Multiple sequence alignment - TraesCS4A01G028000

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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 TraesCS4A01G028000 chr4A 100.000 3541 0 0 1 3541 19657559 19661099 0.000000e+00 6540
1 TraesCS4A01G028000 chr4D 94.417 2042 95 8 662 2693 447340242 447338210 0.000000e+00 3121
2 TraesCS4A01G028000 chr4D 87.622 614 49 16 1 604 447340966 447340370 0.000000e+00 688
3 TraesCS4A01G028000 chr4D 96.684 392 12 1 2778 3168 447338208 447337817 0.000000e+00 651
4 TraesCS4A01G028000 chr4D 91.358 162 9 2 3357 3513 447337821 447337660 2.140000e-52 217
5 TraesCS4A01G028000 chr4D 96.703 91 3 0 2690 2780 41339602 41339512 6.120000e-33 152
6 TraesCS4A01G028000 chr4B 93.147 2043 112 10 662 2694 559856887 559854863 0.000000e+00 2972
7 TraesCS4A01G028000 chr4B 87.394 587 46 15 29 604 559857584 559857015 0.000000e+00 649
8 TraesCS4A01G028000 chr4B 84.577 402 19 17 3146 3541 559845600 559845236 3.360000e-95 359
9 TraesCS4A01G028000 chr4B 93.363 226 8 3 2926 3144 559854547 559854322 9.480000e-86 327
10 TraesCS4A01G028000 chr6D 95.000 100 4 1 2683 2781 45481761 45481860 4.730000e-34 156
11 TraesCS4A01G028000 chr3D 95.789 95 4 0 2684 2778 608805129 608805035 1.700000e-33 154
12 TraesCS4A01G028000 chr1B 92.593 108 7 1 2677 2783 436383767 436383660 1.700000e-33 154
13 TraesCS4A01G028000 chr1B 94.898 98 3 2 2690 2785 392149873 392149776 6.120000e-33 152
14 TraesCS4A01G028000 chr7D 96.703 91 3 0 2688 2778 463109039 463109129 6.120000e-33 152
15 TraesCS4A01G028000 chr5D 93.069 101 7 0 2678 2778 220694077 220693977 7.920000e-32 148
16 TraesCS4A01G028000 chr2D 92.381 105 6 2 2677 2780 645267912 645267809 7.920000e-32 148
17 TraesCS4A01G028000 chr6A 92.381 105 5 2 2676 2777 418953980 418954084 2.850000e-31 147


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 TraesCS4A01G028000 chr4A 19657559 19661099 3540 False 6540.00 6540 100.000000 1 3541 1 chr4A.!!$F1 3540
1 TraesCS4A01G028000 chr4D 447337660 447340966 3306 True 1169.25 3121 92.520250 1 3513 4 chr4D.!!$R2 3512
2 TraesCS4A01G028000 chr4B 559854322 559857584 3262 True 1316.00 2972 91.301333 29 3144 3 chr4B.!!$R2 3115

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
255 260 0.111253 AGGTGGCACTGGGAAGAAAG 59.889 55.0 18.45 0.00 0.00 2.62 F
844 936 0.253044 GATAGCTGTTCCTGTGGGCA 59.747 55.0 0.00 0.00 0.00 5.36 F
1395 1493 0.034767 TCCTTTGATCAGGCTGGCAG 60.035 55.0 15.73 10.94 33.35 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1180 1275 0.038709 TTGCAAAGCGGGTTGTATGC 60.039 50.0 0.00 7.85 0.00 3.14 R
1995 2096 0.665369 GTGCACATGTGGAAGCAAGC 60.665 55.0 26.55 10.55 38.91 4.01 R
2694 2795 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.0 0.00 0.00 0.00 4.30 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
27 29 6.470278 AGTTTACTAATACACAGTGGGGTTC 58.530 40.000 5.31 0.00 0.00 3.62
53 55 4.776795 AACTGGGCGGTTACTTTTATTG 57.223 40.909 0.00 0.00 0.00 1.90
70 72 9.816354 ACTTTTATTGCTTCACAACAAATTACT 57.184 25.926 0.00 0.00 42.27 2.24
72 74 8.586570 TTTATTGCTTCACAACAAATTACTGG 57.413 30.769 0.00 0.00 42.27 4.00
111 113 0.690762 TTACCAGTCCCCTGCTTGTC 59.309 55.000 0.00 0.00 37.38 3.18
121 123 0.830648 CCTGCTTGTCCGGATTCCTA 59.169 55.000 7.81 0.00 0.00 2.94
144 147 2.196595 CTGGGGGACTGGACTTCATTA 58.803 52.381 0.00 0.00 0.00 1.90
154 157 5.999044 ACTGGACTTCATTAGATGCTGATT 58.001 37.500 0.00 0.00 0.00 2.57
158 161 7.765307 TGGACTTCATTAGATGCTGATTTTTC 58.235 34.615 0.00 0.00 0.00 2.29
159 162 7.148018 TGGACTTCATTAGATGCTGATTTTTCC 60.148 37.037 0.00 0.00 0.00 3.13
178 181 2.026915 TCCTGTTCTGTATGTGCTGCAT 60.027 45.455 5.27 0.00 41.42 3.96
188 191 1.108132 TGTGCTGCATGCCTTTGTCA 61.108 50.000 16.68 4.35 42.00 3.58
192 195 2.224329 TGCTGCATGCCTTTGTCAAAAT 60.224 40.909 16.68 0.00 42.00 1.82
194 197 2.997986 CTGCATGCCTTTGTCAAAATCC 59.002 45.455 16.68 0.00 0.00 3.01
198 201 2.028130 TGCCTTTGTCAAAATCCGTGT 58.972 42.857 0.00 0.00 0.00 4.49
203 208 3.428746 TTGTCAAAATCCGTGTGGTTG 57.571 42.857 0.00 0.00 36.30 3.77
207 212 2.032302 TCAAAATCCGTGTGGTTGAACG 59.968 45.455 0.00 0.00 39.48 3.95
211 216 2.248835 CCGTGTGGTTGAACGTCCC 61.249 63.158 0.00 0.00 38.11 4.46
255 260 0.111253 AGGTGGCACTGGGAAGAAAG 59.889 55.000 18.45 0.00 0.00 2.62
260 265 1.620323 GGCACTGGGAAGAAAGCATTT 59.380 47.619 0.00 0.00 43.98 2.32
289 294 3.187432 GCTTGAGCTTGTCAAACCTAGTC 59.813 47.826 0.00 0.00 44.83 2.59
290 295 4.380531 CTTGAGCTTGTCAAACCTAGTCA 58.619 43.478 0.00 0.00 44.83 3.41
291 296 4.623932 TGAGCTTGTCAAACCTAGTCAT 57.376 40.909 0.00 0.00 29.64 3.06
292 297 4.973168 TGAGCTTGTCAAACCTAGTCATT 58.027 39.130 0.00 0.00 29.64 2.57
293 298 6.109156 TGAGCTTGTCAAACCTAGTCATTA 57.891 37.500 0.00 0.00 29.64 1.90
295 300 7.168219 TGAGCTTGTCAAACCTAGTCATTATT 58.832 34.615 0.00 0.00 29.64 1.40
