Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006130.1 Corchorus capsularis cultivar CVL-1 contig06148, 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: 32116
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:4143 original size:58 final size:56
Alignment explanation
Indices: 4077--4200 Score: 135
Period size: 56 Copynumber: 2.2 Consensus size: 56
4067 TTATATATAT
* *
4077 TATATATAT-CCAAAAATCATTTTTATTTTAATATGTAAAATATTTTATTAAATAAG-AA
1 TATATATATACCAAAAA--A-TTTTATTTTAATATATAAAATATATTATT-AATAAGTAA
*** * *
4135 TATATATATATGTAAAAATTTTATTTTAATATATAATATATATTATTAATATGTAA
1 TATATATATACCAAAAAATTTTATTTTAATATATAAAATATATTATTAATAAGTAA
4191 TATATATATA
1 TATATATATA
4201 TGTGTAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
55 5 0.09
56 38 0.67
57 1 0.02
58 9 0.16
59 4 0.07
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (56 bp):
TATATATATACCAAAAAATTTTATTTTAATATATAAAATATATTATTAATAAGTAA
Found at i:4173 original size:7 final size:7
Alignment explanation
Indices: 4161--4201 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
4151 AATTTTATTT
4161 TAATATA
1 TAATATA
4168 TAATATA
1 TAATATA
*
4175 TATTAT-
1 TAATATA
*
4181 TAATATG
1 TAATATA
4188 TAATATA
1 TAATATA
4195 T-ATATA
1 TAATATA
4201 T
1 T
4202 GTGTAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
6 11 0.37
7 19 0.63
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (7 bp):
TAATATA
Found at i:4173 original size:36 final size:35
Alignment explanation
Indices: 4107--4177 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
4097 TTTTATTTTA
4107 ATATGTAAAATATTTTATTAAATAAGAATATATAT
1 ATATGTAAAATATTTTATTAAATAAGAATATATAT
* *
4142 ATATGTAAAA-ATTTTATTTTAATATATAATATATAT
1 ATATGTAAAATATTTTA-TTAAATA-AGAATATATAT
4178 TATTAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 6 0.19
35 16 0.50
36 10 0.31
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (35 bp):
ATATGTAAAATATTTTATTAAATAAGAATATATAT
Found at i:4185 original size:20 final size:19
Alignment explanation
Indices: 4156--4197 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
4146 GTAAAAATTT
4156 TATTTTAATATATAATATA
1 TATTTTAATATATAATATA
*
4175 TATTATTAATATGTAATATA
1 TATT-TTAATATATAATATA
4195 TAT
1 TAT
4198 ATATGTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATTTTAATATATAATATA
Found at i:4207 original size:58 final size:56
Alignment explanation
Indices: 4097--4203 Score: 162
Period size: 56 Copynumber: 1.9 Consensus size: 56
4087 CAAAAATCAT
* *
4097 TTTTATTTTAATATGTAAAATATTTTATTAAATAAGAATATATATATATGTAAAAA
1 TTTTATTTTAATATATAAAATATATTATTAAATAAGAATATATATATATGTAAAAA
* *
4153 TTTTATTTTAATATATAATATATATTATT-AATATGTAATATATATATATGT
1 TTTTATTTTAATATATAAAATATATTATTAAATAAG-AATATATATATATGT
4204 GTAATATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 5 0.11
56 41 0.89
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (56 bp):
TTTTATTTTAATATATAAAATATATTATTAAATAAGAATATATATATATGTAAAAA
Found at i:5349 original size:12 final size:13
Alignment explanation
Indices: 5326--5356 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
5316 TATAATAAAC
5326 AAAGAGACAGGTA
1 AAAGAGACAGGTA
5339 AAAGA-ACAGGTA
1 AAAGAGACAGGTA
