Multiple sequence alignment - TraesCS7B01G414500

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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 TraesCS7B01G414500 chr7B 100.000 2279 0 0 1 2279 682374009 682371731 0.000000e+00 4209
1 TraesCS7B01G414500 chr7B 91.831 355 28 1 1574 1927 602550341 602549987 5.660000e-136 494
2 TraesCS7B01G414500 chr7B 90.323 93 9 0 1293 1385 725172324 725172232 3.070000e-24 122
3 TraesCS7B01G414500 chr7D 92.679 1366 89 4 1 1363 625615508 625616865 0.000000e+00 1958
4 TraesCS7B01G414500 chr7D 77.183 1271 228 38 6 1265 1999830 1998611 0.000000e+00 684
5 TraesCS7B01G414500 chr7A 95.435 701 30 2 1576 2275 25339910 25340609 0.000000e+00 1116
6 TraesCS7B01G414500 chr7A 77.734 1271 216 45 9 1259 63060263 63059040 0.000000e+00 717
7 TraesCS7B01G414500 chr7A 77.424 1258 232 33 15 1262 1690970 1692185 0.000000e+00 702
8 TraesCS7B01G414500 chr4D 92.888 703 48 2 1574 2275 459225918 459225217 0.000000e+00 1020
9 TraesCS7B01G414500 chr4A 78.100 1274 216 38 9 1265 675526192 675524965 0.000000e+00 749
10 TraesCS7B01G414500 chr4A 77.672 1263 229 33 15 1265 742586365 742585144 0.000000e+00 721
11 TraesCS7B01G414500 chr2A 92.113 355 27 1 1574 1927 744291502 744291148 1.220000e-137 499
12 TraesCS7B01G414500 chrUn 92.434 304 22 1 1574 1876 480914865 480915168 1.250000e-117 433
13 TraesCS7B01G414500 chr3A 80.631 222 37 5 1027 1245 102623744 102623526 1.400000e-37 167
14 TraesCS7B01G414500 chr3D 80.000 220 42 2 1027 1245 86341732 86341514 6.520000e-36 161
15 TraesCS7B01G414500 chr3B 79.091 220 44 2 1027 1245 136449184 136448966 1.410000e-32 150


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 TraesCS7B01G414500 chr7B 682371731 682374009 2278 True 4209 4209 100.000 1 2279 1 chr7B.!!$R2 2278
1 TraesCS7B01G414500 chr7D 625615508 625616865 1357 False 1958 1958 92.679 1 1363 1 chr7D.!!$F1 1362
2 TraesCS7B01G414500 chr7D 1998611 1999830 1219 True 684 684 77.183 6 1265 1 chr7D.!!$R1 1259
3 TraesCS7B01G414500 chr7A 25339910 25340609 699 False 1116 1116 95.435 1576 2275 1 chr7A.!!$F2 699
4 TraesCS7B01G414500 chr7A 63059040 63060263 1223 True 717 717 77.734 9 1259 1 chr7A.!!$R1 1250
5 TraesCS7B01G414500 chr7A 1690970 1692185 1215 False 702 702 77.424 15 1262 1 chr7A.!!$F1 1247
6 TraesCS7B01G414500 chr4D 459225217 459225918 701 True 1020 1020 92.888 1574 2275 1 chr4D.!!$R1 701
7 TraesCS7B01G414500 chr4A 675524965 675526192 1227 True 749 749 78.100 9 1265 1 chr4A.!!$R1 1256
8 TraesCS7B01G414500 chr4A 742585144 742586365 1221 True 721 721 77.672 15 1265 1 chr4A.!!$R2 1250

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
359 366 0.320374 TGGCTTCTCCTACAACCACG 59.680 55.0 0.0 0.0 35.26 4.94 F
1234 1245 0.323542 GGAGGACGAGGAGTTCTGGA 60.324 60.0 0.0 0.0 39.26 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1265 1276 0.036875 CCCCGTTCAAGCTTTCCTCT 59.963 55.000 0.00 0.0 0.0 3.69 R
2046 2058 2.558359 GGTTACTTTCAGTTGGCAGCAT 59.442 45.455 3.63 0.0 0.0 3.79 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
58 59 1.563655 CGCGCTCGTCGACTACTAT 59.436 57.895 14.70 0.00 41.67 2.12
87 88 2.877582 CCGCTTCGTAACCGACCG 60.878 66.667 0.00 0.00 44.13 4.79
94 95 1.031571 TCGTAACCGACCGGCACTAT 61.032 55.000 8.55 0.00 38.40 2.12
106 110 1.644786 GGCACTATGGCGGTGAACAC 61.645 60.000 8.79 0.00 36.89 3.32
130 134 1.003355 CGTTGTGGTGGGATGCTCT 60.003 57.895 0.00 0.00 0.00 4.09
134 138 1.448540 GTGGTGGGATGCTCTGTCG 60.449 63.158 0.00 0.00 0.00 4.35
223 227 2.577059 GTGATTCCTCCCGACGCA 59.423 61.111 0.00 0.00 0.00 5.24
