Multiple sequence alignment - TraesCS6D01G228200

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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 TraesCS6D01G228200 chr6D 100.000 5916 0 0 1 5916 319258122 319252207 0.000000e+00 10925.0
1 TraesCS6D01G228200 chr6A 94.915 3284 124 20 505 3767 457091103 457087842 0.000000e+00 5099.0
2 TraesCS6D01G228200 chr6A 90.311 2157 119 37 3825 5916 457087128 457084997 0.000000e+00 2743.0
3 TraesCS6D01G228200 chr6A 94.181 464 19 6 15 476 457091559 457091102 0.000000e+00 701.0
4 TraesCS6D01G228200 chr6B 95.630 2975 81 15 821 3767 503998932 504001885 0.000000e+00 4728.0
5 TraesCS6D01G228200 chr6B 95.177 1161 28 11 4139 5277 504002509 504003663 0.000000e+00 1808.0
6 TraesCS6D01G228200 chr6B 93.541 418 15 7 22 437 503997591 503997998 3.920000e-171 612.0
7 TraesCS6D01G228200 chr6B 93.190 279 14 2 3764 4042 504002240 504002513 7.140000e-109 405.0
8 TraesCS6D01G228200 chr6B 93.208 265 16 2 525 788 503998398 503998661 7.190000e-104 388.0
9 TraesCS6D01G228200 chr6B 80.203 197 11 15 5355 5534 504018615 504018800 8.050000e-24 122.0
10 TraesCS6D01G228200 chr6B 92.537 67 5 0 3764 3830 123824597 123824663 4.880000e-16 97.1
11 TraesCS6D01G228200 chr6B 92.424 66 3 2 3764 3829 523345120 523345183 6.310000e-15 93.5
12 TraesCS6D01G228200 chrUn 91.566 166 12 1 3868 4033 237256550 237256713 1.660000e-55 228.0
13 TraesCS6D01G228200 chrUn 91.566 166 12 1 3868 4033 384915899 384915736 1.660000e-55 228.0
14 TraesCS6D01G228200 chrUn 91.566 166 12 1 3868 4033 399833838 399834001 1.660000e-55 228.0
15 TraesCS6D01G228200 chr4B 91.566 166 12 1 3868 4033 209048135 209047972 1.660000e-55 228.0
16 TraesCS6D01G228200 chr1A 91.566 166 12 1 3868 4033 238108465 238108628 1.660000e-55 228.0
17 TraesCS6D01G228200 chr1A 91.566 166 12 1 3868 4033 238153850 238154013 1.660000e-55 228.0
18 TraesCS6D01G228200 chr1A 91.566 166 12 1 3868 4033 278507627 278507464 1.660000e-55 228.0
19 TraesCS6D01G228200 chr2B 94.318 88 2 1 2732 2816 723392895 723392982 1.340000e-26 132.0
20 TraesCS6D01G228200 chr2B 93.548 62 2 2 3768 3829 302929606 302929547 2.270000e-14 91.6
21 TraesCS6D01G228200 chr3D 94.186 86 2 1 2731 2813 381989073 381989158 1.730000e-25 128.0
22 TraesCS6D01G228200 chr3D 90.426 94 5 2 2730 2819 429306328 429306235 2.900000e-23 121.0
23 TraesCS6D01G228200 chr3D 93.548 62 4 0 3766 3827 6667378 6667439 6.310000e-15 93.5
24 TraesCS6D01G228200 chr2A 93.258 89 2 2 2733 2818 79308226 79308139 1.730000e-25 128.0
25 TraesCS6D01G228200 chr2D 92.135 89 3 3 2731 2815 649818932 649818844 8.050000e-24 122.0
26 TraesCS6D01G228200 chr5B 89.583 96 6 2 2730 2821 364139504 364139409 1.040000e-22 119.0
27 TraesCS6D01G228200 chr7D 93.548 62 4 0 3764 3825 14883660 14883721 6.310000e-15 93.5
28 TraesCS6D01G228200 chr7A 93.548 62 4 0 3764 3825 124795937 124795876 6.310000e-15 93.5
