Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010803.1 Corchorus capsularis cultivar CVL-1 contig10824, 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: 78304
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:982 original size:30 final size:30
Alignment explanation
Indices: 946--1005 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
936 CAAAGGATCA
*
946 AATGGCATCTTTGGTGCGATTCCTCCATCC
1 AATGGCATCTTTGCTGCGATTCCTCCATCC
976 AATGGCATCTTTGCTGCGATTCCTCCATCC
1 AATGGCATCTTTGCTGCGATTCCTCCATCC
1006 TTTGATGTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (30 bp):
AATGGCATCTTTGCTGCGATTCCTCCATCC
Found at i:1673 original size:65 final size:65
Alignment explanation
Indices: 1544--1674 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
1534 GATGAATGTC
*
1544 CAGTAGTGCTATGTATGCTTCTATTGTATGCAAATTCAACATGAGGTAGACAATCCTTCCAAGTT
1 CAGTAGTGCTATGTATGCTTCTATTGTATGCAAATTCAACATGAGGTAGACAATACTTCCAAGTT
* *
1609 CAGTAGTGCTGTGTATGCTTTTATTGTATGCAAATTCAACATGAGGTAGACAATAC-TCCAAAGT
1 CAGTAGTGCTATGTATGCTTCTATTGTATGCAAATTCAACATGAGGTAGACAATACTTCC-AAGT
1673 T
65 T
1674 C
1 C
1675 TTAAGTTCTT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 3 0.05
65 59 0.95
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (65 bp):
CAGTAGTGCTATGTATGCTTCTATTGTATGCAAATTCAACATGAGGTAGACAATACTTCCAAGTT
Found at i:5527 original size:14 final size:14
Alignment explanation
Indices: 5504--5533 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5494 CTTGATTGTG
*
5504 CTCTCGTATTTGCA
1 CTCTCATATTTGCA
5518 CTCTCATATTTGCA
1 CTCTCATATTTGCA
5532 CT
1 CT
5534 TAATTCCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.30, G:0.10, T:0.43
Consensus pattern (14 bp):
CTCTCATATTTGCA
Found at i:8799 original size:10 final size:10
Alignment explanation
Indices: 8786--8811 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
8776 AAATCTCGAT
8786 ATATCCGTAA
1 ATATCCGTAA
8796 ATATCCGTAA
1 ATATCCGTAA
8806 ATATCC
1 ATATCC
8812 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:9393 original size:3 final size:3
Alignment explanation
Indices: 9374--9418 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
9364 GCTCATGGAA
*
9374 GAT G-T GAT GAT GCT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
9419 GGGGAAATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:10512 original size:13 final size:12
Alignment explanation
Indices: 10494--10523 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
10484 CATCGATACC
10494 TCGATATATCCG
1 TCGATATATCCG
10506 TTCGATATATCCG
1 -TCGATATATCCG
10519 TCGAT
1 TCGAT
10524 GCCTGATCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:10926 original size:16 final size:16
Alignment explanation
Indices: 10907--10997 Score: 101
Period size: 16 Copynumber: 5.7 Consensus size: 16
10897 TTTTCATAAA
10907 TTTTCGGATTCGGGTT
1 TTTTCGGATTCGGGTT
* * *
10923 TTTTCGGATTTGAGCT
1 TTTTCGGATTCGGGTT
*
10939 TTTTCGGGTTCGGGTT
1 TTTTCGGATTCGGGTT
* **
10955 TTTTCGGATTTGAATT
1 TTTTCGGATTCGGGTT
* *
10971 TTTTCGGGTTCGGATT
1 TTTTCGGATTCGGGTT
10987 TTTTCGGATTC
1 TTTTCGGATTC
10998 AAGTTCAGAC
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 60 1.00
ACGTcount: A:0.09, C:0.12, G:0.27, T:0.52
Consensus pattern (16 bp):
TTTTCGGATTCGGGTT
Found at i:10951 original size:32 final size:32
Alignment explanation
Indices: 10907--10996 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
10897 TTTTCATAAA
* *
10907 TTTTCGGATTCGGGTTTTTTCGGATTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGATTTGAACT
*
10939 TTTTCGGGTTCGGGTTTTTTCGGATTTGAATT
1 TTTTCGGGTTCGGGTTTTTTCGGATTTGAACT
*
10971 TTTTCGGGTTCGGATTTTTTCGGATT
1 TTTTCGGGTTCGGGTTTTTTCGGATT
