Multiple sequence alignment - TraesCS1A01G217400

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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 TraesCS1A01G217400 chr1A 100.000 2996 0 0 4447 7442 385356475 385353480 0.000000e+00 5533
1 TraesCS1A01G217400 chr1A 100.000 2194 0 0 2041 4234 385358881 385356688 0.000000e+00 4052
2 TraesCS1A01G217400 chr1A 100.000 1778 0 0 1 1778 385360921 385359144 0.000000e+00 3284
3 TraesCS1A01G217400 chr1B 97.999 2199 33 7 2041 4234 414166347 414164155 0.000000e+00 3807
4 TraesCS1A01G217400 chr1B 94.576 2286 86 7 4484 6742 414163854 414161580 0.000000e+00 3500
5 TraesCS1A01G217400 chr1B 93.245 1288 55 11 506 1778 414167966 414166696 0.000000e+00 1868
6 TraesCS1A01G217400 chr1B 90.000 290 16 2 7051 7339 414161278 414161001 5.490000e-96 363
7 TraesCS1A01G217400 chr1B 88.889 288 27 3 6783 7065 414161583 414161296 4.270000e-92 350
8 TraesCS1A01G217400 chr1D 97.090 2199 41 7 2041 4234 306676749 306674569 0.000000e+00 3685
9 TraesCS1A01G217400 chr1D 95.833 1200 42 8 579 1778 306678283 306677092 0.000000e+00 1932
10 TraesCS1A01G217400 chr1D 92.390 1222 56 9 4447 5637 306674517 306673302 0.000000e+00 1707
11 TraesCS1A01G217400 chr1D 95.950 1037 28 6 5614 6640 306673281 306672249 0.000000e+00 1670
12 TraesCS1A01G217400 chr1D 85.316 681 69 18 6640 7315 306672015 306671361 0.000000e+00 675
13 TraesCS1A01G217400 chr1D 86.053 337 44 3 174 509 306679152 306678818 7.100000e-95 359
14 TraesCS1A01G217400 chr7D 96.135 207 8 0 1045 1251 119222411 119222205 9.250000e-89 339
15 TraesCS1A01G217400 chr5B 97.541 122 3 0 1 122 101250236 101250357 7.570000e-50 209
16 TraesCS1A01G217400 chr5B 97.500 120 3 0 1 120 101252918 101253037 9.790000e-49 206
17 TraesCS1A01G217400 chr5B 93.893 131 7 1 1 130 53018358 53018228 5.890000e-46 196
18 TraesCS1A01G217400 chr7B 97.500 120 3 0 1 120 624722618 624722737 9.790000e-49 206
19 TraesCS1A01G217400 chr6B 96.721 122 4 0 1 122 462629124 462629245 3.520000e-48 204
20 TraesCS1A01G217400 chr4B 96.721 122 4 0 1 122 672949026 672948905 3.520000e-48 204
21 TraesCS1A01G217400 chr4B 78.333 180 39 0 328 507 3686671 3686492 4.720000e-22 117
22 TraesCS1A01G217400 chr3B 96.721 122 4 0 1 122 763638221 763638100 3.520000e-48 204
23 TraesCS1A01G217400 chr2B 94.615 130 6 1 1 130 9711662 9711790 4.550000e-47 200
24 TraesCS1A01G217400 chr5D 94.531 128 7 0 1 128 531451239 531451112 1.640000e-46 198


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 TraesCS1A01G217400 chr1A 385353480 385360921 7441 True 4289.666667 5533 100.000000 1 7442 3 chr1A.!!$R1 7441
1 TraesCS1A01G217400 chr1B 414161001 414167966 6965 True 1977.600000 3807 92.941800 506 7339 5 chr1B.!!$R1 6833
2 TraesCS1A01G217400 chr1D 306671361 306679152 7791 True 1671.333333 3685 92.105333 174 7315 6 chr1D.!!$R1 7141
3 TraesCS1A01G217400 chr5B 101250236 101253037 2801 False 207.500000 209 97.520500 1 122 2 chr5B.!!$F1 121

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
965 1438 0.399233 CCTTCCTCCTCCGGATCCTT 60.399 60.0 3.57 0.00 32.02 3.36 F
1733 2212 0.508641 CCGAGCGAAGTTCAGTTGTG 59.491 55.0 3.32 0.00 37.72 3.33 F
3370 4173 0.109913 TATAGGGCTCGGAGAAGCGA 59.890 55.0 9.69 0.00 34.09 4.93 F
4603 6264 0.376152 CCATGCTACAGCGCTTTGAG 59.624 55.0 7.50 6.37 45.83 3.02 F
6333 8960 0.313672 TGTCGCATGAGTTTTTGGCC 59.686 50.0 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2565 3363 0.473755 TTGGTCAGGCATCACACTGT 59.526 50.000 0.00 0.0 36.17 3.55 R
3724 5330 2.076863 CCACTCCTAAAACAGCCTTCG 58.923 52.381 0.00 0.0 0.00 3.79 R
5037 7613 1.006825 TGCAGTCACGCACGACATAC 61.007 55.000 0.00 0.0 38.43 2.39 R
6395 9022 0.179062 ATCTCGAGGCAAGCATGGAC 60.179 55.000 13.56 0.0 0.00 4.02 R
7357 10270 0.108567 GGGCTCTGACGGTCTTCTTC 60.109 60.000 9.88 0.0 0.00 2.87 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
84 85 7.228590 TCATAACCCTTAAAACTGCTACAAGT 58.771 34.615 0.00 0.00 0.00 3.16
122 123 8.005388 TGAGGGTTCTACTAGTAATGCTCTAAT 58.995 37.037 3.76 0.00 0.00 1.73
123 124 9.517868 GAGGGTTCTACTAGTAATGCTCTAATA 57.482 37.037 3.76 0.00 0.00 0.98
125 126 9.517868 GGGTTCTACTAGTAATGCTCTAATAGA 57.482 37.037 3.76 0.00 28.69 1.98
138 139 9.825109 AATGCTCTAATAGATGATCATCATGAG 57.175 33.333 31.99 26.89 37.20 2.90
139 140 7.266400 TGCTCTAATAGATGATCATCATGAGC 58.734 38.462 32.40 32.40 37.20 4.26
140 141 7.124448 TGCTCTAATAGATGATCATCATGAGCT 59.876 37.037 34.72 22.57 37.20 4.09
141 142 7.650504 GCTCTAATAGATGATCATCATGAGCTC 59.349 40.741 32.14 20.25 37.20 4.09
143 144 2.962125 AGATGATCATCATGAGCTCGC 58.038 47.619 31.99 6.99 37.20 5.03
144 145 2.563620 AGATGATCATCATGAGCTCGCT 59.436 45.455 31.99 9.31 37.20 4.93
145 146 2.904697 TGATCATCATGAGCTCGCTT 57.095 45.000 9.64 0.00 33.24 4.68
146 147 2.480845 TGATCATCATGAGCTCGCTTG 58.519 47.619 9.64 7.00 33.24 4.01
147 148 2.101917 TGATCATCATGAGCTCGCTTGA 59.898 45.455 9.64 12.26 33.24 3.02
148 149 2.678471 TCATCATGAGCTCGCTTGAA 57.322 45.000 15.18 0.00 0.00 2.69
149 150 3.189618 TCATCATGAGCTCGCTTGAAT 57.810 42.857 15.18 0.00 0.00 2.57
150 151 2.870411 TCATCATGAGCTCGCTTGAATG 59.130 45.455 15.18 9.75 0.00 2.67
151 152 2.678471 TCATGAGCTCGCTTGAATGA 57.322 45.000 9.64 8.57 0.00 2.57
152 153 2.547826 TCATGAGCTCGCTTGAATGAG 58.452 47.619 9.64 0.00 35.30 2.90
162 163 3.122937 GCTTGAATGAGCGGTACAAAG 57.877 47.619 0.00 0.00 32.23 2.77
163 164 2.729156 GCTTGAATGAGCGGTACAAAGC 60.729 50.000 0.00 0.00 32.23 3.51
