Multiple sequence alignment - TraesCS5A01G417100

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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 TraesCS5A01G417100 chr5A 100.000 2967 0 0 1 2967 605246727 605243761 0.000000e+00 5480
1 TraesCS5A01G417100 chr5B 90.175 2280 131 39 740 2962 595010507 595008264 0.000000e+00 2883
2 TraesCS5A01G417100 chr5B 78.846 260 30 12 442 697 595010869 595010631 5.120000e-33 152
3 TraesCS5A01G417100 chr5D 93.928 1334 71 5 1639 2965 483769579 483768249 0.000000e+00 2006
4 TraesCS5A01G417100 chr5D 94.301 579 25 2 764 1342 483770157 483769587 0.000000e+00 880
5 TraesCS5A01G417100 chr5D 85.588 340 31 8 1 339 483771027 483770705 2.810000e-95 359
6 TraesCS5A01G417100 chr7D 80.821 2023 280 69 794 2741 500776005 500777994 0.000000e+00 1487
7 TraesCS5A01G417100 chr7D 82.903 1550 216 29 998 2514 113583072 113584605 0.000000e+00 1349
8 TraesCS5A01G417100 chr7B 82.276 1749 244 38 998 2697 528873881 528875612 0.000000e+00 1452
9 TraesCS5A01G417100 chr7B 80.719 1836 268 49 777 2558 664399060 664397257 0.000000e+00 1351
10 TraesCS5A01G417100 chr7B 82.732 1025 145 19 1557 2555 528876727 528877745 0.000000e+00 883
11 TraesCS5A01G417100 chr7B 81.667 600 86 11 2103 2691 73139886 73140472 7.440000e-131 477
12 TraesCS5A01G417100 chr7A 82.263 1759 235 40 998 2705 566790506 566792238 0.000000e+00 1448
13 TraesCS5A01G417100 chr7A 82.537 1277 181 32 1270 2514 619305129 619306395 0.000000e+00 1085
14 TraesCS5A01G417100 chr7A 89.841 315 32 0 998 1312 566910405 566910719 3.560000e-109 405
15 TraesCS5A01G417100 chr7A 88.788 330 31 4 998 1327 566989680 566990003 1.660000e-107 399
16 TraesCS5A01G417100 chrUn 81.330 1789 268 47 998 2749 86612161 86613920 0.000000e+00 1393
17 TraesCS5A01G417100 chr3A 82.372 1231 183 23 1354 2558 732404152 732402930 0.000000e+00 1040
18 TraesCS5A01G417100 chr3A 81.275 1020 161 19 1106 2098 728915280 728914264 0.000000e+00 798
19 TraesCS5A01G417100 chr3A 83.250 597 84 10 2164 2749 728914244 728913653 4.350000e-148 534
20 TraesCS5A01G417100 chr3A 86.744 347 43 3 1001 1345 732404533 732404188 1.670000e-102 383
21 TraesCS5A01G417100 chr3D 82.682 1126 164 17 998 2098 598726084 598724965 0.000000e+00 970
22 TraesCS5A01G417100 chr3D 83.389 596 85 8 2164 2749 598724945 598724354 9.360000e-150 540
23 TraesCS5A01G417100 chr3B 82.301 1130 164 22 998 2098 806058470 806057348 0.000000e+00 946
24 TraesCS5A01G417100 chr3B 81.935 310 45 5 2447 2748 805931910 805931604 4.910000e-63 252


