Multiple sequence alignment - TraesCS2A01G058400

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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 TraesCS2A01G058400 chr2A 100.000 3474 0 0 1 3474 24429009 24432482 0.000000e+00 6416
1 TraesCS2A01G058400 chr2A 94.186 86 3 2 1 85 579401662 579401746 2.810000e-26 130
2 TraesCS2A01G058400 chr2B 92.722 1745 107 8 641 2376 37640840 37639107 0.000000e+00 2501
3 TraesCS2A01G058400 chr2B 89.845 581 31 13 76 642 37641440 37640874 0.000000e+00 721
4 TraesCS2A01G058400 chr2B 93.135 437 27 2 3031 3465 37581339 37580904 3.780000e-179 638
5 TraesCS2A01G058400 chrUn 92.212 1605 116 8 1281 2880 62497944 62499544 0.000000e+00 2263
6 TraesCS2A01G058400 chrUn 92.025 1605 119 8 1281 2880 62429563 62431163 0.000000e+00 2246
7 TraesCS2A01G058400 chrUn 91.963 1605 120 8 1281 2880 62557904 62559504 0.000000e+00 2241
8 TraesCS2A01G058400 chrUn 91.963 1605 120 8 1281 2880 62613843 62615443 0.000000e+00 2241
9 TraesCS2A01G058400 chrUn 91.651 1605 125 8 1281 2880 62362489 62364089 0.000000e+00 2213
10 TraesCS2A01G058400 chrUn 91.584 1604 125 10 1282 2880 62312411 62314009 0.000000e+00 2206
11 TraesCS2A01G058400 chrUn 81.435 1115 110 50 147 1244 62612806 62613840 0.000000e+00 822
12 TraesCS2A01G058400 chrUn 86.739 739 77 9 147 875 62556867 62557594 0.000000e+00 802
13 TraesCS2A01G058400 chrUn 86.604 739 78 9 147 875 62361452 62362179 0.000000e+00 797
14 TraesCS2A01G058400 chrUn 86.198 739 81 9 147 875 62428512 62429239 0.000000e+00 780
15 TraesCS2A01G058400 chrUn 80.538 1115 121 47 147 1244 62496906 62497941 0.000000e+00 769
16 TraesCS2A01G058400 chrUn 91.736 484 21 8 2613 3096 62431236 62431700 0.000000e+00 654
17 TraesCS2A01G058400 chrUn 91.736 484 21 8 2613 3096 62559577 62560041 0.000000e+00 654
18 TraesCS2A01G058400 chrUn 91.546 485 21 9 2613 3096 62615516 62615981 0.000000e+00 651
19 TraesCS2A01G058400 chrUn 91.529 484 22 8 2613 3096 62364162 62364626 0.000000e+00 649
20 TraesCS2A01G058400 chrUn 90.928 485 23 10 2613 3096 62499617 62500081 1.760000e-177 632
21 TraesCS2A01G058400 chrUn 79.507 893 86 49 369 1244 62311595 62312407 2.360000e-151 545
22 TraesCS2A01G058400 chrUn 91.791 268 21 1 3199 3465 62431699 62431966 4.230000e-99 372
23 TraesCS2A01G058400 chrUn 84.564 149 17 2 1102 1244 62557753 62557901 3.610000e-30 143
24 TraesCS2A01G058400 chrUn 83.221 149 19 2 1102 1244 62362338 62362486 7.820000e-27 132
25 TraesCS2A01G058400 chr6A 92.087 1605 118 8 1281 2880 4270085 4268485 0.000000e+00 2252
26 TraesCS2A01G058400 chr6A 91.963 1605 120 8 1281 2880 4390102 4388502 0.000000e+00 2241
27 TraesCS2A01G058400 chr6A 91.698 1602 122 11 1285 2880 4335647 4334051 0.000000e+00 2211
28 TraesCS2A01G058400 chr6A 80.974 1109 114 48 153 1244 4391133 4390105 0.000000e+00 789
29 TraesCS2A01G058400 chr6A 86.512 734 76 11 153 875 4271116 4270395 0.000000e+00 785
30 TraesCS2A01G058400 chr6A 91.134 485 23 9 2613 3096 4388429 4387964 1.050000e-179 640
31 TraesCS2A01G058400 chr6A 91.116 484 24 8 2613 3096 4268412 4267948 3.780000e-179 638
32 TraesCS2A01G058400 chr6A 78.396 611 54 38 644 1244 4336196 4335654 3.340000e-85 326
33 TraesCS2A01G058400 chr6A 98.667 75 1 0 1 75 148816411 148816485 2.180000e-27 134
34 TraesCS2A01G058400 chr6A 95.294 85 2 2 1 84 405568982 405568899 2.180000e-27 134
35 TraesCS2A01G058400 chr6A 93.333 90 6 0 1 90 582669509 582669420 2.180000e-27 134
36 TraesCS2A01G058400 chr6A 83.221 149 19 2 1102 1244 4270236 4270088 7.820000e-27 132
37 TraesCS2A01G058400 chr2D 93.359 768 45 3 2698 3464 22841881 22842643 0.000000e+00 1131
38 TraesCS2A01G058400 chr2D 92.427 581 27 6 76 642 22839481 22840058 0.000000e+00 813
39 TraesCS2A01G058400 chr2D 94.805 462 19 2 641 1097 22840092 22840553 0.000000e+00 715
40 TraesCS2A01G058400 chr6D 91.062 772 60 8 2698 3465 5575583 5576349 0.000000e+00 1035
41 TraesCS2A01G058400 chr6D 80.435 230 36 5 1408 1637 5042955 5043175 2.140000e-37 167
42 TraesCS2A01G058400 chr7A 98.684 76 1 0 1 76 122240341 122240266 6.050000e-28 135
43 TraesCS2A01G058400 chr3A 94.444 90 2 3 1 88 480949720 480949632 6.050000e-28 135
44 TraesCS2A01G058400 chr3A 98.667 75 1 0 1 75 101248685 101248759 2.180000e-27 134
45 TraesCS2A01G058400 chr3A 95.181 83 3 1 1 83 585136617 585136698 2.810000e-26 130
46 TraesCS2A01G058400 chr5A 94.186 86 3 2 1 86 16420995 16421078 2.810000e-26 130


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 TraesCS2A01G058400 chr2A 24429009 24432482 3473 False 6416.000000 6416 100.000000 1 3474 1 chr2A.!!$F1 3473
1 TraesCS2A01G058400 chr2B 37639107 37641440 2333 True 1611.000000 2501 91.283500 76 2376 2 chr2B.!!$R2 2300
2 TraesCS2A01G058400 chrUn 62311595 62314009 2414 False 1375.500000 2206 85.545500 369 2880 2 chrUn.!!$F1 2511
3 TraesCS2A01G058400 chrUn 62612806 62615981 3175 False 1238.000000 2241 88.314667 147 3096 3 chrUn.!!$F6 2949
4 TraesCS2A01G058400 chrUn 62496906 62500081 3175 False 1221.333333 2263 87.892667 147 3096 3 chrUn.!!$F4 2949
5 TraesCS2A01G058400 chrUn 62428512 62431966 3454 False 1013.000000 2246 90.437500 147 3465 4 chrUn.!!$F3 3318
