Multiple sequence alignment - TraesCS6A01G211900

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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 TraesCS6A01G211900 chr6A 100.000 5304 0 0 1 5304 384877288 384882591 0.000000e+00 9795.0
1 TraesCS6A01G211900 chr6A 100.000 3085 0 0 6023 9107 384883310 384886394 0.000000e+00 5698.0
2 TraesCS6A01G211900 chr6A 99.420 1551 8 1 6023 7573 574404692 574403143 0.000000e+00 2813.0
3 TraesCS6A01G211900 chr4A 99.220 3974 30 1 1331 5304 16029670 16025698 0.000000e+00 7166.0
4 TraesCS6A01G211900 chr4A 99.120 3976 29 3 1331 5304 170164473 170160502 0.000000e+00 7143.0
5 TraesCS6A01G211900 chr4A 99.420 1551 8 1 6023 7573 59879030 59877481 0.000000e+00 2813.0
6 TraesCS6A01G211900 chr4A 93.826 745 37 4 8371 9107 115559797 115559054 0.000000e+00 1112.0
7 TraesCS6A01G211900 chr4A 81.073 317 51 4 189 498 626924693 626925007 2.540000e-60 244.0
8 TraesCS6A01G211900 chr4A 82.963 270 39 4 189 452 559948641 559948373 4.250000e-58 237.0
9 TraesCS6A01G211900 chr4A 96.203 79 3 0 517 595 603447662 603447584 7.420000e-26 130.0
10 TraesCS6A01G211900 chr2B 99.121 3980 33 2 1325 5304 188823789 188827766 0.000000e+00 7155.0
11 TraesCS6A01G211900 chr2A 99.145 3975 32 2 1331 5304 456651268 456647295 0.000000e+00 7151.0
12 TraesCS6A01G211900 chr2A 99.420 1551 8 1 6023 7573 445574277 445575826 0.000000e+00 2813.0
13 TraesCS6A01G211900 chr2A 99.420 1551 8 1 6023 7573 762876672 762878221 0.000000e+00 2813.0
14 TraesCS6A01G211900 chr2A 90.270 185 16 1 1 185 723640170 723639988 3.290000e-59 241.0
15 TraesCS6A01G211900 chr7B 99.120 3977 32 1 1331 5304 741260659 741256683 0.000000e+00 7147.0
16 TraesCS6A01G211900 chr7B 99.420 1551 8 1 6023 7573 443844915 443843366 0.000000e+00 2813.0
17 TraesCS6A01G211900 chr7B 78.656 253 47 4 185 431 708097393 708097644 2.630000e-35 161.0
18 TraesCS6A01G211900 chr7B 97.403 77 2 0 517 593 701408256 701408180 2.060000e-26 132.0
19 TraesCS6A01G211900 chr7B 97.368 76 2 0 517 592 405051396 405051321 7.420000e-26 130.0
20 TraesCS6A01G211900 chr5B 99.120 3977 32 1 1331 5304 224614631 224610655 0.000000e+00 7147.0
21 TraesCS6A01G211900 chr6B 99.119 3975 34 1 1331 5304 22703593 22707567 0.000000e+00 7145.0
22 TraesCS6A01G211900 chr6B 99.232 1562 10 2 6023 7584 82548022 82549581 0.000000e+00 2817.0
23 TraesCS6A01G211900 chr6B 93.416 805 45 3 7576 8379 432266273 432265476 0.000000e+00 1186.0
24 TraesCS6A01G211900 chr6B 93.842 747 37 4 8369 9107 172316815 172317560 0.000000e+00 1116.0
25 TraesCS6A01G211900 chr6B 90.702 484 33 6 847 1330 432266740 432266269 1.290000e-177 634.0
26 TraesCS6A01G211900 chr3A 99.119 3975 34 1 1330 5304 642392129 642388156 0.000000e+00 7145.0
27 TraesCS6A01G211900 chr3A 99.420 1551 8 1 6023 7573 705364559 705363010 0.000000e+00 2813.0
28 TraesCS6A01G211900 chr3A 93.298 746 41 4 8370 9107 470835443 470836187 0.000000e+00 1092.0
29 TraesCS6A01G211900 chr3A 90.270 185 16 1 1 185 127085026 127084844 3.290000e-59 241.0
30 TraesCS6A01G211900 chr3A 84.434 212 28 4 641 848 12523082 12522872 4.310000e-48 204.0
31 TraesCS6A01G211900 chr3A 89.241 158 15 1 28 185 359364549 359364704 7.210000e-46 196.0
32 TraesCS6A01G211900 chr3A 97.468 79 2 0 518 596 46211581 46211503 1.600000e-27 135.0
33 TraesCS6A01G211900 chr3A 93.590 78 5 0 517 594 99426260 99426183 5.780000e-22 117.0
34 TraesCS6A01G211900 chr1B 99.119 3974 34 1 1331 5304 500583689 500579717 0.000000e+00 7143.0
35 TraesCS6A01G211900 chr1B 93.423 745 40 4 8371 9107 296741558 296742301 0.000000e+00 1096.0
36 TraesCS6A01G211900 chr1B 81.875 320 36 12 186 497 606193771 606194076 5.460000e-62 250.0
37 TraesCS6A01G211900 chr1B 80.455 220 34 8 641 853 534300727 534300944 9.460000e-35 159.0
38 TraesCS6A01G211900 chr1A 98.842 3974 33 2 1331 5304 551799990 551796030 0.000000e+00 7071.0
39 TraesCS6A01G211900 chr1A 99.484 1551 7 1 6023 7573 551796234 551794685 0.000000e+00 2819.0
40 TraesCS6A01G211900 chr1A 94.601 852 31 8 4466 5304 305011458 305012307 0.000000e+00 1304.0
41 TraesCS6A01G211900 chr1A 93.557 745 39 4 8371 9107 593263305 593264048 0.000000e+00 1101.0
42 TraesCS6A01G211900 chr1A 79.921 254 42 5 224 470 52530905 52531156 2.610000e-40 178.0
43 TraesCS6A01G211900 chr3B 99.420 1551 8 1 6023 7573 199965666 199967215 0.000000e+00 2813.0
44 TraesCS6A01G211900 chr6D 94.717 795 34 2 7576 8370 271125659 271124873 0.000000e+00 1229.0
45 TraesCS6A01G211900 chr6D 92.769 484 23 3 847 1330 271126126 271125655 0.000000e+00 689.0
46 TraesCS6A01G211900 chr5D 95.161 744 29 2 8371 9107 243799782 243800525 0.000000e+00 1168.0
47 TraesCS6A01G211900 chr5D 78.618 304 49 11 204 498 109565708 109565412 4.340000e-43 187.0
48 TraesCS6A01G211900 chr5D 93.333 90 6 0 53 142 66294362 66294273 5.740000e-27 134.0
49 TraesCS6A01G211900 chr5D 96.203 79 3 0 514 592 134786410 134786488 7.420000e-26 130.0
50 TraesCS6A01G211900 chr5D 93.976 83 4 1 515 597 194252561 194252642 3.450000e-24 124.0
51 TraesCS6A01G211900 chr7D 94.906 746 28 5 8370 9107 338857970 338858713 0.000000e+00 1158.0
