Multiple sequence alignment - TraesCS2D01G551300

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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 TraesCS2D01G551300 chr2D 100.000 3103 0 0 1 3103 627115596 627112494 0.000000e+00 5731
1 TraesCS2D01G551300 chr2D 94.643 112 6 0 562 673 627114924 627114813 1.140000e-39 174
2 TraesCS2D01G551300 chr2D 94.643 112 6 0 673 784 627115035 627114924 1.140000e-39 174
3 TraesCS2D01G551300 chr2A 96.133 1086 33 7 588 1670 757808013 757806934 0.000000e+00 1764
4 TraesCS2D01G551300 chr2A 88.717 452 26 7 1 429 757808459 757808010 2.120000e-146 529
5 TraesCS2D01G551300 chr2A 90.120 415 25 8 2682 3090 757805979 757805575 2.740000e-145 525
6 TraesCS2D01G551300 chr2A 95.804 286 11 1 1701 1985 757806934 757806649 7.840000e-126 460
7 TraesCS2D01G551300 chr2A 93.532 201 7 4 2240 2440 757806323 757806129 8.420000e-76 294
8 TraesCS2D01G551300 chr2A 90.789 228 4 3 2030 2256 757806551 757806340 3.920000e-74 289
9 TraesCS2D01G551300 chr2A 95.575 113 5 0 562 674 757807928 757807816 6.840000e-42 182
10 TraesCS2D01G551300 chr2A 96.512 86 3 0 699 784 757808013 757807928 3.230000e-30 143
11 TraesCS2D01G551300 chr2B 88.229 977 64 20 573 1540 768549459 768548525 0.000000e+00 1120
12 TraesCS2D01G551300 chr2B 90.208 817 43 11 1 784 768550286 768549474 0.000000e+00 1031
13 TraesCS2D01G551300 chr2B 96.753 308 10 0 1719 2026 768548528 768548221 5.930000e-142 514
14 TraesCS2D01G551300 chr2B 91.266 229 14 3 562 784 768549587 768549359 1.080000e-79 307
15 TraesCS2D01G551300 chr2B 86.220 254 17 10 2243 2490 768547906 768547665 3.070000e-65 259
16 TraesCS2D01G551300 chr2B 84.889 225 23 6 2035 2256 768548140 768547924 1.870000e-52 217
17 TraesCS2D01G551300 chr2B 95.536 112 5 0 562 673 768549359 768549248 2.460000e-41 180
18 TraesCS2D01G551300 chr2B 92.857 112 8 0 673 784 768549698 768549587 2.480000e-36 163
19 TraesCS2D01G551300 chr1D 99.099 111 1 0 2990 3100 316784749 316784639 1.890000e-47 200


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 TraesCS2D01G551300 chr2D 627112494 627115596 3102 True 2026.333333 5731 96.428667 1 3103 3 chr2D.!!$R1 3102
1 TraesCS2D01G551300 chr2A 757805575 757808459 2884 True 523.250000 1764 93.397750 1 3090 8 chr2A.!!$R1 3089
2 TraesCS2D01G551300 chr2B 768547665 768550286 2621 True 473.875000 1120 90.744750 1 2490 8 chr2B.!!$R1 2489

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
211 232 0.039256 CATGTTGTGGTTCTTGCCCG 60.039 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2511 0.033504 AGCTATGGAATGTACCGCCG 59.966 55.0 0.0 0.0 0.0 6.46 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
81 82 3.822167 TGTCTGCTTGAAATCTTGCATGA 59.178 39.130 4.57 4.57 34.79 3.07
123 128 1.733402 TTGCACGGTTGGAAAGCTGG 61.733 55.000 0.00 0.00 43.41 4.85
142 147 1.615392 GGAGGTTTCACAAGCAAGCAT 59.385 47.619 0.00 0.00 32.36 3.79
211 232 0.039256 CATGTTGTGGTTCTTGCCCG 60.039 55.000 0.00 0.00 0.00 6.13
243 264 5.165961 TCCCTTTAGATTCACTCAGGTTG 57.834 43.478 0.00 0.00 31.00 3.77
258 279 7.611467 TCACTCAGGTTGCACTCATTTATTATT 59.389 33.333 0.00 0.00 0.00 1.40
303 330 3.694043 TGGTGTTGTGCTAGCTTGATA 57.306 42.857 17.23 0.00 0.00 2.15
325 352 8.257306 TGATATTTTTCTGGGGTATGCTTTTTC 58.743 33.333 0.00 0.00 0.00 2.29
390 417 4.178540 CCACATCTGCTTGCTATTTTTGG 58.821 43.478 0.00 0.00 0.00 3.28
431 460 0.984230 TCGGCTGATCACCTTTCCTT 59.016 50.000 11.12 0.00 0.00 3.36
434 463 1.203287 GGCTGATCACCTTTCCTTTGC 59.797 52.381 0.00 0.00 0.00 3.68
435 464 1.888512 GCTGATCACCTTTCCTTTGCA 59.111 47.619 0.00 0.00 0.00 4.08
462 491 7.328277 TGTATGAAAAATGGATTAGTTCGGG 57.672 36.000 0.00 0.00 0.00 5.14
465 494 6.902771 TGAAAAATGGATTAGTTCGGGAAA 57.097 33.333 0.00 0.00 0.00 3.13
466 495 6.919721 TGAAAAATGGATTAGTTCGGGAAAG 58.080 36.000 0.00 0.00 0.00 2.62
467 496 6.717540 TGAAAAATGGATTAGTTCGGGAAAGA 59.282 34.615 0.00 0.00 0.00 2.52
468 497 7.396055 TGAAAAATGGATTAGTTCGGGAAAGAT 59.604 33.333 0.00 0.00 0.00 2.40
469 498 6.699575 AAATGGATTAGTTCGGGAAAGATG 57.300 37.500 0.00 0.00 0.00 2.90
471 500 5.174037 TGGATTAGTTCGGGAAAGATGTT 57.826 39.130 0.00 0.00 0.00 2.71
472 501 6.302535 TGGATTAGTTCGGGAAAGATGTTA 57.697 37.500 0.00 0.00 0.00 2.41
482 513 9.717892 GTTCGGGAAAGATGTTATTAAAGAATC 57.282 33.333 0.00 0.00 0.00 2.52
496 527 4.961438 AAAGAATCAAGGGTTGCACATT 57.039 36.364 0.00 0.00 0.00 2.71
512 543 3.738899 GCACATTCATTGGGTAATGGCTG 60.739 47.826 0.00 0.00 43.11 4.85
513 544 3.033184 ACATTCATTGGGTAATGGCTGG 58.967 45.455 0.00 0.00 43.11 4.85
521 552 2.705658 TGGGTAATGGCTGGAGATGTAG 59.294 50.000 0.00 0.00 0.00 2.74
522 553 2.551071 GGGTAATGGCTGGAGATGTAGC 60.551 54.545 0.00 0.00 39.17 3.58
523 554 2.370189 GGTAATGGCTGGAGATGTAGCT 59.630 50.000 0.00 0.00 39.80 3.32
524 555 2.634815 AATGGCTGGAGATGTAGCTG 57.365 50.000 0.00 0.00 39.80 4.24
544 580 9.609950 GTAGCTGAGAGGTACTAATTAATTACG 57.390 37.037 3.71 4.02 43.69 3.18
