Multiple sequence alignment - TraesCS7D01G399300

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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 TraesCS7D01G399300 chr7D 100.000 5361 0 0 1 5361 515466622 515471982 0.000000e+00 9901.0
1 TraesCS7D01G399300 chr7A 89.978 2255 83 60 2095 4258 589133632 589135834 0.000000e+00 2780.0
2 TraesCS7D01G399300 chr7A 92.072 1501 71 16 1 1461 589123283 589124775 0.000000e+00 2069.0
3 TraesCS7D01G399300 chr7A 93.533 866 39 12 4504 5360 589136771 589137628 0.000000e+00 1273.0
4 TraesCS7D01G399300 chr7A 91.165 249 12 3 4252 4493 589135921 589136166 4.000000e-86 329.0
5 TraesCS7D01G399300 chr7A 88.235 272 21 4 1519 1790 589124770 589125030 1.120000e-81 315.0
6 TraesCS7D01G399300 chr7A 90.761 184 8 5 1925 2102 589128141 589128321 2.500000e-58 237.0
7 TraesCS7D01G399300 chr7A 96.429 56 2 0 1873 1928 589125434 589125489 5.720000e-15 93.5
8 TraesCS7D01G399300 chr7A 91.045 67 2 1 1460 1526 78039515 78039453 2.660000e-13 87.9
9 TraesCS7D01G399300 chr7B 91.811 1502 66 16 1 1461 546013415 546014900 0.000000e+00 2039.0
10 TraesCS7D01G399300 chr7B 90.798 1478 58 26 2366 3804 546016123 546017561 0.000000e+00 1905.0
11 TraesCS7D01G399300 chr7B 92.646 1115 54 18 4252 5358 546018128 546019222 0.000000e+00 1580.0
12 TraesCS7D01G399300 chr7B 95.652 437 16 1 3827 4263 546017618 546018051 0.000000e+00 699.0
13 TraesCS7D01G399300 chr7B 86.806 576 40 17 1523 2090 546014899 546015446 1.280000e-170 610.0
14 TraesCS7D01G399300 chr7B 90.909 110 5 3 2235 2340 546016017 546016125 5.600000e-30 143.0
15 TraesCS7D01G399300 chr2D 95.312 64 3 0 1463 1526 649340691 649340628 9.500000e-18 102.0
16 TraesCS7D01G399300 chr5D 91.781 73 2 1 1459 1527 472231955 472232027 1.230000e-16 99.0
17 TraesCS7D01G399300 chrUn 92.537 67 4 1 1439 1504 450660927 450660861 1.590000e-15 95.3
18 TraesCS7D01G399300 chr4B 92.537 67 1 1 1460 1526 340684679 340684617 5.720000e-15 93.5
19 TraesCS7D01G399300 chr4B 91.045 67 2 1 1460 1526 9822559 9822497 2.660000e-13 87.9
20 TraesCS7D01G399300 chr4B 91.045 67 2 1 1460 1526 397903130 397903068 2.660000e-13 87.9
21 TraesCS7D01G399300 chr5A 91.304 69 2 1 1459 1527 591392481 591392545 2.060000e-14 91.6
22 TraesCS7D01G399300 chr3D 91.176 68 3 1 1460 1524 224894413 224894346 7.400000e-14 89.8


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 TraesCS7D01G399300 chr7D 515466622 515471982 5360 False 9901.000000 9901 100.000000 1 5361 1 chr7D.!!$F1 5360
1 TraesCS7D01G399300 chr7A 589133632 589137628 3996 False 1460.666667 2780 91.558667 2095 5360 3 chr7A.!!$F2 3265
2 TraesCS7D01G399300 chr7A 589123283 589128321 5038 False 678.625000 2069 91.874250 1 2102 4 chr7A.!!$F1 2101
3 TraesCS7D01G399300 chr7B 546013415 546019222 5807 False 1162.666667 2039 91.437000 1 5358 6 chr7B.!!$F1 5357

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
144 145 1.076485 GCAGGCTTGGATGGGATGT 60.076 57.895 0.0 0.0 0.0 3.06 F
145 146 1.389609 GCAGGCTTGGATGGGATGTG 61.390 60.000 0.0 0.0 0.0 3.21 F
1464 1513 0.179081 GCCCGTCCATGAACTACTCC 60.179 60.000 0.0 0.0 0.0 3.85 F
2322 5818 0.033504 GTGTGGAAGAAGACGCTCCA 59.966 55.000 0.0 0.0 0.0 3.86 F
2531 6044 0.038435 CCGCATCGCATCTCATCTCT 60.038 55.000 0.0 0.0 0.0 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1375 1423 0.037790 GCGAGAGTCCAAGAACAGCT 60.038 55.0 0.00 0.0 0.00 4.24 R
1555 1604 0.249447 CAGGTCGAACTGTGCTGACA 60.249 55.0 22.63 0.0 33.81 3.58 R
2352 5848 0.401738 TTTTGGGTCTGGCAGAGGAG 59.598 55.0 19.38 0.0 0.00 3.69 R
4232 7866 0.322456 TGGGATCTTTGTTGGAGCCG 60.322 55.0 0.00 0.0 39.85 5.52 R
4493 8227 0.108424 AGTCTTGCAGATCTCCGCAC 60.108 55.0 7.21 0.0 38.00 5.34 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
144 145 1.076485 GCAGGCTTGGATGGGATGT 60.076 57.895 0.00 0.00 0.00 3.06
145 146 1.389609 GCAGGCTTGGATGGGATGTG 61.390 60.000 0.00 0.00 0.00 3.21
167 168 2.423538 GCCTTAGCCACCATTAACACAG 59.576 50.000 0.00 0.00 0.00 3.66
215 216 8.726988 TGTCTACTTATTGGCTTCATTTGTAAC 58.273 33.333 0.00 0.00 0.00 2.50
359 360 5.598417 TGCTATACTAATCCAACTGCAGAGA 59.402 40.000 23.35 14.25 0.00 3.10
532 535 3.547813 CGCAGTTGTACAGTTTGATGCAA 60.548 43.478 0.00 0.00 32.79 4.08
651 677 7.827819 TGTCACAAGTAGTAATGATTAGCAC 57.172 36.000 0.00 0.00 0.00 4.40
765 793 8.503196 CGCCATTTTAGTGAATATATACAAGCA 58.497 33.333 0.00 0.00 0.00 3.91
824 855 9.686683 AAAGTGTTAAGCCTTAGACAATGATAT 57.313 29.630 0.00 0.00 0.00 1.63
855 886 4.272489 GCATATGGCCCTATGCTAAATCA 58.728 43.478 33.50 0.00 46.78 2.57
915 946 3.859961 CGTGCTTGATCTAGTGGTACTTG 59.140 47.826 6.05 0.00 0.00 3.16
