Multiple sequence alignment - TraesCS3A01G477600

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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 TraesCS3A01G477600 chr3A 100.000 3303 0 0 1 3303 709194717 709191415 0.000000e+00 6100
1 TraesCS3A01G477600 chr3A 79.974 769 123 20 1445 2201 710771410 710772159 3.750000e-149 538
2 TraesCS3A01G477600 chr3A 82.266 406 56 12 927 1323 710782449 710782847 1.470000e-88 337
3 TraesCS3A01G477600 chr3A 89.474 152 14 2 2320 2470 709220378 709220228 1.210000e-44 191
4 TraesCS3A01G477600 chr3D 90.347 1699 109 20 708 2377 574242464 574240792 0.000000e+00 2178
5 TraesCS3A01G477600 chr3D 93.475 613 29 6 102 708 574243190 574242583 0.000000e+00 900
6 TraesCS3A01G477600 chr3D 91.874 603 34 9 2708 3303 574240525 574239931 0.000000e+00 828
7 TraesCS3A01G477600 chr3D 88.217 314 24 7 161 469 574292834 574292529 2.420000e-96 363
8 TraesCS3A01G477600 chrUn 90.115 1568 106 19 708 2252 41224648 41226189 0.000000e+00 1991
9 TraesCS3A01G477600 chrUn 90.411 584 45 8 2729 3303 41226513 41227094 0.000000e+00 758
10 TraesCS3A01G477600 chrUn 88.590 631 49 9 87 705 41223907 41224526 0.000000e+00 745
11 TraesCS3A01G477600 chrUn 89.303 402 32 4 87 477 380168715 380169116 8.230000e-136 494
12 TraesCS3A01G477600 chrUn 89.303 402 32 4 87 477 442634265 442634666 8.230000e-136 494
13 TraesCS3A01G477600 chrUn 87.912 91 7 3 2 88 41223748 41223838 1.620000e-18 104
14 TraesCS3A01G477600 chrUn 87.912 91 7 3 2 88 380168556 380168646 1.620000e-18 104
15 TraesCS3A01G477600 chrUn 87.912 91 7 3 2 88 442634106 442634196 1.620000e-18 104
16 TraesCS3A01G477600 chr3B 91.721 459 32 3 1 455 764456569 764457025 1.670000e-177 632
17 TraesCS3A01G477600 chr3B 80.078 773 124 20 1443 2205 765059962 765060714 6.230000e-152 547
18 TraesCS3A01G477600 chr3B 87.805 410 35 9 91 491 764501271 764501674 1.790000e-127 466
19 TraesCS3A01G477600 chr3B 85.909 440 29 13 2 428 764523801 764524220 3.910000e-119 438
20 TraesCS3A01G477600 chr3B 77.872 470 64 17 1954 2395 764458865 764459322 4.230000e-64 255
21 TraesCS3A01G477600 chr3B 87.912 91 7 3 2 88 764501108 764501198 1.620000e-18 104


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 TraesCS3A01G477600 chr3A 709191415 709194717 3302 True 6100.0 6100 100.000000 1 3303 1 chr3A.!!$R1 3302
1 TraesCS3A01G477600 chr3A 710771410 710772159 749 False 538.0 538 79.974000 1445 2201 1 chr3A.!!$F1 756
2 TraesCS3A01G477600 chr3D 574239931 574243190 3259 True 1302.0 2178 91.898667 102 3303 3 chr3D.!!$R2 3201
3 TraesCS3A01G477600 chrUn 41223748 41227094 3346 False 899.5 1991 89.257000 2 3303 4 chrUn.!!$F1 3301
4 TraesCS3A01G477600 chrUn 380168556 380169116 560 False 299.0 494 88.607500 2 477 2 chrUn.!!$F2 475
5 TraesCS3A01G477600 chrUn 442634106 442634666 560 False 299.0 494 88.607500 2 477 2 chrUn.!!$F3 475
6 TraesCS3A01G477600 chr3B 765059962 765060714 752 False 547.0 547 80.078000 1443 2205 1 chr3B.!!$F2 762
7 TraesCS3A01G477600 chr3B 764456569 764459322 2753 False 443.5 632 84.796500 1 2395 2 chr3B.!!$F3 2394
8 TraesCS3A01G477600 chr3B 764501108 764501674 566 False 285.0 466 87.858500 2 491 2 chr3B.!!$F4 489

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
71 75 0.185175 TATAGGCTGGCGTCTCTCCA 59.815 55.0 0.0 0.0 0.00 3.86 F
951 1180 0.410270 AAAGGACCCGTCTCTCCTCT 59.590 55.0 0.0 0.0 35.72 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1108 1579 0.670854 GGAAGTCACTTGGGAGACGC 60.671 60.0 0.00 0.0 37.94 5.19 R
2572 3664 0.032813 TCCCTCCGTCCGGAATTAGT 60.033 55.0 5.23 0.0 44.66 2.24 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
37 38 5.247110 TCTCTTTTCTCATGCTACAAGGAGT 59.753 40.000 0.00 0.00 0.00 3.85
38 39 5.240891 TCTTTTCTCATGCTACAAGGAGTG 58.759 41.667 0.00 0.00 0.00 3.51
40 41 2.820178 TCTCATGCTACAAGGAGTGGA 58.180 47.619 0.00 0.00 0.00 4.02
61 65 4.455877 GGACGAATCCATTTTATAGGCTGG 59.544 45.833 0.00 0.00 45.47 4.85
62 66 3.821033 ACGAATCCATTTTATAGGCTGGC 59.179 43.478 0.00 0.00 0.00 4.85
71 75 0.185175 TATAGGCTGGCGTCTCTCCA 59.815 55.000 0.00 0.00 0.00 3.86
97 172 8.965819 ACCATCACTAATAGCTATATGAGAGTG 58.034 37.037 6.68 14.27 33.14 3.51
118 193 7.831193 AGAGTGAACTATATGCACCAGAATTTT 59.169 33.333 0.00 0.00 33.14 1.82
