Multiple sequence alignment - TraesCS3B01G473700

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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 TraesCS3B01G473700 chr3B 100.000 5124 0 0 1 5124 723027051 723032174 0.000000e+00 9463.0
1 TraesCS3B01G473700 chr3A 89.673 2508 183 34 1 2460 682971180 682973659 0.000000e+00 3127.0
2 TraesCS3B01G473700 chr3A 92.835 1312 67 10 2541 3840 682973639 682974935 0.000000e+00 1877.0
3 TraesCS3B01G473700 chr3A 91.153 633 41 14 4504 5124 682976047 682976676 0.000000e+00 845.0
4 TraesCS3B01G473700 chr3A 95.714 70 3 0 2477 2546 565776370 565776439 4.190000e-21 113.0
5 TraesCS3B01G473700 chr3D 94.777 1570 69 11 901 2460 546244875 546246441 0.000000e+00 2433.0
6 TraesCS3B01G473700 chr3D 93.924 1547 72 9 2550 4090 546246430 546247960 0.000000e+00 2316.0
7 TraesCS3B01G473700 chr3D 88.286 1050 72 21 4085 5124 546247995 546249003 0.000000e+00 1210.0
8 TraesCS3B01G473700 chr3D 85.523 898 95 24 1 868 546243996 546244888 0.000000e+00 905.0
9 TraesCS3B01G473700 chr3D 98.462 65 1 0 2482 2546 549228541 549228477 1.170000e-21 115.0
10 TraesCS3B01G473700 chr4D 91.111 90 5 2 4265 4352 241215298 241215210 9.010000e-23 119.0
11 TraesCS3B01G473700 chr2A 97.143 70 1 1 2477 2546 691479343 691479411 3.240000e-22 117.0
12 TraesCS3B01G473700 chr2A 98.462 65 1 0 2482 2546 456488471 456488407 1.170000e-21 115.0
13 TraesCS3B01G473700 chr5A 94.667 75 2 1 4265 4337 647044724 647044650 1.170000e-21 115.0
14 TraesCS3B01G473700 chr5A 94.444 72 1 2 2475 2546 393879859 393879791 1.950000e-19 108.0
15 TraesCS3B01G473700 chr6B 95.775 71 1 1 2476 2546 637123409 637123341 4.190000e-21 113.0
16 TraesCS3B01G473700 chr6B 95.588 68 3 0 2479 2546 504878393 504878326 5.420000e-20 110.0
17 TraesCS3B01G473700 chr5B 95.652 69 3 0 2478 2546 209646210 209646278 1.510000e-20 111.0
18 TraesCS3B01G473700 chr1A 93.421 76 4 1 2472 2546 33221315 33221240 1.510000e-20 111.0
19 TraesCS3B01G473700 chrUn 93.333 75 3 1 4265 4337 86448597 86448671 5.420000e-20 110.0
20 TraesCS3B01G473700 chrUn 93.333 75 3 1 4265 4337 86454597 86454671 5.420000e-20 110.0
21 TraesCS3B01G473700 chrUn 93.333 75 3 1 4265 4337 222680680 222680606 5.420000e-20 110.0
22 TraesCS3B01G473700 chrUn 93.333 75 3 1 4265 4337 358547246 358547320 5.420000e-20 110.0
23 TraesCS3B01G473700 chrUn 93.333 75 3 1 4265 4337 417500220 417500146 5.420000e-20 110.0
24 TraesCS3B01G473700 chrUn 93.333 75 3 1 4265 4337 427277248 427277322 5.420000e-20 110.0
25 TraesCS3B01G473700 chr5D 100.000 28 0 0 1205 1232 394988550 394988523 9.000000e-03 52.8


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 TraesCS3B01G473700 chr3B 723027051 723032174 5123 False 9463.000000 9463 100.000000 1 5124 1 chr3B.!!$F1 5123
1 TraesCS3B01G473700 chr3A 682971180 682976676 5496 False 1949.666667 3127 91.220333 1 5124 3 chr3A.!!$F2 5123
2 TraesCS3B01G473700 chr3D 546243996 546249003 5007 False 1716.000000 2433 90.627500 1 5124 4 chr3D.!!$F1 5123

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
570 598 0.179097 GAGCCGCGATTTCTTCCTCT 60.179 55.0 8.23 0.0 0.00 3.69 F
1609 1651 0.179205 CGACGAACGTCCTAGGTGAC 60.179 60.0 19.15 0.0 41.76 3.67 F
1661 1705 0.528684 GCACTGAGACATAGCGGGTC 60.529 60.0 0.00 0.0 35.50 4.46 F
2247 2297 0.964358 GCTGCTGCCTTTCCACAGAT 60.964 55.0 3.85 0.0 35.90 2.90 F
3539 3595 0.603439 TGCTTGCTCATCGTGCAGAA 60.603 50.0 0.00 0.0 41.71 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2524 2575 0.103876 ATAATCCCTCCCCAGACCCC 60.104 60.0 0.00 0.00 0.00 4.95 R
3034 3090 0.464735 GCCTAGAGTCGAGCCTCTGA 60.465 60.0 14.17 0.80 41.81 3.27 R
3124 3180 5.010282 ACAAGGTGAAAAGTTTCAGACAGT 58.990 37.5 6.72 2.31 46.80 3.55 R
3731 3794 0.449388 GCAGAACTCCATTTCCTGCG 59.551 55.0 0.00 0.00 0.00 5.18 R
4842 5457 0.182299 CTGGCTCTCCCCTTCCATTC 59.818 60.0 0.00 0.00 0.00 2.67 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
35 36 1.628846 TGGGCTAGGTCCAAGAAAGAC 59.371 52.381 0.00 0.00 32.75 3.01
36 37 1.628846 GGGCTAGGTCCAAGAAAGACA 59.371 52.381 0.00 0.00 35.89 3.41
47 49 2.763249 AGAAAGACAAGCAAGCAACG 57.237 45.000 0.00 0.00 0.00 4.10
69 71 4.626172 CGACAGGAAGCTAAGGTCTAAAAC 59.374 45.833 0.00 0.00 0.00 2.43
74 76 5.932883 AGGAAGCTAAGGTCTAAAACTTTCG 59.067 40.000 0.00 0.00 0.00 3.46
75 77 5.699915 GGAAGCTAAGGTCTAAAACTTTCGT 59.300 40.000 0.00 0.00 0.00 3.85
98 101 4.821260 TGAATTAGCTCAGAGTGTGCAAAA 59.179 37.500 0.00 0.00 39.15 2.44
165 168 2.524569 TGCATTCACAGTCGAGTCAA 57.475 45.000 0.00 0.00 0.00 3.18
234 237 1.212688 ACATTGGCCGAAGATCCATGA 59.787 47.619 1.21 0.00 30.93 3.07
238 241 1.004161 TGGCCGAAGATCCATGAAACA 59.996 47.619 0.00 0.00 0.00 2.83
244 247 5.504665 GCCGAAGATCCATGAAACAAGTATG 60.505 44.000 0.00 0.00 0.00 2.39
248 251 6.668541 AGATCCATGAAACAAGTATGAACG 57.331 37.500 0.00 0.00 0.00 3.95
265 268 0.389426 ACGCTTGCGAGAAACCGTAT 60.389 50.000 22.03 0.00 0.00 3.06
335 338 7.560991 ACCATGAATCAGATAATGCCTTTAACA 59.439 33.333 0.00 0.00 0.00 2.41