52 TraesCS6A01G211900 chr7D 94.765 745 29 5 8371 9107 348119493 348120235 0.000000e+00 1151.0
53 TraesCS6A01G211900 chr7D 94.497 745 28 8 8372 9107 339748692 339747952 0.000000e+00 1136.0
54 TraesCS6A01G211900 chr7D 88.649 185 19 1 1 185 76781049 76780867 3.310000e-54 224.0
55 TraesCS6A01G211900 chr7D 77.830 212 42 4 641 848 626576203 626575993 9.600000e-25 126.0
56 TraesCS6A01G211900 chr4B 94.622 502 18 4 1 497 65593395 65592898 0.000000e+00 769.0
57 TraesCS6A01G211900 chr4B 92.442 172 8 3 684 851 65592585 65592415 3.290000e-59 241.0
58 TraesCS6A01G211900 chr4B 87.179 78 9 1 772 848 578463524 578463447 4.530000e-13 87.9
59 TraesCS6A01G211900 chr2D 94.779 498 18 2 1 497 36662713 36662223 0.000000e+00 769.0
60 TraesCS6A01G211900 chr2D 92.395 263 16 3 589 847 36662226 36661964 1.120000e-98 372.0
61 TraesCS6A01G211900 chrUn 97.403 77 2 0 517 593 36436900 36436976 2.060000e-26 132.0
62 TraesCS6A01G211900 chrUn 85.057 87 10 3 772 856 215033462 215033377 1.630000e-12 86.1
63 TraesCS6A01G211900 chr5A 95.062 81 3 1 517 597 429750511 429750432 9.600000e-25 126.0
64 TraesCS6A01G211900 chr3D 93.103 87 4 2 517 603 253553880 253553796 9.600000e-25 126.0
65 TraesCS6A01G211900 chr7A 85.417 96 7 7 768 860 730912333 730912424 9.740000e-15 93.5
66 TraesCS6A01G211900 chr4D 86.747 83 9 2 772 852 419253396 419253478 3.500000e-14 91.6
67 TraesCS6A01G211900 chr1D 88.406 69 8 0 517 585 59132130 59132062 5.860000e-12 84.2
68 TraesCS6A01G211900 chr1D 81.308 107 8 4 489 595 302256714 302256620 9.810000e-10 76.8


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 TraesCS6A01G211900 chr6A 384877288 384886394 9106 False 7746.5 9795 100.000 1 9107 2 chr6A.!!$F1 9106
1 TraesCS6A01G211900 chr6A 574403143 574404692 1549 True 2813.0 2813 99.420 6023 7573 1 chr6A.!!$R1 1550
2 TraesCS6A01G211900 chr4A 16025698 16029670 3972 True 7166.0 7166 99.220 1331 5304 1 chr4A.!!$R1 3973
3 TraesCS6A01G211900 chr4A 170160502 170164473 3971 True 7143.0 7143 99.120 1331 5304 1 chr4A.!!$R4 3973
4 TraesCS6A01G211900 chr4A 59877481 59879030 1549 True 2813.0 2813 99.420 6023 7573 1 chr4A.!!$R2 1550
5 TraesCS6A01G211900 chr4A 115559054 115559797 743 True 1112.0 1112 93.826 8371 9107 1 chr4A.!!$R3 736
6 TraesCS6A01G211900 chr2B 188823789 188827766 3977 False 7155.0 7155 99.121 1325 5304 1 chr2B.!!$F1 3979
7 TraesCS6A01G211900 chr2A 456647295 456651268 3973 True 7151.0 7151 99.145 1331 5304 1 chr2A.!!$R1 3973
8 TraesCS6A01G211900 chr2A 445574277 445575826 1549 False 2813.0 2813 99.420 6023 7573 1 chr2A.!!$F1 1550
9 TraesCS6A01G211900 chr2A 762876672 762878221 1549 False 2813.0 2813 99.420 6023 7573 1 chr2A.!!$F2 1550
10 TraesCS6A01G211900 chr7B 741256683 741260659 3976 True 7147.0 7147 99.120 1331 5304 1 chr7B.!!$R4 3973
11 TraesCS6A01G211900 chr7B 443843366 443844915 1549 True 2813.0 2813 99.420 6023 7573 1 chr7B.!!$R2 1550
12 TraesCS6A01G211900 chr5B 224610655 224614631 3976 True 7147.0 7147 99.120 1331 5304 1 chr5B.!!$R1 3973
13 TraesCS6A01G211900 chr6B 22703593 22707567 3974 False 7145.0 7145 99.119 1331 5304 1 chr6B.!!$F1 3973
14 TraesCS6A01G211900 chr6B 82548022 82549581 1559 False 2817.0 2817 99.232 6023 7584 1 chr6B.!!$F2 1561
15 TraesCS6A01G211900 chr6B 172316815 172317560 745 False 1116.0 1116 93.842 8369 9107 1 chr6B.!!$F3 738
16 TraesCS6A01G211900 chr6B 432265476 432266740 1264 True 910.0 1186 92.059 847 8379 2 chr6B.!!$R1 7532
17 TraesCS6A01G211900 chr3A 642388156 642392129 3973 True 7145.0 7145 99.119 1330 5304 1 chr3A.!!$R5 3974
18 TraesCS6A01G211900 chr3A 705363010 705364559 1549 True 2813.0 2813 99.420 6023 7573 1 chr3A.!!$R6 1550
19 TraesCS6A01G211900 chr3A 470835443 470836187 744 False 1092.0 1092 93.298 8370 9107 1 chr3A.!!$F2 737
20 TraesCS6A01G211900 chr1B 500579717 500583689 3972 True 7143.0 7143 99.119 1331 5304 1 chr1B.!!$R1 3973
21 TraesCS6A01G211900 chr1B 296741558 296742301 743 False 1096.0 1096 93.423 8371 9107 1 chr1B.!!$F1 736
22 TraesCS6A01G211900 chr1A 551794685 551799990 5305 True 4945.0 7071 99.163 1331 7573 2 chr1A.!!$R1 6242
23 TraesCS6A01G211900 chr1A 305011458 305012307 849 False 1304.0 1304 94.601 4466 5304 1 chr1A.!!$F2 838
24 TraesCS6A01G211900 chr1A 593263305 593264048 743 False 1101.0 1101 93.557 8371 9107 1 chr1A.!!$F3 736
25 TraesCS6A01G211900 chr3B 199965666 199967215 1549 False 2813.0 2813 99.420 6023 7573 1 chr3B.!!$F1 1550
26 TraesCS6A01G211900 chr6D 271124873 271126126 1253 True 959.0 1229 93.743 847 8370 2 chr6D.!!$R1 7523
27 TraesCS6A01G211900 chr5D 243799782 243800525 743 False 1168.0 1168 95.161 8371 9107 1 chr5D.!!$F3 736
28 TraesCS6A01G211900 chr7D 338857970 338858713 743 False 1158.0 1158 94.906 8370 9107 1 chr7D.!!$F1 737
29 TraesCS6A01G211900 chr7D 348119493 348120235 742 False 1151.0 1151 94.765 8371 9107 1 chr7D.!!$F2 736
30 TraesCS6A01G211900 chr7D 339747952 339748692 740 True 1136.0 1136 94.497 8372 9107 1 chr7D.!!$R2 735
31 TraesCS6A01G211900 chr4B 65592415 65593395 980 True 505.0 769 93.532 1 851 2 chr4B.!!$R2 850
32 TraesCS6A01G211900 chr2D 36661964 36662713 749 True 570.5 769 93.587 1 847 2 chr2D.!!$R1 846