172 247 9.479549 AAATCCAACACATAATACCAAGAATCT 57.520 29.630 0.00 0.00 0.00 2.40
211 287 6.371548 GCCACATATGTTCTGAGTTTCTACAA 59.628 38.462 5.37 0.00 0.00 2.41
221 297 6.640518 TCTGAGTTTCTACAACAAGAACTGT 58.359 36.000 0.00 0.00 41.27 3.55
244 320 1.647346 CATGCATGCACCATTGGAAC 58.353 50.000 25.37 1.06 0.00 3.62
270 346 6.793492 ACTACAGAAATCTTTCAGTTGCTC 57.207 37.500 6.11 0.00 37.88 4.26
416 507 1.062488 ACCAAGACAGACCAAGGGCT 61.062 55.000 0.00 0.00 0.00 5.19
428 519 2.041620 ACCAAGGGCTCTCATTTTGCTA 59.958 45.455 0.00 0.00 0.00 3.49
537 629 0.678048 AAGATTGCTTCGGGGCTCAC 60.678 55.000 0.00 0.00 0.00 3.51
598 690 1.370587 GACTCGCGAGCACCTCTACT 61.371 60.000 34.83 13.06 0.00 2.57
621 713 2.014857 CCATCAGGACAATGACTGCAG 58.985 52.381 13.48 13.48 36.89 4.41
662 754 6.787170 TGAGTAGTCCCTACTTCAAGAGTTA 58.213 40.000 5.46 0.00 45.90 2.24
663 755 6.658391 TGAGTAGTCCCTACTTCAAGAGTTAC 59.342 42.308 5.46 0.00 45.90 2.50
665 757 7.926705 AGTAGTCCCTACTTCAAGAGTTACTA 58.073 38.462 0.00 0.00 43.82 1.82
705 797 4.236147 GGTTTGAGAGTAACTTCTCGTCC 58.764 47.826 0.00 0.00 45.26 4.79
735 947 6.311935 GCCACGTGTCACTTCAACTATAATAA 59.688 38.462 15.65 0.00 0.00 1.40
736 948 7.148540 GCCACGTGTCACTTCAACTATAATAAA 60.149 37.037 15.65 0.00 0.00 1.40
792 1013 7.973944 AGTTGAAGTACCAAGATTTTGTGTTTC 59.026 33.333 0.00 0.00 32.21 2.78
845 1066 7.515998 CGTTTGCAACAAAATTCTTCCGTTAAT 60.516 33.333 0.00 0.00 0.00 1.40
907 1128 2.555757 CCCAGAAAGTGAAAGCTTCTGG 59.444 50.000 17.86 17.86 40.01 3.86
951 1180 0.410270 AAAGGACCCGTCTCTCCTCT 59.590 55.000 0.00 0.00 35.72 3.69
954 1183 1.639628 AGGACCCGTCTCTCCTCTTAA 59.360 52.381 0.00 0.00 30.37 1.85
983 1212 2.828549 GCCCGCCCAATACACCTG 60.829 66.667 0.00 0.00 0.00 4.00
1024 1253 4.915298 CTCAGACTGGAGCAGCAG 57.085 61.111 1.81 0.00 34.37 4.24
1167 1931 3.569277 TGTGCTGCTGATTTACACACAAT 59.431 39.130 0.00 0.00 36.39 2.71
1168 1932 4.037803 TGTGCTGCTGATTTACACACAATT 59.962 37.500 0.00 0.00 36.39 2.32
1301 2299 0.870393 ATGTCAGCTGCAACAACGAG 59.130 50.000 9.47 0.00 0.00 4.18
1312 2310 0.938168 AACAACGAGAACTCCGTCGC 60.938 55.000 0.00 0.00 39.57 5.19
1381 2379 2.218603 GAACTGAAGGCCGAAACTGAA 58.781 47.619 0.00 0.00 0.00 3.02
1390 2388 3.379372 AGGCCGAAACTGAATTGATCATG 59.621 43.478 0.00 0.00 37.44 3.07
1397 2395 7.148255 CCGAAACTGAATTGATCATGGTTCTTA 60.148 37.037 0.00 0.00 37.44 2.10
1453 2451 4.669866 TCCACTACCTGAGTTCTTCCTA 57.330 45.455 0.00 0.00 35.64 2.94
1461 2459 2.989840 CTGAGTTCTTCCTAACTGTGCG 59.010 50.000 0.00 0.00 39.78 5.34
1503 2501 0.400525 CTCAGGCCCCCTCATTCCTA 60.401 60.000 0.00 0.00 0.00 2.94
1533 2531 3.368427 CCAACTGAAGAGCCTTCGATACA 60.368 47.826 9.47 0.00 0.00 2.29
1559 2557 0.867746 TTCTACTGCAACTTGCTGCG 59.132 50.000 17.85 10.91 44.72 5.18
1664 2666 3.756434 ACAAAATGAGTGGACCAATACCG 59.244 43.478 0.00 0.00 0.00 4.02
1725 2727 4.713553 TCTTTACAGCAACCATCTCACAA 58.286 39.130 0.00 0.00 0.00 3.33
1728 2730 1.241165 CAGCAACCATCTCACAAGCA 58.759 50.000 0.00 0.00 0.00 3.91
1754 2756 2.792947 GGCCTCGCTCGGGAACATA 61.793 63.158 0.00 0.00 0.00 2.29
1803 2805 1.245732 CTGCAGCAAGCTCCTTTTCT 58.754 50.000 0.00 0.00 45.94 2.52
1807 2809 2.230750 GCAGCAAGCTCCTTTTCTGATT 59.769 45.455 0.00 0.00 41.15 2.57
1819 2821 6.273825 TCCTTTTCTGATTACGAGATGCTAC 58.726 40.000 0.00 0.00 0.00 3.58
1838 2840 2.476873 CGACACCTATCGTCTCCAAG 57.523 55.000 0.00 0.00 37.33 3.61
1921 2923 1.603236 TATACCGGCGTCGTTGGGTT 61.603 55.000 9.28 0.00 34.02 4.11
2013 3015 3.889538 TCTCTCTTGTTCTTGTCGGAGAA 59.110 43.478 0.00 0.00 39.69 2.87
2036 3038 5.899120 TTGACTAAGCTGTGAGTAGTAGG 57.101 43.478 0.00 0.00 0.00 3.18
2037 3039 5.175388 TGACTAAGCTGTGAGTAGTAGGA 57.825 43.478 0.00 0.00 0.00 2.94
2038 3040 5.186942 TGACTAAGCTGTGAGTAGTAGGAG 58.813 45.833 0.00 0.00 0.00 3.69
2039 3041 5.182169 ACTAAGCTGTGAGTAGTAGGAGT 57.818 43.478 0.00 0.00 0.00 3.85
2040 3042 6.070366 TGACTAAGCTGTGAGTAGTAGGAGTA 60.070 42.308 0.00 0.00 0.00 2.59
2050 3053 7.336176 TGTGAGTAGTAGGAGTACATACAGTTG 59.664 40.741 0.00 0.00 36.00 3.16
2181 3197 6.072508 GGCACTGTCAGATCATCTAAACAAAA 60.073 38.462 6.91 0.00 0.00 2.44
2186 3202 7.874940 TGTCAGATCATCTAAACAAAAAGGTG 58.125 34.615 0.00 0.00 0.00 4.00
2201 3218 7.500141 ACAAAAAGGTGGGATGCATATTATTC 58.500 34.615 0.00 0.00 0.00 1.75
