Multiple sequence alignment - TraesCS7A01G406600

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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 TraesCS7A01G406600 chr7A 100.000 2327 0 0 1 2327 591996393 591994067 0.000000e+00 4298
1 TraesCS7A01G406600 chr2D 95.151 1423 59 2 1 1413 33936266 33937688 0.000000e+00 2237
2 TraesCS7A01G406600 chr2D 94.944 1424 59 4 1 1413 630272740 630274161 0.000000e+00 2218
3 TraesCS7A01G406600 chr2D 93.351 752 47 2 1579 2327 574793127 574792376 0.000000e+00 1109
4 TraesCS7A01G406600 chr5A 94.940 1423 60 3 1 1413 482026953 482025533 0.000000e+00 2218
5 TraesCS7A01G406600 chr1D 94.581 1421 64 3 2 1413 254419186 254420602 0.000000e+00 2185
6 TraesCS7A01G406600 chr1D 93.360 753 46 3 1579 2327 360904438 360905190 0.000000e+00 1110
7 TraesCS7A01G406600 chr3B 94.378 1423 64 6 1 1413 201558355 201556939 0.000000e+00 2170
8 TraesCS7A01G406600 chr5B 94.027 1423 72 5 1 1413 413609872 413611291 0.000000e+00 2145
9 TraesCS7A01G406600 chr5B 93.684 1425 74 4 1 1413 429039066 429040486 0.000000e+00 2119
10 TraesCS7A01G406600 chr5B 93.286 1415 86 6 1 1413 432879142 432880549 0.000000e+00 2078
11 TraesCS7A01G406600 chr5B 93.478 184 10 2 1408 1590 127593933 127593751 2.950000e-69 272
12 TraesCS7A01G406600 chr7D 94.002 817 36 4 608 1413 231529011 231529825 0.000000e+00 1225
13 TraesCS7A01G406600 chr7D 94.437 755 42 0 1 755 88619607 88620361 0.000000e+00 1162
14 TraesCS7A01G406600 chr7D 93.493 753 45 3 1579 2327 208401586 208400834 0.000000e+00 1116
15 TraesCS7A01G406600 chr7D 93.227 753 47 4 1579 2327 137937104 137936352 0.000000e+00 1105
16 TraesCS7A01G406600 chr7D 93.227 753 47 3 1579 2327 412951895 412951143 0.000000e+00 1105
17 TraesCS7A01G406600 chr4D 93.360 753 46 3 1579 2327 315063521 315064273 0.000000e+00 1110
18 TraesCS7A01G406600 chr4D 93.360 753 46 3 1579 2327 415010870 415011622 0.000000e+00 1110
19 TraesCS7A01G406600 chr4D 93.218 752 47 3 1580 2327 428734040 428734791 0.000000e+00 1103
20 TraesCS7A01G406600 chr5D 93.227 753 47 3 1579 2327 223919697 223920449 0.000000e+00 1105
21 TraesCS7A01G406600 chr6B 95.977 174 6 1 1406 1579 326490433 326490605 4.900000e-72 281
22 TraesCS7A01G406600 chr6B 95.954 173 6 1 1406 1578 369393398 369393569 1.760000e-71 279
23 TraesCS7A01G406600 chr3A 95.977 174 6 1 1406 1579 201100255 201100083 4.900000e-72 281
24 TraesCS7A01G406600 chr2B 95.455 176 7 1 1404 1579 350760943 350761117 1.760000e-71 279
25 TraesCS7A01G406600 chr2B 93.085 188 7 6 1391 1578 774525281 774525462 1.060000e-68 270
26 TraesCS7A01G406600 chr3D 93.956 182 9 2 1406 1587 246453847 246453668 8.190000e-70 274
27 TraesCS7A01G406600 chr3D 93.158 190 8 5 1391 1580 333320771 333320587 8.190000e-70 274
28 TraesCS7A01G406600 chr2A 93.085 188 8 5 1391 1578 356422439 356422621 1.060000e-68 270


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 TraesCS7A01G406600 chr7A 591994067 591996393 2326 True 4298 4298 100.000 1 2327 1 chr7A.!!$R1 2326
1 TraesCS7A01G406600 chr2D 33936266 33937688 1422 False 2237 2237 95.151 1 1413 1 chr2D.!!$F1 1412
2 TraesCS7A01G406600 chr2D 630272740 630274161 1421 False 2218 2218 94.944 1 1413 1 chr2D.!!$F2 1412