928 959 6.875972 AGTGGTACTTGTAAATCCAGAGAT 57.124 37.500 0.00 0.00 0.00 2.75
974 1005 4.540735 CTTACCCCGCGGCCGATT 62.541 66.667 33.48 9.61 36.29 3.34
1038 1069 2.429971 GCCACTGGTAAGTACTCCTACC 59.570 54.545 14.52 14.52 33.79 3.18
1043 1074 6.126652 CCACTGGTAAGTACTCCTACCTAGTA 60.127 46.154 19.81 4.16 33.79 1.82
1044 1075 7.421147 CCACTGGTAAGTACTCCTACCTAGTAT 60.421 44.444 19.81 3.84 33.79 2.12
1045 1076 7.444792 CACTGGTAAGTACTCCTACCTAGTATG 59.555 44.444 19.81 10.14 33.79 2.39
1260 1299 2.515523 ACAGATGCGGCATCCAGC 60.516 61.111 33.01 14.32 41.36 4.85
1293 1341 2.622942 ACGTCGTTCACTACACCCTAAA 59.377 45.455 0.00 0.00 0.00 1.85
1320 1368 3.534357 TCTGCTTTGGTTTCCCCATTA 57.466 42.857 0.00 0.00 44.74 1.90
1373 1421 1.886542 GGAGCGGTGGTGAAAATTCTT 59.113 47.619 0.00 0.00 0.00 2.52
1374 1422 2.095212 GGAGCGGTGGTGAAAATTCTTC 60.095 50.000 0.00 0.00 0.00 2.87
1375 1423 2.552315 GAGCGGTGGTGAAAATTCTTCA 59.448 45.455 0.00 0.68 0.00 3.02
1376 1424 2.554032 AGCGGTGGTGAAAATTCTTCAG 59.446 45.455 0.00 0.00 0.00 3.02
1377 1425 2.922335 GCGGTGGTGAAAATTCTTCAGC 60.922 50.000 17.88 17.88 44.55 4.26
1378 1426 2.554032 CGGTGGTGAAAATTCTTCAGCT 59.446 45.455 21.78 0.00 44.58 4.24
1379 1427 3.610114 CGGTGGTGAAAATTCTTCAGCTG 60.610 47.826 21.78 7.63 44.58 4.24
1381 1429 4.202151 GGTGGTGAAAATTCTTCAGCTGTT 60.202 41.667 14.67 0.00 44.58 3.16
1382 1430 4.978580 GTGGTGAAAATTCTTCAGCTGTTC 59.021 41.667 14.67 8.73 44.58 3.18
1383 1431 4.889409 TGGTGAAAATTCTTCAGCTGTTCT 59.111 37.500 14.67 0.00 44.58 3.01
1384 1432 5.360714 TGGTGAAAATTCTTCAGCTGTTCTT 59.639 36.000 14.67 0.00 44.58 2.52
1385 1433 5.689068 GGTGAAAATTCTTCAGCTGTTCTTG 59.311 40.000 14.67 1.02 41.98 3.02
1454 1503 0.325296 TTACTCCTCTGCCCGTCCAT 60.325 55.000 0.00 0.00 0.00 3.41
1461 1510 0.535335 TCTGCCCGTCCATGAACTAC 59.465 55.000 0.00 0.00 0.00 2.73
1462 1511 0.537188 CTGCCCGTCCATGAACTACT 59.463 55.000 0.00 0.00 0.00 2.57
1463 1512 0.535335 TGCCCGTCCATGAACTACTC 59.465 55.000 0.00 0.00 0.00 2.59
1464 1513 0.179081 GCCCGTCCATGAACTACTCC 60.179 60.000 0.00 0.00 0.00 3.85
1465 1514 0.464452 CCCGTCCATGAACTACTCCC 59.536 60.000 0.00 0.00 0.00 4.30
1466 1515 1.486211 CCGTCCATGAACTACTCCCT 58.514 55.000 0.00 0.00 0.00 4.20
1467 1516 1.409427 CCGTCCATGAACTACTCCCTC 59.591 57.143 0.00 0.00 0.00 4.30
1468 1517 1.409427 CGTCCATGAACTACTCCCTCC 59.591 57.143 0.00 0.00 0.00 4.30
1469 1518 1.409427 GTCCATGAACTACTCCCTCCG 59.591 57.143 0.00 0.00 0.00 4.63
1470 1519 1.006758 TCCATGAACTACTCCCTCCGT 59.993 52.381 0.00 0.00 0.00 4.69
1471 1520 1.831736 CCATGAACTACTCCCTCCGTT 59.168 52.381 0.00 0.00 0.00 4.44
1472 1521 2.159085 CCATGAACTACTCCCTCCGTTC 60.159 54.545 0.00 0.00 37.02 3.95
1473 1522 1.553706 TGAACTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 35.97 3.62
1474 1523 1.203087 TGAACTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.00 35.97 3.53
1475 1524 1.477295 GAACTACTCCCTCCGTTCCAG 59.523 57.143 0.00 0.00 31.89 3.86
1476 1525 0.702902 ACTACTCCCTCCGTTCCAGA 59.297 55.000 0.00 0.00 0.00 3.86
1477 1526 1.288335 ACTACTCCCTCCGTTCCAGAT 59.712 52.381 0.00 0.00 0.00 2.90
1478 1527 2.292323 ACTACTCCCTCCGTTCCAGATT 60.292 50.000 0.00 0.00 0.00 2.40
1479 1528 2.544844 ACTCCCTCCGTTCCAGATTA 57.455 50.000 0.00 0.00 0.00 1.75
1480 1529 2.108970 ACTCCCTCCGTTCCAGATTAC 58.891 52.381 0.00 0.00 0.00 1.89
1481 1530 2.292323 ACTCCCTCCGTTCCAGATTACT 60.292 50.000 0.00 0.00 0.00 2.24
1482 1531 2.362717 CTCCCTCCGTTCCAGATTACTC 59.637 54.545 0.00 0.00 0.00 2.59
1483 1532 1.067212 CCCTCCGTTCCAGATTACTCG 59.933 57.143 0.00 0.00 0.00 4.18
1484 1533 1.749634 CCTCCGTTCCAGATTACTCGT 59.250 52.381 0.00 0.00 0.00 4.18
1485 1534 2.223525 CCTCCGTTCCAGATTACTCGTC 60.224 54.545 0.00 0.00 0.00 4.20
1486 1535 1.399440 TCCGTTCCAGATTACTCGTCG 59.601 52.381 0.00 0.00 0.00 5.12
1487 1536 1.131883 CCGTTCCAGATTACTCGTCGT 59.868 52.381 0.00 0.00 0.00 4.34
1488 1537 2.174764 CGTTCCAGATTACTCGTCGTG 58.825 52.381 0.00 0.00 0.00 4.35
1489 1538 2.527100 GTTCCAGATTACTCGTCGTGG 58.473 52.381 0.00 0.00 0.00 4.94
1490 1539 1.830279 TCCAGATTACTCGTCGTGGT 58.170 50.000 0.00 0.00 0.00 4.16
1491 1540 2.165167 TCCAGATTACTCGTCGTGGTT 58.835 47.619 0.00 0.00 0.00 3.67
1492 1541 2.559668 TCCAGATTACTCGTCGTGGTTT 59.440 45.455 0.00 0.00 0.00 3.27
1493 1542 3.006110 TCCAGATTACTCGTCGTGGTTTT 59.994 43.478 0.00 0.00 0.00 2.43
1494 1543 4.218200 TCCAGATTACTCGTCGTGGTTTTA 59.782 41.667 0.00 0.00 0.00 1.52
1495 1544 4.561606 CCAGATTACTCGTCGTGGTTTTAG 59.438 45.833 0.00 0.00 0.00 1.85
1496 1545 5.159209 CAGATTACTCGTCGTGGTTTTAGT 58.841 41.667 0.00 0.00 0.00 2.24
1497 1546 5.632347 CAGATTACTCGTCGTGGTTTTAGTT 59.368 40.000 0.00 0.00 0.00 2.24
