Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013137.1 Corchorus olitorius cultivar O-4 contig13170, 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: 31464
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1288 original size:38 final size:38
Alignment explanation
Indices: 1184--1293 Score: 150
Period size: 38 Copynumber: 2.9 Consensus size: 38
1174 TTCTACGGTC
* *
1184 CTCACCATCTGAATTGGAA-AACTGAATATATTAAAGGT
1 CTCATCATCTCAATTGGAATAA-TGAATATATTAAAGGT
* *
1222 CTCATCATCTCAATTGGAATAGTGAATATGTTAAAGGT
1 CTCATCATCTCAATTGGAATAATGAATATATTAAAGGT
* *
1260 CTCATCATCTCAATTGGAATAATTAATATTTTAA
1 CTCATCATCTCAATTGGAATAATGAATATATTAA
1294 TTTAGATAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
38 63 0.98
39 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (38 bp):
CTCATCATCTCAATTGGAATAATGAATATATTAAAGGT
Found at i:1325 original size:21 final size:21
Alignment explanation
Indices: 1280--1339 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1270 CAATTGGAAT
* **
1280 AATTAATATTTTAATTTAGATA
1 AATTAATATATTAA-TTCCATA
1302 AATTAATATATTAATTCCATA
1 AATTAATATATTAATTCCATA
*
1323 AATAAAGT-TATTAATTC
1 AATTAA-TATATTAATTC
1340 TACCAAACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (21 bp):
AATTAATATATTAATTCCATA
Found at i:1829 original size:21 final size:22
Alignment explanation
Indices: 1784--1842 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1774 CAATTGGAAT
* *
1784 AATTAATATTTTAATTTAGATA
1 AATTAATATATTAATTTACATA
1806 AATTAATATATTAATTT-CATA
1 AATTAATATATTAATTTACATA
*
1827 AATGAAGT-TATTAATT
1 AATTAA-TATATTAATT
1843 CTACCCAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
AATTAATATATTAATTTACATA
Found at i:9408 original size:25 final size:25
Alignment explanation
Indices: 9374--9423 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
9364 TAATTGGTTT
*
9374 ATAGAGACCGAGTGAGAGTGCTCAA
1 ATAGAGACCGAGCGAGAGTGCTCAA
9399 ATAGAGACCGAGCGAGAGTGCTCAA
1 ATAGAGACCGAGCGAGAGTGCTCAA
9424 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.32, T:0.14
Consensus pattern (25 bp):
ATAGAGACCGAGCGAGAGTGCTCAA
Found at i:10170 original size:2 final size:2
Alignment explanation
Indices: 10165--10220 Score: 78
Period size: 2 Copynumber: 27.5 Consensus size: 2
10155 AGTTTCTCTA
10165 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG AT- TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -TG TG
*
10207 TT TG CTG TG TG TG T
1 TG TG -TG TG TG TG T
10221 TTGGTTTGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 1 0.02
2 45 0.92
3 3 0.06
ACGTcount: A:0.02, C:0.02, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:11316 original size:31 final size:32
Alignment explanation
Indices: 11278--11351 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
11268 CTTGGGTGGG
11278 TTCGGGTTCGGG-TACT-TCGGGTTCAGACT-TT
1 TTCGGGTTCGGGTTA-TGTCGGGTTC-GACTATT
* *
11309 TTCGGGTTCGGGTTATGTTGGGTTCGAGTATT
1 TTCGGGTTCGGGTTATGTCGGGTTCGACTATT
11341 TTCGGGTTCGG
1 TTCGGGTTCGG
11352 TCTAGGGTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
31 16 0.42
32 22 0.58
ACGTcount: A:0.08, C:0.15, G:0.36, T:0.41
Consensus pattern (32 bp):
TTCGGGTTCGGGTTATGTCGGGTTCGACTATT
Found at i:11347 original size:16 final size:16
Alignment explanation
Indices: 11278--11350 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
11268 CTTGGGTGGG
* *
11278 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGAGTATT
*
11293 TTCGGGTTCAGACT-TT
1 TTCGGGTTC-GAGTATT
* *
11309 TTCGGGTTCGGGTTATG
1 TTCGGGTTCGAG-TATT
