Multiple sequence alignment - TraesCS7B01G016600

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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 TraesCS7B01G016600 chr7B 100.000 3252 0 0 1 3252 14177064 14173813 0.000000e+00 6006.0
1 TraesCS7B01G016600 chr7B 95.451 1473 60 6 672 2139 14214775 14213305 0.000000e+00 2342.0
2 TraesCS7B01G016600 chr7B 95.391 933 23 4 2321 3252 14212817 14211904 0.000000e+00 1467.0
3 TraesCS7B01G016600 chr7B 90.052 191 18 1 2134 2323 14213234 14213044 2.510000e-61 246.0
4 TraesCS7B01G016600 chr7B 90.000 60 4 2 521 578 199313807 199313748 3.480000e-10 76.8
5 TraesCS7B01G016600 chr7B 81.579 76 12 2 517 590 28961837 28961762 9.740000e-06 62.1
6 TraesCS7B01G016600 chr7B 90.909 44 4 0 515 558 147268354 147268311 3.500000e-05 60.2
7 TraesCS7B01G016600 chr7D 92.008 976 64 4 1178 2139 71632596 71631621 0.000000e+00 1358.0
8 TraesCS7B01G016600 chr7D 92.357 942 59 7 2321 3252 71631077 71630139 0.000000e+00 1328.0
9 TraesCS7B01G016600 chr7D 90.307 423 28 7 728 1145 71633013 71632599 2.850000e-150 542.0
10 TraesCS7B01G016600 chr7D 92.147 191 14 1 2134 2323 71631550 71631360 5.350000e-68 268.0
11 TraesCS7B01G016600 chr5D 87.313 402 37 12 2370 2764 99528192 99528586 6.400000e-122 448.0
12 TraesCS7B01G016600 chrUn 100.000 188 0 0 1 188 229607319 229607132 6.680000e-92 348.0
13 TraesCS7B01G016600 chr3D 89.130 276 26 4 2491 2764 419377104 419377377 1.120000e-89 340.0
14 TraesCS7B01G016600 chr2D 85.965 114 13 3 478 590 109728340 109728229 5.700000e-23 119.0
15 TraesCS7B01G016600 chr2D 80.460 87 11 6 526 609 125316271 125316188 9.740000e-06 62.1
16 TraesCS7B01G016600 chr2D 80.682 88 10 7 478 562 644480666 644480749 9.740000e-06 62.1
17 TraesCS7B01G016600 chr7A 93.182 44 3 0 515 558 138734283 138734240 7.530000e-07 65.8
18 TraesCS7B01G016600 chr6A 89.796 49 5 0 530 578 454471652 454471604 2.710000e-06 63.9
19 TraesCS7B01G016600 chr2A 84.127 63 6 3 498 558 78327433 78327493 1.260000e-04 58.4


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 TraesCS7B01G016600 chr7B 14173813 14177064 3251 True 6006.000000 6006 100.000000 1 3252 1 chr7B.!!$R1 3251
1 TraesCS7B01G016600 chr7B 14211904 14214775 2871 True 1351.666667 2342 93.631333 672 3252 3 chr7B.!!$R5 2580
2 TraesCS7B01G016600 chr7D 71630139 71633013 2874 True 874.000000 1358 91.704750 728 3252 4 chr7D.!!$R1 2524

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
678 679 0.036388 AAATTTGAGCGAGGCGAGGA 60.036 50.0 0.0 0.0 0.0 3.71 F
679 680 0.179000 AATTTGAGCGAGGCGAGGAT 59.821 50.0 0.0 0.0 0.0 3.24 F
680 681 0.531532 ATTTGAGCGAGGCGAGGATG 60.532 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1690 0.825010 CCTTCACTTGCAAGCTGGGT 60.825 55.000 26.27 4.24 0.00 4.51 R
1938 1961 1.065709 GGCCGACAACCTAGGATCAAA 60.066 52.381 17.98 0.00 0.00 2.69 R
2319 2420 1.080638 TTTCAGGCCACCCCTATTGT 58.919 50.000 5.01 0.00 44.09 2.71 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
17 18 3.713650 CCCATGTCTGGACGACCT 58.286 61.111 5.33 0.00 46.37 3.85
18 19 1.219124 CCCATGTCTGGACGACCTG 59.781 63.158 5.33 4.88 46.37 4.00
