Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 63 of 131
Found at i:20727443 original size:18 final size:19
Alignment explanation
Indices: 20727420--20727455 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20727410 TCATCCAATG
20727420 ATTAGATTCTCAA-AATCC
1 ATTAGATTCTCAACAATCC
*
20727438 ATTAGATTGTCAACAATC
1 ATTAGATTCTCAACAATC
20727456 ATAGCAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (19 bp):
ATTAGATTCTCAACAATCC
Found at i:20729693 original size:30 final size:29
Alignment explanation
Indices: 20729637--20729826 Score: 139
Period size: 29 Copynumber: 6.5 Consensus size: 29
20729627 TGTTATGTCT
* * *
20729637 CTTTTCATATTCGATGGTCGAAACCATCA
1 CTTTTCATAATCGATGGTCGTAACCATCC
* *
20729666 CTTTTCATTAATCGATAGTCGTCACCATCC
1 CTTTTCA-TAATCGATGGTCGTAACCATCC
* * *
20729696 CTTTTCATAGTTGATGGTCGTTACCATCC
1 CTTTTCATAATCGATGGTCGTAACCATCC
** * * * *
20729725 CTTTTCGCAATAGATAGCCG-AAGCTATCC
1 CTTTTCATAATCGATGGTCGTAA-CCATCC
* * * *
20729754 CGTTTCATATTCGATGGTCATCACCATCC
1 CTTTTCATAATCGATGGTCGTAACCATCC
* * * * *
20729783 CTTTTCACAATTGATGGTCATCACCCTCC
1 CTTTTCATAATCGATGGTCGTAACCATCC
*
20729812 ATTTTCATAATCGAT
1 CTTTTCATAATCGAT
20729827 AGCCGAAGCT
Statistics
Matches: 123, Mismatches: 35, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
28 1 0.01
29 97 0.79
30 25 0.20
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (29 bp):
CTTTTCATAATCGATGGTCGTAACCATCC
Found at i:20729783 original size:87 final size:87
Alignment explanation
Indices: 20729668--20729848 Score: 227
Period size: 87 Copynumber: 2.1 Consensus size: 87
20729658 AACCATCACT
* * * * * * *
20729668 TTTCATTAATCGATAGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTTACCATCCCTTTTCGC
1 TTTCA-TAATCGATAGTCATCACCATCCCTTTTCACAATTGATGGTCATCACCATCCATTTTCAC
20729733 AATAGATAGCCGAAGCTATCCCG
65 AATAGATAGCCGAAGCTATCCCG
* * * *
20729756 TTTCATATTCGATGGTCATCACCATCCCTTTTCACAATTGATGGTCATCACCCTCCATTTTCATA
1 TTTCATAATCGATAGTCATCACCATCCCTTTTCACAATTGATGGTCATCACCATCCATTTTCACA
* * *
20729821 ATCGATAGCCGAAGCTATCTCT
66 ATAGATAGCCGAAGCTATCCCG
20729843 TTTCAT
1 TTTCAT
20729849 TGGTCGATGA
Statistics
Matches: 79, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
87 74 0.94
88 5 0.06
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (87 bp):
TTTCATAATCGATAGTCATCACCATCCCTTTTCACAATTGATGGTCATCACCATCCATTTTCACA
ATAGATAGCCGAAGCTATCCCG
Found at i:20729818 original size:58 final size:58
Alignment explanation
Indices: 20729637--20729826 Score: 163
Period size: 58 Copynumber: 3.3 Consensus size: 58
20729627 TGTTATGTCT
* * * *
20729637 CTTTTCATATTCGATGGTCGA-AACCATCACTTTTCATTAATCGATAGTCGTCACCATCC
1 CTTTTCATATTCGATGGTC-ATAACCATCCCTTTTCA-CAATAGATAGTCATCACCATCC
* * * * *
20729696 CTTTTCATAGTT-GATGGTCGTTACCATCCCTTTTCGCAATAGATAGCCGA--AGCTATCC
1 CTTTTCATA-TTCGATGGTCATAACCATCCCTTTTCACAATAGATAGTC-ATCA-CCATCC
* * * * *
20729754 CGTTTCATATTCGATGGTCATCACCATCCCTTTTCACAATTGATGGTCATCACCCTCC
1 CTTTTCATATTCGATGGTCATAACCATCCCTTTTCACAATAGATAGTCATCACCATCC
* *
20729812 ATTTTCATAATCGAT
1 CTTTTCATATTCGAT
20729827 AGCCGAAGCT
Statistics
Matches: 103, Mismatches: 21, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
57 4 0.04
58 68 0.66
59 29 0.28
60 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (58 bp):
CTTTTCATATTCGATGGTCATAACCATCCCTTTTCACAATAGATAGTCATCACCATCC
Found at i:20733972 original size:23 final size:23
Alignment explanation
Indices: 20733941--20734062 Score: 163
Period size: 23 Copynumber: 5.3 Consensus size: 23
20733931 ATAAGTGCCA
* *
20733941 CACTAATATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
20733964 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
20733987 CACTAAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20734010 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
20734033 CACTGAAATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
20734056 CACTGAT
1 CACTGAT
20734063 CAATAACATT
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 84 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:20734008 original size:46 final size:46
Alignment explanation
Indices: 20733941--20734062 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
20733931 ATAAGTGCCA
* * *
20733941 CACTAATATGTAGTCGAAGCTACCACTGATATGTAGCTGTAGCTAC
1 CACTAAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
20733987 CACTAAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTAAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
* *
20734033 CACTGAAATGTAACCGAAGCTACCACTGAT
1 CACTAAAATGTAGCCGAAGCTACCACTGAT
20734063 CAATAACATT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (46 bp):
CACTAAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
Found at i:20738412 original size:12 final size:12
Alignment explanation
Indices: 20738395--20738419 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20738385 AACCTCACAC
20738395 GCCCGTGTGCTA
1 GCCCGTGTGCTA
20738407 GCCCGTGTGCTA
1 GCCCGTGTGCTA
20738419 G
1 G
20738420 GACATGTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (12 bp):
GCCCGTGTGCTA
Found at i:20744409 original size:36 final size:36
Alignment explanation
Indices: 20744355--20744425 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
20744345 ATTAAACTCT
* * *
20744355 ATTCAGTTAAGCAGCCTTTTGGCTCTATTTTGACTG
1 ATTCAGTTAAGCAACCTTTTGGATCTATTCTGACTG
*
20744391 ATTCAGTTCAA-CAACCTTTTGTATCTATTCTGACT
1 ATTCAGTT-AAGCAACCTTTTGGATCTATTCTGACT
20744426 AATGCGCTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 28 0.93
37 2 0.07
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (36 bp):
ATTCAGTTAAGCAACCTTTTGGATCTATTCTGACTG
Found at i:20752024 original size:26 final size:24
Alignment explanation
Indices: 20751991--20752039 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
20751981 TGCATGTGAG
* *
20751991 CAAAATGAGTTTGTTTTGAATATGA
1 CAAAATGAATATGTTTTG-ATATGA
20752016 CAAATATGAATATGTTTTGATATG
1 CAAA-ATGAATATGTTTTGATATG
20752040 TTCGATTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (24 bp):
CAAAATGAATATGTTTTGATATGA
Found at i:20754771 original size:12 final size:13
Alignment explanation
Indices: 20754747--20754775 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20754737 GGGCTATAAC
20754747 TATTGCATTTATT
1 TATTGCATTTATT
20754760 TATTGC-TTTATT
1 TATTGCATTTATT
20754772 TATT
1 TATT
20754776 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:20759799 original size:34 final size:34
Alignment explanation
Indices: 20759756--20759825 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
20759746 ATTTTCATAC
*
20759756 AGTCAAACGTACACCGTAACTGGTTATTCTATAA
1 AGTCAAACGTACACCATAACTGGTTATTCTATAA
* *
20759790 AGTCAAACGTACACCATAATTGGTTGTTCTATAA
1 AGTCAAACGTACACCATAACTGGTTATTCTATAA
20759824 AG
1 AG
20759826 GCTAATGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (34 bp):
AGTCAAACGTACACCATAACTGGTTATTCTATAA
Found at i:20760933 original size:42 final size:42
Alignment explanation
Indices: 20760837--20760933 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
20760827 CGTTCCAACA
* **
20760837 ACACGGGCATGTGAGGCCATTTCGAAAGTTTCACGGCCTGGT
1 ACACGGGCATGTGAGGCCATTTCGAAAGTTACACGGCCTGAC
* ** * * * *
20760879 AGATTGGTATGTGAGGGCATTTTGAAAGTTACACGGCTTGAC
1 ACACGGGCATGTGAGGCCATTTCGAAAGTTACACGGCCTGAC
20760921 ACACGGGCATGTG
1 ACACGGGCATGTG
20760934 GCTTGGCCAT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.26
Consensus pattern (42 bp):
ACACGGGCATGTGAGGCCATTTCGAAAGTTACACGGCCTGAC
Found at i:20763076 original size:13 final size:14
Alignment explanation
Indices: 20763058--20763086 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20763048 TTTCTACTTG
20763058 TTTAA-TTTTCTTT
1 TTTAATTTTTCTTT
20763071 TTTAATTTTTCTTT
1 TTTAATTTTTCTTT
20763085 TT
1 TT
20763087 GCACTTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTAATTTTTCTTT
Found at i:20770526 original size:41 final size:41
Alignment explanation
Indices: 20770494--20770655 Score: 236
Period size: 41 Copynumber: 4.0 Consensus size: 41
20770484 CCCGTTAGAC
*
20770494 TTATAGCCTGATTCAGATCACCGACACGTAGCCTGCTAGGT
1 TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGT
*
20770535 TTATAACCTGATTTAGATCACC-AGCACGTAGCCTGCTAGGT
1 TTATAACCTGATTCAGATCACCGA-CACGTAGCCTGCTAGGT
* *
20770576 TTATAACCTGATTCAGATCACTGGCACGTAGCCTGCTAGGT
1 TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGT
* * **
20770617 TTATAACCTGATTTAGATCACCGGCAATTAGCCTGCTAG
1 TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAG
20770656 ACTTAAAGTC
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 109 0.99
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGT
Found at i:20770618 original size:82 final size:82
Alignment explanation
Indices: 20770494--20770655 Score: 270
Period size: 82 Copynumber: 2.0 Consensus size: 82
20770484 CCCGTTAGAC
*
20770494 TTATAGCCTGATTCAGATCACCGACACGTAGCCTGCTAGGTTTATAACCTGATTTAGATCACCAG
1 TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGTTTATAACCTGATTTAGATCACCAG
*
20770559 CACGTAGCCTGCTAGGT
66 CAAGTAGCCTGCTAGGT
* * *
20770576 TTATAACCTGATTCAGATCACTGGCACGTAGCCTGCTAGGTTTATAACCTGATTTAGATCACCGG
1 TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGTTTATAACCTGATTTAGATCACCAG
*
20770641 CAATTAGCCTGCTAG
66 CAAGTAGCCTGCTAG
20770656 ACTTAAAGTC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (82 bp):
TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGTTTATAACCTGATTTAGATCACCAG
CAAGTAGCCTGCTAGGT
Found at i:20774027 original size:22 final size:22
Alignment explanation
Indices: 20773995--20774071 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
20773985 TACAGAGGCA
*
20773995 ATGTTGCGACACACCAAGTCCT
1 ATGTTGTGACACACCAAGTCCT
*
20774017 ATGTTGTGACACACCAAGTCAT
1 ATGTTGTGACACACCAAGTCCT
20774039 ATGTTGTGACACACCAAGTCCT
1 ATGTTGTGACACACCAAGTCCT
20774061 ATGTTGTGACA
1 ATGTTGTGACA
20774072 TCCTCAGGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (22 bp):
ATGTTGTGACACACCAAGTCCT
Found at i:20782751 original size:25 final size:26
Alignment explanation
Indices: 20782715--20782769 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
20782705 ATTTTTATTA
*
20782715 TATTATTTATTTTAAACTATTTTAT-
