Multiple sequence alignment - TraesCS4B01G098100

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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 TraesCS4B01G098100 chr4B 100.000 4029 0 0 1 4029 103010168 103014196 0.000000e+00 7441.0
1 TraesCS4B01G098100 chr4D 90.693 3245 203 45 1 3210 69652534 69655714 0.000000e+00 4228.0
2 TraesCS4B01G098100 chr4D 92.749 331 23 1 3494 3824 69656079 69656408 1.010000e-130 477.0
3 TraesCS4B01G098100 chr4D 91.694 301 12 2 3206 3493 69655738 69656038 4.850000e-109 405.0
4 TraesCS4B01G098100 chr4D 94.444 216 11 1 3814 4029 69657067 69657281 8.350000e-87 331.0
5 TraesCS4B01G098100 chr4D 77.098 572 67 39 885 1430 509454080 509453547 5.130000e-69 272.0
6 TraesCS4B01G098100 chr4A 91.514 1968 113 27 277 2221 521845393 521847329 0.000000e+00 2660.0
7 TraesCS4B01G098100 chr4A 90.684 1170 59 13 2364 3490 521862016 521863178 0.000000e+00 1511.0
8 TraesCS4B01G098100 chr4A 93.110 537 31 5 3494 4029 521863223 521863754 0.000000e+00 782.0
9 TraesCS4B01G098100 chr4A 96.186 236 7 1 1 234 521845161 521845396 6.320000e-103 385.0
10 TraesCS4B01G098100 chr4A 91.275 149 6 4 2218 2365 521847409 521847551 3.180000e-46 196.0
11 TraesCS4B01G098100 chr2D 79.012 324 59 6 3495 3815 301377718 301377401 3.150000e-51 213.0
12 TraesCS4B01G098100 chr1D 78.704 324 61 5 3495 3815 120993966 120994284 4.080000e-50 209.0
13 TraesCS4B01G098100 chr5B 97.059 34 1 0 1 34 691740778 691740811 1.560000e-04 58.4
14 TraesCS4B01G098100 chr5A 97.059 34 1 0 1 34 675447277 675447310 1.560000e-04 58.4
15 TraesCS4B01G098100 chr1B 97.059 34 1 0 1 34 593780594 593780627 1.560000e-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 TraesCS4B01G098100 chr4B 103010168 103014196 4028 False 7441.000000 7441 100.000000 1 4029 1 chr4B.!!$F1 4028
1 TraesCS4B01G098100 chr4D 69652534 69657281 4747 False 1360.250000 4228 92.395000 1 4029 4 chr4D.!!$F1 4028
2 TraesCS4B01G098100 chr4D 509453547 509454080 533 True 272.000000 272 77.098000 885 1430 1 chr4D.!!$R1 545
3 TraesCS4B01G098100 chr4A 521862016 521863754 1738 False 1146.500000 1511 91.897000 2364 4029 2 chr4A.!!$F2 1665
4 TraesCS4B01G098100 chr4A 521845161 521847551 2390 False 1080.333333 2660 92.991667 1 2365 3 chr4A.!!$F1 2364

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
543 546 0.041312 CAACCGCTGGTTTCAACGAG 60.041 55.0 9.78 0.0 44.33 4.18 F
960 974 0.322816 TTGGCACCATCCAGAGAAGC 60.323 55.0 0.00 0.0 37.44 3.86 F
2319 2461 0.038599 TACACCTAGACGGACAGCCA 59.961 55.0 0.00 0.0 36.31 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 2045 0.239347 CTTCCGAGCCAAACTGCTTG 59.761 55.0 0.00 0.0 42.95 4.01 R
2798 2942 0.037605 ATCCGTCGGTCTTCACCAAC 60.038 55.0 11.88 0.0 44.02 3.77 R
3362 3552 0.179001 GGGCACAAAGTGGGTACAGT 60.179 55.0 0.00 0.0 33.64 3.55 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
200 201 4.058124 GCACATATCGAGAGGTTGCATTA 58.942 43.478 12.14 0.00 0.00 1.90
282 285 5.910723 GTCAAAAATTGAGCTGCAAAAATGG 59.089 36.000 1.02 0.00 41.01 3.16
445 448 4.056740 GAGTATCATGCACCTCATCACAG 58.943 47.826 0.00 0.00 31.79 3.66
447 450 4.651045 AGTATCATGCACCTCATCACAGTA 59.349 41.667 0.00 0.00 31.79 2.74
470 473 7.981789 AGTATACTGGTCATGTATTTGTGTGAG 59.018 37.037 4.10 0.00 33.32 3.51
540 543 1.299850 GCCAACCGCTGGTTTCAAC 60.300 57.895 9.78 0.00 44.33 3.18
541 544 1.008995 CCAACCGCTGGTTTCAACG 60.009 57.895 9.78 0.47 44.33 4.10