19 20 1.544825 CCCATGTCTGGACGACCTGT 61.545 60.000 5.33 0.00 46.37 4.00
20 21 0.321671 CCATGTCTGGACGACCTGTT 59.678 55.000 5.33 0.00 46.37 3.16
21 22 1.270839 CCATGTCTGGACGACCTGTTT 60.271 52.381 5.33 0.00 46.37 2.83
22 23 2.494059 CATGTCTGGACGACCTGTTTT 58.506 47.619 5.33 0.00 42.13 2.43
23 24 2.702592 TGTCTGGACGACCTGTTTTT 57.297 45.000 5.33 0.00 42.13 1.94
86 87 7.566658 ATTTTCCACTTAAAATGATTGGGGA 57.433 32.000 0.00 0.00 37.60 4.81
87 88 5.993748 TTCCACTTAAAATGATTGGGGAC 57.006 39.130 0.00 0.00 0.00 4.46
88 89 5.269554 TCCACTTAAAATGATTGGGGACT 57.730 39.130 0.00 0.00 0.00 3.85
89 90 5.016173 TCCACTTAAAATGATTGGGGACTG 58.984 41.667 0.00 0.00 0.00 3.51
90 91 5.016173 CCACTTAAAATGATTGGGGACTGA 58.984 41.667 0.00 0.00 0.00 3.41
91 92 5.480073 CCACTTAAAATGATTGGGGACTGAA 59.520 40.000 0.00 0.00 0.00 3.02
92 93 6.014669 CCACTTAAAATGATTGGGGACTGAAA 60.015 38.462 0.00 0.00 0.00 2.69
93 94 7.441017 CACTTAAAATGATTGGGGACTGAAAA 58.559 34.615 0.00 0.00 0.00 2.29
94 95 7.930865 CACTTAAAATGATTGGGGACTGAAAAA 59.069 33.333 0.00 0.00 0.00 1.94
197 198 8.733857 AAAAATGTTCGCAATTTTGAAAACAA 57.266 23.077 12.08 0.00 38.39 2.83
198 199 8.733857 AAAATGTTCGCAATTTTGAAAACAAA 57.266 23.077 12.08 0.00 37.53 2.83
199 200 8.908172 AAATGTTCGCAATTTTGAAAACAAAT 57.092 23.077 12.08 5.33 37.53 2.32
200 201 7.895582 ATGTTCGCAATTTTGAAAACAAATG 57.104 28.000 12.08 0.00 37.53 2.32
201 202 6.835914 TGTTCGCAATTTTGAAAACAAATGT 58.164 28.000 0.00 0.00 33.87 2.71
202 203 7.301054 TGTTCGCAATTTTGAAAACAAATGTT 58.699 26.923 0.00 0.00 40.50 2.71
204 205 7.716738 TCGCAATTTTGAAAACAAATGTTTG 57.283 28.000 11.94 0.00 46.47 2.93
205 206 6.744537 TCGCAATTTTGAAAACAAATGTTTGG 59.255 30.769 11.94 0.00 46.47 3.28
206 207 6.020837 CGCAATTTTGAAAACAAATGTTTGGG 60.021 34.615 11.94 3.33 46.47 4.12
207 208 7.031975 GCAATTTTGAAAACAAATGTTTGGGA 58.968 30.769 11.94 0.00 46.47 4.37
208 209 7.543520 GCAATTTTGAAAACAAATGTTTGGGAA 59.456 29.630 11.94 6.19 46.47 3.97
209 210 9.415544 CAATTTTGAAAACAAATGTTTGGGAAA 57.584 25.926 11.94 12.15 46.47 3.13
294 295 8.961294 TGAATTTTCTCCAATTCAAAACATGT 57.039 26.923 6.41 0.00 45.85 3.21
295 296 9.393512 TGAATTTTCTCCAATTCAAAACATGTT 57.606 25.926 4.92 4.92 45.85 2.71
296 297 9.868389 GAATTTTCTCCAATTCAAAACATGTTC 57.132 29.630 12.39 0.00 41.19 3.18
297 298 8.961294 ATTTTCTCCAATTCAAAACATGTTCA 57.039 26.923 12.39 0.00 0.00 3.18
298 299 8.961294 TTTTCTCCAATTCAAAACATGTTCAT 57.039 26.923 12.39 0.93 0.00 2.57
299 300 7.949903 TTCTCCAATTCAAAACATGTTCATG 57.050 32.000 12.39 13.95 0.00 3.07
300 301 7.287512 TCTCCAATTCAAAACATGTTCATGA 57.712 32.000 12.39 15.98 0.00 3.07
301 302 7.724287 TCTCCAATTCAAAACATGTTCATGAA 58.276 30.769 27.91 27.91 34.82 2.57
302 303 8.369424 TCTCCAATTCAAAACATGTTCATGAAT 58.631 29.630 29.08 29.08 39.02 2.57
303 304 8.905660 TCCAATTCAAAACATGTTCATGAATT 57.094 26.923 33.31 33.31 42.78 2.17
309 310 9.985318 TTCAAAACATGTTCATGAATTGAAAAC 57.015 25.926 26.70 7.18 45.71 2.43
310 311 9.381033 TCAAAACATGTTCATGAATTGAAAACT 57.619 25.926 21.46 3.21 45.71 2.66
