Multiple sequence alignment - TraesCS2A01G324000

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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 TraesCS2A01G324000 chr2A 100.000 3332 0 0 1 3332 554413948 554417279 0.000000e+00 6154.0
1 TraesCS2A01G324000 chr2D 92.812 1906 89 18 641 2513 432081452 432079562 0.000000e+00 2717.0
2 TraesCS2A01G324000 chr2D 84.375 672 88 11 2674 3332 432079382 432078715 0.000000e+00 643.0
3 TraesCS2A01G324000 chr2D 83.673 490 32 19 36 486 432082080 432081600 5.140000e-113 418.0
4 TraesCS2A01G324000 chr2D 90.608 181 16 1 1190 1369 461078665 461078485 4.300000e-59 239.0
5 TraesCS2A01G324000 chr2D 96.721 122 4 0 1608 1729 461078493 461078372 1.570000e-48 204.0
6 TraesCS2A01G324000 chr2D 95.200 125 6 0 1608 1732 352709821 352709945 7.290000e-47 198.0
7 TraesCS2A01G324000 chr2B 90.727 1898 90 29 685 2513 510898450 510896570 0.000000e+00 2451.0
8 TraesCS2A01G324000 chr2B 85.057 261 17 7 5 244 510901910 510901651 2.570000e-61 246.0
9 TraesCS2A01G324000 chr2B 87.047 193 17 5 301 492 510898615 510898430 9.370000e-51 211.0
10 TraesCS2A01G324000 chr6D 92.835 321 23 0 1488 1808 456305687 456305367 1.810000e-127 466.0
11 TraesCS2A01G324000 chr6D 95.690 116 5 0 1915 2030 456305370 456305255 1.580000e-43 187.0
12 TraesCS2A01G324000 chr7D 95.473 243 11 0 1488 1730 171027892 171028134 4.030000e-104 388.0
13 TraesCS2A01G324000 chr7D 95.683 139 6 0 1188 1326 171013670 171013808 1.200000e-54 224.0
14 TraesCS2A01G324000 chr7D 93.985 133 8 0 1317 1449 171027768 171027900 5.640000e-48 202.0
15 TraesCS2A01G324000 chr1D 92.655 177 13 0 1190 1366 307206149 307206325 4.270000e-64 255.0
16 TraesCS2A01G324000 chr1D 95.122 123 6 0 1608 1730 307206321 307206443 9.430000e-46 195.0
17 TraesCS2A01G324000 chr1B 95.082 122 6 0 1608 1729 646571821 646571700 3.390000e-45 193.0
18 TraesCS2A01G324000 chr1B 90.909 121 10 1 1610 1730 646571586 646571467 9.570000e-36 161.0
19 TraesCS2A01G324000 chr6B 87.500 80 7 2 2616 2693 699137716 699137794 4.580000e-14 89.8


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 TraesCS2A01G324000 chr2A 554413948 554417279 3331 False 6154.000000 6154 100.000000 1 3332 1 chr2A.!!$F1 3331
1 TraesCS2A01G324000 chr2D 432078715 432082080 3365 True 1259.333333 2717 86.953333 36 3332 3 chr2D.!!$R1 3296
2 TraesCS2A01G324000 chr2B 510896570 510901910 5340 True 969.333333 2451 87.610333 5 2513 3 chr2B.!!$R1 2508

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
496 3525 0.027194 CGAGATTGCTGCGTGATTGG 59.973 55.0 0.0 0.0 0.00 3.16 F
525 3554 0.037232 GTGGCTCTAACGCTGGTTCT 60.037 55.0 0.0 0.0 37.58 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 5004 0.108585 AAACCGGCTTCTTGCTCTGA 59.891 50.0 0.0 0.0 42.39 3.27 R
2502 5664 0.669625 GGCTAAAAGAGGCGACGTGT 60.670 55.0 0.0 0.0 41.55 4.49 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.199393 GCGGAATAAAGACATAAATGGACAC 58.801 40.000 0.00 0.00 0.00 3.67
68 69 7.814264 ATAATGAGAAACTTTATGGCAGAGG 57.186 36.000 0.00 0.00 30.91 3.69
72 73 3.523564 AGAAACTTTATGGCAGAGGGCTA 59.476 43.478 0.00 0.00 44.01 3.93
74 75 3.778954 ACTTTATGGCAGAGGGCTATC 57.221 47.619 0.00 0.00 43.38 2.08
125 147 1.743252 GTCCCTTTGAGAGGCTGCG 60.743 63.158 0.00 0.00 44.85 5.18
142 164 1.129624 TGCGCCGTGACATGTTTTATC 59.870 47.619 4.18 0.00 0.00 1.75
151 173 4.576463 GTGACATGTTTTATCCCTAGCCTG 59.424 45.833 0.00 0.00 0.00 4.85
168 190 0.755686 CTGGTAGGGCTAGGCAGAAG 59.244 60.000 19.14 4.16 0.00 2.85
206 228 1.615651 CCCGGTGATTTGACATGGGAA 60.616 52.381 0.00 0.00 39.23 3.97
238 287 0.179124 CAGAGCTTCCGTCTAGTGCC 60.179 60.000 0.00 0.00 0.00 5.01
268 317 2.292267 CCATACACACTGAAGCCATCC 58.708 52.381 0.00 0.00 0.00 3.51
271 320 2.119801 ACACACTGAAGCCATCCATC 57.880 50.000 0.00 0.00 0.00 3.51
272 321 1.012086 CACACTGAAGCCATCCATCG 58.988 55.000 0.00 0.00 0.00 3.84
273 322 0.904649 ACACTGAAGCCATCCATCGA 59.095 50.000 0.00 0.00 0.00 3.59
325 3352 3.324117 CGTATCAGGAATGCAGGATGAG 58.676 50.000 0.00 0.00 39.69 2.90
350 3377 1.410882 GAATCAGCTAGCGGTCCTTCT 59.589 52.381 14.70 0.00 0.00 2.85
351 3378 1.036707 ATCAGCTAGCGGTCCTTCTC 58.963 55.000 14.70 0.00 0.00 2.87
380 3407 2.668280 GCAACTCGCCAACCGTCTC 61.668 63.158 0.00 0.00 38.35 3.36
431 3458 1.668237 GAAAGAGAAGCGGAAGATGCC 59.332 52.381 0.00 0.00 0.00 4.40
438 3465 2.658593 CGGAAGATGCCGCCGTAG 60.659 66.667 0.00 0.00 45.38 3.51
439 3466 2.499685 GGAAGATGCCGCCGTAGT 59.500 61.111 0.00 0.00 0.00 2.73
440 3467 1.737816 GGAAGATGCCGCCGTAGTA 59.262 57.895 0.00 0.00 0.00 1.82
441 3468 0.596859 GGAAGATGCCGCCGTAGTAC 60.597 60.000 0.00 0.00 0.00 2.73
