Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 129 of 349
Found at i:41194790 original size:40 final size:40
Alignment explanation
Indices: 41194706--41194890 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
41194696 TCGAATGATG
* *
41194706 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
41194745 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
41194786 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTCACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
41194825 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
41194864 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41194891 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 35 0.28
40 80 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:41194842 original size:79 final size:81
Alignment explanation
Indices: 41194706--41194888 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
41194696 TCGAATGATG
* * *
41194706 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTCACTAAATCCGGACTAAGATCCGAAGGCATT
41194770 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* **
41194785 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTCACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTCACTAAATCCGGACTAAGAT-CCGAAGGCA
41194847 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
41194865 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
41194889 TGAACGAGTA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 60 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTCACTAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:41194912 original size:79 final size:78
Alignment explanation
Indices: 41194707--41194923 Score: 237
Period size: 79 Copynumber: 2.7 Consensus size: 78
41194697 CGAATGATGT
* *
41194707 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAG-TCCGAAGGCATT
*
41194770 TGTGCGAGTTACTAATT
62 TGTGCGAGTTACTAATA
* *
41194787 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTCA-CTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-AGCTATATCC-GGTTAAGT-CCGAAGGCATTT
41194850 GTGCGAGTTACT-ATAA
63 GTGCGAGTTACTAAT-A
* ** *
41194866 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTT-AAGTCCGAAGG
41194924 TACGTGATTC
Statistics
Matches: 117, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
78 3 0.03
79 68 0.58
80 46 0.39
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGTCCGAAGGCATTTGTG
CGAGTTACTAATA
Found at i:41195911 original size:16 final size:16
Alignment explanation
Indices: 41195876--41195916 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
41195866 TTATTTTCCT
* **
41195876 TTATTTACTTCTTTCT
1 TTATTTATTTCTTTAG
41195892 TTATTTATTTCTTTAG
1 TTATTTATTTCTTTAG
41195908 TTATTTATT
1 TTATTTATT
41195917 CATTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTATTTCTTTAG
Found at i:41197524 original size:5 final size:5
Alignment explanation
Indices: 41197514--41197548 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
41197504 ATTGAGTCTG
41197514 TTTTA TTTTA TTTTA TTTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTT
41197549 TCTGATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:41197535 original size:16 final size:16
Alignment explanation
Indices: 41197514--41197549 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
41197504 ATTGAGTCTG
41197514 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
41197530 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
41197546 TTTT
1 TTTT
41197550 CTGATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:41204507 original size:6 final size:6
Alignment explanation
Indices: 41204492--41204548 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
41204482 TGGTTTTCTA
* * * *
41204492 AAAATT AAAATG AAAA-A AGAAATG AAAATG AAAATA AAAATA AAAATG
1 AAAATG AAAATG AAAATG A-AAATG AAAATG AAAATG AAAATG AAAATG
41204540 AGAAATG AA
1 A-AAATG AA
41204549 TTCATTTAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 1 0.02
6 35 0.81
7 7 0.16
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:41204519 original size:18 final size:18
Alignment explanation
Indices: 41204490--41204545 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
41204480 TGTGGTTTTC
*
41204490 TAAAAATTAAAATGAAAA
1 TAAAAATAAAAATGAAAA
*
41204508 -AAGAAATGAAAATGAAAA
1 TAA-AAATAAAAATGAAAA
41204526 TAAAAATAAAAATGAGAAA
1 TAAAAATAAAAATGA-AAA
41204545 T
1 T
41204546 GAATTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 2 0.06
18 25 0.76
19 6 0.18
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (18 bp):
TAAAAATAAAAATGAAAA
Found at i:41204727 original size:26 final size:26
Alignment explanation
Indices: 41204697--41204766 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
41204687 TTGTCTCGAA
*
41204697 AATTTTATCAAGGGTAAAGTTGTCAT
1 AATTTTACCAAGGGTAAAGTTGTCAT
*
41204723 AATTTTACCAGGGGTAAAGTTGTCAT
1 AATTTTACCAAGGGTAAAGTTGTCAT
* *
41204749 TATTTTACCAAAGGTAAA
1 AATTTTACCAAGGGTAAA
41204767 ATTGGGATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (26 bp):
AATTTTACCAAGGGTAAAGTTGTCAT
Found at i:41237367 original size:40 final size:40
Alignment explanation
Indices: 41237305--41237602 Score: 449
Period size: 40 Copynumber: 7.5 Consensus size: 40
41237295 AAGCCAAGTA
* * * *
41237305 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACGAATG
*
41237344 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
*
41237384 CCTTCGGGGCTTAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
*
41237424 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
*
41237464 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
41237504 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* * * *
41237544 CCTTCAGGACTTAGCCCGGA-ACTAGTCACTAGCGCGAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACGAATG
41237584 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
41237603 TTATCATCCA
Statistics
Matches: 239, Mismatches: 17, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
39 13 0.05
40 226 0.95
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
Found at i:41245540 original size:40 final size:40
Alignment explanation
Indices: 41245496--41245760 Score: 426
Period size: 40 Copynumber: 6.6 Consensus size: 40
41245486 GCTACTTGCT
*
41245496 CGAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCA
1 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
41245536 CGAATGCCTTCGGGGCTTAGCCCGGATATAGTAACTCGCA
1 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
41245576 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
41245616 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCA
1 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
41245656 CGAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCA
1 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
41245696 CGAATGCCTTCAGGACTTAGCCCGGA-ACTAGTCACTAGCGA
1 CGAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGC-A
41245737 -GAATGCCTTCGGGACTTAGCCCGG
1 CGAATGCCTTCGGGACTTAGCCCGG
41245761 TTATCATCCA
Statistics
Matches: 210, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
39 1 0.00
40 208 0.99
41 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (40 bp):
CGAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:41257084 original size:21 final size:20
Alignment explanation
Indices: 41257056--41257095 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
41257046 AGTCACACAA
41257056 CCTAACCACAC-GAGCGTGTC
1 CCTAACCACACAG-GCGTGTC
41257076 CCTAGACCACACAGGCGTGT
1 CCTA-ACCACACAGGCGTGT
41257096 GGGTACTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 13 0.72
22 1 0.06
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15
Consensus pattern (20 bp):
CCTAACCACACAGGCGTGTC
Found at i:41258347 original size:22 final size:23
Alignment explanation
Indices: 41258322--41258365 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41258312 AGATTATGAA
*
41258322 ACATAT-AGGGGACTTTATCACC
1 ACATATAAGGGGACTCTATCACC
*
41258344 ACATATAAGTGGACTCTATCAC
1 ACATATAAGGGGACTCTATCAC
41258366 TATACATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (23 bp):
ACATATAAGGGGACTCTATCACC
Found at i:41267742 original size:16 final size:17
Alignment explanation
Indices: 41267721--41267757 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
41267711 TATAAATTAA
41267721 TTTTTGTTTTA-CAATT
1 TTTTTGTTTTAGCAATT
*
41267737 TTTTTGTTTTAGTAATT
1 TTTTTGTTTTAGCAATT
41267754 TTTT
1 TTTT
41267758 ATTGATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.73
Consensus pattern (17 bp):
TTTTTGTTTTAGCAATT
Found at i:41269496 original size:47 final size:46
Alignment explanation
Indices: 41269373--41269739 Score: 225
Period size: 47 Copynumber: 7.8 Consensus size: 46
41269363 TTGGGTGATT
* * * * *
41269373 TGAGTGCCAGTGTAAGA-CATGTCTGGGACATGCTTTGGCCA-CATTA
1 TGAGAGCCAGTGTAAGACCATATCTGGGACATGCATCGG-CATCA-GA
41269419 TGAGAGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCATCCAGA
1 TGAGAGCCAGTGTAAGACCATATCTGGGACAT-GCATCGGCAT-CAGA
* * * * * * *
41269467 CGAGGGCTAGTGTAAGA-CATGTCTAGGACATGCATCAGCCAT-ACTA
1 TGAGAGCCAGTGTAAGACCATATCTGGGACATGCATC-GGCATCA-GA
* *
41269513 TGATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CAGGGA
1 TGAGAGCCAGTGTAAGACCATATCTGGGACAT-GCATCGGCATCA--GA
* *
41269561 TGAGTGCCAGTGTAAGA-CATATCTGGGACATGCATCGGCCTTGACAGA
1 TGAGAGCCAGTGTAAGACCATATCTGGGACATGCATCGG-CAT--CAGA
* * * * * *
41269609 -GATAGCCAGTGTAAGA-CGTGTCTGGGACACGTATCGGC-TAAGAA
