Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018906.1 Corchorus olitorius cultivar O-4 contig18939, 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: 125896
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1613 original size:4 final size:4
Alignment explanation
Indices: 1606--1643 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
1596 AAAAAAAACT
*
1606 AAGG AAGG AAGG AAGG AAGG AAGG AAAG AAGG AAGG AA
1 AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAGG AA
1644 AAAAAACCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (4 bp):
AAGG
Found at i:6152 original size:9 final size:9
Alignment explanation
Indices: 6138--6163 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6128 ATCTCACTTT
6138 TCTTTTTCC
1 TCTTTTTCC
6147 TCTTTTTCC
1 TCTTTTTCC
6156 TCTTTTTC
1 TCTTTTTC
6164 TCTCACAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (9 bp):
TCTTTTTCC
Found at i:8497 original size:29 final size:29
Alignment explanation
Indices: 8455--8510 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
8445 TACAAGTTTA
*
8455 CAACACCACAATTACAAGTTTTCAACAAT
1 CAACACCACAATTACAAGCTTTCAACAAT
8484 CAACACCACAATTACAAGCTTTCAACA
1 CAACACCACAATTACAAGCTTTCAACA
8511 CTGTACAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.30, G:0.04, T:0.21
Consensus pattern (29 bp):
CAACACCACAATTACAAGCTTTCAACAAT
Found at i:12065 original size:39 final size:39
Alignment explanation
Indices: 12022--12106 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
12012 GCTTTATTAG
*
12022 TCGAGCTCGAGTAGCTCGATTCAAGTATCGAACTTGAGC
1 TCGAGCTCGAGTAGCTCGATTCAAGTATCGAACTCGAGC
12061 TCGAGCTCGAGTAGCTCGATTCAAGTATCGAACTCGAGC
1 TCGAGCTCGAGTAGCTCGATTCAAGTATCGAACTCGAGC
12100 TCGAGCT
1 TCGAGCT
12107 TCATAATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (39 bp):
TCGAGCTCGAGTAGCTCGATTCAAGTATCGAACTCGAGC
Found at i:17822 original size:28 final size:29
Alignment explanation
Indices: 17763--17822 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
17753 TTGTATAAGT
* * * *
17763 AAAAATTAATGCATAATTTTTTGTTTTGA
1 AAAAATTAATGCATAATATTTTATTATCA
17792 AAAAATTAATGCATAA-ATTTTATTATCA
1 AAAAATTAATGCATAATATTTTATTATCA
17820 AAA
1 AAA
17823 GAGTGGGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (29 bp):
AAAAATTAATGCATAATATTTTATTATCA
Found at i:31391 original size:14 final size:14
Alignment explanation
Indices: 31372--31398 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31362 GCAATGATTT
31372 TTTGTTTTTGTTTC
1 TTTGTTTTTGTTTC
31386 TTTGTTTTTGTTT
1 TTTGTTTTTGTTT
31399 TTTAAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.81
Consensus pattern (14 bp):
TTTGTTTTTGTTTC
Found at i:31794 original size:6 final size:6
Alignment explanation
Indices: 31783--31807 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31773 TATTGACAAC
31783 CAGAAG CAGAAG CAGAAG CAGAAG C
1 CAGAAG CAGAAG CAGAAG CAGAAG C
31808 TGGAAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.20, G:0.32, T:0.00
Consensus pattern (6 bp):
CAGAAG
Found at i:32232 original size:18 final size:18
Alignment explanation
Indices: 32209--32243 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
32199 GTAATTAATA
32209 ATTATTTCATTTCATTTC
1 ATTATTTCATTTCATTTC
* *
32227 ATTATTTTATTTTATTT
1 ATTATTTCATTTCATTT
32244 TTCTAATCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTATTTCATTTCATTTC
Found at i:33622 original size:45 final size:42
Alignment explanation
Indices: 33529--33622 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 42
33519 AGTGCATTAT
33529 CTAA-ATTCTACTCTATCTCTATGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTATCTCTATGTAATTCATCAAAATAAAG
* *
33570 TTGATATTCTACTCCTCCATCTCTA-GATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CT--ATCTCTATG-TAATTCATCAAAATAAAG
33615 CTAATATT
