Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold182
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: 891401
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.32
Warning! 40281 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:822001 original size:75 final size:73
Alignment explanation
Indices: 821646--822270 Score: 618
Period size: 75 Copynumber: 8.2 Consensus size: 73
821636 AAAGAAAAAG
* * * * * *
821646 AAAA-AGAAATTAAAAAATATCTCAGCTTGACTCGAGGCTCAACTCACCTCTCGGATTATGAGTT
1 AAAACAGAAATT-GAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
821710 TATTTTTTTTTTTG-
65 GA------TTTTTGA
** * * *
821724 AAAACATTAATTGAAAATACCTCAGCGTGACCTGAGGCTTAACTCACCTCTCGCATTATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
821789 ATTTTTGA
66 ATTTTTGA
*
821797 AAAACAGAAAATTGAAAAATACCTC-GACATGTGACCCGAAGCTCAACTCACCTCTCGCAATATG
1 AAAACAG-AAATTG-AAAATACCTCAG-C--GTGACCCGAGGCTCAACTCACCTCTCGCAATATG
* *
821861 AGTTGCTTTTTTTTTTA
61 AGTTG----ATTTTTGA
*
821878 AAAA-AGTAGTAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
1 AAAACAG-A--AATTG-AAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATAT
*
821942 GAGTCGATTTTTGA
60 GAGTTGATTTTTGA
* * * * *
821956 AAAACAGGAATTTAAAATACCTCAGCGTGCGACCTGAGGCCCAACTCACCTCTCACAATATGAGT
1 AAAACAGAAATTGAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
*
822021 TGATTTTTTAA
64 TGA-TTTTTGA
* *
822032 AAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCTCTCGTAATGTGAGTT
1 AAAACAGAAATTGAAAATACCTCAGCG-TGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
822096 GATTTTTGA
65 GATTTTTGA
* * *
822105 AAAA-A-AAATTTAAAAGAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTCGCAATATGA
1 AAAACAGAAA-TT--GA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
*
822168 GTTGATTTTTTAA
62 GTTGA-TTTTTGA
* *
822181 AAAACAGAAATTGAAAATACCTCAG-GATGACCCGAGGCTCAACTCACCTCTCGTAATGTGAGTT
1 AAAACAGAAATTGAAAATACCTCAGCG-TGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
822245 GATTTTTGA
65 GATTTTTGA
*
822254 AAAACAAAAATTGAAAA
1 AAAACAGAAATTGAAAA
822271 ATATAATTCT
Statistics
Matches: 466, Mismatches: 53, Indels: 61
0.80 0.09 0.11
Matches are distributed among these distances:
71 3 0.01
72 9 0.02
73 41 0.09
74 86 0.18
75 105 0.23
76 45 0.10
77 38 0.08
78 63 0.14
79 7 0.02
80 3 0.01
81 10 0.02
82 55 0.12
83 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (73 bp):
AAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGA
Found at i:822105 original size:149 final size:148
Alignment explanation
Indices: 821678--822270 Score: 676
Period size: 149 Copynumber: 3.9 Consensus size: 148
821668 CAGCTTGACT
* * * ** **
821678 CGAGGCTCAACTCACCTCTCGGATTATGAGTTTATTTTTTTTTTTGAAAACATTAATTGAAAATA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTAAAAAACAGAAATTGAAAATA
* * *
821743 CCTCAGCG-TGACCTGAGGCTTAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAA
62 CCTCAGCGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAG-AA
* *
821807 ATTGAAAAATACCTCGACATGTGACC
126 ATT-TAAAATACCTCG-CGTG-GACC
* * * *
821833 CGAAGCTCAACTCACCTCTCGCAATATGAGTTGCTTTTTTTTTTAAAAAAGTAGTAATTGAAAAA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTG----ATTTTTTAAAAAA-CAGAAATTG-AAAA
* * *
821898 TACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAG
60 TACCTCAGCG-ATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAG
*
821963 GAATTTAAAATACCTCAGCGTGCGACC
124 AAATTTAAAATACCTC-GCGTG-GACC
* * *
821990 TGAGGCCCAACTCACCTCTCACAATATGAGTTGATTTTTTAAAAAACAGAAATTGAAAATACCTC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAACAGAAATTGAAAATACCTC
* *
822055 AG-GATGACCCGAGGCTCAACTCACCTCTCGTAATGTGAGTTGATTTTTGAAAAA-A-AAATTTA
66 AGCGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTT-
822117 AAAGAAATACCTCGGCGT-GACC
130 --A-AAATACCTC-GCGTGGACC
*
822139 CGAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAACAGAAATTGAAAATACCTC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAACAGAAATTGAAAATACCTC
* * * *
822204 AG-GATGACCCGAGGCTCAACTCACCTCTCGTAATGTGAGTTGATTTTTGAAAAACAAAAATTGA
66 AGCGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTA
822268 AAA
131 AAA
822271 ATATAATTCT
Statistics
Matches: 386, Mismatches: 37, Indels: 38
