Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006832.1 Corchorus capsularis cultivar CVL-1 contig06853, 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: 15531
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:176 original size:19 final size:19
Alignment explanation
Indices: 152--191 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
142 CTAAATTGTC
152 ATTATTAAATAATATTTTA
1 ATTATTAAATAATATTTTA
** *
171 ATTATTCCATAATTTTTTA
1 ATTATTAAATAATATTTTA
190 AT
1 AT
192 CATAAATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTATTAAATAATATTTTA
Found at i:337 original size:38 final size:37
Alignment explanation
Indices: 265--353 Score: 115
Period size: 38 Copynumber: 2.4 Consensus size: 37
255 AATTTGGCTT
* *
265 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCATAATTAATTTTGCCTTTTGTC
* *
302 TTTGTTTCCAATCGTTATAATTAATTTTGCTTTTTGTC
1 TTTGTTTCCAA-CGTCATAATTAATTTTGCCTTTTGTC
* *
340 TTTGTCTCCTACGT
1 TTTGTTTCCAACGT
354 TCTATTTGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 14 0.31
38 31 0.69
ACGTcount: A:0.15, C:0.19, G:0.11, T:0.55
Consensus pattern (37 bp):
TTTGTTTCCAACGTCATAATTAATTTTGCCTTTTGTC
Found at i:1303 original size:11 final size:11
Alignment explanation
Indices: 1252--1313 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
1242 ATTAAAATTT
1252 ATTATTTAAAA
1 ATTATTTAAAA
1263 ATTAATTATAAAA
1 ATT-ATT-TAAAA
* * *
1276 TTTCAATTTAGAT
1 ATT--ATTTAAAA
1289 ATTATTTAAAA
1 ATTATTTAAAA
*
1300 ATTAATTAAAA
1 ATTATTTAAAA
1311 ATT
1 ATT
1314 TCAATTTAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
11 22 0.54
12 3 0.07
13 12 0.29
14 4 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (11 bp):
ATTATTTAAAA
Found at i:1319 original size:36 final size:37
Alignment explanation
Indices: 1251--1323 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
1241 TATTAAAATT
1251 TATTATTTAAAAATTAATTATAAAATTTCAATTTAGA
1 TATTATTTAAAAATTAATTATAAAATTTCAATTTAGA
1288 TATTATTTAAAAATTAATTA-AAAATTTCAATTTAGA
1 TATTATTTAAAAATTAATTATAAAATTTCAATTTAGA
1324 CCGAATTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 16 0.44
37 20 0.56
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (37 bp):
TATTATTTAAAAATTAATTATAAAATTTCAATTTAGA
Found at i:1411 original size:19 final size:19
Alignment explanation
Indices: 1389--1425 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1379 ACTATAATTT
1389 TTTTAATTT-AATATTTTAC
1 TTTTAATTTCAAT-TTTTAC
1408 TTTTAATTTCAATTTTTA
1 TTTTAATTTCAATTTTTA
1426 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATTTCAATTTTTAC
Found at i:1616 original size:22 final size:23
Alignment explanation
Indices: 1591--1717 Score: 97
Period size: 22 Copynumber: 5.7 Consensus size: 23
1581 TGTCTCTATG
*
1591 TGGTTATCAAAATTTTATGA-GA
1 TGGTTATCAAAATTTCATGAGGA
* *
1613 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCATGAGGA
* *
1636 -GGTTATCAAAATTCCAT-AGTA
1 TGGTTATCAAAATTTCATGAGGA
1657 TGGTTA-CTAAAATTTCAT-ATGGA
1 TGGTTATC-AAAATTTCATGA-GGA
* * * *
1680 -AGTTATCAAAATTCCATAATG-
1 TGGTTATCAAAATTTCATGAGGA
*
1701 TGGTTACCAAAATTTCA
1 TGGTTATCAAAATTTCA
1718 AAGCAAAGTT
Statistics
Matches: 83, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
21 4 0.05
22 73 0.88
23 6 0.07
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (23 bp):
TGGTTATCAAAATTTCATGAGGA
Found at i:1641 original size:44 final size:44
Alignment explanation
Indices: 1592--1717 Score: 148
Period size: 44 Copynumber: 2.9 Consensus size: 44
1582 GTCTCTATGT
** * *
1592 GGTTATCAAAATTTTATGAG-ATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTCCAT-AGTATGGTTACTAAAATTTCAT-ATGGA
1636 GGTTATCAAAATTCCATAGTATGGTTACTAAAATTTCATATGGA
1 GGTTATCAAAATTCCATAGTATGGTTACTAAAATTTCATATGGA
* * * *
1680 AGTTATCAAAATTCCATAATGTGGTTACCAAAATTTCA
1 GGTTATCAAAATTCCATAGTATGGTTACTAAAATTTCA
1718 AAGCAAAGTT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
43 3 0.04
44 69 0.96
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATTCCATAGTATGGTTACTAAAATTTCATATGGA
Found at i:1727 original size:44 final size:44
Alignment explanation
Indices: 1623--1763 Score: 149
Period size: 44 Copynumber: 3.2 Consensus size: 44
1613 TGGTTATTAT
* * * * * *
1623 AATTTCATGAGGAGGTTATCAAAATTCCATAGTATGGTTACTAA
1 AATTTCATAAGAAAGTTATCAAAATTCCATAATGTGGTTACCAA
