Multiple sequence alignment - TraesCS1D01G398000

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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 TraesCS1D01G398000 chr1D 100.000 2008 0 0 450 2457 465259506 465261513 0.000000e+00 3709.0
1 TraesCS1D01G398000 chr1D 100.000 231 0 0 1 231 465259057 465259287 6.280000e-116 427.0
2 TraesCS1D01G398000 chr1D 84.222 469 38 21 2000 2457 403280267 403279824 8.120000e-115 424.0
3 TraesCS1D01G398000 chr2D 96.326 1878 64 3 584 2457 397963572 397961696 0.000000e+00 3081.0
4 TraesCS1D01G398000 chr2D 94.837 1569 74 3 892 2457 54392198 54393762 0.000000e+00 2442.0
5 TraesCS1D01G398000 chr2D 95.692 975 39 1 1486 2457 250920887 250919913 0.000000e+00 1565.0
6 TraesCS1D01G398000 chr7A 95.039 1653 70 7 806 2457 342306033 342304392 0.000000e+00 2588.0
7 TraesCS1D01G398000 chr7A 93.513 1187 68 6 603 1788 533368535 533367357 0.000000e+00 1757.0
8 TraesCS1D01G398000 chr7A 96.637 565 19 0 1784 2348 533341279 533340715 0.000000e+00 939.0
9 TraesCS1D01G398000 chr7A 84.753 446 35 11 663 1103 49819097 49819514 1.360000e-112 416.0
10 TraesCS1D01G398000 chr7A 93.506 154 10 0 603 756 342306633 342306480 1.900000e-56 230.0
11 TraesCS1D01G398000 chr7A 92.593 54 2 2 2128 2180 533340847 533340795 2.620000e-10 76.8
12 TraesCS1D01G398000 chr6D 96.205 975 30 2 1483 2457 288070267 288071234 0.000000e+00 1589.0
13 TraesCS1D01G398000 chr6D 93.662 284 13 4 2175 2457 452251262 452251541 1.050000e-113 420.0
14 TraesCS1D01G398000 chr6D 92.958 284 16 4 2175 2457 67713501 67713221 6.320000e-111 411.0
15 TraesCS1D01G398000 chr7D 93.981 648 38 1 1490 2136 157759016 157759663 0.000000e+00 979.0
16 TraesCS1D01G398000 chr7D 93.333 285 14 5 2175 2457 556661115 556660834 1.360000e-112 416.0
17 TraesCS1D01G398000 chr7D 88.776 294 21 8 1316 1609 157758736 157759017 1.400000e-92 350.0
18 TraesCS1D01G398000 chr7B 87.037 756 64 18 815 1570 359363786 359364507 0.000000e+00 822.0
19 TraesCS1D01G398000 chr7B 86.435 317 33 7 1691 2003 29687924 29688234 3.030000e-89 339.0
20 TraesCS1D01G398000 chr7B 90.625 224 19 2 2 225 99205962 99205741 1.850000e-76 296.0
21 TraesCS1D01G398000 chr7B 85.542 166 16 6 1261 1418 29687741 29687906 1.510000e-37 167.0
22 TraesCS1D01G398000 chr3B 86.242 785 64 23 786 1570 762576222 762576962 0.000000e+00 811.0
23 TraesCS1D01G398000 chr3B 83.049 761 78 24 1264 2006 245922964 245922237 0.000000e+00 643.0
24 TraesCS1D01G398000 chr3B 89.177 231 19 6 2 230 737251295 737251521 1.440000e-72 283.0
25 TraesCS1D01G398000 chr5A 86.761 710 62 20 786 1495 675835738 675836415 0.000000e+00 761.0
26 TraesCS1D01G398000 chr5A 86.591 440 39 8 665 1103 511205050 511205470 3.700000e-128 468.0
27 TraesCS1D01G398000 chr5A 96.154 52 2 0 602 653 1818163 1818112 4.350000e-13 86.1
28 TraesCS1D01G398000 chr1B 87.934 663 50 11 908 1570 126506643 126507275 0.000000e+00 754.0
29 TraesCS1D01G398000 chr4D 87.305 512 36 11 602 1103 295253549 295253057 2.130000e-155 558.0
30 TraesCS1D01G398000 chr4D 93.939 231 14 0 1 231 458012828 458012598 1.400000e-92 350.0
31 TraesCS1D01G398000 chr4D 96.569 204 7 0 1 204 481403657 481403454 3.030000e-89 339.0
32 TraesCS1D01G398000 chr1A 88.235 442 28 7 663 1103 534688541 534688123 7.840000e-140 507.0
33 TraesCS1D01G398000 chr1A 92.574 202 15 0 24 225 522936961 522937162 8.600000e-75 291.0
34 TraesCS1D01G398000 chr4A 86.099 446 30 10 663 1103 238130239 238129821 3.730000e-123 451.0
35 TraesCS1D01G398000 chr4A 83.432 338 40 11 663 986 536319 535984 1.430000e-77 300.0
36 TraesCS1D01G398000 chr4A 100.000 44 0 0 1999 2042 723021348 723021305 5.630000e-12 82.4
37 TraesCS1D01G398000 chr6A 81.603 549 61 18 603 1151 402589147 402589655 3.780000e-113 418.0
38 TraesCS1D01G398000 chr6A 95.238 231 11 0 1 231 601568500 601568270 1.390000e-97 366.0
39 TraesCS1D01G398000 chr6A 96.154 52 2 0 602 653 118180436 118180487 4.350000e-13 86.1
40 TraesCS1D01G398000 chr5D 93.333 225 15 0 1 225 523097094 523096870 1.410000e-87 333.0
41 TraesCS1D01G398000 chr5D 92.593 54 2 2 2128 2180 561346532 561346480 2.620000e-10 76.8
42 TraesCS1D01G398000 chr2B 80.081 492 47 23 1530 2006 152175792 152175337 3.940000e-83 318.0
43 TraesCS1D01G398000 chr2B 89.270 233 23 2 908 1139 49636142 49636373 8.600000e-75 291.0
44 TraesCS1D01G398000 chr6B 89.778 225 20 3 2 225 525256568 525256346 4.000000e-73 285.0
45 TraesCS1D01G398000 chr4B 89.381 226 20 4 2 225 57252898 57252675 5.170000e-72 281.0
46 TraesCS1D01G398000 chr3A 94.231 52 3 0 602 653 569538014 569538065 2.030000e-11 80.5
47 TraesCS1D01G398000 chr3A 94.231 52 3 0 602 653 733310597 733310648 2.030000e-11 80.5
48 TraesCS1D01G398000 chr2A 92.593 54 2 2 2128 2180 487647897 487647949 2.620000e-10 76.8


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 TraesCS1D01G398000 chr1D 465259057 465261513 2456 False 2068.0 3709 100.0000 1 2457 2 chr1D.!!$F1 2456
