Multiple sequence alignment - TraesCS1B01G089200

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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 TraesCS1B01G089200 chr1B 100.000 2552 0 0 1 2552 88480154 88477603 0 4713
1 TraesCS1B01G089200 chr1B 91.727 834 65 3 1720 2552 628772074 628771244 0 1155
2 TraesCS1B01G089200 chr6D 90.388 1987 155 20 594 2552 323166695 323168673 0 2579
3 TraesCS1B01G089200 chr6D 89.878 1887 145 16 595 2447 312544303 312542429 0 2385
4 TraesCS1B01G089200 chr7B 89.824 1985 147 24 596 2552 648212425 648214382 0 2495
5 TraesCS1B01G089200 chr7B 89.608 1992 148 25 596 2552 648202539 648204506 0 2477
6 TraesCS1B01G089200 chr6A 89.511 1983 173 20 594 2547 76046187 76048163 0 2477
7 TraesCS1B01G089200 chr1A 89.608 1886 149 19 596 2447 556201763 556203635 0 2353
8 TraesCS1B01G089200 chr7D 89.388 1894 145 20 596 2447 439707847 439705968 0 2333
9 TraesCS1B01G089200 chr7D 87.540 1870 151 34 588 2404 63995382 63997222 0 2087
10 TraesCS1B01G089200 chr5D 89.691 1843 138 23 594 2404 44511941 44513763 0 2303
11 TraesCS1B01G089200 chr5D 89.876 1373 101 19 596 1935 539819769 539818402 0 1731
12 TraesCS1B01G089200 chr5D 94.842 601 25 2 1 595 483275980 483275380 0 933
13 TraesCS1B01G089200 chr5D 94.640 597 30 2 1 595 534792520 534791924 0 924
14 TraesCS1B01G089200 chr1D 89.966 1744 123 21 841 2552 481625517 481623794 0 2204
15 TraesCS1B01G089200 chr1D 92.529 1111 75 4 596 1701 347252964 347251857 0 1585
16 TraesCS1B01G089200 chr1D 91.737 835 64 5 1720 2552 347251814 347250983 0 1155
17 TraesCS1B01G089200 chr1D 94.631 596 31 1 1 595 86014721 86015316 0 922
18 TraesCS1B01G089200 chr4A 91.070 1131 92 5 596 1720 664111686 664110559 0 1520
19 TraesCS1B01G089200 chr3D 90.221 1043 68 16 1542 2552 4247200 4248240 0 1330
20 TraesCS1B01G089200 chr3D 94.966 596 29 1 1 595 546057775 546057180 0 933
21 TraesCS1B01G089200 chr3D 94.799 596 30 1 1 595 43087221 43086626 0 928
22 TraesCS1B01G089200 chr3D 94.799 596 30 1 1 595 312207297 312206702 0 928
23 TraesCS1B01G089200 chr3B 89.744 936 70 11 1639 2552 821268927 821269858 0 1173
24 TraesCS1B01G089200 chr3B 89.648 937 70 14 1639 2552 821332453 821333385 0 1168
25 TraesCS1B01G089200 chr5B 94.799 596 30 1 1 595 579940042 579940637 0 928
26 TraesCS1B01G089200 chr2D 94.799 596 30 1 1 595 532391583 532390988 0 928
27 TraesCS1B01G089200 chr2D 94.631 596 31 1 1 595 105276589 105275994 0 922


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 TraesCS1B01G089200 chr1B 88477603 88480154 2551 True 4713 4713 100.000 1 2552 1 chr1B.!!$R1 2551