1 TGAGAGCCAGTGTAAGACCATATCTGGGACATGCATCGGCATCAG-A
* * * * * * *
41269653 T-TGTGCTAGTGTAAGA-CATGTCTGGGACATGCATCAGCACGCGTATA
1 TGAGAGCCAGTGTAAGACCATATCTGGGACATGCATCGGCA-TC--AGA
* *
41269700 TGAGAGCCAGTGTAAGACCATGTCAGGGACATGGCATCGG
1 TGAGAGCCAGTGTAAGACCATATCTGGGACAT-GCATCGG
41269740 TAATATATCC
Statistics
Matches: 251, Mismatches: 47, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
43 2 0.01
44 30 0.12
45 2 0.01
46 43 0.17
47 95 0.38
48 56 0.22
49 15 0.06
50 8 0.03
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (46 bp):
TGAGAGCCAGTGTAAGACCATATCTGGGACATGCATCGGCATCAGA
Found at i:41269542 original size:94 final size:93
Alignment explanation
Indices: 41269374--41269739 Score: 386
Period size: 94 Copynumber: 3.9 Consensus size: 93
41269364 TGGGTGATTT
* * ** * *
41269374 GAGTGCCAGTGTAAGACATGTCTGGGACATGCTTTGGCCACATTATGAGAGCCAGTGTAAGACCA
1 GAGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCA
* *
41269439 TATCTGGGACATGGCATCGGCATCCAGAC
66 TGTCTGGGACATGGCATCGGCAT-CAGAA
* * *
41269468 GAGGGCTAGTGTAAGACATGTCTAGGACATGCATCAGCCATACTATGATAGCCAGTGTAAGACCA
1 GAGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCA
*
41269533 TGTCTGGGACATGGCATCGGCA-CAGGGAT
66 TGTCTGGGACATGGCATCGGCATCA--GAA
* * * *
41269562 GAGTGCCAGTGTAAGACATATCTGGGACATGCATCGGCCTTGAC-A-GAGATAGCCAGTGTAAGA
1 GAGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAT-ACTATGAG--AGCCAGTGTAAGA
* * * *
41269625 -CGTGTCTGGGACA-CGTATCGGC-TAAGAA
63 CCATGTCTGGGACATGGCATCGGCATCAGAA
** *
41269653 TTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCGTA-TATGAGAGCCAGTGTAAGA
1 GAGTGCTAGTGTAAGACATGTCTGGGACATGCATCAG--C-CATACTATGAGAGCCAGTGTAAGA
*
41269717 CCATGTCAGGGACATGGCATCGG
63 CCATGTCTGGGACATGGCATCGG
41269740 TAATATATCC
Statistics
Matches: 226, Mismatches: 33, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
91 34 0.15
92 15 0.07
93 24 0.11
94 138 0.61
95 15 0.07
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (93 bp):
GAGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCA
TGTCTGGGACATGGCATCGGCATCAGAA
Found at i:41269631 original size:141 final size:138
Alignment explanation
Indices: 41269376--41269739 Score: 389
Period size: 141 Copynumber: 2.6 Consensus size: 138
41269366 GGTGATTTGA
* * *
41269376 GTGCCAGTGTAAGACATGTCTGGGACATGCTTTGGCCACA-TTATGAGAGCCAGTGTAAGACCAT
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CACAGGTATGAGAGCCAGTGTAAGACCAT
* * * *
41269440 ATCTGGGACATGGCATCGGCATCCAGACGAGGGCTAGTGTAAGACATGTCTAGGACATGCATCAG
65 ATCTGGGACATGGCATCGGCATACAGACGAGAGCCAGTGTAAGACATGTCTAGGACACGCATCAG
*
41269505 CCATACTA-T
130 CCA-ACAATT
* *
41269514 GATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGGGATGAGTGCCAGTGTAAGA-
1 G-T-GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACAGGTATGAGAGCCAGTGTAAGAC
* * * * *
41269578 CATATCTGGGACAT-GCATCGGCCTTGACAGA-GATAGCCAGTGTAAGACGTGTCTGGGACACGT
62 CATATCTGGGACATGGCATCGG-CAT-ACAGACGAGAGCCAGTGTAAGACATGTCTAGGACACGC
* * *
41269641 ATCGGCTAAGAATT
125 ATCAGCCAACAATT
* *
41269655 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCAC-GCGTATATGAGAGCCAGTGTAAGACC
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAG-G--TATGAGAGCCAGTGTAAGACC
* *
41269719 ATGTCAGGGACATGGCATCGG
63 ATATCTGGGACATGGCATCGG
41269740 TAATATATCC
Statistics
Matches: 189, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
136 1 0.01
137 10 0.05
138 15 0.08
139 29 0.15
140 34 0.18
141 74 0.39
142 26 0.14
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (138 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAGGTATGAGAGCCAGTGTAAGACCATA
TCTGGGACATGGCATCGGCATACAGACGAGAGCCAGTGTAAGACATGTCTAGGACACGCATCAGC
CAACAATT
Found at i:41277189 original size:22 final size:22
Alignment explanation
Indices: 41277164--41277208 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41277154 GTTCTTAATA
**
41277164 TTGTATATAAACGTGATTCTTG
1 TTGTATATAAACCAGATTCTTG
41277186 TTGTATATAAACCAGATTCTTG
1 TTGTATATAAACCAGATTCTTG
41277208 T
1 T
41277209 CCAAAACGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (22 bp):
TTGTATATAAACCAGATTCTTG
Found at i:41280197 original size:25 final size:25
Alignment explanation
Indices: 41280168--41280218 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
41280158 TAAAAATAAT
41280168 TATATTAAAATATTATTAAATTATA
1 TATATTAAAATATTATTAAATTATA
*** *
41280193 TATATTATTTTTTTATTAAATTATA
1 TATATTAAAATATTATTAAATTATA
41280218 T
1 T
41280219 TAAATAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TATATTAAAATATTATTAAATTATA
Found at i:41280226 original size:59 final size:55
Alignment explanation
Indices: 41280161--41280271 Score: 168
Period size: 59 Copynumber: 1.9 Consensus size: 55
41280151 TTTAATATAA
* *
41280161 AAATAATTATATTAAAATATTATTAAATTATATATATTATTTTTTTATTAAATTATATT
1 AAATAATAATATTAAAATATGATTAAATTAT-T-TATTA--TTTTTATTAAATTATATT
41280220 AAATAATAATATTAAAATATGATTAAATTATTTATTATTTTTATTAAATTAT
1 AAATAATAATATTAAAATATGATTAAATTATTTATTATTTTTATTAAATTAT
41280272 TTTTAATAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
55 15 0.30
57 5 0.10
58 1 0.02
59 29 0.58
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (55 bp):
AAATAATAATATTAAAATATGATTAAATTATTTATTATTTTTATTAAATTATATT
Found at i:41280255 original size:23 final size:22
Alignment explanation
Indices: 41280204--41280256 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
41280194 ATATTATTTT
*
41280204 TTTATTAAATTATATTAAATAA
1 TTTATTAAAATATATTAAATAA
* *
41280226 TAATATTAAAATATGATTAAATTA
1 T-TTATTAAAATAT-ATTAAATAA
41280250 TTTATTA
1 TTTATTA
41280257 TTTTTATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 15 0.60
24 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTATTAAAATATATTAAATAA
Found at i:41280484 original size:16 final size:16
Alignment explanation
Indices: 41280463--41280500 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
41280453 TGAATTACTG
41280463 ATTACAACCCTATTTC
1 ATTACAACCCTATTTC
*
41280479 ATTACAACTCTATTTC
1 ATTACAACCCTATTTC
41280495 ATTACA
1 ATTACA
41280501 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTACAACCCTATTTC
Found at i:41281745 original size:12 final size:11
Alignment explanation
Indices: 41281722--41281756 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
41281712 ATATTGTATA
41281722 ATTATTATTTT
1 ATTATTATTTT
*
41281733 ATTGTTAATTTT
1 ATTATT-ATTTT
41281745 ATTATTATTTT
1 ATTATTATTTT
41281756 A
1 A
41281757 GAGATATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:41293407 original size:29 final size:31
Alignment explanation
Indices: 41293365--41293429 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
41293355 GTGGATTTAT
* *
41293365 ATTATATTTATATAA-AAAATTTA-AAAAAA
1 ATTATAATAATATAATAAAATTTATAAAAAA
* *
41293394 ATTATAATAATATAATTAATTTTATAAAAAA
1 ATTATAATAATATAATAAAATTTATAAAAAA
41293425 ATTAT
1 ATTAT
41293430 TTTTTAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.43
30 6 0.20
31 11 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
ATTATAATAATATAATAAAATTTATAAAAAA
Found at i:41295782 original size:15 final size:15
Alignment explanation
Indices: 41295681--41295792 Score: 58
Period size: 15 Copynumber: 7.8 Consensus size: 15
41295671 CTTTTTTCGT
*
41295681 TTATTTTCATTTCT-
1 TTATTTTCATTACTA
* *
41295695 TTTTTTTACA-TATTA
1 TTATTTT-CATTACTA
* *
41295710 TTAATATCATTACTA
1 TTATTTTCATTACTA
*
41295725 TTATTTT-ATTTCTA
1 TTATTTTCATTACTA
*
41295739 TTATTATC-TT--TA
1 TTATTTTCATTACTA
* * *
41295751 TTA-TTACTGTTAGTA
1 TTATTTTC-ATTACTA
41295766 TTATTTTCATTACTA
1 TTATTTTCATTACTA
*
41295781 TTATTTTTATTA
1 TTATTTTCATTA
41295793 ACATATTAAT
Statistics
Matches: 72, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
11 2 0.03
12 5 0.07
13 2 0.03
14 24 0.33
15 36 0.50
16 3 0.04
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (15 bp):
TTATTTTCATTACTA
Found at i:41296098 original size:16 final size:16
Alignment explanation
Indices: 41296057--41296129 Score: 67
Period size: 16 Copynumber: 4.4 Consensus size: 16
41296047 TTTAAATATT
*
41296057 ATATTATATATTCTTCT
1 ATATTATATATT-TTCA
*
41296074 ATATATATATGTTTTCA
1 ATAT-TATATATTTTCA
* *
41296091 ATATTATATTTTTTTA
1 ATATTATATATTTTCA
*
41296107 TTATTATATATATTT-A
1 ATATTATATAT-TTTCA
41296123 ATATTAT
1 ATATTAT
41296130 TAGTTATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
16 26 0.55
17 14 0.30
18 7 0.15
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (16 bp):
ATATTATATATTTTCA
Found at i:41296115 original size:32 final size:34
Alignment explanation
Indices: 41296057--41296129 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 34
41296047 TTTAAATATT
*
41296057 ATATTATATATTCTTCTATATATATATGT-TTTCA
1 ATATTATATATTCTTCTATATATATATATATTT-A
*
41296091 ATATTATAT-TT-TTTTAT-TATTATATATATTTA
1 ATATTATATATTCTTCTATATA-TATATATATTTA
41296123 ATATTAT
1 ATATTAT
41296130 TAGTTATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 2 0.06
32 19 0.54
33 5 0.14
34 9 0.26
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (34 bp):
ATATTATATATTCTTCTATATATATATATATTTA
Found at i:41296153 original size:23 final size:22
Alignment explanation
Indices: 41296105--41296205 Score: 86
Period size: 23 Copynumber: 4.7 Consensus size: 22
41296095 TATATTTTTT
*
41296105 TATTATTATATATATTTAATAT
1 TATTATTATATATATTTAATAC
* *
41296127 TATTAGTTATATATTTTTTATAC
1 TATTA-TTATATATATTTAATAC
* *
41296150 TA-T-TTATGTATATTT-ATAA
1 TATTATTATATATATTTAATAC
*
41296169 TATATATTGTATAT-TTCTAATAC
1 TAT-TATTATATATATT-TAATAC
41296192 TATTATT-TATATAT