1 TATTATTCATTTTAAACTATTTTATG
* *
20782740 TATTATTCATTTTAAGCTTTTTTATG
1 TATTATTCATTTTAAACTATTTTATG
20782766 TATT
1 TATT
20782770 TTTTATTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (26 bp):
TATTATTCATTTTAAACTATTTTATG
Found at i:20788384 original size:21 final size:21
Alignment explanation
Indices: 20788358--20788397 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20788348 TGGATTCTAT
*
20788358 AGGTCATGTTCCCCAGAGACC
1 AGGTCATATTCCCCAGAGACC
20788379 AGGTCATATTCCCCAGAGA
1 AGGTCATATTCCCCAGAGA
20788398 ACAAATCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.20
Consensus pattern (21 bp):
AGGTCATATTCCCCAGAGACC
Found at i:20789167 original size:143 final size:143
Alignment explanation
Indices: 20788939--20789497 Score: 764
Period size: 143 Copynumber: 3.9 Consensus size: 143
20788929 GTTATATCAG
* * * * *
20788939 GCGAATCTTATTTCCTTGACGTTGTAGTGGAACA-ATTAAAGCTACCAATTATGGCAGATCTTAT
1 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
* * * * *
20789003 CCTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCTTAAAGTTGCAGCGAAG
66 CTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCTCCCTGAAGTTGCAGCGGAG
20789068 CAGACTGAAGACA
131 CAGACTGAAGACA
* *
20789081 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACCAATTATGGTGGATCTTAT
1 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
* * * *
20789146 CTTTCTAAAGTTGCAGTGGAGCAGATTGGAGCCACAAGCCTTATATCCCTGAAGTTGTAGCGGAG
66 CTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCTCCCTGAAGTTGCAGCGGAG
20789211 CAGACTGAAGACA
131 CAGACTGAAGACA
* * * *
20789224 GCGAATATTATTTCCCTGGCGTTGCAATAGAACAGATTAAAGCTACAAATTGTGGCGGATCTTAT
1 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
* * *
20789289 CTTCCTGAAA-TTGCAGTGGAGTAGATTAAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGA
66 CTTCCT-AAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCTCCCTGAAGTTGCAGCGGA
*
20789353 GCAGACTGAACACA
130 GCAGACTGAAGACA
* * *
20789367 GCGAATCTTACTTCCCTAGCGTTGGAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
1 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
* * * * * * * *
20789432 CTTCCTGAAGTTGCAATAGAGCAAATTGAAGCCACCGATCC-TATCTCCCTGAAGTTGTAGTGGA
66 CTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCA-CAAGCCTTATCTCCCTGAAGTTGCAGCGGA
20789496 GC
130 GC
20789498 GGATTAAAAC
Statistics
Matches: 368, Mismatches: 45, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
142 33 0.09
143 328 0.89
144 7 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (143 bp):
GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
CTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCTCCCTGAAGTTGCAGCGGAG
CAGACTGAAGACA
Found at i:20791140 original size:26 final size:25
Alignment explanation
Indices: 20791069--20791150 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
20791059 CTAACGTTTA
*
20791069 TTTTTATTA-TATTATTTATTTTAAA
1 TTTTT-TTATTATTATTTATTTTAAG
* * *
20791094 CTATTTTATTATTATTCATTTTAAG
1 TTTTTTTATTATTATTTATTTTAAG
* *
20791119 TTTTTTTATGTATTGTTTATTTGAAG
1 TTTTTTTAT-TATTATTTATTTTAAG
*
20791145 TCTTTT
1 TTTTTT
20791151 ATCATTTATT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
24 3 0.07
25 24 0.53
26 18 0.40
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.66
Consensus pattern (25 bp):
TTTTTTTATTATTATTTATTTTAAG
Found at i:20792360 original size:19 final size:19
Alignment explanation
Indices: 20792318--20792362 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
20792308 TTTTACGGAA
* *
20792318 AATGTTTTATACATTTTCC
1 AATGTTTTATACATCTTAC
*
20792337 AATGTTTTATATATCTTAC
1 AATGTTTTATACATCTTAC
*
20792356 TATGTTT
1 AATGTTT
20792363 ACTTCAAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.56
Consensus pattern (19 bp):
AATGTTTTATACATCTTAC
Found at i:20792648 original size:15 final size:15
Alignment explanation
Indices: 20792628--20792684 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
20792618 ATTCAATATT
20792628 AATATTTTAATAATA
1 AATATTTTAATAATA
*
20792643 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
20792662 AATATATTAATAATA
1 AATATTTTAATAATA
*
20792677 AATGTTTT
1 AATATTTT
20792685 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:20802427 original size:101 final size:102
Alignment explanation
Indices: 20802311--20802495 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 102
20802301 AAAGTGATGG
* ** *
20802311 TCACGTGTGTAGTACTATGTACAGGCTACGACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGATAGTGAT-GGTCACATGTGTAGT
20802374 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * *
20802412 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGATAGTGATGGTCACATGTGTAGTA
20802477 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
20802496 TGAACCGGTA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
101 35 0.47
102 35 0.47
103 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (102 bp):
TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:20802430 original size:51 final size:50
Alignment explanation
Indices: 20802311--20802495 Score: 196
Period size: 51 Copynumber: 3.7 Consensus size: 50
20802301 AAAGTGATGG
* * * * * * *
20802311 TCACGTGTGTAGTACTATGTACAGGCTACGACGTGTACCAGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-AT-GA
*
20802361 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-GA
** * *
20802412 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATGA
20802463 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
20802496 TGAACCGGTA
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
50 36 0.32
51 76 0.67
52 1 0.01
53 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATGA
Found at i:20802503 original size:102 final size:101
Alignment explanation
Indices: 20802311--20802503 Score: 271
Period size: 102 Copynumber: 1.9 Consensus size: 101
20802301 AAAGTGATGG
* ** *
20802311 TCACGTGTGTAGTACTATGTACAGGCTACGACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGAATGATAGGTCACATGTGTAGTAC
*
20802376 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
* * * *
20802412 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGA-A-TGATAGGTCACATGTGTAGT
*
20802476 ACTATGTGCAGGCTACTATGTGAACCGG
64 ACTATGTGCAGGCTACTATGCGAACCGG
20802504 TATCATTAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
101 35 0.44
102 41 0.51
103 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
Found at i:20809279 original size:20 final size:23
Alignment explanation
Indices: 20809240--20809280 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
20809230 AATGCAATAT
20809240 TAAAAGTGCTAACTAAAATGTCC
1 TAAAAGTGCTAACTAAAATGTCC
20809263 TAAAA-TGC-AAC-AAAATGT
1 TAAAAGTGCTAACTAAAATGT
20809281 ACTTAAGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 3 0.17
23 5 0.28
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (23 bp):
TAAAAGTGCTAACTAAAATGTCC
Found at i:20811450 original size:82 final size:82
Alignment explanation
Indices: 20811357--20811517 Score: 304
Period size: 82 Copynumber: 2.0 Consensus size: 82
20811347 TTGTATTAAT
*
20811357 TTTTTGGATAAACTTTAATTTTTTAGGGGTATGAGCAACAATAGATTTTTATTTGTTTCTGTGCT
1 TTTTTGAATAAACTTTAATTTTTTAGGGGTATGAGCAACAATAGATTTTTATTTGTTTCTGTGCT
20811422 ATTTTAGAATTTTAGAA
66 ATTTTAGAATTTTAGAA
20811439 TTTTTGAATAAACTTTAATTTTTTAGGGGTATGAGCAACAATAGATTTTTATTTGTTTCTGTGCT
1 TTTTTGAATAAACTTTAATTTTTTAGGGGTATGAGCAACAATAGATTTTTATTTGTTTCTGTGCT
*
20811504 GTTTTAGAATTTTA
66 ATTTTAGAATTTTA
20811518 TATGTAGGAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (82 bp):
TTTTTGAATAAACTTTAATTTTTTAGGGGTATGAGCAACAATAGATTTTTATTTGTTTCTGTGCT
ATTTTAGAATTTTAGAA
Found at i:20822833 original size:19 final size:19
Alignment explanation
Indices: 20822809--20822846 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20822799 TCTTATAAAA
*
20822809 CTAATTAGAAATTTTTATT
1 CTAATTAGAAAATTTTATT
20822828 CTAATTAGAAAATTTTATT
1 CTAATTAGAAAATTTTATT
20822847 AATTACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
CTAATTAGAAAATTTTATT
Found at i:20826115 original size:110 final size:110
Alignment explanation
Indices: 20825922--20826194 Score: 289
Period size: 110 Copynumber: 2.5 Consensus size: 110
20825912 TTATAATGCT
* ** * * *
20825922 AATCAGACTAGTAGTTCATGACATGAAGACATGTGTAAGACCATGTGGTAGAGACCTATGACATT
1 AATCAGACTAGTAGATCACAACATGAAGACATGTGTAAGACCACGTGGTAGAAACCCATGACATT
*
20825987 ATATGACAATGAGGATATTCATGGTGTAGCCTATGGTGAGATGTA
66 ATACGACAATGAGGATATTCATGGTGTAGCCTATGGTGAGATGTA
* * * *
20826032 AATCAGACTAGTAGATCACAACATTAAGATATGTGTAAGACCACGTGGTATAAACCCATGGCATT
1 AATCAGACTAGTAGATCACAACATGAAGACATGTGTAAGACCACGTGGTAGAAACCCATGACATT
* * * * ***
20826097 ATACGACAATGGGGATATTCATGTTGTATCGTCCAGTGAGATGTA
66 ATACGACAATGAGGATATTCATGGTGTAGCCTATGGTGAGATGTA
* * * * * * *
20826142 AA-CCGAACT-GCTGGATCACAATATGAAGATATGTATAAGACCATGTGGGAGAA
1 AATCAG-ACTAG-TAGATCACAACATGAAGACATGTGTAAGACCACGTGGTAGAA
20826195 GCCCCACGGT
Statistics
Matches: 135, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
109 3 0.02
110 132 0.98
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (110 bp):
AATCAGACTAGTAGATCACAACATGAAGACATGTGTAAGACCACGTGGTAGAAACCCATGACATT
ATACGACAATGAGGATATTCATGGTGTAGCCTATGGTGAGATGTA
Found at i:20830326 original size:114 final size:114
Alignment explanation
Indices: 20830126--20830348 Score: 410
Period size: 114 Copynumber: 2.0 Consensus size: 114
20830116 ATGCTAAACC
* *
20830126 CTTATGCAAATTATTGGAGAAGGATACAACATTCAACTTTGATGAAGAATGTTTGAGAGATTTTA
1 CTTATGCAAATTATTGGAGAAGGATACAACATTCAAATTTGATGAAAAATGTTTGAGAGATTTTA
* *
20830191 ATGATTTGAAGAATCGATTAGTTTTAGCACCAATTATCGTCACATAGGA
66 AAGATTTGAAGAATCGATTAGTTTCAGCACCAATTATCGTCACATAGGA
20830240 CTTATGCAAATTATTGGAGAAGGATACAACATTCAAATTTGATGAAAAATGTTTGAGAGATTTTA
1 CTTATGCAAATTATTGGAGAAGGATACAACATTCAAATTTGATGAAAAATGTTTGAGAGATTTTA
20830305 AAGATTTGAAGAATCGATTAGTTTCAGCACCAATTATCGTCACA
66 AAGATTTGAAGAATCGATTAGTTTCAGCACCAATTATCGTCACA
20830349 CGGGATTGGT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (114 bp):
CTTATGCAAATTATTGGAGAAGGATACAACATTCAAATTTGATGAAAAATGTTTGAGAGATTTTA
AAGATTTGAAGAATCGATTAGTTTCAGCACCAATTATCGTCACATAGGA
Found at i:20832541 original size:17 final size:17
Alignment explanation