10997 CAAGTTCAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.09, C:0.11, G:0.28, T:0.52
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCGGATTTGAACT
Found at i:12256 original size:64 final size:64
Alignment explanation
Indices: 12187--12316 Score: 233
Period size: 64 Copynumber: 2.0 Consensus size: 64
12177 GGAAGTAGAA
*
12187 AAAAAGGTAATAGTGACTAAATGGGAAAATGTTGTGAATGGATGCAATATCTTATTCTATCTTC
1 AAAAAGGTAATAGTAACTAAATGGGAAAATGTTGTGAATGGATGCAATATCTTATTCTATCTTC
**
12251 AAAAAGGTAATAGTAACTTGATGGGAAAATGTTGTGAATGGATGCAATATCTTATTCTATCTTC
1 AAAAAGGTAATAGTAACTAAATGGGAAAATGTTGTGAATGGATGCAATATCTTATTCTATCTTC
12315 AA
1 AA
12317 CTTTCTTGAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (64 bp):
AAAAAGGTAATAGTAACTAAATGGGAAAATGTTGTGAATGGATGCAATATCTTATTCTATCTTC
Found at i:16666 original size:70 final size:70
Alignment explanation
Indices: 16553--16695 Score: 241
Period size: 70 Copynumber: 2.0 Consensus size: 70
16543 TGTGGCTAGT
*
16553 TGACTCTTCTACTTAATGCAGATAATATACACACTTAGCATGATTCCCAATCTACAATAAGAGTT
1 TGACTCTTCTACTTAATGCAGATAATATACACACTTAGCATGATTCCCAATCTACAATAAGAGTC
16618 GAGTG
66 GAGTG
* ** *
16623 TGACTCTTCTGCTTAATGCAGATTCTATACACACTTAGCATGATTCCCAATCTACAATTAGAGTC
1 TGACTCTTCTACTTAATGCAGATAATATACACACTTAGCATGATTCCCAATCTACAATAAGAGTC
16688 GAGTG
66 GAGTG
16693 TGA
1 TGA
16696 AAAAAACATC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (70 bp):
TGACTCTTCTACTTAATGCAGATAATATACACACTTAGCATGATTCCCAATCTACAATAAGAGTC
GAGTG
Found at i:53079 original size:35 final size:35
Alignment explanation
Indices: 52979--53452 Score: 359
Period size: 35 Copynumber: 13.3 Consensus size: 35
52969 CCATTTGATT
* *
52979 ATTTACTTAATTACACCGAATTAAGCTAATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
**
53014 ATTTACTTAATTACACCGAATTAAACTGATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
**
53049 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
* * * * * *
53084 AATTACTTAATTTAATTACC-AATTTACTTAATTGCACCG
1 ATTTACTTAA-TT-A-CACCGAATTAAGTTGATT--ACTG
* * * * * * *
53123 AATTAAGTTGATT--ACCAAATT-ACTTAATTACACCG
1 -ATTTACTTAATTACACCGAATTAAGTTGATT--ACTG
* * * ** * * **
53158 AATTAAGTTGATTAC-CAAATTACTTAATTTAATTACCA
1 -ATTTACTTAATTACACCGA--A-TTAAGTTGATTACTG
* **
53196 ATTTACTTAATTACACCGAATCAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
* *
53231 ATTCACTTAATTACACCGAATTAAGTTAATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
53266 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
* *
53301 ATTTACCTAATTTCACCGAATTAAGTTGATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
* * *
53336 ATCTACTTAATCACACCGAATTAAGTT-ATTTACTA
1 ATTTACTTAATTACACCGAATTAAGTTGA-TTACTG
* * * * *
53371 AATCACTTATTTACACCGAATTAAGCTGATTA-TCA
1 ATTTACTTAATTACACCGAATTAAGTTGATTACT-G
**
53406 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
*
53441 AATTACTTAATT
1 ATTTACTTAATT
53453 TAATTATCAA
Statistics
Matches: 367, Mismatches: 54, Indels: 36
0.80 0.12 0.08
Matches are distributed among these distances:
34 2 0.01
35 303 0.83
36 11 0.03
37 22 0.06
38 9 0.02
39 7 0.02
40 13 0.04
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (35 bp):
ATTTACTTAATTACACCGAATTAAGTTGATTACTG
Found at i:53101 original size:21 final size:21
Alignment explanation
Indices: 53077--53116 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53067 AATTAAGTTG
53077 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
53098 ATTACCAATTTACTTAATT
1 ATTACCAAATTACTTAATT
53117 GCACCGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:53109 original size:91 final size:91
Alignment explanation
Indices: 53005--53497 Score: 474