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 TraesCS5A01G417100 chr5A 605243761 605246727 2966 True 5480.000000 5480 100.000000 1 2967 1 chr5A.!!$R1 2966
1 TraesCS5A01G417100 chr5B 595008264 595010869 2605 True 1517.500000 2883 84.510500 442 2962 2 chr5B.!!$R1 2520
2 TraesCS5A01G417100 chr5D 483768249 483771027 2778 True 1081.666667 2006 91.272333 1 2965 3 chr5D.!!$R1 2964
3 TraesCS5A01G417100 chr7D 500776005 500777994 1989 False 1487.000000 1487 80.821000 794 2741 1 chr7D.!!$F2 1947
4 TraesCS5A01G417100 chr7D 113583072 113584605 1533 False 1349.000000 1349 82.903000 998 2514 1 chr7D.!!$F1 1516
5 TraesCS5A01G417100 chr7B 664397257 664399060 1803 True 1351.000000 1351 80.719000 777 2558 1 chr7B.!!$R1 1781
6 TraesCS5A01G417100 chr7B 528873881 528877745 3864 False 1167.500000 1452 82.504000 998 2697 2 chr7B.!!$F2 1699
7 TraesCS5A01G417100 chr7B 73139886 73140472 586 False 477.000000 477 81.667000 2103 2691 1 chr7B.!!$F1 588
8 TraesCS5A01G417100 chr7A 566790506 566792238 1732 False 1448.000000 1448 82.263000 998 2705 1 chr7A.!!$F1 1707
9 TraesCS5A01G417100 chr7A 619305129 619306395 1266 False 1085.000000 1085 82.537000 1270 2514 1 chr7A.!!$F4 1244
10 TraesCS5A01G417100 chrUn 86612161 86613920 1759 False 1393.000000 1393 81.330000 998 2749 1 chrUn.!!$F1 1751
11 TraesCS5A01G417100 chr3A 732402930 732404533 1603 True 711.500000 1040 84.558000 1001 2558 2 chr3A.!!$R2 1557
12 TraesCS5A01G417100 chr3A 728913653 728915280 1627 True 666.000000 798 82.262500 1106 2749 2 chr3A.!!$R1 1643
13 TraesCS5A01G417100 chr3D 598724354 598726084 1730 True 755.000000 970 83.035500 998 2749 2 chr3D.!!$R1 1751
14 TraesCS5A01G417100 chr3B 806057348 806058470 1122 True 946.000000 946 82.301000 998 2098 1 chr3B.!!$R2 1100

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
700 782 0.108709 CACCCACCGGCAAATCATTG 60.109 55.0 0.0 0.0 39.65 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2692 3047 0.1791 CCGGTAGACCATGCTGACAG 60.179 60.0 0.0 0.0 35.14 3.51 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
23 24 1.792367 TCAAAGCATCTCAACACGACG 59.208 47.619 0.00 0.00 0.00 5.12
25 26 1.419374 AAGCATCTCAACACGACGAC 58.581 50.000 0.00 0.00 0.00 4.34
38 39 2.398903 CGACGACGTGCTACAAATTC 57.601 50.000 4.58 0.00 34.56 2.17
46 47 3.000041 CGTGCTACAAATTCTGGCTACA 59.000 45.455 0.00 0.00 0.00 2.74
47 48 3.435327 CGTGCTACAAATTCTGGCTACAA 59.565 43.478 0.00 0.00 0.00 2.41
58 59 6.949352 ATTCTGGCTACAAATATTCACTGG 57.051 37.500 0.00 0.00 0.00 4.00
61 62 5.189736 TCTGGCTACAAATATTCACTGGACT 59.810 40.000 0.00 0.00 0.00 3.85
80 81 2.808543 ACTTTTCCTGAGTTGCATCGAC 59.191 45.455 0.00 0.00 0.00 4.20
