Multiple sequence alignment - TraesCS5A01G545900

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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 TraesCS5A01G545900 chr5A 100.000 2676 0 0 1 2676 700446401 700443726 0 4942
1 TraesCS5A01G545900 chrUn 87.754 2752 186 62 1 2662 110523806 110521116 0 3075
2 TraesCS5A01G545900 chr4B 86.703 2745 197 76 1 2658 660592051 660589388 0 2892


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 TraesCS5A01G545900 chr5A 700443726 700446401 2675 True 4942 4942 100.000 1 2676 1 chr5A.!!$R1 2675
1 TraesCS5A01G545900 chrUn 110521116 110523806 2690 True 3075 3075 87.754 1 2662 1 chrUn.!!$R1 2661
2 TraesCS5A01G545900 chr4B 660589388 660592051 2663 True 2892 2892 86.703 1 2658 1 chr4B.!!$R1 2657

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
504 549 0.038892 GGCAAACACAGCACATGAGG 60.039 55.0 0.0 0.0 0.00 3.86 F
961 1065 0.103208 CAAATAGCCCGTCTCTCGCT 59.897 55.0 0.0 0.0 38.35 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1667 0.39086 GCGGCTGTACTCATCTGGAT 59.609 55.0 0.00 0.0 0.00 3.41 R
2379 2578 0.73288 CACGTCCTTGTAGAGCGTGG 60.733 60.0 7.39 0.0 45.96 4.94 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
42 43 3.313012 ACGACTTTGATTCCATCGTCA 57.687 42.857 0.00 0.00 41.96 4.35
72 73 1.475034 GCGGCATCCTTGGATAACAGA 60.475 52.381 1.37 0.00 0.00 3.41
150 154 6.662865 ATCACTAGATGATGAGGGTTACAG 57.337 41.667 0.00 0.00 46.85 2.74
157 161 2.027192 TGATGAGGGTTACAGCTGTTCC 60.027 50.000 27.06 25.06 0.00 3.62
159 163 1.003718 AGGGTTACAGCTGTTCCGC 60.004 57.895 27.06 21.91 0.00 5.54
190 224 6.662755 AGTTCAATAGGCAATACCAAGATCA 58.337 36.000 0.00 0.00 43.14 2.92
264 298 1.457346 GCAACTCTGCCTGCAAGTAT 58.543 50.000 7.17 0.00 43.26 2.12
275 309 3.941483 GCCTGCAAGTATGTTGTGTAGAT 59.059 43.478 0.00 0.00 0.00 1.98
307 347 2.917933 TGTGTATAAGCCTGTGGATGC 58.082 47.619 0.00 0.00 0.00 3.91
380 425 4.269523 GTGTGGGTGAGCAGGCCA 62.270 66.667 5.01 0.00 0.00 5.36
392 437 3.092511 AGGCCATCCTCCACGCAT 61.093 61.111 5.01 0.00 38.72 4.73
393 438 2.903855 GGCCATCCTCCACGCATG 60.904 66.667 0.00 0.00 0.00 4.06
419 464 0.602905 CGCGTTTCTTGAACCCCTCT 60.603 55.000 0.00 0.00 34.67 3.69
483 528 1.421485 GGTTCGCACGAATCTGCAG 59.579 57.895 7.63 7.63 36.94 4.41
485 530 0.368227 GTTCGCACGAATCTGCAGAG 59.632 55.000 22.96 11.21 36.94 3.35
500 545 0.956633 CAGAGGCAAACACAGCACAT 59.043 50.000 0.00 0.00 0.00 3.21
501 546 0.956633 AGAGGCAAACACAGCACATG 59.043 50.000 0.00 0.00 0.00 3.21
502 547 0.953727 GAGGCAAACACAGCACATGA 59.046 50.000 0.00 0.00 0.00 3.07
503 548 0.956633 AGGCAAACACAGCACATGAG 59.043 50.000 0.00 0.00 0.00 2.90
504 549 0.038892 GGCAAACACAGCACATGAGG 60.039 55.000 0.00 0.00 0.00 3.86
505 550 0.953727 GCAAACACAGCACATGAGGA 59.046 50.000 0.00 0.00 0.00 3.71
506 551 1.337703 GCAAACACAGCACATGAGGAA 59.662 47.619 0.00 0.00 0.00 3.36
507 552 2.029649 GCAAACACAGCACATGAGGAAT 60.030 45.455 0.00 0.00 0.00 3.01
508 553 3.553508 GCAAACACAGCACATGAGGAATT 60.554 43.478 0.00 0.00 0.00 2.17
509 554 4.624015 CAAACACAGCACATGAGGAATTT 58.376 39.130 0.00 0.00 0.00 1.82
