Multiple sequence alignment - TraesCS7D01G073000

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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 TraesCS7D01G073000 chr7D 100.000 3558 0 0 1 3558 42808974 42812531 0.000000e+00 6571
1 TraesCS7D01G073000 chr7A 89.575 2120 137 41 1 2069 42496689 42498775 0.000000e+00 2614
2 TraesCS7D01G073000 chr7A 86.426 943 73 19 2647 3558 42499992 42500910 0.000000e+00 981
3 TraesCS7D01G073000 chr7A 90.669 568 24 8 949 1513 79797851 79798392 0.000000e+00 728
4 TraesCS7D01G073000 chr7A 90.714 560 25 6 957 1513 669446986 669446451 0.000000e+00 721
5 TraesCS7D01G073000 chr7A 82.987 817 100 21 2160 2959 42498785 42499579 0.000000e+00 702
6 TraesCS7D01G073000 chr7A 91.722 302 23 2 957 1257 601863848 601863548 5.490000e-113 418
7 TraesCS7D01G073000 chr2D 89.381 1940 124 33 903 2796 21143040 21141137 0.000000e+00 2366
8 TraesCS7D01G073000 chr4A 89.674 1501 118 22 1759 3240 650368712 650370194 0.000000e+00 1879
9 TraesCS7D01G073000 chr4A 93.289 894 27 14 751 1626 650367730 650368608 0.000000e+00 1288
10 TraesCS7D01G073000 chr4A 90.397 302 27 2 957 1257 418428695 418428395 2.570000e-106 396
11 TraesCS7D01G073000 chr4A 89.545 220 23 0 3314 3533 650370202 650370421 2.700000e-71 279
12 TraesCS7D01G073000 chr4A 94.318 88 5 0 658 745 650367329 650367416 6.200000e-28 135
13 TraesCS7D01G073000 chr4D 89.935 1391 105 19 957 2332 435101794 435100424 0.000000e+00 1760
14 TraesCS7D01G073000 chr4D 97.619 168 4 0 1034 1201 435100427 435100260 4.490000e-74 289
15 TraesCS7D01G073000 chr5A 89.398 1396 103 26 957 2332 512719380 512720750 0.000000e+00 1716
16 TraesCS7D01G073000 chr3B 87.661 1394 130 23 957 2332 710716215 710717584 0.000000e+00 1583
17 TraesCS7D01G073000 chr3B 90.816 196 17 1 1787 1981 754019134 754018939 9.800000e-66 261
18 TraesCS7D01G073000 chr1D 91.373 765 45 7 957 1714 54465728 54466478 0.000000e+00 1027
19 TraesCS7D01G073000 chr1D 96.765 340 11 0 2457 2796 380824710 380825049 5.150000e-158 568
20 TraesCS7D01G073000 chr6A 90.714 560 25 14 957 1513 357869932 357870467 0.000000e+00 721
21 TraesCS7D01G073000 chr3A 88.393 560 37 11 957 1513 704175986 704175452 0.000000e+00 649
22 TraesCS7D01G073000 chr3A 94.408 304 16 1 2029 2332 401132200 401132502 1.930000e-127 466
23 TraesCS7D01G073000 chr6B 96.471 340 12 0 2457 2796 620944045 620943706 2.400000e-156 562
24 TraesCS7D01G073000 chr6B 87.708 301 35 2 1681 1981 35452817 35452519 2.030000e-92 350
25 TraesCS7D01G073000 chr7B 96.176 340 13 0 2457 2796 48226729 48226390 1.120000e-154 556
26 TraesCS7D01G073000 chr7B 96.176 340 13 0 2457 2796 481551121 481550782 1.120000e-154 556
27 TraesCS7D01G073000 chr7B 93.091 275 18 1 957 1231 725212059 725212332 5.530000e-108 401
28 TraesCS7D01G073000 chr7B 89.369 301 31 1 1681 1981 396376420 396376719 9.320000e-101 377
