Multiple sequence alignment - TraesCS7D01G401300

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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 TraesCS7D01G401300 chr7D 100.000 3799 0 0 1 3799 518572635 518576433 0.000000e+00 7016.0
1 TraesCS7D01G401300 chr7D 93.240 1642 90 14 969 2594 518091225 518089589 0.000000e+00 2398.0
2 TraesCS7D01G401300 chr7D 90.716 894 57 15 1963 2846 518558394 518559271 0.000000e+00 1168.0
3 TraesCS7D01G401300 chr7D 90.835 862 54 15 1997 2846 518602073 518602921 0.000000e+00 1131.0
4 TraesCS7D01G401300 chr7D 94.253 696 31 8 2 691 123373202 123372510 0.000000e+00 1055.0
5 TraesCS7D01G401300 chr7D 85.009 587 58 21 3201 3763 518603363 518603943 1.530000e-158 569.0
6 TraesCS7D01G401300 chr7D 90.000 420 27 10 2322 2738 518266899 518267306 2.600000e-146 529.0
7 TraesCS7D01G401300 chr7D 84.494 316 29 13 3213 3511 518559755 518560067 1.030000e-75 294.0
8 TraesCS7D01G401300 chr7D 86.792 212 22 4 3555 3763 518560064 518560272 8.210000e-57 231.0
9 TraesCS7D01G401300 chr7D 94.737 76 4 0 690 765 518616302 518616377 6.670000e-23 119.0
10 TraesCS7D01G401300 chr7B 90.249 2369 154 39 860 3198 551897084 551899405 0.000000e+00 3024.0
11 TraesCS7D01G401300 chr7B 91.185 2076 127 34 870 2908 551538823 551540879 0.000000e+00 2769.0
12 TraesCS7D01G401300 chr7B 87.791 344 34 6 3064 3401 551892885 551893226 2.750000e-106 396.0
13 TraesCS7D01G401300 chr7B 95.484 155 4 3 690 844 551896614 551896765 1.050000e-60 244.0
14 TraesCS7D01G401300 chr7B 94.340 53 2 1 3258 3309 551901027 551901079 3.150000e-11 80.5
15 TraesCS7D01G401300 chr7A 92.247 1780 95 26 869 2625 593016252 593014493 0.000000e+00 2483.0
16 TraesCS7D01G401300 chr7A 95.171 1553 65 8 1070 2617 593376348 593377895 0.000000e+00 2444.0
17 TraesCS7D01G401300 chr1D 97.399 692 16 2 1 691 114689447 114690137 0.000000e+00 1177.0
18 TraesCS7D01G401300 chr1D 94.798 692 30 5 1 691 481805072 481805758 0.000000e+00 1074.0
19 TraesCS7D01G401300 chr1D 78.167 1429 245 46 1140 2526 10936437 10935034 0.000000e+00 848.0
20 TraesCS7D01G401300 chr5A 95.147 680 29 3 14 691 111611579 111610902 0.000000e+00 1070.0
21 TraesCS7D01G401300 chr5A 89.286 84 7 2 1 82 365046061 365045978 1.870000e-18 104.0
22 TraesCS7D01G401300 chr4D 94.109 696 30 8 1 691 23958412 23957723 0.000000e+00 1048.0
23 TraesCS7D01G401300 chr5D 93.678 696 33 8 4 692 52763801 52764492 0.000000e+00 1031.0
24 TraesCS7D01G401300 chr2B 93.543 604 33 5 94 691 782772480 782773083 0.000000e+00 894.0
25 TraesCS7D01G401300 chr2B 93.212 604 35 5 94 691 782898532 782899135 0.000000e+00 883.0
26 TraesCS7D01G401300 chr2A 93.322 599 34 3 94 691 139891776 139891183 0.000000e+00 880.0
