Multiple sequence alignment - TraesCS3B01G251000

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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 TraesCS3B01G251000 chr3B 100.000 5546 0 0 1 5546 401404990 401410535 0.000000e+00 10242
1 TraesCS3B01G251000 chr3D 96.296 5454 140 22 1 5437 317559139 317553731 0.000000e+00 8896
2 TraesCS3B01G251000 chr3D 88.043 184 20 2 420 602 317558553 317558371 3.360000e-52 217
3 TraesCS3B01G251000 chr3A 96.403 4976 113 17 1 4949 447269719 447274655 0.000000e+00 8137
4 TraesCS3B01G251000 chr3A 97.010 2809 50 12 2148 4949 408942751 408945532 0.000000e+00 4691
5 TraesCS3B01G251000 chr3A 94.931 2170 60 10 1 2154 408940580 408942715 0.000000e+00 3352
6 TraesCS3B01G251000 chr3A 97.321 336 5 2 4949 5280 408945815 408946150 8.060000e-158 568
7 TraesCS3B01G251000 chr3A 93.865 163 6 1 5277 5439 408946472 408946630 5.550000e-60 243
8 TraesCS3B01G251000 chr3A 87.317 205 23 3 400 602 408941149 408941352 1.200000e-56 231
9 TraesCS3B01G251000 chr3A 87.317 205 23 3 400 602 447270304 447270507 1.200000e-56 231
10 TraesCS3B01G251000 chr6A 83.849 1325 143 31 3830 5119 1463712 1462424 0.000000e+00 1195
11 TraesCS3B01G251000 chr6A 85.046 1090 116 15 2651 3730 1464766 1463714 0.000000e+00 1066
12 TraesCS3B01G251000 chr6A 83.803 142 22 1 3665 3806 452630057 452630197 3.490000e-27 134
13 TraesCS3B01G251000 chr6D 87.556 450 53 2 3059 3505 465354323 465353874 8.240000e-143 518
14 TraesCS3B01G251000 chr6D 86.444 450 56 3 3059 3505 465352800 465352353 6.460000e-134 488
15 TraesCS3B01G251000 chr4B 84.698 464 53 7 3452 3911 669916317 669915868 1.100000e-121 448
16 TraesCS3B01G251000 chr4B 82.960 446 59 6 3470 3911 669914427 669913995 2.420000e-103 387
17 TraesCS3B01G251000 chr4B 83.099 426 52 12 3268 3689 669912450 669912041 2.440000e-98 370
18 TraesCS3B01G251000 chr4B 82.974 417 52 8 3274 3686 669910747 669911148 5.280000e-95 359
19 TraesCS3B01G251000 chr4B 85.390 308 42 1 3866 4170 669916485 669916792 3.220000e-82 316
20 TraesCS3B01G251000 chr4B 82.000 300 35 9 3360 3654 669912041 669911756 2.580000e-58 237
21 TraesCS3B01G251000 chr5B 99.091 110 1 0 5437 5546 344300954 344301063 1.220000e-46 198
22 TraesCS3B01G251000 chr4A 95.536 112 5 0 5435 5546 21847479 21847590 4.410000e-41 180
23 TraesCS3B01G251000 chr7B 94.017 117 7 0 5430 5546 140609538 140609422 1.590000e-40 178
24 TraesCS3B01G251000 chr7B 90.076 131 8 5 5417 5546 540780766 540780640 1.240000e-36 165
25 TraesCS3B01G251000 chr2A 93.333 120 6 2 5428 5546 749872868 749872750 5.710000e-40 176
26 TraesCS3B01G251000 chr7A 93.220 118 7 1 5429 5546 231553495 231553611 7.390000e-39 172
27 TraesCS3B01G251000 chr7A 90.000 130 12 1 5417 5546 663538341 663538213 3.440000e-37 167
28 TraesCS3B01G251000 chr1A 92.500 120 9 0 5427 5546 481650965 481651084 7.390000e-39 172
29 TraesCS3B01G251000 chr2B 89.313 131 13 1 5416 5546 392896828 392896957 4.450000e-36 163
30 TraesCS3B01G251000 chr2B 85.827 127 17 1 4106 4231 114043405 114043531 3.490000e-27 134


