Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.1, 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: 5666189
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 144833 characters in sequence are not A, C, G, or T
File 5 of 14
Found at i:1590549 original size:26 final size:24
Alignment explanation
Indices: 1590520--1590567 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
1590510 TACAAAGATT
1590520 TTATTTATATATAATTGATATATTAA
1 TTATTTATAT-TAATT-ATATATTAA
* *
1590546 TTATTTTTATTTATTATATATT
1 TTATTTATATTAATTATATATT
1590568 GTCTTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 4 0.20
26 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATTTATATTAATTATATATTAA
Found at i:1599204 original size:26 final size:26
Alignment explanation
Indices: 1599175--1599225 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1599165 ATAAAATTAA
*
1599175 ATTATGATA-AGATTATAATATTATTG
1 ATTATGATACAG-TTACAATATTATTG
1599201 ATTATGATACAGTTACAATATTATT
1 ATTATGATACAGTTACAATATTATT
1599226 AGCTTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (26 bp):
ATTATGATACAGTTACAATATTATTG
Found at i:1612439 original size:16 final size:17
Alignment explanation
Indices: 1612420--1612454 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1612410 TAATAATTTT
1612420 TAAAATTA-ATAAAAAA
1 TAAAATTATATAAAAAA
*
1612436 TAAAATTATATTAAAAA
1 TAAAATTATATAAAAAA
1612453 TA
1 TA
1612455 TTATCACGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAATTATATAAAAAA
Found at i:1612599 original size:16 final size:18
Alignment explanation
Indices: 1612578--1612611 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1612568 GTGTAAAATT
1612578 AAAATTAA-A-ATTTTAA
1 AAAATTAAGATATTTTAA
1612594 AAAATTAAGATATTTTAA
1 AAAATTAAGATATTTTAA
1612612 TTTTTTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAATTAAGATATTTTAA
Found at i:1614149 original size:2 final size:2
Alignment explanation
Indices: 1614142--1614169 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1614132 AAACTTGAAT
1614142 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
1614170 AAAGCCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1622164 original size:2 final size:2
Alignment explanation
Indices: 1622157--1622188 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1622147 TATGGGATGA
1622157 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
1622189 TTAAAAACTT
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:1625629 original size:24 final size:24
Alignment explanation
Indices: 1625602--1625649 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1625592 TTCCAACCAA
*
1625602 CTCTAAAACTAA-AAATTTTGATTC
1 CTCTAAAAC-AACAAATGTTGATTC
1625626 CTCTAAAACAACAAATGTTGATTC
1 CTCTAAAACAACAAATGTTGATTC
1625650 TATTGTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (24 bp):
CTCTAAAACAACAAATGTTGATTC
Found at i:1628986 original size:24 final size:24
Alignment explanation
Indices: 1628953--1629003 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1628943 AAGGTGTGGG
*
1628953 AGTCATGGTGAAACCATTAACGGT
1 AGTCACGGTGAAACCATTAACGGT
* *
1628977 AGTCACGGTGAAACTATTGACGGT
1 AGTCACGGTGAAACCATTAACGGT
1629001 AGT
1 AGT
1629004 GGAGGTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (24 bp):
AGTCACGGTGAAACCATTAACGGT
Found at i:1629482 original size:30 final size:30
Alignment explanation
Indices: 1629448--1629504 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1629438 TTTATACGTA
1629448 AAGAATGAA-GTGAACATTGCACCAAATTAG
1 AAGAAT-AAGGTGAACATTGCACCAAATTAG
1629478 AAGAATAAGGTGAACATTGCACCAAAT
1 AAGAATAAGGTGAACATTGCACCAAAT
1629505 CAAGAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.19
Consensus pattern (30 bp):
AAGAATAAGGTGAACATTGCACCAAATTAG
Found at i:1633232 original size:19 final size:20
Alignment explanation
Indices: 1633208--1633256 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1633198 AAGGAAATTT
1633208 AAAAAGAAAAGGAAAGAAA-
1 AAAAAGAAAAGGAAAGAAAC
* * *
1633227 AAAAAGATAATGAACGAAACC
1 AAAAAGAAAAGGAAAGAAA-C
1633248 AAAAAGAAA
1 AAAAAGAAA
1633257 TTGAAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.67
