Multiple sequence alignment - TraesCS1B01G104100

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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 TraesCS1B01G104100 chr1B 100.000 2291 0 0 1 2291 114679017 114676727 0.000000e+00 4231
1 TraesCS1B01G104100 chr1B 93.981 1379 74 2 1 1377 321687311 321688682 0.000000e+00 2078
2 TraesCS1B01G104100 chr1B 93.059 778 45 2 602 1377 539643143 539643913 0.000000e+00 1129
3 TraesCS1B01G104100 chr3D 94.376 1387 66 5 1 1385 433508738 433510114 0.000000e+00 2119
4 TraesCS1B01G104100 chr3D 85.477 1384 191 3 1 1381 598596188 598597564 0.000000e+00 1434
5 TraesCS1B01G104100 chr7B 94.062 1381 72 3 1 1379 580877353 580875981 0.000000e+00 2087
6 TraesCS1B01G104100 chr7B 89.613 491 42 6 1530 2018 92032783 92033266 1.160000e-172 616
7 TraesCS1B01G104100 chr6B 93.867 1386 74 4 1 1383 159146935 159148312 0.000000e+00 2078
8 TraesCS1B01G104100 chr6B 85.652 1380 187 4 1 1377 412284204 412282833 0.000000e+00 1441
9 TraesCS1B01G104100 chr4A 89.716 1371 130 4 9 1377 67263543 67262182 0.000000e+00 1740
10 TraesCS1B01G104100 chr4A 91.945 658 44 2 729 1384 68129612 68130262 0.000000e+00 913
11 TraesCS1B01G104100 chrUn 92.252 1110 76 4 1 1107 42178997 42177895 0.000000e+00 1565
12 TraesCS1B01G104100 chr2A 88.828 1280 134 2 83 1360 554506905 554508177 0.000000e+00 1563
13 TraesCS1B01G104100 chr2A 89.203 1204 115 7 183 1380 702954008 702955202 0.000000e+00 1489
14 TraesCS1B01G104100 chr4B 90.665 1082 68 10 298 1377 407744133 407745183 0.000000e+00 1408
15 TraesCS1B01G104100 chr5A 91.811 867 60 4 514 1377 572032242 572031384 0.000000e+00 1197
16 TraesCS1B01G104100 chr1D 87.294 787 72 11 1533 2291 464942948 464942162 0.000000e+00 874
17 TraesCS1B01G104100 chr2D 87.261 785 74 5 1533 2291 166198881 166198097 0.000000e+00 872
18 TraesCS1B01G104100 chr2B 87.049 610 55 9 1536 2121 584821399 584822008 0.000000e+00 667
19 TraesCS1B01G104100 chr4D 82.880 736 88 21 1533 2235 221342388 221341658 5.370000e-176 627
20 TraesCS1B01G104100 chr4D 82.745 736 90 20 1533 2235 221364987 221364256 2.500000e-174 621
21 TraesCS1B01G104100 chr4D 82.201 736 84 22 1533 2235 221348953 221348232 7.050000e-165 590
22 TraesCS1B01G104100 chr4D 84.906 159 22 2 1580 1737 245080335 245080178 2.360000e-35 159
23 TraesCS1B01G104100 chr3A 84.277 159 23 2 1580 1737 41266677 41266834 1.100000e-33 154


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 TraesCS1B01G104100 chr1B 114676727 114679017 2290 True 4231 4231 100.000 1 2291 1 chr1B.!!$R1 2290
1 TraesCS1B01G104100 chr1B 321687311 321688682 1371 False 2078 2078 93.981 1 1377 1 chr1B.!!$F1 1376
2 TraesCS1B01G104100 chr1B 539643143 539643913 770 False 1129 1129 93.059 602 1377 1 chr1B.!!$F2 775
3 TraesCS1B01G104100 chr3D 433508738 433510114 1376 False 2119 2119 94.376 1 1385 1 chr3D.!!$F1 1384
4 TraesCS1B01G104100 chr3D 598596188 598597564 1376 False 1434 1434 85.477 1 1381 1 chr3D.!!$F2 1380
5 TraesCS1B01G104100 chr7B 580875981 580877353 1372 True 2087 2087 94.062 1 1379 1 chr7B.!!$R1 1378
