Multiple sequence alignment - TraesCS2D01G499300

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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 TraesCS2D01G499300 chr2D 100.000 2300 0 0 1 2300 594457544 594455245 0.000000e+00 4248.0
1 TraesCS2D01G499300 chr2D 100.000 93 0 0 1235 1327 594456217 594456125 3.040000e-39 172.0
2 TraesCS2D01G499300 chr2D 100.000 93 0 0 1328 1420 594456310 594456218 3.040000e-39 172.0
3 TraesCS2D01G499300 chr2A 91.500 800 52 12 536 1327 729060527 729059736 0.000000e+00 1086.0
4 TraesCS2D01G499300 chr2A 93.305 463 20 8 1 457 729060982 729060525 0.000000e+00 673.0
5 TraesCS2D01G499300 chr2A 84.593 344 46 5 116 453 729119928 729119586 3.660000e-88 335.0
6 TraesCS2D01G499300 chr2A 82.909 275 23 19 1317 1579 729059840 729059578 2.300000e-55 226.0
7 TraesCS2D01G499300 chr2A 78.596 285 33 11 1812 2094 729059561 729059303 1.830000e-36 163.0
8 TraesCS2D01G499300 chr2A 93.478 92 4 2 448 537 617636027 617636118 3.990000e-28 135.0
9 TraesCS2D01G499300 chr2A 89.524 105 6 3 454 554 745552848 745552745 6.670000e-26 128.0
10 TraesCS2D01G499300 chr2B 87.901 810 57 24 539 1327 721726618 721725829 0.000000e+00 915.0
11 TraesCS2D01G499300 chr2B 86.197 355 42 5 105 453 721902210 721901857 6.000000e-101 377.0
12 TraesCS2D01G499300 chr2B 85.251 339 40 7 127 456 721726955 721726618 7.870000e-90 340.0
13 TraesCS2D01G499300 chr2B 88.732 284 7 5 1326 1594 721725922 721725649 7.930000e-85 324.0
14 TraesCS2D01G499300 chr2B 92.105 228 11 4 1812 2033 721725654 721725428 4.770000e-82 315.0
15 TraesCS2D01G499300 chr2B 93.333 105 5 1 2194 2296 721722050 721721946 1.100000e-33 154.0
16 TraesCS2D01G499300 chr2B 91.753 97 2 2 2038 2134 721722152 721722062 1.850000e-26 130.0
17 TraesCS2D01G499300 chr2B 86.585 82 9 2 5 85 721902276 721902196 3.150000e-14 89.8
18 TraesCS2D01G499300 chr3B 95.402 87 3 1 454 539 256200657 256200743 1.110000e-28 137.0
19 TraesCS2D01G499300 chr6B 90.291 103 7 2 452 551 458503481 458503583 5.160000e-27 132.0
20 TraesCS2D01G499300 chr6B 90.909 55 4 1 1764 1818 157022516 157022569 3.170000e-09 73.1
21 TraesCS2D01G499300 chr7D 89.623 106 6 4 448 550 29876464 29876361 1.850000e-26 130.0
22 TraesCS2D01G499300 chr7D 85.000 120 13 4 453 569 235581298 235581181 1.440000e-22 117.0
23 TraesCS2D01G499300 chr7D 82.927 123 15 4 1689 1811 173900874 173900990 3.130000e-19 106.0
24 TraesCS2D01G499300 chr4D 87.156 109 11 2 455 561 282080032 282079925 1.120000e-23 121.0
25 TraesCS2D01G499300 chr7B 85.000 120 13 4 454 570 707519342 707519459 1.440000e-22 117.0
26 TraesCS2D01G499300 chr7B 84.507 71 10 1 1739 1809 165300872 165300941 4.100000e-08 69.4
27 TraesCS2D01G499300 chr5D 85.000 120 13 4 453 569 408763868 408763751 1.440000e-22 117.0
28 TraesCS2D01G499300 chr6A 79.412 136 14 8 1677 1810 602594414 602594291 1.460000e-12 84.2
29 TraesCS2D01G499300 chr5B 83.696 92 12 3 1727 1818 439266658 439266570 1.460000e-12 84.2
30 TraesCS2D01G499300 chr3D 90.196 51 4 1 1756 1805 445790509 445790559 5.300000e-07 65.8


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 TraesCS2D01G499300 chr2D 594455245 594457544 2299 True 1530.666667 4248 100.000000 1 2300 3 chr2D.!!$R1 2299
1 TraesCS2D01G499300 chr2A 729059303 729060982 1679 True 537.000000 1086 86.577500 1 2094 4 chr2A.!!$R3 2093
2 TraesCS2D01G499300 chr2B 721721946 721726955 5009 True 363.000000 915 89.845833 127 2296 6 chr2B.!!$R1 2169

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
847 865 0.179086 GCTAGCTGAAGTGCCTCTCC 60.179 60.0 7.7 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 5542 0.105246 AGGAGGCCCAGATACAGGAG 60.105 60.0 0.0 0.0 33.88 3.69 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
20 21 1.135139 CCAGTACAGCACGACAGCTAT 59.865 52.381 0.00 0.00 44.54 2.97
28 29 6.387041 ACAGCACGACAGCTATAATACTTA 57.613 37.500 0.00 0.00 44.54 2.24
91 93 4.347813 CACGAAACGACAACATTTTTCCT 58.652 39.130 0.00 0.00 0.00 3.36
123 125 7.562454 AAGAAAAGAAACCACGACATTTAGA 57.438 32.000 0.00 0.00 0.00 2.10
125 127 8.166422 AGAAAAGAAACCACGACATTTAGAAT 57.834 30.769 0.00 0.00 0.00 2.40
313 321 1.291132 GCCTTCACGCTCTTATCACC 58.709 55.000 0.00 0.00 0.00 4.02
315 323 2.935238 GCCTTCACGCTCTTATCACCAA 60.935 50.000 0.00 0.00 0.00 3.67
320 328 6.260936 CCTTCACGCTCTTATCACCAAATATT 59.739 38.462 0.00 0.00 0.00 1.28
371 381 3.308438 AGCAATTTGCCATGTTCTGAC 57.692 42.857 17.51 0.00 46.52 3.51
428 440 2.141517 CTCATGATTTAGCCAGCCTCG 58.858 52.381 0.00 0.00 0.00 4.63
432 444 0.753262 GATTTAGCCAGCCTCGGAGA 59.247 55.000 6.58 0.00 0.00 3.71
436 448 2.589610 TAGCCAGCCTCGGAGATGGT 62.590 60.000 22.33 14.92 35.17 3.55
457 469 7.432148 TGGTCATCTTGTGGTACATTATACT 57.568 36.000 0.00 0.00 44.52 2.12
458 470 7.497595 TGGTCATCTTGTGGTACATTATACTC 58.502 38.462 0.00 0.00 44.52 2.59
459 471 6.929606 GGTCATCTTGTGGTACATTATACTCC 59.070 42.308 0.00 0.00 44.52 3.85
460 472 6.929606 GTCATCTTGTGGTACATTATACTCCC 59.070 42.308 0.00 0.00 44.52 4.30
461 473 6.844388 TCATCTTGTGGTACATTATACTCCCT 59.156 38.462 0.00 0.00 44.52 4.20
462 474 6.726490 TCTTGTGGTACATTATACTCCCTC 57.274 41.667 0.00 0.00 44.52 4.30
463 475 6.441222 TCTTGTGGTACATTATACTCCCTCT 58.559 40.000 0.00 0.00 44.52 3.69
464 476 6.323996 TCTTGTGGTACATTATACTCCCTCTG 59.676 42.308 0.00 0.00 44.52 3.35
465 477 5.525484 TGTGGTACATTATACTCCCTCTGT 58.475 41.667 0.00 0.00 44.52 3.41
