Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 122 of 313
Found at i:39417262 original size:6 final size:6
Alignment explanation
Indices: 39417251--39417294 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
39417241 AAAAATAGGT
* * * *
39417251 AAAGGA AAAGGA GAAGGA GAAGGA AAAGGA GAAGGA GAAGGA AA
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AA
39417295 TGACCCATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:39417273 original size:12 final size:12
Alignment explanation
Indices: 39417252--39417292 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
39417242 AAAATAGGTA
*
39417252 AAGGAAAAGGAG
1 AAGGAGAAGGAG
*
39417264 AAGGAGAAGGAA
1 AAGGAGAAGGAG
39417276 AAGGAGAAGGAG
1 AAGGAGAAGGAG
39417288 AAGGA
1 AAGGA
39417293 AATGACCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (12 bp):
AAGGAGAAGGAG
Found at i:39417275 original size:18 final size:18
Alignment explanation
Indices: 39417252--39417294 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
39417242 AAAATAGGTA
39417252 AAGGAAAAGGAGAAGGAG
1 AAGGAAAAGGAGAAGGAG
39417270 AAGGAAAAGGAGAAGGAG
1 AAGGAAAAGGAGAAGGAG
39417288 AAGGAAA
1 AAGGAAA
39417295 TGACCCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (18 bp):
AAGGAAAAGGAGAAGGAG
Found at i:39420520 original size:22 final size:23
Alignment explanation
Indices: 39420490--39420532 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
39420480 TTCAATTTAG
* *
39420490 TTATCTATTATAAT-ATTTTATT
1 TTATATATTAAAATGATTTTATT
39420512 TTATATATTAAAATGATTTTA
1 TTATATATTAAAATGATTTTA
39420533 CACTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATATATTAAAATGATTTTATT
Found at i:39423862 original size:38 final size:38
Alignment explanation
Indices: 39423810--39423885 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
39423800 TGGAAATAAC
* *
39423810 CTACAGGCTTTATGGAATGACAACATGAAAATGGTTAT
1 CTACAGACTCTATGGAATGACAACATGAAAATGGTTAT
* *
39423848 CTACAGACTCTATGGAGTGACACCATGAAAATGGTTAT
1 CTACAGACTCTATGGAATGACAACATGAAAATGGTTAT
39423886 TGACTCATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (38 bp):
CTACAGACTCTATGGAATGACAACATGAAAATGGTTAT
Found at i:39430104 original size:20 final size:21
Alignment explanation
Indices: 39430067--39430106 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
39430057 TTTAATTTTA
39430067 AAAATATTAAATATAAGTAGC
1 AAAATATTAAATATAAGTAGC
39430088 AAAA-ATTAAAT-TGAAGTAG
1 AAAATATTAAATAT-AAGTAG
39430107 AGTAGGGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 13 0.72
21 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (21 bp):
AAAATATTAAATATAAGTAGC
Found at i:39435737 original size:17 final size:18
Alignment explanation
Indices: 39435711--39435765 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
39435701 CAAGGAAAAT
*
39435711 ATGAAAATAAAAATT-AA
1 ATGAATATAAAAATTAAA
*
39435728 ATGAATATAAGAAGTTAAA
1 ATGAATATAA-AAATTAAA
*
39435747 ATTAAT-TAAAAATTTAAA
1 ATGAATATAAAAA-TTAAA
39435765 A
1 A
39435766 ATAAAAACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 11 0.35
18 13 0.42
19 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (18 bp):
ATGAATATAAAAATTAAA
Found at i:39450113 original size:26 final size:26
Alignment explanation
Indices: 39450084--39450165 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
39450074 TGTCCCAGAC
39450084 ATGGTCTTACATGGGATGTTCTCGTG
1 ATGGTCTTACATGGGATGTTCTCGTG
* ** * **
39450110 ATGGTGC--CCATGCCATG-TCCCAGAC
1 ATGGT-CTTACATGGGATGTTCTC-GTG
39450135 ATGGTCTTACATGGGATGTTCTCGTG
1 ATGGTCTTACATGGGATGTTCTCGTG
39450161 ATGGT
1 ATGGT
39450166 GCCCATGCCA
Statistics
Matches: 39, Mismatches: 12, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
24 4 0.10
25 13 0.33
26 18 0.46
27 4 0.10
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (26 bp):
ATGGTCTTACATGGGATGTTCTCGTG
Found at i:39450127 original size:25 final size:25
Alignment explanation
Indices: 39450099--39450178 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
39450089 CTTACATGGG
39450099 ATGTTCTCGTGATGGTGCCCATGCC
1 ATGTTCTCGTGATGGTGCCCATGCC
* ** * **
39450124 ATG-TCCCAGACATGGT-CTTACATGGG
1 ATGTTCTC-GTGATGGTGC--CCATGCC
39450150 ATGTTCTCGTGATGGTGCCCATGCC
1 ATGTTCTCGTGATGGTGCCCATGCC
39450175 ATGT
1 ATGT
39450179 CCCAGACATG
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
24 4 0.11
25 17 0.45
26 13 0.34
27 4 0.11
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.31
Consensus pattern (25 bp):
ATGTTCTCGTGATGGTGCCCATGCC
Found at i:39450142 original size:51 final size:52
Alignment explanation
Indices: 39450070--39450309 Score: 310
Period size: 51 Copynumber: 4.6 Consensus size: 52
39450060 ACATGCCAAA
**
39450070 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGATAGGTGCCCAT
**
39450121 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGATAGGTGCCCAT
* *
39450172 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGT-CTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGATAGGTGCCCAT
* * * *
39450222 GGCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATGATCTTAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGA---T-AGG-TGCCCAT
39450278 GCCATGTCCCAGACATGGTCTTACATGGGATC
1 GCCATGTCCCAGACATGGTCTTACATGGGATC
39450310 TCTTTACCCA
Statistics
Matches: 170, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
49 1 0.01
50 50 0.29
51 81 0.48
54 1 0.01
55 2 0.01
56 34 0.20
57 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.27
Consensus pattern (52 bp):
GCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGATAGGTGCCCAT
Found at i:39450189 original size:25 final size:25
Alignment explanation
Indices: 39450110--39450190 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
39450100 TGTTCTCGTG
39450110 ATGGTGCCCATGCCATGTCCCAGAC
1 ATGGTGCCCATGCCATGTCCCAGAC
* ** * **
39450135 ATGGT-CTTACATGGGATGTTCTC-GTG
1 ATGGTGC--CCATGCCATG-TCCCAGAC
39450161 ATGGTGCCCATGCCATGTCCCAGAC
1 ATGGTGCCCATGCCATGTCCCAGAC
39450186 ATGGT
1 ATGGT
39450191 CTTACATGGG
Statistics
Matches: 39, Mismatches: 12, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
24 4 0.10
25 18 0.46
26 13 0.33
27 4 0.10
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (25 bp):
ATGGTGCCCATGCCATGTCCCAGAC
Found at i:39450428 original size:13 final size:13
Alignment explanation
Indices: 39450407--39450438 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39450397 GCTTGGATCA
*
39450407 TCATCAAATAAAT
1 TCATAAAATAAAT
39450420 TCATAAAATAAAT
1 TCATAAAATAAAT
39450433 TCATAA
1 TCATAA
39450439 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:39450685 original size:30 final size:30
Alignment explanation
Indices: 39450650--39450707 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39450640 CCTCGACTCT
*
39450650 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
39450680 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
39450708 AAGTCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:39454352 original size:23 final size:23
Alignment explanation
Indices: 39454322--39454401 Score: 119
Period size: 23 Copynumber: 3.5 Consensus size: 23
39454312 AAACCCAACT
39454322 AACCTAGCCCAATACCCTAAACC
1 AACCTAGCCCAATACCCTAAACC
39454345 AACCTAGCCCAATACCCTAAACC
1 AACCTAGCCCAATACCCTAAACC
*
39454368 AACCTAGCCCAAT--CCTAAAAC
1 AACCTAGCCCAATACCCTAAACC
*
39454389 TACCTGAGCCCAA
1 AACCT-AGCCCAA
39454402 ATTTTAAAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
21 11 0.20
22 7 0.13
23 36 0.67
ACGTcount: A:0.39, C:0.41, G:0.06, T:0.14
Consensus pattern (23 bp):
AACCTAGCCCAATACCCTAAACC
Found at i:39473162 original size:23 final size:24
Alignment explanation
Indices: 39473136--39473183 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
39473126 GGTGATGGTG
39473136 ATTGAATGTGTTTTATATGT-TGA
1 ATTGAATGTGTTTTATATGTGTGA
* * *
39473159 ATTGATTGTTTTTTATTTGTGTGA
1 ATTGAATGTGTTTTATATGTGTGA
39473183 A
1 A
39473184 GTTTAGGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (24 bp):
ATTGAATGTGTTTTATATGTGTGA
Found at i:39475035 original size:3 final size:3
Alignment explanation
Indices: 39475029--39475082 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
39475019 AGAAAACTTT
39475029 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
39475077 GAA GAA
1 GAA GAA
39475083 AGAGGGTGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:39475946 original size:17 final size:17
Alignment explanation
Indices: 39475901--39475948 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
39475891 TGAGATAGTT
* *
39475901 TATGTTATGTTT-TTGT
1 TATGTTATTTTTATTGA
* *
39475917 TATATTTTTTTTATTGA
1 TATGTTATTTTTATTGA
39475934 TATGTTATTTTTATT
1 TATGTTATTTTTATT
39475949 ATTTTAATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (17 bp):
TATGTTATTTTTATTGA
Found at i:39482000 original size:28 final size:28
Alignment explanation
Indices: 39481968--39482034 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
39481958 TTTATTGATA
*
39481968 TTTATTGATATCTCTACACTTAAAATTT
1 TTTATTGATATCTCTACACTTAAAAATT
*
39481996 TTTATTGATGTCTCTACACTTAAAAATT
1 TTTATTGATATCTCTACACTTAAAAATT
39482024 TTTATTGATAT
1 TTTATTGATAT
39482035 TTTTGATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (28 bp):
TTTATTGATATCTCTACACTTAAAAATT
Found at i:39484533 original size:2 final size:2
Alignment explanation
Indices: 39484526--39484556 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39484516 TCTAAAATCT
39484526 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
39484557 ACCTTTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39487091 original size:43 final size:43
Alignment explanation
Indices: 39486917--39487120 Score: 256
Period size: 42 Copynumber: 4.8 Consensus size: 43
39486907 ACGTCGCTAA
*
39486917 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
39486960 CTTTAGCGTCGC--TTCCCTACAAACGCCACTAAAGACCAAGAC
1 CTTTAGCGACGCTTTTCCC-ACAAACGCCGCTAAAGACCAAGAC
*
39487002 CTTTAGCGGCGC--TTCCTCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGACGCTTTTCC-CACAAACGCCGCTAAAGACCAAGAC
* * *
39487044 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGA-TATTGAG
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCA-AGAC
* **
39487087 CTTTAGCGGCGCTTTTAACACAAACGCCGCTAAA
1 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAA
39487121 AATATATCTT
Statistics
Matches: 144, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
41 5 0.03
42 72 0.50
43 63 0.44
44 4 0.03
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (43 bp):
CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:39487459 original size:43 final size:43
Alignment explanation
Indices: 39487393--39487483 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
39487383 ACATATGCAA
* * * *
39487393 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
39487436 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
39487479 -GTAAT
1 GGTAAT
39487484 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:39491642 original size:7 final size:7
Alignment explanation
Indices: 39491632--39491676 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
39491622 CACTAACTCT
*
39491632 TAACCTC
1 TAACCCC
**
39491639 TAACCTT
1 TAACCCC
39491646 TAACCCC
1 TAACCCC
39491653 TAACCCC
1 TAACCCC
39491660 TAACCCC
1 TAACCCC
39491667 TAACCCC
1 TAACCCC
39491674 TAA
1 TAA
39491677 ATCTTATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.31, C:0.47, G:0.00, T:0.22
Consensus pattern (7 bp):
TAACCCC
Found at i:39491648 original size:14 final size:14
Alignment explanation
Indices: 39491624--39491672 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
39491614 CCCTAAATCA
* *
39491624 CTAACTCTTAACCT
1 CTAACCCTTAACCC
*
39491638 CTAACCTTTAACCC
1 CTAACCCTTAACCC
*
39491652 CTAACCCCTAACCC
1 CTAACCCTTAACCC
39491666 CTAACCC
1 CTAACCC
39491673 CTAAATCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.29, C:0.47, G:0.00, T:0.24
Consensus pattern (14 bp):
CTAACCCTTAACCC
Found at i:39491805 original size:81 final size:83
Alignment explanation
Indices: 39491660--39491815 Score: 226
Period size: 81 Copynumber: 1.9 Consensus size: 83
39491650 CCCTAACCCC
* * *
39491660 TAACCCCTAACCCCTAAATCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAGACCCTA
1 TAACCCCTAACCCCTAAACCTTATTTAATATATAAACTAAAAAACACTAATTAATCTAAACCCTA
39491725 AACCCTAACCCAAATCCT
66 AACCCTAACCCAAATCCT
* * * *
39491743 TAACCCCTAACCCCTACACCTTA-TTCA-ATATAAACTAGAACACACTAATTAATCTAAACCCTA
1 TAACCCCTAACCCCTAAACCTTATTTAATATATAAACTAAAAAACACTAATTAATCTAAACCCTA
*
39491806 AACTCTAACC
66 AACCCTAACC
39491816 TAACACTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
81 41 0.63
82 3 0.05
83 21 0.32
ACGTcount: A:0.42, C:0.30, G:0.01, T:0.26
Consensus pattern (83 bp):
TAACCCCTAACCCCTAAACCTTATTTAATATATAAACTAAAAAACACTAATTAATCTAAACCCTA
AACCCTAACCCAAATCCT
Found at i:39492412 original size:50 final size:51
Alignment explanation
Indices: 39492358--39492463 Score: 169
Period size: 50 Copynumber: 2.1 Consensus size: 51
39492348 ATATATCAAA
* *
39492358 AGCGGGCATTAGCGGCGCTTTTTCAAAAATGCCACTAAAGGCCCAAGCA-T
1 AGCGGGCATTAGCGGCGCTTATTCAAAAACGCCACTAAAGGCCCAAGCATT
* *
39492408 AGCGGGCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGCATT
1 AGCGGGCATTAGCGGCGCTTATTCAAAAACGCCACTAAAGGCCCAAGCATT
39492459 AGCGG
1 AGCGG
39492464 CGCTTCTTCC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 45 0.88
51 6 0.12
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.18
Consensus pattern (51 bp):
AGCGGGCATTAGCGGCGCTTATTCAAAAACGCCACTAAAGGCCCAAGCATT
Found at i:39492478 original size:41 final size:41
Alignment explanation
Indices: 39492413--39492615 Score: 325
Period size: 41 Copynumber: 5.0 Consensus size: 41
39492403 AGCATAGCGG
39492413 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* * *
39492454 GCATTAGCGGCGCTTCTTCCAAAACGCCACTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* * *
39492495 GCATTAGTGGCGCTTCTTCACAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
*
39492536 GCATTAGCGGCGCTTATTCAAAAATGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* *
39492577 GAATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCC
39492616 CAAAAACTCA
Statistics
Matches: 148, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 148 1.00
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.19
Consensus pattern (41 bp):
GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
Found at i:39492723 original size:39 final size:39
Alignment explanation
Indices: 39492680--39492784 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 39
39492670 AAAACACCGG
* *
39492680 TAATGCTTATTTTTAGCGGCATTTTCCA-AAAAGCGCCGC
1 TAATGCTTATTTTTAGTGGCGTTTT-CATAAAAGCGCCGC
* ** *
39492719 TAATGCTCGACCTTTAGTGGCGTTTTTATAAAAGCGCCGC
1 TAATGCT-TATTTTTAGTGGCGTTTTCATAAAAGCGCCGC
39492759 TAATGCTTGATTTTTAGTGGCGTTTT
1 TAATGCTT-ATTTTTAGTGGCGTTTT
39492785 TTGTCTAAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
39 8 0.15
40 46 0.85
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (39 bp):
TAATGCTTATTTTTAGTGGCGTTTTCATAAAAGCGCCGC
Found at i:39492802 original size:41 final size:40
Alignment explanation
Indices: 39492708--39492785 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
39492698 GCATTTTCCA
39492708 AAAAGCGCCGCTAATGCTCGACCTTTAGTGGCGTTTTTAT
1 AAAAGCGCCGCTAATGCTCGACCTTTAGTGGCGTTTTTAT
* **
39492748 AAAAGCGCCGCTAATGCTTGATTTTTAGTGGCGTTTTT
1 AAAAGCGCCGCTAATGCTCGACCTTTAGTGGCGTTTTT
39492786 TGTCTAAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTCGACCTTTAGTGGCGTTTTTAT
Found at i:39492808 original size:12 final size:12
Alignment explanation
Indices: 39492791--39492816 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39492781 TTTTTTGTCT
39492791 AAACGCCGCTAA
1 AAACGCCGCTAA
39492803 AAACGCCGCTAA
1 AAACGCCGCTAA
39492815 AA
1 AA
39492817 GCCTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:39494540 original size:17 final size:18
Alignment explanation
Indices: 39494518--39494559 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
39494508 TTTTCTTGGG
39494518 CCCAAAACCAAT-ACAAA
1 CCCAAAACCAATAACAAA
* *
39494535 CCC-AAACTATTAACAAA
1 CCCAAAACCAATAACAAA
39494552 CCCAAAAC
1 CCCAAAAC
39494560 AAATTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.55, C:0.36, G:0.00, T:0.10
Consensus pattern (18 bp):
CCCAAAACCAATAACAAA
Found at i:39500030 original size:9 final size:9
Alignment explanation
Indices: 39500016--39500044 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
39500006 TCAGACTCAA
39500016 AAAAAAATC
1 AAAAAAATC
39500025 -AAAAAATC
1 AAAAAAATC
39500033 AAAAAAATC
1 AAAAAAATC
39500042 AAA
1 AAA
39500045 GTCAAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:39500078 original size:17 final size:17
Alignment explanation
Indices: 39500056--39500093 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
39500046 TCAAAATAGA
39500056 AAAAAAAAAGAAAAAGG
1 AAAAAAAAAGAAAAAGG
* *
39500073 AAAAAAGAAGAAAAAGT
1 AAAAAAAAAGAAAAAGG
39500090 AAAA
1 AAAA
39500094 GGAGAGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAGG
Found at i:39502664 original size:50 final size:50
Alignment explanation
Indices: 39502586--39503695 Score: 850
Period size: 50 Copynumber: 22.4 Consensus size: 50
39502576 GTCTGCAATT
* * * * * *
39502586 AAAAGATTGAAGCCACAACGGTGAATCTTACCTTTCCAGGCAGTG-AGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTA-CTTTCCAGGCATTGCAATGG
* * * *
39502636 AACAGATTGAAGCTACAACTGCGGATCTTGCTTTCCTA-GTAGTT---A---
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCC-AGGCA-TTGCAATGG
*
39502681 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTA-GCATTGCAATGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGGCATTGCAATGG
* * * * * * **
39502731 AACAGATTGAAGCTACAGCAGCGGACCTTACTTCCCTGACATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCATTGCAATGG
* * * *
39502781 AAAAGATTGAAGCTACAACAGTGGATCTTACTTTCTTA-GCGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGGCATTGCAATGG
* * * * * **
39502831 AACAGATTGAAGCTACAACTGCGGATCTTACTTCCCTGACATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCATTGCAATGG
* * *
39502881 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTA-GCGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGGCATTGCAATGG
* * * * * **
39502931 AACAGATTGAAGCTACAATAGCGGATCTTACTTCCCTGACATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCATTGCAATGG
* * *
39502981 AAAAGATTGAAGCTACAACAACAGATCTTACTTTCCTA-GCATTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCC-AGGCATTGCAATGG
* * * * **
39503031 AATAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCATTGCAATGG
* * *
39503081 AAAAAATTGAAGCTACAACAGCGGATCTTACTTTCTTA-GCGTTGCAATGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGGCATTGCAATGG
* * * **
39503131 AACAGATTGAAGCTACAACAGCGGATCTTAC-TTCCTTGACATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCC-AGGCATTGCAATGG
* * * *
39503181 AAAAGATTGAAGCTACAACAGCGGATTTTACTTTCTTA-ACGTTGCAATGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGGCATTGCAATGG
* * * * *
39503231 AACAGATTGAAGCTACAACAGTGGATCTTAC-TTCCTTGACATTGCAAT-T
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCC-AGGCATTGCAATGG
* * * * * *
39503280 AAAAAATTGAAGCTACAATAGCAGATCTTACTTTCTTA-GCGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGGCATTGCAATGG
* * * * * * **
39503330 AACAGATTGAAGCTGCAACAGCGGATCTTACTTCCCTGACATTACAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCATTGCAATGG
* * * **
39503380 AAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCATTGCAATGG
* * * * *
39503430 AAAAGATTAAAGCCACAACAGCGGATCTTACTTTCTTA-GCGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGGCATTGCAATGG
* * * **
39503480 AACAGATTGAAGCTACAACAGCGGATCTTGC-TTCC---C-CTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCATTGCAATGG
* * ** *
39503525 AAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCATTGCAATGG
* * ** * * **
39503575 AATAGATTGAAGCTACAACGGCAAATCTT-CTTTCCCCGACATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTT-CCAGGCATTGCAATGG
* * *** *
39503625 AAAAGATTGAAG-TCACAACAGCGAATCTTACTTCCCAGGTGGTGTAATGG
1 AAAAGATTGAAGCT-ACAACAGCGGATCTTACTTTCCAGGCATTGCAATGG
* * *
39503675 AATATATTGAAGCTACGACAG
1 AAAAGATTGAAGCTACAACAG
39503696 TAAATCTTAC
Statistics
Matches: 828, Mismatches: 195, Indels: 74
0.75 0.18 0.07
Matches are distributed among these distances:
44 2 0.00
45 67 0.08
46 5 0.01
47 1 0.00
49 56 0.07
50 690 0.83
51 7 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (50 bp):
AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCATTGCAATGG
Found at i:39502807 original size:100 final size:100
Alignment explanation
Indices: 39502579--39503508 Score: 1281
Period size: 100 Copynumber: 9.4 Consensus size: 100
39502569 AACCATAGTC
* * * * *
39502579 TGCAATT-AAAAGATTGAAGCCACAACGGTGAATCTTACCTTTC-CAGGCAG-TG-AGTGGAACA
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTA-CTTTCTTA-GC-GTTGCAGTGGAACA
* * *
39502640 GATTGAAGCTACAACTGCGGATCTTGCTTTCCT---A-
63 GATTGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
* * * *