1498 1547 5.860716 AGATTACTCGTCGTGGTTTTAGTTC 59.139 40.000 0.00 0.00 0.00 3.01
1499 1548 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
1500 1549 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
1501 1550 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
1502 1551 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
1503 1552 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
1504 1553 6.479660 ACTCGTCGTGGTTTTAGTTCAAATTA 59.520 34.615 0.00 0.00 0.00 1.40
1505 1554 7.011295 ACTCGTCGTGGTTTTAGTTCAAATTAA 59.989 33.333 0.00 0.00 0.00 1.40
1506 1555 7.863666 TCGTCGTGGTTTTAGTTCAAATTAAT 58.136 30.769 0.00 0.00 0.00 1.40
1507 1556 8.344098 TCGTCGTGGTTTTAGTTCAAATTAATT 58.656 29.630 0.00 0.00 0.00 1.40
1508 1557 8.960075 CGTCGTGGTTTTAGTTCAAATTAATTT 58.040 29.630 7.64 7.64 0.00 1.82
1510 1559 9.250624 TCGTGGTTTTAGTTCAAATTAATTTGG 57.749 29.630 30.96 17.82 45.39 3.28
1511 1560 9.250624 CGTGGTTTTAGTTCAAATTAATTTGGA 57.749 29.630 30.96 24.54 45.39 3.53
1517 1566 9.685828 TTTAGTTCAAATTAATTTGGAACGGAG 57.314 29.630 30.96 11.30 45.39 4.63
1518 1567 6.687604 AGTTCAAATTAATTTGGAACGGAGG 58.312 36.000 30.96 10.71 45.39 4.30
1519 1568 5.652994 TCAAATTAATTTGGAACGGAGGG 57.347 39.130 30.96 10.10 45.39 4.30
1520 1569 5.326069 TCAAATTAATTTGGAACGGAGGGA 58.674 37.500 30.96 12.42 45.39 4.20
1521 1570 5.417580 TCAAATTAATTTGGAACGGAGGGAG 59.582 40.000 30.96 9.52 45.39 4.30
1522 1571 4.586306 ATTAATTTGGAACGGAGGGAGT 57.414 40.909 0.00 0.00 0.00 3.85
1523 1572 5.703730 ATTAATTTGGAACGGAGGGAGTA 57.296 39.130 0.00 0.00 0.00 2.59
1539 1588 4.971924 AGGGAGTATAATTGAAGGAGCAGT 59.028 41.667 0.00 0.00 0.00 4.40
1555 1604 0.883833 CAGTTCAAGGGATTTGCGCT 59.116 50.000 9.73 0.00 42.29 5.92
1689 1738 3.906014 TCAGTTCAGAGTCGAGACTTG 57.094 47.619 7.23 7.85 42.66 3.16
1707 1756 1.699730 TGACTTGAGTTGAGGTCCGA 58.300 50.000 0.00 0.00 0.00 4.55
1735 1784 3.357079 CCTGCCGGTTGCTGTCAC 61.357 66.667 1.90 0.00 42.00 3.67
1746 1795 2.670934 CTGTCACCAGGCAGGCAC 60.671 66.667 0.00 0.00 43.14 5.01
1779 1829 1.293498 CCGAACCTAGTGTGCTGCT 59.707 57.895 0.00 0.00 0.00 4.24
1803 1857 8.978564 CTCTGTGAGCTTTTATCGTATGATAT 57.021 34.615 5.48 0.00 36.96 1.63
1804 1858 8.748380 TCTGTGAGCTTTTATCGTATGATATG 57.252 34.615 5.48 1.70 36.96 1.78
1806 1860 7.441836 TGTGAGCTTTTATCGTATGATATGGT 58.558 34.615 5.48 5.33 36.96 3.55
1808 1862 7.598869 GTGAGCTTTTATCGTATGATATGGTGA 59.401 37.037 5.48 0.00 36.96 4.02
1809 1863 8.314021 TGAGCTTTTATCGTATGATATGGTGAT 58.686 33.333 5.48 0.00 36.96 3.06
1811 1865 8.314021 AGCTTTTATCGTATGATATGGTGATGA 58.686 33.333 5.48 0.00 36.96 2.92
1812 1866 8.598924 GCTTTTATCGTATGATATGGTGATGAG 58.401 37.037 5.48 0.00 36.96 2.90
1823 1877 1.469703 TGGTGATGAGAAATTGCAGCG 59.530 47.619 0.00 0.00 0.00 5.18
1826 1880 1.469703 TGATGAGAAATTGCAGCGTGG 59.530 47.619 0.00 0.00 0.00 4.94
1828 1882 0.592637 TGAGAAATTGCAGCGTGGTG 59.407 50.000 0.00 0.00 0.00 4.17
1846 1900 1.449778 GCGGTTTGAGAGTAGGGCC 60.450 63.158 0.00 0.00 0.00 5.80
1911 2286 3.427368 GCAAGGCCAAACAAAACAAAAGG 60.427 43.478 5.01 0.00 0.00 3.11
1930 2305 1.065709 GGTTAGGTTGGATGAGGCGAA 60.066 52.381 0.00 0.00 0.00 4.70
2028 5059 5.467063 CCGCTAATCTCCTTTATTTCCTCAC 59.533 44.000 0.00 0.00 0.00 3.51
2031 5062 7.505258 GCTAATCTCCTTTATTTCCTCACTCT 58.495 38.462 0.00 0.00 0.00 3.24
2032 5063 7.655732 GCTAATCTCCTTTATTTCCTCACTCTC 59.344 40.741 0.00 0.00 0.00 3.20
2034 5065 4.402793 TCTCCTTTATTTCCTCACTCTCCG 59.597 45.833 0.00 0.00 0.00 4.63
2035 5066 4.094476 TCCTTTATTTCCTCACTCTCCGT 58.906 43.478 0.00 0.00 0.00 4.69
2036 5067 4.081642 TCCTTTATTTCCTCACTCTCCGTG 60.082 45.833 0.00 0.00 45.18 4.94
2049 5080 4.279671 CACTCTCCGTGAGAAGGCTAATAT 59.720 45.833 9.25 0.00 46.81 1.28
2152 5642 1.516423 GTCGAAGCCTGTACCCCTC 59.484 63.158 0.00 0.00 0.00 4.30
2160 5650 0.767375 CCTGTACCCCTCCATGATGG 59.233 60.000 4.74 4.74 39.43 3.51
2235 5725 1.274447 ACACGGCCTCTTAACCACTAC 59.726 52.381 0.00 0.00 0.00 2.73
2236 5726 1.549170 CACGGCCTCTTAACCACTACT 59.451 52.381 0.00 0.00 0.00 2.57
2237 5727 2.756760 CACGGCCTCTTAACCACTACTA 59.243 50.000 0.00 0.00 0.00 1.82
2261 5751 1.501582 CCTCCTCCCCCTGAAGTTAG 58.498 60.000 0.00 0.00 0.00 2.34
2262 5752 1.273896 CCTCCTCCCCCTGAAGTTAGT 60.274 57.143 0.00 0.00 0.00 2.24
2265 5759 3.447950 TCCTCCCCCTGAAGTTAGTAAC 58.552 50.000 4.78 4.78 0.00 2.50
2270 5764 3.780850 CCCCCTGAAGTTAGTAACCAGAT 59.219 47.826 16.50 0.82 0.00 2.90
2322 5818 0.033504 GTGTGGAAGAAGACGCTCCA 59.966 55.000 0.00 0.00 0.00 3.86
2355 5851 3.093172 CCCCCTTGCCTCCTCTCC 61.093 72.222 0.00 0.00 0.00 3.71