346 349 6.902224 AATGCCTTTAACAAACACTTTGAC 57.098 33.333 1.75 0.00 43.26 3.18
357 360 5.815222 ACAAACACTTTGACAAATTAAGGGC 59.185 36.000 0.05 0.00 43.26 5.19
358 361 5.606348 AACACTTTGACAAATTAAGGGCA 57.394 34.783 0.05 0.00 0.00 5.36
359 362 5.200368 ACACTTTGACAAATTAAGGGCAG 57.800 39.130 0.05 0.00 0.00 4.85
381 384 4.082571 AGCTTGTTTTGTGATGACTATGGC 60.083 41.667 0.00 0.00 0.00 4.40
428 456 3.699411 TTTGGTAGGCCGCTACTTTTA 57.301 42.857 0.00 0.00 37.67 1.52
433 461 1.935933 AGGCCGCTACTTTTACATCG 58.064 50.000 0.00 0.00 0.00 3.84
449 477 2.292016 ACATCGGTCAATTTGTTGCGAA 59.708 40.909 0.00 0.00 0.00 4.70
531 559 5.312079 CCCTCAAACTGTTCATCTTCTTCT 58.688 41.667 0.00 0.00 0.00 2.85
537 565 8.210946 TCAAACTGTTCATCTTCTTCTTCCTAA 58.789 33.333 0.00 0.00 0.00 2.69
544 572 6.467677 TCATCTTCTTCTTCCTAACCAACAG 58.532 40.000 0.00 0.00 0.00 3.16
556 584 1.722011 ACCAACAGAAATACGAGCCG 58.278 50.000 0.00 0.00 0.00 5.52
570 598 0.179097 GAGCCGCGATTTCTTCCTCT 60.179 55.000 8.23 0.00 0.00 3.69
605 633 0.970937 CTCCTACCTCGCCTCCAACA 60.971 60.000 0.00 0.00 0.00 3.33
614 642 2.626780 GCCTCCAACAAGTTCCCGC 61.627 63.158 0.00 0.00 0.00 6.13
618 646 4.038080 CAACAAGTTCCCGCCCGC 62.038 66.667 0.00 0.00 0.00 6.13
661 690 1.532316 TTCCGTCTCCAACTCGGGT 60.532 57.895 0.00 0.00 43.75 5.28
672 701 1.877443 CAACTCGGGTTTCGTCCAATT 59.123 47.619 0.00 0.00 40.32 2.32
673 702 2.265589 ACTCGGGTTTCGTCCAATTT 57.734 45.000 0.00 0.00 40.32 1.82
678 707 2.414957 CGGGTTTCGTCCAATTTAAGCC 60.415 50.000 0.00 0.00 34.04 4.35
714 744 2.773527 CCCCCTCCCAACCACACAA 61.774 63.158 0.00 0.00 0.00 3.33
726 756 0.881118 CCACACAATCAAACCTCCGG 59.119 55.000 0.00 0.00 0.00 5.14
729 759 1.247567 CACAATCAAACCTCCGGCTT 58.752 50.000 0.00 0.00 0.00 4.35
766 796 4.907034 CGTCGTCGATGGCTCCGG 62.907 72.222 7.77 0.00 39.71 5.14
770 800 3.838271 GTCGATGGCTCCGGCTCA 61.838 66.667 0.00 0.00 38.73 4.26
786 816 1.943507 GCTCAGGTGTTGCTTCTCCTC 60.944 57.143 0.00 0.00 0.00 3.71
794 824 2.079925 GTTGCTTCTCCTCTGCGAAAT 58.920 47.619 0.00 0.00 0.00 2.17
812 842 2.154854 ATATCGACTGGCGTGAATGG 57.845 50.000 1.46 0.00 41.80 3.16
814 844 2.593468 ATCGACTGGCGTGAATGGGG 62.593 60.000 1.46 0.00 41.80 4.96
826 856 3.554752 CGTGAATGGGGTTTTCAAGCAAT 60.555 43.478 0.00 0.00 35.03 3.56
830 860 2.402564 TGGGGTTTTCAAGCAATTGGA 58.597 42.857 7.72 0.00 0.00 3.53
836 866 4.632688 GGTTTTCAAGCAATTGGATGATGG 59.367 41.667 7.72 0.00 0.00 3.51
854 884 1.967066 TGGTGAATGGCAAAACCGAAT 59.033 42.857 10.77 0.00 43.94 3.34
910 941 6.070653 TCCTGCAGAGCATTCCAATTTTATTT 60.071 34.615 17.39 0.00 38.13 1.40
993 1024 9.099454 CACTAGAATATTTACCAACTTGGACTC 57.901 37.037 15.14 0.00 40.96 3.36
1465 1499 0.316841 GGATCAGCTCATCCTCCGAC 59.683 60.000 9.80 0.00 39.59 4.79
1551 1593 1.068250 CTCCCTTGCTAGTAGCCGC 59.932 63.158 19.41 0.00 41.51 6.53
1609 1651 0.179205 CGACGAACGTCCTAGGTGAC 60.179 60.000 19.15 0.00 41.76 3.67
1612 1654 0.879765 CGAACGTCCTAGGTGACAGT 59.120 55.000 9.08 0.94 34.88 3.55
1613 1655 2.079158 CGAACGTCCTAGGTGACAGTA 58.921 52.381 9.08 0.00 34.88 2.74
1645 1689 5.349543 GGAATCAAAATGATGAAACTGGCAC 59.650 40.000 0.00 0.00 37.15 5.01
1652 1696 2.104622 TGATGAAACTGGCACTGAGACA 59.895 45.455 0.00 0.00 0.00 3.41
1661 1705 0.528684 GCACTGAGACATAGCGGGTC 60.529 60.000 0.00 0.00 35.50 4.46
1668 1712 1.152525 ACATAGCGGGTCCCTCGAT 60.153 57.895 6.29 0.00 0.00 3.59
1673 1717 3.147595 CGGGTCCCTCGATGCAGA 61.148 66.667 6.29 0.00 0.00 4.26
1816 1864 4.212214 CAGTCACTTGGAACTAACAAGAGC 59.788 45.833 11.65 1.88 46.27 4.09
1817 1865 4.127171 GTCACTTGGAACTAACAAGAGCA 58.873 43.478 11.65 0.00 46.27 4.26
1841 1889 2.799126 TTGACCATTGCCCGTCTATT 57.201 45.000 0.00 0.00 0.00 1.73
1843 1891 4.431416 TTGACCATTGCCCGTCTATTAT 57.569 40.909 0.00 0.00 0.00 1.28
1847 1895 5.654650 TGACCATTGCCCGTCTATTATTTTT 59.345 36.000 0.00 0.00 0.00 1.94
1852 1900 6.439675 TTGCCCGTCTATTATTTTTACACC 57.560 37.500 0.00 0.00 0.00 4.16
1881 1929 5.474189 CCTGCCAATGATTTTGATTTTGGTT 59.526 36.000 0.00 0.00 39.21 3.67
2157 2207 4.211164 TGATGACACTTAAGTTTGTCTGCG 59.789 41.667 20.67 5.95 42.31 5.18
2223 2273 1.216064 TCCAGTGAATCATGGGAGGG 58.784 55.000 10.35 0.00 37.19 4.30
2247 2297 0.964358 GCTGCTGCCTTTCCACAGAT 60.964 55.000 3.85 0.00 35.90 2.90
2289 2339 9.442047 GTTCATCCAAATAATCCTGTCTATAGG 57.558 37.037 0.00 0.00 39.29 2.57
2316 2366 4.584325 TGCATATCCCTAAGGCATTTGTTC 59.416 41.667 0.00 0.00 0.00 3.18
2319 2369 3.085952 TCCCTAAGGCATTTGTTCCAG 57.914 47.619 0.00 0.00 0.00 3.86
2375 2425 6.127535 ACTCCATGAATTTTCCAGTATGCAAG 60.128 38.462 0.00 0.00 31.97 4.01
2394 2444 4.261741 GCAAGATGCAACCACTTATATGGG 60.262 45.833 0.00 0.00 43.05 4.00
2398 2448 6.852404 AGATGCAACCACTTATATGGGTATT 58.148 36.000 0.00 0.00 44.81 1.89
2468 2519 8.777578 AGTAGTATGTTGATCTATACCACCAA 57.222 34.615 0.00 0.00 31.65 3.67
2469 2520 9.209048 AGTAGTATGTTGATCTATACCACCAAA 57.791 33.333 0.00 0.00 31.65 3.28
2470 2521 9.826574 GTAGTATGTTGATCTATACCACCAAAA 57.173 33.333 0.00 0.00 31.65 2.44
