Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_pilon, whole genome shotgun sequence
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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 43
Found at i:5019968 original size:2 final size:2
Alignment explanation
Indices: 5019961--5020009 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5019951 GCAAGGAATC
5019961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5020003 AT AT AT A
1 AT AT AT A
5020010 GGCAATAGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5023331 original size:52 final size:51
Alignment explanation
Indices: 5023262--5023376 Score: 142
Period size: 52 Copynumber: 2.2 Consensus size: 51
5023252 ATATGATATC
* * * *
5023262 CATAAAATTTTCAGATAAAGTCATTTGA-TTTTTGAATAAATGACACAATAAATA
1 CATAAAA--TTCAGATAAAATCATTTAACTTTTGGAA-AAAGGACACAATAAA-A
*
5023316 CATAAAATTCAGATAAAATCATTTAACTTTTGGAAAAAGGACACAATAGAA
1 CATAAAATTCAGATAAAATCATTTAACTTTTGGAAAAAGGACACAATAAAA
5023367 CATAAAATTC
1 CATAAAATTC
5023377 TCTTCGCAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
51 11 0.20
52 30 0.55
53 7 0.13
54 7 0.13
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (51 bp):
CATAAAATTCAGATAAAATCATTTAACTTTTGGAAAAAGGACACAATAAAA
Found at i:5027167 original size:2 final size:2
Alignment explanation
Indices: 5027160--5027198 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5027150 GTGAAAAACA
5027160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5027199 ATCAAAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5027724 original size:20 final size:20
Alignment explanation
Indices: 5027701--5027749 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5027691 GTATGATCAG
* *
5027701 TATCGATACTATGCTAGTAA
1 TATCGATACAAGGCTAGTAA
*
5027721 TATCGATACAAGGCTAGTAG
1 TATCGATACAAGGCTAGTAA
5027741 TATCGATAC
1 TATCGATAC
5027750 CAAACAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (20 bp):
TATCGATACAAGGCTAGTAA
Found at i:5030883 original size:23 final size:23
Alignment explanation
Indices: 5030855--5030908 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
5030845 AGGAACATGA
*
5030855 CGGCGGAGTAGTTGGAGTAGAGG
1 CGGCGGAGCAGTTGGAGTAGAGG
5030878 CGGCGGAGCAGTTGGAGTAGAGG
1 CGGCGGAGCAGTTGGAGTAGAGG
5030901 CGGCGGAG
1 CGGCGGAG
5030909 AAGATGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.13, G:0.54, T:0.13
Consensus pattern (23 bp):
CGGCGGAGCAGTTGGAGTAGAGG
Found at i:5030974 original size:21 final size:21
Alignment explanation
Indices: 5030947--5031022 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
5030937 GGGTCGGGTC
*
5030947 TAGATCTGGGCTTCCGGGTTT
1 TAGATCTGGGCCTCCGGGTTT
* **
5030968 TGGATCTGGGCCTCTAGGTTT
1 TAGATCTGGGCCTCCGGGTTT
*
5030989 TAGATCTGGGCCTCCGGGTTC
1 TAGATCTGGGCCTCCGGGTTT
5031010 TAGATCTGGGCCT
1 TAGATCTGGGCCT
5031023 ATAAAATTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.34
Consensus pattern (21 bp):
TAGATCTGGGCCTCCGGGTTT
Found at i:5031060 original size:3 final size:3
Alignment explanation
Indices: 5031054--5031113 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
5031044 ATTATTTTTT
5031054 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5031101 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
5031114 ATGGGACAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5031504 original size:137 final size:137
Alignment explanation
Indices: 5031355--5031710 Score: 529
Period size: 137 Copynumber: 2.6 Consensus size: 137
5031345 AATCTAGCAA
*
5031355 AAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGATTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * *
5031420 GAACTCCTTCTGGAAATGCTGACCCTCAAAA-GAGGTGTCATTGATTCAACTTCATATATGATGA
66 GAACTCCTTCTGGAAATGCTGACCCTCAAAATAAGG-GTCATTAATTCAACTTCATATATAACGA
5031484 ATTAAAGC
130 ATTAAAGC
5031492 AAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
** ** *** *
5031557 GAACTCCTTCTGGAAATATTGACCCTCAAAATAAGGGTTGTTAATTTGGCTTCATATGTAACGAA
66 GAACTCCTTCTGGAAATGCTGACCCTCAAAATAAGGGTCATTAATTCAACTTCATATATAACGAA
*
5031622 TTAAGGC
131 TTAAAGC
*
5031629 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
*
5031693 TGAAC-ACTTCTGGAAATG
65 TGAACTCCTTCTGGAAATG
5031711 TTGATGCTGA
Statistics
Matches: 200, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
136 14 0.07
137 183 0.92
138 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (137 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCCTTCTGGAAATGCTGACCCTCAAAATAAGGGTCATTAATTCAACTTCATATATAACGAA
TTAAAGC
Found at i:5031983 original size:122 final size:122
Alignment explanation
Indices: 5031629--5032316 Score: 920
Period size: 122 Copynumber: 5.7 Consensus size: 122
5031619 GAATTAAGGC
5031629 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* *
5031693 TGAACACTTCTGGAAATGTTGATGCTGATATATCTCCTTCTGTGATAGAGTCATA-C-A
65 TGAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCA-AGCAA
* *
5031750 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
** * * *
5031815 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
66 GAACACT-TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCAAGCAA
*
5031873 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
5031938 GAACACTTTTGGAAATTTTGATGTTGATCTATCTCTTTCTTTGATAGAATCAAGCAA
66 GAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCAAGCAA
* * * *
5031995 AAGGTTGAACAAATTATTCTCAGTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * *
5032060 GAACACTTCTGGAAATTTTGATGCTGATCTATCTCTTTCTTTGATAGAATCGAGCAA
66 GAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCAAGCAA
* *
5032117 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCCTCTTCAGATGAGTTCTTCTCATTA
* ** **
5032182 TGAACTCTTCCAGAAATGTTGAT-C----C-A--T-C--GAGTGAT-GAATTCAAGCAA
65 TGAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAA-TCAAGCAA
*
5032229 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* *
5032294 TGAACTCTTCCGGAAATGTTGAT
65 TGAACACTTCTGGAAATGTTGAT
5032317 CCATAGAGTG
Statistics
Matches: 515, Mismatches: 45, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
111 6 0.01
112 91 0.18
115 1 0.00
117 1 0.00
118 1 0.00
121 64 0.12
122 238 0.46
123 113 0.22
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCAAGCAA
Found at i:5032237 original size:112 final size:112
Alignment explanation
Indices: 5032112--5032336 Score: 405
Period size: 112 Copynumber: 2.0 Consensus size: 112
5032102 GATAGAATCG
*
5032112 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
5032177 CATTATGAACTCTTCCAGAAATGTTGATCCATCGAGTGATGAATTCA
66 CATTATGAACTCTTCCAGAAATGTTGATCCATAGAGTGATGAATTCA
* *
5032224 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
5032289 CATTATGAACTCTTCCGGAAATGTTGATCCATAGAGTGATGAATTCA
66 CATTATGAACTCTTCCAGAAATGTTGATCCATAGAGTGATGAATTCA
5032336 A
1 A
5032337 ATATTTGCTA
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 108 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (112 bp):
AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTCTTCCAGAAATGTTGATCCATAGAGTGATGAATTCA
Found at i:5033905 original size:15 final size:16
Alignment explanation
Indices: 5033874--5033911 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
5033864 CTTGACCCTC
5033874 TTTTTCTATTATTATT
1 TTTTTCTATTATTATT
5033890 TTTTTC-ATT-TTCATT
1 TTTTTCTATTATT-ATT
5033905 TTTTTCT
1 TTTTTCT
5033912 TCAAGCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 12 0.60
16 6 0.30
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTATTATTATT
Found at i:5041273 original size:15 final size:15
Alignment explanation
Indices: 5041233--5041281 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
5041223 ATACATAAAG
5041233 AAAAT-AATGTAATG-
1 AAAATGAATGT-ATGC
5041247 AATAATGAATGTATGC
1 AA-AATGAATGTATGC
*
5041263 AAAATGCATGTATGC
1 AAAATGAATGTATGC
5041278 AAAA
1 AAAA
5041282 GGTATTGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 2 0.06
15 22 0.71
16 7 0.23
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (15 bp):
AAAATGAATGTATGC
Found at i:5046039 original size:28 final size:30
Alignment explanation
Indices: 5045994--5046061 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
5045984 CTCATTTTGC
5045994 TTCTCTCTCTAAAGAGAGAAAAGCTATCAA
1 TTCTCTCTCTAAAGAGAGAAAAGCTATCAA
*
5046024 TTCTCTCTCTAAAGAGAGAAAAGCTATCAC
1 TTCTCTCTCTAAAGAGAGAAAAGCTATCAA
5046054 TTCTCTCT
1 TTCTCTCT
5046062 AAACTTAGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.31
Consensus pattern (30 bp):
TTCTCTCTCTAAAGAGAGAAAAGCTATCAA
Found at i:5046294 original size:26 final size:26
Alignment explanation
Indices: 5046258--5046312 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
5046248 AATTTACTGA
5046258 CATACTTGGTTTACTGACATGGAATC
1 CATACTTGGTTTACTGACATGGAATC
5046284 CATACTTGGTTTACTGACATGGAATC
1 CATACTTGGTTTACTGACATGGAATC
5046310 CAT
1 CAT
5046313 CTTAGATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (26 bp):
CATACTTGGTTTACTGACATGGAATC
Found at i:5050638 original size:90 final size:90
Alignment explanation
Indices: 5050483--5050658 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 90
5050473 AACACACCCT
* *
5050483 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAACCCATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGAGATTTTATTATTTCAAATTAATTAAACCCATAT
* *
5050548 TTAATTAATTGGAATTTAATAATCC
66 TTAATTAATTGAAATTAAATAATCC
* * * *
5050573 TTTTATATCCAAGTTACCCTAGTCATATTAGAGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGAGATTTTATTATTTCAAATTAATTAAACCCATAT
5050638 TTAATTAATTGAAATTAAATA
66 TTAATTAATTGAAATTAAATA
5050659 TTCAAGATTA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (90 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGAGATTTTATTATTTCAAATTAATTAAACCCATAT
TTAATTAATTGAAATTAAATAATCC
Found at i:5059519 original size:10 final size:10