1 TraesCS1D01G398000 chr2D 397961696 397963572 1876 True 3081.0 3081 96.3260 584 2457 1 chr2D.!!$R2 1873
2 TraesCS1D01G398000 chr2D 54392198 54393762 1564 False 2442.0 2442 94.8370 892 2457 1 chr2D.!!$F1 1565
3 TraesCS1D01G398000 chr2D 250919913 250920887 974 True 1565.0 1565 95.6920 1486 2457 1 chr2D.!!$R1 971
4 TraesCS1D01G398000 chr7A 533367357 533368535 1178 True 1757.0 1757 93.5130 603 1788 1 chr7A.!!$R1 1185
5 TraesCS1D01G398000 chr7A 342304392 342306633 2241 True 1409.0 2588 94.2725 603 2457 2 chr7A.!!$R2 1854
6 TraesCS1D01G398000 chr7A 533340715 533341279 564 True 507.9 939 94.6150 1784 2348 2 chr7A.!!$R3 564
7 TraesCS1D01G398000 chr6D 288070267 288071234 967 False 1589.0 1589 96.2050 1483 2457 1 chr6D.!!$F1 974
8 TraesCS1D01G398000 chr7D 157758736 157759663 927 False 664.5 979 91.3785 1316 2136 2 chr7D.!!$F1 820
9 TraesCS1D01G398000 chr7B 359363786 359364507 721 False 822.0 822 87.0370 815 1570 1 chr7B.!!$F1 755
10 TraesCS1D01G398000 chr3B 762576222 762576962 740 False 811.0 811 86.2420 786 1570 1 chr3B.!!$F2 784
11 TraesCS1D01G398000 chr3B 245922237 245922964 727 True 643.0 643 83.0490 1264 2006 1 chr3B.!!$R1 742
12 TraesCS1D01G398000 chr5A 675835738 675836415 677 False 761.0 761 86.7610 786 1495 1 chr5A.!!$F2 709
13 TraesCS1D01G398000 chr1B 126506643 126507275 632 False 754.0 754 87.9340 908 1570 1 chr1B.!!$F1 662
14 TraesCS1D01G398000 chr6A 402589147 402589655 508 False 418.0 418 81.6030 603 1151 1 chr6A.!!$F2 548

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
545 546 0.033991 CTCTTCCTCCCACCTCTCGA 60.034 60.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 2221 0.03392 TGCATGCATACCTAGAGGCG 59.966 55.0 18.46 0.0 39.32 5.52 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
19 20 4.166011 CGCAGCAAACCCTAGCGC 62.166 66.667 0.00 0.00 41.95 5.92
20 21 2.747855 GCAGCAAACCCTAGCGCT 60.748 61.111 17.26 17.26 35.48 5.92
21 22 2.754995 GCAGCAAACCCTAGCGCTC 61.755 63.158 16.34 0.00 35.48 5.03
22 23 1.078848 CAGCAAACCCTAGCGCTCT 60.079 57.895 16.34 0.00 35.48 4.09
23 24 1.086634 CAGCAAACCCTAGCGCTCTC 61.087 60.000 16.34 0.00 35.48 3.20
24 25 1.079127 GCAAACCCTAGCGCTCTCA 60.079 57.895 16.34 0.00 0.00 3.27
25 26 1.362406 GCAAACCCTAGCGCTCTCAC 61.362 60.000 16.34 0.00 0.00 3.51
26 27 0.037326 CAAACCCTAGCGCTCTCACA 60.037 55.000 16.34 0.00 0.00 3.58
27 28 0.037232 AAACCCTAGCGCTCTCACAC 60.037 55.000 16.34 0.00 0.00 3.82
28 29 1.185618 AACCCTAGCGCTCTCACACA 61.186 55.000 16.34 0.00 0.00 3.72
29 30 1.185618 ACCCTAGCGCTCTCACACAA 61.186 55.000 16.34 0.00 0.00 3.33
30 31 0.737715 CCCTAGCGCTCTCACACAAC 60.738 60.000 16.34 0.00 0.00 3.32
31 32 0.244994 CCTAGCGCTCTCACACAACT 59.755 55.000 16.34 0.00 0.00 3.16
32 33 1.623359 CTAGCGCTCTCACACAACTC 58.377 55.000 16.34 0.00 0.00 3.01
33 34 0.243907 TAGCGCTCTCACACAACTCC 59.756 55.000 16.34 0.00 0.00 3.85
34 35 1.005630 GCGCTCTCACACAACTCCT 60.006 57.895 0.00 0.00 0.00 3.69
35 36 1.011451 GCGCTCTCACACAACTCCTC 61.011 60.000 0.00 0.00 0.00 3.71
36 37 0.389166 CGCTCTCACACAACTCCTCC 60.389 60.000 0.00 0.00 0.00 4.30
37 38 0.972883 GCTCTCACACAACTCCTCCT 59.027 55.000 0.00 0.00 0.00 3.69
38 39 1.346068 GCTCTCACACAACTCCTCCTT 59.654 52.381 0.00 0.00 0.00 3.36
39 40 2.611722 GCTCTCACACAACTCCTCCTTC 60.612 54.545 0.00 0.00 0.00 3.46
40 41 2.896685 CTCTCACACAACTCCTCCTTCT 59.103 50.000 0.00 0.00 0.00 2.85
41 42 2.630098 TCTCACACAACTCCTCCTTCTG 59.370 50.000 0.00 0.00 0.00 3.02
42 43 1.694150 TCACACAACTCCTCCTTCTGG 59.306 52.381 0.00 0.00 0.00 3.86
43 44 1.694150 CACACAACTCCTCCTTCTGGA 59.306 52.381 0.00 0.00 40.69 3.86
44 45 2.304180 CACACAACTCCTCCTTCTGGAT 59.696 50.000 0.00 0.00 42.29 3.41
45 46 2.569404 ACACAACTCCTCCTTCTGGATC 59.431 50.000 0.00 0.00 42.29 3.36
46 47 2.093235 CACAACTCCTCCTTCTGGATCC 60.093 54.545 4.20 4.20 42.29 3.36
47 48 2.191400 CAACTCCTCCTTCTGGATCCA 58.809 52.381 15.27 15.27 42.29 3.41
48 49 1.872773 ACTCCTCCTTCTGGATCCAC 58.127 55.000 11.44 0.00 42.29 4.02
49 50 1.127343 CTCCTCCTTCTGGATCCACC 58.873 60.000 11.44 0.00 42.29 4.61
50 51 0.687757 TCCTCCTTCTGGATCCACCG 60.688 60.000 11.44 1.85 42.29 4.94
51 52 1.144936 CTCCTTCTGGATCCACCGC 59.855 63.158 11.44 0.00 42.29 5.68
52 53 2.190578 CCTTCTGGATCCACCGCC 59.809 66.667 11.44 0.00 42.61 6.13
53 54 2.202932 CTTCTGGATCCACCGCCG 60.203 66.667 11.44 0.12 42.61 6.46
54 55 4.467084 TTCTGGATCCACCGCCGC 62.467 66.667 11.44 0.00 42.61 6.53
75 76 3.339093 CCCCAACCCCACTCCCTC 61.339 72.222 0.00 0.00 0.00 4.30
76 77 3.339093 CCCAACCCCACTCCCTCC 61.339 72.222 0.00 0.00 0.00 4.30
77 78 3.339093 CCAACCCCACTCCCTCCC 61.339 72.222 0.00 0.00 0.00 4.30
78 79 2.204151 CAACCCCACTCCCTCCCT 60.204 66.667 0.00 0.00 0.00 4.20
79 80 2.125225 AACCCCACTCCCTCCCTC 59.875 66.667 0.00 0.00 0.00 4.30
80 81 2.501961 AACCCCACTCCCTCCCTCT 61.502 63.158 0.00 0.00 0.00 3.69
81 82 1.160289 AACCCCACTCCCTCCCTCTA 61.160 60.000 0.00 0.00 0.00 2.43
