Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 14 of 204
Found at i:5451333 original size:16 final size:17
Alignment explanation
Indices: 5451312--5451343 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5451302 AAATATGCAA
5451312 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
5451328 TCACATAACTTCATAT
1 TCACATAACTTCATAT
5451344 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:5451593 original size:41 final size:41
Alignment explanation
Indices: 5451536--5451647 Score: 100
Period size: 41 Copynumber: 2.7 Consensus size: 41
5451526 TCTTACATGT
* * * * *
5451536 AATCACATATGATGCCACTGTCTCAGACAGGGTCTTACACA
1 AATCAAATACGATGCCAATGTCCCAGACAGGATCTTACACA
* * *
5451577 AATCAAATACGATGCCAATGTCCCGGACATGATCTTACACG
1 AATCAAATACGATGCCAATGTCCCAGACAGGATCTTACACA
* *
5451618 TATACACAAGT-CGATGCCAACGTCCCAGAC
1 AAT-CA-AA-TACGATGCCAATGTCCCAGAC
5451648 GTGGTCTTAC
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 35 0.61
42 2 0.04
43 19 0.33
44 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (41 bp):
AATCAAATACGATGCCAATGTCCCAGACAGGATCTTACACA
Found at i:5454101 original size:23 final size:23
Alignment explanation
Indices: 5454071--5454159 Score: 124
Period size: 23 Copynumber: 3.9 Consensus size: 23
5454061 GTTATTGATC
* *
5454071 AGTGGTAGCTTCAGCTACATTTT
1 AGTGGTAGCTACGGCTACATTTT
* *
5454094 AGTGGTAGCTACGACTACATTTC
1 AGTGGTAGCTACGGCTACATTTT
*
5454117 AGTGGTAGCTACGGCTACATATT
1 AGTGGTAGCTACGGCTACATTTT
*
5454140 AGTGGTAGCTTCGGCTACAT
1 AGTGGTAGCTACGGCTACAT
5454160 ATCAGTGTGG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (23 bp):
AGTGGTAGCTACGGCTACATTTT
Found at i:5454122 original size:46 final size:46
Alignment explanation
Indices: 5454068--5454166 Score: 144
Period size: 46 Copynumber: 2.2 Consensus size: 46
5454058 AGTGTTATTG
* *
5454068 ATCAGTGGTAGCTTCAGCTACATTTTAGTGGTAGCTACGACTACAT
1 ATCAGTGGTAGCTACAGCTACATATTAGTGGTAGCTACGACTACAT
* * * *
5454114 TTCAGTGGTAGCTACGGCTACATATTAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACAGCTACATATTAGTGGTAGCTACGACTACAT
5454160 ATCAGTG
1 ATCAGTG
5454167 TGGCACTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTACAGCTACATATTAGTGGTAGCTACGACTACAT
Found at i:5457058 original size:22 final size:20
Alignment explanation
Indices: 5457033--5457072 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
5457023 AAATATTGAG
*
5457033 AAAATAATAAGAAAATAACAGC
1 AAAACAATAA-AAAA-AACAGC
5457055 AAAACAATAAAAAAAACA
1 AAAACAATAAAAAAAACA
5457073 AGAAGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.75, C:0.10, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAACAATAAAAAAAACAGC
Found at i:5461166 original size:2 final size:2
Alignment explanation
Indices: 5461161--5461191 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5461151 GTGTGTGTGT
*
5461161 GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5461192 GGACGGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5463427 original size:32 final size:32
Alignment explanation
Indices: 5463391--5463459 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
5463381 CATGCACACA
5463391 AACATTCATAGGTGAATAAATGACATCCTACT
1 AACATTCATAGGTGAATAAATGACATCCTACT
5463423 AACATTCATAGGTGAATAAATGACATCCTACT
1 AACATTCATAGGTGAATAAATGACATCCTACT
5463455 AACAT
1 AACAT
5463460 ATGGGGCGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (32 bp):
AACATTCATAGGTGAATAAATGACATCCTACT
Found at i:5468325 original size:127 final size:125
Alignment explanation
Indices: 5468025--5468593 Score: 838
Period size: 126 Copynumber: 4.5 Consensus size: 125
5468015 GATAAAATCA
* * * * * * * *
5468025 AAGCAGGATGCT-TTATCAGAAGGATTTCTGAAGTCGCACCCACGTGTACGTGCTTTTGCTACAG
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *
5468089 TGGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* *
5468150 AAGCAGGATG-TTTTATGAGAAGAATTTGTGAAATCGCGCCATCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
5468214 TAGGTCCAGGAATAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
65 TAGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTT-AAAAAACGCTTC
* * * *
5468277 AAGCAAGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTCATGGACGCGCTTTTGCTACAAT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * *
5468342 AGGTCCTGAAAGAAATAATTTTGAGTTGACGTTTCGGAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* * *
5468403 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCATGGACGCGTTTTTACTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
*
5468468 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* *
5468527 TAGCAGGATGCTATTTGAGAAGAATATGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
5468592 AG
66 AG
5468594 CATGTTTGGG
Statistics
Matches: 403, Mismatches: 37, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
124 74 0.18
125 97 0.24
126 118 0.29
127 111 0.28
128 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
Found at i:5471773 original size:21 final size:21
Alignment explanation
Indices: 5471743--5471783 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5471733 TCAAATTATA
*
5471743 TTTAAGTTAAGGGTTAGGGTT
1 TTTAACTTAAGGGTTAGGGTT
*
5471764 TTTAACTTAAGTGTTAGGGT
1 TTTAACTTAAGGGTTAGGGT
5471784 AATCGAGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.44
Consensus pattern (21 bp):
TTTAACTTAAGGGTTAGGGTT
Found at i:5471887 original size:20 final size:20
Alignment explanation
Indices: 5471850--5471887 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5471840 TTTATTTTTA
*
5471850 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
5471870 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
5471888 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:5472898 original size:11 final size:11
Alignment explanation
Indices: 5472884--5472960 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
5472874 TTAAATATGG
5472884 ATTTGAGAGAA
1 ATTTGAGAGAA
*
5472895 ATTTG-GAAGGA
1 ATTTGAG-AGAA
5472906 ATTTGAGAGCAA
1 ATTTGAGAG-AA
5472918 ATTT-AGAGGAA
1 ATTTGAGA-GAA
5472929 ATTT-AGAGGAA
1 ATTTGAGA-GAA
5472940 A-TTGAGAGGAA
1 ATTTGAGA-GAA
5472951 ATTTGAGAGA
1 ATTTGAGAGA
5472961 TGATTAGTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
10 3 0.05
11 42 0.72
12 13 0.22
ACGTcount: A:0.43, C:0.01, G:0.30, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:5472909 original size:22 final size:22
Alignment explanation
Indices: 5472884--5472960 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
5472874 TTAAATATGG
5472884 ATTTGAGAGAAATTTGGAAGG-A
1 ATTTGAGAGAAATTT-GAAGGAA
5472906 ATTTGAGAGCAAATTT-AGAGGAA
1 ATTTGAGAG-AAATTTGA-AGGAA
5472929 ATTT-AGAGGAAA-TTGAGAGGAA
1 ATTTGAGA-GAAATTTGA-AGGAA
5472951 ATTTGAGAGA
1 ATTTGAGAGA
5472961 TGATTAGTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
21 3 0.06
22 31 0.63
23 15 0.31
ACGTcount: A:0.43, C:0.01, G:0.30, T:0.26
Consensus pattern (22 bp):
ATTTGAGAGAAATTTGAAGGAA
Found at i:5472945 original size:33 final size:35
Alignment explanation
Indices: 5472884--5472960 Score: 99
Period size: 33 Copynumber: 2.3 Consensus size: 35
5472874 TTAAATATGG
* *
5472884 ATTT-GAGAGAAATTTGGAAGGAATTTGAGAGCAA
1 ATTTAGAGAGAAATTTAGAAGGAAATTGAGAGCAA
*
5472918 ATTTAGAG-GAAATTTAG-AGGAAATTGAGAGGAA
1 ATTTAGAGAGAAATTTAGAAGGAAATTGAGAGCAA
5472951 ATTT-GAGAGA
1 ATTTAGAGAGA
5472961 TGATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 3 0.08
33 20 0.53
34 12 0.32
35 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.30, T:0.26
Consensus pattern (35 bp):
ATTTAGAGAGAAATTTAGAAGGAAATTGAGAGCAA
Found at i:5478349 original size:18 final size:18
Alignment explanation
Indices: 5478328--5478362 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5478318 ACTTTACTAA
* *