250 257 1.508632 CGGTCGTGGTTCAGTCATTT 58.491 50.000 0.00 0.00 0.00 2.32
259 266 3.960102 TGGTTCAGTCATTTTTCCTGCTT 59.040 39.130 0.00 0.00 0.00 3.91
265 272 4.219070 CAGTCATTTTTCCTGCTTGATGGA 59.781 41.667 0.00 0.00 0.00 3.41
357 364 1.270625 CGTTGGCTTCTCCTACAACCA 60.271 52.381 0.00 0.00 40.04 3.67
358 365 2.152016 GTTGGCTTCTCCTACAACCAC 58.848 52.381 0.00 0.00 39.85 4.16
359 366 0.320374 TGGCTTCTCCTACAACCACG 59.680 55.000 0.00 0.00 35.26 4.94
360 367 1.019805 GGCTTCTCCTACAACCACGC 61.020 60.000 0.00 0.00 0.00 5.34
361 368 1.352156 GCTTCTCCTACAACCACGCG 61.352 60.000 3.53 3.53 0.00 6.01
362 369 1.352156 CTTCTCCTACAACCACGCGC 61.352 60.000 5.73 0.00 0.00 6.86
363 370 2.048597 CTCCTACAACCACGCGCA 60.049 61.111 5.73 0.00 0.00 6.09
364 371 2.048597 TCCTACAACCACGCGCAG 60.049 61.111 5.73 0.00 0.00 5.18
405 412 2.449137 CCTTCTGGGGCTTCATCAAT 57.551 50.000 0.00 0.00 0.00 2.57
702 713 1.004440 GTTTCAGGCGCTGACCTCT 60.004 57.895 7.64 0.00 40.46 3.69
734 745 3.418913 CATCACCCGCGCACGAAA 61.419 61.111 8.75 0.00 43.93 3.46
1128 1139 2.049802 GCGAACAAGGTCGACGGA 60.050 61.111 12.27 0.00 43.86 4.69
1234 1245 0.323542 GGAGGACGAGGAGTTCTGGA 60.324 60.000 0.00 0.00 39.26 3.86
1235 1246 1.686741 GGAGGACGAGGAGTTCTGGAT 60.687 57.143 0.00 0.00 39.26 3.41
1272 1283 3.068881 CCGGTGCTGGAGAGGAAA 58.931 61.111 0.00 0.00 0.00 3.13
1274 1285 1.743252 CGGTGCTGGAGAGGAAAGC 60.743 63.158 0.00 0.00 37.46 3.51
1288 1299 0.536460 GAAAGCTTGAACGGGGGTGA 60.536 55.000 0.00 0.00 0.00 4.02
1291 1302 3.157680 CTTGAACGGGGGTGAGGT 58.842 61.111 0.00 0.00 0.00 3.85
1301 1312 1.216990 GGGGTGAGGTTGGAGATGAT 58.783 55.000 0.00 0.00 0.00 2.45
1302 1313 1.133976 GGGGTGAGGTTGGAGATGATG 60.134 57.143 0.00 0.00 0.00 3.07
1305 1316 2.420687 GGTGAGGTTGGAGATGATGACC 60.421 54.545 0.00 0.00 0.00 4.02
1317 1328 1.191489 TGATGACCCTCTGTTCCGCA 61.191 55.000 0.00 0.00 0.00 5.69
1319 1330 1.194781 ATGACCCTCTGTTCCGCAGT 61.195 55.000 0.00 0.00 45.23 4.40
1324 1335 1.364626 CCTCTGTTCCGCAGTGATGC 61.365 60.000 0.00 0.00 45.23 3.91
1349 1360 4.704833 ATGCTCGCCTTGCCGTGT 62.705 61.111 0.00 0.00 0.00 4.49
1367 1378 1.009335 TCGTGGTGACAACGACTCG 60.009 57.895 11.76 0.00 46.06 4.18
1368 1379 2.014554 CGTGGTGACAACGACTCGG 61.015 63.158 6.68 0.00 46.06 4.63
1369 1380 1.663702 GTGGTGACAACGACTCGGG 60.664 63.158 2.98 0.00 46.06 5.14
1370 1381 2.737376 GGTGACAACGACTCGGGC 60.737 66.667 2.98 0.00 0.00 6.13
1371 1382 2.338984 GTGACAACGACTCGGGCT 59.661 61.111 2.98 0.00 0.00 5.19
1372 1383 2.022129 GTGACAACGACTCGGGCTG 61.022 63.158 2.98 0.07 0.00 4.85
1373 1384 2.338984 GACAACGACTCGGGCTGT 59.661 61.111 2.98 3.32 0.00 4.40
1374 1385 1.300697 GACAACGACTCGGGCTGTT 60.301 57.895 2.98 0.00 0.00 3.16
1375 1386 1.557443 GACAACGACTCGGGCTGTTG 61.557 60.000 16.25 16.25 45.39 3.33
1376 1387 2.030562 AACGACTCGGGCTGTTGG 59.969 61.111 2.98 0.00 0.00 3.77
1377 1388 4.681978 ACGACTCGGGCTGTTGGC 62.682 66.667 2.98 0.00 40.90 4.52
1386 1397 4.752879 GCTGTTGGCCGCCGTCTA 62.753 66.667 4.58 0.00 34.27 2.59
1387 1398 2.186903 CTGTTGGCCGCCGTCTAT 59.813 61.111 4.58 0.00 0.00 1.98
1388 1399 1.449601 CTGTTGGCCGCCGTCTATT 60.450 57.895 4.58 0.00 0.00 1.73
1389 1400 0.179094 CTGTTGGCCGCCGTCTATTA 60.179 55.000 4.58 0.00 0.00 0.98
1390 1401 0.460635 TGTTGGCCGCCGTCTATTAC 60.461 55.000 4.58 0.00 0.00 1.89
1398 1409 3.392440 CGTCTATTACGCGCCGGC 61.392 66.667 19.07 19.07 46.10 6.13
1399 1410 2.278989 GTCTATTACGCGCCGGCA 60.279 61.111 28.98 6.55 39.92 5.69
1400 1411 1.663702 GTCTATTACGCGCCGGCAT 60.664 57.895 28.98 14.62 39.92 4.40
