Multiple sequence alignment - TraesCS2D01G314700

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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 TraesCS2D01G314700 chr2D 100.000 4351 0 0 1 4351 404128491 404124141 0.000000e+00 8035.0
1 TraesCS2D01G314700 chr2A 93.249 1985 94 21 654 2615 542557902 542555935 0.000000e+00 2887.0
2 TraesCS2D01G314700 chr2A 87.161 1106 71 34 2615 3669 542555834 542554749 0.000000e+00 1190.0
3 TraesCS2D01G314700 chr2A 91.468 293 22 3 3789 4080 542554452 542554162 2.440000e-107 399.0
4 TraesCS2D01G314700 chr2A 93.902 82 4 1 4165 4246 542554095 542554015 5.910000e-24 122.0
5 TraesCS2D01G314700 chr2B 89.077 2243 132 59 1909 4080 478192934 478190734 0.000000e+00 2680.0
6 TraesCS2D01G314700 chr2B 90.184 1905 99 44 2 1857 478194801 478192936 0.000000e+00 2401.0
7 TraesCS2D01G314700 chr6B 91.710 193 14 2 3823 4015 657094343 657094153 2.580000e-67 267.0
8 TraesCS2D01G314700 chr6B 90.594 202 16 3 3823 4023 657097247 657097048 9.280000e-67 265.0
9 TraesCS2D01G314700 chr6B 89.604 202 18 3 3823 4023 657166986 657166787 2.010000e-63 254.0
10 TraesCS2D01G314700 chr6D 92.896 183 12 1 3823 4005 434444155 434443974 9.280000e-67 265.0
11 TraesCS2D01G314700 chr6D 88.479 217 23 2 3838 4054 429353488 429353702 1.200000e-65 261.0
12 TraesCS2D01G314700 chr6D 84.733 262 32 8 3823 4080 434450350 434450093 5.580000e-64 255.0
13 TraesCS2D01G314700 chr6D 89.394 198 19 2 3842 4038 350257847 350258043 9.340000e-62 248.0
14 TraesCS2D01G314700 chr5B 88.571 70 7 1 2661 2729 9580153 9580222 2.790000e-12 84.2
15 TraesCS2D01G314700 chr5B 88.571 70 7 1 2661 2729 326960115 326960184 2.790000e-12 84.2


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 TraesCS2D01G314700 chr2D 404124141 404128491 4350 True 8035.0 8035 100.0000 1 4351 1 chr2D.!!$R1 4350
1 TraesCS2D01G314700 chr2A 542554015 542557902 3887 True 1149.5 2887 91.4450 654 4246 4 chr2A.!!$R1 3592
2 TraesCS2D01G314700 chr2B 478190734 478194801 4067 True 2540.5 2680 89.6305 2 4080 2 chr2B.!!$R1 4078
3 TraesCS2D01G314700 chr6B 657094153 657097247 3094 True 266.0 267 91.1520 3823 4023 2 chr6B.!!$R2 200

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
106 116 0.253327 AAGGGAGAAATGGAGGACGC 59.747 55.000 0.00 0.00 0.00 5.19 F
311 321 1.011595 TGACCTCTAAGGGCTCCTCT 58.988 55.000 0.00 0.00 46.32 3.69 F
678 709 1.398174 GGACCGCCTAGGAGTTACCC 61.398 65.000 14.75 3.51 45.00 3.69 F
1336 1380 1.513622 GGAGGAGAGAACGAGTGGC 59.486 63.158 0.00 0.00 0.00 5.01 F
1798 1856 0.107945 GGAGAAGAAGCTGCCGTGAT 60.108 55.000 0.00 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1650 1.003355 CCCTGACACGGCACTTGAT 60.003 57.895 0.00 0.0 0.00 2.57 R
1778 1835 1.004560 CACGGCAGCTTCTTCTCCA 60.005 57.895 0.00 0.0 0.00 3.86 R
1798 1856 1.203758 ACAAGGCATCGACACGACATA 59.796 47.619 0.00 0.0 39.18 2.29 R
3319 3495 0.179181 TTCGGTGTCATCGTAGTCGC 60.179 55.000 5.22 0.0 36.96 5.19 R
3374 3550 0.468400 AAAACCCAGCCGTTTAGCCA 60.468 50.000 0.00 0.0 34.89 4.75 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
76 86 5.238432 GGAAATTTTGGACAAAATGGACCAC 59.762 40.000 20.08 10.16 46.76 4.16
86 96 4.022603 CAAAATGGACCACACATATGGGA 58.977 43.478 13.12 0.00 44.81 4.37
96 106 4.569653 CCACACATATGGGAAAGGGAGAAA 60.570 45.833 13.12 0.00 35.95 2.52
106 116 0.253327 AAGGGAGAAATGGAGGACGC 59.747 55.000 0.00 0.00 0.00 5.19
107 117 1.153147 GGGAGAAATGGAGGACGCC 60.153 63.158 0.00 0.00 0.00 5.68
109 119 1.515954 GAGAAATGGAGGACGCCGA 59.484 57.895 0.00 0.00 0.00 5.54
130 140 1.418637 TGGACGCCCACTTTTTAGAGT 59.581 47.619 0.00 0.00 37.58 3.24
137 147 3.691609 GCCCACTTTTTAGAGTCAGATGG 59.308 47.826 0.00 0.00 0.00 3.51
173 183 4.755411 ACATGTAGTCGAACATACCAAGG 58.245 43.478 0.00 0.00 38.01 3.61
176 186 2.674796 AGTCGAACATACCAAGGCTC 57.325 50.000 0.00 0.00 0.00 4.70
178 188 2.301870 AGTCGAACATACCAAGGCTCAA 59.698 45.455 0.00 0.00 0.00 3.02
209 219 2.234143 GCCCTTTGAGATGCCCTTATC 58.766 52.381 0.00 0.00 0.00 1.75
212 222 3.887716 CCCTTTGAGATGCCCTTATCAAG 59.112 47.826 0.00 0.00 33.53 3.02
246 256 5.827568 TGAAATTTGCAGCGAAAAATCTC 57.172 34.783 0.00 0.00 0.00 2.75
287 297 8.599624 AAAGAAACATTACATGAATCCATCCT 57.400 30.769 0.00 0.00 0.00 3.24
288 298 9.699410 AAAGAAACATTACATGAATCCATCCTA 57.301 29.630 0.00 0.00 0.00 2.94
289 299 9.872684 AAGAAACATTACATGAATCCATCCTAT 57.127 29.630 0.00 0.00 0.00 2.57
290 300 9.872684 AGAAACATTACATGAATCCATCCTATT 57.127 29.630 0.00 0.00 0.00 1.73
294 304 9.645128 ACATTACATGAATCCATCCTATTTTGA 57.355 29.630 0.00 0.00 0.00 2.69
295 305 9.903682 CATTACATGAATCCATCCTATTTTGAC 57.096 33.333 0.00 0.00 0.00 3.18
296 306 6.966534 ACATGAATCCATCCTATTTTGACC 57.033 37.500 0.00 0.00 0.00 4.02
297 307 6.676558 ACATGAATCCATCCTATTTTGACCT 58.323 36.000 0.00 0.00 0.00 3.85
298 308 6.774656 ACATGAATCCATCCTATTTTGACCTC 59.225 38.462 0.00 0.00 0.00 3.85
309 319 2.344093 TTTGACCTCTAAGGGCTCCT 57.656 50.000 0.00 0.00 46.32 3.69
310 320 1.867363 TTGACCTCTAAGGGCTCCTC 58.133 55.000 0.00 0.00 46.32 3.71
311 321 1.011595 TGACCTCTAAGGGCTCCTCT 58.988 55.000 0.00 0.00 46.32 3.69
372 382 2.110578 GCCCAGACAATATTTGCCCTT 58.889 47.619 0.00 0.00 0.00 3.95
