Multiple sequence alignment - TraesCS7D01G171900

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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 TraesCS7D01G171900 chr7D 100.000 4013 0 0 1 4013 124291804 124295816 0.000000e+00 7411.0
1 TraesCS7D01G171900 chr7D 76.561 1297 246 41 1610 2874 123739354 123738084 0.000000e+00 658.0
2 TraesCS7D01G171900 chr7D 74.219 256 54 11 2115 2364 124022540 124022291 3.300000e-16 97.1
3 TraesCS7D01G171900 chr7D 93.182 44 2 1 718 761 37650415 37650373 3.350000e-06 63.9
4 TraesCS7D01G171900 chr7D 92.857 42 3 0 619 660 491298023 491298064 1.200000e-05 62.1
5 TraesCS7D01G171900 chr7A 93.469 3185 127 33 863 4013 126860070 126863207 0.000000e+00 4654.0
6 TraesCS7D01G171900 chr7A 76.011 1434 281 46 1574 2979 126593256 126594654 0.000000e+00 684.0
7 TraesCS7D01G171900 chr7A 75.109 229 47 9 2141 2364 126784481 126784704 9.180000e-17 99.0
8 TraesCS7D01G171900 chr7B 93.287 2607 126 20 760 3350 85939874 85942447 0.000000e+00 3799.0
9 TraesCS7D01G171900 chr7B 89.762 547 46 6 3470 4013 86132486 86133025 0.000000e+00 691.0
10 TraesCS7D01G171900 chr7B 75.878 1310 247 47 1607 2874 85150819 85149537 4.440000e-169 604.0
11 TraesCS7D01G171900 chr7B 84.375 64 9 1 699 762 287920413 287920475 1.200000e-05 62.1
12 TraesCS7D01G171900 chr3A 90.436 711 53 8 1 697 568976039 568975330 0.000000e+00 922.0
13 TraesCS7D01G171900 chr3A 84.000 75 11 1 697 771 479364512 479364439 2.000000e-08 71.3
14 TraesCS7D01G171900 chr2D 86.957 713 68 11 2 696 454825067 454825772 0.000000e+00 778.0
15 TraesCS7D01G171900 chr2D 95.455 44 0 2 728 770 551426468 551426510 7.200000e-08 69.4
16 TraesCS7D01G171900 chr3D 84.300 707 83 19 2 688 577819312 577820010 0.000000e+00 665.0
17 TraesCS7D01G171900 chr1D 86.765 68 7 1 697 764 217291670 217291735 1.550000e-09 75.0
18 TraesCS7D01G171900 chr4A 90.566 53 2 3 723 772 594600205 594600153 2.590000e-07 67.6
19 TraesCS7D01G171900 chr5D 93.182 44 2 1 729 771 481756336 481756293 3.350000e-06 63.9
20 TraesCS7D01G171900 chr2B 82.278 79 9 4 697 774 312841693 312841767 3.350000e-06 63.9
21 TraesCS7D01G171900 chr6B 85.484 62 6 2 697 758 165295828 165295886 1.200000e-05 62.1


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 TraesCS7D01G171900 chr7D 124291804 124295816 4012 False 7411 7411 100.000 1 4013 1 chr7D.!!$F1 4012
1 TraesCS7D01G171900 chr7D 123738084 123739354 1270 True 658 658 76.561 1610 2874 1 chr7D.!!$R2 1264
