Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 182 of 226
Found at i:58286274 original size:25 final size:25
Alignment explanation
Indices: 58286238--58286375 Score: 128
Period size: 25 Copynumber: 5.7 Consensus size: 25
58286228 AGGTTAGAGT
*
58286238 TTTTATTACATCAAATAAACGTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
58286263 TTTTATTTCATCAAAT-AA----TA
1 TTTTATTACATCAAATAAACTTCTA
** * *
58286283 TTAAAATA-ACTCGAAA-AAATTTCTA
1 TTTTATTACA-TC-AAATAAACTTCTA
*
58286308 TTTTATTACTTCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
58286333 TTTTATTACATCAAATAAAATTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
58286358 TTTTATTGCATCAAATAA
1 TTTTATTACATCAAATAA
58286376 TATTTAAATA
Statistics
Matches: 91, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
19 1 0.01
20 8 0.09
21 5 0.05
24 5 0.05
25 72 0.79
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.43
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:58286800 original size:18 final size:18
Alignment explanation
Indices: 58286777--58286811 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58286767 CGGAAAATGA
*
58286777 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
58286795 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
58286812 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:58287461 original size:7 final size:7
Alignment explanation
Indices: 58287449--58287473 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
58287439 TTATGTACAT
58287449 AATACTA
1 AATACTA
58287456 AATACTA
1 AATACTA
58287463 AATACTA
1 AATACTA
58287470 AATA
1 AATA
58287474 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:58288681 original size:11 final size:11
Alignment explanation
Indices: 58288665--58288765 Score: 64
Period size: 11 Copynumber: 8.6 Consensus size: 11
58288655 TAATTTTAGA
58288665 AGGAAATTGAG
1 AGGAAATTGAG
*
58288676 AGGAAATTGAA
1 AGGAAATTGAG
*
58288687 ATGAAATATGAGTTTG
1 AGGAAAT-TGA----G
* *
58288703 AGAGAATTTTAG
1 AG-GAAATTGAG
58288715 AAGGAAATTGAG
1 -AGGAAATTGAG
58288727 A-GAAATTTG-G
1 AGGAAA-TTGAG
58288737 AAGGAAATTGAG
1 -AGGAAATTGAG
58288749 AGG-AATTGAG
1 AGGAAATTGAG
58288759 AGGAAAT
1 AGGAAAT
58288766 ATTAGAGAGG
Statistics
Matches: 70, Mismatches: 8, Indels: 24
0.69 0.08 0.24
Matches are distributed among these distances:
10 15 0.21
11 30 0.43
12 16 0.23
13 2 0.03
16 3 0.04
17 4 0.06
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.24
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:58288728 original size:22 final size:22
Alignment explanation
Indices: 58288700--58288755 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
58288690 AAATATGAGT
58288700 TTGAGAGAATTTTAGAAGGAAA
1 TTGAGAGAATTTTAGAAGGAAA
* *
58288722 TTGAGAGAAATTTGGAAGGAAA
1 TTGAGAGAATTTTAGAAGGAAA
58288744 TTGAGAGGAATT
1 TTGAGA-GAATT
58288756 GAGAGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTAGAAGGAAA
Found at i:58288733 original size:10 final size:11
Alignment explanation
Indices: 58288716--58288765 Score: 61
Period size: 10 Copynumber: 4.6 Consensus size: 11
58288706 GAATTTTAGA
58288716 AGGAAATTGAG
1 AGGAAATTGAG
58288727 A-GAAATTTG-G
1 AGGAAA-TTGAG
58288737 AAGGAAATTGAG
1 -AGGAAATTGAG
58288749 AGG-AATTGAG
1 AGGAAATTGAG
58288759 AGGAAAT
1 AGGAAAT
58288766 ATTAGAGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 15 0.44
11 14 0.41
12 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:58288744 original size:51 final size:51
Alignment explanation
Indices: 58288616--58288733 Score: 168
Period size: 51 Copynumber: 2.3 Consensus size: 51
58288606 TTTAAAAACA
* * *
58288616 GAAATTTAGAGAAAATTGAAATTAAATATG-GATTTGAAATAATTTTAGAAG
1 GAAATTGAGAG-AAATTGAAATGAAATATGAGATTTGAAAGAATTTTAGAAG
*
58288667 GAAATTGAGAGGAAATTGAAATGAAATATGAG-TTTGAGAGAATTTTAGAAG
1 GAAATTGAGA-GAAATTGAAATGAAATATGAGATTTGAAAGAATTTTAGAAG
58288718 GAAATTGAGAGAAATT
1 GAAATTGAGAGAAATT
58288734 TGGAAGGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
50 6 0.10
51 53 0.87
52 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (51 bp):
GAAATTGAGAGAAATTGAAATGAAATATGAGATTTGAAAGAATTTTAGAAG
Found at i:58289035 original size:29 final size:28
Alignment explanation
Indices: 58288977--58289040 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
58288967 CGATTTCCCG
58288977 AAAAAGGACCATTCCAGTAAATAATTAA
1 AAAAAGGACCATTCCAGTAAATAATTAA
* * *
58289005 AAAATAGGCCCATTTCAGTAAAT-TTTGAA
1 AAAA-AGGACCATTCCAGTAAATAATT-AA
58289034 AAAAAGG
1 AAAAAGG
58289041 GCTTTTATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.23
Consensus pattern (28 bp):
AAAAAGGACCATTCCAGTAAATAATTAA
Found at i:58289563 original size:19 final size:19
Alignment explanation
Indices: 58289536--58289577 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
58289526 TTCTCTCATC
* * *
58289536 GCTGGTTCTTTGTTTCTCT
1 GCTGCTTCTTTGATCCTCT
58289555 GCTGCTTCTTTGATCCTCT
1 GCTGCTTCTTTGATCCTCT
58289574 GCTG
1 GCTG
58289578 GTGCTGGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.02, C:0.26, G:0.21, T:0.50
Consensus pattern (19 bp):
GCTGCTTCTTTGATCCTCT
Found at i:58289588 original size:25 final size:25
Alignment explanation
Indices: 58289554--58289682 Score: 213
Period size: 25 Copynumber: 5.2 Consensus size: 25
58289544 TTTGTTTCTC
* *
58289554 TGCTGCTTCTTTGATCCTCTGCTGG
1 TGCTGGTTCTTTGTTCCTCTGCTGG
*
58289579 TGCTGGTTCTTTGTTCTTCTGCTGG
1 TGCTGGTTCTTTGTTCCTCTGCTGG
*
58289604 TGCTGGTTCTTTGTTCCTCTACTGG
1 TGCTGGTTCTTTGTTCCTCTGCTGG
*
58289629 TGCAGGTTCTTTGTTCCTCTGCTGG
1 TGCTGGTTCTTTGTTCCTCTGCTGG
58289654 TGCTGGTTCTTTGTTCCTCTGCTGG
1 TGCTGGTTCTTTGTTCCTCTGCTGG
58289679 TGCT
1 TGCT
58289683 TTGTTCCTCT
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 96 1.00
ACGTcount: A:0.02, C:0.24, G:0.26, T:0.47
Consensus pattern (25 bp):
TGCTGGTTCTTTGTTCCTCTGCTGG
Found at i:58289653 original size:44 final size:44
Alignment explanation
Indices: 58289539--58289654 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 44
58289529 TCTCATCGCT
* * * *
58289539 GGTTCTTTGTTTCTCTGCTGCTTCTTTGATCCTCTGCTGGTGCT
1 GGTTCTTTGTTCCTCTGCTGGTTCTTTGATCCTCTACTGGTGCA
*
58289583 GGTTCTTTGTTCTTCTGCTGGTGCTGGTTCTTTGTTCCTCTACTGGTGCA
1 GGTTCTTTGTTC--CT-C---TGCTGGTTCTTTGATCCTCTACTGGTGCA
58289633 GGTTCTTTGTTCCTCTGCTGGT
1 GGTTCTTTGTTCCTCTGCTGGT
58289655 GCTGGTTCTT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
44 18 0.30
46 2 0.03
47 2 0.03
48 2 0.03
50 37 0.61
ACGTcount: A:0.03, C:0.23, G:0.25, T:0.49
Consensus pattern (44 bp):
GGTTCTTTGTTCCTCTGCTGGTTCTTTGATCCTCTACTGGTGCA
Found at i:58289678 original size:19 final size:19
Alignment explanation
Indices: 58289654--58289692 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
58289644 CCTCTGCTGG
*
58289654 TGCTGGTTCTTTGTTCCTC
1 TGCTGGTGCTTTGTTCCTC
58289673 TGCTGGTGCTTTGTTCCTC
1 TGCTGGTGCTTTGTTCCTC
58289692 T
1 T
58289693 TCTCCACCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.26, G:0.23, T:0.51
Consensus pattern (19 bp):
TGCTGGTGCTTTGTTCCTC
Found at i:58291657 original size:26 final size:26
Alignment explanation
Indices: 58291628--58291678 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
58291618 ACACTCAAAT
* * *
58291628 TTTTTAAAAATACTTCTCAAAAGTAC
1 TTTTCAAAAACACTTCTAAAAAGTAC
*
58291654 TTTTCAACAACACTTCTAAAAAGTA
1 TTTTCAAAAACACTTCTAAAAAGTA
58291679 ATGAAGAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (26 bp):
TTTTCAAAAACACTTCTAAAAAGTAC
Found at i:58294870 original size:25 final size:24
Alignment explanation
Indices: 58294841--58294901 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 24
58294831 TTAATAATTT
*
58294841 TTTTAATTTAATATTCTATAAATTAT
1 TTTTAATTT-ATATTC-ATAAATTAG
*
58294867 TTTATAATTTATATTCATAAACATAG
1 TTT-TAATTTATATTCATAAA-TTAG
58294893 TTTTAATTT
1 TTTTAATTT
58294902 TGTGACTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 11 0.35
26 14 0.45
27 6 0.19
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTAATTTATATTCATAAATTAG
Found at i:58294896 original size:27 final size:27
Alignment explanation
Indices: 58294839--58294901 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
58294829 TGTTAATAAT
* *
58294839 TTTTTTAATTTAATATTCTATAAATTA
1 TTTTATAATTTAATATTCTATAAAATA
58294866 TTTTATAATTT-ATATTC-ATAAACATA
1 TTTTATAATTTAATATTCTATAAA-ATA
*
58294892 GTTT-TAATTT
1 TTTTATAATTT
58294902 TGTGACTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.34
26 11 0.34
27 10 0.31
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTATAATTTAATATTCTATAAAATA
Found at i:58297988 original size:20 final size:21
Alignment explanation
Indices: 58297965--58298015 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 21
58297955 AATGTTTTCT
58297965 TTATACA-ACTTTGTCTAAGC
1 TTATACAGACTTTGTCTAAGC
58297985 TTATACATGTGACTTTGTCTAAGC
1 TTATACA---GACTTTGTCTAAGC
58298009 TTATACA
1 TTATACA
58298016 TGTGATTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.26
24 20 0.74
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
TTATACAGACTTTGTCTAAGC
Found at i:58298004 original size:24 final size:24
Alignment explanation
Indices: 58297972--58298020 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
58297962 TCTTTATACA
58297972 ACTTTGTCTAAGCTTATACATGTG
1 ACTTTGTCTAAGCTTATACATGTG
58297996 ACTTTGTCTAAGCTTATACATGTG
1 ACTTTGTCTAAGCTTATACATGTG
58298020 A
1 A
58298021 TTGTGAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (24 bp):
ACTTTGTCTAAGCTTATACATGTG
Found at i:58298272 original size:43 final size:41
Alignment explanation
