Multiple sequence alignment - TraesCS3D01G395000

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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 TraesCS3D01G395000 chr3D 100.000 4775 0 0 1 4775 510311168 510306394 0.000000e+00 8818.0
1 TraesCS3D01G395000 chr3A 89.310 4200 255 95 570 4672 647194095 647189993 0.000000e+00 5090.0
2 TraesCS3D01G395000 chr3A 82.675 329 52 5 4383 4709 93293517 93293842 2.170000e-73 287.0
3 TraesCS3D01G395000 chr3B 93.585 2229 90 29 1537 3732 672405230 672403022 0.000000e+00 3275.0
4 TraesCS3D01G395000 chr3B 96.224 927 29 3 574 1498 672406381 672405459 0.000000e+00 1513.0
5 TraesCS3D01G395000 chr3B 88.432 389 22 15 3724 4093 672402999 672402615 9.430000e-122 448.0
6 TraesCS3D01G395000 chr3B 84.498 329 47 4 4383 4709 817456501 817456175 5.960000e-84 322.0
7 TraesCS3D01G395000 chr7B 91.993 537 36 2 24 553 723313719 723313183 0.000000e+00 747.0
8 TraesCS3D01G395000 chr7B 88.983 118 13 0 4269 4386 265166837 265166954 3.850000e-31 147.0
9 TraesCS3D01G395000 chr1D 92.164 536 31 4 24 553 467989615 467990145 0.000000e+00 747.0
10 TraesCS3D01G395000 chr1D 87.342 316 30 6 1667 1980 71767168 71766861 2.110000e-93 353.0
11 TraesCS3D01G395000 chr6A 91.636 538 37 3 24 553 401174905 401175442 0.000000e+00 737.0
12 TraesCS3D01G395000 chr6A 91.215 535 34 6 30 553 108949005 108948473 0.000000e+00 715.0
13 TraesCS3D01G395000 chr6A 84.494 316 43 6 4388 4701 617188413 617188102 1.670000e-79 307.0
14 TraesCS3D01G395000 chr6A 82.659 346 46 12 4368 4709 76942595 76942260 1.300000e-75 294.0
15 TraesCS3D01G395000 chr6A 82.675 329 52 5 4383 4709 403342438 403342763 2.170000e-73 287.0
16 TraesCS3D01G395000 chr6A 82.036 334 50 9 4383 4709 158925245 158924915 4.710000e-70 276.0
17 TraesCS3D01G395000 chr6A 79.455 404 67 11 2804 3202 23476900 23476508 6.090000e-69 272.0
18 TraesCS3D01G395000 chr6A 91.509 106 9 0 4269 4374 335752885 335752990 3.850000e-31 147.0
19 TraesCS3D01G395000 chr7A 91.312 541 33 5 20 553 625735997 625736530 0.000000e+00 726.0
20 TraesCS3D01G395000 chr7A 80.198 404 63 11 2801 3198 88967576 88967968 2.170000e-73 287.0
21 TraesCS3D01G395000 chr7A 91.589 107 9 0 4269 4375 6851637 6851531 1.070000e-31 148.0
22 TraesCS3D01G395000 chr5D 90.520 538 41 4 24 553 266688715 266689250 0.000000e+00 702.0
23 TraesCS3D01G395000 chr5D 90.602 532 43 2 27 551 4602213 4602744 0.000000e+00 699.0
24 TraesCS3D01G395000 chr5D 81.132 106 11 5 2611 2707 78604559 78604454 5.120000e-10 76.8
25 TraesCS3D01G395000 chr5D 85.484 62 8 1 4714 4775 432691977 432692037 3.990000e-06 63.9
26 TraesCS3D01G395000 chr4A 90.503 537 44 2 24 553 689216723 689216187 0.000000e+00 702.0
27 TraesCS3D01G395000 chr1A 90.485 536 45 1 24 553 260954894 260954359 0.000000e+00 702.0
28 TraesCS3D01G395000 chr1B 88.169 355 32 6 1667 2019 113023436 113023090 9.560000e-112 414.0
29 TraesCS3D01G395000 chr2D 82.468 462 58 13 4269 4709 422733613 422733154 2.700000e-102 383.0
30 TraesCS3D01G395000 chr6B 82.317 328 52 6 4383 4709 637011981 637011659 3.640000e-71 279.0
31 TraesCS3D01G395000 chr6B 82.609 230 40 0 1244 1473 444542580 444542351 2.250000e-48 204.0
32 TraesCS3D01G395000 chr6B 88.525 122 14 0 4268 4389 501658333 501658212 1.070000e-31 148.0
33 TraesCS3D01G395000 chrUn 79.455 404 67 11 2804 3202 376945435 376945043 6.090000e-69 272.0
34 TraesCS3D01G395000 chrUn 79.361 407 68 11 2801 3202 377019146 377019541 6.090000e-69 272.0
35 TraesCS3D01G395000 chrUn 79.115 407 69 11 2801 3202 452302119 452302514 2.830000e-67 267.0
36 TraesCS3D01G395000 chrUn 91.765 85 5 1 2804 2886 369384308 369384224 3.020000e-22 117.0
37 TraesCS3D01G395000 chrUn 90.909 88 6 1 2801 2886 383861098 383861185 3.020000e-22 117.0
38 TraesCS3D01G395000 chr5A 89.256 121 13 0 4269 4389 40757650 40757530 8.280000e-33 152.0
39 TraesCS3D01G395000 chr4D 90.654 107 10 0 4269 4375 270382993 270382887 4.980000e-30 143.0
40 TraesCS3D01G395000 chr2A 87.705 122 15 0 4268 4389 570055884 570055763 4.980000e-30 143.0
41 TraesCS3D01G395000 chr2A 87.603 121 14 1 4269 4389 617549092 617548973 6.440000e-29 139.0


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 TraesCS3D01G395000 chr3D 510306394 510311168 4774 True 8818.000000 8818 100.000 1 4775 1 chr3D.!!$R1 4774
1 TraesCS3D01G395000 chr3A 647189993 647194095 4102 True 5090.000000 5090 89.310 570 4672 1 chr3A.!!$R1 4102
2 TraesCS3D01G395000 chr3B 672402615 672406381 3766 True 1745.333333 3275 92.747 574 4093 3 chr3B.!!$R2 3519
3 TraesCS3D01G395000 chr7B 723313183 723313719 536 True 747.000000 747 91.993 24 553 1 chr7B.!!$R1 529
4 TraesCS3D01G395000 chr1D 467989615 467990145 530 False 747.000000 747 92.164 24 553 1 chr1D.!!$F1 529
5 TraesCS3D01G395000 chr6A 401174905 401175442 537 False 737.000000 737 91.636 24 553 1 chr6A.!!$F2 529
6 TraesCS3D01G395000 chr6A 108948473 108949005 532 True 715.000000 715 91.215 30 553 1 chr6A.!!$R3 523
7 TraesCS3D01G395000 chr7A 625735997 625736530 533 False 726.000000 726 91.312 20 553 1 chr7A.!!$F2 533
8 TraesCS3D01G395000 chr5D 266688715 266689250 535 False 702.000000 702 90.520 24 553 1 chr5D.!!$F2 529
9 TraesCS3D01G395000 chr5D 4602213 4602744 531 False 699.000000 699 90.602 27 551 1 chr5D.!!$F1 524
10 TraesCS3D01G395000 chr4A 689216187 689216723 536 True 702.000000 702 90.503 24 553 1 chr4A.!!$R1 529