165 166 2.778299 TGAATGAGCGGTACAAAGCTT 58.222 42.857 10.36 0.00 44.69 3.74
166 167 3.932822 TGAATGAGCGGTACAAAGCTTA 58.067 40.909 0.00 7.46 44.69 3.09
167 168 4.513442 TGAATGAGCGGTACAAAGCTTAT 58.487 39.130 0.00 9.16 44.69 1.73
169 170 4.882671 ATGAGCGGTACAAAGCTTATTG 57.117 40.909 0.00 0.00 44.69 1.90
170 171 2.418628 TGAGCGGTACAAAGCTTATTGC 59.581 45.455 0.00 0.00 44.69 3.56
171 172 1.743394 AGCGGTACAAAGCTTATTGCC 59.257 47.619 0.00 1.55 41.52 4.52
172 173 1.531058 GCGGTACAAAGCTTATTGCCG 60.531 52.381 23.96 23.96 44.23 5.69
184 185 5.537188 AGCTTATTGCCGTTCAAAAATTGA 58.463 33.333 0.00 0.00 44.23 2.57
229 230 5.482006 CAAGGGGTCTTGGATTTCAATTTC 58.518 41.667 0.00 0.00 44.89 2.17
232 233 3.511699 GGTCTTGGATTTCAATTTCGCC 58.488 45.455 0.00 0.00 34.45 5.54
236 237 1.204467 TGGATTTCAATTTCGCCCTGC 59.796 47.619 0.00 0.00 0.00 4.85
260 261 2.877691 GAAATGTCAGCACCGGCC 59.122 61.111 0.00 0.00 42.56 6.13
261 262 2.676471 AAATGTCAGCACCGGCCC 60.676 61.111 0.00 0.00 42.56 5.80
270 271 2.440796 CACCGGCCCTGCAATCAT 60.441 61.111 0.00 0.00 0.00 2.45
272 273 2.124193 CCGGCCCTGCAATCATCA 60.124 61.111 0.00 0.00 0.00 3.07
276 277 0.462789 GGCCCTGCAATCATCAAAGG 59.537 55.000 0.00 0.00 0.00 3.11
282 283 4.248058 CCTGCAATCATCAAAGGAAAACC 58.752 43.478 0.00 0.00 0.00 3.27
288 289 3.088532 TCATCAAAGGAAAACCCGATGG 58.911 45.455 0.00 0.00 40.87 3.51
290 291 2.510613 TCAAAGGAAAACCCGATGGAC 58.489 47.619 0.00 0.00 40.87 4.02
301 302 1.517832 CGATGGACCACCTCCTCAC 59.482 63.158 0.00 0.00 40.26 3.51
306 307 1.079750 GACCACCTCCTCACTTCGC 60.080 63.158 0.00 0.00 0.00 4.70
311 312 0.461961 ACCTCCTCACTTCGCTATGC 59.538 55.000 0.00 0.00 0.00 3.14
330 331 3.386486 TGCAGCTTTGCAGATTTTCAAG 58.614 40.909 0.00 0.00 40.23 3.02
337 338 1.888512 TGCAGATTTTCAAGGTGCCTC 59.111 47.619 0.00 0.00 32.99 4.70
339 340 2.494870 GCAGATTTTCAAGGTGCCTCAT 59.505 45.455 0.00 0.00 0.00 2.90
375 376 6.038271 GCCATTACTATTGAACGAATGGAACT 59.962 38.462 14.55 0.00 46.31 3.01
376 377 7.225931 GCCATTACTATTGAACGAATGGAACTA 59.774 37.037 14.55 0.00 46.31 2.24
380 381 2.396590 TGAACGAATGGAACTAGGGC 57.603 50.000 0.00 0.00 0.00 5.19
406 407 1.209128 CAAGACGCGTCACTGAAGTT 58.791 50.000 37.85 20.37 0.00 2.66
407 408 1.593006 CAAGACGCGTCACTGAAGTTT 59.407 47.619 37.85 19.65 0.00 2.66
412 413 3.243336 ACGCGTCACTGAAGTTTAGATC 58.757 45.455 5.58 0.00 0.00 2.75
433 434 0.673644 AGCACCACCGCATGACTAAC 60.674 55.000 0.00 0.00 0.00 2.34
443 444 1.135489 GCATGACTAACACGTCGGAGA 60.135 52.381 0.00 0.00 36.71 3.71
462 463 4.385310 GGAGAAGTAAACCATACCTGCCAT 60.385 45.833 0.00 0.00 0.00 4.40
464 465 5.580022 AGAAGTAAACCATACCTGCCATTT 58.420 37.500 0.00 0.00 0.00 2.32
466 467 7.354312 AGAAGTAAACCATACCTGCCATTTAT 58.646 34.615 0.00 0.00 0.00 1.40
474 475 2.091541 ACCTGCCATTTATGAACCACG 58.908 47.619 0.00 0.00 0.00 4.94
493 494 3.054878 ACGAAACCAACACACGATCTAC 58.945 45.455 0.00 0.00 0.00 2.59
500 501 4.253685 CCAACACACGATCTACCATCTTT 58.746 43.478 0.00 0.00 0.00 2.52
633 1106 2.478134 GAGACTGTGTGTGCAGCTAAAG 59.522 50.000 0.00 0.00 39.96 1.85
638 1111 4.201950 ACTGTGTGTGCAGCTAAAGAAAAG 60.202 41.667 0.00 0.00 39.96 2.27
640 1113 4.035558 TGTGTGTGCAGCTAAAGAAAAGAG 59.964 41.667 0.00 0.00 0.00 2.85
642 1115 4.273480 TGTGTGCAGCTAAAGAAAAGAGAC 59.727 41.667 0.00 0.00 0.00 3.36
643 1116 4.513318 GTGTGCAGCTAAAGAAAAGAGACT 59.487 41.667 0.00 0.00 0.00 3.24
644 1117 4.512944 TGTGCAGCTAAAGAAAAGAGACTG 59.487 41.667 0.00 0.00 0.00 3.51
645 1118 4.513318 GTGCAGCTAAAGAAAAGAGACTGT 59.487 41.667 0.00 0.00 0.00 3.55
649 1122 6.425504 CAGCTAAAGAAAAGAGACTGTTGTG 58.574 40.000 0.00 0.00 0.00 3.33
650 1123 6.037610 CAGCTAAAGAAAAGAGACTGTTGTGT 59.962 38.462 0.00 0.00 0.00 3.72
651 1124 6.037610 AGCTAAAGAAAAGAGACTGTTGTGTG 59.962 38.462 0.00 0.00 0.00 3.82
652 1125 6.183360 GCTAAAGAAAAGAGACTGTTGTGTGT 60.183 38.462 0.00 0.00 0.00 3.72
653 1126 7.011109 GCTAAAGAAAAGAGACTGTTGTGTGTA 59.989 37.037 0.00 0.00 0.00 2.90
668 1141 1.677052 TGTGTAGTGTGTACGAGCACA 59.323 47.619 14.51 11.46 45.85 4.57
705 1178 2.250939 TGTACACTTGCTGCGTGGC 61.251 57.895 11.44 5.49 36.71 5.01
718 1191 1.143183 CGTGGCCCGTAGCAGTTAT 59.857 57.895 0.00 0.00 46.50 1.89
775 1248 3.536917 CGCCCAGATCCACCGCTA 61.537 66.667 0.00 0.00 0.00 4.26
895 1368 0.456221 ATCTCTTCACTACCACCGCG 59.544 55.000 0.00 0.00 0.00 6.46
965 1438 0.399233 CCTTCCTCCTCCGGATCCTT 60.399 60.000 3.57 0.00 32.02 3.36
1581 2060 4.491676 TGGAGAGGTACGATTTTTCTTCG 58.508 43.478 0.00 0.00 42.20 3.79
1612 2091 5.419542 TCATGTTCTTCTAAGAATCACCCG 58.580 41.667 8.31 3.11 45.83 5.28
1733 2212 0.508641 CCGAGCGAAGTTCAGTTGTG 59.491 55.000 3.32 0.00 37.72 3.33
1744 2223 5.438761 AGTTCAGTTGTGGAAAATAGCAC 57.561 39.130 0.00 0.00 0.00 4.40
2231 3029 1.200020 GCAACGACAATCTTCTTGGGG 59.800 52.381 0.00 0.00 0.00 4.96
2299 3097 7.420680 CCATTTAGTGATATTCCTTCCCTCTGT 60.421 40.741 0.00 0.00 0.00 3.41
2338 3136 3.379372 ACATCCATGCAGCAGTTAATGAC 59.621 43.478 0.00 0.00 0.00 3.06
2357 3155 9.967451 TTAATGACATTAGTAGGATTGGTGAAA 57.033 29.630 7.89 0.00 0.00 2.69
2422 3220 4.019771 AGTGAGGATCTGGAAAAGAAGTCC 60.020 45.833 0.00 0.00 38.79 3.85
2745 3543 4.979943 TGAACAAAAGCTCATGTCAACA 57.020 36.364 4.96 4.31 0.00 3.33
2746 3544 5.321959 TGAACAAAAGCTCATGTCAACAA 57.678 34.783 4.96 0.00 0.00 2.83
2747 3545 5.101628 TGAACAAAAGCTCATGTCAACAAC 58.898 37.500 4.96 0.00 0.00 3.32
2748 3546 4.989279 ACAAAAGCTCATGTCAACAACT 57.011 36.364 0.00 0.00 0.00 3.16
