Multiple sequence alignment - TraesCS3B01G058700

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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 TraesCS3B01G058700 chr3B 100.000 2561 0 0 1 2561 30491789 30494349 0.000000e+00 4730.0
1 TraesCS3B01G058700 chr3B 87.868 1088 70 10 1146 2230 30462891 30463919 0.000000e+00 1221.0
2 TraesCS3B01G058700 chr3B 97.143 35 1 0 175 209 71451126 71451092 2.750000e-05 60.2
3 TraesCS3B01G058700 chr3B 100.000 31 0 0 2310 2340 30464086 30464116 9.900000e-05 58.4
4 TraesCS3B01G058700 chr3B 97.059 34 1 0 2313 2346 30494062 30494095 9.900000e-05 58.4
5 TraesCS3B01G058700 chr3B 97.059 34 1 0 2274 2307 30494101 30494134 9.900000e-05 58.4
6 TraesCS3B01G058700 chr3B 100.000 28 0 0 2316 2343 29845231 29845258 5.000000e-03 52.8
7 TraesCS3B01G058700 chr3D 93.997 1999 67 22 57 2047 18876752 18878705 0.000000e+00 2977.0
8 TraesCS3B01G058700 chr3D 90.728 302 21 5 2049 2346 18878814 18879112 1.850000e-106 396.0
9 TraesCS3B01G058700 chr3D 88.462 156 7 7 2417 2561 18880638 18880793 7.280000e-41 178.0
10 TraesCS3B01G058700 chr3D 97.403 77 2 0 2274 2350 18879079 18879155 5.750000e-27 132.0
11 TraesCS3B01G058700 chr3D 98.113 53 1 0 2353 2405 18879192 18879244 2.710000e-15 93.5
12 TraesCS3B01G058700 chr3D 97.059 34 1 0 2310 2343 18699697 18699730 9.900000e-05 58.4
13 TraesCS3B01G058700 chr3A 83.751 997 116 17 813 1789 26459253 26460223 0.000000e+00 902.0
14 TraesCS3B01G058700 chr3A 84.804 204 24 7 457 655 26453233 26453434 5.590000e-47 198.0
15 TraesCS3B01G058700 chr6B 97.222 36 1 0 174 209 697681791 697681826 7.650000e-06 62.1
16 TraesCS3B01G058700 chr6B 97.143 35 1 0 175 209 18170175 18170209 2.750000e-05 60.2
17 TraesCS3B01G058700 chr1B 97.143 35 1 0 175 209 17045660 17045626 2.750000e-05 60.2
18 TraesCS3B01G058700 chr4A 97.059 34 1 0 176 209 31593372 31593339 9.900000e-05 58.4
19 TraesCS3B01G058700 chrUn 100.000 28 0 0 217 244 76653569 76653596 5.000000e-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 TraesCS3B01G058700 chr3B 30491789 30494349 2560 False 1615.6 4730 98.039333 1 2561 3 chr3B.!!$F3 2560
1 TraesCS3B01G058700 chr3B 30462891 30464116 1225 False 639.7 1221 93.934000 1146 2340 2 chr3B.!!$F2 1194
2 TraesCS3B01G058700 chr3D 18876752 18880793 4041 False 755.3 2977 93.740600 57 2561 5 chr3D.!!$F2 2504
3 TraesCS3B01G058700 chr3A 26459253 26460223 970 False 902.0 902 83.751000 813 1789 1 chr3A.!!$F2 976

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