21 8 0.33
ACGTcount: A:0.73, C:0.06, G:0.16, T:0.04
Consensus pattern (20 bp):
AAAAAGAAAAGGAAAGAAAC
Found at i:1634618 original size:13 final size:14
Alignment explanation
Indices: 1634588--1634620 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1634578 AAAAATAAAT
*
1634588 ATAAATATAAATAA
1 ATAAATATAAACAA
1634602 ATAAATA-AAACAA
1 ATAAATATAAACAA
1634615 ATAAAT
1 ATAAAT
1634621 GAGTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
ATAAATATAAACAA
Found at i:1643862 original size:2 final size:2
Alignment explanation
Indices: 1643855--1643881 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1643845 TAAATAAAGG
1643855 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
1643882 CACTCTTATT
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:1644589 original size:19 final size:19
Alignment explanation
Indices: 1644567--1644608 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1644557 TTAAATATAA
*
1644567 TTTTAAATT-TTAATTTAT
1 TTTTTAATTATTAATTTAT
*
1644585 TTTTTATTTATTAATTTAT
1 TTTTTAATTATTAATTTAT
1644604 TTTTT
1 TTTTT
1644609 GTTAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTAATTATTAATTTAT
Found at i:1648022 original size:31 final size:31
Alignment explanation
Indices: 1647964--1648132 Score: 109
Period size: 31 Copynumber: 5.5 Consensus size: 31
1647954 AGTAGAAGCA
* **
1647964 AATATCCAATCCAAAGT-CCAAGGTTGAAACT
1 AATATCAAATCCAAA-TACCAAAATTGAAACT
* *
1647995 AATACCAAATCCAAATGCCAAAATTGAAAC-
1 AATATCAAATCCAAATACCAAAATTGAAACT
* * *
1648025 AACT-TACAAATTCAAACACCAAGATTGAAA-T
1 AA-TAT-CAAATCCAAATACCAAAATTGAAACT
* * * *
1648056 AAAAATCAAATCCAAATATCAAAGTTGAAACA
1 -AATATCAAATCCAAATACCAAAATTGAAACT
* *
1648088 AATATCAAATCCAAAT-CTAAAGA-CGAAAC-
1 AATATCAAATCCAAATACCAAA-ATTGAAACT
1648117 AATTATCAAATCCAAA
1 AA-TATCAAATCCAAA
1648133 AACTAATATC
Statistics
Matches: 108, Mismatches: 21, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
29 2 0.02
30 24 0.22
31 79 0.73
32 3 0.03
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (31 bp):
AATATCAAATCCAAATACCAAAATTGAAACT
Found at i:1648097 original size:62 final size:62
Alignment explanation
Indices: 1647934--1648102 Score: 171
Period size: 62 Copynumber: 2.7 Consensus size: 62
1647924 TAAATCAAAT
* * * * * ** *
1647934 AAACCAAGTCCAAACACCAAAGTAGAAGCAAATATCCAATCCAAAGTCCAAGGTTGAAACTA
1 AAACCAAATCCAAATACCAAAGTTGAAACAAATATCAAATCCAAACACCAAGATTGAAACTA
* * * * *
1647996 ATACCAAATCCAAATGCCAAAATTGAAACAACT-TACAAATTCAAACACCAAGATTGAAA-TAA
1 AAACCAAATCCAAATACCAAAGTTGAAACAAATAT-CAAATCCAAACACCAAGATTGAAACT-A
* *
1648058 AAATCAAATCCAAATATCAAAGTTGAAACAAATATCAAATCCAAA
1 AAACCAAATCCAAATACCAAAGTTGAAACAAATATCAAATCCAAA
1648103 TCTAAAGACG
Statistics
Matches: 84, Mismatches: 20, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
61 2 0.02
62 81 0.96
63 1 0.01
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.18
Consensus pattern (62 bp):
AAACCAAATCCAAATACCAAAGTTGAAACAAATATCAAATCCAAACACCAAGATTGAAACTA
Found at i:1648118 original size:30 final size:31
Alignment explanation
Indices: 1648051--1648132 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 31
1648041 CACCAAGATT
* * **
1648051 GAAATAAAAATCAAATCCAAATATCAAAGTT
1 GAAACAAATATCAAATCCAAATATCAAAGAC
*
1648082 GAAACAAATATCAAATCCAAATCT-AAAGAC
1 GAAACAAATATCAAATCCAAATATCAAAGAC
*
1648112 GAAACAATTATCAAATCCAAA
1 GAAACAAATATCAAATCCAAA
1648133 AACTAATATC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 24 0.53
31 21 0.47
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.20
Consensus pattern (31 bp):
GAAACAAATATCAAATCCAAATATCAAAGAC
Found at i:1658039 original size:16 final size:16
Alignment explanation
Indices: 1658015--1658054 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1658005 AATGGGTAAG
* *
1658015 GAAATAAGATAAAGAA
1 GAAAGAAGAAAAAGAA
*
1658031 GAAAGAAGAAAAATAA
1 GAAAGAAGAAAAAGAA
1658047 GAAAGAAG
1 GAAAGAAG
1658055 CCCGCTTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (16 bp):
GAAAGAAGAAAAAGAA
Found at i:1663413 original size:31 final size:29
Alignment explanation