314 315 8.470040 ACATGTTCATGAATTGAAAACTATGC 57.530 30.769 21.46 3.43 45.71 3.14
315 316 8.308931 ACATGTTCATGAATTGAAAACTATGCT 58.691 29.630 21.46 0.47 45.71 3.79
316 317 9.791820 CATGTTCATGAATTGAAAACTATGCTA 57.208 29.630 12.12 0.00 45.71 3.49
338 339 9.376075 TGCTAAAAATTCAAAAACTGTTCATGA 57.624 25.926 0.00 0.00 0.00 3.07
427 428 9.406113 AGAAAATTTTGATGAATTTTTCCACCA 57.594 25.926 8.47 0.00 44.74 4.17
483 484 6.393720 AAAATCGCCGATTCAAGAAAAATG 57.606 33.333 13.43 0.00 30.29 2.32
484 485 4.701956 ATCGCCGATTCAAGAAAAATGT 57.298 36.364 0.00 0.00 0.00 2.71
485 486 4.497473 TCGCCGATTCAAGAAAAATGTT 57.503 36.364 0.00 0.00 0.00 2.71
486 487 4.472286 TCGCCGATTCAAGAAAAATGTTC 58.528 39.130 0.00 0.00 0.00 3.18
487 488 4.023622 TCGCCGATTCAAGAAAAATGTTCA 60.024 37.500 0.00 0.00 0.00 3.18
488 489 4.088496 CGCCGATTCAAGAAAAATGTTCAC 59.912 41.667 0.00 0.00 0.00 3.18
489 490 4.981674 GCCGATTCAAGAAAAATGTTCACA 59.018 37.500 0.00 0.00 0.00 3.58
490 491 5.461737 GCCGATTCAAGAAAAATGTTCACAA 59.538 36.000 0.00 0.00 0.00 3.33
491 492 6.146021 GCCGATTCAAGAAAAATGTTCACAAT 59.854 34.615 0.00 0.00 0.00 2.71
492 493 7.307337 GCCGATTCAAGAAAAATGTTCACAATT 60.307 33.333 0.00 0.00 0.00 2.32
493 494 8.216453 CCGATTCAAGAAAAATGTTCACAATTC 58.784 33.333 0.00 0.00 0.00 2.17
494 495 8.971321 CGATTCAAGAAAAATGTTCACAATTCT 58.029 29.630 0.00 2.01 32.48 2.40
506 507 9.934190 AATGTTCACAATTCTTAAAAATGTTGC 57.066 25.926 0.00 0.00 0.00 4.17
507 508 8.484641 TGTTCACAATTCTTAAAAATGTTGCA 57.515 26.923 0.00 0.00 0.00 4.08
508 509 8.939929 TGTTCACAATTCTTAAAAATGTTGCAA 58.060 25.926 0.00 0.00 0.00 4.08
509 510 9.766277 GTTCACAATTCTTAAAAATGTTGCAAA 57.234 25.926 0.00 0.00 0.00 3.68
525 526 9.650539 AATGTTGCAAATAGTATAAAATGTGCA 57.349 25.926 0.00 8.63 38.87 4.57
526 527 9.820725 ATGTTGCAAATAGTATAAAATGTGCAT 57.179 25.926 0.00 0.00 40.17 3.96
527 528 9.085250 TGTTGCAAATAGTATAAAATGTGCATG 57.915 29.630 0.00 0.00 40.17 4.06
528 529 8.542132 GTTGCAAATAGTATAAAATGTGCATGG 58.458 33.333 0.00 0.00 40.17 3.66
529 530 8.005192 TGCAAATAGTATAAAATGTGCATGGA 57.995 30.769 8.63 0.00 35.93 3.41
530 531 8.640651 TGCAAATAGTATAAAATGTGCATGGAT 58.359 29.630 8.63 0.00 35.93 3.41
531 532 9.480053 GCAAATAGTATAAAATGTGCATGGATT 57.520 29.630 0.00 0.00 0.00 3.01
537 538 9.941325 AGTATAAAATGTGCATGGATTCAAAAA 57.059 25.926 0.00 0.00 0.00 1.94
585 586 9.670180 GTTTGAAGTTTTAGAAAAATGTTCACG 57.330 29.630 10.18 0.00 30.51 4.35
586 587 9.627395 TTTGAAGTTTTAGAAAAATGTTCACGA 57.373 25.926 10.18 3.82 30.51 4.35
587 588 9.627395 TTGAAGTTTTAGAAAAATGTTCACGAA 57.373 25.926 10.18 0.00 30.51 3.85
588 589 9.796120 TGAAGTTTTAGAAAAATGTTCACGAAT 57.204 25.926 0.00 0.00 0.00 3.34
591 592 9.796120 AGTTTTAGAAAAATGTTCACGAATTCA 57.204 25.926 6.22 0.00 0.00 2.57
601 602 9.689976 AAATGTTCACGAATTCAAATATGTTCA 57.310 25.926 6.22 1.35 0.00 3.18
602 603 8.673626 ATGTTCACGAATTCAAATATGTTCAC 57.326 30.769 6.22 0.00 0.00 3.18
603 604 6.794636 TGTTCACGAATTCAAATATGTTCACG 59.205 34.615 6.22 0.00 0.00 4.35
604 605 6.474819 TCACGAATTCAAATATGTTCACGT 57.525 33.333 6.22 0.00 0.00 4.49
605 606 6.303370 TCACGAATTCAAATATGTTCACGTG 58.697 36.000 9.94 9.94 45.11 4.49
