Multiple sequence alignment - TraesCS7A01G348300

Loading Multiple Alignment...

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 TraesCS7A01G348300 chr7A 100.000 2315 0 0 1 2315 511011277 511013591 0.000000e+00 4276
1 TraesCS7A01G348300 chr5D 86.472 1471 97 32 630 2043 423964348 423965773 0.000000e+00 1520
2 TraesCS7A01G348300 chr5B 86.422 1473 101 46 624 2043 511835144 511836570 0.000000e+00 1520
3 TraesCS7A01G348300 chr5B 83.220 441 52 17 149 572 511830549 511830984 3.610000e-103 385
4 TraesCS7A01G348300 chr5B 83.220 441 52 17 149 572 511832302 511832737 3.610000e-103 385
5 TraesCS7A01G348300 chr5B 83.220 441 52 17 149 572 511833792 511834227 3.610000e-103 385
6 TraesCS7A01G348300 chr5A 88.337 926 57 27 619 1520 537368677 537369575 0.000000e+00 1064
7 TraesCS7A01G348300 chr5A 91.829 257 12 3 1516 1763 537369601 537369857 1.320000e-92 350
8 TraesCS7A01G348300 chr7D 90.598 819 46 12 1516 2315 422151942 422151136 0.000000e+00 1057
9 TraesCS7A01G348300 chr7D 87.500 848 55 15 698 1520 422152789 422151968 0.000000e+00 931
10 TraesCS7A01G348300 chr7B 91.079 695 39 10 839 1520 438950443 438951127 0.000000e+00 918
11 TraesCS7A01G348300 chr7B 86.642 816 60 17 1516 2312 438951153 438951938 0.000000e+00 857
12 TraesCS7A01G348300 chr4B 86.317 877 50 21 1226 2043 4232179 4233044 0.000000e+00 891
13 TraesCS7A01G348300 chr4A 85.860 884 54 22 1226 2049 663652656 663651784 0.000000e+00 874
14 TraesCS7A01G348300 chr6A 83.197 732 77 32 692 1396 49550600 49551312 1.510000e-176 628
15 TraesCS7A01G348300 chr6A 80.220 546 59 31 878 1396 49201970 49202493 4.700000e-97 364
16 TraesCS7A01G348300 chr6A 88.696 115 12 1 683 797 49196543 49196656 3.100000e-29 139
17 TraesCS7A01G348300 chr6A 91.753 97 7 1 692 788 49483553 49483648 1.440000e-27 134
18 TraesCS7A01G348300 chr6D 82.869 718 76 29 692 1390 37933790 37934479 3.290000e-168 601
19 TraesCS7A01G348300 chr6D 82.385 738 69 37 694 1396 37927544 37928255 9.220000e-164 586
20 TraesCS7A01G348300 chr6B 81.424 576 67 23 833 1390 88781204 88781757 3.530000e-118 435


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 TraesCS7A01G348300 chr7A 511011277 511013591 2314 False 4276.00 4276 100.0000 1 2315 1 chr7A.!!$F1 2314
1 TraesCS7A01G348300 chr5D 423964348 423965773 1425 False 1520.00 1520 86.4720 630 2043 1 chr5D.!!$F1 1413
2 TraesCS7A01G348300 chr5B 511830549 511836570 6021 False 668.75 1520 84.0205 149 2043 4 chr5B.!!$F1 1894
3 TraesCS7A01G348300 chr5A 537368677 537369857 1180 False 707.00 1064 90.0830 619 1763 2 chr5A.!!$F1 1144
4 TraesCS7A01G348300 chr7D 422151136 422152789 1653 True 994.00 1057 89.0490 698 2315 2 chr7D.!!$R1 1617
5 TraesCS7A01G348300 chr7B 438950443 438951938 1495 False 887.50 918 88.8605 839 2312 2 chr7B.!!$F1 1473
6 TraesCS7A01G348300 chr4B 4232179 4233044 865 False 891.00 891 86.3170 1226 2043 1 chr4B.!!$F1 817
7 TraesCS7A01G348300 chr4A 663651784 663652656 872 True 874.00 874 85.8600 1226 2049 1 chr4A.!!$R1 823
8 TraesCS7A01G348300 chr6A 49550600 49551312 712 False 628.00 628 83.1970 692 1396 1 chr6A.!!$F4 704
