Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019102.1 Corchorus olitorius cultivar O-4 contig19135, 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: 123927
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4672 original size:12 final size:12
Alignment explanation
Indices: 4655--4680 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4645 AGTATGGATA
4655 TGGGTTCGAGTC
1 TGGGTTCGAGTC
4667 TGGGTTCGAGTC
1 TGGGTTCGAGTC
4679 TG
1 TG
4681 AGTAAACGCA
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:0.08, C:0.15, G:0.42, T:0.35
Consensus pattern (12 bp):
TGGGTTCGAGTC
Found at i:6495 original size:109 final size:109
Alignment explanation
Indices: 6304--6518 Score: 376
Period size: 109 Copynumber: 2.0 Consensus size: 109
6294 TAGTCATTTT
* *
6304 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTATGGTATGTGTGCTT
*
6369 ATTTAATATATTCAATTGAATAAACAACACAATTAATAATAATA
66 ATTTAATAGATTCAATTGAATAAACAACACAATTAATAATAATA
*
6413 GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCATTTTGTATTGTATGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTATGGTATGTGTGCTT
* *
6478 ATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATA
66 ATTTAATAGATTCAATTGAATAAACAACACAATTAATAATA
6519 CTATATATAA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 100 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (109 bp):
GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTATGGTATGTGTGCTT
ATTTAATAGATTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:10547 original size:90 final size:88
Alignment explanation
Indices: 10391--10567 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 88
10381 TGAACTTCAA
10391 ATGTTACTACATAACTACTTGACCGTATAATATTCATACTTGCAAGTATTTTTCATTTAAAATTT
1 ATGTTACTACATAACTACTTGACCGTATAATATTCATACTTGCAAGTATTTTTCATTTAAAATTT
10456 ATACATTATATTCTTATTAACTTTG
66 ATACATTA-A-TCTTATTAACTTTG
* * *
10481 ATGTTACTACATACCTACTTGACCGTATAATATTCATACTTTCAAGTATTTTTCATTTAAAGTTT
1 ATGTTACTACATAACTACTTGACCGTATAATATTCATACTTGCAAGTATTTTTCATTTAAAATTT
*
10546 ATATATTAATCTTATTAACTTT
66 ATACATTAATCTTATTAACTTT
10568 ATTACAGCAA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
88 13 0.16
89 1 0.01
90 69 0.83
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (88 bp):
ATGTTACTACATAACTACTTGACCGTATAATATTCATACTTGCAAGTATTTTTCATTTAAAATTT
ATACATTAATCTTATTAACTTTG
Found at i:10719 original size:13 final size:13
Alignment explanation
Indices: 10701--10734 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
10691 TCTTACTATC
10701 TTATTTTATCTTA
1 TTATTTTATCTTA
10714 TTATTTTATCTTA
1 TTATTTTATCTTA
*
10727 CTATTTTA
1 TTATTTTA
10735 CTACTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTTATCTTA
Found at i:17171 original size:8 final size:7
Alignment explanation
Indices: 17145--17169 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17135 GGCAAGAAAA
17145 TTTTGCT
1 TTTTGCT
17152 TTTTGCT
1 TTTTGCT
17159 TTTTGCT
1 TTTTGCT
17166 TTTT
1 TTTT
17170 TGGAAATTTG
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:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (7 bp):
TTTTGCT
Found at i:17211 original size:15 final size:16
Alignment explanation
Indices: 17191--17220 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17181 TGGCATTTTT
17191 GGTAAATTA-AGGTAA
1 GGTAAATTACAGGTAA
17206 GGTAAATTACAGGTA
1 GGTAAATTACAGGTA
17221 GGATCCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.03, G:0.27, T:0.27
Consensus pattern (16 bp):
GGTAAATTACAGGTAA
Found at i:18375 original size:27 final size:27
Alignment explanation
Indices: 18290--18362 Score: 146
Period size: 27 Copynumber: 2.7 Consensus size: 27
18280 TCCTAAAACT
18290 AATTAATTTAACTATATATTGCCAAAA
1 AATTAATTTAACTATATATTGCCAAAA
18317 AATTAATTTAACTATATATTGCCAAAA
1 AATTAATTTAACTATATATTGCCAAAA
18344 AATTAATTTAACTATATAT
1 AATTAATTTAACTATATAT
18363 ATATAGAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.40
Consensus pattern (27 bp):
AATTAATTTAACTATATATTGCCAAAA
Found at i:20152 original size:38 final size:38
Alignment explanation
Indices: 20101--20177 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
20091 GGATTTATCA
20101 ACATTACTAATAAAGAGAGAAAGGAAATGATTGGAGGG
1 ACATTACTAATAAAGAGAGAAAGGAAATGATTGGAGGG
20139 ACATTACTAATAAAGAGAGAAAGGAAATGATTGGAGGG
1 ACATTACTAATAAAGAGAGAAAGGAAATGATTGGAGGG
20177 A
1 A
20178 TAGAAAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.48, C:0.05, G:0.29, T:0.18
