Multiple sequence alignment - TraesCS3B01G456200

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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 TraesCS3B01G456200 chr3B 100.000 2412 0 0 1 2412 697682251 697684662 0.000000e+00 4455.0
1 TraesCS3B01G456200 chr3B 88.114 1161 65 40 400 1517 808019099 808020229 0.000000e+00 1312.0
2 TraesCS3B01G456200 chr3B 90.878 592 53 1 1822 2412 659511682 659512273 0.000000e+00 793.0
3 TraesCS3B01G456200 chr3B 91.874 443 30 5 3 443 808018670 808019108 4.410000e-172 614.0
4 TraesCS3B01G456200 chr3B 96.032 252 10 0 1521 1772 195352772 195352521 6.210000e-111 411.0
5 TraesCS3B01G456200 chr1B 96.028 579 23 0 1834 2412 635431964 635431386 0.000000e+00 942.0
6 TraesCS3B01G456200 chr1B 96.078 255 9 1 1518 1772 188914037 188914290 4.800000e-112 414.0
7 TraesCS3B01G456200 chr7B 94.426 592 32 1 1822 2412 34129507 34130098 0.000000e+00 909.0
8 TraesCS3B01G456200 chr7B 91.047 592 52 1 1822 2412 654983095 654983686 0.000000e+00 798.0
9 TraesCS3B01G456200 chr7B 87.352 593 72 3 1822 2412 633757432 633756841 0.000000e+00 676.0
10 TraesCS3B01G456200 chr7B 95.984 249 10 0 1518 1766 727918513 727918265 2.890000e-109 405.0
11 TraesCS3B01G456200 chr7B 92.857 42 2 1 116 156 672794448 672794489 2.590000e-05 60.2
12 TraesCS3B01G456200 chr6B 94.877 527 27 0 1886 2412 672638915 672639441 0.000000e+00 824.0
13 TraesCS3B01G456200 chr6B 91.385 592 50 1 1822 2412 102197153 102196562 0.000000e+00 809.0
14 TraesCS3B01G456200 chr6B 95.294 255 12 0 1518 1772 526022745 526022999 2.890000e-109 405.0
15 TraesCS3B01G456200 chr6B 94.902 255 12 1 1518 1772 124390303 124390050 4.830000e-107 398.0
16 TraesCS3B01G456200 chr6B 94.253 261 14 1 1518 1777 144769999 144770259 4.830000e-107 398.0
17 TraesCS3B01G456200 chr3A 96.185 498 17 1 1021 1518 730085774 730086269 0.000000e+00 813.0
18 TraesCS3B01G456200 chr3A 86.436 752 49 24 751 1495 730463072 730463777 0.000000e+00 774.0
19 TraesCS3B01G456200 chr3A 86.303 752 50 25 751 1495 730012416 730011711 0.000000e+00 769.0
20 TraesCS3B01G456200 chr3A 86.303 752 50 24 751 1495 730032260 730031555 0.000000e+00 769.0
21 TraesCS3B01G456200 chr3A 86.303 752 50 24 751 1495 730590853 730591558 0.000000e+00 769.0
22 TraesCS3B01G456200 chr3A 87.706 667 46 17 836 1495 730442715 730443352 0.000000e+00 745.0
23 TraesCS3B01G456200 chr3A 84.808 757 57 26 751 1495 730091792 730092502 0.000000e+00 708.0
24 TraesCS3B01G456200 chr3A 90.800 500 33 8 1 499 730074266 730074753 0.000000e+00 656.0
25 TraesCS3B01G456200 chr3A 95.960 198 6 2 697 894 730085468 730085663 1.080000e-83 320.0
26 TraesCS3B01G456200 chr3A 95.597 159 6 1 542 699 730074738 730074896 1.110000e-63 254.0
27 TraesCS3B01G456200 chr3A 81.871 342 25 15 318 647 730091450 730091766 1.110000e-63 254.0
28 TraesCS3B01G456200 chr3A 95.556 45 1 1 751 795 730442656 730442699 1.200000e-08 71.3
29 TraesCS3B01G456200 chr7A 91.071 560 47 3 1854 2412 10726861 10727418 0.000000e+00 754.0
30 TraesCS3B01G456200 chrUn 87.706 667 46 17 836 1495 358203047 358203684 0.000000e+00 745.0
31 TraesCS3B01G456200 chrUn 95.556 45 1 1 751 795 358202988 358203031 1.200000e-08 71.3
32 TraesCS3B01G456200 chr3D 84.191 816 52 33 742 1515 600654957 600655737 0.000000e+00 721.0
33 TraesCS3B01G456200 chr3D 84.932 657 59 21 874 1517 600665403 600666032 1.570000e-176 628.0
34 TraesCS3B01G456200 chr5A 88.275 597 62 5 1822 2412 34319946 34319352 0.000000e+00 708.0
35 TraesCS3B01G456200 chr5B 96.109 257 10 0 1518 1774 578439931 578440187 1.030000e-113 420.0
36 TraesCS3B01G456200 chr5B 96.016 251 10 0 1518 1768 639761608 639761358 2.230000e-110 409.0
37 TraesCS3B01G456200 chr5B 97.143 35 1 0 119 153 121004659 121004625 2.590000e-05 60.2
38 TraesCS3B01G456200 chr6A 93.609 266 14 1 1518 1780 49765013 49765278 6.250000e-106 394.0
39 TraesCS3B01G456200 chr1D 86.250 80 6 4 80 156 398986962 398986885 5.530000e-12 82.4
40 TraesCS3B01G456200 chr2D 100.000 28 0 0 701 728 311694976 311695003 4.000000e-03 52.8
41 TraesCS3B01G456200 chr2D 96.774 31 1 0 116 146 641275702 641275732 4.000000e-03 52.8


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 TraesCS3B01G456200 chr3B 697682251 697684662 2411 False 4455.00 4455 100.0000 1 2412 1 chr3B.!!$F2 2411
1 TraesCS3B01G456200 chr3B 808018670 808020229 1559 False 963.00 1312 89.9940 3 1517 2 chr3B.!!$F3 1514
2 TraesCS3B01G456200 chr3B 659511682 659512273 591 False 793.00 793 90.8780 1822 2412 1 chr3B.!!$F1 590
3 TraesCS3B01G456200 chr1B 635431386 635431964 578 True 942.00 942 96.0280 1834 2412 1 chr1B.!!$R1 578
4 TraesCS3B01G456200 chr7B 34129507 34130098 591 False 909.00 909 94.4260 1822 2412 1 chr7B.!!$F1 590
5 TraesCS3B01G456200 chr7B 654983095 654983686 591 False 798.00 798 91.0470 1822 2412 1 chr7B.!!$F2 590