6 TraesCS2A01G058400 chrUn 62556867 62560041 3174 False 960.000000 2241 88.750500 147 3096 4 chrUn.!!$F5 2949
7 TraesCS2A01G058400 chrUn 62361452 62364626 3174 False 947.750000 2213 88.251250 147 3096 4 chrUn.!!$F2 2949
8 TraesCS2A01G058400 chr6A 4334051 4336196 2145 True 1268.500000 2211 85.047000 644 2880 2 chr6A.!!$R4 2236
9 TraesCS2A01G058400 chr6A 4387964 4391133 3169 True 1223.333333 2241 88.023667 153 3096 3 chr6A.!!$R5 2943
10 TraesCS2A01G058400 chr6A 4267948 4271116 3168 True 951.750000 2252 88.234000 153 3096 4 chr6A.!!$R3 2943
11 TraesCS2A01G058400 chr2D 22839481 22842643 3162 False 886.333333 1131 93.530333 76 3464 3 chr2D.!!$F1 3388
12 TraesCS2A01G058400 chr6D 5575583 5576349 766 False 1035.000000 1035 91.062000 2698 3465 1 chr6D.!!$F2 767

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
52 53 0.249398 ATAACTGGACGACACCTGGC 59.751 55.0 0.0 0.0 34.01 4.85 F
1016 1087 0.106819 ACAATGGATGCTCTGGAGGC 60.107 55.0 0.0 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1062 1133 1.003118 CAGGACGAAATGAACTGGGGA 59.997 52.381 0.0 0.0 0.00 4.81 R
2657 2742 0.240678 GCAATGGACGATGCACACAA 59.759 50.000 0.0 0.0 42.12 3.33 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
18 19 3.843632 GACACGCAAGCAATGACAA 57.156 47.368 0.84 0.00 45.62 3.18
19 20 1.678360 GACACGCAAGCAATGACAAG 58.322 50.000 0.84 0.00 45.62 3.16
20 21 0.311790 ACACGCAAGCAATGACAAGG 59.688 50.000 0.84 0.00 45.62 3.61
21 22 1.005294 CACGCAAGCAATGACAAGGC 61.005 55.000 0.00 0.00 45.62 4.35
22 23 1.286570 CGCAAGCAATGACAAGGCA 59.713 52.632 4.75 0.00 0.00 4.75
23 24 0.318869 CGCAAGCAATGACAAGGCAA 60.319 50.000 4.75 0.00 0.00 4.52
24 25 1.142474 GCAAGCAATGACAAGGCAAC 58.858 50.000 4.75 0.00 0.00 4.17
25 26 1.538634 GCAAGCAATGACAAGGCAACA 60.539 47.619 4.75 0.00 41.41 3.33
26 27 2.823984 CAAGCAATGACAAGGCAACAA 58.176 42.857 4.75 0.00 41.41 2.83
27 28 2.514205 AGCAATGACAAGGCAACAAC 57.486 45.000 4.75 0.00 41.41 3.32
28 29 1.755959 AGCAATGACAAGGCAACAACA 59.244 42.857 4.75 0.00 41.41 3.33
29 30 2.366266 AGCAATGACAAGGCAACAACAT 59.634 40.909 4.75 0.00 41.41 2.71
30 31 2.733026 GCAATGACAAGGCAACAACATC 59.267 45.455 0.00 0.00 41.41 3.06
31 32 2.981805 CAATGACAAGGCAACAACATCG 59.018 45.455 0.00 0.00 41.41 3.84
32 33 1.960417 TGACAAGGCAACAACATCGA 58.040 45.000 0.00 0.00 41.41 3.59
33 34 2.293170 TGACAAGGCAACAACATCGAA 58.707 42.857 0.00 0.00 41.41 3.71
34 35 2.884012 TGACAAGGCAACAACATCGAAT 59.116 40.909 0.00 0.00 41.41 3.34
35 36 4.068599 TGACAAGGCAACAACATCGAATA 58.931 39.130 0.00 0.00 41.41 1.75
36 37 4.517075 TGACAAGGCAACAACATCGAATAA 59.483 37.500 0.00 0.00 41.41 1.40
37 38 4.794169 ACAAGGCAACAACATCGAATAAC 58.206 39.130 0.00 0.00 41.41 1.89
38 39 4.518970 ACAAGGCAACAACATCGAATAACT 59.481 37.500 0.00 0.00 41.41 2.24
39 40 4.685169 AGGCAACAACATCGAATAACTG 57.315 40.909 0.00 0.00 41.41 3.16
40 41 3.440173 AGGCAACAACATCGAATAACTGG 59.560 43.478 0.00 0.00 41.41 4.00
41 42 3.438781 GGCAACAACATCGAATAACTGGA 59.561 43.478 0.00 0.00 0.00 3.86
42 43 4.403453 GCAACAACATCGAATAACTGGAC 58.597 43.478 0.00 0.00 0.00 4.02
43 44 4.637968 CAACAACATCGAATAACTGGACG 58.362 43.478 0.00 0.00 0.00 4.79
44 45 4.182693 ACAACATCGAATAACTGGACGA 57.817 40.909 0.00 0.00 39.01 4.20
45 46 3.924686 ACAACATCGAATAACTGGACGAC 59.075 43.478 0.00 0.00 37.58 4.34
46 47 3.861276 ACATCGAATAACTGGACGACA 57.139 42.857 0.00 0.00 37.58 4.35
47 48 3.508762 ACATCGAATAACTGGACGACAC 58.491 45.455 0.00 0.00 37.58 3.67
48 49 2.642139 TCGAATAACTGGACGACACC 57.358 50.000 0.00 0.00 0.00 4.16
49 50 2.165167 TCGAATAACTGGACGACACCT 58.835 47.619 0.00 0.00 0.00 4.00
50 51 2.094906 TCGAATAACTGGACGACACCTG 60.095 50.000 0.00 0.00 35.48 4.00
51 52 2.618053 GAATAACTGGACGACACCTGG 58.382 52.381 0.00 0.00 34.01 4.45
52 53 0.249398 ATAACTGGACGACACCTGGC 59.751 55.000 0.00 0.00 34.01 4.85
53 54 1.116536 TAACTGGACGACACCTGGCA 61.117 55.000 0.00 0.00 34.01 4.92
54 55 2.357517 CTGGACGACACCTGGCAC 60.358 66.667 0.00 0.00 0.00 5.01
55 56 3.157949 TGGACGACACCTGGCACA 61.158 61.111 0.00 0.00 0.00 4.57
56 57 2.347490 GGACGACACCTGGCACAT 59.653 61.111 0.00 0.00 38.20 3.21
57 58 1.741770 GGACGACACCTGGCACATC 60.742 63.158 0.00 0.00 38.20 3.06
58 59 1.005037 GACGACACCTGGCACATCA 60.005 57.895 0.00 0.00 38.20 3.07
59 60 1.004560 ACGACACCTGGCACATCAG 60.005 57.895 0.00 0.00 38.20 2.90
60 61 1.004560 CGACACCTGGCACATCAGT 60.005 57.895 0.00 0.00 38.20 3.41
61 62 1.016130 CGACACCTGGCACATCAGTC 61.016 60.000 0.00 0.00 38.20 3.51
62 63 0.322975 GACACCTGGCACATCAGTCT 59.677 55.000 0.00 0.00 38.20 3.24
63 64 0.322975 ACACCTGGCACATCAGTCTC 59.677 55.000 0.00 0.00 38.20 3.36
64 65 0.738762 CACCTGGCACATCAGTCTCG 60.739 60.000 0.00 0.00 38.20 4.04
65 66 1.153489 CCTGGCACATCAGTCTCGG 60.153 63.158 0.00 0.00 38.20 4.63
66 67 1.153489 CTGGCACATCAGTCTCGGG 60.153 63.158 0.00 0.00 38.20 5.14
67 68 2.187946 GGCACATCAGTCTCGGGG 59.812 66.667 0.00 0.00 0.00 5.73
68 69 2.512515 GCACATCAGTCTCGGGGC 60.513 66.667 0.00 0.00 0.00 5.80
69 70 2.202797 CACATCAGTCTCGGGGCG 60.203 66.667 0.00 0.00 0.00 6.13
70 71 2.680352 ACATCAGTCTCGGGGCGT 60.680 61.111 0.00 0.00 0.00 5.68
