Multiple sequence alignment - TraesCS4B01G050100

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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 TraesCS4B01G050100 chr4B 100.000 2318 0 0 1 2318 38781296 38783613 0.000000e+00 4281.0
1 TraesCS4B01G050100 chr4B 85.004 1347 200 2 1 1347 495080516 495081860 0.000000e+00 1367.0
2 TraesCS4B01G050100 chr4B 86.580 842 108 3 509 1345 651808033 651807192 0.000000e+00 924.0
3 TraesCS4B01G050100 chr4B 86.603 836 111 1 509 1343 651870283 651869448 0.000000e+00 922.0
4 TraesCS4B01G050100 chr5A 89.948 1343 134 1 2 1343 708678952 708680294 0.000000e+00 1731.0
5 TraesCS4B01G050100 chr5A 88.318 1344 155 2 2 1343 647000796 647002139 0.000000e+00 1611.0
6 TraesCS4B01G050100 chr4A 89.955 1334 132 2 11 1343 26019041 26017709 0.000000e+00 1720.0
7 TraesCS4B01G050100 chr2A 88.731 1340 150 1 5 1344 41173881 41172543 0.000000e+00 1637.0
8 TraesCS4B01G050100 chr2B 90.141 1065 102 3 1 1064 675504484 675505546 0.000000e+00 1382.0
9 TraesCS4B01G050100 chr1B 85.089 1348 195 3 1 1343 401562558 401563904 0.000000e+00 1371.0
10 TraesCS4B01G050100 chr6A 90.114 526 49 3 820 1343 608259174 608259698 0.000000e+00 680.0
11 TraesCS4B01G050100 chr4D 83.124 557 32 28 1658 2198 26242035 26242545 3.510000e-123 451.0
12 TraesCS4B01G050100 chr4D 89.873 79 1 3 2240 2318 26242620 26242691 6.820000e-16 95.3
13 TraesCS4B01G050100 chr4D 97.959 49 0 1 1617 1664 26241973 26242021 1.480000e-12 84.2


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 TraesCS4B01G050100 chr4B 38781296 38783613 2317 False 4281.000000 4281 100.000000 1 2318 1 chr4B.!!$F1 2317
1 TraesCS4B01G050100 chr4B 495080516 495081860 1344 False 1367.000000 1367 85.004000 1 1347 1 chr4B.!!$F2 1346
2 TraesCS4B01G050100 chr4B 651807192 651808033 841 True 924.000000 924 86.580000 509 1345 1 chr4B.!!$R1 836
3 TraesCS4B01G050100 chr4B 651869448 651870283 835 True 922.000000 922 86.603000 509 1343 1 chr4B.!!$R2 834
4 TraesCS4B01G050100 chr5A 708678952 708680294 1342 False 1731.000000 1731 89.948000 2 1343 1 chr5A.!!$F2 1341
5 TraesCS4B01G050100 chr5A 647000796 647002139 1343 False 1611.000000 1611 88.318000 2 1343 1 chr5A.!!$F1 1341
6 TraesCS4B01G050100 chr4A 26017709 26019041 1332 True 1720.000000 1720 89.955000 11 1343 1 chr4A.!!$R1 1332
7 TraesCS4B01G050100 chr2A 41172543 41173881 1338 True 1637.000000 1637 88.731000 5 1344 1 chr2A.!!$R1 1339
8 TraesCS4B01G050100 chr2B 675504484 675505546 1062 False 1382.000000 1382 90.141000 1 1064 1 chr2B.!!$F1 1063
9 TraesCS4B01G050100 chr1B 401562558 401563904 1346 False 1371.000000 1371 85.089000 1 1343 1 chr1B.!!$F1 1342
10 TraesCS4B01G050100 chr6A 608259174 608259698 524 False 680.000000 680 90.114000 820 1343 1 chr6A.!!$F1 523
11 TraesCS4B01G050100 chr4D 26241973 26242691 718 False 210.166667 451 90.318667 1617 2318 3 chr4D.!!$F1 701

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
245 248 0.168128 GCCACTTACGACCACAATGC 59.832 55.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1507 0.027586 GTGGCAACGATAATGCGGTC 59.972 55.0 0.0 0.0 44.75 4.79 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
52 53 6.642707 ATTGTCGTTTCAATTGGGTTTCTA 57.357 33.333 5.42 0.00 34.86 2.10
87 89 3.289836 CAATGGTGCATGGAGGTATGAA 58.710 45.455 0.00 0.00 0.00 2.57
102 104 2.474410 ATGAACGGTTGAGGGAGTTC 57.526 50.000 0.00 0.77 42.19 3.01
203 206 2.681976 CGGAGAAGAGTGGCCAATTCAT 60.682 50.000 22.04 11.41 0.00 2.57
245 248 0.168128 GCCACTTACGACCACAATGC 59.832 55.000 0.00 0.00 0.00 3.56
371 374 0.246635 AGATGTGCGACAGGTACACC 59.753 55.000 0.00 0.00 44.24 4.16
450 453 2.567615 GTGTGGTGTTGAGGTAGAGGAT 59.432 50.000 0.00 0.00 0.00 3.24
501 504 7.986889 ACCCATGCAAGAATTTTATGGATAAAC 59.013 33.333 0.00 0.00 40.52 2.01
524 527 1.375908 GACGAAGATGGCCACTGCA 60.376 57.895 8.16 0.00 40.13 4.41
571 574 2.095461 GAAAAGAATGGCTGGTCTCCC 58.905 52.381 0.00 0.00 0.00 4.30
614 617 2.038659 TGTCCGTGATATGCTCATCCA 58.961 47.619 0.00 0.00 35.97 3.41
615 618 2.433970 TGTCCGTGATATGCTCATCCAA 59.566 45.455 0.00 0.00 35.97 3.53
616 619 3.071457 TGTCCGTGATATGCTCATCCAAT 59.929 43.478 0.00 0.00 35.97 3.16
659 663 4.615588 TGCGTAATGATATGACCCATGA 57.384 40.909 0.00 0.00 0.00 3.07
697 708 1.086634 GCCGTCTACCGTCGAGTACT 61.087 60.000 0.00 0.00 33.66 2.73
713 724 7.405769 GTCGAGTACTTGGATAGTTACTACAC 58.594 42.308 10.33 0.00 38.33 2.90
733 744 4.012374 CACATCCATCAAGTTAGCTGGTT 58.988 43.478 0.00 0.00 0.00 3.67
756 767 5.121811 TGCTTTTCTGCTGAAGATATCCTC 58.878 41.667 6.13 0.00 33.93 3.71
767 778 4.656112 TGAAGATATCCTCAAGGGGAAGAC 59.344 45.833 1.33 0.00 39.02 3.01
921 932 2.108952 GGGGATGGTGCTTAGGAATGAT 59.891 50.000 0.00 0.00 0.00 2.45
957 968 3.067601 TGATGGCCGCGTATCGATATATT 59.932 43.478 8.66 0.00 41.67 1.28
996 1007 0.532115 TCGAAGCTGAGCTACATGCA 59.468 50.000 7.68 0.00 45.94 3.96
1056 1067 2.871216 TTCCGGTGGTCGTGCAAACA 62.871 55.000 0.00 0.00 37.11 2.83
1072 1083 1.722034 AACAGACTCCTCTGAAGCCA 58.278 50.000 4.73 0.00 46.32 4.75
1077 1088 0.908198 ACTCCTCTGAAGCCATGTCC 59.092 55.000 0.00 0.00 0.00 4.02
1106 1117 1.398692 AATGGTGCGTTGGTTCACTT 58.601 45.000 0.00 0.00 33.91 3.16
1107 1118 2.264005 ATGGTGCGTTGGTTCACTTA 57.736 45.000 0.00 0.00 33.91 2.24
1108 1119 2.264005 TGGTGCGTTGGTTCACTTAT 57.736 45.000 0.00 0.00 33.91 1.73