296 301 8.318412 TGAGCTTGTCAAACCTAGTCATTATTA 58.682 33.333 0.00 0.00 29.64 0.98
349 362 3.701040 AGCTTTGGTGTTTTGACATCTGT 59.299 39.130 0.00 0.00 0.00 3.41
358 371 4.083855 TGTTTTGACATCTGTTGCGAGATC 60.084 41.667 0.00 0.00 29.72 2.75
362 375 3.257393 GACATCTGTTGCGAGATCTTGT 58.743 45.455 11.71 1.26 29.72 3.16
372 385 1.738365 CGAGATCTTGTGCCCTCTGTG 60.738 57.143 0.00 0.00 0.00 3.66
384 397 4.333926 GTGCCCTCTGTGATTTATCTGAAC 59.666 45.833 0.00 0.00 0.00 3.18
389 402 5.587443 CCTCTGTGATTTATCTGAACATGCA 59.413 40.000 0.00 0.00 0.00 3.96
419 432 3.996150 CATCTGTGCAAGTCTTGGTTT 57.004 42.857 14.40 0.00 0.00 3.27
421 434 5.039480 CATCTGTGCAAGTCTTGGTTTAG 57.961 43.478 14.40 0.00 0.00 1.85
422 435 4.415881 TCTGTGCAAGTCTTGGTTTAGA 57.584 40.909 14.40 0.00 0.00 2.10
423 436 4.973168 TCTGTGCAAGTCTTGGTTTAGAT 58.027 39.130 14.40 0.00 0.00 1.98
424 437 6.109156 TCTGTGCAAGTCTTGGTTTAGATA 57.891 37.500 14.40 0.00 0.00 1.98
425 438 6.711277 TCTGTGCAAGTCTTGGTTTAGATAT 58.289 36.000 14.40 0.00 0.00 1.63
506 519 1.470098 GCAGGCACACTATGAACCTTG 59.530 52.381 0.00 0.00 0.00 3.61
519 532 8.246180 CACTATGAACCTTGTTTGAAGCAATAT 58.754 33.333 0.00 0.00 0.00 1.28
558 571 2.839486 TCTGTCTTGTGATGGTGACC 57.161 50.000 0.00 0.00 0.00 4.02
579 592 6.547880 TGACCTGCTATTTCTTTGGTTTACAA 59.452 34.615 0.00 0.00 37.28 2.41
584 597 9.394477 CTGCTATTTCTTTGGTTTACAACTTAC 57.606 33.333 0.00 0.00 39.19 2.34
604 617 9.596308 AACTTACTGGGATTAAGGTAACAAAAT 57.404 29.630 0.00 0.00 41.41 1.82
623 636 6.472163 ACAAAATATATTCGCTTTTTGCCGAG 59.528 34.615 0.00 0.00 40.82 4.63
631 654 2.607635 CGCTTTTTGCCGAGCTCTTATA 59.392 45.455 12.85 0.00 38.78 0.98
636 659 6.197282 GCTTTTTGCCGAGCTCTTATATTTTC 59.803 38.462 12.85 0.00 36.01 2.29
647 670 8.219546 AGCTCTTATATTTTCCTTTCTTCTGC 57.780 34.615 0.00 0.00 0.00 4.26
703 795 5.667172 TCTCATGGTCCTCTTTTGGATATGA 59.333 40.000 0.00 0.00 38.75 2.15
732 824 1.923356 AATTGTCAGGGCGAACCAAT 58.077 45.000 0.00 0.00 43.89 3.16
788 880 2.839486 TCTGACAGTGACATGAACCC 57.161 50.000 0.00 0.00 0.00 4.11
798 890 2.955660 TGACATGAACCCACCTTTTCAC 59.044 45.455 0.00 0.00 34.61 3.18
844 936 0.253044 GATAGCTGTTCCTGTGGGCA 59.747 55.000 0.00 0.00 0.00 5.36
951 1044 3.278574 TCGATCCTGTTAAAATGCCCTG 58.721 45.455 0.00 0.00 0.00 4.45
1006 1101 2.804986 TCCAGCCATACAAATGAGCA 57.195 45.000 0.00 0.00 34.84 4.26
1017 1112 2.369532 ACAAATGAGCACCAAAGCCATT 59.630 40.909 0.00 0.00 37.15 3.16
1028 1123 4.467438 CACCAAAGCCATTTCCCTCTATTT 59.533 41.667 0.00 0.00 0.00 1.40
1098 1193 1.339151 ACCACTTCATTCCTTCGAGCC 60.339 52.381 0.00 0.00 0.00 4.70
1120 1215 2.230508 CTGCTTGATCTTGCAACACCAT 59.769 45.455 12.70 0.00 38.81 3.55
1123 1218 2.885135 TGATCTTGCAACACCATCCT 57.115 45.000 0.00 0.00 0.00 3.24
1140 1235 6.536224 CACCATCCTTTCCATTTAATTTGCTC 59.464 38.462 0.00 0.00 0.00 4.26
1180 1275 2.564771 ACTATCATTGCCATCGTGGTG 58.435 47.619 6.02 0.00 40.46 4.17
1182 1277 0.680601 ATCATTGCCATCGTGGTGCA 60.681 50.000 6.02 0.00 40.46 4.57
1185 1280 1.024271 ATTGCCATCGTGGTGCATAC 58.976 50.000 0.00 0.00 40.46 2.39
1194 1289 1.074072 TGGTGCATACAACCCGCTT 59.926 52.632 0.00 0.00 29.81 4.68
1197 1292 0.732538 GTGCATACAACCCGCTTTGC 60.733 55.000 0.00 0.00 0.00 3.68
1198 1293 1.175347 TGCATACAACCCGCTTTGCA 61.175 50.000 0.00 0.00 37.73 4.08
1209 1304 1.205417 CCGCTTTGCAATGATTTCCCT 59.795 47.619 15.97 0.00 0.00 4.20
1212 1307 2.736400 GCTTTGCAATGATTTCCCTCCG 60.736 50.000 15.97 0.00 0.00 4.63
1228 1323 4.760047 CGGACTTCCCACCGCCTG 62.760 72.222 0.00 0.00 42.55 4.85
1266 1361 3.491619 CGATCTTCTGTGTCGATCCCAAT 60.492 47.826 0.00 0.00 37.55 3.16
1275 1370 1.452651 CGATCCCAATGGCTGCTGT 60.453 57.895 0.00 0.00 0.00 4.40
1287 1382 1.835483 GCTGCTGTGACTTCACCACG 61.835 60.000 6.91 0.00 45.88 4.94
1335 1430 4.021916 CAAGATCCAGCCAAAAGAGGAAT 58.978 43.478 0.00 0.00 33.17 3.01
1339 1434 3.157087 TCCAGCCAAAAGAGGAATGTTC 58.843 45.455 0.00 0.00 0.00 3.18
1350 1445 5.447778 AGAGGAATGTTCTGTGGATCAAT 57.552 39.130 0.00 0.00 0.00 2.57
1362 1457 4.973168 TGTGGATCAATAAGGGCATCTAC 58.027 43.478 0.00 0.00 0.00 2.59
1363 1458 4.202461 TGTGGATCAATAAGGGCATCTACC 60.202 45.833 0.00 0.00 0.00 3.18
1377 1472 5.450550 GGGCATCTACCTGTAAGCAATTTTC 60.451 44.000 0.00 0.00 0.00 2.29
1387 1482 6.810182 CCTGTAAGCAATTTTCCTTTGATCAG 59.190 38.462 0.00 0.00 0.00 2.90
1388 1483 6.690530 TGTAAGCAATTTTCCTTTGATCAGG 58.309 36.000 0.00 0.00 34.86 3.86
1391 1489 3.930848 GCAATTTTCCTTTGATCAGGCTG 59.069 43.478 8.58 8.58 33.35 4.85
1392 1490 4.501071 CAATTTTCCTTTGATCAGGCTGG 58.499 43.478 15.73 0.00 33.35 4.85
1395 1493 0.034767 TCCTTTGATCAGGCTGGCAG 60.035 55.000 15.73 10.94 33.35 4.85
1400 1498 1.818785 GATCAGGCTGGCAGCACTC 60.819 63.158 37.49 23.55 44.75 3.51
1406 1504 2.404995 GCTGGCAGCACTCCATGTC 61.405 63.158 33.33 0.00 41.89 3.06
1421 1519 4.378774 TCCATGTCCAAAGTGCAAAATTG 58.621 39.130 0.00 0.00 0.00 2.32
