Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2248
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: 51742
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:3865 original size:20 final size:20
Alignment explanation
Indices: 3840--3913 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
3830 AAAAAGATAG
3840 AATGTATCAATACATTGAAA
1 AATGTATCAATACATTGAAA
* * * *
3860 AATGTATCGATATATTCATA
1 AATGTATCAATACATTGAAA
* ** *
3880 CATGTATTGATACGTTG-AA
1 AATGTATCAATACATTGAAA
3899 AATGTATCAATACAT
1 AATGTATCAATACAT
3914 CTGCGTAAAA
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
19 12 0.30
20 28 0.70
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCAATACATTGAAA
Found at i:4869 original size:31 final size:31
Alignment explanation
Indices: 4830--4946 Score: 123
Period size: 32 Copynumber: 3.7 Consensus size: 31
4820 CCAGCGACAT
4830 TAGG-TTTAGAAGGGTTGCCACCAACTCGTG
1 TAGGCTTTAGAAGGGTTGCCACCAACTCGTG
* * *
4860 TAGGCTTTAGAGAAGGTTGCTACCAACTTGTG
1 TAGGCTTTAGA-AGGGTTGCCACCAACTCGTG
* * *
4892 TGGGCTTTAGAAGGGTTGCTACCGAC-CTGTG
1 TAGGCTTTAGAAGGGTTGCCACCAACTC-GTG
4923 T-GGACTTTAGAAGAGGTTGCCACC
1 TAGG-CTTTAGAAG-GGTTGCCACC
4947 GACTTGTGGG
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
30 6 0.08
31 32 0.43
32 36 0.49
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (31 bp):
TAGGCTTTAGAAGGGTTGCCACCAACTCGTG
Found at i:4933 original size:63 final size:63
Alignment explanation
Indices: 4834--4954 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
4824 CGACATTAGG
*
4834 TTTAGAAGGGTTGCCACCAACTCGTGTAGGCTTTAG-AGAAGGTTGCTACCAACTTGTGTGGGC
1 TTTAGAAGGGTTGCCACCAACTCGTGTAGGCTTTAGAAG-AGGTTGCCACCAACTTGTGTGGGC
* * *
4897 TTTAGAAGGGTTGCTACCGAC-CTGTGT-GGACTTTAGAAGAGGTTGCCACCGACTTGTG
1 TTTAGAAGGGTTGCCACCAACTC-GTGTAGG-CTTTAGAAGAGGTTGCCACCAACTTGTG
4955 GGCTTTGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
62 3 0.06
63 46 0.90
64 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (63 bp):
TTTAGAAGGGTTGCCACCAACTCGTGTAGGCTTTAGAAGAGGTTGCCACCAACTTGTGTGGGC
Found at i:4948 original size:32 final size:32
Alignment explanation
Indices: 4834--4973 Score: 134
Period size: 31 Copynumber: 4.6 Consensus size: 32
4824 CGACATTAGG
* *
4834 TTTAGAAG-GGTTGCCACC-AACTCGTGTAGGC
1 TTTAGAAGAGGTTGCCACCGACCT-GTGTGGGC
* * *
4865 TTTAG-AGAAGGTTGCTACCAACTTGTGTGGGC
1 TTTAGAAG-AGGTTGCCACCGACCTGTGTGGGC
* *
4897 TTTAGAAG-GGTTGCTACCGACCTGTGTGGAC
1 TTTAGAAGAGGTTGCCACCGACCTGTGTGGGC
4928 TTTAGAAGAGGTTGCCACCGA-CT-TGTGGGC
1 TTTAGAAGAGGTTGCCACCGACCTGTGTGGGC
*
4958 TTT-GAAAAGG-TGCCAC
1 TTTAGAAGAGGTTGCCAC
4974 TGACTTATGG
Statistics
Matches: 94, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
28 6 0.06
29 6 0.06
30 11 0.12
31 35 0.37
32 32 0.34
33 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (32 bp):
TTTAGAAGAGGTTGCCACCGACCTGTGTGGGC
Found at i:4972 original size:28 final size:29
Alignment explanation
Indices: 4921--5085 Score: 171
Period size: 28 Copynumber: 5.9 Consensus size: 29
4911 TACCGACCTG
* * * *
4921 TGTGGACTTTAGAAGAGGTTGCCACCGACT
1 TGTGGGCTTT-GAAAAGGATGCCACTGACT
4951 TGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
4979 TATGGGTTTTGAAATGG-TGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
5007 T-TGGGCTTTG-AAAGGAAGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
5034 TGTGGGCTTTG-AAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
5062 TATAGGCTTTGAAAAAG-TGCCACT
1 TGTGGGCTTTGAAAAGGATGCCACT
