Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015198.1 Kokia drynarioides strain JFW-HI SEQ_130242, 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: 201689
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 102 characters in sequence are not A, C, G, or T
Found at i:871 original size:2 final size:2
Alignment explanation
Indices: 866--894 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
856 GATAGCTGTG
866 TA 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 T
895 TCGAAGTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4954 original size:15 final size:15
Alignment explanation
Indices: 4925--4953 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4915 TTTCGATTTG
4925 TTTTTAAATAAAAAA
1 TTTTTAAATAAAAAA
4940 TTTTT-AATAAAAAA
1 TTTTTAAATAAAAAA
4954 AATATTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTTTAAATAAAAAA
Found at i:11595 original size:23 final size:23
Alignment explanation
Indices: 11495--11596 Score: 116
Period size: 23 Copynumber: 4.4 Consensus size: 23
11485 ACACTAGCGC
*
11495 GCTCTCTGTTTAGCAC-GTTTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
* * * *
11518 GCCCTCTGATCAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * *
11541 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
11564 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
11587 GCTCTCTGTT
1 GCTCTCTGTT
11597 GCCCAGCACT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
23 65 0.97
24 2 0.03
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:18071 original size:20 final size:21
Alignment explanation
Indices: 18025--18073 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
18015 ATGATTAATT
18025 TATTTTTATATAAAATTGTAA
1 TATTTTTATATAAAATTGTAA
*
18046 TA-TTTTA-ACTAAATTTG-AA
1 TATTTTTATA-TAAAATTGTAA
18065 TATTTTTAT
1 TATTTTTAT
18074 TTCACTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 5 0.21
20 17 0.71
21 2 0.08
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TATTTTTATATAAAATTGTAA
Found at i:24165 original size:26 final size:25
Alignment explanation
Indices: 24102--24166 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
24092 AGATAACTAC
*
24102 ATAAAACTATATAAAAAATTAATAA
1 ATAAAAATATATAAAAAATTAATAA
* *
24127 ATAAAAATGTATAAAAATATTAA-AT
1 ATAAAAATATATAAAAA-ATTAATAA
*
24152 ATTAAAATAATATAA
1 ATAAAAAT-ATATAA
24167 TATAAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 23 0.70
26 10 0.30
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
ATAAAAATATATAAAAAATTAATAA
Found at i:30858 original size:20 final size:21
Alignment explanation
Indices: 30831--30870 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30821 AATTAGGTAT
30831 AATTTTTT-TAAAA-ATATAA
1 AATTTTTTATAAAATATATAA
30850 AATTATTTTATAAAATATATA
1 AATT-TTTTATAAAATATATA
30871 CACACTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 4 0.22
21 5 0.28
22 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTTTATAAAATATATAA
Found at i:30870 original size:22 final size:19
Alignment explanation
Indices: 30831--30868 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
30821 AATTAGGTAT
30831 AATTTTTTTAAAAATATAA
1 AATTTTTTTAAAAATATAA
*
30850 AATTATTTTATAAAATATA
1 AATTTTTTTA-AAAATATA
30869 TACACACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTTTTTAAAAATATAA
Found at i:30918 original size:24 final size:25
Alignment explanation
Indices: 30886--30932 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
30876 TTATAATAAT
30886 ATTCATTGAAGGATCTA-ATACCGA
1 ATTCATTGAAGGATCTACATACCGA
*
30910 ATTCGTTGAAGGATCTACATACC
1 ATTCATTGAAGGATCTACATACC
30933 CTCAACGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (25 bp):
ATTCATTGAAGGATCTACATACCGA
Found at i:42843 original size:59 final size:60
Alignment explanation
Indices: 42732--42903 Score: 168
Period size: 59 Copynumber: 2.9 Consensus size: 60
42722 AAATTGATTT
* * * * * * * * *
42732 AAAAAAGGTCTAGGCACCAAATTAGGAAAAAATGCCAAGTTCAAGTATCAAATTGGGTCC
1 AAAAAAGGTTTAGGTACCAAATTAAGAAAAAATGACAAGTTTAGGTACCAAATTAGGTAC
* * *
42792 AAAAAA-GTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTTAGGTACCAAATTAGGTAT
1 AAAAAAGGTTTAGGTACCAAATTAAGAAAAAATGACAAGTTTAGGTACCAAATTAGGTAC
* * * * *
42851 AAAAAAGGATTAGTTATCGAATTAAGAAAAAATGACAAGCTT-GGATACCAAAT
1 AAAAAAGGTTTAGGTACCAAATTAAGAAAAAATGACAAGTTTAGG-TACCAAAT
42904 GATATATTAA
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
59 50 0.54
60 42 0.46
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.23
Consensus pattern (60 bp):