1401 1412 1.372499 TCTATTACGCGCCGGCATC 60.372 57.895 28.98 16.58 39.92 3.91
1402 1413 2.716828 CTATTACGCGCCGGCATCG 61.717 63.158 29.14 29.14 39.92 3.84
1413 1424 3.546407 CGGCATCGGTCTGTACTAC 57.454 57.895 0.00 0.00 0.00 2.73
1414 1425 1.022735 CGGCATCGGTCTGTACTACT 58.977 55.000 0.00 0.00 0.00 2.57
1415 1426 1.002684 CGGCATCGGTCTGTACTACTC 60.003 57.143 0.00 0.00 0.00 2.59
1416 1427 2.022195 GGCATCGGTCTGTACTACTCA 58.978 52.381 0.00 0.00 0.00 3.41
1417 1428 2.223525 GGCATCGGTCTGTACTACTCAC 60.224 54.545 0.00 0.00 0.00 3.51
1418 1429 2.683867 GCATCGGTCTGTACTACTCACT 59.316 50.000 0.00 0.00 0.00 3.41
1419 1430 3.242804 GCATCGGTCTGTACTACTCACTC 60.243 52.174 0.00 0.00 0.00 3.51
1420 1431 3.977134 TCGGTCTGTACTACTCACTCT 57.023 47.619 0.00 0.00 0.00 3.24
1421 1432 3.597255 TCGGTCTGTACTACTCACTCTG 58.403 50.000 0.00 0.00 0.00 3.35
1422 1433 3.007723 TCGGTCTGTACTACTCACTCTGT 59.992 47.826 0.00 0.00 0.00 3.41
1423 1434 4.221482 TCGGTCTGTACTACTCACTCTGTA 59.779 45.833 0.00 0.00 0.00 2.74
1424 1435 4.567558 CGGTCTGTACTACTCACTCTGTAG 59.432 50.000 0.00 0.00 42.07 2.74
1426 1437 5.581874 GGTCTGTACTACTCACTCTGTAGTC 59.418 48.000 9.42 4.09 44.93 2.59
1427 1438 6.164876 GTCTGTACTACTCACTCTGTAGTCA 58.835 44.000 9.42 7.53 44.93 3.41
1428 1439 6.819649 GTCTGTACTACTCACTCTGTAGTCAT 59.180 42.308 9.42 0.00 44.93 3.06
1429 1440 6.819146 TCTGTACTACTCACTCTGTAGTCATG 59.181 42.308 9.42 0.00 44.93 3.07
1430 1441 6.708285 TGTACTACTCACTCTGTAGTCATGA 58.292 40.000 9.42 0.00 44.93 3.07
1431 1442 7.339482 TGTACTACTCACTCTGTAGTCATGAT 58.661 38.462 9.42 0.00 44.93 2.45
1432 1443 6.935741 ACTACTCACTCTGTAGTCATGATC 57.064 41.667 0.00 0.00 44.93 2.92
1433 1444 6.658849 ACTACTCACTCTGTAGTCATGATCT 58.341 40.000 0.00 0.68 44.93 2.75
1434 1445 7.116075 ACTACTCACTCTGTAGTCATGATCTT 58.884 38.462 0.00 0.00 44.93 2.40
1435 1446 6.849085 ACTCACTCTGTAGTCATGATCTTT 57.151 37.500 0.00 0.00 31.97 2.52
1436 1447 7.238486 ACTCACTCTGTAGTCATGATCTTTT 57.762 36.000 0.00 0.00 31.97 2.27
1437 1448 7.319646 ACTCACTCTGTAGTCATGATCTTTTC 58.680 38.462 0.00 0.00 31.97 2.29
1438 1449 6.634805 TCACTCTGTAGTCATGATCTTTTCC 58.365 40.000 0.00 0.00 31.97 3.13
1439 1450 5.518128 CACTCTGTAGTCATGATCTTTTCCG 59.482 44.000 0.00 0.00 31.97 4.30
1440 1451 5.419155 ACTCTGTAGTCATGATCTTTTCCGA 59.581 40.000 0.00 0.00 0.00 4.55
1441 1452 5.651530 TCTGTAGTCATGATCTTTTCCGAC 58.348 41.667 0.00 0.00 0.00 4.79
1442 1453 5.419155 TCTGTAGTCATGATCTTTTCCGACT 59.581 40.000 0.00 0.00 38.75 4.18
1443 1454 6.037786 TGTAGTCATGATCTTTTCCGACTT 57.962 37.500 0.00 0.00 37.33 3.01
1444 1455 6.464222 TGTAGTCATGATCTTTTCCGACTTT 58.536 36.000 0.00 0.00 37.33 2.66
1445 1456 6.934645 TGTAGTCATGATCTTTTCCGACTTTT 59.065 34.615 0.00 0.00 37.33 2.27
1446 1457 6.884280 AGTCATGATCTTTTCCGACTTTTT 57.116 33.333 0.00 0.00 34.22 1.94
1469 1480 8.841444 TTTTCTTCTATTTCTATGATTTGCGC 57.159 30.769 0.00 0.00 0.00 6.09
1470 1481 7.792374 TTCTTCTATTTCTATGATTTGCGCT 57.208 32.000 9.73 0.00 0.00 5.92
1471 1482 7.413475 TCTTCTATTTCTATGATTTGCGCTC 57.587 36.000 9.73 0.00 0.00 5.03
1472 1483 7.212976 TCTTCTATTTCTATGATTTGCGCTCT 58.787 34.615 9.73 0.00 0.00 4.09
1473 1484 7.712639 TCTTCTATTTCTATGATTTGCGCTCTT 59.287 33.333 9.73 0.00 0.00 2.85
1474 1485 7.182361 TCTATTTCTATGATTTGCGCTCTTG 57.818 36.000 9.73 0.00 0.00 3.02
1475 1486 3.680642 TTCTATGATTTGCGCTCTTGC 57.319 42.857 9.73 0.00 0.00 4.01
1476 1487 2.910199 TCTATGATTTGCGCTCTTGCT 58.090 42.857 9.73 0.00 36.97 3.91
1477 1488 4.058721 TCTATGATTTGCGCTCTTGCTA 57.941 40.909 9.73 0.00 36.97 3.49
1478 1489 4.441792 TCTATGATTTGCGCTCTTGCTAA 58.558 39.130 9.73 0.00 36.97 3.09
