Multiple sequence alignment - TraesCS7D01G264800

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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 TraesCS7D01G264800 chr7D 100.000 6751 0 0 1 6751 246029646 246022896 0.000000e+00 12467.0
1 TraesCS7D01G264800 chr7D 89.189 74 8 0 2460 2533 626888189 626888262 7.210000e-15 93.5
2 TraesCS7D01G264800 chr7D 79.464 112 22 1 5049 5159 451198160 451198271 2.020000e-10 78.7
3 TraesCS7D01G264800 chr7D 94.000 50 1 2 3542 3590 306392872 306392920 2.610000e-09 75.0
4 TraesCS7D01G264800 chr7B 94.315 3659 117 25 2534 6171 222303788 222300200 0.000000e+00 5520.0
5 TraesCS7D01G264800 chr7B 94.654 1590 62 14 1 1572 222305365 222303781 0.000000e+00 2444.0
6 TraesCS7D01G264800 chr7B 98.462 130 2 0 6177 6306 726369849 726369720 5.270000e-56 230.0
7 TraesCS7D01G264800 chr7B 94.245 139 8 0 6490 6628 222299570 222299432 5.300000e-51 213.0
8 TraesCS7D01G264800 chr7B 86.224 196 10 1 6302 6497 222300198 222300020 5.340000e-46 196.0
9 TraesCS7D01G264800 chr7A 94.106 3682 127 26 2536 6172 262463406 262459770 0.000000e+00 5515.0
10 TraesCS7D01G264800 chr7A 96.186 1573 58 2 1 1572 262464972 262463401 0.000000e+00 2571.0
11 TraesCS7D01G264800 chr7A 98.237 964 9 4 1572 2534 695630196 695631152 0.000000e+00 1679.0
12 TraesCS7D01G264800 chr7A 94.964 973 30 9 1571 2533 107642890 107643853 0.000000e+00 1507.0
13 TraesCS7D01G264800 chr7A 89.183 453 15 10 6302 6750 262459770 262459348 9.970000e-148 534.0
14 TraesCS7D01G264800 chr7A 95.556 135 6 0 6170 6304 508642927 508643061 4.100000e-52 217.0
15 TraesCS7D01G264800 chr3A 97.541 976 16 4 1565 2539 533087421 533086453 0.000000e+00 1663.0
16 TraesCS7D01G264800 chr4D 94.678 977 26 11 1569 2541 29315742 29316696 0.000000e+00 1493.0
17 TraesCS7D01G264800 chr4D 94.000 50 1 2 3542 3590 243730327 243730375 2.610000e-09 75.0
18 TraesCS7D01G264800 chr6D 93.197 735 38 7 1571 2303 450808939 450809663 0.000000e+00 1070.0
19 TraesCS7D01G264800 chr6D 92.568 148 10 1 2386 2533 450811629 450811775 1.910000e-50 211.0
20 TraesCS7D01G264800 chr6D 94.118 68 3 1 6302 6369 458975446 458975380 1.200000e-17 102.0
21 TraesCS7D01G264800 chr1B 89.766 342 14 8 1751 2090 483989683 483989361 1.050000e-112 418.0
22 TraesCS7D01G264800 chr1B 89.902 307 21 6 2085 2389 483963309 483963011 2.950000e-103 387.0
23 TraesCS7D01G264800 chr1B 96.894 161 5 0 1572 1732 483989831 483989671 3.100000e-68 270.0
24 TraesCS7D01G264800 chr1B 99.219 128 1 0 6176 6303 658923637 658923510 1.460000e-56 231.0
25 TraesCS7D01G264800 chr1B 90.604 149 10 3 2381 2529 483906007 483905863 1.920000e-45 195.0
26 TraesCS7D01G264800 chr1B 94.595 74 2 2 6302 6375 556993852 556993781 5.530000e-21 113.0
27 TraesCS7D01G264800 chr1B 92.157 51 2 2 3541 3590 506824386 506824435 3.380000e-08 71.3
28 TraesCS7D01G264800 chr3B 99.219 128 1 0 6177 6304 493648664 493648791 1.460000e-56 231.0
29 TraesCS7D01G264800 chr5B 96.403 139 4 1 6166 6304 631220169 631220032 1.890000e-55 228.0
30 TraesCS7D01G264800 chr5B 95.714 140 4 2 6166 6305 65594933 65595070 2.450000e-54 224.0
31 TraesCS7D01G264800 chr5B 95.035 141 7 0 6164 6304 598032796 598032936 8.810000e-54 222.0
32 TraesCS7D01G264800 chr2A 97.059 136 3 1 6170 6304 20004788 20004653 1.890000e-55 228.0
33 TraesCS7D01G264800 chr2A 83.251 203 24 9 6176 6373 83031995 83032192 1.930000e-40 178.0
34 TraesCS7D01G264800 chr2A 91.667 72 4 2 6304 6375 609736927 609736858 1.550000e-16 99.0
35 TraesCS7D01G264800 chr4A 94.040 151 4 5 6154 6303 311933214 311933360 2.450000e-54 224.0
36 TraesCS7D01G264800 chr3D 94.118 68 4 0 6307 6374 589702150 589702083 3.330000e-18 104.0
37 TraesCS7D01G264800 chr2D 94.118 68 4 0 6307 6374 19538825 19538892 3.330000e-18 104.0
38 TraesCS7D01G264800 chr2D 92.593 54 1 3 3538 3590 412735605 412735554 2.610000e-09 75.0
39 TraesCS7D01G264800 chr2D 95.556 45 1 1 3547 3590 228817577 228817533 3.380000e-08 71.3
40 TraesCS7D01G264800 chr6B 90.909 77 2 5 6302 6375 40456624 40456698 1.550000e-16 99.0
41 TraesCS7D01G264800 chrUn 90.278 72 5 2 2457 2527 368183055 368183125 7.210000e-15 93.5
42 TraesCS7D01G264800 chrUn 88.312 77 8 1 2457 2533 101929177 101929102 2.590000e-14 91.6
43 TraesCS7D01G264800 chr2B 94.000 50 1 2 3542 3590 736851912 736851960 2.610000e-09 75.0
44 TraesCS7D01G264800 chr6A 97.561 41 1 0 3550 3590 158238688 158238648 3.380000e-08 71.3
45 TraesCS7D01G264800 chr5D 97.561 41 1 0 3550 3590 158225147 158225107 3.380000e-08 71.3
46 TraesCS7D01G264800 chr1D 92.308 52 1 3 3540 3590 216566645 216566596 3.380000e-08 71.3


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 TraesCS7D01G264800 chr7D 246022896 246029646 6750 True 12467.000000 12467 100.000000 1 6751 1 chr7D.!!$R1 6750
1 TraesCS7D01G264800 chr7B 222299432 222305365 5933 True 2093.250000 5520 92.359500 1 6628 4 chr7B.!!$R2 6627
2 TraesCS7D01G264800 chr7A 262459348 262464972 5624 True 2873.333333 5515 93.158333 1 6750 3 chr7A.!!$R1 6749
