Multiple sequence alignment - TraesCS4B01G091300

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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 TraesCS4B01G091300 chr4B 100.000 2660 0 0 1 2660 94187056 94184397 0.000000e+00 4913
1 TraesCS4B01G091300 chr4B 86.990 784 70 12 1000 1762 94202171 94201399 0.000000e+00 854
2 TraesCS4B01G091300 chr4B 95.238 63 2 1 641 703 94204056 94203995 6.060000e-17 99
3 TraesCS4B01G091300 chr2D 96.370 606 21 1 1 606 344999093 344999697 0.000000e+00 996
4 TraesCS4B01G091300 chr2D 94.737 608 30 2 1 607 381205756 381206362 0.000000e+00 944
5 TraesCS4B01G091300 chr2D 94.408 608 33 1 1 608 496490833 496491439 0.000000e+00 933
6 TraesCS4B01G091300 chr2D 90.108 556 46 8 2111 2660 5420107 5419555 0.000000e+00 713
7 TraesCS4B01G091300 chr2D 90.074 544 47 5 2122 2660 549939757 549939216 0.000000e+00 699
8 TraesCS4B01G091300 chr3B 95.724 608 25 1 1 608 617419860 617420466 0.000000e+00 977
9 TraesCS4B01G091300 chr5B 94.780 613 31 1 1 613 706686673 706687284 0.000000e+00 953
10 TraesCS4B01G091300 chr2B 95.033 604 29 1 1 604 88437878 88437276 0.000000e+00 948
11 TraesCS4B01G091300 chr2B 94.842 601 29 2 1 601 23925335 23924737 0.000000e+00 937
12 TraesCS4B01G091300 chr4D 88.596 798 66 8 1000 1776 63580284 63579491 0.000000e+00 946
13 TraesCS4B01G091300 chr4D 90.909 165 15 0 1939 2103 63579263 63579099 3.450000e-54 222
14 TraesCS4B01G091300 chr7D 94.563 607 32 1 1 607 139061835 139061230 0.000000e+00 937
15 TraesCS4B01G091300 chr7D 90.370 540 44 6 2124 2660 371842873 371842339 0.000000e+00 702
16 TraesCS4B01G091300 chr7A 94.399 607 33 1 1 607 78723980 78724585 0.000000e+00 931
17 TraesCS4B01G091300 chr4A 85.932 853 76 16 641 1473 532893021 532893849 0.000000e+00 870
18 TraesCS4B01G091300 chr4A 90.370 540 44 6 2127 2660 576036370 576036907 0.000000e+00 702
19 TraesCS4B01G091300 chr4A 87.709 537 50 10 867 1393 532804602 532805132 1.750000e-171 612
20 TraesCS4B01G091300 chr4A 91.667 396 27 5 1389 1779 532831032 532831426 6.480000e-151 544
21 TraesCS4B01G091300 chr4A 83.597 506 43 14 1456 1948 532894491 532894969 3.140000e-119 438
22 TraesCS4B01G091300 chr4A 91.441 222 14 2 823 1042 532802124 532802342 1.550000e-77 300
23 TraesCS4B01G091300 chr4A 91.304 184 13 2 1939 2121 532895053 532895234 5.690000e-62 248
24 TraesCS4B01G091300 chr4A 86.486 185 17 4 641 821 532804274 532804454 2.090000e-46 196
25 TraesCS4B01G091300 chr1B 92.379 538 37 3 2126 2660 173097311 173096775 0.000000e+00 763
