Multiple sequence alignment - TraesCS6A01G275800

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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 TraesCS6A01G275800 chr6A 100.000 3119 0 0 1 3119 502365179 502368297 0.000000e+00 5760
1 TraesCS6A01G275800 chr6A 94.207 328 16 3 2421 2746 66997202 66997528 6.010000e-137 497
2 TraesCS6A01G275800 chr6D 95.777 2368 53 13 46 2385 361378735 361381083 0.000000e+00 3775
3 TraesCS6A01G275800 chr6D 97.175 177 5 0 2854 3030 361381137 361381313 1.820000e-77 300
4 TraesCS6A01G275800 chr6D 95.833 96 4 0 3024 3119 361409879 361409974 4.160000e-34 156
5 TraesCS6A01G275800 chr6B 94.911 1749 45 9 650 2385 542584867 542586584 0.000000e+00 2697
6 TraesCS6A01G275800 chr6B 92.038 628 19 7 46 651 542584125 542584743 0.000000e+00 854
7 TraesCS6A01G275800 chr6B 95.756 377 15 1 2743 3119 542586593 542586968 9.570000e-170 606
8 TraesCS6A01G275800 chr6B 91.463 328 25 3 2421 2746 123471203 123471529 6.140000e-122 448
9 TraesCS6A01G275800 chr2D 93.558 326 17 4 2425 2746 398414646 398414971 1.680000e-132 483
10 TraesCS6A01G275800 chr4D 78.505 535 106 7 1601 2129 101436892 101437423 2.980000e-90 342
11 TraesCS6A01G275800 chr4B 82.514 366 62 2 1731 2095 145371914 145372278 1.400000e-83 320
12 TraesCS6A01G275800 chr4A 76.952 525 114 5 1610 2129 473946044 473945522 3.040000e-75 292


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 TraesCS6A01G275800 chr6A 502365179 502368297 3118 False 5760.000000 5760 100.000 1 3119 1 chr6A.!!$F2 3118
1 TraesCS6A01G275800 chr6D 361378735 361381313 2578 False 2037.500000 3775 96.476 46 3030 2 chr6D.!!$F2 2984
2 TraesCS6A01G275800 chr6B 542584125 542586968 2843 False 1385.666667 2697 94.235 46 3119 3 chr6B.!!$F2 3073
3 TraesCS6A01G275800 chr4D 101436892 101437423 531 False 342.000000 342 78.505 1601 2129 1 chr4D.!!$F1 528
4 TraesCS6A01G275800 chr4A 473945522 473946044 522 True 292.000000 292 76.952 1610 2129 1 chr4A.!!$R1 519

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
23 24 0.035458 CTCTTCCACACTCCACACCC 59.965 60.000 0.0 0.0 0.0 4.61 F
29 30 0.401738 CACACTCCACACCCCATTCT 59.598 55.000 0.0 0.0 0.0 2.40 F
31 32 0.692476 CACTCCACACCCCATTCTCA 59.308 55.000 0.0 0.0 0.0 3.27 F
32 33 1.073763 CACTCCACACCCCATTCTCAA 59.926 52.381 0.0 0.0 0.0 3.02 F
1071 1226 1.367471 CACGGAGAAGGTGACAGCA 59.633 57.895 7.5 0.0 37.6 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1154 1309 0.388263 GACAGACCGGACGAACTTCC 60.388 60.000 9.46 0.0 0.00 3.46 R
1170 1325 2.511818 ACCGACAGTGAAGGTGACA 58.488 52.632 12.22 0.0 36.81 3.58 R
1454 1609 7.707104 ACATTTGATTACGAGAAAATCATCCC 58.293 34.615 0.00 0.0 41.62 3.85 R
1981 2136 7.825270 TGAAGAGGCAATAAATTCAATGCAAAT 59.175 29.630 10.32 0.0 40.51 2.32 R
2683 2850 0.248843 AGAGAGGCACTAGCACTTGC 59.751 55.000 0.00 0.0 41.55 4.01 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
17 18 4.580835 GCGTCTCTTCCACACTCC 57.419 61.111 0.00 0.00 0.00 3.85
18 19 1.666011 GCGTCTCTTCCACACTCCA 59.334 57.895 0.00 0.00 0.00 3.86
19 20 0.667792 GCGTCTCTTCCACACTCCAC 60.668 60.000 0.00 0.00 0.00 4.02
20 21 0.673985 CGTCTCTTCCACACTCCACA 59.326 55.000 0.00 0.00 0.00 4.17
21 22 1.603172 CGTCTCTTCCACACTCCACAC 60.603 57.143 0.00 0.00 0.00 3.82
22 23 1.048601 TCTCTTCCACACTCCACACC 58.951 55.000 0.00 0.00 0.00 4.16
23 24 0.035458 CTCTTCCACACTCCACACCC 59.965 60.000 0.00 0.00 0.00 4.61
24 25 1.073199 CTTCCACACTCCACACCCC 59.927 63.158 0.00 0.00 0.00 4.95
25 26 1.694525 TTCCACACTCCACACCCCA 60.695 57.895 0.00 0.00 0.00 4.96
26 27 1.065410 TTCCACACTCCACACCCCAT 61.065 55.000 0.00 0.00 0.00 4.00
27 28 1.065410 TCCACACTCCACACCCCATT 61.065 55.000 0.00 0.00 0.00 3.16
28 29 0.609131 CCACACTCCACACCCCATTC 60.609 60.000 0.00 0.00 0.00 2.67
29 30 0.401738 CACACTCCACACCCCATTCT 59.598 55.000 0.00 0.00 0.00 2.40
30 31 0.693049 ACACTCCACACCCCATTCTC 59.307 55.000 0.00 0.00 0.00 2.87
31 32 0.692476 CACTCCACACCCCATTCTCA 59.308 55.000 0.00 0.00 0.00 3.27
32 33 1.073763 CACTCCACACCCCATTCTCAA 59.926 52.381 0.00 0.00 0.00 3.02
33 34 1.780309 ACTCCACACCCCATTCTCAAA 59.220 47.619 0.00 0.00 0.00 2.69
34 35 2.176798 ACTCCACACCCCATTCTCAAAA 59.823 45.455 0.00 0.00 0.00 2.44
35 36 3.230134 CTCCACACCCCATTCTCAAAAA 58.770 45.455 0.00 0.00 0.00 1.94
156 157 2.097038 CGAAGCGAGTTGGGAGCAG 61.097 63.158 0.00 0.00 0.00 4.24
157 158 2.359230 AAGCGAGTTGGGAGCAGC 60.359 61.111 0.00 0.00 0.00 5.25
158 159 3.909086 AAGCGAGTTGGGAGCAGCC 62.909 63.158 0.00 0.00 0.00 4.85
160 161 4.069232 CGAGTTGGGAGCAGCCGA 62.069 66.667 0.00 0.00 37.63 5.54
161 162 2.125350 GAGTTGGGAGCAGCCGAG 60.125 66.667 0.00 0.00 37.63 4.63
162 163 4.400961 AGTTGGGAGCAGCCGAGC 62.401 66.667 0.00 0.00 37.63 5.03
163 164 4.704833 GTTGGGAGCAGCCGAGCA 62.705 66.667 0.00 0.00 37.63 4.26
214 215 3.933722 CCCGCTCCGCCATCAGAT 61.934 66.667 0.00 0.00 0.00 2.90
