Multiple sequence alignment - TraesCS2B01G215000

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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 TraesCS2B01G215000 chr2B 100.000 4444 0 0 1 4444 200381984 200386427 0.000000e+00 8207.0
1 TraesCS2B01G215000 chr2B 90.949 1149 83 14 2484 3629 200471775 200470645 0.000000e+00 1526.0
2 TraesCS2B01G215000 chr2B 88.925 921 79 18 711 1619 200473508 200472599 0.000000e+00 1114.0
3 TraesCS2B01G215000 chr2B 80.851 282 32 12 2201 2475 200472134 200471868 7.540000e-48 202.0
4 TraesCS2B01G215000 chr2D 97.708 1571 30 4 2078 3646 142433505 142431939 0.000000e+00 2697.0
5 TraesCS2B01G215000 chr2D 95.991 1297 34 7 606 1894 142435963 142434677 0.000000e+00 2091.0
6 TraesCS2B01G215000 chr2D 91.454 1135 79 12 2501 3629 142474180 142473058 0.000000e+00 1543.0
7 TraesCS2B01G215000 chr2D 88.042 945 85 21 711 1642 142475898 142474969 0.000000e+00 1094.0
8 TraesCS2B01G215000 chr2D 95.133 452 16 5 1 450 142438646 142438199 0.000000e+00 708.0
9 TraesCS2B01G215000 chr2D 94.879 371 15 1 3729 4099 142431940 142431574 1.070000e-160 577.0
10 TraesCS2B01G215000 chr2D 82.857 280 28 9 2201 2475 142474552 142474288 2.670000e-57 233.0
11 TraesCS2B01G215000 chr2D 93.548 155 10 0 4290 4444 142431529 142431375 9.610000e-57 231.0
12 TraesCS2B01G215000 chr2D 95.876 97 0 3 510 605 142436265 142436172 2.140000e-33 154.0
13 TraesCS2B01G215000 chr2D 98.077 52 1 0 4053 4104 142431577 142431526 1.700000e-14 91.6
14 TraesCS2B01G215000 chr2D 85.333 75 4 6 3662 3733 584666868 584666938 2.220000e-08 71.3
15 TraesCS2B01G215000 chr2A 92.862 1583 64 23 459 2006 158589310 158590878 0.000000e+00 2252.0
16 TraesCS2B01G215000 chr2A 95.102 1123 45 7 2527 3646 158591694 158592809 0.000000e+00 1760.0
17 TraesCS2B01G215000 chr2A 93.894 999 56 4 2484 3481 158554791 158555785 0.000000e+00 1502.0
18 TraesCS2B01G215000 chr2A 89.418 945 67 19 711 1636 158553154 158554084 0.000000e+00 1160.0
19 TraesCS2B01G215000 chr2A 88.403 457 45 7 3888 4342 158595667 158596117 1.090000e-150 544.0
20 TraesCS2B01G215000 chr2A 89.947 378 26 9 70 442 158588979 158589349 1.120000e-130 477.0
21 TraesCS2B01G215000 chr2A 96.476 227 8 0 2085 2311 158591258 158591484 4.200000e-100 375.0
22 TraesCS2B01G215000 chr2A 91.748 206 11 3 2295 2494 158591501 158591706 9.410000e-72 281.0
23 TraesCS2B01G215000 chr2A 95.092 163 8 0 3729 3891 158592808 158592970 1.590000e-64 257.0
24 TraesCS2B01G215000 chr2A 84.000 275 30 5 2202 2475 158554477 158554738 7.380000e-63 252.0
