Multiple sequence alignment - TraesCS3D01G531800

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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 TraesCS3D01G531800 chr3D 100.000 2352 0 0 1 2352 607898072 607900423 0.000000e+00 4344.0
1 TraesCS3D01G531800 chr3D 95.305 788 18 3 1583 2352 540883845 540884631 0.000000e+00 1232.0
2 TraesCS3D01G531800 chr3D 83.806 599 71 18 889 1466 607885614 607886207 1.590000e-151 545.0
3 TraesCS3D01G531800 chr3D 80.408 245 39 4 899 1142 605224115 605223879 6.680000e-41 178.0
4 TraesCS3D01G531800 chr3D 78.838 241 44 2 899 1139 605132236 605132469 3.130000e-34 156.0
5 TraesCS3D01G531800 chr3D 78.205 234 41 7 883 1114 575218747 575218972 8.760000e-30 141.0
6 TraesCS3D01G531800 chr3A 91.410 1525 92 9 1 1492 740103987 740105505 0.000000e+00 2054.0
7 TraesCS3D01G531800 chr3A 84.661 502 51 13 1579 2060 126087275 126087770 5.880000e-131 477.0
8 TraesCS3D01G531800 chr3A 91.391 151 12 1 2196 2345 126087796 126087946 3.060000e-49 206.0
9 TraesCS3D01G531800 chr3A 80.851 188 36 0 952 1139 736903771 736903958 5.240000e-32 148.0
10 TraesCS3D01G531800 chr3A 79.439 214 37 2 899 1112 736268039 736268245 6.770000e-31 145.0
11 TraesCS3D01G531800 chr3B 91.556 1350 99 6 111 1459 817467478 817466143 0.000000e+00 1847.0
12 TraesCS3D01G531800 chr3B 82.505 503 65 12 1584 2069 733254281 733253785 1.010000e-113 420.0
13 TraesCS3D01G531800 chr3B 80.606 495 62 20 1583 2069 15047013 15047481 3.720000e-93 351.0
14 TraesCS3D01G531800 chr3B 91.558 154 11 1 2194 2345 15047496 15047649 6.590000e-51 211.0
15 TraesCS3D01G531800 chr3B 92.053 151 10 1 2197 2345 733253767 733253617 6.590000e-51 211.0
16 TraesCS3D01G531800 chr3B 78.750 240 44 2 900 1139 813022271 813022503 1.130000e-33 154.0
17 TraesCS3D01G531800 chr3B 77.665 197 32 8 986 1177 824230468 824230279 2.470000e-20 110.0
18 TraesCS3D01G531800 chr3B 95.238 42 1 1 81 122 817467533 817467493 5.430000e-07 65.8
19 TraesCS3D01G531800 chr1D 94.577 627 14 2 1583 2193 475240749 475240127 0.000000e+00 952.0
20 TraesCS3D01G531800 chr2B 83.301 509 55 13 1583 2069 542353165 542352665 2.150000e-120 442.0
21 TraesCS3D01G531800 chr2B 82.908 509 56 13 1583 2069 663914723 663915222 1.670000e-116 429.0
22 TraesCS3D01G531800 chr2B 87.437 199 21 4 1583 1777 6733613 6733415 2.350000e-55 226.0
23 TraesCS3D01G531800 chr5B 81.481 405 52 8 1581 1965 514071644 514071243 6.310000e-81 311.0
24 TraesCS3D01G531800 chr5B 84.615 78 11 1 695 772 284165820 284165744 2.510000e-10 76.8
25 TraesCS3D01G531800 chr1B 85.284 299 40 4 1772 2069 581106606 581106311 2.940000e-79 305.0
26 TraesCS3D01G531800 chr1B 90.761 184 13 4 1583 1764 581106827 581106646 2.340000e-60 243.0
27 TraesCS3D01G531800 chr1B 91.892 148 11 1 2199 2345 581106291 581106144 3.060000e-49 206.0