3000 3798 5.435291 AGAAGATAAGGATCAACTTGCAGG 58.565 41.667 0.00 0.00 34.17 4.85
3092 3890 6.619852 TGCCTCCTTTCTATATTCTTAGGGTT 59.380 38.462 0.00 0.00 0.00 4.11
3220 4023 1.352083 ACCACTGCCTAGCTTCAAGA 58.648 50.000 0.00 0.00 0.00 3.02
3276 4079 5.163301 TGAGAGGCCCTATACATTTCTGTTC 60.163 44.000 0.00 0.00 36.79 3.18
3370 4173 0.109913 TATAGGGCTCGGAGAAGCGA 59.890 55.000 9.69 0.00 34.09 4.93
3559 4362 1.623811 GTTTCTACTGCCAGGTCCTCA 59.376 52.381 0.00 0.00 0.00 3.86
3724 5330 7.550906 AGAGGCAAGAGTTTTGTGATTAGATAC 59.449 37.037 0.00 0.00 0.00 2.24
3837 5443 6.827586 TGAATGTTATTTGTCCTACCAACC 57.172 37.500 0.00 0.00 0.00 3.77
4133 5739 0.393077 CTCGTGACCAGACAAAGGGT 59.607 55.000 0.00 0.00 40.96 4.34
4169 5775 4.447290 TCAACTTAGCAAGTGTTAGTGCA 58.553 39.130 2.88 0.00 41.91 4.57
4502 6163 9.762933 ATTGAATTACTGTTTATTTTGTGCTGT 57.237 25.926 0.00 0.00 0.00 4.40
4603 6264 0.376152 CCATGCTACAGCGCTTTGAG 59.624 55.000 7.50 6.37 45.83 3.02
4635 6296 7.227873 TCACTTTGGGATATACTTGTTTGTCA 58.772 34.615 0.00 0.00 0.00 3.58
4671 6332 8.945481 TGAATCAAATGAAACACAAACATCTT 57.055 26.923 0.00 0.00 0.00 2.40
4677 6338 8.745837 CAAATGAAACACAAACATCTTCAGTAC 58.254 33.333 0.00 0.00 30.10 2.73
4705 6366 4.803613 CCAAAATTAGAACCATTAAGCCGC 59.196 41.667 0.00 0.00 0.00 6.53
4906 7482 8.708742 CGTTGTTAGAAATCACTATGAAACAGA 58.291 33.333 0.00 0.00 0.00 3.41
5047 7623 6.978024 TGTTTAAATTGTTGTATGTCGTGC 57.022 33.333 0.00 0.00 0.00 5.34
5499 8075 6.035758 GTGTGGATCGGAAGTTATTTGTACTC 59.964 42.308 0.00 0.00 0.00 2.59
5959 8579 3.586892 AGTTAAAGAGCACGCTAACCTC 58.413 45.455 0.00 0.00 0.00 3.85
6110 8730 4.081142 TCGACACATTGACACCCTATGAAT 60.081 41.667 0.00 0.00 33.24 2.57
6127 8747 8.152898 CCCTATGAATTGATCACTGAATCAGTA 58.847 37.037 16.28 5.40 43.43 2.74
6142 8769 6.240894 TGAATCAGTAATTCTGCCTTTGTCT 58.759 36.000 0.08 0.00 43.61 3.41
6309 8936 1.433879 CAGGATCACGTCGGAGGAC 59.566 63.158 4.48 0.00 39.89 3.85
6333 8960 0.313672 TGTCGCATGAGTTTTTGGCC 59.686 50.000 0.00 0.00 0.00 5.36
6578 9208 7.133891 ACTGCTGTAAATGCTGTACTTAAAG 57.866 36.000 0.00 0.00 40.02 1.85
6617 9247 3.317150 TCTAATGTTCGTGTGTGCTGAG 58.683 45.455 0.00 0.00 0.00 3.35
6632 9262 7.333423 GTGTGTGCTGAGAAGGTTGTTATTATA 59.667 37.037 0.00 0.00 0.00 0.98
6668 9529 5.069251 CCTGATTTACGTATGGAGTTCCTCT 59.931 44.000 0.00 0.00 36.82 3.69
6685 9546 9.232473 GAGTTCCTCTTGTTACTATGGAAATTT 57.768 33.333 0.00 0.00 35.68 1.82
6689 9550 8.325787 TCCTCTTGTTACTATGGAAATTTAGCA 58.674 33.333 0.00 0.00 0.00 3.49
6691 9552 8.506168 TCTTGTTACTATGGAAATTTAGCAGG 57.494 34.615 0.00 0.00 0.00 4.85
6695 9556 9.084533 TGTTACTATGGAAATTTAGCAGGTTTT 57.915 29.630 0.00 0.00 0.00 2.43
6738 9599 1.466167 CACATTTTCTCGGTCTGCCTG 59.534 52.381 0.00 0.00 0.00 4.85
6744 9605 0.680280 TCTCGGTCTGCCTGGTACTC 60.680 60.000 0.00 0.00 0.00 2.59
6745 9606 1.668101 CTCGGTCTGCCTGGTACTCC 61.668 65.000 0.00 0.00 0.00 3.85
6746 9607 1.682684 CGGTCTGCCTGGTACTCCT 60.683 63.158 0.00 0.00 34.23 3.69
6747 9608 1.668101 CGGTCTGCCTGGTACTCCTC 61.668 65.000 0.00 0.00 34.23 3.71
6755 9616 2.167900 GCCTGGTACTCCTCGTGTTATT 59.832 50.000 0.00 0.00 34.23 1.40
6757 9618 4.142093 GCCTGGTACTCCTCGTGTTATTAA 60.142 45.833 0.00 0.00 34.23 1.40
6760 9621 6.534079 CCTGGTACTCCTCGTGTTATTAAAAG 59.466 42.308 0.00 0.00 34.23 2.27
6768 9629 8.638685 TCCTCGTGTTATTAAAAGTAGTATGC 57.361 34.615 0.00 0.00 0.00 3.14
6771 9632 9.901724 CTCGTGTTATTAAAAGTAGTATGCTTG 57.098 33.333 0.00 0.00 41.32 4.01
6834 9695 1.526575 GACCGGTGGTCGTTACAGGA 61.527 60.000 14.63 0.00 43.14 3.86
6894 9757 7.473027 AAAGTCGTTTCGTTCTTCAATAGAA 57.527 32.000 0.00 0.00 40.57 2.10
6898 9761 8.557029 AGTCGTTTCGTTCTTCAATAGAAAAAT 58.443 29.630 0.00 0.00 44.25 1.82
6900 9763 7.322699 TCGTTTCGTTCTTCAATAGAAAAATGC 59.677 33.333 0.00 0.00 44.25 3.56
6902 9765 8.751335 GTTTCGTTCTTCAATAGAAAAATGCAA 58.249 29.630 0.00 0.00 44.25 4.08
6904 9767 8.280909 TCGTTCTTCAATAGAAAAATGCAAAC 57.719 30.769 0.00 0.00 44.25 2.93
6906 9769 8.209869 CGTTCTTCAATAGAAAAATGCAAACAG 58.790 33.333 0.00 0.00 44.25 3.16
6908 9771 9.985730 TTCTTCAATAGAAAAATGCAAACAGAT 57.014 25.926 0.00 0.00 39.90 2.90
6939 9804 6.398918 TCTTCAGAAATAGGTAGAGCACAAC 58.601 40.000 0.00 0.00 0.00 3.32
6949 9814 0.663153 AGAGCACAACTGTTTTCGCC 59.337 50.000 0.00 0.00 0.00 5.54
6956 9821 1.539388 CAACTGTTTTCGCCTGGCATA 59.461 47.619 20.29 2.64 0.00 3.14
7002 9867 2.373169 TGATCACAGGAAAGTCTTGCCT 59.627 45.455 6.25 6.25 0.00 4.75
7023 9888 1.039233 GCCATCCAATCCACCACCAG 61.039 60.000 0.00 0.00 0.00 4.00
7025 9890 1.077501 ATCCAATCCACCACCAGCG 60.078 57.895 0.00 0.00 0.00 5.18
7053 9953 0.529378 CAGGATTGCAGGTTTCAGCC 59.471 55.000 0.00 0.00 0.00 4.85
7057 9957 1.471684 GATTGCAGGTTTCAGCCTCTG 59.528 52.381 0.00 0.00 36.58 3.35
7065 9965 1.801178 GTTTCAGCCTCTGTTTCCTCG 59.199 52.381 0.00 0.00 32.61 4.63
7066 9966 0.321671 TTCAGCCTCTGTTTCCTCGG 59.678 55.000 0.00 0.00 32.61 4.63
7080 9980 1.239296 CCTCGGTGACTACGTGTCCA 61.239 60.000 13.24 0.00 44.75 4.02
7122 10022 3.513662 CATCGCATGATCCTCTCATCTC 58.486 50.000 0.00 0.00 42.91 2.75
7131 10043 5.083122 TGATCCTCTCATCTCCTTATCCAC 58.917 45.833 0.00 0.00 0.00 4.02
7132 10044 4.542906 TCCTCTCATCTCCTTATCCACA 57.457 45.455 0.00 0.00 0.00 4.17
7133 10045 4.883759 TCCTCTCATCTCCTTATCCACAA 58.116 43.478 0.00 0.00 0.00 3.33
7134 10046 4.898265 TCCTCTCATCTCCTTATCCACAAG 59.102 45.833 0.00 0.00 0.00 3.16
7135 10047 4.898265 CCTCTCATCTCCTTATCCACAAGA 59.102 45.833 0.00 0.00 0.00 3.02