11326 TT-GGGTTCGAGTATT
1 TTCGGGTTCGAGTATT
11341 TTCGGGTTCG
1 TTCGGGTTCG
11351 GTCTAGGGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
15 15 0.33
16 27 0.60
17 3 0.07
ACGTcount: A:0.08, C:0.15, G:0.36, T:0.41
Consensus pattern (16 bp):
TTCGGGTTCGAGTATT
Found at i:11903 original size:20 final size:21
Alignment explanation
Indices: 11856--11903 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
11846 ATCAATTCTA
11856 AATTATTGCAAATTAAAAAAATT
1 AATTATT--AAATTAAAAAAATT
*
11879 AATTATTAAATTAAACAAA-T
1 AATTATTAAATTAAAAAAATT
11899 AATTA
1 AATTA
11904 AAATGAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
21 11 0.46
23 7 0.29
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
AATTATTAAATTAAAAAAATT
Found at i:12374 original size:6 final size:6
Alignment explanation
Indices: 12365--12401 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
12355 TATTTAGGGT
12365 TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC T
1 TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC T
12402 GCCTCAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.49, T:0.19
Consensus pattern (6 bp):
TCGGGC
Found at i:12427 original size:16 final size:16
Alignment explanation
Indices: 12408--12447 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12398 GGCTGCCTCA
*
12408 GGTTCGGGTATTTTCG
1 GGTTCGGGTAATTTCG
*
12424 GGTTCGGATAATTTCG
1 GGTTCGGGTAATTTCG
12440 GGTTCGGG
1 GGTTCGGG
12448 ACGTTGACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.10, C:0.12, G:0.40, T:0.38
Consensus pattern (16 bp):
GGTTCGGGTAATTTCG
Found at i:13066 original size:37 final size:37
Alignment explanation
Indices: 13016--13090 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
13006 ATTTTCAATT
13016 AGTTTTTATTTGGGATAATTCCACTTAAATATATTGA
1 AGTTTTTATTTGGGATAATTCCACTTAAATATATTGA
13053 AGTTTTTATTTGGGATAATTCCACTTAAATATATTGA
1 AGTTTTTATTTGGGATAATTCCACTTAAATATATTGA
13090 A
1 A
13091 AGATAAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (37 bp):
AGTTTTTATTTGGGATAATTCCACTTAAATATATTGA
Found at i:15055 original size:20 final size:21
Alignment explanation
Indices: 15009--15058 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
14999 TTGGTGATCT
* *
15009 AGTAAAAAATTAAAAAATTAG
1 AGTAAAAAAATAAAAAATCAG
*
15030 AG-AAAAAAATAATAAATCA-
1 AGTAAAAAAATAAAAAATCAG
15049 AGTAAAAAAA
1 AGTAAAAAAA
15059 AGTAGTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.18
Consensus pattern (21 bp):
AGTAAAAAAATAAAAAATCAG
Found at i:16029 original size:96 final size:96
Alignment explanation
Indices: 15859--16151 Score: 290
Period size: 96 Copynumber: 2.9 Consensus size: 96
15849 ATAAAAGAAA
* * * * *
15859 TTTAATTTTTAAGAGTAAATTAT-GAAATTAA-AGGTTTTTTATTATAGAGTTTTAGAAATAAAA
1 TTTAA-TTTTAAGAGTAAATT-TCAAAATTAATA-ATTTATTGTTATAGGGTTTTAGAAATAAAA
15922 TATAAAACTAATTGCACTAAGTTTAGCCC-TTTAT
63 TATAAAACTAATT-CACTAAGTTTAGCCCATTTAT
*
15956 TTTAATTTTAAGAGTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATAC
1 TTTAATTTTAAGAGTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATAT
16021 AAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTAT
66 AAAACTAA-TTCACTAAGTTTAG-CCC--------A-TTTAT
* * * ** *
16063 TTTTATTTTAAGGGTAAATTCCCTAATTAATAA--TGTTGTTATAGGGTTTTAGAAATAAAATAT
1 TTTAATTTTAAGAGTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATAT
* *
16126 ATAACTAATTTACTAAGTTTAGCCCA
66 AAAACTAATTCACTAAGTTTAGCCCA
16152 AATTAAAATT
Statistics
Matches: 167, Mismatches: 15, Indels: 30
0.79 0.07 0.14