28 TraesCS3D01G531800 chr1B 83.871 186 28 2 580 764 357240997 357240813 2.400000e-40 176.0
29 TraesCS3D01G531800 chr7B 83.206 262 32 9 576 834 393858604 393858856 1.820000e-56 230.0
30 TraesCS3D01G531800 chr7B 92.715 151 9 2 2194 2343 587919334 587919185 1.420000e-52 217.0
31 TraesCS3D01G531800 chr7B 77.564 156 23 9 636 788 641159506 641159360 1.500000e-12 84.2
32 TraesCS3D01G531800 chr7D 92.208 154 8 3 2194 2345 1141479 1141328 5.090000e-52 215.0
33 TraesCS3D01G531800 chr6D 95.349 129 5 1 2069 2196 350568307 350568435 1.100000e-48 204.0
34 TraesCS3D01G531800 chr6D 78.453 181 34 1 651 831 401743407 401743232 1.910000e-21 113.0
35 TraesCS3D01G531800 chrUn 93.798 129 7 1 2069 2196 65117521 65117393 2.390000e-45 193.0
36 TraesCS3D01G531800 chr7A 86.747 83 11 0 669 751 535913466 535913548 2.490000e-15 93.5


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 TraesCS3D01G531800 chr3D 607898072 607900423 2351 False 4344.000000 4344 100.000000 1 2352 1 chr3D.!!$F5 2351
1 TraesCS3D01G531800 chr3D 540883845 540884631 786 False 1232.000000 1232 95.305000 1583 2352 1 chr3D.!!$F1 769
2 TraesCS3D01G531800 chr3D 607885614 607886207 593 False 545.000000 545 83.806000 889 1466 1 chr3D.!!$F4 577
3 TraesCS3D01G531800 chr3A 740103987 740105505 1518 False 2054.000000 2054 91.410000 1 1492 1 chr3A.!!$F3 1491
4 TraesCS3D01G531800 chr3A 126087275 126087946 671 False 341.500000 477 88.026000 1579 2345 2 chr3A.!!$F4 766
5 TraesCS3D01G531800 chr3B 817466143 817467533 1390 True 956.400000 1847 93.397000 81 1459 2 chr3B.!!$R3 1378
6 TraesCS3D01G531800 chr3B 733253617 733254281 664 True 315.500000 420 87.279000 1584 2345 2 chr3B.!!$R2 761
7 TraesCS3D01G531800 chr3B 15047013 15047649 636 False 281.000000 351 86.082000 1583 2345 2 chr3B.!!$F2 762
8 TraesCS3D01G531800 chr1D 475240127 475240749 622 True 952.000000 952 94.577000 1583 2193 1 chr1D.!!$R1 610
9 TraesCS3D01G531800 chr2B 542352665 542353165 500 True 442.000000 442 83.301000 1583 2069 1 chr2B.!!$R2 486
10 TraesCS3D01G531800 chr1B 581106144 581106827 683 True 251.333333 305 89.312333 1583 2345 3 chr1B.!!$R2 762

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
378 405 0.316522 CCCATGATGAGAGCGTCGAT 59.683 55.0 0.0 0.0 32.54 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1566 0.032912 ACCATGAATGAGGCCATGCA 60.033 50.0 5.01 0.0 42.3 3.96 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
139 166 4.142600 GCTACCTAAGTTTTCATGCAGTGG 60.143 45.833 0.00 0.00 0.00 4.00
143 170 6.010219 ACCTAAGTTTTCATGCAGTGGTATT 58.990 36.000 0.00 0.00 0.00 1.89
146 173 5.545658 AGTTTTCATGCAGTGGTATTACG 57.454 39.130 0.00 0.00 0.00 3.18
206 233 2.355010 ACCTATGGCTCCATCAAAGC 57.645 50.000 4.41 0.00 37.82 3.51
225 252 5.873146 AAGCCCCTATACTCTAGAACAAC 57.127 43.478 0.00 0.00 0.00 3.32
