Multiple sequence alignment - TraesCS7A01G552200

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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 TraesCS7A01G552200 chr7A 100.000 2871 0 0 1 2871 725312652 725309782 0.000000e+00 5302.0
1 TraesCS7A01G552200 chr7A 95.164 1282 61 1 635 1915 725232178 725230897 0.000000e+00 2023.0
2 TraesCS7A01G552200 chr7A 84.275 973 117 19 1914 2869 725228416 725227463 0.000000e+00 917.0
3 TraesCS7A01G552200 chr7A 92.308 65 4 1 6 69 28561726 28561662 1.100000e-14 91.6
4 TraesCS7A01G552200 chr7D 95.720 1285 51 2 635 1915 629330834 629329550 0.000000e+00 2065.0
5 TraesCS7A01G552200 chr7D 83.642 972 112 18 1914 2871 629326371 629325433 0.000000e+00 870.0
6 TraesCS7A01G552200 chr7D 88.816 456 48 3 72 524 629331275 629330820 8.990000e-155 556.0
7 TraesCS7A01G552200 chr7D 85.163 337 40 6 942 1274 629422798 629422468 1.270000e-88 337.0
8 TraesCS7A01G552200 chr7B 91.486 1292 82 11 637 1915 732151812 732153088 0.000000e+00 1751.0
9 TraesCS7A01G552200 chr7B 91.099 1292 84 11 637 1915 732193691 732194964 0.000000e+00 1720.0
10 TraesCS7A01G552200 chr7B 87.768 466 49 5 68 529 732151051 732151512 3.250000e-149 538.0
11 TraesCS7A01G552200 chr7B 87.152 467 50 8 68 529 732192930 732193391 3.280000e-144 521.0
12 TraesCS7A01G552200 chr7B 87.186 398 44 4 68 462 732144078 732144471 2.030000e-121 446.0
13 TraesCS7A01G552200 chr7B 81.466 491 83 6 1431 1915 732413297 732412809 2.070000e-106 396.0
14 TraesCS7A01G552200 chr7B 92.920 113 6 2 523 634 478838011 478838122 2.290000e-36 163.0
15 TraesCS7A01G552200 chr7B 90.625 64 6 0 6 69 65749384 65749321 5.100000e-13 86.1
16 TraesCS7A01G552200 chrUn 91.814 794 49 5 637 1419 318736946 318736158 0.000000e+00 1092.0
17 TraesCS7A01G552200 chrUn 88.326 454 45 5 80 529 318737693 318737244 3.250000e-149 538.0
18 TraesCS7A01G552200 chrUn 81.437 501 84 7 1421 1915 88204351 88204848 4.460000e-108 401.0
19 TraesCS7A01G552200 chrUn 81.325 498 85 6 1424 1915 281882333 281881838 5.760000e-107 398.0
20 TraesCS7A01G552200 chrUn 81.238 501 85 7 1421 1915 224362715 224363212 2.070000e-106 396.0
21 TraesCS7A01G552200 chrUn 81.238 501 84 8 1421 1915 234834843 234835339 2.070000e-106 396.0
22 TraesCS7A01G552200 chr4D 86.087 460 58 5 68 524 506411652 506412108 9.240000e-135 490.0
23 TraesCS7A01G552200 chr4B 85.746 456 57 7 74 524 662757533 662757081 2.590000e-130 475.0
24 TraesCS7A01G552200 chr4B 84.914 464 58 11 68 524 663809434 663809892 2.610000e-125 459.0
25 TraesCS7A01G552200 chr4B 94.220 173 10 0 635 807 662757095 662756923 6.100000e-67 265.0
26 TraesCS7A01G552200 chr4B 93.642 173 11 0 635 807 663809878 663810050 2.840000e-65 259.0
27 TraesCS7A01G552200 chr5A 83.974 468 53 14 68 524 702730080 702730536 2.040000e-116 429.0
28 TraesCS7A01G552200 chr2D 78.656 506 97 7 1420 1915 29687171 29687675 2.760000e-85 326.0
29 TraesCS7A01G552200 chr2B 78.614 505 88 14 1420 1916 47698689 47699181 1.660000e-82 316.0
30 TraesCS7A01G552200 chr2B 78.614 505 88 14 1420 1916 47719657 47720149 1.660000e-82 316.0
31 TraesCS7A01G552200 chr2B 78.218 505 89 16 1420 1916 47817787 47818278 1.290000e-78 303.0
32 TraesCS7A01G552200 chr2B 78.020 505 91 14 1420 1916 47746134 47746626 1.670000e-77 300.0
33 TraesCS7A01G552200 chr2B 77.822 505 92 14 1420 1916 47775819 47776311 7.780000e-76 294.0
34 TraesCS7A01G552200 chr3D 92.486 173 12 1 635 807 558787803 558787974 2.210000e-61 246.0
35 TraesCS7A01G552200 chr3D 92.105 114 7 2 523 634 22385918 22385805 2.960000e-35 159.0
36 TraesCS7A01G552200 chr3B 92.262 168 13 0 635 802 741604662 741604829 3.700000e-59 239.0
37 TraesCS7A01G552200 chr1D 96.117 103 3 1 533 634 249620654 249620756 1.770000e-37 167.0
38 TraesCS7A01G552200 chr1D 79.487 195 40 0 1721 1915 100825372 100825178 3.860000e-29 139.0
39 TraesCS7A01G552200 chr6A 92.920 113 6 2 523 634 589466390 589466279 2.290000e-36 163.0
40 TraesCS7A01G552200 chr6A 92.920 113 6 2 523 634 589510736 589510625 2.290000e-36 163.0
41 TraesCS7A01G552200 chr6A 92.920 113 7 1 523 634 589639380 589639268 2.290000e-36 163.0
42 TraesCS7A01G552200 chr5B 92.920 113 7 1 523 634 429187836 429187724 2.290000e-36 163.0
43 TraesCS7A01G552200 chr6D 92.105 114 6 3 523 634 371534941 371535053 1.060000e-34 158.0
44 TraesCS7A01G552200 chr6D 95.238 63 3 0 7 69 35397176 35397238 1.820000e-17 100.0
45 TraesCS7A01G552200 chr1A 90.833 120 7 4 517 633 4852308 4852426 1.060000e-34 158.0
46 TraesCS7A01G552200 chr1A 77.949 195 43 0 1721 1915 104580647 104580841 3.880000e-24 122.0
47 TraesCS7A01G552200 chr1B 78.756 193 41 0 1714 1906 150995004 150995196 2.320000e-26 130.0


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 TraesCS7A01G552200 chr7A 725309782 725312652 2870 True 5302.000000 5302 100.000000 1 2871 1 chr7A.!!$R2 2870
1 TraesCS7A01G552200 chr7A 725227463 725232178 4715 True 1470.000000 2023 89.719500 635 2869 2 chr7A.!!$R3 2234
2 TraesCS7A01G552200 chr7D 629325433 629331275 5842 True 1163.666667 2065 89.392667 72 2871 3 chr7D.!!$R2 2799
