Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011657.1 Corchorus capsularis cultivar CVL-1 contig11678, 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: 103110
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:194 original size:14 final size:14
Alignment explanation
Indices: 175--202 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
165 AGCCTTTAAA
175 GAAGAAAAAAAAAG
1 GAAGAAAAAAAAAG
189 GAAGAAAAAAAAAG
1 GAAGAAAAAAAAAG
203 AACAATGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAGAAAAAAAAAG
Found at i:4714 original size:62 final size:62
Alignment explanation
Indices: 4640--4765 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
4630 TATTTTAGTA
4640 TAAAAAATTTTCATACGTAAAAAGTAAGGCATTTATAATTAAATATAAAAAATATTCTTTAG
1 TAAAAAATTTTCATACGTAAAAAGTAAGGCATTTATAATTAAATATAAAAAATATTCTTTAG
4702 TAAAAAATTTTCATACGTAAAAAGTAAGGCATTTATAATTAAATATAAAAAATATTCTTTAG
1 TAAAAAATTTTCATACGTAAAAAGTAAGGCATTTATAATTAAATATAAAAAATATTCTTTAG
4764 TA
1 TA
4766 TTTATAATTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (62 bp):
TAAAAAATTTTCATACGTAAAAAGTAAGGCATTTATAATTAAATATAAAAAATATTCTTTAG
Found at i:24964 original size:29 final size:29
Alignment explanation
Indices: 24922--24981 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
24912 ACAAACAGAT
* *
24922 TATGCCTCTCCCCAAGGAGCTCGGAGGCC
1 TATGCCTCTCCCCAAGGAACTCAGAGGCC
*
24951 TATGTCTCTCCCCAAGGAACTCAGAGGCC
1 TATGCCTCTCCCCAAGGAACTCAGAGGCC
24980 TA
1 TA
24982 GGATTAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.20
Consensus pattern (29 bp):
TATGCCTCTCCCCAAGGAACTCAGAGGCC
Found at i:27286 original size:37 final size:36
Alignment explanation
Indices: 27244--27341 Score: 101
Period size: 37 Copynumber: 2.7 Consensus size: 36
27234 AAGAGCCTTA
* *
27244 GGCTCAAATCCAAGC-AATCATCAACCACTGAGCCTC
1 GGCTCAAATCCAAACAAAT-ATCAACAACTGAGCCTC
* * *
27280 GTGCTCAAGTCCAAACAAATATCAATAAGTGAGCCTC
1 G-GCTCAAATCCAAACAAATATCAACAACTGAGCCTC
27317 GGACTCAAATCC-AACGAAATATCAA
1 GG-CTCAAATCCAAAC-AAATATCAA
27342 AACATCTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
36 5 0.10
37 44 0.85
38 3 0.06
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (36 bp):
GGCTCAAATCCAAACAAATATCAACAACTGAGCCTC
Found at i:28148 original size:14 final size:13
Alignment explanation
Indices: 28125--28167 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
28115 TAATGCACCC
28125 AAAACATTTAATA
1 AAAACATTTAATA
28138 AAAATCATTT-ATA
1 AAAA-CATTTAATA
*
28151 AAAACAATTTATTA
1 AAAAC-ATTTAATA
28165 AAA
1 AAA
28168 GTAGTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.04
13 15 0.58
14 10 0.38
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAACATTTAATA
Found at i:29378 original size:6 final size:6
Alignment explanation
Indices: 29348--29427 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
29338 TTTCTTTTAA
* * * *
29348 TTTCTC TTTATT TTCCTT ATTCTT TTTCTT TTT-TT TTTC-T TTTCTAT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCT-T