255 282 8.738645 ACTATGGATGTGAAAGTCCTAATTTC 57.261 34.615 0.00 0.00 37.21 2.17
292 319 8.308931 ACACAAATTAGCATCATCATGTCTTTT 58.691 29.630 0.00 0.00 31.86 2.27
318 345 3.158676 ACACGAAAGAAGCTCTACCTCT 58.841 45.455 0.00 0.00 0.00 3.69
367 394 2.283298 CTCGTCTTGTTCCCCATGATG 58.717 52.381 0.00 0.00 36.20 3.07
378 405 0.316522 CCCATGATGAGAGCGTCGAT 59.683 55.000 0.00 0.00 32.54 3.59
409 436 1.655329 CATCCTACTCGGCTCGGAC 59.345 63.158 0.00 0.00 0.00 4.79
431 458 2.496070 TCGATGGACGATGGAGAAACTT 59.504 45.455 0.00 0.00 46.45 2.66
437 464 1.347707 ACGATGGAGAAACTTGCCTCA 59.652 47.619 0.00 0.00 0.00 3.86
703 733 8.044060 AGCGTTGATATTGATATTTGGTATGG 57.956 34.615 0.00 0.00 0.00 2.74
704 734 6.747280 GCGTTGATATTGATATTTGGTATGGC 59.253 38.462 0.00 0.00 0.00 4.40
739 769 1.229428 AACATGTTGAGTGCTCACCG 58.771 50.000 11.07 0.00 39.66 4.94
757 787 1.522668 CGTTGGAGCAATCAAGGTCA 58.477 50.000 0.00 0.00 37.74 4.02
799 829 3.134458 GGCTGGGATTAGTTGAATCTCG 58.866 50.000 0.00 0.00 46.75 4.04
808 838 1.351017 AGTTGAATCTCGCCCTTTGGA 59.649 47.619 0.00 0.00 0.00 3.53
991 1021 2.987232 ACGGGAATAAGAGGTTTGAGC 58.013 47.619 0.00 0.00 0.00 4.26
1092 1123 2.758979 GGAATCACTCTCGTTGTCCCTA 59.241 50.000 0.00 0.00 0.00 3.53
1114 1145 7.366011 CCCTATACATGTTTCCTTTCTCCTCTT 60.366 40.741 2.30 0.00 0.00 2.85
1125 1156 5.365605 TCCTTTCTCCTCTTGAACACAGTAA 59.634 40.000 0.00 0.00 0.00 2.24
1127 1158 6.017852 CCTTTCTCCTCTTGAACACAGTAAAC 60.018 42.308 0.00 0.00 0.00 2.01
1143 1174 8.999431 ACACAGTAAACTAATATTGTCAGTTGG 58.001 33.333 0.00 0.00 32.96 3.77
1163 1194 5.075858 TGGGCTGCATGAATTTCTTTTAG 57.924 39.130 0.50 0.00 0.00 1.85
1252 1302 6.238814 CCACATGCATTGAACTATCTTGCATA 60.239 38.462 8.22 0.00 45.70 3.14
1346 1397 4.887071 TGAATTGTTACTGCAAGGTCTGTT 59.113 37.500 0.00 0.00 39.30 3.16
1347 1398 5.359576 TGAATTGTTACTGCAAGGTCTGTTT 59.640 36.000 0.00 0.00 39.30 2.83
1432 1483 1.814394 TCCTCTTTGTGACATGCATGC 59.186 47.619 26.53 18.59 0.00 4.06
1493 1548 6.869315 TTTTCTTTGTCGTGTGGAATATGA 57.131 33.333 0.00 0.00 0.00 2.15
1494 1549 7.447374 TTTTCTTTGTCGTGTGGAATATGAT 57.553 32.000 0.00 0.00 0.00 2.45
1495 1550 7.447374 TTTCTTTGTCGTGTGGAATATGATT 57.553 32.000 0.00 0.00 0.00 2.57
1496 1551 7.447374 TTCTTTGTCGTGTGGAATATGATTT 57.553 32.000 0.00 0.00 0.00 2.17
1497 1552 6.841119 TCTTTGTCGTGTGGAATATGATTTG 58.159 36.000 0.00 0.00 0.00 2.32
1498 1553 5.559427 TTGTCGTGTGGAATATGATTTGG 57.441 39.130 0.00 0.00 0.00 3.28
1499 1554 3.376859 TGTCGTGTGGAATATGATTTGGC 59.623 43.478 0.00 0.00 0.00 4.52
1500 1555 3.627577 GTCGTGTGGAATATGATTTGGCT 59.372 43.478 0.00 0.00 0.00 4.75
1501 1556 4.814234 GTCGTGTGGAATATGATTTGGCTA 59.186 41.667 0.00 0.00 0.00 3.93
1502 1557 5.470098 GTCGTGTGGAATATGATTTGGCTAT 59.530 40.000 0.00 0.00 0.00 2.97
