Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 182 of 182
Found at i:55708063 original size:14 final size:14
Alignment explanation
Indices: 55708032--55708100 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
55708022 GCTACGGGCT
*
55708032 TCGGGCTTCGGG-C
1 TCGGGGTTCGGGTC
55708045 TTCGGGGTTCGGGTC
1 -TCGGGGTTCGGGTC
55708060 TC-GGGTCTCGGGTC
1 TCGGGGT-TCGGGTC
* *
55708074 TCGGGTTTGGGGT-
1 TCGGGGTTCGGGTC
*
55708087 TTGGGGTCTCGGGT
1 TCGGGGT-TCGGGT
55708101 TTAGGGTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 9 0.20
14 32 0.71
15 4 0.09
ACGTcount: A:0.00, C:0.20, G:0.48, T:0.32
Consensus pattern (14 bp):
TCGGGGTTCGGGTC
Found at i:55708063 original size:21 final size:20
Alignment explanation
Indices: 55707996--55708341 Score: 103
Period size: 21 Copynumber: 16.3 Consensus size: 20
55707986 GGCTTAGGGC
*
55707996 TTCGGGCTTCGGGCTTCGGG
1 TTCGGGCTTCGGGGTTCGGG
* *
55708016 CTTCGGGCTACGGGCTTCGGG
1 -TTCGGGCTTCGGGGTTCGGG
55708037 CTTCGGGCTTCGGGGTTCGGG
1 -TTCGGGCTTCGGGGTTCGGG
55708058 TCTCGGG-TCTC-GGGTCTCGGG
1 T-TCGGGCT-TCGGGGT-TCGGG
* * *
55708079 TTTGGGGTTTGGGGTCTCGGG
1 TTCGGGCTTCGGGGT-TCGGG
* * * *
55708100 TTTAGGGTTTAAGGGGTTAGGG
1 -TTCGGGCTT-CGGGGTTCGGG
* * * ** *
55708122 TTAGGGCCTAGGGCCTAGGG
1 TTCGGGCTTCGGGGTTCGGG
* * * *
55708142 CTAGGGCCTATGGGTTAGGGGTTAGGGG
1 TTCGGG-C------TTCGGGGTT-CGGG
*
55708170 TTAGGG-TTCGGGGTTTCGGG
1 TTCGGGCTTCGGGG-TTCGGG
*
55708190 TTTTCGGGTTTCGGGGTTTCGGG
1 --TTCGGGCTTCGGGG-TTCGGG
*
55708213 TTTCGGGGC-TCGGGGCTCGGGG
1 -TTC-GGGCTTCGGGGTTC-GGG
* *
55708235 CTCGGGC-TCGGGGCTCGGG
1 TTCGGGCTTCGGGGTTCGGG
* *
55708254 TTTCGGGTTTCGGGTTTCGGG
1 -TTCGGGCTTCGGGGTTCGGG
* *
55708275 TTTCGGGTTTC-GGGTTAGGG
1 -TTCGGGCTTCGGGGTTCGGG
** *
55708295 -TCGGGGGTCGGGGGTCGGGG
1 TTCGGGCTTCGGGGTTC-GGG
*
55708315 TTCGGGGTTCGGGGTTCGGGG
1 TTCGGGCTTCGGGGTTC-GGG
55708336 TTCGGG
1 TTCGGG
55708342 GTTTTGGGTT
Statistics
Matches: 262, Mismatches: 37, Indels: 52
0.75 0.11 0.15
Matches are distributed among these distances:
18 7 0.03
19 7 0.03
20 62 0.24
21 121 0.46
22 29 0.11
23 22 0.08
27 6 0.02
28 8 0.03
ACGTcount: A:0.04, C:0.17, G:0.49, T:0.30
Consensus pattern (20 bp):
TTCGGGCTTCGGGGTTCGGG
Found at i:55708133 original size:7 final size:7
Alignment explanation
Indices: 55708123--55708151 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
55708113 GGGTTAGGGT
55708123 TAGGGCC
1 TAGGGCC
55708130 TAGGGCC
1 TAGGGCC
55708137 TAGGG-C
1 TAGGGCC
55708143 TAGGGCC
1 TAGGGCC
55708150 TA
1 TA