1 CTAATATT
33623 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
41 2 0.05
42 8 0.18
43 2 0.05
44 1 0.02
45 31 0.70
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (42 bp):
CTAATATTCTACTCTATCTCTATGTAATTCATCAAAATAAAG
Found at i:39015 original size:6 final size:6
Alignment explanation
Indices: 39004--39032 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
38994 GTTTTGATAG
39004 TCACAT TCACAT TCACAT TCACAT TCACA
1 TCACAT TCACAT TCACAT TCACAT TCACA
39033 AGATATAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (6 bp):
TCACAT
Found at i:56312 original size:3 final size:3
Alignment explanation
Indices: 56304--56346 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
56294 CCACTTATGG
56304 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
56347 GCCATTGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:64078 original size:2 final size:2
Alignment explanation
Indices: 64071--64108 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
64061 AGTGGTGGGT
64071 TA TA TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64109 GTTGCAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:79554 original size:15 final size:15
Alignment explanation
Indices: 79534--79563 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
79524 ATAGCAAATT
79534 TGCCATTGCCTTAGC
1 TGCCATTGCCTTAGC
79549 TGCCATTGCCTTAGC
1 TGCCATTGCCTTAGC
79564 AAAGAACCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.33, G:0.20, T:0.33
Consensus pattern (15 bp):
TGCCATTGCCTTAGC
Found at i:85276 original size:123 final size:126
Alignment explanation
Indices: 85078--85332 Score: 315
Period size: 124 Copynumber: 2.0 Consensus size: 126
85068 ATTGTTTAAA
* * *
85078 CTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATAATT
1 CTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAACCTTATAATT
85143 TTTACCA-TTTT-A-T-TATTTGAATTAAAAAA-CTTATATATATTAGAATTTTTTAAATATG
66 TTT--CATTTTTCATTATATTTGAATTAAAAAATCTTATATATATTAGAATTTTTTAAATATG
* *
85201 CTTTTACAGTTTTATTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATAACCTTATAAC
1 CTTTTACAGTTTTACTCAACTAAAAACTCTA-ATTTTATTTAATTAAATCTAATAACCTTATAA-
* *
85266 TATTTT-ATTTTTACCATTTTACTATTTTATTTAAAAAATCTTATATATATTAGAATTTTTTAAA
64 T-TTTTCATTTTT--CA--TTA-TATTTGAATTAAAAAATCTTATATATATTAGAATTTTTTAAA
85330 TAT
123 TAT
85333 ATTTCTTAAA
Statistics
Matches: 112, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
123 30 0.27
124 33 0.29
125 1 0.01
126 4 0.04
127 1 0.01
130 1 0.01
132 14 0.12
133 28 0.25
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (126 bp):
CTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAACCTTATAATT
TTTCATTTTTCATTATATTTGAATTAAAAAATCTTATATATATTAGAATTTTTTAAATATG
Found at i:85321 original size:133 final size:123
Alignment explanation
Indices: 85078--85332 Score: 357
Period size: 123 Copynumber: 2.0 Consensus size: 123
85068 ATTGTTTAAA
* *
85078 CTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATAATT
1 CTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATACCTTTATAATT
*
85143 TTTACCATTTTATTATTTGAATTAAAAAACTTATATATATTAGAATTTTTTAAATATG
66 TTTACCATTTTACTATTTGAATTAAAAAACTTATATATATTAGAATTTTTTAAATATG
* *
85201 CTTTTACAGTTTTATTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATAACCTTATAAC
1 CTTTTACAGTTTTACTCAACTAAAAACTCTA-ATTTTATTTAATTAAATCTAAT-ACCTT-T-A-
* *
85266 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAATCTTATATATATTAGAATTTTTTAAAT
61 TA----ATTTTTACCATTTTACTATTTGAATTAAAAAA-CTTATATATATTAGAATTTTTTAAAT
85331 AT
121 AT
85333 ATTTCTTAAA
Statistics
Matches: 115, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
123 29 0.25
124 21 0.18
125 4 0.03
126 1 0.01
127 1 0.01
128 2 0.02
132 29 0.25
133 28 0.24
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (123 bp):
CTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATACCTTTATAATT
TTTACCATTTTACTATTTGAATTAAAAAACTTATATATATTAGAATTTTTTAAATATG
Found at i:85355 original size:14 final size:13
Alignment explanation
Indices: 85319--85357 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
85309 TATATATTAG
85319 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
85332 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
85346 AATTTTTTAAAT
1 AATTTTTTAAAT
85358 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:85534 original size:84 final size:85
Alignment explanation
Indices: 85373--85541 Score: 304
Period size: 85 Copynumber: 2.0 Consensus size: 85
85363 AATTTTTTTA
* *
85373 GAAATAAACTTTTACAGTTATTCTACTAAAAAATCTATTTTTATTTAATTAAATTCAATATTATT
1 GAAATAAACTTTTACAATTATTCTACTAAAAAATATATTTTTATTTAATTAAATTCAATATTATT
85438 ATAAATATTTTATTTTTACC
66 ATAAATATTTTATTTTTACC
85458 GAAATAAACTTTTACAATTATTCTACTAAAAAATATATTTTTATTTAATTAAATT-AATATTATT
1 GAAATAAACTTTTACAATTATTCTACTAAAAAATATATTTTTATTTAATTAAATTCAATATTATT
*
85522 ATAACTATTTTATTTTTACC
66 ATAAATATTTTATTTTTACC
85542 ATTTTAATTT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 28 0.35
85 53 0.65
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.49
Consensus pattern (85 bp):
GAAATAAACTTTTACAATTATTCTACTAAAAAATATATTTTTATTTAATTAAATTCAATATTATT
ATAAATATTTTATTTTTACC
Found at i:93830 original size:6 final size:6
Alignment explanation
Indices: 93819--93843 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
93809 CCACCCACCT
93819 CCAAAC CCAAAC CCAAAC CCAAAC C
1 CCAAAC CCAAAC CCAAAC CCAAAC C
93844 ATGCCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAAAC
Found at i:95807 original size:7 final size:7
Alignment explanation
Indices: 95784--95825 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
95774 ATACTTGACG
95784 AATATAT
1 AATATAT
*
95791 AACATAT
1 AATATAT
95798 AATATAT
1 AATATAT
95805 AATA-AT
1 AATATAT
95811 AATATAT
1 AATATAT
*
95818 ACTATAT
1 AATATAT
95825 A
1 A
95826 TTATTTTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (7 bp):
AATATAT
Found at i:95887 original size:51 final size:51
Alignment explanation
Indices: 95811--95915 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
95801 ATATAATAAT
*
95811 AATATATACTATATATTATTTTTAGTGGCTATGGAAATTACTTAAAGGTCA
1 AATATATACTATATATTATTTTTAGTGGCTATGGAAATTACTTAAAGGCCA
95862 AATATATACTATATATTATTTTTAGTGGCTATGGAAATTACTTAAAGGCCA
1 AATATATACTATATATTATTTTTAGTGGCTATGGAAATTACTTAAAGGCCA
95913 AAT
1 AAT
95916 TGAGGATTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (51 bp):
AATATATACTATATATTATTTTTAGTGGCTATGGAAATTACTTAAAGGCCA
Found at i:97969 original size:25 final size:25
Alignment explanation
Indices: 97935--97986 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
97925 GTAGAATATT
97935 AGTTTTATTTTGATGAATTACCTAG
1 AGTTTTATTTTGATGAATTACCTAG
97960 AGTTTTATTTTGATGAATTACCTAG
1 AGTTTTATTTTGATGAATTACCTAG
97985 AG
1 AG
97987 ATGGAGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (25 bp):
AGTTTTATTTTGATGAATTACCTAG
Found at i:104280 original size:6 final size:6
Alignment explanation
Indices: 104271--104295 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
104261 TGGTAGGTGT
104271 GGCAGA GGCAGA GGCAGA GGCAGA G
1 GGCAGA GGCAGA GGCAGA GGCAGA G
104296 CCGAGGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.52, T:0.00
Consensus pattern (6 bp):
GGCAGA
Found at i:105430 original size:27 final size:27
Alignment explanation
Indices: 105373--105431 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
105363 CAAACATGCT
* * *
105373 TTAGAAGTGTAACCTCATACGGGTAGT
1 TTAGAAGTATAACCTCATACGGGGAGA
*
105400 TTAGAAGTATAACCTCATATGGGGAGA
1 TTAGAAGTATAACCTCATACGGGGAGA
105427 TTAGA
1 TTAGA
105432 GCTTCTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (27 bp):