3 TraesCS7A01G552200 chr7B 732151051 732153088 2037 False 1144.500000 1751 89.627000 68 1915 2 chr7B.!!$F3 1847
4 TraesCS7A01G552200 chr7B 732192930 732194964 2034 False 1120.500000 1720 89.125500 68 1915 2 chr7B.!!$F4 1847
5 TraesCS7A01G552200 chrUn 318736158 318737693 1535 True 815.000000 1092 90.070000 80 1419 2 chrUn.!!$R2 1339
6 TraesCS7A01G552200 chr4B 662756923 662757533 610 True 370.000000 475 89.983000 74 807 2 chr4B.!!$R1 733
7 TraesCS7A01G552200 chr4B 663809434 663810050 616 False 359.000000 459 89.278000 68 807 2 chr4B.!!$F1 739
8 TraesCS7A01G552200 chr2D 29687171 29687675 504 False 326.000000 326 78.656000 1420 1915 1 chr2D.!!$F1 495

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
608 618 0.03438 CCAGAGAGTGGTCCGGTCTA 60.034 60.0 0.0 0.0 42.17 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 5750 0.107993 CTGGCGATTCTTCAGGAGCA 60.108 55.0 0.0 0.0 0.0 4.26 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
22 23 3.071874 TGACATAGGCTTCTTTGGTGG 57.928 47.619 0.00 0.00 0.00 4.61
23 24 2.642311 TGACATAGGCTTCTTTGGTGGA 59.358 45.455 0.00 0.00 0.00 4.02
24 25 3.274288 GACATAGGCTTCTTTGGTGGAG 58.726 50.000 0.00 0.00 0.00 3.86
25 26 2.912956 ACATAGGCTTCTTTGGTGGAGA 59.087 45.455 0.00 0.00 0.00 3.71
26 27 3.330701 ACATAGGCTTCTTTGGTGGAGAA 59.669 43.478 0.00 0.00 0.00 2.87
30 31 1.160137 CTTCTTTGGTGGAGAAGCGG 58.840 55.000 1.41 0.00 42.40 5.52
31 32 0.889186 TTCTTTGGTGGAGAAGCGGC 60.889 55.000 0.00 0.00 0.00 6.53
32 33 1.302832 CTTTGGTGGAGAAGCGGCT 60.303 57.895 0.00 0.00 0.00 5.52
33 34 1.580845 CTTTGGTGGAGAAGCGGCTG 61.581 60.000 1.81 0.00 0.00 4.85
34 35 4.704833 TGGTGGAGAAGCGGCTGC 62.705 66.667 10.33 10.33 43.24 5.25
52 53 4.821935 CCCCCAGAAGAAAGCGTT 57.178 55.556 0.00 0.00 0.00 4.84
53 54 2.556286 CCCCCAGAAGAAAGCGTTC 58.444 57.895 3.99 3.99 0.00 3.95
54 55 1.298859 CCCCCAGAAGAAAGCGTTCG 61.299 60.000 6.74 0.00 38.90 3.95
55 56 0.602905 CCCCAGAAGAAAGCGTTCGT 60.603 55.000 6.74 3.44 38.90 3.85
56 57 0.790814 CCCAGAAGAAAGCGTTCGTC 59.209 55.000 17.72 17.72 41.12 4.20
57 58 0.790814 CCAGAAGAAAGCGTTCGTCC 59.209 55.000 20.67 8.60 41.57 4.79
58 59 1.605712 CCAGAAGAAAGCGTTCGTCCT 60.606 52.381 20.67 10.42 41.57 3.85
59 60 1.457303 CAGAAGAAAGCGTTCGTCCTG 59.543 52.381 20.67 16.72 41.57 3.86
60 61 1.068741 AGAAGAAAGCGTTCGTCCTGT 59.931 47.619 20.67 4.20 41.57 4.00
61 62 1.865340 GAAGAAAGCGTTCGTCCTGTT 59.135 47.619 15.30 0.17 36.56 3.16
62 63 1.949465 AGAAAGCGTTCGTCCTGTTT 58.051 45.000 6.74 0.00 38.90 2.83
63 64 2.285977 AGAAAGCGTTCGTCCTGTTTT 58.714 42.857 6.74 0.00 38.90 2.43
64 65 2.031683 AGAAAGCGTTCGTCCTGTTTTG 59.968 45.455 6.74 0.00 38.90 2.44
65 66 0.661020 AAGCGTTCGTCCTGTTTTGG 59.339 50.000 0.00 0.00 0.00 3.28
66 67 1.370051 GCGTTCGTCCTGTTTTGGC 60.370 57.895 0.00 0.00 0.00 4.52
70 71 0.941542 TTCGTCCTGTTTTGGCGAAG 59.058 50.000 0.00 0.00 39.09 3.79
78 79 4.119136 CCTGTTTTGGCGAAGAAAACATT 58.881 39.130 15.68 0.00 46.74 2.71
83 84 5.710613 TTTGGCGAAGAAAACATTTTGAC 57.289 34.783 0.00 0.00 0.00 3.18
96 97 5.300969 ACATTTTGACTGTCATCAATCCG 57.699 39.130 11.86 5.46 38.37 4.18
98 99 3.417069 TTTGACTGTCATCAATCCGGT 57.583 42.857 11.86 0.00 38.37 5.28
99 100 2.672961 TGACTGTCATCAATCCGGTC 57.327 50.000 6.36 0.00 35.51 4.79
100 101 2.179427 TGACTGTCATCAATCCGGTCT 58.821 47.619 6.36 0.00 35.86 3.85
102 103 2.932614 GACTGTCATCAATCCGGTCTTG 59.067 50.000 0.00 7.28 32.84 3.02
103 104 1.667724 CTGTCATCAATCCGGTCTTGC 59.332 52.381 0.00 0.00 0.00 4.01
107 110 2.487762 TCATCAATCCGGTCTTGCAAAC 59.512 45.455 0.00 1.91 0.00 2.93
116 119 1.336755 GGTCTTGCAAACGGACATTGT 59.663 47.619 16.42 0.00 0.00 2.71
126 129 3.870633 ACGGACATTGTAGAAGGACTC 57.129 47.619 0.00 0.00 0.00 3.36
134 137 3.232213 TGTAGAAGGACTCGAATGTGC 57.768 47.619 0.00 0.00 0.00 4.57
153 156 0.688087 CCTTCCGGCTAAGACTCCCT 60.688 60.000 4.50 0.00 0.00 4.20
183 186 0.830444 TACACCCGTGAGCACCTTCT 60.830 55.000 0.96 0.00 0.00 2.85
250 253 9.802039 AAGTTGTTTCCATATGGAGTTTAACTA 57.198 29.630 27.61 21.51 46.36 2.24
260 265 4.824289 TGGAGTTTAACTAAAGGCTACCG 58.176 43.478 0.00 0.00 0.00 4.02
261 266 4.284234 TGGAGTTTAACTAAAGGCTACCGT 59.716 41.667 0.00 0.00 0.00 4.83
262 267 4.628766 GGAGTTTAACTAAAGGCTACCGTG 59.371 45.833 0.00 0.00 0.00 4.94
277 286 2.561956 CGTGTCTGTCCGACCTGGT 61.562 63.158 0.00 0.00 42.13 4.00
305 314 3.193479 GGCTCCCAAACTGATGGTTAAAG 59.807 47.826 4.15 0.00 38.91 1.85
315 324 1.303091 ATGGTTAAAGTCCGCGTGGC 61.303 55.000 11.05 5.67 34.14 5.01
366 376 0.812412 GTATACCGCCACGCCACAAT 60.812 55.000 0.00 0.00 0.00 2.71
384 394 0.326264 ATATCTTCCATGGCCTCCGC 59.674 55.000 6.96 0.00 0.00 5.54
434 444 5.583495 CAACATCAACCGGTTTAAAGACAA 58.417 37.500 19.55 0.00 0.00 3.18
516 526 4.684724 TGTTATAACACTGTCCCTCCTCT 58.315 43.478 14.35 0.00 33.17 3.69
517 527 5.834460 TGTTATAACACTGTCCCTCCTCTA 58.166 41.667 14.35 0.00 33.17 2.43
518 528 5.892119 TGTTATAACACTGTCCCTCCTCTAG 59.108 44.000 14.35 0.00 33.17 2.43
519 529 2.239681 AACACTGTCCCTCCTCTAGG 57.760 55.000 0.00 0.00 46.09 3.02
520 530 1.085715 ACACTGTCCCTCCTCTAGGT 58.914 55.000 0.00 0.00 44.90 3.08
