Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021509.1 Corchorus olitorius cultivar O-4 contig21542, 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: 85730
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:894 original size:124 final size:128
Alignment explanation
Indices: 693--948 Score: 355
Period size: 124 Copynumber: 2.0 Consensus size: 128
683 CATTATTTAA
* *
693 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATGAT
758 TTTTACCATTTTA-C-T-A-T-TTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTA-CATTTTACCTTCACTATTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
817 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-AC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATGA-
* * *
881 CTATTTTA-TTTTTACCATTTCACTATTTTATTTAAAAAACTTATATATATTAGAATTTTTTAAA
65 -T-TTTTACATTTTACC--TTCACTATTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAA
945 TAT
126 TAT
948 A
1 A
949 TTTCTTAAAT
Statistics
Matches: 116, Mismatches: 6, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
123 1 0.01
124 64 0.55
125 2 0.02
126 5 0.04
128 1 0.01
129 1 0.01
130 1 0.01
131 41 0.35
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (128 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATGAT
TTTTACATTTTACCTTCACTATTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:970 original size:14 final size:13
Alignment explanation
Indices: 934--972 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
924 TATATATTAG
934 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
947 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
961 AATTTTTTAAAT
1 AATTTTTTAAAT
973 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:8013 original size:15 final size:15
Alignment explanation
Indices: 7995--8047 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
7985 TTTTTTTATT
7995 ATTATTAAATTTTTA
1 ATTATTAAATTTTTA
*
8010 ATTATTAACTATTATTA
1 ATTATTAA--ATTTTTA
8027 A-T-TTAAATTTTTA
1 ATTATTAAATTTTTA
8040 ATTATTAA
1 ATTATTAA
8048 TTATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 7 0.22
14 1 0.03
15 16 0.50
16 1 0.03
17 7 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATTAAATTTTTA
Found at i:8013 original size:30 final size:30
Alignment explanation
Indices: 7991--8047 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
7981 TTATTTTTTT
7991 TATTATT-A-TTAAATTTTTAATTATTAAC
1 TATTATTAATTTAAATTTTTAATTATTAAC
8019 TATTATTAATTTAAATTTTTAATTATTAA
1 TATTATTAATTTAAATTTTTAATTATTAA
8048 TTATAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 7 0.26
29 1 0.04
30 19 0.70
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
TATTATTAATTTAAATTTTTAATTATTAAC
Found at i:8017 original size:7 final size:7
Alignment explanation
Indices: 7990--8058 Score: 52
Period size: 7 Copynumber: 9.6 Consensus size: 7
7980 ATTATTTTTT
7990 TTATT-A
1 TTATTAA
7996 TTATTAAA
1 TTATT-AA
*
8004 TTTTTAA
1 TTATTAA
8011 TTATTAACTA
1 TTATT-A--A
8021 TTATTAA
1 TTATTAA
*
8028 TT-TAAA
1 TTATTAA
*
8034 TTTTTAA
1 TTATTAA
8041 TTATTAA
1 TTATTAA
*
8048 TTATAAA
1 TTATTAA
8055 TTAT
1 TTAT
8059 ATTTTTAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
6 10 0.20
7 28 0.55
8 6 0.12
9 1 0.02
10 6 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (7 bp):
TTATTAA
Found at i:8133 original size:21 final size:21
Alignment explanation
Indices: 8093--8135 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8083 CAAAATTATC
* **
8093 AAAATGGGGCGGTATTTAGCA
1 AAAAGGGGGCGGTAAATAGCA
8114 AAAAGGGGGCGGTAAATAGCA
1 AAAAGGGGGCGGTAAATAGCA
8135 A
1 A
8136 CTCCCCGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.35, T:0.16
Consensus pattern (21 bp):
AAAAGGGGGCGGTAAATAGCA
Found at i:16265 original size:21 final size:21
Alignment explanation
Indices: 16223--16272 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
16213 GCTTATGGGA
* *
16223 TCAATTGATCGAATAGGCGAG
1 TCAAATGATCGAATAAGCGAG
16244 TCAAATGATCGAATTAAG-GAG
1 TCAAATGATCGAA-TAAGCGAG
*
16265 TCTAATGA
1 TCAAATGA
16273 CTTACTTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (21 bp):
TCAAATGATCGAATAAGCGAG
Found at i:43548 original size:2 final size:2
Alignment explanation
Indices: 43541--43571 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43531 CCACAAACAG
43541 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
43572 AAAGTAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:49231 original size:21 final size:20
