Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008413.1 Hibiscus syriacus cultivar Beakdansim tig00111191_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: 2772818
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1947823 original size:21 final size:20
Alignment explanation
Indices: 1947795--1947839 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1947785 ACATTAATCA
*
1947795 TAAATATTTAGT-AATTATTT
1 TAAATATTT-GTAAATTAGTT
1947815 TAAATTATTTGTAAATTAGTT
1 TAAA-TATTTGTAAATTAGTT
1947836 TAAA
1 TAAA
1947840 GAACAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (20 bp):
TAAATATTTGTAAATTAGTT
Found at i:1950379 original size:21 final size:21
Alignment explanation
Indices: 1950355--1950399 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1950345 AGCAAAGAGG
*
1950355 AAAAAACGAAGAAAAAAAAGC
1 AAAAAACAAAGAAAAAAAAGC
* *
1950376 AAAATACAAAGAAAAAAAGGC
1 AAAAAACAAAGAAAAAAAAGC
1950397 AAA
1 AAA
1950400 GAGAAAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.02
Consensus pattern (21 bp):
AAAAAACAAAGAAAAAAAAGC
Found at i:1953306 original size:55 final size:56
Alignment explanation
Indices: 1953232--1953341 Score: 159
Period size: 55 Copynumber: 2.0 Consensus size: 56
1953222 TTCTCTCGAA
* * * * *
1953232 ACACATTTTATTCTCGCTTGAGATGGTTTTCCCCAAATTTTGAAATCACTTCACTT
1 ACACATTTTAGTCTCGCTTGAGACGATTATCCCCAAATTTTAAAATCACTTCACTT
*
1953288 ACACATTTT-GTCTCGCTTGAGACGATTATCCCCAAATTTTAAAATTACTTCACT
1 ACACATTTTAGTCTCGCTTGAGACGATTATCCCCAAATTTTAAAATCACTTCACT
1953342 CGAAATAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
55 39 0.81
56 9 0.19
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (56 bp):
ACACATTTTAGTCTCGCTTGAGACGATTATCCCCAAATTTTAAAATCACTTCACTT
Found at i:1953830 original size:40 final size:40
Alignment explanation
Indices: 1953786--1953932 Score: 111
Period size: 40 Copynumber: 3.6 Consensus size: 40
1953776 GCTAGACTTC
*
1953786 CTCAACACAAAGGAACAATGTCATCCACCAACCAGATCTT
1 CTCAACGCAAAGGAACAATGTCATCCACCAACCAGATCTT
* * * * *
1953826 CTCAACGCGAATGAGCAGTGTCATCCTCAGACAACCAGA-CTT
1 CTCAACGCAAAGGAACAATGTCAT-C-CA-CCAACCAGATCTT
* * * *
1953868 CCTCAACGCAAA-GAA-TATGTCGTCCACCGACCAGATCTC
1 -CTCAACGCAAAGGAACAATGTCATCCACCAACCAGATCTT
* * * *
1953907 CTCAACCCGAAGGAGCAGTGTCATCC
1 CTCAACGCAAAGGAACAATGTCATCC
1953933 TTAGACAATA
Statistics
Matches: 80, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
38 16 0.20
39 6 0.08
40 27 0.34
41 6 0.08
42 7 0.09
43 18 0.22
ACGTcount: A:0.33, C:0.33, G:0.16, T:0.18
Consensus pattern (40 bp):
CTCAACGCAAAGGAACAATGTCATCCACCAACCAGATCTT
Found at i:1953873 original size:43 final size:43
Alignment explanation
Indices: 1953814--1953960 Score: 110
Period size: 43 Copynumber: 3.5 Consensus size: 43
1953804 TGTCATCCAC
*
1953814 CAACCAGATCTT-CTCAACGCGAATGAGCAGTGTCATCCTCAGA
1 CAACCAGA-CTTCCTCAACGCGAAAGAGCAGTGTCATCCTCAGA
** * *
1953857 CAACCAGACTTCCTCAACGC-AAAGAATA-TGTCGT-C-CA-C
1 CAACCAGACTTCCTCAACGCGAAAGAGCAGTGTCATCCTCAGA
* * * *
1953895 CGACCAGA-TCTCCTCAACCCGAAGGAGCAGTGTCATCCTTAGA
1 CAACCAGACT-TCCTCAACGCGAAAGAGCAGTGTCATCCTCAGA
** * *
1953938 CAATAAGACTTCCTTAACACGAA
1 CAACCAGACTTCCTCAACGCGAA
1953961 GGAACCGTAT
Statistics
Matches: 78, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
37 1 0.01
38 16 0.21
39 7 0.09
40 6 0.08
41 6 0.08
42 9 0.12
43 32 0.41
44 1 0.01
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (43 bp):
CAACCAGACTTCCTCAACGCGAAAGAGCAGTGTCATCCTCAGA
Found at i:1953923 original size:81 final size:83
Alignment explanation
Indices: 1953779--1953965 Score: 252
Period size: 81 Copynumber: 2.3 Consensus size: 83
1953769 TAAAATGGCT
* * *
1953779 AGACTTCCTCAACACAAAGGAACAATGTCATCCACCAACCAGATCTTCTCAACGCGAATGAGCAG
1 AGACTTCCTCAACACAAAGGAACAATGTCATCCACCAACCAGATCTCCTCAACCCGAAGGAGCAG
*
1953844 TGTCATCCTCAGACAACC
66 TGTCATCCTCAGACAACA
* * * *
1953862 AGACTTCCTCAACGCAAA-GAA-TATGTCGTCCACCGACCAGATCTCCTCAACCCGAAGGAGCAG
1 AGACTTCCTCAACACAAAGGAACAATGTCATCCACCAACCAGATCTCCTCAACCCGAAGGAGCAG
* *
1953925 TGTCATCCTTAGACAATA
66 TGTCATCCTCAGACAACA
* *
1953943 AGACTTCCTTAACACGAAGGAAC
1 AGACTTCCTCAACACAAAGGAAC
1953966 CGTATTGTCT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 66 0.74
82 6 0.07
83 17 0.19
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (83 bp):
AGACTTCCTCAACACAAAGGAACAATGTCATCCACCAACCAGATCTCCTCAACCCGAAGGAGCAG
TGTCATCCTCAGACAACA
Found at i:1955723 original size:32 final size:31
Alignment explanation
Indices: 1955687--1955771 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 31
1955677 CCGCTAACTT
1955687 TTCTAACTTTTATTTTATTGTTCATACTAAC
1 TTCTAACTTTTATTTTATTGTTCATACTAAC
* * *
1955718 ATTCTAACTTTTACTTTATCGTTCTTACTAAC
1 -TTCTAACTTTTATTTTATTGTTCATACTAAC
1955750 TTACTAACATTTTATTTTATTG
1 TT-CTAAC-TTTTATTTTATTG
1955772 CACAAACTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 2 0.04
32 33 0.72
33 11 0.24
ACGTcount: A:0.26, C:0.16, G:0.04, T:0.54
Consensus pattern (31 bp):
TTCTAACTTTTATTTTATTGTTCATACTAAC
Found at i:1956534 original size:33 final size:33
Alignment explanation
Indices: 1956497--1956560 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
1956487 TTTGCTTTCT
*
1956497 TTCTATCTTATTATTTTA-CTTTA-TTTTATCTCG
1 TTCTAT-TT-TTATTGTATCTTTATTTTTATCTCG
*
1956530 TTCTATTTTTATTGTATTTTTATTTTTATCT
1 TTCTATTTTTATTGTATCTTTATTTTTATCT
1956561 TTGAGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 7 0.26
32 6 0.22
33 14 0.52
ACGTcount: A:0.17, C:0.11, G:0.03, T:0.69
Consensus pattern (33 bp):
TTCTATTTTTATTGTATCTTTATTTTTATCTCG
Found at i:1957559 original size:17 final size:17
Alignment explanation
Indices: 1957537--1957580 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1957527 TGTAGTGAGT
*
1957537 ATATTAAATACT-GATTC
1 ATATTAAATACTAG-TCC
*
1957554 ATATTATATACTAGTCC
1 ATATTAAATACTAGTCC
1957571 ATATTAAATA
1 ATATTAAATA
1957581 ATACTCCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (17 bp):
ATATTAAATACTAGTCC
Found at i:1962218 original size:2 final size:2
Alignment explanation
Indices: 1962211--1962262 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1962201 AATTAGATTT
1962211 TA TA TA TA TA TA T- 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
1962252 TA TA TA TA TA T
1 TA TA TA TA TA T
1962263 TATTTTAAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1962522 original size:96 final size:99
Alignment explanation
Indices: 1962298--1962541 Score: 327
Period size: 96 Copynumber: 2.5 Consensus size: 99
1962288 AAAAGAGTTC
* * * *
1962298 GATAATTACAATAGTTATCTTTCTTTTAAATATA-AAATGTATCTCAACTCATATTAGGTTATAT
1 GATAATTACAATAATTATCTTTCTTTTAAATATATAAATCTATTTCAACTCAGATTAGGTTATAT
*
1962362 CATATATATATATATATATGTATTAATAGAGTTT
66 CATATATATATATATATATGTATTAATAGAATTT
* * * *
1962396 GATAATTACAATAATTATCTTTATTTTAAATATATAAATTTATTTCAACTTAGATTAGGTTCTAT
1 GATAATTACAATAATTATCTTTCTTTTAAATATATAAATCTATTTCAACTCAGATTAGGTTATAT
* *
1962461 CATATA-A-ATATATAT-T-TTTTAATTTGAATTT
66 CATATATATATATATATATGTATTAA-TAGAATTT
* *
1962492 GATAATTACAATAATTATCTCTCTTTTAAATATATAAACCTATTTCAACT
1 GATAATTACAATAATTATCTTTCTTTTAAATATATAAATCTATTTCAACT
1962542 AGAGATGGGC
Statistics
Matches: 130, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
95 5 0.04
96 53 0.41
97 8 0.06
98 33 0.25
99 31 0.24
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (99 bp):
GATAATTACAATAATTATCTTTCTTTTAAATATATAAATCTATTTCAACTCAGATTAGGTTATAT
CATATATATATATATATATGTATTAATAGAATTT
Found at i:1962845 original size:30 final size:30
Alignment explanation
Indices: 1962811--1962884 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 30
1962801 TCAGGTTAGA
1962811 TCGAGTTTGGGTTTTATCTCAAAAGATAGG
1 TCGAGTTTGGGTTTTATCTCAAAAGATAGG
1962841 TCGAGTTTGGGTTTTATCTCAAAAGATAGG
1 TCGAGTTTGGGTTTTATCTCAAAAGATAGG
*
1962871 TCAAGTTTCGGGTT
1 TCGAGTTT-GGGTT
1962885 GGGTGAAATC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 37 0.88
31 5 0.12
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (30 bp):
TCGAGTTTGGGTTTTATCTCAAAAGATAGG
Found at i:1968512 original size:23 final size:23
Alignment explanation
Indices: 1968486--1968534 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1968476 AAAATAAAAT
*
1968486 GAAAGATAATTAGAAATCAATTA
1 GAAAGATAATTAGAAATCAATCA
* * *
1968509 GAAAGGTAGTTAGGAATCAATCA
1 GAAAGATAATTAGAAATCAATCA
1968532 GAA
1 GAA
1968535 TAAAAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.22
Consensus pattern (23 bp):
GAAAGATAATTAGAAATCAATCA
Found at i:1971872 original size:31 final size:31
Alignment explanation
Indices: 1971837--1971904 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1971827 CAATAGAATG
* *
1971837 AGTTCATAGG-CTAAATTGATATTTCATTTAA
1 AGTTCATAGGTC-AAATTGATATTTAACTTAA
*
1971868 AGTTCATATGTCAAATTGATATTTAACTTAA
1 AGTTCATAGGTCAAATTGATATTTAACTTAA
1971899 AGTTCA
1 AGTTCA
1971905 AGGATTGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (31 bp):
AGTTCATAGGTCAAATTGATATTTAACTTAA
Found at i:1972895 original size:32 final size:30
Alignment explanation
Indices: 1972859--1972934 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 30
1972849 TATTTCCATT
* *
1972859 TTATTTTGATTGTTCGTTTATATATATATATA
1 TTATTTTGATTGTTCGATCATAT-T-TATATA
* * *
1972891 TTATTTTGATTATTTGATCATATTTGTATA
1 TTATTTTGATTGTTCGATCATATTTATATA
1972921 TTATTTTGATTGTT
1 TTATTTTGATTGTT
1972935 TGATAATGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 18 0.47
31 1 0.03
32 19 0.50
ACGTcount: A:0.25, C:0.03, G:0.11, T:0.62
Consensus pattern (30 bp):
TTATTTTGATTGTTCGATCATATTTATATA
Found at i:1972923 original size:30 final size:30
Alignment explanation
Indices: 1972887--1972956 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
1972877 TATATATATA
*
1972887 TATATTATTTTGATTATTTGATCATATTTG
1 TATATTATTTTGATTATTTGATAATATTTG
* *
1972917 TATATTATTTTGATTGTTTGATAATGTTTG
1 TATATTATTTTGATTATTTGATAATATTTG
* *
1972947 CATAATATTT
1 TATATTATTT
1972957 AGATGAGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.59
Consensus pattern (30 bp):
TATATTATTTTGATTATTTGATAATATTTG
Found at i:1974079 original size:19 final size:19
Alignment explanation
Indices: 1974057--1974094 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1974047 AAATACTCAC
*
1974057 TAACTTGTTCGATACATAA
1 TAACATGTTCGATACATAA
*
1974076 TAACATGTTTGATACATAA
1 TAACATGTTCGATACATAA
1974095 AAATTATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (19 bp):
TAACATGTTCGATACATAA
Found at i:1974271 original size:14 final size:14
