Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3594
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: 24486
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:1656 original size:39 final size:40
Alignment explanation
Indices: 1583--1712 Score: 201
Period size: 40 Copynumber: 3.3 Consensus size: 40
1573 GGACTAAGAT
*
1583 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGTTAAGTC
1623 CCGAAGGCATTTGTG-GAGTTACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGTTAAGTC
* * *
1662 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGTTAAGTC
1702 CCGAAGGCATT
1 CCGAAGGCATT
1713 GAACGAGTAG
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
39 40 0.48
40 44 0.52
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGTTAAGTC
Found at i:1732 original size:79 final size:78
Alignment explanation
Indices: 1583--1746 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 78
1573 GGACTAAGAT
* * **
1583 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTTGTGGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGTCCCGAAGGCATTTGACGAGTTACTAA
*
1648 TTCCGGGTTAAGTC
66 TTCC-GGTTAAATC
* *
1662 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCA-TTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAGTCCCGAAGGCATTTG-ACGAGTTA-C
*
1724 T-ATATCCGGTTAAATT
63 TAAT-TCCGGTTAAATC
1740 CCGAAGG
1 CCGAAGG
1747 TACGTGATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
78 23 0.32
79 50 0.68
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGTCCCGAAGGCATTTGACGAGTTACTAA
TTCCGGTTAAATC
Found at i:9647 original size:40 final size:40
Alignment explanation
Indices: 9563--9786 Score: 267
Period size: 40 Copynumber: 5.6 Consensus size: 40
9553 TCGAATGATG
* * * *
9563 TCCGGGATAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
** *
9602 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
9643 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
9683 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
9723 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * * *
9762 AACCAGGCTATGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGGCATT
9787 CGAACGAGTA
Statistics
Matches: 162, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.01
40 150 0.93
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:9795 original size:80 final size:78
Alignment explanation
Indices: 9563--9821 Score: 274
Period size: 80 Copynumber: 3.3 Consensus size: 78
9553 TCGAATGATG
* * * *
9563 TCCGGGATAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGG-CTAAG-TCCCGAAGGCAT
*
9626 TTGTGCGAGATACTAAT
63 TTGTGCGAG-TACTAAA
* *
9643 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTA-ATTCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC-GGCTAAGTCCCGAAGGCATT
9707 TGTGCGAGTTACTAAA
64 TGTGCGAG-TACTAAA
* * *
9723 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCAGGCTATGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC-GGCTAAGTCCCGAAGGCATTT
** *
9788 GAACGAGTAGCTATA
65 GTGCGAGTA-CTAAA
* *
9803 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
9822 TACGTGATTT
Statistics
Matches: 154, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
79 18 0.12
80 126 0.82
81 10 0.06
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCATTTG
TGCGAGTACTAAA
Found at i:11910 original size:3 final size:3
Alignment explanation
Indices: 11902--11959 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
11892 CTTTCTTTTG
11902 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11950 TTA TTA TTA T
1 TTA TTA TTA T
11960 ATTTTAACAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13979 original size:39 final size:40
Alignment explanation
Indices: 13818--14042 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
13808 GCTACTCGTT
* *
13818 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
13858 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
13898 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
13938 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
13977 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
14018 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
14043 CTTCATTCAA
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.19
40 118 0.72
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:14002 original size:119 final size:120
Alignment explanation
Indices: 13818--14042 Score: 296
Period size: 119 Copynumber: 1.9 Consensus size: 120
13808 GCTACTCGTT
**
13818 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
13883 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
13938 CAAATGCCTTCGGG-CTTAGCCCAGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
14000 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
14043 CTTCATTCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
118 3 0.03
119 64 0.70
120 24 0.26
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:21939 original size:39 final size:39
Alignment explanation
Indices: 21851--22015 Score: 210
Period size: 40 Copynumber: 4.2 Consensus size: 39
21841 AAATCACGTA
* * *
21851 CCTTCGGAATTTAACCGGATATAGCT-ACTCGTTCA-AAATG
1 CCTTCGGGACTTAACCGGATTTAG-TAACTCG--CACAAATG
21891 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
21930 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAA-CCGGATTTAGTAACTCGCACAAATG
* * *
21970 CCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATG
1 CCTTCGGGACTTA-ACCGGATTTAGTAACTCGCACAAATG
22009 CCTTCGG
1 CCTTCGG
22016 ATCTTAGTCC
Statistics
Matches: 115, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.02
39 54 0.47
40 59 0.51
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.27
Consensus pattern (39 bp):
CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
Found at i:21988 original size:79 final size:80
Alignment explanation
Indices: 21886--22067 Score: 228
Period size: 79 Copynumber: 2.3 Consensus size: 80
21876 TACTCGTTCA
* *
21886 AAATGCCTTCGGGACTTA-ACCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
21949 ATTTAGTAAC-TCGCAC
64 ATATAGTAACTTAGCAC
* **
21965 AAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
* *
22030 ATGGTCACTTAGCAC
66 ATAGTAACTTAGCAC
*
22045 AAA-GCCTTCGGACTTAGCCCGGA
1 AAATGCCTTCGGGCTTAGCCCGGA
22068 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
78 7 0.08
79 75 0.83
80 8 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
AAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Done.