510 555 4.942761 AACACAGCACATGAGGAATTTT 57.057 36.364 0.00 0.00 0.00 1.82
511 556 4.510038 ACACAGCACATGAGGAATTTTC 57.490 40.909 0.00 0.00 0.00 2.29
512 557 3.890756 ACACAGCACATGAGGAATTTTCA 59.109 39.130 0.00 0.00 0.00 2.69
513 558 4.525487 ACACAGCACATGAGGAATTTTCAT 59.475 37.500 0.00 1.70 35.73 2.57
514 559 5.011329 ACACAGCACATGAGGAATTTTCATT 59.989 36.000 0.00 0.00 33.14 2.57
515 560 5.575606 CACAGCACATGAGGAATTTTCATTC 59.424 40.000 0.00 0.00 38.54 2.67
516 561 4.796830 CAGCACATGAGGAATTTTCATTCG 59.203 41.667 0.00 1.41 39.99 3.34
517 562 4.107622 GCACATGAGGAATTTTCATTCGG 58.892 43.478 0.00 0.00 39.99 4.30
518 563 4.142403 GCACATGAGGAATTTTCATTCGGA 60.142 41.667 0.00 0.00 39.99 4.55
519 564 5.335127 CACATGAGGAATTTTCATTCGGAC 58.665 41.667 0.00 0.00 39.99 4.79
535 580 5.733620 TTCGGACAGATTAACAAGGTAGT 57.266 39.130 0.00 0.00 0.00 2.73
566 611 7.119699 TGCTTCTCATGGTAAGTAATTGAACTG 59.880 37.037 8.97 0.00 0.00 3.16
574 619 1.806542 AGTAATTGAACTGCTGCCGTG 59.193 47.619 0.00 0.00 0.00 4.94
575 620 1.804151 GTAATTGAACTGCTGCCGTGA 59.196 47.619 0.00 0.00 0.00 4.35
576 621 0.877071 AATTGAACTGCTGCCGTGAG 59.123 50.000 0.00 0.00 0.00 3.51
577 622 1.580845 ATTGAACTGCTGCCGTGAGC 61.581 55.000 0.00 0.00 44.14 4.26
610 655 2.908796 GGGGGTCGAGGAATCACC 59.091 66.667 0.00 0.00 39.35 4.02
611 656 2.499685 GGGGTCGAGGAATCACCG 59.500 66.667 0.00 0.00 44.74 4.94
613 658 1.039233 GGGGTCGAGGAATCACCGTA 61.039 60.000 0.00 0.00 44.74 4.02
730 807 3.827898 CAGGCGGAGGAGGTCGTC 61.828 72.222 0.00 0.00 0.00 4.20
833 919 1.388837 GCTCCGTCCTCCCTCTTCTC 61.389 65.000 0.00 0.00 0.00 2.87
834 920 0.753848 CTCCGTCCTCCCTCTTCTCC 60.754 65.000 0.00 0.00 0.00 3.71
836 922 1.758906 CGTCCTCCCTCTTCTCCCC 60.759 68.421 0.00 0.00 0.00 4.81
837 923 1.758906 GTCCTCCCTCTTCTCCCCG 60.759 68.421 0.00 0.00 0.00 5.73
838 924 2.444895 CCTCCCTCTTCTCCCCGG 60.445 72.222 0.00 0.00 0.00 5.73
839 925 2.364961 CTCCCTCTTCTCCCCGGT 59.635 66.667 0.00 0.00 0.00 5.28
840 926 2.038975 TCCCTCTTCTCCCCGGTG 59.961 66.667 0.00 0.00 0.00 4.94
841 927 2.038975 CCCTCTTCTCCCCGGTGA 59.961 66.667 0.00 0.00 0.00 4.02
842 928 2.060980 CCCTCTTCTCCCCGGTGAG 61.061 68.421 7.75 7.75 0.00 3.51
843 929 2.726351 CCTCTTCTCCCCGGTGAGC 61.726 68.421 9.37 0.00 32.22 4.26
844 930 2.683933 TCTTCTCCCCGGTGAGCC 60.684 66.667 9.37 0.00 32.22 4.70
850 936 4.787280 CCCCGGTGAGCCTCTCCT 62.787 72.222 10.85 0.00 0.00 3.69
851 937 2.685380 CCCGGTGAGCCTCTCCTT 60.685 66.667 10.85 0.00 0.00 3.36
860 946 0.715987 AGCCTCTCCTTCTCCTCCTT 59.284 55.000 0.00 0.00 0.00 3.36
876 962 0.251165 CCTTCGGCCTTTTTCCTCCA 60.251 55.000 0.00 0.00 0.00 3.86
904 990 1.453235 CGTCCATGGCCCATCTGAT 59.547 57.895 6.96 0.00 0.00 2.90
910 996 0.400975 ATGGCCCATCTGATCTGAGC 59.599 55.000 0.00 6.17 0.00 4.26
911 997 0.693430 TGGCCCATCTGATCTGAGCT 60.693 55.000 0.00 0.00 0.00 4.09
912 998 0.473326 GGCCCATCTGATCTGAGCTT 59.527 55.000 8.37 0.00 0.00 3.74
913 999 1.696336 GGCCCATCTGATCTGAGCTTA 59.304 52.381 8.37 0.00 0.00 3.09
915 1001 2.289569 GCCCATCTGATCTGAGCTTAGG 60.290 54.545 5.56 5.43 0.00 2.69
