Multiple sequence alignment - TraesCS6B01G206200

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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 TraesCS6B01G206200 chr6B 100.000 5149 0 0 1 5149 259074072 259079220 0.000000e+00 9509.0
1 TraesCS6B01G206200 chr6B 94.578 166 9 0 1693 1858 717891185 717891020 1.840000e-64 257.0
2 TraesCS6B01G206200 chr6A 95.377 2336 54 10 2301 4614 201084240 201086543 0.000000e+00 3666.0
3 TraesCS6B01G206200 chr6A 91.605 1632 94 20 83 1695 201047748 201049355 0.000000e+00 2215.0
4 TraesCS6B01G206200 chr6A 95.815 454 7 6 1855 2306 201049352 201049795 0.000000e+00 723.0
5 TraesCS6B01G206200 chr6A 88.962 453 22 13 4618 5055 201087274 201087713 7.590000e-148 534.0
6 TraesCS6B01G206200 chr6D 96.263 1659 26 8 3518 5149 144874568 144876217 0.000000e+00 2687.0
7 TraesCS6B01G206200 chr6D 92.632 1683 71 21 1855 3491 144872896 144874571 0.000000e+00 2372.0
8 TraesCS6B01G206200 chr6D 92.632 1615 56 27 103 1695 144871326 144872899 0.000000e+00 2265.0
9 TraesCS6B01G206200 chr6D 83.254 209 29 2 4663 4869 53559106 53558902 2.450000e-43 187.0
10 TraesCS6B01G206200 chr6D 88.312 77 4 3 28 99 461008365 461008441 2.550000e-13 87.9
11 TraesCS6B01G206200 chr4D 95.238 168 8 0 1691 1858 93079202 93079369 3.060000e-67 267.0
12 TraesCS6B01G206200 chr4D 94.611 167 8 1 1691 1857 470142786 470142621 1.840000e-64 257.0
13 TraesCS6B01G206200 chr4D 83.981 206 23 6 4664 4865 339482252 339482451 6.810000e-44 189.0
14 TraesCS6B01G206200 chr3B 94.083 169 10 0 1689 1857 775481736 775481568 1.840000e-64 257.0
15 TraesCS6B01G206200 chr3B 83.230 161 25 2 1252 1411 123472945 123472786 4.150000e-31 147.0
16 TraesCS6B01G206200 chr3B 92.000 50 4 0 4618 4667 636736854 636736805 2.570000e-08 71.3
17 TraesCS6B01G206200 chrUn 94.545 165 9 0 1693 1857 74119451 74119615 6.620000e-64 255.0
18 TraesCS6B01G206200 chr5D 94.545 165 9 0 1693 1857 303991596 303991760 6.620000e-64 255.0
19 TraesCS6B01G206200 chr5D 93.529 170 10 1 1688 1857 66671780 66671948 8.560000e-63 252.0
20 TraesCS6B01G206200 chr1B 93.103 174 12 0 1684 1857 619401630 619401457 6.620000e-64 255.0
21 TraesCS6B01G206200 chr1B 96.429 56 2 0 1120 1175 180679146 180679091 5.490000e-15 93.5
22 TraesCS6B01G206200 chr1B 96.429 56 2 0 1120 1175 180687313 180687258 5.490000e-15 93.5
23 TraesCS6B01G206200 chr2D 92.090 177 12 2 1683 1858 623354510 623354685 1.110000e-61 248.0
24 TraesCS6B01G206200 chr2D 86.207 87 7 4 29 110 643235824 643235910 7.100000e-14 89.8
25 TraesCS6B01G206200 chr4B 82.439 205 26 6 4665 4865 419656611 419656809 2.470000e-38 171.0
26 TraesCS6B01G206200 chr3D 82.840 169 24 4 1247 1411 76933444 76933277 4.150000e-31 147.0
27 TraesCS6B01G206200 chr3D 87.356 87 6 4 28 109 434025795 434025881 1.530000e-15 95.3
28 TraesCS6B01G206200 chr3D 83.838 99 10 5 16 108 425066691 425066789 7.100000e-14 89.8
29 TraesCS6B01G206200 chr3A 82.500 160 23 4 1267 1422 91024901 91024743 8.990000e-28 135.0
30 TraesCS6B01G206200 chr1D 96.774 62 2 0 1120 1181 118888606 118888545 2.540000e-18 104.0
31 TraesCS6B01G206200 chr1A 96.774 62 2 0 1120 1181 130912848 130912787 2.540000e-18 104.0
32 TraesCS6B01G206200 chr1A 84.043 94 9 5 29 117 550630542 550630450 9.190000e-13 86.1
33 TraesCS6B01G206200 chr1A 82.178 101 12 5 14 109 15915263 15915164 1.190000e-11 82.4
34 TraesCS6B01G206200 chr7B 88.750 80 5 2 29 108 736761469 736761394 1.530000e-15 95.3
35 TraesCS6B01G206200 chr4A 87.059 85 6 4 29 108 285485451 285485367 1.970000e-14 91.6
36 TraesCS6B01G206200 chr2A 85.556 90 7 5 29 112 94222107 94222196 7.100000e-14 89.8
37 TraesCS6B01G206200 chr5A 80.833 120 14 6 4660 4776 593477778 593477891 9.190000e-13 86.1
38 TraesCS6B01G206200 chr2B 83.333 90 9 3 4659 4748 487240145 487240228 1.540000e-10 78.7
39 TraesCS6B01G206200 chr2B 100.000 30 0 0 4930 4959 779861484 779861455 7.200000e-04 56.5
40 TraesCS6B01G206200 chr5B 87.879 66 7 1 4660 4725 367209041 367209105 5.530000e-10 76.8
41 TraesCS6B01G206200 chr7A 83.871 62 8 2 4926 4985 252538434 252538373 2.000000e-04 58.4


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 TraesCS6B01G206200 chr6B 259074072 259079220 5148 False 9509.000000 9509 100.000000 1 5149 1 chr6B.!!$F1 5148
1 TraesCS6B01G206200 chr6A 201084240 201087713 3473 False 2100.000000 3666 92.169500 2301 5055 2 chr6A.!!$F2 2754
2 TraesCS6B01G206200 chr6A 201047748 201049795 2047 False 1469.000000 2215 93.710000 83 2306 2 chr6A.!!$F1 2223
3 TraesCS6B01G206200 chr6D 144871326 144876217 4891 False 2441.333333 2687 93.842333 103 5149 3 chr6D.!!$F2 5046

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
509 514 0.250513 ATGAGTGGAGCCGAGGTTTC 59.749 55.000 0.00 0.0 0.00 2.78 F