256 257 4.593864 GTCTGATCTCCGCCGCCC 62.594 72.222 0.00 0.00 0.00 6.13
305 320 3.782443 GCGTTCTCCATCCCCGGT 61.782 66.667 0.00 0.00 0.00 5.28
390 405 2.300152 TGTTGCTAGTCTGCTAGTGCTT 59.700 45.455 3.95 0.00 44.93 3.91
397 412 5.988561 GCTAGTCTGCTAGTGCTTGATTAAT 59.011 40.000 3.95 0.00 44.93 1.40
435 450 3.253677 TGCGGCTCTAAATCTAGCTCTAC 59.746 47.826 0.00 0.00 38.80 2.59
474 493 7.362056 CCTTTTTGTGTTCTTCAGAAGTTCAGA 60.362 37.037 10.09 0.00 34.27 3.27
475 494 6.422776 TTTGTGTTCTTCAGAAGTTCAGAC 57.577 37.500 10.09 5.36 34.27 3.51
771 922 4.392754 TGCACTGTTGTATAGCATGTTCAG 59.607 41.667 0.00 0.00 0.00 3.02
776 927 6.936900 ACTGTTGTATAGCATGTTCAGTTCTT 59.063 34.615 0.00 0.00 32.15 2.52
862 1014 5.516339 ACAAAATGCTGTTCTCTTGTTTTCG 59.484 36.000 0.00 0.00 0.00 3.46
864 1016 3.673746 TGCTGTTCTCTTGTTTTCGTG 57.326 42.857 0.00 0.00 0.00 4.35
897 1049 9.026074 CGTCAACTTTGGTTAATTTGTGTAAAT 57.974 29.630 0.00 0.00 34.25 1.40
971 1126 4.686191 ATGTTCCTCTCTTATGCTCAGG 57.314 45.455 0.00 0.00 0.00 3.86
1071 1226 1.367471 CACGGAGAAGGTGACAGCA 59.633 57.895 7.50 0.00 37.60 4.41
1154 1309 2.434336 TCAAGAAGGATATGGGTGTCGG 59.566 50.000 0.00 0.00 0.00 4.79
1170 1325 2.633509 CGGGAAGTTCGTCCGGTCT 61.634 63.158 11.50 0.00 40.07 3.85
1454 1609 3.122445 GCGAAACCACTAAAGTACCTTCG 59.878 47.826 11.98 11.98 35.88 3.79
1468 1623 2.906354 ACCTTCGGGATGATTTTCTCG 58.094 47.619 0.00 0.00 41.01 4.04
1593 1748 3.857157 AAGCTGTTGGACACTAAGGAA 57.143 42.857 0.00 0.00 0.00 3.36
1981 2136 7.824289 AGCATAACTGTGACAAGCTTAAAGATA 59.176 33.333 0.00 0.00 0.00 1.98
2109 2264 0.902516 AGAAGAGAAGCAGGCCTCGT 60.903 55.000 0.00 0.00 34.75 4.18
2144 2302 3.557595 AGCTCATGCGTACTAAAATCAGC 59.442 43.478 0.00 0.00 45.42 4.26
2169 2327 0.249280 GCGGTTGTTGGGGTTTCTTG 60.249 55.000 0.00 0.00 0.00 3.02
2174 2332 3.258228 GTTGTTGGGGTTTCTTGTGTTG 58.742 45.455 0.00 0.00 0.00 3.33
2193 2351 3.228188 TGTCTGCACCTTTCCTGAAAT 57.772 42.857 0.00 0.00 0.00 2.17
2229 2396 9.108284 TGTAATATCATGTGTGGAACTGTTATG 57.892 33.333 0.00 0.00 38.04 1.90
2333 2500 4.131596 ACAACTACTTTATGCAACCGTGT 58.868 39.130 0.00 0.00 0.00 4.49
2341 2508 2.785713 ATGCAACCGTGTTGTTAACC 57.214 45.000 15.22 0.00 0.00 2.85
2374 2541 2.932614 GGAACTGGAAGATGTCACATCG 59.067 50.000 12.25 0.19 37.43 3.84
2385 2552 7.653713 GGAAGATGTCACATCGTATACAATCTT 59.346 37.037 12.25 0.00 0.00 2.40
2386 2553 8.948631 AAGATGTCACATCGTATACAATCTTT 57.051 30.769 12.25 0.00 0.00 2.52
2388 2555 9.383519 AGATGTCACATCGTATACAATCTTTTT 57.616 29.630 12.25 0.00 0.00 1.94
2413 2580 1.620822 TTTGAGGAAAGAAGGCAGGC 58.379 50.000 0.00 0.00 0.00 4.85
2414 2581 0.773644 TTGAGGAAAGAAGGCAGGCT 59.226 50.000 0.00 0.00 0.00 4.58
2415 2582 0.773644 TGAGGAAAGAAGGCAGGCTT 59.226 50.000 9.44 9.44 0.00 4.35
2416 2583 1.145738 TGAGGAAAGAAGGCAGGCTTT 59.854 47.619 11.18 0.00 37.07 3.51
2417 2584 2.375174 TGAGGAAAGAAGGCAGGCTTTA 59.625 45.455 11.18 0.00 34.69 1.85
2418 2585 3.010584 TGAGGAAAGAAGGCAGGCTTTAT 59.989 43.478 11.18 0.00 34.69 1.40
2419 2586 4.019858 GAGGAAAGAAGGCAGGCTTTATT 58.980 43.478 11.18 8.97 34.69 1.40
2420 2587 4.019858 AGGAAAGAAGGCAGGCTTTATTC 58.980 43.478 11.18 16.39 34.69 1.75
2421 2588 3.763897 GGAAAGAAGGCAGGCTTTATTCA 59.236 43.478 24.52 0.00 34.69 2.57
2422 2589 4.403752 GGAAAGAAGGCAGGCTTTATTCAT 59.596 41.667 24.52 7.98 34.69 2.57
2423 2590 5.594317 GGAAAGAAGGCAGGCTTTATTCATA 59.406 40.000 24.52 0.00 34.69 2.15
2424 2591 6.238869 GGAAAGAAGGCAGGCTTTATTCATAG 60.239 42.308 24.52 0.00 34.69 2.23
2425 2592 4.723309 AGAAGGCAGGCTTTATTCATAGG 58.277 43.478 11.18 0.00 0.00 2.57
2426 2593 4.413520 AGAAGGCAGGCTTTATTCATAGGA 59.586 41.667 11.18 0.00 0.00 2.94
2427 2594 5.074239 AGAAGGCAGGCTTTATTCATAGGAT 59.926 40.000 11.18 0.00 0.00 3.24
2428 2595 5.330648 AGGCAGGCTTTATTCATAGGATT 57.669 39.130 0.00 0.00 0.00 3.01
2429 2596 6.454223 AGGCAGGCTTTATTCATAGGATTA 57.546 37.500 0.00 0.00 0.00 1.75
2430 2597 6.241645 AGGCAGGCTTTATTCATAGGATTAC 58.758 40.000 0.00 0.00 0.00 1.89
2431 2598 6.003950 GGCAGGCTTTATTCATAGGATTACA 58.996 40.000 0.00 0.00 0.00 2.41
2432 2599 6.490040 GGCAGGCTTTATTCATAGGATTACAA 59.510 38.462 0.00 0.00 0.00 2.41
2433 2600 7.014230 GGCAGGCTTTATTCATAGGATTACAAA 59.986 37.037 0.00 0.00 0.00 2.83
2434 2601 8.579863 GCAGGCTTTATTCATAGGATTACAAAT 58.420 33.333 0.00 0.00 0.00 2.32
2456 2623 9.520204 CAAATAAATCATGAGGAATACACAACC 57.480 33.333 0.09 0.00 0.00 3.77
2457 2624 8.821686 AATAAATCATGAGGAATACACAACCA 57.178 30.769 0.09 0.00 0.00 3.67
2458 2625 9.425248 AATAAATCATGAGGAATACACAACCAT 57.575 29.630 0.09 0.00 0.00 3.55
2459 2626 6.704289 AATCATGAGGAATACACAACCATG 57.296 37.500 0.09 0.00 33.32 3.66
2460 2627 5.178096 TCATGAGGAATACACAACCATGT 57.822 39.130 0.00 0.00 41.61 3.21
2470 2637 2.561478 ACAACCATGTGTGTCTACCC 57.439 50.000 0.00 0.00 38.69 3.69
2471 2638 2.054799 ACAACCATGTGTGTCTACCCT 58.945 47.619 0.00 0.00 38.69 4.34
