Multiple sequence alignment - TraesCS7A01G238600

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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 TraesCS7A01G238600 chr7A 100.000 3043 0 0 1 3043 211644104 211641062 0 5620
1 TraesCS7A01G238600 chr7D 90.848 3114 168 44 1 3043 156690632 156687565 0 4063
2 TraesCS7A01G238600 chr7B 92.672 1774 89 21 527 2280 118982005 118980253 0 2518
3 TraesCS7A01G238600 chr7B 89.196 759 49 20 2309 3043 118980253 118979504 0 917


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 TraesCS7A01G238600 chr7A 211641062 211644104 3042 True 5620.0 5620 100.000 1 3043 1 chr7A.!!$R1 3042
1 TraesCS7A01G238600 chr7D 156687565 156690632 3067 True 4063.0 4063 90.848 1 3043 1 chr7D.!!$R1 3042
2 TraesCS7A01G238600 chr7B 118979504 118982005 2501 True 1717.5 2518 90.934 527 3043 2 chr7B.!!$R1 2516

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
378 402 0.034477 CCCCAAAGCCGTAGAACCAT 60.034 55.0 0.00 0.00 0.00 3.55 F
1233 1275 0.108424 ATCTCGACTGCTTGCAGTCC 60.108 55.0 35.29 23.49 46.46 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2036 1.004277 GGGGTCTTGTCCTGCACATAA 59.996 52.381 0.0 0.0 33.9 1.90 R
2424 2484 2.102070 TACCCACAAATACCACAGCG 57.898 50.000 0.0 0.0 0.0 5.18 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
40 41 2.618045 CCCCCGACACATTAGAGCTTTT 60.618 50.000 0.00 0.00 0.00 2.27
41 42 3.081804 CCCCGACACATTAGAGCTTTTT 58.918 45.455 0.00 0.00 0.00 1.94
55 56 2.047061 GCTTTTTCCCTTTCCCTGGTT 58.953 47.619 0.00 0.00 0.00 3.67
92 93 1.473257 CGCATCGAGGAGGAAAATCCA 60.473 52.381 0.00 0.00 42.26 3.41
120 121 2.270352 AAAAGACCTCGAACCATGCA 57.730 45.000 0.00 0.00 0.00 3.96
130 131 3.567579 AACCATGCACCGTGGAGGG 62.568 63.158 20.67 20.67 45.39 4.30
245 269 2.799126 TCCATCGCCCTATTGTTGTT 57.201 45.000 0.00 0.00 0.00 2.83
253 277 0.446222 CCTATTGTTGTTGTCGGCCG 59.554 55.000 22.12 22.12 0.00 6.13
303 327 4.599047 TCCATGGATGTGAACCAAAAAC 57.401 40.909 11.44 0.00 40.93 2.43
322 346 4.868195 GGCAACTCGGCAATCAAC 57.132 55.556 0.00 0.00 40.76 3.18
330 354 2.695087 CGGCAATCAACGTTTGTCG 58.305 52.632 10.61 10.61 44.44 4.35
369 393 1.611519 TTTTCTGTACCCCAAAGCCG 58.388 50.000 0.00 0.00 0.00 5.52
370 394 0.475044 TTTCTGTACCCCAAAGCCGT 59.525 50.000 0.00 0.00 0.00 5.68
371 395 1.350071 TTCTGTACCCCAAAGCCGTA 58.650 50.000 0.00 0.00 0.00 4.02
372 396 0.899720 TCTGTACCCCAAAGCCGTAG 59.100 55.000 0.00 0.00 0.00 3.51
373 397 0.899720 CTGTACCCCAAAGCCGTAGA 59.100 55.000 0.00 0.00 0.00 2.59
374 398 1.276989 CTGTACCCCAAAGCCGTAGAA 59.723 52.381 0.00 0.00 0.00 2.10