25 TraesCS2B01G215000 chr2A 86.413 184 19 1 1386 1569 42001376 42001553 3.510000e-46 196.0
26 TraesCS2B01G215000 chr3D 91.398 93 6 2 3645 3737 390200641 390200731 4.670000e-25 126.0
27 TraesCS2B01G215000 chr4A 89.583 96 7 3 3645 3740 646776737 646776645 7.810000e-23 119.0
28 TraesCS2B01G215000 chr6B 89.362 94 6 2 3642 3733 147684315 147684224 1.010000e-21 115.0
29 TraesCS2B01G215000 chr6B 85.393 89 8 3 3644 3730 571723420 571723335 2.200000e-13 87.9
30 TraesCS2B01G215000 chr6B 93.182 44 2 1 3642 3685 474263761 474263803 3.710000e-06 63.9
31 TraesCS2B01G215000 chr6A 83.333 102 12 4 3631 3729 600774202 600774301 6.120000e-14 89.8
32 TraesCS2B01G215000 chr7D 85.057 87 6 5 3645 3731 133687569 133687490 1.020000e-11 82.4
33 TraesCS2B01G215000 chr7D 97.500 40 1 0 3694 3733 170603448 170603487 7.980000e-08 69.4
34 TraesCS2B01G215000 chr4B 95.455 44 1 1 3639 3682 207103915 207103957 7.980000e-08 69.4
35 TraesCS2B01G215000 chr3B 92.105 38 2 1 3698 3734 782996853 782996890 8.000000e-03 52.8


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 TraesCS2B01G215000 chr2B 200381984 200386427 4443 False 8207.000000 8207 100.000000 1 4444 1 chr2B.!!$F1 4443
1 TraesCS2B01G215000 chr2B 200470645 200473508 2863 True 947.333333 1526 86.908333 711 3629 3 chr2B.!!$R1 2918
2 TraesCS2B01G215000 chr2D 142473058 142475898 2840 True 956.666667 1543 87.451000 711 3629 3 chr2D.!!$R2 2918
3 TraesCS2B01G215000 chr2D 142431375 142438646 7271 True 935.657143 2697 95.887429 1 4444 7 chr2D.!!$R1 4443
4 TraesCS2B01G215000 chr2A 158553154 158555785 2631 False 971.333333 1502 89.104000 711 3481 3 chr2A.!!$F2 2770
5 TraesCS2B01G215000 chr2A 158588979 158596117 7138 False 849.428571 2252 92.804286 70 4342 7 chr2A.!!$F3 4272

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
665 2775 1.217942 TCTCCATGAGTAGGGCTGCTA 59.782 52.381 0.00 0.0 0.0 3.49 F
1855 4082 0.243365 TGAATTCAATGCGGCACCAC 59.757 50.000 4.03 0.0 0.0 4.16 F
2028 5135 0.178912 ACCTTGTAGACCGGGGAGTT 60.179 55.000 6.32 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 4142 0.037697 TGTGGCGCACCTTGTAGTAG 60.038 55.000 10.83 0.0 36.63 2.57 R
2746 6474 1.484240 GGTTGGAGATCACAGGAGGAG 59.516 57.143 0.00 0.0 0.00 3.69 R
3975 10416 0.474184 CCCTCTTCCGCCATGGTATT 59.526 55.000 14.67 0.0 39.52 1.89 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
30 31 4.152402 CACTAAGTTCCATCTGTTTCCACG 59.848 45.833 0.00 0.00 0.00 4.94
49 50 2.482721 ACGCCATTTTCGTTCCTAGTTG 59.517 45.455 0.00 0.00 36.72 3.16
68 69 4.563976 AGTTGTACACGTGTTGTCACTTAC 59.436 41.667 28.55 16.29 41.89 2.34