1426 1524 7.360269 CCATGTCCAAAGTGCAAAATTGATAAC 60.360 37.037 8.49 5.35 0.00 1.89
1447 1545 1.541147 TGTGCTGTTAATGAAGCTGCC 59.459 47.619 0.00 0.00 40.21 4.85
1450 1551 2.229543 TGCTGTTAATGAAGCTGCCTTG 59.770 45.455 0.00 0.00 40.21 3.61
1466 1567 3.876914 TGCCTTGTTACAGTGAGAAAGTG 59.123 43.478 0.00 0.00 35.13 3.16
1481 1582 0.977395 AAGTGACAGTCCCTGCTACC 59.023 55.000 0.00 0.00 34.37 3.18
1526 1627 0.179073 AGGGATTTGATCTGACGGCG 60.179 55.000 4.80 4.80 0.00 6.46
1538 1639 0.177836 TGACGGCGATCATGTGGAAT 59.822 50.000 16.62 0.00 0.00 3.01
1553 1654 2.668457 GTGGAATGACACAGCTAACTCG 59.332 50.000 0.00 0.00 40.99 4.18
1580 1681 1.337823 GGAACCTTCTACAGCGCTTCA 60.338 52.381 7.50 0.00 0.00 3.02
1589 1690 1.221414 ACAGCGCTTCAGTTTCTGTC 58.779 50.000 7.50 0.00 33.16 3.51
1595 1696 1.195674 GCTTCAGTTTCTGTCTTCGCC 59.804 52.381 0.00 0.00 32.61 5.54
1596 1697 2.483876 CTTCAGTTTCTGTCTTCGCCA 58.516 47.619 0.00 0.00 32.61 5.69
1628 1729 2.536329 CGCGAAGAACATCAGCTTCATG 60.536 50.000 0.00 1.44 40.31 3.07
1633 1734 5.220548 CGAAGAACATCAGCTTCATGGTAAG 60.221 44.000 7.24 0.00 40.31 2.34
1634 1735 5.171339 AGAACATCAGCTTCATGGTAAGT 57.829 39.130 7.24 0.00 0.00 2.24
1635 1736 5.564550 AGAACATCAGCTTCATGGTAAGTT 58.435 37.500 7.24 0.00 0.00 2.66
1636 1737 5.413833 AGAACATCAGCTTCATGGTAAGTTG 59.586 40.000 7.24 5.06 38.59 3.16
1637 1738 4.012374 ACATCAGCTTCATGGTAAGTTGG 58.988 43.478 9.96 0.67 38.01 3.77
1638 1739 3.788227 TCAGCTTCATGGTAAGTTGGT 57.212 42.857 9.96 0.00 38.01 3.67
1639 1740 4.901197 TCAGCTTCATGGTAAGTTGGTA 57.099 40.909 9.96 0.00 38.01 3.25
1640 1741 5.235850 TCAGCTTCATGGTAAGTTGGTAA 57.764 39.130 9.96 0.00 38.01 2.85
1643 1744 6.014070 TCAGCTTCATGGTAAGTTGGTAACTA 60.014 38.462 9.96 0.00 41.91 2.24
1645 1746 5.935789 GCTTCATGGTAAGTTGGTAACTACA 59.064 40.000 0.00 0.00 45.35 2.74
1650 1751 7.940137 TCATGGTAAGTTGGTAACTACAAACAT 59.060 33.333 9.31 1.00 45.35 2.71
1651 1752 7.733402 TGGTAAGTTGGTAACTACAAACATC 57.267 36.000 9.31 0.82 45.35 3.06
1688 1789 0.250858 TAAGCCACACTGCATGCACT 60.251 50.000 18.46 8.48 0.00 4.40
1701 1802 2.413765 GCATGCACTTTGAGTAGCACTG 60.414 50.000 14.21 0.00 35.96 3.66
1709 1810 5.403766 CACTTTGAGTAGCACTGTAACTCTG 59.596 44.000 14.40 9.33 40.25 3.35
1719 1820 6.109359 AGCACTGTAACTCTGTTAATCATCC 58.891 40.000 0.00 0.00 0.00 3.51
1726 1827 6.365970 AACTCTGTTAATCATCCTGACACT 57.634 37.500 0.00 0.00 0.00 3.55
1755 1856 0.251165 CACCAATTCCAAGACCCGGT 60.251 55.000 0.00 0.00 0.00 5.28
1791 1892 1.077357 AGTCGCTCTGAGGATCGGT 60.077 57.895 6.83 0.00 43.66 4.69
1854 1955 3.061295 CACAAGATACACTGCACGATGAC 59.939 47.826 0.00 0.00 0.00 3.06
1899 2000 3.173953 TGTTTCATTCAGGGCTCCATT 57.826 42.857 0.00 0.00 0.00 3.16
1959 2060 7.509546 AGGTGAGTCAAAGTTATTTCTCAAGA 58.490 34.615 0.00 0.00 33.49 3.02
1995 2096 4.024048 AGCACCGAGTTTGTTCACTAATTG 60.024 41.667 0.00 0.00 0.00 2.32
2012 2113 0.032403 TTGCTTGCTTCCACATGTGC 59.968 50.000 20.81 9.65 0.00 4.57
2112 2213 1.379710 CATGCCCGGGAATCCAACA 60.380 57.895 29.31 11.54 0.00 3.33
2220 2321 4.106909 CCGTGTTGTATTCGCATACACTA 58.893 43.478 7.43 0.00 44.19 2.74
2296 2397 3.139957 AGAGATCAGTATGCCTCTCCTGA 59.860 47.826 0.00 0.00 42.16 3.86
2333 2434 5.011586 TCTGGAATCAATTCAGAATGCACA 58.988 37.500 0.00 0.00 38.53 4.57
2612 2713 4.504097 GCAAAAGGAACAAGTTAGCACAAG 59.496 41.667 0.00 0.00 0.00 3.16
2697 2798 9.525409 CATCATTTGGAATTTCAGAAATACTCC 57.475 33.333 15.74 15.74 31.35 3.85
2698 2799 8.066612 TCATTTGGAATTTCAGAAATACTCCC 57.933 34.615 18.37 13.30 30.17 4.30
2699 2800 7.895429 TCATTTGGAATTTCAGAAATACTCCCT 59.105 33.333 18.37 6.12 30.17 4.20
2700 2801 7.703058 TTTGGAATTTCAGAAATACTCCCTC 57.297 36.000 18.37 8.57 30.17 4.30
2701 2802 5.755849 TGGAATTTCAGAAATACTCCCTCC 58.244 41.667 18.37 15.47 30.17 4.30
2702 2803 4.816925 GGAATTTCAGAAATACTCCCTCCG 59.183 45.833 8.88 0.00 0.00 4.63
2703 2804 5.429130 GAATTTCAGAAATACTCCCTCCGT 58.571 41.667 8.88 0.00 0.00 4.69
2704 2805 4.467198 TTTCAGAAATACTCCCTCCGTC 57.533 45.455 0.00 0.00 0.00 4.79
2705 2806 2.385803 TCAGAAATACTCCCTCCGTCC 58.614 52.381 0.00 0.00 0.00 4.79
2706 2807 1.413077 CAGAAATACTCCCTCCGTCCC 59.587 57.143 0.00 0.00 0.00 4.46
2707 2808 1.007963 AGAAATACTCCCTCCGTCCCA 59.992 52.381 0.00 0.00 0.00 4.37
2708 2809 1.138464 GAAATACTCCCTCCGTCCCAC 59.862 57.143 0.00 0.00 0.00 4.61
2709 2810 0.042131 AATACTCCCTCCGTCCCACA 59.958 55.000 0.00 0.00 0.00 4.17
2710 2811 0.042131 ATACTCCCTCCGTCCCACAA 59.958 55.000 0.00 0.00 0.00 3.33
2711 2812 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
2712 2813 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
2713 2814 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
2714 2815 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
2715 2816 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
2716 2817 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
