Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016905.1 Corchorus olitorius cultivar O-4 contig16938, 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: 109644
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1195 original size:7 final size:7
Alignment explanation
Indices: 1183--1243 Score: 101
Period size: 7 Copynumber: 9.1 Consensus size: 7
1173 ATACTATTTA
1183 AATATAT
1 AATATAT
1190 AATATAT
1 AATATAT
1197 AATATAT
1 AATATAT
1204 AATATAT
1 AATATAT
1211 AATATAT
1 AATATAT
1218 AATATAT
1 AATATAT
1225 -A-ATAT
1 AATATAT
1230 AATATAT
1 AATATAT
1237 -ATATAT
1 AATATAT
1243 A
1 A
1244 TGTGGGTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
5 4 0.08
6 8 0.16
7 39 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATATAT
Found at i:1488 original size:2 final size:2
Alignment explanation
Indices: 1481--1514 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1471 TGAATGCATC
1481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1515 CATTTACCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10826 original size:20 final size:20
Alignment explanation
Indices: 10801--10839 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10791 GAGAATATTA
10801 TGATGGAGAAAGAAGAAGAG
1 TGATGGAGAAAGAAGAAGAG
* *
10821 TGATGGAGGAAGAGGAAGA
1 TGATGGAGAAAGAAGAAGA
10840 AAAAGAAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.44, T:0.10
Consensus pattern (20 bp):
TGATGGAGAAAGAAGAAGAG
Found at i:38111 original size:3 final size:3
Alignment explanation
Indices: 38103--38136 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
38093 CCTGATAAGC
* *
38103 TCT TCT TCT TCT TCT TCT TCT TCC TCC TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
38137 TGTGCCCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:44110 original size:30 final size:30
Alignment explanation
Indices: 44074--44140 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
44064 CGACACGAGG
44074 TTGAGGTTGTATTTGAAGGTGGATAACATT
1 TTGAGGTTGTATTTGAAGGTGGATAACATT
44104 TTGAGGTTGTATTTGAAGGTGGATAACATT
1 TTGAGGTTGTATTTGAAGGTGGATAACATT
44134 TTG-GGTT
1 TTGAGGTT
44141 TTACCTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.11
30 33 0.89
ACGTcount: A:0.24, C:0.03, G:0.31, T:0.42
Consensus pattern (30 bp):
TTGAGGTTGTATTTGAAGGTGGATAACATT
Found at i:44875 original size:55 final size:55
Alignment explanation
Indices: 44810--44920 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
44800 CGTGTTCATT
44810 CTATTTTTCTACGAAAAGCTAATACCACCTAATAAAAATCGTACGAGTTAATTTA
1 CTATTTTTCTACGAAAAGCTAATACCACCTAATAAAAATCGTACGAGTTAATTTA
*
44865 CTATTTTTCTACGAAAAGCTAATACCACCTAATAAAAATCGTACGAGTTACTTTA
1 CTATTTTTCTACGAAAAGCTAATACCACCTAATAAAAATCGTACGAGTTAATTTA
44920 C
1 C
44921 ATGTCCGTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (55 bp):
CTATTTTTCTACGAAAAGCTAATACCACCTAATAAAAATCGTACGAGTTAATTTA
Found at i:56261 original size:18 final size:18
Alignment explanation
Indices: 56226--56261 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56216 GCAGGCAAGT
*
56226 ATGAGTAGCAGGAGGAGC
1 ATGAGTAGCAAGAGGAGC
*
56244 ATGAGTAGCAAGATGAGC
1 ATGAGTAGCAAGAGGAGC
56262 TGGCGTGCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.39, T:0.14
Consensus pattern (18 bp):
ATGAGTAGCAAGAGGAGC
Found at i:68998 original size:21 final size:21
Alignment explanation
Indices: 68974--69041 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
68964 AATTCTCTGT
68974 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
68995 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
69016 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
69037 AAATT
1 AAATT
69042 CTAAATCTTA
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 6 0.18
21 21 0.64
22 6 0.18
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:69020 original size:42 final size:42
Alignment explanation
Indices: 68961--69040 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
68951 GTTAAGTCTT
68961 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
69003 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAAT
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAAT
69041 TCTAAATCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:69179 original size:56 final size:57
Alignment explanation
Indices: 69107--69221 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
69097 TTTATTTTGT
*
69107 AGAATAATTAAGTAGAGATAG-GGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGAGGGGATAAGATTTATTATAACATTTATTGTGTGAA
*
69163 AGAATAATTAAGTAGAGATAGAGGTGATAAGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGAGGGGATAAGATTTATTATAACATTTATTGTGTGAA
