Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022726.1 Corchorus olitorius cultivar O-4 contig22759, 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: 3057
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Found at i:128 original size:7 final size:7
Alignment explanation
Indices: 118--191 Score: 57
Period size: 7 Copynumber: 10.9 Consensus size: 7
108 GCTTAATTTA
118 TTTTTTC
1 TTTTTTC
125 TTTTTTC
1 TTTTTTC
132 ---TTTC
1 TTTTTTC
*
136 TTTTTCC
1 TTTTTTC
143 TTTTTTCC
1 TTTTTT-C
151 TTTTTTC
1 TTTTTTC
158 TTTTTT-
1 TTTTTTC
*
164 TCCTTTTC
1 T-TTTTTC
* *
172 TCTTTTA
1 TTTTTTC
*
179 TTTTTTA
1 TTTTTTC
186 TTTTTT
1 TTTTTT
192 TATAAATGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
4 4 0.07
6 1 0.02
7 43 0.77
8 8 0.14
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:146 original size:16 final size:15
Alignment explanation
Indices: 127--177 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
117 ATTTTTTCTT
127 TTTTCTTTCTTTTTCC
1 TTTT-TTTCTTTTTCC
* *
143 TTTTTTCCTTTTTTC
1 TTTTTTTCTTTTTCC
*
158 TTTTTTTCCTTTTCTC
1 TTTTTTTCTTTTTC-C
174 TTTT
1 TTTT
178 ATTTTTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 20 0.69
16 9 0.31
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTTCTTTTTCC
Found at i:147 original size:8 final size:8
Alignment explanation
Indices: 118--170 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
108 GCTTAATTTA
118 TTTTTT-C
1 TTTTTTCC
*
125 TTTTTTCTT
1 TTTTTTC-C
134 TCTTTTTCC
1 T-TTTTTCC
143 TTTTTTCC
1 TTTTTTCC
*
151 TTTTTTCT
1 TTTTTTCC
159 TTTTTTCC
1 TTTTTTCC
167 TTTT
1 TTTT
171 CTCTTTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
7 6 0.15
8 25 0.64
9 2 0.05
10 6 0.15
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCC
Found at i:761 original size:19 final size:18
Alignment explanation
Indices: 737--776 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
727 AAACCAACCA
*
737 CCGCCGGCCACCACTACCG
1 CCGCCGGCCA-CACCACCG
756 CCGCCGGCCACACCACCG
1 CCGCCGGCCACACCACCG
774 CCG
1 CCG
777 GCTACCATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.15, C:0.60, G:0.23, T:0.03
Consensus pattern (18 bp):
CCGCCGGCCACACCACCG
Found at i:2176 original size:41 final size:39
Alignment explanation
Indices: 2094--3028 Score: 699
Period size: 41 Copynumber: 24.8 Consensus size: 39
2084 GGAAACAACA
* *
2094 TTAAGAAGGCCAACTGATGCCAACTTTGAAAA--C-A-T
1 TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* *
2129 TT-AGAAGGCCAACCGATGCCAAATTTGAAAACTCGAAACT
1 TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCG--ACT
*
2169 TTAAGAAGGCCAACCGATGCCAACTTTGAAAACT----T
1 TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* * *
2204 TTTAGAAGGCCAACTGATACCAACTCTGAAAA--C-ACT
