Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_D_gene_10026503
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: 3402
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Found at i:1770 original size:66 final size:66
Alignment explanation
Indices: 1684--2003 Score: 475
Period size: 66 Copynumber: 4.8 Consensus size: 66
1674 ACCCGCGCAG
* * *
1684 CCAAGTGCAAATCCAC-ATGGCCAGCTTGCTCAGCCCAGTGCTAATCCATATGGCCAAAATGGGC
1 CCAAGTGCTAATCC-CTATGGCCAGCCTGCTCAGCCCAGTGCTAACCCATATGGCCAAAATGGGC
1748 AA
65 AA
* *
1750 CCAAGTGCTAATCCCTATGGCCAGCCTGCGCAGCCCAGTGCTAATCCATATGGCCAAAATGGGCA
1 CCAAGTGCTAATCCCTATGGCCAGCCTGCTCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
1815 A
66 A
*
1816 CCAAGTGCTAATCCCTATGGCCAGCCTGCGCAGCCCAGTGCTAACCCATATGGCCAAAATGGGC-
1 CCAAGTGCTAATCCCTATGGCCAGCCTGCTCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
1880 A
66 A
** *
1881 CTCAAGTGCTAATCCCTATGGCCAGCCTG-TGCAGCCCAGTGCTAACCCATACAGCCAAAACGGG
1 C-CAAGTGCTAATCCCTATGGCCAGCCTGCT-CAGCCCAGTGCTAACCCATATGGCCAAAATGGG
*
1945 CAG
64 CAA
* * *
1948 CCAAGTGCTAATCCCTATGGCCTGCCTGCTCAACCCAGTGCAAACCCATATGGCCA
1 CCAAGTGCTAATCCCTATGGCCAGCCTGCTCAGCCCAGTGCTAACCCATATGGCCA
2004 GTCAAGTGCT
Statistics
Matches: 235, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
65 3 0.01
66 230 0.98
67 2 0.01
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (66 bp):
CCAAGTGCTAATCCCTATGGCCAGCCTGCTCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
A
Found at i:1988 original size:33 final size:33
Alignment explanation
Indices: 1678--2004 Score: 252
Period size: 33 Copynumber: 9.9 Consensus size: 33
1668 GTACCAACCC
* * *
1678 GCGCAGCCAAGTGCAAATCCAC-ATGGCCAGCTT
1 GCGCAGCCCAGTGCTAATCC-CTATGGCCAGCCT
* * ***
1711 GCTCAGCCCAGTGCTAATCCATATGGCCAAAAT
1 GCGCAGCCCAGTGCTAATCCCTATGGCCAGCCT
* * *
1744 GGGCAACCAAGTGCTAATCCCTATGGCCAGCCT
1 GCGCAGCCCAGTGCTAATCCCTATGGCCAGCCT
* ***
1777 GCGCAGCCCAGTGCTAATCCATATGGCCAAAAT
1 GCGCAGCCCAGTGCTAATCCCTATGGCCAGCCT
* * *
1810 GGGCAACCAAGTGCTAATCCCTATGGCCAGCCT
1 GCGCAGCCCAGTGCTAATCCCTATGGCCAGCCT
***
1843 GCGCAGCCCAGTGCTAA-CCCATATGGCCAAAAT
1 GCGCAGCCCAGTGCTAATCCC-TATGGCCAGCCT
* *
1876 GGGCA-CTCAAGTGCTAATCCCTATGGCCAGCCT
1 GCGCAGC-CCAGTGCTAATCCCTATGGCCAGCCT
* ** **
1909 GTGCAGCCCAGTGCTAA-CCCATACAGCCAAAAC-
1 GCGCAGCCCAGTGCTAATCCC-TATGGCC-AGCCT
* * *
1942 GGGCAGCCAAGTGCTAATCCCTATGGCCTGCCT
1 GCGCAGCCCAGTGCTAATCCCTATGGCCAGCCT
* * *
1975 GCTCAACCCAGTGC-AAACCCATATGGCCAG
1 GCGCAGCCCAGTGCTAATCCC-TATGGCCAG
2005 TCAAGTGCTA
Statistics
Matches: 225, Mismatches: 59, Indels: 20
0.74 0.19 0.07
Matches are distributed among these distances:
32 13 0.06
33 203 0.90
34 9 0.04
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.17
Consensus pattern (33 bp):
GCGCAGCCCAGTGCTAATCCCTATGGCCAGCCT
Found at i:2057 original size:33 final size:33
Alignment explanation
Indices: 2010--2183 Score: 150
Period size: 33 Copynumber: 5.3 Consensus size: 33
