Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003963.1 Corchorus capsularis cultivar CVL-1 contig03971, 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: 4255
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Found at i:2031 original size:8 final size:8
Alignment explanation
Indices: 2018--2046 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2008 TTCCCATTCT
2018 AAAAAAGA
1 AAAAAAGA
2026 AAAAAAG-
1 AAAAAAGA
2033 AAAAAAGA
1 AAAAAAGA
2041 AAAAAA
1 AAAAAA
2047 CTTGGCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:2038 original size:15 final size:15
Alignment explanation
Indices: 2018--2046 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2008 TTCCCATTCT
2018 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
2033 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
2047 CTTGGCCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:2131 original size:20 final size:19
Alignment explanation
Indices: 2108--2152 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2098 AAAGAAAAGA
2108 AAAAAGCAACGATGGTTTTC
1 AAAAAG-AACGATGGTTTTC
***
2128 AAAAAGAGTTATGGTTTTC
1 AAAAAGAACGATGGTTTTC
2147 AAAAAG
1 AAAAAG
2153 GTTTTCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (19 bp):
AAAAAGAACGATGGTTTTC
Found at i:2157 original size:12 final size:12
Alignment explanation
Indices: 2140--2164 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2130 AAAGAGTTAT
2140 GGTTTTCAAAAA
1 GGTTTTCAAAAA
2152 GGTTTTCAAAAA
1 GGTTTTCAAAAA
2164 G
1 G
2165 AGTCATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (12 bp):
GGTTTTCAAAAA
Found at i:2195 original size:31 final size:31
Alignment explanation
Indices: 2121--2187 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
2111 AAGCAACGAT
* *
2121 GGTTTTCAAAAAGAGTTATGGTTTTCAAAAA
1 GGTTTTCAAAAAGAGTCATGATTTTCAAAAA
2152 GGTTTTCAAAAAGAGTCATGATTTTC-AAAA
1 GGTTTTCAAAAAGAGTCATGATTTTCAAAAA
2182 GGTTTT
1 GGTTTT
2188 GATAAAAGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.37
Consensus pattern (31 bp):
GGTTTTCAAAAAGAGTCATGATTTTCAAAAA
Found at i:2248 original size:25 final size:24
Alignment explanation
Indices: 2214--2295 Score: 75
Period size: 25 Copynumber: 3.5 Consensus size: 24
2204 AAAAGAATCT
2214 TGGTTTTCAAAATGTTTTGATCAAA
1 TGGTTTTCAAAA-GTTTTGATCAAA
* *
2239 TGGTTTTCAAAA--ATAG-TC--A
1 TGGTTTTCAAAAGTTTTGATCAAA
*
2258 TGGTTTTCAAAAGGTTTTGATAAAA
1 TGGTTTTCAAAA-GTTTTGATCAAA
2283 TGGTTTTCCAAAA
1 TGGTTTT-CAAAA
2296 ATGATTTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 13 0.29
21 2 0.04
22 4 0.09
23 1 0.02
25 20 0.44
26 5 0.11
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (24 bp):
TGGTTTTCAAAAGTTTTGATCAAA
Found at i:2681 original size:27 final size:26
Alignment explanation
Indices: 2626--2675 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2616 GATCCAAAAA
*
2626 AAAAAAAGTGAAAATTGAAAGTGAAG
1 AAAAAAAGTGAAAATAGAAAGTGAAG
* *
2652 AAAAAAATTGAAAA-AGAGAGTGAA
1 AAAAAAAGTGAAAATAGAAAGTGAA
2676 AGGAAAGGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.14
Consensus pattern (26 bp):
AAAAAAAGTGAAAATAGAAAGTGAAG
Found at i:3290 original size:11 final size:11
Alignment explanation
Indices: 3274--3327 Score: 83
Period size: 11 Copynumber: 4.9 Consensus size: 11
3264 GAAGTTCGTG
3274 TTTGAAGATTA
1 TTTGAAGATTA
3285 TTTGAAGA-TA
1 TTTGAAGATTA
3295 GTTTGAAGATTA
1 -TTTGAAGATTA
*
3307 TTTGAAGATAA
1 TTTGAAGATTA
3318 TTTGAAGATT
1 TTTGAAGATT
3328 TGAAGACAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
10 2 0.05
11 35 0.90
12 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:3301 original size:22 final size:22
Alignment explanation
Indices: 3273--3327 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3263 CGAAGTTCGT
3273 GTTTGAAGATTATTTGAAGATA
1 GTTTGAAGATTATTTGAAGATA
3295 GTTTGAAGATTATTTGAAGATA
1 GTTTGAAGATTATTTGAAGATA
*
3317 ATTTGAAGATT
1 GTTTGAAGATT
3328 TGAAGACAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (22 bp):
GTTTGAAGATTATTTGAAGATA
Found at i:3330 original size:19 final size:19
Alignment explanation
Indices: 3284--3343 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 19
3274 TTTGAAGATT
*
3284 ATTTGAAGATAGTTTGAAG
1 ATTTGAAGATAATTTGAAG
3303 ATTATTTGAAGATAATTTGAAG
1 ---ATTTGAAGATAATTTGAAG
*
3325 ATTTGAAGACAA-TTGAAG
1 ATTTGAAGATAATTTGAAG
3343 A
1 A
3344 CTTATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.19
19 11 0.31
22 18 0.50
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTTGAAGATAATTTGAAG
Done.