Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013335.1 Corchorus olitorius cultivar O-4 contig13368, 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: 27847
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:863 original size:213 final size:214
Alignment explanation
Indices: 500--885 Score: 542
Period size: 213 Copynumber: 1.8 Consensus size: 214
490 TTTTTGCTAG
* * * *
500 AAACGCGTTTCGAGGCCCCGACTTAGTTTCGAATGATTTTTGACGCTAAGACTCCTTGAGATATC
1 AAACGCGTTCCGAGGCCCCGACTCAGTTTCGAATGATTTTTGACGCCAAGACTCCTTGAAATATC
* * *
565 CATATTCATCTAATCAAATCTCAATCACATTACATTTAAGGATTTGTTTTTAGGAGCATCTGAAT
66 CATATTCATCTAATCAAATCTCAAGCACATTACATTTAAGGATTTGTTTTTACGAGCATCTAAAT
*
630 CTTGTTTCGATTTAATTAGAAATTAATTAAAAAAAATATGAAAAACGATATTGGGTCATTTTCAC
131 CTTATTTCGATTTAATTAGAAATTAATTAAAAAAAATATGAAAAACGATATTGGGTCATTTTCAC
695 CATTATGGTTTTTGACCAA
196 CATTATGGTTTTTGACCAA
* * * * *
714 AAACGCGTTCCGAGGCCCCGGCTCAG-TTCTGCATTATTTTTGGCGCCGAGACTCCTTGAAATAT
1 AAACGCGTTCCGAGGCCCCGACTCAGTTTC-GAATGATTTTTGACGCCAAGACTCCTTGAAATAT
* * * * * ** * *
778 CTATA-TCATGTAATCAAATGTCAGGCATATTGGATTTAAGGATTTGTTTTTTCGAGCATTTAAA
65 CCATATTCATCTAATCAAATCTCAAGCACATTACATTTAAGGATTTGTTTTTACGAGCATCTAAA
*
842 TCTTATTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAA
130 TCTTATTTCGATTTAATTAGAAATTAATTAAAAAAAATATGAAA
886 CAAAAATTTG
Statistics
Matches: 148, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
213 93 0.63
214 55 0.37
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (214 bp):
AAACGCGTTCCGAGGCCCCGACTCAGTTTCGAATGATTTTTGACGCCAAGACTCCTTGAAATATC
CATATTCATCTAATCAAATCTCAAGCACATTACATTTAAGGATTTGTTTTTACGAGCATCTAAAT
CTTATTTCGATTTAATTAGAAATTAATTAAAAAAAATATGAAAAACGATATTGGGTCATTTTCAC
CATTATGGTTTTTGACCAA
Found at i:2070 original size:35 final size:34
Alignment explanation
Indices: 2024--2093 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 34
2014 TAACAAGAAA
*
2024 ATGATGAAAAAGAAACTCAACGCTTGAATTCGATC
1 ATGATGAAAAAGAAACTCAAAGCTTGAATTC-ATC
2059 ATGATGAAAAAGAAACTCAAAGCTTGAATTCATC
1 ATGATGAAAAAGAAACTCAAAGCTTGAATTCATC
2093 A
1 A
2094 AATGAAGTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 4 0.12
35 30 0.88
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.23
Consensus pattern (34 bp):
ATGATGAAAAAGAAACTCAAAGCTTGAATTCATC
Found at i:2950 original size:49 final size:49
Alignment explanation
Indices: 2877--2975 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
2867 ATTCCATTTT
*
2877 AACCTAACTTGAACCATAACAATATCATGAGAGCGTGTATTTTACGGAA
1 AACCTAACTTGAACCATAACAATATCATGAGAGCATGTATTTTACGGAA
* * *
2926 AACCTAACTTGAGCCATAATAATATCATGAGAGCATTTATTTTACGGAA
1 AACCTAACTTGAACCATAACAATATCATGAGAGCATGTATTTTACGGAA
2975 A
1 A
2976 TGCAAGACAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (49 bp):
AACCTAACTTGAACCATAACAATATCATGAGAGCATGTATTTTACGGAA
Found at i:3129 original size:30 final size:30
Alignment explanation
Indices: 3095--3152 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
3085 ATGTGGCTTG
3095 AAACAACTTAAACCTTC-TATGATTTTATTT