5351 AAAGAG
1 AAAGAG
5357 GGTGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.58, C:0.06, G:0.29, T:0.06
Consensus pattern (13 bp):
AAAGAGACAGGTA
Found at i:23264 original size:32 final size:34
Alignment explanation
Indices: 23108--24087 Score: 178
Period size: 35 Copynumber: 27.6 Consensus size: 34
23098 CGACATTCCA
** * *
23108 CTTAATTGTCCTGAATTAAGTTCTTTACTAACTT
1 CTTAATTACCCTGAATTAAGTTCTTTACTGACCT
* * *
23142 GCTTAATTACCCTAAATTAAGCTCTTTATTGACTCT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGAC-CT
* * *
23178 ACTTAATTACCCTGAATTAAGCTCTTGATTGACTCT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGAC-CT
23214 ACTTAATTAACCCT-AATTAAGTTCTTTACTGA-C-
1 -CTTAATT-ACCCTGAATTAAGTTCTTTACTGACCT
* * *
23247 CTTAATTACCTTGAATTAAGTTCTTTACT--TCA
1 CTTAATTACCCTGAATTAAGTTCTTTACTGACCT
* * * *
23279 CTTAA-TCCCCTTGGATTAAG-TCTCTAACTGATCTT
1 CTTAATTACCC-TGAATTAAGTTCT-TTACTGA-CCT
* * * * * * * **
23314 GCTTAGTCATCTTGGATTAAG-CCTTTGCTGATTTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGA-CCT
* ** * **
23349 ACTTAATTTCTTTGAAATTAAG-TCTTTGCTGATTT
1 -CTTAATTACCCTG-AATTAAGTTCTTTACTGACCT
* * *
23384 ACTTAATTTCCCTGAATTATG-TCTTTGACTG-CTTTTT
1 -CTTAATTACCCTGAATTAAGTTCTTT-ACTGAC---CT
* * *
23421 ATTTAATTACCCTGAATTAAG-TCTTTACTTAGTCT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGA-CCT
* * *
23456 ACTTAATTACCCTGAATTAAG-CCTTTGCTGA-TT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGACCT
***
23489 AACTTAATTACCCTGAATTAAG-TCTTTACCTGTTTT
1 --CTTAATTACCCTGAATTAAGTTCTTTA-CTGACCT
* * *
23525 ACTTAATTACCCTGAATT-AGGTCTTTTACTGTCTGTGTTT
1 -CTTAATTACCCTGAATTAAGTTC-TTTACTGAC-----CT
* *
23565 ACTTAATTACCCTGAATTAAG-TCTTTGCTGACTGTGTTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGAC-----CT
* * ***
23604 ACTTAATTACCTTGAATTAAGTCTTTGTTGACTGTGTTT
1 -CTTAATTACCCTGAATTAAGT-TCT-TT-ACTG-ACCT
* * * * * **
23643 ACCTAATTACCCTTAATTCAG-CCTTTGCTGATTTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGA-CCT
* * * **
23678 ACTTAATTACCTTGAGTTAAGTCCTTTACTGATTTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGA-CCT
* **
23714 ACTTAATTACCCTGAATTAAGTCCTTTACTGAGTTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGA-CCT
* * **
23750 ACTTAATTATCCTGAATTAAG-TCTTTGCTGATTTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGA-CCT
* * * *
23785 ACTTAATTACCTTGAATTAAGTCCTTGACTGATCTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGA-CCT
* ** *
23821 ACTTAATTTCCCTGAATTAAG-TCTTTGTTGACAGTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGAC--CT
* * * * **
23857 ACTTAATT-TCCTCGATTTAAGTCCTTGACTGATTTT
1 -CTTAATTACCCT-GAATTAAGTTCTTTACTGA-CCT
** * **
23893 ACTTAATTACCCTGAATTAAG-TCTTTGTTCATTTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGA-CCT
* * * * *
23928 ACTTACTTACCTTGAATAAAG-TCTTTGCTGACTTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGAC-CT
* * **
23963 ACTTAATTACCCTGAATTAAG-TCTTTGCAGATTTT
1 -CTTAATTACCCTGAATTAAGTTCTTTACTGA-CCT
* **
23998 ACTTAATTACCCTAAATTAAG-TCTTTGA-TGATTT
1 -CTTAATTACCCTGAATTAAGTTCTTT-ACTGACCT
* ***
24032 ACTTAATTACCCTGAATTAAG-TCTTTGCCTGTTTT
1 -CTTAATTACCCTGAATTAAGTTCTTT-ACTGACCT
24067 ACTTAATTACCCTGAATTAAG
1 -CTTAATTACCCTGAATTAAG