1 TraesCS1B01G089200 chr1B 628771244 628772074 830 True 1155 1155 91.727 1720 2552 1 chr1B.!!$R2 832
2 TraesCS1B01G089200 chr6D 323166695 323168673 1978 False 2579 2579 90.388 594 2552 1 chr6D.!!$F1 1958
3 TraesCS1B01G089200 chr6D 312542429 312544303 1874 True 2385 2385 89.878 595 2447 1 chr6D.!!$R1 1852
4 TraesCS1B01G089200 chr7B 648212425 648214382 1957 False 2495 2495 89.824 596 2552 1 chr7B.!!$F2 1956
5 TraesCS1B01G089200 chr7B 648202539 648204506 1967 False 2477 2477 89.608 596 2552 1 chr7B.!!$F1 1956
6 TraesCS1B01G089200 chr6A 76046187 76048163 1976 False 2477 2477 89.511 594 2547 1 chr6A.!!$F1 1953
7 TraesCS1B01G089200 chr1A 556201763 556203635 1872 False 2353 2353 89.608 596 2447 1 chr1A.!!$F1 1851
8 TraesCS1B01G089200 chr7D 439705968 439707847 1879 True 2333 2333 89.388 596 2447 1 chr7D.!!$R1 1851
9 TraesCS1B01G089200 chr7D 63995382 63997222 1840 False 2087 2087 87.540 588 2404 1 chr7D.!!$F1 1816
10 TraesCS1B01G089200 chr5D 44511941 44513763 1822 False 2303 2303 89.691 594 2404 1 chr5D.!!$F1 1810
11 TraesCS1B01G089200 chr5D 539818402 539819769 1367 True 1731 1731 89.876 596 1935 1 chr5D.!!$R3 1339
12 TraesCS1B01G089200 chr5D 483275380 483275980 600 True 933 933 94.842 1 595 1 chr5D.!!$R1 594
13 TraesCS1B01G089200 chr5D 534791924 534792520 596 True 924 924 94.640 1 595 1 chr5D.!!$R2 594
14 TraesCS1B01G089200 chr1D 481623794 481625517 1723 True 2204 2204 89.966 841 2552 1 chr1D.!!$R1 1711
15 TraesCS1B01G089200 chr1D 347250983 347252964 1981 True 1370 1585 92.133 596 2552 2 chr1D.!!$R2 1956
16 TraesCS1B01G089200 chr1D 86014721 86015316 595 False 922 922 94.631 1 595 1 chr1D.!!$F1 594
17 TraesCS1B01G089200 chr4A 664110559 664111686 1127 True 1520 1520 91.070 596 1720 1 chr4A.!!$R1 1124
18 TraesCS1B01G089200 chr3D 4247200 4248240 1040 False 1330 1330 90.221 1542 2552 1 chr3D.!!$F1 1010
19 TraesCS1B01G089200 chr3D 546057180 546057775 595 True 933 933 94.966 1 595 1 chr3D.!!$R3 594
20 TraesCS1B01G089200 chr3D 43086626 43087221 595 True 928 928 94.799 1 595 1 chr3D.!!$R1 594
21 TraesCS1B01G089200 chr3D 312206702 312207297 595 True 928 928 94.799 1 595 1 chr3D.!!$R2 594
22 TraesCS1B01G089200 chr3B 821268927 821269858 931 False 1173 1173 89.744 1639 2552 1 chr3B.!!$F1 913
23 TraesCS1B01G089200 chr3B 821332453 821333385 932 False 1168 1168 89.648 1639 2552 1 chr3B.!!$F2 913
24 TraesCS1B01G089200 chr5B 579940042 579940637 595 False 928 928 94.799 1 595 1 chr5B.!!$F1 594
