Multiple sequence alignment - TraesCS2D01G415200

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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 TraesCS2D01G415200 chr2D 100.000 2318 0 0 1 2318 529030751 529033068 0.000000e+00 4281.0
1 TraesCS2D01G415200 chr6B 95.985 1345 52 2 1 1344 567628563 567629906 0.000000e+00 2183.0
2 TraesCS2D01G415200 chr3A 88.608 1343 151 1 1 1343 423542637 423541297 0.000000e+00 1631.0
3 TraesCS2D01G415200 chr2B 87.302 1323 162 5 1 1321 141160375 141159057 0.000000e+00 1507.0
4 TraesCS2D01G415200 chr2B 75.000 912 210 15 441 1343 478161568 478160666 2.770000e-109 405.0
5 TraesCS2D01G415200 chr2B 80.514 467 85 6 880 1343 736792226 736791763 1.020000e-93 353.0
6 TraesCS2D01G415200 chr2B 94.815 135 7 0 1373 1507 628379557 628379691 6.490000e-51 211.0
7 TraesCS2D01G415200 chr2A 91.387 476 40 1 1843 2318 673954676 673955150 0.000000e+00 651.0
8 TraesCS2D01G415200 chr2A 91.387 476 33 3 1843 2318 673516058 673516525 0.000000e+00 645.0
9 TraesCS2D01G415200 chr2A 86.364 242 24 4 1602 1841 673515769 673516003 2.960000e-64 255.0
10 TraesCS2D01G415200 chr3D 75.314 1353 304 25 5 1343 32309598 32310934 2.530000e-174 621.0
11 TraesCS2D01G415200 chr3D 75.115 1306 293 26 47 1343 68330948 68329666 1.190000e-162 582.0
12 TraesCS2D01G415200 chr1B 84.137 643 80 8 705 1343 584796467 584797091 9.160000e-169 603.0
13 TraesCS2D01G415200 chr4D 76.112 967 214 15 386 1343 464148958 464148000 7.440000e-135 490.0
14 TraesCS2D01G415200 chr1A 89.062 64 2 2 1382 1445 14127472 14127414 8.880000e-10 75.0
15 TraesCS2D01G415200 chr5B 88.525 61 5 2 1366 1426 256951431 256951489 3.190000e-09 73.1


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 TraesCS2D01G415200 chr2D 529030751 529033068 2317 False 4281 4281 100.0000 1 2318 1 chr2D.!!$F1 2317
1 TraesCS2D01G415200 chr6B 567628563 567629906 1343 False 2183 2183 95.9850 1 1344 1 chr6B.!!$F1 1343
2 TraesCS2D01G415200 chr3A 423541297 423542637 1340 True 1631 1631 88.6080 1 1343 1 chr3A.!!$R1 1342
3 TraesCS2D01G415200 chr2B 141159057 141160375 1318 True 1507 1507 87.3020 1 1321 1 chr2B.!!$R1 1320
4 TraesCS2D01G415200 chr2B 478160666 478161568 902 True 405 405 75.0000 441 1343 1 chr2B.!!$R2 902
5 TraesCS2D01G415200 chr2A 673515769 673516525 756 False 450 645 88.8755 1602 2318 2 chr2A.!!$F2 716
6 TraesCS2D01G415200 chr3D 32309598 32310934 1336 False 621 621 75.3140 5 1343 1 chr3D.!!$F1 1338
7 TraesCS2D01G415200 chr3D 68329666 68330948 1282 True 582 582 75.1150 47 1343 1 chr3D.!!$R1 1296
8 TraesCS2D01G415200 chr1B 584796467 584797091 624 False 603 603 84.1370 705 1343 1 chr1B.!!$F1 638
9 TraesCS2D01G415200 chr4D 464148000 464148958 958 True 490 490 76.1120 386 1343 1 chr4D.!!$R1 957

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
633 636 0.317799 TGCTGATTTGGCGCATTTGT 59.682 45.0 10.83 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1576 1582 0.033601 ACACAACTTTGGCACCCTCA 60.034 50.0 0.0 0.0 0.0 3.86 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
50 51 2.210116 CTGCAGACTAAACCGTGTTGT 58.790 47.619 8.42 0.00 0.00 3.32
69 70 8.914654 CGTGTTGTTGATTTTATTGATGACAAT 58.085 29.630 0.00 0.00 46.64 2.71
79 80 2.219080 TGATGACAATGGTGCATGGT 57.781 45.000 0.00 0.00 29.58 3.55
90 91 0.742281 GTGCATGGTGAGCTGATCGT 60.742 55.000 0.00 0.00 0.00 3.73
540 543 2.036475 GCTCCCAAGCGATGATCTTCTA 59.964 50.000 6.99 0.00 39.10 2.10
633 636 0.317799 TGCTGATTTGGCGCATTTGT 59.682 45.000 10.83 0.00 0.00 2.83
649 652 5.225743 CGCATTTGTCACATTCGTAATGAAG 59.774 40.000 12.53 6.55 41.46 3.02
963 969 5.940603 CGGCTTATCGCTATATCTTTCAG 57.059 43.478 0.00 0.00 39.13 3.02
1151 1157 5.360144 TGGAGATTCTACACTTAGCTGGTAC 59.640 44.000 0.00 0.00 0.00 3.34
1275 1281 0.597637 CGGCTCCACCATGTATCGAC 60.598 60.000 0.00 0.00 39.03 4.20
1370 1376 9.325198 ACAATTCCTATTTTCAAAAGGTTTCAC 57.675 29.630 0.00 0.00 0.00 3.18
1371 1377 9.546428 CAATTCCTATTTTCAAAAGGTTTCACT 57.454 29.630 0.00 0.00 0.00 3.41
1375 1381 9.952030 TCCTATTTTCAAAAGGTTTCACTTTTT 57.048 25.926 1.52 0.00 45.61 1.94
1418 1424 7.852971 ATTATTTTCAAATCAGGTGCAATGG 57.147 32.000 0.00 0.00 0.00 3.16
1419 1425 3.681593 TTTCAAATCAGGTGCAATGGG 57.318 42.857 0.00 0.00 0.00 4.00
1420 1426 2.601240 TCAAATCAGGTGCAATGGGA 57.399 45.000 0.00 0.00 0.00 4.37
1421 1427 2.170166 TCAAATCAGGTGCAATGGGAC 58.830 47.619 0.00 0.00 34.10 4.46
1427 1433 2.668632 GTGCAATGGGACCCGAGA 59.331 61.111 5.91 0.00 0.00 4.04
1428 1434 1.745489 GTGCAATGGGACCCGAGAC 60.745 63.158 5.91 0.00 0.00 3.36
1429 1435 2.124695 GCAATGGGACCCGAGACC 60.125 66.667 5.91 0.00 0.00 3.85
1430 1436 2.670148 GCAATGGGACCCGAGACCT 61.670 63.158 5.91 0.00 0.00 3.85
1431 1437 1.335132 GCAATGGGACCCGAGACCTA 61.335 60.000 5.91 0.00 0.00 3.08
1432 1438 1.424638 CAATGGGACCCGAGACCTAT 58.575 55.000 5.91 0.00 30.58 2.57
1433 1439 1.768870 CAATGGGACCCGAGACCTATT 59.231 52.381 5.91 0.00 39.03 1.73
1434 1440 1.424638 ATGGGACCCGAGACCTATTG 58.575 55.000 5.91 0.00 0.00 1.90