916 1002 2.289569 CCCATCTGATCTGAGCTTAGGC 60.290 54.545 5.56 0.00 39.06 3.93
918 1004 1.418334 TCTGATCTGAGCTTAGGCCC 58.582 55.000 5.56 0.00 39.73 5.80
920 1006 0.833287 TGATCTGAGCTTAGGCCCAC 59.167 55.000 5.56 0.00 39.73 4.61
923 1009 0.902984 TCTGAGCTTAGGCCCACGAA 60.903 55.000 5.56 0.00 39.73 3.85
937 1023 3.055719 CGAACAAGCCCACCGCAT 61.056 61.111 0.00 0.00 41.38 4.73
961 1065 0.103208 CAAATAGCCCGTCTCTCGCT 59.897 55.000 0.00 0.00 38.35 4.93
987 1091 0.806492 GCATCTCGACGGAAGGGAAC 60.806 60.000 0.00 0.00 0.00 3.62
988 1092 0.530744 CATCTCGACGGAAGGGAACA 59.469 55.000 0.00 0.00 0.00 3.18
1359 1473 0.108138 CCTACCTCGGCTCCAACTTG 60.108 60.000 0.00 0.00 0.00 3.16
1402 1516 1.279271 CCTTCTCCACCATCTTCGGTT 59.721 52.381 0.00 0.00 37.07 4.44
1403 1517 2.622436 CTTCTCCACCATCTTCGGTTC 58.378 52.381 0.00 0.00 37.07 3.62
1404 1518 0.530744 TCTCCACCATCTTCGGTTCG 59.469 55.000 0.00 0.00 37.07 3.95
1405 1519 0.246635 CTCCACCATCTTCGGTTCGT 59.753 55.000 0.00 0.00 37.07 3.85
1406 1520 0.245539 TCCACCATCTTCGGTTCGTC 59.754 55.000 0.00 0.00 37.07 4.20
1407 1521 1.076533 CCACCATCTTCGGTTCGTCG 61.077 60.000 0.00 0.00 37.07 5.12
1409 1523 0.109412 ACCATCTTCGGTTCGTCGTC 60.109 55.000 0.00 0.00 34.91 4.20
1411 1525 1.399440 CCATCTTCGGTTCGTCGTCTA 59.601 52.381 0.00 0.00 0.00 2.59
1412 1526 2.438583 CATCTTCGGTTCGTCGTCTAC 58.561 52.381 0.00 0.00 0.00 2.59
1414 1528 0.518636 CTTCGGTTCGTCGTCTACCA 59.481 55.000 12.14 1.03 32.12 3.25
1415 1529 0.238289 TTCGGTTCGTCGTCTACCAC 59.762 55.000 12.14 0.00 32.12 4.16
1416 1530 1.154150 CGGTTCGTCGTCTACCACC 60.154 63.158 12.14 0.00 32.12 4.61
1417 1531 1.855213 CGGTTCGTCGTCTACCACCA 61.855 60.000 12.14 0.00 30.96 4.17
1418 1532 0.529378 GGTTCGTCGTCTACCACCAT 59.471 55.000 8.40 0.00 30.96 3.55
1419 1533 1.468736 GGTTCGTCGTCTACCACCATC 60.469 57.143 8.40 0.00 30.96 3.51
1420 1534 1.471684 GTTCGTCGTCTACCACCATCT 59.528 52.381 0.00 0.00 0.00 2.90
1421 1535 1.830279 TCGTCGTCTACCACCATCTT 58.170 50.000 0.00 0.00 0.00 2.40
1422 1536 1.741706 TCGTCGTCTACCACCATCTTC 59.258 52.381 0.00 0.00 0.00 2.87
1423 1537 1.471287 CGTCGTCTACCACCATCTTCA 59.529 52.381 0.00 0.00 0.00 3.02
1424 1538 2.731341 CGTCGTCTACCACCATCTTCAC 60.731 54.545 0.00 0.00 0.00 3.18
1425 1539 2.492484 GTCGTCTACCACCATCTTCACT 59.508 50.000 0.00 0.00 0.00 3.41
1426 1540 3.056749 GTCGTCTACCACCATCTTCACTT 60.057 47.826 0.00 0.00 0.00 3.16
1427 1541 3.192844 TCGTCTACCACCATCTTCACTTC 59.807 47.826 0.00 0.00 0.00 3.01
1428 1542 3.056821 CGTCTACCACCATCTTCACTTCA 60.057 47.826 0.00 0.00 0.00 3.02
1429 1543 4.499183 GTCTACCACCATCTTCACTTCAG 58.501 47.826 0.00 0.00 0.00 3.02
1430 1544 2.191128 ACCACCATCTTCACTTCAGC 57.809 50.000 0.00 0.00 0.00 4.26
1431 1545 1.421268 ACCACCATCTTCACTTCAGCA 59.579 47.619 0.00 0.00 0.00 4.41
1432 1546 2.158623 ACCACCATCTTCACTTCAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
1433 1547 2.227388 CCACCATCTTCACTTCAGCAAC 59.773 50.000 0.00 0.00 0.00 4.17
1434 1548 2.227388 CACCATCTTCACTTCAGCAACC 59.773 50.000 0.00 0.00 0.00 3.77
1435 1549 2.158623 ACCATCTTCACTTCAGCAACCA 60.159 45.455 0.00 0.00 0.00 3.67