466 478 6.675565 TGTGGTACATTATACTCCCTCTGTA 58.324 40.000 0.00 0.00 44.52 2.74
467 479 7.127405 TGTGGTACATTATACTCCCTCTGTAA 58.873 38.462 0.00 0.00 44.52 2.41
468 480 7.620491 TGTGGTACATTATACTCCCTCTGTAAA 59.380 37.037 0.00 0.00 44.52 2.01
469 481 8.142551 GTGGTACATTATACTCCCTCTGTAAAG 58.857 40.741 0.00 0.00 44.52 1.85
470 482 8.063153 TGGTACATTATACTCCCTCTGTAAAGA 58.937 37.037 0.00 0.00 0.00 2.52
471 483 9.091220 GGTACATTATACTCCCTCTGTAAAGAT 57.909 37.037 0.00 0.00 0.00 2.40
481 493 9.250246 ACTCCCTCTGTAAAGATATATAAGAGC 57.750 37.037 0.00 0.00 0.00 4.09
482 494 9.249053 CTCCCTCTGTAAAGATATATAAGAGCA 57.751 37.037 0.00 0.00 0.00 4.26
483 495 9.775539 TCCCTCTGTAAAGATATATAAGAGCAT 57.224 33.333 0.00 0.00 0.00 3.79
532 544 9.566432 AATGCTCTTATATTTCTTTACAGAGGG 57.434 33.333 0.00 0.00 0.00 4.30
533 545 8.319057 TGCTCTTATATTTCTTTACAGAGGGA 57.681 34.615 0.00 0.00 0.00 4.20
534 546 8.424918 TGCTCTTATATTTCTTTACAGAGGGAG 58.575 37.037 0.00 0.00 0.00 4.30
535 547 8.425703 GCTCTTATATTTCTTTACAGAGGGAGT 58.574 37.037 0.00 0.00 0.00 3.85
618 630 3.072038 TGTCCCATGATGAGATCACATCC 59.928 47.826 24.64 12.27 43.96 3.51
619 631 3.327172 GTCCCATGATGAGATCACATCCT 59.673 47.826 24.64 15.53 43.96 3.24
624 636 6.238953 CCCATGATGAGATCACATCCTTTTTC 60.239 42.308 24.64 5.85 43.96 2.29
640 652 5.250543 TCCTTTTTCTCTCATGGGTCATGTA 59.749 40.000 7.63 0.00 41.98 2.29
817 835 9.928618 TTATTAATTACCATTCCAATCCTCACA 57.071 29.630 0.00 0.00 0.00 3.58
827 845 9.573166 CCATTCCAATCCTCACATACTTAATTA 57.427 33.333 0.00 0.00 0.00 1.40
832 850 9.429359 CCAATCCTCACATACTTAATTAGCTAG 57.571 37.037 0.00 0.00 0.00 3.42
833 851 8.930760 CAATCCTCACATACTTAATTAGCTAGC 58.069 37.037 6.62 6.62 0.00 3.42
834 852 7.841282 TCCTCACATACTTAATTAGCTAGCT 57.159 36.000 23.12 23.12 0.00 3.32
835 853 7.661968 TCCTCACATACTTAATTAGCTAGCTG 58.338 38.462 27.68 11.65 0.00 4.24
836 854 7.505923 TCCTCACATACTTAATTAGCTAGCTGA 59.494 37.037 27.68 20.18 0.00 4.26
838 856 9.190858 CTCACATACTTAATTAGCTAGCTGAAG 57.809 37.037 27.68 23.04 0.00 3.02
847 865 0.179086 GCTAGCTGAAGTGCCTCTCC 60.179 60.000 7.70 0.00 0.00 3.71
856 877 1.610673 GTGCCTCTCCCCTCTCACA 60.611 63.158 0.00 0.00 0.00 3.58
861 882 1.000771 TCTCCCCTCTCACACTCGG 60.001 63.158 0.00 0.00 0.00 4.63
882 903 5.895534 TCGGTCCACTATATAAACCTTCACT 59.104 40.000 0.00 0.00 0.00 3.41
913 935 3.430895 CACACAGCAAAGCAAATTGATCC 59.569 43.478 0.00 0.00 31.84 3.36
955 977 1.472376 CCAACAGAGCTACTAGCAGCC 60.472 57.143 11.50 3.57 45.56 4.85
996 1033 3.859961 CAGAGTGCGGTAGTGTATTTCTG 59.140 47.826 0.00 0.00 0.00 3.02
998 1035 1.664151 GTGCGGTAGTGTATTTCTGGC 59.336 52.381 0.00 0.00 0.00 4.85
1008 1045 1.940613 GTATTTCTGGCCATGTCGACC 59.059 52.381 14.12 0.00 0.00 4.79
1009 1046 0.394352 ATTTCTGGCCATGTCGACCC 60.394 55.000 14.12 7.39 0.00 4.46
1011 1048 3.770040 CTGGCCATGTCGACCCGA 61.770 66.667 14.12 0.00 0.00 5.14
1262 1299 4.716003 GCTGGTTAGCTTCCCGTT 57.284 55.556 0.00 0.00 46.57 4.44
1263 1300 2.467962 GCTGGTTAGCTTCCCGTTC 58.532 57.895 0.00 0.00 46.57 3.95
1264 1301 1.359459 GCTGGTTAGCTTCCCGTTCG 61.359 60.000 0.00 0.00 46.57 3.95
1265 1302 0.037605 CTGGTTAGCTTCCCGTTCGT 60.038 55.000 0.00 0.00 0.00 3.85
1266 1303 0.037975 TGGTTAGCTTCCCGTTCGTC 60.038 55.000 0.00 0.00 0.00 4.20
1267 1304 1.074872 GGTTAGCTTCCCGTTCGTCG 61.075 60.000 0.00 0.00 39.52 5.12
1458 1496 2.400399 CACGTGTGGTGTAACGAATCT 58.600 47.619 7.58 0.00 42.32 2.40
1580 1647 2.742053 CCCGTGTAAACAACCAGATCTG 59.258 50.000 16.24 16.24 0.00 2.90
1584 1651 5.334105 CCGTGTAAACAACCAGATCTGAAAG 60.334 44.000 24.62 14.33 0.00 2.62
1588 1662 5.796424 AAACAACCAGATCTGAAAGCAAT 57.204 34.783 24.62 1.87 0.00 3.56
1589 1663 6.899393 AAACAACCAGATCTGAAAGCAATA 57.101 33.333 24.62 0.00 0.00 1.90
1590 1664 6.899393 AACAACCAGATCTGAAAGCAATAA 57.101 33.333 24.62 0.00 0.00 1.40
1591 1665 7.472334 AACAACCAGATCTGAAAGCAATAAT 57.528 32.000 24.62 0.00 0.00 1.28
1592 1666 8.579850 AACAACCAGATCTGAAAGCAATAATA 57.420 30.769 24.62 0.00 0.00 0.98
1593 1667 8.757982 ACAACCAGATCTGAAAGCAATAATAT 57.242 30.769 24.62 0.00 0.00 1.28
1594 1668 8.844244 ACAACCAGATCTGAAAGCAATAATATC 58.156 33.333 24.62 0.00 0.00 1.63
1595 1669 7.992754 ACCAGATCTGAAAGCAATAATATCC 57.007 36.000 24.62 0.00 0.00 2.59
1596 1670 6.652481 ACCAGATCTGAAAGCAATAATATCCG 59.348 38.462 24.62 3.38 0.00 4.18
1597 1671 6.093219 CCAGATCTGAAAGCAATAATATCCGG 59.907 42.308 24.62 0.00 0.00 5.14
1598 1672 6.875726 CAGATCTGAAAGCAATAATATCCGGA 59.124 38.462 18.34 6.61 0.00 5.14
1599 1673 7.551974 CAGATCTGAAAGCAATAATATCCGGAT 59.448 37.037 22.95 22.95 0.00 4.18
1600 1674 7.768120 AGATCTGAAAGCAATAATATCCGGATC 59.232 37.037 23.08 4.36 0.00 3.36
1601 1675 6.173339 TCTGAAAGCAATAATATCCGGATCC 58.827 40.000 23.08 0.00 0.00 3.36
1602 1676 6.013379 TCTGAAAGCAATAATATCCGGATCCT 60.013 38.462 23.08 11.90 0.00 3.24
1603 1677 5.939883 TGAAAGCAATAATATCCGGATCCTG 59.060 40.000 23.08 12.80 0.00 3.86
1604 1678 5.762179 AAGCAATAATATCCGGATCCTGA 57.238 39.130 23.08 9.56 0.00 3.86
1605 1679 5.965033 AGCAATAATATCCGGATCCTGAT 57.035 39.130 23.08 20.86 0.00 2.90
1606 1680 7.437713 AAGCAATAATATCCGGATCCTGATA 57.562 36.000 23.08 23.40 0.00 2.15
1607 1681 7.437713 AGCAATAATATCCGGATCCTGATAA 57.562 36.000 24.53 13.15 0.00 1.75
1608 1682 7.504403 AGCAATAATATCCGGATCCTGATAAG 58.496 38.462 24.53 14.98 0.00 1.73
1609 1683 7.126421 AGCAATAATATCCGGATCCTGATAAGT 59.874 37.037 24.53 18.55 0.00 2.24