2264 3306 4.100529 CACGAATTTCAGATTGGCATCAC 58.899 43.478 0.00 0.00 0.00 3.06
2294 3336 1.201647 CTACGGTCATCCAAGACACGT 59.798 52.381 12.55 12.55 43.06 4.49
2299 3341 2.223377 GGTCATCCAAGACACGTTCAAC 59.777 50.000 0.00 0.00 40.29 3.18
2309 3351 4.861210 AGACACGTTCAACTGAAGACTAG 58.139 43.478 0.00 0.00 34.27 2.57
2332 3375 0.109272 CTGAGCAGCATGGCAAACTG 60.109 55.000 13.97 13.97 35.86 3.16
2378 3424 2.543031 GGTTTTCCGTTCTGAAACTGCC 60.543 50.000 0.00 0.00 34.13 4.85
2380 3426 0.105224 TTCCGTTCTGAAACTGCCGA 59.895 50.000 0.00 0.00 32.95 5.54
2401 3467 0.679002 AGTAGTTGCATGCAGCCTGG 60.679 55.000 28.22 0.00 44.83 4.45
2430 3496 4.458295 TGTAGACCTCTGTTCCGTTAAGAG 59.542 45.833 0.00 0.00 37.73 2.85
2431 3497 3.498334 AGACCTCTGTTCCGTTAAGAGT 58.502 45.455 0.00 0.00 36.51 3.24
2434 3500 3.256136 ACCTCTGTTCCGTTAAGAGTCAG 59.744 47.826 0.00 0.00 36.51 3.51
2435 3501 3.367498 CCTCTGTTCCGTTAAGAGTCAGG 60.367 52.174 0.00 0.00 36.51 3.86
2436 3502 2.561419 TCTGTTCCGTTAAGAGTCAGGG 59.439 50.000 0.00 0.00 30.54 4.45
2437 3503 1.001633 TGTTCCGTTAAGAGTCAGGGC 59.998 52.381 0.00 0.00 0.00 5.19
2438 3504 1.275573 GTTCCGTTAAGAGTCAGGGCT 59.724 52.381 0.00 0.00 0.00 5.19
2439 3505 1.640917 TCCGTTAAGAGTCAGGGCTT 58.359 50.000 0.00 0.00 0.00 4.35
2441 3507 2.494870 TCCGTTAAGAGTCAGGGCTTAC 59.505 50.000 0.00 0.00 0.00 2.34
2442 3508 2.418334 CCGTTAAGAGTCAGGGCTTACC 60.418 54.545 0.00 0.00 40.67 2.85
2453 3519 2.700722 GGGCTTACCTCTCCTTCAAG 57.299 55.000 0.00 0.00 35.85 3.02
2454 3520 2.188817 GGGCTTACCTCTCCTTCAAGA 58.811 52.381 0.00 0.00 35.85 3.02
2455 3521 2.572104 GGGCTTACCTCTCCTTCAAGAA 59.428 50.000 0.00 0.00 35.85 2.52
2456 3522 3.009143 GGGCTTACCTCTCCTTCAAGAAA 59.991 47.826 0.00 0.00 35.85 2.52
2457 3523 4.004314 GGCTTACCTCTCCTTCAAGAAAC 58.996 47.826 0.00 0.00 0.00 2.78
2458 3524 4.505039 GGCTTACCTCTCCTTCAAGAAACA 60.505 45.833 0.00 0.00 0.00 2.83
2459 3525 5.063880 GCTTACCTCTCCTTCAAGAAACAA 58.936 41.667 0.00 0.00 0.00 2.83
2460 3526 5.707764 GCTTACCTCTCCTTCAAGAAACAAT 59.292 40.000 0.00 0.00 0.00 2.71
2461 3527 6.879458 GCTTACCTCTCCTTCAAGAAACAATA 59.121 38.462 0.00 0.00 0.00 1.90
2462 3528 7.065204 GCTTACCTCTCCTTCAAGAAACAATAG 59.935 40.741 0.00 0.00 0.00 1.73
2463 3529 6.688073 ACCTCTCCTTCAAGAAACAATAGA 57.312 37.500 0.00 0.00 0.00 1.98
2464 3530 7.079451 ACCTCTCCTTCAAGAAACAATAGAA 57.921 36.000 0.00 0.00 0.00 2.10
2465 3531 7.164803 ACCTCTCCTTCAAGAAACAATAGAAG 58.835 38.462 0.00 0.00 36.38 2.85
2466 3532 7.016661 ACCTCTCCTTCAAGAAACAATAGAAGA 59.983 37.037 0.00 0.00 38.30 2.87
2467 3533 7.880195 CCTCTCCTTCAAGAAACAATAGAAGAA 59.120 37.037 0.00 0.00 38.30 2.52
2468 3534 9.277783 CTCTCCTTCAAGAAACAATAGAAGAAA 57.722 33.333 0.00 0.00 38.30 2.52
2469 3535 9.799106 TCTCCTTCAAGAAACAATAGAAGAAAT 57.201 29.630 0.00 0.00 38.30 2.17
2487 3553 9.388506 AGAAGAAATACATAGTTGAGTCCATTG 57.611 33.333 0.00 0.00 0.00 2.82
2498 3564 5.882557 AGTTGAGTCCATTGTTATTAGCAGG 59.117 40.000 0.00 0.00 0.00 4.85
2501 3567 6.480763 TGAGTCCATTGTTATTAGCAGGAAA 58.519 36.000 0.00 0.00 0.00 3.13
2506 3572 8.250332 GTCCATTGTTATTAGCAGGAAATTCAA 58.750 33.333 0.00 0.00 0.00 2.69
2507 3573 8.811017 TCCATTGTTATTAGCAGGAAATTCAAA 58.189 29.630 0.00 0.00 0.00 2.69
2543 3635 7.016153 TCCTTGTGGTTTATCTTAGTCACAT 57.984 36.000 0.00 0.00 35.48 3.21
2544 3636 7.103641 TCCTTGTGGTTTATCTTAGTCACATC 58.896 38.462 0.00 0.00 35.48 3.06
2547 3639 6.957631 TGTGGTTTATCTTAGTCACATCCAT 58.042 36.000 0.00 0.00 31.33 3.41
2548 3640 8.084985 TGTGGTTTATCTTAGTCACATCCATA 57.915 34.615 0.00 0.00 31.33 2.74
2549 3641 7.985184 TGTGGTTTATCTTAGTCACATCCATAC 59.015 37.037 0.00 0.00 31.33 2.39
2550 3642 8.204836 GTGGTTTATCTTAGTCACATCCATACT 58.795 37.037 0.00 0.00 0.00 2.12
2551 3643 8.768397 TGGTTTATCTTAGTCACATCCATACTT 58.232 33.333 0.00 0.00 0.00 2.24
2552 3644 9.262358 GGTTTATCTTAGTCACATCCATACTTC 57.738 37.037 0.00 0.00 0.00 3.01
2556 3648 8.768501 ATCTTAGTCACATCCATACTTCTACA 57.231 34.615 0.00 0.00 0.00 2.74
2557 3649 8.768501 TCTTAGTCACATCCATACTTCTACAT 57.231 34.615 0.00 0.00 0.00 2.29
2558 3650 8.851145 TCTTAGTCACATCCATACTTCTACATC 58.149 37.037 0.00 0.00 0.00 3.06
2559 3651 6.412362 AGTCACATCCATACTTCTACATCC 57.588 41.667 0.00 0.00 0.00 3.51