606 607 6.073494 TCACGAATTCAAATATGTTCACGTGT 60.073 34.615 16.51 0.00 44.45 4.49
607 608 6.577055 CACGAATTCAAATATGTTCACGTGTT 59.423 34.615 16.51 0.00 41.08 3.32
608 609 7.112844 CACGAATTCAAATATGTTCACGTGTTT 59.887 33.333 16.51 4.55 41.08 2.83
609 610 8.283992 ACGAATTCAAATATGTTCACGTGTTTA 58.716 29.630 16.51 3.11 0.00 2.01
610 611 9.272901 CGAATTCAAATATGTTCACGTGTTTAT 57.727 29.630 16.51 10.42 0.00 1.40
669 670 8.839947 TCACATAATGTTGATAAATTTGAGCG 57.160 30.769 0.00 0.00 0.00 5.03
670 671 8.672815 TCACATAATGTTGATAAATTTGAGCGA 58.327 29.630 0.00 0.00 0.00 4.93
671 672 8.950961 CACATAATGTTGATAAATTTGAGCGAG 58.049 33.333 0.00 0.00 0.00 5.03
672 673 8.131100 ACATAATGTTGATAAATTTGAGCGAGG 58.869 33.333 0.00 0.00 0.00 4.63
673 674 4.355543 TGTTGATAAATTTGAGCGAGGC 57.644 40.909 0.00 0.00 0.00 4.70
674 675 3.181511 TGTTGATAAATTTGAGCGAGGCG 60.182 43.478 0.00 0.00 0.00 5.52
675 676 2.899976 TGATAAATTTGAGCGAGGCGA 58.100 42.857 0.00 0.00 0.00 5.54
676 677 2.866156 TGATAAATTTGAGCGAGGCGAG 59.134 45.455 0.00 0.00 0.00 5.03
677 678 1.651987 TAAATTTGAGCGAGGCGAGG 58.348 50.000 0.00 0.00 0.00 4.63
678 679 0.036388 AAATTTGAGCGAGGCGAGGA 60.036 50.000 0.00 0.00 0.00 3.71
679 680 0.179000 AATTTGAGCGAGGCGAGGAT 59.821 50.000 0.00 0.00 0.00 3.24
680 681 0.531532 ATTTGAGCGAGGCGAGGATG 60.532 55.000 0.00 0.00 0.00 3.51
681 682 1.888436 TTTGAGCGAGGCGAGGATGT 61.888 55.000 0.00 0.00 0.00 3.06
691 692 2.107953 GAGGATGTGGAGGAGCGC 59.892 66.667 0.00 0.00 0.00 5.92
692 693 3.453070 GAGGATGTGGAGGAGCGCC 62.453 68.421 2.29 0.00 0.00 6.53
719 723 1.527433 GGTTGACAGCAAAGGGAGGC 61.527 60.000 0.00 0.00 35.42 4.70
724 728 1.975407 CAGCAAAGGGAGGCCAGTG 60.975 63.158 5.01 0.00 0.00 3.66
726 730 1.676967 GCAAAGGGAGGCCAGTGAG 60.677 63.158 5.01 0.00 0.00 3.51
738 742 1.004799 CAGTGAGTGCTGCAGAGCT 60.005 57.895 20.43 14.21 46.39 4.09
750 754 3.314635 GCTGCAGAGCTAGCAACAATTAT 59.685 43.478 20.43 0.00 42.17 1.28
785 791 5.180304 CCGACATCGATCAGATAGAGAAAGA 59.820 44.000 2.09 0.00 43.02 2.52
803 809 5.300286 AGAAAGATTCTCAACAACACTTGGG 59.700 40.000 0.00 0.00 34.07 4.12
806 812 2.341846 TCTCAACAACACTTGGGACC 57.658 50.000 0.00 0.00 34.12 4.46
862 868 8.567285 ACAGTATTATTTCTTCCTTCCTTGTG 57.433 34.615 0.00 0.00 0.00 3.33
866 872 3.297134 TTTCTTCCTTCCTTGTGCACT 57.703 42.857 19.41 0.00 0.00 4.40
885 891 2.564947 ACTGAGCAGTTTCCTAGACCTG 59.435 50.000 0.00 0.00 38.83 4.00
893 899 3.196685 AGTTTCCTAGACCTGCTTGCTAG 59.803 47.826 0.00 0.00 33.18 3.42
932 938 7.295322 AGTTGTCTGATGCATATAGAAGCTA 57.705 36.000 13.11 0.00 0.00 3.32
938 944 7.601886 GTCTGATGCATATAGAAGCTAATGTGT 59.398 37.037 13.11 0.00 0.00 3.72
958 964 7.292713 TGTGTAGTACATGTGAAGTTTCCTA 57.707 36.000 9.11 0.00 33.42 2.94
1139 1148 3.440522 TGTGTGACATCAAAAACGGACAA 59.559 39.130 0.00 0.00 0.00 3.18
1154 1163 8.446599 AAAACGGACAATCGGAGAAATATATT 57.553 30.769 0.00 0.00 43.58 1.28
1354 1369 2.763902 CCTGTTCCCCTCAACCCC 59.236 66.667 0.00 0.00 0.00 4.95
1453 1476 6.061441 ACTTGAGTGATACCAACAAACATCA 58.939 36.000 0.00 0.00 0.00 3.07