AAAAAAGGTTTAGGTACCAAATTAAGAAAAAATGACAAGTTTAGGTACCAAATTAGGTAC
Found at i:46522 original size:2 final size:2
Alignment explanation
Indices: 46511--46551 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
46501 TTTAACCTTT
46511 TA TA -A 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
46552 ACTTTAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53291 original size:26 final size:26
Alignment explanation
Indices: 53262--53315 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
53252 ATCTAGGCTA
53262 AACAATCACATCAATAATATCTTTTT
1 AACAATCACATCAATAATATCTTTTT
53288 AACAATCACATCAATAATATCTTTTT
1 AACAATCACATCAATAATATCTTTTT
53314 AA
1 AA
53316 ATATGGGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (26 bp):
AACAATCACATCAATAATATCTTTTT
Found at i:54546 original size:20 final size:20
Alignment explanation
Indices: 54519--54570 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
54509 AAAATTTACG
*
54519 AAATAATTATTAAATTGTTCA
1 AAATAATTATTAAATTATT-A
*
54540 AAA-AATTATTTAATTATTA
1 AAATAATTATTAAATTATTA
54559 AAATAATTATTA
1 AAATAATTATTA
54571 TATAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 20 0.74
21 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
AAATAATTATTAAATTATTA
Found at i:55570 original size:23 final size:23
Alignment explanation
Indices: 55461--55623 Score: 118
Period size: 22 Copynumber: 7.1 Consensus size: 23
55451 AGCGCGCTTA
* *
55461 CTGATCAGCACTGTGTGTG-CTT
1 CTGATCAGCACTTTGTGTGCCCT
* * *
55483 CTGTTCAGCACTGTGTGTG-CTT
1 CTGATCAGCACTTTGTGTGCCCT
* * *
55505 CTGATCATCACTGTGTGTG-CTT
1 CTGATCAGCACTTTGTGTGCCCT
* * * **
55527 TTGTTTAGCACGTTT-AATGCCCT
1 CTGATCAGCAC-TTTGTGTGCCCT
55550 CTGATCAGCACTTTGTGTGCCCT
1 CTGATCAGCACTTTGTGTGCCCT
* * *
55573 CTATTATTAGCACTTCGTGTGCCCT
1 C--TGATCAGCACTTTGTGTGCCCT
*
55598 CTGATTAGCACTTTGTGTGCCCT
1 CTGATCAGCACTTTGTGTGCCCT
55621 CTG
1 CTG
55624 TTACCCAGCA
Statistics
Matches: 115, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
22 53 0.46
23 42 0.37
25 20 0.17
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.39
Consensus pattern (23 bp):
CTGATCAGCACTTTGTGTGCCCT
Found at i:55592 original size:25 final size:24
Alignment explanation
Indices: 55544--55622 Score: 108
Period size: 23 Copynumber: 3.3 Consensus size: 24
55534 GCACGTTTAA
*
55544 TGCCCTC-TGATCAGCACTTTGTG
1 TGCCCTCTTGATTAGCACTTTGTG
* *
55567 TGCCCTCTATTATTAGCACTTCGTG
1 TGCCCTCT-TGATTAGCACTTTGTG
55592 TGCCCTC-TGATTAGCACTTTGTG
1 TGCCCTCTTGATTAGCACTTTGTG
55615 TGCCCTCT
1 TGCCCTCT
55623 GTTACCCAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
23 28 0.58
25 20 0.42
ACGTcount: A:0.13, C:0.30, G:0.19, T:0.38
Consensus pattern (24 bp):
TGCCCTCTTGATTAGCACTTTGTG
Found at i:55599 original size:48 final size:48
Alignment explanation
Indices: 55544--55648 Score: 149
Period size: 48 Copynumber: 2.2 Consensus size: 48
55534 GCACGTTTAA
** *
55544 TGCCCTCTGATCAGCACTTTGTGTGCCCTCTATTA-TTAGCACTTCGTG
1 TGCCCTCTGATCAGCACTTTGTGTGCCCTCTATTACCCAGCACTT-ATG
* *
55592 TGCCCTCTGATTAGCACTTTGTGTGCCCTCTGTTACCCAGCACTTATG
1 TGCCCTCTGATCAGCACTTTGTGTGCCCTCTATTACCCAGCACTTATG
55640 TGCCCTCTG
1 TGCCCTCTG
55649 TTAAGTACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 44 0.86
49 7 0.14
ACGTcount: A:0.13, C:0.31, G:0.19, T:0.36
Consensus pattern (48 bp):
TGCCCTCTGATCAGCACTTTGTGTGCCCTCTATTACCCAGCACTTATG
Found at i:63776 original size:69 final size:69
Alignment explanation
Indices: 63663--63800 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 69
63653 ATTTGCAACA
* * * *
63663 TTGTAAGTTTAGGTTTCCGTCCCCACGAAGATACTATGTTGTTGATTTATAATCGGAAATTTCGT
1 TTGTAAGTTTAGGTTTCCATCCCCACAAAGAAACTATGTCGTTGATTTATAATCGGAAATTTCGT
63728 TTTT
66 TTTT
* ** * * *
63732 TTGTAAGTTTAGGTTTCCATCTCCGTAAAGAAACTGTGTCGTTGATTTATAATTGGAGATTTCGT
1 TTGTAAGTTTAGGTTTCCATCCCCACAAAGAAACTATGTCGTTGATTTATAATCGGAAATTTCGT
63797 TTTT
66 TTTT
63801 AGAAGTGACA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (69 bp):
TTGTAAGTTTAGGTTTCCATCCCCACAAAGAAACTATGTCGTTGATTTATAATCGGAAATTTCGT
TTTT
Found at i:64011 original size:23 final size:24
Alignment explanation
Indices: 63985--64031 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
63975 CATATTAGCA
* *
63985 AATTGATTATT-CTGTTTAAAATT
1 AATTCATTATTACTGTTAAAAATT
*
64008 AATTCATTTTTACTGTTAAAAATT
1 AATTCATTATTACTGTTAAAAATT
64032 GGTTTTTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (24 bp):
AATTCATTATTACTGTTAAAAATT
Found at i:75687 original size:6 final size:6
Alignment explanation
Indices: 75676--75712 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
