Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2458
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: 50195
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:14149 original size:25 final size:26
Alignment explanation
Indices: 14098--14158 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
14088 CATATTGATA
* *
14098 TTCG-ACTGAAATGTCTGATTGATTG
1 TTCGAACTGAAATGTCTGATTAACTG
*
14123 TTC-AACTGAAATGTTTGATTAACTG
1 TTCGAACTGAAATGTCTGATTAACTG
14148 TTCGAA-TGAAA
1 TTCGAACTGAAA
14159 GGCACTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (26 bp):
TTCGAACTGAAATGTCTGATTAACTG
Found at i:17750 original size:13 final size:13
Alignment explanation
Indices: 17732--17756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17722 GGTCATATAA
17732 AAATTTTGTTAAG
1 AAATTTTGTTAAG
17745 AAATTTTGTTAA
1 AAATTTTGTTAA
17757 TTGCATGCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
AAATTTTGTTAAG
Found at i:18863 original size:41 final size:40
Alignment explanation
Indices: 18738--18883 Score: 161
Period size: 40 Copynumber: 3.6 Consensus size: 40
18728 TAATTATACC
* *
18738 TGAATTACACATACATGCCCCTGTTGTACTTCAGTACCCG
1 TGAATTGCACATACGTGCCCCTGTTGTACTTCAGTACCCG
* * * *
18778 TAAATTGCACATACGTGCCCCTATTGTACTT-TGATACCCT
1 TGAATTGCACATACGTGCCCCTGTTGTACTTCAG-TACCCG
* *
18818 TGAATTGCACATACGTGTCTCTGTTTGTACTTCAGTAGCCC-
1 TGAATTGCACATACGTGCCCCTG-TTGTACTTCAGTA-CCCG
* *
18859 TGAATAGCACTTACGTGCCCCTGTT
1 TGAATTGCACATACGTGCCCCTGTT
18884 CACACTCCGG
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
39 1 0.01
40 53 0.61
41 29 0.33
42 4 0.05
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (40 bp):
TGAATTGCACATACGTGCCCCTGTTGTACTTCAGTACCCG
Found at i:27303 original size:26 final size:27
Alignment explanation
Indices: 27267--27371 Score: 142
Period size: 27 Copynumber: 3.9 Consensus size: 27
27257 TAAAATAACA
*
27267 GTAATGCCCCTGTAGGGTAAAATGATC
1 GTAATGCCCCTATAGGGTAAAATGATC
27294 GTAATG-CCCTATAGGGTAAAATGATC
1 GTAATGCCCCTATAGGGTAAAATGATC
27320 GTAATGCCCCTATAGGGTAAAATGA-C
1 GTAATGCCCCTATAGGGTAAAATGATC
* * **
27346 TGTAATACCCCTGTATTGTAAAATGA
1 -GTAATGCCCCTATAGGGTAAAATGA
27372 CGATTATGTC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
26 26 0.37
27 45 0.63
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (27 bp):
GTAATGCCCCTATAGGGTAAAATGATC
Found at i:27759 original size:27 final size:28
Alignment explanation
Indices: 27701--27760 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
27691 ACTGTAGTGA
* *
27701 TACTGTATTGGGCTTAAGCCCACACTGT
1 TACTGTATAGGGCTTAAGCCCACACTGC
*
27729 TACTGTATAGGGC-TAAGGCCCAGACT-C
1 TACTGTATAGGGCTTAA-GCCCACACTGC
27756 TACTG
1 TACTG
27761 ATATTGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.28
Consensus pattern (28 bp):
TACTGTATAGGGCTTAAGCCCACACTGC
Found at i:33208 original size:29 final size:29
Alignment explanation
Indices: 33166--33227 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
33156 AGTGTTGGAA
33166 GTGTAAGAAATGTAGAGATAACCGTTCTG
1 GTGTAAGAAATGTAGAGATAACCGTTCTG
33195 GTGTAAGAAATGTAGAGATAACCGTTCTG
1 GTGTAAGAAATGTAGAGATAACCGTTCTG
33224 GTGT
1 GTGT
33228 GTGATGAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (29 bp):
GTGTAAGAAATGTAGAGATAACCGTTCTG
Found at i:38000 original size:40 final size:38
Alignment explanation
Indices: 37960--38168 Score: 184
Period size: 40 Copynumber: 5.2 Consensus size: 38
37950 ATTATTCCTA
* *
37960 AATTGCACATACGTTCCCTTATTGTACTCTAGTACCCCTA
1 AATTGCACATACGTGCCC-TATTGTACT-TAGTACCCCTG
*
38000 AATTGCACATACGTGGCCCTGTTGTACTTCAGTACCCCTG
1 AATTGCACATACGT-GCCCTATTGTACTT-AGTACCCCTG
* * * *
