Multiple sequence alignment - TraesCS2B01G144900

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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 TraesCS2B01G144900 chr2B 100.000 5658 0 0 1 5658 110851364 110857021 0.000000e+00 10449.0
1 TraesCS2B01G144900 chr2B 88.844 493 51 1 3760 4252 110796198 110795710 2.260000e-168 603.0
2 TraesCS2B01G144900 chr2B 85.714 448 53 8 4249 4689 110778590 110778147 3.990000e-126 462.0
3 TraesCS2B01G144900 chr2B 82.915 398 61 7 2791 3183 236527251 236526856 9.020000e-93 351.0
4 TraesCS2B01G144900 chr2B 89.683 126 13 0 4811 4936 110859348 110859473 1.630000e-35 161.0
5 TraesCS2B01G144900 chr2B 95.522 67 3 0 480 546 110851779 110851845 2.160000e-19 108.0
6 TraesCS2B01G144900 chr2A 94.955 4321 175 19 645 4938 72691295 72695599 0.000000e+00 6732.0
7 TraesCS2B01G144900 chr2A 90.000 600 60 0 5059 5658 133503917 133503318 0.000000e+00 776.0
8 TraesCS2B01G144900 chr2A 89.447 597 61 2 5059 5654 750110742 750111337 0.000000e+00 752.0
9 TraesCS2B01G144900 chr2A 89.936 467 38 9 1 462 758558231 758557769 1.360000e-165 593.0
10 TraesCS2B01G144900 chr2A 90.435 345 32 1 3763 4106 72513246 72512902 2.400000e-123 453.0
11 TraesCS2B01G144900 chr2A 82.872 397 61 7 2791 3182 194129992 194129598 3.240000e-92 350.0
12 TraesCS2B01G144900 chr2D 95.773 2295 83 5 2663 4949 73324007 73321719 0.000000e+00 3688.0
13 TraesCS2B01G144900 chr2D 96.590 1789 55 2 836 2624 73325890 73324108 0.000000e+00 2961.0
14 TraesCS2B01G144900 chr2D 91.685 457 37 1 3760 4215 73207287 73206831 2.880000e-177 632.0
15 TraesCS2B01G144900 chr2D 82.785 395 59 8 2794 3182 179692129 179691738 1.510000e-90 344.0
16 TraesCS2B01G144900 chr2D 94.175 206 10 2 636 841 73326277 73326074 4.260000e-81 313.0
17 TraesCS2B01G144900 chr2D 91.667 60 3 2 4959 5017 636059676 636059618 1.310000e-11 82.4
18 TraesCS2B01G144900 chr7B 94.676 601 31 1 5059 5658 742645221 742645821 0.000000e+00 931.0
19 TraesCS2B01G144900 chr7B 89.951 408 37 4 2797 3202 451353820 451354225 1.810000e-144 523.0
20 TraesCS2B01G144900 chr7B 76.832 764 153 17 1871 2627 451352907 451353653 5.280000e-110 409.0
21 TraesCS2B01G144900 chr7B 80.061 326 61 4 3770 4093 451354684 451355007 7.330000e-59 239.0
22 TraesCS2B01G144900 chr7B 97.959 49 1 0 555 603 638136158 638136110 1.010000e-12 86.1
23 TraesCS2B01G144900 chr6B 94.676 601 31 1 5059 5658 174571542 174572142 0.000000e+00 931.0
24 TraesCS2B01G144900 chr6B 92.833 600 42 1 5059 5658 37269902 37270500 0.000000e+00 869.0
25 TraesCS2B01G144900 chr6B 88.099 605 63 6 5059 5658 101464248 101464848 0.000000e+00 710.0
26 TraesCS2B01G144900 chr4B 94.518 602 31 2 5059 5658 642763157 642762556 0.000000e+00 928.0
27 TraesCS2B01G144900 chr7D 89.127 607 59 6 5056 5658 631182613 631183216 0.000000e+00 749.0
28 TraesCS2B01G144900 chr7D 89.461 408 39 4 2797 3202 434148257 434148662 3.910000e-141 512.0
29 TraesCS2B01G144900 chr7D 78.010 764 144 17 1871 2627 434147341 434148087 5.170000e-125 459.0
30 TraesCS2B01G144900 chr7D 89.655 58 2 4 4955 5010 529690828 529690773 2.830000e-08 71.3
31 TraesCS2B01G144900 chr6A 89.000 600 65 1 5059 5657 13045631 13045032 0.000000e+00 741.0
32 TraesCS2B01G144900 chr3B 93.737 463 23 4 3 464 14974058 14973601 0.000000e+00 689.0
33 TraesCS2B01G144900 chr3B 92.918 466 28 5 1 464 768644754 768645216 0.000000e+00 673.0
34 TraesCS2B01G144900 chr3B 85.612 139 7 2 480 605 14973649 14973511 3.560000e-27 134.0
35 TraesCS2B01G144900 chr4A 92.873 463 28 4 3 464 719303111 719302653 0.000000e+00 667.0
36 TraesCS2B01G144900 chr4A 92.873 463 28 4 3 464 719527655 719527197 0.000000e+00 667.0
37 TraesCS2B01G144900 chr4A 95.122 82 3 1 526 606 719302642 719302561 1.650000e-25 128.0
38 TraesCS2B01G144900 chr4A 95.122 82 3 1 526 606 719527186 719527105 1.650000e-25 128.0
39 TraesCS2B01G144900 chr7A 92.560 457 27 7 1 455 386399616 386400067 0.000000e+00 649.0
40 TraesCS2B01G144900 chr7A 91.775 462 31 6 1 458 386398612 386398154 2.220000e-178 636.0
41 TraesCS2B01G144900 chr7A 90.810 457 34 7 1 455 386455072 386455522 6.270000e-169 604.0
42 TraesCS2B01G144900 chr7A 89.706 408 38 4 2797 3202 484595356 484595761 8.400000e-143 518.0
43 TraesCS2B01G144900 chr7A 78.278 755 143 14 1871 2619 484594444 484595183 3.090000e-127 466.0
44 TraesCS2B01G144900 chr7A 84.800 125 8 5 480 604 386400028 386400141 1.290000e-21 115.0
45 TraesCS2B01G144900 chr3D 90.508 453 34 7 15 464 473470878 473470432 1.760000e-164 590.0
46 TraesCS2B01G144900 chr3D 92.157 51 4 0 550 600 91687417 91687367 7.860000e-09 73.1
47 TraesCS2B01G144900 chrUn 81.618 408 66 9 2781 3182 5436073 5435669 4.230000e-86 329.0
48 TraesCS2B01G144900 chr3A 92.857 56 2 2 4959 5013 33590415 33590361 4.700000e-11 80.5


