Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3799
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: 100985
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:4931 original size:18 final size:18
Alignment explanation
Indices: 4896--4934 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
4886 TAACTTAACT
4896 ATTAATAATCCATATTCA
1 ATTAATAATCCATATTCA
4914 ATTAACTAATCCAT-TTCA
1 ATTAA-TAATCCATATTCA
4932 ATT
1 ATT
4935 TAGGTTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAATAATCCATATTCA
Found at i:29781 original size:29 final size:29
Alignment explanation
Indices: 29718--29785 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
29708 TAATCAACCA
29718 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
29747 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
29776 CGCACACTTA
1 CGCACACTTA
29786 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:29926 original size:29 final size:30
Alignment explanation
Indices: 29887--29965 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
29877 CTTAATAATC
29887 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
29917 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
29946 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
29966 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:36087 original size:17 final size:18
Alignment explanation
Indices: 36059--36097 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
36049 TTAAGGACTA
36059 AATTGAATATGGATTATT
1 AATTGAATATGGATTATT
36077 AATTG-ATATGGATTATT
1 AATTGAATATGGATTATT
36094 AATT
1 AATT
36098 AGAGGTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (18 bp):
AATTGAATATGGATTATT
Found at i:41329 original size:40 final size:41
Alignment explanation
Indices: 41267--41524 Score: 300
Period size: 40 Copynumber: 6.5 Consensus size: 41
41257 AAACCAAGTA
* * * *
41267 CCTTCGGGATTTA-ACCGGATA-TAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATTAG-TAACTCGCACAAATG
** *
41306 CCTTCGGGACTTAGCCCGGATA-TAGTAGTTCGAACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTAACTCGCACAAATG
**
41346 CCTTCGGGACTTAGCCCGGA-ATTAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTAACTCGCACAAATG
*
41386 CCTTCGGGACTTAGCCTGGATA-TAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTAACTCGCACAAATG
41426 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCA-ACAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTAACTCGCACA-AATG
* * * * *
41466 CCTTTGGGACTTAGCCC-GAAATTTGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTAACTCGCACAAATG
41506 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
41525 TTATCATCCA
Statistics
Matches: 193, Mismatches: 17, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
39 18 0.09
40 172 0.89
41 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (41 bp):
CCTTCGGGACTTAGCCCGGATATTAGTAACTCGCACAAATG
Found at i:41501 original size:120 final size:119
Alignment explanation
Indices: 41267--41521 Score: 338
Period size: 120 Copynumber: 2.1 Consensus size: 119
41257 AAACCAAGTA
* * * *
41267 CCTTCGGGATTTAACCGGATATAGCTACTCGCTCGAATGCCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
** * * *
41332 AGTTCGAACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAGTTCGCACAAATG
66 AACTCGAACAAATGCCTTCGGGACTTAGCCCGAAATTAGTAGCTAGCACAAATG
41386 CCTTCGGGACTTAGCCTGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATT
1 CCTTCGGGACTTAGCC-GGATATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-T
* *
41449 AGTAACTCGCAAC-AATGCCTTTGGGACTTAGCCCGAAATTTGTCA-CTAGCACAAATG
63 AGTAACTCG-AACAAATGCCTTCGGGACTTAGCCCGAAATTAGT-AGCTAGCACAAATG
41506 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
41522 CGGTTATCAT
Statistics
Matches: 120, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
119 16 0.13
120 100 0.83
121 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (119 bp):
CCTTCGGGACTTAGCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
AACTCGAACAAATGCCTTCGGGACTTAGCCCGAAATTAGTAGCTAGCACAAATG
Found at i:46900 original size:39 final size:40
Alignment explanation
Indices: 46799--47022 Score: 255
Period size: 40 Copynumber: 5.7 Consensus size: 40
46789 TTGAATGATG
* *