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 TraesCS3B01G251000 chr3B 401404990 401410535 5545 False 10242.0 10242 100.00000 1 5546 1 chr3B.!!$F1 5545
1 TraesCS3B01G251000 chr3D 317553731 317559139 5408 True 4556.5 8896 92.16950 1 5437 2 chr3D.!!$R1 5436
2 TraesCS3B01G251000 chr3A 447269719 447274655 4936 False 8137.0 8137 96.40300 1 4949 1 chr3A.!!$F1 4948
3 TraesCS3B01G251000 chr3A 408940580 408946630 6050 False 1817.0 4691 94.08880 1 5439 5 chr3A.!!$F3 5438
4 TraesCS3B01G251000 chr6A 1462424 1464766 2342 True 1130.5 1195 84.44750 2651 5119 2 chr6A.!!$R1 2468
5 TraesCS3B01G251000 chr6D 465352353 465354323 1970 True 503.0 518 87.00000 3059 3505 2 chr6D.!!$R1 446
6 TraesCS3B01G251000 chr4B 669911756 669916317 4561 True 360.5 448 83.18925 3268 3911 4 chr4B.!!$R1 643

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
285 296 0.398522 AGACCCACACCTCACACTCA 60.399 55.000 0.00 0.0 0.00 3.41 F
799 825 1.115467 AGAAGATGTGGGCTAGACCG 58.885 55.000 10.91 0.0 40.62 4.79 F
1468 1495 0.893270 CAAACCACCGCCTCATCCAA 60.893 55.000 0.00 0.0 0.00 3.53 F
1989 2016 0.401738 CCCCTGTTCCTGCTCAAGAA 59.598 55.000 0.00 0.0 0.00 2.52 F
3004 3076 0.108615 CGTGCAGTCTTACCTGGAGG 60.109 60.000 0.00 0.0 42.17 4.30 F
3300 3378 3.347216 GCTCTACAGGAATCTTGCCAAA 58.653 45.455 0.00 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1237 1264 0.176680 TTGAGGAAGATCTCTGCGCC 59.823 55.000 4.18 0.0 34.98 6.53 R
1983 2010 0.537188 GATCGCCTCCCTGTTCTTGA 59.463 55.000 0.00 0.0 0.00 3.02 R
2541 2613 0.723414 CGTACACATGCTGAAGCCAG 59.277 55.000 0.00 0.0 43.22 4.85 R
3300 3378 2.262774 CTCCATCCTTGCCTTCGCCT 62.263 60.000 0.00 0.0 0.00 5.52 R
4150 7187 3.130633 CACTGTTCATGTCGTTGAAGGA 58.869 45.455 0.00 0.0 36.34 3.36 R
5045 8653 4.286032 TCACCTGGCATGTTTAGTAGTTCT 59.714 41.667 0.00 0.0 0.00 3.01 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
158 159 3.515602 ACTGTGGCTCTTTTCCTCAAT 57.484 42.857 0.00 0.00 0.00 2.57
285 296 0.398522 AGACCCACACCTCACACTCA 60.399 55.000 0.00 0.00 0.00 3.41
417 434 1.287191 CCGCCTGATCATCGACGAT 59.713 57.895 16.18 4.05 0.00 3.73
441 458 4.353437 GACGACGACGGCCACCTT 62.353 66.667 12.58 0.00 42.35 3.50
638 664 4.668118 GGTCGCCACGGTCGGAAA 62.668 66.667 0.00 0.00 0.00 3.13
677 703 3.369400 CGCCGGGGATTTGTTGCA 61.369 61.111 14.46 0.00 0.00 4.08
773 799 1.144565 GAGATCTCCGACGACGACGA 61.145 60.000 20.63 4.95 42.66 4.20
789 815 4.230657 ACGACGAAGAAGAAGAAGATGTG 58.769 43.478 0.00 0.00 0.00 3.21
793 819 3.618507 CGAAGAAGAAGAAGATGTGGGCT 60.619 47.826 0.00 0.00 0.00 5.19
799 825 1.115467 AGAAGATGTGGGCTAGACCG 58.885 55.000 10.91 0.00 40.62 4.79
909 936 2.461945 CGAGAGTACGAGCAGCGGA 61.462 63.158 4.06 0.00 46.49 5.54
930 957 1.153168 CCCCGATGGAACGAGCAAT 60.153 57.895 0.00 0.00 35.39 3.56
972 999 2.359169 GGGTGCCTCTGACGATGGA 61.359 63.158 0.00 0.00 0.00 3.41
1192 1219 2.182842 GTGCTTAGCGATGCCAGGG 61.183 63.158 0.00 0.00 0.00 4.45
