Multiple sequence alignment - TraesCS7B01G272100

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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 TraesCS7B01G272100 chr7B 100.000 2972 0 0 1 2972 498970999 498968028 0.000000e+00 5489.0
1 TraesCS7B01G272100 chr7B 94.382 89 4 1 2547 2635 498968365 498968278 5.170000e-28 135.0
2 TraesCS7B01G272100 chr7B 94.382 89 4 1 2635 2722 498968453 498968365 5.170000e-28 135.0
3 TraesCS7B01G272100 chr7D 90.548 2190 131 38 1 2140 475187167 475185004 0.000000e+00 2828.0
4 TraesCS7B01G272100 chr7D 96.825 63 2 0 2136 2198 475184981 475184919 4.050000e-19 106.0
5 TraesCS7B01G272100 chr7D 100.000 30 0 0 2916 2945 475184398 475184369 4.140000e-04 56.5
6 TraesCS7B01G272100 chr7A 89.201 1389 100 23 783 2140 520832231 520833600 0.000000e+00 1688.0
7 TraesCS7B01G272100 chr7A 78.878 606 89 25 1 591 520798894 520799475 1.010000e-99 374.0
8 TraesCS7B01G272100 chr7A 88.793 116 2 5 2497 2611 520836461 520836566 6.680000e-27 132.0
9 TraesCS7B01G272100 chr7A 98.413 63 1 0 2136 2198 520833627 520833689 8.710000e-21 111.0
10 TraesCS7B01G272100 chr3B 97.744 133 3 0 1 133 32495908 32496040 2.300000e-56 230.0
11 TraesCS7B01G272100 chr3B 97.744 133 3 0 1 133 32564782 32564914 2.300000e-56 230.0
12 TraesCS7B01G272100 chr3B 75.000 252 43 13 2214 2460 32435764 32435528 6.780000e-17 99.0
13 TraesCS7B01G272100 chr5B 79.116 249 39 7 2215 2460 575670134 575669896 3.070000e-35 159.0


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 TraesCS7B01G272100 chr7B 498968028 498970999 2971 True 1919.666667 5489 96.254667 1 2972 3 chr7B.!!$R1 2971
1 TraesCS7B01G272100 chr7D 475184369 475187167 2798 True 996.833333 2828 95.791000 1 2945 3 chr7D.!!$R1 2944
2 TraesCS7B01G272100 chr7A 520832231 520836566 4335 False 643.666667 1688 92.135667 783 2611 3 chr7A.!!$F2 1828
3 TraesCS7B01G272100 chr7A 520798894 520799475 581 False 374.000000 374 78.878000 1 591 1 chr7A.!!$F1 590

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
759 785 0.39382 TCGTTGCTTCGGTTAACCCT 59.606 50.0 19.09 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2710 5278 0.106419 TCCTGGAACCAAACACACCC 60.106 55.0 0.0 0.0 0.0 4.61 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
90 91 3.207778 GTCTAAGAGGAAGAGCGAGCTA 58.792 50.000 0.00 0.00 0.00 3.32
161 162 1.981533 GTACGCGTACTTGTTCACCTC 59.018 52.381 35.66 10.39 33.45 3.85
203 204 9.350357 CTTGTACATGAATTCTTCAGAAAATGG 57.650 33.333 7.05 0.00 43.98 3.16
208 209 8.423349 ACATGAATTCTTCAGAAAATGGAAACA 58.577 29.630 7.05 0.00 44.63 2.83
212 213 9.317936 GAATTCTTCAGAAAATGGAAACAAACT 57.682 29.630 0.00 0.00 40.11 2.66
213 214 8.652810 ATTCTTCAGAAAATGGAAACAAACTG 57.347 30.769 0.00 0.00 40.11 3.16
275 278 9.346725 GCAGGTAGATTAATCAGTTTCTTTTTG 57.653 33.333 17.56 3.64 0.00 2.44
287 290 7.280356 TCAGTTTCTTTTTGCCTAGTTAGTCT 58.720 34.615 0.00 0.00 0.00 3.24
413 424 3.363772 CGACGATGTACCTCTTACCGATC 60.364 52.174 0.00 0.00 0.00 3.69
440 451 4.754667 GGAACGAGCCCGACACCC 62.755 72.222 0.00 0.00 39.50 4.61
472 483 2.029073 CACGGACTCGGCAACAGT 59.971 61.111 0.00 0.00 41.39 3.55
484 495 1.000506 GGCAACAGTGACGAGTAGGAA 59.999 52.381 0.00 0.00 0.00 3.36
494 505 5.535406 AGTGACGAGTAGGAAGAAGAAGAAA 59.465 40.000 0.00 0.00 0.00 2.52
495 506 5.859648 GTGACGAGTAGGAAGAAGAAGAAAG 59.140 44.000 0.00 0.00 0.00 2.62
516 527 0.945265 GAGCAGCTGAGCCATCGATC 60.945 60.000 20.43 0.00 34.23 3.69
517 528 1.227468 GCAGCTGAGCCATCGATCA 60.227 57.895 20.43 0.00 0.00 2.92
529 540 5.674525 AGCCATCGATCAATCAGAACTTAA 58.325 37.500 0.00 0.00 0.00 1.85
538 550 8.446273 CGATCAATCAGAACTTAATGAACACTT 58.554 33.333 0.00 0.00 0.00 3.16
547 561 5.381757 ACTTAATGAACACTTGGTGGCTTA 58.618 37.500 2.75 0.00 37.94 3.09
556 570 4.012374 CACTTGGTGGCTTATGACTGATT 58.988 43.478 0.00 0.00 0.00 2.57
563 578 6.070481 TGGTGGCTTATGACTGATTACTACAA 60.070 38.462 0.00 0.00 0.00 2.41
575 590 2.186532 TACTACAATGTTTGCGGGCA 57.813 45.000 0.00 0.00 0.00 5.36
591 606 2.853210 CACGACGTGGATGTGCAC 59.147 61.111 20.26 10.75 0.00 4.57
593 608 1.227409 ACGACGTGGATGTGCACAA 60.227 52.632 25.72 4.24 0.00 3.33
595 610 1.204062 GACGTGGATGTGCACAACG 59.796 57.895 30.75 30.75 0.00 4.10
597 612 2.255252 GTGGATGTGCACAACGGC 59.745 61.111 25.72 13.18 0.00 5.68
599 614 3.353836 GGATGTGCACAACGGCGT 61.354 61.111 25.72 6.77 36.28 5.68
614 629 1.202604 CGGCGTCATGGTTTATAGGGT 60.203 52.381 0.00 0.00 0.00 4.34
624 639 4.553678 TGGTTTATAGGGTGAGGGAGTAG 58.446 47.826 0.00 0.00 0.00 2.57
632 647 1.549170 GGTGAGGGAGTAGCGAAAGAA 59.451 52.381 0.00 0.00 0.00 2.52
639 654 3.133183 GGGAGTAGCGAAAGAAGAGGATT 59.867 47.826 0.00 0.00 0.00 3.01
645 671 2.095053 GCGAAAGAAGAGGATTGTGAGC 59.905 50.000 0.00 0.00 0.00 4.26
649 675 2.114616 AGAAGAGGATTGTGAGCGGAT 58.885 47.619 0.00 0.00 0.00 4.18
690 716 2.813908 CGCGAGCGGGCTTAGTTT 60.814 61.111 9.90 0.00 35.56 2.66
691 717 2.785258 GCGAGCGGGCTTAGTTTG 59.215 61.111 0.00 0.00 0.00 2.93
692 718 2.033194 GCGAGCGGGCTTAGTTTGT 61.033 57.895 0.00 0.00 0.00 2.83
693 719 1.574702 GCGAGCGGGCTTAGTTTGTT 61.575 55.000 0.00 0.00 0.00 2.83
699 725 1.387756 CGGGCTTAGTTTGTTACGTCG 59.612 52.381 0.00 0.00 0.00 5.12
