Multiple sequence alignment - TraesCS6B01G342200

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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 TraesCS6B01G342200 chr6B 100.000 5941 0 0 1 5941 602820766 602826706 0.000000e+00 10972
1 TraesCS6B01G342200 chr6D 90.355 4728 218 114 301 4910 402115765 402120372 0.000000e+00 5986
2 TraesCS6B01G342200 chr6D 95.773 1041 25 8 4920 5941 402120429 402121469 0.000000e+00 1661
3 TraesCS6B01G342200 chr6D 82.414 290 20 12 1 261 402115473 402115760 2.150000e-54 224
4 TraesCS6B01G342200 chr6A 87.981 2338 126 75 244 2482 548400429 548402710 0.000000e+00 2617
5 TraesCS6B01G342200 chr6A 94.979 1633 57 12 3286 4910 548403487 548405102 0.000000e+00 2538
6 TraesCS6B01G342200 chr6A 95.581 1041 26 9 4920 5941 548405159 548406198 0.000000e+00 1650
7 TraesCS6B01G342200 chr6A 85.859 594 59 16 2678 3252 548402903 548403490 5.090000e-170 608
8 TraesCS6B01G342200 chr5D 89.362 94 7 1 2133 2223 189931081 189930988 1.350000e-21 115
9 TraesCS6B01G342200 chr2D 89.362 94 7 1 2133 2223 477222213 477222120 1.350000e-21 115


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 TraesCS6B01G342200 chr6B 602820766 602826706 5940 False 10972.000000 10972 100.000 1 5941 1 chr6B.!!$F1 5940
1 TraesCS6B01G342200 chr6D 402115473 402121469 5996 False 2623.666667 5986 89.514 1 5941 3 chr6D.!!$F1 5940
2 TraesCS6B01G342200 chr6A 548400429 548406198 5769 False 1853.250000 2617 91.100 244 5941 4 chr6A.!!$F1 5697

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
988 1116 0.036010 CCGCAAGTCAATCCTCACCT 60.036 55.0 0.0 0.0 0.00 4.00 F
1375 1527 0.037790 AGAAGAAGGAGCTGACGCAC 60.038 55.0 0.0 0.0 39.10 5.34 F
2530 2713 0.033504 TGCAAACAGGAGAGACCGTC 59.966 55.0 0.0 0.0 44.74 4.79 F
2879 3121 0.179073 CAAGGACAGATGGCTACCGG 60.179 60.0 0.0 0.0 0.00 5.28 F
4738 5003 0.324552 TAAGGCGGTAGCTGGTGGTA 60.325 55.0 0.0 0.0 44.37 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2511 2694 0.033504 GACGGTCTCTCCTGTTTGCA 59.966 55.000 0.0 0.0 0.0 4.08 R
3279 3539 0.036388 ATCCAATCGTTCACAGCCGT 60.036 50.000 0.0 0.0 0.0 5.68 R
3942 4207 0.107017 CGGCATTCATCCTGTTCCCT 60.107 55.000 0.0 0.0 0.0 4.20 R
4761 5026 0.875059 CTTCTTCTGGTGGCGGTTTC 59.125 55.000 0.0 0.0 0.0 2.78 R
5619 5950 3.260884 TGCCCTCGTTACTTTTCTCATCT 59.739 43.478 0.0 0.0 0.0 2.90 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
82 90 2.167861 GTCCGCAGATTGAGACCGC 61.168 63.158 0.00 0.00 0.00 5.68
83 91 2.125552 CCGCAGATTGAGACCGCA 60.126 61.111 0.00 0.00 0.00 5.69
84 92 2.456119 CCGCAGATTGAGACCGCAC 61.456 63.158 0.00 0.00 0.00 5.34
86 94 1.738099 GCAGATTGAGACCGCACGT 60.738 57.895 0.00 0.00 0.00 4.49
87 95 1.687494 GCAGATTGAGACCGCACGTC 61.687 60.000 0.00 0.00 42.32 4.34
88 96 0.388520 CAGATTGAGACCGCACGTCA 60.389 55.000 3.94 0.00 44.66 4.35
89 97 0.317160 AGATTGAGACCGCACGTCAA 59.683 50.000 3.94 0.00 44.66 3.18
91 99 1.282248 ATTGAGACCGCACGTCAACG 61.282 55.000 0.12 0.12 44.66 4.10
139 167 1.647545 ATGGCATACACACGCAGCAC 61.648 55.000 0.00 0.00 0.00 4.40
185 221 2.283173 TCTGGAGAGCACAGCGGA 60.283 61.111 0.00 0.00 35.94 5.54
186 222 2.183811 CTGGAGAGCACAGCGGAG 59.816 66.667 0.00 0.00 0.00 4.63
209 245 0.597377 CCGAGCAAGGGCAAAAACAC 60.597 55.000 0.00 0.00 44.61 3.32
280 316 2.972505 CAACGTTCGGCCTGCAGT 60.973 61.111 13.81 0.00 0.00 4.40
364 407 4.400109 TGGCGTCGTCTCGTCTGC 62.400 66.667 0.00 0.00 36.35 4.26
366 409 4.104417 GCGTCGTCTCGTCTGCCT 62.104 66.667 0.00 0.00 0.00 4.75
367 410 2.202362 CGTCGTCTCGTCTGCCTG 60.202 66.667 0.00 0.00 0.00 4.85
382 425 1.895238 CCTGCCAGCCAAATTCCAG 59.105 57.895 0.00 0.00 0.00 3.86
389 432 1.097547 AGCCAAATTCCAGATCGCGG 61.098 55.000 6.13 0.00 0.00 6.46
413 456 2.754658 GAGCTCGGGTCTCGGGAA 60.755 66.667 0.00 0.00 43.26 3.97
414 457 2.042843 AGCTCGGGTCTCGGGAAT 60.043 61.111 0.00 0.00 43.26 3.01
415 458 2.077821 GAGCTCGGGTCTCGGGAATC 62.078 65.000 0.00 0.00 43.26 2.52
416 459 3.130227 CTCGGGTCTCGGGAATCC 58.870 66.667 0.00 0.00 43.26 3.01
417 460 2.443390 TCGGGTCTCGGGAATCCC 60.443 66.667 8.64 8.64 41.09 3.85
461 504 2.426752 CGCGCGTCCAAAACCAAG 60.427 61.111 24.19 0.00 0.00 3.61
462 505 2.887889 CGCGCGTCCAAAACCAAGA 61.888 57.895 24.19 0.00 0.00 3.02
463 506 1.082104 GCGCGTCCAAAACCAAGAG 60.082 57.895 8.43 0.00 0.00 2.85
464 507 1.503818 GCGCGTCCAAAACCAAGAGA 61.504 55.000 8.43 0.00 0.00 3.10
487 534 2.583441 CCACCACTCGGGCAGAAGA 61.583 63.158 0.00 0.00 42.05 2.87
493 540 0.107945 ACTCGGGCAGAAGATTGAGC 60.108 55.000 0.00 0.00 0.00 4.26