26 TraesCS4B01G091300 chr5D 91.144 542 41 6 2124 2660 225746685 225747224 0.000000e+00 728
27 TraesCS4B01G091300 chr5D 90.239 543 46 5 2123 2660 142521477 142520937 0.000000e+00 702
28 TraesCS4B01G091300 chr2A 91.231 536 37 5 2128 2660 712705715 712705187 0.000000e+00 721
29 TraesCS4B01G091300 chr2A 90.370 540 45 5 2124 2660 77201237 77200702 0.000000e+00 702


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 TraesCS4B01G091300 chr4B 94184397 94187056 2659 True 4913.000000 4913 100.000000 1 2660 1 chr4B.!!$R1 2659
1 TraesCS4B01G091300 chr4B 94201399 94204056 2657 True 476.500000 854 91.114000 641 1762 2 chr4B.!!$R2 1121
2 TraesCS4B01G091300 chr2D 344999093 344999697 604 False 996.000000 996 96.370000 1 606 1 chr2D.!!$F1 605
3 TraesCS4B01G091300 chr2D 381205756 381206362 606 False 944.000000 944 94.737000 1 607 1 chr2D.!!$F2 606
4 TraesCS4B01G091300 chr2D 496490833 496491439 606 False 933.000000 933 94.408000 1 608 1 chr2D.!!$F3 607
5 TraesCS4B01G091300 chr2D 5419555 5420107 552 True 713.000000 713 90.108000 2111 2660 1 chr2D.!!$R1 549
6 TraesCS4B01G091300 chr2D 549939216 549939757 541 True 699.000000 699 90.074000 2122 2660 1 chr2D.!!$R2 538
7 TraesCS4B01G091300 chr3B 617419860 617420466 606 False 977.000000 977 95.724000 1 608 1 chr3B.!!$F1 607
8 TraesCS4B01G091300 chr5B 706686673 706687284 611 False 953.000000 953 94.780000 1 613 1 chr5B.!!$F1 612
9 TraesCS4B01G091300 chr2B 88437276 88437878 602 True 948.000000 948 95.033000 1 604 1 chr2B.!!$R2 603
10 TraesCS4B01G091300 chr2B 23924737 23925335 598 True 937.000000 937 94.842000 1 601 1 chr2B.!!$R1 600
11 TraesCS4B01G091300 chr4D 63579099 63580284 1185 True 584.000000 946 89.752500 1000 2103 2 chr4D.!!$R1 1103
12 TraesCS4B01G091300 chr7D 139061230 139061835 605 True 937.000000 937 94.563000 1 607 1 chr7D.!!$R1 606
13 TraesCS4B01G091300 chr7D 371842339 371842873 534 True 702.000000 702 90.370000 2124 2660 1 chr7D.!!$R2 536
14 TraesCS4B01G091300 chr7A 78723980 78724585 605 False 931.000000 931 94.399000 1 607 1 chr7A.!!$F1 606
15 TraesCS4B01G091300 chr4A 576036370 576036907 537 False 702.000000 702 90.370000 2127 2660 1 chr4A.!!$F2 533
16 TraesCS4B01G091300 chr4A 532893021 532895234 2213 False 518.666667 870 86.944333 641 2121 3 chr4A.!!$F4 1480
17 TraesCS4B01G091300 chr4A 532802124 532805132 3008 False 369.333333 612 88.545333 641 1393 3 chr4A.!!$F3 752
18 TraesCS4B01G091300 chr1B 173096775 173097311 536 True 763.000000 763 92.379000 2126 2660 1 chr1B.!!$R1 534
