Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold746
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: 30604
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:1654 original size:40 final size:40
Alignment explanation
Indices: 1565--1747 Score: 182
Period size: 39 Copynumber: 4.7 Consensus size: 40
1555 TTACTCGTTT
* *
1565 CAAATGCCTTCGGGAC-AAGCCCGG-TATTAGTAAAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TTAGT--AACTCGCA
* *
1606 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
1646 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
1685 CAAATG-CTTC-GGATCTTAGTCCGGATATGGTCACTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
1724 CAAA-GCCTTC-GGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1748 CATCATTCAA
Statistics
Matches: 121, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
37 2 0.02
38 15 0.12
39 57 0.47
40 20 0.17
41 15 0.12
42 11 0.09
43 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:8801 original size:78 final size:78
Alignment explanation
Indices: 8666--8882 Score: 201
Period size: 78 Copynumber: 2.7 Consensus size: 78
8656 TTGAATGATG
* * * ** *
8666 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTAACTATATCCGGGTTAAG-TCCGAAGGCAAT
8730 TGTGCT-AGATACTA-A
63 TGTG-TGAGATACTATA
* *
8745 TTCCGGGCTAAG-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATT
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTAACTATATCCGGGTTAAGT-CCGAAGGCAATT
*
8809 GTGTGAGTTACTATA
64 GTGTGAGATACTATA
* * ** *
8824 ACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAACTATATCC-GGTTAAATTCCGAAGG
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTAACTATATCCGGGTT-AAGTCCGAAGG
8883 TACGTGATTT
Statistics
Matches: 115, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
77 2 0.02
78 54 0.47
79 19 0.17
80 40 0.35
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (78 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTAACTATATCCGGGTTAAGTCCGAAGGCAATTGT
GTGAGATACTATA
Found at i:8862 original size:40 final size:40
Alignment explanation
Indices: 8667--8868 Score: 182
Period size: 40 Copynumber: 5.1 Consensus size: 40
8657 TGAATGATGT
* * * *
8667 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * * *
8707 CCGGACTAAGAT-CCGAAGGCATTTGTGCTAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
8747 CCGGGCTAAG--CCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* * *
8784 TCCGGGTTAAGTCCCGAAGGCAATTGTGTGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* ** * *
8825 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
8865 CCGG
1 CCGG
8869 TTAAATTCCG
Statistics
Matches: 135, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 33 0.24
39 1 0.01
40 91 0.67
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:21465 original size:26 final size:26
Alignment explanation
Indices: 21419--21500 Score: 110
Period size: 28 Copynumber: 3.0 Consensus size: 26
21409 GATTCAAAAG
* * *
21419 TATATATTAAGTCTGCACACTCAGTGC
1 TATATATCAACTC-GCACACTTAGTGC
21446 TATATATCAACTCGCACACTTAGTGC
1 TATATATCAACTCGCACACTTAGTGC
21472 TATATAATCAAACTCGCACACTTAGTGC
1 TATAT-ATC-AACTCGCACACTTAGTGC
21500 T
1 T
21501 GTACAATTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
26 17 0.34
27 14 0.28
28 19 0.38
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (26 bp):
TATATATCAACTCGCACACTTAGTGC
Found at i:21486 original size:28 final size:28
Alignment explanation
Indices: 21433--21528 Score: 124
Period size: 28 Copynumber: 3.5 Consensus size: 28
21423 TATTAAGTCT
*
21433 GCACACTCAGTGCTATAT-ATC-AACTC
1 GCACACTTAGTGCTATATAATCAAACTC
21459 GCACACTTAGTGCTATATAATCAAACTC
1 GCACACTTAGTGCTATATAATCAAACTC
* * * *
21487 GCACACTTAGTGCTGTACAATTTAAACCC
1 GCACACTTAGTGCTATATAA-TCAAACTC
21516 GCACACTTAGTGC
1 GCACACTTAGTGC
21529 CAATCTCATG
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.27
