Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015122.1 Kokia drynarioides strain JFW-HI SEQ_130166, 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: 135206
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 360 characters in sequence are not A, C, G, or T
Found at i:4897 original size:477 final size:477
Alignment explanation
Indices: 4003--4956 Score: 1809
Period size: 477 Copynumber: 2.0 Consensus size: 477
3993 TATAACAAAA
4003 TTTTCTTTCAAATACTGTGTAATTGAATCGTTTTACTCAAAATATCACAAAATAATCAAGTATAA
1 TTTTCTTTCAAATACTGTGTAATTGAATCGTTTTACTCAAAATATCACAAAATAATCAAGTATAA
4068 TCAAAATCGAGACTTAAAACCAGTTTGAAAATAATGAAAATGAAATTTTTACTCAAAACAGGGCA
66 TCAAAATCGAGACTTAAAACCAGTTTGAAAATAATGAAAATGAAATTTTTACTCAAAACAGGGCA
*
4133 AATATCGATACCACCATAAAAATATTGATACATCTGTTCTAAAATCGAGAAATATAGCTAGAAAC
131 AATATCGATACCACCATAAAAATATTGATACATCTGTTCTAAAATCAAGAAATATAGCTAGAAAC
* *
4198 TTCAAACTAACCCCCTGAAATTATATAAAAACTTTATCAATAAATCAATTCAGTCTAAAACATAA
196 TTCAAACTAACCCCCTGAAATTATATAAAAACTTTACCAATAAATCAATTCAGTCTAAAACACAA
*
4263 TTCCATTCAAAATTCATCATCTTATTTCATAAGTTCATAGTATTCCAAAATAACATTTATAACCC
261 TTCCATTCAAAATTCATCATCTCATTTCATAAGTTCATAGTATTCCAAAATAACATTTATAACCC
*
4328 ATTCATTGAGGATATATAAGTACCATTTGTACATGTCATTTCACACAAAATAAATACACATTGTC
326 ATTCATTGAGGATATATAAGTACCATTTGTACATGCCATTTCACACAAAATAAATACACATTGTC
4393 TTGCAATCTTCCAATGTTGATGTGATTTGATGAGAGACACCTAATCTAACCTTAACTTCTCGGAG
391 TTGCAATCTTCCAATGTTGATGTGATTTGATGAGAGACACCTAATCTAACCTTAACTTCTCGGAG
4458 GTTTTATACCTACGCGTTAAGC
456 GTTTTATACCTACGCGTTAAGC
4480 TTTTCTTTCAAATACTGTGTAATTGAATCGTTTTACTCAAAATATCACAAAATAATCAAGTATAA
1 TTTTCTTTCAAATACTGTGTAATTGAATCGTTTTACTCAAAATATCACAAAATAATCAAGTATAA
4545 TCAAAATCGAGACTTAAAACCAGTTTGAAAATAATGAAAATGAAATTTTTACTCAAAACAGGGCA
66 TCAAAATCGAGACTTAAAACCAGTTTGAAAATAATGAAAATGAAATTTTTACTCAAAACAGGGCA
* *
4610 AATATCGATCCCACCATAAAAATATTGATACATCTGTTCTAAAATCAAGAAATATAGTTAGAAAC
131 AATATCGATACCACCATAAAAATATTGATACATCTGTTCTAAAATCAAGAAATATAGCTAGAAAC
* *
4675 TTCAAACTAACCTCTTGAAATTATATAAAAACTTTACCAATAAATCAATTCAGTCTAAAACACAA
196 TTCAAACTAACCCCCTGAAATTATATAAAAACTTTACCAATAAATCAATTCAGTCTAAAACACAA
4740 TTCCATTCAAAATTCATCATCTCATTTCATAAGTTCATAGTATTCCAAAATAACATTTATAACCC
261 TTCCATTCAAAATTCATCATCTCATTTCATAAGTTCATAGTATTCCAAAATAACATTTATAACCC
4805 ATTCATTGAGGATATATAAGTACCATTTGTACATGCCATTTCACACAAAATAAATACACATTGTC
326 ATTCATTGAGGATATATAAGTACCATTTGTACATGCCATTTCACACAAAATAAATACACATTGTC
*
4870 TTGCAATCTTCCAATGTTGATGTGATTTGATGAGAGACACCTAATCTAACCTTAGCTTCTCGGAG
391 TTGCAATCTTCCAATGTTGATGTGATTTGATGAGAGACACCTAATCTAACCTTAACTTCTCGGAG
*
4935 GTTTTGTACCTACGCGTTAAGC
456 GTTTTATACCTACGCGTTAAGC
4957 CAGTGAAGGC
Statistics
Matches: 466, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
477 466 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (477 bp):
TTTTCTTTCAAATACTGTGTAATTGAATCGTTTTACTCAAAATATCACAAAATAATCAAGTATAA
TCAAAATCGAGACTTAAAACCAGTTTGAAAATAATGAAAATGAAATTTTTACTCAAAACAGGGCA
AATATCGATACCACCATAAAAATATTGATACATCTGTTCTAAAATCAAGAAATATAGCTAGAAAC
TTCAAACTAACCCCCTGAAATTATATAAAAACTTTACCAATAAATCAATTCAGTCTAAAACACAA
TTCCATTCAAAATTCATCATCTCATTTCATAAGTTCATAGTATTCCAAAATAACATTTATAACCC
ATTCATTGAGGATATATAAGTACCATTTGTACATGCCATTTCACACAAAATAAATACACATTGTC
TTGCAATCTTCCAATGTTGATGTGATTTGATGAGAGACACCTAATCTAACCTTAACTTCTCGGAG
GTTTTATACCTACGCGTTAAGC
Found at i:24749 original size:15 final size:16
Alignment explanation
Indices: 24726--24762 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
24716 GTTAAATCCC
24726 AAAAA-ATAT-AATTT
1 AAAAATATATAAATTT
24740 AAAAATATATAAATTT
1 AAAAATATATAAATTT
*
24756 AAGAATA
1 AAAAATA
24763 CATTTAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 5 0.25
15 4 0.20
16 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAAATATATAAATTT
Found at i:24883 original size:27 final size:27
Alignment explanation
Indices: 24845--24902 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
24835 CATATCATTA
* *
24845 GACACGCTCTGTCTTCGTCTGTCTTTT
1 GACACGCTCTGTCTTCCTCTGTCCTTT
24872 GACACGCTCTGTCTTCCTCTGTCCTTT
1 GACACGCTCTGTCTTCCTCTGTCCTTT
24899 GACA
1 GACA
24903 TGTTTTGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.10, C:0.33, G:0.17, T:0.40
Consensus pattern (27 bp):
GACACGCTCTGTCTTCCTCTGTCCTTT
Found at i:37533 original size:25 final size:23
Alignment explanation
Indices: 37490--37535 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
37480 CCAGTTAGGG
37490 AATTATTGTTTAGATTTAATTAA
1 AATTATTGTTTAGATTTAATTAA
*
37513 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
37536 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTAA
Found at i:38624 original size:18 final size:19
Alignment explanation
Indices: 38603--38645 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
38593 TTTAGCCATT
38603 TTTTATTATTT-ATTTTTA
1 TTTTATTATTTCATTTTTA
38621 TTTTATTATTTGCATTTTTA
