Multiple sequence alignment - TraesCS1B01G272900

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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 TraesCS1B01G272900 chr1B 100.000 5889 0 0 1 5889 478726278 478720390 0.000000e+00 10876.0
1 TraesCS1B01G272900 chr1A 91.887 5374 265 71 16 5272 456945270 456939951 0.000000e+00 7350.0
2 TraesCS1B01G272900 chr1A 84.536 582 53 21 5330 5889 456939849 456939283 5.190000e-150 542.0
3 TraesCS1B01G272900 chr1D 93.540 4969 173 44 378 5217 356158504 356153555 0.000000e+00 7262.0
4 TraesCS1B01G272900 chr1D 85.202 223 27 4 16 233 356159858 356159637 2.140000e-54 224.0
5 TraesCS1B01G272900 chr7B 87.668 446 48 3 5446 5889 491198742 491198302 4.070000e-141 512.0
6 TraesCS1B01G272900 chr7B 89.610 77 8 0 5370 5446 140931137 140931061 1.350000e-16 99.0
7 TraesCS1B01G272900 chr3D 87.816 435 46 3 5446 5878 395669676 395670105 2.450000e-138 503.0
8 TraesCS1B01G272900 chr5D 87.558 434 46 4 5446 5876 437083339 437083767 4.100000e-136 496.0
9 TraesCS1B01G272900 chr6B 87.356 435 48 4 5446 5878 545223567 545223996 5.300000e-135 492.0
10 TraesCS1B01G272900 chr4D 87.215 438 49 3 5446 5881 401416508 401416076 5.300000e-135 492.0
11 TraesCS1B01G272900 chr7D 86.986 438 50 3 5446 5881 70150787 70150355 2.470000e-133 486.0
12 TraesCS1B01G272900 chr7D 84.946 93 11 3 5354 5446 175645679 175645590 2.260000e-14 91.6
13 TraesCS1B01G272900 chr7A 87.724 391 45 2 5451 5839 634478713 634478324 2.500000e-123 453.0
14 TraesCS1B01G272900 chr3A 83.857 446 57 6 5446 5889 468005199 468005631 1.530000e-110 411.0
15 TraesCS1B01G272900 chr2B 89.041 73 7 1 5375 5446 32631924 32631996 8.130000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G272900 chr1B 478720390 478726278 5888 True 10876 10876 100.0000 1 5889 1 chr1B.!!$R1 5888
1 TraesCS1B01G272900 chr1A 456939283 456945270 5987 True 3946 7350 88.2115 16 5889 2 chr1A.!!$R1 5873
2 TraesCS1B01G272900 chr1D 356153555 356159858 6303 True 3743 7262 89.3710 16 5217 2 chr1D.!!$R1 5201

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
202 211 0.038892 TACAAACACTCCTCGACCGC 60.039 55.000 0.00 0.0 0.00 5.68 F
481 1511 0.250901 GGTGTGTCCCATTGCTGAGT 60.251 55.000 0.00 0.0 0.00 3.41 F
523 1554 0.386352 GCCCTTACGCCACGAAAAAC 60.386 55.000 0.00 0.0 0.00 2.43 F
953 2020 1.452289 CCTCTCTCTCCTCGGCGAA 60.452 63.158 12.13 0.0 0.00 4.70 F
2739 3842 1.002773 TCCCTCAACTTTTCCTACCGC 59.997 52.381 0.00 0.0 0.00 5.68 F
3963 5111 1.002087 AGGCCTTTGTTCGAGGTACTG 59.998 52.381 0.00 0.0 41.55 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 2662 1.510844 GATCCGCACCCGCAAAATT 59.489 52.632 0.00 0.0 38.40 1.82 R
1974 3069 2.554032 CTCAAGGAGTTTTCGCACCATT 59.446 45.455 0.00 0.0 0.00 3.16 R
2226 3321 7.475015 TCAAATCTAGTAAATGATGCAACTGC 58.525 34.615 0.00 0.0 42.50 4.40 R
2772 3875 3.261643 ACATGTGACAGTAAGGCATGAGA 59.738 43.478 0.00 0.0 37.77 3.27 R
4733 5927 0.036164 TGGTGCATGCCGAGTACTTT 59.964 50.000 16.68 0.0 0.00 2.66 R
5466 6712 0.107993 CTTCTCCAGCTCAATGGCGA 60.108 55.000 0.00 0.0 40.41 5.54 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
34 35 1.133513 AGGATCAGATCAGCCGTCTCT 60.134 52.381 12.66 0.00 0.00 3.10
41 42 0.106469 ATCAGCCGTCTCTAGAGCCA 60.106 55.000 15.35 0.00 0.00 4.75
50 51 3.238597 GTCTCTAGAGCCATTGGATCCT 58.761 50.000 17.14 7.59 39.17 3.24
53 54 0.767375 TAGAGCCATTGGATCCTGCC 59.233 55.000 17.14 0.00 39.17 4.85
65 66 1.965754 ATCCTGCCCGAGAGAGTTGC 61.966 60.000 0.00 0.00 0.00 4.17
66 67 2.654079 CCTGCCCGAGAGAGTTGCT 61.654 63.158 0.00 0.00 0.00 3.91
70 71 1.004560 CCCGAGAGAGTTGCTTGCA 60.005 57.895 0.00 0.00 0.00 4.08
76 77 3.072944 GAGAGAGTTGCTTGCATCAGTT 58.927 45.455 6.47 0.00 0.00 3.16
77 78 3.484407 AGAGAGTTGCTTGCATCAGTTT 58.516 40.909 6.47 0.00 0.00 2.66
142 147 1.431496 GTTTGCAACATGACCCATGC 58.569 50.000 0.00 2.58 44.80 4.06
143 148 0.321021 TTTGCAACATGACCCATGCC 59.679 50.000 0.00 0.00 44.80 4.40
144 149 0.830866 TTGCAACATGACCCATGCCA 60.831 50.000 0.00 0.44 44.80 4.92
146 151 1.507630 CAACATGACCCATGCCACG 59.492 57.895 0.00 0.00 44.80 4.94
180 189 0.310543 TTGACCAATGTTGCGCTCAC 59.689 50.000 9.73 6.11 0.00 3.51
202 211 0.038892 TACAAACACTCCTCGACCGC 60.039 55.000 0.00 0.00 0.00 5.68
231 240 1.657094 CTGGCCGATACGTAACACAAC 59.343 52.381 0.00 0.00 0.00 3.32
233 242 1.404583 GGCCGATACGTAACACAACCT 60.405 52.381 0.00 0.00 0.00 3.50
234 243 1.657094 GCCGATACGTAACACAACCTG 59.343 52.381 0.00 0.00 0.00 4.00