29 TraesCS7D01G073000 chr1A 96.176 340 13 0 2457 2796 154371935 154371596 1.120000e-154 556
30 TraesCS7D01G073000 chr1B 96.165 339 13 0 2457 2795 677151604 677151942 4.010000e-154 555
31 TraesCS7D01G073000 chr2B 88.372 301 31 2 1681 1981 588847728 588848024 3.380000e-95 359


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 TraesCS7D01G073000 chr7D 42808974 42812531 3557 False 6571.000000 6571 100.000000 1 3558 1 chr7D.!!$F1 3557
1 TraesCS7D01G073000 chr7A 42496689 42500910 4221 False 1432.333333 2614 86.329333 1 3558 3 chr7A.!!$F2 3557
2 TraesCS7D01G073000 chr7A 79797851 79798392 541 False 728.000000 728 90.669000 949 1513 1 chr7A.!!$F1 564
3 TraesCS7D01G073000 chr7A 669446451 669446986 535 True 721.000000 721 90.714000 957 1513 1 chr7A.!!$R2 556
4 TraesCS7D01G073000 chr2D 21141137 21143040 1903 True 2366.000000 2366 89.381000 903 2796 1 chr2D.!!$R1 1893
5 TraesCS7D01G073000 chr4A 650367329 650370421 3092 False 895.250000 1879 91.706500 658 3533 4 chr4A.!!$F1 2875
6 TraesCS7D01G073000 chr4D 435100260 435101794 1534 True 1024.500000 1760 93.777000 957 2332 2 chr4D.!!$R1 1375
7 TraesCS7D01G073000 chr5A 512719380 512720750 1370 False 1716.000000 1716 89.398000 957 2332 1 chr5A.!!$F1 1375
8 TraesCS7D01G073000 chr3B 710716215 710717584 1369 False 1583.000000 1583 87.661000 957 2332 1 chr3B.!!$F1 1375
9 TraesCS7D01G073000 chr1D 54465728 54466478 750 False 1027.000000 1027 91.373000 957 1714 1 chr1D.!!$F1 757
10 TraesCS7D01G073000 chr6A 357869932 357870467 535 False 721.000000 721 90.714000 957 1513 1 chr6A.!!$F1 556
11 TraesCS7D01G073000 chr3A 704175452 704175986 534 True 649.000000 649 88.393000 957 1513 1 chr3A.!!$R1 556

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
295 299 0.032813 ATGTTGGAAGATGGCAGGGG 60.033 55.0 0.0 0.0 0.00 4.79 F
690 698 0.107017 ATCATGGAAGGCAAGGACCG 60.107 55.0 0.0 0.0 33.69 4.79 F
1823 2239 0.315568 AGCAGAGTTCTCGACACCAC 59.684 55.0 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1700 0.457853 CGCATCGTTTCGAGGGAGAA 60.458 55.0 6.01 0.0 39.91 2.87 R
2497 3082 0.407139 AGCTTGGTCAGGGCAAGAAT 59.593 50.0 0.00 0.0 0.00 2.40 R
3215 4535 0.185901 ACAGTCAATGTTGCCCACCT 59.814 50.0 0.00 0.0 39.96 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
26 27 9.886132 TTAGTATTAACTGATTGAACTTCCCTC 57.114 33.333 0.00 0.00 36.36 4.30
27 28 7.339482 AGTATTAACTGATTGAACTTCCCTCC 58.661 38.462 0.00 0.00 33.57 4.30
38 39 2.519013 ACTTCCCTCCAACTTTCATGC 58.481 47.619 0.00 0.00 0.00 4.06
40 41 2.905415 TCCCTCCAACTTTCATGCAT 57.095 45.000 0.00 0.00 0.00 3.96
83 84 6.055588 GCATGGTACCTTCTCTGCTAAATTA 58.944 40.000 14.36 0.00 0.00 1.40
90 91 9.465985 GTACCTTCTCTGCTAAATTATGTAGAC 57.534 37.037 0.00 0.00 0.00 2.59
93 94 6.085555 TCTCTGCTAAATTATGTAGACCCG 57.914 41.667 0.00 0.00 0.00 5.28
94 95 5.597182 TCTCTGCTAAATTATGTAGACCCGT 59.403 40.000 0.00 0.00 0.00 5.28
