Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001658.1 Hibiscus syriacus cultivar Beakdansim tig00003316_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 88913
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:90 original size:9 final size:9
Alignment explanation
Indices: 78--136 Score: 61
Period size: 9 Copynumber: 6.9 Consensus size: 9
68 TTTTAATATT
78 TTTATTTAA
1 TTTATTTAA
87 TTTATTTAA
1 TTTATTTAA
*
96 -GTATTTAA
1 TTTATTTAA
104 TTTATTTAA
1 TTTATTTAA
* *
113 TAT-TTTAC
1 TTTATTTAA
*
121 TTTAATTAA
1 TTTATTTAA
130 TTT-TTTA
1 TTTATTTA
137 CAGATAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
8 16 0.40
9 24 0.60
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTATTTAA
Found at i:119 original size:17 final size:17
Alignment explanation
Indices: 82--136 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
72 AATATTTTTA
82 TTTAATTTATTTAAGTA-
1 TTTAATTTATTTAA-TAT
99 TTTAATTTATTTAATAT
1 TTTAATTTATTTAATAT
* * *
116 TTTACTTTAATTAATTT
1 TTTAATTTATTTAATAT
133 TTTA
1 TTTA
137 CAGATAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 2 0.06
17 32 0.94
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTAATTTATTTAATAT
Found at i:949 original size:43 final size:42
Alignment explanation
Indices: 870--995 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 42
860 TTGGCTTTCC
*
870 TGTACAGGGGGATGTGTCGAG-C-CTGACTACAGGCGTAATTCA
1 TGTACAGGGAGA--TGTCGAGCCACTGACTACAGGCGTAATTCA
* *
912 TGTACAGGGAGATGTACGAGCCACTGACTACAAGCGTAATTCC
1 TGTACAGGGAGATGT-CGAGCCACTGACTACAGGCGTAATTCA
* * *
955 TGTATAGGGAGATATGTCGAGCCAATGACTATAGGCGTAAT
1 TGTACAGGGAG--ATGTCGAGCCACTGACTACAGGCGTAAT
996 GTTATCGGCA
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
40 3 0.04
41 4 0.06
42 12 0.17
43 28 0.39
44 21 0.29
45 4 0.06
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (42 bp):
TGTACAGGGAGATGTCGAGCCACTGACTACAGGCGTAATTCA
Found at i:5696 original size:26 final size:25
Alignment explanation
Indices: 5635--5696 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
5625 TTAGTTACTG
*
5635 GAAAAAGACAAAAAAGATAATATTAA
1 GAAAAAGA-AAAAAAGATAATAATAA
* * *
5661 GACAATAGAAACAAAGGTAATAATATA
1 GA-AAAAGAAAAAAAGATAATAATA-A
5688 GAAAAAGAA
1 GAAAAAGAA
5697 TAAAGACAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.15
Consensus pattern (25 bp):
GAAAAAGAAAAAAAGATAATAATAA
Found at i:5705 original size:40 final size:40
Alignment explanation
Indices: 5659--5734 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
5649 AGATAATATT
* *
5659 AAGACAAT-AGAAACAAAGGTAATAATATAGAAAAAGAATA
1 AAGACAATAAAAAACAAAGGTAATAAT-TAAAAAAAGAATA
*
5699 AAGACAATAAAAAACAAGGGTAATAATTAAAAAAAG
1 AAGACAATAAAAAACAAAGGTAATAATTAAAAAAAG
5735 CAACAAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 16 0.50
41 16 0.50
ACGTcount: A:0.66, C:0.05, G:0.14, T:0.14
Consensus pattern (40 bp):
AAGACAATAAAAAACAAAGGTAATAATTAAAAAAAGAATA
Found at i:10577 original size:20 final size:21
Alignment explanation
Indices: 10552--10598 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
10542 GGTTGTAGTT
10552 GTTTCTAG-CCATTGGGGATG
1 GTTTCTAGTCCATTGGGGATG
**
10572 GTTTCTAGTCGTTTGGGGATG
1 GTTTCTAGTCCATTGGGGATG
*
10593 TTTTCT
1 GTTTCT
10599 CTATAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.11, C:0.13, G:0.32, T:0.45
Consensus pattern (21 bp):
GTTTCTAGTCCATTGGGGATG
Found at i:12584 original size:32 final size:32
Alignment explanation
Indices: 12541--12623 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
12531 TGGTTATAGC
*
12541 GCATTCAGATAATGCACAGTAT-AGTCAGGTTT
1 GCATTCAGATAATGCACAATATGA-TCAGGTTT
*
12573 GTATTCAGATAATGCACAATATGATCAGGTTT
1 GCATTCAGATAATGCACAATATGATCAGGTTT
*
12605 GCATTCAGATAATACACAA
1 GCATTCAGATAATGCACAA
12624 GAGTATGAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 45 0.98
33 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (32 bp):
GCATTCAGATAATGCACAATATGATCAGGTTT
Found at i:14473 original size:36 final size:36
Alignment explanation
Indices: 14380--14507 Score: 129
Period size: 36 Copynumber: 3.5 Consensus size: 36
14370 TTTACTTTAG
14380 TATATATTT-TTA-TTTTT-TTAGATTATATATATATA
1 TATATATTTATTATTTTTTATTA-ATT-TATATATATA
* *
14415 TTATATTTTTATTATCAGTTTTATTAATTTATATATATA
1 -TATATATTTATTAT--TTTTTATTAATTTATATATATA
* *
14454 TATATATTTACTATTTTTTATT-TTTTATTATATATA
1 TATATATTTATTATTTTTTATTAATTTA-TATATATA
*
14490 TATATATATATTATTTTT
1 TATATATTTATTATTTTT
14508 ACTTTTTTAT
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
35 4 0.05
36 39 0.50
37 3 0.04
38 12 0.15
39 10 0.13
40 7 0.09
41 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (36 bp):
TATATATTTATTATTTTTTATTAATTTATATATATA
Found at i:14514 original size:36 final size:36
Alignment explanation
Indices: 14433--14520 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 36
14423 TTATTATCAG
* *
14433 TTTTATTAATTTA-TATATATATATATATTTACTATT
1 TTTTATT-TTTTATTATATATATATATATATACTATT
*
14469 TTTTATTTTTTATTATATATATATATATATATTA-T
1 TTTTATTTTTTATTATATATATATATATATACTATT
14504 TTTTACTTTTTTATTAT
1 TTTTA-TTTTTTATTAT
14521 TATTTTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
35 10 0.21
36 37 0.79
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (36 bp):
TTTTATTTTTTATTATATATATATATATATACTATT
Found at i:14520 original size:17 final size:16
Alignment explanation
Indices: 14468--14595 Score: 80
Period size: 17 Copynumber: 7.6 Consensus size: 16
14458 TATTTACTAT
14468 TTTTTATTTTTTATTA
1 TTTTTATTTTTTATTA
* * *
14484 TATATATATATATATATTA
1 T-T-TTTAT-TTTTTATTA
14503 TTTTTACTTTTTTATTA
1 TTTTTA-TTTTTTATTA
* *
14520 TTATT-TTATTTATT-
1 TTTTTATTTTTTATTA
* *
14534 TGTTTTATTTATATATTT
1 T-TTTTATTT-TTTATTA
*
14552 TTTTTATTTTTTTTATTT
1 TTTTTA--TTTTTTATTA
*
14570 TTTTTATTTTTTTTTA
1 TTTTTATTTTTTATTA
*
14586 TATTTATTTT
1 TTTTTATTTT
14596 ACTTACTATT
Statistics
Matches: 87, Mismatches: 15, Indels: 20
0.71 0.12 0.16
Matches are distributed among these distances:
14 1 0.01
15 11 0.13
16 20 0.23
17 25 0.29
18 19 0.22
19 11 0.13
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTTTATTA
Found at i:14532 original size:9 final size:9
Alignment explanation
Indices: 14520--14596 Score: 72
Period size: 9 Copynumber: 8.9 Consensus size: 9
14510 TTTTTTATTA
14520 TTATTTTAT
1 TTATTTTAT