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 TraesCS2B01G144900 chr2B 110851364 110857021 5657 False 10449.000000 10449 100.000000 1 5658 1 chr2B.!!$F1 5657
1 TraesCS2B01G144900 chr2A 72691295 72695599 4304 False 6732.000000 6732 94.955000 645 4938 1 chr2A.!!$F1 4293
2 TraesCS2B01G144900 chr2A 133503318 133503917 599 True 776.000000 776 90.000000 5059 5658 1 chr2A.!!$R2 599
3 TraesCS2B01G144900 chr2A 750110742 750111337 595 False 752.000000 752 89.447000 5059 5654 1 chr2A.!!$F2 595
4 TraesCS2B01G144900 chr2D 73321719 73326277 4558 True 2320.666667 3688 95.512667 636 4949 3 chr2D.!!$R4 4313
5 TraesCS2B01G144900 chr7B 742645221 742645821 600 False 931.000000 931 94.676000 5059 5658 1 chr7B.!!$F1 599
6 TraesCS2B01G144900 chr7B 451352907 451355007 2100 False 390.333333 523 82.281333 1871 4093 3 chr7B.!!$F2 2222
7 TraesCS2B01G144900 chr6B 174571542 174572142 600 False 931.000000 931 94.676000 5059 5658 1 chr6B.!!$F3 599
8 TraesCS2B01G144900 chr6B 37269902 37270500 598 False 869.000000 869 92.833000 5059 5658 1 chr6B.!!$F1 599
9 TraesCS2B01G144900 chr6B 101464248 101464848 600 False 710.000000 710 88.099000 5059 5658 1 chr6B.!!$F2 599
10 TraesCS2B01G144900 chr4B 642762556 642763157 601 True 928.000000 928 94.518000 5059 5658 1 chr4B.!!$R1 599
11 TraesCS2B01G144900 chr7D 631182613 631183216 603 False 749.000000 749 89.127000 5056 5658 1 chr7D.!!$F1 602
12 TraesCS2B01G144900 chr7D 434147341 434148662 1321 False 485.500000 512 83.735500 1871 3202 2 chr7D.!!$F2 1331
13 TraesCS2B01G144900 chr6A 13045032 13045631 599 True 741.000000 741 89.000000 5059 5657 1 chr6A.!!$R1 598
14 TraesCS2B01G144900 chr3B 14973511 14974058 547 True 411.500000 689 89.674500 3 605 2 chr3B.!!$R1 602
15 TraesCS2B01G144900 chr4A 719302561 719303111 550 True 397.500000 667 93.997500 3 606 2 chr4A.!!$R1 603
16 TraesCS2B01G144900 chr4A 719527105 719527655 550 True 397.500000 667 93.997500 3 606 2 chr4A.!!$R2 603
17 TraesCS2B01G144900 chr7A 484594444 484595761 1317 False 492.000000 518 83.992000 1871 3202 2 chr7A.!!$F3 1331
18 TraesCS2B01G144900 chr7A 386399616 386400141 525 False 382.000000 649 88.680000 1 604 2 chr7A.!!$F2 603

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
504 508 0.036765 AATTGTTGCGCGGGAGACTA 60.037 50.000 8.83 0.0 0.00 2.59 F
723 727 0.249868 TTCACCACACAAGCTCTCGG 60.250 55.000 0.00 0.0 0.00 4.63 F
1692 1885 2.585247 GGCGGCATGTACGAGGAC 60.585 66.667 14.63 0.0 0.00 3.85 F
2666 2913 0.392336 TTGCCAAGTTGTTCCCATGC 59.608 50.000 1.45 0.0 0.00 4.06 F
3656 3912 0.391130 CCATCAACATGACCGACCGT 60.391 55.000 0.00 0.0 30.57 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1966 0.030369 ACGTCGGCATCGGTATCTTC 59.970 55.0 0.0 0.0 36.95 2.87 R
2289 2482 0.612174 TGAGGGCGAAGTAGCTGTCT 60.612 55.0 0.0 0.0 37.29 3.41 R
3518 3774 0.398522 AGCCGTAGATCCATCCCACA 60.399 55.0 0.0 0.0 0.00 4.17 R
4468 4736 0.449388 GATGAGCGAGCACCCAAAAG 59.551 55.0 0.0 0.0 0.00 2.27 R
5040 5315 0.179018 AACAGACACCAACTCCCAGC 60.179 55.0 0.0 0.0 0.00 4.85 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
33 34 5.407387 TGTTGTTTAGACAGAACTTATCGGC 59.593 40.000 0.00 0.00 37.04 5.54
80 81 6.768861 CGGGTCAGAATTACCAATGGTATTTA 59.231 38.462 13.55 0.00 38.05 1.40
81 82 7.255001 CGGGTCAGAATTACCAATGGTATTTAC 60.255 40.741 13.55 10.51 38.05 2.01
227 228 2.612212 GTTTTGTCGCCTGAGAGAAACA 59.388 45.455 0.00 0.00 33.91 2.83
320 322 4.156477 AGAGAGAGTTAGCTCAGTTGGTT 58.844 43.478 9.43 0.00 44.00 3.67
321 323 4.021544 AGAGAGAGTTAGCTCAGTTGGTTG 60.022 45.833 9.43 0.00 44.00 3.77
372 374 1.740025 GGTTTGATTCTTGCTAGCGCT 59.260 47.619 17.26 17.26 36.97 5.92
373 375 2.936498 GGTTTGATTCTTGCTAGCGCTA 59.064 45.455 17.75 17.75 36.97 4.26
441 445 2.449031 ATTGTTGCGCGGGAGACTGA 62.449 55.000 8.83 0.00 39.98 3.41
478 482 4.154613 GATAAGCGGATCGAGCGG 57.845 61.111 3.59 3.59 40.04 5.52
479 483 1.286260 GATAAGCGGATCGAGCGGT 59.714 57.895 10.04 0.88 40.04 5.68
480 484 0.729816 GATAAGCGGATCGAGCGGTC 60.730 60.000 10.04 4.06 40.04 4.79
501 505 3.262936 CAATTGTTGCGCGGGAGA 58.737 55.556 8.83 0.00 0.00 3.71
502 506 1.154225 CAATTGTTGCGCGGGAGAC 60.154 57.895 8.83 0.82 0.00 3.36
503 507 1.302511 AATTGTTGCGCGGGAGACT 60.303 52.632 8.83 0.00 0.00 3.24
504 508 0.036765 AATTGTTGCGCGGGAGACTA 60.037 50.000 8.83 0.00 0.00 2.59
505 509 0.460284 ATTGTTGCGCGGGAGACTAG 60.460 55.000 8.83 0.00 0.00 2.57
506 510 1.529152 TTGTTGCGCGGGAGACTAGA 61.529 55.000 8.83 0.00 0.00 2.43
507 511 1.214589 GTTGCGCGGGAGACTAGAA 59.785 57.895 8.83 0.00 0.00 2.10
508 512 0.389426 GTTGCGCGGGAGACTAGAAA 60.389 55.000 8.83 0.00 0.00 2.52
509 513 0.319083 TTGCGCGGGAGACTAGAAAA 59.681 50.000 8.83 0.00 0.00 2.29
510 514 0.319083 TGCGCGGGAGACTAGAAAAA 59.681 50.000 8.83 0.00 0.00 1.94
553 557 4.193334 CGAGCGGTCGCCAGATCA 62.193 66.667 25.07 0.00 43.17 2.92