1 TATTATTATATATAT
41296206 GTATATATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
19 5 0.08
20 10 0.16
21 8 0.13
22 18 0.29
23 22 0.35
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (22 bp):
TATTATTATATATATTTAATAC
Found at i:41296167 original size:19 final size:20
Alignment explanation
Indices: 41296143--41296225 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
41296133 TTATATATTT
* *
41296143 TTTATACTATTTA-TGTATA
1 TTTATAATATATATTGTATA
41296162 TTTATAATATATATTGTATA
1 TTTATAATATATATTGTATA
*
41296182 TTTCTAATACTATTATT-TATA
1 TTTATAATA-TA-TATTGTATA
*
41296203 TATGTAT-ATATATGTGTGTATA
1 T-T-TATAATATATAT-TGTATA
41296225 T
1 T
41296226 ATTTGTGTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
19 11 0.21
20 16 0.31
21 10 0.19
22 13 0.25
23 2 0.04
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTATAATATATATTGTATA
Found at i:41296183 original size:42 final size:41
Alignment explanation
Indices: 41296095--41296225 Score: 115
Period size: 42 Copynumber: 3.1 Consensus size: 41
41296085 TTTTCAATAT
* * *
41296095 TATATTTTTT-TATTATTATATATATTTAATATTAT-TAGTTA
1 TATATTTTTTATACTATTATATATATTT-ATAATATATA-TTG
*
41296136 TATATTTTTTATACTATTTATGTATATTTATAATATATATTG
1 TATATTTTTTATACTA-TTATATATATTTATAATATATATTG
* * * *
41296178 TATATTTCTAATACTATTATTTATATATGTAT-ATATATGTGTG
1 TATATTTTTTATACTATTA--TATATATTTATAATATATAT-TG
41296221 TATAT
1 TATAT
41296226 ATTTGTGTAG
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
41 13 0.17
42 33 0.44
43 29 0.39
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (41 bp):
TATATTTTTTATACTATTATATATATTTATAATATATATTG
Found at i:41301657 original size:407 final size:405
Alignment explanation
Indices: 41300782--41301999 Score: 1623
Period size: 407 Copynumber: 3.0 Consensus size: 405
41300772 TGTACACTTT
* * *
41300782 ATTAAAGTTTTTCTTGAACTCGAAAATGTATTACTTGTACAAGGATTGAAAACTAACGTAATAAG
1 ATTAAAG-TTTTCTTGACCTTGAAAATGTATTACTTGTACAGGGATTGAAAACTAACGTAATAAG
* * * *
41300847 CATAAGTTAAGC-ATGTGGCCAAAGACTTAATAT-ATGATTTAACAAAAATAGTTGTGATGTAAT
65 CATAAGTCAA-CTATGTGACCAAAGGCTTAATATGAT-ATTTAACAAAATTAG-TGTGATGTAAT
* * *
41300910 TAATGAAAAAAATTGTTATAATAAGAGGAGCAAAA-ACTTTTGACAATTACTACAAAGTTTTTAA
127 TAATGAAAAAAAATGTTATAATAAGAGGAGCAAAATA-TTTTGAAAATTGCTACAAAGTTTTTAA
* * ** ** *
41300974 TGAAGTTATTTGCAATAAAACTACTATGCAAGATCTAGATTTGTGACATCGAAAGTTTGGTGGTG
191 TGAAGTTATTTGCAATAAAGCTACTATACAAGATCTAGAGGTGTGACATC-AAAAATTGGTGATG
* *
41301039 TGAATTATTGAAACTT------ACTTGATCAATATGATGCAATTAGAAGACTTTCAAAACTCAAA
255 TGAATTATCGAAACTTACAAAGACTTGATCAATACGATGCAATTAGAAGACTTTCAAAACTCAAA
* * *
41301098 AGTGTTGTGACCAAACTTTGTAGAGATTGTGTTTTGGGGAGACAACACATGGTGACCAATCTAAT
320 AGTGTTGTGACCAAACCTTGTAGAGATTGTGTTTTGGGGAAACAACACATGGTGATCAATCTAAT
41301163 TTTGCCACAAGTAGTGACACA
385 TTTGCCACAAGTAGTGACACA
* * *
41301184 ATTAAATGTTTTCTTGACCTTGAAAATATATTACTTGTATAGGGATTGAAAACTAACTTAATAAG
1 ATTAAA-GTTTTCTTGACCTTGAAAATGTATTACTTGTACAGGGATTGAAAACTAACGTAATAAG
* *
41301249 CATAAGTCAACTATATGACCAAAGGCTTAATATGATATTTAACAAAATTAGTGGAGATGTAATTA
65 CATAAGTCAACTATGTGACCAAAGGCTTAATATGATATTTAACAAAATTAGT-GTGATGTAATTA
* * * *
41301314 ATCAAAAGAACTGTTATAATAAGAGGAGCAAAATTTTTTGAAAATTGCTACAAAGTTTTTAATGA
129 ATGAAAAAAAATGTTATAATAAGAGGAGCAAAATATTTTGAAAATTGCTACAAAGTTTTTAATGA
* *
41301379 AGTTATTTTCAATAAAGCTACTATACAAGATCTAAAGGTGTGACATCAACAAATTGGTGATGTGA
194 AGTTATTTGCAATAAAGCTACTATACAAGATCTAGAGGTGTGACATCAA-AAATTGGTGATGTGA
* * **
41301444 ATTATCGAAACTTACAAAGACTTCATCAATA-AATATAATTAGAAGACTTTCAAAACTCAAAAGT
258 ATTATCGAAACTTACAAAGACTTGATCAATACGATGCAATTAGAAGACTTTCAAAACTCAAAAGT
* * * *
41301508 ATTGTGACCAAACCTTGTGGAGATTGTGTTTTTGGGAAACAACACATGGTGATCTATCTAATTTT
323 GTTGTGACCAAACCTTGTAGAGATTGTGTTTTGGGGAAACAACACATGGTGATCAATCTAATTTT
* *
41301573 GCCACTAGTTGTGACACA
388 GCCACAAGTAGTGACACA
* * *
41301591 ATTAAAGATTTTCTTTACCTTGATAATGTATTACTTGTACAGGGTTTGAAAACTAACGTAATAAG
1 ATTAAAG-TTTTCTTGACCTTGAAAATGTATTACTTGTACAGGGATTGAAAACTAACGTAATAAG
* * *
41301656 CATAAGTCAACTATGTGACCAAAGGCTTAATATGAGATTTAACAAAAATAACTGTGATGTAATTA
65 CATAAGTCAACTATGTGACCAAAGGCTTAATATGATATTTAAC-AAAATTAGTGTGATGTAATTA
** *
41301721 ATGAAAAAAAAT-TTATAATAAGAGGAGCAAAATAAATTGAAAATTGTTACAAAGTTTTTAATGA
129 ATGAAAAAAAATGTTATAATAAGAGGAGCAAAATATTTTGAAAATTGCTACAAAGTTTTTAATGA
* * * * * *
41301785 AGTTATTTGCAATAAAGTTACTATAAAAGATCTAGAGGTGTTACCTCAAAAGATTGGCGATGTGG
194 AGTTATTTGCAATAAAGCTACTATACAAGATCTAGAGGTGTGACATCAAAA-ATTGGTGATGTGA
* ** * * *
41301850 ACTATCGATTCTTACAAAGACTTGATCAATACGATGCAATTAGAAGACTTTCGAAACCCGAAAGT
258 ATTATCGAAACTTACAAAGACTTGATCAATACGATGCAATTAGAAGACTTTCAAAACTCAAAAGT
* * * *
41301915 GTTGTGACTAGACCTTGTAGAGATTGTGTTTTGGGGAAACAACACATGTTG-TCCCATCTAATTT
323 GTTGTGACCAAACCTTGTAGAGATTGTGTTTTGGGGAAACAACACATGGTGAT-CAATCTAATTT
41301979 TGCCACAAGTAGTGACACA
387 TGCCACAAGTAGTGACACA
41301998 AT
1 AT
41302000 GCCCATTGGA
Statistics
Matches: 713, Mismatches: 86, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
401 4 0.01
402 232 0.33
403 3 0.00
405 2 0.00
406 131 0.18
407 323 0.45
408 18 0.03
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (405 bp):
ATTAAAGTTTTCTTGACCTTGAAAATGTATTACTTGTACAGGGATTGAAAACTAACGTAATAAGC
ATAAGTCAACTATGTGACCAAAGGCTTAATATGATATTTAACAAAATTAGTGTGATGTAATTAAT
GAAAAAAAATGTTATAATAAGAGGAGCAAAATATTTTGAAAATTGCTACAAAGTTTTTAATGAAG
TTATTTGCAATAAAGCTACTATACAAGATCTAGAGGTGTGACATCAAAAATTGGTGATGTGAATT
ATCGAAACTTACAAAGACTTGATCAATACGATGCAATTAGAAGACTTTCAAAACTCAAAAGTGTT
GTGACCAAACCTTGTAGAGATTGTGTTTTGGGGAAACAACACATGGTGATCAATCTAATTTTGCC
ACAAGTAGTGACACA
Found at i:41305200 original size:19 final size:18
Alignment explanation
Indices: 41305164--41305204 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
41305154 GAATGCTTAA
*
41305164 AAAATGTAAAAAAAATAT
1 AAAATATAAAAAAAATAT
*
41305182 AAAATATAAAATAATATAT
1 AAAATATAAAA-AAAATAT
41305201 AAAA
1 AAAA
41305205 ATTTAGCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAATATAAAAAAAATAT
Found at i:41307498 original size:69 final size:69
Alignment explanation
Indices: 41307372--41307571 Score: 165
Period size: 68 Copynumber: 2.9 Consensus size: 69
41307362 ACAGAGGTTT
* * * ** * * *
41307372 AAGGTGTAAGACCCTAGCTTGGCTATGGCAACCAATAAAGT-CGACTGAGATAGTAAACATGTGG
1 AAGGTGTAAGACCATAGCTTAGCTATGACAACCAATGGAGTCCGCCAGAGACAGTAAACATG-GG
*
41307436 ATTAC
65 ACTAC
* * *
41307441 AAGGTGTAAGACCATAGCTTAGCTATGAAAACCAATGGAGTCCGCCAG-GACATTAAACATGGGG
1 AAGGTGTAAGACCATAGCTTAGCTATGACAACCAATGGAGTCCGCCAGAGACAGTAAACATGGGA
*
41307505 CTAT
66 CTAC
*** * * * * *
41307509 GTTGTGCAAGACCATAGCTTAGCTATGACAA-CATATGGAGCCCG-CTGGGATAGTAAACATGGG
1 AAGGTGTAAGACCATAGCTTAGCTATGACAACCA-ATGGAGTCCGCCAGAGACAGTAAACATGGG
41307572 GTAGTCCACC
Statistics
Matches: 106, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
67 4 0.04
68 52 0.49
69 46 0.43
70 4 0.04
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (69 bp):
AAGGTGTAAGACCATAGCTTAGCTATGACAACCAATGGAGTCCGCCAGAGACAGTAAACATGGGA
CTAC
Found at i:41310011 original size:45 final size:45
Alignment explanation
Indices: 41309961--41310050 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
41309951 GATGTGTTAA
41309961 TATGTGTTTATATTTCAATTTTGCATTTTGTATTTCTATAATTTG
1 TATGTGTTTATATTTCAATTTTGCATTTTGTATTTCTATAATTTG
41310006 TATGTGTTTATATTTCAATTTTGCATTTTGTATTTCTATAATTTG
1 TATGTGTTTATATTTCAATTTTGCATTTTGTATTTCTATAATTTG
41310051 AACCTAATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.60
Consensus pattern (45 bp):
TATGTGTTTATATTTCAATTTTGCATTTTGTATTTCTATAATTTG
Found at i:41310870 original size:24 final size:24
Alignment explanation
Indices: 41310843--41310895 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
41310833 ATGAATAAAT
41310843 ATATTAATTAGTTAATTGATGTTG
1 ATATTAATTAGTTAATTGATGTTG
41310867 ATATTAATTAGTTAATTGATGTTG
1 ATATTAATTAGTTAATTGATGTTG
*
41310891 TTATT
1 ATATT
41310896 CAAGTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (24 bp):
ATATTAATTAGTTAATTGATGTTG
Found at i:41311833 original size:22 final size:22
Alignment explanation
Indices: 41311807--41311852 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
41311797 ATATTGGTTG
41311807 TATGAACATTTGGTATGGAGAT
1 TATGAACATTTGGTATGGAGAT
*
41311829 TATGAACATTTGGTGTGGAGAT
1 TATGAACATTTGGTATGGAGAT
41311851 TA
1 TA
41311853 CTCATTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.37
Consensus pattern (22 bp):
TATGAACATTTGGTATGGAGAT
Found at i:41312164 original size:20 final size:20
Alignment explanation
Indices: 41312125--41312164 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41312115 CCCCTGCAAC
* *
41312125 TTTGAAAATTTTCTATGTTT
1 TTTGAAAATTTTATAAGTTT
41312145 TTTGAAAATTTTATAAGTTT
1 TTTGAAAATTTTATAAGTTT
41312165 CCTATTTTGT
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:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (20 bp):
TTTGAAAATTTTATAAGTTT
Found at i:41312958 original size:46 final size:45
Alignment explanation
Indices: 41312873--41312962 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 45
41312863 AGTTACTTTT
* **
41312873 TTAAGTATTTAATGTGTTCTAATTAGATTCAGTAATTAATATGTA
1 TTAAGTAATTAATGTGTTCTAATTAGATTCACCAATTAATATGTA
*
41312918 TTAAGTTAATTAATGTGTTCTAATTAG-TTCAACCATTTAATATGT
1 TTAAG-TAATTAATGTGTTCTAATTAGATTC-ACCAATTAATATGT
41312963 CCTATGTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
45 8 0.21
46 31 0.79
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (45 bp):
TTAAGTAATTAATGTGTTCTAATTAGATTCACCAATTAATATGTA
Found at i:41316339 original size:24 final size:24
