Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017691.1 Corchorus olitorius cultivar O-4 contig17724, 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: 100485
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:934 original size:22 final size:22
Alignment explanation
Indices: 909--955 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
899 TTTTTAGTTG
*
909 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
931 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
953 AGT
1 AGT
956 TATAAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:945 original size:91 final size:93
Alignment explanation
Indices: 834--1016 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 93
824 ACTTTTTAAT
* * *
834 TAAATTAGTAATATCGTAAAAATAAAATA-TGTATAAGGATATTAGATTTAATT-AA-AAAAATA
1 TAAAATAGTAAAATCGTAAAAATAAAATAGT-TATAAGAATATTAGATTTAATTAAATAAAAATA
*
896 GAGTTTTTAGTTGAGTAAAACTATAAAAG
65 GAGTTTTTAGTTGACTAAAACTATAAAAG
*
925 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAG
990 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAACTATAAAA
1017 ATTTACACAA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
91 47 0.56
92 3 0.04
93 34 0.40
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:1902 original size:5 final size:6
Alignment explanation
Indices: 1859--1901 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
1849 CATCTCAAGC
1859 AAAGAAA AAAGAA AAAGAA AAAGAA AAAG-A AAAG-A AAAGAA AA
1 AAAG-AA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
1902 GTCTCTACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 10 0.29
6 21 0.60
7 4 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:7950 original size:245 final size:245
Alignment explanation
Indices: 7538--8006 Score: 796
Period size: 245 Copynumber: 1.9 Consensus size: 245
7528 GATTGGTTGA
* *
7538 TCTTTTTCTTTTTCTTTTTTTTTTTTATGGTTTCTTGGATAAATGTTCAAATTGGTCCCTAACGT
1 TCTTTTTCTTTTTCTTTTTTTGTTTCATGGTTTCTTGGATAAATGTTCAAATTGGTCCCTAACGT
** *
7603 TTACAAAAATGCTCAAATAAGGACCTAGTCATTTAATTTCGTTAATTAAGTCCCTGACTTCAAAT
66 TTACAAAAATGCTCAAATAAGGACCTAACCATTTAATTTCGATAATTAAGTCCCTGACTTCAAAT
* *
7668 TGATATCCTAATAAACCCCAAAAATGTTAGGGACTGATTTGAATCGATTTTGCAATATTAGAGAC
131 TGATATCCTAATAAACCCCAAAAATGTTAGGGACTGATTTAAACCGATTTTGCAATATTAGAGAC
*
7733 CGATTGAGCTAATTTTGCAACGTTAGGAACTTTTGATTGGTTGGTCCTTT
196 CAATTGAGCTAATTTTGCAACGTTAGGAACTTTTGATTGGTTGGTCCTTT
7783 TCTTTTTCTTTTTTCTTTTTTTGTTTCATGGTTTCTTGGAT-AATGTTCAAATTGGTCCCTAACG
1 TCTTTTTC-TTTTTCTTTTTTTGTTTCATGGTTTCTTGGATAAATGTTCAAATTGGTCCCTAACG
** * * *
7847 TTTGTAAAAATGTTCAAATAAGGACCTAACCATTTAATTTGGATAATTAAGTCCCTGGCTTCAAA
65 TTTACAAAAATGCTCAAATAAGGACCTAACCATTTAATTTCGATAATTAAGTCCCTGACTTCAAA
*
7912 TTGATATCCTAATAAACCCCAAAAATGTTAGGGACTGATTTAAACCGATTTTGCAATATTAGGGA
130 TTGATATCCTAATAAACCCCAAAAATGTTAGGGACTGATTTAAACCGATTTTGCAATATTAGAGA
7977 CCAATTGAGCTAATTTTGCAACGTTAGGAA
195 CCAATTGAGCTAATTTTGCAACGTTAGGAA
8007 TTTAATTAAC
Statistics
Matches: 209, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
245 179 0.86
246 30 0.14
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (245 bp):
TCTTTTTCTTTTTCTTTTTTTGTTTCATGGTTTCTTGGATAAATGTTCAAATTGGTCCCTAACGT
TTACAAAAATGCTCAAATAAGGACCTAACCATTTAATTTCGATAATTAAGTCCCTGACTTCAAAT
TGATATCCTAATAAACCCCAAAAATGTTAGGGACTGATTTAAACCGATTTTGCAATATTAGAGAC
CAATTGAGCTAATTTTGCAACGTTAGGAACTTTTGATTGGTTGGTCCTTT
Found at i:9438 original size:22 final size:22
Alignment explanation
Indices: 9410--9453 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9400 TCTTGTAAAT
*
9410 TGTATGATACAATCATAAGCTA
1 TGTATGACACAATCATAAGCTA
9432 TGTATGACACAATCATAAGCTA
1 TGTATGACACAATCATAAGCTA
9454 AAGCTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (22 bp):
TGTATGACACAATCATAAGCTA
Found at i:15679 original size:2 final size:2
Alignment explanation
Indices: 15672--15697 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15662 CTATAAAAGA
15672 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
15698 TATTTAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19113 original size:22 final size:21
Alignment explanation
Indices: 19065--19121 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
19055 ATATATTCAC
*
19065 ATTATTAGTAAATTAGTAAAT
1 ATTATTAGTAAATTAATAAAT