2472 2639 2.224523 ACAACCATGTGTGTCTACCCTG 60.225 50.000 0.00 0.00 38.69 4.45
2473 2640 0.984230 ACCATGTGTGTCTACCCTGG 59.016 55.000 0.00 0.00 0.00 4.45
2474 2641 0.253044 CCATGTGTGTCTACCCTGGG 59.747 60.000 12.28 12.28 0.00 4.45
2475 2642 0.984230 CATGTGTGTCTACCCTGGGT 59.016 55.000 24.15 24.15 40.16 4.51
2476 2643 2.184533 CATGTGTGTCTACCCTGGGTA 58.815 52.381 23.77 23.77 37.09 3.69
2487 2654 3.411875 CCTGGGTAGGGTAACACCT 57.588 57.895 0.00 0.00 44.75 4.00
2488 2655 2.555732 CCTGGGTAGGGTAACACCTA 57.444 55.000 0.00 0.00 42.09 3.08
2489 2656 2.395619 CCTGGGTAGGGTAACACCTAG 58.604 57.143 0.00 0.00 43.51 3.02
2496 2663 0.757512 GGGTAACACCTAGCCTAGCC 59.242 60.000 0.00 0.00 43.75 3.93
2497 2664 1.492764 GGTAACACCTAGCCTAGCCA 58.507 55.000 0.00 0.00 34.73 4.75
2498 2665 2.047830 GGTAACACCTAGCCTAGCCAT 58.952 52.381 0.00 0.00 34.73 4.40
2499 2666 2.037381 GGTAACACCTAGCCTAGCCATC 59.963 54.545 0.00 0.00 34.73 3.51
2500 2667 2.182516 AACACCTAGCCTAGCCATCT 57.817 50.000 0.00 0.00 0.00 2.90
2501 2668 2.182516 ACACCTAGCCTAGCCATCTT 57.817 50.000 0.00 0.00 0.00 2.40
2502 2669 3.330126 ACACCTAGCCTAGCCATCTTA 57.670 47.619 0.00 0.00 0.00 2.10
2503 2670 3.863086 ACACCTAGCCTAGCCATCTTAT 58.137 45.455 0.00 0.00 0.00 1.73
2504 2671 3.580458 ACACCTAGCCTAGCCATCTTATG 59.420 47.826 0.00 0.00 0.00 1.90
2505 2672 3.834813 CACCTAGCCTAGCCATCTTATGA 59.165 47.826 0.00 0.00 0.00 2.15
2506 2673 4.081752 CACCTAGCCTAGCCATCTTATGAG 60.082 50.000 0.00 0.00 0.00 2.90
2507 2674 3.118811 CCTAGCCTAGCCATCTTATGAGC 60.119 52.174 0.00 0.00 0.00 4.26
2508 2675 2.618794 AGCCTAGCCATCTTATGAGCT 58.381 47.619 0.00 0.00 39.20 4.09
2509 2676 2.978278 AGCCTAGCCATCTTATGAGCTT 59.022 45.455 7.76 0.00 37.73 3.74
2510 2677 3.007831 AGCCTAGCCATCTTATGAGCTTC 59.992 47.826 7.76 0.00 37.73 3.86
2511 2678 3.244353 GCCTAGCCATCTTATGAGCTTCA 60.244 47.826 7.76 0.00 37.73 3.02
2512 2679 4.744867 GCCTAGCCATCTTATGAGCTTCAA 60.745 45.833 7.76 0.00 37.73 2.69
2513 2680 5.371526 CCTAGCCATCTTATGAGCTTCAAA 58.628 41.667 7.76 0.00 37.73 2.69
2514 2681 5.824624 CCTAGCCATCTTATGAGCTTCAAAA 59.175 40.000 7.76 0.00 37.73 2.44
2515 2682 6.489361 CCTAGCCATCTTATGAGCTTCAAAAT 59.511 38.462 7.76 0.00 37.73 1.82
2516 2683 6.786967 AGCCATCTTATGAGCTTCAAAATT 57.213 33.333 0.00 0.00 34.56 1.82
2517 2684 7.886629 AGCCATCTTATGAGCTTCAAAATTA 57.113 32.000 0.00 0.00 34.56 1.40
2518 2685 8.474710 AGCCATCTTATGAGCTTCAAAATTAT 57.525 30.769 0.00 0.00 34.56 1.28
2519 2686 9.578576 AGCCATCTTATGAGCTTCAAAATTATA 57.421 29.630 0.00 0.00 34.56 0.98
2551 2718 6.206600 CTTCATGAGCAAAAACACATGAAC 57.793 37.500 14.53 0.00 46.07 3.18
2552 2719 5.518848 TCATGAGCAAAAACACATGAACT 57.481 34.783 0.00 0.00 42.28 3.01
2553 2720 6.631971 TCATGAGCAAAAACACATGAACTA 57.368 33.333 0.00 0.00 42.28 2.24
2554 2721 7.036996 TCATGAGCAAAAACACATGAACTAA 57.963 32.000 0.00 0.00 42.28 2.24
2555 2722 7.487484 TCATGAGCAAAAACACATGAACTAAA 58.513 30.769 0.00 0.00 42.28 1.85
2556 2723 7.434897 TCATGAGCAAAAACACATGAACTAAAC 59.565 33.333 0.00 0.00 42.28 2.01
2557 2724 6.625362 TGAGCAAAAACACATGAACTAAACA 58.375 32.000 0.00 0.00 0.00 2.83
2558 2725 7.264221 TGAGCAAAAACACATGAACTAAACAT 58.736 30.769 0.00 0.00 0.00 2.71
2559 2726 8.409371 TGAGCAAAAACACATGAACTAAACATA 58.591 29.630 0.00 0.00 0.00 2.29
2560 2727 9.410556 GAGCAAAAACACATGAACTAAACATAT 57.589 29.630 0.00 0.00 0.00 1.78
2599 2766 7.986085 ATTTATTTGATAACTCCTCCATCCG 57.014 36.000 0.00 0.00 0.00 4.18
2600 2767 2.910688 TTGATAACTCCTCCATCCGC 57.089 50.000 0.00 0.00 0.00 5.54
2601 2768 0.673985 TGATAACTCCTCCATCCGCG 59.326 55.000 0.00 0.00 0.00 6.46
2602 2769 0.667792 GATAACTCCTCCATCCGCGC 60.668 60.000 0.00 0.00 0.00 6.86
2603 2770 2.100879 ATAACTCCTCCATCCGCGCC 62.101 60.000 0.00 0.00 0.00 6.53
2605 2772 4.292178 CTCCTCCATCCGCGCCTC 62.292 72.222 0.00 0.00 0.00 4.70
2608 2775 4.161295 CTCCATCCGCGCCTCCAA 62.161 66.667 0.00 0.00 0.00 3.53
2609 2776 4.467084 TCCATCCGCGCCTCCAAC 62.467 66.667 0.00 0.00 0.00 3.77
2610 2777 4.473520 CCATCCGCGCCTCCAACT 62.474 66.667 0.00 0.00 0.00 3.16
2611 2778 2.892425 CATCCGCGCCTCCAACTC 60.892 66.667 0.00 0.00 0.00 3.01
2612 2779 4.162690 ATCCGCGCCTCCAACTCC 62.163 66.667 0.00 0.00 0.00 3.85
2614 2781 4.473520 CCGCGCCTCCAACTCCAT 62.474 66.667 0.00 0.00 0.00 3.41
2615 2782 2.892425 CGCGCCTCCAACTCCATC 60.892 66.667 0.00 0.00 0.00 3.51
2616 2783 2.586792 GCGCCTCCAACTCCATCT 59.413 61.111 0.00 0.00 0.00 2.90
2617 2784 1.522580 GCGCCTCCAACTCCATCTC 60.523 63.158 0.00 0.00 0.00 2.75
2618 2785 1.227089 CGCCTCCAACTCCATCTCG 60.227 63.158 0.00 0.00 0.00 4.04
2619 2786 1.667154 CGCCTCCAACTCCATCTCGA 61.667 60.000 0.00 0.00 0.00 4.04
2620 2787 0.537188 GCCTCCAACTCCATCTCGAA 59.463 55.000 0.00 0.00 0.00 3.71
2621 2788 1.139853 GCCTCCAACTCCATCTCGAAT 59.860 52.381 0.00 0.00 0.00 3.34
2622 2789 2.365617 GCCTCCAACTCCATCTCGAATA 59.634 50.000 0.00 0.00 0.00 1.75