46799 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
46838 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
46879 TCCGGGCTAAG-CCCGAAGGCATTTGTGGGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
46918 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
46957 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
46996 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
47023 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
39 73 0.45
40 76 0.47
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:46948 original size:78 final size:80
Alignment explanation
Indices: 46799--47022 Score: 253
Period size: 79 Copynumber: 2.8 Consensus size: 80
46789 TTGAATGATG
* * * * *
46799 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGA-T-ACTATAACCGGGCTAAG-TCCCGAAGGCA
*
46861 TTTGTGCGAGATACTAAT
63 TTTGTGCGAGATACTAAA
* * *
46879 TCCGGGCTAAG-CCCGAAGGCATTTGTGGGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGATACTATA-ACCGGGCTAAGTCCCGAAGGCATT
*
46941 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* * *
46957 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTT
47022 G
66 G
47023 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
78 36 0.29
79 54 0.43
80 34 0.27
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:47045 original size:79 final size:78
Alignment explanation
Indices: 46852--47022 Score: 229
Period size: 78 Copynumber: 2.2 Consensus size: 78
46842 GGACTAAGAT
* * *
46852 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGGGAGATACTA
1 CCGAAGGCATTTGTGCGAGATACTAA-TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
*
46916 ATTCCGGGCTAAGC
65 ATACCGGGCTAAGC
* *
46930 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-
1 CCGAAGGCATTTGTGCGAGATACT-AATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
*
46994 ATAACCGGGCTATGTC
65 AT-ACCGGGCTAAG-C
47010 CCGAAGGCATTTG
1 CCGAAGGCATTTG
47023 AACGAGTAGC
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
78 35 0.43
79 33 0.40
80 14 0.17
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGATACTAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTAA
TACCGGGCTAAGC
Found at i:47053 original size:79 final size:79
Alignment explanation
Indices: 46852--47055 Score: 209
Period size: 79 Copynumber: 2.6 Consensus size: 79
46842 GGACTAAGAT
** * * * * * *
46852 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCT-AAGCCCGAAGGCATTTGTGGGAGATACTA
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCAATTGTGCGAGATACTA
*
46916 ATTCCGGGCTAAGC
66 ATACCGGGCTAAGC
** * *
46930 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCAATTGTGCGAGATACTA
*
46994 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
* *
47010 CCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTTAAATCCCGAAGG
47056 TACGTGATTT
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
78 34 0.32
79 48 0.45
80 25 0.23
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCAATTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:56570 original size:27 final size:27
Alignment explanation
Indices: 56537--56607 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
56527 CCAAAGTACG
* * *
56537 CTCGATTTATAGAATTACTGTTTTACC
1 CTCGATTTACAGAATTACTATTTTAAC
* *
56564 CTTGATTTACATAATTACTATTTTAAC
1 CTCGATTTACAGAATTACTATTTTAAC
*
56591 CTCGATTTACAAAATTA
1 CTCGATTTACAGAATTA
56608 TCGTTTAACC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (27 bp):
CTCGATTTACAGAATTACTATTTTAAC
Found at i:56620 original size:27 final size:27
Alignment explanation
Indices: 56537--56620 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
56527 CCAAAGTACG
* * *
56537 CTCGATTTATAGAATTA-CTGTTTTACC
1 CTCGATTTACAAAATTATC-GTTTAACC
* * **
56564 CTTGATTTACATAATTACTATTTTAA-C
1 CTCGATTTACAAAATTA-TCGTTTAACC
56591 CTCGATTTACAAAATTATCGTTTAACC
1 CTCGATTTACAAAATTATCGTTTAACC
56618 CTC
1 CTC
56621 AATTGTGAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
26 6 0.14
27 34 0.77
28 4 0.09
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (27 bp):
CTCGATTTACAAAATTATCGTTTAACC
Found at i:56646 original size:27 final size:27
Alignment explanation
Indices: 56622--56751 Score: 108
Period size: 27 Copynumber: 4.9 Consensus size: 27
56612 TTAACCCTCA
* * *