1109 1120 2.577700 TGGTGCGTTGGTTCACTTATT 58.422 42.857 0.00 0.00 33.91 1.40
1112 1123 4.762765 TGGTGCGTTGGTTCACTTATTATT 59.237 37.500 0.00 0.00 33.91 1.40
1127 1138 9.836076 TCACTTATTATTCGGTCATATAGTTCG 57.164 33.333 0.00 0.00 0.00 3.95
1131 1142 4.785511 ATTCGGTCATATAGTTCGGGAG 57.214 45.455 0.00 0.00 0.00 4.30
1137 1148 5.620205 CGGTCATATAGTTCGGGAGATCAAG 60.620 48.000 0.00 0.00 39.57 3.02
1206 1218 2.286418 CCAAAATAGAGTTGCCGATCGC 60.286 50.000 10.32 6.08 38.31 4.58
1227 1239 3.908737 GGCGAAATATAGCCGGTCT 57.091 52.632 1.90 3.10 44.22 3.85
1231 1243 3.128349 GCGAAATATAGCCGGTCTGAAA 58.872 45.455 1.90 0.00 0.00 2.69
1273 1285 3.053768 TGGTTTGGCTCCATCATGTATCA 60.054 43.478 0.00 0.00 0.00 2.15
1309 1321 6.460399 GCCTCTCGACTGTAACTCTATTCATT 60.460 42.308 0.00 0.00 0.00 2.57
1312 1324 6.752351 TCTCGACTGTAACTCTATTCATTTGC 59.248 38.462 0.00 0.00 0.00 3.68
1335 1347 5.442391 CAATAAAACTCCCTTTATCCCCGA 58.558 41.667 0.00 0.00 31.66 5.14
1357 1369 1.892209 AAAAAGTACCCACTCGGCTG 58.108 50.000 0.00 0.00 32.29 4.85
1358 1370 0.605589 AAAAGTACCCACTCGGCTGC 60.606 55.000 0.00 0.00 32.29 5.25
1359 1371 2.781595 AAAGTACCCACTCGGCTGCG 62.782 60.000 0.00 0.00 32.29 5.18
1360 1372 4.065281 GTACCCACTCGGCTGCGT 62.065 66.667 0.00 0.00 33.26 5.24
1361 1373 3.307906 TACCCACTCGGCTGCGTT 61.308 61.111 0.00 0.00 33.26 4.84
1362 1374 3.291101 TACCCACTCGGCTGCGTTC 62.291 63.158 0.00 0.00 33.26 3.95
1363 1375 4.680237 CCCACTCGGCTGCGTTCA 62.680 66.667 0.00 0.00 0.00 3.18
1364 1376 3.114616 CCACTCGGCTGCGTTCAG 61.115 66.667 0.00 0.00 43.16 3.02
1365 1377 2.049156 CACTCGGCTGCGTTCAGA 60.049 61.111 0.00 0.00 42.95 3.27
1366 1378 1.446792 CACTCGGCTGCGTTCAGAT 60.447 57.895 0.00 0.00 42.95 2.90
1367 1379 0.179137 CACTCGGCTGCGTTCAGATA 60.179 55.000 0.00 0.00 42.95 1.98
1368 1380 0.101399 ACTCGGCTGCGTTCAGATAG 59.899 55.000 0.00 0.00 42.95 2.08
1369 1381 0.101399 CTCGGCTGCGTTCAGATAGT 59.899 55.000 0.00 0.00 42.95 2.12
1370 1382 0.179137 TCGGCTGCGTTCAGATAGTG 60.179 55.000 0.00 0.00 42.95 2.74
1371 1383 1.756375 CGGCTGCGTTCAGATAGTGC 61.756 60.000 0.00 0.00 42.95 4.40
1372 1384 1.432270 GGCTGCGTTCAGATAGTGCC 61.432 60.000 0.00 0.00 42.95 5.01
1373 1385 1.432270 GCTGCGTTCAGATAGTGCCC 61.432 60.000 0.00 0.00 42.95 5.36
1374 1386 0.108186 CTGCGTTCAGATAGTGCCCA 60.108 55.000 0.00 0.00 42.95 5.36
1375 1387 0.391130 TGCGTTCAGATAGTGCCCAC 60.391 55.000 0.00 0.00 0.00 4.61
1376 1388 0.108138 GCGTTCAGATAGTGCCCACT 60.108 55.000 6.17 6.17 45.02 4.00
1377 1389 1.927895 CGTTCAGATAGTGCCCACTC 58.072 55.000 3.88 0.00 42.54 3.51
1378 1390 1.799181 CGTTCAGATAGTGCCCACTCG 60.799 57.143 3.88 0.00 42.54 4.18
1379 1391 0.824109 TTCAGATAGTGCCCACTCGG 59.176 55.000 3.88 0.00 42.54 4.63
1391 1403 2.440539 CCACTCGGGTGTATATGCTC 57.559 55.000 15.66 0.00 41.53 4.26
1392 1404 1.964223 CCACTCGGGTGTATATGCTCT 59.036 52.381 15.66 0.00 41.53 4.09
1393 1405 3.154710 CCACTCGGGTGTATATGCTCTA 58.845 50.000 15.66 0.00 41.53 2.43
1394 1406 3.572682 CCACTCGGGTGTATATGCTCTAA 59.427 47.826 15.66 0.00 41.53 2.10
1395 1407 4.547532 CACTCGGGTGTATATGCTCTAAC 58.452 47.826 7.44 0.00 38.54 2.34
1396 1408 3.573110 ACTCGGGTGTATATGCTCTAACC 59.427 47.826 0.00 0.00 0.00 2.85
1397 1409 2.895404 TCGGGTGTATATGCTCTAACCC 59.105 50.000 6.92 6.92 43.23 4.11
1398 1410 2.631062 CGGGTGTATATGCTCTAACCCA 59.369 50.000 14.71 0.00 46.36 4.51
1399 1411 3.070446 CGGGTGTATATGCTCTAACCCAA 59.930 47.826 14.71 0.00 46.36 4.12
1400 1412 4.386711 GGGTGTATATGCTCTAACCCAAC 58.613 47.826 10.94 0.00 45.51 3.77
1401 1413 4.386711 GGTGTATATGCTCTAACCCAACC 58.613 47.826 0.00 0.00 0.00 3.77
1402 1414 4.141574 GGTGTATATGCTCTAACCCAACCA 60.142 45.833 0.00 0.00 0.00 3.67
1403 1415 5.057149 GTGTATATGCTCTAACCCAACCAG 58.943 45.833 0.00 0.00 0.00 4.00
1404 1416 2.710096 TATGCTCTAACCCAACCAGC 57.290 50.000 0.00 0.00 0.00 4.85
1405 1417 0.392998 ATGCTCTAACCCAACCAGCG 60.393 55.000 0.00 0.00 32.43 5.18
1406 1418 1.003718 GCTCTAACCCAACCAGCGT 60.004 57.895 0.00 0.00 0.00 5.07
1407 1419 0.248289 GCTCTAACCCAACCAGCGTA 59.752 55.000 0.00 0.00 0.00 4.42
1408 1420 1.739371 GCTCTAACCCAACCAGCGTAG 60.739 57.143 0.00 0.00 0.00 3.51
1409 1421 0.899720 TCTAACCCAACCAGCGTAGG 59.100 55.000 0.00 0.00 0.00 3.18
1410 1422 0.107848 CTAACCCAACCAGCGTAGGG 60.108 60.000 0.00 0.00 46.96 3.53
1413 1425 1.074248 CCCAACCAGCGTAGGGTTT 59.926 57.895 5.03 0.00 46.19 3.27
1414 1426 0.538746 CCCAACCAGCGTAGGGTTTT 60.539 55.000 5.03 0.00 46.19 2.43
1415 1427 0.596082 CCAACCAGCGTAGGGTTTTG 59.404 55.000 5.03 0.00 46.19 2.44
1416 1428 0.596082 CAACCAGCGTAGGGTTTTGG 59.404 55.000 5.03 0.00 46.19 3.28
1417 1429 0.184211 AACCAGCGTAGGGTTTTGGT 59.816 50.000 2.31 0.00 46.19 3.67
1418 1430 0.536460 ACCAGCGTAGGGTTTTGGTG 60.536 55.000 0.00 0.00 40.47 4.17
1419 1431 0.536460 CCAGCGTAGGGTTTTGGTGT 60.536 55.000 0.00 0.00 0.00 4.16
1420 1432 0.591170 CAGCGTAGGGTTTTGGTGTG 59.409 55.000 0.00 0.00 0.00 3.82
1421 1433 0.470766 AGCGTAGGGTTTTGGTGTGA 59.529 50.000 0.00 0.00 0.00 3.58
1422 1434 0.872388 GCGTAGGGTTTTGGTGTGAG 59.128 55.000 0.00 0.00 0.00 3.51
1423 1435 1.519408 CGTAGGGTTTTGGTGTGAGG 58.481 55.000 0.00 0.00 0.00 3.86
1424 1436 1.202722 CGTAGGGTTTTGGTGTGAGGT 60.203 52.381 0.00 0.00 0.00 3.85
1425 1437 2.227194 GTAGGGTTTTGGTGTGAGGTG 58.773 52.381 0.00 0.00 0.00 4.00
1426 1438 0.755327 AGGGTTTTGGTGTGAGGTGC 60.755 55.000 0.00 0.00 0.00 5.01
