Multiple sequence alignment - TraesCS3A01G242500

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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 TraesCS3A01G242500 chr3A 100.000 3336 0 0 946 4281 455805284 455801949 0.000000e+00 6161.0
1 TraesCS3A01G242500 chr3A 100.000 682 0 0 1 682 455806229 455805548 0.000000e+00 1260.0
2 TraesCS3A01G242500 chr3A 90.625 128 12 0 2440 2567 427333265 427333138 2.050000e-38 171.0
3 TraesCS3A01G242500 chr3A 86.441 59 6 2 2751 2808 596515549 596515606 3.570000e-06 63.9
4 TraesCS3A01G242500 chr3D 94.365 2804 78 33 1509 4279 337975533 337972777 0.000000e+00 4229.0
5 TraesCS3A01G242500 chr3D 94.707 529 10 6 946 1456 337976056 337975528 0.000000e+00 806.0
6 TraesCS3A01G242500 chr3D 92.481 532 16 9 7 524 337976801 337976280 0.000000e+00 739.0
7 TraesCS3A01G242500 chr3D 95.122 164 4 2 519 682 337976242 337976083 5.490000e-64 255.0
8 TraesCS3A01G242500 chr3D 89.062 128 14 0 2440 2567 308057873 308057746 4.430000e-35 159.0
9 TraesCS3A01G242500 chr3D 84.746 59 7 2 2751 2808 454510142 454510199 1.660000e-04 58.4
10 TraesCS3A01G242500 chr3B 92.786 2800 101 33 1519 4279 435960483 435957746 0.000000e+00 3958.0
11 TraesCS3A01G242500 chr3B 90.496 705 19 15 14 682 435961717 435961025 0.000000e+00 887.0
12 TraesCS3A01G242500 chr3B 97.186 462 12 1 997 1457 435960949 435960488 0.000000e+00 780.0
13 TraesCS3A01G242500 chr3B 90.625 128 12 0 2440 2567 413419083 413419210 2.050000e-38 171.0
14 TraesCS3A01G242500 chr3B 84.746 59 7 2 2751 2808 597089662 597089719 1.660000e-04 58.4
15 TraesCS3A01G242500 chr1D 89.759 166 17 0 2699 2864 471001908 471002073 3.350000e-51 213.0
16 TraesCS3A01G242500 chr1D 91.241 137 10 2 2431 2566 471001666 471001801 7.310000e-43 185.0
17 TraesCS3A01G242500 chr1B 94.891 137 5 2 2431 2566 654716318 654716453 3.350000e-51 213.0
18 TraesCS3A01G242500 chr1B 88.506 174 17 3 2700 2870 654716514 654716687 1.560000e-49 207.0
19 TraesCS3A01G242500 chr1B 86.667 135 12 6 2435 2566 669710467 669710336 1.240000e-30 145.0
20 TraesCS3A01G242500 chr1A 92.617 149 7 4 2419 2566 565293956 565294101 1.210000e-50 211.0
21 TraesCS3A01G242500 chr1A 89.697 165 17 0 2700 2864 565294203 565294367 1.210000e-50 211.0
22 TraesCS3A01G242500 chr2D 100.000 28 0 0 2781 2808 425216036 425216009 8.000000e-03 52.8


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 TraesCS3A01G242500 chr3A 455801949 455806229 4280 True 3710.50 6161 100.000000 1 4281 2 chr3A.!!$R2 4280
1 TraesCS3A01G242500 chr3D 337972777 337976801 4024 True 1507.25 4229 94.168750 7 4279 4 chr3D.!!$R2 4272
2 TraesCS3A01G242500 chr3B 435957746 435961717 3971 True 1875.00 3958 93.489333 14 4279 3 chr3B.!!$R1 4265

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
604 667 0.172352 CACCTCTCGCTGTCTCCTTC 59.828 60.0 0.00 0.00 0.0 3.46 F
606 669 0.682855 CCTCTCGCTGTCTCCTTCCT 60.683 60.0 0.00 0.00 0.0 3.36 F