6 TraesCS1B01G104100 chr6B 159146935 159148312 1377 False 2078 2078 93.867 1 1383 1 chr6B.!!$F1 1382
7 TraesCS1B01G104100 chr6B 412282833 412284204 1371 True 1441 1441 85.652 1 1377 1 chr6B.!!$R1 1376
8 TraesCS1B01G104100 chr4A 67262182 67263543 1361 True 1740 1740 89.716 9 1377 1 chr4A.!!$R1 1368
9 TraesCS1B01G104100 chr4A 68129612 68130262 650 False 913 913 91.945 729 1384 1 chr4A.!!$F1 655
10 TraesCS1B01G104100 chrUn 42177895 42178997 1102 True 1565 1565 92.252 1 1107 1 chrUn.!!$R1 1106
11 TraesCS1B01G104100 chr2A 554506905 554508177 1272 False 1563 1563 88.828 83 1360 1 chr2A.!!$F1 1277
12 TraesCS1B01G104100 chr2A 702954008 702955202 1194 False 1489 1489 89.203 183 1380 1 chr2A.!!$F2 1197
13 TraesCS1B01G104100 chr4B 407744133 407745183 1050 False 1408 1408 90.665 298 1377 1 chr4B.!!$F1 1079
14 TraesCS1B01G104100 chr5A 572031384 572032242 858 True 1197 1197 91.811 514 1377 1 chr5A.!!$R1 863
15 TraesCS1B01G104100 chr1D 464942162 464942948 786 True 874 874 87.294 1533 2291 1 chr1D.!!$R1 758
16 TraesCS1B01G104100 chr2D 166198097 166198881 784 True 872 872 87.261 1533 2291 1 chr2D.!!$R1 758
17 TraesCS1B01G104100 chr2B 584821399 584822008 609 False 667 667 87.049 1536 2121 1 chr2B.!!$F1 585
18 TraesCS1B01G104100 chr4D 221341658 221342388 730 True 627 627 82.880 1533 2235 1 chr4D.!!$R1 702
19 TraesCS1B01G104100 chr4D 221364256 221364987 731 True 621 621 82.745 1533 2235 1 chr4D.!!$R3 702
20 TraesCS1B01G104100 chr4D 221348232 221348953 721 True 590 590 82.201 1533 2235 1 chr4D.!!$R2 702

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
779 810 0.451783 CGCAGTTCTTTGGCCATACC 59.548 55.0 6.09 0.0 39.84 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2142 2.156917 CACTGATTGCTTGCTCCTTGA 58.843 47.619 0.0 0.0 0.0 3.02 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
167 171 5.706833 TGTCTACTACATGACGGTGTTAGAA 59.293 40.000 0.00 0.00 36.10 2.10
180 184 2.934553 GTGTTAGAATTACCGGTGGAGC 59.065 50.000 19.93 4.14 0.00 4.70
327 333 7.508977 TGGGAATCCTAAATCTTGACAAGTTTT 59.491 33.333 21.80 21.80 35.32 2.43
340 346 1.885887 CAAGTTTTCCATCGCCCTTCA 59.114 47.619 0.00 0.00 0.00 3.02
375 381 3.691342 CCGAGTGGCTCAACCCGA 61.691 66.667 0.00 0.00 37.83 5.14
548 555 8.573035 GCCCCTAAAATATATGAATTGTCGAAA 58.427 33.333 0.00 0.00 0.00 3.46
600 631 1.165907 TGGCAACTTCTGGACTTGCG 61.166 55.000 0.00 0.00 41.06 4.85
743 774 4.110036 CATTGATGGACACTACTCGACA 57.890 45.455 0.00 0.00 0.00 4.35
779 810 0.451783 CGCAGTTCTTTGGCCATACC 59.548 55.000 6.09 0.00 39.84 2.73
789 820 1.144057 GGCCATACCGACACTGAGG 59.856 63.158 0.00 0.00 0.00 3.86
834 865 0.530288 GGCGCCTCCTAAATGCAAAA 59.470 50.000 22.15 0.00 0.00 2.44
835 866 1.136891 GGCGCCTCCTAAATGCAAAAT 59.863 47.619 22.15 0.00 0.00 1.82
836 867 2.195922 GCGCCTCCTAAATGCAAAATG 58.804 47.619 0.00 0.00 0.00 2.32
837 868 2.195922 CGCCTCCTAAATGCAAAATGC 58.804 47.619 0.00 0.00 45.29 3.56
864 895 3.896888 TCTTCACTTGGTTGGCAATCAAT 59.103 39.130 24.91 13.08 37.73 2.57
873 904 8.004215 ACTTGGTTGGCAATCAATAATAGGATA 58.996 33.333 24.91 0.29 37.73 2.59
975 1007 2.091885 GGCCCACCTTCTATTCCAATGA 60.092 50.000 0.00 0.00 0.00 2.57
