Multiple sequence alignment - TraesCS6D01G400900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G400900 chr6D 100.000 2429 0 0 1 2429 470353737 470351309 0.000000e+00 4486.0
1 TraesCS6D01G400900 chr6D 85.714 112 9 6 597 707 454889536 454889431 7.100000e-21 111.0
2 TraesCS6D01G400900 chr6D 85.714 112 9 6 597 707 454923091 454922986 7.100000e-21 111.0
3 TraesCS6D01G400900 chr6B 85.340 1603 116 54 885 2429 720975750 720977291 0.000000e+00 1548.0
4 TraesCS6D01G400900 chr6B 84.826 547 68 8 1 538 720974826 720975366 9.880000e-149 536.0
5 TraesCS6D01G400900 chr6B 80.897 602 81 22 1 596 720979258 720979831 6.160000e-121 444.0
6 TraesCS6D01G400900 chr6B 80.800 125 17 6 600 723 93574074 93573956 9.250000e-15 91.6
7 TraesCS6D01G400900 chr6A 87.713 879 63 25 871 1740 615043876 615043034 0.000000e+00 983.0
8 TraesCS6D01G400900 chr6A 80.071 567 71 19 1157 1719 615041439 615040911 1.360000e-102 383.0
9 TraesCS6D01G400900 chr6A 80.922 477 75 12 1 469 615045359 615044891 1.780000e-96 363.0
10 TraesCS6D01G400900 chr6A 79.515 371 58 10 212 576 615041805 615041447 5.190000e-62 248.0
11 TraesCS6D01G400900 chr5D 83.333 120 16 3 597 714 322004935 322004818 9.180000e-20 108.0
12 TraesCS6D01G400900 chr1D 84.071 113 11 4 596 707 53228498 53228604 4.270000e-18 102.0
13 TraesCS6D01G400900 chr7B 82.906 117 15 4 591 707 655569934 655569823 1.540000e-17 100.0
14 TraesCS6D01G400900 chr5B 83.193 119 11 6 598 715 548754391 548754281 1.540000e-17 100.0
15 TraesCS6D01G400900 chr5A 83.036 112 12 3 595 705 693049176 693049281 7.150000e-16 95.3
16 TraesCS6D01G400900 chr2B 81.667 120 16 5 596 715 753838137 753838024 7.150000e-16 95.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G400900 chr6D 470351309 470353737 2428 True 4486.000000 4486 100.000000 1 2429 1 chr6D.!!$R3 2428
1 TraesCS6D01G400900 chr6B 720974826 720979831 5005 False 842.666667 1548 83.687667 1 2429 3 chr6B.!!$F1 2428
2 TraesCS6D01G400900 chr6A 615040911 615045359 4448 True 494.250000 983 82.055250 1 1740 4 chr6A.!!$R1 1739

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
240 246 0.034283 TAGCTCATGCATTGGCCACA 60.034 50.0 3.88 0.0 42.74 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 3036 0.250234 TAGGCTGTGTCCACATGCTC 59.75 55.0 16.05 9.82 41.01 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.213926 GACATGCTCCTCCCCTTCATT 59.786 52.381 0.00 0.00 0.00 2.57
89 91 4.107622 CGGCATCAAATGGAATGAGAAAC 58.892 43.478 0.00 0.00 0.00 2.78
94 96 3.756434 TCAAATGGAATGAGAAACGGGAC 59.244 43.478 0.00 0.00 0.00 4.46
106 108 1.946984 AACGGGACCAGATAGGAACA 58.053 50.000 0.00 0.00 41.22 3.18
123 125 3.463704 GGAACAAGGGAGAAGGGGATATT 59.536 47.826 0.00 0.00 0.00 1.28
143 145 3.371102 TGTGAGGAACGAACAGAGAAG 57.629 47.619 0.00 0.00 0.00 2.85
154 156 3.616076 CGAACAGAGAAGAGGCAGATGTT 60.616 47.826 0.00 0.00 32.46 2.71
205 211 3.947196 TGGAGTAGCGTTTTACCGATCTA 59.053 43.478 0.00 0.00 0.00 1.98
209 215 2.480845 AGCGTTTTACCGATCTATGCC 58.519 47.619 0.00 0.00 0.00 4.40
220 226 1.335810 GATCTATGCCCGTGTGTCGTA 59.664 52.381 0.00 0.00 37.94 3.43
225 231 1.317431 TGCCCGTGTGTCGTATAGCT 61.317 55.000 0.00 0.00 37.94 3.32
227 233 0.736636 CCCGTGTGTCGTATAGCTCA 59.263 55.000 0.00 0.00 37.94 4.26
232 238 3.384668 GTGTGTCGTATAGCTCATGCAT 58.615 45.455 0.00 0.00 42.74 3.96
234 240 3.803778 TGTGTCGTATAGCTCATGCATTG 59.196 43.478 0.00 0.00 42.74 2.82
240 246 0.034283 TAGCTCATGCATTGGCCACA 60.034 50.000 3.88 0.00 42.74 4.17
249 255 0.949397 CATTGGCCACATCAGGATCG 59.051 55.000 3.88 0.00 0.00 3.69
255 261 0.107993 CCACATCAGGATCGTGCAGT 60.108 55.000 10.58 8.37 0.00 4.40
257 263 2.418609 CCACATCAGGATCGTGCAGTTA 60.419 50.000 10.58 0.00 0.00 2.24
274 280 6.021468 GTGCAGTTACACGATTCATATTTTGC 60.021 38.462 0.00 0.00 0.00 3.68
278 284 8.365210 CAGTTACACGATTCATATTTTGCAAAC 58.635 33.333 12.39 0.00 0.00 2.93
315 321 1.282382 TAGTTAGGCCAGGGGTGTTC 58.718 55.000 5.01 0.00 0.00 3.18
413 419 5.897377 AATGTAGCACCAAATGTAGTTCC 57.103 39.130 0.00 0.00 0.00 3.62
418 424 2.785562 CACCAAATGTAGTTCCCGGAA 58.214 47.619 0.73 0.00 0.00 4.30
455 466 5.177696 CCAATAGCTAGTCATAACTTTCGCC 59.822 44.000 0.00 0.00 36.92 5.54
475 486 3.207778 CCGAGGGTGTTGTTTGTTTCTA 58.792 45.455 0.00 0.00 0.00 2.10
500 511 7.706281 TGGCACAAACACTGTATAAATTTTG 57.294 32.000 0.00 0.00 36.10 2.44
502 513 7.766278 TGGCACAAACACTGTATAAATTTTGTT 59.234 29.630 0.00 0.00 35.52 2.83
503 514 8.061268 GGCACAAACACTGTATAAATTTTGTTG 58.939 33.333 0.00 0.00 35.52 3.33
505 516 8.061268 CACAAACACTGTATAAATTTTGTTGGC 58.939 33.333 0.00 0.00 35.52 4.52
506 517 7.043059 ACAAACACTGTATAAATTTTGTTGGCG 60.043 33.333 0.00 0.00 36.10 5.69
507 518 4.920927 ACACTGTATAAATTTTGTTGGCGC 59.079 37.500 0.00 0.00 0.00 6.53
509 520 5.060816 CACTGTATAAATTTTGTTGGCGCAG 59.939 40.000 10.83 0.00 0.00 5.18
510 521 5.048364 ACTGTATAAATTTTGTTGGCGCAGA 60.048 36.000 10.83 0.00 0.00 4.26
511 522 5.773575 TGTATAAATTTTGTTGGCGCAGAA 58.226 33.333 10.83 0.00 0.00 3.02
551 1138 2.475864 TCCGTAAACAACAAATCCGTCG 59.524 45.455 0.00 0.00 0.00 5.12