5478328 TCAAGTGATGCCTTCAAC
1 TCAAATGATGCCCTCAAC
5478346 TCAAATGATGCCCTCAA
1 TCAAATGATGCCCTCAA
5478363 ATTCTGTGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (18 bp):
TCAAATGATGCCCTCAAC
Found at i:5482020 original size:17 final size:17
Alignment explanation
Indices: 5481998--5482049 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5481988 TATAATTTTA
5481998 AAATATATGTTAAATAT
1 AAATATATGTTAAATAT
* *
5482015 AAATATAT-ATAAAAATT
1 AAATATATGTTAAATA-T
* *
5482032 ATATTTATGTTAAATAT
1 AAATATATGTTAAATAT
5482049 A
1 A
5482050 GTCATTAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 5 0.19
17 17 0.63
18 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (17 bp):
AAATATATGTTAAATAT
Found at i:5482144 original size:63 final size:60
Alignment explanation
Indices: 5482025--5482144 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 60
5482015 AAATATATAT
* *
5482025 AAAAATTATATTTATGTTAAATATAGTCATTAAAACGTATAAAATAATATTTATATTTAG
1 AAAAACTATATTTATGTTAAATATAATCATTAAAACGTATAAAATAATATTTATATTTAG
* *
5482085 AAAAACTATATTTATTTTTAAATAATAATCATTAAAA-GTTAATAACATAATATTTATATT
1 AAAAACTATATTTA-TGTTAAAT-ATAATCATTAAAACG-T-ATAAAATAATATTTATATT
5482145 AAAATAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
60 13 0.25
61 8 0.15
62 13 0.25
63 18 0.35
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (60 bp):
AAAAACTATATTTATGTTAAATATAATCATTAAAACGTATAAAATAATATTTATATTTAG
Found at i:5485656 original size:30 final size:30
Alignment explanation
Indices: 5485621--5485684 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
5485611 GGCAAAAAAT
5485621 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
1 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
*
5485651 TCTCAAATTTCTCCTTAAATTTCTCAAAGC
1 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
5485681 TCTC
1 TCTC
5485685 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.28, C:0.30, G:0.03, T:0.39
Consensus pattern (30 bp):
TCTCAAATTTCTCCCTAAATTTCTCAAAGC
Found at i:5487457 original size:18 final size:18
Alignment explanation
Indices: 5487434--5487471 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5487424 TGCCAGCTGC
*
5487434 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
5487452 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
5487470 GT
1 GT
5487472 TTTTTTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:5491207 original size:125 final size:126
Alignment explanation
Indices: 5490984--5491251 Score: 412
Period size: 125 Copynumber: 2.1 Consensus size: 126
5490974 GGTCAAACAT
* *
5490984 GAACTACTGTAGAAAAAGAACGTTGATGTGGGAGCTTTTTTCAATAATTTTGCTAACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCGACGTGGGAGCTTTTTTCAATAATTTTGCTAACAGTGCATC
* *
5491049 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTTAG
66 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
* * * *
5491110 GAACTACTGTAGAAAAAGAGCGTCGACGTGGGAGC-TTTTTCAGTAATTTTGTTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAACGTCGACGTGGGAGCTTTTTTCAATAATTTTGCTAACAGTGCATC
* * *
5491174 TTGCTTGAAGTGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
66 CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
* *
5491235 GAACTATTATAGAAAAA
1 GAACTACTGTAGAAAAA
5491252 AATAAAATCC
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
125 97 0.75
126 32 0.25
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAACGTCGACGTGGGAGCTTTTTTCAATAATTTTGCTAACAGTGCATC
CTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTCAG
Found at i:5491354 original size:33 final size:31
Alignment explanation
Indices: 5491307--5491421 Score: 149
Period size: 33 Copynumber: 3.5 Consensus size: 31
5491297 TAAACACAAT
*
5491307 ATTATTTTTAAAAAAACTAAACCCTAATTTA
1 ATTATTTTTTAAAAAACTAAACCCTAATTTA
5491338 ATTAATTTTCTTAAAAAACTAAACCCTAATTTA
1 ATT-ATTTT-TTAAAAAACTAAACCCTAATTTA
**
5491371 ATTTATTTATTTAAAACCCCTAAACCCTAATTTA
1 A-TTATTT-TTTAAAA-AACTAAACCCTAATTTA
5491405 ATTATTTTTTTAAAAAA
1 ATTA-TTTTTTAAAAAA
5491422 ACACTAAATC
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
31 3 0.04
32 5 0.07
33 43 0.59
34 22 0.30
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (31 bp):
ATTATTTTTTAAAAAACTAAACCCTAATTTA
Found at i:5491515 original size:42 final size:41
Alignment explanation
Indices: 5491467--5491546 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
5491457 AACCTAGAAC
* * *
5491467 CCTAAATTATTTTAGCAAAACCTTAAACCCTACAAACCTAAG
1 CCTAAATTATTATAACAAAACCTT-AACCCTAAAAACCTAAG
*
5491509 CCTAAATTATTATAACAAAATCTTAACCCTAAAAACCT
1 CCTAAATTATTATAACAAAACCTTAACCCTAAAAACCT
5491547 TAAACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 13 0.38
42 21 0.62
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.28
Consensus pattern (41 bp):
CCTAAATTATTATAACAAAACCTTAACCCTAAAAACCTAAG
Found at i:5493450 original size:2 final size:2
Alignment explanation
Indices: 5493443--5493490 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
5493433 CGGGCTTCTT
5493443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5493485 AA TA TA
1 TA TA TA
5493491 ATAATAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5500074 original size:40 final size:40
Alignment explanation
Indices: 5500014--5500089 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
5500004 CTCAGTATGA
* *
5500014 TTTTCTTCACGAAAATACCATACCTACTTTTCACAAATGG
1 TTTTCTTCACCAAAACACCATACCTACTTTTCACAAATGG
5500054 TTTTCTTCACCAAAACACCATACCTACTTTTCACAA
1 TTTTCTTCACCAAAACACCATACCTACTTTTCACAA
5500090 CTCAGTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (40 bp):
TTTTCTTCACCAAAACACCATACCTACTTTTCACAAATGG
Found at i:5500103 original size:25 final size:25
Alignment explanation
Indices: 5500074--5500123 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
5500064 CAAAACACCA
5500074 TACCTACTTTTCACAACTCAGTATG
1 TACCTACTTTTCACAACTCAGTATG
*
5500099 TACCTACTTTTCATAACTCAGTATG
1 TACCTACTTTTCACAACTCAGTATG
5500124 GTTTTCTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (25 bp):
TACCTACTTTTCACAACTCAGTATG
Found at i:5500152 original size:46 final size:46
Alignment explanation
Indices: 5500099--5500251 Score: 252
Period size: 46 Copynumber: 3.3 Consensus size: 46
5500089 ACTCAGTATG
*
5500099 TACCTACTTTTCATAACTCAGTATGGTTTTCTTTACCGAAATACCA
1 TACCTACTTTTCACAACTCAGTATGGTTTTCTTTACCGAAATACCA
* *
5500145 TACCTACTTTTCACAACTCAGTATGGTTTTCTTTATCGAAATATCA
1 TACCTACTTTTCACAACTCAGTATGGTTTTCTTTACCGAAATACCA
* *
5500191 TACCTACTTTTCACAACTCAGTATGGTTTTCTTCACTGAAATACCA
1 TACCTACTTTTCACAACTCAGTATGGTTTTCTTTACCGAAATACCA
*
5500237 TACCTACGTTTCACA
1 TACCTACTTTTCACA
5500252 CTTTGCCATG
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 99 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (46 bp):
TACCTACTTTTCACAACTCAGTATGGTTTTCTTTACCGAAATACCA
Found at i:5500221 original size:111 final size:106
Alignment explanation
Indices: 5500000--5500215 Score: 254
Period size: 117 Copynumber: 1.9 Consensus size: 106
5499990 TCACATTGCT
5500000 ATAACTCAGTATGATTTTCTTCACGAAAATACCATACCTACTTTTCACAAATGGTTTTCTTCACC
1 ATAACTCAGTATGATTTTCTTCACGAAAATACCATACCTACTTTTCACAAATGGTTTTCTTCACC
5500065 AAAACACCATACCTACTTTTCACAACTCAGTATGTACCTACTTTTC
66 AAAACACCATACCTACTTTTCACAACTCAGTATG-----ACTTTTC
* *
5500111 ATAACTCAGTATGGTTTTCTTTACCG-AAATACCATACCTACTTTTCACAACTCAGTATGGTTTT
1 ATAACTCAGTATGATTTTCTTCA-CGAAAATACCATACCTACTTTTCAC-A---A--ATGGTTTT
* * * * *
5500175 CTTTATCGAAATATCATACCTACTTTTCACAACTCAGTATG
59 CTTCACCAAAACACCATACCTACTTTTCACAACTCAGTATG
5500216 GTTTTCTTCA
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
111 43 0.47
112 3 0.03
115 1 0.01
117 44 0.48
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.37
Consensus pattern (106 bp):
ATAACTCAGTATGATTTTCTTCACGAAAATACCATACCTACTTTTCACAAATGGTTTTCTTCACC
