Multiple sequence alignment - TraesCS7B01G401100

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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 TraesCS7B01G401100 chr7B 100.000 2249 0 0 1 2249 667478608 667480856 0.000000e+00 4154
1 TraesCS7B01G401100 chr7A 84.491 1483 105 52 1 1415 686157645 686156220 0.000000e+00 1349
2 TraesCS7B01G401100 chr7A 93.309 807 27 14 1453 2249 686156261 686155472 0.000000e+00 1166
3 TraesCS7B01G401100 chr7D 89.630 974 58 20 471 1415 593370856 593369897 0.000000e+00 1199
4 TraesCS7B01G401100 chr7D 92.346 797 35 14 1466 2249 593369925 593369142 0.000000e+00 1110
5 TraesCS7B01G401100 chr7D 95.726 234 7 2 142 374 593371080 593370849 7.580000e-100 374
6 TraesCS7B01G401100 chr6A 90.833 360 31 2 968 1326 135561310 135561668 4.340000e-132 481
7 TraesCS7B01G401100 chr6A 82.579 442 55 15 1812 2245 135562238 135562665 9.810000e-99 370
8 TraesCS7B01G401100 chr6A 93.689 206 13 0 144 349 135561010 135561215 2.170000e-80 309
9 TraesCS7B01G401100 chr6A 89.573 211 19 3 144 352 492283913 492284122 4.760000e-67 265
10 TraesCS7B01G401100 chr6D 90.556 360 32 2 968 1326 111062154 111062512 2.020000e-130 475
11 TraesCS7B01G401100 chr6D 82.955 440 57 10 1812 2245 111063032 111063459 4.530000e-102 381
12 TraesCS7B01G401100 chr6D 93.333 210 13 1 140 349 111061846 111062054 2.170000e-80 309
13 TraesCS7B01G401100 chr6D 89.671 213 19 3 140 351 351137578 351137368 3.680000e-68 268
14 TraesCS7B01G401100 chr6B 90.000 360 34 2 968 1326 200008688 200009046 4.370000e-127 464
15 TraesCS7B01G401100 chr6B 92.857 210 14 1 140 349 200008391 200008599 1.010000e-78 303
16 TraesCS7B01G401100 chr6B 90.385 208 18 2 145 351 528285888 528286094 2.850000e-69 272


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 TraesCS7B01G401100 chr7B 667478608 667480856 2248 False 4154.000000 4154 100.000000 1 2249 1 chr7B.!!$F1 2248
1 TraesCS7B01G401100 chr7A 686155472 686157645 2173 True 1257.500000 1349 88.900000 1 2249 2 chr7A.!!$R1 2248
2 TraesCS7B01G401100 chr7D 593369142 593371080 1938 True 894.333333 1199 92.567333 142 2249 3 chr7D.!!$R1 2107
3 TraesCS7B01G401100 chr6A 135561010 135562665 1655 False 386.666667 481 89.033667 144 2245 3 chr6A.!!$F2 2101
4 TraesCS7B01G401100 chr6D 111061846 111063459 1613 False 388.333333 475 88.948000 140 2245 3 chr6D.!!$F1 2105
5 TraesCS7B01G401100 chr6B 200008391 200009046 655 False 383.500000 464 91.428500 140 1326 2 chr6B.!!$F2 1186

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