107 108 6.117975 TGTAGACCCGTTTTCTTATTCCTT 57.882 37.500 0.00 0.00 0.00 3.36
108 109 5.935789 TGTAGACCCGTTTTCTTATTCCTTG 59.064 40.000 0.00 0.00 0.00 3.61
162 163 4.000325 GGGTCATTTGTAAATTTGGCCAC 59.000 43.478 3.88 0.00 36.22 5.01
165 166 5.762711 GGTCATTTGTAAATTTGGCCACTTT 59.237 36.000 3.88 11.48 35.05 2.66
231 232 8.868522 TCATGATTCAATTAGTTGTTTCTCCT 57.131 30.769 0.00 0.00 36.69 3.69
233 234 7.364522 TGATTCAATTAGTTGTTTCTCCTCG 57.635 36.000 0.00 0.00 36.69 4.63
250 252 8.795786 TTCTCCTCGTTTTTATGTGATTTTTG 57.204 30.769 0.00 0.00 0.00 2.44
252 254 7.013846 TCTCCTCGTTTTTATGTGATTTTTGGT 59.986 33.333 0.00 0.00 0.00 3.67
253 255 6.920758 TCCTCGTTTTTATGTGATTTTTGGTG 59.079 34.615 0.00 0.00 0.00 4.17
258 262 8.643752 CGTTTTTATGTGATTTTTGGTGTATCC 58.356 33.333 0.00 0.00 0.00 2.59
293 297 1.843368 ACATGTTGGAAGATGGCAGG 58.157 50.000 0.00 0.00 34.27 4.85
295 299 0.032813 ATGTTGGAAGATGGCAGGGG 60.033 55.000 0.00 0.00 0.00 4.79
354 358 9.559732 AGTTTTACCCATTACGTTTACTTTAGT 57.440 29.630 0.00 0.00 0.00 2.24
432 440 7.527457 GTCCTTAAAGATATGTTTGCTTCGTT 58.473 34.615 8.05 0.00 0.00 3.85
437 445 9.906660 TTAAAGATATGTTTGCTTCGTTCATTT 57.093 25.926 8.05 0.00 0.00 2.32
445 453 4.022464 TGCTTCGTTCATTTTGAAACGT 57.978 36.364 7.41 0.00 38.22 3.99
454 462 5.317733 TCATTTTGAAACGTGGTCTGTTT 57.682 34.783 0.00 0.00 41.94 2.83
472 480 7.013529 GTCTGTTTACGGTGTCATTTGATAAC 58.986 38.462 0.00 0.00 0.00 1.89
479 487 4.412207 GGTGTCATTTGATAACGAAAGGC 58.588 43.478 0.00 0.00 0.00 4.35
520 528 5.438761 GCTGTAATTTGGTAGCCCTATTG 57.561 43.478 0.00 0.00 0.00 1.90
523 531 6.068461 TGTAATTTGGTAGCCCTATTGTCA 57.932 37.500 0.00 0.00 0.00 3.58
534 542 3.251972 GCCCTATTGTCAATTAGCAGCTC 59.748 47.826 0.00 0.00 0.00 4.09
545 553 7.718314 TGTCAATTAGCAGCTCAATATGAATCT 59.282 33.333 0.00 0.00 0.00 2.40
563 571 1.369091 CTCATTCCGCCCAGAAACCG 61.369 60.000 0.00 0.00 0.00 4.44
583 591 2.930040 CGTGCAATGGGATATCGATACC 59.070 50.000 7.41 10.85 36.43 2.73
590 598 2.290705 TGGGATATCGATACCGCTCTCA 60.291 50.000 14.40 8.55 39.27 3.27
604 612 1.996191 GCTCTCACGTCTCAAACCATC 59.004 52.381 0.00 0.00 0.00 3.51
612 620 2.234908 CGTCTCAAACCATCCTCTCCTT 59.765 50.000 0.00 0.00 0.00 3.36
613 621 3.604582 GTCTCAAACCATCCTCTCCTTG 58.395 50.000 0.00 0.00 0.00 3.61
622 630 3.212685 CATCCTCTCCTTGATGCCTTTC 58.787 50.000 0.00 0.00 32.71 2.62
626 634 1.004745 TCTCCTTGATGCCTTTCCCAC 59.995 52.381 0.00 0.00 0.00 4.61
628 636 0.322456 CCTTGATGCCTTTCCCACGA 60.322 55.000 0.00 0.00 0.00 4.35
638 646 1.067212 CTTTCCCACGATCTACTCCGG 59.933 57.143 0.00 0.00 0.00 5.14
639 647 1.389609 TTCCCACGATCTACTCCGGC 61.390 60.000 0.00 0.00 0.00 6.13
640 648 1.828660 CCCACGATCTACTCCGGCT 60.829 63.158 0.00 0.00 0.00 5.52
641 649 0.536687 CCCACGATCTACTCCGGCTA 60.537 60.000 0.00 0.00 0.00 3.93
642 650 1.315690 CCACGATCTACTCCGGCTAA 58.684 55.000 0.00 0.00 0.00 3.09
