Multiple sequence alignment - TraesCS1B01G351000

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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 TraesCS1B01G351000 chr1B 100.000 2799 0 0 1 2799 581411194 581413992 0.000000e+00 5169.0
1 TraesCS1B01G351000 chr1D 93.504 1832 87 18 898 2718 430466426 430468236 0.000000e+00 2695.0
2 TraesCS1B01G351000 chr1D 89.493 552 49 7 1 547 430465503 430466050 0.000000e+00 689.0
3 TraesCS1B01G351000 chr1D 84.031 382 26 11 530 882 430466064 430466439 4.470000e-88 335.0
4 TraesCS1B01G351000 chr1A 95.399 1065 33 3 919 1983 528063650 528064698 0.000000e+00 1681.0
5 TraesCS1B01G351000 chr1A 91.240 742 58 4 2015 2752 528064698 528065436 0.000000e+00 1003.0
6 TraesCS1B01G351000 chr1A 97.059 34 1 0 2766 2799 528065483 528065516 1.080000e-04 58.4
7 TraesCS1B01G351000 chrUn 85.194 412 49 9 2272 2674 110690533 110690941 2.010000e-111 412.0
8 TraesCS1B01G351000 chrUn 82.529 435 62 12 2200 2620 110699692 110700126 1.220000e-98 370.0
9 TraesCS1B01G351000 chrUn 84.751 341 45 4 2304 2637 110687551 110687891 4.470000e-88 335.0
10 TraesCS1B01G351000 chrUn 90.909 99 5 1 1582 1680 104133863 104133769 2.260000e-26 130.0
11 TraesCS1B01G351000 chr4B 87.500 336 40 2 2304 2637 660683372 660683707 1.220000e-103 387.0
12 TraesCS1B01G351000 chr4B 88.179 313 36 1 2326 2637 660519842 660519530 3.400000e-99 372.0
13 TraesCS1B01G351000 chr5A 86.111 360 36 3 2340 2688 700785207 700785563 2.630000e-100 375.0
14 TraesCS1B01G351000 chr5A 86.228 334 42 4 2307 2637 700694851 700695183 2.650000e-95 359.0
15 TraesCS1B01G351000 chr7B 84.496 258 34 5 995 1252 80514387 80514136 1.660000e-62 250.0
16 TraesCS1B01G351000 chr7B 85.321 109 9 4 1572 1678 498879301 498879198 3.810000e-19 106.0
17 TraesCS1B01G351000 chr7D 85.020 247 29 7 995 1240 119105993 119105754 7.740000e-61 244.0
18 TraesCS1B01G351000 chr3B 90.909 99 5 1 1582 1680 40134922 40135016 2.260000e-26 130.0
19 TraesCS1B01G351000 chr3B 86.916 107 9 2 1572 1678 828800801 828800902 6.340000e-22 115.0
20 TraesCS1B01G351000 chr2D 88.991 109 7 2 1572 1680 133780427 133780530 2.260000e-26 130.0
21 TraesCS1B01G351000 chr3A 88.073 109 8 2 1572 1680 52048729 52048832 1.050000e-24 124.0


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 TraesCS1B01G351000 chr1B 581411194 581413992 2798 False 5169.000000 5169 100.000000 1 2799 1 chr1B.!!$F1 2798
1 TraesCS1B01G351000 chr1D 430465503 430468236 2733 False 1239.666667 2695 89.009333 1 2718 3 chr1D.!!$F1 2717