6 TraesCS3B01G456200 chr7B 633756841 633757432 591 True 676.00 676 87.3520 1822 2412 1 chr7B.!!$R1 590
7 TraesCS3B01G456200 chr6B 672638915 672639441 526 False 824.00 824 94.8770 1886 2412 1 chr6B.!!$F3 526
8 TraesCS3B01G456200 chr6B 102196562 102197153 591 True 809.00 809 91.3850 1822 2412 1 chr6B.!!$R1 590
9 TraesCS3B01G456200 chr3A 730463072 730463777 705 False 774.00 774 86.4360 751 1495 1 chr3A.!!$F1 744
10 TraesCS3B01G456200 chr3A 730011711 730012416 705 True 769.00 769 86.3030 751 1495 1 chr3A.!!$R1 744
11 TraesCS3B01G456200 chr3A 730031555 730032260 705 True 769.00 769 86.3030 751 1495 1 chr3A.!!$R2 744
12 TraesCS3B01G456200 chr3A 730590853 730591558 705 False 769.00 769 86.3030 751 1495 1 chr3A.!!$F2 744
13 TraesCS3B01G456200 chr3A 730085468 730086269 801 False 566.50 813 96.0725 697 1518 2 chr3A.!!$F4 821
14 TraesCS3B01G456200 chr3A 730091450 730092502 1052 False 481.00 708 83.3395 318 1495 2 chr3A.!!$F5 1177
15 TraesCS3B01G456200 chr3A 730074266 730074896 630 False 455.00 656 93.1985 1 699 2 chr3A.!!$F3 698
16 TraesCS3B01G456200 chr3A 730442656 730443352 696 False 408.15 745 91.6310 751 1495 2 chr3A.!!$F6 744
17 TraesCS3B01G456200 chr7A 10726861 10727418 557 False 754.00 754 91.0710 1854 2412 1 chr7A.!!$F1 558
18 TraesCS3B01G456200 chrUn 358202988 358203684 696 False 408.15 745 91.6310 751 1495 2 chrUn.!!$F1 744
19 TraesCS3B01G456200 chr3D 600654957 600655737 780 False 721.00 721 84.1910 742 1515 1 chr3D.!!$F1 773
20 TraesCS3B01G456200 chr3D 600665403 600666032 629 False 628.00 628 84.9320 874 1517 1 chr3D.!!$F2 643
21 TraesCS3B01G456200 chr5A 34319352 34319946 594 True 708.00 708 88.2750 1822 2412 1 chr5A.!!$R1 590

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
979 1087 0.172803 ACGGACGTACTCCATTGCTC 59.827 55.0 0.0 0.0 39.39 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1990 0.600255 CATGTCGCCCGTTATCCTCC 60.6 60.0 0.0 0.0 0.0 4.3 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
83 85 1.472026 GGTGGATGAATTGCCATGTGC 60.472 52.381 0.00 0.00 36.41 4.57
106 108 7.334421 GTGCTTCAACTAAACTTATCATCCTCA 59.666 37.037 0.00 0.00 0.00 3.86
121 123 6.441093 TCATCCTCACATCACTAAAATTGC 57.559 37.500 0.00 0.00 0.00 3.56
129 132 9.421806 CTCACATCACTAAAATTGCCATAAAAA 57.578 29.630 0.00 0.00 0.00 1.94
130 133 9.202273 TCACATCACTAAAATTGCCATAAAAAC 57.798 29.630 0.00 0.00 0.00 2.43
131 134 8.161610 CACATCACTAAAATTGCCATAAAAACG 58.838 33.333 0.00 0.00 0.00 3.60
134 137 8.288217 TCACTAAAATTGCCATAAAAACGTTC 57.712 30.769 0.00 0.00 0.00 3.95
135 138 7.921214 TCACTAAAATTGCCATAAAAACGTTCA 59.079 29.630 0.00 0.00 0.00 3.18
177 180 0.256464 ACGGGAGTTGTTGGTTTCCA 59.744 50.000 0.00 0.00 43.33 3.53
178 181 1.341187 ACGGGAGTTGTTGGTTTCCAA 60.341 47.619 0.00 0.00 43.33 3.53
225 228 7.043059 TGCTGCTAGTTTTGGAAAATAAAAACG 60.043 33.333 0.00 0.00 46.19 3.60
246 249 1.826385 ATTGCCGCTACTTTCTTGCT 58.174 45.000 0.00 0.00 0.00 3.91
300 303 6.433404 GGAGATGATACTTTAGGTACCGATCA 59.567 42.308 6.18 10.04 32.72 2.92
545 588 4.472833 AGTCTCCATTGCTACTGGAAATCT 59.527 41.667 4.43 1.69 42.12 2.40
610 660 2.477825 CCATTGATCGAGCCACACTAG 58.522 52.381 0.00 0.00 0.00 2.57
837 893 1.603172 CGCCCGTACATGATCTTCTCC 60.603 57.143 0.00 0.00 0.00 3.71
838 894 1.412710 GCCCGTACATGATCTTCTCCA 59.587 52.381 0.00 0.00 0.00 3.86
842 898 3.576118 CCGTACATGATCTTCTCCATCCT 59.424 47.826 0.00 0.00 0.00 3.24
843 899 4.767409 CCGTACATGATCTTCTCCATCCTA 59.233 45.833 0.00 0.00 0.00 2.94
914 995 4.202503 ACACAAACACAGATCCTCATCCTT 60.203 41.667 0.00 0.00 0.00 3.36
979 1087 0.172803 ACGGACGTACTCCATTGCTC 59.827 55.000 0.00 0.00 39.39 4.26
1182 1304 5.113529 GCGTTACATATTACTTGCGCAATTC 59.886 40.000 25.26 1.65 42.63 2.17
1191 1313 2.121786 CTTGCGCAATTCATGGCATAC 58.878 47.619 25.26 0.00 35.87 2.39
1203 1362 4.556233 TCATGGCATACGCATTACTCTAC 58.444 43.478 0.00 0.00 41.24 2.59
1213 1372 6.216801 ACGCATTACTCTACTCATGGTTAA 57.783 37.500 0.00 0.00 0.00 2.01
1384 1549 5.418676 CACAAAAAGAAAGAGGCCAAGAAA 58.581 37.500 5.01 0.00 0.00 2.52
1487 1666 0.896923 TGTACGGCCGGTTACATTCT 59.103 50.000 31.76 7.29 0.00 2.40
1496 1675 5.392165 CGGCCGGTTACATTCTTTCATTTTA 60.392 40.000 20.10 0.00 0.00 1.52
1518 1697 9.787435 TTTTATTGTCTTGTTCCATAGTACTGT 57.213 29.630 5.39 0.00 0.00 3.55
1519 1698 8.771920 TTATTGTCTTGTTCCATAGTACTGTG 57.228 34.615 12.39 12.39 0.00 3.66
1520 1699 5.147330 TGTCTTGTTCCATAGTACTGTGG 57.853 43.478 27.96 27.96 42.43 4.17
1521 1700 4.591498 TGTCTTGTTCCATAGTACTGTGGT 59.409 41.667 30.89 2.73 41.84 4.16
1522 1701 5.071250 TGTCTTGTTCCATAGTACTGTGGTT 59.929 40.000 30.89 0.00 41.84 3.67
1523 1702 5.408604 GTCTTGTTCCATAGTACTGTGGTTG 59.591 44.000 30.89 19.32 41.84 3.77
