Multiple sequence alignment - TraesCS6A01G170000

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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 TraesCS6A01G170000 chr6A 100.000 2207 0 0 1 2207 180313023 180315229 0.000000e+00 4076
1 TraesCS6A01G170000 chr6A 80.846 804 66 41 684 1453 180370824 180371573 3.200000e-153 551
2 TraesCS6A01G170000 chr6A 90.698 86 6 2 1560 1643 149957767 149957682 1.790000e-21 113
3 TraesCS6A01G170000 chr6B 89.331 1181 50 29 422 1559 237108073 237109220 0.000000e+00 1413
4 TraesCS6A01G170000 chr6B 83.395 807 71 38 684 1456 237111552 237112329 0.000000e+00 689
5 TraesCS6A01G170000 chr6B 89.180 305 17 7 1643 1938 237109223 237109520 1.250000e-97 366
6 TraesCS6A01G170000 chr6B 87.375 301 13 5 15 310 237107702 237107982 2.730000e-84 322
7 TraesCS6A01G170000 chr6B 90.909 88 5 3 1565 1650 284188298 284188384 4.980000e-22 115
8 TraesCS6A01G170000 chr6D 87.608 1154 52 32 418 1559 137500740 137501814 0.000000e+00 1254
9 TraesCS6A01G170000 chr6D 82.641 818 67 39 684 1460 137528406 137529189 0.000000e+00 654
10 TraesCS6A01G170000 chr6D 92.000 300 17 5 1643 1942 137501817 137502109 4.380000e-112 414
11 TraesCS6A01G170000 chr3B 90.588 85 7 1 1560 1643 460240941 460240857 6.440000e-21 111
12 TraesCS6A01G170000 chr2D 89.773 88 7 2 1560 1645 74156881 74156968 6.440000e-21 111
13 TraesCS6A01G170000 chr7B 88.889 90 7 3 1563 1650 68514606 68514518 8.330000e-20 108
14 TraesCS6A01G170000 chr1D 90.476 84 5 3 1563 1644 324892748 324892830 8.330000e-20 108
15 TraesCS6A01G170000 chr1B 88.889 90 7 3 1563 1650 463266360 463266272 8.330000e-20 108
16 TraesCS6A01G170000 chr7A 86.735 98 8 5 1549 1644 643877814 643877908 1.080000e-18 104
17 TraesCS6A01G170000 chr4A 85.577 104 10 5 1549 1650 73064062 73063962 1.080000e-18 104


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 TraesCS6A01G170000 chr6A 180313023 180315229 2206 False 4076.0 4076 100.00000 1 2207 1 chr6A.!!$F1 2206
1 TraesCS6A01G170000 chr6A 180370824 180371573 749 False 551.0 551 80.84600 684 1453 1 chr6A.!!$F2 769
2 TraesCS6A01G170000 chr6B 237107702 237112329 4627 False 697.5 1413 87.32025 15 1938 4 chr6B.!!$F2 1923
3 TraesCS6A01G170000 chr6D 137500740 137502109 1369 False 834.0 1254 89.80400 418 1942 2 chr6D.!!$F2 1524
4 TraesCS6A01G170000 chr6D 137528406 137529189 783 False 654.0 654 82.64100 684 1460 1 chr6D.!!$F1 776

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
557 562 0.031178 GCAGACAAGGTGGCAAACAG 59.969 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1727 0.044092 TTGCTACTCCCTCCATCCCA 59.956 55.0 0.0 0.0 0.0 4.37 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
18 19 3.849826 ACCCCTCCCCTACATCAAA 57.150 52.632 0.00 0.00 0.00 2.69
19 20 2.068831 ACCCCTCCCCTACATCAAAA 57.931 50.000 0.00 0.00 0.00 2.44
20 21 2.364190 ACCCCTCCCCTACATCAAAAA 58.636 47.619 0.00 0.00 0.00 1.94
148 149 0.806102 CGTCTACCTTGTGCATCCGG 60.806 60.000 0.00 0.00 0.00 5.14
149 150 0.462047 GTCTACCTTGTGCATCCGGG 60.462 60.000 0.00 0.00 0.00 5.73
150 151 1.819632 CTACCTTGTGCATCCGGGC 60.820 63.158 0.00 0.00 0.00 6.13
151 152 2.257409 CTACCTTGTGCATCCGGGCT 62.257 60.000 0.00 0.00 34.04 5.19
152 153 0.978667 TACCTTGTGCATCCGGGCTA 60.979 55.000 0.00 0.00 34.04 3.93
153 154 1.819632 CCTTGTGCATCCGGGCTAC 60.820 63.158 0.00 0.11 34.04 3.58
154 155 1.221840 CTTGTGCATCCGGGCTACT 59.778 57.895 0.00 0.00 34.04 2.57
155 156 1.078497 TTGTGCATCCGGGCTACTG 60.078 57.895 0.00 0.00 34.04 2.74
156 157 2.203070 GTGCATCCGGGCTACTGG 60.203 66.667 0.00 0.00 45.08 4.00
162 163 4.162690 CCGGGCTACTGGAGGTGC 62.163 72.222 0.00 0.00 46.80 5.01
163 164 4.514577 CGGGCTACTGGAGGTGCG 62.515 72.222 0.00 0.00 0.00 5.34
172 173 2.679996 GGAGGTGCGCCCCAAAAT 60.680 61.111 12.68 0.00 34.57 1.82
190 191 6.926826 CCCAAAATCCCTAAACAACAGTAAAC 59.073 38.462 0.00 0.00 0.00 2.01
193 194 8.813282 CAAAATCCCTAAACAACAGTAAACAAC 58.187 33.333 0.00 0.00 0.00 3.32
220 221 0.942410 ATCCACACGGTGTTTCGTCG 60.942 55.000 11.82 0.00 41.86 5.12
224 225 3.324671 ACGGTGTTTCGTCGCACG 61.325 61.111 2.79 2.79 44.19 5.34
291 296 3.742433 AGGAAATCCTGCTATGAGTCG 57.258 47.619 0.00 0.00 46.55 4.18
316 321 1.981254 AATTTGCGAATTCAGCACCG 58.019 45.000 19.69 1.60 45.10 4.94
317 322 0.881118 ATTTGCGAATTCAGCACCGT 59.119 45.000 19.69 9.56 45.10 4.83
320 325 1.225745 GCGAATTCAGCACCGTTCG 60.226 57.895 14.59 9.12 44.41 3.95
321 326 1.897398 GCGAATTCAGCACCGTTCGT 61.897 55.000 14.59 0.00 43.72 3.85
