Multiple sequence alignment - TraesCS4B01G130500

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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 TraesCS4B01G130500 chr4B 100.000 2408 0 0 1 2408 171120450 171122857 0.000000e+00 4447.0
1 TraesCS4B01G130500 chr4B 95.767 1441 60 1 1 1440 90758864 90760304 0.000000e+00 2322.0
2 TraesCS4B01G130500 chr4B 91.390 813 54 5 1602 2408 43809950 43809148 0.000000e+00 1099.0
3 TraesCS4B01G130500 chr4B 90.954 807 61 7 1603 2408 18434524 18433729 0.000000e+00 1075.0
4 TraesCS4B01G130500 chr4B 91.105 787 48 8 1601 2386 188180501 188181266 0.000000e+00 1046.0
5 TraesCS4B01G130500 chr4B 89.885 781 50 14 1629 2408 325999469 326000221 0.000000e+00 977.0
6 TraesCS4B01G130500 chr4B 90.909 121 11 0 1484 1604 171825861 171825741 1.920000e-36 163.0
7 TraesCS4B01G130500 chr1B 95.417 1440 62 4 4 1440 22438502 22437064 0.000000e+00 2290.0
8 TraesCS4B01G130500 chr1B 95.136 1439 67 3 4 1440 22565145 22563708 0.000000e+00 2266.0
9 TraesCS4B01G130500 chr1B 94.920 1437 70 3 4 1438 22498477 22497042 0.000000e+00 2246.0
10 TraesCS4B01G130500 chr1B 94.367 1438 80 1 4 1440 22378751 22377314 0.000000e+00 2206.0
11 TraesCS4B01G130500 chr1B 92.395 789 39 8 1602 2389 491366531 491365763 0.000000e+00 1105.0
12 TraesCS4B01G130500 chr1B 82.609 414 56 5 1015 1428 447244085 447243688 3.810000e-93 351.0
13 TraesCS4B01G130500 chr4A 95.076 1442 70 1 1 1441 674778437 674779878 0.000000e+00 2268.0
14 TraesCS4B01G130500 chr4A 95.043 807 37 2 1602 2408 651446744 651445941 0.000000e+00 1266.0
15 TraesCS4B01G130500 chr4A 93.277 119 8 0 1484 1602 466917027 466916909 2.460000e-40 176.0
16 TraesCS4B01G130500 chr7D 94.244 1442 80 3 1 1440 89059986 89061426 0.000000e+00 2200.0
17 TraesCS4B01G130500 chr7D 93.741 1438 72 10 4 1440 514921711 514920291 0.000000e+00 2141.0
18 TraesCS4B01G130500 chr4D 94.254 1427 81 1 1 1426 208377431 208378857 0.000000e+00 2180.0
19 TraesCS4B01G130500 chr4D 90.984 122 9 1 1484 1603 109919742 109919863 1.920000e-36 163.0
20 TraesCS4B01G130500 chr7B 92.278 790 40 6 1602 2389 468864770 468864000 0.000000e+00 1101.0
21 TraesCS4B01G130500 chr7B 92.381 735 50 5 1600 2331 733162065 733161334 0.000000e+00 1042.0
22 TraesCS4B01G130500 chr7B 89.550 823 65 10 1596 2408 546883520 546884331 0.000000e+00 1024.0
23 TraesCS4B01G130500 chr2B 90.965 808 62 6 1602 2408 76511628 76510831 0.000000e+00 1077.0
24 TraesCS4B01G130500 chr3B 90.864 810 46 14 1602 2408 678017296 678016512 0.000000e+00 1061.0
25 TraesCS4B01G130500 chr5B 90.959 365 24 4 1605 1969 379362110 379361755 1.290000e-132 483.0
26 TraesCS4B01G130500 chr3D 100.000 28 0 0 1441 1468 2766750 2766723 4.000000e-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 TraesCS4B01G130500 chr4B 171120450 171122857 2407 False 4447 4447 100.000 1 2408 1 chr4B.!!$F2 2407
1 TraesCS4B01G130500 chr4B 90758864 90760304 1440 False 2322 2322 95.767 1 1440 1 chr4B.!!$F1 1439
2 TraesCS4B01G130500 chr4B 43809148 43809950 802 True 1099 1099 91.390 1602 2408 1 chr4B.!!$R2 806
3 TraesCS4B01G130500 chr4B 18433729 18434524 795 True 1075 1075 90.954 1603 2408 1 chr4B.!!$R1 805
4 TraesCS4B01G130500 chr4B 188180501 188181266 765 False 1046 1046 91.105 1601 2386 1 chr4B.!!$F3 785
5 TraesCS4B01G130500 chr4B 325999469 326000221 752 False 977 977 89.885 1629 2408 1 chr4B.!!$F4 779