1 TTTTATTATTT-CATTTTTA
*
38641 ATTTA
1 TTTTA
38646 ATTTGTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
20 11 0.50
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTATTATTTCATTTTTA
Found at i:41525 original size:6 final size:6
Alignment explanation
Indices: 41502--41561 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
41492 ATTTAGTATA
* *
41502 TTTATT TTCATA TTTATT TTTATT TTTATT TTTA-T TTTA-T TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
41548 TTTAGT TTTATT TT
1 TTTATT TTTATT TT
41562 AATTATGCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 10 0.21
6 37 0.79
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:41537 original size:22 final size:22
Alignment explanation
Indices: 41503--41562 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 22
41493 TTTAGTATAT
*
41503 TTATTTTCATATTTATTTTTATTT
1 TTATTTTTAT-TTTA-TTTTATTT
41527 TTATTTTTATTTTATTTTATTT
1 TTATTTTTATTTTATTTTATTT
*
41549 TTAGTTTTATTTTA
1 TTATTTTTATTTTA
41563 ATTATGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 21 0.62
23 4 0.12
24 9 0.26
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (22 bp):
TTATTTTTATTTTATTTTATTT
Found at i:42505 original size:14 final size:14
Alignment explanation
Indices: 42482--42520 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
42472 TTATTGTTTA
42482 GAAAAAAAAAAGTC
1 GAAAAAAAAAAGTC
* *
42496 GAAAAGAAAAA-TT
1 GAAAAAAAAAAGTC
42509 GAAAAAAAAAAG
1 GAAAAAAAAAAG
42521 AAAATTGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.08
Consensus pattern (14 bp):
GAAAAAAAAAAGTC
Found at i:42518 original size:18 final size:18
Alignment explanation
Indices: 42497--42554 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 18
42487 AAAAAAGTCG
42497 AAAAGAAAAATTGAAAAA
1 AAAAGAAAAATTGAAAAA
42515 AAAA-AGAAAATTGAGAAAAA
1 AAAAGA-AAAATT--GAAAAA
42535 AAAAGAAAAA--GAAAAA
1 AAAAGAAAAATTGAAAAA
42551 AAAA
1 AAAA
42555 ACAAAAGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
16 10 0.28
17 1 0.03
18 10 0.28
20 14 0.39
21 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAATTGAAAAA
Found at i:42519 original size:19 final size:19
Alignment explanation
Indices: 42497--42560 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
42487 AAAAAAGTCG
42497 AAAAGAAAAATTGAAAAAA
1 AAAAGAAAAATTGAAAAAA
42516 AAAAG-AAAATTGAGAAAAA
1 AAAAGAAAAATTGA-AAAAA
42535 AAAAGAAAAA--GAAAAAA
1 AAAAGAAAAATTGAAAAAA
*
42552 AAAACAAAA
1 AAAAGAAAA
42561 GTGTGTTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
17 13 0.31
18 10 0.24
19 15 0.36
20 4 0.10
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (19 bp):
AAAAGAAAAATTGAAAAAA
Found at i:43612 original size:25 final size:23
Alignment explanation
Indices: 43571--43616 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
43561 CCAATTAGGT
43571 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
43594 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
43617 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:46781 original size:22 final size:22
Alignment explanation
Indices: 46756--46798 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
46746 AATCTTAAAC
46756 TTGAACCCTAAACTTCAAATCT
1 TTGAACCCTAAACTTCAAATCT
* * *
46778 TTGAATCTTAAACTTTAAATC
1 TTGAACCCTAAACTTCAAATC
46799 CCAAACACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (22 bp):
TTGAACCCTAAACTTCAAATCT
Found at i:46816 original size:21 final size:21
Alignment explanation
Indices: 46786--46825 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46776 CTTTGAATCT
*
46786 TAAACTTTAAATCCCAAACAC
1 TAAACATTAAATCCCAAACAC
*
46807 TAAACATTAAATCTCAAAC
1 TAAACATTAAATCCCAAAC
46826 TGAAACTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACATTAAATCCCAAACAC
Found at i:46858 original size:14 final size:14
Alignment explanation
Indices: 46839--46872 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
46829 AACTCTAAAC
**
46839 TTCAAGGTTTGGGG
1 TTCAAGGTTTAAGG
46853 TTCAAGGTTTAAGG
1 TTCAAGGTTTAAGG
46867 TTCAAG
1 TTCAAG
46873 ATTCGATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (14 bp):
TTCAAGGTTTAAGG
Found at i:48295 original size:21 final size:20
Alignment explanation
Indices: 48271--48309 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
48261 ACACCATTCC
48271 AAACAACAAAACAAAAAATAA
1 AAACAACAAAA-AAAAAATAA
*
48292 AAACAACACAAAAAAAAT
1 AAACAACAAAAAAAAAAT
48310 CAAATAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.05
Consensus pattern (20 bp):
AAACAACAAAAAAAAAATAA
Found at i:52020 original size:59 final size:57
Alignment explanation
Indices: 51952--52284 Score: 253
Period size: 59 Copynumber: 5.7 Consensus size: 57
51942 TGGATACTCG
* * * * * *
51952 GGGGCAAAATGGTAATTTTTGCAAGTTTCGGGATCAAAAATGGAATTTTTGGAGGTTT
1 GGGGTAAAAT-GTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTAGAAGGTTT
* * *
52010 GGAGGTAAAATGTAATTTTTGGAAATTTTGGGGTTAAAAATGGAATTTTCA-AAAGTTT
1 GG-GGTAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTT-AGAAGGTTT
* * * *
52068 AGTGGTAAAAATGTAATTTTTGGAAGTTTGTGGGGTAAAAAATGTAATTTTAGAAGTTTT
1 -GGGGT-AAAATGTAATTTTTGGAAGTTT-TGGGGTCAAAAATGGAATTTTAGAAGGTTT
* * * *
52128 AGGGGTAAAATTGTGATTTTTGGAAGTTTTGAGGTTC-AAAATGGAATTTTCA-AAAGTTC
1 -GGGGTAAAA-TGTAATTTTTGGAAGTTTTG-GGGTCAAAAATGGAATTTT-AGAAGGTTT
* * * * *
52187 GAGGGTAAAAATATAATTTTTGGAAG-TTTAGGGT-AAAAATGTAATTTTCATAAGTTTT
1 G-GGGT-AAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTT-AGAAGGTTT
* * * * *
52245 AGAGTCAAAATGGAATTTTGGAGAAGTTTGGGGGTCAAAA
1 GGGGT-AAAATGTAATTTTTG-GAAGTTTTGGGGTCAAAA
52285 TATAATTTTT
Statistics
Matches: 220, Mismatches: 39, Indels: 30
0.76 0.13 0.10
Matches are distributed among these distances:
57 32 0.15
58 55 0.25
59 75 0.34
60 58 0.26
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (57 bp):
GGGGTAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTAGAAGGTTT
Found at i:52057 original size:30 final size:30
Alignment explanation
Indices: 51957--52303 Score: 191
Period size: 30 Copynumber: 11.7 Consensus size: 30
51947 ACTCGGGGGC
* * * *
51957 AAAATGGTAATTTTTGCAAGTTTCGGGATCA
1 AAAATGG-AATTTTTGGAAGTTTTGGGGTTA
*
51988 AAAATGGAATTTTTGG-AGGTTTGGAGG-T-
1 AAAATGGAATTTTTGGAAGTTTTGG-GGTTA
* *
52016 AAAATGTAATTTTTGGAAATTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
*** * *
52046 AAAATGGAATTTTCAAAAGTTTAGTGG-TA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
* *
52075 AAAATGTAATTTTTGGAAGTTTGTGGGGTAA
1 AAAATGGAATTTTTGGAAGTTT-TGGGGTTA
* *
52106 AAAATGTAA-TTTTAGAAGTTTTAGGGG-TA
1 AAAATGGAATTTTTGGAAGTTTT-GGGGTTA
* * *
52135 AAATTGTG-ATTTTTGGAAGTTTTGAGGTTC
1 AAAATG-GAATTTTTGGAAGTTTTGGGGTTA
*** *
52165 AAAATGGAATTTTCAAAAG-TTCGAGGG-TA
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTTA
** *
52194 AAAATATAATTTTTGGAAG-TTTAGGG-TA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
* *** * * *
52222 AAAATGTAATTTTCATAAGTTTTAGAG-TC
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
* * *
52251 AAAATGGAATTTTGGAGAAGTTTGGGGGTCA
1 AAAATGGAATTTTTG-GAAGTTTTGGGGTTA
52282 AAATAT--AATTTTTGGATAGTTT
1 AAA-ATGGAATTTTTGGA-AGTTT
52304 AGGGACCTCT
Statistics
Matches: 240, Mismatches: 59, Indels: 35
0.72 0.18 0.10
Matches are distributed among these distances:
28 37 0.15
29 86 0.36
30 95 0.40
31 20 0.08
32 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTTA
Found at i:54143 original size:17 final size:17
Alignment explanation
Indices: 54067--54144 Score: 59
Period size: 18 Copynumber: 4.4 Consensus size: 17
54057 AATTGGACTT
* *
54067 TTTAAA-TTCAATTTAA
1 TTTAAACTTAAATTAAA
**
54083 TTTCAAACTTATTTTAAA
1 TTT-AAACTTAAATTAAA
**
54101 TTTAAACTTTAAAAGAAAA
1 TTTAAAC-TT-AAATTAAA
54120 GTTTAAACTTAAATTAAA
1 -TTTAAACTTAAATTAAA
54138 TTTAAAC
1 TTTAAAC
54145 CCAAAATGAA
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
16 3 0.06
17 14 0.30
18 17 0.36
19 6 0.13
20 7 0.15
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (17 bp):
TTTAAACTTAAATTAAA
Found at i:55258 original size:97 final size:98
Alignment explanation
Indices: 55089--55266 Score: 261
Period size: 97 Copynumber: 1.8 Consensus size: 98
55079 TGTATTCTGA
* * * *
55089 TATAATAAATTAAAAGTTGAAAAAGAAATAGATTACAATAGTTATACTAAAAAAAGTTGTTATAA
1 TATAATAAA-TAAAAGCTGAAAAAGAAATAGATTACAATAGTTACAATAAAAAAAGTTGTGATAA
55154 TTATAATATAATTTAGGGAATAGGTTATTATAAT
65 TTATAATATAATTTAGGGAATAGGTTATTATAAT
***
55188 TATAATAAA-AAAAGCTGAAAAAAGAAATAGATTAGGGTAGTTACAATAAAAAAA-TTGTGATAA
1 TATAATAAATAAAAGCTG-AAAAAGAAATAGATTACAATAGTTACAATAAAAAAAGTTGTGATAA
55251 TTATAATATAATTTAG
65 TTATAATATAATTTAG
55267 ATTTATTAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
97 31 0.44
98 31 0.44
99 9 0.13
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (98 bp):
TATAATAAATAAAAGCTGAAAAAGAAATAGATTACAATAGTTACAATAAAAAAAGTTGTGATAAT
TATAATATAATTTAGGGAATAGGTTATTATAAT
Found at i:55691 original size:16 final size:19
Alignment explanation
Indices: 55670--55706 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
55660 AATTATAATT
55670 TAAAAT-TT-TTTAT-TTA
1 TAAAATATTATTTATATTA
55686 TAAAATATTATTTATATTA
1 TAAAATATTATTTATATTA
55705 TA
1 TA
55707 TGCTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 5 0.28
19 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAAAATATTATTTATATTA
Found at i:65297 original size:21 final size:21
Alignment explanation
Indices: 65259--65312 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
65249 TCGAAATATC
65259 ATTATTTCTTTTGATAAAAAAT
1 ATTATTT-TTTTGATAAAAAAT
65281 ATTATTATTTTTG-TAAAAAAT
1 ATTATT-TTTTTGATAAAAAAT
*
65302 AATATTTTTTT
1 ATTATTTTTTT
65313 ATTACATTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 5 0.17
21 13 0.43