2243 2337 0.314302 GAGGCCATACGTATCGCAGT 59.686 55.0 23.62 12.18 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 2331 0.248498 GATCAATCGACCGACTGCGA 60.248 55.000 0.0 0.0 40.82 5.10 R
2590 2692 1.599071 CGGTGCAACTGCCTATGTATG 59.401 52.381 0.0 0.0 41.18 2.39 R
3983 4117 0.179018 AACCACACAAGCAGGGTCTC 60.179 55.000 0.0 0.0 32.01 3.36 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
260 264 5.974751 CCATTACATTACAAATTACGGTGCC 59.025 40.000 0.00 0.00 0.00 5.01
276 283 4.217983 ACGGTGCCATTACTATACTCTAGC 59.782 45.833 0.00 0.00 0.00 3.42
277 284 4.217767 CGGTGCCATTACTATACTCTAGCA 59.782 45.833 0.00 0.00 0.00 3.49
278 285 5.620205 CGGTGCCATTACTATACTCTAGCAG 60.620 48.000 0.00 0.00 0.00 4.24
459 477 5.757886 TCAATTAGCGGTTGTTTCTTTCAG 58.242 37.500 0.00 0.00 0.00 3.02
487 505 3.574354 AGCCAAAAAGCCAATGGAAAA 57.426 38.095 2.05 0.00 36.27 2.29
488 506 3.895998 AGCCAAAAAGCCAATGGAAAAA 58.104 36.364 2.05 0.00 36.27 1.94
603 666 0.540830 ACACCTCTCGCTGTCTCCTT 60.541 55.000 0.00 0.00 0.00 3.36
604 667 0.172352 CACCTCTCGCTGTCTCCTTC 59.828 60.000 0.00 0.00 0.00 3.46
605 668 0.968393 ACCTCTCGCTGTCTCCTTCC 60.968 60.000 0.00 0.00 0.00 3.46
606 669 0.682855 CCTCTCGCTGTCTCCTTCCT 60.683 60.000 0.00 0.00 0.00 3.36
607 670 1.181786 CTCTCGCTGTCTCCTTCCTT 58.818 55.000 0.00 0.00 0.00 3.36
654 717 1.631388 CCACCACCATACCACCACTAA 59.369 52.381 0.00 0.00 0.00 2.24
988 1051 1.135315 CAGCGCCAAGAACAATCGG 59.865 57.895 2.29 0.00 0.00 4.18
989 1052 1.302511 AGCGCCAAGAACAATCGGT 60.303 52.632 2.29 0.00 0.00 4.69
990 1053 0.889186 AGCGCCAAGAACAATCGGTT 60.889 50.000 2.29 0.00 44.10 4.44
1077 1156 2.580867 GCTCGCGTCGCTCTTCAT 60.581 61.111 16.36 0.00 0.00 2.57
1457 1539 6.597280 AGTTGGACTGCATTAATTTCTCTCTC 59.403 38.462 0.00 0.00 0.00 3.20
1458 1540 6.305272 TGGACTGCATTAATTTCTCTCTCT 57.695 37.500 0.00 0.00 0.00 3.10
1459 1541 6.344500 TGGACTGCATTAATTTCTCTCTCTC 58.656 40.000 0.00 0.00 0.00 3.20
1461 1543 6.701400 GGACTGCATTAATTTCTCTCTCTCTC 59.299 42.308 0.00 0.00 0.00 3.20
1462 1544 7.417797 GGACTGCATTAATTTCTCTCTCTCTCT 60.418 40.741 0.00 0.00 0.00 3.10
1463 1545 7.491682 ACTGCATTAATTTCTCTCTCTCTCTC 58.508 38.462 0.00 0.00 0.00 3.20
1464 1546 7.342799 ACTGCATTAATTTCTCTCTCTCTCTCT 59.657 37.037 0.00 0.00 0.00 3.10
1465 1547 7.715657 TGCATTAATTTCTCTCTCTCTCTCTC 58.284 38.462 0.00 0.00 0.00 3.20
1466 1548 7.560991 TGCATTAATTTCTCTCTCTCTCTCTCT 59.439 37.037 0.00 0.00 0.00 3.10
1467 1549 8.078596 GCATTAATTTCTCTCTCTCTCTCTCTC 58.921 40.741 0.00 0.00 0.00 3.20
1468 1550 9.347240 CATTAATTTCTCTCTCTCTCTCTCTCT 57.653 37.037 0.00 0.00 0.00 3.10
1469 1551 8.964476 TTAATTTCTCTCTCTCTCTCTCTCTC 57.036 38.462 0.00 0.00 0.00 3.20
1470 1552 6.821616 ATTTCTCTCTCTCTCTCTCTCTCT 57.178 41.667 0.00 0.00 0.00 3.10
1471 1553 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