390 392 0.904865 TGAGACGCAGGGACCTGAAT 60.905 55.0 22.03 8.43 46.3 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1595 0.339859 ATGCACCCCTCCAGAGAGTA 59.66 55.0 0.0 0.0 38.58 2.59 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
22 23 5.779806 CAAACGTTCGAGAGTTATTGGAT 57.220 39.130 0.00 0.00 0.00 3.41
23 24 6.165659 CAAACGTTCGAGAGTTATTGGATT 57.834 37.500 0.00 0.00 0.00 3.01
24 25 6.241385 CAAACGTTCGAGAGTTATTGGATTC 58.759 40.000 0.00 0.00 0.00 2.52
25 26 4.430908 ACGTTCGAGAGTTATTGGATTCC 58.569 43.478 0.00 0.00 0.00 3.01
26 27 4.159879 ACGTTCGAGAGTTATTGGATTCCT 59.840 41.667 3.95 0.00 0.00 3.36
27 28 5.109903 CGTTCGAGAGTTATTGGATTCCTT 58.890 41.667 3.95 0.00 0.00 3.36
28 29 6.127535 ACGTTCGAGAGTTATTGGATTCCTTA 60.128 38.462 3.95 0.00 0.00 2.69
29 30 6.755141 CGTTCGAGAGTTATTGGATTCCTTAA 59.245 38.462 3.95 0.00 0.00 1.85
30 31 7.277098 CGTTCGAGAGTTATTGGATTCCTTAAA 59.723 37.037 3.95 0.00 0.00 1.52
31 32 8.943002 GTTCGAGAGTTATTGGATTCCTTAAAA 58.057 33.333 3.95 0.00 0.00 1.52
32 33 9.509956 TTCGAGAGTTATTGGATTCCTTAAAAA 57.490 29.630 3.95 0.00 0.00 1.94
80 81 4.262249 CCAGATCTATCTTCGACCTTTCCC 60.262 50.000 0.00 0.00 34.22 3.97
104 105 1.060713 CCACAACTAGCTTGTCGTCG 58.939 55.000 0.07 0.00 41.50 5.12
137 138 4.796038 AATGTCTTGCCTCCAAAATCAG 57.204 40.909 0.00 0.00 0.00 2.90
214 215 1.660264 GCCGACGGCTTTTTGTTGG 60.660 57.895 31.30 0.00 46.69 3.77
228 230 3.395702 TTGGGGCGTCGGCATAGT 61.396 61.111 21.23 0.00 42.47 2.12
247 249 1.123077 TTGGAGATATGCCGACTGCT 58.877 50.000 0.00 0.00 42.00 4.24
390 392 0.904865 TGAGACGCAGGGACCTGAAT 60.905 55.000 22.03 8.43 46.30 2.57
396 398 4.163458 AGACGCAGGGACCTGAATAATAAA 59.837 41.667 22.03 0.00 46.30 1.40
416 418 3.681835 ACTCACGGACTCGCCCAC 61.682 66.667 0.00 0.00 40.63 4.61
430 432 1.743252 CCCACTCTTTCTCAGCGGC 60.743 63.158 0.00 0.00 0.00 6.53
442 444 1.063912 CTCAGCGGCGCATGAATTTTA 59.936 47.619 35.02 10.64 0.00 1.52
449 452 3.786048 CGGCGCATGAATTTTAAGAGTTC 59.214 43.478 10.83 0.00 0.00 3.01
453 456 5.230726 GCGCATGAATTTTAAGAGTTCCATG 59.769 40.000 0.30 0.00 0.00 3.66
487 490 7.814264 AGCTCCTGTATATTGATTTTTCCTG 57.186 36.000 0.00 0.00 0.00 3.86
490 493 7.469181 GCTCCTGTATATTGATTTTTCCTGGTG 60.469 40.741 0.00 0.00 0.00 4.17
576 579 1.078426 TTAGCAAGCGAGGAAGGGC 60.078 57.895 0.00 0.00 0.00 5.19
615 618 7.095229 GCACTTCTATCAACACATACAAGAACA 60.095 37.037 0.00 0.00 0.00 3.18
655 658 5.047377 ACACTGGAAAGCTTTGTTCTTTGAA 60.047 36.000 18.30 0.00 34.24 2.69
656 659 5.289434 CACTGGAAAGCTTTGTTCTTTGAAC 59.711 40.000 18.30 3.74 34.24 3.18
657 660 5.047377 ACTGGAAAGCTTTGTTCTTTGAACA 60.047 36.000 18.30 8.81 34.24 3.18
658 661 5.167845 TGGAAAGCTTTGTTCTTTGAACAC 58.832 37.500 18.30 0.00 34.24 3.32