Period size: 91 Copynumber: 5.5 Consensus size: 91
52995 CGAATTAAGC
** * **
53005 TAATTACTGATTTACTTAATTACACCGAATTAAACTGATTACTGATTTACTTAATTACACCGAAT
1 TAATTACCAATTTACTTAATTACACCGAATTAAGCTGATTACCAATTTACTTAATTACACCGAAT
53070 TAAGTTGATTACCAAATTACTTAATT
66 TAAGTTGATTACCAAATTACTTAATT
* * *
53096 TAATTACCAATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAAT
1 TAATTACCAATTTACTTAATTACACCGAATTAAGCTGATTACCAATTTACTTAATTACACCGAAT
53161 TAAGTTGATTACCAAATTACTTAATT
66 TAAGTTGATTACCAAATTACTTAATT
* * *
53187 TAATTACCAATTTACTTAATTACACCGAATCAAGTTGATTACCAATTCACTTAATTACACCGAAT
1 TAATTACCAATTTACTTAATTACACCGAATTAAGCTGATTACCAATTTACTTAATTACACCGAAT
* ** *
53252 TAAGTTAATTACTGATTTACTTAA-T
66 TAAGTTGATTACCAAATTACTTAATT
* * * * * * * * * * *
53277 T-A-CACCGAATTAAGTTGATT--ACTG-ATTTACCTAATTTCACCGAATTAAGTTGATTACTGA
1 TAATTACC-AATTTACTTAATTACACCGAATTAAGCTGA-TT-ACC-AATTTACTTAATTAC--A
* * * * * * *
53337 TCTACTTAA--TCA-CACCGAATTAAGTT-ATT
60 CCGAATTAAGTTGATTACCAAATT-ACTTAATT
* * * *
53366 T-ACTA--AA-TCACTTATTTACACCGAATTAAGCTGATTATCAATTTACTTAATTACACCGAAT
1 TAATTACCAATTTACTTAATTACACCGAATTAAGCTGATTACCAATTTACTTAATTACACCGAAT
53427 TAAGTTGATTACCAAATTACTTAATT
66 TAAGTTGATTACCAAATTACTTAATT
* *
53453 TAATTATCAATTTACTTAATTACACCGAATTAAGTTGATTACCAA
1 TAATTACCAATTTACTTAATTACACCGAATTAAGCTGATTACCAA
53498 AATGACTTAA
Statistics
Matches: 320, Mismatches: 62, Indels: 40
0.76 0.15 0.09
Matches are distributed among these distances:
84 7 0.02
86 28 0.09
87 20 0.06
88 21 0.07
89 38 0.12
90 5 0.02
91 201 0.63
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (91 bp):
TAATTACCAATTTACTTAATTACACCGAATTAAGCTGATTACCAATTTACTTAATTACACCGAAT
TAAGTTGATTACCAAATTACTTAATT
Found at i:53129 original size:126 final size:122
Alignment explanation
Indices: 52979--53333 Score: 433
Period size: 126 Copynumber: 2.8 Consensus size: 122
52969 CCATTTGATT
* **
52979 ATTTACTTAATTACACCGAATTAAGCTAATTACTGATTTACTTAATTACACCGAATTAAACTGAT
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTGATTTACTTAATTACACCGAATTAAGTTGAT
*
53044 TACTGATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTACCA
66 TACTGATTTACTTAATTACACCGAATTAAGTTGATTACCAAA-T-C--AAGTTAATTACCA
* * ** *
53105 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTGAT
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTGATTTACTTAATTACACCGAATTAAGTTGAT
** * * * * * * *
53170 TACCAAATTACTTAATTTAATTACC-AATTTACTTAATTACACCGAATCAAGTTGATTACCA
66 TACTGATTTACTTAA-TT-A-CACCGAATTAAGTTGATT--ACCAAATCAAGTTAATTACCA
*
53231 ATTCACTTAATTACACCGAATTAAGTTAATTACTGATTTACTTAATTACACCGAATTAAGTTGAT
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTGATTTACTTAATTACACCGAATTAAGTTGAT
* *
53296 TACTGATTTACCTAATTTCACCGAATTAAGTTGATTAC
66 TACTGATTTACTTAATTACACCGAATTAAGTTGATTAC
53334 TGATCTACTT
Statistics
Matches: 190, Mismatches: 33, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
122 2 0.01
123 3 0.02
124 10 0.05
125 2 0.01
126 150 0.79
127 2 0.01
128 12 0.06
129 4 0.02
130 5 0.03
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (122 bp):
ATTTACTTAATTACACCGAATTAAGTTAATTACTGATTTACTTAATTACACCGAATTAAGTTGAT
TACTGATTTACTTAATTACACCGAATTAAGTTGATTACCAAATCAAGTTAATTACCA
Found at i:53192 original size:21 final size:21
Alignment explanation
Indices: 53168--53207 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53158 AATTAAGTTG
53168 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
53189 ATTACCAATTTACTTAATT
1 ATTACCAAATTACTTAATT
53208 ACACCGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:53437 original size:19 final size:19
Alignment explanation
Indices: 53381--53438 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
53371 AATCACTTAT
*
