Multiple sequence alignment - TraesCS1B01G371300

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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 TraesCS1B01G371300 chr1B 100.000 4499 0 0 1 4499 600957175 600961673 0.000000e+00 8309.0
1 TraesCS1B01G371300 chr1D 90.629 4119 196 91 1 4034 442329767 442333780 0.000000e+00 5293.0
2 TraesCS1B01G371300 chr1D 93.208 265 18 0 4235 4499 442334072 442334336 1.520000e-104 390.0
3 TraesCS1B01G371300 chr1D 96.183 131 1 1 4051 4177 442333765 442333895 1.270000e-50 211.0
4 TraesCS1B01G371300 chr1D 91.892 111 8 1 4173 4282 442333966 442334076 2.170000e-33 154.0
5 TraesCS1B01G371300 chr1D 82.576 132 18 2 4357 4488 387422563 387422689 1.320000e-20 111.0
6 TraesCS1B01G371300 chr1A 91.476 3590 162 73 511 4034 536356940 536353429 0.000000e+00 4802.0
7 TraesCS1B01G371300 chr1A 88.281 128 6 4 4052 4177 536353443 536353323 1.300000e-30 145.0
8 TraesCS1B01G371300 chr6D 79.082 196 30 6 4296 4490 422193931 422194116 1.700000e-24 124.0
9 TraesCS1B01G371300 chr6D 74.490 294 56 10 4200 4490 61019584 61019861 4.760000e-20 110.0
10 TraesCS1B01G371300 chr5D 80.392 153 24 2 4339 4490 543832884 543833031 1.320000e-20 111.0
11 TraesCS1B01G371300 chr3A 77.551 196 34 5 4296 4490 25577367 25577553 4.760000e-20 110.0
12 TraesCS1B01G371300 chr6B 83.636 110 11 4 4382 4490 135085342 135085445 3.700000e-16 97.1
13 TraesCS1B01G371300 chr7B 84.536 97 10 2 4381 4477 18226116 18226207 1.720000e-14 91.6
14 TraesCS1B01G371300 chr4D 84.706 85 13 0 4415 4499 440279059 440278975 8.020000e-13 86.1


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 TraesCS1B01G371300 chr1B 600957175 600961673 4498 False 8309.0 8309 100.0000 1 4499 1 chr1B.!!$F1 4498
1 TraesCS1B01G371300 chr1D 442329767 442334336 4569 False 1512.0 5293 92.9780 1 4499 4 chr1D.!!$F2 4498
2 TraesCS1B01G371300 chr1A 536353323 536356940 3617 True 2473.5 4802 89.8785 511 4177 2 chr1A.!!$R1 3666

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
420 445 0.175989 GGGAAGCCTACTCCTTGACG 59.824 60.0 0.0 0.0 0.0 4.35 F
2045 2183 0.179020 TTGCTCTTCTGGTGGGTGTG 60.179 55.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 2260 0.538584 TGTTGCTGAGATCCATCGCT 59.461 50.0 0.0 0.0 0.00 4.93 R
4039 4204 0.106918 ACTGAAAAGGTCACCCGCAA 60.107 50.0 0.0 0.0 35.12 4.85 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
32 33 2.050714 GTGCGAACACGACGAGGA 60.051 61.111 0.00 0.00 36.98 3.71
80 81 4.767255 GGCTCCACCGCAGTCCAG 62.767 72.222 0.00 0.00 0.00 3.86
82 83 3.699894 CTCCACCGCAGTCCAGCT 61.700 66.667 0.00 0.00 0.00 4.24
84 85 2.125512 CCACCGCAGTCCAGCTAC 60.126 66.667 0.00 0.00 0.00 3.58
85 86 2.656646 CACCGCAGTCCAGCTACA 59.343 61.111 0.00 0.00 0.00 2.74
90 115 1.816537 GCAGTCCAGCTACATCGGA 59.183 57.895 0.00 0.00 0.00 4.55
99 124 2.166459 CAGCTACATCGGAAAGTCAGGA 59.834 50.000 0.00 0.00 0.00 3.86
102 127 0.246635 ACATCGGAAAGTCAGGACCG 59.753 55.000 0.00 0.00 45.61 4.79
105 130 1.215647 CGGAAAGTCAGGACCGGAG 59.784 63.158 9.46 0.00 41.41 4.63
211 236 2.895372 GGCGCCGGATGAACGAAT 60.895 61.111 12.58 0.00 35.47 3.34
234 259 4.486503 CCCAGAGGCCAGCTGAGC 62.487 72.222 22.89 16.67 35.39 4.26