659 662 5.047377 TGGAAAGCTTTGTTCTTTGAACACT 60.047 36.000 18.30 4.83 34.24 3.55
660 663 5.289434 GGAAAGCTTTGTTCTTTGAACACTG 59.711 40.000 18.30 9.20 34.24 3.66
661 664 4.376340 AGCTTTGTTCTTTGAACACTGG 57.624 40.909 11.99 7.18 0.00 4.00
662 665 4.016444 AGCTTTGTTCTTTGAACACTGGA 58.984 39.130 11.99 0.00 0.00 3.86
663 666 4.462483 AGCTTTGTTCTTTGAACACTGGAA 59.538 37.500 11.99 4.43 0.00 3.53
664 667 5.047377 AGCTTTGTTCTTTGAACACTGGAAA 60.047 36.000 11.99 4.12 0.00 3.13
665 668 5.637387 GCTTTGTTCTTTGAACACTGGAAAA 59.363 36.000 11.99 3.52 0.00 2.29
666 669 6.401047 GCTTTGTTCTTTGAACACTGGAAAAC 60.401 38.462 11.99 0.00 0.00 2.43
667 670 5.975693 TGTTCTTTGAACACTGGAAAACT 57.024 34.783 8.81 0.00 0.00 2.66
668 671 6.339587 TGTTCTTTGAACACTGGAAAACTT 57.660 33.333 8.81 0.00 0.00 2.66
669 672 6.754193 TGTTCTTTGAACACTGGAAAACTTT 58.246 32.000 8.81 0.00 0.00 2.66
670 673 7.213678 TGTTCTTTGAACACTGGAAAACTTTT 58.786 30.769 8.81 0.00 0.00 2.27
671 674 7.713073 TGTTCTTTGAACACTGGAAAACTTTTT 59.287 29.630 8.81 0.00 0.00 1.94
672 675 7.650834 TCTTTGAACACTGGAAAACTTTTTG 57.349 32.000 0.00 0.00 0.00 2.44
673 676 7.437748 TCTTTGAACACTGGAAAACTTTTTGA 58.562 30.769 0.00 0.00 0.00 2.69
674 677 7.928706 TCTTTGAACACTGGAAAACTTTTTGAA 59.071 29.630 0.00 0.00 0.00 2.69
675 678 7.414814 TTGAACACTGGAAAACTTTTTGAAC 57.585 32.000 0.00 0.00 0.00 3.18
676 679 6.516718 TGAACACTGGAAAACTTTTTGAACA 58.483 32.000 0.00 0.00 0.00 3.18
677 680 6.422400 TGAACACTGGAAAACTTTTTGAACAC 59.578 34.615 0.00 0.00 0.00 3.32
678 681 6.096673 ACACTGGAAAACTTTTTGAACACT 57.903 33.333 0.00 0.00 0.00 3.55
679 682 6.156519 ACACTGGAAAACTTTTTGAACACTC 58.843 36.000 0.00 0.00 0.00 3.51
680 683 6.155827 CACTGGAAAACTTTTTGAACACTCA 58.844 36.000 0.00 0.00 0.00 3.41
681 684 6.813152 CACTGGAAAACTTTTTGAACACTCAT 59.187 34.615 0.00 0.00 0.00 2.90
682 685 6.813152 ACTGGAAAACTTTTTGAACACTCATG 59.187 34.615 0.00 0.00 0.00 3.07
683 686 6.696411 TGGAAAACTTTTTGAACACTCATGT 58.304 32.000 0.00 0.00 42.46 3.21
684 687 7.831753 TGGAAAACTTTTTGAACACTCATGTA 58.168 30.769 0.00 0.00 38.45 2.29
710 713 8.367156 ACTTTGCCATACAATGTACATTTCTTT 58.633 29.630 18.50 6.23 42.92 2.52
731 740 7.765307 TCTTTTTCTCATCATGTTTAGCCATC 58.235 34.615 0.00 0.00 0.00 3.51
764 773 7.501225 TCCCAACTACAAAAGGTAAGAAGAAAG 59.499 37.037 0.00 0.00 0.00 2.62
819 828 1.184970 CCTTGCCCCGTCAATTGGTT 61.185 55.000 5.42 0.00 0.00 3.67
856 870 1.680651 CGACTGCTCCTGGACTCCT 60.681 63.158 0.00 0.00 0.00 3.69
870 888 2.291024 GGACTCCTCTCACTACCACTCA 60.291 54.545 0.00 0.00 0.00 3.41
916 944 3.697190 TCTCCCTGAATTCTAGCTCCT 57.303 47.619 7.05 0.00 0.00 3.69