Alignment explanation
Indices: 1974252--1974283 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1974242 TATCAACATT
1974252 AACATCATAATATC
1 AACATCATAATATC
*
1974266 AACATCATAGTATC
1 AACATCATAATATC
1974280 AACA
1 AACA
1974284 ACTAATAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.22, G:0.03, T:0.25
Consensus pattern (14 bp):
AACATCATAATATC
Found at i:1974901 original size:18 final size:19
Alignment explanation
Indices: 1974873--1974911 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1974863 TTTGTCAATA
*
1974873 TATACTACAAAAATATATT
1 TATACTACAAAAATAGATT
1974892 TATA-TACAAAAATAGATT
1 TATACTACAAAAATAGATT
1974910 TA
1 TA
1974912 ATTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (19 bp):
TATACTACAAAAATAGATT
Found at i:1987538 original size:21 final size:23
Alignment explanation
Indices: 1987511--1987585 Score: 88
Period size: 21 Copynumber: 3.5 Consensus size: 23
1987501 TGATGCATGG
1987511 GGTATCGATACCTATAT-GAACA
1 GGTATCGATACCTATATGGAACA
*
1987533 -GTATCGATACC-ATATGGAAGA
1 GGTATCGATACCTATATGGAACA
* *
1987554 GGTATCGATACCTATGTGG-A-G
1 GGTATCGATACCTATATGGAACA
1987575 GGTATCGATAC
1 GGTATCGATAC
1987586 AAGGGATCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
20 4 0.09
21 26 0.55
22 12 0.26
23 5 0.11
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (23 bp):
GGTATCGATACCTATATGGAACA
Found at i:1988328 original size:45 final size:45
Alignment explanation
Indices: 1988248--1988349 Score: 102
Period size: 45 Copynumber: 2.3 Consensus size: 45
1988238 AACTTGTGAT
* * * *
1988248 ATGAGATATATGATAAGAAGATACGAGACTCTATGT-TAGTATTAC
1 ATGAGATATGTGATAAGAAGACACGAGACTATATGTGTA-TATGAC
* * *
1988293 ATGAGATATGTGATAAGAAGCCATGAG-CTTATATGTGTATATGAT
1 ATGAGATATGTGATAAGAAGACACGAGAC-TATATGTGTATATGAC
1988338 ATGA-ATATGTGA
1 ATGAGATATGTGA
1988350 AAGTGTGATA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
44 9 0.19
45 37 0.77
46 2 0.04
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (45 bp):
ATGAGATATGTGATAAGAAGACACGAGACTATATGTGTATATGAC
Found at i:1992517 original size:22 final size:23
Alignment explanation
Indices: 1992475--1992519 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1992465 AGTGCATATG
*
1992475 TGTATTTGTGATATGAGATGATA
1 TGTACTTGTGATATGAGATGATA
*
1992498 TGTACTTGTG-TATGATATGATA
1 TGTACTTGTGATATGAGATGATA
1992520 GCAGTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.44
Consensus pattern (23 bp):
TGTACTTGTGATATGAGATGATA
Found at i:1992966 original size:2 final size:2
Alignment explanation
Indices: 1992959--1992990 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1992949 AGTATGCTTA
1992959 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
1992991 GAAAATTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1994384 original size:22 final size:22
Alignment explanation
Indices: 1994354--1994435 Score: 130
Period size: 22 Copynumber: 3.7 Consensus size: 22
1994344 TCAAAACCCC
*
1994354 TACTATGGTATCAATATTTCTA
1 TACTATGGTACCAATATTTCTA
*
1994376 TACTGTGGTACCAATATTTCTA
1 TACTATGGTACCAATATTTCTA
1994398 TACTATGGTACCAATATTAT-TA
1 TACTATGGTACCAATATT-TCTA
1994420 TACTATGGTACCAATA
1 TACTATGGTACCAATA
1994436 CTCCGTTTAG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 55 0.98
23 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (22 bp):
TACTATGGTACCAATATTTCTA
Found at i:1994540 original size:21 final size:19
Alignment explanation
Indices: 1994516--1994556 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
1994506 TACCCAGAGC
1994516 AGTATTGATACTACTTGCATT
1 AGTATTGATACTA-TT-CATT
1994537 AGTATTGATACTATTCATT
1 AGTATTGATACTATTCATT
1994556 A
1 A
1994557 AATTTTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (19 bp):
AGTATTGATACTATTCATT
Found at i:2000868 original size:112 final size:111
Alignment explanation
Indices: 2000669--2000898 Score: 379
Period size: 112 Copynumber: 2.1 Consensus size: 111
2000659 ATCGAAGTGC
* *
2000669 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCGAAAATGCACTGT
1 CGAAATGGTAATTCACCTCATTATGAATACCATGAGTGGCACCTTTTATGCCGAAAATGCACTAT
* * *
2000734 TATGCATTAAACAAAATCGATCGTTAACTTTCATACACGAAGTATGT
66 TATGCATTAAACAAAATCGATCGAT-ACTATCATACACAAAGTATGT
2000781 CGAAATGGTAATTCACCTCATTATGAATACCATGAGTGGCACCTTTTATGCCGAAAATGCACTAT
1 CGAAATGGTAATTCACCTCATTATGAATACCATGAGTGGCACCTTTTATGCCGAAAATGCACTAT
* * *
2000846 TATGCATTAAACAAAATTGATCGATACTATGATACGCAAAGTATGT
66 TATGCATTAAACAAAATCGATCGATACTATCATACACAAAGTATGT
2000892 CGAAATG
1 CGAAATG
2000899 CACCTATGAC
Statistics
Matches: 110, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
111 24 0.22
112 86 0.78
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (111 bp):
CGAAATGGTAATTCACCTCATTATGAATACCATGAGTGGCACCTTTTATGCCGAAAATGCACTAT
TATGCATTAAACAAAATCGATCGATACTATCATACACAAAGTATGT
Found at i:2003350 original size:22 final size:22
Alignment explanation
Indices: 2003324--2003365 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2003314 TTAACATGCT
2003324 AAAATTTGTAAGT-TTATATTTA
1 AAAATTT-TAAGTATTATATTTA
*
2003346 AAAATTTTAGGTATTATATT
1 AAAATTTTAAGTATTATATT
2003366 GAATTATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
AAAATTTTAAGTATTATATTTA
Found at i:2006330 original size:2 final size:2
Alignment explanation
Indices: 2006323--2006347 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2006313 CCATCATTAT
2006323 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2006348 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2006481 original size:23 final size:24
Alignment explanation
Indices: 2006443--2006508 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
2006433 TCCTTTTTTG
*
2006443 TTTTTGTTTTTATATTTTTAT-ATAT
1 TTTTTCTTTTT-TATTTTTATCAT-T
*
2006468 TTTTTC-TTTTTA-TTTAATCCATT
1 TTTTTCTTTTTTATTTTTAT-CATT
2006491 TTTTTCTTTTTTATTTTT
1 TTTTTCTTTTTTATTTTT
2006509 TTTTCCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
22 5 0.15
23 9 0.26
24 12 0.35
25 8 0.24
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (24 bp):
TTTTTCTTTTTTATTTTTATCATT
Found at i:2006508 original size:30 final size:27
Alignment explanation
Indices: 2006467--2006522 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
2006457 TTTTTATATA
*
2006467 TTTTTTCTTTTTATTTAATCCATTTTTTTC
1 TTTTTTATTTTT-TTT--TCCATTTTTTTC
2006497 TTTTTTATTTTTTTTTCCATTTTTTT
1 TTTTTTATTTTTTTTTCCATTTTTTT
2006523 TCTCTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 11 0.44
29 3 0.12
30 11 0.44
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTTTATTTTTTTTTCCATTTTTTTC
Found at i:2008647 original size:15 final size:16
Alignment explanation
Indices: 2008621--2008651 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2008611 TTATTCACCT
2008621 TTGGGGGAATTCCTTA
1 TTGGGGGAATTCCTTA
2008637 TTGGGGG-ATTCCTTA
1 TTGGGGGAATTCCTTA
2008652 CTCTAAAATG
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:0.16, C:0.13, G:0.32, T:0.39
Consensus pattern (16 bp):
TTGGGGGAATTCCTTA
Found at i:2040767 original size:12 final size:12
Alignment explanation
Indices: 2040741--2040800 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
2040731 GATACATGAC
* *
2040741 CTGAATTTTGTT
1 CTGAATTCTGAT
*
2040753 CTGATTTCTGAT
1 CTGAATTCTGAT
* *
2040765 CTGGATTCTGTT
1 CTGAATTCTGAT
*
2040777 CTGAATTCTGTT
1 CTGAATTCTGAT
*
2040789 TTGAATTCTGAT
1 CTGAATTCTGAT
2040801 ATCTCCATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.17, C:0.13, G:0.18, T:0.52
Consensus pattern (12 bp):
CTGAATTCTGAT
Found at i:2040796 original size:24 final size:24
Alignment explanation
Indices: 2040741--2040798 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2040731 GATACATGAC
* *
2040741 CTGAATTTTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGAATTCTGAT
* *
2040765 CTGGATTCTGTTCTGAATTCTGTT
1 CTGAATTCTGTTCTGAATTCTGAT
*
2040789 TTGAATTCTG
1 CTGAATTCTG
2040799 ATATCTCCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.52
Consensus pattern (24 bp):
CTGAATTCTGTTCTGAATTCTGAT
Found at i:2051709 original size:24 final size:24
Alignment explanation
Indices: 2051682--2051727 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2051672 ATTGTTGTAA
* * *
2051682 TTAATTTTATTTATTTTAATATAT
1 TTAATATTAATTATTATAATATAT
2051706 TTAATATTAATTATTATAATAT
1 TTAATATTAATTATTATAATAT
2051728 TAATAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTAATATTAATTATTATAATATAT
Found at i:2051715 original size:15 final size:15
Alignment explanation
Indices: 2051697--2051737 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
2051687 TTTATTTATT
2051697 TTAATATATTTAATA
1 TTAATATATTTAATA
2051712 TTAAT-TATTATAATA
1 TTAATATATT-TAATA
2051727 TTAATA-ATTTA
1 TTAATATATTTA
2051738 TTTAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAATATATTTAATA
Found at i:2051835 original size:22 final size:21
Alignment explanation
Indices: 2051810--2051852 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
2051800 TGGGTTGATT
2051810 TTAAAATATAAACATATAAATA
1 TTAAAATATAAACATA-AAATA
* * *
2051832 TTAAGATTTAAACCTAAAATA
1 TTAAAATATAAACATAAAATA
2051853 ATACCAAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAACATAAAATA
Found at i:2053011 original size:42 final size:42
Alignment explanation
Indices: 2052965--2053052 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
2052955 ATATTGACAA
* * * *
2052965 AAAAATAATTGTCGTCGCAACTCACCAACTAAGACTAGTAAC
1 AAAAACAATTATCGTCACAAATCACCAACTAAGACTAGTAAC
* *
2053007 AAAAACAATTATCGTCACAAATCACCAACTAAGACTATTGAC
1 AAAAACAATTATCGTCACAAATCACCAACTAAGACTAGTAAC
2053049 AAAA
1 AAAA
2053053 TGTTTTCGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.20
Consensus pattern (42 bp):
AAAAACAATTATCGTCACAAATCACCAACTAAGACTAGTAAC
Found at i:2062457 original size:30 final size:30
Alignment explanation
Indices: 2062423--2062523 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 30
2062413 AGAAGTTAGT
2062423 TGGGATGTTCTTCTATGTTTCTTAGCCATG
1 TGGGATGTTCTTCTATGTTTCTTAGCCATG
* * * * *
2062453 TGGGATTGTTTTGTTCTCATATTTTCTCTTTAGACTTT
1 TGGGA-TG--TT-CT-TC-TATGTT-TC-TTAGCCATG
2062491 TGGGATGTTCTTCTATGTTTCTTAGCCATG
1 TGGGATGTTCTTCTATGTTTCTTAGCCATG
2062521 TGG
1 TGG
2062524 AATTGTTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
30 14 0.26
31 4 0.08
32 5 0.09
33 4 0.08
34 2 0.04
35 4 0.08
36 5 0.09
37 4 0.08
38 11 0.21
ACGTcount: A:0.13, C:0.15, G:0.22, T:0.50
Consensus pattern (30 bp):
TGGGATGTTCTTCTATGTTTCTTAGCCATG
Found at i:2069059 original size:2 final size:2
