Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1589
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: 51219
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:4168 original size:28 final size:27
Alignment explanation
Indices: 4106--4174 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
4096 ATATTAAGTC
* *
4106 CGCACACTCAGTACTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
4133 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
4161 CGCACACTTAGTGC
1 CGCACACTTAGTGC
4175 CAATCTCATG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:4637 original size:12 final size:12
Alignment explanation
Indices: 4620--4646 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4610 TGGGCATACT
4620 TATGTATATATA
1 TATGTATATATA
4632 TATGTATATATA
1 TATGTATATATA
4644 TAT
1 TAT
4647 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:24771 original size:50 final size:51
Alignment explanation
Indices: 24696--24921 Score: 223
Period size: 50 Copynumber: 4.5 Consensus size: 51
24686 TGAATACACG
**
24696 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAT-ACTGTTAAGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATGACTGTTAAGTCACA
* * ** *
24746 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACT-TCGA-TCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-C-ATGACTGTTAAGTCACA
* * * * *
24797 TGTGTAGTACTAAGTGCAAGCTACTACGTGTATCA-GA-TGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATGACT-GTTAAGTCACA
* * *
24847 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-TGATTGTT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATGACTGTTAAGTCACA
* *
24896 TGTGTAGTACTAAGTACAGACTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
24922 TGCATATCAG
Statistics
Matches: 147, Mismatches: 21, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
47 1 0.01
48 2 0.01
49 31 0.21
50 73 0.50
51 33 0.22
52 4 0.03
53 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATGACTGTTAAGTCACA
Found at i:24930 original size:99 final size:100
Alignment explanation
Indices: 24746--24933 Score: 229
Period size: 99 Copynumber: 1.9 Consensus size: 100
24736 TTAAGTCGTA
* *
24746 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACTTCGATCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACTC-ATGACTTCGATCACATGTGTAGTACTAAG
* **
24811 TGCAAGCTACTACGTGTATCAGATGGTGAGGTCACG
65 TACAAGCTACTACGCATATCAGATGGTGAGGTCACG
* * * * *
24847 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-C-TGATTGTTGGTCGCATGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCATGACT-TCGATCACATGTGTAGTACTAAG
*
24910 TAC-AGACTACTATGCATATCAGAT
65 TACAAG-CTACTACGCATATCAGAT
24934 AGCTTCGGCT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
98 6 0.08
99 36 0.49
100 1 0.01
101 31 0.42
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (100 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGCGTACTCATGACTTCGATCACATGTGTAGTACTAAGT
ACAAGCTACTACGCATATCAGATGGTGAGGTCACG
Found at i:25041 original size:27 final size:26
Alignment explanation
Indices: 25011--25062 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
25001 GGGAAAATCG
25011 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGTGG--ATATGTGCAAAGTTATT
* *
25038 ATAAGGTGGATATGTGCAAATTTAT
1 ATAAAGTGGATATGTGCAAAGTTAT
25063 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (26 bp):
ATAAAGTGGATATGTGCAAAGTTATT
Found at i:30222 original size:29 final size:29
Alignment explanation
Indices: 30183--30261 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
30173 CTTAATAATC
*
30183 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
30213 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
30242 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
30262 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:34202 original size:26 final size:27
Alignment explanation
Indices: 34099--34202 Score: 140
Period size: 27 Copynumber: 3.9 Consensus size: 27
34089 CAAAATCATT
*
34099 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTATC
*
34126 GAAATACCCCTGTAGGGTAGAAATATC
1 GAAATACCCCTGTAGGGTAGAATTATC
*
34153 GAAATACCCCTGTAGGGTGGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTATC
* *
34180 -AAGATACCCTTGTGGGGTA-AATT
1 GAA-ATACCCCTGTAGGGTAGAATT
34203 TACTATTTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
26 6 0.09
27 63 0.91
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTATC
Found at i:34659 original size:25 final size:25
Alignment explanation
Indices: 34628--34697 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 25
34618 GATGACTTTG
*
34628 TGCCACATATTCTGTTAAGTGGCTT
1 TGCCACATATTCTGTTAAGTGGCTC
**
34653 TGCCACAT-TATCTGATTCTGGTGGCTC
1 TGCCACATAT-TCTG-TT-AAGTGGCTC
34680 TGCCACAATATTCTGTTA
1 TGCCAC-ATATTCTGTTA
34698 TTAGCAGCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
24 1 0.03
25 12 0.33
26 2 0.06
27 14 0.39
28 6 0.17
29 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (25 bp):
