Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 84 of 202
Found at i:24907926 original size:28 final size:28
Alignment explanation
Indices: 24907886--24908015 Score: 154
Period size: 28 Copynumber: 4.6 Consensus size: 28
24907876 ATCTTTATTA
24907886 AAAGGAAGTCTTTGTGGCGATCTCTGTT
1 AAAGGAAGTCTTTGTGGCGATCTCTGTT
*
24907914 AAAGGAA-TCCTTTGTGGTGATCTCTGTT
1 AAAGGAAGT-CTTTGTGGCGATCTCTGTT
* ** *
24907942 AAAGGAATTCTTTGTAACGATCTTTGTT
1 AAAGGAAGTCTTTGTGGCGATCTCTGTT
* *
24907970 AAAGGAAGTCTTTATGGCTATCTCTGTT
1 AAAGGAAGTCTTTGTGGCGATCTCTGTT
* *
24907998 AAAAGGATGACTTTGTGG
1 -AAAGGAAGTCTTTGTGG
24908016 TCTCAATTAA
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
27 1 0.01
28 69 0.81
29 15 0.18
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (28 bp):
AAAGGAAGTCTTTGTGGCGATCTCTGTT
Found at i:24909505 original size:14 final size:15
Alignment explanation
Indices: 24909478--24909513 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
24909468 AGGTTTATGA
24909478 ATTATGGAATTAGGG
1 ATTATGGAATTAGGG
24909493 ATTATGG-ATTAGGG
1 ATTATGGAATTAGGG
24909507 ATTATGG
1 ATTATGG
24909514 TTTAAGGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
ATTATGGAATTAGGG
Found at i:24909670 original size:133 final size:132
Alignment explanation
Indices: 24909533--24909772 Score: 340
Period size: 133 Copynumber: 1.8 Consensus size: 132
24909523 TGTGATTTAG
* * * *
24909533 GGGTTAGGGGTTAGATATTAAGAGTTAGGGATTTAAGGTTTATG-GATTCAGTGTTAGGTTAGGG
1 GGGTTAGAGGTTAGATATTAAGAGTTAGGGATTTAAGATTTA-GAGATTCAGGGTCAGGTTAGGG
**
24909597 TTTAGGGTTTAGATTAATTAGTGT-TTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTAGTA
65 TTTAAAGTTTAGATTAATTA-T-TATTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTAGTA
24909661 GTTAA
128 GTTAA
* * ** *
24909666 GGGTTAGAGGTTAGATGTTAAGAGTTAGTGATTTAAGATTTAGAGATTTGGGGTCGGGTTAGGGT
1 GGGTTAGAGGTTAGATATTAAGAGTTAGGGATTTAAGATTTAGAGATTCAGGGTCAGGTTAGGGT
24909731 TTAAAGTTTAGATTAATTATTATTTTTTAATTTATATATTAA
66 TTAAAGTTTAGATTAATTATTATTTTTTAATTTATATATTAA
24909773 TTAAGTTATT
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
131 1 0.01
132 22 0.23
133 71 0.76
ACGTcount: A:0.29, C:0.01, G:0.27, T:0.43
Consensus pattern (132 bp):
GGGTTAGAGGTTAGATATTAAGAGTTAGGGATTTAAGATTTAGAGATTCAGGGTCAGGTTAGGGT
TTAAAGTTTAGATTAATTATTATTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTAGTAGTT
AA
Found at i:24909672 original size:21 final size:21
Alignment explanation
Indices: 24909648--24909693 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
24909638 TAAATAAAGT
* *
24909648 TTAGGGGTTAG-TAGTTAAGGG
1 TTAGAGGTTAGAT-GTTAAGAG
24909669 TTAGAGGTTAGATGTTAAGAG
1 TTAGAGGTTAGATGTTAAGAG
24909690 TTAG
1 TTAG
24909694 TGATTTAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
TTAGAGGTTAGATGTTAAGAG
Found at i:24909810 original size:7 final size:7
Alignment explanation
Indices: 24909798--24909832 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
24909788 ATTGTAAAAG
24909798 AGGGGTT
1 AGGGGTT
24909805 AGGGGTT
1 AGGGGTT
24909812 AGGGGTT
1 AGGGGTT
24909819 AGGGGTT
1 AGGGGTT
*
24909826 ATGGGTT
1 AGGGGTT
24909833 TAGGAGATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.00, G:0.54, T:0.31
Consensus pattern (7 bp):
AGGGGTT
Found at i:24911526 original size:3 final size:3
Alignment explanation
Indices: 24911518--24911550 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
24911508 ACACACCTAT
24911518 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
24911551 TTATTAGCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:24914587 original size:43 final size:43
Alignment explanation
Indices: 24914515--24914799 Score: 326
Period size: 43 Copynumber: 6.7 Consensus size: 43
24914505 GGGAAGGGTT
* *
24914515 GCTAAAGGT-TTGTTCTATAGCGGCATTTGTGGGAAAAGCGCC
1 GCTAAAGGTATTGATCTATAGCGGCGTTTGTGGGAAAAGCGCC
* * * *
24914557 GCTAAAGGTATTGAGCTATAGCGACGTTTGTAGAAAAAGCGCC
1 GCTAAAGGTATTGATCTATAGCGGCGTTTGTGGGAAAAGCGCC
** *
24914600 GCTAAAGGTCGTGATCTATAGCGGCGTTTGTGGGAAAAACGCC
1 GCTAAAGGTATTGATCTATAGCGGCGTTTGTGGGAAAAGCGCC
* * * *
24914643 GCTAAAGGTCTTAAGCTATAGCGGCGTTTGTTGGAAAAGCGCC
1 GCTAAAGGTATTGATCTATAGCGGCGTTTGTGGGAAAAGCGCC
* **
24914686 GCTAAAGGTCA-TGATCTATAGCGCCGTTTGT-CCAAAAGCGCC
1 GCTAAAGGT-ATTGATCTATAGCGGCGTTTGTGGGAAAAGCGCC
** * * *
24914728 GCTAAAGGTCCTGATCTATAGCGGCATTTGTTGCAAAAGCGCC
1 GCTAAAGGTATTGATCTATAGCGGCGTTTGTGGGAAAAGCGCC
*
24914771 GCTAAAGGTCA-TGATCTATAGCAGCGTTT
1 GCTAAAGGT-ATTGATCTATAGCGGCGTTT
24914800 ATTTCTAAAA
Statistics
Matches: 207, Mismatches: 31, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
42 45 0.22
43 162 0.78
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (43 bp):
GCTAAAGGTATTGATCTATAGCGGCGTTTGTGGGAAAAGCGCC
Found at i:24914643 original size:86 final size:86
Alignment explanation
Indices: 24914515--24914799 Score: 394
Period size: 86 Copynumber: 3.3 Consensus size: 86
24914505 GGGAAGGGTT
* * * *
24914515 GCTAAAGGT-TTGTTCTATAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTATTGAGCTATAGC
1 GCTAAAGGTCATGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* *
24914579 GACGTTTGTAGAAAAAGCGCC
66 GGCGTTTGTTGAAAAAGCGCC
* * *
24914600 GCTAAAGGTCGTGATCTATAGCGGCGTTTGTGGGAAAAACGCCGCTAAAGGTCTTAAGCTATAGC
1 GCTAAAGGTCATGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
*
24914665 GGCGTTTGTTGGAAAAGCGCC
66 GGCGTTTGTTGAAAAAGCGCC
* ** * *
24914686 GCTAAAGGTCATGATCTATAGCGCCGTTTGT-CCAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
1 GCTAAAGGTCATGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
* *
24914750 GGCATTTGTTGCAAAAGCGCC
66 GGCGTTTGTTGAAAAAGCGCC
*
24914771 GCTAAAGGTCATGATCTATAGCAGCGTTT
1 GCTAAAGGTCATGATCTATAGCGGCGTTT
24914800 ATTTCTAAAA
Statistics
Matches: 178, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
85 82 0.46
86 96 0.54
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (86 bp):
GCTAAAGGTCATGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGAGCTATAGC
GGCGTTTGTTGAAAAAGCGCC
Found at i:24929855 original size:42 final size:42
Alignment explanation
Indices: 24929808--24929989 Score: 213
Period size: 42 Copynumber: 4.4 Consensus size: 42
24929798 GGCTTAACGC
* *
24929808 CTAGCAGGCTTATTGGCAGTGAAACAATATCAGACTTTACGT
1 CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGT
* * * *
24929850 CTAGCAGGCTTAATGTCAGTGCAATAATTTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGT
* * *
24929892 CTAGCAGGCTTAATACCGGTGAAATAATATCAGACTTTACGT
1 CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGT
* * * * *
24929934 CTAGCAGACTTAATGCCGGTGAAAC-ATTTCAGACTATATGT
1 CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGT
* *
24929975 CTCGCAGGCTAAATG
1 CTAGCAGGCTTAATG
24929990 TCGGTGTTCT
Statistics
Matches: 121, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 25 0.21
42 96 0.79
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (42 bp):
CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGT
Found at i:24929933 original size:84 final size:83
Alignment explanation
Indices: 24929792--24929984 Score: 235
Period size: 84 Copynumber: 2.3 Consensus size: 83
24929782 TGAAATTGAG
* * * * **
24929792 ATTTCAGGCTTAACGCCTAGCAGGCTTATTGGCAGTGAAACAATATCAGACTTTACGTCTAGCAG
1 ATTTCAGACTTTACGTCTAGCAGGCTTAATACCAGTGAAACAATATCAGACTTTACGTCTAGCAG
* *
24929857 GCTTAATGTCAGTGCAATA-
66 ACTTAATGCCAGTG-AA-AC
* *
24929876 ATTTCAGACTTTACGTCTAGCAGGCTTAATACCGGTGAAATAATATCAGACTTTACGTCTAGCAG
1 ATTTCAGACTTTACGTCTAGCAGGCTTAATACCAGTGAAACAATATCAGACTTTACGTCTAGCAG
*
24929941 ACTTAATGCCGGTGAAAC
66 ACTTAATGCCAGTGAAAC
* * *
24929959 ATTTCAGACTATATGTCTCGCAGGCT
1 ATTTCAGACTTTACGTCTAGCAGGCT
24929985 AAATGTCGGT
Statistics
Matches: 94, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
82 1 0.01
83 25 0.27
84 68 0.72
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (83 bp):
ATTTCAGACTTTACGTCTAGCAGGCTTAATACCAGTGAAACAATATCAGACTTTACGTCTAGCAG
ACTTAATGCCAGTGAAAC
Found at i:24931417 original size:344 final size:344
Alignment explanation
Indices: 24930790--24931824 Score: 2016
Period size: 344 Copynumber: 3.0 Consensus size: 344
24930780 TCGTAATTTG
*
24930790 TTATATTGTATATGAATTTAATAGCCATACTAAATTGGTTTATTTCCTCATGGATTTGCTAGTTT
1 TTATATTGTATATGAATTTAATAGCCATACAAAATTGGTTTATTTCCTCATGGATTTGCTAGTTT
24930855 GTAATGTCTTTGTTTTGTTTTAAATGGTCAAAAGAGAAGCTTAAAATTTTGCATGTTTAATATTA
66 GTAATGTCTTTGTTTTGTTTTAAATGGTCAAAAGAGAAGCTTAAAATTTTGCATGTTTAATATTA
24930920 GACCTAGCTTATCATATGTAACTGTTATAATTATTGAACTTTAATGAATGTCTGTTCTGAGTTGT
131 GACCTAGCTTATCATATGTAACTGTTATAATTATTGAACTTTAATGAATGTCTGTTCTGAGTTGT
24930985 GTTTTGATTAGTAATGGCTCTTAACCCTAATTCGGCAACGGATACGGGTTAGGGGTGTTACAAAT
196 GTTTTGATTAGTAATGGCTCTTAACCCTAATTCGGCAACGGATACGGGTTAGGGGTGTTACAAAT
*
24931050 GGTATTTCTACAGAAGTTTTTTCTACTAATAACATAATGAAATTTTTATCAATAGAAAATGGTAA
261 GGTATTTCTACAGAAGTTTTTTCTACTGATAACATAATGAAATTTTTATCAATAGAAAATGGTAA
24931115 ATGTTGATATATAAAATTA
326 ATGTTGATATATAAAATTA
24931134 TTATATTGTATATGAATTTAATAGCCATACAAAATTGGTTTATTTCCTCATGGATTTGCTAGTTT
1 TTATATTGTATATGAATTTAATAGCCATACAAAATTGGTTTATTTCCTCATGGATTTGCTAGTTT
24931199 GTAATGTCTTTGTTTTGTTTTAAATGGTCAAAAGAGAAGCTTAAAATTTTGCATGTTTAATATTA
66 GTAATGTCTTTGTTTTGTTTTAAATGGTCAAAAGAGAAGCTTAAAATTTTGCATGTTTAATATTA
*
24931264 GACCTAGCTTATCATATGTAACTGTTATAATTATTGAACTTTAATGAATGTCTGTTTTGAGTTGT
131 GACCTAGCTTATCATATGTAACTGTTATAATTATTGAACTTTAATGAATGTCTGTTCTGAGTTGT
*
24931329 GTTTTGATTAGTAATGGCTCTTAACCCTAATTCGGCAACGGATACAGGTTAGGGGTGTTACAAAT
196 GTTTTGATTAGTAATGGCTCTTAACCCTAATTCGGCAACGGATACGGGTTAGGGGTGTTACAAAT
24931394 GGTATTTCTACAGAAGTTTTTTCTACTGATAACATAATGAAATTTTTATCAATAGAAAATGGTAA
