Multiple sequence alignment - TraesCS2D01G408900

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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 TraesCS2D01G408900 chr2D 100.000 1777 0 0 1603 3379 523738484 523736708 0.000000e+00 3282.0
1 TraesCS2D01G408900 chr2D 100.000 1257 0 0 1 1257 523740086 523738830 0.000000e+00 2322.0
2 TraesCS2D01G408900 chr2A 93.154 1709 84 16 1686 3379 669558244 669556554 0.000000e+00 2477.0
3 TraesCS2D01G408900 chr2A 92.762 1271 59 16 1 1247 669559836 669558575 0.000000e+00 1807.0
4 TraesCS2D01G408900 chr2B 92.282 1205 75 6 1701 2898 618666576 618665383 0.000000e+00 1694.0
5 TraesCS2D01G408900 chr2B 97.092 447 12 1 773 1219 618667467 618667022 0.000000e+00 752.0
6 TraesCS2D01G408900 chr2B 91.463 410 23 8 2918 3322 618665322 618664920 1.370000e-153 553.0
7 TraesCS2D01G408900 chr4D 84.980 253 35 1 1787 2036 507119692 507119944 1.560000e-63 254.0
8 TraesCS2D01G408900 chr4D 82.540 252 41 3 1788 2036 507124901 507125152 5.680000e-53 219.0
9 TraesCS2D01G408900 chr5A 84.585 253 36 1 1787 2036 692062520 692062268 7.240000e-62 248.0
10 TraesCS2D01G408900 chr5A 82.186 247 41 3 1797 2040 692058237 692057991 3.420000e-50 209.0
11 TraesCS2D01G408900 chr4B 84.585 253 36 1 1787 2036 654466161 654465909 7.240000e-62 248.0
12 TraesCS2D01G408900 chr4B 83.529 255 39 3 1785 2036 654453590 654453336 5.640000e-58 235.0
13 TraesCS2D01G408900 chr1D 94.231 52 3 0 1786 1837 298574169 298574118 2.790000e-11 80.5
14 TraesCS2D01G408900 chr1A 92.308 52 4 0 1786 1837 372241483 372241432 1.300000e-09 75.0


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 TraesCS2D01G408900 chr2D 523736708 523740086 3378 True 2802.000000 3282 100.000000 1 3379 2 chr2D.!!$R1 3378
1 TraesCS2D01G408900 chr2A 669556554 669559836 3282 True 2142.000000 2477 92.958000 1 3379 2 chr2A.!!$R1 3378
2 TraesCS2D01G408900 chr2B 618664920 618667467 2547 True 999.666667 1694 93.612333 773 3322 3 chr2B.!!$R1 2549

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
632 644 0.034756 TTCCACTAGCAAGCGAGCAA 59.965 50.0 6.21 0.0 36.85 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2575 2627 0.181114 TATGCTAGGGTTGCCAGCTG 59.819 55.0 6.78 6.78 36.26 4.24 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
49 50 3.876198 GCCCGTAGCAATGCACGG 61.876 66.667 28.95 28.95 45.37 4.94