2496 2547 8.463930 AAAATGTTGATCTAAAAGGACAGACA 57.536 30.769 0.00 0.00 0.00 3.41
2497 2548 7.440523 AATGTTGATCTAAAAGGACAGACAC 57.559 36.000 0.00 0.00 0.00 3.67
2498 2549 5.924356 TGTTGATCTAAAAGGACAGACACA 58.076 37.500 0.00 0.00 0.00 3.72
2499 2550 5.991606 TGTTGATCTAAAAGGACAGACACAG 59.008 40.000 0.00 0.00 0.00 3.66
2500 2551 5.808366 TGATCTAAAAGGACAGACACAGT 57.192 39.130 0.00 0.00 0.00 3.55
2501 2552 5.541845 TGATCTAAAAGGACAGACACAGTG 58.458 41.667 0.00 0.00 0.00 3.66
2502 2553 3.728845 TCTAAAAGGACAGACACAGTGC 58.271 45.455 0.00 0.00 0.00 4.40
2503 2554 2.418368 AAAAGGACAGACACAGTGCA 57.582 45.000 0.00 0.00 0.00 4.57
2504 2555 2.645838 AAAGGACAGACACAGTGCAT 57.354 45.000 0.00 0.00 0.00 3.96
2505 2556 3.769739 AAAGGACAGACACAGTGCATA 57.230 42.857 0.00 0.00 0.00 3.14
2506 2557 3.325293 AAGGACAGACACAGTGCATAG 57.675 47.619 0.00 0.00 0.00 2.23
2507 2558 2.529632 AGGACAGACACAGTGCATAGA 58.470 47.619 0.00 0.00 0.00 1.98
2508 2559 2.899900 AGGACAGACACAGTGCATAGAA 59.100 45.455 0.00 0.00 0.00 2.10
2509 2560 3.056250 AGGACAGACACAGTGCATAGAAG 60.056 47.826 0.00 0.00 0.00 2.85
2510 2561 2.670414 GACAGACACAGTGCATAGAAGC 59.330 50.000 0.00 0.00 0.00 3.86
2511 2562 2.301296 ACAGACACAGTGCATAGAAGCT 59.699 45.455 0.00 0.00 34.99 3.74
2512 2563 2.928757 CAGACACAGTGCATAGAAGCTC 59.071 50.000 0.00 0.00 34.99 4.09
2513 2564 2.093764 AGACACAGTGCATAGAAGCTCC 60.094 50.000 0.00 0.00 34.99 4.70
2514 2565 1.065854 ACACAGTGCATAGAAGCTCCC 60.066 52.381 0.00 0.00 34.99 4.30
2515 2566 1.065926 CACAGTGCATAGAAGCTCCCA 60.066 52.381 0.00 0.00 34.99 4.37
2516 2567 1.065854 ACAGTGCATAGAAGCTCCCAC 60.066 52.381 0.00 0.00 34.99 4.61
2517 2568 1.065926 CAGTGCATAGAAGCTCCCACA 60.066 52.381 0.00 0.00 34.99 4.17
2518 2569 1.065854 AGTGCATAGAAGCTCCCACAC 60.066 52.381 0.00 0.00 34.99 3.82
2519 2570 0.983467 TGCATAGAAGCTCCCACACA 59.017 50.000 0.00 0.00 34.99 3.72
2520 2571 1.350684 TGCATAGAAGCTCCCACACAA 59.649 47.619 0.00 0.00 34.99 3.33
2521 2572 2.012673 GCATAGAAGCTCCCACACAAG 58.987 52.381 0.00 0.00 0.00 3.16
2522 2573 2.636830 CATAGAAGCTCCCACACAAGG 58.363 52.381 0.00 0.00 0.00 3.61
2523 2574 1.729586 TAGAAGCTCCCACACAAGGT 58.270 50.000 0.00 0.00 0.00 3.50
2531 2582 4.481195 CACACAAGGTGGGGTCTG 57.519 61.111 1.07 0.00 44.04 3.51
2532 2583 1.228245 CACACAAGGTGGGGTCTGG 60.228 63.158 1.07 0.00 44.04 3.86
2533 2584 2.436109 CACAAGGTGGGGTCTGGG 59.564 66.667 0.00 0.00 0.00 4.45
2534 2585 2.858974 ACAAGGTGGGGTCTGGGG 60.859 66.667 0.00 0.00 0.00 4.96
2535 2586 2.531685 CAAGGTGGGGTCTGGGGA 60.532 66.667 0.00 0.00 0.00 4.81
2536 2587 2.204151 AAGGTGGGGTCTGGGGAG 60.204 66.667 0.00 0.00 0.00 4.30
2537 2588 3.891432 AAGGTGGGGTCTGGGGAGG 62.891 68.421 0.00 0.00 0.00 4.30
2539 2590 4.348495 GTGGGGTCTGGGGAGGGA 62.348 72.222 0.00 0.00 0.00 4.20
2544 2595 1.153565 GGGGTCTGGGGAGGGATTATA 59.846 57.143 0.00 0.00 0.00 0.98
2553 2604 4.104831 GGGGAGGGATTATAGTAGCATGT 58.895 47.826 0.00 0.00 0.00 3.21
2557 2608 6.166982 GGAGGGATTATAGTAGCATGTTGAC 58.833 44.000 0.00 0.00 0.00 3.18
2603 2654 9.740239 CTGCTATGTTGATTACATGCTATTTTT 57.260 29.630 0.00 0.00 46.81 1.94
2608 2659 8.870160 TGTTGATTACATGCTATTTTTATGGC 57.130 30.769 0.00 0.00 0.00 4.40
2609 2660 8.473219 TGTTGATTACATGCTATTTTTATGGCA 58.527 29.630 0.00 0.00 42.13 4.92
2610 2661 9.311916 GTTGATTACATGCTATTTTTATGGCAA 57.688 29.630 0.00 0.00 41.28 4.52
2707 2759 9.838339 TTGTTGGACAAAAATATAACACCAATT 57.162 25.926 0.00 0.00 34.76 2.32
2759 2811 5.659440 TTTATGGAAGGCAAAAGATGGTC 57.341 39.130 0.00 0.00 0.00 4.02
2760 2812 1.923356 TGGAAGGCAAAAGATGGTCC 58.077 50.000 0.00 0.00 0.00 4.46
2761 2813 1.146774 TGGAAGGCAAAAGATGGTCCA 59.853 47.619 0.00 0.00 0.00 4.02
2762 2814 1.821136 GGAAGGCAAAAGATGGTCCAG 59.179 52.381 0.00 0.00 0.00 3.86
2763 2815 2.555227 GGAAGGCAAAAGATGGTCCAGA 60.555 50.000 0.00 0.00 0.00 3.86
2764 2816 2.503895 AGGCAAAAGATGGTCCAGAG 57.496 50.000 0.00 0.00 0.00 3.35
2765 2817 1.707427 AGGCAAAAGATGGTCCAGAGT 59.293 47.619 0.00 0.00 0.00 3.24
2766 2818 2.087646 GGCAAAAGATGGTCCAGAGTC 58.912 52.381 0.00 0.00 0.00 3.36
2767 2819 2.087646 GCAAAAGATGGTCCAGAGTCC 58.912 52.381 0.00 0.00 0.00 3.85
2781 2833 3.054728 CCAGAGTCCAGACTAGAGAGACA 60.055 52.174 0.00 0.00 42.66 3.41
2799 2851 5.704515 AGAGACAATTGACCTGTTCTTGATG 59.295 40.000 13.59 0.00 0.00 3.07
2833 2888 6.871844 TGATCTTTTGATTGTGTTCAACCAA 58.128 32.000 0.00 0.00 39.67 3.67
2890 2945 4.322198 GGGCAGATTCATTGCAAAGAGAAA 60.322 41.667 1.71 0.00 43.28 2.52
3034 3090 5.760253 GTCCATGTAGTATACTGCAGCATTT 59.240 40.000 24.87 8.65 43.54 2.32
3460 3516 4.887655 CCTACTTGTCTGGAAGGTTTGTTT 59.112 41.667 0.00 0.00 0.00 2.83
3475 3531 5.062809 AGGTTTGTTTGCACGTGTTTTTATG 59.937 36.000 18.38 0.00 0.00 1.90
3477 3533 6.034683 GGTTTGTTTGCACGTGTTTTTATGTA 59.965 34.615 18.38 0.00 0.00 2.29
3486 3542 8.343366 TGCACGTGTTTTTATGTAAATACAGAA 58.657 29.630 18.38 0.00 37.64 3.02
3539 3595 0.603439 TGCTTGCTCATCGTGCAGAA 60.603 50.000 0.00 0.00 41.71 3.02
3635 3691 4.379243 AGAAGCGACACCTGCCCG 62.379 66.667 0.00 0.00 0.00 6.13
