Multiple sequence alignment - TraesCS2B01G334200

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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 TraesCS2B01G334200 chr2B 100.000 3751 0 0 1 3751 477604316 477608066 0.000000e+00 6927
1 TraesCS2B01G334200 chr2D 93.424 2342 87 26 494 2787 403500598 403502920 0.000000e+00 3410
2 TraesCS2B01G334200 chr2D 92.879 969 43 12 2784 3751 403504498 403505441 0.000000e+00 1384
3 TraesCS2B01G334200 chr2A 89.949 2567 113 61 175 2644 541840433 541842951 0.000000e+00 3177
4 TraesCS2B01G334200 chr2A 93.395 1075 47 10 2679 3751 541842953 541844005 0.000000e+00 1570
5 TraesCS2B01G334200 chr7A 85.249 461 41 11 1152 1612 704049700 704049267 2.050000e-122 449
6 TraesCS2B01G334200 chr3A 93.434 198 13 0 1154 1351 611206628 611206431 1.020000e-75 294
7 TraesCS2B01G334200 chr4D 91.667 204 16 1 1292 1495 375127768 375127970 7.930000e-72 281
8 TraesCS2B01G334200 chr1A 84.314 153 24 0 2040 2192 73352585 73352433 2.330000e-32 150


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 TraesCS2B01G334200 chr2B 477604316 477608066 3750 False 6927.0 6927 100.0000 1 3751 1 chr2B.!!$F1 3750
1 TraesCS2B01G334200 chr2D 403500598 403505441 4843 False 2397.0 3410 93.1515 494 3751 2 chr2D.!!$F1 3257
2 TraesCS2B01G334200 chr2A 541840433 541844005 3572 False 2373.5 3177 91.6720 175 3751 2 chr2A.!!$F1 3576

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
73 74 0.034477 GGAAAGGAATTCAGGCCCGA 60.034 55.0 7.93 0.0 39.98 5.14 F
252 253 0.107017 TACTCTTACTCCCGTCCCCG 60.107 60.0 0.00 0.0 0.00 5.73 F
701 742 0.323629 TAAGGGCCGTGAAACCTCTG 59.676 55.0 0.90 0.0 32.29 3.35 F
938 1022 0.536006 CATTTCCATCTCTCCCCGCC 60.536 60.0 0.00 0.0 0.00 6.13 F
1013 1102 0.834687 TCCTAAACACCAGGACGGCT 60.835 55.0 0.00 0.0 37.27 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1506 1.670949 ATGAGCGAGGTGAGCGTGAT 61.671 55.000 0.00 0.0 40.04 3.06 R
2149 2259 1.302511 GGTGTTGATGGTGGCGTCT 60.303 57.895 0.00 0.0 0.00 4.18 R
2414 2533 1.590932 CCATGATCAGCTACAGTGCC 58.409 55.000 0.09 0.0 0.00 5.01 R
2705 2826 0.391228 TCTGCGCTCAGTTTACACCA 59.609 50.000 9.73 0.0 41.10 4.17 R
2901 4603 2.128535 TGAGGTTCCTGTTGGGTGTTA 58.871 47.619 0.00 0.0 36.25 2.41 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 4.434483 TGAACTCTGGGCTCGCTA 57.566 55.556 0.00 0.00 0.00 4.26
18 19 2.193532 TGAACTCTGGGCTCGCTAG 58.806 57.895 0.00 0.00 0.00 3.42
19 20 1.323271 TGAACTCTGGGCTCGCTAGG 61.323 60.000 0.00 0.00 0.00 3.02
20 21 2.022240 GAACTCTGGGCTCGCTAGGG 62.022 65.000 0.00 0.00 0.00 3.53
21 22 3.922640 CTCTGGGCTCGCTAGGGC 61.923 72.222 1.02 0.00 45.02 5.19
27 28 4.858680 GCTCGCTAGGGCCCAACC 62.859 72.222 27.56 10.22 38.09 3.77
28 29 4.530857 CTCGCTAGGGCCCAACCG 62.531 72.222 27.56 22.14 40.62 4.44
37 38 4.362476 GCCCAACCGCTGCCTTTG 62.362 66.667 0.00 0.00 0.00 2.77
38 39 4.362476 CCCAACCGCTGCCTTTGC 62.362 66.667 0.00 0.00 38.26 3.68
40 41 2.355009 CAACCGCTGCCTTTGCAC 60.355 61.111 0.00 0.00 44.23 4.57
41 42 2.832661 AACCGCTGCCTTTGCACA 60.833 55.556 0.00 0.00 44.23 4.57
42 43 3.137637 AACCGCTGCCTTTGCACAC 62.138 57.895 0.00 0.00 44.23 3.82
43 44 3.594775 CCGCTGCCTTTGCACACA 61.595 61.111 0.00 0.00 44.23 3.72
44 45 2.412525 CGCTGCCTTTGCACACAA 59.587 55.556 0.00 0.00 44.23 3.33
45 46 1.945662 CGCTGCCTTTGCACACAAC 60.946 57.895 0.00 0.00 44.23 3.32
46 47 1.592400 GCTGCCTTTGCACACAACC 60.592 57.895 0.00 0.00 44.23 3.77
47 48 1.067916 CTGCCTTTGCACACAACCC 59.932 57.895 0.00 0.00 44.23 4.11
48 49 2.027460 GCCTTTGCACACAACCCG 59.973 61.111 0.00 0.00 34.87 5.28
49 50 2.027460 CCTTTGCACACAACCCGC 59.973 61.111 0.00 0.00 34.87 6.13
50 51 2.353376 CTTTGCACACAACCCGCG 60.353 61.111 0.00 0.00 34.87 6.46
51 52 3.119709 CTTTGCACACAACCCGCGT 62.120 57.895 4.92 0.00 34.87 6.01
52 53 2.982038 CTTTGCACACAACCCGCGTC 62.982 60.000 4.92 0.00 34.87 5.19
70 71 2.493547 CCGGAAAGGAATTCAGGCC 58.506 57.895 7.93 0.00 44.66 5.19
71 72 1.037579 CCGGAAAGGAATTCAGGCCC 61.038 60.000 7.93 2.27 44.66 5.80
72 73 1.376609 CGGAAAGGAATTCAGGCCCG 61.377 60.000 7.93 10.44 39.98 6.13
73 74 0.034477 GGAAAGGAATTCAGGCCCGA 60.034 55.000 7.93 0.00 39.98 5.14
74 75 1.095600 GAAAGGAATTCAGGCCCGAC 58.904 55.000 7.93 0.00 37.99 4.79
75 76 0.698818 AAAGGAATTCAGGCCCGACT 59.301 50.000 7.93 0.00 0.00 4.18
76 77 0.698818 AAGGAATTCAGGCCCGACTT 59.301 50.000 7.93 0.00 0.00 3.01
77 78 0.253327 AGGAATTCAGGCCCGACTTC 59.747 55.000 9.96 9.96 0.00 3.01