Indices: 58298224--58298326 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 41
58298214 AACGTCGCTA
* **
58298224 ACTTTTGCGGCGTTTTTAGAAACAAACGCAGCTAAAGGTCATG
1 ACTTTTGCGGCGCTTTTA-AAA-AAACGCAGCTAAAGACCATG
* *
58298267 ACTTTTAGCGGCACTTTTAAAAAAACGCCGCTAAAGACCATG
1 ACTTTT-GCGGCGCTTTTAAAAAAACGCAGCTAAAGACCATG
*
58298309 ACCTTTAGCGGCGCTTTT
1 A-CTTTTGCGGCGCTTTT
58298327 CCCACAAACG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
42 28 0.55
43 13 0.25
44 10 0.20
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (41 bp):
ACTTTTGCGGCGCTTTTAAAAAAACGCAGCTAAAGACCATG
Found at i:58298355 original size:43 final size:43
Alignment explanation
Indices: 58298245--58298497 Score: 276
Period size: 43 Copynumber: 5.9 Consensus size: 43
58298235 GTTTTTAGAA
* * * * **
58298245 ACAAACGCAGCTAAAGGTCATGACTTTTAGCGGCACTTTT-AA
1 ACAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCC
* *
58298287 AAAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCC
* * **
58298330 ACAAACGCCGCTAAA-CTCTAGGACCTTTAGCGGCGCTTTTCTT
1 ACAAACGCCGCTAAAGATC-ATGACCTTTAGCGGCGCTTTTCCC
* * ** ***
58298373 ACAAACGCCGCTAAAGGTCAGGACCTTTAGCGATGCTTTTATT
1 ACAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCC
*
58298416 ACAAACGCCGCTAAAAGATCATGACCTTTAGCGGCACTTTTCCC
1 ACAAACGCCGCT-AAAGATCATGACCTTTAGCGGCGCTTTTCCC
* *
58298460 ATAAACGCCGCTAAAGATCATGACCTTTTGCGGCGCTT
1 ACAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTT
58298498 CTGCAAAAAA
Statistics
Matches: 178, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
42 35 0.20
43 107 0.60
44 36 0.20
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCC
Found at i:58298466 original size:130 final size:128
Alignment explanation
Indices: 58298245--58298497 Score: 346
Period size: 130 Copynumber: 2.0 Consensus size: 128
58298235 GTTTTTAGAA
* * *
58298245 ACAAACGCAGCTAAAGGTCATGACTTTTAGCGGCACTTTTAAAAAAACGCCGCTAAAGACCATGA
1 ACAAACGCAGCTAAAGGTCAGGACCTTTAGCGACACTTTTAAAAAAACGCCGCTAAAGACCATGA
* *
58298310 CCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA-CTCTAGGACCTTTAGCGGCGCTTTTCTT
66 CCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGATC-AGGACCTTTAGCGGCGCTTTTCTT
* ** * * *
58298373 ACAAACGCCGCTAAAGGTCAGGACCTTTAGCGATGCTTTTATTACAAACGCCGCTAAAAGATCAT
1 ACAAACGCAGCTAAAGGTCAGGACCTTTAGCGACACTTTTA-AAAAAACGCCGCT-AAAGACCAT
* * *
58298438 GACCTTTAGCGGCACTTTTCCCATAAACGCCGCTAAAGATCATGACCTTTTGCGGCGCTT
64 GACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGATCAGGACCTTTAGCGGCGCTT
58298498 CTGCAAAAAA
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
128 35 0.32
129 11 0.10
130 60 0.56
131 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (128 bp):
ACAAACGCAGCTAAAGGTCAGGACCTTTAGCGACACTTTTAAAAAAACGCCGCTAAAGACCATGA
CCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGATCAGGACCTTTAGCGGCGCTTTTCTT
Found at i:58300033 original size:13 final size:13
Alignment explanation
Indices: 58300016--58300058 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
58300006 GCTTAATGCA
*
58300016 AAATTGTAATTTT
1 AAATTCTAATTTT
* * *
58300029 GAATTTTATTTTT
1 AAATTCTAATTTT
58300042 AAATTCTAATTTT
1 AAATTCTAATTTT
58300055 AAAT
1 AAAT
58300059 CAAAATAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (13 bp):
AAATTCTAATTTT
Found at i:58303105 original size:7 final size:7
Alignment explanation
Indices: 58303093--58303131 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
58303083 ACCAATTAAT
58303093 CTAACCC
1 CTAACCC
58303100 CTAACCC
1 CTAACCC
58303107 CTAACCC
1 CTAACCC
* *
58303114 CTATCTC
1 CTAACCC
*
58303121 CTAAACC
1 CTAACCC
58303128 CTAA
1 CTAA
58303132 ATCATAAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.31, C:0.49, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAACCC
Found at i:58303288 original size:7 final size:7
Alignment explanation
Indices: 58303278--58303339 Score: 79
Period size: 7 Copynumber: 8.9 Consensus size: 7
58303268 CACTAACTTT
*
58303278 TAACCTC
1 TAACCCC
58303285 TAACCCC
1 TAACCCC
58303292 TAACCCC
1 TAACCCC
**
58303299 TAACTAC
1 TAACCCC
58303306 TAACCCC
1 TAACCCC
*
58303313 CAACCCC
1 TAACCCC
*
58303320 TAACCCA
1 TAACCCC
58303327 TAACCCC
1 TAACCCC
58303334 TAACCC
1 TAACCC
58303340 ATAAACATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (7 bp):
TAACCCC
Found at i:58303508 original size:14 final size:15
Alignment explanation
Indices: 58303489--58303521 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
58303479 CTTAAACCAG
58303489 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
58303503 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
58303518 AATC
1 AATC
58303522 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:58304015 original size:41 final size:41
Alignment explanation
Indices: 58303926--58304075 Score: 248
Period size: 41 Copynumber: 3.7 Consensus size: 41
58303916 AAATGTTTTT
* * *
58303926 GCGGCGCTTTTTCAAAAACGCCGCTAAATC-CCGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTCTGAGCATTA
58303966 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTCTGAGCATTA
*
58304007 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTCTGAACATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTCTGAGCATTA
*
58304048 GTGGCGCTTTTCCAAAAACGCCGCTAAA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAA
58304076 TCCCCGAAAG
Statistics
Matches: 104, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
40 28 0.27
41 76 0.73
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTCTGAGCATTA
Found at i:58304169 original size:40 final size:40
Alignment explanation
Indices: 58304114--58304267 Score: 175
Period size: 40 Copynumber: 3.8 Consensus size: 40
58304104 TGGGCTTAGG
* * *
58304114 TTTTTTGCGGCGCTTTTCTAAAAAACACCGCTAATGCT-TA
1 TTTTTAGCGGCGCTTTT-TAAAAAACGCCGCTAATGCTCGA
* *
58304154 TTTTTAGCGGAGCTTTTTTAAAAACGCCGCTAATGCTCGA
1 TTTTTAGCGGCGCTTTTTAAAAAACGCCGCTAATGCTCGA
* * * *
58304194 TCTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGCTTTTTAAAAAACGCCGCTAATGCTCGA
* **
58304234 TTTTTAGCGGCGTTTTTTATCCAAACGCCGCTAA
1 TTTTTAGCGGCGCTTTTTA-AAAAACGCCGCTAA
58304268 AAATGCCGCT
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 18 0.19
40 68 0.70
41 11 0.11
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (40 bp):
TTTTTAGCGGCGCTTTTTAAAAAACGCCGCTAATGCTCGA
Found at i:58306939 original size:14 final size:13
Alignment explanation
Indices: 58306918--58306944 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58306908 TTAGCATTAT
58306918 TTTTAAAAAGTGC
1 TTTTAAAAAGTGC
58306931 TTTTAAAAAGTGC
1 TTTTAAAAAGTGC
58306944 T
1 T
58306945 GTGAAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTTAAAAAGTGC
Found at i:58308273 original size:29 final size:27
Alignment explanation
Indices: 58308241--58308302 Score: 63
Period size: 28 Copynumber: 2.2 Consensus size: 27
58308231 TTACTTATAG
*
58308241 TATTTAATTTCAATAATGT-TTAAATTTAT
1 TATTTAATTT-AA-AATGTAATAAA-TTAT
*
58308270 TATTATAGTTTAAAATGTAATAAATTAT
1 TATT-TAATTTAAAATGTAATAAATTAT
58308298 TATTT
1 TATTT
58308303 TAGTCCGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 1 0.03
28 13 0.45
29 10 0.34
30 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (27 bp):
TATTTAATTTAAAATGTAATAAATTAT
Found at i:58314174 original size:14 final size:14
Alignment explanation
Indices: 58314155--58314194 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
58314145 TCTGAGTCAA
58314155 AAAAATATAAAAAT-
1 AAAAATA-AAAAATG
58314169 AAAAATAAAAAATG
1 AAAAATAAAAAATG
58314183 AAAAAGTAAAAA
1 AAAAA-TAAAAA
58314195 TGGAGAGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.25
14 12 0.50
15 6 0.25
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAAATG
Found at i:58314180 original size:21 final size:21
Alignment explanation
Indices: 58314154--58314195 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
58314144 CTCTGAGTCA
58314154 AAAAAAT-ATAAAAATAAAAAT
1 AAAAAATGA-AAAAATAAAAAT
*
58314175 AAAAAATGAAAAAGTAAAAAT
1 AAAAAATGAAAAAATAAAAAT
58314196 GGAGAGGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAAAATGAAAAAATAAAAAT
Found at i:58315673 original size:129 final size:129
Alignment explanation
Indices: 58315443--58315719 Score: 473
Period size: 129 Copynumber: 2.1 Consensus size: 129
58315433 TCGGTGAAGT
*
58315443 CACAAGTCTTATATCCCTGGTCATCAGTGGAATAAGTTGGGAAATTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATATCCCTGGTCATCAGTGGAATAAGTTGGGAAATTACAGATCTTGTCTCCCTAA
58315508 GCAGTAGCGGAGCAGATCGAAGACGGCGAACCTTATCTTCAAAAGTAAGGAAGCAGATTTAAGC
66 GCAGTAGCGGAGCAGATCGAAGACGGCGAACCTTATCTTCAAAAGTAAGGAAGCAGATTTAAGC
*
58315572 CACAAGTCCTATATCCCTGGTCATCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATATCCCTGGTCATCAGTGGAATAAGTTGGGAAATTACAGATCTTGTCTCCCTAA
* * * **
58315637 GCAGTAGCGGGGTAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
66 GCAGTAGCGGAGCAGATCGAAGACGGCGAACCTTATCTTCAAAAGTAAGGAAGCAGATTTAAGC
* *
58315701 CACAAATCCTATCTCCCTG
1 CACAAGTCCTATATCCCTG
58315720 AAGTTGTAGT
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 139 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (129 bp):
CACAAGTCCTATATCCCTGGTCATCAGTGGAATAAGTTGGGAAATTACAGATCTTGTCTCCCTAA
GCAGTAGCGGAGCAGATCGAAGACGGCGAACCTTATCTTCAAAAGTAAGGAAGCAGATTTAAGC
Found at i:58315779 original size:44 final size:44
Alignment explanation
Indices: 58315710--58316074 Score: 266
Period size: 44 Copynumber: 8.5 Consensus size: 44
58315700 CCACAAATCC
* *
58315710 TATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
** * * * *
58315754 TATCTTACTGAAGTTGCAGTAGAGTGGATT---GTATTAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