53381 TTACACCGAATTAAGCTGA
1 TTACACCGAATTAAGTTGA
* * * *
53400 TT--ATC-AATTTACTTAA
1 TTACACCGAATTAAGTTGA
53416 TTACACCGAATTAAGTTGA
1 TTACACCGAATTAAGTTGA
53435 TTAC
1 TTAC
53439 CAAATTACTT
Statistics
Matches: 27, Mismatches: 9, Indels: 6
0.64 0.21 0.14
Matches are distributed among these distances:
16 9 0.33
17 2 0.07
18 2 0.07
19 14 0.52
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (19 bp):
TTACACCGAATTAAGTTGA
Found at i:53458 original size:21 final size:21
Alignment explanation
Indices: 53434--53530 Score: 64
Period size: 21 Copynumber: 4.9 Consensus size: 21
53424 AATTAAGTTG
53434 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
* *
53455 ATTATCAATTTACTTAA-TT-
1 ATTACCAAATTACTTAATTTA
* * * *
53474 A-CACC-GA--A-TTAAGTTG
1 ATTACCAAATTACTTAATTTA
*
53490 ATTACCAAAATGACTTAATTTA
1 ATTACC-AAATTACTTAATTTA
*
53512 ATTTCCAAATTACTTAATT
1 ATTACCAAATTACTTAATT
53531 ACACCGAATT
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
16 1 0.02
17 3 0.05
18 2 0.04
19 2 0.04
20 2 0.04
21 28 0.50
22 11 0.20
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.41
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:53533 original size:57 final size:56
Alignment explanation
Indices: 53399--53552 Score: 247
Period size: 56 Copynumber: 2.7 Consensus size: 56
53389 AATTAAGCTG
* *
53399 ATTATCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTA
1 ATTATCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATGACTTAATTTA
*
53455 ATTATCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAAATGACTTAATTTA
1 ATTATCAAATTACTTAATTACACCGAATTAAGTTGATTACC-AAATGACTTAATTTA
53512 ATT-TCCAAATTACTTAATTACACCGAATTTAAGTTGATTAC
1 ATTAT-CAAATTACTTAATTACACCGAA-TTAAGTTGATTAC
53553 TAATTTGCTT
Statistics
Matches: 93, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
56 42 0.45
57 38 0.41
58 13 0.14
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (56 bp):
ATTATCAAATTACTTAATTACACCGAATTAAGTTGATTACCAAATGACTTAATTTA
Found at i:55158 original size:1 final size:1
Alignment explanation
Indices: 55152--55184 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
55142 TGAAGGTACC
55152 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
55185 ACACGGTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:57710 original size:27 final size:27
Alignment explanation
Indices: 57654--57731 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
57644 GTAGATTAAG
* *
57654 AATGACCAAAATACCCCCTAAATGCAAA
1 AATGACCAAAAT-GCCCCTAGATGCAAA
**
57682 AATGACCAAAATGCCCCTAGATGTGAA
1 AATGACCAAAATGCCCCTAGATGCAAA
*
57709 AATGACCAAAATGCCCCTGGATG
1 AATGACCAAAATGCCCCTAGATG
57732 ACCCTAATGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 33 0.73
28 12 0.27
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTAGATGCAAA
Found at i:59023 original size:16 final size:15
Alignment explanation
Indices: 58997--59026 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
58987 GCCAAGTGGG
58997 TAAAAAATTAAAAAT
1 TAAAAAATTAAAAAT
59012 TAAAATAATTAAAAA
1 TAAAA-AATTAAAAA
59027 GAAAAACGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAAAATTAAAAAT
Found at i:59183 original size:82 final size:82
Alignment explanation
Indices: 59082--59246 Score: 289
Period size: 82 Copynumber: 2.0 Consensus size: 82
59072 TTTCACAGAA
*
59082 TTCTTTCAACCCTTCTTTTTCAGAA-ACCCAAAACTACGCAACCTAAAATCGATTTCCCCCTTTA
1 TTCTTTCAACCCTTCTTTTT-AGAATACCCAAAACTACACAACCTAAAATCGATTTCCCCCTTTA
59146 TGTTCTAAGTTTCTGGGT
65 TGTTCTAAGTTTCTGGGT
59164 TTCTTTCAACCCCTT-TTTTTAGAATACCCAAAACTACACAACCTAAAATCGATTTCCCCCTTTA
1 TTCTTTCAA-CCCTTCTTTTTAGAATACCCAAAACTACACAACCTAAAATCGATTTCCCCCTTTA
59228 TGTTCTAAGTTTCTGGGT