27 TraesCS7D01G401300 chr1A 77.678 1447 264 46 1111 2523 22755518 22756939 0.000000e+00 828.0
28 TraesCS7D01G401300 chr1B 81.878 905 142 17 1633 2526 16427761 16426868 0.000000e+00 743.0
29 TraesCS7D01G401300 chr1B 79.167 360 59 13 1140 1491 16428261 16427910 6.340000e-58 235.0
30 TraesCS7D01G401300 chr3B 83.359 649 95 10 1892 2533 712559071 712559713 4.230000e-164 588.0
31 TraesCS7D01G401300 chr3A 80.506 395 65 5 1111 1495 673435194 673435586 3.710000e-75 292.0
32 TraesCS7D01G401300 chr6A 89.610 77 6 2 1 76 496585840 496585915 3.120000e-16 97.1


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 TraesCS7D01G401300 chr7D 518572635 518576433 3798 False 7016.000000 7016 100.0000 1 3799 1 chr7D.!!$F2 3798
1 TraesCS7D01G401300 chr7D 518089589 518091225 1636 True 2398.000000 2398 93.2400 969 2594 1 chr7D.!!$R2 1625
2 TraesCS7D01G401300 chr7D 123372510 123373202 692 True 1055.000000 1055 94.2530 2 691 1 chr7D.!!$R1 689
3 TraesCS7D01G401300 chr7D 518602073 518603943 1870 False 850.000000 1131 87.9220 1997 3763 2 chr7D.!!$F5 1766
4 TraesCS7D01G401300 chr7D 518558394 518560272 1878 False 564.333333 1168 87.3340 1963 3763 3 chr7D.!!$F4 1800
5 TraesCS7D01G401300 chr7B 551538823 551540879 2056 False 2769.000000 2769 91.1850 870 2908 1 chr7B.!!$F1 2038
6 TraesCS7D01G401300 chr7B 551892885 551901079 8194 False 936.125000 3024 91.9660 690 3401 4 chr7B.!!$F2 2711
7 TraesCS7D01G401300 chr7A 593014493 593016252 1759 True 2483.000000 2483 92.2470 869 2625 1 chr7A.!!$R1 1756
8 TraesCS7D01G401300 chr7A 593376348 593377895 1547 False 2444.000000 2444 95.1710 1070 2617 1 chr7A.!!$F1 1547
9 TraesCS7D01G401300 chr1D 114689447 114690137 690 False 1177.000000 1177 97.3990 1 691 1 chr1D.!!$F1 690
10 TraesCS7D01G401300 chr1D 481805072 481805758 686 False 1074.000000 1074 94.7980 1 691 1 chr1D.!!$F2 690
11 TraesCS7D01G401300 chr1D 10935034 10936437 1403 True 848.000000 848 78.1670 1140 2526 1 chr1D.!!$R1 1386
12 TraesCS7D01G401300 chr5A 111610902 111611579 677 True 1070.000000 1070 95.1470 14 691 1 chr5A.!!$R1 677
13 TraesCS7D01G401300 chr4D 23957723 23958412 689 True 1048.000000 1048 94.1090 1 691 1 chr4D.!!$R1 690
14 TraesCS7D01G401300 chr5D 52763801 52764492 691 False 1031.000000 1031 93.6780 4 692 1 chr5D.!!$F1 688
15 TraesCS7D01G401300 chr2B 782772480 782773083 603 False 894.000000 894 93.5430 94 691 1 chr2B.!!$F1 597
16 TraesCS7D01G401300 chr2B 782898532 782899135 603 False 883.000000 883 93.2120 94 691 1 chr2B.!!$F2 597
17 TraesCS7D01G401300 chr2A 139891183 139891776 593 True 880.000000 880 93.3220 94 691 1 chr2A.!!$R1 597