* * * ** *
58315795 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGGCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAGTAATAGATCT
*
58315839 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
* * * * * * * *
58315883 TATCTCTCTGAAGTTGTAGTAGAGTGGA-T--CGCATTAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
* ** * ** *
58315924 TATCTCCCTGAGGTTGCAGTGGAGCAAATTGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAG-TAATAGATCT
* *
58315968 TATCTCCCTGAAGTTGTAGTGGAGCGAATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
* * * * *** *
58316012 TATCTCTCTGAACTTGCAGTAGAGTGGATCGCA-TCA-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
*
58316053 TATCTCCCTGAAGTTACAGTGG
1 TATCTCCCTGAAGTTGCAGTGG
58316075 GGCAGACTGT
Statistics
Matches: 249, Mismatches: 62, Indels: 23
0.75 0.19 0.07
Matches are distributed among these distances:
41 83 0.33
42 3 0.01
43 12 0.05
44 145 0.58
45 6 0.02
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATCT
Found at i:58315816 original size:85 final size:85
Alignment explanation
Indices: 58315704--58316067 Score: 286
Period size: 85 Copynumber: 4.2 Consensus size: 85
58315694 TTTAAGCCAC
* * * **
58315704 AAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAGTAATAGATCTTATCTTACTGAAGTT
1 AAATCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGCAATAGATCTTATCTCCCTGAAGTT
*
58315769 GCAGTAGAGTGGATTGTATT
66 GCAGTAGAGCGGATTGTATT
* * * * * *
58315789 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGGCGATA-ATCCTATCTCCCTGAAGT
1 AAATCTTATCTCCCTGAAGTTGTAGTGGAGCGGATT-AAAGCAATAGATCTTATCTCCCTGAAGT
* * *
58315853 TGTAGTGGAGCGGATTAAAGTAAT
65 TGCAGTAGAGCGGATT---GTATT
* * * * * * * *
58315877 AGATCTTATCTCTCTGAAGTTGTAGTAGAGTGGA-T--CGCATTAAATCTTATCTCCCTGAGGTT
1 AAATCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGCAATAGATCTTATCTCCCTGAAGTT
* ** * **
58315939 GCAGTGGAGCAAATTGAAGCCG
66 GCAGTAGAGCGGATTGTA--TT
* * * * *
58315961 ATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGAATTAAAGTAATAGATCTTATCTCTCTGAACT
1 A-AATCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGCAATAGATCTTATCTCCCTGAAGT
* * * *
58316026 TGCAGTAGAGTGGATCGCATC
65 TGCAGTAGAGCGGATTGTATT
*
58316047 AAGTCTTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAAGTT
58316068 ACAGTGGGGC
Statistics
Matches: 212, Mismatches: 56, Indels: 22
0.73 0.19 0.08
Matches are distributed among these distances:
82 2 0.01
84 5 0.02
85 133 0.63
86 8 0.04
87 1 0.00
88 63 0.30
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (85 bp):
AAATCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGCAATAGATCTTATCTCCCTGAAGTT
GCAGTAGAGCGGATTGTATT
Found at i:58315821 original size:129 final size:128
Alignment explanation
Indices: 58315688--58316080 Score: 608
Period size: 129 Copynumber: 3.0 Consensus size: 128
58315678 AGTGTAAGGA
* * *
58315688 AGCAGATTTAAGCCACAAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCA-TAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
* *
58315753 TTATCT-TACTGAAGTTGCAGTAGAGTGGATTGTATTAAATCTTATCTCCCTGAGGTTGCAGTGG
65 TTATCTCT-CTGAAGTTGCAGTAGAGTGGATCGCATTAAATCTTATCTCCCTGAGGTTGCAGTGG
*
58315817 AGCAGATTGAAGGCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
1 AGCAGATTGAA-GCCATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
*
58315882 TTATCTCTCTGAAGTTGTAGTAGAGTGGATCGCATTAAATCTTATCTCCCTGAGGTTGCAGTGG
65 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATTAAATCTTATCTCCCTGAGGTTGCAGTGG
* *
58315946 AGCAAATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGAATTAAAGTAATAGATC
1 AGCAGATTGAAGCC-ATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
* * * * *
58316011 TTATCTCTCTGAACTTGCAGTAGAGTGGATCGCATCAAGTCTTATCTCCCTGAAGTTACAGTGG
65 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATTAAATCTTATCTCCCTGAGGTTGCAGTGG
*
58316075 GGCAGA
1 AGCAGA
58316081 CTGTGAATAG
Statistics
Matches: 243, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
128 2 0.01
129 237 0.98
130 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (128 bp):
AGCAGATTGAAGCCATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
TATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATTAAATCTTATCTCCCTGAGGTTGCAGTGG
Found at i:58316177 original size:50 final size:50
Alignment explanation
Indices: 58316123--58316305 Score: 215
Period size: 50 Copynumber: 3.7 Consensus size: 50
58316113 ACAATGGAAC
* *
58316123 AGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
** * ** ** *
58316173 AGATTAAAGCCACAACAGCGAATCTTACTTCCTTGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * *
58316223 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
58316273 AGATTAAAGCCACAAC-GACGAATCTTACTTCCC
1 AGATTAAAGCCACAACAG-CGAATCTTACTTCCC
58316306 TTGAAGTGTA
Statistics
Matches: 106, Mismatches: 26, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
49 1 0.01
50 105 0.99
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:58316327 original size:50 final size:50
Alignment explanation
Indices: 58316120--58316332 Score: 205
Period size: 50 Copynumber: 4.3 Consensus size: 50
58316110 GGTACAATGG
* * * *
58316120 AACAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGCAGTTA
1 AACAGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACAGTGCAGTGA
* ** * * *
58316170 AAAAGATTAAAGCCACAACAGCGAATCTTACTTCCTTGGCGGTGCAGTGG
1 AACAGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACAGTGCAGTGA
* * * * * * *
58316220 AACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGCAGTTA
1 AACAGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACAGTGCAGTGA
* * * *
58316270 AAAAGATTAAAGCCACAAC-GACGAATCTTACTTCCCTTGA-AGTGTAATGA
1 AACAGATTAAAGCCACAACAG-CGAATCTTACTTCCC-CGACAGTGCAGTGA
58316320 AACAGATTAAAGC
1 AACAGATTAAAGC
58316333 TACGAAGGCA
Statistics
Matches: 127, Mismatches: 34, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
49 1 0.01
50 125 0.98
51 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (50 bp):
AACAGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACAGTGCAGTGA
Found at i:58316347 original size:100 final size:100
Alignment explanation
Indices: 58316114--58316367 Score: 334
Period size: 100 Copynumber: 2.5 Consensus size: 100
58316104 CCAGGCGGTA
* * *
58316114 CAATGGAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAAAGATTA
1 CAATGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
**
58316179 AAGCCACAACAGCGAATCTTACTTCCTTGGCGGTG
66 AAGCCACAACAGCGAATCTTACTTCCTTGGAAGTG
* * *
58316214 CAGTGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTA
1 CAATGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
58316279 AAGCCACAAC-GACGAATCTTACTTCCCTT-GAAGTG
66 AAGCCACAACAG-CGAATCTTACTT-CCTTGGAAGTG
* * * * * *
58316314 TAATGAAACAGATTAAAGCTACGAA-GGCAAATCTTGTTTCGCCGACAATGCAGT
1 CAATGGAACAGATTAAAGCTAC-AACGGCGAATCTTGCTTCCCCGACATTGCAGT
58316368 CAGACAGAAG
Statistics
Matches: 134, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
99 1 0.01
100 127 0.95
101 6 0.04
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (100 bp):
CAATGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
AAGCCACAACAGCGAATCTTACTTCCTTGGAAGTG
Found at i:58317972 original size:29 final size:27
Alignment explanation
Indices: 58317940--58318001 Score: 63
Period size: 28 Copynumber: 2.2 Consensus size: 27
58317930 TTACTTATAG
*
58317940 TATTTAATTTCAATAATGT-TTAAATTTAT
1 TATTTAATTT-AA-AATGTAATAAA-TTAT
*
58317969 TATTATAGTTTAAAATGTAATAAATTAT
1 TATT-TAATTTAAAATGTAATAAATTAT
58317997 TATTT
1 TATTT
58318002 TAGTCCGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 1 0.03
28 13 0.45
29 10 0.34
30 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (27 bp):
TATTTAATTTAAAATGTAATAAATTAT
Found at i:58323369 original size:28 final size:28
Alignment explanation
Indices: 58323291--58323369 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 28
58323281 ATTCATATGG
* * *
58323291 AATTCGCTACAAGGGC-TAATCTTTCAT
1 AATTCGCCACAAAGGCTTATTCTTTCAT
*
58323318 AATTCGCCAC-GAGGCTTATTCTTTCAT
1 AATTCGCCACAAAGGCTTATTCTTTCAT
*
58323345 AGTTCGCCACAAAGGCTTATTCTTT
1 AATTCGCCACAAAGGCTTATTCTTT
58323370 TCTGACATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.07
27 28 0.64
28 13 0.30
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.35
Consensus pattern (28 bp):
AATTCGCCACAAAGGCTTATTCTTTCAT
Found at i:58324120 original size:49 final size:49
Alignment explanation
Indices: 58324043--58324139 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
58324033 TTATGCTATG
* * *
58324043 CATTTCTAAACTTGGCCGTCCATTGTCTACACTCTTATCACTATTTATA
1 CATTGCTAAACTTAGCCGTCCACTGTCTACACTCTTATCACTATTTATA
* *
58324092 CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATTTAT
1 CATTGCTAAACTTAGCCGTCCACTGTCTACACTCTTATCACTATTTAT
58324140 CCCTTCTAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41
Consensus pattern (49 bp):
CATTGCTAAACTTAGCCGTCCACTGTCTACACTCTTATCACTATTTATA
Found at i:58324966 original size:3 final size:3
Alignment explanation
Indices: 58324958--58325003 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
58324948 ATCCACTATC
* *
58324958 ATT ATT ATT -TT -TT CTT -TT ATT ATT ATT ATT ATA ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
58325003 A
1 A
58325004 ACTTTATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:58328098 original size:26 final size:25
Alignment explanation
Indices: 58328068--58328129 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
58328058 TAATAAAACA