2 TraesCS1B01G351000 chr1A 528063650 528065516 1866 False 914.133333 1681 94.566000 919 2799 3 chr1A.!!$F1 1880
3 TraesCS1B01G351000 chrUn 110687551 110690941 3390 False 373.500000 412 84.972500 2272 2674 2 chrUn.!!$F2 402

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
712 765 0.319383 CCGGCTGGATTCAGATCTCG 60.319 60.0 5.28 2.52 43.49 4.04 F
1483 1547 0.179045 ACCACTTCTGCGCTCACTTT 60.179 50.0 9.73 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 1703 0.326264 TCCTTGCTGCTTCCTTCTCC 59.674 55.000 0.00 0.0 0.0 3.71 R
2478 5559 1.532437 CGACACAATTTCAGCTGCAGA 59.468 47.619 20.43 0.0 0.0 4.26 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
64 65 6.759356 AGTTGTGTTACTTTGTATTTTTGCCC 59.241 34.615 0.00 0.00 0.00 5.36
65 66 6.472686 TGTGTTACTTTGTATTTTTGCCCT 57.527 33.333 0.00 0.00 0.00 5.19
66 67 6.508777 TGTGTTACTTTGTATTTTTGCCCTC 58.491 36.000 0.00 0.00 0.00 4.30
193 197 9.677567 TGTTATTCTCTACAAATTTTGAGTTGC 57.322 29.630 15.81 0.00 0.00 4.17
199 203 8.632679 TCTCTACAAATTTTGAGTTGCTCATTT 58.367 29.630 15.81 0.00 40.39 2.32
305 310 9.732130 ATTTAGAAGGATGAATATAGCCAGAAC 57.268 33.333 0.00 0.00 0.00 3.01
352 357 3.706698 ACACATGATGGTCGATCTAACG 58.293 45.455 0.00 0.00 31.55 3.18
373 379 2.475200 GCGGTAGCACCATTTTGATC 57.525 50.000 6.21 0.00 44.35 2.92
374 380 1.268032 GCGGTAGCACCATTTTGATCG 60.268 52.381 6.21 0.00 44.35 3.69
376 382 2.285220 CGGTAGCACCATTTTGATCGAG 59.715 50.000 6.21 0.00 38.47 4.04
382 388 4.107622 GCACCATTTTGATCGAGGAAATG 58.892 43.478 17.34 17.34 39.36 2.32
392 398 6.182039 TGATCGAGGAAATGACACAAAATC 57.818 37.500 0.00 0.00 0.00 2.17
415 421 4.097418 AGTACAACTGAGGCTAGGTCATT 58.903 43.478 0.00 0.00 0.00 2.57
427 433 3.621715 GCTAGGTCATTAGAAAACCACCG 59.378 47.826 0.00 0.00 35.43 4.94
428 434 2.433436 AGGTCATTAGAAAACCACCGC 58.567 47.619 0.00 0.00 35.43 5.68
430 436 1.129811 GTCATTAGAAAACCACCGCCG 59.870 52.381 0.00 0.00 0.00 6.46
445 451 1.833434 CGCCGAACGCTAAAACCACA 61.833 55.000 0.00 0.00 34.21 4.17
447 453 1.727857 GCCGAACGCTAAAACCACATG 60.728 52.381 0.00 0.00 0.00 3.21
457 463 4.262420 GCTAAAACCACATGAAACCACCAT 60.262 41.667 0.00 0.00 0.00 3.55
460 466 6.432403 AAAACCACATGAAACCACCATAAT 57.568 33.333 0.00 0.00 0.00 1.28
498 504 1.328374 ACGTAACACTTTCGCGCTTTT 59.672 42.857 5.56 0.00 0.00 2.27
504 510 1.166531 ACTTTCGCGCTTTTGCCTCT 61.167 50.000 5.56 0.00 43.93 3.69
510 516 0.596082 GCGCTTTTGCCTCTTGGTTA 59.404 50.000 0.00 0.00 43.93 2.85