703 729 4.171754 GGCTTAGTTTGTTACGTCGAGAT 58.828 43.478 0.00 0.00 0.00 2.75
714 740 1.469308 ACGTCGAGATCAAGTGGAGAC 59.531 52.381 0.00 0.00 0.00 3.36
741 767 1.658114 GGTGGACTTTGGCGGTTTC 59.342 57.895 0.00 0.00 0.00 2.78
755 781 1.261089 CGGTTTCGTTGCTTCGGTTAA 59.739 47.619 1.90 0.00 0.00 2.01
757 783 2.602933 GGTTTCGTTGCTTCGGTTAACC 60.603 50.000 15.13 15.13 33.83 2.85
758 784 1.228533 TTCGTTGCTTCGGTTAACCC 58.771 50.000 19.09 5.39 0.00 4.11
759 785 0.393820 TCGTTGCTTCGGTTAACCCT 59.606 50.000 19.09 0.00 0.00 4.34
760 786 0.515564 CGTTGCTTCGGTTAACCCTG 59.484 55.000 19.09 10.00 0.00 4.45
761 787 1.601166 GTTGCTTCGGTTAACCCTGT 58.399 50.000 19.09 0.00 0.00 4.00
762 788 1.534163 GTTGCTTCGGTTAACCCTGTC 59.466 52.381 19.09 6.83 0.00 3.51
763 789 0.759959 TGCTTCGGTTAACCCTGTCA 59.240 50.000 19.09 9.28 0.00 3.58
764 790 1.154197 GCTTCGGTTAACCCTGTCAC 58.846 55.000 19.09 0.45 0.00 3.67
765 791 1.804601 CTTCGGTTAACCCTGTCACC 58.195 55.000 19.09 0.00 0.00 4.02
772 798 1.719529 TAACCCTGTCACCGGAAGAA 58.280 50.000 9.46 0.00 0.00 2.52
775 801 1.423921 ACCCTGTCACCGGAAGAATTT 59.576 47.619 9.46 0.00 0.00 1.82
776 802 2.158519 ACCCTGTCACCGGAAGAATTTT 60.159 45.455 9.46 0.00 0.00 1.82
777 803 2.488153 CCCTGTCACCGGAAGAATTTTC 59.512 50.000 9.46 0.00 0.00 2.29
781 807 5.472137 CCTGTCACCGGAAGAATTTTCTTTA 59.528 40.000 9.46 0.00 46.84 1.85
784 810 4.153475 TCACCGGAAGAATTTTCTTTAGCG 59.847 41.667 9.46 0.00 46.84 4.26
791 817 6.183360 GGAAGAATTTTCTTTAGCGGAGACTC 60.183 42.308 6.98 0.00 46.84 3.36
799 825 1.830279 TAGCGGAGACTCGGAAGAAA 58.170 50.000 13.80 0.00 41.32 2.52
809 835 4.158764 AGACTCGGAAGAAATGGTCTGTAG 59.841 45.833 0.00 0.00 39.51 2.74
813 842 5.014858 TCGGAAGAAATGGTCTGTAGTACT 58.985 41.667 0.00 0.00 36.40 2.73
814 843 5.125097 TCGGAAGAAATGGTCTGTAGTACTC 59.875 44.000 0.00 0.00 36.40 2.59
841 870 2.673775 TCAGGCACCCAAGATTGAAA 57.326 45.000 0.00 0.00 0.00 2.69
896 928 1.673665 CCTGCGAGCTTTGCTTCCT 60.674 57.895 12.38 0.00 39.88 3.36
917 949 1.472662 CCCCCGTAATCCTCATCGCT 61.473 60.000 0.00 0.00 0.00 4.93
949 981 1.301716 ACGGCACTCAACGCATCTT 60.302 52.632 0.00 0.00 0.00 2.40
987 1019 3.493830 TTACATAGCCGCTCGCCCG 62.494 63.158 0.00 0.00 38.78 6.13
1131 1163 4.648626 GCTGCAGCACCACCTCCA 62.649 66.667 33.36 0.00 41.59 3.86
1410 1442 3.483587 GGAGAGGTTCCACCAGCA 58.516 61.111 0.00 0.00 46.01 4.41
1833 1868 2.642139 TAGAGGAACTTGTTACGGCG 57.358 50.000 4.80 4.80 41.55 6.46
1880 1917 1.006043 AGCTGTACAGAGGGAGTAGCA 59.994 52.381 27.08 0.00 0.00 3.49
1896 1933 2.734755 AGCATCCCAATTCATTCGGA 57.265 45.000 0.00 0.00 31.65 4.55
1906 1943 3.526931 ATTCATTCGGACTCGTGACAT 57.473 42.857 0.00 0.00 37.69 3.06
1956 2005 8.196802 TGACTTATTACATGCATGTACAGAAC 57.803 34.615 33.74 24.66 42.48 3.01
1959 2008 9.884636 ACTTATTACATGCATGTACAGAACTTA 57.115 29.630 33.74 19.70 42.48 2.24
2008 2057 8.416329 TCTGAAGAAATTATCGATGATGACAGA 58.584 33.333 8.54 12.64 0.00 3.41
2009 2058 9.205719 CTGAAGAAATTATCGATGATGACAGAT 57.794 33.333 8.54 0.00 0.00 2.90
2013 2062 9.096160 AGAAATTATCGATGATGACAGATATGC 57.904 33.333 8.54 0.00 0.00 3.14
2015 2064 3.599730 TCGATGATGACAGATATGCCC 57.400 47.619 0.00 0.00 0.00 5.36
2016 2065 3.168292 TCGATGATGACAGATATGCCCT 58.832 45.455 0.00 0.00 0.00 5.19
2017 2066 3.194329 TCGATGATGACAGATATGCCCTC 59.806 47.826 0.00 0.00 0.00 4.30
2019 2068 4.505808 GATGATGACAGATATGCCCTCTG 58.494 47.826 5.90 5.90 44.60 3.35
2037 2098 6.295292 GCCCTCTGTGATAGGAAACAATTTTT 60.295 38.462 0.00 0.00 36.08 1.94
2209 2309 2.996155 GCAATCTGAGATTGCCGATTG 58.004 47.619 37.42 15.37 46.21 2.67
2218 2318 2.434336 AGATTGCCGATTGGTGCTACTA 59.566 45.455 0.00 0.00 37.67 1.82
2219 2319 2.018542 TTGCCGATTGGTGCTACTAC 57.981 50.000 0.00 0.00 37.67 2.73
2221 2321 0.532196 GCCGATTGGTGCTACTACCC 60.532 60.000 0.00 0.00 40.09 3.69
2223 2323 0.249322 CGATTGGTGCTACTACCCCG 60.249 60.000 0.00 0.00 40.09 5.73
2224 2324 0.828677 GATTGGTGCTACTACCCCGT 59.171 55.000 0.00 0.00 40.09 5.28
2225 2325 0.828677 ATTGGTGCTACTACCCCGTC 59.171 55.000 0.00 0.00 40.09 4.79
2226 2326 1.259840 TTGGTGCTACTACCCCGTCC 61.260 60.000 0.00 0.00 40.09 4.79
2227 2327 1.380920 GGTGCTACTACCCCGTCCT 60.381 63.158 0.00 0.00 34.56 3.85
2228 2328 1.673808 GGTGCTACTACCCCGTCCTG 61.674 65.000 0.00 0.00 34.56 3.86
2229 2329 0.682209 GTGCTACTACCCCGTCCTGA 60.682 60.000 0.00 0.00 0.00 3.86
2230 2330 0.260816 TGCTACTACCCCGTCCTGAT 59.739 55.000 0.00 0.00 0.00 2.90
2231 2331 1.342674 TGCTACTACCCCGTCCTGATT 60.343 52.381 0.00 0.00 0.00 2.57
2232 2332 1.761198 GCTACTACCCCGTCCTGATTT 59.239 52.381 0.00 0.00 0.00 2.17
2233 2333 2.961062 GCTACTACCCCGTCCTGATTTA 59.039 50.000 0.00 0.00 0.00 1.40
2234 2334 3.577415 GCTACTACCCCGTCCTGATTTAT 59.423 47.826 0.00 0.00 0.00 1.40
2236 2336 5.454329 GCTACTACCCCGTCCTGATTTATTT 60.454 44.000 0.00 0.00 0.00 1.40
2237 2337 4.777463 ACTACCCCGTCCTGATTTATTTG 58.223 43.478 0.00 0.00 0.00 2.32
2238 2338 3.732048 ACCCCGTCCTGATTTATTTGT 57.268 42.857 0.00 0.00 0.00 2.83
2241 2341 3.371595 CCCCGTCCTGATTTATTTGTCCT 60.372 47.826 0.00 0.00 0.00 3.85
2243 2343 4.705023 CCCGTCCTGATTTATTTGTCCTTT 59.295 41.667 0.00 0.00 0.00 3.11
