Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019025.1 Corchorus olitorius cultivar O-4 contig19058, 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: 37161
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:4935 original size:12 final size:12
Alignment explanation
Indices: 4918--4949 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4908 TGAACTTGAA
4918 ATAGCTGAGGTC
1 ATAGCTGAGGTC
4930 ATAGCTGAGGTC
1 ATAGCTGAGGTC
*
4942 AAAGCTGA
1 ATAGCTGA
4950 TTGGCCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (12 bp):
ATAGCTGAGGTC
Found at i:9587 original size:13 final size:13
Alignment explanation
Indices: 9569--9595 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9559 TCCAGGTGGT
9569 AATCTTTCTTTTG
1 AATCTTTCTTTTG
9582 AATCTTTCTTTTG
1 AATCTTTCTTTTG
9595 A
1 A
9596 GGGCTTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (13 bp):
AATCTTTCTTTTG
Found at i:12210 original size:178 final size:177
Alignment explanation
Indices: 11846--12226 Score: 482
Period size: 178 Copynumber: 2.1 Consensus size: 177
11836 CCACAAACAC
* * * *
11846 AAATTATGTAATATTAAGTAAACCGTCTATTTCCGTTAACCGAAACAACTAATTCTTTGGAATAT
1 AAATTATATAATATTAAGTAAACCGTCTATTCCCGTTAACCGAAACAACTAAATCTTTGGAACAT
* * * *
11911 TTTTTATACCTTAAACATTAAATTTAGTTTTTGAGTCCTTCATGAAAGTTGTAGATCATGGAACA
66 TTTTGATACCTTAAACATTAAATTTAGTTTTCGAGTCCTACATGAAAGTTGTAGATAATGGAACA
* * * *
11976 ACCTTTCAAGAGACATTTGAATCATCTCAATCAGACATCTGGAGCAA
131 ACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACTGGAGCAA
* **
12023 AAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAAC-AAATCTTTCGGAAAC
1 AAATTATATAATATTAAGTAAACCGTCTATTCCCGTTAACCGAAACAACTAAATCTTT-GG-AAC
12087 ATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTACATGAAAGTTGTAGATAATGGA
64 ATTTTTGATACCTT-AAACATTAAATTTAGTTTTCGAGTCCTACATGAAAGTTGTAGATAATGGA
* * * * *
12151 ACAATCTTTTAATAGACACTTAAATCACC-CTAATCGGATAACTGGAG-AGA
128 ACAACCTTTCAAGAGACACTTAAATCACCTC-AATCAGACAACTGGAGCA-A
* * *
12201 AAATTATATAATGTTAAATATACCGT
1 AAATTATATAATATTAAGTAAACCGT
12227 TTAGGCAAAC
Statistics
Matches: 174, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
176 7 0.04
177 51 0.29
178 116 0.67
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAAACCGTCTATTCCCGTTAACCGAAACAACTAAATCTTTGGAACAT
TTTTGATACCTTAAACATTAAATTTAGTTTTCGAGTCCTACATGAAAGTTGTAGATAATGGAACA
ACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACTGGAGCAA
Found at i:16357 original size:68 final size:68
Alignment explanation
Indices: 16243--16388 Score: 256
Period size: 68 Copynumber: 2.1 Consensus size: 68
16233 ATTTTTTTCC
*
16243 CAGTTTCACAGTTTGATTTAGTTCATACTTACACATACATGACTTAATCTTTGAGACAAGCATAT
1 CAGTTTCACAGTTTGAATTAGTTCATACTTACACATACATGACTTAATCTTTGAGACAAGCATAT
*
16308 TTG
66 TCG
* *
16311 CAGTTTCACAGTTTGAATTAGTTCATACTTACACATGCATGGCTTAATCTTTGAGACAAGCATAT
1 CAGTTTCACAGTTTGAATTAGTTCATACTTACACATACATGACTTAATCTTTGAGACAAGCATAT
16376 TCG
66 TCG
16379 CAGTTTCACA
1 CAGTTTCACA
16389 TCTTGTAAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 74 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (68 bp):
CAGTTTCACAGTTTGAATTAGTTCATACTTACACATACATGACTTAATCTTTGAGACAAGCATAT
TCG
Found at i:18553 original size:139 final size:139
Alignment explanation
Indices: 18298--18567 Score: 396
Period size: 139 Copynumber: 1.9 Consensus size: 139
18288 CCTATTCAAT
* * *
18298 AATATCCTAAAATCAAGGGATTTACCCTGAAAACCCTTCTTATTTGTAACTAGAAACTAAACCTG
1 AATACCCTAAAATCAAGGGATTTACCCTGAAAACCCTCCTTATTTGTAACTAGAAACTAAACCTA