5086 AATTTTCAGG
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.03
27 19 0.16
28 76 0.64
29 10 0.08
30 9 0.08
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACT
Found at i:5007 original size:56 final size:56
Alignment explanation
Indices: 4940--5302 Score: 301
Period size: 56 Copynumber: 6.6 Consensus size: 56
4930 TAGAAGAGGT
* *
4940 TGCCACCGACTTGTGGGCTTTGAAAAGG-TGCCACTGACTTATGGGTTTTGAAATGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTGAAA-GG
* *
4996 TGCCACTGACTT-TGGGCTTTG-AAAGGAAGCCACTGACTTGTGGGCTTTGAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTGAAAGG
* * * * *
5050 ATGCCACTAACTTATAGGCTTTGAAAAAG-TGCCACT-A---AT----TTT--CAGG
1 -TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTGAAAGG
* * * *
5096 CGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTACGAGCTTTGAAAAAG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTG-AAAGG
** * * * * *
5152 TGCCACTGACTTACGAGCTTTGAAAAGG-TCCCACTGACTTGTTGGTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTG-AAA-GG
* * * * **
5209 TTGCCACTGACTTGTGAGCTCTG-AAAGGATGCCACTGACTTGTAGGCTTTGAAAATA
1 -TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTG-AAAGG
5266 TGCCACTGACTTGTGGGCTTTGAAAAGGGATGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAA-GGATGCCACT
5303 AACTCGGGAG
Statistics
Matches: 246, Mismatches: 39, Indels: 42
0.75 0.12 0.13
Matches are distributed among these distances:
44 4 0.02
45 25 0.10
46 4 0.02
48 3 0.01
49 1 0.00
52 1 0.00
53 3 0.01
54 7 0.03
55 43 0.17
56 85 0.35
57 18 0.07
58 52 0.21
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (56 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTATGGGCTTTGAAAGG
Found at i:5087 original size:28 final size:28
Alignment explanation
Indices: 4940--5085 Score: 172
Period size: 28 Copynumber: 5.2 Consensus size: 28
4930 TAGAAGAGGT
* *
4940 TGCCACCGACTTGTGGGCTTTGAAAAGG
1 TGCCACTGACTTATGGGCTTTGAAAAGG
* *
4968 TGCCACTGACTTATGGGTTTTGAAATGG
1 TGCCACTGACTTATGGGCTTTGAAAAGG
4996 TGCCACTGACTT-TGGGCTTTG-AAAGG
1 TGCCACTGACTTATGGGCTTTGAAAAGG
* *
5022 AAGCCACTGACTTGTGGGCTTTG-AAAGG
1 -TGCCACTGACTTATGGGCTTTGAAAAGG
* * *
5050 ATGCCACTAACTTATAGGCTTTGAAAAAG
1 -TGCCACTGACTTATGGGCTTTGAAAAGG
5079 TGCCACT
1 TGCCACT
5086 AATTTTCAGG
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.04
27 19 0.18
28 76 0.74
29 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (28 bp):
TGCCACTGACTTATGGGCTTTGAAAAGG
Found at i:5143 original size:28 final size:28
Alignment explanation
Indices: 5097--5320 Score: 204
Period size: 28 Copynumber: 7.9 Consensus size: 28
5087 ATTTTCAGGC
*
5097 GCCACTGACTTGTGGGCTTTGAAAGGAT
1 GCCACTGACTTGTGAGCTTTGAAAGGAT
** *
5125 GCCACTGACTTACGAGCTTTGAAA-AAGT
1 GCCACTGACTTGTGAGCTTTGAAAGGA-T
**
5153 GCCACTGACTTACGAGCTTTGAAAAGG-T
1 GCCACTGACTTGTGAGCTTTG-AAAGGAT
* * *
5181 CCCACTGACTTGTTG-GTTTTGAAAAGGGTT
1 GCCACTGACTTG-TGAGCTTTG-AAA-GGAT
*
5211 GCCACTGACTTGTGAGCTCTGAAAGGAT
1 GCCACTGACTTGTGAGCTTTGAAAGGAT
**
5239 GCCACTGACTTGT-AGGCTTTGAAAATAT
1 GCCACTGACTTGTGA-GCTTTGAAAGGAT
*
5267 GCCACTGACTTGTGGGCTTTGAAAAGGGAT
1 GCCACTGACTTGTGAGCTTTG-AAA-GGAT
* * *
5297 GCCACTAACTCGGGAGCTTTGAAA
1 GCCACTGACTTGTGAGCTTTGAAA
5321 ATGTGTCGTA
Statistics
Matches: 162, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
27 2 0.01
28 108 0.67
29 17 0.10
30 35 0.22
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (28 bp):
GCCACTGACTTGTGAGCTTTGAAAGGAT
Found at i:5186 original size:101 final size:100