542 545 1.440938 CCAACCGCTGGTTTCAACGA 61.441 55.000 9.78 0.00 44.33 3.85
543 546 0.041312 CAACCGCTGGTTTCAACGAG 60.041 55.000 9.78 0.00 44.33 4.18
544 547 0.463116 AACCGCTGGTTTCAACGAGT 60.463 50.000 7.08 0.00 44.33 4.18
545 548 1.157870 ACCGCTGGTTTCAACGAGTG 61.158 55.000 7.96 7.96 42.52 3.51
546 549 0.878523 CCGCTGGTTTCAACGAGTGA 60.879 55.000 14.68 0.00 44.66 3.41
815 827 3.886123 AGTTGCTAAGCCCGAATACAAT 58.114 40.909 0.00 0.00 0.00 2.71
827 839 5.406780 GCCCGAATACAATATCACTTGAGAG 59.593 44.000 0.00 0.00 0.00 3.20
943 957 2.879103 AATACCTGACCACCCTGTTG 57.121 50.000 0.00 0.00 0.00 3.33
960 974 0.322816 TTGGCACCATCCAGAGAAGC 60.323 55.000 0.00 0.00 37.44 3.86
961 975 1.300963 GGCACCATCCAGAGAAGCA 59.699 57.895 0.00 0.00 0.00 3.91
1036 1065 1.962807 CTCCAATCATCGCTCTCCTCT 59.037 52.381 0.00 0.00 0.00 3.69
1104 1133 0.530650 CGCTCCATGGCAACGTCTAT 60.531 55.000 6.96 0.00 42.51 1.98
1133 1162 5.596772 TCGGGTATGTATGTTTCTCTGATCA 59.403 40.000 0.00 0.00 0.00 2.92
1172 1209 2.093764 AGCTTTGATCGTCCTTCTCAGG 60.094 50.000 0.00 0.00 42.50 3.86
1244 1282 3.306166 CAGCCACTACTATGTTACGTTGC 59.694 47.826 0.00 0.00 0.00 4.17
1260 1298 2.525368 GTTGCAGATTGGTAAACCCCT 58.475 47.619 0.00 0.00 34.29 4.79
1266 1304 2.378547 AGATTGGTAAACCCCTGAAGCA 59.621 45.455 0.00 0.00 34.29 3.91
1283 1321 3.618690 AGCACTACTTCTTGGACATCC 57.381 47.619 0.00 0.00 0.00 3.51
1318 1356 1.004080 CACCTGGCTGGAGTGTCAG 60.004 63.158 18.12 0.00 39.71 3.51
1443 1489 3.914426 AGTGTTCTGTTCTGTCCAAGT 57.086 42.857 0.00 0.00 0.00 3.16
1445 1491 4.192317 AGTGTTCTGTTCTGTCCAAGTTC 58.808 43.478 0.00 0.00 0.00 3.01
1489 1535 4.445452 TCTTGGCATGATCTTTGCTTTC 57.555 40.909 17.09 5.51 40.03 2.62
1500 1546 5.181056 TGATCTTTGCTTTCGTGCTTGATTA 59.819 36.000 0.00 0.00 0.00 1.75
1507 1553 4.731773 GCTTTCGTGCTTGATTATTCCAGG 60.732 45.833 0.00 0.00 0.00 4.45
1508 1554 2.917933 TCGTGCTTGATTATTCCAGGG 58.082 47.619 0.00 0.00 0.00 4.45
1509 1555 1.949525 CGTGCTTGATTATTCCAGGGG 59.050 52.381 0.00 0.00 0.00 4.79
1511 1557 1.287442 TGCTTGATTATTCCAGGGGCA 59.713 47.619 0.00 0.00 0.00 5.36
1512 1558 2.091166 TGCTTGATTATTCCAGGGGCAT 60.091 45.455 0.00 0.00 0.00 4.40
1519 1565 4.601406 TTATTCCAGGGGCATAAACACT 57.399 40.909 0.00 0.00 0.00 3.55
1522 1568 1.922447 TCCAGGGGCATAAACACTCAT 59.078 47.619 0.00 0.00 0.00 2.90
1534 1580 6.018262 GCATAAACACTCATATTACTCGCCAA 60.018 38.462 0.00 0.00 0.00 4.52
1556 1602 2.863809 ACTTAGCAACTTGAAGGTGGG 58.136 47.619 12.75 0.00 32.34 4.61
1568 1614 2.108075 TGAAGGTGGGATGTCAACACAT 59.892 45.455 0.00 0.00 46.64 3.21
1597 1643 2.970974 GCACTGCGGAAAGACCTGC 61.971 63.158 0.00 0.00 38.17 4.85
1620 1666 2.594131 GGTATTAACCCTCAATGCCCC 58.406 52.381 0.00 0.00 40.21 5.80
1621 1667 2.091555 GGTATTAACCCTCAATGCCCCA 60.092 50.000 0.00 0.00 40.21 4.96
1622 1668 3.437931 GGTATTAACCCTCAATGCCCCAT 60.438 47.826 0.00 0.00 40.21 4.00
1623 1669 2.452600 TTAACCCTCAATGCCCCATC 57.547 50.000 0.00 0.00 0.00 3.51
1627 1673 0.757935 CCCTCAATGCCCCATCAAGG 60.758 60.000 0.00 0.00 37.03 3.61
1655 1701 5.286797 CACATCAATGCCACTACAAAATTCG 59.713 40.000 0.00 0.00 0.00 3.34
1662 1708 4.873827 TGCCACTACAAAATTCGATACCTC 59.126 41.667 0.00 0.00 0.00 3.85
1677 1723 0.611062 ACCTCGATGGGACGACAGAA 60.611 55.000 0.00 0.00 41.11 3.02
1683 1729 1.002087 GATGGGACGACAGAAGGTGTT 59.998 52.381 0.00 0.00 40.56 3.32