2560 3652 5.010112 AGTCACATCCATACTTCTACATCCG 59.990 44.000 0.00 0.00 0.00 4.18
2561 3653 4.893524 TCACATCCATACTTCTACATCCGT 59.106 41.667 0.00 0.00 0.00 4.69
2562 3654 5.362717 TCACATCCATACTTCTACATCCGTT 59.637 40.000 0.00 0.00 0.00 4.44
2563 3655 6.049149 CACATCCATACTTCTACATCCGTTT 58.951 40.000 0.00 0.00 0.00 3.60
2564 3656 6.018751 CACATCCATACTTCTACATCCGTTTG 60.019 42.308 0.00 0.00 0.00 2.93
2565 3657 5.925506 TCCATACTTCTACATCCGTTTGA 57.074 39.130 0.00 0.00 0.00 2.69
2566 3658 5.902681 TCCATACTTCTACATCCGTTTGAG 58.097 41.667 0.00 0.00 0.00 3.02
2567 3659 4.508124 CCATACTTCTACATCCGTTTGAGC 59.492 45.833 0.00 0.00 0.00 4.26
2568 3660 2.607187 ACTTCTACATCCGTTTGAGCG 58.393 47.619 0.00 0.00 0.00 5.03
2575 3667 3.960237 CCGTTTGAGCGGCAACTA 58.040 55.556 1.45 0.00 45.47 2.24
2576 3668 2.240230 CCGTTTGAGCGGCAACTAA 58.760 52.632 1.45 0.00 45.47 2.24
2577 3669 0.802494 CCGTTTGAGCGGCAACTAAT 59.198 50.000 1.45 0.00 45.47 1.73
2578 3670 1.199097 CCGTTTGAGCGGCAACTAATT 59.801 47.619 1.45 0.00 45.47 1.40
2579 3671 2.505866 CGTTTGAGCGGCAACTAATTC 58.494 47.619 1.45 0.00 35.91 2.17
2580 3672 2.727916 CGTTTGAGCGGCAACTAATTCC 60.728 50.000 1.45 0.00 35.91 3.01
2581 3673 1.083489 TTGAGCGGCAACTAATTCCG 58.917 50.000 1.45 0.00 45.46 4.30
2582 3674 0.742990 TGAGCGGCAACTAATTCCGG 60.743 55.000 1.45 0.00 43.11 5.14
2583 3675 0.461339 GAGCGGCAACTAATTCCGGA 60.461 55.000 0.00 0.00 43.11 5.14
2584 3676 0.743345 AGCGGCAACTAATTCCGGAC 60.743 55.000 1.83 0.00 43.11 4.79
2585 3677 2.003672 CGGCAACTAATTCCGGACG 58.996 57.895 1.83 0.00 39.52 4.79
2586 3678 1.426041 CGGCAACTAATTCCGGACGG 61.426 60.000 1.83 3.96 39.52 4.79
2587 3679 0.108041 GGCAACTAATTCCGGACGGA 60.108 55.000 1.83 9.76 43.52 4.69
2588 3680 1.287425 GCAACTAATTCCGGACGGAG 58.713 55.000 13.64 3.57 46.06 4.63
2589 3681 1.935933 CAACTAATTCCGGACGGAGG 58.064 55.000 13.64 8.21 46.06 4.30
2590 3682 0.828677 AACTAATTCCGGACGGAGGG 59.171 55.000 13.64 7.89 46.06 4.30
2591 3683 0.032813 ACTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
2592 3684 0.674534 CTAATTCCGGACGGAGGGAG 59.325 60.000 13.64 8.24 46.06 4.30
2617 3709 3.087031 CACATGGTGCTTCAGGAATCTT 58.913 45.455 0.00 0.00 0.00 2.40
2621 3713 3.415212 TGGTGCTTCAGGAATCTTGAAG 58.585 45.455 25.00 25.00 41.23 3.02
2635 3736 1.666700 CTTGAAGCTCTGATGCTCAGC 59.333 52.381 7.94 0.00 43.95 4.26
2639 3740 1.740297 AGCTCTGATGCTCAGCAAAG 58.260 50.000 1.73 4.69 43.95 2.77
2645 3746 4.190001 TCTGATGCTCAGCAAAGATCTTC 58.810 43.478 1.73 0.00 43.95 2.87
2648 3749 3.413846 TGCTCAGCAAAGATCTTCAGT 57.586 42.857 8.78 0.00 34.76 3.41
2649 3750 3.072211 TGCTCAGCAAAGATCTTCAGTG 58.928 45.455 8.78 4.82 34.76 3.66
2655 3756 2.663879 GCAAAGATCTTCAGTGTGCACG 60.664 50.000 19.48 0.00 36.20 5.34
2657 3758 2.071688 AGATCTTCAGTGTGCACGAC 57.928 50.000 13.13 11.48 36.20 4.34
2658 3759 1.341209 AGATCTTCAGTGTGCACGACA 59.659 47.619 13.13 0.00 36.20 4.35
2659 3760 1.723542 GATCTTCAGTGTGCACGACAG 59.276 52.381 13.13 8.68 34.28 3.51
2660 3761 0.459899 TCTTCAGTGTGCACGACAGT 59.540 50.000 13.13 0.00 38.93 3.55
2662 3763 0.869880 TTCAGTGTGCACGACAGTCG 60.870 55.000 21.62 21.62 46.93 4.18
2664 3765 3.702555 GTGTGCACGACAGTCGCC 61.703 66.667 23.09 14.31 45.12 5.54
2665 3766 4.214327 TGTGCACGACAGTCGCCA 62.214 61.111 23.09 16.73 45.12 5.69
2666 3767 2.964925 GTGCACGACAGTCGCCAA 60.965 61.111 23.09 5.42 45.12 4.52
2667 3768 2.661537 TGCACGACAGTCGCCAAG 60.662 61.111 23.09 11.34 45.12 3.61
2668 3769 3.414700 GCACGACAGTCGCCAAGG 61.415 66.667 23.09 8.59 45.12 3.61
2669 3770 2.338620 CACGACAGTCGCCAAGGA 59.661 61.111 23.09 0.00 45.12 3.36
2671 3772 1.079819 ACGACAGTCGCCAAGGATG 60.080 57.895 23.09 0.00 45.12 3.51
2672 3773 1.215382 CGACAGTCGCCAAGGATGA 59.785 57.895 10.66 0.00 31.14 2.92
2673 3774 0.179100 CGACAGTCGCCAAGGATGAT 60.179 55.000 10.66 0.00 31.14 2.45
2674 3775 1.293924 GACAGTCGCCAAGGATGATG 58.706 55.000 0.00 0.00 0.00 3.07
2675 3776 0.904649 ACAGTCGCCAAGGATGATGA 59.095 50.000 0.00 0.00 0.00 2.92
2676 3777 1.134580 ACAGTCGCCAAGGATGATGAG 60.135 52.381 0.00 0.00 0.00 2.90
2677 3778 1.134580 CAGTCGCCAAGGATGATGAGT 60.135 52.381 0.00 0.00 0.00 3.41
2678 3779 1.134580 AGTCGCCAAGGATGATGAGTG 60.135 52.381 0.00 0.00 0.00 3.51
2679 3780 1.134699 GTCGCCAAGGATGATGAGTGA 60.135 52.381 0.00 0.00 0.00 3.41