690 698 0.107017 ATCATGGAAGGCAAGGACCG 60.107 55.000 0.00 0.00 33.69 4.79
716 724 3.050619 CAATTGGCGACCGATAGAGTAC 58.949 50.000 0.00 0.00 39.76 2.73
774 1090 5.128008 TGACACGAGTATCATGGGTAATTCA 59.872 40.000 0.00 0.00 33.17 2.57
1021 1342 2.645192 GCAAAATCCCCCACCACCG 61.645 63.158 0.00 0.00 0.00 4.94
1290 1643 2.535788 CGACCGCTACCTCTCCTCG 61.536 68.421 0.00 0.00 0.00 4.63
1587 1962 2.105128 GACGAGTCCATGGAGCGG 59.895 66.667 29.80 18.72 0.00 5.52
1616 1993 6.029346 CAGGGTATGCTTGATTCTGTTTTT 57.971 37.500 0.00 0.00 0.00 1.94
1617 1994 5.865552 CAGGGTATGCTTGATTCTGTTTTTG 59.134 40.000 0.00 0.00 0.00 2.44
1618 1995 5.539955 AGGGTATGCTTGATTCTGTTTTTGT 59.460 36.000 0.00 0.00 0.00 2.83
1619 1996 6.041979 AGGGTATGCTTGATTCTGTTTTTGTT 59.958 34.615 0.00 0.00 0.00 2.83
1620 1997 6.705825 GGGTATGCTTGATTCTGTTTTTGTTT 59.294 34.615 0.00 0.00 0.00 2.83
1621 1998 7.226523 GGGTATGCTTGATTCTGTTTTTGTTTT 59.773 33.333 0.00 0.00 0.00 2.43
1622 1999 8.611757 GGTATGCTTGATTCTGTTTTTGTTTTT 58.388 29.630 0.00 0.00 0.00 1.94
1623 2000 9.424659 GTATGCTTGATTCTGTTTTTGTTTTTG 57.575 29.630 0.00 0.00 0.00 2.44
1624 2001 7.432350 TGCTTGATTCTGTTTTTGTTTTTGT 57.568 28.000 0.00 0.00 0.00 2.83
1625 2002 7.869800 TGCTTGATTCTGTTTTTGTTTTTGTT 58.130 26.923 0.00 0.00 0.00 2.83
1626 2003 8.014517 TGCTTGATTCTGTTTTTGTTTTTGTTC 58.985 29.630 0.00 0.00 0.00 3.18
1629 2006 8.824159 TGATTCTGTTTTTGTTTTTGTTCTGA 57.176 26.923 0.00 0.00 0.00 3.27
1639 2016 6.507958 TGTTTTTGTTCTGACAGACATTGA 57.492 33.333 4.15 0.00 37.04 2.57
1672 2057 1.677576 TGCAAGTTCTTCTGTTGCCAG 59.322 47.619 3.98 0.00 44.90 4.85
1714 2110 1.511850 CATCACCACGAGCTTTCACA 58.488 50.000 0.00 0.00 0.00 3.58
1732 2135 7.517259 GCTTTCACACATTTTTCATCTTTCACC 60.517 37.037 0.00 0.00 0.00 4.02
1757 2170 4.142609 TCATGGTCAGACCTTATTCAGC 57.857 45.455 20.82 0.00 39.58 4.26
1779 2195 3.921119 TTCACTGCCTGCTATTTGTTG 57.079 42.857 0.00 0.00 0.00 3.33
1784 2200 2.091541 TGCCTGCTATTTGTTGCTACC 58.908 47.619 0.00 0.00 0.00 3.18
1823 2239 0.315568 AGCAGAGTTCTCGACACCAC 59.684 55.000 0.00 0.00 0.00 4.16
1841 2257 3.063045 ACCACGTTTCTTTGAACTCGTTC 59.937 43.478 2.92 2.92 39.91 3.95
1889 2323 5.094812 TGCGATCGTTGTAAAACGTAGTAT 58.905 37.500 17.41 4.05 45.00 2.12
1943 2377 2.295909 TCCCTTGCAATTTACACACTGC 59.704 45.455 0.00 0.00 35.32 4.40
1953 2388 0.874175 TACACACTGCACGTGACAGC 60.874 55.000 28.26 13.02 46.81 4.40
2099 2540 2.176889 TGTGTACTTCTCTGTAGGGCC 58.823 52.381 0.00 0.00 0.00 5.80
2111 2552 0.540454 GTAGGGCCGGAAAGTAGCTT 59.460 55.000 5.05 0.00 0.00 3.74
2247 2693 9.906660 TTTTCACATTTTTCTCATATGTACCAC 57.093 29.630 1.90 0.00 31.64 4.16
2304 2750 9.307121 CAGATTCTTACTATACTGGACAAACTG 57.693 37.037 0.00 0.00 0.00 3.16
2409 2994 0.833949 GGGAGGGAGATGAACCAGAC 59.166 60.000 0.00 0.00 0.00 3.51
2592 3178 3.529533 GCATAGGCACAGCAGGATATAG 58.470 50.000 0.00 0.00 40.72 1.31