969 997 3.508793 AGATACCTCCTTCGTTTTGTCGA 59.491 43.478 0.00 0.00 38.08 4.20
1150 1178 2.124570 CCCACCCATTCTGGCTCG 60.125 66.667 0.00 0.00 35.79 5.03
1289 1317 2.101582 ACATCTCCTATGAGGAACGCAC 59.898 50.000 0.00 0.00 45.28 5.34
1293 1321 2.628178 CTCCTATGAGGAACGCACCATA 59.372 50.000 0.00 0.00 45.28 2.74
1382 1411 1.815421 CCTCCATCAAACTCGGCCG 60.815 63.158 22.12 22.12 0.00 6.13
1560 1589 4.492611 GTTCAGAAAAGTACGAGGGGTAG 58.507 47.826 0.00 0.00 0.00 3.18
1561 1590 3.771216 TCAGAAAAGTACGAGGGGTAGT 58.229 45.455 0.00 0.00 36.30 2.73
1562 1591 3.508793 TCAGAAAAGTACGAGGGGTAGTG 59.491 47.826 0.00 0.00 34.96 2.74
1563 1592 2.830321 AGAAAAGTACGAGGGGTAGTGG 59.170 50.000 0.00 0.00 34.96 4.00
1564 1593 1.565067 AAAGTACGAGGGGTAGTGGG 58.435 55.000 0.00 0.00 34.96 4.61
1565 1594 0.325016 AAGTACGAGGGGTAGTGGGG 60.325 60.000 0.00 0.00 34.96 4.96
1566 1595 1.000866 GTACGAGGGGTAGTGGGGT 59.999 63.158 0.00 0.00 0.00 4.95
1792 1821 8.745590 GGGCAACTTATTACCTCTAAAAATCAA 58.254 33.333 0.00 0.00 0.00 2.57
1838 1867 4.186159 CCCATGCTCTTAATTTGCTTTGG 58.814 43.478 0.00 0.00 33.61 3.28
2004 2036 4.514441 TCTTCAGGGTAATATCTCGACGAC 59.486 45.833 0.00 0.00 0.00 4.34
2005 2037 2.804527 TCAGGGTAATATCTCGACGACG 59.195 50.000 0.00 0.00 41.26 5.12
2006 2038 2.804527 CAGGGTAATATCTCGACGACGA 59.195 50.000 9.98 9.98 46.56 4.20
2047 2079 5.973565 GGCACTCATGATTTGCATTAACTAC 59.026 40.000 23.73 6.92 38.04 2.73
2120 2259 5.163642 TGCCGAGAGAGAAATACAAGACTAC 60.164 44.000 0.00 0.00 0.00 2.73
2308 2592 6.836007 TCTTAGCCAGATTATTCTCTCACAGA 59.164 38.462 0.00 0.00 0.00 3.41
2342 2626 9.723601 ATTCATTCTTAGCCAGATTATTCTCTC 57.276 33.333 0.00 0.00 0.00 3.20
2350 2634 4.937620 GCCAGATTATTCTCTCACAACACA 59.062 41.667 0.00 0.00 0.00 3.72
2368 2686 2.671396 CACAAGTACGTCTAACATGGGC 59.329 50.000 0.00 0.00 0.00 5.36
2405 2723 0.611896 ATTGACGGGGCAAGGAAAGG 60.612 55.000 0.00 0.00 0.00 3.11
2406 2724 1.710996 TTGACGGGGCAAGGAAAGGA 61.711 55.000 0.00 0.00 0.00 3.36
2407 2725 1.377333 GACGGGGCAAGGAAAGGAG 60.377 63.158 0.00 0.00 0.00 3.69
2408 2726 1.838073 GACGGGGCAAGGAAAGGAGA 61.838 60.000 0.00 0.00 0.00 3.71
2410 2728 1.379176 GGGGCAAGGAAAGGAGAGC 60.379 63.158 0.00 0.00 0.00 4.09
2411 2729 1.379176 GGGCAAGGAAAGGAGAGCC 60.379 63.158 0.00 0.00 41.29 4.70
2413 2731 0.393673 GGCAAGGAAAGGAGAGCCTC 60.394 60.000 0.00 0.00 46.28 4.70
2414 2732 0.617935 GCAAGGAAAGGAGAGCCTCT 59.382 55.000 0.00 0.00 46.28 3.69
2415 2733 1.678425 GCAAGGAAAGGAGAGCCTCTG 60.678 57.143 0.00 0.00 46.28 3.35
2486 4186 0.963856 CATGGTGGCATGCAGAGTGT 60.964 55.000 21.36 0.00 0.00 3.55
2491 4191 0.321919 TGGCATGCAGAGTGTCCTTC 60.322 55.000 21.36 0.00 0.00 3.46
