Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013261.1 Corchorus olitorius cultivar O-4 contig13294, 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: 40296
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1628 original size:6 final size:6
Alignment explanation
Indices: 1617--1663 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
1607 TTGGCTTAAA
*
1617 TGTTTT TGTTTT TGTTTT TGTTTT TG-TTT TGCTTT T-TTTT T-TTTT
1 TGTTTT TGTTTT TGTTTT TGTTTT TGTTTT TGTTTT TGTTTT TGTTTT
1662 TG
1 TG
1664 AAAAAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
5 14 0.37
6 24 0.63
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (6 bp):
TGTTTT
Found at i:1638 original size:18 final size:18
Alignment explanation
Indices: 1617--1663 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 18
1607 TTGGCTTAAA
*
1617 TGTTTTTGTTTTTGTTTT
1 TGTTTTTGTTTTTGCTTT
1635 TGTTTTTG-TTTTGCTTT
1 TGTTTTTGTTTTTGCTTT
1652 T-TTTTT-TTTTTG
1 TGTTTTTGTTTTTG
1664 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 10 0.37
17 9 0.33
18 8 0.30
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (18 bp):
TGTTTTTGTTTTTGCTTT
Found at i:4102 original size:51 final size:51
Alignment explanation
Indices: 4026--4127 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
4016 TACATCACTA
4026 GCTTCCCCCGCACTCTGTTGTCCTGAAACCATGTTTCGATTGCCCAGTTTG
1 GCTTCCCCCGCACTCTGTTGTCCTGAAACCATGTTTCGATTGCCCAGTTTG
4077 GCTTCCCCCGCACTCTGTTGTCCTGAAACCATGTTTCGATTGCCCAGTTTG
1 GCTTCCCCCGCACTCTGTTGTCCTGAAACCATGTTTCGATTGCCCAGTTTG
4128 AACATATCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.33
Consensus pattern (51 bp):
GCTTCCCCCGCACTCTGTTGTCCTGAAACCATGTTTCGATTGCCCAGTTTG
Found at i:6517 original size:102 final size:97
Alignment explanation
Indices: 6381--6566 Score: 291
Period size: 97 Copynumber: 1.9 Consensus size: 97
6371 TGTTTGTGCA
* **
6381 CTATTGGACTGCCTAAACTCTTTCATCAGGGGTGGAGCTATATATAGTTGAGTGGAGTCAAATTA
1 CTATTGGACTGCCTAAACTCTTCCATCACAGGTGGAGC----TATA-TTGAGTGGAGTCAAATTA
*
6446 CTCCACTCAACTTTCAAAAGTTAGTTAATAATACACC
61 CTCCACTCAACTTTCAAAACTTAGTTAATAATACACC
6483 CTATTGGACTGCCTAAACTCTTCCATCACAGGTGGAGCTATATTGAGTGGAGTCAAATTACTCCA
1 CTATTGGACTGCCTAAACTCTTCCATCACAGGTGGAGCTATATTGAGTGGAGTCAAATTACTCCA
6548 CTCAACTTTCAAAACTTAG
66 CTCAACTTTCAAAACTTAG
6567 CTATGTTTGT
Statistics
Matches: 80, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
97 41 0.51
98 4 0.05
102 35 0.44
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (97 bp):
CTATTGGACTGCCTAAACTCTTCCATCACAGGTGGAGCTATATTGAGTGGAGTCAAATTACTCCA
CTCAACTTTCAAAACTTAGTTAATAATACACC
Found at i:8514 original size:2 final size:2
Alignment explanation
Indices: 8507--8534 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8497 TGTATAACCC
8507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8535 CTTTAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13577 original size:20 final size:20
Alignment explanation
Indices: 13552--13593 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
13542 AGTGGCCGTT
13552 TGGTTTGTGGATTGTAGATA
1 TGGTTTGTGGATTGTAGATA
*
13572 TGGTTTGTGGGTTGTAGATA
1 TGGTTTGTGGATTGTAGATA
13592 TG
1 TG
13594 CCCAGGGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (20 bp):
TGGTTTGTGGATTGTAGATA
Found at i:14041 original size:24 final size:24
Alignment explanation
Indices: 14009--14072 Score: 128
Period size: 24 Copynumber: 2.7 Consensus size: 24
13999 CCCTCGAATC
14009 ATTTCTAACTTTCTAATTCAAATT
1 ATTTCTAACTTTCTAATTCAAATT
14033 ATTTCTAACTTTCTAATTCAAATT
1 ATTTCTAACTTTCTAATTCAAATT
14057 ATTTCTAACTTTCTAA
1 ATTTCTAACTTTCTAA
14073 ATTTTTAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTCTAACTTTCTAATTCAAATT
Found at i:14394 original size:13 final size:14