1610 1684 7.225538 GCAATAATATCCGGATCCTGATAAGTG 59.774 40.741 24.53 19.52 0.00 3.16
1611 1685 8.478066 CAATAATATCCGGATCCTGATAAGTGA 58.522 37.037 24.53 13.25 0.00 3.41
1612 1686 8.789767 ATAATATCCGGATCCTGATAAGTGAT 57.210 34.615 24.53 14.52 0.00 3.06
1613 1687 9.883293 ATAATATCCGGATCCTGATAAGTGATA 57.117 33.333 24.53 14.81 0.00 2.15
1614 1688 8.609617 AATATCCGGATCCTGATAAGTGATAA 57.390 34.615 24.53 6.70 0.00 1.75
1615 1689 5.984695 TCCGGATCCTGATAAGTGATAAG 57.015 43.478 10.75 0.00 0.00 1.73
1616 1690 5.394738 TCCGGATCCTGATAAGTGATAAGT 58.605 41.667 10.75 0.00 0.00 2.24
1617 1691 5.243954 TCCGGATCCTGATAAGTGATAAGTG 59.756 44.000 10.75 0.00 0.00 3.16
1618 1692 4.926238 CGGATCCTGATAAGTGATAAGTGC 59.074 45.833 10.75 0.00 0.00 4.40
1619 1693 5.241662 GGATCCTGATAAGTGATAAGTGCC 58.758 45.833 3.84 0.00 0.00 5.01
1620 1694 5.221722 GGATCCTGATAAGTGATAAGTGCCA 60.222 44.000 3.84 0.00 0.00 4.92
1621 1695 5.023533 TCCTGATAAGTGATAAGTGCCAC 57.976 43.478 0.00 0.00 0.00 5.01
1622 1696 4.469586 TCCTGATAAGTGATAAGTGCCACA 59.530 41.667 0.00 0.00 35.84 4.17
1623 1697 4.572389 CCTGATAAGTGATAAGTGCCACAC 59.428 45.833 0.00 0.00 35.84 3.82
1624 1698 5.159273 TGATAAGTGATAAGTGCCACACA 57.841 39.130 0.00 0.00 36.74 3.72
1625 1699 5.744171 TGATAAGTGATAAGTGCCACACAT 58.256 37.500 0.00 0.00 36.74 3.21
1626 1700 6.179756 TGATAAGTGATAAGTGCCACACATT 58.820 36.000 0.00 0.00 36.74 2.71
1627 1701 6.658816 TGATAAGTGATAAGTGCCACACATTT 59.341 34.615 0.00 0.00 36.74 2.32
1628 1702 4.771590 AGTGATAAGTGCCACACATTTG 57.228 40.909 0.00 0.00 36.74 2.32
1629 1703 4.397420 AGTGATAAGTGCCACACATTTGA 58.603 39.130 0.00 0.00 36.74 2.69
1630 1704 4.216257 AGTGATAAGTGCCACACATTTGAC 59.784 41.667 0.00 0.00 36.74 3.18
1631 1705 3.188254 TGATAAGTGCCACACATTTGACG 59.812 43.478 0.00 0.00 36.74 4.35
1632 1706 1.388547 AAGTGCCACACATTTGACGT 58.611 45.000 0.00 0.00 36.74 4.34
1633 1707 0.662619 AGTGCCACACATTTGACGTG 59.337 50.000 0.00 0.00 36.74 4.49
1634 1708 0.660488 GTGCCACACATTTGACGTGA 59.340 50.000 0.00 0.00 37.80 4.35
1635 1709 1.064803 GTGCCACACATTTGACGTGAA 59.935 47.619 0.00 0.00 37.80 3.18
1636 1710 1.064803 TGCCACACATTTGACGTGAAC 59.935 47.619 0.00 0.00 37.80 3.18
1637 1711 1.064803 GCCACACATTTGACGTGAACA 59.935 47.619 0.00 0.00 37.80 3.18
1638 1712 2.715268 CCACACATTTGACGTGAACAC 58.285 47.619 0.00 0.00 37.80 3.32
1639 1713 2.096657 CCACACATTTGACGTGAACACA 59.903 45.455 0.00 0.00 37.80 3.72
1640 1714 3.243035 CCACACATTTGACGTGAACACAT 60.243 43.478 0.00 0.00 37.80 3.21
1641 1715 3.725245 CACACATTTGACGTGAACACATG 59.275 43.478 0.00 0.00 37.80 3.21
1642 1716 3.625313 ACACATTTGACGTGAACACATGA 59.375 39.130 0.00 0.00 37.80 3.07
1643 1717 3.968096 CACATTTGACGTGAACACATGAC 59.032 43.478 0.00 0.00 36.43 3.06
1644 1718 3.625313 ACATTTGACGTGAACACATGACA 59.375 39.130 0.00 0.00 32.16 3.58
1645 1719 4.095632 ACATTTGACGTGAACACATGACAA 59.904 37.500 0.00 0.00 35.06 3.18
1646 1720 4.891627 TTTGACGTGAACACATGACAAT 57.108 36.364 0.00 0.00 36.07 2.71
1647 1721 4.891627 TTGACGTGAACACATGACAATT 57.108 36.364 0.00 0.00 33.24 2.32
1648 1722 4.891627 TGACGTGAACACATGACAATTT 57.108 36.364 0.00 0.00 0.00 1.82
1649 1723 4.843147 TGACGTGAACACATGACAATTTC 58.157 39.130 0.00 0.00 0.00 2.17
1650 1724 3.872354 ACGTGAACACATGACAATTTCG 58.128 40.909 0.00 0.00 0.00 3.46
1651 1725 2.651703 CGTGAACACATGACAATTTCGC 59.348 45.455 0.00 0.37 0.00 4.70
1652 1726 3.626977 GTGAACACATGACAATTTCGCA 58.373 40.909 0.00 0.00 0.00 5.10
1653 1727 4.229096 GTGAACACATGACAATTTCGCAT 58.771 39.130 0.00 0.00 0.00 4.73
1654 1728 4.088923 GTGAACACATGACAATTTCGCATG 59.911 41.667 0.00 0.00 43.70 4.06
1661 1735 6.263615 CATGACAATTTCGCATGTTTATGG 57.736 37.500 0.00 0.00 35.78 2.74
1662 1736 5.384063 TGACAATTTCGCATGTTTATGGT 57.616 34.783 0.00 0.00 34.79 3.55
1663 1737 5.398169 TGACAATTTCGCATGTTTATGGTC 58.602 37.500 0.00 0.00 34.79 4.02
1664 1738 5.048434 TGACAATTTCGCATGTTTATGGTCA 60.048 36.000 0.00 0.51 34.79 4.02
1665 1739 5.401550 ACAATTTCGCATGTTTATGGTCAG 58.598 37.500 0.00 0.00 34.79 3.51
1666 1740 5.048083 ACAATTTCGCATGTTTATGGTCAGT 60.048 36.000 0.00 0.00 34.79 3.41
1667 1741 5.643379 ATTTCGCATGTTTATGGTCAGTT 57.357 34.783 0.00 0.00 34.79 3.16
1668 1742 5.446143 TTTCGCATGTTTATGGTCAGTTT 57.554 34.783 0.00 0.00 34.79 2.66
1669 1743 6.561737 TTTCGCATGTTTATGGTCAGTTTA 57.438 33.333 0.00 0.00 34.79 2.01
1670 1744 6.561737 TTCGCATGTTTATGGTCAGTTTAA 57.438 33.333 0.00 0.00 34.79 1.52
1671 1745 6.751514 TCGCATGTTTATGGTCAGTTTAAT 57.248 33.333 0.00 0.00 34.79 1.40
1672 1746 7.851387 TCGCATGTTTATGGTCAGTTTAATA 57.149 32.000 0.00 0.00 34.79 0.98
1673 1747 8.270080 TCGCATGTTTATGGTCAGTTTAATAA 57.730 30.769 0.00 0.00 34.79 1.40
1674 1748 8.178964 TCGCATGTTTATGGTCAGTTTAATAAC 58.821 33.333 0.00 0.00 34.79 1.89
1675 1749 7.163520 CGCATGTTTATGGTCAGTTTAATAACG 59.836 37.037 0.00 0.00 35.80 3.18
1676 1750 7.044314 GCATGTTTATGGTCAGTTTAATAACGC 60.044 37.037 0.00 0.00 35.80 4.84
1677 1751 6.535811 TGTTTATGGTCAGTTTAATAACGCG 58.464 36.000 3.53 3.53 39.31 6.01
1678 1752 5.721876 TTATGGTCAGTTTAATAACGCGG 57.278 39.130 12.47 0.00 39.31 6.46
1679 1753 2.348660 TGGTCAGTTTAATAACGCGGG 58.651 47.619 12.47 0.00 39.31 6.13
1680 1754 1.667212 GGTCAGTTTAATAACGCGGGG 59.333 52.381 12.47 0.00 39.31 5.73
1681 1755 2.620242 GTCAGTTTAATAACGCGGGGA 58.380 47.619 12.47 0.00 39.31 4.81
1682 1756 3.200483 GTCAGTTTAATAACGCGGGGAT 58.800 45.455 12.47 0.00 39.31 3.85