* *
29395 TTTCTT TTTC-- CTTCTT CTTCTT TTT-TT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
29428 CTTTTCCCGT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
4 3 0.05
5 15 0.25
6 35 0.59
7 6 0.10
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:29389 original size:17 final size:17
Alignment explanation
Indices: 29367--29432 Score: 73
Period size: 17 Copynumber: 3.8 Consensus size: 17
29357 ATTTTCCTTA
*
29367 TTCTTTTTCTTTTTTTT
1 TTCTTCTTCTTTTTTTT
29384 TTCTT-TTCTATTTTCTTT
1 TTCTTCTTCT-TTTT-TTT
29402 TTCCTTCTTCTTCTTTTTT
1 TT-CTTCTTCTT-TTTTTT
29421 TT-TTCTTCTTTT
1 TTCTTCTTCTTTT
29433 CCCGTAGGGC
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.14
17 17 0.39
18 5 0.11
19 9 0.20
20 7 0.16
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (17 bp):
TTCTTCTTCTTTTTTTT
Found at i:29397 original size:23 final size:23
Alignment explanation
Indices: 29348--29424 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
29338 TTTCTTTTAA
*
29348 TTTCTCTTTATTTTCCTTATTCTT
1 TTTCT-TTTTTTTTCCTTATTCTT
*
29372 TTTCTTTTTTTTTTCTT-TTCTAT
1 TTTCTTTTTTTTTCCTTATTCT-T
** *
29395 TTTCTTTTTCCTT-CTTCTTCTT
1 TTTCTTTTTTTTTCCTTATTCTT
29417 TTT-TTTTT
1 TTTCTTTTT
29425 CTTCTTTTCC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 5 0.11
22 11 0.23
23 26 0.55
24 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTCTTTTTTTTTCCTTATTCTT
Found at i:39313 original size:37 final size:38
Alignment explanation
Indices: 39238--39313 Score: 111
Period size: 37 Copynumber: 2.0 Consensus size: 38
39228 TTTAAATCGC
**
39238 AAACTCTTTTTTTTTTAGAAAAATCGGAAAAAGGAAAA
1 AAACTCTTTTTTTTTTAGAAAAATCGGAAAAAACAAAA
39276 AAACT-TTTTTTTTTATAGAAAAA-CGGAAAAAACAAAA
1 AAACTCTTTTTTTTT-TAGAAAAATCGGAAAAAACAAAA
39313 A
1 A
39314 CTAATTCTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
37 22 0.63
38 13 0.37
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (38 bp):
AAACTCTTTTTTTTTTAGAAAAATCGGAAAAAACAAAA
Found at i:43444 original size:59 final size:60
Alignment explanation
Indices: 43335--43450 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
43325 CTCAGTTCTT
* * * *
43335 TTTTCTTTTTTGGTGAATTTGGGAAGTCTACTGTAGAACTTTGGGATTAGGG-TTAGGGA
1 TTTTCTTTTTTGGTGAATTTGAGAACTCTACTATAGAACTCTGGGATTAGGGATTAGGGA
**
43394 TTTTCTTTTTTTGGTGAATTTGAGAACTCTGTTATAGAACTCT-GGATTAGGGATTAG
1 TTTTC-TTTTTTGGTGAATTTGAGAACTCTACTATAGAACTCTGGGATTAGGGATTAG
43451 CAGACTCTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 14 0.29
60 35 0.71
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.44
Consensus pattern (60 bp):
TTTTCTTTTTTGGTGAATTTGAGAACTCTACTATAGAACTCTGGGATTAGGGATTAGGGA
Found at i:49439 original size:19 final size:19
Alignment explanation
Indices: 49419--49455 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
49409 AATTAATTAT
49419 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
49437 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