580 617 3.059603 GCGGTTTGCTAATCCGAGA 57.940 52.632 19.63 0.00 46.05 4.04
581 618 1.583054 GCGGTTTGCTAATCCGAGAT 58.417 50.000 19.63 0.00 46.05 2.75
582 619 1.261619 GCGGTTTGCTAATCCGAGATG 59.738 52.381 19.63 0.00 46.05 2.90
583 620 2.821546 CGGTTTGCTAATCCGAGATGA 58.178 47.619 13.47 0.00 46.05 2.92
584 621 3.393800 CGGTTTGCTAATCCGAGATGAT 58.606 45.455 13.47 0.00 46.05 2.45
587 624 4.999950 GGTTTGCTAATCCGAGATGATGAT 59.000 41.667 0.00 0.00 0.00 2.45
588 625 5.471456 GGTTTGCTAATCCGAGATGATGATT 59.529 40.000 0.00 0.00 33.54 2.57
589 626 6.650807 GGTTTGCTAATCCGAGATGATGATTA 59.349 38.462 0.00 0.00 31.55 1.75
591 628 7.895975 TTGCTAATCCGAGATGATGATTAAG 57.104 36.000 0.00 0.00 32.31 1.85
592 629 5.871524 TGCTAATCCGAGATGATGATTAAGC 59.128 40.000 0.00 0.00 32.31 3.09
593 630 5.871524 GCTAATCCGAGATGATGATTAAGCA 59.128 40.000 0.00 0.00 32.31 3.91
604 649 3.788333 TGATTAAGCAAAGCATCCAGC 57.212 42.857 0.00 0.00 46.19 4.85
626 671 2.855209 AGCTGCATTGACTTGACTCT 57.145 45.000 1.02 0.00 0.00 3.24
627 672 2.424557 AGCTGCATTGACTTGACTCTG 58.575 47.619 1.02 0.00 0.00 3.35
633 678 4.934001 TGCATTGACTTGACTCTGATTCTC 59.066 41.667 0.00 0.00 0.00 2.87
639 684 3.192422 ACTTGACTCTGATTCTCTCCACG 59.808 47.826 0.00 0.00 0.00 4.94
699 752 3.531207 TGGCTCGATCTCCGGCTG 61.531 66.667 0.00 0.00 39.14 4.85
712 765 0.319383 CCGGCTGGATTCAGATCTCG 60.319 60.000 5.28 2.52 43.49 4.04
719 772 5.160641 GCTGGATTCAGATCTCGACTATTC 58.839 45.833 4.75 0.00 43.49 1.75
756 819 1.990563 CGTTCTAATCCGAGTGCGTTT 59.009 47.619 0.00 0.00 35.23 3.60
789 852 1.971695 CTGGTGGCCCCGAAAACTC 60.972 63.158 0.00 0.00 35.15 3.01
790 853 2.114411 GGTGGCCCCGAAAACTCA 59.886 61.111 0.00 0.00 0.00 3.41
856 920 1.192757 CACCGTACGAAACAAATCGCA 59.807 47.619 18.76 0.00 46.51 5.10
909 973 7.831691 TTTTTGAGGTGAATTAATCCAGTGA 57.168 32.000 0.00 0.00 0.00 3.41
910 974 8.421249 TTTTTGAGGTGAATTAATCCAGTGAT 57.579 30.769 0.00 0.00 0.00 3.06
911 975 8.421249 TTTTGAGGTGAATTAATCCAGTGATT 57.579 30.769 0.00 0.00 43.56 2.57
912 976 7.395190 TTGAGGTGAATTAATCCAGTGATTG 57.605 36.000 0.00 0.00 41.31 2.67
931 995 1.202806 TGGTCACCTCTTCAGCAAAGG 60.203 52.381 0.00 0.00 35.54 3.11
932 996 1.528129 GTCACCTCTTCAGCAAAGGG 58.472 55.000 0.00 0.00 35.54 3.95
933 997 1.072331 GTCACCTCTTCAGCAAAGGGA 59.928 52.381 0.53 0.00 37.71 4.20
937 1001 2.290577 ACCTCTTCAGCAAAGGGACATC 60.291 50.000 0.53 0.00 37.71 3.06
1275 1339 2.329379 GACTTCTTCTACCAGTGCGTG 58.671 52.381 0.00 0.00 0.00 5.34