14529 TTATTTGT-T
1 TTATTT-TAT
14538 TTA-TTTAT
1 TTATTTTAT
* *
14546 ATATTTTTT
1 TTATTTTAT
*
14555 TTATTTTTT
1 TTATTTTAT
*
14564 TTATTTTTT
1 TTATTTTAT
14573 TTATTTT-T
1 TTATTTTAT
*
14581 TT-TTATAT
1 TTATTTTAT
14589 TTATTTTA
1 TTATTTTA
14597 CTTACTATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
7 4 0.07
8 11 0.19
9 42 0.72
10 1 0.02
ACGTcount: A:0.18, C:0.00, G:0.01, T:0.81
Consensus pattern (9 bp):
TTATTTTAT
Found at i:14532 original size:12 final size:12
Alignment explanation
Indices: 14512--14609 Score: 66
Period size: 11 Copynumber: 8.5 Consensus size: 12
14502 ATTTTTACTT
14512 TTTTA-TTATTA
1 TTTTATTTATTA
*
14523 TTTTATTTATTTG
1 TTTTATTTA-TTA
14536 TTTTATTTA-TA
1 TTTTATTTATTA
14547 TATTT-TTT-TTA
1 T-TTTATTTATTA
* *
14558 TTTTTTTTATTTT
1 TTTTATTTA-TTA
14571 TTTTATTT-TT-
1 TTTTATTTATTA
*
14581 TTTTATAT-TTA
1 TTTTATTTATTA
* *
14592 TTTTACTTACTA
1 TTTTATTTATTA
14604 TTTTAT
1 TTTTAT
14610 CTTTACTTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
10 12 0.17
11 24 0.35
12 13 0.19
13 20 0.29
ACGTcount: A:0.19, C:0.02, G:0.01, T:0.78
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:14539 original size:13 final size:13
Alignment explanation
Indices: 14512--14579 Score: 68
Period size: 13 Copynumber: 5.3 Consensus size: 13
14502 ATTTTTACTT
14512 TTTTA-TTA-TTA
1 TTTTATTTATTTA
*
14523 TTTTATTTATTTG
1 TTTTATTTATTTA
*
14536 TTTTATTTATATA
1 TTTTATTTATTTA
* *
14549 TTTTTTTTATTTT
1 TTTTATTTATTTA
*
14562 TTTTATTTTTTTTA
1 TTTTA-TTTATTTA
14576 TTTT
1 TTTT
14580 TTTTTATATT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
11 5 0.11
12 3 0.07
13 27 0.60
14 10 0.22
ACGTcount: A:0.18, C:0.00, G:0.01, T:0.81
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:14543 original size:18 final size:18
Alignment explanation
Indices: 14520--14596 Score: 88
Period size: 18 Copynumber: 4.4 Consensus size: 18
14510 TTTTTTATTA
*
14520 TTATTTTATTTATTTGTT
1 TTATTTTATTTATTTTTT
*
14538 TTA-TTTATATATTTTTT
1 TTATTTTATTTATTTTTT
*
14555 TTATTTTTTTTATTTTTT
1 TTATTTTATTTATTTTTT
* *
14573 TTATTTT-TTT-TTATAT
1 TTATTTTATTTATTTTTT
14589 TTATTTTA
1 TTATTTTA
14597 CTTACTATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
16 11 0.22
17 18 0.35
18 22 0.43
ACGTcount: A:0.18, C:0.00, G:0.01, T:0.81
Consensus pattern (18 bp):
TTATTTTATTTATTTTTT
Found at i:14554 original size:47 final size:43
Alignment explanation
Indices: 14450--14600 Score: 107
Period size: 44 Copynumber: 3.4 Consensus size: 43
14440 AATTTATATA
* * * * *
14450 TATATATATATTTAC-TATTTTTTATT-TTTTATTATATATATATA
1 TATATAT-TTTTTACTTATTTTTT-TTATTTTATT-TATTTTTTTT
14494 TATATATTATTTTTACTT-TTTTATTATTATTTTATTTATTTGTTTTATT
1 TATATA-T-TTTTTACTTATTTT-TT-TTATTTTATTTA-TT-TTTT-TT
*
14543 TATATATTTTTT--TTATTTTTTTTATTTTTTTTATTTTTTTT
1 TATATATTTTTTACTTATTTTTTTTATTTTATTTATTTTTTTT
14584 TATAT-TTATTTTACTTA
1 TATATATT-TTTTACTTA
14601 CTATTTTATC
Statistics
Matches: 90, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
40 2 0.02
41 11 0.12
42 4 0.04
43 5 0.06
44 17 0.19
45 16 0.18
46 12 0.13
47 13 0.14
48 3 0.03
49 7 0.08
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.73
Consensus pattern (43 bp):
TATATATTTTTTACTTATTTTTTTTATTTTATTTATTTTTTTT
Found at i:14588 original size:39 final size:41
Alignment explanation
Indices: 14511--14609 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 41
14501 TATTTTTACT
14511 TTTTTATTATTATTTTATTTATTTGTTTTATTTATATATTT
1 TTTTTATTATTATTTTATTTATTTGTTTTATTTATATATTT
* * *
14552 TTTTTATT-TT-TTTTATTT-TTTTTATTTTTTTTTATATTT
1 TTTTTATTATTATTTTATTTATTTGT-TTTATTTATATATTT
* *
14591 ATTTTACTTACTATTTTAT
1 TTTTTA-TTATTATTTTAT
14610 CTTTACTTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
38 4 0.08
39 26 0.53
40 4 0.08
41 9 0.18
42 6 0.12
ACGTcount: A:0.19, C:0.02, G:0.01, T:0.78
Consensus pattern (41 bp):
TTTTTATTATTATTTTATTTATTTGTTTTATTTATATATTT
Found at i:14595 original size:13 final size:13
Alignment explanation
Indices: 14520--14595 Score: 52
Period size: 13 Copynumber: 6.0 Consensus size: 13
14510 TTTTTTATTA
14520 TTAT-TTTATTTAT
1 TTATATTTATTT-T
*
14533 TTGT-TTTA-TTT
1 TTATATTTATTTT
* *
14544 ATATATTTTTTTT
1 TTATATTTATTTT
* *
14557 ATTTTTTTTATTTT
1 -TTATATTTATTTT
*
14571 TTTTATTT-TTTT
1 TTATATTTATTTT
14583 TTATATTTATTTT
1 TTATATTTATTTT
14596 ACTTACTATT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
11 3 0.06
12 16 0.33
13 21 0.43
14 9 0.18
ACGTcount: A:0.17, C:0.00, G:0.01, T:0.82
Consensus pattern (13 bp):
TTATATTTATTTT
Found at i:17791 original size:13 final size:13
Alignment explanation
Indices: 17759--17824 Score: 82
Period size: 13 Copynumber: 5.0 Consensus size: 13
17749 TAATCAAAGC
17759 AAAAAGAGAAAA-
1 AAAAAGAGAAAAT
17771 AAGCAAAGAGAAAAT
1 AA--AAAGAGAAAAT
17786 AAAAAGAGAAAAT
1 AAAAAGAGAAAAT
*
17799 AAAAAGAGAAAAA
1 AAAAAGAGAAAAT
17812 AACAAAG-GAAAAT
1 AA-AAAGAGAAAAT
17825 TAAAGAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
12 2 0.04
13 30 0.62
14 14 0.29
15 2 0.04
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.05
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:17844 original size:40 final size:40
Alignment explanation
Indices: 17759--17845 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
17749 TAATCAAAGC
* * *
17759 AAAAAGAGAAAAAAGCAAAGAGAAAATAAAAAGAGAAAAT
1 AAAAAGAGAAAAAAACAAAGAGAAAATAAAAAGAAAAAAA
*
17799 AAAAAGAGAAAAAAACAAAG-GAAAAT-TAAAGAAAAAAGA
1 AAAAAGAGAAAAAAACAAAGAGAAAATAAAAAGAAAAAA-A
17838 AGAAAAGA
1 A-AAAAGA
17846 TGCATATGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 9 0.22
39 7 0.17
40 25 0.61
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (40 bp):
AAAAAGAGAAAAAAACAAAGAGAAAATAAAAAGAAAAAAA
Found at i:19008 original size:32 final size:31
Alignment explanation
Indices: 18963--19046 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 31
18953 CAATGAGGGA
*
18963 ATCTTTGAAGATTCAACATCAAATGTTGGGGC
1 ATCTTTG-AGATTCAACATCAAATATTGGGGC
* * *
18995 ATTTTTTGAGATTCAATATCGAATATTGGGGC
1 A-TCTTTGAGATTCAACATCAAATATTGGGGC
*
19027 ATCTTTGGGAATTCAACATC
1 ATCTTTGAG-ATTCAACATC
19047 CTGATGCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 6 0.14
32 32 0.74
33 5 0.12
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (31 bp):
ATCTTTGAGATTCAACATCAAATATTGGGGC