Consensus pattern (38 bp):
ACATTACTAATAAAGAGAGAAAGGAAATGATTGGAGGG
Found at i:38533 original size:25 final size:24
Alignment explanation
Indices: 38490--38539 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
38480 TCTCTATAAG
38490 ATCAAACCCAAAACCAAAACACAAA
1 ATCAAACCCAAAACCAAAAC-CAAA
*
38515 ATCAAA-CCAAACCCAAAAACCAAA
1 ATCAAACCCAAAACC-AAAACCAAA
38539 A
1 A
38540 ACCCATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.64, C:0.32, G:0.00, T:0.04
Consensus pattern (24 bp):
ATCAAACCCAAAACCAAAACCAAA
Found at i:40808 original size:81 final size:80
Alignment explanation
Indices: 40673--40833 Score: 236
Period size: 81 Copynumber: 2.0 Consensus size: 80
40663 TTGCTTAAGT
*
40673 TTTCTTTAATTGCAATGAAGAAACGATTTGATTTCATGAATATTAAATATTCAATTTAGCACCCT
1 TTTCTTTAATTGCAATGAAGAAACAATTTGATTTCATGAATATTAAATATTCAATTTAGCACCCT
40738 AAATTTGATTGGTGCA
66 AAATTTGATT-GTGCA
* * *
40754 TTTCTTTAATTGCCATGAAGAAAACAATTTGATTTTCGTTAAT-TT-AATATTCAATTTAGCACC
1 TTTCTTTAATTGCAATGAAG-AAACAATTTGA-TTTCATGAATATTAAATATTCAATTTAGCACC
*
40817 TTAAATTTGATTGTGCA
64 CTAAATTTGATTGTGCA
40834 ATTTGTTTCT
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
80 5 0.07
81 48 0.66
82 12 0.16
83 8 0.11
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (80 bp):
TTTCTTTAATTGCAATGAAGAAACAATTTGATTTCATGAATATTAAATATTCAATTTAGCACCCT
AAATTTGATTGTGCA
Found at i:43014 original size:17 final size:17
Alignment explanation
Indices: 42978--43025 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
42968 ATCATCCTCC
* **
42978 AGATCACTAGTGATTTA
1 AGATCACCAGTGATGCA
42995 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
* *
43012 AGATTACCGGTGAT
1 AGATCACCAGTGAT
43026 CAAAGATTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:54388 original size:79 final size:79
Alignment explanation
Indices: 54297--54451 Score: 292
Period size: 79 Copynumber: 2.0 Consensus size: 79
54287 GTTCATAGTA
*
54297 AAAGTTCTGCTAATCCAGCGATGTTTTCATAATTTTACTATATCAGTGTTTATTTATATTCTTCT
1 AAAGTTCTGCTAATCCAGCGATGTTTTCATAATTTTACTATATCAGTGTTCATTTATATTCTTCT
54362 TTCATTGATGTTGT
66 TTCATTGATGTTGT
*
54376 AAAGTTCTGCTAATCCAGCTATGTTTTCATAATTTTACTATATCAGTGTTCATTTATATTCTTCT
1 AAAGTTCTGCTAATCCAGCGATGTTTTCATAATTTTACTATATCAGTGTTCATTTATATTCTTCT
54441 TTCATTGATGT
66 TTCATTGATGT
54452 AAGCTTTTAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.49
Consensus pattern (79 bp):
AAAGTTCTGCTAATCCAGCGATGTTTTCATAATTTTACTATATCAGTGTTCATTTATATTCTTCT
TTCATTGATGTTGT
Found at i:55454 original size:15 final size:15
Alignment explanation
Indices: 55434--55489 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
55424 AGTAAGTTTG
55434 CTGTTGCTGCTGCCC
1 CTGTTGCTGCTGCCC
55449 CTGTTGCTGCTG---
1 CTGTTGCTGCTGCCC
* *
55461 CTGGTGGTGCTGCCC
1 CTGTTGCTGCTGCCC
*
55476 CTGCTGCTGCTGCC
1 CTGTTGCTGCTGCC
55490 GCACCCGCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 10 0.29
15 24 0.71
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (15 bp):
CTGTTGCTGCTGCCC
Found at i:55471 original size:27 final size:27
Alignment explanation
Indices: 55432--55488 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
55422 CAAGTAAGTT
* *
55432 TGCTGTTGCTGCTGCCCCTGTTGCTGC
1 TGCTGGTGCTGCTGCCCCTGCTGCTGC
*
55459 TGCTGGTGGTGCTGCCCCTGCTGCTGC
1 TGCTGGTGCTGCTGCCCCTGCTGCTGC
55486 TGC
1 TGC
55489 CGCACCCGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (27 bp):
TGCTGGTGCTGCTGCCCCTGCTGCTGC
Found at i:56217 original size:38 final size:38
Alignment explanation
Indices: 56166--56241 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
56156 TTTGGCCGGT
*
56166 GGCCAAATGACCGGTGAATCGGTGCATTAAACATAACC
1 GGCCAAATGACCGGTGAATCGGTGCACTAAACATAACC
56204 GGCCAAATGACCGGTGAATCGGTGCACTAAACATAACC
1 GGCCAAATGACCGGTGAATCGGTGCACTAAACATAACC
56242 TTACAAAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.17
Consensus pattern (38 bp):
GGCCAAATGACCGGTGAATCGGTGCACTAAACATAACC
Found at i:57047 original size:9 final size:9
Alignment explanation
Indices: 57033--57057 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
57023 TAAATGGGGG
57033 TTTCTATCA
1 TTTCTATCA
57042 TTTCTATCA
1 TTTCTATCA
57051 TTTCTAT
1 TTTCTAT
57058 ATATTACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTCTATCA
Found at i:63183 original size:23 final size:23
Alignment explanation
Indices: 63157--63203 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