1373 1437 1.142778 GAGAGGTCGATGCGTTCTGC 61.143 60.000 0.00 0.00 46.70 4.26
1390 1454 1.654137 GCGAGGTGTTGTTTGCACG 60.654 57.895 0.00 0.00 37.70 5.34
1412 1476 5.204673 GACGTTTCGATTATTTGCTCTGT 57.795 39.130 0.00 0.00 0.00 3.41
1426 1490 4.808414 TGCTCTGTACTTCTGCTTATGT 57.192 40.909 0.00 0.00 0.00 2.29
1483 1547 0.179045 ACCACTTCTGCGCTCACTTT 60.179 50.000 9.73 0.00 0.00 2.66
1514 1578 0.973632 ATCAACCCGTGAGTGCAGTA 59.026 50.000 0.00 0.00 40.43 2.74
1577 1641 8.729756 AGTTGATGACAATCGATTCATGTTTTA 58.270 29.630 15.60 1.78 38.32 1.52
1578 1642 9.340695 GTTGATGACAATCGATTCATGTTTTAA 57.659 29.630 15.60 2.79 38.32 1.52
1597 1661 7.483375 TGTTTTAATTACACGATTGCAGCATAC 59.517 33.333 0.00 0.00 0.00 2.39
1639 1703 3.889538 TGTATGGGGATCTAACAGACGAG 59.110 47.826 0.00 0.00 0.00 4.18
1663 1727 2.197283 AGGAAGCAGCAAGGAAGAAG 57.803 50.000 0.00 0.00 0.00 2.85
1685 1749 4.020128 AGGTAGAGGAAATGGACAGTGAAC 60.020 45.833 0.00 0.00 0.00 3.18
1687 1751 5.187186 GGTAGAGGAAATGGACAGTGAACTA 59.813 44.000 0.00 0.00 0.00 2.24
1711 1775 2.902486 TGGACTGCAGTTTGAGATCTCT 59.098 45.455 22.65 0.00 0.00 3.10
1802 1866 2.028112 CACCTTGGGAAGAAGTGATCGA 60.028 50.000 0.00 0.00 0.00 3.59
1906 1970 5.989551 TGATGTAATGATGTGAATGTCCG 57.010 39.130 0.00 0.00 0.00 4.79
1960 2024 0.331616 ACATTGGACCTACCTTGGGC 59.668 55.000 0.00 0.00 39.86 5.36
2024 2088 9.965824 CCAATATTGCCTTTCGTCTAAAATATT 57.034 29.630 10.11 0.00 0.00 1.28
2033 2099 8.463607 CCTTTCGTCTAAAATATTTTGGGCTTA 58.536 33.333 21.76 10.62 32.03 3.09
2039 2105 9.582431 GTCTAAAATATTTTGGGCTTACTTTCC 57.418 33.333 21.19 0.00 31.60 3.13
2086 2152 8.230486 CAGTGTGTTGATTTATTCAGTAGAACC 58.770 37.037 0.00 0.00 36.39 3.62
2088 2154 9.431887 GTGTGTTGATTTATTCAGTAGAACCTA 57.568 33.333 0.00 0.00 36.39 3.08
2170 2239 9.803130 GTAAAAGTCCGAGTTTATCTTTTGTAC 57.197 33.333 1.55 0.00 38.31 2.90
2198 2267 6.485984 CCTCAAGAATACTTTCCATGATCAGG 59.514 42.308 0.09 0.00 33.70 3.86
2213 2282 8.663167 TCCATGATCAGGTGATTAACTAATGAT 58.337 33.333 6.62 0.00 34.37 2.45
2235 2304 9.976776 ATGATTGAGATATATTCCATCAAGCTT 57.023 29.630 14.60 0.00 37.23 3.74
2334 2409 6.153851 TGGTACAACACTACAGTACAGCATAT 59.846 38.462 0.00 0.00 39.78 1.78
2406 5487 0.322187 GCCTAAACCTTCTTCCGCCA 60.322 55.000 0.00 0.00 0.00 5.69
2478 5559 0.666374 GGTACTGCCGTGCAAAGTTT 59.334 50.000 0.00 0.00 38.41 2.66
2490 5571 2.166050 TGCAAAGTTTCTGCAGCTGAAA 59.834 40.909 20.43 20.29 44.67 2.69
2520 5601 3.784338 CACATCTGGTGCAAAAACTGTT 58.216 40.909 0.00 0.00 41.36 3.16
