Multiple sequence alignment - TraesCS7B01G480900

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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 TraesCS7B01G480900 chr7B 100.000 1691 0 0 1 1691 734406735 734408425 0.000000e+00 3123
1 TraesCS7B01G480900 chr7B 100.000 549 0 0 2076 2624 734408810 734409358 0.000000e+00 1014
2 TraesCS7B01G480900 chr7B 78.426 1080 150 41 607 1634 734379023 734380071 6.170000e-176 627
3 TraesCS7B01G480900 chr7B 79.373 606 105 12 905 1507 734426393 734426981 2.430000e-110 409
4 TraesCS7B01G480900 chr7B 89.506 162 17 0 1346 1507 734417022 734417183 3.420000e-49 206
5 TraesCS7B01G480900 chr7D 84.366 1695 147 52 17 1654 638297939 638296306 0.000000e+00 1554
6 TraesCS7B01G480900 chr7D 87.027 740 88 5 912 1647 638288603 638287868 0.000000e+00 828
7 TraesCS7B01G480900 chr7D 80.351 855 123 30 768 1601 638331327 638330497 8.030000e-170 606
8 TraesCS7B01G480900 chr7D 80.502 877 85 32 28 863 638289430 638288599 6.250000e-166 593
9 TraesCS7B01G480900 chr7D 78.479 618 99 20 905 1507 638274535 638273937 8.870000e-100 374
10 TraesCS7B01G480900 chr7D 86.643 277 33 4 2352 2624 638287496 638287220 1.180000e-78 303
11 TraesCS7B01G480900 chr7A 85.727 1093 92 36 589 1646 727773230 727774293 0.000000e+00 1096
12 TraesCS7B01G480900 chr7A 91.047 793 60 6 900 1691 727787900 727788682 0.000000e+00 1061
13 TraesCS7B01G480900 chr7A 81.443 970 135 30 655 1601 727721447 727722394 0.000000e+00 752
14 TraesCS7B01G480900 chr7A 82.460 496 62 19 153 628 727772751 727773241 6.760000e-111 411
15 TraesCS7B01G480900 chr7A 81.621 506 38 15 379 853 727787040 727787521 4.130000e-98 368
16 TraesCS7B01G480900 chr7A 85.921 277 35 4 2352 2624 727789015 727789291 2.550000e-75 292
17 TraesCS7B01G480900 chr7A 84.838 277 38 4 2352 2624 727774861 727775137 2.570000e-70 276
18 TraesCS7B01G480900 chr7A 76.641 518 91 21 1116 1630 727580938 727581428 2.590000e-65 259
19 TraesCS7B01G480900 chr7A 74.757 515 101 22 1117 1630 727583846 727584332 1.230000e-48 204


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 TraesCS7B01G480900 chr7B 734406735 734409358 2623 False 2068.500000 3123 100.000000 1 2624 2 chr7B.!!$F4 2623
1 TraesCS7B01G480900 chr7B 734379023 734380071 1048 False 627.000000 627 78.426000 607 1634 1 chr7B.!!$F1 1027
2 TraesCS7B01G480900 chr7B 734426393 734426981 588 False 409.000000 409 79.373000 905 1507 1 chr7B.!!$F3 602
3 TraesCS7B01G480900 chr7D 638296306 638297939 1633 True 1554.000000 1554 84.366000 17 1654 1 chr7D.!!$R2 1637
4 TraesCS7B01G480900 chr7D 638330497 638331327 830 True 606.000000 606 80.351000 768 1601 1 chr7D.!!$R3 833
