Multiple sequence alignment - TraesCS5A01G334100

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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 TraesCS5A01G334100 chr5A 100.000 2459 0 0 1 2459 543915492 543917950 0.000000e+00 4542
1 TraesCS5A01G334100 chr5A 81.579 342 43 11 860 1189 543714085 543714418 5.210000e-67 265
2 TraesCS5A01G334100 chr5D 94.292 1787 62 12 677 2459 428374639 428376389 0.000000e+00 2699
3 TraesCS5A01G334100 chr5D 91.772 474 30 2 1 474 428374068 428374532 0.000000e+00 651
4 TraesCS5A01G334100 chr5D 79.952 419 56 14 788 1189 428307032 428307439 1.440000e-72 283
5 TraesCS5A01G334100 chr5B 91.213 1525 83 12 950 2459 517557148 517558636 0.000000e+00 2026
6 TraesCS5A01G334100 chr5B 80.191 419 52 14 788 1189 517503416 517503820 4.000000e-73 285
7 TraesCS5A01G334100 chr5B 78.154 325 61 9 1 322 388165334 388165651 5.360000e-47 198
8 TraesCS5A01G334100 chr6D 81.176 340 57 5 1 336 322206218 322205882 1.450000e-67 267
9 TraesCS5A01G334100 chr4A 79.279 333 62 6 1 330 57096820 57097148 2.460000e-55 226
10 TraesCS5A01G334100 chr4A 77.419 341 72 5 1 338 405428764 405428426 5.360000e-47 198
11 TraesCS5A01G334100 chr3D 78.635 337 70 2 1 336 341717396 341717061 3.180000e-54 222
12 TraesCS5A01G334100 chr1A 79.257 323 64 3 1 322 531362943 531363263 3.180000e-54 222
13 TraesCS5A01G334100 chr6B 78.402 338 69 4 1 336 585713067 585712732 1.480000e-52 217
14 TraesCS5A01G334100 chr2D 78.395 324 65 5 1 322 527264234 527263914 3.210000e-49 206


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 TraesCS5A01G334100 chr5A 543915492 543917950 2458 False 4542 4542 100.000 1 2459 1 chr5A.!!$F2 2458
1 TraesCS5A01G334100 chr5D 428374068 428376389 2321 False 1675 2699 93.032 1 2459 2 chr5D.!!$F2 2458
2 TraesCS5A01G334100 chr5B 517557148 517558636 1488 False 2026 2026 91.213 950 2459 1 chr5B.!!$F3 1509

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
689 690 0.03779 TGATCCATCGACGTGTTGCA 60.038 50.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2198 0.106335 CTGATCCCAGCAGCTCGATT 59.894 55.0 0.0 0.0 33.07 3.34 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 0.322997 CCACCCCAAAACCGCTATCA 60.323 55.000 0.00 0.00 0.00 2.15
77 78 7.693969 AAGTTTATAAGAAGCAGAGCATTGT 57.306 32.000 0.00 0.00 0.00 2.71
172 173 9.973246 CTTAGTGACAACAATACAATATGTGTC 57.027 33.333 0.00 0.00 41.98 3.67
188 189 9.698309 CAATATGTGTCTTCGTCCTTATTATCT 57.302 33.333 0.00 0.00 0.00 1.98
189 190 9.915629 AATATGTGTCTTCGTCCTTATTATCTC 57.084 33.333 0.00 0.00 0.00 2.75
190 191 7.589958 ATGTGTCTTCGTCCTTATTATCTCT 57.410 36.000 0.00 0.00 0.00 3.10
191 192 6.796426 TGTGTCTTCGTCCTTATTATCTCTG 58.204 40.000 0.00 0.00 0.00 3.35
192 193 6.183360 TGTGTCTTCGTCCTTATTATCTCTGG 60.183 42.308 0.00 0.00 0.00 3.86
193 194 6.039493 GTGTCTTCGTCCTTATTATCTCTGGA 59.961 42.308 0.00 0.00 0.00 3.86
194 195 6.778069 TGTCTTCGTCCTTATTATCTCTGGAT 59.222 38.462 0.00 0.00 36.07 3.41
195 196 7.287927 TGTCTTCGTCCTTATTATCTCTGGATT 59.712 37.037 0.00 0.00 33.71 3.01
215 216 2.839486 AGAGCACCACGAGATTGAAA 57.161 45.000 0.00 0.00 0.00 2.69
218 219 1.202758 AGCACCACGAGATTGAAACCA 60.203 47.619 0.00 0.00 0.00 3.67