71 72 2.283529 ACATCAGTCTCGGGGCGTT 61.284 57.895 0.00 0.00 0.00 4.84
72 73 0.968901 ACATCAGTCTCGGGGCGTTA 60.969 55.000 0.00 0.00 0.00 3.18
73 74 0.527817 CATCAGTCTCGGGGCGTTAC 60.528 60.000 0.00 0.00 0.00 2.50
74 75 0.968901 ATCAGTCTCGGGGCGTTACA 60.969 55.000 0.00 0.00 0.00 2.41
150 164 2.035576 GCTACGACCCCGAAAGATGTAT 59.964 50.000 0.00 0.00 39.50 2.29
151 165 2.596904 ACGACCCCGAAAGATGTATG 57.403 50.000 0.00 0.00 39.50 2.39
190 204 9.621629 CTTCTCTAACTCTTCATACTCTCCTTA 57.378 37.037 0.00 0.00 0.00 2.69
214 228 2.784347 CAACTGAAACCTTCTCTCCCC 58.216 52.381 0.00 0.00 0.00 4.81
233 247 2.430367 GTCGCCACCACCTCCTTT 59.570 61.111 0.00 0.00 0.00 3.11
296 310 6.013984 TGACCTTAGACGGTAAGATTTCCTTT 60.014 38.462 8.07 0.00 37.42 3.11
346 360 0.400213 ACGAGTGGAATTCAAGGCCA 59.600 50.000 5.01 0.00 0.00 5.36
365 379 6.311735 AGGCCACAAGAGTAATTAAGGAAAA 58.688 36.000 5.01 0.00 0.00 2.29
376 390 8.166422 AGTAATTAAGGAAAACACAAGTGGAG 57.834 34.615 5.08 0.00 34.19 3.86
422 436 9.044150 TGTTTTGGAGATGATGAATTTCAAAAC 57.956 29.630 16.50 16.50 34.86 2.43
532 547 6.335777 ACTTGGCTCATGAGAATAATTTTGC 58.664 36.000 27.04 7.30 0.00 3.68
534 549 4.957954 TGGCTCATGAGAATAATTTTGCCT 59.042 37.500 27.04 0.00 37.69 4.75
660 711 1.002624 TCGTCATGGTGGGCCTTTC 60.003 57.895 4.53 0.00 35.27 2.62
881 936 3.858135 TCCTGTACTCTCCCAGTTTCTT 58.142 45.455 0.00 0.00 36.43 2.52
990 1059 2.032528 CGCAGCTGAGGTGGGAAA 59.967 61.111 22.04 0.00 44.68 3.13
1016 1087 0.106819 ACAATGGATGCTCTGGAGGC 60.107 55.000 0.00 0.00 0.00 4.70
1043 1114 3.637273 ACGGTGAGGCCCTCCAAC 61.637 66.667 8.62 0.00 33.74 3.77
1051 1122 2.674220 GGCCCTCCAACCTCTCCAG 61.674 68.421 0.00 0.00 0.00 3.86
1056 1127 0.457851 CTCCAACCTCTCCAGCTACG 59.542 60.000 0.00 0.00 0.00 3.51
1062 1133 1.608717 CCTCTCCAGCTACGCCTGTT 61.609 60.000 0.00 0.00 0.00 3.16
1081 1152 1.358152 TCCCCAGTTCATTTCGTCCT 58.642 50.000 0.00 0.00 0.00 3.85
1082 1153 1.003118 TCCCCAGTTCATTTCGTCCTG 59.997 52.381 0.00 0.00 0.00 3.86
1099 1177 2.387476 CTGCGGCTGCTGGATGGATA 62.387 60.000 20.27 0.00 43.34 2.59
1108 1186 4.125703 CTGCTGGATGGATAAGTGTTCTC 58.874 47.826 0.00 0.00 0.00 2.87
1141 1219 7.250569 CAACATGTGTCTCAACTTAACTGTTT 58.749 34.615 0.00 0.00 0.00 2.83
1149 1227 6.584563 GTCTCAACTTAACTGTTTTGCAACAA 59.415 34.615 0.00 0.00 42.53 2.83
1198 1282 7.565450 TTCACGCTCATAATTGAACAAATTG 57.435 32.000 0.00 0.00 38.93 2.32
1239 1323 1.518367 TGTCTTCCCCCTGTTTCAGT 58.482 50.000 0.00 0.00 0.00 3.41
1266 1350 8.304596 TCCTGCCGTCTATTTCTGTATAATAAG 58.695 37.037 0.00 0.00 0.00 1.73
1267 1351 7.063544 CCTGCCGTCTATTTCTGTATAATAAGC 59.936 40.741 0.00 0.00 0.00 3.09
1274 1358 8.816894 TCTATTTCTGTATAATAAGCCCCTCTG 58.183 37.037 0.00 0.00 0.00 3.35
1275 1359 5.825593 TTCTGTATAATAAGCCCCTCTGG 57.174 43.478 0.00 0.00 37.09 3.86
1276 1360 5.087923 TCTGTATAATAAGCCCCTCTGGA 57.912 43.478 0.00 0.00 35.39 3.86
1414 1498 1.808234 GCGCGGATGTGTATGTCGAC 61.808 60.000 9.11 9.11 0.00 4.20
1474 1558 2.508526 GATGTTGTCTCCAAGGTGCTT 58.491 47.619 0.00 0.00 0.00 3.91
1492 1576 2.341257 CTTGACGATGACAACCTCCTG 58.659 52.381 0.00 0.00 0.00 3.86
1543 1627 4.680537 ACCCTCGTCCGTGCCTCT 62.681 66.667 0.00 0.00 0.00 3.69
1607 1692 0.036010 CCTCAGCCGTTTCCATGAGT 60.036 55.000 0.00 0.00 37.97 3.41
1654 1739 0.395862 ACCTCGAGGACACCGATGAT 60.396 55.000 37.69 8.38 38.94 2.45
1697 1782 1.817099 CCGATGCTGCCTCAACCTC 60.817 63.158 5.78 0.00 0.00 3.85
1708 1793 0.035881 CTCAACCTCCAGAGCTTGCA 59.964 55.000 0.00 0.00 0.00 4.08
1943 2028 4.163078 TGAATGATCTCCTCCTCTCCAAAC 59.837 45.833 0.00 0.00 0.00 2.93
2198 2283 2.483714 GGCTCAAGCATCTCCACGATTA 60.484 50.000 4.13 0.00 44.36 1.75
2199 2284 2.541762 GCTCAAGCATCTCCACGATTAC 59.458 50.000 0.00 0.00 41.59 1.89
2200 2285 3.126831 CTCAAGCATCTCCACGATTACC 58.873 50.000 0.00 0.00 0.00 2.85
2286 2371 1.134310 TGTGTATCTCAGCCATGCCAG 60.134 52.381 0.00 0.00 0.00 4.85
2358 2443 2.050691 GCACAGTATTTGTTTGCGTGG 58.949 47.619 0.00 0.00 38.16 4.94
2471 2556 4.962362 AGTTTGTTTTCTTGGAGATGGGTT 59.038 37.500 0.00 0.00 0.00 4.11
2476 2561 4.387026 TTTCTTGGAGATGGGTTGATGT 57.613 40.909 0.00 0.00 0.00 3.06
2478 2563 2.644299 TCTTGGAGATGGGTTGATGTGT 59.356 45.455 0.00 0.00 0.00 3.72
2523 2608 5.049680 ACAAGAAACTGCGTAAAGTGTATGG 60.050 40.000 0.00 0.00 0.00 2.74
2525 2610 1.734163 ACTGCGTAAAGTGTATGGCC 58.266 50.000 0.00 0.00 0.00 5.36
2544 2629 2.420372 GCCTGGAAGAAAAAGATCGACC 59.580 50.000 0.00 0.00 34.07 4.79
2601 2686 3.369892 CCTCCCACATTTCCTACACTCAG 60.370 52.174 0.00 0.00 0.00 3.35
2603 2688 2.305927 CCCACATTTCCTACACTCAGGT 59.694 50.000 0.00 0.00 36.99 4.00
2604 2689 3.517901 CCCACATTTCCTACACTCAGGTA 59.482 47.826 0.00 0.00 36.99 3.08
2605 2690 4.164221 CCCACATTTCCTACACTCAGGTAT 59.836 45.833 0.00 0.00 36.99 2.73
2606 2691 5.118990 CCACATTTCCTACACTCAGGTATG 58.881 45.833 0.00 0.00 36.99 2.39
2607 2692 5.104941 CCACATTTCCTACACTCAGGTATGA 60.105 44.000 11.33 0.00 36.99 2.15
2608 2693 6.408548 CCACATTTCCTACACTCAGGTATGAT 60.409 42.308 11.33 0.00 36.99 2.45
2609 2694 6.703607 CACATTTCCTACACTCAGGTATGATC 59.296 42.308 11.33 0.00 36.99 2.92
2610 2695 5.871396 TTTCCTACACTCAGGTATGATCC 57.129 43.478 0.00 0.00 36.99 3.36