380 405 2.107750 CGTCGGCAGATGGATGCT 59.892 61.111 0.00 0.00 45.75 3.79
381 406 1.363807 CGTCGGCAGATGGATGCTA 59.636 57.895 0.00 0.00 45.75 3.49
382 407 0.665670 CGTCGGCAGATGGATGCTAG 60.666 60.000 0.00 0.00 45.75 3.42
395 420 3.447586 TGGATGCTAGTAACAGGAGTGAC 59.552 47.826 0.00 0.00 0.00 3.67
401 426 2.530701 AGTAACAGGAGTGACAGGGAG 58.469 52.381 0.00 0.00 30.87 4.30
402 427 1.550976 GTAACAGGAGTGACAGGGAGG 59.449 57.143 0.00 0.00 0.00 4.30
403 428 0.838122 AACAGGAGTGACAGGGAGGG 60.838 60.000 0.00 0.00 0.00 4.30
404 429 1.079256 CAGGAGTGACAGGGAGGGA 59.921 63.158 0.00 0.00 0.00 4.20
405 430 0.545309 CAGGAGTGACAGGGAGGGAA 60.545 60.000 0.00 0.00 0.00 3.97
406 431 0.252467 AGGAGTGACAGGGAGGGAAG 60.252 60.000 0.00 0.00 0.00 3.46
407 432 1.599576 GAGTGACAGGGAGGGAAGC 59.400 63.158 0.00 0.00 0.00 3.86
408 433 1.904990 GAGTGACAGGGAGGGAAGCC 61.905 65.000 0.00 0.00 0.00 4.35
409 434 1.920835 GTGACAGGGAGGGAAGCCT 60.921 63.158 0.00 0.00 0.00 4.58
410 435 0.617820 GTGACAGGGAGGGAAGCCTA 60.618 60.000 0.00 0.00 0.00 3.93
411 436 0.617820 TGACAGGGAGGGAAGCCTAC 60.618 60.000 0.00 0.00 0.00 3.18
412 437 0.325765 GACAGGGAGGGAAGCCTACT 60.326 60.000 0.00 0.00 0.00 2.57
413 438 0.325765 ACAGGGAGGGAAGCCTACTC 60.326 60.000 0.00 0.00 0.00 2.59
416 441 3.325994 GGAGGGAAGCCTACTCCTT 57.674 57.895 0.00 0.00 45.73 3.36
417 442 0.833949 GGAGGGAAGCCTACTCCTTG 59.166 60.000 0.00 0.00 45.73 3.61
418 443 1.622725 GGAGGGAAGCCTACTCCTTGA 60.623 57.143 0.00 0.00 45.73 3.02
419 444 1.483004 GAGGGAAGCCTACTCCTTGAC 59.517 57.143 0.00 0.00 0.00 3.18
420 445 0.175989 GGGAAGCCTACTCCTTGACG 59.824 60.000 0.00 0.00 0.00 4.35
421 446 1.183549 GGAAGCCTACTCCTTGACGA 58.816 55.000 0.00 0.00 0.00 4.20
422 447 1.135333 GGAAGCCTACTCCTTGACGAG 59.865 57.143 0.00 0.00 35.88 4.18
427 452 0.895530 CTACTCCTTGACGAGGCCAA 59.104 55.000 5.01 0.00 45.87 4.52
431 456 3.793144 CTTGACGAGGCCAAGCGC 61.793 66.667 5.01 0.00 35.23 5.92
447 472 4.899239 GCTGATCTGGGCCGTCGG 62.899 72.222 6.99 6.99 0.00 4.79
458 494 2.989824 CCGTCGGTCTGGTCTGGT 60.990 66.667 2.08 0.00 0.00 4.00
459 495 2.258591 CGTCGGTCTGGTCTGGTG 59.741 66.667 0.00 0.00 0.00 4.17
466 502 4.641645 CTGGTCTGGTGGCCGCAA 62.642 66.667 19.98 5.74 0.00 4.85
473 509 3.419759 GGTGGCCGCAACGTGTAG 61.420 66.667 19.98 0.00 0.00 2.74
474 510 3.419759 GTGGCCGCAACGTGTAGG 61.420 66.667 12.58 0.00 0.00 3.18
475 511 4.690719 TGGCCGCAACGTGTAGGG 62.691 66.667 0.00 0.00 0.00 3.53
476 512 4.692475 GGCCGCAACGTGTAGGGT 62.692 66.667 0.00 0.00 0.00 4.34
477 513 3.419759 GCCGCAACGTGTAGGGTG 61.420 66.667 0.00 0.00 0.00 4.61
478 514 2.029964 CCGCAACGTGTAGGGTGT 59.970 61.111 0.00 0.00 0.00 4.16
479 515 2.314647 CCGCAACGTGTAGGGTGTG 61.315 63.158 0.00 0.00 0.00 3.82
480 516 2.314647 CGCAACGTGTAGGGTGTGG 61.315 63.158 0.00 0.00 0.00 4.17
481 517 1.227734 GCAACGTGTAGGGTGTGGT 60.228 57.895 0.00 0.00 0.00 4.16
482 518 1.503818 GCAACGTGTAGGGTGTGGTG 61.504 60.000 0.00 0.00 0.00 4.17
483 519 1.227734 AACGTGTAGGGTGTGGTGC 60.228 57.895 0.00 0.00 0.00 5.01
484 520 2.358247 CGTGTAGGGTGTGGTGCC 60.358 66.667 0.00 0.00 0.00 5.01
485 521 2.833227 GTGTAGGGTGTGGTGCCA 59.167 61.111 0.00 0.00 0.00 4.92