TGCCACATATTCTGTTAAGTGGCTC
Found at i:34845 original size:25 final size:25
Alignment explanation
Indices: 34817--34878 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
34807 CATTCACGTT
*
34817 CTGATTCTGATTATGTTACCCAATA
1 CTGATTCTGATTATGTCACCCAATA
* * *
34842 CTGATTCTGATTCTGTCACCTAATT
1 CTGATTCTGATTATGTCACCCAATA
34867 CTGATTCTGATT
1 CTGATTCTGATT
34879 TTGATTCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (25 bp):
CTGATTCTGATTATGTCACCCAATA
Found at i:34885 original size:12 final size:12
Alignment explanation
Indices: 34868--34898 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34858 CACCTAATTC
*
34868 TGATTCTGATTT
1 TGATTCTCATTT
34880 TGATTCTCATTT
1 TGATTCTCATTT
34892 TGATTCT
1 TGATTCT
34899 AGTTCTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (12 bp):
TGATTCTCATTT
Found at i:36966 original size:27 final size:26
Alignment explanation
Indices: 36864--36968 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 26
36854 AATACTTTAG
* *
36864 TTTACCAAATTACTGAAATACCCTCGA
1 TTTACAAAATTA-TCAAATACCCTCGA
* ** * *
36891 CTTGTAAAATTACCAAAGTACCCCCGA
1 TTTACAAAATTATCAAA-TACCCTCGA
**
36918 TTTACAAAATTATCAGTTTACCCTCGA
1 TTTACAAAATTATCA-AATACCCTCGA
*
36945 TTTACAAAATTATTGAAATACCCT
1 TTTACAAAATTA-TCAAATACCCT
36969 TGTAGGGTAG
Statistics
Matches: 58, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
26 3 0.05
27 53 0.91
28 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (26 bp):
TTTACAAAATTATCAAATACCCTCGA
Found at i:36982 original size:27 final size:27
Alignment explanation
Indices: 36959--37145 Score: 252
Period size: 27 Copynumber: 7.0 Consensus size: 27
36949 CAAAATTATT
*
36959 GAAATACCCTTGTAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
36986 GAAATACCCCTATAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
*
37013 GAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCTTGTAGGGTAGAATTACC
*
37040 AAAATACCCTTGTAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
*
37067 GAAATACCCTTGTAGGGT-GAAATACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* *
37093 GAAATACCCCTGTAAGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
37120 -AAGATACCCTTCTGGGGTAAAATTAC
1 GAA-ATACCCTTGTAGGGTAGAATTAC
37146 TATTTTGCCT
Statistics
Matches: 140, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
26 25 0.18
27 115 0.82
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
GAAATACCCTTGTAGGGTAGAATTACC
Found at i:37144 original size:80 final size:81
Alignment explanation
Indices: 36960--37145 Score: 266
Period size: 80 Copynumber: 2.3 Consensus size: 81
36950 AAAATTATTG
* * *
36960 AAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATTACCGAAATACCCTTG
1 AAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAAATACCGAAATACCCCTG
*
37025 TAGGGTAGAAATACCA
66 TAAGGTAGAAATACCA
* *
37041 AAATACCCTTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGT-GAAATACCGAAATACCCCTG
1 AAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAAATACCGAAATACCCCTG
*
37105 TAAGGTAGAATTACCA
66 TAAGGTAGAAATACCA
* * * *
37121 AGATACCCTTCTGGGGTAAAATTAC
1 AAATACCCTTGTAGGGTAGAATTAC
37146 TATTTTGCCT
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 53 0.56
81 41 0.44
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (81 bp):
AAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAAATACCGAAATACCCCTG
TAAGGTAGAAATACCA
Found at i:37768 original size:6 final size:6
Alignment explanation
Indices: 37759--37882 Score: 103
Period size: 6 Copynumber: 20.3 Consensus size: 6
37749 TTGCATTCAC
* *
37759 ATTCTG ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG
* * *
37808 -TCACCTA ATTTTG ATTCTG ATTCTG ACTT-TG ATTCTG ATTCTG ATTCTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG A-TTCTG ATTCTG ATTCTG ATTCTG
* *
37857 ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG A-TTCTG AT
37883 AATGTTTCTT
Statistics
Matches: 94, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
5 6 0.06
6 78 0.83
7 8 0.09
8 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:37790 original size:25 final size:24
Alignment explanation
Indices: 37762--37856 Score: 111
Period size: 25 Copynumber: 3.9 Consensus size: 24
37752 CATTCACATT
37762 CTGATTCTGATTCTGATTCTGTTAC
1 CTGATTCTGATTCTGATTCTG-TAC
* *
37787 CTGATACTGATTCTAATTCTGTCAC
1 CTGATTCTGATTCTGATTCTGT-AC
* *
37812 CTAATTTTGATTCTGATTCTG-AC
1 CTGATTCTGATTCTGATTCTGTAC
*
37835 TTTGATTCTGATTCTGATTCTG
1 -CTGATTCTGATTCTGATTCTG
37857 ATTCTCATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.03
24 19 0.32
25 38 0.64
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (24 bp):
CTGATTCTGATTCTGATTCTGTAC
Found at i:41182 original size:40 final size:40
Alignment explanation
Indices: 41098--41281 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
41088 TTGAATGCTG
* * * *
41098 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
41137 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