2611 2696 4.816048 TCCTACACTCAGGTATGATCCT 57.184 45.455 0.00 0.00 36.99 3.24
2619 2704 3.526931 CAGGTATGATCCTGTGACGTT 57.473 47.619 4.75 0.00 46.92 3.99
2620 2705 3.861840 CAGGTATGATCCTGTGACGTTT 58.138 45.455 4.75 0.00 46.92 3.60
2621 2706 5.006153 CAGGTATGATCCTGTGACGTTTA 57.994 43.478 4.75 0.00 46.92 2.01
2622 2707 5.601662 CAGGTATGATCCTGTGACGTTTAT 58.398 41.667 4.75 0.00 46.92 1.40
2623 2708 5.692204 CAGGTATGATCCTGTGACGTTTATC 59.308 44.000 4.75 0.00 46.92 1.75
2624 2709 4.989168 GGTATGATCCTGTGACGTTTATCC 59.011 45.833 0.00 0.00 0.00 2.59
2625 2710 5.221461 GGTATGATCCTGTGACGTTTATCCT 60.221 44.000 0.00 0.00 0.00 3.24
2626 2711 4.819105 TGATCCTGTGACGTTTATCCTT 57.181 40.909 0.00 0.00 0.00 3.36
2627 2712 5.160607 TGATCCTGTGACGTTTATCCTTT 57.839 39.130 0.00 0.00 0.00 3.11
2628 2713 5.556915 TGATCCTGTGACGTTTATCCTTTT 58.443 37.500 0.00 0.00 0.00 2.27
2629 2714 5.411361 TGATCCTGTGACGTTTATCCTTTTG 59.589 40.000 0.00 0.00 0.00 2.44
2630 2715 3.500680 TCCTGTGACGTTTATCCTTTTGC 59.499 43.478 0.00 0.00 0.00 3.68
2631 2716 3.252215 CCTGTGACGTTTATCCTTTTGCA 59.748 43.478 0.00 0.00 0.00 4.08
2632 2717 4.217754 TGTGACGTTTATCCTTTTGCAC 57.782 40.909 0.00 0.00 0.00 4.57
2633 2718 3.003897 TGTGACGTTTATCCTTTTGCACC 59.996 43.478 0.00 0.00 0.00 5.01
2634 2719 2.554893 TGACGTTTATCCTTTTGCACCC 59.445 45.455 0.00 0.00 0.00 4.61
2635 2720 2.817844 GACGTTTATCCTTTTGCACCCT 59.182 45.455 0.00 0.00 0.00 4.34
2636 2721 3.227614 ACGTTTATCCTTTTGCACCCTT 58.772 40.909 0.00 0.00 0.00 3.95
2637 2722 3.005367 ACGTTTATCCTTTTGCACCCTTG 59.995 43.478 0.00 0.00 0.00 3.61
2638 2723 3.005367 CGTTTATCCTTTTGCACCCTTGT 59.995 43.478 0.00 0.00 0.00 3.16
2639 2724 4.556233 GTTTATCCTTTTGCACCCTTGTC 58.444 43.478 0.00 0.00 0.00 3.18
2640 2725 2.380064 ATCCTTTTGCACCCTTGTCA 57.620 45.000 0.00 0.00 0.00 3.58
2641 2726 2.151502 TCCTTTTGCACCCTTGTCAA 57.848 45.000 0.00 0.00 0.00 3.18
2642 2727 2.031120 TCCTTTTGCACCCTTGTCAAG 58.969 47.619 5.53 5.53 0.00 3.02
2643 2728 1.756538 CCTTTTGCACCCTTGTCAAGT 59.243 47.619 11.61 0.00 0.00 3.16
2644 2729 2.168313 CCTTTTGCACCCTTGTCAAGTT 59.832 45.455 11.61 0.00 0.00 2.66
2645 2730 3.369366 CCTTTTGCACCCTTGTCAAGTTT 60.369 43.478 11.61 0.00 0.00 2.66
2646 2731 4.142049 CCTTTTGCACCCTTGTCAAGTTTA 60.142 41.667 11.61 0.00 0.00 2.01
2647 2732 4.647424 TTTGCACCCTTGTCAAGTTTAG 57.353 40.909 11.61 0.55 0.00 1.85
2648 2733 3.569194 TGCACCCTTGTCAAGTTTAGA 57.431 42.857 11.61 0.00 0.00 2.10
2649 2734 3.476552 TGCACCCTTGTCAAGTTTAGAG 58.523 45.455 11.61 0.00 0.00 2.43
2650 2735 3.135712 TGCACCCTTGTCAAGTTTAGAGA 59.864 43.478 11.61 0.00 0.00 3.10
2651 2736 3.498777 GCACCCTTGTCAAGTTTAGAGAC 59.501 47.826 11.61 0.00 0.00 3.36
2652 2737 4.743955 GCACCCTTGTCAAGTTTAGAGACT 60.744 45.833 11.61 0.00 33.56 3.24
2653 2738 5.368989 CACCCTTGTCAAGTTTAGAGACTT 58.631 41.667 11.61 0.00 40.37 3.01
2654 2739 5.823045 CACCCTTGTCAAGTTTAGAGACTTT 59.177 40.000 11.61 0.00 37.76 2.66
2655 2740 6.318900 CACCCTTGTCAAGTTTAGAGACTTTT 59.681 38.462 11.61 0.00 37.76 2.27
2656 2741 6.318900 ACCCTTGTCAAGTTTAGAGACTTTTG 59.681 38.462 11.61 0.00 37.76 2.44
2657 2742 6.318900 CCCTTGTCAAGTTTAGAGACTTTTGT 59.681 38.462 11.61 0.00 37.76 2.83
2658 2743 7.148069 CCCTTGTCAAGTTTAGAGACTTTTGTT 60.148 37.037 11.61 0.00 37.76 2.83
2659 2744 7.698130 CCTTGTCAAGTTTAGAGACTTTTGTTG 59.302 37.037 11.61 0.00 37.76 3.33
2660 2745 7.681939 TGTCAAGTTTAGAGACTTTTGTTGT 57.318 32.000 0.00 0.00 37.76 3.32
2661 2746 7.526608 TGTCAAGTTTAGAGACTTTTGTTGTG 58.473 34.615 0.00 0.00 37.76 3.33
2662 2747 7.174253 TGTCAAGTTTAGAGACTTTTGTTGTGT 59.826 33.333 0.00 0.00 37.76 3.72
2663 2748 7.481798 GTCAAGTTTAGAGACTTTTGTTGTGTG 59.518 37.037 0.00 0.00 37.76 3.82
2664 2749 5.880341 AGTTTAGAGACTTTTGTTGTGTGC 58.120 37.500 0.00 0.00 0.00 4.57
2665 2750 5.414454 AGTTTAGAGACTTTTGTTGTGTGCA 59.586 36.000 0.00 0.00 0.00 4.57
2666 2751 6.095440 AGTTTAGAGACTTTTGTTGTGTGCAT 59.905 34.615 0.00 0.00 0.00 3.96
2667 2752 4.558538 AGAGACTTTTGTTGTGTGCATC 57.441 40.909 0.00 0.00 0.00 3.91
2668 2753 3.002656 AGAGACTTTTGTTGTGTGCATCG 59.997 43.478 0.00 0.00 0.00 3.84
2669 2754 2.682856 AGACTTTTGTTGTGTGCATCGT 59.317 40.909 0.00 0.00 0.00 3.73
2670 2755 3.035942 GACTTTTGTTGTGTGCATCGTC 58.964 45.455 0.00 0.00 0.00 4.20
2671 2756 2.223479 ACTTTTGTTGTGTGCATCGTCC 60.223 45.455 0.00 0.00 0.00 4.79
2672 2757 1.383523 TTTGTTGTGTGCATCGTCCA 58.616 45.000 0.00 0.00 0.00 4.02
2673 2758 1.603456 TTGTTGTGTGCATCGTCCAT 58.397 45.000 0.00 0.00 0.00 3.41
2674 2759 1.603456 TGTTGTGTGCATCGTCCATT 58.397 45.000 0.00 0.00 0.00 3.16
2675 2760 1.266446 TGTTGTGTGCATCGTCCATTG 59.734 47.619 0.00 0.00 0.00 2.82
2676 2761 0.240678 TTGTGTGCATCGTCCATTGC 59.759 50.000 0.00 0.00 39.33 3.56
2677 2762 0.888285 TGTGTGCATCGTCCATTGCA 60.888 50.000 0.00 0.00 46.03 4.08
2681 2766 1.175654 TGCATCGTCCATTGCATTGT 58.824 45.000 7.75 0.00 43.54 2.71
2682 2767 1.545136 TGCATCGTCCATTGCATTGTT 59.455 42.857 7.75 0.00 43.54 2.83
2683 2768 2.751806 TGCATCGTCCATTGCATTGTTA 59.248 40.909 7.75 0.00 43.54 2.41
2684 2769 3.181498 TGCATCGTCCATTGCATTGTTAG 60.181 43.478 7.75 0.00 43.54 2.34