3 TraesCS7D01G264800 chr7A 695630196 695631152 956 False 1679.000000 1679 98.237000 1572 2534 1 chr7A.!!$F3 962
4 TraesCS7D01G264800 chr7A 107642890 107643853 963 False 1507.000000 1507 94.964000 1571 2533 1 chr7A.!!$F1 962
5 TraesCS7D01G264800 chr3A 533086453 533087421 968 True 1663.000000 1663 97.541000 1565 2539 1 chr3A.!!$R1 974
6 TraesCS7D01G264800 chr4D 29315742 29316696 954 False 1493.000000 1493 94.678000 1569 2541 1 chr4D.!!$F1 972
7 TraesCS7D01G264800 chr6D 450808939 450811775 2836 False 640.500000 1070 92.882500 1571 2533 2 chr6D.!!$F1 962

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
94 95 0.178984 AAACCCGGACCGAAAACCAT 60.179 50.000 17.49 0.00 0.00 3.55 F
467 469 1.335142 CCGCTATCTACGAGAAGCACC 60.335 57.143 0.00 0.00 32.02 5.01 F
627 629 1.615424 AGTAGGGCGGTGGTCCAAT 60.615 57.895 0.00 0.00 41.80 3.16 F
1239 1241 1.680735 CTCCACTCCTCTCTCATTCCG 59.319 57.143 0.00 0.00 0.00 4.30 F
1258 1265 1.802880 CGCAGTCGCTATAGGCTTGTT 60.803 52.381 1.04 0.00 39.13 2.83 F
2414 4387 2.328099 CGTGGGAGGCTGCAGTTTC 61.328 63.158 16.64 12.82 0.00 2.78 F
3522 5516 1.106285 CCTTAGTTGCCCCATTCTGC 58.894 55.000 0.00 0.00 0.00 4.26 F
3584 5578 0.034380 TCATCTTCGGTCCTCGGTCT 60.034 55.000 0.00 0.00 39.77 3.85 F
3587 5581 0.251033 TCTTCGGTCCTCGGTCTTGA 60.251 55.000 0.00 0.00 39.77 3.02 F
3975 5973 0.398318 GGTCTTGTTGGGAGCTCTGT 59.602 55.000 14.64 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1505 1.478654 CGGCCAGCCCATAATAAACCT 60.479 52.381 2.24 0.0 0.00 3.50 R
2204 2235 0.970937 CAGTTCTACTCGCCCCCTGA 60.971 60.000 0.00 0.0 0.00 3.86 R
2414 4387 4.279420 CCCTTCCCTCTCAAAGAAAAACAG 59.721 45.833 0.00 0.0 0.00 3.16 R
3217 5211 0.108804 TTCCATCTCCTCGTGTTCGC 60.109 55.000 0.00 0.0 36.96 4.70 R
3357 5351 3.953612 CCTCAGCTCTATCTTGTGTCTCT 59.046 47.826 0.00 0.0 0.00 3.10 R
3565 5559 0.034380 AGACCGAGGACCGAAGATGA 60.034 55.000 0.00 0.0 41.76 2.92 R
5021 7046 0.042581 TCACAGAGGCCTATCCCACA 59.957 55.000 4.42 0.0 34.51 4.17 R
5023 7048 2.050144 GAATCACAGAGGCCTATCCCA 58.950 52.381 4.42 0.0 34.51 4.37 R
5085 7110 2.232208 CCTCCAAATCAAAAGGCTCCAC 59.768 50.000 0.00 0.0 0.00 4.02 R
5875 7900 0.535553 TTACGCCCCAAGAACACACC 60.536 55.000 0.00 0.0 0.00 4.16 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
79 80 3.826729 ACAACTCAAGCCAATCCTAAACC 59.173 43.478 0.00 0.00 0.00 3.27
81 82 2.017049 CTCAAGCCAATCCTAAACCCG 58.983 52.381 0.00 0.00 0.00 5.28
94 95 0.178984 AAACCCGGACCGAAAACCAT 60.179 50.000 17.49 0.00 0.00 3.55
392 394 3.391382 CCGGGAGAAGGAGGCGTT 61.391 66.667 0.00 0.00 0.00 4.84
467 469 1.335142 CCGCTATCTACGAGAAGCACC 60.335 57.143 0.00 0.00 32.02 5.01
525 527 3.336122 ACGGAAGTACGACCTGTCT 57.664 52.632 9.08 0.00 46.88 3.41
627 629 1.615424 AGTAGGGCGGTGGTCCAAT 60.615 57.895 0.00 0.00 41.80 3.16
690 692 2.042831 GTCAGCCCCACATGTCAGC 61.043 63.158 0.00 0.00 0.00 4.26
1239 1241 1.680735 CTCCACTCCTCTCTCATTCCG 59.319 57.143 0.00 0.00 0.00 4.30
1258 1265 1.802880 CGCAGTCGCTATAGGCTTGTT 60.803 52.381 1.04 0.00 39.13 2.83
1357 1376 7.054124 AGGCTTTTGTTGATTCGATCCTATTA 58.946 34.615 0.00 0.00 0.00 0.98
1363 1382 8.972458 TTGTTGATTCGATCCTATTAATCCAA 57.028 30.769 0.00 0.00 0.00 3.53
1412 1431 9.659830 GTTACTGTTGTACTGGAATTTAGTTTG 57.340 33.333 0.00 0.00 0.00 2.93
1540 1559 3.769739 ATCTTCTGGTGTGCAGTACAA 57.230 42.857 0.00 0.00 41.89 2.41
2204 2235 7.067008 CACGTACCATCTCCCAGATAAATTTTT 59.933 37.037 0.00 0.00 32.12 1.94
2414 4387 2.328099 CGTGGGAGGCTGCAGTTTC 61.328 63.158 16.64 12.82 0.00 2.78
2521 4495 2.900337 CCGTTTGCCCGGCCTATC 60.900 66.667 7.03 0.00 41.78 2.08
2606 4580 4.381505 GGCACTGAAACTGGAGAACAAAAA 60.382 41.667 0.00 0.00 0.00 1.94
2730 4723 4.508551 AGCCATATGAGATGTTGTGGAA 57.491 40.909 3.65 0.00 0.00 3.53
2833 4826 4.858850 TGGATATCTCAAGTGCATTTGGT 58.141 39.130 20.34 10.40 0.00 3.67
2839 4832 2.884012 CTCAAGTGCATTTGGTGGTACA 59.116 45.455 20.34 0.14 0.00 2.90
2898 4891 9.062524 TGGTTATCTGTATATTTATGGTGTTGC 57.937 33.333 0.00 0.00 0.00 4.17
3110 5103 6.925610 TGCTTGTTCTGATACATGATAACC 57.074 37.500 0.00 0.00 0.00 2.85
3217 5211 7.099266 TGGTGAACAATATGATGCTTTAAGG 57.901 36.000 0.00 0.00 0.00 2.69
3309 5303 5.873712 TGTTGGTTTTCACTCAAAGTACGTA 59.126 36.000 0.00 0.00 0.00 3.57
3522 5516 1.106285 CCTTAGTTGCCCCATTCTGC 58.894 55.000 0.00 0.00 0.00 4.26
3541 5535 2.694628 TGCATCACTTTTTGCTCCACTT 59.305 40.909 0.00 0.00 39.60 3.16
3555 5549 3.715495 CTCCACTTCATCTGATCTTCCG 58.285 50.000 0.00 0.00 0.00 4.30
3556 5550 3.365472 TCCACTTCATCTGATCTTCCGA 58.635 45.455 0.00 0.00 0.00 4.55
3560 5554 4.565962 CACTTCATCTGATCTTCCGAACTG 59.434 45.833 0.00 0.00 0.00 3.16
3561 5555 4.221703 ACTTCATCTGATCTTCCGAACTGT 59.778 41.667 0.00 0.00 0.00 3.55
3562 5556 4.808414 TCATCTGATCTTCCGAACTGTT 57.192 40.909 0.00 0.00 0.00 3.16
3563 5557 4.748892 TCATCTGATCTTCCGAACTGTTC 58.251 43.478 10.48 10.48 0.00 3.18
3565 5559 4.873746 TCTGATCTTCCGAACTGTTCTT 57.126 40.909 17.60 0.00 0.00 2.52