Alignment explanation
Indices: 2069052--2069084 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2069042 TCAATCTACA
2069052 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
2069085 ATTTACGAAT
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:2084987 original size:19 final size:20
Alignment explanation
Indices: 2084951--2085001 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2084941 ATGTTTGCAT
*
2084951 GGTATCGATACCATCCTT-C
1 GGTATCGATACCACCCTTAC
**
2084970 GGTATCGATATTACCCTTAC
1 GGTATCGATACCACCCTTAC
*
2084990 AGTATCGATACC
1 GGTATCGATACC
2085002 TCTTCAATAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
GGTATCGATACCACCCTTAC
Found at i:2087838 original size:17 final size:17
Alignment explanation
Indices: 2087818--2087853 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2087808 TTTAGGGAAG
2087818 TAGTTCATTCATCAAAT
1 TAGTTCATTCATCAAAT
* *
2087835 TAGTTCATTTATTAAAT
1 TAGTTCATTCATCAAAT
2087852 TA
1 TA
2087854 ACTCTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (17 bp):
TAGTTCATTCATCAAAT
Found at i:2088825 original size:18 final size:18
Alignment explanation
Indices: 2088783--2088826 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2088773 ATTTAACCTT
*
2088783 ACAACACTTACCACGACA
1 ACAACATTTACCACGACA
*
2088801 ACAACATTTGCCACGACA
1 ACAACATTTACCACGACA
2088819 ACAACATT
1 ACAACATT
2088827 CATACTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.34, G:0.07, T:0.16
Consensus pattern (18 bp):
ACAACATTTACCACGACA
Found at i:2093197 original size:21 final size:19
Alignment explanation
Indices: 2093169--2093214 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
2093159 TCATTGAATC
2093169 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
2093189 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
2093208 ACTTAGT
1 A-TTAGT
2093215 AGAATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:2110456 original size:2 final size:2
Alignment explanation
Indices: 2110449--2110481 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2110439 CATTTGATTG
2110449 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
2110482 ATAACCATTT
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:2112001 original size:22 final size:21
Alignment explanation
Indices: 2111974--2112018 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2111964 GTCGTTGGCA
*
2111974 TATTAT-ATGATATTACTATTAT
1 TATTATCAT-ATATTA-TATAAT
2111996 TATTATCATATATTATATAAT
1 TATTATCATATATTATATAAT
2112017 TA
1 TA
2112019 ATAATTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 12 0.57
23 2 0.10
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTATCATATATTATATAAT
Found at i:2112349 original size:29 final size:30
Alignment explanation
Indices: 2112302--2112359 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
2112292 AATCAAAAAC
2112302 TAAATAAAAAAAGTATATAATTGATACAAT
1 TAAATAAAAAAAGTATATAATTGATACAAT
*
2112332 TAAAT-AAAAAAGTGTATAATTGATACAA
1 TAAATAAAAAAAGTATATAATTGATACAA
2112360 GTATCAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (30 bp):
TAAATAAAAAAAGTATATAATTGATACAAT
Found at i:2114473 original size:32 final size:32
Alignment explanation
Indices: 2114432--2114499 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
2114422 AAATTGATTT
2114432 TAAAGTATACTCTTTGTTATTTCAGTGAAATC
1 TAAAGTATACTCTTTGTTATTTCAGTGAAATC
2114464 TAAAGTATACTCTTTGTTATTTCAGTGAAATC
1 TAAAGTATACTCTTTGTTATTTCAGTGAAATC
2114496 TAAA
1 TAAA
2114500 CGATTTGGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (32 bp):
TAAAGTATACTCTTTGTTATTTCAGTGAAATC
Found at i:2115772 original size:24 final size:24
Alignment explanation
Indices: 2115745--2115819 Score: 57
Period size: 25 Copynumber: 3.2 Consensus size: 24
2115735 GTGATAACAC
2115745 GGTTCCTACGTGATGAGGACAGCT
1 GGTTCCTACGTGATGAGGACAGCT
* * * * **
2115769 GGTTATCTATGGGGTGATAACA--T
1 GGTT-CCTACGTGATGAGGACAGCT
2115792 GGTTCCTACGTGATGAGGAC-GACT
1 GGTTCCTACGTGATGAGGACAG-CT
2115816 GGTT
1 GGTT
2115820 ATCTGGGGTG
Statistics
Matches: 35, Mismatches: 12, Indels: 8
0.64 0.22 0.15
Matches are distributed among these distances:
22 10 0.29
23 5 0.14
24 9 0.26
25 11 0.31
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.29
Consensus pattern (24 bp):
GGTTCCTACGTGATGAGGACAGCT
Found at i:2115804 original size:47 final size:45
Alignment explanation
Indices: 2115735--2115860 Score: 154
Period size: 47 Copynumber: 2.8 Consensus size: 45
2115725 TTTAGGAGAT
2115735 GTGATAACACGGTTCCTACGTGATGAGGAC-AGCTGGTTATCTATGGG
1 GTGATAACACGGTTCCTACGTGATGAGGACGA-CTGGTTATC--TGGG
*
2115782 GTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTATCTGGG
1 GTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTGGG
**
2115827 GTG---ACACGACTCCTACGTGATGAGGA-GATCTGGT
1 GTGATAACACGGTTCCTACGTGATGAGGACGA-CTGGT
2115861 CGGGGATGAC
Statistics
Matches: 73, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
41 2 0.03
42 25 0.34
45 7 0.10
47 38 0.52
48 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (45 bp):
GTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTGGG
Found at i:2115883 original size:39 final size:40
Alignment explanation
Indices: 2115798--2115898 Score: 109
Period size: 39 Copynumber: 2.5 Consensus size: 40
2115788 ACATGGTTCC
*
2115798 TACGTGATGAGGACGA-CTGGTTATCTGGGGTGACACGACTCC
1 TACGTGATGAGGA-GATCTGG-T-TCTGGGGTGACACGACTCA
*
2115840 TACGTGATGAGGAGATCTGG-TC-GGGGATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTTCTGGGG-TGACACGACTCA
* *
2115879 TACGTGATGAAGAGTTCTGG
1 TACGTGATGAGGAGATCTGG
2115899 CCAGCTGATG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
38 4 0.08
39 30 0.57
41 2 0.04
42 17 0.32
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (40 bp):
TACGTGATGAGGAGATCTGGTTCTGGGGTGACACGACTCA
Found at i:2124019 original size:30 final size:30
Alignment explanation
Indices: 2123984--2124046 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
2123974 TTAAATTCGA
**
2123984 ATGCATATTATTGGTAATGTGCTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
* * *
2124014 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
2124044 ATG
1 ATG
2124047 AATTTACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (30 bp):
ATGCATATTATTGGTAATGCACTATAAATG
Found at i:2133409 original size:16 final size:16
Alignment explanation
Indices: 2133379--2133409 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2133369 AATATTGAAA
*
2133379 CTTGAACTCGAAAAAG
1 CTTGAACTCAAAAAAG
2133395 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
2133410 AATTTAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:2147407 original size:38 final size:38
Alignment explanation
Indices: 2147365--2147438 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
2147355 AGAGTGTTAC
* *
2147365 TTTGTTGAGTCTCTTGACTATTGAAAGTTATAAAATGG
1 TTTGTTGAGTCCCTTGACTATTGAAAGTTACAAAATGG
*
2147403 TTTGTTGAGTCCCTTGTCTATTGAAAGTTACAAAAT
1 TTTGTTGAGTCCCTTGACTATTGAAAGTTACAAAAT
2147439 AGTCACCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (38 bp):
TTTGTTGAGTCCCTTGACTATTGAAAGTTACAAAATGG
Found at i:2149369 original size:31 final size:31
Alignment explanation
Indices: 2149326--2149416 Score: 123
Period size: 31 Copynumber: 2.9 Consensus size: 31
2149316 ATTACTGAGC
2149326 TCGACTCGAAAACTTTGAAATGAAGCTCGAT
1 TCGACTCGAAAACTTTGAAATGAAGCTCGAT
* *
2149357 TCGATTCGAAAACTTTGAAATTAAGCTCGAT
1 TCGACTCGAAAACTTTGAAATGAAGCTCGAT
*
2149388 TCGAACTCG-AAA-TTCTGAACTGAAGCTCG
1 TCG-ACTCGAAAACTT-TGAAATGAAGCTCG
2149417 TGAGCAGCTC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
30 2 0.04
31 47 0.89
32 4 0.08
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
TCGACTCGAAAACTTTGAAATGAAGCTCGAT
Found at i:2159717 original size:25 final size:22
Alignment explanation
Indices: 2159674--2159718 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 22
2159664 AATCTCAAAA
2159674 TTATTAATTCATTTTATTAATT
1 TTATTAATTCATTTTATTAATT
2159696 TTATTATATATCATTTTAATTAA
1 TTATTA-AT-TCATTTT-ATTAA
2159719 AAATTTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 2 0.10
24 7 0.35
25 5 0.25
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTAATTCATTTTATTAATT
Found at i:2163541 original size:19 final size:20
Alignment explanation
Indices: 2163513--2163555 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2163503 GATGTGGCAA
2163513 TTTT-AATTA-TATTT-TAAT
1 TTTTAAATTATTATTTAT-AT
2163531 TTTTAAATTATTATTTATAT
1 TTTTAAATTATTATTTATAT
2163551 TTTTA
1 TTTTA
2163556 TTTAATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 5 0.23
20 12 0.55
21 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAAATTATTATTTATAT
Found at i:2164154 original size:25 final size:23
Alignment explanation
Indices: 2164104--2164155 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
2164094 TTTTTTAGGT
*
2164104 AAAACAATTAAATATTATTTTAA
1 AAAACAATTAAATATTATTTGAA
* *
2164127 AAAACAATTATAACTTTTATTTGGA
1 AAAACAATTA-AA-TATTATTTGAA
2164152 AAAA
1 AAAA
2164156 TTGAGGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.42
24 2 0.08
25 12 0.50
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (23 bp):
AAAACAATTAAATATTATTTGAA
Found at i:2164990 original size:15 final size:16
Alignment explanation
Indices: 2164972--2165005 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2164962 TATGAACATC
2164972 AAATAAAATAACAA-A
1 AAATAAAATAACAATA
*
2164987 AAATAGAATAACAATA
1 AAATAAAATAACAATA
2165003 AAA
1 AAA
2165006 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:2166689 original size:19 final size:20
Alignment explanation
Indices: 2166657--2166699 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
2166647 ACAAAATGTA
* *
2166657 AATACATATTAAATAATAAT
1 AATACATATAAAATAACAAT
*
2166677 AATA-ATATAAAATGACAAT
1 AATACATATAAAATAACAAT
2166696 AATA
1 AATA
2166700 GTAATAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (20 bp):
AATACATATAAAATAACAAT
Found at i:2168196 original size:23 final size:22
Alignment explanation
Indices: 2168157--2168210 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 22
2168147 TGAACCCTCC
*
2168157 TTTATTTAT-TTTTTCTTCTTT
1 TTTATTTTTCTTTTTCTTCTTT
2168178 TTTCATTTTTCTTTTTCTTCTTT
1 TTT-ATTTTTCTTTTTCTTCTTT
2168201 TTTATTTTTC
1 TTTATTTTTC
2168211 CATCATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 3 0.10
22 12 0.40
23 15 0.50
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTATTTTTCTTTTTCTTCTTT
Found at i:2168202 original size:16 final size:16