1468 1495 0.893270 CAAACCACCGCCTCATCCAA 60.893 55.000 0.00 0.00 0.00 3.53
1563 1590 1.035923 ACGCCGATGATGACTCTGAT 58.964 50.000 0.00 0.00 0.00 2.90
1616 1643 1.659794 GACAAAACGCTGCCCACAT 59.340 52.632 0.00 0.00 0.00 3.21
1641 1668 1.071857 GAAGACTTTGAGGAACCCGGT 59.928 52.381 0.00 0.00 0.00 5.28
1826 1853 2.071262 CAGAGGGATGGGAGCAGCT 61.071 63.158 0.00 0.00 0.00 4.24
1830 1857 3.415087 GGATGGGAGCAGCTGGGT 61.415 66.667 17.12 1.25 0.00 4.51
1983 2010 4.021925 GACGCCCCTGTTCCTGCT 62.022 66.667 0.00 0.00 0.00 4.24
1985 2012 4.020617 CGCCCCTGTTCCTGCTCA 62.021 66.667 0.00 0.00 0.00 4.26
1989 2016 0.401738 CCCCTGTTCCTGCTCAAGAA 59.598 55.000 0.00 0.00 0.00 2.52
2126 2153 1.343142 GGCCGAATCCAACAAGGTTTT 59.657 47.619 0.00 0.00 39.02 2.43
2193 2265 5.931146 TGTGAATTAATTGTCCAATTGTGCC 59.069 36.000 14.02 3.81 40.83 5.01
2211 2283 3.882288 GTGCCACAATTTTTGGTTTGGAT 59.118 39.130 3.64 0.00 36.40 3.41
2224 2296 7.513371 TTTGGTTTGGATCAGTTACGTTTAT 57.487 32.000 0.00 0.00 0.00 1.40
2340 2412 6.863126 AGAACAACACTTTTGTTTCAGTTCTG 59.137 34.615 15.46 0.00 45.57 3.02
2364 2436 2.716217 ACAAGCTAGTGATCCCTTTGC 58.284 47.619 0.00 0.00 0.00 3.68
2470 2542 3.883631 TTCATGATGATCAAATCGGCG 57.116 42.857 0.00 0.00 0.00 6.46
2561 2633 1.298157 TGGCTTCAGCATGTGTACGC 61.298 55.000 0.00 0.00 44.36 4.42
2584 2656 4.084013 CCAGTACGTGTTTCCATTGACTTC 60.084 45.833 0.00 0.00 0.00 3.01
2609 2681 9.806448 TCTCTAGAAATAGAGAGCATCAATACT 57.194 33.333 10.25 0.00 45.38 2.12
2617 2689 9.941325 AATAGAGAGCATCAATACTTCAATAGG 57.059 33.333 0.00 0.00 37.82 2.57
2618 2690 6.229733 AGAGAGCATCAATACTTCAATAGGC 58.770 40.000 0.00 0.00 37.82 3.93
2619 2691 5.933617 AGAGCATCAATACTTCAATAGGCA 58.066 37.500 0.00 0.00 37.82 4.75
2620 2692 5.762218 AGAGCATCAATACTTCAATAGGCAC 59.238 40.000 0.00 0.00 37.82 5.01
2621 2693 4.823989 AGCATCAATACTTCAATAGGCACC 59.176 41.667 0.00 0.00 0.00 5.01
2622 2694 4.823989 GCATCAATACTTCAATAGGCACCT 59.176 41.667 0.00 0.00 0.00 4.00
2670 2742 2.673775 TTCAACAGGCCAAGGAATCA 57.326 45.000 5.01 0.00 0.00 2.57
2745 2817 6.115446 TGACATCCTGAAATCAGTTGGATAC 58.885 40.000 9.43 5.20 42.27 2.24
3004 3076 0.108615 CGTGCAGTCTTACCTGGAGG 60.109 60.000 0.00 0.00 42.17 4.30
3300 3378 3.347216 GCTCTACAGGAATCTTGCCAAA 58.653 45.455 0.00 0.00 0.00 3.28
3486 3564 4.673968 TCCAGAACAACTTCCTAGAGCTA 58.326 43.478 0.00 0.00 0.00 3.32
3499 3580 5.389520 TCCTAGAGCTATACATCTTGTGCT 58.610 41.667 0.00 0.00 31.05 4.40
4452 7489 0.249073 CTACCGGGAGCAATCTGTCG 60.249 60.000 0.00 0.00 0.00 4.35
4480 7517 9.381033 CAGAACTGATATCCAATGATAGGATTC 57.619 37.037 0.00 0.10 43.21 2.52
4563 7656 6.293845 CCCATTGACTGCAGAAATTATAGCTC 60.294 42.308 23.35 3.53 0.00 4.09
4715 7992 6.256757 CGGAATCTTCAGAGTCTCCAAATAAC 59.743 42.308 4.39 0.00 38.97 1.89
5045 8653 3.107601 AGCTTAAGAGACCTACCATGCA 58.892 45.455 6.67 0.00 0.00 3.96
5355 9295 5.357878 TGCAATTTCATGGGATCTCAACTAC 59.642 40.000 0.00 0.00 0.00 2.73
5356 9296 5.504665 GCAATTTCATGGGATCTCAACTACG 60.505 44.000 0.00 0.00 0.00 3.51