0.84 0.08 0.08
Matches are distributed among these distances:
147 8 0.02
148 2 0.01
149 166 0.43
150 3 0.01
151 29 0.08
152 7 0.02
153 12 0.03
155 39 0.10
156 7 0.02
157 59 0.15
158 5 0.01
159 49 0.13
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (148 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAACAGAAATTGAAAATACCTC
AGCGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTA
AAATACCTCGCGTGGACC
Found at i:823170 original size:11 final size:10
Alignment explanation
Indices: 823156--823210 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 10
823146 TTTTTTTTAC
*
823156 TTTTTTTG-C
1 TTTTTTTGTT
823165 TTTTTTTG--
1 TTTTTTTGTT
823173 TTTTTTTGTT
1 TTTTTTTGTT
823183 ATTTTTTTGTT
1 -TTTTTTTGTT
*
823194 TTTTTTCTCTT
1 TTTTTT-TGTT
823205 TTTTTT
1 TTTTTT
823211 AGGCATAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
8 8 0.20
9 8 0.20
10 6 0.15
11 19 0.46
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:823170 original size:19 final size:19
Alignment explanation
Indices: 823146--823211 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 19
823136 TTTTCTTCTT
823146 TTTTTTTTACTTTTTTTGC
1 TTTTTTTTACTTTTTTTGC
* *
823165 -TTTTTTT-GTTTTTTTGT
1 TTTTTTTTACTTTTTTTGC
** *
823182 TATTTTTTTGTTTTTTTTCTC
1 T-TTTTTTTACTTTTTTT-GC
823203 TTTTTTTTA
1 TTTTTTTTA
823212 GGCATAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
17 8 0.22
18 7 0.19
19 7 0.19
20 14 0.38
21 1 0.03
ACGTcount: A:0.05, C:0.06, G:0.06, T:0.83
Consensus pattern (19 bp):
TTTTTTTTACTTTTTTTGC
Found at i:823172 original size:9 final size:9
Alignment explanation
Indices: 823147--823208 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
823137 TTTCTTCTTT
*
823147 TTTTTTTAC
1 TTTTTTTGC
823156 TTTTTTTGC
1 TTTTTTTGC
823165 TTTTTTTG-
1 TTTTTTTGC
*
823173 TTTTTTTGTTA
1 TTTTTTTG--C
823184 TTTTTTTG-
1 TTTTTTTGC
*
823192 TTTTTTTTC
1 TTTTTTTGC
823201 TCTTTTTT
1 T-TTTTTT
823209 TTAGGCATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
8 15 0.33
9 17 0.37
10 6 0.13
11 8 0.17
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.84
Consensus pattern (9 bp):
TTTTTTTGC
Found at i:835847 original size:18 final size:18
Alignment explanation
Indices: 835834--835962 Score: 92
Period size: 18 Copynumber: 7.4 Consensus size: 18
835824 GTTTTTTTTT
835834 AACACGAGAATTTTTGAA
1 AACACGAGAATTTTTGAA
*
835852 AACACGAGAA--TTTGTA
1 AACACGAGAATTTTTGAA
*
835868 AACACGAAAATTTTTG-A
1 AACACGAGAATTTTTGAA
* * *
835885 AACACGACATTTTTTTTAAA
1 AACACGAGA--ATTTTTGAA
*
835905 AACACGGGAATTTTT-AA
1 AACACGAGAATTTTTGAA
* *
835922 AACA-GGGAAATTTT-AGA
1 AACACGAGAATTTTTGA-A
* *
835939 AATACGAAAATTTTT-AA
1 AACACGAGAATTTTTGAA
835956 AACACGA
1 AACACGA
835963 CATTTTTTTT
Statistics
Matches: 90, Mismatches: 14, Indels: 15
0.76 0.12 0.13
Matches are distributed among these distances:
16 24 0.27
17 26 0.29
18 27 0.30
19 5 0.06
20 8 0.09
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.29
Consensus pattern (18 bp):
AACACGAGAATTTTTGAA
Found at i:835865 original size:16 final size:16
Alignment explanation
Indices: 835834--835880 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
835824 GTTTTTTTTT
835834 AACACGAGAATTTTTGAA
1 AACACGAGAA--TTTGAA
*
835852 AACACGAGAATTTGTA
1 AACACGAGAATTTGAA
*
835868 AACACGAAAATTT
1 AACACGAGAATTT
835881 TTGAAACACG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 17 0.63
18 10 0.37
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.26
Consensus pattern (16 bp):
AACACGAGAATTTGAA
Found at i:835900 original size:71 final size:70
Alignment explanation
Indices: 835834--835972 Score: 192
Period size: 71 Copynumber: 2.0 Consensus size: 70
835824 GTTTTTTTTT
*
835834 AACACGAGAATTTTTGAAAACACGAG-AATTTGT-AAACACGAAAATTTTTGAAACACGACATTT
1 AACACGAGAATTTTT-AAAACA-GAGAAATTT-TAAAACACGAAAATTTTTAAAACACGACATTT
835897 TTTTTAAA
63 TTTTTAAA
* * *
835905 AACACGGGAATTTTTAAAACAGGGAAATTTTAGAAATACGAAAATTTTTAAAACACGACATTTTT
1 AACACGAGAATTTTTAAAACAGAGAAATTTTA-AAACACGAAAATTTTTAAAACACGACATTTTT
835970 TTT
65 TTT
835973 GAAACATGAT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
69 3 0.05
70 11 0.18
71 47 0.77
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (70 bp):