29 TraesCS6D01G228200 chr5A 92.063 63 5 0 3764 3826 361871585 361871523 8.170000e-14 89.8
30 TraesCS6D01G228200 chr5A 92.063 63 5 0 3764 3826 414776113 414776175 8.170000e-14 89.8


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 TraesCS6D01G228200 chr6D 319252207 319258122 5915 True 10925.000000 10925 100.000000 1 5916 1 chr6D.!!$R1 5915
1 TraesCS6D01G228200 chr6A 457084997 457091559 6562 True 2847.666667 5099 93.135667 15 5916 3 chr6A.!!$R1 5901
2 TraesCS6D01G228200 chr6B 503997591 504003663 6072 False 1588.200000 4728 94.149200 22 5277 5 chr6B.!!$F4 5255

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
501 505 0.169672 TCGCGCAGAACACTAGGTAC 59.830 55.000 8.75 0.00 0.00 3.34 F
502 506 0.170561 CGCGCAGAACACTAGGTACT 59.829 55.000 8.75 0.00 46.37 2.73 F
738 1057 0.177141 GTACAAGGCATAGGGCGTCA 59.823 55.000 0.00 0.00 46.16 4.35 F
1648 2205 1.198637 GAGACATGCCAGCTGAACAAC 59.801 52.381 17.39 9.05 0.00 3.32 F
2901 3486 0.391228 TGTCTCCACGCTGCTTGTTA 59.609 50.000 5.38 0.00 0.00 2.41 F
3017 3602 0.471591 AAAGGGGTGGCATTGCTTCA 60.472 50.000 8.82 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 3047 0.175760 TGGTAGTCCTGAAGCGATGC 59.824 55.000 0.00 0.00 34.23 3.91 R
2495 3052 3.567478 ATGGAATGGTAGTCCTGAAGC 57.433 47.619 0.00 0.00 36.03 3.86 R
2722 3279 3.198417 GGGACGGAGGGAGTATGTTTTTA 59.802 47.826 0.00 0.00 0.00 1.52 R
2996 3581 1.482748 AAGCAATGCCACCCCTTTGG 61.483 55.000 0.00 0.00 39.98 3.28 R
3845 5451 2.738587 TGGGTCCTAGCTAGTCAGAG 57.261 55.000 19.31 3.92 0.00 3.35 R
4951 6611 1.472728 CGACCTAGAAATTCCACCGGG 60.473 57.143 6.32 0.00 0.00 5.73 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
18 19 3.911989 GCTAGAATCCGACGTTCGA 57.088 52.632 8.63 0.00 43.74 3.71
62 63 5.656859 GGTGATTAATCTGTTTTTAGGGCCT 59.343 40.000 12.58 12.58 0.00 5.19
217 219 4.087892 ACAGCGGCAGCCTCGAAT 62.088 61.111 10.54 0.00 46.67 3.34
228 230 1.211457 AGCCTCGAATCAGCCAGAAAT 59.789 47.619 0.00 0.00 0.00 2.17
346 348 2.708255 GGAGACTAGGTCGTCGCG 59.292 66.667 0.00 0.00 38.90 5.87
392 394 2.284699 CCTCCCCTCCCGTGAAGT 60.285 66.667 0.00 0.00 0.00 3.01
465 469 4.868195 CGCAAGGTAAGGCAAAGC 57.132 55.556 0.00 0.00 0.00 3.51
470 474 2.802247 GCAAGGTAAGGCAAAGCTTTTG 59.198 45.455 9.53 6.62 32.58 2.44
473 477 2.628178 AGGTAAGGCAAAGCTTTTGACC 59.372 45.455 9.53 11.49 0.00 4.02
474 478 2.288825 GGTAAGGCAAAGCTTTTGACCC 60.289 50.000 9.53 7.81 0.00 4.46
475 479 0.758734 AAGGCAAAGCTTTTGACCCC 59.241 50.000 9.53 5.34 0.00 4.95
476 480 1.121407 AGGCAAAGCTTTTGACCCCC 61.121 55.000 9.53 3.60 0.00 5.40
496 500 2.126071 GGCTCGCGCAGAACACTA 60.126 61.111 8.75 0.00 38.10 2.74
497 501 2.161486 GGCTCGCGCAGAACACTAG 61.161 63.158 8.75 0.00 38.10 2.57
498 502 2.161486 GCTCGCGCAGAACACTAGG 61.161 63.158 8.75 0.00 35.78 3.02
499 503 1.213013 CTCGCGCAGAACACTAGGT 59.787 57.895 8.75 0.00 0.00 3.08
500 504 0.450583 CTCGCGCAGAACACTAGGTA 59.549 55.000 8.75 0.00 0.00 3.08
