Multiple sequence alignment - TraesCS7B01G140400

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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 TraesCS7B01G140400 chr7B 100.000 3556 0 0 1 3556 178398847 178402402 0.000000e+00 6567.0
1 TraesCS7B01G140400 chr7B 100.000 3267 0 0 3894 7160 178402740 178406006 0.000000e+00 6034.0
2 TraesCS7B01G140400 chr7D 94.580 3284 119 19 3919 7160 220518450 220515184 0.000000e+00 5024.0
3 TraesCS7B01G140400 chr7D 95.240 2248 91 7 832 3072 220521304 220519066 0.000000e+00 3544.0
4 TraesCS7B01G140400 chr7D 86.316 570 45 16 2980 3543 220519073 220518531 2.220000e-164 590.0
5 TraesCS7B01G140400 chr7D 79.085 306 40 14 6027 6316 618329191 618328894 9.480000e-44 189.0
6 TraesCS7B01G140400 chr7A 95.564 2660 91 9 3926 6567 232753392 232750742 0.000000e+00 4233.0
7 TraesCS7B01G140400 chr7A 94.710 2741 104 19 832 3556 232758687 232755972 0.000000e+00 4220.0
8 TraesCS7B01G140400 chr7A 94.420 448 21 2 6713 7160 232750729 232750286 0.000000e+00 686.0
9 TraesCS7B01G140400 chr2B 94.675 845 33 7 1 833 406539218 406538374 0.000000e+00 1301.0
10 TraesCS7B01G140400 chr2B 92.732 853 48 8 1 839 106924623 106923771 0.000000e+00 1219.0
11 TraesCS7B01G140400 chr2B 91.304 138 12 0 6566 6703 442788208 442788071 9.480000e-44 189.0
12 TraesCS7B01G140400 chr1B 93.437 838 43 10 1 829 576027972 576028806 0.000000e+00 1232.0
13 TraesCS7B01G140400 chr1B 90.580 138 13 0 6566 6703 414091027 414090890 4.410000e-42 183.0
14 TraesCS7B01G140400 chr3D 93.206 839 48 8 1 831 586301436 586300599 0.000000e+00 1225.0
15 TraesCS7B01G140400 chr3D 91.304 138 12 0 6566 6703 537154704 537154841 9.480000e-44 189.0
16 TraesCS7B01G140400 chr5D 93.009 844 44 11 1 831 138810264 138811105 0.000000e+00 1218.0
17 TraesCS7B01G140400 chr5D 92.857 840 44 10 1 831 198441328 198440496 0.000000e+00 1205.0
18 TraesCS7B01G140400 chr4D 92.738 840 51 9 1 831 487160722 487161560 0.000000e+00 1205.0
19 TraesCS7B01G140400 chr4D 100.000 29 0 0 3402 3430 399614156 399614128 4.000000e-03 54.7
20 TraesCS7B01G140400 chrUn 92.628 841 50 11 1 831 22758862 22758024 0.000000e+00 1199.0
21 TraesCS7B01G140400 chr2D 92.417 844 49 13 1 831 381560842 381561683 0.000000e+00 1190.0
22 TraesCS7B01G140400 chr4B 92.029 138 11 0 6566 6703 135218208 135218071 2.040000e-45 195.0
23 TraesCS7B01G140400 chr1D 91.304 138 12 0 6566 6703 463382064 463381927 9.480000e-44 189.0
24 TraesCS7B01G140400 chr1D 79.532 171 29 5 3331 3498 387898819 387898986 4.540000e-22 117.0
25 TraesCS7B01G140400 chr5B 90.647 139 13 0 6566 6704 490757414 490757552 1.230000e-42 185.0
26 TraesCS7B01G140400 chr4A 90.580 138 13 0 6566 6703 517406630 517406493 4.410000e-42 183.0
27 TraesCS7B01G140400 chr1A 90.580 138 13 0 6566 6703 566481167 566481030 4.410000e-42 183.0


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 TraesCS7B01G140400 chr7B 178398847 178406006 7159 False 6300.500000 6567 100.000000 1 7160 2 chr7B.!!$F1 7159