261 GGTATTTCTACAGAAGTTTTTTCTACTGATAACATAATGAAATTTTTATCAATAGAAAATGGTAA
24931459 ATGTTGATATATAAAATTA
326 ATGTTGATATATAAAATTA
*
24931478 TTATATTGTATATGAATTTAATAGCCATACAAAATTGGTTTATTTCCTTATGGATTTGCTAGTTT
1 TTATATTGTATATGAATTTAATAGCCATACAAAATTGGTTTATTTCCTCATGGATTTGCTAGTTT
24931543 GTAATGTCTTTGTTTTGTTTTAAATGGTCAAAAGAGAAGCTTAAAATTTTGCATGTTTAATATTA
66 GTAATGTCTTTGTTTTGTTTTAAATGGTCAAAAGAGAAGCTTAAAATTTTGCATGTTTAATATTA
24931608 GACCTAGCTTATCATATGTAACTGTTATAATTATTGAACTTTAATGAATGTCTGTTCTGAGTTGT
131 GACCTAGCTTATCATATGTAACTGTTATAATTATTGAACTTTAATGAATGTCTGTTCTGAGTTGT
*
24931673 GTTTTGATTAGTAATGGCTCTTAACCCTAATTCGGCAACGGATACGGGTTAGGGTTGTTACAAAT
196 GTTTTGATTAGTAATGGCTCTTAACCCTAATTCGGCAACGGATACGGGTTAGGGGTGTTACAAAT
24931738 GGTATTTCTACAGAAGTTTTTTCTACTGATAACATAATGAAATTTTTATCAATAGAAAATGGTAA
261 GGTATTTCTACAGAAGTTTTTTCTACTGATAACATAATGAAATTTTTATCAATAGAAAATGGTAA
24931803 ATGTTGATATATAAAATTA
326 ATGTTGATATATAAAATTA
24931822 TTA
1 TTA
24931825 CCTAATAATA
Statistics
Matches: 683, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
344 683 1.00
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (344 bp):
TTATATTGTATATGAATTTAATAGCCATACAAAATTGGTTTATTTCCTCATGGATTTGCTAGTTT
GTAATGTCTTTGTTTTGTTTTAAATGGTCAAAAGAGAAGCTTAAAATTTTGCATGTTTAATATTA
GACCTAGCTTATCATATGTAACTGTTATAATTATTGAACTTTAATGAATGTCTGTTCTGAGTTGT
GTTTTGATTAGTAATGGCTCTTAACCCTAATTCGGCAACGGATACGGGTTAGGGGTGTTACAAAT
GGTATTTCTACAGAAGTTTTTTCTACTGATAACATAATGAAATTTTTATCAATAGAAAATGGTAA
ATGTTGATATATAAAATTA
Found at i:24948754 original size:15 final size:15
Alignment explanation
Indices: 24948734--24948762 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24948724 GTCTTATAAC
24948734 AAGTTAAATAACAAT
1 AAGTTAAATAACAAT
24948749 AAGTTAAATAACAA
1 AAGTTAAATAACAA
24948763 GTAAACACAT
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:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (15 bp):
AAGTTAAATAACAAT
Found at i:24951089 original size:26 final size:26
Alignment explanation
Indices: 24951060--24951131 Score: 117
Period size: 26 Copynumber: 2.8 Consensus size: 26
24951050 AACACACCAA
* *
24951060 TATCCCAGCAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
24951086 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
24951112 TATCGTAGCAAAGCTGCCAG
1 TATCGCAGCAAAGCTGCCAG
24951132 CATGTCATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.18
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:24955283 original size:11 final size:11
Alignment explanation
Indices: 24955267--24955297 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
24955257 GTGGAAGGAA
24955267 AATTGTTCATG
1 AATTGTTCATG
24955278 AATTGTTCATG
1 AATTGTTCATG
24955289 AATTGTTCA
1 AATTGTTCA
24955298 AGTGATAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (11 bp):
AATTGTTCATG
Found at i:24955569 original size:23 final size:23
Alignment explanation
Indices: 24955496--24955571 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
24955486 AGTGTTATTG
*
24955496 ATCAGTGGTAGCTTCGGCTATAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
24955519 TTCAATGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
24955542 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
24955565 ATCAGTG
1 ATCAGTG
24955572 TGGCACTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:24960976 original size:26 final size:26
Alignment explanation
Indices: 24960938--24961018 Score: 135
Period size: 26 Copynumber: 3.1 Consensus size: 26
24960928 AACACACCAA
24960938 TATCGCAGTAAAGCTGCTAGTAACAG
1 TATCGCAGTAAAGCTGCTAGTAACAG
* *
24960964 TATCGCAGCAAAGTTGCTAGTAACAG
1 TATCGCAGTAAAGCTGCTAGTAACAG
*
24960990 TATCGCAGTAAAGCTGCCAGTAACAG
1 TATCGCAGTAAAGCTGCTAGTAACAG
24961016 TAT
1 TAT
24961019 ACTTCCTCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (26 bp):
TATCGCAGTAAAGCTGCTAGTAACAG
Found at i:24961540 original size:12 final size:12
Alignment explanation
Indices: 24961508--24961534 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
24961498 TACGGCCAAA
24961508 GCCTATGGAAAT
1 GCCTATGGAAAT
24961520 GCCTATGGAAAT
1 GCCTATGGAAAT
24961532 GCC
1 GCC
24961535 CTTGGAGGCC
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:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (12 bp):
GCCTATGGAAAT
Found at i:24964661 original size:33 final size:33
Alignment explanation
Indices: 24964595--24964663 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
24964585 ATCCTGCCAC
* * *
24964595 TGAGGAGAAGGCCACAAAAGGGCCGAAGGGAGA
1 TGAGCAGAAGGCCACAAAAGGACCGAAGCGAGA
*
24964628 TGAGCAGAAGGCCATAAAAGGACC-AGAGCGAGA
1 TGAGCAGAAGGCCACAAAAGGACCGA-AGCGAGA
24964661 TGA
1 TGA
24964664 AGAGAAGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.41, C:0.16, G:0.38, T:0.06
Consensus pattern (33 bp):
TGAGCAGAAGGCCACAAAAGGACCGAAGCGAGA
Found at i:24969197 original size:2 final size:2
Alignment explanation
Indices: 24969190--24969214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24969180 GAGAATGGAA
24969190 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
24969215 CAAAAACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24969856 original size:5 final size:5
Alignment explanation
Indices: 24969846--24969879 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
24969836 CATACATACA
*
24969846 CATAT CATAT CATAT CATAA CATAT CATAT -ATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT
24969880 AATAAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (5 bp):
CATAT
Found at i:24979876 original size:22 final size:22
Alignment explanation
Indices: 24979846--24979888 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
24979836 ACACCAAAAC
* *
24979846 AGGCTTTTAGCGGTGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
24979868 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
24979889 AGTGGCGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:24980030 original size:43 final size:42
Alignment explanation
Indices: 24979982--24980292 Score: 298
Period size: 43 Copynumber: 7.1 Consensus size: 42
24979972 TTCTAGAAAT
** **
24979982 AAACGCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTT-CAC
* * * *
24980025 AAACGCCGCTAAAAACTAAGACCTTTAGCGGCGCTTTTCCCACCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTT-----TCAC
* *
24980072 AAACACCGCTAAAGACCATGACCTTTAACGGCGCTTTTGTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTT-TCAC
* *
24980115 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTT-TCAC
* * * * *
24980158 AAACGCCGATAAAGACCATGACATTTTATCGGCGAATTTGTCAC
1 AAACGCCGCTAAAGACCATGAC-CTTTAGCGGCG-CTTTTTCAC
* * * *
24980202 AAACGCCGCTATAGAGCATGACCTTTAGGGGCGCTTTTGTCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTT-TCAC
* *
24980245 AAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTTTTTATCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGC-TTTT-TCAC
24980289 AAAC
1 AAAC
24980293 ACTGCTATAG
Statistics
Matches: 217, Mismatches: 42, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
42 3 0.01
43 133 0.61
44 42 0.19
45 3 0.01
47 36 0.17
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTCAC
Found at i:24980289 original size:87 final size:87
Alignment explanation
Indices: 24979982--24980343 Score: 351
Period size: 87 Copynumber: 4.1 Consensus size: 87
24979972 TTCTAGAAAT
** * * * *
24979982 AAACGCCGCTAAAGGTCATG-GTCTTTAGCGGCGCTTTTT-CCACAAACGCCGCTA-AAAACTAA
1 AAACGCCGCTAAAGACCATGACT-TTTAGCGGCGCTTTTTGTCACAAACGCCGCTATAGAAC-AT
24980044 GACCTTTAGCGGCGCTTTTCCCACCCA
64 GACCTTTAGCGGCGCTTTTCCCA---A
* * * *
24980071 CAAACACCGCTAAAGACCATGACCTTTAACGGCGC-TTTTGTCACAAACGCCGCTATAGACCATG
1 -AAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTTGTCACAAACGCCGCTATAGAACATG
*
24980135 ACCTTTAGCGGCGCTTTTCCCAC
65 ACCTTTAGCGGCGCTTTTCCCAA
* * ** *
24980158 AAACGCCGATAAAGACCATGACATTTTATCGGCG-AATTTGTCACAAACGCCGCTATAGAGCATG
1 AAACGCCGCTAAAGACCATGAC-TTTTAGCGGCGCTTTTTGTCACAAACGCCGCTATAGAACATG
* **
24980222 ACCTTTAGGGGCGCTTTTGTCAA
65 ACCTTTAGCGGCGCTTTTCCCAA
* * * * *
24980245 AAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTTTTTATCACAAACACTGCTATAGAACA-AA
1 AAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTTGTCACAAACGCCGCTATAGAACATGA
* ** *
24980309 TCTTTAGCAACG-TTTCTCGCAA
66 CCTTTAGCGGCGCTTT-TCCCAA
24980331 AAACGCCGCTAAA
1 AAACGCCGCTAAA
24980344 AACATATCAT
Statistics
Matches: 228, Mismatches: 37, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
85 3 0.01
86 56 0.25
87 97 0.43
89 4 0.02
90 65 0.29
91 3 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (87 bp):
AAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTTGTCACAAACGCCGCTATAGAACATGA
CCTTTAGCGGCGCTTTTCCCAA
Found at i:24985461 original size:11 final size:11
Alignment explanation
Indices: 24985447--24985506 Score: 56
Period size: 10 Copynumber: 5.7 Consensus size: 11
24985437 AAAATAAAAG
*
24985447 TTTAAAATCTT
1 TTTAAAATCAT
24985458 TTTAAAAT--T
1 TTTAAAATCAT
* *
24985467 TTTAAAA-AAA
1 TTTAAAATCAT
24985477 TTTAAAATC-T
1 TTTAAAATCAT
24985487 TTTAAAATTCAT
1 TTTAAAA-TCAT
24985499 TTTAAAAT
1 TTTAAAAT
24985507 TTTAAATCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
9 8 0.20
10 14 0.34
11 11 0.27
12 8 0.20
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTAAAATCAT
Found at i:24985505 original size:29 final size:29
Alignment explanation
Indices: 24985440--24985514 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 29
24985430 TATTATAAAA
24985440 ATAAAAGTTTAAAATCTTTTTAAAATTTTT
1 ATAAAA-TTTAAAATCTTTTTAAAATTTTT
*
24985470 AAAAAAATTTAAAATC-TTTTAAAATTCATTT
1 -ATAAAATTTAAAATCTTTTTAAAATT--TTT
*
24985501 -TAAAATTTTAAATC