375 399 1.002315 TGTACCCCAAAGCCGTAGAAC 59.998 52.381 0.00 0.00 0.00 3.01
376 400 0.614812 TACCCCAAAGCCGTAGAACC 59.385 55.000 0.00 0.00 0.00 3.62
377 401 1.377229 CCCCAAAGCCGTAGAACCA 59.623 57.895 0.00 0.00 0.00 3.67
378 402 0.034477 CCCCAAAGCCGTAGAACCAT 60.034 55.000 0.00 0.00 0.00 3.55
403 427 5.216648 GTTCTACGGTAATTTTGCTTTGCA 58.783 37.500 0.00 0.00 36.47 4.08
409 433 3.995705 GGTAATTTTGCTTTGCATGCTCA 59.004 39.130 20.33 8.69 38.76 4.26
415 439 1.814394 TGCTTTGCATGCTCACTAAGG 59.186 47.619 20.33 5.86 31.71 2.69
419 443 2.857186 TGCATGCTCACTAAGGAACA 57.143 45.000 20.33 0.00 0.00 3.18
426 450 2.417933 GCTCACTAAGGAACATGTGCTG 59.582 50.000 3.21 0.00 0.00 4.41
428 452 2.371841 TCACTAAGGAACATGTGCTGGT 59.628 45.455 3.21 0.00 0.00 4.00
429 453 3.580895 TCACTAAGGAACATGTGCTGGTA 59.419 43.478 3.21 0.00 0.00 3.25
440 464 5.989477 ACATGTGCTGGTAATAGTATGTGT 58.011 37.500 0.00 0.00 0.00 3.72
443 467 8.044309 ACATGTGCTGGTAATAGTATGTGTTTA 58.956 33.333 0.00 0.00 0.00 2.01
458 482 9.944376 AGTATGTGTTTAAGATTTGCTCTAGAA 57.056 29.630 0.00 0.00 32.41 2.10
463 487 9.387123 GTGTTTAAGATTTGCTCTAGAACAAAG 57.613 33.333 22.06 0.02 39.04 2.77
468 492 4.771590 TTTGCTCTAGAACAAAGCATGG 57.228 40.909 15.64 0.00 44.84 3.66
473 497 4.034975 GCTCTAGAACAAAGCATGGATGTC 59.965 45.833 0.00 0.00 36.06 3.06
477 501 2.183478 ACAAAGCATGGATGTCGTGA 57.817 45.000 0.00 0.00 34.35 4.35
492 516 6.018669 GGATGTCGTGATAGGATTTGTTTCTC 60.019 42.308 0.00 0.00 0.00 2.87
493 517 6.037786 TGTCGTGATAGGATTTGTTTCTCT 57.962 37.500 0.00 0.00 0.00 3.10
495 519 6.100004 GTCGTGATAGGATTTGTTTCTCTCA 58.900 40.000 0.00 0.00 0.00 3.27
496 520 6.590292 GTCGTGATAGGATTTGTTTCTCTCAA 59.410 38.462 0.00 0.00 0.00 3.02
506 530 2.950975 TGTTTCTCTCAATGCAGCACAA 59.049 40.909 0.00 0.00 0.00 3.33
507 531 3.004002 TGTTTCTCTCAATGCAGCACAAG 59.996 43.478 0.00 0.00 0.00 3.16
512 536 2.026542 TCTCAATGCAGCACAAGGATCT 60.027 45.455 0.00 0.00 0.00 2.75
513 537 2.089201 TCAATGCAGCACAAGGATCTG 58.911 47.619 0.00 0.00 0.00 2.90
542 570 1.644786 AATTGCTAAGGTCGCACGGC 61.645 55.000 0.00 0.00 37.07 5.68
584 612 8.830915 TCACTTAATCTCTCATAGTTCTTCCT 57.169 34.615 0.00 0.00 0.00 3.36
589 617 3.948473 TCTCTCATAGTTCTTCCTCCACG 59.052 47.826 0.00 0.00 0.00 4.94
591 619 1.480954 TCATAGTTCTTCCTCCACGCC 59.519 52.381 0.00 0.00 0.00 5.68
627 656 5.021458 AGCCCAAATGATTGATCAGTTCTT 58.979 37.500 3.90 0.00 42.43 2.52
630 659 6.694447 CCCAAATGATTGATCAGTTCTTGTT 58.306 36.000 3.90 0.00 42.43 2.83
668 703 2.457598 TGGGAGCGAGTATATCCATCC 58.542 52.381 0.00 0.00 34.62 3.51
