Multiple sequence alignment - TraesCS5D01G344100

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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 TraesCS5D01G344100 chr5D 100.000 3570 0 0 1 3570 431779999 431783568 0.000000e+00 6593.0
1 TraesCS5D01G344100 chr5D 98.827 2985 32 3 588 3570 513307719 513310702 0.000000e+00 5315.0
2 TraesCS5D01G344100 chr5D 97.688 2985 43 6 588 3570 433685175 433682215 0.000000e+00 5107.0
3 TraesCS5D01G344100 chr5D 94.570 442 7 3 1 431 513307288 513307723 0.000000e+00 667.0
4 TraesCS5D01G344100 chr5D 87.330 442 4 10 1 431 433685571 433685171 3.250000e-125 459.0
5 TraesCS5D01G344100 chr5B 98.598 2995 30 4 588 3570 522862085 522859091 0.000000e+00 5288.0
6 TraesCS5D01G344100 chr5B 93.759 2868 126 20 588 3426 522408009 522410852 0.000000e+00 4255.0
7 TraesCS5D01G344100 chr5B 93.439 442 4 4 1 431 522862508 522862081 1.810000e-177 632.0
8 TraesCS5D01G344100 chr5B 86.595 373 30 7 1 357 522932273 522931905 9.290000e-106 394.0
9 TraesCS5D01G344100 chr5B 92.647 204 14 1 2532 2734 521276716 521276513 3.490000e-75 292.0
10 TraesCS5D01G344100 chr5B 98.361 122 2 0 620 741 522931381 522931260 7.760000e-52 215.0
11 TraesCS5D01G344100 chr5B 95.455 66 2 1 366 431 522931485 522931421 1.750000e-18 104.0
12 TraesCS5D01G344100 chr5A 94.713 2913 124 17 588 3474 546771140 546768232 0.000000e+00 4499.0
13 TraesCS5D01G344100 chr5A 87.713 293 24 6 1 288 546771817 546771532 7.390000e-87 331.0
14 TraesCS5D01G344100 chr5A 92.366 131 9 1 301 431 546771265 546771136 6.090000e-43 185.0
15 TraesCS5D01G344100 chr5A 97.436 39 1 0 3476 3514 546768212 546768174 2.300000e-07 67.6
16 TraesCS5D01G344100 chr2B 82.604 1851 193 53 1030 2817 41137071 41138855 0.000000e+00 1515.0
17 TraesCS5D01G344100 chr2B 87.264 212 21 4 1030 1236 41141186 41141396 1.660000e-58 237.0
18 TraesCS5D01G344100 chr2B 85.714 182 14 4 621 800 41140638 41140809 7.870000e-42 182.0
19 TraesCS5D01G344100 chr2B 84.524 168 16 8 634 801 41132174 41132331 1.330000e-34 158.0
20 TraesCS5D01G344100 chr2B 90.566 53 0 2 919 971 41141059 41141106 8.270000e-07 65.8
21 TraesCS5D01G344100 chr2B 89.091 55 1 1 917 971 41132574 41132623 2.980000e-06 63.9
22 TraesCS5D01G344100 chr2A 83.265 1697 170 47 1030 2678 27956706 27958336 0.000000e+00 1456.0
23 TraesCS5D01G344100 chr2A 84.167 1320 147 29 1318 2594 27952723 27954023 0.000000e+00 1223.0
24 TraesCS5D01G344100 chr2A 84.350 1131 117 36 1030 2122 27963001 27964109 0.000000e+00 1053.0
25 TraesCS5D01G344100 chr2A 89.091 55 1 1 917 971 27952322 27952371 2.980000e-06 63.9
26 TraesCS5D01G344100 chr2D 83.510 1413 156 36 1370 2736 25339348 25340729 0.000000e+00 1247.0
27 TraesCS5D01G344100 chr2D 84.738 1127 110 36 1030 2118 25347630 25348732 0.000000e+00 1072.0
28 TraesCS5D01G344100 chr2D 83.422 567 61 17 2191 2733 25348727 25349284 2.480000e-136 496.0
29 TraesCS5D01G344100 chr2D 98.773 163 2 0 428 590 391812346 391812508 1.250000e-74 291.0
30 TraesCS5D01G344100 chr2D 90.187 214 15 5 1030 1238 25339017 25339229 1.260000e-69 274.0
