Multiple sequence alignment - TraesCS6B01G385800

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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 TraesCS6B01G385800 chr6B 100.000 2728 0 0 1 2728 660454583 660457310 0.000000e+00 5038.0
1 TraesCS6B01G385800 chr6D 92.771 2158 108 17 586 2728 436798170 436800294 0.000000e+00 3077.0
2 TraesCS6B01G385800 chr6D 86.506 541 69 3 1 539 436797634 436798172 2.340000e-165 592.0
3 TraesCS6B01G385800 chr6A 90.959 1283 59 14 601 1857 585056423 585057674 0.000000e+00 1674.0
4 TraesCS6B01G385800 chr6A 90.590 882 62 7 1858 2728 585057745 585058616 0.000000e+00 1149.0
5 TraesCS6B01G385800 chr6A 96.875 32 1 0 545 576 484490 484459 1.000000e-03 54.7
6 TraesCS6B01G385800 chr3D 83.521 534 77 8 1 524 409031661 409031129 3.160000e-134 488.0
7 TraesCS6B01G385800 chr4B 83.752 517 75 9 6 517 472866548 472867060 5.280000e-132 481.0
8 TraesCS6B01G385800 chr5D 82.115 520 87 6 1 516 425038709 425038192 8.970000e-120 440.0
9 TraesCS6B01G385800 chr1B 81.992 522 90 4 3 520 644329243 644328722 8.970000e-120 440.0
10 TraesCS6B01G385800 chr7D 83.656 465 69 7 1 460 512209785 512209323 5.400000e-117 431.0
11 TraesCS6B01G385800 chr5B 82.376 505 80 9 3 501 449199352 449198851 5.400000e-117 431.0
12 TraesCS6B01G385800 chr4D 81.461 534 86 10 4 531 69131949 69131423 2.510000e-115 425.0
13 TraesCS6B01G385800 chr4A 81.034 522 93 6 3 520 666155823 666155304 7.030000e-111 411.0
14 TraesCS6B01G385800 chr1A 88.496 113 12 1 802 914 460970146 460970035 4.740000e-28 135.0
15 TraesCS6B01G385800 chr1D 89.247 93 9 1 802 894 361353194 361353103 6.170000e-22 115.0
16 TraesCS6B01G385800 chr1D 100.000 30 0 0 543 572 246043095 246043066 3.790000e-04 56.5
17 TraesCS6B01G385800 chr7B 92.857 42 1 2 537 577 94407292 94407332 2.930000e-05 60.2
18 TraesCS6B01G385800 chr7B 90.476 42 4 0 535 576 195210320 195210279 3.790000e-04 56.5
19 TraesCS6B01G385800 chr2B 92.857 42 2 1 533 573 41664274 41664315 2.930000e-05 60.2
20 TraesCS6B01G385800 chr3A 92.500 40 3 0 537 576 53216879 53216840 1.060000e-04 58.4
21 TraesCS6B01G385800 chr5A 100.000 30 0 0 543 572 702862638 702862609 3.790000e-04 56.5
22 TraesCS6B01G385800 chr2D 100.000 30 0 0 543 572 86071343 86071314 3.790000e-04 56.5
23 TraesCS6B01G385800 chr3B 100.000 29 0 0 545 573 790348371 790348343 1.000000e-03 54.7