Alignment explanation
Indices: 4997--5186 Score: 258
Period size: 101 Copynumber: 1.9 Consensus size: 100
4987 TTGAAATGGT
** * *
4997 GCCACTGACTTTGGGCTTTGAAAGGAAGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
1 GCCACTGACTTTGGGCTTTGAAAGGAAGCCACTGACTTACGAGCTTTGAAAAGATGCCACTAACT
* *
5062 TATAGGCTTTGAAAAAGTGCCACTAATTTTCAGGC
66 TAGAGGCTTTGAAAAAGTCCCACTAATTTTCAGGC
* *
5097 GCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTACGAGCTTTGAAAA-AGTGCCACTGA
1 GCCACTGACTT-TGGGCTTTGAAAGGAAGCCACTGACTTACGAGCTTTGAAAAGA-TGCCACTAA
*
5161 CTTACGA-GCTTTGAAAAGGTCCCACT
64 CTTA-GAGGCTTTGAAAAAGTCCCACT
5187 GACTTGTTGG
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
100 12 0.15
101 65 0.83
102 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (100 bp):
GCCACTGACTTTGGGCTTTGAAAGGAAGCCACTGACTTACGAGCTTTGAAAAGATGCCACTAACT
TAGAGGCTTTGAAAAAGTCCCACTAATTTTCAGGC
Found at i:5242 original size:86 final size:86
Alignment explanation
Indices: 5098--5321 Score: 269
Period size: 86 Copynumber: 2.6 Consensus size: 86
5088 TTTTCAGGCG
*
5098 CCACTGACTTGTGGGCTTTG-AAA-GGATGCCACTGACTTACGAGCTTTGAAAAAGTGCCACTGA
1 CCACTGACTTGTGGGCTTTGAAAAGGGATGCCACTGACTTGCGAGCTTTGAAAAAGTGCCACTGA
*
5161 C-T-TACGAGCTTTGAAAAGGTC
66 CTTGTA-G-GCTTTGAAAAGATC
* * * * * *
5182 CCACTGACTTGTTGGTTTTGAAAAGGGTTGCCACTGACTTGTGAGCTCTG-AAAGGATGCCACTG
1 CCACTGACTTGTGGGCTTTGAAAAGGGATGCCACTGACTTGCGAGCTTTGAAAAAG-TGCCACTG
* *
5246 ACTTGTAGGCTTTGAAAATATG
65 ACTTGTAGGCTTTGAAAAGATC
* * *
5268 CCACTGACTTGTGGGCTTTGAAAAGGGATGCCACTAACTCGGGAGCTTTGAAAA
1 CCACTGACTTGTGGGCTTTGAAAAGGGATGCCACTGACTTGCGAGCTTTGAAAA
5322 TGTGTCGTAT
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
84 18 0.15
85 7 0.06
86 85 0.73
87 5 0.04
88 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (86 bp):
CCACTGACTTGTGGGCTTTGAAAAGGGATGCCACTGACTTGCGAGCTTTGAAAAAGTGCCACTGA
CTTGTAGGCTTTGAAAAGATC
Found at i:5386 original size:26 final size:26
Alignment explanation
Indices: 5331--5386 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
5321 ATGTGTCGTA
* * *
5331 TTAACAAAAATTTCTTGACAAAGTTT
1 TTAACAAAAATTTCTCGACAAAGCTC
*
5357 TTAACAAACA-TTCTCGACAAAAGCTC
1 TTAACAAAAATTTCTCGAC-AAAGCTC
5383 TTAA
1 TTAA
5387 TGGTAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (26 bp):
TTAACAAAAATTTCTCGACAAAGCTC
Found at i:6635 original size:14 final size:15
Alignment explanation
Indices: 6616--6660 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
6606 GATCCCTCCC
6616 TTTTTG-TATTGTTT
1 TTTTTGTTATTGTTT
*
6630 TTTTTGTTTTTGTTT
1 TTTTTGTTATTGTTT
*
6645 TTTTTTTTATT-TTT
1 TTTTTGTTATTGTTT
6659 TT
1 TT
6661 GCTTTTTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.04, C:0.00, G:0.09, T:0.87
Consensus pattern (15 bp):
TTTTTGTTATTGTTT
Found at i:6641 original size:20 final size:18
Alignment explanation
Indices: 6616--6658 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
6606 GATCCCTCCC
*
6616 TTTTTGTATTGTTTTTTTTG
1 TTTTTGT-TT-TTTTTTTTA
6636 TTTTTGTTTTTTTTTTTA
1 TTTTTGTTTTTTTTTTTA
6654 TTTTT
1 TTTTT
6659 TTGCTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.59
19 2 0.09
20 7 0.32
ACGTcount: A:0.05, C:0.00, G:0.09, T:0.86
Consensus pattern (18 bp):
TTTTTGTTTTTTTTTTTA
Found at i:6659 original size:20 final size:19
Alignment explanation
Indices: 6616--6667 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
6606 GATCCCTCCC
*
6616 TTTTTGTATTGTTTTTTTTG
1 TTTTTGT-TTTTTTTTTTTG
*
6636 TTTTTGTTTTTTTTTTTATT