22 11 0.37
23 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTATTTTTTTGATAAAAAAT
Found at i:66122 original size:20 final size:20
Alignment explanation
Indices: 66077--66123 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
66067 ATTTTTTAAC
*
66077 TAAAAATACTCAAATTTTCT
1 TAAAAATACTCAAATTTTCA
*
66097 TTAAAATA-TCAAAATTTTCA
1 TAAAAATACTC-AAATTTTCA
66117 TAAAAAT
1 TAAAAAT
66124 GCAACAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATACTCAAATTTTCA
Found at i:66420 original size:8 final size:8
Alignment explanation
Indices: 66331--66420 Score: 51
Period size: 9 Copynumber: 10.5 Consensus size: 8
66321 AGATTATGAT
66331 TTTTTTAA
1 TTTTTTAA
*
66339 TTTTTACAA
1 TTTTT-TAA
66348 TTTTTTAA
1 TTTTTTAA
*
66356 -GTTTTAA
1 TTTTTTAA
66363 TATTTTTAGA
1 T-TTTTTA-A
*
66373 TTCTTTTTGGA
1 -T-TTTTT-AA
66384 TTTTTTAA
1 TTTTTTAA
66392 TATTTTTAGA
1 T-TTTTTA-A
66402 TTTTTCT--
1 TTTTT-TAA
66409 TTTTTTAA
1 TTTTTTAA
66417 TTTT
1 TTTT
66421 AAGTAATTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 22
0.69 0.08 0.24
Matches are distributed among these distances:
6 1 0.02
7 11 0.17
8 13 0.20
9 27 0.42
10 5 0.08
11 7 0.11
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (8 bp):
TTTTTTAA
Found at i:67696 original size:2 final size:2
Alignment explanation
Indices: 67689--67716 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
67679 ATTTCAACTC
67689 AT 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 AT
67717 TTGGTGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70067 original size:12 final size:12
Alignment explanation
Indices: 70050--70078 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
70040 TCTCTTCTTC
70050 TTTTTTCTTTTT
1 TTTTTTCTTTTT
70062 TTTTTTCTTTTT
1 TTTTTTCTTTTT
70074 TTTTT
1 TTTTT
70079 AAATTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:70953 original size:31 final size:30
Alignment explanation
Indices: 70918--70975 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
70908 AATAAAAATG
*
70918 TATAAA-ATTATTAAATATTAAAATAATACAA
1 TATAAATATT-TTAAATA-AAAAATAATACAA
*
70949 TATAAATATTTTTAATAAAAAATAATA
1 TATAAATATTTTAAATAAAAAATAATA
70976 TGAGCGGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.38
31 12 0.50
32 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
TATAAATATTTTAAATAAAAAATAATACAA
Found at i:72794 original size:28 final size:27
Alignment explanation
Indices: 72736--72794 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
72726 TTTACTTCTC
* **
72736 TCAAATTGATATTAATTGTTTTTTTTT
1 TCAAATTAATATTAATTGTTTTTTCCT
72763 TCAAATTAATATTTGAATT-TTTTTTCCT
1 TCAAATTAATA-TT-AATTGTTTTTTCCT
72791 TCAA
1 TCAA
72795 CTAAATCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 10 0.37
28 13 0.48
29 4 0.15
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.58
Consensus pattern (27 bp):
TCAAATTAATATTAATTGTTTTTTCCT
Found at i:72870 original size:24 final size:24
Alignment explanation
Indices: 72824--72870 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
72814 TAACATCATT
*
72824 AAATTCATGACACGTGGCAAAATA
1 AAATTCATGACACGTGACAAAATA
72848 AAATT-ATGACACGTGACATAAAT
1 AAATTCATGACACGTGACA-AAAT
72871 GACATCACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (24 bp):
AAATTCATGACACGTGACAAAATA
Found at i:75895 original size:46 final size:46
Alignment explanation
Indices: 75842--75933 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
75832 TCATATTATA
75842 TAAAACTCTAATTTACCCATATTTTATATTTTTCTTATGCTTAGCC
1 TAAAACTCTAATTTACCCATATTTTATATTTTTCTTATGCTTAGCC
75888 TAAAACTCTAATTTACCCATATTTTATATTTTTCTTATGCTTAGCC
1 TAAAACTCTAATTTACCCATATTTTATATTTTTCTTATGCTTAGCC
75934 CCCTTGTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.20, G:0.04, T:0.48
Consensus pattern (46 bp):
TAAAACTCTAATTTACCCATATTTTATATTTTTCTTATGCTTAGCC
Found at i:86262 original size:17 final size:17
Alignment explanation
Indices: 86240--86291 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
86230 AAAATAAATA
86240 TTATTTATTAAATTAAT
1 TTATTTATTAAATTAAT
*
86257 TTATTTAATAAATT-AT
1 TTATTTATTAAATTAAT
86273 TT-TTTCAATTAAA-TAAT
1 TTATTT--ATTAAATTAAT
86290 TT
1 TT
86292 TCTCAACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 3 0.10
16 5 0.17
17 22 0.73
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATTTATTAAATTAAT
Found at i:86292 original size:17 final size:17
Alignment explanation
Indices: 86246--86297 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
86236 AATATTATTT
86246 ATTAAATTAATTTATTT-A
1 ATTAAA-TAATTT-TTTCA
*
86264 A-TAAATTATTTTTTCA
1 ATTAAATAATTTTTTCA
*
86280 ATTAAATAATTTTCTCA
1 ATTAAATAATTTTTTCA
86297 A
1 A
86298 CCCAATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.10
16 7 0.24
17 18 0.62
18 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTAAATAATTTTTTCA
Found at i:97900 original size:17 final size:17
Alignment explanation
Indices: 97874--97907 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
97864 ATATCCTTCC
97874 TAATAATAAAAAGAAAA
1 TAATAATAAAAAGAAAA
* *
97891 TAATAGTAAAAATAAAA
1 TAATAATAAAAAGAAAA
97908 CAAAATAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
TAATAATAAAAAGAAAA
Found at i:98055 original size:17 final size:18
Alignment explanation
Indices: 98025--98111 Score: 68
Period size: 17 Copynumber: 5.3 Consensus size: 18
98015 AAATCTATTT
*
98025 TTTAAAATTTATTTTAAGA
1 TTTAAAA-TTATTTTAAAA
98044 -TTAAAATTA-TTTAAAA
1 TTTAAAATTATTTTAAAA
*
98060 TTTAAAATTGTTTT-AAA
1 TTTAAAATTATTTTAAAA
98077 TTT---A-T-TTTT-AAA
1 TTTAAAATTATTTTAAAA
*
98089 TTTAAAATTATTCT-AAA
1 TTTAAAATTATTTTAAAA
98106 TTTAAA
1 TTTAAA
98112 TAAATAAAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
12 10 0.17
13 1 0.02
14 1 0.02
15 1 0.02
16 7 0.12
17 29 0.50
18 9 0.16
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTAAAATTATTTTAAAA
Found at i:98086 original size:46 final size:46
Alignment explanation
Indices: 98024--98111 Score: 128
Period size: 46 Copynumber: 1.9 Consensus size: 46
98014 TAAATCTATT
98024 TTTTAAAATTTATTTTAAGA-TTAAAATTATT-TAAAATTTAAAATTG
1 TTTTAAAATTTATTTTAA-ATTTAAAATTATTCT-AAATTTAAAATTG
98070 TTTT-AAATTTATTTTTAAATTTAAAATTATTCTAAATTTAAA
1 TTTTAAAATTTA-TTTTAAATTTAAAATTATTCTAAATTTAAA
98112 TAAATAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
45 8 0.21
46 30 0.77
47 1 0.03
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (46 bp):
TTTTAAAATTTATTTTAAATTTAAAATTATTCTAAATTTAAAATTG
Found at i:98096 original size:29 final size:28
Alignment explanation
Indices: 98044--98109 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
98034 TATTTTAAGA
* *
98044 TTAAAATTATTTAAAATTTAAAATTGTT
1 TTAAATTTATTTAAAATTTAAAATTATT
*
98072 TTAAATTTATTTTTAAATTTAAAATTATT
1 TTAAATTTA-TTTAAAATTTAAAATTATT
*
98101 CTAAATTTA
1 TTAAATTTA
98110 AATAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 8 0.24
29 25 0.76
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TTAAATTTATTTAAAATTTAAAATTATT
Found at i:99477 original size:29 final size:29
Alignment explanation
Indices: 99382--99676 Score: 180
Period size: 30 Copynumber: 10.1 Consensus size: 29
99372 CCTAAAAGAT
99382 CCTAAACTGTT-CAAAAATTACATTTTAACC
1 CCTAAACT-TTCCAAAAATTACATTTT-ACC
* * *
99412 TCTAAAC-TTCATAAAAATTATATTTTTA-C
1 CCTAAACTTTC-CAAAAATTACA-TTTTACC
* *
99441 CCTCGAACTTTCCAAAAATTACATTTTGCC
1 CCT-AAACTTTCCAAAAATTACATTTTACC
* ** *
99471 CCTGAACTTTTTAAAAATTACATTTTTATC
1 CCTAAACTTTCCAAAAATTACA-TTTTACC
* * *
99501 CTTAAACTTT-CTAAAATTACCATTTTGCC
1 CCTAAACTTTCCAAAAATTA-CATTTTACC
* * * *
99530 CTTAAACTTTCCAAAAATCAAAATTTTACT
1 CCTAAACTTTCCAAAAAT-TACATTTTACC
*
99560 CTTAAAC-TTCCAAAAATTACCA-TTT--C
1 CCTAAACTTTCCAAAAATTA-CATTTTACC
* *
99586 TCTCGAACTTT-CAAAAATTACATTTTTACC
1 CCT-AAACTTTCCAAAAATTACA-TTTTACC
** *
99616 TTTAAAC-TTCCAAAAATTCCATTTTTAACC
1 CCTAAACTTTCCAAAAATTACA-TTTT-ACC
*
99646 CC-AAACTTTTCAAAAATTACTATTTTACC
1 CCTAAACTTTCCAAAAATTAC-ATTTTACC
99675 CC
1 CC
99677 CCGAGTATCC
Statistics
Matches: 208, Mismatches: 36, Indels: 43
0.72 0.13 0.15
Matches are distributed among these distances:
26 3 0.01
27 12 0.06
28 13 0.06
29 84 0.40
30 87 0.42
31 9 0.04
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (29 bp):
CCTAAACTTTCCAAAAATTACATTTTACC
Found at i:99496 original size:59 final size:58
Alignment explanation
Indices: 99384--99675 Score: 238
Period size: 59 Copynumber: 5.0 Consensus size: 58
99374 TAAAAGATCC
* * * *
99384 TAAACTGTTCAAAAATTACATTTTAACCTCTAAACTTCAT-AAAAATTATATTTTTACCCT
1 TAAACT-TCCAAAAATTACATTTT-ACCCCTAAACTT-TTCAAAAATTACATTTTTACCCT
** * * * *
99444 CGAACTTTCCAAAAATTACATTTTGCCCCTGAACTTTTTAAAAATTACATTTTTATCCT
1 TAAAC-TTCCAAAAATTACATTTTACCCCTAAACTTTTCAAAAATTACATTTTTACCCT
* * * * * * * * *
99503 TAAACTTTCTAAAATTACCATTTTGCCCTTAAACTTTCCAAAAATCAAAATTTTACTCT
1 TAAACTTCCAAAAATTA-CATTTTACCCCTAAACTTTTCAAAAATTACATTTTTACCCT
* * *
99562 TAAACTTCCAAAAATTACCA-TTT--CTCTCGAAC-TTTCAAAAATTACATTTTTACCTT
1 TAAACTTCCAAAAATTA-CATTTTACCCCT-AAACTTTTCAAAAATTACATTTTTACCCT
*
99618 TAAACTTCCAAAAATTCCATTTTTAACCCC-AAACTTTTCAAAAATTAC-TATTTTACCC
1 TAAACTTCCAAAAATTACA-TTTT-ACCCCTAAACTTTTCAAAAATTACAT-TTTTACCC
99676 CCCGAGTATC
Statistics
Matches: 184, Mismatches: 37, Indels: 23
0.75 0.15 0.09
Matches are distributed among these distances:
55 2 0.01
56 36 0.20
57 6 0.03
58 18 0.10
59 100 0.54
60 21 0.11
61 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (58 bp):
TAAACTTCCAAAAATTACATTTTACCCCTAAACTTTTCAAAAATTACATTTTTACCCT
Found at i:111715 original size:209 final size:209
Alignment explanation
Indices: 110955--111967 Score: 1102
Period size: 205 Copynumber: 4.9 Consensus size: 209
110945 AAATAACGAG
* * * * * *