3669 3725 1.950007 CGATATCTCGTGCTCCCGT 59.050 57.895 0.34 0.00 40.07 5.28
3715 3778 1.572085 CTGCAAGCCTGACAACTCCG 61.572 60.000 0.00 0.00 0.00 4.63
3731 3794 2.208431 CTCCGACAATCTGCTGGAATC 58.792 52.381 0.00 0.00 0.00 2.52
3804 3867 2.012673 CATCAGGAAGAGCGGGAAAAG 58.987 52.381 0.00 0.00 0.00 2.27
3845 3908 4.249661 GCTGAAGAGTCTGTAAAGGGAAG 58.750 47.826 0.00 0.00 0.00 3.46
3912 3975 3.629398 AGTTCTTTGCTGTCTGAAACCTG 59.371 43.478 0.00 0.00 0.00 4.00
3934 4000 0.516001 TCGTTCTCGAGACCGACTTG 59.484 55.000 28.22 7.49 41.35 3.16
3943 4009 2.662700 GAGACCGACTTGTGTGTACTG 58.337 52.381 0.00 0.00 0.00 2.74
3950 4016 4.509970 CCGACTTGTGTGTACTGAAATCAA 59.490 41.667 0.00 0.00 0.00 2.57
4025 4091 4.072839 TCAGCGATGGAGTTCGATAGTAT 58.927 43.478 0.00 0.00 41.62 2.12
4205 4344 4.288366 TGTTCATGAGTTAATGGGTCCTCA 59.712 41.667 0.00 0.00 38.24 3.86
4206 4345 5.222027 TGTTCATGAGTTAATGGGTCCTCAA 60.222 40.000 0.00 0.00 37.48 3.02
4207 4346 5.512942 TCATGAGTTAATGGGTCCTCAAA 57.487 39.130 0.00 0.00 37.48 2.69
4208 4347 6.078456 TCATGAGTTAATGGGTCCTCAAAT 57.922 37.500 0.00 0.00 37.48 2.32
4209 4348 7.206789 TCATGAGTTAATGGGTCCTCAAATA 57.793 36.000 0.00 0.00 37.48 1.40
4222 4539 7.065504 GGGTCCTCAAATAGAGTACTAGGTTA 58.934 42.308 0.00 0.00 43.12 2.85
4251 4568 2.831685 TGTTGCGACAATGACCTAGT 57.168 45.000 3.66 0.00 31.49 2.57
4252 4569 3.120321 TGTTGCGACAATGACCTAGTT 57.880 42.857 3.66 0.00 31.49 2.24
4253 4570 4.260139 TGTTGCGACAATGACCTAGTTA 57.740 40.909 3.66 0.00 31.49 2.24
4377 4749 3.873361 CGACAGACCAATGTTGATAGCAT 59.127 43.478 0.00 0.00 36.80 3.79
4386 4758 6.658816 ACCAATGTTGATAGCATTAGTTGTGA 59.341 34.615 0.00 0.00 35.09 3.58
4387 4759 6.968904 CCAATGTTGATAGCATTAGTTGTGAC 59.031 38.462 0.00 0.00 35.09 3.67
4389 4761 5.804639 TGTTGATAGCATTAGTTGTGACCT 58.195 37.500 0.00 0.00 0.00 3.85
4390 4762 6.941857 TGTTGATAGCATTAGTTGTGACCTA 58.058 36.000 0.00 0.00 0.00 3.08
4391 4763 7.041721 TGTTGATAGCATTAGTTGTGACCTAG 58.958 38.462 0.00 0.00 0.00 3.02
4392 4764 6.791867 TGATAGCATTAGTTGTGACCTAGT 57.208 37.500 0.00 0.00 0.00 2.57
4393 4765 7.182817 TGATAGCATTAGTTGTGACCTAGTT 57.817 36.000 0.00 0.00 0.00 2.24
4394 4766 8.301252 TGATAGCATTAGTTGTGACCTAGTTA 57.699 34.615 0.00 0.00 0.00 2.24
4395 4767 8.924303 TGATAGCATTAGTTGTGACCTAGTTAT 58.076 33.333 0.00 0.00 0.00 1.89
4396 4768 9.765795 GATAGCATTAGTTGTGACCTAGTTATT 57.234 33.333 0.00 0.00 0.00 1.40
4397 4769 9.765795 ATAGCATTAGTTGTGACCTAGTTATTC 57.234 33.333 0.00 0.00 0.00 1.75
4398 4770 7.620880 AGCATTAGTTGTGACCTAGTTATTCA 58.379 34.615 0.00 0.00 0.00 2.57
4399 4771 7.549488 AGCATTAGTTGTGACCTAGTTATTCAC 59.451 37.037 0.00 0.00 40.14 3.18
4400 4772 7.333423 GCATTAGTTGTGACCTAGTTATTCACA 59.667 37.037 8.76 8.76 46.11 3.58
4401 4773 9.383519 CATTAGTTGTGACCTAGTTATTCACAT 57.616 33.333 12.07 4.51 46.78 3.21
4402 4774 9.959721 ATTAGTTGTGACCTAGTTATTCACATT 57.040 29.630 12.07 8.18 46.78 2.71
4403 4775 7.907214 AGTTGTGACCTAGTTATTCACATTC 57.093 36.000 12.07 9.59 46.78 2.67
4404 4776 7.450074 AGTTGTGACCTAGTTATTCACATTCA 58.550 34.615 12.07 0.00 46.78 2.57
4405 4777 7.387948 AGTTGTGACCTAGTTATTCACATTCAC 59.612 37.037 12.07 9.00 46.78 3.18
4406 4778 6.170506 TGTGACCTAGTTATTCACATTCACC 58.829 40.000 8.76 0.00 43.63 4.02
4407 4779 6.170506 GTGACCTAGTTATTCACATTCACCA 58.829 40.000 0.00 0.00 39.60 4.17
4408 4780 6.092259 GTGACCTAGTTATTCACATTCACCAC 59.908 42.308 0.00 0.00 39.60 4.16
4409 4781 6.013725 TGACCTAGTTATTCACATTCACCACT 60.014 38.462 0.00 0.00 0.00 4.00
4425 4906 1.171308 CACTCCCGTCCTCGAAGTTA 58.829 55.000 0.00 0.00 39.71 2.24
4426 4907 1.749634 CACTCCCGTCCTCGAAGTTAT 59.250 52.381 0.00 0.00 39.71 1.89
4437 4918 7.064253 CCGTCCTCGAAGTTATAAAATTTCACT 59.936 37.037 0.00 0.00 39.71 3.41
4475 4956 3.932822 TGCTGAAGTGAGCGGTATAAAA 58.067 40.909 0.00 0.00 42.32 1.52
4478 4959 3.869065 TGAAGTGAGCGGTATAAAAGGG 58.131 45.455 0.00 0.00 0.00 3.95
4486 4967 5.006153 AGCGGTATAAAAGGGCAATTTTC 57.994 39.130 3.31 0.00 34.35 2.29
4491 4972 6.348498 GGTATAAAAGGGCAATTTTCAGCAT 58.652 36.000 3.31 0.00 34.35 3.79
4500 4981 7.833786 AGGGCAATTTTCAGCATACATATATG 58.166 34.615 11.29 11.29 41.16 1.78
4549 5126 6.792326 ACTTTGGCTTCTGTTAAACTGTTAC 58.208 36.000 0.00 0.00 0.00 2.50
4638 5249 3.891366 ACTGAGCTAAAGTTGCCAACATT 59.109 39.130 10.69 6.82 0.00 2.71
4639 5250 4.022849 ACTGAGCTAAAGTTGCCAACATTC 60.023 41.667 10.69 0.00 0.00 2.67
4640 5251 3.255642 TGAGCTAAAGTTGCCAACATTCC 59.744 43.478 10.69 0.00 0.00 3.01
4641 5252 3.500343 AGCTAAAGTTGCCAACATTCCT 58.500 40.909 10.69 2.04 0.00 3.36
4642 5253 3.256631 AGCTAAAGTTGCCAACATTCCTG 59.743 43.478 10.69 0.37 0.00 3.86
4643 5254 3.005791 GCTAAAGTTGCCAACATTCCTGT 59.994 43.478 10.69 0.00 37.12 4.00
4644 5255 4.217550 GCTAAAGTTGCCAACATTCCTGTA 59.782 41.667 10.69 0.00 33.36 2.74
4645 5256 5.278758 GCTAAAGTTGCCAACATTCCTGTAA 60.279 40.000 10.69 0.00 33.36 2.41
4646 5257 5.806654 AAAGTTGCCAACATTCCTGTAAT 57.193 34.783 10.69 0.00 33.36 1.89