38040 AATTGCTCATATGTGCCACTATTGTACTTTGGTACCCTTG
1 AATTGCACATACGTGCC-CTATTGTAC-TTAGTACCCCTG
* * * * *
38080 AATTGCCCATACCTACCCTCGTTGTACTTCGGTACCCCTG
1 AATTGCACATACGTGCCCT-ATTGTACTT-AGTACCCCTG
* *
38120 AATTGTACATACGTGCCCCTATTTGTACTTTAGTACCCATG
1 AATTGCACATACGTG-CCCTA-TTGTAC-TTAGTACCCCTG
*
38161 AATAGCAC
1 AATTGCAC
38169 TTATGTAGCC
Statistics
Matches: 137, Mismatches: 23, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
39 8 0.06
40 98 0.72
41 29 0.21
42 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (38 bp):
AATTGCACATACGTGCCCTATTGTACTTAGTACCCCTG
Found at i:38104 original size:80 final size:80
Alignment explanation
Indices: 37960--38168 Score: 235
Period size: 80 Copynumber: 2.6 Consensus size: 80
37950 ATTATTCCTA
* * * * * * *
37960 AATTGCACATACGTTCC-CTTATTGTACTCTAGTACCCCTAAATTGCACATACGTGGCCCTGTTG
1 AATTGTACATACGTGCCAC-TATTGTACTTTAGTACCCATGAATTGCACATACCTGACCCTGTTG
38024 TACTTCAGTACCCCTG
65 TACTTCAGTACCCCTG
* * * *
38040 AATTGCT-CATATGTGCCACTATTGTACTTTGGTACCCTTGAATTGCCCATACCT-ACCCTCGTT
1 AATTG-TACATACGTGCCACTATTGTACTTTAGTACCCATGAATTGCACATACCTGACCCT-GTT
*
38103 GTACTTCGGTACCCCTG
64 GTACTTCAGTACCCCTG
* *
38120 AATTGTACATACGTGCCCCTATTTGTACTTTAGTACCCATGAATAGCAC
1 AATTGTACATACGTGCCACTA-TTGTACTTTAGTACCCATGAATTGCAC
38169 TTATGTAGCC
Statistics
Matches: 107, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
79 5 0.05
80 78 0.73
81 24 0.22
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (80 bp):
AATTGTACATACGTGCCACTATTGTACTTTAGTACCCATGAATTGCACATACCTGACCCTGTTGT
ACTTCAGTACCCCTG
Found at i:38990 original size:13 final size:13
Alignment explanation
Indices: 38972--38997 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38962 CATGTGTGAC
38972 ACACGGCCATGTG
1 ACACGGCCATGTG
38985 ACACGGCCATGTG
1 ACACGGCCATGTG
38998 TCCCCTGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACACGGCCATGTG
Found at i:41417 original size:66 final size:65
Alignment explanation
Indices: 41347--41490 Score: 155
Period size: 66 Copynumber: 2.2 Consensus size: 65
41337 AGGGCTGAGG
* * *
41347 ACACGCCCGTGTGCCAGGCCGTGTGAAAACT-GGAAGGTATACTAACTTATGGAACACGGCCAAG
1 ACACGCCCGTGTGCCAGGCCATGTGAAAACTAGG-AGGTATACTAACTTATAGAACACGACCAA-
41411 TC
64 TC
* * ** * * * * *
41413 ACACGTCCGTGTGCTAGGCCATGTGCCAATTAGGGGGTATACTGACTTGTAGCACACGACCAATC
1 ACACGCCCGTGTGCCAGGCCATGTGAAAACTAGGAGGTATACTAACTTATAGAACACGACCAATC
41478 ACACGCCCGTGTG
1 ACACGCCCGTGTG
41491 TGAGACTGTG
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
65 14 0.22
66 48 0.75
67 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.20
Consensus pattern (65 bp):
ACACGCCCGTGTGCCAGGCCATGTGAAAACTAGGAGGTATACTAACTTATAGAACACGACCAATC
Found at i:44028 original size:27 final size:27
Alignment explanation
Indices: 43998--44229 Score: 306
Period size: 27 Copynumber: 8.6 Consensus size: 27
43988 ATATTGAGTC
* * * *
43998 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
44025 CGCACACTTAGTGCTACGA-AATCAAAT
1 CGCACACTTAGTGCTAC-ATAGTCAAAT
44052 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
44080 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
44107 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
44134 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44161 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44188 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
44215 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44230 GTACAATTTA
Statistics
Matches: 184, Mismatches: 16, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
26 1 0.01
27 158 0.86
28 25 0.14
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Done.