9 TraesCS7A01G348300 chr6A 49201970 49202493 523 False 364.00 364 80.2200 878 1396 1 chr6A.!!$F2 518
10 TraesCS7A01G348300 chr6D 37933790 37934479 689 False 601.00 601 82.8690 692 1390 1 chr6D.!!$F2 698
11 TraesCS7A01G348300 chr6D 37927544 37928255 711 False 586.00 586 82.3850 694 1396 1 chr6D.!!$F1 702
12 TraesCS7A01G348300 chr6B 88781204 88781757 553 False 435.00 435 81.4240 833 1390 1 chr6B.!!$F1 557

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
537 554 0.550147 AATAGTGCTGTGGAGGGGGT 60.55 55.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 6010 1.311403 CCTCCTGCTCCCTCTACCA 59.689 63.158 0.0 0.0 0.0 3.25 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
32 33 9.769093 AGTATCATGAGTTAATAAAACGTTTGC 57.231 29.630 15.46 1.56 0.00 3.68
33 34 7.719689 ATCATGAGTTAATAAAACGTTTGCG 57.280 32.000 15.46 0.00 44.93 4.85
34 35 6.081049 TCATGAGTTAATAAAACGTTTGCGG 58.919 36.000 15.46 0.00 43.45 5.69
35 36 4.785417 TGAGTTAATAAAACGTTTGCGGG 58.215 39.130 15.46 0.00 43.45 6.13
36 37 4.514441 TGAGTTAATAAAACGTTTGCGGGA 59.486 37.500 15.46 0.00 43.45 5.14
37 38 5.181622 TGAGTTAATAAAACGTTTGCGGGAT 59.818 36.000 15.46 0.00 43.45 3.85
38 39 6.370994 TGAGTTAATAAAACGTTTGCGGGATA 59.629 34.615 15.46 2.14 43.45 2.59
39 40 7.066043 TGAGTTAATAAAACGTTTGCGGGATAT 59.934 33.333 15.46 4.61 43.45 1.63
40 41 8.436046 AGTTAATAAAACGTTTGCGGGATATA 57.564 30.769 15.46 0.58 43.45 0.86
41 42 8.891720 AGTTAATAAAACGTTTGCGGGATATAA 58.108 29.630 15.46 3.76 43.45 0.98
42 43 9.500864 GTTAATAAAACGTTTGCGGGATATAAA 57.499 29.630 15.46 0.00 43.45 1.40
44 45 8.983307 AATAAAACGTTTGCGGGATATAAAAA 57.017 26.923 15.46 0.00 43.45 1.94
83 84 6.647212 AAAAGGTTTTCAAGCTCGAAAAAG 57.353 33.333 13.96 0.00 44.24 2.27
84 85 4.983671 AGGTTTTCAAGCTCGAAAAAGT 57.016 36.364 13.96 2.15 44.24 2.66
85 86 5.324784 AGGTTTTCAAGCTCGAAAAAGTT 57.675 34.783 13.96 0.88 44.24 2.66
86 87 5.340803 AGGTTTTCAAGCTCGAAAAAGTTC 58.659 37.500 13.96 2.32 44.24 3.01
87 88 5.099575 GGTTTTCAAGCTCGAAAAAGTTCA 58.900 37.500 13.96 0.00 44.24 3.18
88 89 5.004440 GGTTTTCAAGCTCGAAAAAGTTCAC 59.996 40.000 13.96 1.84 44.24 3.18
89 90 3.585748 TCAAGCTCGAAAAAGTTCACG 57.414 42.857 0.00 0.00 32.89 4.35
90 91 3.191669 TCAAGCTCGAAAAAGTTCACGA 58.808 40.909 0.00 0.00 32.89 4.35
98 99 7.942145 CTCGAAAAAGTTCACGAGTTAAAAA 57.058 32.000 14.05 0.00 44.37 1.94
136 137 5.822584 AAAAATCGCGGTTTTGAAAGATC 57.177 34.783 29.07 0.00 32.02 2.75
137 138 4.497473 AAATCGCGGTTTTGAAAGATCA 57.503 36.364 12.49 0.00 0.00 2.92
138 139 2.961522 TCGCGGTTTTGAAAGATCAC 57.038 45.000 6.13 0.00 34.61 3.06
139 140 2.214347 TCGCGGTTTTGAAAGATCACA 58.786 42.857 6.13 0.00 34.61 3.58
140 141 2.811431 TCGCGGTTTTGAAAGATCACAT 59.189 40.909 6.13 0.00 34.61 3.21
141 142 3.252215 TCGCGGTTTTGAAAGATCACATT 59.748 39.130 6.13 0.00 34.61 2.71
142 143 3.980775 CGCGGTTTTGAAAGATCACATTT 59.019 39.130 0.00 0.00 34.61 2.32
143 144 4.444056 CGCGGTTTTGAAAGATCACATTTT 59.556 37.500 0.00 0.00 34.61 1.82
144 145 5.387342 CGCGGTTTTGAAAGATCACATTTTC 60.387 40.000 0.00 0.00 34.61 2.29
145 146 5.461737 GCGGTTTTGAAAGATCACATTTTCA 59.538 36.000 4.26 4.26 40.46 2.69