2623 2790 3.007398 GCCTCCAACTCCATCTCGAATAT 59.993 47.826 0.00 0.00 0.00 1.28
2624 2791 4.564041 CCTCCAACTCCATCTCGAATATG 58.436 47.826 1.29 1.29 0.00 1.78
2625 2792 4.562347 CCTCCAACTCCATCTCGAATATGG 60.562 50.000 16.84 16.84 44.51 2.74
2626 2793 3.967326 TCCAACTCCATCTCGAATATGGT 59.033 43.478 20.39 5.42 43.72 3.55
2627 2794 4.408921 TCCAACTCCATCTCGAATATGGTT 59.591 41.667 20.39 10.02 43.72 3.67
2628 2795 5.600898 TCCAACTCCATCTCGAATATGGTTA 59.399 40.000 20.39 6.90 43.72 2.85
2629 2796 6.099125 TCCAACTCCATCTCGAATATGGTTAA 59.901 38.462 20.39 6.35 43.72 2.01
2630 2797 6.936900 CCAACTCCATCTCGAATATGGTTAAT 59.063 38.462 20.39 7.98 43.72 1.40
2631 2798 7.095060 CCAACTCCATCTCGAATATGGTTAATG 60.095 40.741 20.39 15.70 43.72 1.90
2632 2799 7.303182 ACTCCATCTCGAATATGGTTAATGA 57.697 36.000 20.39 5.24 43.72 2.57
2633 2800 7.155328 ACTCCATCTCGAATATGGTTAATGAC 58.845 38.462 20.39 0.00 43.72 3.06
2649 2816 8.561738 GGTTAATGACCTCTTTACAATCTGAA 57.438 34.615 0.00 0.00 45.55 3.02
2650 2817 8.669243 GGTTAATGACCTCTTTACAATCTGAAG 58.331 37.037 0.00 0.00 45.55 3.02
2651 2818 6.749923 AATGACCTCTTTACAATCTGAAGC 57.250 37.500 0.00 0.00 0.00 3.86
2652 2819 5.227569 TGACCTCTTTACAATCTGAAGCA 57.772 39.130 0.00 0.00 0.00 3.91
2653 2820 5.620206 TGACCTCTTTACAATCTGAAGCAA 58.380 37.500 0.00 0.00 0.00 3.91
2654 2821 6.240894 TGACCTCTTTACAATCTGAAGCAAT 58.759 36.000 0.00 0.00 0.00 3.56
2655 2822 7.394016 TGACCTCTTTACAATCTGAAGCAATA 58.606 34.615 0.00 0.00 0.00 1.90
2656 2823 8.049117 TGACCTCTTTACAATCTGAAGCAATAT 58.951 33.333 0.00 0.00 0.00 1.28
2657 2824 9.547753 GACCTCTTTACAATCTGAAGCAATATA 57.452 33.333 0.00 0.00 0.00 0.86
2658 2825 9.905713 ACCTCTTTACAATCTGAAGCAATATAA 57.094 29.630 0.00 0.00 0.00 0.98
2664 2831 7.944729 ACAATCTGAAGCAATATAAAGGTGT 57.055 32.000 0.00 0.00 0.00 4.16
2665 2832 8.353423 ACAATCTGAAGCAATATAAAGGTGTT 57.647 30.769 0.00 0.00 0.00 3.32
2666 2833 8.246180 ACAATCTGAAGCAATATAAAGGTGTTG 58.754 33.333 0.00 0.00 0.00 3.33
2667 2834 6.194796 TCTGAAGCAATATAAAGGTGTTGC 57.805 37.500 0.99 0.99 45.37 4.17
2668 2835 5.709631 TCTGAAGCAATATAAAGGTGTTGCA 59.290 36.000 10.97 0.00 46.92 4.08
2669 2836 6.377996 TCTGAAGCAATATAAAGGTGTTGCAT 59.622 34.615 10.97 0.00 46.92 3.96
2670 2837 7.555914 TCTGAAGCAATATAAAGGTGTTGCATA 59.444 33.333 10.97 0.00 46.92 3.14
2671 2838 7.479980 TGAAGCAATATAAAGGTGTTGCATAC 58.520 34.615 10.97 0.00 46.92 2.39
2672 2839 6.391227 AGCAATATAAAGGTGTTGCATACC 57.609 37.500 11.63 11.63 46.92 2.73
2673 2840 5.890985 AGCAATATAAAGGTGTTGCATACCA 59.109 36.000 19.34 0.81 46.92 3.25
2674 2841 6.379703 AGCAATATAAAGGTGTTGCATACCAA 59.620 34.615 19.34 7.74 46.92 3.67
2675 2842 6.697019 GCAATATAAAGGTGTTGCATACCAAG 59.303 38.462 19.34 4.72 44.63 3.61
2676 2843 7.416213 GCAATATAAAGGTGTTGCATACCAAGA 60.416 37.037 19.34 7.01 44.63 3.02
2677 2844 8.632679 CAATATAAAGGTGTTGCATACCAAGAT 58.367 33.333 19.34 12.22 40.74 2.40
2678 2845 6.699575 ATAAAGGTGTTGCATACCAAGATC 57.300 37.500 19.34 0.00 40.74 2.75
2679 2846 3.719268 AGGTGTTGCATACCAAGATCA 57.281 42.857 19.34 0.00 40.74 2.92
2680 2847 4.240881 AGGTGTTGCATACCAAGATCAT 57.759 40.909 19.34 0.00 40.74 2.45
2681 2848 3.949754 AGGTGTTGCATACCAAGATCATG 59.050 43.478 19.34 0.00 40.74 3.07
2682 2849 3.947196 GGTGTTGCATACCAAGATCATGA 59.053 43.478 14.03 0.00 38.12 3.07
2683 2850 4.036027 GGTGTTGCATACCAAGATCATGAG 59.964 45.833 14.03 0.00 38.12 2.90
2684 2851 3.628942 TGTTGCATACCAAGATCATGAGC 59.371 43.478 1.78 1.78 33.21 4.26
2685 2852 3.564053 TGCATACCAAGATCATGAGCA 57.436 42.857 14.38 5.05 0.00 4.26
2686 2853 3.888583 TGCATACCAAGATCATGAGCAA 58.111 40.909 14.38 0.00 0.00 3.91
2687 2854 3.881089 TGCATACCAAGATCATGAGCAAG 59.119 43.478 14.38 4.71 0.00 4.01
2688 2855 3.881688 GCATACCAAGATCATGAGCAAGT 59.118 43.478 14.38 9.50 0.00 3.16
2689 2856 4.261072 GCATACCAAGATCATGAGCAAGTG 60.261 45.833 14.38 7.93 0.00 3.16
2690 2857 2.089980 ACCAAGATCATGAGCAAGTGC 58.910 47.619 14.38 0.00 42.49 4.40
2701 2868 2.761071 GCAAGTGCTAGTGCCTCTC 58.239 57.895 0.00 0.00 38.71 3.20
2702 2869 0.248843 GCAAGTGCTAGTGCCTCTCT 59.751 55.000 0.00 0.00 38.71 3.10
2703 2870 2.006056 GCAAGTGCTAGTGCCTCTCTG 61.006 57.143 0.00 0.00 38.71 3.35
2704 2871 0.248843 AAGTGCTAGTGCCTCTCTGC 59.751 55.000 0.00 0.00 38.71 4.26
2705 2872 0.902048 AGTGCTAGTGCCTCTCTGCA 60.902 55.000 0.00 0.00 39.37 4.41
2706 2873 0.459934 GTGCTAGTGCCTCTCTGCAG 60.460 60.000 7.63 7.63 43.02 4.41
2707 2874 1.521234 GCTAGTGCCTCTCTGCAGC 60.521 63.158 9.47 0.00 43.02 5.25
2708 2875 1.143620 CTAGTGCCTCTCTGCAGCC 59.856 63.158 9.47 0.00 43.02 4.85
2709 2876 1.610379 TAGTGCCTCTCTGCAGCCA 60.610 57.895 9.47 0.00 43.02 4.75
2710 2877 0.979709 TAGTGCCTCTCTGCAGCCAT 60.980 55.000 9.47 0.00 43.02 4.40
2711 2878 0.979709 AGTGCCTCTCTGCAGCCATA 60.980 55.000 9.47 0.00 43.02 2.74
2712 2879 0.532417 GTGCCTCTCTGCAGCCATAG 60.532 60.000 9.47 0.59 43.02 2.23