49456 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:50095 original size:103 final size:102
Alignment explanation
Indices: 49902--50095 Score: 230
Period size: 103 Copynumber: 1.9 Consensus size: 102
49892 TTAAGAAATT
* * * *
49902 CTATAAATAAATATTTAAATTCAAGACATACCCTTAAAATATTTTTTATATCATTTAGGGCTAAA
1 CTATAAATAAATATTTAAATTCAAGACATACCCTTAAAATATCTTTAAGATAATTTAGGGCTAAA
* * * *
49967 GCTTAGTGATTTGGGACTCAGCTTAAACTCTAAAACC
66 GCCTAATGATTTGGGACTAAACTTAAACTCTAAAACC
* * *
50004 CTATAAATAATTATTTTAAATTCAAGACATACCCTTAAATTATCTTTAAGATAATTT-GGGATTA
1 CTATAAATAAATA-TTTAAATTCAAGACATACCCTTAAAATATCTTTAAGATAATTTAGGG-CTA
**
50068 AA-CCTACATGATTTGGGGTTAAACTTAA
64 AAGCCTA-ATGATTTGGGACTAAACTTAA
50096 TTGATTGGGT
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
102 18 0.24
103 58 0.76
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (102 bp):
CTATAAATAAATATTTAAATTCAAGACATACCCTTAAAATATCTTTAAGATAATTTAGGGCTAAA
GCCTAATGATTTGGGACTAAACTTAAACTCTAAAACC
Found at i:56323 original size:2 final size:2
Alignment explanation
Indices: 56316--56344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56306 TCGCCGACTT
56316 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
56345 CTGCTTGGAG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:57510 original size:16 final size:17
Alignment explanation
Indices: 57491--57524 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
57481 AATTCGAGAC
57491 AACCCGAACCCG-CCCG
1 AACCCGAACCCGACCCG
57507 AACCCGAACCCGACCCG
1 AACCCGAACCCGACCCG
57524 A
1 A
57525 GTCCGAGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (17 bp):
AACCCGAACCCGACCCG
Found at i:58309 original size:23 final size:23
Alignment explanation
Indices: 58279--58331 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
58269 TCGAAAATGT
*
58279 ACCCGAACCCGACCCGGGCCCGA
1 ACCCGAACCCGACCCGAGCCCGA
** *
58302 ACCCGAACTTGATCCGAGCCCGA
1 ACCCGAACCCGACCCGAGCCCGA
58325 ACCCGAA
1 ACCCGAA
58332 AAAACCCGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.45, G:0.23, T:0.06
Consensus pattern (23 bp):
ACCCGAACCCGACCCGAGCCCGA
Found at i:58368 original size:15 final size:16
Alignment explanation
Indices: 58320--58376 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
58310 TTGATCCGAG
*
58320 CCCGAACCCGAAAAAA
1 CCCGAACCCGAAAATA
58336 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
58352 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
58367 CCCGAACCCG
1 CCCGAACCCG
58377 CTCGAACCCG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 14 0.36
16 25 0.64
ACGTcount: A:0.39, C:0.42, G:0.16, T:0.04
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:61019 original size:21 final size:20
Alignment explanation
Indices: 60990--61037 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
60980 ATAGTTTAGA
* *
60990 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTA-ATTGCTTTCTT
*
61011 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTTCTT
61031 TTTAATT
1 TTTAATT
