Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018081.1 Corchorus olitorius cultivar O-4 contig18114, 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: 17907
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:853 original size:18 final size:18
Alignment explanation
Indices: 818--854 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
808 TAATTAAAAT
*
818 TTAAAATTTCCAACTTAA
1 TTAAAATTTCCAAATTAA
*
836 TTAAAATTTCTAAATTAA
1 TTAAAATTTCCAAATTAA
854 T
1 T
855 ATAGAGGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAATTTCCAAATTAA
Found at i:1371 original size:6 final size:6
Alignment explanation
Indices: 1355--1417 Score: 99
Period size: 6 Copynumber: 10.0 Consensus size: 6
1345 GTTTAGATTT
1355 ATATAG TATATAG ATATAG TATATAG ATATAG ATATAG ATATAG TATATAG
1 ATATAG -ATATAG ATATAG -ATATAG ATATAG ATATAG ATATAG -ATATAG
1406 ATATAG ATATAG
1 ATATAG ATATAG
1418 TAACTTATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
6 36 0.67
7 18 0.33
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:1386 original size:19 final size:19
Alignment explanation
Indices: 1355--1419 Score: 114
Period size: 19 Copynumber: 3.4 Consensus size: 19
1345 GTTTAGATTT
1355 ATATAGTATATAGATATAG
1 ATATAGTATATAGATATAG
1374 TATATAG-ATATAGATATAG
1 -ATATAGTATATAGATATAG
1393 ATATAGTATATAGATATAG
1 ATATAGTATATAGATATAG
1412 ATATAGTA
1 ATATAGTA
1420 ACTTATATTG
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.14
19 32 0.73
20 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (19 bp):
ATATAGTATATAGATATAG
Found at i:1392 original size:25 final size:25
Alignment explanation
Indices: 1355--1417 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
1345 GTTTAGATTT
1355 ATATAGTATATAGATATAGTATATAG
1 ATATAG-ATATAGATATAGTATATAG
1381 ATATAGATATAGATATAGTATATAG
1 ATATAGATATAGATATAGTATATAG
1406 ATATAGATATAG
1 ATATAGATATAG
1418 TAACTTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 31 0.84
26 6 0.16
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.37
Consensus pattern (25 bp):
ATATAGATATAGATATAGTATATAG
Found at i:8025 original size:17 final size:17
Alignment explanation
Indices: 8003--8039 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
7993 AAAAAAGTGC
8003 ATTATTAGACATTTCAT
1 ATTATTAGACATTTCAT
8020 ATTATTAGACATTTCAT
1 ATTATTAGACATTTCAT
8037 ATT
1 ATT
8040 CAAATAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (17 bp):
ATTATTAGACATTTCAT
Found at i:8501 original size:106 final size:108
Alignment explanation
Indices: 8317--8527 Score: 300
Period size: 106 Copynumber: 2.0 Consensus size: 108
8307 ATTTCCTAAC
* * * * *
8317 CACCTACTCACATATATGATAAGAAACGAGAGAAAAAAAACTCTATAACTAAAATGATTTGCTAA
1 CACCTACGCACATATATGATAAGAAACCAGAGAAAAAAAAATCTAAAACTAAAATAATTTGCTAA
* * *
8382 CCACATATCAAGAATGCTCGACGCGCCAGCGTGAGCCGATAAT
66 CCACAAATCAAGAATGCTCAACACGCCAGCGTGAGCCGATAAT
* * *
8425 CACCTACGCACATATATGATAAG-AACCA-AGAAAAAAAAATCTAAAATTAGAATAATTTGCTAG
1 CACCTACGCACATATATGATAAGAAACCAGAGAAAAAAAAATCTAAAACTAAAATAATTTGCTAA
*
8488 CCACAAATCAAGAATGCTCAACACGTCAGCGTGAGCCGAT
66 CCACAAATCAAGAATGCTCAACACGCCAGCGTGAGCCGAT
8528 CAACTTGTTA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 65 0.71
107 4 0.04
108 22 0.24
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (108 bp):
CACCTACGCACATATATGATAAGAAACCAGAGAAAAAAAAATCTAAAACTAAAATAATTTGCTAA