82 83 1.234529 CCCCACTCCCTCCCTCTAG 59.765 68.421 0.00 0.00 0.00 2.43
83 84 1.297409 CCCCACTCCCTCCCTCTAGA 61.297 65.000 0.00 0.00 0.00 2.43
84 85 0.863956 CCCACTCCCTCCCTCTAGAT 59.136 60.000 0.00 0.00 0.00 1.98
85 86 1.203125 CCCACTCCCTCCCTCTAGATC 60.203 61.905 0.00 0.00 0.00 2.75
86 87 1.786441 CCACTCCCTCCCTCTAGATCT 59.214 57.143 0.00 0.00 0.00 2.75
87 88 2.225017 CCACTCCCTCCCTCTAGATCTC 60.225 59.091 0.00 0.00 0.00 2.75
88 89 1.702957 ACTCCCTCCCTCTAGATCTCG 59.297 57.143 0.00 0.00 0.00 4.04
89 90 1.982226 CTCCCTCCCTCTAGATCTCGA 59.018 57.143 0.00 0.00 0.00 4.04
90 91 1.700739 TCCCTCCCTCTAGATCTCGAC 59.299 57.143 0.00 0.00 0.00 4.20
91 92 1.609580 CCCTCCCTCTAGATCTCGACG 60.610 61.905 0.00 0.00 0.00 5.12
92 93 1.153353 CTCCCTCTAGATCTCGACGC 58.847 60.000 0.00 0.00 0.00 5.19
93 94 0.600518 TCCCTCTAGATCTCGACGCG 60.601 60.000 3.53 3.53 0.00 6.01
94 95 1.205568 CCTCTAGATCTCGACGCGC 59.794 63.158 5.73 0.00 0.00 6.86
95 96 1.205568 CTCTAGATCTCGACGCGCC 59.794 63.158 5.73 0.00 0.00 6.53
96 97 2.127571 CTAGATCTCGACGCGCCG 60.128 66.667 9.05 9.05 0.00 6.46
97 98 4.309347 TAGATCTCGACGCGCCGC 62.309 66.667 10.84 0.00 0.00 6.53
116 117 3.403558 GCCCTCACCCCACTCCTC 61.404 72.222 0.00 0.00 0.00 3.71
117 118 2.689034 CCCTCACCCCACTCCTCC 60.689 72.222 0.00 0.00 0.00 4.30
118 119 3.077556 CCTCACCCCACTCCTCCG 61.078 72.222 0.00 0.00 0.00 4.63
119 120 3.077556 CTCACCCCACTCCTCCGG 61.078 72.222 0.00 0.00 0.00 5.14
124 125 4.452733 CCCACTCCTCCGGCGTTC 62.453 72.222 6.01 0.00 0.00 3.95
125 126 4.452733 CCACTCCTCCGGCGTTCC 62.453 72.222 6.01 0.00 0.00 3.62
126 127 4.452733 CACTCCTCCGGCGTTCCC 62.453 72.222 6.01 0.00 0.00 3.97
137 138 3.486263 CGTTCCCCGCACATTCTC 58.514 61.111 0.00 0.00 0.00 2.87
138 139 1.375396 CGTTCCCCGCACATTCTCA 60.375 57.895 0.00 0.00 0.00 3.27
139 140 1.635663 CGTTCCCCGCACATTCTCAC 61.636 60.000 0.00 0.00 0.00 3.51
140 141 1.002624 TTCCCCGCACATTCTCACC 60.003 57.895 0.00 0.00 0.00 4.02
141 142 2.796483 TTCCCCGCACATTCTCACCG 62.796 60.000 0.00 0.00 0.00 4.94
142 143 3.499737 CCCGCACATTCTCACCGC 61.500 66.667 0.00 0.00 0.00 5.68
143 144 2.434884 CCGCACATTCTCACCGCT 60.435 61.111 0.00 0.00 0.00 5.52
144 145 2.456119 CCGCACATTCTCACCGCTC 61.456 63.158 0.00 0.00 0.00 5.03
145 146 2.792290 CGCACATTCTCACCGCTCG 61.792 63.158 0.00 0.00 0.00 5.03
146 147 2.456119 GCACATTCTCACCGCTCGG 61.456 63.158 6.79 6.79 42.03 4.63
147 148 1.215382 CACATTCTCACCGCTCGGA 59.785 57.895 15.95 0.00 38.96 4.55
148 149 0.803768 CACATTCTCACCGCTCGGAG 60.804 60.000 15.95 7.40 38.96 4.63
149 150 0.965866 ACATTCTCACCGCTCGGAGA 60.966 55.000 15.95 11.66 38.34 3.71
150 151 0.526524 CATTCTCACCGCTCGGAGAC 60.527 60.000 15.95 0.00 39.73 3.36
151 152 1.668101 ATTCTCACCGCTCGGAGACC 61.668 60.000 15.95 0.00 39.73 3.85
152 153 3.827898 CTCACCGCTCGGAGACCC 61.828 72.222 15.95 0.00 38.96 4.46
159 160 4.400251 CTCGGAGACCCCCACCCT 62.400 72.222 0.00 0.00 0.00 4.34
160 161 4.393778 TCGGAGACCCCCACCCTC 62.394 72.222 0.00 0.00 0.00 4.30
166 167 4.741239 ACCCCCACCCTCGCAGAT 62.741 66.667 0.00 0.00 33.89 2.90
167 168 3.866582 CCCCCACCCTCGCAGATC 61.867 72.222 0.00 0.00 33.89 2.75
168 169 3.866582 CCCCACCCTCGCAGATCC 61.867 72.222 0.00 0.00 33.89 3.36
169 170 3.083349 CCCACCCTCGCAGATCCA 61.083 66.667 0.00 0.00 33.89 3.41
170 171 2.669133 CCCACCCTCGCAGATCCAA 61.669 63.158 0.00 0.00 33.89 3.53
171 172 1.450312 CCACCCTCGCAGATCCAAC 60.450 63.158 0.00 0.00 33.89 3.77
172 173 1.811266 CACCCTCGCAGATCCAACG 60.811 63.158 0.00 0.00 33.89 4.10
173 174 2.892425 CCCTCGCAGATCCAACGC 60.892 66.667 0.00 0.00 33.89 4.84
194 195 2.764128 GGTGCCTCCTCCGATCCA 60.764 66.667 0.00 0.00 0.00 3.41
195 196 2.801631 GGTGCCTCCTCCGATCCAG 61.802 68.421 0.00 0.00 0.00 3.86
196 197 1.758514 GTGCCTCCTCCGATCCAGA 60.759 63.158 0.00 0.00 0.00 3.86
197 198 1.118356 GTGCCTCCTCCGATCCAGAT 61.118 60.000 0.00 0.00 0.00 2.90
198 199 0.829602 TGCCTCCTCCGATCCAGATC 60.830 60.000 0.00 0.00 34.56 2.75
206 207 4.327885 GATCCAGATCGACACGCC 57.672 61.111 0.00 0.00 0.00 5.68
207 208 1.300233 GATCCAGATCGACACGCCC 60.300 63.158 0.00 0.00 0.00 6.13
208 209 2.701163 GATCCAGATCGACACGCCCC 62.701 65.000 0.00 0.00 0.00 5.80
209 210 3.461773 CCAGATCGACACGCCCCT 61.462 66.667 0.00 0.00 0.00 4.79
210 211 2.579201 CAGATCGACACGCCCCTT 59.421 61.111 0.00 0.00 0.00 3.95
211 212 1.519455 CAGATCGACACGCCCCTTC 60.519 63.158 0.00 0.00 0.00 3.46
212 213 2.202892 GATCGACACGCCCCTTCC 60.203 66.667 0.00 0.00 0.00 3.46
213 214 3.000819 ATCGACACGCCCCTTCCA 61.001 61.111 0.00 0.00 0.00 3.53
214 215 3.310860 ATCGACACGCCCCTTCCAC 62.311 63.158 0.00 0.00 0.00 4.02
216 217 3.948719 GACACGCCCCTTCCACCA 61.949 66.667 0.00 0.00 0.00 4.17
217 218 4.265056 ACACGCCCCTTCCACCAC 62.265 66.667 0.00 0.00 0.00 4.16
222 223 3.661648 CCCCTTCCACCACCCCTG 61.662 72.222 0.00 0.00 0.00 4.45
223 224 4.366684 CCCTTCCACCACCCCTGC 62.367 72.222 0.00 0.00 0.00 4.85
224 225 4.366684 CCTTCCACCACCCCTGCC 62.367 72.222 0.00 0.00 0.00 4.85