7136 10048 5.365025 CCTCTCATCTCCTTATCCACAAGAA 59.635 44.000 0.00 0.00 0.00 2.52
7137 10049 6.126940 CCTCTCATCTCCTTATCCACAAGAAA 60.127 42.308 0.00 0.00 0.00 2.52
7138 10050 6.644347 TCTCATCTCCTTATCCACAAGAAAC 58.356 40.000 0.00 0.00 0.00 2.78
7139 10051 5.745227 TCATCTCCTTATCCACAAGAAACC 58.255 41.667 0.00 0.00 0.00 3.27
7140 10052 4.569719 TCTCCTTATCCACAAGAAACCC 57.430 45.455 0.00 0.00 0.00 4.11
7141 10053 4.175962 TCTCCTTATCCACAAGAAACCCT 58.824 43.478 0.00 0.00 0.00 4.34
7142 10054 4.601857 TCTCCTTATCCACAAGAAACCCTT 59.398 41.667 0.00 0.00 34.91 3.95
7201 10113 4.695231 CGACGGTTCGCCACTCGT 62.695 66.667 0.00 0.00 38.71 4.18
7231 10144 6.669125 TTTTGTTCTTTCATCATCCATGGT 57.331 33.333 12.58 0.00 32.64 3.55
7248 10161 2.368439 TGGTGCCTGCAGATTTCATAC 58.632 47.619 17.39 3.08 0.00 2.39
7264 10177 3.014623 TCATACCCAGTAGACAGTGACG 58.985 50.000 0.00 0.00 0.00 4.35
7315 10228 6.862608 TGTTGTTTTATGACTGAATGTGATGC 59.137 34.615 0.00 0.00 0.00 3.91
7323 10236 4.151258 ACTGAATGTGATGCTTTTGACG 57.849 40.909 0.00 0.00 0.00 4.35
7339 10252 0.109689 GACGAACAGTAGCGAGCACT 60.110 55.000 0.00 0.00 0.00 4.40
7340 10253 1.129998 GACGAACAGTAGCGAGCACTA 59.870 52.381 0.00 0.00 0.00 2.74
7341 10254 1.130749 ACGAACAGTAGCGAGCACTAG 59.869 52.381 0.00 0.00 0.00 2.57
7342 10255 1.532090 CGAACAGTAGCGAGCACTAGG 60.532 57.143 0.00 0.00 0.00 3.02
7343 10256 1.473278 GAACAGTAGCGAGCACTAGGT 59.527 52.381 0.00 0.00 0.00 3.08
7344 10257 1.546961 ACAGTAGCGAGCACTAGGTT 58.453 50.000 0.00 0.00 0.00 3.50
7345 10258 1.893801 ACAGTAGCGAGCACTAGGTTT 59.106 47.619 0.00 0.00 0.00 3.27
7346 10259 2.094649 ACAGTAGCGAGCACTAGGTTTC 60.095 50.000 0.00 0.00 0.00 2.78
7347 10260 2.094700 CAGTAGCGAGCACTAGGTTTCA 60.095 50.000 0.00 0.00 0.00 2.69
7348 10261 2.761208 AGTAGCGAGCACTAGGTTTCAT 59.239 45.455 0.00 0.00 0.00 2.57
7349 10262 2.770164 AGCGAGCACTAGGTTTCATT 57.230 45.000 0.00 0.00 0.00 2.57
7350 10263 2.622436 AGCGAGCACTAGGTTTCATTC 58.378 47.619 0.00 0.00 0.00 2.67
7351 10264 2.028112 AGCGAGCACTAGGTTTCATTCA 60.028 45.455 0.00 0.00 0.00 2.57
7352 10265 2.742053 GCGAGCACTAGGTTTCATTCAA 59.258 45.455 0.00 0.00 0.00 2.69
7353 10266 3.375299 GCGAGCACTAGGTTTCATTCAAT 59.625 43.478 0.00 0.00 0.00 2.57
7354 10267 4.570772 GCGAGCACTAGGTTTCATTCAATA 59.429 41.667 0.00 0.00 0.00 1.90
7355 10268 5.064707 GCGAGCACTAGGTTTCATTCAATAA 59.935 40.000 0.00 0.00 0.00 1.40
7356 10269 6.403200 GCGAGCACTAGGTTTCATTCAATAAA 60.403 38.462 0.00 0.00 0.00 1.40
7357 10270 7.182761 CGAGCACTAGGTTTCATTCAATAAAG 58.817 38.462 0.00 0.00 0.00 1.85
7358 10271 7.064609 CGAGCACTAGGTTTCATTCAATAAAGA 59.935 37.037 0.00 0.00 0.00 2.52
7359 10272 8.635765 AGCACTAGGTTTCATTCAATAAAGAA 57.364 30.769 0.00 0.00 0.00 2.52
7360 10273 8.734386 AGCACTAGGTTTCATTCAATAAAGAAG 58.266 33.333 0.00 0.00 0.00 2.85
7361 10274 8.730680 GCACTAGGTTTCATTCAATAAAGAAGA 58.269 33.333 0.00 0.00 0.00 2.87
7366 10279 8.797438 AGGTTTCATTCAATAAAGAAGAAGACC 58.203 33.333 0.00 0.00 0.00 3.85
7367 10280 7.750903 GGTTTCATTCAATAAAGAAGAAGACCG 59.249 37.037 0.00 0.00 0.00 4.79
7368 10281 7.979444 TTCATTCAATAAAGAAGAAGACCGT 57.021 32.000 0.00 0.00 0.00 4.83
7369 10282 7.596749 TCATTCAATAAAGAAGAAGACCGTC 57.403 36.000 0.00 0.00 0.00 4.79
7370 10283 7.158697 TCATTCAATAAAGAAGAAGACCGTCA 58.841 34.615 0.40 0.00 0.00 4.35
7371 10284 7.331934 TCATTCAATAAAGAAGAAGACCGTCAG 59.668 37.037 0.40 0.00 0.00 3.51
7372 10285 6.340962 TCAATAAAGAAGAAGACCGTCAGA 57.659 37.500 0.40 0.00 0.00 3.27
7373 10286 6.390721 TCAATAAAGAAGAAGACCGTCAGAG 58.609 40.000 0.40 0.00 0.00 3.35
7374 10287 2.734276 AAGAAGAAGACCGTCAGAGC 57.266 50.000 0.40 0.00 0.00 4.09
7375 10288 0.892063 AGAAGAAGACCGTCAGAGCC 59.108 55.000 0.40 0.00 0.00 4.70
7376 10289 0.108567 GAAGAAGACCGTCAGAGCCC 60.109 60.000 0.40 0.00 0.00 5.19
7377 10290 1.878656 AAGAAGACCGTCAGAGCCCG 61.879 60.000 0.40 0.00 0.00 6.13
7383 10296 2.657237 CGTCAGAGCCCGGAAGTT 59.343 61.111 0.73 0.00 0.00 2.66
7384 10297 1.888018 CGTCAGAGCCCGGAAGTTA 59.112 57.895 0.73 0.00 0.00 2.24
7385 10298 0.458025 CGTCAGAGCCCGGAAGTTAC 60.458 60.000 0.73 0.00 0.00 2.50
7386 10299 0.606604 GTCAGAGCCCGGAAGTTACA 59.393 55.000 0.73 0.00 0.00 2.41
7387 10300 1.001633 GTCAGAGCCCGGAAGTTACAA 59.998 52.381 0.73 0.00 0.00 2.41
7388 10301 1.906574 TCAGAGCCCGGAAGTTACAAT 59.093 47.619 0.73 0.00 0.00 2.71
7389 10302 2.009774 CAGAGCCCGGAAGTTACAATG 58.990 52.381 0.73 0.00 0.00 2.82
7390 10303 1.906574 AGAGCCCGGAAGTTACAATGA 59.093 47.619 0.73 0.00 0.00 2.57
7391 10304 2.093447 AGAGCCCGGAAGTTACAATGAG 60.093 50.000 0.73 0.00 0.00 2.90
7392 10305 1.906574 AGCCCGGAAGTTACAATGAGA 59.093 47.619 0.73 0.00 0.00 3.27
7393 10306 2.304761 AGCCCGGAAGTTACAATGAGAA 59.695 45.455 0.73 0.00 0.00 2.87
7394 10307 3.078837 GCCCGGAAGTTACAATGAGAAA 58.921 45.455 0.73 0.00 0.00 2.52
7395 10308 3.694566 GCCCGGAAGTTACAATGAGAAAT 59.305 43.478 0.73 0.00 0.00 2.17
7396 10309 4.879545 GCCCGGAAGTTACAATGAGAAATA 59.120 41.667 0.73 0.00 0.00 1.40
7397 10310 5.007724 GCCCGGAAGTTACAATGAGAAATAG 59.992 44.000 0.73 0.00 0.00 1.73
7398 10311 5.527582 CCCGGAAGTTACAATGAGAAATAGG 59.472 44.000 0.73 0.00 0.00 2.57
7399 10312 6.113411 CCGGAAGTTACAATGAGAAATAGGT 58.887 40.000 0.00 0.00 0.00 3.08
7400 10313 6.598064 CCGGAAGTTACAATGAGAAATAGGTT 59.402 38.462 0.00 0.00 0.00 3.50
7401 10314 7.414098 CCGGAAGTTACAATGAGAAATAGGTTG 60.414 40.741 0.00 0.00 0.00 3.77