546 582 6.365518 GCTGAGAGGTACTAATTAATTACGGC 59.634 42.308 3.71 5.31 41.55 5.68
547 583 6.752168 TGAGAGGTACTAATTAATTACGGCC 58.248 40.000 3.71 0.00 41.55 6.13
767 1031 3.722728 CCTTGATGAATTTAGGCTGGC 57.277 47.619 0.00 0.00 0.00 4.85
829 1095 2.023888 AGTGATAGTGGTAGGTCAGGCT 60.024 50.000 0.00 0.00 0.00 4.58
879 1145 7.923344 GTGCAGTATTAGATGATACTCAACACT 59.077 37.037 0.00 0.00 40.06 3.55
1109 1380 9.189723 GACCGTATGTCCTCTAATTTACATAAC 57.810 37.037 0.00 0.00 36.77 1.89
1180 1451 2.583520 CTGCAGAGAGCCCTGTCC 59.416 66.667 8.42 0.00 44.83 4.02
1415 1687 2.182537 GCCGCTTTTGCTCCATGG 59.817 61.111 4.97 4.97 44.80 3.66
1531 1806 3.425193 CCGAAATTCCTTTTGCAACTTCG 59.575 43.478 0.00 5.55 35.42 3.79
1535 1810 0.667993 TCCTTTTGCAACTTCGCAGG 59.332 50.000 0.00 0.00 44.14 4.85
1557 1832 5.012148 AGGTAGCTGGTATGGTATTGATGAC 59.988 44.000 0.00 0.00 0.00 3.06
1621 1896 3.320826 GGTTGGCAAACAAACCTGTCTAT 59.679 43.478 11.10 0.00 41.02 1.98
1622 1897 4.521256 GGTTGGCAAACAAACCTGTCTATA 59.479 41.667 11.10 0.00 41.02 1.31
1630 1905 6.560253 AACAAACCTGTCTATACTGCTTTG 57.440 37.500 5.11 5.11 36.73 2.77
1678 1953 1.605753 GATTCGGAACAATAGCCCCC 58.394 55.000 0.00 0.00 0.00 5.40
1702 1977 2.249309 CCCCCTTGTACTGGACTACT 57.751 55.000 6.99 0.00 0.00 2.57
1703 1978 1.831736 CCCCCTTGTACTGGACTACTG 59.168 57.143 6.99 0.00 0.00 2.74
1704 1979 2.537143 CCCCTTGTACTGGACTACTGT 58.463 52.381 6.99 0.00 35.29 3.55
1705 1980 2.904434 CCCCTTGTACTGGACTACTGTT 59.096 50.000 6.99 0.00 33.02 3.16
1706 1981 3.306780 CCCCTTGTACTGGACTACTGTTG 60.307 52.174 6.99 0.00 33.02 3.33
1707 1982 3.326747 CCTTGTACTGGACTACTGTTGC 58.673 50.000 0.00 0.00 33.02 4.17
1708 1983 3.326747 CTTGTACTGGACTACTGTTGCC 58.673 50.000 0.00 0.00 33.02 4.52
1709 1984 1.271379 TGTACTGGACTACTGTTGCCG 59.729 52.381 0.00 0.00 33.02 5.69
1710 1985 1.271656 GTACTGGACTACTGTTGCCGT 59.728 52.381 0.00 0.00 33.02 5.68
1711 1986 1.624336 ACTGGACTACTGTTGCCGTA 58.376 50.000 0.00 0.00 0.00 4.02
1712 1987 1.544691 ACTGGACTACTGTTGCCGTAG 59.455 52.381 0.00 0.00 40.07 3.51
1714 1989 1.965643 TGGACTACTGTTGCCGTAGTT 59.034 47.619 4.56 0.00 45.44 2.24
1715 1990 2.366266 TGGACTACTGTTGCCGTAGTTT 59.634 45.455 4.56 0.00 45.44 2.66
1716 1991 2.735134 GGACTACTGTTGCCGTAGTTTG 59.265 50.000 4.56 0.00 45.44 2.93
1717 1992 3.553508 GGACTACTGTTGCCGTAGTTTGA 60.554 47.826 4.56 0.00 45.44 2.69
1718 1993 4.243270 GACTACTGTTGCCGTAGTTTGAT 58.757 43.478 4.56 0.00 45.44 2.57
1752 2027 9.200817 ACCACTGGTGCTTATATTTATTTGAAT 57.799 29.630 0.00 0.00 32.98 2.57
1998 2274 3.743521 TGTTATGCTGAAGCTTGTCTGT 58.256 40.909 2.10 0.00 42.66 3.41
2026 2302 4.990543 TTGATCTGAGCTTTTACACACG 57.009 40.909 0.00 0.00 0.00 4.49
2027 2303 4.251543 TGATCTGAGCTTTTACACACGA 57.748 40.909 0.00 0.00 0.00 4.35
2028 2304 4.820897 TGATCTGAGCTTTTACACACGAT 58.179 39.130 0.00 0.00 0.00 3.73
2106 2467 2.284190 GCAAGGTGGAAGCATAGTCTC 58.716 52.381 0.00 0.00 36.26 3.36
2117 2491 7.010923 GTGGAAGCATAGTCTCTCTTTACATTG 59.989 40.741 0.00 0.00 0.00 2.82
2118 2492 6.481644 GGAAGCATAGTCTCTCTTTACATTGG 59.518 42.308 0.00 0.00 0.00 3.16
2119 2493 5.363939 AGCATAGTCTCTCTTTACATTGGC 58.636 41.667 0.00 0.00 0.00 4.52
2120 2494 4.210120 GCATAGTCTCTCTTTACATTGGCG 59.790 45.833 0.00 0.00 0.00 5.69
2121 2495 3.252974 AGTCTCTCTTTACATTGGCGG 57.747 47.619 0.00 0.00 0.00 6.13
2122 2496 1.666189 GTCTCTCTTTACATTGGCGGC 59.334 52.381 0.00 0.00 0.00 6.53
2123 2497 0.652592 CTCTCTTTACATTGGCGGCG 59.347 55.000 0.51 0.51 0.00 6.46
2124 2498 0.036765 TCTCTTTACATTGGCGGCGT 60.037 50.000 9.37 0.00 0.00 5.68
2125 2499 0.096976 CTCTTTACATTGGCGGCGTG 59.903 55.000 9.37 8.62 0.00 5.34
2126 2500 1.136565 CTTTACATTGGCGGCGTGG 59.863 57.895 9.37 5.70 0.00 4.94
2127 2501 2.265073 CTTTACATTGGCGGCGTGGG 62.265 60.000 9.37 4.02 0.00 4.61
2128 2502 2.749706 TTTACATTGGCGGCGTGGGA 62.750 55.000 9.37 3.71 0.00 4.37
2129 2503 3.961838 TACATTGGCGGCGTGGGAC 62.962 63.158 9.37 0.00 0.00 4.46
2183 2557 5.654497 ACCAGCTTTCTTTCTTTTCAGTTG 58.346 37.500 0.00 0.00 0.00 3.16
2211 2585 3.256704 TGTTTGGGGGAGATGAAGTACT 58.743 45.455 0.00 0.00 0.00 2.73
2212 2586 4.431378 TGTTTGGGGGAGATGAAGTACTA 58.569 43.478 0.00 0.00 0.00 1.82
2213 2587 4.469945 TGTTTGGGGGAGATGAAGTACTAG 59.530 45.833 0.00 0.00 0.00 2.57
2338 2746 1.348775 GGTGCTCCTTGGCCTCCTAT 61.349 60.000 3.32 0.00 0.00 2.57
2414 2826 2.111043 ACAGAGTGCCGTTGGTGG 59.889 61.111 0.00 0.00 0.00 4.61
2438 2850 2.357424 GATGATGAGTGCGCGCTGTG 62.357 60.000 30.98 0.00 0.00 3.66
2439 2851 3.114616 GATGAGTGCGCGCTGTGT 61.115 61.111 30.98 13.74 0.00 3.72
2440 2852 3.358667 GATGAGTGCGCGCTGTGTG 62.359 63.158 30.98 0.00 0.00 3.82
2451 2863 3.653009 CTGTGTGGGCGCACTGTG 61.653 66.667 30.85 17.77 39.89 3.66
2456 2868 4.994471 TGGGCGCACTGTGCTGAG 62.994 66.667 28.04 15.30 42.25 3.35
2459 2871 3.786586 GCGCACTGTGCTGAGCTC 61.787 66.667 28.04 6.82 42.25 4.09