102 103 9.834628 TCGACATATGCTTTTAAAAACCTAAAG 57.165 29.630 1.58 0.00 33.19 1.85
138 139 0.610232 AGGTGCCCAATCAGAACAGC 60.610 55.000 0.00 0.00 0.00 4.40
147 148 3.006110 CCAATCAGAACAGCCACATTTGT 59.994 43.478 0.00 0.00 0.00 2.83
150 151 5.633830 ATCAGAACAGCCACATTTGTAAG 57.366 39.130 0.00 0.00 0.00 2.34
178 179 4.403453 GGCAAGATACAACACGTTGAATC 58.597 43.478 16.48 0.00 42.93 2.52
215 216 5.942872 ACGCAATAACAAGATTCCAGAAAG 58.057 37.500 0.00 0.00 0.00 2.62
216 217 5.705441 ACGCAATAACAAGATTCCAGAAAGA 59.295 36.000 0.00 0.00 0.00 2.52
217 218 6.206634 ACGCAATAACAAGATTCCAGAAAGAA 59.793 34.615 0.00 0.00 0.00 2.52
218 219 7.083858 CGCAATAACAAGATTCCAGAAAGAAA 58.916 34.615 0.00 0.00 0.00 2.52
219 220 7.272084 CGCAATAACAAGATTCCAGAAAGAAAG 59.728 37.037 0.00 0.00 0.00 2.62
220 221 8.299570 GCAATAACAAGATTCCAGAAAGAAAGA 58.700 33.333 0.00 0.00 0.00 2.52
252 253 9.537848 GAACAACCGTAGTCATAACAAATAAAG 57.462 33.333 0.00 0.00 0.00 1.85
301 302 4.459337 AGTTTTTCCTACTACAGCAATGGC 59.541 41.667 0.00 0.00 41.61 4.40
325 326 6.662616 CGGATGTTTCTGAATATGGTTGATC 58.337 40.000 0.00 0.00 0.00 2.92
347 348 9.256477 TGATCAGTTATTAGTTTACAATAGCGG 57.744 33.333 0.00 0.00 0.00 5.52
351 352 8.325997 CAGTTATTAGTTTACAATAGCGGACAC 58.674 37.037 0.00 0.00 0.00 3.67
388 389 6.594284 AAACGGAACAACTAACAGAGTAAC 57.406 37.500 0.00 0.00 37.44 2.50
389 390 4.625028 ACGGAACAACTAACAGAGTAACC 58.375 43.478 0.00 0.00 37.44 2.85
390 391 4.343239 ACGGAACAACTAACAGAGTAACCT 59.657 41.667 0.00 0.00 37.44 3.50
391 392 5.163374 ACGGAACAACTAACAGAGTAACCTT 60.163 40.000 0.00 0.00 37.44 3.50
392 393 5.756833 CGGAACAACTAACAGAGTAACCTTT 59.243 40.000 0.00 0.00 37.44 3.11
394 395 7.201670 CGGAACAACTAACAGAGTAACCTTTTT 60.202 37.037 0.00 0.00 37.44 1.94
395 396 9.112725 GGAACAACTAACAGAGTAACCTTTTTA 57.887 33.333 0.00 0.00 37.44 1.52
436 474 2.882927 AGTTGAGTACAAGACACGCA 57.117 45.000 0.00 0.00 36.64 5.24
460 538 1.592400 CCGACAGAACACCGAGGCTA 61.592 60.000 0.00 0.00 0.00 3.93
463 541 0.900647 ACAGAACACCGAGGCTAGCT 60.901 55.000 15.72 0.00 0.00 3.32
471 549 1.649815 CGAGGCTAGCTACCTGACG 59.350 63.158 15.72 11.98 37.77 4.35
472 550 1.787057 CGAGGCTAGCTACCTGACGG 61.787 65.000 15.72 0.00 37.77 4.79
473 551 0.465824 GAGGCTAGCTACCTGACGGA 60.466 60.000 15.72 0.00 37.77 4.69
481 561 1.207329 GCTACCTGACGGACCAAGATT 59.793 52.381 0.00 0.00 0.00 2.40
485 565 1.002624 TGACGGACCAAGATTGCCC 60.003 57.895 0.00 0.00 0.00 5.36
512 592 4.643387 AAGCTCCAACGCGCCCTT 62.643 61.111 5.73 0.00 34.40 3.95
525 605 2.178235 GCCCTTAGCCGGTTAAGCG 61.178 63.158 27.48 21.76 34.35 4.68