19 TraesCS4B01G091300 chr5D 225746685 225747224 539 False 728.000000 728 91.144000 2124 2660 1 chr5D.!!$F1 536
20 TraesCS4B01G091300 chr5D 142520937 142521477 540 True 702.000000 702 90.239000 2123 2660 1 chr5D.!!$R1 537
21 TraesCS4B01G091300 chr2A 712705187 712705715 528 True 721.000000 721 91.231000 2128 2660 1 chr2A.!!$R2 532
22 TraesCS4B01G091300 chr2A 77200702 77201237 535 True 702.000000 702 90.370000 2124 2660 1 chr2A.!!$R1 536

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
674 2185 0.03918 TCGAGTCTAGGGCAGTTGGA 59.961 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 5540 0.174845 TGCATGCCTGTAGGTCGTAC 59.825 55.0 16.68 0.0 37.57 3.67 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
50 51 0.599558 AGCTGTGACAATGCGCAAAT 59.400 45.000 17.11 2.99 0.00 2.32
321 322 2.734492 CGATCTACAGGACCGAACAACC 60.734 54.545 0.00 0.00 0.00 3.77
427 429 2.833227 CTTCCACCACCCCAACGA 59.167 61.111 0.00 0.00 0.00 3.85
464 466 6.073314 ACACTAGACAAACCCTAACTACAGA 58.927 40.000 0.00 0.00 0.00 3.41
563 565 1.059584 TGGTGGAGTTGGCCTCAGAA 61.060 55.000 3.32 0.00 42.40 3.02
620 622 2.269978 CGGTTTCTCTCCGTACCCA 58.730 57.895 0.00 0.00 42.62 4.51
624 626 2.612221 GGTTTCTCTCCGTACCCAACTG 60.612 54.545 0.00 0.00 0.00 3.16
625 627 2.005370 TTCTCTCCGTACCCAACTGT 57.995 50.000 0.00 0.00 0.00 3.55
626 628 2.885135 TCTCTCCGTACCCAACTGTA 57.115 50.000 0.00 0.00 0.00 2.74
628 630 3.285484 TCTCTCCGTACCCAACTGTATC 58.715 50.000 0.00 0.00 0.00 2.24
631 633 0.819582 CCGTACCCAACTGTATCGGT 59.180 55.000 0.00 0.00 34.06 4.69
633 635 2.426738 CCGTACCCAACTGTATCGGTTA 59.573 50.000 0.00 0.00 34.06 2.85
634 636 3.068590 CCGTACCCAACTGTATCGGTTAT 59.931 47.826 0.00 0.00 34.06 1.89
635 637 4.441913 CCGTACCCAACTGTATCGGTTATT 60.442 45.833 0.00 0.00 34.06 1.40
637 639 4.146745 ACCCAACTGTATCGGTTATTCC 57.853 45.455 0.00 0.00 31.12 3.01
649 2160 0.643820 GTTATTCCGCTTGGACGTCG 59.356 55.000 9.92 0.00 43.03 5.12
650 2161 0.527113 TTATTCCGCTTGGACGTCGA 59.473 50.000 9.92 1.86 43.03 4.20
674 2185 0.039180 TCGAGTCTAGGGCAGTTGGA 59.961 55.000 0.00 0.00 0.00 3.53
703 2214 4.454678 TGGAGTACGTACCCTACATGTAG 58.545 47.826 23.58 23.58 0.00 2.74
704 2215 4.080356 TGGAGTACGTACCCTACATGTAGT 60.080 45.833 27.07 15.64 0.00 2.73
705 2216 5.130311 TGGAGTACGTACCCTACATGTAGTA 59.870 44.000 27.07 14.71 0.00 1.82
706 2217 6.183361 TGGAGTACGTACCCTACATGTAGTAT 60.183 42.308 27.07 18.29 30.93 2.12