3566 5560 4.810790 TCTGATCTTCCGAACTGTTCTTC 58.189 43.478 17.60 6.33 0.00 2.87
3567 5561 4.280929 TCTGATCTTCCGAACTGTTCTTCA 59.719 41.667 17.60 9.75 0.00 3.02
3569 5563 5.171476 TGATCTTCCGAACTGTTCTTCATC 58.829 41.667 17.60 11.54 0.00 2.92
3570 5564 4.873746 TCTTCCGAACTGTTCTTCATCT 57.126 40.909 17.60 0.00 0.00 2.90
3571 5565 5.215252 TCTTCCGAACTGTTCTTCATCTT 57.785 39.130 17.60 0.00 0.00 2.40
3572 5566 5.230942 TCTTCCGAACTGTTCTTCATCTTC 58.769 41.667 17.60 0.00 0.00 2.87
3573 5567 3.575630 TCCGAACTGTTCTTCATCTTCG 58.424 45.455 17.60 2.70 36.61 3.79
3574 5568 2.668457 CCGAACTGTTCTTCATCTTCGG 59.332 50.000 17.60 8.01 43.37 4.30
3575 5569 3.318017 CGAACTGTTCTTCATCTTCGGT 58.682 45.455 17.60 0.00 34.89 4.69
3576 5570 3.365220 CGAACTGTTCTTCATCTTCGGTC 59.635 47.826 17.60 0.00 34.89 4.79
3577 5571 3.320673 ACTGTTCTTCATCTTCGGTCC 57.679 47.619 0.00 0.00 0.00 4.46
3578 5572 2.900546 ACTGTTCTTCATCTTCGGTCCT 59.099 45.455 0.00 0.00 0.00 3.85
3579 5573 3.056465 ACTGTTCTTCATCTTCGGTCCTC 60.056 47.826 0.00 0.00 0.00 3.71
3580 5574 2.094700 TGTTCTTCATCTTCGGTCCTCG 60.095 50.000 0.00 0.00 40.90 4.63
3581 5575 1.103803 TCTTCATCTTCGGTCCTCGG 58.896 55.000 0.00 0.00 39.77 4.63
3582 5576 0.818296 CTTCATCTTCGGTCCTCGGT 59.182 55.000 0.00 0.00 39.77 4.69
3583 5577 0.815734 TTCATCTTCGGTCCTCGGTC 59.184 55.000 0.00 0.00 39.77 4.79
3584 5578 0.034380 TCATCTTCGGTCCTCGGTCT 60.034 55.000 0.00 0.00 39.77 3.85
3585 5579 0.818296 CATCTTCGGTCCTCGGTCTT 59.182 55.000 0.00 0.00 39.77 3.01
3586 5580 0.818296 ATCTTCGGTCCTCGGTCTTG 59.182 55.000 0.00 0.00 39.77 3.02
3587 5581 0.251033 TCTTCGGTCCTCGGTCTTGA 60.251 55.000 0.00 0.00 39.77 3.02
3588 5582 0.601558 CTTCGGTCCTCGGTCTTGAA 59.398 55.000 0.00 0.00 39.77 2.69
3589 5583 1.000506 CTTCGGTCCTCGGTCTTGAAA 59.999 52.381 0.00 0.00 39.77 2.69
3590 5584 1.263356 TCGGTCCTCGGTCTTGAAAT 58.737 50.000 0.00 0.00 39.77 2.17
3591 5585 2.449464 TCGGTCCTCGGTCTTGAAATA 58.551 47.619 0.00 0.00 39.77 1.40
3592 5586 2.426024 TCGGTCCTCGGTCTTGAAATAG 59.574 50.000 0.00 0.00 39.77 1.73
3593 5587 2.552031 GGTCCTCGGTCTTGAAATAGC 58.448 52.381 0.00 0.00 0.00 2.97
3605 5599 6.317391 GGTCTTGAAATAGCTTTAGATGTGCT 59.683 38.462 0.00 0.00 40.43 4.40
3622 5616 1.134995 TGCTCCTTCTGTCTATGTGCG 60.135 52.381 0.00 0.00 0.00 5.34
3650 5644 3.325870 TGCAATTCCTTCTACGTGTCTG 58.674 45.455 0.00 0.00 0.00 3.51
3673 5667 3.523157 TGGGGAATTTGCTAGATGACTCA 59.477 43.478 0.00 0.00 0.00 3.41
3691 5685 7.252612 TGACTCATTGGTAATCAGGAACTTA 57.747 36.000 0.00 0.00 34.60 2.24
3693 5687 6.415573 ACTCATTGGTAATCAGGAACTTACC 58.584 40.000 4.84 4.84 44.70 2.85
3694 5688 6.215636 ACTCATTGGTAATCAGGAACTTACCT 59.784 38.462 11.54 0.00 44.72 3.08
3739 5734 2.723273 AGTAAATGCCTGCCTGTAACC 58.277 47.619 0.00 0.00 0.00 2.85
3787 5782 9.803315 CAACTGTTGATCTAAGTAAGCATACTA 57.197 33.333 15.26 0.00 41.57 1.82
3791 5786 7.913821 TGTTGATCTAAGTAAGCATACTACACG 59.086 37.037 1.37 0.00 41.57 4.49
3846 5841 8.001881 TGGTTTGTTGCTCTTTATGAGTAAAA 57.998 30.769 0.79 0.00 46.17 1.52
3856 5851 6.049149 TCTTTATGAGTAAAATCCGCTGAGG 58.951 40.000 0.00 0.00 33.67 3.86
3868 5866 6.761099 AATCCGCTGAGGTATATACAGTAG 57.239 41.667 14.70 9.47 41.99 2.57
3876 5874 8.938906 GCTGAGGTATATACAGTAGTCTTAGTC 58.061 40.741 14.70 1.89 34.60 2.59
3930 5928 2.214920 TGCCATGCATTGTGCCCAA 61.215 52.632 0.00 0.00 44.23 4.12
3931 5929 1.448893 GCCATGCATTGTGCCCAAG 60.449 57.895 0.00 0.00 44.23 3.61
3975 5973 0.398318 GGTCTTGTTGGGAGCTCTGT 59.602 55.000 14.64 0.00 0.00 3.41
3976 5974 1.202818 GGTCTTGTTGGGAGCTCTGTT 60.203 52.381 14.64 0.00 0.00 3.16
3977 5975 1.876156 GTCTTGTTGGGAGCTCTGTTG 59.124 52.381 14.64 0.00 0.00 3.33
4032 6030 7.455953 TGATGGGTAAGTAGAGATGCTCATATT 59.544 37.037 0.00 0.00 32.06 1.28
4044 6042 8.045507 AGAGATGCTCATATTGAAGAACTTGAA 58.954 33.333 0.00 0.00 32.06 2.69
4061 6059 8.103305 AGAACTTGAACCTTGCTGATTAATCTA 58.897 33.333 16.24 2.75 0.00 1.98
4125 6139 6.261826 CCTCCTTAGTCCTTGCTGAATATTTG 59.738 42.308 0.00 0.00 0.00 2.32
4131 6145 4.336713 GTCCTTGCTGAATATTTGTCTCCC 59.663 45.833 0.00 0.00 0.00 4.30
4255 6269 8.985315 AGGCATAATCTCATATGAACAAAAGA 57.015 30.769 6.90 0.00 35.69 2.52
4283 6297 3.319122 AGTGTTGTTGGAAGAGGCATTTC 59.681 43.478 0.00 0.00 0.00 2.17
4289 6303 4.522789 TGTTGGAAGAGGCATTTCTTAACC 59.477 41.667 13.29 0.00 37.53 2.85
4292 6306 3.127030 GGAAGAGGCATTTCTTAACCGTG 59.873 47.826 0.00 0.00 37.53 4.94
4309 6323 1.132834 CGTGCACATTGTATGGCATGT 59.867 47.619 18.64 0.00 38.23 3.21
4346 6361 6.660887 TTTGCTTTTTGGTGAATCTGTTTC 57.339 33.333 0.00 0.00 34.72 2.78
4353 6368 5.568685 TTGGTGAATCTGTTTCGTTTTCA 57.431 34.783 0.00 0.00 37.13 2.69
4360 6375 8.230486 GTGAATCTGTTTCGTTTTCATGTATCT 58.770 33.333 0.00 0.00 37.13 1.98
4398 6413 5.188751 ACTTCTAGAAAGAACCAGGGATCAG 59.811 44.000 6.63 0.00 36.80 2.90
4425 6440 7.095355 ACGACTTCTGATTATGGTTTGTACAAC 60.095 37.037 8.07 3.81 0.00 3.32
4439 6454 8.952278 TGGTTTGTACAACCAGATATTTATGAC 58.048 33.333 19.62 7.12 44.74 3.06