529 609 1.143969 CTTAGCCGGTTAAGCGTCCG 61.144 60.000 22.91 10.49 45.42 4.79
541 621 4.088421 CGTCCGCGCTGTTAGATT 57.912 55.556 5.56 0.00 0.00 2.40
561 643 4.473520 CCGCTGGGAATGGCTCGT 62.474 66.667 0.00 0.00 34.06 4.18
563 645 2.268920 GCTGGGAATGGCTCGTCA 59.731 61.111 0.00 0.00 0.00 4.35
564 646 1.817099 GCTGGGAATGGCTCGTCAG 60.817 63.158 0.00 0.00 32.37 3.51
565 647 1.817099 CTGGGAATGGCTCGTCAGC 60.817 63.158 0.00 0.00 46.06 4.26
575 657 2.357034 TCGTCAGCCGAGCCAAAC 60.357 61.111 0.00 0.00 41.60 2.93
576 658 2.664851 CGTCAGCCGAGCCAAACA 60.665 61.111 0.00 0.00 39.56 2.83
577 659 2.671177 CGTCAGCCGAGCCAAACAG 61.671 63.158 0.00 0.00 39.56 3.16
579 661 4.093952 CAGCCGAGCCAAACAGCG 62.094 66.667 0.00 0.00 38.01 5.18
580 662 4.626081 AGCCGAGCCAAACAGCGT 62.626 61.111 0.00 0.00 38.01 5.07
582 664 2.740714 GCCGAGCCAAACAGCGTAG 61.741 63.158 0.00 0.00 38.01 3.51
583 665 1.374252 CCGAGCCAAACAGCGTAGT 60.374 57.895 0.00 0.00 38.01 2.73
584 666 1.626654 CCGAGCCAAACAGCGTAGTG 61.627 60.000 0.00 0.00 38.01 2.74
585 667 1.497722 GAGCCAAACAGCGTAGTGC 59.502 57.895 0.00 0.00 46.98 4.40
594 676 3.617538 GCGTAGTGCCGATGTCGC 61.618 66.667 0.00 0.00 37.76 5.19
595 677 2.102357 CGTAGTGCCGATGTCGCT 59.898 61.111 0.00 0.00 38.18 4.93
596 678 1.354155 CGTAGTGCCGATGTCGCTA 59.646 57.895 0.00 0.00 38.18 4.26
597 679 0.248336 CGTAGTGCCGATGTCGCTAA 60.248 55.000 0.00 0.00 38.18 3.09
598 680 1.197910 GTAGTGCCGATGTCGCTAAC 58.802 55.000 0.00 0.00 38.18 2.34
599 681 1.100510 TAGTGCCGATGTCGCTAACT 58.899 50.000 0.00 3.09 38.18 2.24
600 682 0.179134 AGTGCCGATGTCGCTAACTC 60.179 55.000 0.00 0.00 38.18 3.01
601 683 0.179134 GTGCCGATGTCGCTAACTCT 60.179 55.000 0.00 0.00 38.18 3.24
602 684 0.530744 TGCCGATGTCGCTAACTCTT 59.469 50.000 0.00 0.00 38.18 2.85
609 691 2.433868 GTCGCTAACTCTTGGTGACA 57.566 50.000 7.04 0.00 46.74 3.58
630 712 2.461695 AGTGACATCAACGAGGGAGAT 58.538 47.619 0.00 0.00 0.00 2.75
631 713 2.167281 AGTGACATCAACGAGGGAGATG 59.833 50.000 0.00 0.00 43.56 2.90
650 732 1.550524 TGACAAGCTACGCTGATTCCT 59.449 47.619 0.00 0.00 39.62 3.36
651 733 2.197577 GACAAGCTACGCTGATTCCTC 58.802 52.381 0.00 0.00 39.62 3.71
660 742 3.744660 ACGCTGATTCCTCAAGAACTTT 58.255 40.909 0.00 0.00 37.29 2.66
700 782 0.108709 CACCCACCGGCAAATCATTG 60.109 55.000 0.00 0.00 39.65 2.82
742 848 1.511318 CGAGACGCTCCATCGATCCT 61.511 60.000 0.00 0.00 38.72 3.24
757 929 1.000163 GATCCTGTCCGTGACGCATAT 60.000 52.381 0.00 0.00 34.95 1.78
758 930 0.384309 TCCTGTCCGTGACGCATATC 59.616 55.000 0.00 0.00 34.95 1.63
759 931 0.597637 CCTGTCCGTGACGCATATCC 60.598 60.000 0.00 0.00 34.95 2.59