2680 3781 1.554617 TCGCCAAGGATGATGAGTGAA 59.445 47.619 0.00 0.00 0.00 3.18
2681 3782 2.027285 TCGCCAAGGATGATGAGTGAAA 60.027 45.455 0.00 0.00 0.00 2.69
2682 3783 2.096496 CGCCAAGGATGATGAGTGAAAC 59.904 50.000 0.00 0.00 0.00 2.78
2683 3784 3.084039 GCCAAGGATGATGAGTGAAACA 58.916 45.455 0.00 0.00 41.43 2.83
2684 3785 3.119708 GCCAAGGATGATGAGTGAAACAC 60.120 47.826 0.00 0.00 41.43 3.32
2697 3798 2.750301 GAAACACTCACCCGTTTCAC 57.250 50.000 9.49 0.00 46.57 3.18
2698 3799 2.285977 GAAACACTCACCCGTTTCACT 58.714 47.619 9.49 0.00 46.57 3.41
2699 3800 1.949465 AACACTCACCCGTTTCACTC 58.051 50.000 0.00 0.00 0.00 3.51
2700 3801 0.249322 ACACTCACCCGTTTCACTCG 60.249 55.000 0.00 0.00 0.00 4.18
2701 3802 1.300697 ACTCACCCGTTTCACTCGC 60.301 57.895 0.00 0.00 0.00 5.03
2702 3803 2.027625 CTCACCCGTTTCACTCGCC 61.028 63.158 0.00 0.00 0.00 5.54
2710 3811 0.235926 GTTTCACTCGCCTGAGCAAC 59.764 55.000 0.00 0.00 46.69 4.17
2715 3816 0.108138 ACTCGCCTGAGCAACCATAC 60.108 55.000 0.00 0.00 46.69 2.39
2717 3818 0.541392 TCGCCTGAGCAACCATACAT 59.459 50.000 0.00 0.00 39.83 2.29
2796 3916 3.581755 TGTGTCTACCAAATAGCACGTC 58.418 45.455 0.00 0.00 39.15 4.34
2805 3925 4.155280 ACCAAATAGCACGTCCAAATGTAC 59.845 41.667 0.00 0.00 0.00 2.90
2808 3928 2.831685 AGCACGTCCAAATGTACTGA 57.168 45.000 0.00 0.00 0.00 3.41
2809 3929 3.334583 AGCACGTCCAAATGTACTGAT 57.665 42.857 0.00 0.00 0.00 2.90
2844 3964 9.807921 AACTTTGGTTCAGAGAAATAAAGGATA 57.192 29.630 15.32 0.00 0.00 2.59
2850 3970 6.491714 TCAGAGAAATAAAGGATAGCTGCT 57.508 37.500 7.57 7.57 0.00 4.24
2904 4024 5.536538 ACAGACTAGTTCAAGACTCACATCA 59.463 40.000 0.00 0.00 39.86 3.07
2912 4032 4.959723 TCAAGACTCACATCAATGACACA 58.040 39.130 0.00 0.00 0.00 3.72
2913 4033 5.367302 TCAAGACTCACATCAATGACACAA 58.633 37.500 0.00 0.00 0.00 3.33
2978 4098 3.206964 GTGCTAAATAGGGCAGTCTTCC 58.793 50.000 0.00 0.00 39.22 3.46
2985 4105 2.160721 AGGGCAGTCTTCCGATAGAA 57.839 50.000 0.00 0.00 39.76 2.10
3105 4225 3.054948 TCCCCCTAAAGTAACAACATCGG 60.055 47.826 0.00 0.00 0.00 4.18
3133 4253 5.806654 ACATTAGCAAAGGGAACACAATT 57.193 34.783 0.00 0.00 0.00 2.32
3134 4254 6.909550 ACATTAGCAAAGGGAACACAATTA 57.090 33.333 0.00 0.00 0.00 1.40
3140 4260 4.314961 CAAAGGGAACACAATTAAAGGCC 58.685 43.478 0.00 0.00 0.00 5.19
3159 4279 5.870706 AGGCCTTCCTTTGTATATAAGAGC 58.129 41.667 0.00 0.00 40.66 4.09
3161 4281 5.470437 GGCCTTCCTTTGTATATAAGAGCAC 59.530 44.000 0.00 0.00 0.00 4.40
3167 4294 8.079211 TCCTTTGTATATAAGAGCACAAGAGT 57.921 34.615 0.00 0.00 32.86 3.24
3175 4302 0.036952 GAGCACAAGAGTAGCTGGCA 60.037 55.000 0.00 0.00 39.02 4.92
3181 4308 1.929836 CAAGAGTAGCTGGCACGATTC 59.070 52.381 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.474630 AGCATGAGAAAAGAGAGAAACAGAT 58.525 36.000 0.00 0.00 0.00 2.90
37 38 5.063204 CAGCCTATAAAATGGATTCGTCCA 58.937 41.667 0.00 0.00 44.85 4.02
38 39 4.455877 CCAGCCTATAAAATGGATTCGTCC 59.544 45.833 0.00 0.00 34.60 4.79
40 41 3.821033 GCCAGCCTATAAAATGGATTCGT 59.179 43.478 0.00 0.00 34.60 3.85
61 65 1.103803 TAGTGATGGTGGAGAGACGC 58.896 55.000 0.00 0.00 0.00 5.19
62 66 4.557695 GCTATTAGTGATGGTGGAGAGACG 60.558 50.000 0.00 0.00 0.00 4.18
71 75 8.965819 CACTCTCATATAGCTATTAGTGATGGT 58.034 37.037 12.39 11.59 36.13 3.55
118 193 8.345724 GGATTCTTGGTATCCTATCGTTACTA 57.654 38.462 0.00 0.00 38.81 1.82
172 247 6.112734 ACATATGTGGCAGAGACGATTTTAA 58.887 36.000 7.78 0.00 0.00 1.52
211 287 1.283793 GCATGCGCACAGTTCTTGT 59.716 52.632 14.90 0.00 41.94 3.16
244 320 6.876257 AGCAACTGAAAGATTTCTGTAGTAGG 59.124 38.462 15.41 5.44 44.92 3.18
270 346 2.168106 ACTGCTGGCTACTTGATCTCAG 59.832 50.000 0.00 0.00 0.00 3.35
274 350 2.093764 AGACACTGCTGGCTACTTGATC 60.094 50.000 0.00 0.00 31.87 2.92
380 467 6.127338 TGTCTTGGTCCTAATACATGAGTCAG 60.127 42.308 0.00 0.00 0.00 3.51
416 507 3.191162 AGCGCAACATTAGCAAAATGAGA 59.809 39.130 11.47 0.00 0.00 3.27
428 519 2.923605 GCAGATTTCACAGCGCAACATT 60.924 45.455 11.47 0.00 0.00 2.71
537 629 4.621034 GTGATTAAACCTTGACGCCAATTG 59.379 41.667 0.00 0.00 0.00 2.32
598 690 3.008923 TGCAGTCATTGTCCTGATGGTTA 59.991 43.478 9.33 0.00 34.23 2.85
705 797 1.498865 GAAGTGACACGTGGCAGGTG 61.499 60.000 32.02 32.02 39.65 4.00
792 1013 4.318121 GCGGCTCATGTTCTTCGTATAAAG 60.318 45.833 0.00 0.00 0.00 1.85