225 226 4.722700 CTTCCACCACCCCTGCCG 62.723 72.222 0.00 0.00 0.00 5.69
468 469 2.927553 CATCCAAAGTTACAGCAGGC 57.072 50.000 0.00 0.00 0.00 4.85
469 470 1.131126 CATCCAAAGTTACAGCAGGCG 59.869 52.381 0.00 0.00 0.00 5.52
470 471 1.210155 CCAAAGTTACAGCAGGCGC 59.790 57.895 0.00 0.00 38.99 6.53
481 482 4.292178 CAGGCGCTCCCCTCGATC 62.292 72.222 7.64 0.00 31.24 3.69
485 486 3.299190 CGCTCCCCTCGATCCCTC 61.299 72.222 0.00 0.00 0.00 4.30
486 487 2.920384 GCTCCCCTCGATCCCTCC 60.920 72.222 0.00 0.00 0.00 4.30
487 488 2.203714 CTCCCCTCGATCCCTCCC 60.204 72.222 0.00 0.00 0.00 4.30
488 489 3.033773 TCCCCTCGATCCCTCCCA 61.034 66.667 0.00 0.00 0.00 4.37
489 490 2.844839 CCCCTCGATCCCTCCCAC 60.845 72.222 0.00 0.00 0.00 4.61
490 491 2.844839 CCCTCGATCCCTCCCACC 60.845 72.222 0.00 0.00 0.00 4.61
491 492 3.227276 CCTCGATCCCTCCCACCG 61.227 72.222 0.00 0.00 0.00 4.94
492 493 3.917760 CTCGATCCCTCCCACCGC 61.918 72.222 0.00 0.00 0.00 5.68
502 503 4.452733 CCCACCGCCGTCTCCTTC 62.453 72.222 0.00 0.00 0.00 3.46
503 504 4.452733 CCACCGCCGTCTCCTTCC 62.453 72.222 0.00 0.00 0.00 3.46
504 505 4.452733 CACCGCCGTCTCCTTCCC 62.453 72.222 0.00 0.00 0.00 3.97
505 506 4.698625 ACCGCCGTCTCCTTCCCT 62.699 66.667 0.00 0.00 0.00 4.20
506 507 3.839432 CCGCCGTCTCCTTCCCTC 61.839 72.222 0.00 0.00 0.00 4.30
507 508 3.068691 CGCCGTCTCCTTCCCTCA 61.069 66.667 0.00 0.00 0.00 3.86
508 509 2.896443 GCCGTCTCCTTCCCTCAG 59.104 66.667 0.00 0.00 0.00 3.35
509 510 1.682684 GCCGTCTCCTTCCCTCAGA 60.683 63.158 0.00 0.00 0.00 3.27
510 511 1.045911 GCCGTCTCCTTCCCTCAGAT 61.046 60.000 0.00 0.00 0.00 2.90
511 512 1.036707 CCGTCTCCTTCCCTCAGATC 58.963 60.000 0.00 0.00 0.00 2.75
512 513 0.665835 CGTCTCCTTCCCTCAGATCG 59.334 60.000 0.00 0.00 0.00 3.69
513 514 1.747552 CGTCTCCTTCCCTCAGATCGA 60.748 57.143 0.00 0.00 0.00 3.59
514 515 1.953686 GTCTCCTTCCCTCAGATCGAG 59.046 57.143 7.37 7.37 41.89 4.04
515 516 0.673437 CTCCTTCCCTCAGATCGAGC 59.327 60.000 0.00 0.00 40.78 5.03
516 517 0.260230 TCCTTCCCTCAGATCGAGCT 59.740 55.000 0.00 0.00 40.78 4.09
517 518 0.673437 CCTTCCCTCAGATCGAGCTC 59.327 60.000 0.00 2.73 40.78 4.09
518 519 0.673437 CTTCCCTCAGATCGAGCTCC 59.327 60.000 8.47 0.00 40.78 4.70
519 520 0.757188 TTCCCTCAGATCGAGCTCCC 60.757 60.000 8.47 0.00 40.78 4.30
520 521 2.206536 CCCTCAGATCGAGCTCCCC 61.207 68.421 8.47 0.00 40.78 4.81
521 522 2.206536 CCTCAGATCGAGCTCCCCC 61.207 68.421 8.47 0.00 40.78 5.40
522 523 1.152567 CTCAGATCGAGCTCCCCCT 60.153 63.158 8.47 0.00 34.18 4.79
523 524 1.152652 TCAGATCGAGCTCCCCCTC 60.153 63.158 8.47 0.00 0.00 4.30
524 525 2.200092 AGATCGAGCTCCCCCTCC 59.800 66.667 8.47 0.00 0.00 4.30
525 526 2.920384 GATCGAGCTCCCCCTCCC 60.920 72.222 8.47 0.00 0.00 4.30
526 527 4.565850 ATCGAGCTCCCCCTCCCC 62.566 72.222 8.47 0.00 0.00 4.81
529 530 3.773154 GAGCTCCCCCTCCCCTCT 61.773 72.222 0.87 0.00 0.00 3.69
530 531 3.296737 AGCTCCCCCTCCCCTCTT 61.297 66.667 0.00 0.00 0.00 2.85
531 532 2.770475 GCTCCCCCTCCCCTCTTC 60.770 72.222 0.00 0.00 0.00 2.87
532 533 2.040359 CTCCCCCTCCCCTCTTCC 60.040 72.222 0.00 0.00 0.00 3.46
533 534 2.543637 TCCCCCTCCCCTCTTCCT 60.544 66.667 0.00 0.00 0.00 3.36
534 535 2.040359 CCCCCTCCCCTCTTCCTC 60.040 72.222 0.00 0.00 0.00 3.71
535 536 2.040359 CCCCTCCCCTCTTCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
536 537 2.040359 CCCTCCCCTCTTCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
537 538 2.787866 CCTCCCCTCTTCCTCCCA 59.212 66.667 0.00 0.00 0.00 4.37
538 539 1.690985 CCTCCCCTCTTCCTCCCAC 60.691 68.421 0.00 0.00 0.00 4.61
539 540 1.690985 CTCCCCTCTTCCTCCCACC 60.691 68.421 0.00 0.00 0.00 4.61
540 541 2.184631 TCCCCTCTTCCTCCCACCT 61.185 63.158 0.00 0.00 0.00 4.00
541 542 1.690985 CCCCTCTTCCTCCCACCTC 60.691 68.421 0.00 0.00 0.00 3.85
542 543 1.394151 CCCTCTTCCTCCCACCTCT 59.606 63.158 0.00 0.00 0.00 3.69
543 544 0.689412 CCCTCTTCCTCCCACCTCTC 60.689 65.000 0.00 0.00 0.00 3.20
544 545 1.040339 CCTCTTCCTCCCACCTCTCG 61.040 65.000 0.00 0.00 0.00 4.04
545 546 0.033991 CTCTTCCTCCCACCTCTCGA 60.034 60.000 0.00 0.00 0.00 4.04
546 547 0.323542 TCTTCCTCCCACCTCTCGAC 60.324 60.000 0.00 0.00 0.00 4.20
547 548 0.612174 CTTCCTCCCACCTCTCGACA 60.612 60.000 0.00 0.00 0.00 4.35
548 549 0.898789 TTCCTCCCACCTCTCGACAC 60.899 60.000 0.00 0.00 0.00 3.67
549 550 2.352032 CCTCCCACCTCTCGACACC 61.352 68.421 0.00 0.00 0.00 4.16
550 551 2.283676 TCCCACCTCTCGACACCC 60.284 66.667 0.00 0.00 0.00 4.61
551 552 2.603473 CCCACCTCTCGACACCCA 60.603 66.667 0.00 0.00 0.00 4.51
552 553 2.657237 CCACCTCTCGACACCCAC 59.343 66.667 0.00 0.00 0.00 4.61
553 554 2.207229 CCACCTCTCGACACCCACA 61.207 63.158 0.00 0.00 0.00 4.17
554 555 1.290324 CACCTCTCGACACCCACAG 59.710 63.158 0.00 0.00 0.00 3.66
555 556 1.152525 ACCTCTCGACACCCACAGT 60.153 57.895 0.00 0.00 0.00 3.55
556 557 1.179814 ACCTCTCGACACCCACAGTC 61.180 60.000 0.00 0.00 0.00 3.51
557 558 1.587054 CTCTCGACACCCACAGTCC 59.413 63.158 0.00 0.00 32.41 3.85