230 231 6.054860 AGATTGAAACCAGTACTATGCACT 57.945 37.500 0.00 0.00 0.00 4.40
238 239 3.570550 CCAGTACTATGCACTACTCCCTC 59.429 52.174 0.00 0.00 0.00 4.30
275 276 8.690203 TTATCAATCTTGTCCAGAGAAAACAA 57.310 30.769 0.00 0.00 33.87 2.83
279 280 9.130661 TCAATCTTGTCCAGAGAAAACAAATTA 57.869 29.630 0.00 0.00 33.87 1.40
283 284 9.130661 TCTTGTCCAGAGAAAACAAATTAATCA 57.869 29.630 0.00 0.00 32.89 2.57
333 334 5.971202 TGCAACGAAGAAACTTCAAAAGATC 59.029 36.000 11.20 0.00 0.00 2.75
336 337 6.305693 ACGAAGAAACTTCAAAAGATCCAG 57.694 37.500 11.20 0.00 0.00 3.86
339 340 7.171678 ACGAAGAAACTTCAAAAGATCCAGTAG 59.828 37.037 11.20 0.00 0.00 2.57
354 355 9.482175 AAGATCCAGTAGTCTTGAATAGTTAGT 57.518 33.333 0.00 0.00 33.64 2.24
403 404 2.162681 CTAAGGGCTTTGTGGAACTGG 58.837 52.381 0.00 0.00 38.04 4.00
405 406 0.468029 AGGGCTTTGTGGAACTGGTG 60.468 55.000 0.00 0.00 38.04 4.17
425 426 5.071250 TGGTGTTCTAGTTACTGGTGTGAAT 59.929 40.000 0.00 0.00 0.00 2.57
430 431 6.432607 TCTAGTTACTGGTGTGAATCTACG 57.567 41.667 0.00 0.00 0.00 3.51
431 432 6.175471 TCTAGTTACTGGTGTGAATCTACGA 58.825 40.000 0.00 0.00 0.00 3.43
439 440 4.106197 GGTGTGAATCTACGAGTGATGAC 58.894 47.826 0.00 0.00 0.00 3.06
494 495 9.668497 AAAATAATATTAATAGGCCCGTCTCTC 57.332 33.333 0.00 0.00 0.00 3.20
495 496 4.985538 ATATTAATAGGCCCGTCTCTCG 57.014 45.455 0.00 0.00 39.52 4.04
496 497 2.062971 TTAATAGGCCCGTCTCTCGT 57.937 50.000 0.00 0.00 37.94 4.18
497 498 2.936919 TAATAGGCCCGTCTCTCGTA 57.063 50.000 0.00 0.00 37.94 3.43
498 499 2.062971 AATAGGCCCGTCTCTCGTAA 57.937 50.000 0.00 0.00 37.94 3.18
499 500 2.289592 ATAGGCCCGTCTCTCGTAAT 57.710 50.000 0.00 0.00 37.94 1.89
500 501 1.602311 TAGGCCCGTCTCTCGTAATC 58.398 55.000 0.00 0.00 37.94 1.75
501 502 0.395311 AGGCCCGTCTCTCGTAATCA 60.395 55.000 0.00 0.00 37.94 2.57
502 503 0.674534 GGCCCGTCTCTCGTAATCAT 59.325 55.000 0.00 0.00 37.94 2.45
503 504 1.068741 GGCCCGTCTCTCGTAATCATT 59.931 52.381 0.00 0.00 37.94 2.57
504 505 2.483188 GGCCCGTCTCTCGTAATCATTT 60.483 50.000 0.00 0.00 37.94 2.32
505 506 3.195661 GCCCGTCTCTCGTAATCATTTT 58.804 45.455 0.00 0.00 37.94 1.82
506 507 3.621715 GCCCGTCTCTCGTAATCATTTTT 59.378 43.478 0.00 0.00 37.94 1.94
507 508 4.494199 GCCCGTCTCTCGTAATCATTTTTG 60.494 45.833 0.00 0.00 37.94 2.44
508 509 4.494199 CCCGTCTCTCGTAATCATTTTTGC 60.494 45.833 0.00 0.00 37.94 3.68
509 510 4.092821 CCGTCTCTCGTAATCATTTTTGCA 59.907 41.667 0.00 0.00 37.94 4.08
523 524 6.437928 TCATTTTTGCAGTAGTGATTGTGTC 58.562 36.000 0.42 0.00 0.00 3.67
534 535 2.165845 GTGATTGTGTCTACCTAGCCGT 59.834 50.000 0.00 0.00 0.00 5.68
535 536 2.829720 TGATTGTGTCTACCTAGCCGTT 59.170 45.455 0.00 0.00 0.00 4.44
570 571 1.458064 CGGTAACAACGAGCGTGAAAT 59.542 47.619 0.00 0.00 33.29 2.17
577 578 2.005971 ACGAGCGTGAAATTAGACCC 57.994 50.000 0.00 0.00 0.00 4.46
592 593 9.191995 GAAATTAGACCCAAAACAAGTTACATG 57.808 33.333 0.00 0.00 0.00 3.21
594 595 8.927675 ATTAGACCCAAAACAAGTTACATGTA 57.072 30.769 0.08 0.08 0.00 2.29
595 596 6.628919 AGACCCAAAACAAGTTACATGTAC 57.371 37.500 4.68 1.30 0.00 2.90
596 597 6.123651 AGACCCAAAACAAGTTACATGTACA 58.876 36.000 4.68 0.00 0.00 2.90
