Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 144 of 144
Found at i:38725487 original size:36 final size:36
Alignment explanation
Indices: 38725373--38725487 Score: 124
Period size: 37 Copynumber: 3.2 Consensus size: 36
38725363 AGAGTTTAGA
* *
38725373 GTTTAGGGTTTTAGGGTTTAAGGGCTCGGGGCTCGGG
1 GTTTAGGGTTTT-GGGGTTAAGGGTTCGGGGCTCGGG
* * * *
38725410 GCTTAGGG-CTTAGGGTTTAGGGTTCGGGGCTCGGG
1 GTTTAGGGTTTTGGGGTTAAGGGTTCGGGGCTCGGG
** *
38725445 GCTTTAGGGTTTTGGGGTTCGGGGTTCGGGGTTCGGG
1 G-TTTAGGGTTTTGGGGTTAAGGGTTCGGGGCTCGGG
38725482 GTTTAG
1 GTTTAG
38725488 TTGATCTTTC
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
35 21 0.33
36 13 0.20
37 30 0.47
ACGTcount: A:0.08, C:0.11, G:0.48, T:0.33
Consensus pattern (36 bp):
GTTTAGGGTTTTGGGGTTAAGGGTTCGGGGCTCGGG
Found at i:38727406 original size:30 final size:31
Alignment explanation
Indices: 38727354--38727411 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
38727344 TTGGAGTTTG
38727354 AATTTTTTATAATTATTTA-TTTTAAATTTA
1 AATTTTTTATAATTATTTATTTTTAAATTTA
38727384 AATTTTTTAT-A-TATTTCAATTTTTAAAT
1 AATTTTTTATAATTATTT--ATTTTTAAAT
38727412 ATTTGTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 5 0.20
29 1 0.04
30 11 0.44
31 8 0.32
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (31 bp):
AATTTTTTATAATTATTTATTTTTAAATTTA
Found at i:38734760 original size:14 final size:14
Alignment explanation
Indices: 38734743--38734786 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
38734733 GTTCGGGGTT
38734743 CGGGGTCCGAGG-TC
1 CGGGGTCCG-GGCTC
38734757 CGGGGTTCCGGGCTC
1 CGGGG-TCCGGGCTC
*
38734772 CGGGCTCCGGGCTC
1 CGGGGTCCGGGCTC
38734786 C
1 C
38734787 TTCTCCGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.02, C:0.36, G:0.45, T:0.16
Consensus pattern (14 bp):
CGGGGTCCGGGCTC
Found at i:38734773 original size:22 final size:21
Alignment explanation
Indices: 38734736--38734782 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
38734726 TTTTAGGGTT
*
38734736 CGGGGTTCGGGGTCCGAGG-TC
1 CGGGGTTCGGGCTCCG-GGCTC
38734757 CGGGGTTCCGGGCTCCGGGCTC
1 CGGGGTT-CGGGCTCCGGGCTC
38734779 CGGG
1 CGGG
38734783 CTCCTTCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.02, C:0.30, G:0.51, T:0.17
Consensus pattern (21 bp):
CGGGGTTCGGGCTCCGGGCTC
Found at i:38740933 original size:40 final size:40
Alignment explanation
Indices: 38740888--38740971 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
38740878 TGAACACAGT
*
38740888 AAAATTACAGTTACTTTAAAATATTTGATATATGTATATA
1 AAAATTACAATTACTTTAAAATATTTGATATATGTATATA
*
38740928 AAAATTACAATTATTTTAAAATATTTGATATATGTATATA
1 AAAATTACAATTACTTTAAAATATTTGATATATGTATATA
38740968 AAAA
1 AAAA
38740972 ATATTTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (40 bp):
AAAATTACAATTACTTTAAAATATTTGATATATGTATATA
Found at i:38743878 original size:21 final size:21
Alignment explanation
Indices: 38743818--38743883 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
38743808 GTTTTAATGA
* * *
38743818 TTTAGGGTTTAAGGTTTGAAA
1 TTTAAGGTTTAAGGTTTGGAG
* **
38743839 TTTAAAGTTTGGGGTTTGGAG
1 TTTAAGGTTTAAGGTTTGGAG
*
38743860 TTTAAGGTTTAAGGTTTGGGG
1 TTTAAGGTTTAAGGTTTGGAG
38743881 TTT
1 TTT
38743884 GGGGTTTGGG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (21 bp):
TTTAAGGTTTAAGGTTTGGAG
Found at i:38743896 original size:6 final size:7
Alignment explanation
Indices: 38743845--38743921 Score: 79
Period size: 7 Copynumber: 11.4 Consensus size: 7
38743835 GAAATTTAAA
38743845 GTTTGGG
1 GTTTGGG
*
38743852 GTTTGGA
1 GTTTGGG
**
38743859 GTTTAAG
1 GTTTGGG
**
38743866 GTTTAAG
1 GTTTGGG
38743873 GTTTGGG
1 GTTTGGG
38743880 GTTTGGG
1 GTTTGGG
38743887 GTTT-GG
1 GTTTGGG
38743893 GTTTGGG
1 GTTTGGG
38743900 GTTT-GG
1 GTTTGGG
38743906 GTTT-GG
1 GTTTGGG
*
38743912 GTTTAGG
1 GTTTGGG
38743919 GTT
1 GTT
38743922 AGGGTTTAGG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
6 18 0.29
7 44 0.71
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.45
Consensus pattern (7 bp):
GTTTGGG
Found at i:38743896 original size:13 final size:14
Alignment explanation
Indices: 38743845--38743931 Score: 83
Period size: 13 Copynumber: 6.5 Consensus size: 14
38743835 GAAATTTAAA
* *
38743845 GTTTGGGGTTTGGA
1 GTTTAGGGTTTGGG
* **
38743859 GTTTAAGGTTTAAG
1 GTTTAGGGTTTGGG
*
38743873 GTTTGGGGTTTGGG
1 GTTTAGGGTTTGGG
38743887 GTTT-GGGTTTGGG
1 GTTTAGGGTTTGGG
38743900 GTTT-GGGTTT-GG
1 GTTTAGGGTTTGGG
*
38743912 GTTTAGGG-TTAGG
1 GTTTAGGGTTTGGG
38743925 GTTTAGG
1 GTTTAGG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
12 8 0.13
13 31 0.50
14 23 0.37
ACGTcount: A:0.09, C:0.00, G:0.47, T:0.44
Consensus pattern (14 bp):
GTTTAGGGTTTGGG
Found at i:38743930 original size:7 final size:7
Alignment explanation
Indices: 38743845--38743931 Score: 76
Period size: 7 Copynumber: 13.0 Consensus size: 7
38743835 GAAATTTAAA
*
38743845 GTTTGGG
1 GTTTAGG
38743852 GTTT-GG
1 GTTTAGG
*
38743858 AGTTTAAG
1 -GTTTAGG
*
38743866 GTTTAAG
1 GTTTAGG
*
38743873 GTTTGGG
1 GTTTAGG
*
38743880 GTTTGGG
1 GTTTAGG
38743887 GTTT-GG
1 GTTTAGG
*
38743893 GTTTGGG
1 GTTTAGG
38743900 GTTT-GG
1 GTTTAGG
38743906 GTTT-GG
1 GTTTAGG
38743912 GTTTAGG
1 GTTTAGG
38743919 G-TTAGG
1 GTTTAGG
38743925 GTTTAGG
1 GTTTAGG
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
6 26 0.36
7 45 0.62
8 1 0.01
ACGTcount: A:0.09, C:0.00, G:0.47, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Done.