2396 5900 2.034066 CAACACATGGGGCCTCGT 59.966 61.111 0.84 0.00 0.00 4.18
2529 6042 0.105593 AACCGCATCGCATCTCATCT 59.894 50.000 0.00 0.00 0.00 2.90
2531 6044 0.038435 CCGCATCGCATCTCATCTCT 60.038 55.000 0.00 0.00 0.00 3.10
2563 6101 0.615331 TGGATTCACCACCTCTCTGC 59.385 55.000 0.00 0.00 44.64 4.26
2564 6102 0.908198 GGATTCACCACCTCTCTGCT 59.092 55.000 0.00 0.00 38.79 4.24
2565 6103 1.134551 GGATTCACCACCTCTCTGCTC 60.135 57.143 0.00 0.00 38.79 4.26
2598 6136 3.680786 CAGTGAGTCCGTGGCCGA 61.681 66.667 0.00 0.00 35.63 5.54
2681 6219 1.949847 CTTGGATCGGGCTCGTCAGT 61.950 60.000 5.57 0.00 37.69 3.41
2682 6220 2.105128 GGATCGGGCTCGTCAGTG 59.895 66.667 5.57 0.00 37.69 3.66
2683 6221 2.415608 GGATCGGGCTCGTCAGTGA 61.416 63.158 5.57 0.00 37.69 3.41
2684 6222 1.064946 GATCGGGCTCGTCAGTGAG 59.935 63.158 5.57 0.00 39.05 3.51
2685 6223 1.658686 GATCGGGCTCGTCAGTGAGT 61.659 60.000 5.57 0.00 38.28 3.41
2686 6224 1.658686 ATCGGGCTCGTCAGTGAGTC 61.659 60.000 5.57 0.00 39.90 3.36
2687 6225 2.626780 CGGGCTCGTCAGTGAGTCA 61.627 63.158 0.00 0.00 42.42 3.41
2688 6226 1.214062 GGGCTCGTCAGTGAGTCAG 59.786 63.158 0.00 0.00 42.42 3.51
2871 6422 3.737172 GTCTGCCGCCGCAATGTT 61.737 61.111 0.47 0.00 46.66 2.71
2903 6472 3.268103 TTCGCAGGAAAGGAGCCCC 62.268 63.158 0.00 0.00 0.00 5.80
2921 6490 2.266055 GGCGACCACAAGAGGAGG 59.734 66.667 0.00 0.00 0.00 4.30
3026 6595 2.665603 GTCTCGGCCAGGAGCTTT 59.334 61.111 2.24 0.00 43.05 3.51
3276 6845 3.732788 GCGTCTAGCTAGCTACGTC 57.267 57.895 30.47 22.15 44.04 4.34
3385 6954 2.125912 CTGCTACGGTGAAGCGCT 60.126 61.111 2.64 2.64 43.11 5.92
3552 7147 2.300437 GTCTTCAGAGCCAAGGTACTGT 59.700 50.000 11.88 0.00 40.86 3.55
3564 7159 4.262292 CCAAGGTACTGTTGCTACACTGTA 60.262 45.833 0.00 0.00 40.86 2.74
3565 7160 4.516365 AGGTACTGTTGCTACACTGTAC 57.484 45.455 16.89 16.89 44.95 2.90
3613 7208 4.344679 TGGCATCACTTTGGTCAAGAAAAT 59.655 37.500 0.00 0.00 36.21 1.82
3811 7409 2.506217 AGGTACGCACGCACATCG 60.506 61.111 0.00 0.00 45.38 3.84
3820 7418 3.481903 CGCACATCGTCGCAGCTT 61.482 61.111 0.00 0.00 0.00 3.74
3822 7420 1.510623 GCACATCGTCGCAGCTTTG 60.511 57.895 0.00 0.00 0.00 2.77
3824 7422 0.094216 CACATCGTCGCAGCTTTGAG 59.906 55.000 0.00 0.00 0.00 3.02
3825 7423 1.016130 ACATCGTCGCAGCTTTGAGG 61.016 55.000 0.00 0.00 0.00 3.86
3837 7469 2.831526 AGCTTTGAGGGAGTCTCTTCTC 59.168 50.000 0.00 13.33 42.86 2.87
4043 7677 4.660938 GGGTGGTGGTGGTGAGGC 62.661 72.222 0.00 0.00 0.00 4.70
4232 7866 4.712425 CGTCGTCGGACCACCACC 62.712 72.222 1.91 0.00 40.17 4.61
4242 7876 4.263572 CCACCACCGGCTCCAACA 62.264 66.667 0.00 0.00 0.00 3.33
4273 8000 3.044305 GTGAGCAAGAAGGCGCGT 61.044 61.111 8.43 0.00 39.27 6.01
4293 8020 1.079987 AGAGGGAGGAGAAGCAGCA 59.920 57.895 0.00 0.00 0.00 4.41
4294 8021 0.977108 AGAGGGAGGAGAAGCAGCAG 60.977 60.000 0.00 0.00 0.00 4.24
4295 8022 2.124778 GGGAGGAGAAGCAGCAGC 60.125 66.667 0.00 0.00 42.56 5.25
4372 8105 3.367025 CGGATTACTGAAACCGAGACAAC 59.633 47.826 0.00 0.00 46.94 3.32
4393 8127 4.299155 ACGGAATGATGTACATAGCTTCG 58.701 43.478 8.71 12.52 38.38 3.79
4415 8149 3.126514 GTCAGATCCTGATTGCTGTGTTG 59.873 47.826 0.00 0.00 42.73 3.33
4472 8206 1.473258 TGCTTGGTGCTGAAGTGTTT 58.527 45.000 0.00 0.00 43.37 2.83
4493 8227 7.427606 GTGTTTGATGATTCGAGCTGATTTAAG 59.572 37.037 0.00 0.00 0.00 1.85
4494 8228 7.119699 TGTTTGATGATTCGAGCTGATTTAAGT 59.880 33.333 0.00 0.00 0.00 2.24
4495 8229 6.594284 TGATGATTCGAGCTGATTTAAGTG 57.406 37.500 0.00 0.00 0.00 3.16
4498 8232 1.640428 TCGAGCTGATTTAAGTGCGG 58.360 50.000 0.00 0.00 0.00 5.69
4499 8233 1.203758 TCGAGCTGATTTAAGTGCGGA 59.796 47.619 0.00 0.00 0.00 5.54
4500 8234 1.590238 CGAGCTGATTTAAGTGCGGAG 59.410 52.381 0.00 0.00 0.00 4.63
4501 8235 2.735444 CGAGCTGATTTAAGTGCGGAGA 60.735 50.000 0.00 0.00 0.00 3.71
4560 8888 3.301379 TCACTAAATAAAGTACGCACGCG 59.699 43.478 10.36 10.36 46.03 6.01
4573 8901 4.713946 ACGCGGGTGATGAAACAT 57.286 50.000 12.47 0.00 0.00 2.71
4587 8915 7.096640 GGTGATGAAACATTTGTAAAAGTGTCG 60.097 37.037 0.00 0.00 28.90 4.35
4656 8985 5.103982 ACATCCATGATCCATCCAGTTACAA 60.104 40.000 0.00 0.00 0.00 2.41
4663 8992 1.737793 CCATCCAGTTACAAAGGCGAC 59.262 52.381 0.00 0.00 0.00 5.19
4679 9008 1.244816 CGACTCCCGCCATGACTATA 58.755 55.000 0.00 0.00 0.00 1.31
4680 9009 1.819288 CGACTCCCGCCATGACTATAT 59.181 52.381 0.00 0.00 0.00 0.86
4681 9010 2.159366 CGACTCCCGCCATGACTATATC 60.159 54.545 0.00 0.00 0.00 1.63
4682 9011 2.826128 GACTCCCGCCATGACTATATCA 59.174 50.000 0.00 0.00 43.13 2.15
4683 9012 2.563179 ACTCCCGCCATGACTATATCAC 59.437 50.000 0.00 0.00 41.24 3.06
4684 9013 2.562738 CTCCCGCCATGACTATATCACA 59.437 50.000 0.00 0.00 41.24 3.58