239 248 2.129823 ACGTAACACAACCTGTCTCG 57.870 50.000 0.00 0.00 35.98 4.04
240 249 0.782384 CGTAACACAACCTGTCTCGC 59.218 55.000 0.00 0.00 30.29 5.03
251 260 4.674496 GTCTCGCGCTAGACAGTC 57.326 61.111 30.66 9.06 44.41 3.51
272 281 1.819928 TGCGACACAAGCCATGTTAT 58.180 45.000 0.00 0.00 41.46 1.89
356 388 3.016736 ACCGAGTTCCCATGCTTTATTG 58.983 45.455 0.00 0.00 0.00 1.90
361 393 4.613437 AGTTCCCATGCTTTATTGGTCAT 58.387 39.130 0.00 0.00 0.00 3.06
378 410 6.985188 TGGTCATCTTGATGCTTTAGTAAC 57.015 37.500 5.78 0.00 0.00 2.50
380 412 6.371548 TGGTCATCTTGATGCTTTAGTAACAC 59.628 38.462 5.78 0.00 0.00 3.32
382 414 7.201565 GGTCATCTTGATGCTTTAGTAACACTC 60.202 40.741 5.78 0.00 0.00 3.51
383 415 6.818644 TCATCTTGATGCTTTAGTAACACTCC 59.181 38.462 5.78 0.00 0.00 3.85
384 416 6.109156 TCTTGATGCTTTAGTAACACTCCA 57.891 37.500 0.00 0.00 0.00 3.86
387 419 7.665559 TCTTGATGCTTTAGTAACACTCCATTT 59.334 33.333 0.00 0.00 0.00 2.32
389 421 9.461312 TTGATGCTTTAGTAACACTCCATTTAT 57.539 29.630 0.00 0.00 0.00 1.40
390 422 8.892723 TGATGCTTTAGTAACACTCCATTTATG 58.107 33.333 0.00 0.00 0.00 1.90
391 423 9.109393 GATGCTTTAGTAACACTCCATTTATGA 57.891 33.333 0.00 0.00 0.00 2.15
481 1511 0.250901 GGTGTGTCCCATTGCTGAGT 60.251 55.000 0.00 0.00 0.00 3.41
509 1539 2.238646 TCTCACAAACCATATCGCCCTT 59.761 45.455 0.00 0.00 0.00 3.95
523 1554 0.386352 GCCCTTACGCCACGAAAAAC 60.386 55.000 0.00 0.00 0.00 2.43
557 1588 5.212532 AGCACAAATATCACAAGCCAAAA 57.787 34.783 0.00 0.00 0.00 2.44
558 1589 5.609423 AGCACAAATATCACAAGCCAAAAA 58.391 33.333 0.00 0.00 0.00 1.94
769 1834 4.838152 CAGCCGACCACCCATCCG 62.838 72.222 0.00 0.00 0.00 4.18
953 2020 1.452289 CCTCTCTCTCCTCGGCGAA 60.452 63.158 12.13 0.00 0.00 4.70
1006 2073 2.294536 ACCCATCTAAATCTCACCCCCT 60.295 50.000 0.00 0.00 0.00 4.79
1512 2587 3.746492 GCGAGTTCTGTTTAGGATGTGTT 59.254 43.478 0.00 0.00 0.00 3.32
1514 2589 5.062308 GCGAGTTCTGTTTAGGATGTGTTAG 59.938 44.000 0.00 0.00 0.00 2.34
1555 2631 4.455190 GGGTAAGGCGTTGTTAATTGTACA 59.545 41.667 0.97 0.00 0.00 2.90
1586 2662 4.284746 GGGTTGTTGTGGGGATATTTTTCA 59.715 41.667 0.00 0.00 0.00 2.69
1643 2719 3.734463 TGTGTTTGCTCGAGGAATAACA 58.266 40.909 20.59 21.80 0.00 2.41
1747 2841 7.106439 TGGTTCACTAATTGTTCATTTGTGT 57.894 32.000 8.37 0.00 44.46 3.72
1765 2859 8.739039 CATTTGTGTTTCACCCTAATTGATCTA 58.261 33.333 0.00 0.00 32.73 1.98
1832 2926 5.473504 TCTCCATTTGGTTAACTTCTGCTTC 59.526 40.000 5.42 0.00 36.34 3.86
1940 3034 6.467677 AGTTGCAGTATACAGACAAAGTGAT 58.532 36.000 5.50 0.00 0.00 3.06
1942 3036 5.793817 TGCAGTATACAGACAAAGTGATGT 58.206 37.500 5.50 0.00 35.90 3.06
1974 3069 4.617253 TGGAAACTAGAGTGCTTGCTAA 57.383 40.909 0.00 0.00 0.00 3.09
2201 3296 1.583556 ACATGACATGGAGGGCACTA 58.416 50.000 19.39 0.00 33.60 2.74
2640 3743 6.208007 TCGGTTTCAGTAGACTCACTCAAATA 59.792 38.462 0.00 0.00 0.00 1.40
2739 3842 1.002773 TCCCTCAACTTTTCCTACCGC 59.997 52.381 0.00 0.00 0.00 5.68
2776 3879 3.804036 ACGTTGTCAAGGTTTGATCTCA 58.196 40.909 5.09 0.00 42.47 3.27
2788 3891 4.333926 GGTTTGATCTCATGCCTTACTGTC 59.666 45.833 0.00 0.00 0.00 3.51
3037 4156 3.872511 TTGTGGGCTTCTGCATTATTG 57.127 42.857 0.00 0.00 41.91 1.90
3432 4552 3.959449 CTCCTGGTCAGATCTTCTCATGA 59.041 47.826 0.00 0.00 0.00 3.07
3444 4564 7.277319 CAGATCTTCTCATGATTTGTCGAAGAA 59.723 37.037 20.32 7.28 41.54 2.52
3445 4565 7.821359 AGATCTTCTCATGATTTGTCGAAGAAA 59.179 33.333 20.32 5.78 41.54 2.52
3446 4566 7.356641 TCTTCTCATGATTTGTCGAAGAAAG 57.643 36.000 16.32 0.00 39.69 2.62
3879 5026 5.690865 ACTGTAGAACCTTTTGATGACCAA 58.309 37.500 0.00 0.00 0.00 3.67
3963 5111 1.002087 AGGCCTTTGTTCGAGGTACTG 59.998 52.381 0.00 0.00 41.55 2.74
3979 5127 4.021016 AGGTACTGTCTTGTTCACTCCATC 60.021 45.833 0.00 0.00 37.18 3.51
3993 5141 1.821753 CTCCATCGAGTGTTGTCCTCT 59.178 52.381 0.00 0.00 0.00 3.69
3994 5142 1.546029 TCCATCGAGTGTTGTCCTCTG 59.454 52.381 0.00 0.00 0.00 3.35
3995 5143 1.404717 CCATCGAGTGTTGTCCTCTGG 60.405 57.143 0.00 0.00 0.00 3.86
3996 5144 1.546029 CATCGAGTGTTGTCCTCTGGA 59.454 52.381 0.00 0.00 0.00 3.86
3997 5145 1.699730 TCGAGTGTTGTCCTCTGGAA 58.300 50.000 0.00 0.00 31.38 3.53
4029 5190 6.536731 AGTTCTATCAAAGATTAGCATGCG 57.463 37.500 13.01 0.00 33.05 4.73
4031 5192 6.423302 AGTTCTATCAAAGATTAGCATGCGAG 59.577 38.462 13.01 0.00 33.05 5.03
4047 5208 1.594862 GCGAGGTTCTGACATGCATAC 59.405 52.381 0.00 0.00 0.00 2.39
4118 5279 4.347607 AGGTTTATGCTTTGCTCAAGGAT 58.652 39.130 8.01 8.01 45.14 3.24