2627 3213 7.201652 GCTACTAAATGTCATGGAGAAGAAACC 60.202 40.741 0.00 0.00 0.00 3.27
2921 4238 1.666872 GGTTTCCGTGTCCACCTCG 60.667 63.158 0.00 0.00 0.00 4.63
2923 4240 0.531311 GTTTCCGTGTCCACCTCGTT 60.531 55.000 0.00 0.00 0.00 3.85
2939 4256 0.179215 CGTTGACAAAGCGCTCCATC 60.179 55.000 12.06 9.21 0.00 3.51
2940 4257 1.160137 GTTGACAAAGCGCTCCATCT 58.840 50.000 12.06 0.00 0.00 2.90
2950 4267 2.432146 AGCGCTCCATCTTATCTCAACA 59.568 45.455 2.64 0.00 0.00 3.33
2958 4275 7.244886 TCCATCTTATCTCAACACTTGAAGA 57.755 36.000 0.00 0.00 39.58 2.87
2981 4298 5.352284 ACTGACGATATCTGAAGCGAATTT 58.648 37.500 0.34 0.00 0.00 1.82
2992 4309 1.226746 AGCGAATTTAGCGGGCATAC 58.773 50.000 0.00 0.00 40.04 2.39
3187 4507 2.763448 GGGAGCTGTCTTGTACATCTCT 59.237 50.000 0.00 0.00 46.21 3.10
3219 4539 1.317613 TTGTAGCACAAAGGCAGGTG 58.682 50.000 0.09 0.00 34.76 4.00
3222 4542 3.994853 GCACAAAGGCAGGTGGGC 61.995 66.667 5.56 0.07 43.80 5.36
3240 4560 4.022416 GTGGGCAACATTGACTGTTCATTA 60.022 41.667 0.00 0.00 44.99 1.90
3241 4561 4.586421 TGGGCAACATTGACTGTTCATTAA 59.414 37.500 0.00 0.00 44.99 1.40
3247 4567 8.603181 GCAACATTGACTGTTCATTAACTTTTT 58.397 29.630 0.00 0.00 44.99 1.94
3289 4609 7.360438 CCTGTAAGATTCAGTACAACTTCAAGC 60.360 40.741 0.00 0.00 34.07 4.01
3294 4614 3.740115 TCAGTACAACTTCAAGCTTCCC 58.260 45.455 0.00 0.00 0.00 3.97
3308 4628 4.965119 AGCTTCCCGTGATAAATTGAAC 57.035 40.909 0.00 0.00 0.00 3.18
3326 4646 0.603065 ACGGGCAAATTTTCTGCTCC 59.397 50.000 0.92 0.68 36.93 4.70
3327 4647 0.456653 CGGGCAAATTTTCTGCTCCG 60.457 55.000 12.79 12.79 42.76 4.63
3372 4692 2.312424 TAAATTTGGGCGAAAGGGGT 57.688 45.000 0.00 0.00 0.00 4.95
3414 4734 7.072177 TCAATGGACTCGTTATGATTTGTTC 57.928 36.000 0.00 0.00 0.00 3.18
3420 4740 6.089820 GGACTCGTTATGATTTGTTCGTTACA 59.910 38.462 0.00 0.00 34.12 2.41
3436 4779 6.603237 TCGTTACAATATTGGAGCTGATTG 57.397 37.500 19.37 0.75 35.77 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.943671 TGAAAGTTGGAGGGAAGTTCA 57.056 42.857 5.01 0.00 0.00 3.18
18 19 2.158475 TGCATGAAAGTTGGAGGGAAGT 60.158 45.455 0.00 0.00 0.00 3.01
26 27 3.094572 AGAGGGAATGCATGAAAGTTGG 58.905 45.455 0.00 0.00 0.00 3.77
27 28 3.760151 TGAGAGGGAATGCATGAAAGTTG 59.240 43.478 0.00 0.00 0.00 3.16
38 39 3.067742 GCCAAATCATGTGAGAGGGAATG 59.932 47.826 0.00 0.00 0.00 2.67
40 41 2.041485 TGCCAAATCATGTGAGAGGGAA 59.959 45.455 0.00 0.00 0.00 3.97
83 84 6.309389 AGGAATAAGAAAACGGGTCTACAT 57.691 37.500 0.00 0.00 0.00 2.29
90 91 5.447624 AACACAAGGAATAAGAAAACGGG 57.552 39.130 0.00 0.00 0.00 5.28
93 94 9.366216 ACAAGAAAACACAAGGAATAAGAAAAC 57.634 29.630 0.00 0.00 0.00 2.43
94 95 9.936759 AACAAGAAAACACAAGGAATAAGAAAA 57.063 25.926 0.00 0.00 0.00 2.29
103 104 5.975693 ACTCAAACAAGAAAACACAAGGA 57.024 34.783 0.00 0.00 0.00 3.36
107 108 6.861055 GTGAAGAACTCAAACAAGAAAACACA 59.139 34.615 0.00 0.00 35.22 3.72