1436 1550 2.886523 CCATCTTCACTTCAGCAACCAA 59.113 45.455 0.00 0.00 0.00 3.67
1437 1551 3.318839 CCATCTTCACTTCAGCAACCAAA 59.681 43.478 0.00 0.00 0.00 3.28
1438 1552 4.021719 CCATCTTCACTTCAGCAACCAAAT 60.022 41.667 0.00 0.00 0.00 2.32
1439 1553 5.510179 CCATCTTCACTTCAGCAACCAAATT 60.510 40.000 0.00 0.00 0.00 1.82
1440 1554 6.294675 CCATCTTCACTTCAGCAACCAAATTA 60.295 38.462 0.00 0.00 0.00 1.40
1441 1555 6.072112 TCTTCACTTCAGCAACCAAATTAC 57.928 37.500 0.00 0.00 0.00 1.89
1442 1556 5.827797 TCTTCACTTCAGCAACCAAATTACT 59.172 36.000 0.00 0.00 0.00 2.24
1443 1557 6.321181 TCTTCACTTCAGCAACCAAATTACTT 59.679 34.615 0.00 0.00 0.00 2.24
1444 1558 6.072112 TCACTTCAGCAACCAAATTACTTC 57.928 37.500 0.00 0.00 0.00 3.01
1445 1559 5.827797 TCACTTCAGCAACCAAATTACTTCT 59.172 36.000 0.00 0.00 0.00 2.85
1446 1560 5.916883 CACTTCAGCAACCAAATTACTTCTG 59.083 40.000 0.00 0.00 0.00 3.02
1447 1561 4.503741 TCAGCAACCAAATTACTTCTGC 57.496 40.909 0.00 0.00 0.00 4.26
1448 1562 4.144297 TCAGCAACCAAATTACTTCTGCT 58.856 39.130 0.00 0.00 39.15 4.24
1449 1563 4.216257 TCAGCAACCAAATTACTTCTGCTC 59.784 41.667 0.00 0.00 36.56 4.26
1450 1564 4.217118 CAGCAACCAAATTACTTCTGCTCT 59.783 41.667 0.00 0.00 36.56 4.09
1451 1565 4.457257 AGCAACCAAATTACTTCTGCTCTC 59.543 41.667 0.00 0.00 33.55 3.20
1452 1566 4.457257 GCAACCAAATTACTTCTGCTCTCT 59.543 41.667 0.00 0.00 0.00 3.10
1453 1567 5.643777 GCAACCAAATTACTTCTGCTCTCTA 59.356 40.000 0.00 0.00 0.00 2.43
1454 1568 6.183360 GCAACCAAATTACTTCTGCTCTCTAG 60.183 42.308 0.00 0.00 0.00 2.43
1470 1584 5.599732 CTCTCTAGCTACAACATTGATGCT 58.400 41.667 15.83 15.83 40.73 3.79
1509 1661 6.099125 TGCTCATTTGATCATTTCCATCCATT 59.901 34.615 0.00 0.00 0.00 3.16
1510 1662 6.645415 GCTCATTTGATCATTTCCATCCATTC 59.355 38.462 0.00 0.00 0.00 2.67
1511 1663 7.663043 TCATTTGATCATTTCCATCCATTCA 57.337 32.000 0.00 0.00 0.00 2.57
1512 1664 8.257602 TCATTTGATCATTTCCATCCATTCAT 57.742 30.769 0.00 0.00 0.00 2.57
1513 1665 8.364894 TCATTTGATCATTTCCATCCATTCATC 58.635 33.333 0.00 0.00 0.00 2.92
1514 1666 6.659745 TTGATCATTTCCATCCATTCATCC 57.340 37.500 0.00 0.00 0.00 3.51
1515 1667 5.707495 TGATCATTTCCATCCATTCATCCA 58.293 37.500 0.00 0.00 0.00 3.41
1516 1668 6.319715 TGATCATTTCCATCCATTCATCCAT 58.680 36.000 0.00 0.00 0.00 3.41
1522 1674 3.920841 TCCATCCATTCATCCATCCAGAT 59.079 43.478 0.00 0.00 0.00 2.90
1537 1689 0.593518 CAGATGAGTACAGCCGCGAG 60.594 60.000 8.23 0.00 32.31 5.03
1585 1746 2.720758 CGCGACGGCACAAGAAGAG 61.721 63.158 0.00 0.00 39.92 2.85
1591 1752 0.321671 CGGCACAAGAAGAGGAGGAA 59.678 55.000 0.00 0.00 0.00 3.36
1627 1788 3.588277 GCCGATCGAGCCTATTTCA 57.412 52.632 18.66 0.00 0.00 2.69
1709 1882 1.748879 CATTCCCCACCGTTGCGAT 60.749 57.895 0.00 0.00 0.00 4.58
1721 1894 3.163594 CCGTTGCGATGATTTTTCTGTC 58.836 45.455 0.00 0.00 0.00 3.51
1727 1903 6.110543 TGCGATGATTTTTCTGTCACTATG 57.889 37.500 0.00 0.00 0.00 2.23
1773 1952 3.751479 TCTTCTTACAGTGCTTGCTCA 57.249 42.857 0.00 0.00 0.00 4.26
1808 1989 9.296400 TGTTAAAGAAATGTTTGTCTTGTAAGC 57.704 29.630 0.00 0.00 34.33 3.09