558 559 1.878656 CTCTCGACACCCACAGTCCC 61.879 65.000 0.00 0.00 32.41 4.46
559 560 1.908793 CTCGACACCCACAGTCCCT 60.909 63.158 0.00 0.00 32.41 4.20
560 561 1.878656 CTCGACACCCACAGTCCCTC 61.879 65.000 0.00 0.00 32.41 4.30
561 562 2.943978 CGACACCCACAGTCCCTCC 61.944 68.421 0.00 0.00 32.41 4.30
562 563 2.529389 ACACCCACAGTCCCTCCC 60.529 66.667 0.00 0.00 0.00 4.30
563 564 3.706373 CACCCACAGTCCCTCCCG 61.706 72.222 0.00 0.00 0.00 5.14
564 565 4.250170 ACCCACAGTCCCTCCCGT 62.250 66.667 0.00 0.00 0.00 5.28
565 566 3.391382 CCCACAGTCCCTCCCGTC 61.391 72.222 0.00 0.00 0.00 4.79
566 567 2.283966 CCACAGTCCCTCCCGTCT 60.284 66.667 0.00 0.00 0.00 4.18
567 568 2.352032 CCACAGTCCCTCCCGTCTC 61.352 68.421 0.00 0.00 0.00 3.36
568 569 2.037527 ACAGTCCCTCCCGTCTCC 59.962 66.667 0.00 0.00 0.00 3.71
569 570 2.760385 CAGTCCCTCCCGTCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
570 571 3.273654 AGTCCCTCCCGTCTCCCA 61.274 66.667 0.00 0.00 0.00 4.37
571 572 3.075641 GTCCCTCCCGTCTCCCAC 61.076 72.222 0.00 0.00 0.00 4.61
572 573 4.393778 TCCCTCCCGTCTCCCACC 62.394 72.222 0.00 0.00 0.00 4.61
579 580 4.436998 CGTCTCCCACCCGCACTC 62.437 72.222 0.00 0.00 0.00 3.51
580 581 2.997897 GTCTCCCACCCGCACTCT 60.998 66.667 0.00 0.00 0.00 3.24
581 582 2.680352 TCTCCCACCCGCACTCTC 60.680 66.667 0.00 0.00 0.00 3.20
582 583 2.681778 CTCCCACCCGCACTCTCT 60.682 66.667 0.00 0.00 0.00 3.10
593 594 1.334599 CGCACTCTCTATCTTCCTCGC 60.335 57.143 0.00 0.00 0.00 5.03
654 655 1.992519 GAGCCCATGCCCAGACTCAT 61.993 60.000 0.00 0.00 38.69 2.90
702 703 0.768221 ACTGCTCCTCTTCCCCAACA 60.768 55.000 0.00 0.00 0.00 3.33
767 768 3.700831 ATCGGCGACCTCGTCTCCT 62.701 63.158 13.76 0.00 42.59 3.69
768 769 4.180946 CGGCGACCTCGTCTCCTG 62.181 72.222 0.00 0.00 42.59 3.86
804 806 4.003788 CCACCGCTGACCGACCTT 62.004 66.667 0.00 0.00 40.02 3.50
830 1228 0.179073 CATCTCGTCCATCCACCCAC 60.179 60.000 0.00 0.00 0.00 4.61
918 1316 2.000701 TTCTGGCGATGGATGGGGT 61.001 57.895 0.00 0.00 0.00 4.95
936 1337 0.391130 GTGCACCAGTTCTGGCGATA 60.391 55.000 17.55 0.41 0.00 2.92
938 1339 0.108138 GCACCAGTTCTGGCGATAGT 60.108 55.000 17.55 0.00 39.35 2.12
1158 1559 0.174389 TCTTCTCTCATGCGTGGCTC 59.826 55.000 5.98 0.00 0.00 4.70
1176 1577 3.558411 GCGTGCTGCAGATCCGAC 61.558 66.667 20.43 8.10 45.45 4.79
1238 1639 4.077184 GGGGACGACCGATGTGCA 62.077 66.667 0.00 0.00 41.60 4.57
1288 1706 1.545428 GCCCTCCTTGTTCACATCACA 60.545 52.381 0.00 0.00 0.00 3.58
1343 1769 0.741221 AAGGAAGATGGCGAACGAGC 60.741 55.000 0.00 0.00 0.00 5.03
1386 1824 1.126329 ATCCTCGCCATCATCCTGCT 61.126 55.000 0.00 0.00 0.00 4.24
1393 1831 1.822613 CATCATCCTGCTGCCGCTT 60.823 57.895 0.70 0.00 36.97 4.68
1459 1900 2.831742 CCGGTCCCGTGCTAGCTA 60.832 66.667 17.23 0.00 37.81 3.32
1503 1944 0.820226 CTCTCCTGAGCGTGATTCCA 59.180 55.000 0.00 0.00 33.12 3.53
1578 2137 0.374063 CTGAATCTGCTTGCTGCTCG 59.626 55.000 0.00 0.00 43.37 5.03
1587 2146 0.952497 CTTGCTGCTCGCCTTCTTCA 60.952 55.000 0.00 0.00 38.05 3.02
1660 2219 2.039624 GGGGCTCCTCACCTCTGA 59.960 66.667 0.00 0.00 0.00 3.27
1662 2221 2.363172 GGGCTCCTCACCTCTGACC 61.363 68.421 0.00 0.00 0.00 4.02
2212 2784 9.045745 ACAAATGTAATTTAATTGGATGGTCCT 57.954 29.630 0.00 0.00 46.64 3.85
2220 2792 7.789202 TTTAATTGGATGGTCCTTTTCATCA 57.211 32.000 0.00 0.00 40.94 3.07
2260 2832 2.912956 TGTGCCTCCCTTACTGAAGAAT 59.087 45.455 0.00 0.00 34.25 2.40
2396 2969 0.042731 TCCATCCTTTCCTCCGTCCT 59.957 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.055719 GCTAGGGTTTGCTGCGCA 61.056 61.111 10.98 10.98 36.47 6.09
1 2 4.166011 CGCTAGGGTTTGCTGCGC 62.166 66.667 0.00 0.00 40.15 6.09
3 4 2.747855 AGCGCTAGGGTTTGCTGC 60.748 61.111 8.99 0.00 36.09 5.25
4 5 1.078848 AGAGCGCTAGGGTTTGCTG 60.079 57.895 11.50 0.00 37.91 4.41
5 6 1.219393 GAGAGCGCTAGGGTTTGCT 59.781 57.895 11.50 0.00 41.11 3.91
6 7 1.079127 TGAGAGCGCTAGGGTTTGC 60.079 57.895 11.50 0.00 0.00 3.68
7 8 0.037326 TGTGAGAGCGCTAGGGTTTG 60.037 55.000 11.50 0.00 0.00 2.93
8 9 0.037232 GTGTGAGAGCGCTAGGGTTT 60.037 55.000 11.50 0.00 0.00 3.27
9 10 1.185618 TGTGTGAGAGCGCTAGGGTT 61.186 55.000 11.50 1.59 0.00 4.11
10 11 1.185618 TTGTGTGAGAGCGCTAGGGT 61.186 55.000 11.50 0.00 0.00 4.34
11 12 0.737715 GTTGTGTGAGAGCGCTAGGG 60.738 60.000 11.50 1.65 0.00 3.53
12 13 0.244994 AGTTGTGTGAGAGCGCTAGG 59.755 55.000 11.50 0.00 0.00 3.02
13 14 1.623359 GAGTTGTGTGAGAGCGCTAG 58.377 55.000 11.50 0.00 0.00 3.42
14 15 0.243907 GGAGTTGTGTGAGAGCGCTA 59.756 55.000 11.50 0.00 0.00 4.26
15 16 1.005630 GGAGTTGTGTGAGAGCGCT 60.006 57.895 11.27 11.27 0.00 5.92
16 17 1.005630 AGGAGTTGTGTGAGAGCGC 60.006 57.895 0.00 0.00 0.00 5.92
17 18 0.389166 GGAGGAGTTGTGTGAGAGCG 60.389 60.000 0.00 0.00 0.00 5.03
18 19 0.972883 AGGAGGAGTTGTGTGAGAGC 59.027 55.000 0.00 0.00 0.00 4.09
19 20 2.896685 AGAAGGAGGAGTTGTGTGAGAG 59.103 50.000 0.00 0.00 0.00 3.20
20 21 2.630098 CAGAAGGAGGAGTTGTGTGAGA 59.370 50.000 0.00 0.00 0.00 3.27