456 495 0.171903 GTCCAAGCCATGTGATGTGC 59.828 55.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1524 0.034896 AGAACCCGAACTTGCACGAT 59.965 50.0 0.0 0.0 0.0 3.73 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
21 22 1.899814 ACCACTCGCTCACCTAATCAA 59.100 47.619 0.00 0.00 0.00 2.57
25 26 4.381612 CCACTCGCTCACCTAATCAACTAA 60.382 45.833 0.00 0.00 0.00 2.24
65 83 4.778415 CGTCGTCGCCACTCCTGG 62.778 72.222 0.00 0.00 41.13 4.45
76 94 3.636231 CTCCTGGGCGGTGACCAA 61.636 66.667 1.11 0.00 41.95 3.67
79 97 3.353836 CTGGGCGGTGACCAAACG 61.354 66.667 1.11 0.00 41.95 3.60
80 98 4.178169 TGGGCGGTGACCAAACGT 62.178 61.111 1.11 0.00 38.06 3.99
92 110 3.582120 AAACGTGGTGGCGCTGTG 61.582 61.111 7.64 0.00 34.88 3.66
115 133 5.238214 TGCTATTTTTGGTTGGACATTTTGC 59.762 36.000 0.00 0.00 0.00 3.68
118 136 4.478206 TTTTGGTTGGACATTTTGCTCA 57.522 36.364 0.00 0.00 0.00 4.26
125 164 3.916761 TGGACATTTTGCTCAAGAATGC 58.083 40.909 12.77 0.00 34.86 3.56
128 167 1.657094 CATTTTGCTCAAGAATGCGCC 59.343 47.619 4.18 0.00 36.44 6.53
129 168 0.387112 TTTTGCTCAAGAATGCGCCG 60.387 50.000 4.18 0.00 36.44 6.46
350 389 3.151710 TCATCCCGTACCCCTGCG 61.152 66.667 0.00 0.00 0.00 5.18
354 393 4.483243 CCCGTACCCCTGCGCAAT 62.483 66.667 13.05 0.00 0.00 3.56
355 394 2.502093 CCGTACCCCTGCGCAATA 59.498 61.111 13.05 0.00 0.00 1.90
356 395 1.885850 CCGTACCCCTGCGCAATAC 60.886 63.158 13.05 10.79 0.00 1.89
357 396 1.153529 CGTACCCCTGCGCAATACA 60.154 57.895 13.05 0.00 0.00 2.29
358 397 0.531974 CGTACCCCTGCGCAATACAT 60.532 55.000 13.05 0.00 0.00 2.29
359 398 1.269883 CGTACCCCTGCGCAATACATA 60.270 52.381 13.05 0.00 0.00 2.29
394 433 2.133553 GTGATCATCACCATCAGCTCG 58.866 52.381 6.50 0.00 41.37 5.03
395 434 1.146637 GATCATCACCATCAGCTCGC 58.853 55.000 0.00 0.00 0.00 5.03
396 435 0.466963 ATCATCACCATCAGCTCGCA 59.533 50.000 0.00 0.00 0.00 5.10
414 453 1.069765 AGTCACCACGTTCTGCTGG 59.930 57.895 0.00 0.00 0.00 4.85
416 455 2.591429 CACCACGTTCTGCTGGCA 60.591 61.111 0.00 0.00 0.00 4.92
428 467 0.605050 TGCTGGCAATCAACACGCTA 60.605 50.000 0.00 0.00 0.00 4.26
429 468 0.179189 GCTGGCAATCAACACGCTAC 60.179 55.000 0.00 0.00 0.00 3.58
437 476 4.321745 GCAATCAACACGCTACAATTTCAG 59.678 41.667 0.00 0.00 0.00 3.02
438 477 5.451908 CAATCAACACGCTACAATTTCAGT 58.548 37.500 0.00 0.00 0.00 3.41
441 480 3.120321 ACACGCTACAATTTCAGTCCA 57.880 42.857 0.00 0.00 0.00 4.02
444 483 2.484264 ACGCTACAATTTCAGTCCAAGC 59.516 45.455 0.00 0.00 0.00 4.01
445 484 2.159517 CGCTACAATTTCAGTCCAAGCC 60.160 50.000 0.00 0.00 0.00 4.35
448 487 3.947910 ACAATTTCAGTCCAAGCCATG 57.052 42.857 0.00 0.00 0.00 3.66
450 489 3.006110 ACAATTTCAGTCCAAGCCATGTG 59.994 43.478 0.00 0.00 0.00 3.21