39502674 -GTAGTTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCATTGCAATGGAACAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
* *
39502738 TGAAGCTACAGCAGCGGACCTTACTTCCCTGACAT
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
*
39502773 TGCAATTAAAAAGATTGAAGCTACAACAGTGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
*
39502838 TGAAGCTACAACTGCGGATCTTACTTCCCTGACAT
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
39502873 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
*
39502938 TGAAGCTACAATAGCGGATCTTACTTCCCTGACAT
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
* * * * *
39502973 TGCAATTAAAAAGATTGAAGCTACAACAACAGATCTTACTTTCCTAGCATTGCAGTGGAATAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
39503038 TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
* *
39503073 TGCAATTAAAAAAATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAATGGAACAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
*
39503138 TGAAGCTACAACAGCGGATCTTACTTCCTTGACAT
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
* * *
39503173 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATTTTACTTTCTTAACGTTGCAATGGAACAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
* *
39503238 TGAAGCTACAACAGTGGATCTTACTTCCTTGACAT
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
* *
39503273 TGCAATTAAAAA-ATTGAAGCTACAATAGCAGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
*
39503337 TGAAGCTGCAACAGCGGATCTTACTTCCCTGACAT
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
* * * * * ** *
39503372 TACAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACATTGCAATTAAAAAGA
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAG-CGTTGCAGTGGAACAGA
* * * * *
39503436 TTAAAGCCACAACAGCGGATCTTACTT-TCTTAGCGT
65 TTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CAT
* ** *
39503472 TGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTT
1 TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTT
39503509 GCTTCCCCTG
Statistics
Matches: 751, Mismatches: 72, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
94 13 0.02
95 63 0.08
98 1 0.00
99 94 0.13
100 580 0.77
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (100 bp):
TGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGAT
TGAAGCTACAACAGCGGATCTTACTTCCCTGACAT
Found at i:39503656 original size:100 final size:99
Alignment explanation
Indices: 39503383--39503733 Score: 401
Period size: 100 Copynumber: 3.6 Consensus size: 99
39503373 ACAATTAAAA
** * *
39503383 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAAAAGATTAAAGCCACAA
1 AGATTGAAGCTACAACAGCAAATCTTACTTCCCCGACATTGCAATTAAAAAGATTGAAG-CACAA
* * * *
39503448 CAGCGGATCTTACTTTCTTA-GCGTTGCAGTGGAAC
65 CAGCGAATCTTACTTTC-CAGGCGGTGCAGTGGAAT
** *
39503483 AGATTGAAGCTACAACAGCGGATCTTGCTT-CCC--C--TGCAATTAAAAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCAAATCTTACTTCCCCGACATTGCAATTAAAAAGATTGAAGC-ACAA
*
39503543 CGGCGAATCTTACTTTCCAGGCGGTGCAGTGGAAT
65 CAGCGAATCTTACTTTCCAGGCGGTGCAGTGGAAT
*
39503578 AGATTGAAGCTACAACGGCAAATCTT-CTTTCCCCGACATTGCAATTAAAAAGATTGAAGTCACA
1 AGATTGAAGCTACAACAGCAAATCTTAC-TTCCCCGACATTGCAATTAAAAAGATTGAAG-CACA
* * * *
39503642 ACAGCGAATCTTACTTCCCAGGTGGTGTAATGGAAT
64 ACAGCGAATCTTACTTTCCAGGCGGTGCAGTGGAAT
* * * * * *
39503678 ATATTGAAGCTACGACAGTAAATCTTACTTCCCCAACATTGCAGTTAAACAGATTG
1 AGATTGAAGCTACAACAGCAAATCTTACTTCCCCGACATTGCAATTAAAAAGATTG
39503734 GAGATGGCAG
Statistics
Matches: 218, Mismatches: 23, Indels: 20
0.84 0.09 0.08
Matches are distributed among these distances:
94 3 0.01
95 76 0.35
96 3 0.01
97 1 0.00
98 1 0.00
99 2 0.01
100 130 0.60
101 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (99 bp):
AGATTGAAGCTACAACAGCAAATCTTACTTCCCCGACATTGCAATTAAAAAGATTGAAGCACAAC
AGCGAATCTTACTTTCCAGGCGGTGCAGTGGAAT
Found at i:39503817 original size:18 final size:18
Alignment explanation
Indices: 39503784--39503818 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39503774 GATCGCATCT
* *
39503784 AGTCCTATCTCTCTAAGC
1 AGTCCTATCACCCTAAGC
39503802 AGTCCTATCACCCTAAG
1 AGTCCTATCACCCTAAG
39503819 TAGTAGTGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.29
Consensus pattern (18 bp):
AGTCCTATCACCCTAAGC
Found at i:39504197 original size:131 final size:131
Alignment explanation
Indices: 39503802--39504824 Score: 1767
Period size: 131 Copynumber: 7.8 Consensus size: 131
39503792 CTCTCTAAGC
** * ** * *
39503802 AGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGAAAATTCTGTCACCCTGAGCAGT
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTG-ATATTCTGTCACCCTAAGCAGT
39503867 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
65 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
39503932 TT
130 TT
* ** * ** * * *
39503934 TGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATTCCGTCACCCTATGCAGT
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTG-ATATTCTGTCACCCTAAGCAGT
*
39503999 AGTGGAGCAGATTGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
65 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
39504064 TT
130 TT
39504066 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
39504131 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCAT
66 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCAT
39504196 T
131 T
39504197 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
39504262 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCAT
66 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCAT
39504327 T
131 T
39504328 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
39504393 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCAT
66 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCAT
39504458 T
131 T
39504459 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
39504524 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCAT
66 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCAT
39504589 T
131 T
39504590 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
* * * *
39504655 GTGGAGCAGATCGAATATGGTGAATCTTATCTTTCCAATACAGTGGAGAAGCAGATTTAAGTCGT
66 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCAT
39504720 T
131 T
* * * ** * *
39504721 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCTCCCTAAGCAGT
1 AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTG-ATATTCTGTCACCCTAAGCAGT
39504786 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
65 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
39504825 GTGGAATGGA
Statistics
Matches: 860, Mismatches: 30, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
131 642 0.75
132 218 0.25
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (131 bp):
AGTCCTATCACCCTAAACAGTAGTGGAATAGGTCAAAGATTGATATTCTGTCACCCTAAGCAGTA
GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCAT
T
Found at i:39506161 original size:6 final size:6
Alignment explanation
Indices: 39506150--39506178 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
39506140 TTTATAAATT
39506150 TTGTTA TTGTTA TTGTTA TTGTTA TTGTT
1 TTGTTA TTGTTA TTGTTA TTGTTA TTGTT
39506179 GTATTTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (6 bp):
TTGTTA
Found at i:39520528 original size:2 final size:2
Alignment explanation
Indices: 39520467--39520509 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
39520457 TTGAAGAAGA
39520467 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39520509 A
1 A
39520510 TTAGGTTTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39524663 original size:18 final size:17
Alignment explanation
Indices: 39524637--39524675 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39524627 ATTTTCCTTC
39524637 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
39524654 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
39524672 CACA
1 CACA
39524676 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:39525081 original size:15 final size:15
Alignment explanation
Indices: 39525061--39525089 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39525051 AGTTTAAAAA
39525061 TTACAACTATATCAC
1 TTACAACTATATCAC
39525076 TTACAACTATATCA
1 TTACAACTATATCA
39525090 TGAATGGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.34
Consensus pattern (15 bp):
TTACAACTATATCAC
Found at i:39529621 original size:24 final size:24
Alignment explanation
Indices: 39529606--39529657 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39529596 AATTAATGTC
39529606 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
39529630 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
39529654 AAAT
1 AAAT
39529658 CTTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:39532465 original size:29 final size:30
Alignment explanation
Indices: 39532420--39532477 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
39532410 AACTATGAGC
*
39532420 TCATTCTAAATTGATCCTTAAACT-TCAAA
1 TCATTCTAAATTGATCCCTAAACTATCAAA
*
39532449 TCATTCT-AATTATATCCCTAAACTATCAA
1 TCATTCTAAATT-GATCCCTAAACTATCAA
39532478 GGTTATATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 17 0.68
30 4 0.16
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (30 bp):
TCATTCTAAATTGATCCCTAAACTATCAAA
Found at i:39533333 original size:43 final size:44
Alignment explanation
Indices: 39533278--39533370 Score: 118
Period size: 43 Copynumber: 2.1 Consensus size: 44
39533268 AATATATAAA
* *
39533278 AAAAATATCAAGATATACA-ATAACAT-AACATACTCAATATATC
1 AAAAATACCAAGAAATACAGA-AACATCAACATACTCAATATATC
39533321 AAAAATACCAAGAAATACAGAAACATACCGAACATACTCAATATATC
1 AAAAATACCAAGAAATACAGAAACAT--C-AACATACTCAATATATC
39533368 AAA
1 AAA
39533371 TATATCAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
43 22 0.51
44 1 0.02
47 20 0.47
ACGTcount: A:0.57, C:0.18, G:0.04, T:0.20
Consensus pattern (44 bp):
AAAAATACCAAGAAATACAGAAACATCAACATACTCAATATATC
Found at i:39540415 original size:50 final size:50
Alignment explanation
Indices: 39540304--39540550 Score: 246
Period size: 50 Copynumber: 4.8 Consensus size: 50
39540294 ATTTGGGTAA
*
39540304 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATCGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* **
39540360 AGAGGTTCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
39540410 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
39540460 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * *
39540509 AAACATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39540551 TGTTATTATC
Statistics
Matches: 163, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 38 0.23
50 81 0.50