5357 9297 4.819105 TTTCATGGGATCTCAACTACGT 57.181 40.909 0.00 0.00 0.00 3.57
5358 9298 5.925506 TTTCATGGGATCTCAACTACGTA 57.074 39.130 0.00 0.00 0.00 3.57
5447 9764 8.586879 ATTACTTAAACTAGTACTTCCTCCGT 57.413 34.615 0.00 0.00 30.62 4.69
5448 9765 6.507958 ACTTAAACTAGTACTTCCTCCGTC 57.492 41.667 0.00 0.00 0.00 4.79
5449 9766 5.417266 ACTTAAACTAGTACTTCCTCCGTCC 59.583 44.000 0.00 0.00 0.00 4.79
5450 9767 2.035530 ACTAGTACTTCCTCCGTCCG 57.964 55.000 0.00 0.00 0.00 4.79
5451 9768 1.556911 ACTAGTACTTCCTCCGTCCGA 59.443 52.381 0.00 0.00 0.00 4.55
5452 9769 2.026822 ACTAGTACTTCCTCCGTCCGAA 60.027 50.000 0.00 0.00 0.00 4.30
5454 9771 2.242043 AGTACTTCCTCCGTCCGAAAA 58.758 47.619 0.00 0.00 0.00 2.29
5455 9772 2.830321 AGTACTTCCTCCGTCCGAAAAT 59.170 45.455 0.00 0.00 0.00 1.82
5456 9773 4.019174 AGTACTTCCTCCGTCCGAAAATA 58.981 43.478 0.00 0.00 0.00 1.40
5457 9774 3.242549 ACTTCCTCCGTCCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
5458 9775 2.830321 ACTTCCTCCGTCCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
5460 9777 3.241067 TCCTCCGTCCGAAAATACTTG 57.759 47.619 0.00 0.00 0.00 3.16
5461 9778 2.564062 TCCTCCGTCCGAAAATACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
5462 9779 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5467 9784 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
5468 9785 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
5469 9786 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
5470 9787 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
5471 9788 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
5472 9789 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
5473 9790 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
5476 9793 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
5477 9794 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
5478 9795 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
5479 9796 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
5480 9797 7.538303 ACTTGTCATCAAAATGGACAAAAAC 57.462 32.000 7.70 0.00 34.98 2.43
5481 9798 7.102346 ACTTGTCATCAAAATGGACAAAAACA 58.898 30.769 7.70 0.00 34.98 2.83
5482 9799 7.278424 ACTTGTCATCAAAATGGACAAAAACAG 59.722 33.333 7.70 0.00 34.98 3.16
5483 9800 6.047870 TGTCATCAAAATGGACAAAAACAGG 58.952 36.000 0.00 0.00 33.42 4.00
5484 9801 6.048509 GTCATCAAAATGGACAAAAACAGGT 58.951 36.000 0.00 0.00 33.42 4.00
5485 9802 6.018832 GTCATCAAAATGGACAAAAACAGGTG 60.019 38.462 0.00 0.00 33.42 4.00
5486 9803 5.413309 TCAAAATGGACAAAAACAGGTGT 57.587 34.783 0.00 0.00 0.00 4.16
5487 9804 6.531503 TCAAAATGGACAAAAACAGGTGTA 57.468 33.333 0.00 0.00 0.00 2.90
5489 9806 7.206687 TCAAAATGGACAAAAACAGGTGTATC 58.793 34.615 0.00 0.00 0.00 2.24
5490 9807 6.976934 AAATGGACAAAAACAGGTGTATCT 57.023 33.333 0.00 0.00 0.00 1.98
5491 9808 8.356657 CAAAATGGACAAAAACAGGTGTATCTA 58.643 33.333 0.00 0.00 0.00 1.98
5492 9809 7.687941 AATGGACAAAAACAGGTGTATCTAG 57.312 36.000 0.00 0.00 0.00 2.43