Matches are distributed among these distances:
95 2 0.01
96 70 0.42
97 11 0.07
103 3 0.02
104 13 0.08
105 35 0.21
107 33 0.20
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (96 bp):
TTTAATTTTAAGAGTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATAT
AAAACTAATTCACTAAGTTTAGCCCATTTAT
Found at i:16132 original size:105 final size:104
Alignment explanation
Indices: 15951--16178 Score: 323
Period size: 105 Copynumber: 2.2 Consensus size: 104
15941 AGTTTAGCCC
* * *
15951 TTTATTTTAATTTTAAGAGTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAA
1 TTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAA-TTATTGTTATAGGGTTTTAGAAATAA
16016 AATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAAT
65 AATACAAAACTAATTT-ACTAAGTTTAG-CCCAAATTAAAAT
** *
16058 TTTATTTTTATTTTAAGGGTAAATTCCCTAATTAATAA-TGTTGTTATAGGGTTTTAGAAATAAA
1 TTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAATTATTGTTATAGGGTTTTAGAAATAAA
* *
16122 ATATATAACTAATTTACTAAGTTTAGCCCAAATTAAAAT
66 ATACAAAACTAATTTACTAAGTTTAGCCCAAATTAAAAT
** *
16161 TAAAATTTTATTTTAAGG
1 TTTATTTTTATTTTAAGG
16179 ATTAGAAAAA
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
103 28 0.25
104 11 0.10
105 38 0.35
107 33 0.30
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (104 bp):
TTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAATTATTGTTATAGGGTTTTAGAAATAAA
ATACAAAACTAATTTACTAAGTTTAGCCCAAATTAAAAT
Found at i:16899 original size:21 final size:21
Alignment explanation
Indices: 16875--16941 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
16865 TTAAAATTAC
16875 CTTTGACACCAAAAGTTGTCA
1 CTTTGACACCAAAAGTTGTCA
* ** *
16896 CTTTGGTAAATTAAAA-TTAT--
1 CTTT-G-ACACCAAAAGTTGTCA
16916 CTTTGACACCAAAAGTTGTCA
1 CTTTGACACCAAAAGTTGTCA
16937 CTTTG
1 CTTTG
16942 GTAAATTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 4 0.12
21 9 0.27
22 4 0.12
23 6 0.18
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (21 bp):
CTTTGACACCAAAAGTTGTCA
Found at i:16900 original size:41 final size:41
Alignment explanation
Indices: 16827--16967 Score: 248
Period size: 41 Copynumber: 3.5 Consensus size: 41
16817 AATAATATTG
* *
16827 AAAATTACCTTTGA-AACAGAAGTTGTCACTTTGGTAAATT
1 AAAATTACCTTTGACACCAAAAGTTGTCACTTTGGTAAATT
16867 AAAATTACCTTTGACACCAAAAGTTGTCACTTTGGTAAATT
1 AAAATTACCTTTGACACCAAAAGTTGTCACTTTGGTAAATT
*
16908 AAAATTATCTTTGACACCAAAAGTTGTCACTTTGGTAAATT
1 AAAATTACCTTTGACACCAAAAGTTGTCACTTTGGTAAATT
16949 AAAATTACCTTTGACACCA
1 AAAATTACCTTTGACACCA
16968 GAAATGTTAC
Statistics
Matches: 96, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 14 0.15
41 82 0.85
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (41 bp):
AAAATTACCTTTGACACCAAAAGTTGTCACTTTGGTAAATT
Found at i:25083 original size:24 final size:25
Alignment explanation
Indices: 25037--25085 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
25027 TGCGTTTTAG
* *
25037 AAAAAAAAATGCGTTTTTGCGTTTT
1 AAAAAAAAATGCGTTTATACGTTTT
*
25062 AAAAAAAAAT-TGTTTATACGTTTT
1 AAAAAAAAATGCGTTTATACGTTTT
25086 TAGAAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (25 bp):
AAAAAAAAATGCGTTTATACGTTTT
Found at i:27971 original size:21 final size:21
Alignment explanation
Indices: 27947--27987 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27937 GCCATGGCCC
27947 GGCCACCCGAGCCACATGCCA
1 GGCCACCCGAGCCACATGCCA
* * *
27968 GGCCATCCGCGCCACCTGCC
1 GGCCACCCGAGCCACATGCC
27988 CGGTCAAGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.51, G:0.24, T:0.07
Consensus pattern (21 bp):
GGCCACCCGAGCCACATGCCA
Done.