Multiple sequence alignment - TraesCS2D01G557500

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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 TraesCS2D01G557500 chr2D 100.000 4015 0 0 1 4015 630423402 630427416 0.000000e+00 7415
1 TraesCS2D01G557500 chr2A 91.399 3209 200 41 1 3178 760597020 760600183 0.000000e+00 4327
2 TraesCS2D01G557500 chr2A 80.437 823 98 41 3210 4002 760600546 760601335 1.620000e-158 569
3 TraesCS2D01G557500 chr2B 89.762 3067 204 53 264 3281 773168089 773171094 0.000000e+00 3823
4 TraesCS2D01G557500 chr2B 87.578 161 17 3 1 159 773167916 773168075 2.460000e-42 183
5 TraesCS2D01G557500 chr5B 94.134 358 17 4 1801 2157 473774421 473774775 3.530000e-150 542
6 TraesCS2D01G557500 chr5B 78.462 195 42 0 1297 1491 363669645 363669451 1.170000e-25 128
7 TraesCS2D01G557500 chr6B 78.341 217 45 2 1296 1511 151372668 151372883 5.410000e-29 139
8 TraesCS2D01G557500 chr6A 77.315 216 49 0 1296 1511 94227128 94227343 1.170000e-25 128
9 TraesCS2D01G557500 chr5D 77.949 195 43 0 1297 1491 315485372 315485178 5.450000e-24 122
10 TraesCS2D01G557500 chr6D 77.027 222 43 7 1296 1513 402353142 402352925 1.960000e-23 121
11 TraesCS2D01G557500 chr7B 77.835 194 35 7 1294 1486 409712036 409711850 3.280000e-21 113
12 TraesCS2D01G557500 chr7D 77.320 194 36 7 1294 1486 400171045 400170859 1.530000e-19 108


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 TraesCS2D01G557500 chr2D 630423402 630427416 4014 False 7415 7415 100.000 1 4015 1 chr2D.!!$F1 4014
1 TraesCS2D01G557500 chr2A 760597020 760601335 4315 False 2448 4327 85.918 1 4002 2 chr2A.!!$F1 4001
2 TraesCS2D01G557500 chr2B 773167916 773171094 3178 False 2003 3823 88.670 1 3281 2 chr2B.!!$F1 3280

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
978 1024 0.034960 TGCCCGCTTAATTACCTGCA 60.035 50.0 0.00 0.0 0.00 4.41 F
1575 1631 0.245539 CCTAACTCGGCGTCTTGGAA 59.754 55.0 6.85 0.0 0.00 3.53 F
1802 1858 0.610174 AGCAGATCTTCACCTTCGCA 59.390 50.0 0.00 0.0 0.00 5.10 F
2903 2959 0.815734 ACGACAAGGAGATGTACGGG 59.184 55.0 0.00 0.0 32.57 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 1891 0.179045 AGAACTTCTTGGCGCACTGT 60.179 50.0 10.83 0.0 0.00 3.55 R
2760 2816 0.389296 TAGTGATCCACGCCGTTGTG 60.389 55.0 0.00 0.0 39.64 3.33 R
2912 2968 0.600255 CGTCAAGTCTGGTGACCCAC 60.600 60.0 0.00 0.0 43.91 4.61 R
3949 4399 0.726827 TGCCTCGATTTCATTGCGTC 59.273 50.0 0.00 0.0 0.00 5.19 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
51 52 8.999431 TCTTGTTTGTACAACTATCATCTTTCC 58.001 33.333 8.07 0.00 39.29 3.13
86 91 7.406553 TCAAAGATATTAAGGAAAACGATGCG 58.593 34.615 0.00 0.00 0.00 4.73
105 110 5.530519 TGCGAGAATGTCAACTTTGATAC 57.469 39.130 0.00 0.00 39.73 2.24
172 177 8.497554 TGCGACATAATTTAAAGTCTTACGTTT 58.502 29.630 0.00 0.00 0.00 3.60
234 240 7.466746 TTTCATTGTATTTTGAGGGAAGAGG 57.533 36.000 0.00 0.00 0.00 3.69