AACACGAGAATTTTTAAAACAGAGAAATTTTAAAACACGAAAATTTTTAAAACACGACATTTTTT
TTAAA
Found at i:835970 original size:17 final size:17
Alignment explanation
Indices: 835834--835962 Score: 100
Period size: 17 Copynumber: 7.4 Consensus size: 17
835824 GTTTTTTTTT
*
835834 AACACGAGAATTTTTGAA
1 AACACGAAAATTTTT-AA
* *
835852 AACACGAGAATTTGT-A
1 AACACGAAAATTTTTAA
*
835868 AACACGAAAATTTTTGA
1 AACACGAAAATTTTTAA
**
835885 AACACGACATTTTTTTTAAA
1 AACACGA-A-AATTTTT-AA
**
835905 AACACGGGAATTTTTAA
1 AACACGAAAATTTTTAA
* *
835922 AACAGGGAAA-TTTTAGA
1 AACACGAAAATTTTTA-A
*
835939 AATACGAAAATTTTTAA
1 AACACGAAAATTTTTAA
835956 AACACGA
1 AACACGA
835963 CATTTTTTTT
Statistics
Matches: 89, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
16 19 0.21
17 33 0.37
18 25 0.28
19 5 0.06
20 7 0.08
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.29
Consensus pattern (17 bp):
AACACGAAAATTTTTAA
Found at i:836075 original size:43 final size:42
Alignment explanation
Indices: 836008--836127 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 42
835998 ATGCGAGAAT
* *
836008 ATTTTTGAAACACGAAAAATTTTTTACAAACAC-AAAA-AGTGAA
1 ATTTTTGAAATACG-AAAATTTTTGA-AAACACGAAAACA-TGAA
836051 ATTTTTTGAAATACGAGAAATTTTTGAAAACACGAAAACATGAA
1 A-TTTTTGAAATACGA-AAATTTTTGAAAACACGAAAACATGAA
*
836095 AATTTTGAAAATACGAAAATTTTTG-AAACACGA
1 ATTTTTG-AAATACGAAAATTTTTGAAAACACGA
836128 GAAATTTTGA
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
42 8 0.12
43 22 0.32
44 38 0.55
45 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (42 bp):
ATTTTTGAAATACGAAAATTTTTGAAAACACGAAAACATGAA
Found at i:836087 original size:17 final size:18
Alignment explanation
Indices: 836084--836157 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 18
836074 TTGAAAACAC
*
836084 GAAAACATG-AAAATTTT
1 GAAAACACGAAAAATTTT
* *
836101 GAAAATACGAAAATTTTT
1 GAAAACACGAAAAATTTT
*
836119 G-AAACACGAGAAATTTT
1 GAAAACACGAAAAATTTT
* * *
836136 GAAGACATGAAAATTTTT
1 GAAAACACGAAAAATTTT
836154 GAAA
1 GAAA
836158 CATGATTTAA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
17 21 0.48
18 23 0.52
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (18 bp):
GAAAACACGAAAAATTTT
Found at i:836133 original size:35 final size:34
Alignment explanation
Indices: 836086--836159 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 34
836076 GAAAACACGA
* *
836086 AAACATGAAAATTTTGAAAATACGAAAATTTTTG
1 AAACACGAAAATTTTGAAAACACGAAAATTTTTG
* *
836120 AAACACGAGAAATTTTGAAGACATGAAAATTTTTG
1 AAACACGA-AAATTTTGAAAACACGAAAATTTTTG
836155 AAACA
1 AAACA
836160 TGATTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
34 7 0.20
35 28 0.80
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (34 bp):
AAACACGAAAATTTTGAAAACACGAAAATTTTTG
Found at i:836160 original size:17 final size:16
Alignment explanation
Indices: 836086--836162 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 16
836076 GAAAACACGA
836086 AAACATGAAAATTTTG
1 AAACATGAAAATTTTG
836102 AAA-ATACGAAAATTTTTG
1 AAACAT--GAAAA-TTTTG
*
836120 AAACACGAGAAATTTTG
1 AAACATGA-AAATTTTG
836137 AAGACATGAAAATTTTTG
1 AA-ACATGAAAA-TTTTG
836155 AAACATGA
1 AAACATGA
836163 TTTAAAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.04
16 3 0.06
17 23 0.44
18 23 0.44
19 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (16 bp):
AAACATGAAAATTTTG
Found at i:836164 original size:181 final size:181
Alignment explanation
Indices: 835968--836316 Score: 698
Period size: 181 Copynumber: 1.9 Consensus size: 181
835958 CACGACATTT
835968 TTTTTGAAACATGATTTAAAAAATTTTGAAATGCGAGAATATTTTTGAAACACGAAAAATTTTTT
1 TTTTTGAAACATGATTTAAAAAATTTTGAAATGCGAGAATATTTTTGAAACACGAAAAATTTTTT
836033 ACAAACACAAAAAGTGAAATTTTTTGAAATACGAGAAATTTTTGAAAACACGAAAACATGAAAAT
66 ACAAACACAAAAAGTGAAATTTTTTGAAATACGAGAAATTTTTGAAAACACGAAAACATGAAAAT
836098 TTTGAAAATACGAAAATTTTTGAAACACGAGAAATTTTGAAGACATGAAAA
131 TTTGAAAATACGAAAATTTTTGAAACACGAGAAATTTTGAAGACATGAAAA
836149 TTTTTGAAACATGATTTAAAAAATTTTGAAATGCGAGAATATTTTTGAAACACGAAAAATTTTTT
1 TTTTTGAAACATGATTTAAAAAATTTTGAAATGCGAGAATATTTTTGAAACACGAAAAATTTTTT
836214 ACAAACACAAAAAGTGAAATTTTTTGAAATACGAGAAATTTTTGAAAACACGAAAACATGAAAAT
66 ACAAACACAAAAAGTGAAATTTTTTGAAATACGAGAAATTTTTGAAAACACGAAAACATGAAAAT