61038 AATCTGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTAATTTAATTGCTTTCTT
Found at i:73985 original size:326 final size:330
Alignment explanation
Indices: 73457--74323 Score: 977
Period size: 337 Copynumber: 2.6 Consensus size: 330
73447 TTTACAAAAA
* * * *
73457 AAAAAATGACCCGAAAAATGTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAATTT
1 AAAAATTGACCCGAAAGAT-TTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAATTC
* * * *
73522 AACGCCAAAAAGATTGGATGA--ATTTCACTGTTTTAATATC-----ATTATTTTTT-GAATTAA
65 AACG-AAAAAAGATTGGA-GAGCTTTTCAC-GTTTTAATATCGTTTTCTTATTTTTTCAAATTAA
* * *
73579 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATATGGCT
127 TTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTGCT
* ** * *
73644 GAGATTTGATTAGATGAATATGGATATCTCATGGAGTC-TAGCGCC-AAAA-ATGCAAAACTGAG
192 GAGATTTGATTAGATGAATATAGATATCTCAACGAGTCTTAGAGCCAAAAACATGCAAAACTAAG
* * *
73706 CC-GAGCCCCCAGAATGC-TTTTATAGCCAA-AACTGTGAT-G-GTTATTACACGATTTCAACT-
257 CCAG-GCCCCCAGAACGCGTTTT-TAGCCAATAACCGTGATGGTGTTAGTACACGATTTCAACTA
*
73765 AAAA-TTTTGT
320 AAAACTTTTGC
* * * *
73775 AATAATTGACCCGAAAGATATTTGCTCAATTTTTGGTTAAAATAATCATAAAAAATATATAATTC
1 AAAAATTGACCCGAAAGAT-TTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAATTC
* *
73840 AACGAAAAAAGATTGAAGGGCTTTTCACGTTTCTAATATCGTTTTTCTTATTTTTTACAAATTAA
65 AACGAAAAAAGATTGGAGAGCTTTTCACGTTT-TAATATCG-TTTTCTTATTTTTT-CAAATTAA
* * *
73905 TTTCTATTTAAATCGAAATAAGATGCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCT
127 TTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTGCT
* * * *
73970 GAGATTTGATTAGATGAATATAGATATTTCAACTAGTCTTGGAGCCAAAAATCATGCAAAATTAA
192 GAGATTTGATTAGATGAATATAGATATCTCAACGAGTCTTAGAGCCAAAAA-CATGCAAAACTAA
* * **
74035 GCCAGGTCCCCAGAACGCGTTTTTAGTCAATAACCGTGATGGTTTGTTAGTACACGATTTCGGCT
256 GCCAGGCCCCCAGAACGCGTTTTTAGCCAATAACCGTGATGG--TGTTAGTACACGATTTCAACT
74100 AAAAACTTTTTGC
319 AAAAAC-TTTTGC
** * **
74113 AAAAATTGACATGAAAGATTTCTCCTCAATTTTTGGCTAAAATACTCAT-TGAAATATATAATTC
1 AAAAATTGACCCGAAAGATTT-TCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAATTC
* *
74177 AAC-ACCAGAAAA-ATTGGAGAGCTTTTTACGCTTTTAATATTGTATTTCTTA-TTTTTCTAAAT
65 AACGA--A-AAAAGATTGGAGAGCTTTTCACG-TTTTAATATCGT-TTTCTTATTTTTTC-AAAT
*
74239 TAATTTCTAATTAAATCGACATAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTT
124 TAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTT
*
74304 GCTGAGATTTGGTTAGATGA
189 GCTGAGATTTGATTAGATGA
74324 TGTGAAGTAT
Statistics
Matches: 462, Mismatches: 55, Indels: 45
0.82 0.10 0.08
Matches are distributed among these distances:
316 1 0.00
317 15 0.03
318 73 0.16
324 9 0.02
326 98 0.21
327 5 0.01
328 4 0.01
330 30 0.06
331 13 0.03
332 1 0.00
335 17 0.04
336 6 0.01
337 108 0.23
338 75 0.16
339 7 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (330 bp):
AAAAATTGACCCGAAAGATTTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAATTCA
ACGAAAAAAGATTGGAGAGCTTTTCACGTTTTAATATCGTTTTCTTATTTTTTCAAATTAATTTC
TAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTGCTGAGA
TTTGATTAGATGAATATAGATATCTCAACGAGTCTTAGAGCCAAAAACATGCAAAACTAAGCCAG
GCCCCCAGAACGCGTTTTTAGCCAATAACCGTGATGGTGTTAGTACACGATTTCAACTAAAAACT
TTTGC
Found at i:75448 original size:18 final size:18
Alignment explanation
Indices: 75425--75489 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
75415 ATATGACTAG
75425 TTATAATTAAATATATTA
1 TTATAATTAAATATATTA
*
75443 TTATAATATAAAAATAATTA
1 TTATAAT-TAAATAT-ATTA
* *
75463 TTAGAAGTAAAT-TATTAA
1 TTATAATTAAATATATT-A
*
75481 TTACAATTA
1 TTATAATTA
75490 TAGTGGATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.08
18 16 0.42
19 10 0.26
20 9 0.24
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (18 bp):
TTATAATTAAATATATTA
Found at i:76108 original size:10 final size:10
Alignment explanation
Indices: 76093--76125 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
76083 TAGTAATAAA
76093 ATAGTAAGAT
1 ATAGTAAGAT
76103 ATAGTAAGAT
1 ATAGTAAGAT
76113 A-AGATAAGAT
1 ATAG-TAAGAT
76123 ATA
1 ATA
76126 AAGATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.10
10 18 0.86
11 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (10 bp):
ATAGTAAGAT
Found at i:81067 original size:23 final size:23
Alignment explanation
Indices: 80983--81057 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
80973 CATGGCGGAG
*
80983 ATTTTTTTAAAAAAAAATAGCT-
1 ATTTTTTTAAAAAAAATTAGCTA
** *
81005 A-TTTTAAAAAAAAAATTGGCTA
1 ATTTTTTTAAAAAAAATTAGCTA
81027 ATTTTTTTAAAAAAAATTAGCTA
1 ATTTTTTTAAAAAAAATTAGCTA
81050 ATTTTTTT
1 ATTTTTTT
81058 TTTTAAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 16 0.36
22 2 0.05
23 26 0.59
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (23 bp):
ATTTTTTTAAAAAAAATTAGCTA
Found at i:82766 original size:22 final size:22
Alignment explanation
Indices: 82733--82967 Score: 124
Period size: 22 Copynumber: 10.7 Consensus size: 22
82723 ACTTAAATCT
*
82733 CTATGAAATTTTGATAACCACA
1 CTATAAAATTTTGATAACCACA
* * * **
82755 TTATAAAATTTTGGTAACTATG
1 CTATAAAATTTTGATAACCACA
* * * *
82777 CAATGAAATTTTGAAAACCTC-
1 CTATAAAATTTTGATAACCACA
* * *
82798 CATATTAAATTTTGTTATCC-CGTA
1 C-TATAAAATTTTGATAACCAC--A
* * *
82822 -TATAAAATTTTGACAACCTCC
1 CTATAAAATTTTGATAACCACA
82843 CTATAAAATTTCT-ATAACCACA
1 CTATAAAATTT-TGATAACCACA
* * *
82865 CTATGAAATTTTGATAATCTCA
1 CTATAAAATTTTGATAACCACA
* * *
82887 CTATGAAATTTTGATAATCTCTA
1 CTATAAAATTTTGATAACCAC-A
* *
82910 -TATATAATTTT-AGTAACCTCA
1 CTATAAAATTTTGA-TAACCACA
*
82931 CTATAAAATCTTGATAACCACA
1 CTATAAAATTTTGATAACCACA
*
82953 -TGATGAAATTTTGAT
1 CT-ATAAAATTTTGAT
82968 CAACTCCCTA
Statistics
Matches: 162, Mismatches: 38, Indels: 26
0.72 0.17 0.12
Matches are distributed among these distances:
21 6 0.04
22 152 0.94
23 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (22 bp):
CTATAAAATTTTGATAACCACA
Found at i:82874 original size:44 final size:43
Alignment explanation
Indices: 82821--82984 Score: 122
Period size: 44 Copynumber: 3.8 Consensus size: 43
82811 GTTATCCCGT