2460 2872 2.048409 CGCACTGTGCTGAGCTCT 60.048 61.111 28.04 0.00 42.25 4.09
2461 2873 1.213799 CGCACTGTGCTGAGCTCTA 59.786 57.895 28.04 0.24 42.25 2.43
2462 2874 0.179116 CGCACTGTGCTGAGCTCTAT 60.179 55.000 28.04 0.00 42.25 1.98
2463 2875 1.288350 GCACTGTGCTGAGCTCTATG 58.712 55.000 24.68 6.14 40.96 2.23
2464 2876 1.937278 CACTGTGCTGAGCTCTATGG 58.063 55.000 16.19 3.91 0.00 2.74
2465 2877 0.829333 ACTGTGCTGAGCTCTATGGG 59.171 55.000 16.19 3.69 0.00 4.00
2466 2878 0.106335 CTGTGCTGAGCTCTATGGGG 59.894 60.000 16.19 0.00 0.00 4.96
2467 2879 1.340399 TGTGCTGAGCTCTATGGGGG 61.340 60.000 16.19 0.00 0.00 5.40
2468 2880 2.429494 GCTGAGCTCTATGGGGGC 59.571 66.667 16.19 4.34 0.00 5.80
2469 2881 2.446848 GCTGAGCTCTATGGGGGCA 61.447 63.158 16.19 0.00 0.00 5.36
2470 2882 1.753470 CTGAGCTCTATGGGGGCAG 59.247 63.158 16.19 0.00 0.00 4.85
2471 2883 1.003442 TGAGCTCTATGGGGGCAGT 59.997 57.895 16.19 0.00 0.00 4.40
2472 2884 0.621571 TGAGCTCTATGGGGGCAGTT 60.622 55.000 16.19 0.00 0.00 3.16
2473 2885 0.548510 GAGCTCTATGGGGGCAGTTT 59.451 55.000 6.43 0.00 0.00 2.66
2474 2886 0.548510 AGCTCTATGGGGGCAGTTTC 59.451 55.000 0.00 0.00 0.00 2.78
2475 2887 0.548510 GCTCTATGGGGGCAGTTTCT 59.451 55.000 0.00 0.00 0.00 2.52
2476 2888 1.475930 GCTCTATGGGGGCAGTTTCTC 60.476 57.143 0.00 0.00 0.00 2.87
2477 2889 1.141858 CTCTATGGGGGCAGTTTCTCC 59.858 57.143 0.00 0.00 0.00 3.71
2478 2890 1.216990 CTATGGGGGCAGTTTCTCCT 58.783 55.000 0.00 0.00 0.00 3.69
2479 2891 1.141858 CTATGGGGGCAGTTTCTCCTC 59.858 57.143 0.00 0.00 0.00 3.71
2480 2892 1.915078 ATGGGGGCAGTTTCTCCTCG 61.915 60.000 0.00 0.00 0.00 4.63
2481 2893 2.593956 GGGGGCAGTTTCTCCTCGT 61.594 63.158 0.00 0.00 0.00 4.18
2482 2894 1.375326 GGGGCAGTTTCTCCTCGTT 59.625 57.895 0.00 0.00 0.00 3.85
2483 2895 0.673956 GGGGCAGTTTCTCCTCGTTC 60.674 60.000 0.00 0.00 0.00 3.95
2484 2896 0.673956 GGGCAGTTTCTCCTCGTTCC 60.674 60.000 0.00 0.00 0.00 3.62
2485 2897 0.321996 GGCAGTTTCTCCTCGTTCCT 59.678 55.000 0.00 0.00 0.00 3.36
2486 2898 1.270893 GGCAGTTTCTCCTCGTTCCTT 60.271 52.381 0.00 0.00 0.00 3.36
2487 2899 2.070028 GCAGTTTCTCCTCGTTCCTTC 58.930 52.381 0.00 0.00 0.00 3.46
2488 2900 2.289133 GCAGTTTCTCCTCGTTCCTTCT 60.289 50.000 0.00 0.00 0.00 2.85
2489 2901 3.804063 GCAGTTTCTCCTCGTTCCTTCTT 60.804 47.826 0.00 0.00 0.00 2.52
2490 2902 4.381411 CAGTTTCTCCTCGTTCCTTCTTT 58.619 43.478 0.00 0.00 0.00 2.52
2491 2903 4.816925 CAGTTTCTCCTCGTTCCTTCTTTT 59.183 41.667 0.00 0.00 0.00 2.27
2492 2904 4.816925 AGTTTCTCCTCGTTCCTTCTTTTG 59.183 41.667 0.00 0.00 0.00 2.44
2493 2905 4.682778 TTCTCCTCGTTCCTTCTTTTGA 57.317 40.909 0.00 0.00 0.00 2.69
2494 2906 4.891992 TCTCCTCGTTCCTTCTTTTGAT 57.108 40.909 0.00 0.00 0.00 2.57
2495 2907 4.569943 TCTCCTCGTTCCTTCTTTTGATG 58.430 43.478 0.00 0.00 0.00 3.07
2496 2908 3.674997 TCCTCGTTCCTTCTTTTGATGG 58.325 45.455 0.00 0.00 43.04 3.51
2497 2909 3.326588 TCCTCGTTCCTTCTTTTGATGGA 59.673 43.478 0.00 0.00 46.88 3.41
2506 2918 7.316393 TCCTTCTTTTGATGGAAACTAGAGA 57.684 36.000 0.00 0.00 45.97 3.10
2507 2919 7.745717 TCCTTCTTTTGATGGAAACTAGAGAA 58.254 34.615 0.00 0.00 45.97 2.87
2508 2920 8.386264 TCCTTCTTTTGATGGAAACTAGAGAAT 58.614 33.333 0.00 0.00 45.97 2.40
2509 2921 8.457261 CCTTCTTTTGATGGAAACTAGAGAATG 58.543 37.037 0.00 0.00 44.04 2.67
2510 2922 7.928307 TCTTTTGATGGAAACTAGAGAATGG 57.072 36.000 0.00 0.00 0.00 3.16
2511 2923 7.689299 TCTTTTGATGGAAACTAGAGAATGGA 58.311 34.615 0.00 0.00 0.00 3.41
2512 2924 7.607991 TCTTTTGATGGAAACTAGAGAATGGAC 59.392 37.037 0.00 0.00 0.00 4.02
2513 2925 6.627087 TTGATGGAAACTAGAGAATGGACT 57.373 37.500 0.00 0.00 0.00 3.85
2514 2926 6.227298 TGATGGAAACTAGAGAATGGACTC 57.773 41.667 0.00 0.00 37.19 3.36
2515 2927 5.129485 TGATGGAAACTAGAGAATGGACTCC 59.871 44.000 0.00 0.00 37.60 3.85
2516 2928 4.425772 TGGAAACTAGAGAATGGACTCCA 58.574 43.478 0.00 0.00 37.60 3.86
2517 2929 4.223032 TGGAAACTAGAGAATGGACTCCAC 59.777 45.833 0.00 0.00 35.80 4.02
2518 2930 4.468153 GGAAACTAGAGAATGGACTCCACT 59.532 45.833 0.00 0.00 35.80 4.00
2519 2931 5.413309 AAACTAGAGAATGGACTCCACTG 57.587 43.478 0.00 0.00 35.80 3.66
2520 2932 3.370104 ACTAGAGAATGGACTCCACTGG 58.630 50.000 0.00 0.00 35.80 4.00
2521 2933 1.577736 AGAGAATGGACTCCACTGGG 58.422 55.000 0.00 0.00 35.80 4.45
2522 2934 1.079490 AGAGAATGGACTCCACTGGGA 59.921 52.381 0.00 0.00 42.29 4.37
2523 2935 1.909302 GAGAATGGACTCCACTGGGAA 59.091 52.381 0.00 0.00 44.38 3.97
2524 2936 2.305927 GAGAATGGACTCCACTGGGAAA 59.694 50.000 0.00 0.00 44.38 3.13
2525 2937 2.040412 AGAATGGACTCCACTGGGAAAC 59.960 50.000 0.00 0.00 44.38 2.78
2526 2938 1.444933 ATGGACTCCACTGGGAAACA 58.555 50.000 0.00 0.00 44.38 2.83
2527 2939 0.472471 TGGACTCCACTGGGAAACAC 59.528 55.000 0.00 0.00 44.38 3.32
2528 2940 0.765510 GGACTCCACTGGGAAACACT 59.234 55.000 0.00 0.00 44.38 3.55
2529 2941 1.543429 GGACTCCACTGGGAAACACTG 60.543 57.143 0.00 0.00 44.38 3.66
2530 2942 1.416401 GACTCCACTGGGAAACACTGA 59.584 52.381 0.00 0.00 44.38 3.41