18 TraesCS7D01G401300 chr1A 22755518 22756939 1421 False 828.000000 828 77.6780 1111 2523 1 chr1A.!!$F1 1412
19 TraesCS7D01G401300 chr1B 16426868 16428261 1393 True 489.000000 743 80.5225 1140 2526 2 chr1B.!!$R1 1386
20 TraesCS7D01G401300 chr3B 712559071 712559713 642 False 588.000000 588 83.3590 1892 2533 1 chr3B.!!$F1 641

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
952 4306 0.249826 GCACCAACCCCAACACATTG 60.25 55.0 0.0 0.0 35.4 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2951 6436 0.252197 GGGAGTGGTTGTTATCGCCT 59.748 55.0 0.0 0.0 0.0 5.52 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
112 115 0.401356 TGCAGTCACATGTGGATGGT 59.599 50.000 25.16 3.49 33.39 3.55
672 690 2.601763 GCACGGTCTATTTCTAACCACG 59.398 50.000 0.00 0.00 32.35 4.94
692 710 3.063485 CGGCCCAACAAATAAACAAAGG 58.937 45.455 0.00 0.00 0.00 3.11
727 3768 2.604174 CCGTGCGACTTTGACCACC 61.604 63.158 0.00 0.00 0.00 4.61
728 3769 2.935955 GTGCGACTTTGACCACCG 59.064 61.111 0.00 0.00 0.00 4.94
781 3822 1.767759 CTTGGAGCCTAAACCCCATG 58.232 55.000 0.00 0.00 0.00 3.66
789 3830 4.047883 AGCCTAAACCCCATGATTAGTCT 58.952 43.478 0.00 0.00 0.00 3.24
828 3869 1.136872 TTGTTTTTGTGTGAGCGCGC 61.137 50.000 26.66 26.66 0.00 6.86
844 3885 2.099446 GCGTGTGTGTTGCGTGTT 59.901 55.556 0.00 0.00 0.00 3.32
845 3886 1.513160 GCGTGTGTGTTGCGTGTTT 60.513 52.632 0.00 0.00 0.00 2.83
846 3887 1.728717 GCGTGTGTGTTGCGTGTTTG 61.729 55.000 0.00 0.00 0.00 2.93
879 4222 4.406972 AGCTACTAAATGCCACTGATCTCA 59.593 41.667 0.00 0.00 0.00 3.27
899 4245 2.920384 TCAGTGCACCTACCGGCA 60.920 61.111 14.63 0.00 37.77 5.69
949 4303 2.443016 GGCACCAACCCCAACACA 60.443 61.111 0.00 0.00 0.00 3.72
952 4306 0.249826 GCACCAACCCCAACACATTG 60.250 55.000 0.00 0.00 35.40 2.82
978 4332 8.598041 GGAACTCCAGACATGTCCTATATAAAT 58.402 37.037 22.21 0.00 35.64 1.40
1016 4371 1.068588 GCACACTCACTCCACTACACA 59.931 52.381 0.00 0.00 0.00 3.72
1025 4380 2.291024 ACTCCACTACACATCCTCTCGT 60.291 50.000 0.00 0.00 0.00 4.18
1084 4451 1.494721 AGTCTCTAGCTAGCTGCCTCT 59.505 52.381 27.68 14.89 44.23 3.69
1409 4791 1.735198 GGGCGTCATGTTCGTCGAA 60.735 57.895 2.90 2.90 33.53 3.71
1624 5024 8.795842 TCCAGGTAAATAACGATGTTGTTAAT 57.204 30.769 0.00 0.00 37.81 1.40
1651 5066 1.301716 GCAGGTGACGAGGCTCAAA 60.302 57.895 15.95 0.00 0.00 2.69
1678 5093 2.817423 CTTCATCTTCGGGCAGCGC 61.817 63.158 0.00 0.00 0.00 5.92
2332 5756 4.572571 AGCCACGCCGGGTTCAAA 62.573 61.111 2.18 0.00 45.83 2.69
2344 5768 1.407618 GGGTTCAAAAGCGTGGACTTT 59.592 47.619 0.00 0.00 41.60 2.66
2539 5963 1.066422 CGCCGAGATCTAAGCTGCA 59.934 57.895 13.08 0.00 0.00 4.41
2543 5967 0.526310 CGAGATCTAAGCTGCACGCA 60.526 55.000 1.02 0.00 42.61 5.24