2245 2345 6.295067 CCCGTCCTGATTTATTTGTCCTTTTT 60.295 38.462 0.00 0.00 0.00 1.94
2246 2346 6.586082 CCGTCCTGATTTATTTGTCCTTTTTG 59.414 38.462 0.00 0.00 0.00 2.44
2247 2347 7.145323 CGTCCTGATTTATTTGTCCTTTTTGT 58.855 34.615 0.00 0.00 0.00 2.83
2248 2348 8.293867 CGTCCTGATTTATTTGTCCTTTTTGTA 58.706 33.333 0.00 0.00 0.00 2.41
2280 2694 8.987890 TGCTAAATTTTGAGCAAAGATTTAACC 58.012 29.630 12.24 12.51 45.47 2.85
2281 2695 8.162245 GCTAAATTTTGAGCAAAGATTTAACCG 58.838 33.333 7.88 10.36 38.62 4.44
2288 2702 4.893608 AGCAAAGATTTAACCGGCAAAAT 58.106 34.783 12.98 12.98 0.00 1.82
2293 2707 8.325282 GCAAAGATTTAACCGGCAAAATATTAC 58.675 33.333 17.41 11.65 29.12 1.89
2295 2709 9.581099 AAAGATTTAACCGGCAAAATATTACTG 57.419 29.630 17.41 0.00 29.12 2.74
2296 2710 7.200455 AGATTTAACCGGCAAAATATTACTGC 58.800 34.615 13.07 12.08 35.28 4.40
2297 2711 5.899120 TTAACCGGCAAAATATTACTGCA 57.101 34.783 18.94 0.00 37.83 4.41
2301 2715 4.202010 ACCGGCAAAATATTACTGCATGTC 60.202 41.667 18.94 5.89 37.83 3.06
2302 2716 4.202000 CCGGCAAAATATTACTGCATGTCA 60.202 41.667 18.94 0.00 37.83 3.58
2303 2717 5.339177 CGGCAAAATATTACTGCATGTCAA 58.661 37.500 18.94 0.00 37.83 3.18
2304 2718 5.804473 CGGCAAAATATTACTGCATGTCAAA 59.196 36.000 18.94 0.00 37.83 2.69
2305 2719 6.309980 CGGCAAAATATTACTGCATGTCAAAA 59.690 34.615 18.94 0.00 37.83 2.44
2306 2720 7.148672 CGGCAAAATATTACTGCATGTCAAAAA 60.149 33.333 18.94 0.00 37.83 1.94
2338 2969 7.622893 TCATTGGATTCGTATTTGAACATCA 57.377 32.000 0.00 0.00 0.00 3.07
2340 2971 8.685427 TCATTGGATTCGTATTTGAACATCATT 58.315 29.630 0.00 0.00 0.00 2.57
2343 2974 9.703892 TTGGATTCGTATTTGAACATCATTTTT 57.296 25.926 0.00 0.00 0.00 1.94
2425 3772 8.316214 ACTTATGATCAAAATTTGGCACAGAAT 58.684 29.630 5.83 0.00 42.39 2.40
2429 3776 9.675464 ATGATCAAAATTTGGCACAGAATAAAT 57.325 25.926 5.83 0.00 42.39 1.40
2434 3781 9.381033 CAAAATTTGGCACAGAATAAATATGGA 57.619 29.630 0.00 0.00 42.39 3.41
2436 3783 6.463995 TTTGGCACAGAATAAATATGGACC 57.536 37.500 0.00 0.00 42.39 4.46
2437 3784 5.122707 TGGCACAGAATAAATATGGACCA 57.877 39.130 0.00 0.00 0.00 4.02
2438 3785 5.132502 TGGCACAGAATAAATATGGACCAG 58.867 41.667 0.00 0.00 0.00 4.00
2440 3787 4.580167 GCACAGAATAAATATGGACCAGCA 59.420 41.667 0.00 0.00 0.00 4.41
2441 3788 5.067674 GCACAGAATAAATATGGACCAGCAA 59.932 40.000 0.00 0.00 0.00 3.91
2443 3790 6.974622 CACAGAATAAATATGGACCAGCAAAC 59.025 38.462 0.00 0.00 0.00 2.93
2444 3791 6.096846 ACAGAATAAATATGGACCAGCAAACC 59.903 38.462 0.00 0.00 0.00 3.27
2450 3797 1.966451 GGACCAGCAAACCAGGACG 60.966 63.158 0.00 0.00 0.00 4.79
2453 3800 1.672356 CCAGCAAACCAGGACGGAG 60.672 63.158 0.00 0.00 38.63 4.63
2454 3801 1.672356 CAGCAAACCAGGACGGAGG 60.672 63.158 0.00 0.00 38.63 4.30
2457 3804 0.391263 GCAAACCAGGACGGAGGTAG 60.391 60.000 0.00 0.00 37.07 3.18
2459 3806 2.173519 CAAACCAGGACGGAGGTAGTA 58.826 52.381 0.00 0.00 37.07 1.82
2460 3807 2.764572 CAAACCAGGACGGAGGTAGTAT 59.235 50.000 0.00 0.00 37.07 2.12
2461 3808 2.361643 ACCAGGACGGAGGTAGTATC 57.638 55.000 0.00 0.00 36.07 2.24
2462 3809 1.851653 ACCAGGACGGAGGTAGTATCT 59.148 52.381 0.00 0.00 36.07 1.98
2463 3810 2.231529 CCAGGACGGAGGTAGTATCTG 58.768 57.143 0.00 0.00 36.56 2.90
2468 3815 4.886489 AGGACGGAGGTAGTATCTGTTAAC 59.114 45.833 0.00 0.00 36.41 2.01
2469 3816 4.641989 GGACGGAGGTAGTATCTGTTAACA 59.358 45.833 8.28 8.28 36.41 2.41
2571 5139 1.003839 TTGGTAGCAGCCGGTTCTG 60.004 57.895 1.90 3.65 37.15 3.02
2623 5191 3.716539 TTCGATCGGGAGCGCCTTG 62.717 63.158 16.41 0.00 40.42 3.61
2625 5193 4.918201 GATCGGGAGCGCCTTGGG 62.918 72.222 2.29 0.00 0.00 4.12
2630 5198 4.643387 GGAGCGCCTTGGGTGTGT 62.643 66.667 2.29 0.00 35.34 3.72
2631 5199 2.594592 GAGCGCCTTGGGTGTGTT 60.595 61.111 2.29 0.00 35.34 3.32
2632 5200 2.123897 AGCGCCTTGGGTGTGTTT 60.124 55.556 2.29 0.00 35.34 2.83
2633 5201 2.027460 GCGCCTTGGGTGTGTTTG 59.973 61.111 0.00 0.00 35.34 2.93
2634 5202 2.727544 CGCCTTGGGTGTGTTTGG 59.272 61.111 0.00 0.00 0.00 3.28
2635 5203 2.855514 CGCCTTGGGTGTGTTTGGG 61.856 63.158 0.00 0.00 0.00 4.12
2636 5204 2.506957 GCCTTGGGTGTGTTTGGGG 61.507 63.158 0.00 0.00 0.00 4.96
2637 5205 1.231641 CCTTGGGTGTGTTTGGGGA 59.768 57.895 0.00 0.00 0.00 4.81
2638 5206 0.397816 CCTTGGGTGTGTTTGGGGAA 60.398 55.000 0.00 0.00 0.00 3.97
2639 5207 1.490574 CTTGGGTGTGTTTGGGGAAA 58.509 50.000 0.00 0.00 0.00 3.13
2640 5208 1.412343 CTTGGGTGTGTTTGGGGAAAG 59.588 52.381 0.00 0.00 0.00 2.62
2641 5209 0.336737 TGGGTGTGTTTGGGGAAAGT 59.663 50.000 0.00 0.00 0.00 2.66
2642 5210 1.273324 TGGGTGTGTTTGGGGAAAGTT 60.273 47.619 0.00 0.00 0.00 2.66
2643 5211 1.138069 GGGTGTGTTTGGGGAAAGTTG 59.862 52.381 0.00 0.00 0.00 3.16
2644 5212 1.138069 GGTGTGTTTGGGGAAAGTTGG 59.862 52.381 0.00 0.00 0.00 3.77
2645 5213 1.828595 GTGTGTTTGGGGAAAGTTGGT 59.171 47.619 0.00 0.00 0.00 3.67
2646 5214 3.025262 GTGTGTTTGGGGAAAGTTGGTA 58.975 45.455 0.00 0.00 0.00 3.25
2647 5215 3.067601 GTGTGTTTGGGGAAAGTTGGTAG 59.932 47.826 0.00 0.00 0.00 3.18
2648 5216 2.035449 GTGTTTGGGGAAAGTTGGTAGC 59.965 50.000 0.00 0.00 0.00 3.58
2649 5217 2.312390 GTTTGGGGAAAGTTGGTAGCA 58.688 47.619 0.00 0.00 0.00 3.49