41178 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
41218 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
41258 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41282 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
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:41235 original size:80 final size:81
Alignment explanation
Indices: 41098--41278 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
41088 TTGAATGCTG
* * *
41098 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
41162 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
41178 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
41239 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
41258 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
41279 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:41302 original size:39 final size:38
Alignment explanation
Indices: 41179--41328 Score: 122
Period size: 40 Copynumber: 3.8 Consensus size: 38
41169 GTTATTAATT
* ** * *
41179 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACT-ATA
** * *
41219 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-ATA
*
41258 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAT-A
* *
41298 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
41329 GAGCTATATC
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
39 32 0.35
40 60 0.65
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTATA
Found at i:50003 original size:39 final size:39
Alignment explanation
Indices: 49960--50140 Score: 152
Period size: 40 Copynumber: 4.6 Consensus size: 39
49950 TAACTCATTC
*
49960 ATGCCTTCGGGACTTAACCCGGATTTAAAACTCGCACGA
1 ATGCCTTCGGGACTTAACCCGGATTTAAAACTCGCACAA
*** *
49999 ATGCCTTCGGGACTTAACCCGGAATTGGTATCTCGCACAA
1 ATGCCTTCGGGACTTAACCCGG-ATTTAAAACTCGCACAA
* **
50039 AGGCCTTCGGGACTTAACCC-GAAATAATAACTCGCACAA
1 ATGCCTTCGGGACTTAACCCGGATTTAA-AACTCGCACAA
* ** * ** *
50078 ATACCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAA
1 ATGCCTTCGGGA-CTTAACCCGGATTTA-AAAC-TCGCACAA
*
50119 A-GCCTTCGGGACTTAGCCCGGA
1 ATGCCTTCGGGACTTAACCCGGA
50141 CAGCATTCAA
Statistics
Matches: 113, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
38 4 0.04
39 45 0.40
40 53 0.47
41 11 0.10
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (39 bp):
ATGCCTTCGGGACTTAACCCGGATTTAAAACTCGCACAA
Found at i:50045 original size:40 final size:39
Alignment explanation
Indices: 49962--50087 Score: 137
Period size: 39 Copynumber: 3.2 Consensus size: 39
49952 ACTCATTCAT
* * *
49962 GCCTTCGGGACTTAACCCGGATTTAAAACTCGCACGAAT
1 GCCTTCGGGACTTAACCCGGATTGAAAACTCGCACAAAG
** *
50001 GCCTTCGGGACTTAACCCGGAATTGGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGG-ATTGAAAACTCGCACAAAG
* * *
50041 GCCTTCGGGACTTAACCCGAAAT-AATAACTCGCACAAAT
1 GCCTTCGGGACTTAACCCGGATTGAA-AACTCGCACAAAG
*
50080 ACCTTCGG
1 GCCTTCGG
50088 ATCTTAGTCC
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 40 0.56
40 32 0.44
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (39 bp):
GCCTTCGGGACTTAACCCGGATTGAAAACTCGCACAAAG
Found at i:50100 original size:79 final size:78
Alignment explanation
Indices: 49962--50138 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 78
49952 ACTCATTCAT
** * * *
49962 GCCTTCGGGACTTAACCCGGATTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGA-ATTG
1 GCCTTCGGGACTTAACCC-GAAATAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATA-TA
*
50026 GT-A-TCTCGCACAAA
64 GTCACT-TAGCACAAA
**
50040 GGCCTTCGGGACTTAACCCGAAATAATAACTCGCACAAATACCTTC-GGATCTTAGTCCGGATAT
1 -GCCTTCGGGACTTAACCCGAAATAA-AACTCGCACAAATACCTTCGGGA-CTTAACCCGGATAT
50104 AGTCACTTAGCACAAA
63 AGTCACTTAGCACAAA
*
50120 GCCTTCGGGACTTAGCCCG
1 GCCTTCGGGACTTAACCCG
50139 GACAGCATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
78 8 0.10
79 65 0.77
80 10 0.12
81 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (78 bp):
GCCTTCGGGACTTAACCCGAAATAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATATAGT
CACTTAGCACAAA
Found at i:50134 original size:40 final size:40
Alignment explanation
Indices: 49962--50140 Score: 109
Period size: 39 Copynumber: 4.5 Consensus size: 40
49952 ACTCATTCAT
** * * *
49962 GCCTTCGGGACTTA-ACCCGGATTTAA-AACTCGCACGAAT
1 GCCTTCGGGACTTAGA-CCGGAAATAATAACTAGCACAAAG
* ** * *
50001 GCCTTCGGGACTTA-ACCCGGAATTGGTATCTCGCACAAAG
1 GCCTTCGGGACTTAGA-CCGGAAATAATAACTAGCACAAAG
* * *
50041 GCCTTCGGGACTTA-ACCCGAAATAATAACTCGCACAAAT
1 GCCTTCGGGACTTAGACCGGAAATAATAACTAGCACAAAG
* * * * *
50080 ACCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAA-
1 GCCTTCGGGA-CTTAGACCGGAAATAATAAC-TAGCACAAAG
*
50120 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAGACCGGA
50141 CAGCATTCAA
Statistics
Matches: 114, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
38 3 0.03
39 50 0.44
40 50 0.44
41 11 0.10
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
GCCTTCGGGACTTAGACCGGAAATAATAACTAGCACAAAG
Done.