1553 1576 0.886490 CCGTTCTTGGCAAGCTCACT 60.886 55.000 22.31 0.00 0.00 3.41
1577 1600 4.884744 GCTCTACTCAAGGAGTATGACAGA 59.115 45.833 6.56 1.97 43.08 3.41
1667 1690 2.106566 GATCTCTCACAGCTGGAGGAA 58.893 52.381 23.63 15.85 33.18 3.36
2070 2093 4.082408 AGGAACGTCGTGTCATTTCTATCA 60.082 41.667 0.00 0.00 0.00 2.15
2119 2142 3.214328 CCCTTGCCAATCAGGTATACAC 58.786 50.000 5.01 0.00 40.61 2.90
2156 2255 4.778534 ATTCTTGATGGAAGCAACACAG 57.221 40.909 0.00 0.00 37.27 3.66
2161 2260 2.104622 TGATGGAAGCAACACAGAGTCA 59.895 45.455 0.00 0.00 0.00 3.41
2166 2265 1.959042 AGCAACACAGAGTCAGTTGG 58.041 50.000 18.59 0.00 42.07 3.77
2278 2379 6.683974 AAAGGTATGTCAGTGCATAACATC 57.316 37.500 18.60 7.13 40.49 3.06
2285 2386 4.020662 TGTCAGTGCATAACATCCTGTACA 60.021 41.667 0.00 0.00 31.34 2.90
2292 2393 4.679639 GCATAACATCCTGTACACTTCCGA 60.680 45.833 0.00 0.00 0.00 4.55
2314 2415 3.990959 TTTTTCTTGGGTTGCTTGGTT 57.009 38.095 0.00 0.00 0.00 3.67
2319 2420 3.838565 TCTTGGGTTGCTTGGTTATGAA 58.161 40.909 0.00 0.00 0.00 2.57
2539 2927 9.781633 TTACAAAGTTACCTTCTTAGTTATGCA 57.218 29.630 0.00 0.00 0.00 3.96
2561 2949 5.625197 GCATGCATGAGGTTTCAAAGGTAAT 60.625 40.000 30.64 0.00 36.78 1.89
2614 3002 4.517075 TGATGGCATAAACGTTTTGAGTCA 59.483 37.500 20.19 16.39 0.00 3.41
2615 3003 4.902443 TGGCATAAACGTTTTGAGTCAA 57.098 36.364 20.19 0.08 0.00 3.18
2653 3047 5.484998 ACATTCAGCATGGGGAAGTTTTTAT 59.515 36.000 0.00 0.00 37.17 1.40
2687 3082 5.581126 TTGCTGGGCTATATTTTTCACAG 57.419 39.130 0.00 0.00 0.00 3.66
2689 3084 5.448654 TGCTGGGCTATATTTTTCACAGAT 58.551 37.500 0.00 0.00 0.00 2.90
2697 3092 6.976925 GCTATATTTTTCACAGATTGCTTGCT 59.023 34.615 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 7.237471 AGTCCCCAATCATTTTAAGTGGAAAAT 59.763 33.333 0.00 0.00 39.13 1.82
63 64 6.556874 AGTCCCCAATCATTTTAAGTGGAAAA 59.443 34.615 0.00 0.00 33.04 2.29
64 65 6.014669 CAGTCCCCAATCATTTTAAGTGGAAA 60.015 38.462 0.00 0.00 0.00 3.13
65 66 5.480073 CAGTCCCCAATCATTTTAAGTGGAA 59.520 40.000 0.00 0.00 0.00 3.53
66 67 5.016173 CAGTCCCCAATCATTTTAAGTGGA 58.984 41.667 0.00 0.00 0.00 4.02
67 68 5.016173 TCAGTCCCCAATCATTTTAAGTGG 58.984 41.667 0.00 0.00 0.00 4.00
68 69 6.588719 TTCAGTCCCCAATCATTTTAAGTG 57.411 37.500 0.00 0.00 0.00 3.16
69 70 7.610580 TTTTCAGTCCCCAATCATTTTAAGT 57.389 32.000 0.00 0.00 0.00 2.24
172 173 8.733857 TTGTTTTCAAAATTGCGAACATTTTT 57.266 23.077 11.94 0.00 38.98 1.94
173 174 8.733857 TTTGTTTTCAAAATTGCGAACATTTT 57.266 23.077 11.94 0.00 45.30 1.82
270 271 9.868389 GAACATGTTTTGAATTGGAGAAAATTC 57.132 29.630 13.36 3.29 43.76 2.17
271 272 9.393512 TGAACATGTTTTGAATTGGAGAAAATT 57.606 25.926 13.36 0.00 32.43 1.82
272 273 8.961294 TGAACATGTTTTGAATTGGAGAAAAT 57.039 26.923 13.36 0.00 0.00 1.82
273 274 8.828644 CATGAACATGTTTTGAATTGGAGAAAA 58.171 29.630 13.36 0.00 34.23 2.29
274 275 8.202811 TCATGAACATGTTTTGAATTGGAGAAA 58.797 29.630 13.36 0.00 39.72 2.52
275 276 7.724287 TCATGAACATGTTTTGAATTGGAGAA 58.276 30.769 13.36 0.00 39.72 2.87
276 277 7.287512 TCATGAACATGTTTTGAATTGGAGA 57.712 32.000 13.36 0.00 39.72 3.71