2717 2818 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2718 2819 3.389983 CCCTCCGTCCCACAATATAAGAA 59.610 47.826 0.00 0.00 0.00 2.52
2719 2820 4.377897 CCTCCGTCCCACAATATAAGAAC 58.622 47.826 0.00 0.00 0.00 3.01
2720 2821 4.049186 CTCCGTCCCACAATATAAGAACG 58.951 47.826 0.00 0.00 0.00 3.95
2721 2822 3.448301 TCCGTCCCACAATATAAGAACGT 59.552 43.478 0.00 0.00 0.00 3.99
2722 2823 4.081531 TCCGTCCCACAATATAAGAACGTT 60.082 41.667 0.00 0.00 0.00 3.99
2723 2824 4.632688 CCGTCCCACAATATAAGAACGTTT 59.367 41.667 0.46 0.00 0.00 3.60
2724 2825 5.122711 CCGTCCCACAATATAAGAACGTTTT 59.877 40.000 0.46 0.00 0.00 2.43
2725 2826 6.348704 CCGTCCCACAATATAAGAACGTTTTT 60.349 38.462 9.22 9.22 0.00 1.94
2726 2827 6.521821 CGTCCCACAATATAAGAACGTTTTTG 59.478 38.462 13.87 8.38 0.00 2.44
2727 2828 7.571613 CGTCCCACAATATAAGAACGTTTTTGA 60.572 37.037 13.87 2.81 0.00 2.69
2728 2829 7.536281 GTCCCACAATATAAGAACGTTTTTGAC 59.464 37.037 13.87 5.89 0.00 3.18
2729 2830 7.228906 TCCCACAATATAAGAACGTTTTTGACA 59.771 33.333 13.87 0.01 0.00 3.58
2730 2831 7.325097 CCCACAATATAAGAACGTTTTTGACAC 59.675 37.037 13.87 0.00 0.00 3.67
2731 2832 8.073768 CCACAATATAAGAACGTTTTTGACACT 58.926 33.333 13.87 0.00 0.00 3.55
2737 2838 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
2738 2839 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
2739 2840 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
2752 2853 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
2753 2854 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
2754 2855 6.815142 ACTAGTGTAGTGTCAAAAACGTTCTT 59.185 34.615 0.00 0.00 37.69 2.52
2755 2856 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
2756 2857 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
2757 2858 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
2758 2859 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
2763 2864 9.458374 AGTGTCAAAAACGTTCTTATATTTTGG 57.542 29.630 15.53 0.00 39.94 3.28
2764 2865 8.696175 GTGTCAAAAACGTTCTTATATTTTGGG 58.304 33.333 15.53 0.00 39.94 4.12
2765 2866 8.630917 TGTCAAAAACGTTCTTATATTTTGGGA 58.369 29.630 15.53 4.35 39.94 4.37
2766 2867 8.908678 GTCAAAAACGTTCTTATATTTTGGGAC 58.091 33.333 15.53 7.20 39.94 4.46
2767 2868 8.630917 TCAAAAACGTTCTTATATTTTGGGACA 58.369 29.630 15.53 0.00 39.94 4.02
2768 2869 8.911662 CAAAAACGTTCTTATATTTTGGGACAG 58.088 33.333 0.00 0.00 42.39 3.51
2769 2870 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
2770 2871 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
2771 2872 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
2772 2873 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
2773 2874 6.631766 CGTTCTTATATTTTGGGACAGAGGGA 60.632 42.308 0.00 0.00 42.39 4.20
2774 2875 6.500589 TCTTATATTTTGGGACAGAGGGAG 57.499 41.667 0.00 0.00 42.39 4.30
2775 2876 5.970640 TCTTATATTTTGGGACAGAGGGAGT 59.029 40.000 0.00 0.00 42.39 3.85
2776 2877 7.136885 TCTTATATTTTGGGACAGAGGGAGTA 58.863 38.462 0.00 0.00 42.39 2.59
2782 2883 3.587498 TGGGACAGAGGGAGTATATTGG 58.413 50.000 0.00 0.00 0.00 3.16
2956 3228 9.213777 AGGATACATGTCTTTAAGATAGGTTCA 57.786 33.333 13.52 0.00 32.77 3.18
3031 3303 3.099905 TGTTGCCTGCTATCTACTCTGT 58.900 45.455 0.00 0.00 0.00 3.41
3099 3378 1.548269 CTGGTGAGGTGGAAGAGAGAC 59.452 57.143 0.00 0.00 0.00 3.36
3150 3429 7.911651 TCTTAGCCAAGAGATTATCCCTTATG 58.088 38.462 0.00 0.00 35.82 1.90
3168 3448 9.218525 TCCCTTATGAAGAAAGATAAGAGATGT 57.781 33.333 0.00 0.00 35.12 3.06
3169 3449 9.270640 CCCTTATGAAGAAAGATAAGAGATGTG 57.729 37.037 0.00 0.00 35.12 3.21
3170 3450 9.829507 CCTTATGAAGAAAGATAAGAGATGTGT 57.170 33.333 0.00 0.00 35.12 3.72
3174 3454 8.939201 TGAAGAAAGATAAGAGATGTGTCATC 57.061 34.615 1.98 1.98 0.00 2.92
3175 3455 8.534496 TGAAGAAAGATAAGAGATGTGTCATCA 58.466 33.333 11.47 0.00 0.00 3.07
3176 3456 9.545105 GAAGAAAGATAAGAGATGTGTCATCAT 57.455 33.333 11.47 0.66 0.00 2.45
3177 3457 9.902684 AAGAAAGATAAGAGATGTGTCATCATT 57.097 29.630 11.47 8.33 0.00 2.57
3185 3465 7.803487 AGAGATGTGTCATCATTATATGGGA 57.197 36.000 11.47 0.00 0.00 4.37
3186 3466 8.389979 AGAGATGTGTCATCATTATATGGGAT 57.610 34.615 11.47 0.00 0.00 3.85
3187 3467 8.833734 AGAGATGTGTCATCATTATATGGGATT 58.166 33.333 11.47 0.00 0.00 3.01
3188 3468 9.458727 GAGATGTGTCATCATTATATGGGATTT 57.541 33.333 11.47 0.00 0.00 2.17
3189 3469 9.818270 AGATGTGTCATCATTATATGGGATTTT 57.182 29.630 11.47 0.00 0.00 1.82
3245 3525 8.599624 ATCATTTCATAATTTCAGGGTCTTGT 57.400 30.769 0.00 0.00 0.00 3.16
3246 3526 9.699410 ATCATTTCATAATTTCAGGGTCTTGTA 57.301 29.630 0.00 0.00 0.00 2.41
3247 3527 9.527157 TCATTTCATAATTTCAGGGTCTTGTAA 57.473 29.630 0.00 0.00 0.00 2.41
3256 3536 9.492973 AATTTCAGGGTCTTGTAAATTTGAATG 57.507 29.630 0.00 0.00 0.00 2.67
3257 3537 6.588719 TCAGGGTCTTGTAAATTTGAATGG 57.411 37.500 0.00 0.00 0.00 3.16
3258 3538 6.074648 TCAGGGTCTTGTAAATTTGAATGGT 58.925 36.000 0.00 0.00 0.00 3.55