2613 5694 1.364626 CTACAAGCTCTTGGCCTGCG 61.365 60.000 3.32 0.00 44.45 5.18
2674 5774 7.287696 AGAGTAATTCAACTTGGTGGAAACATT 59.712 33.333 0.00 0.00 46.14 2.71
2690 5796 7.429340 GTGGAAACATTTAGTCATTTATCTGCG 59.571 37.037 0.00 0.00 46.14 5.18
2692 5798 8.345565 GGAAACATTTAGTCATTTATCTGCGAT 58.654 33.333 0.00 0.00 0.00 4.58
2695 5801 7.633621 ACATTTAGTCATTTATCTGCGATGTG 58.366 34.615 0.00 0.06 0.00 3.21
2722 5828 7.012044 GTCTACTTTGTTCAGTTCTAGGCAAAA 59.988 37.037 0.00 0.00 0.00 2.44
2726 5832 4.787551 TGTTCAGTTCTAGGCAAAAAGGA 58.212 39.130 0.00 0.00 0.00 3.36
2763 5896 9.944079 ATAATCTGCTGTATATGTATAGGGAGT 57.056 33.333 0.00 0.00 0.00 3.85
2765 5898 6.552932 TCTGCTGTATATGTATAGGGAGTGT 58.447 40.000 0.00 0.00 0.00 3.55
2767 5900 7.610692 TCTGCTGTATATGTATAGGGAGTGTAC 59.389 40.741 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 9.724839 GCAAAAATACAAAGTAACACAACTAGA 57.275 29.630 0.00 0.00 0.00 2.43
177 181 7.593273 CGGTAAATGAGCAACTCAAAATTTGTA 59.407 33.333 5.56 0.00 44.04 2.41
178 182 6.420604 CGGTAAATGAGCAACTCAAAATTTGT 59.579 34.615 5.56 0.00 44.04 2.83
182 186 4.764823 TCCGGTAAATGAGCAACTCAAAAT 59.235 37.500 0.00 0.00 44.04 1.82
193 197 8.986477 AAATGAAAGAAATTCCGGTAAATGAG 57.014 30.769 0.00 0.00 37.22 2.90
279 284 9.732130 GTTCTGGCTATATTCATCCTTCTAAAT 57.268 33.333 0.00 0.00 0.00 1.40
324 329 7.630242 AGATCGACCATCATGTGTTTAAAAT 57.370 32.000 0.00 0.00 33.29 1.82
332 337 3.964909 TCGTTAGATCGACCATCATGTG 58.035 45.455 0.00 0.00 34.85 3.21
341 346 1.659771 GCTACCGCTCGTTAGATCGAC 60.660 57.143 0.00 0.00 38.15 4.20
352 357 1.448985 TCAAAATGGTGCTACCGCTC 58.551 50.000 0.00 0.00 42.58 5.03
358 364 3.904800 TCCTCGATCAAAATGGTGCTA 57.095 42.857 0.00 0.00 0.00 3.49
366 372 6.384258 TTTGTGTCATTTCCTCGATCAAAA 57.616 33.333 0.00 0.00 0.00 2.44
368 374 6.206438 TGATTTTGTGTCATTTCCTCGATCAA 59.794 34.615 0.00 0.00 0.00 2.57
370 376 6.128172 ACTGATTTTGTGTCATTTCCTCGATC 60.128 38.462 0.00 0.00 0.00 3.69
371 377 5.707298 ACTGATTTTGTGTCATTTCCTCGAT 59.293 36.000 0.00 0.00 0.00 3.59
373 379 5.362556 ACTGATTTTGTGTCATTTCCTCG 57.637 39.130 0.00 0.00 0.00 4.63
374 380 7.202016 TGTACTGATTTTGTGTCATTTCCTC 57.798 36.000 0.00 0.00 0.00 3.71
376 382 7.425606 AGTTGTACTGATTTTGTGTCATTTCC 58.574 34.615 0.00 0.00 0.00 3.13
412 418 1.444836 TCGGCGGTGGTTTTCTAATG 58.555 50.000 7.21 0.00 0.00 1.90
415 421 0.945265 CGTTCGGCGGTGGTTTTCTA 60.945 55.000 7.21 0.00 36.85 2.10
427 433 0.519961 ATGTGGTTTTAGCGTTCGGC 59.480 50.000 0.00 0.00 44.05 5.54