521 531 1.272760 ACACTGTCCCTCCTCTAGGTG 60.273 57.143 0.00 0.00 44.90 4.00
522 532 1.085715 ACTGTCCCTCCTCTAGGTGT 58.914 55.000 0.00 0.00 44.90 4.16
523 533 1.433592 ACTGTCCCTCCTCTAGGTGTT 59.566 52.381 0.00 0.00 44.90 3.32
524 534 2.158143 ACTGTCCCTCCTCTAGGTGTTT 60.158 50.000 0.00 0.00 44.90 2.83
525 535 2.907042 CTGTCCCTCCTCTAGGTGTTTT 59.093 50.000 0.00 0.00 44.90 2.43
526 536 3.323775 TGTCCCTCCTCTAGGTGTTTTT 58.676 45.455 0.00 0.00 44.90 1.94
544 554 2.489938 TTTTGAGAGAATCACCGGGG 57.510 50.000 6.32 0.00 37.77 5.73
545 555 1.651737 TTTGAGAGAATCACCGGGGA 58.348 50.000 9.99 9.99 37.77 4.81
546 556 1.195115 TTGAGAGAATCACCGGGGAG 58.805 55.000 14.24 0.00 37.77 4.30
548 558 0.397254 GAGAGAATCACCGGGGAGGA 60.397 60.000 14.24 0.48 45.00 3.71
549 559 0.397816 AGAGAATCACCGGGGAGGAG 60.398 60.000 14.24 0.00 45.00 3.69
550 560 0.688087 GAGAATCACCGGGGAGGAGT 60.688 60.000 14.24 0.00 45.00 3.85
551 561 0.688087 AGAATCACCGGGGAGGAGTC 60.688 60.000 14.24 9.66 45.00 3.36
552 562 1.687297 GAATCACCGGGGAGGAGTCC 61.687 65.000 14.24 0.00 45.00 3.85
571 581 6.936968 AGTCCCTCCACCTGAATATATTAC 57.063 41.667 0.00 0.00 0.00 1.89
572 582 6.635021 AGTCCCTCCACCTGAATATATTACT 58.365 40.000 0.00 0.00 0.00 2.24
573 583 6.726764 AGTCCCTCCACCTGAATATATTACTC 59.273 42.308 0.00 0.00 0.00 2.59
574 584 6.497259 GTCCCTCCACCTGAATATATTACTCA 59.503 42.308 0.00 0.00 0.00 3.41
575 585 7.016268 GTCCCTCCACCTGAATATATTACTCAA 59.984 40.741 0.00 0.00 0.00 3.02
576 586 7.570982 TCCCTCCACCTGAATATATTACTCAAA 59.429 37.037 0.00 0.00 0.00 2.69
577 587 7.880195 CCCTCCACCTGAATATATTACTCAAAG 59.120 40.741 0.00 0.00 0.00 2.77
578 588 8.432805 CCTCCACCTGAATATATTACTCAAAGT 58.567 37.037 0.00 0.00 0.00 2.66
579 589 9.265901 CTCCACCTGAATATATTACTCAAAGTG 57.734 37.037 0.00 3.99 0.00 3.16
580 590 8.210946 TCCACCTGAATATATTACTCAAAGTGG 58.789 37.037 18.45 18.45 41.06 4.00
581 591 7.041098 CCACCTGAATATATTACTCAAAGTGGC 60.041 40.741 15.30 0.00 37.05 5.01
582 592 6.998673 ACCTGAATATATTACTCAAAGTGGCC 59.001 38.462 0.00 0.00 0.00 5.36
583 593 6.998074 CCTGAATATATTACTCAAAGTGGCCA 59.002 38.462 0.00 0.00 0.00 5.36
584 594 7.667219 CCTGAATATATTACTCAAAGTGGCCAT 59.333 37.037 9.72 0.00 0.00 4.40
585 595 8.995027 TGAATATATTACTCAAAGTGGCCATT 57.005 30.769 9.72 0.00 0.00 3.16
589 599 4.981806 TTACTCAAAGTGGCCATTATGC 57.018 40.909 9.72 0.00 0.00 3.14
606 616 3.289525 CCAGAGAGTGGTCCGGTC 58.710 66.667 0.00 0.00 42.17 4.79
607 617 1.304547 CCAGAGAGTGGTCCGGTCT 60.305 63.158 0.00 0.00 42.17 3.85
608 618 0.034380 CCAGAGAGTGGTCCGGTCTA 60.034 60.000 0.00 0.00 42.17 2.59
609 619 1.410365 CCAGAGAGTGGTCCGGTCTAT 60.410 57.143 0.00 0.00 42.17 1.98
610 620 1.950909 CAGAGAGTGGTCCGGTCTATC 59.049 57.143 0.00 3.48 0.00 2.08
611 621 1.564818 AGAGAGTGGTCCGGTCTATCA 59.435 52.381 0.00 0.00 0.00 2.15
612 622 1.950909 GAGAGTGGTCCGGTCTATCAG 59.049 57.143 0.00 0.00 0.00 2.90
613 623 1.033574 GAGTGGTCCGGTCTATCAGG 58.966 60.000 0.00 0.00 0.00 3.86
614 624 0.397254 AGTGGTCCGGTCTATCAGGG 60.397 60.000 0.00 0.00 32.28 4.45
615 625 0.396695 GTGGTCCGGTCTATCAGGGA 60.397 60.000 0.00 0.00 32.28 4.20
616 626 0.337082 TGGTCCGGTCTATCAGGGAA 59.663 55.000 0.00 0.00 32.28 3.97
617 627 1.273381 TGGTCCGGTCTATCAGGGAAA 60.273 52.381 0.00 0.00 32.28 3.13
618 628 1.138464 GGTCCGGTCTATCAGGGAAAC 59.862 57.143 0.00 0.00 32.28 2.78
706 1037 8.495160 AGGATCATCCCAAATATTTATTTGCA 57.505 30.769 14.74 6.50 46.87 4.08
823 1154 5.812642 CCAGCCTTGTATTCCTAATATAGCG 59.187 44.000 0.00 0.00 0.00 4.26
830 1161 6.707290 TGTATTCCTAATATAGCGCCATTGT 58.293 36.000 2.29 0.00 0.00 2.71
1037 1369 6.205270 GTGATTCTTTGTACGGGAAGGTTTAA 59.795 38.462 0.00 0.00 0.00 1.52
1174 1506 4.343814 TGATCAAGGACAAGTGTGTGACTA 59.656 41.667 0.00 0.00 38.41 2.59
1182 1514 3.882888 ACAAGTGTGTGACTATTGTTGGG 59.117 43.478 0.00 0.00 36.31 4.12
1281 1613 4.448060 CAGACCTTGTTTCTCTCGGTTAAC 59.552 45.833 0.00 0.00 0.00 2.01
1296 1628 5.643300 CGGTTAACGAAATCGAAACATTG 57.357 39.130 10.16 4.39 44.80 2.82
1297 1629 4.551892 CGGTTAACGAAATCGAAACATTGG 59.448 41.667 10.16 1.96 44.80 3.16
1329 1661 8.872845 CCATTTTTCTAAAGCATTCCAATGTAC 58.127 33.333 1.37 0.00 38.65 2.90
1559 1901 6.899393 TTTGCTGAACTCCTTATTCACAAT 57.101 33.333 0.00 0.00 32.40 2.71
1627 1969 6.775629 ACTCCATTGGTACTACAACATGTTTT 59.224 34.615 8.77 5.26 32.39 2.43
1632 1974 8.914654 CATTGGTACTACAACATGTTTTCATTG 58.085 33.333 8.77 0.00 33.04 2.82
1718 2070 7.807433 TCATACATGTGTACATTTCTTTTGTGC 59.193 33.333 9.11 0.00 33.61 4.57
1751 2103 9.077885 AGAGGTTGATTATTTCAAAGTTTGCTA 57.922 29.630 10.90 1.60 45.71 3.49
1858 2210 4.975147 TCCACTACACCCAAGGATCATTAT 59.025 41.667 0.00 0.00 0.00 1.28
1934 5567 7.755373 GCTTTTGTATATTCAGAACAAACCTCC 59.245 37.037 1.14 0.00 41.43 4.30
1954 5589 2.413837 CGGAAGAGAAACGATGTGGTT 58.586 47.619 0.00 0.00 0.00 3.67
1982 5617 3.520721 TCATTCATCCTGTCATGGACACT 59.479 43.478 0.00 0.00 37.67 3.55
1986 5621 0.603065 TCCTGTCATGGACACTGTCG 59.397 55.000 3.04 0.00 37.67 4.35
2040 5675 9.999009 GATATACATGGCATGAAACTATCAATG 57.001 33.333 32.74 4.33 42.54 2.82
2044 5679 7.483307 ACATGGCATGAAACTATCAATGTAAC 58.517 34.615 32.74 0.00 42.54 2.50