1435 1441 0.689745 TGGGACCCGAGACCTATTGG 60.690 60.000 5.91 0.00 39.83 3.16
1449 1455 3.486383 CCTATTGGGTATTTCCGCATGT 58.514 45.455 0.00 0.00 37.00 3.21
1450 1456 3.253188 CCTATTGGGTATTTCCGCATGTG 59.747 47.826 0.00 0.00 37.00 3.21
1451 1457 1.468985 TTGGGTATTTCCGCATGTGG 58.531 50.000 19.75 19.75 37.00 4.17
1452 1458 0.329931 TGGGTATTTCCGCATGTGGT 59.670 50.000 24.28 8.62 37.00 4.16
1453 1459 1.021968 GGGTATTTCCGCATGTGGTC 58.978 55.000 24.28 10.84 37.00 4.02
1454 1460 1.680555 GGGTATTTCCGCATGTGGTCA 60.681 52.381 24.28 12.80 37.00 4.02
1455 1461 1.670811 GGTATTTCCGCATGTGGTCAG 59.329 52.381 24.28 0.00 0.00 3.51
1456 1462 2.356135 GTATTTCCGCATGTGGTCAGT 58.644 47.619 24.28 11.87 0.00 3.41
1457 1463 1.167851 ATTTCCGCATGTGGTCAGTG 58.832 50.000 24.28 0.00 0.00 3.66
1458 1464 0.888736 TTTCCGCATGTGGTCAGTGG 60.889 55.000 24.28 0.00 0.00 4.00
1459 1465 3.434319 CCGCATGTGGTCAGTGGC 61.434 66.667 17.59 0.00 0.00 5.01
1460 1466 3.434319 CGCATGTGGTCAGTGGCC 61.434 66.667 6.88 6.88 0.00 5.36
1461 1467 2.034687 GCATGTGGTCAGTGGCCT 59.965 61.111 16.31 0.00 0.00 5.19
1462 1468 1.604593 GCATGTGGTCAGTGGCCTT 60.605 57.895 16.31 0.00 0.00 4.35
1463 1469 1.589716 GCATGTGGTCAGTGGCCTTC 61.590 60.000 16.31 8.85 0.00 3.46
1464 1470 0.037303 CATGTGGTCAGTGGCCTTCT 59.963 55.000 16.31 0.00 0.00 2.85
1465 1471 0.326264 ATGTGGTCAGTGGCCTTCTC 59.674 55.000 16.31 3.79 0.00 2.87
1466 1472 1.374758 GTGGTCAGTGGCCTTCTCG 60.375 63.158 16.31 0.00 0.00 4.04
1467 1473 1.837051 TGGTCAGTGGCCTTCTCGT 60.837 57.895 16.31 0.00 0.00 4.18
1468 1474 1.371558 GGTCAGTGGCCTTCTCGTT 59.628 57.895 6.49 0.00 0.00 3.85
1469 1475 0.250338 GGTCAGTGGCCTTCTCGTTT 60.250 55.000 6.49 0.00 0.00 3.60
1470 1476 1.594331 GTCAGTGGCCTTCTCGTTTT 58.406 50.000 3.32 0.00 0.00 2.43
1471 1477 1.531578 GTCAGTGGCCTTCTCGTTTTC 59.468 52.381 3.32 0.00 0.00 2.29
1472 1478 0.875059 CAGTGGCCTTCTCGTTTTCC 59.125 55.000 3.32 0.00 0.00 3.13
1473 1479 0.602905 AGTGGCCTTCTCGTTTTCCG 60.603 55.000 3.32 0.00 38.13 4.30
1474 1480 0.601841 GTGGCCTTCTCGTTTTCCGA 60.602 55.000 3.32 0.00 45.00 4.55
1485 1491 4.178545 TCGTTTTCCGAGTAAGGTAAGG 57.821 45.455 0.00 0.00 41.60 2.69
1486 1492 3.573967 TCGTTTTCCGAGTAAGGTAAGGT 59.426 43.478 0.00 0.00 41.60 3.50
1487 1493 3.676646 CGTTTTCCGAGTAAGGTAAGGTG 59.323 47.826 0.00 0.00 39.56 4.00
1488 1494 4.559300 CGTTTTCCGAGTAAGGTAAGGTGA 60.559 45.833 0.00 0.00 39.56 4.02
1489 1495 5.299949 GTTTTCCGAGTAAGGTAAGGTGAA 58.700 41.667 0.00 0.00 0.00 3.18
1490 1496 5.750352 TTTCCGAGTAAGGTAAGGTGAAT 57.250 39.130 0.00 0.00 0.00 2.57
1491 1497 6.855763 TTTCCGAGTAAGGTAAGGTGAATA 57.144 37.500 0.00 0.00 0.00 1.75
1492 1498 6.855763 TTCCGAGTAAGGTAAGGTGAATAA 57.144 37.500 0.00 0.00 0.00 1.40
1493 1499 6.461110 TCCGAGTAAGGTAAGGTGAATAAG 57.539 41.667 0.00 0.00 0.00 1.73
1494 1500 6.189859 TCCGAGTAAGGTAAGGTGAATAAGA 58.810 40.000 0.00 0.00 0.00 2.10
1495 1501 6.664816 TCCGAGTAAGGTAAGGTGAATAAGAA 59.335 38.462 0.00 0.00 0.00 2.52
1496 1502 6.979238 CCGAGTAAGGTAAGGTGAATAAGAAG 59.021 42.308 0.00 0.00 0.00 2.85
1497 1503 6.979238 CGAGTAAGGTAAGGTGAATAAGAAGG 59.021 42.308 0.00 0.00 0.00 3.46
1498 1504 6.651086 AGTAAGGTAAGGTGAATAAGAAGGC 58.349 40.000 0.00 0.00 0.00 4.35
1499 1505 5.780958 AAGGTAAGGTGAATAAGAAGGCT 57.219 39.130 0.00 0.00 0.00 4.58
1500 1506 5.780958 AGGTAAGGTGAATAAGAAGGCTT 57.219 39.130 0.00 0.00 38.15 4.35
1501 1507 6.140968 AGGTAAGGTGAATAAGAAGGCTTT 57.859 37.500 0.00 0.00 35.56 3.51
1502 1508 6.552932 AGGTAAGGTGAATAAGAAGGCTTTT 58.447 36.000 0.00 0.00 35.56 2.27
1503 1509 6.434340 AGGTAAGGTGAATAAGAAGGCTTTTG 59.566 38.462 0.00 0.00 35.56 2.44
1504 1510 6.433093 GGTAAGGTGAATAAGAAGGCTTTTGA 59.567 38.462 0.00 0.00 35.56 2.69
1505 1511 7.122799 GGTAAGGTGAATAAGAAGGCTTTTGAT 59.877 37.037 0.00 0.00 35.56 2.57
1506 1512 6.521151 AGGTGAATAAGAAGGCTTTTGATG 57.479 37.500 0.00 0.00 35.56 3.07
1507 1513 6.012745 AGGTGAATAAGAAGGCTTTTGATGT 58.987 36.000 0.00 0.00 35.56 3.06
1508 1514 6.494835 AGGTGAATAAGAAGGCTTTTGATGTT 59.505 34.615 0.00 0.00 35.56 2.71
1509 1515 6.808704 GGTGAATAAGAAGGCTTTTGATGTTC 59.191 38.462 0.00 3.57 35.56 3.18
1510 1516 6.524586 GTGAATAAGAAGGCTTTTGATGTTCG 59.475 38.462 0.00 0.00 35.56 3.95
1511 1517 3.923017 AAGAAGGCTTTTGATGTTCGG 57.077 42.857 0.00 0.00 0.00 4.30
1512 1518 2.863809 AGAAGGCTTTTGATGTTCGGT 58.136 42.857 0.00 0.00 0.00 4.69
1513 1519 3.222603 AGAAGGCTTTTGATGTTCGGTT 58.777 40.909 0.00 0.00 0.00 4.44
1514 1520 4.394729 AGAAGGCTTTTGATGTTCGGTTA 58.605 39.130 0.00 0.00 0.00 2.85
1515 1521 4.455877 AGAAGGCTTTTGATGTTCGGTTAG 59.544 41.667 0.00 0.00 0.00 2.34
1516 1522 3.751518 AGGCTTTTGATGTTCGGTTAGT 58.248 40.909 0.00 0.00 0.00 2.24
1517 1523 4.142038 AGGCTTTTGATGTTCGGTTAGTT 58.858 39.130 0.00 0.00 0.00 2.24
1518 1524 4.583073 AGGCTTTTGATGTTCGGTTAGTTT 59.417 37.500 0.00 0.00 0.00 2.66
1519 1525 4.915667 GGCTTTTGATGTTCGGTTAGTTTC 59.084 41.667 0.00 0.00 0.00 2.78
1520 1526 4.611366 GCTTTTGATGTTCGGTTAGTTTCG 59.389 41.667 0.00 0.00 0.00 3.46