442 3469 0.101759 GAAGATGCCGCCGTAGTACA 59.898 55.000 0.38 0.00 0.00 2.90
443 3470 0.102481 AAGATGCCGCCGTAGTACAG 59.898 55.000 0.38 0.00 0.00 2.74
444 3471 1.035932 AGATGCCGCCGTAGTACAGT 61.036 55.000 0.38 0.00 0.00 3.55
474 3503 2.163010 GCATATGCATTTCCCCGATGAG 59.837 50.000 22.84 0.00 41.59 2.90
492 3521 2.262603 AGCGAGATTGCTGCGTGA 59.737 55.556 0.00 0.00 45.28 4.35
493 3522 1.153489 AGCGAGATTGCTGCGTGAT 60.153 52.632 0.00 0.00 45.28 3.06
494 3523 0.742281 AGCGAGATTGCTGCGTGATT 60.742 50.000 0.00 0.00 45.28 2.57
495 3524 0.588233 GCGAGATTGCTGCGTGATTG 60.588 55.000 0.00 0.00 0.00 2.67
496 3525 0.027194 CGAGATTGCTGCGTGATTGG 59.973 55.000 0.00 0.00 0.00 3.16
497 3526 1.089920 GAGATTGCTGCGTGATTGGT 58.910 50.000 0.00 0.00 0.00 3.67
498 3527 1.063174 GAGATTGCTGCGTGATTGGTC 59.937 52.381 0.00 0.00 0.00 4.02
499 3528 0.099436 GATTGCTGCGTGATTGGTCC 59.901 55.000 0.00 0.00 0.00 4.46
500 3529 1.315257 ATTGCTGCGTGATTGGTCCC 61.315 55.000 0.00 0.00 0.00 4.46
501 3530 2.045926 GCTGCGTGATTGGTCCCT 60.046 61.111 0.00 0.00 0.00 4.20
502 3531 2.109126 GCTGCGTGATTGGTCCCTC 61.109 63.158 0.00 0.00 0.00 4.30
503 3532 1.450312 CTGCGTGATTGGTCCCTCC 60.450 63.158 0.00 0.00 0.00 4.30
504 3533 2.511600 GCGTGATTGGTCCCTCCG 60.512 66.667 0.00 0.00 39.52 4.63
505 3534 2.978824 CGTGATTGGTCCCTCCGT 59.021 61.111 0.00 0.00 39.52 4.69
506 3535 1.447838 CGTGATTGGTCCCTCCGTG 60.448 63.158 0.00 0.00 39.52 4.94
507 3536 1.677552 GTGATTGGTCCCTCCGTGT 59.322 57.895 0.00 0.00 39.52 4.49
508 3537 0.673644 GTGATTGGTCCCTCCGTGTG 60.674 60.000 0.00 0.00 39.52 3.82
509 3538 1.078426 GATTGGTCCCTCCGTGTGG 60.078 63.158 0.00 0.00 39.52 4.17
510 3539 3.268103 ATTGGTCCCTCCGTGTGGC 62.268 63.158 0.00 0.00 39.52 5.01
511 3540 4.954118 TGGTCCCTCCGTGTGGCT 62.954 66.667 0.00 0.00 39.52 4.75
512 3541 4.083862 GGTCCCTCCGTGTGGCTC 62.084 72.222 0.00 0.00 34.14 4.70
513 3542 2.997897 GTCCCTCCGTGTGGCTCT 60.998 66.667 0.00 0.00 34.14 4.09
514 3543 1.681327 GTCCCTCCGTGTGGCTCTA 60.681 63.158 0.00 0.00 34.14 2.43
515 3544 1.077805 TCCCTCCGTGTGGCTCTAA 59.922 57.895 0.00 0.00 34.14 2.10
516 3545 1.218316 CCCTCCGTGTGGCTCTAAC 59.782 63.158 0.00 0.00 34.14 2.34
517 3546 1.153823 CCTCCGTGTGGCTCTAACG 60.154 63.158 0.00 0.00 37.07 3.18
518 3547 1.805945 CTCCGTGTGGCTCTAACGC 60.806 63.158 0.00 0.00 36.02 4.84
519 3548 2.214181 CTCCGTGTGGCTCTAACGCT 62.214 60.000 0.00 0.00 36.02 5.07
520 3549 2.094659 CCGTGTGGCTCTAACGCTG 61.095 63.158 0.00 0.00 36.02 5.18
521 3550 2.094659 CGTGTGGCTCTAACGCTGG 61.095 63.158 0.00 0.00 0.00 4.85
522 3551 1.004918 GTGTGGCTCTAACGCTGGT 60.005 57.895 0.00 0.00 0.00 4.00
523 3552 0.602905 GTGTGGCTCTAACGCTGGTT 60.603 55.000 0.00 0.00 40.20 3.67
524 3553 0.320421 TGTGGCTCTAACGCTGGTTC 60.320 55.000 0.00 0.00 37.58 3.62
525 3554 0.037232 GTGGCTCTAACGCTGGTTCT 60.037 55.000 0.00 0.00 37.58 3.01
526 3555 0.037326 TGGCTCTAACGCTGGTTCTG 60.037 55.000 0.00 0.00 37.58 3.02
527 3556 1.362406 GGCTCTAACGCTGGTTCTGC 61.362 60.000 0.00 0.00 37.58 4.26
555 3584 2.941453 TGCGTATCAGGTTGAGAGAC 57.059 50.000 0.00 0.00 0.00 3.36
556 3585 1.476891 TGCGTATCAGGTTGAGAGACC 59.523 52.381 0.00 0.00 40.11 3.85
570 3599 1.945354 GAGACCGAGATTCCCACGCA 61.945 60.000 0.00 0.00 0.00 5.24
576 3605 2.518949 CGAGATTCCCACGCAAAAATG 58.481 47.619 0.00 0.00 0.00 2.32
609 3638 2.279517 GTGCTAGGATCACCGGCG 60.280 66.667 0.00 0.00 40.48 6.46
613 3644 2.441348 TAGGATCACCGGCGCTCA 60.441 61.111 7.64 0.00 41.83 4.26
628 3659 0.951040 GCTCACCCTGACGGAAACAG 60.951 60.000 0.00 0.00 34.64 3.16
632 3663 4.285851 CCTGACGGAAACAGGCTC 57.714 61.111 0.00 0.00 46.30 4.70
633 3664 1.674057 CCTGACGGAAACAGGCTCT 59.326 57.895 0.00 0.00 46.30 4.09
634 3665 0.671781 CCTGACGGAAACAGGCTCTG 60.672 60.000 0.00 1.16 46.30 3.35
635 3666 1.294659 CTGACGGAAACAGGCTCTGC 61.295 60.000 2.50 0.00 34.37 4.26
636 3667 1.004440 GACGGAAACAGGCTCTGCT 60.004 57.895 2.50 0.00 34.37 4.24
637 3668 1.004440 ACGGAAACAGGCTCTGCTC 60.004 57.895 2.50 0.76 34.37 4.26
638 3669 1.004560 CGGAAACAGGCTCTGCTCA 60.005 57.895 2.50 0.00 34.37 4.26
639 3670 0.392193 CGGAAACAGGCTCTGCTCAT 60.392 55.000 2.50 0.00 34.37 2.90
658 3733 0.459585 TCGAAAGATGCCGCTGTACC 60.460 55.000 0.00 0.00 33.31 3.34
659 3734 1.752501 CGAAAGATGCCGCTGTACCG 61.753 60.000 0.00 0.00 0.00 4.02
671 3746 1.006832 CTGTACCGTGCTGCATTACC 58.993 55.000 5.27 0.00 0.00 2.85
681 3756 2.358619 GCATTACCCCCTGCCACA 59.641 61.111 0.00 0.00 32.15 4.17
699 3774 0.449388 CAGGTGAAAGCGAGATTGCC 59.551 55.000 0.00 0.00 40.95 4.52
706 3781 4.505217 GCGAGATTGCCGCGTGTG 62.505 66.667 4.92 0.00 43.28 3.82
708 3783 2.667318 CGAGATTGCCGCGTGTGTT 61.667 57.895 4.92 0.00 33.31 3.32
