Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 11 of 141
Found at i:2957730 original size:13 final size:13
Alignment explanation
Indices: 2957702--2957738 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2957692 TGGCCTCTCC
2957702 TTTTTCTGTTTCT-
1 TTTTTCT-TTTCTG
2957715 TTTTT-TTTTCTG
1 TTTTTCTTTTCTG
2957727 TTTTTCTTTTCT
1 TTTTTCTTTTCT
2957739 TTTCTTTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.23
12 6 0.27
13 11 0.50
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTTCTG
Found at i:2957736 original size:18 final size:17
Alignment explanation
Indices: 2957702--2957756 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
2957692 TGGCCTCTCC
2957702 TTTTTCTGTTTCTTTTT
1 TTTTTCTGTTTCTTTTT
2957719 TTTTTCTGTTT-TTCTTT
1 TTTTTCTGTTTCTT-TTT
*
2957736 TCTTTTCT-TTACCTTTTT
1 T-TTTTCTGTT-TCTTTTT
2957754 TTT
1 TTT
2957757 AAAGTGAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 2 0.06
17 19 0.58
18 10 0.30
19 2 0.06
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (17 bp):
TTTTTCTGTTTCTTTTT
Found at i:2957754 original size:24 final size:25
Alignment explanation
Indices: 2957702--2957755 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
2957692 TGGCCTCTCC
* **
2957702 TTTTTCTGTTTCTTTTTTTTTTCTG
1 TTTTTCTGTTTCTTTTCTTTACCTG
*
2957727 TTTTTCT-TTTCTTTTCTTTACCTT
1 TTTTTCTGTTTCTTTTCTTTACCTG
2957751 TTTTT
1 TTTTT
2957756 TAAAGTGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (25 bp):
TTTTTCTGTTTCTTTTCTTTACCTG
Found at i:2962422 original size:12 final size:13
Alignment explanation
Indices: 2962397--2962429 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
2962387 AAGATATATA
2962397 AATAAATAGTAAT
1 AATAAATAGTAAT
2962410 AATAAAT-GTAAT
1 AATAAATAGTAAT
2962422 AATAAATA
1 AATAAATA
2962430 TGGTAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (13 bp):
AATAAATAGTAAT
Found at i:2968746 original size:15 final size:15
Alignment explanation
Indices: 2968726--2968755 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2968716 CAACACCCTG
2968726 ATTTTAGACCCTAAT
1 ATTTTAGACCCTAAT
2968741 ATTTTAGACCCTAAT
1 ATTTTAGACCCTAAT
2968756 TGAAGGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTTTAGACCCTAAT
Found at i:2979828 original size:40 final size:41
Alignment explanation
Indices: 2979772--2979850 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
2979762 TGGCGTTTGG
2979772 ACAACAAACGCCGCTAAAAATCGA-ACACTAGCGGCGCATCT
1 ACAACAAACGCCGCTAAAAATCGAGA-ACTAGCGGCGCATCT
* *
2979813 ACAA-AAACGCCGCTAAAGATCGAGAATTAGCGGCGCAT
1 ACAACAAACGCCGCTAAAAATCGAGAACTAGCGGCGCAT
2979851 TTAGGAAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 30 0.86
41 5 0.14
ACGTcount: A:0.39, C:0.28, G:0.20, T:0.13
Consensus pattern (41 bp):
ACAACAAACGCCGCTAAAAATCGAGAACTAGCGGCGCATCT
Found at i:2980205 original size:114 final size:112
Alignment explanation
Indices: 2979877--2980244 Score: 375
Period size: 114 Copynumber: 3.2 Consensus size: 112
2979867 ATAATAAGCA
* * * * *
2979877 TTAGCAGCGATTTATGAAAAGCACCGCAAAAAAACATAAGGCCAACGACGTCGTTTACTGAGTTT
1 TTAGCGGCGATTTCTGAAAAGCGCCGCAAAAAAACCTAAGGCCAACGACGTCGTTTTCTGAGTTT
* * * *
2979942 TTGGACCTGTAGCGGCGTTTTTCTAAAAACGCCGCTAATGCTCGGGGGAC
66 TTGGACCTTTAGCGGCGTTTTT-GAAAAGCGCCGCTAATGCTC--CGGAC
* * * *
2979992 TTAACGGCGATTTCTAAAAAGCGCCGC-AAAAAACCTAAGGTCAACGACGTC-ATTTCTGAGTTT
1 TTAGCGGCGATTTCTGAAAAGCGCCGCAAAAAAACCTAAGGCCAACGACGTCGTTTTCTGAGTTT
** * * * *
2980055 TTGTCCGCGTT-GCGGCGTTTTTTGAAAAGCACCGCTAATGCTCCTGCC
66 TTGGAC-CTTTAGCGGCG-TTTTTGAAAAGCGCCGCTAATGCTCCGGAC
* * **
2980103 TTTAGCGGCGTTTTCTGAAAAGCGCCGCAAAAAAACCTAAGGCCAACGACGCCGTTTTCTGTTTT
1 -TTAGCGGCGATTTCTGAAAAGCGCCGCAAAAAAACCTAAGGCCAACGACGTCGTTTTCTGAGTT
* * *
2980168 TTTGGGCCTTTAGCGGCGTTTTGTGAAAAGCGTCGCTAATGATCCGGAC
65 TTTGGACCTTTAGCGGCGTTTT-TGAAAAGCGCCGCTAATGCTCCGGAC
* *
2980217 GTTAGCGGCG-TTTTTGAGGAAGCGCCGC
1 -TTAGCGGCGATTTCTGA-AAAGCGCCGC
2980245 TAATAGTAAT
Statistics
Matches: 207, Mismatches: 38, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
111 2 0.01
112 24 0.12
113 72 0.35
114 87 0.42
115 22 0.11
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (112 bp):
TTAGCGGCGATTTCTGAAAAGCGCCGCAAAAAAACCTAAGGCCAACGACGTCGTTTTCTGAGTTT
TTGGACCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTCCGGAC
Found at i:2982300 original size:19 final size:19
Alignment explanation
Indices: 2982276--2982312 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2982266 ATCTCCCTTA
2982276 AATCCCTAA-AATTTCCCCT
1 AATCCCTAACAA-TTCCCCT
2982295 AATCCCTAACAATTCCCC
1 AATCCCTAACAATTCCCC
2982313 AACGTAGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (19 bp):
AATCCCTAACAATTCCCCT
Found at i:2984872 original size:20 final size:20
Alignment explanation
Indices: 2984847--2984908 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
2984837 TACAATTTCT
2984847 TAACTTATATAATATTAAGA
1 TAACTTATATAATATTAAGA
*
2984867 TAACTTATATAATATT-ACA
1 TAACTTATATAATATTAAGA
* *
2984886 TAACTTATATCATGTTAAGA
1 TAACTTATATAATATTAAGA
2984906 TAA
1 TAA
2984909 AAAATCGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (20 bp):
TAACTTATATAATATTAAGA
Found at i:2984991 original size:19 final size:19
Alignment explanation
Indices: 2984967--2985070 Score: 58
Period size: 19 Copynumber: 5.4 Consensus size: 19
2984957 TTTAACTTAC
2984967 AACTTACACAATACATAAT
1 AACTTACACAATACATAAT
*
2984986 AACTTACA-ACTTACATAAT
1 AACTTACACA-ATACATAAT
* * * *
2985005 -ACATA-A-TA-AC-TTAC
1 AACTTACACAATACATAAT
2985019 AACTTACACAATACATTTAACTT
1 AACTTACACAATACA--TAA--T
2985042 GCAACTTACACAATACATAAT
1 --AACTTACACAATACATAAT
2985063 AACTTACA
1 AACTTACA
2985071 ACTTACATAA
Statistics
Matches: 63, Mismatches: 10, Indels: 24
0.65 0.10 0.25
Matches are distributed among these distances:
14 2 0.03
15 6 0.10
16 1 0.02
17 2 0.03
18 7 0.11
19 24 0.38
21 3 0.05
23 3 0.05
25 15 0.24
ACGTcount: A:0.48, C:0.22, G:0.01, T:0.29
Consensus pattern (19 bp):
AACTTACACAATACATAAT
Found at i:2985035 original size:77 final size:77
Alignment explanation
Indices: 2984951--2985179 Score: 424
Period size: 77 Copynumber: 3.0 Consensus size: 77
2984941 TGACTGACAT
2984951 AATACATTTAACTTACAACTTACACAATACATAATAACTTACAACTTACATAATACATAATAACT
1 AATACATTTAACTTACAACTTACACAATACATAATAACTTACAACTTACATAATACATAATAACT
2985016 TACAACTTACAC
66 TACAACTTACAC
*
2985028 AATACATTTAACTTGCAACTTACACAATACATAATAACTTACAACTTACATAATACATAATAACT
1 AATACATTTAACTTACAACTTACACAATACATAATAACTTACAACTTACATAATACATAATAACT
*
2985093 TACAACTTACAT
66 TACAACTTACAC
*
2985105 AATACATTTAACTTACAACTTACACAATACAT-TTAACTTACAACTTACATAATACATAATAACT
1 AATACATTTAACTTACAACTTACACAATACATAATAACTTACAACTTACATAATACATAATAACT
2985169 TACAACTTACA
66 TACAACTTACA
2985180 TTTAACTTAC
Statistics
Matches: 148, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
76 42 0.28
77 106 0.72
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.31
Consensus pattern (77 bp):
AATACATTTAACTTACAACTTACACAATACATAATAACTTACAACTTACATAATACATAATAACT
TACAACTTACAC
Found at i:2985180 original size:26 final size:26
Alignment explanation
Indices: 2984947--2985180 Score: 359
Period size: 26 Copynumber: 9.2 Consensus size: 26
2984937 CATTTGACTG
*
2984947 ACATAATACAT-TTAACTTACAACTT
1 ACATAATACATAATAACTTACAACTT
*
2984972 ACACAATACATAATAACTTACAACTT
1 ACATAATACATAATAACTTACAACTT
2984998 ACATAATACATAATAACTTACAACTT
1 ACATAATACATAATAACTTACAACTT
* * *
2985024 ACACAATACAT-TTAACTTGCAACTT
1 ACATAATACATAATAACTTACAACTT
*
2985049 ACACAATACATAATAACTTACAACTT
1 ACATAATACATAATAACTTACAACTT
2985075 ACATAATACATAATAACTTACAACTT
1 ACATAATACATAATAACTTACAACTT
*
2985101 ACATAATACAT-TTAACTTACAACTT
1 ACATAATACATAATAACTTACAACTT
* *
2985126 ACACAATACAT-TTAACTTACAACTT
1 ACATAATACATAATAACTTACAACTT
2985151 ACATAATACATAATAACTTACAACTT
1 ACATAATACATAATAACTTACAACTT
2985177 ACAT
1 ACAT
2985181 TTAACTTACA
Statistics
Matches: 193, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
25 80 0.41
26 113 0.59
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.31
Consensus pattern (26 bp):
ACATAATACATAATAACTTACAACTT
Found at i:2985188 original size:11 final size:10
Alignment explanation
Indices: 2985172--2985225 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
2985162 AATAACTTAC
2985172 AACTTACATTT
1 AACTTACA-TT
2985183 AACTTACA-T
1 AACTTACATT
2985192 AA--TACATTT
1 AACTTACA-TT
2985201 AACTTACA-T
1 AACTTACATT
2985210 AACTTACA-T
1 AACTTACATT
2985219 AACTTAC
1 AACTTAC
2985226 CATTGCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:2985209 original size:18 final size:18
Alignment explanation
Indices: 2985146--2985211 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
2985136 TTTAACTTAC
*
2985146 AACTTACATAATACATAAT
1 AACTTACATAATACAT-TT
*
2985165 AACTTACA-ACTTACATTT
1 AACTTACATA-ATACATTT
2985183 AACTTACATAATACATTT
1 AACTTACATAATACATTT
2985201 AACTTACATAA
1 AACTTACATAA
2985212 CTTACATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 28 0.67
19 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:2985221 original size:18 final size:18
Alignment explanation
Indices: 2985061--2985225 Score: 69
Period size: 18 Copynumber: 9.5 Consensus size: 18
2985051 ACAATACATA
2985061 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
*
2985077 ATAATACATA-ATAACTTAC
1 AT-A-ACTTACATAACTTAC
2985096 --AACTTACATAA--TAC
1 ATAACTTACATAACTTAC
2985110 ATTTAACTTAC--AACTTAC
1 A--TAACTTACATAACTTAC
*
2985128 ACAA--TACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
*
2985146 --AACTTACATAATACATA-
1 ATAACTTACAT-A-ACTTAC