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 TraesCS6B01G385800 chr6B 660454583 660457310 2727 False 5038.0 5038 100.0000 1 2728 1 chr6B.!!$F1 2727
1 TraesCS6B01G385800 chr6D 436797634 436800294 2660 False 1834.5 3077 89.6385 1 2728 2 chr6D.!!$F1 2727
2 TraesCS6B01G385800 chr6A 585056423 585058616 2193 False 1411.5 1674 90.7745 601 2728 2 chr6A.!!$F1 2127
3 TraesCS6B01G385800 chr3D 409031129 409031661 532 True 488.0 488 83.5210 1 524 1 chr3D.!!$R1 523
4 TraesCS6B01G385800 chr4B 472866548 472867060 512 False 481.0 481 83.7520 6 517 1 chr4B.!!$F1 511
5 TraesCS6B01G385800 chr5D 425038192 425038709 517 True 440.0 440 82.1150 1 516 1 chr5D.!!$R1 515
6 TraesCS6B01G385800 chr1B 644328722 644329243 521 True 440.0 440 81.9920 3 520 1 chr1B.!!$R1 517
7 TraesCS6B01G385800 chr5B 449198851 449199352 501 True 431.0 431 82.3760 3 501 1 chr5B.!!$R1 498
8 TraesCS6B01G385800 chr4D 69131423 69131949 526 True 425.0 425 81.4610 4 531 1 chr4D.!!$R1 527
9 TraesCS6B01G385800 chr4A 666155304 666155823 519 True 411.0 411 81.0340 3 520 1 chr4A.!!$R1 517

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
583 594 0.109723 TCAACTTTGAACGGGAGGGG 59.89 55.0 0.0 0.0 33.55 4.79 F
584 595 0.109723 CAACTTTGAACGGGAGGGGA 59.89 55.0 0.0 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1653 0.179089 CATCGACCTGAGCCTTGAGG 60.179 60.0 0.00 0.0 38.53 3.86 R
2252 2370 0.392863 TGTTATGCTCATGCGCTGGT 60.393 50.0 9.73 0.0 43.34 4.00 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
36 37 3.073678 CGCAATGGATTTCCGATGGATA 58.926 45.455 0.00 0.00 39.43 2.59
114 115 1.456705 GGCCATCTCCTCCTCGAGT 60.457 63.158 12.31 0.00 0.00 4.18
119 120 1.990160 ATCTCCTCCTCGAGTCCGCT 61.990 60.000 12.31 0.00 35.37 5.52
192 194 3.083349 CCATGCCGGAGAGGACCA 61.083 66.667 5.05 0.00 45.00 4.02
203 205 0.178891 AGAGGACCAGAAGGAGCCAA 60.179 55.000 0.00 0.00 38.69 4.52
241 243 3.695825 GGGGAGTGGAGGGGAGGA 61.696 72.222 0.00 0.00 0.00 3.71
247 254 1.687493 GTGGAGGGGAGGAGAGTGG 60.687 68.421 0.00 0.00 0.00 4.00
273 280 2.678190 GCTAGAGTTTGGTCTGGCGAAT 60.678 50.000 0.00 0.00 40.69 3.34
300 308 3.312697 GGGAGAATTTTATGTGAGGTCGC 59.687 47.826 0.00 0.00 0.00 5.19
305 313 0.604073 TTTATGTGAGGTCGCGTGGA 59.396 50.000 5.77 0.00 0.00 4.02
379 388 3.054434 CCCCATATCCGCCTCATATTTGA 60.054 47.826 0.00 0.00 0.00 2.69
380 389 4.567537 CCCCATATCCGCCTCATATTTGAA 60.568 45.833 0.00 0.00 0.00 2.69
406 416 0.252696 ATGAGGGGTACTGGTCAGCA 60.253 55.000 0.00 0.00 0.00 4.41