709 3784 1.574428 GAGATTGCCGCGTGTGTTT 59.426 52.632 4.92 0.00 0.00 2.83
710 3785 0.725784 GAGATTGCCGCGTGTGTTTG 60.726 55.000 4.92 0.00 0.00 2.93
711 3786 1.729131 GATTGCCGCGTGTGTTTGG 60.729 57.895 4.92 0.00 0.00 3.28
735 3810 2.537560 GGTTGATGCCCGATCGCTG 61.538 63.158 10.32 3.88 33.17 5.18
745 3820 1.730902 CGATCGCTGGCTGTATCGG 60.731 63.158 0.26 5.50 38.01 4.18
862 3975 3.597728 GCCTCCGAGCCTCCGTAG 61.598 72.222 0.00 0.00 0.00 3.51
867 3995 4.253257 CGAGCCTCCGTAGTCCGC 62.253 72.222 0.00 0.00 34.38 5.54
971 4104 0.321653 AGCACGACCTTCCATTCCAC 60.322 55.000 0.00 0.00 0.00 4.02
972 4105 1.305930 GCACGACCTTCCATTCCACC 61.306 60.000 0.00 0.00 0.00 4.61
1186 4321 2.364317 CCCTCCCTTCGCTCTCCA 60.364 66.667 0.00 0.00 0.00 3.86
1336 4492 3.744719 TCGCCCTTCACGACCTCG 61.745 66.667 0.00 0.00 46.33 4.63
1344 4500 4.436998 CACGACCTCGGCACCCTC 62.437 72.222 0.00 0.00 44.95 4.30
1719 4875 3.123620 CTCCGCTGCTTGCAGTCC 61.124 66.667 21.55 7.22 43.06 3.85
1845 5001 0.944311 CGTCCGACAAGACCACCAAG 60.944 60.000 0.00 0.00 32.91 3.61
1848 5004 1.594293 CGACAAGACCACCAAGCGT 60.594 57.895 0.00 0.00 0.00 5.07
2059 5215 4.193334 CGGTGCTCTCCATCGCGA 62.193 66.667 13.09 13.09 41.74 5.87
2229 5385 2.035312 AAGAAGCAGCTGCAGGGG 59.965 61.111 38.24 1.04 45.16 4.79
2368 5524 4.886247 ACGATTTTTGACGTTGGAAAGA 57.114 36.364 0.00 0.00 39.75 2.52
2402 5564 8.291032 CCTGATTTTTGATCTGATCTTGATAGC 58.709 37.037 17.82 4.49 0.00 2.97
2481 5643 2.624169 TTTTTGGACTTCGGCGGAG 58.376 52.632 14.98 14.98 0.00 4.63
2530 5716 3.632333 GCCTCTTTTAGCCATTTACCCT 58.368 45.455 0.00 0.00 0.00 4.34
2532 5718 5.386060 GCCTCTTTTAGCCATTTACCCTAT 58.614 41.667 0.00 0.00 0.00 2.57
2552 5738 3.297134 TGGGATTGTAAATCTCAGCCC 57.703 47.619 0.00 0.00 34.25 5.19
2554 5740 1.604278 GGATTGTAAATCTCAGCCCGC 59.396 52.381 0.40 0.00 0.00 6.13
2555 5741 1.604278 GATTGTAAATCTCAGCCCGCC 59.396 52.381 0.00 0.00 0.00 6.13
2556 5742 0.326595 TTGTAAATCTCAGCCCGCCA 59.673 50.000 0.00 0.00 0.00 5.69
2557 5743 0.107703 TGTAAATCTCAGCCCGCCAG 60.108 55.000 0.00 0.00 0.00 4.85
2558 5744 0.107654 GTAAATCTCAGCCCGCCAGT 60.108 55.000 0.00 0.00 0.00 4.00
2559 5745 1.138266 GTAAATCTCAGCCCGCCAGTA 59.862 52.381 0.00 0.00 0.00 2.74
2560 5746 0.618458 AAATCTCAGCCCGCCAGTAA 59.382 50.000 0.00 0.00 0.00 2.24
2561 5747 0.179000 AATCTCAGCCCGCCAGTAAG 59.821 55.000 0.00 0.00 0.00 2.34
2563 5749 1.153549 CTCAGCCCGCCAGTAAGAC 60.154 63.158 0.00 0.00 0.00 3.01
2564 5750 1.608717 CTCAGCCCGCCAGTAAGACT 61.609 60.000 0.00 0.00 0.00 3.24
2565 5751 1.192146 TCAGCCCGCCAGTAAGACTT 61.192 55.000 0.00 0.00 0.00 3.01
2568 5754 1.066358 AGCCCGCCAGTAAGACTTAAC 60.066 52.381 0.00 0.00 0.00 2.01
2569 5755 2.010544 GCCCGCCAGTAAGACTTAACC 61.011 57.143 0.00 0.00 0.00 2.85
2570 5756 1.553704 CCCGCCAGTAAGACTTAACCT 59.446 52.381 0.00 0.00 0.00 3.50
2571 5757 2.762327 CCCGCCAGTAAGACTTAACCTA 59.238 50.000 0.00 0.00 0.00 3.08
2572 5758 3.387050 CCCGCCAGTAAGACTTAACCTAT 59.613 47.826 0.00 0.00 0.00 2.57
2573 5759 4.369182 CCGCCAGTAAGACTTAACCTATG 58.631 47.826 0.00 0.00 0.00 2.23
2574 5760 4.142004 CCGCCAGTAAGACTTAACCTATGT 60.142 45.833 0.00 0.00 0.00 2.29
2576 5762 5.291128 CGCCAGTAAGACTTAACCTATGTTG 59.709 44.000 0.00 0.00 35.87 3.33
2577 5763 6.403878 GCCAGTAAGACTTAACCTATGTTGA 58.596 40.000 0.00 0.00 35.87 3.18
2578 5764 7.048512 GCCAGTAAGACTTAACCTATGTTGAT 58.951 38.462 0.00 0.00 35.87 2.57
2579 5765 7.011482 GCCAGTAAGACTTAACCTATGTTGATG 59.989 40.741 0.00 0.00 35.87 3.07
2580 5766 8.258007 CCAGTAAGACTTAACCTATGTTGATGA 58.742 37.037 0.00 0.00 35.87 2.92
2581 5767 9.653287 CAGTAAGACTTAACCTATGTTGATGAA 57.347 33.333 0.00 0.00 35.87 2.57
2585 5771 8.738645 AGACTTAACCTATGTTGATGAAATCC 57.261 34.615 0.00 0.00 44.73 3.01
2587 5773 9.832445 GACTTAACCTATGTTGATGAAATCCTA 57.168 33.333 0.00 0.00 44.73 2.94
2597 5795 7.453393 TGTTGATGAAATCCTACATAGGGATC 58.547 38.462 5.10 2.70 44.73 3.36
2599 5797 6.090870 TGATGAAATCCTACATAGGGATCCA 58.909 40.000 15.23 0.00 44.73 3.41
2605 5803 4.178339 TCCTACATAGGGATCCATGCAAT 58.822 43.478 15.23 0.00 43.79 3.56
2606 5804 4.603171 TCCTACATAGGGATCCATGCAATT 59.397 41.667 15.23 0.00 43.79 2.32
2660 5858 9.725019 ATGTTATGTCACTTGATTTAGACTTGA 57.275 29.630 0.00 0.00 32.41 3.02
2661 5859 9.725019 TGTTATGTCACTTGATTTAGACTTGAT 57.275 29.630 0.00 0.00 32.41 2.57
2681 5879 7.872993 ACTTGATTAAGTCTCAAATCGACTGAA 59.127 33.333 0.00 0.00 43.53 3.02
2684 5882 7.872993 TGATTAAGTCTCAAATCGACTGAAACT 59.127 33.333 0.50 0.50 40.65 2.66
2702 5900 5.475564 TGAAACTTAGCCACATTCTTTACCC 59.524 40.000 0.00 0.00 0.00 3.69
2728 5926 3.536956 TTGACACGAAGGTTCTCAACT 57.463 42.857 0.00 0.00 0.00 3.16