24088 ACTTTCCTGA
Statistics
Matches: 768, Mismatches: 129, Indels: 96
0.77 0.13 0.10
Matches are distributed among these distances:
31 11 0.01
32 40 0.05
33 1 0.00
34 69 0.09
35 295 0.38
36 227 0.30
37 41 0.05
39 53 0.07
40 22 0.03
41 4 0.01
42 2 0.00
43 3 0.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (34 bp):
CTTAATTACCCTGAATTAAGTTCTTTACTGACCT
Found at i:23392 original size:35 final size:35
Alignment explanation
Indices: 23107--24240 Score: 953
Period size: 36 Copynumber: 31.8 Consensus size: 35
23097 TCGACATTCC
** * **
23107 ACTTAATTGTCCTGAATTAAGTTCTTTACT-AACTT
1 ACTTAATTACCCTGAATTAAG-TCTTTGCTGATTTT
* * ** * *
23142 GCTTAATTACCCTAAATTAAGCTCTTTATTGACTCT
1 ACTTAATTACCCTGAATTAAG-TCTTTGCTGATTTT
* * *
23178 ACTTAATTACCCTGAATTAAG-CTCTTGATTGACTCT
1 ACTTAATTACCCTGAATTAAGTCT-TTG-CTGATTTT
*
23214 ACTTAATTAACCCT-AATTAAGTTCTTTACTGA----
1 ACTTAATT-ACCCTGAATTAAG-TCTTTGCTGATTTT
* * * *
23246 CCTTAATTACCTTGAATTAAGT-TCTT--T-ACTTC
1 ACTTAATTACCCTGAATTAAGTCT-TTGCTGATTTT
* * ** *
23278 ACTTAA-TCCCCTTGGATTAAGTCTCTAACTGATCTT
1 ACTTAATTACCC-TGAATTAAGTCT-TTGCTGATTTT
* * * * * * *
23314 GCTTAGTCATCTTGGATTAAGCCTTTGCTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGATTTT
* **
23349 ACTTAATTTCTTTGAAATTAAGTCTTTGCTGA-TTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGCTGATTTT
* * *
23384 ACTTAATTTCCCTGAATTATGTCTTTGACTGCTTTTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-CTG-ATTTT
* * * * *
23421 ATTTAATTACCCTGAATTAAGTCTTTACTTAGTCT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGATTTT
* *
23456 ACTTAATTACCCTGAATTAAGCCTTTGCTGA-TTA
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGATTTT
*
23490 ACTTAATTACCCTGAATTAAGTCTTTACCTG-TTTT
1 ACTTAATTACCCTGAATTAAGTCTTT-GCTGATTTT
*
23525 ACTTAATTACCCTGAATTAGGTCTTTTACTGTCTG-TGTTT
1 ACTTAATTACCCTGAATTAAGTC--TT--TG-CTGAT-TTT
23565 ACTTAATTACCCTGAATTAAGTCTTTGCTGACTGTGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGA---T-TTT
* *
23604 ACTTAATTACCTTGAATTAAGTCTTTGTTGACTGTGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGA---T-TTT
* * * *
23643 ACCTAATTACCCTTAATTCAGCCTTTGCTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGATTTT
* * *
23678 ACTTAATTACCTTGAGTTAAGTCCTTTACTGATTTT
1 ACTTAATTACCCTGAATTAAGT-CTTTGCTGATTTT
* *
23714 ACTTAATTACCCTGAATTAAGTCCTTTACTGAGTTT
1 ACTTAATTACCCTGAATTAAGT-CTTTGCTGATTTT
*
23750 ACTTAATTATCCTGAATTAAGTCTTTGCTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGATTTT
* * *
23785 ACTTAATTACCTTGAATTAAGTCCTTGACTGATCTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-CTGATTTT
* * **
23821 ACTTAATTTCCCTGAATTAAGTCTTTGTTGACAGTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGA-TTTT
* * *
23857 ACTTAATT-TCCTCGATTTAAGTCCTTGACTGATTTT
1 ACTTAATTACCCT-GAATTAAGTCTTTG-CTGATTTT
* *
23893 ACTTAATTACCCTGAATTAAGTCTTTGTTCATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGATTTT
* * * *
23928 ACTTACTTACCTTGAATAAAGTCTTTGCTGACTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGATTTT
*
23963 ACTTAATTACCCTGAATTAAGTCTTTGCAGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGATTTT
* *
23998 ACTTAATTACCCTAAATTAAGTCTTTGATGA-TTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTGATTTT
24032 ACTTAATTACCCTGAATTAAGTCTTTGCCTG-TTTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-CTGATTTT
* *
24067 ACTTAATTACCCTGAATTAAGACTTTCCTGACTATGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTG---AT-TTT
* *
24106 ACTTAATTACCCTGAATTAAGACTTTGATTG-TGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-CTGAT-TTT
*
24142 ACTTAATTATCCTGAATTAAGTCTTTGACTG-TGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-CTGAT-TTT
*
24178 ACTTAATTACCCTGAATTAAGTCTTTGACAG-TGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-CTGAT-TTT
* *
24214 ACTTAATTACACTGAATTAAATCTTTG
1 ACTTAATTACCCTGAATTAAGTCTTTG
24241 AGTGTATTCT
Statistics
Matches: 916, Mismatches: 135, Indels: 95
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.00
29 1 0.00
30 1 0.00
31 10 0.01
32 28 0.03
33 3 0.00
34 72 0.08
35 303 0.33
36 322 0.35
37 42 0.05
38 5 0.01
39 101 0.11
40 27 0.03
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTCTTTGCTGATTTT
Found at i:23444 original size:143 final size:141
Alignment explanation
Indices: 23143--24240 Score: 929
Period size: 143 Copynumber: 7.7 Consensus size: 141
23133 TACTAACTTG
* * * *
23143 CTTAATTACCCTAAATTAAG-CTCTTTATTGACTCTACTTAATTACCCTGAATTAAG-CTCTTGA
1 CTTAATTACCCTGAATTAAGTCTC-TGACTGA-TTTACTTAATTACCCTGAATTAAGTCT-TTG-
* * * * * * *
23206 TTGACTCTACTTAATTAACCCT-AATTAAGTTCTTTACTGA----CCTTAATTACCTTGAATTAA
62 CTGATTTTACTTAATT-ACCTTGAATTAAG-TCTTTGCTGATTTTACTTAATTACCCTGAATTAA
*
23266 GTTCTTT-AC----TTCA
125 G-TCTTTGACTGTTTTTA
* * * * * * * * * *
23279 CTTAA-TCCCCTTGGATTAAGTCTCTAACTGATCTTGCTTAGTCATCTTGGATTAAGCCTTTGCT
1 CTTAATTACCC-TGAATTAAGTCTCTGACTGAT-TTACTTAATTACCCTGAATTAAGTCTTTGCT
* * * *
23343 GATTTTACTTAATTTCTTTGAAATTAAGTCTTTGCTGA-TTTACTTAATTTCCCTGAATTATGTC
64 GATTTTACTTAATTACCTTG-AATTAAGTCTTTGCTGATTTTACTTAATTACCCTGAATTAAGTC
23407 TTTGACTGCTTTTTA
128 TTTGACTG-TTTTTA
* * * * *
23422 TTTAATTACCCTGAATTAAGTCT-TTACTTAGTCTACTTAATTACCCTGAATTAAGCCTTTGCTG
1 CTTAATTACCCTGAATTAAGTCTCTGACTGA-TTTACTTAATTACCCTGAATTAAGTCTTTGCTG
* * * *
23486 A-TTAACTTAATTACCCTGAATTAAGTCTTTACCTG-TTTTACTTAATTACCCTGAATTAGGTCT
65 ATTTTACTTAATTACCTTGAATTAAGTCTTT-GCTGATTTTACTTAATTACCCTGAATTAAGTCT
*
23549 TTTACTGTCTGTGTTTA
129 TTGACTG--T-T-TTTA
* *
23566 CTTAATTACCCTGAATTAAGTCTTTGCTGACTGTGTTTACTTAATTACCTTGAATTAAGTCTTTG
1 CTTAATTACCCTGAATTAAGTC--T-CTGACTG-ATTTACTTAATTACCCTGAATTAAGTCTTTG
* * * * * *
23631 TTGACTGTGTTTACCTAATTACCCTT-AATTCAGCCTTTGCTGATTTTACTTAATTACCTTGAGT
62 CTGA---T-TTTACTTAATTA-CCTTGAATTAAGTCTTTGCTGATTTTACTTAATTACCCTGAAT
*
23695 TAAGTCCTTT-ACTGATTTTA
122 TAAGT-CTTTGACTGTTTTTA
* *
23715 CTTAATTACCCTGAATTAAGTC-CTTTACTGAGTTTACTTAATTATCCTGAATTAAGTCTTTGCT
1 CTTAATTACCCTGAATTAAGTCTC-TGACTGA-TTTACTTAATTACCCTGAATTAAGTCTTTGCT
* * *
23779 GATTTTACTTAATTACCTTGAATTAAGTCCTTGACTGATCTTACTTAATTTCCCTGAATTAAGTC
64 GATTTTACTTAATTACCTTGAATTAAGTCTTTG-CTGATTTTACTTAATTACCCTGAATTAAGTC
* ***
23844 TTTG-TTGACAGTTA
128 TTTGACTG-TTTTTA
* * *
23858 CTTAATT-TCCTCGATTTAAGTC-CTTGACTGATTTTACTTAATTACCCTGAATTAAGTCTTTGT
1 CTTAATTACCCT-GAATTAAGTCTC-TGACTGA-TTTACTTAATTACCCTGAATTAAGTCTTTGC
* * * *
23921 TCATTTTACTTACTTACCTTGAATAAAGTCTTTGCTGACTTTACTTAATTACCCTGAATTAAGTC