451 490 2.655090 TTTCAGTCCAAGCCATGTGA 57.345 45.000 0.00 0.00 0.00 3.58
452 491 2.885135 TTCAGTCCAAGCCATGTGAT 57.115 45.000 0.00 0.00 0.00 3.06
453 492 2.118313 TCAGTCCAAGCCATGTGATG 57.882 50.000 0.00 0.00 0.00 3.07
455 494 1.471287 CAGTCCAAGCCATGTGATGTG 59.529 52.381 0.00 0.00 0.00 3.21
456 495 0.171903 GTCCAAGCCATGTGATGTGC 59.828 55.000 0.00 0.00 0.00 4.57
457 496 0.251253 TCCAAGCCATGTGATGTGCA 60.251 50.000 0.00 0.00 0.00 4.57
458 497 0.172578 CCAAGCCATGTGATGTGCAG 59.827 55.000 0.00 0.00 0.00 4.41
459 498 0.885879 CAAGCCATGTGATGTGCAGT 59.114 50.000 0.00 0.00 0.00 4.40
460 499 1.271379 CAAGCCATGTGATGTGCAGTT 59.729 47.619 0.00 0.00 0.00 3.16
461 500 1.624336 AGCCATGTGATGTGCAGTTT 58.376 45.000 0.00 0.00 0.00 2.66
462 501 1.542915 AGCCATGTGATGTGCAGTTTC 59.457 47.619 0.00 0.00 0.00 2.78
494 533 0.387202 AGATTCAGACGGCCGAGATG 59.613 55.000 35.90 25.35 0.00 2.90
510 549 2.428890 GAGATGAATCCGTGGTGAGAGT 59.571 50.000 0.00 0.00 0.00 3.24
533 572 3.699538 GACTTGTCCACCCAAAAAGTCTT 59.300 43.478 6.61 0.00 42.13 3.01
534 573 3.447229 ACTTGTCCACCCAAAAAGTCTTG 59.553 43.478 0.00 0.00 0.00 3.02
536 575 1.068588 GTCCACCCAAAAAGTCTTGGC 59.931 52.381 0.00 0.00 43.97 4.52
541 580 1.537202 CCCAAAAAGTCTTGGCGAGAG 59.463 52.381 4.21 0.00 43.97 3.20
563 602 0.175531 AGTTTGTTGGCAACCAGCAC 59.824 50.000 26.31 16.64 44.02 4.40
567 606 0.969917 TGTTGGCAACCAGCACAACT 60.970 50.000 26.31 0.00 46.02 3.16
577 616 1.152902 AGCACAACTCTGGCTTGCA 60.153 52.632 0.00 0.00 35.57 4.08
675 733 1.365699 CGTAAAGGTTGGGATGTCGG 58.634 55.000 0.00 0.00 0.00 4.79
676 734 1.338389 CGTAAAGGTTGGGATGTCGGT 60.338 52.381 0.00 0.00 0.00 4.69
677 735 2.353323 GTAAAGGTTGGGATGTCGGTC 58.647 52.381 0.00 0.00 0.00 4.79
678 736 0.321298 AAAGGTTGGGATGTCGGTCG 60.321 55.000 0.00 0.00 0.00 4.79
727 785 4.298261 CATGCCACCCACCCACCA 62.298 66.667 0.00 0.00 0.00 4.17
805 864 3.439540 CCGATGCCCCAACAACCG 61.440 66.667 0.00 0.00 0.00 4.44
807 866 2.686816 CGATGCCCCAACAACCGTC 61.687 63.158 0.00 0.00 0.00 4.79
814 881 1.076332 CCCAACAACCGTCGATCTTC 58.924 55.000 0.00 0.00 0.00 2.87
884 951 2.526888 ACTGTACCTAGGCTAGTGCA 57.473 50.000 19.68 15.09 41.91 4.57
885 952 2.100989 ACTGTACCTAGGCTAGTGCAC 58.899 52.381 19.68 9.40 41.91 4.57
907 974 3.275338 GCTGGCGTGCCTGATAGC 61.275 66.667 20.34 12.82 37.23 2.97
1285 1366 4.354212 CGCACAGCAACACGTCCG 62.354 66.667 0.00 0.00 0.00 4.79
1286 1367 2.964925 GCACAGCAACACGTCCGA 60.965 61.111 0.00 0.00 0.00 4.55
1314 1395 3.551454 CGAAGTACAAGTTCGGGTTCTCA 60.551 47.826 8.63 0.00 44.74 3.27
1352 1456 4.032786 GCACACACACAAAAATCAGAAACC 59.967 41.667 0.00 0.00 0.00 3.27