188 191 4.892433 AGTCATACATGGCTCTCATAAGC 58.108 43.478 0.00 0.00 38.63 3.09
230 233 6.237901 CAAGCCACAACCTATATTGCCTATA 58.762 40.000 0.00 0.00 32.47 1.31
442 448 8.996988 TTTACGTACATCATTTTGTTCTGTTC 57.003 30.769 0.00 0.00 0.00 3.18
551 2454 6.478344 TGCATTAGGTTTAGTTGTTTTTGCAG 59.522 34.615 0.00 0.00 32.12 4.41
665 2775 1.217942 TCTCCATGAGTAGGGCTGCTA 59.782 52.381 0.00 0.00 0.00 3.49
686 2796 2.032894 ACATGAAAAGTCTTCACACGCG 60.033 45.455 3.53 3.53 0.00 6.01
964 3084 1.905215 ACCCACCAATCTCTCTCTGTG 59.095 52.381 0.00 0.00 0.00 3.66
965 3085 2.182827 CCCACCAATCTCTCTCTGTGA 58.817 52.381 0.00 0.00 0.00 3.58
966 3086 2.770802 CCCACCAATCTCTCTCTGTGAT 59.229 50.000 0.00 0.00 0.00 3.06
970 3090 3.450457 ACCAATCTCTCTCTGTGATCCAC 59.550 47.826 0.00 0.00 34.56 4.02
971 3091 3.450096 CCAATCTCTCTCTGTGATCCACA 59.550 47.826 0.00 0.00 42.45 4.17
985 3105 2.246739 CCACACAGGCACACACTCG 61.247 63.158 0.00 0.00 0.00 4.18
1060 3193 6.415867 GCTGATTACATTGTGTATGTTGCATC 59.584 38.462 0.00 0.00 45.19 3.91
1064 3197 4.973396 ACATTGTGTATGTTGCATCTTCG 58.027 39.130 0.00 0.00 45.19 3.79
1442 3576 2.267642 CCATTCGTGGAGGCCGAA 59.732 61.111 0.00 0.00 46.95 4.30
1570 3704 2.125713 CATGACGGCGCAGGTACA 60.126 61.111 13.26 9.45 0.00 2.90
1850 4077 3.059166 ACAAAAGTGAATTCAATGCGGC 58.941 40.909 10.35 0.00 0.00 6.53
1855 4082 0.243365 TGAATTCAATGCGGCACCAC 59.757 50.000 4.03 0.00 0.00 4.16
1898 4125 5.454329 GGCCGGGTACTTCTTTGATAATACT 60.454 44.000 2.18 0.00 0.00 2.12
1899 4126 5.695363 GCCGGGTACTTCTTTGATAATACTC 59.305 44.000 2.18 0.00 0.00 2.59
1901 4128 6.041751 CCGGGTACTTCTTTGATAATACTCCT 59.958 42.308 0.00 0.00 0.00 3.69
1902 4129 7.418712 CCGGGTACTTCTTTGATAATACTCCTT 60.419 40.741 0.00 0.00 0.00 3.36
1904 4131 9.110502 GGGTACTTCTTTGATAATACTCCTTTG 57.889 37.037 0.00 0.00 0.00 2.77
1915 4142 8.910944 TGATAATACTCCTTTGTACAGTAGTCC 58.089 37.037 0.00 0.00 0.00 3.85
1955 4741 2.037772 AGCAACCTTGTAGACAGGAGTG 59.962 50.000 5.50 0.00 0.00 3.51
2014 4801 0.894835 GGTTGTTATGGCCCACCTTG 59.105 55.000 0.00 0.00 36.63 3.61
2028 5135 0.178912 ACCTTGTAGACCGGGGAGTT 60.179 55.000 6.32 0.00 0.00 3.01
2068 5175 3.055602 TGCTAGTGTGCACATGAATCTCT 60.056 43.478 24.69 15.46 38.12 3.10
2311 5895 8.092687 CCTCATGACATATTGACAGATACATGA 58.907 37.037 0.00 0.00 39.03 3.07
2327 5947 8.982685 CAGATACATGACATTCGCTAATAACTT 58.017 33.333 0.00 0.00 0.00 2.66
2363 5983 1.112113 TGTAGTACCAGCAGCTAGGC 58.888 55.000 9.99 0.00 0.00 3.93
2422 6050 8.964476 ATAGTTGTTAACCTTGATACATCCAG 57.036 34.615 2.48 0.00 0.00 3.86
