Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold596
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: 72025
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1092 original size:35 final size:35
Alignment explanation
Indices: 1018--1092 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
1008 CCAACATTCG
* * * * *
1018 AATAATGGCATGTTTAACATGCGAATCATAATTAG
1 AATAATAGCATGCTCAACATGCGAATCAGAATTAC
*
1053 AATAATAGCATGCTCAACATGTGAATCAGAA-TATC
1 AATAATAGCATGCTCAACATGCGAATCAGAATTA-C
1088 AATAA
1 AATAA
1093 ATTAATGTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (35 bp):
AATAATAGCATGCTCAACATGCGAATCAGAATTAC
Found at i:6804 original size:28 final size:28
Alignment explanation
Indices: 6765--6820 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
6755 AAGAAAAACT
6765 AATTTTTGCACCTCTAATATTACTCCTA
1 AATTTTTGCACCTCTAATATTACTCCTA
*
6793 AATTTTTTCACCTCTAATATTACTCCTA
1 AATTTTTGCACCTCTAATATTACTCCTA
6821 CTAGTCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.02, T:0.45
Consensus pattern (28 bp):
AATTTTTGCACCTCTAATATTACTCCTA
Found at i:8570 original size:15 final size:16
Alignment explanation
Indices: 8547--8603 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
8537 TTATAGCTAA
8547 TTATGATTTCTAGTAG
1 TTATGATTTCTAGTAG
*
8563 TT-TGATTTCTAGTAAT
1 TTATGATTTCTAGT-AG
8579 TTATGATTTCTAGTAG
1 TTATGATTTCTAGTAG
*
8595 TTATTATTT
1 TTATGATTT
8604 ACATCATACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 11 0.31
16 14 0.39
17 11 0.31
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.56
Consensus pattern (16 bp):
TTATGATTTCTAGTAG
Found at i:38811 original size:37 final size:37
Alignment explanation
Indices: 38761--38839 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
38751 TTATTACGAA
* * *
38761 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
38798 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
38835 GTCTT
1 GTCTT
38840 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:39070 original size:47 final size:47
Alignment explanation
Indices: 38958--39502 Score: 786
Period size: 47 Copynumber: 11.4 Consensus size: 47
38948 CCTTTCGGGA
* * * * * * * *
38958 CTTATCACATTTATGCACTTTCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39005 CCT-TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39051 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39098 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
39145 CTTATGACATATATACACTTTCACATTCATCACGTCAGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
39192 CTTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39239 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39286 CTTATTACATATATACATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATAC----ACTTTCACATTCATCACATCGGCCATTAGGC
39337 CTTATCACATATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
39388 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39437 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39484 CTTATCACACATATACACT
1 CTTATCACATATATACACT
39503 CTCTTGGCTG
Statistics
Matches: 461, Mismatches: 28, Indels: 18
0.91 0.06 0.04
Matches are distributed among these distances:
46 37 0.08
47 288 0.62
49 52 0.11
51 76 0.16
53 4 0.01
55 4 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42730 original size:40 final size:40
Alignment explanation
Indices: 42685--42920 Score: 330
Period size: 40 Copynumber: 5.9 Consensus size: 40
42675 CGAATACACG
* * * * *
42685 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * ** * *
42725 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* **
42765 TCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
42805 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
42844 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
42884 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
42921 TTAGTAACTC
Statistics
Matches: 176, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 37 0.21
40 139 0.79
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:42863 original size:79 final size:80
Alignment explanation
Indices: 42685--42920 Score: 330
Period size: 79 Copynumber: 3.0 Consensus size: 80
42675 CGAATACACG
* * * * * * * * *
42685 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTCGGGG
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
* * *
42750 TTTAGCACGGATATA
66 CTTAGCCCGGATACA
* **
42765 TCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTC-GGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
42829 CTTAGCCCGGATACA
66 CTTAGCCCGGATACA
42844 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
42909 CTTAGCCCGGAT
66 CTTAGCCCGGAT
42921 TTAGTAACTC
Statistics
Matches: 137, Mismatches: 18, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
79 72 0.53
80 65 0.47
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
CTTAGCCCGGATACA
Found at i:42863 original size:119 final size:120
Alignment explanation
Indices: 42685--42920 Score: 330
Period size: 119 Copynumber: 2.0 Consensus size: 120
42675 CGAATACACG
* * *
42685 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTCGGGG
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGA
* *
42750 TTTAGCACGGATATATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACA
66 CTTAGCACGGATACATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACA
* * * * * *
42805 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGA
* * **
42869 CTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
66 CTTAGCACGGATACATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGAT
42921 TTAGTAACTC
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
119 82 0.81
120 19 0.19
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGA
CTTAGCACGGATACATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACA
Found at i:42945 original size:40 final size:40
Alignment explanation
Indices: 42698--42999 Score: 294
Period size: 40 Copynumber: 7.6 Consensus size: 40
42688 CCAGCATGAT
* * * * *
42698 TGCTCTTCGGGACCTAGCCCGGACATAACACCAGCA-CGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATC-AA
** * *
42738 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCA-CGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATC-AA
** *
42778 TGCTCTTCGAAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATCAA
*
42818 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATCAA
*
42857 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATCAA
** * * *
42897 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCATCAA
* **
42938 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAA
1 TGCTCTTCGGGA-CTTAGCCCGGATA-CATCAC-TAGCATCAA
*
42978 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
43000 CATCATTCAA
Statistics
Matches: 225, Mismatches: 30, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
39 40 0.18
40 166 0.74
41 19 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATCAA
Found at i:42945 original size:119 final size:118
Alignment explanation
Indices: 42698--42999 Score: 320
Period size: 119 Copynumber: 2.5 Consensus size: 118
42688 CCAGCATGAT
* * * * * ** *
42698 TGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCA-GAATGCTCTTCGGGACTTAGCCCGGATA
* * **
42763 TATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACATCACTAGCATGAA
64 CATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACATAACTAGCACCAA
42818 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATAC
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCA-GAATGCTCTTCGGGACTTAGCCCGGATAC
* ** ** *
42883 ATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
65 ATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACA-TAACTAGCACCAA
* ** * *
42938 TGC-CTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGA-CTTAGCCCGGATA-CATCAC-TAGCAGAATGCTCTTCGGGACTTAGCCCGGA
43000 CATCATTCAA
Statistics
Matches: 154, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
119 90 0.58
120 51 0.33
121 8 0.05
122 5 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (118 bp):
TGCTCTTCGGACTTAGCCCGGATACATCACTAGCAGAATGCTCTTCGGGACTTAGCCCGGATACA
TCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACATAACTAGCACCAA
Found at i:42985 original size:159 final size:160
Alignment explanation
Indices: 42685--42999 Score: 377
Period size: 159 Copynumber: 2.0 Consensus size: 160
42675 CGAATACACG
* * *
42685 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTCGGGG
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGA
* * *
42750 TTTAGCACGGATATATCACTAGCACGAATGCTCTTCGAAACTTAGCCCGGATACATCACTAGCAT
66 CTTAGCACGGATATATAACTAGCACCAATGCTCTTCGAAACTTAGCCCGGATACATCACTAGCAT
* *
42815 GAATGCTCTTC-GGACTTAGCCCGGATACA
131 CAAAGCTCTTCGGGACTTAGCCCGGATACA
* * * * * *
42844 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGA
* * * * * * **
42909 CTTAGCCCGGATTTAGTAACTCGCACCAATGC-CTTCGGATCTTAGTCCGGATATGGTCACTTAG
66 CTTAGCACGGATATA-TAACTAGCACCAATGCTCTTCGAAACTTAGCCCGGATA-CATCAC-TAG
42973 CA-CAAAGC-CTTCGGGACTTAGCCCGGA
128 CATCAAAGCTCTTCGGGACTTAGCCCGGA
43000 CATCATTCAA
Statistics
Matches: 130, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
159 90 0.69
160 35 0.27
161 5 0.04
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (160 bp):
TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGGA
CTTAGCACGGATATATAACTAGCACCAATGCTCTTCGAAACTTAGCCCGGATACATCACTAGCAT
CAAAGCTCTTCGGGACTTAGCCCGGATACA
Found at i:43344 original size:29 final size:29
Alignment explanation
Indices: 43305--43383 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
43295 CTTAATAATC
*
43305 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
43335 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
43364 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
43384 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:43426 original size:43 final size:43
Alignment explanation
Indices: 43365--43467 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
43355 TGCATTTCAA
43365 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
43408 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
43451 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
43468 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:45364 original size:37 final size:37
Alignment explanation
Indices: 45314--45392 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