2 TraesCS7D01G171900 chr7A 126860070 126863207 3137 False 4654 4654 93.469 863 4013 1 chr7A.!!$F3 3150
3 TraesCS7D01G171900 chr7A 126593256 126594654 1398 False 684 684 76.011 1574 2979 1 chr7A.!!$F1 1405
4 TraesCS7D01G171900 chr7B 85939874 85942447 2573 False 3799 3799 93.287 760 3350 1 chr7B.!!$F1 2590
5 TraesCS7D01G171900 chr7B 86132486 86133025 539 False 691 691 89.762 3470 4013 1 chr7B.!!$F2 543
6 TraesCS7D01G171900 chr7B 85149537 85150819 1282 True 604 604 75.878 1607 2874 1 chr7B.!!$R1 1267
7 TraesCS7D01G171900 chr3A 568975330 568976039 709 True 922 922 90.436 1 697 1 chr3A.!!$R2 696
8 TraesCS7D01G171900 chr2D 454825067 454825772 705 False 778 778 86.957 2 696 1 chr2D.!!$F1 694
9 TraesCS7D01G171900 chr3D 577819312 577820010 698 False 665 665 84.300 2 688 1 chr3D.!!$F1 686

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
753 779 0.108089 TACAACGCACGGGCATATGT 60.108 50.000 11.77 13.84 41.24 2.29 F
1436 1479 0.819582 CCAAAGGCCAATCGATTGCT 59.180 50.000 28.90 19.68 36.48 3.91 F
2721 2804 1.068250 GGCCGAGATGTACCTGCTC 59.932 63.158 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1857 0.731514 TTGCAATCGTCGTCGTCCTC 60.732 55.000 0.00 0.00 38.33 3.71 R
2973 3071 0.310854 CCGGGTGAACAAGTTTCAGC 59.689 55.000 7.51 7.51 43.83 4.26 R
3548 3664 3.062639 GCAAGATAACATCTCGTGTGTGG 59.937 47.826 0.00 0.00 41.14 4.17 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
63 68 4.098349 GCACATCATAATCCACAACCACAT 59.902 41.667 0.00 0.00 0.00 3.21
85 90 2.712709 TGTCAACAGAACGAAAACCCA 58.287 42.857 0.00 0.00 0.00 4.51
150 157 0.979187 CCTATACACCACCCACCCGT 60.979 60.000 0.00 0.00 0.00 5.28
151 158 0.906775 CTATACACCACCCACCCGTT 59.093 55.000 0.00 0.00 0.00 4.44
162 169 0.538516 CCACCCGTTGACCAAATCCA 60.539 55.000 0.00 0.00 0.00 3.41
290 298 2.530958 AAATCCGCGGTGGGACGAAT 62.531 55.000 27.15 5.31 39.34 3.34
345 353 4.988716 TGCGTCCCTCACCTCCGT 62.989 66.667 0.00 0.00 0.00 4.69
401 409 1.371183 CCAGGAGAACTTGCGGACA 59.629 57.895 0.00 0.00 0.00 4.02
403 411 1.611673 CCAGGAGAACTTGCGGACAAT 60.612 52.381 0.00 0.00 34.61 2.71
459 470 2.642129 CCAACCGCAATGCACGAA 59.358 55.556 5.91 0.00 0.00 3.85
505 516 0.914417 GGATGGGGGAGTGGAGTTCA 60.914 60.000 0.00 0.00 0.00 3.18
528 539 4.115199 GCATTGGGCGAGAGGGGT 62.115 66.667 0.00 0.00 0.00 4.95
562 575 0.710567 CACTTGTCATCGACGCAGAC 59.289 55.000 11.13 11.13 34.95 3.51
593 607 0.112412 ATGGGAAGGAAACGGCAACT 59.888 50.000 0.00 0.00 0.00 3.16
618 643 1.443194 GAGACGCTGCGAACCGTTA 60.443 57.895 30.47 0.00 37.87 3.18