401 411 1.535028 GTCATCAATGTTGCGGACACA 59.465 47.619 9.96 0.00 42.04 3.72
402 412 1.805943 TCATCAATGTTGCGGACACAG 59.194 47.619 0.00 0.00 42.04 3.66
403 413 1.805943 CATCAATGTTGCGGACACAGA 59.194 47.619 0.00 0.00 42.04 3.41
404 414 1.960417 TCAATGTTGCGGACACAGAA 58.040 45.000 0.00 0.00 42.04 3.02
409 419 3.077229 TGTTGCGGACACAGAAAAATG 57.923 42.857 0.00 0.00 32.00 2.32
411 421 3.042887 GTTGCGGACACAGAAAAATGTC 58.957 45.455 0.00 0.00 43.75 3.06
428 438 5.398603 AATGTCCAAAATCGCATAAACCA 57.601 34.783 0.00 0.00 0.00 3.67
459 475 9.831737 CAAACATTAGTGATTTGGAGAAGTTAG 57.168 33.333 0.00 0.00 31.12 2.34
463 479 5.184892 AGTGATTTGGAGAAGTTAGGCAT 57.815 39.130 0.00 0.00 0.00 4.40
469 485 3.466836 TGGAGAAGTTAGGCATATTGCG 58.533 45.455 0.00 0.00 46.21 4.85
486 502 1.574702 GCGGACACACCAACTTAGCC 61.575 60.000 0.00 0.00 38.90 3.93
492 508 3.995048 GACACACCAACTTAGCCTTAGAC 59.005 47.826 0.00 0.00 0.00 2.59
499 515 2.040178 ACTTAGCCTTAGACCCCATCG 58.960 52.381 0.00 0.00 0.00 3.84
524 540 3.739401 TCCATCTTTTCCCCTTTCTCC 57.261 47.619 0.00 0.00 0.00 3.71
525 541 2.311841 TCCATCTTTTCCCCTTTCTCCC 59.688 50.000 0.00 0.00 0.00 4.30
526 542 2.313041 CCATCTTTTCCCCTTTCTCCCT 59.687 50.000 0.00 0.00 0.00 4.20
527 543 3.245766 CCATCTTTTCCCCTTTCTCCCTT 60.246 47.826 0.00 0.00 0.00 3.95
528 544 3.808834 TCTTTTCCCCTTTCTCCCTTC 57.191 47.619 0.00 0.00 0.00 3.46
534 550 4.114015 TCCCCTTTCTCCCTTCTTTTTC 57.886 45.455 0.00 0.00 0.00 2.29
536 552 3.829026 CCCCTTTCTCCCTTCTTTTTCTG 59.171 47.826 0.00 0.00 0.00 3.02
541 557 4.625607 TCTCCCTTCTTTTTCTGTCTCC 57.374 45.455 0.00 0.00 0.00 3.71
542 558 4.235372 TCTCCCTTCTTTTTCTGTCTCCT 58.765 43.478 0.00 0.00 0.00 3.69
613 641 8.816894 GGGAACATCTAATTCTATCTGTCCATA 58.183 37.037 0.00 0.00 0.00 2.74
614 642 9.868277 GGAACATCTAATTCTATCTGTCCATAG 57.132 37.037 0.00 0.00 0.00 2.23
615 643 9.868277 GAACATCTAATTCTATCTGTCCATAGG 57.132 37.037 0.00 0.00 0.00 2.57
616 644 8.964533 ACATCTAATTCTATCTGTCCATAGGT 57.035 34.615 0.00 0.00 0.00 3.08
678 709 1.398174 GGACCGCCTAGGAGTTACCC 61.398 65.000 14.75 3.51 45.00 3.69
786 824 1.738099 CCACGAACTCCAAGAGGCG 60.738 63.158 0.00 7.34 37.51 5.52
787 825 2.048127 ACGAACTCCAAGAGGCGC 60.048 61.111 0.00 0.00 35.91 6.53
788 826 3.181967 CGAACTCCAAGAGGCGCG 61.182 66.667 0.00 0.00 33.35 6.86
789 827 3.491652 GAACTCCAAGAGGCGCGC 61.492 66.667 25.94 25.94 33.35 6.86
811 852 3.255379 GCGTCGATCCGTTGGAGC 61.255 66.667 0.00 0.00 34.05 4.70
1103 1147 2.283529 GGCGTTGGAGAGGGAGACA 61.284 63.158 0.00 0.00 0.00 3.41
1336 1380 1.513622 GGAGGAGAGAACGAGTGGC 59.486 63.158 0.00 0.00 0.00 5.01
1361 1405 4.687464 GGAGACGGAAAAGGCGAA 57.313 55.556 0.00 0.00 0.00 4.70
1400 1444 4.554036 GGGCGGTGGAGGAGATGC 62.554 72.222 0.00 0.00 0.00 3.91
1454 1498 2.997897 GAGGTGGACGGAGGCTGT 60.998 66.667 0.00 0.00 0.00 4.40
1716 1760 2.892425 GACGCTGCGCTTGCCTAT 60.892 61.111 23.51 0.00 38.03 2.57
1718 1762 4.602696 CGCTGCGCTTGCCTATGC 62.603 66.667 9.88 0.00 38.03 3.14
1778 1835 5.105351 GCCCAAAAGGTTCATAATGCTAGTT 60.105 40.000 0.00 0.00 38.26 2.24
1798 1856 0.107945 GGAGAAGAAGCTGCCGTGAT 60.108 55.000 0.00 0.00 0.00 3.06
1821 1879 0.246360 TCGTGTCGATGCCTTGTGAT 59.754 50.000 0.00 0.00 0.00 3.06
1833 1891 3.181477 TGCCTTGTGATTTGTGGTGAAAG 60.181 43.478 0.00 0.00 0.00 2.62
1834 1892 3.068024 GCCTTGTGATTTGTGGTGAAAGA 59.932 43.478 0.00 0.00 0.00 2.52
1861 1920 5.633830 ACCACTGCTTGAACTATGAAATG 57.366 39.130 0.00 0.00 0.00 2.32
1866 1925 4.088634 TGCTTGAACTATGAAATGCCCTT 58.911 39.130 0.00 0.00 0.00 3.95
1874 1933 7.833682 TGAACTATGAAATGCCCTTTCTGATTA 59.166 33.333 9.47 0.00 43.14 1.75
1875 1934 8.773033 AACTATGAAATGCCCTTTCTGATTAT 57.227 30.769 9.47 0.00 43.14 1.28
1876 1935 8.401490 ACTATGAAATGCCCTTTCTGATTATC 57.599 34.615 9.47 0.00 43.14 1.75
1877 1936 8.223330 ACTATGAAATGCCCTTTCTGATTATCT 58.777 33.333 9.47 0.00 43.14 1.98
1886 1945 7.669722 TGCCCTTTCTGATTATCTTAGTTTTGT 59.330 33.333 0.00 0.00 0.00 2.83
1887 1946 7.970614 GCCCTTTCTGATTATCTTAGTTTTGTG 59.029 37.037 0.00 0.00 0.00 3.33
1920 1979 0.320050 TGTGGTGCGATGACTGCTAA 59.680 50.000 0.00 0.00 0.00 3.09
1928 1987 6.127758 TGGTGCGATGACTGCTAATAAAATTT 60.128 34.615 0.00 0.00 0.00 1.82
1950 2009 6.647334 TTCCAATTTTGCATCAGTAGTTCA 57.353 33.333 0.00 0.00 0.00 3.18
1951 2010 6.012658 TCCAATTTTGCATCAGTAGTTCAC 57.987 37.500 0.00 0.00 0.00 3.18
1978 2037 4.221703 ACTCATAGTTTGGACCTGTGAGAG 59.778 45.833 17.42 4.51 35.12 3.20
2036 2096 4.660352 CTTTCAAGCTGTAGAGTTCTGC 57.340 45.455 0.00 0.00 0.00 4.26
2165 2229 2.481952 GTGGCAGCTCACTTCTGTAAAG 59.518 50.000 6.74 0.00 34.98 1.85
2230 2294 6.357579 ACAGAATGAATCAGAGTTCAGAGT 57.642 37.500 0.00 0.00 41.05 3.24
2304 2368 2.031870 GTGCATTGGGGATAAACCTCC 58.968 52.381 0.00 0.00 38.67 4.30
2366 2430 7.818997 ATGTGAACATCATGATCTGCTATTT 57.181 32.000 4.86 0.00 28.78 1.40
2431 2497 7.495606 TGATGTGTGGATATTGTTAGATGACAC 59.504 37.037 0.00 0.00 33.41 3.67
2547 2613 5.009610 TGAAGAAAATCACAACCAACTAGCC 59.990 40.000 0.00 0.00 0.00 3.93
2736 2912 4.397103 TCTTTCCTGTCATATGCTGCAAAG 59.603 41.667 6.36 1.59 0.00 2.77