Indices: 20832503--20832542 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20832493 AAATAATGTA
20832503 TTATTATATATTATATT
1 TTATTATATATTATATT
*
20832520 ATATTATATATTA-ATTT
1 TTATTATATATTATA-TT
20832537 TTATTA
1 TTATTA
20832543 ACCTTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTATATATTATATT
Found at i:20838325 original size:37 final size:37
Alignment explanation
Indices: 20838275--20838349 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
20838265 CATTAGCCTT
20838275 GCATAACTTCCAAGATTATTATGATTAAATTGTTTTA
1 GCATAACTTCCAAGATTATTATGATTAAATTGTTTTA
20838312 GCATAACTTCCAAGATTATTATGATTAAATTGTTTTA
1 GCATAACTTCCAAGATTATTATGATTAAATTGTTTTA
20838349 G
1 G
20838350 TATAGAGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.43
Consensus pattern (37 bp):
GCATAACTTCCAAGATTATTATGATTAAATTGTTTTA
Found at i:20855612 original size:17 final size:17
Alignment explanation
Indices: 20855587--20855622 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20855577 TATCGGTTAG
*
20855587 AATAAAAAATATT-AAA
1 AATAAAAAAAATTCAAA
20855603 AATAAAAAAAATTCAAA
1 AATAAAAAAAATTCAAA
20855620 AAT
1 AAT
20855623 TTCGGTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
AATAAAAAAAATTCAAA
Found at i:20856971 original size:20 final size:20
Alignment explanation
Indices: 20856926--20856975 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
20856916 ATGCAATACT
20856926 AAAATTTTTAACAAATATCG
1 AAAATTTTTAACAAATATCG
* *
20856946 -ATATTTTTAACATGATAT-G
1 AAAATTTTTAACA-AATATCG
20856965 AAAATTTTTAA
1 AAAATTTTTAA
20856976 TTGATGCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (20 bp):
AAAATTTTTAACAAATATCG
Found at i:20857096 original size:20 final size:19
Alignment explanation
Indices: 20857037--20857101 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
20857027 AGATACACAG
*
20857037 AGAAATTTTGATA-CTCGATT
1 AGAAA-TTTGATATCACG-TT
***
20857057 AGAAATTTGATATTGTGTT
1 AGAAATTTGATATCACGTT
20857076 AGAAATATTGATATCACGTT
1 AGAAAT-TTGATATCACGTT
20857096 A-AAATT
1 AGAAATT
20857102 ATTAGCATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.51
20 17 0.46
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (19 bp):
AGAAATTTGATATCACGTT
Found at i:20857878 original size:17 final size:18
Alignment explanation
Indices: 20857856--20857889 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20857846 GGTGATAAGT
20857856 AAAAG-AATAAGAAAATA
1 AAAAGAAATAAGAAAATA
*
20857873 AAAAGAAATGAGAAAAT
1 AAAAGAAATAAGAAAAT
20857890 CTAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (18 bp):
AAAAGAAATAAGAAAATA
Found at i:20860170 original size:50 final size:50
Alignment explanation
Indices: 20860067--20860183 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
20860057 AGGTATCATA
* * ** *
20860067 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCCCACG
* * *
20860117 TAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCTATG
1 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCCCACG
*
20860167 TAAGACCATATCTGGGA
1 TAAGACCATGTCTGGGA
20860184 TATGACATTG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCCCACG
Found at i:20860497 original size:20 final size:20
Alignment explanation
Indices: 20860459--20860497 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20860449 TAAGCAAGCA
*
20860459 AGTAAGTAAACAAGTAAGTG
1 AGTAAGTAAACAAGAAAGTG
*
20860479 AGTAAGTAAAGAAGAAAGT
1 AGTAAGTAAACAAGAAAGT
20860498 AAAGATCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.26, T:0.18
Consensus pattern (20 bp):
AGTAAGTAAACAAGAAAGTG
Found at i:20863069 original size:432 final size:431
Alignment explanation
Indices: 20862265--20863135 Score: 1733
Period size: 432 Copynumber: 2.0 Consensus size: 431
20862255 ATATAAGATA
20862265 CAAATGACATGTCATTAGGGTTTTAATCTTTCAGCTGCTGGTCCTAAATGTTCTATTGATGGCTG
1 CAAATGACATGTCATTAGGGTTTTAATCTTTCAGCTGCTGGTCCTAAATGTTCTATTGATGGCTG
20862330 AAGTCCCGTATTTGTTGCAAATACTCATCAGCATGTGTGAGCAGCATTGTGTAGCTTACATTCCG
66 AAGTCCCGTATTTGTTGCAAATACTCATCAGCATGTGTGAGCAGCATTGTGTAGCTTACATTCCG
20862395 ATTGTCAGCTTTTGTGAGCAGACCCAAATTACCATGTTTAGGGTGCTGGTCCTGAATGTCCTACC
131 ATTGTCAGCTTTTGTGAGCAGACCCAAATTACCATGTTTAGGGTGCTGGTCCTGAATGTCCTACC
20862460 GATGGCTGAGTTCCAACATTTTTTGTGGATACTCATCATCTTGTGTGAGCGGCATCTTGTAGCAA
196 GATGGCTGAGTTCCAACATTTTTTGTGGATACTCATCATCTTGTGTGAGCGGCATCTTGTAGCAA
20862525 CATTTTGATCGTCAGCTTGTGTGGAAAGACCCATTTATGGCTCGAGTAAGCAATGATAAAAAGGA
261 CATTTTGATCGTCAGCTTGTGTGGAAAGACCCATTTATGGCTCGAGTAAGCAATGATAAAAAGGA
20862590 ATGGTTTCGACTGTATGTTTAGCACACTTTGTGTGAGCTTTCTCGCGTATCCGATATTATTCTAA
326 ATGGTTTCGACTGTATGTTTAGCACACTTTGTGTGAGCTTTCTCGCGTATCCGATATTATTCTAA
20862655 GTGGTTCAACGACCATGAAAAGGGAAGGAAAAATATGCATT
391 GTGGTTCAACGACCATGAAAAGGGAAGGAAAAATATGCATT
20862696 CAAAATGACATGTCATTAGGGTTTTAATCTTTCAGCTGCTGGTCCTAAATGTTCTATTGATGGCT
1 C-AAATGACATGTCATTAGGGTTTTAATCTTTCAGCTGCTGGTCCTAAATGTTCTATTGATGGCT
20862761 GAAGTCCCGTATTTGTTGCAAATACTCATCAGCATGTGTGAGCAGCATTGTGTAGCTTACATTCC
65 GAAGTCCCGTATTTGTTGCAAATACTCATCAGCATGTGTGAGCAGCATTGTGTAGCTTACATTCC
20862826 GATTGTCAGCTTTTGTGAGCAGACCCAAATTACCATGTTTAGGGTGCTGGTCCTGAATGTCCTAC
130 GATTGTCAGCTTTTGTGAGCAGACCCAAATTACCATGTTTAGGGTGCTGGTCCTGAATGTCCTAC
20862891 CGATGGCTGAGTTCCAACATTTTTTGTGGATACTCATCATCTTGTGTGAGCGGCATCTTGTAGCA
195 CGATGGCTGAGTTCCAACATTTTTTGTGGATACTCATCATCTTGTGTGAGCGGCATCTTGTAGCA
20862956 ACATTTTGATCGTCAGCTTGTGTGGAAAGACCCATTTATGGCTCGAGTAAGCAATGATAAAAAGG
260 ACATTTTGATCGTCAGCTTGTGTGGAAAGACCCATTTATGGCTCGAGTAAGCAATGATAAAAAGG
20863021 AATGGTTTCGACTGTATGTTTAGCACACTTTGTGTGAGCTTTCTCGCGTATCCGATATTATTCTA
325 AATGGTTTCGACTGTATGTTTAGCACACTTTGTGTGAGCTTTCTCGCGTATCCGATATTATTCTA
20863086 AGTGGTTCAACGACCATGAAAAGGGAAGGAAAAATATGCATT
390 AGTGGTTCAACGACCATGAAAAGGGAAGGAAAAATATGCATT
20863128 CAAATGAC
1 CAAATGAC
20863136 TTATATCAAG
Statistics
Matches: 439, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
431 8 0.02
432 431 0.98
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (431 bp):
CAAATGACATGTCATTAGGGTTTTAATCTTTCAGCTGCTGGTCCTAAATGTTCTATTGATGGCTG
AAGTCCCGTATTTGTTGCAAATACTCATCAGCATGTGTGAGCAGCATTGTGTAGCTTACATTCCG
ATTGTCAGCTTTTGTGAGCAGACCCAAATTACCATGTTTAGGGTGCTGGTCCTGAATGTCCTACC
GATGGCTGAGTTCCAACATTTTTTGTGGATACTCATCATCTTGTGTGAGCGGCATCTTGTAGCAA
CATTTTGATCGTCAGCTTGTGTGGAAAGACCCATTTATGGCTCGAGTAAGCAATGATAAAAAGGA
ATGGTTTCGACTGTATGTTTAGCACACTTTGTGTGAGCTTTCTCGCGTATCCGATATTATTCTAA
GTGGTTCAACGACCATGAAAAGGGAAGGAAAAATATGCATT
Found at i:20864412 original size:5 final size:5
Alignment explanation
Indices: 20864402--20864440 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
20864392 GCCTAAGATG
* *
20864402 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
20864441 GTTAAGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:20864913 original size:25 final size:25
Alignment explanation
Indices: 20864878--20864988 Score: 99
Period size: 25 Copynumber: 4.5 Consensus size: 25
20864868 ACACATCACA
* *
20864878 GCTCTTAGGAGCGTCTCGATATATG
1 GCTCTTCGGAGCTTCTCGATATATG
20864903 GCTCTTCGGAGCTTAC-CG--ATATG
1 GCTCTTCGGAGCTT-CTCGATATATG
* *
20864926 GCTGGCTT--GAACTTCCCGATATATG
1 GCT--CTTCGGAGCTTCTCGATATATG
*
20864951 GCTATTCGGAGCTTCTCGAT-TAATG
1 GCTCTTCGGAGCTTCTCGATAT-ATG
20864976 GCTCTTCGGAGCT
1 GCTCTTCGGAGCT
20864989 ACCTGTCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
22 1 0.01
23 17 0.24
24 1 0.01
25 50 0.71
26 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.32
Consensus pattern (25 bp):
GCTCTTCGGAGCTTCTCGATATATG
Found at i:20865023 original size:73 final size:73
Alignment explanation
Indices: 20864885--20865023 Score: 160
Period size: 73 Copynumber: 1.9 Consensus size: 73
20864875 ACAGCTCTTA
** *
20864885 GGAGCGTCTCGATATATGGCTCTTCGGAGCTTACCGATATGGCTGGCTTGAACTTCCCGATATAT
1 GGAGCGTCTCGATATATGGCTCTTCGGAGCTTACCGATATGGCTCACATGAACTTCCCGATATAT
20864950 GGCTATTC
66 GGCTATTC
* * *
20864958 GGAGCTTCTCGAT-TAATGGCTCTTCGGAGC-TACCTG-TCATTGGCTCACATGAGCTTCCTGA-
1 GGAGCGTCTCGATAT-ATGGCTCTTCGGAGCTTACC-GAT-A-TGGCTCACATGAACTTCCCGAT
20865019 ATATG
62 ATATG
20865024 ACTTATGAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
72 6 0.11
73 34 0.61
74 16 0.29
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (73 bp):
GGAGCGTCTCGATATATGGCTCTTCGGAGCTTACCGATATGGCTCACATGAACTTCCCGATATAT
GGCTATTC
Found at i:20870805 original size:79 final size:79
Alignment explanation
Indices: 20870714--20870863 Score: 255
Period size: 79 Copynumber: 1.9 Consensus size: 79
20870704 CCGGAAAAAA
* ** *
20870714 TGGTTTTGGGGCCACAAATCCGATGAGTAAGTTCGTAAATATTATTATTTAATATTTATGAGTCA
1 TGGTTTCGGGGCCACAAATCCGACAAGTAAGTTCATAAATATTATTATTTAATATTTATGAGTCA
20870779 AATATGGGAAACAG
66 AATATGGGAAACAG
*
20870793 TGGTTTCGGGGCCACAAATTCGACAAGTAAGTTCATAAATATTATTATTTAATATTTATGAGTCA
1 TGGTTTCGGGGCCACAAATCCGACAAGTAAGTTCATAAATATTATTATTTAATATTTATGAGTCA
20870858 AATATG
66 AATATG
20870864 ATTTTAAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (79 bp):
TGGTTTCGGGGCCACAAATCCGACAAGTAAGTTCATAAATATTATTATTTAATATTTATGAGTCA
AATATGGGAAACAG
Found at i:20875689 original size:27 final size:27
Alignment explanation
Indices: 20875651--20875712 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
20875641 TAACCATATC
*
20875651 ACAAACATATCATCATGCATCCTCAAG
1 ACAACCATATCATCATGCATCCTCAAG
20875678 ACAACCATATCATCATGCATCCTCAAG
1 ACAACCATATCATCATGCATCCTCAAG
20875705 ACAACCAT
1 ACAACCAT
20875713 TTATAATTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.40, C:0.32, G:0.06, T:0.21
Consensus pattern (27 bp):
ACAACCATATCATCATGCATCCTCAAG
Found at i:20878006 original size:12 final size:12
Alignment explanation
Indices: 20877991--20878015 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20877981 CCCAATCAAA
20877991 TAATCAATTAAT
1 TAATCAATTAAT
20878003 TAATCAATTAAT
1 TAATCAATTAAT
20878015 T
1 T
20878016 CATACAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATCAATTAAT
Found at i:20879671 original size:78 final size:79
Alignment explanation
Indices: 20879542--20879716 Score: 235
Period size: 78 Copynumber: 2.2 Consensus size: 79
20879532 AGCACAAAAT
*
20879542 CCTGCTAGGCACTAAGCTTGAATAACACACTGACACGAAGCCTACTAGGCACTAAGCAT-TTAAC
