Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013913.1 Corchorus olitorius cultivar O-4 contig13946, 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: 24192
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:30 original size:7 final size:7
Alignment explanation
Indices: 18--73 Score: 53
Period size: 7 Copynumber: 7.7 Consensus size: 7
8 TTTTTTAATT
18 ATTATTA
1 ATTATTA
25 ATTATTTA
1 ATTA-TTA
33 ATTATTA
1 ATTATTA
40 ATTATT-
1 ATTATTA
46 ATTAATTTAA
1 ATT-A-TT-A
*
56 ATTGTT-
1 ATTATTA
62 ATTATTA
1 ATTATTA
69 ATTAT
1 ATTAT
74 AATAAATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
6 8 0.20
7 19 0.46
8 11 0.27
10 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (7 bp):
ATTATTA
Found at i:46 original size:22 final size:22
Alignment explanation
Indices: 15--73 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
5 TTATTTTTTA
15 ATTATTATTAATTATTT-AATT
1 ATTATTATTAATTATTTAAATT
36 ATTAATTATT-ATTAATTTAAATT
1 ATT-ATTATTAATT-ATTTAAATT
*
59 GTTATTATTAATTAT
1 ATTATTATTAATTAT
74 AATAAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 6 0.18
22 18 0.55
23 9 0.27
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTATTATTAATTATTTAAATT
Found at i:208 original size:29 final size:28
Alignment explanation
Indices: 169--224 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
159 GTTATTCCAC
*
169 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
198 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
225 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:1287 original size:47 final size:48
Alignment explanation
Indices: 1195--1315 Score: 163
Period size: 47 Copynumber: 2.5 Consensus size: 48
1185 TTAATCTAAA
* *
1195 ATGACTAATTAAACACAACTTCTAAAATGAGTATAAAAAAAAAAACAAC
1 ATGACTAATTACACACAACTCCTAAAATGAG-ATAAAAAAAAAAACAAC
* * *
1244 ATGACTAATTACACACAACTCCTAGAATGA-ATATACAAAAAAACAAC
1 ATGACTAATTACACACAACTCCTAAAATGAGATAAAAAAAAAAACAAC
* *
1291 GTGACTAATTACACACAACTTCTAA
1 ATGACTAATTACACACAACTCCTAA
1316 GAAAACAACC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 37 0.58
49 27 0.42
ACGTcount: A:0.53, C:0.19, G:0.07, T:0.21
Consensus pattern (48 bp):
ATGACTAATTACACACAACTCCTAAAATGAGATAAAAAAAAAAACAAC
Found at i:1994 original size:46 final size:46
Alignment explanation
Indices: 1927--2018 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
1917 TACCACCTTG
* *
1927 GCCAGATAATTTGGTGCATGTAACATTACTTTTGAGTGATAAATAA
1 GCCAGATAATTTGGTGCATGTAACATTACTCTTGAGTGAAAAATAA
1973 GCCAGATAATTTGGTGCATGTAACATTACTCTTGAGTGAAAAATAA
1 GCCAGATAATTTGGTGCATGTAACATTACTCTTGAGTGAAAAATAA
2019 AACTAAAACT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (46 bp):
GCCAGATAATTTGGTGCATGTAACATTACTCTTGAGTGAAAAATAA
Found at i:6096 original size:13 final size:13
Alignment explanation
Indices: 6078--6102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6068 TAAATATAAG
6078 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
6091 AAAAAAAAAGAA
1 AAAAAAAAAGAA
6103 TGTTGCTTTT
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:8339 original size:3 final size:3
Alignment explanation
Indices: 8331--8362 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
8321 CGCTCCTGAA
8331 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
8363 TTTGTTCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:17335 original size:20 final size:22
Alignment explanation
Indices: 17310--17350 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17300 TCAAGCTCGG
17310 CTCGAA-TTTTC-CGAGTCGAA
1 CTCGAATTTTTCTCGAGTCGAA
17330 CTCGAATTTTTCTCGAGTCGA
1 CTCGAATTTTTCTCGAGTCGA