245 251 1.134438 GGGAAGAGGGTGTTGGAGGT 61.134 60.000 0.00 0.00 0.00 3.85
250 256 3.979497 GGGTGTTGGAGGTGGGGG 61.979 72.222 0.00 0.00 0.00 5.40
251 257 4.678743 GGTGTTGGAGGTGGGGGC 62.679 72.222 0.00 0.00 0.00 5.80
277 283 7.159372 GGAGGCGTCCTAAATCTTATAATCAA 58.841 38.462 18.26 0.00 40.17 2.57
393 401 6.872547 CACTATACCAACCATCATGATGAGAG 59.127 42.308 32.71 20.82 41.20 3.20
400 408 5.563876 ACCATCATGATGAGAGTTAGCAT 57.436 39.130 32.71 5.76 41.20 3.79
436 444 6.603940 AATTTGTGGCTTAAATGCTTCCTA 57.396 33.333 1.38 0.00 0.00 2.94
438 446 6.603940 TTTGTGGCTTAAATGCTTCCTATT 57.396 33.333 0.00 0.00 0.00 1.73
440 448 5.016173 TGTGGCTTAAATGCTTCCTATTGT 58.984 37.500 0.00 0.00 0.00 2.71
445 453 6.546034 GGCTTAAATGCTTCCTATTGTAAGGA 59.454 38.462 0.00 0.00 44.12 3.36
446 454 7.418408 GCTTAAATGCTTCCTATTGTAAGGAC 58.582 38.462 0.00 0.00 45.49 3.85
476 488 1.029947 GTTGACCAACCATAGGCCGG 61.030 60.000 0.00 0.00 35.36 6.13
478 490 4.123545 ACCAACCATAGGCCGGCC 62.124 66.667 39.29 39.29 0.00 6.13
482 494 1.077625 AACCATAGGCCGGCCAAAA 59.922 52.632 45.13 30.47 38.92 2.44
513 525 7.652909 CCAAAAGAAAGCATTATGTGAGTCAAA 59.347 33.333 0.00 0.00 0.00 2.69
535 548 8.339714 TCAAACTATTTTAGTCCACAAAACTCG 58.660 33.333 0.00 0.00 38.26 4.18
563 577 2.354109 TCACACATCTTCAGCGACTC 57.646 50.000 0.00 0.00 0.00 3.36
582 596 2.427453 CTCTGTGTACGGGCAGAACTAT 59.573 50.000 13.19 0.00 40.68 2.12
584 598 3.379372 TCTGTGTACGGGCAGAACTATAC 59.621 47.826 10.78 0.00 38.61 1.47
588 602 2.910688 ACGGGCAGAACTATACATGG 57.089 50.000 0.00 0.00 0.00 3.66
618 632 7.268199 TGGCAGCATCTGAAGATTTAATTAG 57.732 36.000 0.00 0.00 32.44 1.73
636 650 9.917887 TTTAATTAGTAATTAATGTTCCCCGGA 57.082 29.630 22.66 6.85 41.51 5.14
637 651 9.917887 TTAATTAGTAATTAATGTTCCCCGGAA 57.082 29.630 19.63 0.00 38.16 4.30
638 652 8.826293 AATTAGTAATTAATGTTCCCCGGAAA 57.174 30.769 0.73 0.00 31.81 3.13
639 653 8.826293 ATTAGTAATTAATGTTCCCCGGAAAA 57.174 30.769 0.73 0.00 35.75 2.29
640 654 8.647256 TTAGTAATTAATGTTCCCCGGAAAAA 57.353 30.769 0.73 0.00 35.75 1.94
691 705 7.661127 TTTCGATTATCGGAACAAGAAGAAA 57.339 32.000 14.86 1.22 40.88 2.52
692 706 7.843490 TTCGATTATCGGAACAAGAAGAAAT 57.157 32.000 14.86 0.00 40.88 2.17
695 709 9.031360 TCGATTATCGGAACAAGAAGAAATAAG 57.969 33.333 14.86 0.00 40.88 1.73
696 710 8.818057 CGATTATCGGAACAAGAAGAAATAAGT 58.182 33.333 6.73 0.00 36.00 2.24
704 718 8.175716 GGAACAAGAAGAAATAAGTAATGGTCG 58.824 37.037 0.00 0.00 0.00 4.79
705 719 8.842358 AACAAGAAGAAATAAGTAATGGTCGA 57.158 30.769 0.00 0.00 0.00 4.20
706 720 8.252964 ACAAGAAGAAATAAGTAATGGTCGAC 57.747 34.615 7.13 7.13 0.00 4.20
707 721 7.063074 ACAAGAAGAAATAAGTAATGGTCGACG 59.937 37.037 9.92 0.00 0.00 5.12
708 722 6.040878 AGAAGAAATAAGTAATGGTCGACGG 58.959 40.000 9.92 0.00 0.00 4.79
710 724 5.107133 AGAAATAAGTAATGGTCGACGGTG 58.893 41.667 9.92 0.00 0.00 4.94
