Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019280.1 Corchorus olitorius cultivar O-4 contig19313, 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: 26837
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:982 original size:42 final size:43
Alignment explanation
Indices: 938--1021 Score: 105
Period size: 45 Copynumber: 1.9 Consensus size: 43
928 CCGATCACTA
** * * *
938 CTCCATCTCTAGGTTATTTATCAAAATAAAGCTAATATTCTACTC
1 CTCCATCTCTACATAATTCATCAAAATAAAACTAATATTCTA--C
983 CTCCATCTCTACATAATTCATCAAAATAAAACTAATATT
1 CTCCATCTCTACATAATTCATCAAAATAAAACTAATATT
1022 AATTGTTGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.36
Consensus pattern (43 bp):
CTCCATCTCTACATAATTCATCAAAATAAAACTAATATTCTAC
Found at i:4577 original size:16 final size:16
Alignment explanation
Indices: 4556--4590 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
4546 TGACCACATT
4556 ATGTGCTTAGGTTGTC
1 ATGTGCTTAGGTTGTC
4572 ATGTGCTTAGGTTGTC
1 ATGTGCTTAGGTTGTC
4588 ATG
1 ATG
4591 AGGATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.31, T:0.43
Consensus pattern (16 bp):
ATGTGCTTAGGTTGTC
Found at i:6371 original size:21 final size:21
Alignment explanation
Indices: 6346--6428 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
6336 TATCTTAGAT
6346 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
6367 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
6388 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
6410 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
6429 TTATTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:6379 original size:25 final size:25
Alignment explanation
Indices: 6348--6396 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
6338 TCTTAGATAT
*
6348 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
6373 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
6397 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:8251 original size:133 final size:127
Alignment explanation
Indices: 8086--8324 Score: 329
Period size: 133 Copynumber: 1.8 Consensus size: 127
8076 AGAAATTCTA
*
8086 ATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAATAAAATAGGTATAAGGATATTAG
1 ATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAAT----CA--TA-AA-GATATTAG
* * *
8151 ATTTAATTAAATAAAA-TAGAG-TTTTAGTTGAGTAAAACTGTAAAAGTATATTTAAAAAATTCT
58 ATTTAAATAAATAAAATTAGAGTTTTTAGTTGAATAAAACTATAAAAGTATATTTAAAAAATTCT
8214 AATAT
123 AATAT
* * *
8219 ATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATCATAAAGATATTAGATTTAAAT
1 ATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAATCATAAAGATATTAGATTTAAAT
8284 AAATAAAATTAGAGTTTTTAGTTGAATAAAACTATAAAAGT
66 AAATAAAATTAGAGTTTTTAGTTGAATAAAACTATAAAAGT
8325 TTAAATAATG
Statistics
Matches: 97, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
125 23 0.24
126 7 0.07
127 26 0.27
129 1 0.01
133 40 0.41
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (127 bp):
ATATATATAAGTTTTTAAAATAAAATAATAAAATGGTAAAAATCATAAAGATATTAGATTTAAAT
AAATAAAATTAGAGTTTTTAGTTGAATAAAACTATAAAAGTATATTTAAAAAATTCTAATAT
Found at i:12499 original size:17 final size:17
Alignment explanation
Indices: 12477--12510 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12467 TTTAAGATTC
12477 TGCCCTTATTTGTAAAA
1 TGCCCTTATTTGTAAAA
12494 TGCCCTTATTTGTAAAA
1 TGCCCTTATTTGTAAAA
12511 CCCGAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (17 bp):
TGCCCTTATTTGTAAAA
Found at i:13243 original size:10 final size:10
Alignment explanation
Indices: 13225--13265 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
13215 ACATAAATAT
*
13225 TTATTTATTA
1 TTATATATTA
13235 TTATATATTA
1 TTATATATTA
13245 TTATA-ATTTA
1 TTATATA-TTA
13255 TT-TATATTA
1 TTATATATTA
13264 TT
1 TT
13266 CTACTATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATATATTA
Found at i:18939 original size:18 final size:18
Alignment explanation
Indices: 18916--18954 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
18906 GGTTCCATTC
18916 AAGCAGTTGATTTAGATT
1 AAGCAGTTGATTTAGATT
18934 AAGCAGTTGATTTAGATT
1 AAGCAGTTGATTTAGATT
18952 AAG
1 AAG
18955 AATGGATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (18 bp):
AAGCAGTTGATTTAGATT
Found at i:19677 original size:31 final size:30
Alignment explanation
Indices: 19639--19805 Score: 96
Period size: 31 Copynumber: 5.5 Consensus size: 30
19629 TTTTCGACGC
19639 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTT-GCAAACGT
** **
19670 TAGGCCCTTATTTG-GCTAAATTAAAAGACCG-
1 TAGGCCCTTATTTGAGC-ATTTTGCAA-A-CGT
*
19701 --GGCCCTTATTTGAGCATTTTGGCAAACGA