Alignment explanation
Indices: 5059490--5059522 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
5059480 ACTGCATTTT
*
5059490 TAGTTGCATT
1 TAGTTGCATA
5059500 TAGTTGCATA
1 TAGTTGCATA
5059510 TAGTTGCATA
1 TAGTTGCATA
5059520 TAG
1 TAG
5059523 GTTATATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.42
Consensus pattern (10 bp):
TAGTTGCATA
Found at i:5060680 original size:20 final size:19
Alignment explanation
Indices: 5060655--5060706 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
5060645 GCTGCTGGAA
* *
5060655 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
5060675 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
5060694 AACCGGGTTGACC
1 AACCGGTTTGACC
5060707 CGACCAGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:5060684 original size:10 final size:10
Alignment explanation
Indices: 5060655--5060704 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
5060645 GCTGCTGGAA
5060655 AACCGGTTTG
1 AACCGGTTTG
*
5060665 -ACCAGTTTTG
1 AACC-GGTTTG
5060675 AACCGGTTTG
1 AACCGGTTTG
*
5060685 -ACCGGTCTG
1 AACCGGTTTG
*
5060694 AACCGGGTTG
1 AACCGGTTTG
5060704 A
1 A
5060705 CCCGACCAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 11 0.34
10 18 0.56
11 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:5060722 original size:17 final size:17
Alignment explanation
Indices: 5060700--5060757 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
5060690 TCTGAACCGG
*
5060700 GTTGACCCGACCAGACT
1 GTTGACCCGACCAGACC
*
5060717 GTTGACCCGACCCGACC
1 GTTGACCCGACCAGACC
*
5060734 GTTGACCCGACCTGACC
1 GTTGACCCGACCAGACC
5060751 GTTGACC
1 GTTGACC
5060758 GTTGACCGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.19, C:0.40, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCAGACC
Found at i:5060756 original size:7 final size:7
Alignment explanation
Indices: 5060746--5060796 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
5060736 TGACCCGACC
5060746 TGACCGT
1 TGACCGT
5060753 TGACCGT
1 TGACCGT
5060760 TGACCG-
1 TGACCGT
5060766 TGACCGT
1 TGACCGT
5060773 TGACCG-
1 TGACCGT
5060779 TGACCGT
1 TGACCGT
*
5060786 TGACCAT
1 TGACCGT
5060793 TGAC
1 TGAC
5060797 TTTATTTGAC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 12 0.29
7 29 0.71
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.25
Consensus pattern (7 bp):
TGACCGT
Found at i:5060771 original size:13 final size:13
Alignment explanation
Indices: 5060730--5060790 Score: 83
Period size: 13 Copynumber: 4.8 Consensus size: 13
5060720 GACCCGACCC
*
5060730 GACCGTTGACC-C
1 GACCGTTGACCGT
5060742 GACC--TGACCGTT
1 GACCGTTGACCG-T
5060754 GACCGTTGACCGT
1 GACCGTTGACCGT
5060767 GACCGTTGACCGT
1 GACCGTTGACCGT
5060780 GACCGTTGACC
1 GACCGTTGACC
5060791 ATTGACTTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
10 5 0.11
12 8 0.18
13 25 0.57
14 6 0.14
ACGTcount: A:0.16, C:0.34, G:0.28, T:0.21
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:5060771 original size:20 final size:19
Alignment explanation
Indices: 5060730--5060796 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
5060720 GACCCGACCC
*
5060730 GACCGTTGACC-CGACC-T
1 GACCGTTGACCGTGACCGT
5060747 GACCGTTGACCGTTGACCGT
1 GACCGTTGACCG-TGACCGT
5060767 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCG-T
*
5060787 GACCATTGAC
1 GACCGTTGAC
5060797 TTTATTTGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
17 11 0.25
19 10 0.23
20 23 0.52
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (19 bp):
GACCGTTGACCGTGACCGT
Found at i:5067875 original size:10 final size:10
Alignment explanation
Indices: 5067846--5067914 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
5067836 GCTGCTGGAA
5067846 AACCGGTTTG
1 AACCGGTTTG
*
5067856 -ACCAGTTTTG
1 AACC-GGTTTG
5067866 AACCGGTTTG
1 AACCGGTTTG
*
5067876 -ACCGGTTCG
1 AACCGGTTTG
5067885 AACCGGTTTG
1 AACCGGTTTG
*
5067895 -ACCGGTCTG
1 AACCGGTTTG
*
5067904 AACCGGGTTG
1 AACCGGTTTG
5067914 A
1 A
5067915 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:5067889 original size:19 final size:19
Alignment explanation
Indices: 5067846--5067916 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
5067836 GCTGCTGGAA
* *
5067846 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
5067866 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
5067885 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
5067904 AACCGGGTTGACC
1 AACCGGTTTGACC
5067917 CGACCCGACT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 2 0.04
19 32 0.68
20 13 0.28
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:5067932 original size:17 final size:17
Alignment explanation
Indices: 5067910--5067984 Score: 141
Period size: 17 Copynumber: 4.4 Consensus size: 17
5067900 TCTGAACCGG
*
5067910 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
5067927 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
5067944 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
5067961 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
5067978 GTTGACC
1 GTTGACC
5067985 GTTGACCGGG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.17, C:0.44, G:0.24, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:5067984 original size:7 final size:7
Alignment explanation
Indices: 5067974--5068011 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
5067964 GACCCGACCC
5067974 GACCGTT
1 GACCGTT
5067981 GACCGTT
1 GACCGTT
*
5067988 GACCG-G
1 GACCGTT
5067994 GACCGTT
1 GACCGTT
5068001 GACCCGTT
1 GA-CCGTT
5068009 GAC
1 GAC
5068012 TTCTTTGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 5 0.19
7 15 0.56
8 7 0.26
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.21
Consensus pattern (7 bp):
GACCGTT
Found at i:5082804 original size:119 final size:119
Alignment explanation
Indices: 5082590--5082822 Score: 358
Period size: 119 Copynumber: 2.0 Consensus size: 119
5082580 CTAGGTAACG
* **
5082590 AAAATTTGAATTATGTACATAAATAAGTTAAGTTATTTTTTGCTTTAATATGTTTTAATTTTTAT
1 AAAATTTGAATTATGTACATAAATAAGTTAAGTTATTTTCTGCTTTAATACATTTTAATTTTTAT
* * * *
5082655 TTTCTTCTTTCTTATTGTAGGCAAGGAAGGAACACGTGGTAGCATGGGGCAACA
66 TTTCTTCTTTCTTATTATAGGCAAGCAAGGAACACGTGGCAACATGGGGCAACA
* * *
5082709 AAAATTTGAATTCTGTACATAAATAAGTTAAGTTATTTTCTGCTTTAATCCATTTTATTTTTTAT
1 AAAATTTGAATTATGTACATAAATAAGTTAAGTTATTTTCTGCTTTAATACATTTTAATTTTTAT
* *
5082774 TTTCTTCTTTTTTATTATAGGCAAGCAAGGAACATGTGGCAACATGGGG
66 TTTCTTCTTTCTTATTATAGGCAAGCAAGGAACACGTGGCAACATGGGG
5082823 AGTTGAATCA
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
119 102 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.43
Consensus pattern (119 bp):
AAAATTTGAATTATGTACATAAATAAGTTAAGTTATTTTCTGCTTTAATACATTTTAATTTTTAT
TTTCTTCTTTCTTATTATAGGCAAGCAAGGAACACGTGGCAACATGGGGCAACA
Found at i:5090294 original size:45 final size:45
Alignment explanation
Indices: 5090243--5090352 Score: 152
Period size: 45 Copynumber: 2.4 Consensus size: 45
5090233 TGTTGCCAAA
5090243 ATAAAAGGTGTCACTAATGACAATGCATAACAATGCATTATCGA-C
1 ATAAAAGGTGTCACTAATGACAATGCATAACAATGCATTAT-GAGC
* * * *
5090288 ATAAAAGGTGTCATTAATGATAATGCATAACAGTGCATTATTAGC
1 ATAAAAGGTGTCACTAATGACAATGCATAACAATGCATTATGAGC
5090333 ATAAAAGGT-TCCACTAATGA
1 ATAAAAGGTGT-CACTAATGA
5090353 AAATTATCGA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 2 0.03
45 56 0.97
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (45 bp):
ATAAAAGGTGTCACTAATGACAATGCATAACAATGCATTATGAGC
Found at i:5099464 original size:2 final size:2
Alignment explanation
Indices: 5099457--5099507 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5099447 GCCATCTAAG
5099457 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5099499 GA GA GA GA G
1 GA GA GA GA G
5099508 TTTAATATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5099745 original size:16 final size:16
Alignment explanation
Indices: 5099724--5099757 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5099714 ATATATATAT
5099724 ATATTT-AAGTATTTTA
1 ATATTTGAA-TATTTTA
5099740 ATATTTGAATATTTTA
1 ATATTTGAATATTTTA
5099756 AT
1 AT
5099758 TAAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
ATATTTGAATATTTTA
Found at i:5101022 original size:23 final size:22
Alignment explanation
Indices: 5100996--5101041 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5100986 AAAATTGAAA
*
5100996 TTAAAATTAAAATTGTTAACCAT
1 TTAAAAAT-AAATTGTTAACCAT
*
5101019 TTAAAAATCAATTGTTAACCAT
1 TTAAAAATAAATTGTTAACCAT
5101041 T
1 T
5101042 GTGCAATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (22 bp):
TTAAAAATAAATTGTTAACCAT
Found at i:5104780 original size:13 final size:14
Alignment explanation
Indices: 5104764--5104797 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5104754 CTATGACGCG
5104764 CATTTATGGA-ACA
1 CATTTATGGACACA
5104777 CATTTAT-GACACA
1 CATTTATGGACACA
5104790 CATTTATG
1 CATTTATG
5104798 ATGCGCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (14 bp):
CATTTATGGACACA
Found at i:5104890 original size:85 final size:85
Alignment explanation
Indices: 5104791--5105013 Score: 265
Period size: 85 Copynumber: 2.6 Consensus size: 85
5104781 TATGACACAC
** *
5104791 ATTTATGATGCGCAT-TAATGACGTT-CATTGAGTTTCATTGAAGCCCCCGTCATAAAT-TAAGA
1 ATTTATGACACGCATGT-ATGAC-TTACATTGAGTGTCATTGAAGCCCCCGTCATAAATCT--GA
*
5104853 T-GACACACATTTGTCCGTCATAA
62 TAGACACACATTTATCCGTCATAA
* *
5104876 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATCTGCTAGA
1 ATTTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCGTCATAAATCTGATAGA
* **
5104941 CATACATTTATGTGTCATAA
66 CACACATTTATCCGTCATAA
* * * *
5104961 ATTTATGACACGCATGTATGACTTACATTGCGTGTAATTGAAGCACACGTCAT
1 ATTTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCGTCAT
5105014 TAAAAAAGAC
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