6 TraesCS4B01G130500 chr1B 22437064 22438502 1438 True 2290 2290 95.417 4 1440 1 chr1B.!!$R2 1436
7 TraesCS4B01G130500 chr1B 22563708 22565145 1437 True 2266 2266 95.136 4 1440 1 chr1B.!!$R4 1436
8 TraesCS4B01G130500 chr1B 22497042 22498477 1435 True 2246 2246 94.920 4 1438 1 chr1B.!!$R3 1434
9 TraesCS4B01G130500 chr1B 22377314 22378751 1437 True 2206 2206 94.367 4 1440 1 chr1B.!!$R1 1436
10 TraesCS4B01G130500 chr1B 491365763 491366531 768 True 1105 1105 92.395 1602 2389 1 chr1B.!!$R6 787
11 TraesCS4B01G130500 chr4A 674778437 674779878 1441 False 2268 2268 95.076 1 1441 1 chr4A.!!$F1 1440
12 TraesCS4B01G130500 chr4A 651445941 651446744 803 True 1266 1266 95.043 1602 2408 1 chr4A.!!$R2 806
13 TraesCS4B01G130500 chr7D 89059986 89061426 1440 False 2200 2200 94.244 1 1440 1 chr7D.!!$F1 1439
14 TraesCS4B01G130500 chr7D 514920291 514921711 1420 True 2141 2141 93.741 4 1440 1 chr7D.!!$R1 1436
15 TraesCS4B01G130500 chr4D 208377431 208378857 1426 False 2180 2180 94.254 1 1426 1 chr4D.!!$F2 1425
16 TraesCS4B01G130500 chr7B 468864000 468864770 770 True 1101 1101 92.278 1602 2389 1 chr7B.!!$R1 787
17 TraesCS4B01G130500 chr7B 733161334 733162065 731 True 1042 1042 92.381 1600 2331 1 chr7B.!!$R2 731
18 TraesCS4B01G130500 chr7B 546883520 546884331 811 False 1024 1024 89.550 1596 2408 1 chr7B.!!$F1 812
19 TraesCS4B01G130500 chr2B 76510831 76511628 797 True 1077 1077 90.965 1602 2408 1 chr2B.!!$R1 806
20 TraesCS4B01G130500 chr3B 678016512 678017296 784 True 1061 1061 90.864 1602 2408 1 chr3B.!!$R1 806


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
470 473 0.111253 AAGGCCCTTTGGTCAGTCAG 59.889 55.0 0.0 0.0 39.4 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 1905 0.178873 AGGGGAAGAACTGCCTGGTA 60.179 55.0 0.0 0.0 35.37 3.25 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
34 35 1.347707 TCATCTTCCTTCACTTGGCGT 59.652 47.619 0.00 0.00 0.00 5.68
177 179 1.002544 GATTCTCCCTATTCCGGCTGG 59.997 57.143 4.71 4.71 0.00 4.85
405 407 7.309770 ACTTCTTCTTCTCTACAAGTGGAAT 57.690 36.000 0.00 0.00 0.00 3.01
432 434 2.158755 AGGGTCTGGCTTCCAATATTCG 60.159 50.000 0.00 0.00 30.80 3.34
470 473 0.111253 AAGGCCCTTTGGTCAGTCAG 59.889 55.000 0.00 0.00 39.40 3.51
592 595 2.103432 TGTTTCTTCTGCAACCGGACTA 59.897 45.455 9.46 0.00 0.00 2.59
595 598 1.968493 TCTTCTGCAACCGGACTAAGT 59.032 47.619 9.46 0.00 0.00 2.24
622 625 1.350351 AGCATCTCTTCCTGCTGTGTT 59.650 47.619 0.00 0.00 46.55 3.32
628 631 1.768275 TCTTCCTGCTGTGTTCCTTCA 59.232 47.619 0.00 0.00 0.00 3.02
672 675 2.829741 AAGAGGAGTTCAGTGTCAGC 57.170 50.000 0.00 0.00 0.00 4.26
788 791 5.283763 TCTATGGCATATCTGGGAAGCTAT 58.716 41.667 7.81 0.00 0.00 2.97
904 907 1.632965 GCCTAAACCCGATCCCAGGT 61.633 60.000 0.00 0.00 38.27 4.00
915 918 1.208293 GATCCCAGGTGTGAGTCTTCC 59.792 57.143 0.00 0.00 0.00 3.46
928 931 5.119694 GTGAGTCTTCCTCTTCAACTGTTT 58.880 41.667 0.00 0.00 41.11 2.83
930 933 5.817816 TGAGTCTTCCTCTTCAACTGTTTTC 59.182 40.000 0.00 0.00 41.11 2.29
997 1000 2.803492 GCGCTGTTTCCTTCTATCCGAT 60.803 50.000 0.00 0.00 0.00 4.18
1082 1085 2.371510 AGCTTCAAGGCTTCTCTGAACT 59.628 45.455 0.00 0.00 39.86 3.01
1140 1143 2.632996 TGAGGTTTGTCGATCTGAAGGT 59.367 45.455 0.00 0.00 0.00 3.50
1154 1157 3.003275 TCTGAAGGTTGTTCGTCAATTGC 59.997 43.478 0.00 0.00 38.38 3.56