1521 1527 5.738118 TTTTGATGTTCGGTTAGTTTCGT 57.262 34.783 0.00 0.00 0.00 3.85
1522 1528 4.718858 TTGATGTTCGGTTAGTTTCGTG 57.281 40.909 0.00 0.00 0.00 4.35
1523 1529 3.719924 TGATGTTCGGTTAGTTTCGTGT 58.280 40.909 0.00 0.00 0.00 4.49
1524 1530 3.737266 TGATGTTCGGTTAGTTTCGTGTC 59.263 43.478 0.00 0.00 0.00 3.67
1525 1531 3.441496 TGTTCGGTTAGTTTCGTGTCT 57.559 42.857 0.00 0.00 0.00 3.41
1526 1532 3.784338 TGTTCGGTTAGTTTCGTGTCTT 58.216 40.909 0.00 0.00 0.00 3.01
1527 1533 4.183101 TGTTCGGTTAGTTTCGTGTCTTT 58.817 39.130 0.00 0.00 0.00 2.52
1528 1534 4.630940 TGTTCGGTTAGTTTCGTGTCTTTT 59.369 37.500 0.00 0.00 0.00 2.27
1529 1535 5.122082 TGTTCGGTTAGTTTCGTGTCTTTTT 59.878 36.000 0.00 0.00 0.00 1.94
1530 1536 6.312426 TGTTCGGTTAGTTTCGTGTCTTTTTA 59.688 34.615 0.00 0.00 0.00 1.52
1531 1537 6.900568 TCGGTTAGTTTCGTGTCTTTTTAA 57.099 33.333 0.00 0.00 0.00 1.52
1532 1538 7.301068 TCGGTTAGTTTCGTGTCTTTTTAAA 57.699 32.000 0.00 0.00 0.00 1.52
1533 1539 7.401080 TCGGTTAGTTTCGTGTCTTTTTAAAG 58.599 34.615 0.00 0.00 37.36 1.85
1534 1540 7.064490 TCGGTTAGTTTCGTGTCTTTTTAAAGT 59.936 33.333 2.44 0.00 37.31 2.66
1535 1541 8.327429 CGGTTAGTTTCGTGTCTTTTTAAAGTA 58.673 33.333 2.44 0.00 37.31 2.24
1536 1542 9.425893 GGTTAGTTTCGTGTCTTTTTAAAGTAC 57.574 33.333 2.44 0.00 37.31 2.73
1537 1543 9.136468 GTTAGTTTCGTGTCTTTTTAAAGTACG 57.864 33.333 18.95 18.95 42.72 3.67
1538 1544 7.524294 AGTTTCGTGTCTTTTTAAAGTACGA 57.476 32.000 21.38 21.38 45.18 3.43
1539 1545 7.394099 AGTTTCGTGTCTTTTTAAAGTACGAC 58.606 34.615 23.23 17.70 45.77 4.34
1540 1546 6.884096 TTCGTGTCTTTTTAAAGTACGACA 57.116 33.333 23.23 16.58 45.77 4.35
1541 1547 6.884096 TCGTGTCTTTTTAAAGTACGACAA 57.116 33.333 21.38 9.70 43.78 3.18
1542 1548 7.288317 TCGTGTCTTTTTAAAGTACGACAAA 57.712 32.000 21.38 9.48 43.78 2.83
1543 1549 7.172757 TCGTGTCTTTTTAAAGTACGACAAAC 58.827 34.615 21.38 6.49 43.78 2.93
1544 1550 6.408898 CGTGTCTTTTTAAAGTACGACAAACC 59.591 38.462 19.66 2.51 43.33 3.27
1545 1551 6.688385 GTGTCTTTTTAAAGTACGACAAACCC 59.312 38.462 10.47 0.23 37.31 4.11
1546 1552 6.598850 TGTCTTTTTAAAGTACGACAAACCCT 59.401 34.615 0.00 0.00 37.31 4.34
1547 1553 7.121020 TGTCTTTTTAAAGTACGACAAACCCTT 59.879 33.333 0.00 0.00 37.31 3.95
1548 1554 8.611757 GTCTTTTTAAAGTACGACAAACCCTTA 58.388 33.333 0.00 0.00 37.31 2.69
1549 1555 8.611757 TCTTTTTAAAGTACGACAAACCCTTAC 58.388 33.333 0.00 0.00 37.31 2.34
1550 1556 7.856145 TTTTAAAGTACGACAAACCCTTACA 57.144 32.000 0.00 0.00 0.00 2.41
1551 1557 7.856145 TTTAAAGTACGACAAACCCTTACAA 57.144 32.000 0.00 0.00 0.00 2.41
1552 1558 7.856145 TTAAAGTACGACAAACCCTTACAAA 57.144 32.000 0.00 0.00 0.00 2.83
1553 1559 6.756299 AAAGTACGACAAACCCTTACAAAA 57.244 33.333 0.00 0.00 0.00 2.44
1554 1560 6.756299 AAGTACGACAAACCCTTACAAAAA 57.244 33.333 0.00 0.00 0.00 1.94
1555 1561 6.947644 AGTACGACAAACCCTTACAAAAAT 57.052 33.333 0.00 0.00 0.00 1.82
1556 1562 6.962686 AGTACGACAAACCCTTACAAAAATC 58.037 36.000 0.00 0.00 0.00 2.17
1557 1563 5.838531 ACGACAAACCCTTACAAAAATCA 57.161 34.783 0.00 0.00 0.00 2.57
1558 1564 5.827666 ACGACAAACCCTTACAAAAATCAG 58.172 37.500 0.00 0.00 0.00 2.90
1559 1565 5.591067 ACGACAAACCCTTACAAAAATCAGA 59.409 36.000 0.00 0.00 0.00 3.27
1560 1566 6.264518 ACGACAAACCCTTACAAAAATCAGAT 59.735 34.615 0.00 0.00 0.00 2.90
1561 1567 7.446013 ACGACAAACCCTTACAAAAATCAGATA 59.554 33.333 0.00 0.00 0.00 1.98
1562 1568 7.962918 CGACAAACCCTTACAAAAATCAGATAG 59.037 37.037 0.00 0.00 0.00 2.08
1563 1569 8.934023 ACAAACCCTTACAAAAATCAGATAGA 57.066 30.769 0.00 0.00 0.00 1.98
1564 1570 8.793592 ACAAACCCTTACAAAAATCAGATAGAC 58.206 33.333 0.00 0.00 0.00 2.59
1565 1571 8.792633 CAAACCCTTACAAAAATCAGATAGACA 58.207 33.333 0.00 0.00 0.00 3.41
1566 1572 9.533831 AAACCCTTACAAAAATCAGATAGACAT 57.466 29.630 0.00 0.00 0.00 3.06
1581 1587 9.040259 TCAGATAGACATATAAATCCTTGAGGG 57.960 37.037 0.00 0.00 35.41 4.30
1582 1588 8.820831 CAGATAGACATATAAATCCTTGAGGGT 58.179 37.037 0.00 0.00 36.25 4.34
1583 1589 8.820831 AGATAGACATATAAATCCTTGAGGGTG 58.179 37.037 0.00 0.00 36.25 4.61
1584 1590 5.625150 AGACATATAAATCCTTGAGGGTGC 58.375 41.667 0.00 0.00 36.25 5.01
1585 1591 4.729868 ACATATAAATCCTTGAGGGTGCC 58.270 43.478 0.00 0.00 36.25 5.01
1586 1592 4.167892 ACATATAAATCCTTGAGGGTGCCA 59.832 41.667 0.00 0.00 36.25 4.92
1587 1593 3.756082 ATAAATCCTTGAGGGTGCCAA 57.244 42.857 0.00 0.00 36.25 4.52
1588 1594 2.397044 AAATCCTTGAGGGTGCCAAA 57.603 45.000 0.00 0.00 36.25 3.28
1589 1595 1.928868 AATCCTTGAGGGTGCCAAAG 58.071 50.000 0.00 0.00 36.25 2.77
1590 1596 0.779997 ATCCTTGAGGGTGCCAAAGT 59.220 50.000 0.00 0.00 36.25 2.66
1591 1597 0.555769 TCCTTGAGGGTGCCAAAGTT 59.444 50.000 0.00 0.00 36.25 2.66
1592 1598 0.675633 CCTTGAGGGTGCCAAAGTTG 59.324 55.000 0.00 0.00 0.00 3.16
1593 1599 1.402787 CTTGAGGGTGCCAAAGTTGT 58.597 50.000 0.00 0.00 0.00 3.32
1594 1600 1.067516 CTTGAGGGTGCCAAAGTTGTG 59.932 52.381 0.00 0.00 0.00 3.33
1595 1601 0.033601 TGAGGGTGCCAAAGTTGTGT 60.034 50.000 0.00 0.00 0.00 3.72
1596 1602 1.111277 GAGGGTGCCAAAGTTGTGTT 58.889 50.000 0.00 0.00 0.00 3.32