760 932 0.934901 CTGTCCGTGACGCATATCCG 60.935 60.000 0.00 0.00 34.95 4.18
761 933 1.065273 GTCCGTGACGCATATCCGT 59.935 57.895 0.00 0.00 45.30 4.69
762 934 1.065109 TCCGTGACGCATATCCGTG 59.935 57.895 0.00 0.00 42.24 4.94
804 976 4.458829 TGGGGCTCCGACTCCGAT 62.459 66.667 0.00 0.00 38.22 4.18
832 1011 2.588877 CGCAGGCCCGATTTCGAT 60.589 61.111 0.00 0.00 43.02 3.59
854 1033 2.790433 TGTTTTCCTGCTGGTCCATAC 58.210 47.619 9.73 3.46 34.23 2.39
960 1167 1.133790 GGCGAAAGAGTAGCGGTTAGA 59.866 52.381 0.00 0.00 0.00 2.10
987 1194 2.989840 CAGAAACCAGCAGTTCTCGTAG 59.010 50.000 0.00 0.00 37.88 3.51
990 1197 1.853963 ACCAGCAGTTCTCGTAGGAT 58.146 50.000 0.00 0.00 0.00 3.24
1122 1335 0.669077 AGAAGTCGTCGAGCAACACT 59.331 50.000 0.00 0.00 0.00 3.55
1358 1626 1.083895 TAATCCCTGCCCCTGGTGA 59.916 57.895 0.00 0.00 0.00 4.02
1377 1656 7.202093 CCTGGTGAATCACAATTATCCCTACTA 60.202 40.741 15.86 0.00 35.86 1.82
1402 1681 7.684062 ACTGCTTTATTAATAAATTGCAGCG 57.316 32.000 34.60 24.67 45.55 5.18
1799 2122 5.882557 ACTGCTTATATTGGAAAGGTGACAG 59.117 40.000 0.00 0.00 0.00 3.51
1880 2203 1.338769 ACAACTTGCACCCTATCGGTC 60.339 52.381 0.00 0.00 43.58 4.79
2073 2400 7.966204 GGTACGTATGTATTTTCATGCAAAGTT 59.034 33.333 0.00 0.00 32.11 2.66
2344 2677 1.377202 GACGACATGCACCCCACAT 60.377 57.895 0.00 0.00 0.00 3.21
2370 2703 2.911636 AGGATGGGAGGCTATCATGAAG 59.088 50.000 0.00 0.00 0.00 3.02
2424 2757 6.066032 AGATCAAGACTAGGTAGCTAGGTTC 58.934 44.000 27.89 18.83 0.00 3.62
2692 3047 6.471839 CAATTCCACATCGATTGATTTTTGC 58.528 36.000 0.00 0.00 33.67 3.68
2713 3076 1.001120 TCAGCATGGTCTACCGGGA 59.999 57.895 6.32 0.00 39.43 5.14
2783 3697 3.005539 GGTCAGCCAGAGCCCTCA 61.006 66.667 0.00 0.00 41.25 3.86
2918 4382 4.774124 TGATCACCCATTCTCACAAGATC 58.226 43.478 0.00 0.00 33.19 2.75
2965 4429 7.244886 AGGTTTATTTTTGAGGATCTTTGGG 57.755 36.000 0.00 0.00 34.92 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.076863 AGCCAGAATTTGTAGCACGTC 58.923 47.619 0.00 0.00 0.00 4.34
25 26 3.000041 TGTAGCCAGAATTTGTAGCACG 59.000 45.455 0.00 0.00 0.00 5.34
38 39 5.431765 AGTCCAGTGAATATTTGTAGCCAG 58.568 41.667 0.00 0.00 0.00 4.85
58 59 3.067106 TCGATGCAACTCAGGAAAAGTC 58.933 45.455 0.00 0.00 0.00 3.01
61 62 2.844946 TGTCGATGCAACTCAGGAAAA 58.155 42.857 0.00 0.00 0.00 2.29
91 92 7.724061 TCTTGGTGAGCTATTCTTTAGGTTTTT 59.276 33.333 0.00 0.00 0.00 1.94
101 102 4.917906 ACCTTTCTTGGTGAGCTATTCT 57.082 40.909 0.00 0.00 39.17 2.40
138 139 3.417101 TGCCCAGTACTTACAAATGTGG 58.583 45.455 0.00 0.00 0.00 4.17