11 TraesCS3D01G395000 chr1A 260954359 260954894 535 True 702.000000 702 90.485 24 553 1 chr1A.!!$R1 529

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
542 554 0.764752 GCTCTACCCTGCCCATACCT 60.765 60.000 0.00 0.0 0.00 3.08 F
787 807 1.286553 TCCTCTCCTCCTCCACTTCTC 59.713 57.143 0.00 0.0 0.00 2.87 F
1665 1885 1.453197 GTGGAAAGGCCCCGGTATG 60.453 63.158 0.00 0.0 34.97 2.39 F
1970 2193 0.609681 GGGGGAATTAACGGTGTGCA 60.610 55.000 0.00 0.0 0.00 4.57 F
3163 3391 0.037232 AGGTCAGTACGCCTTTCTGC 60.037 55.000 1.63 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1817 0.250124 TGTGGCCGTAACACTTGGAG 60.250 55.000 0.00 0.00 39.52 3.86 R
1712 1932 1.134128 TGGACCACGAATCCATCCATG 60.134 52.381 0.00 0.00 41.47 3.66 R
2799 3027 1.243902 AAAGTACGGCACAACCATGG 58.756 50.000 11.19 11.19 39.03 3.66 R
3745 4040 0.512952 CCGAAACAAACGCAGAGAGG 59.487 55.000 0.00 0.00 0.00 3.69 R
4711 5077 0.108207 TCCCGGCTCGGTTTGTTTAA 59.892 50.000 11.85 0.00 46.80 1.52 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
39 40 7.126268 AGCTTTCCTAAAGGATGGCAATTTTAT 59.874 33.333 19.13 2.14 44.98 1.40
46 47 4.818447 AGGATGGCAATTTTATCCATGGA 58.182 39.130 18.88 18.88 42.23 3.41
406 412 6.614694 ACATGTGTACTATTTGTCCTACCA 57.385 37.500 0.00 0.00 0.00 3.25
410 416 5.953548 TGTGTACTATTTGTCCTACCAGCTA 59.046 40.000 0.00 0.00 0.00 3.32
412 418 6.320672 GTGTACTATTTGTCCTACCAGCTAGA 59.679 42.308 0.00 0.00 0.00 2.43
506 518 5.981088 TTTTGTACCCACTGACTATACGA 57.019 39.130 0.00 0.00 0.00 3.43
518 530 7.122204 CCACTGACTATACGAATATGGGTATGA 59.878 40.741 8.47 0.00 32.05 2.15
542 554 0.764752 GCTCTACCCTGCCCATACCT 60.765 60.000 0.00 0.00 0.00 3.08
545 557 3.314693 CTCTACCCTGCCCATACCTTAA 58.685 50.000 0.00 0.00 0.00 1.85
553 565 2.291865 TGCCCATACCTTAACCATTGCA 60.292 45.455 0.00 0.00 0.00 4.08
554 566 2.965147 GCCCATACCTTAACCATTGCAT 59.035 45.455 0.00 0.00 0.00 3.96
555 567 3.387699 GCCCATACCTTAACCATTGCATT 59.612 43.478 0.00 0.00 0.00 3.56
556 568 4.141733 GCCCATACCTTAACCATTGCATTT 60.142 41.667 0.00 0.00 0.00 2.32
557 569 5.600696 CCCATACCTTAACCATTGCATTTC 58.399 41.667 0.00 0.00 0.00 2.17
558 570 5.453198 CCCATACCTTAACCATTGCATTTCC 60.453 44.000 0.00 0.00 0.00 3.13
559 571 5.363580 CCATACCTTAACCATTGCATTTCCT 59.636 40.000 0.00 0.00 0.00 3.36
560 572 6.549364 CCATACCTTAACCATTGCATTTCCTA 59.451 38.462 0.00 0.00 0.00 2.94
561 573 5.914898 ACCTTAACCATTGCATTTCCTAC 57.085 39.130 0.00 0.00 0.00 3.18
562 574 5.580022 ACCTTAACCATTGCATTTCCTACT 58.420 37.500 0.00 0.00 0.00 2.57
563 575 5.652452 ACCTTAACCATTGCATTTCCTACTC 59.348 40.000 0.00 0.00 0.00 2.59
564 576 5.220854 CCTTAACCATTGCATTTCCTACTCG 60.221 44.000 0.00 0.00 0.00 4.18
565 577 2.643551 ACCATTGCATTTCCTACTCGG 58.356 47.619 0.00 0.00 0.00 4.63
566 578 2.026262 ACCATTGCATTTCCTACTCGGT 60.026 45.455 0.00 0.00 0.00 4.69
567 579 3.016736 CCATTGCATTTCCTACTCGGTT 58.983 45.455 0.00 0.00 0.00 4.44
568 580 3.443681 CCATTGCATTTCCTACTCGGTTT 59.556 43.478 0.00 0.00 0.00 3.27
569 581 4.414852 CATTGCATTTCCTACTCGGTTTG 58.585 43.478 0.00 0.00 0.00 2.93
570 582 2.432444 TGCATTTCCTACTCGGTTTGG 58.568 47.619 0.00 0.00 0.00 3.28
571 583 2.224670 TGCATTTCCTACTCGGTTTGGT 60.225 45.455 0.00 0.00 0.00 3.67
572 584 2.817844 GCATTTCCTACTCGGTTTGGTT 59.182 45.455 0.00 0.00 0.00 3.67
573 585 3.119955 GCATTTCCTACTCGGTTTGGTTC 60.120 47.826 0.00 0.00 0.00 3.62
574 586 4.324267 CATTTCCTACTCGGTTTGGTTCT 58.676 43.478 0.00 0.00 0.00 3.01
575 587 3.396260 TTCCTACTCGGTTTGGTTCTG 57.604 47.619 0.00 0.00 0.00 3.02
576 588 2.600790 TCCTACTCGGTTTGGTTCTGA 58.399 47.619 0.00 0.00 0.00 3.27
577 589 2.298163 TCCTACTCGGTTTGGTTCTGAC 59.702 50.000 0.00 0.00 0.00 3.51
578 590 2.299297 CCTACTCGGTTTGGTTCTGACT 59.701 50.000 0.00 0.00 0.00 3.41
583 595 1.796459 CGGTTTGGTTCTGACTTACCG 59.204 52.381 0.00 0.00 37.48 4.02
669 686 1.530183 GCTCCATCCCATGCTTCCC 60.530 63.158 0.00 0.00 0.00 3.97
739 756 1.764571 TTCCGTCCACTCCACCCTTG 61.765 60.000 0.00 0.00 0.00 3.61
787 807 1.286553 TCCTCTCCTCCTCCACTTCTC 59.713 57.143 0.00 0.00 0.00 2.87
910 930 4.735132 CGCCCACACCACGATCGT 62.735 66.667 16.60 16.60 0.00 3.73
912 932 1.964373 GCCCACACCACGATCGTTT 60.964 57.895 20.14 5.56 0.00 3.60
923 943 2.929398 CACGATCGTTTCATCCATCACA 59.071 45.455 20.14 0.00 0.00 3.58
1499 1529 1.905894 TCAACCATCCGAGTTCATCCA 59.094 47.619 0.00 0.00 0.00 3.41
1500 1530 2.304470 TCAACCATCCGAGTTCATCCAA 59.696 45.455 0.00 0.00 0.00 3.53
1502 1532 3.652057 ACCATCCGAGTTCATCCAAAT 57.348 42.857 0.00 0.00 0.00 2.32
1504 1534 5.110814 ACCATCCGAGTTCATCCAAATAA 57.889 39.130 0.00 0.00 0.00 1.40
1507 1537 6.263168 ACCATCCGAGTTCATCCAAATAATTC 59.737 38.462 0.00 0.00 0.00 2.17
1512 1542 7.339212 TCCGAGTTCATCCAAATAATTCAACAT 59.661 33.333 0.00 0.00 0.00 2.71
1513 1543 8.620416 CCGAGTTCATCCAAATAATTCAACATA 58.380 33.333 0.00 0.00 0.00 2.29
1571 1791 3.620374 CGATGTCTCATTGGTTTCTCTGG 59.380 47.826 0.00 0.00 0.00 3.86
1588 1808 4.772624 TCTCTGGTCATGTATATGTAGGCC 59.227 45.833 0.00 0.00 35.73 5.19
1665 1885 1.453197 GTGGAAAGGCCCCGGTATG 60.453 63.158 0.00 0.00 34.97 2.39
1692 1912 3.503363 TGTCTTTCCATCACATCAACTGC 59.497 43.478 0.00 0.00 0.00 4.40
1712 1932 5.138125 TGCCTCTTTGATTTGTTTGATCC 57.862 39.130 0.00 0.00 0.00 3.36
1713 1933 4.588106 TGCCTCTTTGATTTGTTTGATCCA 59.412 37.500 0.00 0.00 0.00 3.41
1714 1934 5.246656 TGCCTCTTTGATTTGTTTGATCCAT 59.753 36.000 0.00 0.00 0.00 3.41