7402 10315 7.333423 CGGAAGTTACAATGAGAAATAGGTTGA 59.667 37.037 0.00 0.00 0.00 3.18
7403 10316 8.669243 GGAAGTTACAATGAGAAATAGGTTGAG 58.331 37.037 0.00 0.00 0.00 3.02
7404 10317 9.436957 GAAGTTACAATGAGAAATAGGTTGAGA 57.563 33.333 0.00 0.00 0.00 3.27
7405 10318 9.965902 AAGTTACAATGAGAAATAGGTTGAGAT 57.034 29.630 0.00 0.00 0.00 2.75
7406 10319 9.388506 AGTTACAATGAGAAATAGGTTGAGATG 57.611 33.333 0.00 0.00 0.00 2.90
7407 10320 6.690194 ACAATGAGAAATAGGTTGAGATGC 57.310 37.500 0.00 0.00 0.00 3.91
7408 10321 6.182627 ACAATGAGAAATAGGTTGAGATGCA 58.817 36.000 0.00 0.00 0.00 3.96
7409 10322 6.094603 ACAATGAGAAATAGGTTGAGATGCAC 59.905 38.462 0.00 0.00 0.00 4.57
7410 10323 5.164620 TGAGAAATAGGTTGAGATGCACA 57.835 39.130 0.00 0.00 0.00 4.57
7411 10324 5.559770 TGAGAAATAGGTTGAGATGCACAA 58.440 37.500 0.00 0.00 0.00 3.33
7412 10325 5.645067 TGAGAAATAGGTTGAGATGCACAAG 59.355 40.000 0.00 0.00 0.00 3.16
7413 10326 5.564550 AGAAATAGGTTGAGATGCACAAGT 58.435 37.500 0.00 0.00 0.00 3.16
7414 10327 5.645497 AGAAATAGGTTGAGATGCACAAGTC 59.355 40.000 0.00 0.00 0.00 3.01
7415 10328 2.936919 AGGTTGAGATGCACAAGTCA 57.063 45.000 0.00 0.00 0.00 3.41
7416 10329 2.498167 AGGTTGAGATGCACAAGTCAC 58.502 47.619 0.00 0.00 0.00 3.67
7417 10330 2.105477 AGGTTGAGATGCACAAGTCACT 59.895 45.455 0.00 0.00 0.00 3.41
7418 10331 3.324846 AGGTTGAGATGCACAAGTCACTA 59.675 43.478 0.00 0.00 0.00 2.74
7419 10332 3.433615 GGTTGAGATGCACAAGTCACTAC 59.566 47.826 0.00 0.00 0.00 2.73
7420 10333 4.310769 GTTGAGATGCACAAGTCACTACT 58.689 43.478 0.00 0.00 37.65 2.57
7431 10344 6.147821 GCACAAGTCACTACTAAATGTGATGT 59.852 38.462 8.90 0.00 41.46 3.06
7432 10345 7.513132 CACAAGTCACTACTAAATGTGATGTG 58.487 38.462 12.33 12.33 41.46 3.21
7439 10352 7.877612 TCACTACTAAATGTGATGTGATGTGTT 59.122 33.333 0.00 0.00 38.15 3.32
7440 10353 7.959109 CACTACTAAATGTGATGTGATGTGTTG 59.041 37.037 0.00 0.00 36.38 3.33
7441 10354 5.702865 ACTAAATGTGATGTGATGTGTTGC 58.297 37.500 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 7.002276 ACACTTGTAGCAGTTTTAAGGGTTAT 58.998 34.615 0.00 0.00 31.39 1.89
62 63 6.358991 ACACTTGTAGCAGTTTTAAGGGTTA 58.641 36.000 0.00 0.00 31.39 2.85
84 85 2.243736 AGAACCCTCAAACCCTCAAACA 59.756 45.455 0.00 0.00 0.00 2.83
122 123 3.762823 AGCGAGCTCATGATGATCATCTA 59.237 43.478 30.65 19.72 34.28 1.98
123 124 2.563620 AGCGAGCTCATGATGATCATCT 59.436 45.455 30.65 16.80 34.28 2.90
125 126 3.067833 CAAGCGAGCTCATGATGATCAT 58.932 45.455 15.40 8.25 37.65 2.45
126 127 2.101917 TCAAGCGAGCTCATGATGATCA 59.898 45.455 15.40 0.00 0.00 2.92
127 128 2.752121 TCAAGCGAGCTCATGATGATC 58.248 47.619 15.40 0.00 0.00 2.92
128 129 2.904697 TCAAGCGAGCTCATGATGAT 57.095 45.000 15.40 0.00 0.00 2.45
129 130 2.678471 TTCAAGCGAGCTCATGATGA 57.322 45.000 15.40 9.26 0.00 2.92
130 131 2.870411 TCATTCAAGCGAGCTCATGATG 59.130 45.455 15.40 13.31 0.00 3.07
143 144 2.744202 AGCTTTGTACCGCTCATTCAAG 59.256 45.455 0.00 0.00 0.00 3.02
144 145 2.778299 AGCTTTGTACCGCTCATTCAA 58.222 42.857 0.00 0.00 0.00 2.69
145 146 2.472695 AGCTTTGTACCGCTCATTCA 57.527 45.000 0.00 0.00 0.00 2.57
146 147 5.266242 CAATAAGCTTTGTACCGCTCATTC 58.734 41.667 3.20 0.00 34.96 2.67
147 148 4.438744 GCAATAAGCTTTGTACCGCTCATT 60.439 41.667 3.20 0.00 41.15 2.57
148 149 3.065371 GCAATAAGCTTTGTACCGCTCAT 59.935 43.478 3.20 0.00 41.15 2.90
149 150 2.418628 GCAATAAGCTTTGTACCGCTCA 59.581 45.455 3.20 0.00 41.15 4.26
150 151 2.223272 GGCAATAAGCTTTGTACCGCTC 60.223 50.000 3.20 0.00 44.79 5.03
151 152 1.743394 GGCAATAAGCTTTGTACCGCT 59.257 47.619 3.20 0.00 44.79 5.52
152 153 1.531058 CGGCAATAAGCTTTGTACCGC 60.531 52.381 3.20 0.00 44.79 5.68
153 154 1.735571 ACGGCAATAAGCTTTGTACCG 59.264 47.619 21.73 21.73 44.79 4.02
154 155 3.189702 TGAACGGCAATAAGCTTTGTACC 59.810 43.478 3.20 0.93 44.79 3.34
155 156 4.413495 TGAACGGCAATAAGCTTTGTAC 57.587 40.909 3.20 0.00 44.79 2.90
156 157 5.440234 TTTGAACGGCAATAAGCTTTGTA 57.560 34.783 3.20 0.00 44.79 2.41
157 158 4.314740 TTTGAACGGCAATAAGCTTTGT 57.685 36.364 3.20 0.00 44.79 2.83
158 159 5.649602 TTTTTGAACGGCAATAAGCTTTG 57.350 34.783 3.20 0.00 44.79 2.77
159 160 6.481644 TCAATTTTTGAACGGCAATAAGCTTT 59.518 30.769 3.20 0.00 39.10 3.51
160 161 5.988561 TCAATTTTTGAACGGCAATAAGCTT 59.011 32.000 3.48 3.48 39.10 3.74
161 162 5.537188 TCAATTTTTGAACGGCAATAAGCT 58.463 33.333 0.00 0.00 39.10 3.74
162 163 5.837586 TCAATTTTTGAACGGCAATAAGC 57.162 34.783 0.00 0.00 38.64 3.09
163 164 7.795859 ACAATCAATTTTTGAACGGCAATAAG 58.204 30.769 5.17 0.00 43.95 1.73
164 165 7.721286 ACAATCAATTTTTGAACGGCAATAA 57.279 28.000 5.17 0.00 43.95 1.40
165 166 7.721286 AACAATCAATTTTTGAACGGCAATA 57.279 28.000 5.17 0.00 43.95 1.90
166 167 6.616774 AACAATCAATTTTTGAACGGCAAT 57.383 29.167 5.17 0.00 43.95 3.56
167 168 7.721286 ATAACAATCAATTTTTGAACGGCAA 57.279 28.000 5.17 0.00 43.95 4.52
168 169 7.721286 AATAACAATCAATTTTTGAACGGCA 57.279 28.000 5.17 0.00 43.95 5.69
213 214 3.193267 CAGGGCGAAATTGAAATCCAAGA 59.807 43.478 0.00 0.00 38.31 3.02
215 216 2.353605 GCAGGGCGAAATTGAAATCCAA 60.354 45.455 0.00 0.00 39.41 3.53
236 237 3.508840 GCTGACATTTCGGGGGCG 61.509 66.667 0.00 0.00 0.00 6.13
237 238 2.361104 TGCTGACATTTCGGGGGC 60.361 61.111 0.00 0.00 0.00 5.80
241 242 3.039202 GCCGGTGCTGACATTTCGG 62.039 63.158 1.90 0.00 38.71 4.30
260 261 4.248058 GGTTTTCCTTTGATGATTGCAGG 58.752 43.478 0.00 0.00 36.94 4.85
261 262 4.248058 GGGTTTTCCTTTGATGATTGCAG 58.752 43.478 0.00 0.00 40.46 4.41
267 268 3.088532 CCATCGGGTTTTCCTTTGATGA 58.911 45.455 1.83 0.00 41.64 2.92