5494 9811 6.833041 TGGACAAAAACAGGTGTATCTAGAA 58.167 36.000 0.00 0.00 0.00 2.10
5495 9812 6.708949 TGGACAAAAACAGGTGTATCTAGAAC 59.291 38.462 0.00 0.00 0.00 3.01
5496 9813 6.935208 GGACAAAAACAGGTGTATCTAGAACT 59.065 38.462 0.00 0.00 0.00 3.01
5497 9814 8.092687 GGACAAAAACAGGTGTATCTAGAACTA 58.907 37.037 0.00 0.00 0.00 2.24
5498 9815 9.485206 GACAAAAACAGGTGTATCTAGAACTAA 57.515 33.333 0.00 0.00 0.00 2.24
5499 9816 9.841295 ACAAAAACAGGTGTATCTAGAACTAAA 57.159 29.630 0.00 0.00 0.00 1.85
5504 9821 9.798994 AACAGGTGTATCTAGAACTAAAATACG 57.201 33.333 0.00 0.00 0.00 3.06
5505 9822 8.964772 ACAGGTGTATCTAGAACTAAAATACGT 58.035 33.333 0.00 0.00 0.00 3.57
5506 9823 9.448294 CAGGTGTATCTAGAACTAAAATACGTC 57.552 37.037 0.00 0.00 0.00 4.34
5514 9831 9.117183 TCTAGAACTAAAATACGTCTAGATGCA 57.883 33.333 12.04 0.00 32.48 3.96
5515 9832 9.900710 CTAGAACTAAAATACGTCTAGATGCAT 57.099 33.333 12.04 0.00 0.00 3.96
5516 9833 8.804688 AGAACTAAAATACGTCTAGATGCATC 57.195 34.615 19.37 19.37 0.00 3.91
5518 9835 6.456501 ACTAAAATACGTCTAGATGCATCCC 58.543 40.000 23.06 7.99 0.00 3.85
5519 9836 3.963428 AATACGTCTAGATGCATCCCC 57.037 47.619 23.06 7.64 0.00 4.81
5521 9838 1.794714 ACGTCTAGATGCATCCCCTT 58.205 50.000 23.06 7.24 0.00 3.95
5522 9839 2.119495 ACGTCTAGATGCATCCCCTTT 58.881 47.619 23.06 6.85 0.00 3.11
5523 9840 2.505819 ACGTCTAGATGCATCCCCTTTT 59.494 45.455 23.06 6.10 0.00 2.27
5524 9841 3.709653 ACGTCTAGATGCATCCCCTTTTA 59.290 43.478 23.06 6.97 0.00 1.52
5525 9842 4.348168 ACGTCTAGATGCATCCCCTTTTAT 59.652 41.667 23.06 4.58 0.00 1.40
5526 9843 4.932200 CGTCTAGATGCATCCCCTTTTATC 59.068 45.833 23.06 0.00 0.00 1.75
5529 9846 6.944862 GTCTAGATGCATCCCCTTTTATCAAT 59.055 38.462 23.06 2.35 0.00 2.57
5532 9849 7.441903 AGATGCATCCCCTTTTATCAATTTT 57.558 32.000 23.06 0.00 0.00 1.82
5533 9850 7.277396 AGATGCATCCCCTTTTATCAATTTTG 58.723 34.615 23.06 0.00 0.00 2.44
5534 9851 6.617782 TGCATCCCCTTTTATCAATTTTGA 57.382 33.333 0.00 0.00 42.14 2.69
5536 9853 7.049133 TGCATCCCCTTTTATCAATTTTGATG 58.951 34.615 14.54 0.00 46.68 3.07
5538 9855 7.225341 GCATCCCCTTTTATCAATTTTGATGAC 59.775 37.037 14.54 0.00 46.68 3.06
5539 9856 7.789202 TCCCCTTTTATCAATTTTGATGACA 57.211 32.000 14.54 0.90 46.68 3.58
5541 9858 8.313292 TCCCCTTTTATCAATTTTGATGACAAG 58.687 33.333 14.54 12.31 46.68 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 1.179174 AGAGCCACAGTAGCACGTCA 61.179 55.000 0.00 0.00 0.00 4.35
158 159 1.609501 AGCGGAGTAGCCCTTCACA 60.610 57.895 0.00 0.00 38.01 3.58
565 582 2.356793 GATGATCTCGGCGGGCTG 60.357 66.667 7.21 0.00 0.00 4.85
588 605 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
589 606 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
590 607 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
591 608 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
592 609 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
593 610 4.064491 GGTCGTCGTCGTCGTCGT 62.064 66.667 18.44 0.00 45.27 4.34
733 759 4.496336 GATCTTGGCGGGCTGGCT 62.496 66.667 21.38 0.00 45.14 4.75