1597 1603 1.067060 GAGGGTGCCAAAGTTGTGTTC 59.933 52.381 0.00 0.00 0.00 3.18
1598 1604 0.104120 GGGTGCCAAAGTTGTGTTCC 59.896 55.000 0.00 0.00 0.00 3.62
1599 1605 1.111277 GGTGCCAAAGTTGTGTTCCT 58.889 50.000 0.00 0.00 0.00 3.36
1600 1606 1.067060 GGTGCCAAAGTTGTGTTCCTC 59.933 52.381 0.00 0.00 0.00 3.71
1601 1607 1.067060 GTGCCAAAGTTGTGTTCCTCC 59.933 52.381 0.00 0.00 0.00 4.30
1602 1608 1.064017 TGCCAAAGTTGTGTTCCTCCT 60.064 47.619 0.00 0.00 0.00 3.69
1603 1609 1.338020 GCCAAAGTTGTGTTCCTCCTG 59.662 52.381 0.00 0.00 0.00 3.86
1604 1610 1.338020 CCAAAGTTGTGTTCCTCCTGC 59.662 52.381 0.00 0.00 0.00 4.85
1605 1611 1.338020 CAAAGTTGTGTTCCTCCTGCC 59.662 52.381 0.00 0.00 0.00 4.85
1606 1612 0.846693 AAGTTGTGTTCCTCCTGCCT 59.153 50.000 0.00 0.00 0.00 4.75
1607 1613 0.398318 AGTTGTGTTCCTCCTGCCTC 59.602 55.000 0.00 0.00 0.00 4.70
1608 1614 0.398318 GTTGTGTTCCTCCTGCCTCT 59.602 55.000 0.00 0.00 0.00 3.69
1609 1615 0.397941 TTGTGTTCCTCCTGCCTCTG 59.602 55.000 0.00 0.00 0.00 3.35
1632 1638 1.474320 CCACCACCGTTTCAACAGAGA 60.474 52.381 0.00 0.00 0.00 3.10
1637 1643 3.377172 CCACCGTTTCAACAGAGAAAACT 59.623 43.478 0.00 0.00 39.05 2.66
1639 1645 3.377172 ACCGTTTCAACAGAGAAAACTGG 59.623 43.478 0.00 0.00 41.59 4.00
1653 1659 4.893524 AGAAAACTGGTTTAAACTGGGGAG 59.106 41.667 17.50 8.69 31.63 4.30
1654 1660 2.287977 ACTGGTTTAAACTGGGGAGC 57.712 50.000 17.50 0.39 0.00 4.70
1655 1661 1.497286 ACTGGTTTAAACTGGGGAGCA 59.503 47.619 17.50 4.90 0.00 4.26
1656 1662 2.110011 ACTGGTTTAAACTGGGGAGCAT 59.890 45.455 17.50 0.00 0.00 3.79
1657 1663 2.493278 CTGGTTTAAACTGGGGAGCATG 59.507 50.000 17.50 0.00 0.00 4.06
1658 1664 2.158385 TGGTTTAAACTGGGGAGCATGT 60.158 45.455 17.50 0.00 0.00 3.21
1666 1672 2.509548 ACTGGGGAGCATGTATAAGCAA 59.490 45.455 0.00 0.00 0.00 3.91
1671 1677 3.458189 GGAGCATGTATAAGCAACGACT 58.542 45.455 0.00 0.00 0.00 4.18
1691 1697 7.481642 ACGACTGATAAACTTTCGATGTAGAT 58.518 34.615 0.00 0.00 33.87 1.98
1692 1698 7.974501 ACGACTGATAAACTTTCGATGTAGATT 59.025 33.333 0.00 0.00 33.87 2.40
1722 1728 2.802816 CCGAGAACAAAACACCAGAGAG 59.197 50.000 0.00 0.00 0.00 3.20
1728 1734 0.538287 AAAACACCAGAGAGGGCTGC 60.538 55.000 0.00 0.00 43.89 5.25
1742 1748 2.254464 GCTGCATAACGCCCTAGGC 61.254 63.158 2.05 0.00 46.75 3.93
1753 1759 1.908483 CCCTAGGCCAGTCCAAGAC 59.092 63.158 5.01 0.00 37.29 3.01
1786 1793 0.828022 TCACACACTTCCAACGAGGT 59.172 50.000 0.00 0.00 39.02 3.85
1806 1813 1.548719 TCGATGATGACCAACCTTCGT 59.451 47.619 0.00 0.00 0.00 3.85
1811 1818 1.203052 GATGACCAACCTTCGTCGGTA 59.797 52.381 0.00 0.00 35.89 4.02
1812 1819 0.314935 TGACCAACCTTCGTCGGTAC 59.685 55.000 0.00 0.00 35.89 3.34
1813 1820 0.314935 GACCAACCTTCGTCGGTACA 59.685 55.000 0.00 0.00 35.89 2.90
1816 1823 1.528161 CCAACCTTCGTCGGTACAAAC 59.472 52.381 0.00 0.00 35.89 2.93
1822 1829 0.038892 TCGTCGGTACAAACTGGAGC 60.039 55.000 0.00 0.00 32.40 4.70
1852 1912 7.069578 AGGACTATGTTTTAGTGTCGATATGGT 59.930 37.037 0.00 0.00 0.00 3.55
1862 1922 3.005897 GTGTCGATATGGTGGTGCTCTAT 59.994 47.826 0.00 0.00 0.00 1.98
1869 1929 3.101643 TGGTGGTGCTCTATGAGTAGT 57.898 47.619 0.00 0.00 31.39 2.73
1875 1935 6.001460 GTGGTGCTCTATGAGTAGTAGATCT 58.999 44.000 0.00 0.00 31.39 2.75
1883 1943 7.740805 TCTATGAGTAGTAGATCTCAAGCTCA 58.259 38.462 16.81 16.81 42.67 4.26
1885 1945 5.995446 TGAGTAGTAGATCTCAAGCTCAGA 58.005 41.667 0.00 0.00 37.69 3.27
1929 1989 7.345691 TGATCTTTATTGATTCTACCTGGCAA 58.654 34.615 0.00 0.00 0.00 4.52
1930 1990 8.000709 TGATCTTTATTGATTCTACCTGGCAAT 58.999 33.333 0.00 0.00 34.05 3.56
1935 1995 2.291475 TGATTCTACCTGGCAATGGCAA 60.291 45.455 11.45 0.00 43.71 4.52
1958 2018 7.254286 GCAATTTTTATGTGTCGTTCCTTGTTT 60.254 33.333 0.00 0.00 0.00 2.83
1968 2028 6.197655 GTGTCGTTCCTTGTTTAAAAACCATC 59.802 38.462 3.27 0.00 38.11 3.51
1993 2053 5.587844 ACTTGGATATTGCTTAGACTTGCTG 59.412 40.000 2.59 0.00 0.00 4.41
2042 2102 5.720371 TTAGTGGTTGGATCAAACAATGG 57.280 39.130 14.94 0.00 42.94 3.16
2055 2115 1.113788 ACAATGGTTGTGCTTGTGCT 58.886 45.000 0.00 0.00 43.48 4.40
2058 2118 0.311790 ATGGTTGTGCTTGTGCTTCG 59.688 50.000 0.00 0.00 40.48 3.79
2061 2121 1.466855 GTTGTGCTTGTGCTTCGTTC 58.533 50.000 0.00 0.00 40.48 3.95
2069 2129 2.623878 TGTGCTTCGTTCCCTTTGTA 57.376 45.000 0.00 0.00 0.00 2.41
2074 2134 2.096013 GCTTCGTTCCCTTTGTAGATGC 59.904 50.000 0.00 0.00 0.00 3.91
2077 2137 3.596214 TCGTTCCCTTTGTAGATGCTTC 58.404 45.455 0.00 0.00 0.00 3.86
2083 2143 3.002791 CCTTTGTAGATGCTTCGCTTGA 58.997 45.455 0.00 0.00 0.00 3.02
2140 2200 5.539979 TGGTTGATGTTGATGTTTTCATGG 58.460 37.500 0.00 0.00 41.05 3.66
2182 2242 2.559440 GCATGACTTCTAGGGCTTCAG 58.441 52.381 0.00 0.00 0.00 3.02
2192 2252 0.034089 AGGGCTTCAGTTGGGTATGC 60.034 55.000 0.00 0.00 0.00 3.14
2193 2253 0.034089 GGGCTTCAGTTGGGTATGCT 60.034 55.000 0.00 0.00 0.00 3.79
2194 2254 1.098050 GGCTTCAGTTGGGTATGCTG 58.902 55.000 0.00 0.00 0.00 4.41
2199 2259 3.266510 TCAGTTGGGTATGCTGTCATC 57.733 47.619 0.00 0.00 34.22 2.92
2200 2260 2.571202 TCAGTTGGGTATGCTGTCATCA 59.429 45.455 0.00 0.00 34.22 3.07