1479 1490 4.875536 TCTATGATTTGCGCTCTTGCTAAA 59.124 37.500 9.73 0.00 33.55 1.85
1480 1491 3.201726 TGATTTGCGCTCTTGCTAAAC 57.798 42.857 9.73 0.00 33.55 2.01
1481 1492 2.095263 TGATTTGCGCTCTTGCTAAACC 60.095 45.455 9.73 0.00 33.55 3.27
1482 1493 0.596082 TTTGCGCTCTTGCTAAACCC 59.404 50.000 9.73 0.00 36.97 4.11
1483 1494 0.536233 TTGCGCTCTTGCTAAACCCA 60.536 50.000 9.73 0.00 36.97 4.51
1484 1495 0.536233 TGCGCTCTTGCTAAACCCAA 60.536 50.000 9.73 0.00 36.97 4.12
1485 1496 0.596082 GCGCTCTTGCTAAACCCAAA 59.404 50.000 0.00 0.00 36.97 3.28
1486 1497 1.202348 GCGCTCTTGCTAAACCCAAAT 59.798 47.619 0.00 0.00 36.97 2.32
1487 1498 2.422127 GCGCTCTTGCTAAACCCAAATA 59.578 45.455 0.00 0.00 36.97 1.40
1488 1499 3.119637 GCGCTCTTGCTAAACCCAAATAA 60.120 43.478 0.00 0.00 36.97 1.40
1489 1500 4.440112 GCGCTCTTGCTAAACCCAAATAAT 60.440 41.667 0.00 0.00 36.97 1.28
1490 1501 5.220970 GCGCTCTTGCTAAACCCAAATAATA 60.221 40.000 0.00 0.00 36.97 0.98
1491 1502 6.679392 GCGCTCTTGCTAAACCCAAATAATAA 60.679 38.462 0.00 0.00 36.97 1.40
1492 1503 6.912591 CGCTCTTGCTAAACCCAAATAATAAG 59.087 38.462 0.00 0.00 36.97 1.73
1493 1504 7.415206 CGCTCTTGCTAAACCCAAATAATAAGT 60.415 37.037 0.00 0.00 36.97 2.24
1494 1505 7.702348 GCTCTTGCTAAACCCAAATAATAAGTG 59.298 37.037 0.00 0.00 36.03 3.16
1495 1506 7.543756 TCTTGCTAAACCCAAATAATAAGTGC 58.456 34.615 0.00 0.00 0.00 4.40
1496 1507 6.215495 TGCTAAACCCAAATAATAAGTGCC 57.785 37.500 0.00 0.00 0.00 5.01
1497 1508 5.717178 TGCTAAACCCAAATAATAAGTGCCA 59.283 36.000 0.00 0.00 0.00 4.92
1498 1509 6.382570 TGCTAAACCCAAATAATAAGTGCCAT 59.617 34.615 0.00 0.00 0.00 4.40
1499 1510 7.561722 TGCTAAACCCAAATAATAAGTGCCATA 59.438 33.333 0.00 0.00 0.00 2.74
1500 1511 7.865889 GCTAAACCCAAATAATAAGTGCCATAC 59.134 37.037 0.00 0.00 0.00 2.39
1501 1512 6.385649 AACCCAAATAATAAGTGCCATACG 57.614 37.500 0.00 0.00 0.00 3.06
1502 1513 5.442391 ACCCAAATAATAAGTGCCATACGT 58.558 37.500 0.00 0.00 0.00 3.57
1503 1514 5.298276 ACCCAAATAATAAGTGCCATACGTG 59.702 40.000 0.00 0.00 0.00 4.49
1504 1515 5.212194 CCAAATAATAAGTGCCATACGTGC 58.788 41.667 0.00 0.00 0.00 5.34
1505 1516 5.220951 CCAAATAATAAGTGCCATACGTGCA 60.221 40.000 0.00 0.00 36.12 4.57
1506 1517 5.673337 AATAATAAGTGCCATACGTGCAG 57.327 39.130 0.00 0.00 39.87 4.41
1507 1518 2.979814 ATAAGTGCCATACGTGCAGA 57.020 45.000 0.00 0.00 39.87 4.26
1508 1519 2.979814 TAAGTGCCATACGTGCAGAT 57.020 45.000 0.00 0.00 39.87 2.90
1509 1520 2.979814 AAGTGCCATACGTGCAGATA 57.020 45.000 0.00 0.00 39.87 1.98
1510 1521 2.225068 AGTGCCATACGTGCAGATAC 57.775 50.000 0.00 0.00 39.87 2.24
1511 1522 1.757118 AGTGCCATACGTGCAGATACT 59.243 47.619 0.00 0.00 39.87 2.12
1512 1523 2.168521 AGTGCCATACGTGCAGATACTT 59.831 45.455 0.00 0.00 39.87 2.24
1513 1524 2.936498 GTGCCATACGTGCAGATACTTT 59.064 45.455 0.00 0.00 39.87 2.66
1514 1525 3.374058 GTGCCATACGTGCAGATACTTTT 59.626 43.478 0.00 0.00 39.87 2.27
1515 1526 3.373748 TGCCATACGTGCAGATACTTTTG 59.626 43.478 0.00 0.00 34.05 2.44
1516 1527 3.621268 GCCATACGTGCAGATACTTTTGA 59.379 43.478 0.00 0.00 0.00 2.69
1517 1528 4.094294 GCCATACGTGCAGATACTTTTGAA 59.906 41.667 0.00 0.00 0.00 2.69
1518 1529 5.391523 GCCATACGTGCAGATACTTTTGAAA 60.392 40.000 0.00 0.00 0.00 2.69
1519 1530 6.021596 CCATACGTGCAGATACTTTTGAAAC 58.978 40.000 0.00 0.00 0.00 2.78
1520 1531 6.128282 CCATACGTGCAGATACTTTTGAAACT 60.128 38.462 0.00 0.00 0.00 2.66
1521 1532 7.064134 CCATACGTGCAGATACTTTTGAAACTA 59.936 37.037 0.00 0.00 0.00 2.24
1522 1533 6.854496 ACGTGCAGATACTTTTGAAACTAA 57.146 33.333 0.00 0.00 0.00 2.24