1 TTTTTGTTTTTTTTTTT-TG
6656 TTTTTGCTTTTT
1 TTTTTG-TTTTT
6668 GAGAATGACG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 9 0.32
20 14 0.50
21 5 0.18
ACGTcount: A:0.04, C:0.02, G:0.10, T:0.85
Consensus pattern (19 bp):
TTTTTGTTTTTTTTTTTTG
Found at i:21613 original size:52 final size:51
Alignment explanation
Indices: 21533--21651 Score: 202
Period size: 52 Copynumber: 2.3 Consensus size: 51
21523 AAAAGTTGCT
*
21533 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTACC
* *
21585 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
21636 TGCATGTATCGATACA
1 TGCATGTATCGATACA
21652 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 20 0.31
52 44 0.69
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
Found at i:21678 original size:13 final size:13
Alignment explanation
Indices: 21660--21684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21650 CAAAGATCAG
21660 TGTATCGATACAA
1 TGTATCGATACAA
21673 TGTATCGATACA
1 TGTATCGATACA
21685 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:21762 original size:33 final size:33
Alignment explanation
Indices: 21725--21791 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
21715 AGTAGCTTAA
21725 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
21758 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
21791 A
1 A
21792 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:21765 original size:13 final size:13
Alignment explanation
Indices: 21747--21771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21737 CAAAAAAATA
21747 TGTATCGATACAT
1 TGTATCGATACAT
21760 TGTATCGATACA
1 TGTATCGATACA
21772 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:22736 original size:52 final size:52
Alignment explanation
Indices: 22604--22815 Score: 199
Period size: 52 Copynumber: 4.2 Consensus size: 52
22594 GAAAAGTGAT
* * * * * * * *
22604 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* * *
22658 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
22711 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
22754 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
22806 AAAGGTGCCA
1 AAAGGTGCCA
22816 CCGATTTGTG
Statistics
Matches: 129, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
43 37 0.29
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 42 0.33
53 6 0.05
54 5 0.04
55 35 0.27
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:22772 original size:43 final size:43
Alignment explanation
Indices: 22711--22800 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
22701 TAAAGATGGA
*
22711 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
22754 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
22797 AAAG
1 AAAG
22801 ATGGAAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:22903 original size:28 final size:29
Alignment explanation
Indices: 22835--22974 Score: 187
Period size: 30 Copynumber: 4.9 Consensus size: 29
22825 GGTCTTCGGA
* *
22835 AAAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
22863 -AAGGTTGCCACTGACTTGTGGGCTTTT-
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
22890 AAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
**
22919 AAAAATATGCCACTGACTTGTGGGCTTTTG
1 AAAGGT-TGCCACTGACTTGTGGGCTTTTG
* *
22949 AAAAGGGTGCCACTAACTTGTGGGCT
1 -AAAGGTTGCCACTGACTTGTGGGCT
22975 AAAAAGAGTG
Statistics
Matches: 99, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.21
28 30 0.30
29 4 0.04
30 41 0.41
31 3 0.03