63147 TAAATCTCCA
63157 TAAGATGACTAGTTACCTTGACC
1 TAAGATGACTAGTTACCTTGACC
63180 TAAGATGACTAGTTACCTTGACC
1 TAAGATGACTAGTTACCTTGACC
63203 T
1 T
63204 TAGAAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (23 bp):
TAAGATGACTAGTTACCTTGACC
Found at i:63367 original size:16 final size:17
Alignment explanation
Indices: 63346--63378 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
63336 AAAATTGGTG
63346 AAATTT-TATAAATTTT
1 AAATTTATATAAATTTT
63362 AAATTTATATAAATTTT
1 AAATTTATATAAATTTT
63379 TTTATTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATTTATATAAATTTT
Found at i:73693 original size:112 final size:112
Alignment explanation
Indices: 73496--73714 Score: 402
Period size: 112 Copynumber: 2.0 Consensus size: 112
73486 TTGTTTGATC
**
73496 TTGTATATATAGCTTGAGTGCCAAGGAACAAGTTTCTTCATTTTAACATTTGGTTAATTGAATTG
1 TTGTATATATAGCTTGAGTGCCAAGGAACAAGTTTCTTCATTTTAACATTTGGCCAATTGAATTG
*
73561 TGAATGTTTTAGTAGCTTGATTAGGGTATAGAATATGTTGGCTCTTA
66 TGAATGTTTTAGTAGCTTGATTAGGGTATAGAATATATTGGCTCTTA
73608 TTGTATATATAGCTTGAGTGCCAAGGAACAAGTTTCTTCATTTTAACATTTGGCCAATTGAATTG
1 TTGTATATATAGCTTGAGTGCCAAGGAACAAGTTTCTTCATTTTAACATTTGGCCAATTGAATTG
*
73673 TGAATGTTTTAGTAGCTTGATTAGGGTTTAGAATATATTGGC
66 TGAATGTTTTAGTAGCTTGATTAGGGTATAGAATATATTGGC
73715 CTAGTCTTTC
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 103 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (112 bp):
TTGTATATATAGCTTGAGTGCCAAGGAACAAGTTTCTTCATTTTAACATTTGGCCAATTGAATTG
TGAATGTTTTAGTAGCTTGATTAGGGTATAGAATATATTGGCTCTTA
Found at i:84209 original size:13 final size:13
Alignment explanation
Indices: 84164--84211 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
84154 TCAATTAATT
84164 TAAAAATTTCTGGTA
1 TAAAAATTTCT--TA
* *
84179 TAAAAATTTTTTT
1 TAAAAATTTCTTA
84192 TAAAAATTTCTTA
1 TAAAAATTTCTTA
84205 -AAAAATT
1 TAAAAATT
84212 GCTAAAATCC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 7 0.24
13 12 0.41
15 10 0.34
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (13 bp):
TAAAAATTTCTTA
Found at i:86239 original size:121 final size:121
Alignment explanation
Indices: 86025--86385 Score: 722
Period size: 121 Copynumber: 3.0 Consensus size: 121
86015 CTTAATGACA
86025 CATAAATTAATGTCAAATGTCTTTCTTTTTCAGCACCAATACAACAACTAACTCTTTGGTTGATA
1 CATAAATTAATGTCAAATGTCTTTCTTTTTCAGCACCAATACAACAACTAACTCTTTGGTTGATA
86090 TGGGTTCAAGCACTAGCCTGCTGTAAAATGGACTCTGTAAAGGGTCTCATATGCTG
66 TGGGTTCAAGCACTAGCCTGCTGTAAAATGGACTCTGTAAAGGGTCTCATATGCTG
86146 CATAAATTAATGTCAAATGTCTTTCTTTTTCAGCACCAATACAACAACTAACTCTTTGGTTGATA
1 CATAAATTAATGTCAAATGTCTTTCTTTTTCAGCACCAATACAACAACTAACTCTTTGGTTGATA
86211 TGGGTTCAAGCACTAGCCTGCTGTAAAATGGACTCTGTAAAGGGTCTCATATGCTG
66 TGGGTTCAAGCACTAGCCTGCTGTAAAATGGACTCTGTAAAGGGTCTCATATGCTG
86267 CATAAATTAATGTCAAATGTCTTTCTTTTTCAGCACCAATACAACAACTAACTCTTTGGTTGATA
1 CATAAATTAATGTCAAATGTCTTTCTTTTTCAGCACCAATACAACAACTAACTCTTTGGTTGATA
86332 TGGGTTCAAGCACTAGCCTGCTGTAAAATGGACTCTGTAAAGGGTCTCATATGC
66 TGGGTTCAAGCACTAGCCTGCTGTAAAATGGACTCTGTAAAGGGTCTCATATGC
86386 CTTCAGCTTG
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 240 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (121 bp):
CATAAATTAATGTCAAATGTCTTTCTTTTTCAGCACCAATACAACAACTAACTCTTTGGTTGATA
TGGGTTCAAGCACTAGCCTGCTGTAAAATGGACTCTGTAAAGGGTCTCATATGCTG
Found at i:86617 original size:8 final size:8
Alignment explanation
Indices: 86612--86648 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
86602 TATCTTATCT
86612 TATTATTA
1 TATTATTA
*
86620 TAATA-TA
1 TATTATTA
86627 TA-TATTA
1 TATTATTA
86634 TATTATTA
1 TATTATTA
86642 TATTATT
1 TATTATT
86649 TTATATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 2 0.08
7 8 0.31
8 16 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATTA
Found at i:86919 original size:15 final size:16
Alignment explanation
Indices: 86894--86923 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
86884 AATAATTATT
86894 TTTAGATTATAATATA
1 TTTAGATTATAATATA
86910 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
86924 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:87939 original size:330 final size:328
Alignment explanation
Indices: 87277--91929 Score: 3251
Period size: 330 Copynumber: 14.1 Consensus size: 328
87267 ATACTTTACA
* * * * * *
87277 TCATCAAACCAAATCTCAGCAACATTGAATTTAAGAATTTGTTTTTACGAGTATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