2769 2945 7.981225 CCTAATTTACCATTGCTGCAACTATTT 59.019 33.333 18.51 7.85 0.00 1.40
2776 2952 5.807011 CCATTGCTGCAACTATTTAAGTTCC 59.193 40.000 18.51 0.00 45.64 3.62
2857 3033 4.264352 TGGGAAATTGCTTAATGTCCTCCT 60.264 41.667 8.66 0.00 36.88 3.69
2913 3089 5.407387 GTGGAGAAGTACGTGAAATGCTTTA 59.593 40.000 0.00 0.00 0.00 1.85
3029 3205 4.587520 AGGAACATGCCTCCTCCA 57.412 55.556 10.53 0.00 39.16 3.86
3030 3206 1.994463 AGGAACATGCCTCCTCCAC 59.006 57.895 10.53 0.00 39.16 4.02
3033 3209 1.001641 AACATGCCTCCTCCACAGC 60.002 57.895 0.00 0.00 0.00 4.40
3035 3211 2.285969 ATGCCTCCTCCACAGCCT 60.286 61.111 0.00 0.00 0.00 4.58
3040 3216 3.615811 TCCTCCACAGCCTCCCCT 61.616 66.667 0.00 0.00 0.00 4.79
3041 3217 3.406200 CCTCCACAGCCTCCCCTG 61.406 72.222 0.00 0.00 38.78 4.45
3062 3238 3.681705 CAACAATGCAGCACCTACG 57.318 52.632 0.00 0.00 0.00 3.51
3110 3286 1.067516 GCAAATACCATGCCGATGCTT 59.932 47.619 0.00 0.00 37.85 3.91
3112 3288 3.853307 GCAAATACCATGCCGATGCTTAC 60.853 47.826 0.00 0.00 37.85 2.34
3113 3289 2.928801 ATACCATGCCGATGCTTACA 57.071 45.000 0.00 0.00 38.71 2.41
3135 3311 3.828451 ACAACTTGAGCTTGCATATGGTT 59.172 39.130 4.56 0.00 0.00 3.67
3147 3323 6.404623 GCTTGCATATGGTTTGTTCAGTGATA 60.405 38.462 4.56 0.00 0.00 2.15
3155 3331 4.947388 GGTTTGTTCAGTGATATTGGCCTA 59.053 41.667 3.32 0.00 0.00 3.93
3171 3347 1.544314 GCCTAGATGCCATCCTCAACC 60.544 57.143 0.00 0.00 0.00 3.77
3242 3418 2.278013 GACGGCGACATCGAGGAC 60.278 66.667 16.62 0.00 43.02 3.85
3287 3463 2.509916 GAGCCATGGGAGCCTGAG 59.490 66.667 15.13 0.00 0.00 3.35
3290 3466 0.401105 AGCCATGGGAGCCTGAGTAT 60.401 55.000 15.13 0.00 0.00 2.12
3297 3473 1.394618 GGAGCCTGAGTATCACGAGT 58.605 55.000 0.00 0.00 42.56 4.18
3318 3494 3.190849 CGAGCAGTGGTGGCGATG 61.191 66.667 0.00 0.00 36.08 3.84
3319 3495 2.821366 GAGCAGTGGTGGCGATGG 60.821 66.667 0.00 0.00 36.08 3.51
3374 3550 2.014010 ATGTGGTGCAAAATCCAGGT 57.986 45.000 0.00 0.00 34.16 4.00
3395 3572 0.955905 GCTAAACGGCTGGGTTTTCA 59.044 50.000 0.00 0.00 40.41 2.69
3411 3608 5.047306 GGGTTTTCAGGATCCTTTTGGTTAG 60.047 44.000 13.00 0.00 41.38 2.34
3419 3616 6.660949 CAGGATCCTTTTGGTTAGATGAAACT 59.339 38.462 13.00 0.00 41.38 2.66
3503 3701 5.480422 TGTCTCTGAGGTAATTGCTCTGTAA 59.520 40.000 4.59 0.00 0.00 2.41
3590 3815 4.811908 CATGTGCAATCTTGATTGTTCCA 58.188 39.130 20.23 15.25 34.21 3.53
3599 3824 6.939132 ATCTTGATTGTTCCAGAATGCTAG 57.061 37.500 0.00 0.00 28.37 3.42
3600 3825 5.809001 TCTTGATTGTTCCAGAATGCTAGT 58.191 37.500 0.00 0.00 31.97 2.57
3601 3826 6.946340 TCTTGATTGTTCCAGAATGCTAGTA 58.054 36.000 0.00 0.00 31.97 1.82
3605 3830 6.818644 TGATTGTTCCAGAATGCTAGTACTTC 59.181 38.462 0.00 0.00 31.97 3.01
3608 3833 5.246203 TGTTCCAGAATGCTAGTACTTCTGT 59.754 40.000 20.45 0.00 42.69 3.41
3690 4035 3.611766 AGTCAAAGTAGCGGCTAACAT 57.388 42.857 11.98 0.00 0.00 2.71
3692 4037 5.080969 AGTCAAAGTAGCGGCTAACATAA 57.919 39.130 11.98 0.00 0.00 1.90
3693 4038 5.671493 AGTCAAAGTAGCGGCTAACATAAT 58.329 37.500 11.98 0.00 0.00 1.28
3694 4039 5.523916 AGTCAAAGTAGCGGCTAACATAATG 59.476 40.000 11.98 5.84 0.00 1.90
3695 4040 4.814234 TCAAAGTAGCGGCTAACATAATGG 59.186 41.667 11.98 0.00 0.00 3.16
3696 4041 4.417426 AAGTAGCGGCTAACATAATGGT 57.583 40.909 11.98 0.00 0.00 3.55
3697 4042 4.417426 AGTAGCGGCTAACATAATGGTT 57.583 40.909 11.98 0.00 34.81 3.67
3698 4043 4.777463 AGTAGCGGCTAACATAATGGTTT 58.223 39.130 11.98 0.00 32.29 3.27
3699 4044 5.190677 AGTAGCGGCTAACATAATGGTTTT 58.809 37.500 11.98 0.00 32.29 2.43
3700 4045 4.370364 AGCGGCTAACATAATGGTTTTG 57.630 40.909 0.00 0.00 32.29 2.44
3701 4046 3.130340 AGCGGCTAACATAATGGTTTTGG 59.870 43.478 0.00 0.00 32.29 3.28
3702 4047 3.119280 GCGGCTAACATAATGGTTTTGGT 60.119 43.478 0.00 0.00 32.29 3.67
3708 4053 8.303876 GGCTAACATAATGGTTTTGGTATATGG 58.696 37.037 0.00 0.00 32.29 2.74
3714 4059 5.669164 ATGGTTTTGGTATATGGCGTTTT 57.331 34.783 0.00 0.00 0.00 2.43
3757 4126 8.950208 ATAGTAAGTAAGCTCAGTTCCATTTC 57.050 34.615 0.00 0.00 0.00 2.17
3760 4129 4.583871 AGTAAGCTCAGTTCCATTTCCAG 58.416 43.478 0.00 0.00 0.00 3.86
3810 4230 6.465948 TCATGAACAAAAGGCAGCAAATATT 58.534 32.000 0.00 0.00 0.00 1.28
3812 4232 6.542574 TGAACAAAAGGCAGCAAATATTTG 57.457 33.333 21.54 21.54 41.03 2.32
3903 4325 1.763968 TATGACGTCCACTCTCCCAG 58.236 55.000 14.12 0.00 0.00 4.45
3930 4352 2.989639 TGGTAAGCCAGCGCATCT 59.010 55.556 11.47 0.00 40.46 2.90
3936 4358 0.322456 AAGCCAGCGCATCTACCAAA 60.322 50.000 11.47 0.00 37.52 3.28
4006 4428 2.113807 GACCCCGTCCAGGTAAGTAAT 58.886 52.381 0.00 0.00 37.88 1.89
4019 4441 4.698780 AGGTAAGTAATTTTCAAGGTCGCC 59.301 41.667 0.00 0.00 0.00 5.54
4038 4460 2.774687 CCCCGTGCCTTGGTTATATAC 58.225 52.381 0.00 0.00 0.00 1.47
4050 4473 3.999046 GGTTATATACCACAGTTCCCCG 58.001 50.000 0.00 0.00 46.92 5.73
4055 4478 0.763604 TACCACAGTTCCCCGTCCAA 60.764 55.000 0.00 0.00 0.00 3.53
4080 4503 0.108186 TCAGGCAAGCGATGTGGTAG 60.108 55.000 0.00 0.00 0.00 3.18
4081 4504 0.108186 CAGGCAAGCGATGTGGTAGA 60.108 55.000 0.00 0.00 0.00 2.59
4082 4505 0.176680 AGGCAAGCGATGTGGTAGAG 59.823 55.000 0.00 0.00 0.00 2.43
4092 4539 3.243234 CGATGTGGTAGAGTGACCTGATC 60.243 52.174 0.00 0.00 40.46 2.92