836279 TTTGAAAATACGAAAATTTTTGAAACACGAGAAATTTT
131 TTTGAAAATACGAAAATTTTTGAAACACGAGAAATTTT
836317 TTTTTTGAAA
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
181 168 1.00
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (181 bp):
TTTTTGAAACATGATTTAAAAAATTTTGAAATGCGAGAATATTTTTGAAACACGAAAAATTTTTT
ACAAACACAAAAAGTGAAATTTTTTGAAATACGAGAAATTTTTGAAAACACGAAAACATGAAAAT
TTTGAAAATACGAAAATTTTTGAAACACGAGAAATTTTGAAGACATGAAAA
Found at i:836256 original size:43 final size:42
Alignment explanation
Indices: 836189--836308 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 42
836179 ATGCGAGAAT
* *
836189 ATTTTTGAAACACGAAAAATTTTTTACAAACAC-AAAA-AGTGAA
1 ATTTTTGAAATACG-AAAATTTTTGA-AAACACGAAAACA-TGAA
836232 ATTTTTTGAAATACGAGAAATTTTTGAAAACACGAAAACATGAA
1 A-TTTTTGAAATACGA-AAATTTTTGAAAACACGAAAACATGAA
*
836276 AATTTTGAAAATACGAAAATTTTTG-AAACACGA
1 ATTTTTG-AAATACGAAAATTTTTGAAAACACGA
836309 GAAATTTTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
42 8 0.12
43 22 0.32
44 38 0.55
45 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (42 bp):
ATTTTTGAAATACGAAAATTTTTGAAAACACGAAAACATGAA
Found at i:836285 original size:17 final size:17
Alignment explanation
Indices: 836265--836316 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
836255 TTGAAAACAC
*
836265 GAAAACATGAAAATTTT
1 GAAAACACGAAAATTTT
*
836282 GAAAATACGAAAATTTTT
1 GAAAACACGAAAA-TTTT
836300 G-AAACACGAGAAATTTT
1 GAAAACACGA-AAATTTT
836317 TTTTTTGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 22 0.73
18 8 0.27
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (17 bp):
GAAAACACGAAAATTTT
Found at i:836415 original size:31 final size:30
Alignment explanation
Indices: 836375--836486 Score: 130
Period size: 31 Copynumber: 3.8 Consensus size: 30
836365 GACACGAATA
836375 TATTTTTTGAAACACG-GAAAATTTTATTAT
1 TATTTTTTGAAACACGAG-AAATTTTATTAT
*
836405 TATTATTTTGAAACACGAGAAA-TTT-TGA-
1 TATT-TTTTGAAACACGAGAAATTTTATTAT
836433 -ATTTTTTG-AACACG-GAAAATTTTATTAT
1 TATTTTTTGAAACACGAG-AAATTTTATTAT
836461 TATTATTTTGAAACACGAGAAATTTT
1 TATT-TTTTGAAACACGAGAAATTTT
836487 GAAGACATGA
Statistics
Matches: 70, Mismatches: 2, Indels: 19
0.77 0.02 0.21
Matches are distributed among these distances:
24 1 0.01
25 9 0.13
26 8 0.11
27 5 0.07
29 5 0.07
30 12 0.17
31 28 0.40
32 2 0.03
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.44
Consensus pattern (30 bp):
TATTTTTTGAAACACGAGAAATTTTATTAT
Found at i:836444 original size:25 final size:27
Alignment explanation
Indices: 836406--836489 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 27
836396 TTTTATTATT
836406 ATTATTTTGAAACACGAGAAATTTTGA
1 ATTATTTTGAAACACGAGAAATTTTGA
*
836433 ATT-TTTTG-AACACG-GAAAATTTTATTA
1 ATTATTTTGAAACACGAG-AAA-TTT-TGA
836460 TTATTATTTTGAAACACGAGAAATTTTGA
1 --ATTATTTTGAAACACGAGAAATTTTGA
836489 A
1 A
836490 GACATGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
24 1 0.02
25 9 0.19
26 8 0.17
27 6 0.13
29 5 0.11
30 8 0.17
31 9 0.19
32 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.40
Consensus pattern (27 bp):
ATTATTTTGAAACACGAGAAATTTTGA
Found at i:836446 original size:56 final size:57
Alignment explanation
Indices: 836376--836489 Score: 221
Period size: 56 Copynumber: 2.0 Consensus size: 57
836366 ACACGAATAT
836376 ATTTTTTGAAACACGGAAAATTTTATTATTATTATTTTGAAACACGAGAAATTTTGA
1 ATTTTTTGAAACACGGAAAATTTTATTATTATTATTTTGAAACACGAGAAATTTTGA
836433 ATTTTTTG-AACACGGAAAATTTTATTATTATTATTTTGAAACACGAGAAATTTTGA
1 ATTTTTTGAAACACGGAAAATTTTATTATTATTATTTTGAAACACGAGAAATTTTGA
836489 A
1 A
836490 GACATGAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 49 0.86
57 8 0.14
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (57 bp):
ATTTTTTGAAACACGGAAAATTTTATTATTATTATTTTGAAACACGAGAAATTTTGA
Found at i:836506 original size:18 final size:17
Alignment explanation
Indices: 836465--836513 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
836455 TATTATTATT
836465 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAGAA
*
836482 ATTTTGAAGACATGA-AA
1 ATTTTGAA-ACACGAGAA
836499 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
836514 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (17 bp):
ATTTTGAAACACGAGAA
