Multiple sequence alignment - TraesCS5B01G157200

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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 TraesCS5B01G157200 chr5B 100.000 7174 0 0 1 7174 289702547 289709720 0.000000e+00 13248.0
1 TraesCS5B01G157200 chr5B 92.795 694 44 6 6485 7174 29704291 29703600 0.000000e+00 1000.0
2 TraesCS5B01G157200 chr5A 95.424 4502 144 25 2005 6492 340131890 340136343 0.000000e+00 7116.0
3 TraesCS5B01G157200 chr5A 90.855 1520 119 14 505 2017 340130204 340131710 0.000000e+00 2019.0
4 TraesCS5B01G157200 chr5A 92.651 694 47 4 6484 7174 664309454 664308762 0.000000e+00 996.0
5 TraesCS5B01G157200 chr5A 83.286 353 46 7 4744 5085 104613348 104613698 5.400000e-81 313.0
6 TraesCS5B01G157200 chr5A 80.889 225 34 5 3496 3719 659866463 659866679 1.240000e-37 169.0
7 TraesCS5B01G157200 chr5A 79.268 164 27 5 3548 3705 350805823 350805661 2.740000e-19 108.0
8 TraesCS5B01G157200 chr5A 93.750 64 1 1 1843 1903 340131598 340131661 7.660000e-15 93.5
9 TraesCS5B01G157200 chr5D 95.684 1784 60 6 1903 3682 255943642 255945412 0.000000e+00 2852.0
10 TraesCS5B01G157200 chr5D 95.065 993 31 6 4682 5673 255946728 255947703 0.000000e+00 1546.0
11 TraesCS5B01G157200 chr5D 91.449 842 52 12 5658 6492 255947722 255948550 0.000000e+00 1138.0
12 TraesCS5B01G157200 chr5D 96.482 597 18 3 3720 4313 255945614 255946210 0.000000e+00 983.0
13 TraesCS5B01G157200 chr5D 93.427 639 34 5 1272 1905 255943073 255943708 0.000000e+00 941.0
14 TraesCS5B01G157200 chr5D 97.897 428 7 1 4258 4683 255946210 255946637 0.000000e+00 739.0
15 TraesCS5B01G157200 chr5D 84.511 665 57 19 628 1272 255942395 255943033 3.680000e-172 616.0
16 TraesCS5B01G157200 chr5D 83.186 339 44 5 54 392 255942061 255942386 1.510000e-76 298.0
17 TraesCS5B01G157200 chr1D 88.003 1192 89 28 5226 6404 8731432 8732582 0.000000e+00 1360.0
18 TraesCS5B01G157200 chr1D 92.683 697 45 6 6482 7174 56516139 56516833 0.000000e+00 1000.0
19 TraesCS5B01G157200 chr1D 92.179 537 35 4 4207 4736 8730909 8731445 0.000000e+00 752.0
20 TraesCS5B01G157200 chr1D 85.093 161 15 7 3493 3646 267794484 267794642 9.640000e-34 156.0
21 TraesCS5B01G157200 chr6B 93.768 690 40 3 6487 7174 200326024 200326712 0.000000e+00 1033.0
22 TraesCS5B01G157200 chr6B 93.074 693 45 3 6483 7174 715855372 715856062 0.000000e+00 1011.0
23 TraesCS5B01G157200 chr6B 80.100 201 28 6 3496 3690 387116139 387116333 9.700000e-29 139.0
24 TraesCS5B01G157200 chr4A 93.497 692 41 4 6485 7174 629922549 629921860 0.000000e+00 1026.0
25 TraesCS5B01G157200 chr3B 92.806 695 44 5 6484 7174 172209711 172209019 0.000000e+00 1002.0
26 TraesCS5B01G157200 chr4B 92.775 692 46 4 6485 7174 668413389 668412700 0.000000e+00 998.0
27 TraesCS5B01G157200 chr6A 92.775 692 45 5 6485 7174 613602669 613601981 0.000000e+00 996.0
28 TraesCS5B01G157200 chr6A 88.235 238 24 4 4738 4971 616204290 616204527 1.520000e-71 281.0
29 TraesCS5B01G157200 chr6A 86.667 105 14 0 3487 3591 571847692 571847796 4.550000e-22 117.0
30 TraesCS5B01G157200 chr1B 85.714 161 14 7 3496 3649 345320607 345320449 2.070000e-35 161.0
31 TraesCS5B01G157200 chr1A 85.625 160 15 5 3496 3649 335028702 335028545 2.070000e-35 161.0
32 TraesCS5B01G157200 chr2A 82.558 172 21 8 3496 3660 450883936 450884105 7.500000e-30 143.0
33 TraesCS5B01G157200 chr2B 77.551 147 22 9 3565 3704 422982347 422982489 2.150000e-10 78.7
34 TraesCS5B01G157200 chr7A 94.595 37 2 0 88 124 42689234 42689198 2.800000e-04 58.4


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 TraesCS5B01G157200 chr5B 289702547 289709720 7173 False 13248.000000 13248 100.000000 1 7174 1 chr5B.!!$F1 7173
1 TraesCS5B01G157200 chr5B 29703600 29704291 691 True 1000.000000 1000 92.795000 6485 7174 1 chr5B.!!$R1 689
2 TraesCS5B01G157200 chr5A 340130204 340136343 6139 False 3076.166667 7116 93.343000 505 6492 3 chr5A.!!$F3 5987
3 TraesCS5B01G157200 chr5A 664308762 664309454 692 True 996.000000 996 92.651000 6484 7174 1 chr5A.!!$R2 690
4 TraesCS5B01G157200 chr5D 255942061 255948550 6489 False 1139.125000 2852 92.212625 54 6492 8 chr5D.!!$F1 6438
5 TraesCS5B01G157200 chr1D 8730909 8732582 1673 False 1056.000000 1360 90.091000 4207 6404 2 chr1D.!!$F3 2197
6 TraesCS5B01G157200 chr1D 56516139 56516833 694 False 1000.000000 1000 92.683000 6482 7174 1 chr1D.!!$F1 692