501 505 0.169672 TCGCGCAGAACACTAGGTAC 59.830 55.000 8.75 0.00 0.00 3.34
502 506 0.170561 CGCGCAGAACACTAGGTACT 59.829 55.000 8.75 0.00 46.37 2.73
503 507 1.399440 CGCGCAGAACACTAGGTACTA 59.601 52.381 8.75 0.00 41.75 1.82
533 849 1.425428 CATTCCTTTCGTGCGCCTC 59.575 57.895 4.18 0.00 0.00 4.70
658 976 0.465705 ACATGTCTCGCGGAATGGAT 59.534 50.000 6.13 0.00 0.00 3.41
666 984 2.285083 TCGCGGAATGGATTACTTTGG 58.715 47.619 6.13 0.00 0.00 3.28
677 995 1.154430 TTACTTTGGGGGTTGGAGCT 58.846 50.000 0.00 0.00 0.00 4.09
683 1001 2.677875 GGGGTTGGAGCTTGGCAG 60.678 66.667 0.00 0.00 0.00 4.85
738 1057 0.177141 GTACAAGGCATAGGGCGTCA 59.823 55.000 0.00 0.00 46.16 4.35
788 1140 1.921887 CCGTTTGCTAATCGTTCGCTA 59.078 47.619 0.00 0.00 0.00 4.26
800 1152 1.597663 CGTTCGCTATTTGGGCTTAGG 59.402 52.381 0.00 0.00 0.00 2.69
801 1153 1.947456 GTTCGCTATTTGGGCTTAGGG 59.053 52.381 0.00 0.00 0.00 3.53
1310 1867 3.709653 CCTGTATGCTTTACTAGGGACCA 59.290 47.826 0.00 0.00 0.00 4.02
1330 1887 3.003689 CCAAGAAGGACACACATTGACAC 59.996 47.826 0.00 0.00 41.22 3.67
1433 1990 5.189180 GGTGAAGAAGATGTTAATGCTCCT 58.811 41.667 0.00 0.00 0.00 3.69
1438 1995 8.267183 TGAAGAAGATGTTAATGCTCCTATCAA 58.733 33.333 0.00 0.00 0.00 2.57
1567 2124 1.790387 GCTTGTGCTACTTCCAGCG 59.210 57.895 0.00 0.00 44.88 5.18
1587 2144 2.634940 CGGTATGGACATCAAGGAGGAT 59.365 50.000 0.00 0.00 0.00 3.24
1607 2164 2.045926 CTGCTTCGGAAGGGGTGG 60.046 66.667 18.73 0.00 0.00 4.61
1648 2205 1.198637 GAGACATGCCAGCTGAACAAC 59.801 52.381 17.39 9.05 0.00 3.32
1734 2291 5.547181 AATTAAACGCAGAGGTTTCTAGC 57.453 39.130 0.00 0.00 40.41 3.42
1752 2309 7.812309 TTCTAGCGAATATTCCAATATGTCG 57.188 36.000 9.87 13.67 36.34 4.35
1911 2468 7.942341 CCACCAAATGTACACCAATATACCTAT 59.058 37.037 0.00 0.00 0.00 2.57
1914 2471 8.160765 CCAAATGTACACCAATATACCTATGGA 58.839 37.037 0.00 0.00 0.00 3.41
1941 2498 4.690184 TGTATCTCAGCAGCATTTTGTG 57.310 40.909 0.00 0.00 0.00 3.33
2666 3223 3.541632 TCTCCTTGGGTTATTCATTCGC 58.458 45.455 0.00 0.00 0.00 4.70
2690 3247 9.056306 CGCTTTCTTTCTTTATTTAGAAGCTTC 57.944 33.333 19.11 19.11 35.69 3.86
2756 3313 3.418047 CCTCCGTCCCAAAATAAGTGTT 58.582 45.455 0.00 0.00 0.00 3.32
2892 3477 2.000447 GACAATAACCTGTCTCCACGC 59.000 52.381 0.00 0.00 42.11 5.34
2901 3486 0.391228 TGTCTCCACGCTGCTTGTTA 59.609 50.000 5.38 0.00 0.00 2.41
2996 3581 3.942115 GGAAGGCTTTAGTTGGATGTCTC 59.058 47.826 0.00 0.00 0.00 3.36
3017 3602 0.471591 AAAGGGGTGGCATTGCTTCA 60.472 50.000 8.82 0.00 0.00 3.02
3142 3727 5.972107 AATTCTACATCTGCTTTGCTGTT 57.028 34.783 0.00 0.00 0.00 3.16
3143 3728 5.972107 ATTCTACATCTGCTTTGCTGTTT 57.028 34.783 0.00 0.00 0.00 2.83
3144 3729 5.772825 TTCTACATCTGCTTTGCTGTTTT 57.227 34.783 0.00 0.00 0.00 2.43
3386 3972 6.662755 TCAATGATGCCACTTACCTTAGATT 58.337 36.000 0.00 0.00 0.00 2.40
3432 4019 6.112734 AGCATAATTCAACTACACATTCCGA 58.887 36.000 0.00 0.00 0.00 4.55