597 598 6.775629 AGACCCAAAACAAGTTACATGTACAT 59.224 34.615 4.68 1.41 0.00 2.29
598 599 7.940137 AGACCCAAAACAAGTTACATGTACATA 59.060 33.333 8.32 0.00 0.00 2.29
599 600 8.644374 ACCCAAAACAAGTTACATGTACATAT 57.356 30.769 8.32 0.00 0.00 1.78
600 601 8.736244 ACCCAAAACAAGTTACATGTACATATC 58.264 33.333 8.32 0.00 0.00 1.63
601 602 8.735315 CCCAAAACAAGTTACATGTACATATCA 58.265 33.333 8.32 0.00 0.00 2.15
625 626 9.797556 TCATAGAAATGTGTAGTGTGTACATAC 57.202 33.333 14.37 14.37 34.18 2.39
626 627 9.581099 CATAGAAATGTGTAGTGTGTACATACA 57.419 33.333 22.72 13.47 34.18 2.29
632 633 9.529325 AATGTGTAGTGTGTACATACATATGAC 57.471 33.333 22.72 12.89 38.63 3.06
633 634 7.190871 TGTGTAGTGTGTACATACATATGACG 58.809 38.462 22.72 0.00 38.63 4.35
634 635 7.148205 TGTGTAGTGTGTACATACATATGACGT 60.148 37.037 22.72 5.75 38.63 4.34
635 636 7.165318 GTGTAGTGTGTACATACATATGACGTG 59.835 40.741 22.72 7.38 38.63 4.49
636 637 6.203808 AGTGTGTACATACATATGACGTGT 57.796 37.500 22.72 12.57 38.63 4.49
637 638 7.324354 AGTGTGTACATACATATGACGTGTA 57.676 36.000 22.72 11.64 38.63 2.90
638 639 7.764331 AGTGTGTACATACATATGACGTGTAA 58.236 34.615 22.72 4.45 38.63 2.41
639 640 8.410912 AGTGTGTACATACATATGACGTGTAAT 58.589 33.333 22.72 0.00 38.63 1.89
640 641 8.476925 GTGTGTACATACATATGACGTGTAATG 58.523 37.037 16.95 0.00 38.63 1.90
676 677 1.985473 GCCAATGGCTATGTGATCCA 58.015 50.000 18.47 0.00 46.69 3.41
677 678 2.522185 GCCAATGGCTATGTGATCCAT 58.478 47.619 18.47 0.00 46.69 3.41
678 679 2.490903 GCCAATGGCTATGTGATCCATC 59.509 50.000 18.47 0.00 46.69 3.51
679 680 2.745821 CCAATGGCTATGTGATCCATCG 59.254 50.000 0.00 0.00 39.51 3.84
680 681 3.557686 CCAATGGCTATGTGATCCATCGA 60.558 47.826 0.00 0.00 39.51 3.59
681 682 2.820059 TGGCTATGTGATCCATCGAC 57.180 50.000 0.00 0.00 34.86 4.20
682 683 1.000274 TGGCTATGTGATCCATCGACG 60.000 52.381 0.00 0.00 34.86 5.12
683 684 1.000163 GGCTATGTGATCCATCGACGT 60.000 52.381 0.00 0.00 34.86 4.34
684 685 2.054363 GCTATGTGATCCATCGACGTG 58.946 52.381 0.00 0.00 34.86 4.49
685 686 2.543861 GCTATGTGATCCATCGACGTGT 60.544 50.000 0.00 0.00 34.86 4.49
686 687 2.672961 ATGTGATCCATCGACGTGTT 57.327 45.000 0.00 0.00 0.00 3.32
687 688 1.708822 TGTGATCCATCGACGTGTTG 58.291 50.000 0.00 0.00 0.00 3.33
688 689 0.370273 GTGATCCATCGACGTGTTGC 59.630 55.000 0.00 0.00 0.00 4.17
689 690 0.037790 TGATCCATCGACGTGTTGCA 60.038 50.000 0.00 0.00 0.00 4.08
690 691 1.075542 GATCCATCGACGTGTTGCAA 58.924 50.000 0.00 0.00 0.00 4.08
713 714 2.203098 CGGTTGGACGGGTTGTGT 60.203 61.111 0.00 0.00 0.00 3.72
715 716 2.719354 GTTGGACGGGTTGTGTGC 59.281 61.111 0.00 0.00 0.00 4.57
721 722 0.889186 GACGGGTTGTGTGCTGGATT 60.889 55.000 0.00 0.00 0.00 3.01
735 736 1.271856 TGGATTAACCGGACAGCTCA 58.728 50.000 9.46 0.00 42.61 4.26
736 737 1.066430 TGGATTAACCGGACAGCTCAC 60.066 52.381 9.46 0.00 42.61 3.51
737 738 1.066430 GGATTAACCGGACAGCTCACA 60.066 52.381 9.46 0.00 0.00 3.58
738 739 2.614481 GGATTAACCGGACAGCTCACAA 60.614 50.000 9.46 0.00 0.00 3.33
739 740 2.851263 TTAACCGGACAGCTCACAAT 57.149 45.000 9.46 0.00 0.00 2.71
740 741 2.093306 TAACCGGACAGCTCACAATG 57.907 50.000 9.46 0.00 0.00 2.82
746 747 1.532868 GGACAGCTCACAATGTGTCAC 59.467 52.381 13.55 4.30 40.96 3.67