69220 AG
1 AG
69222 GAAACAGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 21 0.38
57 35 0.62
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.35
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAGAGGGGATAAGATTTATTATAACATTTATTGTGTGAA
Found at i:73231 original size:11 final size:12
Alignment explanation
Indices: 73204--73232 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
73194 TTTCATCTTA
73204 TTAATTTTTAAC
1 TTAATTTTTAAC
73216 TTAATTTTTAAC
1 TTAATTTTTAAC
73228 -TAATT
1 TTAATT
73233 AAGTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAATTTTTAAC
Found at i:96588 original size:21 final size:21
Alignment explanation
Indices: 96563--96603 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
96553 TATGTTCTTA
**
96563 GAATTTTGCTTTGATTGCATC
1 GAATTTTGCTTAAATTGCATC
96584 GAATTTTGCTTAAATTGCAT
1 GAATTTTGCTTAAATTGCAT
96604 TGCATCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.46
Consensus pattern (21 bp):
GAATTTTGCTTAAATTGCATC
Found at i:97406 original size:33 final size:33
Alignment explanation
Indices: 97300--97394 Score: 181
Period size: 33 Copynumber: 2.9 Consensus size: 33
97290 AAAACAAATG
*
97300 GGGTGATCTAAGATTACCACCCAAGATCAACAC
1 GGGTGATCTGAGATTACCACCCAAGATCAACAC
97333 GGGTGATCTGAGATTACCACCCAAGATCAACAC
1 GGGTGATCTGAGATTACCACCCAAGATCAACAC
97366 GGGTGATCTGAGATTACCACCCAAGATCA
1 GGGTGATCTGAGATTACCACCCAAGATCA
97395 CCAGAGGTGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (33 bp):
GGGTGATCTGAGATTACCACCCAAGATCAACAC
Found at i:99627 original size:27 final size:27
Alignment explanation
Indices: 99574--99642 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
99564 CGGGCTTTAT
*
99574 AAAGAT-GGGAAGGGGAACCGAGGAAG
1 AAAGATGGGGAAGGAGAACCGAGGAAG
*
99600 AAAGATGGGGAAGGAGAATC-AGGTAAG
1 AAAGATGGGGAAGGAGAACCGAGG-AAG
99627 AAAGATGGGGAAGGAG
1 AAAGATGGGGAAGGAG
99643 GGTTTGCTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
26 9 0.23
27 30 0.77
ACGTcount: A:0.43, C:0.04, G:0.45, T:0.07
Consensus pattern (27 bp):
AAAGATGGGGAAGGAGAACCGAGGAAG
Found at i:99752 original size:86 final size:85
Alignment explanation
Indices: 99600--99814 Score: 376
Period size: 86 Copynumber: 2.5 Consensus size: 85
99590 ACCGAGGAAG
* *
99600 AAAGATGGGGAAGGAGAATCAGGTAAGAAAGATGGGGAAGGAGGGTTTGCTGTTGTGACTGGTAT
1 AAAGAT-GGGAAGG-GAATCGGGGAAGAAAGATGGGGAAGGAGGGTTTGCTGTTGTGACTGGTAT
99665 GTGTGGTGGGTTCGGGCTTTAT
64 GTGTGGTGGGTTCGGGCTTTAT
99687 AAAGATGGGAATGGGAATCGGGGAAGAAAGATGGGGAAGGAGGGTTTGCTGTTGTGACTGGTATG
1 AAAGATGGGAA-GGGAATCGGGGAAGAAAGATGGGGAAGGAGGGTTTGCTGTTGTGACTGGTATG
99752 TGTGGTGGGTTCGGGCTTTAT
65 TGTGGTGGGTTCGGGCTTTAT
99773 AAAGATGGGAAGGGGAATCGGGGAAGAAAGATGGGGAAGGAG
1 AAAGATGGGAA-GGGAATCGGGGAAGAAAGATGGGGAAGGAG
99815 AATCGGGGAA
Statistics
Matches: 124, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
86 116 0.94
87 8 0.06
ACGTcount: A:0.27, C:0.05, G:0.45, T:0.23
Consensus pattern (85 bp):
AAAGATGGGAAGGGAATCGGGGAAGAAAGATGGGGAAGGAGGGTTTGCTGTTGTGACTGGTATGT
GTGGTGGGTTCGGGCTTTAT
Found at i:99798 original size:14 final size:14
Alignment explanation
Indices: 99779--99840 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
99769 TTATAAAGAT
*
99779 GGGAAGGGGAATCG
1 GGGAAGGAGAATCG
*
99793 GGGAA-GAAAGAT-G
1 GGGAAGGAGA-ATCG
99806 GGGAAGGAGAATCG
1 GGGAAGGAGAATCG
* *
99820 GGGAAGAAAAAT-G
1 GGGAAGGAGAATCG
99833 GGGAAGGA
1 GGGAAGGA
99841 TTGTTTGCTG
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
13 18 0.46
14 21 0.54
ACGTcount: A:0.40, C:0.03, G:0.50, T:0.06
Consensus pattern (14 bp):
GGGAAGGAGAATCG
Found at i:99810 original size:13 final size:13
Alignment explanation
Indices: 99792--99838 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
99782 AAGGGGAATC
99792 GGGGAAGAAAGAT
1 GGGGAAGAAAGAT
*
99805 GGGGAAG-GAGAAT
1 GGGGAAGAAAG-AT
*
99818 CGGGGAAGAAAAAT
1 -GGGGAAGAAAGAT
99832 GGGGAAG
1 GGGGAAG
99839 GATTGTTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 2 0.07
13 16 0.57
14 9 0.32
15 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.49, T:0.06
Consensus pattern (13 bp):
GGGGAAGAAAGAT
Found at i:99817 original size:27 final size:27
Alignment explanation
Indices: 99773--99840 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
99763 CGGGCTTTAT
*
99773 AAAGAT-GGGAAGGGGAATCGGGGAAG
1 AAAGATGGGGAAGGAGAATCGGGGAAG
99799 AAAGATGGGGAAGGAGAATCGGGGAAG
1 AAAGATGGGGAAGGAGAATCGGGGAAG
*
99826 AAAAATGGGGAAGGA
1 AAAGATGGGGAAGGA
99841 TTGTTTGCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 6 0.15
27 33 0.85
ACGTcount: A:0.43, C:0.03, G:0.47, T:0.07
Consensus pattern (27 bp):
AAAGATGGGGAAGGAGAATCGGGGAAG
Done.