7 TraesCS5B01G157200 chr6B 200326024 200326712 688 False 1033.000000 1033 93.768000 6487 7174 1 chr6B.!!$F1 687
8 TraesCS5B01G157200 chr6B 715855372 715856062 690 False 1011.000000 1011 93.074000 6483 7174 1 chr6B.!!$F3 691
9 TraesCS5B01G157200 chr4A 629921860 629922549 689 True 1026.000000 1026 93.497000 6485 7174 1 chr4A.!!$R1 689
10 TraesCS5B01G157200 chr3B 172209019 172209711 692 True 1002.000000 1002 92.806000 6484 7174 1 chr3B.!!$R1 690
11 TraesCS5B01G157200 chr4B 668412700 668413389 689 True 998.000000 998 92.775000 6485 7174 1 chr4B.!!$R1 689
12 TraesCS5B01G157200 chr6A 613601981 613602669 688 True 996.000000 996 92.775000 6485 7174 1 chr6A.!!$R1 689

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
241 242 0.247814 GCCAACTTGTCATCATCGCG 60.248 55.000 0.00 0.0 0.00 5.87 F
973 1004 0.250338 AAAGCTCACCCGAGACAACC 60.250 55.000 0.00 0.0 42.34 3.77 F
1082 1113 0.605589 CAACGACTCAGCCTTCCTCT 59.394 55.000 0.00 0.0 0.00 3.69 F
1086 1117 1.479709 GACTCAGCCTTCCTCTAGCA 58.520 55.000 0.00 0.0 0.00 3.49 F
1792 1864 2.434336 ACAGACCACACTTCTACAAGCA 59.566 45.455 0.00 0.0 32.09 3.91 F
1793 1865 2.802816 CAGACCACACTTCTACAAGCAC 59.197 50.000 0.00 0.0 32.09 4.40 F
3533 3804 1.272147 GCCCAACCTTCTCCATCACTT 60.272 52.381 0.00 0.0 0.00 3.16 F
3624 3895 2.154462 AGTCTCGGTTTTCAGCATTGG 58.846 47.619 0.00 0.0 0.00 3.16 F
4958 5552 0.738412 GCTCAAATGCTTTGCGCCAT 60.738 50.000 4.18 0.0 43.54 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1086 1117 2.357517 CTCTTTGCCGCCGTCAGT 60.358 61.111 0.00 0.00 0.00 3.41 R
1793 1865 3.873361 CCACATCTATACACACTTGGCAG 59.127 47.826 0.00 0.00 0.00 4.85 R
2190 2458 5.340403 CAGAAAACTACAATGCACATGAACG 59.660 40.000 0.00 0.00 0.00 3.95 R
2686 2954 6.543430 TTAAATGACCAGCCAAAGCATTAT 57.457 33.333 0.00 0.00 43.56 1.28 R
3403 3674 0.458669 ACGTGGTGGAAGTATAGGCG 59.541 55.000 0.00 0.00 0.00 5.52 R
3591 3862 2.059541 CCGAGACTTGAAACGAAGACC 58.940 52.381 0.00 0.00 0.00 3.85 R
4627 5123 0.809241 CTTCGTGCTCATCTCCTGGC 60.809 60.000 0.00 0.00 0.00 4.85 R
5090 5684 1.343821 CAAGCAATACGACGCGACC 59.656 57.895 15.93 2.61 0.00 4.79 R
6516 7167 0.250234 TGATTGCTTGGTCCTCGGAG 59.750 55.000 0.00 0.00 0.00 4.63 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
25 26 3.830192 GGCTGCCCGGCAAAGATG 61.830 66.667 14.45 2.10 38.41 2.90
49 50 3.102097 GCCATGCACGAAGGCTAC 58.898 61.111 12.53 0.00 44.92 3.58
50 51 2.813179 GCCATGCACGAAGGCTACG 61.813 63.158 12.53 0.00 44.92 3.51
51 52 1.447838 CCATGCACGAAGGCTACGT 60.448 57.895 0.00 0.00 44.83 3.57
84 85 3.727258 CGGAGGGGGCATTGACCA 61.727 66.667 11.55 0.00 27.52 4.02
85 86 2.276740 GGAGGGGGCATTGACCAG 59.723 66.667 11.55 0.00 27.52 4.00
86 87 2.440980 GAGGGGGCATTGACCAGC 60.441 66.667 11.55 0.00 27.52 4.85
101 102 1.731433 CCAGCGCCCCATCAGATTTG 61.731 60.000 2.29 0.00 0.00 2.32
109 110 2.622452 CCCCATCAGATTTGGCAACTCT 60.622 50.000 13.70 13.70 32.60 3.24
117 118 4.815308 CAGATTTGGCAACTCTAGATCTGG 59.185 45.833 21.45 1.65 36.82 3.86
126 127 1.219213 CTCTAGATCTGGACAGGGGGT 59.781 57.143 4.39 0.00 0.00 4.95
127 128 1.651770 TCTAGATCTGGACAGGGGGTT 59.348 52.381 4.39 0.00 0.00 4.11
174 175 2.892425 CCAGCCATCGTCGCCTTC 60.892 66.667 0.00 0.00 0.00 3.46
175 176 3.257561 CAGCCATCGTCGCCTTCG 61.258 66.667 0.00 0.00 0.00 3.79
188 189 1.528824 CCTTCGGCACCCTCATGAT 59.471 57.895 0.00 0.00 0.00 2.45
194 195 1.450134 GCACCCTCATGATGCGTCA 60.450 57.895 11.83 11.83 39.04 4.35
216 217 3.857038 ACCAACGCCACCAGTCGT 61.857 61.111 0.00 0.00 41.06 4.34
217 218 3.345808 CCAACGCCACCAGTCGTG 61.346 66.667 0.00 0.00 42.62 4.35
234 235 2.676471 GGGCCGCCAACTTGTCAT 60.676 61.111 12.58 0.00 0.00 3.06
241 242 0.247814 GCCAACTTGTCATCATCGCG 60.248 55.000 0.00 0.00 0.00 5.87
243 244 1.325640 CCAACTTGTCATCATCGCGAG 59.674 52.381 16.66 7.11 0.00 5.03
246 247 1.410517 ACTTGTCATCATCGCGAGGAT 59.589 47.619 28.84 28.84 36.69 3.24
247 248 2.057316 CTTGTCATCATCGCGAGGATC 58.943 52.381 31.25 21.71 36.69 3.36
258 259 4.131376 GAGGATCGCACACCCATG 57.869 61.111 0.00 0.00 0.00 3.66
261 262 2.589540 GATCGCACACCCATGGGA 59.410 61.111 38.07 14.50 44.62 4.37
262 263 1.524621 GATCGCACACCCATGGGAG 60.525 63.158 38.07 31.32 43.86 4.30
263 264 1.971505 GATCGCACACCCATGGGAGA 61.972 60.000 38.07 24.60 42.74 3.71
268 269 0.750546 CACACCCATGGGAGAGCATG 60.751 60.000 38.07 24.80 38.96 4.06
276 277 2.439156 GGAGAGCATGCACCACCC 60.439 66.667 21.98 11.37 0.00 4.61
