Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022022.1 Corchorus olitorius cultivar O-4 contig22055, 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: 18359
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:75 original size:36 final size:35
Alignment explanation
Indices: 4--305 Score: 277
Period size: 36 Copynumber: 8.4 Consensus size: 35
1 CCT
* * *
4 TGGATCAACTGAAGTAAAATGAAGAAAAGATCACCC
1 TGGATCAACTGAAATAAACTGAA-ATAAGATCACCC
* *
40 TGGATCAAACTGAAATAAACTGAAATAGGACCACCC
1 TGGATC-AACTGAAATAAACTGAAATAAGATCACCC
* ** *
76 TGGGTCAACAAAAATAAACTGACGAA-AAGATCGCCC
1 TGGATCAACTGAAATAAACTGA--AATAAGATCACCC
* * *
112 TGGATCAACTGAAGTAAAATGAAGAAAAGATCACCC
1 TGGATCAACTGAAATAAACTGAA-ATAAGATCACCC
* * *
148 TGGATACAAACTAAAATAAACTGAAATAGGACCACCC
1 TGGAT-C-AACTGAAATAAACTGAAATAAGATCACCC
* * * *
185 TGGGTCAACTGAAATGAATTG-AATAAGGATCGCCC
1 TGGATCAACTGAAATAAACTGAAATAA-GATCACCC
* *
220 TGGATCAACTGAAATGAATTG-AATAAAGATCACCC
1 TGGATCAACTGAAATAAACTGAAAT-AAGATCACCC
* *
255 TGGATCAAACTGAAATAAACTGAAATAGGACCACCC
1 TGGATC-AACTGAAATAAACTGAAATAAGATCACCC
*
291 TGGGTCAACTGAAAT
1 TGGATCAACTGAAAT
306 GAATTGAAGC
Statistics
Matches: 218, Mismatches: 37, Indels: 23
0.78 0.13 0.08
Matches are distributed among these distances:
34 5 0.02
35 78 0.36
36 87 0.40
37 34 0.16
38 14 0.06
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (35 bp):
TGGATCAACTGAAATAAACTGAAATAAGATCACCC
Found at i:216 original size:108 final size:106
Alignment explanation
Indices: 4--313 Score: 487
Period size: 108 Copynumber: 2.9 Consensus size: 106
1 CCT
4 TGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAAATAGG
1 TGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAAATAGG
** * *
69 ACCACCCTGGGTCAACAAAAATAAACTGACGAAAAGATCGCCC
66 ACCACCCTGGGTCAACTGAAATGAATTGA--AAAAGATCGCCC
*
112 TGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATACAAACTAAAATAAACTGAAATAG
1 TGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGAT-CAAACTGAAATAAACTGAAATAG
*
177 GACCACCCTGGGTCAACTGAAATGAATTGAATAAGGATCGCCC
65 GACCACCCTGGGTCAACTGAAATGAATTGAA-AAAGATCGCCC
* * * *
220 TGGATCAACTGAAATGAATTGAA-TAAAGATCACCCTGGATCAAACTGAAATAAACTGAAATAGG
1 TGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAAATAGG
284 ACCACCCTGGGTCAACTGAAATGAATTGAA
66 ACCACCCTGGGTCAACTGAAATGAATTGAA
314 GCGTCTGAAA
Statistics
Matches: 189, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
106 53 0.28
107 17 0.09
108 71 0.38
109 48 0.25
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (106 bp):
TGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAAATAGG
ACCACCCTGGGTCAACTGAAATGAATTGAAAAAGATCGCCC
Found at i:1854 original size:13 final size:14
Alignment explanation
Indices: 1838--1868 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1828 TGAAAGCAAA
1838 TTTTG-AAAACCAT
1 TTTTGAAAAACCAT
1851 TTTTGAAAAACCAT
1 TTTTGAAAAACCAT
1865 TTTT
1 TTTT
1869 TTGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (14 bp):
TTTTGAAAAACCAT
Found at i:7398 original size:24 final size:24
Alignment explanation
Indices: 7366--7419 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
7356 GTGGGAAGAT
*
7366 TGGAGAGGTTCTGATGATAGGTTA
1 TGGAGAGGTTCTGATGAGAGGTTA
7390 TGGAGAGGTTCTGATGAGAGGTTA
1 TGGAGAGGTTCTGATGAGAGGTTA
7414 TGGAGA
1 TGGAGA
7420 AGTTGAGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.04, G:0.41, T:0.30
Consensus pattern (24 bp):
TGGAGAGGTTCTGATGAGAGGTTA
Found at i:7410 original size:13 final size:13
Alignment explanation
Indices: 7368--7412 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
7358 GGGAAGATTG
7368 GAGAGGTTCTGAT
1 GAGAGGTTCTGAT
* *
7381 GATAGGTTATG--
1 GAGAGGTTCTGAT
7392 GAGAGGTTCTGAT
