Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010826.1 Corchorus olitorius cultivar O-4 contig10858, 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: 22840
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:5661 original size:12 final size:12
Alignment explanation
Indices: 5644--5668 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5634 CTTAGTGTGT
5644 TTAGCATGACTA
1 TTAGCATGACTA
5656 TTAGCATGACTA
1 TTAGCATGACTA
5668 T
1 T
5669 GAGAATTCAC
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TTAGCATGACTA
Found at i:16616 original size:286 final size:288
Alignment explanation
Indices: 16066--16766 Score: 1127
Period size: 286 Copynumber: 2.4 Consensus size: 288
16056 TGAAAGAAGA
* * * * * *
16066 GAGAGAGAGAGACTGACTGACTGATTGATGGGTGATCGATTTAGGCCTGCAGAGTTTGACATGAA
1 GAGAGAGAGAGAC-G--TGACTGACTGATGGGAG-T-GATTTAGACTTGTAGAGTTTGACATGAG
*
16131 AGGTATGTTTCTTAGAAGTCCTTTATATGTAGTTTCACGATACATTTTTGGCAGTATCTTTTATT
61 AGATATGTTTCTTAGAAGTCCTTTATATGTAGTTTCACGATACATTTTTGGCAGTATCTTTTATT
16196 AAATGCAATAAGTTAATTGCATTTTCCTTTATGGACAATTGTAATTACACGAATTGGTACAAGGT
126 AAATGCAATAAGTTAATTGCATTTTCCTTTATGGACAATTGTAATTACACGAATTGGTACAAGGT
*
16261 GAACACCTCAAAAGAAGCGAGCTGTATTAAAAGTTTAGACTTAAATTGAACATTAAGCCCACGAA
191 GAACACCTCAAAAGAAGCGAGCTGTATTAAAAGTTTAGACTTAAATTGAACATTAAGCCCACAAA
* *
16326 AGTAAACGTTCTTAGTTAAATGCTCAATTGATG
256 AGTAAACGTTCTTAGCTAAATGCTCAATTGAGG
*
16359 GAGAGTGAGAGA-G-GACTGACTGATGGGAGTGATTTAGACTTGTAGAGTTTGACATGAGAGATA
1 GAGAGAGAGAGACGTGACTGACTGATGGGAGTGATTTAGACTTGTAGAGTTTGACATGAGAGATA
*
16422 TGTTTCTTAGAAATCCTTTATATGTAGTTTCACGATACATTTTTGGCAGTATCTTTTATTAAATG
66 TGTTTCTTAGAAGTCCTTTATATGTAGTTTCACGATACATTTTTGGCAGTATCTTTTATTAAATG
16487 CAATAAGTTAATTGCATTTTCCTTTATGGACAATTGTAATTACACGAATTGGTACAAGGTGAACA
131 CAATAAGTTAATTGCATTTTCCTTTATGGACAATTGTAATTACACGAATTGGTACAAGGTGAACA
* * *
16552 CCTCTAAAGAAGTGAGTTGTATTAAAAGTTTAGACTTAAATTGAACATTAAGCCCACAAAAGTAA
196 CCTCAAAAGAAGCGAGCTGTATTAAAAGTTTAGACTTAAATTGAACATTAAGCCCACAAAAGTAA
*
16617 ATGTTCTTAGCTAAATGCTCAATTGAGG
261 ACGTTCTTAGCTAAATGCTCAATTGAGG
* * *
16645 GAGAGAGAGAGACTGATTGACTGACTGATGAGAGCGATTTAGACTTGTACAGTTTGACATGAGAG
1 GAGAGAGAGAGAC-G--TGACTGACTGATGGGAGTGATTTAGACTTGTAGAGTTTGACATGAGAG
* *
16710 ATATGTTTCTTAGAAGTCCTTTATATGTAGTTTCATGATGCATTTTTGGCAGTATCT
63 ATATGTTTCTTAGAAGTCCTTTATATGTAGTTTCACGATACATTTTTGGCAGTATCT
16767 CTCATTAATG
Statistics
Matches: 380, Mismatches: 23, Indels: 12
0.92 0.06 0.03
Matches are distributed among these distances:
286 254 0.67
287 1 0.00
288 15 0.04
291 99 0.26
293 11 0.03
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.34
Consensus pattern (288 bp):
GAGAGAGAGAGACGTGACTGACTGATGGGAGTGATTTAGACTTGTAGAGTTTGACATGAGAGATA
TGTTTCTTAGAAGTCCTTTATATGTAGTTTCACGATACATTTTTGGCAGTATCTTTTATTAAATG
CAATAAGTTAATTGCATTTTCCTTTATGGACAATTGTAATTACACGAATTGGTACAAGGTGAACA
CCTCAAAAGAAGCGAGCTGTATTAAAAGTTTAGACTTAAATTGAACATTAAGCCCACAAAAGTAA