1684 1730 0.391597 TGGGACGACAGAAGGTGTTC 59.608 55.000 0.00 0.00 40.56 3.18
1690 1736 1.067495 CGACAGAAGGTGTTCTCTCCC 60.067 57.143 0.00 0.00 41.40 4.30
1697 1743 2.408565 AGGTGTTCTCTCCCTTGACAA 58.591 47.619 0.00 0.00 0.00 3.18
1705 1751 4.022603 TCTCTCCCTTGACAAGATCTCTG 58.977 47.826 16.99 0.00 0.00 3.35
1716 1762 1.490574 AGATCTCTGTCGGGGGAAAG 58.509 55.000 0.00 0.00 0.00 2.62
1722 1768 1.202842 TCTGTCGGGGGAAAGGAAAAC 60.203 52.381 0.00 0.00 0.00 2.43
1723 1769 0.551879 TGTCGGGGGAAAGGAAAACA 59.448 50.000 0.00 0.00 0.00 2.83
1724 1770 1.063867 TGTCGGGGGAAAGGAAAACAA 60.064 47.619 0.00 0.00 0.00 2.83
1725 1777 2.244695 GTCGGGGGAAAGGAAAACAAT 58.755 47.619 0.00 0.00 0.00 2.71
1731 1783 4.180817 GGGGAAAGGAAAACAATATTGCG 58.819 43.478 15.48 0.00 0.00 4.85
1734 1786 6.391537 GGGAAAGGAAAACAATATTGCGTTA 58.608 36.000 15.48 0.00 0.00 3.18
1743 1795 7.690952 AAACAATATTGCGTTAGGGTAAGAA 57.309 32.000 15.48 0.00 0.00 2.52
1744 1796 6.673154 ACAATATTGCGTTAGGGTAAGAAC 57.327 37.500 15.48 0.00 0.00 3.01
1745 1797 6.412214 ACAATATTGCGTTAGGGTAAGAACT 58.588 36.000 15.48 0.00 0.00 3.01
1746 1798 7.558604 ACAATATTGCGTTAGGGTAAGAACTA 58.441 34.615 15.48 0.00 0.00 2.24
1750 1803 3.577848 TGCGTTAGGGTAAGAACTAACCA 59.422 43.478 8.48 5.70 43.72 3.67
1756 1809 5.175388 AGGGTAAGAACTAACCATTCACC 57.825 43.478 0.00 0.00 40.29 4.02
1760 1813 4.618920 AAGAACTAACCATTCACCGTCT 57.381 40.909 0.00 0.00 0.00 4.18
1766 1819 2.169832 ACCATTCACCGTCTGTTCAG 57.830 50.000 0.00 0.00 0.00 3.02
1811 1865 9.026074 GTTGATGATTTTTCACCTTTCGTTTTA 57.974 29.630 0.00 0.00 0.00 1.52
1840 1894 1.024579 GGATACAACCAGCACCCACG 61.025 60.000 0.00 0.00 0.00 4.94
1845 1899 1.826487 AACCAGCACCCACGGAAAC 60.826 57.895 0.00 0.00 0.00 2.78
1857 1914 2.169146 CGGAAACCATCGCCCGTAC 61.169 63.158 0.00 0.00 37.40 3.67
1889 1946 1.378514 CCTTGGGATGGGAACGGTG 60.379 63.158 0.00 0.00 0.00 4.94
1909 1966 0.741915 GGTTTTGTCCCGCAACTCAA 59.258 50.000 0.00 0.00 36.72 3.02
1911 1968 1.404035 GTTTTGTCCCGCAACTCAAGT 59.596 47.619 0.00 0.00 36.72 3.16
1926 1983 6.645790 AACTCAAGTTGCAGAAGATGATTT 57.354 33.333 0.00 0.00 36.80 2.17
1988 2045 1.065345 GGCTACCTCTTCTTTGGGGAC 60.065 57.143 0.00 0.00 0.00 4.46
1989 2046 1.628846 GCTACCTCTTCTTTGGGGACA 59.371 52.381 0.00 0.00 39.83 4.02
1999 2056 4.597032 TGGGGACAAGCAGTTTGG 57.403 55.556 1.70 0.00 41.25 3.28
2001 2058 1.531602 GGGGACAAGCAGTTTGGCT 60.532 57.895 2.45 0.00 44.72 4.75
2002 2059 1.527433 GGGGACAAGCAGTTTGGCTC 61.527 60.000 2.45 0.00 45.31 4.70
2099 2156 9.681692 TTTGTGATCATTAGTTGATGAAGTTTG 57.318 29.630 0.00 0.00 45.29 2.93
2158 2215 7.282224 CCTGTTAGCCTTGCATAACTGTAATAA 59.718 37.037 8.86 0.00 33.86 1.40
2159 2216 8.208718 TGTTAGCCTTGCATAACTGTAATAAG 57.791 34.615 8.86 0.00 33.86 1.73
2163 2220 8.608844 AGCCTTGCATAACTGTAATAAGTATC 57.391 34.615 0.00 0.00 0.00 2.24
2164 2221 8.432805 AGCCTTGCATAACTGTAATAAGTATCT 58.567 33.333 0.00 0.00 0.00 1.98
2165 2222 9.706691 GCCTTGCATAACTGTAATAAGTATCTA 57.293 33.333 0.00 0.00 0.00 1.98
2189 2246 6.522054 AGTAATATGTATGTGTCGAAAGGGG 58.478 40.000 0.00 0.00 0.00 4.79
2210 2267 7.627311 AGGGGTTGTATAGTTAGAAAACGATT 58.373 34.615 0.00 0.00 40.73 3.34
2297 2439 2.703536 TCTACTCACCTGGTCAAGCAAA 59.296 45.455 0.00 0.00 0.00 3.68
2307 2449 4.385825 CTGGTCAAGCAAAACTACACCTA 58.614 43.478 0.00 0.00 33.19 3.08
2308 2450 4.385825 TGGTCAAGCAAAACTACACCTAG 58.614 43.478 0.00 0.00 33.19 3.02