75666 TGTATAGCCT
75676 TTGACA TTGACA TTGACA TTGACA TTGA-A GTTGACA T
1 TTGACA TTGACA TTGACA TTGACA TTGACA -TTGACA T
75713 GCATTGCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 1 0.03
6 27 0.93
7 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (6 bp):
TTGACA
Found at i:78338 original size:104 final size:104
Alignment explanation
Indices: 78158--78352 Score: 354
Period size: 104 Copynumber: 1.9 Consensus size: 104
78148 ATTAATATCA
78158 TCCATTCCTTTCAAATTATAAGCTTATGTTATTAACCATGTTAAACCCAGTTTTCTTTTCTAAAA
1 TCCATTCCTTTCAAATTATAAGCTTATGTTATTAACCATGTTAAACCCAGTTTTCTTTTCTAAAA
*
78223 CCCACCGTAAAAGGTGGCGCGTAGTCCGTCTGTTGGCGG
66 CCCACCGTAAAAGGTGGCGAGTAGTCCGTCTGTTGGCGG
* *
78262 TCCATTGCTTTCAAATTATAAGCTTATGTTGTTAACCATGTTAAACCCAGTTTTCTTTTCTAAAA
1 TCCATTCCTTTCAAATTATAAGCTTATGTTATTAACCATGTTAAACCCAGTTTTCTTTTCTAAAA
*
78327 CCCGCCGTAAAAGGTGGCGAGTAGTC
66 CCCACCGTAAAAGGTGGCGAGTAGTC
78353 GGTGGCTGCT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 87 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (104 bp):
TCCATTCCTTTCAAATTATAAGCTTATGTTATTAACCATGTTAAACCCAGTTTTCTTTTCTAAAA
CCCACCGTAAAAGGTGGCGAGTAGTCCGTCTGTTGGCGG
Found at i:81405 original size:29 final size:30
Alignment explanation
Indices: 81352--81410 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
81342 TTACTGGAGC
* *
81352 AAATCAAAATTTCATGTGTAAAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
* *
81382 AAATC-AAAGTTCATGTATATAATTGCACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
81411 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTACACA
Found at i:85897 original size:123 final size:119
Alignment explanation
Indices: 85682--85909 Score: 294
Period size: 123 Copynumber: 1.9 Consensus size: 119
85672 TCGTTACCGG
* * ** * *
85682 TAATAAATTAAGTTCGAAGGTTACTAAATACATACAAGGAATCCCTGGAGACTGCCTCTAAAGTA
1 TAATAAATGAAGTTCCAAGGTTACTAAATACATACAAGGAATCCAGGGAGACTGCCTCGAAAGAA
* * *
85747 TTATGTGGTTTAAGACCAAGGTGAACAATTTTAGGAGTATTCTCATCATAACAA
66 TGATGTGGTTTAAGACCAAGGCGAACAACTTTAGGAGTATTCTCATCATAACAA
* * *
85801 TAATAAATGAAGTTCCATAGGTTAAACTGAATACATACAAGGTAATCTAGGGAGACTGCCTCGAC
1 TAATAAATGAAGTTCCA-AGGTT--ACTAAATACATACAAGG-AATCCAGGGAGACTGCCTCGAA
* *
85866 GGAATGATGTGGTTTAAGACCAATGCGAACAACTTTAGGAGTAT
62 AGAATGATGTGGTTTAAGACCAAGGCGAACAACTTTAGGAGTAT
85910 ATGCGCGAAC
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
119 15 0.16
120 5 0.05
122 16 0.18
123 55 0.60
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (119 bp):
TAATAAATGAAGTTCCAAGGTTACTAAATACATACAAGGAATCCAGGGAGACTGCCTCGAAAGAA
TGATGTGGTTTAAGACCAAGGCGAACAACTTTAGGAGTATTCTCATCATAACAA
Found at i:89606 original size:29 final size:29
Alignment explanation
Indices: 89564--89621 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
89554 AAACAGAGAC
89564 TTAAAAAAACACACTACCTTCCTCCTCAT
1 TTAAAAAAACACACTACCTTCCTCCTCAT
89593 TTAAAAAAACACACTACCTTCCTCCTCAT
1 TTAAAAAAACACACTACCTTCCTCCTCAT
89622 CTTTTCTCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (29 bp):
TTAAAAAAACACACTACCTTCCTCCTCAT
Found at i:89785 original size:18 final size:18
Alignment explanation
Indices: 89762--89797 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
89752 TTTCTGATTC
*
89762 CAATTCCAAAAACAAAAA
1 CAATTCAAAAAACAAAAA
89780 CAATTCAAAAAACAAAAA
1 CAATTCAAAAAACAAAAA
89798 ACACACACAT
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:0.69, C:0.19, G:0.00, T:0.11
Consensus pattern (18 bp):
CAATTCAAAAAACAAAAA
Found at i:91067 original size:40 final size:39
Alignment explanation
Indices: 91023--91098 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 39
91013 TCATATATTC
91023 GATCACTAAAAGTTTTTATAATTTTTTTTTTTTTTTGTA
1 GATCACTAAAAGTTTTTATAATTTTTTTTTTTTTTTGTA
91062 NGATCACTAAAAGTTTTTATAATTTTTTTTTTTTTTT
1 -GATCACTAAAAGTTTTTATAATTTTTTTTTTTTTTT
91099 TGTAATTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (39 bp):
GATCACTAAAAGTTTTTATAATTTTTTTTTTTTTTTGTA
Found at i:91312 original size:10 final size:10
Alignment explanation
Indices: 91297--91345 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
91287 TTAAAAGTAA
91297 ATTTTTAAAT
1 ATTTTTAAAT
91307 ATTTTTTAAAT
1 A-TTTTTAAAT
*
91318 TTTTTACTAAAT
1 ATTTT--TAAAT
91330 ATTTTTAAAT
1 ATTTTTAAAT
91340 CATTTT
1 -ATTTT
91346 ACCTAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 10 0.30
11 14 0.42
12 9 0.27
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTTTTAAAT
Found at i:91312 original size:11 final size:11
Alignment explanation
Indices: 91298--91345 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