996 1028 9.591792 CAATGAAGATACACTATGAGAGTTTGA 57.408 33.333 0.00 0.00 35.64 2.69
1021 1053 4.209538 CATGATCAAAGATTGGCTGGGTA 58.790 43.478 0.00 0.00 0.00 3.69
1108 1140 2.673368 GCTACCAAGAAGACACAATCGG 59.327 50.000 0.00 0.00 0.00 4.18
1189 1221 7.602644 GGAATGCATGGATCTTTCGTAATACTA 59.397 37.037 0.00 0.00 0.00 1.82
1233 1265 3.384168 TGCTAGGATTAAAGAGGAGGCA 58.616 45.455 0.00 0.00 0.00 4.75
1303 1335 3.365264 GCGAGAGTGATTGTTGCAATTCA 60.365 43.478 0.59 3.95 29.89 2.57
1368 1403 0.161446 GCAAATCTTTTGCCGCGTTG 59.839 50.000 12.74 0.08 39.38 4.10
1394 1429 5.548181 AAAAATATACCCGGAGAGAGACC 57.452 43.478 0.73 0.00 0.00 3.85
1395 1430 3.897657 AATATACCCGGAGAGAGACCA 57.102 47.619 0.73 0.00 0.00 4.02
1396 1431 4.405756 AATATACCCGGAGAGAGACCAT 57.594 45.455 0.73 0.00 0.00 3.55
1397 1432 2.777459 ATACCCGGAGAGAGACCATT 57.223 50.000 0.73 0.00 0.00 3.16
1398 1433 3.897657 ATACCCGGAGAGAGACCATTA 57.102 47.619 0.73 0.00 0.00 1.90
1399 1434 2.074729 ACCCGGAGAGAGACCATTAG 57.925 55.000 0.73 0.00 0.00 1.73
1400 1435 0.676736 CCCGGAGAGAGACCATTAGC 59.323 60.000 0.73 0.00 0.00 3.09
1401 1436 0.676736 CCGGAGAGAGACCATTAGCC 59.323 60.000 0.00 0.00 0.00 3.93
1402 1437 1.403814 CGGAGAGAGACCATTAGCCA 58.596 55.000 0.00 0.00 0.00 4.75
1403 1438 1.067821 CGGAGAGAGACCATTAGCCAC 59.932 57.143 0.00 0.00 0.00 5.01
1404 1439 2.111384 GGAGAGAGACCATTAGCCACA 58.889 52.381 0.00 0.00 0.00 4.17
1405 1440 2.703007 GGAGAGAGACCATTAGCCACAT 59.297 50.000 0.00 0.00 0.00 3.21
1406 1441 3.898123 GGAGAGAGACCATTAGCCACATA 59.102 47.826 0.00 0.00 0.00 2.29
1407 1442 4.530161 GGAGAGAGACCATTAGCCACATAT 59.470 45.833 0.00 0.00 0.00 1.78
1408 1443 5.012561 GGAGAGAGACCATTAGCCACATATT 59.987 44.000 0.00 0.00 0.00 1.28
1409 1444 6.211584 GGAGAGAGACCATTAGCCACATATTA 59.788 42.308 0.00 0.00 0.00 0.98
1410 1445 7.256332 GGAGAGAGACCATTAGCCACATATTAA 60.256 40.741 0.00 0.00 0.00 1.40
1411 1446 8.212259 AGAGAGACCATTAGCCACATATTAAT 57.788 34.615 0.00 0.00 0.00 1.40
1412 1447 9.326489 AGAGAGACCATTAGCCACATATTAATA 57.674 33.333 0.00 0.00 0.00 0.98
1413 1448 9.372369 GAGAGACCATTAGCCACATATTAATAC 57.628 37.037 0.00 0.00 0.00 1.89
1414 1449 8.880244 AGAGACCATTAGCCACATATTAATACA 58.120 33.333 0.00 0.00 0.00 2.29
1415 1450 9.502091 GAGACCATTAGCCACATATTAATACAA 57.498 33.333 0.00 0.00 0.00 2.41
1422 1457 9.964303 TTAGCCACATATTAATACAATTTGCAG 57.036 29.630 0.00 0.00 0.00 4.41
1423 1458 8.236585 AGCCACATATTAATACAATTTGCAGA 57.763 30.769 0.00 0.00 0.00 4.26
1424 1459 8.137437 AGCCACATATTAATACAATTTGCAGAC 58.863 33.333 0.00 0.00 0.00 3.51
1425 1460 8.137437 GCCACATATTAATACAATTTGCAGACT 58.863 33.333 0.00 0.00 0.00 3.24
1426 1461 9.669353 CCACATATTAATACAATTTGCAGACTC 57.331 33.333 0.00 0.00 0.00 3.36
1433 1468 7.878477 AATACAATTTGCAGACTCAAACATG 57.122 32.000 0.00 0.00 38.58 3.21
1434 1469 5.266733 ACAATTTGCAGACTCAAACATGT 57.733 34.783 0.00 0.00 38.58 3.21
1435 1470 5.663456 ACAATTTGCAGACTCAAACATGTT 58.337 33.333 4.92 4.92 38.58 2.71
1436 1471 5.521010 ACAATTTGCAGACTCAAACATGTTG 59.479 36.000 12.82 6.76 38.58 3.33