471 482 1.152631 TGACCGGACAGTGACCAGA 60.153 57.895 9.46 0.00 0.00 3.86
517 528 3.434596 GGATTTAAAGGGTCCGGCTGTAT 60.435 47.826 0.00 0.00 0.00 2.29
548 559 6.851222 CTCTAAAGCATGTATTTCATCCGT 57.149 37.500 0.00 0.00 34.09 4.69
550 561 7.624360 TCTAAAGCATGTATTTCATCCGTTT 57.376 32.000 0.00 0.00 34.09 3.60
551 562 7.693952 TCTAAAGCATGTATTTCATCCGTTTC 58.306 34.615 0.00 0.00 34.09 2.78
552 563 5.895636 AAGCATGTATTTCATCCGTTTCA 57.104 34.783 0.00 0.00 34.09 2.69
553 564 5.895636 AGCATGTATTTCATCCGTTTCAA 57.104 34.783 0.00 0.00 34.09 2.69
554 565 6.266168 AGCATGTATTTCATCCGTTTCAAA 57.734 33.333 0.00 0.00 34.09 2.69
555 566 6.686630 AGCATGTATTTCATCCGTTTCAAAA 58.313 32.000 0.00 0.00 34.09 2.44
556 567 7.322664 AGCATGTATTTCATCCGTTTCAAAAT 58.677 30.769 0.00 0.00 34.09 1.82
557 568 8.465999 AGCATGTATTTCATCCGTTTCAAAATA 58.534 29.630 0.00 0.00 34.09 1.40
558 569 9.081997 GCATGTATTTCATCCGTTTCAAAATAA 57.918 29.630 0.00 0.00 34.09 1.40
564 575 9.927668 ATTTCATCCGTTTCAAAATAAATGACT 57.072 25.926 0.00 0.00 0.00 3.41
565 576 8.964420 TTCATCCGTTTCAAAATAAATGACTC 57.036 30.769 0.00 0.00 0.00 3.36
566 577 8.105097 TCATCCGTTTCAAAATAAATGACTCA 57.895 30.769 0.00 0.00 0.00 3.41
567 578 8.572185 TCATCCGTTTCAAAATAAATGACTCAA 58.428 29.630 0.00 0.00 0.00 3.02
568 579 8.638565 CATCCGTTTCAAAATAAATGACTCAAC 58.361 33.333 0.00 0.00 0.00 3.18
569 580 7.936584 TCCGTTTCAAAATAAATGACTCAACT 58.063 30.769 0.00 0.00 0.00 3.16
570 581 8.410141 TCCGTTTCAAAATAAATGACTCAACTT 58.590 29.630 0.00 0.00 0.00 2.66
571 582 9.030301 CCGTTTCAAAATAAATGACTCAACTTT 57.970 29.630 0.00 0.00 0.00 2.66
572 583 9.833894 CGTTTCAAAATAAATGACTCAACTTTG 57.166 29.630 0.00 0.00 0.00 2.77
576 587 9.232082 TCAAAATAAATGACTCAACTTTGAACG 57.768 29.630 0.00 0.00 36.64 3.95
577 588 8.479280 CAAAATAAATGACTCAACTTTGAACGG 58.521 33.333 0.00 0.00 36.64 4.44
578 589 4.568152 AAATGACTCAACTTTGAACGGG 57.432 40.909 0.00 0.00 36.64 5.28
579 590 2.992124 TGACTCAACTTTGAACGGGA 57.008 45.000 0.00 0.00 36.64 5.14
580 591 2.833794 TGACTCAACTTTGAACGGGAG 58.166 47.619 0.00 0.00 36.64 4.30
581 592 2.143925 GACTCAACTTTGAACGGGAGG 58.856 52.381 0.00 0.00 36.64 4.30
582 593 1.202770 ACTCAACTTTGAACGGGAGGG 60.203 52.381 0.00 0.00 36.64 4.30
583 594 0.109723 TCAACTTTGAACGGGAGGGG 59.890 55.000 0.00 0.00 33.55 4.79
584 595 0.109723 CAACTTTGAACGGGAGGGGA 59.890 55.000 0.00 0.00 0.00 4.81
585 596 0.400594 AACTTTGAACGGGAGGGGAG 59.599 55.000 0.00 0.00 0.00 4.30