52 53 1.520564 CCGTAGCAATGCACGGCTA 60.521 57.895 26.54 15.15 42.39 3.93
93 94 6.017770 ATGTGTTTGACATTTGGAGCAAAATG 60.018 34.615 14.44 14.44 43.20 2.32
230 242 5.284079 TGTAAACCGAGAACACTCTTACAC 58.716 41.667 0.00 0.00 30.88 2.90
233 245 5.779529 AACCGAGAACACTCTTACACTTA 57.220 39.130 0.00 0.00 29.54 2.24
308 320 2.569657 CCACAGCAATGCGCATGT 59.430 55.556 26.09 16.64 46.13 3.21
311 323 0.179148 CACAGCAATGCGCATGTCAT 60.179 50.000 26.09 4.77 46.13 3.06
312 324 0.099968 ACAGCAATGCGCATGTCATC 59.900 50.000 26.09 11.20 46.13 2.92
317 329 1.669265 CAATGCGCATGTCATCTCACT 59.331 47.619 26.09 0.00 0.00 3.41
329 341 6.861065 TGTCATCTCACTTGGTTAAGTTTC 57.139 37.500 0.00 0.00 44.57 2.78
373 385 4.455533 TGTTCACTAATCAGTTGTGATGGC 59.544 41.667 0.00 0.00 43.04 4.40
380 392 1.203287 TCAGTTGTGATGGCGAGAGAG 59.797 52.381 0.00 0.00 0.00 3.20
381 393 1.203287 CAGTTGTGATGGCGAGAGAGA 59.797 52.381 0.00 0.00 0.00 3.10
391 403 3.525537 TGGCGAGAGAGACAATTTGATC 58.474 45.455 2.79 1.17 0.00 2.92
422 434 9.855361 CTGCACATTAGAAATTCGTTATCTTAG 57.145 33.333 0.00 0.00 0.00 2.18
446 458 0.463295 AGCTGCTCGATTCATGTGGG 60.463 55.000 0.00 0.00 0.00 4.61
479 491 2.898705 CGGAGTGCAAAAGCTAGATCT 58.101 47.619 0.00 0.00 0.00 2.75
529 541 1.411246 TGTCACGGGATGTATGGCTAC 59.589 52.381 0.00 0.00 0.00 3.58
544 556 9.941304 ATGTATGGCTACATAGCTAGGTAGGGG 62.941 48.148 34.44 18.95 44.85 4.79
547 559 3.245336 GCTACATAGCTAGGTAGGGGACT 60.245 52.174 34.44 6.87 45.62 3.85
548 560 3.529216 ACATAGCTAGGTAGGGGACTC 57.471 52.381 17.06 0.00 43.67 3.36
555 567 2.019807 AGGTAGGGGACTCGACAAAA 57.980 50.000 0.00 0.00 43.67 2.44
556 568 1.622312 AGGTAGGGGACTCGACAAAAC 59.378 52.381 0.00 0.00 43.67 2.43
632 644 0.034756 TTCCACTAGCAAGCGAGCAA 59.965 50.000 6.21 0.00 36.85 3.91
664 676 5.344743 TGTGCACCAAATTAACTGGAAAA 57.655 34.783 15.69 0.00 37.40 2.29
678 690 4.934356 ACTGGAAAATTGGAGGCTTGATA 58.066 39.130 0.00 0.00 0.00 2.15
708 720 4.386652 TGAGCTAACCGAAAACGACATTAC 59.613 41.667 0.00 0.00 0.00 1.89
733 745 3.326747 ACGCTTTTCAGAGTGATACACC 58.673 45.455 0.00 0.00 34.49 4.16
734 746 2.673368 CGCTTTTCAGAGTGATACACCC 59.327 50.000 0.00 0.00 34.49 4.61
755 774 5.048083 ACCCGTACGTACATTAGAAACTCAA 60.048 40.000 24.50 0.00 0.00 3.02
769 788 0.039798 ACTCAAGCATGCAAGCAACG 60.040 50.000 21.98 3.83 36.85 4.10