Found at i:19759 original size:106 final size:106
Alignment explanation
Indices: 19622--19839 Score: 283
Period size: 106 Copynumber: 2.1 Consensus size: 106
19612 GATATCGTGC
* * * * *
19622 GACTCGAGACAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCC
1 GACTCGAGACAACACAAGCTCAACTTCACAACAAAGGGACGGCTGGCTGTCAACAAACAATTTCC
* *
19687 CAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTG
66 CAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
* * * *
19728 GACTCGAGACAGCACAAGCTCAGCTTCACAACAAAGGGGCGGCTGGCTGTCAACAAACAATTTCT
1 GACTCGAGACAACACAAGCTCAACTTCACAACAAAGGGACGGCTGGCTGTCAACAAACAATTTCC
* * * * * *
19793 TAGTTCCATAGCCAATTTTAACTTCACGACGGAGGATATTG
66 CAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
19834 GACTCG
1 GACTCG
19840 GAACAATACA
Statistics
Matches: 95, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
106 95 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (106 bp):
GACTCGAGACAACACAAGCTCAACTTCACAACAAAGGGACGGCTGGCTGTCAACAAACAATTTCC
CAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
Found at i:20282 original size:37 final size:37
Alignment explanation
Indices: 20207--20395 Score: 132
Period size: 37 Copynumber: 5.4 Consensus size: 37
20197 ATTGAAAACA
* * * * *
20207 TTTCCCTTGAAA-TAAATTTTATCTCGCTTGGGGTAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
20243 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
* * * *
20280 TTTCTCTTGAAACATAAA---------CATTGA-AAACA
1 TTTCCCTTGAAACA-AAATTTTGTCTCCCTTGAGATA-G
* ** *
20309 TTTCCTTTGAAA-TTAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
20345 TTTCCCTTGAAACAAATTTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
20382 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
20396 TAAACCTTGA
Statistics
Matches: 115, Mismatches: 24, Indels: 27
0.69 0.14 0.16
Matches are distributed among these distances:
27 2 0.02
28 2 0.02
29 15 0.13
36 27 0.23
37 66 0.57
38 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
Found at i:20293 original size:102 final size:102
Alignment explanation
Indices: 20187--20421 Score: 380
Period size: 102 Copynumber: 2.3 Consensus size: 102
20177 GTCTCCCTTA
* *
20187 AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCCCTTG
1 AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCCCTTG
20252 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
66 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
* * * *
20289 AAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
1 AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCCCTTG
* *
20354 AAACAAATTTTTGTCTCCCTTGAGATAGTTTCTCTTG
66 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
* *
20391 AAACATAAACCTTGAAAACGTTTCCCTTGAA
1 AAACATAAACATTGAAAACATTTCCCTTGAA
20422 GCACAAAATA
Statistics
Matches: 122, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 122 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCCCTTG
AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
Found at i:20294 original size:87 final size:87
Alignment explanation
Indices: 20100--20272 Score: 283
Period size: 87 Copynumber: 2.0 Consensus size: 87
20090 GTTTCTCTTG
* *
20100 AAACATAAACATTGAAAATATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCCCTTG
1 AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCCCTTG
**
20165 AAATGAAATTTTGTCTCCCTTA
66 AAACAAAATTTTGTCTCCCTTA
* * *
20187 AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCCCTTG
1 AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCCCTTG
20252 AAACAAAATTTTGTCTCCCTT
66 AAACAAAATTTTGTCTCCCTT
20273 GAGACAGTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 79 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (87 bp):
AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCCCTTG
AAACAAAATTTTGTCTCCCTTA
Found at i:20537 original size:36 final size:36
Alignment explanation
Indices: 20458--20693 Score: 202
Period size: 36 Copynumber: 6.7 Consensus size: 36
20448 TTAAAACGAG
*
20458 TTTTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTC
1 TTTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTC
*
20495 TCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTC
1 TTTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTC
*
20531 TTTTGAGACAGTTTCCCTTGAAACAAA------ATC
1 TTTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTC
* * * *
20561 -TTTGA-ATATCTTTTCCTTGAAACAAATTTCGTCTC
1 TTTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTC
** * * * *
20596 CCTTGAGACAGTTT-CTTTTAGAACTAAGTTTCGTCTC
1 TTTTGAGACAGTTTCCCTTGA-AAC-AAATTTTGTCTC
* * ** *
20633 TCTTGATACAGTTTCTTTTGAAACAAATTTTGTCCC
1 TTTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTC
*
20669 TTTTGAGACAGTTTCTCTTGAAACA
1 TTTTGAGACAGTTTCCCTTGAAACA
20694 CAAAAAAAAA
Statistics
Matches: 163, Mismatches: 24, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 20 0.12
30 2 0.01
35 6 0.04
36 78 0.48
37 51 0.31
38 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTC
Found at i:20579 original size:102 final size:102
Alignment explanation
Indices: 20473--20659 Score: 245
Period size: 102 Copynumber: 1.8 Consensus size: 102
20463 AGACAGTTTC
* * *
20473 CCTTGAAACAAAATCTT-GTCTCTCTTGAGACAGTTTCCCTTGA-AAC-AAATTTTGTCTCTTTT
1 CCTTGAAAC-AAAT-TTCGTCTCCCTTGAGACAGTTT-CCTTGAGAACTAAATTTCGTCTCTCTT
20535 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
63 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
* * * *
20575 CCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAGAACTAAGTTTCGTCTCTCTTGAT
1 CCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCTTGAGAACTAAATTTCGTCTCTCTTGAG
**
20640 ACAGTTTCTTTTGAAACAAA
66 ACAGTTTCCCTTGAAACAAA
20660 TTTTGTCCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 6 0.08
101 25 0.34
102 42 0.58
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (102 bp):
CCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCTTGAGAACTAAATTTCGTCTCTCTTGAG
ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
Found at i:20757 original size:39 final size:38
Alignment explanation
Indices: 20679--20773 Score: 133
Period size: 39 Copynumber: 2.6 Consensus size: 38
20669 TTTTGAGACA
*
20679 GTTTCTCTTG-AA-ACACAAAAAAAAACCCTCGAAATT
1 GTTTCTCTTGAAACACACAAAAAAAAACCCTCGAAAAT
* *
20715 GTTTCTCTTGAAACACACACAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACACA-AAAAAAAACCCTCGAAAAT
20754 GTTTCTCTTGAAACAC-CAAA
1 GTTTCTCTTGAAACACACAAA
20774 CCCTTGAGTT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
36 10 0.19
37 4 0.08
38 7 0.13
39 32 0.60
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.26
Consensus pattern (38 bp):
GTTTCTCTTGAAACACACAAAAAAAAACCCTCGAAAAT
Found at i:21794 original size:23 final size:23
Alignment explanation
Indices: 21747--21791 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
21737 GGTCTCTTAC
*
21747 ATTTATATTTTTTAATTATTATT
1 ATTTATATTTTTTAACTATTATT
21770 ATTT-TATTTATTTAACT-TTATT
1 ATTTATATTT-TTTAACTATTATT
21792 TATACGCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTTATATTTTTTAACTATTATT
Found at i:21919 original size:2 final size:2
Alignment explanation
Indices: 21914--22028 Score: 59
Period size: 2 Copynumber: 60.5 Consensus size: 2
21904 TTTTTTAGAT
* *
21914 TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TT TT TA T- TA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* * * *
21954 GT- TT TA T- TA -A TT TA TA TA TA TA TA TA TA CTA T- TT TT TA T-
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
21993 TT TT TA T- TT TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22029 TATTTTTACT
Statistics
Matches: 94, Mismatches: 7, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
1 9 0.10
2 81 0.86
3 3 0.03
4 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (2 bp):
TA
Found at i:21970 original size:44 final size:46
Alignment explanation
Indices: 21914--22035 Score: 178
Period size: 44 Copynumber: 2.7 Consensus size: 46
21904 TTTTTTAGAT
21914 TATATATATATATATATATATATATTATTTTTTA-TTATCAGTTTTA
1 TATATATATATATATATATATATATTATTTTTTATTTATCA-TTTTA
* * * *
21960 T-TA-ATTTATATATATATATATACTATTTTTTATTTTTTATTTTA
1 TATATATATATATATATATATATATTATTTTTTATTTATCATTTTA
22004 TATATATATATATATATATATATATTATTTTT
1 TATATATATATATATATATATATATTATTTTT
22036 ACTTTTTTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
44 33 0.49
45 8 0.12
46 26 0.39
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (46 bp):
TATATATATATATATATATATATATTATTTTTTATTTATCATTTTA
Found at i:22060 original size:9 final size:9
Alignment explanation
Indices: 22048--22201 Score: 50
Period size: 9 Copynumber: 16.7 Consensus size: 9
22038 TTTTTTATTA
22048 TTATTTTAT
1 TTATTTTAT
*
22057 TTATTTTTT
1 TTATTTTAT
22066 TTA-TTTAT
1 TTATTTTAT
*
22074 ATATTTT-T
1 TTATTTTAT
*
22082 TTCTTCTT-T
1 TTATT-TTAT
*
22091 TT-CTTTAT
1 TTATTTTAT
*
22099 TTTTTTATAT
1 TTATTT-TAT
22109 TTATTTTACT
1 TTATTTTA-T
22119 TACTATTTTATAT
1 T--TA-TTT-TAT
* *
22132 TTACTTTCT
1 TTATTTTAT
*
22141 TTATCTTA-
1 TTATTTTAT
*
22149 -TCTTTTAT
1 TTATTTTAT
**
22157 TTAAATTAT
1 TTATTTTAT
*
22166 TTTTTCTTCATT
1 TTATT-TT-A-T
*
22178 TTATTTTAA
1 TTATTTTAT
*
22187 TTAATTTAT
1 TTATTTTAT
22196 TTATTT
1 TTATTT
22202 CTTACCTTTT
Statistics
Matches: 104, Mismatches: 26, Indels: 30
0.65 0.16 0.19
Matches are distributed among these distances:
7 7 0.07
8 14 0.13
9 49 0.47
10 15 0.14
11 5 0.05
12 7 0.07
13 5 0.05
14 2 0.02
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (9 bp):
TTATTTTAT
Found at i:22070 original size:24 final size:24
Alignment explanation
Indices: 22038--22127 Score: 80
Period size: 25 Copynumber: 3.8 Consensus size: 24
22028 TTATTTTTAC
22038 TTTTTTA-TTATTATTTTATTTATT
1 TTTTTTACTTATTATTTT-TTTATT
* *
22062 TTTTTTATTTATATATTTTTTTCTT
1 TTTTTTACTTAT-TATTTTTTTATT
*
22087 CTTTTT-C-T-TTATTTTTTTATAT
1 TTTTTTACTTATTATTTTTTTAT-T
*
22109 TTATTTTACTTACTATTTT
1 TT-TTTTACTTATTATTTT
22128 ATATTTACTT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
21 10 0.19
22 3 0.06
23 5 0.09
24 8 0.15
25 15 0.28
26 12 0.23
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTTACTTATTATTTTTTTATT
Found at i:22070 original size:38 final size:38
Alignment explanation
Indices: 22039--22112 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
22029 TATTTTTACT
22039 TTTTTATTATT-ATTTTATTTATTTTTTTTATTTATATA
1 TTTTT-TTATTCATTTTATTTATTTTTTTTATTTATATA
* * *
22077 TTTTTTTCTTCTTTTTCTTTATTTTTTTATATTTAT
1 TTTTTTTATTCATTTTATTTATTTTTTT-TATTTAT
22113 TTTACTTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 4 0.13
38 20 0.65
39 7 0.23
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (38 bp):
TTTTTTTATTCATTTTATTTATTTTTTTTATTTATATA
Found at i:22078 original size:21 final size:20
Alignment explanation
Indices: 22028--22113 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 20
22018 TATATATATA
22028 TTATT-TTTACTTTTTTATTAT
1 TTATTATTTA-TTTTTT-TTAT
*
22049 TATTTTATTTATTTTTTTTAT
1 T-TATTATTTATTTTTTTTAT
* *
22070 TTA-TATATT-TTTTTCTTCT
1 TTATTAT-TTATTTTTTTTAT
*
22089 TT-TTCTTTATTTTTTTATAT
1 TTATTATTTATTTTTTT-TAT
22109 TTATT
1 TTATT
22114 TTACTTACTA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
18 2 0.04
19 21 0.41
20 7 0.14
21 8 0.16
22 9 0.18
23 4 0.08
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (20 bp):
TTATTATTTATTTTTTTTAT
Found at i:22894 original size:2 final size:2
Alignment explanation
Indices: 22887--22918 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
22877 ATTTTTGAGA
22887 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22919 GTTTTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22963 original size:24 final size:26
Alignment explanation
Indices: 22932--22993 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
22922 TTTGAAAACA
22932 TTTTGAAAACATAT-T-ATATATAGT
1 TTTTGAAAACATATATAATATATAGT
*
22956 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAACATATATAATATATAGT
22982 TTTTGAAAACAT
1 TTTTGAAAACAT
22994 TTTTGAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 13 0.38
25 1 0.03
26 20 0.59
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (26 bp):
TTTTGAAAACATATATAATATATAGT
Found at i:23041 original size:36 final size:35
Alignment explanation
Indices: 22955--23152 Score: 238
Period size: 36 Copynumber: 5.5 Consensus size: 35
22945 TTATATATAG
22955 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAATATATAT--TATATAG-TTTTGAAAACA
*
22993 TTTTTGAGAAATATATATTATATAGTTTTGAAAACGG
1 TTTTTGA-AAATATATATTATATAGTTTTGAAAAC-A
23030 TTTTTGAAAATATATATTATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATTATATAGTTTTGAAAACA
* * *
23065 TTTTTGAAATACATATAATATATAGTTTTGAAAATA
1 TTTTTGAAA-ATATATATTATATAGTTTTGAAAACA
* *
23101 -TTTTGAAAATATATATAACATATAGTTTTTGAAAATA
1 TTTTTGAAAATATATAT--TATATAG-TTTTGAAAACA
*
23138 TTTTT-ATAATATATA
1 TTTTTGAAAATATATA
23153 ATTCTAAAAA
Statistics
Matches: 144, Mismatches: 9, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
34 6 0.04
35 17 0.12
36 66 0.46
37 34 0.24
38 11 0.08
39 10 0.07
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (35 bp):
TTTTTGAAAATATATATTATATAGTTTTGAAAACA
Found at i:23081 original size:72 final size:72
Alignment explanation
Indices: 22953--23142 Score: 262
Period size: 72 Copynumber: 2.6 Consensus size: 72
22943 TATTATATAT
* *
22953 AGTTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAGAAATATATATTATATAG
1 AGTTTTTGAAAATATATAT-ATATATAGTTTTTGAAAACATTTTTGAGAAACATATAATATATAG
23018 TTTTGAAA
65 TTTTGAAA
23026 ACGGTTTTTGAAAATATATAT-TATATAG-TTTTGAAAACATTTTTGA-AATACATATAATATAT
1 A--GTTTTTGAAAATATATATATATATAGTTTTTGAAAACATTTTTGAGAA-ACATATAATATAT
23088 AGTTTTGAAA
63 AGTTTTGAAA
* *
23098 A-TATTTTGAAAATATATATAACATATAGTTTTTGAAAATATTTTT
1 AGT-TTTTGAAAATATATAT-ATATATAGTTTTTGAAAACATTTTT
23143 ATAATATATA
Statistics
Matches: 106, Mismatches: 4, Indels: 14
0.85 0.03 0.11
Matches are distributed among these distances:
69 1 0.01
70 16 0.15
71 2 0.02
72 46 0.43
73 23 0.22
75 18 0.17
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (72 bp):
AGTTTTTGAAAATATATATATATATAGTTTTTGAAAACATTTTTGAGAAACATATAATATATAGT
TTTGAAA
Found at i:24410 original size:17 final size:17
Alignment explanation
Indices: 24390--24434 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
24380 TAGTTATTCC
* *
24390 TTTTTGATTTT-AGCAT
1 TTTTTTATTTTAAACAT
24406 TTTTTTATTTTGAAACAT
1 TTTTTTATTTT-AAACAT
24424 TTTTTTATTTT
1 TTTTTTATTTT
24435 TTTACTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
18 15 0.60
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.69
Consensus pattern (17 bp):
TTTTTTATTTTAAACAT
Found at i:24545 original size:3 final size:3
Alignment explanation
Indices: 24537--24568 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
24527 TATTTAAGGT
24537 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
24569 CTCTAACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:26162 original size:2 final size:2
Alignment explanation
Indices: 26155--26180 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26145 TTTTAAAATA
26155 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
26181 TGTCATAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26222 original size:18 final size:21
Alignment explanation
Indices: 26185--26223 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 21
26175 ATATATTGTC
26185 ATAAACAATTTCATATTTAAA
1 ATAAACAATTTCATATTTAAA
26206 ATAAA-AATTT-A-ATTTAAA
1 ATAAACAATTTCATATTTAAA
26224 TACTTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 5 0.28
21 5 0.28
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAACAATTTCATATTTAAA
Found at i:26426 original size:39 final size:38
Alignment explanation
Indices: 26383--26463 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 38
26373 GAAATTCAAA
26383 TATTAATATCATAAATGAAAGAAATTTAATTAAAATAAT
1 TATTAATATCATAAATGAAAGAAATTTAATT-AAATAAT
*
26422 TATTAATATCATAAATGAAATAAATTTAATTAAATAAT
1 TATTAATATCATAAATGAAAGAAATTTAATTAAATAAT
26460 TATT
1 TATT
26464 TTTACAAGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 11 0.27
39 30 0.73
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (38 bp):
TATTAATATCATAAATGAAAGAAATTTAATTAAATAAT
Found at i:28052 original size:25 final size:26
Alignment explanation
Indices: 28024--28077 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
28014 TCATTATTTT
*
28024 ATAAATT-AAATTCATA-TATAAAATA
1 ATAAATTCAAATCCA-ACTATAAAATA
28049 ATAAATTCAAATCCAACTATAAAATA
1 ATAAATTCAAATCCAACTATAAAATA
28075 ATA
1 ATA
28078 CTTATAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (26 bp):
ATAAATTCAAATCCAACTATAAAATA
Found at i:29095 original size:12 final size:12
Alignment explanation
Indices: 29078--29102 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29068 TATCAAATAT
29078 AAAAATATATAA
1 AAAAATATATAA
29090 AAAAATATATAA
1 AAAAATATATAA
29102 A
1 A
29103 CATCGTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATATATAA
Found at i:35997 original size:26 final size:26
Alignment explanation
Indices: 35963--36017 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
35953 TCCCGTTGCA
35963 CATAGTGAGGGTTAAAGATCACACTG
1 CATAGTGAGGGTTAAAGATCACACTG
35989 CATAGTGAGGGTTAAAGATCACACTG
1 CATAGTGAGGGTTAAAGATCACACTG
36015 CAT
1 CAT
36018 CTATCTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (26 bp):
CATAGTGAGGGTTAAAGATCACACTG
Found at i:37665 original size:20 final size:21
Alignment explanation
Indices: 37640--37691 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
37630 GACCAACAAA
37640 TTCGCAACGCGAG-CTCCAAT
1 TTCGCAACGCGAGTCTCCAAT
*
37660 TTCGCAATC-C-AGTTTCCAAT
1 TTCGCAA-CGCGAGTCTCCAAT
37680 TTCGCAACGCGA
1 TTCGCAACGCGA
37692 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 3 0.11
20 22 0.81
21 2 0.07
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (21 bp):
TTCGCAACGCGAGTCTCCAAT
Found at i:37724 original size:20 final size:20
Alignment explanation
Indices: 37680--37871 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
37670 AGTTTCCAAT
37680 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACGCG-ATA-GTCAAA
*
37701 -TCGCAACACAGA-AGTCAAA
1 TTCGCAACGC-GATAGTCAAA
*
37720 TTCGCAATGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* * *
37740 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
37760 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* *
37780 TTCGCAACTCGATAGCCAAA
1 TTCGCAACGCGATAGTCAAA
* * *
37800 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
37820 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* * *
37840 TTCGTAACGCAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
37860 TTCGCAACGCGA
1 TTCGCAACGCGA
37872 AACACAATAT
Statistics
Matches: 143, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 134 0.94
21 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (20 bp):
TTCGCAACGCGATAGTCAAA