1 AAACAACTTAAACCTTCAT-TGATTTTATTT
3125 AAACAACTTAAACCTTCATTGATTTTAT
1 AAACAACTTAAACCTTCATTGATTTTAT
3153 AACGAATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.41
Consensus pattern (30 bp):
AAACAACTTAAACCTTCATTGATTTTATTT
Found at i:9566 original size:30 final size:30
Alignment explanation
Indices: 9532--9692 Score: 189
Period size: 30 Copynumber: 5.4 Consensus size: 30
9522 TGAACTTGAG
* *
9532 GTTAATGAAGAAGG-GTCTGAGAGAGCGGAA
1 GTTAATGAA-ATGGAGTCTGAGAGAGTGGAA
* *
9562 GTTAATGAAATTGAGTCTGAGAGAGTGGAG
1 GTTAATGAAATGGAGTCTGAGAGAGTGGAA
* *
9592 GTCAATGAGATGGAGTCTGAGAGAGTGGAA
1 GTTAATGAAATGGAGTCTGAGAGAGTGGAA
** *
9622 ACTAATGAAATGGAGTCTGAGAGAGTGGAG
1 GTTAATGAAATGGAGTCTGAGAGAGTGGAA
* * *
9652 GTTAATGTAATGGAGTCTGATAGAGTGGAG
1 GTTAATGAAATGGAGTCTGAGAGAGTGGAA
*
9682 GGTAATGAAAT
1 GTTAATGAAAT
9693 TCAGTCTCTG
Statistics
Matches: 111, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 2 0.02
30 109 0.98
ACGTcount: A:0.35, C:0.05, G:0.37, T:0.23
Consensus pattern (30 bp):
GTTAATGAAATGGAGTCTGAGAGAGTGGAA
Found at i:9599 original size:60 final size:60
Alignment explanation
Indices: 9529--9717 Score: 211
Period size: 60 Copynumber: 3.1 Consensus size: 60
9519 AGCTGAACTT
* * * *
9529 GAGGTTAATGAAGAAGG-GTCTGAGAGAGCGGAAGTTAATGAAATTGAGTCTGAGAGAGTG
1 GAGGTCAATG-AGATGGAGTCTGAGAGAGTGGAAGCTAATGAAATTGAGTCTGAGAGAGTG
* *
9589 GAGGTCAATGAGATGGAGTCTGAGAGAGTGGAAACTAATGAAATGGAGTCTGAGAGAGTG
1 GAGGTCAATGAGATGGAGTCTGAGAGAGTGGAAGCTAATGAAATTGAGTCTGAGAGAGTG
* * * * * ** *
9649 GAGGTTAATGTA-ATGGAGTCTGATAGAGTGGAGGGTAATGAAATTCAGTCTCTGAGAGTT
1 GAGGTCAATG-AGATGGAGTCTGAGAGAGTGGAAGCTAATGAAATTGAGTCTGAGAGAGTG
*
9709 GAGCTCAAT
1 GAGGTCAAT
9718 AGGGAGGCTA
Statistics
Matches: 109, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
59 5 0.05
60 103 0.94
61 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.36, T:0.24
Consensus pattern (60 bp):
GAGGTCAATGAGATGGAGTCTGAGAGAGTGGAAGCTAATGAAATTGAGTCTGAGAGAGTG
Found at i:9620 original size:15 final size:15
Alignment explanation
Indices: 9574--9651 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
9564 TAATGAAATT
9574 GAGTCTGAGAGAGTG
1 GAGTCTGAGAGAGTG
*
9589 GAGGTC-AATGAGA-TG
1 GA-GTCTGA-GAGAGTG
9604 GAGTCTGAGAGAGTG
1 GAGTCTGAGAGAGTG
** * *
9619 GAAACTAATGA-AATG
1 GAGTCTGA-GAGAGTG
9634 GAGTCTGAGAGAGTG
1 GAGTCTGAGAGAGTG
9649 GAG
1 GAG
9652 GTTAATGTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.33, C:0.06, G:0.41, T:0.19
Consensus pattern (15 bp):
GAGTCTGAGAGAGTG
Found at i:9773 original size:96 final size:95
Alignment explanation
Indices: 9646--10023 Score: 299
Period size: 96 Copynumber: 4.0 Consensus size: 95
9636 GTCTGAGAGA
* * * * *
9646 GTGGAGGTTAATGTAATGGAGTCTGATAGAGTGGAGGGTAATGAAATTCAGTCTCTGAGAGTTGA
1 GTGGAAGTTAATGAAATTGAGTCTGAGAGAGTGGA-GGTAATGAAATTCAGTCTCCGAGAGTTGA
* *
9711 GCTCAATAGGGAGGCTAATTTGGATTTAGAT
65 GCTCAATAGGGAGGCTAATATGGATTCAGAT
* * ** * *
9742 GTGGAATTTAATGAAATTGAGTCTGAGAGAGTGGCAGTTAATGTGATTGAGTCTCCGAGATTTGA