25 TraesCS1B01G089200 chr2D 532390988 532391583 595 True 928 928 94.799 1 595 1 chr2D.!!$R2 594
26 TraesCS1B01G089200 chr2D 105275994 105276589 595 True 922 922 94.631 1 595 1 chr2D.!!$R1 594

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
637 645 0.473755 AGTGGTGTCCATGTGCTCAA 59.526 50.0 0.0 0.0 35.28 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 1785 0.325671 TTTGGCCCACAAAGGAACCA 60.326 50.0 0.0 0.0 43.81 3.67 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
115 116 8.989131 ACTAGTATTTGGTTAGAGGATTTGCTA 58.011 33.333 0.00 0.00 0.00 3.49
156 157 4.722700 AGCGCCACACATCCCACC 62.723 66.667 2.29 0.00 0.00 4.61
199 200 1.514087 CATGGAGCATGGTTGGTGC 59.486 57.895 0.00 0.00 41.53 5.01
264 265 3.066621 CGGTTCCATCCATACATTTGTGG 59.933 47.826 0.00 0.00 35.29 4.17
284 285 0.681175 AGTTCCACCAAAATGCAGCC 59.319 50.000 0.00 0.00 0.00 4.85
356 357 3.058224 GGCACTAGTTGATGAAACACACC 60.058 47.826 0.00 0.00 41.61 4.16
361 363 7.202526 CACTAGTTGATGAAACACACCAAATT 58.797 34.615 0.00 0.00 41.61 1.82
403 406 7.522236 GCGATAGTATCATAGTATGCCATGCTA 60.522 40.741 10.71 4.93 39.35 3.49
404 407 8.518702 CGATAGTATCATAGTATGCCATGCTAT 58.481 37.037 15.99 15.99 38.48 2.97
420 423 1.152247 TATGAGGGCGAGATGGGCT 60.152 57.895 0.00 0.00 0.00 5.19
471 479 1.641577 GGAAATCGTCCCAAGTCTCG 58.358 55.000 0.00 0.00 41.10 4.04
582 590 8.276252 TGTAGATCAACTAAAATTAAGCACCC 57.724 34.615 0.00 0.00 32.49 4.61
583 591 7.885922 TGTAGATCAACTAAAATTAAGCACCCA 59.114 33.333 0.00 0.00 32.49 4.51
584 592 7.775053 AGATCAACTAAAATTAAGCACCCAA 57.225 32.000 0.00 0.00 0.00 4.12
585 593 7.830739 AGATCAACTAAAATTAAGCACCCAAG 58.169 34.615 0.00 0.00 0.00 3.61
586 594 6.969993 TCAACTAAAATTAAGCACCCAAGT 57.030 33.333 0.00 0.00 0.00 3.16
591 599 4.414337 AAATTAAGCACCCAAGTTTGCA 57.586 36.364 1.14 0.00 41.48 4.08
592 600 3.665745 ATTAAGCACCCAAGTTTGCAG 57.334 42.857 1.14 0.00 41.48 4.41
637 645 0.473755 AGTGGTGTCCATGTGCTCAA 59.526 50.000 0.00 0.00 35.28 3.02
681 689 1.003696 GCTCAGTTTTGCCCCTAGTCT 59.996 52.381 0.00 0.00 0.00 3.24
717 725 0.976641 TCCGTGAACTCTGCCATCTT 59.023 50.000 0.00 0.00 0.00 2.40
749 757 1.003233 CCTTTTGACTCGGCCCTTACT 59.997 52.381 0.00 0.00 0.00 2.24
784 793 1.025812 CAGAGACGCCCTAGACGATT 58.974 55.000 11.43 0.36 0.00 3.34
932 953 1.747367 ACGGCGAGACAGAGAGAGG 60.747 63.158 16.62 0.00 0.00 3.69
1004 1025 2.586792 GGCTCCGAGCTCCATGTT 59.413 61.111 19.68 0.00 41.99 2.71
1086 1107 1.878522 CGTCTATCCGTGGTGCTGC 60.879 63.158 0.00 0.00 0.00 5.25