1427 1439 0.755327 GGGTTTTGGTGTGAGGTGCT 60.755 55.000 0.00 0.00 0.00 4.40
1428 1440 0.385390 GGTTTTGGTGTGAGGTGCTG 59.615 55.000 0.00 0.00 0.00 4.41
1429 1441 0.249031 GTTTTGGTGTGAGGTGCTGC 60.249 55.000 0.00 0.00 0.00 5.25
1430 1442 1.391157 TTTTGGTGTGAGGTGCTGCC 61.391 55.000 0.00 0.00 37.58 4.85
1431 1443 4.624364 TGGTGTGAGGTGCTGCCG 62.624 66.667 0.00 0.00 43.70 5.69
1443 1455 0.171007 TGCTGCCGCAGATAAAAAGC 59.829 50.000 24.80 7.29 42.25 3.51
1444 1456 0.171007 GCTGCCGCAGATAAAAAGCA 59.829 50.000 24.80 0.00 32.44 3.91
1445 1457 1.402720 GCTGCCGCAGATAAAAAGCAA 60.403 47.619 24.80 0.00 32.44 3.91
1446 1458 2.523015 CTGCCGCAGATAAAAAGCAAG 58.477 47.619 15.74 0.00 32.44 4.01
1447 1459 1.885887 TGCCGCAGATAAAAAGCAAGT 59.114 42.857 0.00 0.00 0.00 3.16
1448 1460 3.078097 TGCCGCAGATAAAAAGCAAGTA 58.922 40.909 0.00 0.00 0.00 2.24
1449 1461 3.119990 TGCCGCAGATAAAAAGCAAGTAC 60.120 43.478 0.00 0.00 0.00 2.73
1450 1462 3.127030 GCCGCAGATAAAAAGCAAGTACT 59.873 43.478 0.00 0.00 0.00 2.73
1451 1463 4.331717 GCCGCAGATAAAAAGCAAGTACTA 59.668 41.667 0.00 0.00 0.00 1.82
1452 1464 5.726963 GCCGCAGATAAAAAGCAAGTACTAC 60.727 44.000 0.00 0.00 0.00 2.73
1453 1465 5.581085 CCGCAGATAAAAAGCAAGTACTACT 59.419 40.000 0.00 0.00 0.00 2.57
1454 1466 6.455646 CCGCAGATAAAAAGCAAGTACTACTG 60.456 42.308 0.00 0.00 0.00 2.74
1455 1467 6.090898 CGCAGATAAAAAGCAAGTACTACTGT 59.909 38.462 0.00 0.00 0.00 3.55
1456 1468 7.274904 CGCAGATAAAAAGCAAGTACTACTGTA 59.725 37.037 0.00 0.00 0.00 2.74
1457 1469 8.381387 GCAGATAAAAAGCAAGTACTACTGTAC 58.619 37.037 0.00 0.00 46.89 2.90
1469 1481 4.382345 ACTACTGTACTACAAATCCGGC 57.618 45.455 0.00 0.00 0.00 6.13
1470 1482 3.765511 ACTACTGTACTACAAATCCGGCA 59.234 43.478 0.00 0.00 0.00 5.69
1471 1483 2.968675 ACTGTACTACAAATCCGGCAC 58.031 47.619 0.00 0.00 0.00 5.01
1472 1484 2.565834 ACTGTACTACAAATCCGGCACT 59.434 45.455 0.00 0.00 0.00 4.40
1473 1485 2.930040 CTGTACTACAAATCCGGCACTG 59.070 50.000 0.00 0.00 0.00 3.66
1474 1486 1.664151 GTACTACAAATCCGGCACTGC 59.336 52.381 0.00 0.00 0.00 4.40
1475 1487 0.676782 ACTACAAATCCGGCACTGCC 60.677 55.000 10.35 10.35 46.75 4.85
1507 1519 1.004918 GGGAGGGACCGCATTATCG 60.005 63.158 0.00 0.00 40.11 2.92
1508 1520 1.746517 GGAGGGACCGCATTATCGT 59.253 57.895 0.00 0.00 0.00 3.73
1509 1521 0.106149 GGAGGGACCGCATTATCGTT 59.894 55.000 0.00 0.00 0.00 3.85
1510 1522 1.217882 GAGGGACCGCATTATCGTTG 58.782 55.000 0.00 0.00 0.00 4.10
1511 1523 0.814010 AGGGACCGCATTATCGTTGC 60.814 55.000 0.00 0.00 36.74 4.17
1512 1524 1.647084 GGACCGCATTATCGTTGCC 59.353 57.895 0.00 0.00 36.75 4.52
1513 1525 1.092921 GGACCGCATTATCGTTGCCA 61.093 55.000 0.00 0.00 36.75 4.92
1514 1526 0.027586 GACCGCATTATCGTTGCCAC 59.972 55.000 0.00 0.00 36.75 5.01
1515 1527 1.355210 CCGCATTATCGTTGCCACC 59.645 57.895 0.00 0.00 36.75 4.61
1516 1528 1.095228 CCGCATTATCGTTGCCACCT 61.095 55.000 0.00 0.00 36.75 4.00
1517 1529 0.732571 CGCATTATCGTTGCCACCTT 59.267 50.000 0.00 0.00 36.75 3.50
1518 1530 1.268032 CGCATTATCGTTGCCACCTTC 60.268 52.381 0.00 0.00 36.75 3.46
1519 1531 1.742831 GCATTATCGTTGCCACCTTCA 59.257 47.619 0.00 0.00 33.95 3.02
1520 1532 2.477863 GCATTATCGTTGCCACCTTCAC 60.478 50.000 0.00 0.00 33.95 3.18
1521 1533 1.434555 TTATCGTTGCCACCTTCACG 58.565 50.000 0.00 0.00 0.00 4.35
1522 1534 0.319083 TATCGTTGCCACCTTCACGT 59.681 50.000 0.00 0.00 0.00 4.49
1523 1535 1.227999 ATCGTTGCCACCTTCACGTG 61.228 55.000 9.94 9.94 0.00 4.49
1524 1536 1.885388 CGTTGCCACCTTCACGTGA 60.885 57.895 15.76 15.76 35.68 4.35
1525 1537 1.433053 CGTTGCCACCTTCACGTGAA 61.433 55.000 28.07 28.07 35.68 3.18
1532 1544 3.972227 CTTCACGTGAAGGCCCAG 58.028 61.111 38.94 21.36 45.79 4.45
1533 1545 2.281484 TTCACGTGAAGGCCCAGC 60.281 61.111 26.53 0.00 0.00 4.85
1534 1546 4.680237 TCACGTGAAGGCCCAGCG 62.680 66.667 17.62 1.51 0.00 5.18
1557 1569 1.006102 GGTGACCACTGACCACTCG 60.006 63.158 0.00 0.00 31.97 4.18
1558 1570 1.664965 GTGACCACTGACCACTCGC 60.665 63.158 0.00 0.00 0.00 5.03
1559 1571 2.430921 GACCACTGACCACTCGCG 60.431 66.667 0.00 0.00 0.00 5.87
1560 1572 2.910479 ACCACTGACCACTCGCGA 60.910 61.111 9.26 9.26 0.00 5.87
1561 1573 2.126307 CCACTGACCACTCGCGAG 60.126 66.667 33.45 33.45 0.00 5.03
1562 1574 2.645567 CACTGACCACTCGCGAGT 59.354 61.111 34.98 34.98 43.61 4.18
1587 1599 3.131478 GGTCGGCCGTTTCATGGG 61.131 66.667 27.15 0.00 0.00 4.00
1588 1600 2.046700 GTCGGCCGTTTCATGGGA 60.047 61.111 27.15 0.00 0.00 4.37
1589 1601 2.046700 TCGGCCGTTTCATGGGAC 60.047 61.111 27.15 0.00 0.00 4.46
1594 1606 4.201951 CGTTTCATGGGACGGAGG 57.798 61.111 12.15 0.00 35.74 4.30
1595 1607 2.106683 CGTTTCATGGGACGGAGGC 61.107 63.158 12.15 0.00 35.74 4.70
1596 1608 1.749258 GTTTCATGGGACGGAGGCC 60.749 63.158 0.00 0.00 0.00 5.19
1597 1609 2.227757 TTTCATGGGACGGAGGCCA 61.228 57.895 5.01 0.00 0.00 5.36
1598 1610 2.478335 TTTCATGGGACGGAGGCCAC 62.478 60.000 5.01 0.00 0.00 5.01
1599 1611 3.402681 CATGGGACGGAGGCCACT 61.403 66.667 5.01 0.00 0.00 4.00
1600 1612 2.610859 ATGGGACGGAGGCCACTT 60.611 61.111 5.01 0.00 0.00 3.16
1601 1613 2.971598 ATGGGACGGAGGCCACTTG 61.972 63.158 5.01 0.00 0.00 3.16
1602 1614 3.637273 GGGACGGAGGCCACTTGT 61.637 66.667 5.01 1.25 0.00 3.16
1603 1615 2.358737 GGACGGAGGCCACTTGTG 60.359 66.667 5.01 0.00 0.00 3.33
1604 1616 3.050275 GACGGAGGCCACTTGTGC 61.050 66.667 5.01 0.00 0.00 4.57