586 597 0.767060 ACTTTGAACGGGAGGGGAGT 60.767 55.000 0.00 0.00 0.00 3.85
587 598 1.272807 CTTTGAACGGGAGGGGAGTA 58.727 55.000 0.00 0.00 0.00 2.59
588 599 0.978907 TTTGAACGGGAGGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
589 600 0.115745 TTGAACGGGAGGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
590 601 1.002069 TGAACGGGAGGGGAGTACTA 58.998 55.000 0.00 0.00 0.00 1.82
591 602 1.341383 TGAACGGGAGGGGAGTACTAC 60.341 57.143 0.00 0.00 0.00 2.73
592 603 1.006020 AACGGGAGGGGAGTACTACT 58.994 55.000 4.77 0.00 0.00 2.57
593 604 1.006020 ACGGGAGGGGAGTACTACTT 58.994 55.000 4.77 0.00 0.00 2.24
594 605 2.208872 ACGGGAGGGGAGTACTACTTA 58.791 52.381 4.77 0.00 0.00 2.24
595 606 2.582636 ACGGGAGGGGAGTACTACTTAA 59.417 50.000 4.77 0.00 0.00 1.85
596 607 2.954989 CGGGAGGGGAGTACTACTTAAC 59.045 54.545 4.77 0.00 0.00 2.01
597 608 2.954989 GGGAGGGGAGTACTACTTAACG 59.045 54.545 4.77 0.00 0.00 3.18
598 609 3.625853 GGAGGGGAGTACTACTTAACGT 58.374 50.000 4.77 0.00 0.00 3.99
634 645 3.827898 CTGGTCCGCTCCGAGTCC 61.828 72.222 0.00 0.00 0.00 3.85
755 789 3.167945 GTCGTAACACGTCGCCGG 61.168 66.667 0.00 0.00 43.14 6.13
796 830 2.890474 GCGCCGAATGTGGACGAT 60.890 61.111 0.00 0.00 32.62 3.73
882 917 1.901159 CAACCAATCAAAGCCCCATCA 59.099 47.619 0.00 0.00 0.00 3.07
894 929 0.609957 CCCCATCACACTGCACACAT 60.610 55.000 0.00 0.00 0.00 3.21
943 980 2.225242 TGCATATCTCCTCTCCCTCTCC 60.225 54.545 0.00 0.00 0.00 3.71
1022 1059 0.995728 TATATGTGTGTGCGTGCGTG 59.004 50.000 0.00 0.00 0.00 5.34
1081 1118 1.065401 CATGACAAAAGCACCACACGT 59.935 47.619 0.00 0.00 0.00 4.49
1168 1205 2.096614 CGGTTTGTTGGTTGTAGCTACG 60.097 50.000 18.74 0.00 0.00 3.51
1169 1206 2.874086 GGTTTGTTGGTTGTAGCTACGT 59.126 45.455 18.74 0.00 0.00 3.57
1170 1207 4.057432 GGTTTGTTGGTTGTAGCTACGTA 58.943 43.478 18.74 6.89 0.00 3.57
1171 1208 4.084380 GGTTTGTTGGTTGTAGCTACGTAC 60.084 45.833 18.74 17.49 0.00 3.67
1259 1296 4.937193 CTCAAGAGCCTGCTCCTG 57.063 61.111 15.23 12.89 43.70 3.86
1262 1299 2.123632 AAGAGCCTGCTCCTGGGA 59.876 61.111 15.23 0.00 43.70 4.37
1544 1581 0.818040 GGACGCAGGTGTTGAAAGGT 60.818 55.000 0.00 0.00 0.00 3.50
1616 1653 2.356553 TTGGACTACGCCGTGTGC 60.357 61.111 0.00 2.06 0.00 4.57
1726 1763 4.184629 GAGTTCGTGGAGATAATGCTTGT 58.815 43.478 0.00 0.00 0.00 3.16
1727 1764 5.339008 AGTTCGTGGAGATAATGCTTGTA 57.661 39.130 0.00 0.00 0.00 2.41