2733 5931 6.751157 TGACACGAAGGTTCTCAACTATTAA 58.249 36.000 0.00 0.00 0.00 1.40
2739 5937 8.512138 ACGAAGGTTCTCAACTATTAAAAATGG 58.488 33.333 0.00 0.00 0.00 3.16
2783 5981 2.223829 ACAAGTCGCCTCCATTAGATCG 60.224 50.000 0.00 0.00 0.00 3.69
2784 5982 0.962489 AGTCGCCTCCATTAGATCGG 59.038 55.000 0.00 0.00 0.00 4.18
2786 5984 0.827925 TCGCCTCCATTAGATCGGCT 60.828 55.000 4.38 0.00 38.58 5.52
2788 5986 0.036858 GCCTCCATTAGATCGGCTCC 60.037 60.000 0.00 0.00 37.76 4.70
2809 6007 1.228862 GCCATGGTTCCCCTTGTGT 60.229 57.895 14.67 0.00 34.77 3.72
2810 6008 0.039035 GCCATGGTTCCCCTTGTGTA 59.961 55.000 14.67 0.00 34.77 2.90
2813 6011 1.004745 CATGGTTCCCCTTGTGTAGCT 59.995 52.381 0.00 0.00 32.53 3.32
2828 6026 3.606662 GCTCCAGCGGGCTATCGA 61.607 66.667 0.00 0.00 0.00 3.59
2829 6027 3.129300 CTCCAGCGGGCTATCGAA 58.871 61.111 0.00 0.00 0.00 3.71
2842 6041 3.056749 GGCTATCGAAACTCATATCCGGT 60.057 47.826 0.00 0.00 0.00 5.28
2846 6045 4.196626 TCGAAACTCATATCCGGTTGTT 57.803 40.909 0.00 0.00 0.00 2.83
2856 6055 2.750350 CGGTTGTTGAGGGCCTCT 59.250 61.111 32.28 0.00 0.00 3.69
2858 6057 0.955919 CGGTTGTTGAGGGCCTCTTC 60.956 60.000 32.28 23.87 0.00 2.87
2868 6067 4.491409 GCCTCTTCCGCTTCCCCC 62.491 72.222 0.00 0.00 0.00 5.40
2871 6070 2.687566 TCTTCCGCTTCCCCCTCC 60.688 66.667 0.00 0.00 0.00 4.30
2908 6107 0.321653 GGGCAATGTTGAGGTCGTCT 60.322 55.000 0.00 0.00 0.00 4.18
2909 6108 1.523758 GGCAATGTTGAGGTCGTCTT 58.476 50.000 0.00 0.00 0.00 3.01
2916 6115 0.396435 TTGAGGTCGTCTTGTGGCAT 59.604 50.000 0.00 0.00 0.00 4.40
2918 6117 0.037326 GAGGTCGTCTTGTGGCATGA 60.037 55.000 0.00 0.00 0.00 3.07
2931 6130 3.181455 TGTGGCATGAAAGCGTAGGATAT 60.181 43.478 0.00 0.00 34.64 1.63
2933 6132 4.627467 GTGGCATGAAAGCGTAGGATATAG 59.373 45.833 0.00 0.00 34.64 1.31
2939 6138 7.598278 CATGAAAGCGTAGGATATAGAAGTCT 58.402 38.462 0.00 0.00 0.00 3.24
2944 6143 4.082136 GCGTAGGATATAGAAGTCTTGGGG 60.082 50.000 0.00 0.00 0.00 4.96
2945 6144 5.322754 CGTAGGATATAGAAGTCTTGGGGA 58.677 45.833 0.00 0.00 0.00 4.81
2946 6145 5.416326 CGTAGGATATAGAAGTCTTGGGGAG 59.584 48.000 0.00 0.00 0.00 4.30
2952 6151 2.999928 AGAAGTCTTGGGGAGGGTTTA 58.000 47.619 0.00 0.00 0.00 2.01
2958 6157 1.128809 TTGGGGAGGGTTTAGCGTCA 61.129 55.000 4.34 0.00 0.00 4.35
2978 6177 0.969917 CGATTTGGGTCCAATGGCCA 60.970 55.000 8.56 8.56 35.70 5.36
2980 6179 1.257055 ATTTGGGTCCAATGGCCACG 61.257 55.000 8.16 1.14 35.70 4.94
2997 6196 0.106167 ACGGGGCTATGCTCTAGTGA 60.106 55.000 0.00 0.00 0.00 3.41
3001 6200 2.311463 GGGCTATGCTCTAGTGAGTCA 58.689 52.381 0.00 0.00 42.13 3.41
3002 6201 2.695666 GGGCTATGCTCTAGTGAGTCAA 59.304 50.000 0.00 0.00 42.13 3.18
3015 6214 2.233922 GTGAGTCAAGGTTGCTAGGCTA 59.766 50.000 0.00 0.00 0.00 3.93
3016 6215 2.233922 TGAGTCAAGGTTGCTAGGCTAC 59.766 50.000 0.00 0.00 33.89 3.58
3017 6216 2.233922 GAGTCAAGGTTGCTAGGCTACA 59.766 50.000 6.46 0.00 36.13 2.74
3018 6217 2.028020 AGTCAAGGTTGCTAGGCTACAC 60.028 50.000 6.46 0.00 36.13 2.90
3022 6221 1.079405 GTTGCTAGGCTACACGGCA 60.079 57.895 2.38 2.38 41.46 5.69
3024 6223 0.251916 TTGCTAGGCTACACGGCAAT 59.748 50.000 13.10 0.00 41.46 3.56
3047 6246 2.201490 CCGAGGAGATGCCCCCTA 59.799 66.667 0.00 0.00 37.37 3.53
3049 6248 2.210711 CGAGGAGATGCCCCCTACC 61.211 68.421 0.00 0.00 37.37 3.18
3050 6249 1.237458 GAGGAGATGCCCCCTACCT 59.763 63.158 0.00 0.00 37.37 3.08
3051 6250 0.834261 GAGGAGATGCCCCCTACCTC 60.834 65.000 0.00 0.00 37.37 3.85
3053 6252 1.843832 GAGATGCCCCCTACCTCCC 60.844 68.421 0.00 0.00 0.00 4.30
3054 6253 2.039831 GATGCCCCCTACCTCCCA 60.040 66.667 0.00 0.00 0.00 4.37
3075 6274 2.125512 GCCGCTACCACCAGTGAG 60.126 66.667 0.00 0.00 0.00 3.51
3076 6275 2.125512 CCGCTACCACCAGTGAGC 60.126 66.667 0.00 0.42 0.00 4.26
3092 6291 1.820519 TGAGCATCATTGGACAAAGCC 59.179 47.619 0.00 0.00 42.56 4.35
3094 6293 0.896923 GCATCATTGGACAAAGCCCA 59.103 50.000 0.00 0.00 0.00 5.36
3096 6295 1.894466 CATCATTGGACAAAGCCCACA 59.106 47.619 0.00 0.00 32.58 4.17
3099 6298 2.768527 TCATTGGACAAAGCCCACAAAA 59.231 40.909 0.00 0.00 32.58 2.44
3100 6299 3.390639 TCATTGGACAAAGCCCACAAAAT 59.609 39.130 0.00 0.00 32.58 1.82
3101 6300 2.906691 TGGACAAAGCCCACAAAATG 57.093 45.000 0.00 0.00 0.00 2.32
3102 6301 2.114616 TGGACAAAGCCCACAAAATGT 58.885 42.857 0.00 0.00 0.00 2.71
3103 6302 3.300388 TGGACAAAGCCCACAAAATGTA 58.700 40.909 0.00 0.00 0.00 2.29
3128 6327 2.755655 CCTTCCTCTAGTGTCGTGACAT 59.244 50.000 5.91 0.00 43.97 3.06
3142 6341 1.750399 GACATGGGAGTTGGCGCAT 60.750 57.895 10.83 0.00 41.44 4.73
3155 6355 1.369091 GGCGCATGGTGACGATTCTT 61.369 55.000 10.83 0.00 0.00 2.52
