Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016424.1 Corchorus olitorius cultivar O-4 contig16457, 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: 55220
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4826 original size:19 final size:19
Alignment explanation
Indices: 4802--4838 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4792 CTATTTAGCA
4802 ACTGTACAAATGAGATTAC
1 ACTGTACAAATGAGATTAC
* *
4821 ACTGTACAGATTAGATTA
1 ACTGTACAAATGAGATTA
4839 TTAAAGCAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
ACTGTACAAATGAGATTAC
Found at i:13719 original size:29 final size:29
Alignment explanation
Indices: 13686--13741 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
13676 GTTAGAGCAA
13686 AGCTTTGGATACCGAATGGGGTACCAAAG
1 AGCTTTGGATACCGAATGGGGTACCAAAG
13715 AGCTTTGGATACCGAATGGGGTACCAA
1 AGCTTTGGATACCGAATGGGGTACCAA
13742 CGAAGAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.21
Consensus pattern (29 bp):
AGCTTTGGATACCGAATGGGGTACCAAAG
Found at i:19383 original size:73 final size:73
Alignment explanation
Indices: 19262--19406 Score: 229
Period size: 73 Copynumber: 2.0 Consensus size: 73
19252 AAAAGTTCAA
* *
19262 ATGAGGGGAGACTGTTACATCTGAACATGTCACAAGTCTTAGAAATGGTTTATAGTGATATTTAC
1 ATGAGGGGAGACCGTTACAACTGAACATGTCACAAGTCTTAGAAATGGTTTATAGTGATATTTAC
19327 AAGGGCAG
66 AAGGGCAG
* *
19335 ATGAGGGGAGACCGTT-CAACTTGAACATGTCACAAGTTTTAGAGATGGTTTATAGTGATATTTA
1 ATGAGGGGAGACCGTTACAAC-TGAACATGTCACAAGTCTTAGAAATGGTTTATAGTGATATTTA
*
19399 CAGGGGCA
65 CAAGGGCA
19407 AGGGATTGGA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 3 0.05
73 63 0.95
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (73 bp):
ATGAGGGGAGACCGTTACAACTGAACATGTCACAAGTCTTAGAAATGGTTTATAGTGATATTTAC
AAGGGCAG
Found at i:19716 original size:5 final size:5
Alignment explanation
Indices: 19708--19735 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
19698 TGGTGAATGG
19708 AGGAA AGGAA AGGAA AGGAA AGGAA AGG
1 AGGAA AGGAA AGGAA AGGAA AGGAA AGG
19736 GTAATTGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
AGGAA
Found at i:28560 original size:79 final size:80
Alignment explanation
Indices: 28407--28561 Score: 195
Period size: 79 Copynumber: 1.9 Consensus size: 80
28397 ATTTCTGCAA
* * * * * * * * *
28407 AAGGAAAATAATACAATCAGATCATGTTATCCACGAATTTTAAGAAAATTAGTAACATAGTACCA
1 AAGGAAAAGAATAAAATCAAATCAAGCTATCCAAGAATTTCAAGAAAATAAGTAACATAATACCA
*
28472 AAGTTAGTAAAGTAG
66 AAGTAAGTAAAGTAG
* *
28487 AAGGAAAAGAATAAAATCAAATCAAGCTATCCAAGAA-TTCAATAAAATAAGTAACCTAATACCA
1 AAGGAAAAGAATAAAATCAAATCAAGCTATCCAAGAATTTCAAGAAAATAAGTAACATAATACCA
28551 AAGTAAGTAAA
66 AAGTAAGTAAA
28562 ATAGCATGAA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
79 32 0.51
80 31 0.49
ACGTcount: A:0.52, C:0.12, G:0.13, T:0.23
Consensus pattern (80 bp):
AAGGAAAAGAATAAAATCAAATCAAGCTATCCAAGAATTTCAAGAAAATAAGTAACATAATACCA
AAGTAAGTAAAGTAG
Found at i:29069 original size:7 final size:7
Alignment explanation
Indices: 29057--29082 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29047 AAATCTTCCG
29057 AGAAAGA
1 AGAAAGA
29064 AGAAAGA
1 AGAAAGA
29071 AGAAAGA
1 AGAAAGA
29078 AGAAA
1 AGAAA
29083 TTAGAATCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AGAAAGA
Found at i:29278 original size:18 final size:17
Alignment explanation
Indices: 29256--29296 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
29246 GCAATCGAGC
*
29256 GTTTTTTTTTTTAAGACT
1 GTTTTTTTTCTTAA-ACT
*
29274 TTTTTTTTTCTTAAACT
1 GTTTTTTTTCTTAAACT
29291 GTTTTT
1 GTTTTT
29297 ATAATATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.71
Consensus pattern (17 bp):
GTTTTTTTTCTTAAACT
Found at i:29279 original size:17 final size:18
Alignment explanation
Indices: 29256--29296 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
29246 GCAATCGAGC
29256 GTTTTTTTTT-TTAAGACT
1 GTTTTTTTTTCTTAA-ACT
29274 -TTTTTTTTTCTTAAACT
1 GTTTTTTTTTCTTAAACT
29291 GTTTTT
1 GTTTTT
29297 ATAATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.71
Consensus pattern (18 bp):
GTTTTTTTTTCTTAAACT
Found at i:39725 original size:13 final size:13
Alignment explanation
Indices: 39707--39738 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
39697 ATTCCACACC
39707 TCGAAAAATTGAT
1 TCGAAAAATTGAT
39720 TCGAAAAATTGAT
1 TCGAAAAATTGAT
39733 TCGAAA
1 TCGAAA
39739 TTTGTTCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (13 bp):
TCGAAAAATTGAT
Found at i:41099 original size:21 final size:19
Alignment explanation
Indices: 41074--41131 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
41064 GCTGCTCTAA
41074 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
41095 TAATCTAATCGGTACAGTG
1 TAATCTCATCTGTACAGTC
41114 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
41132 TGCTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:45675 original size:2 final size:2
Alignment explanation
Indices: 45668--45697 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45658 TTATAGATTC
45668 AT 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 AT
45698 TGATTTGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53081 original size:48 final size:49
Alignment explanation
Indices: 52974--53097 Score: 232
Period size: 48 Copynumber: 2.6 Consensus size: 49
52964 ACATATTTTC
*
52974 TTAATTAATTAATTTTAGTATGATAGATTGATTAATTAGTGATAGTATA
1 TTAATTAATTAATTTTAGTATGATAGACTGATTAATTAGTGATAGTATA
53023 TTAATTAATTAATTTTAGTATGATAGACTGATTAA-TAGTGATAGTATA
1 TTAATTAATTAATTTTAGTATGATAGACTGATTAATTAGTGATAGTATA
53071 TTAATTAATTAATTTTAGTATGATAGA
1 TTAATTAATTAATTTTAGTATGATAGA
53098 TATTTTAGTA
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
48 40 0.54
49 34 0.46
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.46
Consensus pattern (49 bp):
TTAATTAATTAATTTTAGTATGATAGACTGATTAATTAGTGATAGTATA
Found at i:55188 original size:3 final size:3
Alignment explanation
Indices: 55180--55220 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
55170 TTTTTACTTC
55180 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Done.