Multiple sequence alignment - TraesCS6D01G104200

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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 TraesCS6D01G104200 chr6D 100.000 4112 0 0 1 4112 67694049 67698160 0.000000e+00 7594
1 TraesCS6D01G104200 chr6D 94.451 1784 79 13 1778 3557 292046618 292048385 0.000000e+00 2728
2 TraesCS6D01G104200 chr6D 93.031 1148 66 12 2416 3557 318120021 318118882 0.000000e+00 1664
3 TraesCS6D01G104200 chr6D 94.784 556 27 2 3558 4112 292048418 292048972 0.000000e+00 865
4 TraesCS6D01G104200 chr6D 93.896 557 31 3 3558 4112 318118849 318118294 0.000000e+00 837
5 TraesCS6D01G104200 chr6D 95.092 163 8 0 1618 1780 67785411 67785573 1.470000e-64 257
6 TraesCS6D01G104200 chr6D 91.411 163 14 0 1618 1780 422229860 422229698 1.490000e-54 224
7 TraesCS6D01G104200 chr6D 89.941 169 13 4 1778 1945 411458311 411458146 8.950000e-52 215
8 TraesCS6D01G104200 chr7A 93.656 1734 93 15 1829 3557 18869723 18868002 0.000000e+00 2577
9 TraesCS6D01G104200 chr7A 93.073 1588 82 11 1 1582 18871277 18869712 0.000000e+00 2298
10 TraesCS6D01G104200 chr7A 92.308 143 10 1 1803 1944 667398337 667398195 6.970000e-48 202
11 TraesCS6D01G104200 chr3A 92.408 1765 115 16 1803 3557 80292241 80293996 0.000000e+00 2499
12 TraesCS6D01G104200 chr3A 91.857 1793 123 17 1778 3557 623903391 623901609 0.000000e+00 2481
13 TraesCS6D01G104200 chr3A 92.588 1592 93 21 1 1582 623904929 623903353 0.000000e+00 2263
14 TraesCS6D01G104200 chr3A 91.205 1569 110 18 1 1560 80290695 80292244 0.000000e+00 2108
15 TraesCS6D01G104200 chr3A 93.939 132 6 1 1 130 745770120 745769989 9.020000e-47 198
16 TraesCS6D01G104200 chr4A 92.401 1566 101 15 1 1560 510885461 510883908 0.000000e+00 2217
17 TraesCS6D01G104200 chr4D 93.099 1507 86 14 59 1560 86596895 86598388 0.000000e+00 2191
18 TraesCS6D01G104200 chr4D 94.255 557 28 4 3559 4112 285385282 285385837 0.000000e+00 848
19 TraesCS6D01G104200 chr2D 91.677 1586 109 20 1 1582 407951661 407950095 0.000000e+00 2176
20 TraesCS6D01G104200 chr2D 93.398 1136 59 13 2426 3557 525286709 525285586 0.000000e+00 1668
21 TraesCS6D01G104200 chr2D 94.075 557 30 3 3558 4112 525285553 525284998 0.000000e+00 843
22 TraesCS6D01G104200 chr2D 90.423 355 14 7 2096 2434 13210400 13210750 2.250000e-122 449
23 TraesCS6D01G104200 chr2D 90.798 163 15 0 1618 1780 343541772 343541610 6.920000e-53 219
24 TraesCS6D01G104200 chr1D 91.556 1587 104 22 1 1582 165561042 165562603 0.000000e+00 2161
25 TraesCS6D01G104200 chr1D 90.554 1588 124 22 2 1582 96072903 96074471 0.000000e+00 2078
26 TraesCS6D01G104200 chr1D 91.411 163 14 0 1618 1780 96103064 96103226 1.490000e-54 224
27 TraesCS6D01G104200 chr1D 92.308 143 11 0 1803 1945 77358462 77358320 1.940000e-48 204
28 TraesCS6D01G104200 chr3D 90.750 1373 96 20 194 1560 55530731 55529384 0.000000e+00 1803
29 TraesCS6D01G104200 chr3D 93.969 1111 58 8 2451 3557 341451564 341450459 0.000000e+00 1672
30 TraesCS6D01G104200 chr3D 92.469 1142 71 12 2424 3557 610717965 610716831 0.000000e+00 1618
31 TraesCS6D01G104200 chr3D 94.065 556 28 3 3558 4112 341450426 341449875 0.000000e+00 839
32 TraesCS6D01G104200 chr3D 93.896 557 31 3 3558 4112 610716798 610716243 0.000000e+00 837
33 TraesCS6D01G104200 chr3D 94.479 163 9 0 1618 1780 537586319 537586481 6.820000e-63 252
34 TraesCS6D01G104200 chr3D 90.798 163 15 0 1618 1780 610706024 610705862 6.920000e-53 219
35 TraesCS6D01G104200 chr3D 89.844 128 11 2 1992 2118 168503305 168503431 3.290000e-36 163
36 TraesCS6D01G104200 chr5D 93.543 1115 62 7 2451 3557 400771783 400772895 0.000000e+00 1652
37 TraesCS6D01G104200 chr5D 93.447 1114 63 9 2451 3557 333245251 333244141 0.000000e+00 1644
38 TraesCS6D01G104200 chr5D 93.728 558 32 3 3558 4112 545965117 545965674 0.000000e+00 833
39 TraesCS6D01G104200 chr5D 91.287 505 27 7 1943 2434 395251227 395251727 0.000000e+00 673
40 TraesCS6D01G104200 chr7D 94.065 556 30 3 3558 4111 59555976 59555422 0.000000e+00 841
41 TraesCS6D01G104200 chr7D 93.357 557 34 3 3558 4112 59475084 59474529 0.000000e+00 821
42 TraesCS6D01G104200 chr7D 92.638 163 12 0 1618 1780 475989722 475989884 6.870000e-58 235
43 TraesCS6D01G104200 chr7D 89.286 168 15 3 1778 1944 475967697 475967862 1.500000e-49 207
44 TraesCS6D01G104200 chr7D 88.095 168 16 4 1778 1944 475917809 475917973 3.240000e-46 196
45 TraesCS6D01G104200 chr5B 90.891 505 29 7 1943 2434 428106956 428106456 0.000000e+00 662
46 TraesCS6D01G104200 chr5B 90.177 509 30 10 1943 2436 475581589 475582092 0.000000e+00 645
47 TraesCS6D01G104200 chr2A 88.431 510 37 9 1943 2434 655938375 655938880 2.740000e-166 595
48 TraesCS6D01G104200 chr2A 90.854 164 15 0 1617 1780 378392940 378393103 1.920000e-53 220
49 TraesCS6D01G104200 chr5A 86.383 470 52 6 1115 1582 340307980 340308439 1.710000e-138 503
50 TraesCS6D01G104200 chr2B 90.054 372 32 3 1 369 652840479 652840110 1.030000e-130 477
51 TraesCS6D01G104200 chr7B 91.975 162 12 1 1619 1780 731851283 731851443 4.140000e-55 226


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 TraesCS6D01G104200 chr6D 67694049 67698160 4111 False 7594.0 7594 100.0000 1 4112 1 chr6D.!!$F1 4111
1 TraesCS6D01G104200 chr6D 292046618 292048972 2354 False 1796.5 2728 94.6175 1778 4112 2 chr6D.!!$F3 2334
2 TraesCS6D01G104200 chr6D 318118294 318120021 1727 True 1250.5 1664 93.4635 2416 4112 2 chr6D.!!$R3 1696
3 TraesCS6D01G104200 chr7A 18868002 18871277 3275 True 2437.5 2577 93.3645 1 3557 2 chr7A.!!$R2 3556
4 TraesCS6D01G104200 chr3A 623901609 623904929 3320 True 2372.0 2481 92.2225 1 3557 2 chr3A.!!$R2 3556