3259 3539 7.235079 TCAGGGTCTTGTAAATTTGAATGGTA 58.765 34.615 0.00 0.00 0.00 3.25
3260 3540 7.393234 TCAGGGTCTTGTAAATTTGAATGGTAG 59.607 37.037 0.00 0.00 0.00 3.18
3261 3541 7.393234 CAGGGTCTTGTAAATTTGAATGGTAGA 59.607 37.037 0.00 0.00 0.00 2.59
3262 3542 7.611855 AGGGTCTTGTAAATTTGAATGGTAGAG 59.388 37.037 0.00 0.00 0.00 2.43
3263 3543 7.610305 GGGTCTTGTAAATTTGAATGGTAGAGA 59.390 37.037 0.00 0.00 0.00 3.10
3264 3544 9.178758 GGTCTTGTAAATTTGAATGGTAGAGAT 57.821 33.333 0.00 0.00 0.00 2.75
3275 3555 9.739276 TTTGAATGGTAGAGATAACAATTGACT 57.261 29.630 13.59 5.75 0.00 3.41
3316 3596 9.539825 AACATGTACTATTGCTTTCTCTAGATG 57.460 33.333 0.00 0.00 0.00 2.90
3317 3597 8.918116 ACATGTACTATTGCTTTCTCTAGATGA 58.082 33.333 0.00 0.00 0.00 2.92
3318 3598 9.926158 CATGTACTATTGCTTTCTCTAGATGAT 57.074 33.333 0.00 0.00 0.00 2.45
3319 3599 9.926158 ATGTACTATTGCTTTCTCTAGATGATG 57.074 33.333 0.00 0.00 0.00 3.07
3320 3600 8.918116 TGTACTATTGCTTTCTCTAGATGATGT 58.082 33.333 0.00 0.00 0.00 3.06
3321 3601 9.190858 GTACTATTGCTTTCTCTAGATGATGTG 57.809 37.037 0.00 0.00 0.00 3.21
3322 3602 8.016301 ACTATTGCTTTCTCTAGATGATGTGA 57.984 34.615 0.00 0.00 0.00 3.58
3323 3603 8.481314 ACTATTGCTTTCTCTAGATGATGTGAA 58.519 33.333 0.00 0.00 0.00 3.18
3324 3604 9.322773 CTATTGCTTTCTCTAGATGATGTGAAA 57.677 33.333 0.00 0.00 0.00 2.69
3325 3605 8.749026 ATTGCTTTCTCTAGATGATGTGAAAT 57.251 30.769 0.00 0.00 0.00 2.17
3326 3606 9.842775 ATTGCTTTCTCTAGATGATGTGAAATA 57.157 29.630 0.00 0.00 0.00 1.40
3327 3607 8.654230 TGCTTTCTCTAGATGATGTGAAATAC 57.346 34.615 0.00 0.00 0.00 1.89
3328 3608 8.260114 TGCTTTCTCTAGATGATGTGAAATACA 58.740 33.333 0.00 0.00 44.87 2.29
3387 3667 8.002107 CCATACATAAATCAAAGTAACGCTACG 58.998 37.037 0.00 0.00 32.87 3.51
3472 3757 2.597510 GGTGCCCTGTTGTGGTCC 60.598 66.667 0.00 0.00 0.00 4.46
3490 3775 3.621558 GTCCAGGCCAATAGCTAAACTT 58.378 45.455 5.01 0.00 43.05 2.66
3499 3784 4.941263 CCAATAGCTAAACTTGCCTACACA 59.059 41.667 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.517901 TCTGGAACCCCACTGTGTATTAG 59.482 47.826 7.08 0.00 37.58 1.73
13 14 1.809133 TTCTGGAACCCCACTGTGTA 58.191 50.000 7.08 0.00 37.58 2.90
14 15 0.923358 TTTCTGGAACCCCACTGTGT 59.077 50.000 7.08 0.00 37.58 3.72
39 41 6.202937 TGTTGTGAAGCAATAAAAGTAACCG 58.797 36.000 0.00 0.00 39.55 4.44
53 55 4.846779 TCCCAGTAATTTGTTGTGAAGC 57.153 40.909 0.00 0.00 0.00 3.86
70 72 1.565759 CCATCAGTTCCTGGAATCCCA 59.434 52.381 13.07 0.00 40.95 4.37
72 74 3.872459 ATCCATCAGTTCCTGGAATCC 57.128 47.619 13.07 0.31 44.41 3.01
111 113 0.182775 CCCCCAGTTTAGGAATCCGG 59.817 60.000 0.00 0.00 0.00 5.14
121 123 0.771755 GAAGTCCAGTCCCCCAGTTT 59.228 55.000 0.00 0.00 0.00 2.66
144 147 5.075493 ACAGAACAGGAAAAATCAGCATCT 58.925 37.500 0.00 0.00 0.00 2.90
154 157 3.253188 GCAGCACATACAGAACAGGAAAA 59.747 43.478 0.00 0.00 0.00 2.29
158 161 1.812235 TGCAGCACATACAGAACAGG 58.188 50.000 0.00 0.00 0.00 4.00
159 162 2.477357 GCATGCAGCACATACAGAACAG 60.477 50.000 14.21 0.00 44.79 3.16
178 181 2.028130 ACACGGATTTTGACAAAGGCA 58.972 42.857 0.10 0.00 0.00 4.75
188 191 2.018515 ACGTTCAACCACACGGATTTT 58.981 42.857 0.00 0.00 40.84 1.82
192 195 1.227321 GGACGTTCAACCACACGGA 60.227 57.895 0.00 0.00 40.84 4.69
194 197 0.032403 TAGGGACGTTCAACCACACG 59.968 55.000 0.00 0.00 42.29 4.49
198 201 2.435069 TGACTTTAGGGACGTTCAACCA 59.565 45.455 0.00 0.00 0.00 3.67
203 208 3.683340 GTGGAATGACTTTAGGGACGTTC 59.317 47.826 0.00 0.00 0.00 3.95
207 212 3.009143 ACAGGTGGAATGACTTTAGGGAC 59.991 47.826 0.00 0.00 0.00 4.46
211 216 4.003648 GGACACAGGTGGAATGACTTTAG 58.996 47.826 4.24 0.00 34.19 1.85
248 253 2.162408 AGCTGCCGTAAATGCTTTCTTC 59.838 45.455 0.00 0.00 30.96 2.87
255 260 0.524180 GCTCAAGCTGCCGTAAATGC 60.524 55.000 0.00 0.00 38.21 3.56
349 362 0.391661 GAGGGCACAAGATCTCGCAA 60.392 55.000 12.27 0.00 0.00 4.85
358 371 4.334759 CAGATAAATCACAGAGGGCACAAG 59.665 45.833 0.00 0.00 0.00 3.16
362 375 4.019411 TGTTCAGATAAATCACAGAGGGCA 60.019 41.667 0.00 0.00 0.00 5.36
403 416 6.237901 ACATATCTAAACCAAGACTTGCACA 58.762 36.000 9.85 0.00 0.00 4.57
410 423 6.640518 TGACCAGACATATCTAAACCAAGAC 58.359 40.000 0.00 0.00 32.25 3.01
411 424 6.867519 TGACCAGACATATCTAAACCAAGA 57.132 37.500 0.00 0.00 32.25 3.02
412 425 6.017605 GCATGACCAGACATATCTAAACCAAG 60.018 42.308 0.00 0.00 32.25 3.61
413 426 5.822519 GCATGACCAGACATATCTAAACCAA 59.177 40.000 0.00 0.00 32.25 3.67
414 427 5.104569 TGCATGACCAGACATATCTAAACCA 60.105 40.000 0.00 0.00 32.25 3.67
415 428 5.368145 TGCATGACCAGACATATCTAAACC 58.632 41.667 0.00 0.00 32.25 3.27
416 429 6.925610 TTGCATGACCAGACATATCTAAAC 57.074 37.500 0.00 0.00 32.25 2.01
417 430 8.407832 CAATTTGCATGACCAGACATATCTAAA 58.592 33.333 0.00 0.00 32.25 1.85
418 431 7.557358 ACAATTTGCATGACCAGACATATCTAA 59.443 33.333 0.00 0.00 32.25 2.10
419 432 7.012610 CACAATTTGCATGACCAGACATATCTA 59.987 37.037 0.00 0.00 32.25 1.98