Alignment explanation
Indices: 2168165--2168210 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2168155 CCTTTATTTA
*
2168165 TTTTTTCTTCTTTTTTC
1 TTTTTTCTT-TTTCTTC
*
2168182 ATTTTTCTTTTTCTTC
1 TTTTTTCTTTTTCTTC
*
2168198 TTTTTTATTTTTC
1 TTTTTTCTTTTTC
2168211 CATCATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTTTTCTTC
Found at i:2179864 original size:15 final size:16
Alignment explanation
Indices: 2179846--2179882 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2179836 TATGAACATC
2179846 AAATAAAATAACA-AA
1 AAATAAAATAACATAA
*
2179861 AAATAGAATAACATAA
1 AAATAAAATAACATAA
2179877 AAATAA
1 AAATAA
2179883 TTTCTATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATAAAATAACATAA
Found at i:2181554 original size:19 final size:20
Alignment explanation
Indices: 2181522--2181564 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
2181512 ACAAAATGTA
* *
2181522 AATACATATTAAATAATAAT
1 AATACATATAAAATAACAAT
*
2181542 AATA-ATATAAAATGACAAT
1 AATACATATAAAATAACAAT
2181561 AATA
1 AATA
2181565 GTAATAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (20 bp):
AATACATATAAAATAACAAT
Found at i:2181697 original size:15 final size:15
Alignment explanation
Indices: 2181674--2181703 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2181664 TGTTTCTCCT
*
2181674 CTTCCCTCTCTTCCC
1 CTTCACTCTCTTCCC
2181689 CTTCACTCTCTTCCC
1 CTTCACTCTCTTCCC
2181704 ATGCAATCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.57, G:0.00, T:0.40
Consensus pattern (15 bp):
CTTCACTCTCTTCCC
Found at i:2187520 original size:3 final size:3
Alignment explanation
Indices: 2187512--2187547 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2187502 ATCTTCAGCG
*
2187512 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2187548 CCCCAAACCC
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2191437 original size:3 final size:3
Alignment explanation
Indices: 2191423--2191497 Score: 71
Period size: 3 Copynumber: 24.3 Consensus size: 3
2191413 CGAGAGTGTG
*
2191423 GGA GGG GGA GGA GGA GGA GAGA GG- GAGA GGA GGA GAGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA G-GA GGA G-GA GGA GGA G-GA GGA GGA GGA
* * * *
2191470 GGA GAA GGA GGA GAA GAA GGA GAA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
2191498 AAGAAGAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 52 0.87
4 7 0.12
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:2191454 original size:16 final size:17
Alignment explanation
Indices: 2191428--2191482 Score: 82
Period size: 16 Copynumber: 3.5 Consensus size: 17
2191418 GTGTGGGAGG
2191428 GGGAGGAGGAGGAGAGA
1 GGGAGGAGGAGGAGAGA
2191445 GGGA-GAGGAGGAGAGA
1 GGGAGGAGGAGGAGAGA
2191461 -GGAGGAGGAGGAGA-A
1 GGGAGGAGGAGGAGAGA
2191476 -GGAGGAG
1 GGGAGGAG
2191483 AAGAAGGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.30
16 22 0.59
17 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (17 bp):
GGGAGGAGGAGGAGAGA
Found at i:2191498 original size:6 final size:6
Alignment explanation
Indices: 2191431--2191816 Score: 181
Period size: 6 Copynumber: 64.3 Consensus size: 6
2191421 TGGGAGGGGG
* * * * *
2191431 AGGAGG AGGAGA GAGG-GA GAGGAGG AGAGAGG AGGAGG AGGAGA AGGAGG
1 AGGAGA AGGAGA -AGGAGA -AGGAGA AG-GAGA AGGAGA AGGAGA AGGAGA
* * * * **
2191481 AGAAGA AGGAGA AGGAGA AGAAGA AGAAGA AGAAGA AGGAGA AAAAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* * * *
2191529 AGAAGA ATGAGAAGA AGAAGA ATGAGAA AGGAGA A-G-G- AGGAGA AGAAGA
1 AGGAGA A-G-G-AGA AGGAGA AGGAG-A AGGAGA AGGAGA AGGAGA AGGAGA
* * * *
2191578 AGGAGA A-G-GA A-GAGA AGGAGA AGAAGA AGAAGA AGAAGA AGAAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* * * * * *
2191623 AGAAGA AGTAGAAGA AGGAGA AGGAGA A-AAAA AGAAGG AGAAGA AGGAGA
1 AGGAGA AG--G-AGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
* *
2191673 AGGAG- A--AGA AGGAGA AAGAGGA GAGGAGA AGGAGA AGAAGA AGGAGA
1 AGGAGA AGGAGA AGGAGA AGGA-GA -AGGAGA AGGAGA AGGAGA AGGAGA
* ** * * * *
2191720 AGGAGA AGGAGA AGATAGA ATAAG- AGAAGA AGCAGCAA AGCAGA AGAAGA
1 AGGAGA AGGAGA AG-GAGA AGGAGA AGGAGA AGGAG--A AGGAGA AGGAGA
* * * * *
2191770 AGCAGA AGCATA AGGAG- A--AGA AGGAGA AGAAGA AGGAGA AGAAGA
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
2191815 AG
1 AG
2191817 CTGCCACATC
Statistics
Matches: 308, Mismatches: 44, Indels: 56
0.75 0.11 0.14
Matches are distributed among these distances:
3 5 0.02
4 8 0.03
5 15 0.05
6 236 0.77
7 25 0.08
8 10 0.03
9 9 0.03
ACGTcount: A:0.55, C:0.01, G:0.42, T:0.02
Consensus pattern (6 bp):
AGGAGA
Found at i:2191502 original size:3 final size:3
Alignment explanation
Indices: 2191481--2191816 Score: 270
Period size: 3 Copynumber: 111.7 Consensus size: 3
2191471 GAGAAGGAGG
* * * *
2191481 AGA AGA AGG AGA AGG AGA AGA AGA AGA AGA AGA AGA AGG AGA AAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
2191529 AGA AGA ATG- AGA AGA AGA AGA ATG- AGAA AGG AGA AGG AGG AGA AGA
1 AGA AGA A-GA AGA AGA AGA AGA A-GA AG-A AGA AGA AGA AGA AGA AGA
* *
2191575 AGA AGG AGA AGGA AG- AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * *
2191620 AGA AGA AGA AGT AGA AGA AGG AGA AGG AGA A-A AAA AGA AGG AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * *
2191667 AGG AGA AGG AGA AGA AGG AGAA AGA GGA GAGG AGA AGG AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AG-A AGA AGA -AGA AGA AGA AGA AGA AGA
* * * * * *
2191714 AGG AGA AGG AGA AGG AGA AGA TAGA ATA AG- AGA AGA AGC AGC A-A
1 AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * * *
2191758 AGC AGA AGA AGA AGC AGA AGC ATA AGG AGA AGA AGG AGA AGA AGA AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2191806 AGA AGA AGA AG
1 AGA AGA AGA AG
2191817 CTGCCACATC
Statistics
Matches: 259, Mismatches: 61, Indels: 26
0.75 0.18 0.08
Matches are distributed among these distances:
2 9 0.03
3 237 0.92
4 13 0.05
ACGTcount: A:0.58, C:0.01, G:0.39, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:2192063 original size:3 final size:3
Alignment explanation
Indices: 2192055--2192470 Score: 368
Period size: 3 Copynumber: 139.0 Consensus size: 3
2192045 ATATTTTATT
* * * *
2192055 AAG AAG AAG GAG AAG AAG GAG AAG GAG AAG AAG AAG AAG GAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * * * * *
2192103 AAG GAG AAG GAG GAG AAG AAG GAG AAG GAG GAG AAG AAG GAG GAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * *
2192151 GAG GAG AA- AGAG AAG AAG GAG GAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
2192196 AAG AAG AAG AAG -AG GAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * *
2192243 AAAG GAG AAG AAG AAG AAG CAG AAG AAG GAG AAG AAG GAG AAG GAG
1 -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * *
2192289 AATG -AG AAG AAG GAG AAG GAG AAG AAG AAG AATG -AG AAT AGG GAG
1 AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG
* * *
2192334 AAG AAG AAG AAG CAG AAG GAG AAG AATG -AG AAG CAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG
* *
2192379 AAG AAG AAG AAG AAG AAG AAG -AG AAG GAG GAG AAG AATG -AG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG
*
2192423 GAG AATG -AG AA- AGAG AA- AGAG AATG -AG AAG AAG AAG AAG AAG AAG
1 AAG AA-G AAG AAG A-AG AAG A-AG AA-G AAG AAG AAG AAG AAG AAG AAG
2192468 AAG
1 AAG
2192471 CTACCACATC
Statistics
Matches: 339, Mismatches: 53, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
2 13 0.04
3 314 0.93
4 12 0.04
ACGTcount: A:0.57, C:0.01, G:0.40, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:2202980 original size:29 final size:29
Alignment explanation
Indices: 2202946--2203014 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
2202936 TTTATGTTAA
* *
2202946 AGGGGACGAATTTGAACTTTTAAAATTTT
1 AGGGGACGAACTTGAACTTATAAAATTTT
* *
2202975 TGGGGATGAACTTGAACTTATAAAATTTT
1 AGGGGACGAACTTGAACTTATAAAATTTT
*
2203004 AGGGGATGAAC
1 AGGGGACGAAC
2203015 ACAAATTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (29 bp):
AGGGGACGAACTTGAACTTATAAAATTTT
Found at i:2205097 original size:34 final size:34
Alignment explanation
Indices: 2205057--2205229 Score: 176
Period size: 34 Copynumber: 4.9 Consensus size: 34
2205047 CATATATATA
2205057 ATATATAATTTTTAAAATCATTTTGAAAA-ATTAT
1 ATATATAATTTTTAAAA-CATTTTGAAAACATTAT
*
2205091 ATATATAATTTTTGAAAACATTTTTGAAAACA-CAT
1 ATATATAATTTTT-AAAACA-TTTTGAAAACATTAT
* *
2205126 ATATTATAGTTTTGAAAACATTTTGAAAACATTTAT
1 ATA-TATAATTTTTAAAACATTTTGAAAACA-TTAT
*
2205162 ATATTATATAGTTTTTAAAACGTTTTTGAAAAC-TTAT
1 ATA-TATA-A-TTTTTAAAAC-ATTTTGAAAACATTAT
*
2205199 ATA-AT-ATTTTTGAAAACATGTTGAAAACATT
1 ATATATAATTTTT-AAAACATTTTGAAAACATT
2205230 CGTATATTAT
Statistics
Matches: 119, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
32 14 0.12
33 8 0.07
34 26 0.22
35 26 0.22
36 19 0.16
37 7 0.06
38 9 0.08
39 10 0.08
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (34 bp):
ATATATAATTTTTAAAACATTTTGAAAACATTAT
Found at i:2205113 original size:12 final size:12
Alignment explanation
Indices: 2205098--2205122 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2205088 TATATATATA
2205098 ATTTTTGAAAAC
1 ATTTTTGAAAAC
2205110 ATTTTTGAAAAC
1 ATTTTTGAAAAC
2205122 A
1 A
2205123 CATATATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:2205151 original size:11 final size:11
Alignment explanation
Indices: 2205135--2205159 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2205125 TATATTATAG
2205135 TTTTGAAAACA
1 TTTTGAAAACA
2205146 TTTTGAAAACA
1 TTTTGAAAACA
2205157 TTT
1 TTT
2205160 ATATATTATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:2205163 original size:108 final size:105
Alignment explanation
Indices: 2205032--2205227 Score: 277
Period size: 108 Copynumber: 1.8 Consensus size: 105
2205022 TTTTAAAAAA
*
2205032 AAAACGTTTTAAAAACATATATATAATATATAATTTTTAAAATC-ATTTTGAAAAATTATATATA
1 AAAACATTTTAAAAACATATATATAATATATAATTTTTAAAA-CGATTTTGAAAAATTATATA-A
*
2205096 TAATTTTTGAAAACATTTTTGAAAACACATATATTATAGTTTTG
64 T-ATTTTTGAAAACA-TGTTGAAAACACATATATTATAGTTTTG
* * * * * *
2205140 AAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAACGTTTTTGAAAACTTATATAATA
1 AAAACATTTTAAAAACATATATATAATATATAATTTTTAAAACGATTTTGAAAAATTATATAATA
2205205 TTTTTGAAAACATGTTGAAAACA
66 TTTTTGAAAACATGTTGAAAACA
2205228 TTCGTATATT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
105 10 0.13
106 13 0.16
107 3 0.04
108 53 0.67
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (105 bp):
AAAACATTTTAAAAACATATATATAATATATAATTTTTAAAACGATTTTGAAAAATTATATAATA