749 750 0.532640 AGCTCACAATGTGTCACGCA 60.533 50.000 13.55 0.00 34.79 5.24
765 766 0.586319 CGCATTTCACGCCGGAATAT 59.414 50.000 5.05 0.00 0.00 1.28
781 782 5.933463 CCGGAATATGGCTTAACGGTAATTA 59.067 40.000 0.00 0.00 35.47 1.40
785 786 6.774354 ATATGGCTTAACGGTAATTACACG 57.226 37.500 17.16 18.11 0.00 4.49
805 806 0.251916 TGTCGGGCCAAATCGATTCT 59.748 50.000 11.83 0.00 37.73 2.40
808 809 3.322541 TGTCGGGCCAAATCGATTCTATA 59.677 43.478 11.83 0.00 37.73 1.31
903 908 8.940952 AGAGAAATAAAATCCAAGTCTCTTTCG 58.059 33.333 0.00 0.00 37.65 3.46
933 938 5.395214 GCAAGAGGAAAAGGACAAGGAAAAA 60.395 40.000 0.00 0.00 0.00 1.94
938 943 7.785028 AGAGGAAAAGGACAAGGAAAAATAACT 59.215 33.333 0.00 0.00 0.00 2.24
939 944 9.074576 GAGGAAAAGGACAAGGAAAAATAACTA 57.925 33.333 0.00 0.00 0.00 2.24
940 945 9.078990 AGGAAAAGGACAAGGAAAAATAACTAG 57.921 33.333 0.00 0.00 0.00 2.57
941 946 8.857098 GGAAAAGGACAAGGAAAAATAACTAGT 58.143 33.333 0.00 0.00 0.00 2.57
961 966 7.104290 ACTAGTATAGCAACCAAAGAAAGACC 58.896 38.462 0.00 0.00 44.39 3.85
1482 1490 2.222271 AGGAGAGATGAGAGGGGAGAA 58.778 52.381 0.00 0.00 0.00 2.87
1643 1657 1.734465 CTTGTTGTCCGGAGCTGAATC 59.266 52.381 3.06 0.00 0.00 2.52
1668 1682 1.332997 CATGGCGGCTTCTGAATTCTC 59.667 52.381 11.43 0.00 0.00 2.87
1861 1875 8.801715 AGCAATTTTCGCAATTTAGTATATGG 57.198 30.769 0.00 0.00 0.00 2.74
1920 1934 5.950883 TCGTGAAATTTGGTGTTGTGTTTA 58.049 33.333 0.00 0.00 0.00 2.01
1970 1984 2.200067 CACTGATCTGCGAGTCCAATC 58.800 52.381 0.00 0.00 0.00 2.67
1986 2000 2.098117 CCAATCTCCAGCGGAAATGTTC 59.902 50.000 0.00 0.00 0.00 3.18
1994 2008 2.032030 CAGCGGAAATGTTCGTTCTGTT 60.032 45.455 0.00 0.00 34.43 3.16
2034 2054 8.398743 TGGTCCTGTAGATCAATAGATATGGTA 58.601 37.037 0.00 0.00 30.60 3.25
2043 2063 5.655394 TCAATAGATATGGTACTGGAGGCT 58.345 41.667 0.00 0.00 0.00 4.58
2079 2099 0.809241 CATCGCAGTCTCTTGCTCCC 60.809 60.000 0.00 0.00 41.90 4.30
2080 2100 2.290122 ATCGCAGTCTCTTGCTCCCG 62.290 60.000 0.00 0.00 41.90 5.14
2081 2101 2.659610 GCAGTCTCTTGCTCCCGT 59.340 61.111 0.00 0.00 40.89 5.28
2082 2102 1.446966 GCAGTCTCTTGCTCCCGTC 60.447 63.158 0.00 0.00 40.89 4.79
2083 2103 1.216710 CAGTCTCTTGCTCCCGTCC 59.783 63.158 0.00 0.00 0.00 4.79
2138 2158 4.935205 TCTTCATACTGGTTTGGTCGATTG 59.065 41.667 0.00 0.00 0.00 2.67
2140 2160 5.097742 TCATACTGGTTTGGTCGATTGAT 57.902 39.130 0.00 0.00 0.00 2.57
2177 2197 1.306997 ACCCCACAGGACGGATGAT 60.307 57.895 0.00 0.00 39.89 2.45
2178 2198 0.031515 ACCCCACAGGACGGATGATA 60.032 55.000 0.00 0.00 39.89 2.15
2248 2268 3.407046 GAAGCGCCTCCATGCAAGC 62.407 63.158 2.29 0.00 0.00 4.01
2312 2332 3.699538 GGTTTCCTTTCGGATTAAGCCAT 59.300 43.478 10.94 0.00 39.58 4.40
2314 2334 3.924114 TCCTTTCGGATTAAGCCATGA 57.076 42.857 10.94 0.00 33.30 3.07
2315 2335 4.437682 TCCTTTCGGATTAAGCCATGAT 57.562 40.909 10.94 0.00 33.30 2.45
2316 2336 4.389374 TCCTTTCGGATTAAGCCATGATC 58.611 43.478 10.94 0.00 33.30 2.92
2317 2337 4.136796 CCTTTCGGATTAAGCCATGATCA 58.863 43.478 10.94 0.00 0.00 2.92
2318 2338 4.580167 CCTTTCGGATTAAGCCATGATCAA 59.420 41.667 10.94 0.00 0.00 2.57