1422 1538 1.416049 CGTGATCGTGCAAGTTCGG 59.584 57.895 0.00 0.00 0.00 4.30
1423 1539 1.787847 GTGATCGTGCAAGTTCGGG 59.212 57.895 0.00 0.00 0.00 5.14
1424 1540 0.949105 GTGATCGTGCAAGTTCGGGT 60.949 55.000 0.00 0.00 0.00 5.28
1425 1541 0.250124 TGATCGTGCAAGTTCGGGTT 60.250 50.000 0.00 0.00 0.00 4.11
1426 1542 0.442699 GATCGTGCAAGTTCGGGTTC 59.557 55.000 0.00 0.00 0.00 3.62
1427 1543 0.034896 ATCGTGCAAGTTCGGGTTCT 59.965 50.000 0.00 0.00 0.00 3.01
1428 1544 0.599204 TCGTGCAAGTTCGGGTTCTC 60.599 55.000 0.00 0.00 0.00 2.87
1429 1545 1.566018 CGTGCAAGTTCGGGTTCTCC 61.566 60.000 0.00 0.00 0.00 3.71
1442 1558 3.553828 GGTTCTCCCCGTCAATATGAA 57.446 47.619 0.00 0.00 0.00 2.57
1443 1559 3.203716 GGTTCTCCCCGTCAATATGAAC 58.796 50.000 0.00 0.00 33.70 3.18
1444 1560 3.118371 GGTTCTCCCCGTCAATATGAACT 60.118 47.826 0.00 0.00 34.55 3.01
1445 1561 4.514401 GTTCTCCCCGTCAATATGAACTT 58.486 43.478 0.00 0.00 32.32 2.66
1446 1562 4.837093 TCTCCCCGTCAATATGAACTTT 57.163 40.909 0.00 0.00 0.00 2.66
1447 1563 5.174037 TCTCCCCGTCAATATGAACTTTT 57.826 39.130 0.00 0.00 0.00 2.27
1448 1564 5.183228 TCTCCCCGTCAATATGAACTTTTC 58.817 41.667 0.00 0.00 0.00 2.29
1449 1565 5.045869 TCTCCCCGTCAATATGAACTTTTCT 60.046 40.000 0.00 0.00 0.00 2.52
1450 1566 5.566469 TCCCCGTCAATATGAACTTTTCTT 58.434 37.500 0.00 0.00 0.00 2.52
1451 1567 6.007703 TCCCCGTCAATATGAACTTTTCTTT 58.992 36.000 0.00 0.00 0.00 2.52
1452 1568 6.492087 TCCCCGTCAATATGAACTTTTCTTTT 59.508 34.615 0.00 0.00 0.00 2.27
1453 1569 7.014808 TCCCCGTCAATATGAACTTTTCTTTTT 59.985 33.333 0.00 0.00 0.00 1.94
1499 1615 0.605319 AAATGTGATCGTGCGTGGGT 60.605 50.000 0.00 0.00 0.00 4.51
1529 1674 2.440980 GCTGATTGGTGGGCCCTC 60.441 66.667 25.70 20.64 0.00 4.30
1726 2128 4.435651 CGAGAAACGTAAATTGGAAGCTCC 60.436 45.833 0.00 0.00 35.58 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.084519 TCCACTGTTCCATGACTAGTTAGT 58.915 41.667 0.00 0.00 39.71 2.24
25 26 4.081420 GTGATCCACTGTTCCATGACTAGT 60.081 45.833 0.00 0.00 0.00 2.57
65 83 3.656045 CCACGTTTGGTCACCGCC 61.656 66.667 0.00 0.00 38.23 6.13
79 97 1.586154 AAATAGCACAGCGCCACCAC 61.586 55.000 2.29 0.00 44.04 4.16
80 98 0.893270 AAAATAGCACAGCGCCACCA 60.893 50.000 2.29 0.00 44.04 4.17
83 101 0.243365 CCAAAAATAGCACAGCGCCA 59.757 50.000 2.29 0.00 44.04 5.69
87 105 3.243704 TGTCCAACCAAAAATAGCACAGC 60.244 43.478 0.00 0.00 0.00 4.40
92 110 5.469760 AGCAAAATGTCCAACCAAAAATAGC 59.530 36.000 0.00 0.00 0.00 2.97
94 112 6.586344 TGAGCAAAATGTCCAACCAAAAATA 58.414 32.000 0.00 0.00 0.00 1.40
115 133 3.126879 TGCCGGCGCATTCTTGAG 61.127 61.111 23.90 0.00 41.12 3.02