87342 TTCGATTTAATTAAAAATTAATTTAGAAAAATAAGAAATATGATATTAAAAGCATGAAAAGTCCT
66 TTCGATTTAATTAGAAATTAATTCA-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * * *
87407 CCAATATTTTTGGCGTTCAA-CTA-A-ATA-CTTTTATAAGTATTTTAGACAAAAATTGAGGAGA
130 TCAATATTTTTGGCG-TCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA-A
* * * * * *
87468 A-ATTTTTCGTGTCAATTTTTACAAAATTTTAGCCGAAATAGTGTACTAACCATCACGGTTTTTG
193 ATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAACCATCACAGTTTTTT
* * * * * * * * * ** * *
87532 GCTAAAAATGCGTTCCGGGGACCTGCCTCAATTTTACATGATTTATGGCT-CTGAGACTACTTAA
255 GCTAAAAACGCGTTTC-AGGCCCCGGCTCAGTTTTGCATGATTTTTGG-TGCCAAGACTCCTT-G
87596 AATATC-TATAT
317 AATATCATATAT
* *
87607 TCATCTAATCAAATCTCAGCCATATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
87672 TTCGATTTAATTAGAAATTAATTCAAAAAATAGGAAAAACAATATTAGAAA-CGTCAAAAGCCCT
66 TTCGATTTAATTAGAAATTAATTCAAAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGTCCT
** *
87736 TCAACCTTTTTGGCGTCAATATATATATATTTTTTATGAGTATTTTAGCAAAAAATTGAGGAAAT
130 TCAATATTTTTGGCGTCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAT
* *
87801 ATCTTTCGGGTCAATTTTTAC-AAACTTTAGCCGAAATCGTGT-A-CATCACAGTTTTTTGCTAA
195 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCACAGTTTTTTGCTAA
* * * *** * * *
87863 AAAAGCGTTTTAGGTCCTAACTCAGTTTTGCATAACTTTTGGTGCCAAGAATCCTTGAGATATCC
260 AAACGCGTTTCAGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGA-ATAT-C
87928 ATACCATAT
323 AT---ATAT
* *
87937 TCATCTAATCAAATCTTAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
88002 TTCGATTTAATTAGAAATTAATTCAGACTAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTCA-A-AAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * *
88067 TCCAATATTTTTGGAGTTAA-AT-TATATATATTTTATGAGTATTTTATCCAAAAATTGAGGAAA
129 TTCAATATTTTTGGCGTCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * * * *
88130 AAT-TTGTCGGAT-AATTTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCAC-GGTTT
194 TATCTT-TCGGGTCAA--TTTTTGCAAAATTTTAGCCGAAATCGTG---TAACCATCACAGTTTT
* ** * *
88192 TTGCCTAAAAACGCGTTTCGGGACCCCGGCTCAGTTTTGCATGATTTTTAATGTCGAGACTCCTT
253 TTG-CTAAAAACGCGTTTCAGG-CCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTT
*
88257 GAAATATC-TATAC
316 G-AATATCATATAT
* * * * * * * *
88270 TCATATAATTAAATCTTAGCCACATAGCATTTATGGATTTCTTTTTACGAGCATTTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* ** *
88335 TTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAAAATTGTGAAAAGCCCT
66 TTCGATTTAATTAGAAATTAATTC-AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
** * * * *
88400 TCAATATTTTTGGCGTTGA-AT-TATATATTTTTTATGAGTATTGTGGCTAAAAATTCAGGAAAT
130 TCAATATTTTTGGCGTCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAT
** * *
88463 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGATTTTGGCT
195 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCA-CA-GTTTTTTGCT
* * * * ** * *
88528 AAAAACGCGTTCCAGGGCCTGGTTCAGTTTTGCATG-TTTTTTTTGCTTCGAGATCTCATTGAA-
258 AAAAACGCGTTTCAGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGC--CAAGA-CTCCTTGAAT
88591 AT-ATATA-
320 ATCATATAT
* * * * ** * *
88598 T-ATAT-AT--ATTCT-AACCA-ATT---TCTAACCA-TT-TTTTTACAAGCATCTG-ATCATGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
88651 TTCGATTTAATTA-AAAGTTACTTCGGAAAAAAATAGGGAAAACGATATTAGAAGCGTGAAAAGC
66 TTCGATTTAATTAGAAA-TTAATTC---AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT
* ** * * * *
88715 CCTTCAATACTTTTGGTATTGAAT-TATATATA--TTTTATGAGTATTGT-GGCTAAAATTGAGG
127 CCTTCAATATTTTTGG-CGTCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGG
* * * * ** * *
88776 AAAAATATTTCGGGTCAATATTTGCAAAATATTAGATGAAATCGTGT-ACTATCACGGTTTTTTT
191 AAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCACAG----TTT
* * *
88840 TTTGCTAAAAACGCG-TTCTGCGCCCCGGATCAGTTTTGCATGATTTTTGGTGCCAAGACTTCTT
252 TTTGCTAAAAACGCGTTTCAG-GCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTT
*
88904 GAAAAATC-TATAT
316 G-AATATCATATAT
* * *
88917 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTCTTTTTATGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * **
88982 TTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATACTAGAAGCGTAAAAAAAC
66 TTCGATTTAATTAGAAATTAATTC---AAAAAATATGAAAAACGATATTAAAAGCGT-GAAAAGT
* * *
89047 CCTTCAATATTTTTGGCGTTAA-ATTATATATAATTTTTTATTGAGTATTTTAGCCAAGACTTGA
127 CCTTCAATATTTTTGGCGTCAATA-TATATAT-ATTTTTTA-TGAGTATTTTAGCCAAAAATTGA
* * * * *