65 TGTTCTAAGTTTCTGGGT
59246 T
1 T
59247 AGATTTAATG
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
81 4 0.05
82 71 0.89
83 5 0.06
ACGTcount: A:0.26, C:0.27, G:0.09, T:0.38
Consensus pattern (82 bp):
TTCTTTCAACCCTTCTTTTTAGAATACCCAAAACTACACAACCTAAAATCGATTTCCCCCTTTAT
GTTCTAAGTTTCTGGGT
Found at i:61591 original size:23 final size:23
Alignment explanation
Indices: 61544--61592 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
61534 AAATAAAAAT
* *
61544 AAATATAAAAATTAAAAATTTTA
1 AAATATAAAAATTAAAAAATATA
* *
61567 AAATATATATATTAAAAAATATA
1 AAATATAAAAATTAAAAAATATA
61590 AAA
1 AAA
61593 ATACCACGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATAAAAATTAAAAAATATA
Found at i:65308 original size:48 final size:48
Alignment explanation
Indices: 65254--65525 Score: 237
Period size: 48 Copynumber: 5.6 Consensus size: 48
65244 AGATGTGAAG
* *
65254 AAAACCTGCACCTTCCGACCGAGAAGGGCATTTTGGGAAAAAAGATGA
1 AAAACCTGCACCTTCCGACCGGGAAGGGCATTTTGGGAATAAAGATGA
* * * * *
65302 AAAACCTTCACCTTCCAACCGGGAAGGGTATTTTGGGGATAAAGATAAA
1 AAAACCTGCACCTTCCGACCGGGAAGGGCATTTTGGGAATAAAGAT-GA
* *
65351 AAAACTTGCACCTTCCGACCGGGAAGGGCATTTTGGGAATAGAGATGAA
1 AAAACCTGCACCTTCCGACCGGGAAGGGCATTTTGGGAATAAAGATG-A
* * ** * ** *
65400 AAAAACTTCACCTTCCGACCGGGAAGGGCAAAATTGGAAATTGACACT-A
1 AAAACCTGCACCTTCCGACCGGGAAGGGC-ATTTTGGGAATAAAGA-TGA
* *** * * *
65449 AAGA-CTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCG-
1 AAAACCTGCACCTTCCGACCGGGAAGGGC-ATTTTGGGAATAAAGA-TGA
*
65497 AAGA-CTGCACCTTCCGACCGGGAAGGGCA
1 AAAACCTGCACCTTCCGACCGGGAAGGGCA
65526 AAACTGGAAA
Statistics
Matches: 191, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
47 1 0.01
48 106 0.55
49 72 0.38
50 11 0.06
51 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (48 bp):
AAAACCTGCACCTTCCGACCGGGAAGGGCATTTTGGGAATAAAGATGA
Found at i:65373 original size:49 final size:48
Alignment explanation
Indices: 65262--65429 Score: 246
Period size: 49 Copynumber: 3.5 Consensus size: 48
65252 AGAAAACCTG
* * * *
65262 CACCTTCCGACCGAGAAGGGCATTTTGGGAAAAAAGATGAAAAACCTT
1 CACCTTCCGACCGGGAAGGGCATTTTGGGAATAAAGATAAAAAAACTT
* * *
65310 CACCTTCCAACCGGGAAGGGTATTTTGGGGATAAAGATAAAAAAACTT
1 CACCTTCCGACCGGGAAGGGCATTTTGGGAATAAAGATAAAAAAACTT
*
65358 GCACCTTCCGACCGGGAAGGGCATTTTGGGAATAGAGATGAAAAAAACTT
1 -CACCTTCCGACCGGGAAGGGCATTTTGGGAATAAAGAT-AAAAAAACTT
65408 CACCTTCCGACCGGGAAGGGCA
1 CACCTTCCGACCGGGAAGGGCA
65430 AAATTGGAAA
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
48 41 0.38
49 56 0.52
50 10 0.09
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.19
Consensus pattern (48 bp):
CACCTTCCGACCGGGAAGGGCATTTTGGGAATAAAGATAAAAAAACTT
Found at i:65458 original size:97 final size:95
Alignment explanation
Indices: 65254--65477 Score: 263
Period size: 97 Copynumber: 2.3 Consensus size: 95
65244 AGATGTGAAG
* * *
65254 AAAACCTGCACCTTCCGACCGAGAAGGGCATTTTGGGAAAAAAGATGAAAAACCTTCACCTTCCA
1 AAAAACTGCACCTTCCGACCGGGAAGGGCATTTTGGGAAAAAAGATGAAAAAACTTCACCTTCCA
* ** *
65319 ACCGGGAAGGGTATTTTGGGGATAAAGATAA
66 ACCGGGAAGGGAAAATT-GGGATAAAGACAA
* *
65350 AAAAACTTGCACCTTCCGACCGGGAAGGGCATTTTGGGAATAGAGATGAAAAAAACTTCACCTTC
1 AAAAAC-TGCACCTTCCGACCGGGAAGGGCATTTTGGGAAAAAAGATG-AAAAAACTTCACCTTC
* * *
65415 CGACCGGGAAGGGCAAAATT-GGA-AATTGACACT
64 CAACCGGGAAGGG-AAAATTGGGATAA-AGACA-A
*
65448 AAAGACTGCACCTTCCGACCGGGAAGGGCA
1 AAAAACTGCACCTTCCGACCGGGAAGGGCA
65478 AAACTGGAAA
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
96 7 0.06
97 68 0.62
98 32 0.29
99 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.18
Consensus pattern (95 bp):
AAAAACTGCACCTTCCGACCGGGAAGGGCATTTTGGGAAAAAAGATGAAAAAACTTCACCTTCCA