110955 GCGGTCATCTTCCTGATAAGATACAGAAAAGTATACCAACTCAATAAAACCAAGATCAATGTGAG
1 GCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACCAAGCTCAAAGTGAG
* * * * * * *
111020 CGAATCTTAGAACCCCAGCTTTCTGATGAGATACTGAGAAGTAGGCCGAAACAATAAAATGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTA
* * * * ** *
111085 GCTTTTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGAAGAGATATGGAGAAGCGAA
131 CCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
*
111150 TTAAAACAAGTGA-
196 TCAAAACAAGTGAT
* * * *
111163 GACGGTCATCTTCCTGATGAGATAC----AAGTATACCAACTCAATGAAACAAAGCTCAATGTGT
1 G-CGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACCAAGCTCAAAGTGA
* * * *
111224 GCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCGATAAAATGGTT
65 GCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTT
* * *
111289 AACTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGG
130 ACCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGG
** * *
111354 ATTGAAACAAATGAG
195 ATCAAAACAAGTGAT
* * * *
111369 GCGATCATCTTCCTGATGAGATACAAAGAAGTATATC-AA-C--T----CAAAGCTCAAAGTGAG
1 GCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACCAAGCTCAAAGTGAG
* * * *
111426 CGAATCTTCGAACCCTAGCTTCCTGATGATATACTGAAAAGCAAGTCGAAGCAATAAAATGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTA
* * * * *
111491 GCTTCCTGATGAGATACTGAGATGTGAACCAAATTCGTCTTCCTGATGAGACACAGAGAAGTGGA
131 CCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
111556 TCAAAACAAGTGAT
196 TCAAAACAAGTGAT
* * * * *
111570 GCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAACTAGGCTCAAAGTGAG
1 GCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACCAAGCTCAAAGTGAG
* * * * **
111635 CAAAACTTCGAACCTCAGCTTCCTGATGAGATACAGAGAAGCAAGTCGAAGTAATAAAGCGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTA
** * * * * * *
111700 CCTTCTTGATGAGATACAAAGAAGTGAACTAGATCCGTCTTCCTGATGAGATACAAAAAAGTGGA
131 CCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
*
111765 CCAAAACAACGT--T
196 TCAAAACAA-GTGAT
* * ** *
111778 GCGGTCATCTTCCTGATAAGATACTGAGAAGTGGACCAAATCAATGAAACCAGGCTCAAAGTGAG
1 GCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACCAAGCTCAAAGTGAG
* * * * * ***
111843 CAAATCTTTGAACCTCAGCTTCTTGATGAGATAATGAGAAGCAAGTTGAAGCAATAAAGCAGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTA
* * * * * * *
111908 CCTTCCTGATGAGATACAGAGAAGTGAATCAGATCCGTCTTCCTGATAAGATACAAAGAA
131 CCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAA
111968 ATTGACCAAA
Statistics
Matches: 697, Mismatches: 93, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
201 170 0.24
202 2 0.00
203 1 0.00
205 184 0.26
206 1 0.00
207 1 0.00
208 175 0.25
209 161 0.23
210 2 0.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (209 bp):
GCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACCAAGCTCAAAGTGAG
CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTA
CCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
TCAAAACAAGTGAT
Found at i:111977 original size:208 final size:207
Alignment explanation
Indices: 110955--111978 Score: 876
Period size: 208 Copynumber: 5.0 Consensus size: 207
110945 AAATAACGAG
* * * * * * * * *
110955 GCGGTCATCTTCCTGATAAGATACAGAAAAGTATACCAACTCAATAAAACCAAGATCAATGTGAG
1 GCGGTCATCTTCCTAATAAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAG
* * * * * * * * * **
111020 CGAATCTTAGAACCCCAGCTTTCTGATGAGATACTGAGAAGTAGGCCGAAACAATAAAATGGTTA
66 CAAATCTTCGAACCTCAGCTTCCTGATGAGATAATGAGAAGCAAGTCGAAGCAATAAAGCGGTTA
* ** * * * * * *** ** *
111085 GCTTTTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGAAGAGATATGGAGAAGCGAA
131 CCTTCCTGATGAGATACAGAGAAGT-GAACAGATCCGTCTTCCTGATGAGATACAAAGAAATGGA
**
111150 TTAAAACAAGTGA-
195 CCAAAACAAGT-AT
* * * * * * * *
111163 GACGGTCATCTTCCTGATGAGATAC----AAGTATACCAACTCAATGAAACAAAGCTCAATGTGT
1 G-CGGTCATCTTCCTAATAAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGA
* * * * * * **
111224 GCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCGATAAAATGGTT
65 GCAAATCTTCGAACCTCAGCTTCCTGATGAGATAATGAGAAGCAAGTCGAAGCAATAAAGCGGTT
* * * * * * * * **
111289 AACTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGG
130 ACCTTCCTGATGAGATACAGAGAAGT-GAACAGATCCGTCTTCCTGATGAGATACAAAGAAATGG
*** * *
111354 ATTGAAACAAATGAG
194 ACCAAAACAAGT-AT
* * * ** * * *
111369 GCGATCATCTTCCTGATGAGATACAAAGAAGTATATC-AA-C--T-CAA--A-GCTCAAAGTGAG
1 GCGGTCATCTTCCTAATAAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAG
* * * * **
111426 CGAATCTTCGAACC-CTAGCTTCCTGATGATATACTGAAAAGCAAGTCGAAGCAATAAAATGGTT
66 CAAATCTTCGAACCTC-AGCTTCCTGATGAGATAATGAGAAGCAAGTCGAAGCAATAAAGCGGTT
* * * * * * * *
111490 AGCTTCCTGATGAGATACTGAGATGTGAACCAAATTCGTCTTCCTGATGAGACACAGAGAAGTGG
130 ACCTTCCTGATGAGATACAGAGAAGTGAA-CAGATCCGTCTTCCTGATGAGATACAAAGAAATGG
*
111555 ATCAAAACAAGTGAT
194 ACCAAAACAAGT-AT
* *