31 TraesCS5D01G344100 chr2D 85.549 173 14 8 627 799 25338482 25338643 1.700000e-38 171.0
32 TraesCS5D01G344100 chr2D 97.297 37 1 0 935 971 25338888 25338924 2.980000e-06 63.9
33 TraesCS5D01G344100 chr3D 99.387 163 1 0 428 590 486424787 486424949 2.690000e-76 296.0
34 TraesCS5D01G344100 chr7D 98.788 165 2 0 426 590 235502570 235502406 9.690000e-76 294.0
35 TraesCS5D01G344100 chr7D 95.455 176 8 0 427 602 604139343 604139168 7.550000e-72 281.0
36 TraesCS5D01G344100 chr7D 94.944 178 9 0 427 604 422773692 422773515 2.710000e-71 279.0
37 TraesCS5D01G344100 chr1D 98.773 163 2 0 428 590 311986774 311986612 1.250000e-74 291.0
38 TraesCS5D01G344100 chr7B 94.505 182 9 1 423 603 31262389 31262570 2.710000e-71 279.0
39 TraesCS5D01G344100 chr4D 94.944 178 9 0 427 604 361460002 361459825 2.710000e-71 279.0
40 TraesCS5D01G344100 chr7A 93.085 188 12 1 418 604 426204786 426204599 1.260000e-69 274.0
41 TraesCS5D01G344100 chr1B 96.970 33 1 0 2868 2900 458060423 458060391 4.980000e-04 56.5


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 TraesCS5D01G344100 chr5D 431779999 431783568 3569 False 6593.000000 6593 100.000000 1 3570 1 chr5D.!!$F1 3569
1 TraesCS5D01G344100 chr5D 513307288 513310702 3414 False 2991.000000 5315 96.698500 1 3570 2 chr5D.!!$F2 3569
2 TraesCS5D01G344100 chr5D 433682215 433685571 3356 True 2783.000000 5107 92.509000 1 3570 2 chr5D.!!$R1 3569
3 TraesCS5D01G344100 chr5B 522408009 522410852 2843 False 4255.000000 4255 93.759000 588 3426 1 chr5B.!!$F1 2838
4 TraesCS5D01G344100 chr5B 522859091 522862508 3417 True 2960.000000 5288 96.018500 1 3570 2 chr5B.!!$R2 3569
5 TraesCS5D01G344100 chr5B 522931260 522932273 1013 True 237.666667 394 93.470333 1 741 3 chr5B.!!$R3 740
6 TraesCS5D01G344100 chr5A 546768174 546771817 3643 True 1270.650000 4499 93.057000 1 3514 4 chr5A.!!$R1 3513
7 TraesCS5D01G344100 chr2B 41137071 41141396 4325 False 499.950000 1515 86.537000 621 2817 4 chr2B.!!$F2 2196
8 TraesCS5D01G344100 chr2A 27963001 27964109 1108 False 1053.000000 1053 84.350000 1030 2122 1 chr2A.!!$F1 1092
9 TraesCS5D01G344100 chr2A 27952322 27958336 6014 False 914.300000 1456 85.507667 917 2678 3 chr2A.!!$F2 1761
10 TraesCS5D01G344100 chr2D 25347630 25349284 1654 False 784.000000 1072 84.080000 1030 2733 2 chr2D.!!$F3 1703
11 TraesCS5D01G344100 chr2D 25338482 25340729 2247 False 438.975000 1247 89.135750 627 2736 4 chr2D.!!$F2 2109

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
440 1125 0.169894 GACGTGTACTCCCTCCGTTC 59.830 60.000 0.0 0.0 0.0 3.95 F
442 1127 0.964358 CGTGTACTCCCTCCGTTCCT 60.964 60.000 0.0 0.0 0.0 3.36 F
491 1176 1.108776 GGTGGACTACATACGGAGCA 58.891 55.000 0.0 0.0 0.0 4.26 F
492 1177 1.479323 GGTGGACTACATACGGAGCAA 59.521 52.381 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 2481 0.532862 CTGCTGTGACTCGGTTTGGT 60.533 55.000 0.0 0.00 0.00 3.67 R
2260 3177 1.900351 CTCGGGCTTCTGTGATGGA 59.100 57.895 0.0 0.00 0.00 3.41 R
2346 3278 8.768019 CGACATTTATATCTGCAGAAGAATCAA 58.232 33.333 22.5 12.34 38.79 2.57 R