* *
82821 ATATAAAATTTTGA-CAACCTCCCTATAAAATTTCTATAACCAC
1 ATATGAAATTTTGAGCAACCTCACTATAAAATTT-TATAACCAC
* * * * *
82864 ACTATGAAATTTTGA-TAATCTCACTATGAAATTTTGATAATCTC
1 A-TATGAAATTTTGAGCAACCTCACTATAAAATTTT-ATAACCAC
* *
82908 TATAT-ATAATTTT-AGTAACCTCACTATAAAATCTTGATAACCAC
1 -ATATGA-AATTTTGAGCAACCTCACTATAAAAT-TTTATAACCAC
* * *
82952 ATGATGAAATTTTGATCAA-CTCCCTATGAAATT
1 AT-ATGAAATTTTGAGCAACCTCACTATAAAATT
82985 ATGCTAACCA
Statistics
Matches: 96, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
43 7 0.07
44 82 0.85
45 7 0.07
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.37
Consensus pattern (43 bp):
ATATGAAATTTTGAGCAACCTCACTATAAAATTTTATAACCAC
Found at i:82896 original size:66 final size:65
Alignment explanation
Indices: 82826--82984 Score: 173
Period size: 66 Copynumber: 2.4 Consensus size: 65
82816 CCCGTATATA
* *
82826 AAATTTTGACAACCTCCCTATAAAATTTCTA-TAACCACACTATGAAATTTTGATAATCTCAC-T
1 AAATTTTGACAA-CTCCCTATAAAATTT-TAGTAACCACACTATAAAATCTTGATAA-C-CACAT
82889 -ATG
62 GATG
* * *
82892 AAATTTTGATAA-TCTCTATATATAATTTTAGTAACCTCACTATAAAATCTTGATAACCACATGA
1 AAATTTTGACAACTCCCTATA-A-AATTTTAGTAACCACACTATAAAATCTTGATAACCACATGA
82956 TG
64 TG
*
82958 AAATTTTGATCAACTCCCTATGAAATT
1 AAATTTTGA-CAACTCCCTATAAAATT
82985 ATGCTAACCA
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
64 10 0.13
65 5 0.06
66 54 0.69
67 3 0.04
68 6 0.08
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.36
Consensus pattern (65 bp):
AAATTTTGACAACTCCCTATAAAATTTTAGTAACCACACTATAAAATCTTGATAACCACATGATG
Found at i:82967 original size:88 final size:86
Alignment explanation
Indices: 82738--82984 Score: 223
Period size: 88 Copynumber: 2.8 Consensus size: 86
82728 AATCTCTATG
* * * * * * ** * *
82738 AAATTTTGATAACCACATTATAAAATTTTGGTAACTATGCAATGAAATTTTGAAAACCTCCATAT
1 AAATTTTGACAACCTCACTATAAAATTTCGATAACCACACTATGAAATTTTGATAA-CTCC-TAT
* *
82803 TAAATTTTGTTATCCCGTATATA
64 GAAATTTTGTAATCCCGTATATA
* *
82826 AAATTTTGACAACCTCCCTATAAAATTTCTATAACCACACTATGAAATTTTGATAATCTCACTAT
1 AAATTTTGACAACCTCACTATAAAATTTCGATAACCACACTATGAAATTTTGATAA-CTC-CTAT
*
82891 GAAATTTTGATAATCTC-TATATA
64 GAAATTTTG-TAATCCCGTATATA
* *
82914 TAATTTT-AGTAACCTCACTATAAAATCTT-GATAACCACA-TGATGAAATTTTGATCAACTCCC
1 AAATTTTGA-CAACCTCACTATAAAAT-TTCGATAACCACACT-ATGAAATTTTGAT-AACT-CC
82976 TATGAAATT
61 TATGAAATT
82985 ATGCTAACCA
Statistics
Matches: 132, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
87 2 0.02
88 119 0.90
89 11 0.08
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (86 bp):
AAATTTTGACAACCTCACTATAAAATTTCGATAACCACACTATGAAATTTTGATAACTCCTATGA
AATTTTGTAATCCCGTATATA
Found at i:82980 original size:22 final size:21
Alignment explanation
Indices: 82621--82984 Score: 107
Period size: 22 Copynumber: 16.4 Consensus size: 21
82611 AACGAAATAT
* **
82621 TATGAAATTTTGATAATTATAC
1 TATGAAATTTTGATAACT-CCC
* * *
82643 AATGAAATTTTTATAAC-CAC
1 TATGAAATTTTGATAACTCCC
*
82663 TAAGAAATTTTGATAATCTCCC
1 TATGAAATTTTGATAA-CTCCC