2493 4193 1.364626 GCATGCAGAGTGTCCTTCCG 61.365 60.000 14.21 0.00 0.00 4.30
2495 4195 1.134580 CATGCAGAGTGTCCTTCCGAT 60.135 52.381 0.00 0.00 0.00 4.18
2497 4197 1.347707 TGCAGAGTGTCCTTCCGATTT 59.652 47.619 0.00 0.00 0.00 2.17
2499 4199 2.416893 GCAGAGTGTCCTTCCGATTTTC 59.583 50.000 0.00 0.00 0.00 2.29
2500 4200 3.003480 CAGAGTGTCCTTCCGATTTTCC 58.997 50.000 0.00 0.00 0.00 3.13
2501 4201 2.000447 GAGTGTCCTTCCGATTTTCCG 59.000 52.381 0.00 0.00 0.00 4.30
2502 4202 1.346722 AGTGTCCTTCCGATTTTCCGT 59.653 47.619 0.00 0.00 0.00 4.69
2503 4203 1.463444 GTGTCCTTCCGATTTTCCGTG 59.537 52.381 0.00 0.00 0.00 4.94
2506 4217 1.226018 CTTCCGATTTTCCGTGCGC 60.226 57.895 0.00 0.00 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.779806 ATCCAATAACTCTCGAACGTTTG 57.220 39.130 9.40 9.40 0.00 2.93
1 2 5.350640 GGAATCCAATAACTCTCGAACGTTT 59.649 40.000 0.46 0.00 0.00 3.60
2 3 4.868734 GGAATCCAATAACTCTCGAACGTT 59.131 41.667 0.00 0.00 0.00 3.99
3 4 4.159879 AGGAATCCAATAACTCTCGAACGT 59.840 41.667 0.61 0.00 0.00 3.99
4 5 4.683832 AGGAATCCAATAACTCTCGAACG 58.316 43.478 0.61 0.00 0.00 3.95
5 6 8.488651 TTTAAGGAATCCAATAACTCTCGAAC 57.511 34.615 0.61 0.00 0.00 3.95
6 7 9.509956 TTTTTAAGGAATCCAATAACTCTCGAA 57.490 29.630 0.61 0.00 0.00 3.71
30 31 8.805175 TGATCATTTGTACAGGTGATGATTTTT 58.195 29.630 22.30 6.85 37.52 1.94
31 32 8.246180 GTGATCATTTGTACAGGTGATGATTTT 58.754 33.333 22.30 5.65 37.52 1.82
32 33 7.148018 GGTGATCATTTGTACAGGTGATGATTT 60.148 37.037 22.30 6.20 37.52 2.17
33 34 6.319658 GGTGATCATTTGTACAGGTGATGATT 59.680 38.462 22.30 6.49 37.52 2.57
34 35 5.824624 GGTGATCATTTGTACAGGTGATGAT 59.175 40.000 22.30 20.10 39.45 2.45
35 36 5.185454 GGTGATCATTTGTACAGGTGATGA 58.815 41.667 22.30 17.34 31.86 2.92
36 37 4.943093 TGGTGATCATTTGTACAGGTGATG 59.057 41.667 22.30 13.78 31.86 3.07
37 38 5.045651 TCTGGTGATCATTTGTACAGGTGAT 60.046 40.000 19.16 19.16 34.23 3.06
38 39 4.285775 TCTGGTGATCATTTGTACAGGTGA 59.714 41.667 12.76 12.76 0.00 4.02
39 40 4.578871 TCTGGTGATCATTTGTACAGGTG 58.421 43.478 0.00 0.00 0.00 4.00
40 41 4.908601 TCTGGTGATCATTTGTACAGGT 57.091 40.909 0.00 0.00 0.00 4.00
41 42 5.998454 GATCTGGTGATCATTTGTACAGG 57.002 43.478 0.00 0.00 46.20 4.00
47 48 7.116090 GTCGAAGATAGATCTGGTGATCATTTG 59.884 40.741 5.18 2.05 45.06 2.32
48 49 7.151308 GTCGAAGATAGATCTGGTGATCATTT 58.849 38.462 5.18 0.00 45.06 2.32
49 50 6.295011 GGTCGAAGATAGATCTGGTGATCATT 60.295 42.308 5.18 0.00 45.06 2.57
50 51 5.184864 GGTCGAAGATAGATCTGGTGATCAT 59.815 44.000 5.18 0.00 45.06 2.45
51 52 4.520874 GGTCGAAGATAGATCTGGTGATCA 59.479 45.833 5.18 0.00 45.06 2.92