1706 1760 0.108281 GCTTGTACTCCCTCCGTTCC 60.108 60.000 0.00 0.0 0.00 3.62 F
1863 1917 0.113776 AACGGAGGGAGTACCACTGA 59.886 55.000 4.40 0.0 43.89 3.41 F
2890 2975 1.189524 TGGATGTCCGAACCCGACTT 61.190 55.000 0.00 0.0 39.43 3.01 F
3847 3964 2.749044 CACGCTGCAATGGAGGCT 60.749 61.111 3.49 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1898 0.113776 TCAGTGGTACTCCCTCCGTT 59.886 55.0 0.00 0.0 0.00 4.44 R
2890 2975 0.895530 GAGTCAGACACCCGAATCCA 59.104 55.0 2.66 0.0 0.00 3.41 R
3047 3154 1.845266 CAGACACAGCTACGCCATAG 58.155 55.0 0.00 0.0 0.00 2.23 R
3954 4071 0.676466 AATGGATCCAACAAGCGCGA 60.676 50.0 20.67 0.0 0.00 5.87 R
5101 5970 0.099968 CGAACTTACGATCCGCCAGA 59.900 55.0 0.00 0.0 35.09 3.86 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
33 34 8.060931 TGATATCTGCAGTAATCTGATACTCC 57.939 38.462 22.67 6.02 43.76 3.85
34 35 7.892771 TGATATCTGCAGTAATCTGATACTCCT 59.107 37.037 22.67 0.00 43.76 3.69
35 36 6.992664 ATCTGCAGTAATCTGATACTCCTT 57.007 37.500 14.67 0.00 43.76 3.36
36 37 6.398234 TCTGCAGTAATCTGATACTCCTTC 57.602 41.667 14.67 0.00 43.76 3.46
37 38 5.303078 TCTGCAGTAATCTGATACTCCTTCC 59.697 44.000 14.67 0.00 43.76 3.46
38 39 4.038042 TGCAGTAATCTGATACTCCTTCCG 59.962 45.833 0.00 0.00 43.76 4.30
39 40 4.038162 GCAGTAATCTGATACTCCTTCCGT 59.962 45.833 0.00 0.00 43.76 4.69
40 41 5.241064 GCAGTAATCTGATACTCCTTCCGTA 59.759 44.000 0.00 0.00 43.76 4.02
41 42 6.238953 GCAGTAATCTGATACTCCTTCCGTAA 60.239 42.308 0.00 0.00 43.76 3.18
42 43 7.683704 GCAGTAATCTGATACTCCTTCCGTAAA 60.684 40.741 0.00 0.00 43.76 2.01
43 44 7.863375 CAGTAATCTGATACTCCTTCCGTAAAG 59.137 40.741 0.00 0.00 43.76 1.85
44 45 7.778853 AGTAATCTGATACTCCTTCCGTAAAGA 59.221 37.037 0.00 0.00 32.16 2.52
45 46 7.419711 AATCTGATACTCCTTCCGTAAAGAA 57.580 36.000 0.00 0.00 37.12 2.52
46 47 6.845758 TCTGATACTCCTTCCGTAAAGAAA 57.154 37.500 0.00 0.00 37.12 2.52
47 48 7.419711 TCTGATACTCCTTCCGTAAAGAAAT 57.580 36.000 0.00 0.00 37.12 2.17
48 49 8.529424 TCTGATACTCCTTCCGTAAAGAAATA 57.471 34.615 0.00 0.00 37.12 1.40
49 50 9.144298 TCTGATACTCCTTCCGTAAAGAAATAT 57.856 33.333 0.00 0.00 37.12 1.28
55 56 7.927092 ACTCCTTCCGTAAAGAAATATAAGAGC 59.073 37.037 0.00 0.00 37.12 4.09
56 57 7.788026 TCCTTCCGTAAAGAAATATAAGAGCA 58.212 34.615 0.00 0.00 37.12 4.26
57 58 8.429641 TCCTTCCGTAAAGAAATATAAGAGCAT 58.570 33.333 0.00 0.00 37.12 3.79
58 59 9.057089 CCTTCCGTAAAGAAATATAAGAGCATT 57.943 33.333 0.00 0.00 37.12 3.56
128 129 3.307829 TCGATTGCGACGACTTCTC 57.692 52.632 0.00 0.00 42.51 2.87
143 144 3.637694 GACTTCTCCTATCGGGCTACTTT 59.362 47.826 0.00 0.00 34.39 2.66
144 145 3.637694 ACTTCTCCTATCGGGCTACTTTC 59.362 47.826 0.00 0.00 34.39 2.62
145 146 3.308035 TCTCCTATCGGGCTACTTTCA 57.692 47.619 0.00 0.00 34.39 2.69
175 179 4.758674 CCACTTCTCTGATCACATTGTTGT 59.241 41.667 0.00 0.00 36.15 3.32
235 239 9.578439 AATGAGATTTTTGCTATCTTTGCTTAC 57.422 29.630 0.00 0.00 32.64 2.34
315 319 6.947464 ACATGCTACTTTATTACTCCACACT 58.053 36.000 0.00 0.00 0.00 3.55
325 329 7.609760 TTATTACTCCACACTTACTTGCATG 57.390 36.000 0.00 0.00 0.00 4.06
326 330 3.492102 ACTCCACACTTACTTGCATGT 57.508 42.857 10.40 10.40 0.00 3.21
444 449 5.655532 TCACCTACGAAAAACCTAGCTCTAT 59.344 40.000 0.00 0.00 0.00 1.98
454 459 8.814038 AAAAACCTAGCTCTATCATCACATTT 57.186 30.769 0.00 0.00 0.00 2.32
470 475 8.281531 TCATCACATTTCCCTTTTCCTACATAT 58.718 33.333 0.00 0.00 0.00 1.78
478 483 7.931015 TCCCTTTTCCTACATATACAGTGAT 57.069 36.000 0.00 0.00 0.00 3.06
509 514 0.250513 ATGAGTGGAGCCGAGGTTTC 59.749 55.000 0.00 0.00 0.00 2.78
548 569 0.950836 TTCATCGGTGGTTGTTGCTG 59.049 50.000 0.00 0.00 0.00 4.41
553 574 1.021202 CGGTGGTTGTTGCTGAGAAA 58.979 50.000 0.00 0.00 0.00 2.52
554 575 1.403679 CGGTGGTTGTTGCTGAGAAAA 59.596 47.619 0.00 0.00 0.00 2.29
555 576 2.794631 CGGTGGTTGTTGCTGAGAAAAC 60.795 50.000 0.00 0.00 0.00 2.43
556 577 2.165437 GGTGGTTGTTGCTGAGAAAACA 59.835 45.455 0.00 0.00 34.57 2.83
557 578 3.438360 GTGGTTGTTGCTGAGAAAACAG 58.562 45.455 2.22 0.00 37.57 3.16
558 579 3.128589 GTGGTTGTTGCTGAGAAAACAGA 59.871 43.478 0.00 0.00 39.94 3.41
559 580 3.761218 TGGTTGTTGCTGAGAAAACAGAA 59.239 39.130 0.00 0.00 39.94 3.02
560 581 4.142403 TGGTTGTTGCTGAGAAAACAGAAG 60.142 41.667 0.00 0.00 39.94 2.85
561 582 4.354587 GTTGTTGCTGAGAAAACAGAAGG 58.645 43.478 0.00 0.00 39.94 3.46
562 583 3.884895 TGTTGCTGAGAAAACAGAAGGA 58.115 40.909 0.00 0.00 39.94 3.36
572 593 9.801873 CTGAGAAAACAGAAGGAAAACAAATTA 57.198 29.630 0.00 0.00 39.94 1.40
603 624 4.273318 GGGTGAAGCTACAATGGAGAAAT 58.727 43.478 0.00 0.00 0.00 2.17
627 650 2.977829 TCGTGTGATTCGTCGAGAAAAG 59.022 45.455 0.00 0.00 42.91 2.27
629 652 3.314553 GTGTGATTCGTCGAGAAAAGGA 58.685 45.455 0.00 0.00 42.91 3.36