2685 2770 3.793129 GCATCGTCCATTGCATTGTTAGG 60.793 47.826 7.75 2.25 38.72 2.69
2686 2771 3.066291 TCGTCCATTGCATTGTTAGGT 57.934 42.857 7.75 0.00 0.00 3.08
2687 2772 4.209307 TCGTCCATTGCATTGTTAGGTA 57.791 40.909 7.75 0.00 0.00 3.08
2688 2773 3.936453 TCGTCCATTGCATTGTTAGGTAC 59.064 43.478 7.75 0.00 0.00 3.34
2689 2774 3.938963 CGTCCATTGCATTGTTAGGTACT 59.061 43.478 7.75 0.00 46.37 2.73
2690 2775 4.201812 CGTCCATTGCATTGTTAGGTACTG 60.202 45.833 7.75 0.00 41.52 2.74
2691 2776 3.694072 TCCATTGCATTGTTAGGTACTGC 59.306 43.478 7.75 0.00 41.52 4.40
2692 2777 3.696051 CCATTGCATTGTTAGGTACTGCT 59.304 43.478 7.75 0.00 41.52 4.24
2693 2778 4.439153 CCATTGCATTGTTAGGTACTGCTG 60.439 45.833 7.75 0.00 41.52 4.41
2694 2779 3.417069 TGCATTGTTAGGTACTGCTGT 57.583 42.857 0.66 0.66 41.52 4.40
2695 2780 3.750371 TGCATTGTTAGGTACTGCTGTT 58.250 40.909 0.09 0.00 41.52 3.16
2696 2781 3.751175 TGCATTGTTAGGTACTGCTGTTC 59.249 43.478 0.09 0.00 41.52 3.18
2726 2905 8.868522 ATTATGGGTATGTATGGTTCATTCTG 57.131 34.615 0.00 0.00 0.00 3.02
2741 2920 7.065324 TGGTTCATTCTGTAGGCTATTTTAACG 59.935 37.037 0.00 0.00 0.00 3.18
2782 3302 6.947644 AGATAATGCTTGTGTGCAATGATA 57.052 33.333 0.00 0.00 46.61 2.15
2809 3329 6.469410 CAATCACTTACTGGGGTAGTGTTTA 58.531 40.000 0.00 0.00 40.65 2.01
2883 3403 7.816995 GCTTTGTTATGGAACCAAACATAATGA 59.183 33.333 16.03 5.19 40.46 2.57
3055 3579 4.000325 GCCCACAATGGTTTAAAACATCC 59.000 43.478 18.79 2.45 35.17 3.51
3096 3620 5.499004 AGGAAGATGTGTAGCCTTGTTAA 57.501 39.130 0.00 0.00 0.00 2.01
3106 3630 5.008217 GTGTAGCCTTGTTAACATGTTGACA 59.992 40.000 26.94 26.94 37.30 3.58
3183 3707 9.905713 TTAGCTTCCTATTTCATAAACATGACT 57.094 29.630 0.00 0.00 0.00 3.41
3286 3810 1.865865 ATGTTGCTTCACGAGTCGTT 58.134 45.000 17.16 0.00 38.32 3.85
3339 3863 5.570320 ACTTTTATGTGGGTATGCTTGAGT 58.430 37.500 0.00 0.00 0.00 3.41
3371 3895 7.003939 TGCTTTGTGATTCAGATATGTAACG 57.996 36.000 0.00 0.00 0.00 3.18
3378 3902 7.277760 TGTGATTCAGATATGTAACGGTCAAAG 59.722 37.037 0.00 0.00 0.00 2.77
3412 3936 6.908825 TGTATGACAATTGGCAAGTTTCTAC 58.091 36.000 19.96 15.02 36.16 2.59
3419 3943 4.431416 TTGGCAAGTTTCTACTCCAAGA 57.569 40.909 0.00 0.00 34.85 3.02
3465 3989 6.754193 TGTGTGGCGTCTTCATTATATATCA 58.246 36.000 0.00 0.00 0.00 2.15
3466 3990 6.645003 TGTGTGGCGTCTTCATTATATATCAC 59.355 38.462 0.00 0.00 0.00 3.06
3467 3991 6.868864 GTGTGGCGTCTTCATTATATATCACT 59.131 38.462 0.00 0.00 0.00 3.41
3468 3992 6.868339 TGTGGCGTCTTCATTATATATCACTG 59.132 38.462 0.00 0.00 0.00 3.66
3469 3993 6.311445 GTGGCGTCTTCATTATATATCACTGG 59.689 42.308 0.00 0.00 0.00 4.00
3470 3994 6.210584 TGGCGTCTTCATTATATATCACTGGA 59.789 38.462 0.00 0.00 0.00 3.86
3471 3995 7.097192 GGCGTCTTCATTATATATCACTGGAA 58.903 38.462 0.00 0.00 0.00 3.53
3472 3996 7.766278 GGCGTCTTCATTATATATCACTGGAAT 59.234 37.037 0.00 0.00 0.00 3.01
3473 3997 8.598924 GCGTCTTCATTATATATCACTGGAATG 58.401 37.037 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.664016 CCTTGTCATTGCTTGCGTGTC 60.664 52.381 0.00 0.00 0.00 3.67
1 2 0.311790 CCTTGTCATTGCTTGCGTGT 59.688 50.000 0.00 0.00 0.00 4.49
2 3 1.005294 GCCTTGTCATTGCTTGCGTG 61.005 55.000 0.00 0.00 0.00 5.34
3 4 1.286880 GCCTTGTCATTGCTTGCGT 59.713 52.632 0.00 0.00 0.00 5.24
4 5 0.318869 TTGCCTTGTCATTGCTTGCG 60.319 50.000 0.00 0.00 0.00 4.85
5 6 1.142474 GTTGCCTTGTCATTGCTTGC 58.858 50.000 0.00 0.00 0.00 4.01
6 7 2.512485 TGTTGCCTTGTCATTGCTTG 57.488 45.000 0.00 0.00 0.00 4.01
7 8 2.168106 TGTTGTTGCCTTGTCATTGCTT 59.832 40.909 0.00 0.00 0.00 3.91
8 9 1.755959 TGTTGTTGCCTTGTCATTGCT 59.244 42.857 0.00 0.00 0.00 3.91
9 10 2.222007 TGTTGTTGCCTTGTCATTGC 57.778 45.000 0.00 0.00 0.00 3.56
10 11 2.981805 CGATGTTGTTGCCTTGTCATTG 59.018 45.455 0.00 0.00 0.00 2.82
11 12 2.884012 TCGATGTTGTTGCCTTGTCATT 59.116 40.909 0.00 0.00 0.00 2.57
12 13 2.503331 TCGATGTTGTTGCCTTGTCAT 58.497 42.857 0.00 0.00 0.00 3.06
13 14 1.960417 TCGATGTTGTTGCCTTGTCA 58.040 45.000 0.00 0.00 0.00 3.58
14 15 3.559238 ATTCGATGTTGTTGCCTTGTC 57.441 42.857 0.00 0.00 0.00 3.18
15 16 4.518970 AGTTATTCGATGTTGTTGCCTTGT 59.481 37.500 0.00 0.00 0.00 3.16
16 17 4.853196 CAGTTATTCGATGTTGTTGCCTTG 59.147 41.667 0.00 0.00 0.00 3.61
17 18 4.082787 CCAGTTATTCGATGTTGTTGCCTT 60.083 41.667 0.00 0.00 0.00 4.35
18 19 3.440173 CCAGTTATTCGATGTTGTTGCCT 59.560 43.478 0.00 0.00 0.00 4.75
19 20 3.438781 TCCAGTTATTCGATGTTGTTGCC 59.561 43.478 0.00 0.00 0.00 4.52
20 21 4.403453 GTCCAGTTATTCGATGTTGTTGC 58.597 43.478 0.00 0.00 0.00 4.17
21 22 4.387559 TCGTCCAGTTATTCGATGTTGTTG 59.612 41.667 0.00 0.00 0.00 3.33
22 23 4.387862 GTCGTCCAGTTATTCGATGTTGTT 59.612 41.667 0.00 0.00 34.93 2.83
23 24 3.924686 GTCGTCCAGTTATTCGATGTTGT 59.075 43.478 0.00 0.00 34.93 3.32
24 25 3.924073 TGTCGTCCAGTTATTCGATGTTG 59.076 43.478 0.00 0.00 34.93 3.33
25 26 3.924686 GTGTCGTCCAGTTATTCGATGTT 59.075 43.478 0.00 0.00 34.93 2.71
26 27 3.508762 GTGTCGTCCAGTTATTCGATGT 58.491 45.455 0.00 0.00 34.93 3.06
27 28 2.858344 GGTGTCGTCCAGTTATTCGATG 59.142 50.000 0.00 0.00 34.93 3.84
28 29 2.758979 AGGTGTCGTCCAGTTATTCGAT 59.241 45.455 0.00 0.00 34.93 3.59
29 30 2.094906 CAGGTGTCGTCCAGTTATTCGA 60.095 50.000 0.00 0.00 0.00 3.71