Indices: 1663355--1663413 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
1663345 TTCAATGAAA
*
1663355 TTTATTTTTTAAAAACAAAATTAGAAAAG
1 TTTATTTTTTAAAAACAAAAATAGAAAAG
* *
1663384 TTTATTTCTTTTAAAATAAAAATATGAAAA
1 TTTATTT-TTTAAAAACAAAAATA-GAAAA
1663414 TTTCATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (29 bp):
TTTATTTTTTAAAAACAAAAATAGAAAAG
Found at i:1666896 original size:2 final size:2
Alignment explanation
Indices: 1666889--1666925 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1666879 ACAAATAGCA
1666889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1666926 CCTTTGATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1670999 original size:22 final size:21
Alignment explanation
Indices: 1670971--1671020 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1670961 ATTTTATATT
* *
1670971 TTATTATATTTAATTAAATAAA
1 TTATTATA-ATAAATAAATAAA
*
1670993 TTTTTATAATAAATAAATAAA
1 TTATTATAATAAATAAATAAA
1671014 TTATTAT
1 TTATTAT
1671021 TATTAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATTATAATAAATAAATAAA
Found at i:1671235 original size:25 final size:27
Alignment explanation
Indices: 1671205--1671255 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
1671195 GTTAGTTATA
1671205 AAAATTTATTT-TTAAA-A-AATAAAAT
1 AAAATTT-TTTATTAAATATAATAAAAT
1671230 AAAATTTTTTATTAAATATAATAAAA
1 AAAATTTTTTATTAAATATAATAAAA
1671256 GAATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.13
25 12 0.52
26 1 0.04
27 7 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAATTTTTTATTAAATATAATAAAAT
Found at i:1675623 original size:22 final size:23
Alignment explanation
Indices: 1675592--1675637 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1675582 TCTTCCTCCT
*
1675592 CCTCTTCCTCCACCAAACGACAC
1 CCTCTTCCTCCACCAAACAACAC
*
1675615 CCTC-TCCTCCACCCAACAACAC
1 CCTCTTCCTCCACCAAACAACAC
1675637 C
1 C
1675638 ACCTTCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.26, C:0.57, G:0.02, T:0.15
Consensus pattern (23 bp):
CCTCTTCCTCCACCAAACAACAC
Found at i:1678680 original size:27 final size:27
Alignment explanation
Indices: 1678641--1678693 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1678631 AGTGCAAAAG
*
1678641 GCAGAGGTAGTGGATATTAGGTCAGAA
1 GCAGAGGTAGTGGATATTAGATCAGAA
*
1678668 GCAGAGGTGGTGGATATTAGATCAGA
1 GCAGAGGTAGTGGATATTAGATCAGA
1678694 TGATGTTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.38, T:0.23
Consensus pattern (27 bp):
GCAGAGGTAGTGGATATTAGATCAGAA
Found at i:1683480 original size:34 final size:34
Alignment explanation
Indices: 1683437--1683507 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
1683427 TTTATTGGAT
1683437 AAAAGTTGTTG-AAAGTTATTGAAATATTAAATGC
1 AAAAGTTGTTGTAAA-TTATTGAAATATTAAATGC
* *
1683471 AAAAGTTGTTGTAAATTTTTTAAATATTAAATGC
1 AAAAGTTGTTGTAAATTATTGAAATATTAAATGC
1683505 AAA
1 AAA
1683508 TTTATTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 31 0.91
35 3 0.09
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.38
Consensus pattern (34 bp):
AAAAGTTGTTGTAAATTATTGAAATATTAAATGC
Found at i:1684070 original size:27 final size:27
Alignment explanation
Indices: 1684019--1684071 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1684009 CTCCTTACTT
* *
1684019 CACCATGAGCAGGGATAAATCTAGCAC
1 CACCATGAGCAAGGACAAATCTAGCAC
* *
1684046 CACCATGAGCAAGGACAGATTTAGCA
1 CACCATGAGCAAGGACAAATCTAGCA
1684072 ACACGACCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (27 bp):
CACCATGAGCAAGGACAAATCTAGCAC
Found at i:1690779 original size:3 final size:3
Alignment explanation
Indices: 1690771--1690812 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1690761 CCTCGATTGC
1690771 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1690813 TGTTAAACGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1698742 original size:15 final size:15
Alignment explanation
Indices: 1698722--1698776 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
1698712 TTTACAATAC
*
1698722 AATGTGATTG-TAGAT
1 AATGTGATTGCAAG-T
*
1698737 AATGTGATTACAAGT
1 AATGTGATTGCAAGT
1698752 AATGTGATTGCAAGT
1 AATGTGATTGCAAGT
1698767 AATGTGATTG
1 AATGTGATTG