494 541 0.813210 CTCGGGCAGAAGATTGAGCC 60.813 60.000 0.00 0.00 46.28 4.70
506 563 2.753009 ATTGAGCCAAGCACCGCAGA 62.753 55.000 0.00 0.00 0.00 4.26
521 578 1.064803 CGCAGAGCGTTCATACTCTCT 59.935 52.381 1.01 0.00 45.03 3.10
525 582 2.159310 AGAGCGTTCATACTCTCTGCAC 60.159 50.000 1.01 0.00 43.10 4.57
666 762 4.201970 ACGAAAGAGTAGTAGATCAGCAGC 60.202 45.833 0.00 0.00 0.00 5.25
667 763 3.980646 AAGAGTAGTAGATCAGCAGCG 57.019 47.619 0.00 0.00 0.00 5.18
668 764 1.606668 AGAGTAGTAGATCAGCAGCGC 59.393 52.381 0.00 0.00 0.00 5.92
669 765 1.335182 GAGTAGTAGATCAGCAGCGCA 59.665 52.381 11.47 0.00 0.00 6.09
670 766 1.336440 AGTAGTAGATCAGCAGCGCAG 59.664 52.381 11.47 1.31 0.00 5.18
751 850 2.080336 TTGGTTGGCTCCCTCCCTTG 62.080 60.000 0.00 0.00 0.00 3.61
788 900 2.745037 CTTCGTTTCCCGGACCCA 59.255 61.111 0.73 0.00 37.11 4.51
792 904 2.114411 GTTTCCCGGACCCAAGCA 59.886 61.111 0.73 0.00 0.00 3.91
809 921 3.948719 ACCCAACCATCGTGCCGT 61.949 61.111 0.00 0.00 0.00 5.68
813 925 2.024868 CAACCATCGTGCCGTTCGA 61.025 57.895 0.00 0.00 41.45 3.71
835 956 1.610038 CGGACCCAGTAAACAAAACCC 59.390 52.381 0.00 0.00 0.00 4.11
859 980 2.166664 CCCAACCCGAACAAGTCAAAAA 59.833 45.455 0.00 0.00 0.00 1.94
868 989 1.542030 ACAAGTCAAAAACGCACCACA 59.458 42.857 0.00 0.00 0.00 4.17
981 1109 5.406780 AGAATATCGATTCCGCAAGTCAATC 59.593 40.000 1.71 0.00 42.25 2.67
982 1110 1.651987 TCGATTCCGCAAGTCAATCC 58.348 50.000 0.00 0.00 33.40 3.01
983 1111 1.207089 TCGATTCCGCAAGTCAATCCT 59.793 47.619 0.00 0.00 33.40 3.24
984 1112 1.594862 CGATTCCGCAAGTCAATCCTC 59.405 52.381 0.00 0.00 33.40 3.71
985 1113 2.632377 GATTCCGCAAGTCAATCCTCA 58.368 47.619 0.00 0.00 31.72 3.86
986 1114 1.808411 TTCCGCAAGTCAATCCTCAC 58.192 50.000 0.00 0.00 0.00 3.51
987 1115 0.036388 TCCGCAAGTCAATCCTCACC 60.036 55.000 0.00 0.00 0.00 4.02
988 1116 0.036010 CCGCAAGTCAATCCTCACCT 60.036 55.000 0.00 0.00 0.00 4.00
989 1117 1.363744 CGCAAGTCAATCCTCACCTC 58.636 55.000 0.00 0.00 0.00 3.85
990 1118 1.743996 GCAAGTCAATCCTCACCTCC 58.256 55.000 0.00 0.00 0.00 4.30
991 1119 2.009042 GCAAGTCAATCCTCACCTCCG 61.009 57.143 0.00 0.00 0.00 4.63
992 1120 1.276421 CAAGTCAATCCTCACCTCCGT 59.724 52.381 0.00 0.00 0.00 4.69
993 1121 1.187087 AGTCAATCCTCACCTCCGTC 58.813 55.000 0.00 0.00 0.00 4.79
1021 1149 2.377310 CGTCCGTCGCGTTTCCATT 61.377 57.895 5.77 0.00 0.00 3.16
1249 1398 4.180946 CAGTCCGCCTCCTCGTCG 62.181 72.222 0.00 0.00 0.00 5.12
1375 1527 0.037790 AGAAGAAGGAGCTGACGCAC 60.038 55.000 0.00 0.00 39.10 5.34
1376 1528 1.347817 GAAGAAGGAGCTGACGCACG 61.348 60.000 0.00 0.00 39.10 5.34
1377 1529 3.482783 GAAGGAGCTGACGCACGC 61.483 66.667 0.00 0.00 39.10 5.34
1675 1842 3.900601 AGATAGATCAGGAACCGCTCATT 59.099 43.478 0.00 0.00 0.00 2.57
1817 1984 2.229589 GCGATCGCTGTCAGCTCTG 61.230 63.158 31.94 7.52 39.60 3.35
1944 2123 4.901123 CACCACGTCGCCACCACA 62.901 66.667 0.00 0.00 0.00 4.17
1948 2127 4.235762 ACGTCGCCACCACAAGCT 62.236 61.111 0.00 0.00 0.00 3.74
2308 2487 6.886459 TCAAGTAAGCAGCTCCTGAATTAAAT 59.114 34.615 0.00 0.00 32.44 1.40
2340 2519 5.563475 CGCTTCTCATTTCAGTTCACCATTT 60.563 40.000 0.00 0.00 0.00 2.32
2356 2535 2.614481 CCATTTGCCGTAGCCCGTATAT 60.614 50.000 0.00 0.00 38.69 0.86
2363 2542 2.349886 CCGTAGCCCGTATATAGACGTC 59.650 54.545 17.80 7.70 41.31 4.34
2374 2553 7.254050 CCCGTATATAGACGTCTAATTCTCTCG 60.254 44.444 27.90 21.90 41.31 4.04
2376 2555 4.752661 ATAGACGTCTAATTCTCTCGGC 57.247 45.455 27.90 0.00 31.39 5.54
2383 2562 2.427453 TCTAATTCTCTCGGCGCTTCTT 59.573 45.455 7.64 0.00 0.00 2.52
2385 2564 1.086634 ATTCTCTCGGCGCTTCTTGC 61.087 55.000 7.64 0.00 38.57 4.01
2394 2573 2.877582 GCTTCTTGCGCATTGCCG 60.878 61.111 12.75 0.00 45.60 5.69
2404 2583 2.589540 CATTGCCGCTCCCTGGTA 59.410 61.111 0.00 0.00 0.00 3.25
2405 2584 1.819632 CATTGCCGCTCCCTGGTAC 60.820 63.158 0.00 0.00 0.00 3.34
2406 2585 3.385749 ATTGCCGCTCCCTGGTACG 62.386 63.158 0.00 0.00 0.00 3.67
2408 2587 3.766691 GCCGCTCCCTGGTACGAA 61.767 66.667 0.00 0.00 0.00 3.85
2409 2588 2.183555 CCGCTCCCTGGTACGAAC 59.816 66.667 0.00 0.00 0.00 3.95
2410 2589 2.348888 CCGCTCCCTGGTACGAACT 61.349 63.158 0.00 0.00 0.00 3.01
2411 2590 1.153823 CGCTCCCTGGTACGAACTG 60.154 63.158 0.00 0.00 0.00 3.16
2412 2591 1.218316 GCTCCCTGGTACGAACTGG 59.782 63.158 0.00 0.00 0.00 4.00
2482 2665 2.105006 ACAGTGAGTCATGCATGGAC 57.895 50.000 25.97 20.60 35.50 4.02
2495 2678 0.967380 CATGGACCCCTGAACCTTGC 60.967 60.000 0.00 0.00 0.00 4.01
2496 2679 1.434513 ATGGACCCCTGAACCTTGCA 61.435 55.000 0.00 0.00 0.00 4.08