1715 1935 5.579511 GCCTCTTTGATTTGTTTGATCCATG 59.420 40.000 0.00 0.00 0.00 3.66
1737 1957 0.690192 TGGATTCGTGGTCCATGTGT 59.310 50.000 10.97 1.15 40.72 3.72
1750 1970 2.300152 TCCATGTGTTGGTCTCTGTCTC 59.700 50.000 0.00 0.00 46.52 3.36
1751 1971 2.301296 CCATGTGTTGGTCTCTGTCTCT 59.699 50.000 0.00 0.00 40.99 3.10
1752 1972 3.583806 CATGTGTTGGTCTCTGTCTCTC 58.416 50.000 0.00 0.00 0.00 3.20
1756 1976 2.887783 TGTTGGTCTCTGTCTCTCTGAC 59.112 50.000 0.00 0.00 45.54 3.51
1762 1982 2.832733 TCTCTGTCTCTCTGACCGTCTA 59.167 50.000 0.00 0.00 44.75 2.59
1907 2128 7.967303 GTGCAATTTGTTTTCTTTCCATTTTCA 59.033 29.630 0.00 0.00 0.00 2.69
1908 2129 8.182881 TGCAATTTGTTTTCTTTCCATTTTCAG 58.817 29.630 0.00 0.00 0.00 3.02
1970 2193 0.609681 GGGGGAATTAACGGTGTGCA 60.610 55.000 0.00 0.00 0.00 4.57
2095 2318 4.458397 TGCAGATCTCAATCCTCAATTCC 58.542 43.478 0.00 0.00 31.78 3.01
2117 2340 0.698818 ACCCTAAAGAGCCCAACCAG 59.301 55.000 0.00 0.00 0.00 4.00
2128 2351 5.201243 AGAGCCCAACCAGTTTATTTATCC 58.799 41.667 0.00 0.00 0.00 2.59
2207 2432 1.218316 GTTCGAGAAGGTCCGGCAT 59.782 57.895 0.00 0.00 0.00 4.40
2342 2567 9.144298 GGCCATTATATCTAGCTTACATACCTA 57.856 37.037 0.00 0.00 0.00 3.08
2522 2747 7.448588 TCTTTGAAAATTGAAACATGTGTCG 57.551 32.000 11.43 0.00 0.00 4.35
2713 2939 1.203287 GAGGAAATGAAGCAACCTGGC 59.797 52.381 0.00 0.00 0.00 4.85
2720 2948 1.527433 GAAGCAACCTGGCCTTGTCC 61.527 60.000 3.32 0.00 0.00 4.02
2781 3009 2.605338 GCGCACGCATATTTGGATGATT 60.605 45.455 10.65 0.00 41.49 2.57
2785 3013 4.023792 GCACGCATATTTGGATGATTCAGA 60.024 41.667 0.00 0.00 0.00 3.27
2786 3014 5.506151 GCACGCATATTTGGATGATTCAGAA 60.506 40.000 0.00 0.00 0.00 3.02
2988 3216 2.300437 AGTAAGTCCACTCTCAGCAACC 59.700 50.000 0.00 0.00 0.00 3.77
3023 3251 6.345644 CGAGAATCATTTCAGATAGTGCTTCG 60.346 42.308 0.00 0.00 34.08 3.79
3024 3252 5.236047 AGAATCATTTCAGATAGTGCTTCGC 59.764 40.000 0.00 0.00 34.08 4.70
3030 3258 1.134995 CAGATAGTGCTTCGCCTGACA 60.135 52.381 0.00 0.00 0.00 3.58
3033 3261 1.795768 TAGTGCTTCGCCTGACAAAG 58.204 50.000 0.00 0.00 0.00 2.77
3036 3264 0.819259 TGCTTCGCCTGACAAAGCTT 60.819 50.000 10.18 0.00 44.45 3.74
3043 3271 2.927477 CGCCTGACAAAGCTTAATCGTA 59.073 45.455 0.00 0.00 0.00 3.43
3046 3274 5.107133 GCCTGACAAAGCTTAATCGTACTA 58.893 41.667 0.00 0.00 0.00 1.82
3050 3278 7.042658 CCTGACAAAGCTTAATCGTACTATTCC 60.043 40.741 0.00 0.00 0.00 3.01
3154 3382 3.376234 TCATCCTTTACGAGGTCAGTACG 59.624 47.826 0.00 0.00 46.39 3.67
3155 3383 1.470098 TCCTTTACGAGGTCAGTACGC 59.530 52.381 0.00 0.00 46.39 4.42
3163 3391 0.037232 AGGTCAGTACGCCTTTCTGC 60.037 55.000 1.63 0.00 0.00 4.26
3169 3397 2.108168 AGTACGCCTTTCTGCTCCATA 58.892 47.619 0.00 0.00 0.00 2.74
3171 3399 3.895656 AGTACGCCTTTCTGCTCCATATA 59.104 43.478 0.00 0.00 0.00 0.86
3172 3400 4.528596 AGTACGCCTTTCTGCTCCATATAT 59.471 41.667 0.00 0.00 0.00 0.86
3174 3402 2.417933 CGCCTTTCTGCTCCATATATGC 59.582 50.000 7.24 0.00 0.00 3.14
3175 3403 3.415212 GCCTTTCTGCTCCATATATGCA 58.585 45.455 7.24 1.77 35.30 3.96
3218 3446 2.568956 AGCAGAGCAGAGAACATTACCA 59.431 45.455 0.00 0.00 0.00 3.25
3248 3476 7.180748 GGTTTCAGACTTGATAACTTAATCGC 58.819 38.462 0.00 0.00 32.27 4.58
3263 3491 1.062364 ATCGCCCCTGTGATCATCAT 58.938 50.000 0.00 0.00 37.09 2.45
3265 3493 0.107268 CGCCCCTGTGATCATCATCA 59.893 55.000 0.00 0.00 36.62 3.07
3266 3494 1.475571 CGCCCCTGTGATCATCATCAA 60.476 52.381 0.00 0.00 40.90 2.57
3267 3495 1.952296 GCCCCTGTGATCATCATCAAC 59.048 52.381 0.00 0.00 40.90 3.18
3268 3496 2.422519 GCCCCTGTGATCATCATCAACT 60.423 50.000 0.00 0.00 40.90 3.16
3269 3497 3.474600 CCCCTGTGATCATCATCAACTC 58.525 50.000 0.00 0.00 40.90 3.01
3270 3498 3.118149 CCCCTGTGATCATCATCAACTCA 60.118 47.826 0.00 0.00 40.90 3.41
3271 3499 4.520179 CCCTGTGATCATCATCAACTCAA 58.480 43.478 0.00 0.00 40.90 3.02
3279 3507 8.242053 GTGATCATCATCAACTCAATCTTTTGT 58.758 33.333 0.00 0.00 40.90 2.83
3280 3508 8.241367 TGATCATCATCAACTCAATCTTTTGTG 58.759 33.333 0.00 0.00 35.99 3.33
3281 3509 6.916440 TCATCATCAACTCAATCTTTTGTGG 58.084 36.000 0.00 0.00 34.32 4.17
3284 3512 5.593909 TCATCAACTCAATCTTTTGTGGTGT 59.406 36.000 5.92 0.00 42.15 4.16
3440 3671 5.650266 TGCTTCTGAACCTGAAAACACTTTA 59.350 36.000 0.00 0.00 0.00 1.85
3441 3672 6.183360 TGCTTCTGAACCTGAAAACACTTTAG 60.183 38.462 0.00 0.00 0.00 1.85
3442 3673 6.183360 GCTTCTGAACCTGAAAACACTTTAGT 60.183 38.462 0.00 0.00 0.00 2.24
3443 3674 7.628580 GCTTCTGAACCTGAAAACACTTTAGTT 60.629 37.037 0.00 0.00 0.00 2.24
3444 3675 7.316544 TCTGAACCTGAAAACACTTTAGTTC 57.683 36.000 0.00 0.00 33.68 3.01
3445 3676 6.882140 TCTGAACCTGAAAACACTTTAGTTCA 59.118 34.615 0.00 0.00 37.10 3.18
3447 3678 6.657541 TGAACCTGAAAACACTTTAGTTCACT 59.342 34.615 0.00 0.00 35.89 3.41
3448 3679 7.825270 TGAACCTGAAAACACTTTAGTTCACTA 59.175 33.333 0.00 0.00 35.89 2.74
3500 3751 8.410673 TGTTCACTAGATCAGAACTAGAAACT 57.589 34.615 19.06 0.00 41.56 2.66
3551 3814 1.323271 TGATCGAGGAGTGCTGGGAC 61.323 60.000 0.00 0.00 0.00 4.46
3758 4053 3.971032 AGTTTTTCCTCTCTGCGTTTG 57.029 42.857 0.00 0.00 0.00 2.93
3759 4054 3.279434 AGTTTTTCCTCTCTGCGTTTGT 58.721 40.909 0.00 0.00 0.00 2.83
3761 4056 4.157840 AGTTTTTCCTCTCTGCGTTTGTTT 59.842 37.500 0.00 0.00 0.00 2.83
3893 4227 9.373603 ACATGCATACGTACTGTAAAAGATTAA 57.626 29.630 0.00 0.00 36.44 1.40
4054 4411 4.401202 TGGCTTCGTTATCATGTGACTAGA 59.599 41.667 0.00 0.00 0.00 2.43