1 TAGGCCCTTATTTGAGCATTTT-GCAAACGT
** ** *
19730 TAGATCCTTATTT-AGCCAAATT--AAAAGAT
1 TAGGCCCTTATTTGAG-CATTTTGCAAACG-T
* * *
19759 CAGACCCTTATTTGAACATTTTTGCAAACGT
1 TAGGCCCTTATTTGAGCA-TTTTGCAAACGT
19790 TAGGCCCTTATTTGAG
1 TAGGCCCTTATTTGAG
19806 TAATTAGCCT
Statistics
Matches: 99, Mismatches: 23, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
28 6 0.06
29 29 0.29
30 13 0.13
31 45 0.45
32 6 0.06
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (30 bp):
TAGGCCCTTATTTGAGCATTTTGCAAACGT
Found at i:19739 original size:60 final size:60
Alignment explanation
Indices: 19640--19803 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 60
19630 TTTCGACGCT
*
19640 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCTAAATTAAAAGACC
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
* * ** * *
19700 GGGCCCTTATTTGAGCATTTTGGCAAACGATAGATCCTTATTTAGCCAAATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
* * *
19760 AGACCCTTATTTGAACATTTTTGCAAACGTTAGGCCCTTATTTG
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
19804 AGTAATTAGC
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 89 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (60 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
Found at i:21419 original size:43 final size:43
Alignment explanation
Indices: 21360--21686 Score: 399
Period size: 43 Copynumber: 7.8 Consensus size: 43
21350 CCAATAACCA
* * *
21360 AAAGTCCCCAAACACATATGTAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
21403 AAAGTCCTCAAACAC--ATATAACACAGAGGCA-C-CTA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
*
21442 CAAGTCCCCAAACACATATATAACACA-AGGGCAAT-TCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGA-GGC-ATCTCTATTAC
* *
21485 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
21526 AAAGTCCCCAAACACATATATAACATAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
21569 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
21610 AAAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-ATCTCTATTAC
* *
21653 AAAGTCCTCAAATACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
21687 TTCTCCTTAT
Statistics
Matches: 244, Mismatches: 25, Indels: 31
0.81 0.08 0.10
Matches are distributed among these distances:
38 1 0.00
39 17 0.07
40 2 0.01
41 96 0.39
42 11 0.05
43 114 0.47
44 3 0.01
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:21715 original size:84 final size:84
Alignment explanation
Indices: 21360--21686 Score: 552
Period size: 84 Copynumber: 3.9 Consensus size: 84
21350 CCAATAACCA
* *
21360 AAAGTCCCCAAACACATATGTAACACAGGGGC-ATCTCTATTCCAAAGTCCTCAAACAC--ATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAAT-TCTATTACAAAGTCCTCAAACACATATAT
*
21422 AACACAGAGGCACCTATATC
65 AACACAGAGGCATCTATATC
* *
21442 CAAGTCCCCAAACACATATATAACACAAGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
21507 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
* *
21526 AAAGTCCCCAAACACATATATAACATAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
21591 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
*
21610 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAATACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
21675 ACACAGAGGCAT
66 ACACAGAGGCAT
21687 TTCTCCTTAT
Statistics
Matches: 230, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
82 51 0.22
83 2 0.01
84 177 0.77
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:21807 original size:2 final size:2
Alignment explanation
Indices: 21795--21846 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
21785 ACCAAATTCC
21795 TA TA T- TA TA TA TA TA TA TA TA TA 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
* *
21836 CA TA CA TA TA T
1 TA TA TA TA TA T
21847 GTGACAAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:24550 original size:22 final size:24
Alignment explanation
Indices: 24515--24573 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
24505 ATAAATGTTG
* *
24515 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
24537 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
24560 CTTGATAATATCTT
1 C-TGATAAT-TCTT
24574 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:26667 original size:15 final size:16
Alignment explanation
Indices: 26643--26682 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
26633 AGAGGTTGAA
*
26643 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
26658 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
26674 AGAAAACAA
1 AGAAAACAA
26683 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.