2253 2313 5.717078 ATTTGTGTGCATTCTTGATGTCT 57.283 34.783 0.00 0.00 38.07 3.41
2281 2341 7.147312 CCTAGCTTTTGACATTGAATTGTTGA 58.853 34.615 0.00 0.00 0.00 3.18
2282 2342 7.816031 CCTAGCTTTTGACATTGAATTGTTGAT 59.184 33.333 0.00 0.00 0.00 2.57
2283 2343 9.199982 CTAGCTTTTGACATTGAATTGTTGATT 57.800 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 7.384477 TGCACCATTGTCATCAATAAAATCAA 58.616 30.769 0.00 0.00 41.66 2.57
69 70 0.393402 GATCAGCTCACCATGCACCA 60.393 55.000 0.00 0.00 0.00 4.17
79 80 3.879998 ACTCTCTTAGACGATCAGCTCA 58.120 45.455 0.00 0.00 0.00 4.26
540 543 1.079819 CTCCATGCCGTTGTCGACT 60.080 57.895 17.92 0.00 39.71 4.18
633 636 7.148323 CCATGGTAAACTTCATTACGAATGTGA 60.148 37.037 2.57 0.00 39.87 3.58
649 652 0.817654 GCCTCCTTGCCATGGTAAAC 59.182 55.000 16.54 0.00 0.00 2.01
685 688 0.951558 CTGTCCAAAAACTCCACCGG 59.048 55.000 0.00 0.00 0.00 5.28
759 763 1.405463 GAGATCGTTGGCATTTTCCCC 59.595 52.381 0.00 0.00 0.00 4.81
895 901 2.640826 TCCTTAAGACCATTCCAACCGT 59.359 45.455 3.36 0.00 0.00 4.83
963 969 0.527817 CCTCCAGCGGATCGTTACAC 60.528 60.000 0.00 0.00 0.00 2.90
1151 1157 6.770542 AGTTTCTGAGGTAAAAACTCCCTAG 58.229 40.000 0.00 0.00 38.51 3.02
1275 1281 0.034059 AGTTGAGAGGCCACAAGTCG 59.966 55.000 5.01 0.00 0.00 4.18
1344 1350 9.325198 GTGAAACCTTTTGAAAATAGGAATTGT 57.675 29.630 2.81 0.00 33.21 2.71
1345 1351 9.546428 AGTGAAACCTTTTGAAAATAGGAATTG 57.454 29.630 2.81 0.00 37.80 2.32
1348 1354 9.952030 AAAAGTGAAACCTTTTGAAAATAGGAA 57.048 25.926 2.81 0.00 41.75 3.36
1349 1355 9.952030 AAAAAGTGAAACCTTTTGAAAATAGGA 57.048 25.926 2.81 0.00 38.90 2.94
1392 1398 9.381033 CCATTGCACCTGATTTGAAAATAATAA 57.619 29.630 0.00 0.00 0.00 1.40
1393 1399 7.986320 CCCATTGCACCTGATTTGAAAATAATA 59.014 33.333 0.00 0.00 0.00 0.98
1394 1400 6.824704 CCCATTGCACCTGATTTGAAAATAAT 59.175 34.615 0.00 0.00 0.00 1.28
1395 1401 6.013898 TCCCATTGCACCTGATTTGAAAATAA 60.014 34.615 0.00 0.00 0.00 1.40
1396 1402 5.483231 TCCCATTGCACCTGATTTGAAAATA 59.517 36.000 0.00 0.00 0.00 1.40
1397 1403 4.286549 TCCCATTGCACCTGATTTGAAAAT 59.713 37.500 0.00 0.00 0.00 1.82
1398 1404 3.645212 TCCCATTGCACCTGATTTGAAAA 59.355 39.130 0.00 0.00 0.00 2.29
1399 1405 3.006752 GTCCCATTGCACCTGATTTGAAA 59.993 43.478 0.00 0.00 0.00 2.69
1400 1406 2.562298 GTCCCATTGCACCTGATTTGAA 59.438 45.455 0.00 0.00 0.00 2.69
1401 1407 2.170166 GTCCCATTGCACCTGATTTGA 58.830 47.619 0.00 0.00 0.00 2.69
1402 1408 1.205417 GGTCCCATTGCACCTGATTTG 59.795 52.381 0.00 0.00 0.00 2.32
1403 1409 1.560505 GGTCCCATTGCACCTGATTT 58.439 50.000 0.00 0.00 0.00 2.17
1404 1410 0.324645 GGGTCCCATTGCACCTGATT 60.325 55.000 1.78 0.00 32.69 2.57
1405 1411 1.307647 GGGTCCCATTGCACCTGAT 59.692 57.895 1.78 0.00 32.69 2.90
1406 1412 2.763215 GGGTCCCATTGCACCTGA 59.237 61.111 1.78 0.00 32.69 3.86
1407 1413 2.751436 CGGGTCCCATTGCACCTG 60.751 66.667 9.12 1.44 32.69 4.00
1408 1414 2.933287 TCGGGTCCCATTGCACCT 60.933 61.111 9.12 0.00 32.69 4.00
1409 1415 2.438434 CTCGGGTCCCATTGCACC 60.438 66.667 9.12 0.00 0.00 5.01
1410 1416 1.745489 GTCTCGGGTCCCATTGCAC 60.745 63.158 9.12 0.00 0.00 4.57
1411 1417 2.668632 GTCTCGGGTCCCATTGCA 59.331 61.111 9.12 0.00 0.00 4.08
1412 1418 1.335132 TAGGTCTCGGGTCCCATTGC 61.335 60.000 9.12 0.00 0.00 3.56
1413 1419 1.424638 ATAGGTCTCGGGTCCCATTG 58.575 55.000 9.12 0.00 0.00 2.82
1414 1420 1.768870 CAATAGGTCTCGGGTCCCATT 59.231 52.381 9.12 0.00 0.00 3.16
1415 1421 1.424638 CAATAGGTCTCGGGTCCCAT 58.575 55.000 9.12 0.00 0.00 4.00
1416 1422 0.689745 CCAATAGGTCTCGGGTCCCA 60.690 60.000 9.12 0.00 0.00 4.37
1417 1423 1.408453 CCCAATAGGTCTCGGGTCCC 61.408 65.000 0.00 0.00 33.67 4.46
1418 1424 2.134092 CCCAATAGGTCTCGGGTCC 58.866 63.158 0.00 0.00 33.67 4.46
1428 1434 3.253188 CACATGCGGAAATACCCAATAGG 59.747 47.826 0.00 0.00 43.78 2.57
1429 1435 3.253188 CCACATGCGGAAATACCCAATAG 59.747 47.826 0.00 0.00 34.64 1.73
1430 1436 3.218453 CCACATGCGGAAATACCCAATA 58.782 45.455 0.00 0.00 34.64 1.90
1431 1437 2.031120 CCACATGCGGAAATACCCAAT 58.969 47.619 0.00 0.00 34.64 3.16
1432 1438 1.272203 ACCACATGCGGAAATACCCAA 60.272 47.619 6.80 0.00 34.64 4.12
1433 1439 0.329931 ACCACATGCGGAAATACCCA 59.670 50.000 6.80 0.00 34.64 4.51
1434 1440 1.021968 GACCACATGCGGAAATACCC 58.978 55.000 6.80 0.00 34.64 3.69
1435 1441 1.670811 CTGACCACATGCGGAAATACC 59.329 52.381 6.80 0.00 0.00 2.73
1436 1442 2.095853 CACTGACCACATGCGGAAATAC 59.904 50.000 6.80 0.00 0.00 1.89
1437 1443 2.355197 CACTGACCACATGCGGAAATA 58.645 47.619 6.80 0.00 0.00 1.40
1438 1444 1.167851 CACTGACCACATGCGGAAAT 58.832 50.000 6.80 0.00 0.00 2.17
1439 1445 0.888736 CCACTGACCACATGCGGAAA 60.889 55.000 6.80 0.00 0.00 3.13
1440 1446 1.302431 CCACTGACCACATGCGGAA 60.302 57.895 6.80 0.00 0.00 4.30
1441 1447 2.347114 CCACTGACCACATGCGGA 59.653 61.111 6.80 0.00 0.00 5.54
1442 1448 3.434319 GCCACTGACCACATGCGG 61.434 66.667 0.00 0.00 0.00 5.69
1443 1449 3.434319 GGCCACTGACCACATGCG 61.434 66.667 0.00 0.00 0.00 4.73
1444 1450 1.589716 GAAGGCCACTGACCACATGC 61.590 60.000 5.01 0.00 0.00 4.06