147 148 5.484715 GTGTTGTATCTTGCCCAGTACTTA 58.515 41.667 0.00 0.00 0.00 2.24
150 151 2.671396 CGTGTTGTATCTTGCCCAGTAC 59.329 50.000 0.00 0.00 0.00 2.73
178 179 6.815359 TGTTATTGCGTAATTTGTTTGCATG 58.185 32.000 3.47 0.00 35.20 4.06
221 222 7.556733 TGTTATGACTACGGTTGTTCTTTTT 57.443 32.000 0.00 0.00 0.00 1.94
222 223 7.556733 TTGTTATGACTACGGTTGTTCTTTT 57.443 32.000 0.00 0.00 0.00 2.27
223 224 7.556733 TTTGTTATGACTACGGTTGTTCTTT 57.443 32.000 0.00 0.00 0.00 2.52
224 225 7.739498 ATTTGTTATGACTACGGTTGTTCTT 57.261 32.000 0.00 0.00 0.00 2.52
225 226 8.836268 TTATTTGTTATGACTACGGTTGTTCT 57.164 30.769 0.00 0.00 0.00 3.01
226 227 9.537848 CTTTATTTGTTATGACTACGGTTGTTC 57.462 33.333 0.00 0.00 0.00 3.18
227 228 8.508875 CCTTTATTTGTTATGACTACGGTTGTT 58.491 33.333 0.00 0.00 0.00 2.83
228 229 7.879160 TCCTTTATTTGTTATGACTACGGTTGT 59.121 33.333 0.00 0.00 0.00 3.32
229 230 8.259049 TCCTTTATTTGTTATGACTACGGTTG 57.741 34.615 0.00 0.00 0.00 3.77
230 231 8.724229 GTTCCTTTATTTGTTATGACTACGGTT 58.276 33.333 0.00 0.00 0.00 4.44
231 232 7.335171 GGTTCCTTTATTTGTTATGACTACGGT 59.665 37.037 0.00 0.00 0.00 4.83
232 233 7.334921 TGGTTCCTTTATTTGTTATGACTACGG 59.665 37.037 0.00 0.00 0.00 4.02
233 234 8.259049 TGGTTCCTTTATTTGTTATGACTACG 57.741 34.615 0.00 0.00 0.00 3.51
265 266 3.288092 GGAAAAACTGTTCCAGGTGTCT 58.712 45.455 0.00 0.00 45.57 3.41
284 285 0.464036 CCGCCATTGCTGTAGTAGGA 59.536 55.000 0.00 0.00 34.43 2.94
301 302 6.260714 TGATCAACCATATTCAGAAACATCCG 59.739 38.462 0.00 0.00 0.00 4.18
325 326 8.325997 GTGTCCGCTATTGTAAACTAATAACTG 58.674 37.037 0.00 0.00 0.00 3.16
333 334 2.613691 CGGTGTCCGCTATTGTAAACT 58.386 47.619 0.00 0.00 41.17 2.66
364 365 6.037500 GGTTACTCTGTTAGTTGTTCCGTTTT 59.962 38.462 0.00 0.00 39.80 2.43
365 366 5.525012 GGTTACTCTGTTAGTTGTTCCGTTT 59.475 40.000 0.00 0.00 39.80 3.60
366 367 5.052481 GGTTACTCTGTTAGTTGTTCCGTT 58.948 41.667 0.00 0.00 39.80 4.44
367 368 4.343239 AGGTTACTCTGTTAGTTGTTCCGT 59.657 41.667 0.00 0.00 39.80 4.69
369 370 7.563888 AAAAGGTTACTCTGTTAGTTGTTCC 57.436 36.000 0.00 0.00 39.80 3.62
421 459 1.192534 GTTGCTGCGTGTCTTGTACTC 59.807 52.381 0.00 0.00 0.00 2.59
436 474 1.594293 CGGTGTTCTGTCGGTTGCT 60.594 57.895 0.00 0.00 0.00 3.91
460 538 0.251653 TCTTGGTCCGTCAGGTAGCT 60.252 55.000 0.00 0.00 39.05 3.32
463 541 1.066430 GCAATCTTGGTCCGTCAGGTA 60.066 52.381 0.00 0.00 39.05 3.08
471 549 0.039618 TCCTTGGGCAATCTTGGTCC 59.960 55.000 0.00 0.00 0.00 4.46
472 550 1.004745 TCTCCTTGGGCAATCTTGGTC 59.995 52.381 0.00 0.00 0.00 4.02
473 551 1.075601 TCTCCTTGGGCAATCTTGGT 58.924 50.000 0.00 0.00 0.00 3.67
481 561 0.326264 GAGCTTCTTCTCCTTGGGCA 59.674 55.000 0.00 0.00 0.00 5.36