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (29 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTG
Found at i:22910 original size:85 final size:86
Alignment explanation
Indices: 22806--22974 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 86
22796 TAAAGATGGA
* * * * * *
22806 AAAGGTGCCACCGATTTGTGGTCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 AAAGGTGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
22869 GCCACTGACTTGTGGGCTTTT
66 GCCACTAACTTGTGGGCTTTT
* ** *
22890 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGG-TGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGGGCTTTTG-AAAGG
22955 GTGCCACTAACTTGTGGGCT
64 GTGCCACTAACTTGTGGGCT
22975 AAAAAGAGTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
84 5 0.07
85 39 0.56
86 4 0.06
88 22 0.31
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (86 bp):
AAAGGTGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGGGCTTTTGAAAGGGT
GCCACTAACTTGTGGGCTTTT
Found at i:22932 original size:30 final size:29
Alignment explanation
Indices: 22804--22974 Score: 177
Period size: 30 Copynumber: 5.9 Consensus size: 29
22794 CTTAAAGATG
* * * * **
22804 GAAAAGGTGCCACCGATTTGTGGTCTTCG
1 GAAAAGTTGCCACTGACTTGTGGGCTTTT
* *
22833 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAA-GTTGCCACTGACTTGTGGGCTTTT
*
22862 G-AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGTTGCCACTGACTTGTGGGCTTTT
*
22890 -AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGTTGCCACTGACTTGTGGGCTTTT
*
22918 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGT-TGCCACTGACTTGTGGGCTTTT
* *
22948 GAAAAGGGTGCCACTAACTTGTGGGCT
1 GAAAA-GTTGCCACTGACTTGTGGGCT
22975 AAAAAGAGTG
Statistics
Matches: 124, Mismatches: 12, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
27 18 0.15
28 32 0.26
29 11 0.09
30 63 0.51
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (29 bp):
GAAAAGTTGCCACTGACTTGTGGGCTTTT
Found at i:23046 original size:30 final size:30
Alignment explanation
Indices: 23011--23098 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
23001 TTACAAAAGA
* * *
23011 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGAGTGCCACCGACTTGTGGGCTTTGG
*
23041 AAAAGA-TGCCACCGACTTGTGGGCTTCGG
1 AAAAGAGTGCCACCGACTTGTGGGCTTTGG
* * *
23070 AAAAGGGTGCCACTGATTTGTGGGCTTTG
1 AAAAGAGTGCCACCGACTTGTGGGCTTTG
23099 AAGGTTGATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.49
30 25 0.51
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (30 bp):
AAAAGAGTGCCACCGACTTGTGGGCTTTGG
Found at i:24532 original size:1 final size:1
Alignment explanation
Indices: 24528--24616 Score: 52
Period size: 1 Copynumber: 89.0 Consensus size: 1
24518 CCGGACCCCC
* * * * * ** * **
24528 TTTTTTTGTTTTTTTATTGTTTTTGTTTTTTTGTTTTTTTTTTCCTTTTGTTTTTTTTTTGGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** **
24593 TTCATTTTTTTCGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
24617 GGAGGACGCC
Statistics
Matches: 66, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.84
Consensus pattern (1 bp):
T
Found at i:24547 original size:11 final size:10
Alignment explanation
Indices: 24528--24586 Score: 59
Period size: 10 Copynumber: 5.7 Consensus size: 10
24518 CCGGACCCCC
24528 TTTTTTTGTT
1 TTTTTTTGTT
24538 TTTTTATTGTT
1 TTTTT-TTGTT
24549 TTTGTTTT-TT
1 TTT-TTTTGTT
24559 TGTTTTTT-TT
1 T-TTTTTTGTT
*
24569 TTCCTTTTGTT
1 TT-TTTTTGTT
24580 TTTTTTT
1 TTTTTTT