486 522 1.378762 GTGTAGGGTGTGGTGCCAT 59.621 57.895 0.00 0.00 0.00 4.40
487 523 0.676782 GTGTAGGGTGTGGTGCCATC 60.677 60.000 0.00 0.00 0.00 3.51
488 524 1.077716 GTAGGGTGTGGTGCCATCC 60.078 63.158 0.00 0.88 0.00 3.51
489 525 1.540118 TAGGGTGTGGTGCCATCCA 60.540 57.895 14.01 0.00 34.85 3.41
490 526 0.918799 TAGGGTGTGGTGCCATCCAT 60.919 55.000 14.01 10.81 39.81 3.41
491 527 2.053865 GGGTGTGGTGCCATCCATG 61.054 63.158 14.01 0.00 39.81 3.66
517 553 2.740447 GCCGGTGGTTTTTCTAGTAGTG 59.260 50.000 1.90 0.00 0.00 2.74
569 631 0.322906 GGTGGCTGGAAAGAAGGGAG 60.323 60.000 0.00 0.00 0.00 4.30
570 632 0.322906 GTGGCTGGAAAGAAGGGAGG 60.323 60.000 0.00 0.00 0.00 4.30
571 633 1.304617 GGCTGGAAAGAAGGGAGGG 59.695 63.158 0.00 0.00 0.00 4.30
572 634 1.208165 GGCTGGAAAGAAGGGAGGGA 61.208 60.000 0.00 0.00 0.00 4.20
678 744 1.106944 GTCCACACCCCACAACTTGG 61.107 60.000 0.00 0.00 46.47 3.61
681 747 2.917227 CACCCCACAACTTGGCCC 60.917 66.667 0.00 0.00 45.37 5.80
716 784 3.279116 CACACACACACCCGGCAG 61.279 66.667 0.00 0.00 0.00 4.85
786 854 2.177594 CTCCCCACTGTGTCTGCCTC 62.178 65.000 7.08 0.00 0.00 4.70
787 855 2.219875 CCCCACTGTGTCTGCCTCT 61.220 63.158 7.08 0.00 0.00 3.69
788 856 1.004080 CCCACTGTGTCTGCCTCTG 60.004 63.158 7.08 0.00 0.00 3.35
789 857 1.670406 CCACTGTGTCTGCCTCTGC 60.670 63.158 7.08 0.00 38.26 4.26
828 901 4.078516 GGTTCCGTCCCCACCGAG 62.079 72.222 0.00 0.00 0.00 4.63
899 973 3.403558 GCCCGCCTTCCTCTTCCT 61.404 66.667 0.00 0.00 0.00 3.36
900 974 2.904131 CCCGCCTTCCTCTTCCTC 59.096 66.667 0.00 0.00 0.00 3.71
901 975 1.687493 CCCGCCTTCCTCTTCCTCT 60.687 63.158 0.00 0.00 0.00 3.69
902 976 1.681486 CCCGCCTTCCTCTTCCTCTC 61.681 65.000 0.00 0.00 0.00 3.20
903 977 0.686112 CCGCCTTCCTCTTCCTCTCT 60.686 60.000 0.00 0.00 0.00 3.10
904 978 1.190643 CGCCTTCCTCTTCCTCTCTT 58.809 55.000 0.00 0.00 0.00 2.85
905 979 1.136110 CGCCTTCCTCTTCCTCTCTTC 59.864 57.143 0.00 0.00 0.00 2.87
906 980 1.136110 GCCTTCCTCTTCCTCTCTTCG 59.864 57.143 0.00 0.00 0.00 3.79
927 1001 2.164865 CTGCCCCGCATCTAGCTAGG 62.165 65.000 20.58 6.77 42.61 3.02
970 1044 3.760035 GCGAGCTTGGTCGGAGGA 61.760 66.667 20.97 0.00 40.44 3.71
971 1045 2.492090 CGAGCTTGGTCGGAGGAG 59.508 66.667 13.52 0.00 36.26 3.69
1201 1293 4.642429 TCCTTTCTTTCTTTCCTCCTTCG 58.358 43.478 0.00 0.00 0.00 3.79
1244 1336 1.202336 CCAAGCAAGGAATCATTCGCC 60.202 52.381 0.00 0.00 0.00 5.54
1469 1591 2.046292 CACCAAAGGTTCCACCCAATT 58.954 47.619 0.00 0.00 39.75 2.32
1470 1592 3.235200 CACCAAAGGTTCCACCCAATTA 58.765 45.455 0.00 0.00 39.75 1.40
1487 1609 5.189539 CCCAATTAACCACCTCCAAATCAAT 59.810 40.000 0.00 0.00 0.00 2.57
1521 1643 3.711704 AGCCTCAATTAGTTAGCCTAGCA 59.288 43.478 0.00 0.00 0.00 3.49
1522 1644 4.164221 AGCCTCAATTAGTTAGCCTAGCAA 59.836 41.667 0.00 0.00 0.00 3.91
1529 1651 7.764443 TCAATTAGTTAGCCTAGCAAAGTACTG 59.236 37.037 0.00 0.00 0.00 2.74
1630 1755 2.027314 CGATCCTCAGCAGAGCGG 59.973 66.667 0.00 0.00 39.36 5.52
1639 1764 1.228245 AGCAGAGCGGCAAAAAGGA 60.228 52.632 1.45 0.00 35.83 3.36
1669 1794 1.003718 GGCTGTTAGGTGAGCGGTT 60.004 57.895 0.00 0.00 35.95 4.44
1683 1808 2.998949 GGTTGCCCTCGAATCCCT 59.001 61.111 0.00 0.00 0.00 4.20