2545 5969 1.325943 GAGATCTAAGCTGCACGCAAC 59.674 52.381 1.02 0.00 42.61 4.17
2546 5970 0.025513 GATCTAAGCTGCACGCAACG 59.974 55.000 1.02 0.00 42.61 4.10
2565 5989 1.312371 GGCGTACCTACCCACGTACA 61.312 60.000 0.00 0.00 40.25 2.90
2597 6027 3.489813 TGCAGCCGCATATACTACG 57.510 52.632 0.00 0.00 45.36 3.51
2654 6088 2.619074 GGGCCATATAAGTGCATCTCCC 60.619 54.545 4.39 0.00 0.00 4.30
2664 6098 2.359169 GCATCTCCCTGGGTGACGA 61.359 63.158 19.13 9.06 0.00 4.20
2693 6127 8.854614 ATATTCTGACTGACTAAGTTTTGCTT 57.145 30.769 0.00 0.00 40.07 3.91
2705 6139 8.716646 ACTAAGTTTTGCTTTTGTGCTTATTT 57.283 26.923 0.00 0.00 38.57 1.40
2706 6140 9.810545 ACTAAGTTTTGCTTTTGTGCTTATTTA 57.189 25.926 0.00 0.00 38.57 1.40
2717 6162 4.709250 TGTGCTTATTTACCTGTGTGTGA 58.291 39.130 0.00 0.00 0.00 3.58
2748 6194 6.952773 AATTACCAACAGTGTACAACATGT 57.047 33.333 0.00 0.00 0.00 3.21
2784 6230 6.587990 CGTGCAATTTGTATGTAATTTTCCCA 59.412 34.615 0.00 0.00 0.00 4.37
2846 6327 8.065627 TGGATCTACTAGTAAGGAATGAAAGGA 58.934 37.037 3.76 0.00 0.00 3.36
2917 6402 8.773404 ACAACTACACAGTCCATTTTAGATAC 57.227 34.615 0.00 0.00 32.29 2.24
2951 6436 9.719355 TGTTTATCTGAGAAGTACAGCAAAATA 57.281 29.630 0.00 0.00 35.61 1.40
2957 6442 4.770795 AGAAGTACAGCAAAATAGGCGAT 58.229 39.130 0.00 0.00 36.08 4.58
3032 6519 1.138568 TTTGGTTTCCGTGGGGTAGA 58.861 50.000 0.00 0.00 33.83 2.59
3041 6528 1.923909 GTGGGGTAGAGCTTGGGGT 60.924 63.158 0.00 0.00 0.00 4.95
3069 6557 6.164176 GTCCTTTGATCCTAAAAGAAGACGA 58.836 40.000 5.76 0.00 36.88 4.20
3089 6577 4.417506 CGACATCGTTGACACCATACTTA 58.582 43.478 0.00 0.00 34.11 2.24
3092 6580 5.730550 ACATCGTTGACACCATACTTACAT 58.269 37.500 0.00 0.00 0.00 2.29
3097 6585 7.324935 TCGTTGACACCATACTTACATTATGT 58.675 34.615 2.58 2.58 0.00 2.29
3106 6594 7.829211 ACCATACTTACATTATGTGGATATGCC 59.171 37.037 8.26 0.00 37.10 4.40
3108 6596 5.570320 ACTTACATTATGTGGATATGCCCC 58.430 41.667 8.26 0.00 34.97 5.80
3139 6627 2.667969 GCCCAAAATTGTTGCGAAGATC 59.332 45.455 0.00 0.00 0.00 2.75
3141 6629 3.922240 CCCAAAATTGTTGCGAAGATCTG 59.078 43.478 0.00 0.00 0.00 2.90
3155 6643 5.980116 GCGAAGATCTGTCAGTTACATATGT 59.020 40.000 13.93 13.93 37.50 2.29
3156 6644 6.074623 GCGAAGATCTGTCAGTTACATATGTG 60.075 42.308 18.81 1.55 37.50 3.21
3160 6648 7.840931 AGATCTGTCAGTTACATATGTGAACA 58.159 34.615 18.81 10.44 37.50 3.18
3194 6682 9.008965 ACACTAATGCATGTTAAGTTCACAATA 57.991 29.630 0.00 0.00 0.00 1.90
3232 8354 8.195165 TGTTTTGGGATGGACATAATGTTAAA 57.805 30.769 0.00 0.00 0.00 1.52
3233 8355 8.651389 TGTTTTGGGATGGACATAATGTTAAAA 58.349 29.630 0.00 0.00 0.00 1.52
3236 8358 9.664332 TTTGGGATGGACATAATGTTAAAAATG 57.336 29.630 0.00 0.00 0.00 2.32