2319 2339 5.278169 CCTTTCGGATTAAGCCATGATCAAG 60.278 44.000 10.94 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 6.125029 ACTTAATACCTTGAGATGCATGCTT 58.875 36.000 20.33 13.23 0.00 3.91
172 173 9.015367 TCTAATCCAGAGATAATAAGGACGAAG 57.985 37.037 0.00 0.00 30.42 3.79
188 189 1.751351 CTCGTGGTGCTCTAATCCAGA 59.249 52.381 0.00 0.00 31.54 3.86
189 190 1.751351 TCTCGTGGTGCTCTAATCCAG 59.249 52.381 0.00 0.00 31.54 3.86
190 191 1.847328 TCTCGTGGTGCTCTAATCCA 58.153 50.000 0.00 0.00 0.00 3.41
191 192 3.126831 CAATCTCGTGGTGCTCTAATCC 58.873 50.000 0.00 0.00 0.00 3.01
192 193 4.046938 TCAATCTCGTGGTGCTCTAATC 57.953 45.455 0.00 0.00 0.00 1.75
193 194 4.471904 TTCAATCTCGTGGTGCTCTAAT 57.528 40.909 0.00 0.00 0.00 1.73
194 195 3.953712 TTCAATCTCGTGGTGCTCTAA 57.046 42.857 0.00 0.00 0.00 2.10
195 196 3.585862 GTTTCAATCTCGTGGTGCTCTA 58.414 45.455 0.00 0.00 0.00 2.43
204 205 5.109903 GCATAGTACTGGTTTCAATCTCGT 58.890 41.667 5.39 0.00 0.00 4.18
215 216 3.052793 AGGGAGTAGTGCATAGTACTGGT 60.053 47.826 5.39 0.00 41.89 4.00
218 219 4.166337 TCAGAGGGAGTAGTGCATAGTACT 59.834 45.833 0.00 0.00 43.95 2.73
271 272 9.988350 CTACGTATGCTTTCTGATTAATTTGTT 57.012 29.630 0.00 0.00 0.00 2.83
273 274 8.338259 AGCTACGTATGCTTTCTGATTAATTTG 58.662 33.333 12.04 0.00 37.52 2.32
275 276 9.712305 ATAGCTACGTATGCTTTCTGATTAATT 57.288 29.630 19.74 0.00 41.46 1.40
279 280 9.542462 TTAAATAGCTACGTATGCTTTCTGATT 57.458 29.630 19.74 12.44 41.46 2.57
296 297 9.503427 GTTTCTTCGTTGCATAATTAAATAGCT 57.497 29.630 0.00 0.00 0.00 3.32
310 311 5.399596 GGATCTTTTGAAGTTTCTTCGTTGC 59.600 40.000 5.28 0.00 0.00 4.17
333 334 7.339721 TCCAGACTAACTATTCAAGACTACTGG 59.660 40.741 0.00 0.00 39.62 4.00
354 355 7.847096 TGTATGTCAAAGCTAACTATTCCAGA 58.153 34.615 0.00 0.00 0.00 3.86
368 369 4.080863 AGCCCTTAGTCCTGTATGTCAAAG 60.081 45.833 0.00 0.00 0.00 2.77
403 404 6.456501 AGATTCACACCAGTAACTAGAACAC 58.543 40.000 0.00 0.00 0.00 3.32
405 406 6.746364 CGTAGATTCACACCAGTAACTAGAAC 59.254 42.308 0.00 0.00 0.00 3.01
425 426 7.608153 TCTAAATTTTGGTCATCACTCGTAGA 58.392 34.615 0.00 0.00 0.00 2.59
430 431 6.072508 TGCACTCTAAATTTTGGTCATCACTC 60.073 38.462 0.00 0.00 0.00 3.51
431 432 5.769662 TGCACTCTAAATTTTGGTCATCACT 59.230 36.000 0.00 0.00 0.00 3.41
439 440 7.481275 AACAATGTTGCACTCTAAATTTTGG 57.519 32.000 0.00 0.00 0.00 3.28
474 475 4.985538 CGAGAGACGGGCCTATTAATAT 57.014 45.455 0.84 0.00 38.46 1.28
488 489 6.170675 ACTGCAAAAATGATTACGAGAGAC 57.829 37.500 0.00 0.00 0.00 3.36
489 490 7.063426 CACTACTGCAAAAATGATTACGAGAGA 59.937 37.037 0.00 0.00 0.00 3.10
490 491 7.063426 TCACTACTGCAAAAATGATTACGAGAG 59.937 37.037 0.00 0.00 0.00 3.20
491 492 6.871492 TCACTACTGCAAAAATGATTACGAGA 59.129 34.615 0.00 0.00 0.00 4.04
492 493 7.060600 TCACTACTGCAAAAATGATTACGAG 57.939 36.000 0.00 0.00 0.00 4.18
493 494 7.609760 ATCACTACTGCAAAAATGATTACGA 57.390 32.000 0.00 0.00 0.00 3.43
494 495 7.750458 ACAATCACTACTGCAAAAATGATTACG 59.250 33.333 12.85 7.13 35.56 3.18
495 496 8.853345 CACAATCACTACTGCAAAAATGATTAC 58.147 33.333 12.85 0.00 35.56 1.89
496 497 8.575589 ACACAATCACTACTGCAAAAATGATTA 58.424 29.630 12.85 0.00 35.56 1.75
497 498 7.436118 ACACAATCACTACTGCAAAAATGATT 58.564 30.769 9.12 9.12 37.28 2.57
