Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016928.1 Corchorus olitorius cultivar O-4 contig16961, 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: 33277
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:289 original size:16 final size:16
Alignment explanation
Indices: 268--307 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
258 CGGTCCCCGC
268 AATCCGCTTGATCTTA
1 AATCCGCTTGATCTTA
284 AATCCGCTTGATCTTA
1 AATCCGCTTGATCTTA
300 AATCCGCT
1 AATCCGCT
308 GCAACCAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (16 bp):
AATCCGCTTGATCTTA
Found at i:936 original size:27 final size:27
Alignment explanation
Indices: 907--1021 Score: 196
Period size: 27 Copynumber: 4.3 Consensus size: 27
897 ATGTGGCGCC
907 ACCCCAAGTGGCTGCGCTTCATCCGTC-
1 ACCCCAAGTGGCTGCGCTTCATCCG-CA
*
934 ACCCCAAGTGGTTGCGCTTCATCCGCA
1 ACCCCAAGTGGCTGCGCTTCATCCGCA
*
961 ACCCCAAGTAGCTGCGCTTCATCCGCA
1 ACCCCAAGTGGCTGCGCTTCATCCGCA
988 ACCCCAAGTGGCTGCGCTTCATCCGCA
1 ACCCCAAGTGGCTGCGCTTCATCCGCA
1015 ACCCCAA
1 ACCCCAA
1022 TTGAATGGCC
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
26 1 0.01
27 82 0.99
ACGTcount: A:0.20, C:0.41, G:0.20, T:0.19
Consensus pattern (27 bp):
ACCCCAAGTGGCTGCGCTTCATCCGCA
Found at i:1104 original size:15 final size:15
Alignment explanation
Indices: 1084--1137 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1074 AAAAATTGGC
1084 ACCGTTCCAGAAACA
1 ACCGTTCCAGAAACA
* *
1099 ACCGTTGCAAAAACA
1 ACCGTTCCAGAAACA
*
1114 TCATCCGTTTCAGAAACA
1 --A-CCGTTCCAGAAACA
1132 ACCGTT
1 ACCGTT
1138 GTAGAAACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 18 0.56
16 1 0.03
17 1 0.03
18 12 0.38
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20
Consensus pattern (15 bp):
ACCGTTCCAGAAACA
Found at i:1122 original size:33 final size:33
Alignment explanation
Indices: 1085--1151 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1075 AAAATTGGCA
1085 CCGTTCCAGAAACAACCGTTGCAAAAACATCAT
1 CCGTTCCAGAAACAACCGTTGCAAAAACATCAT
* * *
1118 CCGTTTCAGAAACAACCGTTGTAGAAACATCAT
1 CCGTTCCAGAAACAACCGTTGCAAAAACATCAT
1151 C
1 C
1152 TGGTGCAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.21
Consensus pattern (33 bp):
CCGTTCCAGAAACAACCGTTGCAAAAACATCAT
Found at i:1161 original size:33 final size:33
Alignment explanation
Indices: 1091--1162 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
1081 GGCACCGTTC
* *
1091 CAGAAACAACCGTTGCAAAAACATCATCCGTTT
1 CAGAAACAACCGTTGCAAAAACATCATCCGGTG
* * *
1124 CAGAAACAACCGTTGTAGAAACATCATCTGGTG
1 CAGAAACAACCGTTGCAAAAACATCATCCGGTG
1157 CAGAAA
1 CAGAAA
1163 ATTGCAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (33 bp):
CAGAAACAACCGTTGCAAAAACATCATCCGGTG
Found at i:3812 original size:25 final size:25
Alignment explanation
Indices: 3777--3917 Score: 219
Period size: 25 Copynumber: 5.6 Consensus size: 25
3767 TAGCCTATGT
3777 GTTTTCCAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGCTC
* *
3802 GTTTGCTAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGCTC
*
3827 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGCTC
* * *
3852 GTTTTCCAAATGCAAGCACAGGTTT
1 GTTTTCCAAACGCAAGCACAGGCTC
3877 GTTTTCCAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGCTC
*
3902 GTTTTCCAAACACAAG
1 GTTTTCCAAACGCAAG
3918 AACATGAGCG
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 105 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (25 bp):
GTTTTCCAAACGCAAGCACAGGCTC
Found at i:3930 original size:75 final size:75
Alignment explanation
Indices: 3777--3940 Score: 220
Period size: 75 Copynumber: 2.2 Consensus size: 75
3767 TAGCCTATGT
* *
3777 GTTTTCCAAACGCAAGCACAGGCTCGTTTGCTAAACGCAAGCACAGGCTCGTTTTCCAAACGCAA
1 GTTTTCCAAACGCAAGCACAGGCTCGTTTGCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAA
* **
3842 GCACAGGTTC
66 GAACAGGAGC
* * * *
3852 GTTTTCCAAATGCAAGCACAGGTTTGTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAA
1 GTTTTCCAAACGCAAGCACAGGCTCGTTTGCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAA
*
3917 GAACATGAGC
66 GAACAGGAGC
* *
3927 GTTTACCCAACGCA
1 GTTTTCCAAACGCA