** * *
18363 GAATTAATTTGTTATCTTAATTATTAAACAGGATAACTGCCGGTAAAATCAGACGGGGCAATATA
66 GAATTAATTTGTTATCTTAATTATTAAACAAAATAACTGCAGGTAAAATCAGACGGGGCAACATA
18428 TTTTCCGTG
131 TTTTCCGTG
* * *** *
18437 AATACCCTAAAATCAAGGGATTTAGCCTGCAAACCCTCCTTATTTGTAACTAGGGGCTAAATCTA
1 AATACCCTAAAATCAAGGGATTTACCCTGAAAACCCTCCTTATTTGTAACTAGAAACTAAACCTA
* * *
18502 GAATTAATTTGTTATCTTAATTATTAGATAAAATAACTGTAGGTAAAATCAGACGGGGCAACATA
66 GAATTAATTTGTTATCTTAATTATTAAACAAAATAACTGCAGGTAAAATCAGACGGGGCAACATA
18567 T
131 T
18568 AAAAAATTAG
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
139 115 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (139 bp):
AATACCCTAAAATCAAGGGATTTACCCTGAAAACCCTCCTTATTTGTAACTAGAAACTAAACCTA
GAATTAATTTGTTATCTTAATTATTAAACAAAATAACTGCAGGTAAAATCAGACGGGGCAACATA
TTTTCCGTG
Found at i:23042 original size:67 final size:67
Alignment explanation
Indices: 22968--23101 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
22958 CAATATTCAA
* *
22968 AATTGAAACTTTTCCTCATACATATTTATTCAATAAAAATATCAAAGAATAAACCCTAATAGATG
1 AATTGAAACTTGTCCTAATACATATTTATTCAATAAAAATATCAAAGAATAAACCCTAATAGATG
23033 AG
66 AG
*
23035 AATTGAAACTTGTCCTAATTCATATTTATTCAATAAAAATATCAAAGAATAAACCCTAATAGATG
1 AATTGAAACTTGTCCTAATACATATTTATTCAATAAAAATATCAAAGAATAAACCCTAATAGATG
23100 AG
66 AG
23102 CCCAATCAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.31
Consensus pattern (67 bp):
AATTGAAACTTGTCCTAATACATATTTATTCAATAAAAATATCAAAGAATAAACCCTAATAGATG
AG
Found at i:24037 original size:17 final size:17
Alignment explanation
Indices: 24015--24062 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
24005 GATCACCCCT
*
24015 AGATCACTAGTGAT-CTA
1 AGATCACCAGTGATGC-A
24032 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
*
24049 AGATCACCGGTGAT
1 AGATCACCAGTGAT
24063 CAAAAATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 27 0.96
18 1 0.04
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:29282 original size:16 final size:17
Alignment explanation
Indices: 29252--29283 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29242 CTAGTCTTCT
29252 TTTTCCTTATTGTTGCC
1 TTTTCCTTATTGTTGCC
29269 TTTTCCTT-TTGTTGC
1 TTTTCCTTATTGTTGC
29284 TCGAATTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.03, C:0.22, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTTCCTTATTGTTGCC
Found at i:29692 original size:79 final size:81
Alignment explanation
Indices: 29576--29736 Score: 220
Period size: 79 Copynumber: 2.0 Consensus size: 81
29566 TATACATTTG
*
29576 AGCGCCTTTGACTCATAAATGATAGGTCTCATGTTCAAATCTCAATGCATATAAACCGTATATAT
1 AGCGCCTTTGACT-ATAAATGATAGATCTCATGTTCAAATCTCAATGCATATAAACCGTATATAT
29641 ATAAGGAGATATCTAAT
65 ATAAGGAGATATCTAAT
* * * * * *
29658 AGCGCCTTTGACT-T-CATGATAGATCTCA-GCTTCAAGTCTCACTGCATGTAAACTGTATGTAT
1 AGCGCCTTTGACTATAAATGATAGATCTCATG-TTCAAATCTCAATGCATATAAACCGTATATAT
29720 ATAAGGAGATATCTAAT
65 ATAAGGAGATATCTAAT
29737 TGTAATGAGA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
78 1 0.01
79 56 0.79
80 1 0.01
82 13 0.18
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (81 bp):
AGCGCCTTTGACTATAAATGATAGATCTCATGTTCAAATCTCAATGCATATAAACCGTATATATA
TAAGGAGATATCTAAT
Found at i:30650 original size:2 final size:2
Alignment explanation
Indices: 30643--30684 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
30633 TATAAATGTG
30643 TA TA TA TA TA TA TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30683 TA
1 TA
30685 ATACATAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.