Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005890.1 Corchorus capsularis cultivar CVL-1 contig05908, 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: 3756
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:246 original size:53 final size:52
Alignment explanation
Indices: 106--249 Score: 216
Period size: 52 Copynumber: 2.8 Consensus size: 52
96 AAAAATTTTT
*
106 CATCAAGTTTTCAAAGTGTTCAATTTAGGTCTTTTTAAATTGGGAAAGTTCC
1 CATCAAGTTTTCAAAGTGTTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
* * *
158 CATCAAGTTTTCAAAGTTTTCAATTTAGGTTTTTTCAAATTGGGGAAGTTCC
1 CATCAAGTTTTCAAAGTGTTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
* **
210 CATCAAGTTCTTCAAAATGTTCAATTTAAATCTTTTCAAA
1 CATCAAGTT-TTCAAAGTGTTCAATTTAGGTCTTTTCAAA
250 ACATTCAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
52 57 0.70
53 25 0.30
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (52 bp):
CATCAAGTTTTCAAAGTGTTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCC
Found at i:3043 original size:6 final size:6
Alignment explanation
Indices: 3024--3078 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
3014 AATTTCCCAA
* *
3024 AAAAAA AAAGAAG AAAAAG AAAAA- AAAAGG AAAAAG --AAAG AAAAAG
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
3070 AAAAAG AAA
1 AAAAAG AAA
3079 GAAAAGAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 4 0.10
5 4 0.10
6 29 0.69
7 5 0.12
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3046 original size:16 final size:16
Alignment explanation
Indices: 3022--3094 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 16
3012 GCAATTTCCC
3022 AAAAA-AAAAAAGAAG
1 AAAAAGAAAAAAGAAG
*
3037 AAAAAGAAAAAAAAAGG
1 AAAAAGAAAAAAGAA-G
3054 AAAAAGAAAGAAA-AAG
1 AAAAAGAAA-AAAGAAG
3070 AAAAAGAAAGAAAAGAGAG
1 AAAAAG-AA-AAAAGA-AG
3089 AAAAAG
1 AAAAAG
3095 CAACGATGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
15 5 0.10
16 15 0.30
17 17 0.34
18 5 0.10
19 8 0.16
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAG
Found at i:3050 original size:10 final size:10
Alignment explanation
Indices: 3024--3093 Score: 61
Period size: 11 Copynumber: 6.5 Consensus size: 10
3014 AATTTCCCAA
3024 AAAAAAAAAG
1 AAAAAAAAAG
*
3034 -AAGAAAAAG
1 AAAAAAAAAG
3043 AAAAAAAAAGG
1 AAAAAAAAA-G
*
3054 AAAAAGAAAG
1 AAAAAAAAAG
3064 AAAAAGAAAAAG
1 -AAAA-AAAAAG
3076 AAAGAAAAGAGAG
1 AAA-AAAA-A-AG
3089 AAAAA
1 AAAAA
3094 GCAACGATGG
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
9 8 0.16
10 8 0.16
11 19 0.39
12 9 0.18
13 5 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:3065 original size:27 final size:26
Alignment explanation
Indices: 3022--3094 Score: 98
Period size: 27 Copynumber: 2.9 Consensus size: 26
3012 GCAATTTCCC
3022 AAAAAA-AAAAAG-AAGAAAAAGAAA
1 AAAAAAGAAAAAGAAAGAAAAAGAAA
3046 AAAAAAGGAAAAAGAAAGAAAAAGAAA
1 AAAAAA-GAAAAAGAAAGAAAAAGAAA
* *
3073 AAGAAAG-AAAAGAGAGAAAAAG
1 AAAAAAGAAAAAGAAAGAAAAAG
3095 CAACGATGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
24 6 0.14
25 14 0.32
26 7 0.16
27 17 0.39
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAAAAGAAAGAAAAAGAAA
Found at i:3094 original size:10 final size:9
Alignment explanation
Indices: 3028--3094 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
3018 TCCCAAAAAA
3028 AAAAAGAAG
1 AAAAAGAAG
3037 AAAAAGAA-
1 AAAAAGAAG
3045 AAAAA-AAGG
1 AAAAAGAA-G
3054 AAAAAGAA-
1 AAAAAGAAG
*
3062 AGAAA-AAG
1 AAAAAGAAG
3070 AAAAAGAA-
1 AAAAAGAAG
3078 AGAAAAGAGAG
1 A-AAAAGA-AG
3089 AAAAAG
1 AAAAAG
3095 CAACGATGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
7 4 0.08
8 14 0.29
9 21 0.44
10 8 0.17
11 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:3491 original size:18 final size:19
Alignment explanation
Indices: 3470--3518 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
3460 CGATAAAGAT
3470 GAAAAAGA-AAAAAGAAAA
1 GAAAAAGAGAAAAAGAAAA
*
3488 GAAAAA-AGAAAACGAAAA
1 GAAAAAGAGAAAAAGAAAA
3506 -AAAAAGATGAAAA
1 GAAAAAGA-GAAAA
3519 TTGAAAGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.22
18 16 0.59
19 5 0.19
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (19 bp):
GAAAAAGAGAAAAAGAAAA
Found at i:3493 original size:13 final size:12
Alignment explanation
Indices: 3472--3507 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
3462 ATAAAGATGA
3472 AAAAGAAAAAAG
1 AAAAGAAAAAAG
3484 AAAAGAAAAAAG
1 AAAAGAAAAAAG
3496 AAAACGAAAAAA
1 AAAA-GAAAAAA
3508 AAAGATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:3518 original size:25 final size:24
Alignment explanation
Indices: 3464--3540 Score: 58
Period size: 26 Copynumber: 3.3 Consensus size: 24
3454 AAAAGTCGAT
*
3464 AAAGATGAAAAAG--AA-AAAAGA
1 AAAGATGAAAAAGAAAAGAAAAAA
3485 AAAGA--AAAAAGAAAACGAAAAAA
1 AAAGATGAAAAAGAAAA-GAAAAAA
* *
3508 AAAGATGAAAATTGAAAGTGAAAAAA
1 AAAGATGAAAA-AGAAA-AGAAAAAA
3534 AAA-ATGA
1 AAAGATGA
3541 TGAAATGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 6 0.13
21 7 0.16
23 10 0.22
25 8 0.18
26 14 0.31
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (24 bp):
AAAGATGAAAAAGAAAAGAAAAAA
Found at i:3533 original size:28 final size:26
Alignment explanation
Indices: 3502--3556 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 26
3492 AAAGAAAACG
3502 AAAAAAAAAGATGAAAATTGAAAGTGAA
1 AAAAAAAAAGATG-AAA-TGAAAGTGAA
*
3530 AAAAAAAATGATGAAATGAAAGTGAA
1 AAAAAAAAAGATGAAATGAAAGTGAA
3556 A
1 A
3557 GGAAGGGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 11 0.42
27 3 0.12
28 12 0.46
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (26 bp):
AAAAAAAAAGATGAAATGAAAGTGAA
Found at i:3549 original size:26 final size:27
Alignment explanation
Indices: 3502--3556 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
3492 AAAGAAAACG
3502 AAAAAAAAAGATGAAAATTGAAAGTGA
1 AAAAAAAAAGATGAAAATTGAAAGTGA
3529 AAAAAAAAATGATG-AAA-TGAAAGTGA
1 AAAAAAAAA-GATGAAAATTGAAAGTGA
3555 AA
1 AA
3557 GGAAGGGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 11 0.41
27 12 0.44
28 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (27 bp):
AAAAAAAAAGATGAAAATTGAAAGTGA
Done.