1177 1180 1.227205 GCATCTGACTGCCTCCTCG 60.227 63.158 2.04 0.00 36.10 4.63
1321 1324 2.242047 TGTAGCGGCACACAAACTAA 57.758 45.000 1.45 0.00 0.00 2.24
1325 1328 0.941542 GCGGCACACAAACTAACTCA 59.058 50.000 0.00 0.00 0.00 3.41
1343 1346 4.446994 CTCATAGTTGTGAGCACTCTGA 57.553 45.455 1.99 0.00 39.19 3.27
1395 1399 4.345859 TTGTATCAGGGACGAACTTTGT 57.654 40.909 0.00 0.00 0.00 2.83
1405 1409 4.439563 GGGACGAACTTTGTTGTGATGTTT 60.440 41.667 0.00 0.00 0.00 2.83
1458 1462 6.670695 AAAAAGTTCTCCCAATGTGCTTAT 57.329 33.333 0.00 0.00 0.00 1.73
1459 1463 6.670695 AAAAGTTCTCCCAATGTGCTTATT 57.329 33.333 0.00 0.00 0.00 1.40
1460 1464 6.670695 AAAGTTCTCCCAATGTGCTTATTT 57.329 33.333 0.00 0.00 0.00 1.40
1461 1465 5.904362 AGTTCTCCCAATGTGCTTATTTC 57.096 39.130 0.00 0.00 0.00 2.17
1462 1466 5.574188 AGTTCTCCCAATGTGCTTATTTCT 58.426 37.500 0.00 0.00 0.00 2.52
1463 1467 5.416952 AGTTCTCCCAATGTGCTTATTTCTG 59.583 40.000 0.00 0.00 0.00 3.02
1464 1468 4.272489 TCTCCCAATGTGCTTATTTCTGG 58.728 43.478 0.00 0.00 0.00 3.86
1465 1469 4.018506 TCTCCCAATGTGCTTATTTCTGGA 60.019 41.667 0.00 0.00 0.00 3.86
1466 1470 4.870636 TCCCAATGTGCTTATTTCTGGAT 58.129 39.130 0.00 0.00 0.00 3.41
1467 1471 6.012337 TCCCAATGTGCTTATTTCTGGATA 57.988 37.500 0.00 0.00 0.00 2.59
1468 1472 5.827797 TCCCAATGTGCTTATTTCTGGATAC 59.172 40.000 0.00 0.00 0.00 2.24
1469 1473 5.829924 CCCAATGTGCTTATTTCTGGATACT 59.170 40.000 0.00 0.00 37.61 2.12
1470 1474 6.322201 CCCAATGTGCTTATTTCTGGATACTT 59.678 38.462 0.00 0.00 37.61 2.24
1471 1475 7.198390 CCAATGTGCTTATTTCTGGATACTTG 58.802 38.462 0.00 0.00 37.61 3.16
1472 1476 5.818136 TGTGCTTATTTCTGGATACTTGC 57.182 39.130 0.00 0.00 37.61 4.01
1473 1477 4.332543 TGTGCTTATTTCTGGATACTTGCG 59.667 41.667 0.00 0.00 37.61 4.85
1474 1478 3.312421 TGCTTATTTCTGGATACTTGCGC 59.688 43.478 0.00 0.00 37.61 6.09
1475 1479 3.312421 GCTTATTTCTGGATACTTGCGCA 59.688 43.478 5.66 5.66 37.61 6.09
1476 1480 4.553547 GCTTATTTCTGGATACTTGCGCAG 60.554 45.833 11.31 7.81 37.61 5.18
1489 1493 4.767255 CGCAGCCCACTCCCACTC 62.767 72.222 0.00 0.00 0.00 3.51
1490 1494 3.325753 GCAGCCCACTCCCACTCT 61.326 66.667 0.00 0.00 0.00 3.24
1491 1495 1.990060 GCAGCCCACTCCCACTCTA 60.990 63.158 0.00 0.00 0.00 2.43
1492 1496 1.901085 CAGCCCACTCCCACTCTAC 59.099 63.158 0.00 0.00 0.00 2.59
1493 1497 0.904865 CAGCCCACTCCCACTCTACA 60.905 60.000 0.00 0.00 0.00 2.74
1494 1498 0.616111 AGCCCACTCCCACTCTACAG 60.616 60.000 0.00 0.00 0.00 2.74
1495 1499 1.617947 GCCCACTCCCACTCTACAGG 61.618 65.000 0.00 0.00 0.00 4.00
1496 1500 0.252284 CCCACTCCCACTCTACAGGT 60.252 60.000 0.00 0.00 0.00 4.00
1497 1501 1.645710 CCACTCCCACTCTACAGGTT 58.354 55.000 0.00 0.00 0.00 3.50
1498 1502 1.978580 CCACTCCCACTCTACAGGTTT 59.021 52.381 0.00 0.00 0.00 3.27
1499 1503 2.372172 CCACTCCCACTCTACAGGTTTT 59.628 50.000 0.00 0.00 0.00 2.43
1500 1504 3.403038 CACTCCCACTCTACAGGTTTTG 58.597 50.000 0.00 0.00 0.00 2.44
1501 1505 2.372172 ACTCCCACTCTACAGGTTTTGG 59.628 50.000 0.00 0.00 0.00 3.28
1502 1506 1.702957 TCCCACTCTACAGGTTTTGGG 59.297 52.381 0.00 0.00 44.51 4.12
1503 1507 1.702957 CCCACTCTACAGGTTTTGGGA 59.297 52.381 0.00 0.00 45.81 4.37
1504 1508 2.290323 CCCACTCTACAGGTTTTGGGAG 60.290 54.545 0.00 0.00 45.81 4.30
1505 1509 2.637872 CCACTCTACAGGTTTTGGGAGA 59.362 50.000 0.00 0.00 35.85 3.71
1506 1510 3.072476 CCACTCTACAGGTTTTGGGAGAA 59.928 47.826 0.00 0.00 35.85 2.87
