Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009683.1 Corchorus capsularis cultivar CVL-1 contig09704, 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: 8128
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:361 original size:24 final size:24
Alignment explanation
Indices: 334--390 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
324 TCAAGTAGAG
* **
334 GATTCCAACCTCAGTCAAATCCAA
1 GATTGCAACCTCTATCAAATCCAA
358 GATTGCAACCTCTATCAAATCCAA
1 GATTGCAACCTCTATCAAATCCAA
382 GATTGCAAC
1 GATTGCAAC
391 GACAGCCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.23
Consensus pattern (24 bp):
GATTGCAACCTCTATCAAATCCAA
Found at i:2417 original size:16 final size:17
Alignment explanation
Indices: 2377--2421 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
2367 GAAAAACAAT
*
2377 CAATTAGAATGCCTAAAC
1 CAATTAAAATGCCT-AAC
*
2395 AAATTAAAATGCCT-AC
1 CAATTAAAATGCCTAAC
2411 CAATTAAAATG
1 CAATTAAAATG
2422 GAAGTGCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.50
18 12 0.50
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.24
Consensus pattern (17 bp):
CAATTAAAATGCCTAAC
Found at i:7003 original size:16 final size:16
Alignment explanation
Indices: 6865--7010 Score: 154
Period size: 16 Copynumber: 9.2 Consensus size: 16
6855 AGGAAAAGTA
6865 AATGACCCG-AACCCG
1 AATGACCCGAAACCCG
*** *
6880 CCCGACCCGAGACCCG
1 AATGACCCGAAACCCG
*
6896 AATGACCCGCAACCC-
1 AATGACCCGAAACCCG
* *
6911 ATATGACCCGAGACCCA
1 A-ATGACCCGAAACCCG
*
6928 AATGACCCGTAACCC-
1 AATGACCCGAAACCCG
6943 AGATGACCCGAAACCCG
1 A-ATGACCCGAAACCCG
*
6960 AATGACCCGTAACCCG
1 AATGACCCGAAACCCG
6976 AATGACCCGAAACCCG
1 AATGACCCGAAACCCG
* *
6992 TATGACCCGAAAGCCG
1 AATGACCCGAAACCCG
7008 AAT
1 AAT
7011 AATCCGAGAA
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
15 8 0.07
16 97 0.91
17 2 0.02
ACGTcount: A:0.33, C:0.39, G:0.19, T:0.09
Consensus pattern (16 bp):
AATGACCCGAAACCCG
Found at i:7130 original size:2 final size:2
Alignment explanation
Indices: 7123--7161 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
7113 AATACAATAA
7123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
7162 TATTTTTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7316 original size:11 final size:11
Alignment explanation
Indices: 7300--7342 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
7290 TATACTAAAT
7300 CTAATTAATAG
1 CTAATTAATAG
*
7311 CTAATTAATAT
1 CTAATTAATAG
7322 CTAATTAATAG
1 CTAATTAATAG
*
7333 TTAATTAATA
1 CTAATTAATA
7343 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:7326 original size:22 final size:22
Alignment explanation
Indices: 7298--7342 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
7288 ATTATACTAA
7298 ATCTAATTAATAGCTAATTAAT
1 ATCTAATTAATAGCTAATTAAT
*
7320 ATCTAATTAATAGTTAATTAAT
1 ATCTAATTAATAGCTAATTAAT
7342 A
1 A
7343 ATGAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (22 bp):
ATCTAATTAATAGCTAATTAAT
Found at i:7641 original size:24 final size:24
Alignment explanation
Indices: 7614--7694 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
7604 ACTTTAATTC
7614 ATTTTAAGTGTTGAATGATATTTT
1 ATTTTAAGTGTTGAATGATATTTT
** * * *
7638 ATTTTAAGTAAAT-AACT-TTAATTC
1 ATTTTAAGT-GTTGAA-TGATATTTT
7662 ATTTTAAGTGTTGAATGATATTTT
1 ATTTTAAGTGTTGAATGATATTTT
7686 ATTTTAAGT
1 ATTTTAAGT
7695 AAATAATTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
23 2 0.05
24 39 0.91
25 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (24 bp):
ATTTTAAGTGTTGAATGATATTTT
Found at i:7657 original size:48 final size:48
Alignment explanation
Indices: 7603--7700 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
7593 TTTCCTACTC
7603 AACTTTAATTCATTTTAAGTGTTGAATGATATTTTATTTTAAGTAAAT
1 AACTTTAATTCATTTTAAGTGTTGAATGATATTTTATTTTAAGTAAAT
7651 AACTTTAATTCATTTTAAGTGTTGAATGATATTTTATTTTAAGTAAAT
1 AACTTTAATTCATTTTAAGTGTTGAATGATATTTTATTTTAAGTAAAT
7699 AA
1 AA
7701 TTAACAATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (48 bp):
AACTTTAATTCATTTTAAGTGTTGAATGATATTTTATTTTAAGTAAAT
Done.