3242 8364 9.874205 ATGGACATAATGTTAAAAATGGTTCAG 57.126 29.630 0.00 0.00 0.00 3.02
3251 8373 6.206634 TGTTAAAAATGGTTCAGTAGCAGGAG 59.793 38.462 0.00 0.00 37.73 3.69
3303 8433 4.109050 GTTCATTTGTCGTGGCTGAAAAA 58.891 39.130 0.00 0.00 30.03 1.94
3336 8467 5.342806 TGCTAGAAAGAAAATGTCACACG 57.657 39.130 0.00 0.00 0.00 4.49
3339 8470 6.073980 TGCTAGAAAGAAAATGTCACACGTAC 60.074 38.462 0.00 0.00 0.00 3.67
3370 8502 4.469657 GCCACCAACCAAGGATAATCATA 58.530 43.478 0.00 0.00 0.00 2.15
3373 8505 6.041979 GCCACCAACCAAGGATAATCATATTT 59.958 38.462 0.00 0.00 0.00 1.40
3413 8548 8.478066 AGCACATCTCAAGTAGTACATCAAATA 58.522 33.333 2.52 0.00 0.00 1.40
3464 8599 6.628919 AAAACTACTAAATGCAACCGAGTT 57.371 33.333 0.00 0.00 0.00 3.01
3468 8603 9.609346 AAACTACTAAATGCAACCGAGTTATAT 57.391 29.630 0.00 0.00 0.00 0.86
3469 8604 9.609346 AACTACTAAATGCAACCGAGTTATATT 57.391 29.630 0.00 0.00 0.00 1.28
3475 8610 3.619483 TGCAACCGAGTTATATTTCCACG 59.381 43.478 0.00 0.00 0.00 4.94
3480 8616 7.469260 CAACCGAGTTATATTTCCACGAAAAT 58.531 34.615 0.00 0.00 35.11 1.82
3481 8617 7.242914 ACCGAGTTATATTTCCACGAAAATC 57.757 36.000 0.00 0.00 35.11 2.17
3482 8618 7.046033 ACCGAGTTATATTTCCACGAAAATCT 58.954 34.615 0.00 0.00 35.11 2.40
3483 8619 8.199449 ACCGAGTTATATTTCCACGAAAATCTA 58.801 33.333 0.00 0.00 35.11 1.98
3484 8620 8.700644 CCGAGTTATATTTCCACGAAAATCTAG 58.299 37.037 0.00 0.00 35.11 2.43
3524 8664 5.990386 TGCTCAGAAGATGAATAGCTCATTC 59.010 40.000 0.00 0.00 45.23 2.67
3528 8668 7.267857 TCAGAAGATGAATAGCTCATTCGAAA 58.732 34.615 0.00 0.00 45.23 3.46
3606 8747 9.860898 GATTCACATGTATGCTAGTACATATCA 57.139 33.333 0.00 2.23 41.96 2.15
3708 8852 8.298729 AGTTTGAGGGGAAAAGATTGATATTC 57.701 34.615 0.00 0.00 0.00 1.75
3765 8909 5.401550 TGCAAATCTTGGCTCTAAATTTCG 58.598 37.500 0.00 0.00 0.00 3.46
3766 8910 4.266265 GCAAATCTTGGCTCTAAATTTCGC 59.734 41.667 0.00 0.00 0.00 4.70
3767 8911 5.401550 CAAATCTTGGCTCTAAATTTCGCA 58.598 37.500 0.00 0.00 0.00 5.10
3768 8912 5.643379 AATCTTGGCTCTAAATTTCGCAA 57.357 34.783 0.00 0.00 0.00 4.85
3769 8913 5.841957 ATCTTGGCTCTAAATTTCGCAAT 57.158 34.783 0.00 0.00 0.00 3.56
3770 8914 6.942532 ATCTTGGCTCTAAATTTCGCAATA 57.057 33.333 0.00 0.00 0.00 1.90
3771 8915 6.751514 TCTTGGCTCTAAATTTCGCAATAA 57.248 33.333 0.00 0.00 0.00 1.40
3772 8916 7.333528 TCTTGGCTCTAAATTTCGCAATAAT 57.666 32.000 0.00 0.00 0.00 1.28
3773 8917 8.445275 TCTTGGCTCTAAATTTCGCAATAATA 57.555 30.769 0.00 0.00 0.00 0.98
3774 8918 8.898761 TCTTGGCTCTAAATTTCGCAATAATAA 58.101 29.630 0.00 0.00 0.00 1.40
3775 8919 9.683069 CTTGGCTCTAAATTTCGCAATAATAAT 57.317 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 8.028354 TGTGACTGCATGGATTATTTGTTTAAG 58.972 33.333 0.00 0.00 0.00 1.85