78 79 0.748367 GGAATTCAGGCCCGACTTCC 60.748 60.000 19.21 19.21 37.51 3.46
79 80 0.253327 GAATTCAGGCCCGACTTCCT 59.747 55.000 7.65 0.00 0.00 3.36
80 81 0.698818 AATTCAGGCCCGACTTCCTT 59.301 50.000 0.00 0.00 0.00 3.36
81 82 1.580059 ATTCAGGCCCGACTTCCTTA 58.420 50.000 0.00 0.00 0.00 2.69
82 83 0.611714 TTCAGGCCCGACTTCCTTAC 59.388 55.000 0.00 0.00 0.00 2.34
83 84 1.153628 CAGGCCCGACTTCCTTACG 60.154 63.158 0.00 0.00 0.00 3.18
84 85 2.186125 GGCCCGACTTCCTTACGG 59.814 66.667 0.00 0.00 45.24 4.02
95 96 1.272807 TCCTTACGGGAAAGGTCTGG 58.727 55.000 11.72 0.00 45.37 3.86
96 97 0.252197 CCTTACGGGAAAGGTCTGGG 59.748 60.000 5.55 0.00 41.06 4.45
97 98 0.392595 CTTACGGGAAAGGTCTGGGC 60.393 60.000 0.00 0.00 0.00 5.36
98 99 1.844544 TTACGGGAAAGGTCTGGGCC 61.845 60.000 0.00 0.00 0.00 5.80
99 100 2.758852 TACGGGAAAGGTCTGGGCCT 62.759 60.000 4.53 0.00 41.41 5.19
100 101 2.356667 GGGAAAGGTCTGGGCCTG 59.643 66.667 4.53 4.06 39.17 4.85
101 102 2.231380 GGGAAAGGTCTGGGCCTGA 61.231 63.158 9.30 9.30 39.17 3.86
102 103 1.767692 GGAAAGGTCTGGGCCTGAA 59.232 57.895 15.26 0.00 39.17 3.02
103 104 0.609406 GGAAAGGTCTGGGCCTGAAC 60.609 60.000 19.85 19.85 39.17 3.18
104 105 0.609406 GAAAGGTCTGGGCCTGAACC 60.609 60.000 23.17 20.18 39.17 3.62
105 106 1.360393 AAAGGTCTGGGCCTGAACCA 61.360 55.000 23.17 1.60 39.17 3.67
110 111 2.925706 TGGGCCTGAACCAGCGTA 60.926 61.111 4.53 0.00 33.23 4.42
111 112 2.125106 GGGCCTGAACCAGCGTAG 60.125 66.667 0.84 0.00 0.00 3.51
112 113 2.663196 GGCCTGAACCAGCGTAGT 59.337 61.111 0.00 0.00 0.00 2.73
113 114 1.003718 GGCCTGAACCAGCGTAGTT 60.004 57.895 0.00 0.00 0.00 2.24
114 115 0.605589 GGCCTGAACCAGCGTAGTTT 60.606 55.000 0.00 0.00 0.00 2.66
115 116 1.235724 GCCTGAACCAGCGTAGTTTT 58.764 50.000 0.00 0.00 0.00 2.43
116 117 1.197036 GCCTGAACCAGCGTAGTTTTC 59.803 52.381 0.00 0.00 0.00 2.29
117 118 1.804748 CCTGAACCAGCGTAGTTTTCC 59.195 52.381 0.00 0.00 0.00 3.13
118 119 2.550208 CCTGAACCAGCGTAGTTTTCCT 60.550 50.000 0.00 0.00 0.00 3.36
119 120 3.139077 CTGAACCAGCGTAGTTTTCCTT 58.861 45.455 0.00 0.00 0.00 3.36
120 121 3.547746 TGAACCAGCGTAGTTTTCCTTT 58.452 40.909 0.00 0.00 0.00 3.11
121 122 3.562557 TGAACCAGCGTAGTTTTCCTTTC 59.437 43.478 0.00 0.00 0.00 2.62
122 123 3.487120 ACCAGCGTAGTTTTCCTTTCT 57.513 42.857 0.00 0.00 0.00 2.52
123 124 3.400255 ACCAGCGTAGTTTTCCTTTCTC 58.600 45.455 0.00 0.00 0.00 2.87
124 125 3.071167 ACCAGCGTAGTTTTCCTTTCTCT 59.929 43.478 0.00 0.00 0.00 3.10
125 126 3.680458 CCAGCGTAGTTTTCCTTTCTCTC 59.320 47.826 0.00 0.00 0.00 3.20
126 127 4.561105 CAGCGTAGTTTTCCTTTCTCTCT 58.439 43.478 0.00 0.00 0.00 3.10
127 128 4.387256 CAGCGTAGTTTTCCTTTCTCTCTG 59.613 45.833 0.00 0.00 0.00 3.35
128 129 3.123790 GCGTAGTTTTCCTTTCTCTCTGC 59.876 47.826 0.00 0.00 0.00 4.26
129 130 3.680458 CGTAGTTTTCCTTTCTCTCTGCC 59.320 47.826 0.00 0.00 0.00 4.85
130 131 3.864789 AGTTTTCCTTTCTCTCTGCCA 57.135 42.857 0.00 0.00 0.00 4.92
131 132 4.379302 AGTTTTCCTTTCTCTCTGCCAT 57.621 40.909 0.00 0.00 0.00 4.40
132 133 4.331108 AGTTTTCCTTTCTCTCTGCCATC 58.669 43.478 0.00 0.00 0.00 3.51
133 134 3.356529 TTTCCTTTCTCTCTGCCATCC 57.643 47.619 0.00 0.00 0.00 3.51
134 135 0.826715 TCCTTTCTCTCTGCCATCCG 59.173 55.000 0.00 0.00 0.00 4.18
135 136 0.179062 CCTTTCTCTCTGCCATCCGG 60.179 60.000 0.00 0.00 0.00 5.14
145 146 3.190878 CCATCCGGCAGCAGAAAC 58.809 61.111 0.00 0.00 0.00 2.78
146 147 1.675310 CCATCCGGCAGCAGAAACA 60.675 57.895 0.00 0.00 0.00 2.83
147 148 1.651240 CCATCCGGCAGCAGAAACAG 61.651 60.000 0.00 0.00 0.00 3.16
148 149 2.042831 ATCCGGCAGCAGAAACAGC 61.043 57.895 0.00 0.00 0.00 4.40
149 150 2.475371 ATCCGGCAGCAGAAACAGCT 62.475 55.000 0.00 0.00 44.62 4.24
150 151 2.263741 CCGGCAGCAGAAACAGCTT 61.264 57.895 0.00 0.00 41.14 3.74
151 152 1.081641 CGGCAGCAGAAACAGCTTG 60.082 57.895 0.00 0.00 41.14 4.01
152 153 1.288127 GGCAGCAGAAACAGCTTGG 59.712 57.895 0.00 0.00 41.14 3.61
153 154 1.372623 GCAGCAGAAACAGCTTGGC 60.373 57.895 0.00 0.00 41.14 4.52
154 155 1.803366 GCAGCAGAAACAGCTTGGCT 61.803 55.000 0.00 0.00 41.14 4.75
180 181 1.867233 GAACGAGCAGCAGAAACTTCA 59.133 47.619 0.00 0.00 0.00 3.02
186 187 2.122564 GCAGCAGAAACTTCAACTTGC 58.877 47.619 0.00 0.00 0.00 4.01
191 192 1.947456 AGAAACTTCAACTTGCGGTCC 59.053 47.619 0.00 0.00 0.00 4.46
213 214 1.629353 TGGTTAAGGCACGGTATTCCA 59.371 47.619 0.00 0.00 0.00 3.53
216 217 3.697542 GGTTAAGGCACGGTATTCCATTT 59.302 43.478 0.00 0.00 0.00 2.32
220 221 5.514274 AAGGCACGGTATTCCATTTATTG 57.486 39.130 0.00 0.00 0.00 1.90