84 4 0.03
85 116 0.95
86 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCGTCATAAATCTGATAGA
CACACATTTATCCGTCATAA
Found at i:5105051 original size:85 final size:84
Alignment explanation
Indices: 5104869--5105041 Score: 222
Period size: 85 Copynumber: 2.0 Consensus size: 84
5104859 ACATTTGTCC
* * * **
5104869 GTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATC
1 GTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTAATTGAAGCACACGTCATAAAAA
* * *
5104934 TGCTAGACATACATTTATGT
66 AGC-AGACAAACATTCATGT
5104954 GTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTAATTGAAGCACACGTCATTAAAA
1 GTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTAATTGAAGCACACGTCA-TAAAA
* *
5105019 AAG-ACGACAAACGTTCGTGT
65 AAGCA-GACAAACATTCATGT
5105039 GTC
1 GTC
5105042 GTGATTTTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
84 1 0.01
85 70 0.92
86 5 0.07
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (84 bp):
GTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTAATTGAAGCACACGTCATAAAAA
AGCAGACAAACATTCATGT
Found at i:5105068 original size:2 final size:2
Alignment explanation
Indices: 5105061--5105102 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
5105051 TTTTGTAAAT
* * *
5105061 TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA AA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5105103 AATAATCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:5107539 original size:19 final size:19
Alignment explanation
Indices: 5107478--5107539 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
5107468 CTTCAGTGTC
5107478 CCTTCTCCTTT-CTCCTCTT
1 CCTTCTCCTTTAC-CCTCTT
* ** * *
5107497 CCTTTTTCCTTTACGGTGTC
1 CC-TTCTCCTTTACCCTCTT
5107517 CCTTCTCCTTTACCCTCTT
1 CCTTCTCCTTTACCCTCTT
5107536 CCTT
1 CCTT
5107540 TTCTTTCTCT
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
19 18 0.58
20 12 0.39
21 1 0.03
ACGTcount: A:0.03, C:0.42, G:0.05, T:0.50
Consensus pattern (19 bp):
CCTTCTCCTTTACCCTCTT
Found at i:5115530 original size:21 final size:21
Alignment explanation
Indices: 5115506--5115569 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
5115496 GCAAATTCGC
5115506 GTTGCATTTCGCGTTGTGATA
1 GTTGCATTTCGCGTTGTGATA
* ** *
5115527 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGTGATA
* *
5115547 TTTCCATTTCGCGTTGTGATA
1 GTTGCATTTCGCGTTGTGATA
5115568 GT
1 GT
5115570 CTACAGTTGT
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.41
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGTGATA
Found at i:5115589 original size:22 final size:22
Alignment explanation
Indices: 5115558--5115610 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
5115548 TTCCATTTCG
*
5115558 CGTTGTGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
5115580 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
5115602 CGTTGCGAT
1 CGTTGCGAT
5115611 TTTCCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:5115721 original size:6 final size:6
Alignment explanation
Indices: 5115710--5115747 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
5115700 GACACGTATT
5115710 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
5115748 CGAGACAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5116244 original size:5 final size:5
Alignment explanation
Indices: 5116230--5116270 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
5116220 CCGCCGCCGC
5116230 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
5116271 GTTCGGGTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:5116347 original size:6 final size:6
Alignment explanation
Indices: 5116276--5116367 Score: 114
Period size: 6 Copynumber: 15.5 Consensus size: 6
5116266 TCTCGGTTCG
* * * * * *
5116276 GGTCGG GGTCGG GGTCGG GGTCGG GGTCGT GGTCGT GGTCGG GGTCGG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
*
5116324 GGTCGT GGTCGT GGTCGT GGTCGT GGTTG- GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
5116368 AATACGTGTC
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
5 4 0.05
6 76 0.95
ACGTcount: A:0.00, C:0.15, G:0.58, T:0.27
Consensus pattern (6 bp):
GGTCGT
Found at i:5116347 original size:18 final size:18
Alignment explanation
Indices: 5116276--5116367 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
5116266 TCTCGGTTCG
* *
5116276 GGTCGGGGTCGGGGTCGG
1 GGTCGGGGTCGTGGTCGT
5116294 GGTCGGGGTCGTGGTCGT
1 GGTCGGGGTCGTGGTCGT
*
5116312 GGTCGGGGTCGGGGTCGT
1 GGTCGGGGTCGTGGTCGT
*
5116330 GGTCGTGGTCGTGGTCGT
1 GGTCGGGGTCGTGGTCGT
*
5116348 GGT-TGGGTCGTGGTCGT
1 GGTCGGGGTCGTGGTCGT
5116365 GGT
1 GGT
5116368 AATACGTGTC
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
17 15 0.22
18 52 0.78
ACGTcount: A:0.00, C:0.15, G:0.58, T:0.27
Consensus pattern (18 bp):
GGTCGGGGTCGTGGTCGT
Found at i:5116501 original size:20 final size:20
Alignment explanation
Indices: 5116476--5116603 Score: 124
Period size: 20 Copynumber: 6.7 Consensus size: 20
5116466 ACTGTAGACT
5116476 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
5116496 ATCGCAACGTGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
5116516 ATCGCAACGCGATTTTCAAGT
1 ATCGCAACGCGAAATGGAA-A
5116537 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
**
5116557 ATCGCAATACG-AAT-----
1 ATCGCAACGCGAAATGGAAA
*
5116571 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
5116591 ATCGCAACGCGAA
1 ATCGCAACGCGAA
5116604 TTTGCCATAG
Statistics
Matches: 85, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
14 9 0.11
15 3 0.04
19 3 0.04
20 55 0.65
21 15 0.18
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:5116551 original size:41 final size:35
Alignment explanation
Indices: 5116492--5116603 Score: 120
Period size: 34 Copynumber: 3.1 Consensus size: 35
5116482 ACGCGAAATG
*
5116492 GAAA-ATCGCAACGTGAAATGGAAAATCGCAACGC
1 GAAATATCGCAACGCGAAATGGAAAATCGCAACGC
**
5116526 GATTTTCAAGTATCGCAACGCGAAATGGAAAATCGCAATAC
1 GA-----AA-TATCGCAACGCGAAATGGAAAATCGCAACGC
*
5116567 G-AATATCGCAACGCGAAATGAAAAATCGCAACGC
1 GAAATATCGCAACGCGAAATGGAAAATCGCAACGC
5116601 GAA
1 GAA
5116604 TTTGCCATAG
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
34 31 0.48
35 3 0.05
39 2 0.03
41 28 0.44
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.15
Consensus pattern (35 bp):
GAAATATCGCAACGCGAAATGGAAAATCGCAACGC
Found at i:5128328 original size:21 final size:20
Alignment explanation
Indices: 5128303--5128342 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5128293 GAAAGTAAAG
*
5128303 TAAATTATTTATAAGAAAAAT
1 TAAATGATTT-TAAGAAAAAT
*
5128324 TAAATGATTTTGAGAAAAA
1 TAAATGATTTTAAGAAAAA
5128343 GAATATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (20 bp):
TAAATGATTTTAAGAAAAAT
Found at i:5134055 original size:54 final size:53
Alignment explanation
Indices: 5133998--5134200 Score: 291
Period size: 54 Copynumber: 3.8 Consensus size: 53
5133988 CTGTGTATAG
* *
5133998 TATCGACACTATGTGTGCAACCCATGGAATTAATAATGAGTTTATGAATGATCG
1 TATCGACACTATGTGTGCAACCCATGGAATTCATAATGAGTTTATGAATGA-CA
* * * *
5134052 TATCAACACTATGTGTGCAACCCACGAAATTCATAATGGGTTTATGAATGACCA
1 TATCGACACTATGTGTGCAACCCATGGAATTCATAATGAGTTTATGAATGA-CA
5134106 TATCGACACTATGTGTGCAACCCATGGAATTCATAATGAGTTTATGAATGACTA
1 TATCGACACTATGTGTGCAACCCATGGAATTCATAATGAGTTTATGAATGAC-A
* *
5134160 TATCTACACTATAG-GTGTAACCCATGGAATTCATAATGAGT
1 TATCGACACTAT-GTGTGCAACCCATGGAATTCATAATGAGT
5134201 GTGAAAATCC
Statistics
Matches: 134, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 132 0.99
55 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (53 bp):
TATCGACACTATGTGTGCAACCCATGGAATTCATAATGAGTTTATGAATGACA
Found at i:5139233 original size:45 final size:45
Alignment explanation
Indices: 5138907--5139211 Score: 346
Period size: 45 Copynumber: 6.8 Consensus size: 45
5138897 GTTGCCATAA
* * *
5138907 TTGATATGTATATGGGTACATTATCAACAGAAAAGCATACTTTAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
* * * * *
5138952 TTAAAATGTATATGTGTACATTATCAATAGGAAAA-TATGCTAGAG
1 TTGAAATGTATATGGGTACATTATCAACA-GAAAAGTATACTATAG
* * *
5138997 TTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
* * *
5139042 TTGAAATGTATATGGGTGCATTGTCAAC-GCAAAAGTATGCTAGT-G
1 TTGAAATGTATATGGGTACATTATCAACAG-AAAAGTATACTA-TAG
* ** * *
5139087 TTGGAATGTATATTAGTACATTATCAACATAAAAGTATACTATGG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
*
5139132 TTTAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
* * * *
5139177 TTGAAATGCATATGAGTGCATTATCAATAGAAAAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAG
5139212 ATGTTATAGT
Statistics
Matches: 218, Mismatches: 36, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
44 7 0.03
45 206 0.94
46 5 0.02
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (45 bp):
TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
Found at i:5139245 original size:45 final size:45
Alignment explanation
Indices: 5138907--5139250 Score: 293
Period size: 45 Copynumber: 7.6 Consensus size: 45
5138897 GTTGCCATAA
* * * * * *
5138907 TTGATATGTATATGGGTACATTATCAACAGAAAAGCATACTTTAG
1 TTGAAATGCATATGAGTGCATTATCAACAGAAAAGTATACTATAG
* * * * * * *
5138952 TTAAAATGTATATGTGTACATTATCAATAGGAAAA-TATGCTAGAG
1 TTGAAATGCATATGAGTGCATTATCAACA-GAAAAGTATACTATAG
* *
5138997 TTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAG
1 TTGAAATGCATATGAGTGCATTATCAACAGAAAAGTATACTATAG
* * * *
5139042 TTGAAATGTATATGGGTGCATTGTCAAC-GCAAAAGTATGCTAGT-G
1 TTGAAATGCATATGAGTGCATTATCAACAG-AAAAGTATACTA-TAG
* * * * * *
5139087 TTGGAATGTATATTAGTACATTATCAACATAAAAGTATACTATGG
1 TTGAAATGCATATGAGTGCATTATCAACAGAAAAGTATACTATAG
* * * *
5139132 TTTAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
1 TTGAAATGCATATGAGTGCATTATCAACAGAAAAGTATACTATAG
* **
5139177 TTGAAATGCATATGAGTGCATTATCAATAGAAAAG-ATGTTATAG
1 TTGAAATGCATATGAGTGCATTATCAACAGAAAAGTATACTATAG