1 CCTGCTAGGCACTAAGCTTGAATAACACACTGACACGAAGCCTACTAGGCACTAAGCATAATAAC
20879606 ACACAAGCATGAAG
66 ACACAAGCATGAAG
* * * * * *
20879620 CCTGCTAGGCACTATGCTTGAATAATACACTGGCAGGAAGCCTGCTAGGCACTAAGCCTGAATAA
1 CCTGCTAGGCACTAAGCTTGAATAACACACTGACACGAAGCCTACTAGGCACTAAGCAT-AATAA
**
20879685 CACACTGGCATGAAG
65 CACACAAGCATGAAG
* *
20879700 CCTGCTAAGTACTAAGC
1 CCTGCTAGGCACTAAGC
20879717 CTAAACAATC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
78 53 0.64
80 30 0.36
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (79 bp):
CCTGCTAGGCACTAAGCTTGAATAACACACTGACACGAAGCCTACTAGGCACTAAGCATAATAAC
ACACAAGCATGAAG
Found at i:20879717 original size:40 final size:40
Alignment explanation
Indices: 20879542--20879718 Score: 214
Period size: 40 Copynumber: 4.5 Consensus size: 40
20879532 AGCACAAAAT
* * *
20879542 CCTGCTAGGCACTAAGCTTGAATAACACACTGACACGAAG
1 CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
* * * **
20879582 CCTACTAGGCACTAAGCAT--TTAACACACAAGCATGAAG
1 CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
* * * *
20879620 CCTGCTAGGCACTATGCTTGAATAATACACTGGCAGGAAG
1 CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
20879660 CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
1 CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
* *
20879700 CCTGCTAAGTACTAAGCCT
1 CCTGCTAGGCACTAAGCCT
20879719 AAACAATCAT
Statistics
Matches: 114, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
38 30 0.26
40 84 0.74
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (40 bp):
CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
Found at i:20887845 original size:25 final size:25
Alignment explanation
Indices: 20887815--20887863 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
20887805 AAAATTGCCT
* * *
20887815 TTGTGGTAAGTTATCTATAAAGCCA
1 TTGTGGAAAATTATCTAAAAAGCCA
20887840 TTGTGGAAAATTATCTAAAAAGCC
1 TTGTGGAAAATTATCTAAAAAGCC
20887864 TATACGGCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (25 bp):
TTGTGGAAAATTATCTAAAAAGCCA
Found at i:20890578 original size:27 final size:27
Alignment explanation
Indices: 20890540--20890596 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
20890530 TAGAAATGAG
*
20890540 AATGATCCTGGTCTTAACAATAATCCA
1 AATGATCCTGGTCTCAACAATAATCCA
* *
20890567 AATGGTCCTGGTCTCAATAATAATCCA
1 AATGATCCTGGTCTCAACAATAATCCA
20890594 AAT
1 AAT
20890597 TTTTAGGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (27 bp):
AATGATCCTGGTCTCAACAATAATCCA
Found at i:20892325 original size:113 final size:112
Alignment explanation
Indices: 20892184--20892736 Score: 701
Period size: 113 Copynumber: 5.0 Consensus size: 112
20892174 TTTATTTTAT
* * *
20892184 AAAAAATCAATCTAT-AAAAAACAAAATAAAAAATATTTAGCATAGCAAAACGGCGTCATTTTGT
1 AAAAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGT
20892248 TCAAAATGAAATAATATTTTGCGGCGATTTTCATAAAAAACGCCGCAA
66 TCAAAATGAAATAATATTTTGCGGCG-TTTTCATAAAAAACGCCGCAA
* *
20892296 AAAAAATAAATTTATAAAAAAATAAAATAAAAAATTTTTAACATAGCAAAACGGCGTCATTTTGT
1 AAAAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGT
20892361 TCAAAATGAAATAATATTTTGCGGCGATTTTCATAAAAAACGCCGCAA
66 TCAAAATGAAATAATATTTTGCGGCG-TTTTCATAAAAAACGCCGCAA
* * *
20892409 AAAAAATAAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGTAAAACAGCGTCATTTTGT
1 AAAAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGT
* *
20892474 TCAAAATG--A-AATA----GCGGCGTTTT-GTATATAAACGCCGCAAA
66 TCAAAATGAAATAATATTTTGCGGCGTTTTCATA-AAAAACGCCGC-AA
* *
20892515 AAATAAATCAATTTATAGAAAAATAAAAT-AAAAATTTTTAGCATAACAAAACGGCGTCATTTTG
1 AAA-AAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTG
* * * ** *
20892579 TTTAAAAT--AA-AATA----ACGGTGTTTTTTTATAAAAACGCCACAA
65 TTCAAAATGAAATAATATTTTGCGGCGTTTTCATA-AAAAACGCCGCAA
* * *
20892621 AAATTAAATCAATTTATAAAAAAACAAAATAAAAAAATTTTAGCATAGCAAAACGGTGTCATTTT
1 AAA--AAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTT
* *
20892686 GTTCAAAATGAAATAATATTTTGCGGCGTTTTTATGAAAAACGCCG-AA
64 GTTCAAAATGAAATAATATTTTGCGGCGTTTTCATAAAAAACGCCGCAA
20892734 AAA
1 AAA
20892737 GATAAGCAAT
Statistics
Matches: 394, Mismatches: 32, Indels: 29
0.87 0.07 0.06
Matches are distributed among these distances:
104 2 0.01
105 14 0.04
106 68 0.17
107 59 0.15
108 39 0.10
110 6 0.02
111 5 0.01
112 13 0.03
113 169 0.43
114 9 0.02
115 10 0.03
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (112 bp):
AAAAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGT
TCAAAATGAAATAATATTTTGCGGCGTTTTCATAAAAAACGCCGCAA
Found at i:20892874 original size:107 final size:108
Alignment explanation
Indices: 20892754--20892948 Score: 313
Period size: 107 Copynumber: 1.8 Consensus size: 108
20892744 AATAGCGACG
*
20892754 TTTGTTATAAAAACGACGCAAAAAATAAATCAATTTATAAAGAAATAAAATAAAAAAA-ATTTAG
1 TTTGTTATAAAAACGACGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAAATA-TTAG
*
20892818 CATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAGCAGCGA
65 CATAGCAAAACGACGTCATTTTGTTCAAAATGAAATAGCAGCGA
** * *
20892862 TTTG-TATAAAAACGTTGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTATTAGT
1 TTTGTTATAAAAACGACGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAAATATTAGC
20892926 ATAGCAAAACGACGTCATTTTGT
66 ATAGCAAAACGACGTCATTTTGT
20892949 ATAAAAACGC
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
107 75 0.94
108 5 0.06
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (108 bp):
TTTGTTATAAAAACGACGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAAATATTAGC
ATAGCAAAACGACGTCATTTTGTTCAAAATGAAATAGCAGCGA
Found at i:20892948 original size:82 final size:82
Alignment explanation
Indices: 20892861--20893030 Score: 277
Period size: 82 Copynumber: 2.1 Consensus size: 82
20892851 AATAGCAGCG
** *
20892861 ATTTGTATAAAAACGTTGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTATTAGT
1 ATTTGTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTATTAGC
20892926 ATAGCAAAACGACGTCA
66 ATAGCAAAACGACGTCA
* * *
20892943 TTTTGTATAAAAACGCCGTAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGC
1 ATTTGTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTATTAGC
*
20893008 ATAGCAAAACGGCGTCA
66 ATAGCAAAACGACGTCA
20893025 ATTTGT
1 ATTTGT
20893031 TCCAAATGAA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (82 bp):
ATTTGTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTATTAGC
ATAGCAAAACGACGTCA
Found at i:20892991 original size:189 final size:189
Alignment explanation
Indices: 20892754--20893137 Score: 590
Period size: 189 Copynumber: 2.0 Consensus size: 189
20892744 AATAGCGACG
*
20892754 TTTGTTATAAAAACGACGCAAAAAATAAATCAATTTATAAAGAAATAAAATAAAAAAAATTTAGC
1 TTTG-TATAAAAACGACGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAAAATTTAGC
* * ***
20892819 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAGCAGCGATTTG-TATAAAAACGTTGCAAA
65 ATAGCAAAACGGCGTCAATTTGTTCAAAATGAAACAGCAGC-ATTTGTTATAAAAACGCCACAAA
* *
20892883 AAATAAATCAATTTATAAAAAAATAAAATAAAAAATTATTAGTATAGCAAAACGACGTCAT
129 AAATAAATCAATTTATAAAAAAATAAAATAAAAAATTATTAGCATAGCAAAACGACGTCAA
* * **
20892944 TTTGTATAAAAACGCCGTAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCA
1 TTTGTATAAAAACGACGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAAAATTTAGCA
* *
20893009 TAGCAAAACGGCGTCAATTTGTTCCAAATGAAACAGCGGCATTTGTTATAAAAACGCCACAAAAA
66 TAGCAAAACGGCGTCAATTTGTTCAAAATGAAACAGCAGCATTTGTTATAAAAACGCCACAAAAA
* * *
20893074 TTAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCAA
131 ATAAATCAATTTATAAAAAAATAAAATAAAAAATTATTAGCATAGCAAAACGACGTCAA
20893133 TTTGT
1 TTTGT
20893138 TCCAAATGAA
Statistics
Matches: 176, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
188 5 0.03
189 167 0.95
190 4 0.02
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (189 bp):
TTTGTATAAAAACGACGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAAAATTTAGCA
TAGCAAAACGGCGTCAATTTGTTCAAAATGAAACAGCAGCATTTGTTATAAAAACGCCACAAAAA
ATAAATCAATTTATAAAAAAATAAAATAAAAAATTATTAGCATAGCAAAACGACGTCAA
Found at i:20893052 original size:107 final size:107
Alignment explanation
Indices: 20892944--20893254 Score: 545
Period size: 107 Copynumber: 2.9 Consensus size: 107
20892934 ACGACGTCAT
** *
20892944 TTTG-TATAAAAACGCCGTAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGC
1 TTTGTTATAAAAACGCCACAAAAATTAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGC
20893008 ATAGCAAAACGGCGTCAATTTGTTCCAAATGAAACAGCGGCA
66 ATAGCAAAACGGCGTCAATTTGTTCCAAATGAAACAGCGGCA
20893050 TTTGTTATAAAAACGCCACAAAAATTAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGC
1 TTTGTTATAAAAACGCCACAAAAATTAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGC
20893115 ATAGCAAAACGGCGTCAATTTGTTCCAAATGAAACAGCGGCA
66 ATAGCAAAACGGCGTCAATTTGTTCCAAATGAAACAGCGGCA
* *
20893157 TTTGTTATAAAAACGCCACAAAAATTAAATCAATTTAT-AAAAAACAAAATAAAAAAATTTTAGC
1 TTTGTTATAAAAACGCCACAAAAATTAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGC
* *
20893221 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAA
66 ATAGCAAAACGGCGTCAATTTGTTCCAAATGAAA
20893255 TAATATTTTG
Statistics
Matches: 197, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
106 60 0.30
107 137 0.70
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (107 bp):
TTTGTTATAAAAACGCCACAAAAATTAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGC
ATAGCAAAACGGCGTCAATTTGTTCCAAATGAAACAGCGGCA
Found at i:20921336 original size:14 final size:15
Alignment explanation
Indices: 20921310--20921343 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
20921300 AAGAAGAAGC
20921310 AGAAATCTGGAGAAA
1 AGAAATCTGGAGAAA
20921325 AGAAAT-TGGAGAAA
1 AGAAATCTGGAGAAA
20921339 AGAAA
1 AGAAA
20921344 AGAAATGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.59, C:0.03, G:0.26, T:0.12
Consensus pattern (15 bp):
AGAAATCTGGAGAAA
Found at i:20921342 original size:19 final size:22
Alignment explanation
Indices: 20921320--20921364 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
20921310 AGAAATCTGG
20921320 AGAAAAGAAAT-TG-G-AGAAA
1 AGAAAAGAAATGTGAGAAGAAA
20921339 AGAAAAGAAATGTGAGAAGAAA
1 AGAAAAGAAATGTGAGAAGAAA
20921361 AGAA
1 AGAA
20921365 GCTTACAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.48
20 2 0.09
21 1 0.04