1151 1172 2.475818 TCGTCTGTTTTACGTGTGCAT 58.524 42.857 0.00 0.00 41.08 3.96
1165 1186 1.138859 TGTGCATCGAGAATGGGGTAG 59.861 52.381 0.00 0.00 35.77 3.18
1200 1221 2.874751 CCATTTTCGTGGTCGGGC 59.125 61.111 0.00 0.00 37.69 6.13
1201 1222 2.696759 CCATTTTCGTGGTCGGGCC 61.697 63.158 0.00 0.00 37.69 5.80
1330 1355 3.635836 TGAAGAATGGTTGTGCATGTTGA 59.364 39.130 0.00 0.00 0.00 3.18
1413 1438 2.491693 AGACAGAGAGCTAGCTGTTGAC 59.508 50.000 24.99 17.48 44.77 3.18
1492 1517 5.303259 ACCCATTTGCAATTACTTTTGGT 57.697 34.783 0.00 0.00 0.00 3.67
1508 1533 6.548321 ACTTTTGGTCATTTGTAGGTATGGA 58.452 36.000 0.00 0.00 0.00 3.41
1517 1542 3.188159 TGTAGGTATGGAAATCGCACC 57.812 47.619 0.00 0.00 0.00 5.01
1633 1659 8.379902 GTTGGTCAAAGTTGTTTAAATGTTGAG 58.620 33.333 0.00 0.00 0.00 3.02
1636 1663 9.313118 GGTCAAAGTTGTTTAAATGTTGAGAAT 57.687 29.630 0.00 0.00 0.00 2.40
1758 1818 2.356135 GGCCAAATTCAGAGCGTAGAA 58.644 47.619 0.00 0.00 0.00 2.10
1760 1820 3.003480 GCCAAATTCAGAGCGTAGAACT 58.997 45.455 0.00 0.00 0.00 3.01
1781 1841 1.486211 AGTGCCGGCTAGACTAATGT 58.514 50.000 29.70 0.00 0.00 2.71
1784 1844 0.105039 GCCGGCTAGACTAATGTGCT 59.895 55.000 22.15 0.00 0.00 4.40
1787 1847 3.740141 GCCGGCTAGACTAATGTGCTAAA 60.740 47.826 22.15 0.00 0.00 1.85
1793 1854 6.090088 GGCTAGACTAATGTGCTAAATGATCG 59.910 42.308 0.00 0.00 0.00 3.69
1921 1991 8.044060 TGAATTACTCTAGAGCCAAACAATTG 57.956 34.615 19.97 3.24 36.25 2.32
1923 1993 7.617041 ATTACTCTAGAGCCAAACAATTGAC 57.383 36.000 19.97 0.00 38.94 3.18
2035 2109 3.057104 TCATGAAAAATGTGCCTCAGCTG 60.057 43.478 7.63 7.63 40.80 4.24
2068 2142 3.744238 ACACCTGGTGCCAAAATTAAC 57.256 42.857 26.20 0.00 36.98 2.01
2091 2166 6.750148 ACGAACATTTTTAAGGGCATTACAA 58.250 32.000 0.00 0.00 0.00 2.41
2140 2217 0.958091 TGAAGGGTGGAAAATGCACG 59.042 50.000 0.00 0.00 39.79 5.34
2152 2229 4.272261 GGAAAATGCACGAAAAATTGGTGT 59.728 37.500 7.01 0.00 40.87 4.16
2154 2231 3.724508 ATGCACGAAAAATTGGTGTGA 57.275 38.095 7.01 0.00 40.87 3.58
2176 2253 3.003763 GGACTCGAACCCAGGGCT 61.004 66.667 4.91 0.00 0.00 5.19
2198 2275 2.018515 CGTGGGTTTGTGGTGTTTAGT 58.981 47.619 0.00 0.00 0.00 2.24
2233 2310 3.829601 ACCGCTAGGATAGATGGAAAGAG 59.170 47.826 0.00 0.00 42.77 2.85
2238 2315 5.994668 GCTAGGATAGATGGAAAGAGTTTGG 59.005 44.000 0.00 0.00 42.77 3.28
2248 2325 3.561313 GGAAAGAGTTTGGCATGGGTAGA 60.561 47.826 0.00 0.00 0.00 2.59
2285 2386 6.228258 ACATAGTGAGACCGTTTGTTTGTAT 58.772 36.000 0.00 0.00 0.00 2.29
2300 2412 6.825284 TGTTTGTATTGAATGTTTGCACAG 57.175 33.333 0.00 0.00 35.94 3.66