146 147 6.346040 GCGGTTTTGAAAGATCACATTTTCAG 60.346 38.462 7.62 0.00 42.35 3.02
147 148 6.697019 CGGTTTTGAAAGATCACATTTTCAGT 59.303 34.615 7.62 0.00 42.35 3.41
148 149 7.860373 CGGTTTTGAAAGATCACATTTTCAGTA 59.140 33.333 7.62 0.42 42.35 2.74
149 150 9.528018 GGTTTTGAAAGATCACATTTTCAGTAA 57.472 29.630 7.62 5.08 42.35 2.24
154 155 9.748708 TGAAAGATCACATTTTCAGTAAAAAGG 57.251 29.630 4.26 0.00 42.78 3.11
155 156 9.965824 GAAAGATCACATTTTCAGTAAAAAGGA 57.034 29.630 0.00 0.00 40.26 3.36
156 157 9.971922 AAAGATCACATTTTCAGTAAAAAGGAG 57.028 29.630 0.00 0.00 40.26 3.69
157 158 8.924511 AGATCACATTTTCAGTAAAAAGGAGA 57.075 30.769 0.00 0.77 40.26 3.71
158 159 9.354673 AGATCACATTTTCAGTAAAAAGGAGAA 57.645 29.630 0.00 0.00 40.09 2.87
184 185 8.611654 AAAATCTGAGGAAAATCAACAATTGG 57.388 30.769 10.83 0.00 0.00 3.16
196 197 7.729124 AATCAACAATTGGAGGAAAGATCAT 57.271 32.000 10.83 0.00 0.00 2.45
201 202 8.689061 CAACAATTGGAGGAAAGATCATGAATA 58.311 33.333 10.83 0.00 0.00 1.75
227 228 9.696917 ATGAATAACATTCACTTGGAAAAGTTC 57.303 29.630 3.81 0.00 39.39 3.01
237 238 4.570369 ACTTGGAAAAGTTCGCAAAAATGG 59.430 37.500 0.00 0.00 0.00 3.16
312 314 7.712205 AGTTCATGAAATTTGGGAAAAGTTGAG 59.288 33.333 10.35 0.00 0.00 3.02
332 334 9.525409 AGTTGAGAGATTTGAAATGAAAAAGTG 57.475 29.630 0.00 0.00 0.00 3.16
333 335 9.520204 GTTGAGAGATTTGAAATGAAAAAGTGA 57.480 29.630 0.00 0.00 0.00 3.41
343 347 9.837525 TTGAAATGAAAAAGTGAACAAAAATGG 57.162 25.926 0.00 0.00 0.00 3.16
344 348 8.457261 TGAAATGAAAAAGTGAACAAAAATGGG 58.543 29.630 0.00 0.00 0.00 4.00
347 351 7.986085 TGAAAAAGTGAACAAAAATGGGAAA 57.014 28.000 0.00 0.00 0.00 3.13
348 352 8.572855 TGAAAAAGTGAACAAAAATGGGAAAT 57.427 26.923 0.00 0.00 0.00 2.17
392 396 6.983890 AGTTCGCAAAATTGGTAAAAGTTCAT 59.016 30.769 0.00 0.00 0.00 2.57
397 401 8.281893 CGCAAAATTGGTAAAAGTTCATGAATT 58.718 29.630 12.12 4.21 0.00 2.17
398 402 9.949174 GCAAAATTGGTAAAAGTTCATGAATTT 57.051 25.926 12.12 11.05 0.00 1.82
401 405 9.844257 AAATTGGTAAAAGTTCATGAATTTGGA 57.156 25.926 15.98 5.52 0.00 3.53
409 413 9.757227 AAAAGTTCATGAATTTGGATAAAACGA 57.243 25.926 15.98 0.00 0.00 3.85
412 416 9.757227 AGTTCATGAATTTGGATAAAACGAAAA 57.243 25.926 12.12 0.00 0.00 2.29
465 482 7.899178 AAAAAGAAAGAAAGCGAAAAAGGAA 57.101 28.000 0.00 0.00 0.00 3.36
468 485 7.899178 AAGAAAGAAAGCGAAAAAGGAAAAA 57.101 28.000 0.00 0.00 0.00 1.94
501 518 6.894339 AAACCGGTGAAAAGAATCTACATT 57.106 33.333 8.52 0.00 0.00 2.71
537 554 0.550147 AATAGTGCTGTGGAGGGGGT 60.550 55.000 0.00 0.00 0.00 4.95
538 555 1.274703 ATAGTGCTGTGGAGGGGGTG 61.275 60.000 0.00 0.00 0.00 4.61
544 561 4.699522 GTGGAGGGGGTGTGCGTC 62.700 72.222 0.00 0.00 0.00 5.19
550 567 2.030862 GGGGTGTGCGTCGGTTAA 59.969 61.111 0.00 0.00 0.00 2.01
552 569 2.319841 GGGTGTGCGTCGGTTAACC 61.320 63.158 15.13 15.13 0.00 2.85
560 577 1.958417 CGTCGGTTAACCAAATGCAC 58.042 50.000 24.14 9.07 35.14 4.57
561 578 1.264557 CGTCGGTTAACCAAATGCACA 59.735 47.619 24.14 0.00 35.14 4.57
563 580 1.609555 TCGGTTAACCAAATGCACACC 59.390 47.619 24.14 0.00 35.14 4.16
592 1359 2.888834 AATGAATTTACATGGGCCGC 57.111 45.000 0.00 0.00 0.00 6.53