1698777 TAGGGAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 34 0.94
16 2 0.06
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:1699029 original size:33 final size:34
Alignment explanation
Indices: 1698992--1699065 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 34
1698982 TTTTAATGTC
* *
1698992 ATATATTTTATTTTTATTTC-TTAGTATAATCTT
1 ATATATTTTATTTTCATTTCTTTAATATAATCTT
*
1699025 ATATATTTTATTTTCATTTCTTTAATATAATTTT
1 ATATATTTTATTTTCATTTCTTTAATATAATCTT
*
1699059 TTATATT
1 ATATATT
1699066 ATATATTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 19 0.53
34 17 0.47
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.65
Consensus pattern (34 bp):
ATATATTTTATTTTCATTTCTTTAATATAATCTT
Found at i:1699178 original size:33 final size:31
Alignment explanation
Indices: 1699102--1699180 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 31
1699092 TATTATATAA
*
1699102 ATTTTAATTATTTTATTTTATTTTATTTTTTG
1 ATTTTAATTA-TATATTTTATTTTATTTTTTG
1699134 ATTTTTAAATTATATATTTTATTTTAATAATTTTT-
1 A-TTTT-AATTATATATTTTATTTT-AT--TTTTTG
1699169 ATTTTAATTATA
1 ATTTTAATTATA
1699181 ACTTTATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
32 1 0.02
33 23 0.56
34 11 0.27
35 1 0.02
36 5 0.12
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (31 bp):
ATTTTAATTATATATTTTATTTTATTTTTTG
Found at i:1703596 original size:14 final size:14
Alignment explanation
Indices: 1703577--1703616 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1703567 TAAGGGGAGC
1703577 TCTTGTATTTTTTT
1 TCTTGTATTTTTTT
1703591 TCTTG---TTTTTT
1 TCTTGTATTTTTTT
*
1703602 TCTTTTATTTTTTT
1 TCTTGTATTTTTTT
1703616 T
1 T
1703617 GTAATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
11 10 0.45
14 12 0.55
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.82
Consensus pattern (14 bp):
TCTTGTATTTTTTT
Found at i:1706464 original size:27 final size:27
Alignment explanation
Indices: 1706421--1706475 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1706411 ATCGAGGGAA
*
1706421 TTCCTTTGCTACCGCTCAGCTGGATCG
1 TTCCTTTGCTACCGCTCAGATGGATCG
* *
1706448 TTCCTTTGTTACTGCTCAGATGGATCG
1 TTCCTTTGCTACCGCTCAGATGGATCG
1706475 T
1 T
1706476 ATCTGGGCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (27 bp):
TTCCTTTGCTACCGCTCAGATGGATCG
Found at i:1714330 original size:5 final size:5
Alignment explanation
Indices: 1714320--1714356 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
1714310 TAAAATCATA
*
1714320 TATAT TATAT TATAT GATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
1714357 CAAGGTACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:1716379 original size:22 final size:23
Alignment explanation
Indices: 1716322--1716379 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
1716312 ATACGTTATC
* *
1716322 ATTAAAAT-AGAATTAATATAGT
1 ATTAAAATAATAATTAATACAGT
*
1716344 ATTAAAATATTAATTAAT-CAGT
1 ATTAAAATAATAATTAATACAGT
1716366 ATTAAAATAATAAT
1 ATTAAAATAATAAT
1716380 ATTTTAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (23 bp):
ATTAAAATAATAATTAATACAGT
Found at i:1716457 original size:2 final size:2
Alignment explanation
Indices: 1716452--1716490 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1716442 TTCTCTTTTA
1716452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1716491 AAATTTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1717821 original size:15 final size:14
Alignment explanation
Indices: 1717796--1717825 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1717786 TTTACAATTG
1717796 AATA-AAATTTTTA
1 AATATAAATTTTTA
1717809 AATATAAATTTTTA
1 AATATAAATTTTTA
1717823 AAT
1 AAT
1717826 TCGTGAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATAAATTTTTA
Found at i:1722023 original size:18 final size:18
Alignment explanation
Indices: 1721996--1722033 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1721986 CTAATTACTC
* *
1721996 ATTAGTATTAACTAAAAT
1 ATTAGAATTAAATAAAAT
1722014 ATTAGAATTAAATAAAAT
1 ATTAGAATTAAATAAAAT
1722032 AT
1 AT
1722034 GATCTTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (18 bp):
ATTAGAATTAAATAAAAT
Found at i:1723940 original size:19 final size:19