332 333 2.361610 AGCCAAGACGCCATTGGG 60.362 61.111 13.80 0.00 46.09 4.12
351 352 1.144057 CGGGAGCCACTACCATCAC 59.856 63.158 0.00 0.00 33.03 3.06
353 354 1.521681 GGAGCCACTACCATCACGC 60.522 63.158 0.00 0.00 0.00 5.34
354 355 1.521681 GAGCCACTACCATCACGCC 60.522 63.158 0.00 0.00 0.00 5.68
360 361 2.435234 TACCATCACGCCGCCAAC 60.435 61.111 0.00 0.00 0.00 3.77
377 378 4.924187 CCCCCACCGGCCAACAAA 62.924 66.667 0.00 0.00 0.00 2.83
392 393 3.560025 CCAACAAACCATGTAGAGAGGCT 60.560 47.826 0.00 0.00 42.99 4.58
393 394 3.340814 ACAAACCATGTAGAGAGGCTG 57.659 47.619 0.00 0.00 41.63 4.85
395 396 0.543749 AACCATGTAGAGAGGCTGCC 59.456 55.000 11.65 11.65 0.00 4.85
397 398 1.068753 CATGTAGAGAGGCTGCCCG 59.931 63.158 16.57 0.00 35.76 6.13
398 399 2.801631 ATGTAGAGAGGCTGCCCGC 61.802 63.158 16.57 8.14 35.76 6.13
415 416 4.796231 CGTCCCAAGTCGCCCTCG 62.796 72.222 0.00 0.00 0.00 4.63
416 417 4.452733 GTCCCAAGTCGCCCTCGG 62.453 72.222 0.00 0.00 36.13 4.63
443 444 4.340246 CTGGTGGGCAGAGCAGCA 62.340 66.667 0.00 0.00 34.85 4.41
444 445 4.340246 TGGTGGGCAGAGCAGCAG 62.340 66.667 0.00 0.00 35.83 4.24
502 503 3.722295 CCAACACGTCGCGCCATT 61.722 61.111 0.00 0.00 0.00 3.16
503 504 2.384309 CCAACACGTCGCGCCATTA 61.384 57.895 0.00 0.00 0.00 1.90
507 508 1.651132 CACGTCGCGCCATTAATGC 60.651 57.895 10.11 5.03 0.00 3.56
514 515 4.996113 GCCATTAATGCGACCACG 57.004 55.556 10.11 0.00 42.93 4.94
524 525 3.118454 CGACCACGCCATGACCAC 61.118 66.667 0.00 0.00 0.00 4.16
532 533 4.101790 CCATGACCACGCAACCGC 62.102 66.667 0.00 0.00 38.22 5.68
581 583 0.460987 GAAGCACCCTGATCCAGACG 60.461 60.000 0.00 0.00 32.44 4.18
583 585 2.202797 CACCCTGATCCAGACGCG 60.203 66.667 3.53 3.53 32.44 6.01
588 590 3.052620 CTGATCCAGACGCGTCGGT 62.053 63.158 33.21 25.20 32.44 4.69
653 655 4.933064 CGGCTAGGCTTCGCTCGG 62.933 72.222 15.11 0.00 0.00 4.63
700 702 4.442454 GGAGGGGGCGGAAAAGGG 62.442 72.222 0.00 0.00 0.00 3.95
707 709 2.034221 GCGGAAAAGGGAGCTGGT 59.966 61.111 0.00 0.00 0.00 4.00
708 710 2.335712 GCGGAAAAGGGAGCTGGTG 61.336 63.158 0.00 0.00 0.00 4.17
739 741 2.266055 GTTCCTCCCTGTCGCCTG 59.734 66.667 0.00 0.00 0.00 4.85
800 802 7.527084 AACAATTCTCGCTCTTGAGTAATAC 57.473 36.000 0.00 0.00 37.28 1.89
807 816 3.632604 CGCTCTTGAGTAATACTCCCTCA 59.367 47.826 16.89 0.00 44.44 3.86
813 822 8.840200 TCTTGAGTAATACTCCCTCAGTAAAT 57.160 34.615 16.89 0.00 44.44 1.40
814 823 9.931698 TCTTGAGTAATACTCCCTCAGTAAATA 57.068 33.333 16.89 0.00 44.44 1.40
817 826 8.639761 TGAGTAATACTCCCTCAGTAAATAAGC 58.360 37.037 16.89 0.00 44.44 3.09
818 827 8.548880 AGTAATACTCCCTCAGTAAATAAGCA 57.451 34.615 0.00 0.00 41.17 3.91
819 828 8.989131 AGTAATACTCCCTCAGTAAATAAGCAA 58.011 33.333 0.00 0.00 41.17 3.91
820 829 9.609346 GTAATACTCCCTCAGTAAATAAGCAAA 57.391 33.333 0.00 0.00 41.17 3.68
865 888 8.956426 AGACATGAAAGACTTGTAACAAAAGAA 58.044 29.630 0.00 0.00 37.08 2.52
866 889 9.226345 GACATGAAAGACTTGTAACAAAAGAAG 57.774 33.333 0.00 0.00 37.08 2.85
940 963 1.978580 TCCCTCTCCCTTCTCACAAAC 59.021 52.381 0.00 0.00 0.00 2.93
941 964 1.699634 CCCTCTCCCTTCTCACAAACA 59.300 52.381 0.00 0.00 0.00 2.83
942 965 2.106511 CCCTCTCCCTTCTCACAAACAA 59.893 50.000 0.00 0.00 0.00 2.83
944 967 4.401925 CCTCTCCCTTCTCACAAACAAAT 58.598 43.478 0.00 0.00 0.00 2.32
947 978 6.490040 CCTCTCCCTTCTCACAAACAAATTTA 59.510 38.462 0.00 0.00 0.00 1.40
962 993 8.542953 CAAACAAATTTAGGAAGAAAAGCTCAC 58.457 33.333 0.00 0.00 0.00 3.51
964 995 5.984695 AATTTAGGAAGAAAAGCTCACCC 57.015 39.130 0.00 0.00 0.00 4.61
970 1001 1.048601 AGAAAAGCTCACCCGAGACA 58.951 50.000 0.00 0.00 42.34 3.41
973 1004 0.250338 AAAGCTCACCCGAGACAACC 60.250 55.000 0.00 0.00 42.34 3.77
990 1021 0.748729 ACCGGGAGTAGAGAGCTTCG 60.749 60.000 6.32 0.00 0.00 3.79
1082 1113 0.605589 CAACGACTCAGCCTTCCTCT 59.394 55.000 0.00 0.00 0.00 3.69
1086 1117 1.479709 GACTCAGCCTTCCTCTAGCA 58.520 55.000 0.00 0.00 0.00 3.49
1127 1158 2.856032 CGTCTTGGAGCAGCAACG 59.144 61.111 0.00 0.00 0.00 4.10
1410 1481 8.096621 TGATGTTATTTTCAGTAGGGGACATA 57.903 34.615 0.00 0.00 0.00 2.29
1497 1569 6.064846 AGTTTCAAGTGTAATTCTGCAGTG 57.935 37.500 14.67 0.89 0.00 3.66
1551 1623 2.945984 CGCGCATCCACTTTGTGT 59.054 55.556 8.75 0.00 0.00 3.72
1563 1635 4.111916 CCACTTTGTGTACCTTGCAAAAG 58.888 43.478 0.00 0.95 32.64 2.27
1573 1645 7.147983 TGTGTACCTTGCAAAAGTGTTTCTTAT 60.148 33.333 11.14 0.00 35.02 1.73
1604 1676 3.529341 TACTGCAGGGTGTGTGGCG 62.529 63.158 19.93 0.00 0.00 5.69