4175 5336 7.646314 CCTTCCATGTAAGCATTGATTCTTAG 58.354 38.462 0.00 0.00 31.99 2.18
4186 5347 6.485984 AGCATTGATTCTTAGCTACTTCCATG 59.514 38.462 0.00 0.00 33.06 3.66
4200 5363 4.202441 ACTTCCATGATATTGCACTGGTC 58.798 43.478 0.00 0.00 0.00 4.02
4201 5364 3.929955 TCCATGATATTGCACTGGTCA 57.070 42.857 0.00 0.00 0.00 4.02
4218 5381 1.607148 GTCAGGGTTGGTTGCAACTAC 59.393 52.381 27.64 23.31 35.54 2.73
4232 5402 2.494870 GCAACTACTTACCCTCCTTCGA 59.505 50.000 0.00 0.00 0.00 3.71
4319 5489 1.741770 ACGGAAGCGCATGAACTCC 60.742 57.895 11.47 4.39 0.00 3.85
4382 5552 5.420725 ACATGGACTTTCTAGCACACATA 57.579 39.130 0.00 0.00 0.00 2.29
4448 5618 3.137360 AGAGGAAAGCAAGAGAACAGGTT 59.863 43.478 0.00 0.00 0.00 3.50
4449 5619 3.885901 GAGGAAAGCAAGAGAACAGGTTT 59.114 43.478 0.00 0.00 35.87 3.27
4451 5621 3.632145 GGAAAGCAAGAGAACAGGTTTCA 59.368 43.478 15.32 0.00 46.11 2.69
4452 5622 4.498177 GGAAAGCAAGAGAACAGGTTTCAC 60.498 45.833 15.32 4.65 46.11 3.18
4462 5632 2.456577 ACAGGTTTCACAACTGCCTTT 58.543 42.857 0.00 0.00 32.90 3.11
4465 5636 4.649218 ACAGGTTTCACAACTGCCTTTATT 59.351 37.500 0.00 0.00 32.90 1.40
4507 5680 7.223582 CACTCTGGTTATTCTACTAATGTGCAG 59.776 40.741 0.00 0.00 0.00 4.41
4511 5702 5.765182 GGTTATTCTACTAATGTGCAGCCAT 59.235 40.000 0.00 0.00 0.00 4.40
4543 5734 4.389992 AGTGACATGCAAACTAATGACTCG 59.610 41.667 0.00 0.00 0.00 4.18
4544 5735 4.152402 GTGACATGCAAACTAATGACTCGT 59.848 41.667 0.00 0.00 0.00 4.18
4545 5736 4.754618 TGACATGCAAACTAATGACTCGTT 59.245 37.500 0.00 0.00 0.00 3.85
4647 5841 8.993121 AGTGATATAAGCTTTATCATTTGTCCG 58.007 33.333 22.69 0.00 38.11 4.79
4650 5844 4.600012 AAGCTTTATCATTTGTCCGACG 57.400 40.909 0.00 0.00 0.00 5.12
4733 5927 4.576053 CACAGACCAACTTCATTCAGTTCA 59.424 41.667 0.00 0.00 34.60 3.18
4757 5951 0.823356 ACTCGGCATGCACCAAACTT 60.823 50.000 21.36 0.00 0.00 2.66
5031 6226 4.016444 TGCTGTGGTTTCTCTTTGTTTCT 58.984 39.130 0.00 0.00 0.00 2.52
5074 6270 3.244561 TGCCAGTTTCACCTAAGAAGAGG 60.245 47.826 0.00 0.00 42.89 3.69
5097 6293 6.774656 AGGTCTGTTTGATTTCAACATCTCTT 59.225 34.615 0.00 0.00 35.28 2.85
5099 6295 7.592903 GGTCTGTTTGATTTCAACATCTCTTTC 59.407 37.037 0.00 0.00 35.28 2.62
5100 6296 8.131100 GTCTGTTTGATTTCAACATCTCTTTCA 58.869 33.333 0.00 0.00 35.28 2.69
5102 6298 9.472361 CTGTTTGATTTCAACATCTCTTTCATT 57.528 29.630 0.00 0.00 35.28 2.57
5121 6320 9.837525 CTTTCATTTTTGGATCTTGAGTCTTAG 57.162 33.333 0.00 0.00 0.00 2.18
5122 6321 8.924511 TTCATTTTTGGATCTTGAGTCTTAGT 57.075 30.769 0.00 0.00 0.00 2.24
5128 6327 9.547753 TTTTGGATCTTGAGTCTTAGTATATGC 57.452 33.333 0.00 0.00 0.00 3.14
5130 6329 7.890515 TGGATCTTGAGTCTTAGTATATGCTG 58.109 38.462 3.24 0.00 0.00 4.41
5131 6330 7.507277 TGGATCTTGAGTCTTAGTATATGCTGT 59.493 37.037 3.24 0.00 0.00 4.40
5132 6331 8.364142 GGATCTTGAGTCTTAGTATATGCTGTT 58.636 37.037 3.24 0.00 0.00 3.16
5136 6335 9.469807 CTTGAGTCTTAGTATATGCTGTTAAGG 57.530 37.037 3.24 0.00 0.00 2.69
5137 6336 7.434492 TGAGTCTTAGTATATGCTGTTAAGGC 58.566 38.462 3.24 1.25 0.00 4.35
5141 6340 8.358148 GTCTTAGTATATGCTGTTAAGGCTGTA 58.642 37.037 3.24 0.00 0.00 2.74
5142 6341 8.920174 TCTTAGTATATGCTGTTAAGGCTGTAA 58.080 33.333 3.24 0.00 0.00 2.41
5143 6342 9.542462 CTTAGTATATGCTGTTAAGGCTGTAAA 57.458 33.333 3.24 0.00 0.00 2.01
5158 6357 3.853671 GCTGTAAATTTCATCGCTTGTGG 59.146 43.478 0.00 0.00 0.00 4.17
5159 6358 3.832276 TGTAAATTTCATCGCTTGTGGC 58.168 40.909 0.00 0.00 37.64 5.01
5222 6423 8.635765 ACAGAATCTAAAATTTGCTAACCTGA 57.364 30.769 12.01 0.00 0.00 3.86
5226 6427 9.943163 GAATCTAAAATTTGCTAACCTGATCTC 57.057 33.333 0.00 0.00 0.00 2.75
5227 6428 9.466497 AATCTAAAATTTGCTAACCTGATCTCA 57.534 29.630 0.00 0.00 0.00 3.27
5246 6447 6.968131 TCTCAAGAAATTATGTGTCCGAAG 57.032 37.500 0.00 0.00 0.00 3.79
5276 6500 8.582433 AATTTTAACCCATTTTACGTGAACAG 57.418 30.769 0.00 0.00 0.00 3.16
5287 6511 0.504384 CGTGAACAGAACAGAGCACG 59.496 55.000 0.00 0.00 42.17 5.34
5299 6523 0.749649 AGAGCACGCCCTCTAATCAG 59.250 55.000 3.81 0.00 40.30 2.90
5314 6554 5.828747 TCTAATCAGAGACGGAAAATACGG 58.171 41.667 0.00 0.00 35.23 4.02
5315 6555 2.288961 TCAGAGACGGAAAATACGGC 57.711 50.000 0.00 0.00 40.35 5.68
5316 6556 1.134907 TCAGAGACGGAAAATACGGCC 60.135 52.381 0.00 0.00 41.14 6.13
5317 6557 0.899720 AGAGACGGAAAATACGGCCA 59.100 50.000 2.24 0.00 41.14 5.36
5318 6558 1.004595 GAGACGGAAAATACGGCCAC 58.995 55.000 2.24 0.00 41.14 5.01
5319 6559 0.738412 AGACGGAAAATACGGCCACG 60.738 55.000 2.24 0.00 41.14 4.94
5320 6560 0.737019 GACGGAAAATACGGCCACGA 60.737 55.000 2.24 0.00 44.60 4.35
