Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_23086
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: 3005
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Found at i:1753 original size:33 final size:33
Alignment explanation
Indices: 1715--2039 Score: 217
Period size: 33 Copynumber: 9.8 Consensus size: 33
1705 ACCAACCCGC
* * *
1715 GCAGCCAAGTGCGAATCCATATGGCCAGCTTGC
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * ** *
1748 TCAGCCCAGTGCTAATCCATATGGCCAAAATGG
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * *
1781 GCAACCAAGTGCTAATCCCTATGGCCAGCCTGA
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
** *
1814 GCAGCCCAA-TGCTAATCCATATGGCCAAAATGG
1 GCAG-CCAAGTGCTAATCCATATGGCCAGCATGA
* * * *
1847 GCAACCAAGTGCTAATCCCTATGGCCAGCCTGT
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * * ** *
1880 GCAGCCCAGTACTAACCCATATGGCCAAAATGG
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * *
1913 GCA-CTCAAGTGCTAATCCCTATGGCCAGCCTGT
1 GCAGC-CAAGTGCTAATCCATATGGCCAGCATGA
* * ** ** * *
1946 GCAGCCCAGTGCTAACCCATACAGCCAAAACGG
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * *
1979 GCAGCCAAGTGCTAATCTC-TATGGCCTGCCTGC
1 GCAGCCAAGTGCTAATC-CATATGGCCAGCATGA
* * *
2012 GCCA-CCCAGTGCAAACCCATATGGCCAG
1 G-CAGCCAAGTGCTAATCCATATGGCCAG
2040 TCAAGTGCTA
Statistics
Matches: 217, Mismatches: 68, Indels: 14
0.73 0.23 0.05
Matches are distributed among these distances:
32 6 0.03
33 203 0.94
34 8 0.04
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.18
Consensus pattern (33 bp):
GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
Found at i:1804 original size:66 final size:65
Alignment explanation
Indices: 1719--2038 Score: 419
Period size: 66 Copynumber: 4.8 Consensus size: 65
1709 ACCCGCGCAG
* * * *
1719 CCAAGTGCGAATCCATATGGCCAGCTTGCTCAGCCCAGTGCTAATCCATATGGCCAAAATGGGCA
1 CCAAGTGCTAATCCCTATGGCCAGCCTG-TCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
1784 A
65 A
* * *
1785 CCAAGTGCTAATCCCTATGGCCAGCCTGAGCAGCCCAATGCTAATCCATATGGCCAAAATGGGCA
1 CCAAGTGCTAATCCCTATGGCCAGCCTG-TCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
1850 A
65 A
*
1851 CCAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCCAGTACTAACCCATATGGCCAAAATGGGC-
1 CCAAGTGCTAATCCCTATGGCCAGCCTGT-CAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
1915 A
65 A
** *
1916 CTCAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCCAGTGCTAACCCATACAGCCAAAACGGGC
1 C-CAAGTGCTAATCCCTATGGCCAGCCTGT-CAGCCCAGTGCTAACCCATATGGCCAAAATGGGC
*
1981 AG
64 AA
* * * *
1983 CCAAGTGCTAATCTCTATGGCCTGCCTGCGCCA-CCCAGTGCAAACCCATATGGCCA
1 CCAAGTGCTAATCCCTATGGCCAGCCT--GTCAGCCCAGTGCTAACCCATATGGCCA
2039 GTCAAGTGCT
Statistics
Matches: 228, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
65 2 0.01
66 222 0.97
67 3 0.01
68 1 0.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.18
Consensus pattern (65 bp):
CCAAGTGCTAATCCCTATGGCCAGCCTGTCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCAA
Found at i:2779 original size:33 final size:33
Alignment explanation
Indices: 2742--2886 Score: 181
Period size: 33 Copynumber: 4.5 Consensus size: 33