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
910 920 0.035458 CGCCAGAACTTCCTCCTTGT 59.965 55.000 0.0 0.00 0.00 3.16 F
1144 1154 0.324275 GCCTTACATTTCCCCTGGCA 60.324 55.000 0.0 0.00 38.79 4.92 F
1248 1258 1.413767 CTGTGTGCCGACTATGACGC 61.414 60.000 0.0 0.00 0.00 5.19 F
2903 2939 2.910360 CCATGGCTGATCGTCCCA 59.090 61.111 0.0 1.86 0.00 4.37 F
4021 4061 7.881775 ATGAACAACCTGATTATACCTTTCC 57.118 36.000 0.0 0.00 0.00 3.13 F
4231 4273 0.251341 GCCAACCTTCCTGTGTCCAT 60.251 55.000 0.0 0.00 0.00 3.41 F
4867 4921 0.319083 GTGTCCCGACCACATACACA 59.681 55.000 0.0 0.00 40.08 3.72 F
6756 6810 1.913951 TTGTCTCCTGCGGATGCCAT 61.914 55.000 0.0 0.00 41.78 4.40 F
6795 6849 4.102524 TGTTGGTGGACTTCAGTACTTGAT 59.897 41.667 0.0 0.00 35.27 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2903 2939 3.349006 CTGTTGCTTCTGCGGCGT 61.349 61.111 9.37 0.00 43.34 5.68 R
3472 3508 3.990959 GGAAGTTGATGACTCTTCCCT 57.009 47.619 10.86 0.00 46.54 4.20 R
3644 3680 9.491675 AAAAATATCAAACACATCAGATTTGCA 57.508 25.926 0.00 0.00 34.09 4.08 R
4231 4273 0.036164 CAGGGATGGTGGTTCGACAA 59.964 55.000 0.00 0.00 0.00 3.18 R
4867 4921 0.593128 GAAAATGCCACTGCGACTGT 59.407 50.000 0.00 0.00 41.78 3.55 R
6719 6773 3.554934 ACAAAAGCTCACCATCAACAGA 58.445 40.909 0.00 0.00 0.00 3.41 R
6756 6810 3.838317 ACCAACAATGCTCCTGTACTCTA 59.162 43.478 0.00 0.00 0.00 2.43 R
7573 7627 0.108662 CATCTGACCGTGCTGCACTA 60.109 55.000 28.04 12.24 31.34 2.74 R
8637 8697 0.903454 GTGGGAGAGGGGAACGAGAA 60.903 60.000 0.00 0.00 0.00 2.87 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
42 43 8.145767 CCGGTTTATGATACTAAATGAGGTACA 58.854 37.037 0.00 0.00 0.00 2.90
62 63 9.548631 AGGTACATCTATATATAGGTTTGCACT 57.451 33.333 17.81 6.29 0.00 4.40
147 149 4.039124 TGTGCATACTCTGACTTTCAGTGA 59.961 41.667 11.24 0.00 44.58 3.41
172 174 6.385649 TTTTATGAGAACAGGGTTGTCAAC 57.614 37.500 12.09 7.20 36.23 3.18
270 272 0.179073 CTTCAGATGTACCCCCAGCG 60.179 60.000 0.00 0.00 0.00 5.18
355 358 9.578439 AGAATTTGCAAAAGCTTTATATCACTC 57.422 29.630 17.19 5.47 0.00 3.51
497 507 6.025280 CACGGCACATGGTTTTAATAAGTAC 58.975 40.000 0.00 0.00 0.00 2.73
498 508 5.941647 ACGGCACATGGTTTTAATAAGTACT 59.058 36.000 0.00 0.00 0.00 2.73
499 509 6.093082 ACGGCACATGGTTTTAATAAGTACTC 59.907 38.462 0.00 0.00 0.00 2.59
500 510 6.457799 CGGCACATGGTTTTAATAAGTACTCC 60.458 42.308 0.00 0.00 0.00 3.85
501 511 6.183360 GGCACATGGTTTTAATAAGTACTCCC 60.183 42.308 0.00 0.00 0.00 4.30
502 512 6.602009 GCACATGGTTTTAATAAGTACTCCCT 59.398 38.462 0.00 0.00 0.00 4.20
503 513 7.201705 GCACATGGTTTTAATAAGTACTCCCTC 60.202 40.741 0.00 0.00 0.00 4.30
504 514 8.047310 CACATGGTTTTAATAAGTACTCCCTCT 58.953 37.037 0.00 0.00 0.00 3.69
505 515 8.047310 ACATGGTTTTAATAAGTACTCCCTCTG 58.953 37.037 0.00 0.00 0.00 3.35
506 516 7.563724 TGGTTTTAATAAGTACTCCCTCTGT 57.436 36.000 0.00 0.00 0.00 3.41
507 517 8.669055 TGGTTTTAATAAGTACTCCCTCTGTA 57.331 34.615 0.00 0.00 0.00 2.74
508 518 9.103582 TGGTTTTAATAAGTACTCCCTCTGTAA 57.896 33.333 0.00 0.00 0.00 2.41
509 519 9.948964 GGTTTTAATAAGTACTCCCTCTGTAAA 57.051 33.333 0.00 0.00 0.00 2.01
518 528 8.147244 AGTACTCCCTCTGTAAACAAATATGT 57.853 34.615 0.00 0.00 43.14 2.29
519 529 9.263446 AGTACTCCCTCTGTAAACAAATATGTA 57.737 33.333 0.00 0.00 39.40 2.29
520 530 9.880157 GTACTCCCTCTGTAAACAAATATGTAA 57.120 33.333 0.00 0.00 39.40 2.41
522 532 9.227777 ACTCCCTCTGTAAACAAATATGTAAAC 57.772 33.333 0.00 0.00 39.40 2.01
523 533 9.226606 CTCCCTCTGTAAACAAATATGTAAACA 57.773 33.333 0.00 0.00 39.40 2.83
524 534 9.575868 TCCCTCTGTAAACAAATATGTAAACAA 57.424 29.630 0.00 0.00 39.40 2.83
586 596 7.242914 ACGCTTTTATATTTCTTTACGGAGG 57.757 36.000 0.00 0.00 0.00 4.30
587 597 6.259387 ACGCTTTTATATTTCTTTACGGAGGG 59.741 38.462 0.00 0.00 0.00 4.30
588 598 6.480981 CGCTTTTATATTTCTTTACGGAGGGA 59.519 38.462 0.00 0.00 0.00 4.20
589 599 7.307219 CGCTTTTATATTTCTTTACGGAGGGAG 60.307 40.741 0.00 0.00 0.00 4.30
590 600 7.498239 GCTTTTATATTTCTTTACGGAGGGAGT 59.502 37.037 0.00 0.00 0.00 3.85
597 607 4.603131 TCTTTACGGAGGGAGTAGCTTTA 58.397 43.478 0.00 0.00 0.00 1.85
615 625 6.423182 AGCTTTAATTAGAGGTGTGCCAATA 58.577 36.000 6.90 0.00 37.19 1.90
633 643 5.621104 GCCAATATCAATTGTTTGTCGGTGA 60.621 40.000 5.13 0.00 40.84 4.02
638 648 5.856126 TCAATTGTTTGTCGGTGACTATC 57.144 39.130 5.13 0.00 34.32 2.08
647 657 1.200483 CGGTGACTATCGTGCATGAC 58.800 55.000 11.65 0.00 0.00 3.06
649 659 2.032924 CGGTGACTATCGTGCATGACTA 59.967 50.000 11.65 4.54 0.00 2.59
714 724 5.902613 TGGTGCTTCTCTTTAATTGATGG 57.097 39.130 0.00 0.00 0.00 3.51
715 725 4.158394 TGGTGCTTCTCTTTAATTGATGGC 59.842 41.667 0.00 0.00 0.00 4.40
716 726 4.158394 GGTGCTTCTCTTTAATTGATGGCA 59.842 41.667 0.00 0.00 0.00 4.92
717 727 5.336690 GGTGCTTCTCTTTAATTGATGGCAA 60.337 40.000 0.00 0.00 38.60 4.52
718 728 6.158598 GTGCTTCTCTTTAATTGATGGCAAA 58.841 36.000 0.00 0.00 37.59 3.68
719 729 6.089954 GTGCTTCTCTTTAATTGATGGCAAAC 59.910 38.462 0.00 0.00 37.59 2.93
720 730 5.287035 GCTTCTCTTTAATTGATGGCAAACG 59.713 40.000 0.00 0.00 37.59 3.60
721 731 6.567687 TTCTCTTTAATTGATGGCAAACGA 57.432 33.333 0.00 0.00 37.59 3.85