625 650 2.793585 CGCTGCGAACCGTTAGATCTAA 60.794 50.000 18.66 11.24 0.00 2.10
660 686 4.505217 GCGTGCGGATCTGTTGCG 62.505 66.667 2.89 6.77 42.84 4.85
672 698 4.391830 GGATCTGTTGCGAATTTACAGTCA 59.608 41.667 0.00 2.04 0.00 3.41
688 714 4.006319 ACAGTCAGCAGGAATTTAGCTTC 58.994 43.478 0.00 0.00 36.26 3.86
697 723 6.203723 AGCAGGAATTTAGCTTCATCGTATTC 59.796 38.462 0.00 0.00 34.37 1.75
698 724 6.017934 GCAGGAATTTAGCTTCATCGTATTCA 60.018 38.462 0.00 0.00 0.00 2.57
699 725 7.308229 GCAGGAATTTAGCTTCATCGTATTCAT 60.308 37.037 0.00 0.00 0.00 2.57
700 726 8.562892 CAGGAATTTAGCTTCATCGTATTCATT 58.437 33.333 0.00 0.00 0.00 2.57
701 727 9.778741 AGGAATTTAGCTTCATCGTATTCATTA 57.221 29.630 0.00 0.00 0.00 1.90
732 758 8.402472 TGAATGCATATAAAACTTTTACTCCCG 58.598 33.333 0.00 0.00 0.00 5.14
733 759 7.875327 ATGCATATAAAACTTTTACTCCCGT 57.125 32.000 0.00 0.00 0.00 5.28
734 760 7.690952 TGCATATAAAACTTTTACTCCCGTT 57.309 32.000 0.00 0.00 0.00 4.44
735 761 8.789825 TGCATATAAAACTTTTACTCCCGTTA 57.210 30.769 0.00 0.00 0.00 3.18
736 762 8.667463 TGCATATAAAACTTTTACTCCCGTTAC 58.333 33.333 0.00 0.00 0.00 2.50
737 763 8.667463 GCATATAAAACTTTTACTCCCGTTACA 58.333 33.333 0.00 0.00 0.00 2.41
748 774 3.339464 CGTTACAACGCACGGGCA 61.339 61.111 11.77 0.00 46.06 5.36
749 775 2.673114 CGTTACAACGCACGGGCAT 61.673 57.895 11.77 0.00 46.06 4.40
750 776 1.352882 CGTTACAACGCACGGGCATA 61.353 55.000 11.77 0.00 46.06 3.14
751 777 1.011333 GTTACAACGCACGGGCATAT 58.989 50.000 11.77 0.00 41.24 1.78
752 778 1.010580 TTACAACGCACGGGCATATG 58.989 50.000 11.77 7.71 41.24 1.78
753 779 0.108089 TACAACGCACGGGCATATGT 60.108 50.000 11.77 13.84 41.24 2.29
754 780 1.062365 CAACGCACGGGCATATGTG 59.938 57.895 11.77 0.00 41.24 3.21
771 797 7.118390 GGCATATGTGCTAGTAGAACATAAAGG 59.882 40.741 27.62 21.37 46.71 3.11
794 820 5.812127 GGATCATTTCAACATTTTGTAGGCC 59.188 40.000 0.00 0.00 34.02 5.19
812 838 2.391389 CGGAGGAAGTGCGAAAGGC 61.391 63.158 0.00 0.00 44.08 4.35
841 871 2.437518 TAGGCAACCGTAACGCTGCA 62.438 55.000 0.00 0.00 36.42 4.41
1312 1343 2.551270 GAGCCGATAAATGCGCCG 59.449 61.111 4.18 0.00 0.00 6.46
1314 1345 3.649986 GCCGATAAATGCGCCGCT 61.650 61.111 11.67 0.00 0.00 5.52
1364 1395 1.467374 GGCGCGTTTAATCTTGCATGT 60.467 47.619 8.43 0.00 0.00 3.21
1377 1408 1.153784 GCATGTGCCATGTTTCCGG 60.154 57.895 14.21 0.00 34.31 5.14
1387 1418 3.632145 GCCATGTTTCCGGACAAATCTAT 59.368 43.478 1.83 0.00 32.47 1.98
1392 1427 6.249035 TGTTTCCGGACAAATCTATTTCAC 57.751 37.500 1.83 0.00 0.00 3.18