2401 2521 2.293399 GGTTAGAGTGGCACTTGGTTTG 59.707 50.000 22.98 0.00 0.00 2.93
2435 2555 8.366359 AGGGAATAAATTTGCATGTTAGTTCT 57.634 30.769 0.00 0.00 0.00 3.01
2522 2642 7.285566 ACTTGGATAGATAAGATGCAACACAT 58.714 34.615 0.00 0.00 43.54 3.21
2532 2652 1.518325 TGCAACACATCGTACCCTTG 58.482 50.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 2.232452 CTGTGGACGGATCTTTCTCAGT 59.768 50.000 0.00 0.00 0.00 3.41
156 157 3.859118 TTGGCATCCACCACCACCG 62.859 63.158 0.00 0.00 40.19 4.94
199 200 4.231439 GTGTGCCAAGTAAAAATTACCGG 58.769 43.478 0.00 0.00 0.00 5.28
264 265 1.337167 GGCTGCATTTTGGTGGAACTC 60.337 52.381 0.50 0.00 36.74 3.01
284 285 2.811431 TCTGTGCAAACAGGGTTATTCG 59.189 45.455 6.06 0.00 38.23 3.34
403 406 2.447379 AGCCCATCTCGCCCTCAT 60.447 61.111 0.00 0.00 0.00 2.90
404 407 2.298335 TAGAGCCCATCTCGCCCTCA 62.298 60.000 0.00 0.00 46.44 3.86
420 423 1.466856 ACCGTATGAGGCGTTGTAGA 58.533 50.000 0.00 0.00 33.69 2.59
556 564 8.736244 GGGTGCTTAATTTTAGTTGATCTACAA 58.264 33.333 9.96 0.01 36.02 2.41
557 565 7.885922 TGGGTGCTTAATTTTAGTTGATCTACA 59.114 33.333 9.96 0.00 0.00 2.74
558 566 8.276252 TGGGTGCTTAATTTTAGTTGATCTAC 57.724 34.615 0.00 0.00 0.00 2.59
559 567 8.871629 TTGGGTGCTTAATTTTAGTTGATCTA 57.128 30.769 0.00 0.00 0.00 1.98
560 568 7.451566 ACTTGGGTGCTTAATTTTAGTTGATCT 59.548 33.333 0.00 0.00 0.00 2.75
561 569 7.602753 ACTTGGGTGCTTAATTTTAGTTGATC 58.397 34.615 0.00 0.00 0.00 2.92
562 570 7.539034 ACTTGGGTGCTTAATTTTAGTTGAT 57.461 32.000 0.00 0.00 0.00 2.57
563 571 6.969993 ACTTGGGTGCTTAATTTTAGTTGA 57.030 33.333 0.00 0.00 0.00 3.18
564 572 7.518211 GCAAACTTGGGTGCTTAATTTTAGTTG 60.518 37.037 0.00 0.00 37.78 3.16
565 573 6.481976 GCAAACTTGGGTGCTTAATTTTAGTT 59.518 34.615 0.00 0.00 37.78 2.24
566 574 5.989168 GCAAACTTGGGTGCTTAATTTTAGT 59.011 36.000 0.00 0.00 37.78 2.24
567 575 5.988561 TGCAAACTTGGGTGCTTAATTTTAG 59.011 36.000 0.00 0.00 41.48 1.85
568 576 5.918608 TGCAAACTTGGGTGCTTAATTTTA 58.081 33.333 0.00 0.00 41.48 1.52
569 577 4.775236 TGCAAACTTGGGTGCTTAATTTT 58.225 34.783 0.00 0.00 41.48 1.82
570 578 4.100808 TCTGCAAACTTGGGTGCTTAATTT 59.899 37.500 0.00 0.00 41.48 1.82
571 579 3.640967 TCTGCAAACTTGGGTGCTTAATT 59.359 39.130 0.00 0.00 41.48 1.40
572 580 3.230134 TCTGCAAACTTGGGTGCTTAAT 58.770 40.909 0.00 0.00 41.48 1.40
573 581 2.660572 TCTGCAAACTTGGGTGCTTAA 58.339 42.857 0.00 0.00 41.48 1.85
574 582 2.356665 TCTGCAAACTTGGGTGCTTA 57.643 45.000 0.00 0.00 41.48 3.09
575 583 1.410153 CTTCTGCAAACTTGGGTGCTT 59.590 47.619 0.00 0.00 41.48 3.91
