Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_41183
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: 5040
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Found at i:2672 original size:30 final size:30
Alignment explanation
Indices: 2638--2776 Score: 116
Period size: 30 Copynumber: 4.9 Consensus size: 30
2628 GGAACACCTT
*** *
2638 TTGGAACTTCAGTTTCAACAGCAGCGGCAG
1 TTGGAACTTCAGCGACAACAGCAGCAGCAG
*
2668 TTGGAACTTCAGCGACAGCAGCAGCAGCAG
1 TTGGAACTTCAGCGACAACAGCAGCAGCAG
* *
2698 CTGGAACTTCA--G---A-GGCAGCAGCAG
1 TTGGAACTTCAGCGACAACAGCAGCAGCAG
* *
2722 CTGGAACTTCAGCGGCAACAGCAGCAGC--
1 TTGGAACTTCAGCGACAACAGCAGCAGCAG
* *
2750 -TGGAACTACAGCGACAGCAGCAGCAGC
1 TTGGAACTTCAGCGACAACAGCAGCAGC
2777 TAGAGTTACA
Statistics
Matches: 91, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
24 21 0.23
26 1 0.01
27 24 0.26
28 1 0.01
29 1 0.01
30 43 0.47
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.14
Consensus pattern (30 bp):
TTGGAACTTCAGCGACAACAGCAGCAGCAG
Found at i:2774 original size:54 final size:54
Alignment explanation
Indices: 2685--2878 Score: 201
Period size: 51 Copynumber: 3.8 Consensus size: 54
2675 TTCAGCGACA
* * *
2685 GCAGCAGCAGCAGCTGGAACTTCA--GA-GGCAGCAGCAGCTGGAACTT-CAGCG
1 GCAGCAGCAGCAGCTGGAACTACAGCGACAGCAGCAGCAGCTAG-ACTTACAGCG
* *
2736 GCAACAGCAGCAGCTGGAACTACAGCGACAGCAGCAGCAGCTAGAGTTACAGCG
1 GCAGCAGCAGCAGCTGGAACTACAGCGACAGCAGCAGCAGCTAGACTTACAGCG
* ** * *
2790 GCAGCAGCAGCAGCTAGAGTTACAGCG---GCGGCAGCAGCTAGAGTTACAGC-
1 GCAGCAGCAGCAGCTGGAACTACAGCGACAGCAGCAGCAGCTAGACTTACAGCG
* *
2840 G--GCAGCAGCAGTTGGAACTACAGCTACAGCAGCAGCAGC
1 GCAGCAGCAGCAGCTGGAACTACAGCGACAGCAGCAGCAGC
2879 AGCAGTTGGA
Statistics
Matches: 120, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
48 19 0.16
50 1 0.01
51 54 0.45
53 5 0.04
54 41 0.34
ACGTcount: A:0.30, C:0.27, G:0.32, T:0.11
Consensus pattern (54 bp):
GCAGCAGCAGCAGCTGGAACTACAGCGACAGCAGCAGCAGCTAGACTTACAGCG
Found at i:2861 original size:24 final size:24
Alignment explanation
Indices: 2682--2875 Score: 154
Period size: 24 Copynumber: 7.7 Consensus size: 24
2672 AACTTCAGCG
*
2682 ACAGCAGCAGCAGCAGCTGGAACT
1 ACAGCGGCAGCAGCAGCTGGAACT
* *
2706 TCAGAGGCAGCAGCAGCTGGAACT
1 ACAGCGGCAGCAGCAGCTGGAACT
*
2730 TCAGCGGCAACAGCAGCAGCTGGAACT
1 ACAGCGG---CAGCAGCAGCTGGAACT
* **
2757 ACAGCGACAGCAGCAGCAGCTAGAGTT
1 ACAGCG---GCAGCAGCAGCTGGAACT
* **
2784 ACAGCGGCAGCAGCAGCAGCTAGAGTT
1 ACAGC-G--GCAGCAGCAGCTGGAACT
* * **
2811 ACAGCGGCGGCAGCAGCTAGAGTT
1 ACAGCGGCAGCAGCAGCTGGAACT
*
2835 ACAGCGGCAGCAGCAGTTGGAACT
1 ACAGCGGCAGCAGCAGCTGGAACT
**
2859 ACAGCTACAGCAGCAGC
1 ACAGCGGCAGCAGCAGC
2876 AGCAGCAGTT
Statistics
Matches: 146, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
24 77 0.53
26 1 0.01
27 66 0.45
28 1 0.01
30 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.31, T:0.11
Consensus pattern (24 bp):
ACAGCGGCAGCAGCAGCTGGAACT
Found at i:2883 original size:33 final size:33
Alignment explanation
Indices: 2836--2908 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
2826 GCTAGAGTTA
* *
2836 CAGCGGCAGCAGCAGTTGGAACTACAGCTACAG
1 CAGCAGCAGCAGCAGTTGGAACTACAGCGACAG
* *
2869 CAGCAGCAGCAGCAGTTGGAACTTCAGCGGCAG
1 CAGCAGCAGCAGCAGTTGGAACTACAGCGACAG
2902 CAGCAGC
1 CAGCAGC
2909 TTCGTCACCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.32, T:0.11
Consensus pattern (33 bp):
CAGCAGCAGCAGCAGTTGGAACTACAGCGACAG
Found at i:2896 original size:27 final size:27
Alignment explanation
Indices: 2656--2908 Score: 168
Period size: 27 Copynumber: 9.4 Consensus size: 27
2646 TCAGTTTCAA
* *
2656 CAGCAGCGGCAGTTGGAACTTCAGCGACAG
1 CAGCAGCAGCAGCTGGAACTTCA--G-CAG
2686 CAGCAGCAGCAGCTGGAACTTCAG-AG
1 CAGCAGCAGCAGCTGGAACTTCAGCAG
*
2712 --GCAGCAGCAGCTGGAACTTCAGCGG
1 CAGCAGCAGCAGCTGGAACTTCAGCAG
* *
2737 CAACAGCAGCAGCTGGAACTACAGC-G
1 CAGCAGCAGCAGCTGGAACTTCAGCAG
* * *
2763 ACAGCAGCAGCAGCTAG-AGTTACAGCGG
1 -CAGCAGCAGCAGCTGGAACTT-CAGCAG
* *
2791 CAGCAGCAGCAGCTAG-AGTT-A-CAG
1 CAGCAGCAGCAGCTGGAACTTCAGCAG
* * * *
2815 CGGCGGCAGCAGCTAG-AGTT-A-CAG
1 CAGCAGCAGCAGCTGGAACTTCAGCAG
* *
2839 CGGCAGCAGCAGTTGGAACTACAGCTACAGCAG
1 CAGCAGCAGCAGCTGGAACT-----T-CAGCAG
* *
2872 CAGCAGCAGCAGTTGGAACTTCAGCGG
1 CAGCAGCAGCAGCTGGAACTTCAGCAG
2899 CAGCAGCAGC
1 CAGCAGCAGC
2909 TTCGTCACCA
Statistics
Matches: 190, Mismatches: 18, Indels: 33
0.79 0.07 0.14
Matches are distributed among these distances:
24 59 0.31
25 4 0.02
26 5 0.03
27 74 0.39
28 3 0.02
30 22 0.12
32 1 0.01
33 22 0.12
ACGTcount: A:0.29, C:0.27, G:0.32, T:0.11
Consensus pattern (27 bp):
CAGCAGCAGCAGCTGGAACTTCAGCAG
Done.