52 1 0.01
53 3 0.02
55 1 0.01
56 38 0.23
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:39541949 original size:17 final size:17
Alignment explanation
Indices: 39541927--39541960 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39541917 AAATAATTTT
39541927 AAAAATAAAAAATAAAA
1 AAAAATAAAAAATAAAA
* *
39541944 AAAAATCATAAATAAAA
1 AAAAATAAAAAATAAAA
39541961 GATATTAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAATAAAAAATAAAA
Found at i:39541988 original size:9 final size:9
Alignment explanation
Indices: 39541974--39542014 Score: 64
Period size: 9 Copynumber: 4.3 Consensus size: 9
39541964 ATTAGTTCTC
39541974 AAAATTATG
1 AAAATTATG
39541983 AAAATTATG
1 AAAATTATG
39541992 AAATAATTATG
1 -AA-AATTATG
39542003 AAAATTATG
1 AAAATTATG
39542012 AAA
1 AAA
39542015 TAAAGCTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 19 0.63
10 4 0.13
11 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (9 bp):
AAAATTATG
Found at i:39542001 original size:20 final size:20
Alignment explanation
Indices: 39541976--39542017 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39541966 TAGTTCTCAA
39541976 AATTATGAAAATTATGAAAT
1 AATTATGAAAATTATGAAAT
39541996 AATTATGAAAATTATGAAAT
1 AATTATGAAAATTATGAAAT
39542016 AA
1 AA
39542018 AGCTCTTCAA
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:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (20 bp):
AATTATGAAAATTATGAAAT
Found at i:39544478 original size:10 final size:10
Alignment explanation
Indices: 39544463--39544496 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
39544453 TTTTAATTAA
39544463 ATAAATTTTT
1 ATAAATTTTT
39544473 ATAAA-TTTT
1 ATAAATTTTT
39544482 ATAAATTTTT
1 ATAAATTTTT
*
39544492 TTAAA
1 ATAAA
39544497 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATAAATTTTT
Found at i:39545720 original size:20 final size:20
Alignment explanation
Indices: 39545695--39545736 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
39545685 TATGCAATAC
* *
39545695 TTGTTCGCCAAGAGATATAA
1 TTGTTCACCAAGAGACATAA
*
39545715 TTGTTCATCAAGAGACATAA
1 TTGTTCACCAAGAGACATAA
39545735 TT
1 TT
39545737 ATTGTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (20 bp):
TTGTTCACCAAGAGACATAA
Found at i:39546259 original size:19 final size:19
Alignment explanation
Indices: 39546221--39546260 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39546211 TTTCTTATTA
**
39546221 ATATATTTATAATTGTAAT
1 ATATATTTATAATTAAAAT
*
39546240 ATATATTTATTATTAAAAT
1 ATATATTTATAATTAAAAT
39546259 AT
1 AT
39546261 TAATATAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATATATTTATAATTAAAAT
Found at i:39549050 original size:16 final size:16
Alignment explanation
Indices: 39549029--39549065 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
39549019 CCCATAAAGG
39549029 AAATATTTTTTCTTTA
1 AAATATTTTTTCTTTA
39549045 AAATA--TTTTCTTTA
1 AAATATTTTTTCTTTA
39549059 AAA-ATTT
1 AAATATTT
39549066 ATTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.05
14 12 0.63
15 1 0.05
16 5 0.26
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATATTTTTTCTTTA
Found at i:39549425 original size:40 final size:42
Alignment explanation
Indices: 39549379--39549458 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
39549369 AAATCTAGTT
39549379 ATTATAATTTT-AAGATTATCTTCTATTAA-TTTAAAAATAG
1 ATTATAATTTTAAAGATTATCTTCTATTAATTTTAAAAATAG
* *
39549419 ATTATAATTTTAAAATATTATTTTCTATTAATTTTAAAAA
1 ATTATAATTTT-AAAGATTATCTTCTATTAATTTTAAAAA
39549459 AATGGATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 11 0.31
42 16 0.46
43 8 0.23
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (42 bp):
ATTATAATTTTAAAGATTATCTTCTATTAATTTTAAAAATAG
Found at i:39553777 original size:6 final size:6
Alignment explanation
Indices: 39553766--39553811 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
39553756 AACTCAGAAT
39553766 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATA
39553812 AGCTCAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TATACA
Found at i:39563794 original size:52 final size:52
Alignment explanation
Indices: 39563697--39563800 Score: 119
Period size: 52 Copynumber: 2.0 Consensus size: 52
39563687 GACATACATA
39563697 AGTTTACAATAAATAATATGTAAAAGAAATGTAAATAAATTTAATG-TAAAAC
1 AGTTTACAATAAATAATATGTAAAAGAAATGTAAATAAA-TTAATGATAAAAC
39563749 AGTTT-CAACTAAATAATAAATGTGAAAA-AAAT-TAAAATAAA-TAATGATAAAA
1 AGTTTACAA-TAAATAAT--ATGT-AAAAGAAATGT-AAATAAATTAATGATAAAA
39563801 GAGCATTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
51 3 0.07
52 18 0.39
53 6 0.13
54 15 0.33
55 4 0.09
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.29
Consensus pattern (52 bp):
AGTTTACAATAAATAATATGTAAAAGAAATGTAAATAAATTAATGATAAAAC
Found at i:39566438 original size:32 final size:32
Alignment explanation
Indices: 39566397--39566467 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
39566387 ACTAAATTTC
* *
39566397 TAATCAATCTTAATTTCTTCAAGGGTTTGTAT
1 TAATCAATCTTAATTTCTCCAAGGATTTGTAT
*
39566429 TAATCAATCTTAATTTCTCCAATGATTTGTAT
1 TAATCAATCTTAATTTCTCCAAGGATTTGTAT
39566461 TAATCAA
1 TAATCAA
39566468 CCTTTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.45
Consensus pattern (32 bp):
TAATCAATCTTAATTTCTCCAAGGATTTGTAT
Found at i:39569403 original size:21 final size:22
Alignment explanation
Indices: 39569378--39569423 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
39569368 ATCGGCAAAG
*
39569378 CTGAAAT-GACACACGAAGTGC
1 CTGAAATAGACACACAAAGTGC
*
39569399 CTGAAATACGACACATAAAGTGC
1 CTGAAATA-GACACACAAAGTGC
39569422 CT
1 CT
39569424 AATCGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
23 14 0.67
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (22 bp):
CTGAAATAGACACACAAAGTGC
Found at i:39569435 original size:57 final size:57
Alignment explanation
Indices: 39569324--39569435 Score: 188
Period size: 57 Copynumber: 2.0 Consensus size: 57
39569314 TAAGTGCCTA
* **
39569324 AAATGACGCACGAAGTGCCTGAAATACGACACATAAAATGCCTAATCGGCAAAGCTG
1 AAATGACACACGAAGTGCCTGAAATACGACACATAAAATGCCTAATCGAAAAAGCTG
*
39569381 AAATGACACACGAAGTGCCTGAAATACGACACATAAAGTGCCTAATCGAAAAAGC
1 AAATGACACACGAAGTGCCTGAAATACGACACATAAAATGCCTAATCGAAAAAGC
39569436 CCGACTTAGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (57 bp):
AAATGACACACGAAGTGCCTGAAATACGACACATAAAATGCCTAATCGAAAAAGCTG
Found at i:39570140 original size:9 final size:9
Alignment explanation
Indices: 39570121--39570154 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
39570111 AAACTCTAGT
39570121 TTTTCCTTTC
1 TTTT-CTTTC
39570131 TTTTCTTTC
1 TTTTCTTTC
*
39570140 TTTGCTTTC
1 TTTTCTTTC
39570149 TTTTCT
1 TTTTCT
39570155 CCCTATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:39572611 original size:23 final size:23
Alignment explanation
Indices: 39572581--39572635 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
39572571 GCTGATAAAT
* * * *
39572581 GGTAAGCTCTATCGAGTTGACAC
1 GGTAAGCTCCATAGAGCTGAAAC
39572604 GGTAAGCTCCATAGAGCTGAAAC
1 GGTAAGCTCCATAGAGCTGAAAC
39572627 GGTAAGCTC
1 GGTAAGCTC
39572636 ATACAAGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (23 bp):
GGTAAGCTCCATAGAGCTGAAAC
Found at i:39572644 original size:23 final size:23
Alignment explanation
Indices: 39572602--39572645 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
39572592 TCGAGTTGAC
*
39572602 ACGGTAAGCTCCATAGAGCTGAA
1 ACGGTAAGCTCCATAAAGCTGAA
39572625 ACGGTAAGCT-CATACAAGCTG
1 ACGGTAAGCTCCATA-AAGCTG
39572646 TGGTGAGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (23 bp):
ACGGTAAGCTCCATAAAGCTGAA
Found at i:39582545 original size:36 final size:36
Alignment explanation
Indices: 39582504--39582684 Score: 317
Period size: 36 Copynumber: 5.0 Consensus size: 36
39582494 CTAAGGCTAC
39582504 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
39582540 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* * *
39582576 GACTTATCACTTTTTCACATGATCGGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
39582612 CACTTATCACTTTTTCACTTGATCAGATAATTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
39582648 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
39582684 C
1 C
39582685 TAAAGCTACC
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 136 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:39583834 original size:106 final size:106
Alignment explanation
Indices: 39583649--39583860 Score: 361
Period size: 106 Copynumber: 2.0 Consensus size: 106
39583639 CCTGTTTCGC
39583649 TGTCTGACAGTTCCGACCACTCTTCACTAAAAATTAATTATCTCATTGTAAAAAATTCGGATGAT
1 TGTCTGACAGTTCCGACCACTCTTCACTAAAAATTAATTATCTCATTGTAAAAAATTCGGATGAT
* * *
39583714 GTTTCCGTTTGTTTCTTATGAAAATAGACTCATTAAGGATT
66 GTTTCAGCTTGTTTCTTATAAAAATAGACTCATTAAGGATT
* *
39583755 TGTCTGACAGTTCCGACCACTCTTCACTAAAAATTAATTATCTCATTGTACAGAATTCGGATGAT
1 TGTCTGACAGTTCCGACCACTCTTCACTAAAAATTAATTATCTCATTGTAAAAAATTCGGATGAT
* *
39583820 GTTTTAGCTTGTTTCTTCTAAAAATAGACTCATTAAGGATT
66 GTTTCAGCTTGTTTCTTATAAAAATAGACTCATTAAGGATT
39583861 CTAACCATAT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (106 bp):
TGTCTGACAGTTCCGACCACTCTTCACTAAAAATTAATTATCTCATTGTAAAAAATTCGGATGAT
GTTTCAGCTTGTTTCTTATAAAAATAGACTCATTAAGGATT
Found at i:39588215 original size:14 final size:17
Alignment explanation
Indices: 39588196--39588238 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 17
39588186 ATTTATTTCT
39588196 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
39588210 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
39588227 TAATATACATTA
1 TAATATA-ATTA
39588239 GAATTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.32
15 1 0.04
16 4 0.16
17 8 0.32
18 4 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:39596511 original size:20 final size:19
Alignment explanation
Indices: 39596469--39596511 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
39596459 TTAGGGATTT
* * *
39596469 TTTTTTGTATTTTATGAAT
1 TTTTTTATATTTTAAGAAA
39596488 TTTTTTATATTTTAAAGAAA
1 TTTTTTATATTTT-AAGAAA
39596508 TTTT
1 TTTT
39596512 GAGTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (19 bp):
TTTTTTATATTTTAAGAAA
Found at i:39596809 original size:18 final size:18
Alignment explanation
Indices: 39596786--39596821 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39596776 ACTGATATAC
39596786 GAAAAAGGAAAAAAAAAA
1 GAAAAAGGAAAAAAAAAA
39596804 GAAAAAGGAAAAAAAAAA
1 GAAAAAGGAAAAAAAAAA
39596822 ATTGGGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
GAAAAAGGAAAAAAAAAA
Found at i:39596938 original size:107 final size:105
