Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 188 of 322
Found at i:61779110 original size:81 final size:81
Alignment explanation
Indices: 61778971--61779125 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 81
61778961 CTCAACCTAT
* ** * **
61778971 AAAATTATCGAAATACCCTTGATTTGTAAAATTACCAAAATACCCCTAATTTGGAAAATTACCGA
1 AAAATTATAGAAATACCCTTGATTTAAAAAATTACCAAAATACCACTAATTTACAAAATTACCGA
61779036 AATACCCTTAATTTGG
66 AATACCCTTAATTTGG
* * ** *
61779052 AAAATTATAGAAATACCCTTGACTTTAAAAAATTA-TAAAATACCATTGGTTTACAAAATTATCG
1 AAAATTATAGAAATACCCTTGA-TTTAAAAAATTACCAAAATACCACTAATTTACAAAATTACCG
61779116 AAATACCCTT
65 AAATACCCTT
61779126 GGTTTGTAGA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
81 52 0.84
82 10 0.16
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (81 bp):
AAAATTATAGAAATACCCTTGATTTAAAAAATTACCAAAATACCACTAATTTACAAAATTACCGA
AATACCCTTAATTTGG
Found at i:61779657 original size:22 final size:21
Alignment explanation
Indices: 61779608--61779660 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
61779598 AATTGTTCTA
61779608 ATTATGGCTTTGTACCAACCT
1 ATTATGGCTTTGTACCAACCT
*
61779629 ACATATGGCTTTGTACCAACCT
1 A-TTATGGCTTTGTACCAACCT
61779651 GATTATGGCT
1 -ATTATGGCT
61779661 GTGTGCGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.36
Consensus pattern (21 bp):
ATTATGGCTTTGTACCAACCT
Found at i:61791237 original size:26 final size:26
Alignment explanation
Indices: 61791208--61791260 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
61791198 AATCACAAAG
61791208 ATCAATTCAAGCAGATCAATATATTC
1 ATCAATTCAAGCAGATCAATATATTC
61791234 ATCAATTCAAGCAGATCAATATATTC
1 ATCAATTCAAGCAGATCAATATATTC
61791260 A
1 A
61791261 CTAAGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (26 bp):
ATCAATTCAAGCAGATCAATATATTC
Found at i:61793123 original size:51 final size:51
Alignment explanation
Indices: 61793036--61793270 Score: 168
Period size: 51 Copynumber: 4.6 Consensus size: 51
61793026 GTACCTTCTT
* * * * * * * *
61793036 CACAAAGTGGCCTTCACATAGTACCACACTTGTGATCAAAACCATCTGTTA
1 CACATAGTAGCCTGCACTTAGTACTACACATATGATCAAAACCATCTGGTA
** * * * *
61793087 CACATAGTTTCCTGCACTTAGTACTACACATATGATCGAAGCTATCGGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATATGATCAAAACCATCTGGTA
* * * ** **
61793138 CGCATAGTAGCCTGCACTTAATACTATACATGCGA-CCTAACCATCTGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATATGATCAAAACCATCTGGTA
* * * * * **
61793188 CACGTAGTAGCCTGCACTTAGTGCTACACACATGACCTAAAACCATTTGAAA
1 CACATAGTAGCCTGCACTTAGTACTACACATATGATC-AAAACCATCTGGTA
**
61793240 CACATAGTAGCCTAG-AAATAGTACTACACAT
1 CACATAGTAGCCT-GCACTTAGTACTACACAT
61793271 GTGTTCTCAC
Statistics
Matches: 138, Mismatches: 43, Indels: 5
0.74 0.23 0.03
Matches are distributed among these distances:
50 37 0.27
51 67 0.49
52 33 0.24
53 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (51 bp):
CACATAGTAGCCTGCACTTAGTACTACACATATGATCAAAACCATCTGGTA
Found at i:61793225 original size:50 final size:50
Alignment explanation
Indices: 61793075--61793270 Score: 169
Period size: 50 Copynumber: 3.9 Consensus size: 50
61793065 TTGTGATCAA
* ** * *
61793075 AACCATCTGTTACACATAGTTTCCTGCACTTAGTACTACACATATGATCG
1 AACCATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATATGACCT
* * * * * **
61793125 AAGCTATCGGGTACGCATAGTAGCCTGCACTTAATACTATACATGCGACCT
1 AA-CCATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATATGACCT
* * *
61793176 AACCATCTGGTACACGTAGTAGCCTGCACTTAGTGCTACACACATGACCT
1 AACCATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATATGACCT
* ** **
61793226 AAAACCATTTGAAACACATAGTAGCCTAG-AAATAGTACTACACAT
1 --AACCATCTGGTACACATAGTAGCCT-GCACTTAGTACTACACAT
61793271 GTGTTCTCAC
Statistics
Matches: 112, Mismatches: 30, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
50 40 0.36
51 38 0.34
52 33 0.29
53 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (50 bp):
AACCATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATATGACCT
Found at i:61793660 original size:31 final size:30
Alignment explanation
Indices: 61793625--61793683 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
61793615 CTAAATTCAC
*
61793625 ATTTTGGCAAAATTTAAATTTTTGCCCCTCA
1 ATTTTGGC-AAATTTAAACTTTTGCCCCTCA
* * *
61793656 ATTTTGTCATATTTACACTTTTGCCCCT
1 ATTTTGGCAAATTTAAACTTTTGCCCCT
61793684 AGGCTCGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (30 bp):
ATTTTGGCAAATTTAAACTTTTGCCCCTCA
Found at i:61811014 original size:32 final size:31
Alignment explanation
Indices: 61810963--61811042 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 31
61810953 ATACCAATTC
*
61810963 AGACCAGTCCTATATATATATATAATACATTG
1 AGACTAGT-CTATATATATATATAATACATTG
61810995 AGACTAGTC---ATATATATATAATACATTG
1 AGACTAGTCTATATATATATATAATACATTG
61811023 AGACTAGTC-ATATATATATA
1 AGACTAGTCTATATATATATA
61811043 CATGTCATGA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
28 28 0.62
30 9 0.20
31 1 0.02
32 7 0.16
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (31 bp):
AGACTAGTCTATATATATATATAATACATTG
Found at i:61811016 original size:28 final size:28
Alignment explanation
Indices: 61810976--61811042 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
61810966 CCAGTCCTAT
61810976 ATATATATATAATACATTGAGACTAGTC
1 ATATATATATAATACATTGAGACTAGTC
61811004 ATATATATATAATACATTGAGACTAGTC
1 ATATATATATAATACATTGAGACTAGTC
61811032 ATATATATATA
1 ATATATATATA
61811043 CATGTCATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (28 bp):
ATATATATATAATACATTGAGACTAGTC
Found at i:61811116 original size:16 final size:17
Alignment explanation
Indices: 61811088--61811132 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
61811078 TTATAAACAC
61811088 ATATCATATATTTCATT
1 ATATCATATATTTCATT
61811105 ATATCA-ATATTTCA-T
1 ATATCATATATTTCATT
*
61811120 ATACCATA-ATTTC
1 ATATCATATATTTC
61811133 CATGTATTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 11 0.42
16 9 0.35
17 6 0.23
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATCATATATTTCATT
Found at i:61816387 original size:55 final size:55
Alignment explanation
Indices: 61816327--61816435 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
61816317 AACTTACTTG
*
61816327 TTTATAACCTTACCACATCCTGGTCACTTAATG-AACACATCATTCACATAACCAT
1 TTTATAACCTTACCACATCCCGGTCACTTAATGTAA-ACATCATTCACATAACCAT
*
61816382 TTTATAACCTTACCACATCCCGGTCACTTAATGTAAACATCTTTCACATAACCA
1 TTTATAACCTTACCACATCCCGGTCACTTAATGTAAACATCATTCACATAACCA
61816436 AGTTCCTGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
55 49 0.96
56 2 0.04
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (55 bp):
TTTATAACCTTACCACATCCCGGTCACTTAATGTAAACATCATTCACATAACCAT
Found at i:61816640 original size:63 final size:65
Alignment explanation
Indices: 61816561--61816715 Score: 158
Period size: 67 Copynumber: 2.4 Consensus size: 65
61816551 ATATAGTTTG
* * * *
61816561 GCTCTCTTGTAC-ACATGGTGAACAC-TCA-GTACCACCCATGTGACCTAGCCA-ATTTATCTCG
1 GCTCTCTTGT-CTACATGGTG-ACACTTCACGAACCACCCATGCGACCTAGCCACATATATCCCG
61816622 TA
64 TA
* * *
61816624 GCTCTCTTGTCTACATGGTGTC-CTTCACCTGGAACCACGCATGCGACCTAGCTACATATATCCC
1 GCTCTCTTGTCTACATGGTGACACTTCA-C--GAACCACCCATGCGACCTAGCCACATATATCCC
61816688 GTA
63 GTA
61816691 GCTCTCTTGTCTACATGGTGTACAC
1 GCTCTCTTGTCTACATGGTG-ACAC
61816716 ATAGTATCAC
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
61 1 0.01
62 5 0.07
63 18 0.24
66 19 0.25
67 30 0.40
68 1 0.01
69 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.30
Consensus pattern (65 bp):
GCTCTCTTGTCTACATGGTGACACTTCACGAACCACCCATGCGACCTAGCCACATATATCCCGTA
Found at i:61818358 original size:45 final size:44
Alignment explanation
Indices: 61818243--61818364 Score: 156
Period size: 47 Copynumber: 2.7 Consensus size: 44
61818233 AGGTTATTTG
*
61818243 TGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGAGA
1 TGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGACTAGAGA
* *
61818287 TGTAAGCCAGTGTAAAACATTGTCTGGGACATGCATC-GACTGCGAGA
1 TGT--GCCAGTGTAAGACA-TGTCTGGGACATGCATCGGACT-AGAGA
*
61818334 TGTGTCAGTGTAAGACCATGTCTGGGACATG
1 TGTGCCAGTGTAAGA-CATGTCTGGGACATG
61818365 GCATGGGCAT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
44 3 0.04
45 23 0.34
46 18 0.26
47 24 0.35
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (44 bp):
TGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGACTAGAGA
Found at i:61824584 original size:36 final size:36
Alignment explanation
Indices: 61824537--61824609 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
61824527 GCACTTCCTT
61824537 ATCTGCTTCAAAATCTAAGACAATGAAATCAGCAGG
1 ATCTGCTTCAAAATCTAAGACAATGAAATCAGCAGG
61824573 ATCTGCTTCAAAATCTAAGACAATGAAATCAGCAGG
1 ATCTGCTTCAAAATCTAAGACAATGAAATCAGCAGG
61824609 A
1 A
61824610 AAAATAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.22
Consensus pattern (36 bp):
ATCTGCTTCAAAATCTAAGACAATGAAATCAGCAGG
Found at i:61827000 original size:34 final size:34
Alignment explanation
Indices: 61826957--61827028 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
61826947 CCCATACTCG
61826957 TAACCCACGCCAGAGCGAAATACGAGGCATTACC
1 TAACCCACGCCAGAGCGAAATACGAGGCATTACC
61826991 TAACCCACGCCAGAGCGAAATACGAGGCATTACC
1 TAACCCACGCCAGAGCGAAATACGAGGCATTACC
61827025 TAAC
1 TAAC
61827029 TCGATCTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.12
Consensus pattern (34 bp):
TAACCCACGCCAGAGCGAAATACGAGGCATTACC
Found at i:61829580 original size:29 final size:29
Alignment explanation
Indices: 61829538--61829684 Score: 140
Period size: 29 Copynumber: 5.2 Consensus size: 29
61829528 GTGAGCATGA
* *
61829538 ATAT-AAGGTGATTTGGGCCTAACGGGCC
1 ATATGAAGGTGAATTGGGCCTAATGGGCC
* * *
61829566 ATATAAAGGTGATTTGGGCCTAATAGGCC
1 ATATGAAGGTGAATTGGGCCTAATGGGCC
* * *
61829595 ATTTGAAGATGAATTGGGCCTGATGGGCC
1 ATATGAAGGTGAATTGGGCCTAATGGGCC
* * *
61829624 ACATGAATGTGAATTGGGCCTGATGGGCC
1 ATATGAAGGTGAATTGGGCCTAATGGGCC
* *
61829653 ATTTGAA--TGAAATGGGCC-AAGTGGGCC
1 ATATGAAGGTGAATTGGGCCTAA-TGGGCC
61829680 ATATG
1 ATATG
61829685 CATGTATGTA
Statistics
Matches: 100, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
26 1 0.01
27 20 0.20
28 4 0.04
29 75 0.75
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (29 bp):
ATATGAAGGTGAATTGGGCCTAATGGGCC
Found at i:61831145 original size:46 final size:46
Alignment explanation
Indices: 61830951--61831221 Score: 155
Period size: 46 Copynumber: 5.8 Consensus size: 46
61830941 TGGGGTAAAG
* * *
61830951 TGCCGATGCCATATCCCAGACATGGTCTTACAC-ATGCTCTAGCATATCTG-
1 TGCCGATG-CATGTCCCAGACAT-GTCTTACACTA-GCACT--CGTATC-GA
* * * *
61831001 TGCCGATGCTGTGTCCCAGACATAGTCTTACACT-G-ACACATCTCG-
1 TGCCGATGC-ATGTCCCAGACAT-GTCTTACACTAGCACTCGTATCGA
* * * *
61831046 TAGCCGATACATGTCCCAGACATGTCTTACACT-G-ATTTATGTCTCGA
1 T-GCCGATGCATGTCCCAGACATGTCTTACACTAGCA-CT-CGTATCGA
* *
61831093 GGCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTTTCGA
1 TGCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTATCGA
* ** * * * *
61831139 TCCCGATGCCATGTTTCAAACATGGTCTTACACTGGCTCTCATAAT-G-
1 TGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCGT-ATCGA
*
61831186 TGGCTGATGCATGTCCCAGACATGTCTTACACTAGC
1 T-GCCGATGCATGTCCCAGACATGTCTTACACTAGC
61831222 TCAAAATAAC
Statistics
Matches: 177, Mismatches: 32, Indels: 28
0.75 0.14 0.12
Matches are distributed among these distances:
44 12 0.07
45 14 0.08
46 71 0.40
47 25 0.14
48 24 0.14
49 3 0.02
50 28 0.16
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
TGCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTATCGA
Found at i:61835486 original size:43 final size:42
Alignment explanation
Indices: 61835424--61835547 Score: 162
Period size: 43 Copynumber: 3.0 Consensus size: 42
61835414 TACCATACCA
* **
61835424 ATGCCATATCCTAGATATGGTCTTACATGGGATCTCAAATTG
1 ATGCCATATCCTAGATATGGTCTTACACGAAATCTCAAATTG