4060 4417 5.646360 TCGTTATCATGTGACTAGAGTGACA 59.354 40.000 4.41 4.41 45.52 3.58
4069 4426 5.764686 TGTGACTAGAGTGACAAATTGCAAT 59.235 36.000 5.99 5.99 39.12 3.56
4097 4456 4.331443 GGTTGGGTTGTTTGTGTGATTTTC 59.669 41.667 0.00 0.00 0.00 2.29
4100 4459 5.415221 TGGGTTGTTTGTGTGATTTTCTTC 58.585 37.500 0.00 0.00 0.00 2.87
4103 4462 4.664150 TGTTTGTGTGATTTTCTTCCCC 57.336 40.909 0.00 0.00 0.00 4.81
4128 4487 2.178912 TGTTTGGTGACTCGAATCCC 57.821 50.000 0.00 0.00 0.00 3.85
4134 4493 1.482593 GGTGACTCGAATCCCTCACAT 59.517 52.381 0.00 0.00 35.68 3.21
4154 4513 7.925993 TCACATTGTAGGTTGTGAACTTTAAG 58.074 34.615 3.43 0.00 46.75 1.85
4155 4514 7.771361 TCACATTGTAGGTTGTGAACTTTAAGA 59.229 33.333 0.00 0.00 46.75 2.10
4156 4515 8.567948 CACATTGTAGGTTGTGAACTTTAAGAT 58.432 33.333 0.00 0.00 44.74 2.40
4157 4516 9.787435 ACATTGTAGGTTGTGAACTTTAAGATA 57.213 29.630 0.00 0.00 0.00 1.98
4185 4544 2.745281 ACCGATAAATTGTTCCCACGTG 59.255 45.455 9.08 9.08 0.00 4.49
4189 4548 5.106634 CCGATAAATTGTTCCCACGTGTTTA 60.107 40.000 15.65 10.80 0.00 2.01
4193 4552 5.838531 AATTGTTCCCACGTGTTTAGAAA 57.161 34.783 15.65 2.17 0.00 2.52
4233 4596 5.597806 TCCACTTACAAAGCATAGGATACG 58.402 41.667 0.00 0.00 46.39 3.06
4244 4607 4.315803 GCATAGGATACGTAATGCACCTT 58.684 43.478 19.98 0.00 45.49 3.50
4260 4623 2.472861 CACCTTGATGCGCTATAGTTCG 59.527 50.000 9.73 0.00 0.00 3.95
4288 4651 1.971695 GGGCTGGACCAAAACCTCG 60.972 63.158 0.00 0.00 42.05 4.63
4293 4656 0.035739 TGGACCAAAACCTCGTAGCC 59.964 55.000 0.00 0.00 0.00 3.93
4294 4657 0.675837 GGACCAAAACCTCGTAGCCC 60.676 60.000 0.00 0.00 0.00 5.19
4309 4672 2.488355 CCCGCGAGCTTAACGAGA 59.512 61.111 8.23 0.00 32.88 4.04
4310 4673 1.586564 CCCGCGAGCTTAACGAGAG 60.587 63.158 8.23 0.00 32.88 3.20
4356 4719 5.407995 GCTCATAGCTCGCTTCTTAATGAAT 59.592 40.000 0.00 0.00 38.45 2.57
4360 4723 8.982685 TCATAGCTCGCTTCTTAATGAATAAAG 58.017 33.333 0.00 0.00 33.71 1.85
4366 4729 9.643652 CTCGCTTCTTAATGAATAAAGTCAATC 57.356 33.333 0.00 0.00 33.71 2.67
4379 4742 8.826546 AATAAAGTCAATCATCGATTTCAACG 57.173 30.769 0.00 0.00 28.87 4.10
4381 4744 3.684305 AGTCAATCATCGATTTCAACGCA 59.316 39.130 0.00 0.00 28.87 5.24
4386 4749 6.686679 TCAATCATCGATTTCAACGCATTAAC 59.313 34.615 0.00 0.00 28.87 2.01
4391 4754 3.680789 GATTTCAACGCATTAACCTCGG 58.319 45.455 0.00 0.00 0.00 4.63
4401 4764 4.807304 CGCATTAACCTCGGTAGTAACAAT 59.193 41.667 0.00 0.00 0.00 2.71
4405 4768 7.278424 GCATTAACCTCGGTAGTAACAATACAA 59.722 37.037 0.00 0.00 34.29 2.41
4406 4769 8.598075 CATTAACCTCGGTAGTAACAATACAAC 58.402 37.037 0.00 0.00 34.29 3.32
4407 4770 4.737054 ACCTCGGTAGTAACAATACAACG 58.263 43.478 0.00 0.00 34.29 4.10
4444 4807 9.764363 TCTTATATGACAAAATTCTCGTAGCAT 57.236 29.630 0.00 0.00 0.00 3.79
4453 4816 1.007964 CTCGTAGCATCTCAGCCCG 60.008 63.158 0.00 0.00 34.23 6.13
4455 4818 1.299468 CGTAGCATCTCAGCCCGTC 60.299 63.158 0.00 0.00 34.23 4.79
4457 4820 1.319541 GTAGCATCTCAGCCCGTCTA 58.680 55.000 0.00 0.00 34.23 2.59
4464 4829 4.390297 GCATCTCAGCCCGTCTATTTAATC 59.610 45.833 0.00 0.00 0.00 1.75
4540 4906 6.293698 TCTCCTTCTTAAAAACCACACCTAC 58.706 40.000 0.00 0.00 0.00 3.18
4549 4915 3.857157 AACCACACCTACACACTCATT 57.143 42.857 0.00 0.00 0.00 2.57
4551 4917 3.740115 ACCACACCTACACACTCATTTC 58.260 45.455 0.00 0.00 0.00 2.17
4552 4918 3.135712 ACCACACCTACACACTCATTTCA 59.864 43.478 0.00 0.00 0.00 2.69
4559 4925 5.483937 ACCTACACACTCATTTCATAGACCA 59.516 40.000 0.00 0.00 0.00 4.02
4569 4935 8.267183 ACTCATTTCATAGACCATAACACATCA 58.733 33.333 0.00 0.00 0.00 3.07
4570 4936 9.112725 CTCATTTCATAGACCATAACACATCAA 57.887 33.333 0.00 0.00 0.00 2.57
4621 4987 0.942252 AGTTTCAAACGAACCGAGCC 59.058 50.000 0.00 0.00 36.23 4.70
4639 5005 2.045242 GGGGAGGGTTTTCCGCTC 60.045 66.667 2.25 0.00 44.42 5.03
4679 5045 4.187056 AGCCGAGCTTTAACGAGC 57.813 55.556 0.00 0.00 43.02 5.03
4680 5046 1.448013 AGCCGAGCTTTAACGAGCC 60.448 57.895 0.00 0.00 43.74 4.70
4681 5047 2.799540 GCCGAGCTTTAACGAGCCG 61.800 63.158 0.00 0.58 43.74 5.52
4682 5048 1.153901 CCGAGCTTTAACGAGCCGA 60.154 57.895 9.96 0.00 43.74 5.54
4683 5049 1.140407 CCGAGCTTTAACGAGCCGAG 61.140 60.000 9.96 0.00 43.74 4.63
4684 5050 0.179171 CGAGCTTTAACGAGCCGAGA 60.179 55.000 1.50 0.00 43.74 4.04
4685 5051 1.270068 GAGCTTTAACGAGCCGAGAC 58.730 55.000 1.50 0.00 43.74 3.36
4686 5052 0.889306 AGCTTTAACGAGCCGAGACT 59.111 50.000 1.50 0.00 43.74 3.24
4687 5053 1.272769 AGCTTTAACGAGCCGAGACTT 59.727 47.619 1.50 0.00 43.74 3.01
4688 5054 2.490903 AGCTTTAACGAGCCGAGACTTA 59.509 45.455 1.50 0.00 43.74 2.24
4689 5055 3.057033 AGCTTTAACGAGCCGAGACTTAA 60.057 43.478 1.50 0.00 43.74 1.85
4690 5056 3.060496 GCTTTAACGAGCCGAGACTTAAC 59.940 47.826 1.50 0.00 36.66 2.01
4691 5057 2.532531 TAACGAGCCGAGACTTAACG 57.467 50.000 1.50 0.00 0.00 3.18
4692 5058 0.877071 AACGAGCCGAGACTTAACGA 59.123 50.000 1.50 0.00 0.00 3.85
4693 5059 0.877071 ACGAGCCGAGACTTAACGAA 59.123 50.000 1.50 0.00 0.00 3.85
4694 5060 1.257539 CGAGCCGAGACTTAACGAAC 58.742 55.000 0.00 0.00 0.00 3.95
4695 5061 1.400629 CGAGCCGAGACTTAACGAACA 60.401 52.381 0.00 0.00 0.00 3.18
4696 5062 1.984297 GAGCCGAGACTTAACGAACAC 59.016 52.381 0.00 0.00 0.00 3.32
4697 5063 0.706729 GCCGAGACTTAACGAACACG 59.293 55.000 0.00 0.00 0.00 4.49
4698 5064 1.664016 GCCGAGACTTAACGAACACGA 60.664 52.381 0.00 0.00 0.00 4.35
4699 5065 2.240040 CCGAGACTTAACGAACACGAG 58.760 52.381 0.00 0.00 0.00 4.18