561 565 0.527600 GTCGCCAGATCATACGTGCA 60.528 55.000 0.00 0.00 0.00 4.57
606 610 7.072030 GCAGGAAAATAGCATTGTCGTATAAG 58.928 38.462 0.00 0.00 0.00 1.73
607 611 7.254795 GCAGGAAAATAGCATTGTCGTATAAGT 60.255 37.037 0.00 0.00 0.00 2.24
608 612 9.256477 CAGGAAAATAGCATTGTCGTATAAGTA 57.744 33.333 0.00 0.00 0.00 2.24
609 613 9.826574 AGGAAAATAGCATTGTCGTATAAGTAA 57.173 29.630 0.00 0.00 0.00 2.24
649 653 5.106908 GCTGCTATCTTTTTCGAGTCACTTT 60.107 40.000 0.00 0.00 0.00 2.66
653 657 5.830900 ATCTTTTTCGAGTCACTTTCGAG 57.169 39.130 0.00 0.00 46.40 4.04
670 674 4.214986 TCGAGAAATTTACATGGCTCCA 57.785 40.909 0.00 0.00 0.00 3.86
722 726 1.143305 CTTCACCACACAAGCTCTCG 58.857 55.000 0.00 0.00 0.00 4.04
723 727 0.249868 TTCACCACACAAGCTCTCGG 60.250 55.000 0.00 0.00 0.00 4.63
925 1118 3.723348 GGCGCCGTCCAGTTGAAC 61.723 66.667 12.58 0.00 0.00 3.18
1216 1409 3.011517 AGCCCATGAAGGACGGCT 61.012 61.111 5.21 5.21 46.96 5.52
1506 1699 4.459089 GACGGCTGTCTCTGCCCC 62.459 72.222 18.76 0.00 44.00 5.80
1692 1885 2.585247 GGCGGCATGTACGAGGAC 60.585 66.667 14.63 0.00 0.00 3.85
1745 1938 3.197790 CATGCCGGCGGACTTGAG 61.198 66.667 33.44 8.53 0.00 3.02
2358 2551 1.859427 CGGACTTCGTCAAGGACCGA 61.859 60.000 14.64 0.00 46.91 4.69
2595 2791 3.953775 CCTGACCACGCCAAGGGT 61.954 66.667 0.00 0.00 40.96 4.34
2624 2820 1.754803 CGGCATCCTACAGGTACTCAA 59.245 52.381 0.00 0.00 34.60 3.02
2645 2892 1.138859 TCTCAATCATCACGCCGGAAT 59.861 47.619 5.05 0.00 0.00 3.01
2652 2899 1.247419 ATCACGCCGGAATTTTGCCA 61.247 50.000 5.05 0.00 0.00 4.92
2661 2908 2.799978 CGGAATTTTGCCAAGTTGTTCC 59.200 45.455 9.55 9.55 0.00 3.62
2664 2911 4.388485 GAATTTTGCCAAGTTGTTCCCAT 58.612 39.130 1.45 0.00 0.00 4.00
2665 2912 2.906691 TTTGCCAAGTTGTTCCCATG 57.093 45.000 1.45 0.00 0.00 3.66
2666 2913 0.392336 TTGCCAAGTTGTTCCCATGC 59.608 50.000 1.45 0.00 0.00 4.06
2667 2914 0.758310 TGCCAAGTTGTTCCCATGCA 60.758 50.000 1.45 0.00 0.00 3.96
2671 2918 2.299582 CCAAGTTGTTCCCATGCATCAA 59.700 45.455 0.00 0.00 0.00 2.57
2678 2925 3.324268 TGTTCCCATGCATCAAACATGTT 59.676 39.130 4.92 4.92 42.74 2.71
2679 2926 4.525874 TGTTCCCATGCATCAAACATGTTA 59.474 37.500 12.39 0.00 42.74 2.41
2766 3022 1.153489 CATGACGAGGACCAGCTGG 60.153 63.158 31.60 31.60 42.17 4.85
2777 3033 2.268022 CCAGCTGGTCGACTACAGT 58.732 57.895 25.53 3.73 37.07 3.55
2783 3039 2.071540 CTGGTCGACTACAGTGACGTA 58.928 52.381 16.46 0.00 33.45 3.57
2947 3203 2.096417 GCGACCACTACATCAACAACAC 60.096 50.000 0.00 0.00 0.00 3.32
2948 3204 2.154963 CGACCACTACATCAACAACACG 59.845 50.000 0.00 0.00 0.00 4.49
3083 3339 2.404215 CACAACACCGTCTTCTTCGAT 58.596 47.619 0.00 0.00 0.00 3.59
3149 3405 4.329545 ACCGGCTGCATGTTCCGT 62.330 61.111 0.00 6.66 41.46 4.69
3281 3537 0.970937 TCAAGGCGGAGGACTTCGAT 60.971 55.000 3.80 0.00 40.42 3.59
3284 3540 2.956964 GCGGAGGACTTCGATGCG 60.957 66.667 3.80 0.00 0.00 4.73
3626 3882 2.280592 AAACGCGACGCCTTCCTT 60.281 55.556 15.93 0.00 0.00 3.36
3656 3912 0.391130 CCATCAACATGACCGACCGT 60.391 55.000 0.00 0.00 30.57 4.83
3694 3951 5.711976 ACTCCTTTCATTCGAACCATGAATT 59.288 36.000 12.18 0.00 39.76 2.17
3758 4026 4.221041 TGTGTTACCGGTGAATGACTATCA 59.779 41.667 19.93 0.00 0.00 2.15
4109 4377 2.125391 GCTCATCTCAGGCACGCA 60.125 61.111 0.00 0.00 0.00 5.24
4120 4388 1.133598 CAGGCACGCACATCATGAATT 59.866 47.619 0.00 0.00 0.00 2.17
4468 4736 4.103103 GGCGGCGGTTTCTTCAGC 62.103 66.667 9.78 0.00 0.00 4.26
4695 4966 6.630203 AATGTTACTTCCCTGGTGTATGTA 57.370 37.500 0.00 0.00 0.00 2.29
4712 4983 4.879197 ATGTATTGATCCTCGAGCATGA 57.121 40.909 6.99 0.00 0.00 3.07
4735 5006 2.311070 ATGCCAGCACCCATCCAGA 61.311 57.895 0.00 0.00 0.00 3.86
4761 5032 8.250538 TGGTGCATTATACAATACATGATACG 57.749 34.615 0.00 0.00 0.00 3.06
4776 5047 5.932303 ACATGATACGTGAGTTAGCAAAGTT 59.068 36.000 0.00 0.00 46.40 2.66
4786 5057 4.173256 AGTTAGCAAAGTTGTTGTGTTGC 58.827 39.130 0.00 0.00 45.29 4.17
4792 5063 2.825086 AGTTGTTGTGTTGCGTTCTC 57.175 45.000 0.00 0.00 0.00 2.87
4820 5095 5.701855 ACTTGTTCTCTCGTAGACTTAAGC 58.298 41.667 1.29 0.00 32.51 3.09
4859 5134 3.502123 TGAAACTTGAAAGGATCGGGT 57.498 42.857 0.00 0.00 0.00 5.28
4910 5185 6.173339 TCTAAAGCTGAAATTGGTCGAAGAT 58.827 36.000 0.00 0.00 40.67 2.40
4915 5190 6.640518 AGCTGAAATTGGTCGAAGATAACTA 58.359 36.000 0.00 0.00 40.67 2.24
4916 5191 6.758886 AGCTGAAATTGGTCGAAGATAACTAG 59.241 38.462 0.00 0.00 40.67 2.57
4920 5195 8.746530 TGAAATTGGTCGAAGATAACTAGTAGT 58.253 33.333 0.00 0.00 40.67 2.73
4929 5204 6.294787 CGAAGATAACTAGTAGTGCCATGGAT 60.295 42.308 18.40 2.45 0.00 3.41
4946 5221 5.179368 CCATGGATCGTAATATGTGGTGAAC 59.821 44.000 5.56 0.00 0.00 3.18
4949 5224 4.807304 GGATCGTAATATGTGGTGAACGTT 59.193 41.667 0.00 0.00 0.00 3.99
4950 5225 5.978919 GGATCGTAATATGTGGTGAACGTTA 59.021 40.000 0.00 0.00 0.00 3.18