2498 6224 9.344772 TGTGTGGTTTGTACTTTGAGTTATATT 57.655 29.630 0.00 0.00 0.00 1.28
3086 6814 2.030412 ATCGTGCTGACCAACGCA 59.970 55.556 0.00 0.00 0.00 5.24
3114 6842 3.461773 CGGGGGATCTGCTGTCGT 61.462 66.667 0.00 0.00 0.00 4.34
3464 7192 0.956633 CGGCCCAGATTGATTGGATG 59.043 55.000 0.00 0.00 37.96 3.51
3528 7256 7.726033 TTGCATGGGTTTATTAGTATGGTTT 57.274 32.000 0.00 0.00 0.00 3.27
3529 7257 8.824756 TTGCATGGGTTTATTAGTATGGTTTA 57.175 30.769 0.00 0.00 0.00 2.01
3530 7258 9.427821 TTGCATGGGTTTATTAGTATGGTTTAT 57.572 29.630 0.00 0.00 0.00 1.40
3531 7259 9.073475 TGCATGGGTTTATTAGTATGGTTTATC 57.927 33.333 0.00 0.00 0.00 1.75
3532 7260 9.073475 GCATGGGTTTATTAGTATGGTTTATCA 57.927 33.333 0.00 0.00 0.00 2.15
3555 7292 7.419385 TCAGTATGTAACTCTGGTGAGTGTGT 61.419 42.308 0.00 0.00 44.79 3.72
3648 7388 9.226345 GCTTGTAGCAAAATCAATATGTTACTC 57.774 33.333 0.00 0.00 41.89 2.59
3649 7389 9.722056 CTTGTAGCAAAATCAATATGTTACTCC 57.278 33.333 0.00 0.00 33.55 3.85
3650 7390 8.220755 TGTAGCAAAATCAATATGTTACTCCC 57.779 34.615 0.00 0.00 33.55 4.30
3651 7391 8.052748 TGTAGCAAAATCAATATGTTACTCCCT 58.947 33.333 0.00 0.00 33.55 4.20
3652 7392 7.573968 AGCAAAATCAATATGTTACTCCCTC 57.426 36.000 0.00 0.00 0.00 4.30
3653 7393 7.349598 AGCAAAATCAATATGTTACTCCCTCT 58.650 34.615 0.00 0.00 0.00 3.69
3654 7394 7.284034 AGCAAAATCAATATGTTACTCCCTCTG 59.716 37.037 0.00 0.00 0.00 3.35
3655 7395 7.067494 GCAAAATCAATATGTTACTCCCTCTGT 59.933 37.037 0.00 0.00 0.00 3.41
3656 7396 8.616076 CAAAATCAATATGTTACTCCCTCTGTC 58.384 37.037 0.00 0.00 0.00 3.51
3657 7397 5.871396 TCAATATGTTACTCCCTCTGTCC 57.129 43.478 0.00 0.00 0.00 4.02
3658 7398 4.654262 TCAATATGTTACTCCCTCTGTCCC 59.346 45.833 0.00 0.00 0.00 4.46
3659 7399 2.642171 ATGTTACTCCCTCTGTCCCA 57.358 50.000 0.00 0.00 0.00 4.37
3660 7400 2.642171 TGTTACTCCCTCTGTCCCAT 57.358 50.000 0.00 0.00 0.00 4.00
3661 7401 3.769189 TGTTACTCCCTCTGTCCCATA 57.231 47.619 0.00 0.00 0.00 2.74
3662 7402 4.069312 TGTTACTCCCTCTGTCCCATAA 57.931 45.455 0.00 0.00 0.00 1.90
3663 7403 4.631234 TGTTACTCCCTCTGTCCCATAAT 58.369 43.478 0.00 0.00 0.00 1.28
3664 7404 4.408921 TGTTACTCCCTCTGTCCCATAATG 59.591 45.833 0.00 0.00 0.00 1.90
3665 7405 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
3666 7406 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
3667 7407 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
3668 7408 5.036916 ACTCCCTCTGTCCCATAATGTAAA 58.963 41.667 0.00 0.00 0.00 2.01
3669 7409 5.491078 ACTCCCTCTGTCCCATAATGTAAAA 59.509 40.000 0.00 0.00 0.00 1.52