ACCGGGAAGGGAAAATTGGGATAAAGACAA
Found at i:65526 original size:48 final size:48
Alignment explanation
Indices: 65401--65718 Score: 387
Period size: 48 Copynumber: 6.7 Consensus size: 48
65391 AGAGATGAAA
* * **
65401 AAAACTTCACCTTCCGACCGGGAAGGGCAAAATTGGAAATTGACACT-
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
*
65448 AAAGACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACCG
1 AAA-ACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* *
65497 AAGACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATGAACACTG
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* * *
65545 AAAATTAGCACCTTCCGA-C----AGGGCAAAACAGGAAAGAAACACTG
1 AAAACT-GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* * * *
65589 AAAATTAGCACCTTCTGACCGGGAAGGGCAAAACAGGAAAGAAACACTG
1 AAAACT-GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
* * * * *
65638 AAGACAGCACCTTCCGACCGGGAAGGGCAAAATTGGAAGTAGACACTG
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
*
65686 AAAACCGCACCTTCCGACCGGGAAGGGCAAAAC
1 AAAACTGCACCTTCCGACCGGGAAGGGCAAAAC
65719 AGGGAATCGA
Statistics
Matches: 237, Mismatches: 26, Indels: 15
0.85 0.09 0.05
Matches are distributed among these distances:
44 39 0.16
45 1 0.00
47 3 0.01
48 153 0.65
49 41 0.17
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.12
Consensus pattern (48 bp):
AAAACTGCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTG
Found at i:65586 original size:44 final size:45
Alignment explanation
Indices: 65472--65655 Score: 178
Period size: 44 Copynumber: 4.0 Consensus size: 45
65462 CCGACCGGGA
* * * * *
65472 AGGGCAAAACTGGAAATAAACACCGAAGACT-GCACCTTCCGACCGGG
1 AGGGCAAAACAGGAAAGAAACACTGAAAATTAGCACCTTCCGA-C--G
*
65519 AAGGGCAAAACTGGAAATG-AACACTGAAAATTAGCACCTTCCGAC-
1 -AGGGCAAAACAGGAAA-GAAACACTGAAAATTAGCACCTTCCGACG
*
65564 AGGGCAAAACAGGAAAGAAACACTGAAAATTAGCACCTTCTGACCGGG
1 AGGGCAAAACAGGAAAGAAACACTGAAAATTAGCACCTTCCGA-C--G
* *
65612 AAGGGCAAAACAGGAAAGAAACACTGAAGA-CAGCACCTTCCGAC
1 -AGGGCAAAACAGGAAAGAAACACTGAAAATTAGCACCTTCCGAC
65656 CGGGAAGGGC
Statistics
Matches: 119, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
43 1 0.01
44 39 0.33
45 1 0.01
47 1 0.01
48 38 0.32
49 39 0.33
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.11
Consensus pattern (45 bp):
AGGGCAAAACAGGAAAGAAACACTGAAAATTAGCACCTTCCGACG
Found at i:66324 original size:34 final size:34
Alignment explanation
Indices: 66281--66348 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
66271 AGCATTAATC
*
66281 AAAATTCAATCTTTTAGTTCAAAGATTTCATTTT
1 AAAATTCAATCTTTTAGTCCAAAGATTTCATTTT
*
66315 AAAATTCAATTTTTTAGTCCAAAGATTTCATTTT
1 AAAATTCAATCTTTTAGTCCAAAGATTTCATTTT
66349 TATCACAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (34 bp):
AAAATTCAATCTTTTAGTCCAAAGATTTCATTTT
Found at i:66429 original size:51 final size:48
Alignment explanation
Indices: 66326--66568 Score: 139
Period size: 51 Copynumber: 4.9 Consensus size: 48
66316 AAATTCAATT
* * * *
66326 TTTTAGTCCAAAGATTTCATTTTTATCACAAATTAATAAAATTTAATC
1 TTTTAATCCAAAGATCTCATTTCTATCACAAATTAATAAAAGTTAATC
* * *
66374 TTTTAATCCAAGGATCTCATTTCTATTCACAAATTACTTACAAGGTTAATC
1 TTTTAATCCAAAGATCTCATTTCTA-TCACAAATTA-ATA-AAAGTTAATC
* ** * *
66425 TTTTATTTAAAAAATCTCACTTT-TATTTACAAATTAATCAAAAGGTTCAATC
1 TTTTAATCCAAAGATCTCA-TTTCTA-TCACAAATTAAT-AAAA-GTT-AATC
* * * * * * * *
66477 TTTTACTTCACAGATCTCATTTTTATCATAAATCAATCAAAAATTTCATC
1 TTTTAATCCAAAGATCTCATTTCTATCACAAATTAAT--AAAAGTTAATC
* * * * *
66527 TTTT-AGCTTAAAGATCTCATTTTTATCATAAATCAATCAAAA
1 TTTTAATC-CAAAGATCTCATTTCTATCACAAATTAAT-AAAA
66569 ATTTCATCTT
Statistics
Matches: 154, Mismatches: 31, Indels: 19
0.75 0.15 0.09