773 799 4.780021 TCTAGCCCACATCTTCTTCTTCTT 59.220 41.667 0.00 0.00 0.00 2.52
814 841 0.749649 ATGTCATCGACAGGCTCCTC 59.250 55.000 2.95 0.00 46.04 3.71
909 936 3.470888 CTCGTTCCATCGGGGCCT 61.471 66.667 0.84 0.00 36.21 5.19
930 957 0.108804 GCCGACTCGTCTCAATTCCA 60.109 55.000 0.00 0.00 0.00 3.53
972 999 2.018086 CTCCTCCCCCTCCTCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
1232 1259 4.887987 AGATCTCTGCGCCGCTGC 62.888 66.667 11.67 1.30 0.00 5.25
1233 1260 2.202851 AAGATCTCTGCGCCGCTG 60.203 61.111 11.67 10.72 0.00 5.18
1234 1261 2.105930 GAAGATCTCTGCGCCGCT 59.894 61.111 11.67 0.00 0.00 5.52
1235 1262 2.964389 GGAAGATCTCTGCGCCGC 60.964 66.667 4.18 0.00 0.00 6.53
1236 1263 1.299773 GAGGAAGATCTCTGCGCCG 60.300 63.158 4.18 0.00 0.00 6.46
1237 1264 0.176680 TTGAGGAAGATCTCTGCGCC 59.823 55.000 4.18 0.00 34.98 6.53
1238 1265 1.569708 CTTGAGGAAGATCTCTGCGC 58.430 55.000 0.00 0.00 34.98 6.09
1239 1266 1.569708 GCTTGAGGAAGATCTCTGCG 58.430 55.000 0.00 0.00 34.98 5.18
1240 1267 1.569708 CGCTTGAGGAAGATCTCTGC 58.430 55.000 0.00 0.00 34.98 4.26
1241 1268 1.753649 TCCGCTTGAGGAAGATCTCTG 59.246 52.381 0.00 0.00 37.36 3.35
1242 1269 2.151502 TCCGCTTGAGGAAGATCTCT 57.848 50.000 0.00 0.00 37.36 3.10
1243 1270 2.969628 TTCCGCTTGAGGAAGATCTC 57.030 50.000 0.00 0.00 44.66 2.75
1563 1590 2.357034 GCCGTTCTGCCGTCTTCA 60.357 61.111 0.00 0.00 0.00 3.02
1616 1643 3.306780 GGGTTCCTCAAAGTCTTCATCGA 60.307 47.826 0.00 0.00 0.00 3.59
1656 1683 0.617935 GCTGCTTCTCCCTTCTCCTT 59.382 55.000 0.00 0.00 0.00 3.36
1792 1819 3.249189 TGCGGGGAAGTCCTTGCT 61.249 61.111 13.11 0.00 37.62 3.91
1830 1857 3.326006 AGCTCTTCTTGAAGGTGACATCA 59.674 43.478 10.08 0.00 36.03 3.07
1983 2010 0.537188 GATCGCCTCCCTGTTCTTGA 59.463 55.000 0.00 0.00 0.00 3.02
1985 2012 1.908483 GGATCGCCTCCCTGTTCTT 59.092 57.895 0.00 0.00 38.19 2.52
1989 2016 2.240162 GAAACGGATCGCCTCCCTGT 62.240 60.000 0.00 0.00 41.49 4.00
2126 2153 1.679139 CTTGTGGCAGGTGTGAGAAA 58.321 50.000 0.00 0.00 0.00 2.52
2136 2163 5.473504 AGATTGTTTAGTTACCTTGTGGCAG 59.526 40.000 0.00 0.00 36.63 4.85
2155 2224 7.636150 ATTAATTCACAGGAGGAACAGATTG 57.364 36.000 0.00 0.00 0.00 2.67
2193 2265 6.923928 AACTGATCCAAACCAAAAATTGTG 57.076 33.333 0.00 0.00 0.00 3.33
2231 2303 4.414337 AAACAAGGCCACAAATTGCTAA 57.586 36.364 5.01 0.00 0.00 3.09
2340 2412 2.716217 AGGGATCACTAGCTTGTTTGC 58.284 47.619 0.00 0.00 0.00 3.68
2364 2436 2.417933 CTCTGCGTCCTGAATGAAAAGG 59.582 50.000 0.00 0.00 34.65 3.11
2470 2542 8.694039 GATGTAATCGCATTTTCGACATCGAAC 61.694 40.741 15.89 4.51 45.32 3.95
2537 2609 2.522185 ACACATGCTGAAGCCAGATTT 58.478 42.857 0.00 0.00 43.02 2.17
2541 2613 0.723414 CGTACACATGCTGAAGCCAG 59.277 55.000 0.00 0.00 43.22 4.85
2608 2680 5.474876 AGAGAAACAAAGGTGCCTATTGAAG 59.525 40.000 15.09 0.00 0.00 3.02
2609 2681 5.385198 AGAGAAACAAAGGTGCCTATTGAA 58.615 37.500 15.09 0.00 0.00 2.69
2610 2682 4.985538 AGAGAAACAAAGGTGCCTATTGA 58.014 39.130 15.09 0.00 0.00 2.57