1605 1617 4.988598 ACGGAGGCCACTTGTGCG 62.989 66.667 5.01 2.77 0.00 5.34
1606 1618 4.988598 CGGAGGCCACTTGTGCGT 62.989 66.667 5.01 0.00 0.00 5.24
1607 1619 3.357079 GGAGGCCACTTGTGCGTG 61.357 66.667 5.01 0.00 34.71 5.34
1608 1620 4.030452 GAGGCCACTTGTGCGTGC 62.030 66.667 5.01 0.00 33.60 5.34
1611 1623 2.668212 GCCACTTGTGCGTGCCTA 60.668 61.111 0.00 0.00 33.60 3.93
1612 1624 2.680913 GCCACTTGTGCGTGCCTAG 61.681 63.158 0.00 0.00 33.60 3.02
1613 1625 2.680913 CCACTTGTGCGTGCCTAGC 61.681 63.158 0.00 0.00 33.60 3.42
1614 1626 1.669115 CACTTGTGCGTGCCTAGCT 60.669 57.895 0.00 0.00 35.28 3.32
1615 1627 0.389817 CACTTGTGCGTGCCTAGCTA 60.390 55.000 0.00 0.00 35.28 3.32
1616 1628 0.108615 ACTTGTGCGTGCCTAGCTAG 60.109 55.000 14.20 14.20 35.28 3.42
1617 1629 1.424493 CTTGTGCGTGCCTAGCTAGC 61.424 60.000 15.74 6.62 35.28 3.42
1618 1630 2.586357 GTGCGTGCCTAGCTAGCC 60.586 66.667 15.74 4.78 32.78 3.93
1619 1631 4.207281 TGCGTGCCTAGCTAGCCG 62.207 66.667 15.74 16.29 32.78 5.52
1620 1632 4.208686 GCGTGCCTAGCTAGCCGT 62.209 66.667 15.74 0.00 0.00 5.68
1621 1633 2.842256 GCGTGCCTAGCTAGCCGTA 61.842 63.158 15.74 0.00 0.00 4.02
1622 1634 1.283181 CGTGCCTAGCTAGCCGTAG 59.717 63.158 15.74 7.57 0.00 3.51
1685 1716 3.637273 GGTCTCGCCCACCAACCT 61.637 66.667 0.00 0.00 33.63 3.50
1711 1742 4.041762 CCGGTAGGCTTGGGGCAA 62.042 66.667 0.00 0.00 44.01 4.52
1781 1812 0.317603 CCGTTGCGGTAGGTAGATCG 60.318 60.000 0.00 0.00 42.73 3.69
1815 1846 4.000557 CGGTGCGTGTCAGTGTGC 62.001 66.667 0.00 0.00 0.00 4.57
1834 1865 4.608933 CGCGATCGCTTGCTACTA 57.391 55.556 34.69 0.00 39.32 1.82
1835 1866 2.125664 CGCGATCGCTTGCTACTAC 58.874 57.895 34.69 5.29 39.32 2.73
1836 1867 0.317103 CGCGATCGCTTGCTACTACT 60.317 55.000 34.69 0.00 39.32 2.57
1837 1868 1.124462 GCGATCGCTTGCTACTACTG 58.876 55.000 31.94 0.00 38.26 2.74
1838 1869 1.534175 GCGATCGCTTGCTACTACTGT 60.534 52.381 31.94 0.00 38.26 3.55
1839 1870 2.286831 GCGATCGCTTGCTACTACTGTA 60.287 50.000 31.94 0.00 38.26 2.74
1840 1871 3.289911 CGATCGCTTGCTACTACTGTAC 58.710 50.000 0.26 0.00 0.00 2.90
1841 1872 3.002451 CGATCGCTTGCTACTACTGTACT 59.998 47.826 0.26 0.00 0.00 2.73
1842 1873 4.210746 CGATCGCTTGCTACTACTGTACTA 59.789 45.833 0.26 0.00 0.00 1.82
1843 1874 4.871993 TCGCTTGCTACTACTGTACTAC 57.128 45.455 0.00 0.00 0.00 2.73
1844 1875 3.624861 TCGCTTGCTACTACTGTACTACC 59.375 47.826 0.00 0.00 0.00 3.18
1845 1876 3.626670 CGCTTGCTACTACTGTACTACCT 59.373 47.826 0.00 0.00 0.00 3.08
1846 1877 4.813161 CGCTTGCTACTACTGTACTACCTA 59.187 45.833 0.00 0.00 0.00 3.08
1847 1878 5.277250 CGCTTGCTACTACTGTACTACCTAC 60.277 48.000 0.00 0.00 0.00 3.18
1848 1879 5.277250 GCTTGCTACTACTGTACTACCTACG 60.277 48.000 0.00 0.00 0.00 3.51
1849 1880 5.598416 TGCTACTACTGTACTACCTACGA 57.402 43.478 0.00 0.00 0.00 3.43
1850 1881 6.166984 TGCTACTACTGTACTACCTACGAT 57.833 41.667 0.00 0.00 0.00 3.73
1851 1882 6.219473 TGCTACTACTGTACTACCTACGATC 58.781 44.000 0.00 0.00 0.00 3.69
1852 1883 6.183360 TGCTACTACTGTACTACCTACGATCA 60.183 42.308 0.00 0.00 0.00 2.92
1853 1884 6.873076 GCTACTACTGTACTACCTACGATCAT 59.127 42.308 0.00 0.00 0.00 2.45
1854 1885 7.063308 GCTACTACTGTACTACCTACGATCATC 59.937 44.444 0.00 0.00 0.00 2.92
1855 1886 6.229733 ACTACTGTACTACCTACGATCATCC 58.770 44.000 0.00 0.00 0.00 3.51
1870 1901 1.543802 TCATCCATGTTGTTTTCCCGC 59.456 47.619 0.00 0.00 0.00 6.13
1875 1906 2.029110 CCATGTTGTTTTCCCGCTTGAT 60.029 45.455 0.00 0.00 0.00 2.57
1879 1910 3.500680 TGTTGTTTTCCCGCTTGATAGAC 59.499 43.478 0.00 0.00 0.00 2.59
1902 1933 2.845486 CGACGAGGAAGATGATCGATC 58.155 52.381 18.72 18.72 39.66 3.69
1952 1999 0.317799 TACAAGACTTACGGCGCCAA 59.682 50.000 28.98 13.57 0.00 4.52
1973 2020 1.450312 GCGGTAGCTGAGGTTGCAT 60.450 57.895 0.00 0.00 41.01 3.96
1978 2025 2.158755 GGTAGCTGAGGTTGCATGGTAT 60.159 50.000 0.00 0.00 0.00 2.73
1983 2030 3.748668 GCTGAGGTTGCATGGTATGGTAT 60.749 47.826 0.00 0.00 0.00 2.73
1984 2031 3.817084 CTGAGGTTGCATGGTATGGTATG 59.183 47.826 0.00 0.00 0.00 2.39
2044 2091 0.609662 AGTAAGGCGCCCGAAAGTAA 59.390 50.000 26.15 0.00 0.00 2.24
2052 2099 0.733150 GCCCGAAAGTAACCATCTGC 59.267 55.000 0.00 0.00 0.00 4.26
2084 2131 4.094684 AGCGACGCTATGCTTCAC 57.905 55.556 23.15 0.00 38.57 3.18
2085 2132 1.215382 AGCGACGCTATGCTTCACA 59.785 52.632 23.15 0.00 38.57 3.58
2086 2133 0.803768 AGCGACGCTATGCTTCACAG 60.804 55.000 23.15 0.00 38.57 3.66
2087 2134 1.078759 GCGACGCTATGCTTCACAGT 61.079 55.000 13.73 0.00 0.00 3.55
2088 2135 1.350193 CGACGCTATGCTTCACAGTT 58.650 50.000 0.00 0.00 0.00 3.16
2090 2137 2.337583 GACGCTATGCTTCACAGTTCA 58.662 47.619 0.00 0.00 0.00 3.18
2092 2139 2.068519 CGCTATGCTTCACAGTTCACA 58.931 47.619 0.00 0.00 0.00 3.58
2093 2140 2.159787 CGCTATGCTTCACAGTTCACAC 60.160 50.000 0.00 0.00 0.00 3.82
2094 2141 2.160417 GCTATGCTTCACAGTTCACACC 59.840 50.000 0.00 0.00 0.00 4.16
2096 2143 0.465460 TGCTTCACAGTTCACACCCC 60.465 55.000 0.00 0.00 0.00 4.95
2097 2144 0.179018 GCTTCACAGTTCACACCCCT 60.179 55.000 0.00 0.00 0.00 4.79
2098 2145 1.071699 GCTTCACAGTTCACACCCCTA 59.928 52.381 0.00 0.00 0.00 3.53
2099 2146 2.290323 GCTTCACAGTTCACACCCCTAT 60.290 50.000 0.00 0.00 0.00 2.57
2100 2147 3.055385 GCTTCACAGTTCACACCCCTATA 60.055 47.826 0.00 0.00 0.00 1.31
2101 2148 4.759782 CTTCACAGTTCACACCCCTATAG 58.240 47.826 0.00 0.00 0.00 1.31
2102 2149 3.786553 TCACAGTTCACACCCCTATAGT 58.213 45.455 0.00 0.00 0.00 2.12