4700 5066 1.642843 CGAGACTTAACGAACACGAGC 59.357 52.381 0.00 0.00 0.00 5.03
4701 5067 2.664971 CGAGACTTAACGAACACGAGCT 60.665 50.000 0.00 0.00 0.00 4.09
4702 5068 3.306818 GAGACTTAACGAACACGAGCTT 58.693 45.455 0.00 0.00 0.00 3.74
4703 5069 4.470462 GAGACTTAACGAACACGAGCTTA 58.530 43.478 0.00 0.00 0.00 3.09
4704 5070 4.863491 AGACTTAACGAACACGAGCTTAA 58.137 39.130 0.00 0.00 0.00 1.85
4705 5071 4.678742 AGACTTAACGAACACGAGCTTAAC 59.321 41.667 0.00 0.00 0.00 2.01
4706 5072 3.423206 ACTTAACGAACACGAGCTTAACG 59.577 43.478 0.00 0.00 0.00 3.18
4707 5073 2.124011 AACGAACACGAGCTTAACGA 57.876 45.000 0.00 0.00 34.70 3.85
4708 5074 1.682982 ACGAACACGAGCTTAACGAG 58.317 50.000 0.00 0.00 34.70 4.18
4709 5075 1.002033 ACGAACACGAGCTTAACGAGT 60.002 47.619 0.00 0.00 36.31 4.18
4710 5076 2.049228 CGAACACGAGCTTAACGAGTT 58.951 47.619 8.45 8.45 44.05 3.01
4711 5077 2.470257 CGAACACGAGCTTAACGAGTTT 59.530 45.455 9.72 0.00 42.28 2.66
4712 5078 3.060740 CGAACACGAGCTTAACGAGTTTT 60.061 43.478 9.72 0.00 42.28 2.43
4713 5079 4.146961 CGAACACGAGCTTAACGAGTTTTA 59.853 41.667 9.72 0.00 42.28 1.52
4714 5080 5.331756 CGAACACGAGCTTAACGAGTTTTAA 60.332 40.000 9.72 0.00 42.28 1.52
4715 5081 5.971895 ACACGAGCTTAACGAGTTTTAAA 57.028 34.783 0.00 0.00 31.58 1.52
4716 5082 5.731278 ACACGAGCTTAACGAGTTTTAAAC 58.269 37.500 0.00 0.00 31.58 2.01
4717 5083 5.291614 ACACGAGCTTAACGAGTTTTAAACA 59.708 36.000 10.60 0.00 31.58 2.83
4718 5084 6.183360 ACACGAGCTTAACGAGTTTTAAACAA 60.183 34.615 10.60 0.00 31.58 2.83
4719 5085 6.683708 CACGAGCTTAACGAGTTTTAAACAAA 59.316 34.615 10.60 0.00 34.70 2.83
4720 5086 6.684131 ACGAGCTTAACGAGTTTTAAACAAAC 59.316 34.615 10.60 0.91 34.70 2.93
4721 5087 6.139638 CGAGCTTAACGAGTTTTAAACAAACC 59.860 38.462 10.60 0.00 0.00 3.27
4722 5088 5.967088 AGCTTAACGAGTTTTAAACAAACCG 59.033 36.000 10.60 9.72 33.36 4.44
4723 5089 5.964751 GCTTAACGAGTTTTAAACAAACCGA 59.035 36.000 10.60 0.00 32.35 4.69
4724 5090 6.139638 GCTTAACGAGTTTTAAACAAACCGAG 59.860 38.462 10.60 2.97 32.35 4.63
4725 5091 3.943958 ACGAGTTTTAAACAAACCGAGC 58.056 40.909 10.60 0.00 32.35 5.03
4726 5092 3.242837 ACGAGTTTTAAACAAACCGAGCC 60.243 43.478 10.60 0.00 32.35 4.70
4727 5093 3.294102 GAGTTTTAAACAAACCGAGCCG 58.706 45.455 10.60 0.00 0.00 5.52
4743 5109 4.303257 CGGGAGGGTTTTCTGCTC 57.697 61.111 0.00 0.00 0.00 4.26
4744 5110 1.741770 CGGGAGGGTTTTCTGCTCG 60.742 63.158 0.00 0.00 0.00 5.03
4745 5111 1.375326 GGGAGGGTTTTCTGCTCGT 59.625 57.895 0.00 0.00 0.00 4.18
4746 5112 0.250770 GGGAGGGTTTTCTGCTCGTT 60.251 55.000 0.00 0.00 0.00 3.85
4747 5113 1.002773 GGGAGGGTTTTCTGCTCGTTA 59.997 52.381 0.00 0.00 0.00 3.18
4748 5114 2.551504 GGGAGGGTTTTCTGCTCGTTAA 60.552 50.000 0.00 0.00 0.00 2.01
4749 5115 2.742589 GGAGGGTTTTCTGCTCGTTAAG 59.257 50.000 0.00 0.00 0.00 1.85
4773 5139 6.476243 CTTAACAAGCTTAAGCCTTAACGA 57.524 37.500 23.71 4.52 43.38 3.85
4774 5140 6.476243 TTAACAAGCTTAAGCCTTAACGAG 57.524 37.500 23.71 7.52 43.38 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.859112 TTAGGAAAGCTATCAGTGTCTCTT 57.141 37.500 0.00 0.00 0.00 2.85
1 2 6.127196 CCTTTAGGAAAGCTATCAGTGTCTCT 60.127 42.308 0.00 0.00 37.18 3.10
2 3 6.045955 CCTTTAGGAAAGCTATCAGTGTCTC 58.954 44.000 0.00 0.00 37.18 3.36
4 5 5.978814 TCCTTTAGGAAAGCTATCAGTGTC 58.021 41.667 0.00 0.00 42.18 3.67
19 20 6.729690 TGGATAAAATTGCCATCCTTTAGG 57.270 37.500 12.15 0.00 39.24 2.69
20 21 7.015487 TCCATGGATAAAATTGCCATCCTTTAG 59.985 37.037 11.44 3.82 40.29 1.85
21 22 6.843333 TCCATGGATAAAATTGCCATCCTTTA 59.157 34.615 11.44 0.00 40.29 1.85
22 23 5.666718 TCCATGGATAAAATTGCCATCCTTT 59.333 36.000 11.44 1.51 40.29 3.11
225 226 7.390440 AGACGAGTCACATGAAAAATTAATGGA 59.610 33.333 0.00 0.00 0.00 3.41
226 227 7.530010 AGACGAGTCACATGAAAAATTAATGG 58.470 34.615 0.00 0.00 0.00 3.16
470 482 8.557450 AGTGGGTACAAAATTCTATCCATACTT 58.443 33.333 0.00 0.00 0.00 2.24
471 483 7.993183 CAGTGGGTACAAAATTCTATCCATACT 59.007 37.037 0.00 0.00 0.00 2.12
518 530 1.819753 TGGGCAGGGTAGAGCAATAT 58.180 50.000 0.00 0.00 0.00 1.28
542 554 4.638421 CCGAGTAGGAAATGCAATGGTTAA 59.362 41.667 0.00 0.00 45.00 2.01
545 557 2.026262 ACCGAGTAGGAAATGCAATGGT 60.026 45.455 0.00 0.00 45.00 3.55
553 565 4.041198 TCAGAACCAAACCGAGTAGGAAAT 59.959 41.667 0.00 0.00 45.00 2.17
554 566 3.388676 TCAGAACCAAACCGAGTAGGAAA 59.611 43.478 0.00 0.00 45.00 3.13
555 567 2.967201 TCAGAACCAAACCGAGTAGGAA 59.033 45.455 0.00 0.00 45.00 3.36
556 568 2.298163 GTCAGAACCAAACCGAGTAGGA 59.702 50.000 0.00 0.00 45.00 2.94
557 569 8.940004 GGTAAGTCAGAACCAAACCGAGTAGG 62.940 50.000 0.00 0.00 39.83 3.18
558 570 3.662247 AGTCAGAACCAAACCGAGTAG 57.338 47.619 0.00 0.00 0.00 2.57
559 571 4.262164 GGTAAGTCAGAACCAAACCGAGTA 60.262 45.833 0.00 0.00 35.73 2.59
560 572 3.493873 GGTAAGTCAGAACCAAACCGAGT 60.494 47.826 0.00 0.00 35.73 4.18
561 573 3.064931 GGTAAGTCAGAACCAAACCGAG 58.935 50.000 0.00 0.00 35.73 4.63
562 574 2.546373 CGGTAAGTCAGAACCAAACCGA 60.546 50.000 5.09 0.00 43.08 4.69
563 575 1.796459 CGGTAAGTCAGAACCAAACCG 59.204 52.381 0.00 0.00 38.36 4.44
564 576 1.534163 GCGGTAAGTCAGAACCAAACC 59.466 52.381 0.00 0.00 35.35 3.27
565 577 1.534163 GGCGGTAAGTCAGAACCAAAC 59.466 52.381 0.00 0.00 35.35 2.93
566 578 1.874739 CGGCGGTAAGTCAGAACCAAA 60.875 52.381 0.00 0.00 35.35 3.28
567 579 0.320073 CGGCGGTAAGTCAGAACCAA 60.320 55.000 0.00 0.00 35.35 3.67