1617 1689 4.445832 TGGCGAGCCCAACTACTA 57.554 55.556 12.05 0.00 41.82 1.82
1627 1699 3.768215 AGCCCAACTACTACTAAGGTGAC 59.232 47.826 0.00 0.00 33.25 3.67
1740 1812 5.825507 CAGAAACAAAGGACTGGAGAAAAG 58.174 41.667 0.00 0.00 0.00 2.27
1792 1864 2.434336 ACAGACCACACTTCTACAAGCA 59.566 45.455 0.00 0.00 32.09 3.91
1793 1865 2.802816 CAGACCACACTTCTACAAGCAC 59.197 50.000 0.00 0.00 32.09 4.40
1888 1963 9.220767 AGTAAAGAAGGTATGCTCTTTTAACAG 57.779 33.333 3.91 0.00 41.15 3.16
1943 2018 7.444487 AGAAAAGTAAAGACGGTATGCTCTTTT 59.556 33.333 3.91 9.83 37.75 2.27
2075 2343 9.434420 CATCCTTGCCAATTTAATTCTGTTTTA 57.566 29.630 0.00 0.00 0.00 1.52
2190 2458 3.247173 CGCCATAGTCAATCAAGAGAAGC 59.753 47.826 0.00 0.00 0.00 3.86
2240 2508 7.728847 ACCCTCTTGTTTGCAATTAATTTTC 57.271 32.000 0.00 0.00 33.65 2.29
2639 2907 5.988310 ATGAAAAAGAACCTGATGATGCA 57.012 34.783 0.00 0.00 0.00 3.96
2640 2908 5.988310 TGAAAAAGAACCTGATGATGCAT 57.012 34.783 0.00 0.00 0.00 3.96
2641 2909 6.349243 TGAAAAAGAACCTGATGATGCATT 57.651 33.333 0.00 0.00 0.00 3.56
2642 2910 6.761312 TGAAAAAGAACCTGATGATGCATTT 58.239 32.000 0.00 0.00 0.00 2.32
2643 2911 7.894708 TGAAAAAGAACCTGATGATGCATTTA 58.105 30.769 0.00 0.00 0.00 1.40
2644 2912 8.533657 TGAAAAAGAACCTGATGATGCATTTAT 58.466 29.630 0.00 0.00 0.00 1.40
2645 2913 9.374838 GAAAAAGAACCTGATGATGCATTTATT 57.625 29.630 0.00 0.00 0.00 1.40
2646 2914 9.729281 AAAAAGAACCTGATGATGCATTTATTT 57.271 25.926 0.00 0.00 0.00 1.40
2757 3025 9.794685 ATCGAGAATATGTGTCATGTATATCAC 57.205 33.333 0.00 0.00 0.00 3.06
3142 3413 7.039313 GAACAAGGTTGGTCTAAGTGAAAAT 57.961 36.000 0.24 0.00 41.62 1.82
3210 3481 9.605275 CATGCTACATATATATACTTGCCAACT 57.395 33.333 0.00 0.00 0.00 3.16
3289 3560 3.776417 TCCCACTATTTACCACCCTACAC 59.224 47.826 0.00 0.00 0.00 2.90
3293 3564 5.365619 CACTATTTACCACCCTACACCATC 58.634 45.833 0.00 0.00 0.00 3.51
3334 3605 9.014297 AGCTTGTTATTTATGCTTGAAAGTAGT 57.986 29.630 0.00 0.00 0.00 2.73
3533 3804 1.272147 GCCCAACCTTCTCCATCACTT 60.272 52.381 0.00 0.00 0.00 3.16
3556 3827 7.713942 ACTTTAGACTTTTGGTACTACTGGTTG 59.286 37.037 0.00 0.00 0.00 3.77
3624 3895 2.154462 AGTCTCGGTTTTCAGCATTGG 58.846 47.619 0.00 0.00 0.00 3.16
3665 3937 4.354893 TTCTTCCACGTTTAGGCCTTAA 57.645 40.909 12.58 4.88 0.00 1.85
3717 3989 5.310409 AGTATATGTGCATTGCCTAACCT 57.690 39.130 6.12 0.00 0.00 3.50
3786 4222 3.601443 AACACTGAGAGACATGTAGCC 57.399 47.619 0.00 0.00 0.00 3.93
3865 4301 6.612306 AGCTCGAGGAATTTTGACAATAAAC 58.388 36.000 15.58 0.00 0.00 2.01
4012 4448 6.057321 TCAGTATTTGGGAATAAAGGACGT 57.943 37.500 0.00 0.00 29.89 4.34
4067 4503 4.379243 ACGGCAGGGACGAAGCTG 62.379 66.667 0.00 0.00 35.20 4.24
4168 4607 4.965119 AGTATTTCAAAATCCGCTGGTC 57.035 40.909 0.00 0.00 0.00 4.02
4212 4651 3.708220 GAGCTTCGTCCCTGGCTCG 62.708 68.421 0.00 0.00 41.03 5.03
4289 4728 8.766000 TTTGTATTAGTCGCATTCTACTTTCA 57.234 30.769 0.00 0.00 0.00 2.69
4458 4954 3.054878 GCCAAAACTTGCAGAGAATGTG 58.945 45.455 3.37 0.00 0.00 3.21
4627 5123 1.131037 CTCTCGCGTCTGCTTTCTCG 61.131 60.000 5.77 0.00 39.65 4.04
4733 5325 2.098607 CGATTCATTGGCTGCAACATCT 59.901 45.455 0.50 0.00 0.00 2.90
4874 5467 6.609212 AGAGAAATTCATAGAGAGCCTGTACA 59.391 38.462 0.00 0.00 0.00 2.90
4958 5552 0.738412 GCTCAAATGCTTTGCGCCAT 60.738 50.000 4.18 0.00 43.54 4.40
5013 5607 0.895530 GACAGAATGGTCGGGTCTCA 59.104 55.000 0.00 0.00 43.62 3.27
5057 5651 3.726557 TCCACTCATTCCAAATCTGCT 57.273 42.857 0.00 0.00 0.00 4.24
5083 5677 1.984026 CAACATGGCAAGGGTCCCC 60.984 63.158 3.51 0.00 0.00 4.81
5161 5755 0.261696 ATGGGGAAGTATGCCAACCC 59.738 55.000 0.00 0.00 32.29 4.11
5223 5817 4.124851 ACTTCCATATTCCGACAGTGAC 57.875 45.455 0.00 0.00 0.00 3.67
5353 5947 5.643379 TTGGAGTAGTCAATTGGAAATGC 57.357 39.130 5.42 0.00 0.00 3.56
5695 6329 3.377573 ACAATGAATGCTAAATGGGCCT 58.622 40.909 4.53 0.00 0.00 5.19
5716 6350 6.948309 GGCCTGGATAATATTATGTTGACCTT 59.052 38.462 12.74 0.00 0.00 3.50
5729 6363 8.800370 TTATGTTGACCTTATGTTGAATGCTA 57.200 30.769 0.00 0.00 0.00 3.49
5732 6366 8.121305 TGTTGACCTTATGTTGAATGCTAAAT 57.879 30.769 0.00 0.00 0.00 1.40
5733 6367 8.028354 TGTTGACCTTATGTTGAATGCTAAATG 58.972 33.333 0.00 0.00 0.00 2.32
5734 6368 7.099266 TGACCTTATGTTGAATGCTAAATGG 57.901 36.000 0.00 0.00 0.00 3.16
5735 6369 6.096705 TGACCTTATGTTGAATGCTAAATGGG 59.903 38.462 0.00 0.00 0.00 4.00