5 TraesCS6D01G104200 chr3A 80290695 80293996 3301 False 2303.5 2499 91.8065 1 3557 2 chr3A.!!$F1 3556
6 TraesCS6D01G104200 chr4A 510883908 510885461 1553 True 2217.0 2217 92.4010 1 1560 1 chr4A.!!$R1 1559
7 TraesCS6D01G104200 chr4D 86596895 86598388 1493 False 2191.0 2191 93.0990 59 1560 1 chr4D.!!$F1 1501
8 TraesCS6D01G104200 chr4D 285385282 285385837 555 False 848.0 848 94.2550 3559 4112 1 chr4D.!!$F2 553
9 TraesCS6D01G104200 chr2D 407950095 407951661 1566 True 2176.0 2176 91.6770 1 1582 1 chr2D.!!$R2 1581
10 TraesCS6D01G104200 chr2D 525284998 525286709 1711 True 1255.5 1668 93.7365 2426 4112 2 chr2D.!!$R3 1686
11 TraesCS6D01G104200 chr1D 165561042 165562603 1561 False 2161.0 2161 91.5560 1 1582 1 chr1D.!!$F3 1581
12 TraesCS6D01G104200 chr1D 96072903 96074471 1568 False 2078.0 2078 90.5540 2 1582 1 chr1D.!!$F1 1580
13 TraesCS6D01G104200 chr3D 55529384 55530731 1347 True 1803.0 1803 90.7500 194 1560 1 chr3D.!!$R1 1366
14 TraesCS6D01G104200 chr3D 341449875 341451564 1689 True 1255.5 1672 94.0170 2451 4112 2 chr3D.!!$R3 1661
15 TraesCS6D01G104200 chr3D 610716243 610717965 1722 True 1227.5 1618 93.1825 2424 4112 2 chr3D.!!$R4 1688
16 TraesCS6D01G104200 chr5D 400771783 400772895 1112 False 1652.0 1652 93.5430 2451 3557 1 chr5D.!!$F2 1106
17 TraesCS6D01G104200 chr5D 333244141 333245251 1110 True 1644.0 1644 93.4470 2451 3557 1 chr5D.!!$R1 1106
18 TraesCS6D01G104200 chr5D 545965117 545965674 557 False 833.0 833 93.7280 3558 4112 1 chr5D.!!$F3 554
19 TraesCS6D01G104200 chr5D 395251227 395251727 500 False 673.0 673 91.2870 1943 2434 1 chr5D.!!$F1 491
20 TraesCS6D01G104200 chr7D 59555422 59555976 554 True 841.0 841 94.0650 3558 4111 1 chr7D.!!$R2 553
21 TraesCS6D01G104200 chr7D 59474529 59475084 555 True 821.0 821 93.3570 3558 4112 1 chr7D.!!$R1 554
22 TraesCS6D01G104200 chr5B 428106456 428106956 500 True 662.0 662 90.8910 1943 2434 1 chr5B.!!$R1 491
23 TraesCS6D01G104200 chr5B 475581589 475582092 503 False 645.0 645 90.1770 1943 2436 1 chr5B.!!$F1 493
24 TraesCS6D01G104200 chr2A 655938375 655938880 505 False 595.0 595 88.4310 1943 2434 1 chr2A.!!$F2 491

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
66 67 0.250901 CTTGTGGTGGTTCTCCTGGG 60.251 60.0 0.00 0.0 34.23 4.45 F
1642 1678 0.036765 CAGTTGGCCAGCATGCATTT 60.037 50.0 22.64 0.0 31.97 2.32 F
1769 1805 0.036388 CTCAGTTGGCCACGGTACAT 60.036 55.0 3.88 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1750 1786 0.036388 ATGTACCGTGGCCAACTGAG 60.036 55.000 7.24 0.0 0.00 3.35 R
2958 3035 0.970937 TAGTGAGGTCCGCTGGAAGG 60.971 60.000 0.00 0.0 36.85 3.46 R
3577 3702 1.271054 ACTATCCCATGCATTCGCTCC 60.271 52.381 0.00 0.0 39.64 4.70 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
66 67 0.250901 CTTGTGGTGGTTCTCCTGGG 60.251 60.000 0.00 0.00 34.23 4.45
129 132 3.927854 TGTGCAAATTAGTACCTACGCA 58.072 40.909 0.00 0.00 0.00 5.24
131 134 4.569162 TGTGCAAATTAGTACCTACGCATC 59.431 41.667 0.00 0.00 0.00 3.91
157 160 7.897565 CCCAATTTCCCAATATTCTCTATCCAT 59.102 37.037 0.00 0.00 0.00 3.41
202 208 1.524165 TGGTCCGTGTGTTTTCCCG 60.524 57.895 0.00 0.00 0.00 5.14
323 331 2.414994 TGGTGGTCCACGTGTTTTTA 57.585 45.000 15.93 0.00 39.03 1.52
325 333 3.288964 TGGTGGTCCACGTGTTTTTATT 58.711 40.909 15.93 0.00 39.03 1.40
343 351 2.177394 TTCGGCTGTGTGCAAATAGA 57.823 45.000 4.56 0.00 45.15 1.98
346 354 2.093500 TCGGCTGTGTGCAAATAGAGAT 60.093 45.455 4.56 0.00 45.15 2.75
385 393 9.705290 AAATTAGTACCAATGGTTGACAATTTC 57.295 29.630 11.41 0.00 37.09 2.17
424 432 2.074230 TTTCTGCCAGCCTTTGTGCG 62.074 55.000 0.00 0.00 36.02 5.34
527 536 6.208797 GCCAATTTTCCAATATAGTCTACCCC 59.791 42.308 0.00 0.00 0.00 4.95
529 538 7.782644 CCAATTTTCCAATATAGTCTACCCCAA 59.217 37.037 0.00 0.00 0.00 4.12
530 539 9.367160 CAATTTTCCAATATAGTCTACCCCAAT 57.633 33.333 0.00 0.00 0.00 3.16
531 540 9.588096 AATTTTCCAATATAGTCTACCCCAATC 57.412 33.333 0.00 0.00 0.00 2.67
532 541 7.947782 TTTCCAATATAGTCTACCCCAATCT 57.052 36.000 0.00 0.00 0.00 2.40
533 542 6.935240 TCCAATATAGTCTACCCCAATCTG 57.065 41.667 0.00 0.00 0.00 2.90
611 620 3.428862 GGGACCCTTATTTGTGCAAATCG 60.429 47.826 12.72 6.64 40.99 3.34
643 653 8.767478 ATGCTTGCCAATTTCTAATATATTGC 57.233 30.769 8.28 1.18 0.00 3.56
667 677 6.686126 GCACCCAATTGTTTTGCTGGATATAT 60.686 38.462 13.26 0.00 0.00 0.86
690 700 6.783892 TTTCTTGTTGGCTATGCATTTTTC 57.216 33.333 3.54 0.00 0.00 2.29
778 789 9.005777 CCTAGTTATTACTTGCCACAGTTAAAA 57.994 33.333 0.00 0.00 35.78 1.52
964 977 4.921470 TGTTTGCGCATCTTCTAACTAC 57.079 40.909 12.75 0.00 0.00 2.73
1221 1242 2.046892 CGGAGTGTTCAGCAGGGG 60.047 66.667 0.00 0.00 0.00 4.79
1230 1251 1.201429 TTCAGCAGGGGGAGGAAGTC 61.201 60.000 0.00 0.00 0.00 3.01
1367 1400 9.462174 GATGTTGATCAGTTTCATGTTGTAAAA 57.538 29.630 0.00 0.00 0.00 1.52
1411 1444 2.380064 AGGGGAGCTGAGTCATCTAG 57.620 55.000 0.00 0.00 0.00 2.43
1546 1582 3.339253 TGACATCACTGGTCATCTTGG 57.661 47.619 0.00 0.00 40.16 3.61
1566 1602 9.628500 ATCTTGGTCTAAATATAGTTTTCCCAC 57.372 33.333 0.00 0.00 0.00 4.61
1567 1603 8.607713 TCTTGGTCTAAATATAGTTTTCCCACA 58.392 33.333 0.00 0.00 0.00 4.17
1568 1604 9.238368 CTTGGTCTAAATATAGTTTTCCCACAA 57.762 33.333 0.00 0.00 0.00 3.33
1569 1605 8.801882 TGGTCTAAATATAGTTTTCCCACAAG 57.198 34.615 0.00 0.00 0.00 3.16
1570 1606 8.607713 TGGTCTAAATATAGTTTTCCCACAAGA 58.392 33.333 0.00 0.00 0.00 3.02
1571 1607 9.628500 GGTCTAAATATAGTTTTCCCACAAGAT 57.372 33.333 0.00 0.00 0.00 2.40
1575 1611 8.877864 AAATATAGTTTTCCCACAAGATGACA 57.122 30.769 0.00 0.00 0.00 3.58
