Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2390
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: 48458
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Found at i:1128 original size:39 final size:40
Alignment explanation
Indices: 1070--1249 Score: 107
Period size: 40 Copynumber: 4.6 Consensus size: 40
1060 AATCAAGCAT
* * *
1070 CTTCGGGT-TT-AGCCGGATATAACCACTCGCA-CAAGGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
*** *
1107 CTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
* * ** * * *
1147 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
* ** * ** * *
1187 CTTCGGATCTTAGTCCGGATGTAGTCGCTTAGCACAAA-GC
1 CTTCGGGTCTTAACCCGGATATAACCAC-TAGCATAAAGGC
* *
1227 CTTCGGGACTTAGCCCGGATATA
1 CTTCGGGTCTTAACCCGGATATA
1250 GTCGCTTAGC
Statistics
Matches: 119, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
37 8 0.07
38 2 0.02
39 16 0.13
40 84 0.71
41 9 0.08
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
Found at i:1152 original size:40 final size:41
Alignment explanation
Indices: 1105--1289 Score: 252
Period size: 40 Copynumber: 4.6 Consensus size: 41
1095 CTCGCACAAG
* * * * *
1105 GCCTTCGGGTCTTAACCCGGATATGGTCAC-TAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
1145 GCCTTCGGGACTTAGCCCGGATATAGTCGC-TAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
* *
1185 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAA-
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGCTTAGCACAAAT
*
1225 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
*
1266 GCCTTTGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
1290 CATTCGAGTA
Statistics
Matches: 131, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 93 0.71
41 35 0.27
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
Found at i:23421 original size:24 final size:25
Alignment explanation
Indices: 23379--23427 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
23369 ACACAAATGC
*
23379 AGCTCTTCGTGAGCGTCCTGATATG
1 AGCTCTTCATGAGCGTCCTGATATG
*
23404 AGCTCTT-ATGAGCTTCCTGATATG
1 AGCTCTTCATGAGCGTCCTGATATG
23428 GCTTGCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (25 bp):
AGCTCTTCATGAGCGTCCTGATATG
Found at i:23883 original size:16 final size:17
Alignment explanation
Indices: 23864--23896 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
23854 ATGATGGTAT
23864 ATGAAATAT-TGATATA
1 ATGAAATATATGATATA
*
23880 ATGAAATGTATGATATA
1 ATGAAATATATGATATA
23897 TGTTTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATATATGATATA
Found at i:23895 original size:17 final size:17
Alignment explanation
Indices: 23852--23896 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
23842 AAATTCATGA
*
23852 AAATG-ATGGTAT-ATG
1 AAATGTATGATATAATG
*
23867 AAATAT-TGATATAATG
1 AAATGTATGATATAATG
23883 AAATGTATGATATA
1 AAATGTATGATATA
23897 TGTTTATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 9 0.38
16 8 0.33
17 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.36
Consensus pattern (17 bp):
AAATGTATGATATAATG
Found at i:30159 original size:21 final size:21
Alignment explanation
Indices: 30133--30174 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
30123 GAAGGCATTT
*
30133 GTGCGAGTTACTAATTCCGGG
1 GTGCGAGTTACTAAATCCGGG
30154 GTGCGAGTTACTAAATCCGGG
1 GTGCGAGTTACTAAATCCGGG
30175 TTAAGTCCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.26
Consensus pattern (21 bp):
GTGCGAGTTACTAAATCCGGG
Found at i:30214 original size:40 final size:40
Alignment explanation
Indices: 30154--30234 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
30144 TAATTCCGGG
*
30154 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 GTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
*
30194 GTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTT
1 GTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTT
30234 G
1 G
30235 AACGAGTAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 36 0.95
41 2 0.05
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
Found at i:43415 original size:27 final size:27
Alignment explanation
Indices: 43384--43560 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
43374 TAAATTGTAC
43384 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43411 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43437 ATGC-CTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43464 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
43492 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
43519 AGCACTAAGTGTGTGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43546 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43561 GACTCAATAT
Statistics
Matches: 125, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
26 21 0.17
27 81 0.65
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:43447 original size:53 final size:55
Alignment explanation
Indices: 43384--43560 Score: 182
Period size: 53 Copynumber: 3.3 Consensus size: 55
43374 TAAATTGTAC
*
43384 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGA-AATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAATGAATATGT
* * ** ** *
43437 ATGC-CTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAATGAATATGT
* * * * * *
43492 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGTGAG-TTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAATGAATATGT
*
43546 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43561 GACTCAATAT
Statistics
Matches: 103, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
53 36 0.35
54 33 0.32
55 34 0.33
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGAATGAATATGT
Done.