Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023728.1 Corchorus olitorius cultivar O-4 contig23761, 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: 7746
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1612 original size:14 final size:15
Alignment explanation
Indices: 1593--1622 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1583 CAATCAAAGC
1593 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
1607 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
1622 A
1 A
1623 TTAAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:2022 original size:21 final size:21
Alignment explanation
Indices: 1980--2027 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1970 GGAATGGTGA
** *
1980 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGATGG
*
2001 TGGCACGGGCTTAACCGATGG
1 TGGCACGGGCATAACCGATGG
2022 TGGCAC
1 TGGCAC
2028 AGTGAATGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.25, G:0.44, T:0.17
Consensus pattern (21 bp):
TGGCACGGGCATAACCGATGG
Found at i:5208 original size:32 final size:30
Alignment explanation
Indices: 5151--5233 Score: 93
Period size: 32 Copynumber: 2.8 Consensus size: 30
5141 AAAGAAAATA
*
5151 TTTTTTTTCTAAAAACGCAGGAACAAGAATTT
1 TTTTTTTTCTAAAAACGCAGAAAC-A-AATTT
*
5183 TTTTTTTTTTAGAAAACGCA-AAACAAA-TT
1 TTTTTTTTCTA-AAAACGCAGAAACAAATTT
5212 TTTTTTTTC-AAAAACGCA-AAAC
1 TTTTTTTTCTAAAAACGCAGAAAC
5234 TAATAAATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
27 12 0.26
28 1 0.02
29 10 0.21
30 2 0.04
31 1 0.02
32 13 0.28
33 8 0.17
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (30 bp):
TTTTTTTTCTAAAAACGCAGAAACAAATTT
Found at i:5225 original size:27 final size:28
Alignment explanation
Indices: 5140--5233 Score: 91
Period size: 33 Copynumber: 3.2 Consensus size: 28
5130 GACAGAAAAT
* *
5140 AAAAGAAAATATTTTTTTTCTAAAAACGC
1 AAAACAAAATTTTTTTTTTC-AAAAACGC
* *
5169 AGGAACAAGAATTTTTTTTTTTTTAGAAAACGC
1 A-AAACAA-AA--TTTTTTTTTTCA-AAAACGC
5202 AAAAC-AAATTTTTTTTTTCAAAAACGC
1 AAAACAAAATTTTTTTTTTCAAAAACGC
5229 AAAAC
1 AAAAC
5234 TAATAAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
27 12 0.22
28 11 0.20
29 1 0.02
30 6 0.11
31 3 0.06
32 4 0.07
33 17 0.31
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (28 bp):
AAAACAAAATTTTTTTTTTCAAAAACGC
Found at i:5276 original size:28 final size:26
Alignment explanation
Indices: 5243--5297 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
5233 CTAATAAATT
* *
5243 AAAAACGCAAGAAAACTTTCTTTTTATG
1 AAAAACACAA-AAAACCTT-TTTTTATG
*
5271 AAAAACACAAAAACCCTTTTTTTATG
1 AAAAACACAAAAAACCTTTTTTTATG
5297 A
1 A
5298 CGCAGAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.38
27 6 0.25
28 9 0.38
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.31
Consensus pattern (26 bp):
AAAAACACAAAAAACCTTTTTTTATG
Found at i:5681 original size:16 final size:15
Alignment explanation
Indices: 5643--5684 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
5633 ACAGAGATTG
*
5643 ACAGAAATCAATTAA
1 ACAGAAAACAATTAA
5658 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
5673 ACTAGAAAACAA
1 AC-AGAAAACAA
5685 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.