2045 5680 7.122501 ACATGGCATGAAACTATCAATGTAACA 59.877 33.333 32.74 0.00 42.54 2.41
2046 5681 7.087409 TGGCATGAAACTATCAATGTAACAG 57.913 36.000 0.00 0.00 42.54 3.16
2050 5685 7.846107 GCATGAAACTATCAATGTAACAGTACG 59.154 37.037 0.00 0.00 42.54 3.67
2055 5690 7.342769 ACTATCAATGTAACAGTACGGATCA 57.657 36.000 0.00 0.00 32.40 2.92
2056 5691 7.778083 ACTATCAATGTAACAGTACGGATCAA 58.222 34.615 0.00 0.00 32.40 2.57
2065 5700 7.762615 TGTAACAGTACGGATCAAATAAGAAGG 59.237 37.037 0.00 0.00 32.40 3.46
2071 5706 4.764823 ACGGATCAAATAAGAAGGTTGCAA 59.235 37.500 0.00 0.00 0.00 4.08
2083 5718 0.449388 GGTTGCAAGAATCCTCTGCG 59.551 55.000 0.00 0.00 31.92 5.18
2130 5765 2.693069 AGTGTTGCTCCTGAAGAATCG 58.307 47.619 0.00 0.00 0.00 3.34
2135 5770 0.107945 GCTCCTGAAGAATCGCCAGT 60.108 55.000 4.76 0.00 0.00 4.00
2136 5771 1.649664 CTCCTGAAGAATCGCCAGTG 58.350 55.000 4.76 0.00 0.00 3.66
2137 5772 0.391661 TCCTGAAGAATCGCCAGTGC 60.392 55.000 4.76 0.00 0.00 4.40
2138 5773 0.392193 CCTGAAGAATCGCCAGTGCT 60.392 55.000 4.76 0.00 34.43 4.40
2139 5774 1.005340 CTGAAGAATCGCCAGTGCTC 58.995 55.000 0.00 0.00 34.43 4.26
2140 5775 0.391661 TGAAGAATCGCCAGTGCTCC 60.392 55.000 0.00 0.00 34.43 4.70
2141 5776 1.424493 GAAGAATCGCCAGTGCTCCG 61.424 60.000 0.00 0.00 34.43 4.63
2142 5777 2.125512 GAATCGCCAGTGCTCCGT 60.126 61.111 0.00 0.00 34.43 4.69
2143 5778 1.141019 GAATCGCCAGTGCTCCGTA 59.859 57.895 0.00 0.00 34.43 4.02
2144 5779 0.872021 GAATCGCCAGTGCTCCGTAG 60.872 60.000 0.00 0.00 34.43 3.51
2145 5780 1.320344 AATCGCCAGTGCTCCGTAGA 61.320 55.000 0.00 0.00 34.43 2.59
2146 5781 1.320344 ATCGCCAGTGCTCCGTAGAA 61.320 55.000 0.00 0.00 34.43 2.10
2155 5790 1.816835 TGCTCCGTAGAAAGACATCGT 59.183 47.619 0.00 0.00 0.00 3.73
2216 5851 5.161943 TCATGATATGATGGCCAAGAGAG 57.838 43.478 10.96 0.00 33.59 3.20
2217 5852 4.596212 TCATGATATGATGGCCAAGAGAGT 59.404 41.667 10.96 0.00 33.59 3.24
2218 5853 5.781818 TCATGATATGATGGCCAAGAGAGTA 59.218 40.000 10.96 0.00 33.59 2.59
2219 5854 5.474578 TGATATGATGGCCAAGAGAGTAC 57.525 43.478 10.96 0.00 0.00 2.73
2220 5855 5.150715 TGATATGATGGCCAAGAGAGTACT 58.849 41.667 10.96 0.00 0.00 2.73
2221 5856 6.314917 TGATATGATGGCCAAGAGAGTACTA 58.685 40.000 10.96 0.00 0.00 1.82
2222 5857 6.782494 TGATATGATGGCCAAGAGAGTACTAA 59.218 38.462 10.96 0.00 0.00 2.24
2223 5858 4.737855 TGATGGCCAAGAGAGTACTAAC 57.262 45.455 10.96 0.00 0.00 2.34
2224 5859 4.093743 TGATGGCCAAGAGAGTACTAACA 58.906 43.478 10.96 0.00 0.00 2.41
2225 5860 4.160439 TGATGGCCAAGAGAGTACTAACAG 59.840 45.833 10.96 0.00 0.00 3.16
2226 5861 3.507411 TGGCCAAGAGAGTACTAACAGT 58.493 45.455 0.61 0.00 0.00 3.55
2268 5915 3.074412 ACACCTGCAAATTAACGAGGAG 58.926 45.455 0.00 0.00 0.00 3.69
2269 5916 3.244422 ACACCTGCAAATTAACGAGGAGA 60.244 43.478 0.00 0.00 0.00 3.71
2270 5917 3.941483 CACCTGCAAATTAACGAGGAGAT 59.059 43.478 0.00 0.00 0.00 2.75
2276 5923 6.083630 TGCAAATTAACGAGGAGATTTTTCG 58.916 36.000 0.00 0.00 40.02 3.46
2285 5932 5.521735 ACGAGGAGATTTTTCGAGAATGATG 59.478 40.000 0.00 0.00 37.73 3.07
2290 5937 6.094048 GGAGATTTTTCGAGAATGATGTTCCA 59.906 38.462 1.38 0.00 0.00 3.53
2332 5979 6.260050 TGAACTGTCAAAAGAGAATGTGGTAC 59.740 38.462 0.00 0.00 0.00 3.34
2372 6020 6.913673 TGCACGGTAAAGAAAGACAAAATTAC 59.086 34.615 0.00 0.00 0.00 1.89
2377 6025 9.893305 CGGTAAAGAAAGACAAAATTACAGAAT 57.107 29.630 0.00 0.00 0.00 2.40
2389 6037 9.308000 ACAAAATTACAGAATCAACTAATCCCA 57.692 29.630 0.00 0.00 0.00 4.37
2393 6041 5.779241 ACAGAATCAACTAATCCCAAGGA 57.221 39.130 0.00 0.00 35.55 3.36
2394 6042 6.139679 ACAGAATCAACTAATCCCAAGGAA 57.860 37.500 0.00 0.00 34.34 3.36
2397 6045 7.675619 ACAGAATCAACTAATCCCAAGGAAAAT 59.324 33.333 0.00 0.00 34.34 1.82
2431 6079 3.059352 CAGGTTAACTGGAAGGGTGAG 57.941 52.381 5.42 0.00 43.70 3.51
2437 6085 0.113776 ACTGGAAGGGTGAGTCGGTA 59.886 55.000 0.00 0.00 39.30 4.02
2441 6096 1.340568 GGAAGGGTGAGTCGGTATAGC 59.659 57.143 0.00 0.00 0.00 2.97
2450 6105 4.459685 GTGAGTCGGTATAGCTACCATGAT 59.540 45.833 6.48 0.00 46.80 2.45
2460 6115 3.027412 AGCTACCATGATGAACTCGAGT 58.973 45.455 13.58 13.58 0.00 4.18
2464 6119 2.562738 ACCATGATGAACTCGAGTGTCA 59.437 45.455 20.85 22.48 0.00 3.58
2478 6133 2.227388 GAGTGTCAGCTTGTTGGGATTG 59.773 50.000 0.00 0.00 0.00 2.67
2483 6138 3.256631 GTCAGCTTGTTGGGATTGATGTT 59.743 43.478 0.00 0.00 0.00 2.71
2484 6139 3.256383 TCAGCTTGTTGGGATTGATGTTG 59.744 43.478 0.00 0.00 0.00 3.33
2486 6141 4.081862 CAGCTTGTTGGGATTGATGTTGAT 60.082 41.667 0.00 0.00 0.00 2.57
2490 6145 1.391577 TGGGATTGATGTTGATGGCG 58.608 50.000 0.00 0.00 0.00 5.69
2493 6148 2.016318 GGATTGATGTTGATGGCGTGA 58.984 47.619 0.00 0.00 0.00 4.35
2518 6173 3.869623 GCATCCTCTGCCTCTTCAA 57.130 52.632 0.00 0.00 45.66 2.69
2536 6191 2.360475 GCTCTGGCTTGGACCACC 60.360 66.667 0.00 0.00 35.33 4.61
2544 6199 1.898574 CTTGGACCACCACACAGCC 60.899 63.158 0.00 0.00 46.80 4.85
2551 6206 1.754745 CACCACACAGCCTACCACT 59.245 57.895 0.00 0.00 0.00 4.00
2553 6208 0.843984 ACCACACAGCCTACCACTTT 59.156 50.000 0.00 0.00 0.00 2.66
2574 6229 7.228706 CACTTTCCAACATAGACCTGTTTAAGT 59.771 37.037 0.00 0.00 37.25 2.24
