Multiple sequence alignment - TraesCS2B01G390000

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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 TraesCS2B01G390000 chr2B 100.000 5685 0 0 1 5685 553878538 553872854 0.000000e+00 10499.0
1 TraesCS2B01G390000 chr2B 89.041 1095 84 27 4221 5306 553863834 553862767 0.000000e+00 1325.0
2 TraesCS2B01G390000 chr2B 93.578 327 13 3 3303 3622 553866441 553866116 1.110000e-131 481.0
3 TraesCS2B01G390000 chr2B 89.583 336 28 5 5356 5685 553862778 553862444 2.450000e-113 420.0
4 TraesCS2B01G390000 chr2B 85.337 341 24 10 3846 4171 553864490 553864161 4.250000e-86 329.0
5 TraesCS2B01G390000 chr2B 91.534 189 8 3 3667 3850 553866113 553865928 2.630000e-63 254.0
6 TraesCS2B01G390000 chr2A 90.716 4233 233 76 800 4974 615489460 615485330 0.000000e+00 5493.0
7 TraesCS2B01G390000 chr2A 86.833 562 30 15 97 642 615490980 615490447 6.350000e-164 588.0
8 TraesCS2B01G390000 chr2A 89.840 187 11 8 631 815 615490042 615489862 3.420000e-57 233.0
9 TraesCS2B01G390000 chr2A 89.796 147 15 0 5142 5288 615485210 615485064 7.520000e-44 189.0
10 TraesCS2B01G390000 chr2D 92.401 3119 153 43 803 3875 473438062 473434982 0.000000e+00 4370.0
11 TraesCS2B01G390000 chr2D 89.372 1242 76 25 3872 5099 473434716 473433517 0.000000e+00 1511.0
12 TraesCS2B01G390000 chr2D 90.921 760 48 14 4234 4979 473431785 473431033 0.000000e+00 1002.0
13 TraesCS2B01G390000 chr2D 92.074 593 31 9 5103 5684 473432824 473432237 0.000000e+00 821.0
14 TraesCS2B01G390000 chr2D 91.553 438 27 3 325 761 473438617 473438189 3.790000e-166 595.0
15 TraesCS2B01G390000 chr2D 84.720 589 57 7 5103 5685 473428459 473427898 4.970000e-155 558.0
16 TraesCS2B01G390000 chr2D 97.561 41 1 0 5274 5314 536843354 536843394 2.840000e-08 71.3
17 TraesCS2B01G390000 chr6D 89.161 286 28 2 2103 2388 308786449 308786731 2.520000e-93 353.0
18 TraesCS2B01G390000 chr6A 88.850 287 27 4 2103 2388 445413129 445413411 1.170000e-91 348.0
19 TraesCS2B01G390000 chr6B 90.262 267 23 2 2099 2365 476042582 476042845 4.220000e-91 346.0
20 TraesCS2B01G390000 chrUn 95.455 44 2 0 5274 5317 444442286 444442243 2.840000e-08 71.3
21 TraesCS2B01G390000 chr5D 97.561 41 1 0 5274 5314 6212886 6212926 2.840000e-08 71.3
22 TraesCS2B01G390000 chr5D 95.455 44 2 0 5274 5317 6213736 6213693 2.840000e-08 71.3
23 TraesCS2B01G390000 chr5D 97.561 41 1 0 5274 5314 6216669 6216709 2.840000e-08 71.3
24 TraesCS2B01G390000 chr5D 97.561 41 1 0 5274 5314 483800782 483800822 2.840000e-08 71.3
25 TraesCS2B01G390000 chr1D 97.561 41 1 0 5274 5314 12291289 12291329 2.840000e-08 71.3


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 TraesCS2B01G390000 chr2B 553872854 553878538 5684 True 10499.000000 10499 100.00000 1 5685 1 chr2B.!!$R1 5684
1 TraesCS2B01G390000 chr2B 553862444 553866441 3997 True 561.800000 1325 89.81460 3303 5685 5 chr2B.!!$R2 2382
2 TraesCS2B01G390000 chr2A 615485064 615490980 5916 True 1625.750000 5493 89.29625 97 5288 4 chr2A.!!$R1 5191
3 TraesCS2B01G390000 chr2D 473427898 473438617 10719 True 1476.166667 4370 90.17350 325 5685 6 chr2D.!!$R1 5360

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
302 315 0.029300 GCACACGCGGCATTATTGAT 59.971 50.0 12.47 0.0 0.00 2.57 F
762 1206 0.250295 ATCAACACACTGGTCACCCG 60.250 55.0 0.00 0.0 0.00 5.28 F
1162 2039 0.309612 GCGTCGAAGGGAAAAAGCAA 59.690 50.0 0.00 0.0 0.00 3.91 F
2781 3685 0.460987 AGTTAGTCATGCCTCTGCGC 60.461 55.0 0.00 0.0 41.78 6.09 F
3960 6611 0.168348 TCTCGCTCGCTGTCAAGTAC 59.832 55.0 0.00 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2961 0.105964 TCCATCGCCATTAGAACCGG 59.894 55.000 0.00 0.00 0.00 5.28 R
2760 3664 1.134995 CGCAGAGGCATGACTAACTCA 60.135 52.381 0.00 0.00 41.24 3.41 R
3129 4042 0.737219 CCTGCTTTAGCTGCATGGAC 59.263 55.000 1.02 0.00 42.66 4.02 R
3971 6622 0.035458 CGGCCTCTTTGGTCTTCAGT 59.965 55.000 0.00 0.00 38.58 3.41 R
5448 13444 0.175531 GTTACCATTGTGGGCATGGC 59.824 55.000 11.56 11.56 43.37 4.40 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
17 18 4.372235 CCCAACTACGCGTCTACG 57.628 61.111 18.63 5.54 43.27 3.51
32 33 3.833061 CGTCTACGCACAAAAGAAATTCG 59.167 43.478 0.00 0.00 0.00 3.34
33 34 4.375606 CGTCTACGCACAAAAGAAATTCGA 60.376 41.667 0.00 0.00 0.00 3.71
34 35 5.073478 GTCTACGCACAAAAGAAATTCGAG 58.927 41.667 0.00 0.00 0.00 4.04
35 36 3.268013 ACGCACAAAAGAAATTCGAGG 57.732 42.857 0.00 0.00 0.00 4.63
36 37 2.875933 ACGCACAAAAGAAATTCGAGGA 59.124 40.909 0.00 0.00 0.00 3.71
37 38 3.226347 CGCACAAAAGAAATTCGAGGAC 58.774 45.455 0.00 0.00 0.00 3.85
38 39 3.226347 GCACAAAAGAAATTCGAGGACG 58.774 45.455 0.00 0.00 41.26 4.79
39 40 3.303791 GCACAAAAGAAATTCGAGGACGT 60.304 43.478 0.00 0.00 40.69 4.34
40 41 4.084223 GCACAAAAGAAATTCGAGGACGTA 60.084 41.667 0.00 0.00 40.69 3.57
41 42 5.390567 GCACAAAAGAAATTCGAGGACGTAT 60.391 40.000 0.00 0.00 40.69 3.06
42 43 6.599437 CACAAAAGAAATTCGAGGACGTATT 58.401 36.000 0.00 0.00 40.18 1.89
43 44 7.075741 CACAAAAGAAATTCGAGGACGTATTT 58.924 34.615 0.00 0.00 46.30 1.40
44 45 7.059488 CACAAAAGAAATTCGAGGACGTATTTG 59.941 37.037 10.67 2.68 44.71 2.32
45 46 5.796350 AAGAAATTCGAGGACGTATTTGG 57.204 39.130 10.67 0.00 44.71 3.28
46 47 3.621715 AGAAATTCGAGGACGTATTTGGC 59.378 43.478 10.67 0.81 44.71 4.52
47 48 1.949465 ATTCGAGGACGTATTTGGCC 58.051 50.000 0.00 0.00 40.69 5.36