Found at i:37744 original size:60 final size:60
Alignment explanation
Indices: 37713--37867 Score: 249
Period size: 60 Copynumber: 2.6 Consensus size: 60
37703 GCAACACAGA
37713 AGTCAAATTCGCAATGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAATGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
*
37773 AGTCAAATTCGCAACT-CGATAGCCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAA-TGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
* * * *
37833 AGTCAAATTCGTAACGCAAAAGTCAAATTCGCAAC
1 AGTCAAATTCGCAATGCGATAGTCAAATTCGCAAC
37868 GCGAAACACA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
60 86 0.99
61 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (60 bp):
AGTCAAATTCGCAATGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
Found at i:38001 original size:22 final size:22
Alignment explanation
Indices: 37976--38033 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
37966 TCACTCTCTA
37976 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATCTC
*
37998 CGGCGACATCCGTCCCCATTTC
1 CGGCGACATCCGTCCCCATCTC
* *
38020 CAGCGAAATCCGTC
1 CGGCGACATCCGTC
38034 TATCTCCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.45, G:0.19, T:0.19
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATCTC
Found at i:38479 original size:20 final size:19
Alignment explanation
Indices: 38440--38493 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
38430 AAATCGCAAC
*
38440 GCGATTTTAGTTTCGTGTT
1 GCGATTTTAGTTTCGCGTT
*
38459 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
38479 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
38494 AGAAACTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:40740 original size:21 final size:21
Alignment explanation
Indices: 40672--40740 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
40662 GGTGCCTCAT
40672 ATCGTTTAAGAGGCCCCTCTC
1 ATCGTTTAAGAGGCCCCTCTC
* ** * * *
40693 ATCATCGAAAAAGCCCCTCCC
1 ATCGTTTAAGAGGCCCCTCTC
* *
40714 ACCGTTTAAGAGGCCCCTGTC
1 ATCGTTTAAGAGGCCCCTCTC
40735 ATCGTT
1 ATCGTT
40741 CAATAGGTCC
Statistics
Matches: 33, Mismatches: 15, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (21 bp):
ATCGTTTAAGAGGCCCCTCTC
Found at i:42647 original size:18 final size:18
Alignment explanation
Indices: 42624--42659 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42614 AAGCCGGTTG
*
42624 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
42642 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
42660 CCTTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:44066 original size:25 final size:25
Alignment explanation
Indices: 44038--44089 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
44028 ATTATTTTCC
*
44038 AAATAATGTACCCATAACAATGTTT
1 AAATAATGTACCCACAACAATGTTT
44063 AAATAATGTACCCACAACAATGTTT
1 AAATAATGTACCCACAACAATGTTT
44088 AA
1 AA
44090 TTGATTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (25 bp):
AAATAATGTACCCACAACAATGTTT
Found at i:46847 original size:24 final size:24
Alignment explanation
Indices: 46813--46866 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
46803 CCATCACATC
46813 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* *
46837 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
46861 ATCAAA
1 ATCAAA
46867 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:46880 original size:24 final size:24
Alignment explanation
Indices: 46813--46880 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
46803 CCATCACATC
* * * *
46813 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
46837 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
46861 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
46881 TAGTACTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:47043 original size:19 final size:19
Alignment explanation
Indices: 47019--47062 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
47009 ATTGGAAATG
*
47019 TGGTGAAACAAAATTTTCT
1 TGGTGAAACAAAATTTTAT
47038 TGGTGAAACAAAATTTTAT
1 TGGTGAAACAAAATTTTAT
47057 TGGTGA
1 TGGTGA
47063 TGAAATTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.36
Consensus pattern (19 bp):
TGGTGAAACAAAATTTTAT
Found at i:47644 original size:16 final size:16
Alignment explanation
Indices: 47623--47656 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47613 AAATCATTGA
*
47623 AAAATTATATAGAAAT
1 AAAATTATATAAAAAT
*
47639 AAAATTATGTAAAAAT
1 AAAATTATATAAAAAT
47655 AA
1 AA
47657 TTAGAGATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:47876 original size:19 final size:19
Alignment explanation
Indices: 47836--47910 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
47826 TTAAATTCGT
* *
47836 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTG-AAATTTA
47856 GTTGCGAATTTGAAATTTA
1 GTTGCGAATTTGAAATTTA
*
47875 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTTA
47894 GTTGCGAATTTGAAATT
1 GTTGCGAATTTGAAATT
47911 CCGCGTTGCG
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 41 0.79
20 11 0.21
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTTA
Found at i:47911 original size:19 final size:20
Alignment explanation
Indices: 47828--48086 Score: 124
Period size: 20 Copynumber: 13.0 Consensus size: 20
47818 TTGTGAAATT
* *
47828 AAATTCGTGTTGCGAATTCG
1 AAATTCGAGTTGCGAATTTG
* *
47848 AAAATCTAGTTGCGAATTTG
1 AAATTCGAGTTGCGAATTTG
*
47868 AAATT-TAGTTGCGAATTTG
1 AAATTCGAGTTGCGAATTTG
47887 AAATTC-AGTTGCGAATTTG
1 AAATTCGAGTTGCGAATTTG
*
47906 AAATTCCGCGTTGCGAATTTG
1 AAATT-CGAGTTGCGAATTTG
* * *
47927 -ACTTCTGTGTTGCG-ATTTAT
1 AAATTC-GAGTTGCGAATTT-G
* **
47947 AAATTCGTGTTGTAAATTTG
1 AAATTCGAGTTGCGAATTTG
* * *
47967 -ACTATCGCGTTGCAAATTTG
1 AAAT-TCGAGTTGCGAATTTG
* * *
47987 -ACTATCGCGTTACGAATTTG
1 AAAT-TCGAGTTGCGAATTTG
** * *
48007 ACTTTTGTGTTGCGAATTTG
1 AAATTCGAGTTGCGAATTTG
* *
48027 -ACTATCGCGTTGCGAATTTG
1 AAAT-TCGAGTTGCGAATTTG
* *
48047 -ACTTCTGTGTTGCG-ATTT-
1 AAATTC-GAGTTGCGAATTTG
*
48065 ACAGATTCGCGTTGCGAATTTG
1 A-A-ATTCGAGTTGCGAATTTG
48087 GAAAATCACA
Statistics
Matches: 193, Mismatches: 30, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
19 51 0.26
20 114 0.59
21 28 0.15
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (20 bp):
AAATTCGAGTTGCGAATTTG
Found at i:47940 original size:20 final size:19
Alignment explanation
Indices: 47875--48086 Score: 151