63 TGATTTTACTTAATTACCTTGAATTAAGTCTTTGCTGATTTTACTTAATTACCCTGAATTAAGTC
* *
23986 TTTG-CAGATTTTA
128 TTTGACTGTTTTTA
* *
23999 CTTAATTACCCTAAATTAAGTCTTTGA-TGATTTACTTAATTACCCTGAATTAAGTCTTTGCCTG
1 CTTAATTACCCTGAATTAAGTCTCTGACTGATTTACTTAATTACCCTGAATTAAGTCTTTG-CTG
* * *
24063 -TTTTACTTAATTACCCTGAATTAAGACTTTCCTGACTATGTTTACTTAATTACCCTGAATTAAG
65 ATTTTACTTAATTACCTTGAATTAAGTCTTTGCTG---AT-TTTACTTAATTACCCTGAATTAAG
* * *
24127 ACTTTGATTGTGTTTA
126 TCTTTGACTGTTTTTA
* * * *
24143 CTTAATTATCCTGAATTAAGTCTTTGACTGTGTTTACTTAATTACCCTGAATTAAGTCTTTGACA
1 CTTAATTACCCTGAATTAAGTCTCTGACTG-ATTTACTTAATTACCCTGAATTAAGTCTTTG-CT
*
24208 G-TGTTTACTTAATTACAC-TGAATTAAATCTTTG
64 GAT-TTTACTTAATTAC-CTTGAATTAAGTCTTTG
24241 AGTGTATTCT
Statistics
Matches: 786, Mismatches: 122, Indels: 97
0.78 0.12 0.10
Matches are distributed among these distances:
134 2 0.00
135 27 0.03
136 43 0.05
137 10 0.01
138 19 0.02
139 59 0.08
140 16 0.02
141 72 0.09
142 100 0.13
143 162 0.21
144 59 0.08
145 3 0.00
146 70 0.09
147 25 0.03
148 35 0.04
149 26 0.03
150 1 0.00
152 3 0.00
153 47 0.06
154 7 0.01
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (141 bp):
CTTAATTACCCTGAATTAAGTCTCTGACTGATTTACTTAATTACCCTGAATTAAGTCTTTGCTGA
TTTTACTTAATTACCTTGAATTAAGTCTTTGCTGATTTTACTTAATTACCCTGAATTAAGTCTTT
GACTGTTTTTA
Found at i:27449 original size:14 final size:14
Alignment explanation
Indices: 27430--27459 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
27420 CTTTGTTTTG
27430 ATTTTCCTAATGCA
1 ATTTTCCTAATGCA
27444 ATTTTCCTAATGCA
1 ATTTTCCTAATGCA
27458 AT
1 AT
27460 GTGAATGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTTTCCTAATGCA
Found at i:27996 original size:20 final size:22
Alignment explanation
Indices: 27981--28569 Score: 213
Period size: 22 Copynumber: 27.0 Consensus size: 22
27971 CTGCCTTAAG
27981 GTTTGAAAGTCTGCCTTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
*
28003 GTTTGAAAGTCTG-TTGTGAGAC
1 GTTTGAAAGTCTGCCT-TGAGAC
* * * *
28025 GCTTGAAAATATGCCTTGAGAT
1 GTTTGAAAGTCTGCCTTGAGAC
* *
28047 GCTTTGAAAGTCTTCCTTAAGAC
1 G-TTTGAAAGTCTGCCTTGAGAC
* *
28070 GCTTGGAAGTCTGCCTTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
*
28092 GCTTGAAAGTCTGCCCTT-AGAC
1 GTTTGAAAGTCTG-CCTTGAGAC
*
28114 GATTGAAAGTCTGGCCTT-AGAC
1 GTTTGAAAGTCT-GCCTTGAGAC
* *
28136 ATTTAAAAGTCT-CCTTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
* *
28157 ------ACGTCTGCCTTGAAAC
1 GTTTGAAAGTCTGCCTTGAGAC
** * *
28173 ACTTAAAAGTCTGACC-TAAGAC
1 GTTTGAAAGTCTG-CCTTGAGAC
* * *
28195 GTTGGGAAGTCT-ACTTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
* * * * *
28216 GCTTAAAAGTCTACCCTGAAAC
1 GTTTGAAAGTCTGCCTTGAGAC
** *
28238 ACTTGAAAGTCTGCCCTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
** * * **
28260 ACTTAAAATTCTGCCCCGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
* *
28282 GCTTGAAAAGTCTGCCATGAGAC
1 GTTTG-AAAGTCTGCCTTGAGAC
* * *
28305 GCTTGAAAGTTTG-CTCTAAGAC
1 GTTTGAAAGTCTGCCT-TGAGAC
* *
28327 GCTTGGAAAGTCTGCCCTGAGAC
1 G-TTTGAAAGTCTGCCTTGAGAC
** * *
28350 ACTTAAAAGTCTGCCCTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
** ** *
28372 ACTTGGGAGTCTGCCCTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