824 860 1.299976 CAACCTGCCACCTACCCTC 59.700 63.158 0.00 0.00 0.00 4.30
906 944 1.255667 TTACCACCTCACTCGCTCCC 61.256 60.000 0.00 0.00 0.00 4.30
974 1013 1.423921 GTTCCAAGGGTCCTTCCTTCA 59.576 52.381 0.00 0.00 44.70 3.02
986 1025 0.696501 TTCCTTCACTGCCCTAACCC 59.303 55.000 0.00 0.00 0.00 4.11
988 1027 1.550130 CCTTCACTGCCCTAACCCGA 61.550 60.000 0.00 0.00 0.00 5.14
989 1028 0.391263 CTTCACTGCCCTAACCCGAC 60.391 60.000 0.00 0.00 0.00 4.79
990 1029 1.833787 TTCACTGCCCTAACCCGACC 61.834 60.000 0.00 0.00 0.00 4.79
991 1030 3.007323 ACTGCCCTAACCCGACCC 61.007 66.667 0.00 0.00 0.00 4.46
992 1031 3.006728 CTGCCCTAACCCGACCCA 61.007 66.667 0.00 0.00 0.00 4.51
997 1036 2.266689 CTAACCCGACCCAACCCG 59.733 66.667 0.00 0.00 0.00 5.28
1186 1225 5.823861 AGAAGAAGAAGAAGAAGAAGCCT 57.176 39.130 0.00 0.00 0.00 4.58
1465 1511 1.063469 CGTTTTGCTTTCACGTCCACT 59.937 47.619 0.00 0.00 0.00 4.00
1466 1512 2.450160 GTTTTGCTTTCACGTCCACTG 58.550 47.619 0.00 0.00 0.00 3.66
1467 1513 2.031258 TTTGCTTTCACGTCCACTGA 57.969 45.000 0.00 0.00 0.00 3.41
1468 1514 2.254546 TTGCTTTCACGTCCACTGAT 57.745 45.000 0.00 0.00 0.00 2.90
1469 1515 1.511850 TGCTTTCACGTCCACTGATG 58.488 50.000 0.00 0.00 0.00 3.07
1523 1577 0.108992 TAGGTTGTTAGAGCGGTGCG 60.109 55.000 0.00 0.00 0.00 5.34
1557 1611 5.716094 TCGTGATAGAAATGAACCTTTCGA 58.284 37.500 0.00 0.00 39.57 3.71
1591 1645 4.881850 AGATTCAGTTTCGTGAAAGGTTGT 59.118 37.500 0.00 0.00 39.84 3.32
1625 1679 5.730550 ACCGCTGATTCTTGTTCTACATAA 58.269 37.500 0.00 0.00 0.00 1.90
1633 1687 5.836024 TCTTGTTCTACATAAGTGGGGTT 57.164 39.130 0.00 0.00 0.00 4.11
1639 1693 6.012333 TGTTCTACATAAGTGGGGTTATGGTT 60.012 38.462 8.15 0.00 42.45 3.67
1695 1749 1.493022 TGGTGGTCCTTTGCTTGTACT 59.507 47.619 0.00 0.00 34.23 2.73
1696 1750 2.152016 GGTGGTCCTTTGCTTGTACTC 58.848 52.381 0.00 0.00 0.00 2.59
1697 1751 2.152016 GTGGTCCTTTGCTTGTACTCC 58.848 52.381 0.00 0.00 0.00 3.85
1698 1752 1.073284 TGGTCCTTTGCTTGTACTCCC 59.927 52.381 0.00 0.00 0.00 4.30
1699 1753 1.351350 GGTCCTTTGCTTGTACTCCCT 59.649 52.381 0.00 0.00 0.00 4.20
1700 1754 2.615747 GGTCCTTTGCTTGTACTCCCTC 60.616 54.545 0.00 0.00 0.00 4.30
1701 1755 1.628846 TCCTTTGCTTGTACTCCCTCC 59.371 52.381 0.00 0.00 0.00 4.30
1702 1756 1.676014 CCTTTGCTTGTACTCCCTCCG 60.676 57.143 0.00 0.00 0.00 4.63
1703 1757 1.002087 CTTTGCTTGTACTCCCTCCGT 59.998 52.381 0.00 0.00 0.00 4.69
1704 1758 1.053424 TTGCTTGTACTCCCTCCGTT 58.947 50.000 0.00 0.00 0.00 4.44
1705 1759 0.606604 TGCTTGTACTCCCTCCGTTC 59.393 55.000 0.00 0.00 0.00 3.95
1706 1760 0.108281 GCTTGTACTCCCTCCGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
1707 1761 1.558233 CTTGTACTCCCTCCGTTCCT 58.442 55.000 0.00 0.00 0.00 3.36
1708 1762 2.731572 CTTGTACTCCCTCCGTTCCTA 58.268 52.381 0.00 0.00 0.00 2.94
1709 1763 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
1710 1764 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
1711 1765 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
1712 1766 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
1713 1767 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
1714 1768 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
1715 1769 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1716 1770 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1717 1771 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1718 1772 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1719 1773 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1720 1774 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1721 1775 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1722 1776 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
1723 1777 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
1724 1778 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
1725 1779 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
1726 1780 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
1743 1797 9.436957 TCTTTCTAGACATTTCAAATGGACTAC 57.563 33.333 14.70 1.26 0.00 2.73
1744 1798 8.561738 TTTCTAGACATTTCAAATGGACTACC 57.438 34.615 14.70 0.00 0.00 3.18
1745 1799 6.650120 TCTAGACATTTCAAATGGACTACCC 58.350 40.000 14.70 0.00 34.81 3.69
1746 1800 5.520748 AGACATTTCAAATGGACTACCCT 57.479 39.130 14.70 0.00 35.38 4.34
1747 1801 6.636454 AGACATTTCAAATGGACTACCCTA 57.364 37.500 14.70 0.00 35.38 3.53
1748 1802 7.213178 AGACATTTCAAATGGACTACCCTAT 57.787 36.000 14.70 0.00 35.38 2.57
1749 1803 7.056635 AGACATTTCAAATGGACTACCCTATG 58.943 38.462 14.70 0.00 35.38 2.23
1750 1804 5.594317 ACATTTCAAATGGACTACCCTATGC 59.406 40.000 14.70 0.00 35.38 3.14
1751 1805 3.469008 TCAAATGGACTACCCTATGCG 57.531 47.619 0.00 0.00 35.38 4.73