TTTTTGAAAACATGTTGAAAACACATATATTATAGTTTTG
Found at i:2205216 original size:71 final size:74
Alignment explanation
Indices: 2205057--2205246 Score: 231
Period size: 71 Copynumber: 2.7 Consensus size: 74
2205047 CATATATATA
2205057 ATATAT-A-ATTTTT-AAAATCATTTTGAAAA-A-TTATATA-TATA-A-TTTTTGAAAACATTT
1 ATATATAATATTTTTGAAAA-CATTTTGAAAACATTTATATATTATATAGTTTTTGAAAACATTT
2205114 TTGAAAACAC
65 TTGAAAACAC
* * *
2205124 ATATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTT-AAAACGTTTT
1 ATATATAATATTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTTGAAAACATTTT
2205188 TG-AAA-AC
66 TGAAAACAC
* * **
2205195 TTATATAATATTTTTGAAAACATGTTGAAAACATTCGTATATTATATAGTTT
1 ATATATAATATTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTT
2205247 AAGAAAAAAA
Statistics
Matches: 107, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
67 6 0.06
68 1 0.01
69 16 0.15
70 5 0.05
71 55 0.51
72 7 0.07
73 12 0.11
74 5 0.05
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (74 bp):
ATATATAATATTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTTGAAAACATTTT
TGAAAACAC
Found at i:2205277 original size:71 final size:70
Alignment explanation
Indices: 2205057--2205276 Score: 175
Period size: 71 Copynumber: 3.1 Consensus size: 70
2205047 CATATATATA
* * **
2205057 ATATATAATTTTT-AAAATCATTTTGAAAA-ATT-ATATA-TATA-ATTTTTGAAAAC-ATTTTT
1 ATATAT-ATTTTTGAAAA-CATGTTGAAAACATTCATATATTATATAGTTTAAAAAACGA-TTTT
*
2205116 GAAAACACAT
63 G-AAA-ACTT
* * * ** *
2205126 ATATTATAGTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAACGTTTTTGA
1 ATA-TATATTTTTGAAAACATGTTGAAAACATTCATATATTATATAGTTTAAAAAACGATTTTGA
2205191 AAACTT
65 AAACTT
*
2205197 ATATAATATTTTTGAAAACATGTTGAAAACATTCGTATATTATATAGTTTAAGAAAAAAAC-ATT
1 ATAT-ATATTTTTGAAAACATGTTGAAAACATTCATATATTATATAGTTT----AAAAAACGATT
*
2205261 TTGAAAATTT
61 TTGAAAACTT
2205271 ATATAT
1 ATATAT
2205277 TATATGTTTT
Statistics
Matches: 126, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
69 19 0.15
70 11 0.09
71 52 0.41
72 7 0.06
73 17 0.13
74 15 0.12
75 5 0.04
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.43
Consensus pattern (70 bp):
ATATATATTTTTGAAAACATGTTGAAAACATTCATATATTATATAGTTTAAAAAACGATTTTGAA
AACTT
Found at i:2205326 original size:3 final size:3
Alignment explanation
Indices: 2205313--2205342 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
2205303 TATATATATG
2205313 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
2205343 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2206327 original size:13 final size:13
Alignment explanation
Indices: 2206309--2206340 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2206299 TTTGAGAGAC
2206309 GAGAGAGAGCGCA
1 GAGAGAGAGCGCA
2206322 GAGAGAGAGCGCA
1 GAGAGAGAGCGCA
2206335 GAGAGA
1 GAGAGA
2206341 CCAAATGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.47, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGCGCA
Found at i:2206681 original size:26 final size:25
Alignment explanation
Indices: 2206652--2206726 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 25
2206642 TGATCCTAAA
* *
2206652 TTTTATCTTTATTTTTTTATTTTACT
1 TTTTAT-TTTATTTTTTTATTTAACC
*
2206678 TTTTAAATATTT-TTTTTTAATTTAACC
1 TTTT--AT-TTTATTTTTTTATTTAACC
*
2206705 TTTTATTATTATTTTATTATTT
1 TTTTATT-TTATTTTTTTATTT
2206727 CTTTCTTTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
24 1 0.03
25 4 0.10
26 13 0.33
27 16 0.41
28 5 0.13
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTATTTTATTTTTTTATTTAACC
Found at i:2206719 original size:27 final size:26
Alignment explanation
Indices: 2206652--2206726 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
2206642 TGATCCTAAA
* *
2206652 TTTTATCT-TTATTTTTTTATTTTACT
1 TTTTAT-TATTATTTTTTTATTTAACC
*
2206678 TTTTAAATATT-TTTTTTTAATTTAACC
1 TTTT-ATTATTATTTTTTT-ATTTAACC
*
2206705 TTTTATTATTATTTTATTATTT
1 TTTTATTATTATTTTTTTATTT
2206727 CTTTCTTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
26 21 0.52
27 19 0.47
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTATTATTATTTTTTTATTTAACC
Found at i:2212061 original size:85 final size:83
Alignment explanation
Indices: 2211801--2212691 Score: 900
Period size: 85 Copynumber: 10.8 Consensus size: 83
2211791 GCTCAAGGCC
* * *
2211801 AGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCACATCATTT
1 AGAAGGGCTATCTGCCACCAAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTT
* *
2211865 GCAGAATAGCTTAAGTCG
66 GCAGCATAACTTAAGTCG
* * *
2211883 AGAAGGGCTATCTGCCA--AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
1 AGAAGGGCTATCTGCCACCAAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTT
* * * *
2211946 ACAGCATAACTCAAGGCT
66 GCAGCATAACTTAAGTCG
* ** * *
2211964 AGAAGGGTTATCTGTGACCACCAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCA
1 AGAAGGGCTATC--TG-CCACCAAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCA
* *
2212028 TTTGCAGAATAGCTTAAGTCG
63 TTTGCAGCATAACTTAAGTCG
* *
2212049 AGAAGGGCTATCTGCCA--AAGACC-CCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
1 AGAAGGGCTATCTGCCACCAAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTT
* * * *
2212111 ACAGCATAACTCAAGGCT
66 GCAGCATAACTTAAGTCG
* * * *
2212129 AGAAGGGTTATCTGTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCACATCA
1 AGAAGGGCTATC--TG-CCACCAAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCA
* *
2212193 TTTGCAGAATAGCTTAAGTCG
63 TTTGCAGCATAACTTAAGTCG
* *
2212214 AGAAGGGCTATCTGCCA--AAGACC-CCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
1 AGAAGGGCTATCTGCCACCAAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTT
* * * *
2212276 ACAGCATAACTCAAGGCT
66 GCAGCATAACTTAAGTCG
* ** * *
2212294 AGAAGGGTTATCTGTGACCACCAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCA
1 AGAAGGGCTATC--TG-CCACCAAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCA
* *
2212358 TTTGCAGAATAGCTTAAGTCG
63 TTTGCAGCATAACTTAAGTCG
* * * *
2212379 AGAAGGGCTATCTGCCA--AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACACCATTT
1 AGAAGGGCTATCTGCCACCAAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTT
*
2212442 GCAGCATAACTTAAGTCA
66 GCAGCATAACTTAAGTCG
* * * * * *
2212460 AGAAGGGTTATCTGCCCACCAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACACCAT
1 AGAAGGGCTATCTG-CCACC-AAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCAT
*
2212525 TTGCAGCATAACTTAAGTCA
64 TTGCAGCATAACTTAAGTCG
* * * * * * *
2212545 AGAAGAGTTATCTGGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCAT
1 AGAAGGGCTATCT-GCCACC-AAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCAT
* * *
2212609 TTGCAGTATAGCTTAAGTCA
64 TTGCAGCATAACTTAAGTCG
* * * *
2212629 AGAAGGGCTATCTGCCA--AAGA-CTCCCGAGTTCGATTACACTCAACTTCGAAGTCATATCATT
1 AGAAGGGCTATCTGCCACCAAGACCT-CCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATT
2212691 T
65 T
2212692 ATCATGGCAA
Statistics
Matches: 669, Mismatches: 112, Indels: 57
0.80 0.13 0.07
Matches are distributed among these distances:
79 37 0.06
80 156 0.23
81 95 0.14
82 33 0.05
83 17 0.03
84 43 0.06
85 229 0.34
86 59 0.09
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (83 bp):
AGAAGGGCTATCTGCCACCAAGACCTCCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTT
GCAGCATAACTTAAGTCG
Found at i:2212166 original size:165 final size:165
Alignment explanation
Indices: 2211792--2212594 Score: 1238
Period size: 165 Copynumber: 4.8 Consensus size: 165
2211782 TGCAGCTTGG
* * *
2211792 CTCAAGGCCAGAAGGGCTATC--TG-CCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAG
1 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
2211854 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
66 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATT
2211919 ACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
130 ACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
*
2211955 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAG
1 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
2212020 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTA
66 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTA
2212085 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
131 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
*
2212120 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAG
1 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
2212185 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTA
66 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTA
2212250 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
131 CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
*
2212285 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAG
1 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
2212350 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
66 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATT
* *
2212415 ACACTCAGCTTCGAGGGCACACCATTTGCAGCATAA
130 ACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
* * * * ** * * * *
2212451 CTTAAGTCAAGAAGGGTTATC--TGCCCACCAAAGACCCCCAAGTTCGATTACACTCAGCTTCGA
1 CTCAAGGCTAGAAGGGTTATCTGTGACCACC-AAGACCTTCGAGTTCGACTACGCTCAGC-TCCA
* * * * * * * *
2212514 GGGCACACCATTTGCAGCATAACTTAAGTCAAGAAGAGTTATCTGGCAACCAAAGACCTTCGAGT
64 AGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCT-G---CCAAAGACC-CCGAGT
* *
2212579 TCGACTACGCTCAGCT
124 TCGATTACACTCAGCT
2212595 CCAAGGCATA
Statistics
Matches: 598, Mismatches: 31, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
163 19 0.03
164 7 0.01
165 350 0.59
166 193 0.32
167 1 0.00
169 2 0.00
170 26 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (165 bp):
CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG
GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTA
CACTCAGCTTCGAGGGCACATCATTTACAGCATAA
Found at i:2212497 original size:330 final size:327
Alignment explanation
Indices: 2211792--2212594 Score: 1282
Period size: 331 Copynumber: 2.4 Consensus size: 327
2211782 TGCAGCTTGG
* *
2211792 CTCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCA
1 CTCAAGGCAAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCA
2211857 CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACA
66 CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATTACA
2211922 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCACCA
130 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCACCA
2211987 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGA
195 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGA
*
2212052 AGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCA
260 AGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTCGAGGGCACACCATTTACAGCA
2212117 TAA
325 TAA
*
2212120 CTCAAGGCTAGAAGGGTTATCTGTGACCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAG
1 CTCAAGGCAAGAAGGGTTATC--TG-CCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAG
2212185 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTA
63 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTA
2212250 CACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAC
128 CACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAC
2212315 CAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGA
193 CAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGA
*
2212380 GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACACCATTTGCA
258 GAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACACCATTTACA
2212445 GCATAA
322 GCATAA
* * ** * * * * *
2212451 CTTAAGTCAAGAAGGGTTATCTGCCCACCAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGG
1 CTCAAGGCAAGAAGGGTTATCTG-CCACC-AAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAG
* * * * * * *
2212516 GCACACCATTTGCAGCATAACTTAAGTCAAGAAGAGTTATCTGGCAACCAAAGACCTTCGAGTTC
63 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCT-G---CCAAAGACC-CCGAGTTC
* *
2212581 GACTACGCTCAGCT
123 GATTACACTCAGCT
2212595 CCAAGGCATA
Statistics
Matches: 440, Mismatches: 24, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
328 19 0.04
329 7 0.02
330 190 0.43
331 195 0.44
332 1 0.00
335 9 0.02
336 19 0.04
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (327 bp):
CTCAAGGCAAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCA
CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACAC
TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCACCAA
GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAA
GGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTCGAGGGCACACCATTTACAGCAT
AA
Found at i:2213450 original size:12 final size:12
Alignment explanation
Indices: 2213435--2213459 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2213425 TATATATATA
2213435 ATTTTTGAAAAC
1 ATTTTTGAAAAC
2213447 ATTTTTGAAAAC
1 ATTTTTGAAAAC
2213459 A
1 A
2213460 CATATATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:2213465 original size:35 final size:35
Alignment explanation
Indices: 2213394--2213564 Score: 171
Period size: 35 Copynumber: 4.9 Consensus size: 35
2213384 CATATATATA
2213394 ATATATAATTTTT-AAAATCATTTTGAAAA-ATTAT
1 ATATATAATTTTTGAAAA-CATTTTGAAAACATTAT
*
2213428 ATATATAATTTTTGAAAACATTTTTGAAAACA-CAT
1 ATATATAATTTTTGAAAACA-TTTTGAAAACATTAT
*
2213463 ATAT-TATAGTTTTGAAAACA-TTTGAAAACATTTAT
1 ATATATA-ATTTTTGAAAACATTTTGAAAACA-TTAT
* *
2213498 ATATTATATAGTTTT-AAAACGTTTTTGAAAAC-TTAT
1 ATA-TATA-ATTTTTGAAAAC-ATTTTGAAAACATTAT
*
2213534 ATA-AT-ATTTTTGAAAACATGTTGAAAACATT
1 ATATATAATTTTTGAAAACATTTTGAAAACATT
2213565 CGTATATTAT
Statistics
Matches: 118, Mismatches: 7, Indels: 25
0.79 0.05 0.17
Matches are distributed among these distances:
32 14 0.12
33 17 0.14
34 19 0.16
35 36 0.31
36 14 0.12
37 9 0.08
38 9 0.08
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (35 bp):
ATATATAATTTTTGAAAACATTTTGAAAACATTAT
Found at i:2213640 original size:105 final size:101
Alignment explanation
Indices: 2213425--2213641 Score: 221
Period size: 107 Copynumber: 2.1 Consensus size: 101
2213415 TTTGAAAAAT
* *
2213425 TATATATAT-AATTTTTGAAAACATTTTTGAAAACACATATATTATAGTTTTGAAAACATTTGAA
1 TATATATATAAATTTTTGAAAACATTGTTGAAAACACATATATTATAGTTTAGAAAACATTTGAA
* *
2213489 AACATTTATATATTATATAGTTTTAAAACGTTTTTG
66 AACATTTATATATTATATAGTTTTAAAACATTTATG
* * *
2213525 AAAACTTATATAATATTTTTGAAAACA-TGTTGAAAACATTCGTATATTATAGTTTAAGAAAAAA
1 TATA--TATATAA-ATTTTTGAAAACATTGTTGAAAACA--CATATATTATAGTTT-AG---AAA
*
2213589 ACATTTTG-AAA-A-TTATATATTATAT-GTTTTGAAAATATTTATG
57 ACA-TTTGAAAACATTTATATATTATATAGTTTT-AAAACATTTATG
2213632 TATATATATA
1 TATATATATA
2213642 TGTTATTATT
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
100 2 0.02
102 5 0.05
103 11 0.12
104 13 0.14
105 20 0.21
106 6 0.06
107 24 0.25
108 1 0.01
109 9 0.09
110 4 0.04
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (101 bp):
TATATATATAAATTTTTGAAAACATTGTTGAAAACACATATATTATAGTTTAGAAAACATTTGAA
AACATTTATATATTATATAGTTTTAAAACATTTATG
Found at i:2214652 original size:13 final size:13
Alignment explanation
Indices: 2214634--2214665 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2214624 TTTGAGAGAC
2214634 GAGAGAGAGCGCA
1 GAGAGAGAGCGCA
2214647 GAGAGAGAGCGCA
1 GAGAGAGAGCGCA
2214660 GAGAGA
1 GAGAGA
2214666 CCAAATGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.47, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGCGCA
Found at i:2215099 original size:30 final size:33
Alignment explanation
Indices: 2215031--2215100 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
2215021 AATTTAACCT
2215031 TTTATTATTATTTTATTATTTCTTTCTTTCATTA
1 TTTATTATTATTTTATTATTTCTTTCTTT-ATTA
2215065 -TTATTATTATTTT-TTATATT-TTT-TTT-TTA
1 TTTATTATTATTTTATTAT-TTCTTTCTTTATTA
2215094 TTTATTA
1 TTTATTA
2215101 GCATTTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
29 3 0.09
30 6 0.18
31 3 0.09
32 7 0.21
33 15 0.44
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTATTATTATTTTATTATTTCTTTCTTTATTA
Found at i:2216091 original size:179 final size:179
Alignment explanation
Indices: 2215742--2216111 Score: 582
Period size: 179 Copynumber: 2.1 Consensus size: 179
2215732 GATATTCGGG
* *
2215742 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACTGGACCAACCCGAAAATATATATAATT
1 TCGGGTCGGGTCGAGTTCGGATTTAGGGTGAAAAAAACCGGACCAACCCGAAAATATATATAATT
2215807 CAAGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTATTATTTCGGGTCGGG
66 CAA---GGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTATTATTTCGGGTCGGG
* * *
2215872 TCGGATTTTTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGT
128 TAGAATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGT
* * *
2215924 TTGGGTCGGGTCGGGTTCGGATTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATT
1 TCGGGTCGGGTCGAGTTCGGATTTAGGGTGAAAAAAACCGGACCAACCCGAAAATATATATAATT
* *
2215989 C-A-GGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTATTATTATTTCGGGTCGGGT
66 CAAGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACA-ATT-TTATTATTTCGGGTCGGGT
*
2216052 AGAATTTCTAATTCATATATTCGTGTCGGGTCGGATGAAACTTTATTTTGT
129 AGAATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGT
2216103 TCGGGTCGG
1 TCGGGTCGG
2216112 TTTTTTTAAG
Statistics
Matches: 174, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
177 36 0.21
178 2 0.01
179 74 0.43
181 1 0.01
182 61 0.35
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (179 bp):
TCGGGTCGGGTCGAGTTCGGATTTAGGGTGAAAAAAACCGGACCAACCCGAAAATATATATAATT
CAAGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTATTATTTCGGGTCGGGTAG
AATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGT
Found at i:2216347 original size:33 final size:33
Alignment explanation
Indices: 2216290--2216370 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
2216280 TTTATTTTGT
*
2216290 TCGGGTCGGGTC-GGATTTTTTAAGTGTGATAC
1 TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATAC
*
2216322 TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATAC
* *
2216355 TCGAGTCAGGTCGGGT
1 TCGGGTCGGGTCGGGT
2216371 CGGGTTTAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 12 0.27
33 32 0.73
ACGTcount: A:0.14, C:0.12, G:0.37, T:0.37
Consensus pattern (33 bp):
TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATAC
Found at i:2216390 original size:218 final size:207
Alignment explanation
Indices: 2215932--2216407 Score: 521
Period size: 218 Copynumber: 2.2 Consensus size: 207
2215922 GTTTGGGTCG
*
2215932 GGTCGGGTTCGGATTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGG
1 GGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGG
* *
2215997 ATTAAGTCACTGTTTTTATTAAATAAAAATATTTTATTATTATTTCGGGTCGGGTAGAATTTCTA
66 ATTAAGTCACTGTTTTTATTAAATAAAAATATTTTATTATTATTTCAGGTCGGGTAGAA-TTCAA
* * ** *
2216062 ATTCATATATTCGTGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGTTTTTTTAAGTGTGA
130 ATTCATATATTCGGGTCGGGTCGGATGAAACTTTACTCGGGTCGGGTCGGTTTTTTTAAGTGTGA
*
2216127 TATTCGGGTCGAGTCG
195 TATT---GTCGAGTCA
* *
2216143 GGTCGGGTTCGGGTTTAGGGTGAAAAAAAAAACAGACCGACCCGAAAATATATATAATTCGGGTC
1 GGTCGGGTTCGGGTTTAGGGTG--AAAAAAACCGGACCGACCCGAAAATATATATAA-T----TC
* * *
2216208 GGGTCGGATTAAGTCACTGTTTTTATTAAATAAAATTAATTTT-TTATTATTTCAGGTCGGGTCG
59 AGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAAT-ATTTTATTATTATTTCAGGTCGGGTAG
* * * * * ** *
2216272 GA-TGAAACTTTATTTTGTTCGGGTCGGGTCGGATTTTTTAAGTGTGATACTCGGGTCGGGTCGG
123 AATTCAAA-TTCA-TATATTCGGGTCGGGTCGGA---TGAAACT-T--TACTCGGGTCGGGTC-G
2216336 GTTTTTTTAAGTGTGATA-T-TCGAGTCA
179 GTTTTTTTAAGTGTGATATTGTCGAGTCA
*
2216363 GGTCGGG-TCGGGTTTAGGGTGAAAAAAACCGGACTGACCCGAAAA
1 GGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAA
2216408 AAAATATATA
Statistics
Matches: 223, Mismatches: 25, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
211 21 0.09
213 31 0.14
214 1 0.00
216 3 0.01
217 24 0.11
218 74 0.33
219 19 0.09
220 14 0.06
221 4 0.02
222 1 0.00
224 12 0.05
225 19 0.09
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (207 bp):
GGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGG
ATTAAGTCACTGTTTTTATTAAATAAAAATATTTTATTATTATTTCAGGTCGGGTAGAATTCAAA
TTCATATATTCGGGTCGGGTCGGATGAAACTTTACTCGGGTCGGGTCGGTTTTTTTAAGTGTGAT
ATTGTCGAGTCA
Found at i:2218109 original size:14 final size:14
Alignment explanation
Indices: 2218090--2218152 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
2218080 AACTTAATAT
2218090 TATTATTTTTAAAA
1 TATTATTTTTAAAA
* **
2218104 TATTA-TTATAATT
1 TATTATTTTTAAAA
*
2218117 TATTTATTATTAAAA
1 TA-TTATTTTTAAAA
*
2218132 TATTATTTTTATAA
1 TATTATTTTTAAAA
*
2218146 TTTTATT
1 TATTATT
2218153 AATAAAAATA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
13 7 0.19
14 24 0.65
15 6 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTTTTAAAA
Found at i:2218115 original size:28 final size:28
Alignment explanation
Indices: 2218084--2218138 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2218074 TCATAAAACT
*
2218084 TAATATTA-TTATTTTTAAAATATTATTA
1 TAAT-TTATTTATTATTAAAATATTATTA
2218112 TAATTTATTTATTATTAAAATATTATT