1 ATAAAATTTAAAATC
24985515 ACGAAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 22 0.56
30 9 0.23
31 8 0.21
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (29 bp):
ATAAAATTTAAAATCTTTTTAAAATTTTT
Found at i:24985511 original size:30 final size:30
Alignment explanation
Indices: 24985440--24985512 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
24985430 TATTATAAAA
*
24985440 ATAAAAGTTTAAAATCTTTTTAAAATTTTT
1 ATAAAAATTTAAAATCTTTTTAAAATTTTT
*
24985470 AAAAAAATTTAAAATC-TTTTAAAATTCATTT
1 ATAAAAATTTAAAATCTTTTTAAAATT--TTT
*
24985501 -TAAAATTTTAAA
1 ATAAAAATTTAAA
24985513 TCACGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.27
30 24 0.65
31 3 0.08
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (30 bp):
ATAAAAATTTAAAATCTTTTTAAAATTTTT
Found at i:24985512 original size:20 final size:20
Alignment explanation
Indices: 24985447--24985509 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
24985437 AAAATAAAAG
*
24985447 TTTAAAATCTTTTTAAAATT
1 TTTAAAATCATTTTAAAATT
* *
24985467 TTTAAAA-AAATTTAAAATCT
1 TTTAAAATCATTTTAAAAT-T
24985487 TTTAAAATTCATTTTAAAATT
1 TTTAAAA-TCATTTTAAAATT
24985508 TT
1 TT
24985510 AAATCACGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.23
20 15 0.43
21 3 0.09
22 9 0.26
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAATCATTTTAAAATT
Found at i:24985914 original size:7 final size:7
Alignment explanation
Indices: 24985904--24985957 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
24985894 CACTAAAATG
*
24985904 TAAACTC
1 TAAACCC
*
24985911 TAAACCT
1 TAAACCC
*
24985918 TAAACTC
1 TAAACCC
*
24985925 TAATCCC
1 TAAACCC
* *
24985932 CAAGCCC
1 TAAACCC
24985939 TAAACCC
1 TAAACCC
24985946 TAAACCC
1 TAAACCC
24985953 TAAAC
1 TAAAC
24985958 TCAAAACTGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:24986866 original size:41 final size:41
Alignment explanation
Indices: 24986821--24986959 Score: 190
Period size: 41 Copynumber: 3.4 Consensus size: 41
24986811 ACGCTTTTTA
24986821 AAAAACGCCGCTAAAGGTACGAGCATTAGCGGTGCTTCTTC
1 AAAAACGCCGCTAAAGGTACGAGCATTAGCGGTGCTTCTTC
* * *
24986862 AAAAACGCTGCTAAAGGTAGGAGCATTAGCGGCT-CTTCTTA
1 AAAAACGCCGCTAAAGGTACGAGCATTAGCGG-TGCTTCTTC
* * *
24986903 AAAAACTCCGCTAAAGGTACGAGCATTAGCGGCGCTTTTTC
1 AAAAACGCCGCTAAAGGTACGAGCATTAGCGGTGCTTCTTC
* *
24986944 AAAAATGCCACTAAAG
1 AAAAACGCCGCTAAAG
24986960 ACCCCAAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 83 0.99
42 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGGTACGAGCATTAGCGGTGCTTCTTC
Found at i:24986958 original size:82 final size:82
Alignment explanation
Indices: 24986804--24986959 Score: 231
Period size: 82 Copynumber: 1.9 Consensus size: 82
24986794 TGATTTTATT
* *
24986804 ATTAGCGACGCTTTTTAAAAAACGCCGCTAAAGGTACGAGCATTAGCGGTGCTTCTTCAAAAACG
1 ATTAGCGACGCTTCTTAAAAAACGCCGCTAAAGGTACGAGCATTAGCGGCGCTTCTTCAAAAACG
**
24986869 CTGCTAAAGGTAGGAGC
66 CCACTAAAGGTAGGAGC
* * * * *
24986886 ATTAGCGGCTCTTCTTAAAAAACTCCGCTAAAGGTACGAGCATTAGCGGCGCTTTTTCAAAAATG
1 ATTAGCGACGCTTCTTAAAAAACGCCGCTAAAGGTACGAGCATTAGCGGCGCTTCTTCAAAAACG
24986951 CCACTAAAG
66 CCACTAAAG
24986960 ACCCCAAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (82 bp):
ATTAGCGACGCTTCTTAAAAAACGCCGCTAAAGGTACGAGCATTAGCGGCGCTTCTTCAAAAACG
CCACTAAAGGTAGGAGC
Found at i:24987150 original size:41 final size:40
Alignment explanation
Indices: 24986998--24987133 Score: 161
Period size: 40 Copynumber: 3.4 Consensus size: 40
24986988 TGGGCTTAGG
* **
24986998 TTTTTTGCGGCGCTTTTTGGAAAA-CGCCGCTAATGCTT-A
1 TTTTTAGCGGCG-TTTTTCTAAAAGCGCCGCTAATGCTTGA
* *
24987037 TTTTTAGCAGCG-TTTTCTAAAATGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCTAAAA-GCGCCGCTAATGCTTGA
* *
24987077 TCTTTAGCGGCGTTTTTCTAAAAGAGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTCTAAAAGCGCCGCTAATGCTTGA
*
24987117 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
24987134 TGTCCAAACG
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
37 8 0.10
39 23 0.28
40 41 0.50
41 10 0.12
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCTAAAAGCGCCGCTAATGCTTGA
Found at i:24987634 original size:27 final size:27
Alignment explanation
Indices: 24987577--24987637 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
24987567 GACTTTTTTT
* * *
24987577 GGGTGTTGTTTTGCTTTTGTTTGGTTT
1 GGGTTTTGTTTTACTTTTGTTTGGTTC
*
24987604 GGGTTTTGTTTTATTTTTG-TTGTGTTC
1 GGGTTTTGTTTTACTTTTGTTTG-GTTC
24987631 GGGTTTT
1 GGGTTTT
24987638 ATTTGTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.02, C:0.03, G:0.31, T:0.64
Consensus pattern (27 bp):
GGGTTTTGTTTTACTTTTGTTTGGTTC
Found at i:24989134 original size:6 final size:6
Alignment explanation
Indices: 24989125--24989153 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
24989115 AAAAATAAAG
24989125 TATTTA TATTTA TATTTA TATTTA TATTT
1 TATTTA TATTTA TATTTA TATTTA TATTT
24989154 TTTTAACAAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATTTA
Found at i:24989501 original size:30 final size:31
Alignment explanation
Indices: 24989465--24989542 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
24989455 TTAATATAAC
*
24989465 ATTTGGTACCTGAACTTGACA-TTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
* *
24989495 ATTTGGTACCTAAACTTGATACTTTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
* *
24989526 AGTTGGTACTTAAACTT
1 ATTTGGTACCTAAACTT
24989543 TTTTGGGTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 19 0.45
31 23 0.55
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:24989592 original size:59 final size:59
Alignment explanation
Indices: 24989492--24989605 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 59
24989482 GACATTTTTC
* * *
24989492 CTAATTTGGTACCTAAACTTGATACTTTTTCTTAAGTTGGTA-CTTAAACTTTTTTGGGT
1 CTAATTTGATACCTAAACTTGATACTTTCTCCTAAGTTGGTATC-TAAACTTTTTTGGGT
*
24989551 CTAATTTGATACCTAAACTTGACTA-TTTCTCCTAA-TCTGGTATCTAATCTTTTTT
1 CTAATTTGATACCTAAACTTGA-TACTTTCTCCTAAGT-TGGTATCTAAACTTTTTT
24989606 TTGTTTGTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
58 1 0.02
59 44 0.92
60 3 0.06
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (59 bp):
CTAATTTGATACCTAAACTTGATACTTTCTCCTAAGTTGGTATCTAAACTTTTTTGGGT
Found at i:24989986 original size:61 final size:59
Alignment explanation
Indices: 24989887--24990074 Score: 252
Period size: 60 Copynumber: 3.1 Consensus size: 59
24989877 ATTTAATACA
* * *
24989887 TTCAGGTACCATATTGGGCCCAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATGTCAAG
1 TTCAGGTACCATATTGGGCCCAAAAAAAATTT-TGTACCAAATTAAG-AAAAAGTGTCAAG
* *
24989948 TTCAGGTACCATATTGGGCCCAAAAAATACTTTTGTACCAAATTAGGAAAAAGTGTCAAG
1 TTCAGGTACCATATTGGGCCCAAAAAA-AATTTTGTACCAAATTAAGAAAAAGTGTCAAG
* * *
24990008 TTCAGGTACCAAATTGGGCCGAAAAAAAGATTAAT-TACCAAATTAAGAAAAAGTGTCAAG
1 TTCAGGTACCATATTGGGCCCAAAAAAA-ATT-TTGTACCAAATTAAGAAAAAGTGTCAAG
24990068 TTCAGGT
1 TTCAGGT
24990075 CCTAAATGTA
Statistics
Matches: 115, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
59 1 0.01
60 70 0.61
61 40 0.35
62 4 0.03
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (59 bp):
TTCAGGTACCATATTGGGCCCAAAAAAAATTTTGTACCAAATTAAGAAAAAGTGTCAAG
Found at i:24995228 original size:47 final size:46
Alignment explanation
Indices: 24995173--24995263 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
24995163 TAGGATTCTG
**
24995173 CTACTGCATAACTGTTACTGCTACTGATACTATGATGGGCTAAGGTC
1 CTACTGCATAACTGACACTG-TACTGATACTATGATGGGCTAAGGTC
*** *
24995220 CTACTGCATTTTTGACACTGTACTGATACTGTGATGGGCTAAGG
1 CTACTGCATAACTGACACTGTACTGATACTATGATGGGCTAAGG
24995264 CCCAAACTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
46 23 0.61
47 15 0.39
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (46 bp):
CTACTGCATAACTGACACTGTACTGATACTATGATGGGCTAAGGTC
Found at i:24996049 original size:26 final size:26
Alignment explanation
Indices: 24996018--24996079 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
24996008 CCTGTAAGTG
24996018 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATACATGCTATGATA
* *
24996044 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTGATACATGCTATGATA
*
24996070 TTTTGAAACT
1 TTCTGAAACT
24996080 ACTGTAGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGATA
Found at i:25002994 original size:34 final size:35
Alignment explanation
Indices: 25002951--25003017 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
25002941 TGTTACTGCT
** *
25002951 ACTGATACTGTGATGGGCTAAGGCCCAA-ACTGGC
1 ACTGATACTGAAAAGGGCTAAGGCCCAATACTGGC
*
25002985 ACTGATACTGAAAAGGGCTTAGGCCCAATACTG
1 ACTGATACTGAAAAGGGCTAAGGCCCAATACTG
25003018 TTTAACTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (35 bp):
ACTGATACTGAAAAGGGCTAAGGCCCAATACTGGC
Found at i:25025138 original size:2 final size:2
Alignment explanation
Indices: 25025131--25025165 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25025121 CTTTTAGGTT
25025131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25025166 TTATGAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25025327 original size:14 final size:14
Alignment explanation
Indices: 25025304--25025341 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
25025294 GTTTGCCAGT
*
25025304 AAAATGATTTCTAG
1 AAAATGATTTCTAA
*
25025318 AAAATAATTTCTAA
1 AAAATGATTTCTAA
25025332 AAAATGATTT
1 AAAATGATTT
25025342 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCTAA
Found at i:25025357 original size:19 final size:19
Alignment explanation
Indices: 25025333--25025370 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25025323 AATTTCTAAA
25025333 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