3156 6356 1.286501 GCGCATGGTGACGATTCTTA 58.713 50.000 0.30 0.00 0.00 2.10
3157 6357 1.004927 GCGCATGGTGACGATTCTTAC 60.005 52.381 0.30 0.00 0.00 2.34
3162 6362 4.261801 CATGGTGACGATTCTTACCCTTT 58.738 43.478 0.00 0.00 32.20 3.11
3163 6363 3.670625 TGGTGACGATTCTTACCCTTTG 58.329 45.455 0.00 0.00 32.20 2.77
3164 6364 3.325425 TGGTGACGATTCTTACCCTTTGA 59.675 43.478 0.00 0.00 32.20 2.69
3165 6365 4.019681 TGGTGACGATTCTTACCCTTTGAT 60.020 41.667 0.00 0.00 32.20 2.57
3166 6366 4.941873 GGTGACGATTCTTACCCTTTGATT 59.058 41.667 0.00 0.00 0.00 2.57
3169 6369 3.694566 ACGATTCTTACCCTTTGATTGGC 59.305 43.478 0.00 0.00 0.00 4.52
3203 6403 0.325296 TACCGGCAGATTGGAGGACT 60.325 55.000 0.00 0.00 0.00 3.85
3206 6406 0.460987 CGGCAGATTGGAGGACTGAC 60.461 60.000 0.00 0.00 36.45 3.51
3217 6417 1.399089 GAGGACTGACGTGACTAGCTC 59.601 57.143 0.00 0.00 0.00 4.09
3219 6419 2.236644 AGGACTGACGTGACTAGCTCTA 59.763 50.000 0.00 0.00 0.00 2.43
3228 6428 0.465824 GACTAGCTCTAGCACGGGGA 60.466 60.000 4.54 0.00 45.16 4.81
3257 6461 2.494530 AATGGTTTGTGGCGCGGTT 61.495 52.632 8.83 0.00 0.00 4.44
3266 6470 4.204891 GGCGCGGTTGTTCGATCG 62.205 66.667 9.36 9.36 0.00 3.69
3270 6474 2.025418 GCGGTTGTTCGATCGTGGT 61.025 57.895 15.94 0.00 0.00 4.16
3274 6478 0.949105 GTTGTTCGATCGTGGTGGCT 60.949 55.000 15.94 0.00 0.00 4.75
3275 6479 0.250124 TTGTTCGATCGTGGTGGCTT 60.250 50.000 15.94 0.00 0.00 4.35
3277 6481 2.032634 TTCGATCGTGGTGGCTTGC 61.033 57.895 15.94 0.00 0.00 4.01
3278 6482 2.723586 TTCGATCGTGGTGGCTTGCA 62.724 55.000 15.94 0.00 0.00 4.08
3279 6483 2.108514 CGATCGTGGTGGCTTGCAT 61.109 57.895 7.03 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.298276 TGTCCATTTATGTCTTTATTCCGCC 59.702 40.000 0.00 0.00 0.00 6.13
1 2 6.199393 GTGTCCATTTATGTCTTTATTCCGC 58.801 40.000 0.00 0.00 0.00 5.54
2 3 6.418956 CGTGTCCATTTATGTCTTTATTCCG 58.581 40.000 0.00 0.00 0.00 4.30
3 4 6.038271 AGCGTGTCCATTTATGTCTTTATTCC 59.962 38.462 0.00 0.00 0.00 3.01
15 16 5.010933 TGGGAATTTAAGCGTGTCCATTTA 58.989 37.500 0.00 0.00 0.00 1.40
68 69 6.993079 TGAAAAGAAAAAGAAAGGGATAGCC 58.007 36.000 0.00 0.00 0.00 3.93
72 73 6.546034 TCGTCTGAAAAGAAAAAGAAAGGGAT 59.454 34.615 0.00 0.00 0.00 3.85
74 75 6.131544 TCGTCTGAAAAGAAAAAGAAAGGG 57.868 37.500 0.00 0.00 0.00 3.95
80 81 5.453587 CACAGCTTCGTCTGAAAAGAAAAAG 59.546 40.000 8.57 0.00 37.51 2.27
125 147 2.365582 AGGGATAAAACATGTCACGGC 58.634 47.619 0.00 0.00 0.00 5.68
151 173 1.448069 GCTTCTGCCTAGCCCTACC 59.552 63.158 0.00 0.00 32.45 3.18
206 228 0.112025 AGCTCTGCTTTTTGGCTCCT 59.888 50.000 0.00 0.00 33.89 3.69
229 278 1.356938 GGTAAAGCGTGGCACTAGAC 58.643 55.000 16.72 6.30 0.00 2.59
232 281 0.616371 ATGGGTAAAGCGTGGCACTA 59.384 50.000 16.72 0.00 0.00 2.74
238 287 2.415168 CAGTGTGTATGGGTAAAGCGTG 59.585 50.000 0.00 0.00 0.00 5.34
268 317 4.909696 AGTAGAATCAGAGGTGTCGATG 57.090 45.455 0.00 0.00 0.00 3.84
271 320 4.035792 CCTGTAGTAGAATCAGAGGTGTCG 59.964 50.000 0.00 0.00 0.00 4.35
272 321 4.202070 GCCTGTAGTAGAATCAGAGGTGTC 60.202 50.000 0.00 0.00 0.00 3.67
273 322 3.702045 GCCTGTAGTAGAATCAGAGGTGT 59.298 47.826 0.00 0.00 0.00 4.16
325 3352 1.596477 CCGCTAGCTGATTCTGGCC 60.596 63.158 13.93 0.00 37.28 5.36
350 3377 1.587043 CGAGTTGCTCTCCGTCAGGA 61.587 60.000 4.44 0.00 46.11 3.86
351 3378 1.153939 CGAGTTGCTCTCCGTCAGG 60.154 63.158 4.44 0.00 39.84 3.86
431 3458 2.158959 GCAGCACTGTACTACGGCG 61.159 63.158 4.80 4.80 0.00 6.46
444 3471 4.322689 TGCATATGCAGTGCAGCA 57.677 50.000 26.32 23.21 46.76 4.41
474 3503 1.150567 ATCACGCAGCAATCTCGCTC 61.151 55.000 0.00 0.00 41.38 5.03
492 3521 3.077907 CCACACGGAGGGACCAAT 58.922 61.111 0.00 0.00 38.90 3.16
493 3522 3.948719 GCCACACGGAGGGACCAA 61.949 66.667 0.00 0.00 38.90 3.67
494 3523 4.954118 AGCCACACGGAGGGACCA 62.954 66.667 0.00 0.00 38.90 4.02
495 3524 4.083862 GAGCCACACGGAGGGACC 62.084 72.222 0.00 0.00 0.00 4.46
496 3525 1.255667 TTAGAGCCACACGGAGGGAC 61.256 60.000 0.00 0.00 0.00 4.46
497 3526 1.077805 TTAGAGCCACACGGAGGGA 59.922 57.895 0.00 0.00 0.00 4.20
498 3527 1.218316 GTTAGAGCCACACGGAGGG 59.782 63.158 0.00 0.00 0.00 4.30
499 3528 1.153823 CGTTAGAGCCACACGGAGG 60.154 63.158 0.00 0.00 0.00 4.30
500 3529 1.805945 GCGTTAGAGCCACACGGAG 60.806 63.158 0.00 0.00 34.42 4.63
501 3530 2.260434 GCGTTAGAGCCACACGGA 59.740 61.111 0.00 0.00 34.42 4.69
502 3531 2.094659 CAGCGTTAGAGCCACACGG 61.095 63.158 0.00 0.00 38.01 4.94
503 3532 2.094659 CCAGCGTTAGAGCCACACG 61.095 63.158 0.00 0.00 38.01 4.49
504 3533 0.602905 AACCAGCGTTAGAGCCACAC 60.603 55.000 0.00 0.00 38.01 3.82
505 3534 0.320421 GAACCAGCGTTAGAGCCACA 60.320 55.000 0.00 0.00 38.01 4.17
506 3535 0.037232 AGAACCAGCGTTAGAGCCAC 60.037 55.000 0.00 0.00 38.01 5.01