603 1370 4.424711 GGGCCGCCCATCTTCACA 62.425 66.667 24.62 0.00 44.65 3.58
605 1372 1.976474 GGCCGCCCATCTTCACAAA 60.976 57.895 0.00 0.00 0.00 2.83
606 1373 1.212751 GCCGCCCATCTTCACAAAC 59.787 57.895 0.00 0.00 0.00 2.93
607 1374 1.523154 GCCGCCCATCTTCACAAACA 61.523 55.000 0.00 0.00 0.00 2.83
608 1375 0.958091 CCGCCCATCTTCACAAACAA 59.042 50.000 0.00 0.00 0.00 2.83
609 1376 1.339610 CCGCCCATCTTCACAAACAAA 59.660 47.619 0.00 0.00 0.00 2.83
610 1377 2.607771 CCGCCCATCTTCACAAACAAAG 60.608 50.000 0.00 0.00 0.00 2.77
611 1378 2.607771 CGCCCATCTTCACAAACAAAGG 60.608 50.000 0.00 0.00 0.00 3.11
612 1379 2.627699 GCCCATCTTCACAAACAAAGGA 59.372 45.455 0.00 0.00 0.00 3.36
614 1381 4.442753 GCCCATCTTCACAAACAAAGGAAA 60.443 41.667 0.00 0.00 0.00 3.13
615 1382 5.291971 CCCATCTTCACAAACAAAGGAAAG 58.708 41.667 0.00 0.00 0.00 2.62
616 1383 5.068987 CCCATCTTCACAAACAAAGGAAAGA 59.931 40.000 0.00 0.00 0.00 2.52
617 1384 6.211515 CCATCTTCACAAACAAAGGAAAGAG 58.788 40.000 0.00 0.00 0.00 2.85
619 1386 7.416664 CCATCTTCACAAACAAAGGAAAGAGAA 60.417 37.037 0.00 0.00 0.00 2.87
620 1387 7.461182 TCTTCACAAACAAAGGAAAGAGAAA 57.539 32.000 0.00 0.00 0.00 2.52
621 1388 7.891561 TCTTCACAAACAAAGGAAAGAGAAAA 58.108 30.769 0.00 0.00 0.00 2.29
622 1389 7.812669 TCTTCACAAACAAAGGAAAGAGAAAAC 59.187 33.333 0.00 0.00 0.00 2.43
640 1523 3.283259 AACAATTCGAATCTCCCTCCC 57.717 47.619 11.83 0.00 0.00 4.30
642 1525 1.141185 AATTCGAATCTCCCTCCCCC 58.859 55.000 11.83 0.00 0.00 5.40
689 3068 4.475135 GCTCCCCGCACTTCCCTC 62.475 72.222 0.00 0.00 38.92 4.30
690 3069 3.787001 CTCCCCGCACTTCCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
696 4829 3.787001 GCACTTCCCTCCCCTCCG 61.787 72.222 0.00 0.00 0.00 4.63
749 4882 5.024768 TCGCGAAAATTTTCAAGATTCGA 57.975 34.783 26.20 19.74 43.99 3.71
800 4933 1.338200 GCAGGAAACACAGATCCGTCT 60.338 52.381 0.00 0.00 40.78 4.18
821 4955 0.686112 CTCCCTCCACTCCTCTCCAC 60.686 65.000 0.00 0.00 0.00 4.02
837 4971 1.154112 CACGCCGAAATTTTCCCCG 60.154 57.895 12.00 12.00 0.00 5.73
862 4997 5.886960 AACTCAAATCTTTTCATCCTCCG 57.113 39.130 0.00 0.00 0.00 4.63
914 5061 2.293598 ACCCATGGAAGATCCTTCCT 57.706 50.000 21.97 8.83 39.31 3.36
962 5121 2.719979 CGCCGCCTAGTACATCGT 59.280 61.111 0.00 0.00 0.00 3.73
1223 5439 4.719369 GTTGGCGACGACGGAGCT 62.719 66.667 9.67 0.00 40.15 4.09
1224 5440 4.717629 TTGGCGACGACGGAGCTG 62.718 66.667 9.67 0.00 40.15 4.24
1229 5445 4.373116 GACGACGGAGCTGGGCAA 62.373 66.667 0.00 0.00 0.00 4.52
1293 5533 1.069935 GAAGGCCGGCAGATACTCC 59.930 63.158 30.85 8.01 0.00 3.85
1362 5611 8.062065 ACTGTACTTTTCTTTTCATTTGTCCA 57.938 30.769 0.00 0.00 0.00 4.02
1467 5731 9.473640 AAAGCAAAGAAAGAGAAATCTCAAATC 57.526 29.630 12.65 7.41 45.21 2.17
1564 5860 3.271225 TCCAGTTCTCCAGGACTATGGTA 59.729 47.826 5.52 0.00 41.43 3.25
1687 5990 1.537202 AGATGTTGAAACTGCTTCGGC 59.463 47.619 0.00 0.00 36.78 5.54
1707 6010 2.288666 CACAACAAGTACTGTGGCTGT 58.711 47.619 0.00 0.00 39.42 4.40
1774 6078 8.691727 CACACTATATCAGTATACTTTCGTTGC 58.308 37.037 1.56 0.00 34.98 4.17
1803 6107 4.692625 CAGTGATTTCAGGTGTACTTGAGG 59.307 45.833 0.00 0.00 33.43 3.86