* * *
61835466 ATGCCAATAGCCTAGCTATGGTCTTACACGAAATCTCATATTG
1 ATGCC-ATATCCTAGATATGGTCTTACACGAAATCTCAAATTG
61835509 ATGCCATATCC-AGATATGGTCTTACACGTAAA-CTCAAAT
1 ATGCCATATCCTAGATATGGTCTTACACG-AAATCTCAAAT
61835548 AACCCTAATG
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
41 22 0.31
42 13 0.18
43 36 0.51
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCTAGATATGGTCTTACACGAAATCTCAAATTG
Found at i:61843489 original size:28 final size:28
Alignment explanation
Indices: 61843410--61843627 Score: 204
Period size: 24 Copynumber: 8.4 Consensus size: 28
61843400 GGGAAATTAC
61843410 TCACTTAGCACCA-TGCCATGGACTTATT
1 TCACTTAGCA-CATTGCCATGGACTTATT
61843438 TCACTTAG---ATT-CCATGGAC--ATT
1 TCACTTAGCACATTGCCATGGACTTATT
*
61843460 TCACTTAGCACATTGCCGTGGACTTATT
1 TCACTTAGCACATTGCCATGGACTTATT
*
61843488 TCACTTAG---A-TGCCATGGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATT
* *
61843512 TCACTTAGCGCATTGTCATGGACTTATT
1 TCACTTAGCACATTGCCATGGACTTATT
* * *
61843540 TCAC-TA--AGA-TGCCATTGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATT
61843564 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACATTGCCATGGACTTATT
***
61843592 TCACTTAG---A-TGCCATGCTTTTATT
1 TCACTTAGCACATTGCCATGGACTTATT
61843616 TCACTTAGCACA
1 TCACTTAGCACA
61843628 ATGTCATATC
Statistics
Matches: 156, Mismatches: 16, Indels: 37
0.75 0.08 0.18
Matches are distributed among these distances:
22 11 0.07
24 66 0.42
25 9 0.06
26 7 0.04
27 6 0.04
28 57 0.37
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (28 bp):
TCACTTAGCACATTGCCATGGACTTATT
Found at i:61843535 original size:52 final size:52
Alignment explanation
Indices: 61843410--61843627 Score: 325
Period size: 52 Copynumber: 4.2 Consensus size: 52
61843400 GGGAAATTAC
* *
61843410 TCACTTAGCACCA-TGCCATGGACTTATTTCACTTAGATTCCATGGAC--ATT
1 TCACTTAGCA-CATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
*
61843460 TCACTTAGCACATTGCCGTGGACTTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
* * * *
61843512 TCACTTAGCGCATTGTCATGGACTTATTTCACTAAGATGCCATTGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
* *
61843564 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGCTTTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
61843616 TCACTTAGCACA
1 TCACTTAGCACA
61843628 ATGTCATATC
Statistics
Matches: 151, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
49 2 0.01
50 41 0.27
52 108 0.72
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (52 bp):
TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
Found at i:61843558 original size:30 final size:28
Alignment explanation
Indices: 61843426--61843596 Score: 100
Period size: 28 Copynumber: 6.6 Consensus size: 28
61843416 AGCACCATGC
* *
61843426 CATGGACTTATTTCACTTA--G-ATT-C
1 CATGGACTTATTTCACTAAGCGCATTGT
* * *
61843450 CATGGAC--ATTTCACTTAGCACATTGC
1 CATGGACTTATTTCACTAAGCGCATTGT
* * *
61843476 CGTGGACTTATTTCACTTA--G-A-TGC
1 CATGGACTTATTTCACTAAGCGCATTGT
* *
61843500 CATGGTCTTATTTCACTTAGCGCATTGT
1 CATGGACTTATTTCACTAAGCGCATTGT
*
61843528 CATGGACTTATTTCACTAA--G-A-TGC
1 CATGGACTTATTTCACTAAGCGCATTGT
* * * * *
61843552 CATTGTCTTATTTCACTTAGCACATTGC
1 CATGGACTTATTTCACTAAGCGCATTGT
61843580 CATGGACTTATTTCACT
1 CATGGACTTATTTCACT
61843597 TAGATGCCAT
Statistics
Matches: 118, Mismatches: 15, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
22 10 0.08
24 45 0.38
25 5 0.04
26 9 0.08
27 2 0.02
28 47 0.40
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (28 bp):
CATGGACTTATTTCACTAAGCGCATTGT
Found at i:61847811 original size:41 final size:41
Alignment explanation
Indices: 61847753--61847832 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
61847743 TGTGAGAGAG
* *
61847753 CATCTTAAATTTCTTTTATTGATCTATGTTTCCTTTAGTAA
1 CATCTTAAATATCTTTTATTGATCTATGCTTCCTTTAGTAA
* *
61847794 CATCTTAAATCAT-TTTTATTGATTTGTGCTTCCTTTAGT
1 CATCTTAAAT-ATCTTTTATTGATCTATGCTTCCTTTAGT
61847833 CAAAAAGGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 33 0.97
42 1 0.03
ACGTcount: A:0.23, C:0.15, G:0.09, T:0.54
Consensus pattern (41 bp):
CATCTTAAATATCTTTTATTGATCTATGCTTCCTTTAGTAA
Found at i:61854511 original size:99 final size:100
Alignment explanation
Indices: 61854340--61854538 Score: 382
Period size: 99 Copynumber: 2.0 Consensus size: 100
61854330 AGAATGAGAG
61854340 AAAAATCGAAAATTGGGAAAGTTGGTAAAATGGCCGTTTTAATATCAAGGTAAGTTCATACGTAT
1 AAAAATCGAAAATTGGGAAAGTTGGTAAAATGGCCGTTTTAATATCAAGGTAAGTTCATACGTAT
61854405 AATAAGCATTAATTTATGCATGTTTCAATGTAAAA
66 AATAAGCATTAATTTATGCATGTTTCAATGTAAAA
*
61854440 AAAAATCGAAAATTGGGAAAGTTGGT-AAATGGCCGTTTTAATATCAAGGTAAGTTCATATGTAT
1 AAAAATCGAAAATTGGGAAAGTTGGTAAAATGGCCGTTTTAATATCAAGGTAAGTTCATACGTAT
61854504 AATAAGCATTAATTTATGCATGTTTCAATGTAAAA
66 AATAAGCATTAATTTATGCATGTTTCAATGTAAAA
61854539 TTGATATATT
Statistics
Matches: 98, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
99 72 0.73
100 26 0.27
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.33
Consensus pattern (100 bp):
AAAAATCGAAAATTGGGAAAGTTGGTAAAATGGCCGTTTTAATATCAAGGTAAGTTCATACGTAT
AATAAGCATTAATTTATGCATGTTTCAATGTAAAA
Found at i:61855161 original size:64 final size:64
Alignment explanation
Indices: 61855011--61855262 Score: 233
Period size: 68 Copynumber: 3.9 Consensus size: 64
61855001 ATACAGATGG
* ** * * * * * *
61855011 TATGTAGCTAGGTCACATGTATAGTGCTGAGTGCACATCATGT-GTACAAGAGAGCTACAAGACA
1 TATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAG-ACAAGAGAGCTAC--GAGA
61855075 TTA
63 -TA
* *
61855078 TGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
1 T-ATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGATA
* * * *
61855143 TATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGACACCATGTAGACAAGAGAGCTACGAGAT
1 TATGTAGCTAGGTCGCATGGGTGGTACTAAGTG--TACACCATGTAGACAAGAGAGCTACGAGAT
61855208 A
64 A
* * *
61855209 AACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 TA-TGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAG-ACAAGAGAGC
61855263 CGAACTATAT
Statistics
Matches: 155, Mismatches: 24, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
62 1 0.01
63 18 0.12
64 27 0.17
65 26 0.17
66 34 0.22
67 3 0.02
68 45 0.29
69 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (64 bp):
TATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGATA
Found at i:61855196 original size:66 final size:65
Alignment explanation
Indices: 61855056--61855208 Score: 191
Period size: 66 Copynumber: 2.3 Consensus size: 65
61855046 CATCATGTGT
* * * * *
61855056 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TATGATGTAGCTAGGTCGCATGCGTGATACCAAGTGGACACCATG
61855121 TAG
63 TAG
* *
61855124 ACAAGAGAGCTACGAGATAT-ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGACACCATGT
1 ACAAGAGAGCTACGAGATATGATGTAGCTAGGTCGCATGCGTGATACCAAGTG--GACACCATGT
61855188 AG
64 AG
61855190 ACAAGAGAGCTACGAGATA
1 ACAAGAGAGCTACGAGATA
61855209 AACTGGCTAG
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
64 27 0.36
65 3 0.04
66 33 0.43
68 13 0.17
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (65 bp):
ACAAGAGAGCTACGAGATATGATGTAGCTAGGTCGCATGCGTGATACCAAGTGGACACCATGTAG
Found at i:61856482 original size:52 final size:52
Alignment explanation
Indices: 61856404--61856510 Score: 196
Period size: 52 Copynumber: 2.1 Consensus size: 52
61856394 AATTGAATTG
*
61856404 AAATGTTTCAGGCAAACATGTTATTCTGCACATCTGAATCGTAGTATTTTAT
1 AAATGTTTCAGGAAAACATGTTATTCTGCACATCTGAATCGTAGTATTTTAT
*
61856456 AAATGTTTCAGGAAAACATGTTATTCTGCGCATCTGAATCGTAGTATTTTAT
1 AAATGTTTCAGGAAAACATGTTATTCTGCACATCTGAATCGTAGTATTTTAT
61856508 AAA
1 AAA
61856511 GATATGATCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (52 bp):
AAATGTTTCAGGAAAACATGTTATTCTGCACATCTGAATCGTAGTATTTTAT
Found at i:61861101 original size:16 final size:16
Alignment explanation
Indices: 61861080--61861110 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61861070 ATATATTTTC
*
61861080 ATTTGCATCATATATA
1 ATTTGCATCACATATA
61861096 ATTTGCATCACATAT
1 ATTTGCATCACATAT
61861111 CAAATAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATCACATATA
Found at i:61873493 original size:56 final size:56
Alignment explanation
Indices: 61873407--61873526 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
61873397 ACAAGGGATG
61873407 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
61873463 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
61873519 ATGAGCAA
1 ATGGGCAA
61873527 TAAACTAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:61874885 original size:40 final size:40
Alignment explanation
Indices: 61874654--61874878 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
61874644 TCAAATGATG
* * * *
61874654 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
61874694 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
61874734 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
61874773 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
61874813 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
61874854 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
61874879 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 33 0.20
40 120 0.74
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:61874900 original size:119 final size:119
Alignment explanation
Indices: 61874661--61874911 Score: 278
Period size: 119 Copynumber: 2.1 Consensus size: 119
61874651 ATGTCCGGGC
*
61874661 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
* ** *
61874726 ATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCTGGGT
66 ATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATCTCGGT
* * * **
61874780 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
* * * *
61874843 AGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATC-CGGT
64 AGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAATCTCGGT
* *
61874899 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
61874912 TACGTGATTT
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 78 0.70
120 30 0.27
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
ATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATCTCGGT
Found at i:61881607 original size:130 final size:130
Alignment explanation
Indices: 61881374--61881629 Score: 435
Period size: 130 Copynumber: 2.0 Consensus size: 130
61881364 TGGAGTCGAG
61881374 CACGAGATGTTAACGGACTTAATTCATTAATTAAACAGCTCAAACAATTTATTTTAGAATTTCCA
1 CACGAGATGTTAACGGACTTAATTCATTAATTAAACAGCTCAAACAATTTATTTTAGAATTTCCA
* * *
61881439 GACAAGCTGGCTAACTGCGTCACAGTCGCTAAAAAAATCCATATCTCTAGTTACGAAACTTGAAA
66 GACAAGCTGGCCAACTACGTCACAGACGCTAAAAAAATCCATATCTCTAGTTACGAAACTTGAAA
61881504 CACGAGATGTTAACGGACTTAATTCATTAATTAAACAGCTCAAACAATTTATTTTAGAATTTCCA
1 CACGAGATGTTAACGGACTTAATTCATTAATTAAACAGCTCAAACAATTTATTTTAGAATTTCCA
* *
61881569 GACAAGCTGGCCAA-TAATGT-ATCTGACGCTAAAAAAATCCATATCTCTAGTTACGAAACTT
66 GACAAGCTGGCCAACT-ACGTCA-CAGACGCTAAAAAAATCCATATCTCTAGTTACGAAACTT
61881630 TTAATCCAAT
Statistics
Matches: 119, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
129 2 0.02
130 117 0.98
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (130 bp):
CACGAGATGTTAACGGACTTAATTCATTAATTAAACAGCTCAAACAATTTATTTTAGAATTTCCA
GACAAGCTGGCCAACTACGTCACAGACGCTAAAAAAATCCATATCTCTAGTTACGAAACTTGAAA
Found at i:61882899 original size:46 final size:46
Alignment explanation
Indices: 61882777--61882910 Score: 164
Period size: 46 Copynumber: 2.9 Consensus size: 46
61882767 TGTAACCCGC
*
61882777 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGAT
* * * * *
61882823 ACATTTCA-CGAACTCAGACTCAACTCAACGAGTTCGGATG-TTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-AT
*
61882870 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC
61882911 CAAATATCTG
Statistics