CCACAAATCAAGAATGCTCAACACGCCAGCGTGAGCCGATAAT
Found at i:8609 original size:13 final size:13
Alignment explanation
Indices: 8591--8618 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8581 TGAAAACAAG
8591 ATCGCGTAGCCAA
1 ATCGCGTAGCCAA
8604 ATCGCGTAGCCAA
1 ATCGCGTAGCCAA
8617 AT
1 AT
8619 ATATCAGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (13 bp):
ATCGCGTAGCCAA
Found at i:12752 original size:22 final size:23
Alignment explanation
Indices: 12716--12760 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
12706 CACAAAGAAG
*
12716 CTAAATAAGAAAAGAGTTTTGCT
1 CTAAATAAAAAAAGAGTTTTGCT
12739 CTAAA-AAAAAAAGAGTTTTGCT
1 CTAAATAAAAAAAGAGTTTTGCT
12761 ACTTGATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.29
Consensus pattern (23 bp):
CTAAATAAAAAAAGAGTTTTGCT
Found at i:13893 original size:31 final size:32
Alignment explanation
Indices: 13845--13928 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 32
13835 TCCAGAAACT
* * *
13845 TAAAATCAGGATATTTTATCC-CCTAAACTTCC
1 TAAATTCAGGACATTTTA-CCTCATAAACTTCC
*
13877 -AAATTTAGGACATTTTACCTCATAAACTTCC
1 TAAATTCAGGACATTTTACCTCATAAACTTCC
* *
13908 TAAATTCAAGACATTCTACCT
1 TAAATTCAGGACATTTTACCT
13929 ACTGACGGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 2 0.05
31 24 0.56
32 17 0.40
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35
Consensus pattern (32 bp):
TAAATTCAGGACATTTTACCTCATAAACTTCC
Found at i:13921 original size:32 final size:31
Alignment explanation
Indices: 13868--13928 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
13858 TTTTATCCCC
* * *
13868 TAAACTTCCAAATTTAGGACATTTTACCTCA
1 TAAACTTCCAAATTCAAGACATTCTACCTCA
13899 TAAACTTCCTAAATTCAAGACATTCTACCT
1 TAAACTTCC-AAATTCAAGACATTCTACCT
13929 ACTGACGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (31 bp):
TAAACTTCCAAATTCAAGACATTCTACCTCA
Found at i:14457 original size:15 final size:16
Alignment explanation
Indices: 14430--14459 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14420 AAAAGGTTGA
14430 CAAAAGAACTAGTATT
1 CAAAAGAACTAGTATT
14446 CAAAAG-ACTAGTAT
1 CAAAAGAACTAGTAT
14460 AAGCTAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.23
Consensus pattern (16 bp):
CAAAAGAACTAGTATT
Found at i:17418 original size:122 final size:127
Alignment explanation
Indices: 17279--17524 Score: 376
Period size: 122 Copynumber: 2.0 Consensus size: 127
17269 CATTGTTTAC
*
17279 ACTTTTATAATTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAATTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
17340 -TGATTTTTACCATTTCACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTAAATAT
66 TTGATTTTTACCATTTCACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTAAATAT
* *
17401 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAATTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--C
* * *
17466 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAACTTATATATATTAGAATTTTT
64 TA-TTGATTTTTACCATTTCACTATTTTAATTAAAAAACTTATATATATTAGAATTTTT
17525 TGAATATATT
Statistics
Matches: 110, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
122 53 0.48
123 1 0.01
124 1 0.01
125 1 0.01
128 2 0.02
130 52 0.47
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (127 bp):
ACTTTTACAATTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTCACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTAAATAT
Done.