711 725 4.460948 AATAAGTAATGGTCGACGGTGT 57.539 40.909 9.92 0.00 0.00 4.16
712 726 2.358939 AAGTAATGGTCGACGGTGTC 57.641 50.000 9.92 0.13 0.00 3.67
756 801 4.933064 GGCGAGCCCACGATCGAG 62.933 72.222 24.34 14.64 41.40 4.04
945 991 3.626924 ACTCCCAGCACCACGACC 61.627 66.667 0.00 0.00 0.00 4.79
946 992 3.625897 CTCCCAGCACCACGACCA 61.626 66.667 0.00 0.00 0.00 4.02
947 993 3.883744 CTCCCAGCACCACGACCAC 62.884 68.421 0.00 0.00 0.00 4.16
969 1015 3.183259 GCGACATTGCCCGCTTAA 58.817 55.556 14.29 0.00 46.96 1.85
970 1016 1.727467 GCGACATTGCCCGCTTAAT 59.273 52.632 14.29 0.00 46.96 1.40
974 1020 2.286772 CGACATTGCCCGCTTAATTACC 60.287 50.000 0.00 0.00 0.00 2.85
975 1021 2.949644 GACATTGCCCGCTTAATTACCT 59.050 45.455 0.00 0.00 0.00 3.08
976 1022 2.687935 ACATTGCCCGCTTAATTACCTG 59.312 45.455 0.00 0.00 0.00 4.00
977 1023 1.099689 TTGCCCGCTTAATTACCTGC 58.900 50.000 0.00 0.00 0.00 4.85
978 1024 0.034960 TGCCCGCTTAATTACCTGCA 60.035 50.000 0.00 0.00 0.00 4.41
979 1025 0.663153 GCCCGCTTAATTACCTGCAG 59.337 55.000 6.78 6.78 0.00 4.41
980 1026 1.745827 GCCCGCTTAATTACCTGCAGA 60.746 52.381 17.39 0.00 0.00 4.26
981 1027 2.213499 CCCGCTTAATTACCTGCAGAG 58.787 52.381 17.39 8.04 0.00 3.35
982 1028 2.158957 CCCGCTTAATTACCTGCAGAGA 60.159 50.000 17.39 0.00 0.00 3.10
986 1032 4.870426 CGCTTAATTACCTGCAGAGAAGAA 59.130 41.667 17.39 6.43 0.00 2.52
990 1036 7.119846 GCTTAATTACCTGCAGAGAAGAAGAAA 59.880 37.037 17.39 0.00 0.00 2.52
994 1040 3.007831 ACCTGCAGAGAAGAAGAAAGAGG 59.992 47.826 17.39 0.00 0.00 3.69
997 1043 3.181451 TGCAGAGAAGAAGAAAGAGGCAA 60.181 43.478 0.00 0.00 0.00 4.52
1012 1058 3.576356 CAACTATGGCGCGGCTGG 61.576 66.667 33.23 23.09 0.00 4.85
1279 1334 2.945008 TCCGCATTTGCTTATGGAGAAG 59.055 45.455 0.51 0.00 39.32 2.85
1513 1568 1.689582 CCCTCTGGGTCCAGGTACC 60.690 68.421 16.15 2.73 43.75 3.34
1528 1584 1.156803 TACCCAACACTCCCGTCCT 59.843 57.895 0.00 0.00 0.00 3.85
1531 1587 0.903454 CCCAACACTCCCGTCCTACT 60.903 60.000 0.00 0.00 0.00 2.57
1533 1589 1.346722 CCAACACTCCCGTCCTACTTT 59.653 52.381 0.00 0.00 0.00 2.66
1573 1629 1.810030 GCCTAACTCGGCGTCTTGG 60.810 63.158 6.85 5.60 40.79 3.61
1574 1630 1.888018 CCTAACTCGGCGTCTTGGA 59.112 57.895 6.85 0.00 0.00 3.53
1575 1631 0.245539 CCTAACTCGGCGTCTTGGAA 59.754 55.000 6.85 0.00 0.00 3.53
1577 1633 0.675083 TAACTCGGCGTCTTGGAACA 59.325 50.000 6.85 0.00 0.00 3.18
1802 1858 0.610174 AGCAGATCTTCACCTTCGCA 59.390 50.000 0.00 0.00 0.00 5.10
1814 1870 2.357034 TTCGCAGACACCTTCCGC 60.357 61.111 0.00 0.00 34.32 5.54
1835 1891 1.522355 CCGCTACGACGACTCCCTA 60.522 63.158 0.00 0.00 34.06 3.53
1865 1921 1.141234 GAAGTTCTACCCCTCCGCG 59.859 63.158 0.00 0.00 0.00 6.46
2054 2110 2.604686 TCCAAGGTGCTCCTCGCT 60.605 61.111 7.99 0.00 44.35 4.93
2276 2332 2.372690 CGAGTCCGGCGACAAGTTG 61.373 63.158 9.30 0.00 41.87 3.16
2336 2392 4.373116 TTCGCCAGGTCGCAGGTC 62.373 66.667 0.00 0.00 0.00 3.85