1683 1757 3.001939 GTCAGTTTAATAACGCGGGGATG 59.998 47.826 12.47 0.00 39.31 3.51
1684 1758 3.118702 TCAGTTTAATAACGCGGGGATGA 60.119 43.478 12.47 0.00 39.31 2.92
1685 1759 3.001939 CAGTTTAATAACGCGGGGATGAC 59.998 47.826 12.47 0.50 39.31 3.06
1686 1760 2.937799 GTTTAATAACGCGGGGATGACA 59.062 45.455 12.47 0.00 0.00 3.58
1687 1761 2.983907 TAATAACGCGGGGATGACAA 57.016 45.000 12.47 0.00 0.00 3.18
1688 1762 1.663695 AATAACGCGGGGATGACAAG 58.336 50.000 12.47 0.00 0.00 3.16
1689 1763 0.539986 ATAACGCGGGGATGACAAGT 59.460 50.000 12.47 0.00 0.00 3.16
1690 1764 0.322322 TAACGCGGGGATGACAAGTT 59.678 50.000 12.47 0.00 0.00 2.66
1691 1765 0.953960 AACGCGGGGATGACAAGTTC 60.954 55.000 12.47 0.00 0.00 3.01
1692 1766 2.452813 CGCGGGGATGACAAGTTCG 61.453 63.158 0.00 0.00 0.00 3.95
1693 1767 2.106683 GCGGGGATGACAAGTTCGG 61.107 63.158 0.00 0.00 0.00 4.30
1694 1768 1.594833 CGGGGATGACAAGTTCGGA 59.405 57.895 0.00 0.00 0.00 4.55
1695 1769 0.178068 CGGGGATGACAAGTTCGGAT 59.822 55.000 0.00 0.00 0.00 4.18
1696 1770 1.668419 GGGGATGACAAGTTCGGATG 58.332 55.000 0.00 0.00 0.00 3.51
1697 1771 1.668419 GGGATGACAAGTTCGGATGG 58.332 55.000 0.00 0.00 0.00 3.51
1698 1772 1.017387 GGATGACAAGTTCGGATGGC 58.983 55.000 0.00 0.00 0.00 4.40
1699 1773 1.678728 GGATGACAAGTTCGGATGGCA 60.679 52.381 0.00 0.00 39.30 4.92
1700 1774 2.083774 GATGACAAGTTCGGATGGCAA 58.916 47.619 0.00 0.00 38.26 4.52
1701 1775 1.522668 TGACAAGTTCGGATGGCAAG 58.477 50.000 0.00 0.00 29.85 4.01
1702 1776 1.202758 TGACAAGTTCGGATGGCAAGT 60.203 47.619 0.00 0.00 29.85 3.16
1703 1777 1.880027 GACAAGTTCGGATGGCAAGTT 59.120 47.619 0.00 0.00 0.00 2.66
1704 1778 2.293399 GACAAGTTCGGATGGCAAGTTT 59.707 45.455 0.00 0.00 0.00 2.66
1705 1779 2.693074 ACAAGTTCGGATGGCAAGTTTT 59.307 40.909 0.00 0.00 0.00 2.43
1706 1780 3.886505 ACAAGTTCGGATGGCAAGTTTTA 59.113 39.130 0.00 0.00 0.00 1.52
1707 1781 4.023193 ACAAGTTCGGATGGCAAGTTTTAG 60.023 41.667 0.00 0.00 0.00 1.85
1708 1782 3.751518 AGTTCGGATGGCAAGTTTTAGT 58.248 40.909 0.00 0.00 0.00 2.24
1709 1783 4.142038 AGTTCGGATGGCAAGTTTTAGTT 58.858 39.130 0.00 0.00 0.00 2.24
1710 1784 4.583073 AGTTCGGATGGCAAGTTTTAGTTT 59.417 37.500 0.00 0.00 0.00 2.66
1711 1785 5.766174 AGTTCGGATGGCAAGTTTTAGTTTA 59.234 36.000 0.00 0.00 0.00 2.01
1712 1786 6.433093 AGTTCGGATGGCAAGTTTTAGTTTAT 59.567 34.615 0.00 0.00 0.00 1.40
1713 1787 6.827586 TCGGATGGCAAGTTTTAGTTTATT 57.172 33.333 0.00 0.00 0.00 1.40
1714 1788 7.222000 TCGGATGGCAAGTTTTAGTTTATTT 57.778 32.000 0.00 0.00 0.00 1.40
1715 1789 7.662897 TCGGATGGCAAGTTTTAGTTTATTTT 58.337 30.769 0.00 0.00 0.00 1.82
1716 1790 8.145122 TCGGATGGCAAGTTTTAGTTTATTTTT 58.855 29.630 0.00 0.00 0.00 1.94
1741 1815 9.632807 TTTGAGTTTTCTTTTCTTTTCGAATGA 57.367 25.926 0.00 0.00 0.00 2.57
1742 1816 8.614994 TGAGTTTTCTTTTCTTTTCGAATGAC 57.385 30.769 0.00 0.00 0.00 3.06
1743 1817 8.240682 TGAGTTTTCTTTTCTTTTCGAATGACA 58.759 29.630 0.00 0.00 0.00 3.58
1744 1818 8.980143 AGTTTTCTTTTCTTTTCGAATGACAA 57.020 26.923 0.00 0.00 0.00 3.18
1745 1819 9.418045 AGTTTTCTTTTCTTTTCGAATGACAAA 57.582 25.926 0.00 4.42 0.00 2.83
1781 1855 2.724349 CGTTAGGACGGGATTACTTCG 58.276 52.381 0.00 0.00 45.32 3.79
1782 1856 2.098117 CGTTAGGACGGGATTACTTCGT 59.902 50.000 0.00 0.00 45.32 3.85
1783 1857 3.442100 GTTAGGACGGGATTACTTCGTG 58.558 50.000 0.00 0.00 37.25 4.35
1784 1858 1.553706 AGGACGGGATTACTTCGTGT 58.446 50.000 0.00 0.00 37.25 4.49
1785 1859 1.475682 AGGACGGGATTACTTCGTGTC 59.524 52.381 0.00 0.00 37.25 3.67
1786 1860 1.203052 GGACGGGATTACTTCGTGTCA 59.797 52.381 0.00 0.00 37.25 3.58
1787 1861 2.257034 GACGGGATTACTTCGTGTCAC 58.743 52.381 0.00 0.00 37.25 3.67
1788 1862 1.614903 ACGGGATTACTTCGTGTCACA 59.385 47.619 3.42 0.00 35.70 3.58
1789 1863 1.990563 CGGGATTACTTCGTGTCACAC 59.009 52.381 0.00 0.00 0.00 3.82
1790 1864 2.608506 CGGGATTACTTCGTGTCACACA 60.609 50.000 9.06 0.00 33.40 3.72
1791 1865 3.596214 GGGATTACTTCGTGTCACACAT 58.404 45.455 9.06 0.00 33.40 3.21
1792 1866 3.370978 GGGATTACTTCGTGTCACACATG 59.629 47.826 9.06 0.00 36.48 3.21
1793 1867 3.994392 GGATTACTTCGTGTCACACATGT 59.006 43.478 9.06 5.77 36.53 3.21
1794 1868 4.143115 GGATTACTTCGTGTCACACATGTG 60.143 45.833 24.25 24.25 46.91 3.21
1795 1869 1.581934 ACTTCGTGTCACACATGTGG 58.418 50.000 28.64 17.57 45.65 4.17
1804 1878 3.415457 TCACACATGTGGCACTTATCA 57.585 42.857 28.64 0.00 45.65 2.15
1805 1879 3.954200 TCACACATGTGGCACTTATCAT 58.046 40.909 28.64 0.00 45.65 2.45
1806 1880 4.334552 TCACACATGTGGCACTTATCATT 58.665 39.130 28.64 0.98 45.65 2.57
1807 1881 4.766373 TCACACATGTGGCACTTATCATTT 59.234 37.500 28.64 0.77 45.65 2.32
1808 1882 4.860352 CACACATGTGGCACTTATCATTTG 59.140 41.667 28.64 9.95 42.10 2.32
1809 1883 4.766373 ACACATGTGGCACTTATCATTTGA 59.234 37.500 28.64 0.00 34.19 2.69
1810 1884 5.106038 ACACATGTGGCACTTATCATTTGAG 60.106 40.000 28.64 0.00 34.19 3.02
1826 1900 8.845413 ATCATTTGAGTAATATTCTCAGGAGC 57.155 34.615 13.64 0.00 41.87 4.70
1843 1917 2.860293 CGACACCGTCATGTTGCC 59.140 61.111 0.00 0.00 31.24 4.52
1845 1919 1.574428 GACACCGTCATGTTGCCAC 59.426 57.895 0.00 0.00 31.24 5.01
1892 1966 2.856222 TGAGCTAGCTCAGATCGATCA 58.144 47.619 37.64 17.11 46.80 2.92
1942 2018 2.034812 GCAGTAGCTAGCTGGTTACGAT 59.965 50.000 27.68 0.00 37.91 3.73
1943 2019 3.854045 GCAGTAGCTAGCTGGTTACGATC 60.854 52.174 27.68 7.90 37.91 3.69