2611 2683 5.712152 AAGAGAAACAAAGGTGCCTATTG 57.288 39.130 9.80 9.80 0.00 1.90
2612 2684 6.239317 GGAAAAGAGAAACAAAGGTGCCTATT 60.239 38.462 0.00 0.00 0.00 1.73
2613 2685 5.243954 GGAAAAGAGAAACAAAGGTGCCTAT 59.756 40.000 0.00 0.00 0.00 2.57
2614 2686 4.583073 GGAAAAGAGAAACAAAGGTGCCTA 59.417 41.667 0.00 0.00 0.00 3.93
2615 2687 3.384789 GGAAAAGAGAAACAAAGGTGCCT 59.615 43.478 0.00 0.00 0.00 4.75
2616 2688 3.492656 GGGAAAAGAGAAACAAAGGTGCC 60.493 47.826 0.00 0.00 0.00 5.01
2617 2689 3.384789 AGGGAAAAGAGAAACAAAGGTGC 59.615 43.478 0.00 0.00 0.00 5.01
2618 2690 4.644685 TCAGGGAAAAGAGAAACAAAGGTG 59.355 41.667 0.00 0.00 0.00 4.00
2619 2691 4.645136 GTCAGGGAAAAGAGAAACAAAGGT 59.355 41.667 0.00 0.00 0.00 3.50
2620 2692 4.038042 GGTCAGGGAAAAGAGAAACAAAGG 59.962 45.833 0.00 0.00 0.00 3.11
2621 2693 4.889995 AGGTCAGGGAAAAGAGAAACAAAG 59.110 41.667 0.00 0.00 0.00 2.77
2622 2694 4.867086 AGGTCAGGGAAAAGAGAAACAAA 58.133 39.130 0.00 0.00 0.00 2.83
2670 2742 1.689233 TGCTGGCTCCCTATCCGTT 60.689 57.895 0.00 0.00 0.00 4.44
2745 2817 2.978010 ACGTTGCTTGCCCCTTCG 60.978 61.111 0.00 0.00 0.00 3.79
3300 3378 2.262774 CTCCATCCTTGCCTTCGCCT 62.263 60.000 0.00 0.00 0.00 5.52
4150 7187 3.130633 CACTGTTCATGTCGTTGAAGGA 58.869 45.455 0.00 0.00 36.34 3.36
4452 7489 5.879223 CCTATCATTGGATATCAGTTCTGGC 59.121 44.000 4.83 0.00 35.52 4.85
4563 7656 5.936956 AGAAGCTTCCACTTACAAGATTGAG 59.063 40.000 22.81 0.00 28.49 3.02
4715 7992 4.883026 GCAGCAAGATGCCAGTTG 57.117 55.556 0.00 0.00 46.52 3.16
5045 8653 4.286032 TCACCTGGCATGTTTAGTAGTTCT 59.714 41.667 0.00 0.00 0.00 3.01
5439 9756 3.007182 ACAAGTATTTTCGGACGGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
5440 9757 2.564062 ACAAGTATTTTCGGACGGAGGA 59.436 45.455 0.00 0.00 0.00 3.71
5443 9760 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
5447 9764 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
5448 9765 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
5449 9766 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
5450 9767 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
5451 9768 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
5452 9769 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
5454 9771 9.260002 GTTTTTGTCCATTTTGATGACAAGTAT 57.740 29.630 0.00 0.00 37.13 2.12
5455 9772 8.253810 TGTTTTTGTCCATTTTGATGACAAGTA 58.746 29.630 0.00 0.00 37.13 2.24
5456 9773 7.102346 TGTTTTTGTCCATTTTGATGACAAGT 58.898 30.769 0.00 0.00 37.13 3.16
5457 9774 7.254522 CCTGTTTTTGTCCATTTTGATGACAAG 60.255 37.037 0.00 0.00 37.13 3.16
5458 9775 6.538021 CCTGTTTTTGTCCATTTTGATGACAA 59.462 34.615 0.00 0.00 34.47 3.18
5460 9777 6.018832 CACCTGTTTTTGTCCATTTTGATGAC 60.019 38.462 0.00 0.00 0.00 3.06
5461 9778 6.047870 CACCTGTTTTTGTCCATTTTGATGA 58.952 36.000 0.00 0.00 0.00 2.92
5462 9779 5.816777 ACACCTGTTTTTGTCCATTTTGATG 59.183 36.000 0.00 0.00 0.00 3.07
5467 9784 6.976934 AGATACACCTGTTTTTGTCCATTT 57.023 33.333 0.00 0.00 0.00 2.32
5468 9785 7.458397 TCTAGATACACCTGTTTTTGTCCATT 58.542 34.615 0.00 0.00 0.00 3.16