2580 6235 7.118390 CCAACATAGACCTGTTTAAGTGAAGAG 59.882 40.741 0.00 0.00 37.25 2.85
2593 6248 2.110899 AGTGAAGAGAGGTTCTCCAGGA 59.889 50.000 2.60 0.00 44.42 3.86
2626 6281 2.505407 TCACCAAATCGATCCCATGTCT 59.495 45.455 0.00 0.00 0.00 3.41
2672 6327 1.208052 GGTCTGTAGCTTCTGCATGGA 59.792 52.381 0.00 0.00 42.74 3.41
2682 6337 0.328926 TCTGCATGGATCCTTGTGCA 59.671 50.000 26.91 26.91 44.50 4.57
2706 6361 3.181467 ACTTCAGCTCCATGATGCTACTC 60.181 47.826 11.12 0.00 37.81 2.59
2712 6367 2.301296 CTCCATGATGCTACTCCCGATT 59.699 50.000 0.00 0.00 0.00 3.34
2715 6370 3.499918 CCATGATGCTACTCCCGATTTTC 59.500 47.826 0.00 0.00 0.00 2.29
2733 6388 3.303135 AGCCTTGCGAGACACCGA 61.303 61.111 1.22 0.00 0.00 4.69
2736 6391 1.860078 CCTTGCGAGACACCGAAAC 59.140 57.895 1.22 0.00 0.00 2.78
2737 6392 0.878523 CCTTGCGAGACACCGAAACA 60.879 55.000 1.22 0.00 0.00 2.83
2747 6402 2.415512 GACACCGAAACAGATAACTGCC 59.584 50.000 0.00 0.00 46.95 4.85
2748 6403 2.224426 ACACCGAAACAGATAACTGCCA 60.224 45.455 0.00 0.00 46.95 4.92
2765 6420 2.971330 TGCCATCAATCACCAACCTTTT 59.029 40.909 0.00 0.00 0.00 2.27
2780 6441 0.845768 CTTTTGCTTCGTGCGGTTTG 59.154 50.000 0.00 0.00 46.63 2.93
2795 6459 1.269448 GGTTTGCGCCACCCATATATG 59.731 52.381 13.75 5.68 0.00 1.78
2804 6468 4.563374 CGCCACCCATATATGAAGATCACA 60.563 45.833 14.54 0.00 0.00 3.58
2830 6494 2.036256 ACATGGGGCCAAGCACTC 59.964 61.111 4.39 0.00 29.71 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.019174 CCACCAAAGAAGCCTATGTCATT 58.981 43.478 0.00 0.00 0.00 2.57
1 2 3.266772 TCCACCAAAGAAGCCTATGTCAT 59.733 43.478 0.00 0.00 0.00 3.06
2 3 2.642311 TCCACCAAAGAAGCCTATGTCA 59.358 45.455 0.00 0.00 0.00 3.58
3 4 3.055094 TCTCCACCAAAGAAGCCTATGTC 60.055 47.826 0.00 0.00 0.00 3.06
4 5 2.912956 TCTCCACCAAAGAAGCCTATGT 59.087 45.455 0.00 0.00 0.00 2.29
5 6 3.634397 TCTCCACCAAAGAAGCCTATG 57.366 47.619 0.00 0.00 0.00 2.23
6 7 4.227864 CTTCTCCACCAAAGAAGCCTAT 57.772 45.455 0.37 0.00 42.25 2.57
7 8 3.703001 CTTCTCCACCAAAGAAGCCTA 57.297 47.619 0.37 0.00 42.25 3.93
8 9 2.575805 CTTCTCCACCAAAGAAGCCT 57.424 50.000 0.37 0.00 42.25 4.58
12 13 0.889186 GCCGCTTCTCCACCAAAGAA 60.889 55.000 0.00 0.00 0.00 2.52
13 14 1.302511 GCCGCTTCTCCACCAAAGA 60.303 57.895 0.00 0.00 0.00 2.52
14 15 1.302832 AGCCGCTTCTCCACCAAAG 60.303 57.895 0.00 0.00 0.00 2.77
15 16 1.600636 CAGCCGCTTCTCCACCAAA 60.601 57.895 0.00 0.00 0.00 3.28
16 17 2.032528 CAGCCGCTTCTCCACCAA 59.967 61.111 0.00 0.00 0.00 3.67
17 18 4.704833 GCAGCCGCTTCTCCACCA 62.705 66.667 0.00 0.00 34.30 4.17
35 36 1.298859 CGAACGCTTTCTTCTGGGGG 61.299 60.000 1.12 0.00 0.00 5.40
36 37 0.602905 ACGAACGCTTTCTTCTGGGG 60.603 55.000 1.12 0.00 0.00 4.96
37 38 0.790814 GACGAACGCTTTCTTCTGGG 59.209 55.000 1.12 0.00 29.34 4.45
38 39 0.790814 GGACGAACGCTTTCTTCTGG 59.209 55.000 8.94 0.00 31.97 3.86
39 40 1.457303 CAGGACGAACGCTTTCTTCTG 59.543 52.381 8.94 6.17 31.97 3.02
40 41 1.068741 ACAGGACGAACGCTTTCTTCT 59.931 47.619 8.94 0.00 31.97 2.85
41 42 1.499049 ACAGGACGAACGCTTTCTTC 58.501 50.000 1.12 1.19 30.78 2.87
42 43 1.949465 AACAGGACGAACGCTTTCTT 58.051 45.000 1.12 0.00 0.00 2.52
43 44 1.949465 AAACAGGACGAACGCTTTCT 58.051 45.000 1.12 0.00 0.00 2.52
44 45 2.372350 CAAAACAGGACGAACGCTTTC 58.628 47.619 0.00 0.00 0.00 2.62
45 46 1.064952 CCAAAACAGGACGAACGCTTT 59.935 47.619 0.00 0.00 0.00 3.51
46 47 0.661020 CCAAAACAGGACGAACGCTT 59.339 50.000 0.00 0.00 0.00 4.68
47 48 1.782028 GCCAAAACAGGACGAACGCT 61.782 55.000 0.00 0.00 0.00 5.07
48 49 1.370051 GCCAAAACAGGACGAACGC 60.370 57.895 0.00 0.00 0.00 4.84
49 50 1.083015 CGCCAAAACAGGACGAACG 60.083 57.895 0.00 0.00 32.44 3.95
50 51 0.658897 TTCGCCAAAACAGGACGAAC 59.341 50.000 0.00 0.00 40.00 3.95
51 52 0.941542 CTTCGCCAAAACAGGACGAA 59.058 50.000 0.00 0.00 41.41 3.85
52 53 0.105224 TCTTCGCCAAAACAGGACGA 59.895 50.000 0.00 0.00 36.13 4.20
53 54 0.941542 TTCTTCGCCAAAACAGGACG 59.058 50.000 0.00 0.00 0.00 4.79
54 55 3.113322 GTTTTCTTCGCCAAAACAGGAC 58.887 45.455 10.00 0.00 41.48 3.85
55 56 2.755655 TGTTTTCTTCGCCAAAACAGGA 59.244 40.909 12.37 0.00 44.82 3.86
56 57 3.157932 TGTTTTCTTCGCCAAAACAGG 57.842 42.857 12.37 0.00 44.82 4.00
59 60 5.957220 GTCAAAATGTTTTCTTCGCCAAAAC 59.043 36.000 8.61 8.61 41.97 2.43
60 61 5.872070 AGTCAAAATGTTTTCTTCGCCAAAA 59.128 32.000 0.00 0.00 0.00 2.44
61 62 5.290643 CAGTCAAAATGTTTTCTTCGCCAAA 59.709 36.000 0.00 0.00 0.00 3.28
62 63 4.803088 CAGTCAAAATGTTTTCTTCGCCAA 59.197 37.500 0.00 0.00 0.00 4.52
63 64 4.142271 ACAGTCAAAATGTTTTCTTCGCCA 60.142 37.500 0.00 0.00 0.00 5.69
64 65 4.359706 ACAGTCAAAATGTTTTCTTCGCC 58.640 39.130 0.00 0.00 0.00 5.54
65 66 5.034152 TGACAGTCAAAATGTTTTCTTCGC 58.966 37.500 0.00 0.00 0.00 4.70
66 67 6.912051 TGATGACAGTCAAAATGTTTTCTTCG 59.088 34.615 7.50 0.00 0.00 3.79
70 71 7.148918 CGGATTGATGACAGTCAAAATGTTTTC 60.149 37.037 16.02 4.97 41.09 2.29
78 79 3.007940 AGACCGGATTGATGACAGTCAAA 59.992 43.478 9.46 0.00 41.09 2.69
83 84 1.667724 GCAAGACCGGATTGATGACAG 59.332 52.381 22.65 1.14 0.00 3.51
96 97 1.336755 ACAATGTCCGTTTGCAAGACC 59.663 47.619 13.07 0.00 0.00 3.85