25025352 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
25025371 TGTTTGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
AAATGATTTACTTTTCTGG
Found at i:25027584 original size:20 final size:20
Alignment explanation
Indices: 25027559--25027598 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25027549 AATATTTTCT
*
25027559 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
25027579 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
25027599 TCATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:25027601 original size:34 final size:35
Alignment explanation
Indices: 25027547--25027613 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
25027537 CAAACAGCAG
* *
25027547 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
25027582 AAAACATTTTCCAG-AAATCATTTTATAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
25027614 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:25027605 original size:14 final size:14
Alignment explanation
Indices: 25027582--25027621 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
25027572 ACAGAAAAGT
*
25027582 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
25027596 AAATCATTTTATAG
1 AAAACATTTTACAG
25027610 AAAACATTTTAC
1 AAAACATTTTAC
25027622 TGGCAATCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:25028988 original size:30 final size:31
Alignment explanation
Indices: 25028942--25029004 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
25028932 TAAATATTTT
25028942 AATATGTAATTTTTTTATTTCATGTAGTTTC
1 AATATGTAATTTTTTTATTTCATGTAGTTTC
25028973 AATATGTAA-TTTTTTATTTCATGTAGTTTC
1 AATATGTAATTTTTTTATTTCATGTAGTTTC
25029003 AA
1 AA
25029005 ACTTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.56
Consensus pattern (31 bp):
AATATGTAATTTTTTTATTTCATGTAGTTTC
Found at i:25034841 original size:18 final size:18
Alignment explanation
Indices: 25034820--25034862 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
25034810 ACAATTTAAA
25034820 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
25034838 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
25034856 ATGTAAA
1 ATATAAA
25034863 AACAGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:25034966 original size:19 final size:20
Alignment explanation
Indices: 25034942--25034983 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
25034932 CAAACACCAA
*
25034942 AAAAGTAAATCATT-TCCAG
1 AAAAGTAAAACATTCTCCAG
25034961 AAAAGTAAAACATTCTCCAG
1 AAAAGTAAAACATTCTCCAG
25034981 AAA
1 AAA
25034984 TCATTTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (20 bp):
AAAAGTAAAACATTCTCCAG
Found at i:25037604 original size:24 final size:25
Alignment explanation
Indices: 25037548--25037604 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
25037538 TATTTCAAAC
* *
25037548 ATTATAAAAGAAGAGAAATAATATA
1 ATTAGAAAAAAAGAGAAATAATATA
* *
25037573 A-AAGAAAAAAAGAGAAATAATTTA
1 ATTAGAAAAAAAGAGAAATAATATA
25037597 ATTA-AAAA
1 ATTAGAAAA
25037605 TATTTTTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (25 bp):
ATTAGAAAAAAAGAGAAATAATATA
Found at i:25043930 original size:13 final size:13
Alignment explanation
Indices: 25043901--25043929 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25043891 AACAAGTTGC
25043901 TTTTGGCTGAAAT
1 TTTTGGCTGAAAT
25043914 TTTTGGCT-AAAT
1 TTTTGGCTGAAAT
25043926 TTTT
1 TTTT
25043930 TAATTTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (13 bp):
TTTTGGCTGAAAT
Found at i:25047774 original size:23 final size:22
Alignment explanation
Indices: 25047721--25047774 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
25047711 TTTTCTGGAT
*
25047721 AATATATATTAATTAAATGAAAA
1 AATAT-TATTAATTAAATAAAAA
* *
25047744 TATAATTATTAATTACTATAAAAA
1 AAT-ATTATTAATTA-AATAAAAA
25047768 AATATTA
1 AATATTA
25047775 GTATGATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AATATTATTAATTAAATAAAAA
Found at i:25052862 original size:11 final size:11
Alignment explanation
Indices: 25052840--25052883 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
25052830 TGAATGTTTG
25052840 AATAACTTTAAA
1 AATAA-TTTAAA
25052852 AATAATTT-AA
1 AATAATTTAAA
*
25052862 AATCATTTAAA
1 AATAATTTAAA
*
25052873 AATAGTTTAAA
1 AATAATTTAAA
25052884 GTGAATTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 9 0.32
11 14 0.50
12 5 0.18
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (11 bp):
AATAATTTAAA
Found at i:25055010 original size:54 final size:54
Alignment explanation
Indices: 25054880--25055030 Score: 144
Period size: 54 Copynumber: 2.8 Consensus size: 54
25054870 AGCCCACCAA
* * * * ****
25054880 GACAATAAACATTAGATAGTCCACCAGGATAGGAAAAACATTATAGTCCGCTGG
1 GACAGTAAACATGAGATAGTCCACAAGGATAGTAAAAACGGGGTAGTCCGCTGG
* * * *
25054934 GACAGTAAATATGATATTGTCCAC-TGTGATAGTAAAAACGGGGTAGTCCG-TGAG
1 GACAGTAAACATGAGATAGTCCACAAG-GATAGTAAAAACGGGGTAGTCCGCTG-G
* *
25054988 GACAGTAAACATGGGATAGTCCACAAGGATAGTAAAAATGGGG
1 GACAGTAAACATGAGATAGTCCACAAGGATAGTAAAAACGGGG
25055031 CAACCTGCCA
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
53 3 0.04
54 73 0.95
55 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (54 bp):
GACAGTAAACATGAGATAGTCCACAAGGATAGTAAAAACGGGGTAGTCCGCTGG
Found at i:25057419 original size:34 final size:35
Alignment explanation
Indices: 25057376--25057459 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 35
25057366 CATTCACATT
*
25057376 AATCACATATTCAATAGTCCTCCTGCATAGTG-AA
1 AATCACATATTCAATAGTCCTCCTACATAGTGAAA
*
25057410 AATCACATATTCAATGGTCCTCCTACATAGTGAAA
1 AATCACATATTCAATAGTCCTCCTACATAGTGAAA
25057445 AATCACATATT-AATA
1 AATCACATATTCAATA
25057460 AATTAGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
34 33 0.72
35 13 0.28
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (35 bp):
AATCACATATTCAATAGTCCTCCTACATAGTGAAA
Found at i:25077663 original size:71 final size:71
Alignment explanation
Indices: 25077547--25077737 Score: 203
Period size: 71 Copynumber: 2.7 Consensus size: 71
25077537 ATCATATCAT
* *
25077547 CCTACAATTATATACAAAAAGTTATATTACTCCACCACCACACCCAAT-TACACATACAAAAAAG
1 CCTACAATTACATACAAAAAGTGATATTACTCCACCACCACACCC-ATCTACACATACAAAAAAG
25077611 TGCAAAA
65 TGCAAAA
* * **
25077618 CCTACAATTACATACAAAAAGTGATATTAGTTCACCACTGCACCCATCTACACATAC-AAAAAGT
1 CCTACAATTACATACAAAAAGTGATATTACTCCACCACCACACCCATCTACACATACAAAAAAGT
*
25077682 GACGAAA
66 G-CAAAA
* * * *
25077689 -CT-CTATGACATACAAAATGTTATATT-CATCCACCACCACAGCCACATCT
1 CCTACAATTACATACAAAAAGTGATATTAC-TCCACCACCACA-CC-CATCT
25077738 TTAATGGGTA
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
69 29 0.29
70 14 0.14
71 57 0.57
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.23
Consensus pattern (71 bp):
CCTACAATTACATACAAAAAGTGATATTACTCCACCACCACACCCATCTACACATACAAAAAAGT
GCAAAA
Found at i:25080557 original size:40 final size:40
Alignment explanation
Indices: 25080481--25080557 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
25080471 ATTTGAAAAA
* * * * *
25080481 GATTTAAATCGATTGTAACTGGTTTAAATTGCTTGTAACT
1 GATTTAAATCAATTGAAACTGATTTAAATCGATTGTAACT
25080521 GATTTAAATCAATTGAAACAT-ATTTAAATCGATTGTA
1 GATTTAAATCAATTGAAAC-TGATTTAAATCGATTGTA
25080558 GCATATTTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 30 0.97
41 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.40
Consensus pattern (40 bp):
GATTTAAATCAATTGAAACTGATTTAAATCGATTGTAACT
Found at i:25080562 original size:20 final size:20
Alignment explanation
Indices: 25080442--25080565 Score: 83
Period size: 20 Copynumber: 6.2 Consensus size: 20
25080432 GATGAAATAA
** *
25080442 ATTTAAATCGATTGTAGTAG
1 ATTTAAATCGATTGTAACAT
* * * *
25080462 ATTTAAAT-AATTTGAAAAAG
1 ATTTAAATCGA-TTGTAACAT
25080482 ATTTAAATCGATTGTAAC-T
1 ATTTAAATCGATTGTAACAT
* * *
25080501 GGTTTAAATTGCTTGTAAC-T
1 -ATTTAAATCGATTGTAACAT
* *
25080521 GATTTAAATCAATTGAAACAT
1 -ATTTAAATCGATTGTAACAT
*
25080542 ATTTAAATCGATTGTAGCAT
1 ATTTAAATCGATTGTAACAT
25080562 ATTT
1 ATTT
25080566 GGATCGAGTG
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.01
20 78 0.96
21 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (20 bp):
ATTTAAATCGATTGTAACAT
Found at i:25082520 original size:16 final size:18
Alignment explanation
Indices: 25082489--25082521 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
25082479 TAATTTTAGC
25082489 TCTCTATTTAAATTTTTA
1 TCTCTATTTAAATTTTTA
25082507 TCTCT-TTT-AATTTTT
1 TCTCTATTTAAATTTTT
25082522 GAACTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTCTATTTAAATTTTTA
Found at i:25083708 original size:41 final size:39
Alignment explanation
Indices: 25083663--25083754 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
25083653 ACTTGAACTC
* *
25083663 TTAGCGGCGTTTGGATAAAAAATGCCGCTAAAGATCTAGCA
1 TTAGCGGCGTTT-GATAAAAAATGCCGCTAAAAAT-AAGCA
** ** *
25083704 TTAGCGGCGTTTTTTGGAAAATGCCGCTAAAAATAAGTA
1 TTAGCGGCGTTTGATAAAAAATGCCGCTAAAAATAAGCA
25083743 TTAGCGGCGTTT
1 TTAGCGGCGTTT
25083755 TCTAAAAAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 15 0.34
40 17 0.39
41 12 0.27
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (39 bp):
TTAGCGGCGTTTGATAAAAAATGCCGCTAAAAATAAGCA
Found at i:25083929 original size:41 final size:41
Alignment explanation
Indices: 25083814--25084134 Score: 378
Period size: 41 Copynumber: 7.9 Consensus size: 41
25083804 CTTTCGGGGT
* *
25083814 TTTAGCGACGTTTTTGAGAAAGCGCAGCT-ATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * *
25083854 TTTAGCGACG-TTTTGAGAAAGTGCCGCTAGTGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * *
25083894 TTTAGCGGCGTTTCTGAGAAAGCGTCGCTAATGCTCAGGGT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * *
25083935 TTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGATCAAGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * * * *
25083976 TTTAGTGGCATTTTTGAGGAAGCGCTGCTAATGTTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * * *
25084017 TTTAGCGGCGTTTTTGAGGAAGCCCCGCTAATGATCAGGGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
** *
25084058 TTTAGCGGCGTTTTTGAGTTAGCGCCACTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
* * *
25084099 TTTAGCAGTGTTTTTGA-AGTAGCGCCGCTAATGCTC
1 TTTAGCGGCGTTTTTGAGA-AAGCGCCGCTAATGCTC
25084135 TATTTTTAGC
Statistics
Matches: 242, Mismatches: 36, Indels: 5
0.86 0.13 0.02
Matches are distributed among these distances:
39 16 0.07
40 29 0.12
41 197 0.81
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:25084163 original size:40 final size:40
Alignment explanation
Indices: 25084099--25084174 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
25084089 TGCTCAGGGC
**
25084099 TTTAGCAGTGTTTTTGAAGTAGCGCCGCTAATGCTCTATT
1 TTTAGCAGTGTTTTTGAAAAAGCGCCGCTAATGCTCTATT
*
25084139 TTTAGCAGTGTTTTCT-AAAAAGCGCCGCTCATGCTC
1 TTTAGCAGTGTTTT-TGAAAAAGCGCCGCTAATGCTC
25084175 AGAGATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (40 bp):
TTTAGCAGTGTTTTTGAAAAAGCGCCGCTAATGCTCTATT
Found at i:25085014 original size:60 final size:61
Alignment explanation
Indices: 25084919--25085049 Score: 228
Period size: 60 Copynumber: 2.1 Consensus size: 61
25084909 ACTCCATTGA
*
25084919 AATTTCGAAAGCCGAATGTTGAAACAATATGGTGATTCATTTATATAGGACTGAAATTTAAC
1 AATTTC-AAAGCCGAATGTTGAAACAAGATGGTGATTCATTTATATAGGACTGAAATTTAAC
*
25084981 AATTTCAAA-CCGAATGTTGAAACAGGATGGTGATTCATTTATATAGGACTGAAATTTAAC
1 AATTTCAAAGCCGAATGTTGAAACAAGATGGTGATTCATTTATATAGGACTGAAATTTAAC
25085041 AATTTCAAA
1 AATTTCAAA
25085050 AAATATATAT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
60 58 0.87
61 3 0.04
62 6 0.09
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (61 bp):
AATTTCAAAGCCGAATGTTGAAACAAGATGGTGATTCATTTATATAGGACTGAAATTTAAC
Found at i:25085252 original size:7 final size:7
Alignment explanation
Indices: 25085242--25085280 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
25085232 GATTTAAGGT
25085242 TTAGGGG
1 TTAGGGG
*
25085249 TTAGAGG
1 TTAGGGG
25085256 TTAGGGG
1 TTAGGGG
25085263 TTAGGGG
1 TTAGGGG
25085270 TTTAGGGG
1 -TTAGGGG
25085278 TTA
1 TTA
25085281 TGCTTTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.18, C:0.00, G:0.49, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:25085259 original size:14 final size:15
Alignment explanation
Indices: 25085238--25085280 Score: 70
Period size: 14 Copynumber: 2.9 Consensus size: 15
25085228 TTGGGATTTA
25085238 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
25085253 AGG-TTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
25085267 GGGTTTAGGGGTTA
1 AGGTTTAGGGGTTA
25085281 TGCTTTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.19, C:0.00, G:0.49, T:0.33
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:25085272 original size:50 final size:50
Alignment explanation
Indices: 25085218--25085328 Score: 127
Period size: 50 Copynumber: 2.2 Consensus size: 50
25085208 TATGGATTAT
* * *
25085218 GGTTTAAGGGTTGGGATTTAAGGTTTAGGGGTTA-GAGGTTAGGGGTTAGG
1 GGTTTAAGGGTTAGGATTTAAGATTTAGGGGTTATGA-GATAGGGGTTAGG
* * * * *
25085268 GGTTTAGGGGTTATGCTTTATGATTTAGGGTTTATGAGATAGGGGTTAGG
1 GGTTTAAGGGTTAGGATTTAAGATTTAGGGGTTATGAGATAGGGGTTAGG
25085318 GGTTT-AGGGTT
1 GGTTTAAGGGTT
25085329 TAGATTAATT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
49 5 0.10
50 44 0.86
51 2 0.04
ACGTcount: A:0.19, C:0.01, G:0.42, T:0.38
Consensus pattern (50 bp):
GGTTTAAGGGTTAGGATTTAAGATTTAGGGGTTATGAGATAGGGGTTAGG
Found at i:25089612 original size:43 final size:43
Alignment explanation
Indices: 25089564--25089736 Score: 265
Period size: 43 Copynumber: 4.0 Consensus size: 43
25089554 GATAAAAACA
* * *
25089564 CCGCTAAAGATCATGTTCTTTAACGGCGTTTGTGGGTAAAGAG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* *
25089607 TCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGTTAAAGCG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* *
25089650 CCGCTAAAGGTCAGGTTCTTTAGCGACGTTTGTGGGTAAAGCG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
* *
25089693 CCGCTAAATGTCATGTTCTTTAGCGGCGTTTGTAGGTAAAGCG
1 CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
25089736 C
1 C
25089737 AGAGGCGTTT
Statistics
Matches: 117, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 117 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.31
Consensus pattern (43 bp):
CCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCG
Found at i:25100588 original size:12 final size:13
Alignment explanation
Indices: 25100571--25100599 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25100561 CTCATACATG
25100571 AATAAATAAA-GC
1 AATAAATAAATGC
25100583 AATAAATAAATGC
1 AATAAATAAATGC
25100596 AATA
1 AATA
25100600 GTTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:25101831 original size:19 final size:19
Alignment explanation
Indices: 25101809--25101853 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
25101799 ATAAATATTT
25101809 TGATGTATAATATTAAATA
1 TGATGTATAATATTAAATA
* *
25101828 TGATATATTATATTAAATA
1 TGATGTATAATATTAAATA
*
25101847 TAATGTA
1 TGATGTA
25101854 ATATTTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (19 bp):
TGATGTATAATATTAAATA
Found at i:25101862 original size:19 final size:19
Alignment explanation
Indices: 25101818--25101865 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
25101808 TTGATGTATA
* *
25101818 ATATTAAATATGATATATT
1 ATATTAAATATAATATAAT
*
25101837 ATATTAAATATAATGTAAT
1 ATATTAAATATAATATAAT
*
25101856 ATTTTAAATA
1 ATATTAAATA
25101866 CTTCGTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATTAAATATAATATAAT
Found at i:25115975 original size:18 final size:18
Alignment explanation
Indices: 25115952--25115990 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
25115942 TATGGGTAAG
*
25115952 CCACACTGGCATGTGGGC
1 CCACACGGGCATGTGGGC
25115970 CCACACGGGCATGTGGGC
1 CCACACGGGCATGTGGGC
25115988 CCA
1 CCA
25115991 TAGTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.36, G:0.33, T:0.13
Consensus pattern (18 bp):
CCACACGGGCATGTGGGC
Found at i:25116211 original size:13 final size:13
Alignment explanation
Indices: 25116193--25116217 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25116183 AGCATGATAT
25116193 TTCTGTATCTATC
1 TTCTGTATCTATC
25116206 TTCTGTATCTAT
1 TTCTGTATCTAT
25116218 GATTGGGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (13 bp):
TTCTGTATCTATC
Found at i:25127879 original size:25 final size:25
Alignment explanation
Indices: 25127851--25127972 Score: 95
Period size: 25 Copynumber: 4.9 Consensus size: 25
25127841 AGCTCTTCCA
*
25127851 AGCTGAATAACGGGAAGCTCATGTG
1 AGCTGAATATCGGGAAGCTCATGTG
* **
25127876 AGCT-AAGTAACGGGAAGCTCATACG
1 AGCTGAA-TATCGGGAAGCTCATGTG
* * * **
25127901 AGATGTATATCGAGAAGCTCATAAG
1 AGCTGAATATCGGGAAGCTCATGTG
* * *
25127926 AGCTGAA-ATTGGAAAGCTCGTGTG
1 AGCTGAATATCGGGAAGCTCATGTG
* *
25127950 AGCTAAATATCAGGAAGCTCATG
1 AGCTGAATATCGGGAAGCTCATG
25127973 AGAACTTTGG
Statistics
Matches: 74, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
24 19 0.26
25 54 0.73
26 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (25 bp):
AGCTGAATATCGGGAAGCTCATGTG
Found at i:25135467 original size:25 final size:25
Alignment explanation
Indices: 25135439--25135520 Score: 119
Period size: 25 Copynumber: 3.3 Consensus size: 25
25135429 ATGTAAACAT
25135439 GAAGCTCTTCTGAGCTAAATAACGA
1 GAAGCTCTTCTGAGCTAAATAACGA
25135464 GAAGCTCTTCTGAGCTAAATAACGA
1 GAAGCTCTTCTGAGCTAAATAACGA
* * * * *
25135489 GAAGCTCATGTTAGCTAAGTAACGG
1 GAAGCTCTTCTGAGCTAAATAACGA
25135514 GAAGCTC
1 GAAGCTC
25135521 ATACGAGATG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (25 bp):
GAAGCTCTTCTGAGCTAAATAACGA
Found at i:25135627 original size:37 final size:35
Alignment explanation
Indices: 25135570--25135640 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
25135560 CGGGAATCAT
*
25135570 ATTAAATTAATAAAATACTATTAATATAAGTATTAA
1 ATTAAATTAATAAAATACTATTAAGATAA-TATTAA
*
25135606 ATTAAATTTAATATTAA-ACTATTAAGATAATATTA
1 ATTAAA-TTAATA-AAATACTATTAAGATAATATTA
25135641 CTTTTGGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 11 0.35
37 18 0.58
38 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAGATAATATTAA
Found at i:25136619 original size:38 final size:38
Alignment explanation
Indices: 25136568--25136645 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
25136558 AAGTTTGTTA
25136568 TTGTTGAAAAAGTATGGAAATGATGTTATAGTAGAGTT
1 TTGTTGAAAAAGTATGGAAATGATGTTATAGTAGAGTT
25136606 TTGTTGAAAAAGTATGGAAATGATGTTATAGTAGAGTT
1 TTGTTGAAAAAGTATGGAAATGATGTTATAGTAGAGTT
25136644 TT
1 TT
25136646 CTTAAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (38 bp):
TTGTTGAAAAAGTATGGAAATGATGTTATAGTAGAGTT
Found at i:25142932 original size:12 final size:12
Alignment explanation
Indices: 25142917--25142949 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
25142907 ATTTTTATTC
*
25142917 TTATAATTACAT
1 TTATAAATACAT
25142929 TTATAAATACAT
1 TTATAAATACAT
25142941 TTATAAATA
1 TTATAAATA
25142950 AAATTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (12 bp):
TTATAAATACAT
Found at i:25143215 original size:73 final size:73
Alignment explanation
Indices: 25143095--25143240 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
25143085 AAAACCTTAC
25143095 CAGGAAAACTCAATGGGACAAAATCTCGGTTAAGGGAAAAAGAGTACAGTGTGTATTTACTCCCC