1472 1554 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1473 1555 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1474 1556 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1475 1557 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1476 1558 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1477 1559 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1478 1560 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1479 1561 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1480 1562 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1481 1563 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1482 1564 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1483 1565 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1484 1566 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1485 1567 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1486 1568 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1487 1569 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1488 1570 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1489 1571 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1490 1572 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1491 1573 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1492 1574 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1493 1575 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1494 1576 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1495 1577 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1496 1578 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1497 1579 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1498 1580 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1499 1581 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1500 1582 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1501 1583 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1502 1584 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1503 1585 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1504 1586 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1505 1587 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1506 1588 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1507 1589 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1508 1590 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1509 1591 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1510 1592 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1511 1593 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1512 1594 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1513 1595 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1514 1596 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1515 1597 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1516 1598 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1517 1599 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1681 1763 2.162208 CGCTTCCTTGAATTGCTTGCTA 59.838 45.455 0.00 0.00 0.00 3.49
1795 1877 2.665185 GGTTTCACACCGAGCGCT 60.665 61.111 11.27 11.27 35.12 5.92
1798 1880 1.227409 TTTCACACCGAGCGCTCAA 60.227 52.632 34.69 18.72 0.00 3.02
1805 1887 3.184683 CGAGCGCTCAAGCCTCAC 61.185 66.667 34.69 7.57 37.85 3.51
1858 1946 9.743057 AAAAACATAAAATCTGATTTCGTGTCA 57.257 25.926 22.51 6.79 32.29 3.58
1961 2049 9.688592 ATGCTTTGTTCATTTTTCTTCTTCTAG 57.311 29.630 0.00 0.00 0.00 2.43
2239 2333 1.211969 CGGGAGGCCATACGTATCG 59.788 63.158 5.01 0.00 0.00 2.92
2240 2334 1.080025 GGGAGGCCATACGTATCGC 60.080 63.158 15.81 15.81 0.00 4.58
2242 2336 0.388649 GGAGGCCATACGTATCGCAG 60.389 60.000 23.62 5.68 0.00 5.18
2243 2337 0.314302 GAGGCCATACGTATCGCAGT 59.686 55.000 23.62 12.18 0.00 4.40
2244 2338 0.314302 AGGCCATACGTATCGCAGTC 59.686 55.000 23.62 9.14 0.00 3.51
2245 2339 1.002250 GGCCATACGTATCGCAGTCG 61.002 60.000 23.62 3.98 0.00 4.18
2252 2347 0.316772 CGTATCGCAGTCGGTCGATT 60.317 55.000 2.45 0.00 42.03 3.34
2310 2412 8.554011 ACTAGGATTAGGAGTAGATAGCTAAGG 58.446 40.741 0.00 0.00 0.00 2.69
2406 2508 1.021390 ATCTTTTCAGGTCTGCGGCG 61.021 55.000 0.51 0.51 0.00 6.46
2407 2509 2.668212 TTTTCAGGTCTGCGGCGG 60.668 61.111 9.78 1.35 0.00 6.13
2408 2510 3.469863 TTTTCAGGTCTGCGGCGGT 62.470 57.895 9.78 0.00 0.00 5.68
2571 2673 2.426024 CCCATATCCCAGGTACGTATCG 59.574 54.545 0.00 0.00 0.00 2.92
2634 2736 1.408702 GTGCATGGGCGATTTTGGTAT 59.591 47.619 0.00 0.00 45.35 2.73
2635 2737 2.621055 GTGCATGGGCGATTTTGGTATA 59.379 45.455 0.00 0.00 45.35 1.47
2636 2738 3.255642 GTGCATGGGCGATTTTGGTATAT 59.744 43.478 0.00 0.00 45.35 0.86
2637 2739 4.457603 GTGCATGGGCGATTTTGGTATATA 59.542 41.667 0.00 0.00 45.35 0.86
2638 2740 4.457603 TGCATGGGCGATTTTGGTATATAC 59.542 41.667 4.14 4.14 45.35 1.47
2643 2745 7.011499 TGGGCGATTTTGGTATATACTGTAT 57.989 36.000 12.54 5.53 0.00 2.29
2644 2746 6.876789 TGGGCGATTTTGGTATATACTGTATG 59.123 38.462 12.54 0.00 0.00 2.39
2658 2760 8.880991 ATATACTGTATGTAGGGACGAAGAAT 57.119 34.615 10.51 0.00 34.24 2.40
2660 2762 4.099573 ACTGTATGTAGGGACGAAGAATGG 59.900 45.833 0.00 0.00 0.00 3.16
2691 2796 2.749076 TGCTTGTGCTGATAATGGTGAC 59.251 45.455 0.00 0.00 40.48 3.67
2693 2798 2.022764 TGTGCTGATAATGGTGACGG 57.977 50.000 0.00 0.00 0.00 4.79
2697 2802 1.406887 GCTGATAATGGTGACGGGTGT 60.407 52.381 0.00 0.00 0.00 4.16
3331 3451 5.460646 TCGATCTTGTTTTTCCTTGATTGC 58.539 37.500 0.00 0.00 0.00 3.56
3364 3484 4.905429 TGATTTGTTTCCTTCCTCGATCA 58.095 39.130 0.00 0.00 0.00 2.92
3369 3489 2.866762 GTTTCCTTCCTCGATCAATCCG 59.133 50.000 0.00 0.00 0.00 4.18
3590 3712 8.250332 TGATAATTTTATGCTCCTTGTGTTTCC 58.750 33.333 0.00 0.00 0.00 3.13
3625 3747 4.864916 ATGCAACAGTACTAAGAATGCG 57.135 40.909 0.00 0.00 35.18 4.73
3723 3845 2.934886 AATTTGCTGTTGGTGGCAAT 57.065 40.000 0.00 0.00 45.82 3.56
3739 3861 3.648339 GCAATTGTGGCAAGAAGAAGA 57.352 42.857 7.40 0.00 0.00 2.87
3740 3862 4.184079 GCAATTGTGGCAAGAAGAAGAT 57.816 40.909 7.40 0.00 0.00 2.40
3741 3863 4.171754 GCAATTGTGGCAAGAAGAAGATC 58.828 43.478 7.40 0.00 0.00 2.75
3742 3864 4.409570 CAATTGTGGCAAGAAGAAGATCG 58.590 43.478 0.00 0.00 0.00 3.69