2985163 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
2985179 ATTTAACTTACATAA--TAC
1 A--TAACTTACATAACTTAC
2985197 ATTTAACTTACATAACTTAC
1 A--TAACTTACATAACTTAC
2985217 ATAACTTAC
1 ATAACTTAC
2985226 CATTGCAATT
Statistics
Matches: 116, Mismatches: 5, Indels: 54
0.66 0.03 0.31
Matches are distributed among these distances:
14 6 0.05
15 8 0.07
16 16 0.14
17 2 0.02
18 64 0.55
19 14 0.12
20 6 0.05
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:2989090 original size:20 final size:20
Alignment explanation
Indices: 2989065--2989104 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2989055 AACTATTTTA
*
2989065 TGTGTATTGCAGATAAAATG
1 TGTGTATTGCAAATAAAATG
2989085 TGTGTATTGCAAATAAAATG
1 TGTGTATTGCAAATAAAATG
2989105 CCTAGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.35
Consensus pattern (20 bp):
TGTGTATTGCAAATAAAATG
Found at i:2990722 original size:21 final size:21
Alignment explanation
Indices: 2990657--2990716 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
2990647 CTACAACTTA
2990657 AAGCAGAGG-TGGCAGCGAGGG
1 AAGCAGAGGCT-GCAGCGAGGG
2990678 AAGCA-ACGGCTGCAGCGAGGG
1 AAGCAGA-GGCTGCAGCGAGGG
2990699 AAGCAGAGGCTGCAGCGA
1 AAGCAGAGGCTGCAGCGA
2990717 AAGAAGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.03
21 33 0.92
22 2 0.06
ACGTcount: A:0.30, C:0.20, G:0.45, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:2990727 original size:21 final size:21
Alignment explanation
Indices: 2990657--2990727 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
2990647 CTACAACTTA
**
2990657 AAGCAGAGG-TGGCAGCGAGGG
1 AAGCAGAGGCT-GCAGCGAAAG
**
2990678 AAGCA-ACGGCTGCAGCGAGGG
1 AAGCAGA-GGCTGCAGCGAAAG
2990699 AAGCAGAGGCTGCAGCGAAAG
1 AAGCAGAGGCTGCAGCGAAAG
*
2990720 AAGTAGAG
1 AAGCAGAG
2990728 CAGAGCAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.02
21 41 0.93
22 2 0.05
ACGTcount: A:0.34, C:0.17, G:0.44, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAAAG
Found at i:2991091 original size:42 final size:42
Alignment explanation
Indices: 2991053--2991199 Score: 240
Period size: 42 Copynumber: 3.5 Consensus size: 42
2991043 GTAAAAAAGT
*
2991053 GCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAAC
1 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
*
2991095 GCCGCTAAAGACCATGTTCTTTAGCGGTGCTTAGAAAAAAAC
1 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
* *
2991137 GCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGATAAAAAC
1 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
* *
2991179 GCTGCTAAAGATCATGTTCTT
1 GCCGCTAAAGACCATGTTCTT
2991200 ATCTAAGCGC
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 98 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (42 bp):
GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
Found at i:3006582 original size:3 final size:3
Alignment explanation
Indices: 3006574--3006613 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3006564 GAATGATCGC
3006574 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3006614 AAGAACATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3009348 original size:30 final size:31
Alignment explanation
Indices: 3009303--3009362 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
3009293 GGAGGTGGGA
*
3009303 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
3009334 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
3009363 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:3009672 original size:9 final size:9
Alignment explanation
Indices: 3009655--3009685 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3009645 TCGAGTTGAT
3009655 TCGAATAAC
1 TCGAATAAC
*
3009664 TCGATTAAC
1 TCGAATAAC
3009673 TCGAATAAC
1 TCGAATAAC
3009682 TCGA
1 TCGA
3009686 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:3012093 original size:22 final size:23
Alignment explanation
Indices: 3012060--3012107 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3012050 AAACAAGAAA
*
3012060 AAAGAAAAAAAAGGAAAAAAAGG
1 AAAGAAAAAAAAAGAAAAAAAGG
* *
3012083 AAAG-AAAAAAAAGAAACAATGG
1 AAAGAAAAAAAAAGAAAAAAAGG
3012105 AAA
1 AAA
3012108 ATTAGTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (23 bp):
AAAGAAAAAAAAAGAAAAAAAGG
Found at i:3017636 original size:13 final size:14
Alignment explanation
Indices: 3017618--3017646 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3017608 TTTGGATGCA
3017618 TTGTTGTG-TGAAT
1 TTGTTGTGTTGAAT
3017631 TTGTTGTGTTGAAT
1 TTGTTGTGTTGAAT
3017645 TT
1 TT
3017647 CTGAATTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.59
Consensus pattern (14 bp):
TTGTTGTGTTGAAT
Found at i:3018736 original size:7 final size:7
Alignment explanation
Indices: 3018720--3018782 Score: 51
Period size: 7 Copynumber: 8.7 Consensus size: 7
3018710 TATCAATTAT
*
3018720 AGAAACA
1 AGAAAAA
3018727 AGAAAAAA
1 AG-AAAAA
3018735 GAGAAAAA
1 -AGAAAAA
3018743 AGAAAAA
1 AGAAAAA
3018750 AG--AAA
1 AGAAAAA
3018755 AGAAAAA
1 AGAAAAA
3018762 AGGAAAGAA
1 A-GAAA-AA
3018771 A-ACAAAA
1 AGA-AAAA
3018778 AGAAA
1 AGAAA
3018783 CAATGGAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
5 5 0.11
7 21 0.45
8 16 0.34
9 5 0.11
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:3018757 original size:12 final size:12
Alignment explanation
Indices: 3018740--3018782 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
3018730 AAAAAGAGAA
3018740 AAAAGAAAAAAG
1 AAAAGAAAAAAG
3018752 AAAAGAAAAAAG
1 AAAAGAAAAAAG
* *
3018764 GAAAGAAAACA-
1 AAAAGAAAAAAG
3018775 AAAAGAAA
1 AAAAGAAA
3018783 CAATGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:3018762 original size:28 final size:28
Alignment explanation
Indices: 3018726--3018782 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
3018716 TTATAGAAAC
3018726 AAGAAAAAAGAGAAA-AAAGA-AAAAAGAA
1 AAGAAAAAAG-GAAAGAAA-ACAAAAAGAA
3018754 AAGAAAAAAGGAAAGAAAACAAAAAGAA
1 AAGAAAAAAGGAAAGAAAACAAAAAGAA
3018782 A
1 A
3018783 CAATGGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (28 bp):
AAGAAAAAAGGAAAGAAAACAAAAAGAA
Found at i:3018763 original size:19 final size:16
Alignment explanation
Indices: 3018720--3018752 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3018710 TATCAATTAT
*
3018720 AGAAACAAGAAAAAAG
1 AGAAAAAAGAAAAAAG
3018736 AGAAAAAAGAAAAAAG
1 AGAAAAAAGAAAAAAG
3018752 A
1 A
3018753 AAAGAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (16 bp):
AGAAAAAAGAAAAAAG
Found at i:3018790 original size:24 final size:24
Alignment explanation
Indices: 3018741--3018791 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3018731 AAAAGAGAAA
3018741 AAAGAAAAAAGAAAAGAAAAAAGG
1 AAAGAAAAAAGAAAAGAAAAAAGG
* *
3018765 AAAGAAAACA-AAAAGAAACAATGG
1 AAAGAAAAAAGAAAAGAAA-AAAGG
3018789 AAA
1 AAA
3018792 ATTAGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (24 bp):
AAAGAAAAAAGAAAAGAAAAAAGG
Found at i:3034654 original size:27 final size:27
Alignment explanation
Indices: 3034622--3034674 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
3034612 ATTTAAAATA
3034622 ATTAATAAACATAATAACCCTAATATC
1 ATTAATAAACATAATAACCCTAATATC
*
3034649 ATTAATAAAGATAATAACCCTAATAT
1 ATTAATAAACATAATAACCCTAATAT
3034675 GAACTTACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.30
Consensus pattern (27 bp):
ATTAATAAACATAATAACCCTAATATC
Found at i:3040169 original size:45 final size:45
Alignment explanation
Indices: 3040008--3040158 Score: 189
Period size: 45 Copynumber: 3.4 Consensus size: 45
3039998 AAGCCTAAAC
* *
3040008 ATGAGTAAGACCATGGCAGAAAGACACCATGGCATCACACTATCG
1 ATGAGTAAGACCATGGCAGAAAGACACTATGGCATCATACTATCG
* *
3040053 ATAAGTAAGACCATGGCAGAATGACACTATGGCATCATACTATCG
1 ATGAGTAAGACCATGGCAGAAAGACACTATGGCATCATACTATCG
** * *
3040098 ATGAGTAAGACCATAACTA-AAAGATACTATGGCATCATGA-TATAG
1 ATGAGTAAGACCATGGC-AGAAAGACACTATGGCATCAT-ACTATCG
*
3040143 ATGAGTAAGGCCATGG
1 ATGAGTAAGACCATGG
3040159 TTGAAAGATA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
45 89 0.98
46 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.21
Consensus pattern (45 bp):
ATGAGTAAGACCATGGCAGAAAGACACTATGGCATCATACTATCG
Found at i:3045461 original size:289 final size:291
Alignment explanation
Indices: 3044933--3045523 Score: 1078
Period size: 289 Copynumber: 2.0 Consensus size: 291
3044923 TAATTCTTCC
* * *
3044933 AATAGTGTGTTTGAAAAATAGACGAAGACATAATGCATCAAATGTGCCAACATGAAAGAATAAAA
1 AATAGTTTGTTTGAAAAATAGACAAAGACACAATGCATCAAATGTGCCAACATGAAAGAATAAAA
3044998 ATGCTTAACACTAACTTGTCGCTCAAGTCTTCAACTTAATCCAATTTGTCAATTGTAACAAAGTA
66 ATGCTTAACACTAACTTGTCGCTCAAGTCTTCAACTTAATCCAATTTGTCAATTGTAACAAAGTA
3045063 TGTATTAGCCAAAACTAGAAATCATATACCTTTAACCTATTAATGCCTAAAAATGTTATGTTTAT
131 TGTATTAGCCAAAACTAGAAATCATATACCTTTAACCTATTAATGCCTAAAAATGTTATGTTTAT
3045128 TACATTTATTTAAGACATATGTGACAAACGTGATGGAATTTTAGTTCCTTCAAATTCTATTCCTA
196 TACATTTATTTAAGACATATGTGACAAACGTGATGGAATTTTAGTTCCTTCAAATTCTATTCCTA
3045193 AACATGTGGATGAGAATGATTTGCAAGCTAA
261 AACATGTGGATGAGAATGATTTGCAAGCTAA
3045224 AATAGTTTGTTTGAAAAATAGACAAAGACACAATGCATCAAATGTGCCAACATGAAAGAA-AAAA
1 AATAGTTTGTTTGAAAAATAGACAAAGACACAATGCATCAAATGTGCCAACATGAAAGAATAAAA
* * *
3045288 ATGCTTAACGCTAAGTTGTCGCTCAGGT-TTCAACTTAATCCAATTTGTCAATTGTAACAAAGTA
66 ATGCTTAACACTAACTTGTCGCTCAAGTCTTCAACTTAATCCAATTTGTCAATTGTAACAAAGTA
* * *
3045352 TGTATTAGCCAAAACTAGCAATCATATACCTTTAACCTATTGATGCCTAATAATGTTATGTTTAT
131 TGTATTAGCCAAAACTAGAAATCATATACCTTTAACCTATTAATGCCTAAAAATGTTATGTTTAT
3045417 TACATTTATTTAAGACATATGTGACAAACGTGATGGAATTTTAGTTCCTTCAAATTCTATTCCTA
196 TACATTTATTTAAGACATATGTGACAAACGTGATGGAATTTTAGTTCCTTCAAATTCTATTCCTA