89111 GGAAATATCGTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTAATGATCATCACTGCT
189 GGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-A--ACCATCACAGTT
* ** * * ** *
89176 TTTGGCTAAAAACGTATTCCAGGACCCCGAG-TCAGTTTTGCATGATTCTTGACGCCAAGAGTCC
251 TTTTGCTAAAAACGCGTTTCAGG-CCCCG-GCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCC
89240 TTGAGATATCCATAT-T
314 TTGA-ATAT-CATATAT
* * *
89256 T-ATCTAATCAAATCTCATCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
89320 TTCGATTTAATTAGAAATTAATTCAGAAAAAAAATGAAAAACGATATGAAATGTGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTC--AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * * * * *
89385 TCCAATCTTTTTGGCGCTAAAAAAATTATATATATTTCATGATTATTTTAGCCAAAAATTGAGAG
129 TTCAATATTTTTGGCG-TCAATATA-TATATATTTTTTATGAGTATTTTAGCCAAAAATTGAG-G
* * * *** * *
89450 AAAAAT-TTTCGAGTAAATTTTTGCAAAATTTTAATAGAAATCGTGTACTAAGCATCACGGTTAT
191 AAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAACCATCACAGTT-T
* * ** ** * * *
89514 TTTG-TTAAAACGCGTTTCGAGGCCACAACTCAGTTTTGCATGATTTTTGACGTCGAGACTTCTT
252 TTTGCTAAAAACGCGTTTC-AGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTT
89578 GAAATATC-TATAT
316 G-AATATCATATAT
* *
89591 TCATCAAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
89656 ATCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTCCT
66 TTCGATTTAATTAGAAATTAATTCA-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* ** * * *
89721 CCAATATTTTTGGATTTGAAT-TATATATA--TTTTATGAGTATGTTAGCCAAAAATTGAGAAAA
130 TCAATATTTTTGG-CGTCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAG-GAA
* * * *
89783 ATAT-TTT-TGGT-AATTTTTTGC-AAATATTAG-C-----C--G-AA--ATCACGGTTTTTGGC
193 ATATCTTTCGGGTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCACAGTTTTTTGC
* ** * * * ** * * *
89833 TAAAAAAGCG-TTCAGGGAAACCAGTTCAGTGTTATATGATTTTTGCTGGCGAGACTCCTTGAAC
257 TAAAAACGCGTTTCA-GG-CCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAA-
89897 TATC-TATAT
319 TATCATATAT
* * * * * * * *** * * **
89906 TTATCTAAACGACA-CTTAGCTAAATTGAATTTAAGGATTTG-TAAAACAATCATCTGAATCACG
1 TCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * * *
89969 TTTCGATTTAATTAGAAATTAATTTGGAAAATAATAGGAAAAACGATATTAGAAGCATGAAAA-A
65 TTTCGATTTAATTAGAAATTAA-TT-CAAAA-AATATGAAAAACGATATTAAAAGCGTGAAAAGT
* * * * * * *
90033 CCTTCAATCTTTTTGGCGTTGAAT-TATATA-A-TTTTTATGATTATTGTGGCTATAAATTGAGG
127 CCTTCAATATTTTTGGCG-TCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGG
* * * * * * * *
90095 AAATAACTTTCGGG-AAAATTTTGCAAAATATTAGCTGAAATCGTGTAA-TAGTAATCACGGTTT
191 AAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCA-TCA-CA-GTTTT
* ** ** * * * *
90158 TTGACTAAAAACGCATTTTGTGGCCCATGCTAAGTTTTCCATGATTTTTGGCGCCAAGACTCTTT
253 TTG-CTAAAAACGC-GTTTCAGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTT
90223 GAGATATCA-ATAT
316 GA-ATATCATATAT
** * *
90236 TCATCTAATCAAATCTCAGCTTCATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
90301 TTCGATTTAATTAGAAATTAATTTAGAAAATATGAAAGAACGATATTAAAAGCGTGAAAAGTCC-
66 TTCGATTTAATTAGAAATTAATTCAAAAAATATGAAA-AACGATATTAAAAGCGTGAAAAGTCCT
* * * *
90365 TCTAACT-TTTTTGGCGTTCAAT-TATATATA--TTTTATGAGTATTGTGGCTAAAAATTGAGAA
130 TC-AA-TATTTTTGGCG-TCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA
* * ** * *
90426 AAAATATTTTAGGTCAACTTTTACAAAATTTTAGCCGAAATCGTGT-ACCATCACAGTTTTTTGG
192 AATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCACAGTTTTTT-G
* ** * * * ** *
90490 CTGAAAACGCGTTCTGGGGCCCCGGGTTAGTTTTGCATGATTTTCGGTGGTAAAACTCCTTGTAA
256 CTAAAAACGCGTT-TCAGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTG-AA
90555 TATC-TATAT
319 TATCATATAT
* * * * *
90564 TCATCTAA-CGAAATCTCAACCACATTGAATTTAAGGATTTGTTTATACGAGCATCTAAATCTTT
1 TCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * *
90628 TTTCGATTTAATTAGAAATTAATTTAGAAAATATGAAAAACGATATCAAAAGCGTGAAAAGTCCT
65 TTTCGATTTAATTAGAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * * *
90693 CCAATCTTTTTGGTGTTCAATTATATATATATATATATATATATATATATATGAGTATTGTGGCT
130 TCAATATTTTTGGCG-TC--------A-ATATATATATAT-T-T-T-T-TATGAGTATTTTAGC-
* * * * ** * *
90758 AAAAAATTGA-GAAAAATATTTCAGGTCAGCTTTTACAAAATTTTAGTCGAAATCGTGT-ACCAT
179 CAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCAT
* * * * * * *
90821 CACGGTTTTTTG-GAAAAACGCGTTCCGGGGCCCCGGGTCAGTTTTGCATGATTTTCGGTGGCAA
244 CACAGTTTTTTGCTAAAAACGCGTTTC-AGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAA
*