3743 3865 3.401033 TTGTGGCAAGAAGAAGATCGA 57.599 42.857 0.00 0.00 0.00 3.59
3744 3866 3.616956 TGTGGCAAGAAGAAGATCGAT 57.383 42.857 0.00 0.00 0.00 3.59
3899 4033 2.811317 CTTGACCAGGTCGCTCGC 60.811 66.667 15.24 0.00 34.95 5.03
3900 4034 3.288308 CTTGACCAGGTCGCTCGCT 62.288 63.158 15.24 0.00 34.95 4.93
3901 4035 3.282745 TTGACCAGGTCGCTCGCTC 62.283 63.158 15.24 0.00 34.95 5.03
3902 4036 4.838486 GACCAGGTCGCTCGCTCG 62.838 72.222 3.05 0.00 0.00 5.03
3977 4111 4.405680 TCCATAGTGATGTGAACCTACCTG 59.594 45.833 0.00 0.00 0.00 4.00
3978 4112 2.770164 AGTGATGTGAACCTACCTGC 57.230 50.000 0.00 0.00 0.00 4.85
3983 4117 0.396435 TGTGAACCTACCTGCACTGG 59.604 55.000 0.00 0.00 32.69 4.00
4087 4227 1.153489 CGGTCCATGTCTGCCTGAG 60.153 63.158 0.00 0.00 0.00 3.35
4089 4229 0.107945 GGTCCATGTCTGCCTGAGTC 60.108 60.000 0.00 0.00 0.00 3.36
4093 4233 2.432146 TCCATGTCTGCCTGAGTCATAC 59.568 50.000 0.00 0.00 30.28 2.39
4102 4242 4.204799 TGCCTGAGTCATACTACGTATGT 58.795 43.478 12.25 0.00 44.21 2.29
4110 4250 8.718734 TGAGTCATACTACGTATGTAATAGCTG 58.281 37.037 12.25 0.00 44.21 4.24
4218 4360 2.289444 TGGAGTTTAGACGAAGCTTGGG 60.289 50.000 13.38 3.02 0.00 4.12
4220 4362 2.737252 GAGTTTAGACGAAGCTTGGGTG 59.263 50.000 13.38 0.00 0.00 4.61
4227 4369 1.447317 CGAAGCTTGGGTGCAACTGT 61.447 55.000 2.10 0.00 36.74 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.248990 CGTGATCTCTGCTCTGCTCC 60.249 60.000 0.00 0.00 0.00 4.70
161 163 4.802051 CCGGTCACATGCAGGGGG 62.802 72.222 0.00 0.00 0.00 5.40
167 170 2.890474 CGGTAGCCGGTCACATGC 60.890 66.667 1.90 0.00 44.15 4.06
297 305 2.781174 AGTCCAGACCTAGCTAGCTAGT 59.219 50.000 37.50 28.67 43.22 2.57
459 477 3.385193 TGGCTTTTTGGCTAGCTTTTC 57.615 42.857 15.72 0.00 42.34 2.29
517 535 2.091389 TGGGGATTCAGAGAGAGAGAGG 60.091 54.545 0.00 0.00 0.00 3.69
560 621 2.354401 TGCAAGAGAGCGAGAGGGG 61.354 63.158 0.00 0.00 37.31 4.79
603 666 1.064003 TTAGTGAGGCAAGCCAAGGA 58.936 50.000 14.40 0.00 38.92 3.36
604 667 2.019984 GATTAGTGAGGCAAGCCAAGG 58.980 52.381 14.40 0.00 38.92 3.61
605 668 2.421424 GTGATTAGTGAGGCAAGCCAAG 59.579 50.000 14.40 0.00 38.92 3.61
606 669 2.040278 AGTGATTAGTGAGGCAAGCCAA 59.960 45.455 14.40 0.00 38.92 4.52
607 670 1.630369 AGTGATTAGTGAGGCAAGCCA 59.370 47.619 14.40 0.00 38.92 4.75
654 717 3.846588 CAAGCATATGGGGGAGGTACTAT 59.153 47.826 4.56 0.00 41.55 2.12
988 1051 0.951040 CTGCCTGTGGGAACTCGAAC 60.951 60.000 0.00 0.00 33.58 3.95
989 1052 1.371183 CTGCCTGTGGGAACTCGAA 59.629 57.895 0.00 0.00 33.58 3.71
990 1053 3.059982 CTGCCTGTGGGAACTCGA 58.940 61.111 0.00 0.00 33.58 4.04
991 1054 2.743928 GCTGCCTGTGGGAACTCG 60.744 66.667 0.00 0.00 33.58 4.18
992 1055 0.823356 TTTGCTGCCTGTGGGAACTC 60.823 55.000 0.00 0.00 33.58 3.01
993 1056 0.825010 CTTTGCTGCCTGTGGGAACT 60.825 55.000 0.00 0.00 33.58 3.01
994 1057 1.662044 CTTTGCTGCCTGTGGGAAC 59.338 57.895 0.00 0.00 33.58 3.62
995 1058 2.202395 GCTTTGCTGCCTGTGGGAA 61.202 57.895 0.00 0.00 33.58 3.97