1437 1472 4.717233 TTTGCAGACTCAAACATGTTGT 57.283 36.364 12.82 5.75 31.64 3.32
1438 1473 3.969117 TGCAGACTCAAACATGTTGTC 57.031 42.857 12.82 14.81 0.00 3.18
1439 1474 3.544684 TGCAGACTCAAACATGTTGTCT 58.455 40.909 19.20 19.20 38.36 3.41
1441 1476 3.881795 CAGACTCAAACATGTTGTCTGC 58.118 45.455 29.54 15.05 44.90 4.26
1442 1477 3.313249 CAGACTCAAACATGTTGTCTGCA 59.687 43.478 29.54 10.60 44.90 4.41
1443 1478 3.313526 AGACTCAAACATGTTGTCTGCAC 59.686 43.478 22.44 8.91 36.74 4.57
1444 1479 3.016031 ACTCAAACATGTTGTCTGCACA 58.984 40.909 12.82 0.00 0.00 4.57
1445 1480 3.443329 ACTCAAACATGTTGTCTGCACAA 59.557 39.130 12.82 0.00 40.40 3.33
1446 1481 4.031418 TCAAACATGTTGTCTGCACAAG 57.969 40.909 12.82 0.00 43.42 3.16
1447 1482 3.443329 TCAAACATGTTGTCTGCACAAGT 59.557 39.130 12.82 0.00 43.42 3.16
1448 1483 4.637977 TCAAACATGTTGTCTGCACAAGTA 59.362 37.500 12.82 0.00 43.42 2.24
1449 1484 4.552166 AACATGTTGTCTGCACAAGTAC 57.448 40.909 11.07 0.00 43.42 2.73
1450 1485 2.878406 ACATGTTGTCTGCACAAGTACC 59.122 45.455 0.00 0.00 43.42 3.34
1451 1486 1.961793 TGTTGTCTGCACAAGTACCC 58.038 50.000 0.00 0.00 43.42 3.69
1452 1487 1.210722 TGTTGTCTGCACAAGTACCCA 59.789 47.619 0.00 0.00 43.42 4.51
1453 1488 2.294074 GTTGTCTGCACAAGTACCCAA 58.706 47.619 0.00 0.00 43.42 4.12
1454 1489 2.254546 TGTCTGCACAAGTACCCAAG 57.745 50.000 0.00 0.00 0.00 3.61
1455 1490 0.875059 GTCTGCACAAGTACCCAAGC 59.125 55.000 0.00 0.00 0.00 4.01
1456 1491 0.250727 TCTGCACAAGTACCCAAGCC 60.251 55.000 0.00 0.00 0.00 4.35
1457 1492 1.228429 TGCACAAGTACCCAAGCCC 60.228 57.895 0.00 0.00 0.00 5.19
1458 1493 1.074951 GCACAAGTACCCAAGCCCT 59.925 57.895 0.00 0.00 0.00 5.19
1459 1494 0.539669 GCACAAGTACCCAAGCCCTT 60.540 55.000 0.00 0.00 0.00 3.95
1460 1495 1.247567 CACAAGTACCCAAGCCCTTG 58.752 55.000 1.05 1.05 40.05 3.61
1461 1496 0.539669 ACAAGTACCCAAGCCCTTGC 60.540 55.000 2.51 0.00 38.24 4.01
1462 1497 0.539438 CAAGTACCCAAGCCCTTGCA 60.539 55.000 2.51 0.00 41.13 4.08
1463 1498 0.409484 AAGTACCCAAGCCCTTGCAT 59.591 50.000 2.51 0.00 41.13 3.96
1464 1499 0.034089 AGTACCCAAGCCCTTGCATC 60.034 55.000 2.51 0.00 41.13 3.91
1465 1500 0.323360 GTACCCAAGCCCTTGCATCA 60.323 55.000 2.51 0.00 41.13 3.07
1466 1501 0.323360 TACCCAAGCCCTTGCATCAC 60.323 55.000 2.51 0.00 41.13 3.06
1467 1502 1.607178 CCCAAGCCCTTGCATCACA 60.607 57.895 2.51 0.00 41.13 3.58
1468 1503 0.974010 CCCAAGCCCTTGCATCACAT 60.974 55.000 2.51 0.00 41.13 3.21
1469 1504 1.685803 CCCAAGCCCTTGCATCACATA 60.686 52.381 2.51 0.00 41.13 2.29
1470 1505 1.679680 CCAAGCCCTTGCATCACATAG 59.320 52.381 2.51 0.00 41.13 2.23
1471 1506 2.372264 CAAGCCCTTGCATCACATAGT 58.628 47.619 0.00 0.00 41.13 2.12
1472 1507 3.544684 CAAGCCCTTGCATCACATAGTA 58.455 45.455 0.00 0.00 41.13 1.82
1473 1508 4.139786 CAAGCCCTTGCATCACATAGTAT 58.860 43.478 0.00 0.00 41.13 2.12
1474 1509 4.013267 AGCCCTTGCATCACATAGTATC 57.987 45.455 0.00 0.00 41.13 2.24
1475 1510 3.392285 AGCCCTTGCATCACATAGTATCA 59.608 43.478 0.00 0.00 41.13 2.15
1476 1511 4.042560 AGCCCTTGCATCACATAGTATCAT 59.957 41.667 0.00 0.00 41.13 2.45
1477 1512 5.249163 AGCCCTTGCATCACATAGTATCATA 59.751 40.000 0.00 0.00 41.13 2.15