3637 4229 1.114722 ATGCCACACCCCAGTTTGTG 61.115 55.000 0.00 0.00 42.40 3.33
3773 4723 3.926058 ACCCTAAAAGCATCCGTATGT 57.074 42.857 0.00 0.00 35.38 2.29
3782 4732 4.850347 AGCATCCGTATGTAGTCCTTAC 57.150 45.455 0.00 0.00 35.38 2.34
3845 5451 3.434940 TTTTGGAGTAGGGAAGAAGGC 57.565 47.619 0.00 0.00 0.00 4.35
3916 5530 1.340114 GGAGGTACTGCCCAAGGAAAG 60.340 57.143 0.00 0.00 42.57 2.62
3940 5554 3.641434 AATGTGACTTCTGGATCAGGG 57.359 47.619 0.00 0.00 31.51 4.45
3948 5562 7.127186 TGTGACTTCTGGATCAGGGATAATAAA 59.873 37.037 0.00 0.00 31.51 1.40
3949 5563 8.160106 GTGACTTCTGGATCAGGGATAATAAAT 58.840 37.037 0.00 0.00 31.51 1.40
4066 5683 9.830186 TTTCTAGGCAGAGATAGTATATCCTTT 57.170 33.333 1.08 0.00 30.73 3.11
4117 5734 8.341892 AGATTCCTTGTTCTGAAATAAAGTCC 57.658 34.615 0.00 0.00 0.00 3.85
4164 5781 3.072915 TCCATGTCACTCCATGAACAACT 59.927 43.478 0.00 0.00 43.99 3.16
4393 6010 6.795399 ACTGTTTCATTAGTTTGAGGTTGTG 58.205 36.000 0.00 0.00 0.00 3.33
4430 6047 9.561069 TTTAGAGTTCAAGACTGAAAATAAGCT 57.439 29.630 0.00 0.00 43.18 3.74
4718 6364 9.692749 AGGTACAATCATTTATACACGATACTG 57.307 33.333 0.00 0.00 0.00 2.74
4724 6370 6.801575 TCATTTATACACGATACTGCAGACA 58.198 36.000 23.35 8.09 0.00 3.41
5131 6796 7.712639 AGATATAGAAACACAACATGTAGGCAG 59.287 37.037 0.00 0.00 42.31 4.85
5156 6821 7.343833 AGGAGGAATTTTGTATCATGAGCAAAT 59.656 33.333 21.30 12.37 33.00 2.32
5216 6881 3.146066 TGAGTGTATCCTGGTTTTGTGC 58.854 45.455 0.00 0.00 0.00 4.57
5222 6887 2.435372 TCCTGGTTTTGTGCTCTTGT 57.565 45.000 0.00 0.00 0.00 3.16
5223 6888 2.023673 TCCTGGTTTTGTGCTCTTGTG 58.976 47.619 0.00 0.00 0.00 3.33
5226 6891 1.341482 TGGTTTTGTGCTCTTGTGGGA 60.341 47.619 0.00 0.00 0.00 4.37
5227 6892 1.754226 GGTTTTGTGCTCTTGTGGGAA 59.246 47.619 0.00 0.00 0.00 3.97
5228 6893 2.365293 GGTTTTGTGCTCTTGTGGGAAT 59.635 45.455 0.00 0.00 0.00 3.01
5272 6940 5.645929 ACGTTAATATTTCATGTGTGCTGGA 59.354 36.000 0.00 0.00 0.00 3.86
5279 6947 0.037303 CATGTGTGCTGGAAGGGAGT 59.963 55.000 0.00 0.00 0.00 3.85
5287 6955 0.689623 CTGGAAGGGAGTGAGCTTGT 59.310 55.000 0.00 0.00 0.00 3.16
5390 7058 1.924320 GAGCAGTCTACGCGGACAGT 61.924 60.000 12.47 0.00 38.57 3.55
5391 7059 1.801913 GCAGTCTACGCGGACAGTG 60.802 63.158 12.47 3.50 38.57 3.66
5397 7065 1.066645 TCTACGCGGACAGTGACTCTA 60.067 52.381 12.47 0.00 0.00 2.43
5414 7082 4.335416 ACTCTAGCTAGCTCATCCATCTC 58.665 47.826 23.26 0.00 0.00 2.75
5415 7083 4.202556 ACTCTAGCTAGCTCATCCATCTCA 60.203 45.833 23.26 0.00 0.00 3.27
5416 7084 4.734266 TCTAGCTAGCTCATCCATCTCAA 58.266 43.478 23.26 0.00 0.00 3.02
5417 7085 5.143369 TCTAGCTAGCTCATCCATCTCAAA 58.857 41.667 23.26 0.00 0.00 2.69
5418 7086 4.767578 AGCTAGCTCATCCATCTCAAAA 57.232 40.909 12.68 0.00 0.00 2.44
5419 7087 5.108187 AGCTAGCTCATCCATCTCAAAAA 57.892 39.130 12.68 0.00 0.00 1.94
5450 7118 6.353404 AGAAACTCTAGCTAGCTCAGTTTT 57.647 37.500 34.05 25.93 38.41 2.43
5451 7119 6.394809 AGAAACTCTAGCTAGCTCAGTTTTC 58.605 40.000 34.05 28.34 38.41 2.29