1756 1881 1.675310 CGGGCTCCAGATTGCAACA 60.675 57.895 0.00 0.00 0.00 3.33
1826 1953 6.206634 TGAACTTTACCATCTTTTAGGCAGTG 59.793 38.462 0.00 0.00 0.00 3.66
1985 2118 4.766375 TGGTCTAGCTGTTGGTAATTAGC 58.234 43.478 7.74 7.74 36.45 3.09
1988 2121 4.271291 GTCTAGCTGTTGGTAATTAGCTGC 59.729 45.833 15.27 13.06 45.36 5.25
2002 2140 8.458843 GGTAATTAGCTGCTTGAGAATTGTTAA 58.541 33.333 7.79 0.00 0.00 2.01
2045 2183 0.179020 TTGCTCTTCTGGTGGGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
2075 2213 3.425659 ACTCTACTGATGTGTCTGCAGA 58.574 45.455 13.74 13.74 33.94 4.26
2122 2260 1.287503 GAAATGGTCGCCGGCAAAA 59.712 52.632 28.98 8.35 0.00 2.44
2210 2348 4.771590 TGTTCATTTGAATCTGCTGGTC 57.228 40.909 0.00 0.00 36.33 4.02
2256 2394 7.010923 CACTGTTCTATTGAGTCATCTTTAGGC 59.989 40.741 0.00 0.00 0.00 3.93
2296 2457 7.582352 CATATGCATATGTCCAACTCTTTCTG 58.418 38.462 30.55 8.17 36.31 3.02
2312 2473 4.999950 TCTTTCTGTTTCCTCTGATTCAGC 59.000 41.667 8.89 0.00 0.00 4.26
2316 2477 7.423844 TTCTGTTTCCTCTGATTCAGCTATA 57.576 36.000 8.89 0.00 0.00 1.31
2330 2491 7.767659 TGATTCAGCTATATACTTCATGCATCC 59.232 37.037 0.00 0.00 0.00 3.51
2357 2518 2.591715 GGATGACGCGGAATGGGG 60.592 66.667 12.47 0.00 34.15 4.96
2364 2525 2.362375 GCGGAATGGGGGAGCAAA 60.362 61.111 0.00 0.00 0.00 3.68
2568 2729 2.287547 GCTGACGGTGAAATCAAGCAAA 60.288 45.455 0.00 0.00 0.00 3.68
2733 2894 3.713248 AGTTCCTCATCACAGATATGGCA 59.287 43.478 0.00 0.00 0.00 4.92
2793 2954 4.047883 AGCTATCCAACTACCCCTTGATT 58.952 43.478 0.00 0.00 0.00 2.57
2823 2984 6.207221 TCAACAAAGATACTGATGTGCATTGT 59.793 34.615 0.00 0.00 30.81 2.71
2825 2986 5.474532 ACAAAGATACTGATGTGCATTGTGT 59.525 36.000 0.00 0.00 29.54 3.72
3159 3320 2.172082 CTCTGTGGATGTGATGATGGGT 59.828 50.000 0.00 0.00 0.00 4.51
3210 3371 2.652530 CTGCCACACAATGCCACC 59.347 61.111 0.00 0.00 0.00 4.61
3243 3404 2.505982 CCGTGGGGTGGCATAGAG 59.494 66.667 0.00 0.00 0.00 2.43
3300 3461 1.377987 GATGGGCCTGCGGTACAAA 60.378 57.895 4.53 0.00 0.00 2.83
3590 3754 4.797933 GCTCACCGTTCTTCTCTTCTCTTT 60.798 45.833 0.00 0.00 0.00 2.52
3591 3755 5.277857 TCACCGTTCTTCTCTTCTCTTTT 57.722 39.130 0.00 0.00 0.00 2.27
3592 3756 5.290386 TCACCGTTCTTCTCTTCTCTTTTC 58.710 41.667 0.00 0.00 0.00 2.29
3648 3812 3.931578 AGTACATGAGCAAGGAACAGAC 58.068 45.455 0.00 0.00 0.00 3.51
3812 3976 3.305813 GGCATGGAAATATCAGTGCATGG 60.306 47.826 13.66 0.00 38.49 3.66
3892 4056 6.101296 ACCAATAGGAATTTACTAGGTGGAGG 59.899 42.308 20.55 8.02 38.69 4.30
3921 4085 2.703416 TCTGTGCTGTGTGATTCATCC 58.297 47.619 0.00 0.00 0.00 3.51
3988 4153 3.901844 AGGTGTCAGGTGCTAGAAGTTTA 59.098 43.478 0.00 0.00 0.00 2.01
3993 4158 3.055819 TCAGGTGCTAGAAGTTTAGCTGG 60.056 47.826 0.00 0.00 44.99 4.85
4017 4182 5.047021 GCCAGGCCTCTTTCTTTTATTTTCT 60.047 40.000 0.00 0.00 0.00 2.52
4185 4429 5.989777 TGAAGTTGGTTGACTAGAGTAAAGC 59.010 40.000 0.00 2.49 37.39 3.51
4196 4440 1.362932 AGAGTAAAGCCTCCCTCCTCA 59.637 52.381 0.00 0.00 31.53 3.86
4198 4442 1.203313 AGTAAAGCCTCCCTCCTCACA 60.203 52.381 0.00 0.00 0.00 3.58
4208 4452 0.460987 CCTCCTCACAATCTCCGCAC 60.461 60.000 0.00 0.00 0.00 5.34