245 246 3.258622 ACTGTGCAGTTACTCTTACTCCC 59.741 47.826 0.00 0.00 38.83 4.30
246 247 2.230508 TGTGCAGTTACTCTTACTCCCG 59.769 50.000 0.00 0.00 0.00 5.14
247 248 2.230750 GTGCAGTTACTCTTACTCCCGT 59.769 50.000 0.00 0.00 0.00 5.28
248 249 2.490903 TGCAGTTACTCTTACTCCCGTC 59.509 50.000 0.00 0.00 0.00 4.79
249 250 2.159268 GCAGTTACTCTTACTCCCGTCC 60.159 54.545 0.00 0.00 0.00 4.79
250 251 2.426381 CAGTTACTCTTACTCCCGTCCC 59.574 54.545 0.00 0.00 0.00 4.46
251 252 1.753649 GTTACTCTTACTCCCGTCCCC 59.246 57.143 0.00 0.00 0.00 4.81
252 253 0.107017 TACTCTTACTCCCGTCCCCG 60.107 60.000 0.00 0.00 0.00 5.73
253 254 1.077212 CTCTTACTCCCGTCCCCGA 60.077 63.158 0.00 0.00 35.63 5.14
254 255 1.379044 TCTTACTCCCGTCCCCGAC 60.379 63.158 0.00 0.00 35.63 4.79
255 256 2.362889 TTACTCCCGTCCCCGACC 60.363 66.667 0.00 0.00 35.63 4.79
289 290 1.261619 GAACACTTTGCTCCGTGACTG 59.738 52.381 6.80 0.00 35.23 3.51
296 297 2.267006 CTCCGTGACTGGCAGCAT 59.733 61.111 15.89 0.00 0.00 3.79
345 361 2.680352 GAGTCGGGGCACAGGAGA 60.680 66.667 0.00 0.00 0.00 3.71
346 362 2.681778 AGTCGGGGCACAGGAGAG 60.682 66.667 0.00 0.00 0.00 3.20
347 363 3.775654 GTCGGGGCACAGGAGAGG 61.776 72.222 0.00 0.00 0.00 3.69
348 364 3.992641 TCGGGGCACAGGAGAGGA 61.993 66.667 0.00 0.00 0.00 3.71
349 365 3.465403 CGGGGCACAGGAGAGGAG 61.465 72.222 0.00 0.00 0.00 3.69
354 373 1.153667 GCACAGGAGAGGAGCTTCG 60.154 63.158 0.00 0.00 0.00 3.79
380 399 2.586357 GCCCGTGCTAGCTGCTAC 60.586 66.667 17.23 4.47 43.37 3.58
390 409 1.342819 CTAGCTGCTACCCCAGTGATC 59.657 57.143 5.02 0.00 35.28 2.92
394 421 1.000283 CTGCTACCCCAGTGATCGATC 60.000 57.143 18.72 18.72 0.00 3.69
419 446 0.678048 ATCGGCTCCTTGGTTTCTGC 60.678 55.000 0.00 0.00 0.00 4.26
420 447 1.302832 CGGCTCCTTGGTTTCTGCT 60.303 57.895 0.00 0.00 0.00 4.24
423 450 1.322442 GCTCCTTGGTTTCTGCTGTT 58.678 50.000 0.00 0.00 0.00 3.16
425 452 3.084786 GCTCCTTGGTTTCTGCTGTTAT 58.915 45.455 0.00 0.00 0.00 1.89
432 459 5.885230 TGGTTTCTGCTGTTATGATCTTG 57.115 39.130 0.00 0.00 0.00 3.02
439 466 3.937079 TGCTGTTATGATCTTGAGCTGTG 59.063 43.478 0.00 0.00 0.00 3.66
446 473 2.092753 TGATCTTGAGCTGTGGGGATTC 60.093 50.000 0.00 0.00 0.00 2.52
447 474 0.620556 TCTTGAGCTGTGGGGATTCC 59.379 55.000 0.00 0.00 0.00 3.01
448 475 0.745845 CTTGAGCTGTGGGGATTCCG 60.746 60.000 0.00 0.00 38.76 4.30
449 476 1.488705 TTGAGCTGTGGGGATTCCGT 61.489 55.000 0.00 0.00 38.76 4.69
450 477 1.299976 GAGCTGTGGGGATTCCGTT 59.700 57.895 0.00 0.00 38.76 4.44
456 483 3.616219 CTGTGGGGATTCCGTTCATTTA 58.384 45.455 0.00 0.00 38.76 1.40
459 486 3.129813 GTGGGGATTCCGTTCATTTAACC 59.870 47.826 0.00 0.00 38.76 2.85
461 488 2.691526 GGGATTCCGTTCATTTAACCCC 59.308 50.000 0.00 0.00 34.33 4.95
463 490 1.823797 TTCCGTTCATTTAACCCCCG 58.176 50.000 0.00 0.00 34.33 5.73
464 491 0.982704 TCCGTTCATTTAACCCCCGA 59.017 50.000 0.00 0.00 34.33 5.14
477 504 2.975266 ACCCCCGAAACAAAACAAAAC 58.025 42.857 0.00 0.00 0.00 2.43
478 505 2.302157 ACCCCCGAAACAAAACAAAACA 59.698 40.909 0.00 0.00 0.00 2.83
479 506 3.244457 ACCCCCGAAACAAAACAAAACAA 60.244 39.130 0.00 0.00 0.00 2.83
480 507 3.751698 CCCCCGAAACAAAACAAAACAAA 59.248 39.130 0.00 0.00 0.00 2.83
481 508 4.215613 CCCCCGAAACAAAACAAAACAAAA 59.784 37.500 0.00 0.00 0.00 2.44
482 509 5.147865 CCCCGAAACAAAACAAAACAAAAC 58.852 37.500 0.00 0.00 0.00 2.43
483 510 5.277828 CCCCGAAACAAAACAAAACAAAACA 60.278 36.000 0.00 0.00 0.00 2.83
484 511 6.199393 CCCGAAACAAAACAAAACAAAACAA 58.801 32.000 0.00 0.00 0.00 2.83
485 512 6.691388 CCCGAAACAAAACAAAACAAAACAAA 59.309 30.769 0.00 0.00 0.00 2.83
486 513 7.220108 CCCGAAACAAAACAAAACAAAACAAAA 59.780 29.630 0.00 0.00 0.00 2.44
487 514 8.583765 CCGAAACAAAACAAAACAAAACAAAAA 58.416 25.926 0.00 0.00 0.00 1.94
575 603 1.882623 GTCCACCTCCAAGCAAAAGAG 59.117 52.381 0.00 0.00 0.00 2.85
668 700 9.520515 AATCTCATGAGTAAAACAAAGTACCAT 57.479 29.630 21.92 0.00 0.00 3.55
701 742 0.323629 TAAGGGCCGTGAAACCTCTG 59.676 55.000 0.90 0.00 32.29 3.35
708 749 1.404315 CCGTGAAACCTCTGGTCTAGC 60.404 57.143 0.00 0.00 33.12 3.42
715 757 3.290948 ACCTCTGGTCTAGCACTCTAG 57.709 52.381 0.00 0.00 42.87 2.43
716 758 1.953686 CCTCTGGTCTAGCACTCTAGC 59.046 57.143 0.00 0.00 41.59 3.42
717 759 6.408971 AACCTCTGGTCTAGCACTCTAGCT 62.409 50.000 0.00 0.00 41.26 3.32
718 760 3.181449 CCTCTGGTCTAGCACTCTAGCTA 60.181 52.174 0.00 0.00 44.50 3.32
719 761 4.506625 CCTCTGGTCTAGCACTCTAGCTAT 60.507 50.000 0.00 0.00 45.32 2.97
720 762 4.393834 TCTGGTCTAGCACTCTAGCTATG 58.606 47.826 0.00 0.00 45.32 2.23