1478 1513 6.069789 AGCCCTTGCATCACATAGTATCATAT 60.070 38.462 0.00 0.00 41.13 1.78
1479 1514 7.126268 AGCCCTTGCATCACATAGTATCATATA 59.874 37.037 0.00 0.00 41.13 0.86
1480 1515 7.225538 GCCCTTGCATCACATAGTATCATATAC 59.774 40.741 0.00 0.00 37.47 1.47
1481 1516 7.436376 CCCTTGCATCACATAGTATCATATACG 59.564 40.741 0.00 0.00 0.00 3.06
1482 1517 8.190784 CCTTGCATCACATAGTATCATATACGA 58.809 37.037 0.00 0.00 0.00 3.43
1483 1518 9.741647 CTTGCATCACATAGTATCATATACGAT 57.258 33.333 0.00 0.00 0.00 3.73
1499 1534 9.232473 TCATATACGATTTACAGCATAGAGAGT 57.768 33.333 0.00 0.00 0.00 3.24
1503 1538 7.511959 ACGATTTACAGCATAGAGAGTATCA 57.488 36.000 0.00 0.00 37.82 2.15
1504 1539 7.941919 ACGATTTACAGCATAGAGAGTATCAA 58.058 34.615 0.00 0.00 37.82 2.57
1505 1540 8.580720 ACGATTTACAGCATAGAGAGTATCAAT 58.419 33.333 0.00 0.00 37.82 2.57
1510 1545 7.789202 ACAGCATAGAGAGTATCAATATGGT 57.211 36.000 0.00 0.00 42.96 3.55
1511 1546 8.885693 ACAGCATAGAGAGTATCAATATGGTA 57.114 34.615 0.17 0.00 41.44 3.25
1512 1547 9.486123 ACAGCATAGAGAGTATCAATATGGTAT 57.514 33.333 0.17 0.00 41.44 2.73
1594 1629 6.249035 TGAACTTTAATGTTCTAAAGCCGG 57.751 37.500 25.78 0.00 44.63 6.13
1603 1638 7.745620 AATGTTCTAAAGCCGGGAATATAAG 57.254 36.000 2.18 0.00 0.00 1.73
1609 1644 6.958192 TCTAAAGCCGGGAATATAAGGTATCT 59.042 38.462 2.18 0.00 0.00 1.98
1647 1683 6.896021 AATGATGGCATAGAGAGAAAATGG 57.104 37.500 0.00 0.00 33.44 3.16
1844 1902 8.030692 TCAAATAATGAAAAGGAGATGCACTTG 58.969 33.333 0.00 0.00 34.30 3.16
1856 1914 4.543689 AGATGCACTTGATCCAAATCCAT 58.456 39.130 0.00 0.00 0.00 3.41
1905 1963 4.798574 AGAGCCTTAAATTCGCAAACTTG 58.201 39.130 0.00 0.00 0.00 3.16
1911 1969 7.870445 AGCCTTAAATTCGCAAACTTGAAATAA 59.130 29.630 0.00 0.00 0.00 1.40
2000 2059 5.756347 TCGCTAACACAAAGTCAATTAGTGT 59.244 36.000 0.00 0.00 44.53 3.55
2044 2103 9.193806 ACTAGAATTCATACAAGCCAATTTCAT 57.806 29.630 8.44 0.00 0.00 2.57
2046 2105 8.070034 AGAATTCATACAAGCCAATTTCATGA 57.930 30.769 8.44 0.00 0.00 3.07
2049 2108 9.675464 AATTCATACAAGCCAATTTCATGATTT 57.325 25.926 0.00 0.00 0.00 2.17
2112 2176 1.985473 TCAGTGCAGAACAAAGGCAT 58.015 45.000 0.00 0.00 40.05 4.40
2145 2210 0.106519 AAGGAGCAAGCAACTGGTGT 60.107 50.000 0.00 0.00 0.00 4.16
2153 2218 3.315191 GCAAGCAACTGGTGTAGAAAAGA 59.685 43.478 0.00 0.00 0.00 2.52
2200 2272 9.593134 AAACAACAAGCAATATGTAGTTGAAAA 57.407 25.926 9.73 0.00 38.80 2.29
2245 2317 7.765695 AGTTGAATCATTCTCTAAAAAGGCA 57.234 32.000 0.00 0.00 0.00 4.75
2254 2326 8.859090 TCATTCTCTAAAAAGGCAAAGAAATGA 58.141 29.630 0.00 0.00 31.17 2.57
2279 2351 7.730364 AACTTTTGGACACAGTGAACTATAG 57.270 36.000 7.81 0.00 0.00 1.31
2283 2355 3.190874 GGACACAGTGAACTATAGCTGC 58.809 50.000 7.81 0.00 32.65 5.25
2285 2357 2.567169 ACACAGTGAACTATAGCTGCCA 59.433 45.455 7.81 0.00 32.65 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 171 1.568504 TCTTGAGCTCCACCGGTAAT 58.431 50.000 6.87 0.00 0.00 1.89
180 184 3.129871 GGGCATCGATCTTCTTCTTGAG 58.870 50.000 0.00 0.00 0.00 3.02
252 258 5.539955 ACACTTGTTCCCAATTTATCTTGCT 59.460 36.000 0.00 0.00 0.00 3.91