2000 GCCAGTCAAG
* * **
2010 TGCTAATCCCTATGGCCAGCCAACACAACCAAA
1 TGCTAATCCCTATGGTCAACCTGCACAACCAAA
* * *
2043 TGCTATTCCTTATGGTCAATCTGCACAACCAAA
1 TGCTAATCCCTATGGTCAACCTGCACAACCAAA
*
2076 TGCTAATCCGTATGGTCAACCTGCACAACCAAA
1 TGCTAATCCCTATGGTCAACCTGCACAACCAAA
* ** * * *** *
2109 TGCTAATCCATACAGCCAACCTGTACAGGTACA
1 TGCTAATCCCTATGGTCAACCTGCACAACCAAA
* * * * *
2142 TGCTAATCCATATGGCCAACCTGCTCAGCCGAA
1 TGCTAATCCCTATGGTCAACCTGCACAACCAAA
2175 TGCTAATCC
1 TGCTAATCC
2184 ATACAGCCAG
Statistics
Matches: 114, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 114 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (33 bp):
TGCTAATCCCTATGGTCAACCTGCACAACCAAA
Found at i:2145 original size:66 final size:65
Alignment explanation
Indices: 2074--2318 Score: 303
Period size: 66 Copynumber: 3.7 Consensus size: 65
2064 TGCACAACCA
* * * * * **
2074 AATGCTAATCCGTATGGTCAACCTGCACAACCAAATGCTAATCCATACAGCCAACCTGTACAG-G
1 AATGCTAATCCATACGGCCAACCTGCACAGCCAAATGCTAATCCATACAGCCAGCCTACACAGCG
* * *
2138 TACATGCTAATCCATATGGCCAACCTGCTCAGCCGAATGCTAATCCATACAGCCAGCCTACACAG
1 -A-ATGCTAATCCATACGGCCAACCTGCACAGCCAAATGCTAATCCATACAGCCAGCCTACACAG
2203 CCG
64 -CG
* * * *
2206 AATGCTAATCCATACAGCCAGCCTACACAGCCGAATGCTAATCCATACAGCCAGCCTACACAGCC
1 AATGCTAATCCATACGGCCAACCTGCACAGCCAAATGCTAATCCATACAGCCAGCCTACACAG-C
2271 G
65 G
* *
2272 AATGCTAATCCATACGGCCAACCTGTACAGCCAAGTGCTAATCCATA
1 AATGCTAATCCATACGGCCAACCTGCACAGCCAAATGCTAATCCATA
2319 TGCCCAACCC
Statistics
Matches: 158, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.01
66 155 0.98
67 1 0.01
68 1 0.01
ACGTcount: A:0.33, C:0.33, G:0.16, T:0.19
Consensus pattern (65 bp):
AATGCTAATCCATACGGCCAACCTGCACAGCCAAATGCTAATCCATACAGCCAGCCTACACAGCG
Found at i:2182 original size:99 final size:98
Alignment explanation
Indices: 2041--2318 Score: 306
Period size: 99 Copynumber: 2.8 Consensus size: 98
2031 AACACAACCA
* * * * * * * * * *
2041 AATGCTATTCCTTATGGTCAATCTGCACAACCAAATGCTAATCCGTATGGTCAACCTGCACAACC
1 AATGCTAATCCATATGGCCAACCTGCACAGCCGAATGCTAATCCATACGGCCAACCTGCACAGCC
**
2106 AAATGCTAATCCATACAGCCAACCTGTACAG-G
66 AAATGCTAATCCATACAGCCAACCTACACAGCG
* * * *
2138 TACATGCTAATCCATATGGCCAACCTGCTCAGCCGAATGCTAATCCATACAGCCAGCCTACACAG
1 -A-ATGCTAATCCATATGGCCAACCTGCACAGCCGAATGCTAATCCATACGGCCAACCTGCACAG
* *
2203 CCGAATGCTAATCCATACAGCCAGCCTACACAGCCG
64 CCAAATGCTAATCCATACAGCCAACCTACACAG-CG
** * * *
2239 AATGCTAATCCATACAGCCAGCCTACACAGCCGAATGCTAATCCATACGGCCAACCTGTACAGCC
1 AATGCTAATCCATATGGCCAACCTGCACAGCCGAATGCTAATCCATACGGCCAACCTGCACAGCC
*
2304 AAGTGCTAATCCATA
66 AAATGCTAATCCATA
2319 TGCCCAACCC
Statistics
Matches: 148, Mismatches: 29, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
98 1 0.01
99 145 0.98
100 1 0.01
101 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.20
Consensus pattern (98 bp):
AATGCTAATCCATATGGCCAACCTGCACAGCCGAATGCTAATCCATACGGCCAACCTGCACAGCC
AAATGCTAATCCATACAGCCAACCTACACAGCG