2450 2506 4.189188 CCCTCCGTCTACGCCGTG 62.189 72.222 0.00 0.00 38.18 4.94
2744 2800 4.059459 GAGTTCGTGCACGCGGTG 62.059 66.667 33.63 8.46 39.60 4.94
2774 2830 2.742372 GAGCACAACGGCGTGGAT 60.742 61.111 23.33 9.43 37.37 3.41
2840 2896 2.432628 ACGTACCTGAAGCTGCGC 60.433 61.111 0.00 0.00 0.00 6.09
2876 2932 2.331805 CCCATCTACGGCGTCTCG 59.668 66.667 19.21 6.70 0.00 4.04
2903 2959 0.815734 ACGACAAGGAGATGTACGGG 59.184 55.000 0.00 0.00 32.57 5.28
2912 2968 1.041447 AGATGTACGGGTTCCCCTCG 61.041 60.000 1.93 0.00 42.67 4.63
3127 3211 1.766496 TGGTATCCGAGGTCCCAATTC 59.234 52.381 0.00 0.00 0.00 2.17
3225 3640 5.722021 AAGTTTAACATTTTGAGCCGGAT 57.278 34.783 5.05 0.00 0.00 4.18
3247 3662 3.703556 TCTTGATGCTTCGAGAAGGAGAT 59.296 43.478 15.44 0.00 41.97 2.75
3297 3725 3.036091 CGGGACCTCCTAATCCACTTTA 58.964 50.000 0.00 0.00 36.65 1.85
3299 3727 4.102681 CGGGACCTCCTAATCCACTTTATT 59.897 45.833 0.00 0.00 36.65 1.40
3345 3774 1.410882 GTCAGAGGATACACCCTGCTC 59.589 57.143 0.00 0.00 40.05 4.26
3349 3778 2.108425 AGAGGATACACCCTGCTCGATA 59.892 50.000 0.00 0.00 40.05 2.92
3355 3784 2.348998 CCCTGCTCGATATGGGCC 59.651 66.667 0.00 0.00 32.49 5.80
3356 3785 2.348998 CCTGCTCGATATGGGCCC 59.651 66.667 17.59 17.59 0.00 5.80
3376 3805 2.822255 CCATTACGGGGCGTGTGG 60.822 66.667 0.00 0.00 41.39 4.17
3391 3820 2.225963 CGTGTGGGCCATTTTTAACGTA 59.774 45.455 10.70 0.00 0.00 3.57
3412 3841 8.259049 ACGTATCTTTCGGTTTTTCATTATCA 57.741 30.769 0.00 0.00 0.00 2.15
3413 3842 8.388103 ACGTATCTTTCGGTTTTTCATTATCAG 58.612 33.333 0.00 0.00 0.00 2.90
3605 4043 5.224821 TGCAATGATCATGGGTTTCAAAA 57.775 34.783 9.46 0.00 0.00 2.44
3772 4222 9.965748 AAAATGTTCGTGAATTTAAAAACTGTG 57.034 25.926 0.00 0.00 0.00 3.66
3773 4223 8.696410 AATGTTCGTGAATTTAAAAACTGTGT 57.304 26.923 0.00 0.00 0.00 3.72
3775 4225 7.085116 TGTTCGTGAATTTAAAAACTGTGTGT 58.915 30.769 0.00 0.00 0.00 3.72
3776 4226 7.061210 TGTTCGTGAATTTAAAAACTGTGTGTG 59.939 33.333 0.00 0.00 0.00 3.82
3778 4228 7.306213 TCGTGAATTTAAAAACTGTGTGTGAA 58.694 30.769 0.00 0.00 0.00 3.18
3780 4230 8.591312 CGTGAATTTAAAAACTGTGTGTGAATT 58.409 29.630 0.00 0.00 0.00 2.17
3836 4286 7.137426 GCCAAATTCAAACAATGTTTGCATAA 58.863 30.769 28.35 19.77 34.39 1.90
3848 4298 7.644551 ACAATGTTTGCATAATGTTTGCTTTTG 59.355 29.630 0.00 0.00 40.77 2.44
3857 4307 3.409026 TGTTTGCTTTTGTGGTTTGGT 57.591 38.095 0.00 0.00 0.00 3.67
3859 4309 3.748568 TGTTTGCTTTTGTGGTTTGGTTC 59.251 39.130 0.00 0.00 0.00 3.62
3861 4311 3.685139 TGCTTTTGTGGTTTGGTTCAA 57.315 38.095 0.00 0.00 0.00 2.69
3894 4344 8.723942 ATTACATTCTGGAATACAACTCACTC 57.276 34.615 0.00 0.00 26.81 3.51
3952 4402 4.552166 TTTTTGCTTCAAGAAGGAGACG 57.448 40.909 11.44 0.00 39.87 4.18
3974 4424 4.232221 GCAATGAAATCGAGGCAATATGG 58.768 43.478 0.00 0.00 0.00 2.74
3977 4427 6.275335 CAATGAAATCGAGGCAATATGGTTT 58.725 36.000 0.00 0.00 0.00 3.27