270 271 2.510613 GTCCATCGGGTTTTCCTTTGA 58.489 47.619 0.00 0.00 40.46 2.69
272 273 1.146152 TGGTCCATCGGGTTTTCCTTT 59.854 47.619 0.00 0.00 40.46 3.11
276 277 0.037734 AGGTGGTCCATCGGGTTTTC 59.962 55.000 0.00 0.00 35.89 2.29
288 289 1.079750 GCGAAGTGAGGAGGTGGTC 60.080 63.158 0.00 0.00 0.00 4.02
290 291 1.115467 ATAGCGAAGTGAGGAGGTGG 58.885 55.000 0.00 0.00 0.00 4.61
311 312 3.739300 CACCTTGAAAATCTGCAAAGCTG 59.261 43.478 0.00 0.00 0.00 4.24
320 321 4.038271 TGATGAGGCACCTTGAAAATCT 57.962 40.909 0.00 0.00 0.00 2.40
323 324 3.321682 CCTTTGATGAGGCACCTTGAAAA 59.678 43.478 0.00 0.00 0.00 2.29
324 325 2.892852 CCTTTGATGAGGCACCTTGAAA 59.107 45.455 0.00 0.00 0.00 2.69
358 359 4.080807 TGCCCTAGTTCCATTCGTTCAATA 60.081 41.667 0.00 0.00 0.00 1.90
359 360 3.279434 GCCCTAGTTCCATTCGTTCAAT 58.721 45.455 0.00 0.00 0.00 2.57
365 366 1.737793 GTGTTGCCCTAGTTCCATTCG 59.262 52.381 0.00 0.00 0.00 3.34
380 381 1.885388 TGACGCGTCTTGGGTGTTG 60.885 57.895 36.27 0.00 44.90 3.33
388 389 1.935933 AAACTTCAGTGACGCGTCTT 58.064 45.000 36.27 23.24 0.00 3.01
393 394 4.501198 GCTAGATCTAAACTTCAGTGACGC 59.499 45.833 3.57 0.00 0.00 5.19
406 407 1.480789 TGCGGTGGTGCTAGATCTAA 58.519 50.000 3.57 0.00 35.36 2.10
407 408 1.341209 CATGCGGTGGTGCTAGATCTA 59.659 52.381 1.69 1.69 35.36 1.98
412 413 0.459899 TAGTCATGCGGTGGTGCTAG 59.540 55.000 0.00 0.00 35.36 3.42
433 434 2.427232 TGGTTTACTTCTCCGACGTG 57.573 50.000 0.00 0.00 0.00 4.49
443 444 7.122715 TCATAAATGGCAGGTATGGTTTACTT 58.877 34.615 16.08 0.00 0.00 2.24
450 451 4.037923 GTGGTTCATAAATGGCAGGTATGG 59.962 45.833 16.08 3.34 0.00 2.74
462 463 4.398358 TGTGTTGGTTTCGTGGTTCATAAA 59.602 37.500 0.00 0.00 0.00 1.40
464 465 3.312973 GTGTGTTGGTTTCGTGGTTCATA 59.687 43.478 0.00 0.00 0.00 2.15
466 467 1.469308 GTGTGTTGGTTTCGTGGTTCA 59.531 47.619 0.00 0.00 0.00 3.18
474 475 3.395639 TGGTAGATCGTGTGTTGGTTTC 58.604 45.455 0.00 0.00 0.00 2.78
500 501 2.573462 GGGCCCAGAATATAGCATCTGA 59.427 50.000 19.95 0.00 44.64 3.27
511 946 1.428912 TGAGAAAAGTGGGCCCAGAAT 59.571 47.619 29.55 12.19 0.00 2.40
537 972 1.777272 ACTTGGCCCAAAGTCTTCTCT 59.223 47.619 0.00 0.00 35.44 3.10
538 973 1.882623 CACTTGGCCCAAAGTCTTCTC 59.117 52.381 5.51 0.00 38.34 2.87
571 1006 0.240945 GCCAACGCAGCAAGTGTATT 59.759 50.000 0.00 0.00 40.86 1.89
577 1012 3.468266 AACACGCCAACGCAGCAAG 62.468 57.895 0.00 0.00 45.53 4.01
633 1106 5.581085 ACACTACACACAACAGTCTCTTTTC 59.419 40.000 0.00 0.00 0.00 2.29
638 1111 3.782046 ACACACTACACACAACAGTCTC 58.218 45.455 0.00 0.00 0.00 3.36
640 1113 3.484649 CGTACACACTACACACAACAGTC 59.515 47.826 0.00 0.00 0.00 3.51
642 1115 3.697982 TCGTACACACTACACACAACAG 58.302 45.455 0.00 0.00 0.00 3.16
643 1116 3.697982 CTCGTACACACTACACACAACA 58.302 45.455 0.00 0.00 0.00 3.33
644 1117 2.470257 GCTCGTACACACTACACACAAC 59.530 50.000 0.00 0.00 0.00 3.32
645 1118 2.099427 TGCTCGTACACACTACACACAA 59.901 45.455 0.00 0.00 0.00 3.33
649 1122 2.410785 TGTGCTCGTACACACTACAC 57.589 50.000 8.79 0.00 45.36 2.90
668 1141 3.740115 ACACAAAAATAGGAGCTCGTGT 58.260 40.909 18.96 15.18 0.00 4.49
705 1178 0.320697 GGGCCTATAACTGCTACGGG 59.679 60.000 0.84 0.00 0.00 5.28
775 1248 2.668550 GCGAGCGGAGTTTTGGGT 60.669 61.111 0.00 0.00 0.00 4.51
895 1368 0.748367 GGAACCTGGCTTCGAATCCC 60.748 60.000 15.16 11.20 0.00 3.85
965 1438 4.212913 GCTCGGATCTGCGGCTCA 62.213 66.667 0.00 0.00 0.00 4.26
1477 1956 0.178975 ACAAAATTGGCCCAGACGGA 60.179 50.000 0.00 0.00 0.00 4.69
1581 2060 5.473931 TCTTAGAAGAACATGAGCAGTGAC 58.526 41.667 0.00 0.00 30.73 3.67
1733 2212 7.900782 TCTGTAAACTGTAGTGCTATTTTCC 57.099 36.000 0.00 0.00 0.00 3.13
1744 2223 5.844004 ACAGTGAGGTTCTGTAAACTGTAG 58.156 41.667 4.54 0.00 44.66 2.74
2231 3029 4.807834 CCATGTCAGTGTAGATGTCATGTC 59.192 45.833 10.64 0.00 40.39 3.06
2338 3136 7.013655 CCTTCCATTTCACCAATCCTACTAATG 59.986 40.741 0.00 0.00 0.00 1.90
2357 3155 6.662755 TGTAATATGAAAGTGCTCCTTCCAT 58.337 36.000 0.00 0.00 31.27 3.41
2422 3220 2.304180 CACTATCATAGGAAGGGGGCTG 59.696 54.545 0.00 0.00 0.00 4.85
2565 3363 0.473755 TTGGTCAGGCATCACACTGT 59.526 50.000 0.00 0.00 36.17 3.55
2745 3543 4.373156 ACTTTTGTGCCCAGAGATAGTT 57.627 40.909 0.00 0.00 0.00 2.24
2746 3544 4.074970 CAACTTTTGTGCCCAGAGATAGT 58.925 43.478 0.00 0.00 0.00 2.12
2747 3545 4.154918 GTCAACTTTTGTGCCCAGAGATAG 59.845 45.833 0.00 0.00 0.00 2.08
2748 3546 4.072131 GTCAACTTTTGTGCCCAGAGATA 58.928 43.478 0.00 0.00 0.00 1.98
3000 3798 9.045223 AGACAAAAATAACCTTTTGAGCATTTC 57.955 29.630 14.01 2.55 45.25 2.17
3220 4023 3.072476 TCCTCCTCTTCCACGACAAAATT 59.928 43.478 0.00 0.00 0.00 1.82
3724 5330 2.076863 CCACTCCTAAAACAGCCTTCG 58.923 52.381 0.00 0.00 0.00 3.79
4169 5775 4.284234 AGAAAACAAGGGCAAGCAATACAT 59.716 37.500 0.00 0.00 0.00 2.29
4568 6229 5.649782 AGCATGGAGGAAAATGTTGTTAG 57.350 39.130 0.00 0.00 0.00 2.34
4570 6231 4.832266 TGTAGCATGGAGGAAAATGTTGTT 59.168 37.500 0.00 0.00 0.00 2.83
4603 6264 6.775594 AGTATATCCCAAAGTGAAAAAGGC 57.224 37.500 0.00 0.00 0.00 4.35
4644 6305 9.381033 AGATGTTTGTGTTTCATTTGATTCAAA 57.619 25.926 13.88 13.88 37.75 2.69
4671 6332 7.284074 TGGTTCTAATTTTGGACAAGTACTGA 58.716 34.615 0.00 0.00 0.00 3.41
4677 6338 7.545615 GGCTTAATGGTTCTAATTTTGGACAAG 59.454 37.037 0.00 0.00 0.00 3.16
4705 6366 7.851822 ATGCTTTTACAAAAATACAGTGACG 57.148 32.000 0.00 0.00 0.00 4.35
4818 6485 6.591935 ACTTCTCATGACACCTTTCAAACTA 58.408 36.000 0.00 0.00 0.00 2.24
