Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 135 of 135
Found at i:43670861 original size:28 final size:28
Alignment explanation
Indices: 43670821--43670877 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
43670811 AATATTTATG
43670821 ACTCAACTTGTCGGAGTTGTAGTCTCGA
1 ACTCAACTTGTCGGAGTTGTAGTCTCGA
43670849 ACTCAACTTGTCGGAGTTGTAGTCTCGA
1 ACTCAACTTGTCGGAGTTGTAGTCTCGA
43670877 A
1 A
43670878 ACCACTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (28 bp):
ACTCAACTTGTCGGAGTTGTAGTCTCGA
Found at i:43676306 original size:25 final size:25
Alignment explanation
Indices: 43676249--43676308 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
43676239 TGTTAAATGA
*
43676249 TTATATGAAACGGCTATACGAAATC
1 TTATATGGAACGGCTATACGAAATC
*
43676274 TTATATGGATCGGCTATACGAAATC
1 TTATATGGAACGGCTATACGAAATC
43676299 TTATATGGAA
1 TTATATGGAA
43676309 ATAGATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (25 bp):
TTATATGGAACGGCTATACGAAATC
Found at i:43676342 original size:13 final size:13
Alignment explanation
Indices: 43676314--43676349 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
43676304 TGGAAATAGA
*
43676314 TATATGAAATGGT
1 TATATGAAGTGGT
*
43676327 TATATGAAGTGTT
1 TATATGAAGTGGT
43676340 TATATGAAGT
1 TATATGAAGT
43676350 ATTTGTAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (13 bp):
TATATGAAGTGGT
Found at i:43681521 original size:81 final size:81
Alignment explanation
Indices: 43681386--43681541 Score: 303
Period size: 81 Copynumber: 1.9 Consensus size: 81
43681376 ACATTTAAAA
43681386 AAAAAATCTAATTCTTTGTCCTTACACATTAAAATCAAATCCGCATTCTATTTTTTTCTAGGTAT
1 AAAAAATCTAATTCTTTGTCCTTACACATTAAAATCAAATCCGCATTCTATTTTTTTCTAGGTAT
43681451 CAAAACTCACTCGTTT
66 CAAAACTCACTCGTTT
*
43681467 AAAAAATCTAATTCTTTGTCCTTACACATTAAAATCAAATCCGCATTCTATTTTTTTTTAGGTAT
1 AAAAAATCTAATTCTTTGTCCTTACACATTAAAATCAAATCCGCATTCTATTTTTTTCTAGGTAT
43681532 CAAAACTCAC
66 CAAAACTCAC
43681542 CCGATTCCTT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 74 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.39
Consensus pattern (81 bp):
AAAAAATCTAATTCTTTGTCCTTACACATTAAAATCAAATCCGCATTCTATTTTTTTCTAGGTAT
CAAAACTCACTCGTTT
Found at i:43682946 original size:63 final size:63
Alignment explanation
Indices: 43682847--43682974 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
43682837 TCATTAGTGC
43682847 TTGCCCTGCTCAAACTCATTACTTACCTTATTTGCTCTTATTATTATCAAAATATCTTGGTTA
1 TTGCCCTGCTCAAACTCATTACTTACCTTATTTGCTCTTATTATTATCAAAATATCTTGGTTA
43682910 TTGCCCTGCTCAAACTCATTACTTACCTTATTTGCTCTTATTATTATCAAAATATCTTGGTTA
1 TTGCCCTGCTCAAACTCATTACTTACCTTATTTGCTCTTATTATTATCAAAATATCTTGGTTA
43682973 TT
1 TT
43682975 TACTTGTATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (63 bp):
TTGCCCTGCTCAAACTCATTACTTACCTTATTTGCTCTTATTATTATCAAAATATCTTGGTTA
Found at i:43683996 original size:7 final size:7
Alignment explanation
Indices: 43683972--43684068 Score: 68
Period size: 7 Copynumber: 13.9 Consensus size: 7
43683962 GGACTTAAGT
43683972 TTTAGGG
1 TTTAGGG
* *
43683979 CTTAAGG
1 TTTAGGG
43683986 TTTAGGG
1 TTTAGGG
43683993 TTTAGGG
1 TTTAGGG
*
43684000 TTTAGTG
1 TTTAGGG
*
43684007 TTTAAGG
1 TTTAGGG
**
43684014 CCTAGGG
1 TTTAGGG
* *
43684021 CTTAAGG
1 TTTAGGG
* *
43684028 TTTCGTG
1 TTTAGGG
* *
43684035 TCTATGG
1 TTTAGGG
43684042 TTTAGGG
1 TTTAGGG
*
43684049 TTTAAGG
1 TTTAGGG
*
43684056 TTTAAGG
1 TTTAGGG
43684063 TTTAGG
1 TTTAGG
43684069 ATTAAAGTGT
Statistics
Matches: 66, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 66 1.00
