Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005443.1 Corchorus capsularis cultivar CVL-1 contig05461, 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: 2819
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Found at i:1068 original size:2 final size:2
Alignment explanation
Indices: 1061--1095 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1051 AGGTTTTAGG
1061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1096 CTAAGTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2070 original size:22 final size:22
Alignment explanation
Indices: 2043--2267 Score: 135
Period size: 22 Copynumber: 10.1 Consensus size: 22
2033 AAAGTGATGA
2043 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
* *
2065 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAGAGTAA-AATAG
2087 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
** *
2109 TAAAAAGTAATGA-T--AATCAG
1 TAATCAGTAAAGAGTAAAAT-AG
* *
2129 TAA-AAGTAAA-A-TAGTAATCAG
1 TAATCAGTAAAGAGTA-AAAT-AG
** *
2150 TAAAGAGTAAAATAGTAAAAAGTGATG
1 TAATCAGT-AAAGAGT-AAAA-T-A-G
* *
2177 ATAATCAGTAAAAAGTAAAATGG
1 -TAATCAGTAAAGAGTAAAATAG
*
2200 TAATCAGT-AAGAGCAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
* * *
2221 TAAACAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAGAGTAA-AATAG
*
2243 TAATCAGTAAAGAATAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
2265 TAA
1 TAA
2268 AAAAGGTAAT
Statistics
Matches: 160, Mismatches: 26, Indels: 34
0.73 0.12 0.15
Matches are distributed among these distances:
18 2 0.01
19 9 0.06
20 5 0.03
21 31 0.19
22 80 0.50
23 8 0.05
24 1 0.01
25 4 0.03
26 7 0.04
27 7 0.04
28 6 0.04
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.21
Consensus pattern (22 bp):
TAATCAGTAAAGAGTAAAATAG
Found at i:2080 original size:7 final size:7
Alignment explanation
Indices: 2048--2298 Score: 71
Period size: 7 Copynumber: 34.7 Consensus size: 7
2038 GATGATAATC
*
2048 AGTAAAG
1 AGTAAAA
2055 AGTAAAA
1 AGTAAAA
**
2062 TAGTAATC
1 -AGTAAAA
2070 AGTAAAA
1 AGTAAAA
2077 AGTAAGAA
1 AGTAA-AA
* **
2085 GGTAATC
1 AGTAAAA
*
2092 AGTAAAG
1 AGTAAAA
2099 AGTAAAA
1 AGTAAAA
2106 TAGTAAAA
1 -AGTAAAA
**
2114 AGTAATG
1 AGTAAAA
**
2121 A-TAATC
1 AGTAAAA
2127 AGT-AAA
1 AGTAAAA
2133 AGTAAAA
1 AGTAAAA
**
2140 TAGTAATC
1 -AGTAAAA
*
2148 AGTAAAG
1 AGTAAAA
2155 AGTAAAA
1 AGTAAAA
2162 TAGTAAAA
1 -AGTAAAA
* **
2170 AGTGATG
1 AGTAAAA
**
2177 A-TAATC
1 AGTAAAA
2183 AGTAAAA
1 AGTAAAA
2190 AGTAAAA
1 AGTAAAA
* **
2197 TGGTAATC
1 -AGTAAAA
*
2205 AGT-AAG
1 AGTAAAA
*
2211 AGCAAAA
1 AGTAAAA
*
2218 TAGTAAAC
1 -AGTAAAA
2226 AGTAAAA
1 AGTAAAA
2233 AGTAAGAA
1 AGTAA-AA
* **
2241 GGTAATC
1 AGTAAAA
2248 AGTAAAGA
1 AGTAAA-A
2256 A-TAAAA
1 AGTAAAA
2262 TAGTAAAAA
1 -AGT-AAAA
**
2271 AGGTAATC
1 A-GTAAAA
2279 AGTAAAA
1 AGTAAAA
*
2286 GGTAAAA
1 AGTAAAA
2293 TAGTAA
1 -AGTAA
2299 TCGGTAAAGA
Statistics
Matches: 174, Mismatches: 52, Indels: 35
0.67 0.20 0.13
Matches are distributed among these distances:
6 17 0.10
7 96 0.55
8 55 0.32
9 6 0.03
ACGTcount: A:0.57, C:0.04, G:0.19, T:0.21
Consensus pattern (7 bp):
AGTAAAA
Found at i:2146 original size:56 final size:57
Alignment explanation
Indices: 2065--2230 Score: 266
Period size: 56 Copynumber: 2.9 Consensus size: 57
2055 AGTAAAATAG
2065 TAATCAGTAAAAAGTAAGAA-GGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAATGA
1 TAATCAGTAAAAAGTAA-AATGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAATGA
* *
2122 TAATCAGT-AAAAGTAAAATAGTAATCAGTAAAGAGTAAAATAGTAAAAAGTGATGA
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAATGA
* *
2178 TAATCAGTAAAAAGTAAAATGGTAATCAGT-AAGAGCAAAATAGTAAACAGTAA
1 TAATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAA
2231 AAAGTAAGAA
Statistics
Matches: 101, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
55 2 0.02
56 71 0.70
57 28 0.28
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.22
Consensus pattern (57 bp):
TAATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAATGA
Found at i:2284 original size:16 final size:16
Alignment explanation
Indices: 2239--2285 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
2229 AAAAAGTAAG
*
2239 AAGGTAATCAGTAAAG
1 AAGGTAATCAGTAAAA
***
2255 AATAAAAT-AGTAAAA
1 AAGGTAATCAGTAAAA
2270 AAGGTAATCAGTAAAA
1 AAGGTAATCAGTAAAA
2286 GGTAAAATAG
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (16 bp):
AAGGTAATCAGTAAAA
Found at i:2298 original size:22 final size:22
Alignment explanation
Indices: 2264--2349 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
2254 GAATAAAATA
*
2264 GTAAAAAAGGTAATCAGTAAAAG
1 GTAAAATA-GTAATCAGTAAAAG
*
2287 GTAAAATAGTAATCGGT-AAAG
1 GTAAAATAGTAATCAGTAAAAG
* * * * *
2308 AGCAAAATGGTTATTAGTAAGA-
1 -GTAAAATAGTAATCAGTAAAAG
*
2330 GTAAAATAGTAATCTGTAAA
1 GTAAAATAGTAATCAGTAAA
2350 GAGTGAAAGG
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
21 18 0.38
22 20 0.43
23 9 0.19
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (22 bp):
GTAAAATAGTAATCAGTAAAAG
Found at i:2450 original size:30 final size:27
Alignment explanation
Indices: 2416--2476 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
2406 GTAAAAAGTG
*
2416 GTAATCAATAAAAAGAAGAGTAAGGAAAGA
1 GTAATCAAT--AAA-AAGAGTAAGAAAAGA
* *
2446 GTAATTAGTAAAAAGAGTAAGAAAAGA
1 GTAATCAATAAAAAGAGTAAGAAAAGA
2473 GTAA
1 GTAA
2477 AAATGACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 18 0.64
28 3 0.11
30 7 0.25
ACGTcount: A:0.59, C:0.02, G:0.23, T:0.16
Consensus pattern (27 bp):
GTAATCAATAAAAAGAGTAAGAAAAGA
Done.