4906 7482 6.347696 TCATTGTTGAATCTTTTTGTTGGCT 58.652 32.000 0.00 0.00 0.00 4.75
5019 7595 9.872757 ACGACATACAACAATTTAAACAACTAG 57.127 29.630 0.00 0.00 0.00 2.57
5037 7613 1.006825 TGCAGTCACGCACGACATAC 61.007 55.000 0.00 0.00 38.43 2.39
5047 7623 3.065925 TCATATCTCAGTCTGCAGTCACG 59.934 47.826 14.67 3.86 0.00 4.35
5499 8075 3.136123 CGCAGGGGCATTGGAGTG 61.136 66.667 0.00 0.00 41.24 3.51
5959 8579 3.491356 CTGTTGTTCAACATATGCCACG 58.509 45.455 16.89 1.90 31.47 4.94
6066 8686 1.000506 TCAGTTGACCTTGCGTACCTC 59.999 52.381 0.00 0.00 0.00 3.85
6077 8697 3.123621 GTCAATGTGTCGATCAGTTGACC 59.876 47.826 20.53 11.86 41.64 4.02
6127 8747 3.160269 CCTGGAAGACAAAGGCAGAATT 58.840 45.455 0.00 0.00 34.07 2.17
6130 8750 1.349026 CTCCTGGAAGACAAAGGCAGA 59.651 52.381 0.00 0.00 34.07 4.26
6142 8769 4.842531 TGACATCAAATAGCTCCTGGAA 57.157 40.909 0.00 0.00 0.00 3.53
6228 8855 2.716017 CGAGTCAGGGACCTGCTCC 61.716 68.421 24.16 12.72 43.31 4.70
6309 8936 0.792640 AAAACTCATGCGACAGAGCG 59.207 50.000 0.00 0.00 40.67 5.03
6391 9018 1.676635 GAGGCAAGCATGGACAGCA 60.677 57.895 0.00 0.00 0.00 4.41
6392 9019 2.758089 CGAGGCAAGCATGGACAGC 61.758 63.158 0.00 0.00 0.00 4.40
6394 9021 1.078918 CTCGAGGCAAGCATGGACA 60.079 57.895 3.91 0.00 0.00 4.02
6395 9022 0.179062 ATCTCGAGGCAAGCATGGAC 60.179 55.000 13.56 0.00 0.00 4.02
6607 9237 2.418368 AACAACCTTCTCAGCACACA 57.582 45.000 0.00 0.00 0.00 3.72
6632 9262 4.700213 ACGTAAATCAGGCAATAGCACTTT 59.300 37.500 0.00 0.00 44.61 2.66
6668 9529 8.644374 AACCTGCTAAATTTCCATAGTAACAA 57.356 30.769 0.00 0.00 0.00 2.83
6685 9546 7.115663 GCATGAAATTTTCGTTAAAACCTGCTA 59.884 33.333 0.00 0.00 37.41 3.49
6687 9548 6.070829 GCATGAAATTTTCGTTAAAACCTGC 58.929 36.000 0.00 0.00 37.41 4.85
6689 9550 7.708752 TCAAGCATGAAATTTTCGTTAAAACCT 59.291 29.630 0.00 0.00 33.30 3.50
6738 9599 8.246871 ACTACTTTTAATAACACGAGGAGTACC 58.753 37.037 0.00 0.00 0.00 3.34
6744 9605 8.644318 AGCATACTACTTTTAATAACACGAGG 57.356 34.615 0.00 0.00 0.00 4.63
6745 9606 9.901724 CAAGCATACTACTTTTAATAACACGAG 57.098 33.333 0.00 0.00 0.00 4.18
6746 9607 9.426837 ACAAGCATACTACTTTTAATAACACGA 57.573 29.630 0.00 0.00 0.00 4.35
6755 9616 8.038944 CCCTCTGTAACAAGCATACTACTTTTA 58.961 37.037 0.00 0.00 0.00 1.52
6757 9618 6.212791 TCCCTCTGTAACAAGCATACTACTTT 59.787 38.462 0.00 0.00 0.00 2.66
6760 9621 5.127356 ACTCCCTCTGTAACAAGCATACTAC 59.873 44.000 0.00 0.00 0.00 2.73
6771 9632 4.930405 GCTCTTTGTTACTCCCTCTGTAAC 59.070 45.833 9.11 9.11 45.72 2.50
6774 9635 3.243724 AGCTCTTTGTTACTCCCTCTGT 58.756 45.455 0.00 0.00 0.00 3.41
6775 9636 3.971245 AGCTCTTTGTTACTCCCTCTG 57.029 47.619 0.00 0.00 0.00 3.35
6876 9739 8.280909 TGCATTTTTCTATTGAAGAACGAAAC 57.719 30.769 0.00 0.00 44.02 2.78
6878 9741 8.751335 GTTTGCATTTTTCTATTGAAGAACGAA 58.249 29.630 0.00 0.00 44.02 3.85
6894 9757 9.985730 TGAAGAAATTCTATCTGTTTGCATTTT 57.014 25.926 0.00 0.00 0.00 1.82
6898 9761 7.984422 TCTGAAGAAATTCTATCTGTTTGCA 57.016 32.000 0.00 0.00 0.00 4.08
6927 9792 2.349532 GCGAAAACAGTTGTGCTCTACC 60.350 50.000 0.00 0.00 0.00 3.18
6939 9804 1.539388 TGTTATGCCAGGCGAAAACAG 59.461 47.619 17.70 0.00 0.00 3.16
6949 9814 2.030823 CACGTATGCTGTGTTATGCCAG 59.969 50.000 0.00 0.00 32.68 4.85
6956 9821 0.673644 GGCTCCACGTATGCTGTGTT 60.674 55.000 0.00 0.00 35.56 3.32
7002 9867 0.614415 GGTGGTGGATTGGATGGCAA 60.614 55.000 0.00 0.00 0.00 4.52
7023 9888 2.125269 AATCCTGTACACCGCCGC 60.125 61.111 0.00 0.00 0.00 6.53
7025 9890 1.369091 CTGCAATCCTGTACACCGCC 61.369 60.000 0.00 0.00 0.00 6.13
7053 9953 2.414293 CGTAGTCACCGAGGAAACAGAG 60.414 54.545 0.00 0.00 0.00 3.35
7057 9957 1.000938 ACACGTAGTCACCGAGGAAAC 60.001 52.381 0.00 0.00 41.61 2.78
7080 9980 1.303091 GGGTATGCGAAGGCGTTGTT 61.303 55.000 0.00 0.00 44.10 2.83
7132 10044 2.117423 CCGGGGCAAGGGTTTCTT 59.883 61.111 0.00 0.00 35.79 2.52
7133 10045 2.856988 TCCGGGGCAAGGGTTTCT 60.857 61.111 0.00 0.00 0.00 2.52
7134 10046 2.675423 GTCCGGGGCAAGGGTTTC 60.675 66.667 0.00 0.00 0.00 2.78
7135 10047 4.653888 CGTCCGGGGCAAGGGTTT 62.654 66.667 0.00 0.00 0.00 3.27
7138 10050 4.338710 TTTCGTCCGGGGCAAGGG 62.339 66.667 0.00 0.00 0.00 3.95
7139 10051 3.053896 GTTTCGTCCGGGGCAAGG 61.054 66.667 0.00 0.00 0.00 3.61
7140 10052 2.032071 AGTTTCGTCCGGGGCAAG 59.968 61.111 0.00 0.00 0.00 4.01
7141 10053 2.281208 CAGTTTCGTCCGGGGCAA 60.281 61.111 0.00 0.00 0.00 4.52
7201 10113 5.687770 TGATGAAAGAACAAAATCGCAGA 57.312 34.783 0.00 0.00 45.75 4.26
7231 10144 1.284491 TGGGTATGAAATCTGCAGGCA 59.716 47.619 15.13 7.86 0.00 4.75
7248 10161 1.254026 TTCCGTCACTGTCTACTGGG 58.746 55.000 0.00 0.00 0.00 4.45
7264 10177 1.212616 CAGCGATGAGTCCGATTTCC 58.787 55.000 0.00 0.00 0.00 3.13
7315 10228 2.159960 GCTCGCTACTGTTCGTCAAAAG 60.160 50.000 0.00 0.00 0.00 2.27
7323 10236 1.473278 ACCTAGTGCTCGCTACTGTTC 59.527 52.381 0.00 0.00 0.00 3.18
7340 10253 8.797438 GGTCTTCTTCTTTATTGAATGAAACCT 58.203 33.333 0.00 0.00 30.68 3.50
7341 10254 7.750903 CGGTCTTCTTCTTTATTGAATGAAACC 59.249 37.037 0.00 0.00 30.68 3.27
7342 10255 8.290325 ACGGTCTTCTTCTTTATTGAATGAAAC 58.710 33.333 0.00 0.00 30.68 2.78
7343 10256 8.391075 ACGGTCTTCTTCTTTATTGAATGAAA 57.609 30.769 0.00 0.00 30.68 2.69
7344 10257 7.659799 TGACGGTCTTCTTCTTTATTGAATGAA 59.340 33.333 9.88 0.00 0.00 2.57
7345 10258 7.158697 TGACGGTCTTCTTCTTTATTGAATGA 58.841 34.615 9.88 0.00 0.00 2.57
7346 10259 7.331934 TCTGACGGTCTTCTTCTTTATTGAATG 59.668 37.037 9.88 0.00 0.00 2.67
7347 10260 7.386851 TCTGACGGTCTTCTTCTTTATTGAAT 58.613 34.615 9.88 0.00 0.00 2.57
