Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015136.1 Corchorus olitorius cultivar O-4 contig15169, 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: 21383
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7288 original size:50 final size:50
Alignment explanation
Indices: 7204--7353 Score: 201
Period size: 50 Copynumber: 3.0 Consensus size: 50
7194 ATTAATCAAA
* * * *
7204 GCATCTTAAGAAAATCCTAATGGTTAGAAATCGAAATAACACCTACTAAG
1 GCATCTTAAAAAAATCCCAATGATTAGAACTCGAAATAACACCTACTAAG
* * *
7254 GCATCTTAAAAAAAACCCAATGATCAGAACTCGAAATAACACCTACTAAA
1 GCATCTTAAAAAAATCCCAATGATTAGAACTCGAAATAACACCTACTAAG
** * *
7304 GCATCTTAAAAAAATTTCAATGATTAGAACTCGAATTGACACCTACTAAG
1 GCATCTTAAAAAAATCCCAATGATTAGAACTCGAAATAACACCTACTAAG
7354 TACCTTCTGA
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 86 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.23
Consensus pattern (50 bp):
GCATCTTAAAAAAATCCCAATGATTAGAACTCGAAATAACACCTACTAAG
Found at i:11481 original size:1 final size:1
Alignment explanation
Indices: 11475--11502 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
11465 AATTAAGTTG
11475 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
11503 AATAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12145 original size:21 final size:21
Alignment explanation
Indices: 12110--12151 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12100 GGTGTGTGTG
*
12110 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
12132 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
12152 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:12182 original size:25 final size:25
Alignment explanation
Indices: 12148--12196 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
12138 GATTGGTTTG
12148 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
12173 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
12197 GATTGTTTGG
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:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:16671 original size:19 final size:19
Alignment explanation
Indices: 16647--16719 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 19
16637 CTGTTTAGTA
*
16647 ACTGTATAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
16666 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
* *
16687 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
16708 ACTGTACAGATG
1 ACTGTACAGATG
16720 GGATCTTAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.33
21 32 0.67
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:16692 original size:21 final size:21
Alignment explanation
Indices: 16666--16718 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
16656 ATGAGATTAC
16666 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATTAGATTAGGT
16687 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATTAGATTAGGT
16708 ACTGTACAGAT
1 ACTGTACAGAT
16719 GGGATCTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (21 bp):
ACTGTACAGATTAGATTAGGT
Found at i:20049 original size:59 final size:59
Alignment explanation
Indices: 19956--20069 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
19946 ATTTATATAT
* *
19956 ATAAAGACCTAACGTTATCGAAAATGTTTAAATAAGGGTCCGATTTTTTAATTTGATCAA
1 ATAAAGACCTAACGTTATCGAAAATATTTAAATAAGGG-CCGATCTTTTAATTTGATCAA
* *
20016 ATAAAGACCTAATG-TGTCGAAAATATTTAAATAAGGGCCGATCTTTTAATTTGA
1 ATAAAGACCTAACGTTATCGAAAATATTTAAATAAGGGCCGATCTTTTAATTTGA
20070 CCGAATAAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 16 0.32
59 21 0.42
60 13 0.26
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (59 bp):
ATAAAGACCTAACGTTATCGAAAATATTTAAATAAGGGCCGATCTTTTAATTTGATCAA
Found at i:20077 original size:58 final size:60
Alignment explanation
Indices: 19956--20091 Score: 177
Period size: 58 Copynumber: 2.3 Consensus size: 60
19946 ATTTATATAT
* * *
19956 ATAAAGACCTAACGTTATCGAAAATGTTTAAATAAGGGTCCGATTTTTTAATTTGATCAA
1 ATAAAGACCTAACGTTATCGAAAATATTTAAATAAGGGTCCGATCTTTTAATTTGACCAA
* * *
20016 ATAAAGACCTAATG-TGTCGAAAATATTTAAATAAGGG-CCGATCTTTTAATTTGACCGA
1 ATAAAGACCTAACGTTATCGAAAATATTTAAATAAGGGTCCGATCTTTTAATTTGACCAA
* **
20074 ATAAGGGTCTAACGTTAT
1 ATAAAGACCTAACGTTAT
20092 AAAAAATGCT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 28 0.44
59 23 0.36
60 13 0.20
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (60 bp):
ATAAAGACCTAACGTTATCGAAAATATTTAAATAAGGGTCCGATCTTTTAATTTGACCAA
Found at i:20780 original size:43 final size:43
Alignment explanation
Indices: 20719--20803 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
20709 TGAGTAACAA
*
20719 CAGCTTAAACTCAAAAACACATTTTAAAACCAATGAAAATAAT
1 CAGCTGAAACTCAAAAACACATTTTAAAACCAATGAAAATAAT
* ***
20762 CAGCTGAAACTCAAAAACACCTTTTATGGCCAATGAAAATAA
1 CAGCTGAAACTCAAAAACACATTTTAAAACCAATGAAAATAA
20804 GAAGCTTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.22
Consensus pattern (43 bp):
CAGCTGAAACTCAAAAACACATTTTAAAACCAATGAAAATAAT
Found at i:21055 original size:11 final size:10
Alignment explanation
Indices: 21040--21086 Score: 67
Period size: 11 Copynumber: 4.5 Consensus size: 10
21030 AACCATAAAA
21040 GCCCGGCCCG
1 GCCCGGCCCG
21050 AGCCCGGCCCG
1 -GCCCGGCCCG
*
21061 GCCTGAGCCCG
1 GCCCG-GCCCG
21072 GCCCGGCCCG
1 GCCCGGCCCG
21082 GCCCG
1 GCCCG
21087 TATACTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 14 0.42
11 19 0.58
ACGTcount: A:0.04, C:0.55, G:0.38, T:0.02
Consensus pattern (10 bp):
GCCCGGCCCG
Found at i:21059 original size:5 final size:5
Alignment explanation
Indices: 21040--21086 Score: 67
Period size: 5 Copynumber: 9.0 Consensus size: 5
21030 AACCATAAAA
*
21040 GCCCG GCCCG AGCCCG GCCCG GCCTG AGCCCG GCCCG GCCCG GCCCG
1 GCCCG GCCCG -GCCCG GCCCG GCCCG -GCCCG GCCCG GCCCG GCCCG
21087 TATACTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 29 0.76
6 9 0.24
ACGTcount: A:0.04, C:0.55, G:0.38, T:0.02
Consensus pattern (5 bp):
GCCCG
Found at i:21061 original size:16 final size:16
Alignment explanation
Indices: 21040--21086 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
21030 AACCATAAAA
21040 GCCCGGCCCGAGCCCG
1 GCCCGGCCCGAGCCCG
*
21056 GCCCGGCCTGAGCCCG
1 GCCCGGCCCGAGCCCG
21072 GCCCGGCCCG-GCCCG
1 GCCCGGCCCGAGCCCG
21087 TATACTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 5 0.17
16 24 0.83
ACGTcount: A:0.04, C:0.55, G:0.38, T:0.02
Consensus pattern (16 bp):
GCCCGGCCCGAGCCCG
Done.