17351 GCCCGAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
CTCGAATTTTTCTCGAGTCGAA
Found at i:18023 original size:84 final size:81
Alignment explanation
Indices: 17904--18061 Score: 253
Period size: 84 Copynumber: 1.9 Consensus size: 81
17894 AAAACTCTTG
* *
17904 ATACCGGATGGGGTAAAAAAAATATATGCTAAATAGTTAGACTTTAATATAAAAATCATTTATTA
1 ATACCGGATGGGGTAAAAAAAATATATACTAAATAGTTAGACTTTAATATAAAAATAATTTATTA
*
17969 ATTTTTTATATACTAC
66 ATTATTTATATACTAC
*
17985 ATACCGGATGGGGTACCAAAAAAATTATATACTAAATAGTTTGACTTTAATATAAAAATAATTTA
1 ATACCGGATGGGGTA--AAAAAAA-TATATACTAAATAGTTAGACTTTAATATAAAAATAATTTA
18050 TTAATTATTTAT
63 TTAATTATTTAT
18062 TGATTTTTTA
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
81 15 0.21
83 7 0.10
84 48 0.69
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (81 bp):
ATACCGGATGGGGTAAAAAAAATATATACTAAATAGTTAGACTTTAATATAAAAATAATTTATTA
ATTATTTATATACTAC
Found at i:18793 original size:23 final size:25
Alignment explanation
Indices: 18745--18794 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
18735 TGGTAGTAGT
18745 AGTAGTAGATCATATATGAGATAACC
1 AGTAGTAGATCATATAT-AGATAACC
18771 AGTAGTAGATCATATAT-GA-AACC
1 AGTAGTAGATCATATATAGATAACC
18794 A
1 A
18795 TTGGTTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.21
24 2 0.08
26 17 0.71
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (25 bp):
AGTAGTAGATCATATATAGATAACC
Found at i:19898 original size:2 final size:2
Alignment explanation
Indices: 19887--19916 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19877 TTACCTATGT
19887 TA TA -A TA 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 T
19917 CATTAATCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20475 original size:2 final size:2
Alignment explanation
Indices: 20468--20548 Score: 94
Period size: 2 Copynumber: 41.5 Consensus size: 2
20458 CTTCAAGACT
* * * *
20468 TA TA TA TA AA TT TT TA TA T- TA T- TA TA TA TA TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
20508 TA CA TA TA TA TA TA TA CA 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 TA TA TA T
20549 CCTACTCATT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
1 2 0.03
2 65 0.97
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:21170 original size:15 final size:15
Alignment explanation
Indices: 21150--21224 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 15
21140 TAAGAATATA
21150 TATTTTTAAAGGATT
1 TATTTTTAAAGGATT
*
21165 TATTTTTGAAGGA--
1 TATTTTTAAAGGATT
* *
21178 TA--TTTAAA-AATG
1 TATTTTTAAAGGATT
21190 TATTTTTTAAAGGATT
1 TA-TTTTTAAAGGATT
* *
21206 TATTTTTGAAGGATA
1 TATTTTTAAAGGATT
21221 TATT
1 TATT
21225 ATGATGATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
10 1 0.02
11 5 0.11
12 2 0.04
13 2 0.04
15 33 0.70
16 4 0.09
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.51
Consensus pattern (15 bp):
TATTTTTAAAGGATT
Found at i:21176 original size:42 final size:42
Alignment explanation
Indices: 21128--21239 Score: 163
Period size: 41 Copynumber: 2.6 Consensus size: 42
21118 TCCTCCTTTG
21128 TTGAAGGATATTTAAGAATATATATTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGAATATATATTTTTAAAGGATTTATTT
* *
21170 TTGAAGGATATTTAAAAATGTAT-TTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGAATATATATTTTTAAAGGATTTATTT
*
21211 TTGAAGGATATATTATGATGATATATATT
1 TTGAAGGATAT-TTAAGA--ATATATATT
21240 ACATTACTAG
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 29 0.48
42 25 0.41
44 5 0.08
45 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (42 bp):
TTGAAGGATATTTAAGAATATATATTTTTAAAGGATTTATTT
Done.