Alignment explanation
Indices: 1723916--1723953 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1723906 ACTCTCAACC
1723916 TTTTAACGAAAATAAATAA
1 TTTTAACGAAAATAAATAA
1723935 TTTTAACGAAAATAAATAA
1 TTTTAACGAAAATAAATAA
1723954 GGTAAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (19 bp):
TTTTAACGAAAATAAATAA
Found at i:1725854 original size:2 final size:2
Alignment explanation
Indices: 1725847--1725873 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1725837 AAGAATAAAA
1725847 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1725874 AAGGGATCTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1730087 original size:12 final size:12
Alignment explanation
Indices: 1730070--1730096 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1730060 TCTAAACTCC
1730070 ATAAACGGGTTT
1 ATAAACGGGTTT
1730082 ATAAACGGGTTT
1 ATAAACGGGTTT
1730094 ATA
1 ATA
1730097 TAATTGACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (12 bp):
ATAAACGGGTTT
Found at i:1744949 original size:20 final size:21
Alignment explanation
Indices: 1744910--1744950 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1744900 TTTAAATTAA
* *
1744910 TTAATTTAATTTTTTTAAAAT
1 TTAATTTAATTTATTAAAAAT
1744931 TTAA-TTAATTTATTAAAAAT
1 TTAATTTAATTTATTAAAAAT
1744951 AAATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAATTTAATTTATTAAAAAT
Found at i:1744968 original size:26 final size:25
Alignment explanation
Indices: 1744925--1744991 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
1744915 TTAATTTTTT
1744925 TAAA-ATTTAATTAA-TTTATTAAAAA
1 TAAATATTTAA-TAATTTTA-TAAAAA
* **
1744950 TAAATATTTAATAATTTTATATATT
1 TAAATATTTAATAATTTTATAAAAA
1744975 TAAATATTTAAATAATT
1 TAAATATTT-AATAATT
1744992 AATATTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 19 0.53
26 17 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAATATTTAATAATTTTATAAAAA
Found at i:1752246 original size:30 final size:29
Alignment explanation
Indices: 1752212--1752271 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 29
1752202 CTCAGTTCAG
*
1752212 TATTTTGAACTGAAAGGTTGTCAATGAAGA
1 TATTTTGAACTAAAAGGTTGTC-ATGAAGA
1752242 TATTTTGAACTAAAAGGTTGTCATGAAGA
1 TATTTTGAACTAAAAGGTTGTCATGAAGA
1752271 T
1 T
1752272 TTGAAGACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.35
Consensus pattern (29 bp):
TATTTTGAACTAAAAGGTTGTCATGAAGA
Found at i:1754685 original size:3 final size:3
Alignment explanation
Indices: 1754670--1754699 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1754660 ACTGATATAG
*
1754670 TAC TAC CAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1754700 ATCCAATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
TAC
Found at i:1760637 original size:14 final size:15
Alignment explanation
Indices: 1760613--1760641 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1760603 GTAATATTCC
1760613 TAAATAATTAAAAAT
1 TAAATAATTAAAAAT
1760628 TAAA-AATTAAAAAT
1 TAAATAATTAAAAAT
1760642 ATACTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAATAATTAAAAAT
Found at i:1782852 original size:91 final size:91
Alignment explanation
Indices: 1782677--1782855 Score: 227
Period size: 91 Copynumber: 2.0 Consensus size: 91
1782667 TAATTTTTAA
* * * *
1782677 CCTTTTAATCTTTTAGAGTATGAAACTCGATGCAAAAGGATTAAAGTGTCTATATTTCAAGATTC
1 CCTTTTAACCTTTCAGAGTATGAAACTCGATGCAAAAGGATGAAAGTGTCTATATCTCAAGATTC
* * * *
1782742 AACAGATTCTTTTTGATTAGTTTGTG
66 AACAGAGTCTATCTAATTAGTTTGTG
* * *
1782768 CCTTTTAACCTTTCGGAGTATTAAACTCGGTGCAAAAGGATGAAAGTGGT-TAT-TCCTCAAGAT
1 CCTTTTAACCTTTCAGAGTATGAAACTCGATGCAAAAGGATGAAAGT-GTCTATAT-CTCAAGAT
1782831 TCAACAGAGTCTATCTAATTAGTTT
64 TCAACAGAGTCTATCTAATTAGTTT
1782856 ACATAAACTA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
90 1 0.01
91 72 0.96
92 2 0.03
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (91 bp):
CCTTTTAACCTTTCAGAGTATGAAACTCGATGCAAAAGGATGAAAGTGTCTATATCTCAAGATTC
AACAGAGTCTATCTAATTAGTTTGTG
Found at i:1782952 original size:208 final size:207
Alignment explanation
Indices: 1782561--1782972 Score: 494
Period size: 208 Copynumber: 2.0 Consensus size: 207
1782551 ATATTTTTAA
