Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3405
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: 28675
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:6687 original size:27 final size:26
Alignment explanation
Indices: 6656--6833 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
6646 TAAATTGTAC
6656 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
6683 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
6709 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
6737 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
6765 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* * *
6792 GGCACTAAGTGTGCGAGTTGAATATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
6819 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6834 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 99 0.79
28 25 0.20
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:6772 original size:82 final size:81
Alignment explanation
Indices: 6657--6812 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
6647 AAATTGTACA
* * *
6657 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
6721 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
6738 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
6803 TGCGAGTTGA
65 TGCGAATTGA
6813 ATATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:6824 original size:82 final size:81
Alignment explanation
Indices: 6653--6833 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
6643 GATTAAATTG
* * *
6653 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
*
6718 GTGTGCGAATTGACCA
66 GTGTGCGAATTGAACA
* * ** *
6734 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* *
6798 AAGTGTGCGAGTTGAATA
64 AAGTGTGCGAATTGAACA
* *
6816 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
6834 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 20 0.24
82 63 0.76
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGAACA
Found at i:6842 original size:27 final size:27
Alignment explanation
Indices: 6738--6844 Score: 79
Period size: 27 Copynumber: 3.9 Consensus size: 27
6728 TGACCATGCG
* * *
6738 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * ** *
6766 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
6793 GCACTAAGTGTGCGAGTTGAATATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
6820 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
6845 CATTCGTGAA
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
27 50 0.77
28 15 0.23
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:14967 original size:22 final size:21
Alignment explanation
Indices: 14941--14994 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
14931 CGCAAGGCTC
*
14941 ACACGCCCGTGTGGTCCAAGGG
1 ACACGCCCGTGT-GACCAAGGG
* **
14963 ACACGCCCATGTGACCCTGGG
1 ACACGCCCGTGTGACCAAGGG
14984 ACACGCCCGTG
1 ACACGCCCGTG
14995 CTAGAGGCCG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.19, C:0.37, G:0.31, T:0.13
Consensus pattern (21 bp):
ACACGCCCGTGTGACCAAGGG
Found at i:17372 original size:12 final size:12
Alignment explanation
Indices: 17346--17379 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17336 CATAATCTCT
17346 AAACTCATGACCA
1 AAACTCAT-ACCA
*
17359 AATCTCATACCA
1 AAACTCATACCA
17371 AAACTCATA
1 AAACTCATA
17380 AAATTTACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.47, C:0.29, G:0.03, T:0.21
Consensus pattern (12 bp):
AAACTCATACCA
Found at i:19676 original size:80 final size:78
Alignment explanation
Indices: 19592--19763 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 78
19582 GGACTAAGAT
*
19592 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC
* *
19655 TAAATCCGGGTTAAGTC
62 TAAAACCGGGCTAAGTC
* * * *
19672 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
19737 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
19751 CCGAAGGCATTTG
1 CCGAAGGCATTTG
19764 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 38 0.47
80 37 0.46
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:19754 original size:39 final size:39
Alignment explanation
Indices: 19539--19761 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
19529 TTGAATGCTG
* * * * * *
19539 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
19579 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
19619 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
19659 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
19699 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
19738 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
19762 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
39 37 0.24
40 105 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:19781 original size:79 final size:80
Alignment explanation
Indices: 19619--19796 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
19609 AGATACAAGT
* * * *
19619 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
19684 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
19699 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
19763 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
19778 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
19797 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:27235 original size:39 final size:40
Alignment explanation
Indices: 27100--27323 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
27090 TTGAATGCTG
* * * * *
27100 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
27140 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
* *
27180 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAG-TACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
27219 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
27259 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
27298 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
27324 AACGAGGAGC
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
39 66 0.43
40 81 0.52
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:27240 original size:79 final size:78
Alignment explanation
Indices: 27100--27323 Score: 245
Period size: 79 Copynumber: 2.8 Consensus size: 78
27090 TTGAATGCTG
* * * * *
27100 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGC-GAGT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT
*
27164 TGTGCGAGATA-CAAGT
63 TGTGCGAGATATCAA-A
* * *
27180 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
* *
27245 TGCGAGTTATTAAA
65 TGCGAGATATCAAA
* * * *
27259 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAG-TACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
27324 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
78 10 0.08
79 81 0.66
80 23 0.19
81 8 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGATATCAAA
Found at i:27341 original size:79 final size:79
Alignment explanation
Indices: 27180--27356 Score: 198
Period size: 79 Copynumber: 2.3 Consensus size: 79
27170 AGATACAAGT
* * * *
27180 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
** * *
27245 TGCGAGTTATTAAA
66 AACGAGTGACTAAA
* * *
27259 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAG-TACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
27323 GAACGAG-GAGCTATA
65 GAACGAGTGA-CTAAA
*
27338 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
27357 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 25 0.30
79 58 0.70
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
AACGAGTGACTAAA
Done.