30 31 2.259618 CAGGTGTCGTCCAGTTATTCG 58.740 52.381 0.00 0.00 0.00 3.34
31 32 2.618053 CCAGGTGTCGTCCAGTTATTC 58.382 52.381 0.00 0.00 0.00 1.75
32 33 1.338769 GCCAGGTGTCGTCCAGTTATT 60.339 52.381 0.00 0.00 0.00 1.40
33 34 0.249398 GCCAGGTGTCGTCCAGTTAT 59.751 55.000 0.00 0.00 0.00 1.89
34 35 1.116536 TGCCAGGTGTCGTCCAGTTA 61.117 55.000 0.00 0.00 0.00 2.24
35 36 2.426023 GCCAGGTGTCGTCCAGTT 59.574 61.111 0.00 0.00 0.00 3.16
36 37 2.842462 TGCCAGGTGTCGTCCAGT 60.842 61.111 0.00 0.00 0.00 4.00
37 38 2.357517 GTGCCAGGTGTCGTCCAG 60.358 66.667 0.00 0.00 0.00 3.86
38 39 2.449031 GATGTGCCAGGTGTCGTCCA 62.449 60.000 0.00 0.00 0.00 4.02
39 40 1.741770 GATGTGCCAGGTGTCGTCC 60.742 63.158 0.00 0.00 0.00 4.79
40 41 1.005037 TGATGTGCCAGGTGTCGTC 60.005 57.895 0.00 0.00 0.00 4.20
41 42 1.004560 CTGATGTGCCAGGTGTCGT 60.005 57.895 0.00 0.00 0.00 4.34
42 43 1.004560 ACTGATGTGCCAGGTGTCG 60.005 57.895 0.00 0.00 38.44 4.35
43 44 0.322975 AGACTGATGTGCCAGGTGTC 59.677 55.000 0.00 0.00 38.44 3.67
44 45 0.322975 GAGACTGATGTGCCAGGTGT 59.677 55.000 0.00 0.00 38.44 4.16
45 46 0.738762 CGAGACTGATGTGCCAGGTG 60.739 60.000 0.00 0.00 38.44 4.00
46 47 1.593787 CGAGACTGATGTGCCAGGT 59.406 57.895 0.00 0.00 38.44 4.00
47 48 1.153489 CCGAGACTGATGTGCCAGG 60.153 63.158 0.00 0.00 38.44 4.45
48 49 1.153489 CCCGAGACTGATGTGCCAG 60.153 63.158 0.00 0.00 39.93 4.85
49 50 2.659063 CCCCGAGACTGATGTGCCA 61.659 63.158 0.00 0.00 0.00 4.92
50 51 2.187946 CCCCGAGACTGATGTGCC 59.812 66.667 0.00 0.00 0.00 5.01
51 52 2.512515 GCCCCGAGACTGATGTGC 60.513 66.667 0.00 0.00 0.00 4.57
52 53 2.202797 CGCCCCGAGACTGATGTG 60.203 66.667 0.00 0.00 0.00 3.21
53 54 0.968901 TAACGCCCCGAGACTGATGT 60.969 55.000 0.00 0.00 0.00 3.06
54 55 0.527817 GTAACGCCCCGAGACTGATG 60.528 60.000 0.00 0.00 0.00 3.07
55 56 0.968901 TGTAACGCCCCGAGACTGAT 60.969 55.000 0.00 0.00 0.00 2.90
56 57 1.604308 TGTAACGCCCCGAGACTGA 60.604 57.895 0.00 0.00 0.00 3.41
57 58 1.445582 GTGTAACGCCCCGAGACTG 60.446 63.158 0.00 0.00 0.00 3.51
58 59 1.593296 GAGTGTAACGCCCCGAGACT 61.593 60.000 0.00 0.00 45.86 3.24
59 60 1.153881 GAGTGTAACGCCCCGAGAC 60.154 63.158 0.00 0.00 45.86 3.36
60 61 1.303888 AGAGTGTAACGCCCCGAGA 60.304 57.895 0.00 0.00 45.86 4.04
61 62 1.153823 CAGAGTGTAACGCCCCGAG 60.154 63.158 0.00 0.00 45.86 4.63
62 63 2.967397 CAGAGTGTAACGCCCCGA 59.033 61.111 0.00 0.00 45.86 5.14
63 64 2.813908 GCAGAGTGTAACGCCCCG 60.814 66.667 0.00 0.00 45.86 5.73
64 65 2.436115 GGCAGAGTGTAACGCCCC 60.436 66.667 0.00 0.00 45.86 5.80
65 66 2.033194 GTGGCAGAGTGTAACGCCC 61.033 63.158 0.00 0.00 45.86 6.13
66 67 1.004918 AGTGGCAGAGTGTAACGCC 60.005 57.895 0.00 0.00 45.86 5.68
67 68 1.291877 CCAGTGGCAGAGTGTAACGC 61.292 60.000 0.00 0.00 45.86 4.84
68 69 0.033504 ACCAGTGGCAGAGTGTAACG 59.966 55.000 9.78 0.00 45.86 3.18
69 70 1.512926 CACCAGTGGCAGAGTGTAAC 58.487 55.000 9.78 0.00 0.00 2.50
70 71 0.396435 CCACCAGTGGCAGAGTGTAA 59.604 55.000 9.78 0.00 44.73 2.41
71 72 2.057830 CCACCAGTGGCAGAGTGTA 58.942 57.895 9.78 0.00 44.73 2.90
72 73 2.831770 CCACCAGTGGCAGAGTGT 59.168 61.111 9.78 0.00 44.73 3.55
150 164 5.601313 AGTTAGAGAAGTGGGTTAGTTCACA 59.399 40.000 0.00 0.00 40.52 3.58
151 165 6.015265 AGAGTTAGAGAAGTGGGTTAGTTCAC 60.015 42.308 0.00 0.00 40.52 3.18
190 204 3.823304 GGAGAGAAGGTTTCAGTTGCAAT 59.177 43.478 0.59 0.00 0.00 3.56
233 247 4.451150 GTCTGATGCGTGCCGGGA 62.451 66.667 2.18 0.00 0.00 5.14
296 310 8.205512 TCAGTTTGTAGTTTGTATTCCTACACA 58.794 33.333 0.00 0.00 40.39 3.72
346 360 9.185680 ACTTGTGTTTTCCTTAATTACTCTTGT 57.814 29.630 0.00 0.00 0.00 3.16
422 436 5.163416 ACTCCCATGGACAAAAAGAAAACAG 60.163 40.000 15.22 0.00 0.00 3.16
429 443 5.022282 ACAAAACTCCCATGGACAAAAAG 57.978 39.130 15.22 3.16 0.00 2.27
531 546 0.171455 ACTTGTGATCGACTCGAGGC 59.829 55.000 18.41 14.00 39.91 4.70
532 547 2.095212 TGAACTTGTGATCGACTCGAGG 60.095 50.000 18.41 0.00 39.91 4.63
534 549 3.850122 ATGAACTTGTGATCGACTCGA 57.150 42.857 3.06 3.06 41.13 4.04
632 647 2.159226 CCACCATGACGACCTAGTTCTC 60.159 54.545 0.00 0.00 0.00 2.87
634 649 1.134788 CCCACCATGACGACCTAGTTC 60.135 57.143 0.00 0.00 0.00 3.01
635 650 0.902531 CCCACCATGACGACCTAGTT 59.097 55.000 0.00 0.00 0.00 2.24
639 690 3.717294 GGCCCACCATGACGACCT 61.717 66.667 0.00 0.00 35.26 3.85
660 711 6.039717 CCCAAATAAACATGTGACTAGGGATG 59.960 42.308 14.16 0.00 33.23 3.51
774 825 2.833582 GTCGGGGAGATCGCTGGA 60.834 66.667 5.95 0.00 36.04 3.86
881 936 0.109086 CCGCGAGCAGAGAAGAGAAA 60.109 55.000 8.23 0.00 0.00 2.52
974 1043 0.250901 TTCTTTCCCACCTCAGCTGC 60.251 55.000 9.47 0.00 0.00 5.25
990 1059 3.118334 CCAGAGCATCCATTGTCTCTTCT 60.118 47.826 0.00 0.00 36.98 2.85
1016 1087 2.186903 CTCACCGTGGGGGAATCG 59.813 66.667 0.00 0.00 33.19 3.34
1062 1133 1.003118 CAGGACGAAATGAACTGGGGA 59.997 52.381 0.00 0.00 0.00 4.81
1081 1152 1.981951 TTATCCATCCAGCAGCCGCA 61.982 55.000 0.00 0.00 42.27 5.69
1082 1153 1.227943 TTATCCATCCAGCAGCCGC 60.228 57.895 0.00 0.00 38.99 6.53
1141 1219 4.121317 CAATTCCTTCAGCTTTGTTGCAA 58.879 39.130 0.00 0.00 34.99 4.08
1149 1227 1.073923 ACGGGACAATTCCTTCAGCTT 59.926 47.619 0.00 0.00 42.38 3.74
1208 1292 5.775195 CAGGGGGAAGACAAAGAGTAATTTT 59.225 40.000 0.00 0.00 0.00 1.82