2498 2681 1.456287 GACCCCTGAACCTTGCAGT 59.544 57.895 0.00 0.00 0.00 4.40
2500 2683 0.400594 ACCCCTGAACCTTGCAGTAC 59.599 55.000 0.00 0.00 0.00 2.73
2501 2684 0.400213 CCCCTGAACCTTGCAGTACA 59.600 55.000 0.00 0.00 0.00 2.90
2502 2685 1.202879 CCCCTGAACCTTGCAGTACAA 60.203 52.381 0.00 0.00 36.62 2.41
2505 2688 3.214328 CCTGAACCTTGCAGTACAAAGT 58.786 45.455 0.00 0.00 37.96 2.66
2506 2689 3.632145 CCTGAACCTTGCAGTACAAAGTT 59.368 43.478 0.00 0.00 43.94 2.66
2507 2690 4.498009 CCTGAACCTTGCAGTACAAAGTTG 60.498 45.833 0.00 0.00 41.85 3.16
2510 2693 2.099098 ACCTTGCAGTACAAAGTTGCAC 59.901 45.455 6.25 0.00 46.46 4.57
2511 2694 2.358898 CCTTGCAGTACAAAGTTGCACT 59.641 45.455 6.25 0.00 46.46 4.40
2515 2698 3.419264 CAGTACAAAGTTGCACTGCAA 57.581 42.857 12.59 12.59 43.32 4.08
2528 2711 2.832931 CTGCAAACAGGAGAGACCG 58.167 57.895 0.00 0.00 44.74 4.79
2529 2712 0.034059 CTGCAAACAGGAGAGACCGT 59.966 55.000 0.00 0.00 44.74 4.83
2530 2713 0.033504 TGCAAACAGGAGAGACCGTC 59.966 55.000 0.00 0.00 44.74 4.79
2531 2714 0.033504 GCAAACAGGAGAGACCGTCA 59.966 55.000 0.40 0.00 44.74 4.35
2532 2715 1.338200 GCAAACAGGAGAGACCGTCAT 60.338 52.381 0.40 0.00 44.74 3.06
2533 2716 2.094182 GCAAACAGGAGAGACCGTCATA 60.094 50.000 0.40 0.00 44.74 2.15
2534 2717 3.512680 CAAACAGGAGAGACCGTCATAC 58.487 50.000 0.40 0.00 44.74 2.39
2535 2718 2.509166 ACAGGAGAGACCGTCATACA 57.491 50.000 0.40 0.00 44.74 2.29
2536 2719 2.370349 ACAGGAGAGACCGTCATACAG 58.630 52.381 0.40 0.00 44.74 2.74
2537 2720 2.026169 ACAGGAGAGACCGTCATACAGA 60.026 50.000 0.40 0.00 44.74 3.41
2538 2721 2.356382 CAGGAGAGACCGTCATACAGAC 59.644 54.545 0.40 0.00 44.74 3.51
2539 2722 1.677052 GGAGAGACCGTCATACAGACC 59.323 57.143 0.40 0.00 44.66 3.85
2540 2723 2.366533 GAGAGACCGTCATACAGACCA 58.633 52.381 0.40 0.00 44.66 4.02
2541 2724 2.753452 GAGAGACCGTCATACAGACCAA 59.247 50.000 0.40 0.00 44.66 3.67
2542 2725 3.162666 AGAGACCGTCATACAGACCAAA 58.837 45.455 0.40 0.00 44.66 3.28
2543 2726 3.056749 AGAGACCGTCATACAGACCAAAC 60.057 47.826 0.40 0.00 44.66 2.93
2546 2729 2.105134 ACCGTCATACAGACCAAACCAA 59.895 45.455 0.00 0.00 44.66 3.67
2577 2760 5.307196 ACCGAGTAAATCCCACTAGCATTAT 59.693 40.000 0.00 0.00 0.00 1.28
2578 2761 6.183361 ACCGAGTAAATCCCACTAGCATTATT 60.183 38.462 0.00 0.00 0.00 1.40
2579 2762 6.147821 CCGAGTAAATCCCACTAGCATTATTG 59.852 42.308 0.00 0.00 0.00 1.90
2580 2763 6.929049 CGAGTAAATCCCACTAGCATTATTGA 59.071 38.462 0.00 0.00 0.00 2.57
2581 2764 7.604164 CGAGTAAATCCCACTAGCATTATTGAT 59.396 37.037 0.00 0.00 0.00 2.57
2583 2766 9.646522 AGTAAATCCCACTAGCATTATTGATTT 57.353 29.630 0.00 0.00 35.85 2.17
2584 2767 9.899226 GTAAATCCCACTAGCATTATTGATTTC 57.101 33.333 0.00 0.00 34.23 2.17
2585 2768 8.773033 AAATCCCACTAGCATTATTGATTTCT 57.227 30.769 0.00 0.00 0.00 2.52
2586 2769 7.756395 ATCCCACTAGCATTATTGATTTCTG 57.244 36.000 0.00 0.00 0.00 3.02
2590 2773 7.255381 CCCACTAGCATTATTGATTTCTGAAGG 60.255 40.741 0.00 0.00 0.00 3.46
2599 2782 1.921230 GATTTCTGAAGGTCGCTCGAC 59.079 52.381 13.45 13.45 43.87 4.20
2616 2799 4.433615 CTCGACTAGCATTTTTAGCTGGA 58.566 43.478 5.55 0.00 42.44 3.86
2617 2800 4.433615 TCGACTAGCATTTTTAGCTGGAG 58.566 43.478 5.55 0.00 42.44 3.86
2618 2801 4.081642 TCGACTAGCATTTTTAGCTGGAGT 60.082 41.667 5.55 0.00 42.44 3.85
2619 2802 4.033358 CGACTAGCATTTTTAGCTGGAGTG 59.967 45.833 5.55 0.00 42.44 3.51
2621 2804 4.938226 ACTAGCATTTTTAGCTGGAGTGTC 59.062 41.667 5.55 0.00 42.44 3.67
2642 2852 4.090930 GTCGTAGAAACTGAATTAAGCGCA 59.909 41.667 11.47 0.00 39.69 6.09
2643 2853 4.326278 TCGTAGAAACTGAATTAAGCGCAG 59.674 41.667 11.47 0.00 35.81 5.18
2661 2882 2.242043 CAGTGAAAAGGCCCTGAATGT 58.758 47.619 0.00 0.00 0.00 2.71
2670 2891 0.681175 GCCCTGAATGTGCAAAGGTT 59.319 50.000 0.00 0.00 0.00 3.50
2673 2894 2.029649 CCCTGAATGTGCAAAGGTTCAG 60.030 50.000 11.77 11.77 44.36 3.02
2716 2944 2.105984 GCGTGGCAGCCATAATCAA 58.894 52.632 19.75 0.00 35.28 2.57
2717 2945 0.455410 GCGTGGCAGCCATAATCAAA 59.545 50.000 19.75 0.00 35.28 2.69
2728 2956 3.319122 GCCATAATCAAAGGCGGATTCTT 59.681 43.478 5.57 0.00 38.86 2.52
2744 2972 4.444876 GGATTCTTCGATGGGATCAGGAAA 60.445 45.833 13.49 0.00 0.00 3.13
2749 2977 1.685148 GATGGGATCAGGAAACCAGC 58.315 55.000 0.00 0.00 36.27 4.85
2755 2983 2.618816 GGATCAGGAAACCAGCATGTCA 60.619 50.000 0.00 0.00 0.00 3.58
2795 3023 1.078143 GCAGCATCCTCGAAAGGGT 60.078 57.895 0.00 0.00 43.56 4.34
2852 3081 4.751767 ATGTTCTCTCTGGATTCTGGAC 57.248 45.455 0.00 0.00 0.00 4.02