1507 1511 4.319177 CACTCTACAGGTTTTGGGAGAAG 58.681 47.826 0.00 0.00 35.85 2.85
1508 1512 4.040461 CACTCTACAGGTTTTGGGAGAAGA 59.960 45.833 0.00 0.00 35.85 2.87
1509 1513 4.284746 ACTCTACAGGTTTTGGGAGAAGAG 59.715 45.833 0.00 0.00 35.85 2.85
1510 1514 4.489737 TCTACAGGTTTTGGGAGAAGAGA 58.510 43.478 0.00 0.00 0.00 3.10
1511 1515 3.778954 ACAGGTTTTGGGAGAAGAGAG 57.221 47.619 0.00 0.00 0.00 3.20
1512 1516 3.318313 ACAGGTTTTGGGAGAAGAGAGA 58.682 45.455 0.00 0.00 0.00 3.10
1513 1517 3.716872 ACAGGTTTTGGGAGAAGAGAGAA 59.283 43.478 0.00 0.00 0.00 2.87
1514 1518 4.166144 ACAGGTTTTGGGAGAAGAGAGAAA 59.834 41.667 0.00 0.00 0.00 2.52
1515 1519 4.759183 CAGGTTTTGGGAGAAGAGAGAAAG 59.241 45.833 0.00 0.00 0.00 2.62
1516 1520 4.660771 AGGTTTTGGGAGAAGAGAGAAAGA 59.339 41.667 0.00 0.00 0.00 2.52
1517 1521 5.132816 AGGTTTTGGGAGAAGAGAGAAAGAA 59.867 40.000 0.00 0.00 0.00 2.52
1518 1522 5.828328 GGTTTTGGGAGAAGAGAGAAAGAAA 59.172 40.000 0.00 0.00 0.00 2.52
1519 1523 6.321435 GGTTTTGGGAGAAGAGAGAAAGAAAA 59.679 38.462 0.00 0.00 0.00 2.29
1520 1524 7.014711 GGTTTTGGGAGAAGAGAGAAAGAAAAT 59.985 37.037 0.00 0.00 0.00 1.82
1521 1525 7.516198 TTTGGGAGAAGAGAGAAAGAAAATG 57.484 36.000 0.00 0.00 0.00 2.32
1522 1526 6.192970 TGGGAGAAGAGAGAAAGAAAATGT 57.807 37.500 0.00 0.00 0.00 2.71
1523 1527 6.234177 TGGGAGAAGAGAGAAAGAAAATGTC 58.766 40.000 0.00 0.00 0.00 3.06
1524 1528 5.350091 GGGAGAAGAGAGAAAGAAAATGTCG 59.650 44.000 0.00 0.00 0.00 4.35
1525 1529 6.159988 GGAGAAGAGAGAAAGAAAATGTCGA 58.840 40.000 0.00 0.00 0.00 4.20
1526 1530 6.816140 GGAGAAGAGAGAAAGAAAATGTCGAT 59.184 38.462 0.00 0.00 0.00 3.59
1527 1531 7.201513 GGAGAAGAGAGAAAGAAAATGTCGATG 60.202 40.741 0.00 0.00 0.00 3.84
1528 1532 6.593382 AGAAGAGAGAAAGAAAATGTCGATGG 59.407 38.462 0.00 0.00 0.00 3.51
1529 1533 4.633565 AGAGAGAAAGAAAATGTCGATGGC 59.366 41.667 0.00 0.00 0.00 4.40
1530 1534 4.583871 AGAGAAAGAAAATGTCGATGGCT 58.416 39.130 0.00 0.00 0.00 4.75
1531 1535 4.394300 AGAGAAAGAAAATGTCGATGGCTG 59.606 41.667 0.00 0.00 0.00 4.85
1532 1536 2.927553 AAGAAAATGTCGATGGCTGC 57.072 45.000 0.00 0.00 0.00 5.25
1533 1537 1.098050 AGAAAATGTCGATGGCTGCC 58.902 50.000 12.87 12.87 0.00 4.85
1534 1538 0.810648 GAAAATGTCGATGGCTGCCA 59.189 50.000 25.65 25.65 38.19 4.92
1535 1539 0.813184 AAAATGTCGATGGCTGCCAG 59.187 50.000 27.20 14.42 36.75 4.85
1536 1540 1.660560 AAATGTCGATGGCTGCCAGC 61.661 55.000 26.21 26.21 41.46 4.85
1541 1545 3.344215 GATGGCTGCCAGCGATCG 61.344 66.667 27.20 11.69 44.33 3.69
1542 1546 3.797225 GATGGCTGCCAGCGATCGA 62.797 63.158 27.20 0.00 44.33 3.59
1543 1547 3.804153 ATGGCTGCCAGCGATCGAG 62.804 63.158 27.20 10.27 43.62 4.04
1553 1557 4.899239 CGATCGAGGCAGGCCACC 62.899 72.222 10.26 6.01 38.92 4.61
1554 1558 3.785859 GATCGAGGCAGGCCACCA 61.786 66.667 16.52 0.00 38.92 4.17
1555 1559 3.092511 ATCGAGGCAGGCCACCAT 61.093 61.111 16.52 0.00 38.92 3.55
1556 1560 2.615227 GATCGAGGCAGGCCACCATT 62.615 60.000 16.52 0.00 38.92 3.16
1557 1561 2.898920 ATCGAGGCAGGCCACCATTG 62.899 60.000 16.52 0.85 38.92 2.82
1558 1562 2.356278 GAGGCAGGCCACCATTGA 59.644 61.111 16.52 0.00 38.92 2.57
1559 1563 1.076485 GAGGCAGGCCACCATTGAT 60.076 57.895 16.52 0.00 38.92 2.57
1560 1564 1.380785 AGGCAGGCCACCATTGATG 60.381 57.895 16.52 0.00 38.92 3.07
1572 1576 2.581216 CATTGATGGAGATGGGGGAG 57.419 55.000 0.00 0.00 0.00 4.30