Matches: 72, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
45 2 0.03
46 34 0.47
47 34 0.47
48 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGAT
Found at i:61883861 original size:58 final size:58
Alignment explanation
Indices: 61883771--61883886 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
61883761 ATGATCATTT
61883771 TTGTGTTATTTTTCCCATTTTATTTCATTTAATATCCAAATGACCAAAATGCCTTTCC
1 TTGTGTTATTTTTCCCATTTTATTTCATTTAATATCCAAATGACCAAAATGCCTTTCC
61883829 TTGTGTTATTTTTCCCATTTTATTTCATTTAATATCCAAATGACCAAAATGCCTTTCC
1 TTGTGTTATTTTTCCCATTTTATTTCATTTAATATCCAAATGACCAAAATGCCTTTCC
61883887 CTACTAAACT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (58 bp):
TTGTGTTATTTTTCCCATTTTATTTCATTTAATATCCAAATGACCAAAATGCCTTTCC
Found at i:61888384 original size:46 final size:46
Alignment explanation
Indices: 61888317--61888535 Score: 221
Period size: 46 Copynumber: 4.7 Consensus size: 46
61888307 TGTAACCTGC
* * * *
61888317 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCAGG-CATTCTCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* * *
61888363 CCATAAGTGAACTCGGACTCAACTCAATGAGTTTGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T
* *** *
61888409 ACATTTCTCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
61888456 CCATAAGTGAATTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
61888502 CCATAAGTGAACTTGGACTCAACTCAATGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
61888536 AGATGCCCAA
Statistics
Matches: 141, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
43 1 0.01
44 4 0.03
45 2 0.01
46 99 0.70
47 31 0.22
49 3 0.02
50 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:61891879 original size:26 final size:25
Alignment explanation
Indices: 61891849--61891906 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
61891839 TGTTCAAAAC
*
61891849 AGTCATATA-TCATATAGGGGTATATT
1 AGTCATATACTCATA-A-GGGTATAAT
*
61891875 AGTCATTTACTTCATAAGGGTATAAT
1 AGTCATATAC-TCATAAGGGTATAAT
61891901 AGTCAT
1 AGTCAT
61891907 TTAACAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 22 0.79
27 1 0.04
28 5 0.18
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (25 bp):
AGTCATATACTCATAAGGGTATAAT
Found at i:61895510 original size:36 final size:36
Alignment explanation
Indices: 61895470--61895542 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
61895460 TCTCTTGTCT
61895470 AAAGGTAATAATATTTGTTGGTGTTATACTGGACTG
1 AAAGGTAATAATATTTGTTGGTGTTATACTGGACTG
61895506 AAAGGTAATAATATTTGTTGGTGTTATACTGGACTG
1 AAAGGTAATAATATTTGTTGGTGTTATACTGGACTG
61895542 A
1 A
61895543 GGCATTTCGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38
Consensus pattern (36 bp):
AAAGGTAATAATATTTGTTGGTGTTATACTGGACTG
Found at i:61896719 original size:33 final size:33
Alignment explanation
Indices: 61896649--61896720 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
61896639 GCATACTGTG
* **
61896649 CTGATATGGGTTAAGGCCCAGACTACTTTTATCA
1 CTGA-ATGGGCTAAGGCCCAGACTACTACTATCA
* * *
61896683 CTGAATGGGCTAAGGCCCAGACTGCTACTGTTA
1 CTGAATGGGCTAAGGCCCAGACTACTACTATCA
61896716 CTGAA
1 CTGAA
61896721 AAGGTTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (33 bp):
CTGAATGGGCTAAGGCCCAGACTACTACTATCA
Found at i:61901094 original size:15 final size:16
Alignment explanation
Indices: 61901074--61901103 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61901064 CTGTAAAGAT
61901074 TATACATT-TCATATA
1 TATACATTCTCATATA
61901089 TATACATTCTCATAT
1 TATACATTCTCATAT
61901104 CTGGTACTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (16 bp):
TATACATTCTCATATA
Found at i:61901263 original size:42 final size:43
Alignment explanation
Indices: 61901169--61901281 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 43
61901159 CAATGCCTAC
* * **
61901169 GTCCCAGAC-GTGGTCTTACATGTAAGTCAATATCGATGCCTCT
1 GTCCCAGACAG-GGTCTTACACGTAAATCAATATCGATGCCAAT
61901212 GTCCCAGACAGGGTCTTACACG-AAATCACATA-CGATGCCAAT
1 GTCCCAGACAGGGTCTTACACGTAAATCA-ATATCGATGCCAAT
* * *
61901254 GTCCTAGACATGGTCTTACACTTAAATC
1 GTCCCAGACAGGGTCTTACACGTAAATC
61901282 TCAAATTGAG
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 32 0.53
43 27 0.45
44 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
GTCCCAGACAGGGTCTTACACGTAAATCAATATCGATGCCAAT
Found at i:61902021 original size:12 final size:12
Alignment explanation
Indices: 61902004--61902034 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
61901994 AAGAACACGA
61902004 AGAAACGATCAC
1 AGAAACGATCAC
61902016 AGAAACGATCAC
1 AGAAACGATCAC
61902028 AGAAACG
1 AGAAACG
61902035 TAGAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.23, G:0.19, T:0.06
Consensus pattern (12 bp):
AGAAACGATCAC
Found at i:61908387 original size:15 final size:16
Alignment explanation
Indices: 61908369--61908398 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61908359 CTGTAAAGAT
61908369 TATACATT-TCATATA
1 TATACATTCTCATATA
61908384 TATACATTCTCATAT
1 TATACATTCTCATAT
61908399 CTCGTACTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (16 bp):
TATACATTCTCATATA
Found at i:61908556 original size:42 final size:43
Alignment explanation
Indices: 61908456--61908612 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 43
61908446 ATGGAGTACA
* *
61908456 ATGCCTACGTCCCAGAC-GTGGTCTTACATGTAATTC-AATATCG
1 ATGCCTATGTCCCAGACAG-GGTCTTACATGTAAATCAAATA-CG
* *
61908499 ATGGCTCTGTCCCAGACAGGGTCTTACATG-AAATCAAATACG
1 ATGCCTATGTCCCAGACAGGGTCTTACATGTAAATCAAATACG
* * *
61908541 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CG
1 ATGCCTATGTCCCAGACAGGGTCTTACATGTAAA--TCAAATACG
* * * *
61908585 AGGCCTGTGTTCCAGACATGGTCTTACA
1 ATGCCTATGTCCCAGACAGGGTCTTACA
61908613 CGATATTTCA
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
42 31 0.32
43 32 0.33
44 27 0.28
45 6 0.06
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (43 bp):
ATGCCTATGTCCCAGACAGGGTCTTACATGTAAATCAAATACG
Found at i:61908604 original size:44 final size:43
Alignment explanation
Indices: 61908458--61908614 Score: 160
Period size: 42 Copynumber: 3.7 Consensus size: 43
61908448 GGAGTACAAT
* * *
61908458 GCCTACGTCCCAGACGTGGTCTTACATGT-AATTCAATATCGATG
1 GCCTATGTCCCAGACATGGTCTTACACGTAAATTCAA-ATCGA-G
* * * *
61908502 G-CTCTGTCCCAGACAGGGTCTTACATG-AAA-TCAAATACGAT
1 GCCTATGTCCCAGACATGGTCTTACACGTAAATTCAAAT-CGAG
*
61908543 GCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAATCGAG
1 GCCTATGTCCCAGACATGGTCTTACACGTAAAT-TCAAATCGAG
* *
61908587 GCCTGTGTTCCAGACATGGTCTTACACG
1 GCCTATGTCCCAGACATGGTCTTACACG
61908615 ATATTTCAGC
Statistics
Matches: 94, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
41 3 0.03
42 29 0.31
43 27 0.29
44 29 0.31
45 6 0.06
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (43 bp):
GCCTATGTCCCAGACATGGTCTTACACGTAAATTCAAATCGAG
Found at i:61910835 original size:22 final size:24
Alignment explanation
Indices: 61910793--61910844 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
61910783 AAAAGCTTTC
*
61910793 GTAACAAACTCGGTTTTAAAGTTA
1 GTAATAAACTCGGTTTTAAAGTTA
61910817 GTAATAAACT-GG-TTTAAAGTTA
1 GTAATAAACTCGGTTTTAAAGTTA
61910839 GTAATA
1 GTAATA
61910845 TTTTACCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 16 0.59
23 2 0.07
24 9 0.33
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (24 bp):
GTAATAAACTCGGTTTTAAAGTTA
Found at i:61918556 original size:29 final size:29
Alignment explanation
Indices: 61918521--61918594 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
61918511 GTTGTGAGAT
* *
61918521 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
61918550 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
61918579 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
61918595 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:61918989 original size:40 final size:39
Alignment explanation
Indices: 61918944--61919048 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
61918934 AAGTGACCAT
* *
61918944 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGGCTAAG-TCCGAAGGCATTGGTGCGAGATACTAA
* *
61918984 TTCCGGGCTAAG-CCTGAAGGCATTGGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCC-GAAGGCATTGGTGCGAGATACTAA
*
61919023 ATCTGGGCTAAGTCCCGAAGAGCATT
1 ATCCGGGCTAAGT-CCGAAG-GCATT
61919049 CATGCTAGTG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
38 2 0.04
39 32 0.58
40 14 0.25
41 7 0.13
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (39 bp):
ATCCGGGCTAAGTCCGAAGGCATTGGTGCGAGATACTAA
Found at i:61919013 original size:39 final size:40
Alignment explanation
Indices: 61918910--61919122 Score: 127
Period size: 40 Copynumber: 5.3 Consensus size: 40
61918900 TGATGTTCGA
* * * *
61918910 GCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGG
1 GCTAAGTCCCGAAGGCATTGGTGCGAGA-T-ACTAAATCCGG
* * *
61918950 ACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCGG
1 GCTAAG-TCCCGAAGGCATTGGTGCGAGATACTAAATCCGG
* * *
61918990 GCTAAG-CCTGAAGGCATTGGTGCGAGTTACTAAATCTGG
1 GCTAAGTCCCGAAGGCATTGGTGCGAGATACTAAATCCGG
** * **
61919029 GCTAAGTCCCGAAGAGCATTCATGCTAG-TGA-TGTATCCGG
1 GCTAAGTCCCGAAG-GCATTGGTGCGAGAT-ACTAAATCCGG
** * *
61919069 GCTAAGTCCCGAAGAGCATTCATGCTAG-TGA-TATATCCGG
1 GCTAAGTCCCGAAG-GCATTGGTGCGAGAT-ACTAAATCCGG
*
61919109 GCTAGGTCCCGAAG
1 GCTAAGTCCCGAAG
61919123 AGCAATCATG
Statistics
Matches: 146, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
39 33 0.23
40 91 0.62
41 21 0.14
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTGGTGCGAGATACTAAATCCGG
Found at i:61919068 original size:79 final size:80
Alignment explanation
Indices: 61918985--61919139 Score: 197
Period size: 80 Copynumber: 1.9 Consensus size: 80
61918975 AGATACTAAT
* ** * * *
61918985 TCCGGGCTAAG-CCTGAAG-GCATTGGTGCGAGTTACTAAATCTGGGCTAAGTCCCGAAGAGCAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCGAGTGA-TAAATCCGGGCTAAGTCCCGAAGAGCAA
61919048 TCATGCTAGTGATGTA
65 TCATGCTAGTGATGTA
* * *
61919064 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAGGTCCCGAAGAGCAAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCGAGTGATAAATCCGGGCTAAGTCCCGAAGAGCAAT
*
61919129 CATGCTGGTGA
66 CATGCTAGTGA
61919140 CGTGTATTCG
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
79 11 0.17
80 41 0.64
81 12 0.19
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCGAGTGATAAATCCGGGCTAAGTCCCGAAGAGCAAT
CATGCTAGTGATGTA
Found at i:61919073 original size:40 final size:40
Alignment explanation
Indices: 61919027--61919139 Score: 190
Period size: 40 Copynumber: 2.8 Consensus size: 40
61919017 TACTAAATCT
*
61919027 GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCC
1 GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCC
61919067 GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCC
1 GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCC
* * *
61919107 GGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
61919140 CGTGTATTCG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATATCC
Found at i:61922572 original size:47 final size:47
Alignment explanation
Indices: 61922506--61924609 Score: 3470
Period size: 47 Copynumber: 44.1 Consensus size: 47
61922496 GAAATGATAG
* *
61922506 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61922553 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61922600 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61922647 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61922694 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61922741 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61922788 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61922835 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61922882 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61922929 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61922976 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61923023 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61923070 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61923117 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61923164 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61923211 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61923258 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61923305 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61923352 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