91288 TAAAAGTAAA
91298 TTTTTAAATAT
1 TTTTTAAATAT
91309 TTTTTAAAT-T
1 TTTTTAAATAT
91319 TTTTACTAAATA-
1 TTTT--TAAATAT
91331 TTTTTAAATCAT
1 TTTTTAAAT-AT
91343 TTT
1 TTT
91346 ACCTAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.31
11 10 0.31
12 12 0.38
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:91330 original size:23 final size:24
Alignment explanation
Indices: 91302--91354 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
91292 AGTAAATTTT
*
91302 TAAATATTTTTTAAAT-TTTTTA-C
1 TAAATA-TTTTTAAATCATTTTACC
91325 TAAATATTTTTAAATCATTTTACC
1 TAAATATTTTTAAATCATTTTACC
91349 TAAATA
1 TAAATA
91355 AATAAAAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.33
23 11 0.41
24 7 0.26
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAATATTTTTAAATCATTTTACC
Found at i:95443 original size:23 final size:22
Alignment explanation
Indices: 95413--95533 Score: 107
Period size: 23 Copynumber: 5.3 Consensus size: 22
95403 GAAAGCTAGC
95413 GTGCTTACTGTTTCGCACTTTGT
1 GTGCTTACTGTTT-GCACTTTGT
*
95436 GTGCTTACTGTTTCGCACTTCGT
1 GTGCTTACTGTTT-GCACTTTGT
* * *
95459 GTGCCTACTGATTTGCGCTATGT
1 GTGCTTACTG-TTTGCACTTTGT
* * * *
95482 GTGCCTATTGATTGCACTGTGT
1 GTGCTTACTGTTTGCACTTTGT
* * *
95504 GTGCCTACTGGATTGCACTGTGT
1 GTGCTTACT-GTTTGCACTTTGT
95527 GTGCTTA
1 GTGCTTA
95534 TTGTCTCCCC
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.20
23 65 0.76
24 3 0.04
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.41
Consensus pattern (22 bp):
GTGCTTACTGTTTGCACTTTGT
Found at i:96359 original size:11 final size:11
Alignment explanation
Indices: 96328--96370 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
96318 TCACATCAAC
*
96328 AAATGATTTTA
1 AAATTATTTTA
96339 AAATTA--TTA
1 AAATTATTTTA
96348 AAATTATTTTA
1 AAATTATTTTA
*
96359 AAATTAATTTA
1 AAATTATTTTA
96370 A
1 A
96371 TTTTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 9 0.32
11 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:96391 original size:20 final size:19
Alignment explanation
Indices: 96328--96392 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
96318 TCACATCAAC
*
96328 AAATGATTTTAAAATTATTA
1 AAATAATTTT-AAATTATTA
*
96348 AAATTATTTTAAA--ATTA
1 AAATAATTTTAAATTATTA
**
96365 ATTTAATTTTAATATTATTA
1 AAATAATTTTAA-ATTATTA
96385 AAATAATT
1 AAATAATT
96393 ATTTTAAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 13 0.36
18 1 0.03
19 3 0.08
20 19 0.53
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
AAATAATTTTAAATTATTA
Found at i:97047 original size:7 final size:7
Alignment explanation
Indices: 97035--97077 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
97025 AATCAATGAA
97035 GGGAAAG
1 GGGAAAG
97042 GGGAAA-
1 GGGAAAG
97048 GGGAAAG
1 GGGAAAG
97055 GGGAAA-
1 GGGAAAG
*
97061 AGGAAAGG
1 GGGAAA-G
97069 GGGAAAG
1 GGGAAAG
97076 GG
1 GG
97078 CAGAGGAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
6 11 0.35
7 15 0.48
8 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (7 bp):
GGGAAAG
Found at i:97051 original size:13 final size:13
Alignment explanation
Indices: 97033--97077 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
97023 TAAATCAATG
97033 AAGGGAAAGGGGA
1 AAGGGAAAGGGGA
97046 AAGGGAAAGGGGA
1 AAGGGAAAGGGGA
*
97059 AAAGGAAAGGGGGA
1 AAGGGAAA-GGGGA
97073 AAGGG
1 AAGGG
97078 CAGAGGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 20 0.69
14 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (13 bp):
AAGGGAAAGGGGA
Found at i:97085 original size:26 final size:26
Alignment explanation
Indices: 97036--97091 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
97026 ATCAATGAAG
*
97036 GGAAAGGGGAAAGGGAAAGGGGAAAA
1 GGAAAGGGGAAAGGGAAAGAGGAAAA
* *
97062 GGAAAGGGGGAAAGGG-CAGAGGAAGA
1 GGAAA-GGGGAAAGGGAAAGAGGAAAA
97088 GGAA
1 GGAA
97092 GAGGAAGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.46, C:0.02, G:0.52, T:0.00
Consensus pattern (26 bp):
GGAAAGGGGAAAGGGAAAGAGGAAAA
Found at i:97160 original size:16 final size:18
Alignment explanation
Indices: 97139--97172 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
97129 TTTAAATGAT
97139 TATTTT-AA-TAATTTTA
1 TATTTTAAATTAATTTTA
97155 TATTTTAAATTAATTTTA
1 TATTTTAAATTAATTTTA
97173 AAATAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTAAATTAATTTTA
Found at i:97172 original size:11 final size:11
Alignment explanation
Indices: 97156--97221 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
97146 ATAATTTTAT
*
97156 ATTTTAAATTA
1 ATTTTAAAATA
97167 ATTTTAAAATA
1 ATTTTAAAATA