1576 1612 9.479549 AAATATAGTTTTCCCACAAGATGACAT 57.520 29.630 0.00 0.00 0.00 3.06
1577 1613 6.764308 ATAGTTTTCCCACAAGATGACATG 57.236 37.500 0.00 0.00 0.00 3.21
1578 1614 4.728772 AGTTTTCCCACAAGATGACATGA 58.271 39.130 0.00 0.00 0.00 3.07
1579 1615 4.763793 AGTTTTCCCACAAGATGACATGAG 59.236 41.667 0.00 0.00 0.00 2.90
1580 1616 4.371624 TTTCCCACAAGATGACATGAGT 57.628 40.909 0.00 0.00 0.00 3.41
1581 1617 4.371624 TTCCCACAAGATGACATGAGTT 57.628 40.909 0.00 0.00 0.00 3.01
1582 1618 3.942829 TCCCACAAGATGACATGAGTTC 58.057 45.455 0.00 0.00 0.00 3.01
1583 1619 3.327464 TCCCACAAGATGACATGAGTTCA 59.673 43.478 0.00 0.00 0.00 3.18
1584 1620 3.688185 CCCACAAGATGACATGAGTTCAG 59.312 47.826 0.00 0.00 0.00 3.02
1585 1621 4.321718 CCACAAGATGACATGAGTTCAGT 58.678 43.478 0.00 0.00 0.00 3.41
1586 1622 4.758674 CCACAAGATGACATGAGTTCAGTT 59.241 41.667 0.00 0.00 0.00 3.16
1587 1623 5.334646 CCACAAGATGACATGAGTTCAGTTG 60.335 44.000 0.00 4.21 0.00 3.16
1588 1624 4.758674 ACAAGATGACATGAGTTCAGTTGG 59.241 41.667 0.00 0.00 0.00 3.77
1589 1625 3.341823 AGATGACATGAGTTCAGTTGGC 58.658 45.455 0.00 0.00 0.00 4.52
1590 1626 2.936919 TGACATGAGTTCAGTTGGCT 57.063 45.000 0.00 0.00 0.00 4.75
1591 1627 4.223700 AGATGACATGAGTTCAGTTGGCTA 59.776 41.667 0.00 0.00 0.00 3.93
1592 1628 3.930336 TGACATGAGTTCAGTTGGCTAG 58.070 45.455 0.00 0.00 0.00 3.42
1593 1629 2.675348 GACATGAGTTCAGTTGGCTAGC 59.325 50.000 6.04 6.04 0.00 3.42
1594 1630 2.038952 ACATGAGTTCAGTTGGCTAGCA 59.961 45.455 18.24 0.00 0.00 3.49
1595 1631 3.276857 CATGAGTTCAGTTGGCTAGCAT 58.723 45.455 18.24 0.00 0.00 3.79
1596 1632 2.703416 TGAGTTCAGTTGGCTAGCATG 58.297 47.619 18.24 9.42 0.00 4.06
1597 1633 1.399791 GAGTTCAGTTGGCTAGCATGC 59.600 52.381 18.24 10.51 0.00 4.06
1598 1634 1.167851 GTTCAGTTGGCTAGCATGCA 58.832 50.000 21.98 2.09 34.04 3.96
1599 1635 1.747355 GTTCAGTTGGCTAGCATGCAT 59.253 47.619 21.98 7.68 34.04 3.96
1600 1636 1.385528 TCAGTTGGCTAGCATGCATG 58.614 50.000 22.70 22.70 34.04 4.06
1612 1648 1.675552 CATGCATGCTCAGATGGACA 58.324 50.000 20.33 0.00 0.00 4.02
1613 1649 1.604278 CATGCATGCTCAGATGGACAG 59.396 52.381 20.33 0.00 0.00 3.51
1614 1650 0.616891 TGCATGCTCAGATGGACAGT 59.383 50.000 20.33 0.00 0.00 3.55
1615 1651 1.297664 GCATGCTCAGATGGACAGTC 58.702 55.000 11.37 0.00 0.00 3.51
1616 1652 1.406477 GCATGCTCAGATGGACAGTCA 60.406 52.381 11.37 0.00 0.00 3.41
1617 1653 2.938314 GCATGCTCAGATGGACAGTCAA 60.938 50.000 11.37 0.00 0.00 3.18
1618 1654 3.542648 CATGCTCAGATGGACAGTCAAT 58.457 45.455 2.17 0.00 0.00 2.57
1619 1655 2.981898 TGCTCAGATGGACAGTCAATG 58.018 47.619 2.17 0.00 0.00 2.82
1621 1657 2.676839 GCTCAGATGGACAGTCAATGTG 59.323 50.000 8.56 8.56 44.17 3.21
1622 1658 3.867600 GCTCAGATGGACAGTCAATGTGT 60.868 47.826 13.55 0.00 44.17 3.72
1623 1659 3.930336 TCAGATGGACAGTCAATGTGTC 58.070 45.455 13.55 0.00 44.17 3.67
1624 1660 3.324556 TCAGATGGACAGTCAATGTGTCA 59.675 43.478 13.55 0.00 45.24 3.58
1625 1661 3.683340 CAGATGGACAGTCAATGTGTCAG 59.317 47.826 6.88 0.00 45.24 3.51
1626 1662 3.326006 AGATGGACAGTCAATGTGTCAGT 59.674 43.478 2.17 0.00 45.24 3.41
1627 1663 3.558931 TGGACAGTCAATGTGTCAGTT 57.441 42.857 2.17 0.00 45.24 3.16
1628 1664 3.205338 TGGACAGTCAATGTGTCAGTTG 58.795 45.455 2.17 0.00 45.24 3.16
1629 1665 2.549754 GGACAGTCAATGTGTCAGTTGG 59.450 50.000 2.17 0.00 45.24 3.77
1630 1666 1.949525 ACAGTCAATGTGTCAGTTGGC 59.050 47.619 0.00 0.00 41.91 4.52
1631 1667 1.267806 CAGTCAATGTGTCAGTTGGCC 59.732 52.381 0.00 0.00 30.47 5.36
1632 1668 1.133823 AGTCAATGTGTCAGTTGGCCA 60.134 47.619 0.00 0.00 30.47 5.36
1633 1669 1.267806 GTCAATGTGTCAGTTGGCCAG 59.732 52.381 5.11 0.00 0.00 4.85
1634 1670 0.038892 CAATGTGTCAGTTGGCCAGC 60.039 55.000 12.39 12.39 0.00 4.85
1635 1671 0.467844 AATGTGTCAGTTGGCCAGCA 60.468 50.000 22.64 7.11 0.00 4.41
1636 1672 0.251474 ATGTGTCAGTTGGCCAGCAT 60.251 50.000 22.64 1.97 0.00 3.79
1637 1673 1.174078 TGTGTCAGTTGGCCAGCATG 61.174 55.000 22.64 16.01 0.00 4.06
1638 1674 2.270257 TGTCAGTTGGCCAGCATGC 61.270 57.895 22.64 10.51 31.97 4.06
1639 1675 2.115695 TCAGTTGGCCAGCATGCA 59.884 55.556 22.64 0.00 31.97 3.96
1640 1676 1.304630 TCAGTTGGCCAGCATGCAT 60.305 52.632 22.64 1.69 31.97 3.96
1641 1677 0.901114 TCAGTTGGCCAGCATGCATT 60.901 50.000 22.64 0.00 31.97 3.56
1642 1678 0.036765 CAGTTGGCCAGCATGCATTT 60.037 50.000 22.64 0.00 31.97 2.32
1643 1679 0.688487 AGTTGGCCAGCATGCATTTT 59.312 45.000 22.64 0.00 31.97 1.82
1644 1680 1.072648 AGTTGGCCAGCATGCATTTTT 59.927 42.857 22.64 0.00 31.97 1.94
1661 1697 2.798976 TTTTCAGTTGGACAGCATGC 57.201 45.000 10.51 10.51 42.53 4.06
1662 1698 1.689984 TTTCAGTTGGACAGCATGCA 58.310 45.000 21.98 0.00 42.53 3.96
1663 1699 1.913778 TTCAGTTGGACAGCATGCAT 58.086 45.000 21.98 7.42 42.53 3.96
1664 1700 1.170442 TCAGTTGGACAGCATGCATG 58.830 50.000 22.70 22.70 42.53 4.06
1665 1701 0.885879 CAGTTGGACAGCATGCATGT 59.114 50.000 26.79 20.01 42.53 3.21
1666 1702 1.271379 CAGTTGGACAGCATGCATGTT 59.729 47.619 26.79 19.46 42.53 2.71
1667 1703 1.542915 AGTTGGACAGCATGCATGTTC 59.457 47.619 26.79 18.92 42.53 3.18
1668 1704 0.889994 TTGGACAGCATGCATGTTCC 59.110 50.000 26.79 26.05 42.53 3.62
1669 1705 1.307355 TGGACAGCATGCATGTTCCG 61.307 55.000 26.79 13.22 42.53 4.30
1670 1706 1.308069 GGACAGCATGCATGTTCCGT 61.308 55.000 26.79 16.30 42.53 4.69
1671 1707 0.523072 GACAGCATGCATGTTCCGTT 59.477 50.000 26.79 5.93 42.53 4.44
1672 1708 0.241749 ACAGCATGCATGTTCCGTTG 59.758 50.000 26.79 16.81 42.53 4.10
1673 1709 0.457166 CAGCATGCATGTTCCGTTGG 60.457 55.000 26.79 5.29 0.00 3.77
1674 1710 0.608856 AGCATGCATGTTCCGTTGGA 60.609 50.000 26.79 0.00 0.00 3.53