22 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (22 bp):
AGAAAAGAAATGTGAGAAGAAA
Found at i:20926443 original size:50 final size:50
Alignment explanation
Indices: 20926361--20926483 Score: 201
Period size: 50 Copynumber: 2.5 Consensus size: 50
20926351 TTACATTTCT
* *
20926361 AGTAAGGCATGTTAGTTGCTAACCAGCTTGGCGTTATGGGTGATGCCATC
1 AGTAGGGCATGTTAGTTGCTAACCAGCCTGGCGTTATGGGTGATGCCATC
* *
20926411 GGTAGGGCATGTTAGTTACTAACCAGCCTGGCGTTATGGGTGATGCCATC
1 AGTAGGGCATGTTAGTTGCTAACCAGCCTGGCGTTATGGGTGATGCCATC
*
20926461 AGTAGGGTATGTTAGTTGCTAAC
1 AGTAGGGCATGTTAGTTGCTAAC
20926484 AATGGCAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (50 bp):
AGTAGGGCATGTTAGTTGCTAACCAGCCTGGCGTTATGGGTGATGCCATC
Found at i:20926684 original size:66 final size:66
Alignment explanation
Indices: 20926578--20926709 Score: 219
Period size: 66 Copynumber: 2.0 Consensus size: 66
20926568 ATGGGATCCG
* * * *
20926578 AGGTTAGTACAAGGAAGGGCTTGGGAAATAGTGAGAAAATGTGAAAAATGGATTTCTTGTATATA
1 AGGTTAGCACAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
20926643 A
66 A
*
20926644 AGGTTAGCATAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
1 AGGTTAGCACAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
20926709 A
66 A
20926710 TGCATGTTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.41, C:0.05, G:0.29, T:0.26
Consensus pattern (66 bp):
AGGTTAGCACAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
A
Found at i:20928677 original size:35 final size:35
Alignment explanation
Indices: 20928637--20928705 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
20928627 GTGGTAGAAG
* *
20928637 TTAAAATAAGGAGGTAAAATGGTAAAGTGGTTAAA
1 TTAAAATAAGAAGGTAAAATGGTAAAGTGATTAAA
* *
20928672 TTAAAATAAGAAGGTGAAGTGGTAAAGTGATTAA
1 TTAAAATAAGAAGGTAAAATGGTAAAGTGATTAA
20928706 CTGTTTCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (35 bp):
TTAAAATAAGAAGGTAAAATGGTAAAGTGATTAAA
Found at i:20929044 original size:17 final size:16
Alignment explanation
Indices: 20929022--20929063 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
20929012 TCATTTGCTA
20929022 TCATTTTCTCATTTTTT
1 TCATTTTCTCA-TTTTT
20929039 TCA-TTTCTTCATTTTT
1 TCATTTTC-TCATTTTT
20929055 T-ATTTTCTC
1 TCATTTTCTC
20929064 TCTTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.13
16 14 0.61
17 6 0.26
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (16 bp):
TCATTTTCTCATTTTT
Found at i:20929070 original size:17 final size:17
Alignment explanation
Indices: 20929024--20929072 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
20929014 ATTTGCTATC
*
20929024 ATTTTCTCAT-TTTTTTC
1 ATTTTCTC-TCTTTTTTT
*
20929041 A-TTTCT-TCATTTTTT
1 ATTTTCTCTCTTTTTTT
20929056 ATTTTCTCTCTTTTTTT
1 ATTTTCTCTCTTTTTTT
20929073 GAAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
14 1 0.04
15 6 0.23
16 10 0.38
17 9 0.35
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTCTCTCTTTTTTT
Found at i:20930237 original size:14 final size:14
Alignment explanation
Indices: 20930215--20930249 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
20930205 AAATGTGAGC
*
20930215 ATGTTTACATGCAA
1 ATGTGTACATGCAA
20930229 ATGTGTACATGCAA
1 ATGTGTACATGCAA
20930243 ATGTGTA
1 ATGTGTA
20930250 TAATTGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (14 bp):
ATGTGTACATGCAA
Found at i:20930815 original size:19 final size:19
Alignment explanation
Indices: 20930788--20930836 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
20930778 TGCTCTTGGA
*
20930788 TATGAACTTTTTAATAAAT
1 TATGGACTTTTTAATAAAT
* * **
20930807 TATGGACTTTATATTATTT
1 TATGGACTTTTTAATAAAT
20930826 TATGGACTTTT
1 TATGGACTTTT
20930837 ATAGACTTTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (19 bp):
TATGGACTTTTTAATAAAT
Found at i:20931907 original size:18 final size:18
Alignment explanation
Indices: 20931884--20931920 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20931874 ACTCATGTAT
20931884 TATGTTGCTATGCGAACC
1 TATGTTGCTATGCGAACC
* *
20931902 TATGTTGTTTTGCGAACC
1 TATGTTGCTATGCGAACC
20931920 T
1 T
20931921 TAATAATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (18 bp):
TATGTTGCTATGCGAACC
Found at i:20934649 original size:2 final size:2
Alignment explanation
Indices: 20934642--20934666 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20934632 TGATTTTCTT
20934642 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20934667 TCTGTTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20936113 original size:283 final size:284
Alignment explanation
Indices: 20935748--20936316 Score: 1131
Period size: 283 Copynumber: 2.0 Consensus size: 284
20935738 ATTATCGGTC
20935748 TTTTAGCACTTTGGCAGATTTGAAACTTCCCAAACCCATACTTTGATGCCTAGACTTGTCCCGGC
1 TTTTAGCACTTTGGCAGATTTGAAACTTCCCAAACCCATACTTTGATGCCTAGACTTGTCCCGGC
20935813 GGTCGTCCCGAGTTGCCAGCTCGCCTGTCAAAAAGAGCAAAAGATCATTCAAAAAGATAAAGAAG
66 GGTCGTCCCGAGTTGCCAGCTCGCCTGTCAAAAAGAGCAAAAGATCATTCAAAAAGATAAAGAAG
20935878 CATTCAAGTGGCAACTTCTCTAGTGAAAAAGAAACATGCTACTTTAAAAATTTTGTACGCAATAG
131 CATTCAAGTGGCAACTTCTCTAGTGAAAAAGAAACATGCTACTTTAAAAATTTTGTACGCAATAG
20935943 ACTTGAGTTTAAATTTCAGCATTACAATTCATTCCTTTACTTCCATGTTAGAGTCTTTCGACCTC
196 ACTTGAGTTTAAATTTCAGCATTACAATTCATTCCTTTACTTCCATGTTAGAGTCTTTCGACCTC
20936008 TTATATATATTAT-AATATATATA
261 TTATATATATTATAAATATATATA
20936031 TTTTAGCACTTTGGCAGATTTGAAACTTCCCAAACCCATACTTTGATGCCTAGACTTGTCCCGGC
1 TTTTAGCACTTTGGCAGATTTGAAACTTCCCAAACCCATACTTTGATGCCTAGACTTGTCCCGGC
20936096 GGTCGTCCCGAGTTGCCAGCTCGCCTGTCAAAAAGAGCAAAAGATCATTCAAAAAGATAAAGAAG
66 GGTCGTCCCGAGTTGCCAGCTCGCCTGTCAAAAAGAGCAAAAGATCATTCAAAAAGATAAAGAAG
20936161 CATTCAAGTGGCAACTTCTCTAGTGAAAAAGAAACATGCTACTTTAAAAATTTTGTACGCAATAG
131 CATTCAAGTGGCAACTTCTCTAGTGAAAAAGAAACATGCTACTTTAAAAATTTTGTACGCAATAG
20936226 ACTTGAGTTTAAATTTCAGCATTACAATTCATTCCTTTACTTCCATGTTAGAGTCTTTCGACCTC
196 ACTTGAGTTTAAATTTCAGCATTACAATTCATTCCTTTACTTCCATGTTAGAGTCTTTCGACCTC
20936291 TTATATATATTATAAATATATATA
261 TTATATATATTATAAATATATATA
20936315 TT
1 TT
20936317 ACTATATTAT
Statistics
Matches: 285, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
283 273 0.96
284 12 0.04
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (284 bp):
TTTTAGCACTTTGGCAGATTTGAAACTTCCCAAACCCATACTTTGATGCCTAGACTTGTCCCGGC
GGTCGTCCCGAGTTGCCAGCTCGCCTGTCAAAAAGAGCAAAAGATCATTCAAAAAGATAAAGAAG
CATTCAAGTGGCAACTTCTCTAGTGAAAAAGAAACATGCTACTTTAAAAATTTTGTACGCAATAG
ACTTGAGTTTAAATTTCAGCATTACAATTCATTCCTTTACTTCCATGTTAGAGTCTTTCGACCTC
TTATATATATTATAAATATATATA
Found at i:20936658 original size:6 final size:6
Alignment explanation
Indices: 20936648--20936677 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
20936638 ACACATATAC
*
20936648 ATATGC ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA
20936678 TCTCAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (6 bp):
ATATGA
Found at i:20938047 original size:17 final size:19
Alignment explanation
Indices: 20938012--20938049 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
20938002 AATAATTTTT
20938012 AAATTATAAAAAATCTAAA
1 AAATTATAAAAAATCTAAA
*
20938031 AAATTA-AACAAAT-TAAA
1 AAATTATAAAAAATCTAAA
20938048 AA
1 AA
20938050 TTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 6 0.33
19 6 0.33
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATTATAAAAAATCTAAA
Found at i:20939032 original size:37 final size:31
Alignment explanation
Indices: 20938955--20939014 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
20938945 ATTATACTGT
**
20938955 TGGTTTTAATTATGGGGATTGGATGTGAAAA
1 TGGTTTTAATTATGGCCATTGGATGTGAAAA
20938986 TGGTTTTAATTATGGCCATTGGATGTGAA
1 TGGTTTTAATTATGGCCATTGGATGTGAA
20939015 TAAAATAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.03, G:0.30, T:0.40
Consensus pattern (31 bp):
TGGTTTTAATTATGGCCATTGGATGTGAAAA
Found at i:20942497 original size:30 final size:30
Alignment explanation
Indices: 20942462--20942524 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
20942452 ACACTGTTTC
20942462 CATTTACTGAAAGTATGTGATTAGTGAGGA
1 CATTTACTGAAAGTATGTGATTAGTGAGGA
* *
20942492 CATTTATTGAAAGTATGTGATTTGTGAGGA
1 CATTTACTGAAAGTATGTGATTAGTGAGGA
20942522 CAT
1 CAT
20942525 GCTGAGCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (30 bp):
CATTTACTGAAAGTATGTGATTAGTGAGGA
Found at i:20960069 original size:12 final size:13
Alignment explanation
Indices: 20960052--20960081 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
20960042 CTCATACATG
20960052 AATAAATAAA-GC
1 AATAAATAAATGC
20960064 AATAAATAAATGC
1 AATAAATAAATGC
20960077 AATAA
1 AATAA
20960082 TTATAGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:20983401 original size:20 final size:20
Alignment explanation
Indices: 20983378--20983428 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
20983368 TATGTACGTA
*
20983378 TATATATATATTATACTTTC
1 TATATATATATTATAATTTC
* *
20983398 TATACATATTTTATAATTTC
1 TATATATATATTATAATTTC
20983418 TATATATATAT
1 TATATATATAT
20983429 ATATGTAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATATATTATAATTTC
Found at i:20983437 original size:108 final size:113
Alignment explanation
Indices: 20983318--20983543 Score: 309
Period size: 108 Copynumber: 2.0 Consensus size: 113
20983308 TTTTTAAGTT
* * * * *
20983318 TATATATGTAATTATTATTTTTATGATTTATAAATTTATT-AC-CT-TATATATATGTACGTA-T
1 TATATATGTAATCATTATCTTTATGATCTATAAATTTATTAACTATATATATATATATACGTACT
* *
20983379 ATATATATATTATACTTTCTATACATATTTTATAA-TTTCTATATATA
66 ATATACATATTATACTTTCCATACATATTTTATAATTTTCTATATATA
* *
20983426 TATATATGTAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATATATATGTAC
1 TATATATGTAATCATTATCTTTATGATCTATAAATTTATTAAC-TATATATATATATATACGTAC
*
20983491 GTATATACATATTATACTTTCCATACATATTTTATAATTTTCTATATGTA
65 -TATATACATATTATACTTTCCATACATATTTTATAATTTTCTATATATA
20983541 TAT
1 TAT
20983544 TTTCTTTATT
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
108 36 0.36
109 2 0.02
111 1 0.01
112 14 0.14
114 34 0.34
115 14 0.14
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (113 bp):
TATATATGTAATCATTATCTTTATGATCTATAAATTTATTAACTATATATATATATATACGTACT
ATATACATATTATACTTTCCATACATATTTTATAATTTTCTATATATA
Found at i:20983476 original size:54 final size:53
Alignment explanation