5736 6370 5.163416 ACCTTATGTTGAATGCTAAATGGGC 60.163 40.000 0.00 0.00 0.00 5.36
5738 6372 2.533916 TGTTGAATGCTAAATGGGCCA 58.466 42.857 9.61 9.61 0.00 5.36
5739 6373 2.496871 TGTTGAATGCTAAATGGGCCAG 59.503 45.455 13.78 0.00 0.00 4.85
5740 6374 1.779221 TGAATGCTAAATGGGCCAGG 58.221 50.000 13.78 3.22 0.00 4.45
5741 6375 1.287442 TGAATGCTAAATGGGCCAGGA 59.713 47.619 13.78 0.00 0.00 3.86
5742 6376 2.091166 TGAATGCTAAATGGGCCAGGAT 60.091 45.455 13.78 1.38 0.00 3.24
5743 6377 3.139957 TGAATGCTAAATGGGCCAGGATA 59.860 43.478 13.78 3.91 0.00 2.59
5744 6378 3.901570 ATGCTAAATGGGCCAGGATAA 57.098 42.857 13.78 0.00 0.00 1.75
5745 6379 3.901570 TGCTAAATGGGCCAGGATAAT 57.098 42.857 13.78 0.00 0.00 1.28
5818 6452 7.152645 AGAATGTATGTTGTTACGTCTTGAGT 58.847 34.615 0.00 0.00 0.00 3.41
5842 6476 1.442769 CACCACAAACTGCTCGCTAT 58.557 50.000 0.00 0.00 0.00 2.97
5874 6508 8.768955 TGCCAATGTTTTGTTACAATAAATGTC 58.231 29.630 0.00 0.00 42.70 3.06
5911 6545 9.553064 ACTTTAAGGTGCTTATCATAATCTCTG 57.447 33.333 0.00 0.00 0.00 3.35
5924 6558 5.527214 TCATAATCTCTGTGCATTTTACCCG 59.473 40.000 0.00 0.00 0.00 5.28
5935 6569 3.349022 CATTTTACCCGGACCTGCTAAA 58.651 45.455 0.73 0.00 0.00 1.85
5936 6570 2.477845 TTTACCCGGACCTGCTAAAC 57.522 50.000 0.73 0.00 0.00 2.01
5984 6618 1.967319 ACGAACTGCACAAGTGGATT 58.033 45.000 2.00 0.00 39.81 3.01
6149 6783 2.573462 CCCTGAGGACCAAGAATCAGAA 59.427 50.000 0.00 0.00 41.35 3.02
6208 6852 4.635765 CCATGAATCGGTGATGTTTGTAGT 59.364 41.667 0.00 0.00 0.00 2.73
6233 6877 8.947115 GTAAGATAAGATGTTTTGTAGGTTGCT 58.053 33.333 0.00 0.00 0.00 3.91
6243 6887 3.675348 TGTAGGTTGCTAGGGCTAGTA 57.325 47.619 0.00 0.00 39.59 1.82
6286 6930 6.322712 CAGCCTTACAGAGAGATAGTTAGGTT 59.677 42.308 0.00 0.00 35.20 3.50
6303 6947 3.067684 GGTTGGTACCATGTAGCAAGT 57.932 47.619 17.17 0.00 44.36 3.16
6428 7077 6.712095 TCATCTTTTAGAGCAAGTGTGTCATT 59.288 34.615 0.00 0.00 0.00 2.57
6435 7084 6.734104 AGAGCAAGTGTGTCATTAGAAATC 57.266 37.500 0.00 0.00 0.00 2.17
6447 7096 7.809331 GTGTCATTAGAAATCATTGCTGTGAAA 59.191 33.333 0.00 0.00 0.00 2.69
6458 7107 3.540314 TGCTGTGAAAATTGCTGGTTT 57.460 38.095 0.00 0.00 0.00 3.27
6459 7108 4.662468 TGCTGTGAAAATTGCTGGTTTA 57.338 36.364 0.00 0.00 0.00 2.01
6460 7109 4.619973 TGCTGTGAAAATTGCTGGTTTAG 58.380 39.130 0.00 0.00 0.00 1.85
6461 7110 4.340666 TGCTGTGAAAATTGCTGGTTTAGA 59.659 37.500 0.00 0.00 0.00 2.10
6463 7112 5.928264 GCTGTGAAAATTGCTGGTTTAGATT 59.072 36.000 0.00 0.00 0.00 2.40
6464 7113 6.089954 GCTGTGAAAATTGCTGGTTTAGATTC 59.910 38.462 0.00 0.00 0.00 2.52
6465 7114 6.454795 TGTGAAAATTGCTGGTTTAGATTCC 58.545 36.000 0.00 0.00 0.00 3.01
6516 7167 2.202756 GAGGCACACCGTCGATCC 60.203 66.667 0.00 0.00 42.76 3.36
6541 7193 1.003580 AGGACCAAGCAATCACACGAT 59.996 47.619 0.00 0.00 0.00 3.73
6624 7278 3.112205 GCGCTCCTCCCCATGACAT 62.112 63.158 0.00 0.00 0.00 3.06
6656 7310 2.989824 ACCCGGTCACTCTGGACG 60.990 66.667 0.00 0.00 45.09 4.79
6718 7372 7.390440 GCTATTATGTTGGCATAGGTTACATCA 59.610 37.037 3.66 0.00 38.64 3.07
6790 7446 5.516059 AGGACACGACTCCATATCCTATA 57.484 43.478 6.01 0.00 34.77 1.31
6891 7549 2.326428 CGAATATACTCCACCACCCCT 58.674 52.381 0.00 0.00 0.00 4.79
6892 7550 3.117016 ACGAATATACTCCACCACCCCTA 60.117 47.826 0.00 0.00 0.00 3.53
6904 7562 3.458118 CACCACCCCTAGATTTGTCCATA 59.542 47.826 0.00 0.00 0.00 2.74
7147 7805 5.565592 TGAACAACTCACATATTGGATGC 57.434 39.130 0.00 0.00 0.00 3.91
7163 7821 5.372343 TGGATGCCACACATAAGAGTTAT 57.628 39.130 0.00 0.00 39.84 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.830192 CATCTTTGCCGGGCAGCC 61.830 66.667 22.59 1.26 40.61 4.85
9 10 4.503314 GCATCTTTGCCGGGCAGC 62.503 66.667 22.59 17.60 43.38 5.25
30 31 3.697439 TAGCCTTCGTGCATGGCCC 62.697 63.158 15.87 0.00 45.00 5.80
31 32 2.124736 TAGCCTTCGTGCATGGCC 60.125 61.111 15.87 0.00 45.00 5.36
32 33 2.813179 CGTAGCCTTCGTGCATGGC 61.813 63.158 5.98 10.19 44.36 4.40
33 34 1.447838 ACGTAGCCTTCGTGCATGG 60.448 57.895 5.98 0.00 40.07 3.66
34 35 4.185413 ACGTAGCCTTCGTGCATG 57.815 55.556 0.00 0.00 40.07 4.06
79 80 4.100084 CTGATGGGGCGCTGGTCA 62.100 66.667 7.64 6.26 0.00 4.02
84 85 1.454479 CCAAATCTGATGGGGCGCT 60.454 57.895 7.64 0.00 34.15 5.92
85 86 3.122850 CCAAATCTGATGGGGCGC 58.877 61.111 0.00 0.00 34.15 6.53
86 87 3.122850 GCCAAATCTGATGGGGCG 58.877 61.111 14.62 0.00 38.44 6.13
101 102 2.102252 CCTGTCCAGATCTAGAGTTGCC 59.898 54.545 0.00 0.00 0.00 4.52