24587 TGGTTTTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
9 1 0.02
10 23 0.55
11 16 0.38
12 2 0.05
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.86
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:24550 original size:17 final size:16
Alignment explanation
Indices: 24528--24616 Score: 74
Period size: 17 Copynumber: 5.2 Consensus size: 16
24518 CCGGACCCCC
24528 TTTTTTTGTTTTTTTA
1 TTTTTTTGTTTTTTTA
*
24544 TTGTTTTTGTTTTTTTG
1 TT-TTTTTGTTTTTTTA
*
24561 TTTTTTT-TTTCCTTTTG
1 TTTTTTTGTTT--TTTTA
*
24578 TTTTTTTTTTGGTTTTTCA
1 TTTTTTTGTT--TTTTT-A
24597 TTTTTTTCGTTTTTTT-
1 TTTTTTT-GTTTTTTTA
24613 TTTT
1 TTTT
24617 GGAGGACGCC
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
15 3 0.05
16 11 0.18
17 27 0.44
18 11 0.18
19 7 0.11
20 3 0.05
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.84
Consensus pattern (16 bp):
TTTTTTTGTTTTTTTA
Found at i:24556 original size:25 final size:24
Alignment explanation
Indices: 24528--24616 Score: 92
Period size: 25 Copynumber: 3.5 Consensus size: 24
24518 CCGGACCCCC
24528 TTTTTTTGTTTTTTTATTGTTTTTG
1 TTTTTTTGTTTTTTTATT-TTTTTG
24553 TTTTTTTGTTTTTTT-TTTCCTTTTG
1 TTTTTTTGTTTTTTTATTT--TTTTG
*
24578 TTTTTTTTTTGGTTTTTCATTTTTTTCG
1 TTTTTTTGTT--TTTTT-ATTTTTTT-G
24606 TTTTTTT-TTTT
1 TTTTTTTGTTTT
24617 GGAGGACGCC
Statistics
Matches: 56, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
23 1 0.02
24 2 0.04
25 31 0.55
27 11 0.20
28 8 0.14
29 3 0.05
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.84
Consensus pattern (24 bp):
TTTTTTTGTTTTTTTATTTTTTTG
Found at i:24585 original size:29 final size:28
Alignment explanation
Indices: 24548--24617 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
24538 TTTTTATTGT
* *
24548 TTTTGTTTTTTTGTTTTT-TTTTTCCTTTTG
1 TTTT-TTTTTTTGTTTTTCATTTT--TTTCG
*
24578 TTTTTTTTTTGGTTTTTCATTTTTTTCG
1 TTTTTTTTTTTGTTTTTCATTTTTTTCG
24606 TTTTTTTTTTTG
1 TTTTTTTTTTTG
24618 GAGGACGCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 15 0.43
29 12 0.34
30 8 0.23
ACGTcount: A:0.01, C:0.06, G:0.10, T:0.83
Consensus pattern (28 bp):
TTTTTTTTTTTGTTTTTCATTTTTTTCG
Found at i:34318 original size:10 final size:10
Alignment explanation
Indices: 34303--34329 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
34293 ATGTATCAAG
34303 CAAAAACAAA
1 CAAAAACAAA
34313 CAAAAACAAA
1 CAAAAACAAA
34323 CAAAAAC
1 CAAAAAC
34330 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:38552 original size:52 final size:51
Alignment explanation
Indices: 38472--38590 Score: 202
Period size: 52 Copynumber: 2.3 Consensus size: 51
38462 AAAAGTTGCT
*
38472 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTACC
* *
38524 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
38575 TGCATGTATCGATACA
1 TGCATGTATCGATACA
38591 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 20 0.31
52 44 0.69
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
Found at i:38617 original size:13 final size:13
Alignment explanation
Indices: 38599--38623 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38589 CAAAGATCAG
38599 TGTATCGATACAA
1 TGTATCGATACAA
38612 TGTATCGATACA
1 TGTATCGATACA
38624 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:38701 original size:33 final size:33
Alignment explanation
Indices: 38664--38730 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
38654 AGTAGCTTAA
38664 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
38697 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