1108 1187 3.400928 CAGGAGGCCTGCTGCTCT 61.401 66.667 37.26 9.43 45.13 4.09
1354 1436 1.492133 CCTCCTTCTTGCACCTCCCA 61.492 60.000 0.00 0.00 0.00 4.37
1457 1539 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1458 1540 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1459 1541 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1461 1543 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1462 1544 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1463 1545 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1464 1546 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1465 1547 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1466 1548 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1467 1549 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1468 1550 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1469 1551 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1470 1552 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1471 1553 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1472 1554 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1473 1555 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1474 1556 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1475 1557 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1476 1558 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1477 1559 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1478 1560 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1479 1561 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1480 1562 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1481 1563 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1482 1564 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1483 1565 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1484 1566 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1485 1567 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1486 1568 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1487 1569 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1488 1570 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1489 1571 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1490 1572 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1491 1573 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1492 1574 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1493 1575 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1494 1576 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1495 1577 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
1496 1578 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
1497 1579 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
1498 1580 4.403752 CACAGAGAGAGAGAGAGAGAGAGA 59.596 50.000 0.00 0.00 0.00 3.10
1499 1581 4.403752 TCACAGAGAGAGAGAGAGAGAGAG 59.596 50.000 0.00 0.00 0.00 3.20
1500 1582 4.352893 TCACAGAGAGAGAGAGAGAGAGA 58.647 47.826 0.00 0.00 0.00 3.10