2692 3644 9.640963 CTCTGCTGTTAACAAGGGTATATATAC 57.359 37.037 13.6 13.60 0.00 1.47 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
82 87 2.590073 CAGAGTCACTCACGCTACTTG 58.410 52.381 7.77 0.00 32.49 3.16
176 183 2.799126 TCCCTCTCTCTCTCTCACAC 57.201 55.000 0.00 0.00 0.00 3.82
422 1107 7.254522 GCATTTATAGTTTCGGTCGGTTATTGA 60.255 37.037 0.00 0.00 0.00 2.57
426 1111 1.700523 TTCGGTCGGTTATTGACGTG 58.299 50.000 0.00 0.00 37.22 4.49
427 1112 0.597568 TCGGTCGGTTATTGACGTGT 59.402 50.000 0.00 0.00 37.22 4.49
428 1113 1.809547 TCGGTCGGTTATTGACGTGTA 59.190 47.619 0.00 0.00 37.22 2.90
429 1114 1.913403 CGGTCGGTTATTGACGTGTAC 59.087 52.381 0.00 0.00 37.22 2.90
430 1115 2.414559 CGGTCGGTTATTGACGTGTACT 60.415 50.000 0.00 0.00 37.22 2.73
431 1116 3.174375 GGTCGGTTATTGACGTGTACTC 58.826 50.000 0.00 0.00 37.22 2.59
432 1117 3.174375 GTCGGTTATTGACGTGTACTCC 58.826 50.000 0.00 0.00 0.00 3.85
433 1118 2.164219 TCGGTTATTGACGTGTACTCCC 59.836 50.000 0.00 0.00 0.00 4.30
434 1119 2.165030 CGGTTATTGACGTGTACTCCCT 59.835 50.000 0.00 0.00 0.00 4.20
435 1120 3.733077 CGGTTATTGACGTGTACTCCCTC 60.733 52.174 0.00 0.00 0.00 4.30
436 1121 3.429960 GGTTATTGACGTGTACTCCCTCC 60.430 52.174 0.00 0.00 0.00 4.30
437 1122 0.815734 ATTGACGTGTACTCCCTCCG 59.184 55.000 0.00 0.00 0.00 4.63
438 1123 0.538057 TTGACGTGTACTCCCTCCGT 60.538 55.000 0.00 0.00 0.00 4.69
439 1124 0.538057 TGACGTGTACTCCCTCCGTT 60.538 55.000 0.00 0.00 0.00 4.44
440 1125 0.169894 GACGTGTACTCCCTCCGTTC 59.830 60.000 0.00 0.00 0.00 3.95
441 1126 1.246737 ACGTGTACTCCCTCCGTTCC 61.247 60.000 0.00 0.00 0.00 3.62
442 1127 0.964358 CGTGTACTCCCTCCGTTCCT 60.964 60.000 0.00 0.00 0.00 3.36
443 1128 1.679944 CGTGTACTCCCTCCGTTCCTA 60.680 57.143 0.00 0.00 0.00 2.94
444 1129 2.450476 GTGTACTCCCTCCGTTCCTAA 58.550 52.381 0.00 0.00 0.00 2.69
445 1130 2.827921 GTGTACTCCCTCCGTTCCTAAA 59.172 50.000 0.00 0.00 0.00 1.85
446 1131 3.450096 GTGTACTCCCTCCGTTCCTAAAT 59.550 47.826 0.00 0.00 0.00 1.40
447 1132 4.646492 GTGTACTCCCTCCGTTCCTAAATA 59.354 45.833 0.00 0.00 0.00 1.40
448 1133 5.303845 GTGTACTCCCTCCGTTCCTAAATAT 59.696 44.000 0.00 0.00 0.00 1.28
449 1134 6.491403 GTGTACTCCCTCCGTTCCTAAATATA 59.509 42.308 0.00 0.00 0.00 0.86
450 1135 7.014615 GTGTACTCCCTCCGTTCCTAAATATAA 59.985 40.741 0.00 0.00 0.00 0.98
451 1136 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
452 1137 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
453 1138 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
454 1139 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
455 1140 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
456 1141 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
457 1142 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
458 1143 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
474 1159 7.784470 AGTCTTTGTAGAGATTTCACTAGGT 57.216 36.000 0.00 0.00 0.00 3.08
475 1160 7.607250 AGTCTTTGTAGAGATTTCACTAGGTG 58.393 38.462 0.00 0.00 34.45 4.00
476 1161 6.814146 GTCTTTGTAGAGATTTCACTAGGTGG 59.186 42.308 0.00 0.00 33.87 4.61