98 99 3.734463 TCTACAATGTCCGTTTGCAAGA 58.266 40.909 0.00 0.00 0.00 3.02
99 100 4.466828 CTTCTACAATGTCCGTTTGCAAG 58.533 43.478 0.00 0.00 0.00 4.01
100 101 3.252215 CCTTCTACAATGTCCGTTTGCAA 59.748 43.478 0.00 0.00 0.00 4.08
102 103 3.071479 TCCTTCTACAATGTCCGTTTGC 58.929 45.455 0.00 0.00 0.00 3.68
103 104 4.315803 AGTCCTTCTACAATGTCCGTTTG 58.684 43.478 0.00 0.00 0.00 2.93
107 110 2.422479 TCGAGTCCTTCTACAATGTCCG 59.578 50.000 0.00 0.00 0.00 4.79
116 119 2.457598 AGGCACATTCGAGTCCTTCTA 58.542 47.619 0.00 0.00 0.00 2.10
134 137 2.242094 AAGGGAGTCTTAGCCGGAAGG 61.242 57.143 5.05 0.00 44.31 3.46
171 174 0.606604 TTCGGGTAGAAGGTGCTCAC 59.393 55.000 0.00 0.00 34.26 3.51
183 186 6.016108 CCAAGGAAAATAAAACACTTCGGGTA 60.016 38.462 0.00 0.00 0.00 3.69
250 253 0.320697 GGACAGACACGGTAGCCTTT 59.679 55.000 0.00 0.00 0.00 3.11
253 256 2.181021 CGGACAGACACGGTAGCC 59.819 66.667 0.00 0.00 0.00 3.93
315 324 2.709125 TTCTCAGTTCGGTGGGCGTG 62.709 60.000 0.00 0.00 0.00 5.34
321 330 0.969894 AGGACCTTCTCAGTTCGGTG 59.030 55.000 0.00 0.00 0.00 4.94
353 363 0.304705 GAAGATATTGTGGCGTGGCG 59.695 55.000 0.00 0.00 0.00 5.69
366 376 1.754745 GCGGAGGCCATGGAAGATA 59.245 57.895 18.40 0.00 0.00 1.98
384 394 7.573968 AGAATAATTCAAATTCTTCTCCGGG 57.426 36.000 0.00 0.00 40.03 5.73
392 402 9.932207 TGATGTTGCAAGAATAATTCAAATTCT 57.068 25.926 0.00 0.00 43.80 2.40
409 419 3.632604 TCTTTAAACCGGTTGATGTTGCA 59.367 39.130 23.08 0.00 0.00 4.08
448 458 0.040646 ACACGGGACAGTGGGATCTA 59.959 55.000 7.46 0.00 45.80 1.98
524 534 2.373836 TCCCCGGTGATTCTCTCAAAAA 59.626 45.455 0.00 0.00 35.07 1.94
525 535 1.982226 TCCCCGGTGATTCTCTCAAAA 59.018 47.619 0.00 0.00 35.07 2.44
526 536 1.555075 CTCCCCGGTGATTCTCTCAAA 59.445 52.381 0.00 0.00 35.07 2.69
527 537 1.195115 CTCCCCGGTGATTCTCTCAA 58.805 55.000 0.00 0.00 35.07 3.02
528 538 0.687757 CCTCCCCGGTGATTCTCTCA 60.688 60.000 0.00 0.00 0.00 3.27
529 539 0.397254 TCCTCCCCGGTGATTCTCTC 60.397 60.000 0.00 0.00 0.00 3.20
530 540 0.397816 CTCCTCCCCGGTGATTCTCT 60.398 60.000 0.00 0.00 0.00 3.10
531 541 0.688087 ACTCCTCCCCGGTGATTCTC 60.688 60.000 0.00 0.00 0.00 2.87
532 542 0.688087 GACTCCTCCCCGGTGATTCT 60.688 60.000 0.00 0.00 0.00 2.40
533 543 1.687297 GGACTCCTCCCCGGTGATTC 61.687 65.000 0.00 0.00 0.00 2.52
534 544 1.689582 GGACTCCTCCCCGGTGATT 60.690 63.158 0.00 0.00 0.00 2.57
535 545 2.041819 GGACTCCTCCCCGGTGAT 60.042 66.667 0.00 0.00 0.00 3.06
549 559 6.497259 TGAGTAATATATTCAGGTGGAGGGAC 59.503 42.308 0.00 0.00 0.00 4.46
550 560 6.630131 TGAGTAATATATTCAGGTGGAGGGA 58.370 40.000 0.00 0.00 0.00 4.20
551 561 6.935240 TGAGTAATATATTCAGGTGGAGGG 57.065 41.667 0.00 0.00 0.00 4.30
552 562 8.432805 ACTTTGAGTAATATATTCAGGTGGAGG 58.567 37.037 0.00 0.00 0.00 4.30
553 563 9.265901 CACTTTGAGTAATATATTCAGGTGGAG 57.734 37.037 0.00 0.00 32.34 3.86
554 564 8.210946 CCACTTTGAGTAATATATTCAGGTGGA 58.789 37.037 20.94 0.00 43.68 4.02
555 565 7.041098 GCCACTTTGAGTAATATATTCAGGTGG 60.041 40.741 21.06 21.06 43.73 4.61
556 566 7.041098 GGCCACTTTGAGTAATATATTCAGGTG 60.041 40.741 0.00 7.41 33.90 4.00
557 567 6.998673 GGCCACTTTGAGTAATATATTCAGGT 59.001 38.462 0.00 0.00 0.00 4.00
558 568 6.998074 TGGCCACTTTGAGTAATATATTCAGG 59.002 38.462 0.00 0.00 0.00 3.86
559 569 8.627208 ATGGCCACTTTGAGTAATATATTCAG 57.373 34.615 8.16 0.00 0.00 3.02
560 570 8.995027 AATGGCCACTTTGAGTAATATATTCA 57.005 30.769 8.16 0.00 0.00 2.57
563 573 8.960591 GCATAATGGCCACTTTGAGTAATATAT 58.039 33.333 8.16 0.00 0.00 0.86
564 574 8.335532 GCATAATGGCCACTTTGAGTAATATA 57.664 34.615 8.16 0.00 0.00 0.86
565 575 7.219484 GCATAATGGCCACTTTGAGTAATAT 57.781 36.000 8.16 0.00 0.00 1.28
566 576 6.633500 GCATAATGGCCACTTTGAGTAATA 57.367 37.500 8.16 0.00 0.00 0.98
567 577 5.520376 GCATAATGGCCACTTTGAGTAAT 57.480 39.130 8.16 0.00 0.00 1.89
568 578 4.981806 GCATAATGGCCACTTTGAGTAA 57.018 40.909 8.16 0.00 0.00 2.24
580 590 1.133976 ACCACTCTCTGGCATAATGGC 60.134 52.381 0.00 0.00 45.32 4.40
581 591 2.486191 GGACCACTCTCTGGCATAATGG 60.486 54.545 0.00 0.00 45.32 3.16
582 592 2.804572 CGGACCACTCTCTGGCATAATG 60.805 54.545 0.00 0.00 45.32 1.90
583 593 1.414181 CGGACCACTCTCTGGCATAAT 59.586 52.381 0.00 0.00 45.32 1.28
584 594 0.824109 CGGACCACTCTCTGGCATAA 59.176 55.000 0.00 0.00 45.32 1.90
585 595 1.043116 CCGGACCACTCTCTGGCATA 61.043 60.000 0.00 0.00 45.32 3.14
586 596 2.362369 CCGGACCACTCTCTGGCAT 61.362 63.158 0.00 0.00 45.32 4.40
587 597 2.997315 CCGGACCACTCTCTGGCA 60.997 66.667 0.00 0.00 45.32 4.92
588 598 2.997897 ACCGGACCACTCTCTGGC 60.998 66.667 9.46 0.00 45.32 4.85
590 600 1.950909 GATAGACCGGACCACTCTCTG 59.049 57.143 9.46 0.00 0.00 3.35
591 601 1.564818 TGATAGACCGGACCACTCTCT 59.435 52.381 9.46 0.00 0.00 3.10
592 602 1.950909 CTGATAGACCGGACCACTCTC 59.049 57.143 9.46 4.96 0.00 3.20
593 603 1.410365 CCTGATAGACCGGACCACTCT 60.410 57.143 9.46 1.74 0.00 3.24
594 604 1.033574 CCTGATAGACCGGACCACTC 58.966 60.000 9.46 0.00 0.00 3.51
595 605 0.397254 CCCTGATAGACCGGACCACT 60.397 60.000 9.46 4.38 0.00 4.00
596 606 0.396695 TCCCTGATAGACCGGACCAC 60.397 60.000 9.46 0.00 0.00 4.16