677 713 4.561530 CGAGTATATCCATCCACCCAACAG 60.562 50.000 0.00 0.00 0.00 3.16
700 736 5.585047 AGCTACTTTTCGTAAGCTAATTGGG 59.415 40.000 0.00 0.00 33.65 4.12
753 789 2.080286 AACACTCACCTGCACGTATC 57.920 50.000 0.00 0.00 0.00 2.24
849 885 1.666888 CCGTCATTTCAGCCAAGCAAC 60.667 52.381 0.00 0.00 0.00 4.17
940 982 2.087009 CGTCGCGTCTCCACTTTCC 61.087 63.158 5.77 0.00 0.00 3.13
945 987 0.108567 GCGTCTCCACTTTCCTCTCC 60.109 60.000 0.00 0.00 0.00 3.71
946 988 1.257743 CGTCTCCACTTTCCTCTCCA 58.742 55.000 0.00 0.00 0.00 3.86
1095 1137 2.536393 GCTCTTCTTCCGTTCGCTTATC 59.464 50.000 0.00 0.00 0.00 1.75
1178 1220 1.078143 CTGCGCCTTTAGCCTCCTT 60.078 57.895 4.18 0.00 38.78 3.36
1226 1268 3.764434 TCAGGTAAAGATCTCGACTGCTT 59.236 43.478 0.00 0.00 0.00 3.91
1227 1269 3.862267 CAGGTAAAGATCTCGACTGCTTG 59.138 47.826 0.00 0.00 0.00 4.01
1228 1270 2.605366 GGTAAAGATCTCGACTGCTTGC 59.395 50.000 0.00 0.00 0.00 4.01
1229 1271 2.462456 AAAGATCTCGACTGCTTGCA 57.538 45.000 0.00 0.00 0.00 4.08
1230 1272 2.007360 AAGATCTCGACTGCTTGCAG 57.993 50.000 19.62 19.62 0.00 4.41
1231 1273 0.894141 AGATCTCGACTGCTTGCAGT 59.106 50.000 25.73 25.73 38.26 4.40
1232 1274 1.135141 AGATCTCGACTGCTTGCAGTC 60.135 52.381 33.44 33.44 45.90 3.51
1233 1275 0.108424 ATCTCGACTGCTTGCAGTCC 60.108 55.000 35.29 23.49 46.46 3.85
1234 1276 1.739562 CTCGACTGCTTGCAGTCCC 60.740 63.158 35.29 21.33 46.46 4.46
1235 1277 2.743928 CGACTGCTTGCAGTCCCC 60.744 66.667 35.29 20.76 46.46 4.81
1366 1416 9.875708 ATTAGTGGACAAGATAAGAGTAGATCT 57.124 33.333 0.00 0.00 41.27 2.75
1487 1541 2.962421 TGGTCTTGGTTTCATTTGGGTC 59.038 45.455 0.00 0.00 0.00 4.46
1526 1586 4.175962 AGGGGTGAGAAGAGAACCATTTA 58.824 43.478 0.00 0.00 35.56 1.40
1639 1699 9.319143 GTATGATATTGTACCAATCATAGCTCC 57.681 37.037 16.29 6.82 41.11 4.70
1641 1701 7.389232 TGATATTGTACCAATCATAGCTCCTG 58.611 38.462 0.00 0.00 0.00 3.86
1667 1727 5.227569 ACAGGAAGTCATGTGTGTTATCA 57.772 39.130 0.00 0.00 39.61 2.15
1745 1805 6.002062 ACTAGCAATTGTTTAGTGCACTTC 57.998 37.500 27.06 15.95 40.83 3.01
1795 1855 7.516198 AACCTTATCTGCATTGATGGTTATC 57.484 36.000 10.50 0.00 33.63 1.75
1868 1928 9.630098 TGAAACAACCTATACTTCTTAGTAACG 57.370 33.333 0.00 0.00 40.14 3.18
1881 1941 9.924650 ACTTCTTAGTAACGATGTACTGAAATT 57.075 29.630 0.00 0.00 35.85 1.82
1976 2036 3.768922 GAGCACGGCCTCAGAGCT 61.769 66.667 0.00 0.01 38.20 4.09
2036 2096 0.550914 ACAAGTTCTTCACCAGCCCA 59.449 50.000 0.00 0.00 0.00 5.36
2125 2185 9.630098 CTATTTCAAGCATTCAGTAATGTTGTT 57.370 29.630 0.00 0.00 43.75 2.83
2145 2205 3.179443 TGCGTCCATAATTCAGAGGAC 57.821 47.619 0.00 0.00 45.46 3.85
