Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006406.1 Corchorus capsularis cultivar CVL-1 contig06427, 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: 38235
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1849 original size:23 final size:23
Alignment explanation
Indices: 1819--1864 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1809 GTCTTTTTCG
1819 ATCAATAGTCAATCCTATACATT
1 ATCAATAGTCAATCCTATACATT
*
1842 ATCAATAGTCAATTCTATACATT
1 ATCAATAGTCAATCCTATACATT
1865 TTTTTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (23 bp):
ATCAATAGTCAATCCTATACATT
Found at i:2110 original size:22 final size:22
Alignment explanation
Indices: 2068--2110 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2058 TATTTTTTTA
** *
2068 TTAAGTTTAGCCTTAATTTCAC
1 TTAAGTTTAGCCCCAAATTCAC
2090 TTAAGTTTAGCCCCAAATTCA
1 TTAAGTTTAGCCCCAAATTCA
2111 AATTTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (22 bp):
TTAAGTTTAGCCCCAAATTCAC
Found at i:2248 original size:101 final size:99
Alignment explanation
Indices: 2081--2318 Score: 318
Period size: 99 Copynumber: 2.3 Consensus size: 99
2071 AGTTTAGCCT
*
2081 TAATTTCACTTAAGTTTAGCCCCAAATTCAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAAT
1 TAATTTCAC-TAAGTTTAGCCCCAAATT-AAA----A-TTTTATTTTAAGGGTAAATTCCAAAAT
*
2146 TAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
59 TAATAA--TATCGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
2189 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTAAGGGTAAATTCCATAATTAATAAT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTAAGGGTAAATTCCAAAATTAATAAT
* * *
2254 ATCGTTATAGGGTTTTAGAAATAAAATATATAAT
66 ATCGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
2288 TAA-TTCACTAAGTTTAG-CTCAAATTAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATT
2319 AAAATTTTTA
Statistics
Matches: 123, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
97 13 0.11
98 14 0.11
99 34 0.28
101 31 0.25
102 1 0.01
106 3 0.02
107 18 0.15
108 9 0.07
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (99 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTAAGGGTAAATTCCAAAATTAATAAT
ATCGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:5105 original size:2 final size:2
Alignment explanation
Indices: 5098--5124 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5088 AACACAATCA
5098 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
5125 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:7179 original size:2 final size:2
Alignment explanation
Indices: 7172--7198 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7162 AAAACAAAAC
7172 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
7199 AAAGGAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7743 original size:59 final size:59
Alignment explanation
Indices: 7679--7794 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 59
7669 TTTAGATTAC
* *
7679 ATATATATATATATATAGA-ACAAAAAAATCCTCACCAGATTTGCATCCCATCTCCAGAA
1 ATATATATATATATATA-ACAAAAAAAAATCCTCACCAGATTTACATCCCATCTCCAGAA
7738 ATATATATATATATATAACAAAAAAAAATCCTCACCAGATTTACATCCCATCTCCAG
1 ATATATATATATATATAACAAAAAAAAATCCTCACCAGATTTACATCCCATCTCCAG
7795 CTTTTTCCTT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
58 1 0.02
59 53 0.98
ACGTcount: A:0.45, C:0.22, G:0.05, T:0.28
Consensus pattern (59 bp):
ATATATATATATATATAACAAAAAAAAATCCTCACCAGATTTACATCCCATCTCCAGAA
Found at i:9155 original size:26 final size:26
Alignment explanation
Indices: 9126--9176 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
9116 GTTACTGTAG
9126 AAATTAAATTTTTCTAAATAAAATAA