3 TraesCS7A01G406600 chr2D 574792376 574793127 751 True 1109 1109 93.351 1579 2327 1 chr2D.!!$R1 748
4 TraesCS7A01G406600 chr5A 482025533 482026953 1420 True 2218 2218 94.940 1 1413 1 chr5A.!!$R1 1412
5 TraesCS7A01G406600 chr1D 254419186 254420602 1416 False 2185 2185 94.581 2 1413 1 chr1D.!!$F1 1411
6 TraesCS7A01G406600 chr1D 360904438 360905190 752 False 1110 1110 93.360 1579 2327 1 chr1D.!!$F2 748
7 TraesCS7A01G406600 chr3B 201556939 201558355 1416 True 2170 2170 94.378 1 1413 1 chr3B.!!$R1 1412
8 TraesCS7A01G406600 chr5B 413609872 413611291 1419 False 2145 2145 94.027 1 1413 1 chr5B.!!$F1 1412
9 TraesCS7A01G406600 chr5B 429039066 429040486 1420 False 2119 2119 93.684 1 1413 1 chr5B.!!$F2 1412
10 TraesCS7A01G406600 chr5B 432879142 432880549 1407 False 2078 2078 93.286 1 1413 1 chr5B.!!$F3 1412
11 TraesCS7A01G406600 chr7D 231529011 231529825 814 False 1225 1225 94.002 608 1413 1 chr7D.!!$F2 805
12 TraesCS7A01G406600 chr7D 88619607 88620361 754 False 1162 1162 94.437 1 755 1 chr7D.!!$F1 754
13 TraesCS7A01G406600 chr7D 208400834 208401586 752 True 1116 1116 93.493 1579 2327 1 chr7D.!!$R2 748
14 TraesCS7A01G406600 chr7D 137936352 137937104 752 True 1105 1105 93.227 1579 2327 1 chr7D.!!$R1 748
15 TraesCS7A01G406600 chr7D 412951143 412951895 752 True 1105 1105 93.227 1579 2327 1 chr7D.!!$R3 748
16 TraesCS7A01G406600 chr4D 315063521 315064273 752 False 1110 1110 93.360 1579 2327 1 chr4D.!!$F1 748
17 TraesCS7A01G406600 chr4D 415010870 415011622 752 False 1110 1110 93.360 1579 2327 1 chr4D.!!$F2 748
18 TraesCS7A01G406600 chr4D 428734040 428734791 751 False 1103 1103 93.218 1580 2327 1 chr4D.!!$F3 747
19 TraesCS7A01G406600 chr5D 223919697 223920449 752 False 1105 1105 93.227 1579 2327 1 chr5D.!!$F1 748

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
267 269 0.394762 GATGTGAATCTGCCTGCCCA 60.395 55.0 0.0 0.0 0.0 5.36 F
818 830 0.817634 TGCCCGCAATGTATAGTGGC 60.818 55.0 0.0 0.0 34.1 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 1172 0.178990 GTGCTTCCCCATGGGTATCC 60.179 60.0 29.33 14.87 44.74 2.59 R
1853 1874 1.138047 CCATCGTAGCGTCGTTGTCC 61.138 60.0 11.41 0.00 0.00 4.02 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
108 110 4.398044 GGTCCAATGTCACATTCCGTAAAT 59.602 41.667 0.00 0.00 0.00 1.40
187 189 8.287904 TGTATTAGAAATGATACCCTGGGATT 57.712 34.615 22.23 5.57 0.00 3.01
202 204 3.364549 TGGGATTGATGTAAAGCCAAGG 58.635 45.455 0.00 0.00 37.34 3.61
237 239 2.673043 GCCGAGAACCGAAGATTGTGTA 60.673 50.000 0.00 0.00 41.76 2.90
267 269 0.394762 GATGTGAATCTGCCTGCCCA 60.395 55.000 0.00 0.00 0.00 5.36
335 338 5.928839 CACGTAGCATGGCTCTATCTTATTT 59.071 40.000 0.00 0.00 40.44 1.40
504 507 8.707839 CAATACTTGTTGTTTTGCCGATATTTT 58.292 29.630 0.00 0.00 32.58 1.82
554 557 6.761312 TCATAAGGGAAACAAAGTCGTTAGA 58.239 36.000 0.00 0.00 0.00 2.10
631 634 4.599041 TGTTATGATTTCCAACTGGAGGG 58.401 43.478 0.00 0.00 46.36 4.30
686 689 6.425210 TGGATAGATGTCTTCGATTTCCAT 57.575 37.500 0.00 0.00 0.00 3.41
715 718 3.808728 TGGGAATCGATGGACTTTCATC 58.191 45.455 0.00 0.00 39.93 2.92
773 785 1.164411 CAGCTTGGCCAATTACACGA 58.836 50.000 20.85 0.00 0.00 4.35
778 790 3.367630 GCTTGGCCAATTACACGAAATTG 59.632 43.478 20.85 3.19 43.45 2.32