56622 ATTGTGAAATTACTAAAATACCCCTAT
1 ATTGTAAAATTACCAAAATACCCCTAG
**
56649 AGGGTAAAATTACCAAAATACCCCTAG
1 ATTGTAAAATTACCAAAATACCCCTAG
* * *
56676 TTTGTGAAATTACCGAAATA-CCCTCA-
1 ATTGTAAAATTACCAAAATACCCCT-AG
*
56702 ATTTTAAAATTACCAAAATACCCCT-G
1 ATTGTAAAATTACCAAAATACCCCTAG
56728 ATT-TACAAACTTA-CAGAAATACCC
1 ATTGTA-AAA-TTACCA-AAATACCC
56752 TTGACTTTCT
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
25 2 0.02
26 28 0.34
27 53 0.64
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (27 bp):
ATTGTAAAATTACCAAAATACCCCTAG
Found at i:56695 original size:54 final size:53
Alignment explanation
Indices: 56623--56726 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 53
56613 TAACCCTCAA
*
56623 TTGTGAAATTACTAAAATACCC-CTATAGGGTAAAATTACCAAAATACCCCTAGT
1 TTGTGAAATTACCAAAATACCCTC-A-AGGGTAAAATTACCAAAATACCCCTAGT
* ***
56677 TTGTGAAATTACCGAAATACCCTCAATTTTAAAATTACCAAAATACCCCT
1 TTGTGAAATTACCAAAATACCCTCAAGGGTAAAATTACCAAAATACCCCT
56727 GATTTACAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
53 22 0.50
54 21 0.48
55 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (53 bp):
TTGTGAAATTACCAAAATACCCTCAAGGGTAAAATTACCAAAATACCCCTAGT
Found at i:56802 original size:27 final size:27
Alignment explanation
Indices: 56763--56814 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
56753 TGACTTTCTA
56763 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
56790 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
56815 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:56932 original size:27 final size:27
Alignment explanation
Indices: 56855--56932 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
56845 AAATGACTAA
* *
56855 AATACCCCT-AATAGGTAAAAAGACCGC
1 AATACCCCTGTAT-GGTAAAATGACCGC
* * *
56882 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGC
56909 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
56933 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.02
27 38 0.93
28 2 0.05
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGC
Found at i:57762 original size:26 final size:26
Alignment explanation
Indices: 57733--57881 Score: 194
Period size: 26 Copynumber: 5.8 Consensus size: 26
57723 GAGGAAGTGC
* *
57733 AAAAAGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
* *
57759 AAAAGGGCCTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
57785 AAAAGGGCTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
* * *
57811 AAAATGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
* *
57837 AGAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
57862 AAAAGGTCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
57882 ATTAAAGAGG
Statistics
Matches: 107, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
25 30 0.28
26 77 0.72
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACTG
Found at i:58085 original size:42 final size:42
Alignment explanation
Indices: 58026--58114 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
58016 TAGTCTCCCC
* ** *
58026 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
58068 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
58110 AAATG
1 AAATG
58115 AGTCTAAGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:58218 original size:31 final size:31
Alignment explanation
Indices: 58141--58219 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
58131 CGTTTACAGT
*
58141 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
58172 AAAGGGTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
58203 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
58220 AACCGTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:60564 original size:27 final size:27
Alignment explanation
Indices: 60534--60618 Score: 118
Period size: 27 Copynumber: 3.1 Consensus size: 27
60524 AAGTACGCTC
* * *
60534 GATTTATAGAATTACTATTTTACCCTT
1 GATTTACAAAATTACTGTTTTACCCTT
*
60561 GATTTACAAAATTACTGTTTTACCCTC
1 GATTTACAAAATTACTGTTTTACCCTT
60588 GATTTACAAAATTA-TCGTTTTACCCTT
1 GATTTACAAAATTACT-GTTTTACCCTT
60615 GATT
1 GATT
60619 GTGACATTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
26 1 0.02
27 51 0.98
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (27 bp):
GATTTACAAAATTACTGTTTTACCCTT