4270 4515 1.986413 CCTGAGGTGGGGAGTGAAG 59.014 63.158 0.00 0.00 0.00 3.02
4282 4527 2.034221 GTGAAGTCCTGGTGCCCC 59.966 66.667 0.00 0.00 0.00 5.80
4312 4600 5.068855 CAGCTAGTAGGTAGGTTAGGGTTTC 59.931 48.000 0.60 0.00 37.37 2.78
4319 4607 3.586174 GGTAGGTTAGGGTTTCAGTCCTT 59.414 47.826 0.00 0.00 34.75 3.36
4321 4609 3.053826 AGGTTAGGGTTTCAGTCCTTGT 58.946 45.455 0.00 0.00 34.75 3.16
4331 4619 0.888619 CAGTCCTTGTAGAGGCGACA 59.111 55.000 0.00 0.00 45.87 4.35
4364 4652 3.322828 TGGCTACACTTTACCTTCGAGTT 59.677 43.478 0.00 0.00 0.00 3.01
4409 4697 2.104111 TCAAGTTTGTCTGTCGGGACAT 59.896 45.455 1.41 0.00 44.30 3.06
4423 4711 7.122799 TCTGTCGGGACATATTAGATTAGATGG 59.877 40.741 1.41 0.00 41.01 3.51
4447 4735 0.319900 CCGACATAGATTCCTGCCGG 60.320 60.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.319211 AAATCCTCGTCGTGTTCGCA 60.319 50.000 0.00 0.00 36.96 5.10
19 20 1.798813 AGCAAAATCCTCGTCGTGTTC 59.201 47.619 0.00 0.00 0.00 3.18
20 21 1.531149 CAGCAAAATCCTCGTCGTGTT 59.469 47.619 0.00 0.00 0.00 3.32
80 81 2.541556 GTCCTGACTTTCCGATGTAGC 58.458 52.381 0.00 0.00 0.00 3.58
82 83 1.475280 CGGTCCTGACTTTCCGATGTA 59.525 52.381 0.00 0.00 44.86 2.29
84 85 0.460284 CCGGTCCTGACTTTCCGATG 60.460 60.000 4.00 0.00 44.86 3.84
85 86 0.613853 TCCGGTCCTGACTTTCCGAT 60.614 55.000 0.00 0.00 44.86 4.18
90 115 2.943978 CGCCTCCGGTCCTGACTTT 61.944 63.158 0.00 0.00 0.00 2.66
201 226 2.168521 TCTGGGTCTCCATTCGTTCATC 59.831 50.000 0.00 0.00 43.11 2.92
211 236 2.284921 CTGGCCTCTGGGTCTCCA 60.285 66.667 3.32 0.00 41.58 3.86
234 259 1.135431 GCCGATCAGATCCGATCTCAG 60.135 57.143 15.33 6.71 39.78 3.35
298 323 3.854669 AATCCCGCTCGCCTCTGG 61.855 66.667 0.00 0.00 0.00 3.86
375 400 4.440802 CCTGTCACTCCTGTTACTAGCATC 60.441 50.000 0.00 0.00 0.00 3.91
376 401 3.449018 CCTGTCACTCCTGTTACTAGCAT 59.551 47.826 0.00 0.00 0.00 3.79
377 402 2.826128 CCTGTCACTCCTGTTACTAGCA 59.174 50.000 0.00 0.00 0.00 3.49
378 403 2.166664 CCCTGTCACTCCTGTTACTAGC 59.833 54.545 0.00 0.00 0.00 3.42
379 404 3.697045 CTCCCTGTCACTCCTGTTACTAG 59.303 52.174 0.00 0.00 0.00 2.57
380 405 3.563697 CCTCCCTGTCACTCCTGTTACTA 60.564 52.174 0.00 0.00 0.00 1.82
381 406 2.530701 CTCCCTGTCACTCCTGTTACT 58.469 52.381 0.00 0.00 0.00 2.24
382 407 1.550976 CCTCCCTGTCACTCCTGTTAC 59.449 57.143 0.00 0.00 0.00 2.50
395 420 1.051556 GGAGTAGGCTTCCCTCCCTG 61.052 65.000 13.66 0.00 41.75 4.45
401 426 0.175989 CGTCAAGGAGTAGGCTTCCC 59.824 60.000 1.52 0.00 0.00 3.97
402 427 1.135333 CTCGTCAAGGAGTAGGCTTCC 59.865 57.143 0.00 0.00 0.00 3.46
403 428 2.570442 CTCGTCAAGGAGTAGGCTTC 57.430 55.000 0.00 0.00 0.00 3.86
413 438 3.121030 CGCTTGGCCTCGTCAAGG 61.121 66.667 3.32 0.00 44.37 3.61
414 439 3.793144 GCGCTTGGCCTCGTCAAG 61.793 66.667 3.32 0.00 46.59 3.02
415 440 4.314440 AGCGCTTGGCCTCGTCAA 62.314 61.111 2.64 0.00 45.17 3.18
417 442 4.742201 TCAGCGCTTGGCCTCGTC 62.742 66.667 7.50 2.04 45.17 4.20
418 443 4.087892 ATCAGCGCTTGGCCTCGT 62.088 61.111 7.50 0.00 45.17 4.18
419 444 3.267860 GATCAGCGCTTGGCCTCG 61.268 66.667 7.50 6.26 45.17 4.63
420 445 2.178890 CAGATCAGCGCTTGGCCTC 61.179 63.158 7.50 0.00 45.17 4.70
421 446 2.124819 CAGATCAGCGCTTGGCCT 60.125 61.111 7.50 0.00 45.17 5.19