Alignment explanation
Indices: 39596812--39597165 Score: 497
Period size: 103 Copynumber: 3.4 Consensus size: 105
39596802 AAGAAAAAGG
* * *
39596812 AAAAAAAAAAATTGGGTGCTGGCCTGTCAATGGCCGGCACCCGGTAGAATTTAAAAAAAAATTTA
1 AAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTT--AAAAAAATTTA
*
39596877 TTTTTTTCGTGTCAGAATCAGATATCAGTATATGAAAAAAAT
64 TTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
*
39596919 AAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGACACCCAGTACAATTT----AAA-TTATT
1 AAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAATTTA-T
* *
39596979 TTTTTTCGTGTCAAAATCAGATATCAGTATACGAAAAAAGT
65 TTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
* * *
39597020 AAAAAAAAAAATTTTGGGTACTGGCCTATCAATGGCCGGCACCCAGTACAATTTAAAAAAATTTC
1 -AAAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAATTTA
*
39597085 TTTTTTT-GTGTCAGAATCAGATATCAGAATACGAAAAAAAT
64 TTTTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
* *
39597126 -AAAAAAAAATTTGAGTGTTGGCCTGTCAATGGCCGGCACC
1 AAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACC
39597166 ACCTTGTAAT
Statistics
Matches: 221, Mismatches: 18, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
100 3 0.01
101 42 0.19
102 10 0.05
103 66 0.30
104 9 0.04
106 31 0.14
107 58 0.26
108 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (105 bp):
AAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAATTTATT
TTTTTCGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
Found at i:39598212 original size:44 final size:43
Alignment explanation
Indices: 39598158--39598289 Score: 156
Period size: 44 Copynumber: 3.0 Consensus size: 43
39598148 ATAATTGTTC
* *
39598158 TGACTAACTTTTCAAATTTCAATTATTTCTATCCCATCTATCTT
1 TGACTCACTTTTCAAATTTCAATTATTTCTATCCAATCTAT-TT
* * *
39598202 TGACTCACTTTTCAAATTTCATTTGTTTCTATCCAATTTATTT
1 TGACTCACTTTTCAAATTTCAATTATTTCTATCCAATCTATTT
* * * *
39598245 TGACTCACTTTTCAAAATTTCATTTAATTCAATTCAATCTCATTT
1 TGACTCACTTTTC-AAATTTCAATTATTTCTATCCAATCT-ATTT
39598290 ATTAACTCAC
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
43 15 0.20
44 57 0.75
45 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.49
Consensus pattern (43 bp):
TGACTCACTTTTCAAATTTCAATTATTTCTATCCAATCTATTT
Found at i:39599316 original size:108 final size:104
Alignment explanation
Indices: 39598859--39599296 Score: 629
Period size: 95 Copynumber: 4.3 Consensus size: 104
39598849 TGATAAATTT
*
39598859 GGTGCCGGCCATTTACAGGCCAGCACCCAAATTTTTTTTTACTTTTTTCGTATACTGATATCTGA
1 GGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTACTTTTTTCGTATACTGATATCTGA
*
39598924 TTCTGACACG------A--ATTTTTTTTAAATTGTACTA
66 TTCTGACACGAAAAAAATTATTTTTTTTAAATTGTACTG
* * *
39598955 GGTGCTGGCCATTGATAGGCCAGCA-CCAAATTTTTTTTTATTTTTTTCGTATACTGATATCTGA
1 GGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTACTTTTTTCGTATACTGATATCTGA
39599019 TTCTGACACG-----AATT-TTTTTTTTAAATTGTACTG
66 TTCTGACACGAAAAAAATTATTTTTTTTAAATTGTACTG
*
39599052 GGTGCCGGCCATTGACAGGCCAGCACCCAATTTTTTTTTTTACTTTTTTCGTATACTGATATCTG
1 GGTGCCGGCCATTGACAGGCCAGCACCCAA-ATTTTTTTTTACTTTTTTCGTATACTGATATCTG
*
39599117 ATTCTGACACAAAAAAAAGAATT-TTTTTTTTAAAAATTGTACTG
65 ATTCTGACAC--GAAAAA-AATTATTTTTTTT--AAATTGTACTG
*
39599161 GGTGCCAGCCATTGACAGGCCAGCACCCAAATTTTTTTTTACTTTTTTCGTATACTGATATCTGA
1 GGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTACTTTTTTCGTATACTGATATCTGA
39599226 TTCTGACACGAAAAAAATTATTATTTTTTAAATTGTACTG
66 TTCTGACACGAAAAAAATTATT-TTTTTTAAATTGTACTG
39599266 GGTGCCGGCCATTGACAGGCCAGCACCCAAA
1 GGTGCCGGCCATTGACAGGCCAGCACCCAAA
39599297 AAATATTTTT
Statistics
Matches: 311, Mismatches: 14, Indels: 25
0.89 0.04 0.07
Matches are distributed among these distances:
95 48 0.15
96 23 0.07
97 41 0.13
98 4 0.01
99 42 0.14
105 45 0.14
106 7 0.02
107 18 0.06
108 43 0.14
109 40 0.13
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (104 bp):
GGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTACTTTTTTCGTATACTGATATCTGA
TTCTGACACGAAAAAAATTATTTTTTTTAAATTGTACTG
Found at i:39599319 original size:12 final size:12
Alignment explanation
Indices: 39599302--39599328 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39599292 CCAAAAAATA
39599302 TTTTTTTTCCTT
1 TTTTTTTTCCTT
39599314 TTTTTTTTCCTT
1 TTTTTTTTCCTT
39599326 TTT
1 TTT
39599329 CGTATATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTCCTT
Found at i:39615999 original size:22 final size:21
Alignment explanation
Indices: 39615958--39615999 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39615948 TGTTTGGAGT
**
39615958 AATTTAATTTTTTCTTTGAAC
1 AATTTAATTTTTTCAGTGAAC
39615979 AATTTAATTTTTTCGAGTGAA
1 AATTTAATTTTTTC-AGTGAA
39616000 GCGAGCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (21 bp):
AATTTAATTTTTTCAGTGAAC
Found at i:39618082 original size:11 final size:12
Alignment explanation
Indices: 39618068--39618103 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
39618058 TATATTGTCA
39618068 TATGTAT-TTTT
1 TATGTATATTTT
*
39618079 TATGGATATTTT
1 TATGTATATTTT
39618091 TATGTATATTTT
1 TATGTATATTTT
39618103 T
1 T
39618104 CACTGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (12 bp):
TATGTATATTTT
Found at i:39625922 original size:160 final size:160
Alignment explanation
Indices: 39625655--39625970 Score: 524
Period size: 160 Copynumber: 2.0 Consensus size: 160
39625645 TACAATCGAG
* *
39625655 CCAAAATCTTTTACCATACAAAGTAAAGCCAATAAAAGATAATTGTTGGACACAGATTTAATTGC
1 CCAAAATCTTTTACCATACAAAGTAAAGCCAACAAAAAATAATTGTTGGACACAGATTTAATTGC
* *
39625720 TTTCAAAGGGTATTCATCATCAAAAACTTTGACATGATTGAACAGTTTAATCAGGTGCTACCAAT
66 TTTCAAAGGCTATTCATCATCAAAAACTTTGACATGATTGAACAGTTCAATCAGGTGCTACCAAT
*
39625785 GTTGCTCCAACTCTACTTTTCTTGAACAAT
131 GTTACTCCAACTCTACTTTTCTTGAACAAT
*
39625815 CCAAAATCTTTTACCATACGAAGTAAAGCCAACAAAAAATAATTGTTGGACACAGATTTAATTGC
1 CCAAAATCTTTTACCATACAAAGTAAAGCCAACAAAAAATAATTGTTGGACACAGATTTAATTGC
* * * *
39625880 TTTCAACGGCTATTCATCATCTAAAACTTTGACATTATTGAACAGTTCAATCAGGTGCTACCTAT
66 TTTCAAAGGCTATTCATCATCAAAAACTTTGACATGATTGAACAGTTCAATCAGGTGCTACCAAT
**
39625945 GTTACTCTGACTCTACTTTTCTTGAA
131 GTTACTCCAACTCTACTTTTCTTGAA
39625971 GTATCCGTGT
Statistics
Matches: 144, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
160 144 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (160 bp):
CCAAAATCTTTTACCATACAAAGTAAAGCCAACAAAAAATAATTGTTGGACACAGATTTAATTGC
TTTCAAAGGCTATTCATCATCAAAAACTTTGACATGATTGAACAGTTCAATCAGGTGCTACCAAT
GTTACTCCAACTCTACTTTTCTTGAACAAT
Found at i:39631349 original size:18 final size:20
Alignment explanation
Indices: 39631328--39631369 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39631318 TATTTTTTAG
39631328 ATTTCTT-AAA-TATTTTGA
1 ATTTCTTAAAATTATTTTGA
*
39631346 ATTTTTTAAAATTATTTTGA
1 ATTTCTTAAAATTATTTTGA
39631366 ATTT
1 ATTT
39631370 TTTGTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 3 0.14
20 12 0.57
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (20 bp):
ATTTCTTAAAATTATTTTGA
Found at i:39631368 original size:10 final size:9
Alignment explanation
Indices: 39631340--39631382 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
39631330 TTCTTAAATA
39631340 TTTTGAATT
1 TTTTGAATT
*
39631349 TTTTAAAATT
1 TTTT-GAATT
39631359 ATTTTGAATT
1 -TTTTGAATT
39631369 TTTTGTAATT
1 TTTTG-AATT
39631379 TTTT
1 TTTT
39631383 TAGAGGAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 9 0.31
10 16 0.55
11 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (9 bp):
TTTTGAATT
Found at i:39631820 original size:26 final size:26
Alignment explanation
Indices: 39631789--39631840 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39631779 TATAAAACAC
39631789 ATATTT-TACTATTTAAATAATAAAAT
1 ATATTTATA-TATTTAAATAATAAAAT
**
39631815 ATATTTATATATTTTCATAATAAAAT
1 ATATTTATATATTTAAATAATAAAAT
39631841 TTAAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
ATATTTATATATTTAAATAATAAAAT
Found at i:39653027 original size:3 final size:3
Alignment explanation
Indices: 39653021--39653104 Score: 64
Period size: 3 Copynumber: 27.3 Consensus size: 3
39653011 GCAATTTTTT
* *
39653021 TTA TTA TTA TTTA GTTA TTA TTA TTA TTA TCA TTA TTA TCT- TTA CTA
1 TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* * * *
39653068 TTA TTA TTA -TA TTTA TTA ATA CTA TTG TTA GTA TTA T
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T
39653105 GTTTTCTTAT
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
2 3 0.05
3 52 0.81
4 9 0.14
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:39656705 original size:50 final size:50
Alignment explanation
Indices: 39656587--39656879 Score: 264
Period size: 50 Copynumber: 5.8 Consensus size: 50
39656577 TGAATATAAC
* * * ** * * *
39656587 ATGCCAAAGCTATGTCCCAGACATTGTCTTACATGGGATGTTTCTTGTA-
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAG
* * * **
39656636 CTGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAG
* * * ** * *
39656686 GTGCCCATGCCATGTCCCAGAAATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAG
* * * * *
39656736 ATGCCAACGCCATATCCCAGACATGGTCTTATATGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAG
* * *
39656786 GTGCCAATGCCATGTCTCAGACCTGGTCTTACATGGGACCTCTCATAATCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-G
*
39656842 ATGCCAATGCCATGTCCCAGACATGATCTTACATGGGA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
39656880 TCTCATCCTC
Statistics
Matches: 196, Mismatches: 41, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
49 38 0.19
50 122 0.62
53 1 0.01
56 35 0.18
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAG
Found at i:39656749 original size:100 final size:102
Alignment explanation
Indices: 39656637--39656879 Score: 301
Period size: 100 Copynumber: 2.4 Consensus size: 102
39656627 TTTCTTGTAC
* ** *
39656637 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAGGTGCCCATGCCATGTC
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAATGCCATGTC
*
39656702 CCAGAAATGGTCTTACGGGGGACCTCTC-ATCTC-GA
66 CCAGAAATGGTCTTACAGGGGACCTCTCAATCTCAGA
* * * *
39656737 TGCCAACGCCATATCCCAGACATGGTCTTATATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAATGCCATGTC
* ** *
39656802 TCAGACCTGGTCTTACATGGGACCTCTCATAATCTCAATGA
66 CCAGAAATGGTCTTACAGGGGACCTCTC--AATCTC-A-GA
* *
39656843 TGCCAATGCCATGTCCCAGACATGATCTTACATGGGA
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGA
39656880 TCTCATCCTC
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
100 80 0.67
103 5 0.04
106 35 0.29
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (102 bp):
TGCCAATGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAATGCCATGTC
CCAGAAATGGTCTTACAGGGGACCTCTCAATCTCAGA
Found at i:39660072 original size:21 final size:21
Alignment explanation
Indices: 39660046--39660089 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
39660036 GAGTCCTAAA
*
39660046 ACAAAACGAGCTATTTAGCAG
1 ACAAAACGAGCCATTTAGCAG
* *
39660067 ACAAAACGTGCCATTTGGCAG
1 ACAAAACGAGCCATTTAGCAG
39660088 AC
1 AC
39660090 TAAGATTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (21 bp):
ACAAAACGAGCCATTTAGCAG
Found at i:39660200 original size:26 final size:28
Alignment explanation
Indices: 39660140--39660191 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
39660130 AAAATATTGT
*
39660140 TAAATATT-AAAAAATATATAAAAATGA
1 TAAATATTGTAAAAATATATAAAAATGA
39660167 TAAATATTGTAAAAATATA-AAAAAT
1 TAAATATTGTAAAAATATATAAAAAT
39660192 CTAATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (28 bp):
TAAATATTGTAAAAATATATAAAAATGA
Found at i:39668954 original size:41 final size:42
Alignment explanation
Indices: 39668879--39669008 Score: 124
Period size: 41 Copynumber: 3.1 Consensus size: 42
39668869 ATTGGCACTT
* * * *
39668879 AGCCTGCTAGACTTAAAGCCTGATTCA-G-TACACCGACACTT-
1 AGCCTGCTAGACATAAAGTCTGA-TAATGTTTCACCGACA-TTA
* * *
39668920 AGCCTGTTAGACATATAGTCTGA-AATGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGATAATGTTTCACCGACATTA
* * *
39668961 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGATAATGTTTCACCGACATTA
39669003 AGCCTG
1 AGCCTG
39669009 ATAGGCACTG
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
39 1 0.01
40 3 0.04
41 47 0.64
42 23 0.31
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (42 bp):
AGCCTGCTAGACATAAAGTCTGATAATGTTTCACCGACATTA
Found at i:39669004 original size:42 final size:41
Alignment explanation
Indices: 39668920--39669008 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 41
39668910 ACCGACACTT
* *
39668920 AGCCTGTTAGACATATAGTCTGAAATGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATTA
* *
39668961 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCTGA-AATGTTTCACCGGCATTA
39669003 AGCCTG
1 AGCCTG
39669009 ATAGGCACTG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 20 0.47
42 23 0.53
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATTA
Found at i:39674741 original size:59 final size:59
Alignment explanation
Indices: 39674574--39674742 Score: 142
Period size: 59 Copynumber: 2.9 Consensus size: 59
39674564 AATTTGGACC
* * * *** *
39674574 AAAAAAATTCAAACCCCAATATGAGAATAATTAATAAGTTCAAGGT-CTAAATTGGATAA
1 AAAAAAATTCAAACCCCAATGTGAAAACAATTGCCAAATTC-AGGTCCTAAATTGGATAA
* * * * * * *
39674633 AAAAAAGTTCAGACCCCAATGTGAAAACAATTGCCAATTTCAAGACCTAACTTGGTTAA
1 AAAAAAATTCAAACCCCAATGTGAAAACAATTGCCAAATTCAGGTCCTAAATTGGATAA
* ** * * *
39674692 AAAAAAATTCAAACTCTGATGTGAAAATAGTTGCTAAATTCAGGTCCTAAA
1 AAAAAAATTCAAACCCCAATGTGAAAACAATTGCCAAATTCAGGTCCTAAA
39674743 AAGTGATTTA
Statistics
Matches: 84, Mismatches: 25, Indels: 2
0.76 0.23 0.02
Matches are distributed among these distances:
58 2 0.02
59 82 0.98
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (59 bp):
AAAAAAATTCAAACCCCAATGTGAAAACAATTGCCAAATTCAGGTCCTAAATTGGATAA
Found at i:39675725 original size:14 final size:14
Alignment explanation
Indices: 39675708--39675764 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
39675698 TAATATTTAA
39675708 ATAATAACAATAAC
1 ATAATAACAATAAC
39675722 ATAATAACAATATA-
1 ATAATAACAATA-AC
*
39675736 ATAATGA-AATAAC
1 ATAATAACAATAAC
39675749 AGTAAAATAACAATAA
1 A-T--AATAACAATAA
39675765 ATTCAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
12 1 0.03
13 5 0.14
14 19 0.54
15 1 0.03
16 4 0.11
17 5 0.14
ACGTcount: A:0.65, C:0.09, G:0.04, T:0.23
Consensus pattern (14 bp):
ATAATAACAATAAC
Found at i:39679314 original size:26 final size:25
Alignment explanation
Indices: 39679276--39679350 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 25
39679266 CGAATATAAT
39679276 AAATATATATTTTTATTTTTATTTTTA
1 AAATA-AT-TTTTTATTTTTATTTTTA
*
39679303 AAATACTTTTTTATTTTTTATTTTTA
1 AAATAATTTTTTA-TTTTTATTTTTA
* *
39679329 ATATAATTTTTTAATGTTTATT
1 AAATAATTTTTT-ATTTTTATT
39679351 AAAAAATGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 6 0.14
26 30 0.71
27 6 0.14
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (25 bp):
AAATAATTTTTTATTTTTATTTTTA
Found at i:39680365 original size:64 final size:63
Alignment explanation
Indices: 39680290--39680421 Score: 210
Period size: 64 Copynumber: 2.1 Consensus size: 63
39680280 TCTAACTAAA
* ***
39680290 TTTTTGTATCTATACGATTAATAAAATTAAAATTATTTTTATTTATTTATTTTATAAAATATT
1 TTTTTGTATCTATACGATTAATAAAACTAAAATTAAAATTATTTATTTATTTTATAAAATATT
*
39680353 TTTTGTGTATCTATACTATTAATAAAACTAAAATTAAAATTATTTATTTATTTTATAAAATATT
1 TTTT-TGTATCTATACGATTAATAAAACTAAAATTAAAATTATTTATTTATTTTATAAAATATT
39680417 TTTTT
1 TTTTT
39680422 CATACATCCT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 5 0.08
64 58 0.92
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.55
Consensus pattern (63 bp):
TTTTTGTATCTATACGATTAATAAAACTAAAATTAAAATTATTTATTTATTTTATAAAATATT
Found at i:39680660 original size:18 final size:19
Alignment explanation
Indices: 39680639--39680689 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
39680629 TTGAAATTTA
*
39680639 TTTAATATTTTTATAAA-T
1 TTTAATATTTTTACAAATT
39680657 TTTAATAATGTTTTACAAATT
1 TTTAAT-AT-TTTTACAAATT
39680678 TTTAAT-TTTTTA
1 TTTAATATTTTTA
39680690 AAAAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 11 0.38
19 3 0.10
20 8 0.28
21 7 0.24
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTAATATTTTTACAAATT
Found at i:39695809 original size:17 final size:17
Alignment explanation
Indices: 39695787--39695820 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39695777 GACTAATCCC
39695787 TATACATCACTTAGGTA
1 TATACATCACTTAGGTA
*
39695804 TATACATTACTTAGGTA
1 TATACATCACTTAGGTA
39695821 CATGTCACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (17 bp):
TATACATCACTTAGGTA
Found at i:39697741 original size:14 final size:13
Alignment explanation
Indices: 39697715--39697762 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
39697705 GTTTATTTAA
39697715 AATATAATAATAT
1 AATATAATAATAT
39697728 AATATAATTAATAT
1 AATATAA-TAATAT
* *
39697742 AAT-TTACAATAT
1 AATATAATAATAT
*
39697754 AATAAAATA
1 AATATAATA
39697763 GTAACATACT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
12 8 0.29
13 11 0.39
14 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:39698529 original size:30 final size:30
Alignment explanation
Indices: 39698450--39698529 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
39698440 ACGAATTAAT
* * *
39698450 TTCAGCAATGTACAACCATATAAGAATCAA
1 TTCAGCAATGTATAACCATATAACAAACAA
* *
39698480 TTCAGCAACT-TATATCCATATACCAAACAA
1 TTCAGCAA-TGTATAACCATATAACAAACAA
**
39698510 TTTGGCAATGTATAACCATA
1 TTCAGCAATGTATAACCATA
39698530 CACGAATCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 1 0.03
30 38 0.95
31 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (30 bp):
TTCAGCAATGTATAACCATATAACAAACAA
Found at i:39698738 original size:31 final size:30
Alignment explanation
Indices: 39698414--39699127 Score: 308
Period size: 31 Copynumber: 23.4 Consensus size: 30
39698404 CATAATCAAT
* *
39698414 TCAATGTCGACAATATATAACCATGTACGAA
1 TCAAT-TCGGCAATATATAACCATATACGAA
* * * * *
39698445 TTAATTTCAGCAATGTACAACCATATAAGAA
1 TCAA-TTCGGCAATATATAACCATATACGAA
* * *
39698476 TCAATTCAGCAACT-TATATCCATATACCAA
1 TCAATTCGGCAA-TATATAACCATATACGAA
* * * *
39698506 ACAATTTGGCAATGTATAACCATACACGAA
1 TCAATTCGGCAATATATAACCATATACGAA
* * * *
39698536 TCAAGCTCGACAATATATAATCATATACAAA
1 TCAA-TTCGGCAATATATAACCATATACGAA
* ** *
39698567 TCCAATTCGGC-ATCCTATATTCATAAAC-AA
1 T-CAATTCGGCAAT-ATATAACCATATACGAA
* * *
39698597 TTCAATATCGACAATATATAACCATGTACAAA
1 -TCAAT-TCGGCAATATATAACCATATACGAA
* * ** *
39698629 TTAATTTCAGCAAGGTACAA-CATATACGAA
1 TCAA-TTCGGCAATATATAACCATATACGAA
* * * *
39698659 TCAATTCGACAACT-TACATCCATATACCAA
1 TCAATTCGGCAA-TATATAACCATATACGAA
* **
39698689 ACAATTCGGCAAGGTATAACCAT-TCACGAA
1 TCAATTCGGCAATATATAACCATAT-ACGAA
* *
39698719 TCAAGTTCGGCAATATATAATCATATACAAA
1 TCAA-TTCGGCAATATATAACCATATACGAA
* ** *
39698750 TCCAATTCGGC-ATCCTATATTCATAAAC-AA
1 T-CAATTCGGCAAT-ATATAACCATATACGAA
* * *
39698780 TTCAATATCGACAATATATAACCATGTACAAA
1 -TCAAT-TCGGCAATATATAACCATATACGAA
* * ** *
39698812 TTAATTTCAGCAAGGTACAA-CATATACGAA
1 TCAA-TTCGGCAATATATAACCATATACGAA
* * *
39698842 TCAATTCGACAACT-TATATCCATATACCAA
1 TCAATTCGGCAA-TATATAACCATATACGAA
* ** *
39698872 ACAATTCGGCAAGGTATAACAAT-TCACGAA
1 TCAATTCGGCAATATATAACCATAT-ACGAA
* *
39698902 TCAAGTTCGGCAATATATAATCATATACAAA
1 TCAA-TTCGGCAATATATAACCATATACGAA
* ** *
39698933 TCCAATTCGGC-ATCCTATATTCATAAAC-AA
1 T-CAATTCGGCAAT-ATATAACCATATACGAA
* * *
39698963 TTCAATATCGACAATATATAACCATGTACAAA
1 -TCAAT-TCGGCAATATATAACCATATACGAA
* * ** *
39698995 TTAATTTCAGCAAGGTACAA-CATATACGAA
1 TCAA-TTCGGCAATATATAACCATATACGAA
* * *
39699025 TCAATTCGACAACT-TATATCCATATACCAA
1 TCAATTCGGCAA-TATATAACCATATACGAA
* * ** *
39699055 ACAATTCAGCAAGGTATAACCAT-TCATGAA
1 TCAATTCGGCAATATATAACCATAT-ACGAA
* * *
39699085 TCATGTTCGGCAATATATAATCATATACAAA
1 TCA-ATTCGGCAATATATAACCATATACGAA
39699116 TCCAATTCGGCA
1 T-CAATTCGGCA
39699128 TCCTATATTC
Statistics
Matches: 501, Mismatches: 138, Indels: 88
0.69 0.19 0.12
Matches are distributed among these distances:
29 32 0.06
30 199 0.40
31 240 0.48
32 30 0.06
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (30 bp):
TCAATTCGGCAATATATAACCATATACGAA
Found at i:39698746 original size:183 final size:183
Alignment explanation
Indices: 39698358--39699194 Score: 1426
Period size: 183 Copynumber: 4.6 Consensus size: 183
39698348 GCATGTTACA
* * ** * * *
39698358 TCGGCAATGTATAATCATACACAAATTAAATTCGGCATTCTATATTCATAATCAATTCAATGTCG
1 TCGGCAATATATAATCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCG
* * *
39698423 ACAATATATAACCATGTACGAATTAATTTCAGCAATGTACAACCATATAAGAATCAATTC-AGCA
66 ACAATATATAACCATGTACAAATTAATTTCAGCAAGGTACAA-CATATACGAATCAATTCGA-CA
* * * *
39698487 ACTTATATCCATATACCAAACAATTTGGCAATGTATAACCATACACGAATCAAGC
129 ACTTATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGT
*
39698542 TCGACAATATATAATCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCG
1 TCGGCAATATATAATCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCG
39698607 ACAATATATAACCATGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAAC
66 ACAATATATAACCATGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAAC
*
39698672 TTACATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGT
131 TTATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGT
39698725 TCGGCAATATATAATCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCG
1 TCGGCAATATATAATCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCG
39698790 ACAATATATAACCATGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAAC
66 ACAATATATAACCATGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAAC
*
39698855 TTATATCCATATACCAAACAATTCGGCAAGGTATAACAATTCACGAATCAAGT
131 TTATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGT
39698908 TCGGCAATATATAATCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCG
1 TCGGCAATATATAATCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCG
39698973 ACAATATATAACCATGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAAC
66 ACAATATATAACCATGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAAC
* * *
39699038 TTATATCCATATACCAAACAATTCAGCAAGGTATAACCATTCATGAATCATGT
131 TTATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGT
39699091 TCGGCAATATATAATCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCG
1 TCGGCAATATATAATCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCG
* * *
39699156 ATAATTTATAACCATGAAC-AATTAAATTTCAGCAAGGTA
66 ACAATATATAACCATGTACAAATT-AATTTCAGCAAGGTA
39699195 AAAACATTAT
Statistics
Matches: 625, Mismatches: 26, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
182 4 0.01
183 523 0.84
184 98 0.16
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (183 bp):
TCGGCAATATATAATCATATACAAATCCAATTCGGCATCCTATATTCATAAACAATTCAATATCG
ACAATATATAACCATGTACAAATTAATTTCAGCAAGGTACAACATATACGAATCAATTCGACAAC
TTATATCCATATACCAAACAATTCGGCAAGGTATAACCATTCACGAATCAAGT
Found at i:39701214 original size:19 final size:17
Alignment explanation
Indices: 39701173--39701232 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 17
39701163 TTTTCTATAT
*
39701173 TTTTTAATATTTTAAATA
1 TTTTTCATATTTT-AATA
*
39701191 ATTTTCTATATTTTAATCA
1 TTTTTC-ATATTTTAAT-A
*
39701210 TTTTTCATAATTTTTATA
1 TTTTTCAT-ATTTTAATA
39701228 TTTTT
1 TTTTT
39701233 ATAATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 15 0.43
19 20 0.57
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTCATATTTTAATA
Found at i:39701258 original size:22 final size:21
Alignment explanation
Indices: 39701222--39701270 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
39701212 TTTCATAATT
* *
39701222 TTTATATTTTTATAATATATA
1 TTTATTTTTTTATAACATATA
39701243 TTTATTTTTTTCATAACATATA
1 TTTATTTTTTT-ATAACATATA
*
39701265 TATATT
1 TTTATT
39701271 AAAAAATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTATTTTTTTATAACATATA
Found at i:39703745 original size:41 final size:41
Alignment explanation
Indices: 39703684--39703824 Score: 230
Period size: 41 Copynumber: 3.4 Consensus size: 41
39703674 TTTCGGGGGC
39703684 TTTAGCGGCGTTTTGT-TTTAAGCGCCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTT-TATTTAAGCGCCGCTAATGTTCTGGGA
39703725 TTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGA
* * *
39703766 TTTAGTGGCGTTTTTAATTAAGCGCCGCTAATGTTCTGGGC
1 TTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGA
*
39703807 TTTAGCGGCTTTTTTATT
1 TTTAGCGGCGTTTTTATT
39703825 GATGCGTCAC
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 1 0.01
41 92 0.99
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGA
Found at i:39703838 original size:82 final size:80
Alignment explanation
Indices: 39703684--39703861 Score: 221
Period size: 82 Copynumber: 2.2 Consensus size: 80
39703674 TTTCGGGGGC
* * *
39703684 TTTAGCGGCGTTTTGTTTTAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTTATTTAAGCG
1 TTTAGTGGCGTTTT-TATTAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTTATTGAAGCG
* * *
39703749 CCGCTAATGTTCTGGGA
65 CCACTAATGCTCT-GCA
* * *
39703766 TTTAGTGGCGTTTTTAATTAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCTTTTTTATTGATGCG
1 TTTAGTGGCGTTTTT-ATTAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTTATTGAAGCG
* *
39703831 TCACTAATGCTCTTCA
65 CCACTAATGCTCTGCA
*
39703847 TTTAGTGGCATTTTT
1 TTTAGTGGCGTTTTT
39703862 GGAAAGCGCC
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 16 0.19
82 67 0.81
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.42
Consensus pattern (80 bp):
TTTAGTGGCGTTTTTATTAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTTATTGAAGCGC
CACTAATGCTCTGCA
Found at i:39704254 original size:16 final size:16
Alignment explanation
Indices: 39704233--39704302 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
39704223 CTATAGTATG
39704233 TAGTTTAAGGGTTTTA
1 TAGTTTAAGGGTTTTA
*
39704249 TAGTTTAA-GGTTTAA
1 TAGTTTAAGGGTTTTA
** * *
39704264 T-GTTTACTATAG-TATG
1 TAGTTTA--AGGGTTTTA
39704280 TAGTTTAAGGGTTTTA
1 TAGTTTAAGGGTTTTA
39704296 TAGTTTA
1 TAGTTTA
39704303 TGGTTTAGGG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
14 5 0.12
15 9 0.22
16 20 0.50
17 6 0.15
ACGTcount: A:0.27, C:0.01, G:0.21, T:0.50
Consensus pattern (16 bp):
TAGTTTAAGGGTTTTA
Found at i:39704261 original size:23 final size:23
Alignment explanation
Indices: 39704235--39704315 Score: 80
Period size: 23 Copynumber: 3.5 Consensus size: 23
39704225 ATAGTATGTA
39704235 GTTTAAGGGTTTTATAGTTTAAG
1 GTTTAAGGGTTTTATAGTTTAAG
*
39704258 GTTTAA-TGTTTACTATAGTATGT-A-
1 GTTTAAGGGTTT--TATAGT-T-TAAG
*
39704282 GTTTAAGGGTTTTATAGTTTATG
1 GTTTAAGGGTTTTATAGTTTAAG
39704305 GTTT-AGGGTTT
1 GTTTAAGGGTTT
39704316 GTTATATTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
21 1 0.02
22 12 0.25
23 16 0.33
24 12 0.25
25 6 0.12
26 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (23 bp):
GTTTAAGGGTTTTATAGTTTAAG
Found at i:39704351 original size:22 final size:21
Alignment explanation
Indices: 39704326--39704366 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
39704316 GTTATATTGG
39704326 GTTTGTGA-TTTAGTGTTTTAAA
1 GTTTG-GAGTTTAGT-TTTTAAA
39704348 GTTTGGAGTTTAGTTTTTA
1 GTTTGGAGTTTAGTTTTTA
39704367 TAGTCAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (21 bp):
GTTTGGAGTTTAGTTTTTAAA
Found at i:39708520 original size:29 final size:29
Alignment explanation
Indices: 39708478--39708535 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
39708468 TAAATCTTCT
39708478 TCCATTTGTCAACTATTTCATTTCCAAAA
1 TCCATTTGTCAACTATTTCATTTCCAAAA
39708507 TCCATTTGTCAACTATTTCATTTCCAAAA
1 TCCATTTGTCAACTATTTCATTTCCAAAA
39708536 ATATATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (29 bp):
TCCATTTGTCAACTATTTCATTTCCAAAA
Found at i:39708696 original size:9 final size:9
Alignment explanation
Indices: 39708665--39708720 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
39708655 TTAAAGTTCA
39708665 AATTT-CAT
1 AATTTACAT
* *
39708673 AACTTACGT
1 AATTTACAT
*
39708682 ATTTTACAT
1 AATTTACAT
39708691 AATTTACAT
1 AATTTACAT
39708700 AA-TT-CAT
1 AATTTACAT
*
39708707 AATTTACAA
1 AATTTACAT
39708716 AATTT
1 AATTT
39708721 TTACTCAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 5 0.13
8 8 0.21
9 25 0.66
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (9 bp):
AATTTACAT
Found at i:39708709 original size:16 final size:16
Alignment explanation
Indices: 39708688--39708719 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39708678 ACGTATTTTA
*
39708688 CATAATTTACATAATT
1 CATAATTTACAAAATT
39708704 CATAATTTACAAAATT
1 CATAATTTACAAAATT
39708720 TTTACTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
CATAATTTACAAAATT
Found at i:39710664 original size:66 final size:66
Alignment explanation
Indices: 39710594--39710729 Score: 227
Period size: 66 Copynumber: 2.1 Consensus size: 66
39710584 GACCACAGTT
* * *
39710594 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAGAGCAGATGCGGCAGCGAGAGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCAGATGCGGCAGCCAGAGAAGC
39710659 A
66 A
* *
39710660 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCTGATGCGGCATCCAGAGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCAGATGCGGCAGCCAGAGAAGC
39710725 A
66 A
39710726 GAGG
1 GAGG
39710730 CTGCAGCGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.14
Consensus pattern (66 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCAGATGCGGCAGCCAGAGAAGC
A
Found at i:39711083 original size:43 final size:43
Alignment explanation
Indices: 39711030--39711306 Score: 379
Period size: 43 Copynumber: 6.5 Consensus size: 43
39711020 AACCCCAAAA
* * *
39711030 TTAGTGGCGTTTTTTAAAAAAGCGCCGCTAAAGAACAT-TAGCT
1 TTAGCGGCGTTTTGTAAAAAAGCGCCGCTAAAGAACATGT-TCT
* *
39711073 TTAGCGGCGTTTGTGT-TAGAAGCGCCGCTAAAGAACATGTTCT
1 TTAGCGGCGTTT-TGTAAAAAAGCGCCGCTAAAGAACATGTTCT
*
39711116 TTAGCGGCGTTTGTGT-AAAAAGCGCCGCTAGAGAACATGTTCT
1 TTAGCGGCGTTT-TGTAAAAAAGCGCCGCTAAAGAACATGTTCT
39711159 TTAGCGGCG-TTTGTATAAAAAGCGCCGCTAAAGAACATGTTCT
1 TTAGCGGCGTTTTGTA-AAAAAGCGCCGCTAAAGAACATGTTCT
*
39711202 TTAGCGGCGTTTGTGT-AAAAAGCGCCGCTAGAGAACATGTTCT
1 TTAGCGGCGTTT-TGTAAAAAAGCGCCGCTAAAGAACATGTTCT
39711245 TTAGCGGCG-TTTGTATAAAAAGCGCCGCTAAAGAACATGTTCT
1 TTAGCGGCGTTTTGTA-AAAAAGCGCCGCTAAAGAACATGTTCT
*
39711288 TTAGCGGCGCTTT-TAAAAA
1 TTAGCGGCGTTTTGTAAAAA
39711307 TAAACGCCGC
Statistics
Matches: 214, Mismatches: 11, Indels: 19
0.88 0.05 0.08
Matches are distributed among these distances:
41 6 0.03
42 8 0.04
43 189 0.88
44 8 0.04
45 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTTGTAAAAAAGCGCCGCTAAAGAACATGTTCT
Found at i:39711182 original size:86 final size:86
Alignment explanation
Indices: 39711046--39711296 Score: 441
Period size: 86 Copynumber: 2.9 Consensus size: 86
39711036 GCGTTTTTTA
* * * * *
39711046 AAAAAGCGCCGCTAAAGAACAT-TAGCTTTAGCGGCGTTTGTGTTAGAAGCGCCGCTAAAGAACA
1 AAAAAGCGCCGCTAGAGAACATGT-TCTTTAGCGGCGTTTGTATAAAAAGCGCCGCTAAAGAACA
39711110 TGTTCTTTAGCGGCGTTTGTGT
65 TGTTCTTTAGCGGCGTTTGTGT
39711132 AAAAAGCGCCGCTAGAGAACATGTTCTTTAGCGGCGTTTGTATAAAAAGCGCCGCTAAAGAACAT
1 AAAAAGCGCCGCTAGAGAACATGTTCTTTAGCGGCGTTTGTATAAAAAGCGCCGCTAAAGAACAT
39711197 GTTCTTTAGCGGCGTTTGTGT
66 GTTCTTTAGCGGCGTTTGTGT
39711218 AAAAAGCGCCGCTAGAGAACATGTTCTTTAGCGGCGTTTGTATAAAAAGCGCCGCTAAAGAACAT
1 AAAAAGCGCCGCTAGAGAACATGTTCTTTAGCGGCGTTTGTATAAAAAGCGCCGCTAAAGAACAT
39711283 GTTCTTTAGCGGCG
66 GTTCTTTAGCGGCG
39711297 CTTTTAAAAA
Statistics
Matches: 159, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
86 158 0.99
87 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (86 bp):
AAAAAGCGCCGCTAGAGAACATGTTCTTTAGCGGCGTTTGTATAAAAAGCGCCGCTAAAGAACAT
GTTCTTTAGCGGCGTTTGTGT