1 GTGGAAGTTAATGAAATTGAGTCTGAGAGAGTGG-AGGTAATGAAATTCAGTCTCCGAGAGTTGA
*
9807 GCTCAATAGGGAGGCTGATATGGATTCAGAT
65 GCTCAATAGGGAGGCTAATATGGATTCAGAT
* * * ** *
9838 GTGGAAGTTAATGAAATTGAGTGTGAGAGGGTGGAAGTCAATGAAAAACAG--T-C-AGAG-AGA
1 GTGGAAGTTAATGAAATTGAGTCTGAGAGAGTGGAGGT-AATGAAATTCAGTCTCCGAGAGTTGA
** * * * * *
9898 G-TGGA-AGTTGATG--AA-ATTGAGTCTGAGAGA
65 GCTCAATAG-GGAGGCTAATATGGA-T-TCAGA-T
* * * * * ** *
9928 GTGGAGGTTAATGAAGTTGAGTCTGGGAAAGTGGAGGTTAATGTAATGGAGTCTCTGAGAGTTGA
1 GTGGAAGTTAATGAAATTGAGTCTGAGAGAGTGGAGG-TAATGAAATTCAGTCTCCGAGAGTTGA
9993 GCTCAATAGGGAGGCTAATATGGATTCAGAT
65 GCTCAATAGGGAGGCTAATATGGATTCAGAT
10024 TTTTGGAGTG
Statistics
Matches: 211, Mismatches: 54, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
87 4 0.02
88 2 0.01
89 6 0.03
90 43 0.20
91 4 0.02
92 4 0.02
93 1 0.00
94 5 0.02
95 5 0.02
96 123 0.58
97 7 0.03
98 3 0.01
99 4 0.02
ACGTcount: A:0.31, C:0.07, G:0.34, T:0.28
Consensus pattern (95 bp):
GTGGAAGTTAATGAAATTGAGTCTGAGAGAGTGGAGGTAATGAAATTCAGTCTCCGAGAGTTGAG
CTCAATAGGGAGGCTAATATGGATTCAGAT
Found at i:9874 original size:30 final size:30
Alignment explanation
Indices: 9838--9981 Score: 153
Period size: 30 Copynumber: 4.8 Consensus size: 30
9828 GGATTCAGAT
* *
9838 GTGGAAGTTAATGAAATTGAGTGTGAGAGG
1 GTGGAAGTTAATGAAATTGAGTCTGAGAGA
* *** *
9868 GTGGAAGTCAATGAAAAACAGTCAGAGAGA
1 GTGGAAGTTAATGAAATTGAGTCTGAGAGA
*
9898 GTGGAAGTTGATGAAATTGAGTCTGAGAGA
1 GTGGAAGTTAATGAAATTGAGTCTGAGAGA
* * * *
9928 GTGGAGGTTAATGAAGTTGAGTCTGGGAAA
1 GTGGAAGTTAATGAAATTGAGTCTGAGAGA
* * *
9958 GTGGAGGTTAATGTAATGGAGTCT
1 GTGGAAGTTAATGAAATTGAGTCT
9982 CTGAGAGTTG
Statistics
Matches: 93, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 93 1.00
ACGTcount: A:0.34, C:0.04, G:0.37, T:0.25
Consensus pattern (30 bp):
GTGGAAGTTAATGAAATTGAGTCTGAGAGA
Found at i:17580 original size:33 final size:33
Alignment explanation
Indices: 17540--17609 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
17530 AAAATAAAAA
17540 TCATTCTTTTACAATCTAAATTTACATCCTTAT
1 TCATTCTTTTACAATCTAAATTTACATCCTTAT
*
17573 TCATTCTTTTACAATTTAAATTTACATCCTTAT
1 TCATTCTTTTACAATCTAAATTTACATCCTTAT
17606 TCAT
1 TCAT
17610 AAAAATTAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (33 bp):
TCATTCTTTTACAATCTAAATTTACATCCTTAT
Found at i:21247 original size:42 final size:42
Alignment explanation
Indices: 21185--21265 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
21175 GCTAAGTCTT
*
21185 GAAAATTCTCTGTAAGTTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
21227 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
21266 CTAAGTCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:21403 original size:56 final size:57
Alignment explanation
Indices: 21331--21445 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
21321 TTTATTTTGT
21331 AGAATAATTAAGTAGAGATAG-GGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGAGGGGATATGATTTATTATAACATTTATTGTGTGAA
* *
21387 AGAATAATTAAGTAGAGATAGAGGGGATATGATTTATTATAATATTTATTTTGTGAA