58328068 TAAATAGTAAT-AATTATATTATAAAT
1 TAAATA-TAATAAATT-TATTATAAAT
58328094 TAAATATGAATAAATTTATTATAAAT
1 TAAATAT-AATAAATTTATTATAAAT
58328120 T--ATATAATAA
1 TAAATATAATAA
58328130 TGGAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.15
24 4 0.12
25 1 0.03
26 20 0.59
27 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
TAAATATAATAAATTTATTATAAAT
Found at i:58329443 original size:55 final size:57
Alignment explanation
Indices: 58329362--58329507 Score: 165
Period size: 56 Copynumber: 2.6 Consensus size: 57
58329352 CGCGATATAT
** *
58329362 GAATGTATGTAAGACCATGACCTTAAGATCCATGGA-AAGATC-GATATAACTGAAC
1 GAATGTATGTAAGACCATGAGGTTAAGACCCATGGACAAGATCTGATATAACTGAAC
* * * * *
58329417 GAATGCATGTAAGACCATGAGGTTAAGACCCAT-CACAAGATCTGATATTATTGAAT
1 GAATGTATGTAAGACCATGAGGTTAAGACCCATGGACAAGATCTGATATAACTGAAC
* *
58329473 AAATGTATGTAAGACTAT-ATGGTTAAGACCCATGG
1 GAATGTATGTAAGACCATGA-GGTTAAGACCCATGG
58329508 CATTATATGA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
54 1 0.01
55 36 0.48
56 38 0.51
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (57 bp):
GAATGTATGTAAGACCATGAGGTTAAGACCCATGGACAAGATCTGATATAACTGAAC
Found at i:58333332 original size:3 final size:3
Alignment explanation
Indices: 58333324--58333354 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
58333314 TTAACTTTTA
58333324 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
58333355 AATGTGGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:58333675 original size:19 final size:20
Alignment explanation
Indices: 58333650--58333694 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
58333640 AATTATAAAA
58333650 AATAAAAATCAATAAAATTT
1 AATAAAAATCAATAAAATTT
* *
58333670 -ATAAAAATCATTAAACTTT
1 AATAAAAATCAATAAAATTT
58333689 AATAAA
1 AATAAA
58333695 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAAATCAATAAAATTT
Found at i:58333707 original size:13 final size:13
Alignment explanation
Indices: 58333689--58333715 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58333679 ATTAAACTTT
58333689 AATAAATATTTAA
1 AATAAATATTTAA
58333702 AATAAATATTTAA
1 AATAAATATTTAA
58333715 A
1 A
58333716 TTTTACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATAAATATTTAA
Found at i:58334081 original size:21 final size:20
Alignment explanation
Indices: 58334048--58334121 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
58334038 TTTTTCTATA
*
58334048 TTTATAA-TTTTTTAGGATT
1 TTTATAATTTTTTTAGAATT
**
58334067 TTTATAATCTTTTTTCTAATT
1 TTTATAAT-TTTTTTAGAATT
*
58334088 TTTATAATTTTTATT-GATTTT
1 TTTATAATTTTT-TTAGA-ATT
*
58334109 TTTATCATTTTTT
1 TTTATAATTTTTT
58334122 GTCACATGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 7 0.16
20 6 0.13
21 32 0.71
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTATAATTTTTTTAGAATT
Found at i:58334107 original size:19 final size:19
Alignment explanation
Indices: 58334028--58334109 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 19
58334018 ACTTTATAAA
*
58334028 TTTTATATATTTTTTCT-AT
1 TTTTATA-ATTTTTTATGAT
* *
58334047 ATTTATAATTTTTTAGGAT
1 TTTTATAATTTTTTATGAT
* *
58334066 TTTTATAATCTTTTTTCTAAT
1 TTTTATAA--TTTTTTATGAT
58334087 TTTTATAA-TTTTTATTGAT
1 TTTTATAATTTTTTA-TGAT
58334106 TTTT
1 TTTT
58334110 TTATCATTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
18 12 0.24
19 22 0.44
21 16 0.32
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.68
Consensus pattern (19 bp):
TTTTATAATTTTTTATGAT
Found at i:58334107 original size:40 final size:38
Alignment explanation
Indices: 58334028--58334121 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 38
58334018 ACTTTATAAA
58334028 TTTTATATATTTTTTCTATATTTATAATTTTTTAGGAT
1 TTTTATATATTTTTTCTATATTTATAATTTTTTAGGAT
* * *
58334066 TTTTATAATCTTTTTTCTAATTTTTATAA-TTTTTATTGAT
1 TTTTAT-ATATTTTTTCT-ATATTTATAATTTTTTA-GGAT
*
58334106 TTTTTTATCATTTTTT
1 TTTTATAT-ATTTTTT
58334122 GTCACATGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
38 6 0.13
39 18 0.38
40 23 0.49
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.69
Consensus pattern (38 bp):
TTTTATATATTTTTTCTATATTTATAATTTTTTAGGAT
Found at i:58334109 original size:10 final size:9
Alignment explanation
Indices: 58333955--58334101 Score: 54
Period size: 9 Copynumber: 15.4 Consensus size: 9
58333945 GGCATGATAA
58333955 TTATAATTT
1 TTATAATTT
58333964 TTATAATTCTT
1 TTATAA-T-TT
58333975 TTATGAA-TT
1 TTAT-AATTT
58333984 TTAT-ATTT
1 TTATAATTT
* *
58333992 CTTACATTTT
1 -TTATAATTT
*
58334002 TTATCATTT
1 TTATAATTT
*
58334011 TCT-TACGA-CT
1 T-TATA--ATTT
*
58334021 TTATAAATT
1 TTATAATTT
58334030 TTATATATTT
1 TTATA-ATTT
* *
58334040 TT-TCTATAT
1 TTAT-AATTT
58334049 TTATAATTT
1 TTATAATTT
58334058 TT-TAGGATTT
1 TTATA--ATTT
58334068 TTATAATCTTTT
1 TTATAA---TTT
*
58334080 TTCTAATTT
1 TTATAATTT
58334089 TTATAATTT
1 TTATAATTT
58334098 TTAT
1 TTAT
58334102 TGATTTTTTT
Statistics
Matches: 103, Mismatches: 15, Indels: 40
0.65 0.09 0.25
Matches are distributed among these distances:
7 1 0.01
8 5 0.05
9 57 0.55
10 21 0.20
11 9 0.09
12 10 0.10
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (9 bp):
TTATAATTT
Found at i:58336686 original size:20 final size:20
Alignment explanation
Indices: 58336649--58336692 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
58336639 TTAAAAATAT
*
58336649 TTTTATATTTATGTTTTAAA
1 TTTTATATTTATGATTTAAA
*
58336669 TTTTATAATTTAT-ATTTACA
1 TTTTAT-ATTTATGATTTAAA
58336689 TTTT
1 TTTT
58336693 TCTCATCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTATATTTATGATTTAAA
Found at i:58337187 original size:11 final size:11
Alignment explanation
Indices: 58337171--58337195 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58337161 TTATGATTTT
58337171 AATATTTTTAA
1 AATATTTTTAA
58337182 AATATTTTTAA
1 AATATTTTTAA
58337193 AAT
1 AAT
58337196 TTCTATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATATTTTTAA
Found at i:58337384 original size:3 final size:3
Alignment explanation
Indices: 58337376--58337418 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
58337366 TACCCAAAAG
58337376 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
58337419 AGAAGAAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:58342048 original size:5 final size:5
Alignment explanation
Indices: 58342038--58342063 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
58342028 TGAGCATTCG
58342038 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
58342064 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:58345810 original size:225 final size:225
Alignment explanation
Indices: 58345401--58345811 Score: 655
Period size: 225 Copynumber: 1.8 Consensus size: 225
58345391 AAAATTTATT
* *
58345401 TTTGTTTGCTGAAAACTCTTCATCTTCTTCCTCAACACCTGACTATGTTCCAATGTTTGCTCCTC
1 TTTGTTTGCTGAAAACTCTTCATCTTCTACCTCAACACCTGACTATGTTCCAACGTTTGCTCCTC
* * * *
58345466 TTGTATAGTCTCAGTCAAATCACTCTATCTCTCCTAATAGAGATGTCGACATACGAAGTCCTGCA
66 TTGTACAGTCTCAGTCAAATCACTCTATCTCTCCTAAAAGAGATGTCGACATACAAAGTCCTACA
* * * * * *
58345531 GTTTAGTCTCATGGTACCTTAGACTTGCCATTTTTGGAAATTGATGTCAGTGCCTTGGGTCCAGT
131 GTTTAATCTCATGATACCATAGACTCGCCATTTTTGGAAAGTGATGACAGTGCCTTGGGTCCAGT
58345596 AGCAACACCTCTCCCCCAACACTTGAGTTG
196 AGCAACACCTCTCCCCCAACACTTGAGTTG
* *
58345626 TTTGTTTGCTGAGAACTCTTCATCTTCTACCTCAACACCTGACTGTGTTCCAACGTTTGCTCCTC
1 TTTGTTTGCTGAAAACTCTTCATCTTCTACCTCAACACCTGACTATGTTCCAACGTTTGCTCCTC
*
58345691 TTGTACAGTCTCAGTCACATCACTCTATCTCTCCTAAAAGAGATGTCGACATACAAAG-CTCTAC
66 TTGTACAGTCTCAGTCAAATCACTCTATCTCTCCTAAAAGAGATGTCGACATACAAAGTC-CTAC
58345755 AGTTTAATCTCATGATACCATAGACTCGCCATTTTTGGAAAGTGAT-ACAAGTGCCTT
130 AGTTTAATCTCATGATACCATAGACTCGCCATTTTTGGAAAGTGATGAC-AGTGCCTT
58345812 AGATCACAGT
Statistics
Matches: 169, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
224 2 0.01
225 167 0.99
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (225 bp):
TTTGTTTGCTGAAAACTCTTCATCTTCTACCTCAACACCTGACTATGTTCCAACGTTTGCTCCTC
TTGTACAGTCTCAGTCAAATCACTCTATCTCTCCTAAAAGAGATGTCGACATACAAAGTCCTACA
GTTTAATCTCATGATACCATAGACTCGCCATTTTTGGAAAGTGATGACAGTGCCTTGGGTCCAGT
AGCAACACCTCTCCCCCAACACTTGAGTTG
Found at i:58368132 original size:41 final size:40
Alignment explanation
Indices: 58368077--58368226 Score: 230
Period size: 41 Copynumber: 3.7 Consensus size: 40
58368067 TTTCGGGGCT
*
58368077 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGAAGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-AAGC
*
58368118 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAAGC
*
58368158 TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTTAAGGC
1 -TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAA-GC
*
58368200 TTTAGCGGCGTTTTTG-GAAAGCGCCGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGC
58368227 AAAAACATTT
Statistics
Matches: 102, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
40 13 0.13
41 87 0.85
42 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAAGC
Found at i:58368210 original size:82 final size:81
Alignment explanation
Indices: 58368073--58368226 Score: 256
Period size: 82 Copynumber: 1.9 Consensus size: 81
58368063 GACCTTTCGG
*
58368073 GGCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGAAGCTTTAGCGGCGTTTTTGAAAA
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGAAGCTTTAGCGGCGTTTTTG-AAA
58368138 AGCGCCGCTAATGCTCA
65 AGCGCCGCTAATGCTCA
* *
58368155 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCT-TAAGGCTTTAGCGGCGTTTTTGGAA
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGAA-GCTTTAGCGGCGTTTTTGAAA
58368219 AGCGCCGC
65 AGCGCCGC