1752 1806 2.104111 TCAAATGGACTACCCTATGCGG 59.896 50.000 0.00 0.00 35.38 5.69
1753 1807 2.097110 AATGGACTACCCTATGCGGA 57.903 50.000 0.00 0.00 35.38 5.54
1754 1808 2.327325 ATGGACTACCCTATGCGGAT 57.673 50.000 0.00 0.00 35.38 4.18
1755 1809 1.338107 TGGACTACCCTATGCGGATG 58.662 55.000 0.00 0.00 35.38 3.51
1756 1810 1.339097 GGACTACCCTATGCGGATGT 58.661 55.000 0.00 0.00 33.16 3.06
1757 1811 2.158430 TGGACTACCCTATGCGGATGTA 60.158 50.000 0.00 0.00 35.38 2.29
1758 1812 3.097614 GGACTACCCTATGCGGATGTAT 58.902 50.000 0.00 0.00 33.16 2.29
1759 1813 3.119101 GGACTACCCTATGCGGATGTATG 60.119 52.174 0.00 0.00 33.16 2.39
1760 1814 3.507411 ACTACCCTATGCGGATGTATGT 58.493 45.455 0.00 0.00 33.16 2.29
1761 1815 4.669700 ACTACCCTATGCGGATGTATGTA 58.330 43.478 0.00 0.00 33.16 2.29
1762 1816 4.705507 ACTACCCTATGCGGATGTATGTAG 59.294 45.833 0.00 7.75 33.16 2.74
1763 1817 3.774734 ACCCTATGCGGATGTATGTAGA 58.225 45.455 0.00 0.00 33.16 2.59
1764 1818 3.510360 ACCCTATGCGGATGTATGTAGAC 59.490 47.826 0.00 0.00 33.16 2.59
1765 1819 3.509967 CCCTATGCGGATGTATGTAGACA 59.490 47.826 0.00 0.00 33.16 3.41
1766 1820 4.160439 CCCTATGCGGATGTATGTAGACAT 59.840 45.833 0.00 0.08 42.82 3.06
1767 1821 5.359860 CCCTATGCGGATGTATGTAGACATA 59.640 44.000 0.00 0.00 40.18 2.29
1768 1822 6.040955 CCCTATGCGGATGTATGTAGACATAT 59.959 42.308 0.00 0.00 40.18 1.78
1769 1823 7.417911 CCCTATGCGGATGTATGTAGACATATT 60.418 40.741 0.00 0.00 40.18 1.28
1770 1824 7.981789 CCTATGCGGATGTATGTAGACATATTT 59.018 37.037 0.00 0.00 40.18 1.40
1771 1825 9.371136 CTATGCGGATGTATGTAGACATATTTT 57.629 33.333 0.00 0.00 40.18 1.82
1773 1827 8.757164 TGCGGATGTATGTAGACATATTTTAG 57.243 34.615 5.69 0.90 40.18 1.85
1774 1828 8.581578 TGCGGATGTATGTAGACATATTTTAGA 58.418 33.333 5.69 0.00 40.18 2.10
1775 1829 9.077674 GCGGATGTATGTAGACATATTTTAGAG 57.922 37.037 5.69 0.00 40.18 2.43
1799 1853 7.132213 AGTGTACATTCACTCATTTTGTTTCG 58.868 34.615 0.00 0.00 44.07 3.46
1800 1854 6.910433 GTGTACATTCACTCATTTTGTTTCGT 59.090 34.615 0.00 0.00 35.68 3.85
1801 1855 8.065407 GTGTACATTCACTCATTTTGTTTCGTA 58.935 33.333 0.00 0.00 35.68 3.43
1802 1856 8.779303 TGTACATTCACTCATTTTGTTTCGTAT 58.221 29.630 0.00 0.00 0.00 3.06
1803 1857 9.051027 GTACATTCACTCATTTTGTTTCGTATG 57.949 33.333 0.00 0.00 0.00 2.39
1804 1858 7.648142 ACATTCACTCATTTTGTTTCGTATGT 58.352 30.769 0.00 0.00 0.00 2.29
1805 1859 8.779303 ACATTCACTCATTTTGTTTCGTATGTA 58.221 29.630 0.00 0.00 0.00 2.29
1806 1860 9.265938 CATTCACTCATTTTGTTTCGTATGTAG 57.734 33.333 0.00 0.00 0.00 2.74
1807 1861 7.956420 TCACTCATTTTGTTTCGTATGTAGT 57.044 32.000 0.00 0.00 0.00 2.73
1808 1862 8.014322 TCACTCATTTTGTTTCGTATGTAGTC 57.986 34.615 0.00 0.00 0.00 2.59
1809 1863 7.654116 TCACTCATTTTGTTTCGTATGTAGTCA 59.346 33.333 0.00 0.00 0.00 3.41
1810 1864 7.740346 CACTCATTTTGTTTCGTATGTAGTCAC 59.260 37.037 0.00 0.00 0.00 3.67
1811 1865 7.656137 ACTCATTTTGTTTCGTATGTAGTCACT 59.344 33.333 0.00 0.00 0.00 3.41
1812 1866 8.373048 TCATTTTGTTTCGTATGTAGTCACTT 57.627 30.769 0.00 0.00 0.00 3.16
1813 1867 8.279800 TCATTTTGTTTCGTATGTAGTCACTTG 58.720 33.333 0.00 0.00 0.00 3.16
1814 1868 7.542534 TTTTGTTTCGTATGTAGTCACTTGT 57.457 32.000 0.00 0.00 0.00 3.16
1815 1869 7.542534 TTTGTTTCGTATGTAGTCACTTGTT 57.457 32.000 0.00 0.00 0.00 2.83
1816 1870 6.519353 TGTTTCGTATGTAGTCACTTGTTG 57.481 37.500 0.00 0.00 0.00 3.33
1817 1871 6.274579 TGTTTCGTATGTAGTCACTTGTTGA 58.725 36.000 0.00 0.00 0.00 3.18
1818 1872 6.757478 TGTTTCGTATGTAGTCACTTGTTGAA 59.243 34.615 0.00 0.00 35.39 2.69
1819 1873 7.278203 TGTTTCGTATGTAGTCACTTGTTGAAA 59.722 33.333 0.00 0.00 35.39 2.69
1820 1874 6.758593 TCGTATGTAGTCACTTGTTGAAAC 57.241 37.500 0.00 0.00 35.39 2.78
1821 1875 6.274579 TCGTATGTAGTCACTTGTTGAAACA 58.725 36.000 0.00 0.00 37.00 2.83
1822 1876 6.926826 TCGTATGTAGTCACTTGTTGAAACAT 59.073 34.615 0.00 8.00 42.09 2.71
1823 1877 7.115805 TCGTATGTAGTCACTTGTTGAAACATC 59.884 37.037 0.00 0.00 40.13 3.06
1824 1878 7.116376 CGTATGTAGTCACTTGTTGAAACATCT 59.884 37.037 0.00 0.00 40.13 2.90
1825 1879 9.419297 GTATGTAGTCACTTGTTGAAACATCTA 57.581 33.333 0.00 0.00 40.13 1.98
1826 1880 7.946655 TGTAGTCACTTGTTGAAACATCTAG 57.053 36.000 0.00 0.00 38.95 2.43
1827 1881 7.722363 TGTAGTCACTTGTTGAAACATCTAGA 58.278 34.615 0.00 0.00 38.95 2.43
1828 1882 8.201464 TGTAGTCACTTGTTGAAACATCTAGAA 58.799 33.333 0.00 0.00 38.95 2.10
1829 1883 9.042008 GTAGTCACTTGTTGAAACATCTAGAAA 57.958 33.333 0.00 0.00 38.95 2.52
1830 1884 8.147642 AGTCACTTGTTGAAACATCTAGAAAG 57.852 34.615 0.00 0.00 38.95 2.62
1831 1885 7.987458 AGTCACTTGTTGAAACATCTAGAAAGA 59.013 33.333 0.00 0.00 38.95 2.52
1832 1886 8.064814 GTCACTTGTTGAAACATCTAGAAAGAC 58.935 37.037 0.00 1.41 38.95 3.01