707 2218 6.148480 GGAGTACGTACCCTACATGTAGTATG 59.852 46.154 27.07 21.44 30.93 2.39
708 2219 6.595682 AGTACGTACCCTACATGTAGTATGT 58.404 40.000 27.07 24.81 36.13 2.29
722 2251 4.991056 TGTAGTATGTCCCGTATACGAGTC 59.009 45.833 26.37 11.80 43.02 3.36
768 2326 3.574614 GTTGCGTTGCTGATTACCAATT 58.425 40.909 0.00 0.00 0.00 2.32
769 2327 4.670478 CGTTGCGTTGCTGATTACCAATTA 60.670 41.667 0.00 0.00 0.00 1.40
770 2328 5.157781 GTTGCGTTGCTGATTACCAATTAA 58.842 37.500 0.00 0.00 0.00 1.40
772 2330 6.685527 TGCGTTGCTGATTACCAATTAATA 57.314 33.333 0.00 0.00 29.85 0.98
773 2331 6.491394 TGCGTTGCTGATTACCAATTAATAC 58.509 36.000 0.00 0.00 29.85 1.89
821 3266 6.253512 TCACGTCATATCTGAATCGACAAAAG 59.746 38.462 0.00 0.00 31.85 2.27
870 3996 4.222124 AGTTTGAGGGGCAATGTAGTAG 57.778 45.455 0.00 0.00 36.15 2.57
906 4073 1.467342 GGTTAAACCCTGACACGATGC 59.533 52.381 0.00 0.00 30.04 3.91
907 4074 2.423577 GTTAAACCCTGACACGATGCT 58.576 47.619 0.00 0.00 0.00 3.79
938 4118 2.691927 CACGGTACCACCTTTCCTTAC 58.308 52.381 13.54 0.00 35.66 2.34
944 4126 3.790089 ACCACCTTTCCTTACTCCTTG 57.210 47.619 0.00 0.00 0.00 3.61
949 4131 2.302157 CCTTTCCTTACTCCTTGACGGT 59.698 50.000 0.00 0.00 0.00 4.83
1089 4271 1.079543 CGGAGAAGCCACTGTCAGG 60.080 63.158 4.53 0.00 35.94 3.86
1140 4322 2.853914 GTCGTGAAACTGCTCGGC 59.146 61.111 0.00 0.00 31.75 5.54
1239 4422 1.843368 TCTACGAGGTGTTCCCGATT 58.157 50.000 0.00 0.00 38.74 3.34
1261 4444 2.780924 ACCCCAAGGCCACCTTCA 60.781 61.111 5.01 0.00 42.67 3.02
1369 4555 3.644399 GACGAGTTCCTGCCCGACC 62.644 68.421 0.00 0.00 0.00 4.79
1491 5336 2.028112 GGAGTGTTGTATCTGCCTGTCA 60.028 50.000 0.00 0.00 0.00 3.58
1492 5337 3.369892 GGAGTGTTGTATCTGCCTGTCAT 60.370 47.826 0.00 0.00 0.00 3.06
1575 5420 3.490759 CTTACGCCGTGGCTGCAG 61.491 66.667 10.11 10.11 39.32 4.41
1644 5489 2.928334 CTTTACAGCCTCATGCATCCT 58.072 47.619 0.00 0.00 44.83 3.24
1660 5505 2.099141 TCCTCCAAAGCGTCAATGAG 57.901 50.000 0.00 0.00 0.00 2.90
1695 5540 1.069227 TCCGATCGATGTGATGCGTAG 60.069 52.381 18.66 0.00 37.47 3.51
1696 5541 1.335051 CCGATCGATGTGATGCGTAGT 60.335 52.381 18.66 0.00 37.47 2.73
1697 5542 2.095919 CCGATCGATGTGATGCGTAGTA 60.096 50.000 18.66 0.00 37.47 1.82
1715 5560 0.899019 TACGACCTACAGGCATGCAA 59.101 50.000 21.36 0.28 39.32 4.08
1718 5563 1.027357 GACCTACAGGCATGCAATGG 58.973 55.000 21.36 15.24 46.86 3.16
1783 5633 3.817709 AAGGACATTGGTTGGTTGTTG 57.182 42.857 0.00 0.00 0.00 3.33
1786 5636 3.517500 AGGACATTGGTTGGTTGTTGTTT 59.482 39.130 0.00 0.00 0.00 2.83