568 580 1.290955 CGGCGGTAAGTCAGAACCA 59.709 57.895 0.00 0.00 35.35 3.67
569 581 0.320160 AACGGCGGTAAGTCAGAACC 60.320 55.000 13.24 0.00 0.00 3.62
570 582 1.458445 GAAACGGCGGTAAGTCAGAAC 59.542 52.381 13.24 0.00 0.00 3.01
571 583 1.606224 GGAAACGGCGGTAAGTCAGAA 60.606 52.381 13.24 0.00 0.00 3.02
572 584 0.037975 GGAAACGGCGGTAAGTCAGA 60.038 55.000 13.24 0.00 0.00 3.27
573 585 1.017701 GGGAAACGGCGGTAAGTCAG 61.018 60.000 13.24 0.00 0.00 3.51
574 586 1.004679 GGGAAACGGCGGTAAGTCA 60.005 57.895 13.24 0.00 0.00 3.41
575 587 2.096442 CGGGAAACGGCGGTAAGTC 61.096 63.158 13.24 0.00 39.42 3.01
576 588 2.047939 CGGGAAACGGCGGTAAGT 60.048 61.111 13.24 0.00 39.42 2.24
577 589 2.096442 GTCGGGAAACGGCGGTAAG 61.096 63.158 13.24 0.00 44.45 2.34
578 590 2.048316 GTCGGGAAACGGCGGTAA 60.048 61.111 13.24 0.00 44.45 2.85
669 686 1.059838 GTTAAAGTTAGCGCGGGCG 59.940 57.895 19.46 8.99 46.35 6.13
739 756 4.097361 GAAGACGGGAGGTGGGGC 62.097 72.222 0.00 0.00 0.00 5.80
787 807 2.203126 GCGCAGAATGAGGAGGGG 60.203 66.667 0.30 0.00 39.69 4.79
830 850 2.560119 CCGCGGAGATGGAGAGAGG 61.560 68.421 24.07 0.00 0.00 3.69
897 917 1.393539 GGATGAAACGATCGTGGTGTG 59.606 52.381 23.51 0.00 0.00 3.82
910 930 2.239654 GAGAGGGGTGTGATGGATGAAA 59.760 50.000 0.00 0.00 0.00 2.69
912 932 1.500474 GAGAGGGGTGTGATGGATGA 58.500 55.000 0.00 0.00 0.00 2.92
1512 1542 8.264347 GCCAATGAAAGGGGAAAGAAAATATTA 58.736 33.333 0.00 0.00 0.00 0.98
1513 1543 7.112122 GCCAATGAAAGGGGAAAGAAAATATT 58.888 34.615 0.00 0.00 0.00 1.28
1514 1544 6.215227 TGCCAATGAAAGGGGAAAGAAAATAT 59.785 34.615 0.00 0.00 0.00 1.28
1515 1545 5.545723 TGCCAATGAAAGGGGAAAGAAAATA 59.454 36.000 0.00 0.00 0.00 1.40
1516 1546 4.350520 TGCCAATGAAAGGGGAAAGAAAAT 59.649 37.500 0.00 0.00 0.00 1.82
1517 1547 3.713764 TGCCAATGAAAGGGGAAAGAAAA 59.286 39.130 0.00 0.00 0.00 2.29
1518 1548 3.312890 TGCCAATGAAAGGGGAAAGAAA 58.687 40.909 0.00 0.00 0.00 2.52
1519 1549 2.969628 TGCCAATGAAAGGGGAAAGAA 58.030 42.857 0.00 0.00 0.00 2.52
1520 1550 2.692709 TGCCAATGAAAGGGGAAAGA 57.307 45.000 0.00 0.00 0.00 2.52
1521 1551 2.833338 TGATGCCAATGAAAGGGGAAAG 59.167 45.455 0.00 0.00 0.00 2.62
1522 1552 2.833338 CTGATGCCAATGAAAGGGGAAA 59.167 45.455 0.00 0.00 0.00 3.13
1523 1553 2.042842 TCTGATGCCAATGAAAGGGGAA 59.957 45.455 0.00 0.00 0.00 3.97
1524 1554 1.640149 TCTGATGCCAATGAAAGGGGA 59.360 47.619 0.00 0.00 0.00 4.81
1525 1555 1.753073 GTCTGATGCCAATGAAAGGGG 59.247 52.381 0.00 0.00 0.00 4.79
1526 1556 1.402968 CGTCTGATGCCAATGAAAGGG 59.597 52.381 0.00 0.00 0.00 3.95
1527 1557 2.358957 TCGTCTGATGCCAATGAAAGG 58.641 47.619 0.00 0.00 0.00 3.11
1528 1558 3.302935 CGATCGTCTGATGCCAATGAAAG 60.303 47.826 7.03 0.00 34.09 2.62
1571 1791 3.585862 CCACGGCCTACATATACATGAC 58.414 50.000 0.00 0.00 35.96 3.06
1588 1808 2.738521 CACTTGGAGTCGGCCACG 60.739 66.667 2.24 0.00 37.75 4.94
1597 1817 0.250124 TGTGGCCGTAACACTTGGAG 60.250 55.000 0.00 0.00 39.52 3.86
1665 1885 6.820656 AGTTGATGTGATGGAAAGACAGATAC 59.179 38.462 0.00 0.00 0.00 2.24
1692 1912 6.071221 TCCATGGATCAAACAAATCAAAGAGG 60.071 38.462 11.44 0.00 0.00 3.69
1712 1932 1.134128 TGGACCACGAATCCATCCATG 60.134 52.381 0.00 0.00 41.47 3.66
1713 1933 1.212375 TGGACCACGAATCCATCCAT 58.788 50.000 0.00 0.00 41.47 3.41
1714 1934 2.690367 TGGACCACGAATCCATCCA 58.310 52.632 0.00 0.00 41.47 3.41
1750 1970 5.592054 TCTGCAAATTATAGACGGTCAGAG 58.408 41.667 11.27 0.00 0.00 3.35
1751 1971 5.359860 TCTCTGCAAATTATAGACGGTCAGA 59.640 40.000 11.27 0.00 0.00 3.27
1752 1972 5.592054 TCTCTGCAAATTATAGACGGTCAG 58.408 41.667 11.27 0.00 0.00 3.51
1756 1976 6.238211 CCTGTTTCTCTGCAAATTATAGACGG 60.238 42.308 0.00 0.00 0.00 4.79
1762 1982 5.649831 GTCCTCCTGTTTCTCTGCAAATTAT 59.350 40.000 0.00 0.00 0.00 1.28
1880 2100 6.375945 AATGGAAAGAAAACAAATTGCACC 57.624 33.333 0.00 0.00 0.00 5.01
1907 2128 9.107177 CTTCATGCTATTTCTGTTATCTGAACT 57.893 33.333 0.00 0.00 32.71 3.01
1908 2129 7.854916 GCTTCATGCTATTTCTGTTATCTGAAC 59.145 37.037 0.00 0.00 38.95 3.18
1955 2178 1.461237 CGACGTGCACACCGTTAATTC 60.461 52.381 18.64 0.00 38.92 2.17
1970 2193 2.554636 TACGTGCCCTGTTCGACGT 61.555 57.895 0.00 0.00 46.20 4.34
2095 2318 1.340114 GGTTGGGCTCTTTAGGGTGAG 60.340 57.143 0.00 0.00 0.00 3.51
2149 2374 6.638468 CCTGAAAGAGTTTCTGTAACAAATGC 59.362 38.462 0.04 0.00 40.32 3.56
2219 2444 1.248101 TGACGGCTCCGATGAACTGA 61.248 55.000 15.95 0.00 42.83 3.41
2316 2541 8.024145 AGGTATGTAAGCTAGATATAATGGCC 57.976 38.462 0.00 0.00 32.98 5.36
2522 2747 7.266335 CGTCTTTTGTCGAATGAAGAACAATAC 59.734 37.037 7.06 0.00 33.01 1.89
2589 2815 1.438710 CAGCCGCGACGAAAACAAG 60.439 57.895 8.23 0.00 0.00 3.16
2713 2939 1.532868 CAAGCAAGAGAACGGACAAGG 59.467 52.381 0.00 0.00 0.00 3.61
2720 2948 1.717645 GCAAATGCAAGCAAGAGAACG 59.282 47.619 0.00 0.00 41.59 3.95
2764 2992 6.698008 TTTCTGAATCATCCAAATATGCGT 57.302 33.333 0.00 0.00 0.00 5.24
2786 3014 5.412286 GCACAACCATGGCAATTCTATTTTT 59.588 36.000 13.04 0.00 0.00 1.94
2799 3027 1.243902 AAAGTACGGCACAACCATGG 58.756 50.000 11.19 11.19 39.03 3.66
3023 3251 3.933332 AGTACGATTAAGCTTTGTCAGGC 59.067 43.478 3.20 0.00 0.00 4.85
3024 3252 7.042658 GGAATAGTACGATTAAGCTTTGTCAGG 60.043 40.741 3.20 0.00 0.00 3.86
3030 3258 7.436376 GGTTACGGAATAGTACGATTAAGCTTT 59.564 37.037 3.20 0.00 0.00 3.51
3033 3261 6.442112 AGGTTACGGAATAGTACGATTAAGC 58.558 40.000 0.00 0.33 0.00 3.09