1501 1583 4.743057 TCACAGAGAGAGAGAGAGAGAG 57.257 50.000 0.00 0.00 0.00 3.20
1502 1584 5.698741 AATCACAGAGAGAGAGAGAGAGA 57.301 43.478 0.00 0.00 0.00 3.10
1503 1585 6.183360 GGAAAATCACAGAGAGAGAGAGAGAG 60.183 46.154 0.00 0.00 0.00 3.20
1504 1586 5.652014 GGAAAATCACAGAGAGAGAGAGAGA 59.348 44.000 0.00 0.00 0.00 3.10
1505 1587 5.449041 CGGAAAATCACAGAGAGAGAGAGAG 60.449 48.000 0.00 0.00 0.00 3.20
1506 1588 4.397730 CGGAAAATCACAGAGAGAGAGAGA 59.602 45.833 0.00 0.00 0.00 3.10
1507 1589 4.157656 ACGGAAAATCACAGAGAGAGAGAG 59.842 45.833 0.00 0.00 0.00 3.20
1508 1590 4.082517 CACGGAAAATCACAGAGAGAGAGA 60.083 45.833 0.00 0.00 0.00 3.10
1509 1591 4.172505 CACGGAAAATCACAGAGAGAGAG 58.827 47.826 0.00 0.00 0.00 3.20
1510 1592 3.574396 ACACGGAAAATCACAGAGAGAGA 59.426 43.478 0.00 0.00 0.00 3.10
1511 1593 3.919216 ACACGGAAAATCACAGAGAGAG 58.081 45.455 0.00 0.00 0.00 3.20
1512 1594 3.574396 AGACACGGAAAATCACAGAGAGA 59.426 43.478 0.00 0.00 0.00 3.10
1513 1595 3.919216 AGACACGGAAAATCACAGAGAG 58.081 45.455 0.00 0.00 0.00 3.20
1514 1596 4.058124 CAAGACACGGAAAATCACAGAGA 58.942 43.478 0.00 0.00 0.00 3.10
1515 1597 4.058124 TCAAGACACGGAAAATCACAGAG 58.942 43.478 0.00 0.00 0.00 3.35
1516 1598 4.066646 TCAAGACACGGAAAATCACAGA 57.933 40.909 0.00 0.00 0.00 3.41
1517 1599 4.692625 AGATCAAGACACGGAAAATCACAG 59.307 41.667 0.00 0.00 0.00 3.66
1681 1763 3.746045 GGCATGAATGAATGAATGGCT 57.254 42.857 0.00 0.00 41.11 4.75
1793 1875 1.376553 GTCAGGGTGAGGCTTGAGC 60.377 63.158 0.00 0.00 41.14 4.26
1794 1876 0.397941 TTGTCAGGGTGAGGCTTGAG 59.602 55.000 0.00 0.00 0.00 3.02
1795 1877 1.003580 GATTGTCAGGGTGAGGCTTGA 59.996 52.381 0.00 0.00 0.00 3.02
1798 1880 1.004044 CTTGATTGTCAGGGTGAGGCT 59.996 52.381 0.00 0.00 0.00 4.58
1858 1946 7.828223 AGATGAAGCAAGTAATCAAGAGTTCAT 59.172 33.333 0.00 0.00 35.39 2.57
2135 2228 0.251341 AGGAGGTTCACATTGTGCCC 60.251 55.000 12.04 13.30 32.98 5.36
2160 2254 2.365293 TCTATGTATGAGCGCACATGGT 59.635 45.455 27.45 15.99 36.13 3.55
2173 2267 3.267483 GTTGTTGGCGTGGTCTATGTAT 58.733 45.455 0.00 0.00 0.00 2.29
2231 2325 0.805711 TCGACCGACTGCGATACGTA 60.806 55.000 0.00 0.00 40.82 3.57
2234 2328 1.121240 CAATCGACCGACTGCGATAC 58.879 55.000 0.00 0.00 45.50 2.24
2235 2329 1.018910 TCAATCGACCGACTGCGATA 58.981 50.000 0.00 0.00 45.50 2.92
2237 2331 0.248498 GATCAATCGACCGACTGCGA 60.248 55.000 0.00 0.00 40.82 5.10
2252 2347 7.260558 AGAGATTTCGTTCATACTACGATCA 57.739 36.000 0.00 0.00 46.14 2.92
2310 2412 2.906354 ACCATTTGGCTGTCTCGATAC 58.094 47.619 0.00 0.00 39.32 2.24
2586 2688 5.547465 GGTGCAACTGCCTATGTATGTATA 58.453 41.667 0.00 0.00 41.18 1.47
2587 2689 4.389374 GGTGCAACTGCCTATGTATGTAT 58.611 43.478 0.00 0.00 41.18 2.29
2588 2690 3.739830 CGGTGCAACTGCCTATGTATGTA 60.740 47.826 0.00 0.00 41.18 2.29
2589 2691 2.643551 GGTGCAACTGCCTATGTATGT 58.356 47.619 0.00 0.00 41.18 2.29
2590 2692 1.599071 CGGTGCAACTGCCTATGTATG 59.401 52.381 0.00 0.00 41.18 2.39