1573 1577 2.060275 CATTGATGGAGATGGGGGAGA 58.940 52.381 0.00 0.00 0.00 3.71
1574 1578 2.285275 TTGATGGAGATGGGGGAGAA 57.715 50.000 0.00 0.00 0.00 2.87
1575 1579 1.811778 TGATGGAGATGGGGGAGAAG 58.188 55.000 0.00 0.00 0.00 2.85
1576 1580 1.063183 GATGGAGATGGGGGAGAAGG 58.937 60.000 0.00 0.00 0.00 3.46
1577 1581 0.348370 ATGGAGATGGGGGAGAAGGT 59.652 55.000 0.00 0.00 0.00 3.50
1578 1582 0.621571 TGGAGATGGGGGAGAAGGTG 60.622 60.000 0.00 0.00 0.00 4.00
1579 1583 1.348775 GGAGATGGGGGAGAAGGTGG 61.349 65.000 0.00 0.00 0.00 4.61
1580 1584 0.621862 GAGATGGGGGAGAAGGTGGT 60.622 60.000 0.00 0.00 0.00 4.16
1581 1585 0.916358 AGATGGGGGAGAAGGTGGTG 60.916 60.000 0.00 0.00 0.00 4.17
1582 1586 1.926426 GATGGGGGAGAAGGTGGTGG 61.926 65.000 0.00 0.00 0.00 4.61
1583 1587 3.339093 GGGGGAGAAGGTGGTGGG 61.339 72.222 0.00 0.00 0.00 4.61
1584 1588 4.048470 GGGGAGAAGGTGGTGGGC 62.048 72.222 0.00 0.00 0.00 5.36
1585 1589 4.410400 GGGAGAAGGTGGTGGGCG 62.410 72.222 0.00 0.00 0.00 6.13
1586 1590 3.637273 GGAGAAGGTGGTGGGCGT 61.637 66.667 0.00 0.00 0.00 5.68
1587 1591 2.358737 GAGAAGGTGGTGGGCGTG 60.359 66.667 0.00 0.00 0.00 5.34
1588 1592 4.643387 AGAAGGTGGTGGGCGTGC 62.643 66.667 0.00 0.00 0.00 5.34
1643 1647 3.441163 CTGATGCCCAAATCAAATCACG 58.559 45.455 0.00 0.00 36.16 4.35
1686 1690 4.640771 AATTCACTCTGCTGACCCTTTA 57.359 40.909 0.00 0.00 0.00 1.85
1835 1839 0.037697 CTAGGCGCCACACTGTAACA 60.038 55.000 31.54 0.00 0.00 2.41
1931 1937 0.183971 CTTCCCCTCTCCGCTCTCTA 59.816 60.000 0.00 0.00 0.00 2.43
1983 2009 4.169452 CCCCCACATCCCTCTCAA 57.831 61.111 0.00 0.00 0.00 3.02
2044 2070 3.950395 TCCTACTAGGTAAACTCTTCCGC 59.050 47.826 1.83 0.00 36.53 5.54
2069 2095 4.923281 CCCTTTCTTTTGCTCCGTAAATTG 59.077 41.667 0.00 0.00 0.00 2.32
2074 2100 4.339814 TCTTTTGCTCCGTAAATTGGTTGT 59.660 37.500 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.848694 AGGAAGATGATCTTGGCTTGGA 59.151 45.455 13.18 0.00 36.73 3.53
34 35 2.025155 TGACGCCCAAAAAGCAAACTA 58.975 42.857 0.00 0.00 0.00 2.24
390 392 2.265367 TGCCCATTCCACTTGTAGAGA 58.735 47.619 0.00 0.00 0.00 3.10
405 407 3.185203 AAGCCAGACCCTTGCCCA 61.185 61.111 0.00 0.00 0.00 5.36
470 473 7.538303 ACAATCTTCATTTTGTTTGGACAAC 57.462 32.000 0.00 0.00 45.01 3.32
592 595 2.289945 GGAAGAGATGCTCCACACACTT 60.290 50.000 0.00 0.00 0.00 3.16
595 598 1.277273 CAGGAAGAGATGCTCCACACA 59.723 52.381 0.00 0.00 0.00 3.72
650 653 4.241681 GCTGACACTGAACTCCTCTTTAG 58.758 47.826 0.00 0.00 0.00 1.85
672 675 7.362056 CCATTAACCATGTCTTTTCTACACAGG 60.362 40.741 0.00 0.00 33.68 4.00
749 752 4.443457 GCCATAGAGTGATAGCCAAGACAA 60.443 45.833 0.00 0.00 0.00 3.18
788 791 9.844790 CGGTATCATTATTACGTACCTCATTTA 57.155 33.333 0.00 0.00 34.12 1.40
915 918 4.513318 GGAGTCCAGAAAACAGTTGAAGAG 59.487 45.833 3.60 0.00 0.00 2.85
928 931 2.203788 AGGTGGCGGAGTCCAGAA 60.204 61.111 10.49 0.00 34.66 3.02
930 933 4.767255 GCAGGTGGCGGAGTCCAG 62.767 72.222 10.49 3.25 34.66 3.86
997 1000 1.686455 CAAAGCCCATGCCCATCCA 60.686 57.895 0.00 0.00 38.69 3.41
1082 1085 4.704833 GCGCCTCAGCCAACTCCA 62.705 66.667 0.00 0.00 34.57 3.86
1140 1143 2.468831 GCCAAAGCAATTGACGAACAA 58.531 42.857 10.34 0.00 41.85 2.83
1174 1177 4.273480 AGACTTGATTTTGTTCACCACGAG 59.727 41.667 0.00 0.00 0.00 4.18
1175 1178 4.196193 AGACTTGATTTTGTTCACCACGA 58.804 39.130 0.00 0.00 0.00 4.35