2854 3083 3.103742 GTTCTCTCTGGATTCTGGACCT 58.896 50.000 0.00 0.00 0.00 3.85
2855 3084 2.744760 TCTCTCTGGATTCTGGACCTG 58.255 52.381 0.00 0.00 0.00 4.00
2856 3085 2.043664 TCTCTCTGGATTCTGGACCTGT 59.956 50.000 0.00 0.00 0.00 4.00
2857 3086 2.168106 CTCTCTGGATTCTGGACCTGTG 59.832 54.545 0.00 0.00 0.00 3.66
2859 3088 2.568956 CTCTGGATTCTGGACCTGTGAA 59.431 50.000 0.00 0.00 0.00 3.18
2860 3089 2.303022 TCTGGATTCTGGACCTGTGAAC 59.697 50.000 0.00 0.00 0.00 3.18
2870 3112 2.039084 GGACCTGTGAACAAGGACAGAT 59.961 50.000 0.00 0.00 41.90 2.90
2874 3116 1.421268 TGTGAACAAGGACAGATGGCT 59.579 47.619 0.00 0.00 0.00 4.75
2878 3120 0.537188 ACAAGGACAGATGGCTACCG 59.463 55.000 0.00 0.00 0.00 4.02
2879 3121 0.179073 CAAGGACAGATGGCTACCGG 60.179 60.000 0.00 0.00 0.00 5.28
2880 3122 1.338136 AAGGACAGATGGCTACCGGG 61.338 60.000 6.32 0.00 0.00 5.73
2881 3123 2.109181 GACAGATGGCTACCGGGC 59.891 66.667 6.32 0.00 41.27 6.13
2883 3125 3.536917 CAGATGGCTACCGGGCGA 61.537 66.667 6.32 0.00 44.11 5.54
2884 3126 3.227276 AGATGGCTACCGGGCGAG 61.227 66.667 6.32 0.34 44.11 5.03
2885 3127 4.971125 GATGGCTACCGGGCGAGC 62.971 72.222 14.93 14.93 44.11 5.03
2945 3196 2.947448 GTGGAACGGGTATACGAGTT 57.053 50.000 12.49 12.49 37.61 3.01
2990 3242 1.645034 ACGAGCATGGAGTTCATTCG 58.355 50.000 4.28 4.28 40.20 3.34
3128 3387 5.452356 CCAAAGCAATGATGGGAGGATTTAC 60.452 44.000 0.00 0.00 0.00 2.01
3207 3466 2.323968 TGCGCTGGACATAATTAGCA 57.676 45.000 9.73 0.00 35.98 3.49
3279 3539 5.392767 AGAGAATCGTAGCTGAAAGAACA 57.607 39.130 0.00 0.00 42.67 3.18
3289 3549 1.939934 CTGAAAGAACACGGCTGTGAA 59.060 47.619 31.98 7.21 42.98 3.18
3325 3585 7.667219 ACATGATTGGAAACCATATTAGGCTAG 59.333 37.037 0.00 0.00 20.67 3.42
3326 3586 6.003950 TGATTGGAAACCATATTAGGCTAGC 58.996 40.000 6.04 6.04 31.53 3.42
3327 3587 5.646692 TTGGAAACCATATTAGGCTAGCT 57.353 39.130 15.72 3.22 31.53 3.32
3328 3588 6.757173 TTGGAAACCATATTAGGCTAGCTA 57.243 37.500 15.72 2.18 31.53 3.32
3340 3600 4.464069 AGGCTAGCTAGTGTTTCAGAAG 57.536 45.455 21.62 0.00 0.00 2.85
3375 3640 5.874261 TCAGCTTTGTGTATGATCGATTCAA 59.126 36.000 0.00 0.00 38.03 2.69
3380 3645 6.474819 TTGTGTATGATCGATTCAAAACGT 57.525 33.333 0.00 0.00 38.03 3.99
3381 3646 6.474819 TGTGTATGATCGATTCAAAACGTT 57.525 33.333 0.00 0.00 38.03 3.99
3382 3647 6.530567 TGTGTATGATCGATTCAAAACGTTC 58.469 36.000 0.00 0.00 38.03 3.95
3383 3648 6.367695 TGTGTATGATCGATTCAAAACGTTCT 59.632 34.615 0.00 0.00 38.03 3.01
3384 3649 7.542824 TGTGTATGATCGATTCAAAACGTTCTA 59.457 33.333 0.00 0.00 38.03 2.10
3385 3650 7.839837 GTGTATGATCGATTCAAAACGTTCTAC 59.160 37.037 0.00 0.00 38.03 2.59
3676 3941 1.587043 CGTCCTCGAGAAGCTGTCCA 61.587 60.000 15.71 0.00 39.71 4.02
3833 4098 4.260253 GCTGCTATTCAAGGTAAACTACGC 60.260 45.833 0.00 0.00 0.00 4.42
4011 4276 2.545596 CCTCACAGCACTGCGCAAA 61.546 57.895 13.05 0.00 46.13 3.68
4071 4336 2.416747 CTGCACTTTGTCATCGAGGAA 58.583 47.619 0.00 0.00 0.00 3.36
4125 4390 1.079405 CCGCAACTACACCATCCGT 60.079 57.895 0.00 0.00 0.00 4.69
4302 4567 0.972983 AGGCTGCGACTGTGGACTAT 60.973 55.000 0.00 0.00 0.00 2.12
4399 4664 1.139853 ACGATGGATTCTCAAGAGGGC 59.860 52.381 0.00 0.00 0.00 5.19
4461 4726 1.345741 CTGAGTGGAGTGCAGGAGAAA 59.654 52.381 0.00 0.00 0.00 2.52
4479 4744 4.464008 AGAAAGTGCTTGATCTGGTTCAA 58.536 39.130 0.00 0.00 34.55 2.69
4627 4892 0.942884 GCAGCAGCAAAAGAAGCCAC 60.943 55.000 0.00 0.00 41.58 5.01
4651 4916 1.687054 CCCCATCATCACAGCCAACAT 60.687 52.381 0.00 0.00 0.00 2.71
4655 4920 0.324614 TCATCACAGCCAACATCGGT 59.675 50.000 0.00 0.00 0.00 4.69
4695 4960 2.202236 CTAAGGGGCCAGCTGAAGCA 62.202 60.000 17.39 0.00 45.16 3.91
4738 5003 0.324552 TAAGGCGGTAGCTGGTGGTA 60.325 55.000 0.00 0.00 44.37 3.25
4910 5175 5.359194 TGGAGAGGTGTAAATGGAGATTC 57.641 43.478 0.00 0.00 0.00 2.52
4911 5176 4.782691 TGGAGAGGTGTAAATGGAGATTCA 59.217 41.667 0.00 0.00 0.00 2.57
4912 5177 5.250543 TGGAGAGGTGTAAATGGAGATTCAA 59.749 40.000 0.00 0.00 0.00 2.69
4913 5178 5.819901 GGAGAGGTGTAAATGGAGATTCAAG 59.180 44.000 0.00 0.00 0.00 3.02
4914 5179 6.380079 AGAGGTGTAAATGGAGATTCAAGT 57.620 37.500 0.00 0.00 0.00 3.16
4915 5180 7.364762 GGAGAGGTGTAAATGGAGATTCAAGTA 60.365 40.741 0.00 0.00 0.00 2.24
4916 5181 7.560368 AGAGGTGTAAATGGAGATTCAAGTAG 58.440 38.462 0.00 0.00 0.00 2.57
4918 5183 7.106239 AGGTGTAAATGGAGATTCAAGTAGTG 58.894 38.462 0.00 0.00 0.00 2.74
4989 5304 5.037385 CCATGTCGACAACAGTAGATACAG 58.963 45.833 24.13 0.00 42.37 2.74
5021 5336 8.931385 ATATCCAGAAATTGAATTTGAAACCG 57.069 30.769 8.03 0.00 31.47 4.44