781 793 3.570125 TGGCCAATTACACGAAATTGACA 59.430 39.130 0.61 14.42 45.61 3.58
802 814 8.169977 TGACAATTATTCTATTTCCTGATGCC 57.830 34.615 0.00 0.00 0.00 4.40
818 830 0.817634 TGCCCGCAATGTATAGTGGC 60.818 55.000 0.00 0.00 34.10 5.01
937 956 4.430441 GGGGGAGAGGTGTCTATATTCAT 58.570 47.826 0.00 0.00 30.97 2.57
1019 1039 4.289672 AGGTATGGGCTTATATGGTTCCAG 59.710 45.833 0.00 0.00 0.00 3.86
1037 1057 3.134458 CCAGCGAACCAGGATTAGATTC 58.866 50.000 0.00 0.00 0.00 2.52
1152 1172 1.067516 CCCCTACATACGTGGTTACCG 59.932 57.143 0.00 0.00 0.00 4.02
1200 1220 5.754406 TCGTACATGTATGATTTTAACGGGG 59.246 40.000 21.37 0.00 0.00 5.73
1321 1341 5.163814 GGAGCGATCCAAATAATCTATGCAC 60.164 44.000 16.44 0.00 0.00 4.57
1325 1345 6.371548 GCGATCCAAATAATCTATGCACCTTA 59.628 38.462 0.00 0.00 0.00 2.69
1421 1442 7.712204 TTATAGGAATTGGTTCAAAAGACCC 57.288 36.000 0.00 0.00 36.30 4.46
1422 1443 3.922375 AGGAATTGGTTCAAAAGACCCA 58.078 40.909 0.00 0.00 36.30 4.51
1423 1444 4.492646 AGGAATTGGTTCAAAAGACCCAT 58.507 39.130 0.00 0.00 36.30 4.00
1424 1445 5.650283 AGGAATTGGTTCAAAAGACCCATA 58.350 37.500 0.00 0.00 36.30 2.74
1425 1446 5.480422 AGGAATTGGTTCAAAAGACCCATAC 59.520 40.000 0.00 0.00 36.30 2.39
1426 1447 5.245075 GGAATTGGTTCAAAAGACCCATACA 59.755 40.000 0.00 0.00 36.30 2.29
1427 1448 5.722021 ATTGGTTCAAAAGACCCATACAC 57.278 39.130 0.00 0.00 36.30 2.90
1428 1449 3.492337 TGGTTCAAAAGACCCATACACC 58.508 45.455 0.00 0.00 36.30 4.16
1429 1450 3.139397 TGGTTCAAAAGACCCATACACCT 59.861 43.478 0.00 0.00 36.30 4.00
1430 1451 3.506067 GGTTCAAAAGACCCATACACCTG 59.494 47.826 0.00 0.00 0.00 4.00
1431 1452 2.790433 TCAAAAGACCCATACACCTGC 58.210 47.619 0.00 0.00 0.00 4.85
1432 1453 2.107378 TCAAAAGACCCATACACCTGCA 59.893 45.455 0.00 0.00 0.00 4.41
1433 1454 2.890311 CAAAAGACCCATACACCTGCAA 59.110 45.455 0.00 0.00 0.00 4.08
1434 1455 3.456380 AAAGACCCATACACCTGCAAT 57.544 42.857 0.00 0.00 0.00 3.56
1435 1456 3.456380 AAGACCCATACACCTGCAATT 57.544 42.857 0.00 0.00 0.00 2.32
1436 1457 4.584638 AAGACCCATACACCTGCAATTA 57.415 40.909 0.00 0.00 0.00 1.40
1437 1458 4.156455 AGACCCATACACCTGCAATTAG 57.844 45.455 0.00 0.00 0.00 1.73
1438 1459 3.780294 AGACCCATACACCTGCAATTAGA 59.220 43.478 0.00 0.00 0.00 2.10
1439 1460 3.877508 GACCCATACACCTGCAATTAGAC 59.122 47.826 0.00 0.00 0.00 2.59
1440 1461 3.265737 ACCCATACACCTGCAATTAGACA 59.734 43.478 0.00 0.00 0.00 3.41
1441 1462 4.079787 ACCCATACACCTGCAATTAGACAT 60.080 41.667 0.00 0.00 0.00 3.06
1442 1463 4.276678 CCCATACACCTGCAATTAGACATG 59.723 45.833 0.00 0.00 0.00 3.21
1443 1464 4.276678 CCATACACCTGCAATTAGACATGG 59.723 45.833 0.00 0.00 0.00 3.66
1444 1465 2.094675 ACACCTGCAATTAGACATGGC 58.905 47.619 0.00 0.00 0.00 4.40
1445 1466 2.093890 CACCTGCAATTAGACATGGCA 58.906 47.619 0.00 0.00 0.00 4.92
1446 1467 2.094675 ACCTGCAATTAGACATGGCAC 58.905 47.619 0.00 0.00 0.00 5.01
1472 1493 9.097257 CAAAAGTTTGTGATGTAATTTTGTCCT 57.903 29.630 0.00 0.00 33.61 3.85
1473 1494 8.647143 AAAGTTTGTGATGTAATTTTGTCCTG 57.353 30.769 0.00 0.00 0.00 3.86
1474 1495 6.748132 AGTTTGTGATGTAATTTTGTCCTGG 58.252 36.000 0.00 0.00 0.00 4.45
1475 1496 6.549364 AGTTTGTGATGTAATTTTGTCCTGGA 59.451 34.615 0.00 0.00 0.00 3.86