816 835 1.601171 CTTCCTCCTCCACCAGCTG 59.399 63.158 6.78 6.78 0.00 4.24
1101 1125 1.576421 GCGAAGAAAGTGCAGGTGG 59.424 57.895 0.00 0.00 0.00 4.61
1106 1130 2.594592 AAAGTGCAGGTGGTCGCC 60.595 61.111 0.00 0.00 0.00 5.54
1253 1277 4.643387 GGAGGCGGCAACTGTGGT 62.643 66.667 13.08 0.00 0.00 4.16
1254 1278 3.357079 GAGGCGGCAACTGTGGTG 61.357 66.667 13.08 0.00 0.00 4.17
1255 1279 4.954970 AGGCGGCAACTGTGGTGG 62.955 66.667 13.08 0.00 0.00 4.61
1619 1643 3.685435 GTGGTGGCAATGGTGGAG 58.315 61.111 0.00 0.00 0.00 3.86
1620 1644 1.978617 GTGGTGGCAATGGTGGAGG 60.979 63.158 0.00 0.00 0.00 4.30
1621 1645 3.070576 GGTGGCAATGGTGGAGGC 61.071 66.667 0.00 0.00 0.00 4.70
1622 1646 3.443045 GTGGCAATGGTGGAGGCG 61.443 66.667 0.00 0.00 0.00 5.52
1623 1647 4.738998 TGGCAATGGTGGAGGCGG 62.739 66.667 0.00 0.00 0.00 6.13
1624 1648 4.424711 GGCAATGGTGGAGGCGGA 62.425 66.667 0.00 0.00 0.00 5.54
1625 1649 2.361104 GCAATGGTGGAGGCGGAA 60.361 61.111 0.00 0.00 0.00 4.30
1626 1650 1.976474 GCAATGGTGGAGGCGGAAA 60.976 57.895 0.00 0.00 0.00 3.13
1627 1651 1.883021 CAATGGTGGAGGCGGAAAC 59.117 57.895 0.00 0.00 0.00 2.78
1628 1652 0.609131 CAATGGTGGAGGCGGAAACT 60.609 55.000 0.00 0.00 0.00 2.66
1629 1653 0.609131 AATGGTGGAGGCGGAAACTG 60.609 55.000 0.00 0.00 0.00 3.16
1630 1654 1.779061 ATGGTGGAGGCGGAAACTGT 61.779 55.000 0.00 0.00 0.00 3.55
1631 1655 1.671379 GGTGGAGGCGGAAACTGTC 60.671 63.158 0.00 0.00 0.00 3.51
1632 1656 1.671379 GTGGAGGCGGAAACTGTCC 60.671 63.158 0.00 0.00 43.90 4.02
1633 1657 2.046217 GGAGGCGGAAACTGTCCC 60.046 66.667 0.00 0.00 44.60 4.46
1634 1658 2.434359 GAGGCGGAAACTGTCCCG 60.434 66.667 14.67 14.67 44.60 5.14
1635 1659 3.952628 GAGGCGGAAACTGTCCCGG 62.953 68.421 18.74 0.00 44.60 5.73
1636 1660 4.011517 GGCGGAAACTGTCCCGGA 62.012 66.667 18.74 0.00 44.60 5.14
1637 1661 2.434359 GCGGAAACTGTCCCGGAG 60.434 66.667 18.74 0.00 44.60 4.63
1649 1673 2.742372 CCGGAGGCGGAAACTGTG 60.742 66.667 0.00 0.00 46.14 3.66
1650 1674 2.742372 CGGAGGCGGAAACTGTGG 60.742 66.667 0.00 0.00 0.00 4.17
1651 1675 3.056328 GGAGGCGGAAACTGTGGC 61.056 66.667 0.00 0.00 0.00 5.01
1652 1676 3.423154 GAGGCGGAAACTGTGGCG 61.423 66.667 0.00 0.00 0.00 5.69
1655 1679 2.975799 GCGGAAACTGTGGCGGAA 60.976 61.111 0.00 0.00 0.00 4.30
1656 1680 2.548295 GCGGAAACTGTGGCGGAAA 61.548 57.895 0.00 0.00 0.00 3.13