420 433 5.889853 ACAATTTGCATGACCAGACATATCT 59.110 36.000 0.00 0.00 34.57 1.98
421 434 5.975344 CACAATTTGCATGACCAGACATATC 59.025 40.000 0.00 0.00 0.00 1.63
422 435 5.163488 CCACAATTTGCATGACCAGACATAT 60.163 40.000 0.00 0.00 0.00 1.78
423 436 4.158209 CCACAATTTGCATGACCAGACATA 59.842 41.667 0.00 0.00 0.00 2.29
424 437 3.056393 CCACAATTTGCATGACCAGACAT 60.056 43.478 0.00 0.00 0.00 3.06
425 438 2.296752 CCACAATTTGCATGACCAGACA 59.703 45.455 0.00 0.00 0.00 3.41
506 519 8.449397 CAGGCTATAGATGATATTGCTTCAAAC 58.551 37.037 3.21 0.00 0.00 2.93
519 532 8.928448 AGACAGAAATAAACAGGCTATAGATGA 58.072 33.333 3.21 0.00 0.00 2.92
528 541 5.689383 TCACAAGACAGAAATAAACAGGC 57.311 39.130 0.00 0.00 0.00 4.85
611 624 4.820284 ATATAAGAGCTCGGCAAAAAGC 57.180 40.909 8.37 0.00 44.65 3.51
623 636 8.219546 AGCAGAAGAAAGGAAAATATAAGAGC 57.780 34.615 0.00 0.00 0.00 4.09
647 670 8.169268 CGAAAGAGGTGTGCTTAACTATAAAAG 58.831 37.037 0.00 0.00 0.00 2.27
650 673 5.579511 GCGAAAGAGGTGTGCTTAACTATAA 59.420 40.000 0.00 0.00 0.00 0.98
654 677 2.143925 GCGAAAGAGGTGTGCTTAACT 58.856 47.619 0.00 0.00 0.00 2.24
660 683 1.063174 GATCATGCGAAAGAGGTGTGC 59.937 52.381 0.00 0.00 0.00 4.57
720 812 2.162681 CTTCAAAGATTGGTTCGCCCT 58.837 47.619 0.00 0.00 36.08 5.19
721 813 1.402852 GCTTCAAAGATTGGTTCGCCC 60.403 52.381 0.00 0.00 36.08 6.13
732 824 6.524734 TCTGATCAAGTAGTTGCTTCAAAGA 58.475 36.000 5.35 3.96 33.23 2.52
788 880 4.038402 AGCATTTCCTGAAGTGAAAAGGTG 59.962 41.667 6.58 0.00 35.52 4.00
798 890 7.596494 TCTAAACAATGAAGCATTTCCTGAAG 58.404 34.615 0.00 0.00 31.05 3.02
926 1019 4.097892 GGGCATTTTAACAGGATCGAATGT 59.902 41.667 0.00 0.00 0.00 2.71
931 1024 3.278574 TCAGGGCATTTTAACAGGATCG 58.721 45.455 0.00 0.00 0.00 3.69
1006 1101 4.337264 AATAGAGGGAAATGGCTTTGGT 57.663 40.909 0.00 0.00 0.00 3.67
1017 1112 4.081087 GCAGGTACACAGAAATAGAGGGAA 60.081 45.833 0.00 0.00 0.00 3.97
1028 1123 2.038952 AGAAATGCAGCAGGTACACAGA 59.961 45.455 0.00 0.00 0.00 3.41
1098 1193 1.068055 GGTGTTGCAAGATCAAGCAGG 60.068 52.381 0.00 0.00 42.39 4.85
1120 1215 6.267471 ACTGTGAGCAAATTAAATGGAAAGGA 59.733 34.615 0.00 0.00 0.00 3.36
1123 1218 7.495901 TGAACTGTGAGCAAATTAAATGGAAA 58.504 30.769 0.00 0.00 0.00 3.13
1168 1263 0.322008 TTGTATGCACCACGATGGCA 60.322 50.000 0.00 0.00 42.67 4.92
1180 1275 0.038709 TTGCAAAGCGGGTTGTATGC 60.039 50.000 0.00 7.85 0.00 3.14
1182 1277 2.166829 TCATTGCAAAGCGGGTTGTAT 58.833 42.857 1.71 0.00 0.00 2.29
1185 1280 2.083167 AATCATTGCAAAGCGGGTTG 57.917 45.000 1.71 0.00 0.00 3.77
1212 1307 3.319198 TCAGGCGGTGGGAAGTCC 61.319 66.667 0.00 0.00 0.00 3.85
1228 1323 1.361668 ATCGATGTTGCTGCGGTGTC 61.362 55.000 0.00 0.00 0.00 3.67
1266 1361 4.462394 GTGAAGTCACAGCAGCCA 57.538 55.556 6.57 0.00 45.75 4.75
1287 1382 4.980805 TCAACCGCGGACTGCACC 62.981 66.667 35.90 0.00 46.97 5.01
1335 1430 3.010027 TGCCCTTATTGATCCACAGAACA 59.990 43.478 0.00 0.00 0.00 3.18
1339 1434 4.096190 AGATGCCCTTATTGATCCACAG 57.904 45.455 0.00 0.00 0.00 3.66
1350 1445 3.380393 TGCTTACAGGTAGATGCCCTTA 58.620 45.455 0.00 0.00 0.00 2.69
1362 1457 6.690530 TGATCAAAGGAAAATTGCTTACAGG 58.309 36.000 0.00 0.00 37.91 4.00
1363 1458 6.810182 CCTGATCAAAGGAAAATTGCTTACAG 59.190 38.462 0.00 8.02 37.91 2.74
1377 1472 1.664321 GCTGCCAGCCTGATCAAAGG 61.664 60.000 5.06 0.00 40.63 3.11
1387 1482 3.138798 CATGGAGTGCTGCCAGCC 61.139 66.667 15.29 5.62 41.51 4.85
1388 1483 2.360852 ACATGGAGTGCTGCCAGC 60.361 61.111 10.45 10.45 42.82 4.85
1391 1489 0.895100 TTTGGACATGGAGTGCTGCC 60.895 55.000 0.00 0.00 39.64 4.85
1392 1490 0.524862 CTTTGGACATGGAGTGCTGC 59.475 55.000 0.00 0.00 39.64 5.25
1400 1498 4.378774 TCAATTTTGCACTTTGGACATGG 58.621 39.130 0.00 0.00 0.00 3.66
1406 1504 6.564499 GCACAGTTATCAATTTTGCACTTTGG 60.564 38.462 0.00 0.00 0.00 3.28
1421 1519 6.253746 CAGCTTCATTAACAGCACAGTTATC 58.746 40.000 6.04 0.00 38.61 1.75
1426 1524 2.415090 GGCAGCTTCATTAACAGCACAG 60.415 50.000 6.04 0.00 38.61 3.66
1447 1545 5.812642 ACTGTCACTTTCTCACTGTAACAAG 59.187 40.000 0.00 0.00 0.00 3.16
1450 1551 4.745620 GGACTGTCACTTTCTCACTGTAAC 59.254 45.833 10.38 0.00 0.00 2.50
1481 1582 3.581755 CTGAAATGTGATGTTGGGCTTG 58.418 45.455 0.00 0.00 0.00 4.01
1526 1627 3.276857 AGCTGTGTCATTCCACATGATC 58.723 45.455 0.00 0.00 43.91 2.92
1538 1639 1.679153 TGTGACGAGTTAGCTGTGTCA 59.321 47.619 0.00 7.04 35.58 3.58
1544 1645 2.353803 GGTTCCATGTGACGAGTTAGCT 60.354 50.000 0.00 0.00 0.00 3.32
1547 1648 3.576982 AGAAGGTTCCATGTGACGAGTTA 59.423 43.478 0.00 0.00 0.00 2.24
1553 1654 3.003480 GCTGTAGAAGGTTCCATGTGAC 58.997 50.000 0.00 0.00 0.00 3.67
1595 1696 3.295228 CTTCGCGACAAAGCCGGTG 62.295 63.158 9.15 0.00 0.00 4.94
1596 1697 2.981977 TTCTTCGCGACAAAGCCGGT 62.982 55.000 9.15 0.00 0.00 5.28
1628 1729 6.619232 GCGATGTTTGTAGTTACCAACTTACC 60.619 42.308 7.49 0.00 42.81 2.85
1633 1734 4.449743 TCTGCGATGTTTGTAGTTACCAAC 59.550 41.667 0.00 0.66 33.78 3.77