1476 1497 7.233348 AGTTTGTGATGTAATTTTGTCCTGGAT 59.767 33.333 0.00 0.00 0.00 3.41
1477 1498 6.513806 TGTGATGTAATTTTGTCCTGGATG 57.486 37.500 0.00 0.00 0.00 3.51
1478 1499 6.244654 TGTGATGTAATTTTGTCCTGGATGA 58.755 36.000 0.00 0.00 0.00 2.92
1479 1500 6.150976 TGTGATGTAATTTTGTCCTGGATGAC 59.849 38.462 0.00 0.00 35.77 3.06
1480 1501 6.150976 GTGATGTAATTTTGTCCTGGATGACA 59.849 38.462 0.00 0.00 43.26 3.58
1481 1502 6.891361 TGATGTAATTTTGTCCTGGATGACAT 59.109 34.615 0.00 0.00 44.27 3.06
1482 1503 8.052141 TGATGTAATTTTGTCCTGGATGACATA 58.948 33.333 0.00 0.00 44.27 2.29
1483 1504 8.821686 ATGTAATTTTGTCCTGGATGACATAA 57.178 30.769 0.00 0.00 44.27 1.90
1484 1505 8.642935 TGTAATTTTGTCCTGGATGACATAAA 57.357 30.769 0.00 0.00 44.27 1.40
1485 1506 9.253832 TGTAATTTTGTCCTGGATGACATAAAT 57.746 29.630 0.00 1.58 44.27 1.40
1518 1539 6.017400 CACAGTTTGCATTAGAAATCACCT 57.983 37.500 0.00 0.00 0.00 4.00
1519 1540 6.088824 CACAGTTTGCATTAGAAATCACCTC 58.911 40.000 0.00 0.00 0.00 3.85
1520 1541 5.769662 ACAGTTTGCATTAGAAATCACCTCA 59.230 36.000 0.00 0.00 0.00 3.86
1521 1542 6.088824 CAGTTTGCATTAGAAATCACCTCAC 58.911 40.000 0.00 0.00 0.00 3.51
1522 1543 5.769662 AGTTTGCATTAGAAATCACCTCACA 59.230 36.000 0.00 0.00 0.00 3.58
1523 1544 6.265196 AGTTTGCATTAGAAATCACCTCACAA 59.735 34.615 0.00 0.00 0.00 3.33
1524 1545 6.647334 TTGCATTAGAAATCACCTCACAAA 57.353 33.333 0.00 0.00 0.00 2.83
1525 1546 6.839124 TGCATTAGAAATCACCTCACAAAT 57.161 33.333 0.00 0.00 0.00 2.32
1526 1547 7.936496 TGCATTAGAAATCACCTCACAAATA 57.064 32.000 0.00 0.00 0.00 1.40
1527 1548 8.523915 TGCATTAGAAATCACCTCACAAATAT 57.476 30.769 0.00 0.00 0.00 1.28
1528 1549 9.625747 TGCATTAGAAATCACCTCACAAATATA 57.374 29.630 0.00 0.00 0.00 0.86
1529 1550 9.884465 GCATTAGAAATCACCTCACAAATATAC 57.116 33.333 0.00 0.00 0.00 1.47
1537 1558 7.728847 TCACCTCACAAATATACATGTATGC 57.271 36.000 25.48 0.00 0.00 3.14
1538 1559 7.278875 TCACCTCACAAATATACATGTATGCA 58.721 34.615 25.48 9.47 0.00 3.96
1539 1560 7.772757 TCACCTCACAAATATACATGTATGCAA 59.227 33.333 25.48 8.76 0.00 4.08
1540 1561 8.570488 CACCTCACAAATATACATGTATGCAAT 58.430 33.333 25.48 10.63 0.00 3.56
1541 1562 9.791801 ACCTCACAAATATACATGTATGCAATA 57.208 29.630 25.48 8.05 0.00 1.90
1552 1573 6.862209 ACATGTATGCAATATTTTTGGTCGT 58.138 32.000 0.00 0.00 0.00 4.34
1553 1574 7.990917 ACATGTATGCAATATTTTTGGTCGTA 58.009 30.769 0.00 0.00 0.00 3.43
1554 1575 8.629158 ACATGTATGCAATATTTTTGGTCGTAT 58.371 29.630 0.00 0.00 0.00 3.06
1555 1576 9.117145 CATGTATGCAATATTTTTGGTCGTATC 57.883 33.333 0.00 0.00 0.00 2.24
1556 1577 7.644490 TGTATGCAATATTTTTGGTCGTATCC 58.356 34.615 0.00 0.00 0.00 2.59
1557 1578 6.707440 ATGCAATATTTTTGGTCGTATCCA 57.293 33.333 0.00 0.00 35.49 3.41
1558 1579 6.516739 TGCAATATTTTTGGTCGTATCCAA 57.483 33.333 5.65 5.65 44.48 3.53
1559 1580 6.559810 TGCAATATTTTTGGTCGTATCCAAG 58.440 36.000 8.73 0.39 46.27 3.61
1560 1581 5.977129 GCAATATTTTTGGTCGTATCCAAGG 59.023 40.000 8.73 0.00 46.27 3.61
1561 1582 6.405397 GCAATATTTTTGGTCGTATCCAAGGT 60.405 38.462 8.73 4.13 46.27 3.50
1562 1583 7.201750 GCAATATTTTTGGTCGTATCCAAGGTA 60.202 37.037 8.73 5.57 46.27 3.08
1563 1584 8.342634 CAATATTTTTGGTCGTATCCAAGGTAG 58.657 37.037 8.73 0.00 46.27 3.18