1524 1703 4.280436 TGTTCCATAGTACTGTGGTTGG 57.720 45.455 30.89 17.45 41.84 3.77
1525 1704 3.008594 TGTTCCATAGTACTGTGGTTGGG 59.991 47.826 30.89 11.67 41.84 4.12
1526 1705 2.910544 TCCATAGTACTGTGGTTGGGT 58.089 47.619 30.89 0.00 41.84 4.51
1527 1706 4.063851 TCCATAGTACTGTGGTTGGGTA 57.936 45.455 30.89 13.54 41.84 3.69
1528 1707 4.627015 TCCATAGTACTGTGGTTGGGTAT 58.373 43.478 30.89 0.37 41.84 2.73
1529 1708 4.407621 TCCATAGTACTGTGGTTGGGTATG 59.592 45.833 30.89 12.03 41.84 2.39
1530 1709 4.163458 CCATAGTACTGTGGTTGGGTATGT 59.837 45.833 26.14 0.00 37.12 2.29
1531 1710 3.695830 AGTACTGTGGTTGGGTATGTG 57.304 47.619 0.00 0.00 0.00 3.21
1532 1711 2.304761 AGTACTGTGGTTGGGTATGTGG 59.695 50.000 0.00 0.00 0.00 4.17
1533 1712 1.145571 ACTGTGGTTGGGTATGTGGT 58.854 50.000 0.00 0.00 0.00 4.16
1534 1713 1.497286 ACTGTGGTTGGGTATGTGGTT 59.503 47.619 0.00 0.00 0.00 3.67
1535 1714 1.885887 CTGTGGTTGGGTATGTGGTTG 59.114 52.381 0.00 0.00 0.00 3.77
1536 1715 1.215673 TGTGGTTGGGTATGTGGTTGT 59.784 47.619 0.00 0.00 0.00 3.32
1537 1716 1.611491 GTGGTTGGGTATGTGGTTGTG 59.389 52.381 0.00 0.00 0.00 3.33
1538 1717 0.601057 GGTTGGGTATGTGGTTGTGC 59.399 55.000 0.00 0.00 0.00 4.57
1539 1718 1.323412 GTTGGGTATGTGGTTGTGCA 58.677 50.000 0.00 0.00 0.00 4.57
1540 1719 1.683917 GTTGGGTATGTGGTTGTGCAA 59.316 47.619 0.00 0.00 0.00 4.08
1541 1720 1.323412 TGGGTATGTGGTTGTGCAAC 58.677 50.000 6.52 6.52 40.45 4.17
1549 1728 4.702020 GTTGTGCAACCCAACGAC 57.298 55.556 3.25 0.00 35.36 4.34
1550 1729 1.065109 GTTGTGCAACCCAACGACC 59.935 57.895 3.25 0.00 35.36 4.79
1551 1730 2.122167 TTGTGCAACCCAACGACCC 61.122 57.895 0.00 0.00 34.36 4.46
1552 1731 3.656045 GTGCAACCCAACGACCCG 61.656 66.667 0.00 0.00 0.00 5.28
1553 1732 3.862991 TGCAACCCAACGACCCGA 61.863 61.111 0.00 0.00 0.00 5.14
1554 1733 3.047877 GCAACCCAACGACCCGAG 61.048 66.667 0.00 0.00 0.00 4.63
1555 1734 2.424302 CAACCCAACGACCCGAGT 59.576 61.111 0.00 0.00 0.00 4.18
1556 1735 1.227734 CAACCCAACGACCCGAGTT 60.228 57.895 0.00 0.00 0.00 3.01
1557 1736 1.070275 AACCCAACGACCCGAGTTC 59.930 57.895 0.00 0.00 0.00 3.01
1558 1737 1.688269 AACCCAACGACCCGAGTTCA 61.688 55.000 0.00 0.00 0.00 3.18
1559 1738 1.070105 CCCAACGACCCGAGTTCAA 59.930 57.895 0.00 0.00 0.00 2.69
1560 1739 0.321298 CCCAACGACCCGAGTTCAAT 60.321 55.000 0.00 0.00 0.00 2.57
1561 1740 1.519408 CCAACGACCCGAGTTCAATT 58.481 50.000 0.00 0.00 0.00 2.32
1562 1741 1.463444 CCAACGACCCGAGTTCAATTC 59.537 52.381 0.00 0.00 0.00 2.17
1563 1742 1.463444 CAACGACCCGAGTTCAATTCC 59.537 52.381 0.00 0.00 0.00 3.01
1564 1743 0.036671 ACGACCCGAGTTCAATTCCC 60.037 55.000 0.00 0.00 0.00 3.97
1565 1744 0.036765 CGACCCGAGTTCAATTCCCA 60.037 55.000 0.00 0.00 0.00 4.37
1566 1745 1.739067 GACCCGAGTTCAATTCCCAG 58.261 55.000 0.00 0.00 0.00 4.45
1567 1746 1.278127 GACCCGAGTTCAATTCCCAGA 59.722 52.381 0.00 0.00 0.00 3.86
1568 1747 1.702957 ACCCGAGTTCAATTCCCAGAA 59.297 47.619 0.00 0.00 0.00 3.02
1569 1748 2.308866 ACCCGAGTTCAATTCCCAGAAT 59.691 45.455 0.00 0.00 0.00 2.40
1570 1749 3.245264 ACCCGAGTTCAATTCCCAGAATT 60.245 43.478 0.00 0.00 0.00 2.17
1571 1750 3.129287 CCCGAGTTCAATTCCCAGAATTG 59.871 47.826 19.37 19.37 38.60 2.32
1572 1751 4.009675 CCGAGTTCAATTCCCAGAATTGA 58.990 43.478 22.54 22.54 42.82 2.57
1573 1752 4.142600 CCGAGTTCAATTCCCAGAATTGAC 60.143 45.833 24.95 20.09 43.81 3.18
1574 1753 4.455533 CGAGTTCAATTCCCAGAATTGACA 59.544 41.667 24.95 16.29 43.81 3.58
1575 1754 5.391310 CGAGTTCAATTCCCAGAATTGACAG 60.391 44.000 24.95 15.52 43.81 3.51
1576 1755 4.768968 AGTTCAATTCCCAGAATTGACAGG 59.231 41.667 24.95 5.46 43.81 4.00
1577 1756 4.387026 TCAATTCCCAGAATTGACAGGT 57.613 40.909 22.54 0.00 40.53 4.00
1578 1757 4.081406 TCAATTCCCAGAATTGACAGGTG 58.919 43.478 22.54 3.44 40.53 4.00
1579 1758 4.081406 CAATTCCCAGAATTGACAGGTGA 58.919 43.478 20.34 0.00 39.36 4.02
1580 1759 4.598036 ATTCCCAGAATTGACAGGTGAT 57.402 40.909 0.00 0.00 0.00 3.06
1581 1760 3.354948 TCCCAGAATTGACAGGTGATG 57.645 47.619 0.00 0.00 0.00 3.07
1583 1762 3.843619 TCCCAGAATTGACAGGTGATGTA 59.156 43.478 0.00 0.00 44.17 2.29
1584 1763 3.941483 CCCAGAATTGACAGGTGATGTAC 59.059 47.826 0.00 0.00 44.17 2.90
1585 1764 4.565444 CCCAGAATTGACAGGTGATGTACA 60.565 45.833 0.00 0.00 44.17 2.90
1586 1765 4.633126 CCAGAATTGACAGGTGATGTACAG 59.367 45.833 0.33 0.00 44.17 2.74
1587 1766 4.633126 CAGAATTGACAGGTGATGTACAGG 59.367 45.833 0.33 0.00 44.17 4.00
1588 1767 3.634397 ATTGACAGGTGATGTACAGGG 57.366 47.619 0.33 0.00 44.17 4.45
1589 1768 2.319025 TGACAGGTGATGTACAGGGA 57.681 50.000 0.33 0.00 44.17 4.20
1590 1769 2.832838 TGACAGGTGATGTACAGGGAT 58.167 47.619 0.33 0.00 44.17 3.85
1591 1770 3.181329 TGACAGGTGATGTACAGGGATT 58.819 45.455 0.33 0.00 44.17 3.01
1592 1771 3.587061 TGACAGGTGATGTACAGGGATTT 59.413 43.478 0.33 0.00 44.17 2.17