1675 1711 0.456653 GCATGCATGTTCCGTTGGAC 60.457 55.000 26.79 3.32 0.00 4.02
1676 1712 0.880441 CATGCATGTTCCGTTGGACA 59.120 50.000 18.91 0.00 0.00 4.02
1677 1713 1.135603 CATGCATGTTCCGTTGGACAG 60.136 52.381 18.91 0.00 0.00 3.51
1678 1714 0.179032 TGCATGTTCCGTTGGACAGT 60.179 50.000 0.00 0.00 0.00 3.55
1679 1715 0.517316 GCATGTTCCGTTGGACAGTC 59.483 55.000 0.00 0.00 0.00 3.51
1680 1716 1.877637 CATGTTCCGTTGGACAGTCA 58.122 50.000 2.17 0.00 0.00 3.41
1681 1717 2.217750 CATGTTCCGTTGGACAGTCAA 58.782 47.619 2.17 0.00 0.00 3.18
1682 1718 2.631160 TGTTCCGTTGGACAGTCAAT 57.369 45.000 2.17 0.00 0.00 2.57
1683 1719 2.217750 TGTTCCGTTGGACAGTCAATG 58.782 47.619 2.17 1.05 34.41 2.82
1685 1721 1.877637 TCCGTTGGACAGTCAATGTG 58.122 50.000 2.17 0.00 44.17 3.21
1686 1722 1.140052 TCCGTTGGACAGTCAATGTGT 59.860 47.619 2.17 0.00 44.17 3.72
1687 1723 1.946768 CCGTTGGACAGTCAATGTGTT 59.053 47.619 2.17 0.00 44.17 3.32
1688 1724 2.032030 CCGTTGGACAGTCAATGTGTTC 60.032 50.000 2.17 0.00 44.17 3.18
1689 1725 2.611751 CGTTGGACAGTCAATGTGTTCA 59.388 45.455 2.17 0.00 44.17 3.18
1690 1726 3.303329 CGTTGGACAGTCAATGTGTTCAG 60.303 47.826 2.17 0.00 44.17 3.02
1691 1727 3.558931 TGGACAGTCAATGTGTTCAGT 57.441 42.857 2.17 0.00 44.17 3.41
1692 1728 3.884895 TGGACAGTCAATGTGTTCAGTT 58.115 40.909 2.17 0.00 44.17 3.16
1693 1729 3.627123 TGGACAGTCAATGTGTTCAGTTG 59.373 43.478 2.17 0.00 44.17 3.16
1694 1730 3.003689 GGACAGTCAATGTGTTCAGTTGG 59.996 47.826 2.17 0.00 44.17 3.77
1695 1731 2.358898 ACAGTCAATGTGTTCAGTTGGC 59.641 45.455 0.00 0.00 41.91 4.52
1696 1732 2.620115 CAGTCAATGTGTTCAGTTGGCT 59.380 45.455 0.00 0.00 38.24 4.75
1697 1733 3.814842 CAGTCAATGTGTTCAGTTGGCTA 59.185 43.478 5.21 0.00 35.78 3.93
1698 1734 4.067896 AGTCAATGTGTTCAGTTGGCTAG 58.932 43.478 4.08 0.00 36.15 3.42
1699 1735 2.813754 TCAATGTGTTCAGTTGGCTAGC 59.186 45.455 6.04 6.04 0.00 3.42
1700 1736 2.553602 CAATGTGTTCAGTTGGCTAGCA 59.446 45.455 18.24 0.00 0.00 3.49
1701 1737 2.566833 TGTGTTCAGTTGGCTAGCAT 57.433 45.000 18.24 0.00 0.00 3.79
1702 1738 3.694043 TGTGTTCAGTTGGCTAGCATA 57.306 42.857 18.24 1.35 0.00 3.14
1703 1739 3.599343 TGTGTTCAGTTGGCTAGCATAG 58.401 45.455 18.24 1.26 43.09 2.23
1704 1740 2.939103 GTGTTCAGTTGGCTAGCATAGG 59.061 50.000 18.24 1.60 39.70 2.57
1705 1741 2.571653 TGTTCAGTTGGCTAGCATAGGT 59.428 45.455 18.24 0.00 39.70 3.08
1706 1742 2.939103 GTTCAGTTGGCTAGCATAGGTG 59.061 50.000 18.24 7.00 39.70 4.00
1707 1743 2.187958 TCAGTTGGCTAGCATAGGTGT 58.812 47.619 18.24 0.00 39.70 4.16
1708 1744 2.571653 TCAGTTGGCTAGCATAGGTGTT 59.428 45.455 18.24 0.00 39.70 3.32
1709 1745 3.009033 TCAGTTGGCTAGCATAGGTGTTT 59.991 43.478 18.24 0.00 39.70 2.83
1710 1746 3.375299 CAGTTGGCTAGCATAGGTGTTTC 59.625 47.826 18.24 0.00 39.70 2.78
1711 1747 3.009033 AGTTGGCTAGCATAGGTGTTTCA 59.991 43.478 18.24 0.00 39.70 2.69
1712 1748 3.266510 TGGCTAGCATAGGTGTTTCAG 57.733 47.619 18.24 0.00 39.70 3.02
1713 1749 2.571653 TGGCTAGCATAGGTGTTTCAGT 59.428 45.455 18.24 0.00 39.70 3.41
1714 1750 3.009033 TGGCTAGCATAGGTGTTTCAGTT 59.991 43.478 18.24 0.00 39.70 3.16
1715 1751 3.375299 GGCTAGCATAGGTGTTTCAGTTG 59.625 47.826 18.24 0.00 39.70 3.16
1716 1752 3.375299 GCTAGCATAGGTGTTTCAGTTGG 59.625 47.826 10.63 0.00 39.70 3.77
1717 1753 2.162681 AGCATAGGTGTTTCAGTTGGC 58.837 47.619 0.00 0.00 0.00 4.52
1718 1754 1.202348 GCATAGGTGTTTCAGTTGGCC 59.798 52.381 0.00 0.00 0.00 5.36
1719 1755 2.513753 CATAGGTGTTTCAGTTGGCCA 58.486 47.619 0.00 0.00 0.00 5.36
1720 1756 2.270352 TAGGTGTTTCAGTTGGCCAG 57.730 50.000 5.11 0.00 0.00 4.85
1721 1757 0.468029 AGGTGTTTCAGTTGGCCAGG 60.468 55.000 5.11 0.00 0.00 4.45
1722 1758 0.467290 GGTGTTTCAGTTGGCCAGGA 60.467 55.000 5.11 2.15 0.00 3.86
1723 1759 1.620822 GTGTTTCAGTTGGCCAGGAT 58.379 50.000 5.11 0.00 0.00 3.24
1724 1760 1.270550 GTGTTTCAGTTGGCCAGGATG 59.729 52.381 5.11 6.56 0.00 3.51
1725 1761 0.244721 GTTTCAGTTGGCCAGGATGC 59.755 55.000 5.11 0.00 31.97 3.91
1726 1762 0.178967 TTTCAGTTGGCCAGGATGCA 60.179 50.000 5.11 0.00 31.97 3.96
1727 1763 0.040058 TTCAGTTGGCCAGGATGCAT 59.960 50.000 5.11 0.00 31.97 3.96
1728 1764 0.918258 TCAGTTGGCCAGGATGCATA 59.082 50.000 5.11 0.00 31.97 3.14
1729 1765 1.496001 TCAGTTGGCCAGGATGCATAT 59.504 47.619 5.11 0.00 31.97 1.78
1730 1766 2.091720 TCAGTTGGCCAGGATGCATATT 60.092 45.455 5.11 0.00 31.97 1.28
1731 1767 2.295349 CAGTTGGCCAGGATGCATATTC 59.705 50.000 5.11 0.00 31.97 1.75
1732 1768 2.091720 AGTTGGCCAGGATGCATATTCA 60.092 45.455 5.11 0.00 31.97 2.57
1733 1769 2.281539 TGGCCAGGATGCATATTCAG 57.718 50.000 0.00 0.00 31.97 3.02
1734 1770 1.496001 TGGCCAGGATGCATATTCAGT 59.504 47.619 0.00 0.00 31.97 3.41
1735 1771 2.091720 TGGCCAGGATGCATATTCAGTT 60.092 45.455 0.00 0.00 31.97 3.16
1736 1772 2.295349 GGCCAGGATGCATATTCAGTTG 59.705 50.000 0.00 0.00 31.97 3.16
1737 1773 2.295349 GCCAGGATGCATATTCAGTTGG 59.705 50.000 0.00 1.41 31.97 3.77
1738 1774 3.824133 CCAGGATGCATATTCAGTTGGA 58.176 45.455 0.00 0.00 31.97 3.53
1739 1775 3.567164 CCAGGATGCATATTCAGTTGGAC 59.433 47.826 0.00 0.00 31.97 4.02
1740 1776 4.201657 CAGGATGCATATTCAGTTGGACA 58.798 43.478 0.00 0.00 0.00 4.02
1741 1777 4.641541 CAGGATGCATATTCAGTTGGACAA 59.358 41.667 0.00 0.00 0.00 3.18
1742 1778 4.641989 AGGATGCATATTCAGTTGGACAAC 59.358 41.667 0.00 7.08 41.45 3.32
1743 1779 4.398988 GGATGCATATTCAGTTGGACAACA 59.601 41.667 16.58 0.00 43.47 3.33
1744 1780 5.068198 GGATGCATATTCAGTTGGACAACAT 59.932 40.000 16.58 5.12 43.47 2.71
1745 1781 5.313520 TGCATATTCAGTTGGACAACATG 57.686 39.130 16.58 11.57 43.47 3.21
1746 1782 4.107622 GCATATTCAGTTGGACAACATGC 58.892 43.478 16.58 16.48 43.47 4.06