1503 1558 6.017109 GTCGTGTGGAATATGATTTGGCTATT 60.017 38.462 0.00 0.00 0.00 1.73
1504 1559 6.545666 TCGTGTGGAATATGATTTGGCTATTT 59.454 34.615 0.00 0.00 0.00 1.40
1505 1560 7.068103 TCGTGTGGAATATGATTTGGCTATTTT 59.932 33.333 0.00 0.00 0.00 1.82
1506 1561 7.167968 CGTGTGGAATATGATTTGGCTATTTTG 59.832 37.037 0.00 0.00 0.00 2.44
1507 1562 7.981225 GTGTGGAATATGATTTGGCTATTTTGT 59.019 33.333 0.00 0.00 0.00 2.83
1508 1563 7.980662 TGTGGAATATGATTTGGCTATTTTGTG 59.019 33.333 0.00 0.00 0.00 3.33
1509 1564 7.981225 GTGGAATATGATTTGGCTATTTTGTGT 59.019 33.333 0.00 0.00 0.00 3.72
1510 1565 8.538701 TGGAATATGATTTGGCTATTTTGTGTT 58.461 29.630 0.00 0.00 0.00 3.32
1511 1566 9.382275 GGAATATGATTTGGCTATTTTGTGTTT 57.618 29.630 0.00 0.00 0.00 2.83
1513 1568 5.921004 TGATTTGGCTATTTTGTGTTTGC 57.079 34.783 0.00 0.00 0.00 3.68
1514 1569 5.363101 TGATTTGGCTATTTTGTGTTTGCA 58.637 33.333 0.00 0.00 0.00 4.08
1515 1570 5.996513 TGATTTGGCTATTTTGTGTTTGCAT 59.003 32.000 0.00 0.00 0.00 3.96
1516 1571 5.670149 TTTGGCTATTTTGTGTTTGCATG 57.330 34.783 0.00 0.00 0.00 4.06
1517 1572 3.661944 TGGCTATTTTGTGTTTGCATGG 58.338 40.909 0.00 0.00 0.00 3.66
1518 1573 2.416202 GGCTATTTTGTGTTTGCATGGC 59.584 45.455 0.00 0.00 0.00 4.40
1519 1574 2.416202 GCTATTTTGTGTTTGCATGGCC 59.584 45.455 0.00 0.00 0.00 5.36
1520 1575 2.934886 ATTTTGTGTTTGCATGGCCT 57.065 40.000 3.32 0.00 0.00 5.19
1521 1576 2.237393 TTTTGTGTTTGCATGGCCTC 57.763 45.000 3.32 0.00 0.00 4.70
1522 1577 1.117994 TTTGTGTTTGCATGGCCTCA 58.882 45.000 3.32 0.00 0.00 3.86
1523 1578 1.340088 TTGTGTTTGCATGGCCTCAT 58.660 45.000 3.32 0.00 0.00 2.90
1524 1579 1.340088 TGTGTTTGCATGGCCTCATT 58.660 45.000 3.32 0.00 0.00 2.57
1525 1580 1.273048 TGTGTTTGCATGGCCTCATTC 59.727 47.619 3.32 0.00 0.00 2.67
1526 1581 1.273048 GTGTTTGCATGGCCTCATTCA 59.727 47.619 3.32 0.00 0.00 2.57
1527 1582 2.093869 GTGTTTGCATGGCCTCATTCAT 60.094 45.455 3.32 0.00 0.00 2.57
1528 1583 2.093921 TGTTTGCATGGCCTCATTCATG 60.094 45.455 3.32 0.00 42.47 3.07
1529 1584 1.116308 TTGCATGGCCTCATTCATGG 58.884 50.000 3.32 0.00 40.59 3.66
1530 1585 0.032912 TGCATGGCCTCATTCATGGT 60.033 50.000 3.32 0.00 40.59 3.55
1531 1586 1.117150 GCATGGCCTCATTCATGGTT 58.883 50.000 3.32 0.00 40.59 3.67
1532 1587 1.068127 GCATGGCCTCATTCATGGTTC 59.932 52.381 3.32 0.00 40.59 3.62
1533 1588 2.380941 CATGGCCTCATTCATGGTTCA 58.619 47.619 3.32 0.00 37.63 3.18
1534 1589 2.832643 TGGCCTCATTCATGGTTCAT 57.167 45.000 3.32 0.00 0.00 2.57
1535 1590 3.949586 TGGCCTCATTCATGGTTCATA 57.050 42.857 3.32 0.00 0.00 2.15
1536 1591 4.458256 TGGCCTCATTCATGGTTCATAT 57.542 40.909 3.32 0.00 0.00 1.78
1537 1592 4.146564 TGGCCTCATTCATGGTTCATATG 58.853 43.478 3.32 0.00 0.00 1.78
1538 1593 4.147321 GGCCTCATTCATGGTTCATATGT 58.853 43.478 1.90 0.00 0.00 2.29
1539 1594 4.586001 GGCCTCATTCATGGTTCATATGTT 59.414 41.667 1.90 0.00 0.00 2.71