55708152 TGGGTTAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (7 bp):
TAGGGCC
Found at i:55708160 original size:20 final size:19
Alignment explanation
Indices: 55708113--55708161 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
55708103 AGGGTTTAAG
*
55708113 GGGTTAGGGTTAGGGCCTA
1 GGGTTAGGGCTAGGGCCTA
*
55708132 GGGCCTAGGGCTAGGGCCTA
1 GGG-TTAGGGCTAGGGCCTA
55708152 TGGGTTAGGG
1 -GGGTTAGGG
55708162 GTTAGGGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.14, C:0.14, G:0.49, T:0.22
Consensus pattern (19 bp):
GGGTTAGGGCTAGGGCCTA
Found at i:55708182 original size:13 final size:14
Alignment explanation
Indices: 55708076--55708184 Score: 53
Period size: 13 Copynumber: 7.9 Consensus size: 14
55708066 CTCGGGTCTC
* *
55708076 GGGTTTGGGGTTTG
1 GGGTTAGGGGTTAG
* *
55708090 GGGTCTCGGGTTTAG
1 GGGT-TAGGGGTTAG
*
55708105 GGTTTAAGGGGTTA-
1 GGGTT-AGGGGTTAG
**
55708119 GGGTTAGGGCCTAG
1 GGGTTAGGGGTTAG
** *
55708133 GGCCTA-GGGCTAG
1 GGGTTAGGGGTTAG
** *
55708146 GGCCTATGGGTTAG
1 GGGTTAGGGGTTAG
55708160 GGGTTAGGGGTTA-
1 GGGTTAGGGGTTAG
*
55708173 GGGTTCGGGGTT
1 GGGTTAGGGGTT
55708185 TCGGGTTTTC
Statistics
Matches: 74, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
13 29 0.39
14 29 0.39
15 16 0.22
ACGTcount: A:0.11, C:0.09, G:0.50, T:0.30
Consensus pattern (14 bp):
GGGTTAGGGGTTAG
Found at i:55708190 original size:7 final size:7
Alignment explanation
Indices: 55708180--55708359 Score: 125
Period size: 7 Copynumber: 25.9 Consensus size: 7
55708170 TTAGGGTTCG
55708180 GGGTTTC
1 GGGTTTC
55708187 GGGTTTTC
1 GGG-TTTC
55708195 GGGTTTC
1 GGGTTTC
55708202 GGGGTTTC
1 -GGGTTTC
55708210 GGGTTTC
1 GGGTTTC
**
55708217 GGGGCTC
1 GGGTTTC
**
55708224 GGGGCTC
1 GGGTTTC
**
55708231 GGGGCTC
1 GGGTTTC
*
55708238 GGG-CTC
1 GGGTTTC
**
55708244 GGGGCTC
1 GGGTTTC
55708251 GGGTTTC
1 GGGTTTC
55708258 GGGTTTC
1 GGGTTTC
55708265 GGGTTTC
1 GGGTTTC
55708272 GGGTTTC
1 GGGTTTC
55708279 GGGTTTC
1 GGGTTTC
*
55708286 GGG-TTA
1 GGGTTTC
55708292 GGG--TC
1 GGGTTTC
**
55708297 GGGGGTC
1 GGGTTTC
**
55708304 GGGGGTC
1 GGGTTTC
*
55708311 GGGGTTC
1 GGGTTTC
*
55708318 GGGGTTC
1 GGGTTTC
*
55708325 GGGGTTC
1 GGGTTTC
*
55708332 GGGGTTC
1 GGGTTTC
*
55708339 GGGGTTTT
1 -GGGTTTC
*
55708347 GGGTTTT
1 GGGTTTC
55708354 GGGTTT
1 GGGTTT
Statistics
Matches: 158, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
5 4 0.03
6 11 0.07
7 124 0.78
8 19 0.12
ACGTcount: A:0.01, C:0.15, G:0.51, T:0.33
Consensus pattern (7 bp):
GGGTTTC
Found at i:55708243 original size:13 final size:13