21 22 2.289320 CCAGAAGGAGGAGTTGTGTGAG 60.289 54.545 0.00 0.00 36.89 3.51
22 23 1.694150 CCAGAAGGAGGAGTTGTGTGA 59.306 52.381 0.00 0.00 36.89 3.58
23 24 1.694150 TCCAGAAGGAGGAGTTGTGTG 59.306 52.381 0.00 0.00 39.61 3.82
24 25 2.103153 TCCAGAAGGAGGAGTTGTGT 57.897 50.000 0.00 0.00 39.61 3.72
35 36 2.190578 GGCGGTGGATCCAGAAGG 59.809 66.667 16.81 5.79 35.57 3.46
36 37 2.202932 CGGCGGTGGATCCAGAAG 60.203 66.667 16.81 10.65 35.57 2.85
37 38 4.467084 GCGGCGGTGGATCCAGAA 62.467 66.667 16.81 0.00 35.57 3.02
58 59 3.339093 GAGGGAGTGGGGTTGGGG 61.339 72.222 0.00 0.00 0.00 4.96
59 60 3.339093 GGAGGGAGTGGGGTTGGG 61.339 72.222 0.00 0.00 0.00 4.12
60 61 3.339093 GGGAGGGAGTGGGGTTGG 61.339 72.222 0.00 0.00 0.00 3.77
61 62 2.204151 AGGGAGGGAGTGGGGTTG 60.204 66.667 0.00 0.00 0.00 3.77
62 63 1.160289 TAGAGGGAGGGAGTGGGGTT 61.160 60.000 0.00 0.00 0.00 4.11
63 64 1.549322 TAGAGGGAGGGAGTGGGGT 60.549 63.158 0.00 0.00 0.00 4.95
64 65 1.234529 CTAGAGGGAGGGAGTGGGG 59.765 68.421 0.00 0.00 0.00 4.96
65 66 0.863956 ATCTAGAGGGAGGGAGTGGG 59.136 60.000 0.00 0.00 0.00 4.61
66 67 1.786441 AGATCTAGAGGGAGGGAGTGG 59.214 57.143 0.00 0.00 0.00 4.00
67 68 2.552155 CGAGATCTAGAGGGAGGGAGTG 60.552 59.091 0.00 0.00 0.00 3.51
68 69 1.702957 CGAGATCTAGAGGGAGGGAGT 59.297 57.143 0.00 0.00 0.00 3.85
69 70 1.982226 TCGAGATCTAGAGGGAGGGAG 59.018 57.143 0.81 0.00 0.00 4.30
70 71 1.700739 GTCGAGATCTAGAGGGAGGGA 59.299 57.143 5.70 0.00 0.00 4.20
71 72 1.609580 CGTCGAGATCTAGAGGGAGGG 60.610 61.905 15.37 0.00 0.00 4.30
72 73 1.803334 CGTCGAGATCTAGAGGGAGG 58.197 60.000 15.37 2.73 0.00 4.30
73 74 1.153353 GCGTCGAGATCTAGAGGGAG 58.847 60.000 21.89 9.40 0.00 4.30
74 75 0.600518 CGCGTCGAGATCTAGAGGGA 60.601 60.000 21.89 2.61 0.00 4.20
75 76 1.863491 CGCGTCGAGATCTAGAGGG 59.137 63.158 21.89 11.87 0.00 4.30
76 77 1.205568 GCGCGTCGAGATCTAGAGG 59.794 63.158 17.95 17.95 0.00 3.69
77 78 1.205568 GGCGCGTCGAGATCTAGAG 59.794 63.158 8.43 2.42 0.00 2.43
78 79 2.595878 CGGCGCGTCGAGATCTAGA 61.596 63.158 32.09 0.81 0.00 2.43
79 80 2.127571 CGGCGCGTCGAGATCTAG 60.128 66.667 32.09 0.00 0.00 2.43
80 81 4.309347 GCGGCGCGTCGAGATCTA 62.309 66.667 39.63 0.00 0.00 1.98
99 100 3.403558 GAGGAGTGGGGTGAGGGC 61.404 72.222 0.00 0.00 0.00 5.19
100 101 2.689034 GGAGGAGTGGGGTGAGGG 60.689 72.222 0.00 0.00 0.00 4.30
101 102 3.077556 CGGAGGAGTGGGGTGAGG 61.078 72.222 0.00 0.00 0.00 3.86
121 122 1.305930 GGTGAGAATGTGCGGGGAAC 61.306 60.000 0.00 0.00 0.00 3.62
122 123 1.002624 GGTGAGAATGTGCGGGGAA 60.003 57.895 0.00 0.00 0.00 3.97
123 124 2.668632 GGTGAGAATGTGCGGGGA 59.331 61.111 0.00 0.00 0.00 4.81
124 125 2.819595 CGGTGAGAATGTGCGGGG 60.820 66.667 0.00 0.00 0.00 5.73
125 126 3.499737 GCGGTGAGAATGTGCGGG 61.500 66.667 0.00 0.00 0.00 6.13
126 127 2.434884 AGCGGTGAGAATGTGCGG 60.435 61.111 0.00 0.00 0.00 5.69
127 128 2.792290 CGAGCGGTGAGAATGTGCG 61.792 63.158 0.00 0.00 0.00 5.34
128 129 2.456119 CCGAGCGGTGAGAATGTGC 61.456 63.158 0.00 0.00 0.00 4.57
129 130 0.803768 CTCCGAGCGGTGAGAATGTG 60.804 60.000 8.96 0.00 36.47 3.21
130 131 0.965866 TCTCCGAGCGGTGAGAATGT 60.966 55.000 8.96 0.00 34.79 2.71
131 132 0.526524 GTCTCCGAGCGGTGAGAATG 60.527 60.000 13.28 0.00 39.22 2.67
132 133 1.668101 GGTCTCCGAGCGGTGAGAAT 61.668 60.000 13.28 0.00 39.22 2.40
133 134 2.341101 GGTCTCCGAGCGGTGAGAA 61.341 63.158 13.28 0.00 39.22 2.87
134 135 2.750637 GGTCTCCGAGCGGTGAGA 60.751 66.667 13.28 5.20 38.30 3.27
135 136 3.827898 GGGTCTCCGAGCGGTGAG 61.828 72.222 13.28 2.86 38.30 3.51
142 143 4.400251 AGGGTGGGGGTCTCCGAG 62.400 72.222 0.00 0.00 36.01 4.63
143 144 4.393778 GAGGGTGGGGGTCTCCGA 62.394 72.222 0.00 0.00 36.01 4.55
149 150 4.741239 ATCTGCGAGGGTGGGGGT 62.741 66.667 0.00 0.00 0.00 4.95
150 151 3.866582 GATCTGCGAGGGTGGGGG 61.867 72.222 0.00 0.00 0.00 5.40
151 152 3.866582 GGATCTGCGAGGGTGGGG 61.867 72.222 0.00 0.00 0.00 4.96
152 153 2.669133 TTGGATCTGCGAGGGTGGG 61.669 63.158 0.00 0.00 0.00 4.61
153 154 1.450312 GTTGGATCTGCGAGGGTGG 60.450 63.158 0.00 0.00 0.00 4.61
154 155 1.811266 CGTTGGATCTGCGAGGGTG 60.811 63.158 0.00 0.00 0.00 4.61
155 156 2.579201 CGTTGGATCTGCGAGGGT 59.421 61.111 0.00 0.00 0.00 4.34
156 157 2.892425 GCGTTGGATCTGCGAGGG 60.892 66.667 7.94 0.00 0.00 4.30
177 178 2.764128 TGGATCGGAGGAGGCACC 60.764 66.667 0.00 0.00 39.35 5.01
178 179 1.118356 ATCTGGATCGGAGGAGGCAC 61.118 60.000 0.00 0.00 0.00 5.01
179 180 0.829602 GATCTGGATCGGAGGAGGCA 60.830 60.000 0.00 0.00 0.00 4.75
180 181 1.971418 GATCTGGATCGGAGGAGGC 59.029 63.158 0.00 0.00 0.00 4.70
189 190 1.300233 GGGCGTGTCGATCTGGATC 60.300 63.158 0.00 0.83 34.56 3.36
190 191 2.797278 GGGGCGTGTCGATCTGGAT 61.797 63.158 0.00 0.00 0.00 3.41
191 192 3.458163 GGGGCGTGTCGATCTGGA 61.458 66.667 0.00 0.00 0.00 3.86
192 193 2.907897 GAAGGGGCGTGTCGATCTGG 62.908 65.000 0.00 0.00 0.00 3.86
193 194 1.519455 GAAGGGGCGTGTCGATCTG 60.519 63.158 0.00 0.00 0.00 2.90