422 447 3.207669 CCAGATCAGCGCTTGGCC 61.208 66.667 7.50 0.00 45.17 5.36
431 456 3.432051 GACCGACGGCCCAGATCAG 62.432 68.421 15.39 0.00 0.00 2.90
458 494 4.690719 CCCTACACGTTGCGGCCA 62.691 66.667 2.24 0.00 0.00 5.36
459 495 4.692475 ACCCTACACGTTGCGGCC 62.692 66.667 0.00 0.00 0.00 6.13
466 502 2.424302 GCACCACACCCTACACGT 59.576 61.111 0.00 0.00 0.00 4.49
470 506 1.077716 GGATGGCACCACACCCTAC 60.078 63.158 0.00 0.00 0.00 3.18
473 509 2.053865 CATGGATGGCACCACACCC 61.054 63.158 10.34 5.32 43.03 4.61
474 510 2.053865 CCATGGATGGCACCACACC 61.054 63.158 5.56 7.53 43.03 4.16
475 511 3.607163 CCATGGATGGCACCACAC 58.393 61.111 5.56 0.00 43.03 3.82
484 520 0.890542 CCACCGGCATACCATGGATG 60.891 60.000 21.47 17.85 42.29 3.51
485 521 1.352622 ACCACCGGCATACCATGGAT 61.353 55.000 21.47 4.69 42.29 3.41
486 522 1.567208 AACCACCGGCATACCATGGA 61.567 55.000 21.47 2.01 42.29 3.41
487 523 0.682855 AAACCACCGGCATACCATGG 60.683 55.000 11.19 11.19 44.33 3.66
488 524 1.181786 AAAACCACCGGCATACCATG 58.818 50.000 0.00 0.00 34.57 3.66
489 525 1.822371 GAAAAACCACCGGCATACCAT 59.178 47.619 0.00 0.00 34.57 3.55
490 526 1.202952 AGAAAAACCACCGGCATACCA 60.203 47.619 0.00 0.00 34.57 3.25
491 527 1.541379 AGAAAAACCACCGGCATACC 58.459 50.000 0.00 0.00 0.00 2.73
492 528 3.340928 ACTAGAAAAACCACCGGCATAC 58.659 45.455 0.00 0.00 0.00 2.39
493 529 3.706600 ACTAGAAAAACCACCGGCATA 57.293 42.857 0.00 0.00 0.00 3.14
494 530 2.579410 ACTAGAAAAACCACCGGCAT 57.421 45.000 0.00 0.00 0.00 4.40
495 531 2.369532 ACTACTAGAAAAACCACCGGCA 59.630 45.455 0.00 0.00 0.00 5.69
527 585 2.814336 GGCTTTCCTCGTCTCACAAAAT 59.186 45.455 0.00 0.00 0.00 1.82
529 587 1.872237 CGGCTTTCCTCGTCTCACAAA 60.872 52.381 0.00 0.00 0.00 2.83
530 588 0.319555 CGGCTTTCCTCGTCTCACAA 60.320 55.000 0.00 0.00 0.00 3.33
531 589 1.289066 CGGCTTTCCTCGTCTCACA 59.711 57.895 0.00 0.00 0.00 3.58
533 591 2.646175 CCCGGCTTTCCTCGTCTCA 61.646 63.158 0.00 0.00 0.00 3.27
569 631 2.154462 CTTATCATTCCCGCATGTCCC 58.846 52.381 0.00 0.00 0.00 4.46
570 632 2.154462 CCTTATCATTCCCGCATGTCC 58.846 52.381 0.00 0.00 0.00 4.02
571 633 2.154462 CCCTTATCATTCCCGCATGTC 58.846 52.381 0.00 0.00 0.00 3.06
572 634 1.819305 GCCCTTATCATTCCCGCATGT 60.819 52.381 0.00 0.00 0.00 3.21
683 749 2.933287 TGTGTAGGGTGGGGCTGG 60.933 66.667 0.00 0.00 0.00 4.85
684 750 2.351276 GTGTGTAGGGTGGGGCTG 59.649 66.667 0.00 0.00 0.00 4.85
685 751 2.122144 TGTGTGTAGGGTGGGGCT 60.122 61.111 0.00 0.00 0.00 5.19
686 752 2.033602 GTGTGTGTAGGGTGGGGC 59.966 66.667 0.00 0.00 0.00 5.80
716 784 1.637478 GCTCTGCTCTGCTCTTGTGC 61.637 60.000 0.00 0.00 0.00 4.57
786 854 2.409870 GGAATGAACGGGCAGGCAG 61.410 63.158 0.00 0.00 0.00 4.85
787 855 2.361104 GGAATGAACGGGCAGGCA 60.361 61.111 0.00 0.00 0.00 4.75
788 856 3.140814 GGGAATGAACGGGCAGGC 61.141 66.667 0.00 0.00 0.00 4.85
789 857 1.452108 GAGGGAATGAACGGGCAGG 60.452 63.158 0.00 0.00 0.00 4.85
821 894 4.135153 CGTGGAGGAGCTCGGTGG 62.135 72.222 7.83 0.00 0.00 4.61
822 895 4.803426 GCGTGGAGGAGCTCGGTG 62.803 72.222 7.83 0.00 0.00 4.94
826 899 2.107953 GGATGCGTGGAGGAGCTC 59.892 66.667 4.71 4.71 0.00 4.09
828 901 4.899239 CCGGATGCGTGGAGGAGC 62.899 72.222 5.72 0.00 0.00 4.70