Alignment explanation
Indices: 41316310--41316363 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
41316300 GGAAAAAGAG
41316310 AAAGAACAAGAGAAAAAGAATGAA
1 AAAGAACAAGAGAAAAAGAATGAA
*
41316334 AAAGAACAAGAGAGAAAGAATGAA
1 AAAGAACAAGAGAAAAAGAATGAA
41316358 AAAGAA
1 AAAGAA
41316364 AAAAAAAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.70, C:0.04, G:0.22, T:0.04
Consensus pattern (24 bp):
AAAGAACAAGAGAAAAAGAATGAA
Found at i:41316365 original size:30 final size:26
Alignment explanation
Indices: 41316294--41316379 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
41316284 AACAATCTGT
* *
41316294 AGAAAAGGAAAAAGAGAAAGAACAAG
1 AGAAAAAGAAAAAGAAAAAGAACAAG
*
41316320 AGAAAAAG--AATGAAAAAGAACAAGAG
1 AGAAAAAGAAAAAGAAAAAGAAC-A-AG
*
41316346 AGAAAGAATGAAAAAGAAAAA-AAAAAG
1 AGAAA-AA-GAAAAAGAAAAAGAACAAG
41316373 -GAAAAAG
1 AGAAAAAG
41316380 TGAGAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
24 12 0.24
25 3 0.06
26 18 0.37
27 4 0.08
28 2 0.04
29 2 0.04
30 8 0.16
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.02
Consensus pattern (26 bp):
AGAAAAAGAAAAAGAAAAAGAACAAG
Found at i:41319833 original size:48 final size:48
Alignment explanation
Indices: 41319781--41319958 Score: 257
Period size: 48 Copynumber: 3.7 Consensus size: 48
41319771 ATGTGTAACC
* * *
41319781 GTGTAAGACCATATCTGGGACATGGCATTGGCATTGTTATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCA
* *
41319829 GTGTAAGACCATGTCTGGGACATGGCATCGACATCGTTATGTGAGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCA
* * *
41319877 GTGTAAGACCATGTCTGAGACATGGCATCAGCATCGTTATGTAAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCA
* * *
41319925 GTGTAAGACCATGTTTGGGACTTGGCATCTGCAT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCAT
41319959 GAGGCATTGT
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 116 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCA
Found at i:41325781 original size:46 final size:45
Alignment explanation
Indices: 41325715--41325805 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 45
41325705 TTACTTTAGT
41325715 TTAAGTAATTAATGTGTTCTAATTAGATTCAGCAAT-TAATATGTC
1 TTAAGTAATTAATGTGTTCTAATTAG-TTCAGCAATCTAATATGTC
*
41325760 TTAAGTTAATTAATGTGTTCTAATTAGTTCAGCCATCTAATATGTC
1 TTAAG-TAATTAATGTGTTCTAATTAGTTCAGCAATCTAATATGTC
41325806 CTAACTTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
45 13 0.30
46 30 0.70
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (45 bp):
TTAAGTAATTAATGTGTTCTAATTAGTTCAGCAATCTAATATGTC
Found at i:41330101 original size:16 final size:16
Alignment explanation
Indices: 41330080--41330110 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41330070 TTAAATGATA
41330080 TTAGTACATATATATT
1 TTAGTACATATATATT
41330096 TTAGTACATATATAT
1 TTAGTACATATATAT
41330111 GTATACTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTAGTACATATATATT
Found at i:41330337 original size:22 final size:22
Alignment explanation
Indices: 41330289--41330345 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
41330279 TATATTTTCT
* *
41330289 TTTATATATTATGTATATACATT
1 TTTA-ATATTATATATATACATG
* *
41330312 TTTAATATTATATATGTATATG
1 TTTAATATTATATATATACATG
*
41330334 TTT-ATACTATAT
1 TTTAATATTATAT
41330346 TAGTTAGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 8 0.28
22 17 0.59
23 4 0.14
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTAATATTATATATATACATG
Found at i:41330600 original size:22 final size:21
Alignment explanation
Indices: 41330561--41330635 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 21
41330551 ATTTCTAATG
*
41330561 TATATGTATATATCGTATATGTTT
1 TATATATAT-TAT-GTATAT-TTT
41330585 TATATATATTATGTATATATTT
1 TATATATATTATGTATAT-TTT
41330607 TCA-ATATTATTACT-TATATTTT
1 T-ATATA-TATTA-TGTATATTTT
41330629 TATATAT
1 TATATAT
41330636 TATTCCATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.04
22 20 0.44
23 14 0.31
24 9 0.20
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.57
Consensus pattern (21 bp):
TATATATATTATGTATATTTT
Found at i:41330613 original size:24 final size:24
Alignment explanation
Indices: 41330586--41330731 Score: 70
Period size: 24 Copynumber: 5.8 Consensus size: 24
41330576 TATATGTTTT
41330586 ATATATATTATGTATATATTTTCA
1 ATATATATTATGTATATATTTTCA
41330610 ATAT-TATTACT-TATAT-TTTT--
1 ATATATATTA-TGTATATATTTTCA
* *
41330630 ATATATTATTCCATGTACATA-TTTCC
1 ATATA-TATT--ATGTATATATTTTCA
*
41330656 ATATCATCTTATGTATATATTCTTAAACA
1 ATAT-ATATTATGTATATATT-TT---CA
* * * *
41330685 TTATTATATGTATATGTATATTTTTA
1 ATA-TATAT-TATGTATATATTTTCA
*
41330711 ATACCATATTATGTATATATT
1 ATA-TATATTATGTATATATT
41330732 ATTATTACAT
Statistics
Matches: 91, Mismatches: 14, Indels: 33
0.66 0.10 0.24
Matches are distributed among these distances:
20 4 0.04
22 8 0.09
23 11 0.12
24 21 0.23
25 11 0.12
26 16 0.18
27 1 0.01
29 8 0.09
30 11 0.12
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (24 bp):
ATATATATTATGTATATATTTTCA
Found at i:41330615 original size:20 final size:21
Alignment explanation
Indices: 41330588--41330639 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
41330578 TATGTTTTAT
41330588 ATATATTATGTA-TATATTTTC
1 ATATATTAT-TACTATATTTTC
*
41330609 A-ATATTATTACTTATATTTTT
1 ATATATTATTAC-TATATTTTC
41330630 ATATATTATT
1 ATATATTATT
41330640 CCATGTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 7 0.26
21 10 0.37
22 8 0.30
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATATTATTACTATATTTTC
Found at i:41335379 original size:46 final size:45
Alignment explanation
Indices: 41335329--41335501 Score: 188
Period size: 46 Copynumber: 3.8 Consensus size: 45
41335319 TGTTTGGGCA
41335329 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
41335375 TCCGAACTCGTTGAGCTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
41335422 TCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
41335468 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41335502 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
44 3 0.03
45 1 0.01
46 63 0.61
47 31 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:41335488 original size:93 final size:93
Alignment explanation
Indices: 41335325--41335496 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
41335315 AGGATGTTTG
* * *
41335325 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG
41335390 CTGAGTCCGAGTTCGAGAGATGTAACTA
66 CTGAGTCCGAGTTCGAGAGATGTAACTA
* *
41335418 GGCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG
*
41335483 TTGAGTCCGAGTTC
66 CTGAGTCCGAGTTC
41335497 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG
CTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:41338131 original size:161 final size:162
Alignment explanation
Indices: 41337960--41338358 Score: 572
Period size: 176 Copynumber: 2.4 Consensus size: 162
41337950 TTCTATTTTT
* * *
41337960 AAAAATCAACTCATATTGCGAGGGGTAAGTTGAGCCTCAGGTCACACGTTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
* *
41338025 C-ATGTTTCAAAAATCAACTCATATTGCTAGAGGCGAGTTGAGCCTCAGGTCACATGCTGAGGTA
66 CTATGTTTCAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCTGAGGTA
41338089 TTTTCAAATTTCTATTTTTCAATTTATGTTTC
131 TTTTCAAATTTCTATTTTTCAATTTATGTTTC
41338121 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTC--A-
*
41338186 TTCTATTTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
63 ----A---TTC----TATGTTTCAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGT
41338251 CACACGCTGAGGTATTTTCAAATTTCTATTTTTCAATTTATGTTTC
117 CACACGCTGAGGTATTTTCAAATTTCTATTTTTCAATTTATGTTTC
* *
41338297 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG--GCACGCTGA-GTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
41338359 TCTGCTTTTC
Statistics
Matches: 215, Mismatches: 8, Indels: 28
0.86 0.03 0.11
Matches are distributed among these distances:
161 58 0.27
163 3 0.01
166 1 0.00
168 1 0.00
171 4 0.02
173 8 0.04
174 8 0.04
176 132 0.61
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (162 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
CTATGTTTCAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCTGAGGTA
TTTTCAAATTTCTATTTTTCAATTTATGTTTC
Found at i:41338165 original size:88 final size:88
Alignment explanation
Indices: 41338016--41338373 Score: 616
Period size: 88 Copynumber: 4.1 Consensus size: 88
41338006 CGTTGAGGTA
* * * *
41338016 TTTTCAATTCATGTTTCAAAAATCAACTCATATTGCTAGAGGCGAGTTGAGCCTCAGGTCACATG
1 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
41338081 CTGAGGTATTTTCAAATTTCTAT
66 CTGAGGTATTTTCAAATTTCTAT
41338104 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
1 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
41338169 CTGAGGTATTTTCAAATTTCTAT
66 CTGAGGTATTTTCAAATTTCTAT
41338192 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
1 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
41338257 CTGAGGTATTTTCAAATTTCTAT
66 CTGAGGTATTTTCAAATTTCTAT
* *
41338280 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG--GCACG
1 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
**
41338343 CTGA-GTATTTTC-AATTTCTGC
66 CTGAGGTATTTTCAAATTTCTAT
41338364 TTTTCAATTT
1 TTTTCAATTT
41338374 CTATTTTTCA
Statistics
Matches: 262, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
84 17 0.06
85 8 0.03
86 8 0.03
88 229 0.87
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (88 bp):
TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
CTGAGGTATTTTCAAATTTCTAT