2318 2460 0.739561 CTACACCTAGACGGACAGCC 59.260 60.000 0.00 0.00 36.31 4.85
2319 2461 0.038599 TACACCTAGACGGACAGCCA 59.961 55.000 0.00 0.00 36.31 4.75
2320 2462 1.251527 ACACCTAGACGGACAGCCAG 61.252 60.000 0.00 0.00 36.31 4.85
2321 2463 0.965866 CACCTAGACGGACAGCCAGA 60.966 60.000 0.00 0.00 36.31 3.86
2322 2464 0.681564 ACCTAGACGGACAGCCAGAG 60.682 60.000 0.00 0.00 36.31 3.35
2323 2465 1.435515 CTAGACGGACAGCCAGAGC 59.564 63.158 0.00 0.00 40.32 4.09
2324 2466 2.010582 CTAGACGGACAGCCAGAGCC 62.011 65.000 0.00 0.00 41.25 4.70
2325 2467 2.500815 TAGACGGACAGCCAGAGCCT 62.501 60.000 0.00 0.00 41.25 4.58
2465 2607 0.174162 GCCCATGCATTTGGACAGAC 59.826 55.000 14.84 0.00 39.25 3.51
2468 2610 1.135603 CCATGCATTTGGACAGACACG 60.136 52.381 0.00 0.00 39.25 4.49
2469 2611 1.135603 CATGCATTTGGACAGACACGG 60.136 52.381 0.00 0.00 0.00 4.94
2475 2619 0.762418 TTGGACAGACACGGGACATT 59.238 50.000 0.00 0.00 0.00 2.71
2476 2620 0.762418 TGGACAGACACGGGACATTT 59.238 50.000 0.00 0.00 0.00 2.32
2482 2626 3.070446 ACAGACACGGGACATTTAAGTCA 59.930 43.478 0.00 0.00 40.29 3.41
2505 2649 1.820519 GCATTTGGATCTTGCAGGTGA 59.179 47.619 0.00 0.00 36.40 4.02
2506 2650 2.159282 GCATTTGGATCTTGCAGGTGAG 60.159 50.000 0.00 0.00 36.40 3.51
2508 2652 2.479566 TTGGATCTTGCAGGTGAGAC 57.520 50.000 0.00 0.00 0.00 3.36
2528 2672 3.198068 ACATATGATCGGCAGTTCACAC 58.802 45.455 10.38 0.00 0.00 3.82
2529 2673 2.309528 TATGATCGGCAGTTCACACC 57.690 50.000 0.00 0.00 0.00 4.16
2531 2675 2.740714 GATCGGCAGTTCACACCGC 61.741 63.158 6.56 0.00 46.49 5.68
2579 2723 7.437267 CCACATTGCTGGAAATTCAAATCTATC 59.563 37.037 0.00 0.00 32.30 2.08
2609 2753 1.972872 AGAGGTTGTTCAAGCCACTG 58.027 50.000 10.47 0.00 0.00 3.66
2622 2766 1.338973 AGCCACTGTCATTGCAGTTTG 59.661 47.619 9.94 6.92 46.45 2.93
2724 2868 5.508200 AAGAGTGAAACGGCAAATTACAA 57.492 34.783 0.00 0.00 45.86 2.41
2734 2878 5.778862 ACGGCAAATTACAAAAGCTAACAT 58.221 33.333 0.00 0.00 0.00 2.71
2741 2885 9.906660 CAAATTACAAAAGCTAACATGTCCTTA 57.093 29.630 0.00 0.00 0.00 2.69
2774 2918 3.696051 TCAGAGAAGCAATAATTGGTGCC 59.304 43.478 10.57 0.00 41.89 5.01
2798 2942 4.742274 TCCTCAACGGAACACACG 57.258 55.556 0.00 0.00 39.40 4.49
2821 2968 1.630148 GTGAAGACCGACGGATCTTG 58.370 55.000 26.05 1.45 35.29 3.02
2963 3110 5.049828 TGCTTGTGATATACGACAATCAGG 58.950 41.667 0.00 0.00 32.93 3.86
3052 3199 8.264347 TGAGTAAAGTTTGCATGGAGATACATA 58.736 33.333 6.47 0.00 0.00 2.29
3087 3234 1.308216 ATGGGCTTGGGAGTAGGCT 60.308 57.895 0.00 0.00 38.20 4.58
3125 3272 6.936335 TCTTAGCAAGAATGAAGTGATGTTGA 59.064 34.615 0.00 0.00 33.83 3.18
3130 3277 7.280428 AGCAAGAATGAAGTGATGTTGATAGAG 59.720 37.037 0.00 0.00 0.00 2.43
3362 3552 1.738432 TTTTTGCTGCCATGTGCGA 59.262 47.368 0.00 0.00 45.60 5.10
3371 3561 1.295101 CCATGTGCGACTGTACCCA 59.705 57.895 0.00 0.00 0.00 4.51
3382 3572 0.179004 CTGTACCCACTTTGTGCCCA 60.179 55.000 0.00 0.00 31.34 5.36
3386 3576 2.259204 CCACTTTGTGCCCATGCG 59.741 61.111 0.00 0.00 41.78 4.73
3538 3770 3.258372 AGTTAGGAGTGAGCAATCGAACA 59.742 43.478 13.19 0.00 29.85 3.18
3572 3804 2.288457 ACCCGTCGATTGCATCTATCAG 60.288 50.000 0.00 0.00 0.00 2.90
3574 3806 3.057526 CCCGTCGATTGCATCTATCAGTA 60.058 47.826 0.00 0.00 0.00 2.74
3647 3879 6.044404 AGGGATGGACGAATAAATGTAGGAAT 59.956 38.462 0.00 0.00 0.00 3.01
3748 3980 7.014326 GGAACCCTAATCCTCCAAAATTCATAC 59.986 40.741 0.00 0.00 33.98 2.39