1836 2017 6.532657 ACTGTGATTTTTCAGCAAGAAAGTTG 59.467 34.615 4.82 0.00 46.24 3.16
1889 2073 6.263168 CAGTGGTGGATAAATGAATTAGTCCC 59.737 42.308 0.00 0.00 0.00 4.46
1910 2094 5.138125 CCAAAATGGGGATCGGAATATTG 57.862 43.478 0.00 0.00 32.67 1.90
1960 2150 3.320541 CAGAAGACTCCGATAATGGCTCT 59.679 47.826 0.00 0.00 0.00 4.09
1961 2151 3.964031 AGAAGACTCCGATAATGGCTCTT 59.036 43.478 0.00 0.00 31.86 2.85
1995 2185 2.658285 TGCCAGCCTCATCCTTATTTG 58.342 47.619 0.00 0.00 0.00 2.32
2049 2245 6.908870 ATTTTTGGCAAACAAGAAGACTTC 57.091 33.333 13.10 7.14 40.82 3.01
2050 2246 5.659440 TTTTGGCAAACAAGAAGACTTCT 57.341 34.783 13.10 12.12 40.82 2.85
2089 2285 2.012237 GACGATGACGACGGCTCTA 58.988 57.895 0.65 0.00 42.66 2.43
2090 2286 0.587285 GACGATGACGACGGCTCTAT 59.413 55.000 0.65 0.00 42.66 1.98
2123 2322 4.161295 CGGCGGCCTTGATCCTGA 62.161 66.667 18.34 0.00 0.00 3.86
2212 2411 1.668793 CGTGGAGCTGTGCATGTCA 60.669 57.895 0.00 0.00 0.00 3.58
2413 2612 4.120331 GTGGGCATGTGCTTCGCC 62.120 66.667 4.84 0.00 45.47 5.54
2618 2817 5.222007 ACCAACCTCATCAAGTGATCTCTTT 60.222 40.000 7.30 0.00 35.97 2.52
2629 2829 5.480642 AGTGATCTCTTTCTTCTTCAGCA 57.519 39.130 0.00 0.00 0.00 4.41
2637 2837 6.040955 TCTCTTTCTTCTTCAGCAAGTACAGA 59.959 38.462 0.00 0.00 0.00 3.41
2648 2853 5.105187 TCAGCAAGTACAGATCAGTAGCATT 60.105 40.000 9.60 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.547367 GATGCCGCCCGCCTAAGT 62.547 66.667 0.00 0.00 36.24 2.24
72 73 3.386078 ACATCTCAAGTATGGCTGACGAT 59.614 43.478 0.00 0.00 0.00 3.73
129 133 4.343526 AGCTGTAACCCTCATCATCTAGTG 59.656 45.833 0.00 0.00 0.00 2.74
148 152 1.337260 ACTACTTCTGCGGAACAGCTG 60.337 52.381 13.48 13.48 46.76 4.24
150 154 1.727335 GAACTACTTCTGCGGAACAGC 59.273 52.381 3.13 0.00 46.76 4.40
157 161 3.521560 TGCCTATTGAACTACTTCTGCG 58.478 45.455 0.00 0.00 0.00 5.18
159 163 7.047891 TGGTATTGCCTATTGAACTACTTCTG 58.952 38.462 0.00 0.00 38.35 3.02
254 288 4.937620 ACATCTACACAACATACTTGCAGG 59.062 41.667 0.00 0.00 0.00 4.85
298 332 1.250328 TTTCTTGCCTGCATCCACAG 58.750 50.000 0.00 0.00 37.42 3.66
307 347 1.969923 TGACCCCATTTTTCTTGCCTG 59.030 47.619 0.00 0.00 0.00 4.85
380 425 3.092511 AGGGCATGCGTGGAGGAT 61.093 61.111 12.44 0.00 0.00 3.24
392 437 4.947147 AAGAAACGCGGCAGGGCA 62.947 61.111 12.47 0.00 0.00 5.36
393 438 4.404654 CAAGAAACGCGGCAGGGC 62.405 66.667 12.47 0.00 0.00 5.19
483 528 0.953727 TCATGTGCTGTGTTTGCCTC 59.046 50.000 0.00 0.00 0.00 4.70
485 530 0.038892 CCTCATGTGCTGTGTTTGCC 60.039 55.000 0.00 0.00 0.00 4.52
500 545 4.905429 TCTGTCCGAATGAAAATTCCTCA 58.095 39.130 0.00 0.00 0.00 3.86
501 546 6.442513 AATCTGTCCGAATGAAAATTCCTC 57.557 37.500 0.00 0.00 0.00 3.71
502 547 7.393234 TGTTAATCTGTCCGAATGAAAATTCCT 59.607 33.333 0.00 0.00 0.00 3.36
503 548 7.535139 TGTTAATCTGTCCGAATGAAAATTCC 58.465 34.615 0.00 0.00 0.00 3.01
504 549 8.964420 TTGTTAATCTGTCCGAATGAAAATTC 57.036 30.769 0.00 0.00 0.00 2.17
505 550 8.028938 CCTTGTTAATCTGTCCGAATGAAAATT 58.971 33.333 0.00 0.00 0.00 1.82
506 551 7.176690 ACCTTGTTAATCTGTCCGAATGAAAAT 59.823 33.333 0.00 0.00 0.00 1.82