5 TraesCS7B01G480900 chr7D 638287220 638289430 2210 True 574.666667 828 84.724000 28 2624 3 chr7D.!!$R4 2596
6 TraesCS7B01G480900 chr7D 638273937 638274535 598 True 374.000000 374 78.479000 905 1507 1 chr7D.!!$R1 602
7 TraesCS7B01G480900 chr7A 727721447 727722394 947 False 752.000000 752 81.443000 655 1601 1 chr7A.!!$F1 946
8 TraesCS7B01G480900 chr7A 727772751 727775137 2386 False 594.333333 1096 84.341667 153 2624 3 chr7A.!!$F3 2471
9 TraesCS7B01G480900 chr7A 727787040 727789291 2251 False 573.666667 1061 86.196333 379 2624 3 chr7A.!!$F4 2245
10 TraesCS7B01G480900 chr7A 727580938 727584332 3394 False 231.500000 259 75.699000 1116 1630 2 chr7A.!!$F2 514

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
616 664 0.871722 ACACACACACACACACACAC 59.128 50.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2499 3753 0.324614 ACGTCCACATCAGCCATCAA 59.675 50.0 0.0 0.0 0.0 2.57 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
41 42 6.358118 TCTTGTTTGTCATAATATCGTGGC 57.642 37.500 0.00 0.00 0.00 5.01
50 51 8.445275 TGTCATAATATCGTGGCAATTAAAGT 57.555 30.769 0.00 0.00 0.00 2.66
51 52 8.898761 TGTCATAATATCGTGGCAATTAAAGTT 58.101 29.630 0.00 0.00 0.00 2.66
103 109 5.939447 TGGCAAACTCATGATATATGTCCA 58.061 37.500 0.00 3.54 0.00 4.02
106 112 5.413833 GCAAACTCATGATATATGTCCAGGG 59.586 44.000 0.00 0.00 0.00 4.45
111 122 7.815383 ACTCATGATATATGTCCAGGGAAAAA 58.185 34.615 0.00 0.00 0.00 1.94
149 167 8.246184 CGAAGCGTTATTCTTTATGTTTCATC 57.754 34.615 0.00 0.00 0.00 2.92
150 168 8.116753 CGAAGCGTTATTCTTTATGTTTCATCT 58.883 33.333 0.00 0.00 0.00 2.90
151 169 9.774742 GAAGCGTTATTCTTTATGTTTCATCTT 57.225 29.630 0.00 0.00 0.00 2.40
174 192 9.282569 TCTTTTTGACATTCAATATTTTTGGGG 57.717 29.630 0.00 0.00 36.11 4.96
180 198 3.608316 TCAATATTTTTGGGGCTGTGC 57.392 42.857 0.00 0.00 0.00 4.57
195 214 2.677337 GCTGTGCTTTTCTTTTTGGCAA 59.323 40.909 0.00 0.00 34.65 4.52
216 236 0.967380 AAGAATTGCGCTGGGGAAGG 60.967 55.000 9.73 0.00 0.00 3.46
217 237 1.378514 GAATTGCGCTGGGGAAGGA 60.379 57.895 9.73 0.00 0.00 3.36
259 281 2.434884 CCTTGCGTCGCACTGGAT 60.435 61.111 25.66 0.00 38.71 3.41
268 290 3.443045 GCACTGGATGGTTGCCCG 61.443 66.667 0.00 0.00 0.00 6.13
281 303 1.265905 GTTGCCCGAGTGAACGAAAAT 59.734 47.619 0.00 0.00 35.09 1.82
320 343 8.066612 ACATCCCAAATCGAATTATTTGTTCT 57.933 30.769 11.09 0.00 42.68 3.01
322 345 7.095695 TCCCAAATCGAATTATTTGTTCTCC 57.904 36.000 11.09 0.00 42.68 3.71
327 350 2.716398 GAATTATTTGTTCTCCGCGGC 58.284 47.619 23.51 6.96 0.00 6.53