Found at i:60680 original size:27 final size:27
Alignment explanation
Indices: 60650--60772 Score: 137
Period size: 27 Copynumber: 4.6 Consensus size: 27
60640 TATAGGGCAG
60650 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
60677 AATTACCAAAATACCACTAGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
60704 AATTACCGAAATA-CCCTCAATTT-TAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
**
60730 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
60757 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
60773 TTGACTTTCT
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
26 22 0.27
27 60 0.73
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:60691 original size:54 final size:52
Alignment explanation
Indices: 60631--60747 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 52
60621 GACATTACTG
*
60631 AAATACCCCTA-TAGGGCAGAATTACCAAAATACCC-CTAGTTTGTAAAATTACCA
1 AAATACCCCTAGTAGGG-A-AATTACCAAAATACCCTC-AATTT-TAAAATTACCA
* * * *
60685 AAATACCACTAGTTTGTGAAATTACCGAAATACCCTCAATTTTAAAATTACCA
1 AAATACCCCTAG-TAGGGAAATTACCAAAATACCCTCAATTTTAAAATTACCA
60738 AAATACCCCT
1 AAATACCCCT
60748 GATTTACAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
53 20 0.37
54 29 0.54
55 2 0.04
56 3 0.06
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (52 bp):
AAATACCCCTAGTAGGGAAATTACCAAAATACCCTCAATTTTAAAATTACCA
Found at i:60760 original size:53 final size:54
Alignment explanation
Indices: 60650--60829 Score: 161
Period size: 53 Copynumber: 3.3 Consensus size: 54
60640 TATAGGGCAG
* * * ***
60650 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCACT-AGTTTGTGA
1 AATTACCGAAATACCCTC-AATTTCTAAAATTACCAAAATACCACTGA-TTTACAA
*
60704 AATTACCGAAATACCCTCAATTT-TAAAATTACCAAAATACCCCTGATTTACAA
1 AATTACCGAAATACCCTCAATTTCTAAAATTACCAAAATACCACTGATTTACAA
* * * * * *
60757 AATTACAGAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACAA
1 AATTACCGAAATACCC-TCAATTTCT-AAAATTACCA-AAATACCACTGATTTACAA
*
60813 AATTACTGAAATACCCT
1 AATTACCGAAATACCCT
60830 TAGTTTGTAG
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
53 39 0.37
54 25 0.24
55 4 0.04
56 38 0.36
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (54 bp):
AATTACCGAAATACCCTCAATTTCTAAAATTACCAAAATACCACTGATTTACAA
Found at i:60835 original size:27 final size:26
Alignment explanation
Indices: 60650--60835 Score: 115
Period size: 27 Copynumber: 6.9 Consensus size: 26
60640 TATAGGGCAG
* * *
60650 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCGAAATACCCTTAGTTT-CAA
* **
60677 AATTACCAAAATACCAC-TAGTTTGTGA
1 AATTACCGAAATACC-CTTAGTTT-CAA
* * *
60704 AATTACCGAAATACCCTCAATTTTAA
1 AATTACCGAAATACCCTTAGTTTCAA
* *
60730 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCGAAATACCCTTAG-TTT-CAA
* *
60757 AATTACAGAAATACCCTTGACTTTCTAAA
1 AATTACCGAAATACCCTT-AGTTTC--AA
** * *
60786 AATTATAGAAATACCATTGGTTTACAA
1 AATTACCGAAATACCCTTAGTTT-CAA
*
60813 AATTACTGAAATACCCTTAGTTT
1 AATTACCGAAATACCCTTAGTTT
60836 GTAGATTTAC
Statistics
Matches: 128, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
26 21 0.16
27 81 0.63
28 7 0.05
29 19 0.15
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (26 bp):
AATTACCGAAATACCCTTAGTTTCAA
Found at i:61815 original size:52 final size:52
Alignment explanation
Indices: 61754--61899 Score: 235
Period size: 52 Copynumber: 2.8 Consensus size: 52
61744 GAGGAAGTGC
* * *
61754 AAAAGGGCTTATGCCCCAGTTTATCGAAAAGGGCTTATATCCC-AGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTAT-GCCCTAATTTATTG
61806 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCTAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCTAATTTATTG
61858 AAAAGGGCTT-TGCCCCAGTTTACCGAAAAGGGCTT-TGCCCTA
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCTA
61900 GTTATTAAAG
Statistics
Matches: 90, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
50 7 0.08
51 28 0.31
52 55 0.61
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCTAATTTATTG
Found at i:61879 original size:25 final size:26
Alignment explanation
Indices: 61754--61902 Score: 203
Period size: 26 Copynumber: 5.8 Consensus size: 26
61744 GAGGAAGTGC
61754 AAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