1 TAATTTATTTATTATTAAAATATTATT
2218139 TTTATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TAATTTATTTATTATTAAAATATTATTA
Found at i:2218124 original size:17 final size:18
Alignment explanation
Indices: 2218104--2218143 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2218094 ATTTTTAAAA
*
2218104 TATTATTATAAT-TTATT
1 TATTATTAAAATATTATT
2218121 TATTATTAAAATATTATT
1 TATTATTAAAATATTATT
2218139 T-TTAT
1 TATTAT
2218144 AATTTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATTAAAATATTATT
Found at i:2218453 original size:23 final size:23
Alignment explanation
Indices: 2218423--2218490 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 23
2218413 TTAAAATAAA
2218423 AATATAATATATTATATTATTAT
1 AATATAATATATTATATTATTAT
*
2218446 AATATAAT-TGATTATTTTATTAT
1 AATATAATAT-ATTATATTATTAT
*
2218469 AATATTAAAAATATTATATTAT
1 AATA-T-AATATATTATATTAT
2218491 ATTATTAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.03
23 24 0.63
24 1 0.03
25 11 0.29
26 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:2218488 original size:22 final size:22
Alignment explanation
Indices: 2218458--2218506 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2218448 TATAATTGAT
*
2218458 TATTTTATTATAATATTAAAAA
1 TATTATATTATAATATTAAAAA
* *
2218480 TATTATATTATATTATTAGAAA
1 TATTATATTATAATATTAAAAA
2218502 TATTA
1 TATTA
2218507 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTATATTATAATATTAAAAA
Found at i:2218514 original size:22 final size:22
Alignment explanation
Indices: 2218471--2218525 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2218461 TTTATTATAA
*
2218471 TATTAAAAATATTATATTATAT
1 TATTAAAAATATTATATAATAT
*
2218493 TATTAGAAATATTA-ATAAATAT
1 TATTAAAAATATTATAT-AATAT
*
2218515 ATTTTAAAAAT
1 -TATTAAAAAT
2218526 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.07
22 17 0.63
23 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTAAAAATATTATATAATAT
Found at i:2224311 original size:12 final size:12
Alignment explanation
Indices: 2224294--2224318 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2224284 CTATTAGCTC
2224294 ATTTTCCACATA
1 ATTTTCCACATA
2224306 ATTTTCCACATA
1 ATTTTCCACATA
2224318 A
1 A
2224319 ACACATTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTTTCCACATA
Found at i:2237569 original size:2 final size:2
Alignment explanation
Indices: 2237562--2237587 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2237552 TGAAAAACAT
2237562 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
2237588 AACTTCTTAA
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):
TA
Found at i:2240607 original size:106 final size:105
Alignment explanation
Indices: 2240422--2240632 Score: 377
Period size: 106 Copynumber: 2.0 Consensus size: 105
2240412 CGAGTCTCAC
*
2240422 GGTGAGCAATTCATAATTCTGACTGTTGGAGGTCTCCCACGGAAGCTGCTCTCAACCTGGCATTT
1 GGTGAGCAATTCATAATTATGACTGTTGGAGGTCTCCCACGGAAGCTGCTCTCAACCTGGCATTT
*
2240487 GGGGCAGCCTACTATCCTACCTTCCCCTTATCCCATTACAT
66 GGGGCAGCCTACTATCCTACC-TCCCCTTACCCCATTACAT
* *
2240528 GGTGAGCAATTCATAATTATGACTGTTGGAGGTCTCCCACGGAAGTTGCTCTCAACCTGGCGTTT
1 GGTGAGCAATTCATAATTATGACTGTTGGAGGTCTCCCACGGAAGCTGCTCTCAACCTGGCATTT
2240593 GGGGCAGCCTACTATCCTACCTCCCCTTACCCCATTACAT
66 GGGGCAGCCTACTATCCTACCTCCCCTTACCCCATTACAT
2240633 ATGAGAATAG
Statistics
Matches: 101, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 18 0.18
106 83 0.82
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.29
Consensus pattern (105 bp):
GGTGAGCAATTCATAATTATGACTGTTGGAGGTCTCCCACGGAAGCTGCTCTCAACCTGGCATTT
GGGGCAGCCTACTATCCTACCTCCCCTTACCCCATTACAT
Found at i:2246882 original size:20 final size:19
Alignment explanation
Indices: 2246857--2246912 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
2246847 AATTTTCTAT
2246857 TATTTTTATTATAAATATAA
1 TATTTTTATTATAAAT-TAA
*
2246877 TATTTTTA--ATAAATTAT
1 TATTTTTATTATAAATTAA
*
2246894 TAATTTTATT-TAAATTAA
1 TATTTTTATTATAAATTAA
2246912 T
1 T
2246913 TTATTATTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 9 0.29
18 14 0.45
20 8 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTTATTATAAATTAA
Found at i:2247026 original size:23 final size:22
Alignment explanation
Indices: 2247000--2247043 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2246990 TTAGGTTTTT
*
2247000 TTTCTATTCGGGGTTAATTTTGA
1 TTTCGATTC-GGGTTAATTTTGA
* *
2247023 TTTCGGTTCGGGTTAGTTTTG
1 TTTCGATTCGGGTTAATTTTG
2247044 GTTTTGCTAA
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:0.11, C:0.09, G:0.27, T:0.52
Consensus pattern (22 bp):
TTTCGATTCGGGTTAATTTTGA
Found at i:2249728 original size:2 final size:2
Alignment explanation
Indices: 2249723--2249749 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2249713 TAAAGAGAGA
2249723 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 A
2249750 AATAGAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2274144 original size:7 final size:7
Alignment explanation
Indices: 2274105--2274146 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
2274095 TAATTATTCA
2274105 ATTAAAT
1 ATTAAAT
*
2274112 ATT-ATT
1 ATTAAAT
*
2274118 ATTAATT
1 ATTAAAT
*
2274125 ATTGAAT
1 ATTAAAT
2274132 ATTAAAT
1 ATTAAAT
2274139 ATTAAAT
1 ATTAAAT
2274146 A
1 A
2274147 AGATAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
ATTAAAT
Found at i:2274560 original size:6 final size:6
Alignment explanation
Indices: 2274549--2274574 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2274539 TTAGACGTTT
2274549 ATTTTA ATTTTA ATTTTA ATTTTA AT
1 ATTTTA ATTTTA ATTTTA ATTTTA AT
2274575 GGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:2275383 original size:20 final size:21
Alignment explanation
Indices: 2275360--2275404 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2275350 CATTATATGT
**
2275360 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
2275380 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
2275401 ATAT
1 ATAT
2275405 CACTAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:2276838 original size:3 final size:3
Alignment explanation
Indices: 2276830--2276926 Score: 142
Period size: 3 Copynumber: 32.7 Consensus size: 3
2276820 TTAATATATT
* * *
2276830 TAA TAA TAA TAG TAA AAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2276878 TAA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2276925 TA
1 TA
2276927 TGGATAAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2277440 original size:113 final size:114
Alignment explanation
Indices: 2277217--2277480 Score: 451
Period size: 113 Copynumber: 2.3 Consensus size: 114
2277207 AGATAATATC
* * * *
2277217 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTT
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
2277281 TCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTCATGAACCTTCTCTGGCAATGTTGATCCACCAAATGATGAATTT
2277330 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
2277395 TCATT-ATGAACCTTCTCTGGTAATGTTGATCCACCAAATGATGAATTT
66 TCATTCATGAACCTTCTCTGGCAATGTTGATCCACCAAATGATGAATTT
2277443 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCT
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCT
2277481 TCTCTGGTAA
Statistics
Matches: 143, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
113 82 0.57
114 61 0.43
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (114 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTCATGAACCTTCTCTGGCAATGTTGATCCACCAAATGATGAATTT
Found at i:2277474 original size:73 final size:73
Alignment explanation
Indices: 2277387--2277553 Score: 325
Period size: 73 Copynumber: 2.3 Consensus size: 73
2277377 TCTTCAGATG
2277387 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCACCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCACCAAATGATGAATTTAAACAAAAA
2277452 GTTGAACA
66 GTTGAACA
*
2277460 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCACCAAATGATGAATTTAAACAAAAA
2277525 GTTGAACA
66 GTTGAACA
2277533 AGTTCTTCTCATTATGAACCT
1 AGTTCTTCTCATTATGAACCT
2277554 CTTCTTCCTT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 93 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCACCAAATGATGAATTTAAACAAAAA
GTTGAACA
Found at i:2277577 original size:113 final size:113
Alignment explanation
Indices: 2277460--2277892 Score: 857
Period size: 113 Copynumber: 3.8 Consensus size: 113
2277450 AAGTTGAACA
2277460 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2277525 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
2277573 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2277638 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
2277686 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2277751 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
*
2277799 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTAATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2277864 GTTGAACAAGTTCTTCTCATTATGAACCT
66 GTTGAACAAGTTCTTCTCATTATGAACCT
2277893 TCTCTGGTAA
Statistics
Matches: 319, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 319 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
Found at i:2277608 original size:186 final size:186
Alignment explanation
Indices: 2277273--2278078 Score: 873
Period size: 186 Copynumber: 4.1 Consensus size: 186
2277263 TCTTCAGATG
* * *
2277273 AGTTCTTTTCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAA
1 AGTTCTTCTCATT-ATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAA
2277338 AGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
65 AGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
*
2277403 AACCTTCTCTGGTAATGTTGATCCACCAAATGATGAATTTAAACAAAAAGTTGAACA
130 AACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
2277460 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2277525 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
2277590 ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
131 ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
** ** * **
2277646 AGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAA-C-CTTC-T-C-TGGT-A-AT--GTTGATC-CATCA--AA---T-GA
** * ** *** ** ***
2277711 TGGTAATGTTGATCCATCAAA--TGATGAA-TT-TAAACAAAAAGTTGAACAAGTTCTTCTCATT
50 T-G-AAT-TT-AAACA-AAAAGTTGAACAAGTTCTTCTC-ATTA--TGAACCTCTTCTTC-C--T
* *** *** * * *
2277772 ATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTAAT
104 -T---CTTCAGATGAGTTCTTC---TCA----TTAT------GAACCTTCTCTGGTAATGTTGAT
2277837 CCATCAAATGATGAATTTAAACAAAAAGTTGAACA