1944 2020 2.885894 AGTAGCTAGCTGGTTACGATCC 59.114 50.000 27.68 2.24 0.00 3.36
1945 2021 1.776662 AGCTAGCTGGTTACGATCCA 58.223 50.000 18.57 0.00 0.00 3.41
1954 2030 4.730949 TGGTTACGATCCAGAAGTTAGG 57.269 45.455 0.00 0.00 0.00 2.69
1992 2074 2.029290 GCGTACTGTCTCCAGGAAGAAA 60.029 50.000 0.00 0.00 43.36 2.52
1994 2076 3.005472 CGTACTGTCTCCAGGAAGAAACA 59.995 47.826 0.00 0.00 43.36 2.83
2019 2101 2.363172 GGGTGCCCTCTGACCTCTC 61.363 68.421 0.00 0.00 32.33 3.20
2035 2117 4.846040 ACCTCTCTACTTACACATCTCGT 58.154 43.478 0.00 0.00 0.00 4.18
2077 5430 3.192001 CGTAGTACCTACTTGAGCCAACA 59.808 47.826 0.00 0.00 37.73 3.33
2096 5449 4.920640 ACATAGGTATGTGTTCCTCGAG 57.079 45.455 5.13 5.13 44.66 4.04
2124 5477 3.471354 TCGTCACTGGAGCGAGATA 57.529 52.632 0.00 0.00 0.00 1.98
2125 5478 1.746470 TCGTCACTGGAGCGAGATAA 58.254 50.000 0.00 0.00 0.00 1.75
2126 5479 2.089201 TCGTCACTGGAGCGAGATAAA 58.911 47.619 0.00 0.00 0.00 1.40
2127 5480 2.490509 TCGTCACTGGAGCGAGATAAAA 59.509 45.455 0.00 0.00 0.00 1.52
2128 5481 3.057104 TCGTCACTGGAGCGAGATAAAAA 60.057 43.478 0.00 0.00 0.00 1.94
2129 5482 3.060895 CGTCACTGGAGCGAGATAAAAAC 59.939 47.826 0.00 0.00 0.00 2.43
2130 5483 3.060895 GTCACTGGAGCGAGATAAAAACG 59.939 47.826 0.00 0.00 0.00 3.60
2131 5484 2.993899 CACTGGAGCGAGATAAAAACGT 59.006 45.455 0.00 0.00 0.00 3.99
2132 5485 2.993899 ACTGGAGCGAGATAAAAACGTG 59.006 45.455 0.00 0.00 0.00 4.49
2133 5486 2.993899 CTGGAGCGAGATAAAAACGTGT 59.006 45.455 0.00 0.00 0.00 4.49
2134 5487 3.395639 TGGAGCGAGATAAAAACGTGTT 58.604 40.909 0.00 0.00 0.00 3.32
2135 5488 3.810941 TGGAGCGAGATAAAAACGTGTTT 59.189 39.130 9.06 9.06 0.00 2.83
2136 5489 4.273969 TGGAGCGAGATAAAAACGTGTTTT 59.726 37.500 9.41 10.65 43.88 2.43
2159 5512 0.591170 AGGCAAAAACGTGTGATCCG 59.409 50.000 0.00 0.00 0.00 4.18
2164 5517 2.406002 AAAACGTGTGATCCGGGCCT 62.406 55.000 0.84 0.00 0.00 5.19
2165 5518 1.546589 AAACGTGTGATCCGGGCCTA 61.547 55.000 0.84 0.00 0.00 3.93
2166 5519 1.546589 AACGTGTGATCCGGGCCTAA 61.547 55.000 0.84 0.00 0.00 2.69
2167 5520 1.335132 ACGTGTGATCCGGGCCTAAT 61.335 55.000 0.84 0.00 0.00 1.73
2168 5521 0.677288 CGTGTGATCCGGGCCTAATA 59.323 55.000 0.84 0.00 0.00 0.98
2169 5522 1.069513 CGTGTGATCCGGGCCTAATAA 59.930 52.381 0.84 0.00 0.00 1.40
2170 5523 2.767505 GTGTGATCCGGGCCTAATAAG 58.232 52.381 0.84 0.00 0.00 1.73
2171 5524 1.071699 TGTGATCCGGGCCTAATAAGC 59.928 52.381 0.84 0.00 0.00 3.09
2192 5545 3.575965 CAACAATTTGGTGGTAGCTCC 57.424 47.619 6.54 6.07 29.70 4.70
2197 5550 4.018415 ACAATTTGGTGGTAGCTCCTGTAT 60.018 41.667 13.73 2.80 37.07 2.29
2238 5591 2.747855 CTTCAAGGTGGAGCGCCC 60.748 66.667 2.29 5.76 33.99 6.13
2293 5648 2.279741 GATGCAAATACAGAGGCGTGA 58.720 47.619 0.00 0.00 0.00 4.35
2296 5651 2.419673 TGCAAATACAGAGGCGTGATTG 59.580 45.455 0.00 1.65 0.00 2.67
2297 5652 2.792542 GCAAATACAGAGGCGTGATTGC 60.793 50.000 12.61 12.61 35.69 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 127 9.911138 TTTCAAGTACGTGTGATAGTGTTAATA 57.089 29.630 8.68 0.00 0.00 0.98
339 347 9.717942 ACATGGCAAATTGCTTAACTTTAATTA 57.282 25.926 18.04 0.00 44.28 1.40
371 381 2.411069 CGATTGATCGCTAGCTTCCATG 59.589 50.000 13.93 0.00 43.84 3.66
428 440 3.197766 TGTACCACAAGATGACCATCTCC 59.802 47.826 12.40 0.00 46.75 3.71
432 444 8.034313 AGTATAATGTACCACAAGATGACCAT 57.966 34.615 0.00 0.00 0.00 3.55
436 448 6.844388 AGGGAGTATAATGTACCACAAGATGA 59.156 38.462 0.00 0.00 0.00 2.92
457 469 9.775539 ATGCTCTTATATATCTTTACAGAGGGA 57.224 33.333 7.24 0.00 30.36 4.20
506 518 9.566432 CCCTCTGTAAAGAAATATAAGAGCATT 57.434 33.333 0.00 0.00 0.00 3.56
507 519 8.938883 TCCCTCTGTAAAGAAATATAAGAGCAT 58.061 33.333 0.00 0.00 0.00 3.79
508 520 8.319057 TCCCTCTGTAAAGAAATATAAGAGCA 57.681 34.615 0.00 0.00 0.00 4.26
509 521 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
545 557 9.293404 AGCAAAGATTAATGAGCACATATGTAT 57.707 29.630 8.32 0.00 35.50 2.29
597 609 3.327172 AGGATGTGATCTCATCATGGGAC 59.673 47.826 29.34 16.34 44.00 4.46
618 630 6.430925 TGTTACATGACCCATGAGAGAAAAAG 59.569 38.462 13.22 0.00 43.81 2.27
619 631 6.206634 GTGTTACATGACCCATGAGAGAAAAA 59.793 38.462 13.22 0.00 43.81 1.94
624 636 4.478206 AGTGTTACATGACCCATGAGAG 57.522 45.455 13.22 0.00 43.81 3.20
672 684 5.391736 GCCTACCAGTAGTACTACGCATATG 60.392 48.000 23.87 16.86 40.80 1.78
684 696 2.389715 CTAGCAAGGCCTACCAGTAGT 58.610 52.381 5.16 0.00 39.06 2.73
806 824 9.429359 CTAGCTAATTAAGTATGTGAGGATTGG 57.571 37.037 0.00 0.00 0.00 3.16
817 835 6.931840 GGCACTTCAGCTAGCTAATTAAGTAT 59.068 38.462 18.86 1.92 34.17 2.12
827 845 0.823460 GAGAGGCACTTCAGCTAGCT 59.177 55.000 12.68 12.68 41.55 3.32
832 850 2.250741 GAGGGGAGAGGCACTTCAGC 62.251 65.000 0.00 0.00 41.55 4.26
833 851 0.617249 AGAGGGGAGAGGCACTTCAG 60.617 60.000 0.00 0.00 41.55 3.02
834 852 0.616111 GAGAGGGGAGAGGCACTTCA 60.616 60.000 0.00 0.00 41.55 3.02
835 853 0.616111 TGAGAGGGGAGAGGCACTTC 60.616 60.000 0.00 0.00 41.55 3.01
836 854 0.907230 GTGAGAGGGGAGAGGCACTT 60.907 60.000 0.00 0.00 41.55 3.16
838 856 1.610673 TGTGAGAGGGGAGAGGCAC 60.611 63.158 0.00 0.00 0.00 5.01
847 865 1.606601 TGGACCGAGTGTGAGAGGG 60.607 63.158 0.00 0.00 0.00 4.30
856 877 5.895534 TGAAGGTTTATATAGTGGACCGAGT 59.104 40.000 0.00 0.00 35.56 4.18
861 882 6.885922 ACCAGTGAAGGTTTATATAGTGGAC 58.114 40.000 0.00 0.00 39.34 4.02
882 903 2.813754 GCTTTGCTGTGTGATAGAACCA 59.186 45.455 0.00 0.00 0.00 3.67
889 910 4.325028 TCAATTTGCTTTGCTGTGTGAT 57.675 36.364 0.00 0.00 0.00 3.06