277 278 7.949903 TTCATGAACATGTTTTGAATTGGAG 57.050 32.000 23.40 5.34 39.72 3.86
278 279 8.775527 CAATTCATGAACATGTTTTGAATTGGA 58.224 29.630 39.22 23.94 45.32 3.53
279 280 8.775527 TCAATTCATGAACATGTTTTGAATTGG 58.224 29.630 41.29 33.60 46.63 3.16
312 313 9.376075 TCATGAACAGTTTTTGAATTTTTAGCA 57.624 25.926 0.00 0.00 0.00 3.49
401 402 9.406113 TGGTGGAAAAATTCATCAAAATTTTCT 57.594 25.926 0.00 0.00 44.17 2.52
459 460 6.423604 ACATTTTTCTTGAATCGGCGATTTTT 59.576 30.769 32.88 15.23 31.89 1.94
460 461 5.925969 ACATTTTTCTTGAATCGGCGATTTT 59.074 32.000 32.88 16.01 31.89 1.82
461 462 5.469479 ACATTTTTCTTGAATCGGCGATTT 58.531 33.333 32.88 18.52 31.89 2.17
462 463 5.059404 ACATTTTTCTTGAATCGGCGATT 57.941 34.783 32.96 32.96 34.71 3.34
463 464 4.701956 ACATTTTTCTTGAATCGGCGAT 57.298 36.364 18.14 18.14 0.00 4.58
464 465 4.023622 TGAACATTTTTCTTGAATCGGCGA 60.024 37.500 13.87 13.87 0.00 5.54
465 466 4.088496 GTGAACATTTTTCTTGAATCGGCG 59.912 41.667 0.00 0.00 0.00 6.46
466 467 4.981674 TGTGAACATTTTTCTTGAATCGGC 59.018 37.500 0.00 0.00 0.00 5.54
467 468 7.642071 ATTGTGAACATTTTTCTTGAATCGG 57.358 32.000 0.00 0.00 0.00 4.18
468 469 8.971321 AGAATTGTGAACATTTTTCTTGAATCG 58.029 29.630 0.00 0.00 0.00 3.34
480 481 9.934190 GCAACATTTTTAAGAATTGTGAACATT 57.066 25.926 3.69 0.00 0.00 2.71
481 482 9.107177 TGCAACATTTTTAAGAATTGTGAACAT 57.893 25.926 0.00 0.00 0.00 2.71
482 483 8.484641 TGCAACATTTTTAAGAATTGTGAACA 57.515 26.923 0.00 0.00 0.00 3.18
483 484 9.766277 TTTGCAACATTTTTAAGAATTGTGAAC 57.234 25.926 0.00 0.00 0.00 3.18
499 500 9.650539 TGCACATTTTATACTATTTGCAACATT 57.349 25.926 0.00 0.00 35.28 2.71
500 501 9.820725 ATGCACATTTTATACTATTTGCAACAT 57.179 25.926 0.00 0.00 39.87 2.71
501 502 9.085250 CATGCACATTTTATACTATTTGCAACA 57.915 29.630 0.00 0.00 39.87 3.33
502 503 8.542132 CCATGCACATTTTATACTATTTGCAAC 58.458 33.333 0.00 0.00 39.87 4.17
503 504 8.473219 TCCATGCACATTTTATACTATTTGCAA 58.527 29.630 0.00 0.00 39.87 4.08
504 505 8.005192 TCCATGCACATTTTATACTATTTGCA 57.995 30.769 8.65 8.65 40.48 4.08
505 506 9.480053 AATCCATGCACATTTTATACTATTTGC 57.520 29.630 0.00 0.00 0.00 3.68
511 512 9.941325 TTTTTGAATCCATGCACATTTTATACT 57.059 25.926 0.00 0.00 0.00 2.12
559 560 9.670180 CGTGAACATTTTTCTAAAACTTCAAAC 57.330 29.630 0.00 0.00 30.62 2.93
560 561 9.627395 TCGTGAACATTTTTCTAAAACTTCAAA 57.373 25.926 0.00 0.00 30.62 2.69
561 562 9.627395 TTCGTGAACATTTTTCTAAAACTTCAA 57.373 25.926 0.00 0.00 30.62 2.69
562 563 9.796120 ATTCGTGAACATTTTTCTAAAACTTCA 57.204 25.926 0.00 0.00 0.00 3.02
565 566 9.796120 TGAATTCGTGAACATTTTTCTAAAACT 57.204 25.926 0.04 0.00 0.00 2.66
575 576 9.689976 TGAACATATTTGAATTCGTGAACATTT 57.310 25.926 0.04 0.00 0.00 2.32
576 577 9.128107 GTGAACATATTTGAATTCGTGAACATT 57.872 29.630 0.04 0.00 0.00 2.71
577 578 7.481483 CGTGAACATATTTGAATTCGTGAACAT 59.519 33.333 0.04 0.00 0.00 2.71
578 579 6.794636 CGTGAACATATTTGAATTCGTGAACA 59.205 34.615 0.04 0.00 0.00 3.18
579 580 6.795114 ACGTGAACATATTTGAATTCGTGAAC 59.205 34.615 0.04 0.00 0.00 3.18
580 581 6.794636 CACGTGAACATATTTGAATTCGTGAA 59.205 34.615 10.90 0.00 44.51 3.18