327 333 1.748329 CGGAGATGAAGGGCGATGGA 61.748 60.000 0.00 0.00 0.00 3.41
340 346 2.520536 GCCCATAGCCACCGGAGAT 61.521 63.158 9.46 0.00 34.35 2.75
369 375 1.606313 CCCATGGCTTGTTCGGGTT 60.606 57.895 6.09 0.00 31.80 4.11
406 412 9.138062 CAAAAATATTTCGGTCATTGTCATCAA 57.862 29.630 0.10 0.00 37.98 2.57
548 555 6.927381 CCATTCAAACTGAGCAATTCTTCTTT 59.073 34.615 0.00 0.00 0.00 2.52
600 631 0.108138 CCGTGAAGGATGTCCACCTC 60.108 60.000 1.30 0.00 45.00 3.85
675 706 0.320374 GTGTCCATGTCGAGGTGGAA 59.680 55.000 17.67 8.02 45.50 3.53
779 810 1.092348 TCGATACCACCTCAGTGTCG 58.908 55.000 4.01 4.01 42.88 4.35
838 869 9.258336 ATTGATTGCCAACCAAGTGAAGAACTT 62.258 37.037 0.00 0.00 42.96 2.66
839 870 2.435372 TGCCAACCAAGTGAAGAACT 57.565 45.000 0.00 0.00 42.60 3.01
840 871 3.068024 TGATTGCCAACCAAGTGAAGAAC 59.932 43.478 0.00 0.00 36.76 3.01
847 878 6.194235 TCCTATTATTGATTGCCAACCAAGT 58.806 36.000 0.00 0.00 37.63 3.16
864 895 5.833667 CCTATCCGCTGTCCATATCCTATTA 59.166 44.000 0.00 0.00 0.00 0.98
873 904 0.394565 GAAGCCTATCCGCTGTCCAT 59.605 55.000 0.00 0.00 39.64 3.41
975 1007 6.037098 GCGTCAAACTCTCATAGTGTATCTT 58.963 40.000 0.00 0.00 38.88 2.40
996 1028 2.098607 CAGCCAATCTTTGATCATGCGT 59.901 45.455 0.00 0.00 0.00 5.24
1021 1053 3.649502 TCACTAGGATGCACATCATGGAT 59.350 43.478 14.34 0.00 43.10 3.41
1189 1221 0.836400 ATGACTCCAACCGGGACAGT 60.836 55.000 6.32 1.21 42.15 3.55
1384 1419 2.111384 TGTGGCTAATGGTCTCTCTCC 58.889 52.381 0.00 0.00 0.00 3.71
1385 1420 5.736951 ATATGTGGCTAATGGTCTCTCTC 57.263 43.478 0.00 0.00 0.00 3.20
1386 1421 7.618019 TTAATATGTGGCTAATGGTCTCTCT 57.382 36.000 0.00 0.00 0.00 3.10
1387 1422 9.372369 GTATTAATATGTGGCTAATGGTCTCTC 57.628 37.037 0.00 0.00 0.00 3.20
1388 1423 8.880244 TGTATTAATATGTGGCTAATGGTCTCT 58.120 33.333 0.00 0.00 0.00 3.10
1389 1424 9.502091 TTGTATTAATATGTGGCTAATGGTCTC 57.498 33.333 0.00 0.00 0.00 3.36
1396 1431 9.964303 CTGCAAATTGTATTAATATGTGGCTAA 57.036 29.630 0.00 0.00 0.00 3.09
1397 1432 9.348476 TCTGCAAATTGTATTAATATGTGGCTA 57.652 29.630 0.00 0.00 0.00 3.93
1398 1433 8.137437 GTCTGCAAATTGTATTAATATGTGGCT 58.863 33.333 0.00 0.00 0.00 4.75
1399 1434 8.137437 AGTCTGCAAATTGTATTAATATGTGGC 58.863 33.333 0.00 0.20 0.00 5.01
1400 1435 9.669353 GAGTCTGCAAATTGTATTAATATGTGG 57.331 33.333 0.00 0.00 0.00 4.17
1407 1442 9.409312 CATGTTTGAGTCTGCAAATTGTATTAA 57.591 29.630 0.00 0.00 39.65 1.40
1408 1443 8.575589 ACATGTTTGAGTCTGCAAATTGTATTA 58.424 29.630 0.00 0.00 39.65 0.98
1409 1444 7.436118 ACATGTTTGAGTCTGCAAATTGTATT 58.564 30.769 0.00 0.00 39.65 1.89
1410 1445 6.985117 ACATGTTTGAGTCTGCAAATTGTAT 58.015 32.000 0.00 0.00 39.65 2.29
1411 1446 6.389830 ACATGTTTGAGTCTGCAAATTGTA 57.610 33.333 0.00 0.00 39.65 2.41
1412 1447 5.266733 ACATGTTTGAGTCTGCAAATTGT 57.733 34.783 0.00 0.00 39.65 2.71
1413 1448 5.521010 ACAACATGTTTGAGTCTGCAAATTG 59.479 36.000 8.77 0.00 39.65 2.32
1414 1449 5.663456 ACAACATGTTTGAGTCTGCAAATT 58.337 33.333 8.77 0.00 39.65 1.82
1415 1450 5.068198 AGACAACATGTTTGAGTCTGCAAAT 59.932 36.000 22.44 4.73 39.65 2.32
1416 1451 4.398988 AGACAACATGTTTGAGTCTGCAAA 59.601 37.500 22.44 0.00 38.96 3.68