2713 2880 1.597578 GCCTCTCTGCAGCCATAGC 60.598 63.158 9.47 4.29 40.32 2.97
2725 2892 1.826385 GCCATAGCTTCCAACACTGT 58.174 50.000 0.00 0.00 35.50 3.55
2726 2893 2.162681 GCCATAGCTTCCAACACTGTT 58.837 47.619 0.00 0.00 35.50 3.16
2727 2894 2.095059 GCCATAGCTTCCAACACTGTTG 60.095 50.000 14.11 14.11 35.50 3.33
2728 2895 2.489329 CCATAGCTTCCAACACTGTTGG 59.511 50.000 28.67 28.67 40.87 3.77
2729 2896 3.411446 CATAGCTTCCAACACTGTTGGA 58.589 45.455 31.71 31.71 46.08 3.53
2738 2905 5.935945 TCCAACACTGTTGGAGAAATAAGA 58.064 37.500 31.71 12.80 43.17 2.10
2739 2906 5.763204 TCCAACACTGTTGGAGAAATAAGAC 59.237 40.000 31.71 0.00 43.17 3.01
2740 2907 5.048713 CCAACACTGTTGGAGAAATAAGACC 60.049 44.000 30.16 0.00 42.06 3.85
2741 2908 5.568620 ACACTGTTGGAGAAATAAGACCT 57.431 39.130 0.00 0.00 0.00 3.85
2742 2909 5.941788 ACACTGTTGGAGAAATAAGACCTT 58.058 37.500 0.00 0.00 0.00 3.50
2743 2910 5.765182 ACACTGTTGGAGAAATAAGACCTTG 59.235 40.000 0.00 0.00 0.00 3.61
2744 2911 5.997746 CACTGTTGGAGAAATAAGACCTTGA 59.002 40.000 0.00 0.00 0.00 3.02
2745 2912 6.486657 CACTGTTGGAGAAATAAGACCTTGAA 59.513 38.462 0.00 0.00 0.00 2.69
2746 2913 7.013274 CACTGTTGGAGAAATAAGACCTTGAAA 59.987 37.037 0.00 0.00 0.00 2.69
2747 2914 7.559897 ACTGTTGGAGAAATAAGACCTTGAAAA 59.440 33.333 0.00 0.00 0.00 2.29
2748 2915 7.940850 TGTTGGAGAAATAAGACCTTGAAAAG 58.059 34.615 0.00 0.00 45.69 2.27
2841 3008 4.748102 TCGGAAACTTATATGATCGGTTGC 59.252 41.667 0.00 0.00 0.00 4.17
2843 3010 5.558273 CGGAAACTTATATGATCGGTTGCAC 60.558 44.000 0.00 0.00 0.00 4.57
2917 3084 9.555727 TGCAACCCTTAGATGTACTTATATTTC 57.444 33.333 0.00 0.00 0.00 2.17
3040 3207 3.128068 GCCAAACCAGGTTTTACTATCCG 59.872 47.826 15.51 1.46 33.10 4.18
3054 3221 9.760077 GTTTTACTATCCGAGATCAGGATTAAA 57.240 33.333 22.46 18.57 45.59 1.52
3114 3281 7.468141 ACTGATGTAGTCTGTGTTAATCTGA 57.532 36.000 0.00 0.00 37.58 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.667792 GTGGAGTGTGGAAGAGACGC 60.668 60.000 0.00 0.00 0.00 5.19
1 2 0.673985 TGTGGAGTGTGGAAGAGACG 59.326 55.000 0.00 0.00 0.00 4.18
2 3 1.270358 GGTGTGGAGTGTGGAAGAGAC 60.270 57.143 0.00 0.00 0.00 3.36
3 4 1.048601 GGTGTGGAGTGTGGAAGAGA 58.951 55.000 0.00 0.00 0.00 3.10
4 5 0.035458 GGGTGTGGAGTGTGGAAGAG 59.965 60.000 0.00 0.00 0.00 2.85
5 6 1.415672 GGGGTGTGGAGTGTGGAAGA 61.416 60.000 0.00 0.00 0.00 2.87
6 7 1.073199 GGGGTGTGGAGTGTGGAAG 59.927 63.158 0.00 0.00 0.00 3.46
7 8 1.065410 ATGGGGTGTGGAGTGTGGAA 61.065 55.000 0.00 0.00 0.00 3.53
8 9 1.065410 AATGGGGTGTGGAGTGTGGA 61.065 55.000 0.00 0.00 0.00 4.02
9 10 0.609131 GAATGGGGTGTGGAGTGTGG 60.609 60.000 0.00 0.00 0.00 4.17
10 11 0.401738 AGAATGGGGTGTGGAGTGTG 59.598 55.000 0.00 0.00 0.00 3.82
11 12 0.693049 GAGAATGGGGTGTGGAGTGT 59.307 55.000 0.00 0.00 0.00 3.55
12 13 0.692476 TGAGAATGGGGTGTGGAGTG 59.308 55.000 0.00 0.00 0.00 3.51
13 14 1.444933 TTGAGAATGGGGTGTGGAGT 58.555 50.000 0.00 0.00 0.00 3.85
14 15 2.584835 TTTGAGAATGGGGTGTGGAG 57.415 50.000 0.00 0.00 0.00 3.86
15 16 3.320610 TTTTTGAGAATGGGGTGTGGA 57.679 42.857 0.00 0.00 0.00 4.02
150 151 2.894387 GATGTGCTCGGCTGCTCC 60.894 66.667 0.00 0.00 0.00 4.70
157 158 4.457496 ACGCAGGGATGTGCTCGG 62.457 66.667 0.00 0.00 41.62 4.63
158 159 2.887568 GACGCAGGGATGTGCTCG 60.888 66.667 0.00 0.00 41.62 5.03
159 160 2.887568 CGACGCAGGGATGTGCTC 60.888 66.667 0.00 0.00 41.62 4.26
162 163 4.758251 TGGCGACGCAGGGATGTG 62.758 66.667 23.09 0.00 0.00 3.21
163 164 4.760047 GTGGCGACGCAGGGATGT 62.760 66.667 23.09 0.00 41.67 3.06
214 215 0.752009 CTAGGCGAGTAGGTCAGGCA 60.752 60.000 0.00 0.00 0.00 4.75
305 320 0.178987 TTTTTAGGCTGTGCGGGGAA 60.179 50.000 0.00 0.00 0.00 3.97
390 405 7.415095 CGCAAGTTCCTCCAATTGTATTAATCA 60.415 37.037 4.43 0.00 0.00 2.57
397 412 2.432444 CCGCAAGTTCCTCCAATTGTA 58.568 47.619 4.43 0.00 0.00 2.41
435 450 7.707893 AGAACACAAAAAGGAACATGAAAGATG 59.292 33.333 0.00 0.00 0.00 2.90
771 922 7.912250 CCATATGATGTGTGAAAAGCTAAGAAC 59.088 37.037 3.65 0.00 0.00 3.01
776 927 6.539826 CAGACCATATGATGTGTGAAAAGCTA 59.460 38.462 3.65 0.00 0.00 3.32
846 997 5.617187 CGAATTCACGAAAACAAGAGAACAG 59.383 40.000 6.22 0.00 35.09 3.16
862 1014 2.286772 ACCAAAGTTGACGCGAATTCAC 60.287 45.455 15.93 1.46 0.00 3.18
864 1016 2.681152 ACCAAAGTTGACGCGAATTC 57.319 45.000 15.93 0.00 0.00 2.17
897 1049 1.976474 GGCTTGGGCATGGTTTCGA 60.976 57.895 0.00 0.00 40.87 3.71
971 1126 2.838202 TCCAAGAAGGGATAGTGTGGAC 59.162 50.000 0.00 0.00 38.24 4.02
1154 1309 0.388263 GACAGACCGGACGAACTTCC 60.388 60.000 9.46 0.00 0.00 3.46
1170 1325 2.511818 ACCGACAGTGAAGGTGACA 58.488 52.632 12.22 0.00 36.81 3.58
1454 1609 7.707104 ACATTTGATTACGAGAAAATCATCCC 58.293 34.615 0.00 0.00 41.62 3.85
1981 2136 7.825270 TGAAGAGGCAATAAATTCAATGCAAAT 59.175 29.630 10.32 0.00 40.51 2.32
2144 2302 0.608035 ACCCCAACAACCGCATGTAG 60.608 55.000 0.00 0.00 32.02 2.74
2160 2318 1.748493 TGCAGACAACACAAGAAACCC 59.252 47.619 0.00 0.00 0.00 4.11