2531 2943 1.417890 ACTCCACTGGGAAACACTGAG 59.582 52.381 0.00 0.00 44.38 3.35
2532 2944 0.108585 TCCACTGGGAAACACTGAGC 59.891 55.000 0.00 0.00 41.32 4.26
2533 2945 0.109342 CCACTGGGAAACACTGAGCT 59.891 55.000 0.00 0.00 35.59 4.09
2534 2946 1.233019 CACTGGGAAACACTGAGCTG 58.767 55.000 0.00 0.00 0.00 4.24
2535 2947 0.109342 ACTGGGAAACACTGAGCTGG 59.891 55.000 0.00 0.00 0.00 4.85
2536 2948 1.228245 TGGGAAACACTGAGCTGGC 60.228 57.895 0.00 0.00 0.00 4.85
2537 2949 1.073897 GGGAAACACTGAGCTGGCT 59.926 57.895 0.00 0.00 0.00 4.75
2538 2950 1.239968 GGGAAACACTGAGCTGGCTG 61.240 60.000 0.00 0.00 0.00 4.85
2539 2951 1.239968 GGAAACACTGAGCTGGCTGG 61.240 60.000 0.00 0.00 0.00 4.85
2540 2952 1.228367 AAACACTGAGCTGGCTGGG 60.228 57.895 0.00 0.00 0.00 4.45
2541 2953 1.999634 AAACACTGAGCTGGCTGGGT 62.000 55.000 0.00 0.00 0.00 4.51
2542 2954 1.127567 AACACTGAGCTGGCTGGGTA 61.128 55.000 0.00 0.00 0.00 3.69
2543 2955 1.127567 ACACTGAGCTGGCTGGGTAA 61.128 55.000 0.00 0.00 0.00 2.85
2544 2956 0.392193 CACTGAGCTGGCTGGGTAAG 60.392 60.000 0.00 0.00 0.00 2.34
2571 2983 3.569049 CTCGACGCGGGTTCAGGTT 62.569 63.158 12.47 0.00 0.00 3.50
2573 2985 2.029964 GACGCGGGTTCAGGTTCA 59.970 61.111 12.47 0.00 0.00 3.18
2574 2986 2.027625 GACGCGGGTTCAGGTTCAG 61.028 63.158 12.47 0.00 0.00 3.02
2575 2987 2.742372 CGCGGGTTCAGGTTCAGG 60.742 66.667 0.00 0.00 0.00 3.86
2576 2988 2.430367 GCGGGTTCAGGTTCAGGT 59.570 61.111 0.00 0.00 0.00 4.00
2577 2989 1.228154 GCGGGTTCAGGTTCAGGTT 60.228 57.895 0.00 0.00 0.00 3.50
2579 2991 0.107831 CGGGTTCAGGTTCAGGTTCA 59.892 55.000 0.00 0.00 0.00 3.18
2580 2992 1.878102 CGGGTTCAGGTTCAGGTTCAG 60.878 57.143 0.00 0.00 0.00 3.02
2581 2993 1.420138 GGGTTCAGGTTCAGGTTCAGA 59.580 52.381 0.00 0.00 0.00 3.27
2583 2995 3.263425 GGGTTCAGGTTCAGGTTCAGATA 59.737 47.826 0.00 0.00 0.00 1.98
2585 2997 3.868757 TCAGGTTCAGGTTCAGATACG 57.131 47.619 0.00 0.00 0.00 3.06
2586 2998 3.427573 TCAGGTTCAGGTTCAGATACGA 58.572 45.455 0.00 0.00 0.00 3.43
2587 2999 3.830178 TCAGGTTCAGGTTCAGATACGAA 59.170 43.478 0.00 0.00 0.00 3.85
2589 3001 3.576982 AGGTTCAGGTTCAGATACGAACA 59.423 43.478 6.19 0.00 45.82 3.18
2593 3071 2.028476 CAGGTTCAGATACGAACACCCA 60.028 50.000 6.19 0.00 45.82 4.51
2609 3087 4.431131 CACCCGCCTGCTCCCATT 62.431 66.667 0.00 0.00 0.00 3.16
2610 3088 2.690881 ACCCGCCTGCTCCCATTA 60.691 61.111 0.00 0.00 0.00 1.90
2612 3090 2.588877 CCGCCTGCTCCCATTACG 60.589 66.667 0.00 0.00 0.00 3.18
2616 3094 3.272334 CTGCTCCCATTACGCCGC 61.272 66.667 0.00 0.00 0.00 6.53
2617 3095 3.740128 CTGCTCCCATTACGCCGCT 62.740 63.158 0.00 0.00 0.00 5.52
2618 3096 2.513897 GCTCCCATTACGCCGCTT 60.514 61.111 0.00 0.00 0.00 4.68
2619 3097 2.112815 GCTCCCATTACGCCGCTTT 61.113 57.895 0.00 0.00 0.00 3.51
2620 3098 1.654023 GCTCCCATTACGCCGCTTTT 61.654 55.000 0.00 0.00 0.00 2.27
2621 3099 0.808755 CTCCCATTACGCCGCTTTTT 59.191 50.000 0.00 0.00 0.00 1.94
2622 3100 0.523966 TCCCATTACGCCGCTTTTTG 59.476 50.000 0.00 0.00 0.00 2.44
2623 3101 1.075979 CCCATTACGCCGCTTTTTGC 61.076 55.000 0.00 0.00 38.57 3.68
2624 3102 0.109319 CCATTACGCCGCTTTTTGCT 60.109 50.000 0.00 0.00 40.11 3.91
2625 3103 0.984109 CATTACGCCGCTTTTTGCTG 59.016 50.000 0.00 0.00 40.11 4.41
2626 3104 0.878416 ATTACGCCGCTTTTTGCTGA 59.122 45.000 0.00 0.00 40.11 4.26
2627 3105 0.040781 TTACGCCGCTTTTTGCTGAC 60.041 50.000 0.00 0.00 40.11 3.51
2628 3106 2.165362 TACGCCGCTTTTTGCTGACG 62.165 55.000 0.00 0.00 40.11 4.35
2629 3107 3.099574 GCCGCTTTTTGCTGACGC 61.100 61.111 0.00 0.00 40.11 5.19
2630 3108 2.429069 CCGCTTTTTGCTGACGCC 60.429 61.111 0.00 0.00 40.11 5.68
2631 3109 2.796617 CGCTTTTTGCTGACGCCG 60.797 61.111 0.00 0.00 40.11 6.46
2632 3110 3.099574 GCTTTTTGCTGACGCCGC 61.100 61.111 0.00 0.00 38.95 6.53
2633 3111 2.331098 CTTTTTGCTGACGCCGCA 59.669 55.556 0.00 0.00 35.22 5.69
2634 3112 1.727022 CTTTTTGCTGACGCCGCAG 60.727 57.895 4.51 4.51 38.80 5.18
2652 3130 2.336088 CGGTTGGCACAGCTTTGG 59.664 61.111 1.35 0.00 42.39 3.28
2674 3152 4.332637 GTGCGTGGCAGGCAGTTG 62.333 66.667 32.58 0.00 39.87 3.16
2675 3153 4.560743 TGCGTGGCAGGCAGTTGA 62.561 61.111 28.98 7.91 33.67 3.18
2676 3154 3.730761 GCGTGGCAGGCAGTTGAG 61.731 66.667 25.77 0.00 0.00 3.02
2677 3155 2.281070 CGTGGCAGGCAGTTGAGT 60.281 61.111 0.00 0.00 0.00 3.41
2678 3156 2.610694 CGTGGCAGGCAGTTGAGTG 61.611 63.158 0.00 0.00 0.00 3.51
2679 3157 2.595463 TGGCAGGCAGTTGAGTGC 60.595 61.111 2.18 2.18 43.19 4.40
2680 3158 2.282040 GGCAGGCAGTTGAGTGCT 60.282 61.111 10.36 0.00 43.45 4.40
2694 3172 3.767806 TGCTCTCTGCTCTGGCCG 61.768 66.667 0.00 0.00 43.37 6.13
2924 3406 0.744874 TCCAGCTCGAAATCTACCCG 59.255 55.000 0.00 0.00 0.00 5.28
2925 3407 0.249489 CCAGCTCGAAATCTACCCGG 60.249 60.000 0.00 0.00 0.00 5.73
2927 3409 1.594564 GCTCGAAATCTACCCGGCC 60.595 63.158 0.00 0.00 0.00 6.13
2930 3414 2.188469 GAAATCTACCCGGCCGCA 59.812 61.111 22.85 5.81 0.00 5.69