2103 2150 4.938028 TCACAGTTCACACCCCTATAGTA 58.062 43.478 0.00 0.00 0.00 1.82
2144 2191 2.022762 CGCGCGCCCATCTAAAAC 59.977 61.111 27.72 0.00 0.00 2.43
2145 2192 2.461110 CGCGCGCCCATCTAAAACT 61.461 57.895 27.72 0.00 0.00 2.66
2147 2194 1.011333 GCGCGCCCATCTAAAACTAA 58.989 50.000 23.24 0.00 0.00 2.24
2148 2195 1.399089 GCGCGCCCATCTAAAACTAAA 59.601 47.619 23.24 0.00 0.00 1.85
2149 2196 2.159490 GCGCGCCCATCTAAAACTAAAA 60.159 45.455 23.24 0.00 0.00 1.52
2150 2197 3.680789 CGCGCCCATCTAAAACTAAAAG 58.319 45.455 0.00 0.00 0.00 2.27
2151 2198 3.435566 GCGCCCATCTAAAACTAAAAGC 58.564 45.455 0.00 0.00 0.00 3.51
2152 2199 3.680789 CGCCCATCTAAAACTAAAAGCG 58.319 45.455 0.00 0.00 0.00 4.68
2196 2261 1.153647 CACGCACGCCTGATCCTAA 60.154 57.895 0.00 0.00 0.00 2.69
2198 2263 0.036765 ACGCACGCCTGATCCTAAAA 60.037 50.000 0.00 0.00 0.00 1.52
2204 2269 4.058817 CACGCCTGATCCTAAAATACTCC 58.941 47.826 0.00 0.00 0.00 3.85
2209 2274 5.305644 GCCTGATCCTAAAATACTCCTCTGA 59.694 44.000 0.00 0.00 0.00 3.27
2210 2275 6.013812 GCCTGATCCTAAAATACTCCTCTGAT 60.014 42.308 0.00 0.00 0.00 2.90
2211 2276 7.179338 GCCTGATCCTAAAATACTCCTCTGATA 59.821 40.741 0.00 0.00 0.00 2.15
2212 2277 9.094578 CCTGATCCTAAAATACTCCTCTGATAA 57.905 37.037 0.00 0.00 0.00 1.75
2278 2364 1.181001 GAGCATACACGAACGAGACG 58.819 55.000 0.14 0.00 0.00 4.18
2279 2365 0.520404 AGCATACACGAACGAGACGT 59.480 50.000 0.14 0.00 43.97 4.34
2280 2366 0.905839 GCATACACGAACGAGACGTC 59.094 55.000 7.70 7.70 39.99 4.34
2281 2367 1.531912 CATACACGAACGAGACGTCC 58.468 55.000 13.01 2.76 39.99 4.79
2282 2368 1.135888 CATACACGAACGAGACGTCCA 60.136 52.381 13.01 0.00 39.99 4.02
2283 2369 0.943673 TACACGAACGAGACGTCCAA 59.056 50.000 13.01 0.00 39.99 3.53
2284 2370 0.101040 ACACGAACGAGACGTCCAAA 59.899 50.000 13.01 0.00 39.99 3.28
2285 2371 1.269413 ACACGAACGAGACGTCCAAAT 60.269 47.619 13.01 0.00 39.99 2.32
2286 2372 1.790623 CACGAACGAGACGTCCAAATT 59.209 47.619 13.01 1.51 39.99 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 6.780031 TGTCATCAAGGAAATTAGAAACCCAA 59.220 34.615 0.00 0.00 0.00 4.12
52 53 4.283978 TGCACCATTGTCATCAAGGAAATT 59.716 37.500 0.00 0.00 37.51 1.82
87 89 2.572290 CAAAAGAACTCCCTCAACCGT 58.428 47.619 0.00 0.00 0.00 4.83
102 104 6.040729 TGTGCACAATATCCATATCCCAAAAG 59.959 38.462 19.28 0.00 0.00 2.27
162 165 1.200020 GGGTGCCAAGACAGAAAATCG 59.800 52.381 0.00 0.00 0.00 3.34
391 394 1.792949 CGTTGACAAGTGTCTGTAGGC 59.207 52.381 12.43 0.00 44.99 3.93
450 453 5.192927 CAGGTTACTAATGCATGGAAGGAA 58.807 41.667 0.00 0.00 0.00 3.36
501 504 1.134580 AGTGGCCATCTTCGTCTCATG 60.135 52.381 9.72 0.00 0.00 3.07
524 527 0.755686 GATGAGAAGCTCGTCCCCAT 59.244 55.000 5.54 0.00 39.75 4.00
614 617 5.683681 ACTGCCAAATCTTCCAAACAAATT 58.316 33.333 0.00 0.00 0.00 1.82
615 618 5.294734 ACTGCCAAATCTTCCAAACAAAT 57.705 34.783 0.00 0.00 0.00 2.32
616 619 4.751767 ACTGCCAAATCTTCCAAACAAA 57.248 36.364 0.00 0.00 0.00 2.83
626 630 3.081061 TCATTACGCAACTGCCAAATCT 58.919 40.909 0.00 0.00 37.91 2.40
697 708 7.669089 TGATGGATGTGTAGTAACTATCCAA 57.331 36.000 8.17 0.00 45.07 3.53
713 724 3.181493 GCAACCAGCTAACTTGATGGATG 60.181 47.826 5.78 5.35 45.53 3.51
733 744 5.108187 AGGATATCTTCAGCAGAAAAGCA 57.892 39.130 2.05 0.00 34.16 3.91
742 753 2.975489 TCCCCTTGAGGATATCTTCAGC 59.025 50.000 16.14 0.00 38.24 4.26
756 767 0.108138 CAGTAGGCGTCTTCCCCTTG 60.108 60.000 0.00 0.00 32.65 3.61
845 856 4.717629 CAACCGAGAGCGCCACGA 62.718 66.667 17.38 0.00 35.83 4.35
921 932 2.443255 GGCCATCAGAATCTCCCCTTTA 59.557 50.000 0.00 0.00 0.00 1.85
957 968 0.736053 GTGGGTCGTTGCAGTGAAAA 59.264 50.000 0.00 0.00 0.00 2.29
996 1007 0.855598 AGGCCATACCCTGCATGATT 59.144 50.000 5.01 0.00 40.58 2.57
1056 1067 1.830477 GACATGGCTTCAGAGGAGTCT 59.170 52.381 0.00 0.00 0.00 3.24
1072 1083 2.559668 CACCATTTGTCAAGCTGGACAT 59.440 45.455 24.53 8.20 46.37 3.06
1077 1088 0.311790 ACGCACCATTTGTCAAGCTG 59.688 50.000 0.00 0.00 0.00 4.24
1106 1117 7.830697 TCTCCCGAACTATATGACCGAATAATA 59.169 37.037 0.00 0.00 0.00 0.98
1107 1118 6.662234 TCTCCCGAACTATATGACCGAATAAT 59.338 38.462 0.00 0.00 0.00 1.28
1108 1119 6.005823 TCTCCCGAACTATATGACCGAATAA 58.994 40.000 0.00 0.00 0.00 1.40
1109 1120 5.563592 TCTCCCGAACTATATGACCGAATA 58.436 41.667 0.00 0.00 0.00 1.75
1112 1123 3.497103 TCTCCCGAACTATATGACCGA 57.503 47.619 0.00 0.00 0.00 4.69
1127 1138 3.970640 ACCAAGTAGATCCTTGATCTCCC 59.029 47.826 9.74 3.38 45.03 4.30
1131 1142 7.455008 TCCCTATTACCAAGTAGATCCTTGATC 59.545 40.741 11.91 0.00 43.65 2.92
1137 1148 6.997942 AACTCCCTATTACCAAGTAGATCC 57.002 41.667 0.00 0.00 0.00 3.36
1173 1185 7.283354 GCAACTCTATTTTGGAGCCTACTAATT 59.717 37.037 0.00 0.00 34.46 1.40
1182 1194 2.356135 TCGGCAACTCTATTTTGGAGC 58.644 47.619 0.00 0.00 34.46 4.70
1185 1197 2.286418 GCGATCGGCAACTCTATTTTGG 60.286 50.000 18.30 0.00 42.87 3.28
1206 1218 0.034896 ACCGGCTATATTTCGCCAGG 59.965 55.000 0.00 12.22 46.62 4.45
1273 1285 0.984230 TCGAGAGGCCAAATGTCCTT 59.016 50.000 5.01 0.00 31.71 3.36
1287 1299 6.752351 GCAAATGAATAGAGTTACAGTCGAGA 59.248 38.462 0.00 0.00 0.00 4.04
1309 1321 5.423931 GGGGATAAAGGGAGTTTTATTGCAA 59.576 40.000 0.00 0.00 34.31 4.08
1312 1324 5.442391 TCGGGGATAAAGGGAGTTTTATTG 58.558 41.667 0.00 0.00 34.31 1.90
1347 1359 2.842394 ATCTGAACGCAGCCGAGTGG 62.842 60.000 0.00 0.00 42.01 4.00