5022 5337 6.155475 TCCAGAAATTGAATTTGAAACCGT 57.845 33.333 8.03 0.00 31.47 4.83
5023 5338 7.278461 TCCAGAAATTGAATTTGAAACCGTA 57.722 32.000 8.03 0.00 31.47 4.02
5104 5434 4.082949 GCCTACCTACAACAAATGACCAAC 60.083 45.833 0.00 0.00 0.00 3.77
5305 5635 9.001542 GTATAATCGAGCTTAAGGACTCTAAGA 57.998 37.037 4.29 0.00 0.00 2.10
5443 5774 6.294473 AGATATACAGAATCTGCAAACCCAG 58.706 40.000 10.62 0.00 34.37 4.45
5530 5861 5.883685 TTGCAGAGTCCATCATTATCTCT 57.116 39.130 0.00 0.00 36.15 3.10
5602 5933 5.348997 GGTATCTATTTCGCAAGGTATCTGC 59.651 44.000 0.00 0.00 38.47 4.26
5604 5935 4.960938 TCTATTTCGCAAGGTATCTGCAT 58.039 39.130 0.00 0.00 38.47 3.96
5635 5967 6.952935 AGCAAGTAGATGAGAAAAGTAACG 57.047 37.500 0.00 0.00 0.00 3.18
5770 6102 5.749596 TTATGACACCAACAACAACTGAG 57.250 39.130 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 140 0.610509 TGTGTATGCCATTTGCCCGT 60.611 50.000 0.00 0.00 40.16 5.28
154 182 1.139095 CCAGAGCGTTCCGGTACTC 59.861 63.158 9.70 8.40 37.83 2.59
159 187 2.492090 CTCTCCAGAGCGTTCCGG 59.508 66.667 0.00 0.00 35.13 5.14
185 221 3.790416 TTGCCCTTGCTCGGTTGCT 62.790 57.895 0.00 0.00 38.71 3.91
186 222 2.362329 TTTTGCCCTTGCTCGGTTGC 62.362 55.000 0.00 0.00 38.71 4.17
187 223 0.103937 TTTTTGCCCTTGCTCGGTTG 59.896 50.000 0.00 0.00 38.71 3.77
188 224 0.104120 GTTTTTGCCCTTGCTCGGTT 59.896 50.000 0.00 0.00 38.71 4.44
189 225 1.040339 TGTTTTTGCCCTTGCTCGGT 61.040 50.000 0.00 0.00 38.71 4.69
190 226 0.597377 GTGTTTTTGCCCTTGCTCGG 60.597 55.000 0.00 0.00 38.71 4.63
191 227 0.597377 GGTGTTTTTGCCCTTGCTCG 60.597 55.000 0.00 0.00 38.71 5.03
192 228 0.249868 GGGTGTTTTTGCCCTTGCTC 60.250 55.000 0.00 0.00 41.63 4.26
193 229 1.829456 GGGTGTTTTTGCCCTTGCT 59.171 52.632 0.00 0.00 41.63 3.91
209 245 2.182030 GAGTCACGCGGAAGAGGG 59.818 66.667 12.47 0.00 34.72 4.30
280 316 2.099427 GCCAAACGTCCAAAAACCTGTA 59.901 45.455 0.00 0.00 0.00 2.74
364 407 0.612732 TCTGGAATTTGGCTGGCAGG 60.613 55.000 17.64 0.00 0.00 4.85
365 408 1.407979 GATCTGGAATTTGGCTGGCAG 59.592 52.381 10.94 10.94 0.00 4.85
366 409 1.477553 GATCTGGAATTTGGCTGGCA 58.522 50.000 0.00 0.00 0.00 4.92
367 410 0.383231 CGATCTGGAATTTGGCTGGC 59.617 55.000 0.00 0.00 0.00 4.85
389 432 4.539881 GACCCGAGCTCGCGAGAC 62.540 72.222 38.74 27.67 38.18 3.36
397 440 2.042843 ATTCCCGAGACCCGAGCT 60.043 61.111 0.00 0.00 41.76 4.09
398 441 2.417936 GATTCCCGAGACCCGAGC 59.582 66.667 0.00 0.00 41.76 5.03
399 442 2.499827 GGGATTCCCGAGACCCGAG 61.500 68.421 5.84 0.00 41.76 4.63
400 443 2.443390 GGGATTCCCGAGACCCGA 60.443 66.667 5.84 0.00 41.76 5.14
456 499 0.185175 GTGGTGGGGTTTCTCTTGGT 59.815 55.000 0.00 0.00 0.00 3.67
458 501 1.878102 CGAGTGGTGGGGTTTCTCTTG 60.878 57.143 0.00 0.00 0.00 3.02
461 504 1.003718 CCGAGTGGTGGGGTTTCTC 60.004 63.158 0.00 0.00 0.00 2.87
462 505 2.526046 CCCGAGTGGTGGGGTTTCT 61.526 63.158 0.00 0.00 43.39 2.52
463 506 2.033602 CCCGAGTGGTGGGGTTTC 59.966 66.667 0.00 0.00 43.39 2.78
487 534 2.282391 TGCGGTGCTTGGCTCAAT 60.282 55.556 0.00 0.00 0.00 2.57
506 563 1.134965 GGTGCAGAGAGTATGAACGCT 60.135 52.381 0.00 0.00 38.60 5.07
525 582 2.126467 CGTTCCAAATGCACTTTGTGG 58.874 47.619 15.67 5.10 42.29 4.17
570 643 2.837031 GATTGACCACCCGCCCACAT 62.837 60.000 0.00 0.00 0.00 3.21
578 651 0.323629 TTCCTGACGATTGACCACCC 59.676 55.000 0.00 0.00 0.00 4.61
751 850 2.665185 AAGACGCGTTGAGTGGGC 60.665 61.111 15.53 0.00 33.90 5.36
788 900 4.079446 CACGATGGTTGGGTGCTT 57.921 55.556 0.00 0.00 0.00 3.91
809 921 0.318120 GTTTACTGGGTCCGGTCGAA 59.682 55.000 4.52 0.00 36.80 3.71
813 925 2.300433 GTTTTGTTTACTGGGTCCGGT 58.700 47.619 0.00 6.71 39.18 5.28
835 956 0.666374 GACTTGTTCGGGTTGGGTTG 59.334 55.000 0.00 0.00 0.00 3.77
859 980 1.077357 TTGGGACTTTGTGGTGCGT 60.077 52.632 0.00 0.00 0.00 5.24
868 989 0.755327 GTGTGCTGGGTTGGGACTTT 60.755 55.000 0.00 0.00 0.00 2.66
981 1109 2.037367 TGAGGGACGGAGGTGAGG 59.963 66.667 0.00 0.00 0.00 3.86
982 1110 2.352032 GGTGAGGGACGGAGGTGAG 61.352 68.421 0.00 0.00 0.00 3.51
983 1111 2.283676 GGTGAGGGACGGAGGTGA 60.284 66.667 0.00 0.00 0.00 4.02
984 1112 2.283966 AGGTGAGGGACGGAGGTG 60.284 66.667 0.00 0.00 0.00 4.00
985 1113 2.037527 GAGGTGAGGGACGGAGGT 59.962 66.667 0.00 0.00 0.00 3.85
986 1114 2.760385 GGAGGTGAGGGACGGAGG 60.760 72.222 0.00 0.00 0.00 4.30
987 1115 3.141488 CGGAGGTGAGGGACGGAG 61.141 72.222 0.00 0.00 0.00 4.63
988 1116 3.933048 GACGGAGGTGAGGGACGGA 62.933 68.421 0.00 0.00 0.00 4.69
989 1117 3.450115 GACGGAGGTGAGGGACGG 61.450 72.222 0.00 0.00 0.00 4.79
990 1118 3.450115 GGACGGAGGTGAGGGACG 61.450 72.222 0.00 0.00 0.00 4.79