1657 1681 1.281656 CGGAAACTGTGGCGGAAAC 59.718 57.895 0.00 0.00 0.00 2.78
1670 1694 4.629523 GAAACGGTGGCGGTGGGA 62.630 66.667 0.00 0.00 0.00 4.37
1671 1695 4.192453 AAACGGTGGCGGTGGGAA 62.192 61.111 0.00 0.00 0.00 3.97
1672 1696 4.941309 AACGGTGGCGGTGGGAAC 62.941 66.667 0.00 0.00 0.00 3.62
1685 1709 4.011517 GGAACGGTGGCGGAGGAA 62.012 66.667 0.00 0.00 0.00 3.36
1686 1710 2.031465 GAACGGTGGCGGAGGAAA 59.969 61.111 0.00 0.00 0.00 3.13
1687 1711 2.281276 AACGGTGGCGGAGGAAAC 60.281 61.111 0.00 0.00 0.00 2.78
1688 1712 4.675029 ACGGTGGCGGAGGAAACG 62.675 66.667 0.00 0.00 0.00 3.60
1690 1714 4.324991 GGTGGCGGAGGAAACGGT 62.325 66.667 0.00 0.00 0.00 4.83
1691 1715 3.047877 GTGGCGGAGGAAACGGTG 61.048 66.667 0.00 0.00 0.00 4.94
1692 1716 4.323477 TGGCGGAGGAAACGGTGG 62.323 66.667 0.00 0.00 0.00 4.61
1693 1717 4.011517 GGCGGAGGAAACGGTGGA 62.012 66.667 0.00 0.00 0.00 4.02
1694 1718 2.434359 GCGGAGGAAACGGTGGAG 60.434 66.667 0.00 0.00 0.00 3.86
1695 1719 2.264794 CGGAGGAAACGGTGGAGG 59.735 66.667 0.00 0.00 0.00 4.30
1696 1720 2.580601 CGGAGGAAACGGTGGAGGT 61.581 63.158 0.00 0.00 0.00 3.85
1723 1747 4.011517 GGCGGAGGAAACGGTGGA 62.012 66.667 0.00 0.00 0.00 4.02
1844 1883 3.888460 TGCTGGGGCTGCTGAACA 61.888 61.111 0.00 0.00 39.59 3.18
1948 1987 1.009389 CGACGCTGAACCTCAACCTC 61.009 60.000 0.00 0.00 0.00 3.85
1970 2009 0.251341 GGGCATCAACCTGACCTTGT 60.251 55.000 0.00 0.00 41.52 3.16
2136 2179 2.809696 ACCACCACGTACTTAATTGTGC 59.190 45.455 0.00 0.00 0.00 4.57
2153 2196 4.671880 TGTGCGCTTTGATTACGTAATT 57.328 36.364 21.18 6.15 0.00 1.40
2283 2332 2.653890 GTTGTGTGTGTGCATGATGTC 58.346 47.619 0.00 0.00 0.00 3.06
2533 2583 6.316140 TGCACTATTTGTATTGACTTGCCTAG 59.684 38.462 0.00 0.00 0.00 3.02
2575 2627 4.393371 GGAGAAAAGGAGCACTTGTATGAC 59.607 45.833 0.00 0.00 39.96 3.06
2594 2646 0.181114 CAGCTGGCAACCCTAGCATA 59.819 55.000 5.57 0.00 37.58 3.14
2613 2665 2.328819 ACTACCTGATACTCGTCGCT 57.671 50.000 0.00 0.00 0.00 4.93
2621 2673 4.083271 CCTGATACTCGTCGCTGATTATGA 60.083 45.833 0.00 0.00 0.00 2.15
2653 2705 2.178912 AAAGTCGGGCTCATTTCGAA 57.821 45.000 0.00 0.00 34.62 3.71
2686 2738 7.778083 TCTAAGCAAACGATATTGAGAACCTA 58.222 34.615 0.00 0.00 31.84 3.08
2913 2965 9.176460 GTTCAGTGAAGGATTACTAGTAGTAGT 57.824 37.037 14.57 14.57 42.49 2.73
2963 3056 9.219603 CCTCTGTTGTAAATTAGATGACTTTCA 57.780 33.333 0.00 0.00 0.00 2.69