52 53 4.764823 AGGTCGAAGATAGATCTGGTGATC 59.235 45.833 5.18 0.00 43.89 2.92
53 54 4.735369 AGGTCGAAGATAGATCTGGTGAT 58.265 43.478 5.18 0.00 40.67 3.06
54 55 4.171878 AGGTCGAAGATAGATCTGGTGA 57.828 45.455 5.18 0.00 40.67 4.02
55 56 4.927978 AAGGTCGAAGATAGATCTGGTG 57.072 45.455 5.18 0.00 40.67 4.17
71 72 1.954382 GTTGTGGACAAGGGAAAGGTC 59.046 52.381 0.00 0.00 36.39 3.85
104 105 2.669364 CAAGACATTTGGAGCAGCAAC 58.331 47.619 0.00 0.00 0.00 4.17
137 138 4.829064 TTCTGTGTGTTTAACAGGCATC 57.171 40.909 0.00 0.00 44.26 3.91
205 206 3.121019 CCGACGCCCCAACAAAAA 58.879 55.556 0.00 0.00 0.00 1.94
214 215 2.895372 CCAACTATGCCGACGCCC 60.895 66.667 0.00 0.00 0.00 6.13
228 230 3.686622 GCAGTCGGCATATCTCCAA 57.313 52.632 0.00 0.00 43.97 3.53
240 242 1.301677 GGCCTTTCCTCAAGCAGTCG 61.302 60.000 0.00 0.00 0.00 4.18
244 246 1.302511 GACGGCCTTTCCTCAAGCA 60.303 57.895 0.00 0.00 0.00 3.91
247 249 2.345991 CCGACGGCCTTTCCTCAA 59.654 61.111 0.00 0.00 0.00 3.02
266 268 2.607282 CCGTCGGCATATTCTGAGGTAC 60.607 54.545 0.00 0.00 0.00 3.34
390 392 3.922240 GCGAGTCCGTGAGTGTTTTATTA 59.078 43.478 0.00 0.00 38.24 0.98
396 398 2.338984 GGCGAGTCCGTGAGTGTT 59.661 61.111 0.00 0.00 38.24 3.32
416 418 1.812922 ATGCGCCGCTGAGAAAGAG 60.813 57.895 11.67 0.00 0.00 2.85
430 432 5.230726 GCATGGAACTCTTAAAATTCATGCG 59.769 40.000 8.79 0.00 32.53 4.73
453 456 3.778954 ATACAGGAGCTTATTCCAGGC 57.221 47.619 0.00 0.00 39.84 4.85
462 465 7.286316 CCAGGAAAAATCAATATACAGGAGCTT 59.714 37.037 0.00 0.00 0.00 3.74
487 490 3.401033 AAAGCAAACCAAATAGGCACC 57.599 42.857 0.00 0.00 43.14 5.01
490 493 4.221924 TCCCTAAAAGCAAACCAAATAGGC 59.778 41.667 0.00 0.00 43.14 3.93
576 579 6.577103 TGATAGAAGTGCTTCAGTCAATAGG 58.423 40.000 13.58 0.00 41.84 2.57
615 618 1.029681 GTGTTCAAAAAGGGAGGCGT 58.970 50.000 0.00 0.00 0.00 5.68
655 658 6.096673 AGTGTTCAAAAAGTTTTCCAGTGT 57.903 33.333 0.32 0.00 0.00 3.55
656 659 6.155827 TGAGTGTTCAAAAAGTTTTCCAGTG 58.844 36.000 0.32 0.00 0.00 3.66
657 660 6.339587 TGAGTGTTCAAAAAGTTTTCCAGT 57.660 33.333 0.32 0.18 0.00 4.00
658 661 6.813152 ACATGAGTGTTCAAAAAGTTTTCCAG 59.187 34.615 0.00 0.00 36.78 3.86
659 662 6.696411 ACATGAGTGTTCAAAAAGTTTTCCA 58.304 32.000 0.00 0.00 36.78 3.53
660 663 7.973944 AGTACATGAGTGTTCAAAAAGTTTTCC 59.026 33.333 0.00 0.00 39.77 3.13
661 664 8.911247 AGTACATGAGTGTTCAAAAAGTTTTC 57.089 30.769 0.00 0.00 39.77 2.29
662 665 9.705290 AAAGTACATGAGTGTTCAAAAAGTTTT 57.295 25.926 0.00 0.00 39.77 2.43
663 666 9.139174 CAAAGTACATGAGTGTTCAAAAAGTTT 57.861 29.630 0.00 0.00 39.77 2.66
664 667 7.275560 GCAAAGTACATGAGTGTTCAAAAAGTT 59.724 33.333 0.00 0.00 39.77 2.66