3010 3494 2.192861 CAAAAGCACCTGCCCGTGA 61.193 57.895 4.54 0.00 43.38 4.35
3013 3497 4.643387 AGCACCTGCCCGTGAACC 62.643 66.667 4.54 0.00 43.38 3.62
3042 3526 1.202382 GCCAACGATTCTACGCTACCT 60.202 52.381 0.00 0.00 36.70 3.08
3057 3541 2.930682 GCTACCTCAAACTGACGGATTC 59.069 50.000 0.00 0.00 0.00 2.52
3061 3545 2.996621 CCTCAAACTGACGGATTCTGTC 59.003 50.000 17.16 17.16 35.44 3.51
3062 3546 2.996621 CTCAAACTGACGGATTCTGTCC 59.003 50.000 20.33 5.83 44.10 4.02
3091 3575 3.431725 CCGTCCGGCCTCTTTTGC 61.432 66.667 0.00 0.00 0.00 3.68
3092 3576 3.788766 CGTCCGGCCTCTTTTGCG 61.789 66.667 0.00 0.00 0.00 4.85
3093 3577 2.358247 GTCCGGCCTCTTTTGCGA 60.358 61.111 0.00 0.00 0.00 5.10
3094 3578 1.745489 GTCCGGCCTCTTTTGCGAT 60.745 57.895 0.00 0.00 0.00 4.58
3095 3579 0.461339 GTCCGGCCTCTTTTGCGATA 60.461 55.000 0.00 0.00 0.00 2.92
3096 3580 0.250793 TCCGGCCTCTTTTGCGATAA 59.749 50.000 0.00 0.00 0.00 1.75
3097 3581 0.377203 CCGGCCTCTTTTGCGATAAC 59.623 55.000 0.00 0.00 0.00 1.89
3098 3582 0.026285 CGGCCTCTTTTGCGATAACG 59.974 55.000 0.00 0.00 42.93 3.18
3099 3583 1.084289 GGCCTCTTTTGCGATAACGT 58.916 50.000 0.00 0.00 41.98 3.99
3100 3584 2.273557 GGCCTCTTTTGCGATAACGTA 58.726 47.619 0.00 0.00 41.98 3.57
3101 3585 2.284417 GGCCTCTTTTGCGATAACGTAG 59.716 50.000 0.00 0.00 41.98 3.51
3102 3586 2.284417 GCCTCTTTTGCGATAACGTAGG 59.716 50.000 0.00 0.00 41.98 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.161855 TCCACATTTGACACATGCTCC 58.838 47.619 1.40 0.00 0.00 4.70
81 82 2.301009 CAAGCAAGCAAGATCCCCTTTT 59.699 45.455 0.00 0.00 31.42 2.27
123 128 2.669364 CATGCTTGCTTGTGAAACCTC 58.331 47.619 1.03 0.00 34.36 3.85
142 147 2.666272 TCACAAACAACCTATGGGCA 57.334 45.000 0.00 0.00 35.63 5.36
172 193 2.038689 TGCCACCAACCGTTGAGTATTA 59.961 45.455 13.04 0.00 0.00 0.98
211 232 6.207614 AGTGAATCTAAAGGGAAAGAGCAAAC 59.792 38.462 0.00 0.00 0.00 2.93
243 264 8.707938 AAAGGAAGCAAATAATAAATGAGTGC 57.292 30.769 0.00 0.00 0.00 4.40
258 279 7.288810 ACTACATTCATGAAAAAGGAAGCAA 57.711 32.000 13.09 0.00 30.90 3.91
303 330 6.466812 CAGAAAAAGCATACCCCAGAAAAAT 58.533 36.000 0.00 0.00 0.00 1.82
325 352 0.739462 TGCAGTAAATCGCCGTCCAG 60.739 55.000 0.00 0.00 0.00 3.86
390 417 6.214399 CGACTCTGTAATAACAATACCCCTC 58.786 44.000 0.00 0.00 34.49 4.30
456 485 9.717892 GATTCTTTAATAACATCTTTCCCGAAC 57.282 33.333 0.00 0.00 0.00 3.95
465 494 8.470002 GCAACCCTTGATTCTTTAATAACATCT 58.530 33.333 0.00 0.00 0.00 2.90
466 495 8.250332 TGCAACCCTTGATTCTTTAATAACATC 58.750 33.333 0.00 0.00 0.00 3.06
467 496 8.034804 GTGCAACCCTTGATTCTTTAATAACAT 58.965 33.333 0.00 0.00 0.00 2.71
468 497 7.014711 TGTGCAACCCTTGATTCTTTAATAACA 59.985 33.333 0.00 0.00 34.36 2.41
469 498 7.375053 TGTGCAACCCTTGATTCTTTAATAAC 58.625 34.615 0.00 0.00 34.36 1.89
471 500 7.716799 ATGTGCAACCCTTGATTCTTTAATA 57.283 32.000 0.00 0.00 34.36 0.98
472 501 6.610075 ATGTGCAACCCTTGATTCTTTAAT 57.390 33.333 0.00 0.00 34.36 1.40
482 513 2.613474 CCCAATGAATGTGCAACCCTTG 60.613 50.000 0.00 0.00 34.36 3.61
496 527 2.204463 TCTCCAGCCATTACCCAATGA 58.796 47.619 0.00 0.00 43.67 2.57
512 543 3.827722 AGTACCTCTCAGCTACATCTCC 58.172 50.000 0.00 0.00 0.00 3.71
513 544 7.519032 AATTAGTACCTCTCAGCTACATCTC 57.481 40.000 0.00 0.00 0.00 2.75
521 552 6.365518 GCCGTAATTAATTAGTACCTCTCAGC 59.634 42.308 8.18 0.00 0.00 4.26
522 553 6.867293 GGCCGTAATTAATTAGTACCTCTCAG 59.133 42.308 8.18 0.00 0.00 3.35
523 554 6.552350 AGGCCGTAATTAATTAGTACCTCTCA 59.448 38.462 8.18 0.00 0.00 3.27
524 555 6.990798 AGGCCGTAATTAATTAGTACCTCTC 58.009 40.000 8.18 0.00 0.00 3.20
544 580 2.993220 CGAAAGCAAACCAAATTAGGCC 59.007 45.455 0.00 0.00 0.00 5.19
627 663 1.742761 ATTCATCAAGGCACCAGACG 58.257 50.000 0.00 0.00 0.00 4.18
809 1075 2.389715 AGCCTGACCTACCACTATCAC 58.610 52.381 0.00 0.00 0.00 3.06
829 1095 1.063070 TGGAGGGGGTGCACTAACAA 61.063 55.000 17.98 0.00 0.00 2.83
879 1145 3.495983 CCCCAGCAACCGATATGATTACA 60.496 47.826 0.00 0.00 0.00 2.41
956 1222 7.520453 GCAACAAAAGTCTGATCAATACAGTGA 60.520 37.037 0.00 0.00 36.81 3.41
1086 1353 9.454585 TTCGTTATGTAAATTAGAGGACATACG 57.545 33.333 0.00 0.00 35.16 3.06
1109 1380 3.009301 ACTACTGAACCTTCGTGTTCG 57.991 47.619 9.46 7.57 46.04 3.95
1180 1451 2.182537 CGGTTCGGACCCTTACGG 59.817 66.667 7.48 0.00 43.42 4.02
1192 1463 4.856607 CTCCTCTCCGCGCGGTTC 62.857 72.222 44.16 0.00 36.47 3.62
1361 1633 6.867816 GGATCTTGCAATTATGTGTCACAAAA 59.132 34.615 10.28 0.00 0.00 2.44
1396 1668 1.153901 CATGGAGCAAAAGCGGCTG 60.154 57.895 1.81 0.00 42.78 4.85
1415 1687 9.669353 CAGGTTAATGCTCAAAATATGTATGTC 57.331 33.333 0.00 0.00 0.00 3.06
1531 1806 3.071023 TCAATACCATACCAGCTACCTGC 59.929 47.826 0.00 0.00 43.29 4.85
1535 1810 6.102897 AGTCATCAATACCATACCAGCTAC 57.897 41.667 0.00 0.00 0.00 3.58
1630 1905 8.783833 AATTGACTGTGTGGATATATATGCTC 57.216 34.615 14.48 11.54 0.00 4.26
1642 1917 3.424829 CGAATCGGAAATTGACTGTGTGG 60.425 47.826 0.00 0.00 0.00 4.17