4647 5258 5.391312 AAGTTGCCAACATTCCTGTAATC 57.609 39.130 10.69 0.00 33.36 1.75
4648 5259 4.666512 AGTTGCCAACATTCCTGTAATCT 58.333 39.130 10.69 0.00 33.36 2.40
4649 5260 5.079643 AGTTGCCAACATTCCTGTAATCTT 58.920 37.500 10.69 0.00 33.36 2.40
4650 5261 5.047802 AGTTGCCAACATTCCTGTAATCTTG 60.048 40.000 10.69 0.00 33.36 3.02
4651 5262 3.193267 TGCCAACATTCCTGTAATCTTGC 59.807 43.478 0.00 0.00 33.36 4.01
4652 5263 3.731867 GCCAACATTCCTGTAATCTTGCG 60.732 47.826 0.00 0.00 33.36 4.85
4653 5264 3.689161 CCAACATTCCTGTAATCTTGCGA 59.311 43.478 0.00 0.00 33.36 5.10
4654 5265 4.155826 CCAACATTCCTGTAATCTTGCGAA 59.844 41.667 0.00 0.00 33.36 4.70
4655 5266 4.946784 ACATTCCTGTAATCTTGCGAAC 57.053 40.909 0.00 0.00 32.49 3.95
4656 5267 4.323417 ACATTCCTGTAATCTTGCGAACA 58.677 39.130 0.00 0.00 32.49 3.18
4657 5268 4.943705 ACATTCCTGTAATCTTGCGAACAT 59.056 37.500 0.00 0.00 32.49 2.71
4660 5271 5.079689 TCCTGTAATCTTGCGAACATACA 57.920 39.130 0.00 0.00 0.00 2.29
4842 5457 2.094675 ACTGGGAGCATTTCATTTCCG 58.905 47.619 0.00 0.00 0.00 4.30
4885 5501 5.486526 CAAGCTGGCATTTTTATTGGGTAA 58.513 37.500 0.00 0.00 0.00 2.85
5026 5642 1.078848 CCCCTTGAAGGAGCTCACG 60.079 63.158 13.97 0.00 37.67 4.35
5116 5732 1.536284 CCCTCGGCTTCTGATACGTTC 60.536 57.143 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.662619 TTCCTGTCGTTGCTTGCTTG 59.337 50.000 0.00 0.00 0.00 4.01
36 37 0.947244 CTTCCTGTCGTTGCTTGCTT 59.053 50.000 0.00 0.00 0.00 3.91
47 49 5.795972 AGTTTTAGACCTTAGCTTCCTGTC 58.204 41.667 0.00 0.00 0.00 3.51
69 71 4.926238 ACACTCTGAGCTAATTCACGAAAG 59.074 41.667 4.19 0.00 0.00 2.62
74 76 3.329386 TGCACACTCTGAGCTAATTCAC 58.671 45.455 4.19 0.00 34.99 3.18
75 77 3.683365 TGCACACTCTGAGCTAATTCA 57.317 42.857 4.19 0.00 34.99 2.57
101 104 7.147846 CCAACCAAATAAGGCATGAGTCTATTT 60.148 37.037 0.00 0.00 0.00 1.40
102 105 6.322201 CCAACCAAATAAGGCATGAGTCTATT 59.678 38.462 0.00 0.00 0.00 1.73
107 110 3.778265 ACCAACCAAATAAGGCATGAGT 58.222 40.909 0.00 0.00 0.00 3.41
165 168 7.575414 TGTTAGTTTTGTATGTTCATGGTGT 57.425 32.000 0.00 0.00 0.00 4.16
211 214 3.358111 TGGATCTTCGGCCAATGTTAA 57.642 42.857 2.24 0.00 0.00 2.01
212 215 3.118075 TCATGGATCTTCGGCCAATGTTA 60.118 43.478 2.24 0.00 37.78 2.41
213 216 2.026641 CATGGATCTTCGGCCAATGTT 58.973 47.619 2.24 0.00 37.78 2.71
234 237 2.546368 TCGCAAGCGTTCATACTTGTTT 59.454 40.909 14.57 0.00 44.12 2.83
238 241 2.363788 TCTCGCAAGCGTTCATACTT 57.636 45.000 14.57 0.00 40.74 2.24
244 247 1.154654 CGGTTTCTCGCAAGCGTTC 60.155 57.895 14.57 2.21 41.62 3.95
248 251 1.588861 GAGATACGGTTTCTCGCAAGC 59.411 52.381 11.87 0.00 31.07 4.01
265 268 1.078214 CTTGGAGCCGCATTGGAGA 60.078 57.895 0.00 0.00 42.00 3.71
323 326 6.402222 TGTCAAAGTGTTTGTTAAAGGCATT 58.598 32.000 0.00 0.00 41.36 3.56
335 338 5.983540 TGCCCTTAATTTGTCAAAGTGTTT 58.016 33.333 8.48 0.00 0.00 2.83
346 349 4.815846 ACAAAACAAGCTGCCCTTAATTTG 59.184 37.500 15.02 15.02 40.50 2.32
357 360 5.396484 CCATAGTCATCACAAAACAAGCTG 58.604 41.667 0.00 0.00 0.00 4.24
358 361 4.082571 GCCATAGTCATCACAAAACAAGCT 60.083 41.667 0.00 0.00 0.00 3.74
359 362 4.168760 GCCATAGTCATCACAAAACAAGC 58.831 43.478 0.00 0.00 0.00 4.01
404 407 3.918294 AGTAGCGGCCTACCAAAAATA 57.082 42.857 0.00 0.00 44.05 1.40
428 456 1.876799 TCGCAACAAATTGACCGATGT 59.123 42.857 0.00 0.00 38.15 3.06
433 461 2.928694 ACGATTCGCAACAAATTGACC 58.071 42.857 5.86 0.00 38.15 4.02
469 497 3.369997 GGAAGAAGAGGACAATCTGACCC 60.370 52.174 0.00 0.00 32.57 4.46
472 500 3.772025 GGAGGAAGAAGAGGACAATCTGA 59.228 47.826 0.00 0.00 0.00 3.27
506 534 2.887151 AGATGAACAGTTTGAGGGGG 57.113 50.000 0.00 0.00 0.00 5.40
531 559 4.933400 GCTCGTATTTCTGTTGGTTAGGAA 59.067 41.667 0.00 0.00 0.00 3.36
537 565 1.722011 CGGCTCGTATTTCTGTTGGT 58.278 50.000 0.00 0.00 0.00 3.67
544 572 1.859080 AGAAATCGCGGCTCGTATTTC 59.141 47.619 16.54 16.54 40.62 2.17
556 584 2.556257 GAGGGAAGAGGAAGAAATCGC 58.444 52.381 0.00 0.00 0.00 4.58
570 598 1.916777 GAGACGGGTTGGGAGGGAA 60.917 63.158 0.00 0.00 0.00 3.97
626 654 0.798776 GAAGTGACATTGCGTCCCAG 59.201 55.000 0.00 0.00 44.71 4.45
627 655 0.605319 GGAAGTGACATTGCGTCCCA 60.605 55.000 0.00 0.00 44.71 4.37
661 690 3.829601 ACCATGGCTTAAATTGGACGAAA 59.170 39.130 13.04 0.00 33.36 3.46
672 701 5.183140 GCTTTTAACTCTGACCATGGCTTAA 59.817 40.000 13.04 3.42 0.00 1.85
673 702 4.700213 GCTTTTAACTCTGACCATGGCTTA 59.300 41.667 13.04 0.00 0.00 3.09
678 707 2.755103 GGGGCTTTTAACTCTGACCATG 59.245 50.000 0.00 0.00 0.00 3.66
766 796 0.036022 AGGAGAAGCAACACCTGAGC 59.964 55.000 0.00 0.00 30.27 4.26
770 800 0.036022 GCAGAGGAGAAGCAACACCT 59.964 55.000 0.00 0.00 33.84 4.00
786 816 0.504384 CGCCAGTCGATATTTCGCAG 59.496 55.000 0.18 0.00 45.10 5.18
794 824 0.104120 CCCATTCACGCCAGTCGATA 59.896 55.000 0.00 0.00 41.67 2.92
801 831 0.468214 TGAAAACCCCATTCACGCCA 60.468 50.000 0.00 0.00 32.10 5.69
806 836 4.387598 CAATTGCTTGAAAACCCCATTCA 58.612 39.130 0.00 0.00 34.04 2.57
809 839 2.978278 TCCAATTGCTTGAAAACCCCAT 59.022 40.909 0.00 0.00 34.04 4.00
812 842 4.270245 TCATCCAATTGCTTGAAAACCC 57.730 40.909 0.00 0.00 34.04 4.11