48 49 0.108041 TTCGAGGACGTATTTGGCCC 60.108 55.000 0.00 0.00 40.69 5.80
49 50 0.974010 TCGAGGACGTATTTGGCCCT 60.974 55.000 0.00 0.00 40.69 5.19
50 51 0.810031 CGAGGACGTATTTGGCCCTG 60.810 60.000 0.00 0.00 34.56 4.45
51 52 1.077716 AGGACGTATTTGGCCCTGC 60.078 57.895 0.00 0.00 0.00 4.85
52 53 1.077716 GGACGTATTTGGCCCTGCT 60.078 57.895 0.00 0.00 0.00 4.24
53 54 1.095807 GGACGTATTTGGCCCTGCTC 61.096 60.000 0.00 0.00 0.00 4.26
54 55 1.429148 GACGTATTTGGCCCTGCTCG 61.429 60.000 0.00 2.45 0.00 5.03
55 56 1.449601 CGTATTTGGCCCTGCTCGT 60.450 57.895 0.00 0.00 0.00 4.18
56 57 1.024579 CGTATTTGGCCCTGCTCGTT 61.025 55.000 0.00 0.00 0.00 3.85
57 58 0.733150 GTATTTGGCCCTGCTCGTTC 59.267 55.000 0.00 0.00 0.00 3.95
58 59 0.742990 TATTTGGCCCTGCTCGTTCG 60.743 55.000 0.00 0.00 0.00 3.95
59 60 4.697756 TTGGCCCTGCTCGTTCGG 62.698 66.667 0.00 0.00 0.00 4.30
62 63 4.821589 GCCCTGCTCGTTCGGGAG 62.822 72.222 0.00 0.00 40.55 4.30
68 69 3.796443 CTCGTTCGGGAGCGTCGA 61.796 66.667 0.00 0.00 36.41 4.20
69 70 3.318539 CTCGTTCGGGAGCGTCGAA 62.319 63.158 0.00 7.51 43.18 3.71
72 73 4.409218 TTCGGGAGCGTCGAACGG 62.409 66.667 0.00 0.00 42.82 4.44
74 75 4.409218 CGGGAGCGTCGAACGGAA 62.409 66.667 0.00 0.00 42.82 4.30
75 76 2.808321 GGGAGCGTCGAACGGAAC 60.808 66.667 0.00 0.00 42.82 3.62
92 93 4.954092 GGAACGAAAATGAGAAGCTGAT 57.046 40.909 0.00 0.00 0.00 2.90
93 94 4.656041 GGAACGAAAATGAGAAGCTGATG 58.344 43.478 0.00 0.00 0.00 3.07
94 95 3.754188 ACGAAAATGAGAAGCTGATGC 57.246 42.857 0.00 0.00 40.05 3.91
95 96 2.094894 ACGAAAATGAGAAGCTGATGCG 59.905 45.455 0.00 0.00 45.42 4.73
100 101 5.824904 AAATGAGAAGCTGATGCGTTATT 57.175 34.783 0.00 0.00 45.42 1.40
107 108 2.860735 AGCTGATGCGTTATTCTTCGAC 59.139 45.455 0.00 0.00 45.42 4.20
120 121 2.014093 CTTCGACTGATTGCGGACGC 62.014 60.000 10.13 10.13 38.22 5.19
123 124 1.738099 GACTGATTGCGGACGCTGT 60.738 57.895 18.04 6.20 42.51 4.40
133 134 1.664965 GGACGCTGTGAGTGTGACC 60.665 63.158 0.00 0.00 39.36 4.02
135 136 2.027605 CGCTGTGAGTGTGACCGT 59.972 61.111 0.00 0.00 0.00 4.83
136 137 2.302952 CGCTGTGAGTGTGACCGTG 61.303 63.158 0.00 0.00 0.00 4.94
137 138 1.067416 GCTGTGAGTGTGACCGTGA 59.933 57.895 0.00 0.00 0.00 4.35
138 139 0.529773 GCTGTGAGTGTGACCGTGAA 60.530 55.000 0.00 0.00 0.00 3.18
139 140 1.873903 GCTGTGAGTGTGACCGTGAAT 60.874 52.381 0.00 0.00 0.00 2.57
140 141 1.794701 CTGTGAGTGTGACCGTGAATG 59.205 52.381 0.00 0.00 0.00 2.67
141 142 1.410882 TGTGAGTGTGACCGTGAATGA 59.589 47.619 0.00 0.00 0.00 2.57
142 143 2.159028 TGTGAGTGTGACCGTGAATGAA 60.159 45.455 0.00 0.00 0.00 2.57
143 144 2.221055 GTGAGTGTGACCGTGAATGAAC 59.779 50.000 0.00 0.00 0.00 3.18
144 145 1.455786 GAGTGTGACCGTGAATGAACG 59.544 52.381 0.00 0.00 43.20 3.95
145 146 1.067974 AGTGTGACCGTGAATGAACGA 59.932 47.619 2.18 0.00 46.49 3.85
146 147 1.862201 GTGTGACCGTGAATGAACGAA 59.138 47.619 2.18 0.00 46.49 3.85
148 149 1.136336 GTGACCGTGAATGAACGAAGC 60.136 52.381 2.18 0.00 46.49 3.86
151 153 0.366871 CCGTGAATGAACGAAGCGAG 59.633 55.000 2.18 0.00 46.49 5.03
162 164 1.887198 ACGAAGCGAGGAAGAAGAAGA 59.113 47.619 0.00 0.00 0.00 2.87
171 173 5.559225 GCGAGGAAGAAGAAGAAAACTGAAC 60.559 44.000 0.00 0.00 0.00 3.18
179 181 3.630769 AGAAGAAAACTGAACCGGGAAAC 59.369 43.478 6.32 0.00 0.00 2.78
236 246 2.512515 GCTCCATCGGCACCTCAC 60.513 66.667 0.00 0.00 0.00 3.51
237 247 2.202797 CTCCATCGGCACCTCACG 60.203 66.667 0.00 0.00 0.00 4.35
254 264 3.545308 CGCGAATCGTTTCTGACAC 57.455 52.632 0.00 0.00 0.00 3.67
285 298 3.362706 AGTTGAGTACTCTAATCCGGCA 58.637 45.455 23.01 0.00 28.23 5.69
298 311 3.572539 CGGCACACGCGGCATTAT 61.573 61.111 12.47 0.00 39.92 1.28
299 312 2.798009 GGCACACGCGGCATTATT 59.202 55.556 12.47 0.00 39.92 1.40
300 313 1.586042 GGCACACGCGGCATTATTG 60.586 57.895 12.47 0.00 39.92 1.90
301 314 1.427419 GCACACGCGGCATTATTGA 59.573 52.632 12.47 0.00 0.00 2.57
302 315 0.029300 GCACACGCGGCATTATTGAT 59.971 50.000 12.47 0.00 0.00 2.57
303 316 1.921573 GCACACGCGGCATTATTGATC 60.922 52.381 12.47 0.00 0.00 2.92
304 317 0.581529 ACACGCGGCATTATTGATCG 59.418 50.000 12.47 0.00 0.00 3.69
305 318 0.858583 CACGCGGCATTATTGATCGA 59.141 50.000 12.47 0.00 0.00 3.59
306 319 1.460743 CACGCGGCATTATTGATCGAT 59.539 47.619 12.47 0.00 0.00 3.59
307 320 2.666022 CACGCGGCATTATTGATCGATA 59.334 45.455 12.47 0.00 0.00 2.92
308 321 3.306973 CACGCGGCATTATTGATCGATAT 59.693 43.478 12.47 0.00 0.00 1.63
309 322 3.306973 ACGCGGCATTATTGATCGATATG 59.693 43.478 12.47 0.00 0.00 1.78
310 323 3.611517 GCGGCATTATTGATCGATATGC 58.388 45.455 17.86 17.86 0.00 3.14
311 324 3.310774 GCGGCATTATTGATCGATATGCT 59.689 43.478 22.72 3.09 34.36 3.79
312 325 4.201851 GCGGCATTATTGATCGATATGCTT 60.202 41.667 22.72 1.72 34.36 3.91
313 326 5.674569 GCGGCATTATTGATCGATATGCTTT 60.675 40.000 22.72 0.00 34.36 3.51
314 327 6.317088 CGGCATTATTGATCGATATGCTTTT 58.683 36.000 22.72 0.00 34.36 2.27
315 328 6.803320 CGGCATTATTGATCGATATGCTTTTT 59.197 34.615 22.72 0.00 34.36 1.94
384 397 2.023771 TTTCTGCTCGTGCGCTCTG 61.024 57.895 9.73 1.74 43.34 3.35
456 469 3.122971 ACGGCGAGACGATCACGA 61.123 61.111 16.62 0.00 42.66 4.35
505 518 2.026879 GCGTGATCTCTCCTCGCC 59.973 66.667 0.00 0.00 37.59 5.54
574 588 0.675837 GGAGGGCGACAAAAGGGTAC 60.676 60.000 0.00 0.00 0.00 3.34
603 617 1.987770 GCGTGTCCATGCTTCATTTTG 59.012 47.619 4.25 0.00 40.09 2.44
