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. 2004 Feb;2(1):37–45. doi: 10.3121/cmr.2.1.37

Table 3.

TRF profiles for blood isolates and SOD scores for TRF database matches.

Size (bases) of TRF obtained with:
Isolate or organisma Strain Alu Ib Hha Ib Msp Ib Rsa Ib Hha Ic Sum of differences (SOD) scored
6-FAM HEX 6-FAM HEX 6-FAM HEX 6-FAM HEX 6-FAM HEX
MCRF-271 / MCRF-412e 193 560 561 223 537 247 UD UD 321 284 NA
L. rhamnosus DSM 20021 194 556 561 224 535 246 UD UD 325 283 14
L. rhamnosus JCM 1136 194 555 560 224 534 246 UD UD 325 283 17
L. plantarum NCDO 1752 175 558 562 224 536 246 UD UD 320 283 26
L. plantarum JCM 1149 175 556 560 224 534 246 UD UD 325 283 33
L. plantarum ATCC 8014 175 556 560 224 534 246 UD UD 325 283 33
L. manihotivorans LMG 18010 174 556 560 224 534 246 UD UD 325 283 34
L. pentosus JCM 1588 226 556 560 224 534 246 UD UD 325 283 48
L. casei ATCC 334 194 556 561 172 535 246 UD UD 325 283 64
L. casei ATCC 393 194 556 561 172 535 246 UD UD 325 283 64
L. zeae ATCC 15820 194 556 561 172 535 246 UD UD 325 283 64
L. casei JCM 1134 195 555 561 172 535 246 UD UD 325 283 66
L. paracasei JCM 1133 194 555 560 172 534 246 UD UD 325 283 67
L. paracasei JCM 8130 194 555 560 172 534 246 UD UD 325 283 67
L. paracasei JCM 1171 194 555 560 172 534 246 UD UD 325 283 67
MCRF-284e 193 560 561 172 537 247 UD UD 321 284 NA
L. casei ATCC 334 194 556 561 172 535 246 UD UD 325 283 13
L. casei ATCC 393 194 556 561 172 535 246 UD UD 325 283 13
L. zeae ATCC 15820 194 556 561 172 535 246 UD UD 325 283 13
L. casei JCM 1134 195 555 561 172 535 246 UD UD 325 283 15
L. paracasei JCM 1133 194 555 560 172 534 246 UD UD 325 283 16
L. paracasei JCM 8130 194 555 560 172 534 246 UD UD 325 283 16
L. paracasei JCM 1171 194 555 560 172 534 246 UD UD 325 283 16
L. rhamnosus DSM 20021 194 556 561 224 535 246 UD UD 325 283 65
L. paracasei JCM 1181 194 555 612 172 534 246 UD UD 325 283 66
L. rhamnosus JCM 1136 194 555 560 224 534 246 UD UD 325 283 68

UD: Undigested PCR product (6-FAM and HEX fragment sizes were both >700 bases).

aOrganisms are presented in ascending order of the SOD scores relative to the TRF results for each MCRF strain.

bLabeled fragments derived from the PCR product of (6-FAM)-S-D-Bact-0045-b-S-20 and (HEX)-S-D-Bact-0785-a-A-19 or as predicted from sequence data.

cLabeled fragments derived from the PCR product of (6-FAM)-S-D-Bact-0785-a-S-19 and (HEX)-S-D-Bact-1371-a-A-20 or as predicted from sequence data.

dValue calculated from the differences between the size of the experimentally determined TRF and the sequence predicted fragment sizes for a restriction digest of organisms in the TRF database. The SOD for each organism was then calculated.

eEach TRF size reported was determined from the average of at least two digests.