* * *
5139221 TTTAAAGTGCATAATGA-TGTATTATAAACA
1 TTGAAA-TGCAT-ATGAGTGCATTATCAACA
5139251 TAAATGGAGG
Statistics
Matches: 249, Mismatches: 42, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
44 19 0.08
45 221 0.89
46 9 0.04
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (45 bp):
TTGAAATGCATATGAGTGCATTATCAACAGAAAAGTATACTATAG
Found at i:5144679 original size:11 final size:13
Alignment explanation
Indices: 5144653--5144677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5144643 GTTGCAAAAG
5144653 TTTTCTTCCTCTC
1 TTTTCTTCCTCTC
5144666 TTTTCTTCCTCT
1 TTTTCTTCCTCT
5144678 TTCCCGTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTCTTCCTCTC
Found at i:5145439 original size:21 final size:22
Alignment explanation
Indices: 5145413--5145453 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5145403 TATTGATATT
*
5145413 AGTAGGG-GGTATCGATACCAA
1 AGTAGGGTAGTATCGATACCAA
5145434 AGTAGGGTAGTATCGATACC
1 AGTAGGGTAGTATCGATACC
5145454 GTGGTAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.22
Consensus pattern (22 bp):
AGTAGGGTAGTATCGATACCAA
Found at i:5145969 original size:45 final size:45
Alignment explanation
Indices: 5145919--5146230 Score: 307
Period size: 45 Copynumber: 6.8 Consensus size: 45
5145909 AAATGATGCC
*
5145919 ATAGTTGAAATGTATATGGATACATTATCAACAGAAAA-TCATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGT-ATACT
* * *
5145964 TTAGTTGAAATGTATATGGGTACATTATCAACAAAAAAGTATGC-
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
5146008 -TA---GAAATGCATATGGGTGCATTATCAACAGAAAAGTA-AGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATA-CT
* * * * *
5146049 AGAGTTGAAATGCATAAGGGTGCATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
5146094 AGAGTTGAAATGTATATGTGTACATTATCAACAGAAAAATATACTATAGTT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATAC------T
*
5146145 GATATGGTTGAAATGTATATGGGTACATTATCAACATAAAAGTATACT
1 -ATA--GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
5146193 ATAGTTGAAATGCT-TATGGGTGCATTATCAACATAAAA
1 ATAGTTGAAATG-TATATGGGTACATTATCAACAGAAAA
5146231 TATGTTATAG
Statistics
Matches: 227, Mismatches: 22, Indels: 36
0.80 0.08 0.13
Matches are distributed among these distances:
40 33 0.15
42 1 0.00
43 2 0.01
45 144 0.63
46 2 0.01
47 3 0.01
48 1 0.00
51 1 0.00
52 2 0.01
54 38 0.17
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:5146030 original size:40 final size:40
Alignment explanation
Indices: 5145970--5146096 Score: 164
Period size: 40 Copynumber: 3.0 Consensus size: 40
5145960 TACTTTAGTT
* * *
5145970 GAAATGTATATGGGTACATTATCAACAAAAAAGTATGCTA
1 GAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTA
*
5146010 GAAATGCATATGGGTGCATTATCAACAGAAAAGTAAGCTAGA
1 GAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCT--A
*
5146052 GTTGAAATGCATAAGGGTGCATTATCAACAGAAAAGTATGCTA
1 ---GAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTA
5146095 GA
1 GA
5146097 GTTGAAATGT
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
40 37 0.49
42 1 0.01
43 1 0.01
45 37 0.49
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (40 bp):
GAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTA
Found at i:5146030 original size:85 final size:86
Alignment explanation
Indices: 5145924--5146231 Score: 271
Period size: 85 Copynumber: 3.4 Consensus size: 86
5145914 ATGCCATAGT
* *
5145924 TGAAATGTATATGGATACATTATCAACAGAAAATCATACTTTAGTTGAAATGTATATGGGTACAT
1 TGAAATGCATATGGGTACATTATCAACAGAAAATCATACTTTAGTTGAAATGTATATGGGTACAT
5145989 TATCAACAAAAAAGTATGCTA
66 TATCAACAAAAAAGTATGCTA
* ** * * *
5146010 -GAAATGCATATGGGTGCATTATCAACAGAAAAGT-A-AGCTAGAGTTGAAATGCATAAGGGTGC
1 TGAAATGCATATGGGTACATTATCAACAGAAAA-TCATA-CTTTAGTTGAAATGTATATGGGTAC
*
5146072 ATTATCAACAGAAAAGTATGCTAGA
64 ATTATCAACAAAAAAGTATGCT--A
* * *
5146097 GTTGAAATGTATATGTGTACATTATCAACAGAAAAATATACTATAGTTGATATGGTTGAAATGTA
1 --TGAAATGCATATGGGTACATTATCAACAG--AAA-AT-C-ATACTT--TA--GTTGAAATGTA
* *
5146162 TATGGGTACATTATCAACATAAAAGTATACTATA
55 TATGGGTACATTATCAACAAAAAAGTATGC--TA
* * *
5146196 GTTGAAATGCTTATGGGTGCATTATCAACATAAAAT
1 --TGAAATGCATATGGGTACATTATCAACAGAAAAT
5146232 ATGTTATAGT
Statistics
Matches: 177, Mismatches: 25, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
84 1 0.01
85 71 0.40
86 1 0.01
87 1 0.01
90 25 0.14
92 4 0.02
93 1 0.01
95 2 0.01
96 3 0.02
97 4 0.02
99 63 0.36
101 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (86 bp):
TGAAATGCATATGGGTACATTATCAACAGAAAATCATACTTTAGTTGAAATGTATATGGGTACAT
TATCAACAAAAAAGTATGCTA
Found at i:5146179 original size:54 final size:54
Alignment explanation
Indices: 5146097--5146200 Score: 181
Period size: 54 Copynumber: 1.9 Consensus size: 54
5146087 GTATGCTAGA
*
5146097 GTTGAAATGTATATGTGTACATTATCAACAGAAAAATATACTATAGTTGATATG
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAATATACTATAGTTGATATG
* *
5146151 GTTGAAATGTATATGGGTACATTATCAACATAAAAGTATACTATAGTTGA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAATATACTATAGTTGA
5146201 AATGCTTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (54 bp):
GTTGAAATGTATATGGGTACATTATCAACAGAAAAATATACTATAGTTGATATG
Found at i:5146223 original size:99 final size:99
Alignment explanation
Indices: 5146052--5146230 Score: 261
Period size: 99 Copynumber: 1.8 Consensus size: 99
5146042 GTAAGCTAGA
* * *
5146052 GTTGAAATGCATAAGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGTGTAC
1 GTTGAAATGCATAAGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGTATATGGGTAC
5146117 ATTATCAACAGAAAAATATACTATAGTTGATATG
66 ATTATCAACAGAAAAATATACTATAGTTGATATG
* * * * *
5146151 GTTGAAATGTATATGGGTACATTATCAACATAAAAGTATACTATAGTTGAAATGCT-TATGGGTG
1 GTTGAAATGCATAAGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATG-TATATGGGTA
*
5146215 CATTATCAACATAAAA
65 CATTATCAACAGAAAA
5146231 TATGTTATAG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
99 69 0.99
100 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (99 bp):
GTTGAAATGCATAAGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGTATATGGGTAC
ATTATCAACAGAAAAATATACTATAGTTGATATG
Found at i:5146265 original size:45 final size:45
Alignment explanation
Indices: 5146170--5146274 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 45
5146160 TATATGGGTA
** **
5146170 CATTATCAACATAAAAGTATACTATAGTTGAAATGCTTATGGGTG
1 CATTATCAACATAAAAGTATACTATAGTTGAAATGCAAAAAGGTG
** *
5146215 CATTATCAACATAAAA-TATGTTATAGTTTAAAGTGCAAAAAGGTG
1 CATTATCAACATAAAAGTATACTATAGTTGAAA-TGCAAAAAGGTG
* *
5146260 TATTATAAACATAAA
1 CATTATCAACATAAA
5146275 TGGAGGTTAC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 13 0.26
45 37 0.74
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (45 bp):
CATTATCAACATAAAAGTATACTATAGTTGAAATGCAAAAAGGTG
Found at i:5152388 original size:20 final size:20
Alignment explanation
Indices: 5152332--5152392 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 20
5152322 GTATTGATAC
5152332 TGGTAGGGGGTATCGATACCA
1 TGGTA-GGGGTATCGATACCA
**
5152353 AAGTAGGGTAGTATCGATACCA
1 TGGTAGGG--GTATCGATACCA
5152375 TGGTAGGGGTATCGATAC
1 TGGTAGGGGTATCGATAC
5152393 TGAAGGGCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 13 0.38
21 3 0.09
22 18 0.53
ACGTcount: A:0.28, C:0.13, G:0.34, T:0.25
Consensus pattern (20 bp):
TGGTAGGGGTATCGATACCA
Found at i:5153067 original size:45 final size:44
Alignment explanation
Indices: 5152979--5153276 Score: 319
Period size: 45 Copynumber: 6.7 Consensus size: 44
5152969 GCATGAAAGG
* * **
5152979 ATGCATATGGCTACATTATCAACAGAAAACATACTTTAGTTGAA
1 ATGCATATGGGTACATTATCAACAGAAAATATACTAGAGTTGAA
* *
5153023 ATGTATATGGGTACATTATCAACAGGAAAATATGCTAGAGTTGAA
1 ATGCATATGGGTACATTATCAACA-GAAAATATACTAGAGTTGAA
** * * ** *
5153068 ATGCATATGGGGGCATTTTTAACAGGAATGTATGCTAGAGTTGAA
1 ATGCATATGGGTACATTATCAACA-GAAAATATACTAGAGTTGAA
* * *
5153113 ATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTAGAGTTGAA
1 ATGCATATGGGTACATTATCAACAGAAAA-TATACTAGAGTTGAA
* *
5153158 ATGTATATGGGTAAATTATCAACAGAAAAGTATACTATG-GTTGAA
1 ATGCATATGGGTACATTATCAACAGAAAA-TATACTA-GAGTTGAA
* * *
5153203 ATGTATATGGGTACATTATCAACAAAAAAATATACTATAGTTGAA
1 ATGCATATGGGTACATTATCAAC-AGAAAATATACTAGAGTTGAA
* * *
5153248 ATGCATATTGGTTCATTATCAATAGAAAA
1 ATGCATATGGGTACATTATCAACAGAAAA
5153277 GATGTTATAG
Statistics
Matches: 218, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
44 30 0.14
45 182 0.83
46 6 0.03
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (44 bp):
ATGCATATGGGTACATTATCAACAGAAAATATACTAGAGTTGAA
Found at i:5153245 original size:135 final size:135
Alignment explanation
Indices: 5152979--5153277 Score: 352
Period size: 135 Copynumber: 2.2 Consensus size: 135
5152969 GCATGAAAGG
* ** *
5152979 ATGCATATGGCTACATTATCAACAGAAAA-CATACTTTAGTTGAAATGTATATGGGTACATTATC
1 ATGCATATGGGTACATTATCAACAGAAAAGCATACTAGAGTTGAAATGTATATGGGTAAATTATC
* * * * ** ** *
5153043 AACAGGAAAATATGCTAGAGTTGAAATGCATATGGGGGCATTTTTAACAGGAATGTATGCTAGAG
66 AACAGGAAAATATACTAGAGTTGAAATGCATATGGGGACATTATCAACAAAAAAATATACTAGAG
5153108 TTGAA
131 TTGAA
* * * *
5153113 ATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGGTAAATTATC
1 ATGCATATGGGTACATTATCAACAGAAAAGCATACTAGAGTTGAAATGTATATGGGTAAATTATC
* * *
5153178 AACA-GAAAAGTATACTATG-GTTGAAATGTATATGGGTACATTATCAACAAAAAAATATACTAT
66 AACAGGAAAA-TATACTA-GAGTTGAAATGCATATGGGGACATTATCAACAAAAAAATATACTAG
5153241 AGTTGAA
129 AGTTGAA
* * *
5153248 ATGCATATTGGTTCATTATCAATAGAAAAG
1 ATGCATATGGGTACATTATCAACAGAAAAG
5153278 ATGTTATAGT
Statistics
Matches: 138, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
134 31 0.22
135 106 0.77
136 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.30
Consensus pattern (135 bp):
ATGCATATGGGTACATTATCAACAGAAAAGCATACTAGAGTTGAAATGTATATGGGTAAATTATC