1445 1451 0.037303 AGAAGGCCACTGACCACATG 59.963 55.000 5.01 0.00 0.00 3.21
1446 1452 0.326264 GAGAAGGCCACTGACCACAT 59.674 55.000 5.01 0.00 0.00 3.21
1447 1453 1.754745 GAGAAGGCCACTGACCACA 59.245 57.895 5.01 0.00 0.00 4.17
1448 1454 1.374758 CGAGAAGGCCACTGACCAC 60.375 63.158 5.01 0.00 0.00 4.16
1449 1455 1.407656 AACGAGAAGGCCACTGACCA 61.408 55.000 5.01 0.00 0.00 4.02
1450 1456 0.250338 AAACGAGAAGGCCACTGACC 60.250 55.000 5.01 0.00 0.00 4.02
1451 1457 1.531578 GAAAACGAGAAGGCCACTGAC 59.468 52.381 5.01 0.00 0.00 3.51
1452 1458 1.542547 GGAAAACGAGAAGGCCACTGA 60.543 52.381 5.01 0.00 0.00 3.41
1453 1459 0.875059 GGAAAACGAGAAGGCCACTG 59.125 55.000 5.01 2.05 0.00 3.66
1454 1460 3.324207 GGAAAACGAGAAGGCCACT 57.676 52.632 5.01 3.29 0.00 4.00
1465 1471 3.676646 CACCTTACCTTACTCGGAAAACG 59.323 47.826 0.00 0.00 46.11 3.60
1466 1472 4.886579 TCACCTTACCTTACTCGGAAAAC 58.113 43.478 0.00 0.00 0.00 2.43
1467 1473 5.549742 TTCACCTTACCTTACTCGGAAAA 57.450 39.130 0.00 0.00 0.00 2.29
1468 1474 5.750352 ATTCACCTTACCTTACTCGGAAA 57.250 39.130 0.00 0.00 0.00 3.13
1469 1475 6.664816 TCTTATTCACCTTACCTTACTCGGAA 59.335 38.462 0.00 0.00 0.00 4.30
1470 1476 6.189859 TCTTATTCACCTTACCTTACTCGGA 58.810 40.000 0.00 0.00 0.00 4.55
1471 1477 6.461110 TCTTATTCACCTTACCTTACTCGG 57.539 41.667 0.00 0.00 0.00 4.63
1472 1478 6.979238 CCTTCTTATTCACCTTACCTTACTCG 59.021 42.308 0.00 0.00 0.00 4.18
1473 1479 6.762187 GCCTTCTTATTCACCTTACCTTACTC 59.238 42.308 0.00 0.00 0.00 2.59
1474 1480 6.444171 AGCCTTCTTATTCACCTTACCTTACT 59.556 38.462 0.00 0.00 0.00 2.24
1475 1481 6.651086 AGCCTTCTTATTCACCTTACCTTAC 58.349 40.000 0.00 0.00 0.00 2.34
1476 1482 6.886178 AGCCTTCTTATTCACCTTACCTTA 57.114 37.500 0.00 0.00 0.00 2.69
1477 1483 5.780958 AGCCTTCTTATTCACCTTACCTT 57.219 39.130 0.00 0.00 0.00 3.50
1478 1484 5.780958 AAGCCTTCTTATTCACCTTACCT 57.219 39.130 0.00 0.00 0.00 3.08
1479 1485 6.433093 TCAAAAGCCTTCTTATTCACCTTACC 59.567 38.462 0.00 0.00 31.02 2.85
1480 1486 7.448748 TCAAAAGCCTTCTTATTCACCTTAC 57.551 36.000 0.00 0.00 31.02 2.34
1481 1487 7.669722 ACATCAAAAGCCTTCTTATTCACCTTA 59.330 33.333 0.00 0.00 31.02 2.69
1482 1488 6.494835 ACATCAAAAGCCTTCTTATTCACCTT 59.505 34.615 0.00 0.00 31.02 3.50
1483 1489 6.012745 ACATCAAAAGCCTTCTTATTCACCT 58.987 36.000 0.00 0.00 31.02 4.00
1484 1490 6.272822 ACATCAAAAGCCTTCTTATTCACC 57.727 37.500 0.00 0.00 31.02 4.02
1485 1491 6.524586 CGAACATCAAAAGCCTTCTTATTCAC 59.475 38.462 0.00 0.00 31.02 3.18
1486 1492 6.349280 CCGAACATCAAAAGCCTTCTTATTCA 60.349 38.462 0.00 0.00 31.02 2.57
1487 1493 6.030228 CCGAACATCAAAAGCCTTCTTATTC 58.970 40.000 0.00 0.00 31.02 1.75
1488 1494 5.476945 ACCGAACATCAAAAGCCTTCTTATT 59.523 36.000 0.00 0.00 31.02 1.40
1489 1495 5.010282 ACCGAACATCAAAAGCCTTCTTAT 58.990 37.500 0.00 0.00 31.02 1.73
1490 1496 4.394729 ACCGAACATCAAAAGCCTTCTTA 58.605 39.130 0.00 0.00 31.02 2.10
1491 1497 3.222603 ACCGAACATCAAAAGCCTTCTT 58.777 40.909 0.00 0.00 0.00 2.52
1492 1498 2.863809 ACCGAACATCAAAAGCCTTCT 58.136 42.857 0.00 0.00 0.00 2.85
1493 1499 3.643159 AACCGAACATCAAAAGCCTTC 57.357 42.857 0.00 0.00 0.00 3.46
1494 1500 4.142038 ACTAACCGAACATCAAAAGCCTT 58.858 39.130 0.00 0.00 0.00 4.35
1495 1501 3.751518 ACTAACCGAACATCAAAAGCCT 58.248 40.909 0.00 0.00 0.00 4.58
1496 1502 4.499037 AACTAACCGAACATCAAAAGCC 57.501 40.909 0.00 0.00 0.00 4.35
1497 1503 4.611366 CGAAACTAACCGAACATCAAAAGC 59.389 41.667 0.00 0.00 0.00 3.51
1498 1504 5.619607 CACGAAACTAACCGAACATCAAAAG 59.380 40.000 0.00 0.00 0.00 2.27
1499 1505 5.064962 ACACGAAACTAACCGAACATCAAAA 59.935 36.000 0.00 0.00 0.00 2.44
1500 1506 4.571580 ACACGAAACTAACCGAACATCAAA 59.428 37.500 0.00 0.00 0.00 2.69
1501 1507 4.121317 ACACGAAACTAACCGAACATCAA 58.879 39.130 0.00 0.00 0.00 2.57
1502 1508 3.719924 ACACGAAACTAACCGAACATCA 58.280 40.909 0.00 0.00 0.00 3.07
1503 1509 3.985925 AGACACGAAACTAACCGAACATC 59.014 43.478 0.00 0.00 0.00 3.06
1504 1510 3.986277 AGACACGAAACTAACCGAACAT 58.014 40.909 0.00 0.00 0.00 2.71
1505 1511 3.441496 AGACACGAAACTAACCGAACA 57.559 42.857 0.00 0.00 0.00 3.18
1506 1512 4.783959 AAAGACACGAAACTAACCGAAC 57.216 40.909 0.00 0.00 0.00 3.95
1507 1513 5.799681 AAAAAGACACGAAACTAACCGAA 57.200 34.783 0.00 0.00 0.00 4.30
1508 1514 6.900568 TTAAAAAGACACGAAACTAACCGA 57.099 33.333 0.00 0.00 0.00 4.69
1509 1515 7.182089 ACTTTAAAAAGACACGAAACTAACCG 58.818 34.615 9.37 0.00 39.31 4.44
1510 1516 9.425893 GTACTTTAAAAAGACACGAAACTAACC 57.574 33.333 9.37 0.00 39.31 2.85
1511 1517 9.136468 CGTACTTTAAAAAGACACGAAACTAAC 57.864 33.333 19.80 0.00 43.60 2.34
1512 1518 9.081997 TCGTACTTTAAAAAGACACGAAACTAA 57.918 29.630 22.40 9.11 44.89 2.24
1513 1519 8.531530 GTCGTACTTTAAAAAGACACGAAACTA 58.468 33.333 24.40 10.72 46.83 2.24
1514 1520 7.063308 TGTCGTACTTTAAAAAGACACGAAACT 59.937 33.333 24.40 2.03 46.83 2.66
1515 1521 7.172757 TGTCGTACTTTAAAAAGACACGAAAC 58.827 34.615 24.40 18.47 46.83 2.78
1516 1522 7.288317 TGTCGTACTTTAAAAAGACACGAAA 57.712 32.000 24.40 20.38 46.83 3.46