598 1220 6.291067 TCTTAACATGCAGAAAGATATGCG 57.709 37.500 0.00 0.00 46.74 4.73
599 1221 6.048509 TCTTAACATGCAGAAAGATATGCGA 58.951 36.000 0.00 0.00 46.74 5.10
600 1222 6.538381 TCTTAACATGCAGAAAGATATGCGAA 59.462 34.615 0.00 0.00 46.74 4.70
601 1223 5.762825 AACATGCAGAAAGATATGCGAAT 57.237 34.783 0.00 0.00 46.74 3.34
602 1224 5.354054 ACATGCAGAAAGATATGCGAATC 57.646 39.130 0.00 0.00 46.74 2.52
604 1226 5.297527 ACATGCAGAAAGATATGCGAATCAA 59.702 36.000 0.00 0.00 46.74 2.57
605 1227 5.160699 TGCAGAAAGATATGCGAATCAAC 57.839 39.130 0.00 0.00 46.74 3.18
606 1228 4.035558 TGCAGAAAGATATGCGAATCAACC 59.964 41.667 0.00 0.00 46.74 3.77
607 1229 4.274459 GCAGAAAGATATGCGAATCAACCT 59.726 41.667 0.00 0.00 33.54 3.50
609 1231 6.148480 GCAGAAAGATATGCGAATCAACCTAT 59.852 38.462 0.00 0.00 33.54 2.57
610 1232 7.516481 CAGAAAGATATGCGAATCAACCTATG 58.484 38.462 0.00 0.00 0.00 2.23
611 1233 6.652481 AGAAAGATATGCGAATCAACCTATGG 59.348 38.462 0.00 0.00 0.00 2.74
612 1234 5.489792 AGATATGCGAATCAACCTATGGT 57.510 39.130 0.00 0.00 37.65 3.55
614 1236 5.934625 AGATATGCGAATCAACCTATGGTTC 59.065 40.000 0.00 0.00 43.05 3.62
620 1242 4.451900 GAATCAACCTATGGTTCGATGGT 58.548 43.478 0.00 0.00 43.05 3.55
621 1243 3.992943 TCAACCTATGGTTCGATGGTT 57.007 42.857 0.00 0.00 43.05 3.67
622 1244 5.623956 ATCAACCTATGGTTCGATGGTTA 57.376 39.130 0.00 0.00 43.05 2.85
623 1245 5.018539 TCAACCTATGGTTCGATGGTTAG 57.981 43.478 0.00 0.00 43.05 2.34
624 1246 4.127171 CAACCTATGGTTCGATGGTTAGG 58.873 47.826 0.00 9.32 43.05 2.69
625 1247 3.381335 ACCTATGGTTCGATGGTTAGGT 58.619 45.455 10.30 10.30 35.69 3.08
626 1248 3.134081 ACCTATGGTTCGATGGTTAGGTG 59.866 47.826 13.69 0.00 38.35 4.00
627 1249 2.710096 ATGGTTCGATGGTTAGGTGG 57.290 50.000 0.00 0.00 0.00 4.61
628 1250 1.646912 TGGTTCGATGGTTAGGTGGA 58.353 50.000 0.00 0.00 0.00 4.02
629 1251 1.276989 TGGTTCGATGGTTAGGTGGAC 59.723 52.381 0.00 0.00 0.00 4.02
630 1252 1.276989 GGTTCGATGGTTAGGTGGACA 59.723 52.381 0.00 0.00 0.00 4.02
631 1253 2.618053 GTTCGATGGTTAGGTGGACAG 58.382 52.381 0.00 0.00 0.00 3.51
632 1254 1.933021 TCGATGGTTAGGTGGACAGT 58.067 50.000 0.00 0.00 0.00 3.55
633 1255 1.548719 TCGATGGTTAGGTGGACAGTG 59.451 52.381 0.00 0.00 0.00 3.66
634 1256 1.405526 CGATGGTTAGGTGGACAGTGG 60.406 57.143 0.00 0.00 0.00 4.00
635 1257 1.628846 GATGGTTAGGTGGACAGTGGT 59.371 52.381 0.00 0.00 0.00 4.16
636 1258 2.402182 TGGTTAGGTGGACAGTGGTA 57.598 50.000 0.00 0.00 0.00 3.25
637 1259 2.910544 TGGTTAGGTGGACAGTGGTAT 58.089 47.619 0.00 0.00 0.00 2.73
638 1260 2.835764 TGGTTAGGTGGACAGTGGTATC 59.164 50.000 0.00 0.00 0.00 2.24
639 1261 2.169978 GGTTAGGTGGACAGTGGTATCC 59.830 54.545 0.00 0.00 35.37 2.59
640 1262 2.169978 GTTAGGTGGACAGTGGTATCCC 59.830 54.545 0.00 0.00 33.69 3.85
641 1263 0.118346 AGGTGGACAGTGGTATCCCA 59.882 55.000 0.00 0.00 38.87 4.37
642 1264 0.541863 GGTGGACAGTGGTATCCCAG 59.458 60.000 0.00 0.00 42.94 4.45
643 1265 1.276622 GTGGACAGTGGTATCCCAGT 58.723 55.000 0.00 0.00 45.74 4.00
644 1266 1.207329 GTGGACAGTGGTATCCCAGTC 59.793 57.143 0.00 0.00 42.81 3.51
645 1267 0.831307 GGACAGTGGTATCCCAGTCC 59.169 60.000 0.67 0.67 44.37 3.85
646 1268 1.568504 GACAGTGGTATCCCAGTCCA 58.431 55.000 0.00 0.00 42.81 4.02
649 1271 2.587080 GTGGTATCCCAGTCCACGA 58.413 57.895 0.00 0.00 42.94 4.35
650 1272 0.460311 GTGGTATCCCAGTCCACGAG 59.540 60.000 0.00 0.00 42.94 4.18
651 1273 0.686441 TGGTATCCCAGTCCACGAGG 60.686 60.000 0.00 0.00 35.17 4.63
652 1274 1.400530 GGTATCCCAGTCCACGAGGG 61.401 65.000 0.00 4.38 44.22 4.30
660 1282 3.801620 TCCACGAGGGAAGGGTTC 58.198 61.111 0.00 0.00 44.80 3.62
661 1283 1.152204 TCCACGAGGGAAGGGTTCA 60.152 57.895 0.00 0.00 44.80 3.18
662 1284 0.765135 TCCACGAGGGAAGGGTTCAA 60.765 55.000 0.00 0.00 44.80 2.69
663 1285 0.321653 CCACGAGGGAAGGGTTCAAG 60.322 60.000 0.00 0.00 40.01 3.02
664 1286 0.396811 CACGAGGGAAGGGTTCAAGT 59.603 55.000 0.00 0.00 0.00 3.16
665 1287 0.685660 ACGAGGGAAGGGTTCAAGTC 59.314 55.000 0.00 0.00 0.00 3.01
666 1288 0.036294 CGAGGGAAGGGTTCAAGTCC 60.036 60.000 0.00 0.00 0.00 3.85
667 1289 1.363246 GAGGGAAGGGTTCAAGTCCT 58.637 55.000 0.00 0.00 34.29 3.85
668 1290 1.003696 GAGGGAAGGGTTCAAGTCCTG 59.996 57.143 0.00 0.00 32.95 3.86
669 1291 1.064825 GGGAAGGGTTCAAGTCCTGA 58.935 55.000 0.00 0.00 32.95 3.86
670 1292 1.636003 GGGAAGGGTTCAAGTCCTGAT 59.364 52.381 0.00 0.00 32.78 2.90
671 1293 2.844348 GGGAAGGGTTCAAGTCCTGATA 59.156 50.000 0.00 0.00 32.78 2.15
672 1294 3.370633 GGGAAGGGTTCAAGTCCTGATAC 60.371 52.174 0.00 0.00 32.78 2.24
673 1295 3.519913 GGAAGGGTTCAAGTCCTGATACT 59.480 47.826 0.00 0.00 32.78 2.12
674 1296 4.383226 GGAAGGGTTCAAGTCCTGATACTC 60.383 50.000 0.00 0.00 32.78 2.59
675 1297 2.761208 AGGGTTCAAGTCCTGATACTCG 59.239 50.000 0.00 0.00 32.78 4.18
676 1298 2.541556 GGTTCAAGTCCTGATACTCGC 58.458 52.381 0.00 0.00 32.78 5.03
677 1299 2.186076 GTTCAAGTCCTGATACTCGCG 58.814 52.381 0.00 0.00 32.78 5.87
678 1300 1.460504 TCAAGTCCTGATACTCGCGT 58.539 50.000 5.77 0.00 0.00 6.01
679 1301 1.816835 TCAAGTCCTGATACTCGCGTT 59.183 47.619 5.77 0.00 0.00 4.84