AACAGGAAAATATACTAGAGTTGAAATGCATATGGGGACATTATCAACAAAAAAATATACTAGAG
TTGAA
Found at i:5153266 original size:90 final size:90
Alignment explanation
Indices: 5152979--5153277 Score: 359
Period size: 90 Copynumber: 3.3 Consensus size: 90
5152969 GCATGAAAGG
* * * *
5152979 ATGCATATGGCTACATTATCAACAGAAAA-CATACTTTAGTTGAAATGTATATGGGTACATTATC
1 ATGCATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTATC
*
5153043 AACAGGAAAATATGCTAGAGTTGAA
66 AACAGAAAAATATGCTAGAGTTGAA
** * * * * * * * *
5153068 ATGCATATGGGGGCATTTTTAACAGGAATGTATGCTA-GAGTTGAAATGCATATGGGTGCATTGT
1 ATGCATATGGGTACATTATCAACAGAAAAGTATACTATG-GTTGAAATGTATATGGGTACATTAT
*
5153132 CAACAGAAAAGTATGCTAGAGTTGAA
65 CAACAGAAAAATATGCTAGAGTTGAA
* *
5153158 ATGTATATGGGTAAATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTATC
1 ATGCATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTATC
* * *
5153223 AACAAAAAAATATACTATAGTTGAA
66 AACAGAAAAATATGCTAGAGTTGAA
* * *
5153248 ATGCATATTGGTTCATTATCAATAGAAAAG
1 ATGCATATGGGTACATTATCAACAGAAAAG
5153278 ATGTTATAGT
Statistics
Matches: 170, Mismatches: 37, Indels: 5
0.80 0.17 0.02
Matches are distributed among these distances:
89 22 0.13
90 147 0.86
91 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.30
Consensus pattern (90 bp):
ATGCATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTATC
AACAGAAAAATATGCTAGAGTTGAA
Found at i:5153311 original size:90 final size:89
Alignment explanation
Indices: 5152979--5153316 Score: 315
Period size: 90 Copynumber: 3.8 Consensus size: 89
5152969 GCATGAAAGG
* * * * *
5152979 ATGCATATGGCTACATTATCAACAGAAAA-CATACTTTAGTTGAAATGTATATGG-GTACATTAT
1 ATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGCATATGGTGT--ATTAT
*
5153042 CAACAGGAAAATATGCTAGAGTTGAA
64 CAACAGAAAAATATGCTAGAGTTGAA
** * * * * * * *
5153068 ATGCATATGGGGGCATTTTTAACAGGAATGTATGCTAGAGTTGAAATGCATATGGGTGCATTGTC
1 ATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGCATAT-GGTGTATTATC
*
5153133 AACAGAAAAGTATGCTAGAGTTGAA
65 AACAGAAAAATATGCTAGAGTTGAA
* * * * *
5153158 ATGTATATGGGTAAATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGG-GTACATTAT
1 ATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGCATATGGTGT--ATTAT
* * *
5153222 CAACAAAAAAATATACTATAGTTGAA
64 CAACAGAAAAATATGCTAGAGTTGAA
* * * * *
5153248 ATGCATATTGGTTCATTATCAATAGAAAAG-ATGTTATAGTTTAAAGTGCATAATGGTGTATTAT
1 ATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAA-TGCAT-ATGGTGTATTAT
*
5153312 AAACA
64 CAACA
5153317 TAAATGGAGA
Statistics
Matches: 196, Mismatches: 45, Indels: 15
0.77 0.18 0.06
Matches are distributed among these distances:
88 1 0.01
89 35 0.18
90 151 0.77
91 6 0.03
92 3 0.02
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.31
Consensus pattern (89 bp):
ATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGAAATGCATATGGTGTATTATCA
ACAGAAAAATATGCTAGAGTTGAA
Found at i:5155845 original size:20 final size:22
Alignment explanation
Indices: 5155792--5155848 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
5155782 ATACTGAAGA
*
5155792 GAGTATCGATACCATACTAGAG
1 GAGTATCGATACTATACTAGAG
* *
5155814 GAGTATCAATACTATAGTAG-G
1 GAGTATCGATACTATACTAGAG
5155835 G-GTATCGATACTAT
1 GAGTATCGATACTAT
5155849 TTAGTCTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.39
21 2 0.06
22 17 0.55
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (22 bp):
GAGTATCGATACTATACTAGAG
Found at i:5156637 original size:54 final size:54
Alignment explanation
Indices: 5156551--5156806 Score: 332
Period size: 54 Copynumber: 4.7 Consensus size: 54
5156541 CTATTGAAAT
* * * *
5156551 TATGTGTACAACCCACAGAATTCATAATGAGTTTATGAATGACCGTATCAGCAA
1 TATGTGTGCAACCCACGGAATTCATAATGAGTTTATGAATGACCGTATCAACAC
* ***
5156605 TATGTGTGCAACCCACGGAATTCATAACGAGTTTATGAATGACCGTATTGTCAC
1 TATGTGTGCAACCCACGGAATTCATAATGAGTTTATGAATGACCGTATCAACAC
* * *
5156659 TATGTGTGCAACCCACAGAATTCATATTGAGTTTATGAATGACCGTACCAACAC
1 TATGTGTGCAACCCACGGAATTCATAATGAGTTTATGAATGACCGTATCAACAC
* * * *
5156713 TATGTGTGTAACCCACGAAATTCATAATGAGTTTATGAATAATCGTATCAACAC
1 TATGTGTGCAACCCACGGAATTCATAATGAGTTTATGAATGACCGTATCAACAC
* * * * *
5156767 TATGGGTGTAACCCATGGAATTCATAACGAGTTTGTGAAT
1 TATGTGTGCAACCCACGGAATTCATAATGAGTTTATGAAT
5156807 TTCCATATCG
Statistics
Matches: 176, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 176 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (54 bp):
TATGTGTGCAACCCACGGAATTCATAATGAGTTTATGAATGACCGTATCAACAC
Found at i:5159672 original size:23 final size:23
Alignment explanation
Indices: 5159639--5159700 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
5159629 CTCGTATAAA
*
5159639 TGCACCAAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
*
5159662 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
***
5159685 TATTCCGAAGTGCCAT
1 TGCACCGAAGTGCCAT
5159701 ATAAGATGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:5161681 original size:24 final size:25
Alignment explanation
Indices: 5161654--5161701 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5161644 TTAGAGTTAT
*
5161654 CTTTTTCATTTACTTA-TTTATTTC
1 CTTTTTCATGTACTTATTTTATTTC
*
5161678 CTTTTTTATGTACTTATTTTATTT
1 CTTTTTCATGTACTTATTTTATTT
5161702 ACTAGTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.69
Consensus pattern (25 bp):
CTTTTTCATGTACTTATTTTATTTC
Found at i:5161685 original size:12 final size:12
Alignment explanation
Indices: 5161654--5161704 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
5161644 TTAGAGTTAT
*
5161654 CTTTTTCATTTA
1 CTTTTTTATTTA
* *
5161666 CTTATTTATTTC
1 CTTTTTTATTTA
*
5161678 CTTTTTTATGTA
1 CTTTTTTATTTA
5161690 CTTATTTTATTTA
1 CTT-TTTTATTTA
5161703 CT
1 CT
5161705 AGTTAGATGA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 21 0.68
13 10 0.32
ACGTcount: A:0.18, C:0.14, G:0.02, T:0.67
Consensus pattern (12 bp):
CTTTTTTATTTA
Found at i:5163033 original size:19 final size:19
Alignment explanation
Indices: 5162995--5163040 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5162985 ATATGTTGTT
* *
5162995 CAGCTGGATCGGTCTGAAC
1 CAGCTGGATCGATCTAAAC
*
5163014 CAGCTTGATCGATCTAAAC
1 CAGCTGGATCGATCTAAAC
*
5163033 CGGCTGGA
1 CAGCTGGA
5163041 CCAGTCTGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (19 bp):
CAGCTGGATCGATCTAAAC
Found at i:5165177 original size:26 final size:25
Alignment explanation
Indices: 5165129--5165177 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5165119 TTGTATTTTG
* *
5165129 TTTTTATATCTGAGTCTGGAAATCT
1 TTTTTATATCTGAATATGGAAATCT
*
5165154 TTTTTATTTCTGAATATGGTAAAT
1 TTTTTATATCTGAATATGG-AAAT
5165178 TTTACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (25 bp):
TTTTTATATCTGAATATGGAAATCT
Found at i:5170307 original size:11 final size:11
Alignment explanation
Indices: 5170269--5170332 Score: 67
Period size: 11 Copynumber: 5.5 Consensus size: 11
5170259 ACTACATTTG
5170269 TTAAAATA-TT
1 TTAAAATACTT
5170279 TTAAAAGTACCTTT
1 TTAAAA-TA-C-TT
5170293 TTAAAATACTT
1 TTAAAATACTT
*
5170304 TTAAAATATTT
1 TTAAAATACTT
*
5170315 TTTAAATCACTT
1 TTAAAAT-ACTT
5170327 TTAAAA
1 TTAAAA
5170333 AGTAATACTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 6 0.13
11 20 0.44
12 9 0.20
13 2 0.04
14 8 0.18
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.47
Consensus pattern (11 bp):
TTAAAATACTT
Found at i:5171357 original size:70 final size:71
Alignment explanation
Indices: 5171262--5171396 Score: 202
Period size: 70 Copynumber: 1.9 Consensus size: 71
5171252 ATATAAATAT
* *
5171262 AAATTTCAAAAATTATTAATTAAATTTTTATATTATGCAAATTTATTATAAAATTA-ATTTGATA
1 AAATTTCAAAAATTATTAACTAAATTTGTATATTATGCAAATTTATTATAAAATTATA-TTGATA
5171326 TTTAAAA
65 TTTAAAA
* * *
5171333 AAATTT-AAAATTTATTTACTAAATTTGTATATTATGCTAATTTATTATAAAATTATATTGATAT
1 AAATTTCAAAAATTATTAACTAAATTTGTATATTATGCAAATTTATTATAAAATTATATTGATAT
5171397 CTTTTTATGT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
70 51 0.88
71 7 0.12
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (71 bp):
AAATTTCAAAAATTATTAACTAAATTTGTATATTATGCAAATTTATTATAAAATTATATTGATAT
TTAAAA
Found at i:5172285 original size:54 final size:54
Alignment explanation
Indices: 5172220--5172508 Score: 382
Period size: 54 Copynumber: 5.4 Consensus size: 54
5172210 TTCATTGAGA
* ** * * * *
5172220 TGCACACATAGTGCCTATACGGTTATTCATAAATATATTATGAATTTTGT-GGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
* ** * *
5172273 TCGCACACATAGTGCCTATACGACCGTTTATCAACATATGATGAATTTTGTGGGT
1 T-GCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
* *
5172328 TGCACACTTAGTCCCTATACAGTCGTTCATCAACATATGATGAATTCTGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
* * *
5172382 TGCACACTTAGTGCCTATACGGTCGTTCATCAATATATGATGAATTCCGAGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
* *
5172436 TGCACACTTAGTGCCTATACGGTCATTCATCAACATATGCTGAATTCTGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
*
5172490 TGGACACTTAGTGCCTATA
1 TGCACACTTAGTGCCTATA
5172509 GTATATATAT
Statistics
Matches: 208, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
53 1 0.00
54 203 0.98
55 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGT
Found at i:5177463 original size:14 final size:14
Alignment explanation
Indices: 5177444--5177492 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
5177434 AAACATTCAA
5177444 TTATGTTCGTTCGG
1 TTATGTTCGTTCGG
5177458 TTATGTTCG-T---
1 TTATGTTCGTTCGG
5177468 TTATGTTCGTTCGG
1 TTATGTTCGTTCGG
5177482 TTATGTTCGTT
1 TTATGTTCGTT
5177493 TATGTTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.29
11 1 0.03
13 1 0.03
14 20 0.65
ACGTcount: A:0.08, C:0.12, G:0.24, T:0.55
Consensus pattern (14 bp):
TTATGTTCGTTCGG
Found at i:5177471 original size:10 final size:10
Alignment explanation
Indices: 5177452--5177499 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