108 109 6.308041 GGTGAAGAACTCAAACAAGAAAACAC 59.692 38.462 0.00 0.00 35.22 3.32
154 155 4.836825 TGAACAATTCAAAAGTGGCCAAA 58.163 34.783 7.24 0.00 36.59 3.28
185 186 9.725019 TCATGAACAAGAATTACTAGAACATGT 57.275 29.630 0.00 0.00 33.62 3.21
215 216 9.893305 CATAAAAACGAGGAGAAACAACTAATT 57.107 29.630 0.00 0.00 0.00 1.40
224 225 9.243637 CAAAAATCACATAAAAACGAGGAGAAA 57.756 29.630 0.00 0.00 0.00 2.52
231 232 9.400638 GATACACCAAAAATCACATAAAAACGA 57.599 29.630 0.00 0.00 0.00 3.85
233 234 9.705290 AGGATACACCAAAAATCACATAAAAAC 57.295 29.630 0.00 0.00 42.04 2.43
250 252 5.353394 TCAATCACAAGGTAGGATACACC 57.647 43.478 0.00 0.00 45.43 4.16
252 254 6.774673 TGTTTCAATCACAAGGTAGGATACA 58.225 36.000 0.00 0.00 45.43 2.29
253 255 7.336931 ACATGTTTCAATCACAAGGTAGGATAC 59.663 37.037 0.00 0.00 42.04 2.24
258 262 6.016360 TCCAACATGTTTCAATCACAAGGTAG 60.016 38.462 8.77 0.00 0.00 3.18
329 333 9.597999 CACTAAAGTAAACGTAATGGGTAAAAC 57.402 33.333 0.00 0.00 0.00 2.43
354 358 8.668510 AATGCAAACATTACAAAATAACACCA 57.331 26.923 0.00 0.00 44.78 4.17
365 369 7.204496 AGGTAACGTAAATGCAAACATTACA 57.796 32.000 14.17 0.00 44.22 2.41
368 372 8.426881 AAAAAGGTAACGTAAATGCAAACATT 57.573 26.923 0.00 0.00 46.06 2.71
394 398 6.998968 TCTTTAAGGACGTGTTTGGTTAAA 57.001 33.333 0.00 0.00 0.00 1.52
395 399 8.723311 CATATCTTTAAGGACGTGTTTGGTTAA 58.277 33.333 0.00 0.00 0.00 2.01
415 419 7.592938 TCAAAATGAACGAAGCAAACATATCT 58.407 30.769 0.00 0.00 0.00 1.98
432 440 4.974368 AACAGACCACGTTTCAAAATGA 57.026 36.364 1.84 0.00 0.00 2.57
437 445 2.608546 CCGTAAACAGACCACGTTTCAA 59.391 45.455 0.00 0.00 37.69 2.69
445 453 3.478857 AATGACACCGTAAACAGACCA 57.521 42.857 0.00 0.00 0.00 4.02
454 462 5.349270 CCTTTCGTTATCAAATGACACCGTA 59.651 40.000 0.00 0.00 30.24 4.02
514 522 6.630444 ATTGAGCTGCTAATTGACAATAGG 57.370 37.500 0.15 0.00 0.00 2.57
520 528 8.097078 AGATTCATATTGAGCTGCTAATTGAC 57.903 34.615 0.15 0.00 0.00 3.18
523 531 8.865420 ATGAGATTCATATTGAGCTGCTAATT 57.135 30.769 0.15 0.00 34.88 1.40
534 542 4.074259 TGGGCGGAATGAGATTCATATTG 58.926 43.478 0.00 0.00 41.03 1.90
545 553 1.376683 CGGTTTCTGGGCGGAATGA 60.377 57.895 0.00 0.00 0.00 2.57
563 571 2.930040 CGGTATCGATATCCCATTGCAC 59.070 50.000 8.66 0.00 39.00 4.57
577 585 0.042013 GAGACGTGAGAGCGGTATCG 60.042 60.000 4.63 0.00 39.81 2.92
583 591 0.318699 TGGTTTGAGACGTGAGAGCG 60.319 55.000 0.00 0.00 37.94 5.03
590 598 1.550976 GGAGAGGATGGTTTGAGACGT 59.449 52.381 0.00 0.00 0.00 4.34
604 612 1.409381 GGGAAAGGCATCAAGGAGAGG 60.409 57.143 0.00 0.00 0.00 3.69
612 620 0.911769 AGATCGTGGGAAAGGCATCA 59.088 50.000 0.00 0.00 0.00 3.07
613 621 2.103263 AGTAGATCGTGGGAAAGGCATC 59.897 50.000 0.00 0.00 0.00 3.91
622 630 0.536687 TAGCCGGAGTAGATCGTGGG 60.537 60.000 5.05 0.00 0.00 4.61
626 634 1.663445 CGCTTTAGCCGGAGTAGATCG 60.663 57.143 5.05 0.00 37.91 3.69
628 636 1.337387 GACGCTTTAGCCGGAGTAGAT 59.663 52.381 5.05 0.00 37.91 1.98