1 CAGGAAAACTCAATGGGACAAAATCTCGGTTAAGGGAAAAAGAGTACAGTGTGTATTTACTCCCC
25143160 CTCATGAA
66 CTCATGAA
* *
25143168 CAGGAAAACTCAATGGGACAAAATTTCGGTTAAGGGAAAAAGCGTACAGTGTGTATTTACTCCCC
1 CAGGAAAACTCAATGGGACAAAATCTCGGTTAAGGGAAAAAGAGTACAGTGTGTATTTACTCCCC
25143233 CTCATGAA
66 CTCATGAA
25143241 AACATCACAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (73 bp):
CAGGAAAACTCAATGGGACAAAATCTCGGTTAAGGGAAAAAGAGTACAGTGTGTATTTACTCCCC
CTCATGAA
Found at i:25152180 original size:11 final size:11
Alignment explanation
Indices: 25152163--25152199 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
25152153 ATAGGTATAC
25152163 GAAGTATAAAT
1 GAAGTATAAAT
*
25152174 AAAGTAT-AA-
1 GAAGTATAAAT
25152183 GAAGTATAAAT
1 GAAGTATAAAT
25152194 GAAGTA
1 GAAGTA
25152200 GATGTCTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 6 0.27
10 4 0.18
11 12 0.55
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24
Consensus pattern (11 bp):
GAAGTATAAAT
Found at i:25152186 original size:20 final size:20
Alignment explanation
Indices: 25152157--25152199 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
25152147 CTATTTATAG
*
25152157 GTATACGAAGTATAAATAAA
1 GTATAAGAAGTATAAATAAA
*
25152177 GTATAAGAAGTATAAATGAA
1 GTATAAGAAGTATAAATAAA
25152197 GTA
1 GTA
25152200 GATGTCTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.19, T:0.26
Consensus pattern (20 bp):
GTATAAGAAGTATAAATAAA
Found at i:25152459 original size:13 final size:13
Alignment explanation
Indices: 25152441--25152468 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
25152431 TACGCGTTTA
25152441 ATTTTTAATTATT
1 ATTTTTAATTATT
25152454 ATTTTTAATTATT
1 ATTTTTAATTATT
25152467 AT
1 AT
25152469 AATCATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTTAATTATT
Found at i:25153072 original size:17 final size:18
Alignment explanation
Indices: 25153050--25153087 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25153040 ATCACAAATT
25153050 TTATTAAA-TTATAAGTA
1 TTATTAAATTTATAAGTA
*
25153067 TTATTAAATTTATAATTA
1 TTATTAAATTTATAAGTA
25153085 TTA
1 TTA
25153088 AAAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTATTAAATTTATAAGTA
Found at i:25153118 original size:58 final size:58
Alignment explanation
Indices: 25152996--25153115 Score: 143
Period size: 58 Copynumber: 2.1 Consensus size: 58
25152986 ATAATAAATG
* * * **
25152996 TAAATTATAATTATTTTTAAATATATGATTATTAAATTATAATTATCACAAATTTTAT
1 TAAATTATAAGTATTATTAAATATATAATTATTAAAAAATAATTATCACAAATTTTAT
* * *
25153054 TAAATTATAAGTATTATTAAATTTATAATTATTAAAAAATTATTTTACATCAAATTTT-T
1 TAAATTATAAGTATTATTAAATATATAATTATTAAAAAATAATTAT-CA-CAAATTTTAT
25153113 TAA
1 TAA
25153116 TTAATAATTC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
58 38 0.73
59 6 0.12
60 8 0.15
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (58 bp):
TAAATTATAAGTATTATTAAATATATAATTATTAAAAAATAATTATCACAAATTTTAT
Found at i:25155344 original size:16 final size:16
Alignment explanation
Indices: 25155323--25155353 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25155313 TATATTAGTG
25155323 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
25155339 CATATATATTTGAAA
1 CATATAAATTTGAAA
25155354 ATTTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:25155567 original size:19 final size:20
Alignment explanation
Indices: 25155545--25155592 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
25155535 TTTTTATAGA
25155545 TATTTTGAAT-TTT-AAAATT
1 TATTTTGAATATTTGAAAA-T
25155564 TATTTTGAATATTTGAAAAT
1 TATTTTGAATATTTGAAAAT
25155584 TATTTTGAA
1 TATTTTGAA
25155593 CTTTGTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.37
20 13 0.48
21 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TATTTTGAATATTTGAAAAT
Found at i:25155913 original size:20 final size:20
Alignment explanation
Indices: 25155876--25155914 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25155866 AATATAAAAA
* * *
25155876 TAACTAAGTTTTTTATTAAT
1 TAACTAAATTGTTAATTAAT
25155896 TAACTAAATTGTTAATTAA
1 TAACTAAATTGTTAATTAA
25155915 GTAGGAGTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
TAACTAAATTGTTAATTAAT
Found at i:25157713 original size:21 final size:21
Alignment explanation
Indices: 25157688--25157745 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
25157678 TATTTGATTC
25157688 CAATCAAATTGATTTAATTTT
1 CAATCAAATTGATTTAATTTT
25157709 CAATCAAATTGATTTAATTTT
1 CAATCAAATTGATTTAATTTT
*
25157730 TAATCAAATTGATTTA
1 CAATCAAATTGATTTA
25157746 TTAGCTCCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (21 bp):
CAATCAAATTGATTTAATTTT
Found at i:25158660 original size:87 final size:85
Alignment explanation
Indices: 25158520--25158750 Score: 212
Period size: 88 Copynumber: 2.6 Consensus size: 85
25158510 TTATTCCCAC
* * * * *
25158520 ACGGTTTTTATTTCATTTTGTTATTTTATTTCCAAACAGGA-AATTAAAGTTAAATAAGATCCGT
1 ACGG-TTTTATTACATTTTG--ATTTTATTTCCAAA-ACGAGAATTAAAATTAAATAAAATACGT
** * ** *
25158584 TTCGGGATTTATTCTCGCTGTTTA
62 TTCAAGATTTATTCCCGCCATTCA
* * *
25158608 ACAGGTTTTATTCCACTTTTGATTTTATTTCCAAAACGAGTATTAAAATTAAAATAAAATATGTT
1 AC-GGTTTTATTACA-TTTTGATTTTATTTCCAAAACGAGAATTAAAATT-AAATAAAATACGTT
25158673 TCAAGATTTATTCCCGCCATTCA
63 TCAAGATTTATTCCCGCCATTCA
* * * *
25158696 ACTGATTTATTACATTTTGATTATGTTTCCAAAAACGAGAAATTAAAATTAAATA
1 ACGGTTTTATTACATTTTGATTTTATTTCC-AAAACGAG-AATTAAAATTAAATA
25158751 CAATTTTTTT
Statistics
Matches: 118, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
86 17 0.14
87 44 0.37
88 50 0.42
89 7 0.06
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (85 bp):
ACGGTTTTATTACATTTTGATTTTATTTCCAAAACGAGAATTAAAATTAAATAAAATACGTTTCA
AGATTTATTCCCGCCATTCA
Found at i:25158768 original size:87 final size:87
Alignment explanation
Indices: 25158614--25158774 Score: 200
Period size: 87 Copynumber: 1.9 Consensus size: 87
25158604 TTTAACAGGT
* * *
25158614 TTTATTCCACTTTTGATTTTATTTCCAAAACGAGTATTAAAATTAAAATAAAATATGTTTCAAGA
1 TTTATTACACTTTTGATTATATTTCCAAAACGAGAATTAAAATTAAAATAAAATATGTTTCAAGA
*
25158679 TTTATTCCCGCCATTCAACTGA
66 TTTAATCCCGCCATTCAACTGA
* * * * **
25158701 TTTATTACA-TTTTGATTATGTTTCCAAAAACGAGAAATTAAAATT-AAATACAATTTTTTTCGG
1 TTTATTACACTTTTGATTATATTTCC-AAAACGAG-AATTAAAATTAAAATAAAATATGTTTCAA
25158764 GATTTAATCCC
64 GATTTAATCCC
25158775 ATCGTTTAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
86 14 0.23
87 39 0.63
88 9 0.15
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (87 bp):
TTTATTACACTTTTGATTATATTTCCAAAACGAGAATTAAAATTAAAATAAAATATGTTTCAAGA
TTTAATCCCGCCATTCAACTGA
Found at i:25159046 original size:84 final size:84
Alignment explanation
Indices: 25158561--25159136 Score: 533
Period size: 83 Copynumber: 6.8 Consensus size: 84
25158551 CCAAACAGGA
* * * **
25158561 AATTAAAGTTAAATAAGATCCGTTTCGGGATTTATTCTCGC-T-GTTTAAC-AGGTTTTATTCCA
1 AATTAAA-TTAAATAAAATCTGTTTCGGGATTTATTC-C-CATCGTTTAACAAGATTTTATTTGA
* **
25158623 CTTTTGATTTTATTTCCAAAACGAG
63 -TTTT-ATTTTGTTTCC-AAATTAG
* * ** ** * * * **
25158648 TATTAAAATTAAAATAAAATATGTTTCAAGATTTATTCCCGCCATTCAAC-TGA-TTTATTACAT
1 AATT-AAATT-AAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTATTTGAT
* **
25158711 TTTGATTATGTTTCCAAAAACGAG
64 TTT-ATTTTGTTTCC--AAATTAG
* * * * * * *
25158735 AAATTAAAATTAAATACAATTTTTTTCGGGATTTAATCCCATCGTTTAATAAGATTATATTTTAT
1 -AATT-AAATTAAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTATTTGAT
*
25158800 TTTATTTTGTCTCCAAATTAG
64 TTTATTTTGTTTCCAAATTAG
* *
25158821 AATTAGAATGAAATAAAATCTGTTTCGGGATTTATTACCGC-T-GTTTAACAAAATTTTATTTGA
1 AATTA-AATTAAATAAAATCTGTTTCGGGATTTATT-CC-CATCGTTTAACAAGATTTTATTTGA
*
25158884 TTTTATTTTGTTTCTAAATTAG
63 TTTTATTTTGTTTCCAAATTAG
* * *
25158906 AATTAAATTAAA-AAAATATGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTT
1 AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTATTTGATTT
25158970 TATTTTGTTTCCAAATTAG
66 TATTTTGTTTCCAAATTAG
* * *
25158989 AATGAAATTAAATAAAATCTGTTTCGAGATTTATTCCCATCGTTTAACAAGATTTTATTTTATTT
1 AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTATTTGATTT
25159054 TATTTT-TTTCCAAATTAG
66 TATTTTGTTTCCAAATTAG
* * * * *
25159072 AATTAAATGAAATAAAATCTATTTCGGGATTTATTCCCGTTGTTTAAC-ATATTTTATTTTGATT
1 AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTA-TTTGATT
25159136 T
65 T
25159137 AATTATTTAA
Statistics
Matches: 412, Mismatches: 62, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
81 1 0.00
82 10 0.02
83 133 0.32
84 62 0.15
85 71 0.17
86 23 0.06
87 51 0.12
88 51 0.12
89 10 0.02
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (84 bp):
AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTATTTGATTT
TATTTTGTTTCCAAATTAG
Found at i:25159046 original size:167 final size:168
Alignment explanation
Indices: 25158758--25159136 Score: 525
Period size: 167 Copynumber: 2.3 Consensus size: 168
25158748 ATACAATTTT
* * * * *
25158758 TTTCGGGATTTAATCCCATCGTTTAATAAGATTATATTTTATTTTATTTTGTCTCCAAATTAGAA
1 TTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTTTGTCTCCAAATTAGAA
* *
25158823 TTAGAATGAAATAAAATCTGTTTCGGGATTTATTACCGCTGTTTAACAAAATTTTATTTGATTTT
66 TGAGAATGAAATAAAATCTGTTTCGAGATTTATTACCGCTGTTTAACAAAATTTTATTTGATTTT
* * *
25158888 ATTTTGTTTCTAAATTAGAATTAAATTAAA-AAAATATG
131 ATTTT-TTTCCAAATTAGAATTAAATGAAATAAAATATA
* *
25158926 TTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTTTGTTTCCAAATTAGAA
1 TTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTTTGTCTCCAAATTAGAA
* * *
25158991 TGA-AATTAAATAAAATCTGTTTCGAGATTTATT-CC-CATCGTTTAACAAGATTTTATTTTATT
66 TGAGAATGAAATAAAATCTGTTTCGAGATTTATTACCGC-T-GTTTAACAAAATTTTATTTGATT
*
25159053 TTATTTTTTTCCAAATTAGAATTAAATGAAATAAAATCTA