1564 1585 4.895668 TTTTGGTCGTATCCAAGGTAGT 57.104 40.909 8.73 0.00 46.27 2.73
1565 1586 4.460948 TTTGGTCGTATCCAAGGTAGTC 57.539 45.455 8.73 0.00 46.27 2.59
1566 1587 3.090210 TGGTCGTATCCAAGGTAGTCA 57.910 47.619 0.00 0.00 34.24 3.41
1567 1588 3.638860 TGGTCGTATCCAAGGTAGTCAT 58.361 45.455 0.00 0.00 34.24 3.06
1568 1589 3.383505 TGGTCGTATCCAAGGTAGTCATG 59.616 47.826 0.00 0.00 34.24 3.07
1569 1590 3.383825 GGTCGTATCCAAGGTAGTCATGT 59.616 47.826 0.00 0.00 0.00 3.21
1570 1591 4.499357 GGTCGTATCCAAGGTAGTCATGTC 60.499 50.000 0.00 0.00 0.00 3.06
1571 1592 3.635373 TCGTATCCAAGGTAGTCATGTCC 59.365 47.826 0.00 0.00 0.00 4.02
1572 1593 3.637229 CGTATCCAAGGTAGTCATGTCCT 59.363 47.826 0.00 0.00 0.00 3.85
1573 1594 4.261656 CGTATCCAAGGTAGTCATGTCCTC 60.262 50.000 0.00 0.00 0.00 3.71
1574 1595 3.184382 TCCAAGGTAGTCATGTCCTCA 57.816 47.619 0.00 0.00 0.00 3.86
1575 1596 3.724478 TCCAAGGTAGTCATGTCCTCAT 58.276 45.455 0.00 0.00 34.21 2.90
1576 1597 3.706594 TCCAAGGTAGTCATGTCCTCATC 59.293 47.826 0.00 0.00 31.15 2.92
1577 1598 3.452264 CCAAGGTAGTCATGTCCTCATCA 59.548 47.826 0.00 0.00 31.15 3.07
1585 1606 4.288105 AGTCATGTCCTCATCAGGTTCTTT 59.712 41.667 0.00 0.00 41.28 2.52
1653 1674 5.049405 AGAGGACATCTAACTTGTTTTTGCG 60.049 40.000 0.00 0.00 36.10 4.85
1673 1694 2.485426 CGGGGCATGTTGTGATATGATC 59.515 50.000 0.00 0.00 0.00 2.92
1678 1699 4.023450 GGCATGTTGTGATATGATCTGGTG 60.023 45.833 0.00 0.00 0.00 4.17
1699 1720 8.893219 TGGTGAAGACATGATGAGATATAAAC 57.107 34.615 0.00 0.00 0.00 2.01
1774 1795 6.073222 AGCCTTCTAGTTGTCGTTTTATTGTG 60.073 38.462 0.00 0.00 0.00 3.33
1841 1862 5.272397 GGTAGTGATAGTCGTAGAAGCAAC 58.728 45.833 0.00 0.00 39.69 4.17
1853 1874 0.514691 GAAGCAACAGTTGGCGAGAG 59.485 55.000 15.28 0.00 34.54 3.20
1885 1906 3.430929 GCTACGATGGAGATCAAGGTGTT 60.431 47.826 0.00 0.00 0.00 3.32
1886 1907 3.703001 ACGATGGAGATCAAGGTGTTT 57.297 42.857 0.00 0.00 0.00 2.83
2029 2053 8.726870 TTATTTTCTTAGTATGGTGGTAGCAC 57.273 34.615 16.75 16.75 0.00 4.40
2089 2114 5.045942 TGTTCTTCCTGAGTATGCACCATTA 60.046 40.000 0.00 0.00 0.00 1.90
2126 2151 1.135402 CGAGACACCACGTGATGATCA 60.135 52.381 19.08 0.00 36.96 2.92
2134 2159 2.662006 ACGTGATGATCAGGTGTGAG 57.338 50.000 18.73 0.00 42.99 3.51
2157 2182 4.514781 AGCTCTACGTTCACATACAACA 57.485 40.909 0.00 0.00 0.00 3.33
2159 2184 4.217767 AGCTCTACGTTCACATACAACAGA 59.782 41.667 0.00 0.00 0.00 3.41
2201 2226 5.062308 CGTGCAGAATACTCAGGTTAAACTC 59.938 44.000 0.00 0.00 0.00 3.01
2238 2263 3.239449 TGTAGATATGGCCTCGGAACAT 58.761 45.455 3.32 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 88 5.560966 ATTTACGGAATGTGACATTGGAC 57.439 39.130 16.52 4.98 0.00 4.02
187 189 4.527816 AGCAATTTCCTTGGCTTTACATCA 59.472 37.500 0.00 0.00 35.25 3.07
237 239 5.181748 GCAGATTCACATCTCTTACAACCT 58.818 41.667 0.00 0.00 37.71 3.50
286 289 4.774726 TGTTTCAGGCCCTAAATAAATGCA 59.225 37.500 0.00 0.00 0.00 3.96
289 292 6.571537 CGTGTTGTTTCAGGCCCTAAATAAAT 60.572 38.462 0.00 0.00 0.00 1.40
363 366 6.218108 TCTTCGGTAAAGAGGAATTAGACC 57.782 41.667 0.00 0.00 39.12 3.85
368 371 4.906618 TGCTTCTTCGGTAAAGAGGAATT 58.093 39.130 1.57 0.00 44.69 2.17
605 608 6.434028 CCTCCAGTTGGAAATCATAACAGAAA 59.566 38.462 1.99 0.00 44.91 2.52