4002 4452 3.214328 GGAGAAAGTTTGCAAGTGAGGA 58.786 45.455 0.00 0.00 0.00 3.71
4003 4453 3.251972 GGAGAAAGTTTGCAAGTGAGGAG 59.748 47.826 0.00 0.00 0.00 3.69
4004 4454 3.217626 AGAAAGTTTGCAAGTGAGGAGG 58.782 45.455 0.00 0.00 0.00 4.30
4005 4455 2.736670 AAGTTTGCAAGTGAGGAGGT 57.263 45.000 0.00 0.00 0.00 3.85
4006 4456 2.262423 AGTTTGCAAGTGAGGAGGTC 57.738 50.000 0.00 0.00 0.00 3.85
4007 4457 1.490490 AGTTTGCAAGTGAGGAGGTCA 59.510 47.619 0.00 0.00 0.00 4.02
4008 4458 2.092429 AGTTTGCAAGTGAGGAGGTCAA 60.092 45.455 0.00 0.00 36.74 3.18
4009 4459 1.967319 TTGCAAGTGAGGAGGTCAAC 58.033 50.000 0.00 0.00 36.74 3.18
4010 4460 0.836606 TGCAAGTGAGGAGGTCAACA 59.163 50.000 0.00 0.00 36.74 3.33
4011 4461 1.202687 TGCAAGTGAGGAGGTCAACAG 60.203 52.381 0.00 0.00 36.74 3.16
4012 4462 1.517242 CAAGTGAGGAGGTCAACAGC 58.483 55.000 0.00 0.00 36.74 4.40
4013 4463 0.034059 AAGTGAGGAGGTCAACAGCG 59.966 55.000 0.00 0.00 36.74 5.18
4014 4464 0.827925 AGTGAGGAGGTCAACAGCGA 60.828 55.000 0.00 0.00 36.74 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 8.684386 TGGAAAGATGATAGTTGTACAAACAA 57.316 30.769 10.51 0.00 43.32 2.83
62 63 7.406553 TCGCATCGTTTTCCTTAATATCTTTG 58.593 34.615 0.00 0.00 0.00 2.77
70 74 4.693566 ACATTCTCGCATCGTTTTCCTTAA 59.306 37.500 0.00 0.00 0.00 1.85
74 78 2.415168 TGACATTCTCGCATCGTTTTCC 59.585 45.455 0.00 0.00 0.00 3.13
75 79 3.722555 TGACATTCTCGCATCGTTTTC 57.277 42.857 0.00 0.00 0.00 2.29
78 82 2.688507 AGTTGACATTCTCGCATCGTT 58.311 42.857 0.00 0.00 0.00 3.85
114 119 1.658994 AGGCGACGACTTGTGAAAAA 58.341 45.000 0.00 0.00 0.00 1.94
177 183 9.674068 AATGGTGTACCTTTTGTTTATGTTTTT 57.326 25.926 2.32 0.00 36.82 1.94
205 211 9.880157 CTTCCCTCAAAATACAATGAAATTCAT 57.120 29.630 2.07 2.07 39.09 2.57
230 236 1.847968 CCCACCTCCAACACCCTCT 60.848 63.158 0.00 0.00 0.00 3.69
234 240 4.678743 GCCCCCACCTCCAACACC 62.679 72.222 0.00 0.00 0.00 4.16
250 256 0.179081 AAGATTTAGGACGCCTCCGC 60.179 55.000 1.46 0.00 42.22 5.54
251 257 3.662247 ATAAGATTTAGGACGCCTCCG 57.338 47.619 1.46 0.00 42.22 4.63
254 260 7.736893 AGTTGATTATAAGATTTAGGACGCCT 58.263 34.615 3.87 3.87 37.71 5.52
295 302 8.126700 CGTGATGATCAATCTTCAAATCATTCA 58.873 33.333 0.00 0.00 40.97 2.57
317 324 2.835764 AGAATTAAGGTGGTAGGCGTGA 59.164 45.455 0.00 0.00 0.00 4.35
374 382 4.581309 AACTCTCATCATGATGGTTGGT 57.419 40.909 30.54 21.23 39.24 3.67
393 401 9.458374 ACAAATTAACTTGTGTGTTATGCTAAC 57.542 29.630 0.71 0.00 38.12 2.34
429 437 3.617263 CGTGTGTCCTTACAATAGGAAGC 59.383 47.826 0.00 0.00 45.62 3.86
436 444 5.972107 ACTAGTACGTGTGTCCTTACAAT 57.028 39.130 0.00 0.00 37.36 2.71
438 446 4.821260 TCAACTAGTACGTGTGTCCTTACA 59.179 41.667 0.00 0.00 0.00 2.41
440 448 4.216257 GGTCAACTAGTACGTGTGTCCTTA 59.784 45.833 0.00 0.00 0.00 2.69
445 453 3.491447 GGTTGGTCAACTAGTACGTGTGT 60.491 47.826 12.75 0.00 40.94 3.72