1417 1452 4.214437 CGAGAAGAACTTGCATTGAACAC 58.786 43.478 0.00 0.00 0.00 3.32
1418 1453 4.540824 GAGAAGAACTTGCATTGAACACC 58.459 43.478 0.00 0.00 0.00 4.16
1421 1464 4.734398 AGAACTTGCATTGAACACCAAA 57.266 36.364 0.00 0.00 38.43 3.28
1436 1479 0.819582 CCAAAGGCCAATCGATTGCT 59.180 50.000 28.90 19.68 36.48 3.91
1437 1480 1.470285 CCAAAGGCCAATCGATTGCTG 60.470 52.381 28.90 18.72 36.48 4.41
1438 1481 1.473677 CAAAGGCCAATCGATTGCTGA 59.526 47.619 28.90 0.00 36.48 4.26
1448 1491 2.367486 TCGATTGCTGATTGCCATGAA 58.633 42.857 0.00 0.00 42.00 2.57
1603 1653 3.334054 GAGGCCTGCTTGTCCCCT 61.334 66.667 12.00 0.00 0.00 4.79
1803 1853 2.601367 GGCACTGGCACAACCCAT 60.601 61.111 0.00 0.00 43.71 4.00
1804 1854 2.652530 GCACTGGCACAACCCATG 59.347 61.111 0.00 0.00 38.70 3.66
1805 1855 2.652530 CACTGGCACAACCCATGC 59.347 61.111 0.00 0.00 42.62 4.06
1806 1856 1.904865 CACTGGCACAACCCATGCT 60.905 57.895 0.00 0.00 42.93 3.79
1807 1857 1.904865 ACTGGCACAACCCATGCTG 60.905 57.895 0.00 0.00 42.93 4.41
1808 1858 1.604308 CTGGCACAACCCATGCTGA 60.604 57.895 0.00 0.00 42.93 4.26
1820 1870 2.038837 ATGCTGAGGACGACGACGA 61.039 57.895 15.32 0.00 42.66 4.20
2139 2192 2.268920 CACGCCTGCACCTACCAT 59.731 61.111 0.00 0.00 0.00 3.55
2721 2804 1.068250 GGCCGAGATGTACCTGCTC 59.932 63.158 0.00 0.00 0.00 4.26
2737 2820 4.794439 TCAGCATGACCGACGCGG 62.794 66.667 12.47 15.25 42.56 6.46
2973 3071 1.153289 CGAAGACATGAGCTGGGGG 60.153 63.158 0.00 0.00 0.00 5.40
2993 3091 0.310854 CTGAAACTTGTTCACCCGGC 59.689 55.000 0.00 0.00 0.00 6.13
2994 3092 1.104577 TGAAACTTGTTCACCCGGCC 61.105 55.000 0.00 0.00 0.00 6.13
2995 3093 2.125202 GAAACTTGTTCACCCGGCCG 62.125 60.000 21.04 21.04 0.00 6.13
2996 3094 2.612095 AAACTTGTTCACCCGGCCGA 62.612 55.000 30.73 2.40 0.00 5.54
3014 3112 5.751990 CGGCCGAAATAGTACTTAACTGAAT 59.248 40.000 24.07 0.00 39.39 2.57
3034 3132 6.537355 TGAATGGGCCATGTAAAATGAAAAA 58.463 32.000 22.01 0.00 0.00 1.94
3035 3133 6.429385 TGAATGGGCCATGTAAAATGAAAAAC 59.571 34.615 22.01 0.00 0.00 2.43
3036 3134 5.296151 TGGGCCATGTAAAATGAAAAACA 57.704 34.783 0.00 0.00 0.00 2.83
3037 3135 5.059833 TGGGCCATGTAAAATGAAAAACAC 58.940 37.500 0.00 0.00 0.00 3.32
3038 3136 5.163258 TGGGCCATGTAAAATGAAAAACACT 60.163 36.000 0.00 0.00 0.00 3.55
3039 3137 5.408299 GGGCCATGTAAAATGAAAAACACTC 59.592 40.000 4.39 0.00 0.00 3.51
3040 3138 5.118510 GGCCATGTAAAATGAAAAACACTCG 59.881 40.000 0.00 0.00 0.00 4.18