615 618 1.341089 GGGACCCTCCAGTTGGAAATC 60.341 57.143 2.09 0.68 44.91 2.17
658 661 8.713271 GGAAATCGAAGACATCTATCCATTTAC 58.287 37.037 0.00 0.00 42.51 2.01
686 689 2.777114 TCCATCGATTCCCAATCTCCAA 59.223 45.455 0.00 0.00 35.73 3.53
778 790 7.573843 CGGGCATCAGGAAATAGAATAATTGTC 60.574 40.741 0.00 0.00 0.00 3.18
781 793 5.183904 GCGGGCATCAGGAAATAGAATAATT 59.816 40.000 0.00 0.00 0.00 1.40
802 814 1.674359 TTGGCCACTATACATTGCGG 58.326 50.000 3.88 0.00 0.00 5.69
818 830 6.954944 TCGCGAAGAAAATAATCCTATTTGG 58.045 36.000 6.20 0.00 37.70 3.28
956 975 0.037590 AATGGAACCGCCTGCAGTAA 59.962 50.000 13.81 0.00 37.63 2.24
996 1016 4.247814 TGGAACCATATAAGCCCATACCT 58.752 43.478 0.00 0.00 0.00 3.08
1019 1039 2.135933 CCGAATCTAATCCTGGTTCGC 58.864 52.381 8.78 0.00 40.02 4.70
1094 1114 5.744171 TGACAGCATAAGCAATAAGGAAGA 58.256 37.500 0.00 0.00 45.49 2.87
1152 1172 0.178990 GTGCTTCCCCATGGGTATCC 60.179 60.000 29.33 14.87 44.74 2.59
1177 1197 5.754406 TCCCCGTTAAAATCATACATGTACG 59.246 40.000 7.96 6.37 0.00 3.67
1195 1215 6.578439 GCTCCCATCTTTAATAATATCCCCGT 60.578 42.308 0.00 0.00 0.00 5.28
1321 1341 5.054477 TCGTTGACCAAGAGAAGTTTAAGG 58.946 41.667 0.00 0.00 0.00 2.69
1325 1345 6.451064 AATTTCGTTGACCAAGAGAAGTTT 57.549 33.333 0.00 0.00 0.00 2.66
1364 1385 9.621239 AACCCATCTGATATAGAGAGGAATAAA 57.379 33.333 0.00 0.00 39.20 1.40
1413 1434 2.969821 TGCAGGTGTATGGGTCTTTT 57.030 45.000 0.00 0.00 0.00 2.27
1414 1435 2.969821 TTGCAGGTGTATGGGTCTTT 57.030 45.000 0.00 0.00 0.00 2.52
1415 1436 3.456380 AATTGCAGGTGTATGGGTCTT 57.544 42.857 0.00 0.00 0.00 3.01
1416 1437 3.780294 TCTAATTGCAGGTGTATGGGTCT 59.220 43.478 0.00 0.00 0.00 3.85
1417 1438 3.877508 GTCTAATTGCAGGTGTATGGGTC 59.122 47.826 0.00 0.00 0.00 4.46
1418 1439 3.265737 TGTCTAATTGCAGGTGTATGGGT 59.734 43.478 0.00 0.00 0.00 4.51
1419 1440 3.884895 TGTCTAATTGCAGGTGTATGGG 58.115 45.455 0.00 0.00 0.00 4.00
1420 1441 4.276678 CCATGTCTAATTGCAGGTGTATGG 59.723 45.833 0.00 0.00 0.00 2.74
1421 1442 4.261322 GCCATGTCTAATTGCAGGTGTATG 60.261 45.833 0.00 0.00 0.00 2.39
1422 1443 3.885297 GCCATGTCTAATTGCAGGTGTAT 59.115 43.478 0.00 0.00 0.00 2.29
1423 1444 3.278574 GCCATGTCTAATTGCAGGTGTA 58.721 45.455 0.00 0.00 0.00 2.90
1424 1445 2.094675 GCCATGTCTAATTGCAGGTGT 58.905 47.619 0.00 0.00 0.00 4.16
1425 1446 2.093890 TGCCATGTCTAATTGCAGGTG 58.906 47.619 0.00 0.00 0.00 4.00
1426 1447 2.094675 GTGCCATGTCTAATTGCAGGT 58.905 47.619 0.00 0.00 31.69 4.00
1427 1448 2.093890 TGTGCCATGTCTAATTGCAGG 58.906 47.619 0.00 0.00 31.69 4.85
1428 1449 3.853831 TTGTGCCATGTCTAATTGCAG 57.146 42.857 0.00 0.00 31.69 4.41
1429 1450 4.039004 ACTTTTGTGCCATGTCTAATTGCA 59.961 37.500 0.00 0.00 0.00 4.08
1430 1451 4.559153 ACTTTTGTGCCATGTCTAATTGC 58.441 39.130 0.00 0.00 0.00 3.56
1431 1452 6.879962 CAAACTTTTGTGCCATGTCTAATTG 58.120 36.000 0.00 0.00 33.59 2.32
1446 1467 9.097257 AGGACAAAATTACATCACAAACTTTTG 57.903 29.630 0.00 0.00 43.62 2.44
1447 1468 9.097257 CAGGACAAAATTACATCACAAACTTTT 57.903 29.630 0.00 0.00 0.00 2.27
1448 1469 7.710475 CCAGGACAAAATTACATCACAAACTTT 59.290 33.333 0.00 0.00 0.00 2.66
1449 1470 7.069331 TCCAGGACAAAATTACATCACAAACTT 59.931 33.333 0.00 0.00 0.00 2.66
1450 1471 6.549364 TCCAGGACAAAATTACATCACAAACT 59.451 34.615 0.00 0.00 0.00 2.66