135 174 4.397103 AGATCATGAAAGGTACGTACGTCA 59.603 41.667 26.53 20.47 0.00 4.35
136 175 4.733887 CAGATCATGAAAGGTACGTACGTC 59.266 45.833 26.53 15.93 0.00 4.34
137 176 4.439700 CCAGATCATGAAAGGTACGTACGT 60.440 45.833 25.98 25.98 0.00 3.57
138 177 4.042398 CCAGATCATGAAAGGTACGTACG 58.958 47.826 18.98 15.01 0.00 3.67
139 178 5.007385 ACCAGATCATGAAAGGTACGTAC 57.993 43.478 17.56 17.56 0.00 3.67
140 179 5.416083 CAACCAGATCATGAAAGGTACGTA 58.584 41.667 14.98 0.00 31.10 3.57
353 392 7.686438 TCACTCTGTTTTGCAATGTATGTAT 57.314 32.000 0.00 0.00 0.00 2.29
354 393 7.390162 TGATCACTCTGTTTTGCAATGTATGTA 59.610 33.333 0.00 0.00 0.00 2.29
355 394 6.207221 TGATCACTCTGTTTTGCAATGTATGT 59.793 34.615 0.00 0.00 0.00 2.29
356 395 6.614160 TGATCACTCTGTTTTGCAATGTATG 58.386 36.000 0.00 0.00 0.00 2.39
357 396 6.822667 TGATCACTCTGTTTTGCAATGTAT 57.177 33.333 0.00 0.00 0.00 2.29
358 397 6.430616 TGATGATCACTCTGTTTTGCAATGTA 59.569 34.615 0.00 0.00 0.00 2.29
359 398 5.242171 TGATGATCACTCTGTTTTGCAATGT 59.758 36.000 0.00 0.00 0.00 2.71
375 414 1.539712 GCGAGCTGATGGTGATGATCA 60.540 52.381 0.00 0.00 0.00 2.92
384 423 1.812922 GGTGACTGCGAGCTGATGG 60.813 63.158 8.91 0.00 0.00 3.51
386 425 1.079543 GTGGTGACTGCGAGCTGAT 60.080 57.895 8.91 0.00 0.00 2.90
387 426 2.340078 GTGGTGACTGCGAGCTGA 59.660 61.111 8.91 0.00 0.00 4.26
389 428 3.151958 AACGTGGTGACTGCGAGCT 62.152 57.895 6.37 0.00 34.51 4.09
390 429 2.658707 GAACGTGGTGACTGCGAGC 61.659 63.158 6.37 0.00 34.51 5.03
391 430 1.007271 AGAACGTGGTGACTGCGAG 60.007 57.895 6.37 0.00 34.51 5.03
392 431 1.299850 CAGAACGTGGTGACTGCGA 60.300 57.895 6.37 0.00 34.51 5.10
393 432 2.943345 GCAGAACGTGGTGACTGCG 61.943 63.158 13.07 0.00 44.27 5.18
394 433 2.939022 GCAGAACGTGGTGACTGC 59.061 61.111 13.07 13.07 46.25 4.40
395 434 4.758692 AGCAGAACGTGGTGACTG 57.241 55.556 1.65 0.00 34.82 3.51
414 453 4.225984 TGAAATTGTAGCGTGTTGATTGC 58.774 39.130 0.00 0.00 0.00 3.56
416 455 5.334879 GGACTGAAATTGTAGCGTGTTGATT 60.335 40.000 0.00 0.00 0.00 2.57
428 467 3.006110 CACATGGCTTGGACTGAAATTGT 59.994 43.478 5.31 0.00 0.00 2.71
429 468 3.256383 TCACATGGCTTGGACTGAAATTG 59.744 43.478 5.31 0.00 0.00 2.32
437 476 0.171903 GCACATCACATGGCTTGGAC 59.828 55.000 5.31 0.00 33.60 4.02
438 477 0.251253 TGCACATCACATGGCTTGGA 60.251 50.000 5.31 0.33 33.60 3.53
441 480 1.624336 AACTGCACATCACATGGCTT 58.376 45.000 0.00 0.00 33.60 4.35
444 483 3.928727 AAGAAACTGCACATCACATGG 57.071 42.857 0.00 0.00 33.60 3.66
445 484 6.441274 ACTTAAAGAAACTGCACATCACATG 58.559 36.000 0.00 0.00 0.00 3.21