2154 2214 5.994054 CCATAATTCAGAGGACATCGTCAAT 59.006 40.000 4.54 0.00 33.68 2.57
2231 2291 5.532406 TGGTTGATGGCTTCTAAATATCTGC 59.468 40.000 1.86 0.00 0.00 4.26
2265 2325 2.849942 TGGATATTCCATGCTTCCGTG 58.150 47.619 0.00 0.00 42.67 4.94
2370 2430 6.677781 TTTTGAAGTGTGTTCCTGTCTTAG 57.322 37.500 0.00 0.00 0.00 2.18
2376 2436 4.528596 AGTGTGTTCCTGTCTTAGCAGTAT 59.471 41.667 0.00 0.00 34.84 2.12
2380 2440 6.166982 GTGTTCCTGTCTTAGCAGTATCTTT 58.833 40.000 0.00 0.00 34.84 2.52
2381 2441 6.311690 GTGTTCCTGTCTTAGCAGTATCTTTC 59.688 42.308 0.00 0.00 34.84 2.62
2404 2464 5.043248 CACACAACTCCTTTGGAATTTGTC 58.957 41.667 9.16 0.00 36.47 3.18
2409 2469 6.986231 ACAACTCCTTTGGAATTTGTCAATTC 59.014 34.615 7.19 0.00 45.42 2.17
2456 2516 5.720371 TTTGTGGGTATGGAAAATGACTG 57.280 39.130 0.00 0.00 0.00 3.51
2457 2517 4.380843 TGTGGGTATGGAAAATGACTGT 57.619 40.909 0.00 0.00 0.00 3.55
2479 2542 7.399191 ACTGTCTTATAAGTCAATCCTGGTACA 59.601 37.037 12.19 4.17 0.00 2.90
2488 2551 7.448748 AGTCAATCCTGGTACAACATTTTAC 57.551 36.000 0.00 0.00 38.70 2.01
2490 2553 5.712917 TCAATCCTGGTACAACATTTTACCC 59.287 40.000 4.84 0.00 38.70 3.69
2498 2561 3.034635 ACAACATTTTACCCAACAGCCA 58.965 40.909 0.00 0.00 0.00 4.75
2501 2564 2.037121 ACATTTTACCCAACAGCCAAGC 59.963 45.455 0.00 0.00 0.00 4.01
2517 2580 4.065789 GCCAAGCTCTTGTTGTAGTACTT 58.934 43.478 0.00 0.00 38.85 2.24
2540 2603 9.182214 ACTTAGATGCATTTTACATCAGTGATT 57.818 29.630 1.86 0.00 45.19 2.57
2587 2650 4.020218 TGAAGTTGACTAGCATAGCCTGTT 60.020 41.667 0.00 0.00 44.39 3.16
2598 2661 6.759497 AGCATAGCCTGTTAAGGTTTTAAG 57.241 37.500 0.00 0.00 46.43 1.85
2611 2674 5.779241 AGGTTTTAAGATCCAGGTGATGA 57.221 39.130 0.00 0.00 32.41 2.92
2612 2675 5.501156 AGGTTTTAAGATCCAGGTGATGAC 58.499 41.667 0.00 0.00 32.41 3.06
2613 2676 5.014123 AGGTTTTAAGATCCAGGTGATGACA 59.986 40.000 0.00 0.00 32.41 3.58
2614 2677 5.888161 GGTTTTAAGATCCAGGTGATGACAT 59.112 40.000 0.00 0.00 32.41 3.06
2618 2681 5.698741 AAGATCCAGGTGATGACATAACA 57.301 39.130 5.27 0.00 32.41 2.41
2637 2700 8.462016 ACATAACAAAATTAACTCATCAGAGCC 58.538 33.333 0.00 0.00 46.09 4.70
2654 2717 2.476997 GAGCCGACTGAAAAGAACAGAC 59.523 50.000 0.00 0.00 38.55 3.51
2661 2724 7.464710 GCCGACTGAAAAGAACAGACATTATAG 60.465 40.741 0.00 0.00 38.55 1.31
2671 2734 9.911788 AAGAACAGACATTATAGATCAAACCAT 57.088 29.630 0.00 0.00 0.00 3.55
2731 2795 2.870175 TCTCCTCTCTATACAGCTGCC 58.130 52.381 15.27 0.00 0.00 4.85
2734 2798 3.374764 TCCTCTCTATACAGCTGCCAAA 58.625 45.455 15.27 0.00 0.00 3.28