576 584 1.035139 CTTCTGCAAACTTGGGTGCT 58.965 50.000 0.00 0.00 41.48 4.40
577 585 0.032540 CCTTCTGCAAACTTGGGTGC 59.967 55.000 0.00 0.00 41.29 5.01
578 586 0.675633 CCCTTCTGCAAACTTGGGTG 59.324 55.000 0.00 0.00 0.00 4.61
579 587 0.261696 ACCCTTCTGCAAACTTGGGT 59.738 50.000 9.02 9.02 42.52 4.51
580 588 1.413118 AACCCTTCTGCAAACTTGGG 58.587 50.000 7.96 7.96 40.37 4.12
581 589 4.871933 ATTAACCCTTCTGCAAACTTGG 57.128 40.909 0.00 0.00 0.00 3.61
582 590 7.035612 GGATAATTAACCCTTCTGCAAACTTG 58.964 38.462 0.24 0.00 0.00 3.16
583 591 6.954102 AGGATAATTAACCCTTCTGCAAACTT 59.046 34.615 8.09 0.00 0.00 2.66
584 592 6.494059 AGGATAATTAACCCTTCTGCAAACT 58.506 36.000 8.09 0.00 0.00 2.66
585 593 6.775594 AGGATAATTAACCCTTCTGCAAAC 57.224 37.500 8.09 0.00 0.00 2.93
586 594 7.790782 AAAGGATAATTAACCCTTCTGCAAA 57.209 32.000 17.65 0.00 39.21 3.68
591 599 5.661312 GGGCAAAAGGATAATTAACCCTTCT 59.339 40.000 17.65 6.53 39.21 2.85
592 600 5.661312 AGGGCAAAAGGATAATTAACCCTTC 59.339 40.000 17.65 9.33 42.56 3.46
637 645 1.838112 TTCGCATCTGAGGGCAAAAT 58.162 45.000 5.18 0.00 0.00 1.82
681 689 1.378531 GGAATGAGTTGGTGCGCATA 58.621 50.000 15.91 2.58 0.00 3.14
864 873 0.747644 CACCACCACTGTCTGTTGCA 60.748 55.000 0.00 0.00 0.00 4.08
867 876 0.180406 GGTCACCACCACTGTCTGTT 59.820 55.000 0.00 0.00 43.17 3.16
889 898 0.678395 CCGCCATGCTCTCTATCACT 59.322 55.000 0.00 0.00 0.00 3.41
894 903 1.676678 GGTCACCGCCATGCTCTCTA 61.677 60.000 0.00 0.00 0.00 2.43
920 941 0.324275 GCCACTCCCTCTCTCTGTCT 60.324 60.000 0.00 0.00 0.00 3.41
921 942 1.662438 CGCCACTCCCTCTCTCTGTC 61.662 65.000 0.00 0.00 0.00 3.51
922 943 1.680651 CGCCACTCCCTCTCTCTGT 60.681 63.158 0.00 0.00 0.00 3.41
923 944 2.422231 CCGCCACTCCCTCTCTCTG 61.422 68.421 0.00 0.00 0.00 3.35
1066 1087 0.385751 CAGCACCACGGATAGACGAT 59.614 55.000 0.00 0.00 37.61 3.73
1086 1107 3.341043 CTCCGATCAATGCCCGCG 61.341 66.667 0.00 0.00 0.00 6.46
1140 1161 2.267426 CCATTCTCGATGCACACGTAA 58.733 47.619 13.37 10.13 34.25 3.18
1151 1172 1.961394 CGATTCCTACCCCATTCTCGA 59.039 52.381 0.00 0.00 0.00 4.04
1165 1186 1.141665 GTGCAATTGCCCCGATTCC 59.858 57.895 26.94 1.92 41.18 3.01
1200 1221 4.159135 CAGATCAACCCATTTCTCAAAGGG 59.841 45.833 0.00 0.00 46.96 3.95
1201 1222 4.768968 ACAGATCAACCCATTTCTCAAAGG 59.231 41.667 0.00 0.00 0.00 3.11
1330 1355 2.177580 CGACCACTGCCGTTTGTGT 61.178 57.895 0.00 0.00 32.76 3.72
1392 1417 2.491693 GTCAACAGCTAGCTCTCTGTCT 59.508 50.000 16.15 8.41 42.19 3.41
1413 1438 5.810095 ACCTTCTTCTTCAACATCCTAAGG 58.190 41.667 0.00 0.00 37.55 2.69