1523 1534 7.254227 ACGTGCAGATACTTTTGAAACTAAA 57.746 32.000 0.00 0.00 0.00 1.85
1524 1535 7.352739 ACGTGCAGATACTTTTGAAACTAAAG 58.647 34.615 0.00 0.00 38.32 1.85
1525 1536 7.012044 ACGTGCAGATACTTTTGAAACTAAAGT 59.988 33.333 13.42 13.42 45.19 2.66
1526 1537 7.855904 CGTGCAGATACTTTTGAAACTAAAGTT 59.144 33.333 13.92 0.00 41.69 2.66
1527 1538 8.958043 GTGCAGATACTTTTGAAACTAAAGTTG 58.042 33.333 13.92 9.28 41.69 3.16
1528 1539 8.682710 TGCAGATACTTTTGAAACTAAAGTTGT 58.317 29.630 13.92 6.45 41.69 3.32
1529 1540 9.170584 GCAGATACTTTTGAAACTAAAGTTGTC 57.829 33.333 13.92 12.51 41.69 3.18
1567 1578 9.469807 AAAAACAAACCAAAAGGAAATTGAAAC 57.530 25.926 0.00 0.00 0.00 2.78
1568 1579 6.751514 ACAAACCAAAAGGAAATTGAAACC 57.248 33.333 0.00 0.00 0.00 3.27
1569 1580 6.241645 ACAAACCAAAAGGAAATTGAAACCA 58.758 32.000 0.00 0.00 0.00 3.67
1570 1581 6.717084 ACAAACCAAAAGGAAATTGAAACCAA 59.283 30.769 0.00 0.00 0.00 3.67
1571 1582 7.231519 ACAAACCAAAAGGAAATTGAAACCAAA 59.768 29.630 0.00 0.00 0.00 3.28
1572 1583 7.767250 AACCAAAAGGAAATTGAAACCAAAA 57.233 28.000 0.00 0.00 0.00 2.44
1630 1642 6.809689 TGCATAATTTCATTTGAACAGAGCAG 59.190 34.615 0.00 0.00 33.13 4.24
1662 1674 9.902196 GTAATAAATTACCTCTGTAGCTCTCTC 57.098 37.037 0.00 0.00 37.30 3.20
1690 1702 2.092538 CCCTCTCTTGCCAAGATGTGAT 60.093 50.000 7.75 0.00 36.82 3.06
1741 1753 9.730420 TTCTTAGAACAAGAAGTTTTATTGTGC 57.270 29.630 2.96 1.53 41.51 4.57
1778 1790 7.335171 CACAAGATCCACAAGTTATCTGAATGA 59.665 37.037 0.00 0.00 30.50 2.57
1780 1792 6.045318 AGATCCACAAGTTATCTGAATGACG 58.955 40.000 0.00 0.00 0.00 4.35
1828 1840 1.905894 GCTTCACCCTCTTCTCTCCTT 59.094 52.381 0.00 0.00 0.00 3.36
1831 1843 4.605183 CTTCACCCTCTTCTCTCCTTCTA 58.395 47.826 0.00 0.00 0.00 2.10
1837 1849 6.780031 CACCCTCTTCTCTCCTTCTATCATTA 59.220 42.308 0.00 0.00 0.00 1.90
1903 1915 0.958876 GCCTAGGGTTTTGGGACACG 60.959 60.000 11.72 0.00 39.29 4.49
1909 1921 1.906333 GTTTTGGGACACGGGCCAT 60.906 57.895 4.39 0.00 39.29 4.40
1930 1942 2.568623 TTTCCTCTCCTTCAACAGGC 57.431 50.000 0.00 0.00 43.55 4.85
1931 1943 1.434188 TTCCTCTCCTTCAACAGGCA 58.566 50.000 0.00 0.00 43.55 4.75
1933 1945 0.035630 CCTCTCCTTCAACAGGCAGG 60.036 60.000 0.00 0.00 43.55 4.85
1948 1960 0.813210 GCAGGAGGCAGTGCTCATAC 60.813 60.000 16.11 2.24 43.97 2.39
1954 1966 3.539604 GAGGCAGTGCTCATACATCTTT 58.460 45.455 16.11 0.00 0.00 2.52
2086 2098 6.710744 AGTAACCACAAGAACAAGTCCTATTG 59.289 38.462 0.00 0.00 36.22 1.90
2254 2266 2.033801 CCAGTTGTCACTTTTGGCTCTG 59.966 50.000 0.00 0.00 33.18 3.35
2275 2287 7.175347 TCTGTGCTCTTGAACTCTAACATAT 57.825 36.000 0.00 0.00 0.00 1.78
2276 2288 8.293699 TCTGTGCTCTTGAACTCTAACATATA 57.706 34.615 0.00 0.00 0.00 0.86
2277 2289 8.749354 TCTGTGCTCTTGAACTCTAACATATAA 58.251 33.333 0.00 0.00 0.00 0.98
2278 2290 9.539825 CTGTGCTCTTGAACTCTAACATATAAT 57.460 33.333 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 2.582436 CCATAGTGCCGGTCGGTT 59.418 61.111 11.25 0.52 37.65 4.44
87 88 1.376683 TGTTCACCGCCATAGTGCC 60.377 57.895 0.00 0.00 35.14 5.01
118 122 2.512515 GCGACAGAGCATCCCACC 60.513 66.667 0.00 0.00 37.05 4.61
187 191 2.769621 TCCGCCATGGAGATGCCT 60.770 61.111 18.40 0.00 43.74 4.75
234 241 3.563808 CAGGAAAAATGACTGAACCACGA 59.436 43.478 0.00 0.00 34.21 4.35
239 246 5.186996 TCAAGCAGGAAAAATGACTGAAC 57.813 39.130 0.00 0.00 34.21 3.18
250 257 0.405198 TGGCTCCATCAAGCAGGAAA 59.595 50.000 0.00 0.00 44.35 3.13
426 433 3.157252 GATCCGAGGAGCCTGGCA 61.157 66.667 22.65 0.00 0.00 4.92
441 448 4.496336 GGCTGCTCTTGCGGGGAT 62.496 66.667 0.00 0.00 45.30 3.85