597 607 0.337082 TTCCCTGATAGACCGGACCA 59.663 55.000 9.46 0.00 0.00 4.02
598 608 1.138464 GTTTCCCTGATAGACCGGACC 59.862 57.143 9.46 0.00 0.00 4.46
599 609 1.138464 GGTTTCCCTGATAGACCGGAC 59.862 57.143 9.46 0.10 0.00 4.79
600 610 1.273381 TGGTTTCCCTGATAGACCGGA 60.273 52.381 9.46 0.00 33.07 5.14
601 611 1.139058 CTGGTTTCCCTGATAGACCGG 59.861 57.143 0.00 0.00 33.07 5.28
602 612 2.108168 TCTGGTTTCCCTGATAGACCG 58.892 52.381 0.00 0.00 34.10 4.79
603 613 3.243907 CGATCTGGTTTCCCTGATAGACC 60.244 52.174 1.66 0.00 46.18 3.85
604 614 3.637229 TCGATCTGGTTTCCCTGATAGAC 59.363 47.826 7.13 0.00 46.18 2.59
605 615 3.910989 TCGATCTGGTTTCCCTGATAGA 58.089 45.455 7.13 7.13 46.18 1.98
606 616 4.672587 TTCGATCTGGTTTCCCTGATAG 57.327 45.455 1.66 2.64 46.18 2.08
607 617 5.183228 GTTTTCGATCTGGTTTCCCTGATA 58.817 41.667 1.66 0.00 46.18 2.15
609 619 3.408634 GTTTTCGATCTGGTTTCCCTGA 58.591 45.455 0.00 0.00 42.21 3.86
610 620 2.488153 GGTTTTCGATCTGGTTTCCCTG 59.512 50.000 0.00 0.00 0.00 4.45
611 621 2.375509 AGGTTTTCGATCTGGTTTCCCT 59.624 45.455 0.00 0.00 0.00 4.20
612 622 2.791655 AGGTTTTCGATCTGGTTTCCC 58.208 47.619 0.00 0.00 0.00 3.97
613 623 3.688185 GGTAGGTTTTCGATCTGGTTTCC 59.312 47.826 0.00 0.00 0.00 3.13
614 624 4.576879 AGGTAGGTTTTCGATCTGGTTTC 58.423 43.478 0.00 0.00 0.00 2.78
615 625 4.565028 GGAGGTAGGTTTTCGATCTGGTTT 60.565 45.833 0.00 0.00 0.00 3.27
616 626 3.055312 GGAGGTAGGTTTTCGATCTGGTT 60.055 47.826 0.00 0.00 0.00 3.67
617 627 2.500504 GGAGGTAGGTTTTCGATCTGGT 59.499 50.000 0.00 0.00 0.00 4.00
618 628 2.766828 AGGAGGTAGGTTTTCGATCTGG 59.233 50.000 0.00 0.00 0.00 3.86
619 629 3.702045 AGAGGAGGTAGGTTTTCGATCTG 59.298 47.826 0.00 0.00 0.00 2.90
620 630 3.983821 AGAGGAGGTAGGTTTTCGATCT 58.016 45.455 0.00 0.00 0.00 2.75
621 631 4.278919 CCTAGAGGAGGTAGGTTTTCGATC 59.721 50.000 0.00 0.00 40.98 3.69
622 632 4.216708 CCTAGAGGAGGTAGGTTTTCGAT 58.783 47.826 0.00 0.00 40.98 3.59
623 633 3.629087 CCTAGAGGAGGTAGGTTTTCGA 58.371 50.000 0.00 0.00 40.98 3.71
823 1154 3.257127 TGTAAAAGGGTTAGCACAATGGC 59.743 43.478 0.00 0.00 0.00 4.40
830 1161 4.339748 TGCATCATGTAAAAGGGTTAGCA 58.660 39.130 0.00 0.00 0.00 3.49
902 1233 7.256691 CCCAATATGAGTTATAACTAGGCCACT 60.257 40.741 18.03 0.00 39.88 4.00
907 1238 7.016153 TGGCCCAATATGAGTTATAACTAGG 57.984 40.000 18.03 12.19 39.88 3.02
1037 1369 7.147567 GGAATTTGGGTATGTTGGGATAATTGT 60.148 37.037 0.00 0.00 0.00 2.71
1174 1506 4.162131 GGCTGAATTTCCATACCCAACAAT 59.838 41.667 0.00 0.00 0.00 2.71
1182 1514 4.016444 TGTCAAGGGCTGAATTTCCATAC 58.984 43.478 0.00 0.00 35.22 2.39
1260 1592 3.427863 CGTTAACCGAGAGAAACAAGGTC 59.572 47.826 0.00 0.00 39.56 3.85
1274 1606 4.551892 CCAATGTTTCGATTTCGTTAACCG 59.448 41.667 0.00 0.00 40.80 4.44
1281 1613 5.163804 TGGACATACCAATGTTTCGATTTCG 60.164 40.000 0.00 0.00 46.49 3.46
1296 1628 7.706607 GGAATGCTTTAGAAAAATGGACATACC 59.293 37.037 0.00 0.00 39.54 2.73
1297 1629 8.250332 TGGAATGCTTTAGAAAAATGGACATAC 58.750 33.333 0.00 0.00 0.00 2.39
1329 1661 5.746307 ATATAAGCATGATAGGCAATGCG 57.254 39.130 0.00 0.00 44.08 4.73
1534 1876 6.899393 TGTGAATAAGGAGTTCAGCAAAAT 57.101 33.333 0.00 0.00 36.35 1.82
1559 1901 1.486145 GGAGGAAACCTTCACCGGGA 61.486 60.000 6.32 0.00 31.76 5.14
1718 2070 6.968131 TGAAATAATCAACCTCTTCTCACG 57.032 37.500 0.00 0.00 34.30 4.35
1751 2103 5.663106 TCATTGGAATGGAGTAGTAGCTCTT 59.337 40.000 0.00 0.00 37.03 2.85
1868 2220 9.832445 CTCTTTAATAACTATGTTGCCTTCCTA 57.168 33.333 0.00 0.00 0.00 2.94
1934 5567 2.080286 ACCACATCGTTTCTCTTCCG 57.920 50.000 0.00 0.00 0.00 4.30
1954 5589 4.945543 CCATGACAGGATGAATGAACTGAA 59.054 41.667 0.00 0.00 39.69 3.02
1982 5617 3.130633 CTGGATCATATTTTCCGCGACA 58.869 45.455 8.23 0.00 34.58 4.35
1986 5621 2.814336 GTCCCTGGATCATATTTTCCGC 59.186 50.000 0.00 0.00 34.58 5.54
2018 5653 8.620416 GTTACATTGATAGTTTCATGCCATGTA 58.380 33.333 4.31 0.00 35.05 2.29
2019 5654 7.122501 TGTTACATTGATAGTTTCATGCCATGT 59.877 33.333 4.31 4.67 36.51 3.21
2034 5669 9.607988 TTATTTGATCCGTACTGTTACATTGAT 57.392 29.630 0.00 0.00 0.00 2.57
2040 5675 7.763071 ACCTTCTTATTTGATCCGTACTGTTAC 59.237 37.037 0.00 0.00 0.00 2.50
2044 5679 6.456988 GCAACCTTCTTATTTGATCCGTACTG 60.457 42.308 0.00 0.00 0.00 2.74
2045 5680 5.585047 GCAACCTTCTTATTTGATCCGTACT 59.415 40.000 0.00 0.00 0.00 2.73
2046 5681 5.353123 TGCAACCTTCTTATTTGATCCGTAC 59.647 40.000 0.00 0.00 0.00 3.67
2050 5685 6.515272 TCTTGCAACCTTCTTATTTGATCC 57.485 37.500 0.00 0.00 0.00 3.36
2055 5690 6.950619 AGAGGATTCTTGCAACCTTCTTATTT 59.049 34.615 7.68 0.00 32.53 1.40
2056 5691 6.376581 CAGAGGATTCTTGCAACCTTCTTATT 59.623 38.462 7.68 0.00 32.53 1.40
2065 5700 0.179179 GCGCAGAGGATTCTTGCAAC 60.179 55.000 0.30 0.00 34.13 4.17
2097 5732 7.023575 CAGGAGCAACACTTATTACATCAAAC 58.976 38.462 0.00 0.00 0.00 2.93
2111 5746 1.129437 GCGATTCTTCAGGAGCAACAC 59.871 52.381 0.00 0.00 0.00 3.32
2115 5750 0.107993 CTGGCGATTCTTCAGGAGCA 60.108 55.000 0.00 0.00 0.00 4.26
2130 5765 0.246635 TCTTTCTACGGAGCACTGGC 59.753 55.000 0.00 0.00 41.61 4.85
2135 5770 1.816835 ACGATGTCTTTCTACGGAGCA 59.183 47.619 0.00 0.00 0.00 4.26
2136 5771 2.563471 ACGATGTCTTTCTACGGAGC 57.437 50.000 0.00 0.00 0.00 4.70