1805 6109 3.072330 TGATTTCAGGTGTACTTGAGGCA 59.928 43.478 0.00 0.00 33.43 4.75
1898 6202 7.619965 TGAAAATTTAAAGGGCATTAGGAAGG 58.380 34.615 0.00 0.00 0.00 3.46
1918 6222 6.183361 GGAAGGTAACAGAGTTGATGGGATAT 60.183 42.308 0.00 0.00 41.41 1.63
1938 6251 6.382570 GGATATATCTGACTATCCCAGCACTT 59.617 42.308 12.42 0.00 38.19 3.16
1955 6268 3.181485 GCACTTAGATAGCTGAGTTCCGT 60.181 47.826 2.17 0.00 38.76 4.69
2043 6364 3.107601 TGACTATGCTCCTTAACAGGCT 58.892 45.455 0.00 0.00 40.58 4.58
2044 6365 3.519510 TGACTATGCTCCTTAACAGGCTT 59.480 43.478 0.00 0.00 40.58 4.35
2045 6366 4.714802 TGACTATGCTCCTTAACAGGCTTA 59.285 41.667 0.00 0.00 40.58 3.09
2046 6367 5.024785 ACTATGCTCCTTAACAGGCTTAC 57.975 43.478 0.00 0.00 40.58 2.34
2047 6368 4.469945 ACTATGCTCCTTAACAGGCTTACA 59.530 41.667 0.00 0.00 40.58 2.41
2048 6369 3.334583 TGCTCCTTAACAGGCTTACAG 57.665 47.619 0.00 0.00 40.58 2.74
2049 6370 2.027192 TGCTCCTTAACAGGCTTACAGG 60.027 50.000 0.00 0.00 40.58 4.00
2050 6371 2.633488 CTCCTTAACAGGCTTACAGGC 58.367 52.381 0.00 0.00 40.58 4.85
2051 6372 1.982226 TCCTTAACAGGCTTACAGGCA 59.018 47.619 0.00 0.00 44.19 4.75
2178 6506 7.847078 CACAATGCTCAGTTTACATTTGTTTTG 59.153 33.333 0.00 0.00 31.82 2.44
2263 6591 7.428282 TCACTTCTACGATTTGTGCATTTTA 57.572 32.000 0.00 0.00 0.00 1.52
2264 6592 7.866729 TCACTTCTACGATTTGTGCATTTTAA 58.133 30.769 0.00 0.00 0.00 1.52
2288 6619 8.798859 AACTGATGTGAAGCTTGTTCTTATAT 57.201 30.769 2.10 0.00 0.00 0.86
2289 6620 8.206325 ACTGATGTGAAGCTTGTTCTTATATG 57.794 34.615 2.10 0.00 0.00 1.78
2294 6625 3.229697 AGCTTGTTCTTATATGGCCCC 57.770 47.619 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.769093 GCAAACGTTTTATTAACTCATGATACT 57.231 29.630 11.66 0.00 0.00 2.12
7 8 8.721476 CGCAAACGTTTTATTAACTCATGATAC 58.279 33.333 11.66 0.00 33.53 2.24
8 9 7.906010 CCGCAAACGTTTTATTAACTCATGATA 59.094 33.333 11.66 0.00 37.70 2.15
11 12 5.285134 CCCGCAAACGTTTTATTAACTCATG 59.715 40.000 11.66 0.00 37.70 3.07
12 13 5.181622 TCCCGCAAACGTTTTATTAACTCAT 59.818 36.000 11.66 0.00 37.70 2.90
13 14 4.514441 TCCCGCAAACGTTTTATTAACTCA 59.486 37.500 11.66 0.00 37.70 3.41
14 15 5.033326 TCCCGCAAACGTTTTATTAACTC 57.967 39.130 11.66 0.00 37.70 3.01
15 16 5.632244 ATCCCGCAAACGTTTTATTAACT 57.368 34.783 11.66 0.00 37.70 2.24
16 17 9.500864 TTTATATCCCGCAAACGTTTTATTAAC 57.499 29.630 11.66 0.00 37.70 2.01
19 20 8.983307 TTTTTATATCCCGCAAACGTTTTATT 57.017 26.923 11.66 0.00 37.70 1.40
59 60 6.649141 ACTTTTTCGAGCTTGAAAACCTTTTT 59.351 30.769 32.40 15.53 44.92 1.94
60 61 6.163476 ACTTTTTCGAGCTTGAAAACCTTTT 58.837 32.000 32.40 16.90 44.92 2.27
61 62 5.720202 ACTTTTTCGAGCTTGAAAACCTTT 58.280 33.333 32.40 18.30 44.92 3.11
62 63 5.324784 ACTTTTTCGAGCTTGAAAACCTT 57.675 34.783 32.40 20.27 44.92 3.50
63 64 4.983671 ACTTTTTCGAGCTTGAAAACCT 57.016 36.364 32.40 20.91 44.92 3.50
64 65 5.004440 GTGAACTTTTTCGAGCTTGAAAACC 59.996 40.000 32.40 23.00 44.92 3.27
65 66 5.275280 CGTGAACTTTTTCGAGCTTGAAAAC 60.275 40.000 32.40 23.46 44.92 2.43
66 67 4.791163 CGTGAACTTTTTCGAGCTTGAAAA 59.209 37.500 29.98 29.98 43.92 2.29