* ** * *
28394 GCTTGGGAGTCTGCCCTAAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
** *
28416 ACTTAAAAGTCTGCCTTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
* * *
28438 GCTTTCG--AGTCTGCCCTAAGAA
1 G-TTT-GAAAGTCTGCCTTGAGAC
** * * * *
28460 ACTT-ATTAGTCTTCCTTGAAAT
1 GTTTGA-AAGTCTGCCTTGAGAC
* ** *
28482 GCTTGAAAGTCTGCCCAGAGAA
1 GTTTGAAAGTCTGCCTTGAGAC
* * *
28504 GCTTGAAAGTCCGCCCTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
** * *
28526 ACTTAAAAGTTTGCCTTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
* * *
28548 GCTTG-GAGTCTGCCCTGAGAC
1 GTTTGAAAGTCTGCCTTGAGAC
28569 G
1 G
28570 CTTGGGTTAG
Statistics
Matches: 433, Mismatches: 108, Indels: 53
0.73 0.18 0.09
Matches are distributed among these distances:
15 5 0.01
16 8 0.02
20 5 0.01
21 35 0.08
22 319 0.74
23 60 0.14
24 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (22 bp):
GTTTGAAAGTCTGCCTTGAGAC
Found at i:28114 original size:44 final size:44
Alignment explanation
Indices: 27983--28573 Score: 414
Period size: 44 Copynumber: 13.6 Consensus size: 44
27973 GCCTTAAGGT
* ***
27983 TTGAAAGTCTGCCTTGAGACGTTTGAAAGTCTGTTGTGAGACGC
1 TTGAAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
* * * * * *
28027 TTGAAAATATGCCTTGAGATGCTTTGAAAGTCTTCCTTAAGACGC
1 TTGAAAGTCTGCCTTGAGACGC-TTGAAAGTCTGCCCTGAGACGC
* * *
28072 TTGGAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTTAGACGA
1 TTGAAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
** * *
28116 TTGAAAGTCTGGCCTT-AGACATTTAAAAGTCT-CCTTGAGA--C
1 TTGAAAGTCT-GCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
* * * * * *
28157 ----ACGTCTGCCTTGAAACACTTAAAAGTCTGACCTAAGACG-
1 TTGAAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
* * * * * *
28196 TTGGGAAGTCT-ACTTGAGACGCTTAAAAGTCTACCCTGAAACAC
1 TT-GAAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
* * * * *
28240 TTGAAAGTCTGCCCTGAGACACTTAAAATTCTGCCCCGAGACGC
1 TTGAAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
* * * *
28284 TTGAAAAGTCTGCCATGAGACGCTTGAAAGTTTGCTCTAAGACGC
1 TTG-AAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
* * * *
28329 TTGGAAAGTCTGCCCTGAGACACTTAAAAGTCTGCCCTGAGACAC
1 TT-GAAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
** * ** * *
28374 TTGGGAGTCTGCCCTGAGACGCTTGGGAGTCTGCCCTAAGACAC
1 TTGAAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
* *** * **
28418 TTAAAAGTCTGCCTTGAGACGCTTTCGAGTCTGCCCTAAGAAAC
1 TTGAAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
* * * * * *
28462 TT-ATTAGTCTTCCTTGAAATGCTTGAAAGTCTGCCCAGAGAAGC
1 TTGA-AAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
* * * * * *
28506 TTGAAAGTCCGCCCTGAGACACTTAAAAGTTTGCCTTGAGACGC
1 TTGAAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
* *
28550 TTG-GAGTCTGCCCTGAGACGCTTG
1 TTGAAAGTCTGCCTTGAGACGCTTG
28574 GGTTAGGGGT
Statistics
Matches: 427, Mismatches: 103, Indels: 35
0.76 0.18 0.06
Matches are distributed among these distances:
36 5 0.01
37 19 0.04
38 5 0.01
43 55 0.13
44 230 0.54
45 112 0.26
46 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (44 bp):
TTGAAAGTCTGCCTTGAGACGCTTGAAAGTCTGCCCTGAGACGC