4102 5962 1.993370 GTGACCTGATCTGTAACGTGC 59.007 52.381 0.00 0.00 0.00 5.34
4103 5963 1.893137 TGACCTGATCTGTAACGTGCT 59.107 47.619 0.00 0.00 0.00 4.40
4105 5965 2.924290 GACCTGATCTGTAACGTGCTTC 59.076 50.000 0.00 0.00 0.00 3.86
4106 5966 2.563179 ACCTGATCTGTAACGTGCTTCT 59.437 45.455 0.00 0.00 0.00 2.85
4107 5967 3.762288 ACCTGATCTGTAACGTGCTTCTA 59.238 43.478 0.00 0.00 0.00 2.10
4108 5968 4.106197 CCTGATCTGTAACGTGCTTCTAC 58.894 47.826 0.00 0.00 0.00 2.59
4109 5969 4.142359 CCTGATCTGTAACGTGCTTCTACT 60.142 45.833 0.00 0.00 0.00 2.57
4110 5970 4.982999 TGATCTGTAACGTGCTTCTACTC 58.017 43.478 0.00 0.00 0.00 2.59
4111 5971 3.466712 TCTGTAACGTGCTTCTACTCG 57.533 47.619 0.00 0.00 0.00 4.18
4112 5972 1.912110 CTGTAACGTGCTTCTACTCGC 59.088 52.381 0.00 0.00 0.00 5.03
4113 5973 0.905839 GTAACGTGCTTCTACTCGCG 59.094 55.000 0.00 0.00 41.41 5.87
4120 5980 0.248907 GCTTCTACTCGCGTGCCATA 60.249 55.000 5.77 0.00 0.00 2.74
4172 6032 3.878160 TTTATTTCGGGAAACATGGGC 57.122 42.857 0.00 0.00 32.51 5.36
4173 6033 1.770294 TATTTCGGGAAACATGGGCC 58.230 50.000 0.00 0.00 32.51 5.80
4174 6034 0.041090 ATTTCGGGAAACATGGGCCT 59.959 50.000 4.53 0.00 32.51 5.19
4175 6035 0.178947 TTTCGGGAAACATGGGCCTT 60.179 50.000 4.53 0.00 0.00 4.35
4176 6036 0.610785 TTCGGGAAACATGGGCCTTC 60.611 55.000 4.53 0.00 0.00 3.46
4177 6037 1.304052 CGGGAAACATGGGCCTTCA 60.304 57.895 4.53 0.00 0.00 3.02
4178 6038 1.315257 CGGGAAACATGGGCCTTCAG 61.315 60.000 4.53 0.00 0.00 3.02
4179 6039 0.251787 GGGAAACATGGGCCTTCAGT 60.252 55.000 4.53 0.00 0.00 3.41
4197 6057 0.977395 GTAGACCCAGCCAGTTGTCT 59.023 55.000 0.00 0.00 40.87 3.41
4246 6106 2.626840 GAGGTGTCCAATCAGAGAAGC 58.373 52.381 0.00 0.00 0.00 3.86
4247 6107 1.066573 AGGTGTCCAATCAGAGAAGCG 60.067 52.381 0.00 0.00 0.00 4.68
4248 6108 1.363744 GTGTCCAATCAGAGAAGCGG 58.636 55.000 0.00 0.00 0.00 5.52
4249 6109 0.391661 TGTCCAATCAGAGAAGCGGC 60.392 55.000 0.00 0.00 0.00 6.53
4250 6110 0.391661 GTCCAATCAGAGAAGCGGCA 60.392 55.000 1.45 0.00 0.00 5.69
4251 6111 0.107993 TCCAATCAGAGAAGCGGCAG 60.108 55.000 1.45 0.00 0.00 4.85
4252 6112 0.107993 CCAATCAGAGAAGCGGCAGA 60.108 55.000 1.45 0.00 0.00 4.26
4253 6113 1.288350 CAATCAGAGAAGCGGCAGAG 58.712 55.000 1.45 0.00 0.00 3.35
4254 6114 0.177604 AATCAGAGAAGCGGCAGAGG 59.822 55.000 1.45 0.00 0.00 3.69
4255 6115 2.308968 ATCAGAGAAGCGGCAGAGGC 62.309 60.000 1.45 0.00 40.13 4.70
4256 6116 2.999648 AGAGAAGCGGCAGAGGCA 61.000 61.111 1.45 0.00 43.71 4.75
4257 6117 2.817396 GAGAAGCGGCAGAGGCAC 60.817 66.667 1.45 0.00 43.71 5.01
4258 6118 4.400961 AGAAGCGGCAGAGGCACC 62.401 66.667 1.45 0.00 43.71 5.01
4259 6119 4.704833 GAAGCGGCAGAGGCACCA 62.705 66.667 1.45 0.00 43.71 4.17
4260 6120 4.269523 AAGCGGCAGAGGCACCAA 62.270 61.111 1.45 0.00 43.71 3.67
4263 6123 3.357079 CGGCAGAGGCACCAACAC 61.357 66.667 0.00 0.00 43.71 3.32
4264 6124 3.357079 GGCAGAGGCACCAACACG 61.357 66.667 0.00 0.00 43.71 4.49
4265 6125 4.030452 GCAGAGGCACCAACACGC 62.030 66.667 0.00 0.00 40.72 5.34
4266 6126 2.591429 CAGAGGCACCAACACGCA 60.591 61.111 0.00 0.00 0.00 5.24
4267 6127 2.591715 AGAGGCACCAACACGCAC 60.592 61.111 0.00 0.00 0.00 5.34
4268 6128 3.660111 GAGGCACCAACACGCACC 61.660 66.667 0.00 0.00 0.00 5.01
4275 6135 3.722295 CAACACGCACCGCCGATT 61.722 61.111 0.00 0.00 0.00 3.34
4276 6136 3.419759 AACACGCACCGCCGATTC 61.420 61.111 0.00 0.00 0.00 2.52
4279 6139 4.508128 ACGCACCGCCGATTCGAT 62.508 61.111 7.83 0.00 0.00 3.59
4280 6140 2.354188 CGCACCGCCGATTCGATA 60.354 61.111 7.83 0.00 0.00 2.92
4281 6141 2.645510 CGCACCGCCGATTCGATAC 61.646 63.158 7.83 0.00 0.00 2.24
4282 6142 1.590525 GCACCGCCGATTCGATACA 60.591 57.895 7.83 0.00 0.00 2.29
4283 6143 1.818221 GCACCGCCGATTCGATACAC 61.818 60.000 7.83 0.00 0.00 2.90
4284 6144 0.526739 CACCGCCGATTCGATACACA 60.527 55.000 7.83 0.00 0.00 3.72
4285 6145 0.387929 ACCGCCGATTCGATACACAT 59.612 50.000 7.83 0.00 0.00 3.21
4286 6146 1.610038 ACCGCCGATTCGATACACATA 59.390 47.619 7.83 0.00 0.00 2.29
4287 6147 1.983605 CCGCCGATTCGATACACATAC 59.016 52.381 7.83 0.00 0.00 2.39
4288 6148 1.642360 CGCCGATTCGATACACATACG 59.358 52.381 7.83 0.00 0.00 3.06
4289 6149 2.663606 CGCCGATTCGATACACATACGA 60.664 50.000 7.83 0.00 0.00 3.43
4290 6150 3.499048 GCCGATTCGATACACATACGAT 58.501 45.455 7.83 0.00 36.02 3.73
4291 6151 3.918591 GCCGATTCGATACACATACGATT 59.081 43.478 7.83 0.00 36.02 3.34
4292 6152 4.030306 GCCGATTCGATACACATACGATTC 59.970 45.833 7.83 0.00 36.02 2.52
4293 6153 4.557690 CCGATTCGATACACATACGATTCC 59.442 45.833 7.83 0.00 34.90 3.01
4294 6154 5.151389 CGATTCGATACACATACGATTCCA 58.849 41.667 0.00 0.00 34.90 3.53
4295 6155 5.059343 CGATTCGATACACATACGATTCCAC 59.941 44.000 0.00 0.00 34.90 4.02
4296 6156 4.233123 TCGATACACATACGATTCCACC 57.767 45.455 0.00 0.00 0.00 4.61
4297 6157 2.977829 CGATACACATACGATTCCACCG 59.022 50.000 0.00 0.00 0.00 4.94
4298 6158 2.875087 TACACATACGATTCCACCGG 57.125 50.000 0.00 0.00 0.00 5.28
4299 6159 1.187974 ACACATACGATTCCACCGGA 58.812 50.000 9.46 0.00 0.00 5.14
4300 6160 1.134907 ACACATACGATTCCACCGGAC 60.135 52.381 9.46 0.00 0.00 4.79
4301 6161 0.462789 ACATACGATTCCACCGGACC 59.537 55.000 9.46 0.00 0.00 4.46