97178 ATTTT---ATA
1 ATTTTAAAATA
* *
97186 TTTTTAAAAACA
1 ATTTT-AAAATA
97198 ATTTT--AATA
1 ATTTTAAAATA
*
97207 ATTTTAAAATT
1 ATTTTAAAATA
97218 ATTT
1 ATTT
97222 GTTGACGTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
8 7 0.16
9 8 0.19
11 22 0.51
12 6 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:97200 original size:20 final size:21
Alignment explanation
Indices: 97156--97215 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
97146 ATAATTTTAT
*
97156 ATTTTAAATTAATTTT-AAAATA
1 ATTTT-AA-TAATTTTAAAAACA
*
97178 ATTTT-ATATTTTTAAAAACA
1 ATTTTAATAATTTTAAAAACA
97198 ATTTTAATAATTTTAAAA
1 ATTTTAATAATTTTAAAA
97216 TTATTTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 6 0.18
20 11 0.33
21 11 0.33
22 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTAATAATTTTAAAAACA
Found at i:97206 original size:29 final size:27
Alignment explanation
Indices: 97140--97212 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 27
97130 TTAAATGATT
**
97140 ATTTTAATAATTTTATATTTTAAATTA
1 ATTTTAATAATTTTATATTTTAAAACA
97167 ATTTTAAAATAATTTTATATTTTTAAAAACA
1 ATTTT--AATAATTTTATA-TTTT-AAAACA
97198 ATTTTAATAATTTTA
1 ATTTTAATAATTTTA
97213 AAATTATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 22 0.55
30 4 0.10
31 9 0.22
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTTTAATAATTTTATATTTTAAAACA
Found at i:100334 original size:36 final size:36
Alignment explanation
Indices: 100289--100363 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
100279 TGATCGTTTT
100289 AATAAATATTTTATTTATTTTTATTGTTAAAAATTA
1 AATAAATATTTTATTTATTTTTATTGTTAAAAATTA
100325 AATAAATATTTTATTTATTTTTATTGTTAAAAATTA
1 AATAAATATTTTATTTATTTTTATTGTTAAAAATTA
100361 AAT
1 AAT
100364 CTAACATACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (36 bp):
AATAAATATTTTATTTATTTTTATTGTTAAAAATTA
Found at i:101933 original size:1 final size:1
Alignment explanation
Indices: 101889--101913 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
101879 GCATAAACGT
101889 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
101914 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:102130 original size:13 final size:13
Alignment explanation
Indices: 102112--102138 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
102102 ACAGAACCCG
102112 ATTGGTGATTCAT
1 ATTGGTGATTCAT
102125 ATTGGTGATTCAT
1 ATTGGTGATTCAT
102138 A
1 A
102139 GACACATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.44
Consensus pattern (13 bp):
ATTGGTGATTCAT
Found at i:113631 original size:19 final size:19
Alignment explanation
Indices: 113604--113640 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
113594 AATTTCGAAT
* *
113604 GATTCATCTGAAGAACATG
1 GATTAATCTAAAGAACATG
113623 GATTAATCTAAAGAACAT
1 GATTAATCTAAAGAACAT
113641 AAACTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (19 bp):
GATTAATCTAAAGAACATG
Found at i:114408 original size:7 final size:7
Alignment explanation
Indices: 114396--114420 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
114386 TATATATATA
114396 TTTTATT
1 TTTTATT
114403 TTTTATT
1 TTTTATT
114410 TTTTATT
1 TTTTATT
114417 TTTT
1 TTTT
114421 GAGAGTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:119915 original size:59 final size:59
Alignment explanation
Indices: 119840--119971 Score: 165
Period size: 59 Copynumber: 2.2 Consensus size: 59
119830 ATCAAAAACA
* * * *
119840 AAAGTTTCATGTATACATATGAATCACATCCATGTTTCATGTGCATAATTGAACTAAATC
1 AAAG-TTCATGTATACACATGAACCACATCCAAGTTTCATGTGCATAATTGAACCAAATC
* * * * * *
119900 AAAGTTCATGTATACACGTGAACCGCATTCAAGTTTCATGTGTATAATTGCACCAAATT
1 AAAGTTCATGTATACACATGAACCACATCCAAGTTTCATGTGCATAATTGAACCAAATC
119959 AAAGTTCATGTAT
1 AAAGTTCATGTAT
119972 CAAATTGTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 58 0.94
60 4 0.06
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (59 bp):
AAAGTTCATGTATACACATGAACCACATCCAAGTTTCATGTGCATAATTGAACCAAATC
Found at i:120469 original size:31 final size:31
Alignment explanation
Indices: 120426--120489 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
120416 ACTAATAGAC
120426 CAATTACTTAAATAAAAACTTTT-GAATAATT
1 CAATTACTTAAATAAAAA-TTTTCGAATAATT
* *
120457 CAATTA-TATAAATGAAAATTTTCGAATAGTT
1 CAATTACT-TAAATAAAAATTTTCGAATAATT
120488 CA
1 CA
120490 GTAACCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (31 bp):
CAATTACTTAAATAAAAATTTTCGAATAATT
Found at i:129147 original size:31 final size:31
Alignment explanation
Indices: 129107--129166 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
129097 AAGTTTTGTG
* * *