1728 1765 5.918608 AGTTCGTGGAGATAATGCTTGTAT 58.081 37.500 0.00 0.00 0.00 2.29
1729 1766 6.349300 AGTTCGTGGAGATAATGCTTGTATT 58.651 36.000 0.00 0.00 0.00 1.89
1730 1767 7.497595 AGTTCGTGGAGATAATGCTTGTATTA 58.502 34.615 0.00 0.00 0.00 0.98
1786 1823 0.949397 CAACTCACAGCATGCAGTGT 59.051 50.000 33.64 21.95 42.53 3.55
1807 1844 0.683973 AGGGTCAGCGATCATGGATC 59.316 55.000 0.00 0.00 35.88 3.36
1997 2111 3.409026 AGAGTCGACCAAGATTTTGCT 57.591 42.857 13.01 0.00 32.79 3.91
2023 2137 6.275494 TGTTCAAGTCGATGGTACTAATCA 57.725 37.500 8.98 0.00 0.00 2.57
2025 2139 7.327975 TGTTCAAGTCGATGGTACTAATCATT 58.672 34.615 8.98 0.00 0.00 2.57
2028 2142 6.761242 TCAAGTCGATGGTACTAATCATTTGG 59.239 38.462 8.98 0.00 0.00 3.28
2093 2207 2.780010 ACTTGCATCTAATGGCTAGGGT 59.220 45.455 0.00 0.00 37.23 4.34
2100 2214 0.742505 TAATGGCTAGGGTGTCGACG 59.257 55.000 11.62 0.00 0.00 5.12
2105 2219 1.505353 CTAGGGTGTCGACGTGGAC 59.495 63.158 22.17 22.17 37.45 4.02
2130 2245 9.178758 ACATAAGAAAATCTTAGCCAACTTAGG 57.821 33.333 6.07 0.00 41.70 2.69
2232 2350 2.997980 TGAAGCAACTTCAGAACCACA 58.002 42.857 5.94 0.00 44.27 4.17
2245 2363 3.253188 CAGAACCACATACACAAGTTGGG 59.747 47.826 2.79 2.79 0.00 4.12
2250 2368 0.887933 CATACACAAGTTGGGGTGGC 59.112 55.000 10.50 0.00 39.31 5.01
2252 2370 1.436326 TACACAAGTTGGGGTGGCTA 58.564 50.000 10.50 0.00 39.31 3.93
2322 2440 2.105006 AGTCTACGTCTCGGCTAACA 57.895 50.000 0.00 0.00 0.00 2.41
2323 2441 2.641305 AGTCTACGTCTCGGCTAACAT 58.359 47.619 0.00 0.00 0.00 2.71
2324 2442 2.355132 AGTCTACGTCTCGGCTAACATG 59.645 50.000 0.00 0.00 0.00 3.21
2518 2636 7.783090 AACTATTGCTCTGTATGATTGACAG 57.217 36.000 0.00 0.00 44.75 3.51
2538 2656 3.286751 GTGTGGGTGCACATGCGT 61.287 61.111 20.43 0.00 45.83 5.24
2567 2685 6.374333 GGCTCACATTACTTTTGATTAGACCA 59.626 38.462 0.00 0.00 0.00 4.02
2669 2787 2.118403 TCCAAGAGGGGACAAAGAGT 57.882 50.000 0.00 0.00 37.22 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.143594 GACGGTTGCACTCGGACTCT 62.144 60.000 11.74 0.00 0.00 3.24
93 94 0.482887 TCGAGGAGGAGATGGCCATA 59.517 55.000 20.84 0.00 0.00 2.74
133 134 2.248248 TCACCTCCAGATTCGTCAACT 58.752 47.619 0.00 0.00 0.00 3.16
136 138 1.550524 CCTTCACCTCCAGATTCGTCA 59.449 52.381 0.00 0.00 0.00 4.35
192 194 1.343069 ACTCGTCTTTGGCTCCTTCT 58.657 50.000 0.00 0.00 0.00 2.85
203 205 1.597027 CGCCACCCAAACTCGTCTT 60.597 57.895 0.00 0.00 0.00 3.01
241 243 2.564947 CAAACTCTAGCCACTCCACTCT 59.435 50.000 0.00 0.00 0.00 3.24