4302 6162 0.596600 CATACGATTCCACCGGACCG 60.597 60.000 9.46 6.99 0.00 4.79
4314 6174 1.807886 CGGACCGGAGTAAGTGAGG 59.192 63.158 9.46 0.00 0.00 3.86
4315 6175 1.664321 CGGACCGGAGTAAGTGAGGG 61.664 65.000 9.46 0.00 0.00 4.30
4316 6176 0.614134 GGACCGGAGTAAGTGAGGGT 60.614 60.000 9.46 0.00 0.00 4.34
4317 6177 0.531200 GACCGGAGTAAGTGAGGGTG 59.469 60.000 9.46 0.00 0.00 4.61
4318 6178 0.113776 ACCGGAGTAAGTGAGGGTGA 59.886 55.000 9.46 0.00 0.00 4.02
4319 6179 0.818296 CCGGAGTAAGTGAGGGTGAG 59.182 60.000 0.00 0.00 0.00 3.51
4320 6180 0.818296 CGGAGTAAGTGAGGGTGAGG 59.182 60.000 0.00 0.00 0.00 3.86
4321 6181 1.891450 CGGAGTAAGTGAGGGTGAGGT 60.891 57.143 0.00 0.00 0.00 3.85
4322 6182 2.619849 CGGAGTAAGTGAGGGTGAGGTA 60.620 54.545 0.00 0.00 0.00 3.08
4323 6183 3.025262 GGAGTAAGTGAGGGTGAGGTAG 58.975 54.545 0.00 0.00 0.00 3.18
4324 6184 3.308976 GGAGTAAGTGAGGGTGAGGTAGA 60.309 52.174 0.00 0.00 0.00 2.59
4325 6185 3.695556 GAGTAAGTGAGGGTGAGGTAGAC 59.304 52.174 0.00 0.00 0.00 2.59
4326 6186 1.546961 AAGTGAGGGTGAGGTAGACG 58.453 55.000 0.00 0.00 0.00 4.18
4338 6198 1.076923 GTAGACGGAGGAGGAGGCA 60.077 63.158 0.00 0.00 0.00 4.75
4340 6200 0.468214 TAGACGGAGGAGGAGGCATG 60.468 60.000 0.00 0.00 0.00 4.06
4341 6201 2.765807 ACGGAGGAGGAGGCATGG 60.766 66.667 0.00 0.00 0.00 3.66
4342 6202 2.765807 CGGAGGAGGAGGCATGGT 60.766 66.667 0.00 0.00 0.00 3.55
4343 6203 2.914289 GGAGGAGGAGGCATGGTG 59.086 66.667 0.00 0.00 0.00 4.17
4344 6204 1.690633 GGAGGAGGAGGCATGGTGA 60.691 63.158 0.00 0.00 0.00 4.02
4345 6205 1.059006 GGAGGAGGAGGCATGGTGAT 61.059 60.000 0.00 0.00 0.00 3.06
4347 6207 0.622738 AGGAGGAGGCATGGTGATGT 60.623 55.000 0.00 0.00 31.50 3.06
4349 6209 0.465097 GAGGAGGCATGGTGATGTGG 60.465 60.000 0.00 0.00 31.50 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 86 4.586001 CCATTTCTCCCTTTCCCATATGTG 59.414 45.833 1.24 0.00 0.00 3.21
86 96 1.340114 GCGTCCTCCATTTCTCCCTTT 60.340 52.381 0.00 0.00 0.00 3.11
96 106 2.443952 TCCATCGGCGTCCTCCAT 60.444 61.111 6.85 0.00 0.00 3.41
106 116 1.241315 AAAAAGTGGGCGTCCATCGG 61.241 55.000 14.23 0.00 46.09 4.18
107 117 1.396996 CTAAAAAGTGGGCGTCCATCG 59.603 52.381 14.23 0.00 46.09 3.84
109 119 2.039879 ACTCTAAAAAGTGGGCGTCCAT 59.960 45.455 14.23 0.00 46.09 3.41
116 126 4.911390 ACCATCTGACTCTAAAAAGTGGG 58.089 43.478 0.00 0.00 0.00 4.61
130 140 9.104713 ACATGTCCATAGATAAATACCATCTGA 57.895 33.333 0.00 0.00 34.58 3.27
146 156 5.595133 TGGTATGTTCGACTACATGTCCATA 59.405 40.000 17.28 0.00 42.49 2.74
157 167 1.899814 TGAGCCTTGGTATGTTCGACT 59.100 47.619 0.00 0.00 0.00 4.18
158 168 2.380084 TGAGCCTTGGTATGTTCGAC 57.620 50.000 0.00 0.00 0.00 4.20
159 169 3.410631 TTTGAGCCTTGGTATGTTCGA 57.589 42.857 0.00 0.00 0.00 3.71
161 171 7.375053 TGTTAAATTTGAGCCTTGGTATGTTC 58.625 34.615 0.00 0.00 0.00 3.18
169 179 4.392754 GGGCAATGTTAAATTTGAGCCTTG 59.607 41.667 0.00 2.39 40.61 3.61
173 183 5.700373 TCAAAGGGCAATGTTAAATTTGAGC 59.300 36.000 0.00 0.00 32.91 4.26
176 186 7.624764 GCATCTCAAAGGGCAATGTTAAATTTG 60.625 37.037 0.00 0.00 0.00 2.32
178 188 5.876460 GCATCTCAAAGGGCAATGTTAAATT 59.124 36.000 0.00 0.00 0.00 1.82
209 219 9.588774 CTGCAAATTTCATTGTAAATGAACTTG 57.411 29.630 20.11 20.11 37.71 3.16
212 222 6.733280 CGCTGCAAATTTCATTGTAAATGAAC 59.267 34.615 13.51 4.69 37.71 3.18
277 287 7.663493 CCTTAGAGGTCAAAATAGGATGGATTC 59.337 40.741 0.00 0.00 0.00 2.52
287 297 4.371681 AGGAGCCCTTAGAGGTCAAAATA 58.628 43.478 0.00 0.00 31.93 1.40
288 298 3.193782 AGGAGCCCTTAGAGGTCAAAAT 58.806 45.455 0.00 0.00 31.93 1.82
289 299 2.572104 GAGGAGCCCTTAGAGGTCAAAA 59.428 50.000 0.00 0.00 31.76 2.44
290 300 2.188817 GAGGAGCCCTTAGAGGTCAAA 58.811 52.381 0.00 0.00 31.76 2.69
291 301 1.362932 AGAGGAGCCCTTAGAGGTCAA 59.637 52.381 0.00 0.00 31.76 3.18
292 302 1.011595 AGAGGAGCCCTTAGAGGTCA 58.988 55.000 0.00 0.00 31.76 4.02
293 303 2.871453 CTAGAGGAGCCCTTAGAGGTC 58.129 57.143 0.00 0.00 31.76 3.85
294 304 1.133294 GCTAGAGGAGCCCTTAGAGGT 60.133 57.143 0.00 0.00 46.41 3.85
295 305 1.627864 GCTAGAGGAGCCCTTAGAGG 58.372 60.000 0.00 0.00 46.41 3.69
309 319 1.847798 ATTTGGTGGGCCACGCTAGA 61.848 55.000 29.18 14.17 46.01 2.43
310 320 1.376609 GATTTGGTGGGCCACGCTAG 61.377 60.000 29.18 0.00 46.01 3.42
311 321 1.377987 GATTTGGTGGGCCACGCTA 60.378 57.895 29.18 16.94 46.01 4.26
318 328 7.460296 CAAATATTAAAAACGATTTGGTGGGC 58.540 34.615 0.00 0.00 36.22 5.36
331 341 5.452636 GGGCCGCTGATCCAAATATTAAAAA 60.453 40.000 0.00 0.00 0.00 1.94
348 358 1.392589 CAAATATTGTCTGGGCCGCT 58.607 50.000 0.00 0.00 0.00 5.52
372 382 3.503363 GCAACATTGATGACTCCTGTTGA 59.497 43.478 15.62 0.00 41.70 3.18
390 400 3.042887 GACATTTTTCTGTGTCCGCAAC 58.957 45.455 0.00 0.00 38.98 4.17
401 411 7.117667 GGTTTATGCGATTTTGGACATTTTTCT 59.882 33.333 0.00 0.00 0.00 2.52
402 412 7.095439 TGGTTTATGCGATTTTGGACATTTTTC 60.095 33.333 0.00 0.00 0.00 2.29
403 413 6.708054 TGGTTTATGCGATTTTGGACATTTTT 59.292 30.769 0.00 0.00 0.00 1.94
404 414 6.226787 TGGTTTATGCGATTTTGGACATTTT 58.773 32.000 0.00 0.00 0.00 1.82
409 419 4.434713 ACTGGTTTATGCGATTTTGGAC 57.565 40.909 0.00 0.00 0.00 4.02
411 421 4.156922 TGGTACTGGTTTATGCGATTTTGG 59.843 41.667 0.00 0.00 0.00 3.28