Indices: 20983318--20983489 Score: 172
Period size: 54 Copynumber: 3.2 Consensus size: 53
20983308 TTTTTAAGTT
* * * * *
20983318 TATATATGTAATTATTATTTTTATGATTTATAAATTTATTACCTTATATATATG
1 TATATATGTAA-TATTATCTTTATGATCTATATATTTATTAACTTATATATATA
* * * *
20983372 TACGTATATATATATATTATACTTTCT-ATAC-ATAT-TTTA-TAATTTCTATATATA
1 TA--TATATGTA-ATATTAT-CTTTATGAT-CTATATATTTATTAACTTATATATATA
20983426 TATATATGTAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATA
1 TATATATGTAAT-ATTATCTTTATGATCTATATATTTATTAACTTATATATATA
20983480 TATATATGTA
1 TATATATGTA
20983490 CGTATATACA
Statistics
Matches: 95, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
51 8 0.08
52 18 0.19
53 4 0.04
54 38 0.40
55 4 0.04
56 18 0.19
57 5 0.05
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (53 bp):
TATATATGTAATATTATCTTTATGATCTATATATTTATTAACTTATATATATA
Found at i:20983881 original size:16 final size:16
Alignment explanation
Indices: 20983856--20983887 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20983846 CTTTTACTCG
20983856 ATTTTAAAAATAGAAA
1 ATTTTAAAAATAGAAA
*
20983872 ATTTTTAAAATAGAAA
1 ATTTTAAAAATAGAAA
20983888 TAATACTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
ATTTTAAAAATAGAAA
Found at i:20984906 original size:96 final size:96
Alignment explanation
Indices: 20984786--20984969 Score: 305
Period size: 96 Copynumber: 1.9 Consensus size: 96
20984776 TACTTTCTTA
*
20984786 TCTAGTTGGATATTTAATTAGACATTGGAAACCCTTATGATCTTTTGAACTAGACCAATAACATT
1 TCTAGTTGGATATTTAATTAGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATT
**
20984851 GCACAAAAGGTGATTTCTCAATCATCTTCTC
66 GCACAAAAGGTGATAGCTCAATCATCTTCTC
* * * *
20984882 TCTATTTGGATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACTAATAATATT
1 TCTAGTTGGATATTTAATTAGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATT
20984947 GCACAAAAGGTGATAGCTCAATC
66 GCACAAAAGGTGATAGCTCAATC
20984970 GTATTCCTCC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (96 bp):
TCTAGTTGGATATTTAATTAGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATT
GCACAAAAGGTGATAGCTCAATCATCTTCTC
Found at i:20993652 original size:11 final size:12
Alignment explanation
Indices: 20993627--20993653 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20993617 CATTTTAGTA
20993627 TTTTTGTTCATT
1 TTTTTGTTCATT
20993639 TTTTTGTTCATT
1 TTTTTGTTCATT
20993651 TTT
1 TTT
20993654 CCATAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTGTTCATT
Found at i:20999190 original size:10 final size:9
Alignment explanation
Indices: 20999177--20999222 Score: 51
Period size: 8 Copynumber: 5.1 Consensus size: 9
20999167 CTCTTTTTCC
20999177 TTATTTTATT
1 TTATTTTA-T
20999187 TTATTTTAT
1 TTATTTTAT
*
20999196 TTA-TTTAC
1 TTATTTTAT
20999204 TTA-TTTAT
1 TTATTTTAT
20999212 TTATTATTAT
1 TTATT-TTAT
20999222 T
1 T
20999223 CGTATGTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 14 0.44
9 5 0.16
10 13 0.41
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTAT
Found at i:21000981 original size:6 final size:6
Alignment explanation
Indices: 21000970--21001026 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
21000960 AGTTTATTTG
* * *
21000970 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TATTGT TTGTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
21001018 TGTTAT TTT
1 TTTTAT TTT
21001027 CTTCAATTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:21009610 original size:25 final size:24
Alignment explanation
Indices: 21009559--21009612 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
21009549 GTCAGTAGGG
*
21009559 TTACCGATTTCAGCTCGTGAGAGC
1 TTACCGATTTCAGCTCGTGAGACC
*
21009583 TTACTGATTCTCAGCTCGT-ATGACC
1 TTACCGATT-TCAGCTCGTGA-GACC
21009608 TTACC
1 TTACC
21009613 AATATTCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (24 bp):
TTACCGATTTCAGCTCGTGAGACC
Found at i:21009908 original size:24 final size:23
Alignment explanation
Indices: 21009876--21009920 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
21009866 AGGTTATTAC
21009876 ATGATACATAGTTATAT-GAAATGG
1 ATGATACAT-G-TATATGGAAATGG
21009900 ATGATACATGTATATGGAAAT
1 ATGATACATGTATATGGAAAT
21009921 ATGATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.33
Consensus pattern (23 bp):
ATGATACATGTATATGGAAATGG
Found at i:21011837 original size:50 final size:50
Alignment explanation
Indices: 21011720--21011940 Score: 225
Period size: 50 Copynumber: 4.4 Consensus size: 50
21011710 AATGGGTAAA
* * *
21011720 GCCATGTCCCAGACATGGTCTTACATGGGATG-TTTCAT-GCATTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-GCTCTCATCTCAGTGCCAAT
* * * * * * *
21011769 GCCATATCCCAGATATGGTCTTATATGGGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCAGTGCCAAT
** * *
21011819 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCTTCTCAGTGCCAACT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCAGTGCCAA-T
* * *
21011870 -CCATGTCCCAGACATGGTCTTACATGGG-GCCTCTCCTCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGAG-CTCTCATCTCAGTGCCAAT
*
21011919 GCCATGTCCCAGACATGCTCTT
1 GCCATGTCCCAGACATGGTCTT
21011941 CTCGGTGCCA
Statistics
Matches: 141, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 32 0.23
50 107 0.76
51 1 0.01
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATCTCAGTGCCAAT
Found at i:21011897 original size:100 final size:99
Alignment explanation
Indices: 21011720--21011940 Score: 252
Period size: 100 Copynumber: 2.2 Consensus size: 99
21011710 AATGGGTAAA
* * * *
21011720 GCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGCATTGCCAATGCCATATCCCAGATAT
1 GCCATGTCCCAGACATGGTCTTACAGGGGATCTTTCATGCAGTGCCAATGCCATATCCCAGACAT
* * * *
21011785 GGTCTTATATGGGAG-TTCTCATATCGGTGCCCAT
66 GGTCTTACATGGG-GCCTCTCATATCGGTGCCAAC
* *
21011819 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCTTC-T-CAGTGCCAACT-CCATGTCCCAG
1 GCCATGTCCCAGACATGGTCTTACAGGGGA--TCT-TTCATGCAGTGCCAA-TGCCATATCCCAG
* *
21011881 ACATGGTCTTACATGGGGCCTCTCCTCTCGGTGCCAAC
62 ACATGGTCTTACATGGGGCCTCTCATATCGGTGCCAAC
*
21011919 GCCATGTCCCAGACATGCTCTT
1 GCCATGTCCCAGACATGGTCTT
21011941 CTCGGTGCCA
Statistics
Matches: 104, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
99 29 0.28
100 68 0.65
101 4 0.04
102 3 0.03
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.28
Consensus pattern (99 bp):
GCCATGTCCCAGACATGGTCTTACAGGGGATCTTTCATGCAGTGCCAATGCCATATCCCAGACAT
GGTCTTACATGGGGCCTCTCATATCGGTGCCAAC
Found at i:21016887 original size:17 final size:18
Alignment explanation
Indices: 21016859--21016892 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21016849 TCTCCCAAAA
*
21016859 TTCAATTTTATTTAATTT
1 TTCAATTTTATTAAATTT
21016877 TTCAA-TTTATTAAATT
1 TTCAATTTTATTAAATT
21016893 ATTAGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCAATTTTATTAAATTT
Found at i:21031811 original size:31 final size:32
Alignment explanation
Indices: 21031776--21031836 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
21031766 TATTTTATTC
*
21031776 TTAA-TTTTGTTATTATTTTAAAGGCATTTTT
1 TTAATTTTTGTTATTATTTTAAAAGCATTTTT
21031807 TTAATTTTTGTTATTATTTTAAAAGCATTT
1 TTAATTTTTGTTATTATTTTAAAAGCATTT
21031837 ACGTTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (32 bp):
TTAATTTTTGTTATTATTTTAAAAGCATTTTT
Found at i:21031968 original size:11 final size:11
Alignment explanation
Indices: 21031952--21031982 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
21031942 TATATATATT
21031952 TAAAAATTATA
1 TAAAAATTATA
*
21031963 TAAAAATAATA
1 TAAAAATTATA
21031974 TAAAAATTA
1 TAAAAATTA
21031983 ATACGGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:21039295 original size:16 final size:16
Alignment explanation
Indices: 21039271--21039338 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
21039261 TCAAGATAAG
*
21039271 TATTGGATAAATTTAA
1 TATTAGATAAATTTAA
*
21039287 TATTAGATATA-TTAA
1 TATTAGATAAATTTAA
*
21039302 -ATTA-ATAGAATATAA
1 TATTAGATA-AATTTAA
* *
21039317 TATTAAATTTAATTTAA
1 TATTAGA-TAAATTTAA
21039334 TATTA
1 TATTA
21039339 AATTTATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 3 0.07
14 5 0.12
15 7 0.17
16 13 0.32
17 12 0.29
18 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (16 bp):
TATTAGATAAATTTAA
Found at i:21039352 original size:17 final size:17
Alignment explanation
Indices: 21039315--21039349 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21039305 AATAGAATAT
*
21039315 AATATTAAATTTAATTT
1 AATATTAAATTTAATTA
21039332 AATATTAAATTT-ATTA
1 AATATTAAATTTAATTA
21039348 AA
1 AA
21039350 ATAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTAAATTTAATTA
Found at i:21042840 original size:11 final size:11
Alignment explanation
Indices: 21042810--21042843 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
21042800 ATCGCAAGTG
21042810 AATTAATTCTAA
1 AATTAATTC-AA
*
21042822 AATAAATTCAA
1 AATTAATTCAA
21042833 AATTAATTCAA
1 AATTAATTCAA
21042844 CTTGGGTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (11 bp):
AATTAATTCAA
Found at i:21043177 original size:20 final size:19
Alignment explanation
Indices: 21043135--21043181 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
21043125 ACATAAGTTC
21043135 TAATTAAAGTAAGTTAAGT
1 TAATTAAAGTAAGTTAAGT
*
21043154 TAATTAAA-TAAAGATTATGT
1 TAATTAAAGT-AAG-TTAAGT
21043174 TAATTAAA
1 TAATTAAA
21043182 CCAAATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 11 0.44
20 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
TAATTAAAGTAAGTTAAGT
Found at i:21067799 original size:73 final size:73
Alignment explanation
Indices: 21067680--21067834 Score: 242
Period size: 73 Copynumber: 2.1 Consensus size: 73
21067670 AAAAAATATC
*
21067680 AAATAAAATCTTGTTAAACAGCGGGAATAAATTCTGAAACAGATTTTATTTAATTCAATTC-AAT
1 AAATAAAATCTTGTTAAACAGCGGGAATAAATTCTGAAACAGATTTT-TTTAAATCAATTCTAAT
21067744 TTGGAAACA
65 TTGGAAACA
* * *
21067753 AAATAAAATCTTGTTAAATAGTGGGAATAAA-TCTCGAAACAGATTTTTTTAAATCTATTCTAAT
1 AAATAAAATCTTGTTAAACAGCGGGAATAAATTCT-GAAACAGATTTTTTTAAATCAATTCTAAT
21067817 TTGGAAACA
65 TTGGAAACA
21067826 AAATAAAAT
1 AAATAAAAT
21067835 GAAATAAAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
72 14 0.18
73 62 0.82
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.34