Found at i:41338310 original size:176 final size:176
Alignment explanation
Indices: 41338016--41338628 Score: 663
Period size: 176 Copynumber: 3.4 Consensus size: 176
41338006 CGTTGAGGTA
* * *
41338016 TTTTCAATTCATGTTTCAAAAATCAACTCATATTGCTAGAGGCGAGTTGAGCCTCAGGTCACATG
1 TTTTCAATTCATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
41338081 CTGAGGTATTTTCAAATTTCTATTTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGG
66 CTGAGGTATTTTCAAATTTCTATTTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGG
41338146 TGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAAATTTCTAT
131 TGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAAATTTCTAT
*
41338192 TTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
1 TTTTCAATTCATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
*
41338257 CTGAGGTATTTTCAAATTTCTATTTTTCAATTTATGTTTCAAAAATCAACTCATATTGCAAGAGG
66 CTGAGGTATTTTCAAATTTCTATTTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGG
*
41338322 TGAGTTGAGCCTCAGG--GCACGCTGA-GTATTTTCAATTTCTGCTTTTCAATTTCTAT
131 TGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTC-A------------AATTTCTAT
41338378 TTTTCAAATTCA-GTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--AC
1 TTTTC-AATTCATGTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC
* *
41338440 ACGCTGAGGTATTTTC-AATTTCTATTTTTTTTTCTTTTCAATTTATATTTTTCAAAAACCAACT
63 ACGCTGAGGTATTTTCAAATTTCTA--------T-TTTTCAA-TT-TATGTTTCAAAAATCAACT
* * * * * **
41338504 CATATTGCGAGAAGTGAGTTGAGCAT-TGGCTCACATGCTGAGCTATTTTC-AATTTCTGC
117 CATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCACACGCTGAGGTATTTTCAAATTTCTAT
* * * * * *
41338563 TTTT-AATGTCTATTTTTTAAAAGAATTAACTCATATTACGATAAGTGAGTTGAG-CTCAGGATC
1 TTTTCAAT-TC-A-TGTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TC
41338626 ACA
61 ACA
41338629 TGCCGAGTAA
Statistics
Matches: 374, Mismatches: 24, Indels: 66
0.81 0.05 0.14
Matches are distributed among these distances:
173 8 0.02
174 9 0.02
176 141 0.38
183 3 0.01
184 2 0.01
185 29 0.08
186 64 0.17
187 8 0.02
188 44 0.12
193 1 0.00
194 7 0.02
195 4 0.01
196 40 0.11
198 7 0.02
199 7 0.02
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (176 bp):
TTTTCAATTCATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACG
CTGAGGTATTTTCAAATTTCTATTTTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGG
TGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAAATTTCTAT
Found at i:41338381 original size:14 final size:14
Alignment explanation
Indices: 41338350--41338384 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41338340 ACGCTGAGTA
*
41338350 TTTTCAATTTCTGC
1 TTTTCAATTTCTAC
*
41338364 TTTTCAATTTCTAT
1 TTTTCAATTTCTAC
41338378 TTTTCAA
1 TTTTCAA
41338385 ATTCAGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.03, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:41338443 original size:100 final size:98
Alignment explanation
Indices: 41338271--41338579 Score: 364
Period size: 100 Copynumber: 3.1 Consensus size: 98
41338261 GGTATTTTCA
*
41338271 AATTTCTATTTTTC-AATTTATGTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 AATTTCTATTTTTCAAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
*
41338335 AGGGCACGCTGAGTATTTTCAATTTCTGCTTTT
66 AGGACACGCTGAGTATTTTCAATTTCTGCTTTT
*
41338368 CAATTTCTATTTTTCAAATTCA-GTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 -AATTTCTATTTTTCAAATTTATGTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
41338432 CTCAGGACACGCTGAGGTATTTTCAATTTCT-ATTTT
63 CTCAGGACACGCTGA-GTATTTTCAATTTCTGCTTTT
* * * * *
41338468 --TTT-T-TCTTTTCAATTTATATTTTTCAAAAACCAACTCATATTGCGAGAAGTGAGTTGAGCA
1 AATTTCTAT-TTTTCAAATT-TATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* *
41338529 T-TGGCTCACATGCTGAGCTATTTTCAATTTCTGCTTTT
64 TCAGG---ACACGCTGAG-TATTTTCAATTTCTGCTTTT
*
41338567 AATGTCTATTTTT
1 AATTTCTATTTTT
41338580 TAAAAGAATT
Statistics
Matches: 181, Mismatches: 14, Indels: 28
0.81 0.06 0.13
Matches are distributed among these distances:
95 3 0.02
96 44 0.24
97 5 0.03
98 45 0.25
99 9 0.05
100 52 0.29
101 17 0.09
102 5 0.03
103 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (98 bp):
AATTTCTATTTTTCAAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
AGGACACGCTGAGTATTTTCAATTTCTGCTTTT
Found at i:41339318 original size:153 final size:153
Alignment explanation
Indices: 41339038--41339348 Score: 595
Period size: 153 Copynumber: 2.0 Consensus size: 153
41339028 CCAAAATTTA
41339038 AACCCCATTTTACAAAACCCACTTTAGACCCAACATGCATTAAACCCAACTAACAATATAAACCC
1 AACCCCATTTTACAAAACCCACTTTAGACCCAACATGCATTAAACCCAACTAACAATATAAACCC
* *
41339103 CTAAACCTATTTACAACGTAAACCCACTAACCCATCAAAAAACCCAAAAACTCAATAACCCAATT
66 CTAAACCTATTTACAACCTAAACCCACTAACCCATCAAAAAACCCAAAAACCCAATAACCCAATT
41339168 ACACCCTAACCCTAATCAGCCCT
131 ACACCCTAACCCTAATCAGCCCT
41339191 AACCCCATTTTACAAAACCCACTTTAGACCCAACATGCATTAAACCCAACTAACAATATAAACCC
1 AACCCCATTTTACAAAACCCACTTTAGACCCAACATGCATTAAACCCAACTAACAATATAAACCC
*
41339256 CTAAACCTATTTACAACCTAAACCCACTAACCCATCAAAAAACCCAAAAACCCAATAGCCCAATT
66 CTAAACCTATTTACAACCTAAACCCACTAACCCATCAAAAAACCCAAAAACCCAATAACCCAATT
41339321 ACACCCTAACCCTAATCAGCCCT
131 ACACCCTAACCCTAATCAGCCCT
41339344 AACCC
1 AACCC
41339349 GAACACCTCA
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 155 1.00
ACGTcount: A:0.43, C:0.36, G:0.03, T:0.18
Consensus pattern (153 bp):
AACCCCATTTTACAAAACCCACTTTAGACCCAACATGCATTAAACCCAACTAACAATATAAACCC
CTAAACCTATTTACAACCTAAACCCACTAACCCATCAAAAAACCCAAAAACCCAATAACCCAATT
ACACCCTAACCCTAATCAGCCCT
Found at i:41340931 original size:23 final size:23
Alignment explanation
Indices: 41340886--41340931 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41340876 ACACATAAGT
* *
41340886 AAATAAATATAATAATAATACTA
1 AAATAAATATAATAAAAAAACTA
41340909 AAATAAAGTA-AATAAAAAAACTA
1 AAATAAA-TATAATAAAAAAACTA
41340932 TATATAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (23 bp):
AAATAAATATAATAAAAAAACTA
Found at i:41341133 original size:3 final size:3
Alignment explanation
Indices: 41341119--41341216 Score: 62
Period size: 3 Copynumber: 32.7 Consensus size: 3
41341109 TTATACATCA
* * * * *
41341119 AAT AAT ACAT AAT AAT ATT GA- AAT AA- AAT AAT AAGT GAC AAT AGT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
41341164 GA- AAT AAT AAGT AA- AAT AAT AAGT -AT AAT AAT AAGT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AA-T AAT AAT AAT AA-T AAT AAT AAT
41341209 AAT AAT AA
1 AAT AAT AA
41341217 AAAACGATAA
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
2 7 0.10
3 54 0.74
4 12 0.16
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:41341182 original size:12 final size:12
Alignment explanation
Indices: 41341165--41341210 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
41341155 GACAATAGTG
41341165 AAATAATAAGTA
1 AAATAATAAGTA
41341177 AAATAATAAGTA
1 AAATAATAAGTA
*
41341189 TAATAATAAGTA
1 AAATAATAAGTA
41341201 ATAATAATAA
1 A-AATAATAA
41341211 TAATAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 23 0.74
13 8 0.26
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (12 bp):
AAATAATAAGTA
Found at i:41341204 original size:19 final size:19
Alignment explanation
Indices: 41341166--41341216 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
41341156 ACAATAGTGA
41341166 AATAATAAGTAA-AA-TAAT
1 AATAATAA-TAATAAGTAAT
41341184 AAGT-ATAATAATAAGTAAT
1 AA-TAATAATAATAAGTAAT
41341203 AATAATAATAATAA
1 AATAATAATAATAA
41341217 AAAACGATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.10
18 9 0.31
19 17 0.59
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (19 bp):
AATAATAATAATAAGTAAT
Found at i:41341255 original size:21 final size:22
Alignment explanation
Indices: 41341213--41341269 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
41341203 AATAATAATA
*
41341213 ATAAAAAACGATA-ATACTATAT
1 ATAAAAAA-TATATATACTATAT
*
41341235 A-AAAAGTATATATATAC-ATAT
1 ATAAAA-AATATATATACTATAT
41341256 ATAAAAAATATATA
1 ATAAAAAATATATA
41341270 CTAATATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (22 bp):
ATAAAAAATATATATACTATAT
Found at i:41341256 original size:23 final size:22
Alignment explanation
Indices: 41341226--41341269 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
41341216 AAAAACGATA
*
41341226 ATACTATATAAAAAGTATATAT
1 ATACTATATAAAAAATATATAT
41341248 ATACATATATAAAAAATATATA
1 ATAC-TATATAAAAAATATATA
41341270 CTAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (22 bp):
ATACTATATAAAAAATATATAT
Found at i:41341414 original size:9 final size:9
Alignment explanation
Indices: 41341401--41341451 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
41341391 ATATAAAAAA
41341401 AATAATATT
1 AATAATATT
*
41341410 GATAATATT
1 AATAATATT
41341419 AATAATATT
1 AATAATATT
*
41341428 AGA-AATAAT
1 A-ATAATATT
41341437 AATAATATTT
1 AATAATA-TT
41341447 AATAA
1 AATAA
41341452 AGAAACAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 1 0.03
9 27 0.77
10 7 0.20
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (9 bp):
AATAATATT
Found at i:41341414 original size:18 final size:19
Alignment explanation
Indices: 41341401--41341445 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
41341391 ATATAAAAAA
*
41341401 AATAATATT-GATAATATT
1 AATAATATTAGATAATAAT
41341419 AATAATATTAGA-AATAAT
1 AATAATATTAGATAATAAT
41341437 AATAATATT
1 AATAATATT
41341446 TAATAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AATAATATTAGATAATAAT
Found at i:41343479 original size:16 final size:16