814 844 5.121142 CACCATCATCCAATTGCTTGAAAAC 59.879 40.000 11.20 0.00 34.04 2.43
826 856 2.528673 TGCCATTCACCATCATCCAA 57.471 45.000 0.00 0.00 0.00 3.53
830 860 2.094078 CGGTTTTGCCATTCACCATCAT 60.094 45.455 0.00 0.00 36.97 2.45
836 866 4.805219 ACTTATTCGGTTTTGCCATTCAC 58.195 39.130 0.00 0.00 36.97 3.18
872 902 4.560108 GCTCTGCAGGATTGAAAACACAAT 60.560 41.667 15.13 0.00 42.19 2.71
876 906 2.585330 TGCTCTGCAGGATTGAAAACA 58.415 42.857 15.13 0.00 33.32 2.83
877 907 3.863142 ATGCTCTGCAGGATTGAAAAC 57.137 42.857 15.13 0.00 43.65 2.43
910 941 5.155278 TGCTTCGGTTCTAAGAACCATAA 57.845 39.130 18.33 12.73 40.28 1.90
921 952 4.647424 TTTTGTCAAATGCTTCGGTTCT 57.353 36.364 0.00 0.00 0.00 3.01
993 1024 2.878429 CGAGGTCAGTCAGTCCCG 59.122 66.667 0.00 0.00 0.00 5.14
1155 1187 4.430765 GTCGGCGATGGTGACCGT 62.431 66.667 14.79 0.00 46.92 4.83
1248 1280 2.498941 GGATGAGACGGGATGCGGA 61.499 63.158 0.00 0.00 0.00 5.54
1249 1281 2.029666 GGATGAGACGGGATGCGG 59.970 66.667 0.00 0.00 0.00 5.69
1551 1593 2.599082 GCGTCAGACAAATCGAACCTAG 59.401 50.000 0.41 0.00 0.00 3.02
1609 1651 9.256477 CATCATTTTGATTCCATGGAAATACTG 57.744 33.333 30.28 20.60 34.28 2.74
1613 1655 9.169592 GTTTCATCATTTTGATTCCATGGAAAT 57.830 29.630 30.28 18.37 34.28 2.17
1645 1689 0.757188 AGGGACCCGCTATGTCTCAG 60.757 60.000 4.40 0.00 35.60 3.35
1652 1696 2.574955 GCATCGAGGGACCCGCTAT 61.575 63.158 12.91 3.91 0.00 2.97
1661 1705 4.227134 CCCGGTCTGCATCGAGGG 62.227 72.222 0.00 4.74 0.00 4.30
1668 1712 1.760613 CCTCTATAAACCCGGTCTGCA 59.239 52.381 0.00 0.00 0.00 4.41
1673 1717 1.761198 GTGCTCCTCTATAAACCCGGT 59.239 52.381 0.00 0.00 0.00 5.28
1816 1864 0.523072 CGGGCAATGGTCAAAGAGTG 59.477 55.000 0.00 0.00 0.00 3.51
1817 1865 0.110486 ACGGGCAATGGTCAAAGAGT 59.890 50.000 0.00 0.00 0.00 3.24
1841 1889 3.074687 TGGCAGGACAGGGTGTAAAAATA 59.925 43.478 0.00 0.00 0.00 1.40
1843 1891 1.215673 TGGCAGGACAGGGTGTAAAAA 59.784 47.619 0.00 0.00 0.00 1.94
1847 1895 0.327924 CATTGGCAGGACAGGGTGTA 59.672 55.000 0.00 0.00 0.00 2.90
1852 1900 2.827322 TCAAAATCATTGGCAGGACAGG 59.173 45.455 0.00 0.00 0.00 4.00
1881 1929 5.402054 AGGGATAAGATTTGCCACCAATA 57.598 39.130 0.00 0.00 0.00 1.90
2098 2148 6.108015 CCATTAGCTGTTTGGTGCATTAAAT 58.892 36.000 0.00 0.00 0.00 1.40
2102 2152 2.899256 ACCATTAGCTGTTTGGTGCATT 59.101 40.909 14.18 0.00 42.09 3.56
2131 2181 6.662616 CAGACAAACTTAAGTGTCATCAAGG 58.337 40.000 21.68 3.09 45.40 3.61
2223 2273 0.104671 TGGAAAGGCAGCAGCAAAAC 59.895 50.000 2.65 0.00 44.61 2.43
2247 2297 8.592529 TTGGATGAACATATTCCTCAAAATCA 57.407 30.769 0.00 0.00 32.65 2.57
2289 2339 2.517959 TGCCTTAGGGATATGCATTGC 58.482 47.619 3.54 0.46 33.58 3.56
2316 2366 1.203050 ACCCCTCCAAACATGTTCTGG 60.203 52.381 23.17 23.17 0.00 3.86
2319 2369 4.086457 ACATTACCCCTCCAAACATGTTC 58.914 43.478 12.39 0.00 0.00 3.18
2353 2403 6.211587 TCTTGCATACTGGAAAATTCATGG 57.788 37.500 0.00 0.00 0.00 3.66
2354 2404 6.200286 GCATCTTGCATACTGGAAAATTCATG 59.800 38.462 0.00 0.00 44.26 3.07
2375 2425 6.714810 TGAATACCCATATAAGTGGTTGCATC 59.285 38.462 0.00 0.00 37.57 3.91
2398 2448 9.083422 TGGAAACCAAAGATTAAATGTACATGA 57.917 29.630 9.63 0.00 0.00 3.07
2442 2493 9.871175 TTGGTGGTATAGATCAACATACTACTA 57.129 33.333 18.93 14.30 38.47 1.82
2443 2494 8.777578 TTGGTGGTATAGATCAACATACTACT 57.222 34.615 18.93 0.00 38.47 2.57
2444 2495 9.826574 TTTTGGTGGTATAGATCAACATACTAC 57.173 33.333 14.74 14.74 37.99 2.73
2470 2521 8.912988 TGTCTGTCCTTTTAGATCAACATTTTT 58.087 29.630 0.00 0.00 0.00 1.94
2471 2522 8.352942 GTGTCTGTCCTTTTAGATCAACATTTT 58.647 33.333 0.00 0.00 0.00 1.82
2472 2523 7.502226 TGTGTCTGTCCTTTTAGATCAACATTT 59.498 33.333 0.00 0.00 0.00 2.32
2473 2524 6.998074 TGTGTCTGTCCTTTTAGATCAACATT 59.002 34.615 0.00 0.00 0.00 2.71
2474 2525 6.533730 TGTGTCTGTCCTTTTAGATCAACAT 58.466 36.000 0.00 0.00 0.00 2.71
2475 2526 5.924356 TGTGTCTGTCCTTTTAGATCAACA 58.076 37.500 0.00 0.00 0.00 3.33
2476 2527 5.992217 ACTGTGTCTGTCCTTTTAGATCAAC 59.008 40.000 0.00 0.00 0.00 3.18
2477 2528 5.991606 CACTGTGTCTGTCCTTTTAGATCAA 59.008 40.000 0.00 0.00 0.00 2.57
2478 2529 5.541845 CACTGTGTCTGTCCTTTTAGATCA 58.458 41.667 0.00 0.00 0.00 2.92
2479 2530 4.390297 GCACTGTGTCTGTCCTTTTAGATC 59.610 45.833 9.86 0.00 0.00 2.75
2480 2531 4.202357 TGCACTGTGTCTGTCCTTTTAGAT 60.202 41.667 9.86 0.00 0.00 1.98
2481 2532 3.133901 TGCACTGTGTCTGTCCTTTTAGA 59.866 43.478 9.86 0.00 0.00 2.10
2482 2533 3.466836 TGCACTGTGTCTGTCCTTTTAG 58.533 45.455 9.86 0.00 0.00 1.85
2483 2534 3.552132 TGCACTGTGTCTGTCCTTTTA 57.448 42.857 9.86 0.00 0.00 1.52
2484 2535 2.418368 TGCACTGTGTCTGTCCTTTT 57.582 45.000 9.86 0.00 0.00 2.27
2485 2536 2.645838 ATGCACTGTGTCTGTCCTTT 57.354 45.000 9.86 0.00 0.00 3.11
2486 2537 2.899900 TCTATGCACTGTGTCTGTCCTT 59.100 45.455 9.86 0.00 0.00 3.36
2487 2538 2.529632 TCTATGCACTGTGTCTGTCCT 58.470 47.619 9.86 0.00 0.00 3.85
2488 2539 3.257393 CTTCTATGCACTGTGTCTGTCC 58.743 50.000 9.86 0.00 0.00 4.02
2489 2540 2.670414 GCTTCTATGCACTGTGTCTGTC 59.330 50.000 9.86 0.00 0.00 3.51