3045482 AACATGTGGATGAGAATGATTTGCAAGCTAA
261 AACATGTGGATGAGAATGATTTGCAAGCTAA
*
3045513 AATAATTTGTT
1 AATAGTTTGTT
3045524 AATAATCTCT
Statistics
Matches: 290, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
289 204 0.70
290 29 0.10
291 57 0.20
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (291 bp):
AATAGTTTGTTTGAAAAATAGACAAAGACACAATGCATCAAATGTGCCAACATGAAAGAATAAAA
ATGCTTAACACTAACTTGTCGCTCAAGTCTTCAACTTAATCCAATTTGTCAATTGTAACAAAGTA
TGTATTAGCCAAAACTAGAAATCATATACCTTTAACCTATTAATGCCTAAAAATGTTATGTTTAT
TACATTTATTTAAGACATATGTGACAAACGTGATGGAATTTTAGTTCCTTCAAATTCTATTCCTA
AACATGTGGATGAGAATGATTTGCAAGCTAA
Found at i:3047378 original size:20 final size:20
Alignment explanation
Indices: 3047353--3047390 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3047343 TTACTTGGGT
3047353 AATTTTCTATCAGTTCAATC
1 AATTTTCTATCAGTTCAATC
3047373 AATTTTCTATCAGTTCAA
1 AATTTTCTATCAGTTCAA
3047391 AGACTATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (20 bp):
AATTTTCTATCAGTTCAATC
Found at i:3050652 original size:24 final size:25
Alignment explanation
Indices: 3050600--3050646 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3050590 TGTTTCTCAC
*
3050600 GAGCTTCCCGTTATATGGCTCTTGT
1 GAGCTTCCCGTTATATAGCTCTTGT
*
3050625 GAGCTTCTCGTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
3050647 CGGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGT
Found at i:3050738 original size:25 final size:23
Alignment explanation
Indices: 3050710--3050788 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 23
3050700 CTTATAAGCA
*
3050710 TCCCAATAATTGGCTCTTCAGAGCT
1 TCCCGATAA-TGGCTC-TCAGAGCT
3050735 TCCCGATAACTGGCTCGT-ATGAGCT
1 TCCCGATAA-TGGCTC-TCA-GAGCT
*
3050760 TCCCGTTAATGGCTCTCTAGAGCT
1 TCCCGATAATGGCTCTC-AGAGCT
3050784 TCCCG
1 TCCCG
3050789 TTACATGGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.02
24 17 0.36
25 29 0.62
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.30
Consensus pattern (23 bp):
TCCCGATAATGGCTCTCAGAGCT
Found at i:3050782 original size:24 final size:23
Alignment explanation
Indices: 3050720--3050796 Score: 91
Period size: 25 Copynumber: 3.1 Consensus size: 23
3050710 TCCCAATAAT
*
3050720 TGGCTCTTCAGAGCTTCCCGATAA
1 TGGCTCTT-AGAGCTTCCCGTTAA
*
3050744 CTGGCTCGTATGAGCTTCCCGTTAA
1 -TGGCTCTTA-GAGCTTCCCGTTAA
3050769 TGGCTCTCTAGAGCTTCCCGTTACA
1 TGGCTCT-TAGAGCTTCCCGTTA-A
3050794 TGG
1 TGG
3050797 TTCGTATAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 20 0.43
25 26 0.57
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.31
Consensus pattern (23 bp):
TGGCTCTTAGAGCTTCCCGTTAA
Found at i:3050802 original size:49 final size:50
Alignment explanation
Indices: 3050720--3050824 Score: 126
Period size: 49 Copynumber: 2.1 Consensus size: 50
3050710 TCCCAATAAT
* *
3050720 TGGCTCTTCAGAGCTTCCCGATAACTGGCTCGTATGAGCTTCCCGTTA-A
1 TGGCTCTTCAGAGCTTCCCGATAACTGGCTCGTATAAGCTTCCCGGTATA
* * *
3050769 TGGCTC-TCTAGAGCTTCCCG-TTACATGGTTCGTATAAGCTTCTCGGTATA
1 TGGCTCTTC-AGAGCTTCCCGATAAC-TGGCTCGTATAAGCTTCCCGGTATA
3050819 TGGCTC
1 TGGCTC
3050825 GAAAGAGCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
48 5 0.10
49 36 0.75
50 7 0.15
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (50 bp):
TGGCTCTTCAGAGCTTCCCGATAACTGGCTCGTATAAGCTTCCCGGTATA
Found at i:3050808 original size:25 final size:24
Alignment explanation
Indices: 3050731--3050825 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 24
3050721 GGCTCTTCAG
* *
3050731 AGCTTCCCGATAACTGGCTCGTATG
1 AGCTTCCCGTTAA-TGGCTCGTATA
*
3050756 AGCTTCCCGTTAATGGCTC-TCTA
1 AGCTTCCCGTTAATGGCTCGTATA
*
3050779 GAGCTTCCCGTTACATGGTTCGTATA
1 -AGCTTCCCGTTA-ATGGCTCGTATA
* *
3050805 AGCTTCTCGGTATATGGCTCG
1 AGCTTCCCGTTA-ATGGCTCG
3050826 AAAGAGCTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
23 2 0.03
24 18 0.31
25 35 0.60
26 3 0.05
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (24 bp):
AGCTTCCCGTTAATGGCTCGTATA
Found at i:3051978 original size:23 final size:23
Alignment explanation
Indices: 3051952--3051997 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3051942 GGCCTAGCAC
3051952 ACGGGTGTGTGACTTGGCCGTGT
1 ACGGGTGTGTGACTTGGCCGTGT
3051975 ACGGGTGTGTGACTTGGCCGTGT
1 ACGGGTGTGTGACTTGGCCGTGT
3051998 GACCTAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.17, G:0.43, T:0.30
Consensus pattern (23 bp):
ACGGGTGTGTGACTTGGCCGTGT
Found at i:3061131 original size:45 final size:45
Alignment explanation
Indices: 3061062--3061203 Score: 198
Period size: 45 Copynumber: 3.2 Consensus size: 45
3061052 ACGTGTACCG
* *
3061062 GGTACCATTGATTATAAAGGTGGTTGTTGTGTGTTGATTCCACCA
1 GGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACCA
*
3061107 GGTATCATTGATTATAAAGGTGGTTATTGTGTGCTGATTCCACCA
1 GGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACCA
* * *
3061152 GGTA-CTATTGATTATGAAGGTGGTTGCTATGTGCTGATTCCACC-
1 GGTATC-ATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACCA
3061196 GAGTATCA
1 G-GTATCA
3061204 CTAACTATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
44 2 0.02
45 84 0.97
46 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (45 bp):
GGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACCA
Found at i:3073212 original size:24 final size:25
Alignment explanation
Indices: 3073159--3073206 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3073149 TTGGCTCTCA
* *
3073159 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATAGCTCTTG
3073184 CGAGCTTCCCGTTA-ATAGCTCTT
1 CGAGCTTCCCGTTATATAGCTCTT
3073207 CGGAGCATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.38
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGCTCTTG
Found at i:3073298 original size:25 final size:24
Alignment explanation
Indices: 3073270--3073352 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
3073260 CTTATAAGCG
3073270 TCCCGATAATTGGCTCTTCGGAGCT
1 TCCCGATAA-TGGCTCTTCGGAGCT
* **
3073295 TCCCGATAACTGGATCTTATGAGCT
1 TCCCGATAA-TGGCTCTTCGGAGCT
* **
3073320 ACTTGATTAATGGCT-TTCTGGAGCT
1 TCCCGA-TAATGGCTCTTC-GGAGCT
3073345 TCCCGATA
1 TCCCGATA
3073353 CTGCCTCACT
Statistics
Matches: 43, Mismatches: 13, Indels: 5
0.70 0.21 0.08
Matches are distributed among these distances:
24 4 0.09
25 36 0.84
26 3 0.07
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (24 bp):
TCCCGATAATGGCTCTTCGGAGCT
Found at i:3073416 original size:24 final size:24
Alignment explanation
Indices: 3073367--3073470 Score: 70
Period size: 25 Copynumber: 4.2 Consensus size: 24
3073357 CTCACTTGAA
* * *
3073367 CTTCCCATTATTGGCTCGTATGAG
1 CTTCCCATTAATGGCTCCTATAAG
3073391 CTTCCCATTAATGGCTCTCTA-AAG
1 CTTCCCATTAATGGCTC-CTATAAG
* * *
3073415 CTTCTCGTTACATGGCTCAC-ATGAG
1 CTTCCCATTA-ATGGCTC-CTATAAG
* *
3073440 CTTCCTATTACATGGCTCAC-ATGAG
1 CTTCCCATTA-ATGGCTC-CTATAAG
3073465 CTTCCC
1 CTTCCC
3073471 GGTTTATGGC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
24 27 0.41
25 39 0.59
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (24 bp):
CTTCCCATTAATGGCTCCTATAAG
Found at i:3073441 original size:25 final size:25
Alignment explanation
Indices: 3073422--3073469 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
3073412 AAGCTTCTCG
3073422 TTACATGGCTCACATGAGCTTCCTA
1 TTACATGGCTCACATGAGCTTCCTA
3073447 TTACATGGCTCACATGAGCTTCC
1 TTACATGGCTCACATGAGCTTCC
3073470 CGGTTTATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (25 bp):
TTACATGGCTCACATGAGCTTCCTA
Found at i:3079704 original size:20 final size:20
Alignment explanation
Indices: 3079672--3079710 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3079662 AATAATAAGT
3079672 AAATTATACATA-TTATTAC
1 AAATTATACATATTTATTAC
*
3079691 AAATGTATATATATTTATTA
1 AAAT-TATACATATTTATTA
3079711 AATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
AAATTATACATATTTATTAC
Found at i:3082460 original size:48 final size:48
Alignment explanation
Indices: 3082325--3082498 Score: 235
Period size: 48 Copynumber: 3.6 Consensus size: 48
3082315 ATAGTATAAC
*** * * *
3082325 TATGGTCTTACAC-ATCGTCACATATCACATACCGAAGCCATAGCCCAGC
1 TATGGTCTTACACGAAAATCACATATCAC--ACCGATGCCATATCCCAGA
* *
3082374 TATGGTCTTACACGAAAA-CACATATCACACTGATGCCATATCCTAGA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
*
3082421 TATGGTCTTACATGAAAATCACATATCACACCGATGCCATATCCCAGA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
3082469 TATGGTCTTACACGAAAATCACATATCACA
1 TATGGTCTTACACGAAAATCACATATCACA
3082499 TCACACTGAT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
47 31 0.28
48 56 0.50
49 23 0.21
50 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.25
Consensus pattern (48 bp):
TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
Found at i:3083672 original size:48 final size:48
Alignment explanation
Indices: 3083537--3083710 Score: 235
Period size: 48 Copynumber: 3.6 Consensus size: 48
3083527 ATAGTATAAC
*** * * *
3083537 TATGGTCTTACAC-ATCGTCACATATCACATACCGAAGCCATAGCCCAGC
1 TATGGTCTTACACGAAAATCACATATCAC--ACCGATGCCATATCCCAGA
* *
3083586 TATGGTCTTACACGAAAA-CACATATCACACTGATGCCATATCCTAGA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
*
3083633 TATGGTCTTACATGAAAATCACATATCACACCGATGCCATATCCCAGA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
3083681 TATGGTCTTACACGAAAATCACATATCACA
1 TATGGTCTTACACGAAAATCACATATCACA
3083711 TCACACTGAT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
47 31 0.28
48 56 0.50
49 23 0.21
50 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.25
Consensus pattern (48 bp):
TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