331 354 1.816074 ATTTGTTCTCCGCGGCTTAA 58.184 45.000 23.51 11.59 0.00 1.85
342 365 0.951040 GCGGCTTAATCCCAGATCGG 60.951 60.000 0.00 0.00 0.00 4.18
353 376 1.571919 CCAGATCGGACGTCAATTCC 58.428 55.000 18.91 0.00 36.56 3.01
360 383 4.131649 TCGGACGTCAATTCCATATTGT 57.868 40.909 18.91 0.00 31.94 2.71
366 389 6.293081 GGACGTCAATTCCATATTGTCATCTG 60.293 42.308 18.91 0.00 32.82 2.90
367 390 5.528690 ACGTCAATTCCATATTGTCATCTGG 59.471 40.000 0.00 0.00 0.00 3.86
368 391 5.049198 CGTCAATTCCATATTGTCATCTGGG 60.049 44.000 0.00 0.00 29.23 4.45
539 578 2.481276 GGCACCGCAAGTTTTCTTCTTT 60.481 45.455 0.00 0.00 38.17 2.52
540 579 2.789339 GCACCGCAAGTTTTCTTCTTTC 59.211 45.455 0.00 0.00 38.17 2.62
552 592 5.520376 TTTCTTCTTTCTGGGAGCAAAAG 57.480 39.130 0.00 0.00 0.00 2.27
573 621 7.939784 AAAGACAGGTCAAAAGAAGTAAAGT 57.060 32.000 1.84 0.00 0.00 2.66
597 645 4.332543 GTGTCTCATCTTTTCACACACACA 59.667 41.667 0.00 0.00 37.81 3.72
598 646 4.332543 TGTCTCATCTTTTCACACACACAC 59.667 41.667 0.00 0.00 0.00 3.82
599 647 4.332543 GTCTCATCTTTTCACACACACACA 59.667 41.667 0.00 0.00 0.00 3.72
600 648 4.332543 TCTCATCTTTTCACACACACACAC 59.667 41.667 0.00 0.00 0.00 3.82
601 649 4.006319 TCATCTTTTCACACACACACACA 58.994 39.130 0.00 0.00 0.00 3.72
602 650 3.822594 TCTTTTCACACACACACACAC 57.177 42.857 0.00 0.00 0.00 3.82
603 651 3.142174 TCTTTTCACACACACACACACA 58.858 40.909 0.00 0.00 0.00 3.72
604 652 2.979401 TTTCACACACACACACACAC 57.021 45.000 0.00 0.00 0.00 3.82
605 653 1.884235 TTCACACACACACACACACA 58.116 45.000 0.00 0.00 0.00 3.72
616 664 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
698 807 6.455647 TGATCACTACTAGTGTTTCAAGTGG 58.544 40.000 17.17 3.94 46.03 4.00
713 822 6.478512 TTCAAGTGGTTTGCTTAATTTCCT 57.521 33.333 0.00 0.00 36.70 3.36
728 837 5.587388 AATTTCCTCGAATCCACGTAGTA 57.413 39.130 0.00 0.00 41.61 1.82
729 838 5.786264 ATTTCCTCGAATCCACGTAGTAT 57.214 39.130 0.00 0.00 41.61 2.12
733 842 4.993584 TCCTCGAATCCACGTAGTATACTC 59.006 45.833 9.12 0.62 41.61 2.59
757 885 2.227194 CTAAACCAAAAGGAGCCACGT 58.773 47.619 0.00 0.00 0.00 4.49
884 1039 3.161450 ATGACCGGATGACCCCCG 61.161 66.667 9.46 0.00 46.10 5.73
893 1052 1.422402 GGATGACCCCCGGCTATAAAA 59.578 52.381 0.00 0.00 0.00 1.52
894 1053 2.041216 GGATGACCCCCGGCTATAAAAT 59.959 50.000 0.00 0.00 0.00 1.82
895 1054 2.943036 TGACCCCCGGCTATAAAATC 57.057 50.000 0.00 0.00 0.00 2.17
896 1055 1.422402 TGACCCCCGGCTATAAAATCC 59.578 52.381 0.00 0.00 0.00 3.01
914 1420 2.172372 CACGCAGAGCAGAGCATCC 61.172 63.158 0.00 0.00 33.66 3.51
1050 1582 2.659610 GCTCTCGCCAAGACTGGT 59.340 61.111 0.00 0.00 45.53 4.00
