Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021341.1 Corchorus olitorius cultivar O-4 contig21374, 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: 16279
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2557 original size:21 final size:21
Alignment explanation
Indices: 2533--2587 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2523 GGCTTGGAAT
* *
2533 GGTGATGGCACGGGCATGACC
1 GGTGGTGGCACGGGCATAACC
*
2554 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
2575 GGTGGTGGCACGG
1 GGTGGTGGCACGG
2588 TGAATGGCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:2936 original size:75 final size:75
Alignment explanation
Indices: 2856--3027 Score: 227
Period size: 75 Copynumber: 2.3 Consensus size: 75
2846 AGGGTGGCAC
* * * *
2856 GGATGGCCGGGCCATGGCCGGGCATGTATCTCGGCGTGGCTCGGGTATGGCCGATCCTATCCGGG
1 GGATGGCCGGGCCATAGCCGGGCATGTAGCTCGGCGCGGCTCGGGTATGGCCGATCCCATCCGGG
**
2921 CCATGTGTGA
66 CCATGTGCAA
* * * * * * *
2931 TGATGGCCGGGCCATAACCGGGCATGTGGCTCGGGGCGGCTTGGGTATGGCCGGTCCCGTCCGGG
1 GGATGGCCGGGCCATAGCCGGGCATGTAGCTCGGCGCGGCTCGGGTATGGCCGATCCCATCCGGG
2996 CCATGTGCAA
66 CCATGTGCAA
3006 GGATGGCCGGGCCATAGCCGGG
1 GGATGGCCGGGCCATAGCCGGG
3028 TATTGGCCGG
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 82 1.00
ACGTcount: A:0.12, C:0.27, G:0.42, T:0.19
Consensus pattern (75 bp):
GGATGGCCGGGCCATAGCCGGGCATGTAGCTCGGCGCGGCTCGGGTATGGCCGATCCCATCCGGG
CCATGTGCAA
Found at i:5916 original size:30 final size:27
Alignment explanation
Indices: 5833--5918 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 27
5823 CTCTTATAAA
*
5833 TGACGCAAAAAAAAAACTCTTTTTTTTC
1 TGACGCAAAAACAAAACT-TTTTTTTTC
*
5861 -GACGCAAAAACAAACAGGTTTTTTTTTC
1 TGACGCAAAAACAAA-A-CTTTTTTTTTC
5889 TTGACGCAAAACACAAAACTTTATTTTTTC
1 -TGACGCAAAA-ACAAAACTTT-TTTTTTC
5919 AGAAAAACGC
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
27 13 0.27
28 10 0.20
29 4 0.08
30 17 0.35
31 5 0.10
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (27 bp):
TGACGCAAAAACAAAACTTTTTTTTTC
Found at i:6382 original size:16 final size:15
Alignment explanation
Indices: 6344--6385 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
6334 ACAGAGATTT
* *
6344 ACAGAAAGCAATTAA
1 ACAGAAAACAATGAA
6359 ACAGAAAACAATGAA
1 ACAGAAAACAATGAA
6374 ACTAGAAAACAA
1 AC-AGAAAACAA
6386 AGCAAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10
Consensus pattern (15 bp):
ACAGAAAACAATGAA
Found at i:10091 original size:33 final size:33
Alignment explanation
Indices: 10038--10139 Score: 161
Period size: 33 Copynumber: 3.1 Consensus size: 33
10028 GCTCTTACAA
10038 ACAATGAAGTT-ACGGGCCTTCATCACGCCATT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCATT
* * *
10070 CCAATGAAGTTCACGGGCCTTCATCACGTCTTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCATT
*
10103 ACAATGAAGTTCACGGGCCTTCATCACGCCTTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCATT
10136 ACAA
1 ACAA
10140 GTTGAGCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 10 0.16
33 54 0.84
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (33 bp):
ACAATGAAGTTCACGGGCCTTCATCACGCCATT
Done.