Multiple sequence alignment - TraesCS6B01G399200

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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 TraesCS6B01G399200 chr6B 100.000 2342 0 0 1 2342 674841555 674843896 0.000000e+00 4325.0
1 TraesCS6B01G399200 chr6B 92.900 831 54 3 399 1225 674927355 674928184 0.000000e+00 1203.0
2 TraesCS6B01G399200 chr6B 88.517 209 20 3 10 214 674926684 674926892 1.390000e-62 250.0
3 TraesCS6B01G399200 chr6B 87.736 106 7 3 305 405 674927164 674927268 4.090000e-23 119.0
4 TraesCS6B01G399200 chr6B 84.314 102 10 5 1928 2027 674925662 674925759 6.890000e-16 95.3
5 TraesCS6B01G399200 chrUn 91.989 1448 85 13 305 1736 79273132 79274564 0.000000e+00 2002.0
6 TraesCS6B01G399200 chrUn 91.920 1448 85 14 305 1735 79304796 79306228 0.000000e+00 1997.0
7 TraesCS6B01G399200 chrUn 91.731 1415 89 13 399 1800 79246569 79247968 0.000000e+00 1940.0
8 TraesCS6B01G399200 chrUn 90.051 583 35 10 1227 1800 79240016 79240584 0.000000e+00 734.0
9 TraesCS6B01G399200 chrUn 89.545 220 16 6 1 214 79304289 79304507 2.970000e-69 272.0
10 TraesCS6B01G399200 chrUn 89.091 220 17 6 1 214 79272625 79272843 1.380000e-67 267.0
11 TraesCS6B01G399200 chrUn 88.517 209 20 3 10 214 79245898 79246106 1.390000e-62 250.0
12 TraesCS6B01G399200 chrUn 95.192 104 5 0 1 104 479190465 479190568 5.180000e-37 165.0
13 TraesCS6B01G399200 chrUn 87.736 106 7 3 305 405 79246378 79246482 4.090000e-23 119.0
14 TraesCS6B01G399200 chrUn 84.314 102 10 5 1928 2027 79244876 79244973 6.890000e-16 95.3
15 TraesCS6B01G399200 chrUn 82.353 102 12 5 1928 2027 79315705 79315802 1.490000e-12 84.2
16 TraesCS6B01G399200 chr6D 91.088 1369 86 14 305 1647 446476530 446477888 0.000000e+00 1820.0
17 TraesCS6B01G399200 chr6D 92.437 119 3 4 1 114 446463245 446463362 5.180000e-37 165.0
18 TraesCS6B01G399200 chr6D 91.304 115 9 1 1937 2051 446478017 446478130 3.120000e-34 156.0
19 TraesCS6B01G399200 chr6D 93.750 48 3 0 2089 2136 446478119 446478166 3.230000e-09 73.1
20 TraesCS6B01G399200 chr6A 90.639 1378 87 18 305 1647 593234725 593236095 0.000000e+00 1792.0
21 TraesCS6B01G399200 chr6A 89.718 1381 90 22 305 1647 593283921 593285287 0.000000e+00 1716.0
22 TraesCS6B01G399200 chr6A 92.256 1033 58 11 797 1826 593237253 593238266 0.000000e+00 1445.0
23 TraesCS6B01G399200 chr6A 84.948 671 77 16 510 1165 593297060 593297721 0.000000e+00 658.0
24 TraesCS6B01G399200 chr6A 83.284 682 86 13 494 1157 593299588 593300259 9.260000e-169 603.0
25 TraesCS6B01G399200 chr6A 86.444 568 47 11 237 799 593236588 593237130 1.550000e-166 595.0
26 TraesCS6B01G399200 chr6A 81.686 688 90 16 494 1165 593278127 593278794 7.360000e-150 540.0
27 TraesCS6B01G399200 chr6A 94.488 127 7 0 1924 2050 593238620 593238746 1.840000e-46 196.0
28 TraesCS6B01G399200 chr6A 90.984 122 11 0 2089 2210 593285511 593285632 5.180000e-37 165.0
29 TraesCS6B01G399200 chr6A 92.174 115 9 0 1937 2051 593285408 593285522 1.860000e-36 163.0
30 TraesCS6B01G399200 chr6A 79.668 241 19 8 2089 2323 593238736 593238952 1.880000e-31 147.0
31 TraesCS6B01G399200 chr6A 89.565 115 11 1 1937 2051 593236218 593236331 6.750000e-31 145.0
32 TraesCS6B01G399200 chr6A 93.684 95 6 0 2089 2183 593236320 593236414 2.430000e-30 143.0
33 TraesCS6B01G399200 chr6A 86.538 104 10 2 1915 2017 593234197 593234297 6.840000e-21 111.0
34 TraesCS6B01G399200 chr6A 95.000 60 3 0 10 69 593283651 593283710 6.890000e-16 95.3
35 TraesCS6B01G399200 chr6A 89.333 75 7 1 1925 1998 593301384 593301458 2.480000e-15 93.5
36 TraesCS6B01G399200 chr6A 88.571 70 6 1 112 179 593283707 593283776 1.490000e-12 84.2
37 TraesCS6B01G399200 chr6A 90.476 63 5 1 118 179 593234519 593234581 5.360000e-12 82.4
38 TraesCS6B01G399200 chr5D 86.154 65 9 0 1702 1766 289035895 289035831 1.160000e-08 71.3
39 TraesCS6B01G399200 chr2B 85.000 60 4 4 1682 1739 754980145 754980201 3.250000e-04 56.5


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 TraesCS6B01G399200 chr6B 674841555 674843896 2341 False 4325.000000 4325 100.000000 1 2342 1 chr6B.!!$F1 2341
1 TraesCS6B01G399200 chr6B 674925662 674928184 2522 False 416.825000 1203 88.366750 10 2027 4 chr6B.!!$F2 2017
2 TraesCS6B01G399200 chrUn 79272625 79274564 1939 False 1134.500000 2002 90.540000 1 1736 2 chrUn.!!$F5 1735
3 TraesCS6B01G399200 chrUn 79304289 79306228 1939 False 1134.500000 1997 90.732500 1 1735 2 chrUn.!!$F6 1734
4 TraesCS6B01G399200 chrUn 79240016 79240584 568 False 734.000000 734 90.051000 1227 1800 1 chrUn.!!$F1 573