1634 1735 4.633175 TCTGCGATGTTTGTAGTTACCAA 58.367 39.130 0.00 0.00 0.00 3.67
1635 1736 4.260139 TCTGCGATGTTTGTAGTTACCA 57.740 40.909 0.00 0.00 0.00 3.25
1636 1737 4.868171 TGATCTGCGATGTTTGTAGTTACC 59.132 41.667 0.00 0.00 0.00 2.85
1637 1738 6.414079 CATGATCTGCGATGTTTGTAGTTAC 58.586 40.000 0.00 0.00 0.00 2.50
1638 1739 5.006649 GCATGATCTGCGATGTTTGTAGTTA 59.993 40.000 0.00 0.00 41.97 2.24
1639 1740 4.201851 GCATGATCTGCGATGTTTGTAGTT 60.202 41.667 0.00 0.00 41.97 2.24
1640 1741 3.310774 GCATGATCTGCGATGTTTGTAGT 59.689 43.478 0.00 0.00 41.97 2.73
1643 1744 2.838386 GCATGATCTGCGATGTTTGT 57.162 45.000 0.00 0.00 41.97 2.83
1662 1763 2.221169 TGCAGTGTGGCTTAACTGAAG 58.779 47.619 15.71 0.00 45.43 3.02
1688 1789 5.531122 ACAGAGTTACAGTGCTACTCAAA 57.469 39.130 20.91 0.00 40.53 2.69
1719 1820 4.456280 TGGTGCTACATTCTAGTGTCAG 57.544 45.455 0.00 0.00 33.62 3.51
1726 1827 5.880332 GTCTTGGAATTGGTGCTACATTCTA 59.120 40.000 0.00 0.00 0.00 2.10
1755 1856 2.265739 GCCTGAGCACCGACATCA 59.734 61.111 0.00 0.00 39.53 3.07
1791 1892 3.918253 GAATGCCGCCTGGTCACCA 62.918 63.158 0.00 0.00 37.67 4.17
1959 2060 2.618709 CTCGGTGCTTTTTCTTCCAGTT 59.381 45.455 0.00 0.00 0.00 3.16
1995 2096 0.665369 GTGCACATGTGGAAGCAAGC 60.665 55.000 26.55 10.55 38.91 4.01
2012 2113 3.001414 CAATCTGCAGTTCTGAGGAGTG 58.999 50.000 14.67 0.00 0.00 3.51
2112 2213 5.722021 AATGAATAGCCGGTGTTTTCTTT 57.278 34.783 1.90 4.23 0.00 2.52
2296 2397 5.376625 TGATTCCAGAAAACACTAGCAGTT 58.623 37.500 0.00 0.00 0.00 3.16
2333 2434 8.561738 AAATCATAGAACAAACCGATGTTAGT 57.438 30.769 1.96 0.00 43.31 2.24
2694 2795 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2695 2796 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2696 2797 2.969950 TCTTATATTGTGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2697 2798 4.377897 GTTCTTATATTGTGGGACGGAGG 58.622 47.826 0.00 0.00 0.00 4.30
2698 2799 4.049186 CGTTCTTATATTGTGGGACGGAG 58.951 47.826 0.00 0.00 0.00 4.63
2699 2800 3.448301 ACGTTCTTATATTGTGGGACGGA 59.552 43.478 0.00 0.00 0.00 4.69
2700 2801 3.788937 ACGTTCTTATATTGTGGGACGG 58.211 45.455 0.00 0.00 0.00 4.79
2701 2802 5.789710 AAACGTTCTTATATTGTGGGACG 57.210 39.130 0.00 0.00 0.00 4.79
2702 2803 7.536281 GTCAAAAACGTTCTTATATTGTGGGAC 59.464 37.037 0.00 0.00 0.00 4.46
2703 2804 7.228906 TGTCAAAAACGTTCTTATATTGTGGGA 59.771 33.333 0.00 0.00 0.00 4.37
2704 2805 7.325097 GTGTCAAAAACGTTCTTATATTGTGGG 59.675 37.037 0.00 0.00 0.00 4.61
2705 2806 8.073768 AGTGTCAAAAACGTTCTTATATTGTGG 58.926 33.333 0.00 0.00 0.00 4.17
2710 2811 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
2711 2812 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
2712 2813 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
2713 2814 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
2714 2815 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
2715 2816 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
2716 2817 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
2729 2830 6.335777 AGAACGTTTTTGACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
2730 2831 6.823678 AGAACGTTTTTGACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
2731 2832 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
2732 2833 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
2737 2838 9.458374 CCAAAATATAAGAACGTTTTTGACACT 57.542 29.630 13.87 0.00 38.79 3.55
2738 2839 8.696175 CCCAAAATATAAGAACGTTTTTGACAC 58.304 33.333 13.87 0.00 38.79 3.67
2739 2840 8.630917 TCCCAAAATATAAGAACGTTTTTGACA 58.369 29.630 13.87 0.01 38.79 3.58
2740 2841 8.908678 GTCCCAAAATATAAGAACGTTTTTGAC 58.091 33.333 13.87 5.89 38.79 3.18
2741 2842 8.630917 TGTCCCAAAATATAAGAACGTTTTTGA 58.369 29.630 13.87 2.81 38.79 2.69
2742 2843 8.804688 TGTCCCAAAATATAAGAACGTTTTTG 57.195 30.769 13.87 12.16 37.14 2.44
2743 2844 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
2744 2845 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
2745 2846 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
2746 2847 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
2747 2848 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
2748 2849 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
2749 2850 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
2750 2851 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
2751 2852 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
2752 2853 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
2753 2854 7.947782 ATACTCCCTCTGTCCCAAAATATAA 57.052 36.000 0.00 0.00 0.00 0.98
2754 2855 9.629649 AATATACTCCCTCTGTCCCAAAATATA 57.370 33.333 0.00 0.00 0.00 0.86
2755 2856 8.386264 CAATATACTCCCTCTGTCCCAAAATAT 58.614 37.037 0.00 0.00 0.00 1.28
2756 2857 7.202186 CCAATATACTCCCTCTGTCCCAAAATA 60.202 40.741 0.00 0.00 0.00 1.40
2757 2858 6.410853 CCAATATACTCCCTCTGTCCCAAAAT 60.411 42.308 0.00 0.00 0.00 1.82