Period size: 20 Copynumber: 10.6 Consensus size: 19
47865 TTGAAATTTA
* *
47875 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTG-ACTTCGC
*
47894 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTG-ACTT-CGC
*
47915 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTC-GC
* * * *
47935 GTTGCGATTTATAAATTCGT
1 GTTGCGAATT-TGACTTCGC
**
47955 GTTGTAAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
*
47975 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
* * *
47995 GTTACGAATTTGACTTTTGT
1 GTTGCGAATTTGAC-TTCGC
48015 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
*
48035 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTC-GC
48055 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC---TTCGC
48075 GTTGCGAATTTG
1 GTTGCGAATTTG
48087 GAAAATCACA
Statistics
Matches: 158, Mismatches: 22, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.01
19 28 0.18
20 103 0.65
21 25 0.16
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (19 bp):
GTTGCGAATTTGACTTCGC
Found at i:47952 original size:60 final size:60
Alignment explanation
Indices: 47827--48086 Score: 219
Period size: 60 Copynumber: 4.3 Consensus size: 60
47817 GTTGTGAAAT
* ** ** * *
47827 TAAATTCGTGTTGCGAATTCGAAAATCTAGTTGCGAATTTGAAATT-T-AGTTGCGAATTT-
1 TAAATTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTG-ACTTCTGTGTTGCG-ATTTA
* * *
47886 GAAATTC-AGTTGCGAATTTGA-AATTCCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTA
1 TAAATTCGTGTTGCGAATTTGACTA-T-CGCGTTGCGAATTTGACTTCTGTGTTGCGATTTA
** * * *
47946 TAAATTCGTGTTGTAAATTTGACTATCGCGTTGCAAATTTGACTATC-GCGTTACGAATTT-
1 TAAATTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT-TCTGTGTTGCG-ATTTA
* ** *
48006 GACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTA
1 TAAATTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTA
* * *
48066 CAGATTCGCGTTGCGAATTTG
1 TAAATTCGTGTTGCGAATTTG
48087 GAAAATCACA
Statistics
Matches: 161, Mismatches: 29, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
57 2 0.01
58 16 0.10
59 30 0.19
60 94 0.58
61 18 0.11
62 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (60 bp):
TAAATTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTA
Found at i:47965 original size:40 final size:40
Alignment explanation
Indices: 47894--48086 Score: 189
Period size: 40 Copynumber: 4.8 Consensus size: 40
47884 TTGAAATTCA
*
47894 GTTGCGAATTTGA-AATTCCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTA-T-CGCGTTGCGAATTTGACTTCTGT
* * * * ** *
47935 GTTGCGATTTATAAAT-TCGTGTTGTAAATTTGACTATC-GC
1 GTTGCGAATT-TGACTATCGCGTTGCGAATTTGACT-TCTGT
* * *
47975 GTTGCAAATTTGACTATCGCGTTACGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
48015 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
*
48055 GTTGCG-ATTT-ACAGATTCGCGTTGCGAATTTG
1 GTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTG
48087 GAAAATCACA
Statistics
Matches: 124, Mismatches: 21, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
38 2 0.02
39 9 0.07
40 99 0.80
41 12 0.10
42 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
Found at i:48102 original size:21 final size:21
Alignment explanation
Indices: 48078--48123 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
48068 GATTCGCGTT
48078 GCGAATTTGGAAAATCACAAC
1 GCGAATTTGGAAAATCACAAC
*
48099 GCGAATTTGGAAAATCACAAT
1 GCGAATTTGGAAAATCACAAC
48120 GCGA
1 GCGA
48124 TTTACATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
GCGAATTTGGAAAATCACAAC
Found at i:48205 original size:20 final size:20
Alignment explanation
Indices: 48157--48208 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
48147 TGGAAACTGG
* *
48157 GTTGCGAAATTAGAGTTCGC
1 GTTGCGAATTTGGAGTTCGC
48177 GTTGCGAATTTGGAGTTCGC
1 GTTGCGAATTTGGAGTTCGC
48197 GTTGCGAATTTG
1 GTTGCGAATTTG
48209 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGGAGTTCGC
Found at i:49548 original size:19 final size:19
Alignment explanation
Indices: 49506--49553 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
49496 TTTTAAAGAA
* * *
49506 AAATTATAGAAAAATTATC
1 AAATTATATAAAAAATAAC
*
49525 TAATTATATAAAAAATAAC
1 AAATTATATAAAAAATAAC
49544 AAATTA-ATAA
1 AAATTATATAA
49554 TTTAGTTACC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATTATATAAAAAATAAC
Found at i:50223 original size:20 final size:20
Alignment explanation
Indices: 50198--50236 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
50188 TTTAATATTT
50198 ATATTAAATTCAAAATTAAA
1 ATATTAAATTCAAAATTAAA
50218 ATATTAAATTCAAAATTAA
1 ATATTAAATTCAAAATTAA
50237 TATAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATTAAATTCAAAATTAAA
Found at i:52894 original size:13 final size:13
Alignment explanation
Indices: 52876--52900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52866 GTGAGTGCAG
52876 TTTATTTATTTTA
1 TTTATTTATTTTA
52889 TTTATTTATTTT
1 TTTATTTATTTT
52901 GATCTAGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:54069 original size:20 final size:20
Alignment explanation
Indices: 54044--54115 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
54034 ACTCATTTAA
54044 AGTATCGATACTCAACCTAG
1 AGTATCGATACTCAACCTAG
*
54064 AGTATCAATACTCAACCTAG
1 AGTATCGATACTCAACCTAG
54084 AGTATCGATACTCAACCTAG
1 AGTATCGATACTCAACCTAG
*
54104 AGTATCGCTACT
1 AGTATCGATACT
54116 ACCTTACTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (20 bp):
AGTATCGATACTCAACCTAG
Found at i:54765 original size:11 final size:11
Alignment explanation
Indices: 54749--54773 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54739 TATAGTACAT
54749 TTTAGAATATG
1 TTTAGAATATG
54760 TTTAGAATATG
1 TTTAGAATATG
54771 TTT
1 TTT
54774 CTATGCACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (11 bp):
TTTAGAATATG
Found at i:55817 original size:285 final size:284
Alignment explanation
Indices: 55291--55848 Score: 1107
Period size: 285 Copynumber: 2.0 Consensus size: 284
55281 TTTAATTTCA
55291 GATAGAACCTATAGAAACGACCCAACTTATAGTCCGGATGATAGATACGAGAGTCATGCCTCACC
1 GATAGAACCTATAGAAACGACCCAACTTATAGTCCGGATGATAGATACGAGAGTCATGCCTCACC
55356 ACCAACAAATATCAGTGAGGGATTCATCATAGATACCTTTGAGCAAAAGGCTCCAATAGATGCGG
66 ACCAACAAATATCAGTGAGGGATTCATCATAGATACCTTTGAGCAAAAGGCTCCAATAGATGCGG
55421 GGGTTAAGGAGGCTACTTTTTTCAGGGACCTTATCTCTGTACCTAGGCAGATCTCTAGGTCCTTA