5 TraesCS6B01G399200 chrUn 79244876 79247968 3092 False 601.075000 1940 88.074500 10 2027 4 chrUn.!!$F4 2017
6 TraesCS6B01G399200 chr6D 446476530 446478166 1636 False 683.033333 1820 92.047333 305 2136 3 chr6D.!!$F2 1831
7 TraesCS6B01G399200 chr6A 593278127 593278794 667 False 540.000000 540 81.686000 494 1165 1 chr6A.!!$F1 671
8 TraesCS6B01G399200 chr6A 593234197 593238952 4755 False 517.377778 1792 89.306444 118 2323 9 chr6A.!!$F2 2205
9 TraesCS6B01G399200 chr6A 593297060 593301458 4398 False 451.500000 658 85.855000 494 1998 3 chr6A.!!$F4 1504
10 TraesCS6B01G399200 chr6A 593283651 593285632 1981 False 444.700000 1716 91.289400 10 2210 5 chr6A.!!$F3 2200

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
972 4954 1.898472 CCCTCTTCTGAGCTGAAGACA 59.102 52.381 11.44 0.0 45.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 8843 0.253327 ATTTCTTCGGCCTCACCCTC 59.747 55.0 0.0 0.0 33.26 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
31 32 8.443953 AACTAGATGATTGATTGAGCTTAACC 57.556 34.615 0.00 0.00 0.00 2.85
33 34 6.690194 AGATGATTGATTGAGCTTAACCAC 57.310 37.500 0.00 0.00 0.00 4.16
34 35 5.591877 AGATGATTGATTGAGCTTAACCACC 59.408 40.000 0.00 0.00 0.00 4.61
35 36 4.922206 TGATTGATTGAGCTTAACCACCT 58.078 39.130 0.00 0.00 0.00 4.00
36 37 5.324409 TGATTGATTGAGCTTAACCACCTT 58.676 37.500 0.00 0.00 0.00 3.50
41 42 2.660572 TGAGCTTAACCACCTTTTGCA 58.339 42.857 0.00 0.00 0.00 4.08
42 43 3.027412 TGAGCTTAACCACCTTTTGCAA 58.973 40.909 0.00 0.00 0.00 4.08
61 62 3.366374 GCAAGGCAAGGATAAGTGTTGTC 60.366 47.826 0.00 0.00 0.00 3.18
62 63 3.788227 AGGCAAGGATAAGTGTTGTCA 57.212 42.857 0.00 0.00 0.00 3.58
63 64 3.412386 AGGCAAGGATAAGTGTTGTCAC 58.588 45.455 0.00 0.00 44.15 3.67
77 78 6.539649 GTGTTGTCACTAAAGAATGCAGTA 57.460 37.500 0.00 0.00 40.98 2.74
78 79 6.363473 GTGTTGTCACTAAAGAATGCAGTAC 58.637 40.000 0.00 0.00 40.98 2.73
80 81 6.710295 TGTTGTCACTAAAGAATGCAGTACAT 59.290 34.615 0.00 0.00 42.30 2.29
81 82 6.726258 TGTCACTAAAGAATGCAGTACATG 57.274 37.500 0.00 0.00 39.60 3.21
82 83 6.463360 TGTCACTAAAGAATGCAGTACATGA 58.537 36.000 0.00 0.00 39.60 3.07
83 84 6.368791 TGTCACTAAAGAATGCAGTACATGAC 59.631 38.462 0.00 0.00 39.60 3.06
86 87 5.932303 ACTAAAGAATGCAGTACATGACGTT 59.068 36.000 0.00 0.00 39.60 3.99
88 89 4.193826 AGAATGCAGTACATGACGTTCT 57.806 40.909 0.00 3.24 39.60 3.01
90 91 3.592898 ATGCAGTACATGACGTTCTCA 57.407 42.857 0.00 0.00 37.70 3.27
91 92 3.378911 TGCAGTACATGACGTTCTCAA 57.621 42.857 0.00 0.00 30.60 3.02
93 94 3.005367 TGCAGTACATGACGTTCTCAAGA 59.995 43.478 0.00 0.00 30.60 3.02
94 95 4.177026 GCAGTACATGACGTTCTCAAGAT 58.823 43.478 0.00 0.00 30.60 2.40
95 96 5.105917 TGCAGTACATGACGTTCTCAAGATA 60.106 40.000 0.00 0.00 30.60 1.98
97 98 6.556212 CAGTACATGACGTTCTCAAGATAGT 58.444 40.000 0.00 0.00 30.60 2.12
98 99 7.030165 CAGTACATGACGTTCTCAAGATAGTT 58.970 38.462 0.00 0.00 30.60 2.24
99 100 8.182227 CAGTACATGACGTTCTCAAGATAGTTA 58.818 37.037 0.00 0.00 30.60 2.24
100 101 8.737175 AGTACATGACGTTCTCAAGATAGTTAA 58.263 33.333 0.00 0.00 30.60 2.01
103 104 8.035394 ACATGACGTTCTCAAGATAGTTAATGT 58.965 33.333 0.00 9.36 30.60 2.71
105 106 7.375834 TGACGTTCTCAAGATAGTTAATGTGT 58.624 34.615 0.00 0.00 0.00 3.72
106 107 7.328493 TGACGTTCTCAAGATAGTTAATGTGTG 59.672 37.037 0.00 0.00 0.00 3.82
107 108 7.152645 ACGTTCTCAAGATAGTTAATGTGTGT 58.847 34.615 0.00 0.00 0.00 3.72
109 110 8.799091 CGTTCTCAAGATAGTTAATGTGTGTAG 58.201 37.037 0.00 0.00 0.00 2.74
111 112 8.589701 TCTCAAGATAGTTAATGTGTGTAGGA 57.410 34.615 0.00 0.00 0.00 2.94
113 114 9.653287 CTCAAGATAGTTAATGTGTGTAGGAAA 57.347 33.333 0.00 0.00 0.00 3.13
114 115 9.653287 TCAAGATAGTTAATGTGTGTAGGAAAG 57.347 33.333 0.00 0.00 0.00 2.62
115 116 8.883731 CAAGATAGTTAATGTGTGTAGGAAAGG 58.116 37.037 0.00 0.00 0.00 3.11
116 117 8.147244 AGATAGTTAATGTGTGTAGGAAAGGT 57.853 34.615 0.00 0.00 0.00 3.50
117 118 9.263446 AGATAGTTAATGTGTGTAGGAAAGGTA 57.737 33.333 0.00 0.00 0.00 3.08
118 119 9.530633 GATAGTTAATGTGTGTAGGAAAGGTAG 57.469 37.037 0.00 0.00 0.00 3.18
119 120 7.549147 AGTTAATGTGTGTAGGAAAGGTAGA 57.451 36.000 0.00 0.00 0.00 2.59
120 121 7.612677 AGTTAATGTGTGTAGGAAAGGTAGAG 58.387 38.462 0.00 0.00 0.00 2.43
121 122 7.453752 AGTTAATGTGTGTAGGAAAGGTAGAGA 59.546 37.037 0.00 0.00 0.00 3.10
122 123 5.923733 ATGTGTGTAGGAAAGGTAGAGAG 57.076 43.478 0.00 0.00 0.00 3.20
124 125 5.010933 TGTGTGTAGGAAAGGTAGAGAGAG 58.989 45.833 0.00 0.00 0.00 3.20
125 126 5.011586 GTGTGTAGGAAAGGTAGAGAGAGT 58.988 45.833 0.00 0.00 0.00 3.24
127 128 4.333372 GTGTAGGAAAGGTAGAGAGAGTCG 59.667 50.000 0.00 0.00 0.00 4.18