1593 1772 4.042809 TGACAGGTGATGTACAGGGATTTT 59.957 41.667 0.33 0.00 44.17 1.82
1594 1773 4.998051 ACAGGTGATGTACAGGGATTTTT 58.002 39.130 0.33 0.00 41.60 1.94
1595 1774 5.010282 ACAGGTGATGTACAGGGATTTTTC 58.990 41.667 0.33 0.00 41.60 2.29
1596 1775 4.399303 CAGGTGATGTACAGGGATTTTTCC 59.601 45.833 0.33 0.00 0.00 3.13
1597 1776 8.947506 ACAGGTGATGTACAGGGATTTTTCCC 62.948 46.154 0.33 2.66 45.12 3.97
1609 1788 5.928976 GGGATTTTTCCCCATTTATTGAGG 58.071 41.667 0.00 0.00 44.18 3.86
1610 1789 5.665360 GGGATTTTTCCCCATTTATTGAGGA 59.335 40.000 0.00 0.00 44.18 3.71
1611 1790 6.408092 GGGATTTTTCCCCATTTATTGAGGAC 60.408 42.308 0.00 0.00 44.18 3.85
1612 1791 6.408092 GGATTTTTCCCCATTTATTGAGGACC 60.408 42.308 0.00 0.00 0.00 4.46
1613 1792 4.683766 TTTCCCCATTTATTGAGGACCA 57.316 40.909 0.00 0.00 0.00 4.02
1614 1793 4.683766 TTCCCCATTTATTGAGGACCAA 57.316 40.909 0.00 0.00 39.41 3.67
1615 1794 4.249638 TCCCCATTTATTGAGGACCAAG 57.750 45.455 0.00 0.00 38.31 3.61
1616 1795 2.695147 CCCCATTTATTGAGGACCAAGC 59.305 50.000 0.00 0.00 38.31 4.01
1617 1796 3.628257 CCCCATTTATTGAGGACCAAGCT 60.628 47.826 0.00 0.00 38.31 3.74
1618 1797 4.026052 CCCATTTATTGAGGACCAAGCTT 58.974 43.478 0.00 0.00 38.31 3.74
1619 1798 4.142093 CCCATTTATTGAGGACCAAGCTTG 60.142 45.833 19.93 19.93 38.31 4.01
1620 1799 4.706476 CCATTTATTGAGGACCAAGCTTGA 59.294 41.667 28.05 6.10 38.31 3.02
1621 1800 5.361857 CCATTTATTGAGGACCAAGCTTGAT 59.638 40.000 28.05 11.58 38.31 2.57
1622 1801 5.902613 TTTATTGAGGACCAAGCTTGATG 57.097 39.130 28.05 14.26 38.31 3.07
1623 1802 2.957402 TTGAGGACCAAGCTTGATGT 57.043 45.000 28.05 17.53 0.00 3.06
1624 1803 2.189594 TGAGGACCAAGCTTGATGTG 57.810 50.000 28.05 13.14 0.00 3.21
1625 1804 1.421268 TGAGGACCAAGCTTGATGTGT 59.579 47.619 28.05 16.41 0.00 3.72
1626 1805 1.808945 GAGGACCAAGCTTGATGTGTG 59.191 52.381 28.05 12.03 0.00 3.82
1627 1806 0.883833 GGACCAAGCTTGATGTGTGG 59.116 55.000 28.05 12.49 35.39 4.17
1628 1807 1.609208 GACCAAGCTTGATGTGTGGT 58.391 50.000 28.05 15.96 45.23 4.16
1629 1808 1.267806 GACCAAGCTTGATGTGTGGTG 59.732 52.381 28.05 9.83 42.63 4.17
1630 1809 1.133823 ACCAAGCTTGATGTGTGGTGA 60.134 47.619 28.05 0.00 41.05 4.02
1631 1810 1.955778 CCAAGCTTGATGTGTGGTGAA 59.044 47.619 28.05 0.00 0.00 3.18
1632 1811 2.361757 CCAAGCTTGATGTGTGGTGAAA 59.638 45.455 28.05 0.00 0.00 2.69
1633 1812 3.374745 CAAGCTTGATGTGTGGTGAAAC 58.625 45.455 22.31 0.00 0.00 2.78
1652 1831 8.273780 GTGAAACCACTCATCAAGAAATATCT 57.726 34.615 0.00 0.00 37.57 1.98
1653 1832 8.734386 GTGAAACCACTCATCAAGAAATATCTT 58.266 33.333 0.00 0.00 46.91 2.40
1691 1870 8.655935 AAAAATTCTGAGGACCATGTTTATCT 57.344 30.769 0.00 0.00 0.00 1.98
1692 1871 8.655935 AAAATTCTGAGGACCATGTTTATCTT 57.344 30.769 0.00 0.00 0.00 2.40
1693 1872 7.636150 AATTCTGAGGACCATGTTTATCTTG 57.364 36.000 0.00 0.00 0.00 3.02
1694 1873 6.373005 TTCTGAGGACCATGTTTATCTTGA 57.627 37.500 0.00 0.00 0.00 3.02
1695 1874 6.566079 TCTGAGGACCATGTTTATCTTGAT 57.434 37.500 0.00 0.00 0.00 2.57
1696 1875 7.675161 TCTGAGGACCATGTTTATCTTGATA 57.325 36.000 0.00 0.00 0.00 2.15
1697 1876 7.500992 TCTGAGGACCATGTTTATCTTGATAC 58.499 38.462 0.00 0.00 0.00 2.24
1698 1877 7.345653 TCTGAGGACCATGTTTATCTTGATACT 59.654 37.037 0.00 0.00 0.00 2.12
1699 1878 7.500992 TGAGGACCATGTTTATCTTGATACTC 58.499 38.462 0.00 0.00 0.00 2.59
1700 1879 7.125659 TGAGGACCATGTTTATCTTGATACTCA 59.874 37.037 0.00 0.00 0.00 3.41
1701 1880 8.038862 AGGACCATGTTTATCTTGATACTCAT 57.961 34.615 0.00 0.00 0.00 2.90
1702 1881 9.159254 AGGACCATGTTTATCTTGATACTCATA 57.841 33.333 0.00 0.00 0.00 2.15
1703 1882 9.209175 GGACCATGTTTATCTTGATACTCATAC 57.791 37.037 0.00 0.00 0.00 2.39
1704 1883 9.988815 GACCATGTTTATCTTGATACTCATACT 57.011 33.333 0.00 0.00 0.00 2.12
1713 1892 8.854614 ATCTTGATACTCATACTAAAATGGCC 57.145 34.615 0.00 0.00 0.00 5.36
1714 1893 6.929049 TCTTGATACTCATACTAAAATGGCCG 59.071 38.462 0.00 0.00 0.00 6.13
1715 1894 6.169557 TGATACTCATACTAAAATGGCCGT 57.830 37.500 0.00 0.00 0.00 5.68
1716 1895 7.292713 TGATACTCATACTAAAATGGCCGTA 57.707 36.000 0.00 0.00 0.00 4.02
1717 1896 7.903145 TGATACTCATACTAAAATGGCCGTAT 58.097 34.615 0.00 0.00 0.00 3.06
1718 1897 7.817478 TGATACTCATACTAAAATGGCCGTATG 59.183 37.037 16.02 16.02 40.13 2.39
1719 1898 4.755123 ACTCATACTAAAATGGCCGTATGC 59.245 41.667 16.90 0.00 39.17 3.14
1720 1899 4.709250 TCATACTAAAATGGCCGTATGCA 58.291 39.130 16.90 0.00 43.89 3.96
1721 1900 5.312895 TCATACTAAAATGGCCGTATGCAT 58.687 37.500 16.90 3.79 43.89 3.96
1722 1901 5.411361 TCATACTAAAATGGCCGTATGCATC 59.589 40.000 16.90 0.00 43.89 3.91
1723 1902 2.884639 ACTAAAATGGCCGTATGCATCC 59.115 45.455 0.19 0.00 43.89 3.51
1724 1903 2.071778 AAAATGGCCGTATGCATCCT 57.928 45.000 0.19 0.00 43.89 3.24
1725 1904 2.071778 AAATGGCCGTATGCATCCTT 57.928 45.000 0.19 0.00 43.89 3.36