109 110 1.080498 ACAACCCCCTGTCCAGATCTA 59.920 52.381 0.00 0.00 0.00 1.98
117 118 2.034221 GCTGGACAACCCCCTGTC 59.966 66.667 0.00 0.00 44.21 3.51
140 141 4.971125 GCGTGGCCGAGGCTATCC 62.971 72.222 14.33 0.00 41.60 2.59
173 174 2.190313 GCATCATGAGGGTGCCGA 59.810 61.111 9.76 0.00 32.88 5.54
174 175 3.274586 CGCATCATGAGGGTGCCG 61.275 66.667 9.76 0.00 35.51 5.69
175 176 2.124570 ACGCATCATGAGGGTGCC 60.125 61.111 9.76 0.00 35.51 5.01
183 184 0.880441 TGGTGGTTTGACGCATCATG 59.120 50.000 0.00 0.00 33.85 3.07
188 189 3.102985 CGTTGGTGGTTTGACGCA 58.897 55.556 0.00 0.00 0.00 5.24
194 195 2.043852 TGGTGGCGTTGGTGGTTT 60.044 55.556 0.00 0.00 0.00 3.27
216 217 3.505790 ATGACAAGTTGGCGGCCCA 62.506 57.895 17.97 1.48 40.06 5.36
217 218 2.676471 ATGACAAGTTGGCGGCCC 60.676 61.111 17.97 1.16 0.00 5.80
218 219 1.315257 ATGATGACAAGTTGGCGGCC 61.315 55.000 13.32 13.32 0.00 6.13
219 220 0.099436 GATGATGACAAGTTGGCGGC 59.901 55.000 7.96 0.00 0.00 6.53
220 221 0.374758 CGATGATGACAAGTTGGCGG 59.625 55.000 7.96 0.00 0.00 6.13
221 222 0.247814 GCGATGATGACAAGTTGGCG 60.248 55.000 7.96 0.87 0.00 5.69
222 223 0.247814 CGCGATGATGACAAGTTGGC 60.248 55.000 0.00 4.40 0.00 4.52
226 227 0.817654 TCCTCGCGATGATGACAAGT 59.182 50.000 10.36 0.00 0.00 3.16
229 230 0.040067 CGATCCTCGCGATGATGACA 60.040 55.000 28.03 1.95 31.14 3.58
241 242 1.524621 CCATGGGTGTGCGATCCTC 60.525 63.158 2.85 0.00 0.00 3.71
243 244 2.516930 CCCATGGGTGTGCGATCC 60.517 66.667 23.93 0.00 0.00 3.36
246 247 2.606213 TCTCCCATGGGTGTGCGA 60.606 61.111 30.28 16.15 36.47 5.10
247 248 2.124983 CTCTCCCATGGGTGTGCG 60.125 66.667 30.28 15.91 36.47 5.34
252 253 2.311070 TGCATGCTCTCCCATGGGT 61.311 57.895 30.28 7.14 42.18 4.51
256 257 1.077212 GTGGTGCATGCTCTCCCAT 60.077 57.895 20.33 0.00 0.00 4.00
257 258 2.352422 GTGGTGCATGCTCTCCCA 59.648 61.111 20.33 15.85 0.00 4.37
258 259 2.439156 GGTGGTGCATGCTCTCCC 60.439 66.667 20.33 14.62 0.00 4.30
261 262 3.612247 GACGGGTGGTGCATGCTCT 62.612 63.158 20.33 0.00 0.00 4.09
262 263 3.127533 GACGGGTGGTGCATGCTC 61.128 66.667 20.33 15.68 0.00 4.26
263 264 4.722700 GGACGGGTGGTGCATGCT 62.723 66.667 20.33 0.00 36.89 3.79
286 287 4.958897 TTTCGGTGGGTTGGGGCG 62.959 66.667 0.00 0.00 0.00 6.13
296 297 1.281656 GGTTGGCTTCGTTTCGGTG 59.718 57.895 0.00 0.00 0.00 4.94
297 298 1.153127 TGGTTGGCTTCGTTTCGGT 60.153 52.632 0.00 0.00 0.00 4.69
332 333 2.109181 GATGGTAGTGGCTCCCGC 59.891 66.667 0.00 0.00 0.00 6.13
342 343 2.125310 TTGGCGGCGTGATGGTAG 60.125 61.111 9.37 0.00 0.00 3.18
343 344 2.435234 GTTGGCGGCGTGATGGTA 60.435 61.111 9.37 0.00 0.00 3.25
360 361 4.924187 TTTGTTGGCCGGTGGGGG 62.924 66.667 1.90 0.00 35.78 5.40
367 368 1.468520 CTCTACATGGTTTGTTGGCCG 59.531 52.381 0.00 0.00 39.87 6.13
376 377 0.543749 GGCAGCCTCTCTACATGGTT 59.456 55.000 3.29 0.00 0.00 3.67
377 378 1.341156 GGGCAGCCTCTCTACATGGT 61.341 60.000 12.43 0.00 0.00 3.55
398 399 4.796231 CGAGGGCGACTTGGGACG 62.796 72.222 0.00 0.00 40.82 4.79
426 427 4.340246 TGCTGCTCTGCCCACCAG 62.340 66.667 0.00 0.00 43.17 4.00
427 428 4.340246 CTGCTGCTCTGCCCACCA 62.340 66.667 0.00 0.00 0.00 4.17
485 486 1.902716 TTAATGGCGCGACGTGTTGG 61.903 55.000 7.84 0.00 0.00 3.77
486 487 0.096281 ATTAATGGCGCGACGTGTTG 59.904 50.000 7.84 0.00 0.00 3.33
487 488 0.096281 CATTAATGGCGCGACGTGTT 59.904 50.000 7.84 4.63 0.00 3.32
488 489 1.713246 CATTAATGGCGCGACGTGT 59.287 52.632 7.84 0.00 0.00 4.49
489 490 1.651132 GCATTAATGGCGCGACGTG 60.651 57.895 7.84 3.50 0.00 4.49
490 491 2.707039 GCATTAATGGCGCGACGT 59.293 55.556 12.10 5.01 0.00 4.34
497 498 4.996113 CGTGGTCGCATTAATGGC 57.004 55.556 17.02 8.41 0.00 4.40
507 508 3.118454 GTGGTCATGGCGTGGTCG 61.118 66.667 6.90 0.00 40.37 4.79
512 513 3.353836 GTTGCGTGGTCATGGCGT 61.354 61.111 0.00 0.00 0.00 5.68
514 515 4.101790 CGGTTGCGTGGTCATGGC 62.102 66.667 0.00 0.00 0.00 4.40
560 561 1.817099 CTGGATCAGGGTGCTTCGC 60.817 63.158 0.00 0.00 0.00 4.70
571 572 3.047718 GACCGACGCGTCTGGATCA 62.048 63.158 38.06 0.00 0.00 2.92
583 585 3.056328 GCTTTGGGGCAGACCGAC 61.056 66.667 0.00 0.00 41.60 4.79
690 692 2.034221 ACCAGCTCCCTTTTCCGC 59.966 61.111 0.00 0.00 0.00 5.54
691 693 1.675641 CCACCAGCTCCCTTTTCCG 60.676 63.158 0.00 0.00 0.00 4.30
695 697 4.351054 CCGCCACCAGCTCCCTTT 62.351 66.667 0.00 0.00 40.39 3.11
712 714 2.187163 GGAGGAACCCTAGCGCAC 59.813 66.667 11.47 0.00 31.76 5.34
739 741 3.746949 CTCCTGCATCACTCCCGCC 62.747 68.421 0.00 0.00 0.00 6.13