3749 3981 6.980577 ACCCTAATCCTCCAAAATTCATACA 58.019 36.000 0.00 0.00 0.00 2.29
3867 4768 6.566141 TGAAGTCACGTGATCGGATTATTTA 58.434 36.000 23.12 1.60 41.85 1.40
3948 4849 1.889170 CAGGCTCGCTCCATCTGTATA 59.111 52.381 0.00 0.00 0.00 1.47
3959 4860 5.371526 CTCCATCTGTATAATGCACCTTGT 58.628 41.667 0.00 0.00 0.00 3.16
4022 4923 5.514274 AACCCAACATTAACACAGACAAG 57.486 39.130 0.00 0.00 0.00 3.16
4023 4924 4.532834 ACCCAACATTAACACAGACAAGT 58.467 39.130 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 188 8.663025 CATGATACATATGTAATGCAACCTCTC 58.337 37.037 19.11 8.82 33.76 3.20
246 249 8.277713 AGCTCAATTTTTGACATTGAAAATTCG 58.722 29.630 6.22 3.62 41.16 3.34
253 256 4.946445 TGCAGCTCAATTTTTGACATTGA 58.054 34.783 0.00 0.00 38.14 2.57
282 285 3.565902 GTCTAGCAAACTAATGGGCATCC 59.434 47.826 0.00 0.00 0.00 3.51
315 318 7.774157 ACATTTTAAATAAATGATGGCATGCCA 59.226 29.630 40.04 40.04 43.49 4.92
356 359 5.126061 GCAAACATTCCCATGAAGATACTGT 59.874 40.000 0.00 0.00 33.05 3.55
409 412 9.869844 GTGCATGATACTCAAAATTAGTGATAC 57.130 33.333 0.00 0.00 0.00 2.24
445 448 7.764443 ACTCACACAAATACATGACCAGTATAC 59.236 37.037 0.00 0.00 32.19 1.47
447 450 6.711277 ACTCACACAAATACATGACCAGTAT 58.289 36.000 0.00 0.00 33.79 2.12
458 461 9.959749 TCCATTTTTAAGAACTCACACAAATAC 57.040 29.630 0.00 0.00 0.00 1.89
470 473 5.405935 ACCAGCCATCCATTTTTAAGAAC 57.594 39.130 0.00 0.00 0.00 3.01
565 576 7.301789 GGCAAGAAGATTAAGTCAGAAAGAAC 58.698 38.462 0.00 0.00 0.00 3.01
572 583 2.352960 GCCGGCAAGAAGATTAAGTCAG 59.647 50.000 24.80 0.00 0.00 3.51
815 827 8.868522 AATGTTGATTTTCCTCTCAAGTGATA 57.131 30.769 0.00 0.00 32.33 2.15
827 839 7.489574 TTTGTGGCTTTAATGTTGATTTTCC 57.510 32.000 0.00 0.00 0.00 3.13
943 957 1.028868 GTGCTTCTCTGGATGGTGCC 61.029 60.000 0.00 0.00 0.00 5.01
960 974 4.036027 AGCAGTGTGATTTGAAACTCTGTG 59.964 41.667 6.71 0.00 39.15 3.66
961 975 4.036027 CAGCAGTGTGATTTGAAACTCTGT 59.964 41.667 6.71 0.00 39.15 3.41
1036 1065 2.947532 CGAGTGGGAGCAGGAGCAA 61.948 63.158 0.00 0.00 45.49 3.91
1104 1133 4.028131 AGAAACATACATACCCGACAGGA 58.972 43.478 0.00 0.00 41.02 3.86
1133 1162 5.410355 AAGCTTGTCAATTGCCATGTAAT 57.590 34.783 0.00 0.00 0.00 1.89
1172 1209 4.553756 ACGGAGAAAGAAAACTTCAAGC 57.446 40.909 0.00 0.00 0.00 4.01
1244 1282 2.755103 GCTTCAGGGGTTTACCAATCTG 59.245 50.000 0.69 5.71 42.91 2.90
1260 1298 4.563580 GGATGTCCAAGAAGTAGTGCTTCA 60.564 45.833 21.12 2.39 44.59 3.02
1283 1321 1.227823 TGAGGTTGCTTCCGGTGTG 60.228 57.895 0.00 0.00 0.00 3.82
1291 1329 1.228367 CAGCCAGGTGAGGTTGCTT 60.228 57.895 0.00 0.00 33.05 3.91
1397 1442 7.665690 TGGCATCAAACACAAATATTACAGTT 58.334 30.769 0.00 0.00 0.00 3.16
1489 1535 1.949525 CCCCTGGAATAATCAAGCACG 59.050 52.381 0.00 0.00 0.00 5.34
1500 1546 2.311542 TGAGTGTTTATGCCCCTGGAAT 59.688 45.455 0.00 0.00 0.00 3.01
1507 1553 5.107065 GCGAGTAATATGAGTGTTTATGCCC 60.107 44.000 0.00 0.00 0.00 5.36
1508 1554 5.107065 GGCGAGTAATATGAGTGTTTATGCC 60.107 44.000 0.00 0.00 0.00 4.40
1509 1555 5.465390 TGGCGAGTAATATGAGTGTTTATGC 59.535 40.000 0.00 0.00 0.00 3.14
1511 1557 8.395633 GTTTTGGCGAGTAATATGAGTGTTTAT 58.604 33.333 0.00 0.00 0.00 1.40
1512 1558 7.604927 AGTTTTGGCGAGTAATATGAGTGTTTA 59.395 33.333 0.00 0.00 0.00 2.01
1519 1565 6.110033 TGCTAAGTTTTGGCGAGTAATATGA 58.890 36.000 0.00 0.00 40.39 2.15
1522 1568 5.935789 AGTTGCTAAGTTTTGGCGAGTAATA 59.064 36.000 0.00 0.00 40.39 0.98