4442 6457 7.764695 TGTACAACCAGATATTTATGACGTG 57.235 36.000 0.00 0.00 0.00 4.49
4454 6473 9.088512 GATATTTATGACGTGTCTTTCTTGACT 57.911 33.333 0.00 0.00 37.79 3.41
4465 6484 8.873830 CGTGTCTTTCTTGACTTATGATAACAT 58.126 33.333 0.00 0.00 37.83 2.71
4586 6605 1.529438 GCTTGACAAATTCGACCGTGA 59.471 47.619 0.00 0.00 0.00 4.35
4603 6622 3.192844 CCGTGACTCAGGTTAGCTTCTTA 59.807 47.826 0.00 0.00 0.00 2.10
4615 6634 9.052759 CAGGTTAGCTTCTTAGTTTTGTTCTTA 57.947 33.333 0.00 0.00 0.00 2.10
4631 6650 4.699735 TGTTCTTATATGCAACACTGGGTG 59.300 41.667 0.00 0.00 39.75 4.61
4667 6686 8.079211 AGACATTGTACCAGTAGTCATGTATT 57.921 34.615 0.00 0.00 0.00 1.89
4681 6700 6.731467 AGTCATGTATTTACCCCTTGTCAAT 58.269 36.000 0.00 0.00 0.00 2.57
4694 6713 5.009010 CCCCTTGTCAATATGTAATGCACTC 59.991 44.000 0.00 0.00 0.00 3.51
4705 6724 5.222079 TGTAATGCACTCTCCTGTTTGTA 57.778 39.130 0.00 0.00 0.00 2.41
4727 6746 7.913789 TGTAGTGTAAGTCTATTTGATTGGGT 58.086 34.615 0.00 0.00 0.00 4.51
4802 6821 1.792757 TTTCACTCCATGCCCCAGCT 61.793 55.000 0.00 0.00 40.80 4.24
4807 6826 1.288932 ACTCCATGCCCCAGCTTTAAT 59.711 47.619 0.00 0.00 40.80 1.40
4837 6856 6.091441 GCTAAACAGGTTGACTAGTGAGATTG 59.909 42.308 0.00 0.00 0.00 2.67
4887 6906 4.104383 CCATTCATTAGGTATGGTGCCT 57.896 45.455 0.00 0.00 40.00 4.75
4888 6907 4.074970 CCATTCATTAGGTATGGTGCCTC 58.925 47.826 0.00 0.00 37.54 4.70
5021 7046 6.360370 TCTGTAAGCAGTGGACTATTCTTT 57.640 37.500 0.00 0.00 43.05 2.52
5023 7048 5.865085 TGTAAGCAGTGGACTATTCTTTGT 58.135 37.500 0.00 0.00 0.00 2.83
5042 7067 1.771255 GTGGGATAGGCCTCTGTGATT 59.229 52.381 9.68 0.00 36.66 2.57
5043 7068 2.050144 TGGGATAGGCCTCTGTGATTC 58.950 52.381 9.68 0.00 36.66 2.52
5044 7069 2.050144 GGGATAGGCCTCTGTGATTCA 58.950 52.381 9.68 0.00 36.66 2.57
5255 7280 2.076863 GTGCAGCCGAACAACTTCTAT 58.923 47.619 0.00 0.00 0.00 1.98
5264 7289 4.226761 CGAACAACTTCTATTTTGTGCCC 58.773 43.478 0.00 0.00 36.08 5.36
5342 7367 5.067805 CCTATTCCTTGGTTTTAGCCATGTC 59.932 44.000 0.00 0.00 38.48 3.06
5567 7592 1.301954 GTTAGGGGTGCCAATCCGT 59.698 57.895 0.00 0.00 0.00 4.69
5875 7900 2.704572 CAGCCTTACAAGAGGGAACTG 58.295 52.381 0.00 0.00 44.43 3.16
6031 8056 2.092211 CGTGACTAATCGTGGTTCTTGC 59.908 50.000 0.00 0.00 0.00 4.01
6032 8057 3.326747 GTGACTAATCGTGGTTCTTGCT 58.673 45.455 0.00 0.00 0.00 3.91
6033 8058 3.746492 GTGACTAATCGTGGTTCTTGCTT 59.254 43.478 0.00 0.00 0.00 3.91
6034 8059 3.745975 TGACTAATCGTGGTTCTTGCTTG 59.254 43.478 0.00 0.00 0.00 4.01
6171 8196 7.551974 GCTGTCCATTATCTCATTAGCATGTAT 59.448 37.037 0.00 0.00 0.00 2.29
6172 8197 9.445878 CTGTCCATTATCTCATTAGCATGTATT 57.554 33.333 0.00 0.00 0.00 1.89
6173 8198 9.797642 TGTCCATTATCTCATTAGCATGTATTT 57.202 29.630 0.00 0.00 0.00 1.40
6182 8207 8.585881 TCTCATTAGCATGTATTTACTACTCCC 58.414 37.037 0.00 0.00 0.00 4.30
6183 8208 8.492415 TCATTAGCATGTATTTACTACTCCCT 57.508 34.615 0.00 0.00 0.00 4.20
6184 8209 8.585881 TCATTAGCATGTATTTACTACTCCCTC 58.414 37.037 0.00 0.00 0.00 4.30
6185 8210 5.810080 AGCATGTATTTACTACTCCCTCC 57.190 43.478 0.00 0.00 0.00 4.30
6186 8211 4.281182 AGCATGTATTTACTACTCCCTCCG 59.719 45.833 0.00 0.00 0.00 4.63
6187 8212 4.038883 GCATGTATTTACTACTCCCTCCGT 59.961 45.833 0.00 0.00 0.00 4.69
6188 8213 5.452917 GCATGTATTTACTACTCCCTCCGTT 60.453 44.000 0.00 0.00 0.00 4.44
6189 8214 5.841957 TGTATTTACTACTCCCTCCGTTC 57.158 43.478 0.00 0.00 0.00 3.95
6190 8215 4.646492 TGTATTTACTACTCCCTCCGTTCC 59.354 45.833 0.00 0.00 0.00 3.62
6191 8216 1.755179 TTACTACTCCCTCCGTTCCG 58.245 55.000 0.00 0.00 0.00 4.30
6192 8217 0.911769 TACTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
6193 8218 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
6194 8219 1.341778 ACTACTCCCTCCGTTCCGAAT 60.342 52.381 0.00 0.00 0.00 3.34
6195 8220 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
6196 8221 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
6197 8222 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
6198 8223 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
6199 8224 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
6200 8225 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
6201 8226 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
6202 8227 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
6203 8228 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
6204 8229 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
6205 8230 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
6206 8231 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
6207 8232 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
6208 8233 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
6209 8234 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
6210 8235 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
6211 8236 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
6212 8237 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