1833 1887 7.768582 TCACTTGTTGAAACATCTAGAAAGACA 59.231 33.333 0.00 0.00 38.95 3.41
1834 1888 8.397906 CACTTGTTGAAACATCTAGAAAGACAA 58.602 33.333 0.00 1.46 38.95 3.18
1835 1889 8.956426 ACTTGTTGAAACATCTAGAAAGACAAA 58.044 29.630 0.00 0.00 38.95 2.83
1836 1890 9.956720 CTTGTTGAAACATCTAGAAAGACAAAT 57.043 29.630 0.00 0.00 38.95 2.32
1851 1905 8.947115 AGAAAGACAAATATTTAGAAACGGAGG 58.053 33.333 0.00 0.00 0.00 4.30
1852 1906 7.625828 AAGACAAATATTTAGAAACGGAGGG 57.374 36.000 0.00 0.00 0.00 4.30
1853 1907 6.954232 AGACAAATATTTAGAAACGGAGGGA 58.046 36.000 0.00 0.00 0.00 4.20
1854 1908 7.048512 AGACAAATATTTAGAAACGGAGGGAG 58.951 38.462 0.00 0.00 0.00 4.30
1855 1909 6.718294 ACAAATATTTAGAAACGGAGGGAGT 58.282 36.000 0.00 0.00 0.00 3.85
1856 1910 7.854337 ACAAATATTTAGAAACGGAGGGAGTA 58.146 34.615 0.00 0.00 0.00 2.59
1857 1911 7.767659 ACAAATATTTAGAAACGGAGGGAGTAC 59.232 37.037 0.00 0.00 0.00 2.73
1863 1917 0.113776 AACGGAGGGAGTACCACTGA 59.886 55.000 4.40 0.00 43.89 3.41
1955 2023 3.254166 TGAGGTGTCTTCCGTTGTACTAC 59.746 47.826 0.00 0.00 0.00 2.73
1956 2024 3.494332 AGGTGTCTTCCGTTGTACTACT 58.506 45.455 5.91 0.00 0.00 2.57
1957 2025 4.655963 AGGTGTCTTCCGTTGTACTACTA 58.344 43.478 5.91 0.00 0.00 1.82
1984 2052 7.975616 GGTTTGCTATATTTATGCATGGTATGG 59.024 37.037 10.16 7.92 36.55 2.74
2619 2695 5.104527 TGAGGCCTGTGTTGCTAATACTAAT 60.105 40.000 12.00 0.00 0.00 1.73
2874 2959 3.392947 TGTTAGTTGGACAGGAACATGGA 59.607 43.478 0.00 0.00 0.00 3.41
2890 2975 1.189524 TGGATGTCCGAACCCGACTT 61.190 55.000 0.00 0.00 39.43 3.01
3047 3154 6.857956 TGCTTCTGTCTACTTTCTCTATGTC 58.142 40.000 0.00 0.00 0.00 3.06
3050 3157 8.846211 GCTTCTGTCTACTTTCTCTATGTCTAT 58.154 37.037 0.00 0.00 0.00 1.98
3847 3964 2.749044 CACGCTGCAATGGAGGCT 60.749 61.111 3.49 0.00 0.00 4.58
4368 4485 7.420637 CGTAGACGTTTAGATTCTACAAGTG 57.579 40.000 3.61 0.00 41.19 3.16
4922 5776 6.680055 TCGAAACTACATACGAACTGAAAC 57.320 37.500 0.00 0.00 0.00 2.78
4925 5779 6.129378 CGAAACTACATACGAACTGAAACGAA 60.129 38.462 0.00 0.00 0.00 3.85
4926 5780 6.443876 AACTACATACGAACTGAAACGAAC 57.556 37.500 0.00 0.00 0.00 3.95
4927 5781 5.766222 ACTACATACGAACTGAAACGAACT 58.234 37.500 0.00 0.00 0.00 3.01
4928 5782 6.211515 ACTACATACGAACTGAAACGAACTT 58.788 36.000 0.00 0.00 0.00 2.66
5006 5875 7.766278 TGAACAAAGAGAGTAGCATATTTCTCC 59.234 37.037 0.00 0.00 35.82 3.71
5041 5910 6.039605 CACATGCCACCTCATCATATAAACAA 59.960 38.462 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.694540 GGAGTATCAGATTACTGCAGATATCAT 58.305 37.037 23.35 13.77 43.17 2.45
8 9 7.892771 AGGAGTATCAGATTACTGCAGATATCA 59.107 37.037 23.35 7.84 41.48 2.15
9 10 8.292444 AGGAGTATCAGATTACTGCAGATATC 57.708 38.462 23.35 20.40 41.48 1.63
10 11 8.663209 AAGGAGTATCAGATTACTGCAGATAT 57.337 34.615 23.35 12.84 41.48 1.63
11 12 7.177568 GGAAGGAGTATCAGATTACTGCAGATA 59.822 40.741 23.35 7.93 41.48 1.98
12 13 6.014669 GGAAGGAGTATCAGATTACTGCAGAT 60.015 42.308 23.35 3.68 41.48 2.90
13 14 5.303078 GGAAGGAGTATCAGATTACTGCAGA 59.697 44.000 23.35 0.00 41.48 4.26
14 15 5.537188 GGAAGGAGTATCAGATTACTGCAG 58.463 45.833 13.48 13.48 41.48 4.41
15 16 4.038042 CGGAAGGAGTATCAGATTACTGCA 59.962 45.833 11.43 0.00 41.48 4.41
16 17 4.038162 ACGGAAGGAGTATCAGATTACTGC 59.962 45.833 0.00 0.00 43.17 4.40
17 18 5.776173 ACGGAAGGAGTATCAGATTACTG 57.224 43.478 0.00 0.00 44.66 2.74
18 19 7.778853 TCTTTACGGAAGGAGTATCAGATTACT 59.221 37.037 0.00 0.00 36.25 2.24
19 20 7.938715 TCTTTACGGAAGGAGTATCAGATTAC 58.061 38.462 0.00 0.00 36.25 1.89
20 21 8.529424 TTCTTTACGGAAGGAGTATCAGATTA 57.471 34.615 0.00 0.00 36.25 1.75
21 22 7.419711 TTCTTTACGGAAGGAGTATCAGATT 57.580 36.000 0.00 0.00 36.25 2.40
22 23 7.419711 TTTCTTTACGGAAGGAGTATCAGAT 57.580 36.000 0.00 0.00 36.25 2.90
23 24 6.845758 TTTCTTTACGGAAGGAGTATCAGA 57.154 37.500 0.00 0.00 36.25 3.27
29 30 7.927092 GCTCTTATATTTCTTTACGGAAGGAGT 59.073 37.037 0.00 0.00 35.98 3.85
30 31 7.926555 TGCTCTTATATTTCTTTACGGAAGGAG 59.073 37.037 0.00 0.00 35.98 3.69
31 32 7.788026 TGCTCTTATATTTCTTTACGGAAGGA 58.212 34.615 0.00 0.00 35.98 3.36
32 33 8.608844 ATGCTCTTATATTTCTTTACGGAAGG 57.391 34.615 1.66 0.00 35.98 3.46
99 100 3.696281 TCGCAATCGAAATACTCCGTA 57.304 42.857 0.00 0.00 42.44 4.02
111 112 0.179161 AGGAGAAGTCGTCGCAATCG 60.179 55.000 0.00 0.00 0.00 3.34
143 144 4.467438 TGATCAGAGAAGTGGCAATACTGA 59.533 41.667 16.77 16.77 37.33 3.41
144 145 4.569966 GTGATCAGAGAAGTGGCAATACTG 59.430 45.833 0.00 9.31 0.00 2.74
145 146 4.223700 TGTGATCAGAGAAGTGGCAATACT 59.776 41.667 0.00 0.00 0.00 2.12
175 179 3.148412 CATGGTGGTGAAGTGACATTCA 58.852 45.455 0.00 0.00 36.85 2.57
179 183 1.543208 GCTCATGGTGGTGAAGTGACA 60.543 52.381 0.00 0.00 0.00 3.58