448 487 8.850454 TTTTACTTAAAGAAACTGCACATCAC 57.150 30.769 0.00 0.00 0.00 3.06
494 533 1.546476 AGTCACTCTCACCACGGATTC 59.454 52.381 0.00 0.00 0.00 2.52
510 549 3.020984 GACTTTTTGGGTGGACAAGTCA 58.979 45.455 2.29 0.00 41.95 3.41
533 572 1.148273 AACAAACTGCCTCTCGCCA 59.852 52.632 0.00 0.00 36.24 5.69
534 573 1.576421 CAACAAACTGCCTCTCGCC 59.424 57.895 0.00 0.00 36.24 5.54
536 575 1.165907 TGCCAACAAACTGCCTCTCG 61.166 55.000 0.00 0.00 0.00 4.04
541 580 0.530431 CTGGTTGCCAACAAACTGCC 60.530 55.000 10.18 0.00 44.28 4.85
563 602 1.073722 TCCCTGCAAGCCAGAGTTG 59.926 57.895 0.00 0.00 44.64 3.16
567 606 4.020617 CCGTCCCTGCAAGCCAGA 62.021 66.667 0.00 0.00 44.64 3.86
600 639 3.889692 CCACCCCCATGATCCGGG 61.890 72.222 0.00 9.89 44.07 5.73
601 640 4.586235 GCCACCCCCATGATCCGG 62.586 72.222 0.00 0.00 0.00 5.14
602 641 4.935495 CGCCACCCCCATGATCCG 62.935 72.222 0.00 0.00 0.00 4.18
653 711 1.737793 GACATCCCAACCTTTACGCTG 59.262 52.381 0.00 0.00 0.00 5.18
675 733 2.665185 GGTGCGGGATATGGCGAC 60.665 66.667 0.00 0.00 0.00 5.19
676 734 3.936203 GGGTGCGGGATATGGCGA 61.936 66.667 0.00 0.00 0.00 5.54
677 735 3.765894 TTGGGTGCGGGATATGGCG 62.766 63.158 0.00 0.00 0.00 5.69
678 736 1.040339 TTTTGGGTGCGGGATATGGC 61.040 55.000 0.00 0.00 0.00 4.40
727 785 1.507141 CGAGCCAAGGTCGCAGTTTT 61.507 55.000 3.05 0.00 45.89 2.43
761 820 3.936772 TTGGGATGGGTTGGCTCGC 62.937 63.158 0.00 0.00 0.00 5.03
763 822 1.103398 CGATTGGGATGGGTTGGCTC 61.103 60.000 0.00 0.00 0.00 4.70
805 864 3.729462 CGAGTGAACCTCAGAAGATCGAC 60.729 52.174 0.00 0.00 40.48 4.20
807 866 2.791567 CGAGTGAACCTCAGAAGATCG 58.208 52.381 0.00 0.00 40.48 3.69
814 881 3.382111 AGGGCGAGTGAACCTCAG 58.618 61.111 0.00 0.00 40.48 3.35
861 928 3.315749 GCACTAGCCTAGGTACAGTAGTG 59.684 52.174 21.10 21.10 40.13 2.74
900 967 2.686405 TGATTGCTTGCTTGGCTATCAG 59.314 45.455 14.53 0.00 43.06 2.90
904 971 2.166870 CCAATGATTGCTTGCTTGGCTA 59.833 45.455 0.00 0.00 30.85 3.93
906 973 1.066716 TCCAATGATTGCTTGCTTGGC 60.067 47.619 0.00 0.00 37.00 4.52
907 974 3.536956 ATCCAATGATTGCTTGCTTGG 57.463 42.857 0.00 4.75 38.14 3.61
908 975 4.988540 CCATATCCAATGATTGCTTGCTTG 59.011 41.667 0.00 0.00 32.18 4.01
1285 1366 1.280206 AACTTGTACTTCGGCGCGTC 61.280 55.000 8.43 3.30 0.00 5.19
1286 1367 1.280206 GAACTTGTACTTCGGCGCGT 61.280 55.000 8.43 4.26 0.00 6.01
1404 1520 1.416049 CCGAACTTGCACGATCACG 59.584 57.895 0.00 0.00 45.75 4.35
1405 1521 0.949105 ACCCGAACTTGCACGATCAC 60.949 55.000 0.00 0.00 0.00 3.06
1406 1522 0.250124 AACCCGAACTTGCACGATCA 60.250 50.000 0.00 0.00 0.00 2.92
1407 1523 0.442699 GAACCCGAACTTGCACGATC 59.557 55.000 0.00 0.00 0.00 3.69