632 650 1.603931 GCAAAGTGCAAAGAGGAAGCC 60.604 52.381 0.00 0.00 44.26 4.35
672 690 4.344359 TCCTTTGTTTATTTGTTGGGCC 57.656 40.909 0.00 0.00 0.00 5.80
727 3768 0.304098 GGTGGATCTCGTAGTCGTCG 59.696 60.000 0.00 0.00 38.33 5.12
728 3769 0.304098 CGGTGGATCTCGTAGTCGTC 59.696 60.000 0.00 0.00 38.33 4.20
781 3822 3.712218 AGTTAAGGGCCCTGAGACTAATC 59.288 47.826 29.50 13.57 0.00 1.75
789 3830 4.229582 ACAATTCATAGTTAAGGGCCCTGA 59.770 41.667 29.50 17.67 0.00 3.86
828 3869 1.131037 CCAAACACGCAACACACACG 61.131 55.000 0.00 0.00 0.00 4.49
835 3876 2.081462 AGCTATACCCAAACACGCAAC 58.919 47.619 0.00 0.00 0.00 4.17
837 3878 2.740580 GCTAGCTATACCCAAACACGCA 60.741 50.000 7.70 0.00 0.00 5.24
839 3880 3.454371 AGCTAGCTATACCCAAACACG 57.546 47.619 17.69 0.00 0.00 4.49
844 3885 6.295688 GGCATTTAGTAGCTAGCTATACCCAA 60.296 42.308 26.59 15.20 0.00 4.12
845 3886 5.187186 GGCATTTAGTAGCTAGCTATACCCA 59.813 44.000 26.59 11.14 0.00 4.51
846 3887 5.187186 TGGCATTTAGTAGCTAGCTATACCC 59.813 44.000 26.59 18.39 0.00 3.69
879 4222 1.961180 GCCGGTAGGTGCACTGAGAT 61.961 60.000 17.98 0.70 40.50 2.75
899 4245 1.069513 TCGTCGGAGTTCCAATGTGTT 59.930 47.619 0.00 0.00 35.14 3.32
949 4303 2.915604 AGGACATGTCTGGAGTTCCAAT 59.084 45.455 24.50 0.00 46.97 3.16
952 4306 7.540474 TTATATAGGACATGTCTGGAGTTCC 57.460 40.000 24.50 6.82 0.00 3.62
953 4307 9.429359 CATTTATATAGGACATGTCTGGAGTTC 57.571 37.037 24.50 6.84 0.00 3.01
954 4308 7.880195 GCATTTATATAGGACATGTCTGGAGTT 59.120 37.037 24.50 8.92 0.00 3.01
955 4309 7.390027 GCATTTATATAGGACATGTCTGGAGT 58.610 38.462 24.50 11.33 0.00 3.85
956 4310 6.533012 CGCATTTATATAGGACATGTCTGGAG 59.467 42.308 24.50 6.12 0.00 3.86
978 4332 4.089239 TCGCTAACCATGGCCGCA 62.089 61.111 13.04 0.58 0.00 5.69
1016 4371 3.317430 GGGAATGTACGTTACGAGAGGAT 59.683 47.826 13.03 0.00 0.00 3.24
1025 4380 3.429822 GCTAGCTGTGGGAATGTACGTTA 60.430 47.826 7.70 0.00 0.00 3.18
1319 4701 2.832201 GCGAGCGGGTAGTAGGGT 60.832 66.667 0.00 0.00 0.00 4.34
1409 4791 3.735029 GTGAGGTCGACGTCGGCT 61.735 66.667 37.51 25.11 44.45 5.52
1624 5024 0.599060 TCGTCACCTGCACGTCATAA 59.401 50.000 0.00 0.00 38.45 1.90
1651 5066 1.152881 GAAGATGAAGCCCCCGCAT 60.153 57.895 0.00 0.00 37.52 4.73
1822 5237 0.968901 TGTACTCCAGGTGCGGGTAG 60.969 60.000 0.00 0.00 33.14 3.18
2332 5756 1.528309 CCACCCAAAGTCCACGCTT 60.528 57.895 0.00 0.00 0.00 4.68
2543 5967 2.973082 GTGGGTAGGTACGCCGTT 59.027 61.111 0.00 0.00 40.50 4.44
2545 5969 2.112198 TACGTGGGTAGGTACGCCG 61.112 63.158 0.00 11.04 43.63 6.46
2546 5970 1.312371 TGTACGTGGGTAGGTACGCC 61.312 60.000 0.00 0.00 46.13 5.68
2565 5989 0.525668 GCTGCACGAGTACGCTGTAT 60.526 55.000 0.00 0.00 43.96 2.29