2634 2736 7.176165 CCATTCTTCGTCCCTACATACAGTATA 59.824 40.741 0.00 0.00 30.93 1.47
2635 2737 6.015350 CCATTCTTCGTCCCTACATACAGTAT 60.015 42.308 0.00 0.00 30.93 2.12
2636 2738 5.301045 CCATTCTTCGTCCCTACATACAGTA 59.699 44.000 0.00 0.00 0.00 2.74
2637 2739 4.099573 CCATTCTTCGTCCCTACATACAGT 59.900 45.833 0.00 0.00 0.00 3.55
2638 2740 4.099573 ACCATTCTTCGTCCCTACATACAG 59.900 45.833 0.00 0.00 0.00 2.74
2643 2745 4.468510 ACATAACCATTCTTCGTCCCTACA 59.531 41.667 0.00 0.00 0.00 2.74
2644 2746 5.019785 ACATAACCATTCTTCGTCCCTAC 57.980 43.478 0.00 0.00 0.00 3.18
2658 2760 3.439825 CAGCACAAGCACATACATAACCA 59.560 43.478 0.00 0.00 45.49 3.67
2660 2762 4.944962 TCAGCACAAGCACATACATAAC 57.055 40.909 0.00 0.00 45.49 1.89
2691 2796 2.942796 TAGCTCCTGCACACACCCG 61.943 63.158 0.00 0.00 42.74 5.28
2693 2798 0.895530 TAGTAGCTCCTGCACACACC 59.104 55.000 0.00 0.00 42.74 4.16
2697 2802 1.320344 CCGGTAGTAGCTCCTGCACA 61.320 60.000 0.00 0.00 42.74 4.57
3331 3451 6.396829 AGGAAACAAATCAAGAAGTGAAGG 57.603 37.500 0.00 0.00 40.50 3.46
3364 3484 1.522355 CATCTCGCAGCACCGGATT 60.522 57.895 9.46 0.00 0.00 3.01
3369 3489 0.807667 CTGTACCATCTCGCAGCACC 60.808 60.000 0.00 0.00 0.00 5.01
3449 3569 5.107824 TGCTAGTACACTGACTACTACGAG 58.892 45.833 0.00 0.00 0.00 4.18
3587 3709 1.411501 GCATTAATGGAGCCAGGGGAA 60.412 52.381 17.02 0.00 0.00 3.97
3590 3712 1.410153 GTTGCATTAATGGAGCCAGGG 59.590 52.381 17.02 0.00 0.00 4.45
3625 3747 4.444536 ACCAAACATGCAAATGGATATGC 58.555 39.130 14.90 0.00 42.86 3.14
3723 3845 3.401033 TCGATCTTCTTCTTGCCACAA 57.599 42.857 0.00 0.00 0.00 3.33
3739 3861 4.923871 GCCAAGATCGTTGTACATATCGAT 59.076 41.667 21.91 21.91 43.95 3.59
3740 3862 4.037565 AGCCAAGATCGTTGTACATATCGA 59.962 41.667 16.35 16.35 36.77 3.59
3741 3863 4.299155 AGCCAAGATCGTTGTACATATCG 58.701 43.478 0.00 2.85 0.00 2.92
3742 3864 5.346281 GCTAGCCAAGATCGTTGTACATATC 59.654 44.000 2.29 0.85 0.00 1.63
3743 3865 5.011125 AGCTAGCCAAGATCGTTGTACATAT 59.989 40.000 12.13 0.00 0.00 1.78
3744 3866 4.341235 AGCTAGCCAAGATCGTTGTACATA 59.659 41.667 12.13 0.00 0.00 2.29
3977 4111 1.673665 CAAGCAGGGTCTCCAGTGC 60.674 63.158 4.79 4.79 35.89 4.40
3978 4112 0.604780 CACAAGCAGGGTCTCCAGTG 60.605 60.000 0.00 0.00 34.83 3.66
3983 4117 0.179018 AACCACACAAGCAGGGTCTC 60.179 55.000 0.00 0.00 32.01 3.36
4093 4233 8.867112 TTTTTCTCCAGCTATTACATACGTAG 57.133 34.615 0.08 0.00 0.00 3.51
4102 4242 7.604164 GGATCATCGATTTTTCTCCAGCTATTA 59.396 37.037 0.00 0.00 0.00 0.98
4110 4250 7.969536 TTAGATGGATCATCGATTTTTCTCC 57.030 36.000 0.00 0.00 44.67 3.71
4138 4278 8.194104 AGCTAGGTTCACATCAATCGATATATC 58.806 37.037 0.00 2.34 0.00 1.63
4218 4360 1.548986 GCACAGTTCAACAGTTGCAC 58.451 50.000 8.58 8.22 0.00 4.57
4220 4362 0.592247 CCGCACAGTTCAACAGTTGC 60.592 55.000 8.58 0.00 0.00 4.17
4227 4369 0.817229 TGCATCACCGCACAGTTCAA 60.817 50.000 0.00 0.00 36.86 2.69


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

AutoCloner maintained by Alex Coulton.