128 129 4.224594 TGTAGGAAAGGTAGAGAGAGTCGA 59.775 45.833 0.00 0.00 0.00 4.20
129 130 3.613030 AGGAAAGGTAGAGAGAGTCGAC 58.387 50.000 7.70 7.70 0.00 4.20
132 1216 4.379708 GGAAAGGTAGAGAGAGTCGACAAC 60.380 50.000 19.50 11.35 32.61 3.32
180 1264 5.948992 AGCATGGTAGTGTTCTTTTTCTC 57.051 39.130 0.00 0.00 0.00 2.87
189 1273 4.079730 AGTGTTCTTTTTCTCAAGACCCCT 60.080 41.667 0.00 0.00 32.28 4.79
190 1274 4.645136 GTGTTCTTTTTCTCAAGACCCCTT 59.355 41.667 0.00 0.00 32.28 3.95
195 1283 2.723530 TTCTCAAGACCCCTTCCTCT 57.276 50.000 0.00 0.00 0.00 3.69
208 1296 3.055021 CCCTTCCTCTCCTGGTTCTTAAC 60.055 52.174 0.00 0.00 0.00 2.01
231 1477 8.539117 AACCATTAATTAGAAAGCAGGCTAAT 57.461 30.769 0.00 0.00 38.57 1.73
252 1498 4.835284 TGTGGTACTCCAATATTCAGCA 57.165 40.909 0.00 0.00 46.15 4.41
322 1621 9.162764 GCTCTCTGGTATATTTAGTTCAAACAA 57.837 33.333 0.00 0.00 0.00 2.83
346 1646 6.831976 AGACCTATATGATCACCAGGAAAAC 58.168 40.000 20.52 11.28 0.00 2.43
348 1648 7.072961 AGACCTATATGATCACCAGGAAAACAT 59.927 37.037 20.52 2.86 0.00 2.71
462 1858 2.824341 GTCTGTTCTCTTCTCCCCGTAA 59.176 50.000 0.00 0.00 0.00 3.18
477 1881 2.412089 CCCGTAAACGCTTTCAGAAGAG 59.588 50.000 0.00 0.00 38.48 2.85
539 1943 3.175710 ACCGGCACCCAACCTTCT 61.176 61.111 0.00 0.00 0.00 2.85
699 4651 3.380142 CCCAACTTTTGTGGAAACATCG 58.620 45.455 0.00 0.00 46.14 3.84
760 4722 3.255725 TCGAGTTAATTAGTTGCCGTGG 58.744 45.455 0.00 0.00 0.00 4.94
972 4954 1.898472 CCCTCTTCTGAGCTGAAGACA 59.102 52.381 11.44 0.00 45.00 3.41
1047 5032 3.935828 GGAGTTGCAGTTCCAGATACTTC 59.064 47.826 12.32 0.00 33.55 3.01
1147 5132 2.271497 GGGCATCACTCAGCAGCT 59.729 61.111 0.00 0.00 0.00 4.24
1168 5245 1.210155 GGTGGCAACTCAATGTCGC 59.790 57.895 0.00 0.00 34.74 5.19
1191 5268 2.791383 TGCAGAAAACAATTGGGACG 57.209 45.000 10.83 0.00 0.00 4.79
1196 5273 4.236935 CAGAAAACAATTGGGACGAATGG 58.763 43.478 10.83 0.00 0.00 3.16
1197 5274 3.895041 AGAAAACAATTGGGACGAATGGT 59.105 39.130 10.83 0.00 0.00 3.55
1199 5276 4.776795 AAACAATTGGGACGAATGGTAC 57.223 40.909 10.83 0.00 0.00 3.34
1216 5302 4.598894 CCGAGGGATCTGCTGGCG 62.599 72.222 0.00 0.00 0.00 5.69
1325 5411 2.832129 ACTACGGTCCAAGTGATCACAT 59.168 45.455 27.02 13.54 0.00 3.21
1477 7586 6.540551 TGTAAAACTCATGTAAGCTCACACAA 59.459 34.615 0.00 0.00 0.00 3.33
1494 7603 3.281158 CACAATGGGCACATGACATAGA 58.719 45.455 0.00 0.00 37.40 1.98
1567 7679 1.473965 GCCTGCCTCTTGATCGATCAA 60.474 52.381 32.71 32.71 43.94 2.57
1653 7779 5.867903 AGAACCACCAATTTGTTTGATCA 57.132 34.783 0.00 0.00 37.53 2.92
1654 7780 5.846203 AGAACCACCAATTTGTTTGATCAG 58.154 37.500 0.00 0.00 37.53 2.90
1655 7781 5.598005 AGAACCACCAATTTGTTTGATCAGA 59.402 36.000 0.00 0.00 37.53 3.27
1656 7782 5.867903 ACCACCAATTTGTTTGATCAGAA 57.132 34.783 0.00 0.00 37.53 3.02
1657 7783 5.846203 ACCACCAATTTGTTTGATCAGAAG 58.154 37.500 0.00 0.00 37.53 2.85
1658 7784 5.598005 ACCACCAATTTGTTTGATCAGAAGA 59.402 36.000 0.00 0.00 37.53 2.87
1659 7785 5.922544 CCACCAATTTGTTTGATCAGAAGAC 59.077 40.000 0.00 0.00 37.53 3.01
1660 7786 6.239120 CCACCAATTTGTTTGATCAGAAGACT 60.239 38.462 0.00 0.00 37.53 3.24
1756 7887 3.261580 CAAACATGATGAGCGACACCTA 58.738 45.455 0.00 0.00 0.00 3.08
1826 7958 2.490115 CGTAGTTGCAAGACTCTCCTCT 59.510 50.000 0.00 0.00 0.00 3.69
1834 7966 1.502690 AGACTCTCCTCTCGCCTAGA 58.497 55.000 0.00 0.00 0.00 2.43
1845 7977 2.902705 TCGCCTAGAGAGAGAGAGAC 57.097 55.000 0.00 0.00 0.00 3.36
1863 8312 4.648762 AGAGACAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
1864 8313 4.614475 AGACAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
1865 8314 4.648762 AGACAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
1866 8315 4.614475 ACAGAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
1867 8316 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
1868 8317 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
1869 8318 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