1726 1905 2.949177 AATGGCCGTATGCATCCTTA 57.051 45.000 0.19 0.00 43.89 2.69
1727 1906 2.479566 ATGGCCGTATGCATCCTTAG 57.520 50.000 0.19 0.00 43.89 2.18
1728 1907 1.128200 TGGCCGTATGCATCCTTAGT 58.872 50.000 0.19 0.00 43.89 2.24
1729 1908 1.488812 TGGCCGTATGCATCCTTAGTT 59.511 47.619 0.19 0.00 43.89 2.24
1730 1909 1.873591 GGCCGTATGCATCCTTAGTTG 59.126 52.381 0.19 0.00 43.89 3.16
1731 1910 1.873591 GCCGTATGCATCCTTAGTTGG 59.126 52.381 0.19 0.00 40.77 3.77
1732 1911 2.745152 GCCGTATGCATCCTTAGTTGGT 60.745 50.000 0.19 0.00 40.77 3.67
1733 1912 2.872245 CCGTATGCATCCTTAGTTGGTG 59.128 50.000 0.19 0.00 0.00 4.17
1734 1913 2.287915 CGTATGCATCCTTAGTTGGTGC 59.712 50.000 0.19 0.00 35.89 5.01
1735 1914 2.512692 ATGCATCCTTAGTTGGTGCA 57.487 45.000 0.17 0.17 43.02 4.57
1736 1915 1.825090 TGCATCCTTAGTTGGTGCAG 58.175 50.000 0.00 0.00 38.34 4.41
1737 1916 1.350684 TGCATCCTTAGTTGGTGCAGA 59.649 47.619 0.00 0.00 38.34 4.26
1738 1917 2.012673 GCATCCTTAGTTGGTGCAGAG 58.987 52.381 0.00 0.00 35.63 3.35
1739 1918 2.636830 CATCCTTAGTTGGTGCAGAGG 58.363 52.381 0.00 0.00 0.00 3.69
1740 1919 0.324943 TCCTTAGTTGGTGCAGAGGC 59.675 55.000 0.00 0.00 41.68 4.70
1741 1920 0.678048 CCTTAGTTGGTGCAGAGGCC 60.678 60.000 0.00 0.00 40.13 5.19
1742 1921 1.003839 TTAGTTGGTGCAGAGGCCG 60.004 57.895 0.00 0.00 40.13 6.13
1743 1922 2.463589 TTAGTTGGTGCAGAGGCCGG 62.464 60.000 0.00 0.00 40.13 6.13
1747 1926 4.785453 GGTGCAGAGGCCGGGAAG 62.785 72.222 2.18 0.00 40.13 3.46
1748 1927 4.021925 GTGCAGAGGCCGGGAAGT 62.022 66.667 2.18 0.00 40.13 3.01
1749 1928 4.020617 TGCAGAGGCCGGGAAGTG 62.021 66.667 2.18 0.00 40.13 3.16
1750 1929 3.706373 GCAGAGGCCGGGAAGTGA 61.706 66.667 2.18 0.00 0.00 3.41
1751 1930 3.068881 CAGAGGCCGGGAAGTGAA 58.931 61.111 2.18 0.00 0.00 3.18
1752 1931 1.374947 CAGAGGCCGGGAAGTGAAA 59.625 57.895 2.18 0.00 0.00 2.69
1753 1932 0.250727 CAGAGGCCGGGAAGTGAAAA 60.251 55.000 2.18 0.00 0.00 2.29
1754 1933 0.698818 AGAGGCCGGGAAGTGAAAAT 59.301 50.000 2.18 0.00 0.00 1.82
1755 1934 1.095600 GAGGCCGGGAAGTGAAAATC 58.904 55.000 2.18 0.00 0.00 2.17
1756 1935 0.698818 AGGCCGGGAAGTGAAAATCT 59.301 50.000 2.18 0.00 0.00 2.40
1757 1936 1.095600 GGCCGGGAAGTGAAAATCTC 58.904 55.000 2.18 0.00 0.00 2.75
1758 1937 1.613255 GGCCGGGAAGTGAAAATCTCA 60.613 52.381 2.18 0.00 0.00 3.27
1773 1952 8.305046 TGAAAATCTCACCATTTTTATAGGGG 57.695 34.615 0.00 0.00 36.33 4.79
1774 1953 7.344352 TGAAAATCTCACCATTTTTATAGGGGG 59.656 37.037 0.00 0.00 36.33 5.40
1793 1972 4.003788 CCCAACGCCGACTCCTGT 62.004 66.667 0.00 0.00 0.00 4.00
1794 1973 2.738521 CCAACGCCGACTCCTGTG 60.739 66.667 0.00 0.00 0.00 3.66
1795 1974 3.414700 CAACGCCGACTCCTGTGC 61.415 66.667 0.00 0.00 0.00 4.57
1796 1975 3.616721 AACGCCGACTCCTGTGCT 61.617 61.111 0.00 0.00 0.00 4.40
1797 1976 3.575351 AACGCCGACTCCTGTGCTC 62.575 63.158 0.00 0.00 0.00 4.26
1798 1977 3.753434 CGCCGACTCCTGTGCTCT 61.753 66.667 0.00 0.00 0.00 4.09
1799 1978 2.183046 GCCGACTCCTGTGCTCTC 59.817 66.667 0.00 0.00 0.00 3.20
1800 1979 2.487428 CCGACTCCTGTGCTCTCG 59.513 66.667 0.00 0.00 0.00 4.04
1801 1980 2.487428 CGACTCCTGTGCTCTCGG 59.513 66.667 0.00 0.00 0.00 4.63
1802 1981 2.888863 GACTCCTGTGCTCTCGGG 59.111 66.667 0.00 0.00 35.33 5.14
1803 1982 2.681778 ACTCCTGTGCTCTCGGGG 60.682 66.667 0.00 0.00 34.81 5.73
1804 1983 3.465403 CTCCTGTGCTCTCGGGGG 61.465 72.222 0.00 0.00 34.81 5.40
1829 2008 0.759436 AGGAGGATAACGGGCGACAT 60.759 55.000 0.00 0.00 0.00 3.06
2045 2225 3.131933 CGGGATATGATGAGGATGAGGTC 59.868 52.174 0.00 0.00 0.00 3.85
2117 2297 4.735132 CACGCGGGCGAGAGGAAA 62.735 66.667 20.98 0.00 42.83 3.13
2277 2457 3.339141 AGGAAGAAGAAAGCAATCCGAC 58.661 45.455 0.00 0.00 32.22 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 62 3.637694 CACATGGCAATTCATCCACCATA 59.362 43.478 0.00 0.00 39.08 2.74
75 77 3.923017 AGTTTAGTTGAAGCACATGGC 57.077 42.857 0.00 0.00 45.30 4.40
83 85 8.777865 TGTGAGGATGATAAGTTTAGTTGAAG 57.222 34.615 0.00 0.00 0.00 3.02
106 108 7.870445 ACGTTTTTATGGCAATTTTAGTGATGT 59.130 29.630 0.00 0.00 0.00 3.06
121 123 5.914085 TGGCAAATTGAACGTTTTTATGG 57.086 34.783 0.46 0.00 0.00 2.74
129 132 1.959985 TGACCATGGCAAATTGAACGT 59.040 42.857 13.04 0.00 0.00 3.99
130 133 2.721274 TGACCATGGCAAATTGAACG 57.279 45.000 13.04 0.00 0.00 3.95
131 134 5.106594 GGATTTTGACCATGGCAAATTGAAC 60.107 40.000 25.12 14.50 35.41 3.18
134 137 4.325119 TGGATTTTGACCATGGCAAATTG 58.675 39.130 25.12 0.00 35.41 2.32
135 138 4.637387 TGGATTTTGACCATGGCAAATT 57.363 36.364 25.12 22.29 35.41 1.82
225 228 2.162408 AGCAAGAAAGTAGCGGCAATTC 59.838 45.455 1.45 0.97 0.00 2.17
230 233 1.129437 CAAGAGCAAGAAAGTAGCGGC 59.871 52.381 0.00 0.00 0.00 6.53
315 318 9.230932 GAATTACGTACATCTACCTGAAGTAAC 57.769 37.037 0.00 0.00 31.73 2.50
366 369 2.140717 ACCTGTAACTAAGCAACACGC 58.859 47.619 0.00 0.00 42.91 5.34