3131 3228 0.670239 CCCTTGGAAATTGCGGCAAC 60.670 55.000 18.94 5.81 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.961394 CCCTAGTAGAATAGCCGTGCA 59.039 52.381 0.00 0.00 0.00 4.57
47 48 6.039493 CACATATACCCCTAGTAGAATAGCCG 59.961 46.154 0.00 0.00 33.42 5.52
49 50 7.957992 ACACATATACCCCTAGTAGAATAGC 57.042 40.000 0.00 0.00 33.42 2.97
52 53 8.648693 GTCAAACACATATACCCCTAGTAGAAT 58.351 37.037 0.00 0.00 33.42 2.40
118 119 7.964545 AAACTTAACACAACGTCATCTTTTC 57.035 32.000 0.00 0.00 0.00 2.29
268 280 7.544217 GTGGGAATGGTGTGAAAATTGTATAAC 59.456 37.037 0.00 0.00 0.00 1.89
273 285 3.708631 TGTGGGAATGGTGTGAAAATTGT 59.291 39.130 0.00 0.00 0.00 2.71
281 293 1.067425 CATTGCTGTGGGAATGGTGTG 60.067 52.381 2.99 0.00 44.13 3.82
308 320 7.502226 ACAATGAAACTTAACCAAGTGAGATGA 59.498 33.333 0.00 0.00 44.41 2.92
311 323 6.459573 GCACAATGAAACTTAACCAAGTGAGA 60.460 38.462 0.00 0.00 44.41 3.27
312 324 5.687285 GCACAATGAAACTTAACCAAGTGAG 59.313 40.000 0.00 0.00 44.41 3.51
317 329 5.330455 TGTGCACAATGAAACTTAACCAA 57.670 34.783 19.28 0.00 0.00 3.67
373 385 6.034790 CAGTCAAGATCAAATTGTCTCTCTCG 59.965 42.308 0.00 0.00 0.00 4.04
380 392 5.112220 TGTGCAGTCAAGATCAAATTGTC 57.888 39.130 0.00 0.00 0.00 3.18
381 393 5.717078 ATGTGCAGTCAAGATCAAATTGT 57.283 34.783 0.00 0.00 0.00 2.71
391 403 5.931532 ACGAATTTCTAATGTGCAGTCAAG 58.068 37.500 0.00 0.00 0.00 3.02
427 439 0.463295 CCCACATGAATCGAGCAGCT 60.463 55.000 0.00 0.00 0.00 4.24
430 442 1.815003 CGCCCACATGAATCGAGCA 60.815 57.895 0.00 0.00 0.00 4.26
471 483 0.179037 TGGTGCATGGCAGATCTAGC 60.179 55.000 0.00 1.48 40.08 3.42
479 491 2.341875 CGTTGGATGGTGCATGGCA 61.342 57.895 0.00 0.00 35.60 4.92
529 541 2.040012 TCGAGTCCCCTACCTAGCTATG 59.960 54.545 0.00 0.00 0.00 2.23
544 556 7.061210 CCATCATAGATATCGTTTTGTCGAGTC 59.939 40.741 0.00 0.00 43.00 3.36
547 559 6.156519 CCCATCATAGATATCGTTTTGTCGA 58.843 40.000 0.00 0.00 43.86 4.20
548 560 5.348724 CCCCATCATAGATATCGTTTTGTCG 59.651 44.000 0.00 0.00 0.00 4.35
555 567 3.891977 CGATCCCCCATCATAGATATCGT 59.108 47.826 0.00 0.00 32.51 3.73
556 568 3.305676 GCGATCCCCCATCATAGATATCG 60.306 52.174 0.00 0.00 38.33 2.92
664 676 1.765314 AGTCGCTATCAAGCCTCCAAT 59.235 47.619 0.00 0.00 46.68 3.16
678 690 0.601558 TTCGGTTAGCTCAAGTCGCT 59.398 50.000 0.00 0.00 41.35 4.93