722 732 6.757897 TCTCTTTAATTGATGGCAAACGAT 57.242 33.333 0.00 0.00 37.59 3.73
723 733 7.857734 TCTCTTTAATTGATGGCAAACGATA 57.142 32.000 0.00 0.00 37.59 2.92
724 734 7.693952 TCTCTTTAATTGATGGCAAACGATAC 58.306 34.615 0.00 0.00 37.59 2.24
725 735 7.335673 TCTCTTTAATTGATGGCAAACGATACA 59.664 33.333 0.00 0.00 37.59 2.29
726 736 7.247728 TCTTTAATTGATGGCAAACGATACAC 58.752 34.615 0.00 0.00 37.59 2.90
727 737 6.502136 TTAATTGATGGCAAACGATACACA 57.498 33.333 0.00 0.00 37.59 3.72
728 738 5.581126 AATTGATGGCAAACGATACACAT 57.419 34.783 0.00 0.00 37.59 3.21
729 739 6.691754 AATTGATGGCAAACGATACACATA 57.308 33.333 0.00 0.00 37.59 2.29
730 740 6.691754 ATTGATGGCAAACGATACACATAA 57.308 33.333 0.00 0.00 37.59 1.90
731 741 6.502136 TTGATGGCAAACGATACACATAAA 57.498 33.333 0.00 0.00 0.00 1.40
732 742 6.117911 TGATGGCAAACGATACACATAAAG 57.882 37.500 0.00 0.00 0.00 1.85
733 743 4.349663 TGGCAAACGATACACATAAAGC 57.650 40.909 0.00 0.00 0.00 3.51
734 744 4.006989 TGGCAAACGATACACATAAAGCT 58.993 39.130 0.00 0.00 0.00 3.74
735 745 5.179533 TGGCAAACGATACACATAAAGCTA 58.820 37.500 0.00 0.00 0.00 3.32
736 746 5.064198 TGGCAAACGATACACATAAAGCTAC 59.936 40.000 0.00 0.00 0.00 3.58
737 747 5.293569 GGCAAACGATACACATAAAGCTACT 59.706 40.000 0.00 0.00 0.00 2.57
738 748 6.185399 GCAAACGATACACATAAAGCTACTG 58.815 40.000 0.00 0.00 0.00 2.74
739 749 6.183360 GCAAACGATACACATAAAGCTACTGT 60.183 38.462 0.00 0.00 0.00 3.55
740 750 7.009815 GCAAACGATACACATAAAGCTACTGTA 59.990 37.037 0.00 0.00 0.00 2.74
741 751 7.982371 AACGATACACATAAAGCTACTGTAC 57.018 36.000 0.00 0.00 0.00 2.90
742 752 7.092137 ACGATACACATAAAGCTACTGTACA 57.908 36.000 0.00 0.00 0.00 2.90
743 753 7.713750 ACGATACACATAAAGCTACTGTACAT 58.286 34.615 0.00 0.00 0.00 2.29
744 754 8.843262 ACGATACACATAAAGCTACTGTACATA 58.157 33.333 0.00 0.00 0.00 2.29
745 755 9.841880 CGATACACATAAAGCTACTGTACATAT 57.158 33.333 0.00 0.00 0.00 1.78
790 800 9.685276 TCATAGTTCTATTGTTTGAATCATGGT 57.315 29.630 0.00 0.00 0.00 3.55
791 801 9.941664 CATAGTTCTATTGTTTGAATCATGGTC 57.058 33.333 0.00 0.00 0.00 4.02
792 802 9.911788 ATAGTTCTATTGTTTGAATCATGGTCT 57.088 29.630 0.00 0.00 0.00 3.85
794 804 9.167311 AGTTCTATTGTTTGAATCATGGTCTAC 57.833 33.333 0.00 0.00 0.00 2.59
795 805 8.946085 GTTCTATTGTTTGAATCATGGTCTACA 58.054 33.333 0.00 0.00 0.00 2.74
796 806 9.685276 TTCTATTGTTTGAATCATGGTCTACAT 57.315 29.630 0.00 0.00 41.57 2.29
800 810 8.492673 TTGTTTGAATCATGGTCTACATAGTC 57.507 34.615 0.00 0.00 37.84 2.59
801 811 6.756542 TGTTTGAATCATGGTCTACATAGTCG 59.243 38.462 0.00 0.00 37.84 4.18
802 812 4.871513 TGAATCATGGTCTACATAGTCGC 58.128 43.478 0.00 0.00 37.84 5.19
803 813 3.560902 ATCATGGTCTACATAGTCGCG 57.439 47.619 0.00 0.00 37.84 5.87
804 814 2.567985 TCATGGTCTACATAGTCGCGA 58.432 47.619 3.71 3.71 37.84 5.87
805 815 2.289820 TCATGGTCTACATAGTCGCGAC 59.710 50.000 31.30 31.30 37.84 5.19
806 816 1.741528 TGGTCTACATAGTCGCGACA 58.258 50.000 37.85 24.72 0.00 4.35
807 817 2.294979 TGGTCTACATAGTCGCGACAT 58.705 47.619 37.85 25.71 0.00 3.06
808 818 3.469739 TGGTCTACATAGTCGCGACATA 58.530 45.455 37.85 26.27 0.00 2.29
809 819 4.070009 TGGTCTACATAGTCGCGACATAT 58.930 43.478 37.85 27.13 0.00 1.78
810 820 4.083484 TGGTCTACATAGTCGCGACATATG 60.083 45.833 37.85 34.86 33.11 1.78
811 821 4.153655 GGTCTACATAGTCGCGACATATGA 59.846 45.833 37.04 26.78 32.20 2.15
812 822 5.080731 GTCTACATAGTCGCGACATATGAC 58.919 45.833 37.04 30.54 32.20 3.06
813 823 3.982576 ACATAGTCGCGACATATGACA 57.017 42.857 37.04 20.69 35.09 3.58
814 824 3.890128 ACATAGTCGCGACATATGACAG 58.110 45.455 37.04 24.16 35.09 3.51
815 825 3.237628 CATAGTCGCGACATATGACAGG 58.762 50.000 37.85 16.62 35.09 4.00
816 826 0.249073 AGTCGCGACATATGACAGGC 60.249 55.000 37.85 9.43 35.09 4.85
817 827 1.299089 TCGCGACATATGACAGGCG 60.299 57.895 3.71 20.04 44.47 5.52
818 828 1.588932 CGCGACATATGACAGGCGT 60.589 57.895 10.38 0.00 38.90 5.68
819 829 1.811217 CGCGACATATGACAGGCGTG 61.811 60.000 10.38 4.53 38.90 5.34
820 830 1.490693 GCGACATATGACAGGCGTGG 61.491 60.000 10.38 0.00 0.00 4.94
821 831 1.490693 CGACATATGACAGGCGTGGC 61.491 60.000 10.38 8.59 0.00 5.01
822 832 1.490693 GACATATGACAGGCGTGGCG 61.491 60.000 10.38 0.00 32.20 5.69
823 833 1.521457 CATATGACAGGCGTGGCGT 60.521 57.895 12.37 12.37 32.20 5.68
860 870 7.552330 GGGCTAAGCTAGTAATACTCTACGTAT 59.448 40.741 0.00 0.00 40.51 3.06
893 903 4.918201 CCTTCGGGAGGCCATCGC 62.918 72.222 5.01 7.36 39.09 4.58
906 916 0.462759 CCATCGCCAGAACTTCCTCC 60.463 60.000 0.00 0.00 0.00 4.30
907 917 0.539051 CATCGCCAGAACTTCCTCCT 59.461 55.000 0.00 0.00 0.00 3.69
908 918 1.065854 CATCGCCAGAACTTCCTCCTT 60.066 52.381 0.00 0.00 0.00 3.36
909 919 0.321671 TCGCCAGAACTTCCTCCTTG 59.678 55.000 0.00 0.00 0.00 3.61
910 920 0.035458 CGCCAGAACTTCCTCCTTGT 59.965 55.000 0.00 0.00 0.00 3.16
911 921 1.814793 GCCAGAACTTCCTCCTTGTC 58.185 55.000 0.00 0.00 0.00 3.18
912 922 1.349357 GCCAGAACTTCCTCCTTGTCT 59.651 52.381 0.00 0.00 0.00 3.41
913 923 2.614229 GCCAGAACTTCCTCCTTGTCTC 60.614 54.545 0.00 0.00 0.00 3.36
914 924 2.903135 CCAGAACTTCCTCCTTGTCTCT 59.097 50.000 0.00 0.00 0.00 3.10