2169 2327 1.334869 CAGGAAAGGTGCAGACAACAC 59.665 52.381 0.00 0.00 35.21 3.32
2174 2332 4.590850 AAATTTCAGGAAAGGTGCAGAC 57.409 40.909 0.66 0.00 33.32 3.51
2193 2351 8.233868 CCACACATGATATTACACTTCGAAAAA 58.766 33.333 0.00 0.00 0.00 1.94
2210 2377 6.053632 AGATCATAACAGTTCCACACATGA 57.946 37.500 0.00 0.00 0.00 3.07
2319 2486 4.608951 GGTTAACAACACGGTTGCATAAA 58.391 39.130 8.10 4.19 32.29 1.40
2324 2491 0.377905 ACGGTTAACAACACGGTTGC 59.622 50.000 8.10 1.74 32.29 4.17
2333 2500 2.688958 CCCAAAGGAACACGGTTAACAA 59.311 45.455 8.10 0.00 33.47 2.83
2394 2561 1.145738 AGCCTGCCTTCTTTCCTCAAA 59.854 47.619 0.00 0.00 0.00 2.69
2395 2562 0.773644 AGCCTGCCTTCTTTCCTCAA 59.226 50.000 0.00 0.00 0.00 3.02
2396 2563 0.773644 AAGCCTGCCTTCTTTCCTCA 59.226 50.000 0.00 0.00 0.00 3.86
2397 2564 1.916506 AAAGCCTGCCTTCTTTCCTC 58.083 50.000 0.00 0.00 31.99 3.71
2400 2567 5.588958 ATGAATAAAGCCTGCCTTCTTTC 57.411 39.130 0.00 0.00 34.67 2.62
2401 2568 5.595952 CCTATGAATAAAGCCTGCCTTCTTT 59.404 40.000 0.00 0.00 36.58 2.52
2402 2569 5.103940 TCCTATGAATAAAGCCTGCCTTCTT 60.104 40.000 0.00 0.00 31.99 2.52
2403 2570 4.413520 TCCTATGAATAAAGCCTGCCTTCT 59.586 41.667 0.00 0.00 31.99 2.85
2404 2571 4.718961 TCCTATGAATAAAGCCTGCCTTC 58.281 43.478 0.00 0.00 31.99 3.46
2405 2572 4.796110 TCCTATGAATAAAGCCTGCCTT 57.204 40.909 0.00 0.00 34.51 4.35
2406 2573 5.330648 AATCCTATGAATAAAGCCTGCCT 57.669 39.130 0.00 0.00 0.00 4.75
2407 2574 6.003950 TGTAATCCTATGAATAAAGCCTGCC 58.996 40.000 0.00 0.00 0.00 4.85
2408 2575 7.510549 TTGTAATCCTATGAATAAAGCCTGC 57.489 36.000 0.00 0.00 0.00 4.85
2430 2597 9.520204 GGTTGTGTATTCCTCATGATTTATTTG 57.480 33.333 0.00 0.00 0.00 2.32
2431 2598 9.253832 TGGTTGTGTATTCCTCATGATTTATTT 57.746 29.630 0.00 0.00 0.00 1.40
2432 2599 8.821686 TGGTTGTGTATTCCTCATGATTTATT 57.178 30.769 0.00 0.00 0.00 1.40
2433 2600 8.853126 CATGGTTGTGTATTCCTCATGATTTAT 58.147 33.333 0.00 0.00 34.26 1.40
2434 2601 7.833682 ACATGGTTGTGTATTCCTCATGATTTA 59.166 33.333 0.00 0.00 35.74 1.40
2435 2602 6.664816 ACATGGTTGTGTATTCCTCATGATTT 59.335 34.615 0.00 0.00 35.74 2.17
2436 2603 6.095860 CACATGGTTGTGTATTCCTCATGATT 59.904 38.462 0.00 0.00 46.68 2.57
2437 2604 5.591472 CACATGGTTGTGTATTCCTCATGAT 59.409 40.000 0.00 0.00 46.68 2.45
2438 2605 4.943093 CACATGGTTGTGTATTCCTCATGA 59.057 41.667 0.00 0.00 46.68 3.07
2439 2606 5.239359 CACATGGTTGTGTATTCCTCATG 57.761 43.478 0.00 0.00 46.68 3.07
2451 2618 2.054799 AGGGTAGACACACATGGTTGT 58.945 47.619 0.00 0.00 36.15 3.32
2452 2619 2.426522 CAGGGTAGACACACATGGTTG 58.573 52.381 0.00 0.00 0.00 3.77
2453 2620 1.351017 CCAGGGTAGACACACATGGTT 59.649 52.381 0.00 0.00 0.00 3.67
2454 2621 0.984230 CCAGGGTAGACACACATGGT 59.016 55.000 0.00 0.00 0.00 3.55
2455 2622 0.253044 CCCAGGGTAGACACACATGG 59.747 60.000 0.00 0.00 0.00 3.66
2456 2623 0.984230 ACCCAGGGTAGACACACATG 59.016 55.000 10.48 0.00 32.11 3.21
2457 2624 2.634639 TACCCAGGGTAGACACACAT 57.365 50.000 15.22 0.00 37.09 3.21
2469 2636 2.395619 CTAGGTGTTACCCTACCCAGG 58.604 57.143 0.00 0.00 39.75 4.45
2470 2637 1.761198 GCTAGGTGTTACCCTACCCAG 59.239 57.143 0.00 0.00 39.75 4.45
2471 2638 1.623279 GGCTAGGTGTTACCCTACCCA 60.623 57.143 0.00 0.00 39.75 4.51
2472 2639 1.126488 GGCTAGGTGTTACCCTACCC 58.874 60.000 0.00 0.00 39.75 3.69
2473 2640 2.171568 AGGCTAGGTGTTACCCTACC 57.828 55.000 0.00 0.00 39.75 3.18
2474 2641 2.627221 GCTAGGCTAGGTGTTACCCTAC 59.373 54.545 22.40 0.00 39.75 3.18
2475 2642 2.425392 GGCTAGGCTAGGTGTTACCCTA 60.425 54.545 22.40 0.95 39.75 3.53
2476 2643 1.691801 GGCTAGGCTAGGTGTTACCCT 60.692 57.143 22.40 0.00 39.75 4.34
2477 2644 0.757512 GGCTAGGCTAGGTGTTACCC 59.242 60.000 22.40 9.66 39.75 3.69
2478 2645 1.492764 TGGCTAGGCTAGGTGTTACC 58.507 55.000 22.40 13.93 38.99 2.85
2479 2646 2.966516 AGATGGCTAGGCTAGGTGTTAC 59.033 50.000 22.40 4.97 0.00 2.50
2480 2647 3.330126 AGATGGCTAGGCTAGGTGTTA 57.670 47.619 22.40 0.00 0.00 2.41
2481 2648 2.182516 AGATGGCTAGGCTAGGTGTT 57.817 50.000 22.40 0.00 0.00 3.32
2482 2649 2.182516 AAGATGGCTAGGCTAGGTGT 57.817 50.000 22.40 0.00 0.00 4.16
2483 2650 3.834813 TCATAAGATGGCTAGGCTAGGTG 59.165 47.826 22.40 8.84 0.00 4.00
2484 2651 4.093011 CTCATAAGATGGCTAGGCTAGGT 58.907 47.826 22.40 3.32 0.00 3.08
2485 2652 3.118811 GCTCATAAGATGGCTAGGCTAGG 60.119 52.174 22.40 3.33 0.00 3.02
2486 2653 3.768757 AGCTCATAAGATGGCTAGGCTAG 59.231 47.826 17.33 17.33 35.83 3.42
2487 2654 3.784178 AGCTCATAAGATGGCTAGGCTA 58.216 45.455 18.18 4.39 35.83 3.93
2488 2655 2.618794 AGCTCATAAGATGGCTAGGCT 58.381 47.619 18.18 2.81 35.83 4.58
2489 2656 3.244353 TGAAGCTCATAAGATGGCTAGGC 60.244 47.826 9.85 9.85 36.31 3.93
2490 2657 4.613925 TGAAGCTCATAAGATGGCTAGG 57.386 45.455 0.00 0.00 36.31 3.02
2491 2658 6.932356 TTTTGAAGCTCATAAGATGGCTAG 57.068 37.500 0.00 0.00 36.31 3.42
2492 2659 7.886629 AATTTTGAAGCTCATAAGATGGCTA 57.113 32.000 0.00 0.00 36.31 3.93