58368227 AAAAACATTT
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
81 12 0.18
82 56 0.82
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (81 bp):
GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGAAGCTTTAGCGGCGTTTTTGAAAA
GCGCCGCTAATGCTCA
Found at i:58368781 original size:7 final size:7
Alignment explanation
Indices: 58368771--58368803 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
58368761 TAGTAGTTAA
58368771 GGGTTTG
1 GGGTTTG
58368778 GGGTTTG
1 GGGTTTG
58368785 GGGTTTG
1 GGGTTTG
*
58368792 GGGTTAG
1 GGGTTTG
58368799 GGGTT
1 GGGTT
58368804 AAGAGTTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.58, T:0.39
Consensus pattern (7 bp):
GGGTTTG
Found at i:58368788 original size:14 final size:14
Alignment explanation
Indices: 58368766--58368803 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
58368756 AGGGTTAGTA
*
58368766 GTTAAGGGTTTGGG
1 GTTAGGGGTTTGGG
*
58368780 GTTTGGGGTTTGGG
1 GTTAGGGGTTTGGG
58368794 GTTAGGGGTT
1 GTTAGGGGTT
58368804 AAGAGTTAGT
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:0.08, C:0.00, G:0.53, T:0.39
Consensus pattern (14 bp):
GTTAGGGGTTTGGG
Found at i:58368932 original size:7 final size:7
Alignment explanation
Indices: 58368917--58368991 Score: 69
Period size: 7 Copynumber: 10.4 Consensus size: 7
58368907 ATTGTAAAAG
*
58368917 AGGGGTT
1 AGGGTTT
58368924 AGGGTTT
1 AGGGTTT
58368931 AGGGGTTT
1 A-GGGTTT
58368939 AGGGTTT
1 AGGGTTT
58368946 AGGGTTT
1 AGGGTTT
* *
58368953 ATGTTTT
1 AGGGTTT
* *
58368960 ATGATTT
1 AGGGTTT
58368967 AGGGTTT
1 AGGGTTT
* *
58368974 AGGATAT
1 AGGGTTT
58368981 AGGGGTTT
1 A-GGGTTT
58368989 AGG
1 AGG
58368992 AGATAGTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
7 44 0.79
8 12 0.21
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.41
Consensus pattern (7 bp):
AGGGTTT
Found at i:58368986 original size:15 final size:15
Alignment explanation
Indices: 58368968--58368997 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58368958 TTATGATTTA
*
58368968 GGGTTTAGGATATAG
1 GGGTTTAGGAGATAG
58368983 GGGTTTAGGAGATAG
1 GGGTTTAGGAGATAG
58368998 TTTAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.43, T:0.30
Consensus pattern (15 bp):
GGGTTTAGGAGATAG
Found at i:58371163 original size:31 final size:31
Alignment explanation
Indices: 58371125--58371186 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
58371115 TATGTGATAG
*
58371125 AGTCTCGTTTGTGTTTGTTTTTAACCCAGGT
1 AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
58371156 AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
1 AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
58371187 GCTTTTATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.13, C:0.18, G:0.23, T:0.47
Consensus pattern (31 bp):
AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
Found at i:58373200 original size:43 final size:44
Alignment explanation
Indices: 58373102--58373368 Score: 289
Period size: 43 Copynumber: 6.2 Consensus size: 44
58373092 AGGTTATGTT
* ** * *
58373102 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT--TTGTTC
1 TTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCAGTGGTC
* *
58373144 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGT-AGTGGTC
1 TTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCAGTGGTC
*
58373187 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTC-GTGGTC
1 TTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCAGTGGTC
* *
58373230 TTTAGCGGTGTTTGTGAGAAAAGCGCCGCTAAAGGTCAG-GGTC
1 TTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCAGTGGTC
* * ** * * *
58373273 TATCGCGATGTTTATGGGAGAAGCGCCGCTAAAGGTCAG-CGTC
1 TTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCAGTGGTC
* * *
58373316 TTTTGCGGCGTTTGT-AGGAGAAGCGTCGCTAAATGTCA-TGGTC
1 TTTAGCGGCGTTTGTGA-GAGAAGCGCCGCTAAAGGTCAGTGGTC
58373359 TTTAGCGGCG
1 TTTAGCGGCG
58373369 CTTTTCCAAA
Statistics
Matches: 192, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
42 33 0.17
43 158 0.82
44 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (44 bp):
TTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCAGTGGTC
Found at i:58373260 original size:86 final size:87
Alignment explanation
Indices: 58373102--58373368 Score: 321
Period size: 86 Copynumber: 3.1 Consensus size: 87
58373092 AGGTTATGTT
* ** * * *
58373102 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTTGTGATAAAA
1 TTTAGCGGCGTTTATGGGAGAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGAGAAAA
58373166 GCGCCGCTAAAGGT-AGTGGTC
66 GCGCCGCTAAAGGTCAGTGGTC
* *
58373187 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGTGTTTGTGAGAAAA
1 TTTAGCGGCGTTTATGGGAGAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGAGAAAA
58373252 GCGCCGCTAAAGGTCAG-GGTC
66 GCGCCGCTAAAGGTCAGTGGTC
* * ** * * *
58373273 TATCGCGATGTTTATGGGAGAAGCGCCGCTAAAGGTCAG-CGTCTTTTGCGGCGTTTGT-AGGAG
1 TTTAGCGGCGTTTATGGGAGAAGCGCCGCTAAAGGTC-GTGGTCTTTAGCGGCGTTTGTGA-GAA
* *
58373336 AAGCGTCGCTAAATGTCA-TGGTC
64 AAGCGCCGCTAAAGGTCAGTGGTC
58373359 TTTAGCGGCG
1 TTTAGCGGCG
58373369 CTTTTCCAAA
Statistics
Matches: 155, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
85 34 0.22
86 118 0.76
87 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (87 bp):
TTTAGCGGCGTTTATGGGAGAAGCGCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGAGAAAA
GCGCCGCTAAAGGTCAGTGGTC
Found at i:58373893 original size:25 final size:25
Alignment explanation
Indices: 58373853--58373935 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
58373843 GGTCTGCTCC
* * * *
58373853 GTTCCGTTCTATTCTGTTCCCTCTT
1 GTTCTGTTCTACTCTGTTCCATCCT
* *
58373878 GTTTTGTTCTGCTCTGTTCCATCCT
1 GTTCTGTTCTACTCTGTTCCATCCT
* ** *
58373903 GTTCTGTTCTACTCTATTCGGTTCT
1 GTTCTGTTCTACTCTGTTCCATCCT
58373928 GTTCTGTT
1 GTTCTGTT
58373936 TGAATTGCGT
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.05, C:0.27, G:0.16, T:0.53
Consensus pattern (25 bp):
GTTCTGTTCTACTCTGTTCCATCCT
Found at i:58374516 original size:2 final size:2
Alignment explanation
Indices: 58374509--58374537 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58374499 ATATTTAATC
58374509 AT AT 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 AT AT A
58374538 GAATATCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58375573 original size:18 final size:18
Alignment explanation
Indices: 58375540--58375574 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58375530 TATAGAAATG
*
58375540 AAATGATTTACCAATATA
1 AAATGATTTAACAATATA
*
58375558 AAATGATTTAATAATAT
1 AAATGATTTAACAATAT
58375575 TTTTGTATGG
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:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (18 bp):
AAATGATTTAACAATATA
Found at i:58384220 original size:13 final size:14
Alignment explanation
Indices: 58384199--58384231 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
58384189 TATAGGGACC
*
58384199 AATTTATGT-TAAA
1 AATTAATGTATAAA
58384212 AATTAATGTATAAA
1 AATTAATGTATAAA
58384226 AATTAA
1 AATTAA
58384232 AATTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (14 bp):
AATTAATGTATAAA
Found at i:58384356 original size:84 final size:85
Alignment explanation
Indices: 58384196--58384359 Score: 235
Period size: 84 Copynumber: 1.9 Consensus size: 85
58384186 AAATATAGGG
* *
58384196 ACCAATTTATGTTAAAAATTAATGTATAAAAATTAAAATTAAAATTTAGACATTTTAGACTGACC
1 ACCAATTTATGTTAAAAATTAAAGTATAAAAATTAAAATTAAAATTTAGAAATTTTAGACTGACC
* *
58384261 AATATTAAAATTTAATAGAA
66 AAAACTAAAATTTAATAGAA
*
58384281 ACCAATTTATGTTAAAAATTAAAGTAT-AAAATT-AAATTTAAATTATAGAAATTTTAGA-TAGA
1 ACCAATTTATGTTAAAAATTAAAGTATAAAAATTAAAATTAAAATT-TAGAAATTTTAGACT-GA
*
58384343 CCAAAACTGAAATTTAA
64 CCAAAACTAAAATTTAA
58384360 CCAAAATGCA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
83 11 0.15
84 34 0.48
85 26 0.37
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (85 bp):
ACCAATTTATGTTAAAAATTAAAGTATAAAAATTAAAATTAAAATTTAGAAATTTTAGACTGACC
AAAACTAAAATTTAATAGAA
Found at i:58384438 original size:17 final size:17
Alignment explanation
Indices: 58384416--58384450 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
58384406 AAGTAGAAGG
58384416 AAGGTCTTTTGAATCTT
1 AAGGTCTTTTGAATCTT
58384433 AAGGTCTTTTGAATCTT
1 AAGGTCTTTTGAATCTT
58384450 A
1 A
58384451 CACATATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (17 bp):
AAGGTCTTTTGAATCTT
Found at i:58399685 original size:45 final size:45
Alignment explanation
Indices: 58399621--58399712 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
58399611 CTTTGGGGAG
58399621 TTATACAATGAAATCGCGATATCTAAAGGAGGATATCGCAATTTC
1 TTATACAATGAAATCGCGATATCTAAAGGAGGATATCGCAATTTC
* * *
58399666 TTATACAGTGAAATCGCGATATCTAAATGAGGATATCGCGATTTC
1 TTATACAATGAAATCGCGATATCTAAAGGAGGATATCGCAATTTC
58399711 TT
1 TT
58399713 CAACATATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (45 bp):
TTATACAATGAAATCGCGATATCTAAAGGAGGATATCGCAATTTC
Found at i:58399704 original size:22 final size:22
Alignment explanation
Indices: 58399633--58399707 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
58399623 ATACAATGAA
*
58399633 ATCGCGATATCTAAAGGAGGAT
1 ATCGCGATATCTAAATGAGGAT
* * * * *
58399655 ATCGCAATTTCT-TATACAGTGAA
1 ATCGCGATATCTAAAT-GAG-GAT
58399678 ATCGCGATATCTAAATGAGGAT
1 ATCGCGATATCTAAATGAGGAT
58399700 ATCGCGAT
1 ATCGCGAT
58399708 TTCTTCAACA
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
21 1 0.03
22 22 0.56
23 14 0.36
24 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (22 bp):
ATCGCGATATCTAAATGAGGAT
Found at i:58401834 original size:23 final size:23