638 646 0.863144 TTTCGGTGTGACGCTTTAGC 59.137 50.000 0.00 0.00 37.78 3.09
639 647 1.136721 CGTTTCGGTGTGACGCTTTAG 60.137 52.381 0.00 0.00 0.00 1.85
640 648 0.854062 CGTTTCGGTGTGACGCTTTA 59.146 50.000 0.00 0.00 0.00 1.85
641 649 0.806884 TCGTTTCGGTGTGACGCTTT 60.807 50.000 0.00 0.00 36.77 3.51
642 650 0.599204 ATCGTTTCGGTGTGACGCTT 60.599 50.000 0.00 0.00 36.77 4.68
690 698 2.340453 ATCGGTCGCCAATTGCATGC 62.340 55.000 11.82 11.82 41.33 4.06
706 714 8.151141 TGTAATAGTGGTTCTGTACTCTATCG 57.849 38.462 0.00 0.00 0.00 2.92
745 753 3.618594 CCCATGATACTCGTGTCACAAAG 59.381 47.826 3.42 2.44 33.59 2.77
748 756 2.176045 ACCCATGATACTCGTGTCACA 58.824 47.619 3.42 0.00 33.59 3.58
749 757 2.961526 ACCCATGATACTCGTGTCAC 57.038 50.000 0.00 0.00 33.59 3.67
761 1077 5.825532 TCTTGTTGGATGAATTACCCATGA 58.174 37.500 0.00 0.00 0.00 3.07
774 1090 7.669722 TGGTTAGATTTTAGCTTCTTGTTGGAT 59.330 33.333 0.00 0.00 0.00 3.41
950 1271 1.723288 GAGTGGGAAGGGGATAGGAG 58.277 60.000 0.00 0.00 0.00 3.69
951 1272 0.267960 GGAGTGGGAAGGGGATAGGA 59.732 60.000 0.00 0.00 0.00 2.94
952 1273 0.768609 GGGAGTGGGAAGGGGATAGG 60.769 65.000 0.00 0.00 0.00 2.57
998 1319 4.669809 TGGGGGATTTTGCGCCGT 62.670 61.111 4.18 0.00 43.74 5.68
1021 1342 1.298859 AACATCCTCGCTGGTTTCGC 61.299 55.000 0.00 0.00 37.07 4.70
1026 1347 2.990479 GGGAACATCCTCGCTGGT 59.010 61.111 0.00 0.00 36.57 4.00
1206 1559 4.457496 CGGGTCAGCATGTCCGCT 62.457 66.667 0.00 0.00 45.67 5.52
1290 1643 4.451150 TCGGCGATGGTGGTGAGC 62.451 66.667 4.99 0.00 0.00 4.26
1347 1700 0.457853 CGCATCGTTTCGAGGGAGAA 60.458 55.000 6.01 0.00 39.91 2.87
1348 1701 1.138883 CGCATCGTTTCGAGGGAGA 59.861 57.895 6.01 0.00 39.91 3.71
1616 1993 6.321717 GTCAATGTCTGTCAGAACAAAAACA 58.678 36.000 3.51 0.00 34.24 2.83
1617 1994 5.452302 CGTCAATGTCTGTCAGAACAAAAAC 59.548 40.000 3.51 4.84 34.24 2.43
1618 1995 5.123186 ACGTCAATGTCTGTCAGAACAAAAA 59.877 36.000 3.51 0.00 34.24 1.94
1619 1996 4.634004 ACGTCAATGTCTGTCAGAACAAAA 59.366 37.500 3.51 0.00 34.24 2.44
1620 1997 4.033932 CACGTCAATGTCTGTCAGAACAAA 59.966 41.667 3.51 0.00 34.24 2.83
1621 1998 3.555547 CACGTCAATGTCTGTCAGAACAA 59.444 43.478 3.51 0.00 34.24 2.83
1622 1999 3.123050 CACGTCAATGTCTGTCAGAACA 58.877 45.455 3.51 5.90 0.00 3.18
1623 2000 3.123804 ACACGTCAATGTCTGTCAGAAC 58.876 45.455 3.51 0.00 0.00 3.01
1624 2001 3.452755 ACACGTCAATGTCTGTCAGAA 57.547 42.857 3.51 0.00 0.00 3.02
1625 2002 3.452755 AACACGTCAATGTCTGTCAGA 57.547 42.857 0.00 0.00 30.55 3.27
1626 2003 3.119628 CGTAACACGTCAATGTCTGTCAG 59.880 47.826 0.00 0.00 36.74 3.51
1629 2006 2.034939 TCCGTAACACGTCAATGTCTGT 59.965 45.455 0.00 0.00 40.58 3.41
1639 2016 1.873698 ACTTGCATTCCGTAACACGT 58.126 45.000 0.00 0.00 40.58 4.49
1649 2026 3.243501 TGGCAACAGAAGAACTTGCATTC 60.244 43.478 4.18 0.00 46.17 2.67
1714 2110 7.111247 TGAACTGGTGAAAGATGAAAAATGT 57.889 32.000 0.00 0.00 0.00 2.71