Found at i:3084884 original size:48 final size:48
Alignment explanation
Indices: 3084749--3084922 Score: 235
Period size: 48 Copynumber: 3.6 Consensus size: 48
3084739 ATAGTATAAC
*** * * *
3084749 TATGGTCTTACAC-ATCGTCACATATCACATACCGAAGCCATAGCCCAGC
1 TATGGTCTTACACGAAAATCACATATCAC--ACCGATGCCATATCCCAGA
* *
3084798 TATGGTCTTACACGAAAA-CACATATCACACTGATGCCATATCCTAGA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
*
3084845 TATGGTCTTACATGAAAATCACATATCACACCGATGCCATATCCCAGA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
3084893 TATGGTCTTACACGAAAATCACATATCACA
1 TATGGTCTTACACGAAAATCACATATCACA
3084923 TCACACTGAT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
47 31 0.28
48 56 0.50
49 23 0.21
50 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.25
Consensus pattern (48 bp):
TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
Found at i:3086096 original size:48 final size:48
Alignment explanation
Indices: 3085961--3086134 Score: 235
Period size: 48 Copynumber: 3.6 Consensus size: 48
3085951 ATAGTATAAC
*** * * *
3085961 TATGGTCTTACAC-ATCGTCACATATCACATACCGAAGCCATAGCCCAGC
1 TATGGTCTTACACGAAAATCACATATCAC--ACCGATGCCATATCCCAGA
* *
3086010 TATGGTCTTACACGAAAA-CACATATCACACTGATGCCATATCCTAGA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
*
3086057 TATGGTCTTACATGAAAATCACATATCACACCGATGCCATATCCCAGA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
3086105 TATGGTCTTACACGAAAATCACATATCACA
1 TATGGTCTTACACGAAAATCACATATCACA
3086135 TCACACTGAT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
47 31 0.28
48 56 0.50
49 23 0.21
50 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.25
Consensus pattern (48 bp):
TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
Found at i:3087308 original size:48 final size:48
Alignment explanation
Indices: 3087173--3087346 Score: 235
Period size: 48 Copynumber: 3.6 Consensus size: 48
3087163 ATAGTATAAC
*** * * *
3087173 TATGGTCTTACAC-ATCGTCACATATCACATACCGAAGCCATAGCCCAGC
1 TATGGTCTTACACGAAAATCACATATCAC--ACCGATGCCATATCCCAGA
* *
3087222 TATGGTCTTACACGAAAA-CACATATCACACTGATGCCATATCCTAGA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
*
3087269 TATGGTCTTACATGAAAATCACATATCACACCGATGCCATATCCCAGA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
3087317 TATGGTCTTACACGAAAATCACATATCACA
1 TATGGTCTTACACGAAAATCACATATCACA
3087347 TCACACTGAT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
47 31 0.28
48 56 0.50
49 23 0.21
50 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.25
Consensus pattern (48 bp):
TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCAGA
Found at i:3089422 original size:14 final size:14
Alignment explanation
Indices: 3089403--3089454 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
3089393 ATCTAATGAC
3089403 TTAAATAAAATTTT
1 TTAAATAAAATTTT
**
3089417 TTAAATAATTTAATAAT
1 TTAAATAA---AATTTT
*
3089434 TTAAATAAAAATTT
1 TTAAATAAAATTTT
3089448 TTAAATA
1 TTAAATA
3089455 GTTCAATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 18 0.60
17 12 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAATAAAATTTT
Found at i:3089438 original size:31 final size:31
Alignment explanation
Indices: 3089389--3089454 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
3089379 AATAAAAGTT
* *
3089389 AATAATCTAATGACTTAAATAAAATTTTTTA
1 AATAATCTAATAACTTAAATAAAAATTTTTA
* *
3089420 AATAATTTAATAATTTAAATAAAAATTTTTA
1 AATAATCTAATAACTTAAATAAAAATTTTTA
3089451 AATA
1 AATA
3089455 GTTCAATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (31 bp):
AATAATCTAATAACTTAAATAAAAATTTTTA
Found at i:3094929 original size:14 final size:14
Alignment explanation
Indices: 3094910--3094961 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
3094900 ATCTAATGAC
3094910 TTAAATAAAATTTT
1 TTAAATAAAATTTT
**
3094924 TTAAATAATTTAATAAT
1 TTAAATAA---AATTTT
*
3094941 TTAAATAAAAATTT
1 TTAAATAAAATTTT
3094955 TTAAATA
1 TTAAATA
3094962 GTTCAATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 18 0.60
17 12 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAATAAAATTTT
Found at i:3094945 original size:31 final size:31
Alignment explanation
Indices: 3094896--3094961 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
3094886 AATAAAAGTT
* *
3094896 AATAATCTAATGACTTAAATAAAATTTTTTA
1 AATAATCTAATAACTTAAATAAAAATTTTTA
* *
3094927 AATAATTTAATAATTTAAATAAAAATTTTTA
1 AATAATCTAATAACTTAAATAAAAATTTTTA
3094958 AATA
1 AATA
3094962 GTTCAATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (31 bp):
AATAATCTAATAACTTAAATAAAAATTTTTA
Found at i:3102445 original size:56 final size:55
Alignment explanation
Indices: 3102380--3102529 Score: 178
Period size: 53 Copynumber: 2.7 Consensus size: 55
3102370 GTTATGTAGA
* * ** *
3102380 AATCAAATTGCTAAAAGATAACATTCCATAATAATATCCTATAATATCTGATTAAG
1 AATCAAATTGCTAAAAGATAA-ATTCCATAATAATATCCTACAAAATCCCACTAAG
** * *
3102436 AATCAAATTGCTAAGGGAT-AATT-CATAATAATATCTTACAAAATCCCACTAGG
1 AATCAAATTGCTAAAAGATAAATTCCATAATAATATCCTACAAAATCCCACTAAG
*
3102489 AATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTA
1 AATCAAATTGCTAAAAGATAA-ATTCCATAATAATATCCTA
3102530 ACACCCCCTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
53 40 0.51
54 4 0.05
55 3 0.04
56 31 0.40
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (55 bp):
AATCAAATTGCTAAAAGATAAATTCCATAATAATATCCTACAAAATCCCACTAAG
Found at i:3103900 original size:16 final size:16
Alignment explanation
Indices: 3103876--3103917 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3103866 TGGTTCACTA
* *
3103876 TAATGGAATAGGGTTG
1 TAATGGAATAGAGCTG
*
3103892 TAATTGAATAGAGCTG
1 TAATGGAATAGAGCTG
3103908 TAATGGAATA
1 TAATGGAATA
3103918 AAACTGCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.29, T:0.31
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:3104111 original size:25 final size:26
Alignment explanation
Indices: 3104082--3104132 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3104072 ATGATTATTG
*
3104082 TTATTGTT-ATTAAATTTTAATAAAA
1 TTATTGTTAAATAAATTTTAATAAAA
*
3104107 TTATTGTTAAATATATTTTAATAAAA
1 TTATTGTTAAATAAATTTTAATAAAA
3104133 ATAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
TTATTGTTAAATAAATTTTAATAAAA
Found at i:3104191 original size:59 final size:58
Alignment explanation
Indices: 3104095--3104230 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 58
3104085 TTGTTATTAA
* * *
3104095 ATTTTAATAAAATTATTGTTAAATATATTTTAATAAAAATAAAAAAATAATTTAAT-CAT
1 ATTTTAATAAAATTATTATTAAATACAATTTAAT-AAAAT-AAAAAATAATTTAATACAT
* * * * *
3104154 ATTTTAACACAATTATTATTAAATACAATTTAGTAAAATAATATATAATTTAATAACAT
1 ATTTTAATAAAATTATTATTAAATACAATTTAATAAAATAAAAAATAATTTAAT-ACAT
*
3104213 -TTTTAATATAATTATTAT
1 ATTTTAATAAAATTATTAT
3104231 ATGAATTAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
57 13 0.20
58 21 0.32
59 31 0.48
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTTTAATAAAATTATTATTAAATACAATTTAATAAAATAAAAAATAATTTAATACAT
Found at i:3105609 original size:50 final size:50
Alignment explanation
Indices: 3105485--3105780 Score: 281
Period size: 50 Copynumber: 5.8 Consensus size: 50
3105475 GATAATAACA
* ** * * * *
3105485 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGT-AC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* * * ** **
3105534 TACCAATGCCATATCCCAGAAATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* * ** *
3105584 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* ** *
3105634 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCACCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
*
3105684 TGCCAATGCCATGTCCTAGACAT-GTCTTACATGGGACCTCTCATAATCTCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC-A-G
* * *
3105738 ATGCCAATACCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
3105781 TTACCCAAAT
Statistics
Matches: 202, Mismatches: 37, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
49 58 0.29
50 102 0.50
52 2 0.01
54 1 0.00
55 22 0.11
56 17 0.08
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
Found at i:3119243 original size:68 final size:72
Alignment explanation
Indices: 3119139--3119293 Score: 228
Period size: 68 Copynumber: 2.2 Consensus size: 72
3119129 TAGGGTATTC
*
3119139 CATTGAACCAAACAGCTGTTTGTGTGGTCCTATAGAAGAGACTTGTAATAAACTTGTAATGGCAT
1 CATTGAACCAAACAGCTG-TTGTGTGGTCCTATAGAAGAGACTTATAATAAACTTGTAATGGCAT
3119204 AGCCATTA
65 AGCCATTA
* * * *
3119212 CATTGAACCAAACAGC-G-TGTG-GG-CCTGTAGAATATACTTATAATAGACTTGTAATGGCATA
1 CATTGAACCAAACAGCTGTTGTGTGGTCCTATAGAAGAGACTTATAATAAACTTGTAATGGCATA
3119273 GCCATTA
66 GCCATTA
3119280 CATTGAACCAAACA
1 CATTGAACCAAACA
3119294 TTACCTAAGT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
68 54 0.70
69 2 0.03
70 4 0.05
72 1 0.01
73 16 0.21
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (72 bp):
CATTGAACCAAACAGCTGTTGTGTGGTCCTATAGAAGAGACTTATAATAAACTTGTAATGGCATA
GCCATTA
Found at i:3127986 original size:13 final size:13
Alignment explanation
Indices: 3127951--3127988 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
3127941 GATATATTTG
*
3127951 TAATTTGAAAGCT
1 TAATTTGAAAACT
3127964 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
3127978 TAATTTGAAAA
1 TAATTTGAAAA
3127989 TTTGGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:3128325 original size:32 final size:32
Alignment explanation
Indices: 3128236--3128428 Score: 260
Period size: 32 Copynumber: 5.8 Consensus size: 32
3128226 TCACTTGTCT
* * *
3128236 TTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTCTTGCAGGGAATCTCTCCTGTTCA--CATCA