247 254 2.354203 CCAGACCAAACTCTAGCCACTC 60.354 54.545 0.00 0.00 0.00 3.51
273 280 6.493166 ACCTCACATAAAATTCTCCCATTCA 58.507 36.000 0.00 0.00 0.00 2.57
356 364 2.270434 ATATGAGGCGGATATGGGGT 57.730 50.000 0.00 0.00 0.00 4.95
379 388 3.311402 ACCAGTACCCCTCATATCCAGTT 60.311 47.826 0.00 0.00 0.00 3.16
380 389 2.250273 ACCAGTACCCCTCATATCCAGT 59.750 50.000 0.00 0.00 0.00 4.00
471 482 2.134287 ATATGTCCGGGCGAGCTGT 61.134 57.895 0.00 0.00 0.00 4.40
486 497 5.866207 GGACCCTTTAAATCCGTCTCATAT 58.134 41.667 8.49 0.00 0.00 1.78
539 550 9.405587 GAGTCATTTATTTTGAAACGGATGAAA 57.594 29.630 0.00 0.00 0.00 2.69
541 552 8.105097 TGAGTCATTTATTTTGAAACGGATGA 57.895 30.769 0.00 0.00 0.00 2.92
543 554 8.576442 AGTTGAGTCATTTATTTTGAAACGGAT 58.424 29.630 0.00 0.00 0.00 4.18
545 556 8.574196 AAGTTGAGTCATTTATTTTGAAACGG 57.426 30.769 0.00 0.00 0.00 4.44
546 557 9.833894 CAAAGTTGAGTCATTTATTTTGAAACG 57.166 29.630 5.72 0.00 0.00 3.60
550 561 9.232082 CGTTCAAAGTTGAGTCATTTATTTTGA 57.768 29.630 8.92 8.92 38.61 2.69
551 562 8.479280 CCGTTCAAAGTTGAGTCATTTATTTTG 58.521 33.333 0.00 0.00 38.61 2.44
552 563 7.651704 CCCGTTCAAAGTTGAGTCATTTATTTT 59.348 33.333 0.00 0.00 38.61 1.82
553 564 7.013846 TCCCGTTCAAAGTTGAGTCATTTATTT 59.986 33.333 0.00 0.00 38.61 1.40
554 565 6.488683 TCCCGTTCAAAGTTGAGTCATTTATT 59.511 34.615 0.00 0.00 38.61 1.40
555 566 6.001460 TCCCGTTCAAAGTTGAGTCATTTAT 58.999 36.000 0.00 0.00 38.61 1.40
556 567 5.369833 TCCCGTTCAAAGTTGAGTCATTTA 58.630 37.500 0.00 0.00 38.61 1.40
557 568 4.204012 TCCCGTTCAAAGTTGAGTCATTT 58.796 39.130 0.00 0.00 38.61 2.32
558 569 3.815401 CTCCCGTTCAAAGTTGAGTCATT 59.185 43.478 0.00 0.00 38.61 2.57
559 570 3.403038 CTCCCGTTCAAAGTTGAGTCAT 58.597 45.455 0.00 0.00 38.61 3.06
560 571 2.484770 CCTCCCGTTCAAAGTTGAGTCA 60.485 50.000 0.00 0.00 38.61 3.41
561 572 2.143925 CCTCCCGTTCAAAGTTGAGTC 58.856 52.381 0.00 0.00 38.61 3.36
562 573 1.202770 CCCTCCCGTTCAAAGTTGAGT 60.203 52.381 0.00 0.00 38.61 3.41
563 574 1.523758 CCCTCCCGTTCAAAGTTGAG 58.476 55.000 0.00 0.00 38.61 3.02
564 575 0.109723 CCCCTCCCGTTCAAAGTTGA 59.890 55.000 0.00 0.00 34.92 3.18
565 576 0.109723 TCCCCTCCCGTTCAAAGTTG 59.890 55.000 0.00 0.00 0.00 3.16
566 577 0.400594 CTCCCCTCCCGTTCAAAGTT 59.599 55.000 0.00 0.00 0.00 2.66
567 578 0.767060 ACTCCCCTCCCGTTCAAAGT 60.767 55.000 0.00 0.00 0.00 2.66
568 579 1.066358 GTACTCCCCTCCCGTTCAAAG 60.066 57.143 0.00 0.00 0.00 2.77