745 747 2.304056 CCCACCCTCCTGCATCACT 61.304 63.158 0.00 0.00 0.00 3.41
750 752 4.608514 TTCCCCCACCCTCCTGCA 62.609 66.667 0.00 0.00 0.00 4.41
751 753 2.788210 CTTTTCCCCCACCCTCCTGC 62.788 65.000 0.00 0.00 0.00 4.85
782 784 3.884091 GGGAGTATTACTCAAGAGCGAGA 59.116 47.826 22.10 0.00 46.79 4.04
852 875 6.690957 CGTGCTCATTTCTTCTTTTGTTACAA 59.309 34.615 0.00 0.00 0.00 2.41
853 876 6.183360 ACGTGCTCATTTCTTCTTTTGTTACA 60.183 34.615 0.00 0.00 0.00 2.41
863 886 3.125146 TGCATACACGTGCTCATTTCTTC 59.875 43.478 17.22 0.00 45.27 2.87
865 888 2.674852 CTGCATACACGTGCTCATTTCT 59.325 45.455 17.22 0.00 45.27 2.52
866 889 2.416547 ACTGCATACACGTGCTCATTTC 59.583 45.455 17.22 0.00 45.27 2.17
940 963 6.159293 GGGTGAGCTTTTCTTCCTAAATTTG 58.841 40.000 0.00 0.00 0.00 2.32
941 964 5.048013 CGGGTGAGCTTTTCTTCCTAAATTT 60.048 40.000 0.00 0.00 0.00 1.82
942 965 4.459337 CGGGTGAGCTTTTCTTCCTAAATT 59.541 41.667 0.00 0.00 0.00 1.82
944 967 3.071892 TCGGGTGAGCTTTTCTTCCTAAA 59.928 43.478 0.00 0.00 0.00 1.85
947 978 1.002544 CTCGGGTGAGCTTTTCTTCCT 59.997 52.381 0.00 0.00 34.96 3.36
964 995 0.733729 CTCTACTCCCGGTTGTCTCG 59.266 60.000 0.00 0.00 0.00 4.04
970 1001 1.476477 GAAGCTCTCTACTCCCGGTT 58.524 55.000 0.00 0.00 0.00 4.44
973 1004 0.464013 TCCGAAGCTCTCTACTCCCG 60.464 60.000 0.00 0.00 0.00 5.14
990 1021 2.818132 CAGGCCATCTCCTCGTCC 59.182 66.667 5.01 0.00 33.25 4.79
1082 1113 3.523087 TTTGCCGCCGTCAGTGCTA 62.523 57.895 0.00 0.00 0.00 3.49
1086 1117 2.357517 CTCTTTGCCGCCGTCAGT 60.358 61.111 0.00 0.00 0.00 3.41
1127 1158 4.087892 TGCCGGCTGCTTCCTCTC 62.088 66.667 29.70 0.00 42.00 3.20
1393 1464 6.381498 TTCACATATGTCCCCTACTGAAAA 57.619 37.500 5.07 0.00 0.00 2.29
1487 1559 7.093814 TGGATAACAAAATTAGCACTGCAGAAT 60.094 33.333 23.35 6.63 0.00 2.40
1573 1645 6.170506 CACCCTGCAGTAGTAACTCAAAATA 58.829 40.000 13.81 0.00 31.97 1.40
1577 1649 2.969950 ACACCCTGCAGTAGTAACTCAA 59.030 45.455 13.81 0.00 31.97 3.02
1604 1676 4.021916 TCACCTTAGTAGTAGTTGGGCTC 58.978 47.826 0.00 0.00 0.00 4.70
1617 1689 6.012858 TCCATTTGGTTATCTGTCACCTTAGT 60.013 38.462 0.00 0.00 36.34 2.24
1627 1699 6.176183 ACTTCACTCTCCATTTGGTTATCTG 58.824 40.000 0.00 0.00 36.34 2.90
1740 1812 4.938226 CCACTCCTCTCTGAAAACCAATAC 59.062 45.833 0.00 0.00 0.00 1.89
1792 1864 4.507710 CACATCTATACACACTTGGCAGT 58.492 43.478 0.00 0.00 0.00 4.40
1793 1865 3.873361 CCACATCTATACACACTTGGCAG 59.127 47.826 0.00 0.00 0.00 4.85
1908 1983 6.127786 ACCGTCTTTACTTTTCTAGCGAGTAT 60.128 38.462 0.00 0.00 0.00 2.12
1943 2018 9.174166 AGAAAGACTACTTTTGCTCTGTTAAAA 57.826 29.630 0.00 0.00 44.97 1.52
2190 2458 5.340403 CAGAAAACTACAATGCACATGAACG 59.660 40.000 0.00 0.00 0.00 3.95
2240 2508 7.218014 GCGTCTCTATTTCATCATCGATCTAAG 59.782 40.741 0.00 0.00 0.00 2.18
2686 2954 6.543430 TTAAATGACCAGCCAAAGCATTAT 57.457 33.333 0.00 0.00 43.56 1.28
2740 3008 8.565896 ACAACAAAGTGATATACATGACACAT 57.434 30.769 0.00 0.00 35.97 3.21
3289 3560 5.078411 AGCTATATTACTTGCCTCGATGG 57.922 43.478 0.00 0.00 39.35 3.51
3293 3564 7.891183 ATAACAAGCTATATTACTTGCCTCG 57.109 36.000 14.21 0.00 45.74 4.63
3403 3674 0.458669 ACGTGGTGGAAGTATAGGCG 59.541 55.000 0.00 0.00 0.00 5.52
3494 3765 6.204852 TGGGCAATCCAGATATACTTCAAT 57.795 37.500 0.00 0.00 41.46 2.57
3533 3804 6.100134 ACCAACCAGTAGTACCAAAAGTCTAA 59.900 38.462 0.00 0.00 0.00 2.10
3556 3827 8.165239 TGATACCATATTAAGTTTCATGCACC 57.835 34.615 0.00 0.00 0.00 5.01
3591 3862 2.059541 CCGAGACTTGAAACGAAGACC 58.940 52.381 0.00 0.00 0.00 3.85
4012 4448 7.003482 TGCAATTATAGAAGTATTGGATGGCA 58.997 34.615 0.00 0.00 31.54 4.92
4168 4607 2.820059 TACCACTGTTGTCAGCTGAG 57.180 50.000 18.89 7.58 44.77 3.35
4179 4618 4.021368 ACGAAGCTCAAGTATTACCACTGT 60.021 41.667 0.00 0.00 0.00 3.55
4212 4651 4.570772 TGAGAAGCAAATTATGTAGACCGC 59.429 41.667 0.00 0.00 0.00 5.68
4288 4727 5.056480 TCCGGCAAATCTAATATGTGACTG 58.944 41.667 0.00 0.00 0.00 3.51
4289 4728 5.290493 TCCGGCAAATCTAATATGTGACT 57.710 39.130 0.00 0.00 0.00 3.41
4627 5123 0.809241 CTTCGTGCTCATCTCCTGGC 60.809 60.000 0.00 0.00 0.00 4.85
4874 5467 3.804036 TCTGTTTCTCGATGGTGTTTGT 58.196 40.909 0.00 0.00 0.00 2.83
5013 5607 2.314647 CGTGTCGTTCCGCCATGTT 61.315 57.895 0.00 0.00 0.00 2.71
5057 5651 2.356432 CCCTTGCCATGTTGATCTCTGA 60.356 50.000 0.00 0.00 0.00 3.27
5090 5684 1.343821 CAAGCAATACGACGCGACC 59.656 57.895 15.93 2.61 0.00 4.79
5161 5755 2.512692 TCCATGACATTCACCCCAAG 57.487 50.000 0.00 0.00 0.00 3.61