1534 1580 3.636764 CCCACCTTCAAGTTGCTAAGTTT 59.363 43.478 0.00 0.00 0.00 2.66
1568 1614 1.157257 CCGCAGTGCAACACAGTACA 61.157 55.000 16.83 0.00 41.43 2.90
1577 1623 1.148273 AGGTCTTTCCGCAGTGCAA 59.852 52.632 16.83 0.00 41.99 4.08
1584 1630 2.747855 CCTGGCAGGTCTTTCCGC 60.748 66.667 25.74 0.00 41.99 5.54
1597 1643 3.222603 GGCATTGAGGGTTAATACCTGG 58.777 50.000 6.42 0.00 44.38 4.45
1604 1650 1.643286 TGATGGGGCATTGAGGGTTAA 59.357 47.619 0.00 0.00 0.00 2.01
1620 1666 2.223735 GCATTGATGTGGCTCCTTGATG 60.224 50.000 0.00 0.00 0.00 3.07
1621 1667 2.029623 GCATTGATGTGGCTCCTTGAT 58.970 47.619 0.00 0.00 0.00 2.57
1622 1668 1.466856 GCATTGATGTGGCTCCTTGA 58.533 50.000 0.00 0.00 0.00 3.02
1623 1669 0.458669 GGCATTGATGTGGCTCCTTG 59.541 55.000 0.00 0.00 41.09 3.61
1627 1673 1.672881 GTAGTGGCATTGATGTGGCTC 59.327 52.381 0.00 0.00 44.29 4.70
1655 1701 1.267261 CTGTCGTCCCATCGAGGTATC 59.733 57.143 0.00 0.00 40.52 2.24
1662 1708 0.458543 CACCTTCTGTCGTCCCATCG 60.459 60.000 0.00 0.00 0.00 3.84
1677 1723 2.103153 TGTCAAGGGAGAGAACACCT 57.897 50.000 0.00 0.00 35.78 4.00
1683 1729 4.022603 CAGAGATCTTGTCAAGGGAGAGA 58.977 47.826 12.66 0.00 0.00 3.10
1684 1730 3.768757 ACAGAGATCTTGTCAAGGGAGAG 59.231 47.826 12.66 2.30 0.00 3.20
1690 1736 2.417924 CCCCGACAGAGATCTTGTCAAG 60.418 54.545 24.78 18.70 33.20 3.02
1697 1743 1.490574 CTTTCCCCCGACAGAGATCT 58.509 55.000 0.00 0.00 0.00 2.75
1705 1751 1.694844 TTGTTTTCCTTTCCCCCGAC 58.305 50.000 0.00 0.00 0.00 4.79
1716 1762 5.319140 ACCCTAACGCAATATTGTTTTCC 57.681 39.130 16.61 0.00 0.00 3.13
1722 1768 6.920569 AGTTCTTACCCTAACGCAATATTG 57.079 37.500 11.27 11.27 0.00 1.90
1723 1769 7.496920 GGTTAGTTCTTACCCTAACGCAATATT 59.503 37.037 0.00 0.00 42.45 1.28
1724 1770 6.988580 GGTTAGTTCTTACCCTAACGCAATAT 59.011 38.462 0.00 0.00 42.45 1.28
1725 1777 6.070881 TGGTTAGTTCTTACCCTAACGCAATA 60.071 38.462 5.70 0.00 42.45 1.90
1731 1783 6.596888 GGTGAATGGTTAGTTCTTACCCTAAC 59.403 42.308 5.70 0.00 41.36 2.34
1734 1786 4.323257 CGGTGAATGGTTAGTTCTTACCCT 60.323 45.833 5.70 0.00 33.34 4.34
1743 1795 3.070446 TGAACAGACGGTGAATGGTTAGT 59.930 43.478 0.00 0.00 0.00 2.24
1744 1796 3.659786 TGAACAGACGGTGAATGGTTAG 58.340 45.455 0.00 0.00 0.00 2.34
1745 1797 3.070446 ACTGAACAGACGGTGAATGGTTA 59.930 43.478 8.87 0.00 0.00 2.85
1746 1798 2.158813 ACTGAACAGACGGTGAATGGTT 60.159 45.455 8.87 0.00 0.00 3.67
1750 1803 1.070758 AGCACTGAACAGACGGTGAAT 59.929 47.619 8.87 0.00 46.40 2.57
1766 1819 3.059352 ACATCCAAGTCCAGTAAGCAC 57.941 47.619 0.00 0.00 0.00 4.40
1811 1865 1.277842 TGGTTGTATCCACATCTGCGT 59.722 47.619 0.00 0.00 33.76 5.24
1835 1889 3.131478 GGCGATGGTTTCCGTGGG 61.131 66.667 0.00 0.00 0.00 4.61
1840 1894 0.463116 ATGTACGGGCGATGGTTTCC 60.463 55.000 0.00 0.00 0.00 3.13
1845 1899 2.972505 GCCATGTACGGGCGATGG 60.973 66.667 12.01 8.45 42.39 3.51
1871 1928 1.378514 CACCGTTCCCATCCCAAGG 60.379 63.158 0.00 0.00 0.00 3.61
1889 1946 1.104577 TGAGTTGCGGGACAAAACCC 61.105 55.000 0.00 0.00 45.92 4.11
1909 1966 5.319453 TCTTGGAAATCATCTTCTGCAACT 58.681 37.500 0.00 0.00 0.00 3.16
1911 1968 5.535783 TGTTCTTGGAAATCATCTTCTGCAA 59.464 36.000 0.00 0.00 0.00 4.08
1916 1973 7.705325 CCAATGATGTTCTTGGAAATCATCTTC 59.295 37.037 13.02 0.00 43.83 2.87
1925 1982 2.886913 TGCCCAATGATGTTCTTGGAA 58.113 42.857 2.95 0.00 43.83 3.53
1926 1983 2.601240 TGCCCAATGATGTTCTTGGA 57.399 45.000 2.95 0.00 43.83 3.53