1540 1595 5.278660 GGCCTCATTCATGGTTCATATGTTC 60.279 44.000 1.90 0.00 0.00 3.18
1541 1596 5.561532 GCCTCATTCATGGTTCATATGTTCG 60.562 44.000 1.90 0.00 0.00 3.95
1542 1597 5.049198 CCTCATTCATGGTTCATATGTTCGG 60.049 44.000 1.90 0.00 0.00 4.30
1543 1598 5.679601 TCATTCATGGTTCATATGTTCGGA 58.320 37.500 1.90 0.00 0.00 4.55
1544 1599 6.118852 TCATTCATGGTTCATATGTTCGGAA 58.881 36.000 1.90 1.90 0.00 4.30
1545 1600 6.601217 TCATTCATGGTTCATATGTTCGGAAA 59.399 34.615 1.90 0.00 0.00 3.13
1546 1601 5.811399 TCATGGTTCATATGTTCGGAAAC 57.189 39.130 1.90 0.00 35.85 2.78
1547 1602 5.496556 TCATGGTTCATATGTTCGGAAACT 58.503 37.500 1.90 0.00 36.30 2.66
1548 1603 6.645306 TCATGGTTCATATGTTCGGAAACTA 58.355 36.000 1.90 0.00 36.30 2.24
1549 1604 6.761242 TCATGGTTCATATGTTCGGAAACTAG 59.239 38.462 1.90 0.00 36.30 2.57
1550 1605 6.045072 TGGTTCATATGTTCGGAAACTAGT 57.955 37.500 1.90 0.00 36.30 2.57
1551 1606 6.469410 TGGTTCATATGTTCGGAAACTAGTT 58.531 36.000 1.12 1.12 36.30 2.24
1552 1607 6.938030 TGGTTCATATGTTCGGAAACTAGTTT 59.062 34.615 20.67 20.67 36.30 2.66
1553 1608 7.446013 TGGTTCATATGTTCGGAAACTAGTTTT 59.554 33.333 21.40 6.96 36.30 2.43
1554 1609 8.938906 GGTTCATATGTTCGGAAACTAGTTTTA 58.061 33.333 21.40 8.90 36.30 1.52
1555 1610 9.968743 GTTCATATGTTCGGAAACTAGTTTTAG 57.031 33.333 21.40 17.27 36.30 1.85
1556 1611 8.193250 TCATATGTTCGGAAACTAGTTTTAGC 57.807 34.615 21.40 12.55 36.30 3.09
1557 1612 7.820386 TCATATGTTCGGAAACTAGTTTTAGCA 59.180 33.333 21.40 16.90 36.30 3.49
1558 1613 8.612619 CATATGTTCGGAAACTAGTTTTAGCAT 58.387 33.333 21.40 21.20 36.30 3.79
1559 1614 6.870971 TGTTCGGAAACTAGTTTTAGCATT 57.129 33.333 21.40 0.00 36.30 3.56
1560 1615 7.966246 TGTTCGGAAACTAGTTTTAGCATTA 57.034 32.000 21.40 4.51 36.30 1.90
1561 1616 8.556213 TGTTCGGAAACTAGTTTTAGCATTAT 57.444 30.769 21.40 0.00 36.30 1.28
1562 1617 8.662141 TGTTCGGAAACTAGTTTTAGCATTATC 58.338 33.333 21.40 6.01 36.30 1.75
1563 1618 8.880750 GTTCGGAAACTAGTTTTAGCATTATCT 58.119 33.333 21.40 0.00 32.11 1.98
1564 1619 8.420374 TCGGAAACTAGTTTTAGCATTATCTG 57.580 34.615 21.40 10.73 32.11 2.90
1565 1620 8.038944 TCGGAAACTAGTTTTAGCATTATCTGT 58.961 33.333 21.40 0.00 32.11 3.41
1566 1621 8.116753 CGGAAACTAGTTTTAGCATTATCTGTG 58.883 37.037 21.40 0.00 32.11 3.66
1567 1622 8.398665 GGAAACTAGTTTTAGCATTATCTGTGG 58.601 37.037 21.40 0.00 32.11 4.17
1568 1623 9.162764 GAAACTAGTTTTAGCATTATCTGTGGA 57.837 33.333 21.40 0.00 32.11 4.02
1569 1624 9.515226 AAACTAGTTTTAGCATTATCTGTGGAA 57.485 29.630 15.22 0.00 0.00 3.53
1570 1625 9.515226 AACTAGTTTTAGCATTATCTGTGGAAA 57.485 29.630 1.12 0.00 0.00 3.13
1571 1626 8.947115 ACTAGTTTTAGCATTATCTGTGGAAAC 58.053 33.333 0.00 0.00 0.00 2.78
1572 1627 7.759489 AGTTTTAGCATTATCTGTGGAAACA 57.241 32.000 0.00 0.00 38.70 2.83
1804 1895 9.167311 GAACTCTGACATTATTTTCCTACATGT 57.833 33.333 2.69 2.69 0.00 3.21