2597 6027 3.978373 CGTGACGACGTATGCTCC 58.022 61.111 0.00 0.00 40.91 4.70
2654 6088 1.338337 AGAATATCGCTCGTCACCCAG 59.662 52.381 0.00 0.00 0.00 4.45
2664 6098 6.458232 AACTTAGTCAGTCAGAATATCGCT 57.542 37.500 0.00 0.00 32.94 4.93
2693 6127 5.590663 TCACACACAGGTAAATAAGCACAAA 59.409 36.000 0.00 0.00 0.00 2.83
2705 6139 9.386010 GGTAATTTTACATATCACACACAGGTA 57.614 33.333 3.12 0.00 35.37 3.08
2706 6140 7.885922 TGGTAATTTTACATATCACACACAGGT 59.114 33.333 3.12 0.00 35.37 4.00
2707 6141 8.275015 TGGTAATTTTACATATCACACACAGG 57.725 34.615 3.12 0.00 35.37 4.00
2748 6194 5.888691 ACAAATTGCACGGACATAACATA 57.111 34.783 0.00 0.00 0.00 2.29
2754 6200 5.888691 TTACATACAAATTGCACGGACAT 57.111 34.783 0.00 0.00 0.00 3.06
2813 6260 9.939424 ATTCCTTACTAGTAGATCCAGTTAAGT 57.061 33.333 3.59 0.00 0.00 2.24
2817 6264 8.840200 TTCATTCCTTACTAGTAGATCCAGTT 57.160 34.615 3.59 0.00 0.00 3.16
2917 6402 7.702348 TGTACTTCTCAGATAAACATCACATCG 59.298 37.037 0.00 0.00 0.00 3.84
2951 6436 0.252197 GGGAGTGGTTGTTATCGCCT 59.748 55.000 0.00 0.00 0.00 5.52
2952 6437 1.087771 CGGGAGTGGTTGTTATCGCC 61.088 60.000 0.00 0.00 0.00 5.54
2977 6462 3.430042 ACATCCAAAGCTGTCTCATGT 57.570 42.857 0.00 0.00 0.00 3.21
2986 6471 3.825328 ACAGAGTTCAACATCCAAAGCT 58.175 40.909 0.00 0.00 0.00 3.74
3032 6519 0.264657 AAAGGACCAAACCCCAAGCT 59.735 50.000 0.00 0.00 0.00 3.74
3041 6528 7.230712 GTCTTCTTTTAGGATCAAAGGACCAAA 59.769 37.037 0.00 0.00 32.86 3.28
3069 6557 5.142061 TGTAAGTATGGTGTCAACGATGT 57.858 39.130 0.00 0.00 0.00 3.06
3083 6571 7.346471 GGGGCATATCCACATAATGTAAGTAT 58.654 38.462 0.00 0.00 38.47 2.12
3089 6577 2.996021 AGGGGGCATATCCACATAATGT 59.004 45.455 0.00 0.00 41.25 2.71
3092 6580 3.206412 ACAAAGGGGGCATATCCACATAA 59.794 43.478 0.00 0.00 41.25 1.90
3097 6585 0.182537 CGACAAAGGGGGCATATCCA 59.817 55.000 0.00 0.00 36.21 3.41
3108 6596 0.319469 AATTTTGGGCGCGACAAAGG 60.319 50.000 17.00 0.00 38.84 3.11
3121 6609 5.214417 TGACAGATCTTCGCAACAATTTTG 58.786 37.500 0.00 0.00 0.00 2.44
3122 6610 5.009010 ACTGACAGATCTTCGCAACAATTTT 59.991 36.000 10.08 0.00 0.00 1.82
3139 6627 8.484641 AGATTGTTCACATATGTAACTGACAG 57.515 34.615 8.32 0.00 42.79 3.51
3155 6643 9.394767 ACATGCATTAGTGTATTAGATTGTTCA 57.605 29.630 0.00 0.00 0.00 3.18
3194 6682 9.320295 TCCATCCCAAAACAAGAACTATTTAAT 57.680 29.630 0.00 0.00 0.00 1.40
3198 6686 6.074648 TGTCCATCCCAAAACAAGAACTATT 58.925 36.000 0.00 0.00 0.00 1.73
3201 6689 3.909732 TGTCCATCCCAAAACAAGAACT 58.090 40.909 0.00 0.00 0.00 3.01
3202 6690 4.871933 ATGTCCATCCCAAAACAAGAAC 57.128 40.909 0.00 0.00 0.00 3.01
3203 6691 6.496565 ACATTATGTCCATCCCAAAACAAGAA 59.503 34.615 0.00 0.00 0.00 2.52
3204 6692 6.015918 ACATTATGTCCATCCCAAAACAAGA 58.984 36.000 0.00 0.00 0.00 3.02