3036 3264 7.224297 ACCTAGGTTACGGAATAGTACGATTA 58.776 38.462 9.21 0.00 0.00 1.75
3154 3382 3.415212 TGCATATATGGAGCAGAAAGGC 58.585 45.455 14.51 0.00 33.75 4.35
3218 3446 4.042187 AGTTATCAAGTCTGAAACCCAGCT 59.958 41.667 0.00 0.00 42.62 4.24
3248 3476 3.118149 TGAGTTGATGATGATCACAGGGG 60.118 47.826 0.00 0.00 38.38 4.79
3263 3491 4.946772 TCACACCACAAAAGATTGAGTTGA 59.053 37.500 0.00 0.00 38.94 3.18
3265 3493 5.360714 ACATCACACCACAAAAGATTGAGTT 59.639 36.000 0.00 0.00 38.94 3.01
3266 3494 4.889409 ACATCACACCACAAAAGATTGAGT 59.111 37.500 0.00 0.00 38.94 3.41
3267 3495 5.008911 TCACATCACACCACAAAAGATTGAG 59.991 40.000 0.00 0.00 38.94 3.02
3268 3496 4.886489 TCACATCACACCACAAAAGATTGA 59.114 37.500 0.00 0.00 38.94 2.57
3269 3497 5.185668 TCACATCACACCACAAAAGATTG 57.814 39.130 0.00 0.00 42.46 2.67
3270 3498 5.535783 TGATCACATCACACCACAAAAGATT 59.464 36.000 0.00 0.00 33.59 2.40
3271 3499 5.072055 TGATCACATCACACCACAAAAGAT 58.928 37.500 0.00 0.00 33.59 2.40
3500 3751 3.054655 GCATACACCCAGGGTAGAAGAAA 60.055 47.826 12.21 0.00 32.11 2.52
3575 3838 2.409152 GGACGATCATCTCCGAGAAC 57.591 55.000 1.27 0.00 0.00 3.01
3714 3977 3.818773 TCAGTGTTCAGTGACTACGATGA 59.181 43.478 6.27 0.00 0.00 2.92
3745 4040 0.512952 CCGAAACAAACGCAGAGAGG 59.487 55.000 0.00 0.00 0.00 3.69
3758 4053 1.399727 CGTGTCATTTCCTGCCGAAAC 60.400 52.381 0.00 0.00 43.21 2.78
3759 4054 0.871722 CGTGTCATTTCCTGCCGAAA 59.128 50.000 0.00 0.00 44.49 3.46
3761 4056 1.375396 CCGTGTCATTTCCTGCCGA 60.375 57.895 0.00 0.00 0.00 5.54
3893 4227 5.449107 AAGACCGTATACGCTCATGTAAT 57.551 39.130 19.86 2.05 38.18 1.89
3895 4229 4.906065 AAAGACCGTATACGCTCATGTA 57.094 40.909 19.86 0.00 38.18 2.29
3922 4273 3.242091 CGTTCGACAATACATCAGCCAAG 60.242 47.826 0.00 0.00 0.00 3.61
3925 4276 2.536365 TCGTTCGACAATACATCAGCC 58.464 47.619 0.00 0.00 0.00 4.85
3930 4281 5.096169 CAGACTCTTCGTTCGACAATACAT 58.904 41.667 0.00 0.00 0.00 2.29
4009 4364 6.510799 GCCATATTTCTCAAGAAGTGACATCG 60.511 42.308 0.00 0.00 35.21 3.84
4054 4411 6.392354 CAACCATAGATTGCAATTTGTCACT 58.608 36.000 14.33 7.32 0.00 3.41
4060 4417 5.012975 ACAACCCAACCATAGATTGCAATTT 59.987 36.000 14.33 10.78 0.00 1.82
4069 4426 3.634448 CACACAAACAACCCAACCATAGA 59.366 43.478 0.00 0.00 0.00 1.98
4097 4456 1.888512 CACCAAACATCACAGGGGAAG 59.111 52.381 0.00 0.00 0.00 3.46
4100 4459 1.202927 AGTCACCAAACATCACAGGGG 60.203 52.381 0.00 0.00 0.00 4.79
4103 4462 2.754472 TCGAGTCACCAAACATCACAG 58.246 47.619 0.00 0.00 0.00 3.66
4155 4514 9.581289 TGGGAACAATTTATCGGTGATTATTAT 57.419 29.630 0.00 0.00 37.44 1.28
4156 4515 8.842280 GTGGGAACAATTTATCGGTGATTATTA 58.158 33.333 0.00 0.00 46.06 0.98
4157 4516 7.468084 CGTGGGAACAATTTATCGGTGATTATT 60.468 37.037 0.00 0.00 46.06 1.40
4158 4517 6.017440 CGTGGGAACAATTTATCGGTGATTAT 60.017 38.462 0.00 0.00 46.06 1.28
4159 4518 5.294799 CGTGGGAACAATTTATCGGTGATTA 59.705 40.000 0.00 0.00 46.06 1.75
4160 4519 4.095782 CGTGGGAACAATTTATCGGTGATT 59.904 41.667 0.00 0.00 46.06 2.57
4169 4528 6.939132 TTCTAAACACGTGGGAACAATTTA 57.061 33.333 21.57 12.01 46.06 1.40
4170 4529 5.838531 TTCTAAACACGTGGGAACAATTT 57.161 34.783 21.57 11.49 46.06 1.82
4173 4532 3.628487 CCTTTCTAAACACGTGGGAACAA 59.372 43.478 21.57 3.95 46.06 2.83
4189 4548 8.164070 AGTGGAAAACATACAACTATCCTTTCT 58.836 33.333 0.00 0.00 0.00 2.52
4193 4552 8.380099 TGTAAGTGGAAAACATACAACTATCCT 58.620 33.333 0.00 0.00 39.38 3.24
4222 4585 3.926616 AGGTGCATTACGTATCCTATGC 58.073 45.455 18.68 18.68 42.75 3.14
4233 4596 0.734889 AGCGCATCAAGGTGCATTAC 59.265 50.000 11.47 0.00 46.43 1.89
4240 4603 2.100916 ACGAACTATAGCGCATCAAGGT 59.899 45.455 11.47 0.00 0.00 3.50
4244 4607 1.954382 AGGACGAACTATAGCGCATCA 59.046 47.619 11.47 0.00 0.00 3.07
4252 4615 5.479375 CCAGCCCTAATTAGGACGAACTATA 59.521 44.000 29.75 0.00 46.63 1.31
4253 4616 4.283722 CCAGCCCTAATTAGGACGAACTAT 59.716 45.833 29.75 1.27 46.63 2.12
4260 4623 2.124411 TGGTCCAGCCCTAATTAGGAC 58.876 52.381 29.75 20.37 46.63 3.85
4288 4651 2.228914 CGTTAAGCTCGCGGGCTAC 61.229 63.158 37.08 28.21 42.24 3.58
4293 4656 2.224885 GCTCTCGTTAAGCTCGCGG 61.225 63.158 6.13 0.00 36.80 6.46
4294 4657 3.290619 GCTCTCGTTAAGCTCGCG 58.709 61.111 0.00 0.00 36.80 5.87
4309 4672 0.818296 ACGAGCCGAACTATCAAGCT 59.182 50.000 1.50 0.00 37.49 3.74
4310 4673 1.641577 AACGAGCCGAACTATCAAGC 58.358 50.000 1.50 0.00 0.00 4.01
4313 4676 2.805845 GCTTAACGAGCCGAACTATCA 58.194 47.619 1.50 0.00 46.01 2.15
4356 4719 6.128418 TGCGTTGAAATCGATGATTGACTTTA 60.128 34.615 0.00 0.00 32.14 1.85
4360 4723 4.002267 TGCGTTGAAATCGATGATTGAC 57.998 40.909 0.00 0.00 32.14 3.18
4366 4729 4.908736 AGGTTAATGCGTTGAAATCGATG 58.091 39.130 0.00 0.00 0.00 3.84
4377 4740 3.193267 TGTTACTACCGAGGTTAATGCGT 59.807 43.478 0.00 0.00 0.00 5.24
4379 4742 6.757947 TGTATTGTTACTACCGAGGTTAATGC 59.242 38.462 0.00 0.00 0.00 3.56
4381 4744 7.489113 CGTTGTATTGTTACTACCGAGGTTAAT 59.511 37.037 0.00 0.00 32.52 1.40
4386 4749 3.549070 GCGTTGTATTGTTACTACCGAGG 59.451 47.826 0.00 0.00 32.52 4.63
4417 4780 9.764363 TGCTACGAGAATTTTGTCATATAAGAT 57.236 29.630 0.00 0.00 0.00 2.40
4430 4793 3.462021 GGCTGAGATGCTACGAGAATTT 58.538 45.455 0.00 0.00 0.00 1.82
4435 4798 1.007964 CGGGCTGAGATGCTACGAG 60.008 63.158 0.00 0.00 36.18 4.18
4438 4801 1.319541 TAGACGGGCTGAGATGCTAC 58.680 55.000 0.00 0.00 0.00 3.58
4444 4807 6.971726 TTAGATTAAATAGACGGGCTGAGA 57.028 37.500 0.00 0.00 0.00 3.27