38730 A
1 A
38731 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:38704 original size:13 final size:13
Alignment explanation
Indices: 38686--38710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38676 CAAAAAAATA
38686 TGTATCGATACAT
1 TGTATCGATACAT
38699 TGTATCGATACA
1 TGTATCGATACA
38711 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:39182 original size:15 final size:17
Alignment explanation
Indices: 39149--39186 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
39139 AAATCAATCC
39149 TTTTAAAAAAAGTTAAA
1 TTTTAAAAAAAGTTAAA
39166 TTTTAAAAAAA-TT-AA
1 TTTTAAAAAAAGTTAAA
39181 TTTTAA
1 TTTTAA
39187 TATGTATCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.38
16 2 0.10
17 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TTTTAAAAAAAGTTAAA
Found at i:39550 original size:28 final size:27
Alignment explanation
Indices: 39500--39552 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
39490 TTCAAACTAT
** *
39500 TTGATTTAATTAGTTTTAGTTAATTAC
1 TTGATTTAATTAGTTCCAATTAATTAC
39527 TTGATTTTAATTAGTTCCAATTAATT
1 TTGA-TTTAATTAGTTCCAATTAATT
39553 TTAATTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (27 bp):
TTGATTTAATTAGTTCCAATTAATTAC
Found at i:41760 original size:15 final size:13
Alignment explanation
Indices: 41720--41759 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
41710 TAATCTTAAC
*
41720 AATATATATATGT
1 AATATATATATAT
*
41733 AATATAGATATAT
1 AATATATATATAT
41746 AATATATATATAT
1 AATATATATATAT
41759 A
1 A
41760 TCTGAATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (13 bp):
AATATATATATAT
Found at i:42029 original size:25 final size:24
Alignment explanation
Indices: 41990--42050 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
41980 TATTTAGATA
41990 TAAATTAAAATAAAGTTTATTTATG
1 TAAATTAAAATAAAGTTT-TTTATG
*
42015 TAAATATAAAA-AAAGTTTTTTGTG
1 TAAAT-TAAAATAAAGTTTTTTATG
42039 TAAA--AAAATAAA
1 TAAATTAAAATAAA
42051 TTAAAGATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 4 0.12
22 3 0.09
24 9 0.27
25 12 0.36
26 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (24 bp):
TAAATTAAAATAAAGTTTTTTATG
Found at i:42050 original size:26 final size:26
Alignment explanation
Indices: 41995--42044 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
41985 AGATATAAAT
*
41995 TAAAATAAAGTTTATTTATGTAAATA
1 TAAAATAAAGTTTATTTATGTAAAAA
*
42021 TAAAA-AAAGTTT-TTTGTGTAAAAA
1 TAAAATAAAGTTTATTTATGTAAAAA
42045 AATAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 7 0.32
26 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (26 bp):
TAAAATAAAGTTTATTTATGTAAAAA
Found at i:43194 original size:89 final size:85
Alignment explanation
Indices: 43047--43205 Score: 210
Period size: 89 Copynumber: 1.8 Consensus size: 85
43037 ATACACACAT
* * *
43047 AATTAAATAACAAAATAAATAATTATATTTTTATAATGATACATACGCATACCACATAAATTACA
1 AATTAAATAACAAAATAAATAATAATATTTTCATAATAATACATACGCATACCACATAAATTACA
43112 CAATTATACAATATATACTC
66 CAATTATACAATATATACTC
* * * * *
43132 AATTAAATAATAGAATAAATAATAACAATATTTTGCATAATAATACATATGCATATCGCATAAAT
1 AATTAAATAACAAAATAAATAAT---AATATTTT-CATAATAATACATACGCATACCACATAAAT
43197 TACACAATT
62 TACACAATT
43206 TTCAATTACA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 21 0.34
88 7 0.11
89 34 0.55
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.33
Consensus pattern (85 bp):
AATTAAATAACAAAATAAATAATAATATTTTCATAATAATACATACGCATACCACATAAATTACA
CAATTATACAATATATACTC
Done.