322 327 0.093026 CGAATTCAGCACCGTTCGTC 59.907 55.000 6.22 0.00 38.77 4.20
323 328 1.144969 GAATTCAGCACCGTTCGTCA 58.855 50.000 0.00 0.00 0.00 4.35
324 329 1.732259 GAATTCAGCACCGTTCGTCAT 59.268 47.619 0.00 0.00 0.00 3.06
325 330 1.808411 ATTCAGCACCGTTCGTCATT 58.192 45.000 0.00 0.00 0.00 2.57
326 331 1.144969 TTCAGCACCGTTCGTCATTC 58.855 50.000 0.00 0.00 0.00 2.67
327 332 0.317160 TCAGCACCGTTCGTCATTCT 59.683 50.000 0.00 0.00 0.00 2.40
328 333 0.716108 CAGCACCGTTCGTCATTCTC 59.284 55.000 0.00 0.00 0.00 2.87
329 334 0.732880 AGCACCGTTCGTCATTCTCG 60.733 55.000 0.00 0.00 0.00 4.04
330 335 1.683790 GCACCGTTCGTCATTCTCGG 61.684 60.000 0.00 0.00 45.53 4.63
339 344 1.800655 CGTCATTCTCGGCCTTCAGAG 60.801 57.143 0.00 0.00 35.91 3.35
348 353 2.093973 TCGGCCTTCAGAGACATTCTTC 60.094 50.000 0.00 0.00 32.41 2.87
352 357 2.275318 CTTCAGAGACATTCTTCGCCC 58.725 52.381 0.00 0.00 32.41 6.13
357 362 0.105039 AGACATTCTTCGCCCGGATC 59.895 55.000 0.73 0.00 0.00 3.36
359 364 0.541863 ACATTCTTCGCCCGGATCTT 59.458 50.000 0.73 0.00 0.00 2.40
361 366 1.599542 CATTCTTCGCCCGGATCTTTC 59.400 52.381 0.73 0.00 0.00 2.62
367 372 0.733150 CGCCCGGATCTTTCTTTTCC 59.267 55.000 0.73 0.00 0.00 3.13
369 374 2.447443 GCCCGGATCTTTCTTTTCCTT 58.553 47.619 0.73 0.00 0.00 3.36
370 375 3.617284 GCCCGGATCTTTCTTTTCCTTA 58.383 45.455 0.73 0.00 0.00 2.69
371 376 4.207955 GCCCGGATCTTTCTTTTCCTTAT 58.792 43.478 0.73 0.00 0.00 1.73
372 377 4.276183 GCCCGGATCTTTCTTTTCCTTATC 59.724 45.833 0.73 0.00 0.00 1.75
373 378 5.685728 CCCGGATCTTTCTTTTCCTTATCT 58.314 41.667 0.73 0.00 0.00 1.98
374 379 6.122964 CCCGGATCTTTCTTTTCCTTATCTT 58.877 40.000 0.73 0.00 0.00 2.40
376 381 7.773690 CCCGGATCTTTCTTTTCCTTATCTTAA 59.226 37.037 0.73 0.00 0.00 1.85
377 382 9.343539 CCGGATCTTTCTTTTCCTTATCTTAAT 57.656 33.333 0.00 0.00 0.00 1.40
461 466 1.210931 CTCTTGGTGCCAATGCGTG 59.789 57.895 3.91 0.00 41.78 5.34
480 485 3.586892 GTGCTACAGTGTAGAAAGACCC 58.413 50.000 30.32 13.28 0.00 4.46
523 528 2.033194 GTAGGGCGCACCACAGTTC 61.033 63.158 5.73 0.00 43.89 3.01
557 562 0.031178 GCAGACAAGGTGGCAAACAG 59.969 55.000 0.00 0.00 0.00 3.16
655 667 1.736645 CCAGTAACTCGTGCGGTGG 60.737 63.158 0.00 0.00 0.00 4.61
656 668 1.736645 CAGTAACTCGTGCGGTGGG 60.737 63.158 0.00 0.00 0.00 4.61
675 687 4.460683 TGAGGCGCGGGCGTTAAT 62.461 61.111 20.87 2.86 41.24 1.40
676 688 3.937062 GAGGCGCGGGCGTTAATG 61.937 66.667 20.87 0.00 41.24 1.90
677 689 4.770874 AGGCGCGGGCGTTAATGT 62.771 61.111 18.90 0.00 41.24 2.71
678 690 4.530325 GGCGCGGGCGTTAATGTG 62.530 66.667 18.90 0.00 41.24 3.21
679 691 3.492545 GCGCGGGCGTTAATGTGA 61.493 61.111 9.31 0.00 42.09 3.58
680 692 2.819552 GCGCGGGCGTTAATGTGAT 61.820 57.895 9.31 0.00 42.09 3.06
681 693 1.719117 CGCGGGCGTTAATGTGATT 59.281 52.632 4.64 0.00 34.35 2.57
896 939 2.332063 GAAGCATCGAATTCCTCCCA 57.668 50.000 0.00 0.00 0.00 4.37
897 940 2.216898 GAAGCATCGAATTCCTCCCAG 58.783 52.381 0.00 0.00 0.00 4.45
898 941 0.471617 AGCATCGAATTCCTCCCAGG 59.528 55.000 0.00 0.00 36.46 4.45
905 948 2.743183 CGAATTCCTCCCAGGCTAACAG 60.743 54.545 0.00 0.00 34.61 3.16
906 949 1.972588 ATTCCTCCCAGGCTAACAGT 58.027 50.000 0.00 0.00 34.61 3.55
945 992 1.067060 CGATCGAGAGCCCAACATACA 59.933 52.381 10.26 0.00 0.00 2.29
949 996 2.159099 TCGAGAGCCCAACATACATCAC 60.159 50.000 0.00 0.00 0.00 3.06
958 1009 3.555956 CCAACATACATCACCGAAGCTAC 59.444 47.826 0.00 0.00 0.00 3.58
959 1010 4.433615 CAACATACATCACCGAAGCTACT 58.566 43.478 0.00 0.00 0.00 2.57
984 1035 3.193903 ACGAGAGAAGAAGCTAAGAACCC 59.806 47.826 0.00 0.00 0.00 4.11
1008 1059 2.044946 AGGAAGACAATGGGCGGC 60.045 61.111 0.00 0.00 0.00 6.53
1350 1437 5.006386 GGGTGAGCTCCTAATGAATAATGG 58.994 45.833 12.15 0.00 0.00 3.16
1437 1532 8.160342 GTGTGCAGTACGTATATGTAATTATGC 58.840 37.037 17.55 17.55 0.00 3.14
1544 1645 0.387929 ACGCTTCCTCACGACTTCAA 59.612 50.000 0.00 0.00 0.00 2.69
1559 1660 6.146837 CACGACTTCAAGAGAAAATCACATCT 59.853 38.462 0.00 0.00 32.35 2.90
1560 1661 7.329471 CACGACTTCAAGAGAAAATCACATCTA 59.671 37.037 0.00 0.00 32.35 1.98
1561 1662 7.329717 ACGACTTCAAGAGAAAATCACATCTAC 59.670 37.037 0.00 0.00 32.35 2.59
1562 1663 7.543868 CGACTTCAAGAGAAAATCACATCTACT 59.456 37.037 0.00 0.00 32.35 2.57
1563 1664 8.770438 ACTTCAAGAGAAAATCACATCTACTC 57.230 34.615 0.00 0.00 32.35 2.59
1564 1665 7.821846 ACTTCAAGAGAAAATCACATCTACTCC 59.178 37.037 0.00 0.00 32.35 3.85
1565 1666 6.644347 TCAAGAGAAAATCACATCTACTCCC 58.356 40.000 0.00 0.00 0.00 4.30
