Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018501.1 Corchorus olitorius cultivar O-4 contig18534, 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: 41459
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:16399 original size:1 final size:1
Alignment explanation
Indices: 16388--16433 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
16378 ATTATTGATG
* * * *
16388 TTTTGTTTTTTTTTTTTGTTTTTGTTTTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16434 GCGTTTTGGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:16432 original size:14 final size:14
Alignment explanation
Indices: 16388--16432 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
16378 ATTATTGATG
16388 TTTTG-TTTTTTTT
1 TTTTGTTTTTTTTT
*
16401 TTTTGTTTTTGTTT
1 TTTTGTTTTTTTTT
16415 TTTTGTTTTTTTTT
1 TTTTGTTTTTTTTT
16429 TTTT
1 TTTT
16433 TGCGTTTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 5 0.17
14 24 0.83
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (14 bp):
TTTTGTTTTTTTTT
Found at i:16440 original size:14 final size:13
Alignment explanation
Indices: 16388--16431 Score: 79
Period size: 13 Copynumber: 3.3 Consensus size: 13
16378 ATTATTGATG
16388 TTTTGTTTTTTTT
1 TTTTGTTTTTTTT
16401 TTTTGTTTTTGTTT
1 TTTTGTTTTT-TTT
16415 TTTTGTTTTTTTT
1 TTTTGTTTTTTTT
16428 TTTT
1 TTTT
16432 TTGCGTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 17 0.57
14 13 0.43
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (13 bp):
TTTTGTTTTTTTT
Found at i:19255 original size:30 final size:30
Alignment explanation
Indices: 19219--19468 Score: 295
Period size: 30 Copynumber: 8.3 Consensus size: 30
19209 TTGTTTAGCT
* * *
19219 GGTCTCCTAGAAATCGGAGAAGTAGGAGCA
1 GGTCTCCCAGAAATCGCAGAAGCAGGAGCA
* * *
19249 GGTCTCCTAGAAATCGCAGAAGCCGAAGCA
1 GGTCTCCCAGAAATCGCAGAAGCAGGAGCA
* *
19279 GGTCTCCCAGAAATCGCAGAAGCCGAAGCA
1 GGTCTCCCAGAAATCGCAGAAGCAGGAGCA
* * *
19309 GGTCTCCCAGAAATTGTA-AGAGCAGAAGCA
1 GGTCTCCCAGAAATCGCAGA-AGCAGGAGCA
* * *
19339 GGTCGCCCAGAAATCGTAGGAGCAGGAGCA
1 GGTCTCCCAGAAATCGCAGAAGCAGGAGCA
* * *
19369 GGTCGCCCAGAAATCGTAGGAGCAGGAGCA
1 GGTCTCCCAGAAATCGCAGAAGCAGGAGCA
* *
19399 GGTCACCCAGAAATCGCAGGAGCAGGAGCA
1 GGTCTCCCAGAAATCGCAGAAGCAGGAGCA
* *
19429 GGTCGCCCAGAAATCGCAGGAGCAGGAGCA
1 GGTCTCCCAGAAATCGCAGAAGCAGGAGCA
19459 GGTCTCCCAG
1 GGTCTCCCAG
19469 TTTTCGACGT
Statistics
Matches: 202, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
29 1 0.00
30 201 1.00
ACGTcount: A:0.32, C:0.25, G:0.32, T:0.12
Consensus pattern (30 bp):
GGTCTCCCAGAAATCGCAGAAGCAGGAGCA
Found at i:26023 original size:3 final size:3
Alignment explanation
Indices: 26015--26041 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
26005 TTTCTTTTAT
26015 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
26042 AGTGGTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:32345 original size:42 final size:42
Alignment explanation
Indices: 32298--32385 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
32288 GACATTCCAA
*
32298 TTCTGTTTTCCTTTCATCTTCATTTCTATTTGGGTGGGTTTC
1 TTCTGTTTTCCTTTCATCTTCATTTATATTTGGGTGGGTTTC
*
32340 TTCTGTTTTCCTTTCGTCTTCATTTATATTTGGGTGGGTTTC
1 TTCTGTTTTCCTTTCATCTTCATTTATATTTGGGTGGGTTTC
32382 TTCT
1 TTCT
32386 TCCCTAACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.07, C:0.18, G:0.17, T:0.58
Consensus pattern (42 bp):
TTCTGTTTTCCTTTCATCTTCATTTATATTTGGGTGGGTTTC
Found at i:33970 original size:2 final size:2
Alignment explanation
Indices: 33963--34000 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
33953 GATCAATTTG
33963 AT AT 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 AT AT
34001 GCATGTCACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35204 original size:4 final size:4
Alignment explanation
Indices: 35195--35221 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