Found at i:836567 original size:111 final size:110
Alignment explanation
Indices: 836433--836631 Score: 380
Period size: 111 Copynumber: 1.8 Consensus size: 110
836423 GAAATTTTGA
836433 ATTTTTTGAACACGGAAAATTTTATTATTATTATTTTGAAACACGAGAAATTTTGAAGACATGAA
1 ATTTTTTGAACACGGAAAATTTTATTATTATTATTTTGAAACACGAGAAATTTTGAAGACATGAA
836498 AATTTTTGAAACACGATTTTTTTAAAAAGAAAGAGACACGAATAT
66 AATTTTTGAAACACGATTTTTTTAAAAAGAAAGAGACACGAATAT
*
836543 ATTTTTTGAAACACGGAAAATTTTATTATTATTATTTTGAAACACGAGAAATTTTGAAGACCTGA
1 ATTTTTTG-AACACGGAAAATTTTATTATTATTATTTTGAAACACGAGAAATTTTGAAGACATGA
836608 AAATTTTTGAAACACGATTTTTTT
65 AAATTTTTGAAACACGATTTTTTT
836632 TAATACCGTA
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
110 8 0.09
111 79 0.91
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (110 bp):
ATTTTTTGAACACGGAAAATTTTATTATTATTATTTTGAAACACGAGAAATTTTGAAGACATGAA
AATTTTTGAAACACGATTTTTTTAAAAAGAAAGAGACACGAATAT
Found at i:836598 original size:17 final size:16
Alignment explanation
Indices: 836576--836624 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
836566 TATTATTATT
836576 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGA-AA
836593 ATTTTGAAGAC-CTGAAA
1 ATTTTGAA-ACAC-GAAA
836610 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
836625 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (16 bp):
ATTTTGAAACACGAAA
Found at i:837211 original size:19 final size:19
Alignment explanation
Indices: 837187--837234 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
837177 TGCTGTTCTG
*
837187 GGCTTGCTGGACTGGGTCA
1 GGCTTGCTGGACTGGGACA
* * *
837206 GGCTTGTTGGGCTTGGACA
1 GGCTTGCTGGACTGGGACA
*
837225 GGCCTGCTGG
1 GGCTTGCTGG
837235 CCTTTTTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.08, C:0.21, G:0.44, T:0.27
Consensus pattern (19 bp):
GGCTTGCTGGACTGGGACA
Found at i:837409 original size:6 final size:6
Alignment explanation
Indices: 837396--837464 Score: 61
Period size: 6 Copynumber: 11.2 Consensus size: 6
837386 TAGCTTTTTA
* *
837396 TTTT-T TTTTCTT TTTTCT TTCTCT TTTTCT TCTCTCT TTTTCT TCCTTT-T
1 TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT T--TTTCT
*
837446 TTTTCT TTTTCT TCTTCT T
1 TTTTCT TTTTCT TTTTCT T
837465 CCTCGGGCCG
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
5 7 0.13
6 30 0.57
7 13 0.25
8 3 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:837410 original size:11 final size:11
Alignment explanation
Indices: 837396--837455 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
837386 TAGCTTTTTA
837396 TTTTTTTTTCT
1 TTTTTTTTTCT
837407 TTTTTCTTTCTCT
1 TTTTT-TTT-TCT
* *
837420 TTTTCTTCTCT
1 TTTTTTTTTCT
* *
837431 CTTTTTCTTC-
1 TTTTTTTTTCT
*
837441 CTTTTTTTTCT
1 TTTTTTTTTCT
837452 TTTT
1 TTTT
837456 CTTCTTCTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 9 0.24
11 17 0.45
12 5 0.13
13 7 0.18
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:837422 original size:13 final size:13
Alignment explanation
Indices: 837396--837458 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
837386 TAGCTTTTTA
837396 TTTTT-TTT-TCT
1 TTTTTCTTTCTCT
837407 TTTTTCTTTCTC-
1 TTTTTCTTTCTCT
837419 TTTTTC-TTCTCT
1 TTTTTCTTTCTCT
* *
837431 CTTTTTCTTCCTTT
1 -TTTTTCTTTCTCT
*
837445 TTTTTCTTTTTCT
1 TTTTTCTTTCTCT
837458 T
1 T
837459 CTTCTTCCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 10 0.24
12 9 0.21
13 19 0.45
14 4 0.10
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTCTCT
Found at i:837424 original size:19 final size:19
Alignment explanation
Indices: 837390--837464 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
837380 GACTGTTAGC
*
837390 TTTTTATTTTT-TT-TTCT
1 TTTTTCTTTTTCTTCTTCT
* *
837407 TTTTTCTTTCTCTTTTTCT
1 TTTTTCTTTTTCTTCTTCT
* *
837426 TCTCTCTTTTTCTTCCTT-T
1 TTTTTCTTTTTCTT-CTTCT
837445 TTTTTCTTTTTCTTCTTCT
1 TTTTTCTTTTTCTTCTTCT
837464 T
1 T
837465 CCTCGGGCCG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.20
18 5 0.11
19 30 0.65
20 2 0.04
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTTTCTTCTTCT
Found at i:837437 original size:32 final size:30
Alignment explanation
Indices: 837400--837464 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 30
837390 TTTTTATTTT
837400 TTTTTCTT-TTTTCTTTCTCTTTTTCTTCTCTC
