Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020613.1 Corchorus olitorius cultivar O-4 contig20646, 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: 13705
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:242 original size:31 final size:29
Alignment explanation
Indices: 176--255 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
166 CTCATTTTTG
* * *
176 AAACGTAAGGGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
205 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
* *
236 AAACATAAGAGATTTTTTTG
1 AAACATAAGGGATTATTTTG
256 GTATTTAGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 25 0.57
31 19 0.43
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:1011 original size:19 final size:19
Alignment explanation
Indices: 954--1025 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
944 TTTGATATTT
*
954 AAACTCTCAAAACTCCTTC
1 AAACTCTCAAAACTTCTTC
973 AAACT-TC---A-TT-TTC
1 AAACTCTCAAAACTTCTTC
*
986 TAACTCTCAAAACTTCTTC
1 AAACTCTCAAAACTTCTTC
*
1005 AAACTCTCTAAACTTCTTC
1 AAACTCTCAAAACTTCTTC
1024 AA
1 AA
1026 GAACATCATG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
13 7 0.16
14 3 0.07
15 1 0.02
17 1 0.02
18 4 0.09
19 27 0.63
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (19 bp):
AAACTCTCAAAACTTCTTC
Found at i:1616 original size:24 final size:24
Alignment explanation
Indices: 1581--1637 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
1571 CTCCGTCCGT
*
1581 AGGGAGAAACAGGAGCAGTTGCAA
1 AGGGAGAGACAGGAGCAGTTGCAA
*
1605 ATGGAGAGACAGGAGCAGTTGCAA
1 AGGGAGAGACAGGAGCAGTTGCAA
1629 AGGGAGAGA
1 AGGGAGAGA
1638 GAGGCTGAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.40, C:0.11, G:0.40, T:0.09
Consensus pattern (24 bp):
AGGGAGAGACAGGAGCAGTTGCAA
Found at i:5967 original size:26 final size:26
Alignment explanation
Indices: 5938--5996 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
5928 CACCTGCGGA
*
5938 AATAATAAATAAATAC-ATTAATAAAT
1 AATAATAAAT-AATACAACTAATAAAT
* *
5964 AATAATAAATATTACAACTATTAAAT
1 AATAATAAATAATACAACTAATAAAT
5990 AATAATA
1 AATAATA
5997 CCACCTGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (26 bp):
AATAATAAATAATACAACTAATAAAT
Found at i:7361 original size:33 final size:33
Alignment explanation
Indices: 7254--7348 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
7244 CCGCCCTCTA
* * *
7254 AGGGCGGCATGGCCATGGTCATGCCGCCCACCG
1 AGGGCGGCATAGCCATGGTTACGCCGCCCACCG
*
7287 AGGGCGGCATAGCCATGGTTACGTCGCCCACCG
1 AGGGCGGCATAGCCATGGTTACGCCGCCCACCG
7320 AGGGCGGCATAGCCATGGTTACGCCGCCC
1 AGGGCGGCATAGCCATGGTTACGCCGCCC
7349 TCCTTGGGCG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.17, C:0.35, G:0.35, T:0.14
Consensus pattern (33 bp):
AGGGCGGCATAGCCATGGTTACGCCGCCCACCG
Found at i:7909 original size:21 final size:21
Alignment explanation
Indices: 7874--7951 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
7864 CCGTTTAGTA
7874 ATATT-TATA-AT-TAAATAT
1 ATATTATATATATATAAATAT
7892 ATATTATATATATATAAA-AT
1 ATATTATATATATATAAATAT
* * *
7912 AATATTAGATATATATAATTAC
1 -ATATTATATATATATAAATAT
7934 ATA-TATAATAATATATAA
1 ATATTAT-AT-ATATATAA
7952 TTATTAAACG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
18 5 0.10
19 4 0.08
20 6 0.12
21 25 0.51
22 9 0.18
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (21 bp):
ATATTATATATATATAAATAT
Found at i:7939 original size:12 final size:11
Alignment explanation
Indices: 7879--7954 Score: 52
Period size: 12 Copynumber: 6.7 Consensus size: 11
7869 TAGTAATATT
7879 TATAATTAAATA
1 TATAATT-AATA
*
7891 TATATTATATATA
1 TATAAT-TA-ATA
*
7904 TATAAAATAATA
1 TAT-AATTAATA
7916 T-TAGA-T-ATA
1 TATA-ATTAATA
7925 TATAATTACATA
1 TATAATTA-ATA
7937 TATAA-TAATA
1 TATAATTAATA
7947 TATAATTA
1 TATAATTA
7955 TTAAACGGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 19
0.70 0.04 0.26
Matches are distributed among these distances:
9 5 0.10
10 13 0.25
11 6 0.12
12 18 0.35
13 9 0.17
14 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
TATAATTAATA
Found at i:13325 original size:13 final size:13
Alignment explanation
Indices: 13307--13332 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13297 GTTCGATACC
13307 TTTAATAAGGTAT
1 TTTAATAAGGTAT
13320 TTTAATAAGGTAT
1 TTTAATAAGGTAT
13333 GAGATTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTAATAAGGTAT
Done.