913 935 0.588252 CTTTCGAGTGGTGTGCAAGG 59.412 55.000 0.00 0.00 0.00 3.61
955 977 1.067669 TGTTCGGCTCTGCTATAGCTG 59.932 52.381 24.61 23.23 45.87 4.24
1246 1283 0.037605 ACGAACGGGAAGCTAACCAG 60.038 55.000 11.20 9.60 0.00 4.00
1247 1284 0.037975 GACGAACGGGAAGCTAACCA 60.038 55.000 11.20 0.00 0.00 3.67
1248 1285 1.074872 CGACGAACGGGAAGCTAACC 61.075 60.000 0.00 0.00 38.46 2.85
1249 1286 2.356794 CGACGAACGGGAAGCTAAC 58.643 57.895 0.00 0.00 38.46 2.34
1250 1287 4.874534 CGACGAACGGGAAGCTAA 57.125 55.556 0.00 0.00 38.46 3.09
1458 1496 1.538634 CGTCGTGGTTAACTCCCAACA 60.539 52.381 5.42 0.00 32.72 3.33
1540 1605 6.596497 ACACGGGGTTTACAAGAGTATAAATG 59.404 38.462 0.00 0.00 0.00 2.32
1580 1647 6.173339 TCAGGATCCGGATATTATTGCTTTC 58.827 40.000 19.15 0.13 0.00 2.62
1584 1651 7.225538 CACTTATCAGGATCCGGATATTATTGC 59.774 40.741 28.34 2.30 34.22 3.56
1588 1662 9.709387 TTATCACTTATCAGGATCCGGATATTA 57.291 33.333 28.34 17.19 34.22 0.98
1589 1663 8.609617 TTATCACTTATCAGGATCCGGATATT 57.390 34.615 28.34 18.50 34.22 1.28
1590 1664 7.841729 ACTTATCACTTATCAGGATCCGGATAT 59.158 37.037 28.34 19.22 34.22 1.63
1591 1665 7.122799 CACTTATCACTTATCAGGATCCGGATA 59.877 40.741 25.40 25.40 33.28 2.59
1592 1666 6.019748 ACTTATCACTTATCAGGATCCGGAT 58.980 40.000 27.34 27.34 35.25 4.18
1593 1667 5.243954 CACTTATCACTTATCAGGATCCGGA 59.756 44.000 17.36 17.36 0.00 5.14
1594 1668 5.473931 CACTTATCACTTATCAGGATCCGG 58.526 45.833 5.98 5.68 0.00 5.14
1595 1669 4.926238 GCACTTATCACTTATCAGGATCCG 59.074 45.833 5.98 1.36 0.00 4.18
1596 1670 5.221722 TGGCACTTATCACTTATCAGGATCC 60.222 44.000 2.48 2.48 0.00 3.36
1597 1671 5.698545 GTGGCACTTATCACTTATCAGGATC 59.301 44.000 11.13 0.00 0.00 3.36
1598 1672 5.130975 TGTGGCACTTATCACTTATCAGGAT 59.869 40.000 19.83 0.00 35.15 3.24
1599 1673 4.469586 TGTGGCACTTATCACTTATCAGGA 59.530 41.667 19.83 0.00 35.15 3.86
1600 1674 4.572389 GTGTGGCACTTATCACTTATCAGG 59.428 45.833 19.83 0.00 35.15 3.86
1601 1675 5.178061 TGTGTGGCACTTATCACTTATCAG 58.822 41.667 19.83 0.00 35.11 2.90
1602 1676 5.159273 TGTGTGGCACTTATCACTTATCA 57.841 39.130 19.83 0.00 35.11 2.15
1603 1677 6.683974 AATGTGTGGCACTTATCACTTATC 57.316 37.500 19.83 0.00 35.11 1.75
1604 1678 6.658816 TCAAATGTGTGGCACTTATCACTTAT 59.341 34.615 19.83 0.00 35.11 1.73
1605 1679 6.000840 TCAAATGTGTGGCACTTATCACTTA 58.999 36.000 19.83 0.00 35.11 2.24
1606 1680 4.826733 TCAAATGTGTGGCACTTATCACTT 59.173 37.500 19.83 6.41 35.11 3.16
1607 1681 4.216257 GTCAAATGTGTGGCACTTATCACT 59.784 41.667 19.83 0.33 35.11 3.41
1608 1682 4.475944 GTCAAATGTGTGGCACTTATCAC 58.524 43.478 19.83 8.70 35.11 3.06
1609 1683 3.188254 CGTCAAATGTGTGGCACTTATCA 59.812 43.478 19.83 12.55 35.11 2.15
1610 1684 3.188460 ACGTCAAATGTGTGGCACTTATC 59.812 43.478 19.83 7.37 35.11 1.75
1611 1685 3.058293 CACGTCAAATGTGTGGCACTTAT 60.058 43.478 19.83 10.08 35.11 1.73
1612 1686 2.289274 CACGTCAAATGTGTGGCACTTA 59.711 45.455 19.83 8.02 35.11 2.24
1613 1687 1.065401 CACGTCAAATGTGTGGCACTT 59.935 47.619 19.83 1.54 35.11 3.16
1614 1688 0.662619 CACGTCAAATGTGTGGCACT 59.337 50.000 19.83 0.00 35.11 4.40
1615 1689 0.660488 TCACGTCAAATGTGTGGCAC 59.340 50.000 11.55 11.55 36.53 5.01
1616 1690 1.064803 GTTCACGTCAAATGTGTGGCA 59.935 47.619 0.00 0.00 36.53 4.92
1617 1691 1.064803 TGTTCACGTCAAATGTGTGGC 59.935 47.619 0.00 0.00 36.53 5.01
1618 1692 2.096657 TGTGTTCACGTCAAATGTGTGG 59.903 45.455 0.00 0.00 36.53 4.17
1619 1693 3.397405 TGTGTTCACGTCAAATGTGTG 57.603 42.857 0.00 3.32 36.53 3.82
1620 1694 3.625313 TCATGTGTTCACGTCAAATGTGT 59.375 39.130 5.96 0.00 36.53 3.72
1621 1695 3.968096 GTCATGTGTTCACGTCAAATGTG 59.032 43.478 5.96 0.00 36.48 3.21
1622 1696 3.625313 TGTCATGTGTTCACGTCAAATGT 59.375 39.130 5.96 0.00 33.63 2.71
1623 1697 4.208074 TGTCATGTGTTCACGTCAAATG 57.792 40.909 0.48 0.48 33.30 2.32
1624 1698 4.891627 TTGTCATGTGTTCACGTCAAAT 57.108 36.364 0.00 0.00 0.00 2.32
1625 1699 4.891627 ATTGTCATGTGTTCACGTCAAA 57.108 36.364 0.00 0.00 0.00 2.69
1626 1700 4.891627 AATTGTCATGTGTTCACGTCAA 57.108 36.364 0.00 0.00 0.00 3.18
1627 1701 4.551797 CGAAATTGTCATGTGTTCACGTCA 60.552 41.667 0.00 0.00 0.00 4.35
1628 1702 3.900116 CGAAATTGTCATGTGTTCACGTC 59.100 43.478 0.00 0.00 0.00 4.34
1629 1703 3.848191 GCGAAATTGTCATGTGTTCACGT 60.848 43.478 0.00 0.00 0.00 4.49
1630 1704 2.651703 GCGAAATTGTCATGTGTTCACG 59.348 45.455 0.00 0.00 0.00 4.35
1631 1705 3.626977 TGCGAAATTGTCATGTGTTCAC 58.373 40.909 0.00 0.00 0.00 3.18
1632 1706 3.978718 TGCGAAATTGTCATGTGTTCA 57.021 38.095 0.00 0.00 0.00 3.18
1633 1707 4.229096 ACATGCGAAATTGTCATGTGTTC 58.771 39.130 15.39 0.00 46.16 3.18
1634 1708 4.241590 ACATGCGAAATTGTCATGTGTT 57.758 36.364 15.39 0.00 46.16 3.32
1635 1709 3.921119 ACATGCGAAATTGTCATGTGT 57.079 38.095 15.39 0.09 46.16 3.72
1636 1710 6.237622 CCATAAACATGCGAAATTGTCATGTG 60.238 38.462 16.31 7.94 46.92 3.21
1638 1712 5.806502 ACCATAAACATGCGAAATTGTCATG 59.193 36.000 11.16 11.16 42.27 3.07
1639 1713 5.964758 ACCATAAACATGCGAAATTGTCAT 58.035 33.333 0.00 0.00 0.00 3.06
1640 1714 5.048434 TGACCATAAACATGCGAAATTGTCA 60.048 36.000 0.00 0.00 0.00 3.58
1641 1715 5.398169 TGACCATAAACATGCGAAATTGTC 58.602 37.500 0.00 0.00 0.00 3.18
1642 1716 5.048083 ACTGACCATAAACATGCGAAATTGT 60.048 36.000 0.00 0.00 0.00 2.71
1643 1717 5.401550 ACTGACCATAAACATGCGAAATTG 58.598 37.500 0.00 0.00 0.00 2.32