4685 9014 3.173151 TCCCGCCATGACTATATCACAT 58.827 45.455 0.00 0.00 41.24 3.21
4686 9015 3.195610 TCCCGCCATGACTATATCACATC 59.804 47.826 0.00 0.00 41.24 3.06
4687 9016 3.525537 CCGCCATGACTATATCACATCC 58.474 50.000 0.00 0.00 41.24 3.51
4692 9024 6.000219 GCCATGACTATATCACATCCAACTT 59.000 40.000 0.00 0.00 41.24 2.66
4706 9038 1.446907 CAACTTGCTCCACCTAGCTG 58.553 55.000 0.00 0.00 43.19 4.24
4737 9071 5.802956 GCTAAGCTAAGCACTATAATCTCCG 59.197 44.000 0.00 0.00 42.30 4.63
4751 9085 0.251209 TCTCCGGACTACTGCACAGT 60.251 55.000 0.00 8.57 45.02 3.55
4766 9100 3.508402 TGCACAGTTATACTTCTCCGACA 59.492 43.478 0.00 0.00 0.00 4.35
4767 9101 3.858238 GCACAGTTATACTTCTCCGACAC 59.142 47.826 0.00 0.00 0.00 3.67
4768 9102 4.380655 GCACAGTTATACTTCTCCGACACT 60.381 45.833 0.00 0.00 0.00 3.55
4769 9103 5.096169 CACAGTTATACTTCTCCGACACTG 58.904 45.833 0.00 0.00 37.11 3.66
4770 9104 4.158025 ACAGTTATACTTCTCCGACACTGG 59.842 45.833 0.00 0.00 35.69 4.00
4772 9106 1.557099 ATACTTCTCCGACACTGGCA 58.443 50.000 0.00 0.00 0.00 4.92
4773 9107 0.601558 TACTTCTCCGACACTGGCAC 59.398 55.000 0.00 0.00 0.00 5.01
4774 9108 1.374758 CTTCTCCGACACTGGCACC 60.375 63.158 0.00 0.00 0.00 5.01
4775 9109 2.099652 CTTCTCCGACACTGGCACCA 62.100 60.000 0.00 0.00 0.00 4.17
4942 9276 3.192922 CGGTTCGGCGTCCCATTC 61.193 66.667 6.85 0.00 0.00 2.67
4945 9279 2.046700 TTCGGCGTCCCATTCACC 60.047 61.111 6.85 0.00 0.00 4.02
5112 9449 1.851021 TTGAGCAAACATGGGACGCG 61.851 55.000 3.53 3.53 0.00 6.01
5174 9511 2.479275 GGAACGGCACAAAAGAGTACTC 59.521 50.000 15.41 15.41 0.00 2.59
5215 9552 3.169099 CTTCCTCCTTCTCCTGTCTCAA 58.831 50.000 0.00 0.00 0.00 3.02
5285 9622 2.497107 ATGCTGTGTTGTGTTCTTGC 57.503 45.000 0.00 0.00 0.00 4.01
5360 9697 6.769822 AGATATGCATGAAAAGTTAGGTCAGG 59.230 38.462 10.16 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 1.548269 CCTGTCTGAGAGTCCCACTTC 59.452 57.143 0.87 0.00 0.00 3.01
215 216 5.287226 AGTACAGAGAAAACGTACTTGTGG 58.713 41.667 0.00 0.00 42.37 4.17
314 315 4.472690 AGGTTAGCCTGCTAGTACCTAT 57.527 45.455 17.10 0.10 45.05 2.57
334 335 5.847304 TCTGCAGTTGGATTAGTATAGCAG 58.153 41.667 14.67 0.00 45.96 4.24
342 343 6.506500 AAAATGTCTCTGCAGTTGGATTAG 57.493 37.500 14.67 1.43 0.00 1.73
419 421 3.758755 TCAAGCTCAAGACACAGTGAT 57.241 42.857 7.81 0.00 0.00 3.06
532 535 8.828688 AAGCTTGTCTACGAAAACTATTTACT 57.171 30.769 0.00 0.00 0.00 2.24
661 689 6.296026 TGGTAGGCAATACAATCCTTGATAC 58.704 40.000 1.34 0.00 35.96 2.24
730 758 7.807977 ATTCACTAAAATGGCGTAATCTGAT 57.192 32.000 0.00 0.00 0.00 2.90
763 791 3.495377 ACACACATCAAAATGCATGTTGC 59.505 39.130 22.66 0.00 45.29 4.17
765 793 5.816258 TCAAACACACATCAAAATGCATGTT 59.184 32.000 0.00 0.00 42.04 2.71
824 855 3.951563 AGGGCCATATGCTTCAGTTAA 57.048 42.857 6.18 0.00 40.92 2.01
855 886 2.176273 GCATCGATCAAGCGCCTGT 61.176 57.895 2.29 0.00 0.00 4.00
915 946 7.887996 CTGAGAGCATTATCTCTGGATTTAC 57.112 40.000 5.43 0.00 45.03 2.01
928 959 1.342496 CCTCGCATCCTGAGAGCATTA 59.658 52.381 2.76 0.00 41.96 1.90
974 1005 0.397564 TCTCTGCTGCACCAATCACA 59.602 50.000 0.00 0.00 0.00 3.58
1038 1069 5.821470 GGGCCATCAATCATCATCATACTAG 59.179 44.000 4.39 0.00 0.00 2.57
1043 1074 3.431415 CAGGGCCATCAATCATCATCAT 58.569 45.455 6.18 0.00 0.00 2.45
1044 1075 2.871453 CAGGGCCATCAATCATCATCA 58.129 47.619 6.18 0.00 0.00 3.07
1045 1076 1.544691 GCAGGGCCATCAATCATCATC 59.455 52.381 6.18 0.00 0.00 2.92
1260 1299 0.318107 AACGACGTACAACCGGTGAG 60.318 55.000 8.52 6.84 0.00 3.51
1293 1341 4.590850 GGAAACCAAAGCAGAAACTGAT 57.409 40.909 2.81 0.00 32.44 2.90
1360 1408 4.889409 AGAACAGCTGAAGAATTTTCACCA 59.111 37.500 23.35 0.00 0.00 4.17
1363 1411 5.593909 TCCAAGAACAGCTGAAGAATTTTCA 59.406 36.000 23.35 0.00 0.00 2.69
1373 1421 1.270826 CGAGAGTCCAAGAACAGCTGA 59.729 52.381 23.35 0.00 0.00 4.26
1374 1422 1.707632 CGAGAGTCCAAGAACAGCTG 58.292 55.000 13.48 13.48 0.00 4.24
1375 1423 0.037790 GCGAGAGTCCAAGAACAGCT 60.038 55.000 0.00 0.00 0.00 4.24
1376 1424 1.016653 GGCGAGAGTCCAAGAACAGC 61.017 60.000 0.00 0.00 0.00 4.40
1377 1425 0.605589 AGGCGAGAGTCCAAGAACAG 59.394 55.000 0.00 0.00 35.23 3.16
1378 1426 0.603569 GAGGCGAGAGTCCAAGAACA 59.396 55.000 0.00 0.00 35.23 3.18
1379 1427 0.892063 AGAGGCGAGAGTCCAAGAAC 59.108 55.000 0.00 0.00 35.23 3.01
1381 1429 1.027255 CGAGAGGCGAGAGTCCAAGA 61.027 60.000 0.00 0.00 44.57 3.02
1382 1430 1.431440 CGAGAGGCGAGAGTCCAAG 59.569 63.158 0.00 0.00 44.57 3.61
1383 1431 3.592070 CGAGAGGCGAGAGTCCAA 58.408 61.111 0.00 0.00 44.57 3.53
1426 1475 1.686110 AGAGGAGTAACGGCAGGGG 60.686 63.158 0.00 0.00 0.00 4.79
1454 1503 1.203087 TGGAACGGAGGGAGTAGTTCA 60.203 52.381 9.01 0.00 43.24 3.18