1 TraesCS7B01G140400 chr7D 220515184 220521304 6120 True 3052.666667 5024 92.045333 832 7160 3 chr7D.!!$R2 6328
2 TraesCS7B01G140400 chr7A 232750286 232758687 8401 True 3046.333333 4233 94.898000 832 7160 3 chr7A.!!$R1 6328
3 TraesCS7B01G140400 chr2B 406538374 406539218 844 True 1301.000000 1301 94.675000 1 833 1 chr2B.!!$R2 832
4 TraesCS7B01G140400 chr2B 106923771 106924623 852 True 1219.000000 1219 92.732000 1 839 1 chr2B.!!$R1 838
5 TraesCS7B01G140400 chr1B 576027972 576028806 834 False 1232.000000 1232 93.437000 1 829 1 chr1B.!!$F1 828
6 TraesCS7B01G140400 chr3D 586300599 586301436 837 True 1225.000000 1225 93.206000 1 831 1 chr3D.!!$R1 830
7 TraesCS7B01G140400 chr5D 138810264 138811105 841 False 1218.000000 1218 93.009000 1 831 1 chr5D.!!$F1 830
8 TraesCS7B01G140400 chr5D 198440496 198441328 832 True 1205.000000 1205 92.857000 1 831 1 chr5D.!!$R1 830
9 TraesCS7B01G140400 chr4D 487160722 487161560 838 False 1205.000000 1205 92.738000 1 831 1 chr4D.!!$F1 830
10 TraesCS7B01G140400 chrUn 22758024 22758862 838 True 1199.000000 1199 92.628000 1 831 1 chrUn.!!$R1 830
11 TraesCS7B01G140400 chr2D 381560842 381561683 841 False 1190.000000 1190 92.417000 1 831 1 chr2D.!!$F1 830

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
703 742 1.185315 CCCAATTCAGCAAATCCCGT 58.815 50.000 0.00 0.00 0.00 5.28 F
1326 1370 0.767375 ACTGCTTCCACCATGTGAGT 59.233 50.000 0.00 0.00 35.23 3.41 F
1426 1471 0.951558 AGGCAAACCAACGTAGCTTG 59.048 50.000 0.00 0.00 39.06 4.01 F
1888 1933 1.277557 CTAGCAGACCACTTTGCCTCT 59.722 52.381 0.00 0.00 41.17 3.69 F
3212 3354 1.515521 CCACCGCTTTCCCACTGAAC 61.516 60.000 0.00 0.00 31.05 3.18 F
4722 7090 0.478072 TTATGCTGCGGGGGAATGAT 59.522 50.000 0.00 0.00 0.00 2.45 F
5935 8327 1.678970 GAAGATGTGGCCGGGCTTT 60.679 57.895 29.87 13.57 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1854 1.800805 AGCACTGTCGTTCTCAATGG 58.199 50.000 0.0 0.0 0.00 3.16 R
3159 3293 1.071605 GCGAACTCAGTTGGCACTAG 58.928 55.000 18.8 0.0 44.46 2.57 R
3342 3487 2.972267 CCCCATTGCAACGCATGT 59.028 55.556 0.0 0.0 38.76 3.21 R
3507 3654 2.270275 TTTGTTGAAAGCCACACACG 57.730 45.000 0.0 0.0 0.00 4.49 R
5007 7391 1.231221 ATTTCGTTGGCGTTGCTGTA 58.769 45.000 0.0 0.0 39.49 2.74 R
5964 8356 0.032615 CCCAGTCTCTCTGCCCTACT 60.033 60.000 0.0 0.0 42.38 2.57 R
6828 9246 1.402259 CGCGGCATGGGTTAATTTGTA 59.598 47.619 0.0 0.0 0.00 2.41 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
65 68 5.049612 TGCGGACACGTTTTGATACATAAAA 60.050 36.000 0.00 0.00 43.45 1.52
95 98 9.748708 TTCTGAAACCTGAAAATATTTTGTGAG 57.251 29.630 17.98 10.27 0.00 3.51
390 406 5.964958 ATGTGAACCATGTAAAAGAGTGG 57.035 39.130 0.00 0.00 37.74 4.00
633 665 6.208988 AGAAAGCGAAAAAGGAAGAAACTT 57.791 33.333 0.00 0.00 0.00 2.66
703 742 1.185315 CCCAATTCAGCAAATCCCGT 58.815 50.000 0.00 0.00 0.00 5.28
778 817 4.289410 TGATTTCAGGGATTGAGAGTTGGA 59.711 41.667 0.00 0.00 37.07 3.53
867 911 8.428063 TCCCAAAGATTGCTTCAAAAGAAATTA 58.572 29.630 0.00 0.00 36.88 1.40