*
61923399 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
*
61923448 TAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
* * *
61923495 TAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61923542 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
*
61923589 TAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
*
61923636 TAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
*
61923683 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61923732 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61923781 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61923830 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61923879 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61923928 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61923977 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61924026 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61924075 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61924124 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61924173 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61924222 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61924271 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
*
61924320 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTG--AAAGTGTATATACGTGA
61924369 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
*
61924416 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA
* *
61924465 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
* * *
61924512 TAAGGCCTAATGGCCGATGTAATGAATGTGAAAGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
* * * * * * * * *
61924559 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
61924606 TAAG
1 TAAG
61924610 TCCCGAAGGG
Statistics
Matches: 2014, Mismatches: 35, Indels: 16
0.98 0.02 0.01
Matches are distributed among these distances:
47 1252 0.62
49 756 0.38
51 6 0.00
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
Found at i:61924784 original size:37 final size:37
Alignment explanation
Indices: 61924728--61924806 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
61924718 CCGAGCTCTA
* * *
61924728 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
61924765 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
61924802 AAGAC
1 AAGAC
61924807 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:61927010 original size:5 final size:5
Alignment explanation
Indices: 61927000--61927024 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
61926990 AAATAATAAA
61927000 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
61927025 GTAAGGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:61933865 original size:27 final size:27
Alignment explanation
Indices: 61933827--61933954 Score: 152
Period size: 27 Copynumber: 4.7 Consensus size: 27
61933817 TTAGCTTACC
*
61933827 AAATTACTAAAATA-CCCTCGATTAGCA
1 AAATTACCAAAATACCCCT-GATTAGCA
61933854 AAATTACCAAAATA-CCCTCGATTAGCA
1 AAATTACCAAAATACCCCT-GATTAGCA
* * *
61933881 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTAGCA
* * *
61933908 AAATTACCAAAATACCCCTAATTTGTA
1 AAATTACCAAAATACCCCTGATTAGCA
*
61933935 AAATTACCGAAATACCCCTG
1 AAATTACCAAAATACCCCTG
61933955 TAAGGTAGAA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 88 0.96
28 4 0.04
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTAGCA
Found at i:61933966 original size:27 final size:27
Alignment explanation
Indices: 61933936--61934301 Score: 405
Period size: 27 Copynumber: 13.6 Consensus size: 27
61933926 TAATTTGTAA
61933936 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAAGGTAG
* * *
61933963 AATTATCGAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAAGGTAG
** * *
61933990 AATTACTAAAATACTCCTGTAAGATAG
1 AATTACCGAAATACCCCTGTAAGGTAG
*
61934017 AATTACCGAAATACCCTTGT-AGCGTAG
1 AATTACCGAAATACCCCTGTAAG-GTAG
** *
61934044 AATTAGTGAAATACTCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAAGGTAG
*
61934071 AATTACTGAAATACCCCTGT-AGGTAG
1 AATTACCGAAATACCCCTGTAAGGTAG
* ** *
61934097 AATGACTAAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAAGGTAG
* *
61934124 AATTACCGAAATACCCCTGTAGGGCAG
1 AATTACCGAAATACCCCTGTAAGGTAG
* *
61934151 AATTACTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAAGGTAG
* *
61934178 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAAGGTAG
** *
61934205 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAAGGTAG
* * *
61934232 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAAGGTAG
* * * *
61934259 AAATACTGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAAGGTAG
61934286 AATTACC-AAGATACCC
1 AATTACCGAA-ATACCC
61934302 TGTTGGGGTA
Statistics
Matches: 287, Mismatches: 48, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
26 27 0.09
27 258 0.90
28 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAAGGTAG
Found at i:61933967 original size:54 final size:54
Alignment explanation
Indices: 61933936--61934318 Score: 493
Period size: 54 Copynumber: 7.1 Consensus size: 54
61933926 TAATTTGTAA
* * *
61933936 AATTACCGAAATACCCCTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTGG
1 AATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * * * *
61933990 AATTACTAAAATACTCCTGTAAGATAGAATTACCGAAATACCCTTGTAGCGTAG
1 AATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * *
61934044 AATTAGTGAAATACTCCTGTAAGGTAGAATTACTGAAATACCCCTGTA-GGTAG
1 AATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * * *
61934097 AATGACTAAAATACCCCTATAAGGTAGAATTACCGAAATACCCCTGTAGGGCAG
1 AATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* *
61934151 AATTACTGAAATACCCCTATAAGGTAGAATTATCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * * *
61934205 AATTATTGAAATACCCCTGTAGGGTAGAATTATCGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * * * *
61934259 AAATACTGAAATACCCCTGTAGGGTAAAATTACC-AAGATA-CCCTGTTGGGGTAA
1 AATTACTGAAATACCCCTGTAAGGTAGAATTACCGAA-ATACCCCTG-TAGGGTAG
61934313 AATTAC
1 AATTAC
61934319 CGTTTTACCC
Statistics
Matches: 289, Mismatches: 37, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
53 52 0.18
54 237 0.82
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (54 bp):
AATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAG
Found at i:61934913 original size:27 final size:26
Alignment explanation
Indices: 61934883--61935019 Score: 139
Period size: 27 Copynumber: 5.1 Consensus size: 26
61934873 ATTCTGTTAA
* *
61934883 GTGGCTTTGCCACATTATCTGATTCTG
1 GTGGCTCTGCCACAATATCTG-TTCTG
* *
61934910 GTGGCTCTGTCACAATATTCTATTTCTG
1 GTGGCTCTGCCACAATA-TCT-GTTCTG
* * *
61934938 GTGGCTATGCTACAAATATCTGTTTTG
1 GTGGCTCTGCCAC-AATATCTGTTCTG
61934965 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGT-TCTG
* * *
61934992 GTGACTCTGTCACAATATTTGTTCTG
1 GTGGCTCTGCCACAATATCTGTTCTG
61935018 GT
1 GT
61935020 AGCCATGCTG
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
26 15 0.16
27 51 0.56
28 21 0.23
29 4 0.04
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.40
Consensus pattern (26 bp):
GTGGCTCTGCCACAATATCTGTTCTG
Found at i:61934976 original size:82 final size:79
Alignment explanation
Indices: 61934883--61935039 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 79
61934873 ATTCTGTTAA
* * * * * *
61934883 GTGGCTTTGCCACATTATCTG-ATTCTGGTGGCTCTGTCACAATATTCTATTTCTGGTGGCTATG
1 GTGGCTCTGCCACAATATCTGTA-TCTGGTGACTCTGTCACAATATT-T-GTTCTGGTAGCCATG
61934947 CTACAAATATCTGTTTTG
63 CTACAAAT-TCTGTTTTG
*
61934965 GTGGCTCTGCCACAATATCTGTATCTGGTGACTCTGTCACAATATTTGTTCTGGTAGCCATGCTG
1 GTGGCTCTGCCACAATATCTGTATCTGGTGACTCTGTCACAATATTTGTTCTGGTAGCCATGCTA
61935030 CAAATTCTGT
66 CAAATTCTGT
61935040 GGTGTGTAGC
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
79 5 0.07
80 19 0.28
81 1 0.01
82 41 0.61
83 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (79 bp):
GTGGCTCTGCCACAATATCTGTATCTGGTGACTCTGTCACAATATTTGTTCTGGTAGCCATGCTA
CAAATTCTGTTTTG
Found at i:61935214 original size:6 final size:6
Alignment explanation
Indices: 61935205--61935279 Score: 55
Period size: 6 Copynumber: 12.3 Consensus size: 6
61935195 CTGTCACCTA
* * * *
61935205 ATTCTG ATTCTA ATTTTG ATTATG ATTCTG -TCACCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
* *
61935254 ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG A-TTCTG AT
61935280 AATGTTTCTT
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
5 2 0.04
6 46 0.87
7 4 0.08
8 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (6 bp):
ATTCTG
Found at i:61935215 original size:25 final size:25
Alignment explanation
Indices: 61935136--61935197 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
61935126 TTGCATTCAC
* * *
61935136 ATTCTGATTTTGATCCTGTTACCTG
1 ATTCTGATTCTGATCCTGTCACCTA
* *
61935161 ATACTGATTCTGATTCTGTCACCTA
1 ATTCTGATTCTGATCCTGTCACCTA
61935186 ATTCTGATTCTG
1 ATTCTGATTCTG
61935198 TCACCTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTCTGATTCTGATCCTGTCACCTA
Found at i:61935237 original size:37 final size:37
Alignment explanation
Indices: 61935190--61935270 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
61935180 CACCTAATTC
* *
61935190 TGATTCTGTCACCTAATTCTGATTCTAATTTTGATTA
1 TGATTCTGTCACCTAATTCTGATTCTAATTCTCATTA
* * *
61935227 TGATTCTGTCACCTGATTCTGATTCTGATTCTCATTT
1 TGATTCTGTCACCTAATTCTGATTCTAATTCTCATTA
61935264 TGATTCT
1 TGATTCT
61935271 AGTTCTGATA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.49
Consensus pattern (37 bp):
TGATTCTGTCACCTAATTCTGATTCTAATTCTCATTA
Found at i:61935249 original size:19 final size:19
Alignment explanation
Indices: 61935164--61935253 Score: 103
Period size: 19 Copynumber: 4.8 Consensus size: 19
61935154 TTACCTGATA
61935164 CTGATTCTGATTCTGTCAC
1 CTGATTCTGATTCTGTCAC
*
61935183 CTAATTCTGATTCTGTCAC
1 CTGATTCTGATTCTGTCAC
* * *
61935202 CTAATTCTGATTC--TAATT
1 CTGATTCTGATTCTGTCA-C
* *
61935220 TTGATTATGATTCTGTCAC
1 CTGATTCTGATTCTGTCAC
61935239 CTGATTCTGATTCTG
1 CTGATTCTGATTCTG
61935254 ATTCTCATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
17 2 0.03
18 10 0.17
19 44 0.76
20 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.46
Consensus pattern (19 bp):
CTGATTCTGATTCTGTCAC
Found at i:61937388 original size:27 final size:27
Alignment explanation
Indices: 61937291--61937445 Score: 136
Period size: 27 Copynumber: 5.7 Consensus size: 27
61937281 TTAGTTTACC
* * * *
61937291 AAATTACTAAAATA-GCCTCGATTAGCA
1 AAATTACCAAAATACCCCT-GATTTGTA
* * *
61937318 AAATTACCAAAATA-CCTTCGATTAGAA
1 AAATTACCAAAATACCCCT-GATTTGTA
*
61937345 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
61937372 AAATTACCAAAATACCCCTGATTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* *** *
61937399 AAACTATTGAAATACCCCTG-TATGGTA
1 AAATTACCAAAATACCCCTGAT-TTGTA
*
61937426 GAATTACCAAAATACCCCTG
1 AAATTACCAAAATACCCCTG
61937446 TAGGGTGGAA
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
26 1 0.01
27 103 0.96
28 3 0.03
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.27
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:61937446 original size:27 final size:27
Alignment explanation
Indices: 61937407--61937784 Score: 407
Period size: 27 Copynumber: 14.0 Consensus size: 27
61937397 TAAAACTATT
*
61937407 GAAATACCCCTGTATGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