1467 1516 1.131883 ACGACGAGTAATCTGGAACGG 59.868 52.381 0.00 0.00 32.28 4.44
1468 1517 2.174764 CACGACGAGTAATCTGGAACG 58.825 52.381 0.00 0.00 0.00 3.95
1469 1518 2.094854 ACCACGACGAGTAATCTGGAAC 60.095 50.000 0.00 0.00 0.00 3.62
1470 1519 2.165167 ACCACGACGAGTAATCTGGAA 58.835 47.619 0.00 0.00 0.00 3.53
1471 1520 1.830279 ACCACGACGAGTAATCTGGA 58.170 50.000 0.00 0.00 0.00 3.86
1472 1521 2.649331 AACCACGACGAGTAATCTGG 57.351 50.000 0.00 0.00 0.00 3.86
1473 1522 5.159209 ACTAAAACCACGACGAGTAATCTG 58.841 41.667 0.00 0.00 0.00 2.90
1474 1523 5.382618 ACTAAAACCACGACGAGTAATCT 57.617 39.130 0.00 0.00 0.00 2.40
1475 1524 5.630680 TGAACTAAAACCACGACGAGTAATC 59.369 40.000 0.00 0.00 0.00 1.75
1476 1525 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
1477 1526 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
1478 1527 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
1479 1528 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
1480 1529 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
1481 1530 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
1482 1531 8.496872 AATTAATTTGAACTAAAACCACGACG 57.503 30.769 0.00 0.00 0.00 5.12
1498 1547 5.185056 ACTCCCTCCGTTCCAAATTAATTTG 59.815 40.000 27.09 27.09 45.04 2.32
1499 1548 5.330233 ACTCCCTCCGTTCCAAATTAATTT 58.670 37.500 7.64 7.64 0.00 1.82
1500 1549 4.930696 ACTCCCTCCGTTCCAAATTAATT 58.069 39.130 0.00 0.00 0.00 1.40
1501 1550 4.586306 ACTCCCTCCGTTCCAAATTAAT 57.414 40.909 0.00 0.00 0.00 1.40
1502 1551 5.703730 ATACTCCCTCCGTTCCAAATTAA 57.296 39.130 0.00 0.00 0.00 1.40
1503 1552 6.811634 TTATACTCCCTCCGTTCCAAATTA 57.188 37.500 0.00 0.00 0.00 1.40
1504 1553 5.703730 TTATACTCCCTCCGTTCCAAATT 57.296 39.130 0.00 0.00 0.00 1.82
1505 1554 5.906772 ATTATACTCCCTCCGTTCCAAAT 57.093 39.130 0.00 0.00 0.00 2.32
1506 1555 5.190132 TCAATTATACTCCCTCCGTTCCAAA 59.810 40.000 0.00 0.00 0.00 3.28
1507 1556 4.717778 TCAATTATACTCCCTCCGTTCCAA 59.282 41.667 0.00 0.00 0.00 3.53
1508 1557 4.291792 TCAATTATACTCCCTCCGTTCCA 58.708 43.478 0.00 0.00 0.00 3.53
1509 1558 4.950205 TCAATTATACTCCCTCCGTTCC 57.050 45.455 0.00 0.00 0.00 3.62
1510 1559 5.070047 TCCTTCAATTATACTCCCTCCGTTC 59.930 44.000 0.00 0.00 0.00 3.95
1511 1560 4.966805 TCCTTCAATTATACTCCCTCCGTT 59.033 41.667 0.00 0.00 0.00 4.44
1512 1561 4.553678 TCCTTCAATTATACTCCCTCCGT 58.446 43.478 0.00 0.00 0.00 4.69
1513 1562 4.561734 GCTCCTTCAATTATACTCCCTCCG 60.562 50.000 0.00 0.00 0.00 4.63
1514 1563 4.348168 TGCTCCTTCAATTATACTCCCTCC 59.652 45.833 0.00 0.00 0.00 4.30
1515 1564 5.071115 ACTGCTCCTTCAATTATACTCCCTC 59.929 44.000 0.00 0.00 0.00 4.30
1516 1565 4.971924 ACTGCTCCTTCAATTATACTCCCT 59.028 41.667 0.00 0.00 0.00 4.20
1517 1566 5.297569 ACTGCTCCTTCAATTATACTCCC 57.702 43.478 0.00 0.00 0.00 4.30
1518 1567 6.349300 TGAACTGCTCCTTCAATTATACTCC 58.651 40.000 0.00 0.00 0.00 3.85
1519 1568 7.011857 CCTTGAACTGCTCCTTCAATTATACTC 59.988 40.741 5.00 0.00 37.09 2.59
1520 1569 6.825721 CCTTGAACTGCTCCTTCAATTATACT 59.174 38.462 5.00 0.00 37.09 2.12
1521 1570 6.038714 CCCTTGAACTGCTCCTTCAATTATAC 59.961 42.308 5.00 0.00 37.09 1.47
1522 1571 6.069673 TCCCTTGAACTGCTCCTTCAATTATA 60.070 38.462 5.00 0.00 37.09 0.98
1523 1572 4.952335 CCCTTGAACTGCTCCTTCAATTAT 59.048 41.667 5.00 0.00 37.09 1.28
1539 1588 0.881118 GACAGCGCAAATCCCTTGAA 59.119 50.000 11.47 0.00 37.17 2.69
1555 1604 0.249447 CAGGTCGAACTGTGCTGACA 60.249 55.000 22.63 0.00 33.81 3.58
1689 1738 1.670380 GCTCGGACCTCAACTCAAGTC 60.670 57.143 0.00 0.00 0.00 3.01
1707 1756 2.132996 CCGGCAGGATCTCAGAGCT 61.133 63.158 0.00 0.00 41.02 4.09
1779 1829 7.814587 CCATATCATACGATAAAAGCTCACAGA 59.185 37.037 0.00 0.00 37.65 3.41
1802 1856 2.098607 CGCTGCAATTTCTCATCACCAT 59.901 45.455 0.00 0.00 0.00 3.55
1803 1857 1.469703 CGCTGCAATTTCTCATCACCA 59.530 47.619 0.00 0.00 0.00 4.17
1804 1858 1.470098 ACGCTGCAATTTCTCATCACC 59.530 47.619 0.00 0.00 0.00 4.02
1806 1860 1.469703 CCACGCTGCAATTTCTCATCA 59.530 47.619 0.00 0.00 0.00 3.07
1808 1862 1.200716 CACCACGCTGCAATTTCTCAT 59.799 47.619 0.00 0.00 0.00 2.90
1809 1863 0.592637 CACCACGCTGCAATTTCTCA 59.407 50.000 0.00 0.00 0.00 3.27
1811 1865 1.286880 GCACCACGCTGCAATTTCT 59.713 52.632 0.00 0.00 37.11 2.52
1812 1866 2.082366 CGCACCACGCTGCAATTTC 61.082 57.895 0.00 0.00 36.94 2.17
1814 1868 4.041917 CCGCACCACGCTGCAATT 62.042 61.111 0.00 0.00 41.76 2.32
1823 1877 1.429463 CTACTCTCAAACCGCACCAC 58.571 55.000 0.00 0.00 0.00 4.16
1826 1880 1.019805 GCCCTACTCTCAAACCGCAC 61.020 60.000 0.00 0.00 0.00 5.34
1828 1882 1.449778 GGCCCTACTCTCAAACCGC 60.450 63.158 0.00 0.00 0.00 5.68