Alignment explanation
Indices: 49191--49232 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
49181 TTGTAATCTA
**
49191 TGATTATTGATTAATGAAAG
1 TGATTATTGATTAAAAAAAG
49211 TGATTATTTGATTAAAAAAAG
1 TGATTA-TTGATTAAAAAAAG
49232 T
1 T
49233 TTTATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (20 bp):
TGATTATTGATTAAAAAAAG
Found at i:50529 original size:34 final size:34
Alignment explanation
Indices: 50490--50558 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
50480 TTGAGATAAC
50490 AATGGAGAATATATTGTTATATATATATATATAT
1 AATGGAGAATATATTGTTATATATATATATATAT
50524 AATGGAGAATATATTGTTATATATATATATATAT
1 AATGGAGAATATATTGTTATATATATATATATAT
50558 A
1 A
50559 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (34 bp):
AATGGAGAATATATTGTTATATATATATATATAT
Found at i:50587 original size:2 final size:2
Alignment explanation
Indices: 50507--50568 Score: 60
Period size: 2 Copynumber: 33.0 Consensus size: 2
50497 AATATATTGT
* * * *
50507 TA TA TA TA TA TA TA TA TA -A TG GA GA -A TA TA T- TG T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50545 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
50569 AAGAAAATGG
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
1 4 0.08
2 49 0.92
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:53232 original size:10 final size:10
Alignment explanation
Indices: 53217--53246 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
53207 ACCCTTGTAG
53217 AAAAAGAAAA
1 AAAAAGAAAA
53227 AAAAAG-AAA
1 AAAAAGAAAA
53236 AAAAAGAAAA
1 AAAAAGAAAA
53246 A
1 A
53247 GAACAGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:53236 original size:9 final size:9
Alignment explanation
Indices: 53217--53246 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
53207 ACCCTTGTAG
53217 AAAAAGAAAA
1 AAAAAG-AAA
53227 AAAAAGAAA
1 AAAAAGAAA
53236 AAAAAGAAA
1 AAAAAGAAA
53245 AA
1 AA
53247 GAACAGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.70
10 6 0.30
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:60088 original size:67 final size:67
Alignment explanation
Indices: 59979--60473 Score: 467
Period size: 67 Copynumber: 7.4 Consensus size: 67
59969 TAATTTTCTC
* * * *
59979 TTTCCAGAAATACCCTTTCGTTCAAAGGGTCAGTTTCATCTTTTTGCATTTAAGTGTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCTTTTTGCATTTAAGTTTAGTATTTT
60044 CA
66 CA
* * * * * *
60046 TTTCCAAAAATACCCTTTTGGTCAAAGGGTCAATCTT-GTCTTTTCGTATTCAAGTTTTGTATTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGT-TTCGTCTTTTTGCATTTAAGTTTAGTATTT
*
60110 TAA
65 TCA
* * *
60113 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCATTCAAGTTTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCTTTTTGCATTTAAGTTTAGTATTTT
60178 CA
66 CA
* * * *
60180 TTTCCAGAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTGCATTTAGGTTTAGT-TTTA
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCTTTTTGCATTTAAGTTTAGTATTTT
60244 C-
66 CA
* * * * *
60245 TTTTCAAAAATACCC-TTCTGGTCGAAGGGTCAGTTTCATCAGATTGTTGCATTTAAGTCTAGT-
1 TTTCCAAAAATACCCTTTC-GGTCAAAGGGTCAGTTTCGTC---TTTTTGCATTTAAGTTTAGTA
*
60308 CTTTC-
62 TTTTCA
* * * * *
60313 TTTCCAAAGAATACCCTTTCGGTCAAAGGGTCA-ATTCTGTCATTCTTG-AGTTTGAGCTTA--C
1 TTTCCAAA-AATACCCTTTCGGTCAAAGGGTCAGTTTC-GTC-TTTTTGCA-TTTAAGTTTAGTA
*
60374 TTTTGA
62 TTTTCA
* * * * * *
60380 TTTCCAAAAATACCCTTTCGGTGAAATGGTCAGTTTCATCATTTTCGCATTTCAGTTTA-T-TCT
1 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTC-TTTTTGCATTTAAGTTTAGTATTT
*
60443 AC-
65 TCA
*
60445 TTTCCAAAAATGCCCTTTCGGTCAAAGGG
1 TTTCCAAAAATACCCTTTCGGTCAAAGGG
60474 CGAGCTTTGT
Statistics
Matches: 356, Mismatches: 57, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
64 3 0.01
65 59 0.17
66 49 0.14
67 189 0.53
68 32 0.09
69 21 0.06
70 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.41
Consensus pattern (67 bp):
TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTTTCGTCTTTTTGCATTTAAGTTTAGTATTTT
CA
Found at i:68372 original size:21 final size:21
Alignment explanation
Indices: 68348--68395 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
68338 GTAAGCTTGA
68348 CCGGGCAGGTGGCACGGATGG
1 CCGGGCAGGTGGCACGGATGG
* *
68369 CCGGGCAGGTGGCTCGGGTGG
1 CCGGGCAGGTGGCACGGATGG
68390 CCGGGC
1 CCGGGC
68396 CATGGCCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.08, C:0.27, G:0.54, T:0.10
Consensus pattern (21 bp):
CCGGGCAGGTGGCACGGATGG
Done.