444 449 5.886609 TGTAGGAAAAGGGAAATGTGATGA 58.113 37.500 0.00 0.00 0.00 2.92
454 459 7.931015 ATCACTGTATATGTAGGAAAAGGGA 57.069 36.000 0.00 0.00 0.00 4.20
470 475 4.284746 TCATGGTGTGTGGTTATCACTGTA 59.715 41.667 0.00 0.00 46.20 2.74
538 547 4.354587 CTTCTGTTTTCTCAGCAACAACC 58.645 43.478 0.00 0.00 32.53 3.77
548 569 9.031360 GGTAATTTGTTTTCCTTCTGTTTTCTC 57.969 33.333 0.00 0.00 0.00 2.87
553 574 6.183360 CCAGGGTAATTTGTTTTCCTTCTGTT 60.183 38.462 0.00 0.00 0.00 3.16
554 575 5.304357 CCAGGGTAATTTGTTTTCCTTCTGT 59.696 40.000 0.00 0.00 0.00 3.41
555 576 5.538433 TCCAGGGTAATTTGTTTTCCTTCTG 59.462 40.000 0.00 0.00 0.00 3.02
556 577 5.538813 GTCCAGGGTAATTTGTTTTCCTTCT 59.461 40.000 0.00 0.00 0.00 2.85
557 578 5.564063 CGTCCAGGGTAATTTGTTTTCCTTC 60.564 44.000 0.00 0.00 0.00 3.46
558 579 4.279922 CGTCCAGGGTAATTTGTTTTCCTT 59.720 41.667 0.00 0.00 0.00 3.36
559 580 3.824443 CGTCCAGGGTAATTTGTTTTCCT 59.176 43.478 0.00 0.00 0.00 3.36
560 581 3.057104 CCGTCCAGGGTAATTTGTTTTCC 60.057 47.826 0.00 0.00 35.97 3.13
561 582 4.168922 CCGTCCAGGGTAATTTGTTTTC 57.831 45.455 0.00 0.00 35.97 2.29
603 624 0.109919 CTCGACGAATCACACGACCA 60.110 55.000 0.00 0.00 34.70 4.02
696 732 9.367444 CTCTGGTGACTAAAACGTCTTATATTT 57.633 33.333 0.00 0.00 35.00 1.40
697 733 8.529476 ACTCTGGTGACTAAAACGTCTTATATT 58.471 33.333 0.00 0.00 35.00 1.28
698 734 8.064336 ACTCTGGTGACTAAAACGTCTTATAT 57.936 34.615 0.00 0.00 35.00 0.86
699 735 7.458409 ACTCTGGTGACTAAAACGTCTTATA 57.542 36.000 0.00 0.00 35.00 0.98
700 736 6.342338 ACTCTGGTGACTAAAACGTCTTAT 57.658 37.500 0.00 0.00 35.00 1.73
701 737 5.779529 ACTCTGGTGACTAAAACGTCTTA 57.220 39.130 0.00 0.00 35.00 2.10
702 738 4.667519 ACTCTGGTGACTAAAACGTCTT 57.332 40.909 0.00 0.00 35.00 3.01
718 754 5.463724 AGCGTGAGTTTTTCTTTCTACTCTG 59.536 40.000 0.00 0.00 38.23 3.35
974 1013 3.007323 GGGTCGGGTTAGGGCAGT 61.007 66.667 0.00 0.00 0.00 4.40
986 1025 4.692475 GTGGGTCGGGTTGGGTCG 62.692 72.222 0.00 0.00 0.00 4.79
990 1029 4.692475 GTCGGTGGGTCGGGTTGG 62.692 72.222 0.00 0.00 0.00 3.77
991 1030 4.692475 GGTCGGTGGGTCGGGTTG 62.692 72.222 0.00 0.00 0.00 3.77
1275 1317 4.717313 AGAAAACCTCCGGCGGCC 62.717 66.667 23.83 9.54 0.00 6.13
1465 1511 4.565022 TGCGAAACTCTAACATCACATCA 58.435 39.130 0.00 0.00 0.00 3.07
1466 1512 4.493220 GCTGCGAAACTCTAACATCACATC 60.493 45.833 0.00 0.00 0.00 3.06
1467 1513 3.372206 GCTGCGAAACTCTAACATCACAT 59.628 43.478 0.00 0.00 0.00 3.21
1468 1514 2.736721 GCTGCGAAACTCTAACATCACA 59.263 45.455 0.00 0.00 0.00 3.58
1469 1515 2.094417 GGCTGCGAAACTCTAACATCAC 59.906 50.000 0.00 0.00 0.00 3.06
1523 1577 1.884579 TCTATCACGAAGATACCGGCC 59.115 52.381 0.00 0.00 38.19 6.13
1557 1611 7.042321 TCACGAAACTGAATCTTTGTACGATTT 60.042 33.333 0.00 0.00 31.62 2.17
1591 1645 4.270834 AGAATCAGCGGTCTCACTAACTA 58.729 43.478 0.00 0.00 0.00 2.24
1625 1679 5.222463 ACATCCTAAAAACCATAACCCCACT 60.222 40.000 0.00 0.00 0.00 4.00
1633 1687 5.254267 TCTTCCCCACATCCTAAAAACCATA 59.746 40.000 0.00 0.00 0.00 2.74
1639 1693 5.098663 ACTACTCTTCCCCACATCCTAAAA 58.901 41.667 0.00 0.00 0.00 1.52
1695 1749 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1696 1750 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1697 1751 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
1698 1752 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
1699 1753 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
1700 1754 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
1717 1771 9.436957 GTAGTCCATTTGAAATGTCTAGAAAGA 57.563 33.333 15.93 1.84 0.00 2.52
1718 1772 8.669243 GGTAGTCCATTTGAAATGTCTAGAAAG 58.331 37.037 15.93 0.00 0.00 2.62
1719 1773 7.610305 GGGTAGTCCATTTGAAATGTCTAGAAA 59.390 37.037 15.93 0.00 35.00 2.52
1720 1774 7.037586 AGGGTAGTCCATTTGAAATGTCTAGAA 60.038 37.037 15.93 0.00 38.24 2.10
1721 1775 6.443849 AGGGTAGTCCATTTGAAATGTCTAGA 59.556 38.462 15.93 4.16 38.24 2.43
1722 1776 6.653989 AGGGTAGTCCATTTGAAATGTCTAG 58.346 40.000 15.93 1.90 38.24 2.43
1723 1777 6.636454 AGGGTAGTCCATTTGAAATGTCTA 57.364 37.500 15.93 13.97 38.24 2.59
1724 1778 5.520748 AGGGTAGTCCATTTGAAATGTCT 57.479 39.130 15.93 14.81 38.24 3.41
1725 1779 6.238759 GCATAGGGTAGTCCATTTGAAATGTC 60.239 42.308 15.93 9.10 38.24 3.06
1726 1780 5.594317 GCATAGGGTAGTCCATTTGAAATGT 59.406 40.000 15.93 1.43 38.24 2.71
1727 1781 5.277974 CGCATAGGGTAGTCCATTTGAAATG 60.278 44.000 10.84 10.84 38.24 2.32
1728 1782 4.821805 CGCATAGGGTAGTCCATTTGAAAT 59.178 41.667 0.00 0.00 38.24 2.17
1729 1783 4.196193 CGCATAGGGTAGTCCATTTGAAA 58.804 43.478 0.00 0.00 38.24 2.69
1730 1784 3.433031 CCGCATAGGGTAGTCCATTTGAA 60.433 47.826 0.00 0.00 38.24 2.69
1731 1785 2.104111 CCGCATAGGGTAGTCCATTTGA 59.896 50.000 0.00 0.00 38.24 2.69