988 1032 5.167845 ACTTTCGCAAGTGACAACAAAAAT 58.832 33.333 0.00 0.00 42.05 1.82
1072 1116 2.284699 CCTCCTCGTCCCCTGGTT 60.285 66.667 0.00 0.00 0.00 3.67
1122 1166 3.720106 CTTCTCGGTCGACCTCGCG 62.720 68.421 30.92 18.20 39.60 5.87
1326 1370 0.767375 ACTGCTTCCACCATGTGAGT 59.233 50.000 0.00 0.00 35.23 3.41
1342 1386 1.986575 GAGTCTTCTTGCCGCCATGC 61.987 60.000 0.00 0.00 0.00 4.06
1413 1458 7.945664 TCTGGAGGTTATTTTACTTAAGGCAAA 59.054 33.333 7.53 5.68 0.00 3.68
1424 1469 2.554370 TAAGGCAAACCAACGTAGCT 57.446 45.000 0.00 0.00 39.06 3.32
1426 1471 0.951558 AGGCAAACCAACGTAGCTTG 59.048 50.000 0.00 0.00 39.06 4.01
1451 1496 7.547019 TGAACAGTTGTTGCATTCACAATTTAA 59.453 29.630 5.77 0.00 38.56 1.52
1519 1564 4.396357 TTTGAAAAAGATCCCCTGGCTA 57.604 40.909 0.00 0.00 0.00 3.93
1569 1614 7.759465 TCACTGAACTTTAGGATCTACTTACG 58.241 38.462 0.00 0.00 0.00 3.18
1598 1643 7.224557 TGAGCCTTTAAAATTTTCTGACAAAGC 59.775 33.333 6.72 7.72 0.00 3.51
1636 1681 1.944177 TCTTCTGTTCCCAGGAGAGG 58.056 55.000 0.00 0.00 46.45 3.69
1786 1831 4.261572 CCGTTTGACCTTGACAACAATGAT 60.262 41.667 0.00 0.00 35.37 2.45
1809 1854 9.033481 TGATTTTGATGGAAATAATTCGAATGC 57.967 29.630 12.25 0.00 36.36 3.56
1888 1933 1.277557 CTAGCAGACCACTTTGCCTCT 59.722 52.381 0.00 0.00 41.17 3.69
2207 2252 6.305272 ACACTGATGTCTATCAAGGACAAT 57.695 37.500 0.72 0.00 45.09 2.71
2232 2277 9.693739 ATGTTATGAAAATGGTGGTCAGTTATA 57.306 29.630 0.00 0.00 31.92 0.98
2878 2924 7.858382 TCGTAAAATATGCCGTGGATTTTTATG 59.142 33.333 3.12 0.00 35.14 1.90
2925 2971 9.814899 AATTATCTGATCACAAGAGTCTAACAG 57.185 33.333 0.00 0.00 0.00 3.16
2992 3038 6.581171 ATCCTTGGAAGAACAAAAAGCTAG 57.419 37.500 0.00 0.00 0.00 3.42
3008 3054 3.522553 AGCTAGAGTTTGCACCGTTATC 58.477 45.455 0.00 0.00 0.00 1.75
3029 3075 4.621991 TCGAGTTAATGAGCTTATCTGCC 58.378 43.478 0.00 0.00 0.00 4.85
3062 3108 8.877779 CATTAGTATTTGCAGCTGATAGGTATC 58.122 37.037 20.43 0.00 0.00 2.24
3065 3199 1.704641 TGCAGCTGATAGGTATCCGT 58.295 50.000 20.43 0.00 31.71 4.69
3159 3293 4.919754 GCATGAACTTGAAACAGGAACATC 59.080 41.667 0.00 0.00 0.00 3.06
3212 3354 1.515521 CCACCGCTTTCCCACTGAAC 61.516 60.000 0.00 0.00 31.05 3.18
3364 3509 3.301554 CGTTGCAATGGGGCCACA 61.302 61.111 11.97 11.97 30.39 4.17
3386 3531 6.155896 CAAAATAATTTGTACGCGATCACG 57.844 37.500 15.93 0.68 40.84 4.35
3387 3532 5.730802 CAAAATAATTTGTACGCGATCACGT 59.269 36.000 15.93 13.94 42.18 4.49
3445 3590 7.330208 CCAATTGAATCAGCACTTCCTTAAAAG 59.670 37.037 7.12 0.00 0.00 2.27
3516 3663 1.519408 ACCAATAAGACGTGTGTGGC 58.481 50.000 9.47 0.00 0.00 5.01
3537 3684 4.154015 GGCTTTCAACAAAAATATGTGGGC 59.846 41.667 0.00 0.00 32.81 5.36
3544 3691 6.038714 TCAACAAAAATATGTGGGCAAAAACC 59.961 34.615 0.00 0.00 32.81 3.27
3545 3692 5.440610 ACAAAAATATGTGGGCAAAAACCA 58.559 33.333 0.00 0.00 35.14 3.67
3547 3694 5.559148 AAAATATGTGGGCAAAAACCAGA 57.441 34.783 0.00 0.00 39.00 3.86
3548 3695 4.806640 AATATGTGGGCAAAAACCAGAG 57.193 40.909 0.00 0.00 39.00 3.35