708 720 5.061064 GTGTATCACTCTGAAAAGCGTACTG 59.939 44.000 0.00 0.00 0.00 2.74
733 745 5.004156 GCTTGAGTTTCTAATGTACGTACGG 59.996 44.000 21.06 10.53 0.00 4.02
734 746 5.570206 TGCTTGAGTTTCTAATGTACGTACG 59.430 40.000 20.18 15.01 0.00 3.67
755 774 4.409218 CGGCGTTGCTTGCATGCT 62.409 61.111 23.31 0.00 0.00 3.79
816 835 1.139947 GTGAGCCAGCGTCTAGTCC 59.860 63.158 0.00 0.00 0.00 3.85
1070 1094 1.485124 TCTTCGCCATCTCTGCCTAA 58.515 50.000 0.00 0.00 0.00 2.69
1106 1130 4.020617 TTCAGGGCCAGGAGCGTG 62.021 66.667 6.18 0.00 45.17 5.34
1602 1626 1.978617 CCTCCACCATTGCCACCAC 60.979 63.158 0.00 0.00 0.00 4.16
1603 1627 2.440147 CCTCCACCATTGCCACCA 59.560 61.111 0.00 0.00 0.00 4.17
1604 1628 3.070576 GCCTCCACCATTGCCACC 61.071 66.667 0.00 0.00 0.00 4.61
1605 1629 3.443045 CGCCTCCACCATTGCCAC 61.443 66.667 0.00 0.00 0.00 5.01
1606 1630 4.738998 CCGCCTCCACCATTGCCA 62.739 66.667 0.00 0.00 0.00 4.92
1607 1631 3.936772 TTCCGCCTCCACCATTGCC 62.937 63.158 0.00 0.00 0.00 4.52
1608 1632 1.976474 TTTCCGCCTCCACCATTGC 60.976 57.895 0.00 0.00 0.00 3.56
1609 1633 0.609131 AGTTTCCGCCTCCACCATTG 60.609 55.000 0.00 0.00 0.00 2.82
1610 1634 0.609131 CAGTTTCCGCCTCCACCATT 60.609 55.000 0.00 0.00 0.00 3.16
1611 1635 1.002134 CAGTTTCCGCCTCCACCAT 60.002 57.895 0.00 0.00 0.00 3.55
1612 1636 2.391724 GACAGTTTCCGCCTCCACCA 62.392 60.000 0.00 0.00 0.00 4.17
1613 1637 1.671379 GACAGTTTCCGCCTCCACC 60.671 63.158 0.00 0.00 0.00 4.61
1614 1638 1.671379 GGACAGTTTCCGCCTCCAC 60.671 63.158 0.00 0.00 33.46 4.02
1615 1639 2.747686 GGACAGTTTCCGCCTCCA 59.252 61.111 0.00 0.00 33.46 3.86
1622 1646 2.046217 GCCTCCGGGACAGTTTCC 60.046 66.667 0.00 0.00 45.00 3.13
1623 1647 2.434359 CGCCTCCGGGACAGTTTC 60.434 66.667 0.00 0.00 33.58 2.78
1633 1657 2.742372 CCACAGTTTCCGCCTCCG 60.742 66.667 0.00 0.00 0.00 4.63
1634 1658 3.056328 GCCACAGTTTCCGCCTCC 61.056 66.667 0.00 0.00 0.00 4.30
1635 1659 3.423154 CGCCACAGTTTCCGCCTC 61.423 66.667 0.00 0.00 0.00 4.70
1638 1662 2.548295 TTTCCGCCACAGTTTCCGC 61.548 57.895 0.00 0.00 0.00 5.54
1639 1663 1.281656 GTTTCCGCCACAGTTTCCG 59.718 57.895 0.00 0.00 0.00 4.30
1640 1664 1.281656 CGTTTCCGCCACAGTTTCC 59.718 57.895 0.00 0.00 0.00 3.13
1641 1665 1.281656 CCGTTTCCGCCACAGTTTC 59.718 57.895 0.00 0.00 0.00 2.78
1642 1666 1.452470 ACCGTTTCCGCCACAGTTT 60.452 52.632 0.00 0.00 0.00 2.66