5452 7120 5.993748 AACTCTAGCTAGCTCAGTTTTCT 57.006 39.130 25.93 12.17 29.92 2.52
5453 7121 5.993748 ACTCTAGCTAGCTCAGTTTTCTT 57.006 39.130 23.26 0.00 0.00 2.52
5454 7122 6.353404 ACTCTAGCTAGCTCAGTTTTCTTT 57.647 37.500 23.26 0.00 0.00 2.52
5455 7123 6.764379 ACTCTAGCTAGCTCAGTTTTCTTTT 58.236 36.000 23.26 0.00 0.00 2.27
5456 7124 7.220740 ACTCTAGCTAGCTCAGTTTTCTTTTT 58.779 34.615 23.26 0.00 0.00 1.94
5529 7198 2.157701 GCAGCGCTCTCGTTCTCAG 61.158 63.158 7.13 0.00 38.14 3.35
5535 7204 0.869454 GCTCTCGTTCTCAGCCGATG 60.869 60.000 0.00 0.00 31.90 3.84
5541 7210 4.112634 CTCGTTCTCAGCCGATGATTTTA 58.887 43.478 0.00 0.00 37.28 1.52
5542 7211 4.500127 TCGTTCTCAGCCGATGATTTTAA 58.500 39.130 0.00 0.00 37.28 1.52
5543 7212 5.116180 TCGTTCTCAGCCGATGATTTTAAT 58.884 37.500 0.00 0.00 37.28 1.40
5546 7215 6.747280 CGTTCTCAGCCGATGATTTTAATTTT 59.253 34.615 0.00 0.00 37.28 1.82
5547 7216 7.273381 CGTTCTCAGCCGATGATTTTAATTTTT 59.727 33.333 0.00 0.00 37.28 1.94
5618 7290 2.964740 TCTCTCGCTTCTGTCAATTGG 58.035 47.619 5.42 0.00 0.00 3.16
5642 7314 2.025887 AGATCCAACTGTCAACCATCCC 60.026 50.000 0.00 0.00 0.00 3.85
5655 7327 4.706476 TCAACCATCCCAGATGATTTCAAC 59.294 41.667 6.15 0.00 0.00 3.18
5656 7328 3.635591 ACCATCCCAGATGATTTCAACC 58.364 45.455 6.15 0.00 0.00 3.77
5674 7346 9.725019 ATTTCAACCTTTTGTTTTCTTTCTCTT 57.275 25.926 0.00 0.00 34.00 2.85
5730 7402 2.806244 ACAACAAGTATGGACGAGCAAC 59.194 45.455 0.00 0.00 0.00 4.17
5769 7441 0.603569 TCTCTTCTTCGCAGTGGTCC 59.396 55.000 0.00 0.00 0.00 4.46
5770 7442 0.605589 CTCTTCTTCGCAGTGGTCCT 59.394 55.000 0.00 0.00 0.00 3.85
5771 7443 1.819288 CTCTTCTTCGCAGTGGTCCTA 59.181 52.381 0.00 0.00 0.00 2.94
5784 7460 3.394606 AGTGGTCCTATGGTGTCAGTTTT 59.605 43.478 0.00 0.00 0.00 2.43
5861 7537 4.985409 GTCTTCTTTTCTCTCGCTTCTCAA 59.015 41.667 0.00 0.00 0.00 3.02
5866 7542 5.579904 TCTTTTCTCTCGCTTCTCAATCATG 59.420 40.000 0.00 0.00 0.00 3.07
5902 7578 6.434028 AGTGTAAATAGGAGCTTGAATTTGCA 59.566 34.615 12.17 12.17 33.46 4.08
5903 7579 7.039784 AGTGTAAATAGGAGCTTGAATTTGCAA 60.040 33.333 15.59 0.00 36.27 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.402640 ATCGAACGTCGGATTCTAGC 57.597 50.000 0.00 0.00 40.88 3.42
1 2 5.481472 CAAAAATCGAACGTCGGATTCTAG 58.519 41.667 12.67 4.51 40.88 2.43
2 3 4.201647 GCAAAAATCGAACGTCGGATTCTA 60.202 41.667 12.67 0.00 40.88 2.10
3 4 3.424433 GCAAAAATCGAACGTCGGATTCT 60.424 43.478 12.67 0.00 40.88 2.40
4 5 2.838452 GCAAAAATCGAACGTCGGATTC 59.162 45.455 12.67 0.00 40.88 2.52
5 6 2.482721 AGCAAAAATCGAACGTCGGATT 59.517 40.909 7.90 7.90 40.88 3.01
6 7 2.073816 AGCAAAAATCGAACGTCGGAT 58.926 42.857 0.00 2.12 40.88 4.18
7 8 1.504359 AGCAAAAATCGAACGTCGGA 58.496 45.000 0.00 0.00 40.88 4.55
8 9 2.309898 AAGCAAAAATCGAACGTCGG 57.690 45.000 0.00 0.00 40.88 4.79
9 10 4.669588 AAAAAGCAAAAATCGAACGTCG 57.330 36.364 0.00 0.00 42.10 5.12