1 TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* * *
2240 TTTAGAAGGCCGACCGATGCCAACTTTGAAAACT----T
1 TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* * *
2275 TTTAGAAGGCCAACCGATACCAACTTTTAAGAACTCGATTT
1 TTAAGAAGGCCAACCGATACCAACTTTGAA-AACTCGA-CT
* * *
2316 TTAGAGAAGGCCAACCGATATCAACTCTTAAAAACTCGATT
1 TTA-AGAAGGCCAACCGATACCAACT-TTGAAAACTCGACT
* * *
2357 TTAAAGAAGGCCAACCGATACCAACTTTTGGAAATTCGATT
1 TT-AAGAAGGCCAACCGATACCAAC-TTTGAAAACTCGACT
2398 TTAAAGAAGGCCAACCGATACCAACTTTGAAAACT----T
1 TT-AAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* * * *
2434 TTTAGAAGGCCAACCGATACCAACTCTGGAAA--C-ATT
1 TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* * *
2470 TTTAGAAGGCAAACCGATGCCAACTTTGAAAACT----T
1 TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* *
2505 TTTAGAAGGCCAACCGATACCAACTCTT-ATAAACTCGATT
1 TTAAGAAGGCCAACCGATACCAACT-TTGA-AAACTCGACT
* * * *
2545 TTAAAGAAGGCCAACTGATACCAACTTTTGGAAATTCGATT
1 TT-AAGAAGGCCAACCGATACCAAC-TTTGAAAACTCGACT
2586 TTAAAGAAGGCCAACCGATA-CAACTTTGAAAACT----T
1 TT-AAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* * * *
2621 TTTAGAAGGCCAACCGATACCAACTCTGGAAA--C-ATTT
1 TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCGA-CT
*
2658 TTAA-AAGGCCAACCGATGCCAACTTTGAAAACT----T
1 TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* * *
2692 TTTAGAAGGCCAACCGATACCAACTCTTAAAAACTCGATT
1 TTAAGAAGGCCAACCGATACCAACT-TTGAAAACTCGACT
** * * *
2732 TTAAAGAAGGCCAACTTATACCAACTTTTGGAAATTCGATT
1 TT-AAGAAGGCCAACCGATACCAAC-TTTGAAAACTCGACT
2773 TTAAAGAAGGCCAACCGATACCAACTTTGAAAACT----T
1 TT-AAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* * *
2809 TTTAGAAGGCCAACCGATACCAACTCTGGAAA--C-A-T
1 TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* * *
2844 TTGTAGAAGGCCAACCGATGCCAACATTGAAAACT----T
1 TT-AAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* * *
2880 TTTAGAAGGCCAACCGATACCAACTTTTTAAAAACTCGATTT
1 TTAAGAAGGCCAACCGATACCAAC--TTTGAAAACTCGA-CT
* *
2922 TTAGAGAAGGCCAACCGATACCAACTCTTAAAAACTCGATT
1 TTA-AGAAGGCCAACCGATACCAACT-TTGAAAACTCGACT
2963 TTAAAGAAGGCCAACCGATACCAACTTTGAAAACT----T
1 TT-AAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
* *
2999 TTTAGAAGGCCAACCGATGCCAAC-TTGAAA
1 TTAAGAAGGCCAACCGATACCAACTTTGAAA
3029 GGCTCAATTT
Statistics
Matches: 761, Mismatches: 73, Indels: 133
0.79 0.08 0.14
Matches are distributed among these distances:
34 53 0.07
35 214 0.28
36 140 0.18
37 12 0.02
39 9 0.01
40 37 0.05
41 223 0.29
42 48 0.06
43 25 0.03
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (39 bp):
TTAAGAAGGCCAACCGATACCAACTTTGAAAACTCGACT
Found at i:2213 original size:35 final size:35
Alignment explanation
Indices: 2164--3028 Score: 820
Period size: 35 Copynumber: 23.1 Consensus size: 35
2154 TGAAAACTCG
* *