2490 2541 2.301296 AGCTTCTATGCACTGTGTCTGT 59.699 45.455 9.86 0.00 34.99 3.41
2491 2542 2.928757 GAGCTTCTATGCACTGTGTCTG 59.071 50.000 9.86 0.00 34.99 3.51
2492 2543 2.093764 GGAGCTTCTATGCACTGTGTCT 60.094 50.000 9.86 0.00 34.99 3.41
2493 2544 2.275318 GGAGCTTCTATGCACTGTGTC 58.725 52.381 9.86 2.63 34.99 3.67
2494 2545 1.065854 GGGAGCTTCTATGCACTGTGT 60.066 52.381 9.86 0.00 34.99 3.72
2495 2546 1.065926 TGGGAGCTTCTATGCACTGTG 60.066 52.381 2.76 2.76 34.99 3.66
2496 2547 1.065854 GTGGGAGCTTCTATGCACTGT 60.066 52.381 0.00 0.00 34.99 3.55
2497 2548 1.065926 TGTGGGAGCTTCTATGCACTG 60.066 52.381 0.00 0.00 34.99 3.66
2498 2549 1.065854 GTGTGGGAGCTTCTATGCACT 60.066 52.381 0.00 0.00 34.99 4.40
2499 2550 1.339055 TGTGTGGGAGCTTCTATGCAC 60.339 52.381 0.00 0.00 34.99 4.57
2500 2551 0.983467 TGTGTGGGAGCTTCTATGCA 59.017 50.000 0.00 0.00 34.99 3.96
2501 2552 2.012673 CTTGTGTGGGAGCTTCTATGC 58.987 52.381 0.00 0.00 0.00 3.14
2502 2553 2.026822 ACCTTGTGTGGGAGCTTCTATG 60.027 50.000 0.00 0.00 0.00 2.23
2503 2554 2.026822 CACCTTGTGTGGGAGCTTCTAT 60.027 50.000 0.00 0.00 41.52 1.98
2504 2555 1.347707 CACCTTGTGTGGGAGCTTCTA 59.652 52.381 0.00 0.00 41.52 2.10
2505 2556 0.109342 CACCTTGTGTGGGAGCTTCT 59.891 55.000 0.00 0.00 41.52 2.85
2506 2557 2.633860 CACCTTGTGTGGGAGCTTC 58.366 57.895 0.00 0.00 41.52 3.86
2507 2558 4.907457 CACCTTGTGTGGGAGCTT 57.093 55.556 0.00 0.00 41.52 3.74
2514 2565 1.228245 CCAGACCCCACCTTGTGTG 60.228 63.158 0.00 0.00 45.01 3.82
2515 2566 2.460853 CCCAGACCCCACCTTGTGT 61.461 63.158 0.00 0.00 0.00 3.72
2516 2567 2.436109 CCCAGACCCCACCTTGTG 59.564 66.667 0.00 0.00 0.00 3.33
2517 2568 2.858974 CCCCAGACCCCACCTTGT 60.859 66.667 0.00 0.00 0.00 3.16
2518 2569 2.531685 TCCCCAGACCCCACCTTG 60.532 66.667 0.00 0.00 0.00 3.61
2519 2570 2.204151 CTCCCCAGACCCCACCTT 60.204 66.667 0.00 0.00 0.00 3.50
2520 2571 4.354943 CCTCCCCAGACCCCACCT 62.355 72.222 0.00 0.00 0.00 4.00
2522 2573 3.660092 ATCCCTCCCCAGACCCCAC 62.660 68.421 0.00 0.00 0.00 4.61
2523 2574 1.542093 TAATCCCTCCCCAGACCCCA 61.542 60.000 0.00 0.00 0.00 4.96
2524 2575 0.103876 ATAATCCCTCCCCAGACCCC 60.104 60.000 0.00 0.00 0.00 4.95
2525 2576 2.157989 ACTATAATCCCTCCCCAGACCC 60.158 54.545 0.00 0.00 0.00 4.46
2526 2577 3.277416 ACTATAATCCCTCCCCAGACC 57.723 52.381 0.00 0.00 0.00 3.85
2527 2578 3.770388 GCTACTATAATCCCTCCCCAGAC 59.230 52.174 0.00 0.00 0.00 3.51
2528 2579 3.404769 TGCTACTATAATCCCTCCCCAGA 59.595 47.826 0.00 0.00 0.00 3.86
2529 2580 3.791320 TGCTACTATAATCCCTCCCCAG 58.209 50.000 0.00 0.00 0.00 4.45
2530 2581 3.935240 TGCTACTATAATCCCTCCCCA 57.065 47.619 0.00 0.00 0.00 4.96
2531 2582 4.104831 ACATGCTACTATAATCCCTCCCC 58.895 47.826 0.00 0.00 0.00 4.81
2532 2583 5.248477 TCAACATGCTACTATAATCCCTCCC 59.752 44.000 0.00 0.00 0.00 4.30
2533 2584 6.166982 GTCAACATGCTACTATAATCCCTCC 58.833 44.000 0.00 0.00 0.00 4.30
2534 2585 6.014156 AGGTCAACATGCTACTATAATCCCTC 60.014 42.308 0.00 0.00 0.00 4.30
2535 2586 5.846714 AGGTCAACATGCTACTATAATCCCT 59.153 40.000 0.00 0.00 0.00 4.20
2536 2587 6.115448 AGGTCAACATGCTACTATAATCCC 57.885 41.667 0.00 0.00 0.00 3.85
2537 2588 9.726438 AATTAGGTCAACATGCTACTATAATCC 57.274 33.333 0.00 0.00 0.00 3.01
2544 2595 7.136822 TGGATAATTAGGTCAACATGCTACT 57.863 36.000 0.00 0.00 0.00 2.57
2553 2604 6.667414 AGTGGCAATTTGGATAATTAGGTCAA 59.333 34.615 0.00 0.00 0.00 3.18
2557 2608 5.069516 AGCAGTGGCAATTTGGATAATTAGG 59.930 40.000 0.00 0.00 44.61 2.69
2603 2654 3.450096 TGTGCTATTTGCCATTTGCCATA 59.550 39.130 0.00 0.00 42.00 2.74
2604 2655 2.236644 TGTGCTATTTGCCATTTGCCAT 59.763 40.909 0.00 0.00 42.00 4.40
2605 2656 1.622312 TGTGCTATTTGCCATTTGCCA 59.378 42.857 0.00 0.00 42.00 4.92
2606 2657 2.383368 TGTGCTATTTGCCATTTGCC 57.617 45.000 0.00 0.00 42.00 4.52
2607 2658 5.981174 CATATTGTGCTATTTGCCATTTGC 58.019 37.500 0.00 0.00 42.00 3.68
2707 2759 2.267426 CCGATCATTGTACAGTTCGCA 58.733 47.619 6.88 0.00 0.00 5.10
2759 2811 3.054728 TGTCTCTCTAGTCTGGACTCTGG 60.055 52.174 6.52 0.28 42.54 3.86
2760 2812 4.214986 TGTCTCTCTAGTCTGGACTCTG 57.785 50.000 6.52 2.53 42.54 3.35
2761 2813 4.919774 TTGTCTCTCTAGTCTGGACTCT 57.080 45.455 6.52 0.00 42.54 3.24
2762 2814 5.650266 TCAATTGTCTCTCTAGTCTGGACTC 59.350 44.000 6.52 0.00 42.54 3.36
2763 2815 5.417580 GTCAATTGTCTCTCTAGTCTGGACT 59.582 44.000 5.13 8.36 45.02 3.85
2764 2816 5.393678 GGTCAATTGTCTCTCTAGTCTGGAC 60.394 48.000 5.13 0.00 0.00 4.02
2765 2817 4.707448 GGTCAATTGTCTCTCTAGTCTGGA 59.293 45.833 5.13 0.00 0.00 3.86
2766 2818 4.709397 AGGTCAATTGTCTCTCTAGTCTGG 59.291 45.833 5.13 0.00 0.00 3.86
2767 2819 5.184864 ACAGGTCAATTGTCTCTCTAGTCTG 59.815 44.000 5.13 3.09 0.00 3.51
2852 2907 5.573380 ATCTGCCCAGACAATGTGTATAT 57.427 39.130 0.00 0.00 40.75 0.86
2856 2911 2.224843 TGAATCTGCCCAGACAATGTGT 60.225 45.455 0.00 0.00 40.75 3.72
2902 2957 8.916628 TGCCATACATGCTCTATATTTGTTTA 57.083 30.769 0.00 0.00 0.00 2.01
2974 3030 7.617041 ACTGGAGTTAGAATAAACATTCAGC 57.383 36.000 0.65 0.00 31.82 4.26