608 622 5.291971 GTGTCCATGCTTCATTTTGTTTCT 58.708 37.500 0.00 0.00 0.00 2.52
676 1108 9.438163 AATTCTCTATCCTTTTCAGATCTCTCT 57.562 33.333 0.00 0.00 0.00 3.10
679 1111 7.720957 TCTCTATCCTTTTCAGATCTCTCTCAG 59.279 40.741 0.00 0.00 0.00 3.35
680 1112 7.353525 TCTATCCTTTTCAGATCTCTCTCAGT 58.646 38.462 0.00 0.00 0.00 3.41
682 1114 5.579047 TCCTTTTCAGATCTCTCTCAGTCT 58.421 41.667 0.00 0.00 0.00 3.24
683 1115 6.726379 TCCTTTTCAGATCTCTCTCAGTCTA 58.274 40.000 0.00 0.00 0.00 2.59
762 1206 0.250295 ATCAACACACTGGTCACCCG 60.250 55.000 0.00 0.00 0.00 5.28
898 1765 0.979665 CAAGGAAGCCTCTCTGACCA 59.020 55.000 0.00 0.00 30.89 4.02
904 1771 1.758514 GCCTCTCTGACCATCGGGA 60.759 63.158 0.00 0.00 38.05 5.14
937 1804 1.943340 CGAAGCCATAAAAGAGAGGGC 59.057 52.381 0.00 0.00 44.92 5.19
970 1841 1.267121 GAGGAGGCTACCAACACTCA 58.733 55.000 0.00 0.00 0.00 3.41
1091 1968 2.747822 CGCGCTCTGCATTCTGCTT 61.748 57.895 5.56 0.00 45.31 3.91
1103 1980 4.821589 CTGCTTCTCGCGTCCCCC 62.822 72.222 5.77 0.00 43.27 5.40
1157 2034 2.735883 TCGGCGTCGAAGGGAAAA 59.264 55.556 10.97 0.00 43.03 2.29
1158 2035 1.069427 TCGGCGTCGAAGGGAAAAA 59.931 52.632 10.97 0.00 43.03 1.94
1160 2037 1.209383 GGCGTCGAAGGGAAAAAGC 59.791 57.895 0.00 0.00 0.00 3.51
1161 2038 1.512156 GGCGTCGAAGGGAAAAAGCA 61.512 55.000 0.00 0.00 0.00 3.91
1162 2039 0.309612 GCGTCGAAGGGAAAAAGCAA 59.690 50.000 0.00 0.00 0.00 3.91
1163 2040 1.663161 GCGTCGAAGGGAAAAAGCAAG 60.663 52.381 0.00 0.00 0.00 4.01
1164 2041 1.069227 CGTCGAAGGGAAAAAGCAAGG 60.069 52.381 0.00 0.00 0.00 3.61
1165 2042 2.227194 GTCGAAGGGAAAAAGCAAGGA 58.773 47.619 0.00 0.00 0.00 3.36
1307 2191 2.893637 CTAGCTCCGCATTGTTACAGT 58.106 47.619 0.00 0.00 0.00 3.55
1513 2402 9.740239 ATCTGCTGTACAAAAATTATTGCTATG 57.260 29.630 0.00 0.00 33.52 2.23
1540 2429 1.681793 GTCCTATTCGCACCAGAGCTA 59.318 52.381 0.00 0.00 0.00 3.32
1751 2645 1.080501 CGAGTCAAGCGCAGAGGAA 60.081 57.895 11.47 0.00 0.00 3.36
1885 2779 5.507985 GGCTAAAATCTTGGCGATAAATGCT 60.508 40.000 0.00 0.00 39.81 3.79
2044 2938 5.861251 CGCAGTAGATTATCATCTCAGTTCC 59.139 44.000 0.00 0.00 40.53 3.62
2045 2939 6.162777 GCAGTAGATTATCATCTCAGTTCCC 58.837 44.000 0.00 0.00 40.53 3.97
2053 2947 4.796231 CTCAGTTCCCGCCGGACG 62.796 72.222 5.05 8.73 38.14 4.79
2067 2961 1.141234 GGACGGAGGTCGGTTGATC 59.859 63.158 0.00 0.00 44.39 2.92
2221 3116 2.047274 GCGCCTGCTACAAGGTCA 60.047 61.111 0.00 0.00 39.75 4.02
2443 3343 2.069273 GCAGCACGTACACTTCTTCAT 58.931 47.619 0.00 0.00 0.00 2.57
2619 3523 0.531090 TGGACCGTTGTCGAAACAGG 60.531 55.000 9.90 12.08 42.73 4.00
2628 3532 0.796927 GTCGAAACAGGGCAGCTAAC 59.203 55.000 0.00 0.00 0.00 2.34
2629 3533 0.685097 TCGAAACAGGGCAGCTAACT 59.315 50.000 0.00 0.00 0.00 2.24
2651 3555 4.086457 TGCTACTACTGTGGATCTGTGAA 58.914 43.478 0.00 0.00 0.00 3.18
2691 3595 4.702612 TGAAGCGCAGTGGGAATTAAATTA 59.297 37.500 11.47 0.00 0.00 1.40
2725 3629 2.125512 CTAACGGGCTCGCAGCTT 60.126 61.111 5.51 0.00 41.99 3.74
2760 3664 1.421480 TGGATCTATCTGCTGCTGCT 58.579 50.000 17.00 0.00 40.48 4.24
2767 3671 3.828657 TCTGCTGCTGCTGAGTTAG 57.171 52.632 18.88 6.55 41.21 2.34
2781 3685 0.460987 AGTTAGTCATGCCTCTGCGC 60.461 55.000 0.00 0.00 41.78 6.09
2872 3783 1.394917 CAATTCTTCCAGCTCCGTTCG 59.605 52.381 0.00 0.00 0.00 3.95
2909 3820 3.299340 TGGAAAAGCTGTCGTCTCTAC 57.701 47.619 0.00 0.00 0.00 2.59
2920 3831 5.335035 GCTGTCGTCTCTACCTATGTAATCC 60.335 48.000 0.00 0.00 0.00 3.01
2922 3833 6.304624 TGTCGTCTCTACCTATGTAATCCAT 58.695 40.000 0.00 0.00 37.58 3.41
2926 3837 6.166982 GTCTCTACCTATGTAATCCATTGCC 58.833 44.000 0.00 0.00 34.86 4.52
2948 3859 2.703416 CACTGCATGTGTGTACATCCT 58.297 47.619 0.00 0.00 45.53 3.24
3141 4054 1.337384 ACATCGGGTCCATGCAGCTA 61.337 55.000 0.00 0.00 0.00 3.32
3156 4069 2.945890 GCAGCTAAAGCAGGTACCCATT 60.946 50.000 8.74 1.28 45.16 3.16
3157 4070 3.356290 CAGCTAAAGCAGGTACCCATTT 58.644 45.455 8.74 9.81 45.16 2.32
3173 4086 5.385198 ACCCATTTTCTTCTTGTCAAGCTA 58.615 37.500 7.78 0.00 0.00 3.32
3174 4087 6.012745 ACCCATTTTCTTCTTGTCAAGCTAT 58.987 36.000 7.78 0.00 0.00 2.97
3189 4102 6.015519 TGTCAAGCTATTTTACTTTGGTGCAT 60.016 34.615 0.00 0.00 0.00 3.96
3190 4103 6.528072 GTCAAGCTATTTTACTTTGGTGCATC 59.472 38.462 0.00 0.00 0.00 3.91
3253 4167 6.428385 AATCGAGTTATCTTTTGAGCCTTG 57.572 37.500 0.00 0.00 0.00 3.61
3356 4284 2.541588 CGGCGCATATTCTTTCCTTTGG 60.542 50.000 10.83 0.00 0.00 3.28
3505 4433 1.586154 GGCCCATGTCGTGTCCTTTG 61.586 60.000 0.00 0.00 0.00 2.77
3506 4434 0.889186 GCCCATGTCGTGTCCTTTGT 60.889 55.000 0.00 0.00 0.00 2.83
3507 4435 1.609580 GCCCATGTCGTGTCCTTTGTA 60.610 52.381 0.00 0.00 0.00 2.41
3508 4436 2.073816 CCCATGTCGTGTCCTTTGTAC 58.926 52.381 0.00 0.00 0.00 2.90
3509 4437 2.549134 CCCATGTCGTGTCCTTTGTACA 60.549 50.000 0.00 0.00 0.00 2.90
3511 4439 3.059188 CCATGTCGTGTCCTTTGTACAAC 60.059 47.826 8.07 0.00 0.00 3.32
3512 4440 3.248495 TGTCGTGTCCTTTGTACAACA 57.752 42.857 8.07 0.23 0.00 3.33
3514 4442 3.371591 TGTCGTGTCCTTTGTACAACAAC 59.628 43.478 8.07 7.45 37.90 3.32
3581 4511 5.689819 CAGTATTACAGCAAGTGAAACCAC 58.310 41.667 0.00 0.00 37.80 4.16
3594 4524 4.081642 AGTGAAACCACACGTAGCAGATAT 60.082 41.667 0.00 0.00 44.35 1.63
3610 4540 5.178996 AGCAGATATCTAAGCTTCGCAAATG 59.821 40.000 0.00 0.00 32.52 2.32
3624 4554 3.052036 CGCAAATGCTGTATTATTGCCC 58.948 45.455 8.79 0.00 39.32 5.36