680 1302 2.230508 TCAAGTCCTGATACTCGCGTTT 59.769 45.455 5.77 0.00 0.00 3.60
681 1303 3.441222 TCAAGTCCTGATACTCGCGTTTA 59.559 43.478 5.77 0.00 0.00 2.01
682 1304 4.097437 TCAAGTCCTGATACTCGCGTTTAT 59.903 41.667 5.77 3.77 0.00 1.40
683 1305 4.650754 AGTCCTGATACTCGCGTTTATT 57.349 40.909 5.77 0.00 0.00 1.40
684 1306 4.608951 AGTCCTGATACTCGCGTTTATTC 58.391 43.478 5.77 0.00 0.00 1.75
685 1307 3.734735 GTCCTGATACTCGCGTTTATTCC 59.265 47.826 5.77 0.00 0.00 3.01
686 1308 3.635373 TCCTGATACTCGCGTTTATTCCT 59.365 43.478 5.77 0.00 0.00 3.36
687 1309 4.098960 TCCTGATACTCGCGTTTATTCCTT 59.901 41.667 5.77 0.00 0.00 3.36
688 1310 5.300034 TCCTGATACTCGCGTTTATTCCTTA 59.700 40.000 5.77 0.00 0.00 2.69
689 1311 5.981315 CCTGATACTCGCGTTTATTCCTTAA 59.019 40.000 5.77 0.00 0.00 1.85
690 1312 6.645415 CCTGATACTCGCGTTTATTCCTTAAT 59.355 38.462 5.77 0.00 0.00 1.40
691 1313 7.170998 CCTGATACTCGCGTTTATTCCTTAATT 59.829 37.037 5.77 0.00 0.00 1.40
692 1314 8.428186 TGATACTCGCGTTTATTCCTTAATTT 57.572 30.769 5.77 0.00 0.00 1.82
693 1315 9.531942 TGATACTCGCGTTTATTCCTTAATTTA 57.468 29.630 5.77 0.00 0.00 1.40
697 1319 9.712359 ACTCGCGTTTATTCCTTAATTTATTTC 57.288 29.630 5.77 0.00 0.00 2.17
698 1320 9.710979 CTCGCGTTTATTCCTTAATTTATTTCA 57.289 29.630 5.77 0.00 0.00 2.69
699 1321 9.710979 TCGCGTTTATTCCTTAATTTATTTCAG 57.289 29.630 5.77 0.00 0.00 3.02
700 1322 8.953990 CGCGTTTATTCCTTAATTTATTTCAGG 58.046 33.333 0.00 0.00 0.00 3.86
714 1336 7.903995 TTTATTTCAGGATTTCCAACAATGC 57.096 32.000 0.00 0.00 38.89 3.56
715 1337 4.952071 TTTCAGGATTTCCAACAATGCA 57.048 36.364 0.00 0.00 38.89 3.96
716 1338 3.940209 TCAGGATTTCCAACAATGCAC 57.060 42.857 0.00 0.00 38.89 4.57
717 1339 2.562298 TCAGGATTTCCAACAATGCACC 59.438 45.455 0.00 0.00 38.89 5.01
718 1340 2.564062 CAGGATTTCCAACAATGCACCT 59.436 45.455 0.00 0.00 38.89 4.00
719 1341 3.007182 CAGGATTTCCAACAATGCACCTT 59.993 43.478 0.00 0.00 38.89 3.50
720 1342 4.220382 CAGGATTTCCAACAATGCACCTTA 59.780 41.667 0.00 0.00 38.89 2.69
721 1343 4.463891 AGGATTTCCAACAATGCACCTTAG 59.536 41.667 0.00 0.00 38.89 2.18
722 1344 4.381932 GGATTTCCAACAATGCACCTTAGG 60.382 45.833 0.00 0.00 35.64 2.69
723 1345 1.544724 TCCAACAATGCACCTTAGGC 58.455 50.000 0.00 0.00 0.00 3.93
724 1346 1.202989 TCCAACAATGCACCTTAGGCA 60.203 47.619 0.00 0.00 46.66 4.75
730 1352 3.556817 TGCACCTTAGGCATGAGTG 57.443 52.632 0.00 0.00 36.11 3.51
739 1361 2.046892 GCATGAGTGCCCGTGTCT 60.047 61.111 0.00 0.00 45.76 3.41
740 1362 2.393768 GCATGAGTGCCCGTGTCTG 61.394 63.158 0.00 0.00 45.76 3.51
741 1363 1.004560 CATGAGTGCCCGTGTCTGT 60.005 57.895 0.00 0.00 0.00 3.41
742 1364 0.246360 CATGAGTGCCCGTGTCTGTA 59.754 55.000 0.00 0.00 0.00 2.74
743 1365 0.246635 ATGAGTGCCCGTGTCTGTAC 59.753 55.000 0.00 0.00 0.00 2.90
744 1366 0.826256 TGAGTGCCCGTGTCTGTACT 60.826 55.000 0.00 0.00 0.00 2.73
745 1367 0.388649 GAGTGCCCGTGTCTGTACTG 60.389 60.000 0.00 0.00 0.00 2.74
746 1368 1.113517 AGTGCCCGTGTCTGTACTGT 61.114 55.000 0.00 0.00 0.00 3.55
747 1369 0.944311 GTGCCCGTGTCTGTACTGTG 60.944 60.000 0.00 0.00 0.00 3.66
748 1370 1.366366 GCCCGTGTCTGTACTGTGT 59.634 57.895 0.00 0.00 0.00 3.72
749 1371 0.249741 GCCCGTGTCTGTACTGTGTT 60.250 55.000 0.00 0.00 0.00 3.32
750 1372 1.000060 GCCCGTGTCTGTACTGTGTTA 60.000 52.381 0.00 0.00 0.00 2.41
751 1373 2.546373 GCCCGTGTCTGTACTGTGTTAA 60.546 50.000 0.00 0.00 0.00 2.01
752 1374 3.719924 CCCGTGTCTGTACTGTGTTAAA 58.280 45.455 0.00 0.00 0.00 1.52
753 1375 4.121317 CCCGTGTCTGTACTGTGTTAAAA 58.879 43.478 0.00 0.00 0.00 1.52
754 1376 4.571580 CCCGTGTCTGTACTGTGTTAAAAA 59.428 41.667 0.00 0.00 0.00 1.94
778 1400 8.506168 AAAAGATGTAGAAAGATATTTCCGCA 57.494 30.769 9.16 8.86 0.00 5.69
779 1401 8.506168 AAAGATGTAGAAAGATATTTCCGCAA 57.494 30.769 9.16 0.00 0.00 4.85
780 1402 8.506168 AAGATGTAGAAAGATATTTCCGCAAA 57.494 30.769 9.16 0.00 0.00 3.68
781 1403 8.147642 AGATGTAGAAAGATATTTCCGCAAAG 57.852 34.615 9.16 0.00 0.00 2.77
782 1404 7.987458 AGATGTAGAAAGATATTTCCGCAAAGA 59.013 33.333 9.16 0.00 0.00 2.52
783 1405 7.303634 TGTAGAAAGATATTTCCGCAAAGAC 57.696 36.000 9.16 0.00 0.00 3.01
784 1406 6.876789 TGTAGAAAGATATTTCCGCAAAGACA 59.123 34.615 9.16 1.13 0.00 3.41
785 1407 7.552687 TGTAGAAAGATATTTCCGCAAAGACAT 59.447 33.333 9.16 0.00 0.00 3.06
786 1408 7.396540 AGAAAGATATTTCCGCAAAGACATT 57.603 32.000 9.16 0.00 0.00 2.71
787 1409 7.830739 AGAAAGATATTTCCGCAAAGACATTT 58.169 30.769 9.16 0.00 0.00 2.32
797 1419 7.072177 TCCGCAAAGACATTTATGTAGAAAG 57.928 36.000 0.00 0.00 41.95 2.62
889 1557 9.670442 ACTATAATTTGGATAGGAGGAAGTACA 57.330 33.333 0.00 0.00 32.14 2.90
980 2017 5.782925 AGCAGGAGAGGTATATATAAGGGG 58.217 45.833 0.00 0.00 0.00 4.79
981 2018 5.500222 AGCAGGAGAGGTATATATAAGGGGA 59.500 44.000 0.00 0.00 0.00 4.81
995 2032 3.461773 GGGAGCGCTAGCCAGTCA 61.462 66.667 11.50 0.00 46.67 3.41
996 2033 2.105930 GGAGCGCTAGCCAGTCAG 59.894 66.667 11.50 0.00 46.67 3.51
999 2036 2.580867 GCGCTAGCCAGTCAGTCG 60.581 66.667 9.66 0.00 37.42 4.18
1000 2037 3.052620 GCGCTAGCCAGTCAGTCGA 62.053 63.158 9.66 0.00 37.42 4.20