1683 1958 1.831736 CAGTAGTCCAGTACAAGGGGG 59.168 57.143 0.00 0.00 0.00 5.40
1685 1960 3.864921 GCAACAGTAGTCCAGTACAAGGG 60.865 52.174 0.00 0.00 0.00 3.95
1686 1961 3.326747 GCAACAGTAGTCCAGTACAAGG 58.673 50.000 0.00 0.00 0.00 3.61
1688 1963 2.288579 CGGCAACAGTAGTCCAGTACAA 60.289 50.000 0.00 0.00 0.00 2.41
1689 1964 1.271379 CGGCAACAGTAGTCCAGTACA 59.729 52.381 0.00 0.00 0.00 2.90
1690 1965 1.271656 ACGGCAACAGTAGTCCAGTAC 59.728 52.381 0.00 0.00 0.00 2.73
1691 1966 1.624336 ACGGCAACAGTAGTCCAGTA 58.376 50.000 0.00 0.00 0.00 2.74
1692 1967 1.544691 CTACGGCAACAGTAGTCCAGT 59.455 52.381 0.00 0.00 38.23 4.00
1693 1968 1.544691 ACTACGGCAACAGTAGTCCAG 59.455 52.381 4.95 0.00 46.49 3.86
1694 1969 1.624336 ACTACGGCAACAGTAGTCCA 58.376 50.000 4.95 0.00 46.49 4.02
1698 1973 5.408356 ACTATCAAACTACGGCAACAGTAG 58.592 41.667 3.77 3.77 44.11 2.57
1699 1974 5.395682 ACTATCAAACTACGGCAACAGTA 57.604 39.130 0.00 0.00 0.00 2.74
1700 1975 4.267349 ACTATCAAACTACGGCAACAGT 57.733 40.909 0.00 0.00 0.00 3.55
1701 1976 6.903883 ATTACTATCAAACTACGGCAACAG 57.096 37.500 0.00 0.00 0.00 3.16
1702 1977 7.278424 GGTTATTACTATCAAACTACGGCAACA 59.722 37.037 0.00 0.00 0.00 3.33
1703 1978 7.278424 TGGTTATTACTATCAAACTACGGCAAC 59.722 37.037 0.00 0.00 0.00 4.17
1704 1979 7.278424 GTGGTTATTACTATCAAACTACGGCAA 59.722 37.037 0.00 0.00 0.00 4.52
1705 1980 6.757947 GTGGTTATTACTATCAAACTACGGCA 59.242 38.462 0.00 0.00 0.00 5.69
1706 1981 6.982724 AGTGGTTATTACTATCAAACTACGGC 59.017 38.462 0.00 0.00 38.08 5.68
1707 1982 7.437267 CCAGTGGTTATTACTATCAAACTACGG 59.563 40.741 0.00 0.00 38.08 4.02
1708 1983 7.977853 ACCAGTGGTTATTACTATCAAACTACG 59.022 37.037 9.70 0.00 38.08 3.51
1709 1984 9.095065 CACCAGTGGTTATTACTATCAAACTAC 57.905 37.037 13.62 0.00 31.02 2.73
1710 1985 7.767198 GCACCAGTGGTTATTACTATCAAACTA 59.233 37.037 13.62 0.00 31.02 2.24
1711 1986 6.598064 GCACCAGTGGTTATTACTATCAAACT 59.402 38.462 13.62 0.00 31.02 2.66
1712 1987 6.598064 AGCACCAGTGGTTATTACTATCAAAC 59.402 38.462 13.62 0.00 38.24 2.93
1713 1988 6.717289 AGCACCAGTGGTTATTACTATCAAA 58.283 36.000 13.62 0.00 38.24 2.69
1714 1989 6.308015 AGCACCAGTGGTTATTACTATCAA 57.692 37.500 13.62 0.00 38.24 2.57
1715 1990 5.950544 AGCACCAGTGGTTATTACTATCA 57.049 39.130 13.62 0.00 38.24 2.15
1758 2033 1.734465 GAGATGGCACAACTGCAGTAC 59.266 52.381 22.01 10.06 43.03 2.73
1998 2274 3.795688 AAAGCTCAGATCAAACCAGGA 57.204 42.857 0.00 0.00 0.00 3.86
2026 2302 0.524392 CACGCTCGACCTGTCAGATC 60.524 60.000 0.00 0.00 0.00 2.75
2027 2303 1.508545 CACGCTCGACCTGTCAGAT 59.491 57.895 0.00 0.00 0.00 2.90
2028 2304 2.626780 CCACGCTCGACCTGTCAGA 61.627 63.158 0.00 0.00 0.00 3.27
2106 2467 0.096976 CACGCCGCCAATGTAAAGAG 59.903 55.000 0.00 0.00 0.00 2.85
2137 2511 0.033504 AGCTATGGAATGTACCGCCG 59.966 55.000 0.00 0.00 0.00 6.46
2183 2557 1.408969 TCTCCCCCAAACAAAGCAAC 58.591 50.000 0.00 0.00 0.00 4.17
2211 2585 6.552629 GCATCGCTATAATGCTACAGTACTA 58.447 40.000 0.00 0.00 44.83 1.82
2212 2586 5.403246 GCATCGCTATAATGCTACAGTACT 58.597 41.667 0.00 0.00 44.83 2.73
2213 2587 5.688348 GCATCGCTATAATGCTACAGTAC 57.312 43.478 1.00 0.00 44.83 2.73
2367 2775 3.195610 TCACACTGTCACACACTCTTTCT 59.804 43.478 0.00 0.00 0.00 2.52
2414 2826 0.231534 CGCGCACTCATCATCATCAC 59.768 55.000 8.75 0.00 0.00 3.06
2444 2856 1.288350 CATAGAGCTCAGCACAGTGC 58.712 55.000 18.55 18.55 45.46 4.40
2445 2857 1.472904 CCCATAGAGCTCAGCACAGTG 60.473 57.143 17.77 0.00 0.00 3.66
2446 2858 0.829333 CCCATAGAGCTCAGCACAGT 59.171 55.000 17.77 0.00 0.00 3.55
2447 2859 0.106335 CCCCATAGAGCTCAGCACAG 59.894 60.000 17.77 0.00 0.00 3.66
2448 2860 1.340399 CCCCCATAGAGCTCAGCACA 61.340 60.000 17.77 0.00 0.00 4.57
2449 2861 1.449353 CCCCCATAGAGCTCAGCAC 59.551 63.158 17.77 0.00 0.00 4.40
2450 2862 2.446848 GCCCCCATAGAGCTCAGCA 61.447 63.158 17.77 0.23 0.00 4.41
2451 2863 2.394565 CTGCCCCCATAGAGCTCAGC 62.395 65.000 17.77 7.24 0.00 4.26
2452 2864 1.053264 ACTGCCCCCATAGAGCTCAG 61.053 60.000 17.77 4.03 0.00 3.35
2453 2865 0.621571 AACTGCCCCCATAGAGCTCA 60.622 55.000 17.77 2.09 0.00 4.26
2454 2866 0.548510 AAACTGCCCCCATAGAGCTC 59.451 55.000 5.27 5.27 0.00 4.09
2455 2867 0.548510 GAAACTGCCCCCATAGAGCT 59.451 55.000 0.00 0.00 0.00 4.09
2456 2868 0.548510 AGAAACTGCCCCCATAGAGC 59.451 55.000 0.00 0.00 0.00 4.09
2457 2869 1.141858 GGAGAAACTGCCCCCATAGAG 59.858 57.143 0.00 0.00 0.00 2.43
2458 2870 1.213296 GGAGAAACTGCCCCCATAGA 58.787 55.000 0.00 0.00 0.00 1.98
2459 2871 1.141858 GAGGAGAAACTGCCCCCATAG 59.858 57.143 0.00 0.00 0.00 2.23
2460 2872 1.213296 GAGGAGAAACTGCCCCCATA 58.787 55.000 0.00 0.00 0.00 2.74
2461 2873 1.915078 CGAGGAGAAACTGCCCCCAT 61.915 60.000 0.00 0.00 0.00 4.00
2462 2874 2.592993 CGAGGAGAAACTGCCCCCA 61.593 63.158 0.00 0.00 0.00 4.96
2463 2875 2.125766 AACGAGGAGAAACTGCCCCC 62.126 60.000 0.00 0.00 0.00 5.40
2464 2876 0.673956 GAACGAGGAGAAACTGCCCC 60.674 60.000 0.00 0.00 0.00 5.80