1089 1621 0.032678 CGCCGATGAGTATGAAGGCT 59.967 55.000 2.75 0.00 42.16 4.58
1096 1634 3.388552 TGAGTATGAAGGCTCCTGAGA 57.611 47.619 0.00 0.00 0.00 3.27
1098 1636 3.449018 TGAGTATGAAGGCTCCTGAGAAC 59.551 47.826 0.00 0.00 0.00 3.01
1212 1750 1.613317 TAGTCTCCCGGTGCACATGG 61.613 60.000 20.43 19.00 0.00 3.66
1255 1799 4.135153 CCGACCACGCTCCTCCAG 62.135 72.222 0.00 0.00 38.29 3.86
1684 2749 1.140312 TGTGCCCTGTTTTCCTCTCT 58.860 50.000 0.00 0.00 0.00 3.10
2104 3169 5.116983 GGCGTTGTACATTCAATTTGTCTTG 59.883 40.000 0.00 0.00 0.00 3.02
2110 3178 6.545666 TGTACATTCAATTTGTCTTGACAGGT 59.454 34.615 3.61 0.00 34.96 4.00
2111 3179 6.469782 ACATTCAATTTGTCTTGACAGGTT 57.530 33.333 3.61 1.22 34.96 3.50
2112 3180 6.507023 ACATTCAATTTGTCTTGACAGGTTC 58.493 36.000 3.61 0.00 34.96 3.62
2117 3185 6.979817 TCAATTTGTCTTGACAGGTTCATTTG 59.020 34.615 3.61 3.19 32.84 2.32
2129 3197 8.750298 TGACAGGTTCATTTGGTAAAGTAAAAA 58.250 29.630 0.00 0.00 0.00 1.94
2130 3198 8.936070 ACAGGTTCATTTGGTAAAGTAAAAAC 57.064 30.769 0.00 0.00 0.00 2.43
2165 3234 5.803020 AGATTTGTCATTTAGTTCGGCTC 57.197 39.130 0.00 0.00 0.00 4.70
2181 3250 1.475751 GGCTCTATTGCTGGCTTGCTA 60.476 52.381 4.89 0.00 0.00 3.49
2184 3291 2.871022 CTCTATTGCTGGCTTGCTAGTG 59.129 50.000 7.75 0.00 0.00 2.74
2251 3358 3.556004 CCACCTCTTGTCCACTTCTTCTC 60.556 52.174 0.00 0.00 0.00 2.87
2253 3360 2.634940 CCTCTTGTCCACTTCTTCTCCA 59.365 50.000 0.00 0.00 0.00 3.86
2254 3361 3.071602 CCTCTTGTCCACTTCTTCTCCAA 59.928 47.826 0.00 0.00 0.00 3.53
2255 3362 4.263243 CCTCTTGTCCACTTCTTCTCCAAT 60.263 45.833 0.00 0.00 0.00 3.16
2257 3364 4.594920 TCTTGTCCACTTCTTCTCCAATCT 59.405 41.667 0.00 0.00 0.00 2.40
2258 3365 4.982241 TGTCCACTTCTTCTCCAATCTT 57.018 40.909 0.00 0.00 0.00 2.40
2259 3366 4.645535 TGTCCACTTCTTCTCCAATCTTG 58.354 43.478 0.00 0.00 0.00 3.02
2261 3368 5.163205 TGTCCACTTCTTCTCCAATCTTGAA 60.163 40.000 0.00 0.00 0.00 2.69
2263 3370 5.065914 CCACTTCTTCTCCAATCTTGAACA 58.934 41.667 0.00 0.00 0.00 3.18
2264 3371 5.532406 CCACTTCTTCTCCAATCTTGAACAA 59.468 40.000 0.00 0.00 0.00 2.83
2265 3372 6.039717 CCACTTCTTCTCCAATCTTGAACAAA 59.960 38.462 0.00 0.00 0.00 2.83
2266 3373 7.255730 CCACTTCTTCTCCAATCTTGAACAAAT 60.256 37.037 0.00 0.00 0.00 2.32
2269 3492 9.617975 CTTCTTCTCCAATCTTGAACAAATAAC 57.382 33.333 0.00 0.00 0.00 1.89
2278 3501 6.500684 TCTTGAACAAATAACTGAGCATCC 57.499 37.500 0.00 0.00 0.00 3.51
2349 3574 5.833131 GGTGGATGGAATCTATTGCCTTTTA 59.167 40.000 0.00 0.00 44.71 1.52
2350 3575 6.015940 GGTGGATGGAATCTATTGCCTTTTAG 60.016 42.308 0.00 0.00 44.71 1.85
2399 3652 4.024641 TCAGAATCGATTCGCCATTCATTG 60.025 41.667 27.69 18.45 41.56 2.82