62 63 4.705337 AAGTGCACGGTCAAAACTAAAA 57.295 36.364 12.01 0.00 0.00 1.52
217 219 2.577563 TCTCCATGGAATTTCTGGCTGA 59.422 45.455 17.00 2.24 0.00 4.26
357 359 2.520741 CGAGGAGGAGGAGGAGGC 60.521 72.222 0.00 0.00 0.00 4.70
392 394 2.631428 GCTTCGCAACAGTTCGCA 59.369 55.556 8.01 0.00 0.00 5.10
481 485 0.450583 TACCTAGTGTTCTGCGCGAG 59.549 55.000 12.10 4.52 0.00 5.03
482 486 0.169672 GTACCTAGTGTTCTGCGCGA 59.830 55.000 12.10 0.00 0.00 5.87
483 487 0.170561 AGTACCTAGTGTTCTGCGCG 59.829 55.000 0.00 0.00 0.00 6.86
484 488 2.479219 GGTAGTACCTAGTGTTCTGCGC 60.479 54.545 12.41 0.00 34.73 6.09
485 489 3.417690 GGTAGTACCTAGTGTTCTGCG 57.582 52.381 12.41 0.00 34.73 5.18
499 503 5.556857 AGGAATGCCCTCCGAAGGTAGTA 62.557 52.174 0.00 0.00 43.31 1.82
500 504 4.906835 AGGAATGCCCTCCGAAGGTAGT 62.907 54.545 0.00 0.00 43.31 2.73
501 505 2.311604 AGGAATGCCCTCCGAAGGTAG 61.312 57.143 0.00 0.00 43.31 3.18
502 506 0.326238 AGGAATGCCCTCCGAAGGTA 60.326 55.000 0.00 0.00 43.31 3.08
503 507 1.616628 AGGAATGCCCTCCGAAGGT 60.617 57.895 0.00 0.00 43.31 3.50
516 520 2.100631 CGAGGCGCACGAAAGGAAT 61.101 57.895 18.59 0.00 0.00 3.01
658 976 1.154430 AGCTCCAACCCCCAAAGTAA 58.846 50.000 0.00 0.00 0.00 2.24
666 984 2.677875 CTGCCAAGCTCCAACCCC 60.678 66.667 0.00 0.00 0.00 4.95
677 995 0.036164 ACATGAGCGGTAACTGCCAA 59.964 50.000 0.00 0.00 36.90 4.52
683 1001 2.806244 AGACAACAACATGAGCGGTAAC 59.194 45.455 0.00 0.00 0.00 2.50
788 1140 4.881157 ACAATAGTCCCTAAGCCCAAAT 57.119 40.909 0.00 0.00 0.00 2.32
800 1152 6.956202 TGAGCTAGGTACTAACAATAGTCC 57.044 41.667 0.00 0.00 42.17 3.85
801 1153 7.921745 CCTTTGAGCTAGGTACTAACAATAGTC 59.078 40.741 0.00 0.00 42.17 2.59
1293 1850 4.080299 CCTTCTTGGTCCCTAGTAAAGCAT 60.080 45.833 0.00 0.00 0.00 3.79
1310 1867 3.117888 AGGTGTCAATGTGTGTCCTTCTT 60.118 43.478 0.00 0.00 0.00 2.52
1348 1905 1.072331 GGTTTGAGAGTTGAGGCCAGA 59.928 52.381 5.01 0.00 0.00 3.86
1433 1990 2.874086 CCGATCATGTTGCTGCTTGATA 59.126 45.455 0.00 0.00 34.67 2.15
1438 1995 1.651240 GCACCGATCATGTTGCTGCT 61.651 55.000 0.00 0.00 0.00 4.24
1567 2124 3.648067 TCATCCTCCTTGATGTCCATACC 59.352 47.826 0.00 0.00 42.24 2.73
1587 2144 1.841556 ACCCCTTCCGAAGCAGTCA 60.842 57.895 2.27 0.00 0.00 3.41
1607 2164 5.008613 TCTCCTGTTTGATTGCAACAGTTAC 59.991 40.000 13.08 4.65 34.35 2.50
1648 2205 2.091112 CCTCACTTGAGCTCGTGCG 61.091 63.158 14.80 9.96 45.42 5.34
1734 2291 5.179368 ACAAGCCGACATATTGGAATATTCG 59.821 40.000 9.32 12.28 34.91 3.34
1752 2309 1.093159 CCTGCTCTGATGAACAAGCC 58.907 55.000 0.00 0.00 34.35 4.35
1823 2380 3.018423 ACCCTTCAGGCCAAATATGTC 57.982 47.619 5.01 0.00 40.58 3.06
1831 2388 0.251297 CATGTCAACCCTTCAGGCCA 60.251 55.000 5.01 0.00 40.58 5.36
1868 2425 4.269183 TGGTGGGTTAACAATAGCATCAG 58.731 43.478 8.10 0.00 0.00 2.90
1911 2468 3.069300 GCTGCTGAGATACATCTTCTCCA 59.931 47.826 0.00 0.00 39.10 3.86
1914 2471 4.959560 ATGCTGCTGAGATACATCTTCT 57.040 40.909 0.00 0.00 37.25 2.85