3941 CGTGAGTCGT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (75 bp):
GTTTTCCAAACGCAAGCACAGGCTCGTTTGCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAA
GAACAGGAGC
Found at i:3939 original size:50 final size:50
Alignment explanation
Indices: 3777--3940 Score: 211
Period size: 50 Copynumber: 3.3 Consensus size: 50
3767 TAGCCTATGT
* * *
3777 GTTTTCCAAACGCAAGCACAGGCTCGTTTGCTAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACGCAAGCACAGGATC
* * * *
3827 GTTTTCCAAACGCAAGCACAGGTTCGTTTTCCAAATGCAAGCACAGGTTT
1 GTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACGCAAGCACAGGATC
* * * *
3877 GTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACACAAGAACATGAGC
1 GTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACGCAAGCACAGGATC
* *
3927 GTTTACCCAACGCA
1 GTTTTCCAAACGCA
3941 CGTGAGTCGT
Statistics
Matches: 98, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 98 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (50 bp):
GTTTTCCAAACGCAAGCACAGGCTCGTTTTCCAAACGCAAGCACAGGATC
Found at i:12635 original size:50 final size:50
Alignment explanation
Indices: 12577--12678 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
12567 GTTAGTGTTG
*
12577 ACATGAGGCTCTTAATTGTGCCGATTTTGCGACGTTAGGCCATGATTTGA
1 ACATGAGGCTCTTAATTGTGCCGATTTTGCAACGTTAGGCCATGATTTGA
*
12627 ACATGAGGCTCTTAATTGTGCCGATTTTGCAATGTTAGGCCATGATTTGA
1 ACATGAGGCTCTTAATTGTGCCGATTTTGCAACGTTAGGCCATGATTTGA
12677 AC
1 AC
12679 TTTCTTTAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (50 bp):
ACATGAGGCTCTTAATTGTGCCGATTTTGCAACGTTAGGCCATGATTTGA
Found at i:13565 original size:30 final size:30
Alignment explanation
Indices: 13527--13590 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
13517 GCCATCAAAA
* *
13527 AGGGCTTATTTGACC-TTTTTAAAAAGTTT
1 AGGGCTTATTTAACCGTTTTGAAAAAGTTT
**
13556 AGGGACTTATTTAACCGTTTTGAGTAAGTTT
1 AGGG-CTTATTTAACCGTTTTGAAAAAGTTT
13587 AGGG
1 AGGG
13591 GTCTTTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 4 0.14
30 10 0.34
31 15 0.52
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (30 bp):
AGGGCTTATTTAACCGTTTTGAAAAAGTTT
Found at i:14429 original size:23 final size:23
Alignment explanation
Indices: 14403--14465 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
14393 ACACAAGGTA
14403 TTACAAGCTT-TTTTTT-TTAATAT
1 TTACAAG-TTATTTTTTGTT-ATAT
14426 TTACAAGTTAAATTTTTTGTTATAT
1 TTACAAGTT--ATTTTTTGTTATAT
*
14451 TTACAAGTTAATTTT
1 TTACAAGTTATTTTT
14466 GTTCAAGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.06
23 12 0.34
25 19 0.54
26 2 0.06
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.57
Consensus pattern (23 bp):
TTACAAGTTATTTTTTGTTATAT
Found at i:14463 original size:24 final size:26
Alignment explanation
Indices: 14412--14465 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
14402 ATTACAAGCT
*
14412 TTTTTTTTTAATATTTACAAGTTAAA
1 TTTTTTGTTAATATTTACAAGTTAAA
14438 TTTTTTGTT-ATATTTACAAGTT-AA
1 TTTTTTGTTAATATTTACAAGTTAAA
14462 TTTT
1 TTTT
14466 GTTCAAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 6 0.22
25 13 0.48
26 8 0.30
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTTTTGTTAATATTTACAAGTTAAA
Found at i:21720 original size:27 final size:27
Alignment explanation
Indices: 21681--21734 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
21671 CCATCAGGAT
* * *
21681 AATTTGATTGGTGTCGATGATAAAACC
1 AATTGGATCGGTGTCAATGATAAAACC
21708 AATTGGATCGGTGTCAATGATAAAACC
1 AATTGGATCGGTGTCAATGATAAAACC
21735 GAAATATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (27 bp):
AATTGGATCGGTGTCAATGATAAAACC
Found at i:30338 original size:35 final size:35
Alignment explanation
Indices: 30292--30361 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
30282 AAGCGTCTTG
30292 TCCTCTGCTGGATAACTGTATATTTGTAGTTTTGT
1 TCCTCTGCTGGATAACTGTATATTTGTAGTTTTGT
*
30327 TCCTCTGCTGGATAATTGTATATTTGTAGTTTTGT
1 TCCTCTGCTGGATAACTGTATATTTGTAGTTTTGT
30362 ACGTCCTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.13, G:0.20, T:0.50
Consensus pattern (35 bp):
TCCTCTGCTGGATAACTGTATATTTGTAGTTTTGT
Done.