* *
1667 AATTTCATATGGAAGTTATCAAAATTCCATAATGTGGTTACCAA
1 AATTTCATAAGAAAGTTATCAAAATTCCATAATGTGGTTACCAA
* * * * *
1711 AATTTCA-AAGCAAAGTTATCGAAATTACATAATGTGATTATCAG
1 AATTTCATAAG-AAAGTTATCAAAATTCCATAATGTGGTTACCAA
1755 AATTTCATA
1 AATTTCATA
1764 GAGGGGTCAA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
43 2 0.02
44 79 0.96
45 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (44 bp):
AATTTCATAAGAAAGTTATCAAAATTCCATAATGTGGTTACCAA
Found at i:1955 original size:22 final size:22
Alignment explanation
Indices: 1911--2412 Score: 161
Period size: 22 Copynumber: 23.0 Consensus size: 22
1901 TTATGGAGTA
* *
1911 ATCAAAATTTC--AGGAAGGAT
1 ATCAAAATTTCATATGAAGGTT
1931 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* **
1953 ATCGAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* *
1975 TTCAAAATTTCATAAG-AGAGTT
1 ATCAAAATTTCATATGAAG-GTT
* * *
1997 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * * *
2019 ATAAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
2041 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
** * *
2063 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
2085 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * *
2101 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
2123 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* *
2146 ATCAAAATTTTATA-GTAAGATTT
1 ATCAAAATTTCATATG-AAG-GTT
*
2169 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
2191 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* ** *
2213 ATCAAAATTTCAGA-GTCTGATT
1 ATCAAAATTTCATATG-AAGGTT
*
2235 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * * *
2257 TTTAAATTTTCATAACGTA-GTT
1 ATCAAAATTTCAT-ATGAAGGTT
* *
2279 ATCAATATATCATAT-AGAGGTT
1 ATCAAAATTTCATATGA-AGGTT
* * **
2301 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
*
2324 ACCAAAATTTCAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
*
2346 ATCAAAACTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* * * *
2369 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* *
2390 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
2412 A
1 A
2413 AAAAAAATTT
Statistics
Matches: 359, Mismatches: 82, Indels: 80
0.69 0.16 0.15
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 15 0.04
21 15 0.04
22 248 0.69
23 66 0.18
24 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:2149 original size:23 final size:23
Alignment explanation
Indices: 2121--2224 Score: 113
Period size: 23 Copynumber: 4.6 Consensus size: 23
2111 CATAAGAAAG
* *
2121 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGTGAGGT
* * *
2144 TTATCAAAATTTTATAGTAAGAT
1 TTATCAAAATTTCATAGTGAGGT
*
2167 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGTGAGGT
* * *
2189 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTCATAGTGAGGT
2211 TTATCAAAATTTCA
1 TTATCAAAATTTCA
2225 GAGTCTGATT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
21 1 0.01
22 30 0.43
23 38 0.55
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTCATAGTGAGGT
Found at i:2193 original size:45 final size:45
Alignment explanation
Indices: 2099--2224 Score: 148
Period size: 45 Copynumber: 2.8 Consensus size: 45
2089 AAATTTGTAG
* * * *
2099 TTATCAAGATTTCATAAGAAAG-TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCAT-AGTAAGATTATCAAAATTTCATAGCGAGGT
*
2144 TTATCAAAATTTTATAGTAAGATTTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGTAAGA-TTATCAAAATTTCATAGCGAGGT
* **
2189 TTATCACAATTTCATAGTGTGATTATCAAAATTTCA
1 TTATCAAAATTTCATAGTAAGATTATCAAAATTTCA
2225 GAGTCTGATT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 19 0.27
45 31 0.44
46 20 0.29
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAGTAAGATTATCAAAATTTCATAGCGAGGT
Found at i:2432 original size:23 final size:22
Alignment explanation
Indices: 2385--2434 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
2375 TTCCTTAGGG
* *
2385 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAAA
2407 AGGTTAAAAAAAATTT-ATATAAA
1 AGGTT-AAAAAAATTTCATA-AAA
2430 AGGTT
1 AGGTT
2435 CTTGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAAA
Found at i:3049 original size:13 final size:13
Alignment explanation
Indices: 3027--3066 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3017 CAGATAATAT