1787 5637 4.019771 AGGACATTGGTTGGTTGTTGTTTT 60.020 37.500 0.00 0.00 0.00 2.43
1788 5638 4.331443 GGACATTGGTTGGTTGTTGTTTTC 59.669 41.667 0.00 0.00 0.00 2.29
1789 5639 5.159273 ACATTGGTTGGTTGTTGTTTTCT 57.841 34.783 0.00 0.00 0.00 2.52
1790 5640 5.175127 ACATTGGTTGGTTGTTGTTTTCTC 58.825 37.500 0.00 0.00 0.00 2.87
1791 5641 3.878160 TGGTTGGTTGTTGTTTTCTCC 57.122 42.857 0.00 0.00 0.00 3.71
1792 5642 2.498078 TGGTTGGTTGTTGTTTTCTCCC 59.502 45.455 0.00 0.00 0.00 4.30
1793 5643 2.480587 GGTTGGTTGTTGTTTTCTCCCG 60.481 50.000 0.00 0.00 0.00 5.14
1794 5644 0.741915 TGGTTGTTGTTTTCTCCCGC 59.258 50.000 0.00 0.00 0.00 6.13
1795 5645 0.031585 GGTTGTTGTTTTCTCCCGCC 59.968 55.000 0.00 0.00 0.00 6.13
1796 5646 1.029681 GTTGTTGTTTTCTCCCGCCT 58.970 50.000 0.00 0.00 0.00 5.52
1797 5647 1.001706 GTTGTTGTTTTCTCCCGCCTC 60.002 52.381 0.00 0.00 0.00 4.70
1798 5648 0.181587 TGTTGTTTTCTCCCGCCTCA 59.818 50.000 0.00 0.00 0.00 3.86
1799 5649 1.202879 TGTTGTTTTCTCCCGCCTCAT 60.203 47.619 0.00 0.00 0.00 2.90
1807 5657 3.527507 TCTCCCGCCTCATTATAGACT 57.472 47.619 0.00 0.00 0.00 3.24
1818 5668 8.636843 CGCCTCATTATAGACTAAAATTCGTAC 58.363 37.037 0.00 0.00 0.00 3.67
1819 5669 9.694137 GCCTCATTATAGACTAAAATTCGTACT 57.306 33.333 0.00 0.00 0.00 2.73
1862 5712 5.639757 TGCTGTTATTGTGAATGCATGTAC 58.360 37.500 0.00 3.06 0.00 2.90
1870 5720 5.220557 TGTGAATGCATGTACGATTTCAG 57.779 39.130 0.00 0.00 0.00 3.02
1929 5788 8.887717 GCTCATAAATCACATCAAGGATATACC 58.112 37.037 0.00 0.00 39.35 2.73
1935 5794 8.803397 AATCACATCAAGGATATACCATCATG 57.197 34.615 0.00 0.00 42.04 3.07
1937 5796 7.976712 TCACATCAAGGATATACCATCATGAA 58.023 34.615 0.00 0.00 42.04 2.57
2007 5963 1.519455 GTCTTCAGGGATGCGTCGG 60.519 63.158 0.00 0.00 0.00 4.79
2042 5998 1.740025 CTGCAGAAATCGAGTTTCCCC 59.260 52.381 8.42 1.44 45.96 4.81
2051 6007 0.179108 CGAGTTTCCCCGATCAGGTC 60.179 60.000 0.00 0.00 38.74 3.85
2060 6016 0.961753 CCGATCAGGTCCGATGATGA 59.038 55.000 0.00 0.00 37.52 2.92
2109 6066 7.654022 TTTTTGTGGTGGAAGATCTAGTTTT 57.346 32.000 0.00 0.00 0.00 2.43
2110 6067 7.654022 TTTTGTGGTGGAAGATCTAGTTTTT 57.346 32.000 0.00 0.00 0.00 1.94
2207 6164 6.080648 CATAATTAAGATGCACACAGCCAT 57.919 37.500 0.00 0.00 44.83 4.40
2231 6188 0.603569 AGTCCTCTCGCACGAACAAT 59.396 50.000 0.00 0.00 0.00 2.71
2358 6325 0.939577 CGCCGTATCCTCCAATCGTG 60.940 60.000 0.00 0.00 0.00 4.35
2375 6342 1.301423 GTGCACACCTCCGTAAACAA 58.699 50.000 13.17 0.00 0.00 2.83
2381 6348 2.696707 ACACCTCCGTAAACAAGTCTCA 59.303 45.455 0.00 0.00 0.00 3.27