AAAACACCATACCTACTTTTCACAACTCAGTATGACTTTTC
Found at i:5502953 original size:3 final size:3
Alignment explanation
Indices: 5502945--5502980 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
5502935 AAATAATTAA
*
5502945 ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5502981 TTACATATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5502989 original size:12 final size:15
Alignment explanation
Indices: 5502945--5502989 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
5502935 AAATAATTAA
*
5502945 ATTATTATTATTATT
1 ATTATTATTACTATT
5502960 ATTATTATTACTATT
1 ATTATTATTACTATT
5502975 ATTATT-TTACATATT
1 ATTATTATTAC-TATT
5502990 GTGAAATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATTATTACTATT
Found at i:5503154 original size:41 final size:42
Alignment explanation
Indices: 5503066--5503159 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 42
5503056 ACATAAAGAT
* *
5503066 CATGACTTTTAGCGGCTCTTATACCACAAACGCCACTATAAA
1 CATGACTTTTAGCGGCGCTTATACCACAAACGCCACTAAAAA
* *** *
5503108 GATGACTTTTAGCGGCGCTT-TTTGACAAACGCCGCTAAAAA
1 CATGACTTTTAGCGGCGCTTATACCACAAACGCCACTAAAAA
5503149 CATGACTTTTA
1 CATGACTTTTA
5503160 AAAAACATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 26 0.59
42 18 0.41
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (42 bp):
CATGACTTTTAGCGGCGCTTATACCACAAACGCCACTAAAAA
Found at i:5506619 original size:2 final size:2
Alignment explanation
Indices: 5506612--5506644 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5506602 AAGAAAAAGA
5506612 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 A
5506645 ATAGTTTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5518199 original size:22 final size:22
Alignment explanation
Indices: 5518174--5518249 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
5518164 ACACGTGAAA
5518174 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
5518196 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
5518218 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
5518240 CATGAGAGCT
1 CATGAGAGCT
5518250 AAGGAAATCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:5520669 original size:15 final size:15
Alignment explanation
Indices: 5520651--5520697 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5520641 TCCCCCTCCT
5520651 CCCCCTCCACCTTCA
1 CCCCCTCCACCTTCA
*
5520666 CCCCCACCA-C--CA
1 CCCCCTCCACCTTCA
*
5520678 CCTCCTCCACCTTCA
1 CCCCCTCCACCTTCA
5520693 CCCCC
1 CCCCC
5520698 ACCTCCACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
12 9 0.36
13 1 0.04
14 1 0.04
15 14 0.56
ACGTcount: A:0.15, C:0.70, G:0.00, T:0.15
Consensus pattern (15 bp):
CCCCCTCCACCTTCA
Found at i:5520684 original size:27 final size:27
Alignment explanation
Indices: 5520654--5520705 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
5520644 CCCTCCTCCC
5520654 CCTCCACCTTCACCCCCACCACCACCT
1 CCTCCACCTTCACCCCCACCACCACCT
*
5520681 CCTCCACCTTCACCCCCACCTCCAC
1 CCTCCACCTTCACCCCCACCACCAC
5520706 TCGGCATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.15
Consensus pattern (27 bp):
CCTCCACCTTCACCCCCACCACCACCT
Found at i:5521483 original size:6 final size:6
Alignment explanation
Indices: 5521468--5521507 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
5521458 CCTTTTTATG
* *
5521468 TTTCTC TTTCTT TTTCTT TTTCTT TTT-TT TTTTTT TTTCT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCT
5521508 AATCTTCGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:5523111 original size:15 final size:15
Alignment explanation
Indices: 5523086--5523130 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5523076 CTCTTCAAAT
5523086 ATATCTTTTTATTTTA
1 ATAT-TTTTTATTTTA
**
5523102 ATATTTTTTAACTTA
1 ATATTTTTTATTTTA
5523117 ATATTTTTTTATTT
1 ATA-TTTTTTATTT
5523131 AGTTTCTCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATTTTTTATTTTA
Found at i:5525714 original size:17 final size:18
Alignment explanation
Indices: 5525694--5525727 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5525684 TTTTTAAAAT
5525694 AAAATAAT-ATATTTTAC
1 AAAATAATAATATTTTAC
5525711 AAAATAATAATATTTTA
1 AAAATAATAATATTTTA
5525728 GTTATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATAATAATATTTTAC
Found at i:5526392 original size:9 final size:9
Alignment explanation
Indices: 5526378--5526407 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5526368 GTTTATGATG
5526378 AAAAAAATA
1 AAAAAAATA
5526387 AAAAAAATA
1 AAAAAAATA
*
5526396 AAAAAGATA
1 AAAAAAATA
5526405 AAA
1 AAA
5526408 TTATTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:5540228 original size:19 final size:20
Alignment explanation
Indices: 5540196--5540233 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5540186 TGTTCCAGTT
*
5540196 TTTTTTCTTCTCCATTTTCC
1 TTTTCTCTTCTCCATTTTCC
5540216 TTTTCTCTT-TCCATTTTC
1 TTTTCTCTTCTCCATTTTC
5540234 ATTATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTCTCTTCTCCATTTTCC
Found at i:5542591 original size:21 final size:21
Alignment explanation
Indices: 5542567--5542609 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5542557 ATCGATTAAC
*
5542567 ATATTATTTAG-ATTTAAATTT
1 ATATTATTT-GTAATTAAATTT
5542588 ATATTATTTGTAATTAAATTT
1 ATATTATTTGTAATTAAATTT
5542609 A
1 A
5542610 AACAAAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATATTATTTGTAATTAAATTT
Found at i:5544129 original size:17 final size:18
Alignment explanation
Indices: 5544107--5544145 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
5544097 CATTTTAAAA
5544107 TATTTT-AATAAAAAT-AT
1 TATTTTCAA-AAAAATCAT
5544124 TATTTTCAAAAAAATCAT
1 TATTTTCAAAAAAATCAT
5544142 TATT
1 TATT
5544146 ATTTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTTTCAAAAAAATCAT
Found at i:5544848 original size:22 final size:23
Alignment explanation
Indices: 5544814--5544857 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
5544804 ATAAGTATAC
* * *
5544814 AAATTTACTTATA-ATAGTTTTT
1 AAATATACATATATATAATTTTT
5544836 AAATATACATATATATAATTTT
1 AAATATACATATATATAATTTT
5544858 CATTCAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATATACATATATATAATTTTT
Found at i:5545175 original size:7 final size:7
Alignment explanation
Indices: 5545163--5545187 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5545153 TTAAATCATT
5545163 AAAATTA
1 AAAATTA
5545170 AAAATTA
1 AAAATTA
5545177 AAAATTA
1 AAAATTA
5545184 AAAA
1 AAAA
5545188 CGAAAGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:5547280 original size:39 final size:39
Alignment explanation
Indices: 5547232--5547316 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
5547222 AAAAGTATGA
*
5547232 CATGGCACAAATTATGTGATTAAATGCTGACATGAATTC
1 CATGTCACAAATTATGTGATTAAATGCTGACATGAATTC
5547271 CATGTCACAAATTATGTGATTAAATGCTGACATGAATTC
1 CATGTCACAAATTATGTGATTAAATGCTGACATGAATTC
5547310 CATGTCA
1 CATGTCA
5547317 TGGCTATGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (39 bp):
CATGTCACAAATTATGTGATTAAATGCTGACATGAATTC
Found at i:5547993 original size:21 final size:22
Alignment explanation
Indices: 5547952--5547993 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5547942 TTCACATAAA
*
5547952 AATTTAAAAATAATCCTACAAG
1 AATTTAAAAATAATCCAACAAG
*
5547974 AATTTGAAAA-AATCCAACAA
1 AATTTAAAAATAATCCAACAA
5547994 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (22 bp):
AATTTAAAAATAATCCAACAAG
Found at i:5555358 original size:15 final size:15
Alignment explanation
Indices: 5555338--5555368 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5555328 NNNNNACTTT
*
5555338 TTTAAATTTTTTAAA
1 TTTAAATATTTTAAA
5555353 TTTAAATATTTTAAA
1 TTTAAATATTTTAAA
5555368 T
1 T
5555369 ACTTTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATATTTTAAA
Found at i:5557325 original size:9 final size:9
Alignment explanation
Indices: 5557311--5557341 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5557301 GTTAAACGAA
5557311 TCGAGTTAT
1 TCGAGTTAT
*
5557320 TCGAGTTAA
1 TCGAGTTAT
5557329 TCGAGTTAT
1 TCGAGTTAT
5557338 TCGA
1 TCGA
5557342 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5557409 original size:9 final size:9
Alignment explanation
Indices: 5557395--5557422 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5557385 TAAGTTTTCG
5557395 AATTCGAAT
1 AATTCGAAT
5557404 AATTCGAAT
1 AATTCGAAT
5557413 AATTCGAAT
1 AATTCGAAT
5557422 A
1 A
5557423 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5563459 original size:11 final size:11
Alignment explanation
Indices: 5563443--5563467 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5563433 AAAAACACAT
5563443 TTATAATAAAA
1 TTATAATAAAA
5563454 TTATAATAAAA
1 TTATAATAAAA
5563465 TTA
1 TTA
5563468 AGTGAGACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTATAATAAAA
Found at i:5567417 original size:17 final size:17
Alignment explanation
Indices: 5567395--5567428 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5567385 GTATTATATG
5567395 TTTTTAAA-AAGAAATTA
1 TTTTTAAATAA-AAATTA
5567412 TTTTTAAATAAAAATTA
1 TTTTTAAATAAAAATTA
5567429 ATCTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTTTAAATAAAAATTA
Found at i:5567594 original size:57 final size:57
Alignment explanation
Indices: 5567506--5567620 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
5567496 TTTGAACAAA
5567506 AAAGTAAATTGATTTTTGAATCTAGATTGGACCCAAACCGAAAAATTTGATCTACAT
1 AAAGTAAATTGATTTTTGAATCTAGATTGGACCCAAACCGAAAAATTTGATCTACAT
*
5567563 AAAGTAAATTGATTTTTGAATCTAGATTGGACCCAAACCTAAAAATTTGATCTACAT
1 AAAGTAAATTGATTTTTGAATCTAGATTGGACCCAAACCGAAAAATTTGATCTACAT
5567620 A
1 A
5567621 TTTTGCATAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (57 bp):
AAAGTAAATTGATTTTTGAATCTAGATTGGACCCAAACCGAAAAATTTGATCTACAT
Found at i:5568047 original size:24 final size:24
Alignment explanation
Indices: 5568020--5568074 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5568010 GACCTAATTC
5568020 TAATCAAA-GTCAAATATATTATGT
1 TAAT-AAACGTCAAATATATTATGT
* *
5568044 TAATAAACGTTAAATATATTATAT
1 TAATAAACGTCAAATATATTATGT
*
5568068 TTATAAA
1 TAATAAA
5568075 TATTAAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (24 bp):
TAATAAACGTCAAATATATTATGT
Found at i:5568080 original size:24 final size:24
Alignment explanation
Indices: 5568031--5568082 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5568021 AATCAAAGTC
* *
5568031 AAATATATTATGTTAATAAACGTT
1 AAATATATTATATTAATAAACATT
* *
5568055 AAATATATTATATTTATAAATATT
1 AAATATATTATATTAATAAACATT
5568079 AAAT
1 AAAT
5568083 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (24 bp):
AAATATATTATATTAATAAACATT
Found at i:5582602 original size:3 final size:3
Alignment explanation
Indices: 5582594--5582626 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5582584 CATTTATTGT
*
5582594 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5582627 ATAAATTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5591305 original size:13 final size:14
Alignment explanation
Indices: 5591287--5591319 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5591277 CTCATTACTT
*
5591287 TTATTTTTAA-TTA
1 TTATTTTTAACATA
5591300 TTATTTTTAACATA
1 TTATTTTTAACATA
5591314 TTATTT
1 TTATTT
5591320 CCTCTAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTTTAACATA
Found at i:5592572 original size:23 final size:21
Alignment explanation
Indices: 5592531--5592572 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
5592521 TAATATTAAA
*
5592531 ATAATAAAATTACATTTTACT
1 ATAATAAAATTACAATTTACT
5592552 ATAATAAAAATATACAATTTA
1 ATAAT-AAAAT-TACAATTTA
5592573 ATTTTTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 5 0.28
23 8 0.44
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATAAAATTACAATTTACT
Found at i:5592574 original size:81 final size:81
Alignment explanation
Indices: 5592407--5592576 Score: 179
Period size: 81 Copynumber: 2.1 Consensus size: 81
5592397 GTAATAAATT
* * * * *
5592407 TTTAATTTATACTTTTTATAATTTATAAAATTTTAAATTAATAATGATAAAATTACACTTTAGTA
1 TTTAATTTATAATTTTTATAAATTATAAAATTATAAATTAATAATAATAAAATTACACTTTACTA
*
5592472 TTTAAAATAATCAAAA
66 TTAAAAATAATCAAAA
* *
5592488 ATTAATTTA-AATTTTTA-AAATTATAAAGATATATAATATTAA-AATAATAAAATTACATTTTA
1 TTTAATTTATAATTTTTATAAATTATAAA-AT-TATAA-ATTAATAATAATAAAATTACACTTTA
*
5592550 CTATAATAAAAAT-AT-ACAA
63 CTAT--TAAAAATAATCAAAA
5592569 TTTAATTT
1 TTTAATTT
5592577 TTATCAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
79 9 0.12
80 9 0.12
81 43 0.58
82 7 0.09
83 6 0.08
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (81 bp):
TTTAATTTATAATTTTTATAAATTATAAAATTATAAATTAATAATAATAAAATTACACTTTACTA
TTAAAAATAATCAAAA
Found at i:5595221 original size:30 final size:30
Alignment explanation
Indices: 5595187--5595249 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
5595177 ACTTATTTTA
*
5595187 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGCTATTATTTTAAAGACAT
*
5595217 TTGTTAATTTTGCTATTATTTTAAAGTCAT
1 TTGTTAATTTTGCTATTATTTTAAAGACAT
5595247 TTG
1 TTG
5595250 CTTGTTAAGT
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:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGCTATTATTTTAAAGACAT
Found at i:5605449 original size:3 final size:3
Alignment explanation
Indices: 5605438--5605476 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
5605428 ATCAGAAAAG
*
5605438 AGA AG- AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5605477 ATGGACGTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5616638 original size:27 final size:27
Alignment explanation
Indices: 5616599--5616681 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 27
5616589 GCCTGATCAG
* * * *
5616599 GCCAATCACATTGGAGGCACCAAGGGT
1 GCCAATGAGATTGGCGGCACCAATGGT
*
5616626 GCCAATGAGATTGGCGGCATCAATGGT
1 GCCAATGAGATTGGCGGCACCAATGGT
* *
5616653 GCCAATGTGATTGGCGACACCAATGGT
1 GCCAATGAGATTGGCGGCACCAATGGT
5616680 GC
1 GC
5616682 TAAAGAACTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.19
Consensus pattern (27 bp):
GCCAATGAGATTGGCGGCACCAATGGT
Found at i:5617534 original size:28 final size:28
Alignment explanation
Indices: 5617503--5617568 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
5617493 TTTTTTAGGT
5617503 ATATTTTAGTAAATAAAAAAAAT-TTATA
1 ATATTTTAGTAAAT-AAAAAAATGTTATA
5617531 ATATTTT-GATAAATAAAAAAATGTTATA
1 ATATTTTAG-TAAATAAAAAAATGTTATA
5617559 ATATTTTAGT
1 ATATTTTAGT
5617569 TATTTTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 9 0.26
28 25 0.71
29 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (28 bp):
ATATTTTAGTAAATAAAAAAATGTTATA
Found at i:5619021 original size:9 final size:9
Alignment explanation
Indices: 5619009--5619033 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5618999 TTTACATTTA
5619009 TTTTAATAT
1 TTTTAATAT
5619018 TTTTAATAT
1 TTTTAATAT
5619027 TTTTAAT
1 TTTTAAT
5619034 GTATTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAATAT
Found at i:5621204 original size:29 final size:30
Alignment explanation
Indices: 5621172--5621245 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
5621162 TGTATAGTTT
*
5621172 AATCAAAATCAAAGTTTTATATATAT-A-TG
1 AATC-AAATCAAAGTTTCATATATATAATTG
*
5621201 AATCGCAATTCAAA-TTTCATATATATAATTG
1 AAT--CAAATCAAAGTTTCATATATATAATTG
*
5621232 CATCAAATCAAAGT
1 AATCAAATCAAAGT
5621246 AAATATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
29 22 0.61
30 9 0.25
31 5 0.14
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (30 bp):
AATCAAATCAAAGTTTCATATATATAATTG
