Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020373.1 Corchorus olitorius cultivar O-4 contig20406, 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: 78368
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:2067 original size:16 final size:16
Alignment explanation
Indices: 2031--2073 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2021 ACCCTACAAA
2031 AATACTCACTTGGTAC
1 AATACTCACTTGGTAC
* **
2047 CATACTCACTTGGTGT
1 AATACTCACTTGGTAC
2063 AATACTCACTT
1 AATACTCACTT
2074 ACAAAGCCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (16 bp):
AATACTCACTTGGTAC
Found at i:5292 original size:28 final size:31
Alignment explanation
Indices: 5260--5330 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 31
5250 ACGGACTGCT
*
5260 ACTTTGCACCAT-ATTTTTTATTTTGA-T-C
1 ACTTTGCACCATAATGTTTTATTTTGATTCC
* *
5288 ACTTTGCACCTTAATGTTTTATTTTTATTCC
1 ACTTTGCACCATAATGTTTTATTTTGATTCC
*
5319 ACATTGCACCAT
1 ACTTTGCACCAT
5331 CTGTTATCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 11 0.31
29 12 0.34
30 1 0.03
31 11 0.31
ACGTcount: A:0.23, C:0.21, G:0.07, T:0.49
Consensus pattern (31 bp):
ACTTTGCACCATAATGTTTTATTTTGATTCC
Found at i:7112 original size:30 final size:29
Alignment explanation
Indices: 7035--7112 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
7025 GCTTGTAGCG
* *
7035 TTTGGATGTTTTGCCCCTTGAACTTCAAT
1 TTTGGACGTTTTGCCCCCTGAACTTCAAT
* *
7064 TTTGGACATTTTGTCCCCTGAACTTCAAT
1 TTTGGACGTTTTGCCCCCTGAACTTCAAT
7093 TTTGGGACGTTTTGCCCCCT
1 TTT-GGACGTTTTGCCCCCT
7113 CAACCTAACG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 28 0.67
30 14 0.33
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCCTGAACTTCAAT
Found at i:7546 original size:25 final size:25
Alignment explanation
Indices: 7512--7560 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
7502 GTACTGTAGC
7512 AATTGAATTTTTCTAAATAAAATAA
1 AATTGAATTTTTCTAAATAAAATAA
7537 AATTGAATTTTTCTAAATAAAATA
1 AATTGAATTTTTCTAAATAAAATA
7561 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (25 bp):
AATTGAATTTTTCTAAATAAAATAA
Found at i:27655 original size:13 final size:13
Alignment explanation
Indices: 27637--27667 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
27627 CCATTATCAG
27637 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
27650 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
27663 A-AAAA
1 AGAAAA
27668 GCTATACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:29227 original size:9 final size:9
Alignment explanation
Indices: 29182--29235 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
29172 TTTGTTCTAA
*
29182 ATATATTTT
1 ATATATATT
*
29191 ATATAGTATA
1 ATATA-TATT
29201 ATATATATT
1 ATATATATT
* *
29210 GT-GATATT
1 ATATATATT
29218 ATATATATT
1 ATATATATT
29227 ATATATATT
1 ATATATATT
29236 TAGAAATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
8 6 0.17
9 23 0.64
10 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:29274 original size:16 final size:17