3643 4573 4.224433 GCCCGAAACTAAGCTTTGTAAAC 58.776 43.478 13.95 7.71 0.00 2.01
3644 4574 4.261280 GCCCGAAACTAAGCTTTGTAAACA 60.261 41.667 13.95 0.00 0.00 2.83
3645 4575 5.564063 GCCCGAAACTAAGCTTTGTAAACAT 60.564 40.000 13.95 0.00 0.00 2.71
3646 4576 5.856455 CCCGAAACTAAGCTTTGTAAACATG 59.144 40.000 13.95 0.00 0.00 3.21
3647 4577 5.342259 CCGAAACTAAGCTTTGTAAACATGC 59.658 40.000 13.95 0.00 0.00 4.06
3648 4578 5.342259 CGAAACTAAGCTTTGTAAACATGCC 59.658 40.000 13.95 0.00 0.00 4.40
3662 4594 1.274167 ACATGCCAATGAACTGCCAAG 59.726 47.619 0.00 0.00 37.24 3.61
3741 4678 3.548616 CGCACAATGTCACACTGTCAAAT 60.549 43.478 0.00 0.00 0.00 2.32
3938 6589 0.744414 GATGCTGCCGCTTTACCTCA 60.744 55.000 0.70 0.00 36.97 3.86
3949 6600 0.809385 TTTACCTCAGGTCTCGCTCG 59.191 55.000 0.00 0.00 37.09 5.03
3960 6611 0.168348 TCTCGCTCGCTGTCAAGTAC 59.832 55.000 0.00 0.00 0.00 2.73
3961 6612 0.169230 CTCGCTCGCTGTCAAGTACT 59.831 55.000 0.00 0.00 0.00 2.73
3962 6613 0.168348 TCGCTCGCTGTCAAGTACTC 59.832 55.000 0.00 0.00 0.00 2.59
3963 6614 0.798771 CGCTCGCTGTCAAGTACTCC 60.799 60.000 0.00 0.00 0.00 3.85
3964 6615 0.528470 GCTCGCTGTCAAGTACTCCT 59.472 55.000 0.00 0.00 0.00 3.69
3965 6616 1.743958 GCTCGCTGTCAAGTACTCCTA 59.256 52.381 0.00 0.00 0.00 2.94
3971 6622 4.525024 GCTGTCAAGTACTCCTAGTAGGA 58.475 47.826 18.15 18.15 43.43 2.94
3974 6625 5.498393 TGTCAAGTACTCCTAGTAGGACTG 58.502 45.833 15.33 9.21 39.89 3.51
4108 6769 3.029735 CCGTGCGTTTGCTTTGCC 61.030 61.111 0.00 0.00 43.34 4.52
4245 7195 7.881643 ATCTATGAGATTTATCAGTGTTCGC 57.118 36.000 0.00 0.00 28.69 4.70
4246 7196 7.043961 TCTATGAGATTTATCAGTGTTCGCT 57.956 36.000 0.00 0.00 31.44 4.93
4266 7216 3.242543 GCTAGTGCTTATGATGTGTGTGC 60.243 47.826 0.00 0.00 36.03 4.57
4267 7217 3.063510 AGTGCTTATGATGTGTGTGCT 57.936 42.857 0.00 0.00 0.00 4.40
4440 9974 3.822192 CGCGACGTCATCCCCAGA 61.822 66.667 17.16 0.00 0.00 3.86
4502 10036 1.238439 GAGGCCTCTCTCTGATCTCG 58.762 60.000 26.25 0.00 37.07 4.04
4503 10037 0.843309 AGGCCTCTCTCTGATCTCGA 59.157 55.000 0.00 0.00 0.00 4.04
4505 10039 1.812571 GGCCTCTCTCTGATCTCGATC 59.187 57.143 0.00 0.00 38.29 3.69
4506 10040 2.553028 GGCCTCTCTCTGATCTCGATCT 60.553 54.545 0.00 0.00 38.60 2.75
4508 10042 4.323417 GCCTCTCTCTGATCTCGATCTTA 58.677 47.826 8.25 0.00 38.60 2.10
4515 10049 3.632604 TCTGATCTCGATCTTACCACCAC 59.367 47.826 8.25 0.00 38.60 4.16
4516 10050 2.357952 TGATCTCGATCTTACCACCACG 59.642 50.000 8.25 0.00 38.60 4.94
4518 10052 1.100510 CTCGATCTTACCACCACGGA 58.899 55.000 0.00 0.00 38.63 4.69
4519 10053 1.681793 CTCGATCTTACCACCACGGAT 59.318 52.381 0.00 0.00 38.63 4.18
4591 10129 1.376424 ACATGGCGCTCTGTTGGAG 60.376 57.895 7.64 0.00 44.49 3.86
4628 10166 6.105333 AGATTGTGTTTTGTTGCAGCTTAAA 58.895 32.000 1.17 0.00 0.00 1.52
4629 10167 5.523013 TTGTGTTTTGTTGCAGCTTAAAC 57.477 34.783 18.02 18.02 0.00 2.01
4663 10201 1.269154 GCCTAGTCGTAAGCTAGTGGC 60.269 57.143 0.00 0.00 40.27 5.01
4709 10247 1.591703 GTGAGTGATCTGGGTGCGA 59.408 57.895 0.00 0.00 0.00 5.10
4730 10268 1.076024 AGCAGCCATCCTCTCCAAAAA 59.924 47.619 0.00 0.00 0.00 1.94
4765 10303 1.895707 CTGCTGGGAATCCGATGCC 60.896 63.158 0.00 0.00 35.24 4.40
4801 10339 1.412505 GGTTTTGGACCCCTCTTGGTT 60.413 52.381 0.00 0.00 43.06 3.67
4842 10380 7.017498 TGTCGTGTGCTGTTTTTATCTTTTA 57.983 32.000 0.00 0.00 0.00 1.52
4870 10410 6.963796 TCTGTTTTGTTTGCATGTTTGTTTT 58.036 28.000 0.00 0.00 0.00 2.43
4871 10411 6.854892 TCTGTTTTGTTTGCATGTTTGTTTTG 59.145 30.769 0.00 0.00 0.00 2.44
4875 10415 3.755378 TGTTTGCATGTTTGTTTTGCCTT 59.245 34.783 0.00 0.00 35.51 4.35
4877 10417 2.286872 TGCATGTTTGTTTTGCCTTGG 58.713 42.857 0.00 0.00 35.51 3.61
4879 10419 2.682352 GCATGTTTGTTTTGCCTTGGTT 59.318 40.909 0.00 0.00 0.00 3.67
4880 10420 3.873952 GCATGTTTGTTTTGCCTTGGTTA 59.126 39.130 0.00 0.00 0.00 2.85
4881 10421 4.024977 GCATGTTTGTTTTGCCTTGGTTAG 60.025 41.667 0.00 0.00 0.00 2.34
4883 10423 5.153950 TGTTTGTTTTGCCTTGGTTAGTT 57.846 34.783 0.00 0.00 0.00 2.24
4884 10424 4.932200 TGTTTGTTTTGCCTTGGTTAGTTG 59.068 37.500 0.00 0.00 0.00 3.16
4914 10454 2.032799 GGCTCGTGACAAATGTGTTTCA 59.967 45.455 0.00 0.00 38.41 2.69
4915 10455 3.035942 GCTCGTGACAAATGTGTTTCAC 58.964 45.455 0.00 0.00 38.41 3.18
4922 10462 6.321717 GTGACAAATGTGTTTCACTTCTTCA 58.678 36.000 0.00 0.00 38.41 3.02
4938 10478 6.207417 CACTTCTTCAAATGGTGGACTTGTAT 59.793 38.462 0.00 0.00 0.00 2.29
4943 10483 4.221924 TCAAATGGTGGACTTGTATCGAGA 59.778 41.667 0.00 0.00 0.00 4.04
4959 10499 4.478206 TCGAGATCAGAATTCCTGCTTT 57.522 40.909 0.65 0.00 42.62 3.51
5002 10542 2.116366 GACATGCGTGTTTGTTTGGAC 58.884 47.619 13.92 0.00 39.09 4.02
5020 12982 3.074687 TGGACTACTCAGAGAAGACACCT 59.925 47.826 3.79 0.00 0.00 4.00
5035 12997 2.969443 CACCTTCCGTGTGAATGTTC 57.031 50.000 0.00 0.00 37.73 3.18
5036 12998 2.217750 CACCTTCCGTGTGAATGTTCA 58.782 47.619 0.00 0.00 37.73 3.18
5048 13010 4.008074 TGAATGTTCACCTCTCCAGTTC 57.992 45.455 0.00 0.00 31.01 3.01
5087 13049 3.511934 ACCACAAAAAGGTGCACAAGTAA 59.488 39.130 20.43 0.00 38.13 2.24
5107 13069 2.291843 CGTCAAGCAGCTGATACCG 58.708 57.895 20.43 10.69 0.00 4.02
5124 13120 0.982673 CCGACGACTACAGCGAAAAG 59.017 55.000 0.00 0.00 0.00 2.27
5200 13196 0.531974 TCAAGGACTGCGTGACAACC 60.532 55.000 0.00 0.00 0.00 3.77
5226 13222 1.135373 CGGACACGAAGACAGCACTAT 60.135 52.381 0.00 0.00 44.60 2.12