2393 6360 1.734465 CAAGTCTCAATTCTCCACGCC 59.266 52.381 0.00 0.00 0.00 5.68
2431 6398 6.239487 CCATAAATGAAGAGTCCCGGTACATA 60.239 42.308 0.00 0.00 0.00 2.29
2461 6428 4.464069 ACCTGCATCAGAGAAGTACTTC 57.536 45.455 25.24 25.24 39.78 3.01
2579 6546 3.253677 CCGTGTAACCAGTTGCCAAATAA 59.746 43.478 0.00 0.00 0.00 1.40
2588 6555 6.710278 ACCAGTTGCCAAATAAATTAGCAAT 58.290 32.000 13.16 4.28 39.64 3.56
2638 6605 5.104776 GCTATCTGGATGACTGGCCATATAA 60.105 44.000 5.51 0.00 32.89 0.98
2640 6607 4.973168 TCTGGATGACTGGCCATATAAAC 58.027 43.478 5.51 0.00 32.89 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.428219 GAGTACGCGCAGACTGCTA 59.572 57.895 24.36 8.25 42.25 3.49
361 362 1.303806 TCCACTCCCACATCGACGA 60.304 57.895 0.00 0.00 0.00 4.20
427 429 2.754002 GTCTAGTGTCTTCTTAGGGCGT 59.246 50.000 0.00 0.00 0.00 5.68
544 546 1.059584 TTCTGAGGCCAACTCCACCA 61.060 55.000 5.01 0.00 46.01 4.17
608 610 2.033049 CGATACAGTTGGGTACGGAGAG 59.967 54.545 0.00 0.00 0.00 3.20
613 615 2.660189 AACCGATACAGTTGGGTACG 57.340 50.000 0.00 0.00 35.44 3.67
614 616 5.052481 GGAATAACCGATACAGTTGGGTAC 58.948 45.833 0.00 0.00 36.33 3.34
615 617 5.280654 GGAATAACCGATACAGTTGGGTA 57.719 43.478 0.00 0.00 37.96 3.69
616 618 4.146745 GGAATAACCGATACAGTTGGGT 57.853 45.455 0.00 0.00 35.44 4.51
631 633 0.527113 TCGACGTCCAAGCGGAATAA 59.473 50.000 10.58 0.00 45.20 1.40
633 635 1.445582 GTCGACGTCCAAGCGGAAT 60.446 57.895 10.58 0.00 45.20 3.01
634 636 2.049802 GTCGACGTCCAAGCGGAA 60.050 61.111 10.58 0.00 45.20 4.30
635 637 4.394078 CGTCGACGTCCAAGCGGA 62.394 66.667 29.08 0.00 39.79 5.54
637 639 3.164011 GTCGTCGACGTCCAAGCG 61.164 66.667 34.40 9.66 40.80 4.68
638 640 1.796749 GAGTCGTCGACGTCCAAGC 60.797 63.158 34.40 18.80 40.80 4.01
703 2214 2.158449 CCGACTCGTATACGGGACATAC 59.842 54.545 30.99 14.39 43.86 2.39
704 2215 2.416747 CCGACTCGTATACGGGACATA 58.583 52.381 30.99 7.03 43.86 2.29
705 2216 1.233019 CCGACTCGTATACGGGACAT 58.767 55.000 30.99 9.44 43.86 3.06
706 2217 2.694065 CCGACTCGTATACGGGACA 58.306 57.895 30.99 8.17 43.86 4.02
735 2264 2.426752 CGCAACGGCTTGGAAACG 60.427 61.111 0.00 0.00 38.10 3.60
768 2326 9.325198 CAAGGCAAACTCTATGTACATGTATTA 57.675 33.333 18.81 2.02 0.00 0.98
769 2327 7.829211 ACAAGGCAAACTCTATGTACATGTATT 59.171 33.333 18.81 4.83 0.00 1.89
770 2328 7.338710 ACAAGGCAAACTCTATGTACATGTAT 58.661 34.615 18.81 0.00 0.00 2.29
772 2330 5.560724 ACAAGGCAAACTCTATGTACATGT 58.439 37.500 18.81 2.69 0.00 3.21