1001 2038 1.730487 CGCTAGCCAGTCAGTCGAT 59.270 57.895 9.66 0.00 0.00 3.59
1002 2039 0.593518 CGCTAGCCAGTCAGTCGATG 60.594 60.000 9.66 0.00 0.00 3.84
1003 2040 0.741326 GCTAGCCAGTCAGTCGATGA 59.259 55.000 2.29 0.00 34.79 2.92
1018 2055 3.990469 GTCGATGAGACTCAACACAACAT 59.010 43.478 9.70 0.00 46.13 2.71
1368 2446 1.219393 GGAGAAGGCGGTTCAGGAG 59.781 63.158 0.76 0.00 37.67 3.69
1372 2453 0.179070 GAAGGCGGTTCAGGAGGATC 60.179 60.000 0.00 0.00 34.97 3.36
1373 2454 0.909610 AAGGCGGTTCAGGAGGATCA 60.910 55.000 0.00 0.00 36.25 2.92
1468 2553 2.359900 GATCCATCTCGCCTGTTGTTT 58.640 47.619 0.00 0.00 0.00 2.83
1469 2554 1.522668 TCCATCTCGCCTGTTGTTTG 58.477 50.000 0.00 0.00 0.00 2.93
1551 2642 6.767524 AAATTGTTAATCGGCCAAGTCATA 57.232 33.333 2.24 0.00 0.00 2.15
1552 2643 6.959639 AATTGTTAATCGGCCAAGTCATAT 57.040 33.333 2.24 0.00 0.00 1.78
1594 2685 7.645058 TCATGGATAAAAATGGAGAAAGGAC 57.355 36.000 0.00 0.00 0.00 3.85
1628 2720 7.328737 CCGAATTAGCATACTCCTATGTTGTAC 59.671 40.741 0.00 0.00 33.39 2.90
1629 2721 8.082852 CGAATTAGCATACTCCTATGTTGTACT 58.917 37.037 0.00 0.00 33.39 2.73
1720 2812 1.203994 CCGAGGGTAATGTGACGAACT 59.796 52.381 0.00 0.00 0.00 3.01
1721 2813 2.259618 CGAGGGTAATGTGACGAACTG 58.740 52.381 0.00 0.00 0.00 3.16
1722 2814 2.618053 GAGGGTAATGTGACGAACTGG 58.382 52.381 0.00 0.00 0.00 4.00
1723 2815 1.975680 AGGGTAATGTGACGAACTGGT 59.024 47.619 0.00 0.00 0.00 4.00
1724 2816 2.073816 GGGTAATGTGACGAACTGGTG 58.926 52.381 0.00 0.00 0.00 4.17
1725 2817 2.549349 GGGTAATGTGACGAACTGGTGT 60.549 50.000 0.00 0.00 0.00 4.16
1726 2818 2.735134 GGTAATGTGACGAACTGGTGTC 59.265 50.000 0.00 0.00 35.67 3.67
1727 2819 2.613026 AATGTGACGAACTGGTGTCA 57.387 45.000 0.00 0.00 42.49 3.58
1728 2820 2.154854 ATGTGACGAACTGGTGTCAG 57.845 50.000 0.00 0.00 45.08 3.51
1729 2821 0.529773 TGTGACGAACTGGTGTCAGC 60.530 55.000 0.00 0.00 45.08 4.26
1730 2822 0.529773 GTGACGAACTGGTGTCAGCA 60.530 55.000 4.37 4.37 45.08 4.41
1731 2823 0.392706 TGACGAACTGGTGTCAGCAT 59.607 50.000 4.95 0.00 44.59 3.79
1732 2824 1.616374 TGACGAACTGGTGTCAGCATA 59.384 47.619 4.95 0.00 44.59 3.14
1733 2825 2.036604 TGACGAACTGGTGTCAGCATAA 59.963 45.455 4.95 0.00 44.59 1.90
1734 2826 3.262420 GACGAACTGGTGTCAGCATAAT 58.738 45.455 4.95 0.00 44.59 1.28
1735 2827 3.674997 ACGAACTGGTGTCAGCATAATT 58.325 40.909 4.95 0.85 44.59 1.40
1761 2853 3.953612 TGTCAGCACAATTTGGTCTTCTT 59.046 39.130 0.78 0.00 31.87 2.52
1790 2882 5.063944 CAGTTGTAGGAGAATTCGGTCATTG 59.936 44.000 0.00 0.00 0.00 2.82
1809 2901 8.184192 GGTCATTGTTAGTTGAAGATAATGTGG 58.816 37.037 0.00 0.00 0.00 4.17
1812 2904 7.517614 TTGTTAGTTGAAGATAATGTGGCAA 57.482 32.000 0.00 0.00 0.00 4.52
1813 2905 6.908825 TGTTAGTTGAAGATAATGTGGCAAC 58.091 36.000 0.00 0.00 36.72 4.17
1832 2924 4.557205 CAACCTAGGATAACGATGTAGGC 58.443 47.826 17.98 0.00 34.67 3.93
1878 2970 4.936411 TCTCTAGACCTCTCAACACTTACG 59.064 45.833 0.00 0.00 0.00 3.18
1880 2972 1.961394 AGACCTCTCAACACTTACGCA 59.039 47.619 0.00 0.00 0.00 5.24
1895 2987 2.918571 CGCATTCGTAGCATCCCAT 58.081 52.632 0.00 0.00 0.00 4.00
1923 3015 1.882625 TGCACGCACACAGAGACAC 60.883 57.895 0.00 0.00 0.00 3.67
1924 3016 1.882625 GCACGCACACAGAGACACA 60.883 57.895 0.00 0.00 0.00 3.72
1933 3025 3.374402 AGAGACACACCGAGCCCG 61.374 66.667 0.00 0.00 0.00 6.13
1959 3051 1.004560 ACCGAGCATGTGGACACAG 60.005 57.895 11.13 4.75 45.48 3.66
1966 3058 1.089920 CATGTGGACACAGCCTAAGC 58.910 55.000 11.13 0.00 45.48 3.09
1977 3069 1.152943 GCCTAAGCCTAAGCCCACC 60.153 63.158 0.00 0.00 41.25 4.61
1978 3070 1.921869 GCCTAAGCCTAAGCCCACCA 61.922 60.000 0.00 0.00 41.25 4.17
1997 3089 4.476410 GCCCGCCGTGCTTTTAGC 62.476 66.667 0.00 0.00 42.82 3.09
2083 3175 5.722021 TTTCTCTAGAAAAACCAATGGCC 57.278 39.130 0.00 0.00 40.68 5.36
2095 3187 2.092753 ACCAATGGCCTGAGTATGTGAG 60.093 50.000 3.32 0.00 0.00 3.51
2109 3201 1.882912 TGTGAGCATGAACCAGACAC 58.117 50.000 0.00 0.00 0.00 3.67
2114 3206 4.065088 TGAGCATGAACCAGACACTTAAC 58.935 43.478 0.00 0.00 0.00 2.01
2116 3208 4.460263 AGCATGAACCAGACACTTAACAA 58.540 39.130 0.00 0.00 0.00 2.83
2117 3209 5.072741 AGCATGAACCAGACACTTAACAAT 58.927 37.500 0.00 0.00 0.00 2.71
2118 3210 6.237901 AGCATGAACCAGACACTTAACAATA 58.762 36.000 0.00 0.00 0.00 1.90
2119 3211 6.886459 AGCATGAACCAGACACTTAACAATAT 59.114 34.615 0.00 0.00 0.00 1.28
2120 3212 8.046708 AGCATGAACCAGACACTTAACAATATA 58.953 33.333 0.00 0.00 0.00 0.86
2121 3213 8.122952 GCATGAACCAGACACTTAACAATATAC 58.877 37.037 0.00 0.00 0.00 1.47
2122 3214 9.161629 CATGAACCAGACACTTAACAATATACA 57.838 33.333 0.00 0.00 0.00 2.29
2123 3215 9.733556 ATGAACCAGACACTTAACAATATACAA 57.266 29.630 0.00 0.00 0.00 2.41
2124 3216 9.214957 TGAACCAGACACTTAACAATATACAAG 57.785 33.333 0.00 0.00 0.00 3.16
2139 3231 6.974932 ATATACAAGATAGGCAATCAAGCG 57.025 37.500 1.64 0.00 37.03 4.68
2160 3252 3.439129 CGTCCCTACAAGTTCCCAAATTC 59.561 47.826 0.00 0.00 0.00 2.17
2175 3267 8.547894 GTTCCCAAATTCTGTTGTTTAATGAAC 58.452 33.333 0.00 0.00 38.78 3.18
2189 3281 3.495434 AATGAACAAAGGTACGGTCCA 57.505 42.857 1.31 0.00 0.00 4.02