2407 3660 1.806758 GCCATTCATTGCGGCACAC 60.807 57.895 0.05 0.00 45.52 3.82
2421 3674 2.094675 GGCACACCATGATAGCAACTT 58.905 47.619 0.00 0.00 35.26 2.66
2437 3690 3.373439 GCAACTTGACTGATGGAGATCAC 59.627 47.826 0.00 0.00 34.71 3.06
2484 3737 0.031449 GCACATCCTCGGTCTAGCTC 59.969 60.000 0.00 0.00 0.00 4.09
2492 3745 1.300233 CGGTCTAGCTCGATTGCCC 60.300 63.158 0.00 0.00 0.00 5.36
2494 3747 1.329256 GGTCTAGCTCGATTGCCCTA 58.671 55.000 0.00 0.00 0.00 3.53
2495 3748 1.271102 GGTCTAGCTCGATTGCCCTAG 59.729 57.143 0.00 0.00 0.00 3.02
2499 3753 1.490574 AGCTCGATTGCCCTAGAGTT 58.509 50.000 0.00 0.00 33.57 3.01
2535 5404 3.626977 GACGTGATGTCTAGCTGAGATG 58.373 50.000 0.00 0.00 44.58 2.90
2536 5405 2.223688 ACGTGATGTCTAGCTGAGATGC 60.224 50.000 0.00 0.00 36.29 3.91
2541 5410 5.296283 GTGATGTCTAGCTGAGATGCATTTT 59.704 40.000 0.00 0.00 36.29 1.82
2542 5411 6.481313 GTGATGTCTAGCTGAGATGCATTTTA 59.519 38.462 0.00 0.00 36.29 1.52
2545 5414 6.409704 TGTCTAGCTGAGATGCATTTTAGTT 58.590 36.000 10.22 7.15 36.29 2.24
2584 5454 7.607991 CCAGGTATTATGGAATAATGACACCTC 59.392 40.741 8.83 0.00 45.77 3.85
2588 5458 6.942532 TTATGGAATAATGACACCTCTTGC 57.057 37.500 0.00 0.00 32.95 4.01
2596 5467 2.771089 TGACACCTCTTGCAGCTTTAG 58.229 47.619 0.00 0.00 0.00 1.85
2618 5489 3.424962 GCGTTTGATCTACAACTTCTGCC 60.425 47.826 0.00 0.00 38.29 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.173021 ACGATATTATGACAAACAAGAATGGAA 57.827 29.630 0.00 0.00 0.00 3.53
13 14 8.611757 CACGATATTATGACAAACAAGAATGGA 58.388 33.333 0.00 0.00 0.00 3.41
14 15 7.857389 CCACGATATTATGACAAACAAGAATGG 59.143 37.037 0.00 0.00 0.00 3.16
15 16 7.376866 GCCACGATATTATGACAAACAAGAATG 59.623 37.037 0.00 0.00 0.00 2.67
19 20 6.117911 TGCCACGATATTATGACAAACAAG 57.882 37.500 0.00 0.00 0.00 3.16
26 27 9.730420 AAACTTTAATTGCCACGATATTATGAC 57.270 29.630 0.00 0.00 0.00 3.06
68 74 9.918630 ATCATGAGTTTGCCAATTTAATATAGC 57.081 29.630 0.09 0.00 0.00 2.97
76 82 8.362639 GGACATATATCATGAGTTTGCCAATTT 58.637 33.333 0.09 0.00 0.00 1.82
111 122 2.356135 ACGCTTCGCATCTAAACCATT 58.644 42.857 0.00 0.00 0.00 3.16
112 123 2.024176 ACGCTTCGCATCTAAACCAT 57.976 45.000 0.00 0.00 0.00 3.55
122 133 5.539582 AACATAAAGAATAACGCTTCGCA 57.460 34.783 0.00 0.00 0.00 5.10
123 134 6.019152 TGAAACATAAAGAATAACGCTTCGC 58.981 36.000 0.00 0.00 0.00 4.70
124 135 8.116753 AGATGAAACATAAAGAATAACGCTTCG 58.883 33.333 0.00 0.00 0.00 3.79
149 167 8.022550 GCCCCAAAAATATTGAATGTCAAAAAG 58.977 33.333 0.00 0.00 40.12 2.27
150 168 7.723172 AGCCCCAAAAATATTGAATGTCAAAAA 59.277 29.630 0.00 0.00 40.12 1.94