773 2331 6.149308 TGAACAAGGCAAACTCTATGTACATG 59.851 38.462 18.81 8.56 0.00 3.21
779 2501 3.498397 ACGTGAACAAGGCAAACTCTATG 59.502 43.478 0.00 0.00 0.00 2.23
901 4068 2.441462 CGTGCGTATATAGGAGCATCG 58.559 52.381 6.62 9.68 41.88 3.84
904 4071 1.612676 ACCGTGCGTATATAGGAGCA 58.387 50.000 6.62 5.18 37.26 4.26
906 4073 3.076621 TGGTACCGTGCGTATATAGGAG 58.923 50.000 7.57 0.00 0.00 3.69
907 4074 2.813754 GTGGTACCGTGCGTATATAGGA 59.186 50.000 7.57 0.00 0.00 2.94
938 4118 1.739562 GCTGAGCACCGTCAAGGAG 60.740 63.158 0.00 0.00 45.00 3.69
944 4126 0.100682 TAGATTCGCTGAGCACCGTC 59.899 55.000 4.88 0.00 0.00 4.79
949 4131 2.609427 ATTGCTAGATTCGCTGAGCA 57.391 45.000 4.88 0.00 42.98 4.26
1140 4322 1.868251 GTAGCTCGCGACCAACTCG 60.868 63.158 3.71 0.00 45.97 4.18
1381 4567 0.522915 CCGAGGCTACGAAAGACGAC 60.523 60.000 7.73 0.00 45.77 4.34
1387 4573 1.180456 TGGTCACCGAGGCTACGAAA 61.180 55.000 7.73 0.00 35.09 3.46
1414 4600 4.788690 AGAGATATGTCAATGTCGTAGCG 58.211 43.478 2.30 0.00 0.00 4.26
1491 5336 3.041946 GTCTTGATCCTCCACCAGGTAT 58.958 50.000 0.00 0.00 43.95 2.73
1492 5337 2.467880 GTCTTGATCCTCCACCAGGTA 58.532 52.381 0.00 0.00 43.95 3.08
1644 5489 3.394674 TGTACTCATTGACGCTTTGGA 57.605 42.857 0.00 0.00 0.00 3.53
1660 5505 3.797256 CGATCGGATGAGAAACCTTGTAC 59.203 47.826 7.38 0.00 0.00 2.90
1695 5540 0.174845 TGCATGCCTGTAGGTCGTAC 59.825 55.000 16.68 0.00 37.57 3.67
1696 5541 0.899019 TTGCATGCCTGTAGGTCGTA 59.101 50.000 16.68 0.00 37.57 3.43
1697 5542 0.253044 ATTGCATGCCTGTAGGTCGT 59.747 50.000 16.68 0.00 37.57 4.34
1735 5585 9.582431 CCGACTAAGATCTAACTGATTTAACAA 57.418 33.333 0.00 0.00 35.14 2.83
1736 5586 8.963725 TCCGACTAAGATCTAACTGATTTAACA 58.036 33.333 0.00 0.00 35.14 2.41
1737 5587 9.798994 TTCCGACTAAGATCTAACTGATTTAAC 57.201 33.333 0.00 0.00 35.14 2.01
1751 5601 4.225267 ACCAATGTCCTTTCCGACTAAGAT 59.775 41.667 0.00 0.00 33.70 2.40
1756 5606 2.504367 CAACCAATGTCCTTTCCGACT 58.496 47.619 0.00 0.00 33.70 4.18
1759 5609 1.616159 ACCAACCAATGTCCTTTCCG 58.384 50.000 0.00 0.00 0.00 4.30
1783 5633 4.750598 GTCTATAATGAGGCGGGAGAAAAC 59.249 45.833 0.00 0.00 0.00 2.43
1786 5636 3.845860 AGTCTATAATGAGGCGGGAGAA 58.154 45.455 0.00 0.00 0.00 2.87
1787 5637 3.527507 AGTCTATAATGAGGCGGGAGA 57.472 47.619 0.00 0.00 0.00 3.71
1788 5638 5.723672 TTTAGTCTATAATGAGGCGGGAG 57.276 43.478 0.00 0.00 0.00 4.30
1789 5639 6.681729 ATTTTAGTCTATAATGAGGCGGGA 57.318 37.500 0.00 0.00 0.00 5.14
1790 5640 6.090898 CGAATTTTAGTCTATAATGAGGCGGG 59.909 42.308 0.00 0.00 0.00 6.13