1417 1452 3.947196 AGACAACATGTTTGAGTCTGCAA 59.053 39.130 22.44 0.00 38.96 4.08
1418 1453 3.313249 CAGACAACATGTTTGAGTCTGCA 59.687 43.478 29.54 0.00 44.30 4.41
1419 1454 3.881795 CAGACAACATGTTTGAGTCTGC 58.118 45.455 29.54 9.41 44.30 4.26
1421 1456 3.313526 GTGCAGACAACATGTTTGAGTCT 59.686 43.478 19.20 19.20 40.09 3.24
1422 1457 3.065233 TGTGCAGACAACATGTTTGAGTC 59.935 43.478 8.77 13.34 34.75 3.36
1423 1458 3.016031 TGTGCAGACAACATGTTTGAGT 58.984 40.909 8.77 3.83 34.75 3.41
1424 1459 3.696281 TGTGCAGACAACATGTTTGAG 57.304 42.857 8.77 0.07 34.75 3.02
1425 1460 3.443329 ACTTGTGCAGACAACATGTTTGA 59.557 39.130 8.77 0.00 37.15 2.69
1426 1461 3.772932 ACTTGTGCAGACAACATGTTTG 58.227 40.909 8.77 6.36 37.15 2.93
1427 1462 4.202010 GGTACTTGTGCAGACAACATGTTT 60.202 41.667 8.77 0.41 37.15 2.83
1428 1463 3.315191 GGTACTTGTGCAGACAACATGTT 59.685 43.478 4.92 4.92 37.15 2.71
1429 1464 2.878406 GGTACTTGTGCAGACAACATGT 59.122 45.455 0.00 0.00 37.15 3.21
1430 1465 2.226437 GGGTACTTGTGCAGACAACATG 59.774 50.000 0.00 0.00 37.15 3.21
1431 1466 2.158682 TGGGTACTTGTGCAGACAACAT 60.159 45.455 0.00 0.00 37.15 2.71
1432 1467 1.210722 TGGGTACTTGTGCAGACAACA 59.789 47.619 0.00 0.00 37.15 3.33
1433 1468 1.961793 TGGGTACTTGTGCAGACAAC 58.038 50.000 0.00 0.00 37.15 3.32
1434 1469 2.571212 CTTGGGTACTTGTGCAGACAA 58.429 47.619 0.00 0.00 39.88 3.18
1435 1470 1.813862 GCTTGGGTACTTGTGCAGACA 60.814 52.381 0.00 0.00 0.00 3.41
1436 1471 0.875059 GCTTGGGTACTTGTGCAGAC 59.125 55.000 0.00 0.00 0.00 3.51
1437 1472 0.250727 GGCTTGGGTACTTGTGCAGA 60.251 55.000 0.00 0.00 0.00 4.26
1438 1473 1.244019 GGGCTTGGGTACTTGTGCAG 61.244 60.000 0.00 0.00 0.00 4.41
1439 1474 1.228429 GGGCTTGGGTACTTGTGCA 60.228 57.895 0.00 0.00 0.00 4.57
1440 1475 0.539669 AAGGGCTTGGGTACTTGTGC 60.540 55.000 0.00 0.00 0.00 4.57
1441 1476 1.247567 CAAGGGCTTGGGTACTTGTG 58.752 55.000 0.00 0.00 36.47 3.33
1442 1477 0.539669 GCAAGGGCTTGGGTACTTGT 60.540 55.000 0.00 0.00 41.65 3.16
1443 1478 0.539438 TGCAAGGGCTTGGGTACTTG 60.539 55.000 0.00 0.00 42.31 3.16
1444 1479 0.409484 ATGCAAGGGCTTGGGTACTT 59.591 50.000 0.00 0.00 40.74 2.24
1445 1480 0.034089 GATGCAAGGGCTTGGGTACT 60.034 55.000 0.00 0.00 40.74 2.73
1446 1481 0.323360 TGATGCAAGGGCTTGGGTAC 60.323 55.000 0.00 0.00 40.74 3.34
1447 1482 0.323360 GTGATGCAAGGGCTTGGGTA 60.323 55.000 0.00 0.00 40.74 3.69
1448 1483 1.607467 GTGATGCAAGGGCTTGGGT 60.607 57.895 0.00 0.00 40.74 4.51
1449 1484 0.974010 ATGTGATGCAAGGGCTTGGG 60.974 55.000 0.00 0.00 40.74 4.12
1450 1485 1.679680 CTATGTGATGCAAGGGCTTGG 59.320 52.381 0.00 0.00 40.74 3.61
1451 1486 2.372264 ACTATGTGATGCAAGGGCTTG 58.628 47.619 0.00 0.00 43.14 4.01
1452 1487 2.814805 ACTATGTGATGCAAGGGCTT 57.185 45.000 0.00 0.00 41.91 4.35
1453 1488 3.392285 TGATACTATGTGATGCAAGGGCT 59.608 43.478 0.00 0.00 41.91 5.19
1454 1489 3.743521 TGATACTATGTGATGCAAGGGC 58.256 45.455 0.00 0.00 41.68 5.19
1455 1490 7.436376 CGTATATGATACTATGTGATGCAAGGG 59.564 40.741 0.00 0.00 0.00 3.95
1456 1491 8.190784 TCGTATATGATACTATGTGATGCAAGG 58.809 37.037 0.00 0.00 0.00 3.61
1457 1492 9.741647 ATCGTATATGATACTATGTGATGCAAG 57.258 33.333 5.60 0.00 0.00 4.01