5321 6561 0.320596 ACGGAAAATACGGCCACGAA 60.321 50.000 2.24 0.00 44.60 3.85
5324 6564 2.159490 CGGAAAATACGGCCACGAATTT 60.159 45.455 2.24 0.00 44.60 1.82
5325 6565 3.431856 GGAAAATACGGCCACGAATTTC 58.568 45.455 2.24 6.52 44.60 2.17
5326 6566 2.817538 AAATACGGCCACGAATTTCG 57.182 45.000 16.84 16.84 46.93 3.46
5327 6567 1.011333 AATACGGCCACGAATTTCGG 58.989 50.000 21.71 11.09 45.59 4.30
5328 6568 0.812412 ATACGGCCACGAATTTCGGG 60.812 55.000 21.71 18.13 45.59 5.14
5339 6584 1.000843 GAATTTCGGGCAAGCACCTTT 59.999 47.619 0.00 0.00 0.00 3.11
5348 6593 2.273557 GCAAGCACCTTTGGCAATATG 58.726 47.619 0.00 0.96 0.00 1.78
5372 6618 6.919662 TGCACTTTTCTTTGACAAATCATCTC 59.080 34.615 0.05 0.00 33.85 2.75
5374 6620 7.655490 CACTTTTCTTTGACAAATCATCTCCT 58.345 34.615 0.05 0.00 33.85 3.69
5375 6621 7.806960 CACTTTTCTTTGACAAATCATCTCCTC 59.193 37.037 0.05 0.00 33.85 3.71
5376 6622 7.723172 ACTTTTCTTTGACAAATCATCTCCTCT 59.277 33.333 0.05 0.00 33.85 3.69
5414 6660 6.973229 ATTGCATCATTTACAAGAAAAGGC 57.027 33.333 0.00 0.00 0.00 4.35
5427 6673 6.189859 ACAAGAAAAGGCATTATCTCATCCA 58.810 36.000 0.00 0.00 0.00 3.41
5442 6688 0.689623 ATCCAGAGGCGAATCCATCC 59.310 55.000 0.00 0.00 37.29 3.51
5446 6692 1.139654 CAGAGGCGAATCCATCCAGAA 59.860 52.381 0.00 0.00 37.29 3.02
5447 6693 1.139853 AGAGGCGAATCCATCCAGAAC 59.860 52.381 0.00 0.00 37.29 3.01
5448 6694 0.911769 AGGCGAATCCATCCAGAACA 59.088 50.000 0.00 0.00 37.29 3.18
5449 6695 1.134280 AGGCGAATCCATCCAGAACAG 60.134 52.381 0.00 0.00 37.29 3.16
5450 6696 1.407437 GGCGAATCCATCCAGAACAGT 60.407 52.381 0.00 0.00 34.01 3.55
5451 6697 1.936547 GCGAATCCATCCAGAACAGTC 59.063 52.381 0.00 0.00 0.00 3.51
5452 6698 2.677902 GCGAATCCATCCAGAACAGTCA 60.678 50.000 0.00 0.00 0.00 3.41
5453 6699 3.801698 CGAATCCATCCAGAACAGTCAT 58.198 45.455 0.00 0.00 0.00 3.06
5454 6700 4.194640 CGAATCCATCCAGAACAGTCATT 58.805 43.478 0.00 0.00 0.00 2.57
5455 6701 4.034858 CGAATCCATCCAGAACAGTCATTG 59.965 45.833 0.00 0.00 0.00 2.82
5456 6702 4.849813 ATCCATCCAGAACAGTCATTGA 57.150 40.909 0.00 0.00 0.00 2.57
5458 6704 5.183530 TCCATCCAGAACAGTCATTGAAT 57.816 39.130 0.00 0.00 0.00 2.57
5459 6705 6.312141 TCCATCCAGAACAGTCATTGAATA 57.688 37.500 0.00 0.00 0.00 1.75
5461 6707 8.033178 TCCATCCAGAACAGTCATTGAATATA 57.967 34.615 0.00 0.00 0.00 0.86
5463 6709 7.094890 CCATCCAGAACAGTCATTGAATATAGC 60.095 40.741 0.00 0.00 0.00 2.97
5464 6710 6.888105 TCCAGAACAGTCATTGAATATAGCA 58.112 36.000 0.00 0.00 0.00 3.49
5466 6712 6.765036 CCAGAACAGTCATTGAATATAGCACT 59.235 38.462 0.00 0.00 0.00 4.40
5467 6713 7.042187 CCAGAACAGTCATTGAATATAGCACTC 60.042 40.741 0.00 0.00 0.00 3.51
5468 6714 6.699204 AGAACAGTCATTGAATATAGCACTCG 59.301 38.462 0.00 0.00 0.00 4.18
5469 6715 4.747108 ACAGTCATTGAATATAGCACTCGC 59.253 41.667 0.00 0.00 38.99 5.03
5473 6719 5.180117 GTCATTGAATATAGCACTCGCCATT 59.820 40.000 0.00 0.00 39.83 3.16
5474 6720 5.179929 TCATTGAATATAGCACTCGCCATTG 59.820 40.000 0.00 0.00 39.83 2.82
5476 6722 4.309933 TGAATATAGCACTCGCCATTGAG 58.690 43.478 0.00 0.00 41.86 3.02
5478 6724 0.467384 ATAGCACTCGCCATTGAGCT 59.533 50.000 0.00 0.00 39.68 4.09
5510 6773 5.474876 CCTTCCTTCAGAGCATTAACAACTT 59.525 40.000 0.00 0.00 0.00 2.66
5511 6774 6.348868 CCTTCCTTCAGAGCATTAACAACTTC 60.349 42.308 0.00 0.00 0.00 3.01
5512 6775 5.869579 TCCTTCAGAGCATTAACAACTTCT 58.130 37.500 0.00 0.00 0.00 2.85
5513 6776 6.299141 TCCTTCAGAGCATTAACAACTTCTT 58.701 36.000 0.00 0.00 0.00 2.52
5518 6781 7.587629 TCAGAGCATTAACAACTTCTTCATTG 58.412 34.615 0.00 0.00 0.00 2.82
5523 6786 6.346838 GCATTAACAACTTCTTCATTGTTGGC 60.347 38.462 11.56 8.98 46.01 4.52
5546 6809 4.201753 CGACAACCTCAATCTTGCTACATG 60.202 45.833 0.00 0.00 0.00 3.21
5576 6839 7.266400 TGTTTGTGGTAAGTTTAACCCAAATC 58.734 34.615 11.44 8.18 38.38 2.17
5583 6848 6.015772 GGTAAGTTTAACCCAAATCTCAGCAA 60.016 38.462 0.00 0.00 0.00 3.91
5618 6883 6.647895 CAGAAAATGAGCCATAGCAAAAGTTT 59.352 34.615 0.00 0.00 43.56 2.66
5619 6884 6.647895 AGAAAATGAGCCATAGCAAAAGTTTG 59.352 34.615 0.00 0.00 43.56 2.93
5637 6902 0.319083 TGGCCTTTCATTTGCTGCAG 59.681 50.000 10.11 10.11 0.00 4.41
5644 6909 4.381185 CCTTTCATTTGCTGCAGCTATGAA 60.381 41.667 37.67 37.67 43.67 2.57
5650 6915 2.097036 TGCTGCAGCTATGAATTTGCT 58.903 42.857 36.61 0.00 42.66 3.91
5671 6936 9.740239 TTTGCTATTATCATCTTGAAGAATTGC 57.260 29.630 0.00 1.39 36.30 3.56
5677 6942 5.988310 TCATCTTGAAGAATTGCACCAAT 57.012 34.783 0.00 0.00 35.39 3.16