61937434 AAAATACCCCTGTAGGGTGGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
61937461 GAAATACTCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
61937488 GAAATACCCTTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* * **
61937515 GAAATACTCCTATAAAGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * * * *
61937542 AAAATACCCCTATAAGGTAGAATGACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
61937569 GAAATACCCCTATAAGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
61937596 AAAATACCCCTTTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
61937623 GAAATACCCCTGTAAGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
61937650 GAAATACCCCTATAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
61937677 AAAATACCCATGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
61937704 GAAATACCCTTGTAGGGTAGAAATACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* **
61937731 GAAATACCCCTATAGAATAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
61937758 GAGATA-CCCTCGTCGGGTAAAATTACC
1 GAAATACCCCT-GTAGGGTAGAATTACC
61937785 ATTTTGCCCT
Statistics
Matches: 290, Mismatches: 60, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
26 4 0.01
27 286 0.99
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:61937458 original size:81 final size:81
Alignment explanation
Indices: 61937346--61937784 Score: 443
Period size: 81 Copynumber: 5.4 Consensus size: 81
61937336 CGATTAGAAA
** * * ** * * **
61937346 AATTACCAAAATACCCCTGGT-TTGTAAAATTACCAAAATACCCCTG-ATTTGTAAAACTATTGA
1 AATTACCAAAATACCCCT-GTAGGGTAGAATTACCGAAATACCCCTGTA-AGGTAGAATTACCGA
* *
61937409 AATACCCCTGTATGGTAG
64 AATACCCCTATAGGGTAG
* * *
61937427 AATTACCAAAATACCCCTGTAGGGTGGAATTACTGAAATACTCCTGTAAGGTAGAATTACCGAAA
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAAGGTAGAATTACCGAAA
* *
61937492 TACCCTTGTAGGGTAG
66 TACCCCTATAGGGTAG
** * * ** * * * *
61937508 AATTACTGAAATACTCCTATAAAGTAGAATTACCAAAATACCCCTATAAGGTAGAATGACTGAAA
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAAGGTAGAATTACCGAAA
*
61937573 TACCCCTATAAGGTAG
66 TACCCCTATAGGGTAG
* * *
61937589 AATTACCAAAATACCCCTTTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTATCGAAA
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAAGGTAGAATTACCGAAA
61937654 TACCCCTATAGGGTAG
66 TACCCCTATAGGGTAG
* * * * * *
61937670 AATTACTAAAATACCCATGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACTGAAA
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAAGGTAGAATTACCGAAA
**
61937735 TACCCCTATAGAATAG
66 TACCCCTATAGGGTAG
* * * *
61937751 AATTACCGAGATA-CCCTCGTCGGGTAAAATTACC
1 AATTACCAAAATACCCCT-GTAGGGTAGAATTACC
61937785 ATTTTGCCCT
Statistics
Matches: 294, Mismatches: 61, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
80 5 0.02
81 288 0.98
82 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (81 bp):
AATTACCAAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAAGGTAGAATTACCGAAA
TACCCCTATAGGGTAG
Found at i:61937464 original size:54 final size:54
Alignment explanation
Indices: 61937373--61937741 Score: 479
Period size: 54 Copynumber: 6.8 Consensus size: 54
61937363 TGGTTTGTAA
** * * * *
61937373 AATTACCAAAATACCCCTG-ATTTGTAAAACTATTGAAATACCCCTGTATGGTAG
1 AATTACCAAAATACCCCTGTA-GGGTAGAATTACTGAAATACCCCTGTAAGGTAG
* *
61937427 AATTACCAAAATACCCCTGTAGGGTGGAATTACTGAAATACTCCTGTAAGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAG
* * * * *
61937481 AATTACCGAAATACCCTTGTAGGGTAGAATTACTGAAATACTCCTATAAAGTAG
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAG
* * * *
61937535 AATTACCAAAATACCCCTATAAGGTAGAATGACTGAAATACCCCTATAAGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAG
*
61937589 AATTACCAAAATACCCCTTTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAG
* * * * * *
61937643 AATTATCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCATGTAGGGTAG
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAG
* * *
61937697 AATTACCGAAATACCCTTGTAGGGTAGAAATACTGAAATACCCCT
1 AATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCT
61937742 ATAGAATAGA
Statistics
Matches: 278, Mismatches: 36, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
54 277 1.00
55 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (54 bp):
AATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAG
Found at i:61938401 original size:28 final size:28
Alignment explanation
Indices: 61938365--61938484 Score: 99
Period size: 27 Copynumber: 4.4 Consensus size: 28
61938355 TACTACATTA
*
61938365 TCTGATTCTGGTGGCTCTGTCACAATAT
1 TCTGATTCTGGTGGCTCTGCCACAATAT
* *
61938393 TCTGTTTCTGGTGGCTATGCCACAA-AT
1 TCTGATTCTGGTGGCTCTGCCACAATAT
* * *
61938420 ATAT-ATTCTGGTGGCTTTGCCACAGTA-
1 -TCTGATTCTGGTGGCTCTGCCACAATAT
* **
61938447 TCTG-TATCTGGTGACTCTATCACAATAT
1 TCTGAT-TCTGGTGGCTCTGCCACAATAT
61938475 T-TG-TTCTGGT
1 TCTGATTCTGGT
61938485 AGCCATGCTG
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
26 9 0.12
27 39 0.53
28 26 0.35
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (28 bp):
TCTGATTCTGGTGGCTCTGCCACAATAT
Found at i:61938456 original size:27 final size:27
Alignment explanation
Indices: 61938348--61938459 Score: 95
Period size: 27 Copynumber: 4.1 Consensus size: 27
61938338 ATTCTATTAA
* *
61938348 GTGGCTTTACTACATTATCTG-ATTCTG
1 GTGGCTTTGCCACA-TATCTGTATTCTG
* *
61938375 GTGGCTCTGTCACAATATTCTGT-TTCTG
1 GTGGCTTTGCCAC-ATA-TCTGTATTCTG
* * * *
61938403 GTGGCTATGCCACAAATATATATTCTG
1 GTGGCTTTGCCACATATCTGTATTCTG
61938430 GTGGCTTTGCCACAGTATCTGTA-TCTG
1 GTGGCTTTGCCACA-TATCTGTATTCTG
61938457 GTG
1 GTG
61938460 ACTCTATCAC
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
26 3 0.04
27 38 0.57
28 26 0.39
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (27 bp):
GTGGCTTTGCCACATATCTGTATTCTG
Found at i:61938632 original size:25 final size:25
Alignment explanation
Indices: 61938604--61938665 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
61938594 CATTCACATT
* *
61938604 CTGATTTTGATTCTGTTACCTGATA
1 CTGATTTTGATTCTGTCACCTAATA
*
61938629 CTGATTTTGATTCTGTCACCTAATT
1 CTGATTTTGATTCTGTCACCTAATA
*
61938654 CTGATTCTGATT
1 CTGATTTTGATT
61938666 TTGATTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (25 bp):
CTGATTTTGATTCTGTCACCTAATA
Found at i:61938662 original size:6 final size:6
Alignment explanation
Indices: 61938601--61938716 Score: 67
Period size: 6 Copynumber: 18.8 Consensus size: 6
61938591 TTGCATTCAC
* * * * *
61938601 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTTTG ATTCTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
* * *
61938651 ATTCTG ATTCTG ATTTTG ATTATG ATTCTG -TCACCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
* *
61938700 ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCT
61938717 AGTTATGATA
Statistics
Matches: 82, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
5 4 0.05
6 67 0.82
7 8 0.10
8 3 0.04
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:61938664 original size:37 final size:37
Alignment explanation
Indices: 61938623--61938716 Score: 143
Period size: 37 Copynumber: 2.5 Consensus size: 37
61938613 ATTCTGTTAC
*
61938623 CTGATACTGATTTTGATTCTGTCACCTAATTCTGATT
1 CTGATTCTGATTTTGATTCTGTCACCTAATTCTGATT
* * *
61938660 CTGATTTTGATTATGATTCTGTCACCTGATTCTGATT
1 CTGATTCTGATTTTGATTCTGTCACCTAATTCTGATT
*
61938697 CTGATTCTCATTTTGATTCT
1 CTGATTCTGATTTTGATTCT
61938717 AGTTATGATA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (37 bp):
CTGATTCTGATTTTGATTCTGTCACCTAATTCTGATT
Found at i:61949567 original size:54 final size:54
Alignment explanation
Indices: 61949509--61949638 Score: 172
Period size: 54 Copynumber: 2.4 Consensus size: 54
61949499 ATTACCAAAG
* *
61949509 TACCCTCAATTTATAGAATTACCGTTTTAACC-TCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTTTAACCAT-GATCTACAGAATTACCGTTT
* * * *
61949563 TACCCTCGATTTATAGAACTACTGTTTTACCCATGATCTACAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCGTTTTAACCATGATCTACAGAATTACCGTTT
* *
61949617 TACCCTTGATTTATAAAATTAC
1 TACCCTCGATTTATAGAATTAC
61949639 TAAAATACCC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
54 65 0.98
55 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (54 bp):
TACCCTCGATTTATAGAATTACCGTTTTAACCATGATCTACAGAATTACCGTTT
Found at i:61949639 original size:27 final size:27
Alignment explanation
Indices: 61949509--61949639 Score: 156
Period size: 27 Copynumber: 4.9 Consensus size: 27
61949499 ATTACCAAAG
* *
61949509 TACCCTCAATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* * *
61949536 TAACCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
*
61949563 TACCCTCGATTTATAGAACTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* *
61949590 TACCCAT-GATCTACAGAATTACTGTTT
1 TACCC-TCGATTTATAGAATTACTGTTT
* *
61949617 TACCCTTGATTTATAAAATTACT
1 TACCCTCGATTTATAGAATTACT
61949640 AAAATACCCT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.01
27 87 0.98
28 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACTGTTT
Found at i:61949647 original size:27 final size:27
Alignment explanation
Indices: 61949617--61949870 Score: 235
Period size: 27 Copynumber: 9.4 Consensus size: 27
61949607 ATTACTGTTT
* *
61949617 TACCCTTGATTTATAAAATTACTAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* **
61949644 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* **
61949671 TACCCTCGATCAGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* * ***
61949698 TACCCTAG-TCTGTAAAATTGTTAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* * * *
61949724 TACCCCTGGTTTGTAAAATTACCGAAG
1 TACCCTTGATTTGTAAAATTACCAAAA
**
61949751 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
*
61949778 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTGTAAAATTACCAAAA
* * *
61949805 TACCAC-TGGTTTGTGAAATTACCGAAA
1 TACC-CTTGATTTGTAAAATTACCAAAA
**
61949832 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
*
61949859 TACCCCTGATTT
1 TACCCTTGATTT
61949871 ACAACTTTGA
Statistics
Matches: 181, Mismatches: 41, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
26 22 0.12
27 158 0.87
28 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
TACCCTTGATTTGTAAAATTACCAAAA
Found at i:61949664 original size:54 final size:54
Alignment explanation
Indices: 61949543--61949666 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 54
61949533 TTTTAACCTC
* ****
61949543 GATTTACAGAATTACCGTTTTACCCTCGATTTATAGAACTACTGTTTTACCCAT
1 GATTTACAGAATTACCGTTTTACCCTCGATTTATAAAACTACTAAAATACCCAT
* * * * *
61949597 GATCTACAGAATTACTGTTTTACCCTTGATTTATAAAATTACTAAAATACCCTT
1 GATTTACAGAATTACCGTTTTACCCTCGATTTATAAAACTACTAAAATACCCAT
* *
61949651 GGTTTACAAAATTACC
1 GATTTACAGAATTACC
61949667 AAAATACCCT
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (54 bp):
GATTTACAGAATTACCGTTTTACCCTCGATTTATAAAACTACTAAAATACCCAT
Found at i:61949702 original size:81 final size:80
Alignment explanation
Indices: 61949617--61949871 Score: 309
Period size: 81 Copynumber: 3.2 Consensus size: 80
61949607 ATTACTGTTT
* ** * * *
61949617 TACCCTTGATTTATAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGATC
1 TACCCCTGATTTATAAAATTACTAAAATACCC-TGGTTTGTAAAATTACCGAAATACCCTCAATT
*
61949682 AGTAAAATTACCAAAA
65 TGTAAAATTACCAAAA
* * ** *
61949698 TA-CCCT-AGTCTGTAAAATTGTTAAAATACCCCTGGTTTGTAAAATTACCGAAGTACCCTCAAT
1 TACCCCTGA-TTTATAAAATTACTAAAATA-CCCTGGTTTGTAAAATTACCGAAATACCCTCAAT
61949761 TTGTAAAATTACCAAAA
64 TTGTAAAATTACCAAAA
* * *
61949778 TACCCCT-AGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAAT
1 TACCCCTGA-TTTATAAAATTACTAAAATACC-CTGGTTTGTAAAATTACCGAAATACCCTCAAT
61949842 TTGTAAAATTACCAAAA
64 TTGTAAAATTACCAAAA
61949859 TACCCCTGATTTA
1 TACCCCTGATTTA
61949872 CAACTTTGAC
Statistics
Matches: 150, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