5469 9786 7.016153 TCTAGATACACCTGTTTTTGTCCAT 57.984 36.000 0.00 0.00 0.00 3.41
5470 9787 6.428083 TCTAGATACACCTGTTTTTGTCCA 57.572 37.500 0.00 0.00 0.00 4.02
5471 9788 6.935208 AGTTCTAGATACACCTGTTTTTGTCC 59.065 38.462 0.00 0.00 0.00 4.02
5472 9789 7.964604 AGTTCTAGATACACCTGTTTTTGTC 57.035 36.000 0.00 0.00 0.00 3.18
5473 9790 9.841295 TTTAGTTCTAGATACACCTGTTTTTGT 57.159 29.630 0.00 0.00 0.00 2.83
5478 9795 9.798994 CGTATTTTAGTTCTAGATACACCTGTT 57.201 33.333 0.00 0.00 0.00 3.16
5479 9796 8.964772 ACGTATTTTAGTTCTAGATACACCTGT 58.035 33.333 0.00 0.00 0.00 4.00
5480 9797 9.448294 GACGTATTTTAGTTCTAGATACACCTG 57.552 37.037 0.00 0.00 0.00 4.00
5481 9798 9.406113 AGACGTATTTTAGTTCTAGATACACCT 57.594 33.333 0.00 0.00 0.00 4.00
5489 9806 9.900710 ATGCATCTAGACGTATTTTAGTTCTAG 57.099 33.333 0.00 0.00 0.00 2.43
5490 9807 9.894783 GATGCATCTAGACGTATTTTAGTTCTA 57.105 33.333 19.70 0.00 0.00 2.10
5491 9808 7.868415 GGATGCATCTAGACGTATTTTAGTTCT 59.132 37.037 25.28 0.00 0.00 3.01
5492 9809 7.116519 GGGATGCATCTAGACGTATTTTAGTTC 59.883 40.741 25.28 2.81 0.00 3.01
5494 9811 6.456501 GGGATGCATCTAGACGTATTTTAGT 58.543 40.000 25.28 0.00 0.00 2.24
5495 9812 5.869888 GGGGATGCATCTAGACGTATTTTAG 59.130 44.000 25.28 0.00 0.00 1.85
5496 9813 5.542635 AGGGGATGCATCTAGACGTATTTTA 59.457 40.000 25.28 0.00 0.00 1.52
5497 9814 4.348168 AGGGGATGCATCTAGACGTATTTT 59.652 41.667 25.28 0.00 0.00 1.82
5498 9815 3.904339 AGGGGATGCATCTAGACGTATTT 59.096 43.478 25.28 0.00 0.00 1.40
5499 9816 3.511477 AGGGGATGCATCTAGACGTATT 58.489 45.455 25.28 0.13 0.00 1.89
5500 9817 3.176924 AGGGGATGCATCTAGACGTAT 57.823 47.619 25.28 0.00 0.00 3.06
5501 9818 2.677542 AGGGGATGCATCTAGACGTA 57.322 50.000 25.28 0.00 0.00 3.57
5502 9819 1.794714 AAGGGGATGCATCTAGACGT 58.205 50.000 25.28 12.28 0.00 4.34
5503 9820 2.918712 AAAGGGGATGCATCTAGACG 57.081 50.000 25.28 0.00 0.00 4.18
5504 9821 5.869579 TGATAAAAGGGGATGCATCTAGAC 58.130 41.667 25.28 13.29 0.00 2.59
5505 9822 6.514012 TTGATAAAAGGGGATGCATCTAGA 57.486 37.500 25.28 0.00 0.00 2.43
5506 9823 7.771927 AATTGATAAAAGGGGATGCATCTAG 57.228 36.000 25.28 0.00 0.00 2.43
5508 9825 7.126115 TCAAAATTGATAAAAGGGGATGCATCT 59.874 33.333 25.28 7.83 31.01 2.90
5509 9826 7.274447 TCAAAATTGATAAAAGGGGATGCATC 58.726 34.615 18.81 18.81 31.01 3.91
5510 9827 7.197901 TCAAAATTGATAAAAGGGGATGCAT 57.802 32.000 0.00 0.00 31.01 3.96
5511 9828 6.617782 TCAAAATTGATAAAAGGGGATGCA 57.382 33.333 0.00 0.00 31.01 3.96
5512 9829 7.225341 GTCATCAAAATTGATAAAAGGGGATGC 59.775 37.037 8.24 0.00 45.62 3.91
5513 9830 8.259411 TGTCATCAAAATTGATAAAAGGGGATG 58.741 33.333 8.24 0.00 45.62 3.51
5514 9831 8.378115 TGTCATCAAAATTGATAAAAGGGGAT 57.622 30.769 8.24 0.00 45.62 3.85
5515 9832 7.789202 TGTCATCAAAATTGATAAAAGGGGA 57.211 32.000 8.24 0.00 45.62 4.81
5516 9833 8.096414 ACTTGTCATCAAAATTGATAAAAGGGG 58.904 33.333 18.71 5.77 45.62 4.79


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

AutoCloner maintained by Alex Coulton.