* *
19086 ATTTATTAGTATATATAATTAAT
1 A-TTATTAGTAAAT-TAATAAAT
*
19109 ATTATTAATAAAT
1 ATTATTAGTAAAT
19122 AAATTAGTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.03
22 21 0.72
23 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTATTAGTAAATTAATAAAT
Found at i:20410 original size:13 final size:13
Alignment explanation
Indices: 20392--20416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20382 TATTCGTAGG
20392 AAGATATGCAACA
1 AAGATATGCAACA
20405 AAGATATGCAAC
1 AAGATATGCAAC
20417 CCTAATATAA
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:0.16, G:0.16, T:0.16
Consensus pattern (13 bp):
AAGATATGCAACA
Found at i:29395 original size:21 final size:21
Alignment explanation
Indices: 29371--29418 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
29361 TGAGATTGTG
29371 AGATTAAATACTGTACAGATC
1 AGATTAAATACTGTACAGATC
** *
29392 AGATTAGGTACTGTACAGATG
1 AGATTAAATACTGTACAGATC
29413 AGATTA
1 AGATTA
29419 TAATCAGCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (21 bp):
AGATTAAATACTGTACAGATC
Found at i:30967 original size:11 final size:11
Alignment explanation
Indices: 30951--30990 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
30941 CGGACTAACA
30951 AATTGTATAAG
1 AATTGTATAAG
* *
30962 AATTGTCTAACA
1 AATTGTATAA-G
30974 AATTGTATAAG
1 AATTGTATAAG
30985 AATTGT
1 AATTGT
30991 CTGTGCTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (11 bp):
AATTGTATAAG
Found at i:30975 original size:23 final size:23
Alignment explanation
Indices: 30945--30992 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
30935 ATTTTTCGGA
30945 CTAACAAATTGTATAAGAATTGT
1 CTAACAAATTGTATAAGAATTGT
30968 CTAACAAATTGTATAAGAATTGT
1 CTAACAAATTGTATAAGAATTGT
30991 CT
1 CT
30993 GTGCTCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (23 bp):
CTAACAAATTGTATAAGAATTGT
Found at i:31356 original size:22 final size:23
Alignment explanation
Indices: 31300--31367 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
31290 TTTAATAATT
31300 AAATATATATTATTTATTTATTTTA
1 AAATATAT-TTATTTATTTA-TTTA
* *
31325 AACT-CA-TTATTTA-TTATTTA
1 AAATATATTTATTTATTTATTTA
31345 AAATATATTTA-TTATTTATTTA
1 AAATATATTTATTTATTTATTTA
31367 A
1 A
31368 TAGTATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
20 7 0.19
21 7 0.19
22 18 0.50
24 1 0.03
25 3 0.08
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATATATTTATTTATTTATTTA
Found at i:32947 original size:15 final size:16
Alignment explanation
Indices: 32927--32956 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
32917 ATTTCAACCC
32927 CTTTTCTT-TTTTGTT
1 CTTTTCTTGTTTTGTT
32942 CTTTTCTTGTTTTGT
1 CTTTTCTTGTTTTGT
32957 GGCTAAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (16 bp):
CTTTTCTTGTTTTGTT
Found at i:35677 original size:1 final size:1
Alignment explanation
Indices: 35671--35695 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
35661 TAAATTCCAG
35671 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
35696 GTTTCTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41944 original size:19 final size:19
Alignment explanation
Indices: 41920--41975 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
41910 TTTGGTCCCA
*
41920 AAACGGTAGTGAAACGGTC
1 AAACGGTGGTGAAACGGTC
41939 AAACGGTGGTGAAACGGTC
1 AAACGGTGGTGAAACGGTC
41958 AAACGGTGGTGAAACGGT
1 AAACGGTGGTGAAACGGT
41976 TACAGATAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.34, C:0.14, G:0.36, T:0.16
Consensus pattern (19 bp):
AAACGGTGGTGAAACGGTC
Found at i:47084 original size:5 final size:5
Alignment explanation
Indices: 47069--47106 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
47059 TAAGCAAGTG
47069 TTTGTT TTTGT TTTGT TTTGT TTTGT TTT-T TTT-T TTTG
1 TTTG-T TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTG
47107 ACACTTCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 8 0.26
5 19 0.61
6 4 0.13
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
TTTGT
Found at i:57646 original size:28 final size:28
Alignment explanation
Indices: 57606--57689 Score: 168
Period size: 28 Copynumber: 3.0 Consensus size: 28
57596 GTTGCTAACA
57606 GTTTGCTATAGCTTTTGTAATTGGGTAT
1 GTTTGCTATAGCTTTTGTAATTGGGTAT
57634 GTTTGCTATAGCTTTTGTAATTGGGTAT