3670 7410 5.751586 TCCCTCTGTCCCATAATGTAAAAC 58.248 41.667 0.00 0.00 0.00 2.43
3671 7411 4.574828 CCCTCTGTCCCATAATGTAAAACG 59.425 45.833 0.00 0.00 0.00 3.60
3672 7412 5.183228 CCTCTGTCCCATAATGTAAAACGT 58.817 41.667 0.00 0.00 0.00 3.99
3673 7413 5.646360 CCTCTGTCCCATAATGTAAAACGTT 59.354 40.000 0.00 0.00 0.00 3.99
3674 7414 6.150474 CCTCTGTCCCATAATGTAAAACGTTT 59.850 38.462 7.96 7.96 0.00 3.60
3675 7415 7.308951 CCTCTGTCCCATAATGTAAAACGTTTT 60.309 37.037 27.65 27.65 0.00 2.43
3676 7416 7.942990 TCTGTCCCATAATGTAAAACGTTTTT 58.057 30.769 29.42 15.16 0.00 1.94
3695 7435 4.355543 TTTTTGACACTGCACTGAAGTC 57.644 40.909 0.00 0.00 0.00 3.01
3696 7436 2.689553 TTGACACTGCACTGAAGTCA 57.310 45.000 0.00 0.00 37.43 3.41
3697 7437 2.689553 TGACACTGCACTGAAGTCAA 57.310 45.000 0.00 0.00 36.39 3.18
3698 7438 2.984562 TGACACTGCACTGAAGTCAAA 58.015 42.857 0.00 0.00 36.39 2.69
3699 7439 3.342719 TGACACTGCACTGAAGTCAAAA 58.657 40.909 0.00 0.00 36.39 2.44
3700 7440 3.755905 TGACACTGCACTGAAGTCAAAAA 59.244 39.130 0.00 0.00 36.39 1.94
3724 7464 9.688592 AAAACGTCTTATATTATAGAACGGAGG 57.311 33.333 17.17 0.00 0.00 4.30
3725 7465 7.388460 ACGTCTTATATTATAGAACGGAGGG 57.612 40.000 17.17 0.30 0.00 4.30
3726 7466 7.170965 ACGTCTTATATTATAGAACGGAGGGA 58.829 38.462 17.17 0.00 0.00 4.20
3727 7467 7.336427 ACGTCTTATATTATAGAACGGAGGGAG 59.664 40.741 17.17 0.00 0.00 4.30
3728 7468 7.336427 CGTCTTATATTATAGAACGGAGGGAGT 59.664 40.741 10.03 0.00 0.00 3.85
3975 10416 0.108089 ACCCATTATACGCACACGCA 60.108 50.000 0.00 0.00 45.53 5.24
3978 10419 2.803386 CCCATTATACGCACACGCAATA 59.197 45.455 0.00 0.00 45.53 1.90
3998 10439 1.000896 CATGGCGGAAGAGGGGTTT 60.001 57.895 0.00 0.00 0.00 3.27
4033 10474 1.280133 CTTGTCAGGAAGGAGGCATCA 59.720 52.381 0.00 0.00 0.00 3.07
4034 10475 1.361204 TGTCAGGAAGGAGGCATCAA 58.639 50.000 0.00 0.00 0.00 2.57
4035 10476 1.918262 TGTCAGGAAGGAGGCATCAAT 59.082 47.619 0.00 0.00 0.00 2.57
4036 10477 2.092753 TGTCAGGAAGGAGGCATCAATC 60.093 50.000 0.00 0.00 0.00 2.67
4037 10478 2.092753 GTCAGGAAGGAGGCATCAATCA 60.093 50.000 0.00 0.00 0.00 2.57
4129 10613 0.036164 AAGAGTACATGCACGGCCAA 59.964 50.000 2.24 0.00 0.00 4.52
4139 10623 1.725066 CACGGCCAAACGTTGAAGT 59.275 52.632 0.00 0.00 46.25 3.01
4149 10633 0.179105 ACGTTGAAGTACGCACACCA 60.179 50.000 0.00 0.00 45.06 4.17
4161 10645 3.161450 ACACCACACGCTCACCCT 61.161 61.111 0.00 0.00 0.00 4.34
4164 10648 2.283529 ACCACACGCTCACCCTAGG 61.284 63.158 0.06 0.06 0.00 3.02
4191 10675 0.390340 GCGCACACAAGAGAGATGGA 60.390 55.000 0.30 0.00 0.00 3.41