6213 8238 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
6214 8239 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
6215 8240 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
6216 8241 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
6217 8242 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
6218 8243 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
6220 8245 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
6221 8246 7.907389 ACTTGTCTTGGATTTGTCTAGATACA 58.093 34.615 0.00 0.00 0.00 2.29
6222 8247 8.037758 ACTTGTCTTGGATTTGTCTAGATACAG 58.962 37.037 0.00 0.00 0.00 2.74
6223 8248 7.718334 TGTCTTGGATTTGTCTAGATACAGA 57.282 36.000 0.00 0.00 0.00 3.41
6224 8249 8.311395 TGTCTTGGATTTGTCTAGATACAGAT 57.689 34.615 0.00 0.00 0.00 2.90
6225 8250 8.200120 TGTCTTGGATTTGTCTAGATACAGATG 58.800 37.037 0.00 0.00 0.00 2.90
6226 8251 8.200792 GTCTTGGATTTGTCTAGATACAGATGT 58.799 37.037 0.00 0.00 0.00 3.06
6227 8252 9.421399 TCTTGGATTTGTCTAGATACAGATGTA 57.579 33.333 0.00 0.00 34.67 2.29
6257 8282 8.364142 AGACTCATTTTAGTGCTAGATACATCC 58.636 37.037 0.00 0.00 0.00 3.51
6258 8283 7.148641 ACTCATTTTAGTGCTAGATACATCCG 58.851 38.462 0.00 0.00 0.00 4.18
6259 8284 7.050970 TCATTTTAGTGCTAGATACATCCGT 57.949 36.000 0.00 0.00 0.00 4.69
6260 8285 8.173542 TCATTTTAGTGCTAGATACATCCGTA 57.826 34.615 0.00 0.00 0.00 4.02
6261 8286 8.803235 TCATTTTAGTGCTAGATACATCCGTAT 58.197 33.333 0.00 0.00 41.16 3.06
6277 8302 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
6278 8303 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
6279 8304 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
6280 8305 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
6281 8306 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
6282 8307 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
6289 8314 8.480643 AGACAAATCTAAGACAAGTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
6290 8315 8.311836 AGACAAATCTAAGACAAGTAATTCGGA 58.688 33.333 0.00 0.00 31.46 4.55
6291 8316 8.842358 ACAAATCTAAGACAAGTAATTCGGAA 57.158 30.769 0.00 0.00 0.00 4.30
6292 8317 8.718734 ACAAATCTAAGACAAGTAATTCGGAAC 58.281 33.333 0.00 0.00 0.00 3.62
6369 8394 8.398878 TGAACTCCCAAAACGTCTTATATTTT 57.601 30.769 0.00 0.00 0.00 1.82
6370 8395 8.293867 TGAACTCCCAAAACGTCTTATATTTTG 58.706 33.333 0.00 0.00 41.10 2.44
6377 8402 8.142348 CAAAACGTCTTATATTTTGGAACGTC 57.858 34.615 0.00 0.00 38.88 4.34
6378 8403 7.662604 AAACGTCTTATATTTTGGAACGTCT 57.337 32.000 0.00 0.00 0.00 4.18
6379 8404 7.662604 AACGTCTTATATTTTGGAACGTCTT 57.337 32.000 0.00 0.00 0.00 3.01
6380 8405 8.761575 AACGTCTTATATTTTGGAACGTCTTA 57.238 30.769 0.00 0.00 0.00 2.10
6381 8406 8.937634 ACGTCTTATATTTTGGAACGTCTTAT 57.062 30.769 0.00 0.00 0.00 1.73
6458 8483 8.094798 TCGCTAGTTTTCATGTTTGTTTCTAT 57.905 30.769 0.00 0.00 0.00 1.98
6459 8484 8.015087 TCGCTAGTTTTCATGTTTGTTTCTATG 58.985 33.333 0.00 0.00 0.00 2.23
6492 8974 9.775854 ACATTTCTAGAATTGGTGATATCTCTG 57.224 33.333 24.12 1.33 0.00 3.35
6590 9075 6.040842 ACTCCACTTTTATTCATGTTGCTTGT 59.959 34.615 0.00 0.00 0.00 3.16
6629 9114 5.228945 AGTTGTTTCTAGCTTTGCCTCTA 57.771 39.130 0.00 0.00 0.00 2.43
6648 9133 2.593346 AGCCTAGACTCAAATGAGCG 57.407 50.000 10.28 0.00 45.79 5.03
6650 9135 2.697751 AGCCTAGACTCAAATGAGCGAT 59.302 45.455 10.28 0.00 45.79 4.58
6652 9137 3.388308 CCTAGACTCAAATGAGCGATGG 58.612 50.000 10.28 4.88 45.79 3.51
6661 9146 2.202987 GAGCGATGGCAGGACAGG 60.203 66.667 1.50 0.00 43.41 4.00
6706 9191 2.114411 GGGGCCGTGTCTTTTCCA 59.886 61.111 0.00 0.00 0.00 3.53
6718 9203 9.744468 GCCGTGTCTTTTCCATTTTATTATTAT 57.256 29.630 0.00 0.00 0.00 1.28
6750 9235 4.345854 ACTCCCTCCGATCCATATTACTC 58.654 47.826 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 0.802494 CTTCATGGTTTTCGGTCCGG 59.198 55.000 12.29 0.00 0.00 5.14
81 82 1.068541 GTGCTTCATGGTTTTCGGTCC 60.069 52.381 0.00 0.00 0.00 4.46
94 95 0.819259 GTGAGGCCTTGTGTGCTTCA 60.819 55.000 6.77 0.00 41.78 3.02
261 263 2.203070 CCGACCTGCCATACCAGC 60.203 66.667 0.00 0.00 0.00 4.85
421 423 2.261671 GCGGTCATGTGGTCGACT 59.738 61.111 16.46 0.00 32.57 4.18
453 455 1.022735 GATCCGGTGCTTCTCGTAGA 58.977 55.000 0.00 0.00 0.00 2.59
525 527 4.424711 GGGACCCGCATTCTGGCA 62.425 66.667 0.00 0.00 0.00 4.92
627 629 5.204409 TCAGGAAGTTAACGCTGTTTCTA 57.796 39.130 0.00 0.00 0.00 2.10
690 692 3.547868 CCTTCATGATGTACTTCGTGACG 59.452 47.826 25.40 23.23 40.45 4.35
1158 1160 4.717313 GGCTTGTGGTCGGGGTCC 62.717 72.222 0.00 0.00 0.00 4.46
1258 1265 5.595885 CCAATTGTACCACATGAACAAACA 58.404 37.500 0.00 0.00 36.75 2.83
1357 1376 4.985413 CAACATTCGCATACTGTTGGATT 58.015 39.130 9.96 0.00 43.71 3.01
1363 1382 3.436704 CAGAACCAACATTCGCATACTGT 59.563 43.478 0.00 0.00 33.57 3.55
1412 1431 3.701532 TCAAACGACAATTGACCAACC 57.298 42.857 13.59 0.00 32.10 3.77
1486 1505 1.478654 CGGCCAGCCCATAATAAACCT 60.479 52.381 2.24 0.00 0.00 3.50
1540 1559 5.979288 AACTCGTTCAGTCTGTTACCTAT 57.021 39.130 0.00 0.00 32.30 2.57