1492 1517 5.295787 GTGCGATTTCCATACCTACAAATGA 59.704 40.000 0.00 0.00 0.00 2.57
1517 1542 1.066908 ACAATTTCAACACTGCACCCG 59.933 47.619 0.00 0.00 0.00 5.28
1523 1548 5.634859 GCCTTTCCATACAATTTCAACACTG 59.365 40.000 0.00 0.00 0.00 3.66
1525 1550 5.537188 TGCCTTTCCATACAATTTCAACAC 58.463 37.500 0.00 0.00 0.00 3.32
1725 1785 0.325671 TTTGGCCCACAAAGGAACCA 60.326 50.000 0.00 0.00 43.81 3.67
1758 1818 2.431954 TAGTCTAGCCGGCACTTAGT 57.568 50.000 31.54 15.75 0.00 2.24
1760 1820 3.028850 ACATTAGTCTAGCCGGCACTTA 58.971 45.455 31.54 17.68 0.00 2.24
1781 1841 4.072131 GGGCCTAATTCGATCATTTAGCA 58.928 43.478 0.84 0.00 0.00 3.49
1784 1844 6.015519 CCAAATGGGCCTAATTCGATCATTTA 60.016 38.462 4.53 0.00 33.69 1.40
1787 1847 3.828451 CCAAATGGGCCTAATTCGATCAT 59.172 43.478 4.53 0.00 0.00 2.45
1884 1945 9.823647 CTCTAGAGTAATTCAATTAGCTTCCAA 57.176 33.333 11.89 0.00 0.00 3.53
1903 1973 6.566197 AAAGTCAATTGTTTGGCTCTAGAG 57.434 37.500 15.85 15.85 46.93 2.43
1906 1976 8.635765 AATCTAAAGTCAATTGTTTGGCTCTA 57.364 30.769 5.13 0.00 46.93 2.43
2018 2092 3.490348 ACTACAGCTGAGGCACATTTTT 58.510 40.909 23.35 0.00 41.70 1.94
2035 2109 4.620097 GCACCAGGTGTAAACCTCTACTAC 60.620 50.000 21.26 0.00 38.22 2.73
2068 2142 7.543868 TCATTGTAATGCCCTTAAAAATGTTCG 59.456 33.333 0.00 0.00 36.36 3.95
2112 2188 7.174599 TGCATTTTCCACCCTTCATTTTTATTG 59.825 33.333 0.00 0.00 0.00 1.90
2140 2217 2.962421 TCCCCAGTCACACCAATTTTTC 59.038 45.455 0.00 0.00 0.00 2.29
2152 2229 1.911766 GGGTTCGAGTCCCCAGTCA 60.912 63.158 14.49 0.00 40.88 3.41
2154 2231 2.203182 TGGGTTCGAGTCCCCAGT 59.797 61.111 20.23 0.00 46.06 4.00
2174 2251 3.216292 ACCACAAACCCACGCAGC 61.216 61.111 0.00 0.00 0.00 5.25
2176 2253 1.251527 AAACACCACAAACCCACGCA 61.252 50.000 0.00 0.00 0.00 5.24
2233 2310 2.026262 TCCTTCTCTACCCATGCCAAAC 60.026 50.000 0.00 0.00 0.00 2.93
2238 2315 3.636153 ACTTTCCTTCTCTACCCATGC 57.364 47.619 0.00 0.00 0.00 4.06
2248 2325 7.013464 CGGTCTCACTATGTATACTTTCCTTCT 59.987 40.741 4.17 0.00 0.00 2.85
2285 2386 2.757314 TCACACCTGTGCAAACATTCAA 59.243 40.909 0.17 0.00 45.25 2.69
2300 2412 2.640316 AGGAAAACCACTCTCACACC 57.360 50.000 0.00 0.00 0.00 4.16
2401 2521 8.839343 CATGCAAATTTATTCCCTTTAAATCCC 58.161 33.333 0.00 0.00 30.79 3.85
2435 2555 7.889873 TCATTTCTTCCCTAAACAAAGTCAA 57.110 32.000 0.00 0.00 0.00 3.18
2522 2642 1.691976 CCCATCTATGCAAGGGTACGA 59.308 52.381 0.00 0.00 36.52 3.43


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

AutoCloner maintained by Alex Coulton.