1644 1718 5.643379 ACTGACCATAAACATGCGAAATT 57.357 34.783 0.00 0.00 0.00 1.82
1645 1719 5.643379 AACTGACCATAAACATGCGAAAT 57.357 34.783 0.00 0.00 0.00 2.17
1646 1720 5.446143 AAACTGACCATAAACATGCGAAA 57.554 34.783 0.00 0.00 0.00 3.46
1647 1721 6.561737 TTAAACTGACCATAAACATGCGAA 57.438 33.333 0.00 0.00 0.00 4.70
1648 1722 6.751514 ATTAAACTGACCATAAACATGCGA 57.248 33.333 0.00 0.00 0.00 5.10
1649 1723 7.163520 CGTTATTAAACTGACCATAAACATGCG 59.836 37.037 0.00 0.00 33.15 4.73
1650 1724 7.044314 GCGTTATTAAACTGACCATAAACATGC 60.044 37.037 0.00 0.00 33.15 4.06
1651 1725 7.163520 CGCGTTATTAAACTGACCATAAACATG 59.836 37.037 0.00 0.00 33.15 3.21
1652 1726 7.184106 CGCGTTATTAAACTGACCATAAACAT 58.816 34.615 0.00 0.00 33.15 2.71
1653 1727 6.402334 CCGCGTTATTAAACTGACCATAAACA 60.402 38.462 4.92 0.00 33.15 2.83
1654 1728 5.961263 CCGCGTTATTAAACTGACCATAAAC 59.039 40.000 4.92 0.00 33.15 2.01
1655 1729 5.064962 CCCGCGTTATTAAACTGACCATAAA 59.935 40.000 4.92 0.00 33.15 1.40
1656 1730 4.571580 CCCGCGTTATTAAACTGACCATAA 59.428 41.667 4.92 0.00 33.15 1.90
1657 1731 4.121317 CCCGCGTTATTAAACTGACCATA 58.879 43.478 4.92 0.00 33.15 2.74
1658 1732 2.940410 CCCGCGTTATTAAACTGACCAT 59.060 45.455 4.92 0.00 33.15 3.55
1659 1733 2.348660 CCCGCGTTATTAAACTGACCA 58.651 47.619 4.92 0.00 33.15 4.02
1660 1734 1.667212 CCCCGCGTTATTAAACTGACC 59.333 52.381 4.92 0.00 33.15 4.02
1661 1735 2.620242 TCCCCGCGTTATTAAACTGAC 58.380 47.619 4.92 0.00 33.15 3.51
1662 1736 3.118702 TCATCCCCGCGTTATTAAACTGA 60.119 43.478 4.92 0.00 33.15 3.41
1663 1737 3.001939 GTCATCCCCGCGTTATTAAACTG 59.998 47.826 4.92 0.00 33.15 3.16
1664 1738 3.200483 GTCATCCCCGCGTTATTAAACT 58.800 45.455 4.92 0.00 33.15 2.66
1665 1739 2.937799 TGTCATCCCCGCGTTATTAAAC 59.062 45.455 4.92 0.00 0.00 2.01
1666 1740 3.263489 TGTCATCCCCGCGTTATTAAA 57.737 42.857 4.92 0.00 0.00 1.52
1667 1741 2.983907 TGTCATCCCCGCGTTATTAA 57.016 45.000 4.92 0.00 0.00 1.40
1668 1742 2.168936 ACTTGTCATCCCCGCGTTATTA 59.831 45.455 4.92 0.00 0.00 0.98
1669 1743 1.065709 ACTTGTCATCCCCGCGTTATT 60.066 47.619 4.92 0.00 0.00 1.40
1670 1744 0.539986 ACTTGTCATCCCCGCGTTAT 59.460 50.000 4.92 0.00 0.00 1.89
1671 1745 0.322322 AACTTGTCATCCCCGCGTTA 59.678 50.000 4.92 0.00 0.00 3.18
1672 1746 0.953960 GAACTTGTCATCCCCGCGTT 60.954 55.000 4.92 0.00 0.00 4.84
1673 1747 1.375523 GAACTTGTCATCCCCGCGT 60.376 57.895 4.92 0.00 0.00 6.01
1674 1748 2.452813 CGAACTTGTCATCCCCGCG 61.453 63.158 0.00 0.00 0.00 6.46
1675 1749 2.106683 CCGAACTTGTCATCCCCGC 61.107 63.158 0.00 0.00 0.00 6.13
1676 1750 0.178068 ATCCGAACTTGTCATCCCCG 59.822 55.000 0.00 0.00 0.00 5.73
1677 1751 1.668419 CATCCGAACTTGTCATCCCC 58.332 55.000 0.00 0.00 0.00 4.81
1678 1752 1.668419 CCATCCGAACTTGTCATCCC 58.332 55.000 0.00 0.00 0.00 3.85
1679 1753 1.017387 GCCATCCGAACTTGTCATCC 58.983 55.000 0.00 0.00 0.00 3.51
1680 1754 1.737838 TGCCATCCGAACTTGTCATC 58.262 50.000 0.00 0.00 0.00 2.92
1681 1755 2.086869 CTTGCCATCCGAACTTGTCAT 58.913 47.619 0.00 0.00 0.00 3.06
1682 1756 1.202758 ACTTGCCATCCGAACTTGTCA 60.203 47.619 0.00 0.00 0.00 3.58
1683 1757 1.523758 ACTTGCCATCCGAACTTGTC 58.476 50.000 0.00 0.00 0.00 3.18
1684 1758 1.981256 AACTTGCCATCCGAACTTGT 58.019 45.000 0.00 0.00 0.00 3.16
1685 1759 3.369546 AAAACTTGCCATCCGAACTTG 57.630 42.857 0.00 0.00 0.00 3.16
1686 1760 4.142038 ACTAAAACTTGCCATCCGAACTT 58.858 39.130 0.00 0.00 0.00 2.66
1687 1761 3.751518 ACTAAAACTTGCCATCCGAACT 58.248 40.909 0.00 0.00 0.00 3.01
1688 1762 4.499037 AACTAAAACTTGCCATCCGAAC 57.501 40.909 0.00 0.00 0.00 3.95
1689 1763 6.827586 ATAAACTAAAACTTGCCATCCGAA 57.172 33.333 0.00 0.00 0.00 4.30
1690 1764 6.827586 AATAAACTAAAACTTGCCATCCGA 57.172 33.333 0.00 0.00 0.00 4.55
1691 1765 7.883229 AAAATAAACTAAAACTTGCCATCCG 57.117 32.000 0.00 0.00 0.00 4.18
1715 1789 9.632807 TCATTCGAAAAGAAAAGAAAACTCAAA 57.367 25.926 0.00 0.00 42.91 2.69
1716 1790 9.072294 GTCATTCGAAAAGAAAAGAAAACTCAA 57.928 29.630 0.00 0.00 42.91 3.02
1717 1791 8.240682 TGTCATTCGAAAAGAAAAGAAAACTCA 58.759 29.630 0.00 0.00 42.91 3.41
1718 1792 8.614994 TGTCATTCGAAAAGAAAAGAAAACTC 57.385 30.769 0.00 0.00 42.91 3.01
1719 1793 8.980143 TTGTCATTCGAAAAGAAAAGAAAACT 57.020 26.923 0.00 0.00 42.91 2.66
1757 1831 8.672161 ACGAAGTAATCCCGTCCTAACGTTTT 62.672 42.308 5.91 0.00 44.06 2.43
1758 1832 7.290663 ACGAAGTAATCCCGTCCTAACGTTT 62.291 44.000 5.91 0.00 44.06 3.60
1759 1833 5.877842 ACGAAGTAATCCCGTCCTAACGTT 61.878 45.833 5.88 5.88 44.06 3.99
1760 1834 4.429673 ACGAAGTAATCCCGTCCTAACGT 61.430 47.826 0.00 0.00 44.06 3.99
1761 1835 2.098117 ACGAAGTAATCCCGTCCTAACG 59.902 50.000 0.00 0.00 44.87 3.18
1762 1836 3.119352 ACACGAAGTAATCCCGTCCTAAC 60.119 47.826 0.00 0.00 41.61 2.34
1763 1837 3.091545 ACACGAAGTAATCCCGTCCTAA 58.908 45.455 0.00 0.00 41.61 2.69
1764 1838 2.684881 GACACGAAGTAATCCCGTCCTA 59.315 50.000 0.00 0.00 41.61 2.94
1765 1839 1.475682 GACACGAAGTAATCCCGTCCT 59.524 52.381 0.00 0.00 41.61 3.85
1766 1840 1.203052 TGACACGAAGTAATCCCGTCC 59.797 52.381 0.00 0.00 41.61 4.79
1767 1841 2.257034 GTGACACGAAGTAATCCCGTC 58.743 52.381 0.00 0.00 41.61 4.79
1768 1842 1.614903 TGTGACACGAAGTAATCCCGT 59.385 47.619 0.22 0.00 41.61 5.28
1769 1843 1.990563 GTGTGACACGAAGTAATCCCG 59.009 52.381 0.00 0.00 41.61 5.14
1770 1844 3.034721 TGTGTGACACGAAGTAATCCC 57.965 47.619 11.51 0.00 41.61 3.85
1771 1845 3.994392 ACATGTGTGACACGAAGTAATCC 59.006 43.478 11.51 0.00 41.61 3.01