1 AAATTAAATTTTTCTAAATAAAATAA
*
9152 AAATTGAATTTTTCTAAATAAAATA
1 AAATTAAATTTTTCTAAATAAAATA
9177 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (26 bp):
AAATTAAATTTTTCTAAATAAAATAA
Found at i:9497 original size:27 final size:27
Alignment explanation
Indices: 9453--9507 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
9443 AGGTTTGCCG
9453 AAAAACGCAATTCAGGATATAACGTTAC
1 AAAAACGCAATT-AGGATATAACGTTAC
9481 AAAAACGTCAATT-GGATATAACGTTAC
1 AAAAACG-CAATTAGGATATAACGTTAC
9508 CTATTTCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 14 0.54
28 7 0.27
29 5 0.19
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (27 bp):
AAAAACGCAATTAGGATATAACGTTAC
Found at i:18174 original size:11 final size:11
Alignment explanation
Indices: 18131--18168 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
18121 TTCCTATATA
*
18131 AAATAAATTAT
1 AAATTAATTAT
18142 CAAA-TAATTAT
1 -AAATTAATTAT
18153 AAATTAATTAT
1 AAATTAATTAT
18164 AAATT
1 AAATT
18169 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:18332 original size:19 final size:19
Alignment explanation
Indices: 18308--18346 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
18298 TATCTATGTG
*
18308 CCTATAAATAGGTCACTTA
1 CCTATAAATAGGCCACTTA
18327 CCTATAAATAGGCCACTTA
1 CCTATAAATAGGCCACTTA
18346 C
1 C
18347 TTTGTTATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (19 bp):
CCTATAAATAGGCCACTTA
Found at i:24419 original size:13 final size:13
Alignment explanation
Indices: 24401--24431 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
24391 TACTTCTATC
24401 AAGATAATAAGAT
1 AAGATAATAAGAT
*
24414 AAGATAGTAAGAT
1 AAGATAATAAGAT
24427 AAGAT
1 AAGAT
24432 TACGGAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (13 bp):
AAGATAATAAGAT
Found at i:25817 original size:113 final size:113
Alignment explanation
Indices: 25621--25876 Score: 343
Period size: 113 Copynumber: 2.2 Consensus size: 113
25611 TTGAAACTAA
* * * *
25621 TTCAAGACTTGTTATAGTCGACTGAAACATCAATTAGTCCATTTTAGAAAAATGGCTGAATTGAC
1 TTCAGGACTTGTTATAGTCGACTGAAACATCAATTAGTCC--TCTACAAAAATGGCAGAATTGAC
*
25686 AACATCTCGGATGCAGTTTCAACACCAAGGATAGTCGACTGAAAATGATT
64 AACATCTCGGATGCAGTTTCAACACCAAGGATAATCGACTGAAAATGATT
* ** * *
25736 TTCAGGACTTGTTATAATCGACTGAAATTTTAATTAGTCC-CTACAAAAAGTGGCAGAATTGACG
1 TTCAGGACTTGTTATAGTCGACTGAAACATCAATTAGTCCTCTACAAAAA-TGGCAGAATTGACA
* * *
25800 ACATCTCGGTTGTAGTTTCAACGCCAAGGATAATCGACTGAAAATGATT
65 ACATCTCGGATGCAGTTTCAACACCAAGGATAATCGACTGAAAATGATT
*
25849 TTTAGGACTTGCTTATAGTCGACTGAAA
1 TTCAGGACTTG-TTATAGTCGACTGAAA
25877 ATTCTTGTAT
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
112 7 0.06
113 67 0.54
114 15 0.12
115 35 0.28
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (113 bp):
TTCAGGACTTGTTATAGTCGACTGAAACATCAATTAGTCCTCTACAAAAATGGCAGAATTGACAA
CATCTCGGATGCAGTTTCAACACCAAGGATAATCGACTGAAAATGATT
Found at i:29136 original size:13 final size:13
Alignment explanation
Indices: 29118--29142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29108 TCAATAGATT
29118 AGAAAATTTTTAA
1 AGAAAATTTTTAA
29131 AGAAAATTTTTA
1 AGAAAATTTTTA
29143 TGGGATGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
AGAAAATTTTTAA
Found at i:29158 original size:16 final size:16
Alignment explanation
Indices: 29134--29176 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
29124 TTTTTAAAGA
*
29134 AAATTTTTATGGGATG
1 AAATGTTTATGGGATG
29150 AAATGTTTATGGGATG
1 AAATGTTTATGGGATG
29166 AAATGTTTATG
1 AAATGTTTATG
29177 AAATTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.42
Consensus pattern (16 bp):
AAATGTTTATGGGATG
Done.