2752 2816 4.616835 GCCAAATAACACTTTGCTGGAGAG 60.617 45.833 0.00 0.00 35.28 3.20
2761 2825 2.105006 TTGCTGGAGAGAACAGATGC 57.895 50.000 0.00 0.00 38.20 3.91
2764 2828 2.224597 TGCTGGAGAGAACAGATGCAAA 60.225 45.455 0.00 0.00 38.20 3.68
2781 2845 6.489361 AGATGCAAAAAGACTGAAGATGAACT 59.511 34.615 0.00 0.00 0.00 3.01
2789 2853 9.699703 AAAAGACTGAAGATGAACTAAGTAGAC 57.300 33.333 0.00 0.00 0.00 2.59
2795 2879 9.482627 CTGAAGATGAACTAAGTAGACAAAAGT 57.517 33.333 0.00 0.00 0.00 2.66
2801 2885 8.867112 TGAACTAAGTAGACAAAAGTACACTG 57.133 34.615 0.00 0.00 0.00 3.66
2802 2886 7.437267 TGAACTAAGTAGACAAAAGTACACTGC 59.563 37.037 0.00 0.00 0.00 4.40
2804 2888 4.957684 AGTAGACAAAAGTACACTGCCT 57.042 40.909 0.00 0.00 0.00 4.75
2997 3083 3.000727 CAGACCTGCCTAAACTAAACCG 58.999 50.000 0.00 0.00 0.00 4.44
3001 3087 2.353323 CTGCCTAAACTAAACCGTCCC 58.647 52.381 0.00 0.00 0.00 4.46
3004 3090 2.884827 CCTAAACTAAACCGTCCCTCG 58.115 52.381 0.00 0.00 39.52 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.374252 CGGGGGTGACGAGAAAGTG 60.374 63.158 0.00 0.00 0.00 3.16
40 41 0.481128 GTCCAACCAGGGAAAGGGAA 59.519 55.000 0.00 0.00 39.05 3.97
41 42 1.432023 GGTCCAACCAGGGAAAGGGA 61.432 60.000 0.00 0.00 39.05 4.20
55 56 0.608035 GCGGAAATTGTGAGGGTCCA 60.608 55.000 0.00 0.00 0.00 4.02
92 93 7.576861 TGGTTCGAGGTCTTTTTCTTTAAAT 57.423 32.000 0.00 0.00 0.00 1.40
120 121 0.178975 TGAAATTTGCCCTCCACGGT 60.179 50.000 0.00 0.00 0.00 4.83
130 131 9.577110 TGAAATAGACTGAATGATGAAATTTGC 57.423 29.630 0.00 0.00 0.00 3.68
205 206 6.419980 GGATCTAAATGAGTAGATGCATGC 57.580 41.667 11.82 11.82 44.24 4.06
253 277 1.351707 CACGGATTATGGTGCGCAC 59.648 57.895 32.15 32.15 36.31 5.34
300 324 0.598065 GATTGCCGAGTTGCCAGTTT 59.402 50.000 0.00 0.00 0.00 2.66
303 327 0.109597 GTTGATTGCCGAGTTGCCAG 60.110 55.000 0.00 0.00 0.00 4.85
322 346 0.318614 AAGCAAATGGGCGACAAACG 60.319 50.000 0.00 0.00 45.66 3.60
330 354 1.525941 AACATGCAAAGCAAATGGGC 58.474 45.000 0.00 0.00 43.62 5.36
356 380 1.676916 GGTTCTACGGCTTTGGGGTAC 60.677 57.143 0.00 0.00 0.00 3.34
363 387 2.467566 AACGATGGTTCTACGGCTTT 57.532 45.000 0.00 0.00 0.00 3.51
373 397 5.391203 GCAAAATTACCGTAGAACGATGGTT 60.391 40.000 0.15 0.00 46.05 3.67
374 398 4.093850 GCAAAATTACCGTAGAACGATGGT 59.906 41.667 0.15 4.46 46.05 3.55
375 399 4.331717 AGCAAAATTACCGTAGAACGATGG 59.668 41.667 0.15 0.00 46.05 3.51
376 400 5.464965 AGCAAAATTACCGTAGAACGATG 57.535 39.130 0.15 0.00 46.05 3.84
377 401 6.311723 CAAAGCAAAATTACCGTAGAACGAT 58.688 36.000 0.15 0.00 46.05 3.73
378 402 5.681880 CAAAGCAAAATTACCGTAGAACGA 58.318 37.500 0.15 0.00 46.05 3.85