800 1021 1.696832 GGTCGCGGCTCATGTTCTTC 61.697 60.000 11.94 0.00 0.00 2.87
845 1066 3.635373 CCTCTATTGACTGGCTTACCGTA 59.365 47.826 0.00 0.00 39.70 4.02
907 1128 2.625790 TGCAACAATTCCACTGGGTAAC 59.374 45.455 0.00 0.00 34.93 2.50
951 1180 0.938713 CGGGCACACTGAAACGTTAA 59.061 50.000 0.00 0.00 0.00 2.01
954 1183 3.276846 GCGGGCACACTGAAACGT 61.277 61.111 0.00 0.00 0.00 3.99
1024 1253 3.844090 GAGGCTGGCGAGGAGGAC 61.844 72.222 0.00 0.00 0.00 3.85
1056 1285 4.728110 TTGCTGCTGGCGATGGCT 62.728 61.111 0.00 0.00 45.43 4.75
1108 1579 0.670854 GGAAGTCACTTGGGAGACGC 60.671 60.000 0.00 0.00 37.94 5.19
1167 1931 2.164338 GCCTCCGGATACCAACAAAAA 58.836 47.619 3.57 0.00 0.00 1.94
1168 1932 1.828979 GCCTCCGGATACCAACAAAA 58.171 50.000 3.57 0.00 0.00 2.44
1312 2310 2.093658 GGGTGGCATATATACACTCGGG 60.094 54.545 15.37 0.00 35.53 5.14
1381 2379 7.716560 TGAATGTCGATAAGAACCATGATCAAT 59.283 33.333 0.00 0.00 0.00 2.57
1397 2395 3.997021 GTCACAAGGTTCTGAATGTCGAT 59.003 43.478 0.00 0.00 0.00 3.59
1453 2451 1.606313 CCCAAATCCCCGCACAGTT 60.606 57.895 0.00 0.00 0.00 3.16
1461 2459 1.050421 CCTGCATTCCCCAAATCCCC 61.050 60.000 0.00 0.00 0.00 4.81
1503 2501 1.986882 CTCTTCAGTTGGCCCAGTTT 58.013 50.000 0.00 0.00 0.00 2.66
1533 2531 5.613358 GCAAGTTGCAGTAGAACTTACAT 57.387 39.130 22.90 0.00 44.26 2.29
1559 2557 2.191128 ATTTGACAGGTCTGCACTCC 57.809 50.000 0.65 0.00 0.00 3.85
1664 2666 4.699522 AGGTTTCCCAGCGTCGCC 62.700 66.667 14.86 0.00 0.00 5.54
1670 2672 1.349357 AGTCTCTTCAGGTTTCCCAGC 59.651 52.381 0.00 0.00 0.00 4.85
1725 2727 3.900892 CGAGGCCGGTATCGTGCT 61.901 66.667 18.66 0.00 34.56 4.40
1754 2756 3.626924 AGGAAACGCAGCGACCCT 61.627 61.111 24.65 20.09 0.00 4.34
1797 2799 5.971792 TCGTAGCATCTCGTAATCAGAAAAG 59.028 40.000 0.00 0.00 0.00 2.27
1803 2805 3.242969 GGTGTCGTAGCATCTCGTAATCA 60.243 47.826 0.00 0.00 0.00 2.57
1807 2809 2.034104 AGGTGTCGTAGCATCTCGTA 57.966 50.000 0.00 0.00 0.00 3.43
1819 2821 1.743958 ACTTGGAGACGATAGGTGTCG 59.256 52.381 0.00 0.00 46.56 4.35
1838 2840 3.798337 CACCAACAGATTGTTTTCAGCAC 59.202 43.478 0.00 0.00 38.77 4.40
1921 2923 1.270826 CCTGAGAAGCTTCGTCAGACA 59.729 52.381 33.93 22.10 40.21 3.41
1982 2984 1.474879 GAACAAGAGAGAGGACCTCCG 59.525 57.143 18.32 2.85 42.97 4.63
2013 3015 6.188407 TCCTACTACTCACAGCTTAGTCAAT 58.812 40.000 0.00 0.00 0.00 2.57
2036 3038 6.224420 GTGTGAAACCAACTGTATGTACTC 57.776 41.667 0.00 0.00 34.36 2.59
2181 3197 6.209986 CACATGAATAATATGCATCCCACCTT 59.790 38.462 0.19 0.00 0.00 3.50
2186 3202 6.822667 TGTCACATGAATAATATGCATCCC 57.177 37.500 0.19 0.00 0.00 3.85
2201 3218 6.338214 ACCTCTAGCTATACATGTCACATG 57.662 41.667 16.68 16.68 0.00 3.21
2244 3285 4.627611 AGTGATGCCAATCTGAAATTCG 57.372 40.909 0.00 0.00 33.61 3.34
2273 3315 1.201647 CGTGTCTTGGATGACCGTAGT 59.798 52.381 0.00 0.00 39.42 2.73
2287 3329 3.802948 AGTCTTCAGTTGAACGTGTCT 57.197 42.857 0.00 0.00 0.00 3.41
2294 3336 5.777802 CTCAGCTTCTAGTCTTCAGTTGAA 58.222 41.667 0.00 0.00 0.00 2.69
2299 3341 3.772932 CTGCTCAGCTTCTAGTCTTCAG 58.227 50.000 0.00 0.00 0.00 3.02
2351 3394 5.126384 AGTTTCAGAACGGAAAACCATTCAA 59.874 36.000 0.00 0.00 40.75 2.69
2358 3401 2.727777 GGCAGTTTCAGAACGGAAAAC 58.272 47.619 2.21 0.00 40.75 2.43
2378 3424 0.095935 GCTGCATGCAACTACTGTCG 59.904 55.000 22.88 7.64 42.31 4.35
2380 3426 0.037303 AGGCTGCATGCAACTACTGT 59.963 50.000 22.88 0.00 45.15 3.55
2401 3467 3.075148 GGAACAGAGGTCTACAAAAGCC 58.925 50.000 0.00 0.00 0.00 4.35
2405 3471 5.302568 TCTTAACGGAACAGAGGTCTACAAA 59.697 40.000 0.00 0.00 0.00 2.83
2416 3482 2.931320 GCCCTGACTCTTAACGGAACAG 60.931 54.545 0.00 0.00 0.00 3.16
2430 3496 1.483004 GAAGGAGAGGTAAGCCCTGAC 59.517 57.143 0.00 0.00 46.51 3.51
2431 3497 1.078823 TGAAGGAGAGGTAAGCCCTGA 59.921 52.381 0.00 0.00 46.51 3.86
2434 3500 2.188817 TCTTGAAGGAGAGGTAAGCCC 58.811 52.381 0.00 0.00 34.57 5.19
2435 3501 3.983044 TTCTTGAAGGAGAGGTAAGCC 57.017 47.619 0.00 0.00 0.00 4.35
2436 3502 4.642429 TGTTTCTTGAAGGAGAGGTAAGC 58.358 43.478 0.00 0.00 0.00 3.09
2437 3503 8.314751 TCTATTGTTTCTTGAAGGAGAGGTAAG 58.685 37.037 0.00 0.00 0.00 2.34
2438 3504 8.202461 TCTATTGTTTCTTGAAGGAGAGGTAA 57.798 34.615 0.00 0.00 0.00 2.85
2439 3505 7.792364 TCTATTGTTTCTTGAAGGAGAGGTA 57.208 36.000 0.00 0.00 0.00 3.08