67 68 4.093703 TCGTGAACTTTTTCGAGCTTGAAA 59.906 37.500 22.78 22.78 36.12 2.69
68 69 3.619483 TCGTGAACTTTTTCGAGCTTGAA 59.381 39.130 12.62 12.62 34.04 2.69
69 70 3.191669 TCGTGAACTTTTTCGAGCTTGA 58.808 40.909 0.00 0.00 34.04 3.02
70 71 3.535860 CTCGTGAACTTTTTCGAGCTTG 58.464 45.455 0.00 0.00 41.98 4.01
71 72 3.861569 CTCGTGAACTTTTTCGAGCTT 57.138 42.857 0.00 0.00 41.98 3.74
114 115 5.174943 GTGATCTTTCAAAACCGCGATTTTT 59.825 36.000 8.87 10.35 32.48 1.94
115 116 4.679654 GTGATCTTTCAAAACCGCGATTTT 59.320 37.500 5.06 5.06 32.48 1.82
116 117 4.226761 GTGATCTTTCAAAACCGCGATTT 58.773 39.130 8.23 0.00 32.48 2.17
117 118 3.252215 TGTGATCTTTCAAAACCGCGATT 59.748 39.130 8.23 0.00 32.48 3.34
118 119 2.811431 TGTGATCTTTCAAAACCGCGAT 59.189 40.909 8.23 0.00 32.48 4.58
119 120 2.214347 TGTGATCTTTCAAAACCGCGA 58.786 42.857 8.23 0.00 32.48 5.87
120 121 2.679355 TGTGATCTTTCAAAACCGCG 57.321 45.000 0.00 0.00 32.48 6.46
121 122 5.461737 TGAAAATGTGATCTTTCAAAACCGC 59.538 36.000 5.61 0.00 38.32 5.68
122 123 6.697019 ACTGAAAATGTGATCTTTCAAAACCG 59.303 34.615 8.63 1.56 40.16 4.44
123 124 9.528018 TTACTGAAAATGTGATCTTTCAAAACC 57.472 29.630 8.63 0.00 40.16 3.27
128 129 9.748708 CCTTTTTACTGAAAATGTGATCTTTCA 57.251 29.630 7.42 7.42 38.81 2.69
129 130 9.965824 TCCTTTTTACTGAAAATGTGATCTTTC 57.034 29.630 0.00 0.00 36.68 2.62
130 131 9.971922 CTCCTTTTTACTGAAAATGTGATCTTT 57.028 29.630 0.00 0.00 36.68 2.52
131 132 9.354673 TCTCCTTTTTACTGAAAATGTGATCTT 57.645 29.630 0.00 0.00 36.68 2.40
132 133 8.924511 TCTCCTTTTTACTGAAAATGTGATCT 57.075 30.769 0.00 0.00 36.68 2.75
133 134 9.965824 TTTCTCCTTTTTACTGAAAATGTGATC 57.034 29.630 0.00 0.00 36.68 2.92
158 159 9.059260 CCAATTGTTGATTTTCCTCAGATTTTT 57.941 29.630 4.43 0.00 0.00 1.94
164 165 5.477984 TCCTCCAATTGTTGATTTTCCTCAG 59.522 40.000 4.43 0.00 0.00 3.35
167 168 6.554605 TCTTTCCTCCAATTGTTGATTTTCCT 59.445 34.615 4.43 0.00 0.00 3.36
169 170 8.090214 TGATCTTTCCTCCAATTGTTGATTTTC 58.910 33.333 4.43 0.00 0.00 2.29
173 174 6.893554 TCATGATCTTTCCTCCAATTGTTGAT 59.106 34.615 4.43 0.00 0.00 2.57
175 176 6.519679 TCATGATCTTTCCTCCAATTGTTG 57.480 37.500 4.43 0.00 0.00 3.33
178 179 9.074576 TCATATTCATGATCTTTCCTCCAATTG 57.925 33.333 0.00 0.00 36.22 2.32
201 202 9.696917 GAACTTTTCCAAGTGAATGTTATTCAT 57.303 29.630 7.42 0.00 42.89 2.57
286 288 7.563906 TCAACTTTTCCCAAATTTCATGAACT 58.436 30.769 7.89 0.00 0.00 3.01
292 294 7.601705 ATCTCTCAACTTTTCCCAAATTTCA 57.398 32.000 0.00 0.00 0.00 2.69
293 295 8.768019 CAAATCTCTCAACTTTTCCCAAATTTC 58.232 33.333 0.00 0.00 0.00 2.17
307 309 9.520204 TCACTTTTTCATTTCAAATCTCTCAAC 57.480 29.630 0.00 0.00 0.00 3.18
370 374 6.507900 TCATGAACTTTTACCAATTTTGCGA 58.492 32.000 0.00 0.00 0.00 5.10
372 376 9.949174 AAATTCATGAACTTTTACCAATTTTGC 57.051 25.926 11.07 0.00 0.00 3.68
375 379 9.844257 TCCAAATTCATGAACTTTTACCAATTT 57.156 25.926 11.07 0.44 0.00 1.82
468 485 5.592688 TCTTTTCACCGGTTTTCTCATCTTT 59.407 36.000 2.97 0.00 0.00 2.52
471 488 5.432885 TTCTTTTCACCGGTTTTCTCATC 57.567 39.130 2.97 0.00 0.00 2.92
501 518 1.656587 ATTATCTAGATGGGCGGCCA 58.343 50.000 34.65 34.65 0.00 5.36