4194 10678 2.354259 GCACACAAGAGAGATGGAAGG 58.646 52.381 0.00 0.00 0.00 3.46
4197 10681 2.373169 ACACAAGAGAGATGGAAGGCAA 59.627 45.455 0.00 0.00 0.00 4.52
4201 10685 1.012841 GAGAGATGGAAGGCAAAGCG 58.987 55.000 0.00 0.00 0.00 4.68
4232 10716 1.002468 ACTCACGCATCACACAAAAGC 60.002 47.619 0.00 0.00 0.00 3.51
4235 10719 0.316937 ACGCATCACACAAAAGCACG 60.317 50.000 0.00 0.00 0.00 5.34
4236 10720 1.599422 CGCATCACACAAAAGCACGC 61.599 55.000 0.00 0.00 0.00 5.34
4242 10726 0.455972 ACACAAAAGCACGCACACAC 60.456 50.000 0.00 0.00 0.00 3.82
4243 10727 0.179166 CACAAAAGCACGCACACACT 60.179 50.000 0.00 0.00 0.00 3.55
4274 10758 1.468520 CACACAACATTCCCGATGGTC 59.531 52.381 0.00 0.00 40.21 4.02
4279 10763 2.106332 ATTCCCGATGGTCGCGAC 59.894 61.111 30.67 30.67 38.82 5.19
4288 10772 2.534939 CGATGGTCGCGACTTGATTTTC 60.535 50.000 35.50 18.49 31.14 2.29
4294 10778 2.875933 TCGCGACTTGATTTTCTTGGTT 59.124 40.909 3.71 0.00 0.00 3.67
4311 10795 6.469410 TCTTGGTTACTGTATTCAATTCCGT 58.531 36.000 0.00 0.00 0.00 4.69
4386 10870 4.401519 CACTCTAAAGTATCCCTTCGGTGA 59.598 45.833 0.00 0.00 33.25 4.02
4409 10893 3.951563 CAAATATGGAGGTTGGGAGGA 57.048 47.619 0.00 0.00 0.00 3.71
4425 10909 1.472878 GAGGAAGGCGTTGGGATTTTC 59.527 52.381 0.00 0.00 0.00 2.29
4438 10922 3.560636 GGATTTTCCCGAAGAGGATGA 57.439 47.619 0.00 0.00 45.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.453136 TGTACAACTAGGAACGAAAATGGC 59.547 41.667 0.00 0.00 0.00 4.40
198 201 1.888512 AGGTTGTGGCTTGCACTAATG 59.111 47.619 0.00 0.00 0.00 1.90
417 423 8.832521 AGAACAGAACAAAATGATGTACGTAAA 58.167 29.630 0.00 0.00 32.02 2.01
421 427 8.560576 AAAAGAACAGAACAAAATGATGTACG 57.439 30.769 0.00 0.00 32.02 3.67
503 509 9.056005 TGCATAGCATTGTATCCTTAGTTTAAG 57.944 33.333 0.00 0.00 31.71 1.85
665 2775 2.032894 CGCGTGTGAAGACTTTTCATGT 60.033 45.455 0.00 0.00 0.00 3.21
686 2796 4.978099 TGATGAGATTAATTGCTCTCCCC 58.022 43.478 13.49 7.98 37.66 4.81
764 2874 0.958091 CGATGTTGTTTGCTTGGGGA 59.042 50.000 0.00 0.00 0.00 4.81
964 3084 0.250467 AGTGTGTGCCTGTGTGGATC 60.250 55.000 0.00 0.00 38.35 3.36
965 3085 0.250467 GAGTGTGTGCCTGTGTGGAT 60.250 55.000 0.00 0.00 38.35 3.41
966 3086 1.146041 GAGTGTGTGCCTGTGTGGA 59.854 57.895 0.00 0.00 38.35 4.02
970 3090 0.249447 TCTTCGAGTGTGTGCCTGTG 60.249 55.000 0.00 0.00 0.00 3.66
971 3091 0.032678 CTCTTCGAGTGTGTGCCTGT 59.967 55.000 0.00 0.00 0.00 4.00
974 3094 1.140816 GTTCTCTTCGAGTGTGTGCC 58.859 55.000 0.00 0.00 0.00 5.01
975 3095 1.852942 TGTTCTCTTCGAGTGTGTGC 58.147 50.000 0.00 0.00 0.00 4.57