412 422 5.303747 TGGTACTGGTTTATGCGATTTTG 57.696 39.130 0.00 0.00 0.00 2.44
457 473 1.474320 GGTGTGTCCGCAATATGCCTA 60.474 52.381 0.00 0.00 41.12 3.93
458 474 0.748005 GGTGTGTCCGCAATATGCCT 60.748 55.000 0.00 0.00 41.12 4.75
459 475 1.029408 TGGTGTGTCCGCAATATGCC 61.029 55.000 0.00 0.00 41.12 4.40
463 479 2.264005 AAGTTGGTGTGTCCGCAATA 57.736 45.000 0.00 0.00 39.52 1.90
469 485 2.271944 AAGGCTAAGTTGGTGTGTCC 57.728 50.000 0.00 0.00 0.00 4.02
486 502 2.222027 GGATTTGCGATGGGGTCTAAG 58.778 52.381 0.00 0.00 0.00 2.18
492 508 1.696063 AAGATGGATTTGCGATGGGG 58.304 50.000 0.00 0.00 0.00 4.96
499 515 4.223700 AGAAAGGGGAAAAGATGGATTTGC 59.776 41.667 0.00 0.00 0.00 3.68
524 540 5.482163 AGAGAGGAGACAGAAAAAGAAGG 57.518 43.478 0.00 0.00 0.00 3.46
525 541 6.520272 TGAAGAGAGGAGACAGAAAAAGAAG 58.480 40.000 0.00 0.00 0.00 2.85
526 542 6.485830 TGAAGAGAGGAGACAGAAAAAGAA 57.514 37.500 0.00 0.00 0.00 2.52
527 543 6.678568 ATGAAGAGAGGAGACAGAAAAAGA 57.321 37.500 0.00 0.00 0.00 2.52
528 544 6.149142 CCAATGAAGAGAGGAGACAGAAAAAG 59.851 42.308 0.00 0.00 0.00 2.27
534 550 3.513119 TGTCCAATGAAGAGAGGAGACAG 59.487 47.826 0.00 0.00 0.00 3.51
536 552 4.543590 TTGTCCAATGAAGAGAGGAGAC 57.456 45.455 0.00 0.00 0.00 3.36
575 596 3.536956 GATGTTCCCATCGTCCAACTA 57.463 47.619 0.00 0.00 38.28 2.24
576 597 2.403252 GATGTTCCCATCGTCCAACT 57.597 50.000 0.00 0.00 38.28 3.16
584 605 7.821846 GGACAGATAGAATTAGATGTTCCCATC 59.178 40.741 0.00 0.00 46.56 3.51
585 606 7.293299 TGGACAGATAGAATTAGATGTTCCCAT 59.707 37.037 0.00 0.00 0.00 4.00
596 624 9.877222 TGAACTACCTATGGACAGATAGAATTA 57.123 33.333 0.00 0.00 0.00 1.40
641 672 2.293399 GTCCACCAAAACAGACACCATC 59.707 50.000 0.00 0.00 0.00 3.51
642 673 2.306847 GTCCACCAAAACAGACACCAT 58.693 47.619 0.00 0.00 0.00 3.55
678 709 3.914426 AAACTGAGTATAGGTGGGCTG 57.086 47.619 0.00 0.00 0.00 4.85
788 826 4.814294 ACGGATCGACGCCCTTGC 62.814 66.667 0.00 0.00 37.37 4.01
789 827 2.125673 AACGGATCGACGCCCTTG 60.126 61.111 0.00 0.00 37.37 3.61
811 852 3.059472 GATGTGCGACGCGTGTCTG 62.059 63.158 25.28 19.08 43.21 3.51
1069 1113 3.488569 CCCATTAGGCCGCTCCCA 61.489 66.667 0.00 0.00 34.51 4.37
1087 1131 1.216710 GCTGTCTCCCTCTCCAACG 59.783 63.158 0.00 0.00 0.00 4.10
1361 1405 4.473520 CCACGGCCTCGCAAGGAT 62.474 66.667 0.00 0.00 46.67 3.24
1400 1444 2.635229 CTTGACCTCATCGCCCCTCG 62.635 65.000 0.00 0.00 40.15 4.63
1454 1498 1.754745 GCCATTATCTCCGGGCTCA 59.245 57.895 0.00 0.00 43.09 4.26
1606 1650 1.003355 CCCTGACACGGCACTTGAT 60.003 57.895 0.00 0.00 0.00 2.57
1753 1797 3.172339 AGCATTATGAACCTTTTGGGCA 58.828 40.909 0.00 0.00 46.08 5.36
1778 1835 1.004560 CACGGCAGCTTCTTCTCCA 60.005 57.895 0.00 0.00 0.00 3.86
1798 1856 1.203758 ACAAGGCATCGACACGACATA 59.796 47.619 0.00 0.00 39.18 2.29
1861 1920 7.970614 CACAAAACTAAGATAATCAGAAAGGGC 59.029 37.037 0.00 0.00 0.00 5.19
1866 1925 7.446931 TGTGGCACAAAACTAAGATAATCAGAA 59.553 33.333 19.74 0.00 44.16 3.02
1874 1933 9.855021 GTTATAAATGTGGCACAAAACTAAGAT 57.145 29.630 25.95 11.41 44.16 2.40
1875 1934 9.073475 AGTTATAAATGTGGCACAAAACTAAGA 57.927 29.630 25.95 4.23 44.16 2.10
1876 1935 9.128107 CAGTTATAAATGTGGCACAAAACTAAG 57.872 33.333 25.95 13.01 44.16 2.18
1877 1936 8.634444 ACAGTTATAAATGTGGCACAAAACTAA 58.366 29.630 25.95 16.25 44.16 2.24
1897 1956 1.939381 GCAGTCATCGCACCACAGTTA 60.939 52.381 0.00 0.00 0.00 2.24
1928 1987 5.334802 CGTGAACTACTGATGCAAAATTGGA 60.335 40.000 0.00 0.00 0.00 3.53
1943 2002 5.800941 CCAAACTATGAGTCTCGTGAACTAC 59.199 44.000 4.73 0.00 0.00 2.73
1950 2009 3.193691 CAGGTCCAAACTATGAGTCTCGT 59.806 47.826 0.00 0.00 0.00 4.18
1951 2010 3.193691 ACAGGTCCAAACTATGAGTCTCG 59.806 47.826 0.00 0.00 0.00 4.04
2033 2093 1.858091 CACAATAGCTCGTAGGGCAG 58.142 55.000 0.00 0.00 0.00 4.85
2036 2096 2.533266 ATGCACAATAGCTCGTAGGG 57.467 50.000 0.00 0.00 34.99 3.53
2165 2229 4.092821 GGTGTGTTGGCAAAACTTCTTTTC 59.907 41.667 20.59 0.00 0.00 2.29
2304 2368 2.032178 GCCCTTCAGTAGCAAATTAGCG 59.968 50.000 0.00 0.00 40.15 4.26
2366 2430 8.963725 AGCAGATTATCATTCTGTCAAATCAAA 58.036 29.630 0.00 0.00 42.12 2.69
2431 2497 3.230976 AGAAAACAAAGGTTGGCCCTAG 58.769 45.455 0.00 0.00 45.47 3.02
2636 2803 5.980116 ACACAATGTCATAGAGAAGTATCGC 59.020 40.000 0.00 0.00 0.00 4.58
2736 2912 4.081697 AGCAATGGTAAATTAGGTGCCAAC 60.082 41.667 0.00 0.00 32.54 3.77
2804 2980 6.332630 CAGTGGAAATTAACCATCACAATCC 58.667 40.000 7.41 0.00 39.69 3.01
2840 3016 4.446889 GGGATCAGGAGGACATTAAGCAAT 60.447 45.833 0.00 0.00 0.00 3.56
2857 3033 4.579127 TCTCGCTCATCGGGATCA 57.421 55.556 0.00 0.00 43.89 2.92
2913 3089 1.348036 GTCCAACACTCTTAGGGCAGT 59.652 52.381 0.00 0.00 0.00 4.40
3033 3209 1.683365 CATTGTTGCCCAGGGGAGG 60.683 63.158 7.91 0.00 37.50 4.30
3035 3211 2.283821 GCATTGTTGCCCAGGGGA 60.284 61.111 7.91 0.00 43.38 4.81
3061 3237 2.027625 GCCTCGTCTTCAACCACCG 61.028 63.158 0.00 0.00 0.00 4.94
3062 3238 1.671379 GGCCTCGTCTTCAACCACC 60.671 63.158 0.00 0.00 0.00 4.61
3092 3268 3.315191 GTGTAAGCATCGGCATGGTATTT 59.685 43.478 0.00 0.00 39.96 1.40
3110 3286 4.395854 CCATATGCAAGCTCAAGTTGTGTA 59.604 41.667 2.11 0.00 0.00 2.90
3112 3288 3.192001 ACCATATGCAAGCTCAAGTTGTG 59.808 43.478 2.11 1.23 0.00 3.33