Found at i:2184 original size:33 final size:33
Alignment explanation
Indices: 2063--2327 Score: 275
Period size: 33 Copynumber: 8.0 Consensus size: 33
2053 TATGGTCAAT
* * * * *
2063 CTGCACAACCAAATGCTAATCCGTATGGTCAAC
1 CTGCACAGCCGAATGCTAATCCATACGGCCAAC
* * *
2096 CTGCACAACCAAATGCTAATCCATACAGCCAAC
1 CTGCACAGCCGAATGCTAATCCATACGGCCAAC
* *
2129 CTGTACAG--GTACATGCTAATCCATATGGCCAAC
1 CTGCACAGCCG-A-ATGCTAATCCATACGGCCAAC
* * *
2162 CTGCTCAGCCGAATGCTAATCCATACAGCCAGC
1 CTGCACAGCCGAATGCTAATCCATACGGCCAAC
* * *
2195 CTACACAGCCGAATGCTAATCCATACAGCCAGC
1 CTGCACAGCCGAATGCTAATCCATACGGCCAAC
* * *
2228 CTACACAGCCGAATGCTAATCCATACAGCCAGC
1 CTGCACAGCCGAATGCTAATCCATACGGCCAAC
*
2261 CTACACAGCCGAATGCTAATCCATACGGCCAAC
1 CTGCACAGCCGAATGCTAATCCATACGGCCAAC
* * *
2294 CTGTACAGCC-AAGTGCTAATCCATATGCCCAAC
1 CTGCACAGCCGAA-TGCTAATCCATACGGCCAAC
2327 C
1 C
2328 CACACAGTCT
Statistics
Matches: 205, Mismatches: 22, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
32 3 0.01
33 200 0.98
34 1 0.00
35 1 0.00
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.18
Consensus pattern (33 bp):
CTGCACAGCCGAATGCTAATCCATACGGCCAAC
Found at i:2224 original size:20 final size:20
Alignment explanation
Indices: 2199--2257 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
2189 GCCAGCCTAC
2199 ACAGCCGAATGCTAATCCAT
1 ACAGCCGAATGCTAATCCAT
2219 ACAGCC--A-GCCT-A--C--
1 ACAGCCGAATG-CTAATCCAT
2232 ACAGCCGAATGCTAATCCAT
1 ACAGCCGAATGCTAATCCAT
2252 ACAGCC
1 ACAGCC
2258 AGCCTACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 18
0.62 0.00 0.38
Matches are distributed among these distances:
13 6 0.20
15 4 0.13
16 2 0.07
17 2 0.07
18 4 0.13
20 12 0.40
ACGTcount: A:0.34, C:0.36, G:0.15, T:0.15
Consensus pattern (20 bp):
ACAGCCGAATGCTAATCCAT
Found at i:3075 original size:18 final size:17
Alignment explanation
Indices: 3054--3246 Score: 88
Period size: 18 Copynumber: 11.8 Consensus size: 17
3044 TGGGGATGAA
*
3054 CATGGGTATGAACCCAGG
1 CATGGGGATGAA-CCAGG
*
3072 CATGGGGATGAA-CA-A
1 CATGGGGATGAACCAGG
*
3087 CATGGGCATGAATCCAGG
1 CATGGGGATGAA-CCAGG
* *
3105 CATGGGGATG-AGCA-A
1 CATGGGGATGAACCAGG
* *
3120 TATGGGCATGAATCCAGG
1 CATGGGGATGAA-CCAGG
* *
3138 CATGGGGATG-AGCA-A
1 CATGGGGATGAACCAGG
* * *
3153 TATGGGCATGAATCAAGG
1 CATGGGGATGAA-CCAGG
3171 CATGGGGATG-A--A--
1 CATGGGGATGAACCAGG
*
3183 CATGGGCATGAATCCAGG
1 CATGGGGATGAA-CCAGG
*
3201 CATGGGGATGAA-CA-A
1 CATGGGGATGAACCAGG
* *
3216 CATGGGCATGAATCGAGG
1 CATGGGGATGAA-CCAGG
*
3234 CATGGAGATGAAC
1 CATGGGGATGAAC
3247 AATATAGGCA
Statistics
Matches: 127, Mismatches: 30, Indels: 37
0.65 0.15 0.19
Matches are distributed among these distances:
12 9 0.07
13 1 0.01
14 1 0.01
15 38 0.30
16 11 0.09
17 10 0.08
18 57 0.45
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.17
Consensus pattern (17 bp):
CATGGGGATGAACCAGG
Found at i:3098 original size:33 final size:33
Alignment explanation