3070 3168 9.552114 CACAAATTGACAATGAAGATCTTACTC 57.448 33.333 8.25 0.00 0.00 2.59
3185 3283 3.606687 AGCCTACAAATAAGTGGTTCGG 58.393 45.455 0.00 0.00 0.00 4.30
3387 3486 5.337491 GGCATGTCCCTTCATTTTTGTACAT 60.337 40.000 0.00 0.00 0.00 2.29
3388 3487 6.165577 GCATGTCCCTTCATTTTTGTACATT 58.834 36.000 0.00 0.00 0.00 2.71
3389 3488 6.650390 GCATGTCCCTTCATTTTTGTACATTT 59.350 34.615 0.00 0.00 0.00 2.32
3390 3489 7.173047 GCATGTCCCTTCATTTTTGTACATTTT 59.827 33.333 0.00 0.00 0.00 1.82
3391 3490 9.054922 CATGTCCCTTCATTTTTGTACATTTTT 57.945 29.630 0.00 0.00 0.00 1.94
3392 3491 8.430801 TGTCCCTTCATTTTTGTACATTTTTG 57.569 30.769 0.00 0.00 0.00 2.44
3393 3492 8.043710 TGTCCCTTCATTTTTGTACATTTTTGT 58.956 29.630 0.00 0.00 0.00 2.83
3394 3493 9.535878 GTCCCTTCATTTTTGTACATTTTTGTA 57.464 29.630 0.00 0.00 0.00 2.41
3395 3494 9.535878 TCCCTTCATTTTTGTACATTTTTGTAC 57.464 29.630 8.89 8.89 43.49 2.90
3403 3502 5.637006 TGTACATTTTTGTACAGATGCCC 57.363 39.130 13.41 6.98 46.53 5.36
3404 3503 5.321102 TGTACATTTTTGTACAGATGCCCT 58.679 37.500 13.41 1.63 46.53 5.19
3405 3504 5.772672 TGTACATTTTTGTACAGATGCCCTT 59.227 36.000 13.41 1.37 46.53 3.95
3453 3552 3.955101 CGGCTCGACTCGCCCTAG 61.955 72.222 8.46 0.00 44.73 3.02
3500 3612 1.001815 CGCGGATTTTGTTGAACCACT 60.002 47.619 0.00 0.00 0.00 4.00
3545 3661 0.320421 TGCCTGTTGCGAGTAGTTCC 60.320 55.000 0.00 0.00 45.60 3.62
3548 3664 2.271800 CCTGTTGCGAGTAGTTCCATC 58.728 52.381 0.00 0.00 0.00 3.51
3605 3721 5.411781 ACTAGAAGCACTACCAAATTCTCG 58.588 41.667 0.00 0.00 32.69 4.04
3666 3782 1.878522 CGCTCGTGTATGACAGGCC 60.879 63.158 0.00 0.00 34.28 5.19
3879 3998 9.995003 ACTTTTCTTTGCATATAATGTTTCCAA 57.005 25.926 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 68 4.452825 TGGGTTTTCGTTCTGTTGACATA 58.547 39.130 0.00 0.00 0.00 2.29
85 90 9.241919 GTTTAATTTTCCATGGATTTTTCCCAT 57.758 29.630 17.06 0.00 44.75 4.00
162 169 3.934457 GGATTTTGGTTCAATCCGTGT 57.066 42.857 0.00 0.00 40.26 4.49
290 298 3.161866 GTTTTCCCTGTTGCTTATCCCA 58.838 45.455 0.00 0.00 0.00 4.37
392 400 1.938577 CATCTCTCCATTGTCCGCAAG 59.061 52.381 0.00 0.00 38.10 4.01
401 409 2.021639 TCCCCTTCCTCATCTCTCCATT 60.022 50.000 0.00 0.00 0.00 3.16
403 411 1.018840 TCCCCTTCCTCATCTCTCCA 58.981 55.000 0.00 0.00 0.00 3.86
459 470 0.546598 CCGCATTACTTCTCCCCCTT 59.453 55.000 0.00 0.00 0.00 3.95
528 539 4.090588 GTGGGGCCGATCGAACCA 62.091 66.667 18.66 17.95 0.00 3.67
562 575 2.771943 TCCTTCCCATAGCCTTACTGTG 59.228 50.000 0.00 0.00 37.26 3.66
618 643 3.488721 CCGATGTCGTCCGTTTTAGATCT 60.489 47.826 0.00 0.00 37.74 2.75