5237 13233 3.834813 AGACAGCACTATCCTGACTTCAA 59.165 43.478 0.00 0.00 32.81 2.69
5375 13371 4.843220 AAAGGAATCAGCAAGTGAACAG 57.157 40.909 0.00 0.00 39.19 3.16
5407 13403 1.734465 CGGACTCAAAGAAGATGCCAC 59.266 52.381 0.00 0.00 0.00 5.01
5428 13424 2.240667 CCCAAGAGGTTCTGATGATGGT 59.759 50.000 0.00 0.00 0.00 3.55
5432 13428 4.744795 AGAGGTTCTGATGATGGTGTAC 57.255 45.455 0.00 0.00 0.00 2.90
5482 13480 2.569853 TGGTAACCATCACCGAGACAAT 59.430 45.455 0.00 0.00 39.04 2.71
5510 13509 2.047213 AACCCCGCCGAAGAGTTGAA 62.047 55.000 0.00 0.00 0.00 2.69
5513 13512 1.014564 CCCGCCGAAGAGTTGAAGAC 61.015 60.000 0.00 0.00 0.00 3.01
5515 13514 1.782181 GCCGAAGAGTTGAAGACGC 59.218 57.895 0.00 0.00 0.00 5.19
5575 13576 1.969923 CCCATGCAACCTTCAAGGAAA 59.030 47.619 11.59 0.00 37.67 3.13
5612 13613 0.312102 GTTGTTGCTTGGCCAGAGAC 59.688 55.000 5.11 4.58 0.00 3.36
5666 13668 2.158871 GGCATGAACATGGGCAAATGAT 60.159 45.455 15.15 0.00 39.16 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.372235 CGTAGACGCGTAGTTGGG 57.628 61.111 13.97 0.00 0.00 4.12
10 11 3.833061 CGAATTTCTTTTGTGCGTAGACG 59.167 43.478 0.00 0.00 43.27 4.18
11 12 5.013861 TCGAATTTCTTTTGTGCGTAGAC 57.986 39.130 0.00 0.00 0.00 2.59
12 13 4.151689 CCTCGAATTTCTTTTGTGCGTAGA 59.848 41.667 0.00 0.00 0.00 2.59
13 14 4.151689 TCCTCGAATTTCTTTTGTGCGTAG 59.848 41.667 0.00 0.00 0.00 3.51
14 15 4.059511 TCCTCGAATTTCTTTTGTGCGTA 58.940 39.130 0.00 0.00 0.00 4.42
15 16 2.875933 TCCTCGAATTTCTTTTGTGCGT 59.124 40.909 0.00 0.00 0.00 5.24
16 17 3.226347 GTCCTCGAATTTCTTTTGTGCG 58.774 45.455 0.00 0.00 0.00 5.34
17 18 3.226347 CGTCCTCGAATTTCTTTTGTGC 58.774 45.455 0.00 0.00 39.71 4.57
18 19 4.468095 ACGTCCTCGAATTTCTTTTGTG 57.532 40.909 0.00 0.00 40.62 3.33
19 20 6.796705 AATACGTCCTCGAATTTCTTTTGT 57.203 33.333 0.00 0.00 40.62 2.83
20 21 6.523201 CCAAATACGTCCTCGAATTTCTTTTG 59.477 38.462 0.00 0.00 40.62 2.44
21 22 6.608610 CCAAATACGTCCTCGAATTTCTTTT 58.391 36.000 0.00 0.00 40.62 2.27
22 23 5.391629 GCCAAATACGTCCTCGAATTTCTTT 60.392 40.000 0.00 0.00 40.62 2.52
23 24 4.094442 GCCAAATACGTCCTCGAATTTCTT 59.906 41.667 0.00 0.00 40.62 2.52
24 25 3.621715 GCCAAATACGTCCTCGAATTTCT 59.378 43.478 0.00 0.00 40.62 2.52
25 26 3.242641 GGCCAAATACGTCCTCGAATTTC 60.243 47.826 0.00 0.00 40.62 2.17
26 27 2.681344 GGCCAAATACGTCCTCGAATTT 59.319 45.455 0.00 0.00 40.62 1.82
27 28 2.285977 GGCCAAATACGTCCTCGAATT 58.714 47.619 0.00 0.00 40.62 2.17
28 29 1.474498 GGGCCAAATACGTCCTCGAAT 60.474 52.381 4.39 0.00 40.62 3.34
29 30 0.108041 GGGCCAAATACGTCCTCGAA 60.108 55.000 4.39 0.00 40.62 3.71
30 31 0.974010 AGGGCCAAATACGTCCTCGA 60.974 55.000 6.18 0.00 40.62 4.04
31 32 0.810031 CAGGGCCAAATACGTCCTCG 60.810 60.000 6.18 0.00 43.34 4.63
32 33 1.095807 GCAGGGCCAAATACGTCCTC 61.096 60.000 6.18 0.00 0.00 3.71
33 34 1.077716 GCAGGGCCAAATACGTCCT 60.078 57.895 6.18 0.00 0.00 3.85
34 35 1.077716 AGCAGGGCCAAATACGTCC 60.078 57.895 6.18 0.00 0.00 4.79
35 36 1.429148 CGAGCAGGGCCAAATACGTC 61.429 60.000 6.18 0.00 0.00 4.34
36 37 1.449601 CGAGCAGGGCCAAATACGT 60.450 57.895 6.18 0.00 0.00 3.57
37 38 1.024579 AACGAGCAGGGCCAAATACG 61.025 55.000 6.18 7.22 0.00 3.06
38 39 0.733150 GAACGAGCAGGGCCAAATAC 59.267 55.000 6.18 0.00 0.00 1.89
39 40 0.742990 CGAACGAGCAGGGCCAAATA 60.743 55.000 6.18 0.00 0.00 1.40
40 41 2.040544 CGAACGAGCAGGGCCAAAT 61.041 57.895 6.18 0.00 0.00 2.32
41 42 2.668212 CGAACGAGCAGGGCCAAA 60.668 61.111 6.18 0.00 0.00 3.28
42 43 4.697756 CCGAACGAGCAGGGCCAA 62.698 66.667 6.18 0.00 0.00 4.52
45 46 4.821589 CTCCCGAACGAGCAGGGC 62.822 72.222 0.00 0.00 44.70 5.19
51 52 3.318539 TTCGACGCTCCCGAACGAG 62.319 63.158 0.00 0.00 42.77 4.18
52 53 3.356267 TTCGACGCTCCCGAACGA 61.356 61.111 0.00 0.00 40.56 3.85
55 56 4.409218 CCGTTCGACGCTCCCGAA 62.409 66.667 0.00 0.00 40.91 4.30
57 58 4.409218 TTCCGTTCGACGCTCCCG 62.409 66.667 0.00 0.00 40.91 5.14
58 59 2.808321 GTTCCGTTCGACGCTCCC 60.808 66.667 0.00 0.00 40.91 4.30
59 60 3.170585 CGTTCCGTTCGACGCTCC 61.171 66.667 0.00 0.00 40.91 4.70
60 61 1.270777 TTTCGTTCCGTTCGACGCTC 61.271 55.000 0.00 0.00 40.91 5.03
61 62 0.871163 TTTTCGTTCCGTTCGACGCT 60.871 50.000 0.00 0.00 40.91 5.07
62 63 0.162294 ATTTTCGTTCCGTTCGACGC 59.838 50.000 0.00 0.00 40.91 5.19
63 64 1.452773 TCATTTTCGTTCCGTTCGACG 59.547 47.619 0.00 0.00 42.11 5.12
64 65 2.727798 TCTCATTTTCGTTCCGTTCGAC 59.272 45.455 0.00 0.00 37.05 4.20
65 66 3.015934 TCTCATTTTCGTTCCGTTCGA 57.984 42.857 0.00 0.00 35.50 3.71
66 67 3.722123 CTTCTCATTTTCGTTCCGTTCG 58.278 45.455 0.00 0.00 0.00 3.95
67 68 3.186613 AGCTTCTCATTTTCGTTCCGTTC 59.813 43.478 0.00 0.00 0.00 3.95
68 69 3.058914 CAGCTTCTCATTTTCGTTCCGTT 60.059 43.478 0.00 0.00 0.00 4.44
69 70 2.480419 CAGCTTCTCATTTTCGTTCCGT 59.520 45.455 0.00 0.00 0.00 4.69
70 71 2.736721 TCAGCTTCTCATTTTCGTTCCG 59.263 45.455 0.00 0.00 0.00 4.30
71 72 4.656041 CATCAGCTTCTCATTTTCGTTCC 58.344 43.478 0.00 0.00 0.00 3.62
72 73 4.094212 GCATCAGCTTCTCATTTTCGTTC 58.906 43.478 0.00 0.00 37.91 3.95
73 74 3.425359 CGCATCAGCTTCTCATTTTCGTT 60.425 43.478 0.00 0.00 39.10 3.85
74 75 2.094894 CGCATCAGCTTCTCATTTTCGT 59.905 45.455 0.00 0.00 39.10 3.85
75 76 2.094894 ACGCATCAGCTTCTCATTTTCG 59.905 45.455 0.00 0.00 39.10 3.46
76 77 3.754188 ACGCATCAGCTTCTCATTTTC 57.246 42.857 0.00 0.00 39.10 2.29
77 78 5.824904 ATAACGCATCAGCTTCTCATTTT 57.175 34.783 0.00 0.00 39.10 1.82