3113 3289 3.424703 ACCATATGCAAGCTCAAGTTGT 58.575 40.909 2.11 0.00 0.00 3.32
3135 3311 5.692115 TCTAGGCCAATATCACTGAACAA 57.308 39.130 5.01 0.00 0.00 2.83
3155 3331 2.662866 CATTGGTTGAGGATGGCATCT 58.337 47.619 25.48 12.59 0.00 2.90
3297 3473 2.970639 GCCACCACTGCTCGAGTA 59.029 61.111 15.13 8.96 31.73 2.59
3318 3494 1.585521 CGGTGTCATCGTAGTCGCC 60.586 63.158 0.00 0.00 36.96 5.54
3319 3495 0.179181 TTCGGTGTCATCGTAGTCGC 60.179 55.000 5.22 0.00 36.96 5.19
3374 3550 0.468400 AAAACCCAGCCGTTTAGCCA 60.468 50.000 0.00 0.00 34.89 4.75
3395 3572 6.794534 AGTTTCATCTAACCAAAAGGATCCT 58.205 36.000 9.02 9.02 0.00 3.24
3419 3616 8.196771 AGACAACAGTAAGCATTTCAAATTGAA 58.803 29.630 4.03 4.03 34.03 2.69
3503 3701 3.884895 TCCACACAATCAAGAACACACT 58.115 40.909 0.00 0.00 0.00 3.55
3590 3815 7.897864 ACACTAAACAGAAGTACTAGCATTCT 58.102 34.615 0.00 0.00 33.62 2.40
3599 3824 7.924947 ACTCCTACAAACACTAAACAGAAGTAC 59.075 37.037 0.00 0.00 0.00 2.73
3600 3825 8.015185 ACTCCTACAAACACTAAACAGAAGTA 57.985 34.615 0.00 0.00 0.00 2.24
3601 3826 6.885922 ACTCCTACAAACACTAAACAGAAGT 58.114 36.000 0.00 0.00 0.00 3.01
3678 4023 4.336993 CCAAAACCATTATGTTAGCCGCTA 59.663 41.667 0.00 0.00 0.00 4.26
3690 4035 6.777213 AAACGCCATATACCAAAACCATTA 57.223 33.333 0.00 0.00 0.00 1.90
3692 4037 5.669164 AAAACGCCATATACCAAAACCAT 57.331 34.783 0.00 0.00 0.00 3.55
3693 4038 5.230942 CAAAAACGCCATATACCAAAACCA 58.769 37.500 0.00 0.00 0.00 3.67
3694 4039 4.627900 CCAAAAACGCCATATACCAAAACC 59.372 41.667 0.00 0.00 0.00 3.27
3695 4040 5.471257 TCCAAAAACGCCATATACCAAAAC 58.529 37.500 0.00 0.00 0.00 2.43
3696 4041 5.477291 TCTCCAAAAACGCCATATACCAAAA 59.523 36.000 0.00 0.00 0.00 2.44
3697 4042 5.010933 TCTCCAAAAACGCCATATACCAAA 58.989 37.500 0.00 0.00 0.00 3.28
3698 4043 4.396790 GTCTCCAAAAACGCCATATACCAA 59.603 41.667 0.00 0.00 0.00 3.67
3699 4044 3.942748 GTCTCCAAAAACGCCATATACCA 59.057 43.478 0.00 0.00 0.00 3.25
3700 4045 3.314357 GGTCTCCAAAAACGCCATATACC 59.686 47.826 0.00 0.00 0.00 2.73
3701 4046 3.942748 TGGTCTCCAAAAACGCCATATAC 59.057 43.478 0.00 0.00 0.00 1.47
3702 4047 4.223556 TGGTCTCCAAAAACGCCATATA 57.776 40.909 0.00 0.00 0.00 0.86
3714 4059 9.802039 ACTTACTATTAAACATTTGGTCTCCAA 57.198 29.630 0.00 0.00 42.29 3.53
3733 4078 7.038587 TGGAAATGGAACTGAGCTTACTTACTA 60.039 37.037 0.00 0.00 0.00 1.82
3736 4081 6.013725 TCTGGAAATGGAACTGAGCTTACTTA 60.014 38.462 0.00 0.00 0.00 2.24
3903 4325 0.623723 TGGCTTACCATCTCCCCAAC 59.376 55.000 0.00 0.00 42.67 3.77
3930 4352 2.560542 GTGGTCCACATTGCATTTGGTA 59.439 45.455 17.59 0.00 34.08 3.25
3936 4358 1.683011 GGCTAGTGGTCCACATTGCAT 60.683 52.381 24.02 4.62 36.74 3.96
4045 4467 2.284405 GAGGAGGTTGGACGGGGA 60.284 66.667 0.00 0.00 0.00 4.81
4049 4472 2.111999 TTGCCTGAGGAGGTTGGACG 62.112 60.000 0.65 0.00 42.15 4.79
4050 4473 0.322008 CTTGCCTGAGGAGGTTGGAC 60.322 60.000 0.65 0.00 42.15 4.02
4055 4478 1.992277 ATCGCTTGCCTGAGGAGGT 60.992 57.895 0.65 0.00 42.15 3.85
4080 4503 3.502920 CACGTTACAGATCAGGTCACTC 58.497 50.000 0.00 0.00 0.00 3.51
4081 4504 2.352814 GCACGTTACAGATCAGGTCACT 60.353 50.000 0.00 0.00 0.00 3.41
4082 4505 1.993370 GCACGTTACAGATCAGGTCAC 59.007 52.381 0.00 0.00 0.00 3.67
4092 4539 1.912110 GCGAGTAGAAGCACGTTACAG 59.088 52.381 0.00 0.00 0.00 2.74
4108 5968 2.310233 CCCGAATATGGCACGCGAG 61.310 63.158 15.93 5.97 0.00 5.03
4109 5969 2.279851 CCCGAATATGGCACGCGA 60.280 61.111 15.93 0.00 0.00 5.87
4120 5980 1.898330 GCCCATGTTTTGGCCCGAAT 61.898 55.000 0.00 0.00 44.97 3.34
4129 5989 1.710809 AGTACTGGAGGCCCATGTTTT 59.289 47.619 0.00 0.00 42.59 2.43
4130 5990 1.372501 AGTACTGGAGGCCCATGTTT 58.627 50.000 0.00 0.00 42.59 2.83
4150 6010 4.563786 GGCCCATGTTTCCCGAAATAAAAA 60.564 41.667 0.00 0.00 32.36 1.94
4151 6011 3.055747 GGCCCATGTTTCCCGAAATAAAA 60.056 43.478 0.00 0.00 32.36 1.52
4152 6012 2.498078 GGCCCATGTTTCCCGAAATAAA 59.502 45.455 0.00 0.00 32.36 1.40
4153 6013 2.104170 GGCCCATGTTTCCCGAAATAA 58.896 47.619 0.00 0.00 32.36 1.40
4155 6015 0.041090 AGGCCCATGTTTCCCGAAAT 59.959 50.000 0.00 0.00 32.36 2.17
4156 6016 0.178947 AAGGCCCATGTTTCCCGAAA 60.179 50.000 0.00 0.00 0.00 3.46
4157 6017 0.610785 GAAGGCCCATGTTTCCCGAA 60.611 55.000 0.00 0.00 0.00 4.30
4158 6018 1.001393 GAAGGCCCATGTTTCCCGA 60.001 57.895 0.00 0.00 0.00 5.14
4161 6021 2.026262 TCTACTGAAGGCCCATGTTTCC 60.026 50.000 0.00 0.00 0.00 3.13
4163 6023 2.290960 GGTCTACTGAAGGCCCATGTTT 60.291 50.000 0.00 0.00 45.06 2.83
4166 6026 3.788672 GGTCTACTGAAGGCCCATG 57.211 57.895 0.00 0.00 45.06 3.66
4172 6032 0.539051 CTGGCTGGGTCTACTGAAGG 59.461 60.000 0.00 0.00 0.00 3.46
4173 6033 1.270907 ACTGGCTGGGTCTACTGAAG 58.729 55.000 0.00 0.00 0.00 3.02
4174 6034 1.347707 CAACTGGCTGGGTCTACTGAA 59.652 52.381 0.00 0.00 0.00 3.02
4175 6035 0.976641 CAACTGGCTGGGTCTACTGA 59.023 55.000 0.00 0.00 0.00 3.41
4176 6036 0.687354 ACAACTGGCTGGGTCTACTG 59.313 55.000 0.00 0.00 0.00 2.74
4177 6037 0.977395 GACAACTGGCTGGGTCTACT 59.023 55.000 9.93 0.00 0.00 2.57
4178 6038 0.977395 AGACAACTGGCTGGGTCTAC 59.023 55.000 15.67 0.00 38.74 2.59
4179 6039 1.623811 GAAGACAACTGGCTGGGTCTA 59.376 52.381 16.92 0.00 39.55 2.59