1747 1783 4.380761 GCATATTCAGTTGGACAACATGCA 60.381 41.667 22.06 9.49 41.42 3.96
1748 1784 5.680408 GCATATTCAGTTGGACAACATGCAT 60.680 40.000 22.06 13.93 41.42 3.96
1749 1785 3.646611 TTCAGTTGGACAACATGCATG 57.353 42.857 25.09 25.09 43.47 4.06
1750 1786 1.270274 TCAGTTGGACAACATGCATGC 59.730 47.619 26.53 11.82 43.47 4.06
1751 1787 1.271379 CAGTTGGACAACATGCATGCT 59.729 47.619 26.53 12.25 43.47 3.79
1752 1788 1.542915 AGTTGGACAACATGCATGCTC 59.457 47.619 26.53 17.09 43.47 4.26
1753 1789 1.270274 GTTGGACAACATGCATGCTCA 59.730 47.619 26.53 13.97 40.84 4.26
1754 1790 1.170442 TGGACAACATGCATGCTCAG 58.830 50.000 26.53 15.35 0.00 3.35
1755 1791 1.171308 GGACAACATGCATGCTCAGT 58.829 50.000 26.53 18.32 0.00 3.41
1756 1792 1.542915 GGACAACATGCATGCTCAGTT 59.457 47.619 26.53 16.75 0.00 3.16
1757 1793 2.592194 GACAACATGCATGCTCAGTTG 58.408 47.619 30.57 30.57 43.71 3.16
1758 1794 1.271379 ACAACATGCATGCTCAGTTGG 59.729 47.619 32.84 22.82 42.73 3.77
1759 1795 0.245539 AACATGCATGCTCAGTTGGC 59.754 50.000 26.53 0.00 0.00 4.52
1760 1796 1.141019 CATGCATGCTCAGTTGGCC 59.859 57.895 20.33 0.00 0.00 5.36
1761 1797 1.304630 ATGCATGCTCAGTTGGCCA 60.305 52.632 20.33 0.00 0.00 5.36
1762 1798 1.601419 ATGCATGCTCAGTTGGCCAC 61.601 55.000 20.33 0.00 0.00 5.01
1763 1799 2.872557 CATGCTCAGTTGGCCACG 59.127 61.111 3.88 0.00 0.00 4.94
1764 1800 2.360350 ATGCTCAGTTGGCCACGG 60.360 61.111 3.88 1.53 0.00 4.94
1765 1801 3.196207 ATGCTCAGTTGGCCACGGT 62.196 57.895 3.88 0.00 0.00 4.83
1766 1802 1.836999 ATGCTCAGTTGGCCACGGTA 61.837 55.000 3.88 0.00 0.00 4.02
1767 1803 2.033194 GCTCAGTTGGCCACGGTAC 61.033 63.158 3.88 0.00 0.00 3.34
1768 1804 1.369692 CTCAGTTGGCCACGGTACA 59.630 57.895 3.88 0.00 0.00 2.90
1769 1805 0.036388 CTCAGTTGGCCACGGTACAT 60.036 55.000 3.88 0.00 0.00 2.29
1770 1806 0.321210 TCAGTTGGCCACGGTACATG 60.321 55.000 3.88 1.73 0.00 3.21
1771 1807 0.605319 CAGTTGGCCACGGTACATGT 60.605 55.000 3.88 2.69 0.00 3.21
1772 1808 0.109723 AGTTGGCCACGGTACATGTT 59.890 50.000 3.88 0.00 0.00 2.71
1773 1809 0.955905 GTTGGCCACGGTACATGTTT 59.044 50.000 3.88 0.00 0.00 2.83
1774 1810 1.338655 GTTGGCCACGGTACATGTTTT 59.661 47.619 3.88 0.00 0.00 2.43
1775 1811 1.693627 TGGCCACGGTACATGTTTTT 58.306 45.000 0.00 0.00 0.00 1.94
1776 1812 2.860009 TGGCCACGGTACATGTTTTTA 58.140 42.857 0.00 0.00 0.00 1.52
1880 1919 2.106566 ACTGGTCACCATTTTGTGCAA 58.893 42.857 0.00 0.00 36.17 4.08
1918 1957 4.393155 TGCCGCATCTTCCGCAGT 62.393 61.111 0.00 0.00 0.00 4.40
2387 2451 8.976986 ACTGTTGATCTGCTAATTTTTCAATC 57.023 30.769 0.00 0.00 0.00 2.67
2545 2611 6.547880 TGCACATTCCCTAGAACTTTTTGTAA 59.452 34.615 0.00 0.00 33.97 2.41
2710 2783 6.540438 AACTGATCCAAATGATGATTGCTT 57.460 33.333 0.00 0.00 32.41 3.91
2823 2900 1.000396 GGCTGCAGGGGAAGATGTT 60.000 57.895 17.12 0.00 0.00 2.71
2853 2930 0.392998 CACAAGCGGGCAGGATAAGT 60.393 55.000 0.00 0.00 0.00 2.24
2958 3035 5.763698 GGGCCTATTGAACTTATTAGACACC 59.236 44.000 0.84 0.00 0.00 4.16
3177 3255 1.072015 CTGGAGATTCTCATCCCCAGC 59.928 57.143 15.36 0.00 45.61 4.85
3205 3283 2.133281 TGGTGCAAGATGATTCAGGG 57.867 50.000 0.00 0.00 0.00 4.45
3225 3303 2.367567 GGTATGGCTGGAAGAACGGATA 59.632 50.000 0.00 0.00 34.07 2.59
3243 3321 4.023193 CGGATAACACATTCTTTATGGCCC 60.023 45.833 0.00 0.00 38.64 5.80
3305 3383 0.540365 CCCTGAAGCTCAGCCCAAAA 60.540 55.000 0.00 0.00 42.98 2.44
3324 3402 2.295253 ATGCTACGGACTTGTGCTAC 57.705 50.000 0.00 0.00 0.00 3.58
3418 3498 2.519013 GACCAGGAGAAGCAAACCATT 58.481 47.619 0.00 0.00 0.00 3.16
3497 3586 8.559536 TCTTCTTCTTTGTGCAGTTATAGTTTG 58.440 33.333 0.00 0.00 0.00 2.93
3520 3609 8.677148 TTGCTGAAATACTCCTCATAATAACC 57.323 34.615 0.00 0.00 0.00 2.85
3544 3637 3.103742 ACTTGGCTTTTCCTTTGTTGGA 58.896 40.909 0.00 0.00 35.26 3.53
3547 3640 3.303938 TGGCTTTTCCTTTGTTGGATCA 58.696 40.909 0.00 0.00 35.83 2.92
3649 3774 1.546029 CGATCTCTCCTGGTGTGTTCA 59.454 52.381 0.00 0.00 0.00 3.18
3664 3789 4.207019 GTGTGTTCAGCAAATTACAAGTGC 59.793 41.667 0.00 0.00 38.59 4.40
3675 3800 5.751243 AATTACAAGTGCGTTCTCTTTGT 57.249 34.783 0.00 0.00 0.00 2.83
3857 3987 4.644685 ACACCATCTGTTTTAAGTTGCACT 59.355 37.500 0.00 0.00 0.00 4.40
4007 4138 5.412594 CCAGTATCTTGTTGTAGTTGCACAT 59.587 40.000 0.00 0.00 0.00 3.21
4041 4172 5.562506 TGGTTTCGTTCAACACACAAATA 57.437 34.783 0.00 0.00 0.00 1.40
4068 4200 9.364989 TGTTTTGATAACCTTGTTCTTTTCTTG 57.635 29.630 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 2.034558 CACAACAGGGGAAACACATGAC 59.965 50.000 0.00 0.00 34.58 3.06
129 132 8.118600 GGATAGAGAATATTGGGAAATTGGGAT 58.881 37.037 0.00 0.00 0.00 3.85
131 134 7.240897 TGGATAGAGAATATTGGGAAATTGGG 58.759 38.462 0.00 0.00 0.00 4.12
157 160 1.228644 ATCACAAAGGCTGGCAGCA 60.229 52.632 37.49 18.26 44.75 4.41
259 265 8.465999 CAGATTGGGTACACTATATTGCAAAAA 58.534 33.333 1.71 0.00 0.00 1.94
323 331 2.679837 CTCTATTTGCACACAGCCGAAT 59.320 45.455 0.00 0.00 44.83 3.34
325 333 1.275010 TCTCTATTTGCACACAGCCGA 59.725 47.619 0.00 0.00 44.83 5.54
343 351 7.066284 GGTACTAATTTGCACAAGTGATGATCT 59.934 37.037 4.04 0.00 0.00 2.75
346 354 6.000840 TGGTACTAATTTGCACAAGTGATGA 58.999 36.000 4.04 0.00 0.00 2.92
385 393 8.778358 GCAGAAAAATCAGTAGACTATATTGGG 58.222 37.037 0.00 0.00 0.00 4.12
424 432 1.156736 CACACGAACAACCAGATCCC 58.843 55.000 0.00 0.00 0.00 3.85
527 536 3.316029 TCCACAACAAAGACTGCAGATTG 59.684 43.478 23.35 22.14 0.00 2.67
529 538 3.213206 TCCACAACAAAGACTGCAGAT 57.787 42.857 23.35 5.42 0.00 2.90
530 539 2.708216 TCCACAACAAAGACTGCAGA 57.292 45.000 23.35 0.00 0.00 4.26
531 540 2.620115 ACATCCACAACAAAGACTGCAG 59.380 45.455 13.48 13.48 0.00 4.41