1566 1667 6.441924 TCAAGAGAAAATCACATCTACTCCCT 59.558 38.462 0.00 0.00 0.00 4.20
1567 1668 6.478512 AGAGAAAATCACATCTACTCCCTC 57.521 41.667 0.00 0.00 0.00 4.30
1568 1669 6.201591 AGAGAAAATCACATCTACTCCCTCT 58.798 40.000 0.00 0.00 0.00 3.69
1569 1670 6.098124 AGAGAAAATCACATCTACTCCCTCTG 59.902 42.308 0.00 0.00 0.00 3.35
1570 1671 5.723887 AGAAAATCACATCTACTCCCTCTGT 59.276 40.000 0.00 0.00 0.00 3.41
1571 1672 5.606348 AAATCACATCTACTCCCTCTGTC 57.394 43.478 0.00 0.00 0.00 3.51
1572 1673 4.534647 ATCACATCTACTCCCTCTGTCT 57.465 45.455 0.00 0.00 0.00 3.41
1573 1674 3.892284 TCACATCTACTCCCTCTGTCTC 58.108 50.000 0.00 0.00 0.00 3.36
1574 1675 3.267031 TCACATCTACTCCCTCTGTCTCA 59.733 47.826 0.00 0.00 0.00 3.27
1575 1676 4.079500 TCACATCTACTCCCTCTGTCTCAT 60.080 45.833 0.00 0.00 0.00 2.90
1576 1677 5.132816 TCACATCTACTCCCTCTGTCTCATA 59.867 44.000 0.00 0.00 0.00 2.15
1577 1678 5.830457 CACATCTACTCCCTCTGTCTCATAA 59.170 44.000 0.00 0.00 0.00 1.90
1578 1679 6.493115 CACATCTACTCCCTCTGTCTCATAAT 59.507 42.308 0.00 0.00 0.00 1.28
1579 1680 7.667635 CACATCTACTCCCTCTGTCTCATAATA 59.332 40.741 0.00 0.00 0.00 0.98
1580 1681 7.668052 ACATCTACTCCCTCTGTCTCATAATAC 59.332 40.741 0.00 0.00 0.00 1.89
1581 1682 7.150447 TCTACTCCCTCTGTCTCATAATACA 57.850 40.000 0.00 0.00 0.00 2.29
1582 1683 7.583625 TCTACTCCCTCTGTCTCATAATACAA 58.416 38.462 0.00 0.00 0.00 2.41
1583 1684 6.723298 ACTCCCTCTGTCTCATAATACAAG 57.277 41.667 0.00 0.00 0.00 3.16
1584 1685 6.436027 ACTCCCTCTGTCTCATAATACAAGA 58.564 40.000 0.00 0.00 0.00 3.02
1585 1686 6.549364 ACTCCCTCTGTCTCATAATACAAGAG 59.451 42.308 0.00 0.00 0.00 2.85
1586 1687 5.303078 TCCCTCTGTCTCATAATACAAGAGC 59.697 44.000 0.00 0.00 0.00 4.09
1587 1688 5.218885 CCTCTGTCTCATAATACAAGAGCG 58.781 45.833 0.00 0.00 0.00 5.03
1588 1689 5.221145 CCTCTGTCTCATAATACAAGAGCGT 60.221 44.000 0.00 0.00 0.00 5.07
1589 1690 6.208988 TCTGTCTCATAATACAAGAGCGTT 57.791 37.500 0.00 0.00 0.00 4.84
1590 1691 6.631016 TCTGTCTCATAATACAAGAGCGTTT 58.369 36.000 0.00 0.00 0.00 3.60
1591 1692 7.097192 TCTGTCTCATAATACAAGAGCGTTTT 58.903 34.615 0.00 0.00 0.00 2.43
1592 1693 7.060600 TGTCTCATAATACAAGAGCGTTTTG 57.939 36.000 0.00 0.00 0.00 2.44
1593 1694 6.871492 TGTCTCATAATACAAGAGCGTTTTGA 59.129 34.615 5.15 0.00 0.00 2.69
1594 1695 7.148639 TGTCTCATAATACAAGAGCGTTTTGAC 60.149 37.037 5.15 0.00 0.00 3.18
1595 1696 6.871492 TCTCATAATACAAGAGCGTTTTGACA 59.129 34.615 5.15 0.00 0.00 3.58
1596 1697 6.827641 TCATAATACAAGAGCGTTTTGACAC 58.172 36.000 5.15 0.00 0.00 3.67
1597 1698 6.649141 TCATAATACAAGAGCGTTTTGACACT 59.351 34.615 5.15 0.00 0.00 3.55
1598 1699 7.815549 TCATAATACAAGAGCGTTTTGACACTA 59.184 33.333 5.15 0.00 0.00 2.74
1599 1700 6.854496 AATACAAGAGCGTTTTGACACTAA 57.146 33.333 5.15 0.00 0.00 2.24
1600 1701 7.435068 AATACAAGAGCGTTTTGACACTAAT 57.565 32.000 5.15 0.00 0.00 1.73
1601 1702 5.095691 ACAAGAGCGTTTTGACACTAATG 57.904 39.130 5.15 0.00 0.00 1.90
1602 1703 4.574828 ACAAGAGCGTTTTGACACTAATGT 59.425 37.500 5.15 0.00 43.71 2.71
1603 1704 5.756347 ACAAGAGCGTTTTGACACTAATGTA 59.244 36.000 5.15 0.00 39.95 2.29
1604 1705 5.840940 AGAGCGTTTTGACACTAATGTAC 57.159 39.130 0.00 0.00 39.95 2.90
1605 1706 5.539048 AGAGCGTTTTGACACTAATGTACT 58.461 37.500 0.00 0.00 39.95 2.73
1606 1707 5.405571 AGAGCGTTTTGACACTAATGTACTG 59.594 40.000 0.00 0.00 39.95 2.74
1607 1708 5.054477 AGCGTTTTGACACTAATGTACTGT 58.946 37.500 0.00 0.00 39.95 3.55
1608 1709 5.526111 AGCGTTTTGACACTAATGTACTGTT 59.474 36.000 0.00 0.00 39.95 3.16
1609 1710 6.702723 AGCGTTTTGACACTAATGTACTGTTA 59.297 34.615 0.00 0.00 39.95 2.41
1610 1711 7.225145 AGCGTTTTGACACTAATGTACTGTTAA 59.775 33.333 0.00 0.00 39.95 2.01
1611 1712 7.851963 GCGTTTTGACACTAATGTACTGTTAAA 59.148 33.333 0.00 0.00 39.95 1.52
1612 1713 9.705471 CGTTTTGACACTAATGTACTGTTAAAA 57.295 29.630 9.42 9.42 39.95 1.52
1615 1716 9.991388 TTTGACACTAATGTACTGTTAAAACAC 57.009 29.630 0.00 0.00 39.95 3.32
1616 1717 8.951787 TGACACTAATGTACTGTTAAAACACT 57.048 30.769 0.00 0.00 39.95 3.55
1617 1718 9.037737 TGACACTAATGTACTGTTAAAACACTC 57.962 33.333 0.00 0.00 39.95 3.51
1618 1719 9.257651 GACACTAATGTACTGTTAAAACACTCT 57.742 33.333 0.00 0.00 39.95 3.24
1619 1720 9.609346 ACACTAATGTACTGTTAAAACACTCTT 57.391 29.630 0.00 0.00 37.26 2.85
1635 1736 9.799106 AAAACACTCTTATATTATGGGATGGAG 57.201 33.333 0.00 0.00 0.00 3.86
1636 1737 7.502060 ACACTCTTATATTATGGGATGGAGG 57.498 40.000 0.00 0.00 0.00 4.30