1978 2035 2.031120 CAAACTGCTTGTCCCCAAAGA 58.969 47.619 0.00 0.00 0.00 2.52
1988 2045 0.239347 CTTCCGAGCCAAACTGCTTG 59.761 55.000 0.00 0.00 42.95 4.01
1989 2046 0.890996 CCTTCCGAGCCAAACTGCTT 60.891 55.000 0.00 0.00 42.95 3.91
1990 2047 1.302832 CCTTCCGAGCCAAACTGCT 60.303 57.895 0.00 0.00 46.37 4.24
2099 2156 2.877786 CAAAAACTGAAATTGGCACCCC 59.122 45.455 0.00 0.00 0.00 4.95
2162 2219 8.573885 CCCTTTCGACACATACATATTACTAGA 58.426 37.037 0.00 0.00 0.00 2.43
2163 2220 7.813148 CCCCTTTCGACACATACATATTACTAG 59.187 40.741 0.00 0.00 0.00 2.57
2164 2221 7.288389 ACCCCTTTCGACACATACATATTACTA 59.712 37.037 0.00 0.00 0.00 1.82
2165 2222 6.099269 ACCCCTTTCGACACATACATATTACT 59.901 38.462 0.00 0.00 0.00 2.24
2166 2223 6.285990 ACCCCTTTCGACACATACATATTAC 58.714 40.000 0.00 0.00 0.00 1.89
2167 2224 6.488769 ACCCCTTTCGACACATACATATTA 57.511 37.500 0.00 0.00 0.00 0.98
2168 2225 5.367945 ACCCCTTTCGACACATACATATT 57.632 39.130 0.00 0.00 0.00 1.28
2169 2226 5.123227 CAACCCCTTTCGACACATACATAT 58.877 41.667 0.00 0.00 0.00 1.78
2170 2227 4.020039 ACAACCCCTTTCGACACATACATA 60.020 41.667 0.00 0.00 0.00 2.29
2171 2228 3.244770 ACAACCCCTTTCGACACATACAT 60.245 43.478 0.00 0.00 0.00 2.29
2172 2229 2.105134 ACAACCCCTTTCGACACATACA 59.895 45.455 0.00 0.00 0.00 2.29
2173 2230 2.774687 ACAACCCCTTTCGACACATAC 58.225 47.619 0.00 0.00 0.00 2.39
2174 2231 4.829872 ATACAACCCCTTTCGACACATA 57.170 40.909 0.00 0.00 0.00 2.29
2175 2232 3.713826 ATACAACCCCTTTCGACACAT 57.286 42.857 0.00 0.00 0.00 3.21
2176 2233 3.579586 ACTATACAACCCCTTTCGACACA 59.420 43.478 0.00 0.00 0.00 3.72
2177 2234 4.198028 ACTATACAACCCCTTTCGACAC 57.802 45.455 0.00 0.00 0.00 3.67
2178 2235 4.895668 AACTATACAACCCCTTTCGACA 57.104 40.909 0.00 0.00 0.00 4.35
2210 2267 9.921637 AAGTGAAAAGAAAACAAGTATCAACAA 57.078 25.926 0.00 0.00 0.00 2.83
2256 2398 4.685924 AGAAAAGTCTGCAACAAATGGTG 58.314 39.130 0.00 0.00 35.41 4.17
2297 2439 1.817447 GCTGTCCGTCTAGGTGTAGTT 59.183 52.381 0.00 0.00 41.99 2.24
2307 2449 2.500815 TAGGCTCTGGCTGTCCGTCT 62.501 60.000 3.85 0.00 39.30 4.18
2308 2450 1.395826 ATAGGCTCTGGCTGTCCGTC 61.396 60.000 3.85 0.00 39.30 4.79
2318 2460 5.046735 ACTCCATGCTTGTATATAGGCTCTG 60.047 44.000 5.23 3.26 0.00 3.35
2319 2461 5.046735 CACTCCATGCTTGTATATAGGCTCT 60.047 44.000 5.23 0.00 0.00 4.09
2320 2462 5.047021 TCACTCCATGCTTGTATATAGGCTC 60.047 44.000 5.23 0.00 0.00 4.70
2321 2463 4.840680 TCACTCCATGCTTGTATATAGGCT 59.159 41.667 5.23 0.00 0.00 4.58
2322 2464 5.152623 TCACTCCATGCTTGTATATAGGC 57.847 43.478 0.00 0.00 0.00 3.93
2323 2465 6.093219 GCATTCACTCCATGCTTGTATATAGG 59.907 42.308 0.00 0.00 43.26 2.57
2324 2466 7.069852 GCATTCACTCCATGCTTGTATATAG 57.930 40.000 0.00 0.00 43.26 1.31
2461 2603 3.659786 TGACTTAAATGTCCCGTGTCTG 58.340 45.455 0.00 0.00 36.21 3.51
2465 2607 2.097466 GCCATGACTTAAATGTCCCGTG 59.903 50.000 0.00 0.00 36.21 4.94
2468 2610 5.111293 CAAATGCCATGACTTAAATGTCCC 58.889 41.667 0.00 0.00 36.21 4.46
2469 2611 5.105392 TCCAAATGCCATGACTTAAATGTCC 60.105 40.000 0.00 0.00 36.21 4.02
2475 2619 5.394443 GCAAGATCCAAATGCCATGACTTAA 60.394 40.000 0.00 0.00 34.03 1.85
2476 2620 4.098349 GCAAGATCCAAATGCCATGACTTA 59.902 41.667 0.00 0.00 34.03 2.24
2482 2626 1.760613 CCTGCAAGATCCAAATGCCAT 59.239 47.619 7.62 0.00 39.31 4.40
2505 2649 3.132824 TGTGAACTGCCGATCATATGTCT 59.867 43.478 1.90 0.00 0.00 3.41