665 668 6.751888 GCAAAGTACATGAGTGTTCAAAAAGT 59.248 34.615 0.00 0.00 39.77 2.66
666 669 6.198966 GGCAAAGTACATGAGTGTTCAAAAAG 59.801 38.462 0.00 0.00 39.77 2.27
667 670 6.039616 GGCAAAGTACATGAGTGTTCAAAAA 58.960 36.000 0.00 0.00 39.77 1.94
668 671 5.126222 TGGCAAAGTACATGAGTGTTCAAAA 59.874 36.000 0.00 0.00 39.77 2.44
669 672 4.642437 TGGCAAAGTACATGAGTGTTCAAA 59.358 37.500 0.00 0.00 39.77 2.69
670 673 4.203226 TGGCAAAGTACATGAGTGTTCAA 58.797 39.130 0.00 0.00 39.77 2.69
671 674 3.814625 TGGCAAAGTACATGAGTGTTCA 58.185 40.909 0.00 0.00 39.77 3.18
672 675 5.411361 TGTATGGCAAAGTACATGAGTGTTC 59.589 40.000 0.00 0.00 39.77 3.18
673 676 5.312895 TGTATGGCAAAGTACATGAGTGTT 58.687 37.500 0.00 0.00 39.77 3.32
674 677 4.905429 TGTATGGCAAAGTACATGAGTGT 58.095 39.130 0.00 0.00 42.39 3.55
675 678 5.878332 TTGTATGGCAAAGTACATGAGTG 57.122 39.130 0.00 0.00 33.53 3.51
676 679 5.945784 ACATTGTATGGCAAAGTACATGAGT 59.054 36.000 0.00 0.00 40.91 3.41
677 680 6.441093 ACATTGTATGGCAAAGTACATGAG 57.559 37.500 0.00 0.00 40.91 2.90
683 686 8.574251 AGAAATGTACATTGTATGGCAAAGTA 57.426 30.769 21.46 0.00 39.40 2.24
684 687 7.466746 AGAAATGTACATTGTATGGCAAAGT 57.533 32.000 21.46 1.36 41.26 2.66
710 713 7.446319 CCATAGATGGCTAAACATGATGAGAAA 59.554 37.037 0.00 0.00 41.75 2.52
747 756 9.831737 CATACATGTCTTTCTTCTTACCTTTTG 57.168 33.333 0.00 0.00 0.00 2.44
764 773 6.347725 GGACGAAATTATGAGCCATACATGTC 60.348 42.308 0.00 0.00 0.00 3.06
856 870 0.111832 ACGGGTGAGTGGTAGTGAGA 59.888 55.000 0.00 0.00 0.00 3.27
911 939 2.914777 GATCGTGGGCTGTGAGGAGC 62.915 65.000 0.00 0.00 38.34 4.70
916 944 2.230994 GAGCTGATCGTGGGCTGTGA 62.231 60.000 0.00 0.00 36.37 3.58
969 997 7.345392 ACATATAAGGCTTGGAATTGGTTTCAT 59.655 33.333 10.69 0.00 35.94 2.57
1104 1132 2.103042 GTTGCCGCATCTCTTCGCT 61.103 57.895 0.00 0.00 0.00 4.93
1150 1178 1.379309 TTTCCGCCCCCATGTTAGC 60.379 57.895 0.00 0.00 0.00 3.09
1260 1288 4.946772 TCCTCATAGGAGATGTCGATGATC 59.053 45.833 5.84 0.00 44.26 2.92
1289 1317 0.589708 TAGGTCGATGACGCGTATGG 59.410 55.000 13.97 8.00 39.58 2.74
1293 1321 3.108343 CCTAGGTCGATGACGCGT 58.892 61.111 13.85 13.85 39.58 6.01
1382 1411 1.141234 GGGTCGATCCTGAACGGAC 59.859 63.158 7.71 0.00 46.80 4.79
1469 1498 3.288308 CTCAACTCGACCAGCGCCT 62.288 63.158 2.29 0.00 40.61 5.52
1560 1589 0.688087 CCCTCCAGAGAGTACCCCAC 60.688 65.000 0.00 0.00 38.58 4.61
1561 1590 1.704082 CCCTCCAGAGAGTACCCCA 59.296 63.158 0.00 0.00 38.58 4.96
1562 1591 1.075151 CCCCTCCAGAGAGTACCCC 60.075 68.421 0.00 0.00 38.58 4.95
1563 1592 0.688087 CACCCCTCCAGAGAGTACCC 60.688 65.000 0.00 0.00 38.58 3.69
