Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015070.1 Corchorus olitorius cultivar O-4 contig15103, 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: 35739
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:435 original size:16 final size:16
Alignment explanation
Indices: 410--442 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
400 TAAAAAAATC
410 TTATCTTATAT-AAAA
1 TTATCTTATATGAAAA
425 TTATGCTTATATGAAAA
1 TTAT-CTTATATGAAAA
442 T
1 T
443 ACAACACACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TTATCTTATATGAAAA
Found at i:2647 original size:2 final size:2
Alignment explanation
Indices: 2640--2666 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2630 ACATGGACAT
2640 TA 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 T
2667 TTCTAAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4962 original size:7 final size:7
Alignment explanation
Indices: 4950--4980 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
4940 TCTACCATTT
4950 TTTTTCC
1 TTTTTCC
4957 TTTTT-C
1 TTTTTCC
4963 TTTTTCC
1 TTTTTCC
4970 TTTTTCC
1 TTTTTCC
4977 TTTT
1 TTTT
4981 CTTAGGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCC
Found at i:4966 original size:13 final size:13
Alignment explanation
Indices: 4950--4981 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4940 TCTACCATTT
4950 TTTTTCCTTTTTC
1 TTTTTCCTTTTTC
4963 TTTTTCCTTTTTC
1 TTTTTCCTTTTTC
*
4976 CTTTTC
1 TTTTTC
4982 TTAGGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTCCTTTTTC
Found at i:5313 original size:23 final size:23
Alignment explanation
Indices: 5287--5330 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5277 TAAAAATTTT
5287 ATATGCAATTAAAATTTTAAAAA
1 ATATGCAATTAAAATTTTAAAAA
***
5310 ATATGTTTTTAAAATTTTAAA
1 ATATGCAATTAAAATTTTAAA
5331 GTTTAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (23 bp):
ATATGCAATTAAAATTTTAAAAA
Found at i:5349 original size:16 final size:15
Alignment explanation
Indices: 5317--5351 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5307 AAAATATGTT
5317 TTTAAAATTTTAAAG
1 TTTAAAATTTTAAAG
*
5332 TTTAAATTTTTCAAAG
1 TTTAAAATTTT-AAAG
5348 TTTA
1 TTTA
5352 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (15 bp):
TTTAAAATTTTAAAG
Found at i:9155 original size:2 final size:2
Alignment explanation
Indices: 9150--9194 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
9140 GAAAGAGAGC
*
9150 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9190 TA TA T
1 TA TA T
9195 TCTTTGACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23097 original size:71 final size:71
Alignment explanation
Indices: 22947--23090 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 71
22937 ACAATTTTCC
* * *
22947 AAACAATTTACTCTAAGACCCTAAAATTCAGAAATTTTAGTTGCTAAAAACTAGAATGGGGCAAT
1 AAACAATTTACTCTAAAACCCTAAAATTCAGAAATTTTAGTTCCTAAAAACCAGAATGGGGCAAT
23012 AATTGA
66 AATTGA
* * * *
23018 AAACAATTTACTCTAAAACCCTGAAATTCAGAATTTTTTGTTCCTAAAAACCAGAATGGTGCAAT
1 AAACAATTTACTCTAAAACCCTAAAATTCAGAAATTTTAGTTCCTAAAAACCAGAATGGGGCAAT
23083 AATTGA
66 AATTGA
23089 AA
1 AA
23091 TAAATTTGGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (71 bp):
AAACAATTTACTCTAAAACCCTAAAATTCAGAAATTTTAGTTCCTAAAAACCAGAATGGGGCAAT
AATTGA
Found at i:25391 original size:2 final size:2
Alignment explanation
Indices: 25384--25415 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25374 AAAATGAAAC
25384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25416 TGATCAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27769 original size:12 final size:12
Alignment explanation
Indices: 27748--27806 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
27738 TGATTAAAAA
27748 ATATATAAT-AT
1 ATATATAATAAT
*
27759 ATATAATAATATT
1 ATAT-ATAATAAT
*
27772 AGATATATATAATT
1 ATATATA-ATAA-T
27786 ATATATAATAAT
1 ATATATAATAAT
27798 ATATATAAT
1 ATATATAAT
27807 TATTAAACGG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 4 0.10
12 18 0.45
13 11 0.28
14 7 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
ATATATAATAAT
Found at i:27769 original size:19 final size:19
Alignment explanation
Indices: 27747--27806 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
27737 ATGATTAAAA
27747 AATATATAATATATATAAT
1 AATATATAATATATATAAT
27766 AATAT-TAGATATATATAAT
1 AATATATA-ATATATATAAT
*
27785 TATATATAATA-ATATATAT
1 AATATATAATATATATA-AT
27804 AAT
1 AAT
27807 TATTAAACGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 7 0.19
19 27 0.75
20 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATATATAATATATATAAT
Found at i:28267 original size:2 final size:2
Alignment explanation
Indices: 28260--28294 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28250 AAATTTAAAT
28260 TA TA TA TA TA 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 TA TA T
28295 TCAACGGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.