*
1782561 CCTTTTAACCTTTCGAAGCATGAAACTCGATACCAAAAGATTAAAGTGATTATTCCCAAAATTCA
1 CCTTTTAACCTTTCGAAGCATGAAACTCGATACCAAAAGATGAAAGTGATTATTCCCAAAATTCA
* * * * * * *
1782626 ACAAACTCTTTTTGATTAGTTTGCATAAACTATCTTAAGGATAATTTTTAACCTTTTAATCTTTT
66 ACAAACTCTATCTAATTAGTTTACATAAACTATCTTAAGAATAATTTTTAACCTTTTAACCTTTG
** * *
1782691 AGAGTATGAAACTCGATGCAAAAGGATTAAAGTGTCTATATTTCAAGATTCAACAGA-TTCTTTT
131 AGAGTATGAAACTCGATGCAAAAGGATTAAAGTGTCTATACCTCAAAATTCAACAGACTT-TTTC
*
1782755 TGATTAGTTTGTG
195 TAATTAGTTTGTG
* * * * * * *
1782768 CCTTTTAACCTTTCGGAGTATTAAACTCGGT-GCAAAAGGATGAAAGTGGTTATTCCTCAAGATT
1 CCTTTTAACCTTTCGAAGCATGAAACTCGATACCAAAA-GATGAAAGTGATTATTCC-CAAAATT
* *
1782832 CAACAGAGTCTATCTAATTAGTTTACATAAACTATCTTAAGAATAATTTTTAACCTTTTAACCTT
64 CAACAAACTCTATCTAATTAGTTTACATAAACTATCTTAAGAATAATTTTTAACCTTTTAACCTT
* * *
1782897 TCGA-AGTATGAAACTTTG-TGTAAAAGGATTAAAGTGGT-TAT-CCCCTAAAATTCAACAGACT
129 T-GAGAGTATGAAAC-TCGATGCAAAAGGATTAAAGT-GTCTATACCTC-AAAATTCAACAGACT
1782958 TTTTCTAATTAGTTT
190 TTTTCTAATTAGTTT
1782973 ACACAAATTA
Statistics
Matches: 173, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
206 5 0.03
207 44 0.25
208 117 0.68
209 7 0.04
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (207 bp):
CCTTTTAACCTTTCGAAGCATGAAACTCGATACCAAAAGATGAAAGTGATTATTCCCAAAATTCA
ACAAACTCTATCTAATTAGTTTACATAAACTATCTTAAGAATAATTTTTAACCTTTTAACCTTTG
AGAGTATGAAACTCGATGCAAAAGGATTAAAGTGTCTATACCTCAAAATTCAACAGACTTTTTCT
AATTAGTTTGTG
Found at i:1787492 original size:2 final size:2
Alignment explanation
Indices: 1787485--1787577 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
1787475 GTTTATCATA
1787485 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1787527 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1787569 TC TC TC TC T
1 TC TC TC TC T
1787578 ATATATATAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1787614 original size:22 final size:22
Alignment explanation
Indices: 1787586--1787629 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1787576 CTATATATAT
1787586 ATATATATATATATACACACAC
1 ATATATATATATATACACACAC
*
1787608 ATATATATGTATATACACACAC
1 ATATATATATATATACACACAC
1787630 TTGACAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (22 bp):
ATATATATATATATACACACAC
Found at i:1810942 original size:5 final size:5
Alignment explanation
Indices: 1810925--1810986 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
1810915 TCTTCATCTT
* *
1810925 ATTTA ATTT- ATTTA ATTTTA ATTTA CACTTTA ATTCA ATTTT ATTT-
1 ATTTA ATTTA ATTTA A-TTTA ATTTA -A-TTTA ATTTA ATTTA ATTTA
1810971 ATTTA ACTTTA ATTTA
1 ATTTA A-TTTA ATTTA
1810987 TGCTTTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 8 0.17
5 24 0.50
6 12 0.25
7 4 0.08
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:1810974 original size:37 final size:37
Alignment explanation
Indices: 1810925--1811005 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
1810915 TCTTCATCTT
* *
1810925 ATTTAATTTATTTAATTTTAATTTACACTTTAATTCA
1 ATTTTATTTATTTAACTTTAATTTACACTTTAATTCA
**
1810962 ATTTTATTTATTTAACTTTAATTTATGCTTTAATTCA
1 ATTTTATTTATTTAACTTTAATTTACACTTTAATTCA
1810999 ATTTTAT
1 ATTTTAT
1811006 GAAATTAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.59
Consensus pattern (37 bp):
ATTTTATTTATTTAACTTTAATTTACACTTTAATTCA
Found at i:1821239 original size:18 final size:17
Alignment explanation
Indices: 1821199--1821241 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1821189 AATAAACTTT
*
1821199 TATTATTAATAATTAAT
1 TATTATTAATAATTAAA
*
1821216 TAATTATTATTAATTAAAA
1 T-ATTATTAATAATT-AAA
1821235 TATTATT
1 TATTATT
1821242 TATCATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTATTAATAATTAAA
Found at i:1821344 original size:20 final size:20
Alignment explanation
Indices: 1821311--1821349 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1821301 TTTCTATATT
* *
1821311 ATTATATCACGTCATTATAC
1 ATTATAACACGTCAATATAC
*
1821331 ATTATAACATGTCAATATA
1 ATTATAACACGTCAATATA
1821350 TCACCTCAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTATAACACGTCAATATAC
Found at i:1821495 original size:11 final size:11