* *
3128270 TTCTGTTGCAGGGAATCTTTCCTGTTCACATCA
1 TT-TCTTGCAGGGAATCTCTCCTGTTCACATCA
* *
3128303 TTTCTTGTAGGGAATCTCTCCTGTTCACGCATTA
1 TTTCTTGCAGGGAATCTCTCCTGTTCA--CATCA
*
3128337 TTTTGTTGCAGGGAATCTCTCCTGTTCACATCA
1 -TTTCTTGCAGGGAATCTCTCCTGTTCACATCA
3128370 TTTCTTGCAGGGAATCTCTCCTGTTCACATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACATCA
3128402 TTTCTTGCAGGGAATCTCTCCTGTTCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCA
3128429 TGTATTATTT
Statistics
Matches: 144, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
32 80 0.56
33 10 0.07
34 6 0.04
35 48 0.33
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (32 bp):
TTTCTTGCAGGGAATCTCTCCTGTTCACATCA
Found at i:3128344 original size:67 final size:67
Alignment explanation
Indices: 3128236--3128428 Score: 302
Period size: 67 Copynumber: 2.9 Consensus size: 67
3128226 TCACTTGTCT
* * * *
3128236 TTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCACAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACAT
3128301 CA
66 CA
*
3128303 TTTCTTGTAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACAT
3128368 CA
66 CA
* *
3128370 TTTCTTGCAGGGAATCTCTCCTGTTCA--CATCA-TTTCTTGCAGGGAATCTCTCCTGTTCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCA
3128429 TGTATTATTT
Statistics
Matches: 118, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
64 26 0.22
65 4 0.03
67 88 0.75
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (67 bp):
TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACAT
CA
Found at i:3128414 original size:99 final size:101
Alignment explanation
Indices: 3128235--3128438 Score: 304
Period size: 99 Copynumber: 2.0 Consensus size: 101
3128225 TTCACTTGTC
* * * *
3128235 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTCTTGCAGGGAATATCTCCTGTTCAC-CATCATTCTCTTGCAGGGAATCTCTCCTGTTCACA
*
3128300 TCATTTCTTGTAGGGAATCTCTCCTGTTCACGCATTA
65 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
3128337 TTTTGTTGCAGGGAATCTCTCCTGTTCA-CATCATT-TCTTGCAGGGAATCTCTCCTGTTCACAT
1 TTTTCTTGCAGGGAATATCTCCTGTTCACCATCATTCTCTTGCAGGGAATCTCTCCTGTTCACAT
* *
3128400 CATTTCTTGCAGGGAATCTCTCCTGTTCATGTATTA
66 CATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
3128436 TTT
1 TTT
3128439 CTTTTTGGAC
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
99 62 0.67
100 6 0.06
102 25 0.27
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (101 bp):
TTTTCTTGCAGGGAATATCTCCTGTTCACCATCATTCTCTTGCAGGGAATCTCTCCTGTTCACAT
CATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:3131269 original size:21 final size:22
Alignment explanation
Indices: 3131239--3131283 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
3131229 GAGCAAATTG
3131239 TTGATTCTATTTCCTTTTTG-AT
1 TTGATTCTA-TTCCTTTTTGTAT
*
3131261 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCCTTTTTGTAT
3131282 TT
1 TT
3131284 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCCTTTTTGTAT
Found at i:3135632 original size:14 final size:14
Alignment explanation
Indices: 3135594--3135632 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3135584 GATGTATTTG
*
3135594 TAATTTG-AAAGCT
1 TAATTTGAAAACCT
3135607 TAAGTTTGAAAACCT
1 TAA-TTTGAAAACCT
3135622 TAATTTGAAAA
1 TAATTTGAAAA
3135633 TTTGGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 12 0.52
15 8 0.35
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (14 bp):
TAATTTGAAAACCT
Found at i:3144728 original size:42 final size:41
Alignment explanation
Indices: 3144644--3144728 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 41
3144634 TTTTTTTTAA
** *
3144644 TTACTTAACTATTTTTATTATTATTGTTATTATTATTAATG
1 TTACTTAACTATTAGTATTATTATTGTTATTAGTATTAATG
3144685 TTACTATAACTATTAGTATTATTATT-TATATTAGT-TTATATG
1 TTACT-TAACTATTAGTATTATTATTGT-TATTAGTATTA-ATG
3144727 TT
1 TT
3144729 TATTTACCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
41 9 0.24
42 29 0.76
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.59
Consensus pattern (41 bp):
TTACTTAACTATTAGTATTATTATTGTTATTAGTATTAATG
Found at i:3146304 original size:26 final size:26
Alignment explanation
Indices: 3146275--3146342 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
3146265 ATTATATAAC
3146275 TATTTCGTATAACCATCTCATAT-TAG
1 TATTTCGTATAACCATCTCATATAT-G
* ** * *
3146301 TATTTTGTGCAACCATTTCATATATT
1 TATTTCGTATAACCATCTCATATATG
*
3146327 TATTTCGTATAGCCAT
1 TATTTCGTATAACCAT
3146343 TAAATATAAC
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
26 31 0.97
27 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.46
Consensus pattern (26 bp):
TATTTCGTATAACCATCTCATATATG
Found at i:3152907 original size:26 final size:26
Alignment explanation
Indices: 3152884--3152947 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
3152874 GCTAAGATAG
3152884 CCACAAAGGCTTCCTTTCAGAGATCC
1 CCACAAAGGCTTCCTTTCAGAGATCC
3152910 CCACAAAGGCTTCCTTTCAGAGATCC
1 CCACAAAGGCTTCCTTTCAGAGATCC
3152936 CCACAAAGGCTT
1 CCACAAAGGCTT
3152948 TTATTTAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (26 bp):
CCACAAAGGCTTCCTTTCAGAGATCC
Found at i:3152970 original size:29 final size:29
Alignment explanation
Indices: 3152878--3153030 Score: 108
Period size: 26 Copynumber: 5.6 Consensus size: 29
3152868 CATTTAGCTA
* * *
3152878 AGATAGCCACAAAGGC-TTCCTTT--CAG
1 AGATCGCCACAAAGGCTTTCATTTAATAG
* * *
3152904 AGATCCCCACAAAGGC-TTCCTTT--CAG
1 AGATCGCCACAAAGGCTTTCATTTAATAG
* *
3152930 AGATCCCCACAAAGGCTTTTATTTAATAG
1 AGATCGCCACAAAGGCTTTCATTTAATAG
* *
3152959 AGATTGTCACAAAGGCTTTCATTTAATAG
1 AGATCGCCACAAAGGCTTTCATTTAATAG
* * * *
3152988 TGATCGCCATAAAGGC-TTCACTTCATAG
1 AGATCGCCACAAAGGCTTTCATTTAATAG
*
3153016 ATAT--CCACAAAGGCT
1 AGATCGCCACAAAGGCT
3153031 CACTTATACG
Statistics
Matches: 105, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
26 49 0.47
27 5 0.05
28 12 0.11
29 39 0.37
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (29 bp):
AGATCGCCACAAAGGCTTTCATTTAATAG
Found at i:3161152 original size:15 final size:14
Alignment explanation
Indices: 3161132--3161177 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
3161122 AAGGTAGATA
3161132 AAAATAGAACAAAAT
1 AAAATAGAA-AAAAT
*
3161147 AAAATAAAATAAAAT
1 AAAATAGAA-AAAAT
3161162 -AAAT-GAAAAAAT
1 AAAATAGAAAAAAT
3161174 AAAA
1 AAAA
3161178 ATTACCACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
14 4 0.15
15 13 0.48
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAATAGAAAAAAT
Found at i:3161608 original size:28 final size:28
Alignment explanation
Indices: 3161541--3161608 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
3161531 TTAAATTATT
3161541 AATTAAAC-TAATTAAATTAATTATCCTA
1 AATT-AACTTAATTAAATTAATTATCCTA
*
3161569 AAATAA-TATAATTAAATTAATTAAT-CTA
1 AATTAACT-TAATTAAATTAATT-ATCCTA
3161597 AATTAACTTAAT
1 AATTAACTTAAT
3161609 GTAATTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 2 0.06
28 29 0.85
29 3 0.09
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (28 bp):
AATTAACTTAATTAAATTAATTATCCTA
Found at i:3161614 original size:14 final size:14
Alignment explanation
Indices: 3161549--3161608 Score: 63
Period size: 14 Copynumber: 4.3 Consensus size: 14
3161539 TTAATTAAAC
3161549 TAAT-TAAATTAAT
1 TAATCTAAATTAAT
*
3161562 T-ATCCTAAAATAAT
1 TAAT-CTAAATTAAT
3161576 ATAAT-TAAATTAAT
1 -TAATCTAAATTAAT
3161590 TAATCTAAATTAACT
1 TAATCTAAATTAA-T
3161605 TAAT
1 TAAT
3161609 GTAATTTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 2 0.05
13 5 0.13
14 24 0.62
15 6 0.15
16 2 0.05
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATCTAAATTAAT
Found at i:3174126 original size:11 final size:11
Alignment explanation
Indices: 3174110--3174137 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3174100 ATTAAAGGAT
3174110 ATTTGGAGATA
1 ATTTGGAGATA
3174121 ATTTGGAGATA
1 ATTTGGAGATA
3174132 ATTTGG
1 ATTTGG
3174138 TAAATGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (11 bp):
ATTTGGAGATA
Found at i:3180367 original size:94 final size:94
Alignment explanation
Indices: 3180206--3180395 Score: 380
Period size: 94 Copynumber: 2.0 Consensus size: 94
3180196 TTACGATACG
3180206 ATTGGCATGCCAACAGGGTTTAATGCGCACTTGTACGGGATATGTGTTTGTATAAAGATCACTAT
1 ATTGGCATGCCAACAGGGTTTAATGCGCACTTGTACGGGATATGTGTTTGTATAAAGATCACTAT
3180271 AGGTTATACCGGGATCTAGCATTTTTTAC
66 AGGTTATACCGGGATCTAGCATTTTTTAC
3180300 ATTGGCATGCCAACAGGGTTTAATGCGCACTTGTACGGGATATGTGTTTGTATAAAGATCACTAT
1 ATTGGCATGCCAACAGGGTTTAATGCGCACTTGTACGGGATATGTGTTTGTATAAAGATCACTAT
3180365 AGGTTATACCGGGATCTAGCATTTTTTAC
66 AGGTTATACCGGGATCTAGCATTTTTTAC
3180394 AT
1 AT
3180396 ATCACCGAGT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (94 bp):
ATTGGCATGCCAACAGGGTTTAATGCGCACTTGTACGGGATATGTGTTTGTATAAAGATCACTAT
AGGTTATACCGGGATCTAGCATTTTTTAC
Found at i:3181919 original size:21 final size:21
Alignment explanation
Indices: 3181869--3181919 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 21
3181859 TTCAAACATG
*
3181869 GTCA-TGTGGCTACCCCACAC
1 GTCAGTGTGCCTACCCCACAC
** * *
3181889 ACCCGCGTGCCTACCCCACAC
1 GTCAGTGTGCCTACCCCACAC
3181910 GTCAGTGTGC
1 GTCAGTGTGC
3181920 TCACCTGTGT
Statistics
Matches: 21, Mismatches: 9, Indels: 1
0.68 0.29 0.03
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.18
Consensus pattern (21 bp):
GTCAGTGTGCCTACCCCACAC
Found at i:3182816 original size:18 final size:20
Alignment explanation
Indices: 3182771--3182812 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3182761 CAATCACAGC
3182771 TCTCAACAGGTGAGTAATGT
1 TCTCAACAGGTGAGTAATGT
3182791 TCTCAACAGGTGAGTAATGT
1 TCTCAACAGGTGAGTAATGT