152 CCATCAAATGATGAATTTAAACAAAAAGTTGAACA
2277872 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2277937 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
2278002 ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
131 ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
2278058 AGTTCTTCTCATTATGAACCT
1 AGTTCTTCTCATTATGAACCT
2278079 CTTCTTCCTT
Statistics
Matches: 507, Mismatches: 64, Indels: 97
0.76 0.10 0.15
Matches are distributed among these distances:
186 266 0.52
187 13 0.03
188 4 0.01
189 1 0.00
190 1 0.00
191 2 0.00
192 4 0.01
193 2 0.00
195 5 0.01
196 6 0.01
198 2 0.00
199 10 0.02
201 1 0.00
202 2 0.00
203 4 0.01
204 7 0.01
205 11 0.02
206 28 0.06
207 11 0.02
208 7 0.01
209 4 0.01
210 2 0.00
211 1 0.00
213 10 0.02
214 2 0.00
216 6 0.01
217 5 0.01
219 2 0.00
220 4 0.01
221 2 0.00
222 1 0.00
223 1 0.00
224 4 0.01
225 1 0.00
226 75 0.15
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (186 bp):
AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
Found at i:2277886 original size:73 final size:73
Alignment explanation
Indices: 2277799--2277965 Score: 325
Period size: 73 Copynumber: 2.3 Consensus size: 73
2277789 TCTTCAGATG
2277799 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTAATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTAATCCATCAAATGATGAATTTAAACAAAAA
2277864 GTTGAACA
66 GTTGAACA
*
2277872 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTAATCCATCAAATGATGAATTTAAACAAAAA
2277937 GTTGAACA
66 GTTGAACA
2277945 AGTTCTTCTCATTATGAACCT
1 AGTTCTTCTCATTATGAACCT
2277966 CTTCTTCCTT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 93 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTAATCCATCAAATGATGAATTTAAACAAAAA
GTTGAACA
Found at i:2277981 original size:412 final size:412
Alignment explanation
Indices: 2277217--2278260 Score: 1939
Period size: 412 Copynumber: 2.5 Consensus size: 412
2277207 AGATAATATC
* * * *
2277217 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTT
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
2277281 TCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAAC
66 TCATT-ATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAAC
2277346 AAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT
130 AAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT
* *
2277411 CTGGTAATGTTGATCCACCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
195 CTGGTAATGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
2277476 AACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTC
260 AACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTC
2277541 TCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATG
325 TCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATG
2277606 TTGATCCATCAAATGATGAATTT
390 TTGATCCATCAAATGATGAATTT
2277629 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
2277694 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
66 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
2277759 AGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
131 AGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
2277824 TGGTAATGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGA
196 TGGTAATGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGA
2277889 ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCT
261 ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCT
2277954 CATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGT
326 CATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGT
2278019 TGATCCATCAAATGATGAATTT
391 TGATCCATCAAATGATGAATTT
2278041 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
2278106 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
66 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
*
2278171 AGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-
131 AGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-CTTCT
* * **
2278235 CTTGCAATGTTAATCTTTCAAATGAT
195 CTGGTAATGTTAATCCATCAAATGAT
2278261 AGATTTGAAT
Statistics
Matches: 617, Mismatches: 13, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
412 553 0.90
413 64 0.10
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (412 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
AGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
TGGTAATGTTAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGA
ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCT
CATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGT
TGATCCATCAAATGATGAATTT
Found at i:2278111 original size:299 final size:299
Alignment explanation
Indices: 2277273--2278191 Score: 1338
Period size: 299 Copynumber: 3.1 Consensus size: 299
2277263 TCTTCAGATG
* * *
2277273 AGTTCTTTTCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAA
1 AGTTCTTCTCATT-ATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAA
2277338 AGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
65 AGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
*
2277403 AACCTTCTCTGGTAATGTTGATCCACCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTC
130 AACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTC
** * * * * ** * *****
2277468 TCATTATGAA-C-CTTC-T-C-TGGTAATGTTGA-TCCATCAAATGATGAA--TT-TAAACAAAA
195 TCATTATGAACCTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCATTATGAACCTTCT-CTGGTAA
* * * ** * *** **** * **
2277524 AGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTC--CTTCTTCAGATG
258 TGTT----AA-TCCATCAAATGATGAA--T-TTAAACAAAAAGTTGA-ACA
2277573 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2277638 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
2277703 ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCT
131 ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCT
2277768 CATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGT
196 CATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGT
2277833 TAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
261 TAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
2277872 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2277937 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
2278002 ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCT
131 ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCT
2278067 CATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGT
196 CATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGT
*
2278132 TGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
261 TAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
2278171 AGTTCTTCTCATTATGAACCT
1 AGTTCTTCTCATTATGAACCT
2278192 CTTCTTCCTT
Statistics
Matches: 573, Mismatches: 35, Indels: 23
0.91 0.06 0.04
Matches are distributed among these distances:
298 3 0.01
299 509 0.89
300 16 0.03
301 15 0.03
302 3 0.01
303 5 0.01
304 14 0.02
306 7 0.01
307 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (299 bp):
AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCT
CATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGT
TAATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
Found at i:2278260 original size:113 final size:113
Alignment explanation
Indices: 2277872--2278229 Score: 716
Period size: 113 Copynumber: 3.2 Consensus size: 113
2277862 AAGTTGAACA
2277872 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2277937 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
2277985 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2278050 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
2278098 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
2278163 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
2278211 AGTTCTTCTCATTATGAAC
1 AGTTCTTCTCATTATGAAC
2278230 TCTACCTTGC
Statistics
Matches: 245, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 245 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAA
GTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATG
Found at i:2279021 original size:84 final size:84
Alignment explanation
Indices: 2278842--2279153 Score: 590
Period size: 84 Copynumber: 3.7 Consensus size: 84
2278832 GGTTCTGTAA
* *
2278842 GTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTG-GCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCAT
*
2278906 ATTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
2278925 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCAT
2278990 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
2279009 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCAT
2279074 CTTCTAAATTCAATGATTG
66 CTTCTAAATTCAATGATTG
2279093 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACAT
2279154 ATAAAAGGTT
Statistics
Matches: 225, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
83 52 0.23
84 173 0.77
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (84 bp):
GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCAT
CTTCTAAATTCAATGATTG
Found at i:2280108 original size:17 final size:16
Alignment explanation
Indices: 2280083--2280128 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
2280073 CCTTGACCCC
*
2280083 CTTTCTTTTTCTTCTCT
1 CTTTTTTTTTCTT-TCT
2280100 CTTTTTTTTTCTTTCT
1 CTTTTTTTTTCTTTCT
*
2280116 -TTTTTTTTCCTTT
1 CTTTTTTTTTCTTT
2280129 TTTTTTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 12 0.44
16 3 0.11
17 12 0.44
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTTTTTTTTCTTTCT
Found at i:2280111 original size:14 final size:14
Alignment explanation
Indices: 2280088--2280134 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
2280078 ACCCCCTTTC
*
2280088 TTTTTCTTCTCTCT
1 TTTTTTTTCTCTCT
*
2280102 TTTTTTTTCTTTCT
1 TTTTTTTTCTCTCT
2280116 TTTTTTTTC-CT-T
1 TTTTTTTTCTCTCT
2280128 TTTTTTT
1 TTTTTTT
2280135 CTTCAAGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 21 0.70
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTTCTCTCT
Found at i:2280113 original size:27 final size:25
Alignment explanation
Indices: 2280083--2280137 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 25
2280073 CCTTGACCCC
2280083 CTTTCTTTTTCTTCTCTCTTTTTTTTT
1 CTTTCTTTTT-TTCTC-CTTTTTTTTT
*
2280110 CTTTCTTTTTTTTTCCTTTTTTTTT
1 CTTTCTTTTTTTCTCCTTTTTTTTT
2280135 CTT
1 CTT
2280138 CAAGCATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 13 0.48
26 4 0.15
27 10 0.37
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (25 bp):
CTTTCTTTTTTTCTCCTTTTTTTTT
Done.