569 580 0.978907 GTACTCCCCTCCCGTTCAAA 59.021 55.000 0.00 0.00 0.00 2.69
570 581 0.115745 AGTACTCCCCTCCCGTTCAA 59.884 55.000 0.00 0.00 0.00 2.69
571 582 1.002069 TAGTACTCCCCTCCCGTTCA 58.998 55.000 0.00 0.00 0.00 3.18
572 583 1.064091 AGTAGTACTCCCCTCCCGTTC 60.064 57.143 0.00 0.00 0.00 3.95
573 584 1.006020 AGTAGTACTCCCCTCCCGTT 58.994 55.000 0.00 0.00 0.00 4.44
574 585 1.006020 AAGTAGTACTCCCCTCCCGT 58.994 55.000 2.58 0.00 0.00 5.28
575 586 2.954989 GTTAAGTAGTACTCCCCTCCCG 59.045 54.545 2.58 0.00 0.00 5.14
576 587 2.954989 CGTTAAGTAGTACTCCCCTCCC 59.045 54.545 2.58 0.00 0.00 4.30
577 588 3.625853 ACGTTAAGTAGTACTCCCCTCC 58.374 50.000 2.58 0.00 0.00 4.30
578 589 3.311048 CGACGTTAAGTAGTACTCCCCTC 59.689 52.174 2.58 0.00 0.00 4.30
579 590 3.274288 CGACGTTAAGTAGTACTCCCCT 58.726 50.000 2.58 0.00 0.00 4.79
580 591 3.010420 ACGACGTTAAGTAGTACTCCCC 58.990 50.000 2.58 0.00 36.92 4.81
586 597 2.350498 GGCCGTACGACGTTAAGTAGTA 59.650 50.000 18.76 0.00 40.58 1.82
587 598 1.130561 GGCCGTACGACGTTAAGTAGT 59.869 52.381 18.76 0.00 40.58 2.73
588 599 1.531883 GGGCCGTACGACGTTAAGTAG 60.532 57.143 18.76 0.00 40.58 2.57
589 600 0.450184 GGGCCGTACGACGTTAAGTA 59.550 55.000 18.76 0.00 40.58 2.24
590 601 1.212751 GGGCCGTACGACGTTAAGT 59.787 57.895 18.76 0.00 40.58 2.24
591 602 1.517039 GGGGCCGTACGACGTTAAG 60.517 63.158 18.76 0.00 40.58 1.85
592 603 2.571231 GGGGCCGTACGACGTTAA 59.429 61.111 18.76 0.00 40.58 2.01
593 604 3.809775 CGGGGCCGTACGACGTTA 61.810 66.667 18.76 0.00 40.58 3.18
764 798 1.866496 GCGCACGTACGTAGGAGTG 60.866 63.158 22.34 19.43 37.63 3.51
765 799 2.482374 GCGCACGTACGTAGGAGT 59.518 61.111 22.34 7.31 34.88 3.85
769 803 1.584483 ATTCGGCGCACGTACGTAG 60.584 57.895 22.34 18.52 44.69 3.51
770 804 1.868692 CATTCGGCGCACGTACGTA 60.869 57.895 22.34 3.59 44.69 3.57
894 929 3.003171 GTGTGTTCATGTGTGTGTGCATA 59.997 43.478 0.00 0.00 0.00 3.14
943 980 2.978010 GTGCGTGTGAGTTGGGGG 60.978 66.667 0.00 0.00 0.00 5.40
1043 1080 0.100682 TGCGGAGTACAAGCTCGATC 59.899 55.000 0.00 0.00 36.41 3.69
1081 1118 1.335233 CGTGAACTGTAGTGTGCCGTA 60.335 52.381 0.00 0.00 0.00 4.02
1168 1205 1.612463 AGACAGACGACACCAAGGTAC 59.388 52.381 0.00 0.00 0.00 3.34
1169 1206 1.991121 AGACAGACGACACCAAGGTA 58.009 50.000 0.00 0.00 0.00 3.08
1170 1207 1.887198 CTAGACAGACGACACCAAGGT 59.113 52.381 0.00 0.00 0.00 3.50
1171 1208 1.402984 GCTAGACAGACGACACCAAGG 60.403 57.143 0.00 0.00 0.00 3.61