Found at i:5630178 original size:22 final size:22
Alignment explanation
Indices: 5630152--5630205 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
5630142 CTAATCCTCA
*
5630152 TTTAATTATCATAAATATATAT
1 TTTAATTATCAAAAATATATAT
** *
5630174 TTTAAAAATTAAAAATATATAT
1 TTTAATTATCAAAAATATATAT
5630196 TATATAATTA
1 T-T-TAATTA
5630206 AAAATACATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 19 0.79
23 1 0.04
24 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAATTATCAAAAATATATAT
Found at i:5630209 original size:22 final size:22
Alignment explanation
Indices: 5630164--5630211 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
5630154 TAATTATCAT
*
5630164 AAATATATATTTTAAAAATTAA
1 AAATATATATTATAAAAATTAA
*
5630186 AAATATATATTAT-ATAATTAA
1 AAATATATATTATAAAAATTAA
5630207 AAATA
1 AAATA
5630212 CATAAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATATATTATAAAAATTAA
Found at i:5642491 original size:16 final size:15
Alignment explanation
Indices: 5642462--5642492 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
5642452 CCCTTTTCTT
5642462 TGAAAATAGAATGAA
1 TGAAAATAGAATGAA
5642477 TGAAAATATGAATGAA
1 TGAAAATA-GAATGAA
5642493 GGGAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (15 bp):
TGAAAATAGAATGAA
Found at i:5649256 original size:28 final size:28
Alignment explanation
Indices: 5649217--5649270 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5649207 AAATCCCAAA
*
5649217 TTTTCTTCCTTTCCTTCCCT-TTTTCTT
1 TTTTCTTCCTTTCCTCCCCTGTTTTCTT
*
5649244 TTTTCTTTCCTTTTCTCCCCTGTTTTC
1 TTTTC-TTCCTTTCCTCCCCTGTTTTC
5649271 GTTTGCCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 13 0.57
29 5 0.22
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTTCTTCCTTTCCTCCCCTGTTTTCTT
Found at i:5649534 original size:23 final size:21
Alignment explanation
Indices: 5649478--5649535 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
5649468 TATTTATTTA
* *
5649478 AAATATAATAATATAATATAAT
1 AAATATAAT-TTACAATATAAT
5649500 AAATATAATTTACAATATAAT
1 AAATATAATTTACAATATAAT
5649521 AAAATAATAATTTAC
1 -AAAT-ATAATTTAC
5649536 TTTAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 10 0.31
22 13 0.41
23 9 0.28
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATATAATTTACAATATAAT
Found at i:5659390 original size:18 final size:19
Alignment explanation
Indices: 5659339--5659411 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 19
5659329 ACACTAACGA
*
5659339 AATATACAAATTTAAATAT
1 AATATATAAATTTAAATAT
**
5659358 AAT-T-TAAGAAATAAATAT
1 AATATATAA-ATTTAAATAT
*
5659376 AATATATAAATTAAAATATT
1 AATATATAAATTTAAATA-T
5659396 AA-A-ATAAATTTAAATA
1 AATATATAAATTTAAATA
5659412 AATTAACAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.05
18 24 0.56
19 11 0.26
20 6 0.14
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (19 bp):
AATATATAAATTTAAATAT
Found at i:5659439 original size:29 final size:28
Alignment explanation
Indices: 5659381--5659459 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
5659371 AATATAATAT
*
5659381 ATAAATTAAAATATTAAAATAAATTTAA
1 ATAAATTAAAATATTAAAATAAATTGAA
* * *
5659409 ATAAATTAACAATATTGAAATGAGTTGAA
1 ATAAATTAA-AATATTAAAATAAATTGAA
* *
5659438 ATAAGTTAAAGATGTTAAAATA
1 ATAAATTAAA-ATATTAAAATA
5659460 TTTGAAAGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 10 0.24
29 31 0.76
ACGTcount: A:0.57, C:0.01, G:0.09, T:0.33
Consensus pattern (28 bp):
ATAAATTAAAATATTAAAATAAATTGAA
Found at i:5659700 original size:21 final size:21
Alignment explanation
Indices: 5659676--5659725 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
5659666 TTATATATGC
*
5659676 ATATATATAAAATAGTAGATT
1 ATATATATAAAAAAGTAGATT
*
5659697 ATATA-AAAAAAAAGTAGATT
1 ATATATATAAAAAAGTAGATT
5659717 A-ATAT-TAAA
1 ATATATATAAA
5659726 CCAATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 6 0.24
20 14 0.56
21 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (21 bp):
ATATATATAAAAAAGTAGATT
Found at i:5661283 original size:50 final size:50
Alignment explanation
Indices: 5661229--5661502 Score: 241
Period size: 50 Copynumber: 5.5 Consensus size: 50
5661219 TTAGGGAAAC
*
5661229 AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCAGGAAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCAACTGCACCGCCAGGAAAGT
* * * ** * **
5661279 AAGATTCACCGTTGT-GACTTCAATCTATTTAACTGCAATGTC-GGAGAAAC
1 AAGATTCGCCGTCGTAG-CTTCAATCTATTCAACTGCACCGCCAGGA-AAGT
** * * * *
5661329 AAGATTCATCTTCGTAGCTTCAATCTGTTCTACTACACCGCCAAGG-AAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCAACTGCACCGCC-AGGAAAGT
* * ** ** *
5661379 AAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAA-C
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCAACTGCACCG-CCAGGAAAGT
* * * *
5661429 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCAACTGCACCGCCAGGAAAGT
*
5661479 AAGATTCGCCGTTGTAGCTTCAAT
1 AAGATTCGCCGTCGTAGCTTCAAT
5661503 TTGTTTAACT
Statistics
Matches: 170, Mismatches: 46, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
49 9 0.05
50 155 0.91
51 4 0.02
52 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (50 bp):
AAGATTCGCCGTCGTAGCTTCAATCTATTCAACTGCACCGCCAGGAAAGT
Found at i:5661536 original size:100 final size:100
Alignment explanation
Indices: 5661196--5661518 Score: 479
Period size: 100 Copynumber: 3.2 Consensus size: 100
5661186 GGATTGGTTT
* * *
5661196 CTTCAATCTGTTTAACTGCAATGTTAGG-GAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCC
1 CTTCAATCTATTTAACTGCAATG-TCGGAGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCC
* * *
5661260 ACTGCACCGCCAGGAAAGTAAGATTCACCGTTGT-G
65 ACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTAG
** * *
5661295 ACTTCAATCTATTTAACTGCAATGTCGGAGAAACAAGATTCATCTTCGTAGCTTCAATCTGTTCT
1 -CTTCAATCTATTTAACTGCAATGTCGGAGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCC
*
5661360 ACTACACCGCCAAGGAAGTAAGATTCGCCGTTGTAG
65 ACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTAG
*
5661396 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGAGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
5661461 CTACACCGCCAGGGAAGTAAGATTCGCCGTTGTAG
66 CTACACCGCCAGGGAAGTAAGATTCGCCGTTGTAG
* * *
5661496 CTTCAATTTGTTTAACTGTAATG
1 CTTCAATCTATTTAACTGCAATG
5661519 CCAAAGAGAT
Statistics
Matches: 201, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
99 3 0.01
100 197 0.98
101 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (100 bp):
CTTCAATCTATTTAACTGCAATGTCGGAGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
CTACACCGCCAGGGAAGTAAGATTCGCCGTTGTAG
Found at i:5661849 original size:88 final size:88
Alignment explanation
Indices: 5661695--5661869 Score: 287
Period size: 88 Copynumber: 2.0 Consensus size: 88
5661685 GTGATAAGAC
* * * * * *
5661695 TGGTGTCTTCGATCTGCTTTGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCC
1 TGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCC
5661760 ACTGCTACTCAGGGAGACAAGGT
66 ACTGCTACTCAGGGAGACAAGGT
5661783 TGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCC
1 TGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCC
*
5661848 ACTGCTACTCAGGGAGATAAGG
66 ACTGCTACTCAGGGAGACAAGG
5661870 CTGAGGTCTC
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (88 bp):
TGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCC
ACTGCTACTCAGGGAGACAAGGT
Found at i:5663153 original size:28 final size:28
Alignment explanation
Indices: 5663122--5663183 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
5663112 AGCCTCTCCA
5663122 TTTTTAC-TTTTTCCATTTTTCA-TTATTC
1 TTTTTACATTTTTCCA--TTTCATTTATTC
* *
5663150 TTTTT-CATTTTTTCATTTCATTTATTT
1 TTTTTACATTTTTCCATTTCATTTATTC
5663177 TTTTTAC
1 TTTTTAC
5663184 GACTCAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 5 0.17