437 480 1.382522 CTACACGGCTAAGGTACGGA 58.617 55.000 0.00 0.00 0.00 4.69
438 481 0.248784 GCTACACGGCTAAGGTACGG 60.249 60.000 0.00 0.00 0.00 4.02
439 482 0.452987 TGCTACACGGCTAAGGTACG 59.547 55.000 0.00 0.00 0.00 3.67
440 483 1.470458 GGTGCTACACGGCTAAGGTAC 60.470 57.143 0.00 0.00 34.83 3.34
442 485 1.595357 GGTGCTACACGGCTAAGGT 59.405 57.895 0.00 0.00 34.83 3.50
545 588 3.925362 AATGACACGCACGCGGCTA 62.925 57.895 16.70 0.00 44.69 3.93
610 660 6.254589 CCGATCTCAGATATATTTCGCTTTCC 59.745 42.308 0.00 0.00 0.00 3.13
681 732 6.072175 TGTTTTGTGTTTGCTTGAGTACTCTT 60.072 34.615 23.01 0.00 0.00 2.85
682 733 5.414454 TGTTTTGTGTTTGCTTGAGTACTCT 59.586 36.000 23.01 0.00 0.00 3.24
721 774 4.991687 GTGTGCTTTTAGCTACTCTTCTGT 59.008 41.667 0.00 0.00 42.97 3.41
842 898 8.962912 AGGGCATGCATGTCTCTATATATATA 57.037 34.615 29.02 2.49 31.84 0.86
843 899 7.511714 TGAGGGCATGCATGTCTCTATATATAT 59.488 37.037 32.06 11.68 34.10 0.86
850 908 1.499368 TGAGGGCATGCATGTCTCTA 58.501 50.000 32.06 22.99 34.10 2.43
914 995 4.202121 GCGTTGTCTATACAGGAGGAATGA 60.202 45.833 0.00 0.00 36.83 2.57
1182 1304 4.560128 AGTAGAGTAATGCGTATGCCATG 58.440 43.478 4.05 0.00 41.78 3.66
1191 1313 6.273825 AGTTAACCATGAGTAGAGTAATGCG 58.726 40.000 0.88 0.00 0.00 4.73
1203 1362 9.935241 ATTATCAGCACTATAGTTAACCATGAG 57.065 33.333 1.56 0.00 0.00 2.90
1518 1697 1.988293 CACAACCACATACCCAACCA 58.012 50.000 0.00 0.00 0.00 3.67
1519 1698 0.601057 GCACAACCACATACCCAACC 59.399 55.000 0.00 0.00 0.00 3.77
1520 1699 1.323412 TGCACAACCACATACCCAAC 58.677 50.000 0.00 0.00 0.00 3.77
1521 1700 1.683917 GTTGCACAACCACATACCCAA 59.316 47.619 1.97 0.00 35.36 4.12
1522 1701 1.323412 GTTGCACAACCACATACCCA 58.677 50.000 1.97 0.00 35.36 4.51
1532 1711 1.065109 GGTCGTTGGGTTGCACAAC 59.935 57.895 8.27 8.27 43.52 3.32
1533 1712 2.122167 GGGTCGTTGGGTTGCACAA 61.122 57.895 0.00 0.00 0.00 3.33
1534 1713 2.517402 GGGTCGTTGGGTTGCACA 60.517 61.111 0.00 0.00 0.00 4.57
1535 1714 3.656045 CGGGTCGTTGGGTTGCAC 61.656 66.667 0.00 0.00 0.00 4.57
1536 1715 3.818121 CTCGGGTCGTTGGGTTGCA 62.818 63.158 0.00 0.00 0.00 4.08
1537 1716 3.047877 CTCGGGTCGTTGGGTTGC 61.048 66.667 0.00 0.00 0.00 4.17
1538 1717 1.226030 GAACTCGGGTCGTTGGGTTG 61.226 60.000 0.00 0.00 0.00 3.77
1539 1718 1.070275 GAACTCGGGTCGTTGGGTT 59.930 57.895 0.00 0.00 0.00 4.11
1540 1719 1.688269 TTGAACTCGGGTCGTTGGGT 61.688 55.000 0.00 0.00 0.00 4.51
1541 1720 0.321298 ATTGAACTCGGGTCGTTGGG 60.321 55.000 0.00 0.00 0.00 4.12
1542 1721 1.463444 GAATTGAACTCGGGTCGTTGG 59.537 52.381 0.00 0.00 0.00 3.77
1543 1722 1.463444 GGAATTGAACTCGGGTCGTTG 59.537 52.381 0.00 0.00 0.00 4.10
1544 1723 1.609841 GGGAATTGAACTCGGGTCGTT 60.610 52.381 0.00 0.00 0.00 3.85
1545 1724 0.036671 GGGAATTGAACTCGGGTCGT 60.037 55.000 0.00 0.00 0.00 4.34
1546 1725 0.036765 TGGGAATTGAACTCGGGTCG 60.037 55.000 0.00 0.00 0.00 4.79
1547 1726 1.278127 TCTGGGAATTGAACTCGGGTC 59.722 52.381 0.00 0.00 0.00 4.46
1548 1727 1.358152 TCTGGGAATTGAACTCGGGT 58.642 50.000 0.00 0.00 0.00 5.28
1549 1728 2.489938 TTCTGGGAATTGAACTCGGG 57.510 50.000 0.00 0.00 0.00 5.14
1550 1729 4.009675 TCAATTCTGGGAATTGAACTCGG 58.990 43.478 24.34 5.86 41.92 4.63
1551 1730 4.455533 TGTCAATTCTGGGAATTGAACTCG 59.544 41.667 26.66 7.84 45.06 4.18
1552 1731 5.105997 CCTGTCAATTCTGGGAATTGAACTC 60.106 44.000 26.66 18.75 45.06 3.01
1553 1732 4.768968 CCTGTCAATTCTGGGAATTGAACT 59.231 41.667 26.66 0.00 45.06 3.01
1554 1733 4.524328 ACCTGTCAATTCTGGGAATTGAAC 59.476 41.667 26.66 21.66 45.06 3.18
1555 1734 4.523943 CACCTGTCAATTCTGGGAATTGAA 59.476 41.667 26.66 18.77 45.06 2.69
1556 1735 4.081406 CACCTGTCAATTCTGGGAATTGA 58.919 43.478 23.36 23.36 42.44 2.57
1557 1736 4.081406 TCACCTGTCAATTCTGGGAATTG 58.919 43.478 20.45 20.45 38.60 2.32
1558 1737 4.387026 TCACCTGTCAATTCTGGGAATT 57.613 40.909 0.31 0.31 0.00 2.17
1559 1738 4.264083 ACATCACCTGTCAATTCTGGGAAT 60.264 41.667 0.00 0.00 29.94 3.01
1560 1739 3.074390 ACATCACCTGTCAATTCTGGGAA 59.926 43.478 0.00 0.00 29.94 3.97
1561 1740 2.644299 ACATCACCTGTCAATTCTGGGA 59.356 45.455 0.00 0.00 29.94 4.37
1562 1741 3.077484 ACATCACCTGTCAATTCTGGG 57.923 47.619 0.00 0.00 29.94 4.45
1563 1742 4.578871 TGTACATCACCTGTCAATTCTGG 58.421 43.478 0.00 0.00 39.39 3.86
1564 1743 4.633126 CCTGTACATCACCTGTCAATTCTG 59.367 45.833 0.00 0.00 39.39 3.02
1565 1744 4.323792 CCCTGTACATCACCTGTCAATTCT 60.324 45.833 0.00 0.00 39.39 2.40
1566 1745 3.941483 CCCTGTACATCACCTGTCAATTC 59.059 47.826 0.00 0.00 39.39 2.17
1567 1746 3.587061 TCCCTGTACATCACCTGTCAATT 59.413 43.478 0.00 0.00 39.39 2.32
1568 1747 3.181329 TCCCTGTACATCACCTGTCAAT 58.819 45.455 0.00 0.00 39.39 2.57
1569 1748 2.615391 TCCCTGTACATCACCTGTCAA 58.385 47.619 0.00 0.00 39.39 3.18