3182811 TC
1 TC
3182813 AACAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (20 bp):
TCTCAACAGGTGAGTAATGT
Found at i:3194321 original size:5 final size:5
Alignment explanation
Indices: 3194292--3194330 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
3194282 TAAATTTAAC
* *
3194292 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
3194331 CATCCTAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:3218800 original size:17 final size:18
Alignment explanation
Indices: 3218778--3218812 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
3218768 TAAAAAATTG
3218778 TTTTAAAAA-TATAAATA
1 TTTTAAAAATTATAAATA
3218795 TTTTAAAAATTATAAATA
1 TTTTAAAAATTATAAATA
3218813 AATAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTTAAAAATTATAAATA
Found at i:3219269 original size:28 final size:28
Alignment explanation
Indices: 3219224--3219282 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
3219214 AATAAACATT
*
3219224 AAAAAATTATTTTAAAAATAAAAAAATAA
1 AAAAAAGTATTTTAAAAAT-AAAAAATAA
*
3219253 AAAAAAGTATTTT-AAAATTAAAAATAA
1 AAAAAAGTATTTTAAAAATAAAAAATAA
3219280 AAA
1 AAA
3219283 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 11 0.39
28 5 0.18
29 12 0.43
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAAAGTATTTTAAAAATAAAAAATAA
Found at i:3219275 original size:27 final size:27
Alignment explanation
Indices: 3219208--3219282 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 27
3219198 TCCGGCCTAT
* * *
3219208 TTTTAAAA-TAAACAT-TAAAAAATTA
1 TTTTAAAATTAAAAATAAAAAAAAGTA
*
3219233 TTTTAAAAATAAAAAAATAAAAAAAAGTA
1 TTTT-AAAAT-TAAAAATAAAAAAAAGTA
3219262 TTTTAAAATTAAAAATAAAAA
1 TTTTAAAATTAAAAATAAAAA
3219283 TAAAAAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
25 4 0.10
26 4 0.10
27 11 0.27
28 10 0.24
29 12 0.29
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (27 bp):
TTTTAAAATTAAAAATAAAAAAAAGTA
Found at i:3219681 original size:20 final size:22
Alignment explanation
Indices: 3219656--3219709 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
3219646 TATTAATCTT
3219656 TTTATAATTTTTC-TCTAA-TA
1 TTTATAATTTTTCTTCTAATTA
* *
3219676 TTTAT-ATATCTCTTCTAATTTA
1 TTTATAATTTTTCTTCTAA-TTA
3219698 TTTATAATTTTT
1 TTTATAATTTTT
3219710 AAACAATCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 5 0.19
20 10 0.38
22 7 0.27
23 4 0.15
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATAATTTTTCTTCTAATTA
Found at i:3228349 original size:13 final size:14
Alignment explanation
Indices: 3228333--3228361 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3228323 TTATTATAAA
3228333 TTTTAAT-TAATTT
1 TTTTAATATAATTT
3228346 TTTTAATATAATTT
1 TTTTAATATAATTT
3228360 TT
1 TT
3228362 AAAATTACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTAATATAATTT
Found at i:3232706 original size:53 final size:53
Alignment explanation
Indices: 3232594--3232707 Score: 185
Period size: 52 Copynumber: 2.2 Consensus size: 53
3232584 TCAAAAAGAA
* *
3232594 ACAAAAACGAAACCCAAAAAAACGGAGTCAACAAAGATAGTCGAAGCAAGTTC
1 ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATAGTCGAACCAAGTTC
*
3232647 ACAAAAACGAAACCC-AAAAAACAGAGTCAACAAAGATATTCGAACCAAGTTC
1 ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATAGTCGAACCAAGTTC
3232699 ACGAAAAAC
1 AC-AAAAAC
3232708 AGAGCCCCTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 36 0.63
53 21 0.37
ACGTcount: A:0.54, C:0.22, G:0.14, T:0.10
Consensus pattern (53 bp):
ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATAGTCGAACCAAGTTC
Found at i:3234428 original size:33 final size:33
Alignment explanation
Indices: 3234364--3234438 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
3234354 GGAAGTAATC
*
3234364 TTAGGAACAACTAACCTTGGGAACGATATTATG
1 TTAGGAACAACTAACCTTGGGAACGACATTATG
* * *
3234397 TTAGGAACAACTAACTTTTGGAACGGCATTATG
1 TTAGGAACAACTAACCTTGGGAACGACATTATG
* *
3234430 GTGGGAACA
1 TTAGGAACA
3234439 CTTTGGAGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (33 bp):
TTAGGAACAACTAACCTTGGGAACGACATTATG
Found at i:3235240 original size:16 final size:14
Alignment explanation
Indices: 3235196--3235232 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3235186 AAAAAGATCG
3235196 AAAGA-AGAA-AAGA
1 AAAGAGAGAACAA-A
3235209 AAAGAGAGAACAAA
1 AAAGAGAGAACAAA
3235223 AAAGAGAGAA
1 AAAGAGAGAA
3235233 GAGGAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 15 0.68
15 2 0.09
ACGTcount: A:0.73, C:0.03, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAGAGAGAACAAA
Found at i:3245103 original size:11 final size:12
Alignment explanation
Indices: 3245073--3245106 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
3245063 CGGCCCGCCC
3245073 ATATTAATTTTT
1 ATATTAATTTTT
3245085 ATATTAATTTTT
1 ATATTAATTTTT
3245097 ATA-TAATTTT
1 ATATTAATTTT
3245107 AAAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:3245127 original size:17 final size:19
Alignment explanation
Indices: 3245107--3245147 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3245097 ATATAATTTT
*
3245107 AAAATATA-T-AATACATC
1 AAAATATACTAAAAACATC
3245124 AAAA-ATACTAAAAACATC
1 AAAATATACTAAAAACATC
3245142 AAAATA
1 AAAATA
3245148 AATATTTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 5 0.25
18 11 0.55
19 1 0.05
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATATACTAAAAACATC
Found at i:3245272 original size:30 final size:30
Alignment explanation
Indices: 3245228--3245290 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
3245218 ACTTAACAAG
3245228 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
3245258 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
3245288 CAA
1 CAA
3245291 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:3245375 original size:22 final size:22
Alignment explanation
Indices: 3245328--3245375 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
3245318 CAATAATAAC
* *
3245328 AAAATAGTAGCAACATGATAGT
1 AAAATAGTAGCAAAATGAGAGT
*
3245350 AAAATGGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAAT-GAGAGT
3245372 AAAA
1 AAAA
3245376 CAATAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.17
Consensus pattern (22 bp):
AAAATAGTAGCAAAATGAGAGT
Found at i:3251452 original size:23 final size:23
Alignment explanation
Indices: 3251409--3251454 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3251399 TCATGTGAGC
*
3251409 ATTAATGTAAAGGAAAGACTATG
1 ATTAATGTAAAGGAAACACTATG
*
3251432 ATTATATGTAAAGG-CACACTATG
1 ATTA-ATGTAAAGGAAACACTATG
3251455 TGTGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (23 bp):
ATTAATGTAAAGGAAACACTATG
Found at i:3253972 original size:196 final size:196
Alignment explanation
Indices: 3253625--3254053 Score: 488
Period size: 196 Copynumber: 2.2 Consensus size: 196
3253615 CGGAACATCA
* * * **
3253625 GGTACCTCAACTTTTATAATGTCATTGTTAATCTAAATACGCCATTCTGGCTAAAATGTTGACGT
1 GGTACCTCAACTTTTATAATGTCACTGTTAATATAAATACACCATTCTAACTAAAATGTTGACGT
* * *
3253690 GCGCATGTCCAAATACACAACCTTTTACTTAATTTTTGAGATTATACAATAATAGTCAAATTCCA
66 ACACATGTCCAAATACACAACCTTTTACTT-ATTTTTGAGATTATACAACAATAGTCAAATTCCA
*
3253755 ATTTTGGTCCCTATATTATGCTTAAATTTGAAATTTAATCTCTATATTTTAATTTTTTACATAAT
130 ATTTTGGTCCCTATATTATGCTCAAATTTGAAATTTAATCTCTATATTTTAATTTTTTACATAAT
3253820 TC
195 TC
* * ** * * *
3253822 GGTACCTTAACTTTTATAATGTCACTGTTAGTATAAATACATTATTGTAATTAAAATTTTGACGT
1 GGTACCTCAACTTTTATAATGTCACTGTTAATATAAATACACCATTCTAACTAAAATGTTGACGT
* * * * *
3253887 ACACAT-TCCAAATACACAACCTTTTTTCTT-TTCTTTCGA-ATTATATAACAATGGTTAAATTT
66 ACACATGTCCAAATACACAACC-TTTTACTTATT-TTT-GAGATTATACAACAATAGTCAAATTC
* * * *
3253949 CAATTTTGGTCCCTATGTTATGCTCAATTTTGAAATTTAATCTCTATGTTTTAGTTTTTTTTTAC
128 CAATTTTGGTCCCTATATTATGCTCAAATTTGAAATTTAATCTCTATATTTTA---ATTTTTTAC
*
3254014 ATAATTT
190 ATAATTC
** *
3254021 AATACCTCAACATTTT-TAATGTCATTAGTTAAT
1 GGTACCTCAAC-TTTTATAATGTCACT-GTTAAT
3254054 CAAAATATTT
Statistics
Matches: 193, Mismatches: 31, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
195 2 0.01
196 85 0.44
197 66 0.34
199 31 0.16
200 9 0.05
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.44
Consensus pattern (196 bp):
GGTACCTCAACTTTTATAATGTCACTGTTAATATAAATACACCATTCTAACTAAAATGTTGACGT
ACACATGTCCAAATACACAACCTTTTACTTATTTTTGAGATTATACAACAATAGTCAAATTCCAA
TTTTGGTCCCTATATTATGCTCAAATTTGAAATTTAATCTCTATATTTTAATTTTTTACATAATT
C
Found at i:3260409 original size:11 final size:9
Alignment explanation
Indices: 3260367--3260409 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
3260357 AAAAATTACA
*
3260367 AAAAAATAT
1 AAAAAATTT
3260376 AAATAAATTT
1 AAA-AAATTT
3260386 AAAAAATTT
1 AAAAAATTT
3260395 AAAAATATGTT
1 AAAAA-AT-TT
3260406 AAAA
1 AAAA
3260410 CTTTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 14 0.47
10 10 0.33
11 6 0.20
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAAATTT
Found at i:3260966 original size:29 final size:28
Alignment explanation
Indices: 3260929--3260985 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
3260919 TAAAAAATTA
3260929 GTAATTTTTTAT-ATTTATATAATTTTTT
1 GTAATTTTTTATAATTT-TATAATTTTTT
*
3260957 GTAATCTTTTTATAATTTTGTAATTTTTT
1 GTAAT-TTTTTATAATTTTATAATTTTTT
3260986 TAGTTTATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 17 0.65
30 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (28 bp):
GTAATTTTTTATAATTTTATAATTTTTT
Found at i:3260972 original size:11 final size:10
Alignment explanation
Indices: 3260930--3260975 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
3260920 AAAAAATTAG
3260930 TAATTTTTTA
1 TAATTTTTTA
*
3260940 T-A-TTTATA