2650 5218 2.286365 TTGGGGAAAGTTGGTAGCAG 57.714 50.000 0.00 0.00 0.00 4.24
2651 5219 0.251165 TGGGGAAAGTTGGTAGCAGC 60.251 55.000 0.00 0.00 0.00 5.25
2652 5220 0.965866 GGGGAAAGTTGGTAGCAGCC 60.966 60.000 5.05 0.00 0.00 4.85
2653 5221 1.305930 GGGAAAGTTGGTAGCAGCCG 61.306 60.000 5.05 0.00 0.00 5.52
2654 5222 1.305930 GGAAAGTTGGTAGCAGCCGG 61.306 60.000 5.05 0.00 0.00 6.13
2655 5223 0.605589 GAAAGTTGGTAGCAGCCGGT 60.606 55.000 1.90 0.00 0.00 5.28
2656 5224 0.179001 AAAGTTGGTAGCAGCCGGTT 60.179 50.000 1.90 0.00 0.00 4.44
2657 5225 0.605589 AAGTTGGTAGCAGCCGGTTC 60.606 55.000 1.90 0.00 0.00 3.62
2658 5226 1.003718 GTTGGTAGCAGCCGGTTCT 60.004 57.895 1.90 0.00 0.00 3.01
2659 5227 1.003839 TTGGTAGCAGCCGGTTCTG 60.004 57.895 1.90 3.65 37.15 3.02
2660 5228 1.764571 TTGGTAGCAGCCGGTTCTGT 61.765 55.000 1.90 0.00 36.49 3.41
2661 5229 1.003718 GGTAGCAGCCGGTTCTGTT 60.004 57.895 1.90 3.24 36.49 3.16
2662 5230 1.019805 GGTAGCAGCCGGTTCTGTTC 61.020 60.000 1.90 0.00 36.49 3.18
2663 5231 1.080093 TAGCAGCCGGTTCTGTTCG 60.080 57.895 1.90 0.00 36.49 3.95
2664 5232 4.090057 GCAGCCGGTTCTGTTCGC 62.090 66.667 1.90 0.00 36.49 4.70
2665 5233 3.423154 CAGCCGGTTCTGTTCGCC 61.423 66.667 1.90 0.00 0.00 5.54
2666 5234 3.626924 AGCCGGTTCTGTTCGCCT 61.627 61.111 1.90 0.00 0.00 5.52
2667 5235 3.423154 GCCGGTTCTGTTCGCCTG 61.423 66.667 1.90 0.00 0.00 4.85
2668 5236 2.342279 CCGGTTCTGTTCGCCTGA 59.658 61.111 0.00 0.00 0.00 3.86
2669 5237 1.079127 CCGGTTCTGTTCGCCTGAT 60.079 57.895 0.00 0.00 0.00 2.90
2670 5238 1.084370 CCGGTTCTGTTCGCCTGATC 61.084 60.000 0.00 0.00 0.00 2.92
2671 5239 1.413767 CGGTTCTGTTCGCCTGATCG 61.414 60.000 0.00 0.00 0.00 3.69
2672 5240 0.108804 GGTTCTGTTCGCCTGATCGA 60.109 55.000 0.00 0.00 36.60 3.59
2673 5241 1.671850 GGTTCTGTTCGCCTGATCGAA 60.672 52.381 0.00 0.00 44.96 3.71
2678 5246 3.967886 TTCGCCTGATCGAATCCTC 57.032 52.632 0.00 0.00 42.68 3.71
2679 5247 0.030773 TTCGCCTGATCGAATCCTCG 59.969 55.000 0.00 0.00 46.87 4.63
2688 5256 3.568578 GAATCCTCGATGGCCCCT 58.431 61.111 0.00 0.00 35.26 4.79
2689 5257 1.072159 GAATCCTCGATGGCCCCTG 59.928 63.158 0.00 0.00 35.26 4.45
2690 5258 3.125376 AATCCTCGATGGCCCCTGC 62.125 63.158 0.00 0.00 35.26 4.85
2700 5268 2.830370 GCCCCTGCCTTTGATCGG 60.830 66.667 0.00 0.00 0.00 4.18
2701 5269 2.124151 CCCCTGCCTTTGATCGGG 60.124 66.667 0.00 0.00 34.62 5.14
2702 5270 2.679342 CCCCTGCCTTTGATCGGGA 61.679 63.158 1.45 0.00 37.05 5.14
2703 5271 1.153086 CCCTGCCTTTGATCGGGAG 60.153 63.158 0.44 0.44 39.45 4.30
2704 5272 1.821332 CCTGCCTTTGATCGGGAGC 60.821 63.158 1.74 0.00 38.53 4.70
2705 5273 2.125147 TGCCTTTGATCGGGAGCG 60.125 61.111 3.77 0.00 0.00 5.03
2706 5274 3.577313 GCCTTTGATCGGGAGCGC 61.577 66.667 0.00 0.00 0.00 5.92
2707 5275 2.897350 CCTTTGATCGGGAGCGCC 60.897 66.667 2.29 0.00 0.00 6.53
2724 5292 1.744320 GCCCTGGGTGTGTTTGGTTC 61.744 60.000 15.56 0.00 0.00 3.62
2753 5321 3.305064 CCAACCAAAATGTAACGGGTCAG 60.305 47.826 0.00 0.00 0.00 3.51
2770 5338 1.228154 AGACCCGTTCTTTGGCCAC 60.228 57.895 3.88 0.00 0.00 5.01
2777 5345 3.016736 CCGTTCTTTGGCCACATTCTAT 58.983 45.455 3.88 0.00 0.00 1.98
2788 5356 3.485216 GCCACATTCTATCGTTTGGTTCG 60.485 47.826 0.00 0.00 0.00 3.95
2791 5359 4.387559 CACATTCTATCGTTTGGTTCGACA 59.612 41.667 0.00 0.00 40.07 4.35
2807 5375 1.811359 CGACAGAACCTACTCGTTCCT 59.189 52.381 0.00 0.00 42.63 3.36
2813 5381 2.140839 ACCTACTCGTTCCTACCCAG 57.859 55.000 0.00 0.00 0.00 4.45
2815 5383 1.471119 CTACTCGTTCCTACCCAGCA 58.529 55.000 0.00 0.00 0.00 4.41
2822 5390 4.448210 TCGTTCCTACCCAGCAAATATTC 58.552 43.478 0.00 0.00 0.00 1.75
2831 5399 3.629398 CCCAGCAAATATTCCACTGAGAC 59.371 47.826 11.79 0.00 0.00 3.36
2833 5401 4.521146 CAGCAAATATTCCACTGAGACCT 58.479 43.478 6.51 0.00 0.00 3.85
2838 5406 6.623767 GCAAATATTCCACTGAGACCTGAAAC 60.624 42.308 0.00 0.00 0.00 2.78
2843 5411 0.318762 ACTGAGACCTGAAACCGAGC 59.681 55.000 0.00 0.00 0.00 5.03
2864 5432 1.373570 GTCTCTCCAAATTGAGCGGG 58.626 55.000 0.00 0.00 32.22 6.13
2869 5437 0.825425 TCCAAATTGAGCGGGCAACA 60.825 50.000 0.00 0.00 39.74 3.33
2875 5443 3.723348 GAGCGGGCAACACGGAAC 61.723 66.667 0.00 0.00 39.74 3.62
2891 5459 2.820767 GAACCGTCCCTCAGCACTCG 62.821 65.000 0.00 0.00 0.00 4.18
2892 5460 4.803426 CCGTCCCTCAGCACTCGC 62.803 72.222 0.00 0.00 38.99 5.03
2894 5462 4.459089 GTCCCTCAGCACTCGCCC 62.459 72.222 0.00 0.00 39.83 6.13
2904 5472 1.379176 CACTCGCCCCTCTCTCTCA 60.379 63.158 0.00 0.00 0.00 3.27
2906 5474 1.379176 CTCGCCCCTCTCTCTCACA 60.379 63.158 0.00 0.00 0.00 3.58
2907 5475 1.379176 TCGCCCCTCTCTCTCACAG 60.379 63.158 0.00 0.00 0.00 3.66
2908 5476 2.422231 CGCCCCTCTCTCTCACAGG 61.422 68.421 0.00 0.00 0.00 4.00
2909 5477 1.000993 GCCCCTCTCTCTCACAGGA 59.999 63.158 0.00 0.00 0.00 3.86
2910 5478 0.616111 GCCCCTCTCTCTCACAGGAA 60.616 60.000 0.00 0.00 0.00 3.36
2911 5479 1.484038 CCCCTCTCTCTCACAGGAAG 58.516 60.000 0.00 0.00 0.00 3.46
2912 5480 0.823460 CCCTCTCTCTCACAGGAAGC 59.177 60.000 0.00 0.00 0.00 3.86
2914 5482 0.823460 CTCTCTCTCACAGGAAGCCC 59.177 60.000 0.00 0.00 0.00 5.19
2950 5558 2.838225 CCCTCGGTCCGCCAGTAT 60.838 66.667 6.34 0.00 34.09 2.12
2951 5559 2.417516 CCTCGGTCCGCCAGTATG 59.582 66.667 6.34 0.00 34.09 2.39