5680 6945 2.634982 TGAAGAATTGCACCAATCGC 57.365 45.000 0.00 0.00 32.43 4.58
5700 6965 3.314357 CGCACCATTCAGATTGTCATGAT 59.686 43.478 0.00 0.00 0.00 2.45
5701 6966 4.554134 CGCACCATTCAGATTGTCATGATC 60.554 45.833 0.00 0.00 0.00 2.92
5711 6976 5.047872 CAGATTGTCATGATCAAACCCAACA 60.048 40.000 0.00 0.00 0.00 3.33
5720 6985 7.396907 TCATGATCAAACCCAACATCTACATTT 59.603 33.333 0.00 0.00 0.00 2.32
5737 7002 7.214381 TCTACATTTAGTTTCATGTATCCCGG 58.786 38.462 0.00 0.00 35.73 5.73
5756 7021 4.176752 CGGGGCCTAGACCAAGCC 62.177 72.222 0.84 0.00 46.37 4.35
5771 7036 2.123409 AGCCATCGCTCTCCTCTTC 58.877 57.895 0.00 0.00 43.95 2.87
5774 7039 1.299773 CATCGCTCTCCTCTTCGCC 60.300 63.158 0.00 0.00 0.00 5.54
5792 7057 0.179094 CCTTGGGCTTACACGCGATA 60.179 55.000 15.93 1.01 0.00 2.92
5802 7067 2.848562 ACACGCGATAACAAAGTTCG 57.151 45.000 15.93 0.00 36.02 3.95
5815 7080 2.202756 GTTCGCTGCTAGTCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
5817 7082 3.001902 TTCGCTGCTAGTCCCCGTG 62.002 63.158 0.00 0.00 0.00 4.94
5818 7083 3.760035 CGCTGCTAGTCCCCGTGT 61.760 66.667 0.00 0.00 0.00 4.49
5824 7089 1.079127 CTAGTCCCCGTGTTGCCAG 60.079 63.158 0.00 0.00 0.00 4.85
5827 7092 2.203280 TCCCCGTGTTGCCAGTTG 60.203 61.111 0.00 0.00 0.00 3.16
5833 7098 1.533756 CCGTGTTGCCAGTTGAACTTG 60.534 52.381 0.00 0.00 0.00 3.16
5860 7125 5.904941 TGCAGTTTGTGTTTTCTCATCATT 58.095 33.333 0.00 0.00 0.00 2.57
5861 7126 6.339730 TGCAGTTTGTGTTTTCTCATCATTT 58.660 32.000 0.00 0.00 0.00 2.32
5862 7127 6.476380 TGCAGTTTGTGTTTTCTCATCATTTC 59.524 34.615 0.00 0.00 0.00 2.17
5863 7128 6.476380 GCAGTTTGTGTTTTCTCATCATTTCA 59.524 34.615 0.00 0.00 0.00 2.69
5864 7129 7.170320 GCAGTTTGTGTTTTCTCATCATTTCAT 59.830 33.333 0.00 0.00 0.00 2.57
5878 7143 8.408043 TCATCATTTCATGTGTTAGTTTCCTT 57.592 30.769 0.00 0.00 0.00 3.36
5883 7148 6.687081 TTCATGTGTTAGTTTCCTTCGTTT 57.313 33.333 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.512130 TGATCTGATCCTGCTTAATACAACAT 58.488 34.615 14.71 0.00 0.00 2.71
1 2 6.888105 TGATCTGATCCTGCTTAATACAACA 58.112 36.000 14.71 0.00 0.00 3.33
2 3 6.073331 GCTGATCTGATCCTGCTTAATACAAC 60.073 42.308 14.71 0.00 0.00 3.32
4 5 5.512060 GGCTGATCTGATCCTGCTTAATACA 60.512 44.000 22.67 1.50 0.00 2.29
5 6 4.934602 GGCTGATCTGATCCTGCTTAATAC 59.065 45.833 22.67 9.21 0.00 1.89
6 7 4.322273 CGGCTGATCTGATCCTGCTTAATA 60.322 45.833 22.67 1.96 0.00 0.98
7 8 3.556633 CGGCTGATCTGATCCTGCTTAAT 60.557 47.826 22.67 0.00 0.00 1.40
10 11 0.106335 CGGCTGATCTGATCCTGCTT 59.894 55.000 22.67 0.00 0.00 3.91
11 12 1.047596 ACGGCTGATCTGATCCTGCT 61.048 55.000 22.67 9.33 0.00 4.24
12 13 0.599728 GACGGCTGATCTGATCCTGC 60.600 60.000 14.71 16.84 0.00 4.85
13 14 1.000385 GAGACGGCTGATCTGATCCTG 60.000 57.143 14.71 7.96 0.00 3.86
14 15 1.133513 AGAGACGGCTGATCTGATCCT 60.134 52.381 14.71 3.64 0.00 3.24
15 16 1.327303 AGAGACGGCTGATCTGATCC 58.673 55.000 14.71 0.00 0.00 3.36
16 17 3.407698 TCTAGAGACGGCTGATCTGATC 58.592 50.000 10.72 10.72 0.00 2.92
17 18 3.411446 CTCTAGAGACGGCTGATCTGAT 58.589 50.000 15.05 0.00 0.00 2.90
18 19 2.844946 CTCTAGAGACGGCTGATCTGA 58.155 52.381 15.05 8.76 0.00 3.27
19 20 1.266718 GCTCTAGAGACGGCTGATCTG 59.733 57.143 24.24 0.00 0.00 2.90
20 21 1.604604 GCTCTAGAGACGGCTGATCT 58.395 55.000 24.24 4.83 0.00 2.75
21 22 0.596082 GGCTCTAGAGACGGCTGATC 59.404 60.000 24.24 1.86 0.00 2.92
34 35 0.767375 GGCAGGATCCAATGGCTCTA 59.233 55.000 15.82 0.00 38.83 2.43
41 42 0.399091 TCTCTCGGGCAGGATCCAAT 60.399 55.000 15.82 0.00 0.00 3.16
50 51 1.004560 CAAGCAACTCTCTCGGGCA 60.005 57.895 0.00 0.00 0.00 5.36
53 54 1.005340 GATGCAAGCAACTCTCTCGG 58.995 55.000 0.00 0.00 0.00 4.63
142 147 3.211564 CTGCAAACCCCAAGCGTGG 62.212 63.158 12.27 12.27 45.53 4.94
143 148 2.015227 AACTGCAAACCCCAAGCGTG 62.015 55.000 0.00 0.00 0.00 5.34
144 149 1.756561 AACTGCAAACCCCAAGCGT 60.757 52.632 0.00 0.00 0.00 5.07
146 151 0.249447 GTCAACTGCAAACCCCAAGC 60.249 55.000 0.00 0.00 0.00 4.01
180 189 2.056577 GGTCGAGGAGTGTTTGTAACG 58.943 52.381 0.00 0.00 0.00 3.18
215 224 2.919229 GACAGGTTGTGTTACGTATCGG 59.081 50.000 0.00 0.00 40.56 4.18
218 227 3.829948 CGAGACAGGTTGTGTTACGTAT 58.170 45.455 0.00 0.00 40.56 3.06
234 243 0.448593 AAGACTGTCTAGCGCGAGAC 59.551 55.000 34.96 34.96 45.19 3.36
239 248 3.378552 CGCAAGACTGTCTAGCGC 58.621 61.111 11.30 12.79 41.95 5.92
256 265 4.793216 CGCTTTTATAACATGGCTTGTGTC 59.207 41.667 6.80 0.00 38.99 3.67
263 272 2.108700 CGTGCGCTTTTATAACATGGC 58.891 47.619 9.73 0.00 0.00 4.40