129 TTATTTTTTTCCAAATTAGAATTAAATGAAATAAAATATA
* *
25159093 TTTCGGGATTTATTCCCGTTGTTTAAC-ATATTTTATTTTGATTT
1 TTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTA-TTTGATTT
25159137 AATTATTTAA
Statistics
Matches: 188, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
165 1 0.01
166 32 0.17
167 95 0.51
168 60 0.32
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.47
Consensus pattern (168 bp):
TTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTTTGTCTCCAAATTAGAA
TGAGAATGAAATAAAATCTGTTTCGAGATTTATTACCGCTGTTTAACAAAATTTTATTTGATTTT
ATTTTTTTCCAAATTAGAATTAAATGAAATAAAATATA
Found at i:25159902 original size:31 final size:31
Alignment explanation
Indices: 25159861--25159926 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
25159851 TGTTAAGAAA
25159861 ATAATGAAGGAATTATGGACATCGTTGGACC
1 ATAATGAAGGAATTATGGACATCGTTGGACC
*
25159892 ATAATTAAGGAATTATGGACATCGTTGGACC
1 ATAATGAAGGAATTATGGACATCGTTGGACC
25159923 ATAA
1 ATAA
25159927 ATAATTAGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (31 bp):
ATAATGAAGGAATTATGGACATCGTTGGACC
Found at i:25165493 original size:22 final size:22
Alignment explanation
Indices: 25165460--25165504 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
25165450 TTTATTTATA
25165460 TTTATTTTATATATAAATAATTT
1 TTTATTTTATATATAAAT-ATTT
*
25165483 TTTA-TTTATATTTAAATATTT
1 TTTATTTTATATATAAATATTT
25165504 T
1 T
25165505 GTTCGTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 12 0.57
23 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATTTTATATATAAATATTT
Found at i:25169123 original size:18 final size:18
Alignment explanation
Indices: 25169100--25169135 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
25169090 TGCCAGGTGC
*
25169100 GTATCCTATCCCTTATAT
1 GTATCCTAACCCTTATAT
25169118 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
25169136 ATTTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:25169355 original size:21 final size:21
Alignment explanation
Indices: 25169331--25169374 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
25169321 CCCACAACCA
*
25169331 GAGCAACTACAACCCCCGTCG
1 GAGCAACCACAACCCCCGTCG
*
25169352 GAGCAACCAGAACCCCCGTCG
1 GAGCAACCACAACCCCCGTCG
25169373 GA
1 GA
25169375 AGTTGAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.41, G:0.23, T:0.07
Consensus pattern (21 bp):
GAGCAACCACAACCCCCGTCG
Found at i:25170073 original size:126 final size:125
Alignment explanation
Indices: 25169812--25170132 Score: 489
Period size: 125 Copynumber: 2.6 Consensus size: 125
25169802 ATACCGGAAC
* * **
25169812 AAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATAATTTTTTCAGGAACTGTTGTA
1 AAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTA-TTTTTCAGGAACTACTGTA
*
25169877 GAAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGTAATTTTGCTAACAGTGCATCCTACTTG
65 GAAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGTAATTTTGCTAACAATGCATCCTACTTG
*
25169938 AAGCATTTTTGACACTATTTGTTCAAAACCGTATTCTCAAAATTATTTTTCAGGAACTACTGTAG
1 AAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTCAGGAACTACTGTAG
* ** * * * *
25170003 AAAAAGAGCGTCCACGTGGGTGCTTTTTTTAGTAATTTTGCTGACAATGTATCTTGCTTG
66 AAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGTAATTTTGCTAACAATGCATCCTACTTG
* * *
25170063 AAGCGTTTTTTACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTAGGAACTACTGTAG
1 AAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTCAGGAACTACTGTAG
25170128 AAAAA
66 AAAAA
25170133 AATCCTTATT
Statistics
Matches: 178, Mismatches: 17, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
125 136 0.76
126 42 0.24
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (125 bp):
AAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTCAGGAACTACTGTAG
AAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGTAATTTTGCTAACAATGCATCCTACTTG
Found at i:25170235 original size:34 final size:33
Alignment explanation
Indices: 25170187--25170296 Score: 132
Period size: 34 Copynumber: 3.3 Consensus size: 33
25170177 CACAATATTA
*
25170187 TTTTAAAAAAACTAAACCTTAATTTAATTAATT
1 TTTTAAAAACACTAAACCTTAATTTAATTAATT
25170220 TTCTTAAAAACACTAAACCCTT-ATTTAATTAATT
1 TT-TTAAAAACACTAAA-CCTTAATTTAATTAATT
* * * *
25170254 TATTTTAAACCCCTAAACCCTAATTTAATTAATT
1 T-TTTAAAAACACTAAACCTTAATTTAATTAATT
*
25170288 TTTAAAAAA
1 TTTTAAAAA
25170297 GAACACTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
33 10 0.15
34 50 0.77
35 5 0.08
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.41
Consensus pattern (33 bp):
TTTTAAAAACACTAAACCTTAATTTAATTAATT
Found at i:25170397 original size:14 final size:15
Alignment explanation
Indices: 25170360--25170395 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
25170350 TTATTTGAAC
*
25170360 AAAACCCTAACCCTA
1 AAAACCCTAAACCTA
*
25170375 AAAACCCTAAACCAA
1 AAAACCCTAAACCTA
25170390 AAAACC
1 AAAACC
25170396 TAGGGACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (15 bp):
AAAACCCTAAACCTA
Found at i:25171929 original size:38 final size:35
Alignment explanation
Indices: 25171886--25171981 Score: 111
Period size: 38 Copynumber: 2.6 Consensus size: 35
25171876 AACACATTAA
* * *
25171886 AAATATATTAAAAATATTTATATTAAAAACACTACCAT
1 AAATATAATAAATAT-TTTATATTAAAAACAC-A-AAT
25171924 AAATATAATAAATATTTTATCATATTAAAAACACAAAT
1 AAATATAATAAATA-TTT-T-ATATTAAAAACACAAAT
25171962 AAATATAATAAATATTTTAT
1 AAATATAATAAATATTTTAT
25171982 TGTATTAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
35 2 0.04
36 1 0.02
37 3 0.06
38 30 0.58
39 3 0.06
40 13 0.25
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (35 bp):
AAATATAATAAATATTTTATATTAAAAACACAAAT
Found at i:25171988 original size:38 final size:40
Alignment explanation
Indices: 25171905--25171990 Score: 131
Period size: 38 Copynumber: 2.2 Consensus size: 40
25171895 AAAAATATTT
*
25171905 ATATTAAAAACACTACCATAAATATAATAAATATTTTATC
1 ATATTAAAAACACTACAATAAATATAATAAATATTTTATC
*
25171945 ATATTAAAAACAC-A-AATAAATATAATAAATATTTTATT
1 ATATTAAAAACACTACAATAAATATAATAAATATTTTATC
*
25171983 GTATTAAA
1 ATATTAAA
25171991 TATAAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 29 0.67
39 1 0.02
40 13 0.30
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.36
Consensus pattern (40 bp):
ATATTAAAAACACTACAATAAATATAATAAATATTTTATC
Found at i:25172361 original size:2 final size:2
Alignment explanation
Indices: 25172354--25172397 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
25172344 TGAGTTGTAA
25172354 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25172396 AT
1 AT
25172398 TTCTTGTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25173565 original size:9 final size:9
Alignment explanation
Indices: 25173551--25173589 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
25173541 GTTTAAGAGG
25173551 AGAAAAAGA
1 AGAAAAAGA
25173560 AGAAAAAGA
1 AGAAAAAGA
**
25173569 AG-AGGAGA
1 AGAAAAAGA
25173577 AGAAAAAGA
1 AGAAAAAGA
25173586 AGAA
1 AGAA
25173590 GAAGGAGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (9 bp):
AGAAAAAGA
Found at i:25173572 original size:23 final size:23
Alignment explanation
Indices: 25173545--25173606 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
25173535 TTTAGGGTTT
25173545 AAGAGGAGAA-AAAGAAGAAAAAG
1 AAGAGGAGAAGAAA-AAGAAAAAG
*
25173568 AAGAGGAGAAGAAAAAGAAGAAG
1 AAGAGGAGAAGAAAAAGAAAAAG
*
25173591 AAGGAGAAG-AGAAAAA
1 AA-GAGGAGAAGAAAAA
25173607 ATGGAGATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 27 0.77
24 8 0.23
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (23 bp):
AAGAGGAGAAGAAAAAGAAAAAG
Found at i:25173587 original size:26 final size:26
Alignment explanation
Indices: 25173545--25173607 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
25173535 TTTAGGGTTT
*
25173545 AAGAGGAGAAAAAGAAGAAAAAGAAG
1 AAGAGAAGAAAAAGAAGAAAAAGAAG
* * *
25173571 AGGAGAAGAAAAAGAAGAAGAAGGAG
1 AAGAGAAGAAAAAGAAGAAAAAGAAG
25173597 AAGAGAA-AAAA
1 AAGAGAAGAAAA
25173608 TGGAGATGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (26 bp):
AAGAGAAGAAAAAGAAGAAAAAGAAG
Found at i:25174129 original size:3 final size:3
Alignment explanation
Indices: 25174121--25174150 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
25174111 GAAAAGAGCC
*
25174121 AAG AAG AAG AAG AAG AGG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
25174151 GGCAAAGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:25174444 original size:30 final size:31
Alignment explanation
Indices: 25174391--25174459 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
25174381 ACTATTAATC
* *
25174391 AGTGGCTGTTTTGTCATTTTTTTATAACGTT-
1 AGTGACTGTTTTGTCATTTTTTTA-AAAGTTG
*
25174422 AGTGACTGTTTTGTTA-TTTTTTAAAAGTTG
1 AGTGACTGTTTTGTCATTTTTTTAAAAGTTG
25174452 AGTGACTG
1 AGTGACTG
25174460 AAATGAAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 15 0.44
31 14 0.41
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.51
Consensus pattern (31 bp):
AGTGACTGTTTTGTCATTTTTTTAAAAGTTG
Found at i:25175450 original size:32 final size:31
Alignment explanation
Indices: 25175403--25175462 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
25175393 TACTTATCAA
* *
25175403 TTATTTATTATCATTTTAGTATATTTTTATG
1 TTATTAATTATCATTTTAGTAAATTTTTATG
*
25175434 TTATTAATATATCATTTTGGTAAATTTTT
1 TTATTAAT-TATCATTTTAGTAAATTTTT
25175463 TTAATTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (31 bp):
TTATTAATTATCATTTTAGTAAATTTTTATG
Found at i:25179605 original size:88 final size:87
Alignment explanation
Indices: 25179457--25179623 Score: 246
Period size: 88 Copynumber: 1.9 Consensus size: 87
25179447 AAAATTTAAC
* * * * *
