Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1053
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: 43432
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Found at i:6471 original size:27 final size:26
Alignment explanation
Indices: 6434--6487 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
6424 CACCACTGAA
* *
6434 TCGGGGAATCATCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
6460 TCGGGAGAATCAGCACATAGCAACCCC
1 TCGGG-GAATCAGCACATAGCAACCCC
6487 T
1 T
6488 TTTCATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:13924 original size:26 final size:26
Alignment explanation
Indices: 13888--13939 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
13878 CACCACTGAA
* *
13888 TCGGGGAATCATCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
13914 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
13940 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.21, T:0.15
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:14016 original size:70 final size:71
Alignment explanation
Indices: 13900--14050 Score: 241
Period size: 72 Copynumber: 2.1 Consensus size: 71
13890 GGGGAATCAT
*
13900 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTT-CATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACAATGG
13964 ATATCG
66 ATATCG
* ***
13970 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACAATG
14035 GATATCG
65 GATATCG
14042 CACTTAGCA
1 CACTTAGCA
14051 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 16 0.22
71 28 0.38
72 30 0.41
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACAATGG
ATATCG
Found at i:14093 original size:104 final size:104
Alignment explanation
Indices: 13969--14192 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
13959 AATGGATATC
13969 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
14034 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
14073 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
14138 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
14177 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
14193 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:14553 original size:29 final size:29
Alignment explanation
Indices: 14520--14583 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
14510 TAATCCACCA
14520 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
14549 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
14579 CCCAA
1 CCCAA
14584 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:14557 original size:30 final size:30
Alignment explanation
Indices: 14527--14583 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
14517 CCACCCAACT
14527 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
14556 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
14584 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:21472 original size:26 final size:26
Alignment explanation
Indices: 21436--21487 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
21426 CACCACTGAA
* *
21436 TCGGGGAATCATCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
21462 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
21488 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.21, T:0.15
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:21561 original size:70 final size:71
Alignment explanation
Indices: 21448--21597 Score: 248
Period size: 70 Copynumber: 2.1 Consensus size: 71
21438 GGGGAATCAT
* *
21448 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
21512 ATATCG
66 ATATCG
***
21518 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTGG
1 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
21583 ATATCG
66 ATATCG
21589 CACTTAGCA
1 CACTTAGCA
21598 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 44 0.59
71 30 0.41
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
ATATCG
Found at i:21639 original size:103 final size:103
Alignment explanation
Indices: 21517--21738 Score: 374
Period size: 103 Copynumber: 2.2 Consensus size: 103
21507 AATGGATATC
21517 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
21582 GAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
21620 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
21685 GATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
21723 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
21739 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 111 0.99
104 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:21640 original size:26 final size:26
Alignment explanation
Indices: 21610--21660 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
21600 ACCAATGAAC
*
21610 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
21636 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
21661 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:22100 original size:29 final size:29
Alignment explanation
Indices: 22067--22130 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
22057 TAATCCACCA
22067 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
22096 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
22126 CCCAA
1 CCCAA
22131 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:22104 original size:30 final size:30
Alignment explanation
Indices: 22074--22130 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
22064 CCACCCAACT
22074 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
22103 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
22131 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:27929 original size:85 final size:84
Alignment explanation
Indices: 27785--27943 Score: 198
Period size: 85 Copynumber: 1.9 Consensus size: 84
27775 GGTAAGGTGC
* * *
27785 CGATGCCATGTTCCAGACATGGTCTTACACTGGTTCATATCTCACGTTGATGCCATGTCCCGGAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGTTCATATCT-ACGATGATGCCATGTCCCAGAC
27850 ATGGTCTTACTGTCTCGTAAG
65 AT-GTCTTACTGTCTCGTAAG
* * *
27871 CGATG-CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT-GGATGATG-CATGTCCTAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGG-T-TCAT-ATCTACGATGATGCCATGTCCCAG
27933 ACATGTCTTAC
63 ACATGTCTTAC
27944 ACTAGCTCAC
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
84 7 0.11
85 38 0.59
86 12 0.19
87 4 0.06
88 3 0.05
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (84 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGTTCATATCTACGATGATGCCATGTCCCAGACA
TGTCTTACTGTCTCGTAAG
Done.