2164 AAAC-TTTAAGAAGGCCAACCGATGCCAACTTTGA
1 AAACTTTTTAGAAGGCCAACCGATACCAACTTTGA
* *
2198 AAACTTTTTAGAAGGCCAACTGATACCAACTCTGA
1 AAACTTTTTAGAAGGCCAACCGATACCAACTTTGA
* * *
2233 AAACACTTTTAGAAGGCCGACCGATGCCAACTTTGA
1 AAAC-TTTTTAGAAGGCCAACCGATACCAACTTTGA
*
2269 AAACTTTTTAGAAGGCCAACCGATACCAACTTTTA
1 AAACTTTTTAGAAGGCCAACCGATACCAACTTTGA
* *
2304 AGAACTCGATTTTTAGAGAAGGCCAACCGATATCAACTCTTAA
1 A-AA--C--TTTTT--AGAAGGCCAACCGATACCAACT-TTGA
2347 AAACTCGATTTTAAAGAAGGCCAACCGATACCAACTTTTGGA
1 AAACT---TTTT--AGAAGGCCAACCGATACCAAC-TTT-GA
* *
2389 AATTCGATTTTAAAGAAGGCCAACCGATACCAACTTTGA
1 AA-AC--TTTT-TAGAAGGCCAACCGATACCAACTTTGA
* *
2428 AAACTTTTTAGAAGGCCAACCGATACCAACTCTGG
1 AAACTTTTTAGAAGGCCAACCGATACCAACTTTGA
* *
2463 AAACATTTTTAGAAGGCAAACCGATGCCAACTTTGA
1 AAAC-TTTTTAGAAGGCCAACCGATACCAACTTTGA
2499 AAACTTTTTAGAAGGCCAACCGATACCAACTCTT-A
1 AAACTTTTTAGAAGGCCAACCGATACCAACT-TTGA
*
2534 TAAACTCGATTTTAAAGAAGGCCAACTGATACCAACTTTTGGA
1 -AAACT---TTTT--AGAAGGCCAACCGATACCAAC-TTT-GA
* *
2577 AATTCGATTTTAAAGAAGGCCAACCGATA-CAACTTTGA
1 AA-AC--TTTT-TAGAAGGCCAACCGATACCAACTTTGA
* *
2615 AAACTTTTTAGAAGGCCAACCGATACCAACTCTGG
1 AAACTTTTTAGAAGGCCAACCGATACCAACTTTGA
* *
2650 AAACATTTTTAAAAGGCCAACCGATGCCAACTTTGA
1 AAAC-TTTTTAGAAGGCCAACCGATACCAACTTTGA
*
2686 AAACTTTTTAGAAGGCCAACCGATACCAACTCTTAA
1 AAACTTTTTAGAAGGCCAACCGATACCAACT-TTGA
**
2722 AAACTCGATTTTAAAGAAGGCCAACTTATACCAACTTTTGGA
1 AAACT---TTTT--AGAAGGCCAACCGATACCAAC-TTT-GA
* *
2764 AATTCGATTTTAAAGAAGGCCAACCGATACCAACTTTGA
1 AA-AC--TTTT-TAGAAGGCCAACCGATACCAACTTTGA
* *
2803 AAACTTTTTAGAAGGCCAACCGATACCAACTCTGG
1 AAACTTTTTAGAAGGCCAACCGATACCAACTTTGA
* * *
2838 AAACATTTGTAGAAGGCCAACCGATGCCAACATTGA
1 AAAC-TTTTTAGAAGGCCAACCGATACCAACTTTGA
*
2874 AAACTTTTTAGAAGGCCAACCGATACCAACTTTTTAA
1 AAACTTTTTAGAAGGCCAACCGATACCAAC--TTTGA
*
2911 AAACTCGATTTTTAGAGAAGGCCAACCGATACCAACTCTTAA
1 AAA--C--TTTTT--AGAAGGCCAACCGATACCAACT-TTGA
2953 AAACTCGATTTTAAAGAAGGCCAACCGATACCAACTTTGA
1 AAACT---TTTT--AGAAGGCCAACCGATACCAACTTTGA
*
2993 AAACTTTTTAGAAGGCCAACCGATGCCAAC-TTGA
1 AAACTTTTTAGAAGGCCAACCGATACCAACTTTGA
3027 AA
1 AA
3029 GGCTCAATTT
Statistics
Matches: 702, Mismatches: 68, Indels: 122
0.79 0.08 0.14
Matches are distributed among these distances:
34 26 0.04
35 224 0.32
36 147 0.21
37 11 0.02
38 9 0.01
39 20 0.03
40 25 0.04
41 158 0.23
42 50 0.07
43 29 0.04
45 3 0.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (35 bp):
AAACTTTTTAGAAGGCCAACCGATACCAACTTTGA
Found at i:2567 original size:188 final size:188
Alignment explanation
Indices: 2097--3023 Score: 1363
Period size: 188 Copynumber: 4.9 Consensus size: 188
2087 AACAACATTA
* * * * *
2097 AGAAGGCCAACTGATGCCAACTTTGAAAAC-ATTTAGAAGGCCAACCGATGCCAAAT-TTGAAAA
1 AGAAGGCCAACCGATGCCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTTAAAAA
* * * *
2160 CTCGAAACTTT-AAGAAGGCCAACCGATGCCAAC-TTT-GAAA-AC--TTTT-TAGAAGGCCAAC
66 CTCG--ATTTTAAAGAAGGCCAACCGATACCAACTTTTGGAAATTCGATTTTAAAGAAGGCCAAC
* * * * * * *
2218 TGATACCAACTCTGAAAACACTTTTAGAAGGCCGACCGATGCCAACTTTGAAAAC-TTTTT
129 CGATACCAACTTTGAAAAC-TTTTTAGAAGGCCAACCGATACCAACTCTGGAAACATTTTT
* * *
2278 AGAAGGCCAACCGATACCAACTTTTAAGAACTCGATTTTTAGAGAAGGCCAACCGATATCAACTC
1 AGAAGGCCAACCGATGCCAACTTTGAA-AA--C--TTTTT--AGAAGGCCAACCGATACCAACTC
2343 TTAAAAACTCGATTTTAAAGAAGGCCAACCGATACCAACTTTTGGAAATTCGATTTTAAAGAAGG
59 TTAAAAACTCGATTTTAAAGAAGGCCAACCGATACCAACTTTTGGAAATTCGATTTTAAAGAAGG
2408 CCAACCGATACCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTGGAAACATTTTT
124 CCAACCGATACCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTGGAAACATTTTT
* *
2473 AGAAGGCAAACCGATGCCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTTATAAA
1 AGAAGGCCAACCGATGCCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTTAAAAA
*
2538 CTCGATTTTAAAGAAGGCCAACTGATACCAACTTTTGGAAATTCGATTTTAAAGAAGGCCAACCG
66 CTCGATTTTAAAGAAGGCCAACCGATACCAACTTTTGGAAATTCGATTTTAAAGAAGGCCAACCG
2603 ATA-CAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTGGAAACATTTTT
131 ATACCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTGGAAACATTTTT
*
2660 AAAAGGCCAACCGATGCCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTTAAAAA
1 AGAAGGCCAACCGATGCCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTTAAAAA
**
2725 CTCGATTTTAAAGAAGGCCAACTTATACCAACTTTTGGAAATTCGATTTTAAAGAAGGCCAACCG
66 CTCGATTTTAAAGAAGGCCAACCGATACCAACTTTTGGAAATTCGATTTTAAAGAAGGCCAACCG
*
2790 ATACCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTGGAAACATTTGT
131 ATACCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTGGAAACATTTTT
* *
2848 AGAAGGCCAACCGATGCCAACATTGAAAACTTTTTAGAAGGCCAACCGATACCAACTTTTTAAAA
1 AGAAGGCCAACCGATGCCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAAC-TCTTAAAA
* * ** *
2913 ACTCGATTTTTAGAGAAGGCCAACCGATACCAACTCTTAAAAACTCGATTTTAAAGAAGGCCAAC
65 ACTCGA-TTTTAAAGAAGGCCAACCGATACCAACTTTTGGAAATTCGATTTTAAAGAAGGCCAAC
*
2978 CGATACCAACTTTGAAAACTTTTTAGAAGGCCAACCGATGCCAACT
129 CGATACCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACT
3024 TGAAAGGCTC
Statistics
Matches: 685, Mismatches: 41, Indels: 31
0.90 0.05 0.04
Matches are distributed among these distances:
181 24 0.04
182 2 0.00
184 1 0.00
187 186 0.27
188 206 0.30
189 53 0.08
190 114 0.17
191 4 0.01
192 2 0.00
194 36 0.05
195 57 0.08
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (188 bp):
AGAAGGCCAACCGATGCCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTTAAAAA
CTCGATTTTAAAGAAGGCCAACCGATACCAACTTTTGGAAATTCGATTTTAAAGAAGGCCAACCG
ATACCAACTTTGAAAACTTTTTAGAAGGCCAACCGATACCAACTCTGGAAACATTTTT
Done.