27 11 0.38
28 13 0.45
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTTTACATTTTTCCATTTCATTTATTC
Found at i:5663677 original size:19 final size:18
Alignment explanation
Indices: 5663653--5663705 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
5663643 CCTAGTAGAG
5663653 GTTTTTGTTTCTTTTTTTT
1 GTTTTT-TTTCTTTTTTTT
5663672 GTTTTTTGTTCTTCTTTTGTT
1 GTTTTTT-TTCTT-TTTT-TT
*
5663693 -CTTTTTTTCTTTT
1 GTTTTTTTTCTTTT
5663706 GGATTGAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.10
19 16 0.53
20 9 0.30
21 2 0.07
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.81
Consensus pattern (18 bp):
GTTTTTTTTCTTTTTTTT
Found at i:5665727 original size:20 final size:21
Alignment explanation
Indices: 5665690--5665728 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5665680 ATCTGTATTC
5665690 ACATTTGCTCTAATTTCTCCA
1 ACATTTGCTCTAATTTCTCCA
*
5665711 ACATTTGGTCT-ATTTCTC
1 ACATTTGCTCTAATTTCTC
5665729 TAGTCTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.21, C:0.26, G:0.08, T:0.46
Consensus pattern (21 bp):
ACATTTGCTCTAATTTCTCCA
Found at i:5667759 original size:18 final size:19
Alignment explanation
Indices: 5667708--5667780 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 19
5667698 ACACTAACGA
*
5667708 AATATACAAATTTAAATAT
1 AATATATAAATTTAAATAT
**
5667727 AAT-T-TAAGAAATAAATAT
1 AATATATAA-ATTTAAATAT
*
5667745 AATATATAAATTAAAATATT
1 AATATATAAATTTAAATA-T
5667765 AA-A-ATAAATTTAAATA
1 AATATATAAATTTAAATA
5667781 AATTAACAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.05
18 24 0.56
19 11 0.26
20 6 0.14
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (19 bp):
AATATATAAATTTAAATAT
Found at i:5667798 original size:29 final size:28
Alignment explanation
Indices: 5667750--5667828 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
5667740 AATATAATAT
*
5667750 ATAAATTAAAATATTAAAATAAATTTAA
1 ATAAATTAAAATATTAAAATAAATTGAA
* * *
5667778 ATAAATTAACAATATTGAAATGAGTTGAA
1 ATAAATTAA-AATATTAAAATAAATTGAA
*
5667807 ATAAATTAAAGATGTTAAAATA
1 ATAAATTAAA-ATATTAAAATA
5667829 TTTGAAAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 10 0.24
29 32 0.76
ACGTcount: A:0.58, C:0.01, G:0.08, T:0.33
Consensus pattern (28 bp):
ATAAATTAAAATATTAAAATAAATTGAA
Found at i:5679695 original size:24 final size:23
Alignment explanation
Indices: 5679660--5679717 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 23
5679650 AACTCATTTT
5679660 ATTTAAT-TTTTTTATATATTGAC
1 ATTTAATATTTTTTA-ATATTGAC
*
5679683 ATCTTAATATTTTTTAATATTTAC
1 AT-TTAATATTTTTTAATATTGAC
5679707 ATTATAATATT
1 ATT-TAATATT
5679718 ATATATCACC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 3 0.10
24 21 0.68
25 7 0.23
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTTAATATTTTTTAATATTGAC
Found at i:5684380 original size:3 final size:3
Alignment explanation
Indices: 5684374--5684416 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
5684364 CCCAAAAAAC
5684374 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
5684417 GGGCCTACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5686231 original size:21 final size:23
Alignment explanation
Indices: 5686207--5686256 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
5686197 AGCATCAATT
*
5686207 AAATG-TTGAT-CTTCATTACTC
1 AAATGTTTGATCCTTCATTACCC
5686228 AAATGTGTTTGATCCTTCATTACCC
1 AAA--TGTTTGATCCTTCATTACCC
5686253 AAAT
1 AAAT
5686257 CTGCCTATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 3 0.12
23 3 0.12
24 5 0.21
25 13 0.54
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (23 bp):
AAATGTTTGATCCTTCATTACCC
Found at i:5704657 original size:30 final size:30
Alignment explanation
Indices: 5704623--5704685 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
5704613 ACTTATTTTA
5704623 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
5704653 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
5704683 TTG
1 TTG
5704686 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:5708869 original size:26 final size:28
Alignment explanation
Indices: 5708833--5708896 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
5708823 ATGAATTTTC
5708833 TCAAAATTTTAAC-G-GGTG-TAAAATCG
1 TCAAAATTTTAACTGAGG-GATAAAATCG
5708859 TCAAAATTTT-ACTGAGGGATAAAATCG
1 TCAAAATTTTAACTGAGGGATAAAATCG
5708886 TCAAAATTTTA
1 TCAAAATTTTA
5708897 CTAGGGTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 2 0.06
26 12 0.35
27 20 0.59
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (28 bp):
TCAAAATTTTAACTGAGGGATAAAATCG
Found at i:5708888 original size:27 final size:26
Alignment explanation
Indices: 5708851--5708902 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
5708841 TTAACGGGTG
5708851 TAAAATCGTCAAAATTTTACTGAGGGA
1 TAAAATCGTCAAAATTTTACT-AGGGA
5708878 TAAAATCGTCAAAATTTTACTAGGG
1 TAAAATCGTCAAAATTTTACTAGGG
5708903 TAACATTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (26 bp):
TAAAATCGTCAAAATTTTACTAGGGA
Found at i:5729013 original size:24 final size:24
Alignment explanation
Indices: 5728985--5729096 Score: 161
Period size: 24 Copynumber: 4.7 Consensus size: 24
5728975 TTGTTCTTTG
*
5728985 GTAAAGGATGAATTGACGAAAAAT
1 GTAAAGGATGAATTGACGGAAAAT
*
5729009 GTAAAGGATAAATTGACGGAAAAT
1 GTAAAGGATGAATTGACGGAAAAT
* * * *
5729033 ATAAAGGAGGAACTGGCGGAAAAT
1 GTAAAGGATGAATTGACGGAAAAT
5729057 GTAAAGGATGAATTGACGGAAAAT
1 GTAAAGGATGAATTGACGGAAAAT
*
5729081 GTAAATGATGAATTGA
1 GTAAAGGATGAATTGA
5729097 TGGCAATTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.47, C:0.04, G:0.28, T:0.21
Consensus pattern (24 bp):
GTAAAGGATGAATTGACGGAAAAT
Found at i:5729850 original size:9 final size:9
Alignment explanation
Indices: 5729836--5729947 Score: 152
Period size: 9 Copynumber: 12.4 Consensus size: 9
5729826 TTTGGTTAAA
5729836 AATTAACCG
1 AATTAACCG
**
5729845 AATTAATTG
1 AATTAACCG
*
5729854 AATTAACTG
1 AATTAACCG
5729863 AATTAACCG
1 AATTAACCG
*
5729872 AATTACCCG
1 AATTAACCG
*
5729881 AATTACCCG
1 AATTAACCG
*
5729890 AATTAACTG
1 AATTAACCG
5729899 AATTAACCG
1 AATTAACCG
*
5729908 AATTACCCG
1 AATTAACCG
*
5729917 AATTACCCG
1 AATTAACCG
5729926 AATTAACCG
1 AATTAACCG
5729935 AATTAACCG
1 AATTAACCG
5729944 AATT
1 AATT
5729948 GAATCACTAC
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 93 1.00
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:5729882 original size:36 final size:36
Alignment explanation
Indices: 5729853--5729947 Score: 181
Period size: 36 Copynumber: 2.6 Consensus size: 36
5729843 CGAATTAATT
5729853 GAATTAACTGAATTAACCGAATTACCCGAATTACCC
1 GAATTAACTGAATTAACCGAATTACCCGAATTACCC
5729889 GAATTAACTGAATTAACCGAATTACCCGAATTACCC
1 GAATTAACTGAATTAACCGAATTACCCGAATTACCC
*
5729925 GAATTAACCGAATTAACCGAATT
1 GAATTAACTGAATTAACCGAATT
5729948 GAATCACTAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (36 bp):
GAATTAACTGAATTAACCGAATTACCCGAATTACCC
Found at i:5732415 original size:2 final size:2
Alignment explanation
Indices: 5732408--5732441 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5732398 NTAATAATAG
5732408 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5732442 ACTATGGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5733315 original size:22 final size:25
Alignment explanation
Indices: 5733287--5733337 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
5733277 TGATTTGACA
5733287 AAAAAATA-TAAAT-TT-AATAACT
1 AAAAAATATTAAATATTAAATAACT
*
5733309 AAAAAATATTAAATATTAAATAATT
1 AAAAAATATTAAATATTAAATAACT
5733334 AAAA
1 AAAA
5733338 CTATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
23 5 0.20
24 2 0.08
25 10 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAAATATTAAATATTAAATAACT
Found at i:5733625 original size:13 final size:13