532 541 2.358582 CACATCCACAACAAAGACTGCA 59.641 45.455 0.00 0.00 0.00 4.41
533 542 2.287788 CCACATCCACAACAAAGACTGC 60.288 50.000 0.00 0.00 0.00 4.40
642 652 1.202627 TCCAGCAAAACAATTGGGTGC 60.203 47.619 17.63 17.63 36.78 5.01
643 653 2.906691 TCCAGCAAAACAATTGGGTG 57.093 45.000 10.83 7.45 37.65 4.61
667 677 5.404968 CGAAAAATGCATAGCCAACAAGAAA 59.595 36.000 0.00 0.00 0.00 2.52
690 700 2.184448 CTTGTGCAACTGGAACAAACG 58.816 47.619 0.00 0.00 38.70 3.60
778 789 5.940617 TGGACAGCATATAAGCCAACTAAT 58.059 37.500 0.00 0.00 34.23 1.73
964 977 5.464057 GGGGGAAATACAACAAAAGAAAACG 59.536 40.000 0.00 0.00 0.00 3.60
1221 1242 1.477295 CCACTTACCTCGACTTCCTCC 59.523 57.143 0.00 0.00 0.00 4.30
1230 1251 0.108186 TCAGCATGCCACTTACCTCG 60.108 55.000 15.66 0.00 34.76 4.63
1255 1276 7.281100 CCAAACAAAACCAAAATAAGGTGCTTA 59.719 33.333 0.00 0.00 39.86 3.09
1367 1400 2.201436 CTGCTGCACGTCTAGTCCGT 62.201 60.000 0.00 4.72 39.52 4.69
1566 1602 4.379186 GCCAACTGAACTCATGTCATCTTG 60.379 45.833 0.00 0.00 0.00 3.02
1567 1603 3.755378 GCCAACTGAACTCATGTCATCTT 59.245 43.478 0.00 0.00 0.00 2.40
1568 1604 3.008813 AGCCAACTGAACTCATGTCATCT 59.991 43.478 0.00 0.00 0.00 2.90
1569 1605 3.341823 AGCCAACTGAACTCATGTCATC 58.658 45.455 0.00 0.00 0.00 2.92
1570 1606 3.430042 AGCCAACTGAACTCATGTCAT 57.570 42.857 0.00 0.00 0.00 3.06
1571 1607 2.936919 AGCCAACTGAACTCATGTCA 57.063 45.000 0.00 0.00 0.00 3.58
1572 1608 2.675348 GCTAGCCAACTGAACTCATGTC 59.325 50.000 2.29 0.00 0.00 3.06
1573 1609 2.038952 TGCTAGCCAACTGAACTCATGT 59.961 45.455 13.29 0.00 0.00 3.21
1574 1610 2.703416 TGCTAGCCAACTGAACTCATG 58.297 47.619 13.29 0.00 0.00 3.07
1575 1611 3.276857 CATGCTAGCCAACTGAACTCAT 58.723 45.455 13.29 0.00 0.00 2.90
1576 1612 2.703416 CATGCTAGCCAACTGAACTCA 58.297 47.619 13.29 0.00 0.00 3.41
1577 1613 1.399791 GCATGCTAGCCAACTGAACTC 59.600 52.381 13.29 0.00 0.00 3.01
1578 1614 1.271543 TGCATGCTAGCCAACTGAACT 60.272 47.619 20.33 0.00 0.00 3.01
1579 1615 1.167851 TGCATGCTAGCCAACTGAAC 58.832 50.000 20.33 0.00 0.00 3.18
1580 1616 1.746787 CATGCATGCTAGCCAACTGAA 59.253 47.619 20.33 0.00 0.00 3.02
1581 1617 1.385528 CATGCATGCTAGCCAACTGA 58.614 50.000 20.33 0.00 0.00 3.41
1582 1618 3.938653 CATGCATGCTAGCCAACTG 57.061 52.632 20.33 5.83 0.00 3.16
1593 1629 1.604278 CTGTCCATCTGAGCATGCATG 59.396 52.381 22.70 22.70 0.00 4.06
1594 1630 1.212195 ACTGTCCATCTGAGCATGCAT 59.788 47.619 21.98 4.75 0.00 3.96
1595 1631 0.616891 ACTGTCCATCTGAGCATGCA 59.383 50.000 21.98 0.00 0.00 3.96
1596 1632 1.297664 GACTGTCCATCTGAGCATGC 58.702 55.000 10.51 10.51 0.00 4.06
1597 1633 2.685850 TGACTGTCCATCTGAGCATG 57.314 50.000 5.17 0.00 0.00 4.06
1598 1634 3.054582 ACATTGACTGTCCATCTGAGCAT 60.055 43.478 5.17 0.00 29.94 3.79
1599 1635 2.303890 ACATTGACTGTCCATCTGAGCA 59.696 45.455 5.17 0.00 29.94 4.26
1600 1636 2.676839 CACATTGACTGTCCATCTGAGC 59.323 50.000 5.17 0.00 35.29 4.26
1601 1637 3.931468 GACACATTGACTGTCCATCTGAG 59.069 47.826 5.17 0.00 35.29 3.35
1602 1638 3.324556 TGACACATTGACTGTCCATCTGA 59.675 43.478 5.17 0.00 37.79 3.27
1603 1639 3.667360 TGACACATTGACTGTCCATCTG 58.333 45.455 5.17 0.61 37.79 2.90
1604 1640 3.326006 ACTGACACATTGACTGTCCATCT 59.674 43.478 5.17 0.00 37.79 2.90
1605 1641 3.668447 ACTGACACATTGACTGTCCATC 58.332 45.455 5.17 0.00 37.79 3.51
1606 1642 3.777106 ACTGACACATTGACTGTCCAT 57.223 42.857 5.17 0.00 37.79 3.41
1607 1643 3.205338 CAACTGACACATTGACTGTCCA 58.795 45.455 5.17 0.00 37.79 4.02
1608 1644 2.549754 CCAACTGACACATTGACTGTCC 59.450 50.000 5.17 0.00 37.79 4.02
1609 1645 2.031682 GCCAACTGACACATTGACTGTC 60.032 50.000 0.00 0.00 38.86 3.51
1610 1646 1.949525 GCCAACTGACACATTGACTGT 59.050 47.619 0.00 0.00 39.20 3.55
1611 1647 1.267806 GGCCAACTGACACATTGACTG 59.732 52.381 0.00 0.00 0.00 3.51
1612 1648 1.133823 TGGCCAACTGACACATTGACT 60.134 47.619 0.61 0.00 0.00 3.41
1613 1649 1.267806 CTGGCCAACTGACACATTGAC 59.732 52.381 7.01 0.00 0.00 3.18
1614 1650 1.608055 CTGGCCAACTGACACATTGA 58.392 50.000 7.01 0.00 0.00 2.57
1615 1651 0.038892 GCTGGCCAACTGACACATTG 60.039 55.000 7.01 0.00 0.00 2.82
1616 1652 0.467844 TGCTGGCCAACTGACACATT 60.468 50.000 7.01 0.00 0.00 2.71
1617 1653 0.251474 ATGCTGGCCAACTGACACAT 60.251 50.000 7.01 0.00 0.00 3.21
1618 1654 1.151221 ATGCTGGCCAACTGACACA 59.849 52.632 7.01 0.00 0.00 3.72
1619 1655 1.582968 CATGCTGGCCAACTGACAC 59.417 57.895 7.01 0.00 0.00 3.67
1620 1656 2.270257 GCATGCTGGCCAACTGACA 61.270 57.895 11.37 0.16 0.00 3.58
1621 1657 1.601419 ATGCATGCTGGCCAACTGAC 61.601 55.000 20.33 0.00 0.00 3.51
1622 1658 0.901114 AATGCATGCTGGCCAACTGA 60.901 50.000 20.33 0.00 0.00 3.41
1623 1659 0.036765 AAATGCATGCTGGCCAACTG 60.037 50.000 20.33 5.65 0.00 3.16
1624 1660 0.688487 AAAATGCATGCTGGCCAACT 59.312 45.000 20.33 0.00 0.00 3.16
1625 1661 1.525941 AAAAATGCATGCTGGCCAAC 58.474 45.000 20.33 1.82 0.00 3.77
1641 1677 2.429971 TGCATGCTGTCCAACTGAAAAA 59.570 40.909 20.33 0.00 0.00 1.94
1642 1678 2.030371 TGCATGCTGTCCAACTGAAAA 58.970 42.857 20.33 0.00 0.00 2.29
1643 1679 1.689984 TGCATGCTGTCCAACTGAAA 58.310 45.000 20.33 0.00 0.00 2.69
1644 1680 1.542472 CATGCATGCTGTCCAACTGAA 59.458 47.619 20.33 0.00 0.00 3.02
1645 1681 1.170442 CATGCATGCTGTCCAACTGA 58.830 50.000 20.33 0.00 0.00 3.41
1646 1682 0.885879 ACATGCATGCTGTCCAACTG 59.114 50.000 26.53 0.00 0.00 3.16
1647 1683 1.542915 GAACATGCATGCTGTCCAACT 59.457 47.619 26.53 0.28 0.00 3.16
1648 1684 1.403249 GGAACATGCATGCTGTCCAAC 60.403 52.381 27.56 12.68 30.86 3.77
1649 1685 0.889994 GGAACATGCATGCTGTCCAA 59.110 50.000 27.56 0.00 30.86 3.53