512 592 2.491152 CGGACGCTTAACCGGCTA 59.509 61.111 0.00 0.00 44.59 3.93
525 605 1.348594 GCAATCTAACAGCGCGGAC 59.651 57.895 16.26 0.00 0.00 4.79
529 609 2.709475 CGGGCAATCTAACAGCGC 59.291 61.111 0.00 0.00 37.79 5.92
536 616 0.179020 CATTCCCAGCGGGCAATCTA 60.179 55.000 8.57 0.00 43.94 1.98
537 617 1.454479 CATTCCCAGCGGGCAATCT 60.454 57.895 8.57 0.00 43.94 2.40
559 641 2.664851 TGTTTGGCTCGGCTGACG 60.665 61.111 0.00 0.00 46.11 4.35
561 643 2.669569 GCTGTTTGGCTCGGCTGA 60.670 61.111 0.00 0.00 34.72 4.26
563 645 3.234630 TACGCTGTTTGGCTCGGCT 62.235 57.895 7.01 0.00 35.32 5.52
564 646 2.740714 CTACGCTGTTTGGCTCGGC 61.741 63.158 0.00 0.00 0.00 5.54
565 647 1.374252 ACTACGCTGTTTGGCTCGG 60.374 57.895 0.00 0.00 0.00 4.63
567 649 1.497722 GCACTACGCTGTTTGGCTC 59.502 57.895 0.00 0.00 37.77 4.70
568 650 1.966451 GGCACTACGCTGTTTGGCT 60.966 57.895 0.00 0.00 41.91 4.75
570 652 2.860293 CGGCACTACGCTGTTTGG 59.140 61.111 0.00 0.00 42.55 3.28
576 658 2.102357 CGACATCGGCACTACGCT 59.898 61.111 0.00 0.00 41.91 5.07
577 659 2.657484 TAGCGACATCGGCACTACGC 62.657 60.000 3.08 0.00 45.03 4.42
579 661 1.197910 GTTAGCGACATCGGCACTAC 58.802 55.000 3.08 0.00 40.23 2.73
580 662 1.065102 GAGTTAGCGACATCGGCACTA 59.935 52.381 3.08 0.00 40.23 2.74
582 664 0.179134 AGAGTTAGCGACATCGGCAC 60.179 55.000 3.08 0.00 40.23 5.01
583 665 0.530744 AAGAGTTAGCGACATCGGCA 59.469 50.000 3.08 0.00 40.23 5.69
584 666 0.924090 CAAGAGTTAGCGACATCGGC 59.076 55.000 3.08 0.00 40.23 5.54
585 667 1.135083 ACCAAGAGTTAGCGACATCGG 60.135 52.381 3.08 0.00 40.23 4.18
586 668 1.920574 CACCAAGAGTTAGCGACATCG 59.079 52.381 0.00 0.00 43.27 3.84
587 669 2.924290 GTCACCAAGAGTTAGCGACATC 59.076 50.000 0.00 0.00 0.00 3.06
588 670 2.299013 TGTCACCAAGAGTTAGCGACAT 59.701 45.455 0.00 0.00 0.00 3.06
589 671 1.684450 TGTCACCAAGAGTTAGCGACA 59.316 47.619 0.00 0.00 0.00 4.35
590 672 2.433868 TGTCACCAAGAGTTAGCGAC 57.566 50.000 0.00 0.00 0.00 5.19
601 683 2.611751 CGTTGATGTCACTTGTCACCAA 59.388 45.455 0.00 0.00 0.00 3.67
602 684 2.159028 TCGTTGATGTCACTTGTCACCA 60.159 45.455 0.00 0.00 0.00 4.17
609 691 2.248248 TCTCCCTCGTTGATGTCACTT 58.752 47.619 0.00 0.00 0.00 3.16
612 694 2.166459 GTCATCTCCCTCGTTGATGTCA 59.834 50.000 0.00 0.00 38.78 3.58
650 732 0.383949 GGCGTTGGCAAAGTTCTTGA 59.616 50.000 14.46 0.00 42.47 3.02
651 733 0.934436 CGGCGTTGGCAAAGTTCTTG 60.934 55.000 14.46 0.00 42.47 3.02
660 742 2.203084 TCTTTGACGGCGTTGGCA 60.203 55.556 16.19 4.58 42.47 4.92
700 782 2.447887 CGACGCTGCAGTGGATGTC 61.448 63.158 29.60 17.20 0.00 3.06