1835 1889 0.473326 TCTCCTACGGCCCTACTCTC 59.527 60.000 0.00 0.00 0.00 3.20
1846 1900 0.468400 CCCTTCTCCCCTCTCCTACG 60.468 65.000 0.00 0.00 0.00 3.51
1856 1910 1.202940 GCACCCATATTCCCTTCTCCC 60.203 57.143 0.00 0.00 0.00 4.30
1858 1912 2.576615 GTGCACCCATATTCCCTTCTC 58.423 52.381 5.22 0.00 0.00 2.87
1859 1913 1.215423 GGTGCACCCATATTCCCTTCT 59.785 52.381 26.31 0.00 0.00 2.85
1911 2286 2.280628 CTTCGCCTCATCCAACCTAAC 58.719 52.381 0.00 0.00 0.00 2.34
1938 4969 1.211457 ACTGGATCCTCACATGGCTTC 59.789 52.381 14.23 0.00 0.00 3.86
1951 4982 0.733150 GCGCCCTTTTACACTGGATC 59.267 55.000 0.00 0.00 0.00 3.36
2028 5059 6.207810 ACTTATATTAGCCTTCTCACGGAGAG 59.792 42.308 1.10 1.10 46.14 3.20
2031 5062 7.523380 GCTTACTTATATTAGCCTTCTCACGGA 60.523 40.741 0.00 0.00 0.00 4.69
2032 5063 6.586844 GCTTACTTATATTAGCCTTCTCACGG 59.413 42.308 0.00 0.00 0.00 4.94
2049 5080 0.905809 TGTCGGCAGGGGCTTACTTA 60.906 55.000 0.00 0.00 40.87 2.24
2058 5089 1.227764 CATGGATCTGTCGGCAGGG 60.228 63.158 18.55 0.00 42.78 4.45
2107 5156 3.706373 TCGACCTCTTGCCTGGGC 61.706 66.667 4.43 4.43 42.35 5.36
2152 5642 3.819337 GTCAGTCCATTCATCCATCATGG 59.181 47.826 0.00 0.00 39.17 3.66
2160 5650 2.093973 AGTCACCGTCAGTCCATTCATC 60.094 50.000 0.00 0.00 0.00 2.92
2221 5711 3.453717 GGGGGTTAGTAGTGGTTAAGAGG 59.546 52.174 0.00 0.00 0.00 3.69
2235 5725 2.039724 GGGGGAGGAGGGGGTTAG 60.040 72.222 0.00 0.00 0.00 2.34
2236 5726 2.545293 AGGGGGAGGAGGGGGTTA 60.545 66.667 0.00 0.00 0.00 2.85
2237 5727 4.371231 CAGGGGGAGGAGGGGGTT 62.371 72.222 0.00 0.00 0.00 4.11
2261 5751 7.360575 ACATGTTCTAAAACGATCTGGTTAC 57.639 36.000 0.00 0.00 38.28 2.50
2262 5752 6.592607 GGACATGTTCTAAAACGATCTGGTTA 59.407 38.462 0.00 0.00 38.28 2.85
2265 5759 4.935205 TGGACATGTTCTAAAACGATCTGG 59.065 41.667 5.55 0.00 38.28 3.86
2270 5764 6.017440 CCTCTTTTGGACATGTTCTAAAACGA 60.017 38.462 13.64 8.42 39.15 3.85
2349 5845 2.063378 GGGTCTGGCAGAGGAGAGG 61.063 68.421 19.38 0.00 0.00 3.69
2351 5847 0.473694 TTTGGGTCTGGCAGAGGAGA 60.474 55.000 19.38 1.76 0.00 3.71
2352 5848 0.401738 TTTTGGGTCTGGCAGAGGAG 59.598 55.000 19.38 0.00 0.00 3.69
2353 5849 0.401738 CTTTTGGGTCTGGCAGAGGA 59.598 55.000 19.38 1.28 0.00 3.71
2355 5851 2.276732 TTCTTTTGGGTCTGGCAGAG 57.723 50.000 19.38 4.24 0.00 3.35
2396 5900 2.907458 TGATGACAGACAGGGAGAGA 57.093 50.000 0.00 0.00 0.00 3.10
2529 6042 2.380064 ATCCAACCAAAACAGGCAGA 57.620 45.000 0.00 0.00 0.00 4.26
2531 6044 2.102252 GTGAATCCAACCAAAACAGGCA 59.898 45.455 0.00 0.00 0.00 4.75
2598 6136 4.109675 GCACCACCACCCGGCTAT 62.110 66.667 0.00 0.00 34.57 2.97
2681 6219 2.640302 GCCCTGACTCGCTGACTCA 61.640 63.158 0.00 0.00 0.00 3.41
2682 6220 2.183046 GCCCTGACTCGCTGACTC 59.817 66.667 0.00 0.00 0.00 3.36
2683 6221 3.386237 GGCCCTGACTCGCTGACT 61.386 66.667 0.00 0.00 0.00 3.41
2684 6222 2.948720 AAGGCCCTGACTCGCTGAC 61.949 63.158 0.00 0.00 0.00 3.51
2685 6223 2.604686 AAGGCCCTGACTCGCTGA 60.605 61.111 0.00 0.00 0.00 4.26
2686 6224 2.435586 CAAGGCCCTGACTCGCTG 60.436 66.667 0.00 0.00 0.00 5.18
2687 6225 3.710722 CCAAGGCCCTGACTCGCT 61.711 66.667 1.80 0.00 0.00 4.93
2713 6251 2.043953 GAGGCCCATGGGTGAACC 60.044 66.667 31.58 23.13 40.81 3.62
2871 6422 3.006859 TCCTGCGAAGAAGAAGAATGTCA 59.993 43.478 0.00 0.00 0.00 3.58
2903 6472 2.125912 CTCCTCTTGTGGTCGCCG 60.126 66.667 0.00 0.00 0.00 6.46
2921 6490 2.686835 AGCCTCAGAGAGCCCCAC 60.687 66.667 0.00 0.00 0.00 4.61
2948 6517 4.717629 TTCTCGTCGCCGCACAGG 62.718 66.667 0.00 0.00 44.97 4.00
2949 6518 3.470567 GTTCTCGTCGCCGCACAG 61.471 66.667 0.00 0.00 0.00 3.66
3026 6595 2.181777 GTCATCGCGCAGGTCTCA 59.818 61.111 8.75 0.00 0.00 3.27
3276 6845 3.564644 GCACCATGATCTTCATTCAGGAG 59.435 47.826 0.00 0.00 34.28 3.69
3385 6954 3.393970 CCGAGGCAGGGCTCTTGA 61.394 66.667 18.95 0.00 0.00 3.02
3564 7159 1.344763 GTCAAGTCCCTGTGTGCTAGT 59.655 52.381 0.00 0.00 0.00 2.57
3565 7160 1.620819 AGTCAAGTCCCTGTGTGCTAG 59.379 52.381 0.00 0.00 0.00 3.42
3613 7208 4.760715 TGCCAAATTAAGCCGTAACACTAA 59.239 37.500 0.00 0.00 0.00 2.24
3663 7261 7.770433 CACTCCTCCTGAAACATCACATTTATA 59.230 37.037 0.00 0.00 0.00 0.98
3664 7262 6.600822 CACTCCTCCTGAAACATCACATTTAT 59.399 38.462 0.00 0.00 0.00 1.40
3811 7409 1.004440 ACTCCCTCAAAGCTGCGAC 60.004 57.895 0.00 0.00 0.00 5.19
3814 7412 0.612744 AGAGACTCCCTCAAAGCTGC 59.387 55.000 0.00 0.00 44.40 5.25
3816 7414 2.831526 GAGAAGAGACTCCCTCAAAGCT 59.168 50.000 14.31 0.00 44.40 3.74
3817 7415 2.564947 TGAGAAGAGACTCCCTCAAAGC 59.435 50.000 17.82 0.00 44.40 3.51
3818 7416 4.283212 AGTTGAGAAGAGACTCCCTCAAAG 59.717 45.833 26.44 0.00 44.24 2.77