1870 8319 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1871 8320 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1872 8321 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1873 8322 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1874 8323 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1875 8324 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1876 8325 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1877 8326 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1878 8327 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1879 8328 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1880 8329 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1881 8330 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1882 8331 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1883 8332 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1884 8333 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1885 8334 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1886 8335 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1887 8336 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1888 8337 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1889 8338 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1890 8339 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1891 8340 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1892 8341 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1893 8342 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1894 8343 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1895 8344 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1896 8345 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1897 8346 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1904 8353 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
1910 8359 4.326826 AGAGAGAGAGAGAGAGTGTTGTG 58.673 47.826 0.00 0.00 0.00 3.33
1912 8361 3.073798 AGAGAGAGAGAGAGTGTTGTGGA 59.926 47.826 0.00 0.00 0.00 4.02
1913 8362 3.153919 AGAGAGAGAGAGTGTTGTGGAC 58.846 50.000 0.00 0.00 0.00 4.02
1914 8363 3.153919 GAGAGAGAGAGTGTTGTGGACT 58.846 50.000 0.00 0.00 0.00 3.85
1915 8364 3.153919 AGAGAGAGAGTGTTGTGGACTC 58.846 50.000 0.00 0.00 40.25 3.36
1916 8365 1.883275 AGAGAGAGTGTTGTGGACTCG 59.117 52.381 0.00 0.00 43.95 4.18
1918 8367 0.959553 GAGAGTGTTGTGGACTCGGA 59.040 55.000 0.00 0.00 43.95 4.55
1919 8368 0.674534 AGAGTGTTGTGGACTCGGAC 59.325 55.000 0.00 0.00 43.95 4.79
1920 8369 0.319641 GAGTGTTGTGGACTCGGACC 60.320 60.000 0.00 0.00 31.01 4.46
1921 8370 1.301479 GTGTTGTGGACTCGGACCC 60.301 63.158 0.00 0.00 0.00 4.46
1922 8371 2.346365 GTTGTGGACTCGGACCCC 59.654 66.667 0.00 0.00 0.00 4.95
1923 8372 2.122769 TTGTGGACTCGGACCCCA 60.123 61.111 0.00 0.00 0.00 4.96
1979 8526 1.393487 ATGCTGCAGTGTTGTTGGCA 61.393 50.000 16.64 4.61 32.94 4.92
1988 8536 1.476488 GTGTTGTTGGCAAAGGACTGT 59.524 47.619 0.00 0.00 36.22 3.55
2034 8582 2.290323 ACGGCTCACTAAAGCATTTCCT 60.290 45.455 0.00 0.00 44.35 3.36
2037 8585 5.163343 ACGGCTCACTAAAGCATTTCCTATA 60.163 40.000 0.00 0.00 44.35 1.31
2039 8587 5.470437 GGCTCACTAAAGCATTTCCTATACC 59.530 44.000 0.00 0.00 44.35 2.73
2051 8599 8.705594 AGCATTTCCTATACCGCATAGTATATT 58.294 33.333 0.00 0.00 35.26 1.28
2052 8600 9.326413 GCATTTCCTATACCGCATAGTATATTT 57.674 33.333 0.00 0.00 35.26 1.40
2081 8629 9.194972 TGACAAATGGTATATTTTATTGGCTCA 57.805 29.630 0.00 0.00 0.00 4.26
2088 8636 8.986991 TGGTATATTTTATTGGCTCAAAATGGT 58.013 29.630 11.77 6.01 35.64 3.55
2089 8637 9.260002 GGTATATTTTATTGGCTCAAAATGGTG 57.740 33.333 11.77 0.00 35.64 4.17
2090 8638 7.790823 ATATTTTATTGGCTCAAAATGGTGC 57.209 32.000 11.77 0.00 35.64 5.01
2091 8639 4.613925 TTTATTGGCTCAAAATGGTGCA 57.386 36.364 0.00 0.00 0.00 4.57
2092 8640 4.822685 TTATTGGCTCAAAATGGTGCAT 57.177 36.364 0.00 0.00 0.00 3.96
2093 8641 5.929058 TTATTGGCTCAAAATGGTGCATA 57.071 34.783 0.00 0.00 0.00 3.14
2094 8642 4.822685 ATTGGCTCAAAATGGTGCATAA 57.177 36.364 0.00 0.00 0.00 1.90
2095 8643 4.822685 TTGGCTCAAAATGGTGCATAAT 57.177 36.364 0.00 0.00 0.00 1.28
2096 8644 5.929058 TTGGCTCAAAATGGTGCATAATA 57.071 34.783 0.00 0.00 0.00 0.98
2097 8645 6.482898 TTGGCTCAAAATGGTGCATAATAT 57.517 33.333 0.00 0.00 0.00 1.28
2098 8646 5.845103 TGGCTCAAAATGGTGCATAATATG 58.155 37.500 0.00 0.00 0.00 1.78
2099 8647 5.363292 TGGCTCAAAATGGTGCATAATATGT 59.637 36.000 1.92 0.00 0.00 2.29
2136 8684 5.583457 TCTCACACATGCTCAATGATAACTG 59.417 40.000 0.00 0.00 38.72 3.16
2155 8703 2.374504 CTGGATGATTGATGGGGCTAGT 59.625 50.000 0.00 0.00 0.00 2.57
2192 8740 7.118723 TGGAAGGCAAAGATAAGTGATGTAAT 58.881 34.615 0.00 0.00 0.00 1.89
2213 8761 8.673711 TGTAATTAAAGAATGCAGTACATCACC 58.326 33.333 0.00 0.00 38.34 4.02
2214 8762 7.944729 AATTAAAGAATGCAGTACATCACCT 57.055 32.000 0.00 0.00 38.34 4.00
2215 8763 6.741992 TTAAAGAATGCAGTACATCACCTG 57.258 37.500 0.00 0.00 38.34 4.00
2216 8764 2.636830 AGAATGCAGTACATCACCTGC 58.363 47.619 4.75 4.75 38.34 4.85
2221 8769 3.641437 GCAGTACATCACCTGCAAAAA 57.359 42.857 6.75 0.00 41.89 1.94
2248 8796 9.778741 AAAACAGTACATGACTTTCTCAAGATA 57.221 29.630 0.00 0.00 35.64 1.98