2952 5560 2.279517 CTCGGTCCGCCAGTATGC 60.280 66.667 6.34 0.00 31.97 3.14
2953 5561 3.071837 TCGGTCCGCCAGTATGCA 61.072 61.111 6.34 0.00 31.97 3.96
2954 5562 2.125310 CGGTCCGCCAGTATGCAA 60.125 61.111 0.00 0.00 31.97 4.08
2955 5563 2.461110 CGGTCCGCCAGTATGCAAC 61.461 63.158 0.00 0.00 31.97 4.17
2956 5564 2.461110 GGTCCGCCAGTATGCAACG 61.461 63.158 0.00 0.00 31.97 4.10
2957 5565 2.817834 TCCGCCAGTATGCAACGC 60.818 61.111 0.00 0.00 31.97 4.84
2958 5566 2.819595 CCGCCAGTATGCAACGCT 60.820 61.111 0.00 0.00 31.97 5.07
2959 5567 2.703409 CGCCAGTATGCAACGCTC 59.297 61.111 0.00 0.00 31.97 5.03
2960 5568 2.100031 CGCCAGTATGCAACGCTCA 61.100 57.895 0.00 0.00 31.97 4.26
2961 5569 1.717937 GCCAGTATGCAACGCTCAG 59.282 57.895 0.00 0.00 31.97 3.35
2962 5570 1.021390 GCCAGTATGCAACGCTCAGT 61.021 55.000 0.00 0.00 31.97 3.41
2963 5571 1.442769 CCAGTATGCAACGCTCAGTT 58.557 50.000 0.00 0.00 45.45 3.16
2964 5572 1.806542 CCAGTATGCAACGCTCAGTTT 59.193 47.619 0.00 0.00 42.02 2.66
2965 5573 2.159653 CCAGTATGCAACGCTCAGTTTC 60.160 50.000 0.00 0.00 42.02 2.78
2966 5574 2.076863 AGTATGCAACGCTCAGTTTCC 58.923 47.619 0.00 0.00 42.02 3.13
2967 5575 1.075542 TATGCAACGCTCAGTTTCCG 58.924 50.000 0.00 0.00 42.02 4.30
2968 5576 0.884704 ATGCAACGCTCAGTTTCCGT 60.885 50.000 0.00 0.00 42.02 4.69
2969 5577 1.204312 GCAACGCTCAGTTTCCGTC 59.796 57.895 0.00 0.00 42.02 4.79
2970 5578 1.860078 CAACGCTCAGTTTCCGTCC 59.140 57.895 0.00 0.00 42.02 4.79
2971 5579 1.301479 AACGCTCAGTTTCCGTCCC 60.301 57.895 0.00 0.00 40.88 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 0.670546 CTACCACTGCAACTGGACGG 60.671 60.000 15.55 0.74 32.55 4.79
201 202 6.072064 TCGTTAAAAACTCCAGTTTGTTTCCA 60.072 34.615 5.46 0.00 46.47 3.53
203 204 7.980742 ATCGTTAAAAACTCCAGTTTGTTTC 57.019 32.000 5.46 0.00 46.47 2.78
237 238 0.796312 CTACCTGCGTGCATTTCGTT 59.204 50.000 0.00 0.00 0.00 3.85
239 240 1.290203 ATCTACCTGCGTGCATTTCG 58.710 50.000 0.00 0.00 0.00 3.46
240 241 4.875544 TTAATCTACCTGCGTGCATTTC 57.124 40.909 0.00 0.00 0.00 2.17
275 278 5.672421 TTGGTAAGGAAGACTAACTAGGC 57.328 43.478 0.00 0.00 0.00 3.93
287 290 2.500098 CGAGGACTCCATTGGTAAGGAA 59.500 50.000 1.86 0.00 32.57 3.36
386 389 3.122250 GAGGTACATCGTCGGCGCT 62.122 63.158 3.52 0.00 38.14 5.92
468 479 3.752665 TCTTCTTCCTACTCGTCACTGT 58.247 45.455 0.00 0.00 0.00 3.55
472 483 5.535406 ACTTTCTTCTTCTTCCTACTCGTCA 59.465 40.000 0.00 0.00 0.00 4.35
484 495 3.070734 TCAGCTGCTCACTTTCTTCTTCT 59.929 43.478 9.47 0.00 0.00 2.85
494 505 1.221293 GATGGCTCAGCTGCTCACT 59.779 57.895 9.47 0.00 0.00 3.41
495 506 2.172372 CGATGGCTCAGCTGCTCAC 61.172 63.158 9.47 0.00 0.00 3.51
516 527 7.592533 CACCAAGTGTTCATTAAGTTCTGATTG 59.407 37.037 0.00 0.00 0.00 2.67
517 528 7.255590 CCACCAAGTGTTCATTAAGTTCTGATT 60.256 37.037 0.00 0.00 0.00 2.57
529 540 3.758554 GTCATAAGCCACCAAGTGTTCAT 59.241 43.478 0.00 0.00 0.00 2.57
538 550 5.423931 TGTAGTAATCAGTCATAAGCCACCA 59.576 40.000 0.00 0.00 0.00 4.17
547 561 6.183360 CCGCAAACATTGTAGTAATCAGTCAT 60.183 38.462 0.00 0.00 0.00 3.06
556 570 1.807742 GTGCCCGCAAACATTGTAGTA 59.192 47.619 0.00 0.00 0.00 1.82
563 578 3.722295 CGTCGTGCCCGCAAACAT 61.722 61.111 0.00 0.00 0.00 2.71
575 590 1.227409 TTGTGCACATCCACGTCGT 60.227 52.632 22.39 0.00 38.55 4.34
591 606 2.286833 CCTATAAACCATGACGCCGTTG 59.713 50.000 0.00 0.00 0.00 4.10
593 608 1.202604 CCCTATAAACCATGACGCCGT 60.203 52.381 0.00 0.00 0.00 5.68
595 610 2.158871 TCACCCTATAAACCATGACGCC 60.159 50.000 0.00 0.00 0.00 5.68
597 612 3.494398 CCCTCACCCTATAAACCATGACG 60.494 52.174 0.00 0.00 0.00 4.35
599 614 3.973973 CTCCCTCACCCTATAAACCATGA 59.026 47.826 0.00 0.00 0.00 3.07
614 629 2.755655 CTCTTCTTTCGCTACTCCCTCA 59.244 50.000 0.00 0.00 0.00 3.86
624 639 2.095053 GCTCACAATCCTCTTCTTTCGC 59.905 50.000 0.00 0.00 0.00 4.70
632 647 1.411977 CTCATCCGCTCACAATCCTCT 59.588 52.381 0.00 0.00 0.00 3.69
639 654 0.737367 CTTTCGCTCATCCGCTCACA 60.737 55.000 0.00 0.00 0.00 3.58
645 671 1.795286 GCCTATTCTTTCGCTCATCCG 59.205 52.381 0.00 0.00 0.00 4.18
649 675 1.831106 TCCTGCCTATTCTTTCGCTCA 59.169 47.619 0.00 0.00 0.00 4.26
679 705 1.387756 CGACGTAACAAACTAAGCCCG 59.612 52.381 0.00 0.00 0.00 6.13
682 708 4.855388 TGATCTCGACGTAACAAACTAAGC 59.145 41.667 0.00 0.00 0.00 3.09
683 709 6.581542 ACTTGATCTCGACGTAACAAACTAAG 59.418 38.462 0.00 0.00 0.00 2.18
684 710 6.361481 CACTTGATCTCGACGTAACAAACTAA 59.639 38.462 0.00 0.00 0.00 2.24
685 711 5.854866 CACTTGATCTCGACGTAACAAACTA 59.145 40.000 0.00 0.00 0.00 2.24
686 712 4.680110 CACTTGATCTCGACGTAACAAACT 59.320 41.667 0.00 0.00 0.00 2.66
687 713 4.143389 CCACTTGATCTCGACGTAACAAAC 60.143 45.833 0.00 0.00 0.00 2.93
688 714 3.985279 CCACTTGATCTCGACGTAACAAA 59.015 43.478 0.00 0.00 0.00 2.83
689 715 3.253921 TCCACTTGATCTCGACGTAACAA 59.746 43.478 0.00 0.00 0.00 2.83
690 716 2.815503 TCCACTTGATCTCGACGTAACA 59.184 45.455 0.00 0.00 0.00 2.41
691 717 3.126514 TCTCCACTTGATCTCGACGTAAC 59.873 47.826 0.00 0.00 0.00 2.50
692 718 3.126514 GTCTCCACTTGATCTCGACGTAA 59.873 47.826 0.00 0.00 0.00 3.18
693 719 2.676839 GTCTCCACTTGATCTCGACGTA 59.323 50.000 0.00 0.00 0.00 3.57