449 456 2.269241 GGCGTAAGGGCTGCTCTT 59.731 61.111 20.00 20.00 38.40 2.85
450 457 4.148825 CGGCGTAAGGGCTGCTCT 62.149 66.667 0.00 0.00 39.52 4.09
634 645 3.334054 GGTGGCCAGGAGCTCCTT 61.334 66.667 33.33 15.54 46.09 3.36
702 713 0.829990 TGATGCAACGCCATAGGAGA 59.170 50.000 0.00 0.00 0.00 3.71
732 743 1.515521 CCTTTTCCGGCGACAGCTTT 61.516 55.000 9.30 0.00 44.37 3.51
733 744 1.966451 CCTTTTCCGGCGACAGCTT 60.966 57.895 9.30 0.00 44.37 3.74
734 745 2.358737 CCTTTTCCGGCGACAGCT 60.359 61.111 9.30 0.00 44.37 4.24
1128 1139 1.823169 ATGGGTACAACGACGTGCCT 61.823 55.000 0.00 0.00 41.09 4.75
1265 1276 0.036875 CCCCGTTCAAGCTTTCCTCT 59.963 55.000 0.00 0.00 0.00 3.69
1267 1278 1.074951 CCCCCGTTCAAGCTTTCCT 59.925 57.895 0.00 0.00 0.00 3.36
1272 1283 2.750350 CTCACCCCCGTTCAAGCT 59.250 61.111 0.00 0.00 0.00 3.74
1274 1285 0.889186 CAACCTCACCCCCGTTCAAG 60.889 60.000 0.00 0.00 0.00 3.02
1288 1299 2.122768 GAGGGTCATCATCTCCAACCT 58.877 52.381 0.00 0.00 0.00 3.50
1291 1302 2.837947 ACAGAGGGTCATCATCTCCAA 58.162 47.619 0.00 0.00 0.00 3.53
1317 1328 4.511246 CATGGCCCCGGCATCACT 62.511 66.667 8.23 0.00 45.69 3.41
1349 1360 1.009335 CGAGTCGTTGTCACCACGA 60.009 57.895 3.82 0.00 0.00 4.35
1359 1370 2.030562 CCAACAGCCCGAGTCGTT 59.969 61.111 12.31 0.00 0.00 3.85
1369 1380 4.752879 TAGACGGCGGCCAACAGC 62.753 66.667 20.71 0.00 42.60 4.40
1370 1381 0.179094 TAATAGACGGCGGCCAACAG 60.179 55.000 20.71 4.85 0.00 3.16
1371 1382 0.460635 GTAATAGACGGCGGCCAACA 60.461 55.000 20.71 0.58 0.00 3.33
1372 1383 2.304428 GTAATAGACGGCGGCCAAC 58.696 57.895 20.71 11.91 0.00 3.77
1373 1384 4.840168 GTAATAGACGGCGGCCAA 57.160 55.556 20.71 0.00 0.00 4.52
1382 1393 1.615107 GATGCCGGCGCGTAATAGAC 61.615 60.000 23.90 0.00 38.08 2.59
1383 1394 1.372499 GATGCCGGCGCGTAATAGA 60.372 57.895 23.90 0.00 38.08 1.98
1384 1395 2.716828 CGATGCCGGCGCGTAATAG 61.717 63.158 27.17 10.75 38.08 1.73
1385 1396 2.731721 CGATGCCGGCGCGTAATA 60.732 61.111 27.17 8.07 38.08 0.98
1395 1406 1.002684 GAGTAGTACAGACCGATGCCG 60.003 57.143 2.52 0.00 0.00 5.69
1396 1407 2.022195 TGAGTAGTACAGACCGATGCC 58.978 52.381 2.52 0.00 0.00 4.40
1397 1408 2.683867 AGTGAGTAGTACAGACCGATGC 59.316 50.000 2.52 0.00 0.00 3.91
1398 1409 4.034626 CAGAGTGAGTAGTACAGACCGATG 59.965 50.000 2.52 0.00 0.00 3.84
1399 1410 4.193090 CAGAGTGAGTAGTACAGACCGAT 58.807 47.826 2.52 0.00 0.00 4.18
1400 1411 3.007723 ACAGAGTGAGTAGTACAGACCGA 59.992 47.826 2.52 0.00 0.00 4.69
1401 1412 3.336468 ACAGAGTGAGTAGTACAGACCG 58.664 50.000 2.52 0.00 0.00 4.79
1410 1421 7.566760 AAGATCATGACTACAGAGTGAGTAG 57.433 40.000 0.00 0.00 43.51 2.57
1411 1422 7.946381 AAAGATCATGACTACAGAGTGAGTA 57.054 36.000 0.00 0.00 35.45 2.59
1412 1423 6.849085 AAAGATCATGACTACAGAGTGAGT 57.151 37.500 0.00 0.00 35.45 3.41
1413 1424 6.756074 GGAAAAGATCATGACTACAGAGTGAG 59.244 42.308 0.00 0.00 35.45 3.51
1414 1425 6.625960 CGGAAAAGATCATGACTACAGAGTGA 60.626 42.308 0.00 0.00 35.45 3.41
1415 1426 5.518128 CGGAAAAGATCATGACTACAGAGTG 59.482 44.000 0.00 0.00 35.45 3.51
1416 1427 5.419155 TCGGAAAAGATCATGACTACAGAGT 59.581 40.000 0.00 0.00 39.20 3.24
1417 1428 5.746245 GTCGGAAAAGATCATGACTACAGAG 59.254 44.000 0.00 0.00 34.13 3.35
1418 1429 5.419155 AGTCGGAAAAGATCATGACTACAGA 59.581 40.000 0.00 0.00 41.07 3.41
1419 1430 5.655488 AGTCGGAAAAGATCATGACTACAG 58.345 41.667 0.00 0.00 41.07 2.74
1420 1431 5.661056 AGTCGGAAAAGATCATGACTACA 57.339 39.130 0.00 0.00 41.07 2.74
1421 1432 6.969828 AAAGTCGGAAAAGATCATGACTAC 57.030 37.500 0.00 0.00 41.64 2.73
1422 1433 7.979444 AAAAAGTCGGAAAAGATCATGACTA 57.021 32.000 0.00 0.00 41.64 2.59