45304 TTATTACGAA
* * *
45314 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
45351 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
45388 GTCTT
1 GTCTT
45393 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:45597 original size:47 final size:47
Alignment explanation
Indices: 45510--46047 Score: 823
Period size: 47 Copynumber: 11.4 Consensus size: 47
45500 GCCTTCGGGA
* * * * * * * *
45510 CTTATCACATTTATGCACTTTCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45557 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45604 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45651 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45698 CTTAT-ACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45744 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45791 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45838 CTTAT-ACATATACATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
45886 CTTATCACATATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45937 CTTATCACATATACATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45984 CTTAT-ACATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
46029 CTTATCACACATATACACT
1 CTTATCACATATATACACT
46048 CTCTTGGCTG
Statistics
Matches: 461, Mismatches: 23, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
45 13 0.03
46 92 0.20
47 264 0.57
48 38 0.08
49 6 0.01
51 48 0.10
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:45728 original size:140 final size:140
Alignment explanation
Indices: 45510--46047 Score: 835
Period size: 140 Copynumber: 3.8 Consensus size: 140
45500 GCCTTCGGGA
* * * * * * * * * *
45510 CTTATCACATTTATGCACTTTCACATCCATTACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-ACATATATACAC
*
45575 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
65 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
45640 GGCCATTAGGC
130 GGCCATTAGGC
45651 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATACATATATACACT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATACATATATACACT
*
45716 TTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG
66 TTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG
*
45781 GCTATTAGGC
131 GCCATTAGGC
* * *
45791 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATACATATACATATA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATACATAT--ATACA
*
45856 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACATACACTTTCACATTCATC
64 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ACAT--ATACACTTTCACATTCATC
45921 ACATCGGCCATTAGGC
125 ACATCGGCCATTAGGC
* *
45937 CTTATCACATATACATACTTTCACATTCATCACATCGGCCATTAGGCCTTATACATATATACACT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATACATATATACACT
46002 TTCACATTCATCACATCGG-CATTAGGCCTTATCACACATATACACT
66 TTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACT
46048 CTCTTGGCTG
Statistics
Matches: 366, Mismatches: 25, Indels: 14
0.90 0.06 0.03
Matches are distributed among these distances:
139 7 0.02
140 141 0.39
141 45 0.12
142 41 0.11
143 16 0.04
144 28 0.08
146 88 0.24
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (140 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATACATATATACACT
TTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCG
GCCATTAGGC
Found at i:45991 original size:40 final size:41
Alignment explanation
Indices: 45946--46033 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 41
45936 CCTTATCACA
45946 TATAC-AT-ACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATACAATAACTTTCACATTCATCACATCGG-CATTAGGCCT
45986 TATACATATATACACTTTCACATTCATCACATCGGCATTAGGCCT
1 TATAC--A-ATA-ACTTTCACATTCATCACATCGGCATTAGGCCT
46031 TAT
1 TAT
46034 CACACATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
40 5 0.12
44 2 0.05
45 13 0.31
46 22 0.52
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (41 bp):
TATACAATAACTTTCACATTCATCACATCGGCATTAGGCCT
Found at i:53816 original size:21 final size:20
Alignment explanation
Indices: 53778--53818 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
53768 AAAAGAAATT
53778 GAAAAGAGTTGAAGAAAGAA
1 GAAAAGAGTTGAAGAAAGAA
53798 GAAAATGAGTTAGAA-AAAGAA
1 GAAAA-GAGTT-GAAGAAAGAA
53819 ACAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 11 0.58
22 3 0.16
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (20 bp):
GAAAAGAGTTGAAGAAAGAA
Found at i:66657 original size:70 final size:69
Alignment explanation
Indices: 66544--66688 Score: 254
Period size: 70 Copynumber: 2.1 Consensus size: 69
66534 GTGTGTTGAT
66544 TTACTTTCTTCCATATTTAGGGTCTCTATTTTGATTATCTGGCTCACAAAGTTTTTTAAATAAAA
1 TTACTTTCTTCCATATTTAGGGTCTCTATTTTGATTATCTGGCTCACAAAGTTTTTTAAAT-AAA
66609 AAAAC
65 AAAAC
* * *
66614 TTACTTTCTTCCGTATTTGGGGTCTCTATTTTGATTATCTGGCTCATAAAGTTTTTTAAATAAAA
1 TTACTTTCTTCCATATTTAGGGTCTCTATTTTGATTATCTGGCTCACAAAGTTTTTTAAATAAAA
66679 AAAC
66 AAAC
66683 TTACTT
1 TTACTT
66689 GAAGATAATA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
69 14 0.19
70 58 0.81
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (69 bp):
TTACTTTCTTCCATATTTAGGGTCTCTATTTTGATTATCTGGCTCACAAAGTTTTTTAAATAAAA
AAAC
Done.