194 195 2.722201 GGAAGGGGCGTGTCGATCT 61.722 63.158 0.00 0.00 0.00 2.75
195 196 2.202892 GGAAGGGGCGTGTCGATC 60.203 66.667 0.00 0.00 0.00 3.69
196 197 3.000819 TGGAAGGGGCGTGTCGAT 61.001 61.111 0.00 0.00 0.00 3.59
197 198 3.998672 GTGGAAGGGGCGTGTCGA 61.999 66.667 0.00 0.00 0.00 4.20
199 200 3.948719 TGGTGGAAGGGGCGTGTC 61.949 66.667 0.00 0.00 0.00 3.67
200 201 4.265056 GTGGTGGAAGGGGCGTGT 62.265 66.667 0.00 0.00 0.00 4.49
205 206 3.661648 CAGGGGTGGTGGAAGGGG 61.662 72.222 0.00 0.00 0.00 4.79
206 207 4.366684 GCAGGGGTGGTGGAAGGG 62.367 72.222 0.00 0.00 0.00 3.95
207 208 4.366684 GGCAGGGGTGGTGGAAGG 62.367 72.222 0.00 0.00 0.00 3.46
208 209 4.722700 CGGCAGGGGTGGTGGAAG 62.723 72.222 0.00 0.00 0.00 3.46
449 450 1.131126 CGCCTGCTGTAACTTTGGATG 59.869 52.381 0.00 0.00 0.00 3.51
450 451 1.453155 CGCCTGCTGTAACTTTGGAT 58.547 50.000 0.00 0.00 0.00 3.41
451 452 1.234615 GCGCCTGCTGTAACTTTGGA 61.235 55.000 0.00 0.00 38.39 3.53
452 453 1.210155 GCGCCTGCTGTAACTTTGG 59.790 57.895 0.00 0.00 38.39 3.28
453 454 4.847255 GCGCCTGCTGTAACTTTG 57.153 55.556 0.00 0.00 38.39 2.77
464 465 4.292178 GATCGAGGGGAGCGCCTG 62.292 72.222 11.11 4.12 0.00 4.85
468 469 3.299190 GAGGGATCGAGGGGAGCG 61.299 72.222 0.00 0.00 0.00 5.03
469 470 2.920384 GGAGGGATCGAGGGGAGC 60.920 72.222 0.00 0.00 0.00 4.70
470 471 2.203714 GGGAGGGATCGAGGGGAG 60.204 72.222 0.00 0.00 0.00 4.30
471 472 3.033773 TGGGAGGGATCGAGGGGA 61.034 66.667 0.00 0.00 0.00 4.81
472 473 2.844839 GTGGGAGGGATCGAGGGG 60.845 72.222 0.00 0.00 0.00 4.79
473 474 2.844839 GGTGGGAGGGATCGAGGG 60.845 72.222 0.00 0.00 0.00 4.30
474 475 3.227276 CGGTGGGAGGGATCGAGG 61.227 72.222 0.00 0.00 0.00 4.63
475 476 3.917760 GCGGTGGGAGGGATCGAG 61.918 72.222 0.00 0.00 0.00 4.04
485 486 4.452733 GAAGGAGACGGCGGTGGG 62.453 72.222 13.24 0.00 0.00 4.61
486 487 4.452733 GGAAGGAGACGGCGGTGG 62.453 72.222 13.24 0.00 0.00 4.61
487 488 4.452733 GGGAAGGAGACGGCGGTG 62.453 72.222 13.24 0.00 0.00 4.94
488 489 4.698625 AGGGAAGGAGACGGCGGT 62.699 66.667 13.24 0.00 0.00 5.68
489 490 3.839432 GAGGGAAGGAGACGGCGG 61.839 72.222 13.24 0.00 0.00 6.13
490 491 3.068691 TGAGGGAAGGAGACGGCG 61.069 66.667 4.80 4.80 0.00 6.46
491 492 1.045911 ATCTGAGGGAAGGAGACGGC 61.046 60.000 0.00 0.00 0.00 5.68
492 493 1.036707 GATCTGAGGGAAGGAGACGG 58.963 60.000 0.00 0.00 0.00 4.79
493 494 0.665835 CGATCTGAGGGAAGGAGACG 59.334 60.000 0.00 0.00 0.00 4.18
494 495 1.953686 CTCGATCTGAGGGAAGGAGAC 59.046 57.143 6.66 0.00 41.29 3.36
495 496 1.752436 GCTCGATCTGAGGGAAGGAGA 60.752 57.143 13.84 0.00 45.38 3.71
496 497 0.673437 GCTCGATCTGAGGGAAGGAG 59.327 60.000 13.84 1.59 45.38 3.69
497 498 0.260230 AGCTCGATCTGAGGGAAGGA 59.740 55.000 13.84 0.00 45.38 3.36
498 499 0.673437 GAGCTCGATCTGAGGGAAGG 59.327 60.000 0.00 0.00 45.38 3.46
499 500 0.673437 GGAGCTCGATCTGAGGGAAG 59.327 60.000 7.83 0.00 45.38 3.46
500 501 0.757188 GGGAGCTCGATCTGAGGGAA 60.757 60.000 7.83 0.00 45.38 3.97
501 502 1.152652 GGGAGCTCGATCTGAGGGA 60.153 63.158 7.83 0.00 45.38 4.20
502 503 2.206536 GGGGAGCTCGATCTGAGGG 61.207 68.421 7.83 0.00 45.38 4.30
503 504 2.206536 GGGGGAGCTCGATCTGAGG 61.207 68.421 7.83 0.60 45.38 3.86
505 506 1.152652 GAGGGGGAGCTCGATCTGA 60.153 63.158 7.83 0.00 0.00 3.27
506 507 2.206536 GGAGGGGGAGCTCGATCTG 61.207 68.421 7.83 0.00 0.00 2.90
507 508 2.200092 GGAGGGGGAGCTCGATCT 59.800 66.667 7.83 4.32 0.00 2.75
508 509 2.920384 GGGAGGGGGAGCTCGATC 60.920 72.222 7.83 2.71 0.00 3.69
509 510 4.565850 GGGGAGGGGGAGCTCGAT 62.566 72.222 7.83 0.00 0.00 3.59
512 513 3.339951 AAGAGGGGAGGGGGAGCTC 62.340 68.421 4.71 4.71 0.00 4.09
513 514 3.296737 AAGAGGGGAGGGGGAGCT 61.297 66.667 0.00 0.00 0.00 4.09
514 515 2.770475 GAAGAGGGGAGGGGGAGC 60.770 72.222 0.00 0.00 0.00 4.70
515 516 2.040359 GGAAGAGGGGAGGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
516 517 2.543637 AGGAAGAGGGGAGGGGGA 60.544 66.667 0.00 0.00 0.00 4.81
517 518 2.040359 GAGGAAGAGGGGAGGGGG 60.040 72.222 0.00 0.00 0.00 5.40
518 519 2.040359 GGAGGAAGAGGGGAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
519 520 2.040359 GGGAGGAAGAGGGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
520 521 1.690985 GTGGGAGGAAGAGGGGAGG 60.691 68.421 0.00 0.00 0.00 4.30
521 522 1.690985 GGTGGGAGGAAGAGGGGAG 60.691 68.421 0.00 0.00 0.00 4.30
522 523 2.182858 GAGGTGGGAGGAAGAGGGGA 62.183 65.000 0.00 0.00 0.00 4.81
523 524 1.690985 GAGGTGGGAGGAAGAGGGG 60.691 68.421 0.00 0.00 0.00 4.79
524 525 0.689412 GAGAGGTGGGAGGAAGAGGG 60.689 65.000 0.00 0.00 0.00 4.30
525 526 1.040339 CGAGAGGTGGGAGGAAGAGG 61.040 65.000 0.00 0.00 0.00 3.69
526 527 0.033991 TCGAGAGGTGGGAGGAAGAG 60.034 60.000 0.00 0.00 0.00 2.85
527 528 0.323542 GTCGAGAGGTGGGAGGAAGA 60.324 60.000 0.00 0.00 0.00 2.87
528 529 0.612174 TGTCGAGAGGTGGGAGGAAG 60.612 60.000 0.00 0.00 0.00 3.46
529 530 0.898789 GTGTCGAGAGGTGGGAGGAA 60.899 60.000 0.00 0.00 0.00 3.36
530 531 1.304217 GTGTCGAGAGGTGGGAGGA 60.304 63.158 0.00 0.00 0.00 3.71