991 1119 3.450115 CGGACGGAGGTGAGGGAC 61.450 72.222 0.00 0.00 0.00 4.46
992 1120 3.933048 GACGGACGGAGGTGAGGGA 62.933 68.421 0.00 0.00 0.00 4.20
993 1121 3.450115 GACGGACGGAGGTGAGGG 61.450 72.222 0.00 0.00 0.00 4.30
1249 1398 2.182030 CGCTTCGTGGAGGAGGAC 59.818 66.667 0.00 0.00 0.00 3.85
1807 1974 2.997315 CGGGGGACAGAGCTGACA 60.997 66.667 4.21 0.00 0.00 3.58
1944 2123 1.691823 GGTGGGCCTTTAGGAGCTT 59.308 57.895 4.53 0.00 37.39 3.74
2056 2235 0.617820 CTCCCTTCTTTCCTCCGGGA 60.618 60.000 0.00 0.00 41.47 5.14
2095 2274 3.330720 CCCTTCTTGCCTCCGGGT 61.331 66.667 0.00 0.00 34.45 5.28
2101 2280 3.342477 GGCCCTCCCTTCTTGCCT 61.342 66.667 0.00 0.00 39.05 4.75
2182 2361 4.373116 TTCGCCAGGTCGTCTGCC 62.373 66.667 3.62 0.00 42.05 4.85
2356 2535 2.543012 CGCCGAGAGAATTAGACGTCTA 59.457 50.000 21.25 21.25 0.00 2.59
2363 2542 2.500509 AGAAGCGCCGAGAGAATTAG 57.499 50.000 2.29 0.00 0.00 1.73
2391 2570 3.766691 TTCGTACCAGGGAGCGGC 61.767 66.667 0.00 0.00 0.00 6.53
2393 2572 1.153823 CAGTTCGTACCAGGGAGCG 60.154 63.158 0.00 0.00 0.00 5.03
2394 2573 1.218316 CCAGTTCGTACCAGGGAGC 59.782 63.158 0.00 0.00 0.00 4.70
2397 2576 0.533951 GTACCCAGTTCGTACCAGGG 59.466 60.000 15.84 15.84 42.79 4.45
2402 2581 0.109132 CACCGGTACCCAGTTCGTAC 60.109 60.000 6.87 0.00 36.22 3.67
2403 2582 0.251121 TCACCGGTACCCAGTTCGTA 60.251 55.000 6.87 0.00 0.00 3.43
2404 2583 0.901580 ATCACCGGTACCCAGTTCGT 60.902 55.000 6.87 0.00 0.00 3.85
2405 2584 0.248289 AATCACCGGTACCCAGTTCG 59.752 55.000 6.87 0.00 0.00 3.95
2406 2585 2.498885 AGTAATCACCGGTACCCAGTTC 59.501 50.000 6.87 0.00 0.00 3.01
2407 2586 2.235402 CAGTAATCACCGGTACCCAGTT 59.765 50.000 6.87 0.00 0.00 3.16
2408 2587 1.829222 CAGTAATCACCGGTACCCAGT 59.171 52.381 6.87 0.71 0.00 4.00
2409 2588 2.104967 TCAGTAATCACCGGTACCCAG 58.895 52.381 6.87 0.00 0.00 4.45
2410 2589 2.234896 TCAGTAATCACCGGTACCCA 57.765 50.000 6.87 0.00 0.00 4.51
2411 2590 3.463944 CAATCAGTAATCACCGGTACCC 58.536 50.000 6.87 0.00 0.00 3.69
2412 2591 2.870411 GCAATCAGTAATCACCGGTACC 59.130 50.000 6.87 0.16 0.00 3.34
2421 2600 8.715998 CACTACATTCCTATGCAATCAGTAATC 58.284 37.037 0.00 0.00 35.03 1.75
2456 2635 3.599343 TGCATGACTCACTGTTCATACC 58.401 45.455 0.00 0.00 0.00 2.73
2460 2639 2.038820 TCCATGCATGACTCACTGTTCA 59.961 45.455 28.31 0.00 0.00 3.18
2482 2665 0.400213 TGTACTGCAAGGTTCAGGGG 59.600 55.000 0.00 0.00 39.30 4.79
2506 2689 0.469494 TCTCTCCTGTTTGCAGTGCA 59.531 50.000 15.37 15.37 41.02 4.57
2507 2690 0.871057 GTCTCTCCTGTTTGCAGTGC 59.129 55.000 8.58 8.58 41.02 4.40
2510 2693 0.034059 ACGGTCTCTCCTGTTTGCAG 59.966 55.000 0.00 0.00 42.22 4.41
2511 2694 0.033504 GACGGTCTCTCCTGTTTGCA 59.966 55.000 0.00 0.00 0.00 4.08
2512 2695 0.033504 TGACGGTCTCTCCTGTTTGC 59.966 55.000 9.88 0.00 0.00 3.68
2513 2696 2.751166 ATGACGGTCTCTCCTGTTTG 57.249 50.000 9.88 0.00 0.00 2.93
2514 2697 3.162666 TGTATGACGGTCTCTCCTGTTT 58.837 45.455 9.88 0.00 0.00 2.83
2515 2698 2.755655 CTGTATGACGGTCTCTCCTGTT 59.244 50.000 9.88 0.00 0.00 3.16
2516 2699 2.026169 TCTGTATGACGGTCTCTCCTGT 60.026 50.000 9.88 0.00 0.00 4.00
2517 2700 2.356382 GTCTGTATGACGGTCTCTCCTG 59.644 54.545 9.88 0.11 35.81 3.86
2518 2701 2.645802 GTCTGTATGACGGTCTCTCCT 58.354 52.381 9.88 0.00 35.81 3.69
2519 2702 1.677052 GGTCTGTATGACGGTCTCTCC 59.323 57.143 9.88 0.00 46.24 3.71
2520 2703 2.366533 TGGTCTGTATGACGGTCTCTC 58.633 52.381 9.88 0.52 46.24 3.20
2521 2704 2.509166 TGGTCTGTATGACGGTCTCT 57.491 50.000 9.88 0.00 46.24 3.10
2522 2705 3.251571 GTTTGGTCTGTATGACGGTCTC 58.748 50.000 9.88 1.20 46.24 3.36
2523 2706 2.028385 GGTTTGGTCTGTATGACGGTCT 60.028 50.000 9.88 0.00 46.24 3.85
2524 2707 2.289195 TGGTTTGGTCTGTATGACGGTC 60.289 50.000 0.00 0.00 46.24 4.79
2525 2708 1.695242 TGGTTTGGTCTGTATGACGGT 59.305 47.619 0.00 0.00 46.24 4.83
2526 2709 2.465860 TGGTTTGGTCTGTATGACGG 57.534 50.000 0.00 0.00 46.24 4.79
2527 2710 2.159627 GCTTGGTTTGGTCTGTATGACG 59.840 50.000 0.00 0.00 46.24 4.35
2528 2711 3.146066 TGCTTGGTTTGGTCTGTATGAC 58.854 45.455 0.00 0.00 44.63 3.06
2529 2712 3.500448 TGCTTGGTTTGGTCTGTATGA 57.500 42.857 0.00 0.00 0.00 2.15
2530 2713 3.758023 TCATGCTTGGTTTGGTCTGTATG 59.242 43.478 0.00 0.00 0.00 2.39
2531 2714 4.032960 TCATGCTTGGTTTGGTCTGTAT 57.967 40.909 0.00 0.00 0.00 2.29
2532 2715 3.500448 TCATGCTTGGTTTGGTCTGTA 57.500 42.857 0.00 0.00 0.00 2.74
2533 2716 2.362077 GTTCATGCTTGGTTTGGTCTGT 59.638 45.455 0.00 0.00 0.00 3.41
2534 2717 2.288395 GGTTCATGCTTGGTTTGGTCTG 60.288 50.000 0.00 0.00 0.00 3.51