Alignment explanation
Indices: 5733609--5733652 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
5733599 AGTTGATTTG
*
5733609 ATTAATTAATTCT
1 ATTAATTGATTCT
5733622 ATTAATTGATT-T
1 ATTAATTGATTCT
*
5733634 AATTAATTGATACT
1 -ATTAATTGATTCT
5733648 ATTAA
1 ATTAA
5733653 CTGTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 1 0.04
13 25 0.93
14 1 0.04
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (13 bp):
ATTAATTGATTCT
Found at i:5733638 original size:26 final size:26
Alignment explanation
Indices: 5733601--5733652 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5733591 ATTATAGTAG
* *
5733601 TTGATTTGATTAATTAATTCTATTAA
1 TTGATTTAATTAATTAATACTATTAA
*
5733627 TTGATTTAATTAATTGATACTATTAA
1 TTGATTTAATTAATTAATACTATTAA
5733653 CTGTTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (26 bp):
TTGATTTAATTAATTAATACTATTAA
Found at i:5733801 original size:26 final size:28
Alignment explanation
Indices: 5733753--5733820 Score: 106
Period size: 26 Copynumber: 2.5 Consensus size: 28
5733743 AAAATAAAAA
5733753 TTACCAAAATAT-TATAAATTTTTTTAT
1 TTACCAAAATATATATAAATTTTTTTAT
*
5733780 TTATCAAAATATATAT-AA-TTTTTTAT
1 TTACCAAAATATATATAAATTTTTTTAT
5733806 TTACCAAAATATATA
1 TTACCAAAATATATA
5733821 AAAAACAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 22 0.58
27 13 0.34
28 3 0.08
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAAATTTTTTTAT
Found at i:5738704 original size:94 final size:93
Alignment explanation
Indices: 5738543--5738732 Score: 353
Period size: 94 Copynumber: 2.0 Consensus size: 93
5738533 ATAACGAGCT
*
5738543 TCAAGGTTGGATAGCTGCTATGCGGGAGTATGTATCGGGGACTGTGATTGAGTTGCAGGGAAGAC
1 TCAAGGTTGGATAGCTGCTATGCGGGAGTATGTACCGGGGACTGTGATTGAGTTGCAGGGAAGAC
5738608 CATATTACGGCCCGGACGGCCAATTACAG
66 CATATTACGGCCCGGACGG-CAATTACAG
5738637 TCAAGGTTGGATAGCTGCTATGCGGGAGTATGTACCGGGGACTGTGATTGAGTTGCAGGGAAGAC
1 TCAAGGTTGGATAGCTGCTATGCGGGAGTATGTACCGGGGACTGTGATTGAGTTGCAGGGAAGAC
*
5738702 CATATTACGGCCCGGACGGTAATTACAG
66 CATATTACGGCCCGGACGGCAATTACAG
5738730 TCA
1 TCA
5738733 GTAAAAATGA
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
93 11 0.12
94 83 0.88
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.24
Consensus pattern (93 bp):
TCAAGGTTGGATAGCTGCTATGCGGGAGTATGTACCGGGGACTGTGATTGAGTTGCAGGGAAGAC
CATATTACGGCCCGGACGGCAATTACAG
Found at i:5740333 original size:15 final size:15
Alignment explanation
Indices: 5740309--5740347 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5740299 CAATAACCAC
*
5740309 AATAACTAAAACTAG
1 AATAATTAAAACTAG
*
5740324 AATAATT-AAATTAG
1 AATAATTAAAACTAG
5740338 AATAATTAAA
1 AATAATTAAA
5740348 TTGATACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (15 bp):
AATAATTAAAACTAG
Found at i:5740340 original size:14 final size:14
Alignment explanation
Indices: 5740321--5740349 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5740311 TAACTAAAAC
5740321 TAGAATAATTAAAT
1 TAGAATAATTAAAT
5740335 TAGAATAATTAAAT
1 TAGAATAATTAAAT
5740349 T
1 T
5740350 GATACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:5741336 original size:17 final size:17
Alignment explanation
Indices: 5741314--5741350 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
5741304 AGTAAGATGT
5741314 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
5741331 CATGAATATTAGAATAG
1 CATGAATATTAGAATAG
5741348 CAT
1 CAT
5741351 CTTACCCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (17 bp):
CATGAATATTAGAATAG
Found at i:5742681 original size:16 final size:16
Alignment explanation
Indices: 5742655--5742694 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
5742645 TTTAGTGTGT
5742655 TTTTTTCTGTTTTTTTA-
1 TTTTTT-TG-TTTTTTAC
5742672 TTTTTTTGTTTTTTAC
1 TTTTTTTGTTTTTTAC
5742688 TTTTTTT
1 TTTTTTT
5742695 TGATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
16 9 0.41
17 6 0.27
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.85
Consensus pattern (16 bp):
TTTTTTTGTTTTTTAC
Found at i:5742727 original size:27 final size:29
Alignment explanation
Indices: 5742697--5742765 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 29
5742687 CTTTTTTTTG
5742697 ATATATTTTGGTAAAT-AAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
5742724 ATATATTTTGGTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
5742753 A-ATATTTTGGTAA
1 ATATATTTTGGTAA
5742766 TTTTTTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.40
28 19 0.47
29 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:5742789 original size:13 final size:13
Alignment explanation
Indices: 5742771--5742796 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5742761 GGTAATTTTT
5742771 TTATTTTTTTATA
1 TTATTTTTTTATA
5742784 TTATTTTTTTATA
1 TTATTTTTTTATA
5742797 AAAACGCCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTTTTATA
Found at i:5743423 original size:10 final size:10
Alignment explanation
Indices: 5743410--5743470 Score: 50
Period size: 10 Copynumber: 5.5 Consensus size: 10
5743400 TTTTCTATCC
5743410 TTCTTTTTCT
1 TTCTTTTTCT
5743420 TTCTTTCCTCTCCT
1 TTCTTT--T-T-CT
* *
5743434 TTCCTTTTCC
1 TTCTTTTTCT
5743444 TTCTTTTTCT
1 TTCTTTTTCT
5743454 TTCTTCCTTTCT
1 TTCTT--TTTCT
5743466 TTCTT
1 TTCTT
5743471 CTTCCCCTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 20 0.49
11 1 0.02
12 12 0.29
13 1 0.02
14 7 0.17
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
TTCTTTTTCT
Found at i:5743464 original size:38 final size:38
Alignment explanation
Indices: 5743375--5743458 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 38
5743365 NNNNNNNTTA
5743375 TTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTATCCTTC
1 TTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTATCCTTC
*
5743413 TTTTTCTTTCTTTCCTCTCCTTTCC--TT-T-TCCTTC
1 TTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTATCCTTC
5743447 TTTTTCTTTCTT
1 TTTTTCTTTCTT
5743459 CCTTTCTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
34 18 0.40
35 1 0.02
36 2 0.04
38 24 0.53
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.65
Consensus pattern (38 bp):
TTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTATCCTTC
Found at i:5743651 original size:17 final size:17
Alignment explanation
Indices: 5743629--5743670 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
5743619 TCAGTTCACG
5743629 TTTTTTTCAGTTTTTTA
1 TTTTTTTCAGTTTTTTA
**
5743646 TTTTTTTTTGTTTTTTA
1 TTTTTTTCAGTTTTTTA
5743663 TTTATTTT
1 TTT-TTTT
5743671 TATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.10, C:0.02, G:0.05, T:0.83
Consensus pattern (17 bp):
TTTTTTTCAGTTTTTTA
Found at i:5743671 original size:17 final size:17
Alignment explanation
Indices: 5743638--5743671 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5743628 GTTTTTTTCA
*
5743638 GTTTTTTATTTTTTTTT
1 GTTTTTTATTTATTTTT
5743655 GTTTTTTATTTATTTTT
1 GTTTTTTATTTATTTTT
5743672 ATATATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (17 bp):
GTTTTTTATTTATTTTT
Found at i:5743701 original size:27 final size:28
Alignment explanation
Indices: 5743671--5743739 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
5743661 TATTTATTTT
5743671 TATATATTTTGGTAAATAAAAAAA-TTA
1 TATATATTTTGGTAAATAAAAAAAGTTA
5743698 TATATATTTTGGTAAATAAAAAAAGTTA
1 TATATATTTTGGTAAATAAAAAAAGTTA
*
5743726 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
5743740 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAAGTTA
Found at i:5746462 original size:26 final size:27
Alignment explanation
Indices: 5746417--5746468 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5746407 AAATCCCAAA
*
5746417 TTTTCTTCCTTTGCTTCCCT-TTTTCT
1 TTTTCTTCCTTTGCTCCCCTGTTTTCT
5746443 TTTTCTTTCCTTT-CTCCCCTGTTTTC