699 725 2.035321 GGATCGGTCTCCACTTGATCTC 59.965 54.545 0.00 0.00 35.96 2.75
703 729 1.945354 GCGGATCGGTCTCCACTTGA 61.945 60.000 0.00 0.00 34.78 3.02
727 753 0.933047 GCAACGAAACCGCCAAAGTC 60.933 55.000 0.00 0.00 0.00 3.01
729 755 0.248866 AAGCAACGAAACCGCCAAAG 60.249 50.000 0.00 0.00 0.00 2.77
738 764 1.603326 GGGTTAACCGAAGCAACGAAA 59.397 47.619 18.39 0.00 37.27 3.46
741 767 0.515564 CAGGGTTAACCGAAGCAACG 59.484 55.000 18.39 0.00 46.96 4.10
755 781 1.064825 AATTCTTCCGGTGACAGGGT 58.935 50.000 0.00 0.00 0.00 4.34
757 783 3.412386 AGAAAATTCTTCCGGTGACAGG 58.588 45.455 0.00 0.00 32.55 4.00
758 784 5.438761 AAAGAAAATTCTTCCGGTGACAG 57.561 39.130 8.74 0.00 46.22 3.51
759 785 5.048991 GCTAAAGAAAATTCTTCCGGTGACA 60.049 40.000 8.74 0.00 46.22 3.58
760 786 5.391449 GCTAAAGAAAATTCTTCCGGTGAC 58.609 41.667 8.74 0.00 46.22 3.67
761 787 4.153475 CGCTAAAGAAAATTCTTCCGGTGA 59.847 41.667 8.74 0.00 46.22 4.02
762 788 4.403453 CGCTAAAGAAAATTCTTCCGGTG 58.597 43.478 8.74 5.68 46.22 4.94
763 789 3.439129 CCGCTAAAGAAAATTCTTCCGGT 59.561 43.478 21.64 8.03 46.22 5.28
764 790 3.687698 TCCGCTAAAGAAAATTCTTCCGG 59.312 43.478 22.79 22.79 46.22 5.14
765 791 4.630069 TCTCCGCTAAAGAAAATTCTTCCG 59.370 41.667 8.74 11.09 46.22 4.30
772 798 3.194968 TCCGAGTCTCCGCTAAAGAAAAT 59.805 43.478 0.00 0.00 0.00 1.82
775 801 1.830279 TCCGAGTCTCCGCTAAAGAA 58.170 50.000 0.00 0.00 0.00 2.52
776 802 1.743958 CTTCCGAGTCTCCGCTAAAGA 59.256 52.381 0.00 0.00 0.00 2.52
777 803 1.743958 TCTTCCGAGTCTCCGCTAAAG 59.256 52.381 0.00 0.00 0.00 1.85
781 807 1.134965 CATTTCTTCCGAGTCTCCGCT 60.135 52.381 0.00 0.00 0.00 5.52
784 810 2.498078 AGACCATTTCTTCCGAGTCTCC 59.502 50.000 0.00 0.00 28.69 3.71
791 817 5.326200 AGTACTACAGACCATTTCTTCCG 57.674 43.478 0.00 0.00 28.96 4.30
799 825 3.027412 CTGCAGGAGTACTACAGACCAT 58.973 50.000 8.10 0.00 42.22 3.55
821 850 2.827921 GTTTCAATCTTGGGTGCCTGAT 59.172 45.455 0.00 0.00 0.00 2.90
841 870 2.798847 GCTCCGTCAAGTTAACTTTCGT 59.201 45.455 26.44 6.78 33.11 3.85
917 949 3.059982 CCGTGGGAGAAGACTGCA 58.940 61.111 0.00 0.00 36.18 4.41
1001 1033 1.656818 CGCGTTTCTGGCATGGGATT 61.657 55.000 0.00 0.00 0.00 3.01
1357 1389 3.352338 GAGCACCTCCGGGTACGTG 62.352 68.421 0.00 4.13 45.41 4.49
1360 1392 4.509737 GCGAGCACCTCCGGGTAC 62.510 72.222 0.00 0.00 45.41 3.34
1880 1917 2.170607 ACGAGTCCGAATGAATTGGGAT 59.829 45.455 9.62 0.86 44.65 3.85
1885 1922 3.313012 TGTCACGAGTCCGAATGAATT 57.687 42.857 0.00 0.00 39.50 2.17
1896 1933 9.665264 GAAAAATAAGAAAGAAATGTCACGAGT 57.335 29.630 0.00 0.00 0.00 4.18
2008 2057 4.660303 TGTTTCCTATCACAGAGGGCATAT 59.340 41.667 0.00 0.00 34.56 1.78
2009 2058 4.037222 TGTTTCCTATCACAGAGGGCATA 58.963 43.478 0.00 0.00 34.56 3.14
2010 2059 2.846206 TGTTTCCTATCACAGAGGGCAT 59.154 45.455 0.00 0.00 34.56 4.40
2011 2060 2.265367 TGTTTCCTATCACAGAGGGCA 58.735 47.619 0.00 0.00 34.56 5.36
2012 2061 3.350219 TTGTTTCCTATCACAGAGGGC 57.650 47.619 0.00 0.00 34.56 5.19
2013 2062 6.840780 AAAATTGTTTCCTATCACAGAGGG 57.159 37.500 0.00 0.00 34.56 4.30
2015 2064 7.039784 TCCCAAAAATTGTTTCCTATCACAGAG 60.040 37.037 0.00 0.00 0.00 3.35
2016 2065 6.780031 TCCCAAAAATTGTTTCCTATCACAGA 59.220 34.615 0.00 0.00 0.00 3.41
2017 2066 6.991938 TCCCAAAAATTGTTTCCTATCACAG 58.008 36.000 0.00 0.00 0.00 3.66
2019 2068 9.936759 TTTATCCCAAAAATTGTTTCCTATCAC 57.063 29.630 0.00 0.00 0.00 3.06
2037 2098 9.031537 GGAAAAACTAAGGATTCTTTTATCCCA 57.968 33.333 0.00 0.00 44.34 4.37
2047 2108 7.027778 ACGCATATGGAAAAACTAAGGATTC 57.972 36.000 4.56 0.00 0.00 2.52
2049 2110 7.226720 CAGTACGCATATGGAAAAACTAAGGAT 59.773 37.037 4.56 0.00 0.00 3.24
2055 2116 5.001232 ACACAGTACGCATATGGAAAAACT 58.999 37.500 4.56 0.00 0.00 2.66
2056 2117 5.291293 ACACAGTACGCATATGGAAAAAC 57.709 39.130 4.56 0.00 0.00 2.43
2057 2118 5.950758 AACACAGTACGCATATGGAAAAA 57.049 34.783 4.56 0.00 0.00 1.94
2068 2129 6.196571 AGTTTAACATTCAAACACAGTACGC 58.803 36.000 0.00 0.00 38.16 4.42
2205 2305 0.828677 ACGGGGTAGTAGCACCAATC 59.171 55.000 1.13 0.00 40.65 2.67
2209 2309 1.380920 AGGACGGGGTAGTAGCACC 60.381 63.158 1.13 0.00 37.91 5.01
2218 2318 3.617284 GACAAATAAATCAGGACGGGGT 58.383 45.455 0.00 0.00 0.00 4.95
2219 2319 2.949644 GGACAAATAAATCAGGACGGGG 59.050 50.000 0.00 0.00 0.00 5.73
2221 2321 5.897377 AAAGGACAAATAAATCAGGACGG 57.103 39.130 0.00 0.00 0.00 4.79
2223 2323 9.974980 TTACAAAAAGGACAAATAAATCAGGAC 57.025 29.630 0.00 0.00 0.00 3.85
2255 2355 8.162245 CGGTTAAATCTTTGCTCAAAATTTAGC 58.838 33.333 6.07 6.07 39.25 3.09
2256 2356 8.647226 CCGGTTAAATCTTTGCTCAAAATTTAG 58.353 33.333 0.00 0.00 32.22 1.85
2258 2358 6.073276 GCCGGTTAAATCTTTGCTCAAAATTT 60.073 34.615 1.90 14.01 32.01 1.82
2259 2359 5.408299 GCCGGTTAAATCTTTGCTCAAAATT 59.592 36.000 1.90 0.00 0.00 1.82
2260 2360 4.929211 GCCGGTTAAATCTTTGCTCAAAAT 59.071 37.500 1.90 0.00 0.00 1.82
2262 2362 3.319405 TGCCGGTTAAATCTTTGCTCAAA 59.681 39.130 1.90 0.00 0.00 2.69
2263 2363 2.887783 TGCCGGTTAAATCTTTGCTCAA 59.112 40.909 1.90 0.00 0.00 3.02
2264 2364 2.509569 TGCCGGTTAAATCTTTGCTCA 58.490 42.857 1.90 0.00 0.00 4.26
2265 2365 3.569250 TTGCCGGTTAAATCTTTGCTC 57.431 42.857 1.90 0.00 0.00 4.26