1348 1360 0.179137 TATCTGAACGCAGCCGAGTG 60.179 55.000 0.00 0.00 42.01 3.51
1349 1361 0.101399 CTATCTGAACGCAGCCGAGT 59.899 55.000 0.00 0.00 42.01 4.18
1350 1362 0.101399 ACTATCTGAACGCAGCCGAG 59.899 55.000 0.00 0.00 42.01 4.63
1351 1363 0.179137 CACTATCTGAACGCAGCCGA 60.179 55.000 0.00 0.00 42.01 5.54
1352 1364 1.756375 GCACTATCTGAACGCAGCCG 61.756 60.000 0.00 0.00 42.01 5.52
1353 1365 1.432270 GGCACTATCTGAACGCAGCC 61.432 60.000 0.00 0.00 42.01 4.85
1354 1366 1.432270 GGGCACTATCTGAACGCAGC 61.432 60.000 0.00 0.00 42.01 5.25
1355 1367 0.108186 TGGGCACTATCTGAACGCAG 60.108 55.000 0.00 0.00 43.67 5.18
1356 1368 0.391130 GTGGGCACTATCTGAACGCA 60.391 55.000 0.00 0.00 0.00 5.24
1357 1369 0.108138 AGTGGGCACTATCTGAACGC 60.108 55.000 0.00 0.00 40.43 4.84
1358 1370 1.799181 CGAGTGGGCACTATCTGAACG 60.799 57.143 0.00 0.00 42.66 3.95
1359 1371 1.471676 CCGAGTGGGCACTATCTGAAC 60.472 57.143 0.00 0.00 42.66 3.18
1360 1372 0.824109 CCGAGTGGGCACTATCTGAA 59.176 55.000 0.00 0.00 42.66 3.02
1361 1373 2.504920 CCGAGTGGGCACTATCTGA 58.495 57.895 0.00 0.00 42.66 3.27
1374 1386 3.573110 GGTTAGAGCATATACACCCGAGT 59.427 47.826 0.00 0.00 0.00 4.18
1375 1387 3.056749 GGGTTAGAGCATATACACCCGAG 60.057 52.174 0.00 0.00 34.76 4.63
1376 1388 2.895404 GGGTTAGAGCATATACACCCGA 59.105 50.000 0.00 0.00 34.76 5.14
1377 1389 2.631062 TGGGTTAGAGCATATACACCCG 59.369 50.000 0.00 0.00 46.13 5.28
1378 1390 4.386711 GTTGGGTTAGAGCATATACACCC 58.613 47.826 0.00 0.00 43.80 4.61
1379 1391 4.141574 TGGTTGGGTTAGAGCATATACACC 60.142 45.833 0.00 0.00 0.00 4.16
1380 1392 5.031066 TGGTTGGGTTAGAGCATATACAC 57.969 43.478 0.00 0.00 0.00 2.90
1381 1393 4.444306 GCTGGTTGGGTTAGAGCATATACA 60.444 45.833 0.00 0.00 0.00 2.29
1382 1394 4.065789 GCTGGTTGGGTTAGAGCATATAC 58.934 47.826 0.00 0.00 0.00 1.47
1383 1395 3.244078 CGCTGGTTGGGTTAGAGCATATA 60.244 47.826 0.00 0.00 0.00 0.86
1384 1396 2.485479 CGCTGGTTGGGTTAGAGCATAT 60.485 50.000 0.00 0.00 0.00 1.78
1385 1397 1.134521 CGCTGGTTGGGTTAGAGCATA 60.135 52.381 0.00 0.00 0.00 3.14
1386 1398 0.392998 CGCTGGTTGGGTTAGAGCAT 60.393 55.000 0.00 0.00 0.00 3.79
1387 1399 1.003839 CGCTGGTTGGGTTAGAGCA 60.004 57.895 0.00 0.00 0.00 4.26
1388 1400 0.248289 TACGCTGGTTGGGTTAGAGC 59.752 55.000 0.00 0.00 42.13 4.09
1389 1401 1.134788 CCTACGCTGGTTGGGTTAGAG 60.135 57.143 0.00 0.00 42.13 2.43
1390 1402 0.899720 CCTACGCTGGTTGGGTTAGA 59.100 55.000 0.00 0.00 42.13 2.10
1391 1403 3.453559 CCTACGCTGGTTGGGTTAG 57.546 57.895 0.00 0.00 42.13 2.34
1396 1408 0.596082 CAAAACCCTACGCTGGTTGG 59.404 55.000 4.79 0.00 45.23 3.77
1397 1409 0.596082 CCAAAACCCTACGCTGGTTG 59.404 55.000 4.79 0.00 45.23 3.77
1399 1411 0.536460 CACCAAAACCCTACGCTGGT 60.536 55.000 0.00 0.00 41.08 4.00
1400 1412 0.536460 ACACCAAAACCCTACGCTGG 60.536 55.000 0.00 0.00 0.00 4.85
1401 1413 0.591170 CACACCAAAACCCTACGCTG 59.409 55.000 0.00 0.00 0.00 5.18
1402 1414 0.470766 TCACACCAAAACCCTACGCT 59.529 50.000 0.00 0.00 0.00 5.07
1403 1415 0.872388 CTCACACCAAAACCCTACGC 59.128 55.000 0.00 0.00 0.00 4.42
1404 1416 1.202722 ACCTCACACCAAAACCCTACG 60.203 52.381 0.00 0.00 0.00 3.51
1405 1417 2.227194 CACCTCACACCAAAACCCTAC 58.773 52.381 0.00 0.00 0.00 3.18
1406 1418 1.477923 GCACCTCACACCAAAACCCTA 60.478 52.381 0.00 0.00 0.00 3.53
1407 1419 0.755327 GCACCTCACACCAAAACCCT 60.755 55.000 0.00 0.00 0.00 4.34
1408 1420 0.755327 AGCACCTCACACCAAAACCC 60.755 55.000 0.00 0.00 0.00 4.11
1409 1421 0.385390 CAGCACCTCACACCAAAACC 59.615 55.000 0.00 0.00 0.00 3.27
1410 1422 0.249031 GCAGCACCTCACACCAAAAC 60.249 55.000 0.00 0.00 0.00 2.43
1411 1423 1.391157 GGCAGCACCTCACACCAAAA 61.391 55.000 0.00 0.00 34.51 2.44
1412 1424 1.827789 GGCAGCACCTCACACCAAA 60.828 57.895 0.00 0.00 34.51 3.28
1413 1425 2.203337 GGCAGCACCTCACACCAA 60.203 61.111 0.00 0.00 34.51 3.67
1414 1426 4.624364 CGGCAGCACCTCACACCA 62.624 66.667 0.00 0.00 35.61 4.17
1425 1437 0.171007 TGCTTTTTATCTGCGGCAGC 59.829 50.000 24.78 12.04 45.41 5.25
1426 1438 2.095059 ACTTGCTTTTTATCTGCGGCAG 60.095 45.455 23.72 23.72 0.00 4.85
1427 1439 1.885887 ACTTGCTTTTTATCTGCGGCA 59.114 42.857 1.29 1.29 0.00 5.69
1428 1440 2.636768 ACTTGCTTTTTATCTGCGGC 57.363 45.000 0.00 0.00 0.00 6.53
1429 1441 4.946784 AGTACTTGCTTTTTATCTGCGG 57.053 40.909 0.00 0.00 0.00 5.69
1430 1442 6.090898 ACAGTAGTACTTGCTTTTTATCTGCG 59.909 38.462 0.00 0.00 0.00 5.18
1431 1443 7.365840 ACAGTAGTACTTGCTTTTTATCTGC 57.634 36.000 0.00 0.00 0.00 4.26
1447 1459 4.949238 TGCCGGATTTGTAGTACAGTAGTA 59.051 41.667 5.05 0.00 0.00 1.82
1448 1460 3.765511 TGCCGGATTTGTAGTACAGTAGT 59.234 43.478 5.05 0.00 0.00 2.73
1449 1461 4.110482 GTGCCGGATTTGTAGTACAGTAG 58.890 47.826 5.05 0.00 0.00 2.57
1450 1462 3.765511 AGTGCCGGATTTGTAGTACAGTA 59.234 43.478 5.05 0.00 0.00 2.74
1451 1463 2.565834 AGTGCCGGATTTGTAGTACAGT 59.434 45.455 5.05 0.00 0.00 3.55
1452 1464 2.930040 CAGTGCCGGATTTGTAGTACAG 59.070 50.000 5.05 0.00 0.00 2.74
1453 1465 2.933492 GCAGTGCCGGATTTGTAGTACA 60.933 50.000 5.05 0.00 0.00 2.90
1454 1466 1.664151 GCAGTGCCGGATTTGTAGTAC 59.336 52.381 5.05 0.00 0.00 2.73
1455 1467 1.406341 GGCAGTGCCGGATTTGTAGTA 60.406 52.381 20.55 0.00 39.62 1.82
1456 1468 0.676782 GGCAGTGCCGGATTTGTAGT 60.677 55.000 20.55 0.00 39.62 2.73
1457 1469 2.098293 GGCAGTGCCGGATTTGTAG 58.902 57.895 20.55 0.00 39.62 2.74
1458 1470 4.312052 GGCAGTGCCGGATTTGTA 57.688 55.556 20.55 0.00 39.62 2.41