890 964 0.333312 AGCCGAAGAGAGGAAGAGGA 59.667 55.000 0.00 0.00 0.00 3.71
905 979 4.976925 CTAGATGCGGGGCAGCCG 62.977 72.222 5.00 0.00 46.90 5.52
954 1028 2.492090 CTCCTCCGACCAAGCTCG 59.508 66.667 0.00 0.00 0.00 5.03
956 1030 2.685380 CCCTCCTCCGACCAAGCT 60.685 66.667 0.00 0.00 0.00 3.74
958 1032 3.083997 CCCCCTCCTCCGACCAAG 61.084 72.222 0.00 0.00 0.00 3.61
1163 1248 2.789409 AGGAAGAAAGAATCGTGGGG 57.211 50.000 0.00 0.00 0.00 4.96
1201 1293 5.866092 GGTTGCAAGAAGGAAATGAAGAATC 59.134 40.000 0.00 0.00 0.00 2.52
1244 1336 3.126343 GTCAGTTACCATTTTACCAGCGG 59.874 47.826 0.00 0.00 0.00 5.52
1280 1373 4.776322 TCACTGCGAATGGGGGCG 62.776 66.667 0.00 0.00 0.00 6.13
1469 1591 5.016173 CAGGAATTGATTTGGAGGTGGTTA 58.984 41.667 0.00 0.00 0.00 2.85
1470 1592 3.834231 CAGGAATTGATTTGGAGGTGGTT 59.166 43.478 0.00 0.00 0.00 3.67
1514 1636 6.986904 AGATAAAACAGTACTTTGCTAGGC 57.013 37.500 0.00 0.00 0.00 3.93
1529 1651 8.029642 TCAGTCGAGAAATTCCAAGATAAAAC 57.970 34.615 0.00 0.00 0.00 2.43
1630 1755 1.205655 GGGATTCAGGCTCCTTTTTGC 59.794 52.381 0.00 0.00 33.05 3.68
1647 1772 2.656069 GCTCACCTAACAGCCGGGA 61.656 63.158 2.18 0.00 0.00 5.14
1669 1794 1.801242 TATTGAGGGATTCGAGGGCA 58.199 50.000 0.00 0.00 0.00 5.36
1683 1808 5.163561 GGGCATCGGACAAAGAAATTATTGA 60.164 40.000 5.77 0.00 0.00 2.57
1756 1881 2.162681 CGTTTCAAGGAGGCCAAATCT 58.837 47.619 5.01 0.00 0.00 2.40
1826 1953 0.840722 TTCTCCCCTTCACCTCCACC 60.841 60.000 0.00 0.00 0.00 4.61
1943 2076 8.140112 AGACCAAGAAACATGAGAAGTACTAT 57.860 34.615 0.00 0.00 0.00 2.12
1944 2077 7.540474 AGACCAAGAAACATGAGAAGTACTA 57.460 36.000 0.00 0.00 0.00 1.82
2002 2140 6.418101 AGCAAGTACCATCACAGTCATTAAT 58.582 36.000 0.00 0.00 0.00 1.40
2045 2183 4.172505 CACATCAGTAGAGTCAAGTCAGC 58.827 47.826 0.00 0.00 0.00 4.26
2075 2213 3.695830 TTTCTGTTTCCGGTCTGCTAT 57.304 42.857 0.00 0.00 0.00 2.97
2081 2219 5.048991 TCAAGCTTATTTTCTGTTTCCGGTC 60.049 40.000 0.00 0.00 0.00 4.79
2122 2260 0.538584 TGTTGCTGAGATCCATCGCT 59.461 50.000 0.00 0.00 0.00 4.93
2127 2265 2.906389 ACTACCTTGTTGCTGAGATCCA 59.094 45.455 0.00 0.00 0.00 3.41
2196 2334 3.149196 GGAACAAGACCAGCAGATTCAA 58.851 45.455 0.00 0.00 0.00 2.69
2210 2348 4.999950 AGTGTGCTCTGAATTAGGAACAAG 59.000 41.667 0.00 0.00 0.00 3.16
2256 2394 6.944234 ATGCATATGCCAATATCTCATCAG 57.056 37.500 24.54 0.00 41.18 2.90
2296 2457 9.418045 GAAGTATATAGCTGAATCAGAGGAAAC 57.582 37.037 15.38 4.44 32.44 2.78
2330 2491 1.769098 CGCGTCATCCCAATCTGCAG 61.769 60.000 7.63 7.63 0.00 4.41
2357 2518 3.733443 AATCACAAAGTGGTTTGCTCC 57.267 42.857 0.00 0.00 46.13 4.70
2364 2525 6.152661 TGAAGTTTGAGAAATCACAAAGTGGT 59.847 34.615 12.37 1.41 39.09 4.16
2568 2729 0.762842 TGGTACACTCAGGTGCCACT 60.763 55.000 0.00 0.00 46.64 4.00
2640 2801 0.031585 CGGTGAAGTCGTGGAACAGA 59.968 55.000 0.00 0.00 41.80 3.41
2733 2894 4.149598 GGTACTTCCTTGTCCACCAAATT 58.850 43.478 0.00 0.00 31.20 1.82
2793 2954 7.040548 TGCACATCAGTATCTTTGTTGAAATCA 60.041 33.333 0.00 0.00 0.00 2.57
3168 3329 2.594303 CAGTTTGTGAGCCCGGCA 60.594 61.111 13.15 0.00 0.00 5.69
3189 3350 4.972591 GCATTGTGTGGCAGGAAC 57.027 55.556 0.00 0.00 0.00 3.62