Found at i:39711265 original size:129 final size:129
Alignment explanation
Indices: 39711046--39711296 Score: 432
Period size: 129 Copynumber: 1.9 Consensus size: 129
39711036 GCGTTTTTTA
* *
39711046 AAAAAGCGCCGCTAAAGAACATTAGCTTTAGCGGCGTTTGTGTTAGAAGCGCCGCTAAAGAACAT
1 AAAAAGCGCCGCTAAAGAACATTAGCTTTAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGAACAT
* *
39711111 GTTCTTTAGCGGCGTTTGTGTAAAAAGCGCCGCTAGAGAACATGTTCTTTAGCGGCGTTTGTAT
66 GTTCTTTAGCGGCGTTTGTATAAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAT
* *
39711175 AAAAAGCGCCGCTAAAGAACATGT-TCTTTAGCGGCGTTTGTGTAAAAAGCGCCGCTAGAGAACA
1 AAAAAGCGCCGCTAAAGAACAT-TAGCTTTAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGAACA
39711239 TGTTCTTTAGCGGCGTTTGTATAAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG
65 TGTTCTTTAGCGGCGTTTGTATAAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG
39711297 CTTTTAAAAA
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
129 114 0.99
130 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (129 bp):
AAAAAGCGCCGCTAAAGAACATTAGCTTTAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGAACAT
GTTCTTTAGCGGCGTTTGTATAAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAT
Found at i:39712175 original size:6 final size:6
Alignment explanation
Indices: 39712166--39712190 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39712156 TATAATAACA
39712166 ATATTT ATATTT ATATTT ATATTT A
1 ATATTT ATATTT ATATTT ATATTT A
39712191 ATCAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:39716764 original size:42 final size:42
Alignment explanation
Indices: 39716633--39716770 Score: 118
Period size: 42 Copynumber: 3.3 Consensus size: 42
39716623 CGAAGCAATC
* * * **
39716633 ATACTGGTACATAAGTGCATCATCTG-ATGTACCAAAGAAAAT
1 ATACTGGCACGTAAGTGAATCAT-TGAATGTACTGAAGAAAAT
* * * * * *
39716675 ATTCTGACACGTAAGTGAATCATCGAGGTATACTGAAG-CAAT
1 ATACTGGCACGTAAGTGAATCATTGA-ATGTACTGAAGAAAAT
* *
39716717 CATACTGGCATGTAAGTGTATCATTGAATGTACTGAAGAAAAT
1 -ATACTGGCACGTAAGTGAATCATTGAATGTACTGAAGAAAAT
39716760 ATACTGGCACG
1 ATACTGGCACG
39716771 CAACTGCATC
Statistics
Matches: 72, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
41 1 0.01
42 40 0.56
43 31 0.43
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (42 bp):
ATACTGGCACGTAAGTGAATCATTGAATGTACTGAAGAAAAT
Found at i:39716782 original size:85 final size:85
Alignment explanation
Indices: 39716624--39716782 Score: 203
Period size: 85 Copynumber: 1.9 Consensus size: 85
39716614 CGGTTAAACC
* * *
39716624 GAAGCAATCATACTGGTACATAAGTGCATCATCTGATGTACCAAAGAAAATATTCTGACACGTAA
1 GAAGCAATCATACTGGCACATAAGTGCATCATCTGATGTACCAAAGAAAATATACTGACACGCAA
*
39716689 GTGAATCATCGAGGTATACT
66 CTGAATCATCGAGGTATACT
** * ** *
39716709 GAAGCAATCATACTGGCATGTAAGTGTATCAT-TGAATGTACTGAAGAAAATATACTGGCACGCA
1 GAAGCAATCATACTGGCACATAAGTGCATCATCTG-ATGTACCAAAGAAAATATACTGACACGCA
*
39716773 ACTGCATCAT
65 ACTGAATCAT
39716783 TAGCTAAACC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
84 2 0.03
85 60 0.97
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (85 bp):
GAAGCAATCATACTGGCACATAAGTGCATCATCTGATGTACCAAAGAAAATATACTGACACGCAA
CTGAATCATCGAGGTATACT
Found at i:39721384 original size:3 final size:3
Alignment explanation
Indices: 39721376--39721404 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39721366 GATGTAAAGT
39721376 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
39721405 TTCTTTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:39725673 original size:20 final size:19
Alignment explanation
Indices: 39725627--39725665 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
39725617 TTTATTCGAA
* *
39725627 TCCAAAAAAGTAAATCATT
1 TCCAGAAAAGTAAACCATT
39725646 TCCAGAAAAGTAAACCATT
1 TCCAGAAAAGTAAACCATT
39725665 T
1 T
39725666 TTCTGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.26
Consensus pattern (19 bp):
TCCAGAAAAGTAAACCATT
Found at i:39728609 original size:23 final size:23
Alignment explanation
Indices: 39728583--39728628 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
39728573 TTTATTTCTC
39728583 TTCAACTCACTATACTATTTTTA
1 TTCAACTCACTATACTATTTTTA
*
39728606 TTCAACTCACTATATTATTTTTA
1 TTCAACTCACTATACTATTTTTA
39728629 AACAAGCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (23 bp):
TTCAACTCACTATACTATTTTTA
Found at i:39736900 original size:246 final size:243
Alignment explanation
Indices: 39736442--39736906 Score: 544
Period size: 243 Copynumber: 1.9 Consensus size: 243
39736432 TAATATGCAA
* * * ** *
39736442 TACCTAGATTCATTTAGTCACATTTCAATTATTAATGATAAAATGAACTTTTTTTTATACACAAT
1 TACCCAGATCCATTTAGTCACATTTCAATTATCAATGATAAAATGAAAATTCTTTTATACACAAT
* * * * *
39736507 TATATTCATAATAAAAATGCAGAATTAGATAATTGGTGAATACAAGTGAATAAGACACTATAATA
66 TATATTCACAACAAAAAGGCAGAATTAGATAATTGGTAAATACAAATGAATAAGACACTATAATA
* * * *
39736572 ATACTCCTTTCTTGTATCTCTATATCTATTCGACTGCTCTCTAGACATGTCTTGTTAAATCGAAT
131 ATACTCCTTTCTTGCATCTCTATATCAATTCAACTGCTCTCTAGA-ATGTCTTATTAAATCGAAT
39736637 TATGCATCACCATTGATAAGGTATTAAAATATCTAACAATTATATGTAG
195 TATGCATCACCATTGATAAGGTATTAAAATATCTAACAATTATATGTAG
* *
39736686 TACCCAGATCCATTTAGTCACATTTCAATTATCAATGATAAAAT-AAAATTCTTTTATTCACTAT
1 TACCCAGATCCATTTAGTCACATTTCAATTATCAATGATAAAATGAAAATTCTTTTATACACAAT
* * *
39736750 TATATTCACAACAAAAAGGCATAATTGGA-ACATTGGTAAATATAAATGAATGAA-ACACTATAA
66 TATATTCACAACAAAAAGGCAGAATTAGATA-ATTGGTAAATACAAATGAAT-AAGACACTATAA
** ** * *
39736813 TGATATTTTATTTTTCTTGCATCACTCTATTTCAA-TCTAATTGCTCTCTAG-ATGTCTTATTAA
129 T-A-ATACT-CCTTTCTTGCAT--CTCTATATCAATTC-AACTGCTCTCTAGAATGTCTTATTAA
** * *
39736876 ATCGAATTATGTGTGACTATTGATAAGGTAT
188 ATCGAATTATGCATCACCATTGATAAGGTAT
39736907 CGAGATAGTT
Statistics
Matches: 183, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
242 1 0.01
243 66 0.36
244 44 0.24
245 3 0.02
246 47 0.26
247 2 0.01
248 20 0.11
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (243 bp):
TACCCAGATCCATTTAGTCACATTTCAATTATCAATGATAAAATGAAAATTCTTTTATACACAAT
TATATTCACAACAAAAAGGCAGAATTAGATAATTGGTAAATACAAATGAATAAGACACTATAATA
ATACTCCTTTCTTGCATCTCTATATCAATTCAACTGCTCTCTAGAATGTCTTATTAAATCGAATT
ATGCATCACCATTGATAAGGTATTAAAATATCTAACAATTATATGTAG
Found at i:39737803 original size:20 final size:20
Alignment explanation
Indices: 39737758--39737806 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
39737748 TTCATTCTTT
39737758 TTTTTTTAAGATTTTATGAA
1 TTTTTTTAAGATTTTATGAA
** *
39737778 AATTTTTATAG-TTTTTTGAA
1 TTTTTTTA-AGATTTTATGAA
39737798 TTTTTTTAA
1 TTTTTTTAA
39737807 ATATTTTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
19 1 0.04
20 20 0.87
21 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTTTTTAAGATTTTATGAA
Found at i:39743229 original size:21 final size:21
Alignment explanation
Indices: 39743177--39743300 Score: 69
Period size: 21 Copynumber: 6.0 Consensus size: 21
39743167 TCGTGTTTAC
*
39743177 TTTCCGTTTAGCT-CTCATGAG
1 TTTCCGTTTAACTCCT-ATGAG
* * *
39743198 CTTCAG-TTAACTCATATGAG
1 TTTCCGTTTAACTCCTATGAG
39743218 TTTCCGTTTAAC-CCTA-GTAGG
1 TTTCCGTTTAACTCCTATG-A-G
* * *
39743239 TTTCCGTTTAGCTCTTTTGAG
1 TTTCCGTTTAACTCCTATGAG
* * *
39743260 CTTCAGTTTAAC-CCTTATGGG
1 TTTCCGTTTAACTCC-TATGAG
* *
39743281 TTTCCATTTAGCTCCTATGA
1 TTTCCGTTTAACTCCTATGA
39743301 ACTTCTGTTC
Statistics
Matches: 74, Mismatches: 21, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
19 1 0.01
20 19 0.26
21 48 0.65
22 5 0.07
23 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TTTCCGTTTAACTCCTATGAG
Found at i:39743283 original size:42 final size:42
Alignment explanation
Indices: 39743212--39743334 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
39743202 AGTTAACTCA
* * * *
39743212 TATGAGTTTCCGTTTAACCC-TAGTAGGTTTCCGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTA-TGGGTTTCCGTTTAGCTCC
* *
39743254 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCCATTTAGCTCC
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTTAGCTCC
* * * *
39743296 TATGAACTTCTGTTCAACCCTTATGGGTTTCTGTTTAGC
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTTAGC
39743335 ACTCATGTGC
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 66 0.97
43 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTTAGCTCC
Found at i:39743348 original size:42 final size:42
Alignment explanation
Indices: 39743237--39743350 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
39743227 AACCCTAGTA
* * * * * *
39743237 GGTTTCCGTTTAGCTCTTTTGAGCTTCAGTTTAACCCTTATG
1 GGTTTCCATTTAGCACCTATGAGCTTCTGTTCAACCCTTATG
* *
39743279 GGTTTCCATTTAGCTCCTATGAACTTCTGTTCAACCCTTATG
1 GGTTTCCATTTAGCACCTATGAGCTTCTGTTCAACCCTTATG
** *
39743321 GGTTTCTGTTTAGCA-CTCATGTGCTTCTGT
1 GGTTTCCATTTAGCACCT-ATGAGCTTCTGT
39743351 ATAGCCTTCG
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.03
42 58 0.97
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (42 bp):
GGTTTCCATTTAGCACCTATGAGCTTCTGTTCAACCCTTATG
Found at i:39744873 original size:50 final size:50
Alignment explanation
Indices: 39744749--39744997 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
39744739 GATAATAACA
* *** * *
39744749 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-GGGGACCTCTCAT-CTCGG
* *
39744800 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
39744850 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
39744900 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAAGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T--CGG
* *
39744956 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
39744998 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 96 0.57
51 29 0.17
53 2 0.01
54 1 0.01
56 40 0.24
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:39744926 original size:100 final size:103
Alignment explanation
Indices: 39744748--39744997 Score: 337
Period size: 100 Copynumber: 2.4 Consensus size: 103
39744738 TGATAATAAC
***
39744748 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCGTGATGGTGCCCATGCCATG
* *
39744813 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAG
* * *
39744849 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
39744913 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAAG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTT-AAG
* *
39744955 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
39744998 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
99 1 0.01
100 53 0.40
101 32 0.24
103 3 0.02
104 1 0.01
106 41 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (103 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAG
Done.