78 79 5.587844 AGAATAACGCATCAGCTTCTCATTT 59.412 36.000 0.00 0.00 39.10 2.32
79 80 5.121811 AGAATAACGCATCAGCTTCTCATT 58.878 37.500 0.00 0.00 39.10 2.57
80 81 4.701765 AGAATAACGCATCAGCTTCTCAT 58.298 39.130 0.00 0.00 39.10 2.90
81 82 4.128925 AGAATAACGCATCAGCTTCTCA 57.871 40.909 0.00 0.00 39.10 3.27
82 83 4.317698 CGAAGAATAACGCATCAGCTTCTC 60.318 45.833 0.00 0.00 39.10 2.87
83 84 3.553511 CGAAGAATAACGCATCAGCTTCT 59.446 43.478 0.00 0.00 39.10 2.85
84 85 3.551890 TCGAAGAATAACGCATCAGCTTC 59.448 43.478 0.00 0.00 39.10 3.86
85 86 3.307242 GTCGAAGAATAACGCATCAGCTT 59.693 43.478 0.00 0.00 39.69 3.74
86 87 2.860735 GTCGAAGAATAACGCATCAGCT 59.139 45.455 0.00 0.00 39.69 4.24
87 88 2.860735 AGTCGAAGAATAACGCATCAGC 59.139 45.455 0.00 0.00 39.69 4.26
88 89 4.105486 TCAGTCGAAGAATAACGCATCAG 58.895 43.478 0.00 0.00 39.69 2.90
89 90 4.104696 TCAGTCGAAGAATAACGCATCA 57.895 40.909 0.00 0.00 39.69 3.07
90 91 5.427082 CAATCAGTCGAAGAATAACGCATC 58.573 41.667 0.00 0.00 39.69 3.91
91 92 4.260375 GCAATCAGTCGAAGAATAACGCAT 60.260 41.667 0.00 0.00 39.69 4.73
92 93 3.062099 GCAATCAGTCGAAGAATAACGCA 59.938 43.478 0.00 0.00 39.69 5.24
93 94 3.598330 GCAATCAGTCGAAGAATAACGC 58.402 45.455 0.00 0.00 39.69 4.84
94 95 3.301835 CCGCAATCAGTCGAAGAATAACG 60.302 47.826 0.00 0.00 39.69 3.18
95 96 3.863424 TCCGCAATCAGTCGAAGAATAAC 59.137 43.478 0.00 0.00 39.69 1.89
100 101 0.456142 CGTCCGCAATCAGTCGAAGA 60.456 55.000 0.00 0.00 0.00 2.87
107 108 1.690283 CTCACAGCGTCCGCAATCAG 61.690 60.000 14.70 0.78 44.88 2.90
120 121 1.794701 CATTCACGGTCACACTCACAG 59.205 52.381 0.00 0.00 0.00 3.66
123 124 2.479837 GTTCATTCACGGTCACACTCA 58.520 47.619 0.00 0.00 0.00 3.41
133 134 0.366871 CCTCGCTTCGTTCATTCACG 59.633 55.000 0.00 0.00 41.78 4.35
135 136 2.029380 TCTTCCTCGCTTCGTTCATTCA 60.029 45.455 0.00 0.00 0.00 2.57
136 137 2.607187 TCTTCCTCGCTTCGTTCATTC 58.393 47.619 0.00 0.00 0.00 2.67
137 138 2.743636 TCTTCCTCGCTTCGTTCATT 57.256 45.000 0.00 0.00 0.00 2.57
138 139 2.231478 TCTTCTTCCTCGCTTCGTTCAT 59.769 45.455 0.00 0.00 0.00 2.57
139 140 1.611977 TCTTCTTCCTCGCTTCGTTCA 59.388 47.619 0.00 0.00 0.00 3.18
140 141 2.349297 TCTTCTTCCTCGCTTCGTTC 57.651 50.000 0.00 0.00 0.00 3.95
141 142 2.296471 TCTTCTTCTTCCTCGCTTCGTT 59.704 45.455 0.00 0.00 0.00 3.85
142 143 1.887198 TCTTCTTCTTCCTCGCTTCGT 59.113 47.619 0.00 0.00 0.00 3.85
143 144 2.638556 TCTTCTTCTTCCTCGCTTCG 57.361 50.000 0.00 0.00 0.00 3.79
144 145 4.752604 AGTTTTCTTCTTCTTCCTCGCTTC 59.247 41.667 0.00 0.00 0.00 3.86
145 146 4.513318 CAGTTTTCTTCTTCTTCCTCGCTT 59.487 41.667 0.00 0.00 0.00 4.68
146 147 4.061596 CAGTTTTCTTCTTCTTCCTCGCT 58.938 43.478 0.00 0.00 0.00 4.93
148 149 5.050023 GGTTCAGTTTTCTTCTTCTTCCTCG 60.050 44.000 0.00 0.00 0.00 4.63
151 153 4.023963 CCGGTTCAGTTTTCTTCTTCTTCC 60.024 45.833 0.00 0.00 0.00 3.46
179 181 1.424403 TAACGCATATCGCATTCCCG 58.576 50.000 0.00 0.00 42.60 5.14
185 187 0.934496 GCCAGTTAACGCATATCGCA 59.066 50.000 0.00 0.00 42.60 5.10
199 201 3.379445 CCGTACAGTCCGGCCAGT 61.379 66.667 2.24 0.00 38.85 4.00
237 247 1.144969 TGGTGTCAGAAACGATTCGC 58.855 50.000 5.86 0.00 40.63 4.70
246 256 2.980568 ACTTGTTCGTTGGTGTCAGAA 58.019 42.857 0.00 0.00 0.00 3.02
247 257 2.675844 CAACTTGTTCGTTGGTGTCAGA 59.324 45.455 0.00 0.00 40.35 3.27
253 263 4.117685 GAGTACTCAACTTGTTCGTTGGT 58.882 43.478 18.20 4.20 43.36 3.67
254 264 4.369182 AGAGTACTCAACTTGTTCGTTGG 58.631 43.478 24.44 0.00 43.36 3.77
285 298 0.581529 CGATCAATAATGCCGCGTGT 59.418 50.000 4.92 0.00 0.00 4.49
313 326 5.063204 CAGCATATCGATCACCCCTAAAAA 58.937 41.667 0.00 0.00 0.00 1.94
314 327 4.102524 ACAGCATATCGATCACCCCTAAAA 59.897 41.667 0.00 0.00 0.00 1.52
315 328 3.646162 ACAGCATATCGATCACCCCTAAA 59.354 43.478 0.00 0.00 0.00 1.85
316 329 3.239449 ACAGCATATCGATCACCCCTAA 58.761 45.455 0.00 0.00 0.00 2.69
317 330 2.889512 ACAGCATATCGATCACCCCTA 58.110 47.619 0.00 0.00 0.00 3.53
318 331 1.722034 ACAGCATATCGATCACCCCT 58.278 50.000 0.00 0.00 0.00 4.79
319 332 2.549754 CAAACAGCATATCGATCACCCC 59.450 50.000 0.00 0.00 0.00 4.95
320 333 3.002656 CACAAACAGCATATCGATCACCC 59.997 47.826 0.00 0.00 0.00 4.61
321 334 3.871006 TCACAAACAGCATATCGATCACC 59.129 43.478 0.00 0.00 0.00 4.02
322 335 4.805719 TCTCACAAACAGCATATCGATCAC 59.194 41.667 0.00 0.00 0.00 3.06
323 336 5.009854 TCTCACAAACAGCATATCGATCA 57.990 39.130 0.00 0.00 0.00 2.92
330 343 4.081254 AGAGCAGATCTCACAAACAGCATA 60.081 41.667 0.00 0.00 44.35 3.14
331 344 3.008330 GAGCAGATCTCACAAACAGCAT 58.992 45.455 0.00 0.00 41.51 3.79
505 518 3.204827 CGGATCCAGCTTTGGCGG 61.205 66.667 13.41 0.00 44.37 6.13
574 588 0.110238 CATGGACACGCTTTTCACCG 60.110 55.000 0.00 0.00 0.00 4.94
658 1090 6.197168 AGACTGAGAGAGATCTGAAAAGGAT 58.803 40.000 0.00 0.00 0.00 3.24
672 1104 5.356426 CAACGAGAGAGATAGACTGAGAGA 58.644 45.833 0.00 0.00 0.00 3.10
674 1106 3.874543 GCAACGAGAGAGATAGACTGAGA 59.125 47.826 0.00 0.00 0.00 3.27
676 1108 3.610911 TGCAACGAGAGAGATAGACTGA 58.389 45.455 0.00 0.00 0.00 3.41
679 1111 5.164954 ACTTTTGCAACGAGAGAGATAGAC 58.835 41.667 14.22 0.00 0.00 2.59
680 1112 5.048013 TGACTTTTGCAACGAGAGAGATAGA 60.048 40.000 14.22 0.00 0.00 1.98
682 1114 5.134202 TGACTTTTGCAACGAGAGAGATA 57.866 39.130 14.22 0.00 0.00 1.98
683 1115 3.995199 TGACTTTTGCAACGAGAGAGAT 58.005 40.909 14.22 0.00 0.00 2.75
762 1206 0.109226 GACCACCACTCTCTACGTGC 60.109 60.000 0.00 0.00 0.00 5.34