TTAGAAGTATAACCTCATACGGGGAGA
Found at i:109296 original size:6 final size:6
Alignment explanation
Indices: 109285--109312 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
109275 AAAGGAATAG
109285 AAAAGC AAAAGC AAAAGC AAAAGC AAAA
1 AAAAGC AAAAGC AAAAGC AAAAGC AAAA
109313 TCCAAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.14, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGC
Found at i:109782 original size:4 final size:4
Alignment explanation
Indices: 109773--109804 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
109763 CATTAATTTA
*
109773 AAAT AAAT AAAT AAAT AAAT AAAT ATAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
109805 CTGAATCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:112363 original size:92 final size:91
Alignment explanation
Indices: 112206--112374 Score: 302
Period size: 92 Copynumber: 1.8 Consensus size: 91
112196 TTATCAAAGA
* *
112206 TTGCATTCTAGACTTTGTGTTATACAATGGTTGAAGTATCTTTCATCTGTTTGGAATCACATTTA
1 TTGCATTCTAGACTTTGTGTTATACAATGGTTGAAGCATCTCTCATCTGTTTGGAATCACATTTA
112271 AAAACGTGTTTTTTTTTTTTTTTTTTT
66 AAAACGT-TTTTTTTTTTTTTTTTTTT
*
112298 TTGCATTTTAGACTTTGTGTTATACAATGGTTGAAGCATCTCTCATCTGTTTGGAATCACATTTA
1 TTGCATTCTAGACTTTGTGTTATACAATGGTTGAAGCATCTCTCATCTGTTTGGAATCACATTTA
112363 AAAACGTTTTTT
66 AAAACGTTTTTT
112375 ATTATATTTG
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 5 0.07
92 69 0.93
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (91 bp):
TTGCATTCTAGACTTTGTGTTATACAATGGTTGAAGCATCTCTCATCTGTTTGGAATCACATTTA
AAAACGTTTTTTTTTTTTTTTTTTTT
Found at i:113121 original size:81 final size:81
Alignment explanation
Indices: 112986--113149 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
112976 CATGTTTACT
112986 TTGTGAGTTGAATATTTTAGATTTTGTCCAGAATTATGAGGAAAAGAAAAGAAAGAATGCATGAG
1 TTGTGAGTTGAATATTTTAGATTTTGTCCAGAATTATGAGGAAAAGAAAAGAAAGAATGCATGAG
113051 GATTTCTGTGGTTGCA
66 GATTTCTGTGGTTGCA
113067 TTGTGAGTTGAATATTTTAGATTTTGTCCAGAATTATGAGGAAAAGAAAAGAAAGAATGCATGAG
1 TTGTGAGTTGAATATTTTAGATTTTGTCCAGAATTATGAGGAAAAGAAAAGAAAGAATGCATGAG
113132 GATTTCTGTGGTTGCA
66 GATTTCTGTGGTTGCA
113148 TT
1 TT
113150 CCTCCTGGCT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (81 bp):
TTGTGAGTTGAATATTTTAGATTTTGTCCAGAATTATGAGGAAAAGAAAAGAAAGAATGCATGAG
GATTTCTGTGGTTGCA
Found at i:122236 original size:27 final size:27
Alignment explanation
Indices: 122184--122236 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
122174 ATTCCACACT
*
122184 AAAAATCCTACTCCAATTTCAACAACAA
1 AAAAATCCTACTCCAATCTC-ACAACAA
122212 AAAAATCCTACTCCAAGTCTC-CAAC
1 AAAAATCCTACTCCAA-TCTCACAAC
122237 TCTCTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 16 0.70
29 3 0.13
ACGTcount: A:0.45, C:0.32, G:0.02, T:0.21
Consensus pattern (27 bp):
AAAAATCCTACTCCAATCTCACAACAA
Found at i:122435 original size:19 final size:19
Alignment explanation
Indices: 122411--122450 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
122401 ACAGTCCCCA
122411 TTAGAAGTTTGAAATAAAT
1 TTAGAAGTTTGAAATAAAT
122430 TTAGAAGTTTGAAATAAAT
1 TTAGAAGTTTGAAATAAAT
122449 TT
1 TT
122451 TTACATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (19 bp):
TTAGAAGTTTGAAATAAAT
Found at i:122841 original size:32 final size:33
Alignment explanation
Indices: 122803--122877 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
122793 CGTCCTGGTG
* * * * *
122803 GGGCGGCACCGCCGTGG-CGTGCCGCACCATCT
1 GGGCGGCACAGCCATGGCCATGCCGCACCACCA
*
122835 GGGCGGCACAGCCATGGCCATGCCGCCCCACCA
1 GGGCGGCACAGCCATGGCCATGCCGCACCACCA
122868 GGGCGGCACA
1 GGGCGGCACA
122878 ACCAATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 15 0.42
33 21 0.58
ACGTcount: A:0.15, C:0.41, G:0.36, T:0.08
Consensus pattern (33 bp):
GGGCGGCACAGCCATGGCCATGCCGCACCACCA
Done.