1 TTTTTCTTCTTTT-TTT-TCTTTTTCTTCT-TC
837432 TTTTTCTTCCTTTTTTTTCTTTTTCTTCTTC
1 TTTTTCTT-CTTTTTTTTCTTTTTCTTCTTC
837463 TT
1 TT
837465 CCTCGGGCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 4 0.13
32 20 0.65
33 3 0.10
34 4 0.13
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTTCTTCTTTTTTTTCTTTTTCTTCTTC
Found at i:837447 original size:25 final size:24
Alignment explanation
Indices: 837396--837467 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
837386 TAGCTTTTTA
*
837396 TTTTTT-TTTCT-TTTTTCTTTCT
1 TTTTTTCTTTCTCTTTTTCTTCCT
*
837418 CTTTTTCTTCTCTCTTTTTCTTCCTT
1 TTTTTTCTT-TCTCTTTTTCTTCC-T
* *
837444 TTTTTTCTTTTTCTTCTTCTTCCT
1 TTTTTTCTTTCTCTTTTTCTTCCT
837468 CGGGCCGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 5 0.12
23 2 0.05
24 4 0.10
25 21 0.51
26 9 0.22
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTTCTTTCTCTTTTTCTTCCT
Found at i:837573 original size:22 final size:22
Alignment explanation
Indices: 837545--837590 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
837535 GCGCCTCCCC
*
837545 TTCTCTTCCTCTTTTCTTTCTT
1 TTCTCTTCCTCTTTTCTCTCTT
* *
837567 TTCTCTTCTTTTTTTCTCTCTT
1 TTCTCTTCCTCTTTTCTCTCTT
837589 TT
1 TT
837591 TCCTTTGGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (22 bp):
TTCTCTTCCTCTTTTCTCTCTT
Found at i:837583 original size:13 final size:13
Alignment explanation
Indices: 837558--837591 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
837548 TCTTCCTCTT
837558 TTCTTTCTTTTCTC
1 TTCTTT-TTTTCTC
837572 TTCTTTTTTTCTC
1 TTCTTTTTTTCTC
837585 -TCTTTTT
1 TTCTTTTT
837592 CCTTTGGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 7 0.35
14 6 0.30
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCTTTTTTTCTC
Found at i:837809 original size:24 final size:24
Alignment explanation
Indices: 837764--837809 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
837754 TCCCCTTTCT
*
837764 TCTCTTCCATTTTCTTCTTTTTAA
1 TCTCTTCCATTTTCTTCCTTTTAA
*
837788 TCTCTT-CATTTTTTGTCCTTTT
1 TCTCTTCCATTTTCT-TCCTTTT
837810 TCTTCTTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.09, C:0.24, G:0.02, T:0.65
Consensus pattern (24 bp):
TCTCTTCCATTTTCTTCCTTTTAA
Found at i:838030 original size:59 final size:58
Alignment explanation
Indices: 837954--838093 Score: 176
Period size: 59 Copynumber: 2.4 Consensus size: 58
837944 ACGCAAAATA
*
837954 TTTGGGGTAAAAATGTAATTTT-AGGAAAATATGGGGCCAAAATGTAATTTTCA-AAAAG
1 TTTGGGGTCAAAATGTAATTTTGA-GAAAATATGGGGCCAAAATGTAATTTT-AGAAAAG
* * * *
838012 TTTAGGGGTCAAAGTGTAATTTTGAGAAAGTTTGGGGCCAAAATGTAATTTTAGCAAAG
1 TTT-GGGGTCAAAATGTAATTTTGAGAAAATATGGGGCCAAAATGTAATTTTAGAAAAG
*
838071 TTTGGGGTCAAAATATAAATTTT
1 TTTGGGGTCAAAATGT-AATTTT
838094 TATTTTTTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
58 15 0.21
59 55 0.77
60 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.34
Consensus pattern (58 bp):
TTTGGGGTCAAAATGTAATTTTGAGAAAATATGGGGCCAAAATGTAATTTTAGAAAAG
Found at i:838032 original size:30 final size:28
Alignment explanation
Indices: 837954--838093 Score: 129
Period size: 29 Copynumber: 4.8 Consensus size: 28
837944 ACGCAAAATA
**
837954 TTTGGGGTAAAAATGTAATTTTAGGAAAA-
1 TTTGGGGCCAAAATGTAATTTTA--AAAAG
*
837983 TATGGGGCCAAAATGTAATTTTCAAAAAG
1 TTTGGGGCCAAAATGTAATTTT-AAAAAG
* * *
838012 TTTAGGGGTCAAAGTGTAATTTTGAGAAAG
1 TTT-GGGGCCAAAATGTAATTTT-AAAAAG
*
838042 TTTGGGGCCAAAATGTAATTTTAGCAAAG
1 TTTGGGGCCAAAATGTAATTTTA-AAAAG
* *
838071 TTTGGGGTCAAAATATAAATTTT
1 TTTGGGGCCAAAATGT-AATTTT
838094 TATTTTTTGT
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
28 5 0.05
29 56 0.60
30 32 0.34
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.34
Consensus pattern (28 bp):
TTTGGGGCCAAAATGTAATTTTAAAAAG
Found at i:841131 original size:89 final size:89
Alignment explanation
Indices: 841055--841764 Score: 876
Period size: 89 Copynumber: 8.0 Consensus size: 89
841045 TGAACTCAGA
* *
841055 GAGGCAAGGCTGGTGT-TGTCGATCTGCTTCGCTGCCAGTACAGGAAGACAAGATTTGCTATCTT
1 GAGGCAAGGCTGGTGTCT-TCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTT
* * *
841119 CAATCTGCTCCACTGCAAACCCAGT
65 CAGTCTGCTCCGCTGCAAACCCAGG
* * * *
841144 GAGGCAAAGTTGGTGTCTTCAATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTT
1 GAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTC
* *
841209 AGTCTGTTCCGCTGCAAACTCAGG
66 AGTCTGCTCCGCTGCAAACCCAGG
* ** * * * ** *
841233 GATGCAAGGCTGGTGTCTTCGATCTGCTTCGCTATCAGTATAGGAAGGCAATATCTACGGTTTTC
1 GAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTC
* * *
841298 AGTTTGCTCCACTGCAAATCCAGG
66 AGTCTGCTCCGCTGCAAACCCAGG
* ** * * ** *
841322 GAGGCAAGGGTGGTGTCTTCGATCTGCTTCGCTATCAGTATAGAAAGGCAAGATCTGCGGTTTTC
1 GAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTC
* **
841387 AGTTTAATCCGCTGCAAACCCAGG
66 AGTCTGCTCCGCTGCAAACCCAGG
* *
841411 GAGGCAAGACTGGTGTCTTCGATCTGCTTCGCTGCCAGTGCAGGAAGGCAAGATCTGCTATCTTC
1 GAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTC
*
841476 AGTCTGCTCCGCTGCAAACCCAGA
66 AGTCTGCTCCGCTGCAAACCCAGG
* * * * *
841500 GAGGTAAGGCTGGTGTCTTCCATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTAT-ATC
1 GAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTC
*
841564 AGTCTGCTCCGCCGCAAACCCAGG
66 AGTCTGCTCCGCTGCAAACCCAGG
* * * *
841588 GAGGCAAGGCTAGTGTCTTCAATCTGTTTCGCTGCCAGTACAGGAAGGCAAGATATGCTATCTTC
1 GAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTC
* *
841653 AGTCTGCTCCGCTACAAACCTAGG
66 AGTCTGCTCCGCTGCAAACCCAGG
* * * *
841677 AAGGCAAGACT-G-G---TCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTC
1 GAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTC
*
841737 AGTCTGCTCCGTTGCAAACCCAGG
66 AGTCTGCTCCGCTGCAAACCCAGG
841761 GAGG
1 GAGG
841765 GAAGACTTGT
Statistics
Matches: 536, Mismatches: 83, Indels: 9
0.85 0.13 0.01
Matches are distributed among these distances:
84 66 0.12
87 1 0.00
88 79 0.15
89 389 0.73
90 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (89 bp):
GAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTC
AGTCTGCTCCGCTGCAAACCCAGG
Found at i:841193 original size:44 final size:45
Alignment explanation
Indices: 841076--841665 Score: 154
Period size: 44 Copynumber: 13.3 Consensus size: 45
841066 GGTGTTGTCG
* *
841076 ATCTGCTTCGCTGCCAGTACAGGAAGACAAGATTTGCTATCTTCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAGTTGCTATCTTCA
* * * *** * *
841121 ATCTGCTCCACTGCAAACCCAGTG-AGGCAA-AGTTGGTGTCTTCA
1 ATCTGCTTCGCTGCCAGTACAG-GAAGGCAAGAGTTGCTATCTTCA
*
841165 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGA-TCTGCTATCTTTA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAGT-TGCTATCTTCA
* * * * * * * * *
841210 GTCTG-TTCCGCTGCAAACT-CAGGGATGCAAG-GCTGGTGTCTTCG
1 ATCTGCTT-CGCTGC-CAGTACAGGAAGGCAAGAGTTGCTATCTTCA
** * * * ** *
841254 ATCTGCTTCGCTATCAGTATAGGAAGGCAATA-TCTACGGTTTTCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAGT-TGCTATCTTCA
* * * * * * * * * * * *
841299 GTTTGCTCCACTGCAAATCCAGGGAGGCAAG-GGTGGTGTCTTCG
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAGTTGCTATCTTCA
** * * ** *
841343 ATCTGCTTCGCTATCAGTATAGAAAGGCAAGA-TCTGCGGTTTTCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAGT-TGCTATCTTCA
* * ** * * *** * * * * *
841388 GTTTAATCCGCTGCAAACCCAGGGAGGCAAGA-CTGGTGTCTTCG
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAGTTGCTATCTTCA
*
841432 ATCTGCTTCGCTGCCAGTGCAGGAAGGCAAGA-TCTGCTATCTTCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAGT-TGCTATCTTCA
* * * *** * * * * *
841477 GTCTGCTCCGCTGCAAACCCA-GAGAGGTAAG-GCTGGTGTCTTCC
1 ATCTGCTTCGCTGCCAGTACAGGA-AGGCAAGAGTTGCTATCTTCA
* * *
841521 ATCTACTTCGCTGTCAGTACAGGAAGGCAAGA-TCTGCTAT-ATCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAGT-TGCTATCTTCA
* * * * *** * * *
841565 GTCTGCTCCGCCGCAAACCCAGGGAGGCAAG-GCTAG-TGTCTTCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAG-TTGCTATCTTCA
*
841609 ATCTGTTTCGCTGCCAGTACAGGAAGGCAAGA-TATGCTATCTTCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAGT-TGCTATCTTCA
* *
841654 GTCTGCTCCGCT
1 ATCTGCTTCGCT
841666 ACAAACCTAG
Statistics
Matches: 355, Mismatches: 164, Indels: 52
0.62 0.29 0.09
Matches are distributed among these distances:
43 6 0.02
44 192 0.54
45 154 0.43
46 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (45 bp):
ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAGTTGCTATCTTCA
Found at i:843117 original size:19 final size:17
Alignment explanation