383 407 4.031652 GCATGCAAAGCAAAATTACCGTAG 59.968 41.667 14.21 0.00 43.62 3.51
403 427 3.012518 GCACATGTTCCTTAGTGAGCAT 58.987 45.455 0.00 0.00 36.74 3.79
409 433 4.634012 TTACCAGCACATGTTCCTTAGT 57.366 40.909 0.00 0.00 0.00 2.24
415 439 6.538742 ACACATACTATTACCAGCACATGTTC 59.461 38.462 0.00 0.00 0.00 3.18
419 443 9.109393 CTTAAACACATACTATTACCAGCACAT 57.891 33.333 0.00 0.00 0.00 3.21
440 464 8.165239 TGCTTTGTTCTAGAGCAAATCTTAAA 57.835 30.769 28.11 10.96 42.89 1.52
458 482 2.183478 TCACGACATCCATGCTTTGT 57.817 45.000 0.00 0.00 0.00 2.83
463 487 2.820059 TCCTATCACGACATCCATGC 57.180 50.000 0.00 0.00 0.00 4.06
468 492 6.758886 AGAGAAACAAATCCTATCACGACATC 59.241 38.462 0.00 0.00 0.00 3.06
473 497 6.968131 TTGAGAGAAACAAATCCTATCACG 57.032 37.500 0.00 0.00 29.22 4.35
477 501 6.183360 GCTGCATTGAGAGAAACAAATCCTAT 60.183 38.462 0.00 0.00 0.00 2.57
492 516 2.097629 CAGATCCTTGTGCTGCATTGAG 59.902 50.000 5.27 4.31 0.00 3.02
493 517 2.089201 CAGATCCTTGTGCTGCATTGA 58.911 47.619 5.27 0.60 0.00 2.57
495 519 1.816835 CACAGATCCTTGTGCTGCATT 59.183 47.619 5.27 0.00 41.65 3.56
496 520 1.460504 CACAGATCCTTGTGCTGCAT 58.539 50.000 5.27 0.00 41.65 3.96
506 530 3.441572 GCAATTACAAGCACACAGATCCT 59.558 43.478 0.00 0.00 0.00 3.24
507 531 3.441572 AGCAATTACAAGCACACAGATCC 59.558 43.478 0.00 0.00 0.00 3.36
512 536 4.141287 ACCTTAGCAATTACAAGCACACA 58.859 39.130 0.00 0.00 0.00 3.72
513 537 4.669197 CGACCTTAGCAATTACAAGCACAC 60.669 45.833 0.00 0.00 0.00 3.82
515 539 3.727970 GCGACCTTAGCAATTACAAGCAC 60.728 47.826 0.00 0.00 34.19 4.40
520 544 1.996898 CGTGCGACCTTAGCAATTACA 59.003 47.619 0.00 0.00 46.97 2.41
542 570 5.757850 AAGTGAAGGCAAGTTAAGAAGTG 57.242 39.130 0.00 0.00 0.00 3.16
584 612 0.884259 CACTGATTGTGTGGCGTGGA 60.884 55.000 0.00 0.00 41.53 4.02
591 619 1.608055 TTGGGCTCACTGATTGTGTG 58.392 50.000 0.00 0.00 46.27 3.82
644 673 5.305644 GGATGGATATACTCGCTCCCATTAT 59.694 44.000 0.00 0.00 34.83 1.28
645 674 4.649674 GGATGGATATACTCGCTCCCATTA 59.350 45.833 0.00 0.00 34.83 1.90
652 687 2.180276 GGGTGGATGGATATACTCGCT 58.820 52.381 0.00 0.00 0.00 4.93
668 703 2.218603 ACGAAAAGTAGCTGTTGGGTG 58.781 47.619 0.00 0.00 0.00 4.61
677 713 5.729732 GCCCAATTAGCTTACGAAAAGTAGC 60.730 44.000 0.00 0.00 36.56 3.58
700 736 8.725405 AAAGGATTAGCTAGTTTTCTCTTAGC 57.275 34.615 0.00 0.00 0.00 3.09
753 789 4.862902 AGAGACAAGTGGATATGATCGG 57.137 45.455 0.00 0.00 0.00 4.18
849 885 1.803519 GTTGCTCAGTCGCTCGGAG 60.804 63.158 0.00 0.00 40.44 4.63
928 970 3.103742 AGATGGAGAGGAAAGTGGAGAC 58.896 50.000 0.00 0.00 0.00 3.36