915 925 3.056179 CCAGAACTTCCTCCTTGTCTCTC 60.056 52.174 0.00 0.00 0.00 3.20
916 926 3.831911 CAGAACTTCCTCCTTGTCTCTCT 59.168 47.826 0.00 0.00 0.00 3.10
917 927 4.082245 CAGAACTTCCTCCTTGTCTCTCTC 60.082 50.000 0.00 0.00 0.00 3.20
918 928 2.815158 ACTTCCTCCTTGTCTCTCTCC 58.185 52.381 0.00 0.00 0.00 3.71
919 929 2.107366 CTTCCTCCTTGTCTCTCTCCC 58.893 57.143 0.00 0.00 0.00 4.30
963 973 5.133153 TCTTGGATTCTTGATCATCCATCCA 59.867 40.000 19.34 19.34 46.78 3.41
1066 1076 1.880796 CGACCAACGTGACAGCACA 60.881 57.895 0.00 0.00 45.41 4.57
1090 1100 4.331968 ACTTTTATGCCATGTTCCGAGAA 58.668 39.130 0.00 0.00 0.00 2.87
1099 1109 1.810030 GTTCCGAGAAATCGCCGCT 60.810 57.895 0.00 0.00 0.00 5.52
1140 1150 1.212250 ACCGGCCTTACATTTCCCCT 61.212 55.000 0.00 0.00 0.00 4.79
1144 1154 0.324275 GCCTTACATTTCCCCTGGCA 60.324 55.000 0.00 0.00 38.79 4.92
1160 1170 2.430921 CACACGTCGTCCCTGAGC 60.431 66.667 0.00 0.00 0.00 4.26
1161 1171 2.910479 ACACGTCGTCCCTGAGCA 60.910 61.111 0.00 0.00 0.00 4.26
1248 1258 1.413767 CTGTGTGCCGACTATGACGC 61.414 60.000 0.00 0.00 0.00 5.19
1351 1361 7.867909 GTGCATGTTAGACTATGTATAGCTTCA 59.132 37.037 0.00 0.00 33.68 3.02
1471 1507 5.585820 TGTCTTACATGGTATCACGCTAA 57.414 39.130 0.00 0.00 0.00 3.09
2393 2429 3.005897 GTGTCAGAAGCTTGACTCCACTA 59.994 47.826 17.26 0.00 46.00 2.74
2903 2939 2.910360 CCATGGCTGATCGTCCCA 59.090 61.111 0.00 1.86 0.00 4.37
3644 3680 8.692710 GCTTTACCTGGCTTTACCTTATTAAAT 58.307 33.333 0.00 0.00 40.22 1.40
4021 4061 7.881775 ATGAACAACCTGATTATACCTTTCC 57.118 36.000 0.00 0.00 0.00 3.13
4231 4273 0.251341 GCCAACCTTCCTGTGTCCAT 60.251 55.000 0.00 0.00 0.00 3.41
4619 4673 2.374830 CTTCATCAGCGGATCGGCCT 62.375 60.000 20.46 6.53 0.00 5.19
4761 4815 2.439701 CCGAGTCCGAGGCTACCA 60.440 66.667 0.00 0.00 38.22 3.25
4802 4856 2.050714 GACTCGTCAACGTCGCCA 60.051 61.111 2.09 0.00 40.80 5.69
4867 4921 0.319083 GTGTCCCGACCACATACACA 59.681 55.000 0.00 0.00 40.08 3.72
6756 6810 1.913951 TTGTCTCCTGCGGATGCCAT 61.914 55.000 0.00 0.00 41.78 4.40
6795 6849 4.102524 TGTTGGTGGACTTCAGTACTTGAT 59.897 41.667 0.00 0.00 35.27 2.57
7330 7384 6.825610 ACTCCAGATCAAGTTTATCTCATCC 58.174 40.000 0.00 0.00 31.22 3.51
7573 7627 7.013834 TGGTTCCCCAAAACTTATTGTCTTAT 58.986 34.615 0.00 0.00 37.98 1.73
7574 7628 8.171400 TGGTTCCCCAAAACTTATTGTCTTATA 58.829 33.333 0.00 0.00 37.98 0.98
7575 7629 8.683615 GGTTCCCCAAAACTTATTGTCTTATAG 58.316 37.037 0.00 0.00 0.00 1.31
7576 7630 9.239551 GTTCCCCAAAACTTATTGTCTTATAGT 57.760 33.333 0.00 0.00 0.00 2.12
7577 7631 8.801882 TCCCCAAAACTTATTGTCTTATAGTG 57.198 34.615 0.00 0.00 0.00 2.74
7578 7632 7.338449 TCCCCAAAACTTATTGTCTTATAGTGC 59.662 37.037 0.00 0.00 0.00 4.40
7642 7696 5.191522 TCAGATGGATGTATTTCTTCACCCA 59.808 40.000 0.00 0.00 0.00 4.51
7707 7761 1.298938 GTCGACCGGTTCCTATCGC 60.299 63.158 9.42 0.00 34.59 4.58
7709 7763 2.487532 CGACCGGTTCCTATCGCCT 61.488 63.158 9.42 0.00 0.00 5.52
7710 7764 1.363080 GACCGGTTCCTATCGCCTC 59.637 63.158 9.42 0.00 0.00 4.70
7813 7867 0.685097 TACACCACCCTGAAGCTGAC 59.315 55.000 0.00 0.00 0.00 3.51
7819 7873 1.078567 CCCTGAAGCTGACCTCTGC 60.079 63.158 0.00 0.00 40.53 4.26
7820 7874 1.675801 CCTGAAGCTGACCTCTGCA 59.324 57.895 6.90 0.00 42.33 4.41
7821 7875 0.252479 CCTGAAGCTGACCTCTGCAT 59.748 55.000 6.90 0.00 42.33 3.96
7947 8001 2.203523 TCGACCACTTCACCCGGA 60.204 61.111 0.73 0.00 0.00 5.14
8013 8067 3.231736 ACTTGGCGGACCTCACGT 61.232 61.111 0.00 0.00 36.63 4.49
8056 8110 4.082523 CCTGCCGTCCACCGTCAT 62.083 66.667 0.00 0.00 33.66 3.06
8101 8155 1.618487 TGCACAATCAACCAGATGCA 58.382 45.000 0.00 0.00 36.96 3.96
8124 8178 3.524648 TTCAGGTGGAACGACGGCC 62.525 63.158 0.00 0.00 38.12 6.13
8135 8189 2.185608 GACGGCCTGAAGGAGCTC 59.814 66.667 4.71 4.71 37.39 4.09
8264 8318 2.868964 ACCAGAGGCATTACTCCCTA 57.131 50.000 0.00 0.00 38.26 3.53
8266 8320 2.022918 ACCAGAGGCATTACTCCCTACT 60.023 50.000 0.00 0.00 38.26 2.57
8272 8326 4.298626 AGGCATTACTCCCTACTTGATCA 58.701 43.478 0.00 0.00 0.00 2.92
8273 8327 4.346418 AGGCATTACTCCCTACTTGATCAG 59.654 45.833 0.00 0.00 0.00 2.90
8324 8384 2.036604 GGATTAGGACCTAGAGCAGTGC 59.963 54.545 7.13 7.13 0.00 4.40
8325 8385 1.486211 TTAGGACCTAGAGCAGTGCC 58.514 55.000 12.58 3.25 0.00 5.01
8326 8386 0.335019 TAGGACCTAGAGCAGTGCCA 59.665 55.000 12.58 0.00 0.00 4.92
8327 8387 1.219393 GGACCTAGAGCAGTGCCAC 59.781 63.158 12.58 6.65 0.00 5.01
8328 8388 1.261238 GGACCTAGAGCAGTGCCACT 61.261 60.000 12.58 14.10 0.00 4.00
8340 8400 2.162681 AGTGCCACTGAATTTGTAGGC 58.837 47.619 0.00 0.00 42.32 3.93
8401 8461 1.001181 ACGTTGGTACCATACTTGCGT 59.999 47.619 17.17 15.54 0.00 5.24
8537 8597 3.256960 AGGTCGGGCCCACATGTT 61.257 61.111 24.92 0.00 38.26 2.71
8637 8697 2.497770 CGCCGGTTCGAACCCTAT 59.502 61.111 35.50 0.00 46.53 2.57
8655 8716 0.042731 ATTCTCGTTCCCCTCTCCCA 59.957 55.000 0.00 0.00 0.00 4.37
8815 8882 1.215382 CGAGGGCGACAGTTCATCA 59.785 57.895 0.00 0.00 40.82 3.07
8842 8909 1.483424 CGAGCGGCGAGGAAGAAATC 61.483 60.000 12.98 0.00 44.57 2.17
8959 9026 1.903183 GGAGTGCTGTAAGTCCTCCTT 59.097 52.381 0.00 0.00 44.47 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 8.870116 TGACACAGTGCAAACCTATATATAGAT 58.130 33.333 19.51 0.60 32.05 1.98