1852 1943 3.340953 CTGGGTCGCGGCAAAATGG 62.341 63.158 14.93 0.00 0.00 3.16
1853 1944 4.794439 GGGTCGCGGCAAAATGGC 62.794 66.667 14.93 0.00 39.85 4.40
1976 2073 0.528924 AATAAAAAGTTCGCCGCCCC 59.471 50.000 0.00 0.00 0.00 5.80
2028 2125 1.129879 CAGCGCGTGCACAAATCATC 61.130 55.000 24.79 0.00 46.23 2.92
2140 2237 8.748412 AGTTTCATTATGCCTTTTGTAATAGCA 58.252 29.630 0.00 0.00 37.94 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 8.414003 TGCACATAGTTTGGTTGTACATTTTTA 58.586 29.630 0.00 0.00 0.00 1.52
139 166 3.335579 GGAATCCATGGAGCCGTAATAC 58.664 50.000 21.33 3.45 0.00 1.89
143 170 1.415672 GGGGAATCCATGGAGCCGTA 61.416 60.000 21.33 0.00 35.00 4.02
146 173 0.756815 GTTGGGGAATCCATGGAGCC 60.757 60.000 21.33 21.98 46.52 4.70
206 233 6.749036 ATTGGTTGTTCTAGAGTATAGGGG 57.251 41.667 0.00 0.00 0.00 4.79
225 252 6.595682 AGGACTTTCACATCCATAGTATTGG 58.404 40.000 0.00 0.00 37.47 3.16
243 270 5.411669 GTGTGATCCAACGAAATTAGGACTT 59.588 40.000 0.00 0.00 32.04 3.01
255 282 4.158384 GCTAATTTGTGTGTGATCCAACG 58.842 43.478 0.00 0.00 0.00 4.10
292 319 3.179443 AGAGCTTCTTTCGTGTCACAA 57.821 42.857 3.42 0.00 0.00 3.33
318 345 0.911769 CAGTCATAGGGTGGCCTTGA 59.088 55.000 3.32 0.00 30.86 3.02
326 353 3.143741 AGGATCCTCATCAGTCATAGGGT 59.856 47.826 9.02 0.00 0.00 4.34
367 394 0.948678 AAGAGGCTATCGACGCTCTC 59.051 55.000 8.25 11.65 0.00 3.20
378 405 1.762957 GTAGGATGGTGCAAGAGGCTA 59.237 52.381 0.00 0.00 45.15 3.93
431 458 1.044790 TCATCCTGCTCGATGAGGCA 61.045 55.000 10.97 1.28 42.89 4.75
437 464 2.064628 CCCCATCATCCTGCTCGAT 58.935 57.895 0.00 0.00 0.00 3.59
704 734 6.307558 TCAACATGTTTAGCGTGCAATTAATG 59.692 34.615 8.77 0.00 37.62 1.90
739 769 3.367703 CCAATGACCTTGATTGCTCCAAC 60.368 47.826 0.00 0.00 36.97 3.77
757 787 4.578928 GCCGTAAAACCATGTCTATCCAAT 59.421 41.667 0.00 0.00 0.00 3.16
799 829 4.617253 AACATAAAAAGGTCCAAAGGGC 57.383 40.909 0.00 0.00 0.00 5.19
991 1021 4.140536 GCTTTTCCCTCCATAAGATCAGG 58.859 47.826 0.00 0.00 0.00 3.86
1092 1123 7.020827 TCAAGAGGAGAAAGGAAACATGTAT 57.979 36.000 0.00 0.00 0.00 2.29
1114 1145 9.772973 ACTGACAATATTAGTTTACTGTGTTCA 57.227 29.630 0.00 0.00 0.00 3.18
1143 1174 7.425577 AAAACTAAAAGAAATTCATGCAGCC 57.574 32.000 0.00 0.00 0.00 4.85
1237 1287 4.823442 CAGGCCAATATGCAAGATAGTTCA 59.177 41.667 5.01 0.00 0.00 3.18
1252 1302 1.000396 GGACTTCTGGCAGGCCAAT 60.000 57.895 15.73 0.14 46.63 3.16
1492 1547 5.921004 TGCAAACACAAAATAGCCAAATC 57.079 34.783 0.00 0.00 0.00 2.17
1493 1548 5.181622 CCATGCAAACACAAAATAGCCAAAT 59.818 36.000 0.00 0.00 0.00 2.32
1494 1549 4.514441 CCATGCAAACACAAAATAGCCAAA 59.486 37.500 0.00 0.00 0.00 3.28
1495 1550 4.063689 CCATGCAAACACAAAATAGCCAA 58.936 39.130 0.00 0.00 0.00 4.52
1496 1551 3.661944 CCATGCAAACACAAAATAGCCA 58.338 40.909 0.00 0.00 0.00 4.75
