Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022004.1 Corchorus olitorius cultivar O-4 contig22037, 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: 8704
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Found at i:1054 original size:21 final size:21
Alignment explanation
Indices: 1021--1069 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1011 AAGAATTGTA
**
1021 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
1041 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
1062 GCATTCCT
1 GC-TTCCT
1070 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:2233 original size:18 final size:18
Alignment explanation
Indices: 2210--2252 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2200 AAAATAAACG
2210 AAAATAAAAGAAAAAGAA
1 AAAATAAAAGAAAAAGAA
* *
2228 AAAAT-AACGAAAAATAA
1 AAAATAAAAGAAAAAGAA
2245 AAAGATAA
1 AAA-ATAA
2253 GGGTAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 13 0.62
18 7 0.33
19 1 0.05
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.09
Consensus pattern (18 bp):
AAAATAAAAGAAAAAGAA
Found at i:3856 original size:21 final size:21
Alignment explanation
Indices: 3832--3876 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
3822 GGCGCCCACA
*
3832 TGGTTTCCTTGAGCACCCATG
1 TGGTTTCCTTGAGAACCCATG
*
3853 TGGTTTGCTTGAGAACCCATG
1 TGGTTTCCTTGAGAACCCATG
3874 TGG
1 TGG
3877 GCGGTGTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TGGTTTCCTTGAGAACCCATG
Found at i:5135 original size:83 final size:84
Alignment explanation
Indices: 4974--5173 Score: 287
Period size: 83 Copynumber: 2.4 Consensus size: 84
4964 GCCTATGTCA
* * *
4974 CATTAGAATTAGCTTAAGCTACCTAAATCTATAAATAATATGTGTGACATGAAATTTAAACCCTA
1 CATTAAAATTAGCTTAAGATACCTAAATCTATAAATAATATGTGTGACATGAAATTTAAACCATA
* *
5039 GGTGAGAAAAAATGAATAT
66 AGTGAGAAAAAATGAATAC
*
5058 CATTAAAATTAGCTTAAGATACCTAAATCTATACA-AATAATG-GTGACATGAAATTTAAACCAT
1 CATTAAAATTAGCTTAAGATACCTAAATCTATAAATAAT-ATGTGTGACATGAAATTTAAACCAT
*
5121 AAGTGAGAGAAAATGAATAC
65 AAGTGAGAAAAAATGAATAC
* * *
5141 CATTAAAATTAACTTAAGGTATCTAAATCTATA
1 CATTAAAATTAGCTTAAGATACCTAAATCTATA
5174 TTATAAATCT
Statistics
Matches: 105, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
83 70 0.67
84 35 0.33
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (84 bp):
CATTAAAATTAGCTTAAGATACCTAAATCTATAAATAATATGTGTGACATGAAATTTAAACCATA
AGTGAGAAAAAATGAATAC
Found at i:5250 original size:28 final size:29
Alignment explanation
Indices: 5218--5286 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
5208 AGACTAATCA
5218 ATAATTAATTAACAA-CACTAACAAAATG-
1 ATAATT-ATTAACAATCACTAACAAAATGT
* * *
5246 ATAATGTATCAACAATCACTAATAAGATGT
1 ATAAT-TATTAACAATCACTAACAAAATGT
5276 ATAATTATTAA
1 ATAATTATTAA
5287 TTCCAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 12 0.35
29 17 0.50
30 5 0.15
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (29 bp):
ATAATTATTAACAATCACTAACAAAATGT
Found at i:5540 original size:16 final size:17
Alignment explanation
Indices: 5511--5542 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5501 GTTAGCAAAA
5511 AAATTAATATAAGAAAC
1 AAATTAATATAAGAAAC
5528 AAATTAA-ATAAGAAA
1 AAATTAATATAAGAAA
5543 AACAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (17 bp):
AAATTAATATAAGAAAC
Found at i:5545 original size:18 final size:18
Alignment explanation
Indices: 5507--5548 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
5497 TCTAGTTAGC
5507 AAAA-AAATTAATATAAG
1 AAAACAAATTAATATAAG
5524 -AAACAAATTAA-ATAAG
1 AAAACAAATTAATATAAG
5540 AAAAACAAA
1 -AAAACAAA
5549 AATAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.36
17 7 0.32
18 7 0.32
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.17
Consensus pattern (18 bp):
AAAACAAATTAATATAAG
Found at i:6700 original size:22 final size:23
Alignment explanation
Indices: 6675--6720 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
6665 TAATATCCAC
6675 ACACAATTAAT-ATGTAAT-TAAA
1 ACACAATTAATCATG-AATATAAA
*
6697 ACACACTTAATCATGAATATAAA
1 ACACAATTAATCATGAATATAAA
6720 A
1 A
6721 ATAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.28
Consensus pattern (23 bp):
ACACAATTAATCATGAATATAAA
Found at i:7794 original size:162 final size:164
Alignment explanation
Indices: 7537--7858 Score: 436
Period size: 163 Copynumber: 2.0 Consensus size: 164
7527 CGCCGCCGTA
* *
7537 TTAATACATGGAGGGAGAGATTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAAA
1 TTAATACATGGAGGGAGAGATTTTTTTCTCCTTTGTTTGGAGGGAAAAATTCACTCCCCACTAAA
*
7602 AGAAAGAAAGCTTCCAACTCTAAACCTATAATATATAGCGGCG-TTTTAAAACCAGACGCCGTTA
66 AGAAAGAAAGCTTCCAACTCTAAACCTATAATATATAGCGGCGTTTTTAAAACCAGACGCCGCTA
* * *
7666 ATTAGTGGCGTCTAGAA-CAGTAAACGCCGCTATT
131 ATTAGAGGCGTCT-GAAGAAGGAAACGCCGCTATT
* * * * *
7700 TTAATATATGGAGGGAGAGTTTTTTTTTTTTCTTTGTTTGGAGGGAAAAATTCACTCTCC-CTAA
1 TTAATACATGGAGGGAGAG-ATTTTTTTCTCCTTTGTTTGGAGGGAAAAATTCACTCCCCACTAA
** ** ***
7764 AA-AAAGAAATTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTTCTCACCAGACGCCGCT
65 AAGAAAGAAAGCTTCCAACTCTAAACCTATAATATATAGCGGCGTTTTTAAAACCAGACGCCGCT
7828 AATTAGAGGCGTCTGAAGAAGGAAACGCCGC
130 AATTAGAGGCGTCTGAAGAAGGAAACGCCGC
7859 AATTGTCAGA
Statistics
Matches: 138, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
162 40 0.29
163 64 0.46
164 34 0.25
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (164 bp):
TTAATACATGGAGGGAGAGATTTTTTTCTCCTTTGTTTGGAGGGAAAAATTCACTCCCCACTAAA
AGAAAGAAAGCTTCCAACTCTAAACCTATAATATATAGCGGCGTTTTTAAAACCAGACGCCGCTA
ATTAGAGGCGTCTGAAGAAGGAAACGCCGCTATT
Done.