Alignment explanation
Indices: 55708215--55708253 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
55708205 GTTTCGGGTT
55708215 TCGGGGCTCGGGGC
1 TCGGGGCTC-GGGC
55708229 TCGGGGCTCGGGC
1 TCGGGGCTCGGGC
55708242 TCGGGGCTCGGG
1 TCGGGGCTCGGG
55708254 TTTCGGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.00, C:0.28, G:0.56, T:0.15
Consensus pattern (13 bp):
TCGGGGCTCGGGC
Found at i:55708351 original size:14 final size:14
Alignment explanation
Indices: 55708153--55708344 Score: 151
Period size: 14 Copynumber: 13.9 Consensus size: 14
55708143 TAGGGCCTAT
* *
55708153 GGGTTAGGGGTTAG
1 GGGTTCGGGGTTCG
*
55708167 GGGTT-AGGGTTCG
1 GGGTTCGGGGTTCG
*
55708180 GGGTTTCGGGTTTTCG
1 GGG-TTCGGG-GTTCG
*
55708196 GGTTTCGGGGTTTCG
1 GGGTTCGGGG-TTCG
* *
55708211 GGTTTCGGGGCTCG
1 GGGTTCGGGGTTCG
* *
55708225 GGGCTCGGGGCTC-
1 GGGTTCGGGGTTCG
* *
55708238 GGGCTCGGGGCTCG
1 GGGTTCGGGGTTCG
* *
55708252 GGTTTCGGGTTTCG
1 GGGTTCGGGGTTCG
* *
55708266 GGTTTCGGGTTTCG
1 GGGTTCGGGGTTCG
* *
55708280 GGTTTC-GGGTT-A
1 GGGTTCGGGGTTCG
*
55708292 GGG-TCGGGGGTCG
1 GGGTTCGGGGTTCG
*
55708305 GGGGTCGGGGTTCG
1 GGGTTCGGGGTTCG
55708319 GGGTTCGGGGTTCG
1 GGGTTCGGGGTTCG
55708333 GGGTTCGGGGTT
1 GGGTTCGGGGTT
55708345 TTGGGTTTTG
Statistics
Matches: 150, Mismatches: 20, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
11 2 0.01
12 6 0.04
13 29 0.19
14 85 0.57
15 22 0.15
16 6 0.04
ACGTcount: A:0.02, C:0.15, G:0.53, T:0.31
Consensus pattern (14 bp):
GGGTTCGGGGTTCG
Found at i:55708358 original size:21 final size:21
Alignment explanation
Indices: 55708153--55708344 Score: 151
Period size: 21 Copynumber: 9.2 Consensus size: 21
55708143 TAGGGCCTAT
* * *
55708153 GGGTTAGGGGTTAGGGGTT-A
1 GGGTTCGGGGTTCGGGGTTCG
*
55708173 GGGTTCGGGGTTTCGGGTTTTCG
1 GGGTTCGGGG-TTCGGG-GTTCG
* *
55708196 GGTTTCGGGGTTTCGGGTTTCG
1 GGGTTCGGGG-TTCGGGGTTCG
* * *
55708218 GGGCTCGGGGCTCGGGGCTC-
1 GGGTTCGGGGTTCGGGGTTCG
* * *
55708238 GGGCTCGGGGCTCGGGTTTCG
1 GGGTTCGGGGTTCGGGGTTCG
* * *
55708259 GGTTTCGGGTTTCGGGTTTCG
1 GGGTTCGGGGTTCGGGGTTCG
* *
55708280 GGTTTC-GGGTT-AGGG-TCG
1 GGGTTCGGGGTTCGGGGTTCG
* *
55708298 GGGGTCGGGGGTCGGGGTTCG
1 GGGTTCGGGGTTCGGGGTTCG
55708319 GGGTTCGGGGTTCGGGGTTCG
1 GGGTTCGGGGTTCGGGGTTCG
55708340 GGGTT
1 GGGTT
55708345 TTGGGTTTTG
Statistics
Matches: 140, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.05
19 6 0.04
20 34 0.24
21 62 0.44
22 15 0.11
23 16 0.11
ACGTcount: A:0.02, C:0.15, G:0.53, T:0.31
Consensus pattern (21 bp):
GGGTTCGGGGTTCGGGGTTCG
Done.