722 764 3.885901 TGGTCTAGCACTCTAGCTATGTG 59.114 47.826 17.58 17.58 45.32 3.21
767 825 9.823647 TTTAAGGAAAATTGTGCTGTTGATTAA 57.176 25.926 0.00 0.00 0.00 1.40
768 826 9.995003 TTAAGGAAAATTGTGCTGTTGATTAAT 57.005 25.926 0.00 0.00 0.00 1.40
771 829 9.643693 AGGAAAATTGTGCTGTTGATTAATTAG 57.356 29.630 0.00 0.00 0.00 1.73
812 892 0.860533 CATGTTTGGCAAAAGGCGTG 59.139 50.000 15.29 10.23 46.16 5.34
873 955 3.750371 TCCCAATTTGACATATAGGCCG 58.250 45.455 0.00 0.00 0.00 6.13
916 1000 3.752665 TGTCTCTCCGTTTCTCTGTAGT 58.247 45.455 0.00 0.00 0.00 2.73
917 1001 4.903054 TGTCTCTCCGTTTCTCTGTAGTA 58.097 43.478 0.00 0.00 0.00 1.82
918 1002 4.936411 TGTCTCTCCGTTTCTCTGTAGTAG 59.064 45.833 0.00 0.00 0.00 2.57
937 1021 1.169034 GCATTTCCATCTCTCCCCGC 61.169 60.000 0.00 0.00 0.00 6.13
938 1022 0.536006 CATTTCCATCTCTCCCCGCC 60.536 60.000 0.00 0.00 0.00 6.13
939 1023 1.709994 ATTTCCATCTCTCCCCGCCC 61.710 60.000 0.00 0.00 0.00 6.13
940 1024 2.840203 TTTCCATCTCTCCCCGCCCT 62.840 60.000 0.00 0.00 0.00 5.19
941 1025 3.554342 CCATCTCTCCCCGCCCTG 61.554 72.222 0.00 0.00 0.00 4.45
955 1039 0.962855 GCCCTGGAGAGCAAGGAAAC 60.963 60.000 0.00 0.00 35.40 2.78
1013 1102 0.834687 TCCTAAACACCAGGACGGCT 60.835 55.000 0.00 0.00 37.27 5.52
1057 1146 3.694535 AGGATACGATCGACAAGACAC 57.305 47.619 24.34 3.40 46.39 3.67
1070 1161 3.998672 GACACGGGGCCGAGAACA 61.999 66.667 0.00 0.00 42.83 3.18
1265 1361 1.080772 GATGTGCGTCGACCACTCA 60.081 57.895 26.61 18.97 34.38 3.41
1556 1652 4.704833 GCCTGCTTCGTCCTGCCA 62.705 66.667 0.00 0.00 0.00 4.92
1993 2089 1.803998 GCTGCTGTACATGCTCGATCA 60.804 52.381 15.28 0.00 0.00 2.92
2016 2112 8.352752 TCATCTGTTCATTCGACATATTGTAC 57.647 34.615 0.00 0.00 0.00 2.90
2385 2504 8.972127 AGGTAAGCATGATGTATTCTATCGTAT 58.028 33.333 0.00 0.00 0.00 3.06
2414 2533 2.412770 GGTTTGATTTCGCCATTGCAAG 59.587 45.455 4.94 0.00 37.32 4.01
2492 2611 2.355481 ACGGTGTTCGGCTTCGTC 60.355 61.111 0.00 0.00 44.45 4.20
2495 2614 2.654912 GGTGTTCGGCTTCGTCGTG 61.655 63.158 0.00 0.00 35.06 4.35
2651 2772 3.435275 CATCCAGCTCCTATACCTGCTA 58.565 50.000 0.00 0.00 34.10 3.49
2654 2775 2.560542 CCAGCTCCTATACCTGCTACAG 59.439 54.545 0.00 0.00 34.10 2.74
2681 2802 5.778862 TGTCATTCATGTACTGTCGAGAAA 58.221 37.500 0.00 0.00 0.00 2.52
2693 2814 4.156190 ACTGTCGAGAAACATGTAGATCGT 59.844 41.667 19.61 4.73 0.00 3.73
2705 2826 2.026169 TGTAGATCGTCACCCTCTCAGT 60.026 50.000 0.00 0.00 0.00 3.41
2746 2867 7.708752 GCAGATAGCTAAGTAAACTCATGTTCT 59.291 37.037 0.00 0.00 41.15 3.01
2770 2891 2.911819 ATAAACCGTGTTCATTGCCG 57.088 45.000 0.00 0.00 0.00 5.69
2802 4504 4.040339 TCTGCTTACCTGATGACAAACTGA 59.960 41.667 0.00 0.00 0.00 3.41
2806 4508 5.562890 GCTTACCTGATGACAAACTGAAACC 60.563 44.000 0.00 0.00 0.00 3.27
2811 4513 5.180117 CCTGATGACAAACTGAAACCTACTG 59.820 44.000 0.00 0.00 0.00 2.74
2812 4514 5.680619 TGATGACAAACTGAAACCTACTGT 58.319 37.500 0.00 0.00 0.00 3.55
2813 4515 6.119536 TGATGACAAACTGAAACCTACTGTT 58.880 36.000 0.00 0.00 39.43 3.16
2841 4543 2.884639 TGGGAAAACTAGCTTGCAAGTC 59.115 45.455 26.55 18.45 0.00 3.01
2870 4572 4.189639 ACTCCTAACAAGTTGGATCGAC 57.810 45.455 7.96 0.00 0.00 4.20
2881 4583 2.165301 GGATCGACGGAACCGCAAG 61.165 63.158 13.32 5.17 44.19 4.01
2890 4592 1.444119 GGAACCGCAAGTCAGCACAA 61.444 55.000 0.00 0.00 0.00 3.33
2901 4603 2.433604 AGTCAGCACAATGAGATCGGAT 59.566 45.455 0.00 0.00 0.00 4.18
2909 4611 3.454447 ACAATGAGATCGGATAACACCCA 59.546 43.478 0.00 0.00 0.00 4.51
2921 4623 0.923358 AACACCCAACAGGAACCTCA 59.077 50.000 0.00 0.00 39.89 3.86
2951 4653 5.786401 AGTCGAGCAATATGTCAAAAGAC 57.214 39.130 0.00 0.00 0.00 3.01
2954 4656 6.036517 AGTCGAGCAATATGTCAAAAGACATC 59.963 38.462 13.76 1.45 43.89 3.06
2955 4657 5.874261 TCGAGCAATATGTCAAAAGACATCA 59.126 36.000 13.76 3.15 43.89 3.07
3024 4727 2.733956 AGAGTTGGGTTGTGCTTTTCA 58.266 42.857 0.00 0.00 0.00 2.69
3092 4795 4.184629 ACGCTGCTTCTATTCTACTTTGG 58.815 43.478 0.00 0.00 0.00 3.28
3124 4827 8.073768 GGAAATAAAAGAAACGTCATTCACAGA 58.926 33.333 3.01 0.00 0.00 3.41
3132 4835 4.456280 ACGTCATTCACAGATCTAGCAA 57.544 40.909 0.00 0.00 0.00 3.91
3203 4907 2.053747 AACCCACCCTCTATGACCAA 57.946 50.000 0.00 0.00 0.00 3.67
3215 4919 6.003950 CCTCTATGACCAAACCAGAAAGAAA 58.996 40.000 0.00 0.00 0.00 2.52
3238 4942 9.455847 GAAACATGCTAAAGGATTCATGAATAC 57.544 33.333 21.26 21.26 31.71 1.89
3241 4945 7.776969 ACATGCTAAAGGATTCATGAATACTGT 59.223 33.333 29.82 26.83 40.97 3.55
3249 4953 2.276201 TCATGAATACTGTTTCCGCCG 58.724 47.619 0.00 0.00 0.00 6.46