1177 1180 5.440685 CGTAGACTTGATTTTGTTCACCAC 58.559 41.667 0.00 0.00 0.00 4.16
1321 1324 3.829026 TCAGAGTGCTCACAACTATGAGT 59.171 43.478 2.63 0.00 46.65 3.41
1325 1328 7.358770 AGATTATCAGAGTGCTCACAACTAT 57.641 36.000 2.63 0.00 0.00 2.12
1356 1360 0.251165 AATCCGGAACCACACCAAGG 60.251 55.000 9.01 0.00 0.00 3.61
1441 1445 4.706476 CCAGAAATAAGCACATTGGGAGAA 59.294 41.667 0.00 0.00 0.00 2.87
1442 1446 4.018506 TCCAGAAATAAGCACATTGGGAGA 60.019 41.667 0.00 0.00 0.00 3.71
1443 1447 4.272489 TCCAGAAATAAGCACATTGGGAG 58.728 43.478 0.00 0.00 0.00 4.30
1444 1448 4.314522 TCCAGAAATAAGCACATTGGGA 57.685 40.909 0.00 0.00 0.00 4.37
1445 1449 5.829924 AGTATCCAGAAATAAGCACATTGGG 59.170 40.000 0.00 0.00 0.00 4.12
1446 1450 6.949352 AGTATCCAGAAATAAGCACATTGG 57.051 37.500 0.00 0.00 0.00 3.16
1447 1451 6.694411 GCAAGTATCCAGAAATAAGCACATTG 59.306 38.462 0.00 0.00 0.00 2.82
1448 1452 6.458751 CGCAAGTATCCAGAAATAAGCACATT 60.459 38.462 0.00 0.00 0.00 2.71
1449 1453 5.008019 CGCAAGTATCCAGAAATAAGCACAT 59.992 40.000 0.00 0.00 0.00 3.21
1450 1454 4.332543 CGCAAGTATCCAGAAATAAGCACA 59.667 41.667 0.00 0.00 0.00 4.57
1451 1455 4.786609 GCGCAAGTATCCAGAAATAAGCAC 60.787 45.833 0.30 0.00 41.68 4.40
1452 1456 3.312421 GCGCAAGTATCCAGAAATAAGCA 59.688 43.478 0.30 0.00 41.68 3.91
1453 1457 3.312421 TGCGCAAGTATCCAGAAATAAGC 59.688 43.478 8.16 0.00 41.68 3.09
1454 1458 4.553547 GCTGCGCAAGTATCCAGAAATAAG 60.554 45.833 13.05 0.00 41.68 1.73
1455 1459 3.312421 GCTGCGCAAGTATCCAGAAATAA 59.688 43.478 13.05 0.00 41.68 1.40
1456 1460 2.872245 GCTGCGCAAGTATCCAGAAATA 59.128 45.455 13.05 0.00 41.68 1.40
1457 1461 1.672881 GCTGCGCAAGTATCCAGAAAT 59.327 47.619 13.05 0.00 41.68 2.17
1458 1462 1.086696 GCTGCGCAAGTATCCAGAAA 58.913 50.000 13.05 0.00 41.68 2.52
1459 1463 0.744414 GGCTGCGCAAGTATCCAGAA 60.744 55.000 13.05 0.00 38.19 3.02
1460 1464 1.153369 GGCTGCGCAAGTATCCAGA 60.153 57.895 13.05 0.00 38.19 3.86
1461 1465 2.182842 GGGCTGCGCAAGTATCCAG 61.183 63.158 13.05 0.00 40.22 3.86
1462 1466 2.124736 GGGCTGCGCAAGTATCCA 60.125 61.111 13.05 0.00 40.22 3.41
1463 1467 2.124736 TGGGCTGCGCAAGTATCC 60.125 61.111 17.53 9.26 37.52 2.59
1464 1468 1.432270 GAGTGGGCTGCGCAAGTATC 61.432 60.000 21.38 12.67 41.68 2.24
1465 1469 1.450312 GAGTGGGCTGCGCAAGTAT 60.450 57.895 21.38 7.74 41.68 2.12
1466 1470 2.047274 GAGTGGGCTGCGCAAGTA 60.047 61.111 21.38 0.00 41.68 2.24
1472 1476 4.767255 GAGTGGGAGTGGGCTGCG 62.767 72.222 0.00 0.00 33.52 5.18
1473 1477 1.990060 TAGAGTGGGAGTGGGCTGC 60.990 63.158 0.00 0.00 0.00 5.25
1474 1478 0.904865 TGTAGAGTGGGAGTGGGCTG 60.905 60.000 0.00 0.00 0.00 4.85
1475 1479 0.616111 CTGTAGAGTGGGAGTGGGCT 60.616 60.000 0.00 0.00 0.00 5.19
1476 1480 1.617947 CCTGTAGAGTGGGAGTGGGC 61.618 65.000 0.00 0.00 0.00 5.36
1477 1481 0.252284 ACCTGTAGAGTGGGAGTGGG 60.252 60.000 0.00 0.00 0.00 4.61
1478 1482 1.645710 AACCTGTAGAGTGGGAGTGG 58.354 55.000 0.00 0.00 0.00 4.00
1479 1483 3.403038 CAAAACCTGTAGAGTGGGAGTG 58.597 50.000 0.00 0.00 0.00 3.51
1480 1484 2.372172 CCAAAACCTGTAGAGTGGGAGT 59.628 50.000 0.00 0.00 0.00 3.85
1481 1485 3.059352 CCAAAACCTGTAGAGTGGGAG 57.941 52.381 0.00 0.00 0.00 4.30
1483 1487 1.702957 TCCCAAAACCTGTAGAGTGGG 59.297 52.381 6.90 6.90 46.01 4.61
1484 1488 2.637872 TCTCCCAAAACCTGTAGAGTGG 59.362 50.000 0.00 0.00 0.00 4.00
1485 1489 4.040461 TCTTCTCCCAAAACCTGTAGAGTG 59.960 45.833 0.00 0.00 0.00 3.51