1612 1631 2.726822 GAACAAGGGCCCTCGACGTT 62.727 60.000 28.84 24.63 0.00 3.99
2204 2235 0.970937 CAGTTCTACTCGCCCCCTGA 60.971 60.000 0.00 0.00 0.00 3.86
2414 4387 4.279420 CCCTTCCCTCTCAAAGAAAAACAG 59.721 45.833 0.00 0.00 0.00 3.16
2730 4723 2.912771 TGAAAACTGTGTGGATGTCGT 58.087 42.857 0.00 0.00 0.00 4.34
2741 4734 9.814899 TGTTATTTCATTTGACATGAAAACTGT 57.185 25.926 10.39 0.00 46.84 3.55
2833 4826 4.343231 AGCATTTGGATTCACATGTACCA 58.657 39.130 0.00 3.60 34.49 3.25
2839 4832 7.771183 ACGTTAAATAGCATTTGGATTCACAT 58.229 30.769 4.89 0.00 0.00 3.21
2967 4960 6.012658 TGCCAGTCAGATAAACAAATTGAC 57.987 37.500 0.00 0.00 38.68 3.18
3110 5103 8.788813 GCACACTGAATGAAGAAAAATAATACG 58.211 33.333 0.00 0.00 0.00 3.06
3217 5211 0.108804 TTCCATCTCCTCGTGTTCGC 60.109 55.000 0.00 0.00 36.96 4.70
3357 5351 3.953612 CCTCAGCTCTATCTTGTGTCTCT 59.046 47.826 0.00 0.00 0.00 3.10
3416 5410 4.346709 TGTATCCAAGACCTGAAAGTGTCA 59.653 41.667 0.00 0.00 36.84 3.58
3522 5516 4.572985 TGAAGTGGAGCAAAAAGTGATG 57.427 40.909 0.00 0.00 0.00 3.07
3541 5535 4.464244 AGAACAGTTCGGAAGATCAGATGA 59.536 41.667 7.68 0.00 41.60 2.92
3555 5549 3.680458 GGACCGAAGATGAAGAACAGTTC 59.320 47.826 5.00 5.00 0.00 3.01
3556 5550 3.325135 AGGACCGAAGATGAAGAACAGTT 59.675 43.478 0.00 0.00 0.00 3.16
3560 5554 2.531206 CGAGGACCGAAGATGAAGAAC 58.469 52.381 0.00 0.00 41.76 3.01
3561 5555 1.476891 CCGAGGACCGAAGATGAAGAA 59.523 52.381 0.00 0.00 41.76 2.52
3562 5556 1.103803 CCGAGGACCGAAGATGAAGA 58.896 55.000 0.00 0.00 41.76 2.87
3563 5557 0.818296 ACCGAGGACCGAAGATGAAG 59.182 55.000 0.00 0.00 41.76 3.02
3565 5559 0.034380 AGACCGAGGACCGAAGATGA 60.034 55.000 0.00 0.00 41.76 2.92
3566 5560 0.818296 AAGACCGAGGACCGAAGATG 59.182 55.000 0.00 0.00 41.76 2.90
3567 5561 0.818296 CAAGACCGAGGACCGAAGAT 59.182 55.000 0.00 0.00 41.76 2.40
3569 5563 0.601558 TTCAAGACCGAGGACCGAAG 59.398 55.000 0.00 0.00 41.76 3.79
3570 5564 1.042229 TTTCAAGACCGAGGACCGAA 58.958 50.000 0.00 0.00 41.76 4.30
3571 5565 1.263356 ATTTCAAGACCGAGGACCGA 58.737 50.000 0.00 0.00 41.76 4.69
3572 5566 2.810650 CTATTTCAAGACCGAGGACCG 58.189 52.381 0.00 0.00 38.18 4.79
3573 5567 2.168728 AGCTATTTCAAGACCGAGGACC 59.831 50.000 0.00 0.00 0.00 4.46
3574 5568 3.528597 AGCTATTTCAAGACCGAGGAC 57.471 47.619 0.00 0.00 0.00 3.85
3575 5569 4.553330 AAAGCTATTTCAAGACCGAGGA 57.447 40.909 0.00 0.00 0.00 3.71
3576 5570 5.661458 TCTAAAGCTATTTCAAGACCGAGG 58.339 41.667 0.00 0.00 0.00 4.63
3577 5571 6.758886 ACATCTAAAGCTATTTCAAGACCGAG 59.241 38.462 0.00 0.00 0.00 4.63
3578 5572 6.535150 CACATCTAAAGCTATTTCAAGACCGA 59.465 38.462 0.00 0.00 0.00 4.69
3579 5573 6.709643 CACATCTAAAGCTATTTCAAGACCG 58.290 40.000 0.00 0.00 0.00 4.79
3580 5574 6.317391 AGCACATCTAAAGCTATTTCAAGACC 59.683 38.462 0.00 0.00 36.73 3.85
3581 5575 7.313951 AGCACATCTAAAGCTATTTCAAGAC 57.686 36.000 0.00 0.00 36.73 3.01
3582 5576 6.540189 GGAGCACATCTAAAGCTATTTCAAGA 59.460 38.462 0.00 0.00 39.02 3.02
3583 5577 6.541641 AGGAGCACATCTAAAGCTATTTCAAG 59.458 38.462 0.00 0.00 39.02 3.02
3584 5578 6.418101 AGGAGCACATCTAAAGCTATTTCAA 58.582 36.000 0.00 0.00 39.02 2.69
3585 5579 5.994250 AGGAGCACATCTAAAGCTATTTCA 58.006 37.500 0.00 0.00 39.02 2.69
3586 5580 6.765512 AGAAGGAGCACATCTAAAGCTATTTC 59.234 38.462 0.00 0.00 39.02 2.17
3587 5581 6.541641 CAGAAGGAGCACATCTAAAGCTATTT 59.458 38.462 0.00 0.00 39.02 1.40
3588 5582 6.054295 CAGAAGGAGCACATCTAAAGCTATT 58.946 40.000 0.00 0.00 39.02 1.73
3589 5583 5.130145 ACAGAAGGAGCACATCTAAAGCTAT 59.870 40.000 0.00 0.00 39.02 2.97
3590 5584 4.467795 ACAGAAGGAGCACATCTAAAGCTA 59.532 41.667 0.00 0.00 39.02 3.32
3591 5585 3.262915 ACAGAAGGAGCACATCTAAAGCT 59.737 43.478 0.00 0.00 42.17 3.74
3592 5586 3.604582 ACAGAAGGAGCACATCTAAAGC 58.395 45.455 0.00 0.00 0.00 3.51
3593 5587 5.083533 AGACAGAAGGAGCACATCTAAAG 57.916 43.478 0.00 0.00 0.00 1.85
3605 5599 1.186200 AGCGCACATAGACAGAAGGA 58.814 50.000 11.47 0.00 0.00 3.36
3622 5616 3.914364 CGTAGAAGGAATTGCAAACAAGC 59.086 43.478 1.71 0.00 39.69 4.01
3650 5644 3.879892 GAGTCATCTAGCAAATTCCCCAC 59.120 47.826 0.00 0.00 0.00 4.61
3739 5734 1.873591 GACAGTTAACAGTGCACAGGG 59.126 52.381 21.04 10.59 0.00 4.45
3787 5782 1.886542 GGGATTGAAGAAAAGGCGTGT 59.113 47.619 0.00 0.00 0.00 4.49
3791 5786 4.463891 TCATCAAGGGATTGAAGAAAAGGC 59.536 41.667 0.00 0.00 34.24 4.35
3846 5841 5.817784 ACTACTGTATATACCTCAGCGGAT 58.182 41.667 10.38 0.00 36.31 4.18
3931 5929 9.683069 CCATAAAACATAATAAAGACCATCTGC 57.317 33.333 0.00 0.00 0.00 4.26
3959 5957 1.972872 ACAACAGAGCTCCCAACAAG 58.027 50.000 10.93 0.00 0.00 3.16
3975 5973 8.358895 CAACCAATGCATATCATATACCAACAA 58.641 33.333 0.00 0.00 34.33 2.83
3976 5974 7.723172 TCAACCAATGCATATCATATACCAACA 59.277 33.333 0.00 0.00 34.33 3.33
3977 5975 8.109705 TCAACCAATGCATATCATATACCAAC 57.890 34.615 0.00 0.00 34.33 3.77
4032 6030 3.884895 TCAGCAAGGTTCAAGTTCTTCA 58.115 40.909 0.00 0.00 0.00 3.02
4125 6139 4.407296 ACATCTGAGGATAACAAGGGAGAC 59.593 45.833 0.00 0.00 0.00 3.36