940 982 2.951642 GGAGAGTGAGTGAGATGGAGAG 59.048 54.545 0.00 0.00 0.00 3.20
945 987 1.118838 GGGGGAGAGTGAGTGAGATG 58.881 60.000 0.00 0.00 0.00 2.90
946 988 1.014804 AGGGGGAGAGTGAGTGAGAT 58.985 55.000 0.00 0.00 0.00 2.75
1067 1109 1.807573 CGGAAGAAGAGCGAGTGGC 60.808 63.158 0.00 0.00 44.05 5.01
1095 1137 2.336809 GGCCGCGAGACAGGATAG 59.663 66.667 8.23 0.00 0.00 2.08
1169 1211 0.901827 TGATGTTGCGAAGGAGGCTA 59.098 50.000 0.00 0.00 0.00 3.93
1178 1220 2.281139 TTGCCGGTGATGTTGCGA 60.281 55.556 1.90 0.00 0.00 5.10
1234 1276 1.159664 CAGGGATAGGAGGAGGGGG 59.840 68.421 0.00 0.00 0.00 5.40
1235 1277 1.159664 CCAGGGATAGGAGGAGGGG 59.840 68.421 0.00 0.00 0.00 4.79
1250 1296 5.123820 TCTCAATCAAGAAATAAACGGCCAG 59.876 40.000 2.24 0.00 0.00 4.85
1350 1400 7.854166 AATCCAGCAGATCTACTCTTATCTT 57.146 36.000 0.00 0.00 32.47 2.40
1366 1416 1.746861 CGAACAGGCCATAATCCAGCA 60.747 52.381 5.01 0.00 0.00 4.41
1407 1457 1.330521 GCAGCGAAGTCAACACTCAAA 59.669 47.619 0.00 0.00 29.93 2.69
1462 1516 4.383552 CCCAAATGAAACCAAGACCACAAA 60.384 41.667 0.00 0.00 0.00 2.83
1487 1541 1.064296 CTCGTGGACCGATTCTCCG 59.936 63.158 0.00 0.00 46.23 4.63
1526 1586 2.794286 AGATATCTCCCCCAAAAGGCT 58.206 47.619 0.00 0.00 0.00 4.58
1639 1699 2.074576 CACATGACTTCCTGTCTGCAG 58.925 52.381 7.63 7.63 45.54 4.41
1641 1701 1.802960 CACACATGACTTCCTGTCTGC 59.197 52.381 0.00 0.00 45.54 4.26
1745 1805 2.721859 TCGTCTCCCGATCATGCG 59.278 61.111 0.00 0.00 41.60 4.73
1795 1855 7.486647 AGATGAGCTGCCACAAATTTATTAAG 58.513 34.615 0.00 0.00 0.00 1.85
1881 1941 4.299586 TGTTGACCCTGCAGATGAAATA 57.700 40.909 17.39 0.00 0.00 1.40
1976 2036 1.004277 GGGGTCTTGTCCTGCACATAA 59.996 52.381 0.00 0.00 33.90 1.90
2036 2096 6.543831 ACAGACAGACTAAAGTGCTTCATTTT 59.456 34.615 0.00 0.00 0.00 1.82
2125 2185 3.179443 GTCCTCTGAATTATGGACGCA 57.821 47.619 0.00 0.00 39.39 5.24
2145 2205 9.098355 TCTTTCAATAAGAGGTAATTGACGATG 57.902 33.333 0.00 0.00 40.77 3.84
2149 2209 9.010029 TGGTTCTTTCAATAAGAGGTAATTGAC 57.990 33.333 0.00 0.00 40.77 3.18
2154 2214 8.160765 TCACATGGTTCTTTCAATAAGAGGTAA 58.839 33.333 0.00 0.00 0.00 2.85
2231 2291 7.812690 TGGAATATCCACAATCTCAATGAAG 57.187 36.000 0.00 0.00 42.67 3.02
2265 2325 2.422127 ACAACCACAACACAGCAACTAC 59.578 45.455 0.00 0.00 0.00 2.73
2307 2367 2.679837 CCAAATGTCTGCAGTAATCGCT 59.320 45.455 14.67 0.00 0.00 4.93
2370 2430 4.319177 AGGAGTTGTGTGAAAGATACTGC 58.681 43.478 0.00 0.00 0.00 4.40
2376 2436 4.229304 TCCAAAGGAGTTGTGTGAAAGA 57.771 40.909 0.00 0.00 35.23 2.52
2380 2440 4.709397 ACAAATTCCAAAGGAGTTGTGTGA 59.291 37.500 13.26 0.00 39.03 3.58