1732 1786 2.104111 TCCGCATAGGGTAGTCCATTTG 59.896 50.000 0.00 0.00 41.52 2.32
1733 1787 2.404559 TCCGCATAGGGTAGTCCATTT 58.595 47.619 0.00 0.00 41.52 2.32
1734 1788 2.097110 TCCGCATAGGGTAGTCCATT 57.903 50.000 0.00 0.00 41.52 3.16
1735 1789 1.902508 CATCCGCATAGGGTAGTCCAT 59.097 52.381 0.00 0.00 41.52 3.41
1736 1790 1.338107 CATCCGCATAGGGTAGTCCA 58.662 55.000 0.00 0.00 41.52 4.02
1737 1791 1.339097 ACATCCGCATAGGGTAGTCC 58.661 55.000 0.00 0.00 41.52 3.85
1738 1792 3.510360 ACATACATCCGCATAGGGTAGTC 59.490 47.826 0.00 0.00 41.52 2.59
1739 1793 3.507411 ACATACATCCGCATAGGGTAGT 58.493 45.455 0.00 0.00 41.52 2.73
1740 1794 4.948004 TCTACATACATCCGCATAGGGTAG 59.052 45.833 0.00 0.00 41.52 3.18
1741 1795 4.703575 GTCTACATACATCCGCATAGGGTA 59.296 45.833 0.00 0.00 41.52 3.69
1742 1796 3.510360 GTCTACATACATCCGCATAGGGT 59.490 47.826 0.00 0.00 41.52 4.34
1743 1797 3.509967 TGTCTACATACATCCGCATAGGG 59.490 47.826 0.00 0.00 41.52 3.53
1744 1798 4.783764 TGTCTACATACATCCGCATAGG 57.216 45.455 0.00 0.00 42.97 2.57
1745 1799 8.932945 AAATATGTCTACATACATCCGCATAG 57.067 34.615 4.98 0.00 41.15 2.23
1747 1801 9.371136 CTAAAATATGTCTACATACATCCGCAT 57.629 33.333 4.98 0.00 41.15 4.73
1748 1802 8.581578 TCTAAAATATGTCTACATACATCCGCA 58.418 33.333 4.98 0.00 41.15 5.69
1749 1803 8.981724 TCTAAAATATGTCTACATACATCCGC 57.018 34.615 4.98 0.00 41.15 5.54
1775 1829 6.910433 ACGAAACAAAATGAGTGAATGTACAC 59.090 34.615 0.00 0.00 40.60 2.90
1776 1830 7.022055 ACGAAACAAAATGAGTGAATGTACA 57.978 32.000 0.00 0.00 0.00 2.90
1777 1831 9.051027 CATACGAAACAAAATGAGTGAATGTAC 57.949 33.333 0.00 0.00 0.00 2.90
1778 1832 8.779303 ACATACGAAACAAAATGAGTGAATGTA 58.221 29.630 0.00 0.00 0.00 2.29
1779 1833 7.648142 ACATACGAAACAAAATGAGTGAATGT 58.352 30.769 0.00 0.00 0.00 2.71
1780 1834 9.265938 CTACATACGAAACAAAATGAGTGAATG 57.734 33.333 0.00 0.00 0.00 2.67
1781 1835 8.999431 ACTACATACGAAACAAAATGAGTGAAT 58.001 29.630 0.00 0.00 0.00 2.57
1782 1836 8.373048 ACTACATACGAAACAAAATGAGTGAA 57.627 30.769 0.00 0.00 0.00 3.18
1783 1837 7.654116 TGACTACATACGAAACAAAATGAGTGA 59.346 33.333 0.00 0.00 0.00 3.41
1784 1838 7.740346 GTGACTACATACGAAACAAAATGAGTG 59.260 37.037 0.00 0.00 0.00 3.51
1785 1839 7.656137 AGTGACTACATACGAAACAAAATGAGT 59.344 33.333 0.00 0.00 0.00 3.41
1786 1840 8.018677 AGTGACTACATACGAAACAAAATGAG 57.981 34.615 0.00 0.00 0.00 2.90
1787 1841 7.956420 AGTGACTACATACGAAACAAAATGA 57.044 32.000 0.00 0.00 0.00 2.57
1788 1842 8.067784 ACAAGTGACTACATACGAAACAAAATG 58.932 33.333 0.00 0.00 0.00 2.32
1789 1843 8.149973 ACAAGTGACTACATACGAAACAAAAT 57.850 30.769 0.00 0.00 0.00 1.82
1790 1844 7.542534 ACAAGTGACTACATACGAAACAAAA 57.457 32.000 0.00 0.00 0.00 2.44
1791 1845 7.278203 TCAACAAGTGACTACATACGAAACAAA 59.722 33.333 0.00 0.00 0.00 2.83
1792 1846 6.757478 TCAACAAGTGACTACATACGAAACAA 59.243 34.615 0.00 0.00 0.00 2.83
1793 1847 6.274579 TCAACAAGTGACTACATACGAAACA 58.725 36.000 0.00 0.00 0.00 2.83
1794 1848 6.758593 TCAACAAGTGACTACATACGAAAC 57.241 37.500 0.00 0.00 0.00 2.78
1795 1849 7.278203 TGTTTCAACAAGTGACTACATACGAAA 59.722 33.333 0.00 0.00 35.39 3.46
1796 1850 6.757478 TGTTTCAACAAGTGACTACATACGAA 59.243 34.615 0.00 0.00 35.39 3.85
1797 1851 6.274579 TGTTTCAACAAGTGACTACATACGA 58.725 36.000 0.00 0.00 35.39 3.43
1798 1852 6.519353 TGTTTCAACAAGTGACTACATACG 57.481 37.500 0.00 0.00 35.39 3.06
1799 1853 8.311650 AGATGTTTCAACAAGTGACTACATAC 57.688 34.615 0.00 0.00 43.03 2.39
1800 1854 9.639601 CTAGATGTTTCAACAAGTGACTACATA 57.360 33.333 0.00 0.00 43.03 2.29
1801 1855 8.367911 TCTAGATGTTTCAACAAGTGACTACAT 58.632 33.333 0.00 0.00 43.03 2.29
1802 1856 7.722363 TCTAGATGTTTCAACAAGTGACTACA 58.278 34.615 0.00 0.00 43.03 2.74
1803 1857 8.589335 TTCTAGATGTTTCAACAAGTGACTAC 57.411 34.615 0.00 0.00 43.03 2.73
1804 1858 9.261180 CTTTCTAGATGTTTCAACAAGTGACTA 57.739 33.333 0.00 0.00 43.03 2.59
1805 1859 7.987458 TCTTTCTAGATGTTTCAACAAGTGACT 59.013 33.333 0.00 0.00 43.03 3.41
1806 1860 8.064814 GTCTTTCTAGATGTTTCAACAAGTGAC 58.935 37.037 0.00 0.00 43.03 3.67
1807 1861 7.768582 TGTCTTTCTAGATGTTTCAACAAGTGA 59.231 33.333 0.00 0.00 43.03 3.41
1808 1862 7.919690 TGTCTTTCTAGATGTTTCAACAAGTG 58.080 34.615 0.00 0.00 43.03 3.16
1809 1863 8.506168 TTGTCTTTCTAGATGTTTCAACAAGT 57.494 30.769 0.00 0.00 43.03 3.16
1810 1864 9.956720 ATTTGTCTTTCTAGATGTTTCAACAAG 57.043 29.630 0.00 0.00 43.03 3.16
1825 1879 8.947115 CCTCCGTTTCTAAATATTTGTCTTTCT 58.053 33.333 11.05 0.00 0.00 2.52
1826 1880 8.182227 CCCTCCGTTTCTAAATATTTGTCTTTC 58.818 37.037 11.05 0.00 0.00 2.62
1827 1881 7.886446 TCCCTCCGTTTCTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
1828 1882 7.399634 TCCCTCCGTTTCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