79 1 0.01
80 64 0.43
81 84 0.56
82 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (80 bp):
TACCCCTGATTTATAAAATTACTAAAATACCCTGGTTTGTAAAATTACCGAAATACCCTCAATTT
GTAAAATTACCAAAA
Found at i:61949927 original size:27 final size:27
Alignment explanation
Indices: 61949888--61949939 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
61949878 TGACTTTCTA
61949888 AAAATTATGGAAATACCATTGGTTTAC
1 AAAATTATGGAAATACCATTGGTTTAC
*
61949915 AAAATTACT-GAAATACCTTTGGTTT
1 AAAATTA-TGGAAATACCATTGGTTT
61949940 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (27 bp):
AAAATTATGGAAATACCATTGGTTTAC
Found at i:61950016 original size:27 final size:27
Alignment explanation
Indices: 61949984--61950062 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
61949974 GACTAAAATA
61949984 CCCCTATTA-GGTAAAAAGACCGTAAAG
1 CCCCTA-TAGGGTAAAAAGACCGTAAAG
** *
61950011 CCCCTATAGGGTAAAGTGATCGTAAAG
1 CCCCTATAGGGTAAAAAGACCGTAAAG
* **
61950038 CCCCTGTAGGGTAAAGTGACCGTAA
1 CCCCTATAGGGTAAAAAGACCGTAA
61950063 TACCCTTGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 2 0.04
27 44 0.96
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (27 bp):
CCCCTATAGGGTAAAAAGACCGTAAAG
Found at i:61950072 original size:27 final size:27
Alignment explanation
Indices: 61950001--61950084 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
61949991 TAGGTAAAAA
*
61950001 GACCGTAAAGCCCCTATAGGGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
*
61950028 GATCGTAAAGCCCCTGTAGGGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
* * *
61950055 GACCGTAATA-CCCTTGTATGGTAAAAT
1 GACCGTAA-AGCCCCTGTAGGGTAAAGT
61950082 GAC
1 GAC
61950085 GAATATGCCC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (27 bp):
GACCGTAAAGCCCCTGTAGGGTAAAGT
Found at i:61950989 original size:25 final size:26
Alignment explanation
Indices: 61950887--61951022 Score: 188
Period size: 26 Copynumber: 5.2 Consensus size: 26
61950877 GAGGAAATGC
61950887 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
61950913 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
61950939 AAAAGGGCTTACGCCCCAGCAGTTTATTG
1 AAAAGGGCTTATG-CCC--CAGTTTATTG
**
61950968 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
61950993 AAAAGGGCTT-TGCCCCAG-TTATTA
1 AAAAGGGCTTATGCCCCAGTTTATTG
61951017 AAAAGG
1 AAAAGG
61951023 CTAGGCCTCC
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
24 9 0.09
25 26 0.26
26 38 0.38
27 6 0.06
28 1 0.01
29 20 0.20
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:61950999 original size:54 final size:55
Alignment explanation
Indices: 61950887--61951010 Score: 186
Period size: 54 Copynumber: 2.3 Consensus size: 55
61950877 GAGGAAATGC
**
61950887 AAAAGGGCTTATG-CCC--CAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
61950939 AAAAGGGCTTACGCCCCAGCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
61950993 AAAAGGGCTT-TGCCCCAG
1 AAAAGGGCTTATGCCCCAG
61951011 TTATTAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
52 12 0.18
53 10 0.15
54 23 0.35
55 20 0.31
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (55 bp):
AAAAGGGCTTATGCCCCAGCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:61951246 original size:42 final size:42
Alignment explanation
Indices: 61951181--61951272 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
61951171 TAGTCTCCCC
* * ** *
61951181 AAATAGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
61951223 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
61951265 AAATGGGC
1 AAATGGGC
61951273 CTAAGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:61953716 original size:27 final size:27
Alignment explanation
Indices: 61953683--61954083 Score: 196
Period size: 27 Copynumber: 14.8 Consensus size: 27
61953673 CCTCAAATTG
*
61953683 TAAAATTACCAAAGTACCCTTGATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* **** *
61953710 TAGAATTACCGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* **** *
61953737 TAGAATTACCGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* ***
61953764 TAAAATTACTATCTTACCCTTGATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* * * *** *
61953791 CAGAATTACTATTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* ** *
61953818 CAAAATTATTAAAATACCCTTGGTTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* * *
61953845 CAAAATTACCAAAATACCCTCGA-TCA
1 TAAAATTACCAAAATACCCTTGATTTA
* * *
61953871 GTAAAATTACCAAAATACCCTAG-TCTG
1 -TAAAATTACCAAAATACCCTTGATTTA
* * * * *
61953898 TAAAATTGCTAAAATACCCCTGGTTTG
1 TAAAATTACCAAAATACCCTTGATTTA
* ** *
61953925 TAAAATTACCGAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTTGATTTA
61953952 TAAAATTACCAAAATACCCTTGATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* * * *
61953979 TAAAGTTA-CAGAAGTACCATTGACTTTC
1 TAAAATTACCA-AAATACCCTTGA-TTTA
* *** * *
61954007 TAGAATTTATGGAAATACCATTGGTTTA
1 TA-AAATTACCAAAATACCCTTGATTTA
* ** * * *
61954035 CAAAATTACTGAAATACGCTTGGTTTG
1 TAAAATTACCAAAATACCCTTGATTTA
* *
61954062 TAAATTTACCAAAACACCCTTG
1 TAAAATTACCAAAATACCCTTG
61954084 TAGGATGAAA
Statistics
Matches: 296, Mismatches: 71, Indels: 14
0.78 0.19 0.04
Matches are distributed among these distances:
26 22 0.07
27 250 0.84
28 9 0.03
29 15 0.05
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTTGATTTA
Found at i:61954144 original size:27 final size:27
Alignment explanation
Indices: 61954114--61954173 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
61954104 ACCCCTACTA
61954114 GGTAAAAAGA-CTGCAAAGCCCCTGTAG
1 GGTAAAAAGATC-GCAAAGCCCCTGTAG
** * *
61954141 GGTAAAGTGATCGTAAAGCCCTTGTAG
1 GGTAAAAAGATCGCAAAGCCCCTGTAG
61954168 GGTAAA
1 GGTAAA
61954174 GTGACCGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (27 bp):
GGTAAAAAGATCGCAAAGCCCCTGTAG
Found at i:61954174 original size:27 final size:27
Alignment explanation
Indices: 61954128--61954205 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
61954118 AAAAGACTGC
*
61954128 AAAGCCCCTGTAGGGTAAAGTGATCGT
1 AAAGCCCCTGTAGGGTAAAGTGACCGT
*
61954155 AAAGCCCTTGTAGGGTAAAGTGACCGT
1 AAAGCCCCTGTAGGGTAAAGTGACCGT
* *
61954182 AATA-CCCCTGTATGGTAAAATGAC
1 AA-AGCCCCTGTAGGGTAAAGTGAC
61954206 GAATATGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
27 44 0.98
28 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (27 bp):
AAAGCCCCTGTAGGGTAAAGTGACCGT
Found at i:61955089 original size:55 final size:54
Alignment explanation
Indices: 61955008--61955127 Score: 194
Period size: 54 Copynumber: 2.3 Consensus size: 54
61954998 GAGGAAGTGC
*
61955008 AAAAGGGCTTAT---GCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
61955060 AAAAGGGCTTATGCCGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
61955114 AAAAGGGCTT-TGCC
1 AAAAGGGCTTATGCC
61955128 CCAGTTAATA
Statistics
Matches: 64, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
52 12 0.19
53 4 0.06
54 24 0.38
55 24 0.38
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (54 bp):
AAAAGGGCTTATGCCGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:61955108 original size:25 final size:26
Alignment explanation
Indices: 61955008--61955133 Score: 184
Period size: 26 Copynumber: 4.8 Consensus size: 26
61954998 GAGGAAGTGC
*
61955008 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATCG
61955034 AAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
*
61955060 AAAAGGGCTTATGCCGCCCCAGTTTATTG
1 AAAAGGGCTTAT---GCCCCAGTTTATCG
*
61955089 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATCG
61955114 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
61955134 AATAAAGAGG
Statistics
Matches: 93, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
25 32 0.34
26 37 0.40
28 1 0.01
29 23 0.25
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATCG
Found at i:61955337 original size:42 final size:42
Alignment explanation
Indices: 61955278--61955369 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
61955268 TAGTCTCCCC
* ** *
61955278 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
61955320 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
61955362 AAATGGGC
1 AAATGGGC
61955370 CTAAGGGCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:61957720 original size:27 final size:27
Alignment explanation
Indices: 61957676--61958045 Score: 182
Period size: 27 Copynumber: 13.7 Consensus size: 27
61957666 CCTCAAATTG
* *
61957676 TAAAATTACCAAACTACCCTCGACTTA
1 TAAAATTACCAAATTACCCTCGATTTA
**
61957703 TAAAATTACCATTTTACCCTCGATTTA
1 TAAAATTACCAAATTACCCTCGATTTA
* * ** *
61957730 TAGAATTACTATTTTACCCTTGATTTA
1 TAAAATTACCAAATTACCCTCGATTTA
* * * **
61957757 CAGAATTACTATTTTACCCTCGATTTA
1 TAAAATTACCAAATTACCCTCGATTTA
* * * * *
61957784 CAAAATTACTAAAATACCCTTGGTTTA
1 TAAAATTACCAAATTACCCTCGATTTA
*
61957811 TAAAATTACCAAAATACCCTCGA-TTA
1 TAAAATTACCAAATTACCCTCGATTTA
* * * *
61957837 GTAAAATTACCAAAATACCCTAG-TCTG
1 -TAAAATTACCAAATTACCCTCGATTTA
* * * * *
61957864 TAAAATTGCTAAAATACCC-CTGGTTTG
1 TAAAATTACCAAATTACCCTC-GATTTA
* * *
61957891 TAAAATTATCGAAA-TACCCTCAATTTG
1 TAAAATTA-CCAAATTACCCTCGATTTA
* * *
61957918 TAAAATTACCAAAATA-CCTCTAGTTTG
1 TAAAATTACCAAATTACCCTCGA-TTTA
* * *
61957945 TAAAATTACCAAAATACCACT-GGTTTG
1 TAAAATTACCAAATTACC-CTCGATTTA
* * * *
61957972 TGAAATTACCGAAA-TACCCTCAAATTG
1 TAAAATTACC-AAATTACCCTCGATTTA
*
61957999 TCAAATTACCAGAA-TACCC-CTGATTTA
1 TAAAATTACCA-AATTACCCTC-GATTTA
* * * *
61958026 CAAAGTTACAAAAATACCCT
1 TAAAATTACCAAATTACCCT
61958046 TGAGTTTCTA
Statistics
Matches: 281, Mismatches: 46, Indels: 31
0.78 0.13 0.09
Matches are distributed among these distances:
26 36 0.13
27 234 0.83
28 9 0.03
29 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (27 bp):
TAAAATTACCAAATTACCCTCGATTTA
Found at i:61957845 original size:81 final size:80
Alignment explanation
Indices: 61957771--61958072 Score: 306
Period size: 81 Copynumber: 3.7 Consensus size: 80
61957761 ATTACTATTT
* * *
61957771 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTCGATT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATT
61957836 AGTAAAATTACCAAAA
66 -GTAAAATTACCAAAA
* * ** * * *
61957852 TACCCTAG-TCTGTAAAATTGCTAAAATACCCCTGGTTTGTAAAATTATCGAAATACCCTCAATT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAA-T
61957916 TGTAAAATTACCAAAA
65 TGTAAAATTACCAAAA
* ** * *
61957932 TA-CCTCTAGTTTGTAAAATTACCAAAATACCAC-TGGTTTGTGAAATTACCGAAATACCCTCAA
1 TACCCTCGA-TTTACAAAATTACTAAAATACC-CTTGGTTTGTAAAATTACCGAAATACCCTC-A
* *
61957995 ATTGTCAAATTACCAGAA
63 ATTGTAAAATTACCAAAA
* * * **
61958013 TACCC-CTGATTTACAAAGTTACAAAAATACCCTTGAGTTTCTAAAAATTATGGAAATACC
1 TACCCTC-GATTTACAAAATTACTAAAATACCCTTG-GTTTGT-AAAATTACCGAAATACC
61958073 ATTGGTTTAC
Statistics
Matches: 183, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
79 3 0.02
80 63 0.34
81 92 0.50
82 11 0.06
83 14 0.08
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (80 bp):
TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATT
GTAAAATTACCAAAA
Found at i:61957944 original size:54 final size:52
Alignment explanation
Indices: 61957785--61958017 Score: 232
Period size: 54 Copynumber: 4.3 Consensus size: 52
61957775 CTCGATTTAC
* * * * *
61957785 AAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTCGATTAGT
1 AAAATTACCAAAATACCC-TAGTTTGTAAAATTACCAAAATACCCTAG-TTTGT
* * * *
61957839 AAAATTACCAAAATACCCTAGTCTGTAAAATTGCTAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCTAGTTTGTAAAATTACCAAAATA-CCCTAGTTTGT
* * *
61957892 AAAATTATCGAAATACCCTCAATTTGTAAAATTACCAAAATACCTCTAGTTTGT
1 AAAATTACCAAAATACCCT-AGTTTGTAAAATTACCAAAATACC-CTAGTTTGT
* * * **
61957946 AAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAAATTGT
1 AAAATTACCAAAATACC-CTAGTTTGTAAAATTACCAAAATACCCT-AGTTTGT
* *
61958000 CAAATTACCAGAATACCC
1 AAAATTACCAAAATACCC
61958018 CTGATTTACA
Statistics