446 454 3.054878 GGTTGGTCAACTAGTACGTGTG 58.945 50.000 12.75 0.00 40.94 3.82
482 494 6.991531 TCACATAATGCTTTCTTTTGGCTTTT 59.008 30.769 0.00 0.00 0.00 2.27
513 525 5.107220 CGCGAGTTTTGTGGACTAAAATAGT 60.107 40.000 0.00 0.00 42.86 2.12
520 532 1.774639 GTCGCGAGTTTTGTGGACTA 58.225 50.000 10.24 0.00 0.00 2.59
563 577 2.961526 ATAGTTCTGCCCGTACACAG 57.038 50.000 0.00 0.00 35.15 3.66
582 596 0.911053 TGCTGCCATCTGACCATGTA 59.089 50.000 0.00 0.00 0.00 2.29
584 598 0.952280 GATGCTGCCATCTGACCATG 59.048 55.000 0.00 0.00 43.62 3.66
660 674 9.320352 TCTTGTTCCGATAATCGAAAATAATCA 57.680 29.630 0.00 0.00 43.74 2.57
663 677 9.373603 TCTTCTTGTTCCGATAATCGAAAATAA 57.626 29.630 0.00 0.00 43.74 1.40
664 678 8.936070 TCTTCTTGTTCCGATAATCGAAAATA 57.064 30.769 0.00 0.00 43.74 1.40
665 679 7.843490 TCTTCTTGTTCCGATAATCGAAAAT 57.157 32.000 0.00 0.00 43.74 1.82
666 680 7.661127 TTCTTCTTGTTCCGATAATCGAAAA 57.339 32.000 0.00 0.00 43.74 2.29
667 681 7.661127 TTTCTTCTTGTTCCGATAATCGAAA 57.339 32.000 0.00 0.00 43.74 3.46
668 682 7.843490 ATTTCTTCTTGTTCCGATAATCGAA 57.157 32.000 0.00 0.00 43.74 3.71
669 683 8.936070 TTATTTCTTCTTGTTCCGATAATCGA 57.064 30.769 0.00 0.00 43.74 3.59
670 684 8.818057 ACTTATTTCTTCTTGTTCCGATAATCG 58.182 33.333 0.00 0.00 40.07 3.34
678 692 8.175716 CGACCATTACTTATTTCTTCTTGTTCC 58.824 37.037 0.00 0.00 0.00 3.62
679 693 8.932791 TCGACCATTACTTATTTCTTCTTGTTC 58.067 33.333 0.00 0.00 0.00 3.18
691 705 4.037858 GACACCGTCGACCATTACTTAT 57.962 45.455 10.58 0.00 0.00 1.73
692 706 3.492421 GACACCGTCGACCATTACTTA 57.508 47.619 10.58 0.00 0.00 2.24
704 718 3.924686 ACATTAGACATTTCGACACCGTC 59.075 43.478 0.00 0.00 37.05 4.79
705 719 3.921677 ACATTAGACATTTCGACACCGT 58.078 40.909 0.00 0.00 37.05 4.83
706 720 3.001070 CGACATTAGACATTTCGACACCG 60.001 47.826 0.00 0.00 37.07 4.94
707 721 4.171005 TCGACATTAGACATTTCGACACC 58.829 43.478 0.00 0.00 33.95 4.16
708 722 5.756950 TTCGACATTAGACATTTCGACAC 57.243 39.130 0.00 0.00 38.37 3.67
710 724 6.459330 GTCTTTCGACATTAGACATTTCGAC 58.541 40.000 9.88 0.00 38.37 4.20
711 725 5.285370 CGTCTTTCGACATTAGACATTTCGA 59.715 40.000 13.38 0.00 42.86 3.71
712 726 5.285370 TCGTCTTTCGACATTAGACATTTCG 59.715 40.000 13.38 0.00 44.01 3.46
756 801 4.759096 GGTCGCACGCACAATGGC 62.759 66.667 0.00 0.00 0.00 4.40
813 859 1.309006 GGGGTAGAGGGGAGACGAA 59.691 63.158 0.00 0.00 0.00 3.85
853 899 4.388499 GTGACCGACATGGGGCGT 62.388 66.667 0.00 0.00 44.64 5.68
945 991 4.147322 GGCAATGTCGCCGTCGTG 62.147 66.667 0.00 0.00 43.52 4.35
964 1010 6.109359 TCTTCTTCTCTGCAGGTAATTAAGC 58.891 40.000 15.13 0.00 0.00 3.09
969 1015 6.365970 TCTTTCTTCTTCTCTGCAGGTAAT 57.634 37.500 15.13 0.00 0.00 1.89
970 1016 5.279708 CCTCTTTCTTCTTCTCTGCAGGTAA 60.280 44.000 15.13 7.65 0.00 2.85
974 1020 3.002102 GCCTCTTTCTTCTTCTCTGCAG 58.998 50.000 7.63 7.63 0.00 4.41
975 1021 2.369860 TGCCTCTTTCTTCTTCTCTGCA 59.630 45.455 0.00 0.00 0.00 4.41