1791 5641 6.645415 ACGAATTTTAGTCTATAATGAGGCGG 59.355 38.462 0.00 0.00 0.00 6.13
1792 5642 7.639162 ACGAATTTTAGTCTATAATGAGGCG 57.361 36.000 0.00 0.00 0.00 5.52
1793 5643 9.694137 AGTACGAATTTTAGTCTATAATGAGGC 57.306 33.333 0.00 0.00 0.00 4.70
1826 5676 9.665719 TCACAATAACAGCATTTATACTCTCAA 57.334 29.630 0.00 0.00 0.00 3.02
1827 5677 9.665719 TTCACAATAACAGCATTTATACTCTCA 57.334 29.630 0.00 0.00 0.00 3.27
1833 5683 9.465985 CATGCATTCACAATAACAGCATTTATA 57.534 29.630 0.00 0.00 39.00 0.98
1837 5687 5.726397 ACATGCATTCACAATAACAGCATT 58.274 33.333 0.00 0.00 39.00 3.56
1848 5698 4.094739 CCTGAAATCGTACATGCATTCACA 59.905 41.667 0.00 0.00 0.00 3.58
1849 5699 4.332543 TCCTGAAATCGTACATGCATTCAC 59.667 41.667 0.00 0.00 0.00 3.18
1903 5757 8.887717 GGTATATCCTTGATGTGATTTATGAGC 58.112 37.037 0.00 0.00 0.00 4.26
1929 5788 7.448420 AGGAGTTCATAGGTGTATTCATGATG 58.552 38.462 0.00 0.00 0.00 3.07
1931 5790 7.255486 CGTAGGAGTTCATAGGTGTATTCATGA 60.255 40.741 0.00 0.00 0.00 3.07
1935 5794 6.388435 ACGTAGGAGTTCATAGGTGTATTC 57.612 41.667 0.00 0.00 31.33 1.75
1937 5796 7.886629 TTTACGTAGGAGTTCATAGGTGTAT 57.113 36.000 8.80 0.00 33.97 2.29
2007 5963 3.281240 CAGGTTGACATGCAGGCC 58.719 61.111 0.00 0.00 0.00 5.19
2042 5998 1.664302 CGTCATCATCGGACCTGATCG 60.664 57.143 0.00 0.00 31.00 3.69
2051 6007 1.143838 TCAAGGGCGTCATCATCGG 59.856 57.895 0.00 0.00 0.00 4.18
2060 6016 2.665185 GCAAGTCGTCAAGGGCGT 60.665 61.111 0.00 0.00 0.00 5.68
2173 6130 5.311265 CATCTTAATTATGCAGAGGCCAGA 58.689 41.667 5.01 0.00 40.13 3.86
2358 6325 1.529865 GACTTGTTTACGGAGGTGTGC 59.470 52.381 0.00 0.00 0.00 4.57
2375 6342 1.270907 AGGCGTGGAGAATTGAGACT 58.729 50.000 0.00 0.00 0.00 3.24
2393 6360 5.630415 TCATTTATGGTCCCCTCTACAAG 57.370 43.478 0.00 0.00 0.00 3.16
2431 6398 6.326064 ACTTCTCTGATGCAGGTTATCTACAT 59.674 38.462 0.00 0.00 32.37 2.29
2477 6444 4.096382 CGCTTTGGCTATGTAGAAATGGTT 59.904 41.667 0.00 0.00 36.09 3.67
2479 6446 3.876914 TCGCTTTGGCTATGTAGAAATGG 59.123 43.478 0.00 0.00 36.09 3.16
2579 6546 8.934697 TGTATCCTCCTTGTAGTATTGCTAATT 58.065 33.333 0.00 0.00 0.00 1.40
2588 6555 4.616553 TGGCTTGTATCCTCCTTGTAGTA 58.383 43.478 0.00 0.00 0.00 1.82
2630 6597 4.298332 CAAATTGGCTCGGTTTATATGGC 58.702 43.478 0.00 0.00 0.00 4.40
2638 6605 1.338011 CCAATGCAAATTGGCTCGGTT 60.338 47.619 6.34 0.00 43.81 4.44
2640 6607 3.053662 CCAATGCAAATTGGCTCGG 57.946 52.632 6.34 0.00 43.81 4.63


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

AutoCloner maintained by Alex Coulton.