Consensus pattern (73 bp):
AAATAAAATCTTGTTAAACAGCGGGAATAAATTCTGAAACAGATTTTTTTAAATCAATTCTAATT
TGGAAACA
Found at i:21067984 original size:87 final size:88
Alignment explanation
Indices: 21067822--21068009 Score: 236
Period size: 87 Copynumber: 2.1 Consensus size: 88
21067812 CTAATTTGGA
* * * *
21067822 AACAAAATAAAATGAAATAAAATATTGTTAAATGACGAGAAAAAAAATCCCAAAATAGATTTTAT
1 AACAAAATCAAATCAAATAAAATATTATTAAATGACGAG-AAAAAAATCACAAAATAGATTTTAT
21067887 TTAATTTAATTTCTC-GTTTTTGAC
65 TTAATTTAATTTCTCAGTTTTTG-C
* * * * * *
21067911 AACAAAATCAAATCAAATAAATTTTTATTAAATGATGAG-AATAAATCACGAAATATATTTTATT
1 AACAAAATCAAATCAAATAAAATATTATTAAATGACGAGAAAAAAATCACAAAATAGATTTTATT
* *
21067975 TAATTTAATTTTTCATTTTTTGC
66 TAATTTAATTTCTCAGTTTTTGC
21067998 AACAAAATCAAA
1 AACAAAATCAAA
21068010 ATGTAATAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
87 47 0.55
88 6 0.07
89 33 0.38
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (88 bp):
AACAAAATCAAATCAAATAAAATATTATTAAATGACGAGAAAAAAATCACAAAATAGATTTTATT
TAATTTAATTTCTCAGTTTTTGC
Found at i:21070649 original size:39 final size:39
Alignment explanation
Indices: 21070606--21070693 Score: 90
Period size: 39 Copynumber: 2.2 Consensus size: 39
21070596 GGCCCATTTT
*
21070606 TAAAATAAA-CATTAAAAAATTATTTTAAAAATAAAAAAA
1 TAAAATAAATCATTAAAAAAGTATTTT-AAAATAAAAAAA
* ** *
21070645 TAAAA-AAATTTATTTTAAAAGTATTTTAAAATTAAAAAA
1 TAAAATAAA-TCATTAAAAAAGTATTTTAAAATAAAAAAA
21070684 TAAAAATAAA
1 T-AAAATAAA
21070694 AAATATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
38 3 0.08
39 17 0.43
40 17 0.43
41 3 0.08
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (39 bp):
TAAAATAAATCATTAAAAAAGTATTTTAAAATAAAAAAA
Found at i:21070655 original size:25 final size:25
Alignment explanation
Indices: 21070601--21070655 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 25
21070591 GGCCCGGCCC
* * *
21070601 ATTTTTAAAATAAACATTAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAA-T
21070627 ATTTTAAAAATAAAAAAATAAAAAA-
1 ATTTTAAAAAT-AAAAAATAAAAAAT
21070652 ATTT
1 ATTT
21070656 ATTTTAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.16
26 10 0.40
27 11 0.44
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
ATTTTAAAAATAAAAAATAAAAAAT
Found at i:21070664 original size:28 final size:25
Alignment explanation
Indices: 21070603--21070664 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 25
21070593 CCCGGCCCAT
* *
21070603 TTTTAAAATAAACATTAAAAAATTA
1 TTTTAAAATAAAAATAAAAAAATTA
21070628 TTTTAAAAATAAAAAAATAAAAAAATTTA
1 TTTT-AAAAT--AAAAATAAAAAAA-TTA
21070657 TTTTAAAA
1 TTTTAAAA
21070665 GTATTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 4 0.13
26 5 0.16
28 15 0.48
29 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
TTTTAAAATAAAAATAAAAAAATTA
Found at i:21077229 original size:20 final size:20
Alignment explanation
Indices: 21077206--21077245 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21077196 TATATAAAAA
21077206 TAAAATTACATATAGAGGAG
1 TAAAATTACATATAGAGGAG
21077226 TAAAATTACATATAGAGGAG
1 TAAAATTACATATAGAGGAG
21077246 CTCTTTTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (20 bp):
TAAAATTACATATAGAGGAG
Found at i:21078276 original size:152 final size:152
Alignment explanation
Indices: 21077995--21078311 Score: 528
Period size: 152 Copynumber: 2.1 Consensus size: 152
21077985 AAGTCTAAAT
* *
21077995 ACCATAAGAAATTAGTTTAAATATAACAAAAATATTATTAAGCACATAATAATCAAACATGCAAT
1 ACCAAAAGAAATTAGTTTAAATATAACAAAAAGATTATTAAGCACATAATAATCAAACATGCAAT
*
21078060 CTTTATGTGCATGATTATGATAATCCAAATATTTTTATAAAACATATATGCAAGTTTTCTAAAAT
66 CTTTATGTGCATGATTACGATAATCCAAATATTTTTATAAAACATATATGCAAGTTTTCTAAAAT
*
21078125 TTCCTACCCATTTCCGCTGCAC
131 TTCCTACCCATTTCCGCTACAC
* *
21078147 ACTAAAAGAAATTAGTTTAAATATAACAAAAAGATTGTTAAGCACATAATAATCAAACATGCAAT
1 ACCAAAAGAAATTAGTTTAAATATAACAAAAAGATTATTAAGCACATAATAATCAAACATGCAAT
*
21078212 CTTTATGTGCATGATTACGATAATGCAAATATTTTTATAAAACATATATG-ACAGTTTTCTAAAA
66 CTTTATGTGCATGATTACGATAATCCAAATATTTTTATAAAACATATATGCA-AGTTTTCTAAAA
* *
21078276 TTTCTTACCCATTTCTGCTACAC
130 TTTCCTACCCATTTCCGCTACAC
*
21078299 ACCAAAAGGAATT
1 ACCAAAAGAAATT
21078312 CCTCAAAAAT
Statistics
Matches: 153, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
151 1 0.01
152 152 0.99
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (152 bp):
ACCAAAAGAAATTAGTTTAAATATAACAAAAAGATTATTAAGCACATAATAATCAAACATGCAAT
CTTTATGTGCATGATTACGATAATCCAAATATTTTTATAAAACATATATGCAAGTTTTCTAAAAT
TTCCTACCCATTTCCGCTACAC
Found at i:21086190 original size:21 final size:23
Alignment explanation
Indices: 21086166--21086218 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
21086156 CTAATTATTC
21086166 TAAAAAAA-T-ACAAAAATAAAA
1 TAAAAAAATTAACAAAAATAAAA
21086187 TAAAATGAAATTGAACAAAAATAAAA
1 TAAAA--AAATT-AACAAAAATAAAA
21086213 TAAAAA
1 TAAAAA
21086219 GAAAATTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 5 0.19
23 3 0.11
24 2 0.07
26 17 0.63
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (23 bp):
TAAAAAAATTAACAAAAATAAAA
Found at i:21092111 original size:23 final size:23
Alignment explanation
Indices: 21092077--21092121 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
21092067 ACGCCAGTTC
*
21092077 TGTAATATCCTGAAAATTACTAT
1 TGTAATACCCTGAAAATTACTAT
21092100 TGTAATACCCTGAAAATTACTA
1 TGTAATACCCTGAAAATTACTA
21092122 CAGTGAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (23 bp):
TGTAATACCCTGAAAATTACTAT
Found at i:21095216 original size:50 final size:50
Alignment explanation
Indices: 21095119--21095406 Score: 326
Period size: 50 Copynumber: 5.6 Consensus size: 50
21095109 TGTGAGCCAG
* *
21095119 TGTAAGACCATGTCTGGAACATGGCATTGGCATTCTTGAGATTATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA--C-CGAG---ATGAGAGGTCCCA
21095175 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * *
21095225 TGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGTGGGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * * * *
21095275 TGTAAAACCATGTTTGGGACATGGCGTTGGCACCGGGATGATAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * * **
21095325 CGTATGACCATGTCTAGGACATGGCATGGGCACCG-GTATGAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG-ATGAGAGGTCCCA
* *
21095375 TGTAAGACCATATCTGGGATATGGCATTGGCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA
21095407 GTATAGAAAA
Statistics
Matches: 200, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
49 1 0.00
50 164 0.82
53 3 0.01
54 1 0.00
56 31 0.16
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.23
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
Found at i:21110142 original size:41 final size:41
Alignment explanation
Indices: 21110096--21110179 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
21110086 TATTATATAA
21110096 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
1 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
21110137 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
1 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
21110178 CC
1 CC
21110180 GTATCGAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (41 bp):
CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
Found at i:21119256 original size:25 final size:25
Alignment explanation
Indices: 21119239--21119350 Score: 161
Period size: 25 Copynumber: 4.5 Consensus size: 25
21119229 CAGCTCATAT
*
21119239 GAGCTTACCGTTATTCAGCTTGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
* * * *
21119264 AAGCTTCCCGTTATTCAACTCAGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
* *
21119289 GAGTTTACCATTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
21119314 GAGCTTACCGTTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
21119339 GAGCTTACCGTT
1 GAGCTTACCGTT
21119351 TACAGCTTGT
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.30
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCGGAG
Found at i:21126817 original size:54 final size:54
Alignment explanation
Indices: 21126690--21126818 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 54
21126680 CAGAATAGGT
* * * *** *
21126690 CTTACACAATGTGGTCTTCATTACCCCATATGATGCCACAGCAAATGGCTAGGC
1 CTTACACTATATGGTCTTCTTTACCCCATATGATGCCACAGCAAACAACTAAGC
* * ** *
21126744 CTTACACTATATGCTCTTCTTTTCCCTGTATGATGCCATAGCAAACAACTAAGC
1 CTTACACTATATGGTCTTCTTTACCCCATATGATGCCACAGCAAACAACTAAGC
21126798 CTTACACTATATGGTCTTCTT
1 CTTACACTATATGGTCTTCTT
21126819 GCCATGGTCA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (54 bp):
CTTACACTATATGGTCTTCTTTACCCCATATGATGCCACAGCAAACAACTAAGC
Found at i:21128111 original size:20 final size:20
Alignment explanation
Indices: 21128086--21128124 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
21128076 TACTTTCTTT
21128086 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
21128106 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
21128125 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:21128492 original size:50 final size:49
Alignment explanation
Indices: 21128420--21128541 Score: 147
Period size: 49 Copynumber: 2.5 Consensus size: 49
21128410 TACCCCAGAT
* **
21128420 ATGGTCTTACATGGGAGTTCTCATATCGGTGCC-CATGCCATGTCCCAGGC
1 ATGGTCTTACGTGGGACCTCTCATATCGGTGCCACA--CCATGTCCCAGGC
* * * * *
21128470 ATGGTCTTACGGGGGACCTCTCATCTTGGTGCCACACCATGTCCCTGTC
1 ATGGTCTTACGTGGGACCTCTCATATCGGTGCCACACCATGTCCCAGGC
21128519 ATGGTCTTACGTGGGACCTCTCA
1 ATGGTCTTACGTGGGACCTCTCA
21128542 AAATCTCAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 33 0.53
50 27 0.44
51 2 0.03
ACGTcount: A:0.16, C:0.30, G:0.25, T:0.29
Consensus pattern (49 bp):
ATGGTCTTACGTGGGACCTCTCATATCGGTGCCACACCATGTCCCAGGC
Found at i:21132707 original size:16 final size:16
Alignment explanation
Indices: 21132686--21132716 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21132676 GGCACTAATA
*
21132686 TTACTTTCTCCAACTG
1 TTACTTGCTCCAACTG
21132702 TTACTTGCTCCAACT
1 TTACTTGCTCCAACT
21132717 CCCAGATTCC
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:0.19, C:0.32, G:0.06, T:0.42
Consensus pattern (16 bp):
TTACTTGCTCCAACTG
Found at i:21140051 original size:14 final size:14
Alignment explanation