3549 3696 2.086610 ATGTGGGCAAAAACCAGAGT 57.913 45.000 0.00 0.00 39.00 3.24
3910 4057 2.280524 TGGGGAGCGAAACACGTG 60.281 61.111 15.48 15.48 44.60 4.49
3911 4058 3.047877 GGGGAGCGAAACACGTGG 61.048 66.667 21.57 2.48 44.60 4.94
4071 6431 3.288809 AGCAAGGAATTTCTGCGTTTC 57.711 42.857 5.33 0.00 0.00 2.78
4074 6434 1.165270 AGGAATTTCTGCGTTTCCGG 58.835 50.000 0.00 0.00 43.01 5.14
4476 6836 1.374252 GTGGCTGACCCGTACAGTG 60.374 63.158 0.00 0.00 37.64 3.66
4485 6845 2.928116 GACCCGTACAGTGCTTGATTAC 59.072 50.000 0.00 0.00 0.00 1.89
4579 6939 9.573166 AATCTATAGCTTAACATTATGTGGCAA 57.427 29.630 16.00 4.75 0.00 4.52
4594 6954 0.894835 GGCAAATACCACACCCCTTG 59.105 55.000 0.00 0.00 0.00 3.61
4608 6968 2.764010 ACCCCTTGACAAGTTTTTGGTC 59.236 45.455 14.03 0.00 38.66 4.02
4628 6988 9.771534 TTTGGTCAATTTTCTAACAAAATAGGG 57.228 29.630 0.00 0.00 30.38 3.53
4629 6989 7.382898 TGGTCAATTTTCTAACAAAATAGGGC 58.617 34.615 0.00 0.00 30.38 5.19
4630 6990 7.015682 TGGTCAATTTTCTAACAAAATAGGGCA 59.984 33.333 0.00 0.00 30.38 5.36
4631 6991 8.040727 GGTCAATTTTCTAACAAAATAGGGCAT 58.959 33.333 0.00 0.00 30.38 4.40
4632 6992 8.872845 GTCAATTTTCTAACAAAATAGGGCATG 58.127 33.333 0.00 0.00 30.38 4.06
4633 6993 7.548780 TCAATTTTCTAACAAAATAGGGCATGC 59.451 33.333 9.90 9.90 30.38 4.06
4634 6994 5.991933 TTTCTAACAAAATAGGGCATGCA 57.008 34.783 21.36 0.00 0.00 3.96
4635 6995 5.581126 TTCTAACAAAATAGGGCATGCAG 57.419 39.130 21.36 3.36 0.00 4.41
4636 6996 4.599041 TCTAACAAAATAGGGCATGCAGT 58.401 39.130 21.36 8.22 0.00 4.40
4719 7087 1.529244 GCTTATGCTGCGGGGGAAT 60.529 57.895 0.00 0.00 36.03 3.01
4722 7090 0.478072 TTATGCTGCGGGGGAATGAT 59.522 50.000 0.00 0.00 0.00 2.45
4770 7153 4.619973 TGTGCTGAATTCAATTCCAACAC 58.380 39.130 9.88 15.38 38.50 3.32
4921 7304 2.835764 TGCTCCGGGTAACTTCATTACT 59.164 45.455 0.00 0.00 42.58 2.24
4990 7374 5.007682 GCCTAGTTGTTTCCCTTTGTGATA 58.992 41.667 0.00 0.00 0.00 2.15
5007 7391 4.142038 GTGATACAGAAAAGGTGGTTGGT 58.858 43.478 0.00 0.00 0.00 3.67
5132 7516 5.936956 AGCTACAAAATGAGACTTCAGAAGG 59.063 40.000 14.90 0.00 36.61 3.46
5141 7525 4.952957 TGAGACTTCAGAAGGAGAGGTATG 59.047 45.833 14.90 0.00 0.00 2.39
5179 7564 3.716601 TCGCTCGATTTCTTGATGCATA 58.283 40.909 0.00 0.00 0.00 3.14
5191 7577 6.839124 TCTTGATGCATATTTTTGTCTGGT 57.161 33.333 0.00 0.00 0.00 4.00
5336 7722 4.457949 AGTTACCAGGCAAAAAGGATTACG 59.542 41.667 0.00 0.00 0.00 3.18
5353 7739 6.042781 AGGATTACGGCACTCCATCTTTATTA 59.957 38.462 0.00 0.00 0.00 0.98
5484 7871 8.801299 TGGTCATGTTTTCTATTTAATGCAGAA 58.199 29.630 0.00 0.00 0.00 3.02
5549 7937 6.202516 AGACTAGCTAGATTCAACTGTGAC 57.797 41.667 27.45 0.00 31.90 3.67
5796 8188 4.662179 ACATCACCAGATTATCCTGATGGT 59.338 41.667 20.03 11.82 45.00 3.55
5862 8254 3.330701 TCTTACCCAAAGAGGATGCAGTT 59.669 43.478 0.00 0.00 39.36 3.16
5935 8327 1.678970 GAAGATGTGGCCGGGCTTT 60.679 57.895 29.87 13.57 0.00 3.51
6006 8398 2.265739 GTGATGCTGCCGGACTCA 59.734 61.111 5.05 0.00 0.00 3.41