537 554 1.264557 CATTTGGTTAACCGACGCACA 59.735 47.619 19.65 2.92 39.43 4.57
538 555 1.958417 CATTTGGTTAACCGACGCAC 58.042 50.000 19.65 0.00 39.43 5.34
544 561 1.338337 TGGTGTGCATTTGGTTAACCG 59.662 47.619 19.65 6.53 39.43 4.44
550 567 1.739049 CGGTTGGTGTGCATTTGGT 59.261 52.632 0.00 0.00 0.00 3.67
552 569 4.651585 CCGGTTGGTGTGCATTTG 57.348 55.556 0.00 0.00 0.00 2.32
563 580 5.576384 CCATGTAAATTCATTTCACCGGTTG 59.424 40.000 2.97 0.00 0.00 3.77
572 589 2.158971 GGCGGCCCATGTAAATTCATTT 60.159 45.455 8.12 0.00 0.00 2.32
573 590 1.412343 GGCGGCCCATGTAAATTCATT 59.588 47.619 8.12 0.00 0.00 2.57
575 592 1.040339 GGGCGGCCCATGTAAATTCA 61.040 55.000 32.90 0.00 44.65 2.57
576 593 1.739667 GGGCGGCCCATGTAAATTC 59.260 57.895 32.90 0.48 44.65 2.17
592 1359 4.935352 TTCCTTTGTTTGTGAAGATGGG 57.065 40.909 0.00 0.00 0.00 4.00
595 1362 7.645058 TTCTCTTTCCTTTGTTTGTGAAGAT 57.355 32.000 0.00 0.00 0.00 2.40
596 1363 7.461182 TTTCTCTTTCCTTTGTTTGTGAAGA 57.539 32.000 0.00 0.00 0.00 2.87
597 1364 7.598493 TGTTTTCTCTTTCCTTTGTTTGTGAAG 59.402 33.333 0.00 0.00 0.00 3.02
598 1365 7.437748 TGTTTTCTCTTTCCTTTGTTTGTGAA 58.562 30.769 0.00 0.00 0.00 3.18
601 1368 8.846943 AATTGTTTTCTCTTTCCTTTGTTTGT 57.153 26.923 0.00 0.00 0.00 2.83
602 1369 8.110002 CGAATTGTTTTCTCTTTCCTTTGTTTG 58.890 33.333 0.00 0.00 0.00 2.93
603 1370 8.032451 TCGAATTGTTTTCTCTTTCCTTTGTTT 58.968 29.630 0.00 0.00 0.00 2.83
605 1372 7.095695 TCGAATTGTTTTCTCTTTCCTTTGT 57.904 32.000 0.00 0.00 0.00 2.83
606 1373 7.985634 TTCGAATTGTTTTCTCTTTCCTTTG 57.014 32.000 0.00 0.00 0.00 2.77
607 1374 8.633561 AGATTCGAATTGTTTTCTCTTTCCTTT 58.366 29.630 12.81 0.00 0.00 3.11
608 1375 8.171164 AGATTCGAATTGTTTTCTCTTTCCTT 57.829 30.769 12.81 0.00 0.00 3.36
609 1376 7.094592 GGAGATTCGAATTGTTTTCTCTTTCCT 60.095 37.037 12.81 0.00 32.23 3.36
610 1377 7.024171 GGAGATTCGAATTGTTTTCTCTTTCC 58.976 38.462 12.81 0.00 32.23 3.13
611 1378 7.024171 GGGAGATTCGAATTGTTTTCTCTTTC 58.976 38.462 12.81 1.96 32.23 2.62
612 1379 6.717084 AGGGAGATTCGAATTGTTTTCTCTTT 59.283 34.615 12.81 4.13 32.23 2.52
614 1381 5.810095 AGGGAGATTCGAATTGTTTTCTCT 58.190 37.500 12.81 2.51 32.23 3.10
615 1382 5.065346 GGAGGGAGATTCGAATTGTTTTCTC 59.935 44.000 12.81 13.17 0.00 2.87
616 1383 4.944317 GGAGGGAGATTCGAATTGTTTTCT 59.056 41.667 12.81 4.11 0.00 2.52
617 1384 4.096532 GGGAGGGAGATTCGAATTGTTTTC 59.903 45.833 12.81 8.00 0.00 2.29
619 1386 3.621558 GGGAGGGAGATTCGAATTGTTT 58.378 45.455 12.81 0.00 0.00 2.83
620 1387 2.092375 GGGGAGGGAGATTCGAATTGTT 60.092 50.000 12.81 1.22 0.00 2.83
621 1388 1.490910 GGGGAGGGAGATTCGAATTGT 59.509 52.381 12.81 2.69 0.00 2.71
622 1389 1.202818 GGGGGAGGGAGATTCGAATTG 60.203 57.143 12.81 0.00 0.00 2.32
650 1533 1.602668 CGCTGAAAACATTGGTGTGGG 60.603 52.381 0.00 0.00 38.92 4.61
652 1535 1.130955 GCGCTGAAAACATTGGTGTG 58.869 50.000 0.00 0.00 38.92 3.82
653 1536 0.317770 CGCGCTGAAAACATTGGTGT 60.318 50.000 5.56 0.00 41.28 4.16
679 1568 3.787001 CGGAGGGGAGGGAAGTGC 61.787 72.222 0.00 0.00 0.00 4.40
696 4829 2.388494 GAAATCGGAATTCGGGGCGC 62.388 60.000 12.54 0.00 39.77 6.53
707 4840 3.438781 CGAAATGTTTGGAGGAAATCGGA 59.561 43.478 0.00 0.00 0.00 4.55