3560 3721 2.618709 AGAAGAACGGTGAGCCAAAAAG 59.381 45.455 0.00 0.00 34.09 2.27
3567 3731 2.230266 AGAGAAGAGAAGAACGGTGAGC 59.770 50.000 0.00 0.00 0.00 4.26
3568 3732 4.513198 AAGAGAAGAGAAGAACGGTGAG 57.487 45.455 0.00 0.00 0.00 3.51
3648 3812 9.254133 CCATGTGTACAATTCTAGACAGATAAG 57.746 37.037 0.00 0.00 0.00 1.73
3665 3829 4.067896 CCCAGCTTCATATCCATGTGTAC 58.932 47.826 0.00 0.00 33.57 2.90
3666 3830 3.973305 TCCCAGCTTCATATCCATGTGTA 59.027 43.478 0.00 0.00 33.57 2.90
3667 3831 2.779430 TCCCAGCTTCATATCCATGTGT 59.221 45.455 0.00 0.00 33.57 3.72
3668 3832 3.497103 TCCCAGCTTCATATCCATGTG 57.503 47.619 0.00 0.00 33.57 3.21
3768 3932 3.006940 CAATACGGCAACAGGTGTACAT 58.993 45.455 0.00 0.00 0.00 2.29
3812 3976 0.459237 CTGACCTGATCACCACGCTC 60.459 60.000 0.00 0.00 32.37 5.03
3847 4011 2.579201 CCGGTGTCAGTAGGCCTG 59.421 66.667 17.99 0.00 42.97 4.85
3864 4028 5.531287 CACCTAGTAAATTCCTATTGGTGCC 59.469 44.000 0.00 0.00 36.48 5.01
3899 4063 3.126514 GGATGAATCACACAGCACAGAAG 59.873 47.826 0.00 0.00 0.00 2.85
3963 4128 3.258622 ACTTCTAGCACCTGACACCTAAC 59.741 47.826 0.00 0.00 0.00 2.34
3993 4158 4.808414 AAATAAAAGAAAGAGGCCTGGC 57.192 40.909 12.00 11.05 0.00 4.85
4037 4202 1.407258 CTGAAAAGGTCACCCGCAAAA 59.593 47.619 0.00 0.00 35.12 2.44
4038 4203 1.028905 CTGAAAAGGTCACCCGCAAA 58.971 50.000 0.00 0.00 35.12 3.68
4039 4204 0.106918 ACTGAAAAGGTCACCCGCAA 60.107 50.000 0.00 0.00 35.12 4.85
4040 4205 0.106918 AACTGAAAAGGTCACCCGCA 60.107 50.000 0.00 0.00 35.12 5.69
4041 4206 1.029681 AAACTGAAAAGGTCACCCGC 58.970 50.000 0.00 0.00 35.12 6.13
4042 4207 3.443976 CAAAAACTGAAAAGGTCACCCG 58.556 45.455 0.00 0.00 35.12 5.28
4043 4208 3.118775 AGCAAAAACTGAAAAGGTCACCC 60.119 43.478 0.00 0.00 31.13 4.61
4044 4209 3.865164 CAGCAAAAACTGAAAAGGTCACC 59.135 43.478 0.00 0.00 40.25 4.02
4045 4210 3.865164 CCAGCAAAAACTGAAAAGGTCAC 59.135 43.478 0.00 0.00 40.25 3.67
4046 4211 3.513515 ACCAGCAAAAACTGAAAAGGTCA 59.486 39.130 0.00 0.00 40.25 4.02
4047 4212 3.865164 CACCAGCAAAAACTGAAAAGGTC 59.135 43.478 0.00 0.00 40.25 3.85
4048 4213 3.513515 TCACCAGCAAAAACTGAAAAGGT 59.486 39.130 0.00 0.00 40.25 3.50
4049 4214 4.114794 CTCACCAGCAAAAACTGAAAAGG 58.885 43.478 0.00 0.00 40.25 3.11
4185 4429 1.127343 GGAGATTGTGAGGAGGGAGG 58.873 60.000 0.00 0.00 0.00 4.30
4196 4440 1.738099 GCTCACGTGCGGAGATTGT 60.738 57.895 11.67 0.00 34.24 2.71
4198 4442 1.738099 GTGCTCACGTGCGGAGATT 60.738 57.895 11.67 0.00 34.24 2.40
4254 4499 0.836400 GGACTTCACTCCCCACCTCA 60.836 60.000 0.00 0.00 0.00 3.86
4256 4501 0.838122 CAGGACTTCACTCCCCACCT 60.838 60.000 0.00 0.00 0.00 4.00
4282 4527 1.240256 CTACCTACTAGCTGGAGCCG 58.760 60.000 3.17 0.00 43.38 5.52
4319 4607 0.243907 GCTCAAGTGTCGCCTCTACA 59.756 55.000 0.00 0.00 0.00 2.74
4321 4609 1.506718 CGCTCAAGTGTCGCCTCTA 59.493 57.895 0.00 0.00 0.00 2.43
4352 4640 3.006537 CCAGAAGACCAACTCGAAGGTAA 59.993 47.826 4.06 0.00 38.50 2.85
4364 4652 3.251484 AGGATCAAAGACCAGAAGACCA 58.749 45.455 0.00 0.00 0.00 4.02
4409 4697 8.651589 ATGTCGGAACTCCATCTAATCTAATA 57.348 34.615 0.00 0.00 35.14 0.98
4423 4711 3.385577 GCAGGAATCTATGTCGGAACTC 58.614 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.