267 276 3.061322 ACTCACGTGCGCTTTTATAACA 58.939 40.909 11.67 0.00 0.00 2.41
272 281 1.790755 ATCACTCACGTGCGCTTTTA 58.209 45.000 11.67 0.00 40.99 1.52
290 299 3.807622 CCGTCCGAACAGCAATACAATAT 59.192 43.478 0.00 0.00 0.00 1.28
293 302 1.270412 ACCGTCCGAACAGCAATACAA 60.270 47.619 0.00 0.00 0.00 2.41
294 303 0.319083 ACCGTCCGAACAGCAATACA 59.681 50.000 0.00 0.00 0.00 2.29
295 304 0.997196 GACCGTCCGAACAGCAATAC 59.003 55.000 0.00 0.00 0.00 1.89
296 305 0.457166 CGACCGTCCGAACAGCAATA 60.457 55.000 0.00 0.00 0.00 1.90
297 306 1.736645 CGACCGTCCGAACAGCAAT 60.737 57.895 0.00 0.00 0.00 3.56
331 362 2.690778 GCATGGGAACTCGGTGTGC 61.691 63.158 0.00 0.00 0.00 4.57
338 369 4.016444 TGACCAATAAAGCATGGGAACTC 58.984 43.478 0.00 0.00 41.17 3.01
356 388 6.595716 AGTGTTACTAAAGCATCAAGATGACC 59.404 38.462 13.93 0.00 41.20 4.02
361 393 6.109156 TGGAGTGTTACTAAAGCATCAAGA 57.891 37.500 0.00 0.00 0.00 3.02
481 1511 0.534877 ATGGTTTGTGAGACGCTGCA 60.535 50.000 0.00 0.00 0.00 4.41
509 1539 2.133553 TCGATTGTTTTTCGTGGCGTA 58.866 42.857 0.00 0.00 37.82 4.42
523 1554 6.020984 TGATATTTGTGCTTCGTTTCGATTG 58.979 36.000 0.00 0.00 35.23 2.67
557 1588 4.449229 GGAGGAAATGGTGGGGCTTATATT 60.449 45.833 0.00 0.00 0.00 1.28
558 1589 3.076032 GGAGGAAATGGTGGGGCTTATAT 59.924 47.826 0.00 0.00 0.00 0.86
782 1847 3.009033 CACTGTCATTGGGTAGGAGGAAA 59.991 47.826 0.00 0.00 0.00 3.13
953 2020 1.519455 GCGATACAGCGAGGCAGTT 60.519 57.895 0.00 0.00 29.63 3.16
1555 2631 1.600023 CCACAACAACCCACGTACAT 58.400 50.000 0.00 0.00 0.00 2.29
1586 2662 1.510844 GATCCGCACCCGCAAAATT 59.489 52.632 0.00 0.00 38.40 1.82
1643 2719 3.260740 CCAACGACGAGACTACTACTCT 58.739 50.000 0.00 0.00 32.87 3.24
1719 2795 7.285401 ACAAATGAACAATTAGTGAACCAGTCT 59.715 33.333 0.00 0.00 0.00 3.24
1792 2886 7.655328 CCAAATGGAGATAGAAGTGATCACTAC 59.345 40.741 28.10 16.15 37.88 2.73
1832 2926 4.022068 ACAACAACACTAGCATTTCCATGG 60.022 41.667 4.97 4.97 0.00 3.66
1923 3017 6.752351 ACATCGACATCACTTTGTCTGTATAC 59.248 38.462 0.00 0.00 43.10 1.47
1940 3034 4.765339 TCTAGTTTCCAAGAGACATCGACA 59.235 41.667 0.00 0.00 0.00 4.35
1942 3036 5.010933 ACTCTAGTTTCCAAGAGACATCGA 58.989 41.667 6.36 0.00 41.51 3.59
1974 3069 2.554032 CTCAAGGAGTTTTCGCACCATT 59.446 45.455 0.00 0.00 0.00 3.16
2056 3151 7.568349 TCATTATTGTAGTTCATCAAGCTCCT 58.432 34.615 0.00 0.00 0.00 3.69
2226 3321 7.475015 TCAAATCTAGTAAATGATGCAACTGC 58.525 34.615 0.00 0.00 42.50 4.40
2430 3525 7.942341 ACCAAATAACTAACAGTCAAGGATGAA 59.058 33.333 0.00 0.00 37.30 2.57
2772 3875 3.261643 ACATGTGACAGTAAGGCATGAGA 59.738 43.478 0.00 0.00 37.77 3.27
2776 3879 4.883585 CCATAACATGTGACAGTAAGGCAT 59.116 41.667 0.00 0.00 37.77 4.40
2788 3891 6.972722 TGTCATATTGATGCCATAACATGTG 58.027 36.000 0.00 0.00 32.62 3.21
2855 3958 5.005740 ACAGCAGCAACATTCTGAATAGAA 58.994 37.500 1.98 0.00 46.32 2.10
3098 4217 2.825532 TGCCCAACTTCATAAAAGAGGC 59.174 45.455 0.00 0.00 0.00 4.70
3432 4552 7.066284 CCATATGTCCTTCTTTCTTCGACAAAT 59.934 37.037 1.24 0.00 37.05 2.32
3444 4564 4.273318 GGAAACTGCCATATGTCCTTCTT 58.727 43.478 1.24 0.00 0.00 2.52
3445 4565 3.372025 GGGAAACTGCCATATGTCCTTCT 60.372 47.826 1.24 0.00 0.00 2.85
3446 4566 2.952310 GGGAAACTGCCATATGTCCTTC 59.048 50.000 1.24 0.00 0.00 3.46
3497 4617 6.472163 CCCAAACATGCTATTACGAAACAATC 59.528 38.462 0.00 0.00 0.00 2.67
3706 4853 7.524912 CATCGAGAAAATCAGAGACACAAATT 58.475 34.615 0.00 0.00 0.00 1.82
3954 5102 3.566523 GAGTGAACAAGACAGTACCTCG 58.433 50.000 0.00 0.00 0.00 4.63
3979 5127 2.751166 ATTCCAGAGGACAACACTCG 57.249 50.000 0.00 0.00 39.90 4.18
4024 5185 0.376152 GCATGTCAGAACCTCGCATG 59.624 55.000 0.00 0.00 39.68 4.06
4029 5190 3.165058 TCGTATGCATGTCAGAACCTC 57.835 47.619 10.16 0.00 0.00 3.85
4031 5192 4.808895 TGTAATCGTATGCATGTCAGAACC 59.191 41.667 10.16 0.00 0.00 3.62
4047 5208 5.617973 CGATGTACCTCTCATCCTGTAATCG 60.618 48.000 0.00 0.00 38.60 3.34
4118 5279 4.521639 AGAATGTCATCTTGCTTTGCTTGA 59.478 37.500 0.00 0.00 0.00 3.02
4175 5336 4.214971 CCAGTGCAATATCATGGAAGTAGC 59.785 45.833 0.00 0.00 32.55 3.58
4186 5347 2.684881 CAACCCTGACCAGTGCAATATC 59.315 50.000 0.00 0.00 0.00 1.63
4218 5381 1.271656 ACACGTTCGAAGGAGGGTAAG 59.728 52.381 23.56 7.17 0.00 2.34
4319 5489 1.414158 AGTGGTATGACCCCTGATCG 58.586 55.000 0.00 0.00 37.50 3.69
4448 5618 7.517614 TGTTGATAATAAAGGCAGTTGTGAA 57.482 32.000 0.00 0.00 0.00 3.18
4449 5619 7.701539 ATGTTGATAATAAAGGCAGTTGTGA 57.298 32.000 0.00 0.00 0.00 3.58