Alignment explanation
Indices: 29244--29276 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29234 TTTAGAAATA
*
29244 ATAAAGATATGTATTAT
1 ATAAAGATATATATTAT
29261 ATAAA-ATATATATTAT
1 ATAAAGATATATATTAT
29277 TATGTTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
ATAAAGATATATATTAT
Found at i:30772 original size:208 final size:209
Alignment explanation
Indices: 30377--30842 Score: 864
Period size: 208 Copynumber: 2.2 Consensus size: 209
30367 AACAAGTCCA
* * **
30377 TTTTGTAGCTACTAGTATTTAATACCAAAACATAATTATTTTGTTCTTTATTGATTCCATTATTT
1 TTTTCTAGCTACTAGTATTTAGTACCAAAACATAAGCATTTTGTTCTTTATTGATTCCATTATTT
30442 GTTGGAGGGAAAAGTGGTGCAATTATAATACAATATTGGAAGAAAAGAAATTACACCTACATAAT
66 GTTGGAGGGAAAAGTGGTGCAATTATAATACAATATTGGAAGAAAAGAAATTACACCTACATAAT
30507 TATATTTATAATCTGCAATTGCTAGCCAGACTCCATTATATCACTTTGTTGAGTCTCAGTCCTAT
131 TATATTTATAATCTGCAATTGCTAGCCAGACTCCATTATATCACTTTGTTGAGTCTCAGTCCTAT
30572 AACCAACCCTTTTC
196 AACCAACCCTTTTC
* *
30586 TTTTCTAGCTACTAGTATTTAGTA-AAAAAAATAAGCATTTTGTTCTTTATTGATTCCATTATTT
1 TTTTCTAGCTACTAGTATTTAGTACCAAAACATAAGCATTTTGTTCTTTATTGATTCCATTATTT
30650 GTTGGAGGGAAAAGTGGTGCAATTATAATACAATATTGGAAGAAAAGAAATTACACCTACATAAT
66 GTTGGAGGGAAAAGTGGTGCAATTATAATACAATATTGGAAGAAAAGAAATTACACCTACATAAT
30715 TATATTTATAATCTGCAATTGCTAGCCAGACTCCATTATATCACTTTGTTGAGTCTCAGTCCTAT
131 TATATTTATAATCTGCAATTGCTAGCCAGACTCCATTATATCACTTTGTTGAGTCTCAGTCCTAT
30780 AACCAACCCTTTTC
196 AACCAACCCTTTTC
30794 TTTTCTAGCTACTAGTATTTAGTACCAAAACATAAGCA-TTTGTTCTTTA
1 TTTTCTAGCTACTAGTATTTAGTACCAAAACATAAGCATTTTGTTCTTTA
30843 AGTCTAACTT
Statistics
Matches: 248, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
208 215 0.87
209 33 0.13
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (209 bp):
TTTTCTAGCTACTAGTATTTAGTACCAAAACATAAGCATTTTGTTCTTTATTGATTCCATTATTT
GTTGGAGGGAAAAGTGGTGCAATTATAATACAATATTGGAAGAAAAGAAATTACACCTACATAAT
TATATTTATAATCTGCAATTGCTAGCCAGACTCCATTATATCACTTTGTTGAGTCTCAGTCCTAT
AACCAACCCTTTTC
Found at i:31317 original size:12 final size:12
Alignment explanation
Indices: 31300--31324 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31290 TAATATGTAG
31300 TGTATATATATA
1 TGTATATATATA
31312 TGTATATATATA
1 TGTATATATATA
31324 T
1 T
31325 ATTATTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGTATATATATA
Found at i:32779 original size:91 final size:91
Alignment explanation
Indices: 32624--32805 Score: 247
Period size: 91 Copynumber: 2.0 Consensus size: 91
32614 AGATTCGAGC
* * * * * *
32624 CCTTTTCTGATGCTGCCCGCTAGCGGGTACACTTGCTCGCTCCTGGGTACCACCAAAAGCTTCAA
1 CCTTTTCTGATGCTGCCCACTAGCGAGTACACCTGCCCGCCCCTAGGTACCACCAAAAGCTTCAA
* * *
32689 TGTTTCACTTTGTTGCTCTCGTGTCA
66 TGCTTCACTTCGTTGCTCCCGTGTCA
* * *
32715 CCTTTTCTGATGTTGCCCACTAGCGAGTACGCCTGCCCGCCCCTAGGTACCACCAAATGCTTCAA
1 CCTTTTCTGATGCTGCCCACTAGCGAGTACACCTGCCCGCCCCTAGGTACCACCAAAAGCTTCAA
*
32780 TGCTTCCCTTCGTTGCTCCCGTGTCA
66 TGCTTCACTTCGTTGCTCCCGTGTCA