498 499 6.985117 ACACAATCACTACTGCAAAAATGAT 58.015 32.000 0.00 0.00 0.00 2.45
499 500 6.262944 AGACACAATCACTACTGCAAAAATGA 59.737 34.615 0.00 0.00 0.00 2.57
500 501 6.441274 AGACACAATCACTACTGCAAAAATG 58.559 36.000 0.00 0.00 0.00 2.32
501 502 6.639632 AGACACAATCACTACTGCAAAAAT 57.360 33.333 0.00 0.00 0.00 1.82
502 503 6.017440 GGTAGACACAATCACTACTGCAAAAA 60.017 38.462 0.00 0.00 37.32 1.94
503 504 5.468746 GGTAGACACAATCACTACTGCAAAA 59.531 40.000 0.00 0.00 37.32 2.44
504 505 4.994852 GGTAGACACAATCACTACTGCAAA 59.005 41.667 0.00 0.00 37.32 3.68
505 506 4.283467 AGGTAGACACAATCACTACTGCAA 59.717 41.667 0.00 0.00 37.32 4.08
506 507 3.832490 AGGTAGACACAATCACTACTGCA 59.168 43.478 0.00 0.00 37.32 4.41
507 508 4.457834 AGGTAGACACAATCACTACTGC 57.542 45.455 0.00 0.00 37.32 4.40
508 509 5.450688 GGCTAGGTAGACACAATCACTACTG 60.451 48.000 0.00 0.00 37.32 2.74
509 510 4.645588 GGCTAGGTAGACACAATCACTACT 59.354 45.833 0.00 0.00 37.32 2.57
523 524 2.736144 TTCACACAACGGCTAGGTAG 57.264 50.000 0.00 0.00 0.00 3.18
534 535 4.515567 TGTTACCGTTGCATATTCACACAA 59.484 37.500 0.00 0.00 0.00 3.33
535 536 4.065789 TGTTACCGTTGCATATTCACACA 58.934 39.130 0.00 0.00 0.00 3.72
552 553 5.303485 GTCTAATTTCACGCTCGTTGTTAC 58.697 41.667 0.00 0.00 0.00 2.50
570 571 7.774157 TGTACATGTAACTTGTTTTGGGTCTAA 59.226 33.333 7.25 0.00 0.00 2.10
599 600 9.797556 GTATGTACACACTACACATTTCTATGA 57.202 33.333 0.00 0.00 34.78 2.15
600 601 9.581099 TGTATGTACACACTACACATTTCTATG 57.419 33.333 5.77 0.00 34.78 2.23
606 607 9.529325 GTCATATGTATGTACACACTACACATT 57.471 33.333 5.77 0.00 39.30 2.71
607 608 7.860872 CGTCATATGTATGTACACACTACACAT 59.139 37.037 5.77 7.76 39.30 3.21
608 609 7.148205 ACGTCATATGTATGTACACACTACACA 60.148 37.037 5.77 0.00 39.30 3.72
609 610 7.165318 CACGTCATATGTATGTACACACTACAC 59.835 40.741 5.77 0.00 39.30 2.90
610 611 7.148205 ACACGTCATATGTATGTACACACTACA 60.148 37.037 5.77 7.96 39.30 2.74
611 612 7.191551 ACACGTCATATGTATGTACACACTAC 58.808 38.462 5.77 2.12 39.30 2.73
612 613 7.324354 ACACGTCATATGTATGTACACACTA 57.676 36.000 5.77 0.00 39.30 2.74
613 614 6.203808 ACACGTCATATGTATGTACACACT 57.796 37.500 5.77 0.00 39.30 3.55
614 615 7.974243 TTACACGTCATATGTATGTACACAC 57.026 36.000 0.00 0.00 39.30 3.82
615 616 8.407064 TCATTACACGTCATATGTATGTACACA 58.593 33.333 0.00 0.00 39.30 3.72
616 617 8.688184 GTCATTACACGTCATATGTATGTACAC 58.312 37.037 0.00 8.57 39.30 2.90
617 618 7.863877 GGTCATTACACGTCATATGTATGTACA 59.136 37.037 0.00 0.00 40.98 2.90
618 619 8.080417 AGGTCATTACACGTCATATGTATGTAC 58.920 37.037 12.78 7.11 32.70 2.90
619 620 8.173542 AGGTCATTACACGTCATATGTATGTA 57.826 34.615 1.90 7.36 32.70 2.29
620 621 7.050970 AGGTCATTACACGTCATATGTATGT 57.949 36.000 1.90 8.27 32.70 2.29
621 622 7.651704 TGAAGGTCATTACACGTCATATGTATG 59.348 37.037 1.90 2.68 32.70 2.39
622 623 7.722363 TGAAGGTCATTACACGTCATATGTAT 58.278 34.615 1.90 0.00 32.70 2.29
623 624 7.102847 TGAAGGTCATTACACGTCATATGTA 57.897 36.000 1.90 0.00 0.00 2.29
624 625 5.972935 TGAAGGTCATTACACGTCATATGT 58.027 37.500 1.90 0.00 0.00 2.29
625 626 6.507929 CGTTGAAGGTCATTACACGTCATATG 60.508 42.308 0.00 0.00 0.00 1.78