2535 2718 1.963515 GGTTCATGCTTGGTTTGGTCT 59.036 47.619 0.00 0.00 0.00 3.85
2536 2719 1.335872 CGGTTCATGCTTGGTTTGGTC 60.336 52.381 0.00 0.00 0.00 4.02
2537 2720 0.673437 CGGTTCATGCTTGGTTTGGT 59.327 50.000 0.00 0.00 0.00 3.67
2538 2721 0.958091 TCGGTTCATGCTTGGTTTGG 59.042 50.000 0.00 0.00 0.00 3.28
2539 2722 1.608590 ACTCGGTTCATGCTTGGTTTG 59.391 47.619 0.00 0.00 0.00 2.93
2540 2723 1.981256 ACTCGGTTCATGCTTGGTTT 58.019 45.000 0.00 0.00 0.00 3.27
2541 2724 2.851263 TACTCGGTTCATGCTTGGTT 57.149 45.000 0.00 0.00 0.00 3.67
2542 2725 2.851263 TTACTCGGTTCATGCTTGGT 57.149 45.000 0.00 0.00 0.00 3.67
2543 2726 3.065371 GGATTTACTCGGTTCATGCTTGG 59.935 47.826 0.00 0.00 0.00 3.61
2546 2729 2.238646 TGGGATTTACTCGGTTCATGCT 59.761 45.455 0.00 0.00 0.00 3.79
2577 2760 2.029380 TCGAGCGACCTTCAGAAATCAA 60.029 45.455 0.00 0.00 0.00 2.57
2578 2761 1.544246 TCGAGCGACCTTCAGAAATCA 59.456 47.619 0.00 0.00 0.00 2.57
2579 2762 1.921230 GTCGAGCGACCTTCAGAAATC 59.079 52.381 11.70 0.00 39.08 2.17
2580 2763 1.546476 AGTCGAGCGACCTTCAGAAAT 59.454 47.619 18.28 0.00 45.59 2.17
2581 2764 0.959553 AGTCGAGCGACCTTCAGAAA 59.040 50.000 18.28 0.00 45.59 2.52
2583 2766 1.370609 CTAGTCGAGCGACCTTCAGA 58.629 55.000 18.28 0.00 45.59 3.27
2584 2767 0.248296 GCTAGTCGAGCGACCTTCAG 60.248 60.000 18.28 11.77 45.59 3.02
2585 2768 1.801332 GCTAGTCGAGCGACCTTCA 59.199 57.895 18.28 2.43 45.59 3.02
2586 2769 4.694102 GCTAGTCGAGCGACCTTC 57.306 61.111 18.28 5.08 45.59 3.46
2599 2782 4.033358 CGACACTCCAGCTAAAAATGCTAG 59.967 45.833 0.00 0.00 38.92 3.42
2607 2790 4.280174 AGTTTCTACGACACTCCAGCTAAA 59.720 41.667 0.00 0.00 0.00 1.85
2609 2792 3.190744 CAGTTTCTACGACACTCCAGCTA 59.809 47.826 0.00 0.00 0.00 3.32
2610 2793 2.029828 CAGTTTCTACGACACTCCAGCT 60.030 50.000 0.00 0.00 0.00 4.24
2611 2794 2.030185 TCAGTTTCTACGACACTCCAGC 60.030 50.000 0.00 0.00 0.00 4.85
2612 2795 3.917329 TCAGTTTCTACGACACTCCAG 57.083 47.619 0.00 0.00 0.00 3.86
2613 2796 4.866508 ATTCAGTTTCTACGACACTCCA 57.133 40.909 0.00 0.00 0.00 3.86
2614 2797 6.183360 GCTTAATTCAGTTTCTACGACACTCC 60.183 42.308 0.00 0.00 0.00 3.85
2616 2799 5.345202 CGCTTAATTCAGTTTCTACGACACT 59.655 40.000 0.00 0.00 0.00 3.55
2617 2800 5.539207 CGCTTAATTCAGTTTCTACGACAC 58.461 41.667 0.00 0.00 0.00 3.67
2618 2801 4.090930 GCGCTTAATTCAGTTTCTACGACA 59.909 41.667 0.00 0.00 0.00 4.35
2619 2802 4.090930 TGCGCTTAATTCAGTTTCTACGAC 59.909 41.667 9.73 0.00 0.00 4.34
2621 2804 4.091509 ACTGCGCTTAATTCAGTTTCTACG 59.908 41.667 9.73 0.00 37.78 3.51
2634 2844 0.596082 GGCCTTTTCACTGCGCTTAA 59.404 50.000 9.73 0.00 0.00 1.85
2635 2845 1.241315 GGGCCTTTTCACTGCGCTTA 61.241 55.000 9.73 0.00 35.34 3.09
2636 2846 2.564721 GGGCCTTTTCACTGCGCTT 61.565 57.895 9.73 0.00 35.34 4.68
2637 2847 2.985847 GGGCCTTTTCACTGCGCT 60.986 61.111 9.73 0.00 35.34 5.92
2638 2848 2.985847 AGGGCCTTTTCACTGCGC 60.986 61.111 0.00 0.00 38.13 6.09
2639 2849 1.172180 TTCAGGGCCTTTTCACTGCG 61.172 55.000 1.32 0.00 0.00 5.18
2642 2852 2.242043 CACATTCAGGGCCTTTTCACT 58.758 47.619 1.32 0.00 0.00 3.41
2643 2853 1.337167 GCACATTCAGGGCCTTTTCAC 60.337 52.381 1.32 0.00 42.32 3.18
2700 2928 1.202452 GCCTTTGATTATGGCTGCCAC 60.202 52.381 25.99 12.00 42.38 5.01
2711 2939 2.985896 TCGAAGAATCCGCCTTTGATT 58.014 42.857 0.00 0.00 35.21 2.57
2716 2944 0.179045 CCCATCGAAGAATCCGCCTT 60.179 55.000 0.00 0.00 43.58 4.35
2717 2945 1.048724 TCCCATCGAAGAATCCGCCT 61.049 55.000 0.00 0.00 43.58 5.52
2728 2956 1.486310 CTGGTTTCCTGATCCCATCGA 59.514 52.381 0.00 0.00 0.00 3.59
2744 2972 1.238439 CGGAAAAGTGACATGCTGGT 58.762 50.000 0.00 0.00 0.00 4.00
2749 2977 1.535462 GTCCACCGGAAAAGTGACATG 59.465 52.381 9.46 0.00 37.42 3.21
2755 2983 0.249741 CGTGAGTCCACCGGAAAAGT 60.250 55.000 9.46 0.00 40.12 2.66
2795 3023 1.905843 CCGTGATTTGGGTTGGGCA 60.906 57.895 0.00 0.00 0.00 5.36
2852 3081 2.430465 CCATCTGTCCTTGTTCACAGG 58.570 52.381 0.00 0.00 40.49 4.00
2854 3083 1.421268 AGCCATCTGTCCTTGTTCACA 59.579 47.619 0.00 0.00 0.00 3.58
2855 3084 2.191128 AGCCATCTGTCCTTGTTCAC 57.809 50.000 0.00 0.00 0.00 3.18
2856 3085 2.027192 GGTAGCCATCTGTCCTTGTTCA 60.027 50.000 0.00 0.00 0.00 3.18
2857 3086 2.633488 GGTAGCCATCTGTCCTTGTTC 58.367 52.381 0.00 0.00 0.00 3.18
2859 3088 0.537188 CGGTAGCCATCTGTCCTTGT 59.463 55.000 0.00 0.00 0.00 3.16
2860 3089 0.179073 CCGGTAGCCATCTGTCCTTG 60.179 60.000 0.00 0.00 0.00 3.61
2881 3123 2.978452 CTACGAAGCCCCCATGCTCG 62.978 65.000 0.00 0.00 41.80 5.03
2883 3125 1.271840 TTCTACGAAGCCCCCATGCT 61.272 55.000 0.00 0.00 45.43 3.79