625 650 1.082117 GCATCCGATGTCGTCCGTTT 61.082 55.000 10.10 0.00 37.74 3.60
660 686 6.969473 GCTAAATTCCTGCTGACTGTAAATTC 59.031 38.462 0.00 0.00 0.00 2.17
672 698 3.878778 ACGATGAAGCTAAATTCCTGCT 58.121 40.909 0.00 0.00 38.87 4.24
706 732 8.402472 CGGGAGTAAAAGTTTTATATGCATTCA 58.598 33.333 3.54 0.00 0.00 2.57
707 733 8.403236 ACGGGAGTAAAAGTTTTATATGCATTC 58.597 33.333 3.54 0.00 44.60 2.67
708 734 8.288689 ACGGGAGTAAAAGTTTTATATGCATT 57.711 30.769 3.54 0.00 44.60 3.56
709 735 7.875327 ACGGGAGTAAAAGTTTTATATGCAT 57.125 32.000 11.12 3.79 44.60 3.96
710 736 7.690952 AACGGGAGTAAAAGTTTTATATGCA 57.309 32.000 11.12 0.00 46.69 3.96
711 737 8.667463 TGTAACGGGAGTAAAAGTTTTATATGC 58.333 33.333 11.12 8.45 46.69 3.14
732 758 1.011333 ATATGCCCGTGCGTTGTAAC 58.989 50.000 0.00 0.00 41.78 2.50
733 759 1.010580 CATATGCCCGTGCGTTGTAA 58.989 50.000 0.00 0.00 41.78 2.41
734 760 0.108089 ACATATGCCCGTGCGTTGTA 60.108 50.000 1.58 0.00 41.78 2.41
735 761 1.376683 ACATATGCCCGTGCGTTGT 60.377 52.632 1.58 0.00 41.78 3.32
736 762 1.062365 CACATATGCCCGTGCGTTG 59.938 57.895 1.58 0.00 41.78 4.10
737 763 3.496711 CACATATGCCCGTGCGTT 58.503 55.556 1.58 0.00 41.78 4.84
747 773 9.935241 ATCCTTTATGTTCTACTAGCACATATG 57.065 33.333 8.76 0.00 35.04 1.78
749 775 9.143155 TGATCCTTTATGTTCTACTAGCACATA 57.857 33.333 4.88 4.88 34.14 2.29
750 776 8.023021 TGATCCTTTATGTTCTACTAGCACAT 57.977 34.615 6.59 6.59 36.17 3.21
751 777 7.418337 TGATCCTTTATGTTCTACTAGCACA 57.582 36.000 0.00 0.00 0.00 4.57
752 778 8.894768 AATGATCCTTTATGTTCTACTAGCAC 57.105 34.615 0.00 0.00 0.00 4.40
753 779 9.547753 GAAATGATCCTTTATGTTCTACTAGCA 57.452 33.333 0.00 0.00 0.00 3.49
754 780 9.547753 TGAAATGATCCTTTATGTTCTACTAGC 57.452 33.333 0.00 0.00 0.00 3.42
757 783 9.739276 TGTTGAAATGATCCTTTATGTTCTACT 57.261 29.630 0.00 0.00 0.00 2.57
771 797 5.516339 CGGCCTACAAAATGTTGAAATGATC 59.484 40.000 1.62 0.00 38.20 2.92
781 807 0.988832 TCCTCCGGCCTACAAAATGT 59.011 50.000 0.00 0.00 0.00 2.71
794 820 2.391389 GCCTTTCGCACTTCCTCCG 61.391 63.158 0.00 0.00 37.47 4.63
809 835 2.037121 GGTTGCCTATTGTTTGTTGCCT 59.963 45.455 0.00 0.00 0.00 4.75
812 838 3.363341 ACGGTTGCCTATTGTTTGTTG 57.637 42.857 0.00 0.00 0.00 3.33
818 844 1.081094 GCGTTACGGTTGCCTATTGT 58.919 50.000 6.94 0.00 0.00 2.71
874 904 7.264947 AGGAAAAATATCCGCTGTAAAAATGG 58.735 34.615 0.00 0.00 44.60 3.16
1293 1324 2.551270 GCGCATTTATCGGCTCGG 59.449 61.111 0.30 0.00 0.00 4.63