507 3536 0.037326 CAGAACCAGCGTTAGAGCCA 60.037 55.000 0.00 0.00 38.01 4.75
508 3537 1.362406 GCAGAACCAGCGTTAGAGCC 61.362 60.000 0.00 0.00 38.01 4.70
509 3538 0.670546 TGCAGAACCAGCGTTAGAGC 60.671 55.000 0.00 0.00 30.30 4.09
510 3539 1.728971 CTTGCAGAACCAGCGTTAGAG 59.271 52.381 0.00 0.00 30.30 2.43
511 3540 1.795768 CTTGCAGAACCAGCGTTAGA 58.204 50.000 0.00 0.00 30.30 2.10
512 3541 0.166814 GCTTGCAGAACCAGCGTTAG 59.833 55.000 0.00 0.00 30.30 2.34
513 3542 0.533978 TGCTTGCAGAACCAGCGTTA 60.534 50.000 3.06 0.00 30.30 3.18
514 3543 1.823470 TGCTTGCAGAACCAGCGTT 60.823 52.632 3.06 0.00 33.88 4.84
515 3544 2.203195 TGCTTGCAGAACCAGCGT 60.203 55.556 3.06 0.00 33.85 5.07
516 3545 1.859427 ATGTGCTTGCAGAACCAGCG 61.859 55.000 3.06 0.00 33.85 5.18
517 3546 0.316204 AATGTGCTTGCAGAACCAGC 59.684 50.000 0.21 0.21 0.00 4.85
518 3547 2.060326 CAATGTGCTTGCAGAACCAG 57.940 50.000 0.00 0.00 0.00 4.00
527 3556 1.739466 ACCTGATACGCAATGTGCTTG 59.261 47.619 0.00 0.00 42.25 4.01
555 3584 0.878416 TTTTTGCGTGGGAATCTCGG 59.122 50.000 0.00 0.00 33.48 4.63
556 3585 2.161410 TCATTTTTGCGTGGGAATCTCG 59.839 45.455 0.00 0.00 35.69 4.04
594 3623 3.850095 GAGCGCCGGTGATCCTAGC 62.850 68.421 22.49 0.00 0.00 3.42
609 3638 0.951040 CTGTTTCCGTCAGGGTGAGC 60.951 60.000 0.00 0.00 38.33 4.26
628 3659 2.237393 ATCTTTCGATGAGCAGAGCC 57.763 50.000 0.00 0.00 0.00 4.70
638 3669 1.571919 GTACAGCGGCATCTTTCGAT 58.428 50.000 1.45 0.00 0.00 3.59
639 3670 0.459585 GGTACAGCGGCATCTTTCGA 60.460 55.000 1.45 0.00 0.00 3.71
658 3733 2.114670 CAGGGGGTAATGCAGCACG 61.115 63.158 0.00 0.00 0.00 5.34
659 3734 2.418083 GCAGGGGGTAATGCAGCAC 61.418 63.158 0.00 0.00 42.11 4.40
681 3756 1.021390 CGGCAATCTCGCTTTCACCT 61.021 55.000 0.00 0.00 0.00 4.00
699 3774 2.892334 CTGGGACCAAACACACGCG 61.892 63.158 3.53 3.53 0.00 6.01
702 3777 0.744281 CAACCTGGGACCAAACACAC 59.256 55.000 0.00 0.00 0.00 3.82
705 3780 1.993956 CATCAACCTGGGACCAAACA 58.006 50.000 0.00 0.00 0.00 2.83
706 3781 0.603065 GCATCAACCTGGGACCAAAC 59.397 55.000 0.00 0.00 0.00 2.93
708 3783 1.076549 GGCATCAACCTGGGACCAA 59.923 57.895 0.00 0.00 0.00 3.67
709 3784 2.763215 GGCATCAACCTGGGACCA 59.237 61.111 0.00 0.00 0.00 4.02
710 3785 2.043953 GGGCATCAACCTGGGACC 60.044 66.667 0.00 0.00 0.00 4.46
711 3786 2.270874 ATCGGGCATCAACCTGGGAC 62.271 60.000 0.00 0.00 36.66 4.46
735 3810 3.792053 CTGCCCGACCGATACAGCC 62.792 68.421 0.00 0.00 0.00 4.85
857 3970 1.148157 CTCTGCAATGCGGACTACGG 61.148 60.000 13.45 0.00 39.19 4.02
858 3971 0.458543 ACTCTGCAATGCGGACTACG 60.459 55.000 13.45 6.07 39.19 3.51
859 3972 1.281899 GACTCTGCAATGCGGACTAC 58.718 55.000 13.45 3.84 39.19 2.73
860 3973 0.179137 CGACTCTGCAATGCGGACTA 60.179 55.000 13.45 0.00 39.19 2.59
861 3974 1.446792 CGACTCTGCAATGCGGACT 60.447 57.895 13.45 4.11 39.19 3.85
862 3975 3.084579 CGACTCTGCAATGCGGAC 58.915 61.111 13.45 3.56 39.19 4.79
867 3995 4.175599 AGTCGCGACTCTGCAATG 57.824 55.556 34.98 0.00 36.92 2.82
913 4045 0.878961 GGGCCTATTTGTACGCGGAG 60.879 60.000 12.47 0.00 0.00 4.63
914 4046 1.144496 GGGCCTATTTGTACGCGGA 59.856 57.895 12.47 0.00 0.00 5.54
915 4047 1.890510 GGGGCCTATTTGTACGCGG 60.891 63.158 12.47 0.00 0.00 6.46
996 4131 1.000283 CGCGGGAGAAGCTTCATCTAT 60.000 52.381 27.57 7.06 0.00 1.98
997 4132 0.385751 CGCGGGAGAAGCTTCATCTA 59.614 55.000 27.57 0.00 0.00 1.98
998 4133 1.142748 CGCGGGAGAAGCTTCATCT 59.857 57.895 27.57 7.76 0.00 2.90
999 4134 2.529619 GCGCGGGAGAAGCTTCATC 61.530 63.158 27.57 19.89 33.33 2.92
1320 4476 4.796231 CCGAGGTCGTGAAGGGCG 62.796 72.222 0.00 0.00 37.74 6.13
1326 4482 4.988716 AGGGTGCCGAGGTCGTGA 62.989 66.667 0.00 0.00 37.74 4.35
1344 4500 4.477975 GAGGTGGACGTCGGCTCG 62.478 72.222 9.92 0.00 0.00 5.03
1461 4617 2.266055 GAAGAGACCCGCCACAGG 59.734 66.667 0.00 0.00 0.00 4.00
1542 4698 4.011517 TTGGACGGGAGCGGGAAC 62.012 66.667 0.00 0.00 0.00 3.62
1845 5001 2.734673 CGGCTTCTTGCTCTGACGC 61.735 63.158 0.00 0.00 42.39 5.19
1848 5004 0.108585 AAACCGGCTTCTTGCTCTGA 59.891 50.000 0.00 0.00 42.39 3.27
1944 5100 3.426117 ATCGTTGCCGCCGGAGTAG 62.426 63.158 7.68 0.00 0.00 2.57
2229 5385 1.227002 GTCATCGCCGTCTTCTCCC 60.227 63.158 0.00 0.00 0.00 4.30
2250 5406 3.470888 ACCCTCCATTCCTCGCCG 61.471 66.667 0.00 0.00 0.00 6.46
2288 5444 2.607750 ACCAGACCCGCACCTCAT 60.608 61.111 0.00 0.00 0.00 2.90
2289 5445 3.311110 GACCAGACCCGCACCTCA 61.311 66.667 0.00 0.00 0.00 3.86
2368 5524 7.587037 TCAGATCAAAAATCAGGAAAACACT 57.413 32.000 0.00 0.00 0.00 3.55
2402 5564 4.324135 CGACCGTACGTATCTCTATCTCAG 59.676 50.000 15.21 0.00 0.00 3.35
2479 5641 2.783135 TGGATTCACCACAAGAAGCTC 58.217 47.619 0.00 0.00 44.64 4.09