3034 3090 0.464735 GCCTAGAGTCGAGCCTCTGA 60.465 60.000 14.17 0.80 41.81 3.27
3124 3180 5.010282 ACAAGGTGAAAAGTTTCAGACAGT 58.990 37.500 6.72 2.31 46.80 3.55
3289 3345 6.389830 TTCTTTTGAGCAGCTAAATGTTCA 57.610 33.333 0.00 0.00 38.46 3.18
3292 3348 6.040842 TCCTTTTCTTTTGAGCAGCTAAATGT 59.959 34.615 0.00 0.00 0.00 2.71
3460 3516 7.862648 TCTGTATTTACATAAAAACACGTGCA 58.137 30.769 17.22 0.00 35.36 4.57
3635 3691 5.855045 AGATATCGTACCTTCCCACAAATC 58.145 41.667 0.00 0.00 0.00 2.17
3701 3764 0.687354 ATTGTCGGAGTTGTCAGGCT 59.313 50.000 0.00 0.00 0.00 4.58
3715 3778 1.372582 TGCGATTCCAGCAGATTGTC 58.627 50.000 0.00 0.00 40.01 3.18
3731 3794 0.449388 GCAGAACTCCATTTCCTGCG 59.551 55.000 0.00 0.00 0.00 5.18
3804 3867 1.531423 CATCCCATGCTGCAGATACC 58.469 55.000 20.43 0.00 0.00 2.73
3827 3890 7.676468 AGATACTTCTTCCCTTTACAGACTCTT 59.324 37.037 0.00 0.00 0.00 2.85
3873 3936 8.333186 GCAAAGAACTACGGTATTATTTACAGG 58.667 37.037 0.00 0.00 0.00 4.00
3927 3990 4.055360 TGATTTCAGTACACACAAGTCGG 58.945 43.478 0.00 0.00 0.00 4.79
3934 4000 7.667043 TTGGTAGATTGATTTCAGTACACAC 57.333 36.000 0.00 0.00 0.00 3.82
3967 4033 8.826710 CAACAATATACACACGAAATATCCAGT 58.173 33.333 0.00 0.00 0.00 4.00
4208 4347 9.863650 ACAATAATGAGCTAACCTAGTACTCTA 57.136 33.333 0.00 0.00 0.00 2.43
4209 4348 8.770010 ACAATAATGAGCTAACCTAGTACTCT 57.230 34.615 0.00 0.00 0.00 3.24
4244 4561 6.313905 CAGTGGTGAATGTGAATAACTAGGTC 59.686 42.308 0.00 0.00 0.00 3.85
4245 4562 6.173339 CAGTGGTGAATGTGAATAACTAGGT 58.827 40.000 0.00 0.00 0.00 3.08
4250 4567 4.759693 TGGACAGTGGTGAATGTGAATAAC 59.240 41.667 0.00 0.00 0.00 1.89
4251 4568 4.979335 TGGACAGTGGTGAATGTGAATAA 58.021 39.130 0.00 0.00 0.00 1.40
4252 4569 4.632327 TGGACAGTGGTGAATGTGAATA 57.368 40.909 0.00 0.00 0.00 1.75
4253 4570 3.507162 TGGACAGTGGTGAATGTGAAT 57.493 42.857 0.00 0.00 0.00 2.57
4386 4758 6.374417 AGTGGTGAATGTGAATAACTAGGT 57.626 37.500 0.00 0.00 0.00 3.08
4387 4759 5.817816 GGAGTGGTGAATGTGAATAACTAGG 59.182 44.000 0.00 0.00 0.00 3.02
4389 4761 5.625886 CGGGAGTGGTGAATGTGAATAACTA 60.626 44.000 0.00 0.00 0.00 2.24
4390 4762 4.589908 GGGAGTGGTGAATGTGAATAACT 58.410 43.478 0.00 0.00 0.00 2.24
4391 4763 3.374058 CGGGAGTGGTGAATGTGAATAAC 59.626 47.826 0.00 0.00 0.00 1.89
4392 4764 3.008594 ACGGGAGTGGTGAATGTGAATAA 59.991 43.478 0.00 0.00 44.82 1.40
4393 4765 2.569853 ACGGGAGTGGTGAATGTGAATA 59.430 45.455 0.00 0.00 44.82 1.75
4394 4766 1.351017 ACGGGAGTGGTGAATGTGAAT 59.649 47.619 0.00 0.00 44.82 2.57
4395 4767 0.762418 ACGGGAGTGGTGAATGTGAA 59.238 50.000 0.00 0.00 44.82 3.18
4396 4768 2.447630 ACGGGAGTGGTGAATGTGA 58.552 52.632 0.00 0.00 44.82 3.58
4408 4780 4.644103 TTTATAACTTCGAGGACGGGAG 57.356 45.455 0.00 0.00 40.21 4.30
4409 4781 5.603170 ATTTTATAACTTCGAGGACGGGA 57.397 39.130 0.00 0.00 40.21 5.14
4475 4956 7.093640 CCATATATGTATGCTGAAAATTGCCCT 60.094 37.037 11.73 0.00 37.06 5.19
4478 4959 9.132521 GAACCATATATGTATGCTGAAAATTGC 57.867 33.333 11.73 0.00 37.06 3.56
4486 4967 8.846943 TTTGTAGGAACCATATATGTATGCTG 57.153 34.615 11.73 0.00 37.06 4.41
4491 4972 7.750655 TGCCATTTGTAGGAACCATATATGTA 58.249 34.615 11.73 0.00 0.00 2.29
4500 4981 6.715347 ATCTTTATGCCATTTGTAGGAACC 57.285 37.500 0.00 0.00 0.00 3.62
4502 5079 9.474313 AAGTAATCTTTATGCCATTTGTAGGAA 57.526 29.630 0.00 0.00 0.00 3.36
4549 5126 6.645415 ACGGACACTTTGATCTAACTAAACAG 59.355 38.462 0.00 0.00 0.00 3.16
4647 5258 6.128553 ACTGTTGTTATCTGTATGTTCGCAAG 60.129 38.462 0.00 0.00 0.00 4.01
4648 5259 5.699001 ACTGTTGTTATCTGTATGTTCGCAA 59.301 36.000 0.00 0.00 0.00 4.85
4649 5260 5.234752 ACTGTTGTTATCTGTATGTTCGCA 58.765 37.500 0.00 0.00 0.00 5.10
4650 5261 5.779806 ACTGTTGTTATCTGTATGTTCGC 57.220 39.130 0.00 0.00 0.00 4.70
4651 5262 7.758076 TCCTTACTGTTGTTATCTGTATGTTCG 59.242 37.037 0.00 0.00 0.00 3.95
4652 5263 8.997621 TCCTTACTGTTGTTATCTGTATGTTC 57.002 34.615 0.00 0.00 0.00 3.18
4653 5264 8.812972 TCTCCTTACTGTTGTTATCTGTATGTT 58.187 33.333 0.00 0.00 0.00 2.71
4654 5265 8.362464 TCTCCTTACTGTTGTTATCTGTATGT 57.638 34.615 0.00 0.00 0.00 2.29
4655 5266 9.653287 TTTCTCCTTACTGTTGTTATCTGTATG 57.347 33.333 0.00 0.00 0.00 2.39
4657 5268 9.653287 CATTTCTCCTTACTGTTGTTATCTGTA 57.347 33.333 0.00 0.00 0.00 2.74
4660 5271 7.168219 TGCATTTCTCCTTACTGTTGTTATCT 58.832 34.615 0.00 0.00 0.00 1.98
4754 5366 3.625764 TGTGTAACTGAGGTTTGTTGCTC 59.374 43.478 0.00 0.00 38.04 4.26
4763 5375 3.403038 GCTGTCATTGTGTAACTGAGGT 58.597 45.455 0.00 0.00 38.04 3.85
4842 5457 0.182299 CTGGCTCTCCCCTTCCATTC 59.818 60.000 0.00 0.00 0.00 2.67
4852 5467 2.438075 CCAGCTTGCTGGCTCTCC 60.438 66.667 25.97 0.00 41.00 3.71
4885 5501 2.764314 GCGCTGGCCATCAAACGAT 61.764 57.895 5.51 0.00 0.00 3.73
4925 5541 3.418047 ACCTGTAGGCGCTAAAATTGTT 58.582 40.909 7.64 0.00 39.32 2.83
4927 5543 3.427503 CCAACCTGTAGGCGCTAAAATTG 60.428 47.826 7.64 3.98 39.32 2.32
5101 5717 1.917921 CGCGAACGTATCAGAAGCC 59.082 57.895 0.00 0.00 33.53 4.35


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

AutoCloner maintained by Alex Coulton.