1643 1667 2.184167 CACCGTTTCCGCCACAGTT 61.184 57.895 0.00 0.00 0.00 3.16
1644 1668 2.590575 CACCGTTTCCGCCACAGT 60.591 61.111 0.00 0.00 0.00 3.55
1645 1669 3.353836 CCACCGTTTCCGCCACAG 61.354 66.667 0.00 0.00 0.00 3.66
1653 1677 4.629523 TCCCACCGCCACCGTTTC 62.630 66.667 0.00 0.00 0.00 2.78
1654 1678 4.192453 TTCCCACCGCCACCGTTT 62.192 61.111 0.00 0.00 0.00 3.60
1655 1679 4.941309 GTTCCCACCGCCACCGTT 62.941 66.667 0.00 0.00 0.00 4.44
1668 1692 3.540367 TTTCCTCCGCCACCGTTCC 62.540 63.158 0.00 0.00 0.00 3.62
1669 1693 2.031465 TTTCCTCCGCCACCGTTC 59.969 61.111 0.00 0.00 0.00 3.95
1670 1694 2.281276 GTTTCCTCCGCCACCGTT 60.281 61.111 0.00 0.00 0.00 4.44
1671 1695 4.675029 CGTTTCCTCCGCCACCGT 62.675 66.667 0.00 0.00 0.00 4.83
1673 1697 4.324991 ACCGTTTCCTCCGCCACC 62.325 66.667 0.00 0.00 0.00 4.61
1674 1698 3.047877 CACCGTTTCCTCCGCCAC 61.048 66.667 0.00 0.00 0.00 5.01
1675 1699 4.323477 CCACCGTTTCCTCCGCCA 62.323 66.667 0.00 0.00 0.00 5.69
1676 1700 3.952628 CTCCACCGTTTCCTCCGCC 62.953 68.421 0.00 0.00 0.00 6.13
1677 1701 2.434359 CTCCACCGTTTCCTCCGC 60.434 66.667 0.00 0.00 0.00 5.54
1678 1702 2.264794 CCTCCACCGTTTCCTCCG 59.735 66.667 0.00 0.00 0.00 4.63
1679 1703 1.003718 CACCTCCACCGTTTCCTCC 60.004 63.158 0.00 0.00 0.00 4.30
1680 1704 1.003718 CCACCTCCACCGTTTCCTC 60.004 63.158 0.00 0.00 0.00 3.71
1681 1705 2.526046 CCCACCTCCACCGTTTCCT 61.526 63.158 0.00 0.00 0.00 3.36
1682 1706 2.033602 CCCACCTCCACCGTTTCC 59.966 66.667 0.00 0.00 0.00 3.13
1683 1707 0.887836 GTTCCCACCTCCACCGTTTC 60.888 60.000 0.00 0.00 0.00 2.78
1684 1708 1.149854 GTTCCCACCTCCACCGTTT 59.850 57.895 0.00 0.00 0.00 3.60
1685 1709 2.833957 GTTCCCACCTCCACCGTT 59.166 61.111 0.00 0.00 0.00 4.44
1686 1710 3.622826 CGTTCCCACCTCCACCGT 61.623 66.667 0.00 0.00 0.00 4.83
1687 1711 4.388499 CCGTTCCCACCTCCACCG 62.388 72.222 0.00 0.00 0.00 4.94
1688 1712 3.246880 ACCGTTCCCACCTCCACC 61.247 66.667 0.00 0.00 0.00 4.61
1689 1713 2.032071 CACCGTTCCCACCTCCAC 59.968 66.667 0.00 0.00 0.00 4.02
1690 1714 3.246112 CCACCGTTCCCACCTCCA 61.246 66.667 0.00 0.00 0.00 3.86
1691 1715 4.717313 GCCACCGTTCCCACCTCC 62.717 72.222 0.00 0.00 0.00 4.30
1711 1735 2.526046 CCCACCTCCACCGTTTCCT 61.526 63.158 0.00 0.00 0.00 3.36
1723 1747 4.047125 CCGCCACCATTCCCACCT 62.047 66.667 0.00 0.00 0.00 4.00
1831 1870 1.037579 GGGTAATGTTCAGCAGCCCC 61.038 60.000 0.00 0.00 33.89 5.80