1423 1434 6.884280 AAAAAGTCGGAAAAGATCATGACT 57.116 33.333 0.00 0.00 43.26 3.41
1443 1454 9.289303 GCGCAAATCATAGAAATAGAAGAAAAA 57.711 29.630 0.30 0.00 0.00 1.94
1444 1455 8.677300 AGCGCAAATCATAGAAATAGAAGAAAA 58.323 29.630 11.47 0.00 0.00 2.29
1445 1456 8.213518 AGCGCAAATCATAGAAATAGAAGAAA 57.786 30.769 11.47 0.00 0.00 2.52
1446 1457 7.712639 AGAGCGCAAATCATAGAAATAGAAGAA 59.287 33.333 11.47 0.00 0.00 2.52
1447 1458 7.212976 AGAGCGCAAATCATAGAAATAGAAGA 58.787 34.615 11.47 0.00 0.00 2.87
1448 1459 7.418840 AGAGCGCAAATCATAGAAATAGAAG 57.581 36.000 11.47 0.00 0.00 2.85
1449 1460 7.633621 CAAGAGCGCAAATCATAGAAATAGAA 58.366 34.615 11.47 0.00 0.00 2.10
1450 1461 6.293081 GCAAGAGCGCAAATCATAGAAATAGA 60.293 38.462 11.47 0.00 0.00 1.98
1451 1462 5.850128 GCAAGAGCGCAAATCATAGAAATAG 59.150 40.000 11.47 0.00 0.00 1.73
1452 1463 5.751680 GCAAGAGCGCAAATCATAGAAATA 58.248 37.500 11.47 0.00 0.00 1.40
1453 1464 4.604976 GCAAGAGCGCAAATCATAGAAAT 58.395 39.130 11.47 0.00 0.00 2.17
1454 1465 4.019919 GCAAGAGCGCAAATCATAGAAA 57.980 40.909 11.47 0.00 0.00 2.52
1455 1466 3.680642 GCAAGAGCGCAAATCATAGAA 57.319 42.857 11.47 0.00 0.00 2.10
1461 1472 9.903977 TATTTGGGTTTAGCAAGAGCGCAAATC 62.904 40.741 19.85 0.00 45.08 2.17
1462 1473 8.241317 TATTTGGGTTTAGCAAGAGCGCAAAT 62.241 38.462 11.47 20.01 46.60 2.32
1468 1479 7.702348 CACTTATTATTTGGGTTTAGCAAGAGC 59.298 37.037 0.00 0.00 42.56 4.09
1469 1480 7.702348 GCACTTATTATTTGGGTTTAGCAAGAG 59.298 37.037 0.00 0.00 0.00 2.85
1470 1481 7.363443 GGCACTTATTATTTGGGTTTAGCAAGA 60.363 37.037 0.00 0.00 0.00 3.02
1471 1482 6.756542 GGCACTTATTATTTGGGTTTAGCAAG 59.243 38.462 0.00 0.00 0.00 4.01
1472 1483 6.211584 TGGCACTTATTATTTGGGTTTAGCAA 59.788 34.615 0.00 0.00 0.00 3.91
1473 1484 5.717178 TGGCACTTATTATTTGGGTTTAGCA 59.283 36.000 0.00 0.00 0.00 3.49
1474 1485 6.215495 TGGCACTTATTATTTGGGTTTAGC 57.785 37.500 0.00 0.00 0.00 3.09
1475 1486 8.073768 CGTATGGCACTTATTATTTGGGTTTAG 58.926 37.037 0.00 0.00 0.00 1.85
1476 1487 7.556996 ACGTATGGCACTTATTATTTGGGTTTA 59.443 33.333 0.00 0.00 0.00 2.01
1477 1488 6.378848 ACGTATGGCACTTATTATTTGGGTTT 59.621 34.615 0.00 0.00 0.00 3.27
1478 1489 5.889289 ACGTATGGCACTTATTATTTGGGTT 59.111 36.000 0.00 0.00 0.00 4.11
1479 1490 5.298276 CACGTATGGCACTTATTATTTGGGT 59.702 40.000 0.00 0.00 0.00 4.51
1480 1491 5.757886 CACGTATGGCACTTATTATTTGGG 58.242 41.667 0.00 0.00 0.00 4.12
1481 1492 5.212194 GCACGTATGGCACTTATTATTTGG 58.788 41.667 0.00 0.00 0.00 3.28
1482 1493 5.815850 TGCACGTATGGCACTTATTATTTG 58.184 37.500 0.00 0.00 36.11 2.32
1483 1494 5.820423 TCTGCACGTATGGCACTTATTATTT 59.180 36.000 0.00 0.00 36.11 1.40
1484 1495 5.364778 TCTGCACGTATGGCACTTATTATT 58.635 37.500 0.00 0.00 36.11 1.40
1485 1496 4.956085 TCTGCACGTATGGCACTTATTAT 58.044 39.130 0.00 0.00 36.11 1.28
1486 1497 4.394439 TCTGCACGTATGGCACTTATTA 57.606 40.909 0.00 0.00 36.11 0.98
1487 1498 3.260475 TCTGCACGTATGGCACTTATT 57.740 42.857 0.00 0.00 36.11 1.40
1488 1499 2.979814 TCTGCACGTATGGCACTTAT 57.020 45.000 0.00 0.00 36.11 1.73
1489 1500 2.979814 ATCTGCACGTATGGCACTTA 57.020 45.000 0.00 0.00 36.11 2.24
1490 1501 2.168521 AGTATCTGCACGTATGGCACTT 59.831 45.455 0.00 0.00 36.11 3.16
1491 1502 1.757118 AGTATCTGCACGTATGGCACT 59.243 47.619 0.00 0.00 36.11 4.40
1492 1503 2.225068 AGTATCTGCACGTATGGCAC 57.775 50.000 0.00 0.00 36.11 5.01
1493 1504 2.979814 AAGTATCTGCACGTATGGCA 57.020 45.000 0.00 0.00 39.32 4.92
1494 1505 3.621268 TCAAAAGTATCTGCACGTATGGC 59.379 43.478 0.00 0.00 0.00 4.40
1495 1506 5.794687 TTCAAAAGTATCTGCACGTATGG 57.205 39.130 0.00 0.00 0.00 2.74