147 149 7.287696 AGTTGACAACCCTGTTCTCATAAAAAT 59.712 33.333 14.72 0.00 35.30 1.82
270 272 0.247736 AGGATCTTCGCTGTGTGGAC 59.752 55.000 0.00 0.00 0.00 4.02
355 358 8.771920 TCCCGCAATATTAGTGAATGTAATAG 57.228 34.615 0.00 0.00 0.00 1.73
364 367 2.047061 AGCCTCCCGCAATATTAGTGA 58.953 47.619 0.00 0.00 41.38 3.41
365 368 2.550830 AGCCTCCCGCAATATTAGTG 57.449 50.000 0.00 0.00 41.38 2.74
366 369 4.161754 GGTATAGCCTCCCGCAATATTAGT 59.838 45.833 0.00 0.00 41.38 2.24
367 370 4.161565 TGGTATAGCCTCCCGCAATATTAG 59.838 45.833 0.00 0.00 41.38 1.73
372 379 0.687354 CTGGTATAGCCTCCCGCAAT 59.313 55.000 0.00 0.00 41.38 3.56
377 384 2.327325 TCATCCTGGTATAGCCTCCC 57.673 55.000 0.00 0.00 38.35 4.30
497 507 9.226606 TGTTTACATATTTGTTTACAGAGGGAG 57.773 33.333 0.00 0.00 37.28 4.30
498 508 9.575868 TTGTTTACATATTTGTTTACAGAGGGA 57.424 29.630 0.00 0.00 37.28 4.20
560 570 8.179615 CCTCCGTAAAGAAATATAAAAGCGTTT 58.820 33.333 2.53 2.53 0.00 3.60
561 571 7.201670 CCCTCCGTAAAGAAATATAAAAGCGTT 60.202 37.037 0.00 0.00 0.00 4.84
562 572 6.259387 CCCTCCGTAAAGAAATATAAAAGCGT 59.741 38.462 0.00 0.00 0.00 5.07
563 573 6.480981 TCCCTCCGTAAAGAAATATAAAAGCG 59.519 38.462 0.00 0.00 0.00 4.68
564 574 7.498239 ACTCCCTCCGTAAAGAAATATAAAAGC 59.502 37.037 0.00 0.00 0.00 3.51
565 575 8.959705 ACTCCCTCCGTAAAGAAATATAAAAG 57.040 34.615 0.00 0.00 0.00 2.27
567 577 8.146412 GCTACTCCCTCCGTAAAGAAATATAAA 58.854 37.037 0.00 0.00 0.00 1.40
568 578 7.508296 AGCTACTCCCTCCGTAAAGAAATATAA 59.492 37.037 0.00 0.00 0.00 0.98
569 579 7.008941 AGCTACTCCCTCCGTAAAGAAATATA 58.991 38.462 0.00 0.00 0.00 0.86
570 580 5.839606 AGCTACTCCCTCCGTAAAGAAATAT 59.160 40.000 0.00 0.00 0.00 1.28
571 581 5.206587 AGCTACTCCCTCCGTAAAGAAATA 58.793 41.667 0.00 0.00 0.00 1.40
572 582 4.031611 AGCTACTCCCTCCGTAAAGAAAT 58.968 43.478 0.00 0.00 0.00 2.17
573 583 3.438183 AGCTACTCCCTCCGTAAAGAAA 58.562 45.455 0.00 0.00 0.00 2.52
574 584 3.097342 AGCTACTCCCTCCGTAAAGAA 57.903 47.619 0.00 0.00 0.00 2.52
575 585 2.822707 AGCTACTCCCTCCGTAAAGA 57.177 50.000 0.00 0.00 0.00 2.52
576 586 3.889520 AAAGCTACTCCCTCCGTAAAG 57.110 47.619 0.00 0.00 0.00 1.85
577 587 5.945144 ATTAAAGCTACTCCCTCCGTAAA 57.055 39.130 0.00 0.00 0.00 2.01
578 588 5.945144 AATTAAAGCTACTCCCTCCGTAA 57.055 39.130 0.00 0.00 0.00 3.18
579 589 6.367983 TCTAATTAAAGCTACTCCCTCCGTA 58.632 40.000 0.00 0.00 0.00 4.02
580 590 5.206587 TCTAATTAAAGCTACTCCCTCCGT 58.793 41.667 0.00 0.00 0.00 4.69
581 591 5.279056 CCTCTAATTAAAGCTACTCCCTCCG 60.279 48.000 0.00 0.00 0.00 4.63
582 592 5.603395 ACCTCTAATTAAAGCTACTCCCTCC 59.397 44.000 0.00 0.00 0.00 4.30
583 593 6.098552 ACACCTCTAATTAAAGCTACTCCCTC 59.901 42.308 0.00 0.00 0.00 4.30
584 594 5.965091 ACACCTCTAATTAAAGCTACTCCCT 59.035 40.000 0.00 0.00 0.00 4.20
585 595 6.049790 CACACCTCTAATTAAAGCTACTCCC 58.950 44.000 0.00 0.00 0.00 4.30
586 596 5.524281 GCACACCTCTAATTAAAGCTACTCC 59.476 44.000 0.00 0.00 0.00 3.85
587 597 5.524281 GGCACACCTCTAATTAAAGCTACTC 59.476 44.000 0.00 0.00 0.00 2.59
588 598 5.045869 TGGCACACCTCTAATTAAAGCTACT 60.046 40.000 0.00 0.00 36.63 2.57
589 599 5.183228 TGGCACACCTCTAATTAAAGCTAC 58.817 41.667 0.00 0.00 36.63 3.58
590 600 5.429681 TGGCACACCTCTAATTAAAGCTA 57.570 39.130 0.00 0.00 36.63 3.32
591 601 4.301072 TGGCACACCTCTAATTAAAGCT 57.699 40.909 0.00 0.00 36.63 3.74
597 607 7.342799 ACAATTGATATTGGCACACCTCTAATT 59.657 33.333 13.59 0.00 44.42 1.40
615 625 5.063438 CGATAGTCACCGACAAACAATTGAT 59.937 40.000 13.59 0.00 38.94 2.57
688 698 8.636213 CCATCAATTAAAGAGAAGCACCAATAT 58.364 33.333 0.00 0.00 0.00 1.28
689 699 7.416664 GCCATCAATTAAAGAGAAGCACCAATA 60.417 37.037 0.00 0.00 0.00 1.90
690 700 6.628844 GCCATCAATTAAAGAGAAGCACCAAT 60.629 38.462 0.00 0.00 0.00 3.16
691 701 5.336690 GCCATCAATTAAAGAGAAGCACCAA 60.337 40.000 0.00 0.00 0.00 3.67
692 702 4.158394 GCCATCAATTAAAGAGAAGCACCA 59.842 41.667 0.00 0.00 0.00 4.17
693 703 4.158394 TGCCATCAATTAAAGAGAAGCACC 59.842 41.667 0.00 0.00 0.00 5.01
694 704 5.314923 TGCCATCAATTAAAGAGAAGCAC 57.685 39.130 0.00 0.00 0.00 4.40
695 705 5.981088 TTGCCATCAATTAAAGAGAAGCA 57.019 34.783 0.00 0.00 0.00 3.91
696 706 5.287035 CGTTTGCCATCAATTAAAGAGAAGC 59.713 40.000 0.00 0.00 31.33 3.86
697 707 6.611381 TCGTTTGCCATCAATTAAAGAGAAG 58.389 36.000 0.00 0.00 31.33 2.85
698 708 6.567687 TCGTTTGCCATCAATTAAAGAGAA 57.432 33.333 0.00 0.00 31.33 2.87
699 709 6.757897 ATCGTTTGCCATCAATTAAAGAGA 57.242 33.333 0.00 0.00 31.33 3.10
700 710 7.429340 GTGTATCGTTTGCCATCAATTAAAGAG 59.571 37.037 0.00 0.00 31.33 2.85
701 711 7.094592 TGTGTATCGTTTGCCATCAATTAAAGA 60.095 33.333 0.00 0.00 31.33 2.52
702 712 7.026562 TGTGTATCGTTTGCCATCAATTAAAG 58.973 34.615 0.00 0.00 31.33 1.85
703 713 6.914259 TGTGTATCGTTTGCCATCAATTAAA 58.086 32.000 0.00 0.00 31.33 1.52
704 714 6.502136 TGTGTATCGTTTGCCATCAATTAA 57.498 33.333 0.00 0.00 31.33 1.40
705 715 6.691754 ATGTGTATCGTTTGCCATCAATTA 57.308 33.333 0.00 0.00 31.33 1.40
706 716 5.581126 ATGTGTATCGTTTGCCATCAATT 57.419 34.783 0.00 0.00 31.33 2.32
707 717 6.691754 TTATGTGTATCGTTTGCCATCAAT 57.308 33.333 0.00 0.00 31.33 2.57