111570 GCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAACTAGGCTCAAAGTGAG
1 GCGGTCATCTTCCTAATAAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAG
* *
111635 CAAAACTTCGAACCTCAGCTTCCTGATGAGATACA-GAGAAGCAAGTCGAAGTAATAAAGCGGTT
66 CAAATCTTCGAACCTCAGCTTCCTGATGAGATA-ATGAGAAGCAAGTCGAAGCAATAAAGCGGTT
* *
111699 ACCTTCTTGATGAGATACAAAGAAGTGAACTAGATCCGTCTTCCTGATGAGATACAAA-AAAGTG
130 ACCTTCCTGATGAGATACAGAGAAGTGAAC-AGATCCGTCTTCCTGATGAGATACAAAGAAA-TG
111763 GACCAAAACAACGT-T
193 GACCAAAACAA-GTAT
* *
111778 GCGGTCATCTTCCTGATAAGATACTGAGAAGTGGACCAAATCAATGAAACCAGGCTCAAAGTGAG
1 GCGGTCATCTTCCTAATAAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAG
* * * *
111843 CAAATCTTTGAACCTCAGCTTCTTGATGAGATAATGAGAAGCAAGTTGAAGCAATAAAGCAGTTA
66 CAAATCTTCGAACCTCAGCTTCCTGATGAGATAATGAGAAGCAAGTCGAAGCAATAAAGCGGTTA
* *
111908 CCTTCCTGATGAGATACAGAGAAGTGAATCAGATCCGTCTTCCTGATAAGATACAAAGAAATTGA
131 CCTTCCTGATGAGATACAGAGAAGTGAA-CAGATCCGTCTTCCTGATGAGATACAAAGAAATGGA
111973 CCAAAA
195 CCAAAA
111979 AAATGAAGTC
Statistics
Matches: 707, Mismatches: 85, Indels: 48
0.84 0.10 0.06
Matches are distributed among these distances:
200 3 0.00
201 162 0.23
202 3 0.00
203 1 0.00
204 2 0.00
205 184 0.26
206 3 0.00
207 2 0.00
208 186 0.26
209 158 0.22
210 3 0.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (207 bp):
GCGGTCATCTTCCTAATAAGATACTGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAG
CAAATCTTCGAACCTCAGCTTCCTGATGAGATAATGAGAAGCAAGTCGAAGCAATAAAGCGGTTA
CCTTCCTGATGAGATACAGAGAAGTGAACAGATCCGTCTTCCTGATGAGATACAAAGAAATGGAC
CAAAACAAGTAT
Found at i:112370 original size:17 final size:17
Alignment explanation
Indices: 112348--112483 Score: 110
Period size: 17 Copynumber: 8.2 Consensus size: 17
112338 CCCATTTTTA
112348 AAATTTATTTTAAGA-TT
1 AAATTTATTTTAA-ATTT
112365 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
112382 -AA---A-TTTAAATTT
1 AAATTTATTTTAAATTT
** *
112394 -GTTTTAAATTTAAATTT
1 AAATTT-ATTTTAAATTT
*
112411 AAATTTGTTTTAAATTT
1 AAATTTATTTTAAATTT
112428 AAATTT-TATTTAAGA-TT
1 AAATTTAT-TTTAA-ATTT
112445 AAATTTATTTTTAAATTT
1 AAATTTA-TTTTAAATTT
* *
112463 AAAATTATTCTAAATTT
1 AAATTTATTTTAAATTT
112480 AAAT
1 AAAT
112484 AAATAAAAGC
Statistics
Matches: 98, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
12 9 0.09
13 1 0.01
16 5 0.05
17 65 0.66
18 17 0.17
19 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:112382 original size:6 final size:6
Alignment explanation
Indices: 112363--112483 Score: 94
Period size: 6 Copynumber: 21.0 Consensus size: 6
112353 TATTTTAAGA
* **
112363 TTAAAT TT-ATT TTAAAT TTAAAT TTAAAT TT-GTT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
** * **
112409 TTAAAT TT-GTT TTAAAT TTAAAT TT-TAT TTAAGA- TTAAAT TTATTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT
*
112455 TTAAAT TTAAAA TT--AT TCTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT
112484 AAATAAAAGC
Statistics
Matches: 88, Mismatches: 18, Indels: 18
0.71 0.15 0.15
Matches are distributed among these distances:
4 2 0.02
5 16 0.18
6 66 0.75
7 4 0.05
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:112389 original size:23 final size:23
Alignment explanation
Indices: 112363--112433 Score: 133
Period size: 23 Copynumber: 3.1 Consensus size: 23
112353 TATTTTAAGA
*
112363 TTAAATTTATTTTAAATTTAAAT
1 TTAAATTTGTTTTAAATTTAAAT
112386 TTAAATTTGTTTTAAATTTAAAT
1 TTAAATTTGTTTTAAATTTAAAT
112409 TTAAATTTGTTTTAAATTTAAAT
1 TTAAATTTGTTTTAAATTTAAAT
112432 TT
1 TT
112434 TATTTAAGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (23 bp):
TTAAATTTGTTTTAAATTTAAAT
Found at i:112731 original size:12 final size:12
Alignment explanation
Indices: 112714--112739 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
112704 ACAGTACCAC
112714 CTTCAACTTGAG
1 CTTCAACTTGAG
112726 CTTCAACTTGAG
1 CTTCAACTTGAG
112738 CT
1 CT
112740 GCCACCGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (12 bp):
CTTCAACTTGAG
Found at i:114374 original size:29 final size:29
Alignment explanation
Indices: 114293--114557 Score: 238
Period size: 29 Copynumber: 8.9 Consensus size: 29
114283 AAGGTCTCTT
114293 AACTGTTC-AAAAATTACATTTTGACCCCTA
1 AACT-TTCTAAAAATTACATTTT-ACCCCTA
* *
114323 AAC-TTCATAAAAATTATAATTTTACCCCCA
1 AACTTTC-TAAAAATTA-CATTTTACCCCTA
114353 AACTTTCTAAAAATTACATTTTACCCTCTTA
1 AACTTTCTAAAAATTACATTTTACCC-C-TA
*
114384 AACTTTCTAAAAATTACATTTTTACCCTTA
1 AACTTTCTAAAAATTACA-TTTTACCCCTA
* *
114414 AAC-TTCTTAAAATTACCATTTTGCCCCTA
1 AACTTTCTAAAAATTA-CATTTTACCCCTA
*
114443 AACTTTCAAAAAATTACATTTTA-CCCTCA
1 AACTTTCTAAAAATTACATTTTACCCCT-A
* **
114472 AAC-TTCCAAAAATTACCATTTTACCTTTA
1 AACTTTCTAAAAATTA-CATTTTACCCCTA
* * *
114501 AAC-TTCCAAAAATTTCATTTTTGACCCC-G
1 AACTTTCTAAAAATTACA-TTTT-ACCCCTA
* *
114530 AATTTTCCAAAAATTACCATTTTACCCC
1 AACTTTCTAAAAATTA-CATTTTACCCC
114558 CGGGCATCCA