2493 2660 6.786967 AATTTTGAAGCTCATAAGATGGCT 57.213 33.333 0.00 0.00 38.06 4.75
2530 2697 5.518848 AGTTCATGTGTTTTTGCTCATGA 57.481 34.783 0.00 0.00 43.32 3.07
2531 2698 7.222417 TGTTTAGTTCATGTGTTTTTGCTCATG 59.778 33.333 0.00 0.00 40.00 3.07
2532 2699 7.264221 TGTTTAGTTCATGTGTTTTTGCTCAT 58.736 30.769 0.00 0.00 0.00 2.90
2533 2700 6.625362 TGTTTAGTTCATGTGTTTTTGCTCA 58.375 32.000 0.00 0.00 0.00 4.26
2534 2701 7.698836 ATGTTTAGTTCATGTGTTTTTGCTC 57.301 32.000 0.00 0.00 0.00 4.26
2573 2740 9.502091 CGGATGGAGGAGTTATCAAATAAATAA 57.498 33.333 0.00 0.00 0.00 1.40
2574 2741 7.606456 GCGGATGGAGGAGTTATCAAATAAATA 59.394 37.037 0.00 0.00 0.00 1.40
2575 2742 6.431234 GCGGATGGAGGAGTTATCAAATAAAT 59.569 38.462 0.00 0.00 0.00 1.40
2576 2743 5.763204 GCGGATGGAGGAGTTATCAAATAAA 59.237 40.000 0.00 0.00 0.00 1.40
2577 2744 5.305585 GCGGATGGAGGAGTTATCAAATAA 58.694 41.667 0.00 0.00 0.00 1.40
2578 2745 4.560716 CGCGGATGGAGGAGTTATCAAATA 60.561 45.833 0.00 0.00 0.00 1.40
2579 2746 3.744660 GCGGATGGAGGAGTTATCAAAT 58.255 45.455 0.00 0.00 0.00 2.32
2580 2747 2.483013 CGCGGATGGAGGAGTTATCAAA 60.483 50.000 0.00 0.00 0.00 2.69
2581 2748 1.068588 CGCGGATGGAGGAGTTATCAA 59.931 52.381 0.00 0.00 0.00 2.57
2582 2749 0.673985 CGCGGATGGAGGAGTTATCA 59.326 55.000 0.00 0.00 0.00 2.15
2583 2750 0.667792 GCGCGGATGGAGGAGTTATC 60.668 60.000 8.83 0.00 0.00 1.75
2584 2751 1.367840 GCGCGGATGGAGGAGTTAT 59.632 57.895 8.83 0.00 0.00 1.89
2585 2752 2.792947 GGCGCGGATGGAGGAGTTA 61.793 63.158 8.83 0.00 0.00 2.24
2586 2753 4.162690 GGCGCGGATGGAGGAGTT 62.163 66.667 8.83 0.00 0.00 3.01
2588 2755 4.292178 GAGGCGCGGATGGAGGAG 62.292 72.222 8.83 0.00 0.00 3.69
2591 2758 4.161295 TTGGAGGCGCGGATGGAG 62.161 66.667 8.83 0.00 0.00 3.86
2592 2759 4.467084 GTTGGAGGCGCGGATGGA 62.467 66.667 8.83 0.00 0.00 3.41
2593 2760 4.473520 AGTTGGAGGCGCGGATGG 62.474 66.667 8.83 0.00 0.00 3.51
2594 2761 2.892425 GAGTTGGAGGCGCGGATG 60.892 66.667 8.83 0.00 0.00 3.51
2595 2762 4.162690 GGAGTTGGAGGCGCGGAT 62.163 66.667 8.83 0.00 0.00 4.18
2597 2764 4.473520 ATGGAGTTGGAGGCGCGG 62.474 66.667 8.83 0.00 0.00 6.46
2598 2765 2.892425 GATGGAGTTGGAGGCGCG 60.892 66.667 0.00 0.00 0.00 6.86
2599 2766 1.522580 GAGATGGAGTTGGAGGCGC 60.523 63.158 0.00 0.00 0.00 6.53
2600 2767 1.227089 CGAGATGGAGTTGGAGGCG 60.227 63.158 0.00 0.00 0.00 5.52
2601 2768 0.537188 TTCGAGATGGAGTTGGAGGC 59.463 55.000 0.00 0.00 0.00 4.70
2602 2769 4.562347 CCATATTCGAGATGGAGTTGGAGG 60.562 50.000 19.01 0.00 45.89 4.30
2603 2770 4.039730 ACCATATTCGAGATGGAGTTGGAG 59.960 45.833 26.73 6.13 45.89 3.86
2604 2771 3.967326 ACCATATTCGAGATGGAGTTGGA 59.033 43.478 26.73 0.00 45.89 3.53
2605 2772 4.342862 ACCATATTCGAGATGGAGTTGG 57.657 45.455 26.73 11.65 45.89 3.77
2606 2773 7.657354 TCATTAACCATATTCGAGATGGAGTTG 59.343 37.037 26.73 18.89 45.89 3.16
2607 2774 7.657761 GTCATTAACCATATTCGAGATGGAGTT 59.342 37.037 26.73 17.12 45.89 3.01
2608 2775 7.155328 GTCATTAACCATATTCGAGATGGAGT 58.845 38.462 26.73 18.38 45.89 3.85
2609 2776 7.588143 GTCATTAACCATATTCGAGATGGAG 57.412 40.000 26.73 14.52 45.89 3.86
2625 2792 8.178313 GCTTCAGATTGTAAAGAGGTCATTAAC 58.822 37.037 0.00 0.00 0.00 2.01
2626 2793 7.882791 TGCTTCAGATTGTAAAGAGGTCATTAA 59.117 33.333 0.00 0.00 0.00 1.40
2627 2794 7.394016 TGCTTCAGATTGTAAAGAGGTCATTA 58.606 34.615 0.00 0.00 0.00 1.90
2628 2795 6.240894 TGCTTCAGATTGTAAAGAGGTCATT 58.759 36.000 0.00 0.00 0.00 2.57
2629 2796 5.809001 TGCTTCAGATTGTAAAGAGGTCAT 58.191 37.500 0.00 0.00 0.00 3.06
2630 2797 5.227569 TGCTTCAGATTGTAAAGAGGTCA 57.772 39.130 0.00 0.00 0.00 4.02
2631 2798 6.749923 ATTGCTTCAGATTGTAAAGAGGTC 57.250 37.500 0.00 0.00 0.00 3.85
2632 2799 9.905713 TTATATTGCTTCAGATTGTAAAGAGGT 57.094 29.630 0.00 0.00 0.00 3.85
2638 2805 9.461312 ACACCTTTATATTGCTTCAGATTGTAA 57.539 29.630 0.00 0.00 0.00 2.41
2639 2806 9.461312 AACACCTTTATATTGCTTCAGATTGTA 57.539 29.630 0.00 0.00 0.00 2.41
2640 2807 7.944729 ACACCTTTATATTGCTTCAGATTGT 57.055 32.000 0.00 0.00 0.00 2.71
2641 2808 7.221452 GCAACACCTTTATATTGCTTCAGATTG 59.779 37.037 0.70 0.00 43.26 2.67
2642 2809 7.093814 TGCAACACCTTTATATTGCTTCAGATT 60.094 33.333 9.02 0.00 46.06 2.40
2643 2810 6.377996 TGCAACACCTTTATATTGCTTCAGAT 59.622 34.615 9.02 0.00 46.06 2.90
2644 2811 5.709631 TGCAACACCTTTATATTGCTTCAGA 59.290 36.000 9.02 0.00 46.06 3.27
2645 2812 5.953183 TGCAACACCTTTATATTGCTTCAG 58.047 37.500 9.02 0.00 46.06 3.02
2646 2813 5.973899 TGCAACACCTTTATATTGCTTCA 57.026 34.783 9.02 0.00 46.06 3.02
2647 2814 6.918022 GGTATGCAACACCTTTATATTGCTTC 59.082 38.462 12.46 0.80 46.06 3.86
2648 2815 6.379703 TGGTATGCAACACCTTTATATTGCTT 59.620 34.615 18.64 5.59 46.06 3.91
2649 2816 5.890985 TGGTATGCAACACCTTTATATTGCT 59.109 36.000 18.64 0.00 46.06 3.91
2650 2817 6.142818 TGGTATGCAACACCTTTATATTGC 57.857 37.500 18.64 0.94 46.08 3.56
2651 2818 7.995289 TCTTGGTATGCAACACCTTTATATTG 58.005 34.615 18.64 4.18 36.96 1.90