Alignment explanation
Indices: 58401785--58401834 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
58401775 ATGCACATAT
*
58401785 TTTTATATGTTTTAGTTTTTTAC
1 TTTTATATGTTTTAGTTGTTTAC
58401808 TTTTATATTGTTTT-GTATGTTTA-
1 TTTTATA-TGTTTTAGT-TGTTTAC
58401831 TTTT
1 TTTT
58401835 CATTTTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.72
Consensus pattern (23 bp):
TTTTATATGTTTTAGTTGTTTAC
Found at i:58411675 original size:20 final size:20
Alignment explanation
Indices: 58411647--58411687 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
58411637 TGTTGGTTAC
*
58411647 TGGGTATTTGGTTGGTTCGT
1 TGGGCATTTGGTTGGTTCGT
58411667 TGGGCATTTGGTTGGTTCGT
1 TGGGCATTTGGTTGGTTCGT
58411687 T
1 T
58411688 TGGTAGTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.07, G:0.39, T:0.49
Consensus pattern (20 bp):
TGGGCATTTGGTTGGTTCGT
Found at i:58414361 original size:21 final size:21
Alignment explanation
Indices: 58414337--58414391 Score: 56
Period size: 27 Copynumber: 2.3 Consensus size: 21
58414327 CTTGTACAAC
58414337 ATTTAGTTGATTTAGATTTAA
1 ATTTAGTTGATTTAGATTTAA
58414358 ATTTAGTATTCGTTGATTTAGATTTAA
1 A-TT--TA---GTTGATTTAGATTTAA
58414385 ATTTAGT
1 ATTTAGT
58414392 AATCTAACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
21 3 0.11
22 2 0.07
24 4 0.14
26 2 0.07
27 17 0.61
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.53
Consensus pattern (21 bp):
ATTTAGTTGATTTAGATTTAA
Found at i:58415424 original size:48 final size:49
Alignment explanation
Indices: 58415351--58415452 Score: 145
Period size: 48 Copynumber: 2.1 Consensus size: 49
58415341 TGTGTTATGA
* * *
58415351 AATTATATATAGTGTTAAGCTTTTGATTCATGATATTTAACTT-AATTAT
1 AATTTTATAAAGTGTTAAGCTTTTGATTCATGATATTAAACTTAAATT-T
*
58415400 AATTTTATAAAGTGTTCA-CTTTTGATTCATGATATTAAACTTAAATTT
1 AATTTTATAAAGTGTTAAGCTTTTGATTCATGATATTAAACTTAAATTT
58415448 AATTT
1 AATTT
58415453 GTTTTTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
48 29 0.60
49 19 0.40
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (49 bp):
AATTTTATAAAGTGTTAAGCTTTTGATTCATGATATTAAACTTAAATTT
Found at i:58416751 original size:47 final size:47
Alignment explanation
Indices: 58416698--58416838 Score: 134
Period size: 47 Copynumber: 3.1 Consensus size: 47
58416688 TCATATAAGA
*
58416698 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
* * *
58416745 ATATTTA--A-TAACAATTATT-TTAAATTATACA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATT-TTATGAAATTATATATAATT-AT-TAA-ATT
* * *
58416789 AAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
58416836 ATA
1 ATA
58416839 CAAATTCATA
Statistics
Matches: 72, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
43 3 0.04
44 25 0.35
45 7 0.10
46 7 0.10
47 27 0.38
48 3 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
Found at i:58416817 original size:38 final size:36
Alignment explanation
Indices: 58416775--58416887 Score: 91
Period size: 37 Copynumber: 3.3 Consensus size: 36
58416765 TAAATTATAC
58416775 AAATTCATATAAGAAAATTTATTATCAAGAATTTTATG
1 AAATT-ATATAAGAAAATTTATTAT-AAGAATTTTATG
* * *
58416813 AAATTATAT------A-TTATTATTA-AATTATA-C
1 AAATTATATAAGAAAATTTATTATAAGAATTTTATG
*
58416840 AAATTCATATAAGAAAATTTATTAGTAAGAGTTTTATG
1 AAATT-ATATAAGAAAATTTATTA-TAAGAATTTTATG
58416878 AAATTATATA
1 AAATTATATA
58416888 TTTATTATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 23
0.66 0.08 0.26
Matches are distributed among these distances:
27 5 0.09
28 10 0.18
29 1 0.02
30 7 0.12
31 1 0.02
34 1 0.02
35 6 0.11
36 2 0.04
37 14 0.25
38 10 0.18
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.42
Consensus pattern (36 bp):
AAATTATATAAGAAAATTTATTATAAGAATTTTATG
Found at i:58416844 original size:65 final size:65
Alignment explanation
Indices: 58416758--58416904 Score: 253
Period size: 65 Copynumber: 2.3 Consensus size: 65
58416748 TTTAATAACA
58416758 ATTATT-TTAAATTATACAAATTCATATAAGAAAATTTATTA-TCAAGAATTTTATGAAATTATA
1 ATTATTATTAAATTATACAAATTCATATAAGAAAATTTATTAGT-AAGAATTTTATGAAATTATA
58416821 T
65 T
*
58416822 ATTATTATTAAATTATACAAATTCATATAAGAAAATTTATTAGTAAGAGTTTTATGAAATTATAT
1 ATTATTATTAAATTATACAAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATAT
58416887 ATTTATTATTAAATTATA
1 A-TTATTATTAAATTATA
58416905 TTTAATATTA
Statistics
Matches: 79, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
64 6 0.08
65 56 0.71
66 17 0.22
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (65 bp):
ATTATTATTAAATTATACAAATTCATATAAGAAAATTTATTAGTAAGAATTTTATGAAATTATAT
Found at i:58416906 original size:17 final size:16
Alignment explanation
Indices: 58416884--58416928 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
58416874 TATGAAATTA
*
58416884 TATATTTATTATTAAAT
1 TATATTTAATATT-AAT
58416901 TATATTTAATATTAAT
1 TATATTTAATATTAAT
58416917 TAT-TTTAA-ATTA
1 TATATTTAATATTA
58416929 TACAAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 4 0.15
15 5 0.19
16 6 0.22
17 12 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATTTAATATTAAT
Found at i:58416967 original size:47 final size:48
Alignment explanation
Indices: 58416822--58416974 Score: 158
Period size: 47 Copynumber: 3.3 Consensus size: 48
58416812 GAAATTATAT
*
58416822 ATTATTATTAAATTATACAAATTCATATAAGAAAATTTATTAGTAAGA
1 ATTATTATTAAATTATACAAATTCATATAAGAAAATTTATTAGTAATA
* * * * ** * *
58416870 GTT-TTATGAAATTAT--ATATT--TATTATTAAATTATATTTAATATTA
1 ATTATTATTAAATTATACAAATTCATATAAGAAAATT-TA-TTAGTAATA
58416915 ATTATT-TTAAATTATACAAATTCATATAAGAAAATTTATTAGTAATA
1 ATTATTATTAAATTATACAAATTCATATAAGAAAATTTATTAGTAATA
58416962 ATTATT-TTAAATT
1 ATTATTATTAAATT
58416975 TTATTAAATC
Statistics
Matches: 81, Mismatches: 17, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
43 9 0.11
44 2 0.02
45 20 0.25
46 2 0.02
47 35 0.43
48 4 0.05
49 9 0.11
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.47
Consensus pattern (48 bp):
ATTATTATTAAATTATACAAATTCATATAAGAAAATTTATTAGTAATA
Found at i:58417000 original size:18 final size:15
Alignment explanation
Indices: 58416972--58417022 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
58416962 ATTATTTTAA
58416972 ATTTTATTAAATCATAT
1 ATTTTATTAAA--ATAT
58416989 ATTTTAATTAAAATAT
1 ATTTT-ATTAAAATAT
* *
58417005 ATTTAATAAAAAT-T
1 ATTTTATTAAAATAT
58417019 ATTT
1 ATTT
58417023 CAAATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 8 0.26
17 5 0.16
18 6 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTTATTAAAATAT
Found at i:58417006 original size:16 final size:16
Alignment explanation
Indices: 58416972--58417022 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
58416962 ATTATTTTAA
58416972 ATTTT-ATTAAATCATAT
1 ATTTTAATTAAA--ATAT
58416989 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
58417005 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
58417019 ATTT
1 ATTT
58417023 CAAATTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 2 0.06
15 13 0.42
16 5 0.16
17 5 0.16
18 6 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:58417033 original size:120 final size:119
Alignment explanation
Indices: 58416928--58417260 Score: 426
Period size: 120 Copynumber: 2.8 Consensus size: 119
58416918 ATTTTAAATT
*
58416928 ATACAA-ATTCATATAAGAAAATT-TATTAGTAATAATT-ATT-TT-A-AATTTTATTAAATCAT
1 ATACAATA-TCATATAAGAAAATTATATAAG-AAT-ATTGATTATTAAGAATTTTATTAAATCAT
58416987 ATATTTTAATTAAAATATATTTAATAAAAATTATTTCAAATTATATTTTATAGTATC
63 ATATTTTAATTAAAATATATTTAATAAAAATTATTTCAAATTATATTTTATAGTATC
* * * * * *
58417044 ATACATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATAT
1 ATACAATATCATATAAGAAAATT-ATATAAGAATATTGATTATTAAGAATTTTATTAAATCATAT
* *
58417109 ATTTTAGTTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATC
65 ATTTTAATTAAAATATATTTAATAAAAATTATTTCAAATTATATTTTATAGTATC
* * * * * * *
58417164 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATAT
1 ATACAATATCATATAAGAAAATT-ATATAAGAATATTGATTATTAAGAATTTTATTAAATCATAT
*
58417229 ATTTTAATTAAAATATATTTAATAATAATTAT
65 ATTTTAATTAAAATATATTTAATAAAAATTAT
58417261 GTTAAAATAT
Statistics
Matches: 199, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
116 19 0.10
117 7 0.04
118 7 0.04
119 1 0.01
120 165 0.83
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (119 bp):
ATACAATATCATATAAGAAAATTATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATA
TTTTAATTAAAATATATTTAATAAAAATTATTTCAAATTATATTTTATAGTATC
Found at i:58417046 original size:59 final size:59
Alignment explanation
Indices: 58416982--58417170 Score: 170
Period size: 59 Copynumber: 3.2 Consensus size: 59
58416972 ATTTTATTAA
58416982 ATCATATATTTTAATTAAAATATATTTAATAAAAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAAAAATTATTTCAAATTATATTTTATAGT
* * * ** * * * * * *
58417041 ATCATACATTATGATTTTAGTAAATTCATATAAGAATATTGATTAT-TAA-GA-ATTTTATTA-A
1 ATCATATATTTTAATTAAAATATATTTA-ATAA-AA-ATT-ATT-TCAAATTATATTTTA-TAGT
* * *
58417102 ATTATATATTTTAGTTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAAAAATTATTTCAAATTATATTTTATAGT
58417161 ATCATATATT
1 ATCATATATT
58417171 ATGATTTTAG
Statistics
Matches: 94, Mismatches: 26, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
56 1 0.01
57 5 0.05
58 6 0.06
59 36 0.38
60 8 0.09
61 26 0.28
62 6 0.06
63 5 0.05
64 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (59 bp):
ATCATATATTTTAATTAAAATATATTTAATAAAAATTATTTCAAATTATATTTTATAGT
Found at i:58417068 original size:130 final size:120
Alignment explanation
Indices: 58416971--58417260 Score: 544
Period size: 120 Copynumber: 2.4 Consensus size: 120