ACGTTCTTAGCTAAATGCTCAATTGAGG
Found at i:17228 original size:24 final size:24
Alignment explanation
Indices: 17201--17250 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
17191 TTCTAAGTAC
* *
17201 TTTGCAACGGAATCAAAAACGGAA
1 TTTGCAACAGAATCAAAAAAGGAA
*
17225 TTTGCAATAGAATCAAAAAAGGAA
1 TTTGCAACAGAATCAAAAAAGGAA
17249 TT
1 TT
17251 CTATCTATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (24 bp):
TTTGCAACAGAATCAAAAAAGGAA
Found at i:17605 original size:45 final size:45
Alignment explanation
Indices: 17534--17642 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
17524 AAAACTAAAC
** * * *
17534 CCTATACAAAATAAAGGCCTTTTCTAGATCATTGCAAGTT-AGTGA
1 CCTATACAAAATAAAGGCCTCCTCTAGATAATGGCAAATTAAG-GA
* *
17579 TCTATACAAAATAAATGCCTCCTCTAGATAATGGCAAATTAAGGA
1 CCTATACAAAATAAAGGCCTCCTCTAGATAATGGCAAATTAAGGA
17624 CCTATACAAAATAAGAGGC
1 CCTATACAAAATAA-AGGC
17643 TGCCTTTCTA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
45 48 0.91
46 5 0.09
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (45 bp):
CCTATACAAAATAAAGGCCTCCTCTAGATAATGGCAAATTAAGGA
Found at i:19617 original size:2 final size:2
Alignment explanation
Indices: 19610--19637 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19600 CTATAGTTTA
19610 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
19638 TAATCACGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21075 original size:97 final size:97
Alignment explanation
Indices: 20859--21140 Score: 379
Period size: 97 Copynumber: 2.9 Consensus size: 97
20849 ACTAGCAAAT
* * * *
20859 TTATTATC-ATTTGGAAGCGGATTTGGATACGGATATGTACTTTCCGTGTTAAATTTCGTTTCAA
1 TTATTATCAATTT-GAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTTCGTTCCAA
*
20923 ATGAAATAAAAAATTTATATATAGAATAATTTTA
65 ATGAAAT-AAAAATTTATTTATAGAATAATTTTA
* * *
20957 CTATTATCAATTAGAAGCGGATTTAGACACGGATATGTAGTTTCTGTGTTAAATTTCGCTTCCAA
1 TTATTATCAATTTGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTTCG-TTCCAA
*
21022 ATGAAAT-AAAATTTATTTATAGAATTATTTTA
65 ATGAAATAAAAATTTATTTATAGAATAATTTTA
* * *
21054 TTATTATCAATTTGAATCGGATTTAGACACGGATATGCAGTTTCCGTGTTAAATTCCGTTTCCAA
1 TTATTATCAATTTGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTTCG-TTCCAA
* *
21119 GTGAAATAGAAAATTAATTTAT
65 ATGAAATA-AAAATTTATTTAT
21141 GTAAGATAGT
Statistics
Matches: 162, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
97 87 0.54
98 48 0.30
99 27 0.17
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (97 bp):
TTATTATCAATTTGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTTCGTTCCAAA
TGAAATAAAAATTTATTTATAGAATAATTTTA
Found at i:22736 original size:2 final size:2
Alignment explanation
Indices: 22725--22778 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
22715 AATGCTCAAT
22725 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
22766 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
22779 CTGATGGGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.