1451 1472 6.744112 TCCAGGACAAAATTACATCACAAAC 58.256 36.000 0.00 0.00 0.00 2.93
1452 1473 6.968263 TCCAGGACAAAATTACATCACAAA 57.032 33.333 0.00 0.00 0.00 2.83
1453 1474 6.718912 TCATCCAGGACAAAATTACATCACAA 59.281 34.615 0.00 0.00 0.00 3.33
1454 1475 6.150976 GTCATCCAGGACAAAATTACATCACA 59.849 38.462 0.00 0.00 37.73 3.58
1455 1476 6.150976 TGTCATCCAGGACAAAATTACATCAC 59.849 38.462 0.00 0.00 44.34 3.06
1456 1477 6.244654 TGTCATCCAGGACAAAATTACATCA 58.755 36.000 0.00 0.00 44.34 3.07
1457 1478 6.757897 TGTCATCCAGGACAAAATTACATC 57.242 37.500 0.00 0.00 44.34 3.06
1495 1516 6.017400 AGGTGATTTCTAATGCAAACTGTG 57.983 37.500 0.00 0.00 0.00 3.66
1496 1517 5.769662 TGAGGTGATTTCTAATGCAAACTGT 59.230 36.000 0.00 0.00 0.00 3.55
1497 1518 6.088824 GTGAGGTGATTTCTAATGCAAACTG 58.911 40.000 0.00 0.00 0.00 3.16
1498 1519 5.769662 TGTGAGGTGATTTCTAATGCAAACT 59.230 36.000 0.00 0.00 0.00 2.66
1499 1520 6.012658 TGTGAGGTGATTTCTAATGCAAAC 57.987 37.500 0.00 0.00 0.00 2.93
1500 1521 6.647334 TTGTGAGGTGATTTCTAATGCAAA 57.353 33.333 0.00 0.00 0.00 3.68
1501 1522 6.647334 TTTGTGAGGTGATTTCTAATGCAA 57.353 33.333 0.00 0.00 0.00 4.08
1502 1523 6.839124 ATTTGTGAGGTGATTTCTAATGCA 57.161 33.333 0.00 0.00 0.00 3.96
1503 1524 9.884465 GTATATTTGTGAGGTGATTTCTAATGC 57.116 33.333 0.00 0.00 0.00 3.56
1511 1532 8.786898 GCATACATGTATATTTGTGAGGTGATT 58.213 33.333 17.86 0.00 0.00 2.57
1512 1533 7.938490 TGCATACATGTATATTTGTGAGGTGAT 59.062 33.333 17.86 0.00 0.00 3.06
1513 1534 7.278875 TGCATACATGTATATTTGTGAGGTGA 58.721 34.615 17.86 0.00 0.00 4.02
1514 1535 7.495135 TGCATACATGTATATTTGTGAGGTG 57.505 36.000 17.86 4.39 0.00 4.00
1515 1536 8.696043 ATTGCATACATGTATATTTGTGAGGT 57.304 30.769 17.86 0.00 0.00 3.85
1526 1547 8.629158 ACGACCAAAAATATTGCATACATGTAT 58.371 29.630 12.75 12.75 0.00 2.29
1527 1548 7.990917 ACGACCAAAAATATTGCATACATGTA 58.009 30.769 8.27 8.27 0.00 2.29
1528 1549 6.862209 ACGACCAAAAATATTGCATACATGT 58.138 32.000 2.69 2.69 0.00 3.21
1529 1550 9.117145 GATACGACCAAAAATATTGCATACATG 57.883 33.333 0.00 0.00 0.00 3.21
1530 1551 8.296713 GGATACGACCAAAAATATTGCATACAT 58.703 33.333 0.00 0.00 0.00 2.29
1531 1552 7.283354 TGGATACGACCAAAAATATTGCATACA 59.717 33.333 0.00 0.00 36.96 2.29
1532 1553 7.644490 TGGATACGACCAAAAATATTGCATAC 58.356 34.615 0.00 0.00 36.96 2.39
1533 1554 7.809546 TGGATACGACCAAAAATATTGCATA 57.190 32.000 0.00 0.00 36.96 3.14
1534 1555 6.707440 TGGATACGACCAAAAATATTGCAT 57.293 33.333 0.00 0.00 36.96 3.96
1535 1556 6.516739 TTGGATACGACCAAAAATATTGCA 57.483 33.333 9.96 0.00 45.36 4.08
1545 1566 3.433343 TGACTACCTTGGATACGACCAA 58.567 45.455 11.35 11.35 46.02 3.67
1546 1567 3.090210 TGACTACCTTGGATACGACCA 57.910 47.619 0.00 0.00 42.51 4.02
1547 1568 3.383825 ACATGACTACCTTGGATACGACC 59.616 47.826 0.00 0.00 42.51 4.79
1548 1569 4.499357 GGACATGACTACCTTGGATACGAC 60.499 50.000 0.00 0.00 42.51 4.34
1549 1570 3.635373 GGACATGACTACCTTGGATACGA 59.365 47.826 0.00 0.00 42.51 3.43
1550 1571 3.637229 AGGACATGACTACCTTGGATACG 59.363 47.826 0.00 0.00 42.51 3.06
1551 1572 4.649674 TGAGGACATGACTACCTTGGATAC 59.350 45.833 0.00 0.00 33.89 2.24
1552 1573 4.878968 TGAGGACATGACTACCTTGGATA 58.121 43.478 0.00 0.00 33.89 2.59