1941 2498 0.318784 ACTCTGACGAACGCTTGTCC 60.319 55.000 3.78 0.00 34.18 4.02
2246 2803 6.208402 TGCCAAGCATGAAAAATTCTACTGTA 59.792 34.615 0.00 0.00 31.71 2.74
2247 2804 5.010922 TGCCAAGCATGAAAAATTCTACTGT 59.989 36.000 0.00 0.00 31.71 3.55
2248 2805 5.472148 TGCCAAGCATGAAAAATTCTACTG 58.528 37.500 0.00 0.00 31.71 2.74
2249 2806 5.726980 TGCCAAGCATGAAAAATTCTACT 57.273 34.783 0.00 0.00 31.71 2.57
2250 2807 6.783892 TTTGCCAAGCATGAAAAATTCTAC 57.216 33.333 0.00 0.00 38.76 2.59
2490 3047 0.175760 TGGTAGTCCTGAAGCGATGC 59.824 55.000 0.00 0.00 34.23 3.91
2495 3052 3.567478 ATGGAATGGTAGTCCTGAAGC 57.433 47.619 0.00 0.00 36.03 3.86
2722 3279 3.198417 GGGACGGAGGGAGTATGTTTTTA 59.802 47.826 0.00 0.00 0.00 1.52
2788 3370 5.721232 ACTCCCTCTGTAAAATAAGTGTCG 58.279 41.667 0.00 0.00 0.00 4.35
2884 3469 2.248280 TTTAACAAGCAGCGTGGAGA 57.752 45.000 13.26 0.00 0.00 3.71
2892 3477 7.859598 TGTTGCCAAATAAATTTAACAAGCAG 58.140 30.769 1.21 0.00 28.46 4.24
2996 3581 1.482748 AAGCAATGCCACCCCTTTGG 61.483 55.000 0.00 0.00 39.98 3.28
3086 3671 6.262496 GGACTAGGGAGTAAATTGTAATTGCC 59.738 42.308 0.00 0.00 35.45 4.52
3087 3672 6.262496 GGGACTAGGGAGTAAATTGTAATTGC 59.738 42.308 0.00 0.00 35.45 3.56
3386 3972 8.856153 TGCTCAACCTGAAGTATTAACATTAA 57.144 30.769 0.00 0.00 0.00 1.40
3406 3993 6.037062 CGGAATGTGTAGTTGAATTATGCTCA 59.963 38.462 0.00 0.00 0.00 4.26
3432 4019 7.907841 AAAGGGAGTTTACCACACTAAAATT 57.092 32.000 0.00 0.00 0.00 1.82
3816 4766 4.037927 TCCCTACTCCAAAATACTCCCTG 58.962 47.826 0.00 0.00 0.00 4.45
3845 5451 2.738587 TGGGTCCTAGCTAGTCAGAG 57.261 55.000 19.31 3.92 0.00 3.35
3916 5530 4.397417 CCTGATCCAGAAGTCACATTTTCC 59.603 45.833 0.00 0.00 32.44 3.13
4100 5717 7.523709 GCTCCAAATGGACTTTATTTCAGAACA 60.524 37.037 0.00 0.00 39.78 3.18
4135 5752 4.019051 TCATGGAGTGACATGGAGAACAAT 60.019 41.667 0.00 0.00 46.33 2.71
4164 5781 7.880105 TGATTATTTGTTTGTCATAGTGTGCA 58.120 30.769 0.00 0.00 0.00 4.57
4393 6010 8.787852 AGTCTTGAACTCTAAAATCATTGGAAC 58.212 33.333 0.00 0.00 30.02 3.62
4430 6047 3.943671 TGACCTTGGACTCTGGAAAAA 57.056 42.857 0.00 0.00 0.00 1.94
4510 6156 6.374333 GGTAAACAAGCCATCAGAAGTGATAA 59.626 38.462 0.00 0.00 41.85 1.75
4718 6364 5.504665 GCATCCAGTAACATTGTATGTCTGC 60.505 44.000 0.00 0.00 44.07 4.26
4724 6370 7.148086 ACGAATTTGCATCCAGTAACATTGTAT 60.148 33.333 0.00 0.00 0.00 2.29
4951 6611 1.472728 CGACCTAGAAATTCCACCGGG 60.473 57.143 6.32 0.00 0.00 5.73
5025 6689 6.824196 TGATGTACACTGGTTTGTTACAAGAA 59.176 34.615 0.00 0.00 31.69 2.52
5131 6796 6.455360 TTGCTCATGATACAAAATTCCTCC 57.545 37.500 8.44 0.00 0.00 4.30
5156 6821 5.801350 CGCAAGGAAATCTACATCTCAAA 57.199 39.130 0.00 0.00 0.00 2.69
5216 6881 4.692625 CAGTGACACTTATTCCCACAAGAG 59.307 45.833 5.04 0.00 0.00 2.85
5222 6887 5.630121 ACAATTCAGTGACACTTATTCCCA 58.370 37.500 5.04 0.00 0.00 4.37
5223 6888 6.575162 AACAATTCAGTGACACTTATTCCC 57.425 37.500 5.04 0.00 0.00 3.97