3252 4956 1.208535 TGAATACTGTTTCCGCCGGAT 59.791 47.619 6.69 0.00 0.00 4.18
3274 4978 1.912043 AGCTCTCATGGTAAGGTGCTT 59.088 47.619 0.00 0.00 0.00 3.91
3275 4979 2.012673 GCTCTCATGGTAAGGTGCTTG 58.987 52.381 0.00 0.00 0.00 4.01
3323 5027 4.015084 CTCCCATTTCTCAGCTGTCATTT 58.985 43.478 14.67 0.00 0.00 2.32
3347 5051 1.283321 GATCTTGCTTGTCTCCCCCTT 59.717 52.381 0.00 0.00 0.00 3.95
3388 5092 4.740822 ACCAACCTGCGGCCATCC 62.741 66.667 2.24 0.00 0.00 3.51
3584 5288 7.510343 TCATCACTCCAATCAGAGTTATCCATA 59.490 37.037 0.00 0.00 44.83 2.74
3590 5294 9.270640 CTCCAATCAGAGTTATCCATAAAAGAG 57.729 37.037 0.00 0.00 0.00 2.85
3719 5423 1.287146 AGCTCCTTCCATTCAGCCAAT 59.713 47.619 0.00 0.00 31.81 3.16
3725 5429 0.322366 TCCATTCAGCCAATCGTGCA 60.322 50.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.323271 CCTAGCGAGCCCAGAGTTCA 61.323 60.000 0.00 0.00 0.00 3.18
1 2 1.439644 CCTAGCGAGCCCAGAGTTC 59.560 63.158 0.00 0.00 0.00 3.01
2 3 2.060980 CCCTAGCGAGCCCAGAGTT 61.061 63.158 0.00 0.00 0.00 3.01
3 4 2.443016 CCCTAGCGAGCCCAGAGT 60.443 66.667 0.00 0.00 0.00 3.24
4 5 3.922640 GCCCTAGCGAGCCCAGAG 61.923 72.222 0.00 0.00 0.00 3.35
10 11 4.858680 GGTTGGGCCCTAGCGAGC 62.859 72.222 25.70 9.56 41.24 5.03
11 12 4.530857 CGGTTGGGCCCTAGCGAG 62.531 72.222 42.24 21.29 43.01 5.03
20 21 4.362476 CAAAGGCAGCGGTTGGGC 62.362 66.667 0.00 0.00 0.00 5.36
21 22 4.362476 GCAAAGGCAGCGGTTGGG 62.362 66.667 8.37 0.00 40.72 4.12
31 32 2.027460 CGGGTTGTGTGCAAAGGC 59.973 61.111 0.00 0.00 36.22 4.35
32 33 2.027460 GCGGGTTGTGTGCAAAGG 59.973 61.111 0.00 0.00 36.22 3.11
33 34 2.353376 CGCGGGTTGTGTGCAAAG 60.353 61.111 0.00 0.00 36.22 2.77
34 35 3.114647 GACGCGGGTTGTGTGCAAA 62.115 57.895 12.47 0.00 42.62 3.68
35 36 3.578272 GACGCGGGTTGTGTGCAA 61.578 61.111 12.47 0.00 42.62 4.08
40 41 4.973055 TTCCGGACGCGGGTTGTG 62.973 66.667 12.47 0.00 0.00 3.33
41 42 4.238654 TTTCCGGACGCGGGTTGT 62.239 61.111 12.47 0.00 0.00 3.32
42 43 3.419759 CTTTCCGGACGCGGGTTG 61.420 66.667 12.47 2.52 0.00 3.77
43 44 4.692475 CCTTTCCGGACGCGGGTT 62.692 66.667 12.47 0.00 33.16 4.11
45 46 3.675619 ATTCCTTTCCGGACGCGGG 62.676 63.158 12.47 4.08 42.97 6.13
46 47 1.702491 GAATTCCTTTCCGGACGCGG 61.702 60.000 12.47 4.89 42.97 6.46
47 48 1.017177 TGAATTCCTTTCCGGACGCG 61.017 55.000 1.83 3.53 42.97 6.01
48 49 0.727398 CTGAATTCCTTTCCGGACGC 59.273 55.000 1.83 0.00 42.97 5.19
49 50 1.369625 CCTGAATTCCTTTCCGGACG 58.630 55.000 1.83 0.00 42.97 4.79
50 51 1.095600 GCCTGAATTCCTTTCCGGAC 58.904 55.000 1.83 0.00 42.97 4.79
51 52 0.034477 GGCCTGAATTCCTTTCCGGA 60.034 55.000 0.00 0.00 40.23 5.14
52 53 1.037579 GGGCCTGAATTCCTTTCCGG 61.038 60.000 0.84 0.00 40.63 5.14
53 54 1.376609 CGGGCCTGAATTCCTTTCCG 61.377 60.000 5.28 7.85 33.04 4.30
54 55 0.034477 TCGGGCCTGAATTCCTTTCC 60.034 55.000 13.31 0.00 33.04 3.13
55 56 1.095600 GTCGGGCCTGAATTCCTTTC 58.904 55.000 18.11 0.00 34.72 2.62
56 57 0.698818 AGTCGGGCCTGAATTCCTTT 59.301 50.000 18.11 0.00 0.00 3.11
57 58 0.698818 AAGTCGGGCCTGAATTCCTT 59.301 50.000 21.38 14.66 0.00 3.36
58 59 0.253327 GAAGTCGGGCCTGAATTCCT 59.747 55.000 34.58 18.28 37.07 3.36
59 60 2.781911 GAAGTCGGGCCTGAATTCC 58.218 57.895 34.58 21.04 37.07 3.01
60 61 0.253327 AGGAAGTCGGGCCTGAATTC 59.747 55.000 35.98 35.98 41.04 2.17
61 62 0.698818 AAGGAAGTCGGGCCTGAATT 59.301 50.000 26.62 26.62 34.00 2.17
62 63 1.209747 GTAAGGAAGTCGGGCCTGAAT 59.790 52.381 18.11 13.63 34.00 2.57
63 64 0.611714 GTAAGGAAGTCGGGCCTGAA 59.388 55.000 18.11 0.00 34.00 3.02
64 65 1.601419 CGTAAGGAAGTCGGGCCTGA 61.601 60.000 11.27 11.27 34.00 3.86
65 66 1.153628 CGTAAGGAAGTCGGGCCTG 60.154 63.158 4.71 4.71 34.00 4.85
66 67 3.295800 CGTAAGGAAGTCGGGCCT 58.704 61.111 0.84 0.00 35.61 5.19
78 79 0.392595 GCCCAGACCTTTCCCGTAAG 60.393 60.000 0.00 0.00 0.00 2.34
79 80 1.681076 GCCCAGACCTTTCCCGTAA 59.319 57.895 0.00 0.00 0.00 3.18
80 81 2.295602 GGCCCAGACCTTTCCCGTA 61.296 63.158 0.00 0.00 0.00 4.02
81 82 3.647771 GGCCCAGACCTTTCCCGT 61.648 66.667 0.00 0.00 0.00 5.28
82 83 3.330720 AGGCCCAGACCTTTCCCG 61.331 66.667 0.00 0.00 36.28 5.14
83 84 1.789576 TTCAGGCCCAGACCTTTCCC 61.790 60.000 0.00 0.00 38.26 3.97
84 85 0.609406 GTTCAGGCCCAGACCTTTCC 60.609 60.000 0.00 0.00 38.26 3.13
85 86 0.609406 GGTTCAGGCCCAGACCTTTC 60.609 60.000 0.00 0.00 38.26 2.62
86 87 1.360393 TGGTTCAGGCCCAGACCTTT 61.360 55.000 17.10 0.00 38.26 3.11
87 88 1.774217 TGGTTCAGGCCCAGACCTT 60.774 57.895 17.10 0.00 38.26 3.50
88 89 2.121963 TGGTTCAGGCCCAGACCT 60.122 61.111 17.10 0.00 42.30 3.85