2267 2367 6.902224 ATATTTTGCCGGTTAAATCTTTGC 57.098 33.333 16.02 0.00 0.00 3.68
2268 2368 9.581099 AGTAATATTTTGCCGGTTAAATCTTTG 57.419 29.630 16.02 0.00 0.00 2.77
2270 2370 7.704899 GCAGTAATATTTTGCCGGTTAAATCTT 59.295 33.333 16.02 14.90 31.79 2.40
2271 2371 7.147983 TGCAGTAATATTTTGCCGGTTAAATCT 60.148 33.333 16.02 7.15 37.03 2.40
2272 2372 6.975772 TGCAGTAATATTTTGCCGGTTAAATC 59.024 34.615 16.02 5.78 37.03 2.17
2273 2373 6.868622 TGCAGTAATATTTTGCCGGTTAAAT 58.131 32.000 17.10 16.55 37.03 1.40
2274 2374 6.268825 TGCAGTAATATTTTGCCGGTTAAA 57.731 33.333 17.10 4.31 37.03 1.52
2275 2375 5.899120 TGCAGTAATATTTTGCCGGTTAA 57.101 34.783 17.10 0.00 37.03 2.01
2280 2694 4.919206 TGACATGCAGTAATATTTTGCCG 58.081 39.130 17.10 12.50 37.03 5.69
2281 2695 7.593875 TTTTGACATGCAGTAATATTTTGCC 57.406 32.000 17.10 6.82 37.03 4.52
2312 2726 9.336171 TGATGTTCAAATACGAATCCAATGATA 57.664 29.630 0.00 0.00 0.00 2.15
2314 2728 7.622893 TGATGTTCAAATACGAATCCAATGA 57.377 32.000 0.00 0.00 0.00 2.57
2316 2730 9.874205 AAAATGATGTTCAAATACGAATCCAAT 57.126 25.926 0.00 0.00 0.00 3.16
2317 2731 9.703892 AAAAATGATGTTCAAATACGAATCCAA 57.296 25.926 0.00 0.00 0.00 3.53
2393 3045 9.995003 TGCCAAATTTTGATCATAAGTTTAACT 57.005 25.926 10.72 0.00 0.00 2.24
2396 3048 9.421806 CTGTGCCAAATTTTGATCATAAGTTTA 57.578 29.630 10.72 0.00 0.00 2.01
2400 3052 8.712285 ATTCTGTGCCAAATTTTGATCATAAG 57.288 30.769 10.72 9.43 0.00 1.73
2408 3060 9.381033 TCCATATTTATTCTGTGCCAAATTTTG 57.619 29.630 1.99 1.99 0.00 2.44
2410 3062 7.986889 GGTCCATATTTATTCTGTGCCAAATTT 59.013 33.333 0.00 0.00 0.00 1.82
2411 3063 7.125507 TGGTCCATATTTATTCTGTGCCAAATT 59.874 33.333 0.00 0.00 0.00 1.82
2412 3064 6.610830 TGGTCCATATTTATTCTGTGCCAAAT 59.389 34.615 0.00 0.00 0.00 2.32
2414 3066 5.514169 TGGTCCATATTTATTCTGTGCCAA 58.486 37.500 0.00 0.00 0.00 4.52
2415 3067 5.122707 TGGTCCATATTTATTCTGTGCCA 57.877 39.130 0.00 0.00 0.00 4.92
2416 3068 4.022849 GCTGGTCCATATTTATTCTGTGCC 60.023 45.833 0.00 0.00 0.00 5.01
2418 3765 6.698008 TTGCTGGTCCATATTTATTCTGTG 57.302 37.500 0.00 0.00 0.00 3.66
2420 3767 6.096705 TGGTTTGCTGGTCCATATTTATTCTG 59.903 38.462 0.00 0.00 0.00 3.02
2425 3772 4.017958 TCCTGGTTTGCTGGTCCATATTTA 60.018 41.667 0.00 0.00 0.00 1.40
2429 3776 1.004277 GTCCTGGTTTGCTGGTCCATA 59.996 52.381 0.00 0.00 0.00 2.74
2434 3781 2.113139 CCGTCCTGGTTTGCTGGT 59.887 61.111 0.00 0.00 0.00 4.00
2436 3783 1.672356 CCTCCGTCCTGGTTTGCTG 60.672 63.158 0.00 0.00 39.52 4.41
2437 3784 0.834687 TACCTCCGTCCTGGTTTGCT 60.835 55.000 0.00 0.00 39.52 3.91
2438 3785 0.391263 CTACCTCCGTCCTGGTTTGC 60.391 60.000 0.00 0.00 39.52 3.68
2440 3787 2.610438 TACTACCTCCGTCCTGGTTT 57.390 50.000 0.00 0.00 39.52 3.27
2441 3788 2.244252 AGATACTACCTCCGTCCTGGTT 59.756 50.000 0.00 0.00 39.52 3.67
2443 3790 2.231529 CAGATACTACCTCCGTCCTGG 58.768 57.143 0.00 0.00 40.09 4.45
2444 3791 2.933573 ACAGATACTACCTCCGTCCTG 58.066 52.381 0.00 0.00 0.00 3.86
2474 4741 5.982356 TCATCAGGCAATATACAGATAGCC 58.018 41.667 0.00 0.00 42.31 3.93
2478 4987 7.177921 CCCAAATTCATCAGGCAATATACAGAT 59.822 37.037 0.00 0.00 0.00 2.90
2599 5167 2.419198 CTCCCGATCGAAGGCAGG 59.581 66.667 18.66 8.17 0.00 4.85
2619 5187 0.397816 TTCCCCAAACACACCCAAGG 60.398 55.000 0.00 0.00 0.00 3.61
2623 5191 1.138069 CAACTTTCCCCAAACACACCC 59.862 52.381 0.00 0.00 0.00 4.61
2624 5192 1.138069 CCAACTTTCCCCAAACACACC 59.862 52.381 0.00 0.00 0.00 4.16
2625 5193 1.828595 ACCAACTTTCCCCAAACACAC 59.171 47.619 0.00 0.00 0.00 3.82
2626 5194 2.239681 ACCAACTTTCCCCAAACACA 57.760 45.000 0.00 0.00 0.00 3.72
2627 5195 2.035449 GCTACCAACTTTCCCCAAACAC 59.965 50.000 0.00 0.00 0.00 3.32
2628 5196 2.312390 GCTACCAACTTTCCCCAAACA 58.688 47.619 0.00 0.00 0.00 2.83
2629 5197 2.296190 CTGCTACCAACTTTCCCCAAAC 59.704 50.000 0.00 0.00 0.00 2.93
2630 5198 2.593026 CTGCTACCAACTTTCCCCAAA 58.407 47.619 0.00 0.00 0.00 3.28
2631 5199 1.821666 GCTGCTACCAACTTTCCCCAA 60.822 52.381 0.00 0.00 0.00 4.12
2632 5200 0.251165 GCTGCTACCAACTTTCCCCA 60.251 55.000 0.00 0.00 0.00 4.96
2633 5201 0.965866 GGCTGCTACCAACTTTCCCC 60.966 60.000 0.00 0.00 0.00 4.81
2634 5202 1.305930 CGGCTGCTACCAACTTTCCC 61.306 60.000 0.00 0.00 0.00 3.97
2635 5203 1.305930 CCGGCTGCTACCAACTTTCC 61.306 60.000 0.00 0.00 0.00 3.13
2636 5204 0.605589 ACCGGCTGCTACCAACTTTC 60.606 55.000 0.00 0.00 0.00 2.62
2637 5205 0.179001 AACCGGCTGCTACCAACTTT 60.179 50.000 0.00 0.00 0.00 2.66
2638 5206 0.605589 GAACCGGCTGCTACCAACTT 60.606 55.000 0.00 0.00 0.00 2.66
2639 5207 1.003718 GAACCGGCTGCTACCAACT 60.004 57.895 0.00 0.00 0.00 3.16
2640 5208 1.003718 AGAACCGGCTGCTACCAAC 60.004 57.895 0.00 0.00 0.00 3.77
2641 5209 1.003839 CAGAACCGGCTGCTACCAA 60.004 57.895 0.00 0.00 0.00 3.67
2642 5210 1.764571 AACAGAACCGGCTGCTACCA 61.765 55.000 0.00 0.00 39.51 3.25
2643 5211 1.003718 AACAGAACCGGCTGCTACC 60.004 57.895 0.00 0.00 39.51 3.18
2644 5212 1.352156 CGAACAGAACCGGCTGCTAC 61.352 60.000 0.00 0.00 39.51 3.58
2645 5213 1.080093 CGAACAGAACCGGCTGCTA 60.080 57.895 0.00 0.00 39.51 3.49
2646 5214 2.357517 CGAACAGAACCGGCTGCT 60.358 61.111 0.00 0.00 39.51 4.24
2647 5215 4.090057 GCGAACAGAACCGGCTGC 62.090 66.667 0.00 0.00 39.51 5.25
