Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1363
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: 53965
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1964 original size:39 final size:39
Alignment explanation
Indices: 1834--2014 Score: 165
Period size: 40 Copynumber: 4.6 Consensus size: 39
1824 TTGAATGCTG
* * *
1834 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACTAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACAAT
** * **
1873 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAG-TATTAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACAAT
*
1912 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACAAT
* * *
1951 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTA-AAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAG--ATACAAT
1991 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
2015 GAATGAGTTA
Statistics
Matches: 120, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
37 1 0.01
38 26 0.22
39 38 0.32
40 44 0.37
41 11 0.09
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACAAT
Found at i:2006 original size:40 final size:39
Alignment explanation
Indices: 1887--2014 Score: 163
Period size: 39 Copynumber: 3.3 Consensus size: 39
1877 GGACTAAGAT
*
1887 CCGAAGGTATTTGTGCGAGTATT--ATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGT-TTAAATTCCGGGTTAAGTC
* *
1925 CCGAAGGCCTTTGTGCGAG-ATACAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTTA-AATTCCGGGTTAAGTC
* *
1964 CCGAAGGCATTCGTGCGAGTTTTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAG-TTTAAATTCCGGGTTAAGTC
2004 CCGAAGGCATT
1 CCGAAGGCATT
2015 GAATGAGTTA
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
36 1 0.01
38 17 0.22
39 32 0.41
40 26 0.33
41 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGTTTAAATTCCGGGTTAAGTC
Found at i:9787 original size:40 final size:40
Alignment explanation
Indices: 9703--9885 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
9693 TTGAATGCTG
* * * *
9703 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
9742 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
9783 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATA-CAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
9822 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
9862 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
9886 GAATGAGTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.29
40 76 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:9854 original size:79 final size:81
Alignment explanation
Indices: 9703--9882 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 81
9693 TTGAATGCTG
* * * *
9703 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
* *
9767 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
9783 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACAAT-TCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACAATATCCGGACTAAGAT-CCGAAGGCA
9844 TTCGTGCGAGTTTTAAAA
64 TTCGTGCGAGTTTTAAAA
9862 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
9883 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
78 3 0.03
79 51 0.58
80 25 0.28
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:9906 original size:39 final size:39
Alignment explanation
Indices: 9783--9932 Score: 117
Period size: 39 Copynumber: 3.8 Consensus size: 39
9773 AGTTATTAAT
* ** * *
9783 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAG--ATACAAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTCTA-AAA
** *
9822 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
9862 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
9902 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
9933 GAGCTATATC
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
38 3 0.03
39 52 0.55
40 37 0.39
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:9906 original size:79 final size:79
Alignment explanation
Indices: 9756--9922 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
9746 GGACTAAGAT
* * * * **
9756 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACAA
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAA
* *
9821 TTCCGGGTTAAGTC
66 TACCGGGCTAAGTC
* * *
9835 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGG-CATTGAATGAGTTACT
1 CCGAAGGCATTCGTGCGAGTTATT-AAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACA
*
9898 ATGACCGGGCTATGTC
65 AT-ACCGGGCTAAGTC
9914 CCGAAGGCA
1 CCGAAGGCA
9923 CTTGAACGAG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
78 14 0.19
79 60 0.81
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAA
TACCGGGCTAAGTC
Found at i:14025 original size:45 final size:45
Alignment explanation
Indices: 13901--14025 Score: 146
Period size: 45 Copynumber: 2.8 Consensus size: 45
13891 CACTAGGAAT
* *
13901 TTAGAAATCCGAACTCATTGAGTTGGTCCGAGTTTGTGATATATG