Alignment explanation
Indices: 41343458--41343488 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41343448 TTAAATGATA
41343458 TTAGTACATATATATT
1 TTAGTACATATATATT
41343474 TTAGTACATATATAT
1 TTAGTACATATATAT
41343489 GTATGCTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTAGTACATATATATT
Found at i:41343715 original size:22 final size:22
Alignment explanation
Indices: 41343667--41343723 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
41343657 TATATTTTCT
* *
41343667 TTTATATATTATGTATATACATT
1 TTTA-ATATTATATATATACATG
* *
41343690 TTTAATATTATATATGTATATG
1 TTTAATATTATATATATACATG
*
41343712 TTT-ATACTATAT
1 TTTAATATTATAT
41343724 TAGTTAGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 8 0.28
22 17 0.59
23 4 0.14
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTAATATTATATATATACATG
Found at i:41343977 original size:22 final size:21
Alignment explanation
Indices: 41343938--41344012 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 21
41343928 ATTTCTAATG
*
41343938 TATATGTATATATCGTATATGTTT
1 TATATATAT-TAT-GTATAT-TTT
41343962 TATATATATTATGTATATATTT
1 TATATATATTATGTATAT-TTT
41343984 TCA-ATATTATTACT-TATATTTT
1 T-ATATA-TATTA-TGTATATTTT
41344006 TATATAT
1 TATATAT
41344013 TATTCCATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.04
22 20 0.44
23 14 0.31
24 9 0.20
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.57
Consensus pattern (21 bp):
TATATATATTATGTATATTTT
Found at i:41343990 original size:24 final size:24
Alignment explanation
Indices: 41343963--41344076 Score: 69
Period size: 26 Copynumber: 4.7 Consensus size: 24
41343953 TATATGTTTT
41343963 ATATATATTATGTATATATTTTCA
1 ATATATATTATGTATATATTTTCA
41343987 ATAT-TATTACT-TATAT-TTTT--
1 ATATATATTA-TGTATATATTTTCA
* *
41344007 ATATATTATTCCATGTACATA-TTTCC
1 ATATA-TATT--ATGTATATATTTTCA
* *
41344033 ATATCATCTTATGTATATATTCTTAA
1 ATAT-ATATTATGTATATATT-TTCA
* *
41344059 ACATTATTTTATGTATAT
1 ATA-TATATTATGTATAT
41344077 GTATATTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
20 4 0.06
22 8 0.11
23 11 0.16
24 21 0.30
25 1 0.01
26 23 0.33
27 2 0.03
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATATATTATGTATATATTTTCA
Found at i:41343992 original size:20 final size:21
Alignment explanation
Indices: 41343965--41344016 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
41343955 TATGTTTTAT
41343965 ATATATTATGTA-TATATTTTC
1 ATATATTAT-TACTATATTTTC
*
41343986 A-ATATTATTACTTATATTTTT
1 ATATATTATTAC-TATATTTTC
41344007 ATATATTATT
1 ATATATTATT
41344017 CCATGTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 7 0.26
21 10 0.37
22 8 0.30
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATATTATTACTATATTTTC
Found at i:41344229 original size:31 final size:29
Alignment explanation
Indices: 41344155--41344230 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 29
41344145 TTAATATTAG
*
41344155 TATATATATT-TTATTATTCTTGTATACA
1 TATATTTATTATTATTATTCTTGTATACA
*
41344183 TATTTTATATATATTATTATT-TTCGTATATCA
1 TATATT-TAT-TATTATTATTCTT-GTATA-CA
41344215 TTATATTTATTATTAT
1 -TATATTTATTATTAT
41344231 ACCTATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 4 0.10
29 3 0.08
30 3 0.08
31 19 0.49
32 5 0.13
33 5 0.13
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (29 bp):
TATATTTATTATTATTATTCTTGTATACA
Found at i:41344351 original size:11 final size:11
Alignment explanation
Indices: 41344331--41344359 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41344321 ATATTTATTT
41344331 TATATA-TATG
1 TATATATTATG
41344341 TATATATTATG
1 TATATATTATG
41344352 TATATATT
1 TATATATT
41344360 TTAAAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (11 bp):
TATATATTATG
Found at i:41352661 original size:21 final size:22
Alignment explanation
Indices: 41352635--41352681 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
41352625 ACTATTACTC
41352635 ATATTTTAAATT-CAT-TTAAAA
1 ATATTTT-AATTCCATCTTAAAA
*
41352656 ATATTTTAATTCCATCTTAAAT
1 ATATTTTAATTCCATCTTAAAA
41352678 ATAT
1 ATAT
41352682 CAATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 10 0.43
22 9 0.39
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTTTAATTCCATCTTAAAA
Found at i:41355116 original size:32 final size:32
Alignment explanation
Indices: 41355079--41355143 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
41355069 GAATAAATTT
*
41355079 ACGGCAACTCAGTAATTTTCTAACTTATGAAC
1 ACGGCAACTCAGTAAATTTCTAACTTATGAAC
41355111 ACGGCAACTCAGTAAATTTCTAACTTATGAAC
1 ACGGCAACTCAGTAAATTTCTAACTTATGAAC
41355143 A
1 A
41355144 TACTTACTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (32 bp):
ACGGCAACTCAGTAAATTTCTAACTTATGAAC
Found at i:41356008 original size:18 final size:18
Alignment explanation
Indices: 41355985--41356025 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
41355975 TCAAATGACC
41355985 AGCAATAACTACTATAAT
1 AGCAATAACTACTATAAT
41356003 AGCAATAACTACTATAAT
1 AGCAATAACTACTATAAT
41356021 AGCAA
1 AGCAA
41356026 AAATAGACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.24
Consensus pattern (18 bp):
AGCAATAACTACTATAAT
Found at i:41359274 original size:22 final size:20
Alignment explanation
Indices: 41359235--41359281 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
41359225 TGTAAAGTTG
41359235 ATAATAATTAATATATATT-
1 ATAATAATTAATATATATTA
41359254 ATAATAGATATAATTATATATTA
1 ATAATA-AT-TAA-TATATATTA
41359277 ATAAT
1 ATAAT
41359282 TATCATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 3 0.12
22 8 0.33
23 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATAATAATTAATATATATTA
Found at i:41366789 original size:22 final size:22
Alignment explanation
Indices: 41366763--41366806 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
41366753 GAAAATAATC
*
41366763 AAAATTAA-TCAAAATTTATTAT
1 AAAATTAAGT-AAAATTCATTAT
41366785 AAAATTAAGTAAAATTCATTAT
1 AAAATTAAGTAAAATTCATTAT
41366807 GTTAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATTAAGTAAAATTCATTAT
Found at i:41366841 original size:27 final size:27
Alignment explanation
Indices: 41366789--41366842 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
41366779 TATTATAAAA
* *
41366789 TTAAGTAAAATTCATTATGTTAATAAT
1 TTAAGTAAAAATAATTATGTTAATAAT
*
41366816 TTAAGTACAAAATAATTAT-TTTATAAT
1 TTAAGTA-AAAATAATTATGTTAATAAT
41366843 ATTTATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (27 bp):
TTAAGTAAAAATAATTATGTTAATAAT
Found at i:41368197 original size:14 final size:14
Alignment explanation
Indices: 41368178--41368205 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41368168 TATATTGAAA
41368178 AAGGGTGCGTGTGG
1 AAGGGTGCGTGTGG
41368192 AAGGGTGCGTGTGG
1 AAGGGTGCGTGTGG
41368206 TAGCTCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.57, T:0.21
Consensus pattern (14 bp):
AAGGGTGCGTGTGG
Found at i:41371026 original size:21 final size:21
Alignment explanation
Indices: 41370976--41371027 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
41370966 TATATATAGA
*
41370976 TATTTTATATATACTTCTTAC
1 TATTTTATGTATACTTCTTAC
* *
41370997 -ATTTT-TGTATATTTCTTTC
1 TATTTTATGTATACTTCTTAC
41371016 TATTTTATGTAT
1 TATTTTATGTAT
41371028 TTTTATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 11 0.42
20 10 0.38
21 5 0.19
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63
Consensus pattern (21 bp):
TATTTTATGTATACTTCTTAC
Found at i:41381579 original size:19 final size:19
Alignment explanation
Indices: 41381542--41381579 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41381532 ACCTGTCAGA
*
41381542 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
41381561 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
41381580 TAAATTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:41381726 original size:72 final size:72
Alignment explanation
Indices: 41381630--41381776 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 72
41381620 CAAGTGTTCC
41381630 TAATATCCTAGTTCCCCGGCAACGGCGTCAAAAACTTGATGCGTGATATTCGTAATAGGTTTTAA
1 TAATATCCTAGTTCCCCGGCAACGGCGTCAAAAACTTGATGCGTGATATTCGTAATAGGTTTTAA
*
41381695 AAATTTA
66 AAAATTA
41381702 TAATATCCTAGTTCCCCGGCAACGGCGTCAAAAACTTGATGCGTGATATTCGTAATAGGTTTTAA
1 TAATATCCTAGTTCCCCGGCAACGGCGTCAAAAACTTGATGCGTGATATTCGTAATAGGTTTTAA
41381767 AAAATTA
66 AAAATTA
41381774 TAA
1 TAA
41381777 ATGAATCATT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (72 bp):
TAATATCCTAGTTCCCCGGCAACGGCGTCAAAAACTTGATGCGTGATATTCGTAATAGGTTTTAA
AAAATTA
Found at i:41382881 original size:13 final size:13
Alignment explanation
Indices: 41382863--41382890 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41382853 TTGCCAAAGG
41382863 GACACGCCCGTGT
1 GACACGCCCGTGT
41382876 GACACGCCCGTGT
1 GACACGCCCGTGT
41382889 GA
1 GA
41382891 GAAAGTCCAG
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:0.18, C:0.36, G:0.32, T:0.14
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:41383385 original size:16 final size:16
Alignment explanation
Indices: 41383364--41383395 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41383354 ACTAGCATCT
41383364 TTACCAACAATATGCC
1 TTACCAACAATATGCC
41383380 TTACCAACAATATGCC
1 TTACCAACAATATGCC
41383396 AATACTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (16 bp):
TTACCAACAATATGCC
Found at i:41387066 original size:22 final size:21
Alignment explanation
Indices: 41387033--41387080 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
41387023 GTATTTTTAT
41387033 AATTTTTAATAATCTTT-TAGTA
1 AATTTTTAATAAT-TTTAT-GTA