1312 1343 2.547007 GGCGGAGGAAGATAAAGAGAGC 60.547 54.545 0.00 0.00 0.00 4.09
1314 1345 1.681793 CGGCGGAGGAAGATAAAGAGA 59.318 52.381 0.00 0.00 0.00 3.10
1364 1395 1.543802 GATTTGTCCGGAAACATGGCA 59.456 47.619 5.23 0.00 0.00 4.92
1377 1408 3.863424 TCTCGCCGTGAAATAGATTTGTC 59.137 43.478 0.00 0.00 0.00 3.18
1387 1418 1.864711 CAAGTTCTTCTCGCCGTGAAA 59.135 47.619 3.06 0.00 0.00 2.69
1392 1427 0.798776 AATGCAAGTTCTTCTCGCCG 59.201 50.000 0.00 0.00 0.00 6.46
1415 1450 1.736696 GCAATCGATTGGCCTTTGGTG 60.737 52.381 33.05 10.62 38.21 4.17
1417 1452 0.819582 AGCAATCGATTGGCCTTTGG 59.180 50.000 33.05 11.18 38.21 3.28
1418 1453 1.473677 TCAGCAATCGATTGGCCTTTG 59.526 47.619 33.05 20.39 38.21 2.77
1421 1464 1.679680 CAATCAGCAATCGATTGGCCT 59.320 47.619 33.05 22.15 43.90 5.19
1448 1491 1.466167 GCGCAATGTCTGTCATGAGTT 59.534 47.619 0.30 0.00 36.81 3.01
1483 1532 6.692681 GTGTAACGCATATCTCCTACGTTAAA 59.307 38.462 7.74 0.58 46.77 1.52
1801 1851 1.869574 CGTCGTCGTCCTCAGCATG 60.870 63.158 0.00 0.00 37.54 4.06
1802 1852 1.377366 ATCGTCGTCGTCCTCAGCAT 61.377 55.000 1.33 0.00 38.33 3.79
1803 1853 1.583495 AATCGTCGTCGTCCTCAGCA 61.583 55.000 1.33 0.00 38.33 4.41
1804 1854 1.134530 CAATCGTCGTCGTCCTCAGC 61.135 60.000 1.33 0.00 38.33 4.26
1805 1855 1.134530 GCAATCGTCGTCGTCCTCAG 61.135 60.000 1.33 0.00 38.33 3.35
1806 1856 1.154093 GCAATCGTCGTCGTCCTCA 60.154 57.895 1.33 0.00 38.33 3.86
1807 1857 0.731514 TTGCAATCGTCGTCGTCCTC 60.732 55.000 0.00 0.00 38.33 3.71
1808 1858 0.732880 CTTGCAATCGTCGTCGTCCT 60.733 55.000 0.00 0.00 38.33 3.85
1820 1870 1.442769 CAGCACGAGGTACTTGCAAT 58.557 50.000 0.00 0.00 45.68 3.56
1938 1988 3.708220 GAAGAGGTCGGGCAGCGAG 62.708 68.421 0.00 0.00 0.00 5.03
2016 2066 3.358076 CTCGCCGGTCAGGTTCTCC 62.358 68.421 1.90 0.00 43.70 3.71
2139 2192 1.886542 TCGCAGTAGAAGAGCTTGTCA 59.113 47.619 0.00 0.00 0.00 3.58
2649 2732 3.947132 CTGGTGCTCCTCGTGGCTG 62.947 68.421 6.34 0.00 34.23 4.85
2790 2873 1.146930 CATGATCCACGGGGTGAGG 59.853 63.158 2.12 0.00 35.23 3.86
2973 3071 0.310854 CCGGGTGAACAAGTTTCAGC 59.689 55.000 7.51 7.51 43.83 4.26
2993 3091 6.018180 GCCCATTCAGTTAAGTACTATTTCGG 60.018 42.308 0.00 0.00 34.56 4.30
2994 3092 6.018180 GGCCCATTCAGTTAAGTACTATTTCG 60.018 42.308 0.00 0.00 34.56 3.46
2995 3093 6.826741 TGGCCCATTCAGTTAAGTACTATTTC 59.173 38.462 0.00 0.00 34.56 2.17
2996 3094 6.727394 TGGCCCATTCAGTTAAGTACTATTT 58.273 36.000 0.00 0.00 34.56 1.40
3014 3112 5.059833 GTGTTTTTCATTTTACATGGCCCA 58.940 37.500 0.00 0.00 0.00 5.36