5177442 AATTATGTTC
*
5177452 GTTCGGTTAT
1 GTTCGTTTAT
5177462 GTTCGTTTAT
1 GTTCGTTTAT
5177472 GTTCGTTCGGTTAT
1 GTTCG-T---TTAT
5177486 GTTCGTTTAT
1 GTTCGTTTAT
5177496 GTTC
1 GTTC
5177500 ATTCATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.54
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:5177512 original size:24 final size:24
Alignment explanation
Indices: 5177444--5177499 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
5177434 AAACATTCAA
5177444 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGT
5177468 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGT
5177492 TTATGTTC
1 TTATGTTC
5177500 ATTCATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.09, C:0.12, G:0.23, T:0.55
Consensus pattern (24 bp):
TTATGTTCGTTCGGTTATGTTCGT
Found at i:5177980 original size:16 final size:16
Alignment explanation
Indices: 5177959--5178025 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
5177949 ATCTCCAACG
5177959 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
* *
5177975 TTTATGTTCGGGTTCG
1 TTTATGTTCGTGTTCA
*
5177991 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
5178007 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
5178021 TTTAT
1 TTTAT
5178026 TAAATGAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:5179975 original size:54 final size:54
Alignment explanation
Indices: 5179914--5180362 Score: 580
Period size: 54 Copynumber: 8.3 Consensus size: 54
5179904 CGTTGAGATA
* * * * * *
5179914 CACACATAGTGCCGATACGGTCATTCATAAACATATTATGAATTTTGT-GGTTCG
1 CACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTT-G
* * * * *
5179968 TACACATAGTTCTTATACGGTCGTTCATCAACATATGATGAATTATGTGAGTTG
1 CACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTG
* * *
5180022 CACACTTAGTGTCTATACGGCCATTCATCAACATATGATGAATT-TCGTGGGTTG
1 CACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTAT-GTGGGTTG
* ***
5180076 CACACTTAGTGCCTATACAGTCGTTCATCAACATATGATGAATTCCATGGGTTG
1 CACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTG
*
5180130 CACACTTAGTGCCTATACGGTCGTTCATCAACATATGATTAATTATGTGGGTTG
1 CACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTG
* *
5180184 CACACTTAGTGTCTATACGGTCGTTCTTCAACATATGATGAATTATGTGGGTTG
1 CACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTG
* *
5180238 CACACTTAGTGCATATACGGTCGTTCATCAACATTTGATGAATT-TCGTGGGTTG
1 CACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTAT-GTGGGTTG
* * * * ***
5180292 TACGCTTAGTGCCTATACAGTCGTTCATTAACATATGATGAATTCCATGGGTTG
1 CACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTG
5180346 CACACTTAGTGCCTATA
1 CACACTTAGTGCCTATA
5180363 TTGTAATACC
Statistics
Matches: 345, Mismatches: 45, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
53 2 0.01
54 340 0.99
55 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (54 bp):
CACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTG
Found at i:5181335 original size:94 final size:95
Alignment explanation
Indices: 5181188--5181368 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 95
5181178 CAATACTAAA
* * *
5181188 AAGGAAAGTATCAATGCCATGGATTCTAGAATGCCAAAATGGTTTCGATACTGAAAGGGAGTATC
1 AAGGAAAGTATCAATACCATGGATTCCAGAATACCAAAATGGTTTCGATACTGAAAGGGAGTATC
** *
5181253 AGTACCGTATTATAGAAGTATCGGTATTAG
66 AGTACCACAGTATAGAAGTATCGGTATTAG
* ***
5181283 AAGGAAAGTATCGATACCATGGA-TCCAGAATATTGAAATGGTATT-GATACTGAAAGGGAGTAT
1 AAGGAAAGTATCAATACCATGGATTCCAGAATACCAAAATGGT-TTCGATACTGAAAGGGAGTAT
5181346 CAGTACCACAGTATAGAAGTATC
65 CAGTACCACAGTATAGAAGTATC
5181369 AATACGATGG
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
94 52 0.69
95 23 0.31
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.26
Consensus pattern (95 bp):
AAGGAAAGTATCAATACCATGGATTCCAGAATACCAAAATGGTTTCGATACTGAAAGGGAGTATC
AGTACCACAGTATAGAAGTATCGGTATTAG
Found at i:5181885 original size:81 final size:81
Alignment explanation
Indices: 5181776--5182349 Score: 752
Period size: 81 Copynumber: 7.1 Consensus size: 81
5181766 TTGTTTTAAA
* * * * * *
5181776 TAAAATATTAATTGTCTAGCTGTACATTTGATAGAAATGTGTCAATTATGCCAATTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
5181841 GTTAAATACCTTTGAG
66 GTTAAATGCCTTTGAG
* * * * *
5181857 TAAAAGATTAATTGCCTAGTTTTGCATTTGACAAAAAGGTTTCAATTAGGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
5181922 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * *
5181938 TAAAAGATTAATTGCATAGCTGTGCATTTGACAGAAAGGTGTCAATTATGACAGTTAGATGGAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
5182003 GTTAAATTCCTTTGAG
66 GTTAAATGCCTTTGAG
* * * * * * *
5182019 TAAAACATTAATTACCTAGTTGTACATTTGACCGAAAGATGCCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
5182084 GTTAAACGGCTTTGAG
66 GTTAAATGCCTTTGAG
* * **
5182100 TAAAAGATTAATTGTCTAGCTCTGCATTTGACAGAAATATGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
5182165 GTTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * * *
5182181 TAAAAGATTAATTGCCTAGCTGTGCATTTCACAGAAAGGTTTCAATTATGTCAGTTAAATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
5182246 GCTAAATGCCTTTGAG
66 GTTAAATGCCTTTGAG
* * * * * * *
5182262 TTAAAGATTAAATGTCTAGCTGTGCATTGGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
5182327 GCTAAATGTCTTTGGG
66 GTTAAATGCCTTTGAG
5182343 TAAAAGA
1 TAAAAGA
5182350 CTAAATGTGT
Statistics
Matches: 425, Mismatches: 68, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 425 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATGCCTTTGAG
Found at i:5184038 original size:13 final size:14
Alignment explanation
Indices: 5184014--5184043 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5184004 TTTAGTAATT
5184014 TTAAGATTTTGAAA
1 TTAAGATTTTGAAA
5184028 TTAAG-TTTTGAAA
1 TTAAGATTTTGAAA
5184041 TTA
1 TTA
5184044 CTCCCCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TTAAGATTTTGAAA
Found at i:5184761 original size:18 final size:18
Alignment explanation
Indices: 5184709--5184749 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
5184699 AGGCATTTGA
*
5184709 TCCTCTGGTCGTGCTTGT
1 TCCTCTGGTTGTGCTTGT
5184727 TCCTCTGGTTGTGCTTGT
1 TCCTCTGGTTGTGCTTGT
5184745 TCCTC
1 TCCTC
5184750 GTGTTGTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.29, G:0.24, T:0.46
Consensus pattern (18 bp):
TCCTCTGGTTGTGCTTGT
Found at i:5186340 original size:22 final size:22
Alignment explanation
Indices: 5186315--5186397 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
5186305 CAGAACCCTC
* * *
5186315 AGGGGGTATCGATCCCCCTACA
1 AGGGGGAATCGATTCCCCTTCA
5186337 A-GGGGAATC-AGTTCCCCTTCAA
1 AGGGGGAATCGA-TTCCCCTTC-A
*
5186359 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
* *
5186381 AAGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
5186398 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 1 0.02
21 14 0.28
22 18 0.36
23 17 0.34
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.22
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:5186368 original size:23 final size:23
Alignment explanation
Indices: 5186338--5186386 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
5186328 CCCCCTACAA
5186338 GGGGAATCAGTTCCCCTTCAAAG
1 GGGGAATCAGTTCCCCTTCAAAG
*
5186361 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCAGTTCCCCTTCAAAG
5186384 GGG
1 GGG
5186387 TATCGATTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.20
Consensus pattern (23 bp):
GGGGAATCAGTTCCCCTTCAAAG
Found at i:5192173 original size:22 final size:22
Alignment explanation
Indices: 5192122--5192176 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
5192112 CGTTGATCAA
** *
5192122 GGGGAATAAGTACCCCCTTGGG
1 GGGGAATCGGTACCCCCTAGGG
5192144 GGGGAATCGGTACCCCCTAGGG
1 GGGGAATCGGTACCCCCTAGGG
5192166 GGGGAATCGGT
1 GGGGAATCGGT
5192177 TCCCTCCGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.16
Consensus pattern (22 bp):
GGGGAATCGGTACCCCCTAGGG
Found at i:5194401 original size:9 final size:9
Alignment explanation
Indices: 5194387--5194468 Score: 50
Period size: 9 Copynumber: 9.6 Consensus size: 9
5194377 TTGGAAATTA
5194387 AATAAGAAT
1 AATAAGAAT
*
5194396 AATAAGATT
1 AATAAGAAT
*
5194405 AA-AATAAT
1 AATAAGAAT
5194413 AA-ATAGAA-
1 AATA-AGAAT
5194421 AATAA-AGAT
1 AATAAGA-AT
*
5194430 AA-GAGAA-
1 AATAAGAAT
*
5194437 AATAATAAT
1 AATAAGAAT
*
5194446 AATAATAAT
1 AATAAGAAT
*
5194455 AATAATAAT
1 AATAAGAAT
5194464 AATAA
1 AATAA
5194469 TATGATATGA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
7 3 0.05
8 16 0.27
9 40 0.68
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (9 bp):
AATAAGAAT
Found at i:5194445 original size:3 final size:3
Alignment explanation
Indices: 5194437--5194470 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5194427 GATAAGAGAA
5194437 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5194471 TGATATGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5199623 original size:22 final size:22
Alignment explanation
Indices: 5199595--5199638 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5199585 TTCTTCTATG
5199595 ATAACTCTCCAAAAAAGTTATC
1 ATAACTCTCCAAAAAAGTTATC
5199617 ATAACTCTCCAAAAAAGTTATC
1 ATAACTCTCCAAAAAAGTTATC
5199639 TTTTATGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.27
Consensus pattern (22 bp):
ATAACTCTCCAAAAAAGTTATC
Found at i:5201213 original size:21 final size:21
Alignment explanation
Indices: 5201188--5201261 Score: 98
Period size: 21 Copynumber: 3.5 Consensus size: 21
5201178 AATATATATA
5201188 ATTTATAAAAGTAAAATATTT
1 ATTTATAAAAGTAAAATATTT
*
5201209 ATTTA-AAAA-TAATATATATATA
1 ATTTATAAAAGTAA-A-ATAT-TT
5201231 ATTTATAAAAGTAAAATATTT
1 ATTTATAAAAGTAAAATATTT
5201252 ATTTATAAAA
1 ATTTATAAAA
5201262 AAAATCAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 3 0.07
20 5 0.11
21 20 0.43
22 10 0.22
23 5 0.11