129107 AGTTCTAATTAATCCTCTCAAAACTTTTAAA
1 AGTTCTAATTAAACCTCCCAAAACATTTAAA
*
129138 AGTTTTAATTAAACCTCCCAAAACATTTA
1 AGTTCTAATTAAACCTCCCAAAACATTTA
129167 GAAAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (31 bp):
AGTTCTAATTAAACCTCCCAAAACATTTAAA
Found at i:132027 original size:106 final size:105
Alignment explanation
Indices: 131832--132028 Score: 304
Period size: 105 Copynumber: 1.9 Consensus size: 105
131822 CTATTGTTTC
* * * *
131832 GGTTGATTCGGTTCGGTTCAAGGACTTTTGTGGATGAAAACATGTCCTAAATTCAATATGCAGAG
1 GGTTGATTCGGTTCGGTTCAAGAACTTTTATCGATAAAAACATGTCCTAAATTCAATATGCAGAG
* *
131897 TGCATGCTTCAATGTTACAATGTCTCATAATGTTCGTTCT
66 TGCATACTACAATGTTACAATGTCTCATAATGTTCGTTCT
* **
131937 GGTTGTTTCGGTTCGGTTTGAGAACTTTTATCGATAAAAACATGTCCTAAAATTCAATATGCAGA
1 GGTTGATTCGGTTCGGTTCAAGAACTTTTATCGATAAAAACATGTCCT-AAATTCAATATGCAGA
132002 GTGCATACTACAATGTTACAATGTCTC
65 GTGCATACTACAATGTTACAATGTCTC
132029 GTATGGTAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
105 41 0.50
106 41 0.50
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (105 bp):
GGTTGATTCGGTTCGGTTCAAGAACTTTTATCGATAAAAACATGTCCTAAATTCAATATGCAGAG
TGCATACTACAATGTTACAATGTCTCATAATGTTCGTTCT
Found at i:135816 original size:31 final size:30
Alignment explanation
Indices: 135766--135824 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
135756 TGTACGCGTG
**
135766 AAATTTTAATTTTGGTTTAAAT-ATATACTT
1 AAATTTTAATTTTAATTT-AATCATATACTT
135796 AAATATTTAATTTTAATTTAATCATATAC
1 AAAT-TTTAATTTTAATTTAATCATATAC
135825 ATTTAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (30 bp):
AAATTTTAATTTTAATTTAATCATATACTT
Found at i:136873 original size:15 final size:14
Alignment explanation
Indices: 136853--136898 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
136843 ATAAAAAAAA
136853 ATTTATCTATTTTTT
1 ATTTAT-TATTTTTT
*
136868 ATTTATAATTTTTT
1 ATTTATTATTTTTT
136882 -TTTA-TATTTTATT
1 ATTTATTATTTT-TT
136895 ATTT
1 ATTT
136899 TAAAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 5 0.19
13 6 0.22
14 10 0.37
15 6 0.22
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTATTATTTTTT
Found at i:136885 original size:13 final size:13
Alignment explanation
Indices: 136860--136898 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
136850 AAAATTTATC
136860 TATTTTTTATTTA
1 TATTTTTTATTTA
136873 TAATTTTTT-TTTA
1 T-ATTTTTTATTTA
136886 TATTTTATTATTT
1 TATTTT-TTATTT
136899 TAAAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.22
13 8 0.35
14 10 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTTTTATTTA
Found at i:143042 original size:16 final size:16
Alignment explanation
Indices: 143021--143055 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
143011 TAAAAGTCAG
*
143021 AATTGAAGATTATTTC
1 AATTGAAGATTATATC
143037 AATTGAAGATTATATC
1 AATTGAAGATTATATC
143053 AAT
1 AAT
143056 AAAAAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (16 bp):
AATTGAAGATTATATC
Found at i:146005 original size:31 final size:30
Alignment explanation
Indices: 145940--146005 Score: 71
Period size: 31 Copynumber: 2.1 Consensus size: 30
145930 TAAAGAAAAC
* * *
145940 AATTTGACTCTTTTTGAAAGTGGAAAGGTCA
1 AATTCGACTCTTTTTAAAAGT-GAAAGGGCA
145971 AATTCGACTCTTTTTAAAAAGT-AAAGGGCTA
1 AATTCGACTCTTTTT-AAAAGTGAAAGGGC-A
146002 AATT
1 AATT
146006 TAGGTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 6 0.20
31 19 0.63
32 5 0.17
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (30 bp):
AATTCGACTCTTTTTAAAAGTGAAAGGGCA
Found at i:150801 original size:20 final size:21
Alignment explanation
Indices: 150776--150823 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
150766 ATAAAAATTA
150776 TTTTAT-ATTAAAATTT-ATAT
1 TTTTATAATT-AAATTTAATAT
150796 TTTTATAATTAAATTTAAATAT
1 TTTTATAATTAAATTT-AATAT
150818 TTTTAT
1 TTTTAT
150824 TTTTAATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.48
21 3 0.12
22 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATAATTAAATTTAATAT
Found at i:150829 original size:22 final size:20
Alignment explanation
Indices: 150776--150829 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
150766 ATAAAAATTA
*
150776 TTTTATATTAAAATTTATAT
1 TTTTATATTTAAATTTATAT
*
150796 TTTTATAATTAAATTTAAATAT
1 TTTTATATTTAAATTT--ATAT
*
150818 TTTTATTTTTAA
1 TTTTATATTTAA
150830 TAGTAAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 14 0.50
22 14 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTATATTTAAATTTATAT
Found at i:150836 original size:28 final size:27
Alignment explanation