800 4933 1.000993 GAGAGGAGTGGAGGGAGCA 59.999 63.158 0.00 0.00 0.00 4.26
821 4955 1.587933 TTCCGGGGAAAATTTCGGCG 61.588 55.000 0.00 0.00 41.98 6.46
837 4971 6.623767 CGGAGGATGAAAAGATTTGAGTTTCC 60.624 42.308 0.00 0.00 31.57 3.13
862 4997 1.124780 GTAGGAGGGAAGAAGAGGGC 58.875 60.000 0.00 0.00 0.00 5.19
1186 5390 4.827087 CTCGTGCGGCTGCTGGAT 62.827 66.667 20.27 0.00 43.34 3.41
1218 5434 3.991725 CTCTGCCTTGCCCAGCTCC 62.992 68.421 0.00 0.00 0.00 4.70
1219 5435 2.438075 CTCTGCCTTGCCCAGCTC 60.438 66.667 0.00 0.00 0.00 4.09
1220 5436 4.737177 GCTCTGCCTTGCCCAGCT 62.737 66.667 0.00 0.00 31.93 4.24
1263 5494 1.679898 GGCCTTCAGTACAGCACCT 59.320 57.895 0.00 0.00 0.00 4.00
1354 5603 7.248743 AGTCCAATGAATCATTTGGACAAAT 57.751 32.000 33.15 22.18 44.51 2.32
1355 5604 6.669125 AGTCCAATGAATCATTTGGACAAA 57.331 33.333 33.15 14.41 44.51 2.83
1356 5605 7.174413 TCTAGTCCAATGAATCATTTGGACAA 58.826 34.615 33.15 24.04 44.51 3.18
1357 5606 6.720309 TCTAGTCCAATGAATCATTTGGACA 58.280 36.000 33.15 24.94 44.51 4.02
1358 5607 7.814264 ATCTAGTCCAATGAATCATTTGGAC 57.186 36.000 29.35 29.35 43.64 4.02
1359 5608 7.286087 CCAATCTAGTCCAATGAATCATTTGGA 59.714 37.037 17.24 17.24 31.05 3.53
1360 5609 7.069085 ACCAATCTAGTCCAATGAATCATTTGG 59.931 37.037 5.63 10.27 31.05 3.28
1362 5611 8.472413 CAACCAATCTAGTCCAATGAATCATTT 58.528 33.333 5.63 0.00 31.05 2.32
1445 5709 9.837525 ATTCGATTTGAGATTTCTCTTTCTTTG 57.162 29.630 8.91 0.00 43.25 2.77
1687 5990 2.032054 CACAGCCACAGTACTTGTTGTG 59.968 50.000 14.91 14.91 43.27 3.33
1707 6010 1.311403 CCTCCTGCTCCCTCTACCA 59.689 63.158 0.00 0.00 0.00 3.25
1774 6078 4.000331 ACACCTGAAATCACTGAGACTG 58.000 45.455 0.00 0.00 0.00 3.51
1803 6107 4.201841 ACAGCACAAGAAATTTTTGCTTGC 60.202 37.500 14.72 14.35 41.60 4.01
1805 6109 6.316319 CAAACAGCACAAGAAATTTTTGCTT 58.684 32.000 12.31 1.03 41.60 3.91
1898 6202 8.807118 TCAGATATATCCCATCAACTCTGTTAC 58.193 37.037 9.18 0.00 32.65 2.50
1918 6222 5.953571 TCTAAGTGCTGGGATAGTCAGATA 58.046 41.667 0.00 0.00 34.36 1.98
1938 6251 6.927416 TGTTAAAACGGAACTCAGCTATCTA 58.073 36.000 0.00 0.00 0.00 1.98
1947 6260 4.142881 GCAGATCCTGTTAAAACGGAACTC 60.143 45.833 3.19 2.50 37.48 3.01
1955 6268 7.068103 TCAGAAACAAAGCAGATCCTGTTAAAA 59.932 33.333 0.00 0.00 33.43 1.52
2050 6371 8.144478 ACTAGTTACCACAAGATGCACTATATG 58.856 37.037 0.00 0.00 0.00 1.78
2051 6372 8.251383 ACTAGTTACCACAAGATGCACTATAT 57.749 34.615 0.00 0.00 0.00 0.86
2063 6384 9.352191 GGATAGAGAGAATACTAGTTACCACAA 57.648 37.037 0.00 0.00 0.00 3.33
2064 6385 7.943447 GGGATAGAGAGAATACTAGTTACCACA 59.057 40.741 0.00 0.00 0.00 4.17
2178 6506 3.492756 TGCCAGAAAAATAACAAAAGCGC 59.507 39.130 0.00 0.00 0.00 5.92
2263 6591 8.671921 CATATAAGAACAAGCTTCACATCAGTT 58.328 33.333 0.00 0.00 0.00 3.16
2264 6592 7.281774 CCATATAAGAACAAGCTTCACATCAGT 59.718 37.037 0.00 0.00 0.00 3.41
2288 6619 2.704190 TCCAAACTTTTATGGGGCCA 57.296 45.000 4.39 0.00 37.31 5.36
2289 6620 2.236146 CCTTCCAAACTTTTATGGGGCC 59.764 50.000 0.00 0.00 37.31 5.80


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

AutoCloner maintained by Alex Coulton.