90885 AACTCCTTG-------TA-A-
308 GACTCCTTGAATATCATATAT
* * * *
90897 T-ATCT-AT---AT-T------CATTGGATTTAAGGA-TGGTTTTTATGAGCATTTGAATCATGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * ** * *
90949 TTCGATTTAATTAGAAATTAATTTGAAAAGAAATAGGAAAAACGATATTTGAAGCATGAGAAG-C
66 TTCGATTTAATTAGAAATTAA-TT-CAAA-AAATATGAAAAACGATATTAAAAGCGTGAAAAGTC
* * * * * * * **
91013 CTTTGAATCTTTTTGGCGTTGAAT-T-T-TATACTTTTTATGAGTATTGTGGCCAAAAATTTAAA
128 C-TTCAATATTTTTGGCG-TCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGG
* * * * *
91075 AAAAATATTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAATCGTAT-ACCATCACGGGTTTTTG
191 AAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCAC-AGTTTTTT
* * * * * * *
91138 GCTAAAAACGTGTTCCGGGGCCCCAGATCAGTTTTGCATGATTTTTTGTGCCAAGACTCCTTAAA
255 GCTAAAAACGCGTTTC-AGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTT-GA
91203 ATAT-ATCTATAT
318 ATATCA--TATAT
* * * * * *
91215 TCATCTAACCAAATCTCAGGCACATTGTATTTAAGGATTTGTTTTCACGAGTATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
91280 TTCGACTTAATCAAAAATTAATTTGGAAGTAAAATAGGAAAAACGATATTAGAAA-CGTGAAAAA
66 TTCGATTTAATTAGAAATTAA-TT-CAA--AAAATATGAAAAACGATATTA-AAAGCGTG-AAAA
* * * ** * * ** * *
91344 GACTTTCAATTTTTTTTGGCGTTGA-A-CTATATATTTTGTATGAGTATTTTCTCTAGAAATTGA
125 GTCCTTCAA-TATTTTTGGCGTCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGA
* * * * * *
91407 GGAAATGTCTTTCGGCTCATTTTTTGTAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTT
189 GGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAACCATCACAGTT
** * * * * * * *
91472 TTCAGCTAAAAATGCATTCCGGGGCCCGGCTTAGTTTTGTATGATTTTTGGTGCCAAGACTCCTT
251 TTTTGCTAAAAACGCGTTTCAGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTT
91537 GAAATATC-TATAT
316 G-AATATCATATAT
* * * * * * *
91550 TCATATAACCAAATCTCAACCACATTGGATTTAAAGATTCG-TTTTACGAGCATTTGAATCTGGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * * * *
91614 TTCGATTTAATAAGAAACTAGTTCAGAAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCC
66 TTCGATTTAATTAGAAATTAATTC---AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTC
*** * * * * *
91679 CTTCAATATTTTTTATGTCGA-AT-TATATATTTTTTCTGAGTATTTTATCCAAAAATTAAGAAA
128 CTTCAATATTTTTGGCGTCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAA
* *
91742 ATATCTTTCGGGTCATTTTTTGCAAAATTTTAGCTGAAATCGTGTACTGACCATCACCATTTTTT
193 ATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA---ACCATCA-CA------
* * ** ** * * * * * *
91807 TTTTTTTGGCTAAAAACGCATTCTGGGGCTACGGCTCTGTTTTGCATTATTTTTTGCGACGAGAC
248 GTTTTTT-GCTAAAAACGCGTT-TCAGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGAC
*
91872 TCCTTGAAATATC-TCTAT
311 TCCTTG-AATATCATATAT
* * *
91890 TTATCTAATTAAATCTCAACCACATTGGATTTAAGGATTT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTT
91930 AATTAGAAAT
Statistics
Matches: 3493, Mismatches: 597, Indels: 456
0.77 0.13 0.10
Matches are distributed among these distances:
305 31 0.01
306 48 0.01
307 53 0.02
308 1 0.00
309 1 0.00
310 1 0.00
311 4 0.00
312 1 0.00
313 2 0.00
314 56 0.02
315 154 0.04
316 80 0.02
317 77 0.02
318 104 0.03
319 20 0.01
320 51 0.01
321 19 0.01
322 7 0.00
323 53 0.02
324 12 0.00
325 39 0.01
326 30 0.01
327 50 0.01
328 190 0.05
329 118 0.03
330 420 0.12
331 374 0.11
332 274 0.08
333 136 0.04
334 100 0.03
335 117 0.03
336 234 0.07
337 188 0.05
338 190 0.05
339 27 0.01
340 83 0.02
341 8 0.00
342 55 0.02
343 2 0.00
344 74 0.02
345 9 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (328 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTT
CAATATTTTTGGCGTCAATATATATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATA
TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCACAGTTTTTTGCTAAA
AACGCGTTTCAGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAATATCATA
TAT
Found at i:90721 original size:2 final size:2
Alignment explanation
Indices: 90714--90744 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
90704 GGTGTTCAAT
90714 TA 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 TA T
90745 GAGTATTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:91771 original size:331 final size:332
Alignment explanation
Indices: 90907--91798 Score: 987
Period size: 331 Copynumber: 2.7 Consensus size: 332
90897 TATCTATATT
* * *
90907 CATTGGATTTAAGGA-TGGTTTTTATGAGCATTTGAATCATGTTTCGATTTAATTAGAAATTAAT
1 CATTGGATTTAAGGATTCG-TTTTACGAGCATTTGAATC-TGTTTCGATTTAATAAGAAATTAAT