4951 5226 6.143438 GGATCGTAATATGTGGTGAACGTTAG 59.857 42.308 0.00 0.00 0.00 2.34
4952 5227 6.193514 TCGTAATATGTGGTGAACGTTAGA 57.806 37.500 0.00 0.00 0.00 2.10
4953 5228 6.619744 TCGTAATATGTGGTGAACGTTAGAA 58.380 36.000 0.00 0.00 0.00 2.10
4954 5229 7.259882 TCGTAATATGTGGTGAACGTTAGAAT 58.740 34.615 0.00 0.00 0.00 2.40
4955 5230 7.760794 TCGTAATATGTGGTGAACGTTAGAATT 59.239 33.333 0.00 0.00 0.00 2.17
4956 5231 8.385111 CGTAATATGTGGTGAACGTTAGAATTT 58.615 33.333 0.00 0.00 0.00 1.82
4958 5233 8.964420 AATATGTGGTGAACGTTAGAATTTTG 57.036 30.769 0.00 0.00 0.00 2.44
4959 5234 5.176407 TGTGGTGAACGTTAGAATTTTGG 57.824 39.130 0.00 0.00 0.00 3.28
4960 5235 4.641094 TGTGGTGAACGTTAGAATTTTGGT 59.359 37.500 0.00 0.00 0.00 3.67
4961 5236 5.125739 TGTGGTGAACGTTAGAATTTTGGTT 59.874 36.000 0.00 0.00 0.00 3.67
4962 5237 6.037726 GTGGTGAACGTTAGAATTTTGGTTT 58.962 36.000 0.00 0.00 0.00 3.27
4963 5238 6.532302 GTGGTGAACGTTAGAATTTTGGTTTT 59.468 34.615 0.00 0.00 0.00 2.43
4964 5239 6.531948 TGGTGAACGTTAGAATTTTGGTTTTG 59.468 34.615 0.00 0.00 0.00 2.44
4965 5240 6.407623 GTGAACGTTAGAATTTTGGTTTTGC 58.592 36.000 0.00 0.00 0.00 3.68
4966 5241 6.254804 GTGAACGTTAGAATTTTGGTTTTGCT 59.745 34.615 0.00 0.00 0.00 3.91
4967 5242 7.432838 GTGAACGTTAGAATTTTGGTTTTGCTA 59.567 33.333 0.00 0.00 0.00 3.49
4968 5243 8.138712 TGAACGTTAGAATTTTGGTTTTGCTAT 58.861 29.630 0.00 0.00 0.00 2.97
4969 5244 8.880878 AACGTTAGAATTTTGGTTTTGCTATT 57.119 26.923 0.00 0.00 0.00 1.73
4970 5245 8.880878 ACGTTAGAATTTTGGTTTTGCTATTT 57.119 26.923 0.00 0.00 0.00 1.40
4971 5246 9.320352 ACGTTAGAATTTTGGTTTTGCTATTTT 57.680 25.926 0.00 0.00 0.00 1.82
4976 5251 9.394767 AGAATTTTGGTTTTGCTATTTTTCAGT 57.605 25.926 0.00 0.00 0.00 3.41
4977 5252 9.650371 GAATTTTGGTTTTGCTATTTTTCAGTC 57.350 29.630 0.00 0.00 0.00 3.51
4978 5253 6.820470 TTTGGTTTTGCTATTTTTCAGTCG 57.180 33.333 0.00 0.00 0.00 4.18
4979 5254 5.759506 TGGTTTTGCTATTTTTCAGTCGA 57.240 34.783 0.00 0.00 0.00 4.20
4980 5255 5.757886 TGGTTTTGCTATTTTTCAGTCGAG 58.242 37.500 0.00 0.00 0.00 4.04
4981 5256 5.298276 TGGTTTTGCTATTTTTCAGTCGAGT 59.702 36.000 0.00 0.00 0.00 4.18
4982 5257 5.625311 GGTTTTGCTATTTTTCAGTCGAGTG 59.375 40.000 14.33 14.33 0.00 3.51
4983 5258 6.427150 GTTTTGCTATTTTTCAGTCGAGTGA 58.573 36.000 18.99 18.99 0.00 3.41
4984 5259 6.801539 TTTGCTATTTTTCAGTCGAGTGAT 57.198 33.333 23.05 11.14 0.00 3.06
4985 5260 6.801539 TTGCTATTTTTCAGTCGAGTGATT 57.198 33.333 23.05 11.22 0.00 2.57
4986 5261 6.801539 TGCTATTTTTCAGTCGAGTGATTT 57.198 33.333 23.05 10.90 0.00 2.17
4987 5262 7.899178 TGCTATTTTTCAGTCGAGTGATTTA 57.101 32.000 23.05 11.59 0.00 1.40
4988 5263 7.739295 TGCTATTTTTCAGTCGAGTGATTTAC 58.261 34.615 23.05 10.11 0.00 2.01
4989 5264 7.386573 TGCTATTTTTCAGTCGAGTGATTTACA 59.613 33.333 23.05 12.28 0.00 2.41
4990 5265 7.900352 GCTATTTTTCAGTCGAGTGATTTACAG 59.100 37.037 23.05 17.18 0.00 2.74
4991 5266 7.730364 ATTTTTCAGTCGAGTGATTTACAGT 57.270 32.000 23.05 4.35 34.52 3.55
4992 5267 7.548196 TTTTTCAGTCGAGTGATTTACAGTT 57.452 32.000 23.05 0.00 31.63 3.16
4993 5268 6.525121 TTTCAGTCGAGTGATTTACAGTTG 57.475 37.500 23.05 0.00 35.29 3.16
4994 5269 4.556233 TCAGTCGAGTGATTTACAGTTGG 58.444 43.478 18.99 0.00 34.86 3.77
4995 5270 4.038763 TCAGTCGAGTGATTTACAGTTGGT 59.961 41.667 18.99 0.00 34.86 3.67
4996 5271 4.386049 CAGTCGAGTGATTTACAGTTGGTC 59.614 45.833 15.40 0.00 34.86 4.02
4997 5272 4.281182 AGTCGAGTGATTTACAGTTGGTCT 59.719 41.667 0.00 0.00 34.86 3.85
4998 5273 4.989168 GTCGAGTGATTTACAGTTGGTCTT 59.011 41.667 0.00 0.00 34.86 3.01
4999 5274 5.118817 GTCGAGTGATTTACAGTTGGTCTTC 59.881 44.000 0.00 0.00 34.86 2.87
5000 5275 4.988540 CGAGTGATTTACAGTTGGTCTTCA 59.011 41.667 0.00 0.00 31.63 3.02
5001 5276 5.639506 CGAGTGATTTACAGTTGGTCTTCAT 59.360 40.000 0.00 0.00 31.63 2.57
5002 5277 6.147821 CGAGTGATTTACAGTTGGTCTTCATT 59.852 38.462 0.00 0.00 31.63 2.57
5003 5278 7.440523 AGTGATTTACAGTTGGTCTTCATTC 57.559 36.000 0.00 0.00 0.00 2.67
5004 5279 6.998074 AGTGATTTACAGTTGGTCTTCATTCA 59.002 34.615 0.00 0.00 0.00 2.57
5005 5280 7.502226 AGTGATTTACAGTTGGTCTTCATTCAA 59.498 33.333 0.00 0.00 0.00 2.69
5006 5281 8.134895 GTGATTTACAGTTGGTCTTCATTCAAA 58.865 33.333 0.00 0.00 0.00 2.69
5007 5282 8.859090 TGATTTACAGTTGGTCTTCATTCAAAT 58.141 29.630 0.00 0.00 0.00 2.32
5008 5283 9.696917 GATTTACAGTTGGTCTTCATTCAAATT 57.303 29.630 0.00 0.00 0.00 1.82
5010 5285 8.870160 TTACAGTTGGTCTTCATTCAAATTTG 57.130 30.769 12.15 12.15 0.00 2.32
5011 5286 6.877236 ACAGTTGGTCTTCATTCAAATTTGT 58.123 32.000 17.47 0.00 0.00 2.83
5012 5287 6.757947 ACAGTTGGTCTTCATTCAAATTTGTG 59.242 34.615 17.47 9.89 0.00 3.33
5013 5288 6.979817 CAGTTGGTCTTCATTCAAATTTGTGA 59.020 34.615 17.47 12.01 0.00 3.58
5014 5289 6.980397 AGTTGGTCTTCATTCAAATTTGTGAC 59.020 34.615 17.47 14.76 0.00 3.67
5015 5290 5.841810 TGGTCTTCATTCAAATTTGTGACC 58.158 37.500 17.47 20.93 37.69 4.02