1650 1686 1.307355 CGGAACATGCATGCTGTCCA 61.307 55.000 29.68 0.00 30.86 4.02
1651 1687 1.308069 ACGGAACATGCATGCTGTCC 61.308 55.000 26.53 25.43 0.00 4.02
1652 1688 0.523072 AACGGAACATGCATGCTGTC 59.477 50.000 26.53 19.48 0.00 3.51
1653 1689 0.241749 CAACGGAACATGCATGCTGT 59.758 50.000 26.53 18.28 0.00 4.40
1654 1690 0.457166 CCAACGGAACATGCATGCTG 60.457 55.000 26.53 17.64 0.00 4.41
1655 1691 0.608856 TCCAACGGAACATGCATGCT 60.609 50.000 26.53 15.25 0.00 3.79
1656 1692 0.456653 GTCCAACGGAACATGCATGC 60.457 55.000 26.53 11.82 31.38 4.06
1657 1693 0.880441 TGTCCAACGGAACATGCATG 59.120 50.000 25.09 25.09 31.38 4.06
1658 1694 1.167851 CTGTCCAACGGAACATGCAT 58.832 50.000 0.00 0.00 31.38 3.96
1659 1695 0.179032 ACTGTCCAACGGAACATGCA 60.179 50.000 0.00 0.00 31.38 3.96
1660 1696 0.517316 GACTGTCCAACGGAACATGC 59.483 55.000 0.00 0.00 31.38 4.06
1661 1697 1.877637 TGACTGTCCAACGGAACATG 58.122 50.000 5.17 0.00 31.38 3.21
1662 1698 2.631160 TTGACTGTCCAACGGAACAT 57.369 45.000 5.17 0.00 31.38 2.71
1663 1699 2.217750 CATTGACTGTCCAACGGAACA 58.782 47.619 5.17 0.00 31.38 3.18
1664 1700 2.032030 CACATTGACTGTCCAACGGAAC 60.032 50.000 5.17 0.00 35.29 3.62
1665 1701 2.217750 CACATTGACTGTCCAACGGAA 58.782 47.619 5.17 0.00 35.29 4.30
1666 1702 1.140052 ACACATTGACTGTCCAACGGA 59.860 47.619 5.17 0.00 35.29 4.69
1667 1703 1.593196 ACACATTGACTGTCCAACGG 58.407 50.000 5.17 0.00 35.29 4.44
1668 1704 2.611751 TGAACACATTGACTGTCCAACG 59.388 45.455 5.17 0.00 35.29 4.10
1669 1705 3.627577 ACTGAACACATTGACTGTCCAAC 59.372 43.478 5.17 0.00 35.29 3.77
1670 1706 3.884895 ACTGAACACATTGACTGTCCAA 58.115 40.909 5.17 0.52 35.29 3.53
1671 1707 3.558931 ACTGAACACATTGACTGTCCA 57.441 42.857 5.17 0.00 35.29 4.02
1672 1708 3.003689 CCAACTGAACACATTGACTGTCC 59.996 47.826 5.17 0.00 35.29 4.02
1673 1709 3.548818 GCCAACTGAACACATTGACTGTC 60.549 47.826 0.00 0.00 35.29 3.51
1674 1710 2.358898 GCCAACTGAACACATTGACTGT 59.641 45.455 0.00 0.00 39.20 3.55
1675 1711 2.620115 AGCCAACTGAACACATTGACTG 59.380 45.455 0.00 0.00 0.00 3.51
1676 1712 2.936202 AGCCAACTGAACACATTGACT 58.064 42.857 0.00 0.00 0.00 3.41
1677 1713 3.365364 GCTAGCCAACTGAACACATTGAC 60.365 47.826 2.29 0.00 0.00 3.18
1678 1714 2.813754 GCTAGCCAACTGAACACATTGA 59.186 45.455 2.29 0.00 0.00 2.57
1679 1715 2.553602 TGCTAGCCAACTGAACACATTG 59.446 45.455 13.29 0.00 0.00 2.82
1680 1716 2.862541 TGCTAGCCAACTGAACACATT 58.137 42.857 13.29 0.00 0.00 2.71
1681 1717 2.566833 TGCTAGCCAACTGAACACAT 57.433 45.000 13.29 0.00 0.00 3.21
1682 1718 2.566833 ATGCTAGCCAACTGAACACA 57.433 45.000 13.29 0.00 0.00 3.72
1683 1719 2.939103 CCTATGCTAGCCAACTGAACAC 59.061 50.000 13.29 0.00 0.00 3.32
1684 1720 2.571653 ACCTATGCTAGCCAACTGAACA 59.428 45.455 13.29 0.00 0.00 3.18
1685 1721 2.939103 CACCTATGCTAGCCAACTGAAC 59.061 50.000 13.29 0.00 0.00 3.18
1686 1722 2.571653 ACACCTATGCTAGCCAACTGAA 59.428 45.455 13.29 0.00 0.00 3.02
1687 1723 2.187958 ACACCTATGCTAGCCAACTGA 58.812 47.619 13.29 0.00 0.00 3.41
1688 1724 2.698855 ACACCTATGCTAGCCAACTG 57.301 50.000 13.29 3.72 0.00 3.16
1689 1725 3.009033 TGAAACACCTATGCTAGCCAACT 59.991 43.478 13.29 0.00 0.00 3.16
1690 1726 3.343617 TGAAACACCTATGCTAGCCAAC 58.656 45.455 13.29 0.00 0.00 3.77
1691 1727 3.009033 ACTGAAACACCTATGCTAGCCAA 59.991 43.478 13.29 0.00 0.00 4.52
1692 1728 2.571653 ACTGAAACACCTATGCTAGCCA 59.428 45.455 13.29 0.24 0.00 4.75
1693 1729 3.268023 ACTGAAACACCTATGCTAGCC 57.732 47.619 13.29 0.00 0.00 3.93
1694 1730 3.375299 CCAACTGAAACACCTATGCTAGC 59.625 47.826 8.10 8.10 0.00 3.42
1695 1731 3.375299 GCCAACTGAAACACCTATGCTAG 59.625 47.826 0.00 0.00 0.00 3.42
1696 1732 3.343617 GCCAACTGAAACACCTATGCTA 58.656 45.455 0.00 0.00 0.00 3.49
1697 1733 2.162681 GCCAACTGAAACACCTATGCT 58.837 47.619 0.00 0.00 0.00 3.79
1698 1734 1.202348 GGCCAACTGAAACACCTATGC 59.798 52.381 0.00 0.00 0.00 3.14
1699 1735 2.489329 CTGGCCAACTGAAACACCTATG 59.511 50.000 7.01 0.00 0.00 2.23
1700 1736 2.555227 CCTGGCCAACTGAAACACCTAT 60.555 50.000 7.01 0.00 0.00 2.57
1701 1737 1.202879 CCTGGCCAACTGAAACACCTA 60.203 52.381 7.01 0.00 0.00 3.08
1702 1738 0.468029 CCTGGCCAACTGAAACACCT 60.468 55.000 7.01 0.00 0.00 4.00
1703 1739 0.467290 TCCTGGCCAACTGAAACACC 60.467 55.000 7.01 0.00 0.00 4.16
1704 1740 1.270550 CATCCTGGCCAACTGAAACAC 59.729 52.381 7.01 0.00 0.00 3.32
1705 1741 1.619654 CATCCTGGCCAACTGAAACA 58.380 50.000 7.01 0.00 0.00 2.83
1706 1742 0.244721 GCATCCTGGCCAACTGAAAC 59.755 55.000 7.01 0.00 0.00 2.78
1707 1743 0.178967 TGCATCCTGGCCAACTGAAA 60.179 50.000 7.01 0.00 0.00 2.69
1708 1744 0.040058 ATGCATCCTGGCCAACTGAA 59.960 50.000 7.01 0.00 0.00 3.02
1709 1745 0.918258 TATGCATCCTGGCCAACTGA 59.082 50.000 7.01 4.06 0.00 3.41
1710 1746 1.991121 ATATGCATCCTGGCCAACTG 58.009 50.000 7.01 5.65 0.00 3.16
1711 1747 2.091720 TGAATATGCATCCTGGCCAACT 60.092 45.455 7.01 0.00 0.00 3.16
1712 1748 2.295349 CTGAATATGCATCCTGGCCAAC 59.705 50.000 7.01 0.00 0.00 3.77
1713 1749 2.091720 ACTGAATATGCATCCTGGCCAA 60.092 45.455 7.01 0.00 0.00 4.52
1714 1750 1.496001 ACTGAATATGCATCCTGGCCA 59.504 47.619 4.71 4.71 0.00 5.36
1715 1751 2.283145 ACTGAATATGCATCCTGGCC 57.717 50.000 0.19 0.00 0.00 5.36
1716 1752 2.295349 CCAACTGAATATGCATCCTGGC 59.705 50.000 0.19 0.00 0.00 4.85
1717 1753 3.567164 GTCCAACTGAATATGCATCCTGG 59.433 47.826 0.19 0.96 0.00 4.45
1718 1754 4.201657 TGTCCAACTGAATATGCATCCTG 58.798 43.478 0.19 0.77 0.00 3.86
1719 1755 4.508551 TGTCCAACTGAATATGCATCCT 57.491 40.909 0.19 0.00 0.00 3.24
1720 1756 4.398988 TGTTGTCCAACTGAATATGCATCC 59.601 41.667 0.19 0.00 41.67 3.51
1721 1757 5.565592 TGTTGTCCAACTGAATATGCATC 57.434 39.130 0.19 0.00 41.67 3.91