1497 1552 2.416202 GCCATGCAAACACAAAATAGCC 59.584 45.455 0.00 0.00 0.00 3.93
1498 1553 2.416202 GGCCATGCAAACACAAAATAGC 59.584 45.455 0.00 0.00 0.00 2.97
1499 1554 3.928375 GAGGCCATGCAAACACAAAATAG 59.072 43.478 5.01 0.00 0.00 1.73
1500 1555 3.323115 TGAGGCCATGCAAACACAAAATA 59.677 39.130 5.01 0.00 0.00 1.40
1501 1556 2.104451 TGAGGCCATGCAAACACAAAAT 59.896 40.909 5.01 0.00 0.00 1.82
1502 1557 1.483827 TGAGGCCATGCAAACACAAAA 59.516 42.857 5.01 0.00 0.00 2.44
1503 1558 1.117994 TGAGGCCATGCAAACACAAA 58.882 45.000 5.01 0.00 0.00 2.83
1504 1559 1.340088 ATGAGGCCATGCAAACACAA 58.660 45.000 5.01 0.00 0.00 3.33
1505 1560 1.273048 GAATGAGGCCATGCAAACACA 59.727 47.619 5.01 0.00 32.36 3.72
1506 1561 1.273048 TGAATGAGGCCATGCAAACAC 59.727 47.619 5.01 0.00 35.42 3.32
1507 1562 1.630223 TGAATGAGGCCATGCAAACA 58.370 45.000 5.01 2.39 35.42 2.83
1508 1563 2.546778 CATGAATGAGGCCATGCAAAC 58.453 47.619 5.01 0.00 41.47 2.93
1509 1564 1.483004 CCATGAATGAGGCCATGCAAA 59.517 47.619 5.01 0.00 41.47 3.68
1510 1565 1.116308 CCATGAATGAGGCCATGCAA 58.884 50.000 5.01 0.00 41.47 4.08
1511 1566 0.032912 ACCATGAATGAGGCCATGCA 60.033 50.000 5.01 0.00 42.30 3.96
1512 1567 1.068127 GAACCATGAATGAGGCCATGC 59.932 52.381 5.01 0.00 38.95 4.06
1513 1568 2.380941 TGAACCATGAATGAGGCCATG 58.619 47.619 5.01 0.00 39.72 3.66
1514 1569 2.832643 TGAACCATGAATGAGGCCAT 57.167 45.000 5.01 0.00 33.66 4.40
1515 1570 2.832643 ATGAACCATGAATGAGGCCA 57.167 45.000 5.01 0.00 0.00 5.36
1516 1571 4.147321 ACATATGAACCATGAATGAGGCC 58.853 43.478 10.38 0.00 0.00 5.19
1517 1572 5.561532 CGAACATATGAACCATGAATGAGGC 60.562 44.000 10.38 0.00 0.00 4.70
1518 1573 5.049198 CCGAACATATGAACCATGAATGAGG 60.049 44.000 10.38 0.00 0.00 3.86
1519 1574 5.759763 TCCGAACATATGAACCATGAATGAG 59.240 40.000 10.38 0.00 0.00 2.90
1520 1575 5.679601 TCCGAACATATGAACCATGAATGA 58.320 37.500 10.38 0.00 0.00 2.57
1521 1576 6.375945 TTCCGAACATATGAACCATGAATG 57.624 37.500 10.38 0.00 0.00 2.67
1522 1577 6.603201 AGTTTCCGAACATATGAACCATGAAT 59.397 34.615 10.38 0.00 38.26 2.57
1523 1578 5.943416 AGTTTCCGAACATATGAACCATGAA 59.057 36.000 10.38 1.89 38.26 2.57
1524 1579 5.496556 AGTTTCCGAACATATGAACCATGA 58.503 37.500 10.38 0.00 38.26 3.07
1525 1580 5.818136 AGTTTCCGAACATATGAACCATG 57.182 39.130 10.38 0.00 38.26 3.66
1526 1581 6.650120 ACTAGTTTCCGAACATATGAACCAT 58.350 36.000 10.38 0.00 38.26 3.55
1527 1582 6.045072 ACTAGTTTCCGAACATATGAACCA 57.955 37.500 10.38 0.00 38.26 3.67
1528 1583 6.980051 AACTAGTTTCCGAACATATGAACC 57.020 37.500 10.38 0.00 38.26 3.62
1529 1584 9.968743 CTAAAACTAGTTTCCGAACATATGAAC 57.031 33.333 20.78 2.13 38.26 3.18
1530 1585 8.662141 GCTAAAACTAGTTTCCGAACATATGAA 58.338 33.333 20.78 0.00 38.26 2.57
1531 1586 7.820386 TGCTAAAACTAGTTTCCGAACATATGA 59.180 33.333 20.78 0.00 38.26 2.15