1496 1507 6.831769 AGTTTCAAAAGTATCTGCACGTATG 58.168 36.000 0.00 0.00 0.00 2.39
1497 1508 8.542497 TTAGTTTCAAAAGTATCTGCACGTAT 57.458 30.769 0.00 0.00 0.00 3.06
1498 1509 7.949903 TTAGTTTCAAAAGTATCTGCACGTA 57.050 32.000 0.00 0.00 0.00 3.57
1499 1510 6.854496 TTAGTTTCAAAAGTATCTGCACGT 57.146 33.333 0.00 0.00 0.00 4.49
1500 1511 7.352739 ACTTTAGTTTCAAAAGTATCTGCACG 58.647 34.615 0.00 0.00 43.54 5.34
1501 1512 8.958043 CAACTTTAGTTTCAAAAGTATCTGCAC 58.042 33.333 1.96 0.00 44.35 4.57
1502 1513 8.682710 ACAACTTTAGTTTCAAAAGTATCTGCA 58.317 29.630 1.96 0.00 44.35 4.41
1503 1514 9.170584 GACAACTTTAGTTTCAAAAGTATCTGC 57.829 33.333 1.96 0.00 44.35 4.26
1541 1552 9.469807 GTTTCAATTTCCTTTTGGTTTGTTTTT 57.530 25.926 0.00 0.00 41.38 1.94
1542 1553 8.085296 GGTTTCAATTTCCTTTTGGTTTGTTTT 58.915 29.630 0.00 0.00 41.38 2.43
1543 1554 7.231519 TGGTTTCAATTTCCTTTTGGTTTGTTT 59.768 29.630 0.00 0.00 41.38 2.83
1544 1555 6.717084 TGGTTTCAATTTCCTTTTGGTTTGTT 59.283 30.769 0.00 0.00 41.38 2.83
1545 1556 6.241645 TGGTTTCAATTTCCTTTTGGTTTGT 58.758 32.000 0.00 0.00 41.38 2.83
1546 1557 6.749923 TGGTTTCAATTTCCTTTTGGTTTG 57.250 33.333 0.00 0.00 41.38 2.93
1547 1558 7.767250 TTTGGTTTCAATTTCCTTTTGGTTT 57.233 28.000 0.00 0.00 35.30 3.27
1548 1559 7.576666 GCTTTTGGTTTCAATTTCCTTTTGGTT 60.577 33.333 0.00 0.00 35.30 3.67
1549 1560 6.127758 GCTTTTGGTTTCAATTTCCTTTTGGT 60.128 34.615 0.00 0.00 35.30 3.67
1550 1561 6.127786 TGCTTTTGGTTTCAATTTCCTTTTGG 60.128 34.615 0.00 0.00 35.16 3.28
1551 1562 6.850555 TGCTTTTGGTTTCAATTTCCTTTTG 58.149 32.000 0.00 0.00 32.28 2.44
1552 1563 7.459795 TTGCTTTTGGTTTCAATTTCCTTTT 57.540 28.000 0.00 0.00 32.28 2.27
1553 1564 7.459795 TTTGCTTTTGGTTTCAATTTCCTTT 57.540 28.000 0.00 0.00 32.28 3.11
1554 1565 7.643569 ATTTGCTTTTGGTTTCAATTTCCTT 57.356 28.000 0.00 0.00 32.28 3.36
1555 1566 8.744568 TTATTTGCTTTTGGTTTCAATTTCCT 57.255 26.923 0.00 0.00 32.28 3.36
1556 1567 9.794685 TTTTATTTGCTTTTGGTTTCAATTTCC 57.205 25.926 0.00 0.00 32.28 3.13
1562 1573 9.823647 TGTCTATTTTATTTGCTTTTGGTTTCA 57.176 25.926 0.00 0.00 0.00 2.69
1587 1598 8.891671 ATTATGCACCTATTTTGCCTAATTTG 57.108 30.769 0.00 0.00 37.44 2.32
1603 1615 6.035327 GCTCTGTTCAAATGAAATTATGCACC 59.965 38.462 0.00 0.00 33.67 5.01
1654 1666 3.011708 AGAGAGGGAGAAAAGAGAGAGCT 59.988 47.826 0.00 0.00 0.00 4.09
1662 1674 2.867109 TGGCAAGAGAGGGAGAAAAG 57.133 50.000 0.00 0.00 0.00 2.27
1702 1714 9.475620 TCTTGTTCTAAGAATGGAGATAGTACA 57.524 33.333 0.00 0.00 0.00 2.90
1741 1753 1.064685 GGATCTTGTGGTGGTAAGGGG 60.065 57.143 0.00 0.00 0.00 4.79
1778 1790 1.668419 AAGAAACTGAGCAAGCACGT 58.332 45.000 0.00 0.00 0.00 4.49
1780 1792 2.226674 GGGTAAGAAACTGAGCAAGCAC 59.773 50.000 0.00 0.00 0.00 4.40
1828 1840 8.695456 GGGCAAAGGAAAAAGAATAATGATAGA 58.305 33.333 0.00 0.00 0.00 1.98
1831 1843 7.333323 CAGGGCAAAGGAAAAAGAATAATGAT 58.667 34.615 0.00 0.00 0.00 2.45
1837 1849 2.038952 GCCAGGGCAAAGGAAAAAGAAT 59.961 45.455 5.20 0.00 41.49 2.40
1903 1915 2.103373 GAAGGAGAGGAAAAATGGCCC 58.897 52.381 0.00 0.00 0.00 5.80
1930 1942 0.538584 TGTATGAGCACTGCCTCCTG 59.461 55.000 0.00 0.00 0.00 3.86
1931 1943 1.415659 GATGTATGAGCACTGCCTCCT 59.584 52.381 0.00 0.00 0.00 3.69
1933 1945 2.906691 AGATGTATGAGCACTGCCTC 57.093 50.000 0.00 0.00 0.00 4.70
2046 2058 2.558359 GGTTACTTTCAGTTGGCAGCAT 59.442 45.455 3.63 0.00 0.00 3.79
2086 2098 5.869888 CAGGAGGTACACAGTAAATCTTGAC 59.130 44.000 0.00 0.00 0.00 3.18
2206 2218 4.680702 GCACAATTTGCCCAAACATTTTT 58.319 34.783 0.00 0.00 46.63 1.94


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

AutoCloner maintained by Alex Coulton.