* * * * * * * *
90971 TTGAAAAGAAATAGGAAAAACGATATTTGAAGCATGAGAAGCCTTTGAATCTTTTTGGCGTTGAA
64 TAGAAAA-AAATAGGAAAAACGATATTAGAAGCGTAAAAAGCCTTTCAATATTTTTTGCGTTGAA
* * * ** * * *
91036 TTTTATACTTTTTATGAGTATTGTGGCCAAAAATTTAA-AAAAAATATTTCGGGTCAATTTTTGC
128 TTATATATTTTTTATGAGTATTTTATCCAAAAA-TTAAGAAAATATCTTTCGGGTCATTTTTTGC
* ** **
91100 AAAA-TTTAGCCGAAATC--GTA-TACCATCACGGGTTTTTGGCTAAAAACGTGTTCCGGGGCCC
192 AAAATTTTAGCTGAAATCGTGTACTACCATCACGGGTTTTCAGCTAAAAACGCATTCCGGGGCCC
* *
91161 CAGATCAGTTTTGCATGATTTTTTGTGCCAAGACTCCTTAAAATATATCTATATTCATCTAACCA
257 CAGATCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTAAAATATATCTATATTCATATAACCA
**
91226 AATCTCAGGCA
322 AATCTCAACCA
* * * * * *
91237 CATTGTATTTAAGGATTTGTTTTCACGAGTATCTAAATCTTGTTTCGACTTAATCAA-AAATTAA
1 CATTGGATTTAAGGATTCGTTTT-ACGAGCATTTGAATC-TGTTTCGATTTAAT-AAGAAATTAA
* * * * *
91301 TTTGGAAGTAAAATAGGAAAAACGATATTAGAAACGTGAAAAAGACTTTCAATTTTTTTTGGCGT
63 -TTAGAA-AAAAATAGGAAAAACGATATTAGAAGCGT-AAAAAGCCTTTCAATATTTTTT-GCGT
* * * * * * * * *
91366 TGAACTATATATTTTGTATGAGTATTTTCTCTAGAAATTGAGGAAATGTCTTTCGGCTCATTTTT
124 TGAATTATATATTTTTTATGAGTATTTTATCCAAAAATTAAGAAAATATCTTTCGGGTCATTTTT
* *
91431 TGTAAAATTTTAGCTGAAATCGTGTACTAACCATCAC-GGTTTTCAGCTAAAAATGCATTCCGGG
189 TGCAAAATTTTAGCTGAAATCGTGTACT-ACCATCACGGGTTTTCAGCTAAAAACGCATTCCGGG
* * * * *
91495 G-CCCGGCTTAGTTTTGTATGATTTTTGGTGCCAAGACTCCTT-GAA-ATATCTATATTCATATA
253 GCCCCAGATCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTAAAATATATCTATATTCATATA
91557 ACCAAATCTCAACCA
318 ACCAAATCTCAACCA
* * *
91572 CATTGGATTTAAAGATTCGTTTTACGAGCATTTGAATCTGGTTTCGATTTAATAAGAAACTAGTT
1 CATTGGATTTAAGGATTCGTTTTACGAGCATTTGAATCT-GTTTCGATTTAATAAGAAATTAATT
* * * ** *
91637 CAGAAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATATTTTTTATGTCGAAT
65 -AGAAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAAGCCTTTCAATATTTTTTGCGTTGAAT
*
91702 TATATATTTTTTCTGAGTATTTTATCCAAAAATTAAGAAAATATCTTTCGGGTCATTTTTTGCAA
129 TATATATTTTTTATGAGTATTTTATCCAAAAATTAAGAAAATATCTTTCGGGTCATTTTTTGCAA
91767 AATTTTAGCTGAAATCGTGTACTGACCATCAC
194 AATTTTAGCTGAAATCGTGTACT-ACCATCAC
91799 CATTTTTTTT
Statistics
Matches: 462, Mismatches: 84, Indels: 31
0.80 0.15 0.05
Matches are distributed among these distances:
330 18 0.04
331 124 0.27
332 48 0.10
333 51 0.11
334 87 0.19
335 61 0.13
336 2 0.00
337 39 0.08
338 24 0.05
339 8 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (332 bp):
CATTGGATTTAAGGATTCGTTTTACGAGCATTTGAATCTGTTTCGATTTAATAAGAAATTAATTA
GAAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAAGCCTTTCAATATTTTTTGCGTTGAATTA
TATATTTTTTATGAGTATTTTATCCAAAAATTAAGAAAATATCTTTCGGGTCATTTTTTGCAAAA
TTTTAGCTGAAATCGTGTACTACCATCACGGGTTTTCAGCTAAAAACGCATTCCGGGGCCCCAGA
TCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTAAAATATATCTATATTCATATAACCAAATC
TCAACCA
Found at i:93112 original size:13 final size:13
Alignment explanation
Indices: 93094--93118 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93084 ATGGCCGAGT
93094 TTTATTATTATTA
1 TTTATTATTATTA
93107 TTTATTATTATT
1 TTTATTATTATT
93119 TCCTCGTAAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:95958 original size:18 final size:18
Alignment explanation
Indices: 95918--95963 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
95908 TTTGAACTCA
*
95918 TTATTTAGTATTTAAAAT
1 TTATTTATTATTTAAAAT
* **
95936 ATATTTATTATTTATTAT
1 TTATTTATTATTTAAAAT
95954 TTATTTATTA
1 TTATTTATTA
95964 ATATATATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATTTATTATTTAAAAT
Found at i:96889 original size:15 final size:15
Alignment explanation
Indices: 96871--96901 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
96861 TAAATTGGTA
96871 ACGATTCAATTCATG
1 ACGATTCAATTCATG
96886 ACGATTCAATTCATG
1 ACGATTCAATTCATG
96901 A
1 A
96902 TTGAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (15 bp):
ACGATTCAATTCATG
Found at i:114054 original size:31 final size:32
Alignment explanation
Indices: 114019--114099 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 32
114009 TATGATGCTG
* * *
114019 ACGTGGCATGCCACGTCAGA-TGAAAATTGCC
1 ACGTGGCATGCCATGTCAAACCGAAAATTGCC
*
114050 ACGTGGCATGCCATGT-AAACCGAAAATTGCG
1 ACGTGGCATGCCATGTCAAACCGAAAATTGCC
*
114081 ACGGGGCATGCCATGTCAA
1 ACGTGGCATGCCATGTCAA
114100 CATAAAAAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.05
31 39 0.91
32 2 0.05
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.19