2732 AGGCTATGTT
** * **
2742 GGCATGGGGATGAGTAATATGGGCATGAATAAA
1 GGCATGGGGATGAACAACATGGGCATGAATCCA
2775 GGCATGGGGATG---AACATGGGCATGAATCCA
1 GGCATGGGGATGAACAACATGGGCATGAATCCA
2805 GGCATGGGGATGAACAACATGGGCATGAATCCA
1 GGCATGGGGATGAACAACATGGGCATGAATCCA
* * *
2838 GGCATGGAGATGAACAATATGGGCATG-AGCGCA
1 GGCATGGGGATGAACAACATGGGCATGAATC-CA
2871 GGCATGGGGATGAACA
1 GGCATGGGGATGAACA
2887 TGGGAATGGG
Statistics
Matches: 101, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
30 27 0.27
32 2 0.02
33 72 0.71
ACGTcount: A:0.33, C:0.14, G:0.37, T:0.17
Consensus pattern (33 bp):
GGCATGGGGATGAACAACATGGGCATGAATCCA
Found at i:2810 original size:18 final size:18
Alignment explanation
Indices: 2789--2844 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
2779 TGGGGATGAA
2789 CATGGGCATGAATCCAGG
1 CATGGGCATGAATCCAGG
* *
2807 CATGGGGATGAA--CA-A
1 CATGGGCATGAATCCAGG
2822 CATGGGCATGAATCCAGG
1 CATGGGCATGAATCCAGG
2840 CATGG
1 CATGG
2845 AGATGAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 11 0.35
16 2 0.06
17 2 0.06
18 16 0.52
ACGTcount: A:0.30, C:0.20, G:0.34, T:0.16
Consensus pattern (18 bp):
CATGGGCATGAATCCAGG
Found at i:2814 original size:63 final size:64
Alignment explanation
Indices: 2742--2886 Score: 186
Period size: 63 Copynumber: 2.2 Consensus size: 64
2732 AGGCTATGTT
** * * *
2742 GGCATGGGGATGAGTAATATGGGCATGAATAAAGGCATGGGGATGAAC-ATGGGCATGAATC-CA
1 GGCATGGGGATGAACAACATGGGCATGAATAAAGGCATGGAGATGAACAATGGGCATG-AGCGCA
**
2805 GGCATGGGGATGAACAACATGGGCATGAATCCAGGCATGGAGATGAACAATATGGGCATGAGCGC
1 GGCATGGGGATGAACAACATGGGCATGAATAAAGGCATGGAGATGAAC-A-ATGGGCATGAGCGC
2870 A
64 A
2871 GGCATGGGGATGAACA
1 GGCATGGGGATGAACA
2887 TGGGAATGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
63 42 0.59
65 2 0.03
66 27 0.38
ACGTcount: A:0.33, C:0.14, G:0.37, T:0.17
Consensus pattern (64 bp):
GGCATGGGGATGAACAACATGGGCATGAATAAAGGCATGGAGATGAACAATGGGCATGAGCGCA
Found at i:2827 original size:15 final size:15
Alignment explanation
Indices: 2787--2865 Score: 52
Period size: 18 Copynumber: 4.9 Consensus size: 15
2777 CATGGGGATG
2787 AACATGGGCATGAATCC
1 AACATGGGCATGAA--C
* *
2804 AGGCATGGGGATGAAC
1 A-ACATGGGCATGAAC
2820 AACATGGGCATGAATCC
1 AACATGGGCATGAA--C
*
2837 AGGCATGGAG-ATGAAC
1 A-ACATGG-GCATGAAC
*
2853 AATATGGGCATGA
1 AACATGGGCATGA
2866 GCGCAGGCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 1 0.02
15 19 0.39
16 4 0.08
17 3 0.06
18 21 0.43
19 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.32, T:0.16
Consensus pattern (15 bp):
AACATGGGCATGAAC
Found at i:2850 original size:18 final size:17
Alignment explanation
Indices: 2789--2851 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
2779 TGGGGATGAA
2789 CATGGGCATGAATCCAGG
1 CATGGG-ATGAATCCAGG
*
2807 CATGGGGATGAA--CA-A
1 CAT-GGGATGAATCCAGG
2822 CATGGGCATGAATCCAGG
1 CATGGG-ATGAATCCAGG
2840 CATGGAGATGAA
1 CATGG-GATGAA
2852 CAATATGGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
14 3 0.08
15 8 0.22
16 2 0.05
17 2 0.05
18 18 0.49
19 4 0.11
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.16
Consensus pattern (17 bp):
CATGGGATGAATCCAGG
Done.