5016 5291 4.917415 GGTCTTCATTCAAATTTGTGACCG 59.083 41.667 17.47 8.82 32.59 4.79
5017 5292 4.382754 GTCTTCATTCAAATTTGTGACCGC 59.617 41.667 17.47 4.60 0.00 5.68
5018 5293 4.278170 TCTTCATTCAAATTTGTGACCGCT 59.722 37.500 17.47 0.00 0.00 5.52
5019 5294 4.159377 TCATTCAAATTTGTGACCGCTC 57.841 40.909 17.47 0.00 0.00 5.03
5020 5295 3.567585 TCATTCAAATTTGTGACCGCTCA 59.432 39.130 17.47 0.00 0.00 4.26
5021 5296 4.037327 TCATTCAAATTTGTGACCGCTCAA 59.963 37.500 17.47 2.21 0.00 3.02
5022 5297 4.582701 TTCAAATTTGTGACCGCTCAAT 57.417 36.364 17.47 0.00 0.00 2.57
5023 5298 4.159377 TCAAATTTGTGACCGCTCAATC 57.841 40.909 17.47 0.00 0.00 2.67
5024 5299 3.820467 TCAAATTTGTGACCGCTCAATCT 59.180 39.130 17.47 0.00 0.00 2.40
5025 5300 4.278170 TCAAATTTGTGACCGCTCAATCTT 59.722 37.500 17.47 0.00 0.00 2.40
5026 5301 3.837213 ATTTGTGACCGCTCAATCTTG 57.163 42.857 0.00 0.00 0.00 3.02
5027 5302 0.874390 TTGTGACCGCTCAATCTTGC 59.126 50.000 0.00 0.00 0.00 4.01
5032 5307 3.478226 CGCTCAATCTTGCGCAGA 58.522 55.556 11.31 11.19 45.50 4.26
5033 5308 2.012237 CGCTCAATCTTGCGCAGAT 58.988 52.632 11.31 13.12 45.03 2.90
5034 5309 1.211743 CGCTCAATCTTGCGCAGATA 58.788 50.000 11.31 0.00 41.93 1.98
5035 5310 1.797046 CGCTCAATCTTGCGCAGATAT 59.203 47.619 11.31 2.45 41.93 1.63
5036 5311 2.222678 CGCTCAATCTTGCGCAGATATT 59.777 45.455 11.31 9.12 41.93 1.28
5037 5312 3.663754 CGCTCAATCTTGCGCAGATATTC 60.664 47.826 11.31 5.91 41.93 1.75
5038 5313 3.663754 GCTCAATCTTGCGCAGATATTCG 60.664 47.826 11.31 6.55 41.93 3.34
5039 5314 3.457234 TCAATCTTGCGCAGATATTCGT 58.543 40.909 11.31 0.00 41.93 3.85
5040 5315 3.245990 TCAATCTTGCGCAGATATTCGTG 59.754 43.478 11.31 10.40 41.93 4.35
5041 5316 0.930310 TCTTGCGCAGATATTCGTGC 59.070 50.000 11.31 4.40 39.10 5.34
5042 5317 0.933097 CTTGCGCAGATATTCGTGCT 59.067 50.000 11.31 0.00 39.38 4.40
5043 5318 0.652071 TTGCGCAGATATTCGTGCTG 59.348 50.000 11.31 0.00 39.38 4.41
5044 5319 1.153597 TGCGCAGATATTCGTGCTGG 61.154 55.000 5.66 0.00 39.38 4.85
5045 5320 1.835483 GCGCAGATATTCGTGCTGGG 61.835 60.000 0.30 0.00 43.10 4.45
5046 5321 0.249447 CGCAGATATTCGTGCTGGGA 60.249 55.000 0.00 0.00 42.95 4.37
5047 5322 1.506493 GCAGATATTCGTGCTGGGAG 58.494 55.000 0.00 0.00 36.71 4.30
5048 5323 1.202580 GCAGATATTCGTGCTGGGAGT 60.203 52.381 0.00 0.00 36.71 3.85
5049 5324 2.743183 GCAGATATTCGTGCTGGGAGTT 60.743 50.000 0.00 0.00 36.71 3.01
5050 5325 2.868583 CAGATATTCGTGCTGGGAGTTG 59.131 50.000 0.00 0.00 0.00 3.16
5051 5326 2.158900 AGATATTCGTGCTGGGAGTTGG 60.159 50.000 0.00 0.00 0.00 3.77
5052 5327 0.981183 TATTCGTGCTGGGAGTTGGT 59.019 50.000 0.00 0.00 0.00 3.67
5053 5328 0.606401 ATTCGTGCTGGGAGTTGGTG 60.606 55.000 0.00 0.00 0.00 4.17
5054 5329 1.978455 TTCGTGCTGGGAGTTGGTGT 61.978 55.000 0.00 0.00 0.00 4.16
5055 5330 1.961277 CGTGCTGGGAGTTGGTGTC 60.961 63.158 0.00 0.00 0.00 3.67
5056 5331 1.451936 GTGCTGGGAGTTGGTGTCT 59.548 57.895 0.00 0.00 0.00 3.41
5057 5332 0.886490 GTGCTGGGAGTTGGTGTCTG 60.886 60.000 0.00 0.00 0.00 3.51
5086 5362 9.743581 TTTTTAGGGTAACTAGGGACTTTATTG 57.256 33.333 0.00 0.00 41.75 1.90
5218 5495 4.901197 TTGCTTCCCTACACTCATAACA 57.099 40.909 0.00 0.00 0.00 2.41
5293 5570 5.334182 CCAGCGAGTAAGAAGAAAAAGTTCC 60.334 44.000 0.00 0.00 33.92 3.62
5320 5597 5.537188 GTTTAAATCCATCACCACTTGCAA 58.463 37.500 0.00 0.00 0.00 4.08
5419 5697 3.503363 GCTCGCTGCATCCACCAC 61.503 66.667 0.00 0.00 42.31 4.16
5595 5873 7.524912 TCGATTCTCTGTACTTGTAGTGTTAC 58.475 38.462 0.00 0.00 0.00 2.50
5615 5893 0.250209 CCGCTGGCTTCATAGATGCT 60.250 55.000 5.12 0.00 33.95 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 228 5.008712 GTGGAAAGGAAAAACAACTCGATCT 59.991 40.000 0.00 0.00 0.00 2.75
321 323 2.124736 TTGAGGCCATAGCACGCC 60.125 61.111 5.01 0.00 46.09 5.68
408 412 2.086869 CAACAATTGCTCGATCTGGGT 58.913 47.619 5.05 0.00 0.00 4.51
409 413 2.838386 CAACAATTGCTCGATCTGGG 57.162 50.000 5.05 0.00 0.00 4.45
421 425 1.302511 AGTCTCCCGCGCAACAATT 60.303 52.632 8.75 0.00 0.00 2.32
449 453 1.487482 CGCTTATCGCTCGATCCAAA 58.513 50.000 8.14 0.00 36.17 3.28
464 468 4.554363 CGACCGCTCGATCCGCTT 62.554 66.667 0.00 0.00 43.06 4.68
471 475 1.805539 CAATTGCTCGACCGCTCGA 60.806 57.895 2.39 2.39 46.85 4.04
472 476 1.626654 AACAATTGCTCGACCGCTCG 61.627 55.000 5.05 0.00 41.65 5.03
473 477 0.179215 CAACAATTGCTCGACCGCTC 60.179 55.000 5.05 0.00 0.00 5.03
474 478 1.868997 CAACAATTGCTCGACCGCT 59.131 52.632 5.05 0.00 0.00 5.52
475 479 4.440214 CAACAATTGCTCGACCGC 57.560 55.556 5.05 0.00 0.00 5.68
484 488 1.154225 GTCTCCCGCGCAACAATTG 60.154 57.895 8.75 3.24 0.00 2.32
485 489 0.036765 TAGTCTCCCGCGCAACAATT 60.037 50.000 8.75 0.00 0.00 2.32
486 490 0.460284 CTAGTCTCCCGCGCAACAAT 60.460 55.000 8.75 0.00 0.00 2.71
487 491 1.080093 CTAGTCTCCCGCGCAACAA 60.080 57.895 8.75 0.00 0.00 2.83