1 TTTTC-TTCCTTTGCTCCCCTGTTTTC
5746469 GTTTGCCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.00, C:0.33, G:0.04, T:0.63
Consensus pattern (27 bp):
TTTTCTTCCTTTGCTCCCCTGTTTTCT
Found at i:5746701 original size:14 final size:13
Alignment explanation
Indices: 5746675--5746725 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
5746665 GTTTATTTGA
5746675 AATATAATAATAT
1 AATATAATAATAT
5746688 AATATAATTAATAT
1 AATATAA-TAATAT
* *
5746702 AAT-TTACAATAT
1 AATATAATAATAT
*
5746714 AATAAAATAATA
1 AATATAATAATA
5746726 ATATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:5751849 original size:30 final size:30
Alignment explanation
Indices: 5751800--5751879 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
5751790 GGAGGGAGAT
5751800 TCGAACCTAGTGT--TTTTTTTCTTAGAAA
1 TCGAACCTAGTGTAATTTTTTTCTTAGAAA
5751828 TCGAACCTAGTGTAATTTTTTTCTTAGAAA
1 TCGAACCTAGTGTAATTTTTTTCTTAGAAA
*
5751858 TTGAACCTAGTGTAATTTTTTT
1 TCGAACCTAGTGTAATTTTTTT
5751880 AGTACAATAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 13 0.27
30 36 0.73
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (30 bp):
TCGAACCTAGTGTAATTTTTTTCTTAGAAA
Found at i:5758372 original size:17 final size:17
Alignment explanation
Indices: 5758350--5758396 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
5758340 TTAATAAATG
5758350 TAAATATATAAAATTAT
1 TAAATATATAAAATTAT
*
5758367 TAAATA-ATAAATATTTT
1 TAAATATATAAA-ATTAT
5758384 TAAA-ATATTAAAA
1 TAAATATA-TAAAA
5758397 ATAATATGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 6 0.23
17 16 0.62
18 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATATATAAAATTAT
Found at i:5763140 original size:24 final size:24
Alignment explanation
Indices: 5763108--5763161 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
5763098 TCTTTCTAGA
5763108 ATATTTAGTATTTATTAGCATAAT
1 ATATTTAGTATTTATTAGCATAAT
5763132 ATATTTAGTATTTATTAGCATAAT
1 ATATTTAGTATTTATTAGCATAAT
*
5763156 TTATTT
1 ATATTT
5763162 GACCTACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (24 bp):
ATATTTAGTATTTATTAGCATAAT
Found at i:5765220 original size:24 final size:24
Alignment explanation
Indices: 5765193--5765241 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5765183 GCCTATAATA
5765193 GGTAGCTCCAAAGAGCAATTAACG
1 GGTAGCTCCAAAGAGCAATTAACG
*
5765217 GGTAGCTCCGAAGAGCAATTAACG
1 GGTAGCTCCAAAGAGCAATTAACG
5765241 G
1 G
5765242 CAAGTACCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (24 bp):
GGTAGCTCCAAAGAGCAATTAACG
Found at i:5765348 original size:26 final size:26
Alignment explanation
Indices: 5765290--5765349 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
5765280 GGACTAACGG
* *
5765290 GAAGCTCACAAAGAGCCTTTAATCGG
1 GAAGCTCACAAAGAGCCTATAATCGA
*
5765316 GAAGCTCACGAAGAGCCATATAAT-GA
1 GAAGCTCACAAAGAGCC-TATAATCGA
*
5765342 GATGCTCA
1 GAAGCTCA
5765350 TAAGAGTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
GAAGCTCACAAAGAGCCTATAATCGA
Found at i:5765627 original size:13 final size:13
Alignment explanation
Indices: 5765609--5765633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5765599 TATTTTAATA
5765609 TTATTTTGTGTGT
1 TTATTTTGTGTGT
5765622 TTATTTTGTGTG
1 TTATTTTGTGTG
5765634 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:5766947 original size:114 final size:114
Alignment explanation
Indices: 5766707--5766928 Score: 408
Period size: 114 Copynumber: 1.9 Consensus size: 114
5766697 AAATCAGCAT
*
5766707 ATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAATATATGAATTGAAATTAGT
1 ATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAATATATAAATTGAAATTAGT
5766772 TAAGTATGAATATTATATATATGCATAAATGAAGTTCGAATATATGTAA
66 TAAGTATGAATATTATATATATGCATAAATGAAGTTCGAATATATGTAA
* *
5766821 ATATATATGTATATCTATTGTATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGT
1 ATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAATATATAAATTGAAATTAGT
*
5766886 TAAGTATGAATGTTATATATATGCATAAATGAAGTTCGAATAT
66 TAAGTATGAATATTATATATATGCATAAATGAAGTTCGAATAT
5766929 GTATATATGA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.41
Consensus pattern (114 bp):
ATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAATATATAAATTGAAATTAGT
TAAGTATGAATATTATATATATGCATAAATGAAGTTCGAATATATGTAA
Found at i:5767468 original size:41 final size:41
Alignment explanation
Indices: 5767417--5767563 Score: 233
Period size: 41 Copynumber: 3.6 Consensus size: 41
5767407 CAGACTTTAC
*
5767417 GTCTAGCAGGCTAAGTGCCGGTGATCTGAAACAGGCTATAA
1 GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
*
5767458 GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
1 GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
**
5767499 ACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
1 GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
*
5767540 G-CTTAGCAGGTTAAGTGCCGGTGA
1 GTC-TAGCAGGCTAAGTGCCGGTGA
5767564 ATATGTTAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
40 1 0.01
41 97 0.99
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (41 bp):
GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
Found at i:5769252 original size:21 final size:20
Alignment explanation
Indices: 5769207--5769256 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
5769197 AATAAATAAA
*
5769207 ATCATTCATGTCAATTCCCT
1 ATCATTCATGACAATTCCCT
*
5769227 ATCATTCACTGACAATTTCCT
1 ATCATTCA-TGACAATTCCCT
*
5769248 GTCATTCAT
1 ATCATTCAT
5769257 AACTTCTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.40
Consensus pattern (20 bp):
ATCATTCATGACAATTCCCT
Found at i:5773910 original size:2 final size:2
Alignment explanation
Indices: 5773898--5773931 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5773888 CTTAACTTTT
5773898 TA TA T- TA TA 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 TA TA TA TA TA T
5773932 GTTTTATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5782338 original size:18 final size:18
Alignment explanation
Indices: 5782289--5782340 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
5782279 TGTGTAATAT
*
5782289 ATTTATAAAA-GAAACTTA
1 ATTTATAAAATTAAA-TTA
* *
5782307 ACTTAT-AGATTAAATTA
1 ATTTATAAAATTAAATTA
5782324 ATTTATAAAATTAAATT
1 ATTTATAAAATTAAATT
5782341 TTAATATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (18 bp):
ATTTATAAAATTAAATTA
Found at i:5782377 original size:18 final size:18
Alignment explanation
Indices: 5782309--5782381 Score: 53
Period size: 18 Copynumber: 3.9 Consensus size: 18
5782299 GAAACTTAAC
* *
5782309 TTATAGATTAAATTAA-T
1 TTATAAATTAATTTAATT
5782326 TTATAAAATTAAATTTTAATAT
1 TTAT-AAATT-AA-TTTAAT-T
*
5782348 ATTATTAA--AATTTAATT
1 -TTATAAATTAATTTAATT
5782365 TTATAAATTAATTTAAT
1 TTATAAATTAATTTAAT
5782382 GTATTTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
16 6 0.14
17 5 0.11
18 18 0.41
19 4 0.09
20 4 0.09
22 3 0.07
23 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (18 bp):
TTATAAATTAATTTAATT
Found at i:5782397 original size:18 final size:19
Alignment explanation
Indices: 5782376--5782412 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5782366 TATAAATTAA
5782376 TTTAA-TGTATTTAAAATT
1 TTTAAGTGTATTTAAAATT
*
5782394 TTTAAGTTTATTTAAAATT
1 TTTAAGTGTATTTAAAATT
5782413 AAATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTAAGTGTATTTAAAATT
Found at i:5785074 original size:24 final size:24
Alignment explanation
Indices: 5785047--5785100 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
5785037 ATAATAAAAA
*
5785047 TTATTTTTTTTCATTTTTCTATTT
1 TTATTTTTTTTCATTTTTCAATTT
**
5785071 TTATAATTTTTCATTTTTCAATTT
1 TTATTTTTTTTCATTTTTCAATTT
5785095 TT-TTTT
1 TTATTTT
5785101 CATTCTATCA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (24 bp):
TTATTTTTTTTCATTTTTCAATTT
Done.