6051 8443 3.707458 TGGTACCGGAATGCGGCA 61.707 61.111 14.43 4.58 0.00 5.69
6265 8659 6.558771 TGGTTGTACATGTCATCTGAAAAG 57.441 37.500 0.00 0.00 0.00 2.27
6400 8794 6.775142 TGAAAACTGTCCCAGAAAATATGTCA 59.225 34.615 0.00 0.00 35.18 3.58
6639 9044 6.988580 ACATGAGGATGTACACAGACATATTG 59.011 38.462 0.00 0.00 41.27 1.90
6645 9050 7.014711 AGGATGTACACAGACATATTGTAGAGG 59.985 40.741 0.00 0.00 40.18 3.69
6655 9060 8.811017 CAGACATATTGTAGAGGGTAGATTCAT 58.189 37.037 0.00 0.00 0.00 2.57
6668 9073 5.506317 GGGTAGATTCATTCATTTTGCTCCG 60.506 44.000 0.00 0.00 0.00 4.63
6679 9084 5.109210 TCATTTTGCTCCGTATGTAGTCTG 58.891 41.667 0.00 0.00 0.00 3.51
6696 9101 5.317733 AGTCTGTAGTGGAATCTCGAAAG 57.682 43.478 0.00 0.00 0.00 2.62
6757 9175 3.368495 GCACAACCTTTTCGAAATTCGT 58.632 40.909 15.34 5.38 41.35 3.85
6781 9199 7.436673 CGTATGATTTCTCTCAAAGGTTAGGAG 59.563 40.741 0.00 0.00 0.00 3.69
6798 9216 6.126565 GGTTAGGAGGGGATGTACAGTAAATT 60.127 42.308 0.33 0.00 0.00 1.82
6825 9243 8.687292 TTCTTTCTTATATCATGCAAGCATCT 57.313 30.769 4.24 0.00 33.90 2.90
6826 9244 9.783081 TTCTTTCTTATATCATGCAAGCATCTA 57.217 29.630 4.24 0.81 33.90 1.98
6827 9245 9.212641 TCTTTCTTATATCATGCAAGCATCTAC 57.787 33.333 4.24 0.00 33.90 2.59
6828 9246 9.217278 CTTTCTTATATCATGCAAGCATCTACT 57.783 33.333 4.24 0.00 33.90 2.57
6877 9295 1.321474 TTCTTTCTTGGTGCTGCTGG 58.679 50.000 0.00 0.00 0.00 4.85
6895 9313 2.693591 CTGGCAGCTGGATTTGATGAAT 59.306 45.455 17.12 0.00 0.00 2.57
6989 9407 2.770802 CTCATGAGGATGAAGACTGGGT 59.229 50.000 15.38 0.00 38.17 4.51
7086 9504 0.668401 GCATCAGCCTGCCAAACAAC 60.668 55.000 0.00 0.00 36.10 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 21 7.412455 CGCACTTTAAAATTTTGTTCAGGTTGT 60.412 33.333 13.76 0.00 0.00 3.32
222 235 5.574830 CACAAACACAATTTTTGGAACTCGA 59.425 36.000 6.16 0.00 38.12 4.04
567 587 8.157476 ACACATGTCTAATTTTTCTCAGTACCT 58.843 33.333 0.00 0.00 0.00 3.08
615 647 7.980742 TTTTCTAAGTTTCTTCCTTTTTCGC 57.019 32.000 0.00 0.00 0.00 4.70
633 665 3.369756 CGCGCACTAATCTGGTTTTTCTA 59.630 43.478 8.75 0.00 0.00 2.10
728 767 6.373216 CACACCAAACTCTTTAATCCCGATTA 59.627 38.462 0.00 0.00 32.50 1.75
729 768 5.183140 CACACCAAACTCTTTAATCCCGATT 59.817 40.000 0.00 0.00 34.93 3.34
731 770 4.069304 CACACCAAACTCTTTAATCCCGA 58.931 43.478 0.00 0.00 0.00 5.14
867 911 6.009115 ACCGAGCAAACGATTTCTAAAAAT 57.991 33.333 0.00 0.00 37.80 1.82
988 1032 4.935205 CCTTGTTGTCATCGGTGAGAATAA 59.065 41.667 11.82 13.81 39.47 1.40
1188 1232 2.438975 TCGTACCTCCGCACGGAT 60.439 61.111 12.94 0.94 44.24 4.18
1326 1370 2.751436 GGCATGGCGGCAAGAAGA 60.751 61.111 18.31 0.00 40.76 2.87
1342 1386 3.982576 AACGCAACCAGTAAAAGAAGG 57.017 42.857 0.00 0.00 0.00 3.46
1413 1458 2.612212 CAACTGTTCAAGCTACGTTGGT 59.388 45.455 0.00 0.00 32.08 3.67
1424 1469 4.446994 TGTGAATGCAACAACTGTTCAA 57.553 36.364 0.00 0.00 35.83 2.69
1426 1471 5.971895 AATTGTGAATGCAACAACTGTTC 57.028 34.783 4.62 0.00 35.83 3.18