Found at i:28132 original size:67 final size:67
Alignment explanation
Indices: 27983--28439 Score: 184
Period size: 67 Copynumber: 7.0 Consensus size: 67
27973 GCCTTAAGGT
* * * *
27983 TTGAAAGTCTGCCTTGAGACGTTTGAAAGTCTGTTGTGAGACGCTTGAAAATATGCCTTGAGATG
1 TTGAAAGTCTGCCTTAAGACGCTTGAAAGTCTGCTGTGAGACGCTTGAAAATATGCCTTGAGACG
*
28048 CT
66 CA
* * * *
28050 TTGAAAGTCTTCCTTAAGACGCTTGGAAGTCTGCCT-TGAGACGCTTGAAAGTCTGCCCTT-AGA
1 TTGAAAGTCTGCCTTAAGACGCTTGAAAGTCTG-CTGTGAGACGCTTGAAAATATG-CCTTGAGA
28113 CG-A
64 CGCA
** * * * * *
28116 TTGAAAGTCTGGCCTT-AGACATTTAAAAGTCTCCT-TGAGACAC--G----TCTGCCTTGAAAC
1 TTGAAAGTCT-GCCTTAAGACGCTTGAAAGTCTGCTGTGAGACGCTTGAAAATATGCCTTGAGAC
*
28173 AC-
65 GCA
* * * * * * *
28175 TTAAAAGTCTGACC-TAAGACG-TTGGGAAGTCTACT-TGAGACGCTT-AAAAGTCTACCCTGAA
1 TTGAAAGTCTG-CCTTAAGACGCTT-GAAAGTCTGCTGTGAGACGCTTGAAAA-TATGCCTTGAG
*
28236 ACAC-
63 ACGCA
* * * * * *** * *
28240 TTGAAAGTCTGCCCTGAGACACTTAAAATTCTGCCCCGAGACGCTTGAAAAGTCTGCCATGAGAC
1 TTGAAAGTCTGCCTTAAGACGCTTGAAAGTCTGCTGTGAGACGCTTGAAAA-TATGCCTTGAGAC
28305 GC-
65 GCA
* ** * * *
28307 TTGAAAGTTTG-CTCTAAGACGCTTGGAAAGTCTGCCCTGAGACACTT-AAAAGTCTGCCCTGAG
1 TTGAAAGTCTGCCT-TAAGACGCTT-GAAAGTCTGCTGTGAGACGCTTGAAAA-TATGCCTTGAG
*
28370 ACAC-
63 ACGCA
** * * ** ** * * *
28374 TTGGGAGTCTGCCCTGAGACGCTTGGGAGTCTGCCCTAAGACACTT-AAAAGTCTGCCTTGAGAC
1 TTGAAAGTCTGCCTTAAGACGCTTGAAAGTCTGCTGTGAGACGCTTGAAAA-TATGCCTTGAGAC
28438 GC
65 GC
28440 TTTCGAGTCT
Statistics
Matches: 309, Mismatches: 59, Indels: 45
0.75 0.14 0.11
Matches are distributed among these distances:
58 8 0.03
59 37 0.12
63 1 0.00
64 2 0.01
65 43 0.14
66 71 0.23
67 123 0.40
68 24 0.08
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (67 bp):
TTGAAAGTCTGCCTTAAGACGCTTGAAAGTCTGCTGTGAGACGCTTGAAAATATGCCTTGAGACG
CA
Found at i:28249 original size:22 final size:22
Alignment explanation
Indices: 28210--28573 Score: 284
Period size: 22 Copynumber: 16.5 Consensus size: 22
28200 GAAGTCTACT
* * *
28210 TGAGACGCTTAAAAGTCTACCC
1 TGAGACACTTGAAAGTCTGCCC
*
28232 TGAAACACTTGAAAGTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
* *
28254 TGAGACACTTAAAATTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
* * *
28276 CGAGACGCTTGAAAAGTCTGCCA
1 TGAGACACTTG-AAAGTCTGCCC
* * *
28299 TGAGACGCTTGAAAGTTTGCTC
1 TGAGACACTTGAAAGTCTGCCC
* *
28321 TAAGACGCTTGGAAAGTCTGCCC
1 TGAGACACTT-GAAAGTCTGCCC
*
28344 TGAGACACTTAAAAGTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
**
28366 TGAGACACTTGGGAGTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
* **
28388 TGAGACGCTTGGGAGTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
* * *
28410 TAAGACACTTAAAAGTCTGCCT
1 TGAGACACTTGAAAGTCTGCCC
* ***
28432 TGAGACGCTTTCGAGTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
* * * * *
28454 TAAGAAACTT-ATTAGTCTTCCT
1 TGAGACACTTGA-AAGTCTGCCC
* **
28476 TGAAATGCTTGAAAGTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
* *
28498 AGAGA-AGCTTGAAAGTCCGCCC
1 TGAGACA-CTTGAAAGTCTGCCC
* * *
28520 TGAGACACTTAAAAGTTTGCCT
1 TGAGACACTTGAAAGTCTGCCC
* *
28542 TGAGACGCTTG-GAGTCTGCCC
1 TGAGACACTTGAAAGTCTGCCC
*
28563 TGAGACGCTTG
1 TGAGACACTTG
28574 GGTTAGGGGT
Statistics
Matches: 270, Mismatches: 66, Indels: 13