Matches are distributed among these distances:
48 21 0.14
49 14 0.09
50 39 0.25
51 52 0.34
52 28 0.18
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.42
Consensus pattern (48 bp):
TTTTAATCCAAAGATCTCATTTCTATCACAAATTAATAAAAGTTAATC
Found at i:66531 original size:30 final size:29
Alignment explanation
Indices: 66493--66581 Score: 70
Period size: 29 Copynumber: 3.3 Consensus size: 29
66483 TTCACAGATC
66493 TCATTTTTATCATAAATCAATCAAAAATT
1 TCATTTTTATCATAAATCAATCAAAAATT
* * *
66522 TCATCTTTTAGC-----T---T-AAAGATC
1 TCAT-TTTTATCATAAATCAATCAAAAATT
66543 TCATTTTTATCATAAATCAATCAAAAATT
1 TCATTTTTATCATAAATCAATCAAAAATT
66572 TCATCTTTTA
1 TCAT-TTTTA
66582 GCTTAAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 21
0.61 0.09 0.30
Matches are distributed among these distances:
20 6 0.14
21 9 0.21
22 1 0.02
25 2 0.05
28 1 0.02
29 13 0.30
30 11 0.26
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (29 bp):
TCATTTTTATCATAAATCAATCAAAAATT
Found at i:66621 original size:49 final size:50
Alignment explanation
Indices: 66455--66599 Score: 213
Period size: 50 Copynumber: 2.9 Consensus size: 50
66445 TTTTATTTAC
* ** *
66455 AAATTAATCAAAAGGTTCAATCTTTTA-CTTCACAGATCTCATTTTTATCAT
1 AAATCAATCAAAAATTTC-ATCTTTTAGCTT-AAAGATCTCATTTTTATCAT
66506 AAATCAATCAAAAATTTCATCTTTTAGCTTAAAGATCTCATTTTTATCAT
1 AAATCAATCAAAAATTTCATCTTTTAGCTTAAAGATCTCATTTTTATCAT
*
66556 AAATCAATCAAAAATTTCATCTTTTAGCTTAAA-ATTTCATTTTT
1 AAATCAATCAAAAATTTCATCTTTTAGCTTAAAGATCTCATTTTT
66600 TATTGCTAAC
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
49 10 0.11
50 60 0.68
51 18 0.20
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (50 bp):
AAATCAATCAAAAATTTCATCTTTTAGCTTAAAGATCTCATTTTTATCAT
Found at i:67875 original size:38 final size:35
Alignment explanation
Indices: 67796--67865 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
67786 GGGAGAGCTT
* *
67796 TATTTCGTCTCCATGTGTGATGTGTGTTGTTGAAG
1 TATTTTGTCTCCATGTATGATGTGTGTTGTTGAAG
67831 TATTTTGTCTCCATGTATG-TGTGTGTGTGTTGAAG
1 TATTTTGTCTCCATGTATGATGTGTGT-TGTTGAAG
67866 GGTGATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 7 0.22
35 25 0.78
ACGTcount: A:0.14, C:0.10, G:0.29, T:0.47
Consensus pattern (35 bp):
TATTTTGTCTCCATGTATGATGTGTGTTGTTGAAG
Found at i:67972 original size:2 final size:2
Alignment explanation
Indices: 67965--67996 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
67955 AAATGCCATA
67965 AT AT 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 AT AT
67997 GCACCGCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72308 original size:33 final size:33
Alignment explanation
Indices: 72271--72387 Score: 155
Period size: 33 Copynumber: 3.8 Consensus size: 33
72261 TAGTTAAAGG
72271 ATCATGTGGCCGGTTGTGGCCGGGCATGGCCGA
1 ATCATGTGGCCGGTTGTGGCCGGGCATGGCCGA
72304 ATCA----------TGTGGCCGGGCATGGCCGA
1 ATCATGTGGCCGGTTGTGGCCGGGCATGGCCGA
*
72327 ATCATGTGGCCGGTTGTGGCCGGGCATGTCCGA
1 ATCATGTGGCCGGTTGTGGCCGGGCATGGCCGA
72360 ATCATGTGGCCGGTTGTGGCCGGGCATG
1 ATCATGTGGCCGGTTGTGGCCGGGCATG
72388 TCCTTGTCGC
Statistics
Matches: 73, Mismatches: 1, Indels: 20
0.78 0.01 0.21
Matches are distributed among these distances:
23 23 0.32
33 50 0.68
ACGTcount: A:0.13, C:0.24, G:0.41, T:0.22
Consensus pattern (33 bp):
ATCATGTGGCCGGTTGTGGCCGGGCATGGCCGA
Found at i:72348 original size:23 final size:23
Alignment explanation
Indices: 72285--72339 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
72275 TGTGGCCGGT
72285 TGTGGCCGGGCATGGCCGAATCA
1 TGTGGCCGGGCATGGCCGAATCA
72308 TGTGGCCGGGCATGGCCGAATCA
1 TGTGGCCGGGCATGGCCGAATCA
72331 TGTGGCCGG
1 TGTGGCCGG
72340 TTGTGGCCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.42, T:0.18