4452 5622 8.971321 GCATAATGTTGATAATAAAGGCAGTTG 58.029 33.333 0.00 0.00 0.00 3.16
4462 5632 7.879677 CCAGAGTGAGGCATAATGTTGATAATA 59.120 37.037 0.00 0.00 0.00 0.98
4465 5636 5.130975 ACCAGAGTGAGGCATAATGTTGATA 59.869 40.000 0.00 0.00 0.00 2.15
4507 5680 3.304257 GCATGTCACTGCAGTAATATGGC 60.304 47.826 23.63 17.30 41.87 4.40
4550 5741 2.713167 AGACATTATCCATCCCTGTGGG 59.287 50.000 0.00 0.00 46.11 4.61
4551 5742 3.392285 TCAGACATTATCCATCCCTGTGG 59.608 47.826 0.00 0.00 40.76 4.17
4633 5827 3.613494 TCCCGTCGGACAAATGATAAA 57.387 42.857 14.39 0.00 31.13 1.40
4647 5841 9.706691 TGTATGAAAGAAATATCTTATCCCGTC 57.293 33.333 0.00 0.00 45.19 4.79
4733 5927 0.036164 TGGTGCATGCCGAGTACTTT 59.964 50.000 16.68 0.00 0.00 2.66
4757 5951 5.728937 ACTATCCCTACTAGTCTCACCAA 57.271 43.478 0.00 0.00 0.00 3.67
4790 5984 6.072175 GCTCTATAGAGTTGAGATGGTACCAG 60.072 46.154 26.73 1.10 43.85 4.00
4876 6070 2.430694 ACCAGACGCATATACAAGAGCA 59.569 45.455 0.00 0.00 0.00 4.26
5031 6226 2.983907 TTACAACAACCGGAGTCACA 57.016 45.000 9.46 0.00 0.00 3.58
5074 6270 8.131100 TGAAAGAGATGTTGAAATCAAACAGAC 58.869 33.333 0.00 0.00 37.63 3.51
5097 6293 8.924511 ACTAAGACTCAAGATCCAAAAATGAA 57.075 30.769 0.00 0.00 0.00 2.57
5102 6298 9.547753 GCATATACTAAGACTCAAGATCCAAAA 57.452 33.333 0.00 0.00 0.00 2.44
5121 6320 9.665264 GAAATTTACAGCCTTAACAGCATATAC 57.335 33.333 0.00 0.00 0.00 1.47
5122 6321 9.402320 TGAAATTTACAGCCTTAACAGCATATA 57.598 29.630 0.00 0.00 0.00 0.86
5123 6322 8.292444 TGAAATTTACAGCCTTAACAGCATAT 57.708 30.769 0.00 0.00 0.00 1.78
5124 6323 7.695480 TGAAATTTACAGCCTTAACAGCATA 57.305 32.000 0.00 0.00 0.00 3.14
5125 6324 6.588719 TGAAATTTACAGCCTTAACAGCAT 57.411 33.333 0.00 0.00 0.00 3.79
5128 6327 5.739161 GCGATGAAATTTACAGCCTTAACAG 59.261 40.000 0.00 0.00 0.00 3.16
5130 6329 5.880341 AGCGATGAAATTTACAGCCTTAAC 58.120 37.500 0.00 0.00 0.00 2.01
5131 6330 6.072175 ACAAGCGATGAAATTTACAGCCTTAA 60.072 34.615 0.00 0.00 0.00 1.85
5132 6331 5.414454 ACAAGCGATGAAATTTACAGCCTTA 59.586 36.000 0.00 0.00 0.00 2.69
5133 6332 4.218417 ACAAGCGATGAAATTTACAGCCTT 59.782 37.500 0.00 0.00 0.00 4.35
5134 6333 3.758554 ACAAGCGATGAAATTTACAGCCT 59.241 39.130 0.00 0.00 0.00 4.58
5136 6335 3.853671 CCACAAGCGATGAAATTTACAGC 59.146 43.478 0.00 0.00 0.00 4.40
5137 6336 3.853671 GCCACAAGCGATGAAATTTACAG 59.146 43.478 0.00 0.00 0.00 2.74
5159 6358 1.079543 CCTGCTGTTCGAGGTCCAG 60.080 63.158 0.00 0.00 0.00 3.86
5222 6423 6.540189 CCTTCGGACACATAATTTCTTGAGAT 59.460 38.462 0.00 0.00 0.00 2.75
5246 6447 8.513774 TCACGTAAAATGGGTTAAAATTAGTCC 58.486 33.333 0.00 0.00 0.00 3.85
5259 6460 4.513692 TCTGTTCTGTTCACGTAAAATGGG 59.486 41.667 0.00 0.00 0.00 4.00
5276 6500 0.246635 TTAGAGGGCGTGCTCTGTTC 59.753 55.000 0.00 0.00 0.00 3.18
5299 6523 1.004595 GTGGCCGTATTTTCCGTCTC 58.995 55.000 0.00 0.00 0.00 3.36
5304 6544 3.431856 GAAATTCGTGGCCGTATTTTCC 58.568 45.455 0.00 1.53 41.95 3.13
5315 6555 1.154035 GCTTGCCCGAAATTCGTGG 60.154 57.895 14.58 15.02 38.40 4.94
5316 6556 0.729140 GTGCTTGCCCGAAATTCGTG 60.729 55.000 14.58 3.85 38.40 4.35
5317 6557 1.579429 GTGCTTGCCCGAAATTCGT 59.421 52.632 14.58 0.00 38.40 3.85
5318 6558 1.154035 GGTGCTTGCCCGAAATTCG 60.154 57.895 8.62 8.62 40.07 3.34
5319 6559 0.603065 AAGGTGCTTGCCCGAAATTC 59.397 50.000 0.00 0.00 0.00 2.17
5320 6560 1.047801 AAAGGTGCTTGCCCGAAATT 58.952 45.000 0.00 0.00 0.00 1.82
5321 6561 0.318120 CAAAGGTGCTTGCCCGAAAT 59.682 50.000 0.00 0.00 0.00 2.17
5324 6564 2.597217 CCAAAGGTGCTTGCCCGA 60.597 61.111 0.00 0.00 0.00 5.14
5325 6565 4.362476 GCCAAAGGTGCTTGCCCG 62.362 66.667 0.00 0.00 0.00 6.13
5326 6566 2.115734 ATTGCCAAAGGTGCTTGCCC 62.116 55.000 0.00 0.00 0.00 5.36
5327 6567 0.607620 TATTGCCAAAGGTGCTTGCC 59.392 50.000 0.00 0.00 0.00 4.52
5328 6568 2.273557 CATATTGCCAAAGGTGCTTGC 58.726 47.619 0.00 0.00 0.00 4.01
5339 6584 5.221402 TGTCAAAGAAAAGTGCATATTGCCA 60.221 36.000 0.00 0.00 44.23 4.92
5343 6588 9.715121 ATGATTTGTCAAAGAAAAGTGCATATT 57.285 25.926 4.03 0.00 0.00 1.28
5348 6593 6.364435 GGAGATGATTTGTCAAAGAAAAGTGC 59.636 38.462 4.03 0.00 0.00 4.40
5352 6597 8.469309 AAGAGGAGATGATTTGTCAAAGAAAA 57.531 30.769 4.03 0.00 0.00 2.29
5355 6600 9.745018 ATAAAAGAGGAGATGATTTGTCAAAGA 57.255 29.630 4.03 0.00 0.00 2.52
5372 6618 8.712285 ATGCAATTGTGATTGAATAAAAGAGG 57.288 30.769 7.40 0.00 44.37 3.69
5374 6620 9.878667 ATGATGCAATTGTGATTGAATAAAAGA 57.121 25.926 7.40 0.00 40.85 2.52
5414 6660 3.949842 TCGCCTCTGGATGAGATAATG 57.050 47.619 0.00 0.00 45.39 1.90