2648 5216 3.423154 GGCGAACAGAACCGGCTG 61.423 66.667 0.00 4.06 45.94 4.85
2651 5219 1.079127 ATCAGGCGAACAGAACCGG 60.079 57.895 0.00 0.00 0.00 5.28
2652 5220 1.413767 CGATCAGGCGAACAGAACCG 61.414 60.000 0.00 0.00 0.00 4.44
2653 5221 0.108804 TCGATCAGGCGAACAGAACC 60.109 55.000 0.00 0.00 37.35 3.62
2654 5222 1.710013 TTCGATCAGGCGAACAGAAC 58.290 50.000 0.00 0.00 44.43 3.01
2671 5239 1.072159 CAGGGGCCATCGAGGATTC 59.928 63.158 4.39 0.00 41.22 2.52
2672 5240 3.125376 GCAGGGGCCATCGAGGATT 62.125 63.158 4.39 0.00 41.22 3.01
2673 5241 3.564218 GCAGGGGCCATCGAGGAT 61.564 66.667 4.39 0.00 41.22 3.24
2683 5251 2.830370 CCGATCAAAGGCAGGGGC 60.830 66.667 0.00 0.00 40.13 5.80
2684 5252 2.124151 CCCGATCAAAGGCAGGGG 60.124 66.667 0.00 0.00 38.44 4.79
2685 5253 1.153086 CTCCCGATCAAAGGCAGGG 60.153 63.158 0.00 0.00 43.32 4.45
2686 5254 1.821332 GCTCCCGATCAAAGGCAGG 60.821 63.158 0.00 0.00 0.00 4.85
2687 5255 2.176273 CGCTCCCGATCAAAGGCAG 61.176 63.158 0.00 0.00 36.29 4.85
2688 5256 2.125147 CGCTCCCGATCAAAGGCA 60.125 61.111 0.00 0.00 36.29 4.75
2689 5257 3.577313 GCGCTCCCGATCAAAGGC 61.577 66.667 0.00 0.00 36.29 4.35
2690 5258 2.897350 GGCGCTCCCGATCAAAGG 60.897 66.667 7.64 0.00 36.29 3.11
2691 5259 2.897350 GGGCGCTCCCGATCAAAG 60.897 66.667 7.64 0.00 43.94 2.77
2701 5269 4.643387 AACACACCCAGGGCGCTC 62.643 66.667 4.91 1.48 0.00 5.03
2702 5270 4.204028 AAACACACCCAGGGCGCT 62.204 61.111 4.91 0.00 0.00 5.92
2703 5271 3.977244 CAAACACACCCAGGGCGC 61.977 66.667 4.91 0.00 0.00 6.53
2704 5272 3.294493 CCAAACACACCCAGGGCG 61.294 66.667 4.91 0.00 0.00 6.13
2705 5273 1.744320 GAACCAAACACACCCAGGGC 61.744 60.000 4.91 0.00 0.00 5.19
2706 5274 1.112916 GGAACCAAACACACCCAGGG 61.113 60.000 2.85 2.85 0.00 4.45
2707 5275 0.396417 TGGAACCAAACACACCCAGG 60.396 55.000 0.00 0.00 0.00 4.45
2708 5276 1.032014 CTGGAACCAAACACACCCAG 58.968 55.000 0.00 0.00 35.75 4.45
2709 5277 0.396417 CCTGGAACCAAACACACCCA 60.396 55.000 0.00 0.00 0.00 4.51
2710 5278 0.106419 TCCTGGAACCAAACACACCC 60.106 55.000 0.00 0.00 0.00 4.61
2724 5292 4.627058 GTTACATTTTGGTTGGTTCCTGG 58.373 43.478 0.00 0.00 0.00 4.45
2753 5321 0.893727 ATGTGGCCAAAGAACGGGTC 60.894 55.000 7.24 0.00 0.00 4.46
2761 5329 4.414852 CAAACGATAGAATGTGGCCAAAG 58.585 43.478 7.24 0.00 41.38 2.77
2762 5330 3.192422 CCAAACGATAGAATGTGGCCAAA 59.808 43.478 7.24 0.15 41.38 3.28
2764 5332 2.290641 ACCAAACGATAGAATGTGGCCA 60.291 45.455 0.00 0.00 41.38 5.36
2770 5338 5.131168 CTGTCGAACCAAACGATAGAATG 57.869 43.478 0.00 0.00 46.36 2.67
2788 5356 3.128415 GGTAGGAACGAGTAGGTTCTGTC 59.872 52.174 5.54 0.00 44.45 3.51
2791 5359 2.042162 TGGGTAGGAACGAGTAGGTTCT 59.958 50.000 5.54 0.00 44.45 3.01
2807 5375 4.473196 TCTCAGTGGAATATTTGCTGGGTA 59.527 41.667 11.76 1.59 0.00 3.69
2813 5381 4.517285 TCAGGTCTCAGTGGAATATTTGC 58.483 43.478 0.00 0.00 0.00 3.68
2815 5383 5.946377 GGTTTCAGGTCTCAGTGGAATATTT 59.054 40.000 0.00 0.00 0.00 1.40
2822 5390 0.679505 TCGGTTTCAGGTCTCAGTGG 59.320 55.000 0.00 0.00 0.00 4.00
2838 5406 0.108138 AATTTGGAGAGACCGCTCGG 60.108 55.000 6.79 6.79 45.98 4.63
2843 5411 1.002366 CGCTCAATTTGGAGAGACCG 58.998 55.000 0.00 0.00 42.61 4.79
2851 5419 0.667184 GTGTTGCCCGCTCAATTTGG 60.667 55.000 0.00 0.00 0.00 3.28
2864 5432 3.351416 GGGACGGTTCCGTGTTGC 61.351 66.667 21.61 6.92 43.94 4.17
2869 5437 3.692406 GCTGAGGGACGGTTCCGT 61.692 66.667 16.91 16.91 43.94 4.69
2875 5443 4.803426 GCGAGTGCTGAGGGACGG 62.803 72.222 0.00 0.00 38.85 4.79
2885 5453 2.757917 AGAGAGAGGGGCGAGTGC 60.758 66.667 0.00 0.00 41.71 4.40
2891 5459 0.616111 TTCCTGTGAGAGAGAGGGGC 60.616 60.000 0.00 0.00 35.68 5.80
2892 5460 1.484038 CTTCCTGTGAGAGAGAGGGG 58.516 60.000 0.00 0.00 35.68 4.79
2894 5462 0.823460 GGCTTCCTGTGAGAGAGAGG 59.177 60.000 0.00 0.00 36.36 3.69
2907 5475 2.791868 GCGAGAGAGAGGGGCTTCC 61.792 68.421 0.00 0.00 0.00 3.46
2908 5476 2.055042 TGCGAGAGAGAGGGGCTTC 61.055 63.158 0.00 0.00 0.00 3.86
2909 5477 2.038007 TGCGAGAGAGAGGGGCTT 59.962 61.111 0.00 0.00 0.00 4.35
2910 5478 2.757917 GTGCGAGAGAGAGGGGCT 60.758 66.667 0.00 0.00 0.00 5.19
2911 5479 2.570582 CTTGTGCGAGAGAGAGGGGC 62.571 65.000 0.00 0.00 0.00 5.80
2912 5480 1.515020 CTTGTGCGAGAGAGAGGGG 59.485 63.158 0.00 0.00 0.00 4.79
2914 5482 1.153667 GCCTTGTGCGAGAGAGAGG 60.154 63.158 0.00 0.00 0.00 3.69
2945 5553 2.159653 GGAAACTGAGCGTTGCATACTG 60.160 50.000 0.00 0.00 35.61 2.74
2946 5554 2.076863 GGAAACTGAGCGTTGCATACT 58.923 47.619 0.00 0.00 35.61 2.12
2947 5555 1.201921 CGGAAACTGAGCGTTGCATAC 60.202 52.381 0.00 0.00 35.61 2.39
2948 5556 1.075542 CGGAAACTGAGCGTTGCATA 58.924 50.000 0.00 0.00 35.61 3.14
2949 5557 0.884704 ACGGAAACTGAGCGTTGCAT 60.885 50.000 0.00 0.00 35.61 3.96
2950 5558 1.495584 GACGGAAACTGAGCGTTGCA 61.496 55.000 0.00 0.00 35.61 4.08
2951 5559 1.204312 GACGGAAACTGAGCGTTGC 59.796 57.895 0.00 0.00 35.61 4.17
2952 5560 1.566018 GGGACGGAAACTGAGCGTTG 61.566 60.000 0.00 0.00 35.61 4.10
2953 5561 1.301479 GGGACGGAAACTGAGCGTT 60.301 57.895 0.00 0.00 37.47 4.84
2954 5562 2.342648 GGGACGGAAACTGAGCGT 59.657 61.111 0.00 0.00 0.00 5.07


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

AutoCloner maintained by Alex Coulton.