5226 6891 8.149973 ACGTTAACAATTCAGTGACACTTATT 57.850 30.769 5.04 6.16 0.00 1.40
5227 6892 7.724305 ACGTTAACAATTCAGTGACACTTAT 57.276 32.000 5.04 0.00 0.00 1.73
5228 6893 7.542534 AACGTTAACAATTCAGTGACACTTA 57.457 32.000 5.04 0.00 0.00 2.24
5272 6940 1.073897 GCCACAAGCTCACTCCCTT 59.926 57.895 0.00 0.00 38.99 3.95
5279 6947 3.535629 CTCCGTGGCCACAAGCTCA 62.536 63.158 34.16 10.52 43.05 4.26
5287 6955 1.306654 ATAACCTCCTCCGTGGCCA 60.307 57.895 0.00 0.00 35.26 5.36
5390 7058 3.584733 TGGATGAGCTAGCTAGAGTCA 57.415 47.619 25.15 23.20 0.00 3.41
5391 7059 4.335416 AGATGGATGAGCTAGCTAGAGTC 58.665 47.826 25.15 18.67 0.00 3.36
5397 7065 4.767578 TTTTGAGATGGATGAGCTAGCT 57.232 40.909 19.45 19.45 0.00 3.32
5424 7092 6.353404 ACTGAGCTAGCTAGAGTTTCTTTT 57.647 37.500 25.15 0.00 0.00 2.27
5428 7096 6.394809 AGAAAACTGAGCTAGCTAGAGTTTC 58.605 40.000 33.68 28.52 37.61 2.78
5443 7111 8.931775 GCTCCAAAAAGTTAAAAAGAAAACTGA 58.068 29.630 0.00 0.00 36.12 3.41
5444 7112 7.897800 CGCTCCAAAAAGTTAAAAAGAAAACTG 59.102 33.333 0.00 0.00 36.12 3.16
5445 7113 7.601130 ACGCTCCAAAAAGTTAAAAAGAAAACT 59.399 29.630 0.00 0.00 37.54 2.66
5446 7114 7.735500 ACGCTCCAAAAAGTTAAAAAGAAAAC 58.264 30.769 0.00 0.00 0.00 2.43
5454 7122 9.321562 CCTAGATATACGCTCCAAAAAGTTAAA 57.678 33.333 0.00 0.00 0.00 1.52
5455 7123 8.480501 ACCTAGATATACGCTCCAAAAAGTTAA 58.519 33.333 0.00 0.00 0.00 2.01
5456 7124 8.015185 ACCTAGATATACGCTCCAAAAAGTTA 57.985 34.615 0.00 0.00 0.00 2.24
5598 7270 2.354103 CCCAATTGACAGAAGCGAGAGA 60.354 50.000 7.12 0.00 0.00 3.10
5599 7271 2.005451 CCCAATTGACAGAAGCGAGAG 58.995 52.381 7.12 0.00 0.00 3.20
5601 7273 0.449388 GCCCAATTGACAGAAGCGAG 59.551 55.000 7.12 0.00 0.00 5.03
5605 7277 2.686915 GGATCTGCCCAATTGACAGAAG 59.313 50.000 25.35 11.70 43.23 2.85
5618 7290 1.168714 GGTTGACAGTTGGATCTGCC 58.831 55.000 0.00 0.00 38.84 4.85
5630 7302 4.263860 TGAAATCATCTGGGATGGTTGACA 60.264 41.667 6.77 7.74 0.00 3.58
5642 7314 8.652810 AGAAAACAAAAGGTTGAAATCATCTG 57.347 30.769 0.00 0.00 40.35 2.90
5655 7327 7.038048 AGAAGCAAGAGAAAGAAAACAAAAGG 58.962 34.615 0.00 0.00 0.00 3.11
5656 7328 9.741647 ATAGAAGCAAGAGAAAGAAAACAAAAG 57.258 29.630 0.00 0.00 0.00 2.27
5674 7346 4.261155 GGATGTGCGCAATTTATAGAAGCA 60.261 41.667 14.00 0.49 0.00 3.91
5684 7356 0.810648 ATCGTTGGATGTGCGCAATT 59.189 45.000 14.00 1.09 0.00 2.32
5709 7381 2.806244 GTTGCTCGTCCATACTTGTTGT 59.194 45.455 0.00 0.00 0.00 3.32
5730 7402 7.527568 AGAGAAGGTAGGAGGAAAATATACG 57.472 40.000 0.00 0.00 0.00 3.06
5743 7415 2.494073 ACTGCGAAGAAGAGAAGGTAGG 59.506 50.000 0.00 0.00 0.00 3.18
5866 7542 8.371699 AGCTCCTATTTACACTAATTGGATCTC 58.628 37.037 0.00 0.00 38.27 2.75
5878 7554 6.620678 TGCAAATTCAAGCTCCTATTTACAC 58.379 36.000 0.00 0.00 0.00 2.90
5882 7558 6.210185 AGAGTTGCAAATTCAAGCTCCTATTT 59.790 34.615 0.00 0.00 34.65 1.40


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

AutoCloner maintained by Alex Coulton.