2249 8797 8.994429 AACAGTACATGACTTTCTCAAGATAG 57.006 34.615 0.00 0.00 35.64 2.08
2259 8807 8.097038 TGACTTTCTCAAGATAGCAGTTTGTAT 58.903 33.333 0.00 0.00 33.72 2.29
2294 8843 2.683362 GGAGTTAAAGAGGAAATGGCGG 59.317 50.000 0.00 0.00 0.00 6.13
2299 8853 1.208165 AAGAGGAAATGGCGGAGGGT 61.208 55.000 0.00 0.00 0.00 4.34
2304 8858 3.645268 AAATGGCGGAGGGTGAGGC 62.645 63.158 0.00 0.00 0.00 4.70
2314 8868 0.698818 AGGGTGAGGCCGAAGAAATT 59.301 50.000 0.00 0.00 38.44 1.82
2323 8877 2.262211 GCCGAAGAAATTGGTTCATGC 58.738 47.619 0.00 0.49 38.86 4.06
2324 8878 2.352617 GCCGAAGAAATTGGTTCATGCA 60.353 45.455 0.00 0.00 38.86 3.96
2325 8879 3.676873 GCCGAAGAAATTGGTTCATGCAT 60.677 43.478 0.00 0.00 38.86 3.96
2326 8880 4.439974 GCCGAAGAAATTGGTTCATGCATA 60.440 41.667 0.00 0.00 38.86 3.14
2327 8881 5.649557 CCGAAGAAATTGGTTCATGCATAA 58.350 37.500 0.00 0.00 38.86 1.90
2328 8882 6.275335 CCGAAGAAATTGGTTCATGCATAAT 58.725 36.000 0.00 0.00 38.86 1.28
2329 8883 6.757947 CCGAAGAAATTGGTTCATGCATAATT 59.242 34.615 0.00 0.00 38.86 1.40
2330 8884 7.278424 CCGAAGAAATTGGTTCATGCATAATTT 59.722 33.333 14.15 14.15 38.86 1.82
2331 8885 8.658609 CGAAGAAATTGGTTCATGCATAATTTT 58.341 29.630 15.01 4.37 38.86 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.591877 GGTGGTTAAGCTCAATCAATCATCT 59.408 40.000 6.19 0.00 0.00 2.90
12 13 5.513233 AGGTGGTTAAGCTCAATCAATCAT 58.487 37.500 6.19 0.00 27.29 2.45
13 14 4.922206 AGGTGGTTAAGCTCAATCAATCA 58.078 39.130 6.19 0.00 27.29 2.57
14 15 5.904362 AAGGTGGTTAAGCTCAATCAATC 57.096 39.130 6.19 0.00 34.84 2.67
16 17 5.738783 GCAAAAGGTGGTTAAGCTCAATCAA 60.739 40.000 6.19 0.00 34.84 2.57
17 18 4.261994 GCAAAAGGTGGTTAAGCTCAATCA 60.262 41.667 6.19 0.00 34.84 2.57
18 19 4.237724 GCAAAAGGTGGTTAAGCTCAATC 58.762 43.478 6.19 0.00 34.84 2.67
20 21 3.027412 TGCAAAAGGTGGTTAAGCTCAA 58.973 40.909 6.19 0.00 34.84 3.02
21 22 2.660572 TGCAAAAGGTGGTTAAGCTCA 58.339 42.857 6.19 0.00 34.84 4.26
22 23 3.552890 CCTTGCAAAAGGTGGTTAAGCTC 60.553 47.826 0.00 2.00 34.84 4.09
23 24 2.365293 CCTTGCAAAAGGTGGTTAAGCT 59.635 45.455 0.00 0.00 38.63 3.74
24 25 2.754472 CCTTGCAAAAGGTGGTTAAGC 58.246 47.619 0.00 0.00 35.22 3.09
25 26 2.102252 TGCCTTGCAAAAGGTGGTTAAG 59.898 45.455 6.32 0.00 42.00 1.85
26 27 2.111384 TGCCTTGCAAAAGGTGGTTAA 58.889 42.857 6.32 0.00 42.00 2.01
27 28 1.781786 TGCCTTGCAAAAGGTGGTTA 58.218 45.000 6.32 0.00 42.00 2.85
28 29 0.908198 TTGCCTTGCAAAAGGTGGTT 59.092 45.000 6.32 0.00 45.96 3.67
29 30 2.601664 TTGCCTTGCAAAAGGTGGT 58.398 47.368 6.32 0.00 45.96 4.16
41 42 3.821033 GTGACAACACTTATCCTTGCCTT 59.179 43.478 0.00 0.00 42.99 4.35
42 43 3.412386 GTGACAACACTTATCCTTGCCT 58.588 45.455 0.00 0.00 42.99 4.75
61 62 5.348724 ACGTCATGTACTGCATTCTTTAGTG 59.651 40.000 0.00 0.00 35.19 2.74
62 63 5.479306 ACGTCATGTACTGCATTCTTTAGT 58.521 37.500 0.00 0.00 35.19 2.24
63 64 6.311445 AGAACGTCATGTACTGCATTCTTTAG 59.689 38.462 0.00 0.00 35.19 1.85
64 65 6.163476 AGAACGTCATGTACTGCATTCTTTA 58.837 36.000 0.00 0.00 35.19 1.85
65 66 4.997395 AGAACGTCATGTACTGCATTCTTT 59.003 37.500 0.00 0.00 35.19 2.52
66 67 4.569943 AGAACGTCATGTACTGCATTCTT 58.430 39.130 0.00 0.00 35.19 2.52
68 69 3.926527 TGAGAACGTCATGTACTGCATTC 59.073 43.478 0.00 0.00 35.19 2.67
69 70 3.925379 TGAGAACGTCATGTACTGCATT 58.075 40.909 0.00 0.00 35.19 3.56
70 71 3.592898 TGAGAACGTCATGTACTGCAT 57.407 42.857 0.00 0.00 38.60 3.96
71 72 3.005367 TCTTGAGAACGTCATGTACTGCA 59.995 43.478 0.00 0.00 34.17 4.41
72 73 3.575630 TCTTGAGAACGTCATGTACTGC 58.424 45.455 0.00 0.00 34.17 4.40
73 74 6.556212 ACTATCTTGAGAACGTCATGTACTG 58.444 40.000 0.00 0.00 34.17 2.74
74 75 6.761099 ACTATCTTGAGAACGTCATGTACT 57.239 37.500 0.00 0.00 34.17 2.73
75 76 8.906636 TTAACTATCTTGAGAACGTCATGTAC 57.093 34.615 0.00 0.00 34.17 2.90
77 78 8.035394 ACATTAACTATCTTGAGAACGTCATGT 58.965 33.333 0.00 0.00 34.17 3.21
78 79 8.323854 CACATTAACTATCTTGAGAACGTCATG 58.676 37.037 0.00 0.00 34.17 3.07
80 81 7.328493 CACACATTAACTATCTTGAGAACGTCA 59.672 37.037 0.00 0.00 0.00 4.35
81 82 7.328737 ACACACATTAACTATCTTGAGAACGTC 59.671 37.037 0.00 0.00 0.00 4.34
82 83 7.152645 ACACACATTAACTATCTTGAGAACGT 58.847 34.615 0.00 0.00 0.00 3.99
83 84 7.582435 ACACACATTAACTATCTTGAGAACG 57.418 36.000 0.00 0.00 0.00 3.95
86 87 8.589701 TCCTACACACATTAACTATCTTGAGA 57.410 34.615 0.00 0.00 0.00 3.27
88 89 9.653287 CTTTCCTACACACATTAACTATCTTGA 57.347 33.333 0.00 0.00 0.00 3.02
90 91 8.603304 ACCTTTCCTACACACATTAACTATCTT 58.397 33.333 0.00 0.00 0.00 2.40
91 92 8.147244 ACCTTTCCTACACACATTAACTATCT 57.853 34.615 0.00 0.00 0.00 1.98