32806 TTTGTCTTCG
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
91 78 1.00
ACGTcount: A:0.15, C:0.34, G:0.20, T:0.31
Consensus pattern (91 bp):
CCTTTTCTGATGCTGCCCACTAGCGAGTACACCTGCCCGCCCCTAGGTACCACCAAAAGCTTCAA
TGCTTCACTTCGTTGCTCCCGTGTCA
Found at i:45011 original size:15 final size:15
Alignment explanation
Indices: 44991--45022 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44981 CAACTTGGGT
44991 TGATCCTATATACGC
1 TGATCCTATATACGC
*
45006 TGATCCTATATAGGC
1 TGATCCTATATACGC
45021 TG
1 TG
45023 CTGGATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (15 bp):
TGATCCTATATACGC
Found at i:49039 original size:20 final size:22
Alignment explanation
Indices: 49001--49050 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
48991 AAAAATGCTC
*
49001 TCTCTCTCTCCTTGGTTGAGAG
1 TCTCTCTCTCCTTGCTTGAGAG
49023 TCTCTCTCTCC-T-CTTGAGAG
1 TCTCTCTCTCCTTGCTTGAGAG
*
49043 TTTCTCTC
1 TCTCTCTC
49051 GCGTTTTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 14 0.54
21 1 0.04
22 11 0.42
ACGTcount: A:0.08, C:0.32, G:0.16, T:0.44
Consensus pattern (22 bp):
TCTCTCTCTCCTTGCTTGAGAG
Found at i:69090 original size:32 final size:32
Alignment explanation
Indices: 69054--69163 Score: 127
Period size: 32 Copynumber: 3.3 Consensus size: 32
69044 TTGATTATTG
69054 GGGACTTTGGATTCTGTTTTTGCTTGGAAGTT
1 GGGACTTTGGATTCTGTTTTTGCTTGGAAGTT
* *
69086 GGGACTTTGGAATT-T-TTTGTAGCTTTTGATTA-TT
1 GGGACTTTGG-ATTCTGTTT-TTGC-TTGGA--AGTT
69120 GGGGACTTTGGATTCTGTTTTTGCTTGGAAGTT
1 -GGGACTTTGGATTCTGTTTTTGCTTGGAAGTT
69153 GGGACTTTGGA
1 GGGACTTTGGA
69164 AGTTTTTGCT
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
31 3 0.05
32 26 0.40
33 9 0.14
34 9 0.14
35 15 0.23
36 3 0.05
ACGTcount: A:0.15, C:0.08, G:0.31, T:0.46
Consensus pattern (32 bp):
GGGACTTTGGATTCTGTTTTTGCTTGGAAGTT
Found at i:69139 original size:67 final size:67
Alignment explanation
Indices: 69031--69171 Score: 273
Period size: 67 Copynumber: 2.1 Consensus size: 67
69021 ACCTATGATC
69031 TTTTTTGTAGCTTTTGATTATTGGGGACTTTGGATTCTGTTTTTGCTTGGAAGTTGGGACTTTGG
1 TTTTTTGTAGCTTTTGATTATTGGGGACTTTGGATTCTGTTTTTGCTTGGAAGTTGGGACTTTGG
69096 AA
66 AA
69098 TTTTTTGTAGCTTTTGATTATTGGGGACTTTGGATTCTGTTTTTGCTTGGAAGTTGGGACTTTGG
1 TTTTTTGTAGCTTTTGATTATTGGGGACTTTGGATTCTGTTTTTGCTTGGAAGTTGGGACTTTGG
69163 AA
66 AA
*
69165 GTTTTTG
1 TTTTTTG
69172 CTGGTTCTGT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 73 1.00
ACGTcount: A:0.14, C:0.07, G:0.28, T:0.50
Consensus pattern (67 bp):
TTTTTTGTAGCTTTTGATTATTGGGGACTTTGGATTCTGTTTTTGCTTGGAAGTTGGGACTTTGG
AA
Found at i:69381 original size:14 final size:14
Alignment explanation
Indices: 69362--69388 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
69352 GGAAGTTTTG
69362 GTATGCTCTGCTTC
1 GTATGCTCTGCTTC
69376 GTATGCTCTGCTT
1 GTATGCTCTGCTT
69389 TGCAAAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.26, G:0.22, T:0.44
Consensus pattern (14 bp):
GTATGCTCTGCTTC
Done.