1517 1523 6.884096 TGTCGTACTTTAAAAAGACACGAA 57.116 33.333 24.40 17.10 46.83 3.85
1518 1524 6.884096 TTGTCGTACTTTAAAAAGACACGA 57.116 33.333 21.56 21.56 45.24 4.35
1519 1525 6.408898 GGTTTGTCGTACTTTAAAAAGACACG 59.591 38.462 19.06 19.06 42.97 4.49
1520 1526 6.688385 GGGTTTGTCGTACTTTAAAAAGACAC 59.312 38.462 9.37 5.87 38.18 3.67
1521 1527 6.598850 AGGGTTTGTCGTACTTTAAAAAGACA 59.401 34.615 9.37 5.02 39.31 3.41
1522 1528 7.019774 AGGGTTTGTCGTACTTTAAAAAGAC 57.980 36.000 9.37 3.07 39.31 3.01
1523 1529 7.628769 AAGGGTTTGTCGTACTTTAAAAAGA 57.371 32.000 9.37 0.00 39.31 2.52
1524 1530 8.397148 TGTAAGGGTTTGTCGTACTTTAAAAAG 58.603 33.333 0.90 0.90 41.73 2.27
1525 1531 8.273780 TGTAAGGGTTTGTCGTACTTTAAAAA 57.726 30.769 0.00 0.00 0.00 1.94
1526 1532 7.856145 TGTAAGGGTTTGTCGTACTTTAAAA 57.144 32.000 0.00 0.00 0.00 1.52
1527 1533 7.856145 TTGTAAGGGTTTGTCGTACTTTAAA 57.144 32.000 0.00 0.00 0.00 1.52
1528 1534 7.856145 TTTGTAAGGGTTTGTCGTACTTTAA 57.144 32.000 0.00 0.00 0.00 1.52
1529 1535 7.856145 TTTTGTAAGGGTTTGTCGTACTTTA 57.144 32.000 0.00 0.00 0.00 1.85
1530 1536 6.756299 TTTTGTAAGGGTTTGTCGTACTTT 57.244 33.333 0.00 0.00 0.00 2.66
1531 1537 6.756299 TTTTTGTAAGGGTTTGTCGTACTT 57.244 33.333 0.00 0.00 0.00 2.24
1532 1538 6.543100 TGATTTTTGTAAGGGTTTGTCGTACT 59.457 34.615 0.00 0.00 0.00 2.73
1533 1539 6.727215 TGATTTTTGTAAGGGTTTGTCGTAC 58.273 36.000 0.00 0.00 0.00 3.67
1534 1540 6.766944 TCTGATTTTTGTAAGGGTTTGTCGTA 59.233 34.615 0.00 0.00 0.00 3.43
1535 1541 5.591067 TCTGATTTTTGTAAGGGTTTGTCGT 59.409 36.000 0.00 0.00 0.00 4.34
1536 1542 6.067263 TCTGATTTTTGTAAGGGTTTGTCG 57.933 37.500 0.00 0.00 0.00 4.35
1537 1543 9.010029 TCTATCTGATTTTTGTAAGGGTTTGTC 57.990 33.333 0.00 0.00 0.00 3.18
1538 1544 8.793592 GTCTATCTGATTTTTGTAAGGGTTTGT 58.206 33.333 0.00 0.00 0.00 2.83
1539 1545 8.792633 TGTCTATCTGATTTTTGTAAGGGTTTG 58.207 33.333 0.00 0.00 0.00 2.93
1540 1546 8.934023 TGTCTATCTGATTTTTGTAAGGGTTT 57.066 30.769 0.00 0.00 0.00 3.27
1555 1561 9.040259 CCCTCAAGGATTTATATGTCTATCTGA 57.960 37.037 0.00 0.00 38.24 3.27
1556 1562 8.820831 ACCCTCAAGGATTTATATGTCTATCTG 58.179 37.037 0.00 0.00 39.89 2.90
1557 1563 8.820831 CACCCTCAAGGATTTATATGTCTATCT 58.179 37.037 0.00 0.00 39.89 1.98
1558 1564 7.550906 GCACCCTCAAGGATTTATATGTCTATC 59.449 40.741 0.00 0.00 39.89 2.08
1559 1565 7.398024 GCACCCTCAAGGATTTATATGTCTAT 58.602 38.462 0.00 0.00 39.89 1.98
1560 1566 6.239887 GGCACCCTCAAGGATTTATATGTCTA 60.240 42.308 0.00 0.00 39.89 2.59
1561 1567 5.456763 GGCACCCTCAAGGATTTATATGTCT 60.457 44.000 0.00 0.00 39.89 3.41
1562 1568 4.762251 GGCACCCTCAAGGATTTATATGTC 59.238 45.833 0.00 0.00 39.89 3.06
1563 1569 4.167892 TGGCACCCTCAAGGATTTATATGT 59.832 41.667 0.00 0.00 39.89 2.29
1564 1570 4.728772 TGGCACCCTCAAGGATTTATATG 58.271 43.478 0.00 0.00 39.89 1.78
1565 1571 5.402054 TTGGCACCCTCAAGGATTTATAT 57.598 39.130 0.00 0.00 39.89 0.86
1566 1572 4.871871 TTGGCACCCTCAAGGATTTATA 57.128 40.909 0.00 0.00 39.89 0.98
1567 1573 3.756082 TTGGCACCCTCAAGGATTTAT 57.244 42.857 0.00 0.00 39.89 1.40
1568 1574 3.181423 ACTTTGGCACCCTCAAGGATTTA 60.181 43.478 0.00 0.00 39.89 1.40
1569 1575 2.250924 CTTTGGCACCCTCAAGGATTT 58.749 47.619 0.00 0.00 39.89 2.17
1570 1576 1.147817 ACTTTGGCACCCTCAAGGATT 59.852 47.619 0.00 0.00 39.89 3.01
1571 1577 0.779997 ACTTTGGCACCCTCAAGGAT 59.220 50.000 0.00 0.00 39.89 3.24
1572 1578 0.555769 AACTTTGGCACCCTCAAGGA 59.444 50.000 0.00 0.00 39.89 3.36
1573 1579 0.675633 CAACTTTGGCACCCTCAAGG 59.324 55.000 0.00 0.00 43.78 3.61
1574 1580 1.067516 CACAACTTTGGCACCCTCAAG 59.932 52.381 0.00 0.00 0.00 3.02
1575 1581 1.110442 CACAACTTTGGCACCCTCAA 58.890 50.000 0.00 0.00 0.00 3.02
1576 1582 0.033601 ACACAACTTTGGCACCCTCA 60.034 50.000 0.00 0.00 0.00 3.86
1577 1583 1.067060 GAACACAACTTTGGCACCCTC 59.933 52.381 0.00 0.00 0.00 4.30
1578 1584 1.111277 GAACACAACTTTGGCACCCT 58.889 50.000 0.00 0.00 0.00 4.34
1579 1585 0.104120 GGAACACAACTTTGGCACCC 59.896 55.000 0.00 0.00 0.00 4.61
1580 1586 1.067060 GAGGAACACAACTTTGGCACC 59.933 52.381 0.00 0.00 0.00 5.01
1581 1587 1.067060 GGAGGAACACAACTTTGGCAC 59.933 52.381 0.00 0.00 0.00 5.01
1582 1588 1.064017 AGGAGGAACACAACTTTGGCA 60.064 47.619 0.00 0.00 0.00 4.92
1583 1589 1.338020 CAGGAGGAACACAACTTTGGC 59.662 52.381 0.00 0.00 0.00 4.52
1584 1590 1.338020 GCAGGAGGAACACAACTTTGG 59.662 52.381 0.00 0.00 0.00 3.28
1585 1591 1.338020 GGCAGGAGGAACACAACTTTG 59.662 52.381 0.00 0.00 0.00 2.77
1586 1592 1.215423 AGGCAGGAGGAACACAACTTT 59.785 47.619 0.00 0.00 0.00 2.66
1587 1593 0.846693 AGGCAGGAGGAACACAACTT 59.153 50.000 0.00 0.00 0.00 2.66
1588 1594 0.398318 GAGGCAGGAGGAACACAACT 59.602 55.000 0.00 0.00 0.00 3.16
1589 1595 0.398318 AGAGGCAGGAGGAACACAAC 59.602 55.000 0.00 0.00 0.00 3.32
1590 1596 0.397941 CAGAGGCAGGAGGAACACAA 59.602 55.000 0.00 0.00 0.00 3.33
1591 1597 1.483595 CCAGAGGCAGGAGGAACACA 61.484 60.000 0.00 0.00 0.00 3.72
1592 1598 1.298014 CCAGAGGCAGGAGGAACAC 59.702 63.158 0.00 0.00 0.00 3.32