ACGTcount: A:0.19, C:0.06, G:0.34, T:0.41
Consensus pattern (7 bp):
TTTAGGG
Found at i:43684064 original size:14 final size:14
Alignment explanation
Indices: 43683942--43684066 Score: 106
Period size: 14 Copynumber: 8.9 Consensus size: 14
43683932 TTGTATTATT
* *
43683942 GGTTTGGGGTCTAA
1 GGTTTAGGGTTTAA
**
43683956 GGTTTAGGACTTAA
1 GGTTTAGGGTTTAA
* *
43683970 GTTTTAGGGCTTAA
1 GGTTTAGGGTTTAA
*
43683984 GGTTTAGGGTTTAG
1 GGTTTAGGGTTTAA
*
43683998 GGTTTAGTGTTTAA
1 GGTTTAGGGTTTAA
** *
43684012 GGCCTAGGGCTTAA
1 GGTTTAGGGTTTAA
* * * *
43684026 GGTTTCGTGTCTAT
1 GGTTTAGGGTTTAA
43684040 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
*
43684054 GGTTTAAGGTTTA
1 GGTTTAGGGTTTA
43684067 GGATTAAAGT
Statistics
Matches: 84, Mismatches: 27, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 84 1.00
ACGTcount: A:0.19, C:0.06, G:0.34, T:0.41
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:43687032 original size:20 final size:18
Alignment explanation
Indices: 43686995--43687037 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
43686985 GATCGAGACT
43686995 TAAAATTGATTTAAAATAA
1 TAAAATTGATTTAAAAT-A
**
43687014 TAAAATATGATTTTTAATA
1 TAAAAT-TGATTTAAAATA
43687033 TAAAA
1 TAAAA
43687038 CACAAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
TAAAATTGATTTAAAATA
Found at i:43687606 original size:23 final size:22
Alignment explanation
Indices: 43687574--43687677 Score: 75
Period size: 23 Copynumber: 4.6 Consensus size: 22
43687564 GTTGGGGAAA
* *
43687574 CAGTAAGCACACACAATGTAAT
1 CAGTAGGCACACACAATGCAAT
*
43687596 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAATGCAAT
** * **
43687619 CAGTAGGTGCACATAGCGCAAAT
1 CAGTAGGCACACACAATGC-AAT
*
43687642 CAGTAGGCACACA-AAGTGCGAAA
1 CAGTAGGCACACACAA-TGC-AAT
*
43687665 CAGTAAGCACACA
1 CAGTAGGCACACA
43687678 AAGTGCGAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
22 16 0.25
23 49 0.75
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.13
Consensus pattern (22 bp):
CAGTAGGCACACACAATGCAAT
Found at i:43687678 original size:23 final size:23
Alignment explanation
Indices: 43687642--43687695 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
43687632 TAGCGCAAAT
*
43687642 CAGTAGGCACACAAAGTGCGAAA
1 CAGTAAGCACACAAAGTGCGAAA
43687665 CAGTAAGCACACAAAGTGCGAAA
1 CAGTAAGCACACAAAGTGCGAAA
43687688 CAGTAAGC
1 CAGTAAGC
43687696 GCGCTAGCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (23 bp):
CAGTAAGCACACAAAGTGCGAAA
Found at i:43692143 original size:24 final size:26
Alignment explanation
Indices: 43692116--43692166 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
43692106 GTTTAAAATG
43692116 AATATT-AAAAAAA-TTTAAGTATAA
1 AATATTCAAAAAAACTTTAAGTATAA
43692140 AATATTCAAAAAAACTTTAAGTATAA
1 AATATTCAAAAAAACTTTAAGTATAA
43692166 A
1 A
43692167 TAAATCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 6 0.24
25 7 0.28
26 12 0.48
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (26 bp):
AATATTCAAAAAAACTTTAAGTATAA
Found at i:43695145 original size:18 final size:18
Alignment explanation
Indices: 43695122--43695158 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
43695112 TTAATTTTTA
*
43695122 TGAATTATATATATATTT
1 TGAATTATATAAATATTT
*
43695140 TGAATTTTATAAATATTT
1 TGAATTATATAAATATTT
43695158 T
1 T
43695159 TTATATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TGAATTATATAAATATTT
Found at i:43696805 original size:20 final size:20
Alignment explanation