7348 10261 6.755206 TCTGACGGTCTTCTTCTTTATTGAA 58.245 36.000 9.88 0.00 0.00 2.69
7349 10262 6.340962 TCTGACGGTCTTCTTCTTTATTGA 57.659 37.500 9.88 0.00 0.00 2.57
7350 10263 5.062809 GCTCTGACGGTCTTCTTCTTTATTG 59.937 44.000 9.88 0.00 0.00 1.90
7351 10264 5.172205 GCTCTGACGGTCTTCTTCTTTATT 58.828 41.667 9.88 0.00 0.00 1.40
7352 10265 4.382147 GGCTCTGACGGTCTTCTTCTTTAT 60.382 45.833 9.88 0.00 0.00 1.40
7353 10266 3.056749 GGCTCTGACGGTCTTCTTCTTTA 60.057 47.826 9.88 0.00 0.00 1.85
7354 10267 2.289133 GGCTCTGACGGTCTTCTTCTTT 60.289 50.000 9.88 0.00 0.00 2.52
7355 10268 1.273886 GGCTCTGACGGTCTTCTTCTT 59.726 52.381 9.88 0.00 0.00 2.52
7356 10269 0.892063 GGCTCTGACGGTCTTCTTCT 59.108 55.000 9.88 0.00 0.00 2.85
7357 10270 0.108567 GGGCTCTGACGGTCTTCTTC 60.109 60.000 9.88 0.00 0.00 2.87
7358 10271 1.878656 CGGGCTCTGACGGTCTTCTT 61.879 60.000 9.88 0.00 0.00 2.52
7359 10272 2.344203 CGGGCTCTGACGGTCTTCT 61.344 63.158 9.88 0.00 0.00 2.85
7360 10273 2.182030 CGGGCTCTGACGGTCTTC 59.818 66.667 9.88 0.00 0.00 2.87
7361 10274 3.382832 CCGGGCTCTGACGGTCTT 61.383 66.667 9.88 0.00 44.85 3.01
7366 10279 0.458025 GTAACTTCCGGGCTCTGACG 60.458 60.000 0.00 0.00 0.00 4.35
7367 10280 0.606604 TGTAACTTCCGGGCTCTGAC 59.393 55.000 0.00 0.00 0.00 3.51
7368 10281 1.344065 TTGTAACTTCCGGGCTCTGA 58.656 50.000 0.00 0.00 0.00 3.27
7369 10282 2.009774 CATTGTAACTTCCGGGCTCTG 58.990 52.381 0.00 0.00 0.00 3.35
7370 10283 1.906574 TCATTGTAACTTCCGGGCTCT 59.093 47.619 0.00 0.00 0.00 4.09
7371 10284 2.093658 TCTCATTGTAACTTCCGGGCTC 60.094 50.000 0.00 0.00 0.00 4.70
7372 10285 1.906574 TCTCATTGTAACTTCCGGGCT 59.093 47.619 0.00 0.00 0.00 5.19
7373 10286 2.396590 TCTCATTGTAACTTCCGGGC 57.603 50.000 0.00 0.00 0.00 6.13
7374 10287 5.527582 CCTATTTCTCATTGTAACTTCCGGG 59.472 44.000 0.00 0.00 0.00 5.73
7375 10288 6.113411 ACCTATTTCTCATTGTAACTTCCGG 58.887 40.000 0.00 0.00 0.00 5.14
7376 10289 7.333423 TCAACCTATTTCTCATTGTAACTTCCG 59.667 37.037 0.00 0.00 0.00 4.30
7377 10290 8.561738 TCAACCTATTTCTCATTGTAACTTCC 57.438 34.615 0.00 0.00 0.00 3.46
7378 10291 9.436957 TCTCAACCTATTTCTCATTGTAACTTC 57.563 33.333 0.00 0.00 0.00 3.01
7379 10292 9.965902 ATCTCAACCTATTTCTCATTGTAACTT 57.034 29.630 0.00 0.00 0.00 2.66
7380 10293 9.388506 CATCTCAACCTATTTCTCATTGTAACT 57.611 33.333 0.00 0.00 0.00 2.24
7381 10294 8.125448 GCATCTCAACCTATTTCTCATTGTAAC 58.875 37.037 0.00 0.00 0.00 2.50
7382 10295 7.828717 TGCATCTCAACCTATTTCTCATTGTAA 59.171 33.333 0.00 0.00 0.00 2.41
7383 10296 7.280876 GTGCATCTCAACCTATTTCTCATTGTA 59.719 37.037 0.00 0.00 0.00 2.41
7384 10297 6.094603 GTGCATCTCAACCTATTTCTCATTGT 59.905 38.462 0.00 0.00 0.00 2.71
7385 10298 6.094464 TGTGCATCTCAACCTATTTCTCATTG 59.906 38.462 0.00 0.00 0.00 2.82
7386 10299 6.182627 TGTGCATCTCAACCTATTTCTCATT 58.817 36.000 0.00 0.00 0.00 2.57
7387 10300 5.748402 TGTGCATCTCAACCTATTTCTCAT 58.252 37.500 0.00 0.00 0.00 2.90
7388 10301 5.164620 TGTGCATCTCAACCTATTTCTCA 57.835 39.130 0.00 0.00 0.00 3.27
7389 10302 5.645497 ACTTGTGCATCTCAACCTATTTCTC 59.355 40.000 0.00 0.00 0.00 2.87
7390 10303 5.564550 ACTTGTGCATCTCAACCTATTTCT 58.435 37.500 0.00 0.00 0.00 2.52
7391 10304 5.412594 TGACTTGTGCATCTCAACCTATTTC 59.587 40.000 0.00 0.00 0.00 2.17
7392 10305 5.182001 GTGACTTGTGCATCTCAACCTATTT 59.818 40.000 0.00 0.00 0.00 1.40
7393 10306 4.697352 GTGACTTGTGCATCTCAACCTATT 59.303 41.667 0.00 0.00 0.00 1.73
7394 10307 4.019860 AGTGACTTGTGCATCTCAACCTAT 60.020 41.667 0.00 0.00 0.00 2.57
7395 10308 3.324846 AGTGACTTGTGCATCTCAACCTA 59.675 43.478 0.00 0.00 0.00 3.08
7396 10309 2.105477 AGTGACTTGTGCATCTCAACCT 59.895 45.455 0.00 0.00 0.00 3.50
7397 10310 2.498167 AGTGACTTGTGCATCTCAACC 58.502 47.619 0.00 0.00 0.00 3.77
7398 10311 4.310769 AGTAGTGACTTGTGCATCTCAAC 58.689 43.478 0.00 0.00 28.61 3.18
7399 10312 4.607293 AGTAGTGACTTGTGCATCTCAA 57.393 40.909 0.00 0.00 28.61 3.02
7400 10313 5.722021 TTAGTAGTGACTTGTGCATCTCA 57.278 39.130 0.00 0.00 37.10 3.27
7401 10314 6.591834 ACATTTAGTAGTGACTTGTGCATCTC 59.408 38.462 0.00 0.00 37.10 2.75
7402 10315 6.369890 CACATTTAGTAGTGACTTGTGCATCT 59.630 38.462 0.00 0.00 35.96 2.90
7403 10316 6.368791 TCACATTTAGTAGTGACTTGTGCATC 59.631 38.462 7.72 0.00 39.92 3.91
7404 10317 6.230472 TCACATTTAGTAGTGACTTGTGCAT 58.770 36.000 7.72 0.00 39.92 3.96
7405 10318 5.606505 TCACATTTAGTAGTGACTTGTGCA 58.393 37.500 7.72 0.00 39.92 4.57
7406 10319 6.147821 ACATCACATTTAGTAGTGACTTGTGC 59.852 38.462 7.72 0.00 46.38 4.57
7407 10320 7.384932 TCACATCACATTTAGTAGTGACTTGTG 59.615 37.037 16.92 16.92 46.65 3.33
7408 10321 7.441836 TCACATCACATTTAGTAGTGACTTGT 58.558 34.615 0.00 0.00 46.38 3.16
7409 10322 7.889589 TCACATCACATTTAGTAGTGACTTG 57.110 36.000 0.00 0.00 46.38 3.16
7410 10323 8.097038 ACATCACATCACATTTAGTAGTGACTT 58.903 33.333 0.00 0.00 46.38 3.01
7411 10324 7.547019 CACATCACATCACATTTAGTAGTGACT 59.453 37.037 0.00 0.00 46.38 3.41
7412 10325 7.331934 ACACATCACATCACATTTAGTAGTGAC 59.668 37.037 0.00 0.00 46.38 3.67
7414 10327 7.601073 ACACATCACATCACATTTAGTAGTG 57.399 36.000 0.00 0.00 37.10 2.74
7415 10328 7.361201 GCAACACATCACATCACATTTAGTAGT 60.361 37.037 0.00 0.00 0.00 2.73
7416 10329 6.963242 GCAACACATCACATCACATTTAGTAG 59.037 38.462 0.00 0.00 0.00 2.57
7417 10330 6.841119 GCAACACATCACATCACATTTAGTA 58.159 36.000 0.00 0.00 0.00 1.82
7418 10331 5.702865 GCAACACATCACATCACATTTAGT 58.297 37.500 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.