477 1162 6.724441 TCTTTGTAGAGATTTCACTAGGTGGA 59.276 38.462 0.00 0.00 33.87 4.02
478 1163 5.916661 TGTAGAGATTTCACTAGGTGGAC 57.083 43.478 0.00 0.00 33.87 4.02
479 1164 5.580998 TGTAGAGATTTCACTAGGTGGACT 58.419 41.667 0.00 0.00 33.87 3.85
480 1165 6.728411 TGTAGAGATTTCACTAGGTGGACTA 58.272 40.000 0.00 0.00 33.87 2.59
481 1166 6.602406 TGTAGAGATTTCACTAGGTGGACTAC 59.398 42.308 0.00 0.00 33.87 2.73
482 1167 5.580998 AGAGATTTCACTAGGTGGACTACA 58.419 41.667 0.00 0.00 33.87 2.74
483 1168 6.198639 AGAGATTTCACTAGGTGGACTACAT 58.801 40.000 0.00 0.00 33.87 2.29
484 1169 7.355101 AGAGATTTCACTAGGTGGACTACATA 58.645 38.462 0.00 0.00 33.87 2.29
485 1170 7.285858 AGAGATTTCACTAGGTGGACTACATAC 59.714 40.741 0.00 0.00 33.87 2.39
486 1171 5.571784 TTTCACTAGGTGGACTACATACG 57.428 43.478 0.00 0.00 33.87 3.06
487 1172 3.548770 TCACTAGGTGGACTACATACGG 58.451 50.000 0.00 0.00 33.87 4.02
488 1173 3.200605 TCACTAGGTGGACTACATACGGA 59.799 47.826 0.00 0.00 33.87 4.69
489 1174 3.564644 CACTAGGTGGACTACATACGGAG 59.435 52.174 0.00 0.00 0.00 4.63
490 1175 1.400737 AGGTGGACTACATACGGAGC 58.599 55.000 0.00 0.00 0.00 4.70
491 1176 1.108776 GGTGGACTACATACGGAGCA 58.891 55.000 0.00 0.00 0.00 4.26
492 1177 1.479323 GGTGGACTACATACGGAGCAA 59.521 52.381 0.00 0.00 0.00 3.91
493 1178 2.093869 GGTGGACTACATACGGAGCAAA 60.094 50.000 0.00 0.00 0.00 3.68
494 1179 3.592059 GTGGACTACATACGGAGCAAAA 58.408 45.455 0.00 0.00 0.00 2.44
495 1180 4.189231 GTGGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
496 1181 4.034048 GTGGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
497 1182 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
498 1183 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
499 1184 5.527582 GGACTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
500 1185 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
501 1186 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
502 1187 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
503 1188 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
504 1189 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
505 1190 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
506 1191 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
507 1192 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
508 1193 5.647658 ACGGAGCAAAATGAATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
509 1194 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
510 1195 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
511 1196 7.542025 GGAGCAAAATGAATGAATCTACACTT 58.458 34.615 0.00 0.00 0.00 3.16
512 1197 8.677300 GGAGCAAAATGAATGAATCTACACTTA 58.323 33.333 0.00 0.00 0.00 2.24
540 1225 9.788889 AATGCATCTATATACATCCATATGTGG 57.211 33.333 0.00 1.19 45.99 4.17
541 1226 8.322905 TGCATCTATATACATCCATATGTGGT 57.677 34.615 8.51 0.00 45.99 4.16
542 1227 8.771286 TGCATCTATATACATCCATATGTGGTT 58.229 33.333 8.51 0.00 45.99 3.67
543 1228 9.265901 GCATCTATATACATCCATATGTGGTTC 57.734 37.037 8.51 0.00 45.99 3.62
550 1235 6.499106 ACATCCATATGTGGTTCATAGTGA 57.501 37.500 8.51 0.00 44.79 3.41