508 512 5.452302 CGCTTATCGCTCGATTCAAATTTTT 59.548 36.000 10.18 0.00 36.17 1.94
509 513 4.963953 CGCTTATCGCTCGATTCAAATTTT 59.036 37.500 10.18 0.00 36.17 1.82
510 514 4.518217 CGCTTATCGCTCGATTCAAATTT 58.482 39.130 10.18 0.00 36.17 1.82
511 515 3.059597 CCGCTTATCGCTCGATTCAAATT 60.060 43.478 10.18 0.00 36.17 1.82
512 516 2.476619 CCGCTTATCGCTCGATTCAAAT 59.523 45.455 10.18 0.00 36.17 2.32
513 517 1.858458 CCGCTTATCGCTCGATTCAAA 59.142 47.619 10.18 0.00 36.17 2.69
514 518 1.066454 TCCGCTTATCGCTCGATTCAA 59.934 47.619 10.18 0.00 36.17 2.69
515 519 0.666374 TCCGCTTATCGCTCGATTCA 59.334 50.000 10.18 0.00 36.17 2.57
516 520 1.914700 GATCCGCTTATCGCTCGATTC 59.085 52.381 10.18 0.00 36.17 2.52
517 521 1.729472 CGATCCGCTTATCGCTCGATT 60.729 52.381 10.18 0.00 41.93 3.34
518 522 0.179187 CGATCCGCTTATCGCTCGAT 60.179 55.000 9.81 9.81 41.93 3.59
519 523 1.206831 CGATCCGCTTATCGCTCGA 59.793 57.895 4.86 0.00 41.93 4.04
520 524 0.791238 CTCGATCCGCTTATCGCTCG 60.791 60.000 11.45 0.00 46.51 5.03
521 525 1.068287 GCTCGATCCGCTTATCGCTC 61.068 60.000 11.45 3.89 46.51 5.03
522 526 1.081108 GCTCGATCCGCTTATCGCT 60.081 57.895 11.45 0.00 46.51 4.93
523 527 2.429351 CGCTCGATCCGCTTATCGC 61.429 63.158 11.45 0.51 46.51 4.58
528 532 4.554363 CGACCGCTCGATCCGCTT 62.554 66.667 0.00 0.00 43.06 4.68
561 565 0.667993 CGACTGGTGGTTTGCAACAT 59.332 50.000 0.00 0.00 0.00 2.71
620 624 4.083581 TCGAAAAAGATAGCAGCTTTGC 57.916 40.909 0.00 0.00 35.86 3.68
621 625 5.106948 TGACTCGAAAAAGATAGCAGCTTTG 60.107 40.000 0.00 0.00 35.86 2.77
622 626 4.997395 TGACTCGAAAAAGATAGCAGCTTT 59.003 37.500 0.00 0.00 37.18 3.51
623 627 4.390297 GTGACTCGAAAAAGATAGCAGCTT 59.610 41.667 0.00 0.00 0.00 3.74
624 628 3.929610 GTGACTCGAAAAAGATAGCAGCT 59.070 43.478 0.00 0.00 0.00 4.24
625 629 3.929610 AGTGACTCGAAAAAGATAGCAGC 59.070 43.478 0.00 0.00 0.00 5.25
626 630 6.473397 AAAGTGACTCGAAAAAGATAGCAG 57.527 37.500 0.00 0.00 0.00 4.24
627 631 5.118664 CGAAAGTGACTCGAAAAAGATAGCA 59.881 40.000 0.00 0.00 38.61 3.49
628 632 5.345202 TCGAAAGTGACTCGAAAAAGATAGC 59.655 40.000 0.00 0.00 42.07 2.97
629 633 6.802348 TCTCGAAAGTGACTCGAAAAAGATAG 59.198 38.462 0.00 0.00 44.18 2.08
630 634 6.675026 TCTCGAAAGTGACTCGAAAAAGATA 58.325 36.000 0.00 0.00 44.18 1.98
631 635 5.529791 TCTCGAAAGTGACTCGAAAAAGAT 58.470 37.500 0.00 0.00 44.18 2.40
632 636 4.928601 TCTCGAAAGTGACTCGAAAAAGA 58.071 39.130 0.00 0.00 44.18 2.52
633 637 5.637104 TTCTCGAAAGTGACTCGAAAAAG 57.363 39.130 0.00 0.00 44.18 2.27
634 638 6.598753 ATTTCTCGAAAGTGACTCGAAAAA 57.401 33.333 0.00 0.00 44.18 1.94
635 639 6.598753 AATTTCTCGAAAGTGACTCGAAAA 57.401 33.333 0.00 3.78 44.18 2.29
636 640 6.598753 AAATTTCTCGAAAGTGACTCGAAA 57.401 33.333 0.00 0.00 44.18 3.46
637 641 6.698329 TGTAAATTTCTCGAAAGTGACTCGAA 59.302 34.615 8.34 0.00 44.18 3.71
638 642 6.210796 TGTAAATTTCTCGAAAGTGACTCGA 58.789 36.000 8.34 0.00 42.75 4.04
649 653 4.214986 TGGAGCCATGTAAATTTCTCGA 57.785 40.909 0.00 0.00 0.00 4.04
681 685 5.397360 AGGAGAAGAAACCATGAACCAAAT 58.603 37.500 0.00 0.00 0.00 2.32
684 688 4.141274 TGAAGGAGAAGAAACCATGAACCA 60.141 41.667 0.00 0.00 0.00 3.67
686 690 4.216472 GGTGAAGGAGAAGAAACCATGAAC 59.784 45.833 0.00 0.00 0.00 3.18
688 692 3.394274 TGGTGAAGGAGAAGAAACCATGA 59.606 43.478 0.00 0.00 32.88 3.07
689 693 3.503748 GTGGTGAAGGAGAAGAAACCATG 59.496 47.826 0.00 0.00 39.70 3.66
690 694 3.138283 TGTGGTGAAGGAGAAGAAACCAT 59.862 43.478 0.00 0.00 39.70 3.55
691 695 2.507886 TGTGGTGAAGGAGAAGAAACCA 59.492 45.455 0.00 0.00 35.39 3.67
693 697 3.541632 TGTGTGGTGAAGGAGAAGAAAC 58.458 45.455 0.00 0.00 0.00 2.78
694 698 3.924114 TGTGTGGTGAAGGAGAAGAAA 57.076 42.857 0.00 0.00 0.00 2.52
737 741 6.916705 TGGCTATATTAAGGCACAAAGCAGAT 60.917 38.462 0.00 0.00 46.09 2.90
740 744 4.531854 TGGCTATATTAAGGCACAAAGCA 58.468 39.130 0.00 0.00 46.09 3.91
834 838 1.072930 GGGGAGGGATATGGTGGGT 60.073 63.158 0.00 0.00 0.00 4.51
925 1118 2.777972 CGCATGGCTGGGATGGTTG 61.778 63.158 0.00 0.00 37.51 3.77
1429 1622 2.267681 CTACACTCGCAGGGGTCGAC 62.268 65.000 7.13 7.13 32.08 4.20
1734 1927 1.743252 CTTCTGGCTCAAGTCCGCC 60.743 63.158 0.00 0.00 46.46 6.13
1735 1928 2.394563 GCTTCTGGCTCAAGTCCGC 61.395 63.158 0.00 0.00 38.06 5.54
1736 1929 1.743252 GGCTTCTGGCTCAAGTCCG 60.743 63.158 0.00 0.00 41.46 4.79
1737 1930 1.743252 CGGCTTCTGGCTCAAGTCC 60.743 63.158 0.00 0.00 41.46 3.85
1741 1934 0.179032 TTGAACGGCTTCTGGCTCAA 60.179 50.000 0.00 0.00 41.46 3.02
1745 1938 2.563427 GCTTGAACGGCTTCTGGC 59.437 61.111 0.00 0.00 40.90 4.85
1773 1966 0.030369 ACGTCGGCATCGGTATCTTC 59.970 55.000 0.00 0.00 36.95 2.87
1875 2068 1.522092 CCAGAGCGCCTCCATGTTA 59.478 57.895 2.29 0.00 0.00 2.41
2289 2482 0.612174 TGAGGGCGAAGTAGCTGTCT 60.612 55.000 0.00 0.00 37.29 3.41
2511 2704 2.838202 CCAGGTAGCCTTCTTCACCTTA 59.162 50.000 0.00 0.00 39.40 2.69