93 94 2.925706 TACGCTGGTTCAGGCCCA 60.926 61.111 0.00 0.00 31.21 5.36
94 95 2.125106 CTACGCTGGTTCAGGCCC 60.125 66.667 0.00 0.00 31.21 5.80
95 96 0.605589 AAACTACGCTGGTTCAGGCC 60.606 55.000 0.00 0.00 31.21 5.19
96 97 1.197036 GAAAACTACGCTGGTTCAGGC 59.803 52.381 0.00 0.00 31.21 4.85
97 98 1.804748 GGAAAACTACGCTGGTTCAGG 59.195 52.381 0.00 0.00 31.21 3.86
98 99 2.767505 AGGAAAACTACGCTGGTTCAG 58.232 47.619 0.00 0.00 34.12 3.02
99 100 2.922740 AGGAAAACTACGCTGGTTCA 57.077 45.000 0.00 0.00 0.00 3.18
100 101 3.813724 AGAAAGGAAAACTACGCTGGTTC 59.186 43.478 0.00 0.00 0.00 3.62
101 102 3.813724 GAGAAAGGAAAACTACGCTGGTT 59.186 43.478 0.00 0.00 0.00 3.67
102 103 3.071167 AGAGAAAGGAAAACTACGCTGGT 59.929 43.478 0.00 0.00 0.00 4.00
103 104 3.665190 AGAGAAAGGAAAACTACGCTGG 58.335 45.455 0.00 0.00 0.00 4.85
104 105 4.387256 CAGAGAGAAAGGAAAACTACGCTG 59.613 45.833 0.00 0.00 0.00 5.18
105 106 4.561105 CAGAGAGAAAGGAAAACTACGCT 58.439 43.478 0.00 0.00 0.00 5.07
106 107 3.123790 GCAGAGAGAAAGGAAAACTACGC 59.876 47.826 0.00 0.00 0.00 4.42
107 108 3.680458 GGCAGAGAGAAAGGAAAACTACG 59.320 47.826 0.00 0.00 0.00 3.51
108 109 4.642429 TGGCAGAGAGAAAGGAAAACTAC 58.358 43.478 0.00 0.00 0.00 2.73
109 110 4.974645 TGGCAGAGAGAAAGGAAAACTA 57.025 40.909 0.00 0.00 0.00 2.24
110 111 3.864789 TGGCAGAGAGAAAGGAAAACT 57.135 42.857 0.00 0.00 0.00 2.66
111 112 3.441922 GGATGGCAGAGAGAAAGGAAAAC 59.558 47.826 0.00 0.00 0.00 2.43
112 113 3.690460 GGATGGCAGAGAGAAAGGAAAA 58.310 45.455 0.00 0.00 0.00 2.29
113 114 2.355108 CGGATGGCAGAGAGAAAGGAAA 60.355 50.000 0.00 0.00 0.00 3.13
114 115 1.208052 CGGATGGCAGAGAGAAAGGAA 59.792 52.381 0.00 0.00 0.00 3.36
115 116 0.826715 CGGATGGCAGAGAGAAAGGA 59.173 55.000 0.00 0.00 0.00 3.36
116 117 0.179062 CCGGATGGCAGAGAGAAAGG 60.179 60.000 0.00 0.00 0.00 3.11
117 118 3.376218 CCGGATGGCAGAGAGAAAG 57.624 57.895 0.00 0.00 0.00 2.62
128 129 1.651240 CTGTTTCTGCTGCCGGATGG 61.651 60.000 5.05 0.00 38.77 3.51
129 130 1.798735 CTGTTTCTGCTGCCGGATG 59.201 57.895 5.05 0.00 0.00 3.51
130 131 2.042831 GCTGTTTCTGCTGCCGGAT 61.043 57.895 5.05 0.00 0.00 4.18
131 132 2.669569 GCTGTTTCTGCTGCCGGA 60.670 61.111 5.05 0.00 0.00 5.14
132 133 2.263741 AAGCTGTTTCTGCTGCCGG 61.264 57.895 0.00 0.00 38.59 6.13
133 134 1.081641 CAAGCTGTTTCTGCTGCCG 60.082 57.895 0.00 0.00 38.59 5.69
134 135 1.288127 CCAAGCTGTTTCTGCTGCC 59.712 57.895 0.00 0.00 38.59 4.85
135 136 1.372623 GCCAAGCTGTTTCTGCTGC 60.373 57.895 0.00 0.00 38.59 5.25
136 137 2.338381 AGCCAAGCTGTTTCTGCTG 58.662 52.632 0.00 0.00 38.59 4.41
137 138 4.916358 AGCCAAGCTGTTTCTGCT 57.084 50.000 0.00 0.00 40.24 4.24
148 149 4.697756 TCGTTCCCGCCAGCCAAG 62.698 66.667 0.00 0.00 0.00 3.61
149 150 4.697756 CTCGTTCCCGCCAGCCAA 62.698 66.667 0.00 0.00 0.00 4.52
156 157 4.742201 TCTGCTGCTCGTTCCCGC 62.742 66.667 0.00 0.00 0.00 6.13
157 158 1.667830 TTTCTGCTGCTCGTTCCCG 60.668 57.895 0.00 0.00 0.00 5.14
158 159 0.603975 AGTTTCTGCTGCTCGTTCCC 60.604 55.000 0.00 0.00 0.00 3.97
159 160 1.195674 GAAGTTTCTGCTGCTCGTTCC 59.804 52.381 0.00 0.00 0.00 3.62
160 161 1.867233 TGAAGTTTCTGCTGCTCGTTC 59.133 47.619 0.00 0.00 0.00 3.95
161 162 1.953559 TGAAGTTTCTGCTGCTCGTT 58.046 45.000 0.00 0.00 0.00 3.85
162 163 1.599542 GTTGAAGTTTCTGCTGCTCGT 59.400 47.619 0.00 0.00 0.00 4.18
163 164 1.869767 AGTTGAAGTTTCTGCTGCTCG 59.130 47.619 0.00 0.00 0.00 5.03
164 165 3.625938 CAAGTTGAAGTTTCTGCTGCTC 58.374 45.455 0.00 0.00 0.00 4.26
165 166 2.223665 GCAAGTTGAAGTTTCTGCTGCT 60.224 45.455 7.16 0.00 0.00 4.24
166 167 2.122564 GCAAGTTGAAGTTTCTGCTGC 58.877 47.619 7.16 0.00 0.00 5.25
167 168 2.378806 CGCAAGTTGAAGTTTCTGCTG 58.621 47.619 7.16 0.00 0.00 4.41
168 169 1.334869 CCGCAAGTTGAAGTTTCTGCT 59.665 47.619 7.16 0.00 0.00 4.24
169 170 1.065551 ACCGCAAGTTGAAGTTTCTGC 59.934 47.619 7.16 0.00 0.00 4.26
170 171 2.287009 GGACCGCAAGTTGAAGTTTCTG 60.287 50.000 7.16 0.00 0.00 3.02
171 172 1.947456 GGACCGCAAGTTGAAGTTTCT 59.053 47.619 7.16 0.00 0.00 2.52
172 173 1.333791 CGGACCGCAAGTTGAAGTTTC 60.334 52.381 7.16 0.00 0.00 2.78
173 174 0.661020 CGGACCGCAAGTTGAAGTTT 59.339 50.000 7.16 0.00 0.00 2.66
180 181 0.179051 TTAACCACGGACCGCAAGTT 60.179 50.000 15.39 16.76 0.00 2.66
186 187 2.030958 GTGCCTTAACCACGGACCG 61.031 63.158 13.61 13.61 0.00 4.79
207 208 7.531524 ACTGCACAGTGCCAATAAATGGAATA 61.532 38.462 23.06 0.00 45.82 1.75
213 214 4.766891 AGTAACTGCACAGTGCCAATAAAT 59.233 37.500 23.06 4.89 44.23 1.40
216 217 3.007940 AGAGTAACTGCACAGTGCCAATA 59.992 43.478 23.06 9.79 44.23 1.90