151 169 7.174599 CAGCCCCAAAAATATTGAATGTCAAAA 59.825 33.333 0.00 0.00 40.12 2.44
152 170 6.654161 CAGCCCCAAAAATATTGAATGTCAAA 59.346 34.615 0.00 0.00 40.12 2.69
153 171 6.171921 CAGCCCCAAAAATATTGAATGTCAA 58.828 36.000 0.00 0.00 41.09 3.18
154 172 5.248020 ACAGCCCCAAAAATATTGAATGTCA 59.752 36.000 0.00 0.00 0.00 3.58
155 173 5.581874 CACAGCCCCAAAAATATTGAATGTC 59.418 40.000 0.00 0.00 0.00 3.06
156 174 5.490159 CACAGCCCCAAAAATATTGAATGT 58.510 37.500 0.00 0.00 0.00 2.71
157 175 4.333372 GCACAGCCCCAAAAATATTGAATG 59.667 41.667 0.00 0.00 0.00 2.67
162 180 4.639078 AAAGCACAGCCCCAAAAATATT 57.361 36.364 0.00 0.00 0.00 1.28
174 192 2.278854 TGCCAAAAAGAAAAGCACAGC 58.721 42.857 0.00 0.00 0.00 4.40
195 214 1.273327 CTTCCCCAGCGCAATTCTTTT 59.727 47.619 11.47 0.00 0.00 2.27
207 227 1.318158 GCATTGCTGTCCTTCCCCAG 61.318 60.000 0.16 0.00 0.00 4.45
208 228 1.304381 GCATTGCTGTCCTTCCCCA 60.304 57.895 0.16 0.00 0.00 4.96
216 236 1.080298 GGCCACTTGCATTGCTGTC 60.080 57.895 10.49 0.00 43.89 3.51
217 237 0.251297 TAGGCCACTTGCATTGCTGT 60.251 50.000 5.01 6.15 43.89 4.40
311 334 2.676632 TAAGCCGCGGAGAACAAATA 57.323 45.000 33.48 5.94 0.00 1.40
315 338 0.461339 GGATTAAGCCGCGGAGAACA 60.461 55.000 33.48 8.30 0.00 3.18
320 343 1.407656 ATCTGGGATTAAGCCGCGGA 61.408 55.000 33.48 8.40 36.51 5.54
322 345 1.284982 CGATCTGGGATTAAGCCGCG 61.285 60.000 3.16 0.00 0.00 6.46
327 350 2.361119 TGACGTCCGATCTGGGATTAAG 59.639 50.000 14.12 0.00 38.61 1.85
331 354 1.414158 ATTGACGTCCGATCTGGGAT 58.586 50.000 14.12 0.00 38.61 3.85
342 365 6.293081 CCAGATGACAATATGGAATTGACGTC 60.293 42.308 9.11 9.11 46.42 4.34
353 376 5.287674 ACTCTGTCCCAGATGACAATATG 57.712 43.478 0.00 0.00 44.19 1.78
360 383 5.130705 AGTGTATACTCTGTCCCAGATGA 57.869 43.478 6.65 0.00 39.92 2.92
539 578 1.072331 GACCTGTCTTTTGCTCCCAGA 59.928 52.381 0.00 0.00 0.00 3.86
540 579 1.202806 TGACCTGTCTTTTGCTCCCAG 60.203 52.381 0.00 0.00 0.00 4.45
552 592 6.093633 ACACACTTTACTTCTTTTGACCTGTC 59.906 38.462 0.00 0.00 0.00 3.51
573 621 4.332543 GTGTGTGTGAAAAGATGAGACACA 59.667 41.667 0.00 0.00 43.44 3.72
597 645 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
598 646 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
599 647 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
600 648 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
601 649 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
602 650 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
603 651 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
604 652 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