2595 2791 2.059190 TAGGATGCCGGCGTGGTTA 61.059 57.895 29.48 12.43 41.21 2.85
2624 2820 0.752658 TCCGGCGTGATGATTGAGAT 59.247 50.000 6.01 0.00 0.00 2.75
2661 2908 5.456497 GTCGATTAACATGTTTGATGCATGG 59.544 40.000 17.78 2.13 45.68 3.66
2664 2911 5.619625 TGTCGATTAACATGTTTGATGCA 57.380 34.783 17.78 6.84 0.00 3.96
2703 2959 2.513204 CGGCCTCAGCATCACCTG 60.513 66.667 0.00 0.00 42.56 4.00
2704 2960 4.479993 GCGGCCTCAGCATCACCT 62.480 66.667 0.00 0.00 42.56 4.00
2766 3022 2.733552 TGTCTACGTCACTGTAGTCGAC 59.266 50.000 7.70 7.70 42.01 4.20
2777 3033 2.282674 AGCCGGGTGTCTACGTCA 60.283 61.111 4.72 0.00 0.00 4.35
3158 3414 2.104530 GGGTCGAAGCCGTAGAGC 59.895 66.667 0.00 0.00 37.05 4.09
3197 3453 1.356124 TCTTCTTGAAGAGCCAGCCT 58.644 50.000 8.80 0.00 0.00 4.58
3518 3774 0.398522 AGCCGTAGATCCATCCCACA 60.399 55.000 0.00 0.00 0.00 4.17
3656 3912 0.764369 AGGAGTGAACCTGGTGCAGA 60.764 55.000 8.05 0.00 39.01 4.26
3758 4026 1.812571 GCAACACCTGATCGATGGTTT 59.187 47.619 0.54 0.00 33.75 3.27
4109 4377 6.699204 GTCGTCAGTATCAGAATTCATGATGT 59.301 38.462 21.11 11.48 37.91 3.06
4120 4388 3.562343 AGCTAGGTCGTCAGTATCAGA 57.438 47.619 0.00 0.00 0.00 3.27
4294 4562 3.119955 CGTAGATGTCCTCGTTGTCTTCA 60.120 47.826 0.00 0.00 0.00 3.02
4468 4736 0.449388 GATGAGCGAGCACCCAAAAG 59.551 55.000 0.00 0.00 0.00 2.27
4712 4983 1.682451 GATGGGTGCTGGCATGCATT 61.682 55.000 21.36 0.00 45.23 3.56
4718 4989 2.311070 ATCTGGATGGGTGCTGGCA 61.311 57.895 0.00 0.00 0.00 4.92
4735 5006 8.882736 CGTATCATGTATTGTATAATGCACCAT 58.117 33.333 5.17 3.81 40.83 3.55
4761 5032 4.981794 ACACAACAACTTTGCTAACTCAC 58.018 39.130 0.00 0.00 0.00 3.51
4776 5047 1.454201 TTGGAGAACGCAACACAACA 58.546 45.000 0.00 0.00 0.00 3.33
4854 5129 1.894466 TCTACGGAAACATTGACCCGA 59.106 47.619 17.71 5.98 44.29 5.14
4855 5130 2.268298 CTCTACGGAAACATTGACCCG 58.732 52.381 12.09 12.09 46.65 5.28
4910 5185 4.212716 ACGATCCATGGCACTACTAGTTA 58.787 43.478 6.96 0.00 0.00 2.24
4915 5190 5.246203 ACATATTACGATCCATGGCACTACT 59.754 40.000 6.96 0.00 0.00 2.57
4916 5191 5.348724 CACATATTACGATCCATGGCACTAC 59.651 44.000 6.96 0.00 0.00 2.73
4920 5195 3.072330 ACCACATATTACGATCCATGGCA 59.928 43.478 6.96 0.00 0.00 4.92
4929 5204 6.193514 TCTAACGTTCACCACATATTACGA 57.806 37.500 2.82 0.00 33.60 3.43
4950 5225 9.394767 ACTGAAAAATAGCAAAACCAAAATTCT 57.605 25.926 0.00 0.00 0.00 2.40
4951 5226 9.650371 GACTGAAAAATAGCAAAACCAAAATTC 57.350 29.630 0.00 0.00 0.00 2.17
4952 5227 8.334632 CGACTGAAAAATAGCAAAACCAAAATT 58.665 29.630 0.00 0.00 0.00 1.82
4953 5228 7.708752 TCGACTGAAAAATAGCAAAACCAAAAT 59.291 29.630 0.00 0.00 0.00 1.82
4954 5229 7.036220 TCGACTGAAAAATAGCAAAACCAAAA 58.964 30.769 0.00 0.00 0.00 2.44
4955 5230 6.565234 TCGACTGAAAAATAGCAAAACCAAA 58.435 32.000 0.00 0.00 0.00 3.28
4956 5231 6.137794 TCGACTGAAAAATAGCAAAACCAA 57.862 33.333 0.00 0.00 0.00 3.67
4957 5232 5.298276 ACTCGACTGAAAAATAGCAAAACCA 59.702 36.000 0.00 0.00 0.00 3.67
4958 5233 5.625311 CACTCGACTGAAAAATAGCAAAACC 59.375 40.000 0.00 0.00 0.00 3.27
4959 5234 6.427150 TCACTCGACTGAAAAATAGCAAAAC 58.573 36.000 0.00 0.00 0.00 2.43
4960 5235 6.612247 TCACTCGACTGAAAAATAGCAAAA 57.388 33.333 0.00 0.00 0.00 2.44
4961 5236 6.801539 ATCACTCGACTGAAAAATAGCAAA 57.198 33.333 0.00 0.00 0.00 3.68
4962 5237 6.801539 AATCACTCGACTGAAAAATAGCAA 57.198 33.333 0.00 0.00 0.00 3.91
4963 5238 6.801539 AAATCACTCGACTGAAAAATAGCA 57.198 33.333 0.00 0.00 0.00 3.49
4964 5239 7.739295 TGTAAATCACTCGACTGAAAAATAGC 58.261 34.615 0.00 0.00 0.00 2.97
4965 5240 8.926710 ACTGTAAATCACTCGACTGAAAAATAG 58.073 33.333 0.00 0.00 0.00 1.73
4966 5241 8.827177 ACTGTAAATCACTCGACTGAAAAATA 57.173 30.769 0.00 0.00 0.00 1.40
4967 5242 7.730364 ACTGTAAATCACTCGACTGAAAAAT 57.270 32.000 0.00 0.00 0.00 1.82
4968 5243 7.406553 CAACTGTAAATCACTCGACTGAAAAA 58.593 34.615 0.00 0.00 0.00 1.94
4969 5244 6.018262 CCAACTGTAAATCACTCGACTGAAAA 60.018 38.462 0.00 0.00 0.00 2.29
4970 5245 5.465390 CCAACTGTAAATCACTCGACTGAAA 59.535 40.000 0.00 0.00 0.00 2.69
4971 5246 4.988540 CCAACTGTAAATCACTCGACTGAA 59.011 41.667 0.00 0.00 0.00 3.02
4972 5247 4.038763 ACCAACTGTAAATCACTCGACTGA 59.961 41.667 0.00 0.00 0.00 3.41
4973 5248 4.307432 ACCAACTGTAAATCACTCGACTG 58.693 43.478 0.00 0.00 0.00 3.51
4974 5249 4.281182 AGACCAACTGTAAATCACTCGACT 59.719 41.667 0.00 0.00 0.00 4.18
4975 5250 4.557205 AGACCAACTGTAAATCACTCGAC 58.443 43.478 0.00 0.00 0.00 4.20
4976 5251 4.866508 AGACCAACTGTAAATCACTCGA 57.133 40.909 0.00 0.00 0.00 4.04
4977 5252 4.988540 TGAAGACCAACTGTAAATCACTCG 59.011 41.667 0.00 0.00 0.00 4.18
4978 5253 7.173218 TGAATGAAGACCAACTGTAAATCACTC 59.827 37.037 0.00 0.00 0.00 3.51
4979 5254 6.998074 TGAATGAAGACCAACTGTAAATCACT 59.002 34.615 0.00 0.00 0.00 3.41
4980 5255 7.202016 TGAATGAAGACCAACTGTAAATCAC 57.798 36.000 0.00 0.00 0.00 3.06