2465 2877 0.673956 GGAACGAGGAGAAACTGCCC 60.674 60.000 0.00 0.00 0.00 5.36
2466 2878 0.321996 AGGAACGAGGAGAAACTGCC 59.678 55.000 0.00 0.00 0.00 4.85
2467 2879 2.070028 GAAGGAACGAGGAGAAACTGC 58.930 52.381 0.00 0.00 0.00 4.40
2468 2880 3.669251 AGAAGGAACGAGGAGAAACTG 57.331 47.619 0.00 0.00 0.00 3.16
2469 2881 4.691326 AAAGAAGGAACGAGGAGAAACT 57.309 40.909 0.00 0.00 0.00 2.66
2470 2882 4.814771 TCAAAAGAAGGAACGAGGAGAAAC 59.185 41.667 0.00 0.00 0.00 2.78
2471 2883 5.031066 TCAAAAGAAGGAACGAGGAGAAA 57.969 39.130 0.00 0.00 0.00 2.52
2472 2884 4.682778 TCAAAAGAAGGAACGAGGAGAA 57.317 40.909 0.00 0.00 0.00 2.87
2473 2885 4.563580 CCATCAAAAGAAGGAACGAGGAGA 60.564 45.833 0.00 0.00 0.00 3.71
2474 2886 3.686726 CCATCAAAAGAAGGAACGAGGAG 59.313 47.826 0.00 0.00 0.00 3.69
2475 2887 3.326588 TCCATCAAAAGAAGGAACGAGGA 59.673 43.478 0.00 0.00 0.00 3.71
2476 2888 3.674997 TCCATCAAAAGAAGGAACGAGG 58.325 45.455 0.00 0.00 0.00 4.63
2477 2889 5.239525 AGTTTCCATCAAAAGAAGGAACGAG 59.760 40.000 2.03 0.00 39.69 4.18
2478 2890 5.130350 AGTTTCCATCAAAAGAAGGAACGA 58.870 37.500 2.03 0.00 39.69 3.85
2479 2891 5.438761 AGTTTCCATCAAAAGAAGGAACG 57.561 39.130 2.03 0.00 39.69 3.95
2480 2892 7.661847 TCTCTAGTTTCCATCAAAAGAAGGAAC 59.338 37.037 2.03 0.00 39.69 3.62
2481 2893 7.745717 TCTCTAGTTTCCATCAAAAGAAGGAA 58.254 34.615 0.00 0.00 38.31 3.36
2482 2894 7.316393 TCTCTAGTTTCCATCAAAAGAAGGA 57.684 36.000 0.00 0.00 0.00 3.36
2483 2895 7.986085 TTCTCTAGTTTCCATCAAAAGAAGG 57.014 36.000 0.00 0.00 0.00 3.46
2484 2896 8.457261 CCATTCTCTAGTTTCCATCAAAAGAAG 58.543 37.037 0.00 0.00 0.00 2.85
2485 2897 8.163408 TCCATTCTCTAGTTTCCATCAAAAGAA 58.837 33.333 0.00 0.00 0.00 2.52
2486 2898 7.607991 GTCCATTCTCTAGTTTCCATCAAAAGA 59.392 37.037 0.00 0.00 0.00 2.52
2487 2899 7.609532 AGTCCATTCTCTAGTTTCCATCAAAAG 59.390 37.037 0.00 0.00 0.00 2.27
2488 2900 7.461749 AGTCCATTCTCTAGTTTCCATCAAAA 58.538 34.615 0.00 0.00 0.00 2.44
2489 2901 7.020827 AGTCCATTCTCTAGTTTCCATCAAA 57.979 36.000 0.00 0.00 0.00 2.69
2490 2902 6.352222 GGAGTCCATTCTCTAGTTTCCATCAA 60.352 42.308 3.60 0.00 35.11 2.57
2491 2903 5.129485 GGAGTCCATTCTCTAGTTTCCATCA 59.871 44.000 3.60 0.00 35.11 3.07
2492 2904 5.129485 TGGAGTCCATTCTCTAGTTTCCATC 59.871 44.000 8.12 0.00 35.11 3.51
2493 2905 5.032846 TGGAGTCCATTCTCTAGTTTCCAT 58.967 41.667 8.12 0.00 35.11 3.41
2494 2906 4.223032 GTGGAGTCCATTCTCTAGTTTCCA 59.777 45.833 16.67 0.00 35.28 3.53
2495 2907 4.468153 AGTGGAGTCCATTCTCTAGTTTCC 59.532 45.833 16.67 0.00 35.28 3.13
2496 2908 5.415221 CAGTGGAGTCCATTCTCTAGTTTC 58.585 45.833 16.67 0.00 35.28 2.78
2497 2909 4.223923 CCAGTGGAGTCCATTCTCTAGTTT 59.776 45.833 16.67 0.00 35.28 2.66
2498 2910 3.772025 CCAGTGGAGTCCATTCTCTAGTT 59.228 47.826 16.67 0.00 35.28 2.24
2499 2911 3.370104 CCAGTGGAGTCCATTCTCTAGT 58.630 50.000 16.67 0.00 35.28 2.57
2500 2912 2.697751 CCCAGTGGAGTCCATTCTCTAG 59.302 54.545 16.67 0.38 35.28 2.43
2501 2913 2.314852 TCCCAGTGGAGTCCATTCTCTA 59.685 50.000 16.67 0.00 35.28 2.43
2502 2914 1.079490 TCCCAGTGGAGTCCATTCTCT 59.921 52.381 16.67 4.50 35.28 3.10
2503 2915 1.573108 TCCCAGTGGAGTCCATTCTC 58.427 55.000 16.67 1.77 35.28 2.87
2504 2916 2.040412 GTTTCCCAGTGGAGTCCATTCT 59.960 50.000 16.67 5.73 43.07 2.40
2505 2917 2.224769 TGTTTCCCAGTGGAGTCCATTC 60.225 50.000 16.67 3.02 43.07 2.67
2506 2918 1.780309 TGTTTCCCAGTGGAGTCCATT 59.220 47.619 16.67 8.56 43.07 3.16
2507 2919 1.073923 GTGTTTCCCAGTGGAGTCCAT 59.926 52.381 16.67 1.47 43.07 3.41
2508 2920 0.472471 GTGTTTCCCAGTGGAGTCCA 59.528 55.000 11.95 8.12 43.07 4.02
2509 2921 0.765510 AGTGTTTCCCAGTGGAGTCC 59.234 55.000 11.95 0.73 43.07 3.85
2510 2922 1.416401 TCAGTGTTTCCCAGTGGAGTC 59.584 52.381 11.95 0.00 43.52 3.36
2511 2923 1.417890 CTCAGTGTTTCCCAGTGGAGT 59.582 52.381 11.95 0.00 43.52 3.85
2512 2924 1.879796 GCTCAGTGTTTCCCAGTGGAG 60.880 57.143 11.95 0.34 43.52 3.86
2513 2925 0.108585 GCTCAGTGTTTCCCAGTGGA 59.891 55.000 11.95 0.00 43.52 4.02
2514 2926 0.109342 AGCTCAGTGTTTCCCAGTGG 59.891 55.000 0.63 0.63 43.52 4.00
2515 2927 1.233019 CAGCTCAGTGTTTCCCAGTG 58.767 55.000 0.00 0.00 44.51 3.66
2516 2928 0.109342 CCAGCTCAGTGTTTCCCAGT 59.891 55.000 0.00 0.00 0.00 4.00
2517 2929 1.239968 GCCAGCTCAGTGTTTCCCAG 61.240 60.000 0.00 0.00 0.00 4.45
2518 2930 1.228245 GCCAGCTCAGTGTTTCCCA 60.228 57.895 0.00 0.00 0.00 4.37
2519 2931 1.073897 AGCCAGCTCAGTGTTTCCC 59.926 57.895 0.00 0.00 0.00 3.97
2520 2932 1.239968 CCAGCCAGCTCAGTGTTTCC 61.240 60.000 0.00 0.00 0.00 3.13
2521 2933 1.239968 CCCAGCCAGCTCAGTGTTTC 61.240 60.000 0.00 0.00 0.00 2.78
2522 2934 1.228367 CCCAGCCAGCTCAGTGTTT 60.228 57.895 0.00 0.00 0.00 2.83
2523 2935 1.127567 TACCCAGCCAGCTCAGTGTT 61.128 55.000 0.00 0.00 0.00 3.32
2524 2936 1.127567 TTACCCAGCCAGCTCAGTGT 61.128 55.000 0.00 0.00 0.00 3.55
2525 2937 0.392193 CTTACCCAGCCAGCTCAGTG 60.392 60.000 0.00 0.00 0.00 3.66
2526 2938 1.986413 CTTACCCAGCCAGCTCAGT 59.014 57.895 0.00 0.00 0.00 3.41