93 94 9.263446 TCTACCTTTCCTACACACATTAACTAT 57.737 33.333 0.00 0.00 0.00 2.12
94 95 8.654485 TCTACCTTTCCTACACACATTAACTA 57.346 34.615 0.00 0.00 0.00 2.24
95 96 7.453752 TCTCTACCTTTCCTACACACATTAACT 59.546 37.037 0.00 0.00 0.00 2.24
97 98 7.672660 TCTCTCTACCTTTCCTACACACATTAA 59.327 37.037 0.00 0.00 0.00 1.40
98 99 7.179966 TCTCTCTACCTTTCCTACACACATTA 58.820 38.462 0.00 0.00 0.00 1.90
99 100 6.017192 TCTCTCTACCTTTCCTACACACATT 58.983 40.000 0.00 0.00 0.00 2.71
100 101 5.580998 TCTCTCTACCTTTCCTACACACAT 58.419 41.667 0.00 0.00 0.00 3.21
103 104 5.254901 GACTCTCTCTACCTTTCCTACACA 58.745 45.833 0.00 0.00 0.00 3.72
105 106 4.224594 TCGACTCTCTCTACCTTTCCTACA 59.775 45.833 0.00 0.00 0.00 2.74
106 107 4.571984 GTCGACTCTCTCTACCTTTCCTAC 59.428 50.000 8.70 0.00 0.00 3.18
107 108 4.224594 TGTCGACTCTCTCTACCTTTCCTA 59.775 45.833 17.92 0.00 0.00 2.94
109 110 3.345414 TGTCGACTCTCTCTACCTTTCC 58.655 50.000 17.92 0.00 0.00 3.13
111 112 4.142790 TGTTGTCGACTCTCTCTACCTTT 58.857 43.478 17.92 0.00 0.00 3.11
113 114 3.420300 TGTTGTCGACTCTCTCTACCT 57.580 47.619 17.92 0.00 0.00 3.08
114 115 3.119779 CCTTGTTGTCGACTCTCTCTACC 60.120 52.174 17.92 0.00 0.00 3.18
115 116 3.671164 GCCTTGTTGTCGACTCTCTCTAC 60.671 52.174 17.92 4.31 0.00 2.59
116 117 2.488545 GCCTTGTTGTCGACTCTCTCTA 59.511 50.000 17.92 0.00 0.00 2.43
117 118 1.271102 GCCTTGTTGTCGACTCTCTCT 59.729 52.381 17.92 0.00 0.00 3.10
118 119 1.000163 TGCCTTGTTGTCGACTCTCTC 60.000 52.381 17.92 3.43 0.00 3.20
119 120 1.040646 TGCCTTGTTGTCGACTCTCT 58.959 50.000 17.92 0.00 0.00 3.10
120 121 1.865865 TTGCCTTGTTGTCGACTCTC 58.134 50.000 17.92 7.60 0.00 3.20
121 122 2.325583 TTTGCCTTGTTGTCGACTCT 57.674 45.000 17.92 0.00 0.00 3.24
122 123 3.414549 TTTTTGCCTTGTTGTCGACTC 57.585 42.857 17.92 10.45 0.00 3.36
180 1264 0.908198 CAGGAGAGGAAGGGGTCTTG 59.092 60.000 0.00 0.00 32.52 3.02
208 1296 7.864379 CACATTAGCCTGCTTTCTAATTAATGG 59.136 37.037 0.00 0.00 34.33 3.16
231 1477 4.835284 TGCTGAATATTGGAGTACCACA 57.165 40.909 0.00 0.00 46.80 4.17
269 1515 5.476599 AGCACACACAATATACAACATGGTT 59.523 36.000 0.00 0.00 0.00 3.67
270 1516 5.009631 AGCACACACAATATACAACATGGT 58.990 37.500 0.00 0.00 0.00 3.55
322 1621 6.386927 TGTTTTCCTGGTGATCATATAGGTCT 59.613 38.462 17.29 0.00 0.00 3.85
348 1648 9.168451 GCTCTAGCTCTGTACATGTTCTATATA 57.832 37.037 2.30 0.00 38.21 0.86
421 1817 3.596214 ACTGGCGGTTATGTTGAACTAG 58.404 45.455 0.00 0.00 0.00 2.57
426 1822 1.346395 ACAGACTGGCGGTTATGTTGA 59.654 47.619 7.51 0.00 0.00 3.18
462 1858 1.517242 CTGCCTCTTCTGAAAGCGTT 58.483 50.000 0.00 0.00 32.18 4.84
477 1881 2.745492 GCACTGACAGAGGCTGCC 60.745 66.667 11.65 11.65 34.37 4.85
502 1906 3.560896 GGTCTGTCTAGTCTAGCTAACGG 59.439 52.174 1.60 1.41 0.00 4.44
539 1943 3.395702 ACGCATTGCCCGGTCCTA 61.396 61.111 0.00 0.00 0.00 2.94
564 1968 3.642141 AGGTTCTTGTGTTTGGTTCCAT 58.358 40.909 0.00 0.00 0.00 3.41
631 4582 8.583296 CACTAGTTTGTTCCTTAGTACCTAACT 58.417 37.037 0.00 0.00 42.62 2.24
636 4587 4.934001 GCCACTAGTTTGTTCCTTAGTACC 59.066 45.833 0.00 0.00 0.00 3.34
756 4718 1.926511 GCAAATGGCTCTGGACCACG 61.927 60.000 0.00 0.00 40.82 4.94
760 4722 2.113860 TAGTGCAAATGGCTCTGGAC 57.886 50.000 0.00 0.00 45.38 4.02
972 4954 7.579105 ACTAGATGGAGAGTATACTTCAGTGT 58.421 38.462 6.88 0.00 0.00 3.55
1047 5032 2.593725 ACAGCTGCAGCCAGTGTG 60.594 61.111 34.39 26.41 43.38 3.82
1147 5132 1.514678 GACATTGAGTTGCCACCGCA 61.515 55.000 0.00 0.00 45.49 5.69
1168 5245 3.747529 GTCCCAATTGTTTTCTGCATTGG 59.252 43.478 4.43 4.75 38.51 3.16
1191 5268 1.270358 GCAGATCCCTCGGTACCATTC 60.270 57.143 13.54 0.00 0.00 2.67
1196 5273 1.742768 CCAGCAGATCCCTCGGTAC 59.257 63.158 0.00 0.00 0.00 3.34
1197 5274 2.134287 GCCAGCAGATCCCTCGGTA 61.134 63.158 0.00 0.00 0.00 4.02
1199 5276 4.598894 CGCCAGCAGATCCCTCGG 62.599 72.222 0.00 0.00 0.00 4.63
1216 5302 0.436531 CTCTTTGTCTCGCTTGTCGC 59.563 55.000 0.00 0.00 38.27 5.19
1325 5411 0.846015 CCATCAATGGTGCCTAGGGA 59.154 55.000 11.72 4.36 43.05 4.20
1432 7530 1.839424 AAGTAATTCTGGCAGGTGGC 58.161 50.000 15.73 0.00 43.74 5.01
1433 7531 3.157087 ACAAAGTAATTCTGGCAGGTGG 58.843 45.455 15.73 0.00 0.00 4.61
1434 7532 5.957842 TTACAAAGTAATTCTGGCAGGTG 57.042 39.130 15.73 3.23 0.00 4.00
1435 7533 6.549736 AGTTTTACAAAGTAATTCTGGCAGGT 59.450 34.615 15.73 3.58 0.00 4.00
1436 7534 6.981722 AGTTTTACAAAGTAATTCTGGCAGG 58.018 36.000 15.73 0.00 0.00 4.85
1477 7586 3.200605 TCAACTCTATGTCATGTGCCCAT 59.799 43.478 0.00 0.00 0.00 4.00
1494 7603 4.082571 GCCAAGAATGTTAGCACATCAACT 60.083 41.667 0.00 0.00 43.34 3.16
1567 7679 1.672356 GTGCAAGCCCACACGAGAT 60.672 57.895 0.00 0.00 35.80 2.75