220 221 1.884235 AAGAGTAACTGCACAGTGCC 58.116 50.000 23.06 6.85 44.23 5.01
221 222 3.654414 AGTAAGAGTAACTGCACAGTGC 58.346 45.455 19.37 19.37 45.29 4.40
268 269 0.232303 GTCACGGAGCAAAGTGTTCG 59.768 55.000 5.58 0.00 39.25 3.95
269 270 1.261619 CAGTCACGGAGCAAAGTGTTC 59.738 52.381 5.58 0.00 39.25 3.18
289 290 2.751436 TCGCCAAAGGATGCTGCC 60.751 61.111 0.00 0.00 0.00 4.85
296 297 0.606604 GAGGTACAGTCGCCAAAGGA 59.393 55.000 0.00 0.00 0.00 3.36
345 361 2.437359 GCATGCACCGAAGCTCCT 60.437 61.111 14.21 0.00 34.99 3.69
346 362 3.869272 CGCATGCACCGAAGCTCC 61.869 66.667 19.57 0.00 34.99 4.70
347 363 4.527157 GCGCATGCACCGAAGCTC 62.527 66.667 19.57 0.00 42.15 4.09
407 434 4.946157 AGATCATAACAGCAGAAACCAAGG 59.054 41.667 0.00 0.00 0.00 3.61
408 435 6.149973 TCAAGATCATAACAGCAGAAACCAAG 59.850 38.462 0.00 0.00 0.00 3.61
409 436 6.003326 TCAAGATCATAACAGCAGAAACCAA 58.997 36.000 0.00 0.00 0.00 3.67
419 446 3.875727 CCCACAGCTCAAGATCATAACAG 59.124 47.826 0.00 0.00 0.00 3.16
420 447 3.370846 CCCCACAGCTCAAGATCATAACA 60.371 47.826 0.00 0.00 0.00 2.41
423 450 2.763039 TCCCCACAGCTCAAGATCATA 58.237 47.619 0.00 0.00 0.00 2.15
425 452 1.588239 ATCCCCACAGCTCAAGATCA 58.412 50.000 0.00 0.00 0.00 2.92
432 459 0.744771 GAACGGAATCCCCACAGCTC 60.745 60.000 0.00 0.00 34.14 4.09
439 466 2.691526 GGGTTAAATGAACGGAATCCCC 59.308 50.000 0.00 0.00 39.12 4.81
446 473 1.823797 TTCGGGGGTTAAATGAACGG 58.176 50.000 0.00 0.00 39.12 4.44
447 474 2.553172 TGTTTCGGGGGTTAAATGAACG 59.447 45.455 0.00 0.00 39.12 3.95
448 475 4.587584 TTGTTTCGGGGGTTAAATGAAC 57.412 40.909 0.00 0.00 37.31 3.18
449 476 5.105064 TGTTTTGTTTCGGGGGTTAAATGAA 60.105 36.000 0.00 0.00 0.00 2.57
450 477 4.404715 TGTTTTGTTTCGGGGGTTAAATGA 59.595 37.500 0.00 0.00 0.00 2.57
456 483 3.244457 TGTTTTGTTTTGTTTCGGGGGTT 60.244 39.130 0.00 0.00 0.00 4.11
459 486 5.147865 GTTTTGTTTTGTTTTGTTTCGGGG 58.852 37.500 0.00 0.00 0.00 5.73
461 488 7.665080 TTTGTTTTGTTTTGTTTTGTTTCGG 57.335 28.000 0.00 0.00 0.00 4.30
484 511 3.026694 AGAGAAGCCAAGTGCAGTTTTT 58.973 40.909 3.38 0.00 44.83 1.94
485 512 2.659428 AGAGAAGCCAAGTGCAGTTTT 58.341 42.857 3.38 0.00 44.83 2.43
486 513 2.355010 AGAGAAGCCAAGTGCAGTTT 57.645 45.000 3.38 0.00 44.83 2.66
487 514 2.355010 AAGAGAAGCCAAGTGCAGTT 57.645 45.000 0.00 0.00 44.83 3.16
488 515 2.355010 AAAGAGAAGCCAAGTGCAGT 57.645 45.000 0.00 0.00 44.83 4.40
575 603 1.891919 TGCGAGGCACAGAAACACC 60.892 57.895 0.00 0.00 31.71 4.16
676 717 0.393808 TTTCACGGCCCTTATCAGCC 60.394 55.000 0.00 0.00 46.17 4.85
701 742 4.497473 CACATAGCTAGAGTGCTAGACC 57.503 50.000 14.03 0.00 46.89 3.85
715 757 3.367395 GGAAGGAAAAACCAGCACATAGC 60.367 47.826 0.00 0.00 42.04 2.97
716 758 4.082125 AGGAAGGAAAAACCAGCACATAG 58.918 43.478 0.00 0.00 42.04 2.23
717 759 4.112634 AGGAAGGAAAAACCAGCACATA 57.887 40.909 0.00 0.00 42.04 2.29
718 760 2.962859 AGGAAGGAAAAACCAGCACAT 58.037 42.857 0.00 0.00 42.04 3.21
719 761 2.452600 AGGAAGGAAAAACCAGCACA 57.547 45.000 0.00 0.00 42.04 4.57
720 762 3.819564 AAAGGAAGGAAAAACCAGCAC 57.180 42.857 0.00 0.00 42.04 4.40
743 801 9.995003 AATTAATCAACAGCACAATTTTCCTTA 57.005 25.926 0.00 0.00 0.00 2.69
744 802 8.907222 AATTAATCAACAGCACAATTTTCCTT 57.093 26.923 0.00 0.00 0.00 3.36
746 804 9.638239 TCTAATTAATCAACAGCACAATTTTCC 57.362 29.630 0.00 0.00 0.00 3.13
788 868 3.250521 CGCCTTTTGCCAAACATGAAATT 59.749 39.130 0.00 0.00 36.24 1.82
793 873 0.860533 CACGCCTTTTGCCAAACATG 59.139 50.000 0.00 0.00 36.24 3.21
796 876 0.179124 TGACACGCCTTTTGCCAAAC 60.179 50.000 0.00 0.00 36.24 2.93
885 967 8.110271 AGAGAAACGGAGAGACATATATATCCA 58.890 37.037 0.00 0.00 0.00 3.41
916 1000 1.694150 CGGGGAGAGATGGAAATGCTA 59.306 52.381 0.00 0.00 0.00 3.49
917 1001 0.471617 CGGGGAGAGATGGAAATGCT 59.528 55.000 0.00 0.00 0.00 3.79
918 1002 1.169034 GCGGGGAGAGATGGAAATGC 61.169 60.000 0.00 0.00 0.00 3.56
937 1021 0.695347 AGTTTCCTTGCTCTCCAGGG 59.305 55.000 0.00 0.00 41.86 4.45
938 1022 2.039613 AGAAGTTTCCTTGCTCTCCAGG 59.960 50.000 0.00 0.00 0.00 4.45
939 1023 3.415457 AGAAGTTTCCTTGCTCTCCAG 57.585 47.619 0.00 0.00 0.00 3.86
940 1024 3.480470 CAAGAAGTTTCCTTGCTCTCCA 58.520 45.455 0.00 0.00 35.23 3.86
955 1039 5.461737 GCTGTAGTATTGAGCTAGCAAGAAG 59.538 44.000 18.83 1.64 0.00 2.85
1057 1146 2.824041 CCAATGTTCTCGGCCCCG 60.824 66.667 0.00 0.00 41.35 5.73
1410 1506 1.670949 ATGAGCGAGGTGAGCGTGAT 61.671 55.000 0.00 0.00 40.04 3.06
1523 1619 2.726351 GGCGAGGAGGTGGAAGGAG 61.726 68.421 0.00 0.00 0.00 3.69