5223 5817 4.508461 TGGACAAAATGATGTTGCAGAG 57.492 40.909 0.00 0.00 32.57 3.35
5516 6113 8.988064 TTGATAGACAATAGTTCAGTCTGAAC 57.012 34.615 30.45 30.45 43.59 3.18
5608 6205 7.129457 ACAATGTAGCTCTCATTCAATCCTA 57.871 36.000 12.25 0.00 33.92 2.94
5662 6259 6.105397 AGCATTCATTGTCAAATCCTTGTT 57.895 33.333 0.00 0.00 33.94 2.83
5716 6350 4.285020 TGGCCCATTTAGCATTCAACATA 58.715 39.130 0.00 0.00 0.00 2.29
5724 6358 3.901570 TTATCCTGGCCCATTTAGCAT 57.098 42.857 0.00 0.00 0.00 3.79
5725 6359 3.901570 ATTATCCTGGCCCATTTAGCA 57.098 42.857 0.00 0.00 0.00 3.49
5726 6360 7.229506 GTCATATATTATCCTGGCCCATTTAGC 59.770 40.741 0.00 0.00 0.00 3.09
5727 6361 8.274322 TGTCATATATTATCCTGGCCCATTTAG 58.726 37.037 0.00 0.00 0.00 1.85
5729 6363 7.036644 TCTGTCATATATTATCCTGGCCCATTT 60.037 37.037 0.00 0.00 0.00 2.32
5732 6366 5.349690 TCTGTCATATATTATCCTGGCCCA 58.650 41.667 0.00 0.00 0.00 5.36
5733 6367 5.957771 TCTGTCATATATTATCCTGGCCC 57.042 43.478 0.00 0.00 0.00 5.80
5734 6368 9.905713 TTATTTCTGTCATATATTATCCTGGCC 57.094 33.333 0.00 0.00 0.00 5.36
5743 6377 9.725019 TTCCTCGCATTATTTCTGTCATATATT 57.275 29.630 0.00 0.00 0.00 1.28
5744 6378 9.896645 ATTCCTCGCATTATTTCTGTCATATAT 57.103 29.630 0.00 0.00 0.00 0.86
5745 6379 9.725019 AATTCCTCGCATTATTTCTGTCATATA 57.275 29.630 0.00 0.00 0.00 0.86
5795 6429 7.724305 AACTCAAGACGTAACAACATACATT 57.276 32.000 0.00 0.00 0.00 2.71
5818 6452 1.604604 GAGCAGTTTGTGGTGCCTAA 58.395 50.000 0.00 0.00 40.81 2.69
5842 6476 1.786937 ACAAAACATTGGCACCCTCA 58.213 45.000 0.00 0.00 0.00 3.86
5874 6508 4.454504 AGCACCTTAAAGTTACATGAACCG 59.545 41.667 0.00 0.00 39.02 4.44
5911 6545 0.808755 CAGGTCCGGGTAAAATGCAC 59.191 55.000 0.00 0.00 0.00 4.57
5924 6558 3.334583 TGATGTCTGTTTAGCAGGTCC 57.665 47.619 0.00 0.00 45.08 4.46
5935 6569 4.758688 TCTGCATAAACGATGATGTCTGT 58.241 39.130 0.00 0.00 37.82 3.41
5936 6570 5.292834 AGTTCTGCATAAACGATGATGTCTG 59.707 40.000 6.49 0.00 37.82 3.51
5984 6618 3.866910 GGTACGAATCGAGCACCATTTTA 59.133 43.478 10.55 0.00 31.34 1.52
6149 6783 4.731313 AAATTCTGGTTCTTCCCTGTCT 57.269 40.909 0.00 0.00 34.77 3.41
6233 6877 7.073854 ACTTCATAAGACCAATACTAGCCCTA 58.926 38.462 0.00 0.00 0.00 3.53
6243 6887 6.067217 AGGCTGTAACTTCATAAGACCAAT 57.933 37.500 0.00 0.00 0.00 3.16
6286 6930 4.287585 ACCTTAACTTGCTACATGGTACCA 59.712 41.667 18.99 18.99 0.00 3.25
6293 6937 7.848128 TCTAGCTAAACCTTAACTTGCTACAT 58.152 34.615 0.00 0.00 0.00 2.29
6332 6977 7.793888 GCATACGAACATGTAATCAGTGTAATG 59.206 37.037 0.00 0.56 0.00 1.90
6428 7077 7.329962 CAGCAATTTTCACAGCAATGATTTCTA 59.670 33.333 0.00 0.00 0.00 2.10
6435 7084 3.395639 ACCAGCAATTTTCACAGCAATG 58.604 40.909 0.00 0.00 0.00 2.82
6447 7096 4.463891 CCACAGGAATCTAAACCAGCAATT 59.536 41.667 0.00 0.00 0.00 2.32
6458 7107 6.832384 CACCTAGTAGTAACCACAGGAATCTA 59.168 42.308 0.00 0.00 0.00 1.98
6459 7108 5.657302 CACCTAGTAGTAACCACAGGAATCT 59.343 44.000 0.00 0.00 0.00 2.40
6460 7109 5.421374 ACACCTAGTAGTAACCACAGGAATC 59.579 44.000 0.00 0.00 0.00 2.52
6461 7110 5.187186 CACACCTAGTAGTAACCACAGGAAT 59.813 44.000 0.00 0.00 0.00 3.01
6463 7112 4.084287 CACACCTAGTAGTAACCACAGGA 58.916 47.826 0.00 0.00 0.00 3.86
6464 7113 3.830755 ACACACCTAGTAGTAACCACAGG 59.169 47.826 0.00 0.00 0.00 4.00
6465 7114 5.464030 AACACACCTAGTAGTAACCACAG 57.536 43.478 0.00 0.00 0.00 3.66
6496 7145 2.214181 GATCGACGGTGTGCCTCAGT 62.214 60.000 0.00 0.00 0.00 3.41
6498 7147 2.571757 GATCGACGGTGTGCCTCA 59.428 61.111 0.00 0.00 0.00 3.86
6516 7167 0.250234 TGATTGCTTGGTCCTCGGAG 59.750 55.000 0.00 0.00 0.00 4.63
6541 7193 2.519377 AACAAATCTCGGTGTCGTGA 57.481 45.000 0.00 0.00 41.99 4.35
6624 7278 1.473610 CCGGGTGCGGTATTGTAATGA 60.474 52.381 0.00 0.00 0.00 2.57
6649 7303 4.758251 CATGTGCCGGCGTCCAGA 62.758 66.667 23.90 2.12 0.00 3.86
6685 7339 1.873591 GCCAACATAATAGCACCGGAG 59.126 52.381 9.46 0.00 0.00 4.63
6718 7372 5.516044 TCATATATAGCGGGGTAGACACAT 58.484 41.667 0.00 0.00 0.00 3.21
6891 7549 6.592607 GGAAGTTTGACGTATGGACAAATCTA 59.407 38.462 10.94 0.00 36.25 1.98
6892 7550 5.411669 GGAAGTTTGACGTATGGACAAATCT 59.588 40.000 10.94 8.36 36.25 2.40
6904 7562 4.215399 CCAATGTACATGGAAGTTTGACGT 59.785 41.667 12.11 0.00 40.56 4.34
7147 7805 7.323420 TGAGTTCAGATAACTCTTATGTGTGG 58.677 38.462 16.40 0.00 45.13 4.17


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

AutoCloner maintained by Alex Coulton.