1 GAGAGGTTCTGAT
7405 GAGAGGTT
1 GAGAGGTT
7413 ATGGAGAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.35
13 17 0.65
ACGTcount: A:0.24, C:0.04, G:0.40, T:0.31
Consensus pattern (13 bp):
GAGAGGTTCTGAT
Found at i:9402 original size:13 final size:13
Alignment explanation
Indices: 9386--9416 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9376 CAATTTGGTC
9386 CTTTAATTTATTT
1 CTTTAATTTATTT
*
9399 CTTTAATTTTTTT
1 CTTTAATTTATTT
9412 CTTTA
1 CTTTA
9417 TAAATTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (13 bp):
CTTTAATTTATTT
Found at i:15204 original size:42 final size:40
Alignment explanation
Indices: 15147--15371 Score: 252
Period size: 42 Copynumber: 5.4 Consensus size: 40
15137 TCAATCACCA
*
15147 AAATTTTGATAGTCAAACCCTAAATTTTGATGGTCAATTCCC
1 AAATTTTGATAGTCAAACCC-AAATTTTGATGGTCAA-CCCC
* * *
15189 AAATTTCGATGGTCAAACCCCAAATTTTGATGGTCAAACCTC
1 AAATTTTGATAGTCAAA-CCCAAATTTTGATGGTC-AACCCC
* *
15231 AAAATTTGATAGTGAAACACCAAATTTTGATGGTCAACCCCC
1 AAATTTTGATAGTCAAAC-CCAAATTTTGATGGTCAA-CCCC
* * * *
15273 AAATTTTGATAATTAACACCCAAAGTTTGATTGTCAAACCCC
1 AAATTTTGATAGTCAA-ACCCAAATTTTGATGGTC-AACCCC
* *
15315 AAATTTTGATTGTCAAACCCAAAGTTTGATGGTCAACCTCC
1 AAATTTTGATAGTCAAACCCAAATTTTGATGGTCAACC-CC
*
15356 AAATTTAGATAGTCAA
1 AAATTTTGATAGTCAA
15372 CCCCCAAAGT
Statistics
Matches: 156, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
40 4 0.03
41 36 0.23
42 107 0.69
43 9 0.06
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (40 bp):
AAATTTTGATAGTCAAACCCAAATTTTGATGGTCAACCCC
Found at i:15378 original size:21 final size:21
Alignment explanation
Indices: 15147--15379 Score: 216
Period size: 21 Copynumber: 11.1 Consensus size: 21
15137 TCAATCACCA
* * *
15147 AAATTTTGATAGTCAAACCCT
1 AAATTTTGATGGTCAACCCCC
**
15168 AAATTTTGATGGTCAATTCCC
1 AAATTTTGATGGTCAACCCCC
* *
15189 AAATTTCGATGGTCAAACCCC
1 AAATTTTGATGGTCAACCCCC
* *
15210 AAATTTTGATGGTCAAACCTC
1 AAATTTTGATGGTCAACCCCC
* * * * *
15231 AAAATTTGATAGTGAAACACC
1 AAATTTTGATGGTCAACCCCC
15252 AAATTTTGATGGTCAACCCCC
1 AAATTTTGATGGTCAACCCCC
** * *
15273 AAATTTTGATAATTAACACCC
1 AAATTTTGATGGTCAACCCCC
* * *
15294 AAAGTTTGATTGTCAAACCCC
1 AAATTTTGATGGTCAACCCCC
* *
15315 AAATTTTGATTGTCAA-ACCC
1 AAATTTTGATGGTCAACCCCC
* *
15335 AAAGTTTGATGGTCAACCTCC
1 AAATTTTGATGGTCAACCCCC
* *
15356 AAATTTAGATAGTCAACCCCC
1 AAATTTTGATGGTCAACCCCC
15377 AAA
1 AAA
15380 GTATCATATA
Statistics
Matches: 172, Mismatches: 39, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
20 17 0.10
21 155 0.90
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (21 bp):
AAATTTTGATGGTCAACCCCC
Found at i:15861 original size:45 final size:45
Alignment explanation
Indices: 15812--15942 Score: 208
Period size: 45 Copynumber: 2.9 Consensus size: 45
15802 CTAAATTCTA
15812 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
* *
15857 CTCCATCTCTAGGTAATTCATCAAAATAAAACTAATATTCTACTC
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
* * **
15902 TTTCATCTCTAGGTAATTCATTGAAATAAAGCTAATATTAT
1 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTAT
15943 TTGTTGCTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (45 bp):
CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
Found at i:17166 original size:41 final size:41
Alignment explanation
Indices: 17120--17201 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
17110 TTCCACTAAG
17120 TCATCAATTAGAAAATTGAGATATACATCTTTTTAGCAAAA
1 TCATCAATTAGAAAATTGAGATATACATCTTTTTAGCAAAA
17161 TCATCAATTAGAAAATTGAGATATACATCTTTTTAGCAAAA
1 TCATCAATTAGAAAATTGAGATATACATCTTTTTAGCAAAA
17202 GATAATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (41 bp):
TCATCAATTAGAAAATTGAGATATACATCTTTTTAGCAAAA
Done.