Indices: 21140027--21140060 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
21140017 GGTAGCTTGT
21140027 TTGTGTCACTTTAGG
1 TTGT-TCACTTTAGG
21140042 TTGTTCACTTTAGG
1 TTGTTCACTTTAGG
21140056 TTGTT
1 TTGTT
21140061 TGTGTTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.53
Consensus pattern (14 bp):
TTGTTCACTTTAGG
Found at i:21148533 original size:51 final size:52
Alignment explanation
Indices: 21148444--21148542 Score: 150
Period size: 51 Copynumber: 1.9 Consensus size: 52
21148434 TACATGACTA
*
21148444 AATTTAATGATGTAAACTTTAACTAACATAGGAGTTACATAAATGCATGTCAT
1 AATTTAATGATGCAAACTTTAACTAACATAGGAGTTACAT-AATGCATGTCAT
21148497 AATTT-ATGATGCAAAC-TTAACTAACAT-GAGAGTTACATAATGCATG
1 AATTTAATGATGCAAACTTTAACTAACATAG-GAGTTACATAATGCATG
21148543 ACTTTATTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
50 9 0.20
51 20 0.45
52 10 0.23
53 5 0.11
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (52 bp):
AATTTAATGATGCAAACTTTAACTAACATAGGAGTTACATAATGCATGTCAT
Found at i:21153221 original size:20 final size:22
Alignment explanation
Indices: 21153196--21153243 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
21153186 TGAATCTGTC
21153196 AAAAATAA-T-AAAAATTCACT
1 AAAAATAATTGAAAAATTCACT
* *
21153216 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGAAAAATTCACT
21153238 AAAAAT
1 AAAAAT
21153244 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGAAAAATTCACT
Found at i:21153281 original size:19 final size:19
Alignment explanation
Indices: 21153257--21153336 Score: 69
Period size: 18 Copynumber: 4.3 Consensus size: 19
21153247 CATGTTCAAA
* *
21153257 ATTTTAATATAATTTAATT
1 ATTTTAATAAAAATTAATT
*
21153276 ATTTT-ATAAAAATTAA-A
1 ATTTTAATAAAAATTAATT
*
21153293 ATTTTTAA-AATAATTTAATT
1 A-TTTTAATAA-AAATTAATT
*
21153313 ATTTT-ATAAAAATTATTT
1 ATTTTAATAAAAATTAATT
21153331 ATTTTA
1 ATTTTA
21153337 TGACAAAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
17 1 0.02
18 28 0.58
19 18 0.38
20 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTAATAAAAATTAATT
Found at i:21153336 original size:37 final size:36
Alignment explanation
Indices: 21153254--21153327 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 36
21153244 TAACATGTTC
*
21153254 AAAATTTTAATATAATTTAATTATTTTATAAAAATT
1 AAAATTTTAAAATAATTTAATTATTTTATAAAAATT
21153290 AAAATTTTTAAAATAATTTAATTATTTTATAAAAATT
1 AAAA-TTTTAAAATAATTTAATTATTTTATAAAAATT
21153327 A
1 A
21153328 TTTATTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 4 0.11
37 32 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
AAAATTTTAAAATAATTTAATTATTTTATAAAAATT
Found at i:21153482 original size:24 final size:25
Alignment explanation
Indices: 21153441--21153487 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
21153431 AAATTCCAGA
*
21153441 AAGAATTTCTCAGAAAC-ACTTTTG
1 AAGAATTCCTCAGAAACAACTTTTG
21153465 AAGAATTCCTTCAG-AACAACTTT
1 AAGAATTCC-TCAGAAACAACTTT
21153488 CTTCTCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (25 bp):
AAGAATTCCTCAGAAACAACTTTTG
Found at i:21163640 original size:22 final size:21
Alignment explanation
Indices: 21163615--21163658 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
21163605 TGATAAACTT
21163615 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
21163637 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
21163658 T
1 T
21163659 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:21167041 original size:42 final size:41
Alignment explanation
Indices: 21166985--21167200 Score: 185
Period size: 33 Copynumber: 5.5 Consensus size: 41
21166975 ATTCCCACAA
21166985 GGGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAG
1 GGGGTTGCTAAGTGCTGATTCCACCGTA-TTTAAATGTGAAG
* * *
21167027 GGGGTTGCTAAGTGCTGATTCC-TCG-A-AT-CAT-T---G
1 GGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAG
* *
21167060 GTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAA
1 GGGGTTGCTAAGTGCTGATTCCACCGTAT-TTAAATGTGAAG
* *
21167102 GGGGTTGCTAAGTGCTGATTCC-CAG-A-TT-CAT-T---G
1 GGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAG
* * *
21167135 GTGGTTGCTAAGTGCTGATTCCACCATATTTTTAAATGTGGAAA
1 GGGGTTGCTAAGTGCTGATTCCACCGTA--TTTAAATGT-GAAG
21167179 GGGGTTGCTAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATTCC
21167201 CCGAATCATT
Statistics
Matches: 136, Mismatches: 18, Indels: 38
0.71 0.09 0.20
Matches are distributed among these distances:
33 43 0.32
34 3 0.02
35 2 0.01
36 2 0.01
37 5 0.04
38 7 0.05
39 3 0.02
40 3 0.02
41 4 0.03
42 43 0.32
44 21 0.15
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (41 bp):
GGGGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAG
Found at i:21167071 original size:33 final size:33
Alignment explanation
Indices: 21167029--21167229 Score: 143
Period size: 33 Copynumber: 5.5 Consensus size: 33
21167019 ATGTGAAGGG
*
21167029 GGTTGCTAAGTGCTGATTCCTCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
21167062 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
* *
21167104 GGTTGCTAAGTGCTGATTCCCAGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
21167137 GGTTGCTAAGTGCTGATTCCACC-ATATTTTTAAATGTGGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGA-A----T-CAT-T-G---GT
21167181 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
21167214 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
21167230 ATCCACCGGT
Statistics
Matches: 133, Mismatches: 13, Indels: 44
0.70 0.07 0.23
Matches are distributed among these distances:
33 59 0.44
34 6 0.05
36 3 0.02
37 3 0.02
38 5 0.04
39 5 0.04
40 1 0.01
41 5 0.04
42 21 0.16
43 3 0.02
44 22 0.17
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:21167086 original size:75 final size:74
Alignment explanation
Indices: 21166958--21167237 Score: 426
Period size: 75 Copynumber: 3.8 Consensus size: 74
21166948 GAAAATAAAG
*
21166958 GGGGTTGCTAAGTGCTGATTCCC--A-CA-AGG-GGTTGCTAAGTGCTGATTCCACCGTATTTTA
1 GGGGTTGCTAAGTGCTGATTCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTA
*
21167018 AATGTGAAG
66 AATGTGAAA
*
21167027 GGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCC-CGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTT
21167092 AAATGTGAAA
65 AAATGTGAAA
* *
21167102 GGGGTTGCTAAGTGCTGATTCCCAGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCC-GAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA-TTT
21167167 TAAATGTGGAAA
64 TAAATGT-GAAA
*
21167179 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAATCCACCG
1 GGGGTTGCTAAGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
21167238 GTAACGGATA
Statistics
Matches: 192, Mismatches: 9, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
69 22 0.11
70 1 0.01
72 1 0.01
73 2 0.01
74 3 0.02
75 95 0.49
76 9 0.05
77 56 0.29
78 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (74 bp):
GGGGTTGCTAAGTGCTGATTCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTA
AATGTGAAA
Found at i:21167221 original size:152 final size:144
Alignment explanation
Indices: 21166958--21167237 Score: 443
Period size: 152 Copynumber: 1.9 Consensus size: 144
21166948 GAAAATAAAG
*
21166958 GGGGTTGCTAAGTGCTGATTCCCACAAGGGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGT
1 GGGGTTGCTAAGTGCTGATTCCCACAAGGGGTTGCTAAGTGCTGATTCCACCATATTTTAAATGT
* * *
21167023 GAAGGGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA
66 GAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAATCCACCGTA
21167088 TCTTAAATGTGAAA
131 TCTTAAATGTGAAA
*
21167102 GGGGTTGCTAAGTGCTGATTCCCAGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCC--A--CA-AGG-GGTTGCTAAGTGCTGATTCCACCATA-TTT
21167167 TAAATGTGGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAAT
59 TAAATGT-GAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAAT
21167232 CCACCG
123 CCACCG
21167238 GTAACGGATA
Statistics
Matches: 123, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
144 23 0.19
146 1 0.01
148 2 0.02
149 2 0.02
150 25 0.20
151 10 0.08
152 60 0.49
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (144 bp):
GGGGTTGCTAAGTGCTGATTCCCACAAGGGGTTGCTAAGTGCTGATTCCACCATATTTTAAATGT
GAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAATCCACCGTA
TCTTAAATGTGAAA
Found at i:21169415 original size:12 final size:13
Alignment explanation
Indices: 21169400--21169432 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
21169390 TTATTTTTAT
21169400 TTTTTAA-CTTAG
1 TTTTTAACCTTAG
21169412 TTTTTAACCCTTAG
1 TTTTTAA-CCTTAG
21169426 TTTTTAA
1 TTTTTAA
21169433 TCATCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (13 bp):
TTTTTAACCTTAG
Found at i:21175384 original size:50 final size:50
Alignment explanation
Indices: 21175311--21175501 Score: 235
Period size: 51 Copynumber: 3.8 Consensus size: 50
21175301 TATTATCATT
*
21175311 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
1 CGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
* * *
21175361 CGATCCACATAGTAGCCTCCACATAGAACTACACACGTGATCAAAGGTTTT-
1 CGATACACATAGTAGCCTTCACATAGTACTACACACGTGATC-AA-GTTTTA
* * * *
21175412 C-AGTACACATAGTAGCCTTCACTTAGTACTACACATGTGA-CCATTATTTA
1 CGA-TACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTA
*
21175462 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
1 -CGATACACATAGTAGCCTTCACATAGTACTACACACGTG
21175502 TTCATCGATA
Statistics
Matches: 120, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
48 1 0.01
49 4 0.03
50 40 0.33
51 69 0.57
52 6 0.05
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (50 bp):
CGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
Found at i:21175446 original size:26 final size:26
Alignment explanation
Indices: 21175415--21175497 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
21175405 AGGTTTTCAG
21175415 TACACATAGTAGCCTTCACTTAGTAC
1 TACACATAGTAGCCTTCACTTAGTAC
*
21175441 TACACAT-GT-GACCATT-ATTTA-T-C
1 TACACATAGTAG-CC-TTCACTTAGTAC
* *
21175464 GATACACGTAGTAGCCTTCACATAGTAC
1 --TACACATAGTAGCCTTCACTTAGTAC
21175492 TACACA
1 TACACA
21175498 CGTGTTCATC
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
23 1 0.02
24 2 0.05
25 16 0.37
26 21 0.49
27 2 0.05
28 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (26 bp):
TACACATAGTAGCCTTCACTTAGTAC
Done.