581 582 6.073494 ACACGTGAACATATTTGAATTCGTGA 60.073 34.615 25.01 0.00 44.51 4.35
582 583 6.077197 ACACGTGAACATATTTGAATTCGTG 58.923 36.000 25.01 17.68 46.20 4.35
583 584 6.236017 ACACGTGAACATATTTGAATTCGT 57.764 33.333 25.01 0.00 0.00 3.85
584 585 7.547285 AAACACGTGAACATATTTGAATTCG 57.453 32.000 25.01 0.00 0.00 3.34
643 644 9.288124 CGCTCAAATTTATCAACATTATGTGAA 57.712 29.630 0.00 0.00 0.00 3.18
644 645 8.672815 TCGCTCAAATTTATCAACATTATGTGA 58.327 29.630 0.00 0.00 0.00 3.58
645 646 8.839947 TCGCTCAAATTTATCAACATTATGTG 57.160 30.769 0.00 0.00 0.00 3.21
646 647 8.131100 CCTCGCTCAAATTTATCAACATTATGT 58.869 33.333 0.00 0.00 0.00 2.29
647 648 7.113965 GCCTCGCTCAAATTTATCAACATTATG 59.886 37.037 0.00 0.00 0.00 1.90
648 649 7.141363 GCCTCGCTCAAATTTATCAACATTAT 58.859 34.615 0.00 0.00 0.00 1.28
649 650 6.494842 GCCTCGCTCAAATTTATCAACATTA 58.505 36.000 0.00 0.00 0.00 1.90
650 651 5.343249 GCCTCGCTCAAATTTATCAACATT 58.657 37.500 0.00 0.00 0.00 2.71
651 652 4.496341 CGCCTCGCTCAAATTTATCAACAT 60.496 41.667 0.00 0.00 0.00 2.71
652 653 3.181511 CGCCTCGCTCAAATTTATCAACA 60.182 43.478 0.00 0.00 0.00 3.33
653 654 3.063452 TCGCCTCGCTCAAATTTATCAAC 59.937 43.478 0.00 0.00 0.00 3.18
654 655 3.266636 TCGCCTCGCTCAAATTTATCAA 58.733 40.909 0.00 0.00 0.00 2.57
655 656 2.866156 CTCGCCTCGCTCAAATTTATCA 59.134 45.455 0.00 0.00 0.00 2.15
656 657 2.221981 CCTCGCCTCGCTCAAATTTATC 59.778 50.000 0.00 0.00 0.00 1.75
657 658 2.158957 TCCTCGCCTCGCTCAAATTTAT 60.159 45.455 0.00 0.00 0.00 1.40
658 659 1.206132 TCCTCGCCTCGCTCAAATTTA 59.794 47.619 0.00 0.00 0.00 1.40
659 660 0.036388 TCCTCGCCTCGCTCAAATTT 60.036 50.000 0.00 0.00 0.00 1.82
660 661 0.179000 ATCCTCGCCTCGCTCAAATT 59.821 50.000 0.00 0.00 0.00 1.82
661 662 0.531532 CATCCTCGCCTCGCTCAAAT 60.532 55.000 0.00 0.00 0.00 2.32
662 663 1.153568 CATCCTCGCCTCGCTCAAA 60.154 57.895 0.00 0.00 0.00 2.69
663 664 2.351244 ACATCCTCGCCTCGCTCAA 61.351 57.895 0.00 0.00 0.00 3.02
664 665 2.755876 ACATCCTCGCCTCGCTCA 60.756 61.111 0.00 0.00 0.00 4.26
665 666 2.279120 CACATCCTCGCCTCGCTC 60.279 66.667 0.00 0.00 0.00 5.03
666 667 3.842923 CCACATCCTCGCCTCGCT 61.843 66.667 0.00 0.00 0.00 4.93
667 668 3.781770 CTCCACATCCTCGCCTCGC 62.782 68.421 0.00 0.00 0.00 5.03
668 669 2.415010 CTCCACATCCTCGCCTCG 59.585 66.667 0.00 0.00 0.00 4.63
669 670 1.743321 CTCCTCCACATCCTCGCCTC 61.743 65.000 0.00 0.00 0.00 4.70
670 671 1.760086 CTCCTCCACATCCTCGCCT 60.760 63.158 0.00 0.00 0.00 5.52
671 672 2.818132 CTCCTCCACATCCTCGCC 59.182 66.667 0.00 0.00 0.00 5.54
672 673 2.107953 GCTCCTCCACATCCTCGC 59.892 66.667 0.00 0.00 0.00 5.03
673 674 2.415010 CGCTCCTCCACATCCTCG 59.585 66.667 0.00 0.00 0.00 4.63
674 675 2.107953 GCGCTCCTCCACATCCTC 59.892 66.667 0.00 0.00 0.00 3.71
675 676 3.474570 GGCGCTCCTCCACATCCT 61.475 66.667 7.64 0.00 0.00 3.24
676 677 3.746949 CTGGCGCTCCTCCACATCC 62.747 68.421 7.64 0.00 0.00 3.51
677 678 2.202987 CTGGCGCTCCTCCACATC 60.203 66.667 7.64 0.00 0.00 3.06
678 679 3.790437 CCTGGCGCTCCTCCACAT 61.790 66.667 7.64 0.00 0.00 3.21
692 693 3.357079 GCTGTCAACCACGCCCTG 61.357 66.667 0.00 0.00 0.00 4.45