2527 2939 1.451028 GCTTACCCAGCCAGCTCAG 60.451 63.158 0.00 0.00 43.65 3.35
2528 2940 2.671070 GCTTACCCAGCCAGCTCA 59.329 61.111 0.00 0.00 43.65 4.26
2535 2947 0.895559 AGCAACTTGGCTTACCCAGC 60.896 55.000 0.00 0.00 46.39 4.85
2536 2948 1.168714 GAGCAACTTGGCTTACCCAG 58.831 55.000 0.00 0.00 46.39 4.45
2537 2949 0.605319 CGAGCAACTTGGCTTACCCA 60.605 55.000 0.00 0.00 45.99 4.51
2538 2950 0.321298 TCGAGCAACTTGGCTTACCC 60.321 55.000 0.00 0.00 45.99 3.69
2539 2951 0.796927 GTCGAGCAACTTGGCTTACC 59.203 55.000 0.00 0.00 45.99 2.85
2540 2952 0.438830 CGTCGAGCAACTTGGCTTAC 59.561 55.000 0.00 0.00 45.99 2.34
2541 2953 1.289109 GCGTCGAGCAACTTGGCTTA 61.289 55.000 0.00 0.00 45.99 3.09
2542 2954 2.607892 GCGTCGAGCAACTTGGCTT 61.608 57.895 0.00 0.00 45.99 4.35
2569 2981 3.678548 GGTGTTCGTATCTGAACCTGAAC 59.321 47.826 4.37 7.87 46.04 3.18
2571 2983 2.232941 GGGTGTTCGTATCTGAACCTGA 59.767 50.000 4.37 0.00 46.04 3.86
2573 2985 2.028385 GTGGGTGTTCGTATCTGAACCT 60.028 50.000 4.37 0.00 46.04 3.50
2574 2986 2.344025 GTGGGTGTTCGTATCTGAACC 58.656 52.381 4.37 0.00 46.04 3.62
2575 2987 2.344025 GGTGGGTGTTCGTATCTGAAC 58.656 52.381 0.00 0.00 46.63 3.18
2576 2988 1.276989 GGGTGGGTGTTCGTATCTGAA 59.723 52.381 0.00 0.00 0.00 3.02
2577 2989 0.899720 GGGTGGGTGTTCGTATCTGA 59.100 55.000 0.00 0.00 0.00 3.27
2579 2991 1.895238 CGGGTGGGTGTTCGTATCT 59.105 57.895 0.00 0.00 0.00 1.98
2580 2992 1.812507 GCGGGTGGGTGTTCGTATC 60.813 63.158 0.00 0.00 0.00 2.24
2581 2993 2.266689 GCGGGTGGGTGTTCGTAT 59.733 61.111 0.00 0.00 0.00 3.06
2593 3071 2.690881 TAATGGGAGCAGGCGGGT 60.691 61.111 0.00 0.00 0.00 5.28
2604 3082 1.075979 GCAAAAAGCGGCGTAATGGG 61.076 55.000 9.37 0.00 0.00 4.00
2605 3083 2.358791 GCAAAAAGCGGCGTAATGG 58.641 52.632 9.37 0.00 0.00 3.16
2632 3110 2.848858 AAAGCTGTGCCAACCGCTG 61.849 57.895 0.00 0.00 45.03 5.18
2634 3112 2.355009 CAAAGCTGTGCCAACCGC 60.355 61.111 0.00 0.00 36.83 5.68
2635 3113 2.336088 CCAAAGCTGTGCCAACCG 59.664 61.111 0.00 0.00 0.00 4.44
2636 3114 2.029518 GCCAAAGCTGTGCCAACC 59.970 61.111 0.00 0.00 35.50 3.77
2637 3115 1.300388 CTGCCAAAGCTGTGCCAAC 60.300 57.895 0.00 0.00 40.80 3.77
2638 3116 2.500714 CCTGCCAAAGCTGTGCCAA 61.501 57.895 0.00 0.00 40.80 4.52
2639 3117 2.913578 CCTGCCAAAGCTGTGCCA 60.914 61.111 0.00 0.00 40.80 4.92
2640 3118 3.688159 CCCTGCCAAAGCTGTGCC 61.688 66.667 0.00 0.00 40.80 5.01
2641 3119 2.914097 ACCCTGCCAAAGCTGTGC 60.914 61.111 0.00 0.00 40.80 4.57
2642 3120 3.045142 CACCCTGCCAAAGCTGTG 58.955 61.111 0.00 0.00 40.80 3.66
2643 3121 2.914097 GCACCCTGCCAAAGCTGT 60.914 61.111 0.00 0.00 37.42 4.40
2644 3122 4.047059 CGCACCCTGCCAAAGCTG 62.047 66.667 0.00 0.00 41.12 4.24
2645 3123 4.586235 ACGCACCCTGCCAAAGCT 62.586 61.111 0.00 0.00 41.12 3.74
2646 3124 4.347453 CACGCACCCTGCCAAAGC 62.347 66.667 0.00 0.00 41.12 3.51
2647 3125 3.673484 CCACGCACCCTGCCAAAG 61.673 66.667 0.00 0.00 41.12 2.77
2667 3145 1.297456 GCAGAGAGCACTCAACTGCC 61.297 60.000 25.36 14.97 46.14 4.85
2668 3146 2.160946 GCAGAGAGCACTCAACTGC 58.839 57.895 23.34 23.34 45.99 4.40
2678 3156 4.527583 CCGGCCAGAGCAGAGAGC 62.528 72.222 2.24 0.00 42.56 4.09
2679 3157 2.654079 AACCGGCCAGAGCAGAGAG 61.654 63.158 0.00 0.00 42.56 3.20
2680 3158 2.604686 AACCGGCCAGAGCAGAGA 60.605 61.111 0.00 0.00 42.56 3.10
2745 3223 0.942252 AGGAAAAAGTTGACGGCGTC 59.058 50.000 31.68 31.68 0.00 5.19
2750 3228 2.159310 TGCCAACAGGAAAAAGTTGACG 60.159 45.455 6.85 0.00 46.01 4.35
2752 3230 3.096092 AGTGCCAACAGGAAAAAGTTGA 58.904 40.909 6.85 0.00 46.01 3.18
2754 3232 3.096092 TGAGTGCCAACAGGAAAAAGTT 58.904 40.909 0.00 0.00 0.00 2.66
2902 3384 3.606687 GGGTAGATTTCGAGCTGGAAAA 58.393 45.455 24.91 8.73 39.19 2.29
2905 3387 0.744874 CGGGTAGATTTCGAGCTGGA 59.255 55.000 0.00 0.00 0.00 3.86
2910 3392 1.299926 CGGCCGGGTAGATTTCGAG 60.300 63.158 20.10 0.00 0.00 4.04
2911 3393 2.809706 CGGCCGGGTAGATTTCGA 59.190 61.111 20.10 0.00 0.00 3.71
2912 3394 2.965462 GCGGCCGGGTAGATTTCG 60.965 66.667 29.38 0.00 0.00 3.46
2913 3395 1.436983 CTTGCGGCCGGGTAGATTTC 61.437 60.000 29.38 7.00 0.00 2.17
2915 3397 1.696097 ATCTTGCGGCCGGGTAGATT 61.696 55.000 29.38 0.00 0.00 2.40
2917 3399 2.762459 ATCTTGCGGCCGGGTAGA 60.762 61.111 29.38 7.13 0.00 2.59
2918 3400 2.280186 GATCTTGCGGCCGGGTAG 60.280 66.667 29.38 0.00 0.00 3.18
2924 3406 2.746277 ACAACGGATCTTGCGGCC 60.746 61.111 0.00 0.00 34.75 6.13
2925 3407 2.480555 CACAACGGATCTTGCGGC 59.519 61.111 0.00 0.00 34.75 6.53
2927 3409 1.062587 GATTCCACAACGGATCTTGCG 59.937 52.381 0.00 0.00 45.80 4.85
2930 3414 3.600388 GACAGATTCCACAACGGATCTT 58.400 45.455 0.00 0.00 45.80 2.40
2981 3465 0.928451 GTGCTTTTGAACGGTCGTGC 60.928 55.000 0.00 0.00 0.00 5.34
3013 3497 3.788333 AGAATCGTTGGCCAATCATTG 57.212 42.857 23.66 9.68 0.00 2.82
3042 3526 3.040147 GGACAGAATCCGTCAGTTTGA 57.960 47.619 0.00 0.00 37.88 2.69


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

AutoCloner maintained by Alex Coulton.