27 3 0.05
28 23 0.37
29 19 0.31
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (28 bp):
GCACACTTAGTGCTATATAATCAAACTC
Found at i:21991 original size:12 final size:12
Alignment explanation
Indices: 21974--22000 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21964 TGGGCATACT
21974 TATGTATATATA
1 TATGTATATATA
21986 TATGTATATATA
1 TATGTATATATA
21998 TAT
1 TAT
22001 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:27232 original size:63 final size:59
Alignment explanation
Indices: 27129--27360 Score: 209
Period size: 63 Copynumber: 3.8 Consensus size: 59
27119 AACAAATTAG
* * * *
27129 AAAAAAAAGAAAAAAAAGAAAAA-CAAA-AAATAAAAAAAAAAAATTAAAAAAAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAATTAAATCAA-AAAAAAAAAAAATTAAAAAAAAAATAA
* *
27187 AAAAAAAAAAAAAAAAAAAAAAATATAGGAA-CAAAAAAATCAAAAATATTAAAAAAATAATGAA
1 AAAAAAAAAAAAAAAAAAAAAAAT-TA--AATCAAAAAAA--AAAAAAATTAAAAAAAAAAT-AA
* **
27251 AAACAAGAAAAAAAAAAAAAAAAAATTAAATTTAAAAAAAAAAAAAAAAAAAAAAAAAATAA
1 AAA-AA-AAAAAAAAAAAAAAAAAATTAAA-TCAAAAAAAAAAAAAATTAAAAAAAAAATAA
* ** *
27313 AAAAAAATTAAAAAAAAGAAAAAAAAATATTTTAAAAAAAAAAAAAAT
1 AAAAAAA--AAAAAAAA-AAAAAAAATTAAATCAAAAAAAAAAAAAAT
27361 AGATAGAATA
Statistics
Matches: 145, Mismatches: 15, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
58 21 0.14
60 3 0.02
61 7 0.05
62 33 0.23
63 46 0.32
64 5 0.03
65 11 0.08
66 19 0.13
ACGTcount: A:0.84, C:0.02, G:0.03, T:0.11
Consensus pattern (59 bp):
AAAAAAAAAAAAAAAAAAAAAAATTAAATCAAAAAAAAAAAAAATTAAAAAAAAAATAA
Found at i:27348 original size:109 final size:108
Alignment explanation
Indices: 27124--27359 Score: 297
Period size: 110 Copynumber: 2.2 Consensus size: 108
27114 AAAGAAACAA
27124 ATTAGAAAAAAAAGAAAAAAAAGAAAAACAAAAAATAAAAAAAAAAAATTAAAAAAAAAATAAAA
1 ATTA-AAAAAAAAGAAAAAAAAGAAAAACAAAAAATAAAAAAAAAAAATTAAAAAAAAAATAAAA
**
27189 AAAAAAAAAAAAAAAAAAAAATATAGGAACAAAAAAATCAAAAAT
65 AAAAAAAAAAAAAAAAAAAAATATA-GAACAAAAAAAAAAAAAAT
* * *
27234 ATTAAAAAAATAATGAAAAACAAGAAAAA-AAAAAA-AAAAAAATTAAATTTAAAAAAAAAA-AA
1 ATTAAAAAAA-AA-GAAAAAAAAGAAAAACAAAAAATAAAAAAA-AAAAATTAAAAAAAAAATAA
27296 AAAAAAAAAAAAAATAAAAAAAAAT-TA-AA-AAAAAGAAAAAAAAAT
63 AAAAAAAAAAAAAA-AAAAAAAAATATAGAACAAAAA-AAAAAAAAAT
**
27341 ATTTTAAAAAAA-AAAAAAA
1 ATTAAAAAAAAAGAAAAAAA
27360 TAGATAGAAT
Statistics
Matches: 113, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
104 6 0.05
106 7 0.06
107 18 0.16
109 31 0.27
110 37 0.33
111 14 0.12
ACGTcount: A:0.83, C:0.02, G:0.03, T:0.11
Consensus pattern (108 bp):
ATTAAAAAAAAAGAAAAAAAAGAAAAACAAAAAATAAAAAAAAAAAATTAAAAAAAAAATAAAAA
AAAAAAAAAAAAAAAAAAAATATAGAACAAAAAAAAAAAAAAT
Found at i:27359 original size:1 final size:1
Alignment explanation
Indices: 27129--27339 Score: 143
Period size: 1 Copynumber: 211.0 Consensus size: 1
27119 AACAAATTAG
* * * * ** *
27129 AAAAAAAAGAAAAAAAAGAAAAACAAAAAATAAAAAAAAAAAATTAAAAAAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** * ** * ** * ** * *
27194 AAAAAAAAAAAAAAAATATAGGAACAAAAAAATCAAAAATATTAAAAAAATAATGAAAAACAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** *** * **
27259 AAAAAAAAAAAAAAAAATTAAATTTAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAATTAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
27324 AAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAA
27340 TATTTTAAAA
Statistics
Matches: 164, Mismatches: 46, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 164 1.00
ACGTcount: A:0.85, C:0.02, G:0.03, T:0.09
Consensus pattern (1 bp):
A
Found at i:30162 original size:12 final size:12
Alignment explanation
Indices: 30145--30171 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30135 TGGGCATACT
30145 TATGTATATATA
1 TATGTATATATA
30157 TATGTATATATA
1 TATGTATATATA
30169 TAT
1 TAT
30172 ACTTGGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Done.