1732 2135 5.491070 TGAATAAGGTCTGACCATGAACTG 58.509 41.667 27.48 0.00 41.95 3.16
1757 2170 4.171005 CAACAAATAGCAGGCAGTGAATG 58.829 43.478 0.00 0.00 0.00 2.67
1779 2195 4.617875 AGCAACGATGGTGGTAGC 57.382 55.556 0.00 0.00 35.55 3.58
1813 2229 2.198406 TCAAAGAAACGTGGTGTCGAG 58.802 47.619 0.00 0.00 34.70 4.04
1823 2239 2.285371 TGCGAACGAGTTCAAAGAAACG 60.285 45.455 15.20 1.76 39.46 3.60
1841 2257 4.380531 AGGTAGTATTGAATGGTCATGCG 58.619 43.478 0.00 0.00 32.48 4.73
1943 2377 2.052237 GCAAACGGCTGTCACGTG 60.052 61.111 9.94 9.94 44.83 4.49
1953 2388 2.489971 TGTAACCAGAGAAGCAAACGG 58.510 47.619 0.00 0.00 0.00 4.44
2247 2693 5.805486 TGAATCGGTTAGACAAAGATCTTCG 59.195 40.000 8.78 0.00 0.00 3.79
2304 2750 1.209261 CTCTGCTCCCTTTCCTCCTTC 59.791 57.143 0.00 0.00 0.00 3.46
2497 3082 0.407139 AGCTTGGTCAGGGCAAGAAT 59.593 50.000 0.00 0.00 0.00 2.40
2592 3178 4.566004 TGACATTTAGTAGCACACAGGAC 58.434 43.478 0.00 0.00 0.00 3.85
2627 3213 6.980397 ACAGTTTCTTTTTACTTGCCATCTTG 59.020 34.615 0.00 0.00 0.00 3.02
2921 4238 1.160137 AGATGGAGCGCTTTGTCAAC 58.840 50.000 13.26 7.22 0.00 3.18
2923 4240 2.760634 TAAGATGGAGCGCTTTGTCA 57.239 45.000 13.26 8.80 0.00 3.58
2939 4256 6.088749 CGTCAGTCTTCAAGTGTTGAGATAAG 59.911 42.308 0.00 0.00 41.38 1.73
2940 4257 5.920840 CGTCAGTCTTCAAGTGTTGAGATAA 59.079 40.000 0.00 0.00 41.38 1.75
2950 4267 6.516739 TTCAGATATCGTCAGTCTTCAAGT 57.483 37.500 0.00 0.00 0.00 3.16
2958 4275 4.576216 ATTCGCTTCAGATATCGTCAGT 57.424 40.909 0.00 0.00 0.00 3.41
2992 4309 4.649088 TCTGGTGAACATGGTACGATAG 57.351 45.455 0.00 0.00 46.19 2.08
3152 4472 3.573967 ACAGCTCCCAAACCAAATACAAG 59.426 43.478 0.00 0.00 0.00 3.16
3187 4507 7.277539 CCTTTGTGCTACAAAACATTTTGAAGA 59.722 33.333 20.95 7.29 46.15 2.87
3215 4535 0.185901 ACAGTCAATGTTGCCCACCT 59.814 50.000 0.00 0.00 39.96 4.00
3247 4567 1.770110 AGGACAGGACTGCCACCAA 60.770 57.895 12.88 0.00 36.29 3.67
3248 4568 2.122413 AGGACAGGACTGCCACCA 60.122 61.111 12.88 0.00 36.29 4.17
3255 4575 4.421131 ACTGAATCTTACAGGACAGGACT 58.579 43.478 0.00 0.00 39.38 3.85
3289 4609 4.273005 CCGTTCAATTTATCACGGGAAG 57.727 45.455 0.00 0.00 46.92 3.46
3294 4614 3.479505 TTGCCCGTTCAATTTATCACG 57.520 42.857 0.00 0.00 0.00 4.35
3308 4628 0.456653 CGGAGCAGAAAATTTGCCCG 60.457 55.000 12.79 12.79 43.52 6.13
3311 4631 3.288809 AGAACGGAGCAGAAAATTTGC 57.711 42.857 0.00 0.00 41.83 3.68
3326 4646 1.710249 CGCACTGCATTTTGAAGAACG 59.290 47.619 1.11 0.00 0.00 3.95
3327 4647 2.053627 CCGCACTGCATTTTGAAGAAC 58.946 47.619 1.11 0.00 0.00 3.01
3372 4692 5.528690 CCATTGAATTTGCAGCTAGCTACTA 59.471 40.000 18.86 5.87 45.94 1.82
3414 4734 6.363577 ACAATCAGCTCCAATATTGTAACG 57.636 37.500 14.25 0.00 39.96 3.18
3420 4740 7.175641 GCCTAACATACAATCAGCTCCAATATT 59.824 37.037 0.00 0.00 0.00 1.28
3436 4779 4.392138 AGTTTCTTCAAGCGCCTAACATAC 59.608 41.667 2.29 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.