2506 2650 3.246226 GTGTGAACTGCCGATCATATGTC 59.754 47.826 1.90 0.00 0.00 3.06
2508 2652 2.545526 GGTGTGAACTGCCGATCATATG 59.454 50.000 0.00 0.00 0.00 1.78
2528 2672 1.596203 ATGATCATGCACCTCGCGG 60.596 57.895 7.59 0.00 46.97 6.46
2529 2673 0.877213 TCATGATCATGCACCTCGCG 60.877 55.000 27.68 0.00 46.97 5.87
2531 2675 1.202615 AGGTCATGATCATGCACCTCG 60.203 52.381 32.47 14.22 41.29 4.63
2544 2688 0.172578 CAGCAATGTGGCAGGTCATG 59.827 55.000 0.00 0.00 35.83 3.07
2579 2723 2.719426 ACAACCTCTTAACCTCGTCG 57.281 50.000 0.00 0.00 0.00 5.12
2609 2753 5.776519 TTTTGTTGTCAAACTGCAATGAC 57.223 34.783 16.13 16.13 44.84 3.06
2622 2766 5.006941 GGATATGCATGGCAATTTTGTTGTC 59.993 40.000 10.16 0.00 43.62 3.18
2724 2868 8.421002 ACAAATTTGTAAGGACATGTTAGCTTT 58.579 29.630 22.10 0.00 40.16 3.51
2734 2878 6.353323 TCTCTGACACAAATTTGTAAGGACA 58.647 36.000 22.87 15.43 39.91 4.02
2741 2885 5.581126 TTGCTTCTCTGACACAAATTTGT 57.419 34.783 18.13 18.13 43.36 2.83
2774 2918 2.989639 TCCGTTGAGGATGGCCAG 59.010 61.111 13.05 0.00 45.98 4.85
2794 2938 0.529119 GTCGGTCTTCACCAACGTGT 60.529 55.000 0.00 0.00 44.02 4.49
2797 2941 3.534160 CGTCGGTCTTCACCAACG 58.466 61.111 0.00 0.00 46.40 4.10
2798 2942 0.037605 ATCCGTCGGTCTTCACCAAC 60.038 55.000 11.88 0.00 44.02 3.77
2800 2944 0.611062 AGATCCGTCGGTCTTCACCA 60.611 55.000 11.88 0.00 44.02 4.17
2801 2945 0.531200 AAGATCCGTCGGTCTTCACC 59.469 55.000 17.89 1.51 39.69 4.02
2802 2946 1.201647 TCAAGATCCGTCGGTCTTCAC 59.798 52.381 19.72 5.50 32.60 3.18
2821 2968 4.008074 TGTCAAGTTCAGACCTCCAATC 57.992 45.455 0.00 0.00 35.15 2.67
2963 3110 1.062488 ACCCATCCCAGCCTACCATC 61.062 60.000 0.00 0.00 0.00 3.51
2993 3140 1.451028 GATGAGGCCTGGTGCACTC 60.451 63.158 12.00 7.60 43.89 3.51
3052 3199 6.521527 AGCCCATCTCTATCTTTTACCAAT 57.478 37.500 0.00 0.00 0.00 3.16
3066 3213 0.761802 CCTACTCCCAAGCCCATCTC 59.238 60.000 0.00 0.00 0.00 2.75
3087 3234 5.525484 TCTTGCTAAGAGTTATGACCCCTA 58.475 41.667 0.00 0.00 32.71 3.53
3125 3272 5.543405 AGCAAGAGGATCATACAAGCTCTAT 59.457 40.000 0.00 0.00 37.82 1.98
3130 3277 3.801698 TGAGCAAGAGGATCATACAAGC 58.198 45.455 0.00 0.00 36.91 4.01
3285 3463 4.644234 TGCAAGAAAAAGTCAGGAATGTGA 59.356 37.500 0.00 0.00 0.00 3.58
3362 3552 0.179001 GGGCACAAAGTGGGTACAGT 60.179 55.000 0.00 0.00 33.64 3.55
3371 3561 2.598394 AGCGCATGGGCACAAAGT 60.598 55.556 33.01 11.56 41.24 2.66
3382 3572 1.949525 ACTGAAAACACAAGAGCGCAT 59.050 42.857 11.47 0.00 0.00 4.73
3386 3576 5.825507 AGATTTCACTGAAAACACAAGAGC 58.174 37.500 8.28 0.00 35.11 4.09
3473 3664 3.068732 TCTGAGTAATTCTGGCGATGAGG 59.931 47.826 0.00 0.00 0.00 3.86
3572 3804 1.212195 GGGGGATGAAGGTGGTTCTAC 59.788 57.143 0.00 0.00 35.99 2.59
3574 3806 0.477597 TGGGGGATGAAGGTGGTTCT 60.478 55.000 0.00 0.00 35.99 3.01
3627 3859 8.473358 TCTCTATTCCTACATTTATTCGTCCA 57.527 34.615 0.00 0.00 0.00 4.02
3719 3951 0.619255 TGGAGGATTAGGGTTCCGCA 60.619 55.000 0.00 0.00 38.36 5.69
3726 3958 7.896383 TTGTATGAATTTTGGAGGATTAGGG 57.104 36.000 0.00 0.00 0.00 3.53
3805 4037 4.439968 GGTACTTACCATGTTAGTGGCTC 58.560 47.826 0.17 0.00 45.73 4.70
3917 4818 2.263741 CGAGCCTGTTTTGCCTGCT 61.264 57.895 0.00 0.00 34.40 4.24
3948 4849 3.387374 TCAATTTGTCCACAAGGTGCATT 59.613 39.130 0.00 0.00 37.15 3.56
3959 4860 4.706476 GGTGATGGAGATTCAATTTGTCCA 59.294 41.667 8.43 8.43 41.50 4.02


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

AutoCloner maintained by Alex Coulton.