Indices: 43696780--43696819 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43696770 GATTCACGGT
*
43696780 TCATGTTTTAGGGTTTGAGC
1 TCATGTTTTAGGGTTGGAGC
*
43696800 TCATGTTTTATGGTTGGAGC
1 TCATGTTTTAGGGTTGGAGC
43696820 AATTTTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.30, T:0.45
Consensus pattern (20 bp):
TCATGTTTTAGGGTTGGAGC
Found at i:43696985 original size:22 final size:24
Alignment explanation
Indices: 43696946--43696995 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
43696936 TTGATTGATG
* *
43696946 TTTT-GGGTTTGAGAGTTT-ATGT
1 TTTTAGGGTTTAAGAGTTTAATAT
43696968 TTTTAGGGTTTAAG-GTTTAATAT
1 TTTTAGGGTTTAAGAGTTTAATAT
43696991 TTTTA
1 TTTTA
43696996 TGTTATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (24 bp):
TTTTAGGGTTTAAGAGTTTAATAT
Found at i:43698370 original size:26 final size:26
Alignment explanation
Indices: 43698318--43698370 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
43698308 ATAATAAAAC
*
43698318 TAAAAGTCTAATATTTGTAATTCTTT
1 TAAAAGTCTAATATTTGTAATTATTT
* *
43698344 TAAAAGTCTTATTATTTGT-TTTATTT
1 TAAAAGTC-TAATATTTGTAATTATTT
43698370 T
1 T
43698371 TGAACTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.57
Consensus pattern (26 bp):
TAAAAGTCTAATATTTGTAATTATTT
Found at i:43701892 original size:15 final size:15
Alignment explanation
Indices: 43701872--43701913 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
43701862 AAATTAAAAT
* *
43701872 TATTTAATAATTTTA
1 TATTTAAAAAATTTA
43701887 TATTTAAAAAAATTTA
1 TATTT-AAAAAATTTA
43701903 TATTTAAAAAA
1 TATTTAAAAAA
43701914 AATAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTAAAAAATTTA
Found at i:43701916 original size:17 final size:16
Alignment explanation
Indices: 43701883--43701914 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43701873 ATTTAATAAT
43701883 TTTATATTTAAAAAAA
1 TTTATATTTAAAAAAA
43701899 TTTATATTTAAAAAAA
1 TTTATATTTAAAAAAA
43701915 ATAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTATATTTAAAAAAA
Found at i:43701923 original size:15 final size:16
Alignment explanation
Indices: 43701886--43701924 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
43701876 TAATAATTTT
* *
43701886 ATATTTAAAAAAATTT
1 ATATTTAAAAAAAATA
43701902 ATATTTAAAAAAAATA
1 ATATTTAAAAAAAATA
43701918 AT-TTTAA
1 ATATTTAA
43701925 TAACTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTTAAAAAAAATA
Found at i:43711153 original size:7 final size:7
Alignment explanation
Indices: 43711136--43711324 Score: 371
Period size: 7 Copynumber: 27.1 Consensus size: 7
43711126 TTGATTTTAA
43711136 GGCTC-G
1 GGCTCGG
43711142 GGCTCGG
1 GGCTCGG
43711149 GGCTCGG
1 GGCTCGG
43711156 GGCTCGG
1 GGCTCGG
43711163 GGCTCGG
1 GGCTCGG
43711170 GGCTCGG
1 GGCTCGG
43711177 GGCTCGG
1 GGCTCGG
43711184 GGCTCGG
1 GGCTCGG
43711191 GGCTCGG
1 GGCTCGG
43711198 GGCTCGG
1 GGCTCGG
43711205 GGCTCGG
1 GGCTCGG
43711212 GGCTCGG
1 GGCTCGG
43711219 GGCTCGG
1 GGCTCGG
43711226 GGCTCGG
1 GGCTCGG
43711233 GGCTCGG
1 GGCTCGG
43711240 GGCTCGG
1 GGCTCGG
43711247 GGCTCGG
1 GGCTCGG
43711254 GGCTCGG
1 GGCTCGG
43711261 GGCTCGG
1 GGCTCGG
43711268 GGCTCGG
1 GGCTCGG
43711275 GGCTCGG
1 GGCTCGG
43711282 GGCTCGG
1 GGCTCGG
43711289 GGCTCGG
1 GGCTCGG
43711296 GGCTCGG
1 GGCTCGG
43711303 GGCTCGG
1 GGCTCGG
43711310 GGCTCGG
1 GGCTCGG
43711317 GGCTCGG
1 GGCTCGG
43711324 G
1 G
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
6 5 0.03
7 177 0.97
ACGTcount: A:0.00, C:0.29, G:0.57, T:0.14
Consensus pattern (7 bp):
GGCTCGG
Done.