1486 1490 4.232091 TCTTCTCCCAAAACCTGTAGAGT 58.768 43.478 0.00 0.00 0.00 3.24
1487 1491 4.528596 TCTCTTCTCCCAAAACCTGTAGAG 59.471 45.833 0.00 0.00 0.00 2.43
1488 1492 4.489737 TCTCTTCTCCCAAAACCTGTAGA 58.510 43.478 0.00 0.00 0.00 2.59
1489 1493 4.528596 TCTCTCTTCTCCCAAAACCTGTAG 59.471 45.833 0.00 0.00 0.00 2.74
1490 1494 4.489737 TCTCTCTTCTCCCAAAACCTGTA 58.510 43.478 0.00 0.00 0.00 2.74
1491 1495 3.318313 TCTCTCTTCTCCCAAAACCTGT 58.682 45.455 0.00 0.00 0.00 4.00
1492 1496 4.357918 TTCTCTCTTCTCCCAAAACCTG 57.642 45.455 0.00 0.00 0.00 4.00
1493 1497 4.660771 TCTTTCTCTCTTCTCCCAAAACCT 59.339 41.667 0.00 0.00 0.00 3.50
1494 1498 4.974399 TCTTTCTCTCTTCTCCCAAAACC 58.026 43.478 0.00 0.00 0.00 3.27
1495 1499 6.944234 TTTCTTTCTCTCTTCTCCCAAAAC 57.056 37.500 0.00 0.00 0.00 2.43
1496 1500 7.561356 ACATTTTCTTTCTCTCTTCTCCCAAAA 59.439 33.333 0.00 0.00 0.00 2.44
1497 1501 7.062957 ACATTTTCTTTCTCTCTTCTCCCAAA 58.937 34.615 0.00 0.00 0.00 3.28
1498 1502 6.605119 ACATTTTCTTTCTCTCTTCTCCCAA 58.395 36.000 0.00 0.00 0.00 4.12
1499 1503 6.192970 ACATTTTCTTTCTCTCTTCTCCCA 57.807 37.500 0.00 0.00 0.00 4.37
1500 1504 5.350091 CGACATTTTCTTTCTCTCTTCTCCC 59.650 44.000 0.00 0.00 0.00 4.30
1501 1505 6.159988 TCGACATTTTCTTTCTCTCTTCTCC 58.840 40.000 0.00 0.00 0.00 3.71
1502 1506 7.201513 CCATCGACATTTTCTTTCTCTCTTCTC 60.202 40.741 0.00 0.00 0.00 2.87
1503 1507 6.593382 CCATCGACATTTTCTTTCTCTCTTCT 59.407 38.462 0.00 0.00 0.00 2.85
1504 1508 6.674278 GCCATCGACATTTTCTTTCTCTCTTC 60.674 42.308 0.00 0.00 0.00 2.87
1505 1509 5.123027 GCCATCGACATTTTCTTTCTCTCTT 59.877 40.000 0.00 0.00 0.00 2.85
1506 1510 4.633565 GCCATCGACATTTTCTTTCTCTCT 59.366 41.667 0.00 0.00 0.00 3.10
1507 1511 4.633565 AGCCATCGACATTTTCTTTCTCTC 59.366 41.667 0.00 0.00 0.00 3.20
1508 1512 4.394300 CAGCCATCGACATTTTCTTTCTCT 59.606 41.667 0.00 0.00 0.00 3.10
1509 1513 4.656041 CAGCCATCGACATTTTCTTTCTC 58.344 43.478 0.00 0.00 0.00 2.87
1510 1514 3.119708 GCAGCCATCGACATTTTCTTTCT 60.120 43.478 0.00 0.00 0.00 2.52
1511 1515 3.174375 GCAGCCATCGACATTTTCTTTC 58.826 45.455 0.00 0.00 0.00 2.62
1512 1516 2.094545 GGCAGCCATCGACATTTTCTTT 60.095 45.455 6.55 0.00 0.00 2.52
1513 1517 1.474077 GGCAGCCATCGACATTTTCTT 59.526 47.619 6.55 0.00 0.00 2.52
1514 1518 1.098050 GGCAGCCATCGACATTTTCT 58.902 50.000 6.55 0.00 0.00 2.52
1515 1519 0.810648 TGGCAGCCATCGACATTTTC 59.189 50.000 11.22 0.00 0.00 2.29
1516 1520 0.813184 CTGGCAGCCATCGACATTTT 59.187 50.000 16.64 0.00 30.82 1.82
1517 1521 1.660560 GCTGGCAGCCATCGACATTT 61.661 55.000 28.87 0.00 34.48 2.32
1518 1522 2.117156 GCTGGCAGCCATCGACATT 61.117 57.895 28.87 0.00 34.48 2.71
1519 1523 2.515523 GCTGGCAGCCATCGACAT 60.516 61.111 28.87 0.00 34.48 3.06
1521 1525 4.819761 TCGCTGGCAGCCATCGAC 62.820 66.667 31.66 13.83 45.23 4.20
1523 1527 3.344215 GATCGCTGGCAGCCATCG 61.344 66.667 32.08 28.28 43.38 3.84
1524 1528 3.344215 CGATCGCTGGCAGCCATC 61.344 66.667 29.85 29.85 38.18 3.51
1525 1529 3.804153 CTCGATCGCTGGCAGCCAT 62.804 63.158 32.08 26.20 38.18 4.40
1526 1530 4.519437 CTCGATCGCTGGCAGCCA 62.519 66.667 32.08 22.26 38.18 4.75
1536 1540 4.899239 GGTGGCCTGCCTCGATCG 62.899 72.222 9.36 9.36 36.94 3.69
1537 1541 2.615227 AATGGTGGCCTGCCTCGATC 62.615 60.000 16.05 0.00 36.94 3.69
1538 1542 2.683465 AATGGTGGCCTGCCTCGAT 61.683 57.895 16.05 5.84 36.94 3.59