1593 1599 1.920325 CCCAGAGGCAGGAGGAACA 60.920 63.158 0.00 0.00 0.00 3.18
1594 1600 2.993853 CCCAGAGGCAGGAGGAAC 59.006 66.667 0.00 0.00 0.00 3.62
1605 1611 3.491598 AAACGGTGGTGGCCCAGAG 62.492 63.158 0.00 0.00 42.94 3.35
1606 1612 3.485346 GAAACGGTGGTGGCCCAGA 62.485 63.158 0.00 0.00 42.94 3.86
1607 1613 2.983592 GAAACGGTGGTGGCCCAG 60.984 66.667 0.00 0.00 42.94 4.45
1608 1614 3.360423 TTGAAACGGTGGTGGCCCA 62.360 57.895 0.00 0.00 38.87 5.36
1609 1615 2.519780 TTGAAACGGTGGTGGCCC 60.520 61.111 0.00 0.00 0.00 5.80
1615 1621 3.377172 AGTTTTCTCTGTTGAAACGGTGG 59.623 43.478 2.10 0.00 35.91 4.61
1632 1638 3.386726 GCTCCCCAGTTTAAACCAGTTTT 59.613 43.478 14.72 0.00 34.23 2.43
1637 1643 2.158385 ACATGCTCCCCAGTTTAAACCA 60.158 45.455 14.72 4.37 0.00 3.67
1639 1645 6.459710 GCTTATACATGCTCCCCAGTTTAAAC 60.460 42.308 10.47 10.47 0.00 2.01
1653 1659 6.525121 TTATCAGTCGTTGCTTATACATGC 57.475 37.500 0.00 0.00 0.00 4.06
1654 1660 8.131455 AGTTTATCAGTCGTTGCTTATACATG 57.869 34.615 0.00 0.00 0.00 3.21
1655 1661 8.718102 AAGTTTATCAGTCGTTGCTTATACAT 57.282 30.769 0.00 0.00 0.00 2.29
1656 1662 8.542497 AAAGTTTATCAGTCGTTGCTTATACA 57.458 30.769 0.00 0.00 0.00 2.29
1657 1663 7.839837 CGAAAGTTTATCAGTCGTTGCTTATAC 59.160 37.037 0.00 0.00 0.00 1.47
1658 1664 7.756272 TCGAAAGTTTATCAGTCGTTGCTTATA 59.244 33.333 0.00 0.00 33.55 0.98
1666 1672 6.849502 TCTACATCGAAAGTTTATCAGTCGT 58.150 36.000 0.00 0.00 33.55 4.34
1691 1697 5.049680 GTGTTTTGTTCTCGGCATCTTCTAA 60.050 40.000 0.00 0.00 0.00 2.10
1692 1698 4.451096 GTGTTTTGTTCTCGGCATCTTCTA 59.549 41.667 0.00 0.00 0.00 2.10
1742 1748 0.602905 GTGTTCCCGTCTTGGACTGG 60.603 60.000 2.42 2.42 42.00 4.00
1744 1750 0.834612 TTGTGTTCCCGTCTTGGACT 59.165 50.000 0.00 0.00 42.00 3.85
1746 1752 0.834612 AGTTGTGTTCCCGTCTTGGA 59.165 50.000 0.00 0.00 42.00 3.53
1753 1759 1.217882 GTGTGAGAGTTGTGTTCCCG 58.782 55.000 0.00 0.00 0.00 5.14
1786 1793 1.548719 ACGAAGGTTGGTCATCATCGA 59.451 47.619 0.00 0.00 33.42 3.59
1800 1807 1.000060 TCCAGTTTGTACCGACGAAGG 60.000 52.381 0.00 0.00 29.08 3.46
1806 1813 1.290955 CGGCTCCAGTTTGTACCGA 59.709 57.895 0.00 0.00 43.19 4.69
1811 1818 1.841556 TCCTCCGGCTCCAGTTTGT 60.842 57.895 0.00 0.00 0.00 2.83
1812 1819 1.376037 GTCCTCCGGCTCCAGTTTG 60.376 63.158 0.00 0.00 0.00 2.93
1813 1820 0.252103 TAGTCCTCCGGCTCCAGTTT 60.252 55.000 0.00 0.00 0.00 2.66
1816 1823 0.757188 ACATAGTCCTCCGGCTCCAG 60.757 60.000 0.00 0.00 0.00 3.86
1822 1829 4.430908 GACACTAAAACATAGTCCTCCGG 58.569 47.826 0.00 0.00 0.00 5.14
1831 1838 6.759356 CACCACCATATCGACACTAAAACATA 59.241 38.462 0.00 0.00 0.00 2.29
1833 1840 4.932799 CACCACCATATCGACACTAAAACA 59.067 41.667 0.00 0.00 0.00 2.83
1835 1842 3.936453 GCACCACCATATCGACACTAAAA 59.064 43.478 0.00 0.00 0.00 1.52
1841 1848 1.485124 AGAGCACCACCATATCGACA 58.515 50.000 0.00 0.00 0.00 4.35
1852 1912 6.183361 TGAGATCTACTACTCATAGAGCACCA 60.183 42.308 0.00 0.00 37.50 4.17
1862 1922 5.995446 TCTGAGCTTGAGATCTACTACTCA 58.005 41.667 14.05 14.05 40.66 3.41
1869 1929 4.826733 GTCATCCTCTGAGCTTGAGATCTA 59.173 45.833 16.25 3.21 33.51 1.98
1875 1935 1.552337 GGTGTCATCCTCTGAGCTTGA 59.448 52.381 0.00 1.60 33.51 3.02
1885 1945 5.723887 AGATCAAAACTAGAGGTGTCATCCT 59.276 40.000 0.00 0.00 40.97 3.24
1929 1989 5.047377 AGGAACGACACATAAAAATTGCCAT 60.047 36.000 0.00 0.00 0.00 4.40
1930 1990 4.279671 AGGAACGACACATAAAAATTGCCA 59.720 37.500 0.00 0.00 0.00 4.92
1935 1995 9.804758 TTTAAACAAGGAACGACACATAAAAAT 57.195 25.926 0.00 0.00 0.00 1.82
1968 2028 5.587844 AGCAAGTCTAAGCAATATCCAAGTG 59.412 40.000 0.67 0.00 0.00 3.16
1993 2053 4.574013 CAGATCATGGTTTTAGCTCCAGAC 59.426 45.833 0.00 0.00 37.14 3.51
2042 2102 1.466855 GAACGAAGCACAAGCACAAC 58.533 50.000 0.00 0.00 45.49 3.32
2055 2115 3.695830 AGCATCTACAAAGGGAACGAA 57.304 42.857 0.00 0.00 0.00 3.85
2074 2134 3.658709 AGAAAGTTCTCCTCAAGCGAAG 58.341 45.455 0.00 0.00 29.94 3.79
2077 2137 3.431572 CAGAAGAAAGTTCTCCTCAAGCG 59.568 47.826 0.00 0.00 36.28 4.68
2083 2143 3.049344 ACACCCAGAAGAAAGTTCTCCT 58.951 45.455 0.00 0.00 36.28 3.69
2124 2184 4.281435 AGATGCACCATGAAAACATCAACA 59.719 37.500 15.58 0.00 42.54 3.33
2125 2185 4.813027 AGATGCACCATGAAAACATCAAC 58.187 39.130 15.58 0.00 42.54 3.18
2126 2186 4.523558 TGAGATGCACCATGAAAACATCAA 59.476 37.500 15.58 5.58 42.54 2.57
2127 2187 4.080687 TGAGATGCACCATGAAAACATCA 58.919 39.130 15.58 2.09 43.67 3.07
2128 2188 4.707030 TGAGATGCACCATGAAAACATC 57.293 40.909 0.00 2.16 37.89 3.06
2129 2189 5.186215 TCAATGAGATGCACCATGAAAACAT 59.814 36.000 0.00 0.00 0.00 2.71
2140 2200 3.066342 CCCAACTGATCAATGAGATGCAC 59.934 47.826 9.22 0.00 37.00 4.57
2182 2242 3.813443 AGATGATGACAGCATACCCAAC 58.187 45.455 6.10 0.00 34.11 3.77
2231 2291 5.336213 GGAGACATCAAGAATGCACACAAAT 60.336 40.000 0.00 0.00 39.12 2.32
2236 2296 2.618816 GGGGAGACATCAAGAATGCACA 60.619 50.000 0.00 0.00 39.12 4.57
2242 2302 3.121929 AGCTAGGGGAGACATCAAGAA 57.878 47.619 0.00 0.00 0.00 2.52
2253 2313 4.380843 TTCAATGTCAAAAGCTAGGGGA 57.619 40.909 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.