1637 1738 6.445139 ACACTCTTATATTATGGGATGGAGGG 59.555 42.308 0.00 0.00 0.00 4.30
1638 1739 6.673978 CACTCTTATATTATGGGATGGAGGGA 59.326 42.308 0.00 0.00 0.00 4.20
1639 1740 6.905776 ACTCTTATATTATGGGATGGAGGGAG 59.094 42.308 0.00 0.00 0.00 4.30
1640 1741 6.826727 TCTTATATTATGGGATGGAGGGAGT 58.173 40.000 0.00 0.00 0.00 3.85
1641 1742 7.961940 TCTTATATTATGGGATGGAGGGAGTA 58.038 38.462 0.00 0.00 0.00 2.59
1648 1749 2.979678 GGGATGGAGGGAGTAGCAATTA 59.020 50.000 0.00 0.00 0.00 1.40
1651 1752 3.926058 TGGAGGGAGTAGCAATTAACC 57.074 47.619 0.00 0.00 0.00 2.85
1676 1777 2.500582 GCGAGCGAAAGTTGCAGC 60.501 61.111 0.00 0.00 33.85 5.25
1718 1824 5.221224 TGTGTTTTCTGGTGATTGATCAACC 60.221 40.000 11.07 9.27 43.80 3.77
1743 1849 4.446371 CACTGAAAAGACTAGCTATGGGG 58.554 47.826 0.00 0.00 0.00 4.96
1784 1890 4.889112 ATGCATCCGGCCTGGCAG 62.889 66.667 22.05 17.07 43.89 4.85
1833 1939 4.679373 TGCCAGGCATGTTTAAGAAAAA 57.321 36.364 11.22 0.00 31.71 1.94
1879 1989 2.171027 TCAAACTGGTCACCGGTAACTT 59.829 45.455 9.35 0.00 43.15 2.66
1894 2004 4.921515 CGGTAACTTCTTCAGTTCGATCAA 59.078 41.667 0.00 0.00 42.62 2.57
1928 2038 5.278061 AGTAGGTAAGATTTCTGCACCCTA 58.722 41.667 7.62 0.00 34.24 3.53
1957 2067 9.772973 AAATTACCATGTTTTTCCTTAGGTTTC 57.227 29.630 0.00 0.00 0.00 2.78
1958 2068 8.721133 ATTACCATGTTTTTCCTTAGGTTTCT 57.279 30.769 0.00 0.00 0.00 2.52
1959 2069 6.650427 ACCATGTTTTTCCTTAGGTTTCTC 57.350 37.500 0.00 0.00 0.00 2.87
1960 2070 6.133356 ACCATGTTTTTCCTTAGGTTTCTCA 58.867 36.000 0.00 0.00 0.00 3.27
1961 2071 6.782494 ACCATGTTTTTCCTTAGGTTTCTCAT 59.218 34.615 0.00 0.00 0.00 2.90
1962 2072 7.290014 ACCATGTTTTTCCTTAGGTTTCTCATT 59.710 33.333 0.00 0.00 0.00 2.57
1963 2073 7.814587 CCATGTTTTTCCTTAGGTTTCTCATTC 59.185 37.037 0.00 0.00 0.00 2.67
1964 2074 8.579863 CATGTTTTTCCTTAGGTTTCTCATTCT 58.420 33.333 0.00 0.00 0.00 2.40
1965 2075 8.166422 TGTTTTTCCTTAGGTTTCTCATTCTC 57.834 34.615 0.00 0.00 0.00 2.87
1966 2076 7.777910 TGTTTTTCCTTAGGTTTCTCATTCTCA 59.222 33.333 0.00 0.00 0.00 3.27
1967 2077 8.630037 GTTTTTCCTTAGGTTTCTCATTCTCAA 58.370 33.333 0.00 0.00 0.00 3.02
1968 2078 7.986085 TTTCCTTAGGTTTCTCATTCTCAAG 57.014 36.000 0.00 0.00 0.00 3.02
1969 2079 6.935240 TCCTTAGGTTTCTCATTCTCAAGA 57.065 37.500 0.00 0.00 0.00 3.02
1970 2080 7.316393 TCCTTAGGTTTCTCATTCTCAAGAA 57.684 36.000 0.00 0.00 38.56 2.52
1971 2081 7.390027 TCCTTAGGTTTCTCATTCTCAAGAAG 58.610 38.462 0.00 0.00 37.48 2.85
1972 2082 7.016661 TCCTTAGGTTTCTCATTCTCAAGAAGT 59.983 37.037 0.00 0.00 37.48 3.01
1973 2083 7.663493 CCTTAGGTTTCTCATTCTCAAGAAGTT 59.337 37.037 0.00 0.00 37.48 2.66
1974 2084 8.980481 TTAGGTTTCTCATTCTCAAGAAGTTT 57.020 30.769 0.00 0.00 37.48 2.66
1975 2085 7.269477 AGGTTTCTCATTCTCAAGAAGTTTG 57.731 36.000 0.00 0.00 37.48 2.93
1976 2086 6.830838 AGGTTTCTCATTCTCAAGAAGTTTGT 59.169 34.615 0.00 0.00 37.48 2.83
1977 2087 6.914757 GGTTTCTCATTCTCAAGAAGTTTGTG 59.085 38.462 0.00 0.00 37.48 3.33
1978 2088 7.415653 GGTTTCTCATTCTCAAGAAGTTTGTGT 60.416 37.037 0.00 0.00 37.48 3.72
1979 2089 7.630242 TTCTCATTCTCAAGAAGTTTGTGTT 57.370 32.000 0.00 0.00 37.48 3.32
1980 2090 7.251704 TCTCATTCTCAAGAAGTTTGTGTTC 57.748 36.000 0.00 0.00 37.48 3.18
1981 2091 6.823182 TCTCATTCTCAAGAAGTTTGTGTTCA 59.177 34.615 0.00 0.00 37.48 3.18
1982 2092 7.500227 TCTCATTCTCAAGAAGTTTGTGTTCAT 59.500 33.333 0.00 0.00 37.48 2.57
1983 2093 8.675705 TCATTCTCAAGAAGTTTGTGTTCATA 57.324 30.769 0.00 0.00 37.48 2.15
1984 2094 9.288576 TCATTCTCAAGAAGTTTGTGTTCATAT 57.711 29.630 0.00 0.00 37.48 1.78
1985 2095 9.338291 CATTCTCAAGAAGTTTGTGTTCATATG 57.662 33.333 0.00 0.00 37.48 1.78
1986 2096 8.450578 TTCTCAAGAAGTTTGTGTTCATATGT 57.549 30.769 1.90 0.00 0.00 2.29
1987 2097 8.450578 TCTCAAGAAGTTTGTGTTCATATGTT 57.549 30.769 1.90 0.00 0.00 2.71
1988 2098 8.902806 TCTCAAGAAGTTTGTGTTCATATGTTT 58.097 29.630 1.90 0.00 0.00 2.83
1989 2099 9.520204 CTCAAGAAGTTTGTGTTCATATGTTTT 57.480 29.630 1.90 0.00 0.00 2.43
1990 2100 9.868277 TCAAGAAGTTTGTGTTCATATGTTTTT 57.132 25.926 1.90 0.00 0.00 1.94
2031 2141 3.888930 TCATATGTGATCTACGAGTGGCA 59.111 43.478 1.90 0.00 0.00 4.92
2033 2143 2.584492 TGTGATCTACGAGTGGCATG 57.416 50.000 0.00 0.00 0.00 4.06
2048 2158 1.410153 GGCATGCCTATGGAAAACCTG 59.590 52.381 29.98 0.00 34.79 4.00
2055 2165 5.083122 TGCCTATGGAAAACCTGAATCAAA 58.917 37.500 0.00 0.00 0.00 2.69
2112 2222 1.604693 CCGGTTGTATCTCGTATGGCC 60.605 57.143 0.00 0.00 0.00 5.36
2117 2227 3.746045 TGTATCTCGTATGGCCCTTTC 57.254 47.619 0.00 0.00 0.00 2.62