1539 1543 3.329889 AATGGTGGCCTGCCTCGA 61.330 61.111 16.05 3.46 36.94 4.04
1540 1544 2.898920 ATCAATGGTGGCCTGCCTCG 62.899 60.000 16.05 6.51 36.94 4.63
1541 1545 1.076485 ATCAATGGTGGCCTGCCTC 60.076 57.895 16.05 5.67 36.94 4.70
1542 1546 1.380785 CATCAATGGTGGCCTGCCT 60.381 57.895 16.05 1.95 36.94 4.75
1543 1547 2.428925 CCATCAATGGTGGCCTGCC 61.429 63.158 3.32 7.19 43.05 4.85
1544 1548 3.213264 CCATCAATGGTGGCCTGC 58.787 61.111 3.32 0.00 43.05 4.85
1553 1557 2.060275 TCTCCCCCATCTCCATCAATG 58.940 52.381 0.00 0.00 0.00 2.82
1554 1558 2.520188 TCTCCCCCATCTCCATCAAT 57.480 50.000 0.00 0.00 0.00 2.57
1555 1559 2.130193 CTTCTCCCCCATCTCCATCAA 58.870 52.381 0.00 0.00 0.00 2.57
1556 1560 1.696965 CCTTCTCCCCCATCTCCATCA 60.697 57.143 0.00 0.00 0.00 3.07
1557 1561 1.063183 CCTTCTCCCCCATCTCCATC 58.937 60.000 0.00 0.00 0.00 3.51
1558 1562 0.348370 ACCTTCTCCCCCATCTCCAT 59.652 55.000 0.00 0.00 0.00 3.41
1559 1563 0.621571 CACCTTCTCCCCCATCTCCA 60.622 60.000 0.00 0.00 0.00 3.86
1560 1564 1.348775 CCACCTTCTCCCCCATCTCC 61.349 65.000 0.00 0.00 0.00 3.71
1561 1565 0.621862 ACCACCTTCTCCCCCATCTC 60.622 60.000 0.00 0.00 0.00 2.75
1562 1566 0.916358 CACCACCTTCTCCCCCATCT 60.916 60.000 0.00 0.00 0.00 2.90
1563 1567 1.609783 CACCACCTTCTCCCCCATC 59.390 63.158 0.00 0.00 0.00 3.51
1564 1568 1.930656 CCACCACCTTCTCCCCCAT 60.931 63.158 0.00 0.00 0.00 4.00
1565 1569 2.531685 CCACCACCTTCTCCCCCA 60.532 66.667 0.00 0.00 0.00 4.96
1566 1570 3.339093 CCCACCACCTTCTCCCCC 61.339 72.222 0.00 0.00 0.00 5.40
1567 1571 4.048470 GCCCACCACCTTCTCCCC 62.048 72.222 0.00 0.00 0.00 4.81
1568 1572 4.410400 CGCCCACCACCTTCTCCC 62.410 72.222 0.00 0.00 0.00 4.30
1569 1573 3.637273 ACGCCCACCACCTTCTCC 61.637 66.667 0.00 0.00 0.00 3.71
1570 1574 2.358737 CACGCCCACCACCTTCTC 60.359 66.667 0.00 0.00 0.00 2.87
1571 1575 4.643387 GCACGCCCACCACCTTCT 62.643 66.667 0.00 0.00 0.00 2.85
1584 1588 3.792047 CTCATGCCACACCGCACG 61.792 66.667 0.00 0.00 42.70 5.34
1585 1589 3.434319 CCTCATGCCACACCGCAC 61.434 66.667 0.00 0.00 42.70 5.34
1588 1592 3.129502 CTGCCTCATGCCACACCG 61.130 66.667 0.00 0.00 40.16 4.94
1589 1593 0.895100 TTTCTGCCTCATGCCACACC 60.895 55.000 0.00 0.00 40.16 4.16
1590 1594 1.133790 GATTTCTGCCTCATGCCACAC 59.866 52.381 0.00 0.00 40.16 3.82
1591 1595 1.005097 AGATTTCTGCCTCATGCCACA 59.995 47.619 0.00 0.00 40.16 4.17
1592 1596 1.674962 GAGATTTCTGCCTCATGCCAC 59.325 52.381 0.00 0.00 40.16 5.01
1593 1597 1.282738 TGAGATTTCTGCCTCATGCCA 59.717 47.619 0.00 0.00 40.16 4.92
1594 1598 2.048444 TGAGATTTCTGCCTCATGCC 57.952 50.000 0.00 0.00 40.16 4.40
1611 1615 3.949586 TGGGCATCAGGTCAAATATGA 57.050 42.857 0.00 0.00 0.00 2.15
1643 1647 3.963383 TTTTCGAAAGCAGGTCAGTTC 57.037 42.857 10.98 0.00 0.00 3.01
1798 1802 2.032528 AGCTTAGGCGCTGCACAA 59.967 55.556 7.64 0.00 44.37 3.33
1835 1839 0.471617 CTAAGGGCTAGGCACTGCAT 59.528 55.000 19.14 0.00 43.87 3.96
1900 1905 0.178873 AGGGGAAGAACTGCCTGGTA 60.179 55.000 0.00 0.00 35.37 3.25
1931 1937 4.127040 CGCCGCTGCTCTCTGTCT 62.127 66.667 0.00 0.00 34.43 3.41
1983 2009 7.040617 CGAATCCATGGATCAAATCTTCAGATT 60.041 37.037 27.45 7.43 38.92 2.40
2044 2070 1.897560 ACGGAGCAAAAGAAAGGGAG 58.102 50.000 0.00 0.00 0.00 4.30
2069 2095 7.214467 TGGACAAATCTCTAAAATGACAACC 57.786 36.000 0.00 0.00 0.00 3.77



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

AutoCloner maintained by Alex Coulton.