3205 6693 6.284891 ACATTATGTCCATCCCAAAACAAG 57.715 37.500 0.00 0.00 0.00 3.16
3206 6694 6.678568 AACATTATGTCCATCCCAAAACAA 57.321 33.333 0.00 0.00 0.00 2.83
3207 6695 7.782897 TTAACATTATGTCCATCCCAAAACA 57.217 32.000 0.00 0.00 0.00 2.83
3214 8309 9.313118 GAACCATTTTTAACATTATGTCCATCC 57.687 33.333 0.00 0.00 0.00 3.51
3232 8354 4.042187 AGAACTCCTGCTACTGAACCATTT 59.958 41.667 0.00 0.00 0.00 2.32
3233 8355 3.584848 AGAACTCCTGCTACTGAACCATT 59.415 43.478 0.00 0.00 0.00 3.16
3236 8358 3.764972 ACTAGAACTCCTGCTACTGAACC 59.235 47.826 0.00 0.00 0.00 3.62
3242 8364 6.452494 TCATTGTACTAGAACTCCTGCTAC 57.548 41.667 0.00 0.00 0.00 3.58
3251 8373 7.148641 ACATGGATCGATCATTGTACTAGAAC 58.851 38.462 25.93 5.26 0.00 3.01
3303 8433 8.932791 CATTTTCTTTCTAGCATGCTTCATTTT 58.067 29.630 28.02 1.31 0.00 1.82
3336 8467 1.730612 GTTGGTGGCGCTTTAGAGTAC 59.269 52.381 7.64 0.00 0.00 2.73
3339 8470 0.605319 TGGTTGGTGGCGCTTTAGAG 60.605 55.000 7.64 0.00 0.00 2.43
3398 8533 9.036980 ACTTGGTTCTCTATTTGATGTACTACT 57.963 33.333 0.00 0.00 0.00 2.57
3413 8548 7.993183 TGACTCAGAATTTTAACTTGGTTCTCT 59.007 33.333 0.00 0.00 0.00 3.10
3415 8550 8.519799 TTGACTCAGAATTTTAACTTGGTTCT 57.480 30.769 0.00 0.00 0.00 3.01
3444 8579 9.609346 AAATATAACTCGGTTGCATTTAGTAGT 57.391 29.630 0.00 0.00 0.00 2.73
3459 8594 9.459640 TCTAGATTTTCGTGGAAATATAACTCG 57.540 33.333 0.00 0.00 31.34 4.18
3464 8599 9.929180 CTCCATCTAGATTTTCGTGGAAATATA 57.071 33.333 10.86 0.00 35.52 0.86
3468 8603 6.294361 TCTCCATCTAGATTTTCGTGGAAA 57.706 37.500 10.86 0.00 35.52 3.13
3469 8604 5.932619 TCTCCATCTAGATTTTCGTGGAA 57.067 39.130 10.86 1.92 35.52 3.53
3471 8606 8.662781 TTATTTCTCCATCTAGATTTTCGTGG 57.337 34.615 1.33 1.67 0.00 4.94
3480 8616 9.334947 CTGAGCAATTTTATTTCTCCATCTAGA 57.665 33.333 0.00 0.00 0.00 2.43
3481 8617 9.334947 TCTGAGCAATTTTATTTCTCCATCTAG 57.665 33.333 0.00 0.00 0.00 2.43
3482 8618 9.685276 TTCTGAGCAATTTTATTTCTCCATCTA 57.315 29.630 0.00 0.00 0.00 1.98
3483 8619 8.585471 TTCTGAGCAATTTTATTTCTCCATCT 57.415 30.769 0.00 0.00 0.00 2.90
3484 8620 8.680903 TCTTCTGAGCAATTTTATTTCTCCATC 58.319 33.333 0.00 0.00 0.00 3.51
3623 8764 8.976986 ATGTTTAAAGCAATTTTTGTGCAAAA 57.023 23.077 6.04 6.04 44.74 2.44
3656 8800 9.167311 AGACATGTAAAAATGTTTCTAGCTAGG 57.833 33.333 20.58 2.51 40.87 3.02
3731 8875 8.248945 AGAGCCAAGATTTGCATATATAATTGC 58.751 33.333 1.98 1.98 39.33 3.56
3739 8883 7.864379 CGAAATTTAGAGCCAAGATTTGCATAT 59.136 33.333 0.00 0.00 0.00 1.78
3744 8888 5.401550 TGCGAAATTTAGAGCCAAGATTTG 58.598 37.500 2.11 0.00 0.00 2.32
3746 8890 5.643379 TTGCGAAATTTAGAGCCAAGATT 57.357 34.783 2.11 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.