531 532 2.352032 GGTGTCGAGAGGTGGGAGG 61.352 68.421 0.00 0.00 0.00 4.30
532 533 2.352032 GGGTGTCGAGAGGTGGGAG 61.352 68.421 0.00 0.00 0.00 4.30
533 534 2.283676 GGGTGTCGAGAGGTGGGA 60.284 66.667 0.00 0.00 0.00 4.37
534 535 2.603473 TGGGTGTCGAGAGGTGGG 60.603 66.667 0.00 0.00 0.00 4.61
535 536 2.159819 CTGTGGGTGTCGAGAGGTGG 62.160 65.000 0.00 0.00 0.00 4.61
536 537 1.290324 CTGTGGGTGTCGAGAGGTG 59.710 63.158 0.00 0.00 0.00 4.00
537 538 1.152525 ACTGTGGGTGTCGAGAGGT 60.153 57.895 0.00 0.00 0.00 3.85
538 539 1.587054 GACTGTGGGTGTCGAGAGG 59.413 63.158 0.00 0.00 0.00 3.69
539 540 1.587054 GGACTGTGGGTGTCGAGAG 59.413 63.158 0.00 0.00 35.45 3.20
540 541 1.906824 GGGACTGTGGGTGTCGAGA 60.907 63.158 0.00 0.00 35.45 4.04
541 542 1.878656 GAGGGACTGTGGGTGTCGAG 61.879 65.000 0.00 0.00 41.55 4.04
542 543 1.906824 GAGGGACTGTGGGTGTCGA 60.907 63.158 0.00 0.00 41.55 4.20
543 544 2.657237 GAGGGACTGTGGGTGTCG 59.343 66.667 0.00 0.00 41.55 4.35
544 545 2.593956 GGGAGGGACTGTGGGTGTC 61.594 68.421 0.00 0.00 41.55 3.67
545 546 2.529389 GGGAGGGACTGTGGGTGT 60.529 66.667 0.00 0.00 41.55 4.16
546 547 3.706373 CGGGAGGGACTGTGGGTG 61.706 72.222 0.00 0.00 41.55 4.61
547 548 4.250170 ACGGGAGGGACTGTGGGT 62.250 66.667 0.00 0.00 41.55 4.51
548 549 3.391382 GACGGGAGGGACTGTGGG 61.391 72.222 0.00 0.00 41.55 4.61
549 550 2.283966 AGACGGGAGGGACTGTGG 60.284 66.667 0.00 0.00 41.55 4.17
550 551 2.352032 GGAGACGGGAGGGACTGTG 61.352 68.421 0.00 0.00 41.55 3.66
551 552 2.037527 GGAGACGGGAGGGACTGT 59.962 66.667 0.00 0.00 41.55 3.55
552 553 2.760385 GGGAGACGGGAGGGACTG 60.760 72.222 0.00 0.00 41.55 3.51
554 555 3.075641 GTGGGAGACGGGAGGGAC 61.076 72.222 0.00 0.00 0.00 4.46
555 556 4.393778 GGTGGGAGACGGGAGGGA 62.394 72.222 0.00 0.00 0.00 4.20
562 563 4.436998 GAGTGCGGGTGGGAGACG 62.437 72.222 0.00 0.00 0.00 4.18
563 564 2.997897 AGAGTGCGGGTGGGAGAC 60.998 66.667 0.00 0.00 0.00 3.36
564 565 1.859841 TAGAGAGTGCGGGTGGGAGA 61.860 60.000 0.00 0.00 0.00 3.71
565 566 0.757188 ATAGAGAGTGCGGGTGGGAG 60.757 60.000 0.00 0.00 0.00 4.30
566 567 0.755698 GATAGAGAGTGCGGGTGGGA 60.756 60.000 0.00 0.00 0.00 4.37
567 568 0.757188 AGATAGAGAGTGCGGGTGGG 60.757 60.000 0.00 0.00 0.00 4.61
568 569 1.067821 GAAGATAGAGAGTGCGGGTGG 59.932 57.143 0.00 0.00 0.00 4.61
569 570 1.067821 GGAAGATAGAGAGTGCGGGTG 59.932 57.143 0.00 0.00 0.00 4.61
570 571 1.063567 AGGAAGATAGAGAGTGCGGGT 60.064 52.381 0.00 0.00 0.00 5.28
571 572 1.611491 GAGGAAGATAGAGAGTGCGGG 59.389 57.143 0.00 0.00 0.00 6.13
572 573 1.265635 CGAGGAAGATAGAGAGTGCGG 59.734 57.143 0.00 0.00 0.00 5.69
573 574 1.334599 GCGAGGAAGATAGAGAGTGCG 60.335 57.143 0.00 0.00 0.00 5.34
574 575 1.953686 AGCGAGGAAGATAGAGAGTGC 59.046 52.381 0.00 0.00 0.00 4.40
575 576 2.223144 CGAGCGAGGAAGATAGAGAGTG 59.777 54.545 0.00 0.00 0.00 3.51
576 577 2.103432 TCGAGCGAGGAAGATAGAGAGT 59.897 50.000 0.00 0.00 0.00 3.24
577 578 2.761559 TCGAGCGAGGAAGATAGAGAG 58.238 52.381 0.00 0.00 0.00 3.20
578 579 2.912690 TCGAGCGAGGAAGATAGAGA 57.087 50.000 0.00 0.00 0.00 3.10
579 580 3.119990 GGAATCGAGCGAGGAAGATAGAG 60.120 52.174 0.00 0.00 0.00 2.43
580 581 2.814919 GGAATCGAGCGAGGAAGATAGA 59.185 50.000 0.00 0.00 0.00 1.98
581 582 2.094957 GGGAATCGAGCGAGGAAGATAG 60.095 54.545 0.00 0.00 0.00 2.08
582 583 1.887198 GGGAATCGAGCGAGGAAGATA 59.113 52.381 0.00 0.00 0.00 1.98
593 594 0.029035 CGTCTACGGTGGGAATCGAG 59.971 60.000 0.00 0.00 35.37 4.04
630 631 3.839353 CTGGGCATGGGCTCGATCC 62.839 68.421 0.00 0.00 46.33 3.36
702 703 2.043227 GAGATTGGAGAGGAATCGGGT 58.957 52.381 0.00 0.00 35.36 5.28
794 796 0.041238 ATGAGGAGGAAGGTCGGTCA 59.959 55.000 0.00 0.00 0.00 4.02
804 806 1.479573 GGATGGACGAGATGAGGAGGA 60.480 57.143 0.00 0.00 0.00 3.71
830 1228 1.002502 GTGGAAGAGGGGGTTTCCG 60.003 63.158 0.00 0.00 44.66 4.30
1238 1639 1.925455 CCACCTCCTGGTCCACCAT 60.925 63.158 0.00 0.00 46.60 3.55
1288 1706 1.432807 TCCAAGGGAAAGCAAAGGGAT 59.567 47.619 0.00 0.00 0.00 3.85
1343 1769 2.827051 CGATGCAGTTGGCCATCCG 61.827 63.158 6.09 0.00 43.89 4.18
1393 1831 0.319555 CGAACTTGAGGAAGACGCCA 60.320 55.000 0.00 0.00 32.98 5.69
1459 1900 7.773690 AGAACCTACTGTGAAGTTTAAACATGT 59.226 33.333 20.06 10.78 0.00 3.21
1503 1944 3.576982 TGTCAGTTAACCCAACTCTCGAT 59.423 43.478 0.88 0.00 44.48 3.59
1578 2137 0.179234 GGGAGGTAGCTGAAGAAGGC 59.821 60.000 0.00 0.00 0.00 4.35
1587 2146 0.401105 ATGATGCCAGGGAGGTAGCT 60.401 55.000 0.00 0.00 39.36 3.32
1660 2219 0.681733 CATGCATACCTAGAGGCGGT 59.318 55.000 0.00 0.00 39.32 5.68
1662 2221 0.033920 TGCATGCATACCTAGAGGCG 59.966 55.000 18.46 0.00 39.32 5.52
1789 2349 9.455847 GTTGTTAAGAATACGACGGACTATATT 57.544 33.333 0.00 0.00 0.00 1.28
2303 2875 2.494073 GACACTGCCTAGAGTGCTTACT 59.506 50.000 10.67 0.00 46.28 2.24
2387 2960 2.185004 AACAATGACAAGGACGGAGG 57.815 50.000 0.00 0.00 0.00 4.30
2396 2969 5.020132 CCCAGGGGTAAATAACAATGACAA 58.980 41.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.