24 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTTATAAAAGTAAAATATTT
Found at i:5201214 original size:47 final size:44
Alignment explanation
Indices: 5201163--5201262 Score: 157
Period size: 43 Copynumber: 2.2 Consensus size: 44
5201153 AAAAAAATAT
5201163 TTTAAAAAATAGATTAATATATATAATTTATAAAAGTAAAATATTTA
1 TTTAAAAAATA-A-T-ATATATATAATTTATAAAAGTAAAATATTTA
5201210 TTT-AAAAATAATATATATATAATTTATAAAAGTAAAATATTTA
1 TTTAAAAAATAATATATATATAATTTATAAAAGTAAAATATTTA
5201253 TTTATAAAAA
1 TTTA-AAAAA
5201263 AAATCAGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
43 34 0.67
44 1 0.02
45 6 0.12
46 7 0.14
47 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (44 bp):
TTTAAAAAATAATATATATATAATTTATAAAAGTAAAATATTTA
Found at i:5201239 original size:43 final size:44
Alignment explanation
Indices: 5201179--5201261 Score: 159
Period size: 43 Copynumber: 1.9 Consensus size: 44
5201169 AAATAGATTA
5201179 ATATATATAATTTATAAAAGTAAAATATTTATTTA-AAAATAAT
1 ATATATATAATTTATAAAAGTAAAATATTTATTTATAAAATAAT
5201222 ATATATATAATTTATAAAAGTAAAATATTTATTTATAAAA
1 ATATATATAATTTATAAAAGTAAAATATTTATTTATAAAA
5201262 AAAATCAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
43 35 0.90
44 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (44 bp):
ATATATATAATTTATAAAAGTAAAATATTTATTTATAAAATAAT
Found at i:5202489 original size:44 final size:45
Alignment explanation
Indices: 5202439--5202539 Score: 123
Period size: 45 Copynumber: 2.3 Consensus size: 45
5202429 GGTTGATGCT
* ** *
5202439 TGCTGGAAGCTGTTGGAA-TGGGGACGTGGAAGGGCTGCTAGCAG
1 TGCTGGAAGCTGCTGGAATTGGCAACATGGAAGGGCTGCTAGCAG
* * *
5202483 TGCTGGAAGCTGCTGGAATTTGCAACATGGAGGGGCTGCTGGCAG
1 TGCTGGAAGCTGCTGGAATTGGCAACATGGAAGGGCTGCTAGCAG
*
5202528 TGCTAGAAGCTG
1 TGCTGGAAGCTG
5202540 ATGGGATTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 17 0.35
45 31 0.65
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.22
Consensus pattern (45 bp):
TGCTGGAAGCTGCTGGAATTGGCAACATGGAAGGGCTGCTAGCAG
Found at i:5212836 original size:54 final size:54
Alignment explanation
Indices: 5212756--5213077 Score: 432
Period size: 54 Copynumber: 5.9 Consensus size: 54
5212746 ATGGGAACTA
*
5212756 TGTGTGAAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTG
** *
5212810 TGTGTATAACTTAAAAAATTCATAATAAGTTTATGAA-TTTCTGTATTGGCACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATTGGCACTG
* * *
5212864 TGTGTGCAACTTAATAAATTCATAATAAGTTTATGAA-TTTCTGTATTGACACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATTGGCACTG
*
5212918 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTG
* * * *
5212972 TGTGTGCAACCTAAGAAATTCATAATAAGTTTGTGAATTTCCGTATTGGCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTG
** * * * * *
5213026 TGTGTGCAACCCCACGTAATTCATAATAAGTTTGTGAATTATCGTATCGGCA
1 TGTGTGCAA-CTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCA
5213078 TTACGTGTGC
Statistics
Matches: 242, Mismatches: 23, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
53 4 0.02
54 199 0.82
55 39 0.16
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (54 bp):
TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTG
Found at i:5213479 original size:23 final size:23
Alignment explanation
Indices: 5213436--5213479 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5213426 TAAGTTAATG
* **
5213436 AATGTTTTATTATTATTAAACTT
1 AATGTTTTATGATTAGAAAACTT
5213459 AATGTTTTATGATTAGAAAAC
1 AATGTTTTATGATTAGAAAAC
5213480 AAAATTTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (23 bp):
AATGTTTTATGATTAGAAAACTT
Found at i:5220531 original size:20 final size:20
Alignment explanation
Indices: 5220506--5220545 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5220496 TCATAACCAT
5220506 AAATTACAACTAATCCAAAC
1 AAATTACAACTAATCCAAAC
5220526 AAATTACAACTAATCCAAAC
1 AAATTACAACTAATCCAAAC
5220546 CCTTCATTCA
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:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATTACAACTAATCCAAAC
Found at i:5233424 original size:35 final size:35
Alignment explanation
Indices: 5233385--5233504 Score: 152
Period size: 35 Copynumber: 3.4 Consensus size: 35
5233375 CCTTAGATCC
5233385 ATAAGGAATTACCAATTGATCGGTACTGAACCTAT
1 ATAAGGAATTACCAATTGATCGGTACTGAACCTAT
** *
5233420 ATAAGGAATTACCAATTGATCGGTGTTGAACCTGT
1 ATAAGGAATTACCAATTGATCGGTACTGAACCTAT
* * *
5233455 ATAAGGAATTATCAACTTGATCAG-AGCAGAACCTAT
1 ATAAGGAATTACCAA-TTGATCGGTA-CTGAACCTAT
*
5233491 ATAATGAATTACCA
1 ATAAGGAATTACCA
5233505 GCTTGATCAA
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
35 46 0.64
36 26 0.36
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (35 bp):
ATAAGGAATTACCAATTGATCGGTACTGAACCTAT
Found at i:5233487 original size:36 final size:35
Alignment explanation
Indices: 5233385--5233525 Score: 149
Period size: 35 Copynumber: 4.0 Consensus size: 35
5233375 CCTTAGATCC
*
5233385 ATAAGGAATTACCAATTGATCGGTA-CTGAACCTAT
1 ATAAGGAATTACCAATTGATCAG-AGCTGAACCTAT
* * * *
5233420 ATAAGGAATTACCAATTGATCGGTGTTGAACCTGT
1 ATAAGGAATTACCAATTGATCAGAGCTGAACCTAT
* *
5233455 ATAAGGAATTATCAACTTGATCAGAGCAGAACCTAT
1 ATAAGGAATTACCAA-TTGATCAGAGCTGAACCTAT
* * * *
5233491 ATAATGAATTACCAGCTTGATCAAAGCTAAACCTA
1 ATAAGGAATTACCA-ATTGATCAGAGCTGAACCTA
5233526 CAGAGCCTTC
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
35 45 0.51
36 43 0.49
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (35 bp):
ATAAGGAATTACCAATTGATCAGAGCTGAACCTAT
Found at i:5237049 original size:41 final size:41
Alignment explanation
Indices: 5236999--5237150 Score: 202
Period size: 41 Copynumber: 3.7 Consensus size: 41
5236989 GGCCATCAAT
5236999 AGTCTTTCGAGCATGATGTTAAATCCTTCGGGTCATCAGTA
1 AGTCTTTCGAGCATGATGTTAAATCCTTCGGGTCATCAGTA
5237040 AGTCTTTCGAGCATGATGTTAAATCCTTCGGGTCATCAGTA
1 AGTCTTTCGAGCATGATGTTAAATCCTTCGGGTCATCAGTA
* * * *
5237081 AGTCTTTCGAGCGTGATGTTAAGTCCTCCGGG-CAATCACTA
1 AGTCTTTCGAGCATGATGTTAAATCCTTCGGGTC-ATCAGTA
*
5237122 AGTCCTTTGGGAGCGATGAT-TTAAA-CCTT
1 AGT-CTTT-CGAGC-ATGATGTTAAATCCTT
5237151 TGTGTACACT
Statistics
Matches: 99, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
40 1 0.01
41 79 0.80
42 7 0.07
43 8 0.08
44 4 0.04
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (41 bp):
AGTCTTTCGAGCATGATGTTAAATCCTTCGGGTCATCAGTA
Found at i:5237103 original size:21 final size:21
Alignment explanation
Indices: 5236999--5237105 Score: 64
Period size: 21 Copynumber: 5.2 Consensus size: 21
5236989 GGCCATCAAT
*
5236999 AGTCTTTCGAGCATGATGTTA
1 AGTCTTTCGAGCGTGATGTTA
* * *
5237020 AATCCTTCG-G-GTCATCAG-TA
1 AGTCTTTCGAGCGTGAT--GTTA
*
5237040 AGTCTTTCGAGCATGATGTTA
1 AGTCTTTCGAGCGTGATGTTA
* * *
5237061 AATCCTTCG-G-GTCATCAG-TA
1 AGTCTTTCGAGCGTGAT--GTTA
5237081 AGTCTTTCGAGCGTGATGTTA
1 AGTCTTTCGAGCGTGATGTTA
5237102 AGTC
1 AGTC
5237106 CTCCGGGCAA
Statistics
Matches: 61, Mismatches: 15, Indels: 20
0.64 0.16 0.21
Matches are distributed among these distances:
19 6 0.10
20 22 0.36
21 26 0.43
22 7 0.11
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (21 bp):
AGTCTTTCGAGCGTGATGTTA
Found at i:5237124 original size:82 final size:83
Alignment explanation
Indices: 5236976--5237150 Score: 207
Period size: 82 Copynumber: 2.1 Consensus size: 83
5236966 TTTCTCAATT
* * * * *
5236976 TTTAAGACCTTCAGGCCATCAAT-AGTCTTTCGAGCATGATGTTAAATCCTTCGGGTCATCAGTA
1 TTTAA-ACCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGTTAAATCCTCCGGGTCATCACTA
5237040 AGT-CTTT-CGAGC-ATGA
65 AGTCCTTTGCGAGCGATGA
* *
5237056 TGTTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCGTGATGTTAAGTCCTCCGGG-CAATCAC
1 T-TTAAA-CCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGTTAAATCCTCCGGGTC-ATCAC
*
5237120 TAAGTCCTTTGGGAGCGATGA
63 TAAGTCCTTTGCGAGCGATGA
5237141 TTTAAACCTT
1 TTTAAACCTT
5237151 TGTGTACACT
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
80 2 0.03
81 18 0.22
82 38 0.47
83 8 0.10
84 9 0.11
85 5 0.06
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (83 bp):
TTTAAACCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGTTAAATCCTCCGGGTCATCACTAA
GTCCTTTGCGAGCGATGA
Found at i:5240426 original size:6 final size:6
Alignment explanation
Indices: 5240412--5240466 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
5240402 GACACGTATT
* * * *
5240412 ACCATG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
5240460 ACCACG A
1 ACCACG A
5240467 GCCGAGTCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.29, C:0.47, G:0.16, T:0.07
Consensus pattern (6 bp):
ACCACG
Found at i:5240484 original size:15 final size:15
Alignment explanation
Indices: 5240464--5240512 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5240454 ACCACGACCA
5240464 CGAGCCGAGTCGAGC
1 CGAGCCGAGTCGAGC
*
5240479 CGAGCCGTACT-GAGC
1 CGAGCCG-AGTCGAGC
* *
5240494 CGAGCCGAGACGAGA
1 CGAGCCGAGTCGAGC
5240509 CGAG
1 CGAG
5240513 ACGAACGGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.04
15 25 0.89
16 2 0.07
ACGTcount: A:0.24, C:0.31, G:0.39, T:0.06
Consensus pattern (15 bp):
CGAGCCGAGTCGAGC
Found at i:5246384 original size:6 final size:6
Alignment explanation
Indices: 5246373--5246433 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
5246363 GACACGTATT
* * *
5246373 ACCACG ACCACG ACCACG ACCACA ACCACG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
5246421 ACCACG ACCACG A
1 ACCACG ACCACG A
5246434 GCCAAGCCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.49, G:0.15, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:5246446 original size:5 final size:5
Alignment explanation
Indices: 5246431--5246474 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
5246421 ACCACGACCA
* * * *
5246431 CGAGC CAAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
5246475 ACAGACGGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.39, T:0.02