35185 ATTGAAAATT
35195 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
35222 TATATGCGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:37730 original size:22 final size:22
Alignment explanation
Indices: 37677--37736 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
37667 AGCTATAACC
*
37677 ACACTATGAAATTGTGATAATT
1 ACACTATGAAATTTTGATAATT
37699 ACACTATGAAATTTTGATAATCT
1 ACACTATGAAATTTTGATAAT-T
* *
37722 -CCCTCTGAAATTTTG
1 ACACTATGAAATTTTG
37737 GCAACGACGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (22 bp):
ACACTATGAAATTTTGATAATT
Found at i:37825 original size:22 final size:22
Alignment explanation
Indices: 37800--37845 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
37790 CTATGAAAAA
37800 TTTTCAACCTTCCCAT-GAAATT
1 TTTTCAACCTTCCCATAG-AATT
*
37822 TTTTTAACCTTCCCATAGAATT
1 TTTTCAACCTTCCCATAGAATT
37844 TT
1 TT
37846 GAAAACCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.26, C:0.24, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTTCAACCTTCCCATAGAATT
Found at i:37882 original size:23 final size:22
Alignment explanation
Indices: 37840--37913 Score: 98
Period size: 22 Copynumber: 3.3 Consensus size: 22
37830 CTTCCCATAG
37840 AATTTTGA-AAACCTCACTATGA
1 AATTTTGATAAACCTC-CTATGA
*
37862 AATTTTGATAAACCGTCCTATAA
1 AATTTTGATAAACC-TCCTATGA
37885 AATTTTGAT-AACCTCCTTATGA
1 AATTTTGATAAACCTCC-TATGA
37907 AATTTTG
1 AATTTTG
37914 TTTACCTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
21 3 0.06
22 23 0.49
23 19 0.40
24 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
AATTTTGATAAACCTCCTATGA
Found at i:37898 original size:45 final size:45
Alignment explanation
Indices: 37814--37913 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
37804 CAACCTTCCC
* * * *
37814 ATGAAATTTT-TTTAACCTTCCCATAGAATTTTGAAAACCTCAC-T
1 ATGAAATTTTGATAAACCGTCCCATAAAATTTTGAAAACCTC-CTT
* *
37858 ATGAAATTTTGATAAACCGTCCTATAAAATTTTGATAACCTCCTT
1 ATGAAATTTTGATAAACCGTCCCATAAAATTTTGAAAACCTCCTT
37903 ATGAAATTTTG
1 ATGAAATTTTG
37914 TTTACCTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 11 0.23
45 37 0.77
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (45 bp):
ATGAAATTTTGATAAACCGTCCCATAAAATTTTGAAAACCTCCTT
Found at i:37909 original size:22 final size:21
Alignment explanation
Indices: 37805--37913 Score: 94
Period size: 22 Copynumber: 4.9 Consensus size: 21
37795 AAAAATTTTC
* **
37805 AACCTTCCCATGAAATTTTTTT
1 AACC-TCCTATGAAATTTTGAT
* *
37827 AACCTTCCCAT-AGAATTTTGAA
1 AACC-TCCTATGA-AATTTTGAT
37849 AACCTCACTATGAAATTTTGAT
1 AACCTC-CTATGAAATTTTGAT
*
37871 AAACCGTCCTATAAAATTTTGAT
1 -AACC-TCCTATGAAATTTTGAT
37894 AACCTCCTTATGAAATTTTG
1 AACCTCC-TATGAAATTTTG
37914 TTTACCTTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
21 6 0.08
22 47 0.64
23 19 0.26
24 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (21 bp):
AACCTCCTATGAAATTTTGAT
Found at i:37964 original size:22 final size:21
Alignment explanation
Indices: 37934--37995 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 21
37924 ATCTGTTTTG
*
37934 ATACCCTATGAAATTTTGATC
1 ATACACTATGAAATTTTGATC
* * *
37955 TATACACTATGAGATTTTAAAC
1 -ATACACTATGAAATTTTGATC
*
37977 -CACACTATGAAATTTTGAT
1 ATACACTATGAAATTTTGAT
37996 AACCCCCCTA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 15 0.47
22 17 0.53
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (21 bp):
ATACACTATGAAATTTTGATC
Found at i:38348 original size:21 final size:21
Alignment explanation
Indices: 38322--38369 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
38312 CAAGATTGCT
38322 GAAGAATTCTAGGATGGTAAG
1 GAAGAATTCTAGGATGGTAAG
38343 GAAGAATTCTAGGATGGTAAG
1 GAAGAATTCTAGGATGGTAAG
*
38364 GCAGAA
1 GAAGAA
38370 ATTGAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.06, G:0.33, T:0.21
Consensus pattern (21 bp):
GAAGAATTCTAGGATGGTAAG
Done.