738 844 1.000163 GATATGCGTCACGGACAGGAT 60.000 52.381 0.00 6.52 32.09 3.24
742 848 1.065109 CGGATATGCGTCACGGACA 59.935 57.895 8.66 0.00 32.09 4.02
757 929 3.663176 GTCGGACACGGACACGGA 61.663 66.667 2.62 0.00 46.48 4.69
758 930 4.712425 GGTCGGACACGGACACGG 62.712 72.222 10.76 0.00 46.48 4.94
760 932 2.257676 GAGGTCGGACACGGACAC 59.742 66.667 10.76 0.00 41.39 3.67
761 933 2.987547 GGAGGTCGGACACGGACA 60.988 66.667 10.76 0.00 41.39 4.02
762 934 4.112341 CGGAGGTCGGACACGGAC 62.112 72.222 10.76 0.00 41.39 4.79
803 975 3.034878 CCTGCGACCTCGATCGAT 58.965 61.111 19.78 4.24 45.13 3.59
804 976 3.889044 GCCTGCGACCTCGATCGA 61.889 66.667 18.32 18.32 45.13 3.59
832 1011 2.151502 TGGACCAGCAGGAAAACAAA 57.848 45.000 0.35 0.00 38.69 2.83
854 1033 7.921214 TCTCGCTTCAATTTATAGAACTACTGG 59.079 37.037 0.00 0.00 0.00 4.00
960 1167 2.203337 TGCTGGTTTCTGCGGCTT 60.203 55.556 0.00 0.00 40.18 4.35
990 1197 1.115467 GAAGCTTCATCGAGGGAGGA 58.885 55.000 21.67 0.00 0.00 3.71
1122 1335 3.900446 GTCCCCGAAGACGAAGAAA 57.100 52.632 0.00 0.00 42.66 2.52
1348 1600 1.560505 AATTGTGATTCACCAGGGGC 58.439 50.000 14.05 0.00 32.73 5.80
1358 1626 7.806180 AGCAGTTAGTAGGGATAATTGTGATT 58.194 34.615 0.00 0.00 0.00 2.57
1377 1656 7.973388 TCGCTGCAATTTATTAATAAAGCAGTT 59.027 29.630 34.41 21.20 44.63 3.16
1394 1673 0.244450 CCCAACATTGTCGCTGCAAT 59.756 50.000 0.00 0.00 39.42 3.56
1402 1681 1.203001 TCCTCCAACCCCAACATTGTC 60.203 52.381 0.00 0.00 0.00 3.18
1671 1975 2.832838 TGATACTCACATCACTGGGGT 58.167 47.619 0.00 0.00 29.93 4.95
1770 2093 8.271458 TCACCTTTCCAATATAAGCAGTAATCA 58.729 33.333 0.00 0.00 0.00 2.57
1776 2099 6.115446 TCTGTCACCTTTCCAATATAAGCAG 58.885 40.000 0.00 0.00 0.00 4.24
1799 2122 1.789464 CACATTAGCCGCGATCTCTTC 59.211 52.381 8.23 0.00 0.00 2.87
1880 2203 4.659874 GGTTTGTGACGGCGTGCG 62.660 66.667 21.19 0.00 0.00 5.34
2101 2429 9.851686 AAGCATACAATCAAACTCCATCTAATA 57.148 29.630 0.00 0.00 0.00 0.98
2161 2493 5.130350 TGAGCCTTTACCTACATTAATGCC 58.870 41.667 15.48 0.00 0.00 4.40
2344 2677 2.191400 GATAGCCTCCCATCCTGCATA 58.809 52.381 0.00 0.00 0.00 3.14
2370 2703 1.039856 TCAAGGGCTTTTCCAACTGC 58.960 50.000 0.00 0.00 36.21 4.40
2666 3019 4.987408 AATCAATCGATGTGGAATTGCA 57.013 36.364 0.00 0.00 30.13 4.08
2692 3047 0.179100 CCGGTAGACCATGCTGACAG 60.179 60.000 0.00 0.00 35.14 3.51
2713 3076 3.070446 TCATCACCCTTAGAACACGTTGT 59.930 43.478 0.00 0.00 0.00 3.32
2783 3697 9.904198 AAGCAGCCCAAATAAAATAAATACATT 57.096 25.926 0.00 0.00 0.00 2.71
2918 4382 8.428063 ACCTTATTCTTATCTGAACATCCTCTG 58.572 37.037 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.