1844 1883 2.772622 CGGGCTCCCCAGGGTAAT 60.773 66.667 4.22 0.00 45.83 1.89
1948 1987 1.379044 GGTCAGGTTGATGCCCAGG 60.379 63.158 0.00 0.00 0.00 4.45
1970 2009 3.157252 GAGGCTGAGGGCGATGGA 61.157 66.667 0.00 0.00 42.94 3.41
2058 2097 1.577922 GTATGGCGGATGCAGCATG 59.422 57.895 14.22 0.00 45.35 4.06
2059 2098 1.601759 GGTATGGCGGATGCAGCAT 60.602 57.895 7.91 7.91 45.35 3.79
2060 2099 2.203195 GGTATGGCGGATGCAGCA 60.203 61.111 3.51 0.00 45.35 4.41
2061 2100 1.963338 GAGGTATGGCGGATGCAGC 60.963 63.158 0.00 0.00 45.35 5.25
2136 2179 6.787515 CAGCAGATAATTACGTAATCAAAGCG 59.212 38.462 20.57 9.54 0.00 4.68
2153 2196 4.157656 GCCACACATAAAAACCAGCAGATA 59.842 41.667 0.00 0.00 0.00 1.98
2283 2332 4.903638 AACATGTGACGATTACGACAAG 57.096 40.909 0.00 0.00 44.04 3.16
2406 2455 6.820470 GCACAGTGCAAAAATAGTAAAACA 57.180 33.333 21.22 0.00 44.26 2.83
2450 2500 4.144297 ACCATTCAAACACACTACATGCT 58.856 39.130 0.00 0.00 0.00 3.79
2460 2510 3.430218 CGAGAGTGAGACCATTCAAACAC 59.570 47.826 0.00 0.00 32.14 3.32
2538 2588 5.241506 TCCTTTTCTCCTCTCGTAACGTTAA 59.758 40.000 10.11 0.00 0.00 2.01
2543 2593 3.056749 TGCTCCTTTTCTCCTCTCGTAAC 60.057 47.826 0.00 0.00 0.00 2.50
2575 2627 0.181114 TATGCTAGGGTTGCCAGCTG 59.819 55.000 6.78 6.78 36.26 4.24
2594 2646 1.941294 CAGCGACGAGTATCAGGTAGT 59.059 52.381 0.00 0.00 33.17 2.73
2653 2705 3.695830 TCGTTTGCTTAGAGGAATGGT 57.304 42.857 0.00 0.00 0.00 3.55
2686 2738 6.490381 GGGAGAATTAGTTTTCCAGTTCACTT 59.510 38.462 9.39 0.00 39.71 3.16
2813 2865 8.506168 TTCTGAACTAGCTTATTAATGGTTGG 57.494 34.615 0.00 0.00 0.00 3.77
2911 2963 7.499895 GGACAGTTGTCTAGCTATCTAGTAACT 59.500 40.741 11.67 14.51 43.47 2.24
2913 2965 6.771749 GGGACAGTTGTCTAGCTATCTAGTAA 59.228 42.308 11.67 0.00 44.20 2.24
2970 3067 5.474876 AGTTTGAAAGTGTTGATCCCATCTC 59.525 40.000 0.00 0.00 0.00 2.75
3040 3137 1.768275 ACACAGTCATGGAACCTGACA 59.232 47.619 18.15 0.00 44.37 3.58
3041 3138 2.550830 ACACAGTCATGGAACCTGAC 57.449 50.000 12.20 12.20 42.68 3.51
3221 3322 8.251026 TCTAAGTTGATCGAACACATATCACTT 58.749 33.333 11.37 11.37 36.98 3.16
3323 3424 9.093970 CACCGTTGAGAACTGTTCAATTATATA 57.906 33.333 21.50 0.00 36.96 0.86
3324 3425 7.822334 TCACCGTTGAGAACTGTTCAATTATAT 59.178 33.333 21.50 0.00 36.96 0.86


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

AutoCloner maintained by Alex Coulton.