551 1236 6.899089 ACATCCATATGTGGTTCATAGTGAA 58.101 36.000 8.51 0.00 44.79 3.18
552 1237 7.345691 ACATCCATATGTGGTTCATAGTGAAA 58.654 34.615 8.51 0.00 44.79 2.69
553 1238 8.000709 ACATCCATATGTGGTTCATAGTGAAAT 58.999 33.333 8.51 0.00 44.79 2.17
554 1239 8.509690 CATCCATATGTGGTTCATAGTGAAATC 58.490 37.037 8.51 0.00 46.16 2.17
555 1240 7.805163 TCCATATGTGGTTCATAGTGAAATCT 58.195 34.615 8.51 0.00 46.16 2.40
556 1241 7.933577 TCCATATGTGGTTCATAGTGAAATCTC 59.066 37.037 8.51 0.00 46.16 2.75
557 1242 7.935755 CCATATGTGGTTCATAGTGAAATCTCT 59.064 37.037 0.00 0.00 41.55 3.10
558 1243 9.987272 CATATGTGGTTCATAGTGAAATCTCTA 57.013 33.333 0.00 0.00 41.55 2.43
559 1244 9.988815 ATATGTGGTTCATAGTGAAATCTCTAC 57.011 33.333 0.00 0.00 41.55 2.59
560 1245 7.239763 TGTGGTTCATAGTGAAATCTCTACA 57.760 36.000 0.00 0.00 38.22 2.74
561 1246 7.676004 TGTGGTTCATAGTGAAATCTCTACAA 58.324 34.615 0.00 0.00 38.22 2.41
562 1247 8.154203 TGTGGTTCATAGTGAAATCTCTACAAA 58.846 33.333 0.00 0.00 38.22 2.83
563 1248 8.660373 GTGGTTCATAGTGAAATCTCTACAAAG 58.340 37.037 0.00 0.00 38.22 2.77
564 1249 8.593679 TGGTTCATAGTGAAATCTCTACAAAGA 58.406 33.333 0.00 0.00 38.22 2.52
565 1250 8.874816 GGTTCATAGTGAAATCTCTACAAAGAC 58.125 37.037 0.00 0.00 38.22 3.01
566 1251 9.646427 GTTCATAGTGAAATCTCTACAAAGACT 57.354 33.333 0.00 0.00 38.22 3.24
583 1268 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
584 1269 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
585 1270 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
586 1271 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
807 1556 4.743151 CAGCATTAAACTAATCGCGGTAGA 59.257 41.667 20.14 0.00 31.81 2.59
1325 2193 2.641815 AGGCTAGGAATTAGGATGCTGG 59.358 50.000 0.00 0.00 0.00 4.85
1774 2662 2.334977 TCAGGCTTCCTTCACTAACCA 58.665 47.619 0.00 0.00 0.00 3.67
2260 3177 3.055675 CCATCTTGCCATTCCAAACACAT 60.056 43.478 0.00 0.00 0.00 3.21
2346 3278 2.575279 AGCAGATCACTGGATTTCTGGT 59.425 45.455 0.00 0.00 43.62 4.00
2912 4413 8.482943 TCTGAATTTTGAACCGAGATTATCCTA 58.517 33.333 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.352127 CGTGAGTGACTCTGCTGATGAA 60.352 50.000 14.42 0.00 0.00 2.57
176 183 0.589479 CATGCGTGTGTGTGTGTGTG 60.589 55.000 0.00 0.00 0.00 3.82
376 1061 3.753272 TGCAACTCTTTATTGAGCACCTC 59.247 43.478 0.00 0.00 37.58 3.85
422 1107 1.246737 GGAACGGAGGGAGTACACGT 61.247 60.000 0.00 0.00 39.74 4.49
426 1111 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
427 1112 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
428 1113 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
429 1114 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
430 1115 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
431 1116 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
432 1117 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
433 1118 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
448 1133 9.310449 ACCTAGTGAAATCTCTACAAAGACTTA 57.690 33.333 0.00 0.00 0.00 2.24
449 1134 8.091449 CACCTAGTGAAATCTCTACAAAGACTT 58.909 37.037 0.00 0.00 35.23 3.01