41387055 AATTCTTT-ATAATTTTATGTA
1 AATT-TTTAATAATTTTATGTA
41387076 AATTT
1 AATTT
41387081 AATATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
22 10 0.42
23 3 0.12
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (21 bp):
AATTTTTAATAATTTTATGTA
Found at i:41389011 original size:12 final size:13
Alignment explanation
Indices: 41388994--41389023 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
41388984 TATTTTTACA
41388994 TATTTTT-ATAAT
1 TATTTTTAATAAT
41389006 TATTTTTAATAAT
1 TATTTTTAATAAT
41389019 TATTT
1 TATTT
41389024 GATACATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTTAATAAT
Found at i:41389547 original size:6 final size:6
Alignment explanation
Indices: 41389537--41389575 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
41389527 CACTTGATCT
*
41389537 CCCTTT CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCC
41389576 CATCCTTGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCCTTC
Found at i:41394109 original size:15 final size:15
Alignment explanation
Indices: 41394089--41394119 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41394079 CCAACCTTCA
41394089 AATTTTACCTCAATT
1 AATTTTACCTCAATT
41394104 AATTTTACCTCAATT
1 AATTTTACCTCAATT
41394119 A
1 A
41394120 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:41397544 original size:27 final size:27
Alignment explanation
Indices: 41397514--41397691 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
41397504 ATATTGAGTC
* * * *
41397514 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41397541 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
41397568 CGCACACTTAGTGCTACATAGTCAATCT
1 CGCACACTTAGTGCTACATAGTCAA-AT
** * *
41397596 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41397623 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41397650 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41397677 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41397692 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41397653 original size:82 final size:81
Alignment explanation
Indices: 41397535--41397690 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
41397525 TGCTATATAA
* * *
41397535 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAATCTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAA-ATCGCA
41397600 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41397617 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41397681 CACTTAGTGC
65 CACTTAGTGC
41397691 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41405434 original size:27 final size:27
Alignment explanation
Indices: 41405404--41405581 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41405394 ATATTGAGTC
* * * *
41405404 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41405431 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41405458 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41405486 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41405513 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41405540 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41405567 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41405582 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41405543 original size:82 final size:81
Alignment explanation
Indices: 41405425--41405580 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41405415 TGCTATATAA
* *
41405425 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41405490 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41405507 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41405571 CACTTAGTGC
65 CACTTAGTGC
41405581 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41407376 original size:11 final size:11
Alignment explanation
Indices: 41407360--41407386 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41407350 TAGAAATTAG
41407360 TTTGTGAAACT
1 TTTGTGAAACT
41407371 TTTGTGAAACT
1 TTTGTGAAACT
41407382 TTTGT
1 TTTGT
41407387 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:41408919 original size:93 final size:92
Alignment explanation
Indices: 41408787--41408981 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
41408777 TTGATTTTAG
* *
41408787 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
41408851 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
41408879 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
41408944 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
41408972 CAAATTCATA
1 TAAATTCATA
41408982 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:41409039 original size:17 final size:17
Alignment explanation
Indices: 41409014--41409047 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41409004 ATAATTTTAA
*
41409014 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
41409031 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
41409048 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:41409049 original size:15 final size:16
Alignment explanation
Indices: 41409014--41409052 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
41409004 ATAATTTTAA
*
41409014 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
41409031 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
41409046 ATTTAAT
1 ATTTAAT
41409053 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:41409056 original size:17 final size:18
Alignment explanation
Indices: 41409018--41409057 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
41409008 TTTTAAATTT
*
41409018 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
41409036 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
41409052 TATTAA
1 TATTAA
41409058 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:41409172 original size:15 final size:15
Alignment explanation
Indices: 41409137--41409271 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 15
41409127 TTAAGAATTT
*
41409137 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41409151 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41409165 TATTTAATAATAAT-
1 TATTTAATTATAATA
41409179 TATGTTAATT-T-ATA
1 TAT-TTAATTATAATA
* *
41409193 T-TTTACAGTATCATA
1 TATTTA-ATTATAATA
*
41409208 TATTATGATTTGAGTAAATTCA
1 TATT-T-AATT-A-T-AA-T-A
*
41409230 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41409244 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41409258 TATTTAATAATAAT
1 TATTTAATTATAAT
41409272 TATGTTTAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 33
0.68 0.08 0.24
Matches are distributed among these distances:
12 3 0.03
13 21 0.23
14 17 0.18
15 32 0.34
16 3 0.03
17 2 0.02
18 3 0.03
19 2 0.02
20 4 0.04
21 1 0.01
22 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41409179 original size:120 final size:119
Alignment explanation
Indices: 41409013--41409231 Score: 345
Period size: 120 Copynumber: 1.8 Consensus size: 119
41409003 AATAATTTTA
* *
41409013 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATATTAATTAT-TTGAAATTT-TCTTT
1 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATGTT--AATTTATATTT
*
41409076 TATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
64 TACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
*
41409132 AATTTTATTAAATTATATATTTTAATTATAAT-ATATTTAATAATAATTATGTTAATTTATATTT
1 AATTTTATTAAATCATATA-TTTAATTA-AATCATATTTAATAATAATTATGTTAATTTATATTT
41409196 TACAGTATCATATATTATGATTTGAGTAAATTCATA
64 TACAGTATCATATATTATGATTTGAGTAAATTCATA
41409232 TTAAATTATA
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
119 23 0.25
120 64 0.70
121 5 0.05
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATGTTAATTTATATTTTA
CAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
Found at i:41409260 original size:16 final size:16
Alignment explanation
Indices: 41409239--41409280 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41409229 ATATTAAATT
*
41409239 ATATATTTTAATTATA
1 ATATATTTTAATAATA
41409255 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
41409270 AT-TATGTTTAA
1 ATATAT-TTTAA
41409281 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:41409388 original size:154 final size:156
Alignment explanation
Indices: 41409230--41409527 Score: 546
Period size: 154 Copynumber: 1.9 Consensus size: 156
41409220 AGTAAATTCA
*
41409230 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
41409295 TTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
66 TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
41409358 AAATTTATGCTAATTATTAAGAATTT
131 AAATTTATGCTAATTATTAAGAATTT
41409384 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
*
41409449 TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAA
66 TTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
*
41409514 CAAATTTCTGCTAA
130 CAAATTTATGCTAA
41409528 GGGTATTCTA
Statistics
Matches: 138, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
154 76 0.55
155 2 0.01
157 60 0.43
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (156 bp):
TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
AAATTTATGCTAATTATTAAGAATTT
Found at i:41409408 original size:18 final size:17
Alignment explanation
Indices: 41409380--41409414 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41409370 ATTATTAAGA
*
41409380 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41409397 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41409415 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:41409668 original size:16 final size:16