898 1765 1.041437 GAGAAATCCCGAGTCCCGAT 58.959 55.000 0.00 0.00 41.76 4.18
904 1771 0.175989 GGCTTCGAGAAATCCCGAGT 59.824 55.000 0.00 0.00 36.11 4.18
937 1804 2.044946 CCTCCTTTTGGGGCCTCG 60.045 66.667 0.84 0.00 39.29 4.63
1146 2023 2.227194 GTCCTTGCTTTTTCCCTTCGA 58.773 47.619 0.00 0.00 0.00 3.71
1154 2031 0.389025 CCGCCTTGTCCTTGCTTTTT 59.611 50.000 0.00 0.00 0.00 1.94
1157 2034 2.985847 GCCGCCTTGTCCTTGCTT 60.986 61.111 0.00 0.00 0.00 3.91
1161 2038 4.699522 GACCGCCGCCTTGTCCTT 62.700 66.667 0.00 0.00 0.00 3.36
1247 2130 1.594310 GGAGGCGAGTTGAGAGCTT 59.406 57.895 0.00 0.00 0.00 3.74
1307 2191 0.974010 ACGCCGGAGTAATCAAGGGA 60.974 55.000 9.91 0.00 0.00 4.20
1422 2306 4.454504 GTCATGAAGCCGGTAAAGAAAAGA 59.545 41.667 1.90 0.00 0.00 2.52
1513 2402 1.141019 TGCGAATAGGACGGCTCAC 59.859 57.895 0.00 0.00 0.00 3.51
1619 2511 8.876303 AGAGCTAATCAATCCTTCTTCTTTTT 57.124 30.769 0.00 0.00 0.00 1.94
1621 2513 7.555914 GGAAGAGCTAATCAATCCTTCTTCTTT 59.444 37.037 10.14 0.00 34.77 2.52
1622 2514 7.053498 GGAAGAGCTAATCAATCCTTCTTCTT 58.947 38.462 10.14 0.00 34.77 2.52
1623 2515 6.409120 GGGAAGAGCTAATCAATCCTTCTTCT 60.409 42.308 10.14 0.00 36.75 2.85
1624 2516 5.762711 GGGAAGAGCTAATCAATCCTTCTTC 59.237 44.000 7.28 3.42 36.75 2.87
1625 2517 5.686124 CGGGAAGAGCTAATCAATCCTTCTT 60.686 44.000 7.28 0.00 36.75 2.52
1634 2526 1.739035 CGCAACGGGAAGAGCTAATCA 60.739 52.381 0.00 0.00 0.00 2.57
1667 2559 0.597637 CACGGGATATGCAGACGTCC 60.598 60.000 13.01 0.00 35.36 4.79
1725 2618 1.805945 CGCTTGACTCGTGTAGGGC 60.806 63.158 0.00 0.00 0.00 5.19
1751 2645 4.287186 ACGAATCGTAAAGCCACGGAGT 62.287 50.000 6.47 0.00 39.60 3.85
1885 2779 2.989253 TGAACGGAGGCGCAGAGA 60.989 61.111 10.83 0.00 0.00 3.10
1979 2873 4.574527 CTGACTTCAGAGTGTAAATGCG 57.425 45.455 0.00 0.00 46.59 4.73
2032 2926 2.721167 CCGGCGGGAACTGAGATGA 61.721 63.158 20.56 0.00 36.31 2.92
2063 2957 1.116308 TCGCCATTAGAACCGGATCA 58.884 50.000 9.46 0.00 0.00 2.92
2067 2961 0.105964 TCCATCGCCATTAGAACCGG 59.894 55.000 0.00 0.00 0.00 5.28
2578 3481 4.707448 CACTGACTGACCCATCTAACTAGT 59.293 45.833 0.00 0.00 0.00 2.57
2579 3482 4.098654 CCACTGACTGACCCATCTAACTAG 59.901 50.000 0.00 0.00 0.00 2.57
2580 3483 4.023980 CCACTGACTGACCCATCTAACTA 58.976 47.826 0.00 0.00 0.00 2.24
2581 3484 2.834549 CCACTGACTGACCCATCTAACT 59.165 50.000 0.00 0.00 0.00 2.24
2628 3532 3.696548 TCACAGATCCACAGTAGTAGCAG 59.303 47.826 0.00 0.00 0.00 4.24
2629 3533 3.697166 TCACAGATCCACAGTAGTAGCA 58.303 45.455 0.00 0.00 0.00 3.49
2630 3534 4.720649 TTCACAGATCCACAGTAGTAGC 57.279 45.455 0.00 0.00 0.00 3.58
2633 3537 5.248640 CCAAATTCACAGATCCACAGTAGT 58.751 41.667 0.00 0.00 0.00 2.73
2651 3555 2.684001 TCAAGATACGACGGCCAAAT 57.316 45.000 2.24 0.00 0.00 2.32
2691 3595 3.118371 CGTTAGAGTTAAAGGCCCTGGAT 60.118 47.826 0.00 0.00 0.00 3.41
2725 3629 7.561722 AGATAGATCCAAGTTAAGACAGCTGTA 59.438 37.037 21.73 0.32 0.00 2.74
2760 3664 1.134995 CGCAGAGGCATGACTAACTCA 60.135 52.381 0.00 0.00 41.24 3.41
2781 3685 2.110967 CCTCTGCCCGAGTTGCATG 61.111 63.158 0.00 0.00 38.22 4.06
2800 3705 1.131638 GGGACAGGTATCCATCTGCA 58.868 55.000 0.00 0.00 40.96 4.41
2872 3783 6.183360 GCTTTTCCATGGTCAGATAGGTTAAC 60.183 42.308 12.58 0.00 0.00 2.01
2909 3820 2.226437 GTGCGGCAATGGATTACATAGG 59.774 50.000 3.23 0.00 39.40 2.57
2948 3859 6.790232 AGGAAAAGAAACACCAAATCTCAA 57.210 33.333 0.00 0.00 0.00 3.02
3129 4042 0.737219 CCTGCTTTAGCTGCATGGAC 59.263 55.000 1.02 0.00 42.66 4.02
3157 4070 9.950680 CAAAGTAAAATAGCTTGACAAGAAGAA 57.049 29.630 19.51 0.88 0.00 2.52
3173 4086 2.825532 AGGCGATGCACCAAAGTAAAAT 59.174 40.909 0.00 0.00 0.00 1.82
3174 4087 2.235016 AGGCGATGCACCAAAGTAAAA 58.765 42.857 0.00 0.00 0.00 1.52
3200 4113 5.335113 CCATTCGCTTTGTCAATTCTTCAGA 60.335 40.000 0.00 0.00 0.00 3.27
3201 4114 4.855388 CCATTCGCTTTGTCAATTCTTCAG 59.145 41.667 0.00 0.00 0.00 3.02
3205 4118 2.493278 CCCCATTCGCTTTGTCAATTCT 59.507 45.455 0.00 0.00 0.00 2.40
3206 4119 2.417243 CCCCCATTCGCTTTGTCAATTC 60.417 50.000 0.00 0.00 0.00 2.17
3207 4120 1.550072 CCCCCATTCGCTTTGTCAATT 59.450 47.619 0.00 0.00 0.00 2.32
3208 4121 1.185315 CCCCCATTCGCTTTGTCAAT 58.815 50.000 0.00 0.00 0.00 2.57
3209 4122 0.178975 ACCCCCATTCGCTTTGTCAA 60.179 50.000 0.00 0.00 0.00 3.18
3210 4123 0.693622 TACCCCCATTCGCTTTGTCA 59.306 50.000 0.00 0.00 0.00 3.58
3211 4124 1.828979 TTACCCCCATTCGCTTTGTC 58.171 50.000 0.00 0.00 0.00 3.18
3218 4132 2.614829 ACTCGATTTACCCCCATTCG 57.385 50.000 0.00 0.00 0.00 3.34
3253 4167 1.004679 CCACCACCAAAGGCAATGC 60.005 57.895 0.00 0.00 0.00 3.56
3356 4284 1.068333 ACTCACATGCACGCATTTTCC 60.068 47.619 0.72 0.00 33.90 3.13
3514 4442 5.428184 AGTTTCATTCTAGAACCTCAGGG 57.572 43.478 7.48 0.00 38.88 4.45
3581 4511 4.848841 CGAAGCTTAGATATCTGCTACGTG 59.151 45.833 15.79 4.05 35.09 4.49
3610 4540 5.744666 TTAGTTTCGGGCAATAATACAGC 57.255 39.130 0.00 0.00 0.00 4.40
3624 4554 5.342259 GGCATGTTTACAAAGCTTAGTTTCG 59.658 40.000 0.00 0.00 33.36 3.46
3646 4576 1.200948 GTCTCTTGGCAGTTCATTGGC 59.799 52.381 0.00 0.00 43.38 4.52
3647 4577 1.466167 CGTCTCTTGGCAGTTCATTGG 59.534 52.381 0.00 0.00 0.00 3.16
3648 4578 2.158449 GTCGTCTCTTGGCAGTTCATTG 59.842 50.000 0.00 0.00 0.00 2.82
3662 4594 1.996191 GCTGATTTCCAGTGTCGTCTC 59.004 52.381 0.00 0.00 44.71 3.36
3741 4678 2.103153 AGGGTGTCTTCAGTCAAGGA 57.897 50.000 0.00 0.00 32.22 3.36