4197 6057 1.070786 GACGGCTGGACAGTTGGAA 59.929 57.895 0.00 0.00 0.00 3.53
4223 6083 0.543749 CTCTGATTGGACACCTCCCC 59.456 60.000 0.00 0.00 35.34 4.81
4231 6091 0.391661 TGCCGCTTCTCTGATTGGAC 60.392 55.000 0.00 0.00 0.00 4.02
4246 6106 3.357079 GTGTTGGTGCCTCTGCCG 61.357 66.667 0.00 0.00 36.33 5.69
4247 6107 3.357079 CGTGTTGGTGCCTCTGCC 61.357 66.667 0.00 0.00 36.33 4.85
4248 6108 4.030452 GCGTGTTGGTGCCTCTGC 62.030 66.667 0.00 0.00 38.26 4.26
4249 6109 2.591429 TGCGTGTTGGTGCCTCTG 60.591 61.111 0.00 0.00 0.00 3.35
4250 6110 2.591715 GTGCGTGTTGGTGCCTCT 60.592 61.111 0.00 0.00 0.00 3.69
4251 6111 3.660111 GGTGCGTGTTGGTGCCTC 61.660 66.667 0.00 0.00 0.00 4.70
4258 6118 3.645157 GAATCGGCGGTGCGTGTTG 62.645 63.158 7.21 0.00 0.00 3.33
4259 6119 3.419759 GAATCGGCGGTGCGTGTT 61.420 61.111 7.21 0.00 0.00 3.32
4262 6122 3.128632 TATCGAATCGGCGGTGCGT 62.129 57.895 21.49 10.51 0.00 5.24
4263 6123 2.354188 TATCGAATCGGCGGTGCG 60.354 61.111 15.89 15.89 0.00 5.34
4264 6124 1.590525 TGTATCGAATCGGCGGTGC 60.591 57.895 7.21 0.00 0.00 5.01
4265 6125 0.526739 TGTGTATCGAATCGGCGGTG 60.527 55.000 7.21 0.00 0.00 4.94
4266 6126 0.387929 ATGTGTATCGAATCGGCGGT 59.612 50.000 7.21 0.00 0.00 5.68
4267 6127 1.983605 GTATGTGTATCGAATCGGCGG 59.016 52.381 7.21 0.00 0.00 6.13
4268 6128 1.642360 CGTATGTGTATCGAATCGGCG 59.358 52.381 0.00 0.00 0.00 6.46
4269 6129 2.924903 TCGTATGTGTATCGAATCGGC 58.075 47.619 1.76 0.00 0.00 5.54
4270 6130 4.557690 GGAATCGTATGTGTATCGAATCGG 59.442 45.833 1.76 0.00 35.30 4.18
4271 6131 5.059343 GTGGAATCGTATGTGTATCGAATCG 59.941 44.000 0.00 0.00 35.30 3.34
4272 6132 5.345202 GGTGGAATCGTATGTGTATCGAATC 59.655 44.000 0.00 0.00 37.16 2.52
4273 6133 5.227908 GGTGGAATCGTATGTGTATCGAAT 58.772 41.667 0.00 0.00 37.16 3.34
4274 6134 4.613944 GGTGGAATCGTATGTGTATCGAA 58.386 43.478 0.00 0.00 37.16 3.71
4275 6135 3.304190 CGGTGGAATCGTATGTGTATCGA 60.304 47.826 0.00 0.00 37.96 3.59
4276 6136 2.977829 CGGTGGAATCGTATGTGTATCG 59.022 50.000 0.00 0.00 0.00 2.92
4277 6137 3.005050 TCCGGTGGAATCGTATGTGTATC 59.995 47.826 0.00 0.00 0.00 2.24
4278 6138 2.960384 TCCGGTGGAATCGTATGTGTAT 59.040 45.455 0.00 0.00 0.00 2.29
4279 6139 2.099592 GTCCGGTGGAATCGTATGTGTA 59.900 50.000 0.00 0.00 31.38 2.90
4280 6140 1.134907 GTCCGGTGGAATCGTATGTGT 60.135 52.381 0.00 0.00 31.38 3.72
4281 6141 1.567504 GTCCGGTGGAATCGTATGTG 58.432 55.000 0.00 0.00 31.38 3.21
4282 6142 0.462789 GGTCCGGTGGAATCGTATGT 59.537 55.000 0.00 0.00 31.38 2.29
4283 6143 0.596600 CGGTCCGGTGGAATCGTATG 60.597 60.000 2.34 0.00 31.38 2.39
4284 6144 1.737816 CGGTCCGGTGGAATCGTAT 59.262 57.895 2.34 0.00 31.38 3.06
4285 6145 2.417257 CCGGTCCGGTGGAATCGTA 61.417 63.158 23.02 0.00 42.73 3.43
4286 6146 3.766691 CCGGTCCGGTGGAATCGT 61.767 66.667 23.02 0.00 42.73 3.73
4296 6156 1.664321 CCCTCACTTACTCCGGTCCG 61.664 65.000 3.60 3.60 0.00 4.79
4297 6157 0.614134 ACCCTCACTTACTCCGGTCC 60.614 60.000 0.00 0.00 0.00 4.46
4298 6158 0.531200 CACCCTCACTTACTCCGGTC 59.469 60.000 0.00 0.00 0.00 4.79
4299 6159 0.113776 TCACCCTCACTTACTCCGGT 59.886 55.000 0.00 0.00 0.00 5.28
4300 6160 0.818296 CTCACCCTCACTTACTCCGG 59.182 60.000 0.00 0.00 0.00 5.14
4301 6161 0.818296 CCTCACCCTCACTTACTCCG 59.182 60.000 0.00 0.00 0.00 4.63
4302 6162 1.939980 ACCTCACCCTCACTTACTCC 58.060 55.000 0.00 0.00 0.00 3.85
4303 6163 3.695556 GTCTACCTCACCCTCACTTACTC 59.304 52.174 0.00 0.00 0.00 2.59
4304 6164 3.699413 GTCTACCTCACCCTCACTTACT 58.301 50.000 0.00 0.00 0.00 2.24
4305 6165 2.422832 CGTCTACCTCACCCTCACTTAC 59.577 54.545 0.00 0.00 0.00 2.34
4306 6166 2.619849 CCGTCTACCTCACCCTCACTTA 60.620 54.545 0.00 0.00 0.00 2.24
4307 6167 1.546961 CGTCTACCTCACCCTCACTT 58.453 55.000 0.00 0.00 0.00 3.16
4308 6168 0.323542 CCGTCTACCTCACCCTCACT 60.324 60.000 0.00 0.00 0.00 3.41
4309 6169 0.323178 TCCGTCTACCTCACCCTCAC 60.323 60.000 0.00 0.00 0.00 3.51
4310 6170 0.034380 CTCCGTCTACCTCACCCTCA 60.034 60.000 0.00 0.00 0.00 3.86
4311 6171 0.752376 CCTCCGTCTACCTCACCCTC 60.752 65.000 0.00 0.00 0.00 4.30
4312 6172 1.212934 TCCTCCGTCTACCTCACCCT 61.213 60.000 0.00 0.00 0.00 4.34
4313 6173 0.752376 CTCCTCCGTCTACCTCACCC 60.752 65.000 0.00 0.00 0.00 4.61
4314 6174 0.752376 CCTCCTCCGTCTACCTCACC 60.752 65.000 0.00 0.00 0.00 4.02
4315 6175 0.255318 TCCTCCTCCGTCTACCTCAC 59.745 60.000 0.00 0.00 0.00 3.51
4316 6176 0.547075 CTCCTCCTCCGTCTACCTCA 59.453 60.000 0.00 0.00 0.00 3.86
4317 6177 0.179012 CCTCCTCCTCCGTCTACCTC 60.179 65.000 0.00 0.00 0.00 3.85
4318 6178 1.924352 CCTCCTCCTCCGTCTACCT 59.076 63.158 0.00 0.00 0.00 3.08
4319 6179 1.829096 GCCTCCTCCTCCGTCTACC 60.829 68.421 0.00 0.00 0.00 3.18
4320 6180 0.468400 ATGCCTCCTCCTCCGTCTAC 60.468 60.000 0.00 0.00 0.00 2.59
4321 6181 0.468214 CATGCCTCCTCCTCCGTCTA 60.468 60.000 0.00 0.00 0.00 2.59
4322 6182 1.760086 CATGCCTCCTCCTCCGTCT 60.760 63.158 0.00 0.00 0.00 4.18
4323 6183 2.801631 CCATGCCTCCTCCTCCGTC 61.802 68.421 0.00 0.00 0.00 4.79
4324 6184 2.765807 CCATGCCTCCTCCTCCGT 60.766 66.667 0.00 0.00 0.00 4.69
4325 6185 2.765807 ACCATGCCTCCTCCTCCG 60.766 66.667 0.00 0.00 0.00 4.63
4326 6186 1.059006 ATCACCATGCCTCCTCCTCC 61.059 60.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.