428 434 1.801771 TCATGTGGTTTTAGCGTTCGG 59.198 47.619 0.00 0.00 0.00 4.30
430 436 3.978855 GGTTTCATGTGGTTTTAGCGTTC 59.021 43.478 0.00 0.00 0.00 3.95
445 451 2.771372 GCCCCAATTATGGTGGTTTCAT 59.229 45.455 0.00 0.00 46.01 2.57
447 453 2.168313 CTGCCCCAATTATGGTGGTTTC 59.832 50.000 0.00 0.00 46.01 2.78
457 463 0.840617 TCGCATACCTGCCCCAATTA 59.159 50.000 0.00 0.00 46.07 1.40
460 466 2.270850 GTCGCATACCTGCCCCAA 59.729 61.111 0.00 0.00 46.07 4.12
498 504 2.492881 TCGATTACGTAACCAAGAGGCA 59.507 45.455 10.81 0.00 38.51 4.75
526 532 6.361114 GTTTAGCAAAAGACTTAAGGACGAC 58.639 40.000 7.53 0.00 0.00 4.34
567 604 6.369890 GCTTAATCATCATCTCGGATTAGCAA 59.630 38.462 0.00 0.00 35.58 3.91
568 605 5.871524 GCTTAATCATCATCTCGGATTAGCA 59.128 40.000 0.00 0.00 35.58 3.49
569 606 5.871524 TGCTTAATCATCATCTCGGATTAGC 59.128 40.000 0.00 0.00 35.58 3.09
570 607 7.895975 TTGCTTAATCATCATCTCGGATTAG 57.104 36.000 0.00 0.00 35.58 1.73
571 608 7.095060 GCTTTGCTTAATCATCATCTCGGATTA 60.095 37.037 0.00 0.00 33.59 1.75
572 609 6.293845 GCTTTGCTTAATCATCATCTCGGATT 60.294 38.462 0.00 0.00 35.57 3.01
573 610 5.180868 GCTTTGCTTAATCATCATCTCGGAT 59.819 40.000 0.00 0.00 0.00 4.18
574 611 4.512944 GCTTTGCTTAATCATCATCTCGGA 59.487 41.667 0.00 0.00 0.00 4.55
576 613 5.413969 TGCTTTGCTTAATCATCATCTCG 57.586 39.130 0.00 0.00 0.00 4.04
577 614 6.016527 TGGATGCTTTGCTTAATCATCATCTC 60.017 38.462 13.86 7.07 39.85 2.75
578 615 5.831525 TGGATGCTTTGCTTAATCATCATCT 59.168 36.000 13.86 0.00 39.85 2.90
580 617 5.509163 GCTGGATGCTTTGCTTAATCATCAT 60.509 40.000 13.86 0.00 39.85 2.45
581 618 4.202080 GCTGGATGCTTTGCTTAATCATCA 60.202 41.667 13.86 4.53 39.85 3.07
582 619 4.296690 GCTGGATGCTTTGCTTAATCATC 58.703 43.478 7.16 7.16 38.21 2.92
583 620 3.243301 CGCTGGATGCTTTGCTTAATCAT 60.243 43.478 0.00 0.00 40.11 2.45
584 621 2.097954 CGCTGGATGCTTTGCTTAATCA 59.902 45.455 0.00 0.00 40.11 2.57
587 624 1.533625 ACGCTGGATGCTTTGCTTAA 58.466 45.000 0.00 0.00 40.11 1.85
588 625 2.279741 CTACGCTGGATGCTTTGCTTA 58.720 47.619 0.00 0.00 40.11 3.09
589 626 1.089920 CTACGCTGGATGCTTTGCTT 58.910 50.000 0.00 0.00 40.11 3.91
591 628 1.063166 GCTACGCTGGATGCTTTGC 59.937 57.895 0.00 0.00 40.11 3.68
592 629 2.772739 AGCTACGCTGGATGCTTTG 58.227 52.632 0.00 0.00 37.57 2.77
604 649 2.341257 AGTCAAGTCAATGCAGCTACG 58.659 47.619 0.00 0.00 0.00 3.51
639 684 4.822026 ACTGTAAGCTTGTGTATCCACTC 58.178 43.478 9.86 0.00 39.18 3.51
657 702 3.631686 TGCTGCAGTGATTAACAAACTGT 59.368 39.130 16.64 0.00 42.65 3.55