507 552 6.488683 ACCTTGTTAATCTGTCCGAATGAAAA 59.511 34.615 0.00 0.00 0.00 2.29
508 553 6.001460 ACCTTGTTAATCTGTCCGAATGAAA 58.999 36.000 0.00 0.00 0.00 2.69
509 554 5.556915 ACCTTGTTAATCTGTCCGAATGAA 58.443 37.500 0.00 0.00 0.00 2.57
510 555 5.160607 ACCTTGTTAATCTGTCCGAATGA 57.839 39.130 0.00 0.00 0.00 2.57
511 556 6.036083 CACTACCTTGTTAATCTGTCCGAATG 59.964 42.308 0.00 0.00 0.00 2.67
512 557 6.070995 TCACTACCTTGTTAATCTGTCCGAAT 60.071 38.462 0.00 0.00 0.00 3.34
513 558 5.244402 TCACTACCTTGTTAATCTGTCCGAA 59.756 40.000 0.00 0.00 0.00 4.30
514 559 4.768448 TCACTACCTTGTTAATCTGTCCGA 59.232 41.667 0.00 0.00 0.00 4.55
515 560 5.068234 TCACTACCTTGTTAATCTGTCCG 57.932 43.478 0.00 0.00 0.00 4.79
516 561 7.626452 GCAAATCACTACCTTGTTAATCTGTCC 60.626 40.741 0.00 0.00 0.00 4.02
517 562 7.119846 AGCAAATCACTACCTTGTTAATCTGTC 59.880 37.037 0.00 0.00 0.00 3.51
518 563 6.942576 AGCAAATCACTACCTTGTTAATCTGT 59.057 34.615 0.00 0.00 0.00 3.41
519 564 7.383102 AGCAAATCACTACCTTGTTAATCTG 57.617 36.000 0.00 0.00 0.00 2.90
535 580 8.461222 CAATTACTTACCATGAGAAGCAAATCA 58.539 33.333 0.00 0.00 0.00 2.57
566 611 1.300971 TGATTCAAGCTCACGGCAGC 61.301 55.000 0.00 0.00 44.79 5.25
599 644 1.299165 CGCCTACGGTGATTCCTCG 60.299 63.158 0.00 0.00 34.74 4.63
600 645 4.732106 CGCCTACGGTGATTCCTC 57.268 61.111 0.00 0.00 34.74 3.71
610 655 1.664306 GACCCCTATTCCGCCTACG 59.336 63.158 0.00 0.00 39.67 3.51
611 656 1.111715 ACGACCCCTATTCCGCCTAC 61.112 60.000 0.00 0.00 0.00 3.18
613 658 2.042230 ACGACCCCTATTCCGCCT 60.042 61.111 0.00 0.00 0.00 5.52
833 919 4.787280 AGGAGAGGCTCACCGGGG 62.787 72.222 22.71 0.00 42.76 5.73
834 920 2.685380 AAGGAGAGGCTCACCGGG 60.685 66.667 22.71 0.00 42.76 5.73
836 922 1.671901 GGAGAAGGAGAGGCTCACCG 61.672 65.000 22.71 0.00 42.76 4.94
837 923 0.325203 AGGAGAAGGAGAGGCTCACC 60.325 60.000 21.74 21.74 31.08 4.02
838 924 1.111277 GAGGAGAAGGAGAGGCTCAC 58.889 60.000 18.26 10.70 31.08 3.51
839 925 0.032615 GGAGGAGAAGGAGAGGCTCA 60.033 60.000 18.26 0.00 31.08 4.26
840 926 0.261696 AGGAGGAGAAGGAGAGGCTC 59.738 60.000 6.34 6.34 0.00 4.70
841 927 0.715987 AAGGAGGAGAAGGAGAGGCT 59.284 55.000 0.00 0.00 0.00 4.58
842 928 1.119684 GAAGGAGGAGAAGGAGAGGC 58.880 60.000 0.00 0.00 0.00 4.70
843 929 1.398692 CGAAGGAGGAGAAGGAGAGG 58.601 60.000 0.00 0.00 0.00 3.69
860 946 0.323360 CCATGGAGGAAAAAGGCCGA 60.323 55.000 5.56 0.00 41.22 5.54
886 972 0.604780 GATCAGATGGGCCATGGACG 60.605 60.000 26.77 9.21 0.00 4.79
889 975 0.769247 TCAGATCAGATGGGCCATGG 59.231 55.000 26.77 16.03 0.00 3.66
892 978 0.693430 AGCTCAGATCAGATGGGCCA 60.693 55.000 9.61 9.61 45.69 5.36
910 996 1.305930 GGCTTGTTCGTGGGCCTAAG 61.306 60.000 4.53 0.00 41.20 2.18
911 997 1.302993 GGCTTGTTCGTGGGCCTAA 60.303 57.895 4.53 0.00 41.20 2.69
912 998 2.349755 GGCTTGTTCGTGGGCCTA 59.650 61.111 4.53 0.00 41.20 3.93
913 999 4.660938 GGGCTTGTTCGTGGGCCT 62.661 66.667 4.53 0.00 43.62 5.19
915 1001 3.670377 GTGGGCTTGTTCGTGGGC 61.670 66.667 0.00 0.00 0.00 5.36
916 1002 2.983592 GGTGGGCTTGTTCGTGGG 60.984 66.667 0.00 0.00 0.00 4.61
918 1004 4.025401 GCGGTGGGCTTGTTCGTG 62.025 66.667 0.00 0.00 39.11 4.35