2155 2277 3.705579 CCAAGTGATGGCAAAATATCCCA 59.294 43.478 0.00 0.00 43.80 4.37
2160 2282 4.037208 GTGATGGCAAAATATCCCAGTCAG 59.963 45.833 0.00 0.00 31.12 3.51
2161 2283 3.737559 TGGCAAAATATCCCAGTCAGT 57.262 42.857 0.00 0.00 0.00 3.41
2162 2284 4.046286 TGGCAAAATATCCCAGTCAGTT 57.954 40.909 0.00 0.00 0.00 3.16
2163 2285 5.186256 TGGCAAAATATCCCAGTCAGTTA 57.814 39.130 0.00 0.00 0.00 2.24
2184 2306 3.223674 ACTGGATTTCTCAAAACCGGT 57.776 42.857 0.00 0.00 33.76 5.28
2185 2307 2.884639 ACTGGATTTCTCAAAACCGGTG 59.115 45.455 8.52 0.00 35.57 4.94
2196 2318 5.086104 TCAAAACCGGTGAAAATTCCAAA 57.914 34.783 8.52 0.00 0.00 3.28
2201 2323 3.127589 CCGGTGAAAATTCCAAACCAAC 58.872 45.455 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.068831 TTTTGATGTAGGGGAGGGGT 57.931 50.000 0.00 0.00 0.00 4.95
22 23 0.849540 ATCGGGGAGGGGTCCTTTTT 60.850 55.000 0.00 0.00 31.76 1.94
23 24 0.849540 AATCGGGGAGGGGTCCTTTT 60.850 55.000 0.00 0.00 31.76 2.27
24 25 1.230182 AATCGGGGAGGGGTCCTTT 60.230 57.895 0.00 0.00 31.76 3.11
25 26 2.001269 CAATCGGGGAGGGGTCCTT 61.001 63.158 0.00 0.00 31.76 3.36
26 27 2.366972 CAATCGGGGAGGGGTCCT 60.367 66.667 0.00 0.00 36.03 3.85
27 28 3.489513 CCAATCGGGGAGGGGTCC 61.490 72.222 0.00 0.00 0.00 4.46
28 29 4.191015 GCCAATCGGGGAGGGGTC 62.191 72.222 0.00 0.00 37.04 4.46
38 39 1.470098 CCTTCTTTGACTGGCCAATCG 59.530 52.381 10.07 0.00 0.00 3.34
148 149 4.840005 GGCGCACCTCCAGTAGCC 62.840 72.222 10.83 0.00 42.07 3.93
149 150 4.840005 GGGCGCACCTCCAGTAGC 62.840 72.222 10.83 0.00 35.85 3.58
150 151 4.162690 GGGGCGCACCTCCAGTAG 62.163 72.222 24.98 0.00 40.03 2.57
153 154 4.659172 TTTGGGGCGCACCTCCAG 62.659 66.667 32.18 0.00 37.52 3.86
154 155 3.521765 ATTTTGGGGCGCACCTCCA 62.522 57.895 32.18 18.00 34.30 3.86
155 156 2.679996 ATTTTGGGGCGCACCTCC 60.680 61.111 32.18 15.46 34.30 4.30
156 157 2.710902 GGATTTTGGGGCGCACCTC 61.711 63.158 32.18 19.15 40.03 3.85
157 158 2.679996 GGATTTTGGGGCGCACCT 60.680 61.111 32.18 9.68 40.03 4.00
158 159 2.847366 TAGGGATTTTGGGGCGCACC 62.847 60.000 25.59 25.59 39.11 5.01
159 160 0.968393 TTAGGGATTTTGGGGCGCAC 60.968 55.000 10.83 4.83 0.00 5.34
160 161 0.251832 TTTAGGGATTTTGGGGCGCA 60.252 50.000 10.83 0.00 0.00 6.09
161 162 0.174845 GTTTAGGGATTTTGGGGCGC 59.825 55.000 0.00 0.00 0.00 6.53
162 163 1.551452 TGTTTAGGGATTTTGGGGCG 58.449 50.000 0.00 0.00 0.00 6.13
163 164 2.635427 TGTTGTTTAGGGATTTTGGGGC 59.365 45.455 0.00 0.00 0.00 5.80
190 191 0.784178 CGTGTGGATGTCGTCAGTTG 59.216 55.000 0.00 0.00 0.00 3.16
193 194 1.008875 CACCGTGTGGATGTCGTCAG 61.009 60.000 0.00 0.00 39.21 3.51
220 221 9.476761 GAATCAAATTTGGATTTAAAATCGTGC 57.523 29.630 17.90 0.00 35.23 5.34
291 296 5.250332 GTGCTGAATTCGCAAATTTATTGC 58.750 37.500 20.96 3.16 39.39 3.56
310 315 0.732880 CGAGAATGACGAACGGTGCT 60.733 55.000 0.00 0.00 0.00 4.40
311 316 1.683790 CCGAGAATGACGAACGGTGC 61.684 60.000 0.00 0.00 38.97 5.01
316 321 1.000145 GAAGGCCGAGAATGACGAAC 59.000 55.000 0.00 0.00 0.00 3.95
317 322 0.606096 TGAAGGCCGAGAATGACGAA 59.394 50.000 0.00 0.00 0.00 3.85
320 325 1.478510 TCTCTGAAGGCCGAGAATGAC 59.521 52.381 5.68 0.00 33.62 3.06
321 326 1.478510 GTCTCTGAAGGCCGAGAATGA 59.521 52.381 9.37 0.00 37.96 2.57
322 327 1.205655 TGTCTCTGAAGGCCGAGAATG 59.794 52.381 9.37 0.00 37.96 2.67
323 328 1.561643 TGTCTCTGAAGGCCGAGAAT 58.438 50.000 9.37 0.00 37.96 2.40
324 329 1.561643 ATGTCTCTGAAGGCCGAGAA 58.438 50.000 9.37 2.32 37.96 2.87
325 330 1.478510 GAATGTCTCTGAAGGCCGAGA 59.521 52.381 4.14 4.14 34.12 4.04
326 331 1.480137 AGAATGTCTCTGAAGGCCGAG 59.520 52.381 0.00 0.00 31.12 4.63
327 332 1.561643 AGAATGTCTCTGAAGGCCGA 58.438 50.000 0.00 0.00 31.12 5.54
328 333 2.275318 GAAGAATGTCTCTGAAGGCCG 58.725 52.381 0.00 0.00 33.37 6.13
329 334 2.275318 CGAAGAATGTCTCTGAAGGCC 58.725 52.381 0.00 0.00 33.37 5.19
330 335 1.663135 GCGAAGAATGTCTCTGAAGGC 59.337 52.381 0.00 0.00 33.37 4.35
339 344 0.105039 AGATCCGGGCGAAGAATGTC 59.895 55.000 0.00 0.00 0.00 3.06
348 353 0.733150 GGAAAAGAAAGATCCGGGCG 59.267 55.000 0.00 0.00 0.00 6.13
409 414 8.980481 TCAAGTTCCAGAAGTTTCTCTAATTT 57.020 30.769 0.00 0.00 34.74 1.82
410 415 8.214364 ACTCAAGTTCCAGAAGTTTCTCTAATT 58.786 33.333 0.00 0.00 34.74 1.40
411 416 7.740805 ACTCAAGTTCCAGAAGTTTCTCTAAT 58.259 34.615 0.00 0.00 34.74 1.73
413 418 6.732896 ACTCAAGTTCCAGAAGTTTCTCTA 57.267 37.500 0.00 0.00 34.74 2.43
414 419 5.622346 ACTCAAGTTCCAGAAGTTTCTCT 57.378 39.130 0.00 0.00 34.74 3.10