2198 3290 5.471116 ACAAAGGTACGGTCCAATAAACTTC 59.529 40.000 1.31 0.00 0.00 3.01
2228 3320 5.591643 TCTTTTCACTAGTTAGCGCAAAG 57.408 39.130 11.47 6.68 0.00 2.77
2242 3334 2.789208 CGCAAAGCCATTACTGACATG 58.211 47.619 0.00 0.00 0.00 3.21
2285 3377 8.700051 TCAATATACCAAAACATACCCAAATGG 58.300 33.333 0.00 0.00 41.37 3.16
2303 3395 3.154827 TGGGTTCTAGCTTTGGGAAAG 57.845 47.619 0.00 0.00 41.46 2.62
2311 3403 2.745968 AGCTTTGGGAAAGTTGGTTGA 58.254 42.857 0.00 0.00 40.64 3.18
2312 3404 3.308401 AGCTTTGGGAAAGTTGGTTGAT 58.692 40.909 0.00 0.00 40.64 2.57
2313 3405 4.479158 AGCTTTGGGAAAGTTGGTTGATA 58.521 39.130 0.00 0.00 40.64 2.15
2350 3463 4.627900 GGTTTCCAAAAAGCTTGTCGAAAA 59.372 37.500 11.52 3.82 39.30 2.29
2354 3467 7.458038 TTCCAAAAAGCTTGTCGAAAAATAC 57.542 32.000 0.00 0.00 0.00 1.89
2357 3470 5.523438 AAAAGCTTGTCGAAAAATACCCA 57.477 34.783 0.00 0.00 0.00 4.51
2361 3474 5.709966 AGCTTGTCGAAAAATACCCAAATC 58.290 37.500 0.00 0.00 0.00 2.17
2374 3488 6.726490 ATACCCAAATCGAGTCTAGCTTTA 57.274 37.500 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.024176 TGAAGGTCAAGTAGGAGCCA 57.976 50.000 0.00 0.00 35.95 4.75
76 78 1.633432 TGGTCCCGTTTCTCATTCCAT 59.367 47.619 0.00 0.00 0.00 3.41
89 91 1.139058 CCTTGTTCCTATCTGGTCCCG 59.861 57.143 0.00 0.00 37.07 5.14
94 96 3.135530 CCTTCTCCCTTGTTCCTATCTGG 59.864 52.174 0.00 0.00 37.10 3.86
106 108 3.718956 CTCACAATATCCCCTTCTCCCTT 59.281 47.826 0.00 0.00 0.00 3.95
123 125 2.956333 TCTTCTCTGTTCGTTCCTCACA 59.044 45.455 0.00 0.00 0.00 3.58
154 156 3.679389 GATGTCTCTCTCCCAGCAAAAA 58.321 45.455 0.00 0.00 0.00 1.94
159 161 1.066908 CTTCGATGTCTCTCTCCCAGC 59.933 57.143 0.00 0.00 0.00 4.85
188 191 3.553508 GGGCATAGATCGGTAAAACGCTA 60.554 47.826 0.00 0.00 0.00 4.26
209 215 3.419969 GCATGAGCTATACGACACACGG 61.420 54.545 0.00 0.00 41.39 4.94
220 226 1.325355 GTGGCCAATGCATGAGCTAT 58.675 50.000 7.24 0.00 42.74 2.97
225 231 1.107945 CTGATGTGGCCAATGCATGA 58.892 50.000 7.24 0.00 40.13 3.07
227 233 0.032912 TCCTGATGTGGCCAATGCAT 60.033 50.000 7.24 7.11 40.13 3.96
232 238 0.392863 CACGATCCTGATGTGGCCAA 60.393 55.000 7.24 0.00 0.00 4.52
234 240 2.182842 GCACGATCCTGATGTGGCC 61.183 63.158 0.00 0.00 34.24 5.36
240 246 2.893637 GTGTAACTGCACGATCCTGAT 58.106 47.619 0.00 0.00 0.00 2.90
249 255 6.021468 GCAAAATATGAATCGTGTAACTGCAC 60.021 38.462 0.00 0.00 36.12 4.57
255 261 8.803201 TTGTTTGCAAAATATGAATCGTGTAA 57.197 26.923 14.67 0.00 0.00 2.41
257 263 7.706281 TTTGTTTGCAAAATATGAATCGTGT 57.294 28.000 14.67 0.00 41.15 4.49
278 284 8.531530 GCCTAACTAATATTGCGTCAAATTTTG 58.468 33.333 2.59 2.59 0.00 2.44
288 294 3.074412 CCCTGGCCTAACTAATATTGCG 58.926 50.000 3.32 0.00 0.00 4.85
301 307 0.264657 AAAAAGAACACCCCTGGCCT 59.735 50.000 3.32 0.00 0.00 5.19
322 328 1.352114 CAGAAATGCCATTTGTGCCG 58.648 50.000 13.52 0.00 36.84 5.69
413 419 9.449719 AGCTATTGGTATCTTTTTATATTCCGG 57.550 33.333 0.00 0.00 0.00 5.14
448 454 1.164041 AACAACACCCTCGGCGAAAG 61.164 55.000 12.13 7.73 0.00 2.62
455 466 4.320202 CCATAGAAACAAACAACACCCTCG 60.320 45.833 0.00 0.00 0.00 4.63
475 486 7.930865 ACAAAATTTATACAGTGTTTGTGCCAT 59.069 29.630 0.00 0.00 41.10 4.40
482 493 6.074034 GCGCCAACAAAATTTATACAGTGTTT 60.074 34.615 0.00 0.00 0.00 2.83
495 506 4.519540 AACTATTCTGCGCCAACAAAAT 57.480 36.364 4.18 0.00 0.00 1.82
500 511 4.939509 TTAGAAACTATTCTGCGCCAAC 57.060 40.909 4.18 0.00 45.47 3.77
502 513 6.509418 AATTTTAGAAACTATTCTGCGCCA 57.491 33.333 4.18 0.00 45.47 5.69
503 514 8.560374 AGATAATTTTAGAAACTATTCTGCGCC 58.440 33.333 4.18 0.00 45.47 6.53
532 949 3.060406 TGTCGACGGATTTGTTGTTTACG 60.060 43.478 11.62 0.00 0.00 3.18
596 1218 2.546778 TCGAACCATAGGTTGATTCGC 58.453 47.619 6.10 0.00 46.95 4.70
598 1220 4.451900 ACCATCGAACCATAGGTTGATTC 58.548 43.478 6.10 0.00 46.95 2.52
599 1221 4.503714 ACCATCGAACCATAGGTTGATT 57.496 40.909 6.10 0.00 46.95 2.57
600 1222 4.503714 AACCATCGAACCATAGGTTGAT 57.496 40.909 6.10 7.02 46.95 2.57
601 1223 3.992943 AACCATCGAACCATAGGTTGA 57.007 42.857 6.10 5.06 46.95 3.18
602 1224 4.127171 CCTAACCATCGAACCATAGGTTG 58.873 47.826 6.10 0.00 46.95 3.77
604 1226 3.134081 CACCTAACCATCGAACCATAGGT 59.866 47.826 14.20 14.20 42.85 3.08
605 1227 3.494398 CCACCTAACCATCGAACCATAGG 60.494 52.174 13.21 13.21 36.75 2.57
606 1228 3.386726 TCCACCTAACCATCGAACCATAG 59.613 47.826 0.00 0.00 0.00 2.23
607 1229 3.133362 GTCCACCTAACCATCGAACCATA 59.867 47.826 0.00 0.00 0.00 2.74
609 1231 1.276989 GTCCACCTAACCATCGAACCA 59.723 52.381 0.00 0.00 0.00 3.67
610 1232 1.276989 TGTCCACCTAACCATCGAACC 59.723 52.381 0.00 0.00 0.00 3.62
611 1233 2.028385 ACTGTCCACCTAACCATCGAAC 60.028 50.000 0.00 0.00 0.00 3.95
612 1234 2.028476 CACTGTCCACCTAACCATCGAA 60.028 50.000 0.00 0.00 0.00 3.71
613 1235 1.548719 CACTGTCCACCTAACCATCGA 59.451 52.381 0.00 0.00 0.00 3.59
614 1236 1.405526 CCACTGTCCACCTAACCATCG 60.406 57.143 0.00 0.00 0.00 3.84
615 1237 1.628846 ACCACTGTCCACCTAACCATC 59.371 52.381 0.00 0.00 0.00 3.51
616 1238 1.742308 ACCACTGTCCACCTAACCAT 58.258 50.000 0.00 0.00 0.00 3.55
617 1239 2.402182 TACCACTGTCCACCTAACCA 57.598 50.000 0.00 0.00 0.00 3.67