699 752 7.027161 GCTTAGAATAGTCGAGATCTGAATCC 58.973 42.308 0.00 0.00 31.78 3.01
712 765 9.694137 ACGAATAATTAGGTGCTTAGAATAGTC 57.306 33.333 0.00 0.00 0.00 2.59
789 852 1.001520 GGGGTCCCGGTTTTCAAATTG 59.998 52.381 0.48 0.00 0.00 2.32
790 853 1.344065 GGGGTCCCGGTTTTCAAATT 58.656 50.000 0.48 0.00 0.00 1.82
833 896 0.110554 ATTTGTTTCGTACGGTGCGC 60.111 50.000 16.52 0.00 0.00 6.09
840 903 2.230864 GTGCTGCGATTTGTTTCGTAC 58.769 47.619 0.00 0.00 41.16 3.67
841 904 1.195900 GGTGCTGCGATTTGTTTCGTA 59.804 47.619 0.00 0.00 41.16 3.43
842 905 0.040425 GGTGCTGCGATTTGTTTCGT 60.040 50.000 0.00 0.00 41.16 3.85
843 906 1.059657 CGGTGCTGCGATTTGTTTCG 61.060 55.000 0.00 0.00 41.99 3.46
844 907 0.729140 CCGGTGCTGCGATTTGTTTC 60.729 55.000 0.00 0.00 0.00 2.78
845 908 1.285641 CCGGTGCTGCGATTTGTTT 59.714 52.632 0.00 0.00 0.00 2.83
885 949 7.831691 TCACTGGATTAATTCACCTCAAAAA 57.168 32.000 0.00 0.00 0.00 1.94
886 950 8.306038 CAATCACTGGATTAATTCACCTCAAAA 58.694 33.333 0.00 0.00 41.78 2.44
887 951 7.829725 CAATCACTGGATTAATTCACCTCAAA 58.170 34.615 0.00 0.00 41.78 2.69
888 952 7.395190 CAATCACTGGATTAATTCACCTCAA 57.605 36.000 0.00 0.00 41.78 3.02
906 970 7.273361 CTTTGCTGAAGAGGTGACCAATCAC 62.273 48.000 3.63 0.00 44.86 3.06
907 971 1.699083 TGCTGAAGAGGTGACCAATCA 59.301 47.619 3.63 4.10 0.00 2.57
908 972 2.479566 TGCTGAAGAGGTGACCAATC 57.520 50.000 3.63 0.00 0.00 2.67
909 973 2.957402 TTGCTGAAGAGGTGACCAAT 57.043 45.000 3.63 0.00 0.00 3.16
910 974 2.575532 CTTTGCTGAAGAGGTGACCAA 58.424 47.619 3.63 0.00 37.57 3.67
911 975 1.202806 CCTTTGCTGAAGAGGTGACCA 60.203 52.381 3.63 0.00 37.57 4.02
912 976 1.528129 CCTTTGCTGAAGAGGTGACC 58.472 55.000 0.00 0.00 37.57 4.02
913 977 1.072331 TCCCTTTGCTGAAGAGGTGAC 59.928 52.381 2.50 0.00 37.57 3.67
931 995 0.744771 GTGGGAAGCCGAAGATGTCC 60.745 60.000 0.00 0.00 0.00 4.02
932 996 0.744771 GGTGGGAAGCCGAAGATGTC 60.745 60.000 0.00 0.00 0.00 3.06
933 997 1.299976 GGTGGGAAGCCGAAGATGT 59.700 57.895 0.00 0.00 0.00 3.06
937 1001 4.778143 CGGGGTGGGAAGCCGAAG 62.778 72.222 0.00 0.00 0.00 3.79
1275 1339 1.829096 GGGCTCGAGGAGGAGGTAC 60.829 68.421 15.58 0.00 34.56 3.34
1373 1437 0.315869 GTCGTGCAAACAACACCTCG 60.316 55.000 0.00 0.00 34.45 4.63
1381 1445 4.957363 CGAAACGTCGTGCAAACA 57.043 50.000 0.00 0.00 42.53 2.83
1390 1454 5.204673 ACAGAGCAAATAATCGAAACGTC 57.795 39.130 0.00 0.00 0.00 4.34
1412 1476 8.749354 TCAGATAACTTGACATAAGCAGAAGTA 58.251 33.333 0.00 0.00 0.00 2.24