4981 5256 7.815840 TTGAATGAAGACCAACTGTAAATCA 57.184 32.000 0.00 0.00 0.00 2.57
4982 5257 9.696917 AATTTGAATGAAGACCAACTGTAAATC 57.303 29.630 0.00 0.00 0.00 2.17
4984 5259 9.311916 CAAATTTGAATGAAGACCAACTGTAAA 57.688 29.630 13.08 0.00 0.00 2.01
4985 5260 8.474025 ACAAATTTGAATGAAGACCAACTGTAA 58.526 29.630 24.64 0.00 0.00 2.41
4986 5261 7.920151 CACAAATTTGAATGAAGACCAACTGTA 59.080 33.333 24.64 0.00 0.00 2.74
4987 5262 6.757947 CACAAATTTGAATGAAGACCAACTGT 59.242 34.615 24.64 0.00 0.00 3.55
4988 5263 6.979817 TCACAAATTTGAATGAAGACCAACTG 59.020 34.615 24.64 7.18 0.00 3.16
4989 5264 6.980397 GTCACAAATTTGAATGAAGACCAACT 59.020 34.615 24.64 0.00 0.00 3.16
4990 5265 6.200854 GGTCACAAATTTGAATGAAGACCAAC 59.799 38.462 24.64 5.77 41.00 3.77
4991 5266 6.279882 GGTCACAAATTTGAATGAAGACCAA 58.720 36.000 24.64 0.00 41.00 3.67
4992 5267 5.507149 CGGTCACAAATTTGAATGAAGACCA 60.507 40.000 24.64 0.00 41.18 4.02
4993 5268 4.917415 CGGTCACAAATTTGAATGAAGACC 59.083 41.667 24.64 23.14 39.54 3.85
4994 5269 4.382754 GCGGTCACAAATTTGAATGAAGAC 59.617 41.667 24.64 17.99 0.00 3.01
4995 5270 4.278170 AGCGGTCACAAATTTGAATGAAGA 59.722 37.500 24.64 9.07 0.00 2.87
4996 5271 4.549458 AGCGGTCACAAATTTGAATGAAG 58.451 39.130 24.64 15.21 0.00 3.02
4997 5272 4.037327 TGAGCGGTCACAAATTTGAATGAA 59.963 37.500 24.64 0.53 0.00 2.57
4998 5273 3.567585 TGAGCGGTCACAAATTTGAATGA 59.432 39.130 24.64 15.24 0.00 2.57
4999 5274 3.899734 TGAGCGGTCACAAATTTGAATG 58.100 40.909 24.64 13.17 0.00 2.67
5000 5275 4.582701 TTGAGCGGTCACAAATTTGAAT 57.417 36.364 24.64 0.00 30.10 2.57
5001 5276 4.278170 AGATTGAGCGGTCACAAATTTGAA 59.722 37.500 24.64 9.32 30.10 2.69
5002 5277 3.820467 AGATTGAGCGGTCACAAATTTGA 59.180 39.130 24.64 0.00 30.10 2.69
5003 5278 4.164822 AGATTGAGCGGTCACAAATTTG 57.835 40.909 18.42 16.67 30.10 2.32
5004 5279 4.549458 CAAGATTGAGCGGTCACAAATTT 58.451 39.130 18.42 0.62 30.10 1.82
5005 5280 3.612479 GCAAGATTGAGCGGTCACAAATT 60.612 43.478 18.42 7.23 30.10 1.82
5006 5281 2.095059 GCAAGATTGAGCGGTCACAAAT 60.095 45.455 18.42 8.51 30.10 2.32
5007 5282 1.266718 GCAAGATTGAGCGGTCACAAA 59.733 47.619 18.42 2.91 30.10 2.83
5008 5283 0.874390 GCAAGATTGAGCGGTCACAA 59.126 50.000 18.42 3.77 30.10 3.33
5009 5284 2.543578 GCAAGATTGAGCGGTCACA 58.456 52.632 18.42 9.27 30.10 3.58
5017 5292 3.492383 ACGAATATCTGCGCAAGATTGAG 59.508 43.478 21.71 14.28 43.52 3.02
5018 5293 3.245990 CACGAATATCTGCGCAAGATTGA 59.754 43.478 21.71 12.25 43.52 2.57
5019 5294 3.538780 CACGAATATCTGCGCAAGATTG 58.461 45.455 21.71 12.91 43.52 2.67
5020 5295 2.032549 GCACGAATATCTGCGCAAGATT 60.033 45.455 21.71 16.23 43.52 2.40
5022 5297 0.930310 GCACGAATATCTGCGCAAGA 59.070 50.000 13.05 11.87 39.94 3.02
5023 5298 0.933097 AGCACGAATATCTGCGCAAG 59.067 50.000 13.05 5.99 38.51 4.01
5024 5299 0.652071 CAGCACGAATATCTGCGCAA 59.348 50.000 13.05 2.72 38.51 4.85
5025 5300 1.153597 CCAGCACGAATATCTGCGCA 61.154 55.000 10.98 10.98 38.51 6.09
5026 5301 1.566563 CCAGCACGAATATCTGCGC 59.433 57.895 0.00 0.00 38.51 6.09
5027 5302 0.249447 TCCCAGCACGAATATCTGCG 60.249 55.000 0.00 0.00 38.51 5.18
5028 5303 1.202580 ACTCCCAGCACGAATATCTGC 60.203 52.381 0.00 0.00 0.00 4.26
5029 5304 2.868583 CAACTCCCAGCACGAATATCTG 59.131 50.000 0.00 0.00 0.00 2.90
5030 5305 2.158900 CCAACTCCCAGCACGAATATCT 60.159 50.000 0.00 0.00 0.00 1.98
5031 5306 2.213499 CCAACTCCCAGCACGAATATC 58.787 52.381 0.00 0.00 0.00 1.63
5032 5307 1.559682 ACCAACTCCCAGCACGAATAT 59.440 47.619 0.00 0.00 0.00 1.28
5033 5308 0.981183 ACCAACTCCCAGCACGAATA 59.019 50.000 0.00 0.00 0.00 1.75
5034 5309 0.606401 CACCAACTCCCAGCACGAAT 60.606 55.000 0.00 0.00 0.00 3.34
5035 5310 1.227823 CACCAACTCCCAGCACGAA 60.228 57.895 0.00 0.00 0.00 3.85
5036 5311 2.377628 GACACCAACTCCCAGCACGA 62.378 60.000 0.00 0.00 0.00 4.35
5037 5312 1.961277 GACACCAACTCCCAGCACG 60.961 63.158 0.00 0.00 0.00 5.34
5038 5313 0.886490 CAGACACCAACTCCCAGCAC 60.886 60.000 0.00 0.00 0.00 4.40
5039 5314 1.344953 ACAGACACCAACTCCCAGCA 61.345 55.000 0.00 0.00 0.00 4.41
5040 5315 0.179018 AACAGACACCAACTCCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
5041 5316 2.348411 AAACAGACACCAACTCCCAG 57.652 50.000 0.00 0.00 0.00 4.45
5042 5317 2.818751 AAAACAGACACCAACTCCCA 57.181 45.000 0.00 0.00 0.00 4.37
5086 5362 0.951558 TGCTCCGGCTTTGAACTTTC 59.048 50.000 0.00 0.00 39.59 2.62
5293 5570 4.261801 AGTGGTGATGGATTTAAACGGAG 58.738 43.478 0.00 0.00 0.00 4.63
5320 5597 1.000827 CGATGATAGCTTCGGACTGCT 60.001 52.381 8.28 9.22 42.67 4.24
5498 5776 1.407437 GGGGCTATATCTCGCAATGGG 60.407 57.143 0.00 0.00 0.00 4.00
5595 5873 1.233285 GCATCTATGAAGCCAGCGGG 61.233 60.000 0.00 0.00 37.18 6.13
5615 5893 1.951209 TGGAGGACCTGAACATAGCA 58.049 50.000 0.00 0.00 37.04 3.49


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

AutoCloner maintained by Alex Coulton.