Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023578.1 Corchorus olitorius cultivar O-4 contig23611, 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: 13638
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:496 original size:31 final size:31
Alignment explanation
Indices: 458--519 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
448 CCTTTTATTT
458 CAATCATATTTATCTTTGTTCAAAATCTGCA
1 CAATCATATTTATCTTTGTTCAAAATCTGCA
*
489 CAATCATATTTATCTTTGTTCAAAATTTGCA
1 CAATCATATTTATCTTTGTTCAAAATCTGCA
520 GAAGTTACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (31 bp):
CAATCATATTTATCTTTGTTCAAAATCTGCA
Found at i:1759 original size:22 final size:22
Alignment explanation
Indices: 1733--1774 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1723 TAAAAAATTG
*
1733 AAAACGAAACAAAAATAAAATA
1 AAAACGAAACAAAAACAAAATA
1755 AAAACGAAACAAAAACAAAA
1 AAAACGAAACAAAAACAAAA
1775 AACAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.79, C:0.12, G:0.05, T:0.05
Consensus pattern (22 bp):
AAAACGAAACAAAAACAAAATA
Found at i:2579 original size:28 final size:28
Alignment explanation
Indices: 2541--2621 Score: 94
Period size: 27 Copynumber: 2.9 Consensus size: 28
2531 TCATGAATTT
* * *
2541 ATAAGATTATAGTCATTTTTTTTGAAAA
1 ATAAGACTATAATCATTCTTTTTGAAAA
*
2569 ATAAGACTATAATAATTCTTTTTG--AA
1 ATAAGACTATAATCATTCTTTTTGAAAA
*
2595 ATGAAGACTATAATCATTCTATTTGAA
1 AT-AAGACTATAATCATTCTTTTTGAA
2622 CATGAAATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.09
27 20 0.45
28 20 0.45
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (28 bp):
ATAAGACTATAATCATTCTTTTTGAAAA
Found at i:2601 original size:27 final size:27
Alignment explanation
Indices: 2567--2646 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
2557 TTTTTTTGAA
2567 AAAT-AAGACTATAATAATTCTTTTTG
1 AAATGAAGACTATAATAATTCTTTTTG
* *
2593 AAATGAAGACTATAATCATTCTATTTG
1 AAATGAAGACTATAATAATTCTTTTTG
* *
2620 AACATGAA-ATGTATAATAATGCTTTTT
1 AA-ATGAAGA-CTATAATAATTCTTTTT
2647 TTTTCAAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.09
27 23 0.51
28 18 0.40
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (27 bp):
AAATGAAGACTATAATAATTCTTTTTG
Found at i:6794 original size:167 final size:168
Alignment explanation
Indices: 6503--6811 Score: 559
Period size: 167 Copynumber: 1.8 Consensus size: 168
6493 CTCTATAACC
6503 TCATAAATCATCTTTATTATATTTAAACCCATAGAAAACGCGTTCACATTTACAGAGTAAAAAAA
1 TCATAAATCATCTTTATTATATTTAAACCCATAGAAAACGCGTTCACATTTACAGAGTAAAAAAA
*
6568 AATTTATACAAATTGACTCATATGATAATAACAAATTTTAATTAGAGTGATTATGAGTAGTTTTT
66 AATCTATACAAATTGACTCATATGATAATAACAAATTTTAATTAGAGTGATTATGAGTAGTTTTT
6633 AAGTAAAAATGTTCTCTCTATAACCTCATAAATCATAT
131 AAGTAAAAATGTTCTCTCTATAACCTCATAAATCATAT
*
6671 TCATAAATCATTTTTATTATATTTAAACCCATTA-AAAACGCGTTCACATTTACAGAGT-AAAAA
1 TCATAAATCATCTTTATTATATTTAAACCCA-TAGAAAACGCGTTCACATTTACAGAGTAAAAAA
* *
6734 AAATCTATACAAATTGACTCATATGATAATAACGAATTTTAATTAGATTGATTATGAGTAGTTTT
65 AAATCTATACAAATTGACTCATATGATAATAACAAATTTTAATTAGAGTGATTATGAGTAGTTTT
6799 TAAGTAAAAATGT
130 TAAGTAAAAATGT
6812 AATATATAAA
Statistics
Matches: 136, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
167 80 0.59
168 54 0.40
169 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (168 bp):
TCATAAATCATCTTTATTATATTTAAACCCATAGAAAACGCGTTCACATTTACAGAGTAAAAAAA
AATCTATACAAATTGACTCATATGATAATAACAAATTTTAATTAGAGTGATTATGAGTAGTTTTT
AAGTAAAAATGTTCTCTCTATAACCTCATAAATCATAT
Found at i:6827 original size:19 final size:18
Alignment explanation
Indices: 6798--6839 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
6788 TGAGTAGTTT
* *
6798 TTAAGTAAAAATGTAATA
1 TTAAATAAAAATATAATA
6816 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
6835 TTAAA
1 TTAAA
6840 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:6843 original size:19 final size:19
Alignment explanation
Indices: 6803--6839 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6793 AGTTTTTAAG
*
6803 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
6822 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
6840 ATAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:7078 original size:24 final size:24
Alignment explanation
Indices: 7030--7079 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
7020 CTTGCATCCC
*
7030 TAAGATTTATTTTTGAAGGATATT
1 TAAGATTTATTTTTGAAGGAGATT
*
7054 TAAGAATTTATTTTTTAAGG-GATT
1 TAAG-ATTTATTTTTGAAGGAGATT
7078 TA
1 TA
7080 TTTTTGAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (24 bp):
TAAGATTTATTTTTGAAGGAGATT
Found at i:7091 original size:15 final size:15
Alignment explanation
Indices: 7033--7091 Score: 56
Period size: 16 Copynumber: 4.2 Consensus size: 15
7023 GCATCCCTAA
7033 GATTTATTTTTGAAG
1 GATTTATTTTTGAAG
7048 GA--TA--TTT-AAG
1 GATTTATTTTTGAAG
* *
7058 AATTTATTTTTTAAGG
1 GATTTATTTTTGAA-G
7074 GATTTATTTTTGAAG
1 GATTTATTTTTGAAG
7089 GAT
1 GAT
7092 ATATAATGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
10 4 0.11
11 3 0.09
12 2 0.06
13 2 0.06
14 3 0.09
15 8 0.23
16 13 0.37
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.51
Consensus pattern (15 bp):
GATTTATTTTTGAAG
Found at i:9018 original size:24 final size:25
Alignment explanation
Indices: 8972--9022 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
8962 ATTGGAGTAT
*
8972 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
8997 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
9021 TT
1 TT
9023 GTTCACATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:12259 original size:18 final size:16
Alignment explanation
Indices: 12216--12247 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12206 ATCTTGATTT
*
12216 TTCAGGGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
12232 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
12248 CTTGTAGAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44
Consensus pattern (16 bp):
TTCAGAGCTTTTCTGC
Done.