1239 1323 6.474140 TTATACAGAAATAGACGGCAGGAA 57.526 37.500 0.00 0.00 0.00 3.36
1274 1358 2.527875 ATCCATCCGCCCCTCTCC 60.528 66.667 0.00 0.00 0.00 3.71
1275 1359 2.746359 CATCCATCCGCCCCTCTC 59.254 66.667 0.00 0.00 0.00 3.20
1276 1360 3.564218 GCATCCATCCGCCCCTCT 61.564 66.667 0.00 0.00 0.00 3.69
1414 1498 2.154462 GTCAGGGAATGGTGTTGTGAG 58.846 52.381 0.00 0.00 0.00 3.51
1474 1558 1.546029 CTCAGGAGGTTGTCATCGTCA 59.454 52.381 6.07 0.00 0.00 4.35
1492 1576 4.358851 CGACACAAAGGATGATCTCTCTC 58.641 47.826 0.00 0.00 0.00 3.20
1535 1619 2.202544 GCAGACGAGAGAGGCACG 60.203 66.667 0.00 0.00 36.62 5.34
1543 1627 1.664649 CCAACGCTTGCAGACGAGA 60.665 57.895 16.17 0.00 0.00 4.04
1607 1692 3.948719 GAGGTGGGACGGGTTGCA 61.949 66.667 0.00 0.00 0.00 4.08
1697 1782 1.467734 GATGACAGTTGCAAGCTCTGG 59.532 52.381 17.06 3.13 34.02 3.86
1708 1793 3.972227 GCAGTGCGGATGACAGTT 58.028 55.556 0.00 0.00 0.00 3.16
1943 2028 1.372087 GACAAGCCATCGCCTTCCTG 61.372 60.000 0.00 0.00 34.57 3.86
2286 2371 3.495753 CCAAATGCAAAGTTGAAGCTTCC 59.504 43.478 23.42 9.23 0.00 3.46
2343 2428 2.230266 ACCATCCCACGCAAACAAATAC 59.770 45.455 0.00 0.00 0.00 1.89
2358 2443 3.350219 TCCTCAAACTAGCAACCATCC 57.650 47.619 0.00 0.00 0.00 3.51
2523 2608 2.420372 GGTCGATCTTTTTCTTCCAGGC 59.580 50.000 0.00 0.00 0.00 4.85
2525 2610 5.335191 CCAAAGGTCGATCTTTTTCTTCCAG 60.335 44.000 20.94 7.33 35.04 3.86
2544 2629 5.448654 TGAAAGGATGGATATCACCCAAAG 58.551 41.667 4.83 0.00 37.22 2.77
2601 2686 4.989168 GGATAAACGTCACAGGATCATACC 59.011 45.833 0.00 0.00 0.00 2.73
2603 2688 6.479972 AAGGATAAACGTCACAGGATCATA 57.520 37.500 0.00 0.00 0.00 2.15
2604 2689 5.359194 AAGGATAAACGTCACAGGATCAT 57.641 39.130 0.00 0.00 0.00 2.45
2605 2690 4.819105 AAGGATAAACGTCACAGGATCA 57.181 40.909 0.00 0.00 0.00 2.92
2606 2691 5.673818 GCAAAAGGATAAACGTCACAGGATC 60.674 44.000 0.00 0.00 0.00 3.36
2607 2692 4.156008 GCAAAAGGATAAACGTCACAGGAT 59.844 41.667 0.00 0.00 0.00 3.24
2608 2693 3.500680 GCAAAAGGATAAACGTCACAGGA 59.499 43.478 0.00 0.00 0.00 3.86
2609 2694 3.252215 TGCAAAAGGATAAACGTCACAGG 59.748 43.478 0.00 0.00 0.00 4.00
2610 2695 4.219033 GTGCAAAAGGATAAACGTCACAG 58.781 43.478 0.00 0.00 0.00 3.66
2611 2696 3.003897 GGTGCAAAAGGATAAACGTCACA 59.996 43.478 0.00 0.00 0.00 3.58
2612 2697 3.561503 GGTGCAAAAGGATAAACGTCAC 58.438 45.455 0.00 0.00 0.00 3.67
2613 2698 2.554893 GGGTGCAAAAGGATAAACGTCA 59.445 45.455 0.00 0.00 0.00 4.35
2614 2699 2.817844 AGGGTGCAAAAGGATAAACGTC 59.182 45.455 0.00 0.00 0.00 4.34
2615 2700 2.871453 AGGGTGCAAAAGGATAAACGT 58.129 42.857 0.00 0.00 0.00 3.99
2616 2701 3.005367 ACAAGGGTGCAAAAGGATAAACG 59.995 43.478 0.00 0.00 0.00 3.60
2617 2702 4.038642 TGACAAGGGTGCAAAAGGATAAAC 59.961 41.667 0.00 0.00 0.00 2.01
2618 2703 4.219115 TGACAAGGGTGCAAAAGGATAAA 58.781 39.130 0.00 0.00 0.00 1.40
2619 2704 3.838565 TGACAAGGGTGCAAAAGGATAA 58.161 40.909 0.00 0.00 0.00 1.75
2620 2705 3.517296 TGACAAGGGTGCAAAAGGATA 57.483 42.857 0.00 0.00 0.00 2.59
2621 2706 2.380064 TGACAAGGGTGCAAAAGGAT 57.620 45.000 0.00 0.00 0.00 3.24
2622 2707 2.031120 CTTGACAAGGGTGCAAAAGGA 58.969 47.619 7.35 0.00 0.00 3.36
2623 2708 1.756538 ACTTGACAAGGGTGCAAAAGG 59.243 47.619 19.16 0.00 0.00 3.11
2624 2709 3.525268 AACTTGACAAGGGTGCAAAAG 57.475 42.857 19.16 0.00 0.00 2.27
2625 2710 3.971245 AAACTTGACAAGGGTGCAAAA 57.029 38.095 19.16 0.00 0.00 2.44
2626 2711 4.274147 TCTAAACTTGACAAGGGTGCAAA 58.726 39.130 19.16 0.00 0.00 3.68
2627 2712 3.882888 CTCTAAACTTGACAAGGGTGCAA 59.117 43.478 19.16 0.10 0.00 4.08
2628 2713 3.135712 TCTCTAAACTTGACAAGGGTGCA 59.864 43.478 19.16 0.00 0.00 4.57
2629 2714 3.498777 GTCTCTAAACTTGACAAGGGTGC 59.501 47.826 19.16 0.00 0.00 5.01
2630 2715 4.962155 AGTCTCTAAACTTGACAAGGGTG 58.038 43.478 19.16 6.75 33.56 4.61
2631 2716 5.632034 AAGTCTCTAAACTTGACAAGGGT 57.368 39.130 19.16 8.84 38.06 4.34
2632 2717 6.318900 ACAAAAGTCTCTAAACTTGACAAGGG 59.681 38.462 19.16 6.74 39.40 3.95
2633 2718 7.321745 ACAAAAGTCTCTAAACTTGACAAGG 57.678 36.000 19.16 1.74 39.40 3.61
2634 2719 8.237267 ACAACAAAAGTCTCTAAACTTGACAAG 58.763 33.333 13.77 13.77 39.40 3.16
2635 2720 8.020819 CACAACAAAAGTCTCTAAACTTGACAA 58.979 33.333 0.00 0.00 39.40 3.18
2636 2721 7.174253 ACACAACAAAAGTCTCTAAACTTGACA 59.826 33.333 0.00 0.00 39.40 3.58
2637 2722 7.481798 CACACAACAAAAGTCTCTAAACTTGAC 59.518 37.037 0.00 0.00 39.40 3.18
2638 2723 7.526608 CACACAACAAAAGTCTCTAAACTTGA 58.473 34.615 0.00 0.00 39.40 3.02
2639 2724 6.251376 GCACACAACAAAAGTCTCTAAACTTG 59.749 38.462 0.00 0.00 39.40 3.16
2640 2725 6.072175 TGCACACAACAAAAGTCTCTAAACTT 60.072 34.615 0.00 0.00 41.20 2.66
2641 2726 5.414454 TGCACACAACAAAAGTCTCTAAACT 59.586 36.000 0.00 0.00 0.00 2.66
2642 2727 5.636837 TGCACACAACAAAAGTCTCTAAAC 58.363 37.500 0.00 0.00 0.00 2.01
2643 2728 5.888691 TGCACACAACAAAAGTCTCTAAA 57.111 34.783 0.00 0.00 0.00 1.85
2644 2729 5.277297 CGATGCACACAACAAAAGTCTCTAA 60.277 40.000 0.00 0.00 0.00 2.10
2645 2730 4.211164 CGATGCACACAACAAAAGTCTCTA 59.789 41.667 0.00 0.00 0.00 2.43
2646 2731 3.002656 CGATGCACACAACAAAAGTCTCT 59.997 43.478 0.00 0.00 0.00 3.10