2884 3126 1.095807 GTTCTACGAAGCCCCCATGC 61.096 60.000 0.00 0.00 0.00 4.06
2885 3127 0.810031 CGTTCTACGAAGCCCCCATG 60.810 60.000 0.00 0.00 46.05 3.66
2886 3128 1.520666 CGTTCTACGAAGCCCCCAT 59.479 57.895 0.00 0.00 46.05 4.00
2920 3171 1.478105 GTATACCCGTTCCACGAAGGT 59.522 52.381 0.00 0.38 46.05 3.50
2921 3172 1.534595 CGTATACCCGTTCCACGAAGG 60.535 57.143 0.00 0.00 46.05 3.46
2922 3173 1.401552 TCGTATACCCGTTCCACGAAG 59.598 52.381 0.00 0.00 46.05 3.79
2923 3174 1.401552 CTCGTATACCCGTTCCACGAA 59.598 52.381 0.00 0.00 46.05 3.85
2924 3175 1.016627 CTCGTATACCCGTTCCACGA 58.983 55.000 0.00 0.00 46.05 4.35
2925 3176 0.734889 ACTCGTATACCCGTTCCACG 59.265 55.000 0.00 0.00 42.11 4.94
2990 3242 2.989166 GTCAAGGTAGCAAAGCAAATGC 59.011 45.455 0.00 0.00 44.15 3.56
3038 3294 7.702772 CGAGATCAAACAAGCTAACAGTAGTAT 59.297 37.037 0.00 0.00 0.00 2.12
3062 3319 2.698797 GTCCCCATCCAGATTCTTACGA 59.301 50.000 0.00 0.00 0.00 3.43
3128 3387 2.100631 GGCGTCCACATCCTGTTCG 61.101 63.158 0.00 0.00 0.00 3.95
3200 3459 1.156736 GTGACGTGGCAGTGCTAATT 58.843 50.000 16.11 0.00 0.00 1.40
3207 3466 3.626924 GAGGGGTGACGTGGCAGT 61.627 66.667 0.00 0.00 0.00 4.40
3253 3513 8.035394 TGTTCTTTCAGCTACGATTCTCTTATT 58.965 33.333 0.00 0.00 0.00 1.40
3279 3539 0.036388 ATCCAATCGTTCACAGCCGT 60.036 50.000 0.00 0.00 0.00 5.68
3289 3549 5.299279 GGTTTCCAATCATGTATCCAATCGT 59.701 40.000 0.00 0.00 0.00 3.73
3313 3573 7.661968 TCTGAAACACTAGCTAGCCTAATATG 58.338 38.462 20.91 11.66 0.00 1.78
3325 3585 4.820284 AAACAGCTTCTGAAACACTAGC 57.180 40.909 0.29 0.00 35.18 3.42
3363 3628 7.545965 AGAAGTAGAACGTTTTGAATCGATCAT 59.454 33.333 0.46 0.00 38.03 2.45
3375 3640 4.936891 ACACCGTTAGAAGTAGAACGTTT 58.063 39.130 0.46 0.00 45.35 3.60
3380 3645 7.013655 AGAGTAACAACACCGTTAGAAGTAGAA 59.986 37.037 0.00 0.00 32.15 2.10
3381 3646 6.488006 AGAGTAACAACACCGTTAGAAGTAGA 59.512 38.462 0.00 0.00 32.15 2.59
3382 3647 6.581542 CAGAGTAACAACACCGTTAGAAGTAG 59.418 42.308 0.00 0.00 32.15 2.57
3383 3648 6.262944 TCAGAGTAACAACACCGTTAGAAGTA 59.737 38.462 0.00 0.00 32.15 2.24
3384 3649 5.068198 TCAGAGTAACAACACCGTTAGAAGT 59.932 40.000 0.00 0.00 32.15 3.01
3385 3650 5.401674 GTCAGAGTAACAACACCGTTAGAAG 59.598 44.000 0.00 0.00 32.15 2.85
3564 3829 3.135348 GGAGGATGATGGAGATGTTGTGA 59.865 47.826 0.00 0.00 0.00 3.58
3654 3919 0.889638 ACAGCTTCTCGAGGACGTCA 60.890 55.000 18.91 0.00 40.69 4.35
3676 3941 0.619832 TCCTTGGAGATGCTGAGCCT 60.620 55.000 0.23 0.00 0.00 4.58
3833 4098 2.696506 TGAGCACAGCAATCTCAGAAG 58.303 47.619 0.00 0.00 33.42 2.85
3942 4207 0.107017 CGGCATTCATCCTGTTCCCT 60.107 55.000 0.00 0.00 0.00 4.20
3945 4210 1.031571 TGCCGGCATTCATCCTGTTC 61.032 55.000 29.03 0.00 0.00 3.18
3949 4214 2.514592 CGTGCCGGCATTCATCCT 60.515 61.111 35.23 0.00 0.00 3.24
4011 4276 2.408050 GTGCTCTTCACGTCATTGAGT 58.592 47.619 0.00 0.00 35.76 3.41
4053 4318 2.417719 ACTTCCTCGATGACAAAGTGC 58.582 47.619 0.00 0.00 0.00 4.40
4102 4367 2.356135 GATGGTGTAGTTGCGGTTGAT 58.644 47.619 0.00 0.00 0.00 2.57
4302 4567 2.164827 GCATTCATTGGCAGTCACATCA 59.835 45.455 0.00 0.00 0.00 3.07
4399 4664 2.161808 CAGCATTGACAAAGCCTCTCAG 59.838 50.000 11.57 0.00 0.00 3.35
4461 4726 2.146342 CGTTGAACCAGATCAAGCACT 58.854 47.619 0.00 0.00 39.84 4.40
4479 4744 1.168714 GGTAGTACTCCGTTGTCCGT 58.831 55.000 0.00 0.00 33.66 4.69
4627 4892 1.454479 GCTGTGATGATGGGGGTGG 60.454 63.158 0.00 0.00 0.00 4.61
4761 5026 0.875059 CTTCTTCTGGTGGCGGTTTC 59.125 55.000 0.00 0.00 0.00 2.78
4914 5179 9.689976 CCAACACAAACAATTTCATTATCACTA 57.310 29.630 0.00 0.00 0.00 2.74
4915 5180 8.203485 ACCAACACAAACAATTTCATTATCACT 58.797 29.630 0.00 0.00 0.00 3.41
4916 5181 8.364129 ACCAACACAAACAATTTCATTATCAC 57.636 30.769 0.00 0.00 0.00 3.06
4918 5183 9.260002 AGAACCAACACAAACAATTTCATTATC 57.740 29.630 0.00 0.00 0.00 1.75
5104 5434 3.242188 GCCTGTAAATTGTAAGTACCGCG 60.242 47.826 0.00 0.00 0.00 6.46
5437 5768 3.182152 AGCTCAGGTATGTTACTGGGTT 58.818 45.455 0.00 0.00 37.52 4.11
5443 5774 7.723324 TGGATTTACTAGCTCAGGTATGTTAC 58.277 38.462 0.00 0.00 0.00 2.50
5602 5933 3.943381 TCATCTACTTGCTTCTTGGCATG 59.057 43.478 0.00 0.00 42.09 4.06
5604 5935 3.261643 TCTCATCTACTTGCTTCTTGGCA 59.738 43.478 0.00 0.00 40.74 4.92
5619 5950 3.260884 TGCCCTCGTTACTTTTCTCATCT 59.739 43.478 0.00 0.00 0.00 2.90
5635 5967 7.094377 TGTGTCTTTAAATCAATAGTTGCCCTC 60.094 37.037 0.00 0.00 0.00 4.30
5770 6102 3.608474 GCAGTTTTGTGTATGAACCGTCC 60.608 47.826 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.