Matches: 149, Mismatches: 25, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
53 44 0.30
54 103 0.69
55 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.30
Consensus pattern (52 bp):
AAAATTACCAAAATACCCTAGTTTGTAAAATTACCAAAATACCCTAGTTTGT
Found at i:61958202 original size:27 final size:27
Alignment explanation
Indices: 61958169--61958252 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
61958159 TAGGTAAAAA
*
61958169 GACCGTAAAGCCCTTGTAGGGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
*
61958196 GATCGTAAAGCCCCTGTAGGGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
* *
61958223 GACCGTAATA-CCCCTGTATGGTAAAAT
1 GACCGTAA-AGCCCCTGTAGGGTAAAGT
61958250 GAC
1 GAC
61958253 GAATATGCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 50 0.98
28 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (27 bp):
GACCGTAAAGCCCCTGTAGGGTAAAGT
Found at i:61959084 original size:26 final size:26
Alignment explanation
Indices: 61959055--61959272 Score: 251
Period size: 26 Copynumber: 8.8 Consensus size: 26
61959045 GAGGAAGTGC
*
61959055 AAAATGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
61959081 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
61959107 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* * * * *
61959133 GAAAGGGATTATACCCCTGTTTA-TC
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
61959158 AAAA------A--CCTCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
61959176 AAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
61959202 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
61959228 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
61959253 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
61959273 ATTAAAGAGG
Statistics
Matches: 164, Mismatches: 19, Indels: 19
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.05
18 5 0.03
19 1 0.01
24 1 0.01
25 37 0.23
26 112 0.68
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:61959138 original size:52 final size:52
Alignment explanation
Indices: 61959055--61959272 Score: 287
Period size: 52 Copynumber: 4.4 Consensus size: 52
61959045 GAGGAAGTGC
*
61959055 AAAATGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
* * * * *
61959107 AAAAGGGCTTATGCCCCAGTTTATTGGAAAGGGATTATACCCCTGTTTATC-
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
* *
61959158 AAAA------A--CCTCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
61959202 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
61959253 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
61959273 ATTAAAGAGG
Statistics
Matches: 144, Mismatches: 13, Indels: 20
0.81 0.07 0.11
Matches are distributed among these distances:
43 33 0.23
44 4 0.03
45 1 0.01
50 11 0.08
51 28 0.19
52 67 0.47
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:61959208 original size:69 final size:69
Alignment explanation
Indices: 61959097--61959225 Score: 195
Period size: 69 Copynumber: 1.9 Consensus size: 69
61959087 GCTTATGCCC
* * *
61959097 CAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGGAAAGGGATTATACCCCTGTTTATCAAAA
1 CAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATCGAAAAGGGATTATACCCCAGTTTATCAAAA
61959162 ACCT
66 ACCT
** * *
61959166 CAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATCGAAAAGGGCTTATGCCCCAGTTTAT
1 CAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATCGAAAAGGGATTATACCCCAGTTTAT
61959226 TGAAAAGGGC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (69 bp):
CAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATCGAAAAGGGATTATACCCCAGTTTATCAAAA
ACCT
Found at i:61959258 original size:51 final size:51
Alignment explanation
Indices: 61959166--61959272 Score: 189
Period size: 51 Copynumber: 2.1 Consensus size: 51
61959156 TCAAAAACCT
*
61959166 CAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATCGAAAAGGGCTTATGCCC
1 CAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTT-TGCCC
61959218 CAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCGAAAAGGGCTTTGCCC
1 CAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTTGCCC
61959268 CAGTT
1 CAGTT
61959273 ATTAAAGAGG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
50 10 0.19
51 24 0.44
52 20 0.37
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.29
Consensus pattern (51 bp):
CAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTTGCCC
Found at i:61959493 original size:42 final size:42
Alignment explanation
Indices: 61959424--61959505 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
61959414 CCCAAATAGG
** *
61959424 CTTGCATACATTCATTGGTATTTCATGTGATATTGAAATGAA
1 CTTGCATACATTCATTGACATTACATGTGATATTGAAATGAA
61959466 CTTGCATACA-TCTATTGACATTACATGTGATATTGAAATG
1 CTTGCATACATTC-ATTGACATTACATGTGATATTGAAATG
61959506 GGTCTAAGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (42 bp):
CTTGCATACATTCATTGACATTACATGTGATATTGAAATGAA
Found at i:61959624 original size:78 final size:79
Alignment explanation
Indices: 61959488--61959644 Score: 262
Period size: 78 Copynumber: 2.0 Consensus size: 79
61959478 TATTGACATT
* **
61959488 ACATGTGATATTGAAATGGGTCTAAGGGCCATACCGTTTACAGTAAAGGCTTTGGCCCAATGATA
1 ACATGTGATATTGAAATGGGCCTAAGGGCCATACCGTTTACAGTAAAGGCTCCGGCCCAATGATA
* *
61959553 TGATTTATGAAAAG
66 TAATCTATGAAAAG
61959567 ACATGTGATATTGAAATGGGCCTAAGGG-CATACCGTTTACAGTAAAGGCTCCGGCCCAATGATA
1 ACATGTGATATTGAAATGGGCCTAAGGGCCATACCGTTTACAGTAAAGGCTCCGGCCCAATGATA
61959631 TAATCTATGAAAAG
66 TAATCTATGAAAAG
61959645 GCTTCGGCCC
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
78 46 0.63
79 27 0.37
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (79 bp):
ACATGTGATATTGAAATGGGCCTAAGGGCCATACCGTTTACAGTAAAGGCTCCGGCCCAATGATA
TAATCTATGAAAAG
Found at i:61962052 original size:27 final size:27
Alignment explanation
Indices: 61961923--61962051 Score: 177
Period size: 27 Copynumber: 4.8 Consensus size: 27
61961913 TACCAAAATT
* *
61961923 CCCTAGATTTATAGAATTACTGTTTTA
1 CCCTCGATTTACAGAATTACTGTTTTA
*
61961950 CCCTCGATTTACAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACTGTTTTA
* *
61961977 CCCTCGATTTATAGAATTATTGTTTTA
1 CCCTCGATTTACAGAATTACTGTTTTA
* * *
61962004 CCCTTGATCTACAGAATTACTATTTTA
1 CCCTCGATTTACAGAATTACTGTTTTA
*
61962031 CCCTCGATTTACAAAATTACT
1 CCCTCGATTTACAGAATTACT
61962052 AAAATACCTT
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACTGTTTTA
Found at i:61962059 original size:27 final size:27
Alignment explanation
Indices: 61962029--61962386 Score: 206
Period size: 27 Copynumber: 13.2 Consensus size: 27
61962019 ATTACTATTT
* *
61962029 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * * *
61962056 TACCTTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
*
61962083 TACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAA
* * *
61962110 TACCATAG-TTTATAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * *
61962136 TACCC-CTGGTTTGTAAAATTACCTAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* ** *
61962163 TACCTTTAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* *
61962190 TACCCT-TAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
* * * *
61962217 TACCACT-GGTTTGTGAAATTACCGAAA
1 TACC-CTCGATTTATAAAATTACCAAAA
* * *
61962244 TGCCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * *
61962271 TACCC-CTGATTTACAAAGTTACAAAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* * ***
61962298 TACCCTTGACTTTCTAAAAATTATGGAAA
1 TACCCTCGA-TTTAT-AAAATTACCAAAA
* * * * *
61962327 TACCATTGGTTTACAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * * * *
61962354 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
*
61962381 CACCCT
1 TACCCT
61962387 TGTAGGATGA
Statistics
Matches: 258, Mismatches: 61, Indels: 24
0.75 0.18 0.07
Matches are distributed among these distances:
26 24 0.09
27 210 0.81
28 8 0.03
29 16 0.06
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCAAAA
Found at i:61962087 original size:54 final size:54
Alignment explanation
Indices: 61962029--61962380 Score: 296
Period size: 54 Copynumber: 6.5 Consensus size: 54
61962019 ATTACTATTT
** * *
61962029 TACCCTCGATTTACAAAATTACTAAAATACCTTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCATTGGTTTACAAAATTACCAAAA
** * * *
61962083 TACCCTCGATCAGTAAAATTACCAAAATACCA-TAGTTTATAAAATTACTAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCATTGGTTTACAAAATTACCAAAA
* * * ** **
61962136 TACCC-CTGGTTTGTAAAATTACCTAAATACCTTTAATTTGTAAAATTACCAAAA
1 TACCCTC-GATTTGTAAAATTACCAAAATACCATTGGTTTACAAAATTACCAAAA
* * *** *
61962190 TACCCT-TAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAA
1 TACCCTCGA-TTTGTAAAATTACCAAAATACCATTGGTTTACAAAATTACCAAAA
* * ** * * *
61962244 TGCCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAGTTACAAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCATTGGTTTACAAAATTACCAAAA
* * *** *
61962298 TACCCTTGACTTTCTAAAAATTATGGAAATACCATTGGTTTACAAAATTACTAAAA
1 TACCCTCGA-TTTGT-AAAATTACCAAAATACCATTGGTTTACAAAATTACCAAAA
* * * *
61962354 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTCGATTTGTAAAATTACCAAAA
61962381 CACCCTTGTA
Statistics
Matches: 236, Mismatches: 55, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
52 1 0.00
53 43 0.18
54 143 0.61
55 9 0.04
56 40 0.17
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.32
Consensus pattern (54 bp):
TACCCTCGATTTGTAAAATTACCAAAATACCATTGGTTTACAAAATTACCAAAA
Found at i:61962236 original size:81 final size:81
Alignment explanation
Indices: 61962038--61962301 Score: 298
Period size: 81 Copynumber: 3.3 Consensus size: 81
61962028 TTACCCTCGA
* * ** ** * * **
61962038 TTTACAAAATTACTAAAATACCTTTGGTTTACAAAATTACCAAAATACCCTCGATCAGTAAAATT
1 TTTATAAAATTACCAAAATACCACTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATT
61962103 ACCAAAATA-CCATAG
66 ACCAAAATACCCATAG
* * * * *
61962118 TTTATAAAATTACTAAAATACCCCTGGTTTGTAAAATTACCTAAATACCTTTAATTTGTAAAATT
1 TTTATAAAATTACCAAAATACCACTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATT
*
61962183 ACCAAAATACCCTTAG
66 ACCAAAATACCCATAG
* * *
61962199 TTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATGCCCTCAATTTGTAAAATT
1 TTTATAAAATTACCAAAATACCACTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATT
*
61962264 ACCAAAATACCCCT-G
66 ACCAAAATACCCATAG
* * *
61962279 ATTTACAAAGTTACAAAAATACC
1 -TTTATAAAATTACCAAAATACC
61962302 CTTGACTTTC
Statistics
Matches: 157, Mismatches: 25, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
80 64 0.41
81 93 0.59
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (81 bp):
TTTATAAAATTACCAAAATACCACTGGTTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATT
ACCAAAATACCCATAG
Found at i:61962440 original size:27 final size:27
Alignment explanation
Indices: 61962410--61962506 Score: 79
Period size: 27 Copynumber: 3.6 Consensus size: 27
61962400 GACTAAAATA
* *
61962410 CCCCTATTAGTTAAAAAGACCGTAAAG
1 CCCCTATAAGGTAAAAAGACCGTAAAG
* ** *
61962437 CCCCTGTAAGGTAAAGTGATCGTAAAG
1 CCCCTATAAGGTAAAAAGACCGTAAAG
* * *
61962464 CCCCTGTAGGGTAAAATGACCGTAATA-
1 CCCCTATAAGGTAAAAAGACCGTAA-AG
* *
61962491 CCCCTGTATGGTAAAA
1 CCCCTATAAGGTAAAA
61962507 TGACAAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 58 0.98
28 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (27 bp):
CCCCTATAAGGTAAAAAGACCGTAAAG
Found at i:61962507 original size:27 final size:27
Alignment explanation
Indices: 61962421--61962510 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
61962411 CCCTATTAGT
*
61962421 TAAAAAGACCGTAAAGCCCCTGTAAGG
1 TAAAATGACCGTAAAGCCCCTGTAAGG
* * *
61962448 TAAAGTGATCGTAAAGCCCCTGTAGGG
1 TAAAATGACCGTAAAGCCCCTGTAAGG
*
61962475 TAAAATGACCGTAATA-CCCCTGTATGG
1 TAAAATGACCGTAA-AGCCCCTGTAAGG
61962502 TAAAATGAC
1 TAAAATGAC
61962511 AAATATGCCC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 54 0.98