25179457 TTCTTCTGTGCCTAAAAACATTACTCATAAATTGATTTTTCCAATAATTGCTATTAGACCAGGTT
1 TTCTTCTATACCTAAAAACACTACTCATAAATTAATTTTTCCAATAATTGCTATAAGACCAGGTT
25179522 GTG-TCATGTTTATAGTATAAAA
66 GTGCT-ATGTTTATAGTATAAAA
* *
25179544 TTCTTCTATACCTAAAAACACTGCTCACTAAATTAATTTTTCCAATAATTGGTATAAGACCAGGT
1 TTCTTCTATACCTAAAAACACTACTCA-TAAATTAATTTTTCCAATAATTGCTATAAGACCAGGT
25179609 TGTGCTATGTTTATA
65 TGTGCTATGTTTATA
25179624 ATAAATTGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
87 23 0.32
88 47 0.66
89 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (87 bp):
TTCTTCTATACCTAAAAACACTACTCATAAATTAATTTTTCCAATAATTGCTATAAGACCAGGTT
GTGCTATGTTTATAGTATAAAA
Found at i:25181083 original size:27 final size:27
Alignment explanation
Indices: 25181053--25181125 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
25181043 GGGGGTGGTG
*
25181053 CCTATCTGATAGGCGGTACTAGTGACC
1 CCTATCTGATAGGCGGCACTAGTGACC
* * * *
25181080 CCTATCTGGTAGGCAGCATTGGTGACC
1 CCTATCTGATAGGCGGCACTAGTGACC
* *
25181107 CCTATTTAATAGGCGGCAC
1 CCTATCTGATAGGCGGCAC
25181126 CAGTATTAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (27 bp):
CCTATCTGATAGGCGGCACTAGTGACC
Found at i:25181224 original size:22 final size:22
Alignment explanation
Indices: 25181209--25181251 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
25181199 AAGAAGAGAG
25181209 GAAG-AAGAAAGAAAGAAAGGA
1 GAAGAAAGAAAGAAAGAAAGGA
25181230 GAAGAAAGAAAGAAAGGAAAGG
1 GAAGAAAGAAAGAAA-GAAAGG
25181252 TATTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 10 0.50
23 6 0.30
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (22 bp):
GAAGAAAGAAAGAAAGAAAGGA
Found at i:25181232 original size:18 final size:18
Alignment explanation
Indices: 25181211--25181247 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
25181201 GAAGAGAGGA
25181211 AGAAGAAAGAAAGAAAGG
1 AGAAGAAAGAAAGAAAGG
25181229 AGAAGAAAGAAAGAAAGG
1 AGAAGAAAGAAAGAAAGG
25181247 A
1 A
25181248 AAGGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AGAAGAAAGAAAGAAAGG
Found at i:25181720 original size:20 final size:19
Alignment explanation
Indices: 25181695--25181732 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
25181685 TTAGCACAAA
25181695 ATGAGA-AAGTTGATAAGATG
1 ATGAGAGAA-TTG-TAAGATG
25181715 ATGAGAGAATTGTAAGAT
1 ATGAGAGAATTGTAAGAT
25181733 TACCATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 9 0.53
21 2 0.12
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (19 bp):
ATGAGAGAATTGTAAGATG
Found at i:25182844 original size:20 final size:20
Alignment explanation
Indices: 25182789--25182845 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
25182779 GGTGAAGAAC
*
25182789 ATGGAGCTCAAGAAACGTGT
1 ATGGAGCTCAAGAACCGTGT
* *
25182809 ATGGTGGCTTAAGAACCGTGT
1 ATGG-AGCTCAAGAACCGTGT
25182830 ATGGAGCTCAAGAACC
1 ATGGAGCTCAAGAACC
25182846 ATTGATAGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.21
Consensus pattern (20 bp):
ATGGAGCTCAAGAACCGTGT
Found at i:25185264 original size:98 final size:97
Alignment explanation
Indices: 25184976--25185340 Score: 595
Period size: 97 Copynumber: 3.7 Consensus size: 97
25184966 AATTTAAACT
** * * * *
25184976 ACAAAGTTTGTTCCTCGTTTTAATGTTGTAATGCATCTAATTTATATTACAAAATTTTTTCCAAG
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATATCACAAAGTTTGTTCCAAG
* *
25185041 TTTTAATGTTGTAATGTATCTAATATATGATC
66 TTTTAATGTTGTAATGTATCTAATTTATGACC
* *
25185073 ACAAAGTTTGTTCCAACTTTTAATGTTGTAATGTATCTAATTTATATTACAAAGTTTGTTCCAAG
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATATCACAAAGTTTGTTCCAAG
25185138 TTTTAATGTTGTAATGTATCTAATTTATGACC
66 TTTTAATGTTGTAATGTATCTAATTTATGACC
*
25185170 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCCACAAAGTTTGTTCCAA
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATAT-CACAAAGTTTGTTCCAA
*
25185235 GTTTTAATGTTGTAATGTATCTAATTTATGTCC
65 GTTTTAATGTTGTAATGTATCTAATTTATGACC
*
25185268 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCCACAAAGTTTGTTCCAA
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATAT-CACAAAGTTTGTTCCAA
25185333 GTTTTAAT
65 GTTTTAAT
25185341 ATTTCAATTA
Statistics
Matches: 255, Mismatches: 12, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
97 134 0.53
98 121 0.47
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (97 bp):
ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATATCACAAAGTTTGTTCCAAG
TTTTAATGTTGTAATGTATCTAATTTATGACC
Found at i:25185358 original size:49 final size:49
Alignment explanation
Indices: 25184976--25185340 Score: 592
Period size: 49 Copynumber: 7.5 Consensus size: 49
25184966 AATTTAAACT
** * * *
25184976 ACAAAGTTTGTTCCTCGTTTTAATGTTGTAATGCATCTAATTTATAT-T
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCC
* * *
25185024 ACAAAATTTTTTCCAAGTTTTAATGTTGTAATGTATCTAATATATGAT-C
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATG-TCC
* * *
25185073 ACAAAGTTTGTTCCAACTTTTAATGTTGTAATGTATCTAATTTATAT-T
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCC
*
25185121 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGACC
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCC
25185170 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCC
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCC
25185219 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCC
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCC
25185268 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCC
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCC
25185317 ACAAAGTTTGTTCCAAGTTTTAAT
1 ACAAAGTTTGTTCCAAGTTTTAAT
25185341 ATTTCAATTA
Statistics
Matches: 296, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
48 84 0.28
49 212 0.72
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (49 bp):
ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCC
Found at i:25185657 original size:33 final size:33
Alignment explanation
Indices: 25185615--25185677 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
25185605 CGATGAACTT
* * *
25185615 GAGCCGGGAGGAGTGGAGTACTGTGGTGGATAC
1 GAGCCGGGAGGACTGGAGTAATGCGGTGGATAC
25185648 GAGCCGGGAGGACTGGAGTAATGCGGTGGA
1 GAGCCGGGAGGACTGGAGTAATGCGGTGGA
25185678 CATGGGCCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.13, G:0.49, T:0.16
Consensus pattern (33 bp):
GAGCCGGGAGGACTGGAGTAATGCGGTGGATAC
Found at i:25192630 original size:30 final size:30
Alignment explanation
Indices: 25192596--25192668 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
25192586 ACAAGCTATC
* * *
25192596 ACACGGCCGTGTGACACACACGGCTTGGTG
1 ACACGGCCGTGTGACACACACGACCTAGTG
* *
25192626 ACACGACCGTGTGACACGCACGACCTAGTG
1 ACACGGCCGTGTGACACACACGACCTAGTG
25192656 ACACGGCCGTGTG
1 ACACGGCCGTGTG
25192669 TCATTTGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.15
Consensus pattern (30 bp):
ACACGGCCGTGTGACACACACGACCTAGTG
Found at i:25192647 original size:17 final size:17
Alignment explanation
Indices: 25192627--25192660 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
25192617 GGCTTGGTGA
25192627 CACGACCGT-GTGACACG
1 CACGACC-TAGTGACACG
25192644 CACGACCTAGTGACACG
1 CACGACCTAGTGACACG
25192661 GCCGTGTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.26, C:0.35, G:0.26, T:0.12
Consensus pattern (17 bp):
CACGACCTAGTGACACG
Found at i:25200719 original size:17 final size:17
Alignment explanation
Indices: 25200699--25200736 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
25200689 TAGAATTTGG
25200699 TTGAGAAAAAAATTTAA
1 TTGAGAAAAAAATTTAA
*
25200716 TTGAGAAAAAACTTTAA
1 TTGAGAAAAAAATTTAA
25200733 TTGA
1 TTGA
25200737 AGTTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (17 bp):
TTGAGAAAAAAATTTAA
Found at i:25202693 original size:68 final size:68
Alignment explanation
Indices: 25202492--25202886 Score: 414
Period size: 68 Copynumber: 5.8 Consensus size: 68
25202482 AGTTTAATGA
* *** * * * *
25202492 GTAAGACCATAGCTCGACTATGGCAACTAATAGAGTCCAATAGGGCATTAAATAT-GTGTTACAA
1 GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
*
25202556 AGT
66 GGT
* * * * ** *
25202559 GTAAGATCATAGCTCGACTATGACAACAAAATAGAGTCTGCCAAAATGTTAAACATGGGGTTACA
1 GTAAGACCATAGCTCGACTATGGCAAC-CAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACA
25202624 AGGT
65 AGGT
*
25202628 GTAAGACCATAGCTCGGCTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
1 GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
25202693 GGT
66 GGT
* ** ** * *
25202696 GTAAGTCCATAGCTCGGTTATGGCAACCAATAGAGTCCTTCAGGAAGTTAAACATGAGGTTACAA
1 GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
25202761 GGT
66 GGT
* * ** * * * *
25202764 GTAAAACCATTGCTCGGTTATGGAAACCAATAAAGTCCTCCAGGATGTTAAACATGGGGTTACAA
1 GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
25202829 GGT
66 GGT
* * ** * * **
25202832 GTAAGACCATGGCTCAACCCTGACAACCAATAGAGTTCGCCAAAACGTTAAACAT
1 GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACAT
25202887 AGGTTCAAAT
Statistics
Matches: 274, Mismatches: 52, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
67 25 0.09
68 215 0.78
69 34 0.12
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (68 bp):
GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
GGT
Found at i:25205422 original size:32 final size:32
Alignment explanation
Indices: 25205381--25205442 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
25205371 CATCTATTTT
*
25205381 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTATTTGACAACACGAAAAATC
* *
25205413 CATTGTTCAACTATTTGACTACATGAAAAA
1 CATTGTTCAACTATTTGACAACACGAAAAA
25205443 AACCAAAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (32 bp):
CATTGTTCAACTATTTGACAACACGAAAAATC
Done.