2441 3507 7.390027 TCTTCTATTGTTTCTTGAAGGAGAGG 58.610 38.462 0.00 0.00 35.98 3.69
2442 3508 8.839310 TTCTTCTATTGTTTCTTGAAGGAGAG 57.161 34.615 0.00 0.00 35.98 3.20
2443 3509 9.799106 ATTTCTTCTATTGTTTCTTGAAGGAGA 57.201 29.630 0.00 0.00 35.98 3.71
2461 3527 9.388506 CAATGGACTCAACTATGTATTTCTTCT 57.611 33.333 0.00 0.00 0.00 2.85
2462 3528 9.167311 ACAATGGACTCAACTATGTATTTCTTC 57.833 33.333 0.00 0.00 0.00 2.87
2463 3529 9.520515 AACAATGGACTCAACTATGTATTTCTT 57.479 29.630 0.00 0.00 0.00 2.52
2469 3535 9.542462 GCTAATAACAATGGACTCAACTATGTA 57.458 33.333 0.00 0.00 0.00 2.29
2470 3536 8.046708 TGCTAATAACAATGGACTCAACTATGT 58.953 33.333 0.00 0.00 0.00 2.29
2471 3537 8.437360 TGCTAATAACAATGGACTCAACTATG 57.563 34.615 0.00 0.00 0.00 2.23
2472 3538 7.716998 CCTGCTAATAACAATGGACTCAACTAT 59.283 37.037 0.00 0.00 0.00 2.12
2473 3539 7.047891 CCTGCTAATAACAATGGACTCAACTA 58.952 38.462 0.00 0.00 0.00 2.24
2474 3540 5.882557 CCTGCTAATAACAATGGACTCAACT 59.117 40.000 0.00 0.00 0.00 3.16
2475 3541 5.880332 TCCTGCTAATAACAATGGACTCAAC 59.120 40.000 0.00 0.00 0.00 3.18
2476 3542 6.061022 TCCTGCTAATAACAATGGACTCAA 57.939 37.500 0.00 0.00 0.00 3.02
2477 3543 5.692115 TCCTGCTAATAACAATGGACTCA 57.308 39.130 0.00 0.00 0.00 3.41
2478 3544 7.573968 ATTTCCTGCTAATAACAATGGACTC 57.426 36.000 0.00 0.00 0.00 3.36
2501 3567 9.826574 CCACAAGGATGAATCATTATTTTGAAT 57.173 29.630 0.00 0.00 36.89 2.57
2515 3581 7.606456 GTGACTAAGATAAACCACAAGGATGAA 59.394 37.037 0.00 0.00 38.69 2.57
2524 3616 8.204836 AGTATGGATGTGACTAAGATAAACCAC 58.795 37.037 0.00 0.00 0.00 4.16
2543 3635 5.681437 GCTCAAACGGATGTAGAAGTATGGA 60.681 44.000 0.00 0.00 0.00 3.41
2544 3636 4.508124 GCTCAAACGGATGTAGAAGTATGG 59.492 45.833 0.00 0.00 0.00 2.74
2547 3639 3.766151 CGCTCAAACGGATGTAGAAGTA 58.234 45.455 0.00 0.00 0.00 2.24
2548 3640 2.607187 CGCTCAAACGGATGTAGAAGT 58.393 47.619 0.00 0.00 0.00 3.01
2559 3651 2.505866 GAATTAGTTGCCGCTCAAACG 58.494 47.619 0.00 0.00 36.26 3.60
2560 3652 2.727916 CGGAATTAGTTGCCGCTCAAAC 60.728 50.000 0.00 0.00 38.46 2.93
2561 3653 1.466950 CGGAATTAGTTGCCGCTCAAA 59.533 47.619 0.00 0.00 38.46 2.69
2562 3654 1.083489 CGGAATTAGTTGCCGCTCAA 58.917 50.000 0.00 0.00 38.46 3.02
2563 3655 0.742990 CCGGAATTAGTTGCCGCTCA 60.743 55.000 0.00 0.00 43.52 4.26
2564 3656 0.461339 TCCGGAATTAGTTGCCGCTC 60.461 55.000 0.00 0.00 43.52 5.03
2565 3657 0.743345 GTCCGGAATTAGTTGCCGCT 60.743 55.000 5.23 0.00 43.52 5.52
2566 3658 1.719709 GTCCGGAATTAGTTGCCGC 59.280 57.895 5.23 0.00 43.52 6.53
2567 3659 1.426041 CCGTCCGGAATTAGTTGCCG 61.426 60.000 5.23 1.25 44.42 5.69
2568 3660 0.108041 TCCGTCCGGAATTAGTTGCC 60.108 55.000 5.23 0.00 42.05 4.52
2569 3661 1.287425 CTCCGTCCGGAATTAGTTGC 58.713 55.000 5.23 0.00 44.66 4.17
2570 3662 1.472728 CCCTCCGTCCGGAATTAGTTG 60.473 57.143 5.23 0.00 44.66 3.16
2571 3663 0.828677 CCCTCCGTCCGGAATTAGTT 59.171 55.000 5.23 0.00 44.66 2.24
2572 3664 0.032813 TCCCTCCGTCCGGAATTAGT 60.033 55.000 5.23 0.00 44.66 2.24
2573 3665 0.674534 CTCCCTCCGTCCGGAATTAG 59.325 60.000 5.23 3.15 44.66 1.73
2574 3666 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
2575 3667 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
2576 3668 0.467659 CTACTCCCTCCGTCCGGAAT 60.468 60.000 5.23 0.00 44.66 3.01
2577 3669 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
2578 3670 2.593978 CTACTCCCTCCGTCCGGA 59.406 66.667 0.00 0.00 42.90 5.14
2579 3671 3.217743 GCTACTCCCTCCGTCCGG 61.218 72.222 0.00 0.00 0.00 5.14
2580 3672 2.439701 TGCTACTCCCTCCGTCCG 60.440 66.667 0.00 0.00 0.00 4.79
2581 3673 1.043673 ATGTGCTACTCCCTCCGTCC 61.044 60.000 0.00 0.00 0.00 4.79
2582 3674 0.103208 CATGTGCTACTCCCTCCGTC 59.897 60.000 0.00 0.00 0.00 4.79
2583 3675 1.330655 CCATGTGCTACTCCCTCCGT 61.331 60.000 0.00 0.00 0.00 4.69
2584 3676 1.330655 ACCATGTGCTACTCCCTCCG 61.331 60.000 0.00 0.00 0.00 4.63
2585 3677 0.179000 CACCATGTGCTACTCCCTCC 59.821 60.000 0.00 0.00 0.00 4.30
2586 3678 3.768633 CACCATGTGCTACTCCCTC 57.231 57.895 0.00 0.00 0.00 4.30
2635 3736 2.802247 TCGTGCACACTGAAGATCTTTG 59.198 45.455 18.64 6.75 0.00 2.77
2639 3740 1.723542 CTGTCGTGCACACTGAAGATC 59.276 52.381 18.64 1.09 0.00 2.75
2645 3746 2.932083 GCGACTGTCGTGCACACTG 61.932 63.158 28.38 18.22 42.81 3.66