4131 6145 7.854557 TCAATGAACATCTGAGGATAACAAG 57.145 36.000 0.00 0.00 0.00 3.16
4255 6269 5.362430 TGCCTCTTCCAACAACACTTATTTT 59.638 36.000 0.00 0.00 0.00 1.82
4283 6297 3.730662 GCCATACAATGTGCACGGTTAAG 60.731 47.826 13.13 1.26 0.00 1.85
4289 6303 1.132834 ACATGCCATACAATGTGCACG 59.867 47.619 13.13 0.00 38.58 5.34
4292 6306 1.750206 TGGACATGCCATACAATGTGC 59.250 47.619 0.00 0.94 43.33 4.57
4309 6323 7.153985 CCAAAAAGCAAAACTCTGATAATGGA 58.846 34.615 0.00 0.00 0.00 3.41
4346 6361 5.584649 TCAGGCCTAAAGATACATGAAAACG 59.415 40.000 3.98 0.00 0.00 3.60
4353 6368 6.567602 AGTTCTTCAGGCCTAAAGATACAT 57.432 37.500 19.49 3.14 31.89 2.29
4360 6375 6.681729 TTCTAGAAGTTCTTCAGGCCTAAA 57.318 37.500 11.40 0.00 0.00 1.85
4398 6413 6.588756 TGTACAAACCATAATCAGAAGTCGTC 59.411 38.462 0.00 0.00 0.00 4.20
4425 6440 8.331022 CAAGAAAGACACGTCATAAATATCTGG 58.669 37.037 0.00 0.00 0.00 3.86
4439 6454 8.239681 TGTTATCATAAGTCAAGAAAGACACG 57.760 34.615 0.00 0.00 40.98 4.49
4586 6605 6.592870 ACAAAACTAAGAAGCTAACCTGAGT 58.407 36.000 0.00 0.00 0.00 3.41
4603 6622 7.370383 CCAGTGTTGCATATAAGAACAAAACT 58.630 34.615 0.00 0.00 40.40 2.66
4615 6634 1.616725 CCACCACCCAGTGTTGCATAT 60.617 52.381 0.00 0.00 35.93 1.78
4631 6650 4.196971 GGTACAATGTCTATGTTCCCACC 58.803 47.826 0.00 0.00 33.52 4.61
4667 6686 6.320164 GTGCATTACATATTGACAAGGGGTAA 59.680 38.462 0.00 9.42 0.00 2.85
4681 6700 5.804639 ACAAACAGGAGAGTGCATTACATA 58.195 37.500 0.00 0.00 0.00 2.29
4694 6713 8.926710 CAAATAGACTTACACTACAAACAGGAG 58.073 37.037 0.00 0.00 0.00 3.69
4705 6724 6.779860 ACACCCAATCAAATAGACTTACACT 58.220 36.000 0.00 0.00 0.00 3.55
4727 6746 2.284263 TGCAATGCAAAACGACAACA 57.716 40.000 5.01 0.00 34.76 3.33
4802 6821 6.040391 AGTCAACCTGTTTAGCAGCAATTAAA 59.960 34.615 0.00 0.00 43.71 1.52
4807 6826 2.930950 AGTCAACCTGTTTAGCAGCAA 58.069 42.857 0.00 0.00 43.71 3.91
4828 6847 7.796054 ACTAAATGGCATACTACAATCTCACT 58.204 34.615 0.00 0.00 0.00 3.41
4837 6856 8.459911 AAAACCCATACTAAATGGCATACTAC 57.540 34.615 0.00 0.00 37.85 2.73
4872 6891 4.018415 ACAAACAGAGGCACCATACCTAAT 60.018 41.667 0.00 0.00 37.77 1.73
4883 6902 0.753867 TACGGACACAAACAGAGGCA 59.246 50.000 0.00 0.00 0.00 4.75
4884 6903 1.429463 CTACGGACACAAACAGAGGC 58.571 55.000 0.00 0.00 0.00 4.70
4885 6904 1.939838 GCCTACGGACACAAACAGAGG 60.940 57.143 0.00 0.00 0.00 3.69
4886 6905 1.270094 TGCCTACGGACACAAACAGAG 60.270 52.381 0.00 0.00 0.00 3.35
4887 6906 0.753867 TGCCTACGGACACAAACAGA 59.246 50.000 0.00 0.00 0.00 3.41
4888 6907 1.148310 CTGCCTACGGACACAAACAG 58.852 55.000 0.00 0.00 0.00 3.16
5021 7046 0.042581 TCACAGAGGCCTATCCCACA 59.957 55.000 4.42 0.00 34.51 4.17
5023 7048 2.050144 GAATCACAGAGGCCTATCCCA 58.950 52.381 4.42 0.00 34.51 4.37
5042 7067 4.844349 AAATCCTCCGAAATTCCTCTGA 57.156 40.909 0.00 0.00 0.00 3.27
5043 7068 7.255277 GGAATAAAATCCTCCGAAATTCCTCTG 60.255 40.741 0.00 0.00 38.44 3.35
5044 7069 6.773200 GGAATAAAATCCTCCGAAATTCCTCT 59.227 38.462 0.00 0.00 38.44 3.69
5085 7110 2.232208 CCTCCAAATCAAAAGGCTCCAC 59.768 50.000 0.00 0.00 0.00 4.02
5255 7280 4.347583 AGGAATTCAAATGAGGGCACAAAA 59.652 37.500 7.93 0.00 0.00 2.44
5342 7367 7.440556 CAGGTGAATACATTATCTCTTGTCCTG 59.559 40.741 0.00 0.00 30.97 3.86
5463 7488 2.475864 TGCAAAACTGCAATGCGATTTC 59.524 40.909 0.00 0.00 42.40 2.17
5567 7592 2.426024 GCTTCGGTCTAGGTACATCACA 59.574 50.000 0.00 0.00 0.00 3.58
5752 7777 2.655090 TGGTGTTTCATCAGCCAGAA 57.345 45.000 0.00 0.00 35.31 3.02
5856 7881 1.630878 CCAGTTCCCTCTTGTAAGGCT 59.369 52.381 0.00 0.00 34.88 4.58
5875 7900 0.535553 TTACGCCCCAAGAACACACC 60.536 55.000 0.00 0.00 0.00 4.16
6031 8056 9.639601 GGAGTAAATAATTCAGGGAAAAACAAG 57.360 33.333 0.00 0.00 0.00 3.16
6032 8057 9.374711 AGGAGTAAATAATTCAGGGAAAAACAA 57.625 29.630 0.00 0.00 0.00 2.83
6033 8058 8.950007 AGGAGTAAATAATTCAGGGAAAAACA 57.050 30.769 0.00 0.00 0.00 2.83
6034 8059 9.244292 AGAGGAGTAAATAATTCAGGGAAAAAC 57.756 33.333 0.00 0.00 0.00 2.43
6186 8211 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
6187 8212 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
6188 8213 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
6189 8214 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
6190 8215 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
6191 8216 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
6192 8217 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
6194 8219 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
6195 8220 9.031537 TGTATCTAGACAAATCCAAGACAAGTA 57.968 33.333 0.00 0.00 0.00 2.24
6196 8221 7.907389 TGTATCTAGACAAATCCAAGACAAGT 58.093 34.615 0.00 0.00 0.00 3.16
6197 8222 8.253810 TCTGTATCTAGACAAATCCAAGACAAG 58.746 37.037 0.00 0.00 0.00 3.16
6198 8223 8.134202 TCTGTATCTAGACAAATCCAAGACAA 57.866 34.615 0.00 0.00 0.00 3.18
6199 8224 7.718334 TCTGTATCTAGACAAATCCAAGACA 57.282 36.000 0.00 0.00 0.00 3.41
6200 8225 8.200792 ACATCTGTATCTAGACAAATCCAAGAC 58.799 37.037 0.00 0.00 0.00 3.01