2652 2819 8.766994 ATCTTGGTATGCAACACCTTTATATT 57.233 30.769 18.64 0.00 36.96 1.28
2653 2820 7.998383 TGATCTTGGTATGCAACACCTTTATAT 59.002 33.333 18.64 7.88 36.96 0.86
2654 2821 7.342581 TGATCTTGGTATGCAACACCTTTATA 58.657 34.615 18.64 0.00 36.96 0.98
2655 2822 6.186957 TGATCTTGGTATGCAACACCTTTAT 58.813 36.000 18.64 10.59 36.96 1.40
2656 2823 5.565509 TGATCTTGGTATGCAACACCTTTA 58.434 37.500 18.64 7.07 36.96 1.85
2657 2824 4.406456 TGATCTTGGTATGCAACACCTTT 58.594 39.130 18.64 4.48 36.96 3.11
2658 2825 4.032960 TGATCTTGGTATGCAACACCTT 57.967 40.909 18.64 4.76 36.96 3.50
2659 2826 3.719268 TGATCTTGGTATGCAACACCT 57.281 42.857 18.64 2.06 36.96 4.00
2660 2827 3.947196 TCATGATCTTGGTATGCAACACC 59.053 43.478 12.76 12.76 36.54 4.16
2661 2828 4.497006 GCTCATGATCTTGGTATGCAACAC 60.497 45.833 8.60 0.00 0.00 3.32
2662 2829 3.628942 GCTCATGATCTTGGTATGCAACA 59.371 43.478 8.60 0.00 0.00 3.33
2663 2830 3.628942 TGCTCATGATCTTGGTATGCAAC 59.371 43.478 8.60 0.00 0.00 4.17
2664 2831 3.888583 TGCTCATGATCTTGGTATGCAA 58.111 40.909 8.60 0.00 0.00 4.08
2665 2832 3.564053 TGCTCATGATCTTGGTATGCA 57.436 42.857 8.60 10.61 0.00 3.96
2666 2833 3.881688 ACTTGCTCATGATCTTGGTATGC 59.118 43.478 8.60 8.60 0.00 3.14
2667 2834 4.261072 GCACTTGCTCATGATCTTGGTATG 60.261 45.833 8.60 0.00 38.21 2.39
2668 2835 3.881688 GCACTTGCTCATGATCTTGGTAT 59.118 43.478 8.60 0.00 38.21 2.73
2669 2836 3.273434 GCACTTGCTCATGATCTTGGTA 58.727 45.455 8.60 0.00 38.21 3.25
2670 2837 2.089980 GCACTTGCTCATGATCTTGGT 58.910 47.619 8.60 0.00 38.21 3.67
2671 2838 2.846039 GCACTTGCTCATGATCTTGG 57.154 50.000 8.60 1.65 38.21 3.61
2683 2850 0.248843 AGAGAGGCACTAGCACTTGC 59.751 55.000 0.00 0.00 41.55 4.01
2684 2851 2.006056 GCAGAGAGGCACTAGCACTTG 61.006 57.143 4.43 0.00 41.55 3.16
2685 2852 0.248843 GCAGAGAGGCACTAGCACTT 59.751 55.000 4.43 0.00 41.55 3.16
2686 2853 0.902048 TGCAGAGAGGCACTAGCACT 60.902 55.000 7.30 0.00 41.55 4.40
2687 2854 0.459934 CTGCAGAGAGGCACTAGCAC 60.460 60.000 8.42 0.00 41.55 4.40
2688 2855 1.895966 CTGCAGAGAGGCACTAGCA 59.104 57.895 8.42 10.23 41.55 3.49
2689 2856 1.521234 GCTGCAGAGAGGCACTAGC 60.521 63.158 20.43 0.00 41.55 3.42
2690 2857 1.143620 GGCTGCAGAGAGGCACTAG 59.856 63.158 20.43 0.00 41.55 2.57
2691 2858 1.610379 TGGCTGCAGAGAGGCACTA 60.610 57.895 20.43 0.00 43.18 2.74
2692 2859 2.926779 TGGCTGCAGAGAGGCACT 60.927 61.111 20.43 0.00 43.18 4.40
2695 2862 1.597578 GCTATGGCTGCAGAGAGGC 60.598 63.158 20.43 10.45 38.99 4.70
2696 2863 4.775295 GCTATGGCTGCAGAGAGG 57.225 61.111 20.43 3.84 35.22 3.69
2706 2873 1.826385 ACAGTGTTGGAAGCTATGGC 58.174 50.000 0.00 0.00 39.06 4.40
2707 2874 2.489329 CCAACAGTGTTGGAAGCTATGG 59.511 50.000 40.59 18.20 42.06 2.74
2708 2875 3.411446 TCCAACAGTGTTGGAAGCTATG 58.589 45.455 42.26 22.03 44.90 2.23
2709 2876 3.327757 TCTCCAACAGTGTTGGAAGCTAT 59.672 43.478 42.26 5.87 46.85 2.97
2710 2877 2.703536 TCTCCAACAGTGTTGGAAGCTA 59.296 45.455 42.26 29.81 46.85 3.32
2711 2878 1.490490 TCTCCAACAGTGTTGGAAGCT 59.510 47.619 42.26 7.35 46.85 3.74
2712 2879 1.967319 TCTCCAACAGTGTTGGAAGC 58.033 50.000 42.26 0.00 46.85 3.86
2713 2880 6.486657 TCTTATTTCTCCAACAGTGTTGGAAG 59.513 38.462 42.26 35.76 46.85 3.46
2714 2881 6.262273 GTCTTATTTCTCCAACAGTGTTGGAA 59.738 38.462 42.26 33.23 46.85 3.53
2715 2882 5.763204 GTCTTATTTCTCCAACAGTGTTGGA 59.237 40.000 41.38 41.38 45.61 3.53
2716 2883 5.048713 GGTCTTATTTCTCCAACAGTGTTGG 60.049 44.000 38.68 38.68 40.87 3.77
2717 2884 5.765182 AGGTCTTATTTCTCCAACAGTGTTG 59.235 40.000 26.06 26.06 0.00 3.33
2718 2885 5.941788 AGGTCTTATTTCTCCAACAGTGTT 58.058 37.500 1.64 1.64 0.00 3.32
2719 2886 5.568620 AGGTCTTATTTCTCCAACAGTGT 57.431 39.130 0.00 0.00 0.00 3.55
2720 2887 5.997746 TCAAGGTCTTATTTCTCCAACAGTG 59.002 40.000 0.00 0.00 0.00 3.66
2721 2888 6.187727 TCAAGGTCTTATTTCTCCAACAGT 57.812 37.500 0.00 0.00 0.00 3.55
2722 2889 7.510549 TTTCAAGGTCTTATTTCTCCAACAG 57.489 36.000 0.00 0.00 0.00 3.16
2723 2890 7.777910 TCTTTTCAAGGTCTTATTTCTCCAACA 59.222 33.333 0.00 0.00 0.00 3.33
2724 2891 8.166422 TCTTTTCAAGGTCTTATTTCTCCAAC 57.834 34.615 0.00 0.00 0.00 3.77
2725 2892 8.760980 TTCTTTTCAAGGTCTTATTTCTCCAA 57.239 30.769 0.00 0.00 0.00 3.53
2726 2893 8.760980 TTTCTTTTCAAGGTCTTATTTCTCCA 57.239 30.769 0.00 0.00 0.00 3.86
2835 3002 5.228579 TCACAATGTTATATGTGCAACCG 57.771 39.130 0.00 0.00 45.08 4.44
2841 3008 9.673454 CATTCATTCCTCACAATGTTATATGTG 57.327 33.333 0.00 0.00 46.44 3.21
2917 3084 4.037446 GCTCAGTTCAGTAGTATCCCAGAG 59.963 50.000 0.00 0.00 0.00 3.35
2969 3136 9.959749 GAAATTAAACAGTTTATCAAGTGACCA 57.040 29.630 6.58 0.00 36.87 4.02
3040 3207 6.932356 TTGATGTGCTTTAATCCTGATCTC 57.068 37.500 0.00 0.00 0.00 2.75
3050 3217 5.362430 ACCTTTCCAGTTTGATGTGCTTTAA 59.638 36.000 0.00 0.00 0.00 1.52
3054 3221 2.949447 ACCTTTCCAGTTTGATGTGCT 58.051 42.857 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.