Alignment explanation
Indices: 14366--14397 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
14356 TTAGAATCGA
14366 TATTA-GTATTATT
1 TATTATGTATTATT
14379 TATTATGTATTA-T
1 TATTATGTATTATT
14392 TATTAT
1 TATTAT
14398 TAGGCCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (14 bp):
TATTATGTATTATT
Found at i:15842 original size:22 final size:21
Alignment explanation
Indices: 15817--15886 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
15807 CATACTTAGA
*
15817 TTATTATATATTGTTATTACTG
1 TTATTATATATT-TTATTAATG
* *
15839 TTATTATTTTTTATTATTAGAT-
1 TTATTATATATT-TTATTA-ATG
*
15861 TTATT-TA-ATTTTATTATTG
1 TTATTATATATTTTATTAATG
15880 TTATTAT
1 TTATTAT
15887 TAGTATTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.03
19 11 0.29
20 3 0.08
21 1 0.03
22 21 0.55
23 1 0.03
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (21 bp):
TTATTATATATTTTATTAATG
Found at i:15855 original size:3 final size:3
Alignment explanation
Indices: 15816--15972 Score: 72
Period size: 3 Copynumber: 52.3 Consensus size: 3
15806 ACATACTTAG
* * * *
15816 ATT ATT ATAT ATT GTT ATT ACT GTT ATT ATT -TT -TT ATT ATT A-G
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
15859 ATTT ATT -TA ATT -TT ATT ATT GTT ATT ATT AGT ATT ATT ATGT ATT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
* * ** * * * * *
15904 ATT AGT AGT AGC ATTT ATT ATT AAT GTT ATT ATT ATT TTT AAT GTT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
15950 ATTT ATT ATT GTT ATA ATT ATT A
1 A-TT ATT ATT ATT ATT ATT ATT A
15973 ATATAAATGT
Statistics
Matches: 113, Mismatches: 32, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
2 8 0.07
3 94 0.83
4 11 0.10
ACGTcount: A:0.30, C:0.01, G:0.08, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:15922 original size:19 final size:19
Alignment explanation
Indices: 15880--15926 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
15870 TTTATTATTG
* **
15880 TTATTATTAGTATTATTAT
1 TTATTATTAGTAGTAGCAT
*
15899 GTATTATTAGTAGTAGCAT
1 TTATTATTAGTAGTAGCAT
15918 TTATTATTA
1 TTATTATTA
15927 ATGTTATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (19 bp):
TTATTATTAGTAGTAGCAT
Found at i:19135 original size:30 final size:30
Alignment explanation
Indices: 19099--19173 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
19089 TTCAATTTAC
19099 TCAATTGAATTTCTTTAATCAATTAAGTAA
1 TCAATTGAATTTCTTTAATCAATTAAGTAA
* *
19129 TCAATTGAATTTATTTAATCAATTATGTAA
1 TCAATTGAATTTCTTTAATCAATTAAGTAA
19159 TCAATTGAATTTCTT
1 TCAATTGAATTTCTT
19174 GAGGCAGACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (30 bp):
TCAATTGAATTTCTTTAATCAATTAAGTAA
Found at i:20536 original size:12 final size:12
Alignment explanation
Indices: 20519--20560 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
20509 GAGTTGTGAT
*
20519 AGCAATTATAAA
1 AGCAATAATAAA
*
20531 AGCAATAAGAAA
1 AGCAATAATAAA
20543 A-CAATAATAAA
1 AGCAATAATAAA
*
20554 GGCAATA
1 AGCAATA
20561 CTTCTCTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.17
Consensus pattern (12 bp):
AGCAATAATAAA
Found at i:27163 original size:15 final size:15
Alignment explanation
Indices: 27145--27173 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27135 GTTTCTAGTA
27145 TAATTGTTTTCTTTT
1 TAATTGTTTTCTTTT
27160 TAATTGTTTTCTTT
1 TAATTGTTTTCTTT
27174 CAACCTCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TAATTGTTTTCTTTT
Found at i:36848 original size:6 final size:6
Alignment explanation
Indices: 36829--36860 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
36819 CGAATATAGC
*
36829 AAAGAA AAACAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
36861 TAATACACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAGAA
Done.