Indices: 150783--150836 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
150773 TTATTTTATA
*
150783 TTAAAATTTATATTTTTATAATTAAAT
1 TTAAAATTTATATTTTTATAAGTAAAT
*
150810 TTAAATATTTTTATTTTTA-ATAGTAAA
1 TTAAA-ATTTATATTTTTATA-AGTAAA
150837 ACGAGTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAAAATTTATATTTTTATAAGTAAAT
Found at i:151101 original size:16 final size:17
Alignment explanation
Indices: 151076--151108 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
151066 AAAAATGTTT
151076 ATATTATTTTTAATTTA
1 ATATTATTTTTAATTTA
*
151093 ATATT-TTTTTCATTTA
1 ATATTATTTTTAATTTA
151109 TTAAAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATTTTTAATTTA
Found at i:154521 original size:24 final size:24
Alignment explanation
Indices: 154485--154533 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
154475 GCCTAATAAT
*
154485 TTCCACAAACAAAACCACACAAAA
1 TTCCACAAACAAAACAACACAAAA
* * *
154509 TTCCTCAATCAAATCAACACAAAA
1 TTCCACAAACAAAACAACACAAAA
154533 T
1 T
154534 ATATTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.31, G:0.00, T:0.16
Consensus pattern (24 bp):
TTCCACAAACAAAACAACACAAAA
Found at i:160062 original size:31 final size:31
Alignment explanation
Indices: 160025--160084 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
160015 AAAAAAAAAC
160025 TGAAAAGTACGACGACTAAAATTGACCAATT
1 TGAAAAGTACGACGACTAAAATTGACCAATT
* * *
160056 TGAAAAGTACGAGGATTAGAATTGACCAA
1 TGAAAAGTACGACGACTAAAATTGACCAA
160085 ATTAAAGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (31 bp):
TGAAAAGTACGACGACTAAAATTGACCAATT
Found at i:167100 original size:158 final size:158
Alignment explanation
Indices: 166812--167121 Score: 425
Period size: 158 Copynumber: 2.0 Consensus size: 158
166802 TATTTCAACA
* **
166812 TATGATACACTACCTAACTAACCTCTAAAATGAACATAAAGTAAACTTCATTCAAACATGAAAAA
1 TATGATACACTACCTAACTAACCTCGAAAACAAACATAAAGTAAACTTCATTCAAACATGAAAAA
* * *
166877 TCACGCACTAAAAAATGCAATGATACTTTTGAGAAGTTCAATGGCTGACCCTCACAGAGAATAAA
66 TCACGCACTAAAAAATGCAATGATACTTATGAAAAGTTCAATGGCTGAACCTCACAGAGAATAAA
*
166942 ATCAA-GTACAGGATTACCACACCAGAAC
131 ATCAAGGAACA-GATTACCACACCAGAAC
* *
166970 TATGATACACTACCTAACTAACCTCGAAAACAAACATAAAGTAACCTTTCATTCAAACATGAACC
1 TATGATACACTACCTAACTAACCTCGAAAACAAACATAAAGTAAAC-TTCATTCAAACATGAA-A
* *
167035 AA-CA-GTCA-TCAAACAATGCAATGTTACTTATGAAAAGTTCAATGGCT-AACCTCACAG-GTA
64 AATCACG-CACT-AAAAAATGCAATGATACTTATGAAAAGTTCAATGGCTGAACCTCACAGAG-A
167095 ATAAAATCAAGGAACAGATTACCACAC
126 ATAAAATCAAGGAACAGATTACCACAC
167122 AACACCAGAG
Statistics
Matches: 135, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
157 1 0.01
158 75 0.56
159 57 0.42
160 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (158 bp):
TATGATACACTACCTAACTAACCTCGAAAACAAACATAAAGTAAACTTCATTCAAACATGAAAAA
TCACGCACTAAAAAATGCAATGATACTTATGAAAAGTTCAATGGCTGAACCTCACAGAGAATAAA
ATCAAGGAACAGATTACCACACCAGAAC
Found at i:167289 original size:187 final size:190
Alignment explanation
Indices: 166974--167349 Score: 546
Period size: 187 Copynumber: 2.0 Consensus size: 190
166964 CAGAACTATG
* * *
166974 ATACACTACCTAACTAACCTCGAAAACAAACATAAAGTAACCTTTCATTCAAACATGAACCAACA
1 ATACACTACCTAACTAACCTCAAAAACAAACATAAAGTAAACTTCCATTCAAACATGAACCAACA
* *
167039 GTCATCAAACAATGCAATGTTACTTATGAAAAGTTCAATGGCTAACCTCACAGGTAATAAAATCA
66 GTCATCAAACAATGCAATGTTACTTATGAAAAGTTCAATAGCTAACCTCACAGGGAATAAAATCA
* * *
167104 AGGAACAGATTA-C-CA-CACAACACCAGAGAGGAAGCAAATACACATTTCAGTTCCATA
131 AGGAACAGATTACCACACCACAACACCAAAGAGGAAACAAATACACATTCCAGTTCCATA
* * * *
167161 ATACACTACCTACCTAACCTCAAAAACGAACATAAAGTAAACTTCCATTCAAACATTAACCATCA
1 ATACACTACCTAACTAACCTCAAAAACAAACATAAAGTAAACTTCCATTCAAACATGAACCAACA
* *
167226 -TGCATCAAACAATTCAATGTTACTT-TCGAGAAGTTCAATAGCTAACCTCACAGGGAATAAAAT
66 GT-CATCAAACAATGCAATGTTACTTAT-GAAAAGTTCAATAGCTAACCTCACAGGGAATAAAAT
* * *
167289 CAAGTATCGGATTACCACACCACAACACCAAAGAGGAAACAAATACACATTCCAGTTCCAT
129 CAAGGAACAGATTACCACACCACAACACCAAAGAGGAAACAAATACACATTCCAGTTCCAT
167350 GGTTCAGGAG
Statistics
Matches: 167, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
186 2 0.01
187 124 0.74
188 1 0.01
189 2 0.01
190 38 0.23
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (190 bp):
ATACACTACCTAACTAACCTCAAAAACAAACATAAAGTAAACTTCCATTCAAACATGAACCAACA
GTCATCAAACAATGCAATGTTACTTATGAAAAGTTCAATAGCTAACCTCACAGGGAATAAAATCA
AGGAACAGATTACCACACCACAACACCAAAGAGGAAACAAATACACATTCCAGTTCCATA
Found at i:173744 original size:28 final size:29
Alignment explanation
Indices: 173696--173776 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 29
173686 TGAAAGGATA
*