708 718 6.502136 TTTATGTGTATCGTTTGCCATCAA 57.498 33.333 0.00 0.00 0.00 2.57
709 719 5.448496 GCTTTATGTGTATCGTTTGCCATCA 60.448 40.000 0.00 0.00 0.00 3.07
710 720 4.970003 GCTTTATGTGTATCGTTTGCCATC 59.030 41.667 0.00 0.00 0.00 3.51
711 721 4.640201 AGCTTTATGTGTATCGTTTGCCAT 59.360 37.500 0.00 0.00 0.00 4.40
712 722 4.006989 AGCTTTATGTGTATCGTTTGCCA 58.993 39.130 0.00 0.00 0.00 4.92
713 723 4.616181 AGCTTTATGTGTATCGTTTGCC 57.384 40.909 0.00 0.00 0.00 4.52
714 724 6.183360 ACAGTAGCTTTATGTGTATCGTTTGC 60.183 38.462 0.00 0.00 0.00 3.68
715 725 7.290857 ACAGTAGCTTTATGTGTATCGTTTG 57.709 36.000 0.00 0.00 0.00 2.93
716 726 8.030692 TGTACAGTAGCTTTATGTGTATCGTTT 58.969 33.333 0.00 0.00 0.00 3.60
717 727 7.541162 TGTACAGTAGCTTTATGTGTATCGTT 58.459 34.615 0.00 0.00 0.00 3.85
718 728 7.092137 TGTACAGTAGCTTTATGTGTATCGT 57.908 36.000 0.00 0.00 0.00 3.73
719 729 9.841880 ATATGTACAGTAGCTTTATGTGTATCG 57.158 33.333 0.33 0.00 0.00 2.92
764 774 9.685276 ACCATGATTCAAACAATAGAACTATGA 57.315 29.630 0.00 0.00 0.00 2.15
765 775 9.941664 GACCATGATTCAAACAATAGAACTATG 57.058 33.333 0.00 0.00 0.00 2.23
766 776 9.911788 AGACCATGATTCAAACAATAGAACTAT 57.088 29.630 0.00 0.00 0.00 2.12
768 778 9.167311 GTAGACCATGATTCAAACAATAGAACT 57.833 33.333 0.00 0.00 0.00 3.01
769 779 8.946085 TGTAGACCATGATTCAAACAATAGAAC 58.054 33.333 0.00 0.00 0.00 3.01
770 780 9.685276 ATGTAGACCATGATTCAAACAATAGAA 57.315 29.630 0.00 0.00 30.69 2.10
774 784 9.113838 GACTATGTAGACCATGATTCAAACAAT 57.886 33.333 0.00 0.00 34.86 2.71
775 785 7.277760 CGACTATGTAGACCATGATTCAAACAA 59.722 37.037 0.00 0.00 34.86 2.83
776 786 6.756542 CGACTATGTAGACCATGATTCAAACA 59.243 38.462 0.00 0.07 34.86 2.83
777 787 6.292381 GCGACTATGTAGACCATGATTCAAAC 60.292 42.308 0.00 0.00 34.86 2.93
778 788 5.753438 GCGACTATGTAGACCATGATTCAAA 59.247 40.000 0.00 0.00 34.86 2.69
779 789 5.289595 GCGACTATGTAGACCATGATTCAA 58.710 41.667 0.00 0.00 34.86 2.69
780 790 4.556699 CGCGACTATGTAGACCATGATTCA 60.557 45.833 0.00 0.00 34.86 2.57
781 791 3.914966 CGCGACTATGTAGACCATGATTC 59.085 47.826 0.00 0.00 34.86 2.52
782 792 3.568430 TCGCGACTATGTAGACCATGATT 59.432 43.478 3.71 0.00 34.86 2.57
783 793 3.058155 GTCGCGACTATGTAGACCATGAT 60.058 47.826 31.12 0.00 34.86 2.45
784 794 2.289820 GTCGCGACTATGTAGACCATGA 59.710 50.000 31.12 0.00 34.86 3.07
785 795 2.032924 TGTCGCGACTATGTAGACCATG 59.967 50.000 36.27 0.00 34.86 3.66
786 796 2.294979 TGTCGCGACTATGTAGACCAT 58.705 47.619 36.27 0.00 37.58 3.55
787 797 1.741528 TGTCGCGACTATGTAGACCA 58.258 50.000 36.27 12.51 0.00 4.02
788 798 4.153655 TCATATGTCGCGACTATGTAGACC 59.846 45.833 33.03 15.16 31.02 3.85
789 799 5.080731 GTCATATGTCGCGACTATGTAGAC 58.919 45.833 33.03 28.43 31.02 2.59
790 800 4.753107 TGTCATATGTCGCGACTATGTAGA 59.247 41.667 33.03 24.54 31.02 2.59
791 801 5.030874 TGTCATATGTCGCGACTATGTAG 57.969 43.478 33.03 23.29 31.02 2.74
792 802 4.083484 CCTGTCATATGTCGCGACTATGTA 60.083 45.833 33.03 26.75 31.02 2.29
793 803 3.304726 CCTGTCATATGTCGCGACTATGT 60.305 47.826 33.03 24.43 31.02 2.29
794 804 3.237628 CCTGTCATATGTCGCGACTATG 58.762 50.000 36.27 33.18 0.00 2.23
795 805 2.351835 GCCTGTCATATGTCGCGACTAT 60.352 50.000 36.27 28.05 0.00 2.12
796 806 1.001706 GCCTGTCATATGTCGCGACTA 60.002 52.381 36.27 25.64 0.00 2.59
797 807 0.249073 GCCTGTCATATGTCGCGACT 60.249 55.000 36.27 24.47 0.00 4.18
798 808 1.540607 CGCCTGTCATATGTCGCGAC 61.541 60.000 31.66 31.66 42.03 5.19
799 809 1.299089 CGCCTGTCATATGTCGCGA 60.299 57.895 3.71 3.71 42.03 5.87
800 810 1.588932 ACGCCTGTCATATGTCGCG 60.589 57.895 19.27 19.27 44.78 5.87
801 811 1.490693 CCACGCCTGTCATATGTCGC 61.491 60.000 1.90 0.00 0.00 5.19
802 812 1.490693 GCCACGCCTGTCATATGTCG 61.491 60.000 1.90 3.14 0.00 4.35
803 813 1.490693 CGCCACGCCTGTCATATGTC 61.491 60.000 1.90 0.00 0.00 3.06
804 814 1.521457 CGCCACGCCTGTCATATGT 60.521 57.895 1.90 0.00 0.00 2.29
805 815 1.521457 ACGCCACGCCTGTCATATG 60.521 57.895 0.00 0.00 0.00 1.78
806 816 1.521457 CACGCCACGCCTGTCATAT 60.521 57.895 0.00 0.00 0.00 1.78
807 817 2.125713 CACGCCACGCCTGTCATA 60.126 61.111 0.00 0.00 0.00 2.15
808 818 4.314440 ACACGCCACGCCTGTCAT 62.314 61.111 0.00 0.00 0.00 3.06
809 819 4.961511 GACACGCCACGCCTGTCA 62.962 66.667 9.83 0.00 41.64 3.58
829 839 2.672908 TTACTAGCTTAGCCCGCGCG 62.673 60.000 25.67 25.67 41.18 6.86
830 840 0.319641 ATTACTAGCTTAGCCCGCGC 60.320 55.000 0.00 0.00 0.00 6.86
831 841 2.228343 AGTATTACTAGCTTAGCCCGCG 59.772 50.000 0.00 0.00 0.00 6.46
832 842 3.506844 AGAGTATTACTAGCTTAGCCCGC 59.493 47.826 0.00 0.00 0.00 6.13
833 843 5.163874 CGTAGAGTATTACTAGCTTAGCCCG 60.164 48.000 0.00 0.00 0.00 6.13
834 844 5.704978 ACGTAGAGTATTACTAGCTTAGCCC 59.295 44.000 0.00 0.00 0.00 5.19
835 845 6.799926 ACGTAGAGTATTACTAGCTTAGCC 57.200 41.667 0.00 0.00 0.00 3.93
836 846 9.149225 TCATACGTAGAGTATTACTAGCTTAGC 57.851 37.037 0.08 0.00 43.12 3.09
840 850 9.504708 ACAATCATACGTAGAGTATTACTAGCT 57.495 33.333 0.08 0.00 43.12 3.32
893 903 2.903135 AGAGACAAGGAGGAAGTTCTGG 59.097 50.000 2.25 0.00 0.00 3.86
906 916 3.545703 GAGAGAGAGGGAGAGAGACAAG 58.454 54.545 0.00 0.00 0.00 3.16