1451 1496 9.289782 AGAACAAGCAAAGTAATCTTGTATTCT 57.710 29.630 7.20 5.36 46.63 2.40
1488 1533 7.947890 AGGGGATCTTTTTCAAAATACAGTACA 59.052 33.333 0.00 0.00 0.00 2.90
1489 1534 8.244113 CAGGGGATCTTTTTCAAAATACAGTAC 58.756 37.037 0.00 0.00 0.00 2.73
1490 1535 7.396055 CCAGGGGATCTTTTTCAAAATACAGTA 59.604 37.037 0.00 0.00 0.00 2.74
1491 1536 6.211384 CCAGGGGATCTTTTTCAAAATACAGT 59.789 38.462 0.00 0.00 0.00 3.55
1492 1537 6.633856 CCAGGGGATCTTTTTCAAAATACAG 58.366 40.000 0.00 0.00 0.00 2.74
1568 1613 7.221838 TGTCAGAAAATTTTAAAGGCTCAAACG 59.778 33.333 2.75 0.00 0.00 3.60
1569 1614 8.419076 TGTCAGAAAATTTTAAAGGCTCAAAC 57.581 30.769 2.75 0.00 0.00 2.93
1598 1643 2.416547 AGAATCCACTTGAAATCGCACG 59.583 45.455 0.00 0.00 0.00 5.34
1747 1792 2.590092 GGCTCCAATGGGTAGCGT 59.410 61.111 6.85 0.00 37.87 5.07
1786 1831 7.326454 TGGCATTCGAATTATTTCCATCAAAA 58.674 30.769 8.21 0.00 0.00 2.44
1804 1849 2.744202 ACTGTCGTTCTCAATGGCATTC 59.256 45.455 10.36 0.00 30.54 2.67
1809 1854 1.800805 AGCACTGTCGTTCTCAATGG 58.199 50.000 0.00 0.00 0.00 3.16
1888 1933 2.368875 GACACCTTCTGAGACAAAGGGA 59.631 50.000 3.89 0.00 45.27 4.20
2207 2252 9.173021 CTATAACTGACCACCATTTTCATAACA 57.827 33.333 0.00 0.00 0.00 2.41
2232 2277 2.608988 CTCACTGGCCACCTCCCT 60.609 66.667 0.00 0.00 0.00 4.20
2470 2515 8.043113 TGAAGCTGTATCACAAGTTCTTCATAT 58.957 33.333 0.00 0.00 35.28 1.78
2789 2835 9.701098 CTACCAACTACATTCACTACTTAACAA 57.299 33.333 0.00 0.00 0.00 2.83
2839 2885 7.148423 GGCATATTTTACGATATGATGACTGCA 60.148 37.037 8.61 0.00 40.74 4.41
2842 2888 7.063426 CACGGCATATTTTACGATATGATGACT 59.937 37.037 8.61 0.00 40.74 3.41
2851 2897 6.385649 AAAATCCACGGCATATTTTACGAT 57.614 33.333 0.00 0.00 32.51 3.73
2906 2952 9.244292 AGTTATACTGTTAGACTCTTGTGATCA 57.756 33.333 0.00 0.00 0.00 2.92
2935 2981 9.463443 AAGCACACAAGAATTAACATTTTACTC 57.537 29.630 0.00 0.00 0.00 2.59
2992 3038 2.334838 ACTCGATAACGGTGCAAACTC 58.665 47.619 0.00 0.00 40.21 3.01
3008 3054 3.743396 GGGCAGATAAGCTCATTAACTCG 59.257 47.826 0.00 0.00 34.32 4.18
3029 3075 5.468072 CAGCTGCAAATACTAATGAGTAGGG 59.532 44.000 0.00 0.00 41.50 3.53
3075 3209 6.478673 TGGAAGTACAAATAGATATGTGTGCG 59.521 38.462 6.01 0.00 40.22 5.34
3159 3293 1.071605 GCGAACTCAGTTGGCACTAG 58.928 55.000 18.80 0.00 44.46 2.57
3170 3312 4.329545 GCCCCCACAGCGAACTCA 62.330 66.667 0.00 0.00 0.00 3.41
3212 3354 5.185635 TGGGCCAATTCTCTACTTTTCAATG 59.814 40.000 2.13 0.00 0.00 2.82
3342 3487 2.972267 CCCCATTGCAACGCATGT 59.028 55.556 0.00 0.00 38.76 3.21
3344 3489 3.773404 GGCCCCATTGCAACGCAT 61.773 61.111 0.00 0.00 38.76 4.73
3364 3509 5.860641 ACGTGATCGCGTACAAATTATTTT 58.139 33.333 31.31 3.08 43.83 1.82
3445 3590 6.753744 GGCAAGTCAATAAATGTTGATTCTCC 59.246 38.462 0.00 0.00 39.99 3.71
3446 3591 7.315142 TGGCAAGTCAATAAATGTTGATTCTC 58.685 34.615 0.00 0.00 39.99 2.87
3507 3654 2.270275 TTTGTTGAAAGCCACACACG 57.730 45.000 0.00 0.00 0.00 4.49
3511 3658 5.757320 CCACATATTTTTGTTGAAAGCCACA 59.243 36.000 0.00 0.00 0.00 4.17