976 1022 3.051081 TGCCTCTTTCTTCTTCTCTGC 57.949 47.619 0.00 0.00 0.00 4.26
977 1023 4.640364 AGTTGCCTCTTTCTTCTTCTCTG 58.360 43.478 0.00 0.00 0.00 3.35
978 1024 4.972751 AGTTGCCTCTTTCTTCTTCTCT 57.027 40.909 0.00 0.00 0.00 3.10
979 1025 5.584251 CCATAGTTGCCTCTTTCTTCTTCTC 59.416 44.000 0.00 0.00 0.00 2.87
980 1026 5.495640 CCATAGTTGCCTCTTTCTTCTTCT 58.504 41.667 0.00 0.00 0.00 2.85
981 1027 4.095632 GCCATAGTTGCCTCTTTCTTCTTC 59.904 45.833 0.00 0.00 0.00 2.87
982 1028 4.013050 GCCATAGTTGCCTCTTTCTTCTT 58.987 43.478 0.00 0.00 0.00 2.52
986 1032 2.014068 GCGCCATAGTTGCCTCTTTCT 61.014 52.381 0.00 0.00 0.00 2.52
990 1036 2.202932 CGCGCCATAGTTGCCTCT 60.203 61.111 0.00 0.00 0.00 3.69
994 1040 4.241999 CAGCCGCGCCATAGTTGC 62.242 66.667 0.00 0.00 0.00 4.17
1279 1334 0.813184 CACCTGCACACATCCATTCC 59.187 55.000 0.00 0.00 0.00 3.01
1353 1408 4.807039 GGTCACCGCGTACGCCAT 62.807 66.667 32.64 19.17 38.22 4.40
1528 1584 3.316029 CCGGGCTGGGCTAAAGTA 58.684 61.111 3.77 0.00 0.00 2.24
1559 1615 0.179067 TTGTTCCAAGACGCCGAGTT 60.179 50.000 0.00 0.00 0.00 3.01
1573 1629 1.269051 CGCCCACCTTCAAAGTTGTTC 60.269 52.381 0.00 0.00 0.00 3.18
1574 1630 0.744281 CGCCCACCTTCAAAGTTGTT 59.256 50.000 0.00 0.00 0.00 2.83
1575 1631 0.106918 TCGCCCACCTTCAAAGTTGT 60.107 50.000 0.00 0.00 0.00 3.32
1577 1633 1.164041 CGTCGCCCACCTTCAAAGTT 61.164 55.000 0.00 0.00 0.00 2.66
1578 1634 1.597027 CGTCGCCCACCTTCAAAGT 60.597 57.895 0.00 0.00 0.00 2.66
1579 1635 2.325082 CCGTCGCCCACCTTCAAAG 61.325 63.158 0.00 0.00 0.00 2.77
1580 1636 2.281208 CCGTCGCCCACCTTCAAA 60.281 61.111 0.00 0.00 0.00 2.69
1581 1637 3.552384 ACCGTCGCCCACCTTCAA 61.552 61.111 0.00 0.00 0.00 2.69
1814 1870 4.883300 GAGTCGTCGTAGCGGCCG 62.883 72.222 24.05 24.05 37.15 6.13
1835 1891 0.179045 AGAACTTCTTGGCGCACTGT 60.179 50.000 10.83 0.00 0.00 3.55
1865 1921 1.509923 CTCGTCTTGGTACCCGGAC 59.490 63.158 18.71 18.71 0.00 4.79
1871 1927 0.528470 AGAGCAGCTCGTCTTGGTAC 59.472 55.000 16.99 0.00 35.36 3.34
1877 1933 3.073735 CCCCAGAGCAGCTCGTCT 61.074 66.667 16.99 0.00 35.36 4.18
2698 2754 2.202987 CTCCGATGTGCAGGGAGC 60.203 66.667 9.36 0.00 45.96 4.70
2700 2756 3.785859 GCCTCCGATGTGCAGGGA 61.786 66.667 0.00 0.00 0.00 4.20
2723 2779 2.661866 GCGTGCACGAACTCCAGT 60.662 61.111 41.19 0.00 43.02 4.00
2744 2800 1.668151 GTGCTCCCACGAGTTGGTC 60.668 63.158 0.00 0.00 45.25 4.02
2760 2816 0.389296 TAGTGATCCACGCCGTTGTG 60.389 55.000 0.00 0.00 39.64 3.33
2840 2896 4.227134 CCGGTCAGCCCCTCGATG 62.227 72.222 0.00 0.00 0.00 3.84
2876 2932 4.980805 TCCTTGTCGTGCGTGGCC 62.981 66.667 0.00 0.00 0.00 5.36
2912 2968 0.600255 CGTCAAGTCTGGTGACCCAC 60.600 60.000 0.00 0.00 43.91 4.61
3051 3114 9.746711 GCAAAAATCATAGTAATATAGACGCAG 57.253 33.333 0.00 0.00 0.00 5.18
3057 3120 9.236006 AGCAGGGCAAAAATCATAGTAATATAG 57.764 33.333 0.00 0.00 0.00 1.31