626 627 5.518847 CGTTGAAGGTCATTACACGTCATAT 59.481 40.000 0.00 0.00 0.00 1.78
627 628 4.860352 CGTTGAAGGTCATTACACGTCATA 59.140 41.667 0.00 0.00 0.00 2.15
628 629 3.678072 CGTTGAAGGTCATTACACGTCAT 59.322 43.478 0.00 0.00 0.00 3.06
629 630 3.054166 CGTTGAAGGTCATTACACGTCA 58.946 45.455 0.00 0.00 0.00 4.35
630 631 2.159881 GCGTTGAAGGTCATTACACGTC 60.160 50.000 0.00 0.00 31.82 4.34
631 632 1.796459 GCGTTGAAGGTCATTACACGT 59.204 47.619 3.49 0.00 31.82 4.49
632 633 1.201769 CGCGTTGAAGGTCATTACACG 60.202 52.381 0.00 0.00 32.18 4.49
633 634 2.063266 TCGCGTTGAAGGTCATTACAC 58.937 47.619 5.77 0.00 0.00 2.90
634 635 2.442212 TCGCGTTGAAGGTCATTACA 57.558 45.000 5.77 0.00 0.00 2.41
635 636 2.671396 ACATCGCGTTGAAGGTCATTAC 59.329 45.455 23.12 0.00 0.00 1.89
636 637 2.670905 CACATCGCGTTGAAGGTCATTA 59.329 45.455 23.12 0.00 0.00 1.90
637 638 1.464608 CACATCGCGTTGAAGGTCATT 59.535 47.619 23.12 0.00 0.00 2.57
638 639 1.078709 CACATCGCGTTGAAGGTCAT 58.921 50.000 23.12 0.00 0.00 3.06
639 640 1.565156 GCACATCGCGTTGAAGGTCA 61.565 55.000 23.12 0.00 0.00 4.02
640 641 1.132640 GCACATCGCGTTGAAGGTC 59.867 57.895 23.12 4.16 0.00 3.85
665 666 3.355626 ACACGTCGATGGATCACATAG 57.644 47.619 9.90 0.00 40.72 2.23
666 667 3.443976 CAACACGTCGATGGATCACATA 58.556 45.455 9.90 0.00 40.72 2.29
667 668 2.270923 CAACACGTCGATGGATCACAT 58.729 47.619 9.90 0.00 44.18 3.21
671 672 1.075542 TTGCAACACGTCGATGGATC 58.924 50.000 9.90 0.00 0.00 3.36
672 673 1.518325 TTTGCAACACGTCGATGGAT 58.482 45.000 9.90 0.00 0.00 3.41
673 674 1.300481 TTTTGCAACACGTCGATGGA 58.700 45.000 9.90 0.00 0.00 3.41
674 675 1.778591 GTTTTTGCAACACGTCGATGG 59.221 47.619 9.90 0.57 0.00 3.51
676 677 2.598907 CGAGTTTTTGCAACACGTCGAT 60.599 45.455 12.73 0.00 31.38 3.59
677 678 1.267136 CGAGTTTTTGCAACACGTCGA 60.267 47.619 12.73 0.00 31.38 4.20
678 679 1.101454 CGAGTTTTTGCAACACGTCG 58.899 50.000 0.00 2.14 31.38 5.12
679 680 1.202098 ACCGAGTTTTTGCAACACGTC 60.202 47.619 0.00 0.00 33.51 4.34
680 681 0.806241 ACCGAGTTTTTGCAACACGT 59.194 45.000 0.00 0.00 33.51 4.49
681 682 1.581602 CAACCGAGTTTTTGCAACACG 59.418 47.619 0.00 0.00 34.77 4.49
682 683 1.923864 CCAACCGAGTTTTTGCAACAC 59.076 47.619 0.00 0.00 0.00 3.32
683 684 1.819288 TCCAACCGAGTTTTTGCAACA 59.181 42.857 0.00 0.00 0.00 3.33
684 685 2.190161 GTCCAACCGAGTTTTTGCAAC 58.810 47.619 0.00 0.00 0.00 4.17
685 686 1.202200 CGTCCAACCGAGTTTTTGCAA 60.202 47.619 0.00 0.00 0.00 4.08
686 687 0.378962 CGTCCAACCGAGTTTTTGCA 59.621 50.000 0.00 0.00 0.00 4.08
687 688 0.317519 CCGTCCAACCGAGTTTTTGC 60.318 55.000 0.00 0.00 0.00 3.68
688 689 0.309612 CCCGTCCAACCGAGTTTTTG 59.690 55.000 0.00 0.00 0.00 2.44
689 690 0.107066 ACCCGTCCAACCGAGTTTTT 60.107 50.000 0.00 0.00 0.00 1.94
690 691 0.107066 AACCCGTCCAACCGAGTTTT 60.107 50.000 0.00 0.00 0.00 2.43
713 714 0.392461 GCTGTCCGGTTAATCCAGCA 60.392 55.000 17.40 0.00 45.94 4.41
715 716 1.207089 TGAGCTGTCCGGTTAATCCAG 59.793 52.381 0.00 0.67 35.57 3.86
721 722 1.346395 ACATTGTGAGCTGTCCGGTTA 59.654 47.619 0.00 0.00 0.00 2.85
731 732 0.518636 ATGCGTGACACATTGTGAGC 59.481 50.000 23.12 19.58 36.96 4.26
733 734 2.615912 TGAAATGCGTGACACATTGTGA 59.384 40.909 23.12 0.00 37.78 3.58