2647 2732 3.242739 ACGATGCACACAACAAAAGTCTC 60.243 43.478 0.00 0.00 0.00 3.36
2648 2733 2.682856 ACGATGCACACAACAAAAGTCT 59.317 40.909 0.00 0.00 0.00 3.24
2649 2734 3.035942 GACGATGCACACAACAAAAGTC 58.964 45.455 0.00 0.00 0.00 3.01
2650 2735 2.223479 GGACGATGCACACAACAAAAGT 60.223 45.455 0.00 0.00 0.00 2.66
2651 2736 2.223456 TGGACGATGCACACAACAAAAG 60.223 45.455 0.00 0.00 0.00 2.27
2652 2737 1.745653 TGGACGATGCACACAACAAAA 59.254 42.857 0.00 0.00 0.00 2.44
2653 2738 1.383523 TGGACGATGCACACAACAAA 58.616 45.000 0.00 0.00 0.00 2.83
2654 2739 1.603456 ATGGACGATGCACACAACAA 58.397 45.000 0.00 0.00 0.00 2.83
2655 2740 1.266446 CAATGGACGATGCACACAACA 59.734 47.619 0.00 0.00 0.00 3.33
2656 2741 1.967762 CAATGGACGATGCACACAAC 58.032 50.000 0.00 0.00 0.00 3.32
2657 2742 0.240678 GCAATGGACGATGCACACAA 59.759 50.000 0.00 0.00 42.12 3.33
2658 2743 0.888285 TGCAATGGACGATGCACACA 60.888 50.000 0.00 0.00 46.87 3.72
2659 2744 1.875262 TGCAATGGACGATGCACAC 59.125 52.632 0.00 0.00 46.87 3.82
2660 2745 4.393693 TGCAATGGACGATGCACA 57.606 50.000 0.00 0.00 46.87 4.57
2663 2748 2.282701 AACAATGCAATGGACGATGC 57.717 45.000 6.73 0.00 42.86 3.91
2664 2749 3.378112 ACCTAACAATGCAATGGACGATG 59.622 43.478 6.73 0.00 0.00 3.84
2665 2750 3.620488 ACCTAACAATGCAATGGACGAT 58.380 40.909 6.73 0.00 0.00 3.73
2666 2751 3.066291 ACCTAACAATGCAATGGACGA 57.934 42.857 6.73 0.00 0.00 4.20
2667 2752 3.938963 AGTACCTAACAATGCAATGGACG 59.061 43.478 6.73 0.00 0.00 4.79
2668 2753 4.438744 GCAGTACCTAACAATGCAATGGAC 60.439 45.833 6.73 0.00 36.88 4.02
2669 2754 3.694072 GCAGTACCTAACAATGCAATGGA 59.306 43.478 6.73 0.00 36.88 3.41
2670 2755 3.696051 AGCAGTACCTAACAATGCAATGG 59.304 43.478 6.73 0.00 39.34 3.16
2671 2756 4.156556 ACAGCAGTACCTAACAATGCAATG 59.843 41.667 0.00 0.00 39.34 2.82
2672 2757 4.335416 ACAGCAGTACCTAACAATGCAAT 58.665 39.130 0.00 0.00 39.34 3.56
2673 2758 3.750371 ACAGCAGTACCTAACAATGCAA 58.250 40.909 0.00 0.00 39.34 4.08
2674 2759 3.417069 ACAGCAGTACCTAACAATGCA 57.583 42.857 4.14 0.00 39.34 3.96
2675 2760 3.751175 TGAACAGCAGTACCTAACAATGC 59.249 43.478 0.00 0.00 37.15 3.56
2676 2761 5.940192 TTGAACAGCAGTACCTAACAATG 57.060 39.130 0.00 0.00 0.00 2.82
2677 2762 6.237901 TCATTGAACAGCAGTACCTAACAAT 58.762 36.000 0.00 0.00 0.00 2.71
2678 2763 5.616270 TCATTGAACAGCAGTACCTAACAA 58.384 37.500 0.00 0.00 0.00 2.83
2679 2764 5.222079 TCATTGAACAGCAGTACCTAACA 57.778 39.130 0.00 0.00 0.00 2.41
2680 2765 6.743575 AATCATTGAACAGCAGTACCTAAC 57.256 37.500 0.00 0.00 0.00 2.34
2681 2766 7.498900 CCATAATCATTGAACAGCAGTACCTAA 59.501 37.037 0.00 0.00 0.00 2.69
2682 2767 6.992123 CCATAATCATTGAACAGCAGTACCTA 59.008 38.462 0.00 0.00 0.00 3.08
2683 2768 5.824624 CCATAATCATTGAACAGCAGTACCT 59.175 40.000 0.00 0.00 0.00 3.08
2684 2769 5.009010 CCCATAATCATTGAACAGCAGTACC 59.991 44.000 0.00 0.00 0.00 3.34
2685 2770 5.590259 ACCCATAATCATTGAACAGCAGTAC 59.410 40.000 0.00 0.00 0.00 2.73
2686 2771 5.754782 ACCCATAATCATTGAACAGCAGTA 58.245 37.500 0.00 0.00 0.00 2.74
2687 2772 4.603131 ACCCATAATCATTGAACAGCAGT 58.397 39.130 0.00 0.00 0.00 4.40
2688 2773 6.263842 ACATACCCATAATCATTGAACAGCAG 59.736 38.462 0.00 0.00 0.00 4.24
2689 2774 6.128486 ACATACCCATAATCATTGAACAGCA 58.872 36.000 0.00 0.00 0.00 4.41
2690 2775 6.639632 ACATACCCATAATCATTGAACAGC 57.360 37.500 0.00 0.00 0.00 4.40
2691 2776 8.733458 CCATACATACCCATAATCATTGAACAG 58.267 37.037 0.00 0.00 0.00 3.16
2692 2777 8.224025 ACCATACATACCCATAATCATTGAACA 58.776 33.333 0.00 0.00 0.00 3.18
2693 2778 8.635765 ACCATACATACCCATAATCATTGAAC 57.364 34.615 0.00 0.00 0.00 3.18
2694 2779 9.295825 GAACCATACATACCCATAATCATTGAA 57.704 33.333 0.00 0.00 0.00 2.69
2695 2780 8.443979 TGAACCATACATACCCATAATCATTGA 58.556 33.333 0.00 0.00 0.00 2.57
2696 2781 8.634335 TGAACCATACATACCCATAATCATTG 57.366 34.615 0.00 0.00 0.00 2.82
2782 3302 3.523564 ACTACCCCAGTAAGTGATTGCAT 59.476 43.478 0.00 0.00 34.98 3.96
2849 3369 5.129485 TGGTTCCATAACAAAGCTTTGGAAA 59.871 36.000 35.65 23.29 45.34 3.13
2850 3370 4.651503 TGGTTCCATAACAAAGCTTTGGAA 59.348 37.500 35.65 28.02 42.58 3.53
2851 3371 4.219115 TGGTTCCATAACAAAGCTTTGGA 58.781 39.130 35.65 24.50 42.34 3.53
2852 3372 4.599047 TGGTTCCATAACAAAGCTTTGG 57.401 40.909 35.65 22.76 42.34 3.28
2883 3403 1.632589 GGGGTGGCAGTTTCAAGAAT 58.367 50.000 0.00 0.00 0.00 2.40
3073 3597 4.373156 AACAAGGCTACACATCTTCCTT 57.627 40.909 0.00 0.00 37.61 3.36
3180 3704 6.030228 GGCAGTAGAAAACAATGCAATAGTC 58.970 40.000 0.00 0.00 38.63 2.59
3182 3706 6.199937 AGGCAGTAGAAAACAATGCAATAG 57.800 37.500 0.00 0.00 38.63 1.73
3183 3707 6.094881 GGTAGGCAGTAGAAAACAATGCAATA 59.905 38.462 0.00 0.00 38.63 1.90
3286 3810 5.063204 CCACTAGTGTTCCAGAAAACATGA 58.937 41.667 21.18 0.00 40.96 3.07
3339 3863 6.270156 TCTGAATCACAAAGCATGCATAAA 57.730 33.333 21.98 0.00 0.00 1.40
3371 3895 7.657336 TGTCATACAAAAGGAAATCTTTGACC 58.343 34.615 1.80 0.00 44.30 4.02
3378 3902 6.873076 TGCCAATTGTCATACAAAAGGAAATC 59.127 34.615 14.41 2.30 41.96 2.17
3412 3936 6.322201 ACAAATTGCCCACTATTATCTTGGAG 59.678 38.462 0.00 0.00 31.39 3.86
3419 3943 6.873076 CACAAACACAAATTGCCCACTATTAT 59.127 34.615 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.