Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012662.1 Corchorus capsularis cultivar CVL-1 contig12683, 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: 2451
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Found at i:233 original size:28 final size:27
Alignment explanation
Indices: 200--253 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
190 ATTACTATGC
*
200 TAAAATTTCTAAGAATGCAAGGTTACT
1 TAAAAATTCTAAGAATGCAAGGTTACT
* **
227 TAAAAATTCTTAGAATGTGAGGTTACT
1 TAAAAATTCTAAGAATGCAAGGTTACT
254 AAATTTATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (27 bp):
TAAAAATTCTAAGAATGCAAGGTTACT
Found at i:637 original size:27 final size:27
Alignment explanation
Indices: 607--706 Score: 132
Period size: 27 Copynumber: 3.7 Consensus size: 27
597 AGGAAAAAAA
607 ACATAATATGATTTCAAAAATTCCAAT
1 ACATAATATGATTTCAAAAATTCCAAT
* *
634 ACATAATATGATTTCAAAAATTTCAAA
1 ACATAATATGATTTCAAAAATTCCAAT
* *
661 ACTTCCAATA--ATTTCCAAAATTCCAAT
1 ACAT--AATATGATTTCAAAAATTCCAAT
688 ACATAATATGATTTCAAAA
1 ACATAATATGATTTCAAAA
707 CACTAAGTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
25 4 0.07
27 53 0.87
29 4 0.07
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (27 bp):
ACATAATATGATTTCAAAAATTCCAAT
Found at i:675 original size:18 final size:18
Alignment explanation
Indices: 652--688 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
642 TGATTTCAAA
652 AATTT-CAAAACTTCCAAT
1 AATTTCCAAAA-TTCCAAT
670 AATTTCCAAAATTCCAAT
1 AATTTCCAAAATTCCAAT
688 A
1 A
689 CATAATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTTCCAAAATTCCAAT
Found at i:2347 original size:199 final size:200
Alignment explanation
Indices: 1695--2451 Score: 974
Period size: 199 Copynumber: 3.8 Consensus size: 200
1685 TTGGCACAAA
* * * * *
1695 AACTTCTTAATTCGCTTATGGAATCCAAAATTTACATTGACAGTGTATTGTATAATAATCCTACA
1 AACTTCTTAATCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAATAATCCTATA
* * *
1760 AGAAAATTTATACAATACACCGTAAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAA
66 AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAAACTGCACGTGCGGGG------TTTAA
* *
1825 GGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATT-AA-ATAT--TTAATAAT-AAAATG
125 GGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATAATTAATTATGAAAATG
1885 GGGTATGTGTC
190 GGGTATGTGTC
* * *
1896 AACTTCTTAATCTGCTTATGGAGTCCAAAATTTACACTGACTATGTAATATTATATAATAATTCT
1 AACTTCTTAATCCGCTTATGGAGTCCAAAATTTACACTGAC-A-GT-ATATTGTATAATAATCCT
* * * *
1961 ATAAGAAAAATTATACAATAC-CCGTCAGTGAATTTTAGCAAACTGCACGTGCAGGATTTAAGGG
63 ATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAAACTGCACGTGCGGGGTTTAAGGG
* *
2025 TTGATATGTGTCCCCTTAGGAAATATGTATTAATATTAAATATATAATTAATTATG-AAATGGGG
128 TTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATAATTAATTATGAAAATGGGG
2089 TATGTGTC
193 TATGTGTC
* * * * * *
2097 AACTTCTTAATCCGCTTATGAAGTTCAAAATTTATACTAACAGTGTATTGTATAATAATCCTGTA
1 AACTTCTTAATCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAATAATCCTATA
** * * * * * *
2162 AGAAAAATTATGTAATACACAGTTAGTGTAGTTTAGCAGACTGCACATGCGGGGGTTAAGGGTTG
66 AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAAACTGCACGTGCGGGGTTTAAGGGTTG
* *
2227 ACATGTATTCCCTTA-GGAATATGTATTAATATTAAATATATAATTAATTATGAAAAT-GGGTAT
131 ACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATAATTAATTATGAAAATGGGGTAT
2290 GTGTC
196 GTGTC
* * * * *
2295 AAATTTCTTAACCCGCTTATGGCGTCCAAAATTTATACTGACAGTATATTGTATAATAACCCTAT
1 -AACTTCTTAATCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAATAATCCTAT
**
2360 AAGAAAAATTATGGAATACACCGTCAGTGGAGTTTAAGCAAACTGCACGTGCGGGGTTTAAGGGT
65 AAGAAAAATTATACAATACACCGTCAGTGGAGTTT-AGCAAACTGCACGTGCGGGGTTTAAGGGT
2425 TGACATGTGTCCCCTTAGGGAATATGT
129 TGACATGTGTCCCCTTAGGGAATATGT
Statistics
Matches: 482, Mismatches: 61, Indels: 26
0.85 0.11 0.05
Matches are distributed among these distances:
197 42 0.09
198 82 0.17
199 145 0.30
200 42 0.09
201 105 0.22
202 1 0.00
203 31 0.06
204 34 0.07
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (200 bp):
AACTTCTTAATCCGCTTATGGAGTCCAAAATTTACACTGACAGTATATTGTATAATAATCCTATA
AGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAAACTGCACGTGCGGGGTTTAAGGGTTG
ACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATAATTAATTATGAAAATGGGGTAT
GTGTC
Done.