1553 1574 3.724478 TGAGGACATGACTACCTTGGAT 58.276 45.455 0.00 0.00 33.89 3.41
1554 1575 3.184382 TGAGGACATGACTACCTTGGA 57.816 47.619 0.00 0.00 33.89 3.53
1555 1576 3.452264 TGATGAGGACATGACTACCTTGG 59.548 47.826 0.00 0.00 36.82 3.61
1556 1577 4.442612 CCTGATGAGGACATGACTACCTTG 60.443 50.000 0.00 0.00 42.93 3.61
1557 1578 3.708631 CCTGATGAGGACATGACTACCTT 59.291 47.826 0.00 0.00 42.93 3.50
1558 1579 3.303938 CCTGATGAGGACATGACTACCT 58.696 50.000 0.00 2.34 42.93 3.08
1559 1580 3.034635 ACCTGATGAGGACATGACTACC 58.965 50.000 4.75 0.00 42.93 3.18
1560 1581 4.404073 AGAACCTGATGAGGACATGACTAC 59.596 45.833 4.75 0.00 42.93 2.73
1561 1582 4.614475 AGAACCTGATGAGGACATGACTA 58.386 43.478 4.75 0.00 42.93 2.59
1562 1583 3.448934 AGAACCTGATGAGGACATGACT 58.551 45.455 4.75 0.00 42.93 3.41
1563 1584 3.902881 AGAACCTGATGAGGACATGAC 57.097 47.619 4.75 0.00 42.93 3.06
1564 1585 4.533707 AGAAAGAACCTGATGAGGACATGA 59.466 41.667 4.75 0.00 42.93 3.07
1565 1586 4.841422 AGAAAGAACCTGATGAGGACATG 58.159 43.478 4.75 0.00 42.93 3.21
1566 1587 5.960811 TCTAGAAAGAACCTGATGAGGACAT 59.039 40.000 4.75 0.00 42.93 3.06
1567 1588 5.333581 TCTAGAAAGAACCTGATGAGGACA 58.666 41.667 4.75 0.00 42.93 4.02
1568 1589 5.923733 TCTAGAAAGAACCTGATGAGGAC 57.076 43.478 4.75 0.00 42.93 3.85
1569 1590 5.105146 GCTTCTAGAAAGAACCTGATGAGGA 60.105 44.000 4.75 0.00 43.31 3.71
1570 1591 5.115480 GCTTCTAGAAAGAACCTGATGAGG 58.885 45.833 6.63 0.00 46.21 3.86
1571 1592 5.115480 GGCTTCTAGAAAGAACCTGATGAG 58.885 45.833 6.63 0.00 36.80 2.90
1572 1593 4.080863 GGGCTTCTAGAAAGAACCTGATGA 60.081 45.833 6.63 0.00 36.80 2.92
1573 1594 4.195416 GGGCTTCTAGAAAGAACCTGATG 58.805 47.826 6.63 0.00 36.80 3.07
1574 1595 3.118592 CGGGCTTCTAGAAAGAACCTGAT 60.119 47.826 6.63 0.00 39.34 2.90
1575 1596 2.233922 CGGGCTTCTAGAAAGAACCTGA 59.766 50.000 6.63 0.00 39.34 3.86
1576 1597 2.028020 ACGGGCTTCTAGAAAGAACCTG 60.028 50.000 6.63 12.36 40.93 4.00
1577 1598 2.258109 ACGGGCTTCTAGAAAGAACCT 58.742 47.619 6.63 0.00 36.80 3.50
1585 1606 1.392710 GGCTGCTACGGGCTTCTAGA 61.393 60.000 0.00 0.00 42.39 2.43
1653 1674 3.504906 CAGATCATATCACAACATGCCCC 59.495 47.826 0.00 0.00 0.00 5.80
1673 1694 8.986847 GTTTATATCTCATCATGTCTTCACCAG 58.013 37.037 0.00 0.00 0.00 4.00
1755 1776 8.891928 CATTTCACACAATAAAACGACAACTAG 58.108 33.333 0.00 0.00 0.00 2.57
1774 1795 2.282701 ACATGGCGATTGCATTTCAC 57.717 45.000 7.38 0.00 45.35 3.18
1841 1862 1.284982 CGTTGTCCTCTCGCCAACTG 61.285 60.000 0.00 0.00 37.04 3.16
1853 1874 1.138047 CCATCGTAGCGTCGTTGTCC 61.138 60.000 11.41 0.00 0.00 4.02
1885 1906 1.271856 TCTCCATTGTCACCGGCTAA 58.728 50.000 0.00 0.00 0.00 3.09
1886 1907 1.412710 GATCTCCATTGTCACCGGCTA 59.587 52.381 0.00 0.00 0.00 3.93
2029 2053 4.963318 TTCAGTGAGGGCCATCTTATAG 57.037 45.455 19.75 4.39 0.00 1.31
2089 2114 4.959446 GGCACGACGAACTGTAGT 57.041 55.556 0.00 0.00 36.82 2.73
2126 2151 1.912417 ACGTAGAGCTTCTCACACCT 58.088 50.000 0.00 0.00 32.06 4.00
2134 2159 4.921515 TGTTGTATGTGAACGTAGAGCTTC 59.078 41.667 0.00 0.00 0.00 3.86
2157 2182 3.900446 GCAAAACTGGCTTGCATCT 57.100 47.368 10.08 0.00 46.78 2.90
2201 2226 2.742589 TCTACATATGCTAGGCTCGTCG 59.257 50.000 1.58 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.