1756 7887 0.179936 GGACTTGCTATGCAGAGGCT 59.820 55.000 10.92 0.00 40.61 4.58
1826 7958 2.102420 CTGTCTCTCTCTCTCTAGGCGA 59.898 54.545 0.00 0.00 0.00 5.54
1834 7966 4.614475 TCTCTCTCTCTGTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
1835 7967 4.646945 TCTCTCTCTCTCTGTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
1836 7968 4.614475 TCTCTCTCTCTCTGTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
1837 7969 4.646945 TCTCTCTCTCTCTCTGTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
1838 7970 4.614475 TCTCTCTCTCTCTCTGTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
1839 7971 4.646945 TCTCTCTCTCTCTCTCTGTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
1840 7972 4.614475 TCTCTCTCTCTCTCTCTGTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
1841 7973 4.646945 TCTCTCTCTCTCTCTCTCTGTCTC 59.353 50.000 0.00 0.00 0.00 3.36
1842 7974 4.614475 TCTCTCTCTCTCTCTCTCTGTCT 58.386 47.826 0.00 0.00 0.00 3.41
1843 7975 4.646945 TCTCTCTCTCTCTCTCTCTCTGTC 59.353 50.000 0.00 0.00 0.00 3.51
1844 7976 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
1845 7977 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
1863 8312 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1864 8313 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1865 8314 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1866 8315 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1867 8316 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1868 8317 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1869 8318 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1870 8319 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1871 8320 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1872 8321 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1873 8322 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1874 8323 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1875 8324 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1876 8325 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1877 8326 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1878 8327 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1879 8328 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1880 8329 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1881 8330 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
1882 8331 4.648762 CACTCTCTCTCTCTCTCTCTCTCT 59.351 50.000 0.00 0.00 0.00 3.10
1883 8332 4.404073 ACACTCTCTCTCTCTCTCTCTCTC 59.596 50.000 0.00 0.00 0.00 3.20
1884 8333 4.357325 ACACTCTCTCTCTCTCTCTCTCT 58.643 47.826 0.00 0.00 0.00 3.10
1885 8334 4.744795 ACACTCTCTCTCTCTCTCTCTC 57.255 50.000 0.00 0.00 0.00 3.20
1886 8335 4.287067 ACAACACTCTCTCTCTCTCTCTCT 59.713 45.833 0.00 0.00 0.00 3.10
1887 8336 4.393062 CACAACACTCTCTCTCTCTCTCTC 59.607 50.000 0.00 0.00 0.00 3.20
1888 8337 4.326826 CACAACACTCTCTCTCTCTCTCT 58.673 47.826 0.00 0.00 0.00 3.10
1889 8338 3.440173 CCACAACACTCTCTCTCTCTCTC 59.560 52.174 0.00 0.00 0.00 3.20
1890 8339 3.073798 TCCACAACACTCTCTCTCTCTCT 59.926 47.826 0.00 0.00 0.00 3.10
1891 8340 3.190535 GTCCACAACACTCTCTCTCTCTC 59.809 52.174 0.00 0.00 0.00 3.20
1892 8341 3.153919 GTCCACAACACTCTCTCTCTCT 58.846 50.000 0.00 0.00 0.00 3.10
1893 8342 3.153919 AGTCCACAACACTCTCTCTCTC 58.846 50.000 0.00 0.00 0.00 3.20
1894 8343 3.153919 GAGTCCACAACACTCTCTCTCT 58.846 50.000 0.00 0.00 37.82 3.10
1895 8344 2.095466 CGAGTCCACAACACTCTCTCTC 60.095 54.545 0.00 0.00 38.55 3.20
1896 8345 1.883275 CGAGTCCACAACACTCTCTCT 59.117 52.381 0.00 0.00 38.55 3.10
1897 8346 1.068194 CCGAGTCCACAACACTCTCTC 60.068 57.143 0.00 0.00 38.55 3.20
1904 8353 2.513259 GGGGTCCGAGTCCACAACA 61.513 63.158 0.00 0.00 0.00 3.33
1910 8359 1.407656 TATGCATGGGGTCCGAGTCC 61.408 60.000 10.16 0.00 0.00 3.85
1912 8361 1.696097 GGTATGCATGGGGTCCGAGT 61.696 60.000 10.16 0.00 0.00 4.18
1913 8362 1.071471 GGTATGCATGGGGTCCGAG 59.929 63.158 10.16 0.00 0.00 4.63
1914 8363 1.275421 TTGGTATGCATGGGGTCCGA 61.275 55.000 10.16 1.40 0.00 4.55
1915 8364 1.101049 GTTGGTATGCATGGGGTCCG 61.101 60.000 10.16 0.00 0.00 4.79
1916 8365 0.755327 GGTTGGTATGCATGGGGTCC 60.755 60.000 10.16 2.96 0.00 4.46
1918 8367 1.309688 GGGTTGGTATGCATGGGGT 59.690 57.895 10.16 0.00 0.00 4.95
1919 8368 1.457455 GGGGTTGGTATGCATGGGG 60.457 63.158 10.16 0.00 0.00 4.96
1920 8369 0.325110 TTGGGGTTGGTATGCATGGG 60.325 55.000 10.16 0.00 0.00 4.00
1921 8370 0.823460 GTTGGGGTTGGTATGCATGG 59.177 55.000 10.16 0.00 0.00 3.66