1 GTTTGCTATAGCTTTTGTAATTGGGTAT
57662 GTTTGCTATAGCTTTTGTAATTGGGTAT
1 GTTTGCTATAGCTTTTGTAATTGGGTAT
57690 ATTATTGTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.18, C:0.07, G:0.25, T:0.50
Consensus pattern (28 bp):
GTTTGCTATAGCTTTTGTAATTGGGTAT
Found at i:58247 original size:6 final size:6
Alignment explanation
Indices: 58236--58260 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58226 ATTATTATAT
58236 ATTTTC ATTTTC ATTTTC ATTTTC A
1 ATTTTC ATTTTC ATTTTC ATTTTC A
58261 AGCCTCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTTC
Found at i:61910 original size:12 final size:12
Alignment explanation
Indices: 61886--61918 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
61876 TAGAGGTGAA
61886 AAAAAG-AAA-G
1 AAAAAGAAAAGG
61896 AAAAAGAAAAGG
1 AAAAAGAAAAGG
61908 AAAAAGAAAAG
1 AAAAAGAAAAG
61919 AGAGGGATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.29
11 3 0.14
12 12 0.57
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGG
Found at i:66075 original size:21 final size:19
Alignment explanation
Indices: 66048--66106 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
66038 TGTTGCTCTA
*
66048 ATAATCTCATCTATACAAT
1 ATAATCTCATCTGTACAAT
* *
66067 ATCTAATCTAATCTGTACAGT
1 A--TAATCTCATCTGTACAAT
*
66088 ATAATCTCATATGTACAAT
1 ATAATCTCATCTGTACAAT
66107 TGCTAAACAG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAAT
Found at i:66214 original size:73 final size:73
Alignment explanation
Indices: 66084--66231 Score: 224
Period size: 73 Copynumber: 2.0 Consensus size: 73
66074 CTAATCTGTA
* *
66084 CAGTATAATCTCATATGTACAATTGCTAAACAGTGTCAATCGTACTGCTACCACACCGTTCTAGT
1 CAGTATAATCTCATATGTACAATTGCTAAACAGTGTCAATCGTACTGCTACCACACCGCTCTAAT
*
66149 AAATGCAG
66 AAACGCAG
* * * * *
66157 CAGTGTAATCTCATCTGTACAGTTGCTAAACAGTGTCAATCGTACTGTTACCGCACCGCTCTAAT
1 CAGTATAATCTCATATGTACAATTGCTAAACAGTGTCAATCGTACTGCTACCACACCGCTCTAAT
66222 AAACGCAG
66 AAACGCAG
66230 CA
1 CA
66232 TAAGAAGATG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (73 bp):
CAGTATAATCTCATATGTACAATTGCTAAACAGTGTCAATCGTACTGCTACCACACCGCTCTAAT
AAACGCAG
Found at i:92832 original size:3 final size:3
Alignment explanation
Indices: 92824--92864 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
92814 ACCTTTTGCA
92824 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
92865 TTTTGATGTA
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:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:97856 original size:35 final size:35
Alignment explanation
Indices: 97810--97881 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
97800 CAGAATTGAA
97810 GAGCAATGAATCTGAGGCCATTACGATTCTTGGTC
1 GAGCAATGAATCTGAGGCCATTACGATTCTTGGTC
97845 GAGCAATGAATCTGAGGCCATTACGATTCTTGGTC
1 GAGCAATGAATCTGAGGCCATTACGATTCTTGGTC
97880 GA
1 GA
97882 TGGTTCTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (35 bp):
GAGCAATGAATCTGAGGCCATTACGATTCTTGGTC
Found at i:99085 original size:15 final size:16
Alignment explanation
Indices: 99062--99109 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
99052 CATCTTCTTA
*
99062 TTATAATTATTA-AAC
1 TTATTATTATTATAAC
99077 TTATTATTATTATAAC
1 TTATTATTATTATAAC
99093 AATTATTATTAGTTATA
1 --TTATTATTA-TTATA
99110 TGATCACACG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
18 9 0.32
19 5 0.18
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATTATTATTATAAC
Found at i:99098 original size:18 final size:17
Alignment explanation
Indices: 99059--99109 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
99049 AAACATCTTC
* *
99059 TTATTATAATTATTAAAC
1 TTATTATTATTA-TAAAA
99077 TTATTATTATTATAACAA
1 TTATTATTATTATAA-AA
99095 TTATTATTAGTTATA
1 TTATTATTA-TTATA
99110 TGATCACACG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 21 0.72
19 5 0.17
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTATTATTATTATAAAA
Found at i:100334 original size:22 final size:22
Alignment explanation
Indices: 100309--100350 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
100299 AAGATAATAA
* *
100309 TATAGTTTTTAAAATAATCACT
1 TATACTTTTTAAAACAATCACT
*
100331 TATACTTTTTAGAACAATCA
1 TATACTTTTTAAAACAATCA
100351 TTGAAGCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (22 bp):
TATACTTTTTAAAACAATCACT
Done.