1570 1749 2.319025 TCCCTGTACATCACCTGTCA 57.681 50.000 0.00 0.00 39.39 3.58
1571 1750 3.914426 AATCCCTGTACATCACCTGTC 57.086 47.619 0.00 0.00 39.39 3.51
1572 1751 4.657814 AAAATCCCTGTACATCACCTGT 57.342 40.909 0.00 0.00 42.13 4.00
1573 1752 4.399303 GGAAAAATCCCTGTACATCACCTG 59.601 45.833 0.00 0.00 0.00 4.00
1574 1753 4.569865 GGGAAAAATCCCTGTACATCACCT 60.570 45.833 6.65 0.00 46.39 4.00
1575 1754 3.699538 GGGAAAAATCCCTGTACATCACC 59.300 47.826 6.65 0.00 46.39 4.02
1576 1755 4.983671 GGGAAAAATCCCTGTACATCAC 57.016 45.455 6.65 0.00 46.39 3.06
1596 1775 3.635591 AGCTTGGTCCTCAATAAATGGG 58.364 45.455 0.00 0.00 34.45 4.00
1597 1776 4.706476 TCAAGCTTGGTCCTCAATAAATGG 59.294 41.667 25.73 0.00 34.45 3.16
1598 1777 5.902613 TCAAGCTTGGTCCTCAATAAATG 57.097 39.130 25.73 0.00 34.45 2.32
1599 1778 5.954150 ACATCAAGCTTGGTCCTCAATAAAT 59.046 36.000 25.73 4.91 34.45 1.40
1600 1779 5.183713 CACATCAAGCTTGGTCCTCAATAAA 59.816 40.000 25.73 2.53 34.45 1.40
1601 1780 4.701651 CACATCAAGCTTGGTCCTCAATAA 59.298 41.667 25.73 3.07 34.45 1.40
1602 1781 4.263462 ACACATCAAGCTTGGTCCTCAATA 60.263 41.667 25.73 3.84 34.45 1.90
1603 1782 3.087031 CACATCAAGCTTGGTCCTCAAT 58.913 45.455 25.73 7.63 34.45 2.57
1604 1783 2.158623 ACACATCAAGCTTGGTCCTCAA 60.159 45.455 25.73 5.39 0.00 3.02
1605 1784 1.421268 ACACATCAAGCTTGGTCCTCA 59.579 47.619 25.73 6.16 0.00 3.86
1606 1785 1.808945 CACACATCAAGCTTGGTCCTC 59.191 52.381 25.73 0.00 0.00 3.71
1607 1786 1.546323 CCACACATCAAGCTTGGTCCT 60.546 52.381 25.73 3.53 0.00 3.85
1608 1787 0.883833 CCACACATCAAGCTTGGTCC 59.116 55.000 25.73 0.00 0.00 4.46
1609 1788 1.267806 CACCACACATCAAGCTTGGTC 59.732 52.381 25.73 0.00 38.56 4.02
1610 1789 1.133823 TCACCACACATCAAGCTTGGT 60.134 47.619 25.73 17.40 41.40 3.67
1611 1790 1.608055 TCACCACACATCAAGCTTGG 58.392 50.000 25.73 13.43 0.00 3.61
1612 1791 3.374745 GTTTCACCACACATCAAGCTTG 58.625 45.455 20.81 20.81 0.00 4.01
1613 1792 2.362077 GGTTTCACCACACATCAAGCTT 59.638 45.455 0.00 0.00 38.42 3.74
1614 1793 1.956477 GGTTTCACCACACATCAAGCT 59.044 47.619 0.00 0.00 38.42 3.74
1615 1794 1.680735 TGGTTTCACCACACATCAAGC 59.319 47.619 0.00 0.00 44.79 4.01
1626 1805 5.712152 ATTTCTTGATGAGTGGTTTCACC 57.288 39.130 0.00 0.00 44.64 4.02
1627 1806 8.273780 AGATATTTCTTGATGAGTGGTTTCAC 57.726 34.615 0.00 0.00 43.93 3.18
1628 1807 8.868522 AAGATATTTCTTGATGAGTGGTTTCA 57.131 30.769 0.00 0.00 40.74 2.69
1666 1845 8.655935 AGATAAACATGGTCCTCAGAATTTTT 57.344 30.769 0.00 0.00 0.00 1.94
1667 1846 8.526147 CAAGATAAACATGGTCCTCAGAATTTT 58.474 33.333 0.00 0.00 0.00 1.82
1668 1847 7.890127 TCAAGATAAACATGGTCCTCAGAATTT 59.110 33.333 0.00 0.00 0.00 1.82
1669 1848 7.405292 TCAAGATAAACATGGTCCTCAGAATT 58.595 34.615 0.00 0.00 0.00 2.17
1670 1849 6.962182 TCAAGATAAACATGGTCCTCAGAAT 58.038 36.000 0.00 0.00 0.00 2.40
1671 1850 6.373005 TCAAGATAAACATGGTCCTCAGAA 57.627 37.500 0.00 0.00 0.00 3.02
1672 1851 6.566079 ATCAAGATAAACATGGTCCTCAGA 57.434 37.500 0.00 0.00 0.00 3.27
1673 1852 7.504403 AGTATCAAGATAAACATGGTCCTCAG 58.496 38.462 0.00 0.00 0.00 3.35
1674 1853 7.125659 TGAGTATCAAGATAAACATGGTCCTCA 59.874 37.037 0.00 0.00 45.97 3.86
1675 1854 7.500992 TGAGTATCAAGATAAACATGGTCCTC 58.499 38.462 0.00 0.00 45.97 3.71
1676 1855 7.437713 TGAGTATCAAGATAAACATGGTCCT 57.562 36.000 0.00 0.00 45.97 3.85
1693 1872 7.201530 GCATACGGCCATTTTAGTATGAGTATC 60.202 40.741 22.80 7.37 45.38 2.24
1694 1873 6.594159 GCATACGGCCATTTTAGTATGAGTAT 59.406 38.462 22.80 7.56 45.38 2.12
1695 1874 5.929992 GCATACGGCCATTTTAGTATGAGTA 59.070 40.000 22.80 5.76 45.38 2.59
1696 1875 4.755123 GCATACGGCCATTTTAGTATGAGT 59.245 41.667 22.80 3.85 45.38 3.41
1697 1876 4.754618 TGCATACGGCCATTTTAGTATGAG 59.245 41.667 22.80 5.28 45.38 2.90
1698 1877 4.709250 TGCATACGGCCATTTTAGTATGA 58.291 39.130 22.80 10.38 45.38 2.15
1699 1878 5.391950 GGATGCATACGGCCATTTTAGTATG 60.392 44.000 17.22 17.22 45.34 2.39
1700 1879 4.700213 GGATGCATACGGCCATTTTAGTAT 59.300 41.667 2.24 0.00 43.89 2.12
1701 1880 4.069304 GGATGCATACGGCCATTTTAGTA 58.931 43.478 2.24 0.00 43.89 1.82
1702 1881 2.884639 GGATGCATACGGCCATTTTAGT 59.115 45.455 2.24 0.00 43.89 2.24
1703 1882 3.149196 AGGATGCATACGGCCATTTTAG 58.851 45.455 2.24 0.00 43.89 1.85
1704 1883 3.222173 AGGATGCATACGGCCATTTTA 57.778 42.857 2.24 0.00 43.89 1.52
1705 1884 2.071778 AGGATGCATACGGCCATTTT 57.928 45.000 2.24 0.00 43.89 1.82
1706 1885 2.071778 AAGGATGCATACGGCCATTT 57.928 45.000 2.24 0.00 43.89 2.32
1707 1886 2.106511 ACTAAGGATGCATACGGCCATT 59.893 45.455 2.24 0.00 43.89 3.16
1708 1887 1.699634 ACTAAGGATGCATACGGCCAT 59.300 47.619 2.24 0.00 43.89 4.40
1709 1888 1.128200 ACTAAGGATGCATACGGCCA 58.872 50.000 2.24 0.00 43.89 5.36
1710 1889 1.873591 CAACTAAGGATGCATACGGCC 59.126 52.381 2.46 0.00 43.89 6.13
1711 1890 1.873591 CCAACTAAGGATGCATACGGC 59.126 52.381 2.46 0.00 45.13 5.68