2758 2859 5.104109 CCAATATACTCCCTCTGTCCCAAAA 60.104 44.000 0.00 0.00 0.00 2.44
2759 2860 4.412199 CCAATATACTCCCTCTGTCCCAAA 59.588 45.833 0.00 0.00 0.00 3.28
2760 2861 3.973973 CCAATATACTCCCTCTGTCCCAA 59.026 47.826 0.00 0.00 0.00 4.12
2761 2862 3.051341 ACCAATATACTCCCTCTGTCCCA 60.051 47.826 0.00 0.00 0.00 4.37
2762 2863 3.588569 ACCAATATACTCCCTCTGTCCC 58.411 50.000 0.00 0.00 0.00 4.46
2763 2864 5.612351 GAAACCAATATACTCCCTCTGTCC 58.388 45.833 0.00 0.00 0.00 4.02
2764 2865 5.068723 TCGAAACCAATATACTCCCTCTGTC 59.931 44.000 0.00 0.00 0.00 3.51
2765 2866 4.960469 TCGAAACCAATATACTCCCTCTGT 59.040 41.667 0.00 0.00 0.00 3.41
2766 2867 5.163447 TGTCGAAACCAATATACTCCCTCTG 60.163 44.000 0.00 0.00 0.00 3.35
2767 2868 4.960469 TGTCGAAACCAATATACTCCCTCT 59.040 41.667 0.00 0.00 0.00 3.69
2768 2869 5.272283 TGTCGAAACCAATATACTCCCTC 57.728 43.478 0.00 0.00 0.00 4.30
2769 2870 5.687166 TTGTCGAAACCAATATACTCCCT 57.313 39.130 0.00 0.00 0.00 4.20
2770 2871 6.110707 TCTTTGTCGAAACCAATATACTCCC 58.889 40.000 0.00 0.00 0.00 4.30
2771 2872 7.787725 ATCTTTGTCGAAACCAATATACTCC 57.212 36.000 0.00 0.00 0.00 3.85
2772 2873 8.122952 CCAATCTTTGTCGAAACCAATATACTC 58.877 37.037 0.00 0.00 0.00 2.59
2773 2874 7.827236 TCCAATCTTTGTCGAAACCAATATACT 59.173 33.333 0.00 0.00 0.00 2.12
2774 2875 7.981142 TCCAATCTTTGTCGAAACCAATATAC 58.019 34.615 0.00 0.00 0.00 1.47
2775 2876 8.746052 ATCCAATCTTTGTCGAAACCAATATA 57.254 30.769 0.00 0.00 0.00 0.86
2776 2877 7.645058 ATCCAATCTTTGTCGAAACCAATAT 57.355 32.000 0.00 0.00 0.00 1.28
2956 3228 5.245531 TGTGAACTTTCTTCTCACACTTGT 58.754 37.500 0.16 0.00 43.36 3.16
3031 3303 2.076100 CAGCTGATGTTACCGAAAGCA 58.924 47.619 8.42 0.00 33.08 3.91
3144 3423 9.829507 ACACATCTCTTATCTTTCTTCATAAGG 57.170 33.333 0.00 0.00 34.55 2.69
3150 3429 8.939201 TGATGACACATCTCTTATCTTTCTTC 57.061 34.615 11.98 0.00 0.00 2.87
3163 3443 9.818270 AAAATCCCATATAATGATGACACATCT 57.182 29.630 11.98 0.00 0.00 2.90
3219 3499 9.039165 ACAAGACCCTGAAATTATGAAATGATT 57.961 29.630 0.00 0.00 33.50 2.57
3220 3500 8.599624 ACAAGACCCTGAAATTATGAAATGAT 57.400 30.769 0.00 0.00 0.00 2.45
3221 3501 9.527157 TTACAAGACCCTGAAATTATGAAATGA 57.473 29.630 0.00 0.00 0.00 2.57
3230 3510 9.492973 CATTCAAATTTACAAGACCCTGAAATT 57.507 29.630 0.00 0.00 32.50 1.82
3231 3511 8.096414 CCATTCAAATTTACAAGACCCTGAAAT 58.904 33.333 0.00 0.00 0.00 2.17
3232 3512 7.070571 ACCATTCAAATTTACAAGACCCTGAAA 59.929 33.333 0.00 0.00 0.00 2.69
3233 3513 6.553100 ACCATTCAAATTTACAAGACCCTGAA 59.447 34.615 0.00 0.00 0.00 3.02
3234 3514 6.074648 ACCATTCAAATTTACAAGACCCTGA 58.925 36.000 0.00 0.00 0.00 3.86
3235 3515 6.345096 ACCATTCAAATTTACAAGACCCTG 57.655 37.500 0.00 0.00 0.00 4.45
3236 3516 7.466804 TCTACCATTCAAATTTACAAGACCCT 58.533 34.615 0.00 0.00 0.00 4.34
3237 3517 7.610305 TCTCTACCATTCAAATTTACAAGACCC 59.390 37.037 0.00 0.00 0.00 4.46
3238 3518 8.561738 TCTCTACCATTCAAATTTACAAGACC 57.438 34.615 0.00 0.00 0.00 3.85
3249 3529 9.739276 AGTCAATTGTTATCTCTACCATTCAAA 57.261 29.630 5.13 0.00 0.00 2.69
3290 3570 9.539825 CATCTAGAGAAAGCAATAGTACATGTT 57.460 33.333 2.30 0.00 0.00 2.71
3291 3571 8.918116 TCATCTAGAGAAAGCAATAGTACATGT 58.082 33.333 2.69 2.69 0.00 3.21
3292 3572 9.926158 ATCATCTAGAGAAAGCAATAGTACATG 57.074 33.333 0.00 0.00 0.00 3.21
3293 3573 9.926158 CATCATCTAGAGAAAGCAATAGTACAT 57.074 33.333 0.00 0.00 0.00 2.29
3294 3574 8.918116 ACATCATCTAGAGAAAGCAATAGTACA 58.082 33.333 0.00 0.00 0.00 2.90
3295 3575 9.190858 CACATCATCTAGAGAAAGCAATAGTAC 57.809 37.037 0.00 0.00 0.00 2.73
3296 3576 9.136323 TCACATCATCTAGAGAAAGCAATAGTA 57.864 33.333 0.00 0.00 0.00 1.82
3297 3577 8.016301 TCACATCATCTAGAGAAAGCAATAGT 57.984 34.615 0.00 0.00 0.00 2.12
3298 3578 8.883954 TTCACATCATCTAGAGAAAGCAATAG 57.116 34.615 0.00 0.00 0.00 1.73
3299 3579 9.842775 ATTTCACATCATCTAGAGAAAGCAATA 57.157 29.630 0.00 0.00 0.00 1.90
3300 3580 8.749026 ATTTCACATCATCTAGAGAAAGCAAT 57.251 30.769 0.00 0.00 0.00 3.56
3301 3581 9.102757 GTATTTCACATCATCTAGAGAAAGCAA 57.897 33.333 0.00 0.00 0.00 3.91
3302 3582 8.260114 TGTATTTCACATCATCTAGAGAAAGCA 58.740 33.333 0.00 3.04 30.04 3.91
3303 3583 8.654230 TGTATTTCACATCATCTAGAGAAAGC 57.346 34.615 0.00 0.74 30.04 3.51
3337 3617 9.671279 TGGCATATACAATTATCGATGAAATCT 57.329 29.630 8.54 0.00 42.58 2.40
3341 3621 9.883142 TGTATGGCATATACAATTATCGATGAA 57.117 29.630 10.92 0.00 32.19 2.57
3387 3667 8.600625 TGCATTTTCGTGTTATGAGTAACTATC 58.399 33.333 0.00 0.00 40.66 2.08
3396 3676 7.484641 GCTAGAAATTGCATTTTCGTGTTATGA 59.515 33.333 21.93 6.61 39.93 2.15
3420 3700 4.556898 CGACCACTATTACTCGCAATAGCT 60.557 45.833 0.00 0.00 40.64 3.32
3429 3710 1.334243 AGCGAGCGACCACTATTACTC 59.666 52.381 0.00 0.00 0.00 2.59
3472 3757 2.099756 GGCAAGTTTAGCTATTGGCCTG 59.900 50.000 17.13 3.24 42.00 4.85


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

AutoCloner maintained by Alex Coulton.