976 3096 3.642705 TGATGTTCTCTTCGAGTGTGTG 58.357 45.455 0.00 0.00 0.00 3.82
977 3097 4.322080 TTGATGTTCTCTTCGAGTGTGT 57.678 40.909 0.00 0.00 0.00 3.72
978 3098 5.657470 TTTTGATGTTCTCTTCGAGTGTG 57.343 39.130 0.00 0.00 0.00 3.82
985 3105 6.376978 CACTCACCATTTTGATGTTCTCTTC 58.623 40.000 0.00 0.00 0.00 2.87
992 3112 1.068333 GCGCACTCACCATTTTGATGT 60.068 47.619 0.30 0.00 0.00 3.06
1060 3193 6.627690 ACGAGTAATATGAACAACACGAAG 57.372 37.500 0.00 0.00 31.72 3.79
1064 3197 6.021153 GGACGTACGAGTAATATGAACAACAC 60.021 42.308 24.41 0.00 0.00 3.32
1850 4077 3.988379 AGCAGTACATGTTTTGTGGTG 57.012 42.857 2.30 0.00 39.48 4.17
1855 4082 2.668279 GCCGGAAGCAGTACATGTTTTG 60.668 50.000 5.05 4.18 42.97 2.44
1910 4137 1.747355 GCGCACCTTGTAGTAGGACTA 59.253 52.381 0.30 0.00 38.73 2.59
1912 4139 0.459759 GGCGCACCTTGTAGTAGGAC 60.460 60.000 10.83 0.00 38.73 3.85
1914 4141 0.739813 GTGGCGCACCTTGTAGTAGG 60.740 60.000 10.83 0.00 41.31 3.18
1915 4142 0.037697 TGTGGCGCACCTTGTAGTAG 60.038 55.000 10.83 0.00 36.63 2.57
1927 4446 2.187599 CTACAAGGTTGCTGTGGCGC 62.188 60.000 0.00 0.00 42.25 6.53
1955 4741 1.002544 CCCAGTCCTCAACTCTTGACC 59.997 57.143 0.00 0.00 35.45 4.02
2014 4801 2.364780 CCCCAACTCCCCGGTCTAC 61.365 68.421 0.00 0.00 0.00 2.59
2028 5135 2.358619 CCCAGAAATTCGCCCCCA 59.641 61.111 0.00 0.00 0.00 4.96
2104 5641 7.238710 ACCTCTGTACCAGGAAAACATATTTT 58.761 34.615 13.68 0.00 40.83 1.82
2311 5895 8.902540 TGATTGGATAAGTTATTAGCGAATGT 57.097 30.769 1.88 0.00 36.32 2.71
2327 5947 7.071824 TGGTACTACATGTTGGATGATTGGATA 59.928 37.037 2.30 0.00 0.00 2.59
2363 5983 7.017645 CGATTAATCTTGTGTGAGTTTTGGAG 58.982 38.462 13.45 0.00 0.00 3.86
2422 6050 4.379793 CAGCGTTTTGACTAATTTGAGTGC 59.620 41.667 0.00 0.00 0.00 4.40
2746 6474 1.484240 GGTTGGAGATCACAGGAGGAG 59.516 57.143 0.00 0.00 0.00 3.69
3555 7292 7.490840 CCATGCTGGTTGATAATTAAATGACA 58.509 34.615 0.00 0.00 31.35 3.58
3674 7414 3.755905 TGACTTCAGTGCAGTGTCAAAAA 59.244 39.130 20.73 6.90 35.15 1.94
3675 7415 3.342719 TGACTTCAGTGCAGTGTCAAAA 58.657 40.909 20.73 7.26 35.15 2.44
3676 7416 2.984562 TGACTTCAGTGCAGTGTCAAA 58.015 42.857 20.73 7.61 35.15 2.69
3677 7417 2.689553 TGACTTCAGTGCAGTGTCAA 57.310 45.000 20.73 8.32 35.15 3.18
3678 7418 2.689553 TTGACTTCAGTGCAGTGTCA 57.310 45.000 20.73 14.32 36.10 3.58
3679 7419 4.355543 TTTTTGACTTCAGTGCAGTGTC 57.644 40.909 20.73 11.92 0.00 3.67
3698 7438 9.688592 CCTCCGTTCTATAATATAAGACGTTTT 57.311 33.333 11.48 0.00 0.00 2.43
3699 7439 8.302438 CCCTCCGTTCTATAATATAAGACGTTT 58.698 37.037 11.48 0.00 0.00 3.60