1218 1255 2.034879 CCCGCTTGAACTGCATCGT 61.035 57.895 0.00 0.00 0.00 3.73
1304 1341 3.438017 GATGGCGCGCTTCCTCTCT 62.438 63.158 32.29 6.51 0.00 3.10
1616 1653 0.179089 CATCGACCTGAGCCTTGAGG 60.179 60.000 0.00 0.00 38.53 3.86
1628 1665 2.286294 CAGAAGCTGCATTACATCGACC 59.714 50.000 1.02 0.00 0.00 4.79
1631 1668 2.031314 CACCAGAAGCTGCATTACATCG 59.969 50.000 1.02 0.00 0.00 3.84
1728 1765 8.648693 GGTAGAGAAGGCTTTGGTATCTTATAA 58.351 37.037 0.00 0.00 0.00 0.98
1729 1766 8.011290 AGGTAGAGAAGGCTTTGGTATCTTATA 58.989 37.037 0.00 0.00 0.00 0.98
1730 1767 6.847036 AGGTAGAGAAGGCTTTGGTATCTTAT 59.153 38.462 0.00 0.00 0.00 1.73
1786 1823 0.687427 TCCATGATCGCTGACCCTCA 60.687 55.000 0.00 0.00 0.00 3.86
1895 2002 6.255670 GCAACAGGTCCTTTAACTTCTTTTTG 59.744 38.462 0.00 0.00 0.00 2.44
1937 2051 5.048782 TCCACATTTTGACGGAGAATTTCAG 60.049 40.000 0.00 0.00 0.00 3.02
1997 2111 8.471609 TGATTAGTACCATCGACTTGAACATTA 58.528 33.333 0.00 0.00 0.00 1.90
2023 2137 6.091076 TGGGGAGAATCAAGATTACCAAAT 57.909 37.500 15.37 0.00 36.25 2.32
2025 2139 5.732331 ATGGGGAGAATCAAGATTACCAA 57.268 39.130 15.37 5.86 36.25 3.67
2028 2142 6.830838 ACAAGAATGGGGAGAATCAAGATTAC 59.169 38.462 0.00 0.00 36.25 1.89
2093 2207 3.646611 TTTCTTATGTCCACGTCGACA 57.353 42.857 18.33 18.33 46.36 4.35
2100 2214 7.121315 AGTTGGCTAAGATTTTCTTATGTCCAC 59.879 37.037 10.17 4.76 38.20 4.02
2105 2219 9.178758 ACCTAAGTTGGCTAAGATTTTCTTATG 57.821 33.333 0.00 0.00 38.20 1.90
2130 2245 7.809665 TGTTATAGCTTTCGGTTTTCCTAAAC 58.190 34.615 0.00 0.00 42.34 2.01
2216 2334 3.563808 TGTGTATGTGGTTCTGAAGTTGC 59.436 43.478 0.00 0.00 0.00 4.17
2232 2350 0.777446 AGCCACCCCAACTTGTGTAT 59.223 50.000 0.00 0.00 0.00 2.29
2245 2363 3.204827 CATGCGCTGGTAGCCACC 61.205 66.667 9.73 0.00 46.00 4.61
2250 2368 1.528586 GTTATGCTCATGCGCTGGTAG 59.471 52.381 9.73 1.87 43.34 3.18
2252 2370 0.392863 TGTTATGCTCATGCGCTGGT 60.393 50.000 9.73 0.00 43.34 4.00
2295 2413 3.365767 GCCGAGACGTAGACTTTGTACTT 60.366 47.826 0.00 0.00 29.49 2.24
2516 2634 2.516695 TGTGCACCCACACTGCTG 60.517 61.111 15.69 0.00 46.51 4.41
2538 2656 8.318412 TCTAATCAAAAGTAATGTGAGCCTACA 58.682 33.333 0.00 0.00 34.63 2.74
2648 2766 2.989571 ACTCTTTGTCCCCTCTTGGATT 59.010 45.455 0.00 0.00 36.63 3.01
2698 2816 4.199310 AGACTGGCGCATATTACAATTGT 58.801 39.130 16.68 16.68 0.00 2.71


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

AutoCloner maintained by Alex Coulton.