605 653 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
616 664 1.102809 ACCAGCCATGTGTGTGTGTG 61.103 55.000 0.00 0.00 0.00 3.82
698 807 5.800438 GTGGATTCGAGGAAATTAAGCAAAC 59.200 40.000 0.00 0.00 0.00 2.93
713 822 4.371786 ACGAGTATACTACGTGGATTCGA 58.628 43.478 21.54 0.00 38.79 3.71
728 837 6.104665 GCTCCTTTTGGTTTAGTACGAGTAT 58.895 40.000 0.00 0.00 41.38 2.12
729 838 5.473039 GCTCCTTTTGGTTTAGTACGAGTA 58.527 41.667 0.00 0.00 41.38 2.59
733 842 3.187842 GTGGCTCCTTTTGGTTTAGTACG 59.812 47.826 0.00 0.00 41.38 3.67
757 885 1.423794 GGGGTGTTTCCTCCTCCACA 61.424 60.000 0.00 0.00 36.25 4.17
761 889 1.145119 ACTTTGGGGTGTTTCCTCCTC 59.855 52.381 0.00 0.00 35.35 3.71
884 1039 2.224314 GCTCTGCGTGGATTTTATAGCC 59.776 50.000 0.00 0.00 0.00 3.93
893 1052 1.969200 ATGCTCTGCTCTGCGTGGAT 61.969 55.000 0.00 0.00 0.00 3.41
894 1053 2.569072 GATGCTCTGCTCTGCGTGGA 62.569 60.000 0.00 0.00 0.00 4.02
895 1054 2.125229 ATGCTCTGCTCTGCGTGG 60.125 61.111 0.00 0.00 0.00 4.94
896 1055 2.172372 GGATGCTCTGCTCTGCGTG 61.172 63.158 0.00 0.00 0.00 5.34
914 1420 3.705638 CTGAGCGTGCGTGTGTGG 61.706 66.667 0.00 0.00 0.00 4.17
1075 1607 3.921104 TCTCAGGAGCCTTCATACTCAT 58.079 45.455 0.00 0.00 34.48 2.90
1089 1621 1.536073 CCGTCTGCTGGTTCTCAGGA 61.536 60.000 0.00 0.00 43.54 3.86
1110 1648 1.002430 GAGTTCACTGCCATCACAGGA 59.998 52.381 0.00 0.00 42.21 3.86
1194 1732 2.665000 CATGTGCACCGGGAGACT 59.335 61.111 15.69 0.00 0.00 3.24
1228 1766 2.786495 CGTGGTCGGAGGATGAGGG 61.786 68.421 0.00 0.00 0.00 4.30
1527 2074 3.472726 ACCACGACCACCACCGTT 61.473 61.111 0.00 0.00 36.83 4.44
1638 2434 9.787435 AGAACAATACTACAATTCTACAAACCA 57.213 29.630 0.00 0.00 0.00 3.67
1648 2444 6.010219 AGGGCACAAGAACAATACTACAATT 58.990 36.000 0.00 0.00 0.00 2.32
1655 2720 4.584327 AAACAGGGCACAAGAACAATAC 57.416 40.909 0.00 0.00 0.00 1.89
1656 2721 4.038642 GGAAAACAGGGCACAAGAACAATA 59.961 41.667 0.00 0.00 0.00 1.90
2080 3145 4.794169 AGACAAATTGAATGTACAACGCC 58.206 39.130 0.00 0.00 32.50 5.68
2104 3169 9.027129 GTTTTTACTTTACCAAATGAACCTGTC 57.973 33.333 0.00 0.00 0.00 3.51
2142 3211 6.640518 AGAGCCGAACTAAATGACAAATCTA 58.359 36.000 0.00 0.00 0.00 1.98
2157 3226 0.462759 AGCCAGCAATAGAGCCGAAC 60.463 55.000 0.00 0.00 34.23 3.95
2165 3234 1.332997 GCACTAGCAAGCCAGCAATAG 59.667 52.381 0.55 0.00 41.58 1.73
2184 3291 1.602377 ACGGACTAGTTTTGCACAAGC 59.398 47.619 0.00 0.00 42.57 4.01
2196 3303 6.696441 AAGGTAGAGAAATACACGGACTAG 57.304 41.667 0.00 0.00 0.00 2.57
2198 3305 5.997384 AAAGGTAGAGAAATACACGGACT 57.003 39.130 0.00 0.00 0.00 3.85
2251 3358 6.680810 TGCTCAGTTATTTGTTCAAGATTGG 58.319 36.000 0.00 0.00 0.00 3.16