1 TAATTTTTTA
*
3260948 TAATTTTTTG
1 TAATTTTTTA
3260958 TAATCTTTTTA
1 TAAT-TTTTTA
3260969 TAATTTT
1 TAATTTT
3260976 GTAATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
8 6 0.21
9 2 0.07
10 12 0.41
11 9 0.31
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:3260999 original size:24 final size:22
Alignment explanation
Indices: 3260965--3261010 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3260955 TTGTAATCTT
3260965 TTTATAATTTTGTAATTTTTTTAG
1 TTTATAATTTT-T-ATTTTTTTAG
*
3260989 TTTATACTTTTTATTTTTTTAG
1 TTTATAATTTTTATTTTTTTAG
3261011 GTTTTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 1 0.05
24 10 0.48
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.70
Consensus pattern (22 bp):
TTTATAATTTTTATTTTTTTAG
Found at i:3262114 original size:25 final size:25
Alignment explanation
Indices: 3262081--3262137 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
3262071 CGTTGACATG
3262081 GTCG-TTAACAGATGCCACGCTAAT
1 GTCGATTAACAGATGCCACGCTAAT
*
3262105 GTCGATTAACAGATGCCACTCTAAT
1 GTCGATTAACAGATGCCACGCTAAT
3262130 GTCGATTA
1 GTCGATTA
3262138 CTAACATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (25 bp):
GTCGATTAACAGATGCCACGCTAAT
Found at i:3263351 original size:26 final size:24
Alignment explanation
Indices: 3263321--3263373 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
3263311 TTGAATATTA
*
3263321 TTTAAAAAATTTTTCATTTATGTAAT
1 TTTAAAAAATTTTT-ATTT-TATAAT
**
3263347 TTTAATTAATTTTTATTTTATAAT
1 TTTAAAAAATTTTTATTTTATAAT
3263371 TTT
1 TTT
3263374 TTATAACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.33
25 4 0.17
26 12 0.50
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTAAAAAATTTTTATTTTATAAT
Found at i:3264936 original size:18 final size:18
Alignment explanation
Indices: 3264913--3264948 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3264903 TGCCAAGTGC
* *
3264913 ATATCCTATCCCTTATAT
1 ATATCCTAACCATTATAT
3264931 ATATCCTAACCATTATAT
1 ATATCCTAACCATTATAT
3264949 GTTTCCTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATCCTAACCATTATAT
Found at i:3265442 original size:62 final size:59
Alignment explanation
Indices: 3265326--3265446 Score: 145
Period size: 62 Copynumber: 2.0 Consensus size: 59
3265316 TTGTACAAAC
* ****
3265326 TATTTTTATATTGTTTCATTTAATAAAATAGAAGTTGTTTTAAATATTTTAATAGTAAAT
1 TATTTTTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTAAATAAGGCAATAG-AAAT
*
3265386 TATTTTTATATT-TTGTCCTATTTAATAAAATAGAAGTTCTTTTGAATAAGGCAATAGAAAT
1 TATTTTTATATTGTT-T-C-ATTTAATAAAATAGAAGTTCTTTTAAATAAGGCAATAGAAAT
3265447 GATGCAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
59 2 0.04
60 13 0.25
61 5 0.10
62 32 0.62
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (59 bp):
TATTTTTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTAAATAAGGCAATAGAAAT
Found at i:3268780 original size:125 final size:122
Alignment explanation
Indices: 3268559--3268841 Score: 422
Period size: 125 Copynumber: 2.3 Consensus size: 122
3268549 TTCTCAAAAT
* * * *
3268559 TATTTTTTTAGAGCCGTGTTTTCAAAATTATTTTTTCAGAAACTACTAAAAAAAGTGCGTCAAGT
1 TATTTTTTTAGAACCGTCTTTTCAAAATTA-TTTTACAGAAACTACTAAAAAAAGAGCGTCAAGT
* * *
3268624 GGGAGCTTTTTTCAGTACTTTTGCTGGTAGTGCATCCTGCTTGAAGTGTTTTTGACAC
65 GGGAGCTTCTTTCAGTACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACAC
* *
3268682 TATTTTTTTAGAACCGTCTTTTCAAAATTATTTTACAGAAACTACTGTAGAAAAAGAGCGTCCAC
1 TATTTTTTTAGAACCGTCTTTTCAAAATTATTTTACAGAAACTAC--TAAAAAAAGAGCGT-CAA
3268747 GTGGGAGCTTCTTTCAGTACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACAC
63 GTGGGAGCTTCTTTCAGTACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACAC
* *
3268807 TATTTTTTCAGAACCGTCTTCTCAAAATTAATTTT
1 TATTTTTTTAGAACCGTCTTTTCAAAATT-ATTTT
3268842 TTAGAAATTA
Statistics
Matches: 145, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
122 14 0.10
123 28 0.19
124 12 0.08
125 86 0.59
126 5 0.03
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (122 bp):
TATTTTTTTAGAACCGTCTTTTCAAAATTATTTTACAGAAACTACTAAAAAAAGAGCGTCAAGTG
GGAGCTTCTTTCAGTACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACAC
Found at i:3268993 original size:32 final size:31
Alignment explanation
Indices: 3268946--3269038 Score: 111
Period size: 32 Copynumber: 3.0 Consensus size: 31
3268936 CTAAATACAA
*
3268946 AATTATTTTTAAAAACCCTAAACCCTAATTT
1 AATTATTTTTTAAAACCCTAAACCCTAATTT
*
3268977 AATTTATTTTTTAAAACCCTAAACCTTAATTT
1 AA-TTATTTTTTAAAACCCTAAACCCTAATTT
* *
3269009 -A-T-TTTTTTAAAATTCCTAAACCCTGATTT
1 AATTATTTTTTAAAA-CCCTAAACCCTAATTT
3269038 A
1 A
3269039 TTTTTTAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
28 10 0.19
29 14 0.26
31 3 0.06
32 27 0.50
ACGTcount: A:0.38, C:0.17, G:0.01, T:0.44
Consensus pattern (31 bp):
AATTATTTTTTAAAACCCTAAACCCTAATTT
Found at i:3269010 original size:27 final size:27
Alignment explanation
Indices: 3268975--3269054 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 27
3268965 AAACCCTAAT
3268975 TTAATTTATTTTTTAAAACCCTAAACC
1 TTAATTTATTTTTTAAAACCCTAAACC
*
3269002 TTAATTTATTTTTTTAAAATTCCTAAACC
1 TTAATTTA-TTTTTTAAAA-CCCTAAACC
* * *
3269031 CTGATTTATTTTTTAAATCCCTAA
1 TTAATTTATTTTTTAAAACCCTAA
3269055 CCCATAACCC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 13 0.28
28 19 0.41
29 14 0.30
ACGTcount: A:0.34, C:0.16, G:0.01, T:0.49
Consensus pattern (27 bp):
TTAATTTATTTTTTAAAACCCTAAACC
Found at i:3272608 original size:138 final size:138
Alignment explanation
Indices: 3272436--3272699 Score: 456
Period size: 138 Copynumber: 1.9 Consensus size: 138
3272426 GAGAACATAG
* ***
3272436 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTTTATATTTTACCGAATTTATT
1 ATATAATTAATATATAAATTTAATTCATACAAAATATTAATTACATATATTTTACCGAATTTATT
* * *
3272501 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
66 AATATAAACAATTATATTAATTAATTTCAGCCAAAATATAAAAGACAGGGAAATTAATATTCTTT
3272566 GGTAAAAA
131 GGTAAAAA
*
3272574 ATATAATTAATATATGAATTTAATTCATACAAAATATTAATTACATATATTTTACCGAATTTATT
1 ATATAATTAATATATAAATTTAATTCATACAAAATATTAATTACATATATTTTACCGAATTTATT
3272639 AATATAAACAATTATATTAATTAATTTCAGCCAAAATATAAAAGACAGGGAAATTAATATT
66 AATATAAACAATTATATTAATTAATTTCAGCCAAAATATAAAAGACAGGGAAATTAATATT
3272700 GTTTTGGAAA
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 118 1.00
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.39
Consensus pattern (138 bp):
ATATAATTAATATATAAATTTAATTCATACAAAATATTAATTACATATATTTTACCGAATTTATT
AATATAAACAATTATATTAATTAATTTCAGCCAAAATATAAAAGACAGGGAAATTAATATTCTTT
GGTAAAAA
Found at i:3272677 original size:67 final size:67
Alignment explanation
Indices: 3272459--3272677 Score: 160
Period size: 67 Copynumber: 3.2 Consensus size: 67
3272449 ATAAATTTGA
* ***
3272459 TTCATACAAAATATTAATTGTTTATATTTTACCGAATTTATTAATATAAACAATTATATTAATTA
1 TTCAGACAAAATATTAATTACATATATTTTACCGAATTTATTAATATAAACAATTATATTAATTA
3272524 AT
66 AT
* * * ** * * * ** * *
3272526 TTCGGTCAAAATATAAAAGACATGGAAATTAATATTC---TTTGGTAA-AAAATATAATTAATAT
1 TTCAGACAAAATATTAATTACAT--ATATT-TTA-CCGAATTTATTAATATAA-ACAATT-ATAT
3272587 ATGAATTTAA-
60 -T-AA-TTAAT
*
3272597 TTCATACAAAATATTAATTACATATATTTTACCGAATTTATTAATATAAACAATTATATTAATTA
1 TTCAGACAAAATATTAATTACATATATTTTACCGAATTTATTAATATAAACAATTATATTAATTA
3272662 AT
66 AT
*
3272664 TTCAGCCAAAATAT
1 TTCAGACAAAATAT
3272678 AAAAGACAGG
Statistics
Matches: 107, Mismatches: 31, Indels: 28
0.64 0.19 0.17
Matches are distributed among these distances:
66 4 0.04
67 32 0.30
68 14 0.13
69 16 0.15
70 14 0.13
71 23 0.21
72 4 0.04
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (67 bp):
TTCAGACAAAATATTAATTACATATATTTTACCGAATTTATTAATATAAACAATTATATTAATTA
AT
Found at i:3274585 original size:25 final size:25
Alignment explanation
Indices: 3274529--3274588 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
3274519 ATAGATAAAA
3274529 ATTTTAATTTTAGTTATTTTAATTTG
1 ATTTTAATTTTAGTTA-TTTAATTTG
* *
3274555 A-ATTAATTTGTAGTTA-TTAATTTT
1 ATTTTAATTT-TAGTTATTTAATTTG
3274579 ATTTTAATTT
1 ATTTTAATTT
3274589 CTCTGATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 8 0.28
25 14 0.48
26 7 0.24
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (25 bp):
ATTTTAATTTTAGTTATTTAATTTG
Found at i:3277559 original size:25 final size:25
Alignment explanation
Indices: 3277522--3277636 Score: 117
Period size: 25 Copynumber: 4.6 Consensus size: 25
3277512 CGGACACACC
*
3277522 ACAGCTCGTATGAGCTTCTTGATTT
1 ACAGCTCGTATGAGCTTCTCGATTT
**
3277547 ACAGCTCACATGAGCTTCTCGATTT
1 ACAGCTCGTATGAGCTTCTCGATTT
* * *
3277572 ACAGCTCGTATGAGCTTCCCAATTC
1 ACAGCTCGTATGAGCTTCTCGATTT
* *
3277597 ATAGCTCGTGA-GAGCATACT-GATTT
1 ACAGCTCGT-ATGAGC-TTCTCGATTT
*
3277622 AGAGCTCGTATGAGC
1 ACAGCTCGTATGAGC
3277637 ATACATGAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
24 1 0.01
25 69 0.95
26 3 0.04
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (25 bp):
ACAGCTCGTATGAGCTTCTCGATTT
Found at i:3279539 original size:19 final size:21
Alignment explanation
Indices: 3279503--3279541 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
3279493 TTAAATTAAG
3279503 AACTAATATGCAAATGAAATA
1 AACTAATATGCAAATGAAATA
3279524 AACTAA-ATGC-AATGAAAT
1 AACTAATATGCAAATGAAAT
3279542 GGTTTAGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (21 bp):
AACTAATATGCAAATGAAATA
Found at i:3280973 original size:59 final size:58
Alignment explanation
Indices: 3280887--3281000 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 58
3280877 ATAATCAAAG
* * * *
3280887 TTTCTTGTCATCACAGTTCATAGTAGGTGAGTCTATACTCAAACAAGAATATGATCAT