2381 2441 5.009854 ACAAATTCCAAAGGAGTTGTGTG 57.990 39.130 13.26 4.09 39.03 3.82
2424 2484 2.102070 TACCCACAAATACCACAGCG 57.898 50.000 0.00 0.00 0.00 5.18
2456 2516 8.038944 TGTTGTACCAGGATTGACTTATAAGAC 58.961 37.037 19.38 13.32 0.00 3.01
2457 2517 8.141298 TGTTGTACCAGGATTGACTTATAAGA 57.859 34.615 19.38 0.00 0.00 2.10
2479 2542 3.494223 GCTTGGCTGTTGGGTAAAATGTT 60.494 43.478 0.00 0.00 0.00 2.71
2488 2551 4.507969 AAGAGCTTGGCTGTTGGG 57.492 55.556 1.21 0.00 40.60 4.12
2498 2561 6.814146 GCATCTAAGTACTACAACAAGAGCTT 59.186 38.462 0.00 0.00 0.00 3.74
2501 2564 8.709386 AATGCATCTAAGTACTACAACAAGAG 57.291 34.615 0.00 0.00 0.00 2.85
2546 2609 9.507329 TCAACTTCAACAGAATAAGCTAGAAAT 57.493 29.630 0.00 0.00 0.00 2.17
2568 2631 4.811557 CCTTAACAGGCTATGCTAGTCAAC 59.188 45.833 0.00 0.00 31.53 3.18
2587 2650 7.110155 GTCATCACCTGGATCTTAAAACCTTA 58.890 38.462 0.00 0.00 32.57 2.69
2598 2661 6.757897 TTTTGTTATGTCATCACCTGGATC 57.242 37.500 0.00 0.00 32.57 3.36
2611 2674 8.462016 GGCTCTGATGAGTTAATTTTGTTATGT 58.538 33.333 0.00 0.00 42.13 2.29
2612 2675 7.641411 CGGCTCTGATGAGTTAATTTTGTTATG 59.359 37.037 0.00 0.00 42.13 1.90
2613 2676 7.552687 TCGGCTCTGATGAGTTAATTTTGTTAT 59.447 33.333 0.00 0.00 42.13 1.89
2614 2677 6.876789 TCGGCTCTGATGAGTTAATTTTGTTA 59.123 34.615 0.00 0.00 42.13 2.41
2618 2681 5.352569 CAGTCGGCTCTGATGAGTTAATTTT 59.647 40.000 0.00 0.00 42.13 1.82
2633 2696 2.476997 GTCTGTTCTTTTCAGTCGGCTC 59.523 50.000 0.00 0.00 34.86 4.70
2637 2700 8.689251 TCTATAATGTCTGTTCTTTTCAGTCG 57.311 34.615 0.00 0.00 34.86 4.18
2649 2712 7.500227 CCACATGGTTTGATCTATAATGTCTGT 59.500 37.037 0.00 0.00 0.00 3.41
2671 2734 4.653801 TGAGGCTAGCATATAAAGACCACA 59.346 41.667 18.24 0.00 0.00 4.17
2731 2795 5.947228 TCTCTCCAGCAAAGTGTTATTTG 57.053 39.130 0.00 0.00 42.00 2.32
2734 2798 4.973168 TGTTCTCTCCAGCAAAGTGTTAT 58.027 39.130 0.00 0.00 0.00 1.89
2752 2816 6.064846 TCTTCAGTCTTTTTGCATCTGTTC 57.935 37.500 0.00 0.00 0.00 3.18
2764 2828 8.861086 TGTCTACTTAGTTCATCTTCAGTCTTT 58.139 33.333 0.00 0.00 0.00 2.52
2781 2845 6.415206 AGGCAGTGTACTTTTGTCTACTTA 57.585 37.500 0.00 0.00 29.87 2.24
2812 2896 8.668510 AATAATGATACACTTGACTGTCCATC 57.331 34.615 5.17 0.18 0.00 3.51
2947 3033 4.193826 TCAGTTCTTGTAGGCAGATCAC 57.806 45.455 0.00 0.00 0.00 3.06
3001 3087 2.268298 CACGGGAATAAACCTCACGAG 58.732 52.381 0.87 0.00 42.40 4.18
3004 3090 4.824289 TCTTACACGGGAATAAACCTCAC 58.176 43.478 0.00 0.00 0.00 3.51
3012 3098 5.069516 GGTACTTGGATCTTACACGGGAATA 59.930 44.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.