907 917 2.241176 GGAGAGAGAGGGAGAGAGACAA 59.759 54.545 0.00 0.00 0.00 3.18
908 918 1.843851 GGAGAGAGAGGGAGAGAGACA 59.156 57.143 0.00 0.00 0.00 3.41
909 919 1.143073 GGGAGAGAGAGGGAGAGAGAC 59.857 61.905 0.00 0.00 0.00 3.36
910 920 1.010793 AGGGAGAGAGAGGGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
911 921 1.421646 GAGGGAGAGAGAGGGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
912 922 1.010793 AGAGGGAGAGAGAGGGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
913 923 1.421646 GAGAGGGAGAGAGAGGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
914 924 1.010793 AGAGAGGGAGAGAGAGGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
915 925 1.522900 AGAGAGGGAGAGAGAGGGAG 58.477 60.000 0.00 0.00 0.00 4.30
916 926 1.568597 CAAGAGAGGGAGAGAGAGGGA 59.431 57.143 0.00 0.00 0.00 4.20
917 927 1.411501 CCAAGAGAGGGAGAGAGAGGG 60.412 61.905 0.00 0.00 0.00 4.30
918 928 1.287739 ACCAAGAGAGGGAGAGAGAGG 59.712 57.143 0.00 0.00 0.00 3.69
919 929 2.826674 ACCAAGAGAGGGAGAGAGAG 57.173 55.000 0.00 0.00 0.00 3.20
1034 1044 2.668550 GTCGGGGAGCAAACGCTT 60.669 61.111 0.00 0.00 40.78 4.68
1066 1076 4.764823 TCTCGGAACATGGCATAAAAGTTT 59.235 37.500 0.00 0.00 0.00 2.66
1134 1144 4.308458 CGACGTGTGCCAGGGGAA 62.308 66.667 0.00 0.00 0.00 3.97
1144 1154 2.910479 TGCTCAGGGACGACGTGT 60.910 61.111 4.58 0.00 36.39 4.49
1248 1258 0.592754 GAGGCTTTCGTCGATCTCCG 60.593 60.000 0.00 0.00 40.25 4.63
2393 2429 3.454812 ACCTTGTTGTAGAACTCAGTGGT 59.545 43.478 4.21 2.89 32.79 4.16
2903 2939 3.349006 CTGTTGCTTCTGCGGCGT 61.349 61.111 9.37 0.00 43.34 5.68
3472 3508 3.990959 GGAAGTTGATGACTCTTCCCT 57.009 47.619 10.86 0.00 46.54 4.20
3644 3680 9.491675 AAAAATATCAAACACATCAGATTTGCA 57.508 25.926 0.00 0.00 34.09 4.08
4231 4273 0.036164 CAGGGATGGTGGTTCGACAA 59.964 55.000 0.00 0.00 0.00 3.18
4586 4628 1.251527 ATGAAGGCGACGTGAGGACT 61.252 55.000 0.00 0.00 0.00 3.85
4761 4815 1.608717 GGTGACGAGGAGCCAGTCAT 61.609 60.000 16.77 0.00 45.13 3.06
4802 4856 3.329889 TGCAACGGGCTGGAGGAT 61.330 61.111 0.00 0.00 45.15 3.24
4867 4921 0.593128 GAAAATGCCACTGCGACTGT 59.407 50.000 0.00 0.00 41.78 3.55
6719 6773 3.554934 ACAAAAGCTCACCATCAACAGA 58.445 40.909 0.00 0.00 0.00 3.41
6756 6810 3.838317 ACCAACAATGCTCCTGTACTCTA 59.162 43.478 0.00 0.00 0.00 2.43
6795 6849 4.979335 AGAGATATCTGGTCTCGTGATCA 58.021 43.478 10.74 0.00 45.26 2.92
7330 7384 5.426504 AGATGTCTGCAAGTTGATCCTTAG 58.573 41.667 7.16 0.00 33.76 2.18
7573 7627 0.108662 CATCTGACCGTGCTGCACTA 60.109 55.000 28.04 12.24 31.34 2.74
7574 7628 1.375140 CATCTGACCGTGCTGCACT 60.375 57.895 28.04 12.58 31.34 4.40
7575 7629 2.393768 CCATCTGACCGTGCTGCAC 61.394 63.158 22.38 22.38 0.00 4.57
7576 7630 2.046988 CCATCTGACCGTGCTGCA 60.047 61.111 0.00 0.00 0.00 4.41
7577 7631 2.103042 GTCCATCTGACCGTGCTGC 61.103 63.158 0.00 0.00 38.09 5.25
7578 7632 0.320683 TTGTCCATCTGACCGTGCTG 60.321 55.000 0.00 0.00 43.78 4.41
7642 7696 2.431942 CGGCGAGGTTGTAGCGTT 60.432 61.111 0.00 0.00 0.00 4.84
7720 7774 3.268330 AGCTCGTAGTCGTCAGTAATCA 58.732 45.455 0.00 0.00 38.33 2.57
7727 7781 3.482809 CGGAGCTCGTAGTCGTCA 58.517 61.111 7.83 0.00 38.33 4.35
7813 7867 1.299468 GACGCGACCTATGCAGAGG 60.299 63.158 25.77 25.77 42.89 3.69
7819 7873 1.002250 GCCATACGACGCGACCTATG 61.002 60.000 15.93 16.09 0.00 2.23
7820 7874 1.285023 GCCATACGACGCGACCTAT 59.715 57.895 15.93 3.36 0.00 2.57
7821 7875 2.717485 GCCATACGACGCGACCTA 59.283 61.111 15.93 0.46 0.00 3.08
8055 8109 2.203070 GAAGACCGCCGATGCCAT 60.203 61.111 0.00 0.00 0.00 4.40
8056 8110 4.812476 CGAAGACCGCCGATGCCA 62.812 66.667 0.00 0.00 0.00 4.92
8079 8133 2.164827 GCATCTGGTTGATTGTGCATCA 59.835 45.455 0.00 0.00 40.43 3.07
8101 8155 2.030562 CGTTCCACCTGAAGCCGT 59.969 61.111 0.00 0.00 32.37 5.68
8124 8178 1.018226 CACGCCAAGAGCTCCTTCAG 61.018 60.000 10.93 2.19 40.39 3.02
8192 8246 1.153958 CTCGAGCTCGTGCATGTCA 60.154 57.895 33.33 12.56 42.74 3.58
8264 8318 4.222366 TGAGTCATCTCAAGCTGATCAAGT 59.778 41.667 0.00 0.00 46.17 3.16
8266 8320 4.813750 TGAGTCATCTCAAGCTGATCAA 57.186 40.909 0.00 0.00 46.17 2.57
8324 8384 1.821216 ACCGCCTACAAATTCAGTGG 58.179 50.000 0.00 0.00 0.00 4.00
8325 8385 6.146184 CAGATATACCGCCTACAAATTCAGTG 59.854 42.308 0.00 0.00 0.00 3.66
8326 8386 6.223852 CAGATATACCGCCTACAAATTCAGT 58.776 40.000 0.00 0.00 0.00 3.41
8327 8387 5.639506 CCAGATATACCGCCTACAAATTCAG 59.360 44.000 0.00 0.00 0.00 3.02
8328 8388 5.305902 TCCAGATATACCGCCTACAAATTCA 59.694 40.000 0.00 0.00 0.00 2.57
8329 8389 5.790593 TCCAGATATACCGCCTACAAATTC 58.209 41.667 0.00 0.00 0.00 2.17
8340 8400 7.224753 GCCAATGTATACAATCCAGATATACCG 59.775 40.741 10.14 0.00 32.89 4.02
8401 8461 4.637534 GTGGTACTGATTCGTGAGTAGGTA 59.362 45.833 0.00 0.00 0.00 3.08
8537 8597 4.063967 CGGCCAGCGTGTCACCTA 62.064 66.667 2.24 0.00 0.00 3.08
8637 8697 0.903454 GTGGGAGAGGGGAACGAGAA 60.903 60.000 0.00 0.00 0.00 2.87
8669 8730 1.021390 GTCGCCATTGACACAGAGGG 61.021 60.000 0.00 0.00 38.75 4.30
8815 8882 4.451241 TCGCCGCTCGAGTAGTAT 57.549 55.556 15.13 0.00 43.16 2.12
8959 9026 3.835395 GGAAGAAAGAACAGAGGAGAGGA 59.165 47.826 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.