450 1135 7.310113 CCACCTAGTGAAATCTCTACAAAGACT 60.310 40.741 0.00 0.00 35.23 3.24
451 1136 6.814146 CCACCTAGTGAAATCTCTACAAAGAC 59.186 42.308 0.00 0.00 35.23 3.01
452 1137 6.724441 TCCACCTAGTGAAATCTCTACAAAGA 59.276 38.462 0.00 0.00 35.23 2.52
453 1138 6.814146 GTCCACCTAGTGAAATCTCTACAAAG 59.186 42.308 0.00 0.00 35.23 2.77
454 1139 6.497259 AGTCCACCTAGTGAAATCTCTACAAA 59.503 38.462 0.00 0.00 35.23 2.83
455 1140 6.017192 AGTCCACCTAGTGAAATCTCTACAA 58.983 40.000 0.00 0.00 35.23 2.41
456 1141 5.580998 AGTCCACCTAGTGAAATCTCTACA 58.419 41.667 0.00 0.00 35.23 2.74
457 1142 6.602406 TGTAGTCCACCTAGTGAAATCTCTAC 59.398 42.308 0.00 0.00 35.23 2.59
458 1143 6.728411 TGTAGTCCACCTAGTGAAATCTCTA 58.272 40.000 0.00 0.00 35.23 2.43
459 1144 5.580998 TGTAGTCCACCTAGTGAAATCTCT 58.419 41.667 0.00 0.00 35.23 3.10
460 1145 5.916661 TGTAGTCCACCTAGTGAAATCTC 57.083 43.478 0.00 0.00 35.23 2.75
461 1146 6.039493 CGTATGTAGTCCACCTAGTGAAATCT 59.961 42.308 0.00 0.00 35.23 2.40
462 1147 6.207213 CGTATGTAGTCCACCTAGTGAAATC 58.793 44.000 0.00 0.00 35.23 2.17
463 1148 5.068723 CCGTATGTAGTCCACCTAGTGAAAT 59.931 44.000 0.00 0.00 35.23 2.17
464 1149 4.400251 CCGTATGTAGTCCACCTAGTGAAA 59.600 45.833 0.00 0.00 35.23 2.69
465 1150 3.949754 CCGTATGTAGTCCACCTAGTGAA 59.050 47.826 0.00 0.00 35.23 3.18
466 1151 3.200605 TCCGTATGTAGTCCACCTAGTGA 59.799 47.826 0.00 0.00 35.23 3.41
467 1152 3.548770 TCCGTATGTAGTCCACCTAGTG 58.451 50.000 0.00 0.00 0.00 2.74
468 1153 3.818180 CTCCGTATGTAGTCCACCTAGT 58.182 50.000 0.00 0.00 0.00 2.57
469 1154 2.553172 GCTCCGTATGTAGTCCACCTAG 59.447 54.545 0.00 0.00 0.00 3.02
470 1155 2.092267 TGCTCCGTATGTAGTCCACCTA 60.092 50.000 0.00 0.00 0.00 3.08
471 1156 1.341679 TGCTCCGTATGTAGTCCACCT 60.342 52.381 0.00 0.00 0.00 4.00
472 1157 1.108776 TGCTCCGTATGTAGTCCACC 58.891 55.000 0.00 0.00 0.00 4.61
473 1158 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
474 1159 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
475 1160 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
476 1161 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
477 1162 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
478 1163 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
479 1164 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
480 1165 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
481 1166 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
482 1167 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
483 1168 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
484 1169 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
485 1170 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
486 1171 7.093322 AGTGTAGATTCATTCATTTTGCTCC 57.907 36.000 0.00 0.00 0.00 4.70
532 1217 8.899427 AGAGATTTCACTATGAACCACATATG 57.101 34.615 0.00 0.00 40.18 1.78
533 1218 9.988815 GTAGAGATTTCACTATGAACCACATAT 57.011 33.333 0.00 0.00 40.18 1.78
534 1219 8.977412 TGTAGAGATTTCACTATGAACCACATA 58.023 33.333 0.00 0.00 35.89 2.29
535 1220 7.851228 TGTAGAGATTTCACTATGAACCACAT 58.149 34.615 0.00 0.00 35.89 3.21