706 710 1.975407 CACTGGCCTCCCTTTGCTG 60.975 63.158 3.32 0.00 0.00 4.41
719 723 2.033755 GCTCTGCAGCACTCACTGG 61.034 63.158 9.47 0.00 46.06 4.00
738 742 2.426738 GCTGGCACCATAATTGTTGCTA 59.573 45.455 0.00 0.00 0.00 3.49
764 768 8.408043 AGAATCTTTCTCTATCTGATCGATGT 57.592 34.615 0.54 0.00 34.07 3.06
785 791 3.222603 GGTCCCAAGTGTTGTTGAGAAT 58.777 45.455 0.00 0.00 0.00 2.40
803 809 0.034089 ATACCTTGCTGGCCTTGGTC 60.034 55.000 3.32 0.00 40.22 4.02
806 812 2.134789 AGAATACCTTGCTGGCCTTG 57.865 50.000 3.32 0.00 40.22 3.61
809 815 5.598416 AATTTTAGAATACCTTGCTGGCC 57.402 39.130 0.00 0.00 40.22 5.36
810 816 8.251026 ACTAAAATTTTAGAATACCTTGCTGGC 58.749 33.333 34.09 0.00 42.05 4.85
837 843 7.121315 GCACAAGGAAGGAAGAAATAATACTGT 59.879 37.037 0.00 0.00 0.00 3.55
862 868 2.342179 GTCTAGGAAACTGCTCAGTGC 58.658 52.381 2.97 0.00 41.58 4.40
885 891 4.766404 ATTGTTGTTGGTACTAGCAAGC 57.234 40.909 8.74 5.39 36.14 4.01
932 938 7.224297 AGGAAACTTCACATGTACTACACATT 58.776 34.615 0.00 0.00 41.31 2.71
938 944 6.985117 ACGTTAGGAAACTTCACATGTACTA 58.015 36.000 0.00 0.00 43.67 1.82
958 964 2.028748 ACTAAAGCCACCATCGTACGTT 60.029 45.455 16.05 3.67 0.00 3.99
1139 1148 7.329746 TCCCTTCCAAATATATTTCTCCGAT 57.670 36.000 7.76 0.00 0.00 4.18
1154 1163 1.710244 TGCATTCTTCCTCCCTTCCAA 59.290 47.619 0.00 0.00 0.00 3.53
1354 1369 4.749245 AAGCATGAAACGTAGAAACTGG 57.251 40.909 0.00 0.00 0.00 4.00
1453 1476 0.109342 CTCTGCTCTGTGGGTGGTTT 59.891 55.000 0.00 0.00 0.00 3.27
1514 1537 2.620234 GGTCATCACCCCCATCAGA 58.380 57.895 0.00 0.00 36.54 3.27
1553 1576 4.600062 TGTCATACTCCTTGAGTAGAGCA 58.400 43.478 9.57 5.58 46.35 4.26
1577 1600 0.915364 GAGGATGGAGGCCTTTGAGT 59.085 55.000 6.77 0.00 35.44 3.41
1667 1690 0.825010 CCTTCACTTGCAAGCTGGGT 60.825 55.000 26.27 4.24 0.00 4.51
1865 1888 3.827625 CCGATCATTAACCTCTAGAGCG 58.172 50.000 14.73 10.11 37.79 5.03
1938 1961 1.065709 GGCCGACAACCTAGGATCAAA 60.066 52.381 17.98 0.00 0.00 2.69
2119 2142 7.538678 CCATCAAGAATTTACTTTTGACTTCCG 59.461 37.037 0.00 0.00 32.90 4.30
2161 2260 2.779755 TGTGTTGACTGTCACCAACT 57.220 45.000 10.56 0.00 42.16 3.16
2166 2265 3.466836 TCCTTGATGTGTTGACTGTCAC 58.533 45.455 10.56 6.70 35.43 3.67
2278 2379 5.941948 AGAAAAATTCGGAAGTGTACAGG 57.058 39.130 0.00 0.00 34.02 4.00
2285 2386 4.739436 GCAACCCAAGAAAAATTCGGAAGT 60.739 41.667 0.00 0.00 34.02 3.01
2292 2393 4.502105 ACCAAGCAACCCAAGAAAAATT 57.498 36.364 0.00 0.00 0.00 1.82
2314 2415 2.174639 CAGGCCACCCCTATTGTTCATA 59.825 50.000 5.01 0.00 44.09 2.15
2319 2420 1.080638 TTTCAGGCCACCCCTATTGT 58.919 50.000 5.01 0.00 44.09 2.71
2443 2829 7.792383 TCTTCTCAACGTTATTAAGAAGACG 57.208 36.000 25.20 12.57 44.16 4.18
2539 2927 7.716799 TTATTACCTTTGAAACCTCATGCAT 57.283 32.000 0.00 0.00 0.00 3.96
2653 3047 2.011046 GCCCAGCAAACAAAGCAAACA 61.011 47.619 0.00 0.00 0.00 2.83
2687 3082 8.707938 ATTAGTTTTATTCCAAGCAAGCAATC 57.292 30.769 0.00 0.00 0.00 2.67
3098 3493 3.914426 AAGAGAATTACGCACCCTCAT 57.086 42.857 0.00 0.00 0.00 2.90
3183 3578 5.488341 TCTTCAAATAGCAAGGTAGGTCAC 58.512 41.667 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.