5427 6673 1.139853 GTTCTGGATGGATTCGCCTCT 59.860 52.381 0.00 0.00 37.63 3.69
5442 6688 7.306457 CGAGTGCTATATTCAATGACTGTTCTG 60.306 40.741 0.00 0.00 0.00 3.02
5446 6692 4.747108 GCGAGTGCTATATTCAATGACTGT 59.253 41.667 0.00 0.00 38.39 3.55
5447 6693 4.151335 GGCGAGTGCTATATTCAATGACTG 59.849 45.833 0.00 0.00 42.25 3.51
5448 6694 4.202253 TGGCGAGTGCTATATTCAATGACT 60.202 41.667 0.00 0.00 42.25 3.41
5449 6695 4.058124 TGGCGAGTGCTATATTCAATGAC 58.942 43.478 0.00 0.00 42.25 3.06
5450 6696 4.335400 TGGCGAGTGCTATATTCAATGA 57.665 40.909 0.00 0.00 42.25 2.57
5451 6697 5.179929 TCAATGGCGAGTGCTATATTCAATG 59.820 40.000 0.00 0.00 42.05 2.82
5452 6698 5.308014 TCAATGGCGAGTGCTATATTCAAT 58.692 37.500 0.00 0.00 42.05 2.57
5453 6699 4.702831 TCAATGGCGAGTGCTATATTCAA 58.297 39.130 0.00 0.00 42.05 2.69
5454 6700 4.309933 CTCAATGGCGAGTGCTATATTCA 58.690 43.478 0.00 0.00 42.05 2.57
5455 6701 3.124297 GCTCAATGGCGAGTGCTATATTC 59.876 47.826 0.00 0.00 42.05 1.75
5456 6702 3.070018 GCTCAATGGCGAGTGCTATATT 58.930 45.455 0.00 0.00 42.05 1.28
5458 6704 1.688735 AGCTCAATGGCGAGTGCTATA 59.311 47.619 0.00 0.00 42.05 1.31
5459 6705 0.467384 AGCTCAATGGCGAGTGCTAT 59.533 50.000 0.00 0.00 45.18 2.97
5461 6707 1.744368 CAGCTCAATGGCGAGTGCT 60.744 57.895 0.00 0.00 42.25 4.40
5463 6709 1.078918 TCCAGCTCAATGGCGAGTG 60.079 57.895 0.00 0.00 40.41 3.51
5464 6710 1.220206 CTCCAGCTCAATGGCGAGT 59.780 57.895 0.00 0.00 40.41 4.18
5466 6712 0.107993 CTTCTCCAGCTCAATGGCGA 60.108 55.000 0.00 0.00 40.41 5.54
5467 6713 1.712977 GCTTCTCCAGCTCAATGGCG 61.713 60.000 0.00 0.00 46.27 5.69
5468 6714 2.105124 GCTTCTCCAGCTCAATGGC 58.895 57.895 0.00 0.00 46.27 4.40
5478 6724 1.905215 CTCTGAAGGAAGGCTTCTCCA 59.095 52.381 25.25 18.20 37.29 3.86
5520 6783 1.522668 CAAGATTGAGGTTGTCGCCA 58.477 50.000 0.00 0.00 0.00 5.69
5523 6786 3.325870 TGTAGCAAGATTGAGGTTGTCG 58.674 45.455 0.00 0.00 0.00 4.35
5559 6822 6.569179 TGCTGAGATTTGGGTTAAACTTAC 57.431 37.500 0.00 0.00 0.00 2.34
5590 6855 4.155063 TGCTATGGCTCATTTTCTGCTA 57.845 40.909 1.68 0.00 39.59 3.49
5604 6869 3.683365 AAGGCCAAACTTTTGCTATGG 57.317 42.857 5.01 0.00 36.86 2.74
5618 6883 0.319083 CTGCAGCAAATGAAAGGCCA 59.681 50.000 5.01 0.00 0.00 5.36
5619 6884 1.017701 GCTGCAGCAAATGAAAGGCC 61.018 55.000 33.36 0.00 41.59 5.19
5621 6886 3.129813 TCATAGCTGCAGCAAATGAAAGG 59.870 43.478 35.61 20.61 45.16 3.11
5650 6915 8.750515 TGGTGCAATTCTTCAAGATGATAATA 57.249 30.769 0.00 0.00 0.00 0.98
5663 6928 1.067635 GGTGCGATTGGTGCAATTCTT 60.068 47.619 0.00 0.00 45.23 2.52
5671 6936 1.452110 TCTGAATGGTGCGATTGGTG 58.548 50.000 0.00 0.00 0.00 4.17
5677 6942 2.470983 TGACAATCTGAATGGTGCGA 57.529 45.000 0.00 0.00 0.00 5.10
5680 6945 6.445357 TTGATCATGACAATCTGAATGGTG 57.555 37.500 0.00 0.00 0.00 4.17
5700 6965 8.472007 AAACTAAATGTAGATGTTGGGTTTGA 57.528 30.769 0.00 0.00 0.00 2.69
5701 6966 8.356657 TGAAACTAAATGTAGATGTTGGGTTTG 58.643 33.333 0.00 0.00 0.00 2.93
5711 6976 7.878127 CCGGGATACATGAAACTAAATGTAGAT 59.122 37.037 0.00 0.00 41.31 1.98
5720 6985 1.069513 CGGCCGGGATACATGAAACTA 59.930 52.381 20.10 0.00 39.74 2.24
5737 7002 4.176752 CTTGGTCTAGGCCCCGGC 62.177 72.222 11.80 0.00 41.06 6.13
5756 7021 1.299773 GGCGAAGAGGAGAGCGATG 60.300 63.158 0.00 0.00 0.00 3.84
5774 7039 1.326548 GTTATCGCGTGTAAGCCCAAG 59.673 52.381 5.77 0.00 0.00 3.61
5792 7057 2.143925 GGACTAGCAGCGAACTTTGTT 58.856 47.619 0.00 0.00 0.00 2.83
5802 7067 1.741770 CAACACGGGGACTAGCAGC 60.742 63.158 0.00 0.00 0.00 5.25
5815 7080 1.202405 CCCAAGTTCAACTGGCAACAC 60.202 52.381 0.00 0.00 46.17 3.32
5817 7082 0.249447 GCCCAAGTTCAACTGGCAAC 60.249 55.000 12.96 0.00 37.28 4.17
5818 7083 0.396974 AGCCCAAGTTCAACTGGCAA 60.397 50.000 18.64 0.00 39.12 4.52
5824 7089 0.746659 AACTGCAGCCCAAGTTCAAC 59.253 50.000 15.27 0.00 0.00 3.18
5827 7092 0.746659 ACAAACTGCAGCCCAAGTTC 59.253 50.000 15.27 0.00 0.00 3.01
5833 7098 1.136891 AGAAAACACAAACTGCAGCCC 59.863 47.619 15.27 0.00 0.00 5.19
5860 7125 6.316640 TCAAACGAAGGAAACTAACACATGAA 59.683 34.615 0.00 0.00 42.68 2.57
5861 7126 5.818336 TCAAACGAAGGAAACTAACACATGA 59.182 36.000 0.00 0.00 42.68 3.07
5862 7127 6.055231 TCAAACGAAGGAAACTAACACATG 57.945 37.500 0.00 0.00 42.68 3.21
5863 7128 6.459161 GGTTCAAACGAAGGAAACTAACACAT 60.459 38.462 0.00 0.00 42.68 3.21
5864 7129 5.163733 GGTTCAAACGAAGGAAACTAACACA 60.164 40.000 0.00 0.00 42.68 3.72


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

AutoCloner maintained by Alex Coulton.