1408 1524 0.034896 AGAACCCGAACTTGCACGAT 59.965 50.000 0.00 0.00 0.00 3.73
1409 1525 0.599204 GAGAACCCGAACTTGCACGA 60.599 55.000 0.00 0.00 0.00 4.35
1410 1526 1.566018 GGAGAACCCGAACTTGCACG 61.566 60.000 0.00 0.00 0.00 5.34
1411 1527 2.244946 GGAGAACCCGAACTTGCAC 58.755 57.895 0.00 0.00 0.00 4.57
1412 1528 4.792087 GGAGAACCCGAACTTGCA 57.208 55.556 0.00 0.00 0.00 4.08
1422 1538 3.118371 AGTTCATATTGACGGGGAGAACC 60.118 47.826 0.00 0.00 35.68 3.62
1423 1539 4.138487 AGTTCATATTGACGGGGAGAAC 57.862 45.455 0.00 0.00 35.40 3.01
1424 1540 4.837093 AAGTTCATATTGACGGGGAGAA 57.163 40.909 0.00 0.00 0.00 2.87
1425 1541 4.837093 AAAGTTCATATTGACGGGGAGA 57.163 40.909 0.00 0.00 0.00 3.71
1426 1542 5.186198 AGAAAAGTTCATATTGACGGGGAG 58.814 41.667 0.00 0.00 0.00 4.30
1427 1543 5.174037 AGAAAAGTTCATATTGACGGGGA 57.826 39.130 0.00 0.00 0.00 4.81
1428 1544 5.897377 AAGAAAAGTTCATATTGACGGGG 57.103 39.130 0.00 0.00 0.00 5.73
1452 1568 3.822996 TCAAACTTTGTCGACGCAAAAA 58.177 36.364 11.62 4.88 37.82 1.94
1453 1569 3.473093 TCAAACTTTGTCGACGCAAAA 57.527 38.095 11.62 5.25 37.82 2.44
1454 1570 3.473093 TTCAAACTTTGTCGACGCAAA 57.527 38.095 11.62 13.92 36.93 3.68
1455 1571 3.684103 ATTCAAACTTTGTCGACGCAA 57.316 38.095 11.62 5.45 0.00 4.85
1456 1572 3.064134 TCAATTCAAACTTTGTCGACGCA 59.936 39.130 11.62 0.00 0.00 5.24
1457 1573 3.613563 TCAATTCAAACTTTGTCGACGC 58.386 40.909 11.62 0.00 0.00 5.19
1458 1574 6.547493 TTTTCAATTCAAACTTTGTCGACG 57.453 33.333 11.62 0.00 0.00 5.12
1459 1575 8.379902 ACATTTTTCAATTCAAACTTTGTCGAC 58.620 29.630 9.11 9.11 0.00 4.20
1460 1576 8.379161 CACATTTTTCAATTCAAACTTTGTCGA 58.621 29.630 1.44 0.00 0.00 4.20
1461 1577 8.379161 TCACATTTTTCAATTCAAACTTTGTCG 58.621 29.630 1.44 0.00 0.00 4.35
1464 1580 9.360514 CGATCACATTTTTCAATTCAAACTTTG 57.639 29.630 0.00 0.00 0.00 2.77
1465 1581 9.097257 ACGATCACATTTTTCAATTCAAACTTT 57.903 25.926 0.00 0.00 0.00 2.66
1547 1692 0.679505 GGATCGGATCGGATTGGACA 59.320 55.000 16.07 0.00 0.00 4.02
1726 2128 3.878667 GATCCTTCGGGGCCAGGG 61.879 72.222 4.39 0.00 35.37 4.45
1775 2178 4.570663 CTCCCCGCTACGCTTCCG 62.571 72.222 0.00 0.00 41.14 4.30
1795 2207 2.125188 GTCAGCTCAGCCTCAGCC 60.125 66.667 0.00 0.00 41.25 4.85
1959 2392 3.033764 GCCTCGCGTTCAACGACA 61.034 61.111 15.79 0.00 46.05 4.35
1997 2430 2.129146 TGGTCACCGTCGACAAGGT 61.129 57.895 17.16 12.82 42.34 3.50
2000 2433 2.026445 CGTGGTCACCGTCGACAA 59.974 61.111 17.16 0.00 37.66 3.18
2001 2434 3.968568 CCGTGGTCACCGTCGACA 61.969 66.667 17.16 0.00 37.66 4.35


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

AutoCloner maintained by Alex Coulton.