2648 3749 3.724914 TTGGCGACTGTCGTGCACA 62.725 57.895 28.38 19.50 42.81 4.57
2649 3750 2.943345 CTTGGCGACTGTCGTGCAC 61.943 63.158 28.38 17.48 42.81 4.57
2655 3756 1.134699 TCATCATCCTTGGCGACTGTC 60.135 52.381 0.00 0.00 0.00 3.51
2657 3758 1.134580 ACTCATCATCCTTGGCGACTG 60.135 52.381 0.00 0.00 0.00 3.51
2658 3759 1.134580 CACTCATCATCCTTGGCGACT 60.135 52.381 0.00 0.00 0.00 4.18
2659 3760 1.134699 TCACTCATCATCCTTGGCGAC 60.135 52.381 0.00 0.00 0.00 5.19
2660 3761 1.194218 TCACTCATCATCCTTGGCGA 58.806 50.000 0.00 0.00 0.00 5.54
2662 3763 3.084039 TGTTTCACTCATCATCCTTGGC 58.916 45.455 0.00 0.00 0.00 4.52
2679 3780 2.285977 GAGTGAAACGGGTGAGTGTTT 58.714 47.619 0.00 0.00 45.86 2.83
2680 3781 1.805120 CGAGTGAAACGGGTGAGTGTT 60.805 52.381 0.00 0.00 45.86 3.32
2681 3782 0.249322 CGAGTGAAACGGGTGAGTGT 60.249 55.000 0.00 0.00 45.86 3.55
2682 3783 1.557443 GCGAGTGAAACGGGTGAGTG 61.557 60.000 0.00 0.00 45.86 3.51
2683 3784 1.300697 GCGAGTGAAACGGGTGAGT 60.301 57.895 0.00 0.00 45.86 3.41
2684 3785 2.027625 GGCGAGTGAAACGGGTGAG 61.028 63.158 0.00 0.00 45.86 3.51
2685 3786 2.029964 GGCGAGTGAAACGGGTGA 59.970 61.111 0.00 0.00 45.86 4.02
2686 3787 2.030562 AGGCGAGTGAAACGGGTG 59.969 61.111 0.00 0.00 45.86 4.61
2687 3788 2.030562 CAGGCGAGTGAAACGGGT 59.969 61.111 0.00 0.00 45.86 5.28
2688 3789 1.738099 CTCAGGCGAGTGAAACGGG 60.738 63.158 0.00 0.00 45.86 5.28
2689 3790 2.383527 GCTCAGGCGAGTGAAACGG 61.384 63.158 7.88 0.00 45.86 4.44
2690 3791 1.221466 TTGCTCAGGCGAGTGAAACG 61.221 55.000 7.88 0.00 41.74 3.60
2691 3792 0.235926 GTTGCTCAGGCGAGTGAAAC 59.764 55.000 7.88 6.93 41.71 2.78
2692 3793 0.884704 GGTTGCTCAGGCGAGTGAAA 60.885 55.000 7.88 0.11 41.71 2.69
2693 3794 1.301716 GGTTGCTCAGGCGAGTGAA 60.302 57.895 7.88 0.62 41.71 3.18
2694 3795 1.830587 ATGGTTGCTCAGGCGAGTGA 61.831 55.000 7.88 0.00 41.71 3.41
2695 3796 0.108186 TATGGTTGCTCAGGCGAGTG 60.108 55.000 7.88 0.00 41.71 3.51
2696 3797 0.108138 GTATGGTTGCTCAGGCGAGT 60.108 55.000 7.88 0.00 41.71 4.18
2697 3798 0.108186 TGTATGGTTGCTCAGGCGAG 60.108 55.000 0.00 2.61 42.25 5.03
2698 3799 0.541392 ATGTATGGTTGCTCAGGCGA 59.459 50.000 0.00 0.00 42.25 5.54
2699 3800 0.659427 CATGTATGGTTGCTCAGGCG 59.341 55.000 0.00 0.00 42.25 5.52
2700 3801 2.042686 TCATGTATGGTTGCTCAGGC 57.957 50.000 0.00 0.00 39.26 4.85
2701 3802 3.877559 TCTTCATGTATGGTTGCTCAGG 58.122 45.455 0.00 0.00 0.00 3.86
2702 3803 5.181009 TCTTCTTCATGTATGGTTGCTCAG 58.819 41.667 0.00 0.00 0.00 3.35
2710 3811 7.383572 GTGCTATGTACTCTTCTTCATGTATGG 59.616 40.741 0.00 0.00 0.00 2.74
2715 3816 6.101997 TGTGTGCTATGTACTCTTCTTCATG 58.898 40.000 0.00 0.00 0.00 3.07
2717 3818 5.476945 TCTGTGTGCTATGTACTCTTCTTCA 59.523 40.000 0.00 0.00 0.00 3.02
2783 3903 3.848272 ACATTTGGACGTGCTATTTGG 57.152 42.857 8.99 0.00 0.00 3.28
2785 3905 5.242434 TCAGTACATTTGGACGTGCTATTT 58.758 37.500 8.99 0.00 0.00 1.40
2796 3916 6.317140 AGTTGTGATGCTATCAGTACATTTGG 59.683 38.462 0.00 0.00 40.53 3.28
2805 3925 5.181811 TGAACCAAAGTTGTGATGCTATCAG 59.818 40.000 0.00 0.00 36.71 2.90
2808 3928 5.316167 TCTGAACCAAAGTTGTGATGCTAT 58.684 37.500 0.00 0.00 35.94 2.97
2809 3929 4.713553 TCTGAACCAAAGTTGTGATGCTA 58.286 39.130 0.00 0.00 35.94 3.49
2859 3979 6.153680 TCTGTTAAGTTTGTGGGTCATTGTTT 59.846 34.615 0.00 0.00 0.00 2.83
2978 4098 4.514441 AGGCTGCATTTCTGATTTCTATCG 59.486 41.667 0.50 0.00 33.23 2.92
2985 4105 3.022406 GAGGAAGGCTGCATTTCTGATT 58.978 45.455 13.26 0.00 0.00 2.57
3105 4225 5.863935 GTGTTCCCTTTGCTAATGTTTGATC 59.136 40.000 0.00 0.00 0.00 2.92
3140 4260 8.948631 TCTTGTGCTCTTATATACAAAGGAAG 57.051 34.615 0.00 0.00 33.19 3.46
3150 4270 5.510520 GCCAGCTACTCTTGTGCTCTTATAT 60.511 44.000 0.00 0.00 34.51 0.86
3155 4275 0.248843 GCCAGCTACTCTTGTGCTCT 59.751 55.000 0.00 0.00 34.51 4.09
3156 4276 0.036952 TGCCAGCTACTCTTGTGCTC 60.037 55.000 0.00 0.00 34.51 4.26
3159 4279 0.038251 TCGTGCCAGCTACTCTTGTG 60.038 55.000 0.00 0.00 0.00 3.33
3161 4281 1.929836 GAATCGTGCCAGCTACTCTTG 59.070 52.381 0.00 0.00 0.00 3.02
3167 4294 0.101759 GTACCGAATCGTGCCAGCTA 59.898 55.000 0.82 0.00 0.00 3.32
3240 4367 4.973055 CGGAACCGGAACACGCCA 62.973 66.667 9.46 0.00 42.52 5.69


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

AutoCloner maintained by Alex Coulton.