4515 4881 5.762279 AGGTGTGGTTTTTAAGAAGGAGAA 58.238 37.500 0.00 0.00 0.00 2.87
4517 4883 6.017357 GTGTAGGTGTGGTTTTTAAGAAGGAG 60.017 42.308 0.00 0.00 0.00 3.69
4540 4906 7.334171 TGTGTTATGGTCTATGAAATGAGTGTG 59.666 37.037 0.00 0.00 0.00 3.82
4549 4915 9.295825 AGTTTTTGATGTGTTATGGTCTATGAA 57.704 29.630 0.00 0.00 0.00 2.57
4569 4935 5.049954 TCGTGAGCGCTTGTTAATAGTTTTT 60.050 36.000 13.26 0.00 38.14 1.94
4570 4936 4.449743 TCGTGAGCGCTTGTTAATAGTTTT 59.550 37.500 13.26 0.00 38.14 2.43
4573 4939 3.179830 CTCGTGAGCGCTTGTTAATAGT 58.820 45.455 13.26 0.00 38.14 2.12
4604 4970 1.500512 CCGGCTCGGTTCGTTTGAAA 61.501 55.000 5.56 0.00 42.73 2.69
4605 4971 1.957186 CCGGCTCGGTTCGTTTGAA 60.957 57.895 5.56 0.00 42.73 2.69
4621 4987 3.971109 GAGCGGAAAACCCTCCCCG 62.971 68.421 0.00 0.00 44.34 5.73
4623 4989 2.436115 CGAGCGGAAAACCCTCCC 60.436 66.667 0.00 0.00 31.03 4.30
4669 5035 3.300066 CGTTAAGTCTCGGCTCGTTAAAG 59.700 47.826 0.00 0.00 0.00 1.85
4670 5036 3.058293 TCGTTAAGTCTCGGCTCGTTAAA 60.058 43.478 0.00 0.00 0.00 1.52
4673 5039 0.877071 TCGTTAAGTCTCGGCTCGTT 59.123 50.000 0.00 0.00 0.00 3.85
4674 5040 0.877071 TTCGTTAAGTCTCGGCTCGT 59.123 50.000 0.00 0.00 0.00 4.18
4675 5041 1.257539 GTTCGTTAAGTCTCGGCTCG 58.742 55.000 0.00 0.00 0.00 5.03
4676 5042 1.984297 GTGTTCGTTAAGTCTCGGCTC 59.016 52.381 0.00 0.00 0.00 4.70
4677 5043 1.665161 CGTGTTCGTTAAGTCTCGGCT 60.665 52.381 0.00 0.00 0.00 5.52
4678 5044 0.706729 CGTGTTCGTTAAGTCTCGGC 59.293 55.000 0.00 0.00 0.00 5.54
4679 5045 2.240040 CTCGTGTTCGTTAAGTCTCGG 58.760 52.381 0.00 0.00 38.33 4.63
4680 5046 1.642843 GCTCGTGTTCGTTAAGTCTCG 59.357 52.381 0.00 0.00 38.33 4.04
4681 5047 2.931228 AGCTCGTGTTCGTTAAGTCTC 58.069 47.619 0.00 0.00 38.33 3.36
4682 5048 3.366440 AAGCTCGTGTTCGTTAAGTCT 57.634 42.857 0.00 0.00 38.33 3.24
4683 5049 4.430830 CGTTAAGCTCGTGTTCGTTAAGTC 60.431 45.833 0.00 0.00 38.33 3.01
4684 5050 3.423206 CGTTAAGCTCGTGTTCGTTAAGT 59.577 43.478 0.00 0.00 38.33 2.24
4685 5051 3.665409 TCGTTAAGCTCGTGTTCGTTAAG 59.335 43.478 0.00 0.00 38.33 1.85
4686 5052 3.626977 TCGTTAAGCTCGTGTTCGTTAA 58.373 40.909 0.00 0.00 38.33 2.01
4687 5053 3.228749 CTCGTTAAGCTCGTGTTCGTTA 58.771 45.455 0.00 0.00 38.33 3.18
4688 5054 2.049228 CTCGTTAAGCTCGTGTTCGTT 58.951 47.619 0.00 0.00 38.33 3.85
4689 5055 1.002033 ACTCGTTAAGCTCGTGTTCGT 60.002 47.619 0.00 0.00 38.33 3.85
4690 5056 1.682982 ACTCGTTAAGCTCGTGTTCG 58.317 50.000 0.00 0.00 32.52 3.95
4691 5057 4.448363 AAAACTCGTTAAGCTCGTGTTC 57.552 40.909 12.30 0.00 41.66 3.18
4692 5058 5.971895 TTAAAACTCGTTAAGCTCGTGTT 57.028 34.783 7.64 7.64 43.35 3.32
4693 5059 5.291614 TGTTTAAAACTCGTTAAGCTCGTGT 59.708 36.000 0.00 0.00 36.77 4.49
4694 5060 5.730269 TGTTTAAAACTCGTTAAGCTCGTG 58.270 37.500 0.00 0.00 0.00 4.35
4695 5061 5.971895 TGTTTAAAACTCGTTAAGCTCGT 57.028 34.783 0.00 0.00 0.00 4.18
4696 5062 6.139638 GGTTTGTTTAAAACTCGTTAAGCTCG 59.860 38.462 0.00 0.00 30.70 5.03
4697 5063 6.139638 CGGTTTGTTTAAAACTCGTTAAGCTC 59.860 38.462 0.00 0.00 31.18 4.09
4698 5064 5.967088 CGGTTTGTTTAAAACTCGTTAAGCT 59.033 36.000 0.00 0.00 31.18 3.74
4699 5065 5.964751 TCGGTTTGTTTAAAACTCGTTAAGC 59.035 36.000 0.00 0.00 31.18 3.09
4700 5066 6.139638 GCTCGGTTTGTTTAAAACTCGTTAAG 59.860 38.462 0.00 0.38 31.18 1.85
4701 5067 5.964751 GCTCGGTTTGTTTAAAACTCGTTAA 59.035 36.000 0.00 0.00 31.18 2.01
4702 5068 5.500825 GCTCGGTTTGTTTAAAACTCGTTA 58.499 37.500 0.00 0.00 31.18 3.18
4703 5069 4.345288 GCTCGGTTTGTTTAAAACTCGTT 58.655 39.130 0.00 0.00 31.18 3.85
4704 5070 3.242837 GGCTCGGTTTGTTTAAAACTCGT 60.243 43.478 0.00 0.00 31.18 4.18
4705 5071 3.294102 GGCTCGGTTTGTTTAAAACTCG 58.706 45.455 0.00 3.98 31.18 4.18
4706 5072 3.294102 CGGCTCGGTTTGTTTAAAACTC 58.706 45.455 0.00 0.00 31.18 3.01
4707 5073 2.033675 CCGGCTCGGTTTGTTTAAAACT 59.966 45.455 5.56 0.00 42.73 2.66
4708 5074 2.387185 CCGGCTCGGTTTGTTTAAAAC 58.613 47.619 5.56 0.00 42.73 2.43
4709 5075 1.337387 CCCGGCTCGGTTTGTTTAAAA 59.663 47.619 11.85 0.00 46.80 1.52
4710 5076 0.953003 CCCGGCTCGGTTTGTTTAAA 59.047 50.000 11.85 0.00 46.80 1.52
4711 5077 0.108207 TCCCGGCTCGGTTTGTTTAA 59.892 50.000 11.85 0.00 46.80 1.52
4712 5078 0.320946 CTCCCGGCTCGGTTTGTTTA 60.321 55.000 11.85 0.00 46.80 2.01
4713 5079 1.599797 CTCCCGGCTCGGTTTGTTT 60.600 57.895 11.85 0.00 46.80 2.83
4714 5080 2.032071 CTCCCGGCTCGGTTTGTT 59.968 61.111 11.85 0.00 46.80 2.83
4715 5081 4.016706 CCTCCCGGCTCGGTTTGT 62.017 66.667 11.85 0.00 46.80 2.83
4716 5082 4.778143 CCCTCCCGGCTCGGTTTG 62.778 72.222 11.85 2.95 46.80 2.93
4721 5087 2.436115 GAAAACCCTCCCGGCTCG 60.436 66.667 0.00 0.00 33.26 5.03
4722 5088 1.377333 CAGAAAACCCTCCCGGCTC 60.377 63.158 0.00 0.00 33.26 4.70
4723 5089 2.757077 CAGAAAACCCTCCCGGCT 59.243 61.111 0.00 0.00 33.26 5.52
4724 5090 3.062466 GCAGAAAACCCTCCCGGC 61.062 66.667 0.00 0.00 33.26 6.13
4725 5091 1.377333 GAGCAGAAAACCCTCCCGG 60.377 63.158 0.00 0.00 37.81 5.73
4726 5092 1.741770 CGAGCAGAAAACCCTCCCG 60.742 63.158 0.00 0.00 0.00 5.14
4727 5093 0.250770 AACGAGCAGAAAACCCTCCC 60.251 55.000 0.00 0.00 0.00 4.30
4728 5094 2.467566 TAACGAGCAGAAAACCCTCC 57.532 50.000 0.00 0.00 0.00 4.30
4750 5116 6.476243 TCGTTAAGGCTTAAGCTTGTTAAG 57.524 37.500 25.88 17.51 41.70 1.85
4751 5117 6.476243 CTCGTTAAGGCTTAAGCTTGTTAA 57.524 37.500 25.88 21.26 41.70 2.01


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

AutoCloner maintained by Alex Coulton.