Alignment explanation
Indices: 1821479--1821529 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
1821469 AAAAAAAATA
1821479 AAAATTTATTT
1 AAAATTTATTT
1821490 AAAATTT-TTT
1 AAAATTTATTT
*
1821500 -AAA-TAATTT
1 AAAATTTATTT
*
1821509 AAAATTTTTTT
1 AAAATTTATTT
1821520 AAAATATTAT
1 AAAAT-TTAT
1821530 ACTAAAGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
8 1 0.03
9 6 0.19
10 6 0.19
11 16 0.50
12 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AAAATTTATTT
Found at i:1824596 original size:2 final size:2
Alignment explanation
Indices: 1824589--1824626 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1824579 CAATAATGGG
1824589 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1824627 CATTCCATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1824935 original size:2 final size:2
Alignment explanation
Indices: 1824928--1824975 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1824918 TGATTAGACA
1824928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1824970 AT AT AT
1 AT AT AT
1824976 CCGGTAAGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1835393 original size:45 final size:45
Alignment explanation
Indices: 1835324--1835420 Score: 185
Period size: 45 Copynumber: 2.2 Consensus size: 45
1835314 GTGTCACTTT
*
1835324 TTAAGTTAATTTGTGGGAAGCCCTGCATTTTTGTTTTTCCTCTTA
1 TTAACTTAATTTGTGGGAAGCCCTGCATTTTTGTTTTTCCTCTTA
1835369 TTAACTTAATTTGTGGGAAGCCCTGCATTTTTGTTTTTCCTCTTA
1 TTAACTTAATTTGTGGGAAGCCCTGCATTTTTGTTTTTCCTCTTA
1835414 TTAACTT
1 TTAACTT
1835421 CATTAATTAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.49
Consensus pattern (45 bp):
TTAACTTAATTTGTGGGAAGCCCTGCATTTTTGTTTTTCCTCTTA
Found at i:1848898 original size:2 final size:2
Alignment explanation
Indices: 1848893--1848925 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1848883 CTTCCCCAAT
*
1848893 TA TA TA TA TA TA TA TA TA T- TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1848926 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1851216 original size:20 final size:21
Alignment explanation
Indices: 1851187--1851230 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1851177 ATTTGTATTA
* *
1851187 ATTTTCAAAATAA-ATATTTT
1 ATTTTAAAAAAAACATATTTT
1851207 ATTTTAAAAAAAACATATTTT
1 ATTTTAAAAAAAACATATTTT
1851228 ATT
1 ATT
1851231 ATACATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTTAAAAAAAACATATTTT
Found at i:1852116 original size:16 final size:17
Alignment explanation
Indices: 1852088--1852120 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1852078 AATATTAGTA
1852088 TTTAACTTTAAAATATT
1 TTTAACTTTAAAATATT
1852105 TTTAAC-TTAAAATATT
1 TTTAACTTTAAAATATT
1852121 AATATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAACTTTAAAATATT
Found at i:1853652 original size:22 final size:22
Alignment explanation
Indices: 1853612--1853653 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1853602 AAATAAATTC
* **
1853612 AAATATGTAAAAAGTATGTTAT
1 AAATATGAAAAAAAAATGTTAT
1853634 AAATATGAAAAAAAAATGTT
1 AAATATGAAAAAAAAATGTT
1853654 CATTTTCTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (22 bp):
AAATATGAAAAAAAAATGTTAT
Found at i:1878657 original size:14 final size:15
Alignment explanation
Indices: 1878634--1878671 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1878624 GTTAAGTTTG
*
1878634 GAAAAGGAAGGAAT-
1 GAAAAAGAAGGAATA
1878648 GAAAAAGAAGGAATA
1 GAAAAAGAAGGAATA
*
1878663 GAAGAAGAA
1 GAAAAAGAA
1878672 AGCCATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.32, T:0.05
Consensus pattern (15 bp):
GAAAAAGAAGGAATA
Found at i:1884284 original size:30 final size:30
Alignment explanation
Indices: 1884248--1884311 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
1884238 ATCCTCTTCA
1884248 TCATGATTTCTACAATCATTTTGAATCTCT
1 TCATGATTTCTACAATCATTTTGAATCTCT
**
1884278 TCATGATTTCTATGATCATTTTGAATCTCT
1 TCATGATTTCTACAATCATTTTGAATCTCT
1884308 TCAT
1 TCAT
1884312 TAACTTATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (30 bp):
TCATGATTTCTACAATCATTTTGAATCTCT
Found at i:1908563 original size:20 final size:20
Alignment explanation