Alignment explanation
Indices: 41409647--41409685 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41409637 TTGATTTGCT
*
41409647 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
41409663 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
41409679 ATTACAC
1 ATTACAC
41409686 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:41409686 original size:16 final size:16
Alignment explanation
Indices: 41409660--41409716 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
41409650 ACACAGCTTT
* *
41409660 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
41409676 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
41409692 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
41409708 TCCAATACA
1 TCCAATACA
41409717 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:41411437 original size:10 final size:11
Alignment explanation
Indices: 41411410--41411436 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41411400 CTTTATATAT
41411410 TTTTTTAGAAA
1 TTTTTTAGAAA
41411421 TTTTTTAGAAA
1 TTTTTTAGAAA
41411432 TTTTT
1 TTTTT
41411437 ATAATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (11 bp):
TTTTTTAGAAA
Found at i:41411437 original size:21 final size:21
Alignment explanation
Indices: 41411411--41411453 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41411401 TTTATATATT
*
41411411 TTTTTAGAAATTTTTTAGAAA
1 TTTTTAGAAATTTTTTAAAAA
* *
41411432 TTTTTATAATTTTTTTAAAAA
1 TTTTTAGAAATTTTTTAAAAA
41411453 T
1 T
41411454 ATAAATTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (21 bp):
TTTTTAGAAATTTTTTAAAAA
Found at i:41411471 original size:27 final size:27
Alignment explanation
Indices: 41411439--41411499 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
41411429 AAATTTTTAT
41411439 AATTTTTTTAAA-AATATAAATTTTGG
1 AATTTTTTTAAATAATATAAATTTTGG
* * * *
41411465 AATTTTTATAAATATTTTAAATTTTTG
1 AATTTTTTTAAATAATATAAATTTTGG
41411492 AATTTTTT
1 AATTTTTT
41411500 GTTAAGAGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (27 bp):
AATTTTTTTAAATAATATAAATTTTGG
Found at i:41411764 original size:13 final size:12
Alignment explanation
Indices: 41411738--41411771 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 12
41411728 TGCTCACCCC
41411738 TAATATTTTTTT
1 TAATATTTTTTT
41411750 TAATATTTATTTT
1 TAATATTT-TTTT
41411763 TAATATTTT
1 TAATATTTT
41411772 ACTATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TAATATTTTTTT
Found at i:41412284 original size:3 final size:3
Alignment explanation
Indices: 41412276--41412309 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
41412266 AACATGCCTT
41412276 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA -AA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
41412310 TTAACACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:41421901 original size:42 final size:42
Alignment explanation
Indices: 41421839--41421940 Score: 177
Period size: 42 Copynumber: 2.4 Consensus size: 42
41421829 GGGAATACTT
41421839 CACAGCTCGTGTGAGTAGCATCGTGTAGCTTACATTCCGATC
1 CACAGCTCGTGTGAGTAGCATCGTGTAGCTTACATTCCGATC
* * *
41421881 CATAGCTCATGTGAGTAGCATCGTGTAGCTTACATTCTGATC
1 CACAGCTCGTGTGAGTAGCATCGTGTAGCTTACATTCCGATC
41421923 CACAGCTCGTGTGAGTAG
1 CACAGCTCGTGTGAGTAG
41421941 ACCCATTTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.29
Consensus pattern (42 bp):
CACAGCTCGTGTGAGTAGCATCGTGTAGCTTACATTCCGATC
Found at i:41423665 original size:28 final size:28
Alignment explanation
Indices: 41423633--41423691 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
41423623 GCCTAATAGT
* ** *
41423633 TGCTTTCAAATTGTGCTCTAATCGCCAA
1 TGCTTGCAAATTGCACTCCAATCGCCAA
*
41423661 TGCTTGCAAATTGCACTCCAATTGCCAA
1 TGCTTGCAAATTGCACTCCAATCGCCAA
41423689 TGC
1 TGC
41423692 CCACAACCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.32
Consensus pattern (28 bp):
TGCTTGCAAATTGCACTCCAATCGCCAA
Found at i:41425174 original size:18 final size:18
Alignment explanation
Indices: 41425153--41425190 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41425143 GGTTGTAAAC
41425153 TAGTTTAAGGTGATAGAA
1 TAGTTTAAGGTGATAGAA
41425171 TAGTTTAAGGTGATAGAA
1 TAGTTTAAGGTGATAGAA
41425189 TA
1 TA
41425191 AAGTGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.34
Consensus pattern (18 bp):
TAGTTTAAGGTGATAGAA
Found at i:41428829 original size:63 final size:67
Alignment explanation
Indices: 41428761--41428899 Score: 151
Period size: 68 Copynumber: 2.1 Consensus size: 67
41428751 AAATAATATT
* * * *
41428761 ATTTTAAT-A-GAT-TTAGTATTAAATTAAATTTAATACTTATCTTAAT-AGTATTTTATTAATT
1 ATTTTAATCATGATCTTAATATTAAATTAAATCTAATACTTATCTTAATAAGTACTATATTAATT
41428822 TA
66 TA
* * * *
41428824 ATTTTAAAATCATTATCTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTACTATATTAA
1 ATTTT--AATCATGATCTTAATATTAAATTAAATCTAATACTTATCTTAATAAGTACTATATTAA
41428889 TTTA
64 TTTA
*
41428893 ATATTAA
1 ATTTTAA
41428900 AGTGATTAAC
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
63 5 0.08
65 3 0.05
66 1 0.02
67 4 0.07
68 29 0.48
69 19 0.31
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (67 bp):
ATTTTAATCATGATCTTAATATTAAATTAAATCTAATACTTATCTTAATAAGTACTATATTAATT
TA
Found at i:41428846 original size:39 final size:38
Alignment explanation
Indices: 41428758--41428846 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 38
41428748 TAAAAATAAT
* *
41428758 ATTATTTTAATAGATTTAGTATTAAATTAAATTTAATAC
1 ATTATCTTAATAGATTTA-TATTAAATTAAATTTAAAAC
* *
41428797 -TTATCTTAATAGTATTT-TATTAATTTAATTTTAAAATC
1 ATTATCTTAATAG-ATTTATATTAAATTAAATTTAAAA-C
41428835 ATTATCTTAATA
1 ATTATCTTAATA
41428847 TTAAATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
37 16 0.37
38 12 0.28
39 15 0.35
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.52
Consensus pattern (38 bp):
ATTATCTTAATAGATTTATATTAAATTAAATTTAAAAC
Found at i:41429411 original size:21 final size:23
Alignment explanation
Indices: 41429386--41429433 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
41429376 TCGCATTTTT
*
41429386 AAAATTA-TAAAAATCAAA-TAA
1 AAAATTACTAAAAATAAAATTAA
*
41429407 AAAATTACTAAATATAAAATTAA
1 AAAATTACTAAAAATAAAATTAA
41429430 AAAA
1 AAAA
41429434 ACAAGAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 9 0.39
23 7 0.30
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAATTACTAAAAATAAAATTAA
Found at i:41429484 original size:15 final size:15
Alignment explanation
Indices: 41429464--41429499 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
41429454 GAAAGAAAAA
41429464 TTGAGAACAAAATAG
1 TTGAGAACAAAATAG
41429479 TTGAGAACAAAATAG
1 TTGAGAACAAAATAG
41429494 TTGAGA
1 TTGAGA
41429500 GAATAGATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (15 bp):
TTGAGAACAAAATAG
Found at i:41430444 original size:29 final size:29
Alignment explanation
Indices: 41430411--41430470 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
41430401 ATATCATTGA
41430411 TAAAATTACCAAACGATATAAAAGCGTAT
1 TAAAATTACCAAACGATATAAAAGCGTAT
* * * *
41430440 TAAAATTAGCGAATGATATAAAATCGTAT
1 TAAAATTACCAAACGATATAAAAGCGTAT
41430469 TA
1 TA
41430471 GTTTTACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (29 bp):
TAAAATTACCAAACGATATAAAAGCGTAT
Found at i:41430542 original size:24 final size:24
Alignment explanation
Indices: 41430496--41430542 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41430486 GATTATTTTC
*
41430496 TATTTATTTATTTGTTTTTTACAA
1 TATTTATTTATTTGTTTTCTACAA
41430520 TATTTATTTATTT-TTATTCTACA
1 TATTTATTTATTTGTT-TTCTACA
41430543 TCGTATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTTATTTATTTGTTTTCTACAA
Found at i:41448017 original size:25 final size:25
Alignment explanation
Indices: 41447989--41448055 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
41447979 AGACTCACCA
*
41447989 TAGCTCGCATAAGCTTACCGATATT
1 TAGCTCGGATAAGCTTACCGATATT
*
41448014 TAGCTCGGA-AGAGCTTACTGATATT
1 TAGCTCGGATA-AGCTTACCGATATT
* *
41448039 CAGCTCGGATGAGCTTA
1 TAGCTCGGATAAGCTTA
41448056 TCGTTTACCG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (25 bp):
TAGCTCGGATAAGCTTACCGATATT
Found at i:41448718 original size:45 final size:45
Alignment explanation
Indices: 41448669--41448791 Score: 138
Period size: 45 Copynumber: 2.7 Consensus size: 45
41448659 ACCGGAAATA
* * *
41448669 AGTAAGACCATAATTGAAAGACGTTATGGCATCACGATTCTAACG
1 AGTAAGACCATAGTTGAAAGACGCTATGGCATCACGAATCTAACG
* * * * *
41448714 AGTAAGACCTTAGCTGAAAGATGCTATGGCATCATGAATCTGACG
1 AGTAAGACCATAGTTGAAAGACGCTATGGCATCACGAATCTAACG
* * * *
41448759 AATAAGACCATTGTTGAAAGACACTATGACATC
1 AGTAAGACCATAGTTGAAAGACGCTATGGCATC
41448792 CTTTAACCAA
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (45 bp):
AGTAAGACCATAGTTGAAAGACGCTATGGCATCACGAATCTAACG
Found at i:41449759 original size:13 final size:13
Alignment explanation
Indices: 41449741--41449766 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41449731 CCATGCGCAC
41449741 GGGCGTGTAGTTT
1 GGGCGTGTAGTTT
41449754 GGGCGTGTAGTTT
1 GGGCGTGTAGTTT
41449767 AGCCGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.46, T:0.38
Consensus pattern (13 bp):
GGGCGTGTAGTTT
Found at i:41455137 original size:14 final size:14
Alignment explanation
Indices: 41455118--41455149 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
41455108 ATTAAGGTAG
41455118 AATTTTCTATTTAT
1 AATTTTCTATTTAT
41455132 AATTTTCTATTTAT
1 AATTTTCTATTTAT
41455146 AATT
1 AATT
41455150 GTTTCTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTTTCTATTTAT
Done.