58416961 AATTATTTTA
* *
58416971 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAAAAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
58417036 ATAGTATCATACATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATACATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
58417091 AATTTTATTAAATTATATATTTTAGTTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
58417156 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATACATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
58417211 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
58417261 GTTAAAATAT
Statistics
Matches: 165, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 165 1.00
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATACATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:58417125 original size:18 final size:17
Alignment explanation
Indices: 58417092--58417126 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58417082 ATTATTAAGA
*
58417092 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
58417109 ATTTTAGTTAAAATATAT
1 ATTTTA-TTAAAATATAT
58417127 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:58417217 original size:61 final size:61
Alignment explanation
Indices: 58417031--58417218 Score: 196
Period size: 63 Copynumber: 3.1 Consensus size: 61
58417021 TTCAAATTAT
*
58417031 ATTTTATAGTATCATACATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGA
* * * *
58417092 ATTTTAT--TA-AAT-TA-TAT-ATTTTAGTTAAAATAT-ATTTAATAATAATT-ATT-TCAAAT
1 ATTTTATAGTATCATATATTATGATTTTAG-T-AAAT-TCATATAAGAAT-ATTGATTAT-TAA-
*
58417148 TA
60 GA
58417150 TATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGA
1 -ATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGA
58417212 ATTTTAT
1 ATTTTAT
58417219 TAAATTATAT
Statistics
Matches: 100, Mismatches: 11, Indels: 32
0.70 0.08 0.22
Matches are distributed among these distances:
55 7 0.07
56 5 0.05
57 18 0.18
58 7 0.07
59 9 0.09
61 16 0.16
62 7 0.07
63 19 0.19
64 5 0.05
65 7 0.07
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (61 bp):
ATTTTATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGA
Found at i:58417229 original size:61 final size:61
Alignment explanation
Indices: 58417048--58417231 Score: 186
Period size: 61 Copynumber: 3.0 Consensus size: 61
58417038 AGTATCATAC
58417048 ATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATAT
1 ATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATAT
* * * * * * * *
58417109 ATT-TTA-GTTA--AAATAT-ATTTAATAATAATT-ATT-TCAAATTATATTTTA-TAGTATCAT
1 ATTATGATTTTAGTAAAT-TCATATAAGAAT-ATTGATTAT-TAA-GA-ATTTTATTA-AATTAT
58417166 AT
60 AT
58417168 ATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATAT
1 ATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATAT
58417229 ATT
1 ATT
58417232 TTAATTAAAA
Statistics
Matches: 93, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
56 1 0.01
57 17 0.18
58 7 0.08
59 18 0.19
60 4 0.04
61 21 0.23
62 7 0.08
63 17 0.18
64 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATAT
Found at i:58417240 original size:18 final size:17
Alignment explanation
Indices: 58417212--58417246 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58417202 ATTATTAAGA
*
58417212 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
58417229 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
58417247 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:58417473 original size:44 final size:46
Alignment explanation
Indices: 58417406--58417493 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 46
58417396 TTACACATCC
* * * *
58417406 ATTCCATTCAACTAAGCACAAGAA-TA-CTATTACGTCTCTATTCT
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCT
58417450 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATT
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATT
58417494 TCATTACATC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 21 0.55
45 2 0.05
46 15 0.39
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCT
Found at i:58425837 original size:26 final size:25
Alignment explanation
Indices: 58425808--58425857 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
58425798 TTGATTTAAA
*
58425808 TAGATTCACGGTGGAGTTTGTTTTTG
1 TAGATTCACGATGGAGTTT-TTTTTG
* *
58425834 TAGATTTATGATGGAGTTTTTTTT
1 TAGATTCACGATGGAGTTTTTTTT
58425858 CTTTTTTGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.18, C:0.04, G:0.26, T:0.52
Consensus pattern (25 bp):
TAGATTCACGATGGAGTTTTTTTTG
Found at i:58433573 original size:20 final size:21
Alignment explanation
Indices: 58433528--58433566 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
58433518 CAATATAAGT
58433528 ATATATTAATTATTATTTAAC
1 ATATATTAATTATTATTTAAC
58433549 ATATA-TAATTGATT-TTTA
1 ATATATTAATT-ATTATTTA
58433567 TAATATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (21 bp):
ATATATTAATTATTATTTAAC
Found at i:58433800 original size:25 final size:24
Alignment explanation
Indices: 58433755--58433802 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
58433745 AATTTAAAGG
* * *
58433755 TTTAACTAAATTTAAACTATTTAC
1 TTTAACTAAAATAAAAATATTTAC
58433779 TTTAACTAAAATAAAATATATTTA
1 TTTAACTAAAATAAAA-ATATTTA
58433803 ATATCATAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTAACTAAAATAAAAATATTTAC
Found at i:58434320 original size:21 final size:21
Alignment explanation
Indices: 58434294--58434347 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
58434284 AATAACGGTG
*
58434294 GCGGTGAGATT-AGTTACTGTA
1 GCGGTGAGATTGA-ATACTGTA
58434315 GCGGTGAGATTGAATACTGTA
1 GCGGTGAGATTGAATACTGTA
58434336 GCGGTGAGATTG
1 GCGGTGAGATTG
58434348 GAAACAATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.24, C:0.09, G:0.37, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTGAATACTGTA
Found at i:58435298 original size:22 final size:22
Alignment explanation
Indices: 58435270--58435331 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
58435260 TTTATTGTTC
58435270 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
58435292 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
58435314 AGCCATGAGAGCTTAGTA
1 AAACATGAGAGCTTAGTA
58435332 GAAGCCAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:58437860 original size:14 final size:13
Alignment explanation
Indices: 58437826--58437854 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
58437816 ATATTTTTAA
58437826 TTACTTAATATTT
1 TTACTTAATATTT
58437839 TTACTTAATATTT
1 TTACTTAATATTT
58437852 TTA
1 TTA
58437855 AGTTAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (13 bp):
TTACTTAATATTT
Found at i:58437920 original size:16 final size:17
Alignment explanation
Indices: 58437901--58437933 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
58437891 AAACTTGAAA
58437901 AGTATATATAA-ATATT
1 AGTATATATAATATATT
*
58437917 AGTATTTATAATATATT
1 AGTATATATAATATATT
58437934 TAAGAGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
AGTATATATAATATATT
Found at i:58444518 original size:13 final size:13
Alignment explanation
Indices: 58444500--58444526 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58444490 AATTTTATAC
58444500 TTGTGCAAGTGGA
1 TTGTGCAAGTGGA
58444513 TTGTGCAAGTGGA
1 TTGTGCAAGTGGA
58444526 T
1 T
58444527 CCCTTCCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.37, T:0.33
Consensus pattern (13 bp):
TTGTGCAAGTGGA
Found at i:58447282 original size:29 final size:30
Alignment explanation
Indices: 58447223--58447280 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
58447213 TCCGAGCCTT
*
58447223 GGGGAAAAAATGTAATTATGTAAAAGTTTA
1 GGGGAAAAAATGTAATTATGAAAAAGTTTA
* * *
58447253 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAAATGTAATTATGAAAAAGTT
58447281 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGAAAAAATGTAATTATGAAAAAGTTTA
Found at i:58447511 original size:13 final size:13
Alignment explanation
Indices: 58447493--58447523 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58447483 TTCCAGCAAC
58447493 TATGAATTTATTT
1 TATGAATTTATTT
58447506 TATGAATTTATTT
1 TATGAATTTATTT
*
58447519 GATGA
1 TATGA
58447524 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:58447732 original size:50 final size:50
Alignment explanation
Indices: 58447618--58447859 Score: 268
Period size: 50 Copynumber: 4.7 Consensus size: 50
58447608 ATTTGGGTAA
* * *
58447618 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* *
58447674 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * * *
58447724 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * * *
58447774 AGAGGTCCCCTATAAGACCATCTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
58447824 AGAAAATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
58447860 TTTGGCATGT
Statistics
Matches: 162, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
50 89 0.55
51 28 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.24
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:58447810 original size:100 final size:103
Alignment explanation
Indices: 58447618--58447867 Score: 335
Period size: 100 Copynumber: 2.4 Consensus size: 103
58447608 ATTTGGGTAA
58447618 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
* * * *
58447683 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATCTCTGGGACATGGCATGGGCACCAACACG
* * * * *
58447724 AGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
*
58447786 TAAGACCATCTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATCTCTGGGACATGGCATGGGCACCAACACG
* *
58447824 AGAAAATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