2502 5664 0.669625 GGCTAAAAGAGGCGACGTGT 60.670 55.000 0.00 0.00 41.55 4.49
2530 5716 4.504864 CGGGCTGAGATTTACAATCCCATA 60.505 45.833 0.00 0.00 33.00 2.74
2532 5718 2.421388 CGGGCTGAGATTTACAATCCCA 60.421 50.000 0.00 0.00 33.00 4.37
2549 5735 1.366679 GTTAAGTCTTACTGGCGGGC 58.633 55.000 0.00 0.00 0.00 6.13
2550 5736 1.553704 AGGTTAAGTCTTACTGGCGGG 59.446 52.381 0.00 0.00 0.00 6.13
2552 5738 5.007385 ACATAGGTTAAGTCTTACTGGCG 57.993 43.478 0.00 0.00 0.00 5.69
2554 5740 8.258007 TCATCAACATAGGTTAAGTCTTACTGG 58.742 37.037 0.00 0.00 34.87 4.00
2555 5741 9.653287 TTCATCAACATAGGTTAAGTCTTACTG 57.347 33.333 0.00 0.00 34.87 2.74
2559 5745 9.178758 GGATTTCATCAACATAGGTTAAGTCTT 57.821 33.333 0.00 0.00 34.87 3.01
2560 5746 8.552296 AGGATTTCATCAACATAGGTTAAGTCT 58.448 33.333 0.00 0.00 34.87 3.24
2561 5747 8.738645 AGGATTTCATCAACATAGGTTAAGTC 57.261 34.615 0.00 0.00 34.87 3.01
2563 5749 9.613428 TGTAGGATTTCATCAACATAGGTTAAG 57.387 33.333 0.00 0.00 34.87 1.85
2569 5755 8.597167 TCCCTATGTAGGATTTCATCAACATAG 58.403 37.037 19.67 19.67 46.63 2.23
2570 5756 8.504811 TCCCTATGTAGGATTTCATCAACATA 57.495 34.615 7.66 9.24 46.63 2.29
2571 5757 7.392766 TCCCTATGTAGGATTTCATCAACAT 57.607 36.000 7.66 8.28 46.63 2.71
2572 5758 6.823286 TCCCTATGTAGGATTTCATCAACA 57.177 37.500 7.66 0.00 46.63 3.33
2573 5759 6.881602 GGATCCCTATGTAGGATTTCATCAAC 59.118 42.308 0.00 0.00 46.63 3.18
2574 5760 6.562223 TGGATCCCTATGTAGGATTTCATCAA 59.438 38.462 9.90 0.00 46.63 2.57
2576 5762 6.627087 TGGATCCCTATGTAGGATTTCATC 57.373 41.667 9.90 1.92 46.63 2.92
2577 5763 6.579849 GCATGGATCCCTATGTAGGATTTCAT 60.580 42.308 9.90 2.70 46.63 2.57
2578 5764 5.280676 GCATGGATCCCTATGTAGGATTTCA 60.281 44.000 9.90 0.53 46.63 2.69
2579 5765 5.189180 GCATGGATCCCTATGTAGGATTTC 58.811 45.833 9.90 1.98 46.63 2.17
2580 5766 4.603171 TGCATGGATCCCTATGTAGGATTT 59.397 41.667 9.90 0.00 46.63 2.17
2581 5767 4.178339 TGCATGGATCCCTATGTAGGATT 58.822 43.478 9.90 0.00 46.63 3.01
2582 5768 3.806975 TGCATGGATCCCTATGTAGGAT 58.193 45.455 9.90 0.00 46.63 3.24
2583 5769 3.274281 TGCATGGATCCCTATGTAGGA 57.726 47.619 9.90 0.00 46.63 2.94
2584 5770 4.581309 ATTGCATGGATCCCTATGTAGG 57.419 45.455 9.90 0.00 43.25 3.18
2585 5771 6.906157 AAAATTGCATGGATCCCTATGTAG 57.094 37.500 9.90 0.00 0.00 2.74
2640 5838 9.778741 ACTTAATCAAGTCTAAATCAAGTGACA 57.221 29.630 0.00 0.00 41.25 3.58
2660 5858 8.608844 AAGTTTCAGTCGATTTGAGACTTAAT 57.391 30.769 24.51 11.10 45.74 1.40
2661 5859 9.193133 CTAAGTTTCAGTCGATTTGAGACTTAA 57.807 33.333 27.06 18.71 44.58 1.85
2662 5860 7.328737 GCTAAGTTTCAGTCGATTTGAGACTTA 59.671 37.037 26.34 26.34 45.74 2.24
2663 5861 6.146347 GCTAAGTTTCAGTCGATTTGAGACTT 59.854 38.462 26.71 26.71 45.74 3.01
2665 5863 5.163943 GGCTAAGTTTCAGTCGATTTGAGAC 60.164 44.000 12.67 12.67 38.81 3.36
2666 5864 4.929808 GGCTAAGTTTCAGTCGATTTGAGA 59.070 41.667 0.00 0.00 0.00 3.27
2667 5865 4.690748 TGGCTAAGTTTCAGTCGATTTGAG 59.309 41.667 0.00 0.00 0.00 3.02
2668 5866 4.451096 GTGGCTAAGTTTCAGTCGATTTGA 59.549 41.667 0.00 0.00 0.00 2.69
2669 5867 4.213270 TGTGGCTAAGTTTCAGTCGATTTG 59.787 41.667 0.00 0.00 0.00 2.32
2670 5868 4.385825 TGTGGCTAAGTTTCAGTCGATTT 58.614 39.130 0.00 0.00 0.00 2.17
2671 5869 4.002906 TGTGGCTAAGTTTCAGTCGATT 57.997 40.909 0.00 0.00 0.00 3.34
2672 5870 3.678056 TGTGGCTAAGTTTCAGTCGAT 57.322 42.857 0.00 0.00 0.00 3.59
2678 5876 5.475564 GGGTAAAGAATGTGGCTAAGTTTCA 59.524 40.000 0.00 0.00 0.00 2.69
2681 5879 5.256806 AGGGTAAAGAATGTGGCTAAGTT 57.743 39.130 0.00 0.00 0.00 2.66
2684 5882 6.630203 TCTTAGGGTAAAGAATGTGGCTAA 57.370 37.500 0.00 0.00 32.59 3.09
2702 5900 5.470368 TGAGAACCTTCGTGTCAATCTTAG 58.530 41.667 0.00 0.00 0.00 2.18
2798 5996 0.984230 CTGGAGCTACACAAGGGGAA 59.016 55.000 0.00 0.00 0.00 3.97
2801 5999 1.448540 CGCTGGAGCTACACAAGGG 60.449 63.158 0.00 0.00 39.32 3.95
2809 6007 2.268802 CGATAGCCCGCTGGAGCTA 61.269 63.158 0.00 8.87 45.17 3.32
2810 6008 3.610669 CGATAGCCCGCTGGAGCT 61.611 66.667 0.00 7.02 43.20 4.09
2813 6011 1.143183 GTTTCGATAGCCCGCTGGA 59.857 57.895 0.00 0.00 0.00 3.86
2819 6017 3.512680 CGGATATGAGTTTCGATAGCCC 58.487 50.000 0.00 0.00 28.34 5.19
2827 6025 4.332819 CCTCAACAACCGGATATGAGTTTC 59.667 45.833 9.46 0.00 36.61 2.78
2828 6026 4.261801 CCTCAACAACCGGATATGAGTTT 58.738 43.478 9.46 0.00 36.61 2.66
2829 6027 3.370527 CCCTCAACAACCGGATATGAGTT 60.371 47.826 9.46 0.00 36.61 3.01
2842 6041 1.374947 CGGAAGAGGCCCTCAACAA 59.625 57.895 14.46 0.00 32.06 2.83
2846 6045 2.607750 AAGCGGAAGAGGCCCTCA 60.608 61.111 14.46 0.00 32.06 3.86
2895 6094 0.531974 GCCACAAGACGACCTCAACA 60.532 55.000 0.00 0.00 0.00 3.33