536 1221 7.239763 TGTAGAGATTTCACTATGAACCACA 57.760 36.000 0.00 0.00 35.89 4.17
537 1222 8.547967 TTTGTAGAGATTTCACTATGAACCAC 57.452 34.615 0.00 0.00 35.89 4.16
538 1223 8.593679 TCTTTGTAGAGATTTCACTATGAACCA 58.406 33.333 0.00 0.00 35.89 3.67
539 1224 8.874816 GTCTTTGTAGAGATTTCACTATGAACC 58.125 37.037 0.00 0.00 35.89 3.62
540 1225 9.646427 AGTCTTTGTAGAGATTTCACTATGAAC 57.354 33.333 0.00 0.00 35.89 3.18
558 1243 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
559 1244 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
560 1245 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
561 1246 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
562 1247 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
563 1248 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
564 1249 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
565 1250 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
566 1251 7.232127 CAGTACTCCCTCCGTTCCTAAATATAA 59.768 40.741 0.00 0.00 0.00 0.98
567 1252 6.718454 CAGTACTCCCTCCGTTCCTAAATATA 59.282 42.308 0.00 0.00 0.00 0.86
568 1253 5.539193 CAGTACTCCCTCCGTTCCTAAATAT 59.461 44.000 0.00 0.00 0.00 1.28
569 1254 4.891756 CAGTACTCCCTCCGTTCCTAAATA 59.108 45.833 0.00 0.00 0.00 1.40
570 1255 3.705072 CAGTACTCCCTCCGTTCCTAAAT 59.295 47.826 0.00 0.00 0.00 1.40
571 1256 3.094572 CAGTACTCCCTCCGTTCCTAAA 58.905 50.000 0.00 0.00 0.00 1.85
572 1257 2.622452 CCAGTACTCCCTCCGTTCCTAA 60.622 54.545 0.00 0.00 0.00 2.69
573 1258 1.064166 CCAGTACTCCCTCCGTTCCTA 60.064 57.143 0.00 0.00 0.00 2.94
574 1259 0.324460 CCAGTACTCCCTCCGTTCCT 60.324 60.000 0.00 0.00 0.00 3.36
575 1260 0.324091 TCCAGTACTCCCTCCGTTCC 60.324 60.000 0.00 0.00 0.00 3.62
576 1261 1.553706 TTCCAGTACTCCCTCCGTTC 58.446 55.000 0.00 0.00 0.00 3.95
577 1262 2.236395 CAATTCCAGTACTCCCTCCGTT 59.764 50.000 0.00 0.00 0.00 4.44
578 1263 1.831736 CAATTCCAGTACTCCCTCCGT 59.168 52.381 0.00 0.00 0.00 4.69
579 1264 1.473434 GCAATTCCAGTACTCCCTCCG 60.473 57.143 0.00 0.00 0.00 4.63
580 1265 1.559682 TGCAATTCCAGTACTCCCTCC 59.440 52.381 0.00 0.00 0.00 4.30
581 1266 3.209410 CATGCAATTCCAGTACTCCCTC 58.791 50.000 0.00 0.00 0.00 4.30
582 1267 2.578021 ACATGCAATTCCAGTACTCCCT 59.422 45.455 0.00 0.00 0.00 4.20
583 1268 2.945668 GACATGCAATTCCAGTACTCCC 59.054 50.000 0.00 0.00 0.00 4.30
584 1269 3.878778 AGACATGCAATTCCAGTACTCC 58.121 45.455 0.00 0.00 0.00 3.85
585 1270 5.886960 AAAGACATGCAATTCCAGTACTC 57.113 39.130 0.00 0.00 0.00 2.59
586 1271 6.568462 CGAAAAAGACATGCAATTCCAGTACT 60.568 38.462 0.00 0.00 0.00 2.73
1593 2481 0.532862 CTGCTGTGACTCGGTTTGGT 60.533 55.000 0.00 0.00 0.00 3.67
1774 2662 3.054065 GGTCTCTTGGGAAGTGATGGATT 60.054 47.826 0.00 0.00 34.02 3.01
2260 3177 1.900351 CTCGGGCTTCTGTGATGGA 59.100 57.895 0.00 0.00 0.00 3.41
2346 3278 8.768019 CGACATTTATATCTGCAGAAGAATCAA 58.232 33.333 22.50 12.34 38.79 2.57
2692 3644 9.640963 CTCTGCTGTTAACAAGGGTATATATAC 57.359 37.037 13.60 13.60 0.00 1.47


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

AutoCloner maintained by Alex Coulton.