Indices: 3052--3280 Score: 313
Period size: 33 Copynumber: 7.0 Consensus size: 33
3042 AATGGGGATG
* *
3052 AACATGGGTATGAACCCAGGCATGGGGATGAAC
1 AACATGGGCATGAATCCAGGCATGGGGATGAAC
*
3085 AACATGGGCATGAATCCAGGCATGGGGATGAGC
1 AACATGGGCATGAATCCAGGCATGGGGATGAAC
* *
3118 AATATGGGCATGAATCCAGGCATGGGGATGAGC
1 AACATGGGCATGAATCCAGGCATGGGGATGAAC
* *
3151 AATATGGGCATGAATCAAGGCATGGGGATG---
1 AACATGGGCATGAATCCAGGCATGGGGATGAAC
3181 AACATGGGCATGAATCCAGGCATGGGGATGAAC
1 AACATGGGCATGAATCCAGGCATGGGGATGAAC
* *
3214 AACATGGGCATGAATCGAGGCATGGAGATGAAC
1 AACATGGGCATGAATCCAGGCATGGGGATGAAC
* * *
3247 AATATAGGCATG-AGCGCAGGCATGGGGATGAAC
1 AACATGGGCATGAATC-CAGGCATGGGGATGAAC
3280 A
1 A
3281 TGGGAATGGG
Statistics
Matches: 178, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
30 28 0.16
32 2 0.01
33 148 0.83
ACGTcount: A:0.33, C:0.16, G:0.35, T:0.16
Consensus pattern (33 bp):
AACATGGGCATGAATCCAGGCATGGGGATGAAC
Found at i:3225 original size:129 final size:129
Alignment explanation
Indices: 3043--3277 Score: 391
Period size: 129 Copynumber: 1.8 Consensus size: 129
3033 GGGCATGGGA
*
3043 ATGGGGATGAACATGGGTATGAACCCAGGCATGGGGATGAACAACATGGGCATGAATCCAGGCAT
1 ATGGGGATGAACATGGGCATGAACCCAGGCATGGGGATGAACAACATGGGCATGAATCCAGGCAT
* * * *
3108 GGGGATGAGCAATATGGGCATGAATC-CAGGCATGGGGATGAGCAATATGGGCATGAATCAAGGC
66 GGAGATGAACAATATAGGCATG-AGCGCAGGCATGGGGATGAGCAATATGGGCATGAATCAAGGC
* *
3172 ATGGGGATGAACATGGGCATGAATCCAGGCATGGGGATGAACAACATGGGCATGAATCGAGGCAT
1 ATGGGGATGAACATGGGCATGAACCCAGGCATGGGGATGAACAACATGGGCATGAATCCAGGCAT
3237 GGAGATGAACAATATAGGCATGAGCGCAGGCATGGGGATGA
66 GGAGATGAACAATATAGGCATGAGCGCAGGCATGGGGATGA
3278 ACATGGGAAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
128 2 0.02
129 96 0.98
ACGTcount: A:0.32, C:0.15, G:0.36, T:0.17
Consensus pattern (129 bp):
ATGGGGATGAACATGGGCATGAACCCAGGCATGGGGATGAACAACATGGGCATGAATCCAGGCAT
GGAGATGAACAATATAGGCATGAGCGCAGGCATGGGGATGAGCAATATGGGCATGAATCAAGGC
Found at i:3281 original size:96 final size:96
Alignment explanation
Indices: 3061--3284 Score: 324
Period size: 96 Copynumber: 2.3 Consensus size: 96
3051 GAACATGGGT
* * *
3061 ATGAACCCAGGCATGGGGATGAACAACATGGGCATGAATCCAGGCATGGGGATGAGCAATATGGG
1 ATGAAGCCAGGCATGGGGATG---AACATGGGCATGAATCCAGGCATGGGGATGAACAACATGGG
* * *
3126 CATGAATCCAGGCATGGGGATGAGCAATATGGGC
63 CATGAATCCAGGCATGGAGATGAACAATATAGGC
* *
3160 ATGAATCAAGGCATGGGGATGAACATGGGCATGAATCCAGGCATGGGGATGAACAACATGGGCAT
1 ATGAAGCCAGGCATGGGGATGAACATGGGCATGAATCCAGGCATGGGGATGAACAACATGGGCAT
*
3225 GAATCGAGGCATGGAGATGAACAATATAGGC
66 GAATCCAGGCATGGAGATGAACAATATAGGC
3256 ATG-AGCGCAGGCATGGGGATGAACATGGG
1 ATGAAGC-CAGGCATGGGGATGAACATGGG
3285 AATGGGGCAG
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
95 2 0.02
96 93 0.82
99 19 0.17
ACGTcount: A:0.33, C:0.16, G:0.36, T:0.16
Consensus pattern (96 bp):
ATGAAGCCAGGCATGGGGATGAACATGGGCATGAATCCAGGCATGGGGATGAACAACATGGGCAT
GAATCCAGGCATGGAGATGAACAATATAGGC
Done.