Consensus pattern (5 bp):
CGAGC
Found at i:5247818 original size:24 final size:24
Alignment explanation
Indices: 5247791--5247837 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5247781 AAAGTGACTA
* *
5247791 TTTAATAAAATATTAAAAATATTT
1 TTTAACAAAATATAAAAAATATTT
**
5247815 TTTAACATTATATAAAAAATATT
1 TTTAACAAAATATAAAAAATATT
5247838 ATGGTTGGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAACAAAATATAAAAAATATTT
Found at i:5248643 original size:15 final size:14
Alignment explanation
Indices: 5248621--5248655 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
5248611 GTAAATTTTT
*
5248621 TAAAATAAATATTA
1 TAAAATAAAAATTA
5248635 TAGAAATAAAAATTA
1 TA-AAATAAAAATTA
5248650 TAAAAT
1 TAAAAT
5248656 TACAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
TAAAATAAAAATTA
Found at i:5251302 original size:16 final size:16
Alignment explanation
Indices: 5251277--5251311 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5251267 CAAACGAATC
5251277 TTTAAAATTTAATATT
1 TTTAAAATTTAATATT
* *
5251293 TTTAACATTTTATATT
1 TTTAAAATTTAATATT
5251309 TTT
1 TTT
5251312 TTCTAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAAAATTTAATATT
Found at i:5251342 original size:20 final size:21
Alignment explanation
Indices: 5251317--5251366 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
5251307 TTTTTTTCTA
5251317 AATATTTTA-AATAATTATT-T
1 AATATTTTAGAATAATT-TTGT
5251337 AATATTTTAGAATAATTTTGT
1 AATATTTTAGAATAATTTTGT
*
5251358 ATTATTTTA
1 AATATTTTA
5251367 TGATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
AATATTTTAGAATAATTTTGT
Found at i:5251578 original size:2 final size:2
Alignment explanation
Indices: 5251538--5251563 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5251528 GACTTTTTGA
5251538 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5251564 TCAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5252525 original size:14 final size:14
Alignment explanation
Indices: 5252506--5252533 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5252496 GAACCGGTCT
5252506 GACCCGACCCGACC
1 GACCCGACCCGACC
5252520 GACCCGACCCGACC
1 GACCCGACCCGACC
5252534 CGAAGGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.57, G:0.21, T:0.00
Consensus pattern (14 bp):
GACCCGACCCGACC
Found at i:5252554 original size:5 final size:5
Alignment explanation
Indices: 5252506--5252536 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5252496 GAACCGGTCT
5252506 GACCC GACCC GA-CC GACCC GACCC GACCC GA
1 GACCC GACCC GACCC GACCC GACCC GACCC GA
5252537 AGGTTGACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.23, C:0.55, G:0.23, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:5259810 original size:9 final size:9
Alignment explanation
Indices: 5259766--5259826 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 9
5259756 CAGCTGGAAA
5259766 ACCGGTTTG
1 ACCGGTTTG
*
5259775 ACCAGTTTTG
1 ACC-GGTTTG
*
5259785 AACCGGTTTTA
1 -ACCGG-TTTG
5259796 ACCGGTTTG
1 ACCGGTTTG
*
5259805 ACCGGTCTG
1 ACCGGTTTG
*
5259814 AACCGGTCTG
1 -ACCGGTTTG
5259824 ACC
1 ACC
5259827 CGACCCGACC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 17 0.40
10 20 0.47
11 6 0.14
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:5259810 original size:19 final size:19
Alignment explanation
Indices: 5259781--5259826 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5259771 TTTGACCAGT
* *
5259781 TTTGAACCGGTTTTAACCGG
1 TTTG-ACCGGTCTGAACCGG
5259801 TTTGACCGGTCTGAACCGG
1 TTTGACCGGTCTGAACCGG
*
5259820 TCTGACC
1 TTTGACC
5259827 CGACCCGACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (19 bp):
TTTGACCGGTCTGAACCGG
Found at i:5259833 original size:5 final size:5
Alignment explanation
Indices: 5259823--5259872 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
5259813 GAACCGGTCT
**
5259823 GACCC GACCC GA-CC GACCC GACCC GACCC GAACGTT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC G-AC-CC GACCC GACCC GACC
5259873 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 4 0.11
5 29 0.76
6 4 0.11
7 1 0.03
ACGTcount: A:0.22, C:0.52, G:0.22, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:5259842 original size:14 final size:14
Alignment explanation
Indices: 5259823--5259850 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5259813 GAACCGGTCT
5259823 GACCCGACCCGACC
1 GACCCGACCCGACC
5259837 GACCCGACCCGACC
1 GACCCGACCCGACC
5259851 CGAACGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.57, G:0.21, T:0.00
Consensus pattern (14 bp):
GACCCGACCCGACC
Found at i:5259864 original size:17 final size:17
Alignment explanation
Indices: 5259842--5259879 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5259832 CGACCGACCC
5259842 GACCCGACCCGAACGTT
1 GACCCGACCCGAACGTT
*
5259859 GACCCGACCCGACCGTT
1 GACCCGACCCGAACGTT
5259876 GACC
1 GACC
5259880 GTTAACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.45, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGAACGTT
Found at i:5266674 original size:3 final size:3
Alignment explanation
Indices: 5266666--5266767 Score: 132
Period size: 3 Copynumber: 33.3 Consensus size: 3
5266656 TGTATTTATT
5266666 TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * **
5266712 TGTA TAT TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TTT TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5266758 AAA TAA TAA T
1 TAA TAA TAA T
5266768 TTAAGTAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
3 80 0.94
4 5 0.06
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5266947 original size:45 final size:45
Alignment explanation
Indices: 5266883--5267806 Score: 1407
Period size: 45 Copynumber: 20.5 Consensus size: 45
5266873 GATGGAAATG
* * *
5266883 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGC
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * *
5266928 TTTGAAAACATCATGCACTGAACGACTTACAGATTACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * *
5266973 TTTGAAAACATCATGCAGTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
*
5267018 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
5267063 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * ** *
5267108 TTTGAAGACATCAAGCACTGAATGACAAACAGATGACCCGAAGAT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * *
5267153 TTTGAAGACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * *
5267198 TTTGAAAATATCAAGCACTGAAGGACTTATAGATGGCCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
5267243 TTTGAAGACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
*
5267288 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
5267333 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
*
5267378 TTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
5267423 TTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCCGAAGAT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * * *
5267468 TTTGAAGACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
*
5267513 TTTGAAAACATCAAGCACTAAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * * *
5267558 TTTGAAGACATCAAGAACTGAAGGGCTTACAGATTACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * * *
5267603 TTTGAAAACATGAAGCACTGAAGGGCCTACAGATGACTCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
*
5267648 TTTGAAAACATCAAGCACTGAAGAACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
5267693 TTTGAAGACATCAAGCACTAAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * *
5267738 TTTGAAGACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * *
5267783 TTTGAAGACACCATGCACTGAAGG
1 TTTGAAAACATCAAGCACTGAAGG
5267807 TTTTGAAGAC
Statistics
Matches: 810, Mismatches: 69, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 810 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (45 bp):
TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
Found at i:5267811 original size:25 final size:25
Alignment explanation
Indices: 5267777--5267831 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
5267767 CAGATGACCC
5267777 GAAGGTTTTGAAGACACCATGCACT
1 GAAGGTTTTGAAGACACCATGCACT
*
5267802 GAAGGTTTTGAAGACATCATGCACT
1 GAAGGTTTTGAAGACACCATGCACT
5267827 GAAGG
1 GAAGG
5267832 GCTTACAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (25 bp):
GAAGGTTTTGAAGACACCATGCACT
Found at i:5268523 original size:22 final size:22
Alignment explanation
Indices: 5268498--5268577 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 22
5268488 AATAAAGCTT
5268498 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
5268520 TCATCTTT--AAAGAGATATGTTA
1 TCATCTTTGAAAAGAGA-AT-CTA
*
5268542 TCATCTTTGAAGAA-ATAATCTA
1 TCATCTTTGAA-AAGAGAATCTA
*
5268564 TCATATTTGAAAAG
1 TCATCTTTGAAAAG
5268578 TGTAGATGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.15
21 4 0.08
22 30 0.62
23 2 0.04
24 3 0.06
25 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:5280749 original size:3 final size:3
Alignment explanation
Indices: 5280741--5280818 Score: 84
Period size: 3 Copynumber: 25.3 Consensus size: 3
5280731 TGTATTTATT
* *
5280741 TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TGTA TAT TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* ** *
5280788 CAA TAA TAA TAA TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5280819 TTATATAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
3 56 0.92
4 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5281849 original size:19 final size:19
Alignment explanation
Indices: 5281827--5281871 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
5281817 ACAATTATTA
* **
5281827 TTAAAATATATTATATTTT
1 TTAAAATATATAATAAGTT
*
5281846 TTAAAAAATATAATAAGTT
1 TTAAAATATATAATAAGTT
5281865 TTAAAAT
1 TTAAAAT
5281872 TAGCTTGGCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTAAAATATATAATAAGTT
Done.