618 1240 2.169978 GGATACCACTGTCCACCTAACC 59.830 54.545 0.00 0.00 34.57 2.85
619 1241 3.538634 GGATACCACTGTCCACCTAAC 57.461 52.381 0.00 0.00 34.57 2.34
634 1256 0.396695 TCCCTCGTGGACTGGGATAC 60.397 60.000 4.76 0.00 44.37 2.24
635 1257 2.012569 TCCCTCGTGGACTGGGATA 58.987 57.895 4.76 0.00 44.37 2.59
636 1258 2.777853 TCCCTCGTGGACTGGGAT 59.222 61.111 4.76 0.00 44.37 3.85
637 1259 1.609501 CTTCCCTCGTGGACTGGGA 60.610 63.158 4.76 0.00 45.11 4.37
638 1260 2.660064 CCTTCCCTCGTGGACTGGG 61.660 68.421 4.76 0.00 45.11 4.45
639 1261 2.660064 CCCTTCCCTCGTGGACTGG 61.660 68.421 4.76 6.55 45.11 4.00
640 1262 1.481056 AACCCTTCCCTCGTGGACTG 61.481 60.000 4.76 0.00 45.11 3.51
641 1263 1.152096 AACCCTTCCCTCGTGGACT 60.152 57.895 4.76 0.00 45.11 3.85
642 1264 1.295746 GAACCCTTCCCTCGTGGAC 59.704 63.158 4.76 0.00 45.11 4.02
643 1265 0.765135 TTGAACCCTTCCCTCGTGGA 60.765 55.000 4.76 0.00 43.18 4.02
644 1266 0.321653 CTTGAACCCTTCCCTCGTGG 60.322 60.000 0.00 0.00 0.00 4.94
645 1267 0.396811 ACTTGAACCCTTCCCTCGTG 59.603 55.000 0.00 0.00 0.00 4.35
646 1268 0.685660 GACTTGAACCCTTCCCTCGT 59.314 55.000 0.00 0.00 0.00 4.18
647 1269 0.036294 GGACTTGAACCCTTCCCTCG 60.036 60.000 0.00 0.00 0.00 4.63
648 1270 1.003696 CAGGACTTGAACCCTTCCCTC 59.996 57.143 0.00 0.00 0.00 4.30
649 1271 1.068121 CAGGACTTGAACCCTTCCCT 58.932 55.000 0.00 0.00 0.00 4.20
650 1272 1.064825 TCAGGACTTGAACCCTTCCC 58.935 55.000 0.00 0.00 31.34 3.97
651 1273 3.519913 AGTATCAGGACTTGAACCCTTCC 59.480 47.826 0.00 0.00 39.77 3.46
652 1274 4.678309 CGAGTATCAGGACTTGAACCCTTC 60.678 50.000 0.00 0.00 39.77 3.46
653 1275 3.195825 CGAGTATCAGGACTTGAACCCTT 59.804 47.826 0.00 0.00 39.77 3.95
654 1276 2.761208 CGAGTATCAGGACTTGAACCCT 59.239 50.000 0.00 0.00 39.77 4.34
655 1277 2.738964 GCGAGTATCAGGACTTGAACCC 60.739 54.545 0.00 0.00 39.77 4.11
656 1278 2.541556 GCGAGTATCAGGACTTGAACC 58.458 52.381 0.00 0.00 39.77 3.62
657 1279 2.186076 CGCGAGTATCAGGACTTGAAC 58.814 52.381 0.00 0.00 39.77 3.18
658 1280 1.816835 ACGCGAGTATCAGGACTTGAA 59.183 47.619 15.93 0.00 46.88 2.69
659 1281 1.460504 ACGCGAGTATCAGGACTTGA 58.539 50.000 15.93 0.00 46.88 3.02
672 1294 9.710979 TGAAATAAATTAAGGAATAAACGCGAG 57.289 29.630 15.93 0.00 0.00 5.03
673 1295 9.710979 CTGAAATAAATTAAGGAATAAACGCGA 57.289 29.630 15.93 0.00 0.00 5.87
674 1296 8.953990 CCTGAAATAAATTAAGGAATAAACGCG 58.046 33.333 3.53 3.53 0.00 6.01
688 1310 8.949177 GCATTGTTGGAAATCCTGAAATAAATT 58.051 29.630 0.44 0.00 36.82 1.82
689 1311 8.102047 TGCATTGTTGGAAATCCTGAAATAAAT 58.898 29.630 0.44 0.00 36.82 1.40
690 1312 7.387397 GTGCATTGTTGGAAATCCTGAAATAAA 59.613 33.333 0.44 0.00 36.82 1.40
691 1313 6.873076 GTGCATTGTTGGAAATCCTGAAATAA 59.127 34.615 0.44 0.00 36.82 1.40
692 1314 6.397272 GTGCATTGTTGGAAATCCTGAAATA 58.603 36.000 0.44 0.00 36.82 1.40
693 1315 5.240121 GTGCATTGTTGGAAATCCTGAAAT 58.760 37.500 0.44 0.00 36.82 2.17
694 1316 4.502950 GGTGCATTGTTGGAAATCCTGAAA 60.503 41.667 0.44 0.00 36.82 2.69
695 1317 3.006752 GGTGCATTGTTGGAAATCCTGAA 59.993 43.478 0.44 0.00 36.82 3.02
696 1318 2.562298 GGTGCATTGTTGGAAATCCTGA 59.438 45.455 0.44 0.00 36.82 3.86
697 1319 2.564062 AGGTGCATTGTTGGAAATCCTG 59.436 45.455 0.44 0.00 36.82 3.86
698 1320 2.893424 AGGTGCATTGTTGGAAATCCT 58.107 42.857 0.44 0.00 36.82 3.24
699 1321 3.683365 AAGGTGCATTGTTGGAAATCC 57.317 42.857 0.00 0.00 0.00 3.01
700 1322 4.747810 CCTAAGGTGCATTGTTGGAAATC 58.252 43.478 0.00 0.00 0.00 2.17
701 1323 3.055891 GCCTAAGGTGCATTGTTGGAAAT 60.056 43.478 0.00 0.00 0.00 2.17
702 1324 2.298729 GCCTAAGGTGCATTGTTGGAAA 59.701 45.455 0.00 0.00 0.00 3.13
703 1325 1.892474 GCCTAAGGTGCATTGTTGGAA 59.108 47.619 0.00 0.00 0.00 3.53
704 1326 1.202989 TGCCTAAGGTGCATTGTTGGA 60.203 47.619 0.00 0.00 32.85 3.53
705 1327 1.255882 TGCCTAAGGTGCATTGTTGG 58.744 50.000 0.00 0.00 32.85 3.77
706 1328 2.492881 TCATGCCTAAGGTGCATTGTTG 59.507 45.455 0.00 0.00 46.91 3.33
707 1329 2.756760 CTCATGCCTAAGGTGCATTGTT 59.243 45.455 0.00 0.00 46.91 2.83
708 1330 2.291153 ACTCATGCCTAAGGTGCATTGT 60.291 45.455 0.00 0.00 46.91 2.71
709 1331 2.098607 CACTCATGCCTAAGGTGCATTG 59.901 50.000 0.00 0.00 46.91 2.82
710 1332 2.372264 CACTCATGCCTAAGGTGCATT 58.628 47.619 0.00 0.00 46.91 3.56
712 1334 3.556817 CACTCATGCCTAAGGTGCA 57.443 52.632 0.00 0.00 43.97 4.57
713 1335 2.101700 GCACTCATGCCTAAGGTGC 58.898 57.895 0.00 0.00 46.97 5.01
723 1345 0.246360 TACAGACACGGGCACTCATG 59.754 55.000 0.00 0.00 0.00 3.07
724 1346 0.246635 GTACAGACACGGGCACTCAT 59.753 55.000 0.00 0.00 0.00 2.90
725 1347 0.826256 AGTACAGACACGGGCACTCA 60.826 55.000 0.00 0.00 0.00 3.41
726 1348 0.388649 CAGTACAGACACGGGCACTC 60.389 60.000 0.00 0.00 0.00 3.51
727 1349 1.113517 ACAGTACAGACACGGGCACT 61.114 55.000 0.00 0.00 0.00 4.40
728 1350 0.944311 CACAGTACAGACACGGGCAC 60.944 60.000 0.00 0.00 0.00 5.01
729 1351 1.365999 CACAGTACAGACACGGGCA 59.634 57.895 0.00 0.00 0.00 5.36
730 1352 0.249741 AACACAGTACAGACACGGGC 60.250 55.000 0.00 0.00 0.00 6.13
731 1353 3.374220 TTAACACAGTACAGACACGGG 57.626 47.619 0.00 0.00 0.00 5.28