3127 3211 6.630015 CAAACAATTCAACGATGTTGTTCTG 58.370 36.000 12.61 10.09 42.17 3.02
3194 3284 7.647715 GCTCAAAATGTTAAACTTTGCTCTACA 59.352 33.333 0.00 0.00 31.51 2.74
3198 3288 5.107875 CGGCTCAAAATGTTAAACTTTGCTC 60.108 40.000 0.00 0.00 31.51 4.26
3199 3289 4.744631 CGGCTCAAAATGTTAAACTTTGCT 59.255 37.500 0.00 0.00 31.51 3.91
3200 3290 4.084589 CCGGCTCAAAATGTTAAACTTTGC 60.085 41.667 0.00 0.00 31.51 3.68
3205 3620 5.310720 AGATCCGGCTCAAAATGTTAAAC 57.689 39.130 8.23 0.00 0.00 2.01
3207 3622 5.007034 TCAAGATCCGGCTCAAAATGTTAA 58.993 37.500 8.23 0.00 0.00 2.01
3208 3623 4.584874 TCAAGATCCGGCTCAAAATGTTA 58.415 39.130 8.23 0.00 0.00 2.41
3225 3640 3.092301 TCTCCTTCTCGAAGCATCAAGA 58.908 45.455 1.13 0.00 37.11 3.02
3247 3662 3.129113 CACATCGCCTCAATTTCATTGGA 59.871 43.478 0.00 0.00 40.61 3.53
3325 3753 1.410882 GAGCAGGGTGTATCCTCTGAC 59.589 57.143 0.00 0.00 36.96 3.51
3374 3803 5.392165 CGAAAGATACGTTAAAAATGGCCCA 60.392 40.000 0.00 0.00 0.00 5.36
3376 3805 5.032220 CCGAAAGATACGTTAAAAATGGCC 58.968 41.667 0.00 0.00 0.00 5.36
3391 3820 9.981114 AAAACTGATAATGAAAAACCGAAAGAT 57.019 25.926 0.00 0.00 0.00 2.40
3567 4004 8.837389 TGATCATTGCATGAACATTTTTCAAAA 58.163 25.926 0.00 0.00 43.50 2.44
3568 4005 8.379457 TGATCATTGCATGAACATTTTTCAAA 57.621 26.923 0.00 0.00 43.50 2.69
3569 4006 7.964604 TGATCATTGCATGAACATTTTTCAA 57.035 28.000 0.00 0.00 43.50 2.69
3570 4007 7.065204 CCATGATCATTGCATGAACATTTTTCA 59.935 33.333 5.16 8.13 46.49 2.69
3571 4008 7.406553 CCATGATCATTGCATGAACATTTTTC 58.593 34.615 5.16 4.18 46.49 2.29
3808 4258 5.229678 GCAAACATTGTTTGAATTTGGCAAC 59.770 36.000 35.02 16.22 32.17 4.17
3809 4259 5.106038 TGCAAACATTGTTTGAATTTGGCAA 60.106 32.000 35.02 13.28 32.17 4.52
3810 4260 4.397103 TGCAAACATTGTTTGAATTTGGCA 59.603 33.333 35.02 24.24 32.17 4.92
3811 4261 4.918037 TGCAAACATTGTTTGAATTTGGC 58.082 34.783 35.02 22.42 32.17 4.52
3812 4262 9.119329 CATTATGCAAACATTGTTTGAATTTGG 57.881 29.630 35.02 21.80 37.74 3.28
3813 4263 9.666626 ACATTATGCAAACATTGTTTGAATTTG 57.333 25.926 35.02 29.71 37.74 2.32
3823 4273 7.644551 ACAAAAGCAAACATTATGCAAACATTG 59.355 29.630 0.00 0.00 46.22 2.82
3836 4286 3.949132 ACCAAACCACAAAAGCAAACAT 58.051 36.364 0.00 0.00 0.00 2.71
3848 4298 4.712122 TCTTTGTCTTGAACCAAACCAC 57.288 40.909 0.00 0.00 0.00 4.16
3857 4307 8.690203 TTCCAGAATGTAATCTTTGTCTTGAA 57.310 30.769 0.00 0.00 0.00 2.69
3859 4309 9.994432 GTATTCCAGAATGTAATCTTTGTCTTG 57.006 33.333 3.10 0.00 32.50 3.02
3861 4311 9.739276 TTGTATTCCAGAATGTAATCTTTGTCT 57.261 29.630 3.10 0.00 32.50 3.41
3949 4399 0.726827 TGCCTCGATTTCATTGCGTC 59.273 50.000 0.00 0.00 0.00 5.19
3952 4402 4.232221 CCATATTGCCTCGATTTCATTGC 58.768 43.478 0.00 0.00 0.00 3.56
3974 4424 3.414549 TGCAAACTTTCTCCGACAAAC 57.585 42.857 0.00 0.00 0.00 2.93
3977 4427 2.354510 CACTTGCAAACTTTCTCCGACA 59.645 45.455 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.