1722 1758 5.680408 GCATGTTGTCCAACTGAATATGCAT 60.680 40.000 19.30 3.79 41.42 3.96
1723 1759 4.380761 GCATGTTGTCCAACTGAATATGCA 60.381 41.667 19.30 0.00 41.42 3.96
1724 1760 4.107622 GCATGTTGTCCAACTGAATATGC 58.892 43.478 13.26 13.26 41.67 3.14
1725 1761 5.313520 TGCATGTTGTCCAACTGAATATG 57.686 39.130 11.14 7.22 41.67 1.78
1726 1762 5.680408 GCATGCATGTTGTCCAACTGAATAT 60.680 40.000 26.79 0.00 41.67 1.28
1727 1763 4.380761 GCATGCATGTTGTCCAACTGAATA 60.381 41.667 26.79 0.00 41.67 1.75
1728 1764 3.615592 GCATGCATGTTGTCCAACTGAAT 60.616 43.478 26.79 4.96 41.67 2.57
1729 1765 2.288334 GCATGCATGTTGTCCAACTGAA 60.288 45.455 26.79 3.05 41.67 3.02
1730 1766 1.270274 GCATGCATGTTGTCCAACTGA 59.730 47.619 26.79 0.00 41.67 3.41
1731 1767 1.271379 AGCATGCATGTTGTCCAACTG 59.729 47.619 26.79 0.00 41.67 3.16
1732 1768 1.542915 GAGCATGCATGTTGTCCAACT 59.457 47.619 26.79 13.09 41.67 3.16
1733 1769 1.270274 TGAGCATGCATGTTGTCCAAC 59.730 47.619 26.79 9.35 41.50 3.77
1734 1770 1.542472 CTGAGCATGCATGTTGTCCAA 59.458 47.619 26.79 7.02 0.00 3.53
1735 1771 1.170442 CTGAGCATGCATGTTGTCCA 58.830 50.000 26.79 14.58 0.00 4.02
1736 1772 1.171308 ACTGAGCATGCATGTTGTCC 58.829 50.000 26.79 10.75 0.00 4.02
1737 1773 2.592194 CAACTGAGCATGCATGTTGTC 58.408 47.619 26.79 20.13 34.91 3.18
1738 1774 1.271379 CCAACTGAGCATGCATGTTGT 59.729 47.619 30.05 13.86 37.04 3.32
1739 1775 1.990799 CCAACTGAGCATGCATGTTG 58.009 50.000 27.96 27.96 38.08 3.33
1740 1776 0.245539 GCCAACTGAGCATGCATGTT 59.754 50.000 26.79 22.13 0.00 2.71
1741 1777 1.601419 GGCCAACTGAGCATGCATGT 61.601 55.000 26.79 14.24 0.00 3.21
1742 1778 1.141019 GGCCAACTGAGCATGCATG 59.859 57.895 22.70 22.70 0.00 4.06
1743 1779 1.304630 TGGCCAACTGAGCATGCAT 60.305 52.632 21.98 4.75 0.00 3.96
1744 1780 2.115695 TGGCCAACTGAGCATGCA 59.884 55.556 21.98 0.00 0.00 3.96
1745 1781 2.570181 GTGGCCAACTGAGCATGC 59.430 61.111 7.24 10.51 0.00 4.06
1746 1782 2.693762 CCGTGGCCAACTGAGCATG 61.694 63.158 7.24 0.00 0.00 4.06
1747 1783 1.836999 TACCGTGGCCAACTGAGCAT 61.837 55.000 7.24 0.00 0.00 3.79
1748 1784 2.512355 TACCGTGGCCAACTGAGCA 61.512 57.895 7.24 0.00 0.00 4.26
1749 1785 2.033194 GTACCGTGGCCAACTGAGC 61.033 63.158 7.24 0.00 0.00 4.26
1750 1786 0.036388 ATGTACCGTGGCCAACTGAG 60.036 55.000 7.24 0.00 0.00 3.35
1751 1787 0.321210 CATGTACCGTGGCCAACTGA 60.321 55.000 7.24 0.00 0.00 3.41
1752 1788 0.605319 ACATGTACCGTGGCCAACTG 60.605 55.000 7.24 0.39 0.00 3.16
1753 1789 0.109723 AACATGTACCGTGGCCAACT 59.890 50.000 7.24 0.00 0.00 3.16
1754 1790 0.955905 AAACATGTACCGTGGCCAAC 59.044 50.000 7.24 1.63 0.00 3.77
1755 1791 1.693627 AAAACATGTACCGTGGCCAA 58.306 45.000 7.24 0.00 0.00 4.52
1756 1792 1.693627 AAAAACATGTACCGTGGCCA 58.306 45.000 0.00 0.00 0.00 5.36
1757 1793 4.082679 TCAATAAAAACATGTACCGTGGCC 60.083 41.667 0.00 0.00 0.00 5.36
1758 1794 5.049398 TCAATAAAAACATGTACCGTGGC 57.951 39.130 0.00 0.00 0.00 5.01
1759 1795 7.083875 AGATCAATAAAAACATGTACCGTGG 57.916 36.000 0.00 0.00 0.00 4.94
1798 1834 3.814625 TGCCAACTCATGTCAACTTGTA 58.185 40.909 0.00 0.00 0.00 2.41
2082 2124 7.886629 AAACACTAGCAATATTGACATGGAT 57.113 32.000 19.73 2.85 0.00 3.41
2187 2236 5.885230 TTGACAAGGATCATGTGCTTTAG 57.115 39.130 7.99 0.00 36.20 1.85
2295 2359 6.727824 ATTCTGTGTACTCATGCTTGTAAC 57.272 37.500 0.00 0.00 0.00 2.50
2387 2451 7.856145 AGTACTCCATTTGATAAAGCAGAAG 57.144 36.000 0.00 0.00 0.00 2.85
2482 2547 7.909641 TGATATTGCAACAAGATAACATCAACG 59.090 33.333 0.00 0.00 0.00 4.10
2527 2593 7.447238 CCTGACAATTACAAAAAGTTCTAGGGA 59.553 37.037 0.00 0.00 0.00 4.20
2579 2649 2.605257 AGACTACCAGTGTGCAACCTA 58.395 47.619 0.00 0.00 34.36 3.08
2637 2707 6.545567 TGGATCATGCCAACTAATATGATGT 58.454 36.000 0.00 0.00 39.60 3.06
2687 2759 6.070995 ACAAGCAATCATCATTTGGATCAGTT 60.071 34.615 0.00 0.00 32.57 3.16
2767 2844 1.200948 GCTGGCCTGTTGATGAGAAAC 59.799 52.381 11.69 0.00 0.00 2.78
2823 2900 1.737735 CGCTTGTGATGGTCGCTCA 60.738 57.895 0.00 0.00 0.00 4.26
2958 3035 0.970937 TAGTGAGGTCCGCTGGAAGG 60.971 60.000 0.00 0.00 36.85 3.46
3035 3112 2.309755 TCAGCATCAACAGGGATCCTTT 59.690 45.455 12.58 0.00 0.00 3.11
3044 3121 2.874086 TGAACACTGTCAGCATCAACAG 59.126 45.455 0.00 1.17 46.61 3.16
3048 3125 2.486918 CTGTGAACACTGTCAGCATCA 58.513 47.619 0.00 0.00 0.00 3.07
3177 3255 3.865446 TCATCTTGCACCATGTAGTGAG 58.135 45.455 6.31 0.00 40.34 3.51
3205 3283 2.622064 ATCCGTTCTTCCAGCCATAC 57.378 50.000 0.00 0.00 0.00 2.39
3225 3303 2.099405 CCGGGCCATAAAGAATGTGTT 58.901 47.619 4.39 0.00 33.34 3.32
3273 3351 4.263572 CAGGGCCGTGGTTGGTGA 62.264 66.667 17.92 0.00 0.00 4.02
3305 3383 1.548719 TGTAGCACAAGTCCGTAGCAT 59.451 47.619 0.00 0.00 0.00 3.79
3324 3402 5.705902 TGTGTTCTTGAGCATTTCATGATG 58.294 37.500 0.00 0.00 39.07 3.07
3418 3498 2.189594 AGTGATACAAGCAGCAGCAA 57.810 45.000 3.17 0.00 45.49 3.91
3497 3586 7.152645 TCGGTTATTATGAGGAGTATTTCAGC 58.847 38.462 0.00 0.00 0.00 4.26
3520 3609 3.436700 ACAAAGGAAAAGCCAAGTTCG 57.563 42.857 0.00 0.00 40.02 3.95
3544 3637 2.502947 TGCTTACTGATCTGCACCTGAT 59.497 45.455 0.00 0.00 0.00 2.90
3547 3640 2.304180 AGTTGCTTACTGATCTGCACCT 59.696 45.455 0.00 0.00 35.19 4.00
3577 3702 1.271054 ACTATCCCATGCATTCGCTCC 60.271 52.381 0.00 0.00 39.64 4.70
3649 3774 3.815401 AGAGAACGCACTTGTAATTTGCT 59.185 39.130 0.00 0.00 33.90 3.91
3776 3905 5.821204 ACTTAAAGCTACAAGTTGTGCAAG 58.179 37.500 18.90 17.95 30.89 4.01
4007 4138 8.188799 TGTTGAACGAAACCAAACATTATAACA 58.811 29.630 0.00 0.00 0.00 2.41
4086 4220 6.039493 CCGTGCCTCTATACTTCTCTTTAAGA 59.961 42.308 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.