3034 3132 3.738982 TGTCAATTTGTGATCCGAGTGT 58.261 40.909 0.00 0.00 38.90 3.55
3035 3133 4.747540 TTGTCAATTTGTGATCCGAGTG 57.252 40.909 0.00 0.00 38.90 3.51
3036 3134 5.003160 TCATTGTCAATTTGTGATCCGAGT 58.997 37.500 0.00 0.00 38.90 4.18
3037 3135 5.550232 TCATTGTCAATTTGTGATCCGAG 57.450 39.130 0.00 0.00 38.90 4.63
3038 3136 5.704978 TCTTCATTGTCAATTTGTGATCCGA 59.295 36.000 0.00 0.00 38.90 4.55
3039 3137 5.941733 TCTTCATTGTCAATTTGTGATCCG 58.058 37.500 0.00 0.00 38.90 4.18
3040 3138 7.769220 AGATCTTCATTGTCAATTTGTGATCC 58.231 34.615 16.11 6.53 38.90 3.36
3070 3168 1.260561 GACATGCCTAATTGCGTACGG 59.739 52.381 18.39 0.00 0.00 4.02
3185 3283 1.468520 TGCATCGCTAAGGCAAGTTTC 59.531 47.619 0.00 0.00 38.60 2.78
3361 3460 3.259123 ACAAAAATGAAGGGACATGCCTC 59.741 43.478 0.00 0.00 36.66 4.70
3387 3486 7.395772 TGATATGAAAGGGCATCTGTACAAAAA 59.604 33.333 0.00 0.00 0.00 1.94
3388 3487 6.889177 TGATATGAAAGGGCATCTGTACAAAA 59.111 34.615 0.00 0.00 0.00 2.44
3389 3488 6.318648 GTGATATGAAAGGGCATCTGTACAAA 59.681 38.462 0.00 0.00 0.00 2.83
3390 3489 5.822519 GTGATATGAAAGGGCATCTGTACAA 59.177 40.000 0.00 0.00 0.00 2.41
3391 3490 5.104569 TGTGATATGAAAGGGCATCTGTACA 60.105 40.000 0.00 0.00 0.00 2.90
3392 3491 5.368145 TGTGATATGAAAGGGCATCTGTAC 58.632 41.667 0.00 0.00 0.00 2.90
3393 3492 5.628797 TGTGATATGAAAGGGCATCTGTA 57.371 39.130 0.00 0.00 0.00 2.74
3394 3493 4.508551 TGTGATATGAAAGGGCATCTGT 57.491 40.909 0.00 0.00 0.00 3.41
3395 3494 5.840243 TTTGTGATATGAAAGGGCATCTG 57.160 39.130 0.00 0.00 0.00 2.90
3396 3495 6.855763 TTTTTGTGATATGAAAGGGCATCT 57.144 33.333 0.00 0.00 0.00 2.90
3424 3523 1.391485 GTCGAGCCGCTATAATGCATG 59.609 52.381 0.00 0.00 0.00 4.06
3462 3566 1.032657 CGGGTCAGTGATCGTCTCCT 61.033 60.000 0.00 0.00 0.00 3.69
3464 3568 1.226717 GCGGGTCAGTGATCGTCTC 60.227 63.158 16.44 0.00 0.00 3.36
3500 3612 2.312390 TGTGATACGCCAGCATACCTA 58.688 47.619 0.00 0.00 0.00 3.08
3511 3627 2.936498 ACAGGCAAAGTATGTGATACGC 59.064 45.455 0.00 0.00 40.64 4.42
3545 3661 4.686972 AGATAACATCTCGTGTGTGGATG 58.313 43.478 0.00 0.00 41.14 3.51
3548 3664 3.062639 GCAAGATAACATCTCGTGTGTGG 59.937 47.826 0.00 0.00 41.14 4.17
3666 3782 5.636121 TGTACTGGTAGTAATTTGCAACGAG 59.364 40.000 0.00 0.00 31.62 4.18
3938 4057 7.905604 TCTCAAGAGAAAATGAATCGCTAAA 57.094 32.000 0.00 0.00 33.91 1.85
3939 4058 7.905604 TTCTCAAGAGAAAATGAATCGCTAA 57.094 32.000 9.93 0.00 43.79 3.09


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

AutoCloner maintained by Alex Coulton.