28 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (27 bp):
TAAAATGACCGTAAAGCCCCTGTAAGG
Found at i:61963350 original size:26 final size:26
Alignment explanation
Indices: 61963313--61963487 Score: 228
Period size: 26 Copynumber: 6.8 Consensus size: 26
61963303 GAGGAAGTGC
*
61963313 AAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* * * **
61963339 CAAAGGGATTATGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
61963365 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
61963391 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
61963417 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
61963443 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
61963468 AAAAGGGCTT-TGCCTCAGTT
1 AAAAGGGCTTATGCCCCAGTT
61963488 ATTAAAGAGG
Statistics
Matches: 131, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 31 0.24
26 100 0.76
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:61963396 original size:52 final size:52
Alignment explanation
Indices: 61963313--61963487 Score: 282
Period size: 52 Copynumber: 3.4 Consensus size: 52
61963303 GAGGAAGTGC
* * * *
61963313 AAAAGGGCTTATGCCCCAATTTATTGCAAAGGGATTATGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
61963365 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
61963417 AAAAGGGCTTATGCCCTAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
61963468 AAAAGGGCTT-TGCCTCAGTT
1 AAAAGGGCTTATGCCCCAGTT
61963488 ATTAAAGAGG
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
50 8 0.07
51 25 0.22
52 83 0.72
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:61963697 original size:42 final size:42
Alignment explanation
Indices: 61963632--61963723 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
61963622 TAGTCTCCCC
* * ** *
61963632 AAATGGGCTTGGATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
*
61963674 GAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
61963716 AAATGGGC
1 AAATGGGC
61963724 CTAAGGGCCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:61967606 original size:46 final size:45
Alignment explanation
Indices: 61967538--61967712 Score: 165
Period size: 46 Copynumber: 3.8 Consensus size: 45
61967528 TGTAACCCGC
*
61967538 CCATAAGTGAAGTCGGACTCAACTCAACGAGCTCAGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
* * *
61967584 CCATAAGTGAACTCGGAATCAACTCAATGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** * * * *
61967630 ACATCTCTCGAACTCGGACTTAACTCAACGAGTTTGGACATTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
*
61967677 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
61967713 ATGCTCAACC
Statistics
Matches: 101, Mismatches: 21, Indels: 14
0.74 0.15 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 2 0.02
46 62 0.61
47 28 0.28
49 3 0.03
50 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:61970148 original size:30 final size:30
Alignment explanation
Indices: 61970104--61970192 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
61970094 CAAAGATAAC
*
61970104 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
61970133 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
61970163 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
61970193 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:61970152 original size:15 final size:14
Alignment explanation
Indices: 61970104--61970186 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
61970094 CAAAGATAAC
*
61970104 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
61970118 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
61970133 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
61970148 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
61970163 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
61970178 AAGAAACCC
1 AAGAAACCC
61970187 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:61970192 original size:15 final size:15
Alignment explanation
Indices: 61970115--61970192 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
61970105 AGAAAACCGA
61970115 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
61970130 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
61970144 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
61970159 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
61970175 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
61970190 ATA
1 ATA
61970193 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:61973277 original size:46 final size:46
Alignment explanation
Indices: 61973105--61973280 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
61973095 TGTAACCCGC
* * * *
61973105 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* *
61973151 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* *
61973201 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* *
61973244 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
61973281 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 1 0.01
43 8 0.07
44 1 0.01
46 63 0.58
47 28 0.26
49 1 0.01
50 6 0.06
51 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:61973280 original size:93 final size:93
Alignment explanation
Indices: 61973113--61973283 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
61973103 GCCCATAAGT
* *
61973113 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
61973178 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CAAGCTCGGATGCCTAGTTACATCTCTC
* * *
61973206 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
61973271 CAAGTTCGGATGC
66 CAAGCTCGGATGC
61973284 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CAAGCTCGGATGCCTAGTTACATCTCTC
Found at i:61978841 original size:16 final size:17
Alignment explanation
Indices: 61978820--61978858 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
61978810 CTTTTATTAA
61978820 GTTTTTAAGACTCATTC
1 GTTTTTAAGACTCATTC
* *
61978837 GTTTTTAAGATTCATTT
1 GTTTTTAAGACTCATTC
61978854 GTTTT
1 GTTTT
61978859 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.56
Consensus pattern (17 bp):
GTTTTTAAGACTCATTC
Found at i:61984603 original size:20 final size:19
Alignment explanation
Indices: 61984578--61984616 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
61984568 GTTGCAAATC
61984578 ATATATAATGTAAATGAAAA
1 ATATAT-ATGTAAATGAAAA
* *
61984598 ATATATGTGTATATGAAAA
1 ATATATATGTAAATGAAAA
61984617 GTACATTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (19 bp):
ATATATATGTAAATGAAAA
Found at i:61987248 original size:35 final size:35
Alignment explanation
Indices: 61987197--61987269 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
61987187 AGATTCGAAA
61987197 ATAGGTTGAACAAAAACATTAAACTGCTAGTTGGC
1 ATAGGTTGAACAAAAACATTAAACTGCTAGTTGGC
*
61987232 ATAGGTTGAACGAAAACATTAAACTGCTAGTTGGC
1 ATAGGTTGAACAAAAACATTAAACTGCTAGTTGGC
61987267 ATA
1 ATA
61987270 CTTGGAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (35 bp):
ATAGGTTGAACAAAAACATTAAACTGCTAGTTGGC
Found at i:61991641 original size:37 final size:37
Alignment explanation
Indices: 61991599--61991673 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
61991589 AATAATTAAA
61991599 AGCCATACATGTTTATATTTGATAGCTAAAATTAGCT
1 AGCCATACATGTTTATATTTGATAGCTAAAATTAGCT
* *
61991636 AGCCATGCATGTTTATATTTGATAGCTGAAATTAGCT
1 AGCCATACATGTTTATATTTGATAGCTAAAATTAGCT
61991673 A
1 A
61991674 AAGGAAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (37 bp):
AGCCATACATGTTTATATTTGATAGCTAAAATTAGCT
Found at i:61993820 original size:27 final size:28
Alignment explanation
Indices: 61993787--61993843 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
61993777 TGGTATGTAA
*
61993787 ATAATACAACTA-AATGCTAATTTATGT
1 ATAATACAACTACAATACTAATTTATGT
*
61993814 ATAATACAACTACATTACTAATTTATGT
1 ATAATACAACTACAATACTAATTTATGT
61993842 AT
1 AT
61993844 TGAATTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATACAACTACAATACTAATTTATGT
Found at i:61994169 original size:45 final size:46
Alignment explanation
Indices: 61993984--61994204 Score: 186
Period size: 46 Copynumber: 4.8 Consensus size: 46
61993974 GGGTTATTGT
* * * *
61993984 GAGCTAGTGTAAGAGATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACGA-GATGA
* * * *
61994030 GAGCCAGTGTAAGATCATGTTTGGGACATGGCATCGGC-ATTGAGATGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTA-CGAGATGA
* * * *
61994078 GTGCTAGTGTATGACATGTCTGGGACATGCATCAGCCT-TGAAATGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGATG-A
61994125 -AGCTAGTGTAAGACATGTC-GGGACATGCATCAGCTACGAGATG-
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGATGA
* * *
61994168 TA-TTAGTGTAAGACTACGTCTGGGACATGGCATCAGC
1 GAGCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCAGC
61994205 ACCTTACCCA
Statistics
Matches: 146, Mismatches: 17, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
43 11 0.08
44 7 0.05
45 26 0.18
46 50 0.34
47 28 0.19
48 23 0.16
49 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGATGA
Found at i:62014281 original size:40 final size:40
Alignment explanation
Indices: 62014226--62014493 Score: 455
Period size: 40 Copynumber: 6.7 Consensus size: 40
62014216 GAGCATTGGA
*
62014226 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
62014266 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
62014306 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
62014346 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * * *
62014386 ATATGTCCGAGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
62014426 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
62014466 ATATATCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
62014494 ATGTGTTTGC
Statistics
Matches: 213, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 213 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:62018980 original size:46 final size:44
Alignment explanation
Indices: 62018927--62019099 Score: 188
Period size: 46 Copynumber: 3.8 Consensus size: 44
62018917 TTATTGTGAA
*
62018927 CTAGTGTAAGACGTGTCTGGGACATGCATCGGCCACATTATGA-GAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTA-GACGAG
62018973 CTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGAGACGAGTG
1 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCATT-AGACGA--G
* * * *
62019021 CTAGTGAAAGACATGTCTGGGACATGCATCTGCCTTTAGATGTAAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTAGACG--AG
*
62019067 CCAGTGTAAGACATGTCTGGGACATGCATCGGC
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGC
62019100 TACGAGATGT
Statistics
Matches: 110, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
45 6 0.05
46 55 0.50
47 30 0.27
48 19 0.17
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (44 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTAGACGAG
Found at i:62019108 original size:46 final size:46
Alignment explanation
Indices: 62018929--62019141 Score: 170
Period size: 46 Copynumber: 4.6 Consensus size: 46
62018919 ATTGTGAACT
* * * *
62018929 AGTGTAAGACGTGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGAGAGCC
* * * *
62018975 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ATTGAGACGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CGAGATGAGAGCC
* * **
62019023 AGTGAAAGACATGTCTGGGACATGCATCTGCCT-TTAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCTACGAGATG-AGAGCC
* *
62019069 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGAT--GTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGAGAGCC
*
62019113 A-TGTAAGACCATGTCCGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
62019142 AGCACCTTAC
Statistics
Matches: 138, Mismatches: 18, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
43 7 0.05
44 16 0.12
45 8 0.06
46 52 0.38
47 31 0.22
48 23 0.17
49 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGAGAGCC
Done.