416 421 5.745227 TCAACTCAAGTTCCAGAAGTTTCT 58.255 37.500 0.00 0.00 35.83 2.52
461 466 3.851098 CAGGGTCTTTCTACACTGTAGC 58.149 50.000 10.92 0.00 44.37 3.58
480 485 1.858091 CAGCTGGGCGTAGTAATCAG 58.142 55.000 5.57 0.00 0.00 2.90
523 528 0.040514 TCTGCAATGCCGTGAAAACG 60.041 50.000 1.53 0.00 0.00 3.60
570 575 4.021981 GGTGAACCATTCTTTTTCCTCCAG 60.022 45.833 0.00 0.00 35.64 3.86
663 675 0.315869 GAATCACATTAACGCCCGCG 60.316 55.000 7.69 7.69 46.03 6.46
894 937 4.443034 GGAGTTGGTATACTGTTAGCCTGG 60.443 50.000 2.25 0.00 0.00 4.45
896 939 4.161754 GTGGAGTTGGTATACTGTTAGCCT 59.838 45.833 2.25 0.00 0.00 4.58
897 940 4.081309 TGTGGAGTTGGTATACTGTTAGCC 60.081 45.833 2.25 0.00 0.00 3.93
898 941 5.080969 TGTGGAGTTGGTATACTGTTAGC 57.919 43.478 2.25 0.00 0.00 3.09
905 948 1.287425 GCGCTGTGGAGTTGGTATAC 58.713 55.000 0.00 0.00 0.00 1.47
906 949 0.177141 GGCGCTGTGGAGTTGGTATA 59.823 55.000 7.64 0.00 0.00 1.47
945 992 2.915349 TCGTAGAGTAGCTTCGGTGAT 58.085 47.619 0.00 0.00 37.89 3.06
959 1010 5.354792 GGTTCTTAGCTTCTTCTCTCGTAGA 59.645 44.000 0.00 0.00 0.00 2.59
984 1035 2.751806 GCCCATTGTCTTCCTCTTCTTG 59.248 50.000 0.00 0.00 0.00 3.02
1008 1059 1.153745 CCCGGACGAAGAGAAGCAG 60.154 63.158 0.73 0.00 0.00 4.24
1117 1177 2.508663 GTAGACGCCGGCCTTGTC 60.509 66.667 23.46 22.14 0.00 3.18
1129 1189 2.354821 GGTGGAAATTGGCGATGTAGAC 59.645 50.000 0.00 0.00 0.00 2.59
1143 1203 1.675219 GGACTGGTAGCGGTGGAAA 59.325 57.895 11.96 0.00 0.00 3.13
1229 1289 3.726557 TGGAACCATCTTGCTCTTCAT 57.273 42.857 0.00 0.00 0.00 2.57
1350 1437 4.878397 CACAACCCCTCATCTTCACTAATC 59.122 45.833 0.00 0.00 0.00 1.75
1437 1532 6.007936 TCCGGTCTTGAACAAATTTACATG 57.992 37.500 0.00 0.00 0.00 3.21
1495 1590 3.452627 AGATCGAATCCCAGTGCTAAACT 59.547 43.478 0.00 0.00 40.93 2.66
1496 1591 3.798202 AGATCGAATCCCAGTGCTAAAC 58.202 45.455 0.00 0.00 0.00 2.01
1497 1592 4.162320 AGAAGATCGAATCCCAGTGCTAAA 59.838 41.667 0.00 0.00 0.00 1.85
1498 1593 3.706594 AGAAGATCGAATCCCAGTGCTAA 59.293 43.478 0.00 0.00 0.00 3.09
1499 1594 3.300388 AGAAGATCGAATCCCAGTGCTA 58.700 45.455 0.00 0.00 0.00 3.49
1500 1595 2.114616 AGAAGATCGAATCCCAGTGCT 58.885 47.619 0.00 0.00 0.00 4.40
1501 1596 2.611225 AGAAGATCGAATCCCAGTGC 57.389 50.000 0.00 0.00 0.00 4.40
1544 1645 6.098124 CAGAGGGAGTAGATGTGATTTTCTCT 59.902 42.308 0.00 0.00 0.00 3.10
1559 1660 7.583625 TCTTGTATTATGAGACAGAGGGAGTA 58.416 38.462 0.00 0.00 0.00 2.59
1560 1661 6.436027 TCTTGTATTATGAGACAGAGGGAGT 58.564 40.000 0.00 0.00 0.00 3.85
1561 1662 6.516527 GCTCTTGTATTATGAGACAGAGGGAG 60.517 46.154 11.06 7.50 33.55 4.30
1562 1663 5.303078 GCTCTTGTATTATGAGACAGAGGGA 59.697 44.000 11.06 0.00 33.55 4.20
1563 1664 5.537188 GCTCTTGTATTATGAGACAGAGGG 58.463 45.833 11.06 3.43 33.55 4.30
1564 1665 5.218885 CGCTCTTGTATTATGAGACAGAGG 58.781 45.833 11.06 0.00 33.55 3.69
1565 1666 5.826586 ACGCTCTTGTATTATGAGACAGAG 58.173 41.667 7.09 7.09 33.55 3.35
1566 1667 5.836821 ACGCTCTTGTATTATGAGACAGA 57.163 39.130 0.00 0.00 33.55 3.41
1567 1668 6.893958 AAACGCTCTTGTATTATGAGACAG 57.106 37.500 0.00 0.00 33.55 3.51
1568 1669 6.871492 TCAAAACGCTCTTGTATTATGAGACA 59.129 34.615 0.00 0.00 33.55 3.41
1569 1670 7.148639 TGTCAAAACGCTCTTGTATTATGAGAC 60.149 37.037 0.00 0.00 33.55 3.36
1570 1671 6.871492 TGTCAAAACGCTCTTGTATTATGAGA 59.129 34.615 0.00 0.00 33.55 3.27
1571 1672 6.955963 GTGTCAAAACGCTCTTGTATTATGAG 59.044 38.462 0.00 0.00 34.55 2.90
1572 1673 6.649141 AGTGTCAAAACGCTCTTGTATTATGA 59.351 34.615 0.00 0.00 42.59 2.15
1573 1674 6.831769 AGTGTCAAAACGCTCTTGTATTATG 58.168 36.000 0.00 0.00 42.59 1.90
1574 1675 8.542497 TTAGTGTCAAAACGCTCTTGTATTAT 57.458 30.769 0.00 0.00 42.59 1.28
1575 1676 7.949903 TTAGTGTCAAAACGCTCTTGTATTA 57.050 32.000 0.00 0.00 42.59 0.98
1576 1677 6.854496 TTAGTGTCAAAACGCTCTTGTATT 57.146 33.333 0.00 0.00 42.59 1.89
1577 1678 6.426937 ACATTAGTGTCAAAACGCTCTTGTAT 59.573 34.615 0.00 0.00 42.59 2.29
1578 1679 5.756347 ACATTAGTGTCAAAACGCTCTTGTA 59.244 36.000 0.00 0.00 42.59 2.41
1579 1680 4.574828 ACATTAGTGTCAAAACGCTCTTGT 59.425 37.500 0.00 0.00 42.59 3.16
1580 1681 5.095691 ACATTAGTGTCAAAACGCTCTTG 57.904 39.130 0.00 0.00 42.59 3.02
1581 1682 5.989777 AGTACATTAGTGTCAAAACGCTCTT 59.010 36.000 0.00 0.00 42.59 2.85
1582 1683 5.405571 CAGTACATTAGTGTCAAAACGCTCT 59.594 40.000 0.00 0.00 42.59 4.09
1583 1684 5.176958 ACAGTACATTAGTGTCAAAACGCTC 59.823 40.000 0.00 0.00 42.59 5.03
1585 1686 5.338614 ACAGTACATTAGTGTCAAAACGC 57.661 39.130 0.00 0.00 37.83 4.84