3700 7440 7.667219 TCCCTCCGTTCTATAATATAAGACGTT 59.333 37.037 11.48 0.00 0.00 3.99
3701 7441 7.170965 TCCCTCCGTTCTATAATATAAGACGT 58.829 38.462 11.48 0.00 0.00 4.34
3702 7442 7.336427 ACTCCCTCCGTTCTATAATATAAGACG 59.664 40.741 7.63 7.63 0.00 4.18
3703 7443 8.578448 ACTCCCTCCGTTCTATAATATAAGAC 57.422 38.462 0.00 0.00 0.00 3.01
3713 7453 9.543231 TTCAATAATATACTCCCTCCGTTCTAT 57.457 33.333 0.00 0.00 0.00 1.98
3714 7454 8.945195 TTCAATAATATACTCCCTCCGTTCTA 57.055 34.615 0.00 0.00 0.00 2.10
3715 7455 7.850935 TTCAATAATATACTCCCTCCGTTCT 57.149 36.000 0.00 0.00 0.00 3.01
3716 7456 8.936864 CATTTCAATAATATACTCCCTCCGTTC 58.063 37.037 0.00 0.00 0.00 3.95
3717 7457 8.656806 TCATTTCAATAATATACTCCCTCCGTT 58.343 33.333 0.00 0.00 0.00 4.44
3718 7458 8.202461 TCATTTCAATAATATACTCCCTCCGT 57.798 34.615 0.00 0.00 0.00 4.69
3822 7562 5.984725 TCCATAATTCTTTGAAGGACGCTA 58.015 37.500 0.00 0.00 0.00 4.26
3975 10416 0.474184 CCCTCTTCCGCCATGGTATT 59.526 55.000 14.67 0.00 39.52 1.89
3978 10419 3.411517 CCCCTCTTCCGCCATGGT 61.412 66.667 14.67 0.00 39.52 3.55
3986 10427 0.476771 TGACACCAAACCCCTCTTCC 59.523 55.000 0.00 0.00 0.00 3.46
4017 10458 2.092753 GTGATTGATGCCTCCTTCCTGA 60.093 50.000 0.00 0.00 0.00 3.86
4083 10567 1.321474 CAATGTGGTGGTCTTGCAGT 58.679 50.000 0.00 0.00 0.00 4.40
4129 10613 0.932399 GGTGTGCGTACTTCAACGTT 59.068 50.000 4.97 0.00 44.64 3.99
4139 10623 2.355363 GAGCGTGTGGTGTGCGTA 60.355 61.111 0.00 0.00 0.00 4.42
4149 10633 3.760035 CGCCTAGGGTGAGCGTGT 61.760 66.667 11.72 0.00 44.65 4.49
4191 10675 1.943116 TTGTGTGTGCGCTTTGCCTT 61.943 50.000 9.73 0.00 45.60 4.35
4194 10678 1.515952 TGTTGTGTGTGCGCTTTGC 60.516 52.632 9.73 0.00 46.70 3.68
4197 10681 1.024046 TGAGTGTTGTGTGTGCGCTT 61.024 50.000 9.73 0.00 0.00 4.68
4201 10685 1.297598 GCGTGAGTGTTGTGTGTGC 60.298 57.895 0.00 0.00 0.00 4.57
4236 10720 1.223417 TGACGCATGAGCAGTGTGTG 61.223 55.000 0.00 0.00 40.14 3.82
4242 10726 0.110509 GTTGTGTGACGCATGAGCAG 60.111 55.000 0.00 0.00 42.27 4.24
4243 10727 0.813210 TGTTGTGTGACGCATGAGCA 60.813 50.000 0.00 0.00 42.27 4.26
4274 10758 2.969443 ACCAAGAAAATCAAGTCGCG 57.031 45.000 0.00 0.00 0.00 5.87
4288 10772 6.737254 ACGGAATTGAATACAGTAACCAAG 57.263 37.500 0.00 0.00 0.00 3.61
4294 10778 5.105635 ACCTCGAACGGAATTGAATACAGTA 60.106 40.000 0.00 0.00 0.00 2.74
4311 10795 3.502123 AATTTCCTCAACCACCTCGAA 57.498 42.857 0.00 0.00 0.00 3.71
4401 10885 2.434331 CCAACGCCTTCCTCCCAA 59.566 61.111 0.00 0.00 0.00 4.12
4403 10887 2.211468 AATCCCAACGCCTTCCTCCC 62.211 60.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.