3819 7417 4.227197 AGTTGAGAAGAGACTCCCTCAAA 58.773 43.478 26.44 15.32 44.24 2.69
3820 7418 3.829601 GAGTTGAGAAGAGACTCCCTCAA 59.170 47.826 23.40 23.40 44.40 3.02
3822 7420 2.422127 CGAGTTGAGAAGAGACTCCCTC 59.578 54.545 12.96 12.96 42.28 4.30
3824 7422 2.162809 GACGAGTTGAGAAGAGACTCCC 59.837 54.545 0.00 0.00 37.17 4.30
3825 7423 3.078837 AGACGAGTTGAGAAGAGACTCC 58.921 50.000 0.00 0.00 37.17 3.85
3837 7469 0.994995 CTGCCGATCAAGACGAGTTG 59.005 55.000 0.00 0.00 0.00 3.16
4144 7778 4.537433 CCGGGCCTGTAGCAGCTC 62.537 72.222 11.58 0.00 46.50 4.09
4230 7864 0.322546 GGATCTTTGTTGGAGCCGGT 60.323 55.000 1.90 0.00 29.47 5.28
4231 7865 1.032114 GGGATCTTTGTTGGAGCCGG 61.032 60.000 0.00 0.00 39.85 6.13
4232 7866 0.322456 TGGGATCTTTGTTGGAGCCG 60.322 55.000 0.00 0.00 39.85 5.52
4242 7876 1.425066 TGCTCACCTTGTGGGATCTTT 59.575 47.619 0.00 0.00 35.82 2.52
4273 8000 0.975040 GCTGCTTCTCCTCCCTCTGA 60.975 60.000 0.00 0.00 0.00 3.27
4293 8020 2.239150 ACTTGATGATCCTTCTGCAGCT 59.761 45.455 9.47 0.00 0.00 4.24
4294 8021 2.613133 GACTTGATGATCCTTCTGCAGC 59.387 50.000 9.47 0.00 0.00 5.25
4295 8022 2.864946 CGACTTGATGATCCTTCTGCAG 59.135 50.000 7.63 7.63 0.00 4.41
4372 8105 4.299155 ACGAAGCTATGTACATCATTCCG 58.701 43.478 12.68 13.70 37.91 4.30
4393 8127 2.983229 ACACAGCAATCAGGATCTGAC 58.017 47.619 0.00 0.00 43.63 3.51
4472 8206 5.007039 GCACTTAAATCAGCTCGAATCATCA 59.993 40.000 0.00 0.00 0.00 3.07
4493 8227 0.108424 AGTCTTGCAGATCTCCGCAC 60.108 55.000 7.21 0.00 38.00 5.34
4494 8228 0.108472 CAGTCTTGCAGATCTCCGCA 60.108 55.000 3.70 3.70 36.05 5.69
4495 8229 0.174389 TCAGTCTTGCAGATCTCCGC 59.826 55.000 0.00 0.00 0.00 5.54
4498 8232 3.924144 ACTTGTCAGTCTTGCAGATCTC 58.076 45.455 0.00 0.00 0.00 2.75
4499 8233 3.613671 CGACTTGTCAGTCTTGCAGATCT 60.614 47.826 0.00 0.00 46.67 2.75
4500 8234 2.665537 CGACTTGTCAGTCTTGCAGATC 59.334 50.000 1.59 0.00 46.67 2.75
4501 8235 2.611473 CCGACTTGTCAGTCTTGCAGAT 60.611 50.000 1.59 0.00 46.67 2.90
4560 8888 6.983890 ACACTTTTACAAATGTTTCATCACCC 59.016 34.615 0.00 0.00 0.00 4.61
4573 8901 8.231837 GCTATGAATAACCGACACTTTTACAAA 58.768 33.333 0.00 0.00 0.00 2.83
4663 8992 2.562738 TGTGATATAGTCATGGCGGGAG 59.437 50.000 0.00 0.00 39.48 4.30
4679 9008 2.440409 GTGGAGCAAGTTGGATGTGAT 58.560 47.619 4.75 0.00 0.00 3.06
4680 9009 1.545428 GGTGGAGCAAGTTGGATGTGA 60.545 52.381 4.75 0.00 0.00 3.58
4681 9010 0.883833 GGTGGAGCAAGTTGGATGTG 59.116 55.000 4.75 0.00 0.00 3.21
4682 9011 0.773644 AGGTGGAGCAAGTTGGATGT 59.226 50.000 4.75 0.00 0.00 3.06
4683 9012 2.636830 CTAGGTGGAGCAAGTTGGATG 58.363 52.381 4.75 0.00 0.00 3.51
4684 9013 1.065126 GCTAGGTGGAGCAAGTTGGAT 60.065 52.381 4.75 0.00 42.36 3.41
4685 9014 0.324943 GCTAGGTGGAGCAAGTTGGA 59.675 55.000 4.75 0.00 42.36 3.53
4686 9015 0.326264 AGCTAGGTGGAGCAAGTTGG 59.674 55.000 4.75 0.00 45.43 3.77
4687 9016 1.002430 TCAGCTAGGTGGAGCAAGTTG 59.998 52.381 21.22 0.00 45.43 3.16
4716 9048 4.833380 TCCGGAGATTATAGTGCTTAGCTT 59.167 41.667 0.00 0.00 0.00 3.74
4717 9049 4.218852 GTCCGGAGATTATAGTGCTTAGCT 59.781 45.833 3.06 0.00 0.00 3.32
4718 9050 4.218852 AGTCCGGAGATTATAGTGCTTAGC 59.781 45.833 3.06 0.00 0.00 3.09
4719 9051 5.968528 AGTCCGGAGATTATAGTGCTTAG 57.031 43.478 3.06 0.00 0.00 2.18
4725 9057 4.519730 GTGCAGTAGTCCGGAGATTATAGT 59.480 45.833 3.06 0.00 0.00 2.12
4737 9071 6.210287 AGAAGTATAACTGTGCAGTAGTCC 57.790 41.667 5.18 0.00 41.58 3.85
4751 9085 3.093814 TGCCAGTGTCGGAGAAGTATAA 58.906 45.455 0.00 0.00 39.69 0.98
4770 9104 1.361668 CTGACACGTATGGCTGGTGC 61.362 60.000 0.00 0.00 33.48 5.01
4772 9106 1.596934 CCTGACACGTATGGCTGGT 59.403 57.895 0.00 0.00 45.78 4.00
4773 9107 4.521075 CCTGACACGTATGGCTGG 57.479 61.111 0.00 0.00 45.68 4.85
4774 9108 0.802222 CGACCTGACACGTATGGCTG 60.802 60.000 0.00 0.00 33.48 4.85
4775 9109 0.963856 TCGACCTGACACGTATGGCT 60.964 55.000 0.00 0.00 33.48 4.75
4776 9110 0.108992 TTCGACCTGACACGTATGGC 60.109 55.000 0.00 0.00 0.00 4.40
4777 9111 1.471287 TCTTCGACCTGACACGTATGG 59.529 52.381 0.00 0.00 0.00 2.74
4778 9112 2.516923 GTCTTCGACCTGACACGTATG 58.483 52.381 7.31 0.00 33.75 2.39
4779 9113 1.129998 CGTCTTCGACCTGACACGTAT 59.870 52.381 11.33 0.00 39.71 3.06
4780 9114 0.514255 CGTCTTCGACCTGACACGTA 59.486 55.000 11.33 0.00 39.71 3.57
4782 9116 2.081212 GCGTCTTCGACCTGACACG 61.081 63.158 11.33 3.80 39.71 4.49
5112 9449 2.540265 ATGTCCAGCGAATCATCTCC 57.460 50.000 0.00 0.00 0.00 3.71
5174 9511 2.093764 AGAGAAGCGAAGAATGAGGGTG 60.094 50.000 0.00 0.00 0.00 4.61
5215 9552 4.626042 GATGCTGGACGAATACAGAATCT 58.374 43.478 5.59 0.00 45.73 2.40
5252 9589 1.153628 AGCATTCACCTACGACGGC 60.154 57.895 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.