2253 3360 7.363268 GGGATGCTCAGTTATTTGTTCAAGATT 60.363 37.037 0.00 0.00 0.00 2.40
2254 3361 6.096001 GGGATGCTCAGTTATTTGTTCAAGAT 59.904 38.462 0.00 0.00 0.00 2.40
2255 3362 5.415701 GGGATGCTCAGTTATTTGTTCAAGA 59.584 40.000 0.00 0.00 0.00 3.02
2257 3364 4.155826 CGGGATGCTCAGTTATTTGTTCAA 59.844 41.667 0.00 0.00 0.00 2.69
2258 3365 3.689161 CGGGATGCTCAGTTATTTGTTCA 59.311 43.478 0.00 0.00 0.00 3.18
2259 3366 3.938963 TCGGGATGCTCAGTTATTTGTTC 59.061 43.478 0.00 0.00 0.00 3.18
2261 3368 3.627395 TCGGGATGCTCAGTTATTTGT 57.373 42.857 0.00 0.00 0.00 2.83
2263 3370 6.147821 CGATTAATCGGGATGCTCAGTTATTT 59.852 38.462 26.61 0.00 45.93 1.40
2264 3371 5.639506 CGATTAATCGGGATGCTCAGTTATT 59.360 40.000 26.61 0.00 45.93 1.40
2265 3372 5.171476 CGATTAATCGGGATGCTCAGTTAT 58.829 41.667 26.61 0.00 45.93 1.89
2266 3373 4.556233 CGATTAATCGGGATGCTCAGTTA 58.444 43.478 26.61 0.00 45.93 2.24
2310 3533 5.429762 TCCATCCACCAAATATTCAGAGTCT 59.570 40.000 0.00 0.00 0.00 3.24
2327 3552 6.672593 ACTAAAAGGCAATAGATTCCATCCA 58.327 36.000 0.00 0.00 0.00 3.41
2330 3555 8.494433 TGACTACTAAAAGGCAATAGATTCCAT 58.506 33.333 0.00 0.00 29.20 3.41
2399 3652 1.375853 TTGCTATCATGGTGTGCCGC 61.376 55.000 0.00 0.00 37.67 6.53
2401 3654 1.755179 AGTTGCTATCATGGTGTGCC 58.245 50.000 0.00 0.00 0.00 5.01
2407 3660 4.275196 CCATCAGTCAAGTTGCTATCATGG 59.725 45.833 0.00 7.54 0.00 3.66
2437 3690 5.418310 TTGCACTTTAGTTTTCCTTCGAG 57.582 39.130 0.00 0.00 0.00 4.04
2484 3737 2.874701 CCATCAAACTCTAGGGCAATCG 59.125 50.000 0.00 0.00 0.00 3.34
2492 3745 3.875727 CCACATCAGCCATCAAACTCTAG 59.124 47.826 0.00 0.00 0.00 2.43
2494 3747 2.306805 TCCACATCAGCCATCAAACTCT 59.693 45.455 0.00 0.00 0.00 3.24
2495 3748 2.421424 GTCCACATCAGCCATCAAACTC 59.579 50.000 0.00 0.00 0.00 3.01
2499 3753 0.324614 ACGTCCACATCAGCCATCAA 59.675 50.000 0.00 0.00 0.00 2.57
2535 5404 9.884465 CTGGCTATTATCAACTAACTAAAATGC 57.116 33.333 0.00 0.00 0.00 3.56
2545 5414 9.555411 TCCATAATACCTGGCTATTATCAACTA 57.445 33.333 13.78 2.82 30.10 2.24
2563 5433 8.217111 TGCAAGAGGTGTCATTATTCCATAATA 58.783 33.333 0.00 0.00 33.86 0.98
2565 5435 6.422333 TGCAAGAGGTGTCATTATTCCATAA 58.578 36.000 0.00 0.00 0.00 1.90
2570 5440 3.944015 AGCTGCAAGAGGTGTCATTATTC 59.056 43.478 1.02 0.00 34.07 1.75
2584 5454 2.686558 TCAAACGCTAAAGCTGCAAG 57.313 45.000 1.02 0.00 39.32 4.01
2588 5458 5.120830 AGTTGTAGATCAAACGCTAAAGCTG 59.879 40.000 0.00 0.00 37.81 4.24
2596 5467 3.424962 GGCAGAAGTTGTAGATCAAACGC 60.425 47.826 0.00 0.00 37.81 4.84


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

AutoCloner maintained by Alex Coulton.