2898 6097 0.320683 CATGCCACAAGACGACCTCA 60.321 55.000 0.00 0.00 0.00 3.86
2908 6107 1.164411 CCTACGCTTTCATGCCACAA 58.836 50.000 0.00 0.00 0.00 3.33
2909 6108 0.323302 TCCTACGCTTTCATGCCACA 59.677 50.000 0.00 0.00 0.00 4.17
2916 6115 7.426410 CAAGACTTCTATATCCTACGCTTTCA 58.574 38.462 0.00 0.00 0.00 2.69
2918 6117 6.239345 CCCAAGACTTCTATATCCTACGCTTT 60.239 42.308 0.00 0.00 0.00 3.51
2931 6130 2.735259 AACCCTCCCCAAGACTTCTA 57.265 50.000 0.00 0.00 0.00 2.10
2933 6132 2.618302 GCTAAACCCTCCCCAAGACTTC 60.618 54.545 0.00 0.00 0.00 3.01
2939 6138 1.128809 TGACGCTAAACCCTCCCCAA 61.129 55.000 0.00 0.00 0.00 4.12
2944 6143 2.005971 AATCGTGACGCTAAACCCTC 57.994 50.000 0.00 0.00 0.00 4.30
2945 6144 2.073816 CAAATCGTGACGCTAAACCCT 58.926 47.619 0.00 0.00 0.00 4.34
2946 6145 1.129811 CCAAATCGTGACGCTAAACCC 59.870 52.381 0.00 0.00 0.00 4.11
2952 6151 1.375523 GGACCCAAATCGTGACGCT 60.376 57.895 0.00 0.00 0.00 5.07
2958 6157 0.970427 GGCCATTGGACCCAAATCGT 60.970 55.000 6.95 0.00 39.55 3.73
2978 6177 0.106167 TCACTAGAGCATAGCCCCGT 60.106 55.000 0.00 0.00 0.00 5.28
2980 6179 1.616374 GACTCACTAGAGCATAGCCCC 59.384 57.143 0.00 0.00 46.09 5.80
2982 6181 3.243704 CCTTGACTCACTAGAGCATAGCC 60.244 52.174 0.00 0.00 46.09 3.93
2997 6196 2.028020 GTGTAGCCTAGCAACCTTGACT 60.028 50.000 0.00 0.00 0.00 3.41
3001 6200 0.249398 CCGTGTAGCCTAGCAACCTT 59.751 55.000 0.00 0.00 0.00 3.50
3002 6201 1.898154 CCGTGTAGCCTAGCAACCT 59.102 57.895 0.00 0.00 0.00 3.50
3030 6229 2.201490 TAGGGGGCATCTCCTCGG 59.799 66.667 0.00 0.00 35.59 4.63
3031 6230 2.210711 GGTAGGGGGCATCTCCTCG 61.211 68.421 0.00 0.00 35.59 4.63
3045 6244 4.162690 GCGGCCTGTGGGAGGTAG 62.163 72.222 0.00 0.00 44.97 3.18
3046 6245 3.305619 TAGCGGCCTGTGGGAGGTA 62.306 63.158 0.00 0.00 44.97 3.08
3047 6246 4.715130 TAGCGGCCTGTGGGAGGT 62.715 66.667 0.00 0.00 44.97 3.85
3049 6248 4.162690 GGTAGCGGCCTGTGGGAG 62.163 72.222 0.00 0.00 33.58 4.30
3051 6250 4.778143 GTGGTAGCGGCCTGTGGG 62.778 72.222 0.00 0.00 0.00 4.61
3053 6252 3.958147 CTGGTGGTAGCGGCCTGTG 62.958 68.421 0.00 0.00 0.00 3.66
3054 6253 3.706373 CTGGTGGTAGCGGCCTGT 61.706 66.667 0.00 0.00 0.00 4.00
3059 6258 2.125512 GCTCACTGGTGGTAGCGG 60.126 66.667 0.70 0.00 0.00 5.52
3063 6262 2.356022 CCAATGATGCTCACTGGTGGTA 60.356 50.000 5.74 0.00 38.83 3.25
3075 6274 0.896923 TGGGCTTTGTCCAATGATGC 59.103 50.000 0.00 0.00 32.75 3.91
3076 6275 1.894466 TGTGGGCTTTGTCCAATGATG 59.106 47.619 0.00 0.00 39.82 3.07
3080 6279 3.136260 ACATTTTGTGGGCTTTGTCCAAT 59.864 39.130 0.00 0.00 39.82 3.16
3092 6291 1.824852 GGAAGGCCCTACATTTTGTGG 59.175 52.381 0.00 0.00 0.00 4.17
3128 6327 3.965258 ACCATGCGCCAACTCCCA 61.965 61.111 4.18 0.00 0.00 4.37
3142 6341 3.325425 TCAAAGGGTAAGAATCGTCACCA 59.675 43.478 3.99 0.00 32.42 4.17
3155 6355 3.010027 TGATCACTGCCAATCAAAGGGTA 59.990 43.478 0.00 0.00 0.00 3.69
3156 6356 2.225091 TGATCACTGCCAATCAAAGGGT 60.225 45.455 0.00 0.00 0.00 4.34
3157 6357 2.426024 CTGATCACTGCCAATCAAAGGG 59.574 50.000 0.00 0.00 31.81 3.95
3162 6362 0.994247 ACCCTGATCACTGCCAATCA 59.006 50.000 0.00 0.00 0.00 2.57
3163 6363 1.065199 TGACCCTGATCACTGCCAATC 60.065 52.381 0.00 0.00 0.00 2.67
3164 6364 0.994247 TGACCCTGATCACTGCCAAT 59.006 50.000 0.00 0.00 0.00 3.16
3165 6365 0.994247 ATGACCCTGATCACTGCCAA 59.006 50.000 0.00 0.00 0.00 4.52
3166 6366 1.486310 GTATGACCCTGATCACTGCCA 59.514 52.381 0.00 0.00 0.00 4.92
3169 6369 1.069204 CCGGTATGACCCTGATCACTG 59.931 57.143 0.00 0.00 33.75 3.66
3203 6403 1.738350 GTGCTAGAGCTAGTCACGTCA 59.262 52.381 2.72 0.00 42.66 4.35
3206 6406 3.518017 CGTGCTAGAGCTAGTCACG 57.482 57.895 24.93 24.93 46.13 4.35
3217 6417 0.034059 GGACATCATCCCCGTGCTAG 59.966 60.000 0.00 0.00 42.46 3.42
3219 6419 2.911143 GGACATCATCCCCGTGCT 59.089 61.111 0.00 0.00 42.46 4.40
3228 6428 3.765511 CCACAAACCATTGAGGACATCAT 59.234 43.478 0.00 0.00 46.64 2.45
3257 6461 0.948623 CAAGCCACCACGATCGAACA 60.949 55.000 24.34 0.00 0.00 3.18
3266 6470 1.005867 CACCAATGCAAGCCACCAC 60.006 57.895 0.00 0.00 0.00 4.16
3270 6474 2.267351 CGACCACCAATGCAAGCCA 61.267 57.895 0.00 0.00 0.00 4.75
3274 6478 1.900981 CACCCGACCACCAATGCAA 60.901 57.895 0.00 0.00 0.00 4.08
3275 6479 2.282110 CACCCGACCACCAATGCA 60.282 61.111 0.00 0.00 0.00 3.96
3277 6481 3.061848 GCCACCCGACCACCAATG 61.062 66.667 0.00 0.00 0.00 2.82
3278 6482 4.715523 CGCCACCCGACCACCAAT 62.716 66.667 0.00 0.00 40.02 3.16
3304 6515 1.631072 CCATTAAGTCTCACGCGCG 59.369 57.895 30.96 30.96 0.00 6.86
3308 6519 1.473434 GGGGAGCCATTAAGTCTCACG 60.473 57.143 0.00 0.00 31.26 4.35


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

AutoCloner maintained by Alex Coulton.