1 AGAATAATTAAGTAGAGATAGAGGGGATATGATTTATTATAACATTTATTGTGTGAA
21444 AG
1 AG
21446 GAAACAGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 21 0.38
57 35 0.62
ACGTcount: A:0.40, C:0.01, G:0.23, T:0.37
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAGAGGGGATATGATTTATTATAACATTTATTGTGTGAA
Found at i:22930 original size:121 final size:126
Alignment explanation
Indices: 22723--22971 Score: 375
Period size: 121 Copynumber: 2.0 Consensus size: 126
22713 TAAGAAATAA
*
22723 ATTTAAAAATTCTTATATATATAAGTTTTTTAATTAAAATATTAAAATGGTAAAAATAAAATAGG
1 ATTTAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-G
*
22788 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTGTAAAAGTAT
62 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAGTAT
22853 ATTTAAAAAATTC-TA-ATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-
1 ATTT-AAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTAT
* *
22913 AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGT
65 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAGT
22972 TTAAACAATG
Statistics
Matches: 114, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
121 54 0.47
122 2 0.02
123 2 0.02
125 2 0.02
129 40 0.35
130 6 0.05
131 8 0.07
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (126 bp):
ATTTAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATA
AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAGTAT
Found at i:25849 original size:76 final size:76
Alignment explanation
Indices: 25723--25870 Score: 235
Period size: 76 Copynumber: 1.9 Consensus size: 76
25713 AAACCTCTAT
* *
25723 AAATTAATAATGTTGGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAAT-TAATCGAGTAC
1 AAATTAATAATATTAGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATGT-ATCGAGTAC
25787 TAATTTATATAG
65 TAATTTATATAG
* * *
25799 AAATTAATGATATTAGGACTATGAAAAATTATTAATTTAGAGAGGTTATTAATGTATCGAGTATT
1 AAATTAATAATATTAGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATGTATCGAGTACT
25864 AATTTAT
66 AATTTAT
25871 GGAGGTTGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
76 65 0.98
77 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.39
Consensus pattern (76 bp):
AAATTAATAATATTAGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATGTATCGAGTACT
AATTTATATAG
Found at i:27262 original size:12 final size:13
Alignment explanation
Indices: 27242--27279 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
27232 GTTTTACATG
*
27242 TAATTTATAT-TA
1 TAATATATATATA
27254 TAATATATATATA
1 TAATATATATATA
27267 T-ATATATATATA
1 TAATATATATATA
27279 T
1 T
27280 GGTTTATGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 21 0.88
13 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TAATATATATATA
Found at i:27263 original size:2 final size:2
Alignment explanation
Indices: 27247--27279 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
27237 ACATGTAATT
27247 TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27280 GGTTTATGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.