** *
61780 AAAAGGGCTTATATCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
61806 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
* * *
61832 AAAAGGGCTTATGCCCTAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
61858 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
61883 AAAAGGGCTT-TGCCCTAGTT
1 AAAAGGGCTTATGCCCCAGTT
61903 ATTAAAGAGG
Statistics
Matches: 107, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
25 30 0.28
26 77 0.72
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATCG
Found at i:62106 original size:42 final size:42
Alignment explanation
Indices: 62047--62138 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
62037 TAGTCTCCCC
* ** *
62047 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
62089 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
62131 AAATGGGC
1 AAATGGGC
62139 CTAAGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:62199 original size:31 final size:31
Alignment explanation
Indices: 62162--62271 Score: 184
Period size: 31 Copynumber: 3.5 Consensus size: 31
62152 CGTTTACAGT
* *
62162 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGACCCAGTGATATGATTTATGA
* *
62193 ACAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGACCCAGTGATATGATTTATGA
62224 AAAGGCTTCGACCCAGTGATATGATTTATGA
1 AAAGGCTTCGACCCAGTGATATGATTTATGA
62255 AAAGGCTTCGACCCAGT
1 AAAGGCTTCGACCCAGT
62272 AACCGTTAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGACCCAGTGATATGATTTATGA
Found at i:66111 original size:34 final size:34
Alignment explanation
Indices: 66031--66112 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
66021 TATACTGAAT
* **
66031 TGGGCTAAGGCCTACACAGATACTGGTACTGTAA
1 TGGGCTAAGGCCCACACAGATACTGCCACTGTAA
* * * *
66065 TAGGCTAGGGCCCACACTGATATTGCCACTG-ATA
1 TGGGCTAAGGCCCACACAGATACTGCCACTGTA-A
66099 TGGGCTAAGGCCCA
1 TGGGCTAAGGCCCA
66113 GACCATTTTG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
33 1 0.03
34 37 0.97
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (34 bp):
TGGGCTAAGGCCCACACAGATACTGCCACTGTAA
Found at i:69953 original size:44 final size:42
Alignment explanation
Indices: 69880--69989 Score: 105
Period size: 44 Copynumber: 2.5 Consensus size: 42
69870 GTATTGATCT
* * * * * *
69880 AAATTATCGTGTAAGACCGTATTTGGGACA-CTGGCATCGATTTG
1 AAATT-TCGTGTAAGACCATGTCTAGGACATC-GGCATC-ATATC
69924 AAATTTACGTGTAAGACCATGTCTAGGACATCGGCATCATATC
1 AAATTT-CGTGTAAGACCATGTCTAGGACATCGGCATCATATC
* *
69967 TAATTTCGTGTAAGACCCTGTCT
1 AAATTTCGTGTAAGACCATGTCT
69990 GAGATAGAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
42 16 0.29
43 9 0.16
44 30 0.54
45 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (42 bp):
AAATTTCGTGTAAGACCATGTCTAGGACATCGGCATCATATC
Found at i:74095 original size:27 final size:27
Alignment explanation
Indices: 74065--74241 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
74055 ATATTGAGTC
* * *
74065 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
74092 CGCACACTTAGTGCTACGTAATCAA-T
1 CGCACACTTAGTGCTACATAGTCAACT
74118 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
** * *
74146 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
74173 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
74200 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
74227 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
74242 GTACAATTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 22 0.17
27 85 0.66
28 22 0.17
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:74230 original size:81 final size:81
Alignment explanation
Indices: 74086--74240 Score: 233
Period size: 81 Copynumber: 1.9 Consensus size: 81
74076 TGCTATATAA
* *
74086 TCAACTCGCACACTTAGTGCTACGTAATCAATCGCACACTTAGTGCTACATAGTCAAACTCGCAC
1 TCAACTCGCACACTTAGTGCTACATAATCAATCGCACACTTAGTGCAACATAGTCAAACTCGCAC
74151 ACTTAGTGCCGCATGG
66 ACTTAGTGCCGCATGG
* * *
74167 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAA-TCGC
1 TCAACTCGCACACTTAGTGCTA-CATAATCA-ATCGCACACTTAGTGCAACATAGTCAAACTCGC
74230 ACACTTAGTGC
64 ACACTTAGTGC
74241 TGTACAATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
80 1 0.01
81 40 0.60
82 26 0.39
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAATCGCACACTTAGTGCAACATAGTCAAACTCGCAC
ACTTAGTGCCGCATGG
Done.