Indices: 843082--843140 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
843072 GACCTCTCTA
*
843082 TTTTTTATTATTGTTAT
1 TTTTTTATTATTATTAT
843099 TTTTGTTATATATTATTAT
1 TTTT-TTAT-TATTATTAT
* * *
843118 TATTAT-TTATTATAAT
1 TTTTTTATTATTATTAT
843134 TTTTTTA
1 TTTTTTA
843141 GGAATCAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
16 12 0.36
17 5 0.15
18 5 0.15
19 11 0.33
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTTATTATTATTAT
Found at i:855373 original size:120 final size:121
Alignment explanation
Indices: 855228--855475 Score: 482
Period size: 120 Copynumber: 2.1 Consensus size: 121
855218 TGACTAATAA
855228 TTTATCATATAAAAATGTTAAACTAATAAAATAACATAAATATTTAATTTTTAACAATAATACTT
1 TTTATCATATAAAAATGTTAAACTAATAAAATAACATAAATATTTAATTTTTAACAATAATACTT
855293 TTAAAAGAATTATATAAGTTAAAATTAATTAATATTATTCATATTTATAACTTCAC
66 TTAAAAGAATTATATAAGTTAAAATTAATTAATATTATTCATATTTATAACTTCAC
855349 TTTATCATAT-AAAATGTTAAACTAATAAAATAACATAAATATTTAATTTTTAACAATAATACTT
1 TTTATCATATAAAAATGTTAAACTAATAAAATAACATAAATATTTAATTTTTAACAATAATACTT
855413 TTAAAAGAATTATATAAGTTAAAATTAATTAATATTATTCATATTTATAACTTCAC
66 TTAAAAGAATTATATAAGTTAAAATTAATTAATATTATTCATATTTATAACTTCAC
855469 TTT-TCAT
1 TTTATCAT
855476 TTTAGGTATC
Statistics
Matches: 127, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
119 4 0.03
120 113 0.89
121 10 0.08
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (121 bp):
TTTATCATATAAAAATGTTAAACTAATAAAATAACATAAATATTTAATTTTTAACAATAATACTT
TTAAAAGAATTATATAAGTTAAAATTAATTAATATTATTCATATTTATAACTTCAC
Found at i:861051 original size:19 final size:20
Alignment explanation
Indices: 861007--861051 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
860997 ACTTGATTGG
*
861007 TGATATTTGAAATATGTGAT
1 TGATATTCGAAATATGTGAT
* *
861027 TAATATTCGAAAT-TGTGTT
1 TGATATTCGAAATATGTGAT
861046 TGATAT
1 TGATAT
861052 GTATATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (20 bp):
TGATATTCGAAATATGTGAT
Found at i:876449 original size:22 final size:21
Alignment explanation
Indices: 876413--876454 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
876403 AAATTTTTTT
**
876413 TTTTTAAAATGATTAATAAATA
1 TTTTTAAAAAAATTAA-AAATA
876435 TTTTTAAAAAAATTAAAAAT
1 TTTTTAAAAAAATTAAAAAT
876455 TATAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTTTAAAAAAATTAAAAATA
Found at i:876595 original size:10 final size:11
Alignment explanation
Indices: 876549--876595 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
876539 AAGAATTTAG
876549 AAATTATTAAA
1 AAATTATTAAA
876560 AAA-TATT-AA
1 AAATTATTAAA
*
876569 TAATTATTAAA
1 AAATTATTAAA
876580 AGAATTA-TAAA
1 A-AATTATTAAA
876591 AAATT
1 AAATT
876596 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 4 0.13
10 12 0.39
11 10 0.32
12 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
AAATTATTAAA
Found at i:877611 original size:18 final size:20
Alignment explanation
Indices: 877588--877643 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
877578 AATTACTAAA
877588 ATTTAATTTTTTTAAT-A-T
1 ATTTAATTTTTTTAATGATT
* *
877606 ATTTAAAATTTTTAAATGATT
1 ATTT-AATTTTTTTAATGATT
*
877627 ATTAATATTTTTTTAAT
1 ATTTA-ATTTTTTTAAT
877644 TTTTAAAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 4 0.14
19 10 0.34
20 2 0.07
21 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTAATTTTTTTAATGATT
Found at i:887163 original size:18 final size:19
Alignment explanation
Indices: 887131--887183 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
887121 AATAAAAATC
*
887131 AATAAAAATTGTTAAATTTA-
1 AATAAAAA-T-TTAAAATTAG
887151 AATAAAAATTTAAAATTAG
1 AATAAAAATTTAAAATTAG
*
887170 AA-AAAAATATAAAA
1 AATAAAAATTTAAAA
887184 CTTTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 19 0.63
19 3 0.10
20 8 0.27
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AATAAAAATTTAAAATTAG
Found at i:887194 original size:19 final size:20
Alignment explanation
Indices: 887172--887215 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
887162 AAAATTAGAA
* *
887172 AAAAATATAA-AACTTTTAT
1 AAAAATACAATAAATTTTAT
887191 AAAAA-ACAATAAATTTTAT
1 AAAAATACAATAAATTTTAT
887210 AAAAAT
1 AAAAAT
887216 CGTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATACAATAAATTTTAT
Done.