1426 1490 5.181811 CACCTGCAACATTCAGATAACTTGA 59.818 40.000 0.00 0.00 33.54 3.02
1477 1541 4.705110 TGATCTCTGAAACCCAAAGTGA 57.295 40.909 0.00 0.00 0.00 3.41
1577 1641 5.513376 CATGTATGCTGCAATCGTGTAATT 58.487 37.500 6.36 0.00 0.00 1.40
1578 1642 5.099484 CATGTATGCTGCAATCGTGTAAT 57.901 39.130 6.36 0.00 0.00 1.89
1597 1661 1.381928 GGAGGCTGACATGTGGCATG 61.382 60.000 18.23 7.48 29.25 4.06
1609 1673 0.689623 GATCCCCATACAGGAGGCTG 59.310 60.000 0.00 0.00 41.22 4.85
1639 1703 0.326264 TCCTTGCTGCTTCCTTCTCC 59.674 55.000 0.00 0.00 0.00 3.71
1663 1727 4.020128 AGTTCACTGTCCATTTCCTCTACC 60.020 45.833 0.00 0.00 0.00 3.18
1685 1749 4.462508 TCTCAAACTGCAGTCCAGATAG 57.537 45.455 21.95 11.82 44.64 2.08
1687 1751 3.518705 AGATCTCAAACTGCAGTCCAGAT 59.481 43.478 24.66 24.66 44.64 2.90
1711 1775 2.259618 GTTCGATAAAGTGCGAGCTCA 58.740 47.619 15.40 0.00 37.85 4.26
1802 1866 3.843027 AGAAGCATATCATCGGGAGGAAT 59.157 43.478 0.00 0.00 0.00 3.01
1906 1970 1.398958 TTCAAAGCAACAGGGGTGCC 61.399 55.000 2.08 0.00 0.00 5.01
1986 2050 6.909550 AGGCAATATTGGTCAACTTTGTAA 57.090 33.333 17.02 0.00 0.00 2.41
2024 2088 7.368198 AGTTATTTTGGAAAGTAAGCCCAAA 57.632 32.000 0.00 0.00 45.16 3.28
2079 2145 9.788960 CCTGCTTTTCATTTTAATAGGTTCTAC 57.211 33.333 0.00 0.00 0.00 2.59
2097 2163 5.454755 TAGTTTCTACTCAGCACCTGCTTTT 60.455 40.000 0.00 0.00 41.74 2.27
2151 2220 5.482878 AGGGAGTACAAAAGATAAACTCGGA 59.517 40.000 0.00 0.00 37.93 4.55
2153 2222 6.395629 TGAGGGAGTACAAAAGATAAACTCG 58.604 40.000 0.00 0.00 37.93 4.18
2170 2239 5.994250 TCATGGAAAGTATTCTTGAGGGAG 58.006 41.667 0.00 0.00 35.79 4.30
2311 2380 9.745880 ATTATATGCTGTACTGTAGTGTTGTAC 57.254 33.333 1.46 0.00 37.60 2.90
2313 2382 7.710907 CCATTATATGCTGTACTGTAGTGTTGT 59.289 37.037 1.46 0.00 0.00 3.32
2406 5487 2.307098 CTGTCAAAGGGAAGGTGGATCT 59.693 50.000 0.00 0.00 0.00 2.75
2478 5559 1.532437 CGACACAATTTCAGCTGCAGA 59.468 47.619 20.43 0.00 0.00 4.26
2520 5601 2.300967 CCAGCAACTAGGCAGGGGA 61.301 63.158 0.00 0.00 36.85 4.81
2674 5774 5.670485 ACCACATCGCAGATAAATGACTAA 58.330 37.500 0.00 0.00 45.12 2.24
2690 5796 5.992217 AGAACTGAACAAAGTAGACCACATC 59.008 40.000 0.00 0.00 0.00 3.06
2692 5798 5.353394 AGAACTGAACAAAGTAGACCACA 57.647 39.130 0.00 0.00 0.00 4.17
2695 5801 4.930405 GCCTAGAACTGAACAAAGTAGACC 59.070 45.833 0.00 0.00 0.00 3.85
2722 5828 9.153479 ACAGCAGATTATATTAGAAGACTCCTT 57.847 33.333 0.00 0.00 34.81 3.36
2765 5898 9.802039 ATACTGGTTTTGAAGAGTTTTATGGTA 57.198 29.630 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.