Consensus pattern (23 bp):
TGTGGCCGGGCATGGCCGAATCA
Found at i:72388 original size:33 final size:33
Alignment explanation
Indices: 72308--72390 Score: 157
Period size: 33 Copynumber: 2.5 Consensus size: 33
72298 GGCCGAATCA
*
72308 TGTGGCCGGGCATGGCCGAATCATGTGGCCGGT
1 TGTGGCCGGGCATGTCCGAATCATGTGGCCGGT
72341 TGTGGCCGGGCATGTCCGAATCATGTGGCCGGT
1 TGTGGCCGGGCATGTCCGAATCATGTGGCCGGT
72374 TGTGGCCGGGCATGTCC
1 TGTGGCCGGGCATGTCC
72391 TTGTCGCGTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.11, C:0.25, G:0.41, T:0.23
Consensus pattern (33 bp):
TGTGGCCGGGCATGTCCGAATCATGTGGCCGGT
Found at i:74514 original size:36 final size:37
Alignment explanation
Indices: 74453--74525 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
74443 TTAATTACCA
74453 TTTTACTGATTACTTCTTTACTTTTTACCATTTTACT
1 TTTTACTGATTACTTCTTTACTTTTTACCATTTTACT
*
74490 TTTTACTGA-T-CTCTCTTTATTTTTTACCATTTTACT
1 TTTTACTGATTACT-TCTTTACTTTTTACCATTTTACT
74526 GGTTACTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 2 0.06
36 23 0.68
37 9 0.26
ACGTcount: A:0.18, C:0.19, G:0.03, T:0.60
Consensus pattern (37 bp):
TTTTACTGATTACTTCTTTACTTTTTACCATTTTACT
Found at i:74559 original size:26 final size:26
Alignment explanation
Indices: 74528--74580 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
74518 ATTTTACTGG
*
74528 TTACTATTTT-ACTCTCTTGAATTTAA
1 TTACTATTTTCACTCT-TTGAACTTAA
74554 TTACTATTTTCACTCTTTGAACTTAA
1 TTACTATTTTCACTCTTTGAACTTAA
74580 T
1 T
74581 CACCATTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.26, C:0.17, G:0.04, T:0.53
Consensus pattern (26 bp):
TTACTATTTTCACTCTTTGAACTTAA
Found at i:74588 original size:26 final size:26
Alignment explanation
Indices: 74533--74588 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
74523 ACTGGTTACT
* * *
74533 ATTTTACTCTCTTGAATTTAATTACT
1 ATTTTACTCTCTTGAACTTAATCACC
74559 ATTTTCACTCT-TTGAACTTAATCACC
1 ATTTT-ACTCTCTTGAACTTAATCACC
74585 ATTT
1 ATTT
74589 GCCATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.50
Consensus pattern (26 bp):
ATTTTACTCTCTTGAACTTAATCACC
Found at i:74603 original size:32 final size:33
Alignment explanation
Indices: 74554--74636 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
74544 TTGAATTTAA
*
74554 TTACTATTTTCACTCTTTGAACTTAATCACCA-T
1 TTACCATTTT-ACTCTTTGAACTTAATCACCATT
* * * *
74587 TTGCCATTTTATTCTTTGAATTTAATTACCATT
1 TTACCATTTTACTCTTTGAACTTAATCACCATT
74620 TTACCATTTTACTCTTT
1 TTACCATTTTACTCTTT
74637 ACCGGTTTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 18 0.43
33 24 0.57
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (33 bp):
TTACCATTTTACTCTTTGAACTTAATCACCATT
Found at i:74752 original size:40 final size:42
Alignment explanation
Indices: 74682--74760 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 42
74672 CTTTTACCGA
*
74682 TTTACTGATCACTTTCTTTTACTTTTACTC-TTAATTACCAT
1 TTTACTGATCACTTTCTTTTACTTTGACTCTTTAATTACCAT
*
74723 TTTACTGATTAC-TTCTTTTACTTTGACTCTTTAATTAC
1 TTTACTGATCACTTTCTTTTACTTTGACTCTTTAATTAC
74761 TGATTTCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 16 0.46
41 19 0.54
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.54
Consensus pattern (42 bp):
TTTACTGATCACTTTCTTTTACTTTGACTCTTTAATTACCAT
Found at i:77116 original size:19 final size:19
Alignment explanation
Indices: 77092--77135 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
77082 GTTCTGCACT
77092 TGTGCATGTGTGTATGGCA
1 TGTGCATGTGTGTATGGCA
77111 TGTGCATGTGTGTATGGCA
1 TGTGCATGTGTGTATGGCA
77130 TGTGCA
1 TGTGCA
77136 GGCCTGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.11, G:0.36, T:0.36
Consensus pattern (19 bp):
TGTGCATGTGTGTATGGCA
Done.