1489 1501 1.004918 CGATAATGCGGTCCCTCCC 60.005 63.158 0.00 0.00 0.00 4.30
1490 1502 0.106149 AACGATAATGCGGTCCCTCC 59.894 55.000 0.00 0.00 35.12 4.30
1491 1503 1.217882 CAACGATAATGCGGTCCCTC 58.782 55.000 0.00 0.00 35.12 4.30
1492 1504 0.814010 GCAACGATAATGCGGTCCCT 60.814 55.000 0.00 0.00 33.57 4.20
1493 1505 1.647084 GCAACGATAATGCGGTCCC 59.353 57.895 0.00 0.00 33.57 4.46
1494 1506 1.092921 TGGCAACGATAATGCGGTCC 61.093 55.000 0.00 0.00 44.75 4.46
1495 1507 0.027586 GTGGCAACGATAATGCGGTC 59.972 55.000 0.00 0.00 44.75 4.79
1496 1508 1.373590 GGTGGCAACGATAATGCGGT 61.374 55.000 0.00 0.00 44.75 5.68
1497 1509 1.095228 AGGTGGCAACGATAATGCGG 61.095 55.000 0.00 0.00 44.75 5.69
1498 1510 0.732571 AAGGTGGCAACGATAATGCG 59.267 50.000 0.00 0.00 44.75 4.73
1499 1511 1.742831 TGAAGGTGGCAACGATAATGC 59.257 47.619 0.00 0.00 43.08 3.56
1500 1512 2.223021 CGTGAAGGTGGCAACGATAATG 60.223 50.000 2.64 0.00 42.51 1.90
1501 1513 2.006888 CGTGAAGGTGGCAACGATAAT 58.993 47.619 2.64 0.00 42.51 1.28
1502 1514 1.270412 ACGTGAAGGTGGCAACGATAA 60.270 47.619 14.84 0.00 42.51 1.75
1503 1515 0.319083 ACGTGAAGGTGGCAACGATA 59.681 50.000 14.84 0.00 42.51 2.92
1504 1516 1.070786 ACGTGAAGGTGGCAACGAT 59.929 52.632 14.84 0.00 42.51 3.73
1505 1517 1.885388 CACGTGAAGGTGGCAACGA 60.885 57.895 10.90 0.00 42.51 3.85
1506 1518 1.433053 TTCACGTGAAGGTGGCAACG 61.433 55.000 26.53 7.08 38.46 4.10
1507 1519 0.307760 CTTCACGTGAAGGTGGCAAC 59.692 55.000 38.94 0.00 45.79 4.17
1508 1520 2.701587 CTTCACGTGAAGGTGGCAA 58.298 52.632 38.94 15.07 45.79 4.52
1509 1521 4.454948 CTTCACGTGAAGGTGGCA 57.545 55.556 38.94 15.76 45.79 4.92
1516 1528 2.281484 GCTGGGCCTTCACGTGAA 60.281 61.111 28.07 28.07 0.00 3.18
1517 1529 4.680237 CGCTGGGCCTTCACGTGA 62.680 66.667 15.76 15.76 0.00 4.35
1536 1548 3.936203 TGGTCAGTGGTCACCCGC 61.936 66.667 0.00 0.00 41.87 6.13
1537 1549 2.030562 GTGGTCAGTGGTCACCCG 59.969 66.667 0.00 0.00 0.00 5.28
1538 1550 1.371558 GAGTGGTCAGTGGTCACCC 59.628 63.158 11.37 0.00 32.29 4.61
1539 1551 1.006102 CGAGTGGTCAGTGGTCACC 60.006 63.158 11.37 0.00 32.29 4.02
1540 1552 1.664965 GCGAGTGGTCAGTGGTCAC 60.665 63.158 8.17 8.17 0.00 3.67
1541 1553 2.734591 GCGAGTGGTCAGTGGTCA 59.265 61.111 0.00 0.00 0.00 4.02
1542 1554 2.430921 CGCGAGTGGTCAGTGGTC 60.431 66.667 0.00 0.00 0.00 4.02
1543 1555 2.910479 TCGCGAGTGGTCAGTGGT 60.910 61.111 3.71 0.00 0.00 4.16
1544 1556 2.126307 CTCGCGAGTGGTCAGTGG 60.126 66.667 27.79 0.00 0.00 4.00
1545 1557 2.645567 ACTCGCGAGTGGTCAGTG 59.354 61.111 38.89 12.87 40.75 3.66
1570 1582 3.131478 CCCATGAAACGGCCGACC 61.131 66.667 35.90 19.94 0.00 4.79
1571 1583 2.046700 TCCCATGAAACGGCCGAC 60.047 61.111 35.90 22.05 0.00 4.79
1572 1584 2.046700 GTCCCATGAAACGGCCGA 60.047 61.111 35.90 10.13 0.00 5.54
1573 1585 3.496131 CGTCCCATGAAACGGCCG 61.496 66.667 26.86 26.86 35.32 6.13
1577 1589 2.106683 GCCTCCGTCCCATGAAACG 61.107 63.158 11.48 11.48 38.58 3.60
1578 1590 1.749258 GGCCTCCGTCCCATGAAAC 60.749 63.158 0.00 0.00 0.00 2.78
1579 1591 2.227757 TGGCCTCCGTCCCATGAAA 61.228 57.895 3.32 0.00 0.00 2.69
1580 1592 2.609299 TGGCCTCCGTCCCATGAA 60.609 61.111 3.32 0.00 0.00 2.57
1581 1593 3.399181 GTGGCCTCCGTCCCATGA 61.399 66.667 3.32 0.00 32.95 3.07
1582 1594 2.971598 AAGTGGCCTCCGTCCCATG 61.972 63.158 3.32 0.00 32.95 3.66
1583 1595 2.610859 AAGTGGCCTCCGTCCCAT 60.611 61.111 3.32 0.00 32.95 4.00
1584 1596 3.636231 CAAGTGGCCTCCGTCCCA 61.636 66.667 3.32 0.00 0.00 4.37
1585 1597 3.637273 ACAAGTGGCCTCCGTCCC 61.637 66.667 3.32 0.00 0.00 4.46
1586 1598 2.358737 CACAAGTGGCCTCCGTCC 60.359 66.667 3.32 0.00 0.00 4.79
1587 1599 3.050275 GCACAAGTGGCCTCCGTC 61.050 66.667 3.32 0.00 0.00 4.79
1588 1600 4.988598 CGCACAAGTGGCCTCCGT 62.989 66.667 3.32 0.00 0.00 4.69
1589 1601 4.988598 ACGCACAAGTGGCCTCCG 62.989 66.667 3.32 1.17 0.00 4.63
1590 1602 3.357079 CACGCACAAGTGGCCTCC 61.357 66.667 3.32 0.00 38.40 4.30
1591 1603 4.030452 GCACGCACAAGTGGCCTC 62.030 66.667 3.32 0.00 42.09 4.70
1595 1607 2.680913 GCTAGGCACGCACAAGTGG 61.681 63.158 2.00 0.00 42.09 4.00
1596 1608 0.389817 TAGCTAGGCACGCACAAGTG 60.390 55.000 0.00 0.00 44.47 3.16
1597 1609 0.108615 CTAGCTAGGCACGCACAAGT 60.109 55.000 13.32 0.00 0.00 3.16
1598 1610 1.424493 GCTAGCTAGGCACGCACAAG 61.424 60.000 22.10 0.00 0.00 3.16
1599 1611 1.447838 GCTAGCTAGGCACGCACAA 60.448 57.895 22.10 0.00 0.00 3.33
1600 1612 2.184322 GCTAGCTAGGCACGCACA 59.816 61.111 22.10 0.00 0.00 4.57
1601 1613 2.586357 GGCTAGCTAGGCACGCAC 60.586 66.667 35.27 12.28 46.94 5.34
1607 1619 2.651945 GGCTACGGCTAGCTAGGC 59.348 66.667 31.90 31.90 44.46 3.93
1608 1620 0.604780 TACGGCTACGGCTAGCTAGG 60.605 60.000 22.10 9.03 44.46 3.02
1609 1621 0.797542 CTACGGCTACGGCTAGCTAG 59.202 60.000 16.84 16.84 44.46 3.42
1610 1622 0.107456 ACTACGGCTACGGCTAGCTA 59.893 55.000 15.72 0.00 44.46 3.32
1611 1623 0.107456 TACTACGGCTACGGCTAGCT 59.893 55.000 15.72 0.00 44.46 3.32
1612 1624 0.516439 CTACTACGGCTACGGCTAGC 59.484 60.000 6.04 6.04 46.48 3.42
1613 1625 1.797635 GTCTACTACGGCTACGGCTAG 59.202 57.143 0.00 0.00 46.48 3.42
1614 1626 1.871080 GTCTACTACGGCTACGGCTA 58.129 55.000 0.00 0.00 46.48 3.93
1615 1627 2.700329 GTCTACTACGGCTACGGCT 58.300 57.895 0.00 0.00 46.48 5.52
1718 1749 1.820581 CAGGAAATGCCATGCCCAG 59.179 57.895 0.00 0.00 40.02 4.45
1798 1829 4.000557 GCACACTGACACGCACCG 62.001 66.667 0.00 0.00 0.00 4.94