173696 AATTTACTCTTTAATTTAATATAT-AATACT
1 AATTTACT-TTT-TTTTAATATATAAATACT
173726 AATTTACTTTTTTTTAATAAATATACAATACT
1 AATTTACTTTTTTTTAAT--ATATA-AATACT
173758 AATTTA-TTATTTTTTAATA
1 AATTTACTT-TTTTTTAATA
173777 AAGGAATAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
28 6 0.13
29 3 0.07
30 13 0.29
31 2 0.04
32 21 0.47
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (29 bp):
AATTTACTTTTTTTTAATATATAAATACT
Found at i:173756 original size:32 final size:32
Alignment explanation
Indices: 173713--173778 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
173703 TCTTTAATTT
*
173713 AATATATAATACTAATTTACTT-TTTTTTAATA
1 AATATACAATACTAATTTA-TTATTTTTTAATA
173745 AATATACAATACTAATTTATTATTTTTTAATA
1 AATATACAATACTAATTTATTATTTTTTAATA
173777 AA
1 AA
173779 GGAATAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (32 bp):
AATATACAATACTAATTTATTATTTTTTAATA
Found at i:174471 original size:10 final size:10
Alignment explanation
Indices: 174453--174483 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
174443 TCCGGTACGG
174453 TTTTCATTTT
1 TTTTCATTTT
*
174463 TTTTAATTTT
1 TTTTCATTTT
174473 TTTTCATTTT
1 TTTTCATTTT
174483 T
1 T
174484 GTGTAAGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:176350 original size:264 final size:264
Alignment explanation
Indices: 175880--176403 Score: 863
Period size: 264 Copynumber: 2.0 Consensus size: 264
175870 TAAAATTTCT
* *
175880 GTTCCACTTATGTATTATATATGTTTTGGTAGAAAAACAGAACATATCACTAAGTTGCAATTATG
1 GTTCCACTTATGTATTATATATGTTTTGGCAGAAAAACAAAACATATCACTAAGTTGCAATTATG
* *
175945 GAGACAAACATTAATGTTAGAAAACCAGTAATCCATAATGACCAGGCATTGGTTTAAAAGGTTTC
66 GAGACAAACATTAATGTTAGAAAACCAGTAATCCATAAGGACCAGGCATTGGTTTAAAAGGCTTC
* * *
176010 AGTGGTTTGTAGACATATAGTATTAATGTCATATGTTGAAGGATGATCTTTGATCTATCTTTTCA
131 AGTGGTTTCTAGACATATAGTATTAATATCATATGTTGAAGGATGATCATTGATCTATCTTTTCA
* * *
176075 TATGTTAAAAGTAACTATGATGGTCTATTTGGACTTGAAACAAGCACAATATTTGAAATCTGACA
196 TATGTTAAAAGTAACTATAATGGTCTATTTGGACTTGAAACAAGCACAAAATTTGAAATATGACA
176140 CTAA
261 CTAA
* *
176144 GTTCCACTTATGTATTATATATGTTTTGGCAGAAAAACAAAACATATCAGTAAGTTGCAATTGTG
1 GTTCCACTTATGTATTATATATGTTTTGGCAGAAAAACAAAACATATCACTAAGTTGCAATTATG
** *
176209 GAGACAGGCA-TAATGTTAGAAAACCAGT-ATCCATAAGGACCAGGCATTGGTTTACAAGGCTTC
66 GAGACAAACATTAATGTTAGAAAACCAGTAATCCATAAGGACCAGGCATTGGTTTAAAAGGCTTC
*
176272 AGTGGTCTTTCTGGACATATAGTATTAATATCATATGTTGAAGGATGATCATTGATCTATCTTTT
131 AGTGG--TTTCTAGACATATAGTATTAATATCATATGTTGAAGGATGATCATTGATCTATCTTTT
*
176337 CATATGTTAAAAGTAACTATAATGGTCTATTTGGGCTTGAAACAAGCACAAAATTTGAAATATGA
194 CATATGTTAAAAGTAACTATAATGGTCTATTTGGACTTGAAACAAGCACAAAATTTGAAATATGA
176402 CA
259 CA
176404 ATTTCTTCCC
Statistics
Matches: 241, Mismatches: 17, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
262 37 0.15
263 18 0.07
264 186 0.77
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (264 bp):
GTTCCACTTATGTATTATATATGTTTTGGCAGAAAAACAAAACATATCACTAAGTTGCAATTATG
GAGACAAACATTAATGTTAGAAAACCAGTAATCCATAAGGACCAGGCATTGGTTTAAAAGGCTTC
AGTGGTTTCTAGACATATAGTATTAATATCATATGTTGAAGGATGATCATTGATCTATCTTTTCA
TATGTTAAAAGTAACTATAATGGTCTATTTGGACTTGAAACAAGCACAAAATTTGAAATATGACA
CTAA
Found at i:180587 original size:3 final size:3
Alignment explanation
Indices: 180579--180604 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
180569 ATGGCATTGA
180579 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
180605 GATCACCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:197638 original size:13 final size:13
Alignment explanation
Indices: 197620--197646 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
197610 TAGATTCCCA
197620 TATATATATATAT
1 TATATATATATAT
197633 TATATATATATAT
1 TATATATATATAT
197646 T
1 T
197647 CTTTTAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATATATATAT
Found at i:198358 original size:17 final size:17
Alignment explanation
Indices: 198332--198370 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
198322 ATAAAATAAG
198332 TATTAAATTGTTTAAA-T
1 TATTAAATTG-TTAAATT
*
198349 TATTAGATTGTTAAATT
1 TATTAAATTGTTAAATT
198366 TATTA
1 TATTA
198371 TTGTATGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (17 bp):
TATTAAATTGTTAAATT
Found at i:200998 original size:15 final size:15
Alignment explanation
Indices: 200978--201010 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
200968 TAATAATAGC
200978 ATTTCAATACGAATA
1 ATTTCAATACGAATA
200993 ATTTCAATACGAATA
1 ATTTCAATACGAATA
201008 ATT
1 ATT
201011 AAAGATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (15 bp):
ATTTCAATACGAATA
Done.