1981 2077 3.531934 TGAACAGATGATCGAGCATGT 57.468 42.857 22.75 15.12 0.00 3.21
1993 2089 8.716646 TTGTACAATATGTCGAATGAACAGAT 57.283 30.769 3.59 0.00 0.00 2.90
2016 2112 7.061094 GCTGAAGAAAATTCCAGACGTTAATTG 59.939 37.037 0.00 0.00 0.00 2.32
2149 2259 1.302511 GGTGTTGATGGTGGCGTCT 60.303 57.895 0.00 0.00 0.00 4.18
2245 2364 3.052082 TCGTCCGACTGGTCCGAC 61.052 66.667 10.58 10.58 35.72 4.79
2370 2489 5.571741 CCGCAAACGATACGATAGAATACAT 59.428 40.000 0.00 0.00 43.93 2.29
2371 2490 4.913345 CCGCAAACGATACGATAGAATACA 59.087 41.667 0.00 0.00 43.93 2.29
2372 2491 4.913924 ACCGCAAACGATACGATAGAATAC 59.086 41.667 0.00 0.00 43.93 1.89
2373 2492 5.112220 ACCGCAAACGATACGATAGAATA 57.888 39.130 0.00 0.00 43.93 1.75
2374 2493 3.973657 ACCGCAAACGATACGATAGAAT 58.026 40.909 0.00 0.00 43.93 2.40
2375 2494 3.425577 ACCGCAAACGATACGATAGAA 57.574 42.857 0.00 0.00 43.93 2.10
2376 2495 3.425577 AACCGCAAACGATACGATAGA 57.574 42.857 0.00 0.00 43.93 1.98
2377 2496 3.548668 TCAAACCGCAAACGATACGATAG 59.451 43.478 0.00 0.00 43.93 2.08
2378 2497 3.509740 TCAAACCGCAAACGATACGATA 58.490 40.909 0.00 0.00 43.93 2.92
2385 2504 2.025544 CGAAATCAAACCGCAAACGA 57.974 45.000 0.00 0.00 43.93 3.85
2414 2533 1.590932 CCATGATCAGCTACAGTGCC 58.409 55.000 0.09 0.00 0.00 5.01
2654 2775 3.549471 CGACAGTACATGAATGACAGAGC 59.451 47.826 0.00 0.00 0.00 4.09
2681 2802 2.952978 GAGAGGGTGACGATCTACATGT 59.047 50.000 2.69 2.69 0.00 3.21
2705 2826 0.391228 TCTGCGCTCAGTTTACACCA 59.609 50.000 9.73 0.00 41.10 4.17
2746 2867 5.464057 CGGCAATGAACACGGTTTATATCTA 59.536 40.000 0.00 0.00 0.00 1.98
2806 4508 8.880750 GCTAGTTTTCCCAGTAATAAACAGTAG 58.119 37.037 0.00 0.00 33.94 2.57
2811 4513 7.027760 GCAAGCTAGTTTTCCCAGTAATAAAC 58.972 38.462 0.00 0.00 0.00 2.01
2812 4514 6.717540 TGCAAGCTAGTTTTCCCAGTAATAAA 59.282 34.615 0.00 0.00 0.00 1.40
2813 4515 6.242396 TGCAAGCTAGTTTTCCCAGTAATAA 58.758 36.000 0.00 0.00 0.00 1.40
2814 4516 5.811190 TGCAAGCTAGTTTTCCCAGTAATA 58.189 37.500 0.00 0.00 0.00 0.98
2841 4543 2.218603 ACTTGTTAGGAGTTGGTTGCG 58.781 47.619 0.00 0.00 0.00 4.85
2870 4572 2.664851 TGCTGACTTGCGGTTCCG 60.665 61.111 6.90 6.90 35.36 4.30
2881 4583 2.299993 TCCGATCTCATTGTGCTGAC 57.700 50.000 0.00 0.00 0.00 3.51
2890 4592 3.454447 TGTTGGGTGTTATCCGATCTCAT 59.546 43.478 0.00 0.00 0.00 2.90
2901 4603 2.128535 TGAGGTTCCTGTTGGGTGTTA 58.871 47.619 0.00 0.00 36.25 2.41
2909 4611 5.238650 CGACTTGTATTTTGAGGTTCCTGTT 59.761 40.000 0.00 0.00 0.00 3.16
2921 4623 7.609760 TGACATATTGCTCGACTTGTATTTT 57.390 32.000 0.00 0.00 0.00 1.82
2951 4653 9.520204 GACCATTTTGTTATATGTTTCCTGATG 57.480 33.333 0.00 0.00 0.00 3.07
2954 4656 8.739039 TCAGACCATTTTGTTATATGTTTCCTG 58.261 33.333 0.00 0.00 0.00 3.86
2955 4657 8.739972 GTCAGACCATTTTGTTATATGTTTCCT 58.260 33.333 0.00 0.00 0.00 3.36
3024 4727 3.778265 AGCCATTGGTGTTATTGTCCTT 58.222 40.909 4.26 0.00 0.00 3.36
3066 4769 6.642707 AAGTAGAATAGAAGCAGCGTATCT 57.357 37.500 4.21 4.21 0.00 1.98
3067 4770 6.144724 CCAAAGTAGAATAGAAGCAGCGTATC 59.855 42.308 0.00 0.00 0.00 2.24
3124 4827 4.056740 CTCTGATGAATGCGTTGCTAGAT 58.943 43.478 0.00 0.00 0.00 1.98
3132 4835 5.471456 ACTTCTTTTTCTCTGATGAATGCGT 59.529 36.000 0.00 0.00 0.00 5.24
3181 4885 2.719705 TGGTCATAGAGGGTGGGTTTTT 59.280 45.455 0.00 0.00 0.00 1.94
3185 4889 1.633945 GTTTGGTCATAGAGGGTGGGT 59.366 52.381 0.00 0.00 0.00 4.51
3191 4895 5.165961 TCTTTCTGGTTTGGTCATAGAGG 57.834 43.478 0.00 0.00 0.00 3.69
3203 4907 5.833131 TCCTTTAGCATGTTTCTTTCTGGTT 59.167 36.000 0.00 0.00 0.00 3.67
3215 4919 7.776969 ACAGTATTCATGAATCCTTTAGCATGT 59.223 33.333 23.95 8.76 39.22 3.21
3238 4942 2.464459 GCTGATCCGGCGGAAACAG 61.464 63.158 37.87 37.87 40.40 3.16
3241 4945 2.186903 GAGCTGATCCGGCGGAAA 59.813 61.111 34.58 22.66 41.21 3.13
3249 4953 2.703007 ACCTTACCATGAGAGCTGATCC 59.297 50.000 0.00 0.00 0.00 3.36
3252 4956 1.208052 GCACCTTACCATGAGAGCTGA 59.792 52.381 0.00 0.00 0.00 4.26
3274 4978 3.239464 TGCCAGGAAGCAGACACA 58.761 55.556 0.00 0.00 38.00 3.72
3323 5027 1.003580 GGGAGACAAGCAAGATCCACA 59.996 52.381 0.00 0.00 0.00 4.17
3347 5051 1.953231 CTCTGTCAGCTCGGATGCCA 61.953 60.000 0.00 0.00 0.00 4.92
3388 5092 1.302033 AGAAGCAGTGGAAGGCGTG 60.302 57.895 0.00 0.00 34.54 5.34
3584 5288 1.227943 TGGCAGCAGCGACTCTTTT 60.228 52.632 0.00 0.00 43.41 2.27
3719 5423 0.531974 GTGAAGTTGACCCTGCACGA 60.532 55.000 0.00 0.00 31.48 4.35
3725 5429 1.129058 AACCTCGTGAAGTTGACCCT 58.871 50.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.