Statistics
Matches: 199, Mismatches: 20, Indels: 33
0.79 0.08 0.13
Matches are distributed among these distances:
28 20 0.10
29 75 0.38
30 67 0.34
31 29 0.15
32 8 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (29 bp):
AACTTTCTAAAAATTACATTTTACCCCTA
Found at i:114551 original size:59 final size:58
Alignment explanation
Indices: 114300--114557 Score: 265
Period size: 59 Copynumber: 4.4 Consensus size: 58
114290 CTTAACTGTT
* *
114300 CAAAAATTA-CATTTTGACCCCTAAAC-TTCATAAAAATTATAATTTTACCCCCAAACTTTC
1 CAAAAATTACCATTTT-ACCCCTAAACTTTC-TAAAAATTACATTTTTA-CCCCAAAC-TTC
* *
114360 TAAAAATTA-CATTTTACCCTCTTAAACTTTCTAAAAATTACATTTTTACCCTTAAACTTC
1 CAAAAATTACCATTTTACCC-C-TAAACTTTCTAAAAATTACATTTTTACCC-CAAACTTC
** * *
114420 TTAAAATTACCATTTTGCCCCTAAACTTTCAAAAAATTACA-TTTTACCCTCAAACTTC
1 CAAAAATTACCATTTTACCCCTAAACTTTCTAAAAATTACATTTTTACCC-CAAACTTC
** * * **
114478 CAAAAATTACCATTTTACCTTTAAAC-TTCCAAAAATTTCATTTTTGACCCCGAATTTTC
1 CAAAAATTACCATTTTACCCCTAAACTTTCTAAAAATTACATTTTT-ACCCC-AAACTTC
114537 CAAAAATTACCATTTTACCCC
1 CAAAAATTACCATTTTACCCC
114558 CGGGCATCCA
Statistics
Matches: 171, Mismatches: 19, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
57 12 0.07
58 42 0.25
59 51 0.30
60 30 0.18
61 33 0.19
62 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCTAAAAATTACATTTTTACCCCAAACTTC
Found at i:114559 original size:30 final size:30
Alignment explanation
Indices: 114300--114559 Score: 157
Period size: 30 Copynumber: 8.8 Consensus size: 30
114290 CTTAACTGTT
*
114300 CAAAAATTA-CATTTTGA-CCCCTAAACTTC
1 CAAAAATTACCATTTT-ACCCCCGAAACTTC
* **
114329 ATAAAAATTATAATTTTACCCCC-AAACTTTC
1 -CAAAAATTACCATTTTACCCCCGAAAC-TTC
* **
114360 TAAAAATTA-CATTTTACCCTCTTAAACTTTC
1 CAAAAATTACCATTTTACCC-CCGAAAC-TTC
* **
114391 TAAAAATTA-CATTTTTA-CCCTTAAACTTC
1 CAAAAATTACCA-TTTTACCCCCGAAACTTC
** * *
114420 TTAAAATTACCATTTT-GCCCCTAAACTTTC
1 CAAAAATTACCATTTTACCCCCGAAAC-TTC
* *
114450 AAAAAATTA-CATTTTACCCTC-AAACTTC
1 CAAAAATTACCATTTTACCCCCGAAACTTC
***
114478 CAAAAATTACCATTTTA-CCTTTAAACTTC
1 CAAAAATTACCATTTTACCCCCGAAACTTC
* **
114507 CAAAAATT-TCATTTTTGA-CCCCGAATTTTC
1 CAAAAATTACCA-TTTT-ACCCCCGAAACTTC
114537 CAAAAATTACCATTTTACCCCCG
1 CAAAAATTACCATTTTACCCCCG
114560 GGCATCCAAA
Statistics
Matches: 195, Mismatches: 19, Indels: 32
0.79 0.08 0.13
Matches are distributed among these distances:
28 16 0.08
29 69 0.35
30 70 0.36
31 35 0.18
32 5 0.03
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
CAAAAATTACCATTTTACCCCCGAAACTTC
Found at i:120513 original size:27 final size:25
Alignment explanation
Indices: 120483--120543 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 25
120473 TATTTTATAA
120483 AAATTAATTATATTAATTATATATGTT
1 AAATTAATTATA-TAATTATATAT-TT
120510 AAA-TAA-TA-ATAATTATATATTT
1 AAATTAATTATATAATTATATATTT
*
120532 ATATTAAATTAT
1 AAATT-AATTAT
120544 TAACTCAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
22 4 0.14
23 12 0.41
24 3 0.10
25 4 0.14
26 3 0.10
27 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
AAATTAATTATATAATTATATATTT
Found at i:132349 original size:12 final size:12
Alignment explanation
Indices: 132320--132364 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
132310 ATGATTAATA
*
132320 AATAAATGAGTC
1 AATAAACGAGTC
132332 -ATAAACGAGTC
1 AATAAACGAGTC
*
132343 AATAAACGAATC
1 AATAAACGAGTC
132355 AATAAACGAG
1 AATAAACGAG
132365 CTTGTTTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:132974 original size:29 final size:30
Alignment explanation
Indices: 132919--132988 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
132909 ATTTTAAAAT
* *
132919 TATATATGAATTTTGATTTAATATGTAATTA
1 TATATATGAATATTGATTT-AGATGTAATTA
*
132950 TATATATGAATATTGATTT-GGTGTAATTA
1 TATATATGAATATTGATTTAGATGTAATTA
132979 TATATATGAA
1 TATATATGAA
132989 ATTCTAATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 18 0.50
31 18 0.50
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.49
Consensus pattern (30 bp):
TATATATGAATATTGATTTAGATGTAATTA
Found at i:134715 original size:14 final size:14
Alignment explanation
Indices: 134698--134724 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
134688 CTGTTTTACT
134698 GAAAATGATTTATG
1 GAAAATGATTTATG
134712 GAAAATGATTTAT
1 GAAAATGATTTAT
134725 CTTTTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (14 bp):
GAAAATGATTTATG
Found at i:135179 original size:15 final size:16
Alignment explanation
Indices: 135158--135206 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 16
135148 TATACTACAA
135158 AATATTTATTATTAAT
1 AATATTTATTATTAAT
*
135174 -ATATTTATAATTGTAAT
1 AATATTTATTA-T-TAAT
135191 AAATATTTATTATTAA
1 -AATATTTATTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 9 0.33
16 1 0.04
17 7 0.26
18 1 0.04
19 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
AATATTTATTATTAAT
Done.