1712 1891 2.872245 CACCAACTAAGGATGCATACGG 59.128 50.000 2.46 0.00 0.00 4.02
1713 1892 2.287915 GCACCAACTAAGGATGCATACG 59.712 50.000 2.46 0.00 36.30 3.06
1714 1893 3.278574 TGCACCAACTAAGGATGCATAC 58.721 45.455 0.00 0.00 41.18 2.39
1715 1894 3.199727 TCTGCACCAACTAAGGATGCATA 59.800 43.478 0.00 2.75 44.73 3.14
1716 1895 2.025981 TCTGCACCAACTAAGGATGCAT 60.026 45.455 0.00 0.00 44.73 3.96
1717 1896 1.350684 TCTGCACCAACTAAGGATGCA 59.649 47.619 0.00 0.00 43.70 3.96
1718 1897 2.012673 CTCTGCACCAACTAAGGATGC 58.987 52.381 0.00 0.00 36.81 3.91
1719 1898 2.636830 CCTCTGCACCAACTAAGGATG 58.363 52.381 0.00 0.00 0.00 3.51
1720 1899 1.065126 GCCTCTGCACCAACTAAGGAT 60.065 52.381 0.00 0.00 37.47 3.24
1721 1900 0.324943 GCCTCTGCACCAACTAAGGA 59.675 55.000 0.00 0.00 37.47 3.36
1722 1901 0.678048 GGCCTCTGCACCAACTAAGG 60.678 60.000 0.00 0.00 40.13 2.69
1723 1902 1.021390 CGGCCTCTGCACCAACTAAG 61.021 60.000 0.00 0.00 40.13 2.18
1724 1903 1.003839 CGGCCTCTGCACCAACTAA 60.004 57.895 0.00 0.00 40.13 2.24
1725 1904 2.662596 CGGCCTCTGCACCAACTA 59.337 61.111 0.00 0.00 40.13 2.24
1726 1905 4.335647 CCGGCCTCTGCACCAACT 62.336 66.667 0.00 0.00 40.13 3.16
1730 1909 4.785453 CTTCCCGGCCTCTGCACC 62.785 72.222 0.00 0.00 40.13 5.01
1731 1910 4.021925 ACTTCCCGGCCTCTGCAC 62.022 66.667 0.00 0.00 40.13 4.57
1732 1911 4.020617 CACTTCCCGGCCTCTGCA 62.021 66.667 0.00 0.00 40.13 4.41
1733 1912 2.748058 TTTCACTTCCCGGCCTCTGC 62.748 60.000 0.00 0.00 0.00 4.26
1734 1913 0.250727 TTTTCACTTCCCGGCCTCTG 60.251 55.000 0.00 0.00 0.00 3.35
1735 1914 0.698818 ATTTTCACTTCCCGGCCTCT 59.301 50.000 0.00 0.00 0.00 3.69
1736 1915 1.095600 GATTTTCACTTCCCGGCCTC 58.904 55.000 0.00 0.00 0.00 4.70
1737 1916 0.698818 AGATTTTCACTTCCCGGCCT 59.301 50.000 0.00 0.00 0.00 5.19
1738 1917 1.095600 GAGATTTTCACTTCCCGGCC 58.904 55.000 0.00 0.00 0.00 6.13
1739 1918 1.821216 TGAGATTTTCACTTCCCGGC 58.179 50.000 0.00 0.00 0.00 6.13
1748 1927 7.344352 CCCCCTATAAAAATGGTGAGATTTTCA 59.656 37.037 0.00 0.00 35.01 2.69
1749 1928 7.726216 CCCCCTATAAAAATGGTGAGATTTTC 58.274 38.462 0.00 0.00 35.01 2.29
1750 1929 7.675161 CCCCCTATAAAAATGGTGAGATTTT 57.325 36.000 0.00 0.00 37.16 1.82
1776 1955 4.003788 ACAGGAGTCGGCGTTGGG 62.004 66.667 6.85 0.00 0.00 4.12
1777 1956 2.738521 CACAGGAGTCGGCGTTGG 60.739 66.667 6.85 0.00 0.00 3.77
1778 1957 3.414700 GCACAGGAGTCGGCGTTG 61.415 66.667 6.85 1.82 0.00 4.10
1779 1958 3.575351 GAGCACAGGAGTCGGCGTT 62.575 63.158 6.85 0.00 0.00 4.84
1780 1959 4.057428 GAGCACAGGAGTCGGCGT 62.057 66.667 6.85 0.00 0.00 5.68
1781 1960 3.691744 GAGAGCACAGGAGTCGGCG 62.692 68.421 0.00 0.00 0.00 6.46
1782 1961 2.183046 GAGAGCACAGGAGTCGGC 59.817 66.667 0.00 0.00 0.00 5.54
1783 1962 2.487428 CGAGAGCACAGGAGTCGG 59.513 66.667 0.00 0.00 0.00 4.79
1784 1963 2.487428 CCGAGAGCACAGGAGTCG 59.513 66.667 0.00 0.00 0.00 4.18
1785 1964 2.716017 CCCCGAGAGCACAGGAGTC 61.716 68.421 0.00 0.00 0.00 3.36
1786 1965 2.681778 CCCCGAGAGCACAGGAGT 60.682 66.667 0.00 0.00 0.00 3.85
1787 1966 3.465403 CCCCCGAGAGCACAGGAG 61.465 72.222 0.00 0.00 0.00 3.69
1802 1981 3.231736 TTATCCTCCTCGCGGCCC 61.232 66.667 6.13 0.00 0.00 5.80
1803 1982 2.029221 GTTATCCTCCTCGCGGCC 59.971 66.667 6.13 0.00 0.00 6.13
1804 1983 2.354773 CGTTATCCTCCTCGCGGC 60.355 66.667 6.13 0.00 0.00 6.53
1805 1984 2.335369 CCGTTATCCTCCTCGCGG 59.665 66.667 6.13 0.00 0.00 6.46
1806 1985 2.335369 CCCGTTATCCTCCTCGCG 59.665 66.667 0.00 0.00 0.00 5.87
1807 1986 2.029221 GCCCGTTATCCTCCTCGC 59.971 66.667 0.00 0.00 0.00 5.03
1808 1987 2.191513 TCGCCCGTTATCCTCCTCG 61.192 63.158 0.00 0.00 0.00 4.63
1809 1988 1.363080 GTCGCCCGTTATCCTCCTC 59.637 63.158 0.00 0.00 0.00 3.71
1810 1989 0.759436 ATGTCGCCCGTTATCCTCCT 60.759 55.000 0.00 0.00 0.00 3.69
1811 1990 0.600255 CATGTCGCCCGTTATCCTCC 60.600 60.000 0.00 0.00 0.00 4.30
1812 1991 0.600255 CCATGTCGCCCGTTATCCTC 60.600 60.000 0.00 0.00 0.00 3.71
1813 1992 1.445942 CCATGTCGCCCGTTATCCT 59.554 57.895 0.00 0.00 0.00 3.24
1814 1993 1.597027 CCCATGTCGCCCGTTATCC 60.597 63.158 0.00 0.00 0.00 2.59
1815 1994 1.597027 CCCCATGTCGCCCGTTATC 60.597 63.158 0.00 0.00 0.00 1.75
1816 1995 2.508928 CCCCATGTCGCCCGTTAT 59.491 61.111 0.00 0.00 0.00 1.89
1817 1996 3.788145 CCCCCATGTCGCCCGTTA 61.788 66.667 0.00 0.00 0.00 3.18
1961 2141 3.620785 GGAGATGCCGCCGGATCT 61.621 66.667 7.68 12.57 0.00 2.75
2056 2236 2.202932 CCGGCAAGATCCTGTCCG 60.203 66.667 15.86 15.86 36.43 4.79
2117 2297 3.685214 GACGCGACGCACCATCTCT 62.685 63.158 21.35 0.00 0.00 3.10
2207 2387 4.261801 GGATCAAATCGAAAAGGGTGAGA 58.738 43.478 0.00 0.00 0.00 3.27
2277 2457 2.124570 CCGGGATTCACCAGCAGG 60.125 66.667 0.00 0.00 41.20 4.85


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

AutoCloner maintained by Alex Coulton.