1586 1687 9.705471 TTTTAACAGTACATTAGTGTCAAAACG 57.295 29.630 0.00 0.00 41.27 3.60
1589 1690 9.991388 GTGTTTTAACAGTACATTAGTGTCAAA 57.009 29.630 0.00 0.00 41.27 2.69
1590 1691 9.386010 AGTGTTTTAACAGTACATTAGTGTCAA 57.614 29.630 0.00 0.00 41.27 3.18
1591 1692 8.951787 AGTGTTTTAACAGTACATTAGTGTCA 57.048 30.769 0.00 0.00 41.27 3.58
1592 1693 9.257651 AGAGTGTTTTAACAGTACATTAGTGTC 57.742 33.333 3.07 0.00 42.36 3.67
1593 1694 9.609346 AAGAGTGTTTTAACAGTACATTAGTGT 57.391 29.630 3.07 0.00 42.36 3.55
1609 1710 9.799106 CTCCATCCCATAATATAAGAGTGTTTT 57.201 33.333 0.00 0.00 0.00 2.43
1610 1711 8.386264 CCTCCATCCCATAATATAAGAGTGTTT 58.614 37.037 0.00 0.00 0.00 2.83
1611 1712 7.037297 CCCTCCATCCCATAATATAAGAGTGTT 60.037 40.741 0.00 0.00 0.00 3.32
1612 1713 6.445139 CCCTCCATCCCATAATATAAGAGTGT 59.555 42.308 0.00 0.00 0.00 3.55
1613 1714 6.673978 TCCCTCCATCCCATAATATAAGAGTG 59.326 42.308 0.00 0.00 0.00 3.51
1614 1715 6.826727 TCCCTCCATCCCATAATATAAGAGT 58.173 40.000 0.00 0.00 0.00 3.24
1615 1716 6.905776 ACTCCCTCCATCCCATAATATAAGAG 59.094 42.308 0.00 0.00 0.00 2.85
1616 1717 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
1617 1718 7.202047 GCTACTCCCTCCATCCCATAATATAAG 60.202 44.444 0.00 0.00 0.00 1.73
1618 1719 6.615726 GCTACTCCCTCCATCCCATAATATAA 59.384 42.308 0.00 0.00 0.00 0.98
1619 1720 6.143915 GCTACTCCCTCCATCCCATAATATA 58.856 44.000 0.00 0.00 0.00 0.86
1620 1721 4.971924 GCTACTCCCTCCATCCCATAATAT 59.028 45.833 0.00 0.00 0.00 1.28
1621 1722 4.202890 TGCTACTCCCTCCATCCCATAATA 60.203 45.833 0.00 0.00 0.00 0.98
1622 1723 3.185455 GCTACTCCCTCCATCCCATAAT 58.815 50.000 0.00 0.00 0.00 1.28
1623 1724 2.090210 TGCTACTCCCTCCATCCCATAA 60.090 50.000 0.00 0.00 0.00 1.90
1624 1725 1.507742 TGCTACTCCCTCCATCCCATA 59.492 52.381 0.00 0.00 0.00 2.74
1625 1726 0.268869 TGCTACTCCCTCCATCCCAT 59.731 55.000 0.00 0.00 0.00 4.00
1626 1727 0.044092 TTGCTACTCCCTCCATCCCA 59.956 55.000 0.00 0.00 0.00 4.37
1627 1728 1.439543 ATTGCTACTCCCTCCATCCC 58.560 55.000 0.00 0.00 0.00 3.85
1628 1729 4.390264 GTTAATTGCTACTCCCTCCATCC 58.610 47.826 0.00 0.00 0.00 3.51
1629 1730 4.390264 GGTTAATTGCTACTCCCTCCATC 58.610 47.826 0.00 0.00 0.00 3.51
1630 1731 3.181454 CGGTTAATTGCTACTCCCTCCAT 60.181 47.826 0.00 0.00 0.00 3.41
1631 1732 2.169769 CGGTTAATTGCTACTCCCTCCA 59.830 50.000 0.00 0.00 0.00 3.86
1632 1733 2.484947 CCGGTTAATTGCTACTCCCTCC 60.485 54.545 0.00 0.00 0.00 4.30
1633 1734 2.433239 TCCGGTTAATTGCTACTCCCTC 59.567 50.000 0.00 0.00 0.00 4.30
1634 1735 2.474112 TCCGGTTAATTGCTACTCCCT 58.526 47.619 0.00 0.00 0.00 4.20
1635 1736 2.994186 TCCGGTTAATTGCTACTCCC 57.006 50.000 0.00 0.00 0.00 4.30
1636 1737 3.808174 GTGATCCGGTTAATTGCTACTCC 59.192 47.826 0.00 0.00 0.00 3.85
1637 1738 3.489785 CGTGATCCGGTTAATTGCTACTC 59.510 47.826 0.00 0.00 0.00 2.59
1638 1739 3.454375 CGTGATCCGGTTAATTGCTACT 58.546 45.455 0.00 0.00 0.00 2.57
1639 1740 2.033151 GCGTGATCCGGTTAATTGCTAC 60.033 50.000 0.00 0.00 36.94 3.58
1640 1741 2.206750 GCGTGATCCGGTTAATTGCTA 58.793 47.619 0.00 0.00 36.94 3.49
1641 1742 1.014352 GCGTGATCCGGTTAATTGCT 58.986 50.000 0.00 0.00 36.94 3.91
1651 1752 2.849966 CTTTCGCTCGCGTGATCCG 61.850 63.158 13.13 5.97 40.74 4.18
1718 1824 2.086054 AGCTAGTCTTTTCAGTGCCG 57.914 50.000 0.00 0.00 0.00 5.69
1743 1849 2.862347 GAATCAGCAAGGCAGCGCAC 62.862 60.000 11.47 0.00 40.15 5.34
1791 1897 3.333029 AATTAATGGCCAAACCTGCAC 57.667 42.857 10.96 0.00 40.22 4.57
1792 1898 3.672808 CAAATTAATGGCCAAACCTGCA 58.327 40.909 10.96 0.00 40.22 4.41
1794 1900 3.009026 GGCAAATTAATGGCCAAACCTG 58.991 45.455 20.83 3.90 46.92 4.00
1795 1901 3.348647 GGCAAATTAATGGCCAAACCT 57.651 42.857 20.83 0.00 46.92 3.50
1833 1939 7.765695 TGATAAAGAATCTCAGTGCCTTTTT 57.234 32.000 0.00 0.00 35.45 1.94
1904 2014 4.536489 AGGGTGCAGAAATCTTACCTACTT 59.464 41.667 11.37 0.00 33.47 2.24
1938 2048 8.579863 AGAATGAGAAACCTAAGGAAAAACATG 58.420 33.333 0.00 0.00 0.00 3.21
1939 2049 8.712228 AGAATGAGAAACCTAAGGAAAAACAT 57.288 30.769 0.00 0.00 0.00 2.71
1940 2050 7.777910 TGAGAATGAGAAACCTAAGGAAAAACA 59.222 33.333 0.00 0.00 0.00 2.83
1941 2051 8.166422 TGAGAATGAGAAACCTAAGGAAAAAC 57.834 34.615 0.00 0.00 0.00 2.43
1942 2052 8.760980 TTGAGAATGAGAAACCTAAGGAAAAA 57.239 30.769 0.00 0.00 0.00 1.94
1943 2053 8.217799 TCTTGAGAATGAGAAACCTAAGGAAAA 58.782 33.333 0.00 0.00 0.00 2.29
1944 2054 7.745717 TCTTGAGAATGAGAAACCTAAGGAAA 58.254 34.615 0.00 0.00 0.00 3.13
1945 2055 7.316393 TCTTGAGAATGAGAAACCTAAGGAA 57.684 36.000 0.00 0.00 0.00 3.36