1473 1508 9.232473 ACTCTCTATGCTGTAAATCGTATATGA 57.768 33.333 0.00 0.00 0.00 2.15
1477 1512 9.232473 TGATACTCTCTATGCTGTAAATCGTAT 57.768 33.333 0.00 0.00 0.00 3.06
1478 1513 8.617290 TGATACTCTCTATGCTGTAAATCGTA 57.383 34.615 0.00 0.00 0.00 3.43
1479 1514 7.511959 TGATACTCTCTATGCTGTAAATCGT 57.488 36.000 0.00 0.00 0.00 3.73
1480 1515 8.978564 ATTGATACTCTCTATGCTGTAAATCG 57.021 34.615 0.00 0.00 0.00 3.34
1484 1519 9.314133 ACCATATTGATACTCTCTATGCTGTAA 57.686 33.333 0.00 0.00 0.00 2.41
1485 1520 8.885693 ACCATATTGATACTCTCTATGCTGTA 57.114 34.615 0.00 0.00 0.00 2.74
1486 1521 7.789202 ACCATATTGATACTCTCTATGCTGT 57.211 36.000 0.00 0.00 0.00 4.40
1625 1661 6.002704 GTCCATTTTCTCTCTATGCCATCAT 58.997 40.000 0.00 0.00 36.73 2.45
1631 1667 5.505324 GCACATGTCCATTTTCTCTCTATGC 60.505 44.000 0.00 0.00 0.00 3.14
1632 1668 5.277202 CGCACATGTCCATTTTCTCTCTATG 60.277 44.000 0.00 0.00 0.00 2.23
1636 1672 3.002791 TCGCACATGTCCATTTTCTCTC 58.997 45.455 0.00 0.00 0.00 3.20
1647 1683 2.363788 TCAGTAACCTCGCACATGTC 57.636 50.000 0.00 0.00 0.00 3.06
1684 1720 9.787532 CTCAACCCATACTTTTGTGTAAATATG 57.212 33.333 0.00 0.00 0.00 1.78
1691 1727 6.777580 AGATTTCTCAACCCATACTTTTGTGT 59.222 34.615 0.00 0.00 0.00 3.72
1696 1732 7.039714 GGTTTCAGATTTCTCAACCCATACTTT 60.040 37.037 6.84 0.00 33.29 2.66
1705 1741 4.516698 TGCTCAGGTTTCAGATTTCTCAAC 59.483 41.667 0.00 0.00 0.00 3.18
1761 1797 7.760794 TGCTAAGACTTGCCATAAATTCAAATG 59.239 33.333 0.00 0.00 0.00 2.32
1863 1921 6.377146 GGCTCTACCATCATACAAAGGAAAAA 59.623 38.462 0.00 0.00 38.86 1.94
1867 1925 4.298626 AGGCTCTACCATCATACAAAGGA 58.701 43.478 0.00 0.00 43.14 3.36
1905 1963 9.943163 GCTAATTGTTTCATCCTCTCTTATTTC 57.057 33.333 0.00 0.00 0.00 2.17
1911 1969 5.189180 GGTGCTAATTGTTTCATCCTCTCT 58.811 41.667 0.00 0.00 0.00 3.10
1967 2026 4.336993 ACTTTGTGTTAGCGATTGGTTTCA 59.663 37.500 0.00 0.00 0.00 2.69
1976 2035 5.756347 ACACTAATTGACTTTGTGTTAGCGA 59.244 36.000 0.00 0.00 46.94 4.93
1977 2036 5.985781 ACACTAATTGACTTTGTGTTAGCG 58.014 37.500 0.00 0.00 46.94 4.26
2014 2073 9.851686 AATTGGCTTGTATGAATTCTAGTATCA 57.148 29.630 7.05 0.00 0.00 2.15
2018 2077 8.579850 TGAAATTGGCTTGTATGAATTCTAGT 57.420 30.769 7.05 0.00 0.00 2.57
2025 2084 9.806203 CTAAATCATGAAATTGGCTTGTATGAA 57.194 29.630 0.00 0.00 0.00 2.57
2049 2108 9.656040 TTTGTGTGTAGTGTTTCTTTTCTACTA 57.344 29.630 0.00 0.00 35.31 1.82
2070 2129 3.719924 TGCTTGCTCCTTGATTTTTGTG 58.280 40.909 0.00 0.00 0.00 3.33
2078 2142 2.156917 CACTGATTGCTTGCTCCTTGA 58.843 47.619 0.00 0.00 0.00 3.02
2104 2168 6.091169 CCTTGCACTAATTGTTAATGCCTTTG 59.909 38.462 1.38 0.00 35.37 2.77
2109 2173 4.800471 GCTCCTTGCACTAATTGTTAATGC 59.200 41.667 0.00 0.00 42.31 3.56
2153 2218 7.659186 TGTTTGGTGTTTAGTTTGTAGTGTTT 58.341 30.769 0.00 0.00 0.00 2.83
2222 2294 8.816640 TTTGCCTTTTTAGAGAATGATTCAAC 57.183 30.769 8.03 1.43 0.00 3.18
2245 2317 7.331687 CACTGTGTCCAAAAGTTTCATTTCTTT 59.668 33.333 0.00 0.00 35.73 2.52
2254 2326 7.255139 GCTATAGTTCACTGTGTCCAAAAGTTT 60.255 37.037 7.79 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.