1 TTTCCTGTCATCACAGTTCACAATAGGTAAGTCTATACTCAAACAAGAATATGATCAT
* *
3280945 TTTCCTGTCAATCACAGTTCACAATAGGTAAGTTTATACTTAAACAAGAATATGAT
1 TTTCCTGTC-ATCACAGTTCACAATAGGTAAGTCTATACTCAAACAAGAATATGAT
3281001 TATTCATTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 8 0.16
59 41 0.84
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (58 bp):
TTTCCTGTCATCACAGTTCACAATAGGTAAGTCTATACTCAAACAAGAATATGATCAT
Found at i:3287825 original size:75 final size:74
Alignment explanation
Indices: 3287694--3288025 Score: 274
Period size: 75 Copynumber: 4.4 Consensus size: 74
3287684 TATAGATCGA
* * * ** *
3287694 GCATTAGCGGCGCTTCTTGAAAAACGCCGCAAAAAAATTAAGCACAATTTCGTCGTTTTATGTTG
1 GCATTAGCGACGCTTTTTGAAAAACGCTGCAAAAAAATTAAGCACAAGCT-ATCGTTTTATGTTG
*
3287759 AACTTTAGTG
65 AGCTTTAGTG
*
3287769 GCACTAGCGACGCTTTTTGAAAAACGCTGCAAAAAAATTAAGCACAACGCTATCGTTTTATGTTG
1 GCATTAGCGACGCTTTTTGAAAAACGCTGCAAAAAAATTAAGCACAA-GCTATCGTTTTATGTTG
3287834 AGCTTTAGTG
65 AGCTTTAGTG
* * * * * ** * * * *
3287844 ACATTAGC-AGCGCTTTTTGAAAAACGC--CACTATAGATTGAGCATTAGCGGAGCTTTTTGAAA
1 GCATTAGCGA-CGCTTTTTGAAAAACGCTGCA-AAAAAATTAAGCACAAGC-TATCGTTTT--AT
** * *
3287906 AATGCCGCTATAGGTTG
61 GTTG-AGCTTTA-G-TG
* ** * **
3287923 ACCATTAGCGGTGCTTTTCGAAAAACGCTGCAAAAAAATTAAGCACAACGCCGTCGTTTTATGTT
1 -GCATTAGCGACGCTTTTTGAAAAACGCTGCAAAAAAATTAAGCACAA-GCTATCGTTTTATGTT
3287988 GAGCTTTAGTG
64 GAGCTTTAGTG
3287999 GCATTAGCGACGCTTTTTGAAAAACGC
1 GCATTAGCGACGCTTTTTGAAAAACGC
3288026 CGCTATAGAT
Statistics
Matches: 196, Mismatches: 47, Indels: 28
0.72 0.17 0.10
Matches are distributed among these distances:
73 4 0.02
74 17 0.09
75 111 0.57
76 6 0.03
77 6 0.03
78 6 0.03
79 5 0.03
80 22 0.11
81 15 0.08
82 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (74 bp):
GCATTAGCGACGCTTTTTGAAAAACGCTGCAAAAAAATTAAGCACAAGCTATCGTTTTATGTTGA
GCTTTAGTG
Found at i:3287900 original size:40 final size:40
Alignment explanation
Indices: 3287845--3287950 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
3287835 GCTTTAGTGA
* * *
3287845 CATTAGCAGCGCTTTTTGAAAAACGCCACTATAGATTGAG
1 CATTAGCGGAGCTTTTTGAAAAACGCCACTATAGATTGAC
* * *
3287885 CATTAGCGGAGCTTTTTGAAAAATGCCGCTATAGGTTGAC
1 CATTAGCGGAGCTTTTTGAAAAACGCCACTATAGATTGAC
* *
3287925 CATTAGCGGTGCTTTTCGAAAAACGC
1 CATTAGCGGAGCTTTTTGAAAAACGC
3287951 TGCAAAAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (40 bp):
CATTAGCGGAGCTTTTTGAAAAACGCCACTATAGATTGAC
Found at i:3287972 original size:155 final size:155
Alignment explanation
Indices: 3287773--3288128 Score: 588
Period size: 155 Copynumber: 2.3 Consensus size: 155
3287763 TTAGTGGCAC
* * *
3287773 TAGCGACGCTTTTTGAAAAACGCTGCAAAAAAATTAAGCACAACGCTATCGTTTTATGTTGAGCT
1 TAGCGGCGCTTTTCGAAAAACGCTGCAAAAAAATTAAGCACAACGCCATCGTTTTATGTTGAGCT
*
3287838 TTAGTGACATTAGC-AGCGCTTTTTGAAAAACGCCACTATAGATTGAGCATTAGCGGAGCTTTTT
66 TTAGTGACATTAGCGA-CGCTTTTTGAAAAACGCCACTATAGATCGAGCATTAGCGGAGCTTTTT
*
3287902 GAAAAATGCCGCTATAGGTTGACCAT
130 GAAAAATGCCGCTATAGGTCGACCAT
* *
3287928 TAGCGGTGCTTTTCGAAAAACGCTGCAAAAAAATTAAGCACAACGCCGTCGTTTTATGTTGAGCT
1 TAGCGGCGCTTTTCGAAAAACGCTGCAAAAAAATTAAGCACAACGCCATCGTTTTATGTTGAGCT
* * * *
3287993 TTAGTGGCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGTGGCGCTTTTTG
66 TTAGTGACATTAGCGACGCTTTTTGAAAAACGCCACTATAGATCGAGCATTAGCGGAGCTTTTTG
3288058 AAAAATGCCGCTATAGGTCGACCAT
131 AAAAATGCCGCTATAGGTCGACCAT
*
3288083 TAGCGGCGCTTTTCGAAAAACGCCGCAAAAAAATTAAGCACAACGC
1 TAGCGGCGCTTTTCGAAAAACGCTGCAAAAAAATTAAGCACAACGC
3288129 GAGCTTTAGT
Statistics
Matches: 187, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
155 186 0.99
156 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (155 bp):
TAGCGGCGCTTTTCGAAAAACGCTGCAAAAAAATTAAGCACAACGCCATCGTTTTATGTTGAGCT
TTAGTGACATTAGCGACGCTTTTTGAAAAACGCCACTATAGATCGAGCATTAGCGGAGCTTTTTG
AAAAATGCCGCTATAGGTCGACCAT
Found at i:3288054 original size:40 final size:40
Alignment explanation
Indices: 3287999--3288228 Score: 201
Period size: 40 Copynumber: 5.6 Consensus size: 40
3287989 AGCTTTAGTG
*
3287999 GCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGA
* * *
3288039 GCATTAGTGGCGCTTTTTGAAAAATGCCGCTATAGGTCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGA
* * * * * **
3288079 CCATTAGCGGCGCTTTTCGAAAAACGCCGCAAAAAAATTAA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGC-TATAGATCGA
* * * * *
3288120 GCA-CAACGCGAGCTTTAGTGGCATTAGAACGCCGCTATAGATCGA
1 GCATTAGCG-GCGCTTT--TTG-A--AAAACGCCGCTATAGATCGA
* * *
3288165 GCATTAGTGGCGCTTTTTGAAAAATGCCGCTATAGGTCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGA
* *
3288205 CCATTAGCGGCGCTTTTCGAAAAA
1 GCATTAGCGGCGCTTTTTGAAAAA
3288229 AGTCGCAAAA
Statistics
Matches: 146, Mismatches: 36, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
40 103 0.71
41 12 0.08
42 1 0.01
43 4 0.03
44 1 0.01
45 14 0.10
46 11 0.08
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGA
Found at i:3288246 original size:126 final size:126
Alignment explanation
Indices: 3288021--3288254 Score: 450
Period size: 126 Copynumber: 1.9 Consensus size: 126
3288011 CTTTTTGAAA
3288021 AACGCCGCTATAGATCGAGCATTAGTGGCGCTTTTTGAAAAATGCCGCTATAGGTCGACCATTAG
1 AACGCCGCTATAGATCGAGCATTAGTGGCGCTTTTTGAAAAATGCCGCTATAGGTCGACCATTAG
*
3288086 CGGCGCTTTTCGAAAAACGCCGCAAAAAAATTAAGCACAACGCGAGCTTTAGTGGCATTAG
66 CGGCGCTTTTCGAAAAAAGCCGCAAAAAAATTAAGCACAACGCGAGCTTTAGTGGCATTAG
3288147 AACGCCGCTATAGATCGAGCATTAGTGGCGCTTTTTGAAAAATGCCGCTATAGGTCGACCATTAG
1 AACGCCGCTATAGATCGAGCATTAGTGGCGCTTTTTGAAAAATGCCGCTATAGGTCGACCATTAG
*
3288212 CGGCGCTTTTCGAAAAAAGTCGCAAAAAAATTAAGCACAACGC
66 CGGCGCTTTTCGAAAAAAGCCGCAAAAAAATTAAGCACAACGC
3288255 TGTCGCTTTA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 106 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (126 bp):
AACGCCGCTATAGATCGAGCATTAGTGGCGCTTTTTGAAAAATGCCGCTATAGGTCGACCATTAG
CGGCGCTTTTCGAAAAAAGCCGCAAAAAAATTAAGCACAACGCGAGCTTTAGTGGCATTAG
Found at i:3288701 original size:14 final size:14
Alignment explanation
Indices: 3288664--3288833 Score: 51
Period size: 14 Copynumber: 12.0 Consensus size: 14
3288654 ATAGTGTAGA
3288664 GTTTATGGTTTAGG
1 GTTTATGGTTTAGG
* *
3288678 ATATATGGTTTAGG
1 GTTTATGGTTTAGG
* * *
3288692 GTTTAAGGTTCAAGA
1 GTTTATGGTT-TAGG
*
3288707 GTTACTAT--TTTAAG
1 GTT--TATGGTTTAGG
* *
3288721 GTTTATAGATTATGG
1 GTTTATGGTTTA-GG
** * *
3288736 GTTTACAGATTATG
1 GTTTATGGTTTAGG
*
3288750 GTTTATGGCTTAAGG
1 GTTTATGG-TTTAGG
**
3288765 G-TTGGGGTTTAGGG
1 GTTTATGGTTTA-GG
* *
3288779 GTTTATGTTTTA-T
1 GTTTATGGTTTAGG
* *
3288792 GATTAGGGTTTAGG
1 GTTTATGGTTTAGG
* *
3288806 GTTTATGTTTTATG
1 GTTTATGGTTTAGG
* *
3288820 ATTTAGGGTTTAGG
1 GTTTATGGTTTAGG
3288834 TAATAGGGAT
Statistics
Matches: 107, Mismatches: 39, Indels: 20
0.64 0.23 0.12
Matches are distributed among these distances:
12 3 0.03
13 12 0.11
14 60 0.56
15 30 0.28
17 2 0.02
ACGTcount: A:0.22, C:0.02, G:0.30, T:0.46
Consensus pattern (14 bp):
GTTTATGGTTTAGG
Found at i:3288740 original size:15 final size:14
Alignment explanation
Indices: 3288720--3288755 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
3288710 ACTATTTTAA
3288720 GGTTTATAGATTAT
1 GGTTTATAGATTAT
*
3288734 GGGTTTACAGATTAT
1 -GGTTTATAGATTAT
3288749 GGTTTAT
1 GGTTTAT
3288756 GGCTTAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (14 bp):
GGTTTATAGATTAT
Found at i:3288804 original size:28 final size:29
Alignment explanation
Indices: 3288769--3288833 Score: 116
Period size: 27 Copynumber: 2.3 Consensus size: 29
3288759 TTAAGGGTTG
3288769 GGGTTTAGGGGTTTATGTTTTATGA-TTA
1 GGGTTTAGGGGTTTATGTTTTATGATTTA
3288797 GGGTTTA-GGGTTTATGTTTTATGATTTA
1 GGGTTTAGGGGTTTATGTTTTATGATTTA
3288825 GGGTTTAGG
1 GGGTTTAGG
3288834 TAATAGGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 17 0.49
28 17 0.49
29 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (29 bp):
GGGTTTAGGGGTTTATGTTTTATGATTTA
Found at i:3288813 original size:27 final size:28
Alignment explanation
Indices: 3288769--3288833 Score: 114
Period size: 28 Copynumber: 2.3 Consensus size: 28
3288759 TTAAGGGTTG
3288769 GGGTTTAGGGGTTTATGTTTTATGA-TTA
1 GGGTTTA-GGGTTTATGTTTTATGATTTA
3288797 GGGTTTAGGGTTTATGTTTTATGATTTA
1 GGGTTTAGGGTTTATGTTTTATGATTTA
3288825 GGGTTTAGG
1 GGGTTTAGG
3288834 TAATAGGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 17 0.47
28 19 0.53
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (28 bp):
GGGTTTAGGGTTTATGTTTTATGATTTA
Found at i:3288832 original size:7 final size:7
Alignment explanation
Indices: 3288794--3288854 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
3288784 TGTTTTATGA
3288794 TTAGGGT
1 TTAGGGT
3288801 TTAGGGT
1 TTAGGGT
* *
3288808 TTATGTT
1 TTAGGGT
* *
3288815 TTATGAT
1 TTAGGGT
3288822 TTAGGGT
1 TTAGGGT
3288829 TTA-GGT
1 TTAGGGT
*
3288835 AATAGGGAT
1 -TTAGGG-T
3288844 TTAGGGT
1 TTAGGGT
3288851 TTAG
1 TTAG
3288855 ATTAATTAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
6 3 0.07
7 33 0.75
8 7 0.16
9 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (7 bp):
TTAGGGT
Found at i:3289470 original size:41 final size:40
Alignment explanation
Indices: 3289406--3289482 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 40
3289396 TTTTCCGCAA
* *
3289406 AAAAGTTGAGCAATAATGGCGTTTTTTGTCCAAACGCTGCT
1 AAAAGTCGAGCAATAATGACGTTTTTT-TCCAAACGCTGCT
*
3289447 AAAAGTCGAGCAATAGTGACGTTTTTTTCCAAACGC
1 AAAAGTCGAGCAATAATGACGTTTTTTTCCAAACGC
3289483 CACGAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 9 0.27
41 24 0.73
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (40 bp):
AAAAGTCGAGCAATAATGACGTTTTTTTCCAAACGCTGCT
Done.