3516 3663 6.857777 TTGCCCACATATTTTTGTTGAAAG 57.142 33.333 0.00 0.00 0.00 2.62
3893 4040 2.280524 CACGTGTTTCGCTCCCCA 60.281 61.111 7.58 0.00 44.19 4.96
3894 4041 3.047877 CCACGTGTTTCGCTCCCC 61.048 66.667 15.65 0.00 44.19 4.81
3895 4042 3.047877 CCCACGTGTTTCGCTCCC 61.048 66.667 15.65 0.00 44.19 4.30
3896 4043 2.280592 ACCCACGTGTTTCGCTCC 60.281 61.111 15.65 0.00 44.19 4.70
3897 4044 1.155424 TTCACCCACGTGTTTCGCTC 61.155 55.000 15.65 0.00 44.19 5.03
3898 4045 0.745128 TTTCACCCACGTGTTTCGCT 60.745 50.000 15.65 0.00 44.19 4.93
3901 4048 2.486592 CCCTATTTCACCCACGTGTTTC 59.513 50.000 15.65 0.00 41.09 2.78
3904 4051 1.354101 TCCCTATTTCACCCACGTGT 58.646 50.000 15.65 0.00 41.09 4.49
3905 4052 2.081462 GTTCCCTATTTCACCCACGTG 58.919 52.381 9.08 9.08 41.72 4.49
3906 4053 1.003928 GGTTCCCTATTTCACCCACGT 59.996 52.381 0.00 0.00 0.00 4.49
3908 4055 3.451402 AAGGTTCCCTATTTCACCCAC 57.549 47.619 0.00 0.00 31.13 4.61
3910 4057 5.045066 AGACTTAAGGTTCCCTATTTCACCC 60.045 44.000 7.53 0.00 31.13 4.61
3911 4058 6.063496 AGACTTAAGGTTCCCTATTTCACC 57.937 41.667 7.53 0.00 31.13 4.02
4071 6431 1.375523 GTAACACCTCTGTGCCCGG 60.376 63.158 0.00 0.00 46.86 5.73
4074 6434 2.028112 TGATCTGTAACACCTCTGTGCC 60.028 50.000 0.00 0.00 46.86 5.01
4294 6654 1.380380 TGGCATCGAGCTCCTCTGA 60.380 57.895 8.47 0.00 44.79 3.27
4476 6836 2.706890 TCTTTCCCACCGTAATCAAGC 58.293 47.619 0.00 0.00 0.00 4.01
4485 6845 1.877443 ACGAAACATTCTTTCCCACCG 59.123 47.619 0.00 0.00 0.00 4.94
4545 6905 7.639162 ATGTTAAGCTATAGATTCCGAAACG 57.361 36.000 6.50 0.00 0.00 3.60
4579 6939 2.445525 ACTTGTCAAGGGGTGTGGTATT 59.554 45.455 16.85 0.00 0.00 1.89
4594 6954 9.145865 TGTTAGAAAATTGACCAAAAACTTGTC 57.854 29.630 0.00 0.00 0.00 3.18
4608 6968 7.333921 TGCATGCCCTATTTTGTTAGAAAATTG 59.666 33.333 16.68 4.08 32.64 2.32
4626 6986 2.057137 TATCTTTGGACTGCATGCCC 57.943 50.000 16.68 10.02 0.00 5.36
4628 6988 2.099756 GGGTTATCTTTGGACTGCATGC 59.900 50.000 11.82 11.82 0.00 4.06
4629 6989 3.624777 AGGGTTATCTTTGGACTGCATG 58.375 45.455 0.00 0.00 0.00 4.06
4630 6990 4.322057 AAGGGTTATCTTTGGACTGCAT 57.678 40.909 0.00 0.00 0.00 3.96
4631 6991 3.806949 AAGGGTTATCTTTGGACTGCA 57.193 42.857 0.00 0.00 0.00 4.41
4632 6992 4.809673 CAAAAGGGTTATCTTTGGACTGC 58.190 43.478 0.00 0.00 37.09 4.40
4633 6993 4.524328 AGCAAAAGGGTTATCTTTGGACTG 59.476 41.667 0.00 0.00 37.09 3.51
4634 6994 4.740902 AGCAAAAGGGTTATCTTTGGACT 58.259 39.130 0.00 0.00 37.09 3.85
4635 6995 5.468540 AAGCAAAAGGGTTATCTTTGGAC 57.531 39.130 0.00 0.00 37.09 4.02
4636 6996 6.493189 AAAAGCAAAAGGGTTATCTTTGGA 57.507 33.333 0.00 0.00 37.09 3.53
4676 7044 5.228945 AGTAACATAACCACTCAACAGCT 57.771 39.130 0.00 0.00 0.00 4.24
4746 7129 5.049167 TGTTGGAATTGAATTCAGCACAAC 58.951 37.500 24.73 24.73 41.03 3.32
4764 7147 2.930040 CTGCCTATTCTACACGTGTTGG 59.070 50.000 28.55 19.37 0.00 3.77
4770 7153 2.307768 TCCCTCTGCCTATTCTACACG 58.692 52.381 0.00 0.00 0.00 4.49
4921 7304 5.798132 ACTGACATCAAGCAACTATTCAGA 58.202 37.500 8.74 0.00 34.58 3.27