732 1354 5.721876 TTTTTAACACAGTACAGACACGG 57.278 39.130 0.00 0.00 0.00 4.94
752 1374 8.956426 TGCGGAAATATCTTTCTACATCTTTTT 58.044 29.630 3.86 0.00 40.55 1.94
753 1375 8.506168 TGCGGAAATATCTTTCTACATCTTTT 57.494 30.769 3.86 0.00 40.55 2.27
754 1376 8.506168 TTGCGGAAATATCTTTCTACATCTTT 57.494 30.769 3.86 0.00 40.55 2.52
755 1377 8.506168 TTTGCGGAAATATCTTTCTACATCTT 57.494 30.769 0.00 0.00 40.55 2.40
756 1378 7.987458 TCTTTGCGGAAATATCTTTCTACATCT 59.013 33.333 1.45 0.00 40.55 2.90
757 1379 8.064814 GTCTTTGCGGAAATATCTTTCTACATC 58.935 37.037 1.45 0.00 40.55 3.06
758 1380 7.552687 TGTCTTTGCGGAAATATCTTTCTACAT 59.447 33.333 1.45 0.00 40.55 2.29
759 1381 6.876789 TGTCTTTGCGGAAATATCTTTCTACA 59.123 34.615 1.45 0.68 40.55 2.74
760 1382 7.303634 TGTCTTTGCGGAAATATCTTTCTAC 57.696 36.000 1.45 0.00 40.55 2.59
761 1383 8.506168 AATGTCTTTGCGGAAATATCTTTCTA 57.494 30.769 1.45 0.00 40.55 2.10
762 1384 7.396540 AATGTCTTTGCGGAAATATCTTTCT 57.603 32.000 1.45 0.00 40.55 2.52
763 1385 9.736023 ATAAATGTCTTTGCGGAAATATCTTTC 57.264 29.630 1.45 0.00 40.09 2.62
764 1386 9.520204 CATAAATGTCTTTGCGGAAATATCTTT 57.480 29.630 1.45 4.33 0.00 2.52
765 1387 8.686334 ACATAAATGTCTTTGCGGAAATATCTT 58.314 29.630 1.45 0.00 35.87 2.40
766 1388 8.225603 ACATAAATGTCTTTGCGGAAATATCT 57.774 30.769 1.45 0.00 35.87 1.98
767 1389 9.599322 CTACATAAATGTCTTTGCGGAAATATC 57.401 33.333 1.45 0.00 41.97 1.63
768 1390 9.337396 TCTACATAAATGTCTTTGCGGAAATAT 57.663 29.630 1.45 0.00 41.97 1.28
769 1391 8.725405 TCTACATAAATGTCTTTGCGGAAATA 57.275 30.769 1.45 0.00 41.97 1.40
770 1392 7.624360 TCTACATAAATGTCTTTGCGGAAAT 57.376 32.000 1.45 0.00 41.97 2.17
771 1393 7.441890 TTCTACATAAATGTCTTTGCGGAAA 57.558 32.000 1.05 1.05 41.97 3.13
772 1394 7.389330 TCTTTCTACATAAATGTCTTTGCGGAA 59.611 33.333 0.00 0.00 41.97 4.30
773 1395 6.876789 TCTTTCTACATAAATGTCTTTGCGGA 59.123 34.615 0.00 0.00 41.97 5.54
774 1396 7.072177 TCTTTCTACATAAATGTCTTTGCGG 57.928 36.000 0.00 0.00 41.97 5.69
786 1408 9.892444 TGGAGGGAGTAATATCTTTCTACATAA 57.108 33.333 0.00 0.00 0.00 1.90
787 1409 9.892444 TTGGAGGGAGTAATATCTTTCTACATA 57.108 33.333 0.00 0.00 0.00 2.29
826 1449 7.807687 ACTAAAGTTGTACTAAGTATGCGTG 57.192 36.000 0.00 0.00 0.00 5.34
863 1486 9.670442 TGTACTTCCTCCTATCCAAATTATAGT 57.330 33.333 0.00 0.00 0.00 2.12
877 1512 8.611051 ATGACTAGTTATTTGTACTTCCTCCT 57.389 34.615 0.00 0.00 0.00 3.69
965 2002 4.267341 AGCGCTCCCCTTATATATACCT 57.733 45.455 2.64 0.00 0.00 3.08
980 2017 1.226831 GACTGACTGGCTAGCGCTC 60.227 63.158 16.34 0.00 36.09 5.03
981 2018 2.888863 GACTGACTGGCTAGCGCT 59.111 61.111 17.26 17.26 36.09 5.92
996 2033 3.381045 TGTTGTGTTGAGTCTCATCGAC 58.619 45.455 2.68 8.15 43.17 4.20
999 2036 4.993584 AGTGATGTTGTGTTGAGTCTCATC 59.006 41.667 2.68 3.57 0.00 2.92
1000 2037 4.965814 AGTGATGTTGTGTTGAGTCTCAT 58.034 39.130 2.68 0.00 0.00 2.90
1001 2038 4.406648 AGTGATGTTGTGTTGAGTCTCA 57.593 40.909 0.00 0.00 0.00 3.27
1002 2039 5.773575 TCTAGTGATGTTGTGTTGAGTCTC 58.226 41.667 0.00 0.00 0.00 3.36
1003 2040 5.791336 TCTAGTGATGTTGTGTTGAGTCT 57.209 39.130 0.00 0.00 0.00 3.24
1018 2055 3.017442 CCTGTTGGTCTCGATCTAGTGA 58.983 50.000 0.00 0.00 0.00 3.41
1065 2143 2.034879 GTCCACGGTGCTGTCCATG 61.035 63.158 1.68 0.00 0.00 3.66
1327 2405 4.489771 CTCACGGTGGCCATCCCC 62.490 72.222 9.72 4.35 0.00 4.81
1328 2406 4.489771 CCTCACGGTGGCCATCCC 62.490 72.222 9.72 5.27 0.00 3.85
1329 2407 3.391665 CTCCTCACGGTGGCCATCC 62.392 68.421 9.72 11.73 0.00 3.51
1330 2408 1.899437 TTCTCCTCACGGTGGCCATC 61.899 60.000 9.72 7.61 0.00 3.51
1331 2409 1.903877 CTTCTCCTCACGGTGGCCAT 61.904 60.000 9.72 0.00 0.00 4.40
1332 2410 2.525629 TTCTCCTCACGGTGGCCA 60.526 61.111 0.00 0.00 0.00 5.36
1333 2411 2.266055 CTTCTCCTCACGGTGGCC 59.734 66.667 8.50 0.00 0.00 5.36
1334 2412 2.232298 CTCCTTCTCCTCACGGTGGC 62.232 65.000 8.50 0.00 0.00 5.01
1335 2413 0.612174 TCTCCTTCTCCTCACGGTGG 60.612 60.000 8.50 0.00 0.00 4.61
1336 2414 1.203523 CTTCTCCTTCTCCTCACGGTG 59.796 57.143 0.56 0.56 0.00 4.94
1337 2415 1.551452 CTTCTCCTTCTCCTCACGGT 58.449 55.000 0.00 0.00 0.00 4.83
1352 2430 0.618968 ATCCTCCTGAACCGCCTTCT 60.619 55.000 0.00 0.00 0.00 2.85
1435 2516 4.137872 GGATCGACCGCCCGAACA 62.138 66.667 0.00 0.00 42.22 3.18
1468 2553 2.687425 CTCAACATCACACCCAACAACA 59.313 45.455 0.00 0.00 0.00 3.33
1469 2554 2.687935 ACTCAACATCACACCCAACAAC 59.312 45.455 0.00 0.00 0.00 3.32
1594 2685 2.918712 ATGCTAATTCGGTCCTCCTG 57.081 50.000 0.00 0.00 0.00 3.86
1657 2749 8.576442 ACTGACAATAACATCAAGGTAAAAAGG 58.424 33.333 0.00 0.00 0.00 3.11
1658 2750 9.398170 CACTGACAATAACATCAAGGTAAAAAG 57.602 33.333 0.00 0.00 0.00 2.27
1677 2769 4.442706 GTGTTCTTCTCTTTCCACTGACA 58.557 43.478 0.00 0.00 0.00 3.58
1715 2807 4.406069 CAAATTATGCTGACACCAGTTCG 58.594 43.478 0.00 0.00 42.35 3.95
1720 2812 3.495331 ACACCAAATTATGCTGACACCA 58.505 40.909 0.00 0.00 0.00 4.17
1721 2813 3.505680 TGACACCAAATTATGCTGACACC 59.494 43.478 0.00 0.00 0.00 4.16
1722 2814 4.726416 CTGACACCAAATTATGCTGACAC 58.274 43.478 0.00 0.00 0.00 3.67