Consensus pattern (32 bp):
ACGTGGCATGCCATGTCAAACCGAAAATTGCC
Found at i:119421 original size:17 final size:16
Alignment explanation
Indices: 119395--119446 Score: 70
Period size: 17 Copynumber: 3.2 Consensus size: 16
119385 CCGGCAAAAA
119395 TATTATTTTATAGAGAT
1 TATTATTTTATAGAG-T
*
119412 TATTAATTTATAGAG-
1 TATTATTTTATAGAGT
119427 TATTATTTTATAGAGGT
1 TATTATTTTATAGA-GT
119444 TAT
1 TAT
119447 ATTGTATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 13 0.42
16 1 0.03
17 17 0.55
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (16 bp):
TATTATTTTATAGAGT
Found at i:119436 original size:15 final size:16
Alignment explanation
Indices: 119394--119441 Score: 71
Period size: 15 Copynumber: 3.0 Consensus size: 16
119384 ACCGGCAAAA
119394 ATATTATTTTATAGAG
1 ATATTATTTTATAGAG
*
119410 ATTATTAATTTATAGAG
1 A-TATTATTTTATAGAG
119427 -TATTATTTTATAGAG
1 ATATTATTTTATAGAG
119442 GTTATATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 14 0.48
16 1 0.03
17 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
ATATTATTTTATAGAG
Found at i:123125 original size:30 final size:31
Alignment explanation
Indices: 123089--123171 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 31
123079 TGTCACCAAA
*
123089 ATTTTAACAGTTTAGGGGTAAAACA-TCAAG
1 ATTTTAAGAGTTTAGGGGTAAAACATTCAAG
* *
123119 ATTTTAAGAGTTTAGGGGAAAAACATTCAGG
1 ATTTTAAGAGTTTAGGGGTAAAACATTCAAG
*
123150 GTTTTAAGAGTTTA-GGGTAAAA
1 ATTTTAAGAGTTTAGGGGTAAAA
123172 TGATTAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 30 0.64
31 17 0.36
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (31 bp):
ATTTTAAGAGTTTAGGGGTAAAACATTCAAG
Found at i:123158 original size:31 final size:30
Alignment explanation
Indices: 123089--123171 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 30
123079 TGTCACCAAA
* *
123089 ATTTTAACAGTTTAGGGGTAAAACATCAAG
1 ATTTTAAGAGTTTAGGGGAAAAACATCAAG
*
123119 ATTTTAAGAGTTTAGGGGAAAAACATTCAGG
1 ATTTTAAGAGTTTAGGGGAAAAACA-TCAAG
* *
123150 GTTTTAAGAGTTTAGGGTAAAA
1 ATTTTAAGAGTTTAGGGGAAAA
123172 TGATTAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 23 0.49
31 24 0.51
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (30 bp):
ATTTTAAGAGTTTAGGGGAAAAACATCAAG
Found at i:123391 original size:16 final size:16
Alignment explanation
Indices: 123355--123489 Score: 143
Period size: 16 Copynumber: 8.5 Consensus size: 16
123345 GGACTCGGGA
*
123355 GGGTTCGGGTA-CTTC
1 GGGTTCGGGTATTTTC
123370 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
* **
123386 GTGTTCGGGT-TAAGTC
1 GGGTTCGGGTAT-TTTC
123402 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
**
123418 GGGTTCGGGT-TAAGTC
1 GGGTTCGGGTAT-TTTC
123434 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
* *
123450 GGGCTCGGGT-TATGTC
1 GGGTTCGGGTAT-TTTC
123466 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
123482 GGGTTCGG
1 GGGTTCGG
123490 TCTCAGGTAG
Statistics
Matches: 98, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
15 14 0.14
16 81 0.83
17 3 0.03
ACGTcount: A:0.07, C:0.14, G:0.41, T:0.38
Consensus pattern (16 bp):
GGGTTCGGGTATTTTC
Found at i:123407 original size:32 final size:32
Alignment explanation
Indices: 123355--123489 Score: 218
Period size: 32 Copynumber: 4.2 Consensus size: 32
123345 GGACTCGGGA
**
123355 GGGTTCGGG-TACTTCGGGTTCGGGTATTTTC
1 GGGTTCGGGTTAAGTCGGGTTCGGGTATTTTC
*
123386 GTGTTCGGGTTAAGTCGGGTTCGGGTATTTTC
1 GGGTTCGGGTTAAGTCGGGTTCGGGTATTTTC
123418 GGGTTCGGGTTAAGTCGGGTTCGGGTATTTTC
1 GGGTTCGGGTTAAGTCGGGTTCGGGTATTTTC
* *
123450 GGGCTCGGGTTATGTCGGGTTCGGGTATTTTC
1 GGGTTCGGGTTAAGTCGGGTTCGGGTATTTTC
123482 GGGTTCGG
1 GGGTTCGG
123490 TCTCAGGTAG
Statistics
Matches: 96, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
31 8 0.08
32 88 0.92
ACGTcount: A:0.07, C:0.14, G:0.41, T:0.38
Consensus pattern (32 bp):
GGGTTCGGGTTAAGTCGGGTTCGGGTATTTTC
Found at i:123686 original size:13 final size:12
Alignment explanation
Indices: 123663--123716 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 12
123653 AAGTTTATTG
123663 ATAATATATAAT
1 ATAATATATAAT
123675 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
123688 ATAACAT-TATT
1 ATAATATATAAT
123699 ATCAATATATATAT
1 AT-AATATATA-AT
123713 ATAA
1 ATAA
123717 AGATTGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
11 5 0.15
12 11 0.32
13 15 0.44
14 3 0.09
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAATATATAAT
Done.