58447868 GTTATTATCA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
100 49 0.38
101 38 0.30
105 2 0.02
106 39 0.30
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
TAAGACCATCTCTGGGACATGGCATGGGCACCAACACG
Found at i:58453098 original size:29 final size:30
Alignment explanation
Indices: 58453039--58453096 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
58453029 TCCGAGCCTT
* *
58453039 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATATAATTATGAAAAAGTTTA
* *
58453069 GGGGCAAAATTATAATTTTGAAAAAGTT
1 GGGGCAAAAATATAATTATGAAAAAGTT
58453097 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATATAATTATGAAAAAGTTTA
Found at i:58453327 original size:13 final size:13
Alignment explanation
Indices: 58453309--58453339 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58453299 TTCCAGCAAC
58453309 TATGAATTTATTT
1 TATGAATTTATTT
58453322 TATGAATTTATTT
1 TATGAATTTATTT
*
58453335 GATGA
1 TATGA
58453340 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:58453548 original size:50 final size:50
Alignment explanation
Indices: 58453434--58453675 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
58453424 ATTTGGGTAA
* * *
58453434 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* *
58453490 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
58453540 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
58453590 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
58453640 AGAAAATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
58453676 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 92 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:58453626 original size:100 final size:103
Alignment explanation
Indices: 58453434--58453683 Score: 353
Period size: 100 Copynumber: 2.4 Consensus size: 103
58453424 ATTTGGGTAA
58453434 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
* * *
58453499 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * * *
58453540 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
*
58453602 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
58453640 AGAAAATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
58453684 GTTATTATCA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:58465845 original size:22 final size:22
Alignment explanation
Indices: 58465798--58465845 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
58465788 TTAGTCTTTT
* **
58465798 AAATTTCTAACTCTAATCTCTT
1 AAATTTCTAACTCTAATATCGG
58465820 AAATTTCTAACTCTAAGTAT-GG
1 AAATTTCTAACTCTAA-TATCGG
58465842 AAAT
1 AAAT
58465846 GACTTGAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (22 bp):
AAATTTCTAACTCTAATATCGG
Found at i:58470144 original size:17 final size:17
Alignment explanation
Indices: 58470122--58470174 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
58470112 TCTAAAAGAA
58470122 ACATAATTAAAAATCCT
1 ACATAATTAAAAATCCT
*
58470139 ACATAA-TAAATAT--T
1 ACATAATTAAAAATCCT
58470153 --ATAATTAAAAATCCT
1 ACATAATTAAAAATCCT
58470168 ACATAAT
1 ACATAAT
58470175 AAATATTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 1 0.03
15 1 0.03
16 6 0.21
17 11 0.38
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (17 bp):
ACATAATTAAAAATCCT
Found at i:58470166 original size:29 final size:29
Alignment explanation
Indices: 58470124--58470182 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
58470114 TAAAAGAAAC
58470124 ATAATTAAAAATCCTACATAATAAATATT
1 ATAATTAAAAATCCTACATAATAAATATT
58470153 ATAATTAAAAATCCTACATAATAAATATT
1 ATAATTAAAAATCCTACATAATAAATATT
58470182 A
1 A
58470183 AGACAATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (29 bp):
ATAATTAAAAATCCTACATAATAAATATT
Found at i:58473534 original size:17 final size:19
Alignment explanation
Indices: 58473503--58473537 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
58473493 GGGGTAGCAA
58473503 AAAAATATAATAATAAAAT
1 AAAAATATAATAATAAAAT
58473522 AAAAATA-AA-AATAAAA
1 AAAAATATAATAATAAAA
58473538 GGAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAAATATAATAATAAAAT
Found at i:58473543 original size:17 final size:19
Alignment explanation
Indices: 58473503--58473544 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
58473493 GGGGTAGCAA
*
58473503 AAAAATATAATAATAAAAT
1 AAAAATATAATAATAAAAG
58473522 AAAAATA-AA-AATAAAAGG
1 AAAAATATAATAATAAAA-G
58473540 AAAAA
1 AAAAA
58473545 GAAAGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 7 0.33
18 7 0.33
19 7 0.33
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (19 bp):
AAAAATATAATAATAAAAG
Found at i:58474360 original size:30 final size:29
Alignment explanation
Indices: 58474321--58474387 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
58474311 ACCAAAAAAA
58474321 GCCACTTTTTTTAAAAAATTACCGAAATGG
1 GCCA-TTTTTTTAAAAAATTACCGAAATGG
* ** * *
58474351 GCCAGTTTTTTAATTATTTACCGGAATGG
1 GCCATTTTTTTAAAAAATTACCGAAATGG
58474380 GCCATTTT
1 GCCATTTT
58474388 CCCCGAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (29 bp):
GCCATTTTTTTAAAAAATTACCGAAATGG
Found at i:58474880 original size:124 final size:123
Alignment explanation
Indices: 58474700--58474953 Score: 366
Period size: 124 Copynumber: 2.1 Consensus size: 123
58474690 AAATAGTGGG
** * * * *
58474700 AAATCGCTTCTACCAGGATGCTATTTGAGAAAAAATTGTGAAATAGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATA
* *
58474765 TCGCTACAG-TGGTCATGTAAGAAATAATTTTTTTTGACTTTTACTGAGCAACTAGTATA
66 TCGCTACAGTTGGTCATGTAAGAAATAA-TTTTTTTGACGTTT-CTGAGCAAATAGTATA
* *
58474824 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATA
1 AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATA
* * *
58474889 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTGTC
66 TCGCTACAGTTGGTCATGTAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATA
58474947 AAATCGC
1 AAATCGC
58474954 GCCCTCGTGA
Statistics
Matches: 116, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
123 20 0.17
124 79 0.68
125 17 0.15
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (123 bp):
AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAGCGCCCTCGTGGACGCGATA
TCGCTACAGTTGGTCATGTAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:58480906 original size:14 final size:15
Alignment explanation
Indices: 58480889--58480922 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
58480879 AATAAATATC
58480889 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
58480903 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
58480918 TAAAA
1 TAAAA
58480923 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:58481148 original size:22 final size:22
Alignment explanation
Indices: 58481118--58481159 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58481108 ATTTGGAGAT
*
58481118 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
58481140 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
58481160 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:58481167 original size:30 final size:30
Alignment explanation
Indices: 58481131--58481189 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
58481121 TTGAAGGAAA
* * *
58481131 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGAAAATTGAGAGT
58481161 TTGAGAGAATTTTGGAAGAAAATTGAGAG
1 TTGAGAGAATTTTGGAAGAAAATTGAGAG
58481190 AATTTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGAAAATTGAGAGT
Found at i:58481184 original size:52 final size:51
Alignment explanation
Indices: 58481109--58481211 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
58481099 TTAATATGTA
* * * *
58481109 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGAAAATTGAGAGAATTTTGGAAGGGAA-TTGAGAG
*
58481160 TTTGAGAGAATTTTGGAAGAAAATTGAGAGAATTTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGAAAATTGAGAGAATTTTGGAAGGGAATTGAGAG
58481212 AATTTTTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 37 0.82
53 4 0.09
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGAAAATTGAGAGAATTTTGGAAGGGAATTGAGAG
Found at i:58481186 original size:22 final size:22
Alignment explanation
Indices: 58481161--58481230 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
58481151 ATTTGAGAGT
* *
58481161 TTGAGAGAATTTTGGAAGAAAA
1 TTGAGAGAATTTTTGAAGGAAA
*
58481183 TTGAGAGAATTTTTGAAGGGAA
1 TTGAGAGAATTTTTGAAGGAAA
58481205 TTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTTGAAGGAAA
58481227 TTGA
1 TTGA
58481231 TATTGAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (22 bp):
TTGAGAGAATTTTTGAAGGAAA
Found at i:58482160 original size:112 final size:111
Alignment explanation
Indices: 58482031--58482255 Score: 423
Period size: 112 Copynumber: 2.0 Consensus size: 111
58482021 AGGCTAAAAT
* *
58482031 ATAAATAATTTAGTGACAACTACTTAAGTAGACAACCTTATTAAAAGTATATGTACAATTAGTGA
1 ATAAATAATTTAGTGACAACTACTCAAGTAGACAACCCTATTAAAAGTATATGTACAATTAGTG-
58482096 AAAAATAATTAATATTATATATAGGCATACTATACTAAAAGTCAAAG
65 AAAAATAATTAATATTATATATAGGCATACTATACTAAAAGTCAAAG
58482143 ATAAATAATTTAGTGACAACTACTCAAGTAGACAACCCTATTAAAAGTATATGTACAATTAGTGA
1 ATAAATAATTTAGTGACAACTACTCAAGTAGACAACCCTATTAAAAGTATATGTACAATTAGTGA
58482208 AAAATAATTAATATTATATATAGGCATACTATACTAAAAGTCAAAG
66 AAAATAATTAATATTATATATAGGCATACTATACTAAAAGTCAAAG
58482254 AT
1 AT
58482256 TCTCTTATAT
Statistics
Matches: 111, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
111 49 0.44
112 62 0.56
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.31
Consensus pattern (111 bp):
ATAAATAATTTAGTGACAACTACTCAAGTAGACAACCCTATTAAAAGTATATGTACAATTAGTGA
AAAATAATTAATATTATATATAGGCATACTATACTAAAAGTCAAAG
Done.