3027 TATCAACAGAAGA
1 TATCAACAGAAGA
*
3040 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
3053 TTTCAACTGAAGA
1 TATCAACAGAAGA
3066 T
1 T
3067 TATCTGAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:3497 original size:41 final size:41
Alignment explanation
Indices: 3440--3637 Score: 222
Period size: 41 Copynumber: 4.8 Consensus size: 41
3430 AATAATATTG
3440 AAAATTACCT-TTGACACCAGAAGTTGTCACTTTGGTAAATT
1 AAAATTA-CTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
* * * *
3481 AAAATTACTGCTGACACTAGAAGTTGTCACCTTGCTAAATT
1 AAAATTACTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
* * *
3522 GAAATTACTTTTGACACCAGAAGTTGTCAATTTGGTAAATT
1 AAAATTACTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
* ***
3563 AAAATTACCT-TTGACACCAGAAG-TGTTACTCCAGTAAATT
1 AAAATTA-CTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
* * *
3603 ATAATTACTGTTAACACCAGAAATTGTCACCTTTG
1 AAAATTACTGTTGACACCAGAAGTTGTCA-CTTTG
3638 AATTACCCCG
Statistics
Matches: 128, Mismatches: 24, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
39 2 0.02
40 31 0.24
41 91 0.71
42 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (41 bp):
AAAATTACTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
Found at i:8229 original size:13 final size:13
Alignment explanation
Indices: 8207--8246 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
8197 CAGAGAATAT
8207 TATCAACAGAAGA
1 TATCAACAGAAGA
*
8220 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
8233 TTTCAACTGAAGA
1 TATCAACAGAAGA
8246 T
1 T
8247 TATTTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:12234 original size:97 final size:97
Alignment explanation
Indices: 12068--12262 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
12058 ACAATGTTGT
12068 TAATATAGAAAAGTTTCAATAATAAACTTAACCGTTTATTGACGAAGGAAGCTCAAGCTACTTGG
1 TAATATAGAAAAGTTTCAATAATAAACTTAACCGTTTATTGACGAAGGAAGCTCAAGCTACTTGG
12133 GAGGTAGGGAAGATGTTAGAAATCTCATTTGA
66 GAGGTAGGGAAGATGTTAGAAATCTCATTTGA
12165 TAATATAGAAAAGTTTCAATAATAAACTTAACCGTTTATTGACGAAGGAAGCTCAAGCTACTTGG
1 TAATATAGAAAAGTTTCAATAATAAACTTAACCGTTTATTGACGAAGGAAGCTCAAGCTACTTGG
12230 GAGGTAGGGAAGATGTTAGAAATCTCATTTGA
66 GAGGTAGGGAAGATGTTAGAAATCTCATTTGA
12262 T
1 T
12263 TGCGATGAAA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (97 bp):
TAATATAGAAAAGTTTCAATAATAAACTTAACCGTTTATTGACGAAGGAAGCTCAAGCTACTTGG
GAGGTAGGGAAGATGTTAGAAATCTCATTTGA
Found at i:12863 original size:6 final size:6
Alignment explanation
Indices: 12854--12902 Score: 71
Period size: 6 Copynumber: 7.8 Consensus size: 6
12844 CTTGTTTTAT
*
12854 TATATC TATATC TATATC GATATATC TATATT TATATC TATATC TATAT
1 TATATC TATATC TATATC --TATATC TATATC TATATC TATATC TATAT
12903 ATTATATAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 33 0.85
8 6 0.15
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (6 bp):
TATATC
Found at i:12879 original size:14 final size:13
Alignment explanation
Indices: 12854--12909 Score: 64
Period size: 12 Copynumber: 4.4 Consensus size: 13
12844 CTTGTTTTAT
12854 TATATC-TATATC
1 TATATCATATATC
12866 TATATCGATATATC
1 TATATC-ATATATC
*
12880 TATAT-TTATATC
1 TATATCATATATC
12892 TATATCTATATAT-
1 TATATC-ATATATC
12905 TATAT
1 TATAT
12910 AAGTTTAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 17 0.45
13 5 0.13
14 16 0.42
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (13 bp):
TATATCATATATC
Found at i:12879 original size:20 final size:18
Alignment explanation
Indices: 12854--12902 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 18
12844 CTTGTTTTAT
12854 TATATCTATATCTATATC
1 TATATCTATATCTATATC
*
12872 GATATATCTATATTTATATC
1 --TATATCTATATCTATATC
12892 TATATCTATAT
1 TATATCTATAT
12903 ATTATATAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 11 0.39
20 17 0.61
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (18 bp):
TATATCTATATCTATATC
Found at i:15261 original size:20 final size:19
Alignment explanation
Indices: 15236--15273 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
15226 GAATTTATTA
15236 ATAACCTTATAATTGTTTTG
1 ATAACC-TATAATTGTTTTG
*
15256 ATAACCTCTAATTGTTTT
1 ATAACCTATAATTGTTTT
15274 TTTAGTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (19 bp):
ATAACCTATAATTGTTTTG
Done.