1564 1593 1.331399 GCACCCCTCCAGAGAGTACC 61.331 65.000 0.00 0.00 38.58 3.34
1565 1594 0.614979 TGCACCCCTCCAGAGAGTAC 60.615 60.000 0.00 0.00 38.58 2.73
1566 1595 0.339859 ATGCACCCCTCCAGAGAGTA 59.660 55.000 0.00 0.00 38.58 2.59
1657 1686 1.203287 GCCATTTCAAGAGGAAGCCAC 59.797 52.381 0.00 0.00 36.72 5.01
1683 1712 2.161012 CGAGCTTACCAGTAACAGACGA 59.839 50.000 0.00 0.00 0.00 4.20
1792 1821 7.093245 GGGTGAAGAGTAGAGAAAGAAGGTATT 60.093 40.741 0.00 0.00 0.00 1.89
1793 1822 6.381707 GGGTGAAGAGTAGAGAAAGAAGGTAT 59.618 42.308 0.00 0.00 0.00 2.73
1838 1867 5.873164 ACCGTGGATAATTAGTTCAACACTC 59.127 40.000 0.00 0.00 36.88 3.51
1987 2016 2.805099 AGTCGTCGTCGAGATATTACCC 59.195 50.000 4.68 0.00 46.96 3.69
2004 2036 5.297278 AGTGCCTCTAGTCAGTAATTAGTCG 59.703 44.000 0.00 0.00 0.00 4.18
2005 2037 6.319152 TGAGTGCCTCTAGTCAGTAATTAGTC 59.681 42.308 4.21 0.00 0.00 2.59
2006 2038 6.188407 TGAGTGCCTCTAGTCAGTAATTAGT 58.812 40.000 4.21 0.00 0.00 2.24
2047 2079 8.717821 TCCAAGTTTCTTCACAAGATAAATACG 58.282 33.333 0.00 0.00 37.38 3.06
2120 2259 0.954449 GAGATGCCGGGCAGATCATG 60.954 60.000 27.62 0.00 43.65 3.07
2264 2406 4.640771 AGAATGAAAGGCACTCCACTAA 57.359 40.909 0.00 0.00 38.49 2.24
2308 2592 6.309357 TCTGGCTAAGAATGAATGGCATATT 58.691 36.000 0.00 0.00 35.78 1.28
2342 2626 5.333035 CCATGTTAGACGTACTTGTGTTGTG 60.333 44.000 0.00 0.00 0.00 3.33
2350 2634 2.565834 AGTGCCCATGTTAGACGTACTT 59.434 45.455 0.00 0.00 0.00 2.24
2368 2686 5.063438 CGTCAATTGGTATACTTGTGGAGTG 59.937 44.000 5.42 0.00 39.48 3.51
2408 2726 1.398958 GGAGGAGCGATTCAGAGGCT 61.399 60.000 0.00 0.00 40.29 4.58
2410 2728 1.745264 GGGAGGAGCGATTCAGAGG 59.255 63.158 0.00 0.00 0.00 3.69
2411 2729 1.361993 CGGGAGGAGCGATTCAGAG 59.638 63.158 0.00 0.00 0.00 3.35
2412 2730 2.786495 GCGGGAGGAGCGATTCAGA 61.786 63.158 0.00 0.00 0.00 3.27
2413 2731 2.279784 GCGGGAGGAGCGATTCAG 60.280 66.667 0.00 0.00 0.00 3.02
2414 2732 3.849951 GGCGGGAGGAGCGATTCA 61.850 66.667 0.00 0.00 35.00 2.57
2415 2733 3.170490 ATGGCGGGAGGAGCGATTC 62.170 63.158 0.00 0.00 35.00 2.52
2483 4183 1.463444 CACGGAAAATCGGAAGGACAC 59.537 52.381 0.00 0.00 0.00 3.67
2486 4186 1.017177 CGCACGGAAAATCGGAAGGA 61.017 55.000 0.00 0.00 0.00 3.36
2500 4200 1.744811 TAGTTAAATCCGCGCGCACG 61.745 55.000 32.61 20.43 44.07 5.34
2501 4201 0.580104 ATAGTTAAATCCGCGCGCAC 59.420 50.000 32.61 19.42 0.00 5.34
2502 4202 0.579630 CATAGTTAAATCCGCGCGCA 59.420 50.000 32.61 11.60 0.00 6.09
2503 4203 0.110823 CCATAGTTAAATCCGCGCGC 60.111 55.000 27.36 23.91 0.00 6.86
2506 4217 1.878953 AGGCCATAGTTAAATCCGCG 58.121 50.000 5.01 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.