734 735 2.720578 GTGAAATGCGTGACACATTGTG 59.279 45.455 15.18 15.18 37.78 3.33
735 736 2.601979 CGTGAAATGCGTGACACATTGT 60.602 45.455 6.37 0.00 37.78 2.71
736 737 1.971284 CGTGAAATGCGTGACACATTG 59.029 47.619 6.37 0.00 37.78 2.82
737 738 1.662876 GCGTGAAATGCGTGACACATT 60.663 47.619 6.37 0.00 40.15 2.71
738 739 0.110238 GCGTGAAATGCGTGACACAT 60.110 50.000 6.37 0.00 40.15 3.21
739 740 1.278337 GCGTGAAATGCGTGACACA 59.722 52.632 6.37 0.00 40.15 3.72
740 741 4.115287 GCGTGAAATGCGTGACAC 57.885 55.556 0.00 0.00 40.15 3.67
749 750 0.951558 GCCATATTCCGGCGTGAAAT 59.048 50.000 6.01 5.42 40.35 2.17
765 766 3.679025 CACGTGTAATTACCGTTAAGCCA 59.321 43.478 21.71 0.00 33.21 4.75
781 782 1.964373 GATTTGGCCCGACACGTGT 60.964 57.895 23.64 23.64 0.00 4.49
785 786 0.377203 GAATCGATTTGGCCCGACAC 59.623 55.000 12.81 0.00 37.64 3.67
938 943 7.011499 TGGTCTTTCTTTGGTTGCTATACTA 57.989 36.000 0.00 0.00 0.00 1.82
939 944 5.876357 TGGTCTTTCTTTGGTTGCTATACT 58.124 37.500 0.00 0.00 0.00 2.12
940 945 5.938125 TCTGGTCTTTCTTTGGTTGCTATAC 59.062 40.000 0.00 0.00 0.00 1.47
941 946 5.938125 GTCTGGTCTTTCTTTGGTTGCTATA 59.062 40.000 0.00 0.00 0.00 1.31
942 947 4.762251 GTCTGGTCTTTCTTTGGTTGCTAT 59.238 41.667 0.00 0.00 0.00 2.97
961 966 5.233263 GCTAATTTCGCCTCTTTCTAGTCTG 59.767 44.000 0.00 0.00 0.00 3.51
1410 1415 0.609131 CACTGCGACCCCCAATTTCT 60.609 55.000 0.00 0.00 0.00 2.52
1482 1490 6.126863 TCATGTGAATTACAAGAAGGTCCT 57.873 37.500 0.00 0.00 43.77 3.85
1630 1644 0.690744 TGGATGGATTCAGCTCCGGA 60.691 55.000 2.93 2.93 38.21 5.14
1668 1682 6.699642 ACGAACCAAATTAACCAATTCAGTTG 59.300 34.615 0.00 0.00 33.09 3.16
1861 1875 3.195698 GAATCGCACCCGCACTCC 61.196 66.667 0.00 0.00 38.40 3.85
1970 1984 1.128692 GAACGAACATTTCCGCTGGAG 59.871 52.381 0.00 0.00 31.21 3.86
1994 2008 3.201266 ACAGGACCAAAGTTCTACCACAA 59.799 43.478 0.00 0.00 27.33 3.33
2090 2110 1.654105 GGAGTTGTATCGAACGCACAG 59.346 52.381 0.00 0.00 0.00 3.66
2138 2158 1.063174 GCAACAGATTGGACTCGCATC 59.937 52.381 0.00 0.00 36.23 3.91
2140 2160 0.250252 TGCAACAGATTGGACTCGCA 60.250 50.000 0.00 0.00 36.23 5.10
2177 2197 1.342496 CTGATCCCAGCAGCTCGATTA 59.658 52.381 0.00 0.00 33.07 1.75
2178 2198 0.106335 CTGATCCCAGCAGCTCGATT 59.894 55.000 0.00 0.00 33.07 3.34
2214 2234 3.790123 GCGCTTCTAGAACATTCCATTGC 60.790 47.826 0.00 0.00 0.00 3.56
2215 2235 3.242870 GGCGCTTCTAGAACATTCCATTG 60.243 47.826 7.64 0.00 0.00 2.82
2248 2268 2.504244 GAACTCTCGCACGACCGG 60.504 66.667 0.00 0.00 0.00 5.28
2312 2332 7.732996 TCAGATGATAAGCTTGATCTTGATCA 58.267 34.615 9.86 8.72 0.00 2.92
2314 2334 7.874016 GTCTCAGATGATAAGCTTGATCTTGAT 59.126 37.037 9.86 0.00 0.00 2.57
2315 2335 7.069702 AGTCTCAGATGATAAGCTTGATCTTGA 59.930 37.037 9.86 10.14 0.00 3.02
2316 2336 7.211573 AGTCTCAGATGATAAGCTTGATCTTG 58.788 38.462 9.86 8.30 0.00 3.02
2317 2337 7.364149 AGTCTCAGATGATAAGCTTGATCTT 57.636 36.000 9.86 6.62 0.00 2.40
2318 2338 6.982160 AGTCTCAGATGATAAGCTTGATCT 57.018 37.500 9.86 10.09 0.00 2.75
2319 2339 7.809331 CAGTAGTCTCAGATGATAAGCTTGATC 59.191 40.741 9.86 7.93 0.00 2.92


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

AutoCloner maintained by Alex Coulton.