1922 8371 1.477700 CTGTTGGGGTTGGTATGCATG 59.522 52.381 10.16 0.00 0.00 4.06
1923 8372 1.077005 ACTGTTGGGGTTGGTATGCAT 59.923 47.619 3.79 3.79 0.00 3.96
1979 8526 6.062095 ACATAGCAAAGTACAACAGTCCTTT 58.938 36.000 0.00 0.00 0.00 3.11
1988 8536 2.937873 GCCCGGACATAGCAAAGTACAA 60.938 50.000 0.73 0.00 0.00 2.41
2055 8603 9.194972 TGAGCCAATAAAATATACCATTTGTCA 57.805 29.630 0.00 0.00 0.00 3.58
2062 8610 8.986991 ACCATTTTGAGCCAATAAAATATACCA 58.013 29.630 0.00 0.00 35.40 3.25
2063 8611 9.260002 CACCATTTTGAGCCAATAAAATATACC 57.740 33.333 0.00 0.00 35.40 2.73
2064 8612 8.764287 GCACCATTTTGAGCCAATAAAATATAC 58.236 33.333 0.00 0.00 35.40 1.47
2065 8613 8.481314 TGCACCATTTTGAGCCAATAAAATATA 58.519 29.630 0.00 0.00 35.40 0.86
2066 8614 7.337167 TGCACCATTTTGAGCCAATAAAATAT 58.663 30.769 0.00 0.00 35.40 1.28
2067 8615 6.705302 TGCACCATTTTGAGCCAATAAAATA 58.295 32.000 0.00 0.00 35.40 1.40
2068 8616 5.558818 TGCACCATTTTGAGCCAATAAAAT 58.441 33.333 0.00 0.00 37.06 1.82
2069 8617 4.965814 TGCACCATTTTGAGCCAATAAAA 58.034 34.783 0.00 0.00 0.00 1.52
2070 8618 4.613925 TGCACCATTTTGAGCCAATAAA 57.386 36.364 0.00 0.00 0.00 1.40
2071 8619 4.822685 ATGCACCATTTTGAGCCAATAA 57.177 36.364 0.00 0.00 0.00 1.40
2072 8620 5.929058 TTATGCACCATTTTGAGCCAATA 57.071 34.783 0.00 0.00 0.00 1.90
2073 8621 4.822685 TTATGCACCATTTTGAGCCAAT 57.177 36.364 0.00 0.00 0.00 3.16
2074 8622 4.822685 ATTATGCACCATTTTGAGCCAA 57.177 36.364 0.00 0.00 0.00 4.52
2075 8623 5.363292 ACATATTATGCACCATTTTGAGCCA 59.637 36.000 3.52 0.00 0.00 4.75
2076 8624 5.846203 ACATATTATGCACCATTTTGAGCC 58.154 37.500 3.52 0.00 0.00 4.70
2077 8625 7.379529 GTGTACATATTATGCACCATTTTGAGC 59.620 37.037 0.00 0.00 0.00 4.26
2078 8626 7.862372 GGTGTACATATTATGCACCATTTTGAG 59.138 37.037 20.12 0.00 46.29 3.02
2079 8627 7.711846 GGTGTACATATTATGCACCATTTTGA 58.288 34.615 20.12 0.00 46.29 2.69
2080 8628 7.928908 GGTGTACATATTATGCACCATTTTG 57.071 36.000 20.12 0.00 46.29 2.44
2086 8634 4.515191 CAGTGGGTGTACATATTATGCACC 59.485 45.833 18.20 18.20 46.31 5.01
2087 8635 5.123227 ACAGTGGGTGTACATATTATGCAC 58.877 41.667 0.00 2.05 37.75 4.57
2088 8636 5.366482 ACAGTGGGTGTACATATTATGCA 57.634 39.130 0.00 0.00 37.75 3.96
2089 8637 6.542370 AGAAACAGTGGGTGTACATATTATGC 59.458 38.462 0.00 0.00 39.03 3.14
2090 8638 7.768582 TGAGAAACAGTGGGTGTACATATTATG 59.231 37.037 0.00 2.03 39.03 1.90
2091 8639 7.769044 GTGAGAAACAGTGGGTGTACATATTAT 59.231 37.037 0.00 0.00 39.03 1.28
2092 8640 7.101054 GTGAGAAACAGTGGGTGTACATATTA 58.899 38.462 0.00 0.00 39.03 0.98
2093 8641 5.938125 GTGAGAAACAGTGGGTGTACATATT 59.062 40.000 0.00 0.00 39.03 1.28
2094 8642 5.012664 TGTGAGAAACAGTGGGTGTACATAT 59.987 40.000 0.00 0.00 39.03 1.78
2095 8643 4.345547 TGTGAGAAACAGTGGGTGTACATA 59.654 41.667 0.00 0.00 39.03 2.29
2096 8644 3.135712 TGTGAGAAACAGTGGGTGTACAT 59.864 43.478 0.00 0.00 39.03 2.29
2097 8645 2.502130 TGTGAGAAACAGTGGGTGTACA 59.498 45.455 0.00 0.00 39.03 2.90
2098 8646 2.870411 GTGTGAGAAACAGTGGGTGTAC 59.130 50.000 0.00 0.00 40.26 2.90
2099 8647 2.502130 TGTGTGAGAAACAGTGGGTGTA 59.498 45.455 0.00 0.00 40.26 2.90
2136 8684 3.515602 AACTAGCCCCATCAATCATCC 57.484 47.619 0.00 0.00 0.00 3.51
2192 8740 6.741992 CAGGTGATGTACTGCATTCTTTAA 57.258 37.500 0.00 0.00 38.06 1.52
2221 8769 8.506168 TCTTGAGAAAGTCATGTACTGTTTTT 57.494 30.769 0.00 0.00 38.88 1.94
2222 8770 8.682936 ATCTTGAGAAAGTCATGTACTGTTTT 57.317 30.769 0.00 0.00 38.88 2.43
2223 8771 9.429359 CTATCTTGAGAAAGTCATGTACTGTTT 57.571 33.333 0.00 0.00 38.88 2.83
2224 8772 7.547370 GCTATCTTGAGAAAGTCATGTACTGTT 59.453 37.037 0.00 0.00 38.88 3.16
2225 8773 7.038659 GCTATCTTGAGAAAGTCATGTACTGT 58.961 38.462 0.00 0.00 38.88 3.55
2226 8774 7.038048 TGCTATCTTGAGAAAGTCATGTACTG 58.962 38.462 0.00 0.00 38.88 2.74
2227 8775 7.093552 ACTGCTATCTTGAGAAAGTCATGTACT 60.094 37.037 0.00 0.00 41.49 2.73
2228 8776 7.038659 ACTGCTATCTTGAGAAAGTCATGTAC 58.961 38.462 0.00 0.00 34.17 2.90
2229 8777 7.175347 ACTGCTATCTTGAGAAAGTCATGTA 57.825 36.000 0.00 0.00 34.17 2.29
2230 8778 6.047511 ACTGCTATCTTGAGAAAGTCATGT 57.952 37.500 0.00 0.00 34.17 3.21
2231 8779 6.981762 AACTGCTATCTTGAGAAAGTCATG 57.018 37.500 0.00 0.00 34.17 3.07
2232 8780 6.939163 ACAAACTGCTATCTTGAGAAAGTCAT 59.061 34.615 0.00 0.00 34.17 3.06
2294 8843 0.253327 ATTTCTTCGGCCTCACCCTC 59.747 55.000 0.00 0.00 33.26 4.30
2299 8853 2.159382 GAACCAATTTCTTCGGCCTCA 58.841 47.619 0.00 0.00 0.00 3.86
2304 8858 3.574284 TGCATGAACCAATTTCTTCGG 57.426 42.857 0.00 0.00 34.97 4.30


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

AutoCloner maintained by Alex Coulton.