0.77 0.19 0.04
Matches are distributed among these distances:
21 18 0.07
22 213 0.79
23 39 0.14
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.25
Consensus pattern (22 bp):
TGAGACACTTGAAAGTCTGCCC
Found at i:28471 original size:66 final size:66
Alignment explanation
Indices: 28212--28464 Score: 202
Period size: 67 Copynumber: 3.8 Consensus size: 66
28202 AGTCTACTTG
* * * ** * * ** * *
28212 AGACGCTTAAAAGTCTACCCTGAAACACTTGAAAGTCTGCCCTGAGACACTTAAAATTCTGCCCC
1 AGACACTTAAAAGTCTGCCCTGAGACACTTGCGAGTCTGCCCTAAGAAACTTAGGAGTCTGCCCT
*
28277 G
66 A
* * * ** * * **
28278 AGACGCTTGAAAAGTCTGCCATGAGACGCTTGAAAGTTTGCTCTAAGACGCTT-GGAAAGTCTGC
1 AGACACTT-AAAAGTCTGCCCTGAGACACTTGCGAGTCTGCCCTAAGAAACTTAGG--AGTCTGC
*
28342 CCTG
63 CCTA
* * ** *
28346 AGACACTTAAAAGTCTGCCCTGAGACACTTGGGAGTCTGCCCTGAGACGCTTGGGAGTCTGCCCT
1 AGACACTTAAAAGTCTGCCCTGAGACACTTGCGAGTCTGCCCTAAGAAACTTAGGAGTCTGCCCT
28411 A
66 A
* * *
28412 AGACACTTAAAAGTCTGCCTTGAGACGCTTTCGAGTCTGCCCTAAGAAACTTA
1 AGACACTTAAAAGTCTGCCCTGAGACACTTGCGAGTCTGCCCTAAGAAACTTA
28465 TTAGTCTTCC
Statistics
Matches: 154, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
66 63 0.41
67 73 0.47
68 18 0.12
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (66 bp):
AGACACTTAAAAGTCTGCCCTGAGACACTTGCGAGTCTGCCCTAAGAAACTTAGGAGTCTGCCCT
A
Found at i:29082 original size:15 final size:15
Alignment explanation
Indices: 29062--29115 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
29052 ACCCAAAACC
29062 TTTTGAAAACTCATT
1 TTTTGAAAACTCATT
*
29077 TTTTGAAAAC-CTTTT
1 TTTTGAAAACTC-ATT
*
29092 TTTTGAAAA-TAATT
1 TTTTGAAAACTCATT
29106 TTCTTGAAAA
1 TT-TTGAAAA
29116 ATGTCTCTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 5 0.15
15 28 0.85
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (15 bp):
TTTTGAAAACTCATT
Found at i:30472 original size:53 final size:53
Alignment explanation
Indices: 30411--30523 Score: 217
Period size: 53 Copynumber: 2.1 Consensus size: 53
30401 TCGAGCTCGA
30411 CTCGAGCTCAATGTCAAGCCGAACTCGAACAGTAAAAATATCACTCGGCCGAG
1 CTCGAGCTCAATGTCAAGCCGAACTCGAACAGTAAAAATATCACTCGGCCGAG
*
30464 CTCGAGCTCGATGTCAAGCCGAACTCGAACAGTAAAAATATCACTCGGCCGAG
1 CTCGAGCTCAATGTCAAGCCGAACTCGAACAGTAAAAATATCACTCGGCCGAG
30517 CTCGAGC
1 CTCGAGC
30524 CCGAGCTCGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (53 bp):
CTCGAGCTCAATGTCAAGCCGAACTCGAACAGTAAAAATATCACTCGGCCGAG
Found at i:30925 original size:20 final size:22
Alignment explanation
Indices: 30891--30934 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
30881 CAAATTATGC
*
30891 ATATTTTTATAGCTATTTTTAT
1 ATATTTTTATAGCTACTTTTAT
30913 ATATTTTT-T-GCTACTTTTAT
1 ATATTTTTATAGCTACTTTTAT
30933 AT
1 AT
30935 GTGTTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (22 bp):
ATATTTTTATAGCTACTTTTAT
Found at i:30941 original size:20 final size:20
Alignment explanation
Indices: 30902--30941 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
30892 TATTTTTATA
* *
30902 GCTATTTTTATATATTTTTT
1 GCTACTTTTATATATGTTTT
*
30922 GCTACTTTTATATGTGTTTT
1 GCTACTTTTATATATGTTTT
30942 TACCCTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.65
Consensus pattern (20 bp):
GCTACTTTTATATATGTTTT
Done.