3748 4685 3.624861 GCAATCATGTAGGGTGTCTTCAG 59.375 47.826 0.00 0.00 0.00 3.02
3755 4692 3.793129 GCGAAATGCAATCATGTAGGGTG 60.793 47.826 0.00 0.00 45.45 4.61
3938 6589 2.206515 CTTGACAGCGAGCGAGACCT 62.207 60.000 0.00 0.00 0.00 3.85
3949 6600 4.336153 GTCCTACTAGGAGTACTTGACAGC 59.664 50.000 4.91 0.00 46.90 4.40
3960 6611 4.237976 TGGTCTTCAGTCCTACTAGGAG 57.762 50.000 4.91 0.00 46.90 3.69
3961 6612 4.669866 TTGGTCTTCAGTCCTACTAGGA 57.330 45.455 0.03 0.03 43.43 2.94
3962 6613 5.017490 TCTTTGGTCTTCAGTCCTACTAGG 58.983 45.833 0.00 0.00 36.46 3.02
3963 6614 5.126384 CCTCTTTGGTCTTCAGTCCTACTAG 59.874 48.000 0.00 0.00 0.00 2.57
3964 6615 5.017490 CCTCTTTGGTCTTCAGTCCTACTA 58.983 45.833 0.00 0.00 0.00 1.82
3965 6616 3.835395 CCTCTTTGGTCTTCAGTCCTACT 59.165 47.826 0.00 0.00 0.00 2.57
3971 6622 0.035458 CGGCCTCTTTGGTCTTCAGT 59.965 55.000 0.00 0.00 38.58 3.41
3974 6625 1.377333 CCCGGCCTCTTTGGTCTTC 60.377 63.158 0.00 0.00 38.58 2.87
4010 6661 2.552338 GCATTAGCAGGTGCAAGAGCA 61.552 52.381 4.48 0.00 44.82 4.26
4108 6769 4.760047 CCAAGTCCACGAGGCCGG 62.760 72.222 0.00 0.00 40.78 6.13
4245 7195 4.186926 AGCACACACATCATAAGCACTAG 58.813 43.478 0.00 0.00 0.00 2.57
4246 7196 4.206477 AGCACACACATCATAAGCACTA 57.794 40.909 0.00 0.00 0.00 2.74
4266 7216 2.853457 CGCACCACGTGAACAAAAG 58.147 52.632 19.30 0.00 35.23 2.27
4502 10036 2.240493 CCATCCGTGGTGGTAAGATC 57.760 55.000 0.00 0.00 40.83 2.75
4591 10129 3.568538 ACACAATCTACGTACGTCCAAC 58.431 45.455 26.53 0.00 0.00 3.77
4628 10166 1.959985 CTAGGCGATCATCAGACCAGT 59.040 52.381 0.00 0.00 0.00 4.00
4629 10167 1.959985 ACTAGGCGATCATCAGACCAG 59.040 52.381 0.00 0.00 0.00 4.00
4663 10201 0.511221 CCAAAACTACTCACACCGCG 59.489 55.000 0.00 0.00 0.00 6.46
4665 10203 3.659786 TGATCCAAAACTACTCACACCG 58.340 45.455 0.00 0.00 0.00 4.94
4709 10247 0.700564 TTTGGAGAGGATGGCTGCTT 59.299 50.000 0.00 0.00 0.00 3.91
4765 10303 2.203070 CCCTCCCAATCGGCTTCG 60.203 66.667 0.00 0.00 0.00 3.79
4801 10339 3.630013 AGCAGGAGTGAAGCGGCA 61.630 61.111 1.45 0.00 0.00 5.69
4842 10380 7.592051 ACAAACATGCAAACAAAACAGAAAAT 58.408 26.923 0.00 0.00 0.00 1.82
4860 10400 5.351948 ACTAACCAAGGCAAAACAAACAT 57.648 34.783 0.00 0.00 0.00 2.71
4870 10410 4.280677 CCTTCAATTCAACTAACCAAGGCA 59.719 41.667 0.00 0.00 0.00 4.75
4871 10411 4.321974 CCCTTCAATTCAACTAACCAAGGC 60.322 45.833 0.00 0.00 0.00 4.35
4875 10415 4.079253 GAGCCCTTCAATTCAACTAACCA 58.921 43.478 0.00 0.00 0.00 3.67
4877 10417 3.751698 ACGAGCCCTTCAATTCAACTAAC 59.248 43.478 0.00 0.00 0.00 2.34
4879 10419 3.007506 TCACGAGCCCTTCAATTCAACTA 59.992 43.478 0.00 0.00 0.00 2.24
4880 10420 2.154462 CACGAGCCCTTCAATTCAACT 58.846 47.619 0.00 0.00 0.00 3.16
4881 10421 2.095718 GTCACGAGCCCTTCAATTCAAC 60.096 50.000 0.00 0.00 0.00 3.18
4883 10423 1.071542 TGTCACGAGCCCTTCAATTCA 59.928 47.619 0.00 0.00 0.00 2.57
4884 10424 1.808411 TGTCACGAGCCCTTCAATTC 58.192 50.000 0.00 0.00 0.00 2.17
4914 10454 4.536765 ACAAGTCCACCATTTGAAGAAGT 58.463 39.130 0.00 0.00 0.00 3.01
4915 10455 6.402550 CGATACAAGTCCACCATTTGAAGAAG 60.403 42.308 0.00 0.00 0.00 2.85
4922 10462 4.819105 TCTCGATACAAGTCCACCATTT 57.181 40.909 0.00 0.00 0.00 2.32
4938 10478 4.478206 AAAGCAGGAATTCTGATCTCGA 57.522 40.909 5.23 0.00 46.18 4.04
4943 10483 3.426695 CGCGAAAAAGCAGGAATTCTGAT 60.427 43.478 0.00 0.00 46.18 2.90
4959 10499 4.625742 CCATAAGAAGAGAGAAACGCGAAA 59.374 41.667 15.93 0.00 0.00 3.46
5002 10542 3.127895 CGGAAGGTGTCTTCTCTGAGTAG 59.872 52.174 4.32 4.72 46.42 2.57
5070 13032 2.425668 ACGCTTACTTGTGCACCTTTTT 59.574 40.909 15.69 0.00 0.00 1.94
5082 13044 1.151668 CAGCTGCTTGACGCTTACTT 58.848 50.000 0.00 0.00 40.11 2.24
5087 13049 0.460987 GGTATCAGCTGCTTGACGCT 60.461 55.000 9.47 0.00 40.11 5.07
5107 13069 2.658285 TGTCTTTTCGCTGTAGTCGTC 58.342 47.619 0.00 0.00 0.00 4.20
5138 13134 2.029649 CCATTTGTGGCTTGAGGTTCAG 60.030 50.000 0.00 0.00 0.00 3.02
5200 13196 0.874175 TGTCTTCGTGTCCGCTGTTG 60.874 55.000 0.00 0.00 0.00 3.33
5226 13222 2.224378 CCAGCTTGAGTTGAAGTCAGGA 60.224 50.000 15.28 0.00 27.06 3.86
5237 13233 1.598130 GCGTTGACCCAGCTTGAGT 60.598 57.895 0.00 0.00 0.00 3.41
5267 13263 0.736325 ATCGACCGTTGCTGCACTAC 60.736 55.000 0.00 0.00 0.00 2.73
5375 13371 1.671379 GAGTCCGGTTGGTTCCTGC 60.671 63.158 0.00 0.00 36.30 4.85
5407 13403 2.240667 ACCATCATCAGAACCTCTTGGG 59.759 50.000 0.00 0.00 41.89 4.12
5428 13424 4.728102 CTCCGGGCGCAACGTACA 62.728 66.667 19.81 5.36 0.00 2.90
5448 13444 0.175531 GTTACCATTGTGGGCATGGC 59.824 55.000 11.56 11.56 43.37 4.40
5461 13457 1.634960 TGTCTCGGTGATGGTTACCA 58.365 50.000 6.53 6.53 38.11 3.25
5462 13458 2.754946 TTGTCTCGGTGATGGTTACC 57.245 50.000 0.00 0.00 34.81 2.85
5482 13480 3.551407 GGCGGGGTTTTGGGCAAA 61.551 61.111 0.00 0.00 0.00 3.68
5510 13509 0.907704 TATTGGAGGTGGTGGCGTCT 60.908 55.000 0.00 0.00 0.00 4.18
5513 13512 0.180171 TGATATTGGAGGTGGTGGCG 59.820 55.000 0.00 0.00 0.00 5.69
5515 13514 3.652057 AGTTGATATTGGAGGTGGTGG 57.348 47.619 0.00 0.00 0.00 4.61
5592 13593 1.165907 TCTCTGGCCAAGCAACAACG 61.166 55.000 7.01 0.00 0.00 4.10
5593 13594 0.312102 GTCTCTGGCCAAGCAACAAC 59.688 55.000 7.01 0.00 0.00 3.32
5612 13613 1.817357 GGTCAAAACCTTAGGTCGGG 58.183 55.000 3.62 0.00 42.80 5.14


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

AutoCloner maintained by Alex Coulton.