1 TTAGAAATCTGAACTCATTGAGTTGGTCCGAGTTCGTGATATATG
** **
13946 TTAGAAATCTGAACTTGTTGAGTTGGTCAAAGTTCGTGATATATG
1 TTAGAAATCTGAACTCATTGAGTTGGTCCGAGTTCGTGATATATG
* *
13991 -T-GAAGCATCTGAGCTCATTGAGTTCGTCCGAGTTC
1 TTAGAA--ATCTGAACTCATTGAGTTGGTCCGAGTTC
14026 ATTATGGATG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 3 0.05
44 1 0.02
45 62 0.94
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (45 bp):
TTAGAAATCTGAACTCATTGAGTTGGTCCGAGTTCGTGATATATG
Found at i:16805 original size:15 final size:15
Alignment explanation
Indices: 16785--16828 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16775 ATTATGATAT
*
16785 TGTATCTTGGATTTG
1 TGTATCTTGGATTTC
* *
16800 TGTATCTCGGTTTTC
1 TGTATCTTGGATTTC
*
16815 TTTATCTTGGATTT
1 TGTATCTTGGATTT
16829 TTTTGTTCTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (15 bp):
TGTATCTTGGATTTC
Found at i:21356 original size:45 final size:45
Alignment explanation
Indices: 21293--21403 Score: 127
Period size: 45 Copynumber: 2.5 Consensus size: 45
21283 AACGGTAGCA
* * * *
21293 GTAACAGTAATAGCAACAGTATTCA-ACACATAAAGTG-CTGAATCT
1 GTAACAGTAACAGTAACAGTATT-AGACACACAAAGTGTC-GAATCG
* *
21338 GTAACAGTAACGGTAACAGGATTAGACACACAAAGTGTCGAATCG
1 GTAACAGTAACAGTAACAGTATTAGACACACAAAGTGTCGAATCG
*
21383 GTAATAGTAACAGTAACAGTA
1 GTAACAGTAACAGTAACAGTA
21404 ACAGTAACAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 1 0.02
45 53 0.96
46 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTAGACACACAAAGTGTCGAATCG
Found at i:21397 original size:6 final size:6
Alignment explanation
Indices: 21383--21412 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
21373 TGTCGAATCG
*
21383 GTAATA GTAACA GTAACA GTAACA GTAACA
1 GTAACA GTAACA GTAACA GTAACA GTAACA
21413 TAAGTGCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (6 bp):
GTAACA
Found at i:21661 original size:21 final size:21
Alignment explanation
Indices: 21596--21663 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
21586 AATTCATTAC
* *
21596 TTCAGTAATTTCACAGTTCAA
1 TTCAGTAACTTCACAATTCAA
* * *
21617 TGCAGTACACATAACAA-T--A
1 TTCAGTA-ACTTCACAATTCAA
21636 TTCAGTAACTTCACAATTCAA
1 TTCAGTAACTTCACAATTCAA
21657 TTCAGTA
1 TTCAGTA
21664 TCAGTCTCGA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 7 0.20
19 8 0.23
21 15 0.43
22 5 0.14
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (21 bp):
TTCAGTAACTTCACAATTCAA
Found at i:22566 original size:3 final size:3
Alignment explanation
Indices: 22558--22589 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
22548 TGTTTTATTC
22558 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
22590 TATTTTACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:22644 original size:26 final size:24
Alignment explanation
Indices: 22626--22683 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
22616 ATTTATTAAT
*
22626 TTACATTTGTATTCATATTCATTA
1 TTACACTTGTATTCATATTCATTA
*
22650 TTACACTTGTATTTA-ATT-ATTA
1 TTACACTTGTATTCATATTCATTA
22672 CCTTACACTTGT
1 --TTACACTTGT
22684 CACTCCTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 4 0.13
23 3 0.10
24 23 0.77
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.52
Consensus pattern (24 bp):
TTACACTTGTATTCATATTCATTA
Found at i:43684 original size:6 final size:6
Alignment explanation
Indices: 43632--43706 Score: 62
Period size: 6 Copynumber: 12.3 Consensus size: 6
43622 CATTATGCCT
* * * * **
43632 TAACAG TACACAG TACCTG -AACAA TAATCAG TAACGG TAGTAG TAACAG
1 TAACAG TA-ACAG TAACAG TAACAG TAA-CAG TAACAG TAACAG TAACAG
*
43681 TAACAT TAACAG TAACAG TAACAG TA
1 TAACAG TAACAG TAACAG TAACAG TA
43707 TTCAACACAC
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
5 2 0.04
6 39 0.75
7 11 0.21
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.21
Consensus pattern (6 bp):
TAACAG
Found at i:43737 original size:45 final size:45
Alignment explanation
Indices: 43687--43790 Score: 158
Period size: 45 Copynumber: 2.3 Consensus size: 45
43677 ACAGTAACAT
*
43687 TAACAGTAACAGTAACAGTATTCAACACAC-AAA-GTACTGAATCTG
1 TAACAGTAACAGTAACAGTATTCAACACACAAAATGT-C-GAATCGG
*
43732 TAACAGTAACGGTAACAGTATTCAACACACAAAATGTCGAATCGG
1 TAACAGTAACAGTAACAGTATTCAACACACAAAATGTCGAATCGG
43777 TAACAGTAACAGTA
1 TAACAGTAACAGTA
43791 GTCGGCACAT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
45 48 0.89
46 4 0.07
47 2 0.04
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (45 bp):
TAACAGTAACAGTAACAGTATTCAACACACAAAATGTCGAATCGG
Found at i:44650 original size:30 final size:30
Alignment explanation
Indices: 44614--44674 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
44604 TTCCCGAGCC
*
44614 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
44644 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
44674 T
1 T
44675 GTTTTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Done.