920 1006 1.705337 CTATGCGGTGGGCTTGTTCG 61.705 60.000 0.00 0.00 44.05 3.95
923 1009 2.438434 GCTATGCGGTGGGCTTGT 60.438 61.111 0.00 0.00 44.05 3.16
937 1023 0.756903 GAGACGGGCTATTTGGGCTA 59.243 55.000 0.00 0.00 0.00 3.93
965 1069 2.956964 CTTCCGTCGAGATGCGGC 60.957 66.667 7.28 0.00 46.79 6.53
987 1091 1.067000 GGATCCATCCGATCTGCTCTG 60.067 57.143 6.95 0.00 45.90 3.35
988 1092 1.265236 GGATCCATCCGATCTGCTCT 58.735 55.000 6.95 0.00 45.90 4.09
1402 1516 1.741706 GAAGATGGTGGTAGACGACGA 59.258 52.381 0.00 0.00 0.00 4.20
1403 1517 1.471287 TGAAGATGGTGGTAGACGACG 59.529 52.381 0.00 0.00 0.00 5.12
1404 1518 2.492484 AGTGAAGATGGTGGTAGACGAC 59.508 50.000 0.00 0.00 0.00 4.34
1405 1519 2.803956 AGTGAAGATGGTGGTAGACGA 58.196 47.619 0.00 0.00 0.00 4.20
1406 1520 3.056821 TGAAGTGAAGATGGTGGTAGACG 60.057 47.826 0.00 0.00 0.00 4.18
1407 1521 4.499183 CTGAAGTGAAGATGGTGGTAGAC 58.501 47.826 0.00 0.00 0.00 2.59
1409 1523 3.265791 GCTGAAGTGAAGATGGTGGTAG 58.734 50.000 0.00 0.00 0.00 3.18
1411 1525 1.421268 TGCTGAAGTGAAGATGGTGGT 59.579 47.619 0.00 0.00 0.00 4.16
1412 1526 2.189594 TGCTGAAGTGAAGATGGTGG 57.810 50.000 0.00 0.00 0.00 4.61
1414 1528 2.158623 TGGTTGCTGAAGTGAAGATGGT 60.159 45.455 0.00 0.00 0.00 3.55
1415 1529 2.507484 TGGTTGCTGAAGTGAAGATGG 58.493 47.619 0.00 0.00 0.00 3.51
1416 1530 4.572985 TTTGGTTGCTGAAGTGAAGATG 57.427 40.909 0.00 0.00 0.00 2.90
1417 1531 5.796424 AATTTGGTTGCTGAAGTGAAGAT 57.204 34.783 0.00 0.00 0.00 2.40
1418 1532 5.827797 AGTAATTTGGTTGCTGAAGTGAAGA 59.172 36.000 0.00 0.00 31.05 2.87
1419 1533 6.076981 AGTAATTTGGTTGCTGAAGTGAAG 57.923 37.500 0.00 0.00 31.05 3.02
1420 1534 6.321181 AGAAGTAATTTGGTTGCTGAAGTGAA 59.679 34.615 0.00 0.00 32.72 3.18
1421 1535 5.827797 AGAAGTAATTTGGTTGCTGAAGTGA 59.172 36.000 0.00 0.00 32.72 3.41
1422 1536 5.916883 CAGAAGTAATTTGGTTGCTGAAGTG 59.083 40.000 0.00 0.00 32.72 3.16
1423 1537 5.507985 GCAGAAGTAATTTGGTTGCTGAAGT 60.508 40.000 0.00 0.00 32.72 3.01
1424 1538 4.919754 GCAGAAGTAATTTGGTTGCTGAAG 59.080 41.667 0.00 0.00 32.72 3.02
1425 1539 4.584325 AGCAGAAGTAATTTGGTTGCTGAA 59.416 37.500 0.00 0.00 38.82 3.02
1426 1540 4.144297 AGCAGAAGTAATTTGGTTGCTGA 58.856 39.130 0.00 0.00 38.82 4.26
1427 1541 4.217118 AGAGCAGAAGTAATTTGGTTGCTG 59.783 41.667 8.98 0.00 40.19 4.41
1428 1542 4.401925 AGAGCAGAAGTAATTTGGTTGCT 58.598 39.130 5.32 5.32 42.53 3.91
1429 1543 4.457257 AGAGAGCAGAAGTAATTTGGTTGC 59.543 41.667 0.00 0.00 0.00 4.17
1430 1544 7.301068 CTAGAGAGCAGAAGTAATTTGGTTG 57.699 40.000 0.00 0.00 0.00 3.77
1445 1559 9.969367 GAGCATCAATGTTGTAGCTAGAGAGCA 62.969 44.444 12.16 0.00 43.43 4.26
1446 1560 7.713916 GAGCATCAATGTTGTAGCTAGAGAGC 61.714 46.154 12.16 0.00 41.99 4.09
1447 1561 5.599732 AGCATCAATGTTGTAGCTAGAGAG 58.400 41.667 0.00 0.00 37.51 3.20
1448 1562 5.362143 AGAGCATCAATGTTGTAGCTAGAGA 59.638 40.000 12.16 0.00 38.64 3.10
1449 1563 5.599732 AGAGCATCAATGTTGTAGCTAGAG 58.400 41.667 12.16 0.00 38.64 2.43
1450 1564 5.127682 TGAGAGCATCAATGTTGTAGCTAGA 59.872 40.000 12.16 0.00 38.64 2.43