* * * *
82685 TTTTGAAATTTTGGTAATTTCTC
1 -TATGAAATTTTGATAA-CTCCC
* * *
82708 TATGTAATTTTAGTAACTTAAATCTC
1 TATGAAATTTT-G--A--TAACTCCC
*
82734 TATGAAATTTTGATAAC-CACAT
1 TATGAAATTTTGATAACTC-C-C
* * **
82756 TATAAAATTTTGGTAACTATGC
1 TATGAAATTTTGATAACT-CCC
* * *
82778 AATGAAATTTTGAAAACCTCCA
1 TATGAAATTTTGATAA-CTCCC
* *
82800 TATTAAATTTTG-TTA-TCCC
1 TATGAAATTTTGATAACTCCC
* *
82819 GTATATAAAATTTTGACAACCTCCC
1 ---TATGAAATTTTGATAA-CTCCC
*
82844 TATAAAATTTCT-ATAAC-CACAC
1 TATGAAATTT-TGATAACTC-C-C
*
82866 TATGAAATTTTGATAATCTCAC
1 TATGAAATTTTGATAA-CTCCC
*
82888 TATGAAATTTTGATAA-TCTC
1 TATGAAATTTTGATAACTCCC
* *
82908 TATATATAATTTT-AGTAACCTCAC
1 TAT-GA-AATTTTGA-TAA-CTCCC
* * *
82932 TATAAAATCTTGATAAC-CACA
1 TATGAAATTTTGATAACTC-CC
82953 TGATGAAATTTTGATCAACTCCC
1 T-ATGAAATTTTGAT-AACTCCC
82976 TATGAAATT
1 TATGAAATT
82985 ATGCTAACCA
Statistics
Matches: 253, Mismatches: 54, Indels: 70
0.67 0.14 0.19
Matches are distributed among these distances:
19 3 0.01
20 24 0.09
21 12 0.05
22 153 0.60
23 31 0.12
24 8 0.03
25 5 0.02
26 14 0.06
27 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTGATAACTCCC
Found at i:83007 original size:88 final size:88
Alignment explanation
Indices: 82836--83037 Score: 220
Period size: 88 Copynumber: 2.3 Consensus size: 88
82826 AAATTTTGAC
* * *
82836 AACCTCCCTATAAAATTTCTATAACCACACTATGAAATTTTGATAATCTCACTATGAAATTTTGA
1 AACCTCACTATAAAATTTCGATAACCACACTATGAAATTTTGATAATCTCACTATGAAATTATGA
82901 TAATCTCTATATATAATTTTAGT
66 TAATCTCTATATATAATTTTAGT
*
82924 AACCTCACTATAAAATCTT-GATAACCACA-TGATGAAATTTTGATCAA-CTCCCTATGAAATTA
1 AACCTCACTATAAAAT-TTCGATAACCACACT-ATGAAATTTTGAT-AATCTCACTATGAAATTA
* *
82986 TGCTAA-C-C-ATA-ATTCGAAATTTTGGT
63 TGATAATCTCTATATA-T---AATTTTAGT
* *
83012 AACCTCACTTTAAATTTTCGATAACC
1 AACCTCACTATAAAATTTCGATAACC
83038 TGCCTACAAA
Statistics
Matches: 98, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
84 1 0.01
85 4 0.04
86 1 0.01
87 4 0.04
88 84 0.86
89 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (88 bp):
AACCTCACTATAAAATTTCGATAACCACACTATGAAATTTTGATAATCTCACTATGAAATTATGA
TAATCTCTATATATAATTTTAGT
Found at i:83335 original size:22 final size:22
Alignment explanation
Indices: 83307--83425 Score: 120
Period size: 22 Copynumber: 5.3 Consensus size: 22
83297 TAACCTCTTG
* *
83307 TGATAACCTCCATTTGAAATTT
1 TGATAACCACCATATGAAATTT
83329 TGATAACCA-CATTATGAAATTT
1 TGATAACCACCA-TATGAAATTT
83351 TGATAACCAACC-TATGAAATTT
1 TGATAACC-ACCATATGAAATTT
*
83373 TAATAACCACACTATATGAAATTT
1 TGATAACCAC-C-ATATGAAATTT
*
83397 TAATAACCA-CACTATG-AATTT
1 TGATAACCACCA-TATGAAATTT
83418 GTGATAAC
1 -TGATAAC
83426 TCTGTATGAA
Statistics
Matches: 85, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
21 10 0.12
22 54 0.64
23 1 0.01
24 20 0.24
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.34
Consensus pattern (22 bp):
TGATAACCACCATATGAAATTT
Found at i:83395 original size:24 final size:24
Alignment explanation
Indices: 83321--83411 Score: 127