4990 7374 3.551846 CTGTACCAACCACCTTTTCTGT 58.448 45.455 0.00 0.00 0.00 3.41
5007 7391 1.231221 ATTTCGTTGGCGTTGCTGTA 58.769 45.000 0.00 0.00 39.49 2.74
5132 7516 5.367060 AGAAACTTATGGGACCATACCTCTC 59.633 44.000 10.48 6.19 38.48 3.20
5141 7525 3.344515 AGCGAAAGAAACTTATGGGACC 58.655 45.455 0.00 0.00 0.00 4.46
5179 7564 9.975218 ATACTAACTCCAATACCAGACAAAAAT 57.025 29.630 0.00 0.00 0.00 1.82
5336 7722 6.396829 AAGCAATAATAAAGATGGAGTGCC 57.603 37.500 0.00 0.00 0.00 5.01
5484 7871 7.733402 TTTTACGGACAAAAATAGCTACACT 57.267 32.000 0.00 0.00 0.00 3.55
5549 7937 2.292569 GGTGCAAGTCATATGCCATCTG 59.707 50.000 0.00 0.00 43.16 2.90
5807 8199 5.175859 CGAGTAATTTCCAGTTTAGGAGCA 58.824 41.667 0.00 0.00 39.25 4.26
5862 8254 3.444742 CCATGCATAAGAGGAGCACAAAA 59.555 43.478 0.00 0.00 41.60 2.44
5935 8327 1.342555 CGTATTCTTCGTCGCACCAA 58.657 50.000 0.00 0.00 0.00 3.67
5964 8356 0.032615 CCCAGTCTCTCTGCCCTACT 60.033 60.000 0.00 0.00 42.38 2.57
6006 8398 1.760405 AATGAGGGTCAAGGGAAGGT 58.240 50.000 0.00 0.00 0.00 3.50
6048 8440 1.400242 GCAGAGATCAAAACACGTGCC 60.400 52.381 17.22 0.00 0.00 5.01
6051 8443 3.062763 CTCTGCAGAGATCAAAACACGT 58.937 45.455 35.69 0.00 44.74 4.49
6265 8659 3.177997 ACACAACAACAAATCAAGCCC 57.822 42.857 0.00 0.00 0.00 5.19
6353 8747 5.104527 TCAAACATGTTCCGGGATATCTTCT 60.105 40.000 12.39 0.00 0.00 2.85
6365 8759 4.142049 TGGGACAGTTTTCAAACATGTTCC 60.142 41.667 12.39 17.26 41.28 3.62
6400 8794 4.881850 CCAGTGACAACTTTAACAGTTCCT 59.118 41.667 0.00 0.00 44.60 3.36
6515 8917 9.967451 TGATGAAGGTTCTGGTTGTTATTATTA 57.033 29.630 0.00 0.00 0.00 0.98
6639 9044 7.500559 AGCAAAATGAATGAATCTACCCTCTAC 59.499 37.037 0.00 0.00 0.00 2.59
6645 9050 5.066505 ACGGAGCAAAATGAATGAATCTACC 59.933 40.000 0.00 0.00 0.00 3.18
6655 9060 5.580691 CAGACTACATACGGAGCAAAATGAA 59.419 40.000 0.00 0.00 0.00 2.57
6659 9064 4.530710 ACAGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
6668 9073 6.482641 TCGAGATTCCACTACAGACTACATAC 59.517 42.308 0.00 0.00 0.00 2.39
6696 9101 6.266558 ACCCATGTACATATCTCTCAAGTCTC 59.733 42.308 8.32 0.00 0.00 3.36
6757 9175 7.147479 CCCTCCTAACCTTTGAGAGAAATCATA 60.147 40.741 0.00 0.00 0.00 2.15
6781 9199 9.628500 AGAAAGAATAATTTACTGTACATCCCC 57.372 33.333 0.00 0.00 0.00 4.81
6825 9243 3.628487 GCGGCATGGGTTAATTTGTAGTA 59.372 43.478 0.00 0.00 0.00 1.82
6826 9244 2.425668 GCGGCATGGGTTAATTTGTAGT 59.574 45.455 0.00 0.00 0.00 2.73
6827 9245 2.540769 CGCGGCATGGGTTAATTTGTAG 60.541 50.000 0.00 0.00 0.00 2.74
6828 9246 1.402259 CGCGGCATGGGTTAATTTGTA 59.598 47.619 0.00 0.00 0.00 2.41
6877 9295 2.470821 GCATTCATCAAATCCAGCTGC 58.529 47.619 8.66 0.00 0.00 5.25
6989 9407 1.418097 TTCCTGGGTTCAGCAGCAGA 61.418 55.000 0.00 0.00 39.61 4.26
7103 9521 9.616156 TGTCACCTTTTTGAGTTAAGTAACATA 57.384 29.630 4.14 0.00 38.62 2.29
7123 9541 3.157087 ACTGAATTTGATGGGTGTCACC 58.843 45.455 14.13 14.13 37.60 4.02


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

AutoCloner maintained by Alex Coulton.