1451 1565 5.354767 TGAGAGCATCAATGTTGTAGCTAG 58.645 41.667 12.16 0.00 38.64 3.42
1452 1566 5.343307 TGAGAGCATCAATGTTGTAGCTA 57.657 39.130 12.16 0.00 38.64 3.32
1453 1567 4.212143 TGAGAGCATCAATGTTGTAGCT 57.788 40.909 12.07 12.07 40.20 3.32
1454 1568 4.952262 TTGAGAGCATCAATGTTGTAGC 57.048 40.909 0.59 4.75 43.09 3.58
1470 1584 6.571605 TCAAATGAGCAACAACAAATTGAGA 58.428 32.000 0.00 0.00 39.30 3.27
1509 1661 3.323115 GCTGTACTCATCTGGATGGATGA 59.677 47.826 10.22 6.92 46.50 2.92
1510 1662 3.556633 GGCTGTACTCATCTGGATGGATG 60.557 52.174 10.22 0.00 43.01 3.51
1511 1663 2.636893 GGCTGTACTCATCTGGATGGAT 59.363 50.000 10.22 2.69 39.24 3.41
1512 1664 2.042464 GGCTGTACTCATCTGGATGGA 58.958 52.381 10.22 0.00 39.24 3.41
1513 1665 1.269988 CGGCTGTACTCATCTGGATGG 60.270 57.143 10.22 4.65 39.24 3.51
1514 1666 1.871408 GCGGCTGTACTCATCTGGATG 60.871 57.143 4.36 4.36 40.09 3.51
1515 1667 0.390860 GCGGCTGTACTCATCTGGAT 59.609 55.000 0.00 0.00 0.00 3.41
1516 1668 1.816537 GCGGCTGTACTCATCTGGA 59.183 57.895 0.00 0.00 0.00 3.86
1522 1674 4.476410 CGCTCGCGGCTGTACTCA 62.476 66.667 6.13 0.00 39.13 3.41
1576 1737 5.151454 TCTTCTTCTTCCTCCTCTTCTTGT 58.849 41.667 0.00 0.00 0.00 3.16
1585 1746 1.550976 TCCGCTTCTTCTTCTTCCTCC 59.449 52.381 0.00 0.00 0.00 4.30
1591 1752 0.534873 GCCTCTCCGCTTCTTCTTCT 59.465 55.000 0.00 0.00 0.00 2.85
1621 1782 5.761726 GTGATGGATGCTGATGTCTGAAATA 59.238 40.000 0.00 0.00 0.00 1.40
1627 1788 3.135895 TGATGTGATGGATGCTGATGTCT 59.864 43.478 0.00 0.00 0.00 3.41
1709 1882 6.595326 CAGCTACCATAGTGACAGAAAAATCA 59.405 38.462 0.00 0.00 0.00 2.57
1727 1903 3.797184 GCACTACTGCACTATCAGCTACC 60.797 52.174 0.00 0.00 43.62 3.18
1773 1952 9.665719 ACAAACATTTCTTTAACAGAATTTGGT 57.334 25.926 17.51 9.82 40.41 3.67
1794 1973 6.539649 TCACAGTATGCTTACAAGACAAAC 57.460 37.500 11.89 0.00 42.53 2.93
1808 1989 7.864379 ACTTTCTTGCTGAAAAATCACAGTATG 59.136 33.333 0.00 0.00 43.25 2.39
1836 2017 7.381139 GCTATGTATAGACTCAAGAAGCTCAAC 59.619 40.741 3.15 0.00 32.05 3.18
1889 2073 5.769662 TCTCAATATTCCGATCCCCATTTTG 59.230 40.000 0.00 0.00 0.00 2.44
1901 2085 2.816087 CCCATGGCTTCTCAATATTCCG 59.184 50.000 6.09 0.00 0.00 4.30
1944 2134 2.630580 GGAGAAGAGCCATTATCGGAGT 59.369 50.000 0.00 0.00 0.00 3.85
1960 2150 2.124983 GCATGGCAGAGCGGAGAA 60.125 61.111 0.00 0.00 0.00 2.87
1961 2151 4.166888 GGCATGGCAGAGCGGAGA 62.167 66.667 15.47 0.00 0.00 3.71
1995 2185 4.743057 AAATTATGAGGGAAGCAAAGCC 57.257 40.909 0.00 0.00 0.00 4.35
2049 2245 3.241900 CGTCGCTGTCTTCATTGATTCAG 60.242 47.826 8.11 8.11 0.00 3.02
2050 2246 2.667969 CGTCGCTGTCTTCATTGATTCA 59.332 45.455 0.00 0.00 0.00 2.57
2379 2578 0.732880 CACGTCCTTGTAGAGCGTGG 60.733 60.000 7.39 0.00 45.96 4.94
2413 2612 3.071459 GATCTGGTCGTGCGCGTTG 62.071 63.158 20.50 8.39 39.49 4.10
2414 2613 2.809601 GATCTGGTCGTGCGCGTT 60.810 61.111 20.50 0.00 39.49 4.84
2415 2614 3.567478 TTGATCTGGTCGTGCGCGT 62.567 57.895 20.50 0.00 39.49 6.01
2618 2817 5.244851 ACTGATCTGTACTTGCTGAAGAAGA 59.755 40.000 3.02 0.00 32.98 2.87


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

AutoCloner maintained by Alex Coulton.