131 GGGTTAAGGAGGCTACTTTTTTCAGGGACCTTATCTCTGTACCTAGGCAGATCTCTAGGTCCTTA
55486 CCTAGTTTCTCAACTGAACCACCTCCCCCACCAGTACATCCAGCTAAGCCAGTGACCATACCCCA
196 CCTAGTTTCTCAACTGAACCACCTCCCCCACCAGTACATCCAGCTAAGCCAGTGACCATACCCCA
55551 TGAGTCCCTAGTAACTACTGGAAT
261 TGAGTCCCTAGTAACTACTGGAAT
55575 GATAGAACCTATAGAAGACGACCCAACTTATAGTCCGGATGATAGATACGAGAGTCATGCCTCAC
1 GATAGAACCTATAGAA-ACGACCCAACTTATAGTCCGGATGATAGATACGAGAGTCATGCCTCAC
55640 CACCAACAAATATCAGTGAGGGATTCATCATAGATACCTTTGAGCAAAAGGCTCCAATAGATGCG
65 CACCAACAAATATCAGTGAGGGATTCATCATAGATACCTTTGAGCAAAAGGCTCCAATAGATGCG
55705 GGGGTTAAGGAGGCTACTTTTTTCAGGGACCTTATCTCTGTACCTAGGCAGATCTCTAGGTCCTT
130 GGGGTTAAGGAGGCTACTTTTTTCAGGGACCTTATCTCTGTACCTAGGCAGATCTCTAGGTCCTT
55770 ACCTAGTTTCTCAACTGAACCACCTCCCCCACCAGTACATCCAGCTAAGCCAGTGACCATACCCC
195 ACCTAGTTTCTCAACTGAACCACCTCCCCCACCAGTACATCCAGCTAAGCCAGTGACCATACCCC
55835 ATGAGTCCCTAGTA
260 ATGAGTCCCTAGTA
55849 GAGCGACTCC
Statistics
Matches: 273, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
284 16 0.06
285 257 0.94
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (284 bp):
GATAGAACCTATAGAAACGACCCAACTTATAGTCCGGATGATAGATACGAGAGTCATGCCTCACC
ACCAACAAATATCAGTGAGGGATTCATCATAGATACCTTTGAGCAAAAGGCTCCAATAGATGCGG
GGGTTAAGGAGGCTACTTTTTTCAGGGACCTTATCTCTGTACCTAGGCAGATCTCTAGGTCCTTA
CCTAGTTTCTCAACTGAACCACCTCCCCCACCAGTACATCCAGCTAAGCCAGTGACCATACCCCA
TGAGTCCCTAGTAACTACTGGAAT
Found at i:58992 original size:17 final size:17
Alignment explanation
Indices: 58970--59005 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
58960 TTCTAATATA
58970 TTTTTTACTTGTTATTT
1 TTTTTTACTTGTTATTT
* *
58987 TTTTTTATTTTTTATTT
1 TTTTTTACTTGTTATTT
59004 TT
1 TT
59006 CAGGCTCTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTTTTACTTGTTATTT
Found at i:70695 original size:20 final size:19
Alignment explanation
Indices: 70672--70709 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
70662 ACAAGTTAGG
*
70672 GGGTATTAATACCAGAAGGA
1 GGGTATCAATACCA-AAGGA
70692 GGGTATCAATACCAAAGG
1 GGGTATCAATACCAAAGG
70710 TTTAGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.18
Consensus pattern (19 bp):
GGGTATCAATACCAAAGGA
Found at i:78209 original size:12 final size:12
Alignment explanation
Indices: 78194--78277 Score: 64
Period size: 12 Copynumber: 7.0 Consensus size: 12
78184 GATACATTAC
78194 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
78206 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
78218 ATGGATTCTGTT
1 CTGAATTCTGTT
* *
78230 ATGATATT-TGAT
1 CTGA-ATTCTGTT
78242 CTGAATTCTGTT
1 CTGAATTCTGTT
*
78254 CTGATATT-TGAT
1 CTGA-ATTCTGTT
*
78266 CTAAATTCTGTT
1 CTGAATTCTGTT
78278 TTAATTTCTG
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
11 6 0.11
12 43 0.78
13 6 0.11
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:78289 original size:24 final size:24
Alignment explanation
Indices: 78157--78277 Score: 131
Period size: 24 Copynumber: 5.0 Consensus size: 24
78147 AAATATTTTA
*
78157 TCTGATTTTTGA-CTTGAATTCTGT
1 TCTGATATTTGATC-TGAATTCTGT
* *
78181 TCTGATACATT-ACCTGAATTCTGT
1 TCTGATA-TTTGATCTGAATTCTGT
* *
78205 TCTGAT-TTCTGATATGGATTCTGT
1 TCTGATATT-TGATCTGAATTCTGT
*
78229 TATGATATTTGATCTGAATTCTGT
1 TCTGATATTTGATCTGAATTCTGT
*
78253 TCTGATATTTGATCTAAATTCTGT
1 TCTGATATTTGATCTGAATTCTGT
78277 T
1 T
78278 TTAATTTCTG
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 74 0.91
25 5 0.06
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (24 bp):
TCTGATATTTGATCTGAATTCTGT
Found at i:80311 original size:18 final size:18
Alignment explanation
Indices: 80290--80459 Score: 259
Period size: 18 Copynumber: 9.4 Consensus size: 18
80280 TTTATCCCAT
80290 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
80308 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
* *
80326 AGGACCATTATGTCTCGA
1 AGGACCACTATGTCCCGA
**
80344 AGGAAAACTATGTCCCGA
1 AGGACCACTATGTCCCGA
80362 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
80380 AGGACCACTATTTCCCGA
1 AGGACCACTATGTCCCGA
*
80398 AGGACCATTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
80416 AAGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
80434 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
80452 AGGACCAC
1 AGGACCAC
80460 GTAGACCCTC
Statistics
Matches: 135, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 135 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:81398 original size:19 final size:19
Alignment explanation
Indices: 81374--81425 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
81364 TTTTAAGGGG
81374 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
81393 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
81412 ATGCATCGATGCAC
1 ATGCATCGATGCAC
81426 CAATTGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:81416 original size:83 final size:82
Alignment explanation
Indices: 81311--81469 Score: 187
Period size: 83 Copynumber: 1.9 Consensus size: 82
81301 CTTTAACATG
* * * *
81311 TGCATCGATGCACTACCCATGCATTGATACACAAATCACCTTCGATGTTTTCAT-TTTAAGGGGA
1 TGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATG-TTTCATCTTTAAAGAG-
81375 TGCATCGATGCACTCCTTA
64 TGCATCGATGCACTCCTTA
* * * ** *
81394 TGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGAGT
1 TGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCGATGTTTCATCTTTAAAGAGT
81458 GCATCGATGCAC
65 GCATCGATGCAC
81470 ATTGATGCAC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
82 20 0.31
83 44 0.69
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (82 bp):
TGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCATCTTTAAAGAGTG
CATCGATGCACTCCTTA
Found at i:82392 original size:2 final size:2
Alignment explanation
Indices: 82385--82429 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
82375 GACAGCCAGC
82385 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82427 TA T
1 TA T
82430 TGCAAGGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:85555 original size:18 final size:18
Alignment explanation
Indices: 85529--85563 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
85519 TACTCCTAAA
* *
85529 CTTGTGTATCGATACTAT
1 CTTGAGTATCAATACTAT
85547 CTTGAGTATCAATACTA
1 CTTGAGTATCAATACTA
85564 AAATTTTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (18 bp):
CTTGAGTATCAATACTAT
Done.