6201 8226 8.311395 ACATCTGTATCTAGACAAATCCAAGA 57.689 34.615 0.00 0.00 0.00 3.02
6231 8256 8.364142 GGATGTATCTAGCACTAAAATGAGTCT 58.636 37.037 0.00 0.00 0.00 3.24
6232 8257 7.327275 CGGATGTATCTAGCACTAAAATGAGTC 59.673 40.741 0.00 0.00 0.00 3.36
6233 8258 7.148641 CGGATGTATCTAGCACTAAAATGAGT 58.851 38.462 0.00 0.00 0.00 3.41
6234 8259 7.148641 ACGGATGTATCTAGCACTAAAATGAG 58.851 38.462 0.00 0.00 0.00 2.90
6235 8260 7.050970 ACGGATGTATCTAGCACTAAAATGA 57.949 36.000 0.00 0.00 0.00 2.57
6236 8261 8.988064 ATACGGATGTATCTAGCACTAAAATG 57.012 34.615 0.00 0.00 36.56 2.32
6251 8276 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
6252 8277 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
6253 8278 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
6254 8279 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
6255 8280 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
6256 8281 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
6263 8288 9.582431 CCGAATTACTTGTCTTAGATTTGTCTA 57.418 33.333 0.00 0.00 0.00 2.59
6264 8289 8.311836 TCCGAATTACTTGTCTTAGATTTGTCT 58.688 33.333 0.00 0.00 0.00 3.41
6265 8290 8.475331 TCCGAATTACTTGTCTTAGATTTGTC 57.525 34.615 0.00 0.00 0.00 3.18
6266 8291 8.718734 GTTCCGAATTACTTGTCTTAGATTTGT 58.281 33.333 0.00 0.00 0.00 2.83
6267 8292 7.898309 CGTTCCGAATTACTTGTCTTAGATTTG 59.102 37.037 0.00 0.00 0.00 2.32
6268 8293 7.064253 CCGTTCCGAATTACTTGTCTTAGATTT 59.936 37.037 0.00 0.00 0.00 2.17
6269 8294 6.534079 CCGTTCCGAATTACTTGTCTTAGATT 59.466 38.462 0.00 0.00 0.00 2.40
6270 8295 6.040878 CCGTTCCGAATTACTTGTCTTAGAT 58.959 40.000 0.00 0.00 0.00 1.98
6271 8296 5.183713 TCCGTTCCGAATTACTTGTCTTAGA 59.816 40.000 0.00 0.00 0.00 2.10
6272 8297 5.404946 TCCGTTCCGAATTACTTGTCTTAG 58.595 41.667 0.00 0.00 0.00 2.18
6273 8298 5.389859 TCCGTTCCGAATTACTTGTCTTA 57.610 39.130 0.00 0.00 0.00 2.10
6274 8299 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
6275 8300 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
6276 8301 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
6277 8302 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
6278 8303 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
6279 8304 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
6280 8305 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
6281 8306 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
6282 8307 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
6283 8308 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
6284 8309 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
6285 8310 0.967380 GGTACTCCCTCCGTTCCGAA 60.967 60.000 0.00 0.00 0.00 4.30
6286 8311 1.379044 GGTACTCCCTCCGTTCCGA 60.379 63.158 0.00 0.00 0.00 4.55
6287 8312 1.379576 AGGTACTCCCTCCGTTCCG 60.380 63.158 0.00 0.00 40.71 4.30
6288 8313 4.781264 AGGTACTCCCTCCGTTCC 57.219 61.111 0.00 0.00 40.71 3.62
6369 8394 7.162761 TCTGTTCCAAAATATAAGACGTTCCA 58.837 34.615 0.00 0.00 0.00 3.53
6370 8395 7.201617 CCTCTGTTCCAAAATATAAGACGTTCC 60.202 40.741 0.00 0.00 0.00 3.62
6371 8396 7.201617 CCCTCTGTTCCAAAATATAAGACGTTC 60.202 40.741 0.00 0.00 0.00 3.95
6372 8397 6.598064 CCCTCTGTTCCAAAATATAAGACGTT 59.402 38.462 0.00 0.00 0.00 3.99
6373 8398 6.113411 CCCTCTGTTCCAAAATATAAGACGT 58.887 40.000 0.00 0.00 0.00 4.34
6374 8399 6.037172 CACCCTCTGTTCCAAAATATAAGACG 59.963 42.308 0.00 0.00 0.00 4.18
6375 8400 6.884836 ACACCCTCTGTTCCAAAATATAAGAC 59.115 38.462 0.00 0.00 0.00 3.01
6376 8401 7.027874 ACACCCTCTGTTCCAAAATATAAGA 57.972 36.000 0.00 0.00 0.00 2.10
6377 8402 8.980481 ATACACCCTCTGTTCCAAAATATAAG 57.020 34.615 0.00 0.00 33.91 1.73
6381 8406 8.656806 CCTATATACACCCTCTGTTCCAAAATA 58.343 37.037 0.00 0.00 33.91 1.40
6382 8407 7.349859 TCCTATATACACCCTCTGTTCCAAAAT 59.650 37.037 0.00 0.00 33.91 1.82
6383 8408 6.674861 TCCTATATACACCCTCTGTTCCAAAA 59.325 38.462 0.00 0.00 33.91 2.44
6384 8409 6.206787 TCCTATATACACCCTCTGTTCCAAA 58.793 40.000 0.00 0.00 33.91 3.28
6385 8410 5.784023 TCCTATATACACCCTCTGTTCCAA 58.216 41.667 0.00 0.00 33.91 3.53
6386 8411 5.412617 TCCTATATACACCCTCTGTTCCA 57.587 43.478 0.00 0.00 33.91 3.53
6458 8483 4.576053 CCAATTCTAGAAATGTCCATCGCA 59.424 41.667 17.29 0.00 0.00 5.10
6459 8484 4.576463 ACCAATTCTAGAAATGTCCATCGC 59.424 41.667 17.29 0.00 0.00 4.58
6492 8974 6.106673 TGAAAGCTAATTCTGTAGTACTGGC 58.893 40.000 5.39 0.00 0.00 4.85
6629 9114 2.103373 TCGCTCATTTGAGTCTAGGCT 58.897 47.619 0.00 0.00 43.85 4.58
6648 9133 1.065199 TCATTCACCTGTCCTGCCATC 60.065 52.381 0.00 0.00 0.00 3.51
6650 9135 0.994247 ATCATTCACCTGTCCTGCCA 59.006 50.000 0.00 0.00 0.00 4.92
6652 9137 1.065199 TCCATCATTCACCTGTCCTGC 60.065 52.381 0.00 0.00 0.00 4.85
6661 9146 4.019174 ACCATTCCAGTTCCATCATTCAC 58.981 43.478 0.00 0.00 0.00 3.18
6718 9203 3.595190 TCGGAGGGAGTATGAGATTCA 57.405 47.619 0.00 0.00 0.00 2.57
6719 9204 3.445805 GGATCGGAGGGAGTATGAGATTC 59.554 52.174 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.