1723 2815 3.191162 GCTGACACCAAATTATGCTGACA 59.809 43.478 0.00 0.00 0.00 3.58
1724 2816 3.191162 TGCTGACACCAAATTATGCTGAC 59.809 43.478 0.00 0.00 0.00 3.51
1725 2817 3.191162 GTGCTGACACCAAATTATGCTGA 59.809 43.478 0.00 0.00 41.21 4.26
1726 2818 3.057386 TGTGCTGACACCAAATTATGCTG 60.057 43.478 0.00 0.00 46.86 4.41
1727 2819 3.156293 TGTGCTGACACCAAATTATGCT 58.844 40.909 0.00 0.00 46.86 3.79
1728 2820 3.574284 TGTGCTGACACCAAATTATGC 57.426 42.857 0.00 0.00 46.86 3.14
1729 2821 6.128499 CCAAATTGTGCTGACACCAAATTATG 60.128 38.462 0.00 0.00 46.86 1.90
1730 2822 5.933463 CCAAATTGTGCTGACACCAAATTAT 59.067 36.000 0.00 0.00 46.86 1.28
1731 2823 5.163364 ACCAAATTGTGCTGACACCAAATTA 60.163 36.000 0.00 0.00 46.86 1.40
1732 2824 4.128643 CCAAATTGTGCTGACACCAAATT 58.871 39.130 0.00 0.00 46.86 1.82
1733 2825 3.134442 ACCAAATTGTGCTGACACCAAAT 59.866 39.130 0.00 0.00 46.86 2.32
1734 2826 2.499289 ACCAAATTGTGCTGACACCAAA 59.501 40.909 0.00 0.00 46.86 3.28
1735 2827 2.100584 GACCAAATTGTGCTGACACCAA 59.899 45.455 0.00 0.00 46.86 3.67
1761 2853 6.942976 ACCGAATTCTCCTACAACTGATTTA 58.057 36.000 3.52 0.00 0.00 1.40
1774 2866 5.642063 TCAACTAACAATGACCGAATTCTCC 59.358 40.000 3.52 0.00 0.00 3.71
1790 2882 6.151144 AGGTTGCCACATTATCTTCAACTAAC 59.849 38.462 0.00 0.00 35.48 2.34
1809 2901 4.557205 CCTACATCGTTATCCTAGGTTGC 58.443 47.826 9.08 0.00 0.00 4.17
1812 2904 2.818432 CGCCTACATCGTTATCCTAGGT 59.182 50.000 9.08 0.00 0.00 3.08
1813 2905 3.079578 TCGCCTACATCGTTATCCTAGG 58.920 50.000 0.82 0.82 0.00 3.02
1904 2996 1.882625 TGTCTCTGTGTGCGTGCAC 60.883 57.895 17.72 17.72 46.33 4.57
1905 2997 1.882625 GTGTCTCTGTGTGCGTGCA 60.883 57.895 0.00 0.00 0.00 4.57
1908 3000 1.227263 GGTGTGTCTCTGTGTGCGT 60.227 57.895 0.00 0.00 0.00 5.24
1910 3002 0.941463 CTCGGTGTGTCTCTGTGTGC 60.941 60.000 0.00 0.00 0.00 4.57
1914 3006 2.574955 GGGCTCGGTGTGTCTCTGT 61.575 63.158 0.00 0.00 0.00 3.41
1935 3027 2.821366 CACATGCTCGGTGGGCTC 60.821 66.667 0.00 0.00 32.65 4.70
1940 3032 1.293963 CTGTGTCCACATGCTCGGTG 61.294 60.000 0.00 0.00 41.01 4.94
1941 3033 1.004560 CTGTGTCCACATGCTCGGT 60.005 57.895 0.00 0.00 41.01 4.69
1942 3034 2.393768 GCTGTGTCCACATGCTCGG 61.394 63.158 0.00 0.00 41.01 4.63
1943 3035 2.393768 GGCTGTGTCCACATGCTCG 61.394 63.158 16.05 2.03 41.01 5.03
1944 3036 0.250234 TAGGCTGTGTCCACATGCTC 59.750 55.000 16.05 9.82 41.01 4.26
1945 3037 0.692476 TTAGGCTGTGTCCACATGCT 59.308 50.000 16.05 8.86 41.01 3.79
1946 3038 1.089920 CTTAGGCTGTGTCCACATGC 58.910 55.000 0.00 6.89 41.01 4.06
1947 3039 1.089920 GCTTAGGCTGTGTCCACATG 58.910 55.000 0.00 0.00 41.01 3.21
1959 3051 1.152943 GGTGGGCTTAGGCTTAGGC 60.153 63.158 17.67 17.67 38.73 3.93
1966 3058 2.043953 GGGCTTGGTGGGCTTAGG 60.044 66.667 0.00 0.00 0.00 2.69
2031 3123 7.613801 ACCATAAGTTGCCTTGTTAATGTATCA 59.386 33.333 0.00 0.00 31.89 2.15
2044 3136 8.548877 TCTAGAGAAAATAACCATAAGTTGCCT 58.451 33.333 0.00 0.00 39.67 4.75
2045 3137 8.732746 TCTAGAGAAAATAACCATAAGTTGCC 57.267 34.615 0.00 0.00 39.67 4.52
2065 3157 4.202567 ACTCAGGCCATTGGTTTTTCTAGA 60.203 41.667 5.01 0.00 0.00 2.43
2082 3174 3.201290 GGTTCATGCTCACATACTCAGG 58.799 50.000 0.00 0.00 33.67 3.86
2083 3175 3.865446 TGGTTCATGCTCACATACTCAG 58.135 45.455 0.00 0.00 33.67 3.35
2095 3187 4.829064 TTGTTAAGTGTCTGGTTCATGC 57.171 40.909 0.00 0.00 0.00 4.06
2114 3206 7.095060 ACGCTTGATTGCCTATCTTGTATATTG 60.095 37.037 0.00 0.00 34.17 1.90
2116 3208 6.467677 ACGCTTGATTGCCTATCTTGTATAT 58.532 36.000 0.00 0.00 34.17 0.86
2117 3209 5.853936 ACGCTTGATTGCCTATCTTGTATA 58.146 37.500 0.00 0.00 34.17 1.47
2118 3210 4.708177 ACGCTTGATTGCCTATCTTGTAT 58.292 39.130 0.00 0.00 34.17 2.29
2119 3211 4.119862 GACGCTTGATTGCCTATCTTGTA 58.880 43.478 0.00 0.00 34.17 2.41
2120 3212 2.939103 GACGCTTGATTGCCTATCTTGT 59.061 45.455 0.00 0.00 34.17 3.16
2121 3213 2.289002 GGACGCTTGATTGCCTATCTTG 59.711 50.000 0.00 0.00 34.17 3.02
2122 3214 2.565841 GGACGCTTGATTGCCTATCTT 58.434 47.619 0.00 0.00 34.17 2.40
2123 3215 1.202698 GGGACGCTTGATTGCCTATCT 60.203 52.381 0.00 0.00 34.17 1.98
2124 3216 1.202698 AGGGACGCTTGATTGCCTATC 60.203 52.381 0.00 0.00 30.46 2.08
2135 3227 0.323957 GGGAACTTGTAGGGACGCTT 59.676 55.000 0.00 0.00 0.00 4.68
2139 3231 4.459337 CAGAATTTGGGAACTTGTAGGGAC 59.541 45.833 0.00 0.00 0.00 4.46
2175 3267 5.470777 TGAAGTTTATTGGACCGTACCTTTG 59.529 40.000 0.00 0.00 0.00 2.77
2198 3290 7.636359 GCGCTAACTAGTGAAAAGATGTTATTG 59.364 37.037 0.00 0.00 35.92 1.90
2228 3320 7.502120 AATAGATGAACATGTCAGTAATGGC 57.498 36.000 0.00 0.00 40.43 4.40
2285 3377 3.255888 CCAACTTTCCCAAAGCTAGAACC 59.744 47.826 0.00 0.00 42.27 3.62
2286 3378 3.889538 ACCAACTTTCCCAAAGCTAGAAC 59.110 43.478 0.00 0.00 42.27 3.01
2303 3395 5.897377 ACTTTGGTGCTATATCAACCAAC 57.103 39.130 13.58 0.00 39.80 3.77
2350 3463 5.615925 AAGCTAGACTCGATTTGGGTATT 57.384 39.130 0.00 0.00 0.00 1.89
2354 3467 6.737254 TTTTAAAGCTAGACTCGATTTGGG 57.263 37.500 0.00 0.00 0.00 4.12
2382 3496 5.092781 GCAACTTTGGTGTTATATGAACCG 58.907 41.667 0.00 0.00 36.73 4.44


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.