Period size: 22 Copynumber: 4.0 Consensus size: 24
83311 AACCTCCATT
*
83321 TGAAATTTTGATAACCACA-T-TA
1 TGAAATTTTAATAACCACACTATA
* *
83343 TGAAATTTTGATAACCA-AC-CTA
1 TGAAATTTTAATAACCACACTATA
83365 TGAAATTTTAATAACCACACTATA
1 TGAAATTTTAATAACCACACTATA
83389 TGAAATTTTAATAACCACACTAT
1 TGAAATTTTAATAACCACACTAT
83412 GAATTTGTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
21 1 0.02
22 35 0.56
23 2 0.03
24 25 0.40
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (24 bp):
TGAAATTTTAATAACCACACTATA
Found at i:83425 original size:46 final size:44
Alignment explanation
Indices: 83321--83425 Score: 142
Period size: 46 Copynumber: 2.3 Consensus size: 44
83311 AACCTCCATT
*
83321 TGAAATTTTGATAACCACATTATGAAATTTTGATAACCAACCTA
1 TGAAATTTTGATAACCACATTATGAAATTTTAATAACCAACCTA
*
83365 TGAAATTTTAATAACCACACTATATGAAATTTTAATAACC-ACACTA
1 TGAAATTTTGATAACCACA-T-TATGAAATTTTAATAACCAAC-CTA
83411 TG-AATTTGTGATAAC
1 TGAAATTT-TGATAAC
83426 TCTGTATGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
44 18 0.33
45 8 0.15
46 28 0.52
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (44 bp):
TGAAATTTTGATAACCACATTATGAAATTTTAATAACCAACCTA
Found at i:85324 original size:134 final size:131
Alignment explanation
Indices: 85168--85433 Score: 406
Period size: 134 Copynumber: 2.0 Consensus size: 131
85158 CATTGTTTAA
* * *
85168 ACTTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATATCCTTATA
1 ACTTTTATAGTTTTACTCAACTAAAAACACTATTTTTATCTAATTAAATCT-A-ATATCCTTATA
* * * * *
85233 ACTGTTTTATTTTTACCATTTTTATTATTTTAAATAAAAAACTTATATATATTAGAATTTTTAAA
64 ACTATTTTATTTTTACCA-TTTTACTAATTTAAATAAAAAACTTAGATATATTACAATTTTTAAA
85298 ATAT
128 ATAT
85302 ACTTTTATAGTTTTACTCAACTAAAAACACTATTTTTATCTAATTAAATCTAATATCCTTATAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACACTATTTTTATCTAATTAAATCTAATATCCTTATAAC
* * *
85367 TATTTTATTTTTACTATTTTACTAATTTAATTAAAAAACTTAGATATATTACAATTTTTAGAATA
66 TATTTTATTTTTACCATTTTACTAATTTAAATAAAAAACTTAGATATATTACAATTTTTAAAATA
85432 T
131 T
85433 A
1 A
85434 TTTCTTAAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
131 45 0.37
132 27 0.22
133 1 0.01
134 48 0.40
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (131 bp):
ACTTTTATAGTTTTACTCAACTAAAAACACTATTTTTATCTAATTAAATCTAATATCCTTATAAC
TATTTTATTTTTACCATTTTACTAATTTAAATAAAAAACTTAGATATATTACAATTTTTAAAATA
T
Found at i:88320 original size:33 final size:33
Alignment explanation
Indices: 88283--88396 Score: 228
Period size: 33 Copynumber: 3.5 Consensus size: 33
88273 TGCAATTGCC
88283 TCATGGTAAAAACTCTAAAATATAGCCTAATTG
1 TCATGGTAAAAACTCTAAAATATAGCCTAATTG
88316 TCATGGTAAAAACTCTAAAATATAGCCTAATTG
1 TCATGGTAAAAACTCTAAAATATAGCCTAATTG
88349 TCATGGTAAAAACTCTAAAATATAGCCTAATTG
1 TCATGGTAAAAACTCTAAAATATAGCCTAATTG
88382 TCATGGTAAAAACTC
1 TCATGGTAAAAACTC
88397 CTACCTCCAC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 81 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (33 bp):
TCATGGTAAAAACTCTAAAATATAGCCTAATTG
Done.