1777 1851 4.493280 GTGCCACATGTGTGACACGAAG 62.493 54.545 23.79 6.82 46.28 3.79
1778 1852 2.668976 GTGCCACATGTGTGACACGAA 61.669 52.381 23.79 0.00 46.28 3.85
1779 1853 1.157257 GTGCCACATGTGTGACACGA 61.157 55.000 23.79 0.76 46.28 4.35
1780 1854 1.279539 GTGCCACATGTGTGACACG 59.720 57.895 23.79 8.95 46.28 4.49
1785 1859 4.707030 AATGATAAGTGCCACATGTGTG 57.293 40.909 23.79 15.96 45.23 3.82
1786 1860 4.766373 TCAAATGATAAGTGCCACATGTGT 59.234 37.500 23.79 8.06 32.04 3.72
1787 1861 5.106038 ACTCAAATGATAAGTGCCACATGTG 60.106 40.000 19.31 19.31 31.55 3.21
1788 1862 5.012239 ACTCAAATGATAAGTGCCACATGT 58.988 37.500 0.00 0.00 0.00 3.21
1789 1863 5.571784 ACTCAAATGATAAGTGCCACATG 57.428 39.130 0.00 0.00 0.00 3.21
1790 1864 7.886629 ATTACTCAAATGATAAGTGCCACAT 57.113 32.000 0.00 0.00 0.00 3.21
1791 1865 8.978874 ATATTACTCAAATGATAAGTGCCACA 57.021 30.769 0.00 0.00 0.00 4.17
1792 1866 9.884465 GAATATTACTCAAATGATAAGTGCCAC 57.116 33.333 0.00 0.00 0.00 5.01
1793 1867 9.851686 AGAATATTACTCAAATGATAAGTGCCA 57.148 29.630 0.00 0.00 0.00 4.92
1800 1874 9.935241 GCTCCTGAGAATATTACTCAAATGATA 57.065 33.333 14.48 0.00 42.58 2.15
1801 1875 7.601886 CGCTCCTGAGAATATTACTCAAATGAT 59.398 37.037 14.48 0.00 42.58 2.45
1802 1876 6.925718 CGCTCCTGAGAATATTACTCAAATGA 59.074 38.462 14.48 11.40 42.58 2.57
1803 1877 6.925718 TCGCTCCTGAGAATATTACTCAAATG 59.074 38.462 14.48 10.06 42.58 2.32
1804 1878 6.926272 GTCGCTCCTGAGAATATTACTCAAAT 59.074 38.462 14.48 0.00 42.58 2.32
1805 1879 6.127451 TGTCGCTCCTGAGAATATTACTCAAA 60.127 38.462 14.48 8.20 42.58 2.69
1806 1880 5.359860 TGTCGCTCCTGAGAATATTACTCAA 59.640 40.000 14.48 5.00 42.58 3.02
1807 1881 4.887655 TGTCGCTCCTGAGAATATTACTCA 59.112 41.667 13.49 13.49 41.26 3.41
1808 1882 5.216648 GTGTCGCTCCTGAGAATATTACTC 58.783 45.833 0.00 7.55 35.26 2.59
1809 1883 4.038162 GGTGTCGCTCCTGAGAATATTACT 59.962 45.833 0.00 0.00 0.00 2.24
1810 1884 4.299978 GGTGTCGCTCCTGAGAATATTAC 58.700 47.826 0.00 0.00 0.00 1.89
1826 1900 1.958715 TGGCAACATGACGGTGTCG 60.959 57.895 0.00 0.00 46.17 4.35
1942 2018 2.054799 AGCACCAACCTAACTTCTGGA 58.945 47.619 0.00 0.00 32.97 3.86
1943 2019 2.554032 CAAGCACCAACCTAACTTCTGG 59.446 50.000 0.00 0.00 34.95 3.86
1944 2020 2.030805 GCAAGCACCAACCTAACTTCTG 60.031 50.000 0.00 0.00 0.00 3.02
1945 2021 2.230660 GCAAGCACCAACCTAACTTCT 58.769 47.619 0.00 0.00 0.00 2.85
1946 2022 1.953686 TGCAAGCACCAACCTAACTTC 59.046 47.619 0.00 0.00 0.00 3.01
1947 2023 1.956477 CTGCAAGCACCAACCTAACTT 59.044 47.619 0.00 0.00 0.00 2.66
2019 2101 4.611310 TTCCGACGAGATGTGTAAGTAG 57.389 45.455 0.00 0.00 0.00 2.57
2077 5430 3.117246 TCCCTCGAGGAACACATACCTAT 60.117 47.826 33.39 0.00 43.78 2.57
2096 5449 1.891150 TCCAGTGACGAGTACTTTCCC 59.109 52.381 0.00 0.00 0.00 3.97
2135 5488 5.044558 GGATCACACGTTTTTGCCTAAAAA 58.955 37.500 0.00 0.00 41.96 1.94
2136 5489 4.612943 GGATCACACGTTTTTGCCTAAAA 58.387 39.130 0.00 0.00 34.13 1.52
2137 5490 3.304123 CGGATCACACGTTTTTGCCTAAA 60.304 43.478 0.00 0.00 0.00 1.85
2138 5491 2.224549 CGGATCACACGTTTTTGCCTAA 59.775 45.455 0.00 0.00 0.00 2.69
2139 5492 1.801771 CGGATCACACGTTTTTGCCTA 59.198 47.619 0.00 0.00 0.00 3.93
2140 5493 0.591170 CGGATCACACGTTTTTGCCT 59.409 50.000 0.00 0.00 0.00 4.75
2141 5494 0.386731 CCGGATCACACGTTTTTGCC 60.387 55.000 0.00 0.00 0.00 4.52
2142 5495 0.386731 CCCGGATCACACGTTTTTGC 60.387 55.000 0.73 0.00 0.00 3.68
2143 5496 0.386731 GCCCGGATCACACGTTTTTG 60.387 55.000 0.73 0.00 0.00 2.44
2144 5497 1.520600 GGCCCGGATCACACGTTTTT 61.521 55.000 0.73 0.00 0.00 1.94
2172 5525 3.057315 CAGGAGCTACCACCAAATTGTTG 60.057 47.826 0.00 0.00 42.04 3.33
2173 5526 3.157087 CAGGAGCTACCACCAAATTGTT 58.843 45.455 0.00 0.00 42.04 2.83
2174 5527 2.108250 ACAGGAGCTACCACCAAATTGT 59.892 45.455 0.00 0.00 42.04 2.71
2175 5528 2.795329 ACAGGAGCTACCACCAAATTG 58.205 47.619 0.00 0.00 42.04 2.32
2176 5529 4.475016 AGATACAGGAGCTACCACCAAATT 59.525 41.667 0.00 0.00 42.04 1.82
2177 5530 4.040755 AGATACAGGAGCTACCACCAAAT 58.959 43.478 0.00 0.00 42.04 2.32
2178 5531 3.197766 CAGATACAGGAGCTACCACCAAA 59.802 47.826 0.00 0.00 42.04 3.28
2179 5532 2.766263 CAGATACAGGAGCTACCACCAA 59.234 50.000 0.00 0.00 42.04 3.67
2180 5533 2.388735 CAGATACAGGAGCTACCACCA 58.611 52.381 0.00 0.00 42.04 4.17
2181 5534 1.689273 CCAGATACAGGAGCTACCACC 59.311 57.143 0.00 0.00 42.04 4.61
2182 5535 1.689273 CCCAGATACAGGAGCTACCAC 59.311 57.143 0.00 0.00 42.04 4.16
2183 5536 2.034799 GCCCAGATACAGGAGCTACCA 61.035 57.143 0.00 0.00 42.04 3.25
2184 5537 0.682292 GCCCAGATACAGGAGCTACC 59.318 60.000 0.00 0.00 39.35 3.18
2185 5538 0.682292 GGCCCAGATACAGGAGCTAC 59.318 60.000 0.00 0.00 0.00 3.58
2186 5539 0.563173 AGGCCCAGATACAGGAGCTA 59.437 55.000 0.00 0.00 0.00 3.32
2187 5540 0.762461 GAGGCCCAGATACAGGAGCT 60.762 60.000 0.00 0.00 0.00 4.09
2188 5541 1.751563 GAGGCCCAGATACAGGAGC 59.248 63.158 0.00 0.00 0.00 4.70
2189 5542 0.105246 AGGAGGCCCAGATACAGGAG 60.105 60.000 0.00 0.00 33.88 3.69
2190 5543 0.399091 CAGGAGGCCCAGATACAGGA 60.399 60.000 0.00 0.00 33.88 3.86
2191 5544 2.049627 GCAGGAGGCCCAGATACAGG 62.050 65.000 0.00 0.00 36.11 4.00
2192 5545 1.449353 GCAGGAGGCCCAGATACAG 59.551 63.158 0.00 0.00 36.11 2.74
2224 5577 3.868200 AAAGGGGCGCTCCACCTTG 62.868 63.158 31.81 0.00 40.14 3.61
2252 5605 1.790755 TCGAACAATAACAGCAGCGT 58.209 45.000 0.00 0.00 0.00 5.07


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

AutoCloner maintained by Alex Coulton.