1825 1856 6.045318 TCGTAGGTAGTACAGTAGTAGCAAG 58.955 44.000 21.52 13.89 35.18 4.01
1827 1858 5.598416 TCGTAGGTAGTACAGTAGTAGCA 57.402 43.478 21.52 9.04 35.18 3.49
1828 1859 6.219473 TGATCGTAGGTAGTACAGTAGTAGC 58.781 44.000 14.51 14.51 33.42 3.58
1829 1860 7.545265 GGATGATCGTAGGTAGTACAGTAGTAG 59.455 44.444 2.06 0.00 0.00 2.57
1830 1861 7.015584 TGGATGATCGTAGGTAGTACAGTAGTA 59.984 40.741 2.06 0.00 0.00 1.82
1831 1862 6.183361 TGGATGATCGTAGGTAGTACAGTAGT 60.183 42.308 2.06 0.00 0.00 2.73
1832 1863 6.228995 TGGATGATCGTAGGTAGTACAGTAG 58.771 44.000 2.06 0.00 0.00 2.57
1833 1864 6.178607 TGGATGATCGTAGGTAGTACAGTA 57.821 41.667 2.06 0.00 0.00 2.74
1834 1865 5.045012 TGGATGATCGTAGGTAGTACAGT 57.955 43.478 2.06 0.00 0.00 3.55
1835 1866 5.473846 ACATGGATGATCGTAGGTAGTACAG 59.526 44.000 2.06 0.00 0.00 2.74
1836 1867 5.382616 ACATGGATGATCGTAGGTAGTACA 58.617 41.667 2.06 0.00 0.00 2.90
1837 1868 5.961396 ACATGGATGATCGTAGGTAGTAC 57.039 43.478 0.00 0.00 0.00 2.73
1838 1869 5.831525 ACAACATGGATGATCGTAGGTAGTA 59.168 40.000 7.66 0.00 0.00 1.82
1839 1870 4.649674 ACAACATGGATGATCGTAGGTAGT 59.350 41.667 7.66 0.00 0.00 2.73
1840 1871 5.201713 ACAACATGGATGATCGTAGGTAG 57.798 43.478 7.66 0.00 0.00 3.18
1841 1872 5.607939 AACAACATGGATGATCGTAGGTA 57.392 39.130 7.66 0.00 0.00 3.08
1842 1873 4.487714 AACAACATGGATGATCGTAGGT 57.512 40.909 7.66 0.00 0.00 3.08
1843 1874 5.220854 GGAAAACAACATGGATGATCGTAGG 60.221 44.000 7.66 0.00 0.00 3.18
1844 1875 5.220854 GGGAAAACAACATGGATGATCGTAG 60.221 44.000 7.66 0.00 0.00 3.51
1845 1876 4.638421 GGGAAAACAACATGGATGATCGTA 59.362 41.667 7.66 0.00 0.00 3.43
1846 1877 3.443681 GGGAAAACAACATGGATGATCGT 59.556 43.478 7.66 0.00 0.00 3.73
1847 1878 3.487376 CGGGAAAACAACATGGATGATCG 60.487 47.826 7.66 0.00 0.00 3.69
1848 1879 3.734902 GCGGGAAAACAACATGGATGATC 60.735 47.826 7.66 0.00 0.00 2.92
1849 1880 2.166254 GCGGGAAAACAACATGGATGAT 59.834 45.455 7.66 0.00 0.00 2.45
1850 1881 1.543802 GCGGGAAAACAACATGGATGA 59.456 47.619 7.66 0.00 0.00 2.92
1851 1882 1.545582 AGCGGGAAAACAACATGGATG 59.454 47.619 0.00 0.00 0.00 3.51
1852 1883 1.923356 AGCGGGAAAACAACATGGAT 58.077 45.000 0.00 0.00 0.00 3.41
1853 1884 1.339610 CAAGCGGGAAAACAACATGGA 59.660 47.619 0.00 0.00 0.00 3.41
1854 1885 1.339610 TCAAGCGGGAAAACAACATGG 59.660 47.619 0.00 0.00 0.00 3.66
1855 1886 2.791383 TCAAGCGGGAAAACAACATG 57.209 45.000 0.00 0.00 0.00 3.21
1870 1901 1.671328 TCCTCGTCGCTGTCTATCAAG 59.329 52.381 0.00 0.00 0.00 3.02
1875 1906 1.671328 CATCTTCCTCGTCGCTGTCTA 59.329 52.381 0.00 0.00 0.00 2.59
1879 1910 1.764851 GATCATCTTCCTCGTCGCTG 58.235 55.000 0.00 0.00 0.00 5.18
1952 1999 2.995574 AACCTCAGCTACCGCCGT 60.996 61.111 0.00 0.00 36.60 5.68
2016 2063 2.937799 CGGGCGCCTTACTTAAAATACA 59.062 45.455 28.56 0.00 0.00 2.29
2082 2129 4.441634 GCTACTATAGGGGTGTGAACTGTG 60.442 50.000 4.43 0.00 0.00 3.66
2084 2131 3.961408 AGCTACTATAGGGGTGTGAACTG 59.039 47.826 4.43 0.00 0.00 3.16
2085 2132 4.267341 AGCTACTATAGGGGTGTGAACT 57.733 45.455 4.43 0.00 0.00 3.01
2086 2133 5.383476 TCTAGCTACTATAGGGGTGTGAAC 58.617 45.833 4.43 0.00 0.00 3.18
2087 2134 5.133999 ACTCTAGCTACTATAGGGGTGTGAA 59.866 44.000 4.43 0.00 0.00 3.18
2088 2135 4.664064 ACTCTAGCTACTATAGGGGTGTGA 59.336 45.833 4.43 5.12 0.00 3.58
2090 2137 6.090186 TCTACTCTAGCTACTATAGGGGTGT 58.910 44.000 4.43 0.57 0.00 4.16
2092 2139 6.214005 CACTCTACTCTAGCTACTATAGGGGT 59.786 46.154 4.43 4.97 0.00 4.95
2093 2140 6.646267 CACTCTACTCTAGCTACTATAGGGG 58.354 48.000 4.43 0.00 0.00 4.79
2094 2141 6.110707 GCACTCTACTCTAGCTACTATAGGG 58.889 48.000 4.43 0.00 0.00 3.53
2096 2143 8.500773 GTTTGCACTCTACTCTAGCTACTATAG 58.499 40.741 0.00 0.00 0.00 1.31
2097 2144 7.171167 CGTTTGCACTCTACTCTAGCTACTATA 59.829 40.741 0.00 0.00 0.00 1.31
2098 2145 6.017770 CGTTTGCACTCTACTCTAGCTACTAT 60.018 42.308 0.00 0.00 0.00 2.12
2099 2146 5.293814 CGTTTGCACTCTACTCTAGCTACTA 59.706 44.000 0.00 0.00 0.00 1.82
2100 2147 4.095185 CGTTTGCACTCTACTCTAGCTACT 59.905 45.833 0.00 0.00 0.00 2.57
2101 2148 4.094590 TCGTTTGCACTCTACTCTAGCTAC 59.905 45.833 0.00 0.00 0.00 3.58
2102 2149 4.259356 TCGTTTGCACTCTACTCTAGCTA 58.741 43.478 0.00 0.00 0.00 3.32
2103 2150 3.082548 TCGTTTGCACTCTACTCTAGCT 58.917 45.455 0.00 0.00 0.00 3.32
2151 2198 1.896193 GTTTATGCGCGTTTTCACTCG 59.104 47.619 7.78 0.00 0.00 4.18
2152 2199 2.239201 GGTTTATGCGCGTTTTCACTC 58.761 47.619 7.78 0.00 0.00 3.51
2214 2279 8.662141 GCCCGTTGATCGTGTATTATTATTATT 58.338 33.333 0.00 0.00 37.94 1.40
2263 2349 1.159285 TGGACGTCTCGTTCGTGTAT 58.841 50.000 16.46 0.00 41.37 2.29
2278 2364 3.242518 GAGCGGCTTTGTTAATTTGGAC 58.757 45.455 2.97 0.00 0.00 4.02
2279 2365 2.095466 CGAGCGGCTTTGTTAATTTGGA 60.095 45.455 2.97 0.00 0.00 3.53
2280 2366 2.250188 CGAGCGGCTTTGTTAATTTGG 58.750 47.619 2.97 0.00 0.00 3.28
2281 2367 1.648681 GCGAGCGGCTTTGTTAATTTG 59.351 47.619 2.97 0.00 39.11 2.32
2282 2368 1.268352 TGCGAGCGGCTTTGTTAATTT 59.732 42.857 2.97 0.00 44.05 1.82
2283 2369 0.878416 TGCGAGCGGCTTTGTTAATT 59.122 45.000 2.97 0.00 44.05 1.40
2284 2370 0.878416 TTGCGAGCGGCTTTGTTAAT 59.122 45.000 2.97 0.00 44.05 1.40
2285 2371 0.040781 GTTGCGAGCGGCTTTGTTAA 60.041 50.000 2.97 0.00 44.05 2.01
2286 2372 1.572447 GTTGCGAGCGGCTTTGTTA 59.428 52.632 2.97 0.00 44.05 2.41


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

AutoCloner maintained by Alex Coulton.