2137 5772 3.834610 ACAACGATGTCTTTCTACGGAG 58.165 45.455 0.00 0.00 33.41 4.63
2138 5773 3.928727 ACAACGATGTCTTTCTACGGA 57.071 42.857 0.00 0.00 33.41 4.69
2139 5774 4.978186 TCTACAACGATGTCTTTCTACGG 58.022 43.478 0.00 0.00 41.05 4.02
2140 5775 6.255950 TCATCTACAACGATGTCTTTCTACG 58.744 40.000 0.00 0.00 41.17 3.51
2141 5776 7.968956 TCTTCATCTACAACGATGTCTTTCTAC 59.031 37.037 0.00 0.00 41.17 2.59
2142 5777 8.051901 TCTTCATCTACAACGATGTCTTTCTA 57.948 34.615 0.00 0.00 41.17 2.10
2143 5778 6.925211 TCTTCATCTACAACGATGTCTTTCT 58.075 36.000 0.00 0.00 41.17 2.52
2144 5779 7.763172 ATCTTCATCTACAACGATGTCTTTC 57.237 36.000 0.00 0.00 41.17 2.62
2145 5780 9.469807 GATATCTTCATCTACAACGATGTCTTT 57.530 33.333 0.00 0.00 41.17 2.52
2146 5781 8.633561 TGATATCTTCATCTACAACGATGTCTT 58.366 33.333 0.00 0.00 41.17 3.01
2198 5833 5.736951 AGTACTCTCTTGGCCATCATATC 57.263 43.478 6.09 0.00 0.00 1.63
2201 5836 4.716784 TGTTAGTACTCTCTTGGCCATCAT 59.283 41.667 6.09 0.00 0.00 2.45
2204 5839 4.097418 ACTGTTAGTACTCTCTTGGCCAT 58.903 43.478 6.09 0.00 0.00 4.40
2256 5903 7.900782 TTCTCGAAAAATCTCCTCGTTAATT 57.099 32.000 0.00 0.00 34.27 1.40
2268 5915 7.308435 AGTTGGAACATCATTCTCGAAAAATC 58.692 34.615 0.00 0.00 39.30 2.17
2269 5916 7.040478 TGAGTTGGAACATCATTCTCGAAAAAT 60.040 33.333 0.00 0.00 39.30 1.82
2270 5917 6.262049 TGAGTTGGAACATCATTCTCGAAAAA 59.738 34.615 0.00 0.00 39.30 1.94
2285 5932 5.239306 TCAAGTTGTGATGATGAGTTGGAAC 59.761 40.000 2.11 0.00 0.00 3.62
2290 5937 5.824624 ACAGTTCAAGTTGTGATGATGAGTT 59.175 36.000 2.11 0.00 35.70 3.01
2332 5979 5.342806 ACCGTGCATACATATTGATTTCG 57.657 39.130 0.00 0.00 0.00 3.46
2372 6020 7.466746 TTTTCCTTGGGATTAGTTGATTCTG 57.533 36.000 0.00 0.00 0.00 3.02
2400 6048 9.159364 CCTTCCAGTTAACCTGTATTTAGTTAC 57.841 37.037 0.88 0.00 39.74 2.50
2404 6052 6.598064 CACCCTTCCAGTTAACCTGTATTTAG 59.402 42.308 0.88 0.00 39.74 1.85
2407 6055 4.600111 TCACCCTTCCAGTTAACCTGTATT 59.400 41.667 0.88 0.00 39.74 1.89
2408 6056 4.172807 TCACCCTTCCAGTTAACCTGTAT 58.827 43.478 0.88 0.00 39.74 2.29
2410 6058 2.372172 CTCACCCTTCCAGTTAACCTGT 59.628 50.000 0.88 0.00 39.74 4.00
2411 6059 2.372172 ACTCACCCTTCCAGTTAACCTG 59.628 50.000 0.88 0.24 41.15 4.00
2412 6060 2.638363 GACTCACCCTTCCAGTTAACCT 59.362 50.000 0.88 0.00 0.00 3.50
2413 6061 2.612221 CGACTCACCCTTCCAGTTAACC 60.612 54.545 0.88 0.00 0.00 2.85
2419 6067 1.486211 ATACCGACTCACCCTTCCAG 58.514 55.000 0.00 0.00 0.00 3.86
2437 6085 4.830046 ACTCGAGTTCATCATGGTAGCTAT 59.170 41.667 13.58 0.00 0.00 2.97
2441 6096 4.142381 TGACACTCGAGTTCATCATGGTAG 60.142 45.833 17.26 2.24 0.00 3.18
2450 6105 1.409064 ACAAGCTGACACTCGAGTTCA 59.591 47.619 17.26 19.91 0.00 3.18
2460 6115 2.655090 TCAATCCCAACAAGCTGACA 57.345 45.000 0.00 0.00 0.00 3.58
2464 6119 3.499338 TCAACATCAATCCCAACAAGCT 58.501 40.909 0.00 0.00 0.00 3.74
2478 6133 2.987413 TTTGTCACGCCATCAACATC 57.013 45.000 0.00 0.00 0.00 3.06
2483 6138 0.957362 TGCAATTTGTCACGCCATCA 59.043 45.000 0.00 0.00 0.00 3.07
2484 6139 2.187707 GATGCAATTTGTCACGCCATC 58.812 47.619 0.00 0.00 0.00 3.51
2486 6141 0.243365 GGATGCAATTTGTCACGCCA 59.757 50.000 0.00 0.00 0.00 5.69
2536 6191 1.202758 TGGAAAGTGGTAGGCTGTGTG 60.203 52.381 0.00 0.00 0.00 3.82
2544 6199 5.178797 CAGGTCTATGTTGGAAAGTGGTAG 58.821 45.833 0.00 0.00 0.00 3.18
2551 6206 7.284074 TCACTTAAACAGGTCTATGTTGGAAA 58.716 34.615 0.00 0.00 42.49 3.13
2553 6208 6.428083 TCACTTAAACAGGTCTATGTTGGA 57.572 37.500 0.00 0.00 42.49 3.53
2574 6229 2.158310 TGTCCTGGAGAACCTCTCTTCA 60.158 50.000 0.00 0.00 42.95 3.02
2580 6235 3.046968 GACTTTGTCCTGGAGAACCTC 57.953 52.381 5.67 0.28 37.04 3.85
2593 6248 4.582656 TCGATTTGGTGATTTGGACTTTGT 59.417 37.500 0.00 0.00 0.00 2.83
2626 6281 5.252547 TGAGGTTATTTTATCAGTGCAGCA 58.747 37.500 0.00 0.00 0.00 4.41
2672 6327 2.555757 GAGCTGAAGTTTGCACAAGGAT 59.444 45.455 0.00 0.00 0.00 3.24
2682 6337 3.083122 AGCATCATGGAGCTGAAGTTT 57.917 42.857 11.26 0.00 40.13 2.66
2706 6361 1.137404 CGCAAGGCTGAAAATCGGG 59.863 57.895 0.00 0.00 0.00 5.14
2712 6367 0.884704 GGTGTCTCGCAAGGCTGAAA 60.885 55.000 0.00 0.00 38.47 2.69
2715 6370 3.114616 CGGTGTCTCGCAAGGCTG 61.115 66.667 0.00 0.00 38.47 4.85
2733 6388 5.126061 GGTGATTGATGGCAGTTATCTGTTT 59.874 40.000 2.85 0.00 43.05 2.83
2736 6391 4.201657 TGGTGATTGATGGCAGTTATCTG 58.798 43.478 0.00 0.00 43.87 2.90
2737 6392 4.508551 TGGTGATTGATGGCAGTTATCT 57.491 40.909 0.00 0.00 0.00 1.98
2747 6402 4.261578 AGCAAAAGGTTGGTGATTGATG 57.738 40.909 0.00 0.00 43.72 3.07
2748 6403 4.559300 CGAAGCAAAAGGTTGGTGATTGAT 60.559 41.667 0.00 0.00 44.60 2.57
2765 6420 4.306471 CGCAAACCGCACGAAGCA 62.306 61.111 0.00 0.00 46.13 3.91
2780 6441 2.472695 TCTTCATATATGGGTGGCGC 57.527 50.000 12.78 0.00 0.00 6.53
2804 6468 0.915872 TGGCCCCATGTCATCACTCT 60.916 55.000 0.00 0.00 0.00 3.24
2813 6477 2.036256 GAGTGCTTGGCCCCATGT 59.964 61.111 0.00 0.00 0.00 3.21
2818 6482 2.747855 CCTTCGAGTGCTTGGCCC 60.748 66.667 0.00 0.00 0.00 5.80
2819 6483 2.032681 ACCTTCGAGTGCTTGGCC 59.967 61.111 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.