1532 1587 7.970384 TGCTAAAACTAGTTTCCGAACATATG 58.030 34.615 20.78 0.00 38.26 1.78
1533 1588 8.732746 ATGCTAAAACTAGTTTCCGAACATAT 57.267 30.769 20.78 5.11 38.26 1.78
1534 1589 8.556213 AATGCTAAAACTAGTTTCCGAACATA 57.444 30.769 20.78 7.30 38.26 2.29
1535 1590 7.448748 AATGCTAAAACTAGTTTCCGAACAT 57.551 32.000 20.78 15.83 38.26 2.71
1536 1591 6.870971 AATGCTAAAACTAGTTTCCGAACA 57.129 33.333 20.78 14.47 38.26 3.18
1537 1592 8.880750 AGATAATGCTAAAACTAGTTTCCGAAC 58.119 33.333 20.78 9.84 35.97 3.95
1538 1593 8.879759 CAGATAATGCTAAAACTAGTTTCCGAA 58.120 33.333 20.78 10.14 31.45 4.30
1539 1594 8.038944 ACAGATAATGCTAAAACTAGTTTCCGA 58.961 33.333 20.78 8.95 31.45 4.55
1540 1595 8.116753 CACAGATAATGCTAAAACTAGTTTCCG 58.883 37.037 20.78 15.02 31.45 4.30
1541 1596 8.398665 CCACAGATAATGCTAAAACTAGTTTCC 58.601 37.037 20.78 12.61 31.45 3.13
1542 1597 9.162764 TCCACAGATAATGCTAAAACTAGTTTC 57.837 33.333 20.78 9.61 31.45 2.78
1543 1598 9.515226 TTCCACAGATAATGCTAAAACTAGTTT 57.485 29.630 15.22 15.22 0.00 2.66
1544 1599 9.515226 TTTCCACAGATAATGCTAAAACTAGTT 57.485 29.630 1.12 1.12 0.00 2.24
1545 1600 8.947115 GTTTCCACAGATAATGCTAAAACTAGT 58.053 33.333 0.00 0.00 0.00 2.57
1546 1601 8.946085 TGTTTCCACAGATAATGCTAAAACTAG 58.054 33.333 0.00 0.00 32.26 2.57
1547 1602 8.726988 GTGTTTCCACAGATAATGCTAAAACTA 58.273 33.333 0.00 0.00 41.44 2.24
1548 1603 7.230510 TGTGTTTCCACAGATAATGCTAAAACT 59.769 33.333 0.00 0.00 46.45 2.66
1549 1604 7.367285 TGTGTTTCCACAGATAATGCTAAAAC 58.633 34.615 0.00 0.00 46.45 2.43
1550 1605 7.517614 TGTGTTTCCACAGATAATGCTAAAA 57.482 32.000 0.00 0.00 46.45 1.52
1564 1619 2.513753 TCCATGGACATGTGTTTCCAC 58.486 47.619 11.44 0.00 44.80 4.02
1565 1620 2.967745 TCCATGGACATGTGTTTCCA 57.032 45.000 11.44 4.47 46.06 3.53
1566 1621 4.599047 TTTTCCATGGACATGTGTTTCC 57.401 40.909 15.91 0.00 37.11 3.13
1567 1622 5.600696 ACTTTTTCCATGGACATGTGTTTC 58.399 37.500 15.91 0.00 37.11 2.78
1568 1623 5.453198 GGACTTTTTCCATGGACATGTGTTT 60.453 40.000 15.91 0.00 45.10 2.83
1569 1624 4.039124 GGACTTTTTCCATGGACATGTGTT 59.961 41.667 15.91 0.00 45.10 3.32
1570 1625 3.573967 GGACTTTTTCCATGGACATGTGT 59.426 43.478 15.91 9.99 45.10 3.72
1571 1626 4.178545 GGACTTTTTCCATGGACATGTG 57.821 45.455 15.91 6.67 45.10 3.21
1623 1678 5.477607 TTTCGACTTGAGGGTTCATTCTA 57.522 39.130 0.00 0.00 32.27 2.10
1804 1895 1.452470 GGGCGAGGCGGGAAAATTA 60.452 57.895 0.00 0.00 0.00 1.40
1976 2073 3.713902 CCCAGATTCGAATCCTGGG 57.286 57.895 35.47 35.47 42.23 4.45
2024 2121 3.480505 ACAGATCGATTGGCATGATGA 57.519 42.857 0.00 0.00 0.00 2.92
2028 2125 3.791122 GCTCAAACAGATCGATTGGCATG 60.791 47.826 0.00 0.00 0.00 4.06
2140 2237 5.483685 TCTTAGCCAACAGTGTTACATCT 57.516 39.130 8.49 6.04 0.00 2.90
2271 2370 6.072175 CCCGAAGAATACCAAACATCTGAAAA 60.072 38.462 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.