1829 1883 6.954232 TCCCTCCGTTTCTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
1830 1884 6.822170 ACTCCCTCCGTTTCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
1831 1885 6.718294 ACTCCCTCCGTTTCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
1832 1886 7.226128 GGTACTCCCTCCGTTTCTAAATATTTG 59.774 40.741 11.05 1.65 0.00 2.32
1833 1887 7.092757 TGGTACTCCCTCCGTTTCTAAATATTT 60.093 37.037 5.89 5.89 0.00 1.40
1834 1888 6.384886 TGGTACTCCCTCCGTTTCTAAATATT 59.615 38.462 0.00 0.00 0.00 1.28
1835 1889 5.901276 TGGTACTCCCTCCGTTTCTAAATAT 59.099 40.000 0.00 0.00 0.00 1.28
1836 1890 5.127682 GTGGTACTCCCTCCGTTTCTAAATA 59.872 44.000 0.00 0.00 0.00 1.40
1837 1891 4.081254 GTGGTACTCCCTCCGTTTCTAAAT 60.081 45.833 0.00 0.00 0.00 1.40
1838 1892 3.259123 GTGGTACTCCCTCCGTTTCTAAA 59.741 47.826 0.00 0.00 0.00 1.85
1839 1893 2.827921 GTGGTACTCCCTCCGTTTCTAA 59.172 50.000 0.00 0.00 0.00 2.10
1840 1894 2.042162 AGTGGTACTCCCTCCGTTTCTA 59.958 50.000 0.00 0.00 0.00 2.10
1841 1895 1.203149 AGTGGTACTCCCTCCGTTTCT 60.203 52.381 0.00 0.00 0.00 2.52
1842 1896 1.067071 CAGTGGTACTCCCTCCGTTTC 60.067 57.143 0.00 0.00 0.00 2.78
1843 1897 0.974383 CAGTGGTACTCCCTCCGTTT 59.026 55.000 0.00 0.00 0.00 3.60
1844 1898 0.113776 TCAGTGGTACTCCCTCCGTT 59.886 55.000 0.00 0.00 0.00 4.44
1845 1899 0.335361 ATCAGTGGTACTCCCTCCGT 59.665 55.000 0.00 0.00 0.00 4.69
1846 1900 0.747255 CATCAGTGGTACTCCCTCCG 59.253 60.000 0.00 0.00 0.00 4.63
1847 1901 1.123928 CCATCAGTGGTACTCCCTCC 58.876 60.000 0.00 0.00 40.83 4.30
1848 1902 2.035632 CTCCATCAGTGGTACTCCCTC 58.964 57.143 0.00 0.00 46.16 4.30
1849 1903 1.362932 ACTCCATCAGTGGTACTCCCT 59.637 52.381 0.00 0.00 46.16 4.20
1850 1904 1.867363 ACTCCATCAGTGGTACTCCC 58.133 55.000 0.00 0.00 46.16 4.30
1863 1917 3.627577 GGCATCGTTAATTGTCACTCCAT 59.372 43.478 0.00 0.00 0.00 3.41
1955 2023 8.340618 ACCATGCATAAATATAGCAAACCTAG 57.659 34.615 0.00 0.00 42.15 3.02
1956 2024 9.973661 ATACCATGCATAAATATAGCAAACCTA 57.026 29.630 0.00 0.00 42.15 3.08
1957 2025 8.742777 CATACCATGCATAAATATAGCAAACCT 58.257 33.333 0.00 0.00 42.15 3.50
1984 2052 1.740025 GTCAAGCTGTCTGCCCATTAC 59.260 52.381 0.00 0.00 44.23 1.89
2371 2441 2.806244 CCAGGACAACTTCGTAAAGTGG 59.194 50.000 0.00 0.00 45.07 4.00
2748 2830 3.009723 ACAAAGAGCATACATCAACCGG 58.990 45.455 0.00 0.00 0.00 5.28
2874 2959 1.189524 TCCAAGTCGGGTTCGGACAT 61.190 55.000 0.00 0.00 36.95 3.06
2890 2975 0.895530 GAGTCAGACACCCGAATCCA 59.104 55.000 2.66 0.00 0.00 3.41
2950 3057 8.857694 TCACTATCAGATATTATACACGTCCA 57.142 34.615 0.00 0.00 0.00 4.02
3004 3111 2.165845 GCAGTTCTACACGGACACCTAT 59.834 50.000 0.00 0.00 0.00 2.57
3047 3154 1.845266 CAGACACAGCTACGCCATAG 58.155 55.000 0.00 0.00 0.00 2.23
3050 3157 2.048222 GCAGACACAGCTACGCCA 60.048 61.111 0.00 0.00 0.00 5.69
3530 3641 7.725251 TCAGCTGAAAAGTACCAAAATCAAAT 58.275 30.769 15.67 0.00 0.00 2.32
3649 3760 6.387192 TTGGAATCCTTAGATGGTTTCTCA 57.613 37.500 0.00 0.00 36.54 3.27
3838 3955 2.507944 CTAGCGGCAGCCTCCATT 59.492 61.111 10.54 0.00 46.67 3.16
3954 4071 0.676466 AATGGATCCAACAAGCGCGA 60.676 50.000 20.67 0.00 0.00 5.87
4020 4137 6.710295 TGTTAAGTAATCTGAAGCAAGCAGAA 59.290 34.615 7.17 0.00 44.71 3.02
4330 4447 4.815040 CGTCTACGTACCAGATGAGAAT 57.185 45.455 0.50 0.00 31.81 2.40
4368 4485 6.340522 ACCAAATGATAAGGCATAAAAGCAC 58.659 36.000 0.00 0.00 35.83 4.40
4794 5648 5.815740 TCGAAAGTTTGTAGCAAAGTTCTCT 59.184 36.000 13.05 1.35 0.00 3.10
4922 5776 8.899776 GGATGTATATAGACACGTTTAAGTTCG 58.100 37.037 1.52 0.00 30.52 3.95
4925 5779 8.072567 GTCGGATGTATATAGACACGTTTAAGT 58.927 37.037 1.52 0.00 30.52 2.24
4926 5780 8.288208 AGTCGGATGTATATAGACACGTTTAAG 58.712 37.037 1.52 0.00 34.56 1.85
4927 5781 8.158169 AGTCGGATGTATATAGACACGTTTAA 57.842 34.615 1.52 0.00 34.56 1.52
4928 5782 7.442062 TGAGTCGGATGTATATAGACACGTTTA 59.558 37.037 1.52 0.00 34.56 2.01
5006 5875 1.200716 GGTGGCATGTGTGAATGTGAG 59.799 52.381 0.00 0.00 0.00 3.51
5101 5970 0.099968 CGAACTTACGATCCGCCAGA 59.900 55.000 0.00 0.00 35.09 3.86
5110 5979 2.746904 TCCGATGGTTACGAACTTACGA 59.253 45.455 0.00 0.00 37.03 3.43
5111 5980 3.135414 TCCGATGGTTACGAACTTACG 57.865 47.619 0.00 0.00 39.31 3.18
5112 5981 3.244579 GCATCCGATGGTTACGAACTTAC 59.755 47.826 10.41 0.00 0.00 2.34
5113 5982 3.450578 GCATCCGATGGTTACGAACTTA 58.549 45.455 10.41 0.00 0.00 2.24
5114 5983 2.277084 GCATCCGATGGTTACGAACTT 58.723 47.619 10.41 0.00 0.00 2.66
5115 5984 1.472728 GGCATCCGATGGTTACGAACT 60.473 52.381 10.41 0.00 0.00 3.01
5116 5985 0.935196 GGCATCCGATGGTTACGAAC 59.065 55.000 10.41 0.00 0.00 3.95
5117 5986 0.179067 GGGCATCCGATGGTTACGAA 60.179 55.000 10.41 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.