1946 2056 6.935240 TCTTGAGAATGAGAAACCTAAGGA 57.065 37.500 0.00 0.00 0.00 3.36
1947 2057 7.164803 ACTTCTTGAGAATGAGAAACCTAAGG 58.835 38.462 0.00 0.00 31.99 2.69
1948 2058 8.614469 AACTTCTTGAGAATGAGAAACCTAAG 57.386 34.615 0.00 0.00 31.99 2.18
1949 2059 8.840321 CAAACTTCTTGAGAATGAGAAACCTAA 58.160 33.333 0.00 0.00 31.99 2.69
1950 2060 7.993183 ACAAACTTCTTGAGAATGAGAAACCTA 59.007 33.333 0.00 0.00 31.99 3.08
1951 2061 6.830838 ACAAACTTCTTGAGAATGAGAAACCT 59.169 34.615 0.00 0.00 31.99 3.50
1952 2062 6.914757 CACAAACTTCTTGAGAATGAGAAACC 59.085 38.462 0.00 0.00 31.99 3.27
1953 2063 7.475840 ACACAAACTTCTTGAGAATGAGAAAC 58.524 34.615 0.00 0.00 31.99 2.78
1954 2064 7.630242 ACACAAACTTCTTGAGAATGAGAAA 57.370 32.000 0.00 0.00 31.99 2.52
1955 2065 7.336679 TGAACACAAACTTCTTGAGAATGAGAA 59.663 33.333 0.00 0.00 33.01 2.87
1956 2066 6.823182 TGAACACAAACTTCTTGAGAATGAGA 59.177 34.615 0.00 0.00 33.01 3.27
1957 2067 7.019774 TGAACACAAACTTCTTGAGAATGAG 57.980 36.000 0.00 0.00 33.01 2.90
1958 2068 7.572523 ATGAACACAAACTTCTTGAGAATGA 57.427 32.000 0.00 0.00 33.01 2.57
1959 2069 9.338291 CATATGAACACAAACTTCTTGAGAATG 57.662 33.333 0.00 0.00 33.01 2.67
1960 2070 9.071276 ACATATGAACACAAACTTCTTGAGAAT 57.929 29.630 10.38 0.00 33.01 2.40
1961 2071 8.450578 ACATATGAACACAAACTTCTTGAGAA 57.549 30.769 10.38 0.00 0.00 2.87
1962 2072 8.450578 AACATATGAACACAAACTTCTTGAGA 57.549 30.769 10.38 0.00 0.00 3.27
1963 2073 9.520204 AAAACATATGAACACAAACTTCTTGAG 57.480 29.630 10.38 0.00 0.00 3.02
1964 2074 9.868277 AAAAACATATGAACACAAACTTCTTGA 57.132 25.926 10.38 0.00 0.00 3.02
1998 2108 9.249457 CGTAGATCACATATGAACACAAACTAT 57.751 33.333 10.38 0.00 38.69 2.12
1999 2109 8.463607 TCGTAGATCACATATGAACACAAACTA 58.536 33.333 10.38 0.05 38.69 2.24
2000 2110 7.320399 TCGTAGATCACATATGAACACAAACT 58.680 34.615 10.38 0.92 38.69 2.66
2001 2111 7.275779 ACTCGTAGATCACATATGAACACAAAC 59.724 37.037 10.38 0.00 38.69 2.93
2002 2112 7.275560 CACTCGTAGATCACATATGAACACAAA 59.724 37.037 10.38 0.00 38.69 2.83
2003 2113 6.751888 CACTCGTAGATCACATATGAACACAA 59.248 38.462 10.38 0.00 38.69 3.33
2004 2114 6.265577 CACTCGTAGATCACATATGAACACA 58.734 40.000 10.38 0.00 38.69 3.72
2005 2115 5.687730 CCACTCGTAGATCACATATGAACAC 59.312 44.000 10.38 0.00 38.69 3.32
2006 2116 5.736207 GCCACTCGTAGATCACATATGAACA 60.736 44.000 10.38 0.00 38.69 3.18
2007 2117 4.681942 GCCACTCGTAGATCACATATGAAC 59.318 45.833 10.38 0.00 38.69 3.18
2008 2118 4.340950 TGCCACTCGTAGATCACATATGAA 59.659 41.667 10.38 0.00 38.69 2.57
2009 2119 3.888930 TGCCACTCGTAGATCACATATGA 59.111 43.478 10.38 0.00 39.83 2.15
2010 2120 4.243007 TGCCACTCGTAGATCACATATG 57.757 45.455 0.00 0.00 33.89 1.78
2011 2121 4.814147 CATGCCACTCGTAGATCACATAT 58.186 43.478 0.00 0.00 33.89 1.78
2012 2122 3.552890 GCATGCCACTCGTAGATCACATA 60.553 47.826 6.36 0.00 33.89 2.29
2013 2123 2.804572 GCATGCCACTCGTAGATCACAT 60.805 50.000 6.36 0.00 33.89 3.21
2014 2124 1.471501 GCATGCCACTCGTAGATCACA 60.472 52.381 6.36 0.00 33.89 3.58
2015 2125 1.212616 GCATGCCACTCGTAGATCAC 58.787 55.000 6.36 0.00 33.89 3.06
2016 2126 0.104855 GGCATGCCACTCGTAGATCA 59.895 55.000 32.08 0.00 33.16 2.92
2017 2127 0.390860 AGGCATGCCACTCGTAGATC 59.609 55.000 37.18 6.78 38.92 2.75
2018 2128 1.704641 TAGGCATGCCACTCGTAGAT 58.295 50.000 37.18 16.55 38.92 1.98
2019 2129 1.341209 CATAGGCATGCCACTCGTAGA 59.659 52.381 37.18 12.51 38.92 2.59
2031 2141 4.870636 TGATTCAGGTTTTCCATAGGCAT 58.129 39.130 0.00 0.00 43.73 4.40
2033 2143 5.659440 TTTGATTCAGGTTTTCCATAGGC 57.341 39.130 0.00 0.00 43.73 3.93
2076 2186 5.949735 ACAACCGGCACTTCAATTAATTAG 58.050 37.500 0.00 0.00 0.00 1.73
2085 2195 1.403647 CGAGATACAACCGGCACTTCA 60.404 52.381 0.00 0.00 0.00 3.02
2094 2204 1.692519 AGGGCCATACGAGATACAACC 59.307 52.381 6.18 0.00 0.00 3.77
2112 2222 3.498777 GGACTCGGTTTCTTCAAGAAAGG 59.501 47.826 13.09 8.45 44.07 3.11
2117 2227 3.248602 CACTTGGACTCGGTTTCTTCAAG 59.751 47.826 0.00 0.00 36.96 3.02
2155 2277 7.013369 GGTTTTGAGAAATCCAGTTAACTGACT 59.987 37.037 32.50 21.78 46.59 3.41
2160 2282 5.009310 ACCGGTTTTGAGAAATCCAGTTAAC 59.991 40.000 0.00 0.00 0.00 2.01
2161 2283 5.009210 CACCGGTTTTGAGAAATCCAGTTAA 59.991 40.000 2.97 0.00 0.00 2.01
2162 2284 4.517453 CACCGGTTTTGAGAAATCCAGTTA 59.483 41.667 2.97 0.00 0.00 2.24
2163 2285 3.317993 CACCGGTTTTGAGAAATCCAGTT 59.682 43.478 2.97 0.00 0.00 3.16
2174 2296 4.737855 TTGGAATTTTCACCGGTTTTGA 57.262 36.364 2.97 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.