Indices: 1908538--1908578 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1908528 AAGTCTATGT
1908538 ATGAACAATTAAAAAAGGCA
1 ATGAACAATTAAAAAAGGCA
1908558 ATGAACAATTAAAAAAGGCA
1 ATGAACAATTAAAAAAGGCA
1908578 A
1 A
1908579 ACTTTAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (20 bp):
ATGAACAATTAAAAAAGGCA
Found at i:1911915 original size:14 final size:14
Alignment explanation
Indices: 1911896--1912055 Score: 57
Period size: 14 Copynumber: 11.1 Consensus size: 14
1911886 TAATGTTATA
1911896 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
1911910 ATTAAAATAAAATATAT
1 ATTAAAAT-AAA-A-AT
*
1911927 AATATAAAATTCAAAA-
1 -AT-TAAAA-TAAAAAT
1911943 ATTAAAAT-AAAAT
1 ATTAAAATAAAAAT
1911956 A--AAATATAAAAA-
1 ATTAAA-ATAAAAAT
** *
1911968 ATTAAAATTTATAT
1 ATTAAAATAAAAAT
* * *
1911982 AATATAAGTAAAATAA
1 ATTA-AAATAAAA-AT
1911998 ATTAAAAT-AAAAT
1 ATTAAAATAAAAAT
*
1912011 ATATAATATAAAAA-
1 AT-TAAAATAAAAAT
* *
1912025 ATTATATTAAAGAA-
1 ATTAAAATAAA-AAT
*
1912039 ATAAAAATAAAATAT
1 ATTAAAATAAAA-AT
1912054 AT
1 AT
1912056 AAGATTATAA
Statistics
Matches: 107, Mismatches: 20, Indels: 37
0.65 0.12 0.23
Matches are distributed among these distances:
11 3 0.03
12 7 0.07
13 20 0.19
14 40 0.37
15 18 0.17
16 5 0.05
17 3 0.03
18 3 0.03
19 7 0.07
20 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.31
Consensus pattern (14 bp):
ATTAAAATAAAAAT
Found at i:1911920 original size:5 final size:5
Alignment explanation
Indices: 1911898--1912011 Score: 58
Period size: 5 Copynumber: 23.4 Consensus size: 5
1911888 ATGTTATAAT
* * * * ** *
1911898 TAAAA TAAAA -ATAT TAAAA TAAAA T-ATA TAATA TAAAA TTCAA -AAAT
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
* ** * *
1911945 TAAAA TAAAA TAAAA TATAAA -AAAT TAAAA T-TTA TATAA TATAAG TAAAA
1 TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA
*
1911995 TAAAT TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TA
1912012 TATAATATAA
Statistics
Matches: 80, Mismatches: 22, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
4 10 0.12
5 64 0.80
6 6 0.08
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (5 bp):
TAAAA
Found at i:1911947 original size:33 final size:33
Alignment explanation
Indices: 1911892--1912023 Score: 112
Period size: 33 Copynumber: 4.4 Consensus size: 33
1911882 TTTATAATGT
1911892 TATAAT-TAAAATAAAAATATTAAAATAAAATA
1 TATAATATAAAATAAAAATATTAAAATAAAATA
*
1911924 TATAATATAAAATTCAAAA-ATTAAAAT-AAA-A
1 TATAATATAAAA-TAAAAATATTAAAATAAAATA
*
1911955 TA-AA-AT---ATAAAAA-ATTAAAAT---TTA
1 TATAATATAAAATAAAAATATTAAAATAAAATA
* *
1911979 TATAATAT-AAGTAAAATAAATTAAAATAAAATA
1 TATAATATAAAATAAAA-ATATTAAAATAAAATA
1912012 TATAATATAAAA
1 TATAATATAAAA
1912024 AATTATATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
24 3 0.04
25 15 0.19
26 3 0.04
28 5 0.06
29 3 0.04
30 10 0.12
31 3 0.04
32 9 0.11
33 23 0.28
34 7 0.09
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (33 bp):
TATAATATAAAATAAAAATATTAAAATAAAATA
Found at i:1911957 original size:24 final size:25
Alignment explanation
Indices: 1911939--1912028 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 25
1911929 TATAAAATTC
1911939 AAAAATTAAAATAAAATAAAATATA
1 AAAAATTAAAATAAAATAAAATATA
*
1911964 AAAAATTAAAATTTATATAATATAAGTA-A
1 AAAAATTAAAA--TA-A-AATA-AAATATA
1911993 AATAAATTAAAATAAAATATATAATATA
1 AA-AAATTAAAATAAAATA-A-AATATA
1912021 AAAAATTA
1 AAAAATTA
1912029 TATTAAAGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
25 11 0.20
26 6 0.11
27 12 0.22
28 6 0.11
29 7 0.13
30 13 0.24
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (25 bp):
AAAAATTAAAATAAAATAAAATATA
Found at i:1912044 original size:50 final size:51
Alignment explanation
Indices: 1911898--1912052 Score: 133
Period size: 50 Copynumber: 3.0 Consensus size: 51
1911888 ATGTTATAAT
* *
1911898 TAAAATAAAA-ATATTAAAAT--AAAA-TATATAATATAAAATTCAAAAATTAAAA
1 TAAAATAAAATATA-AAAAATAAAAAATTATATAATA-GAAA-T-AAAAA-TAAAA
* * * * *
1911950 TAAAATAAAATATAAAAAATTAAAATTTATATAATATAAGT-AAAATAAAT
1 TAAAATAAAATATAAAAAATAAAAAATTATATAATAGAAATAAAAATAAAA
* *
1912000 TAAAATAAAATATATAATATAAAAAATTATATTAA-AGAAATAAAAATAAAA
1 TAAAATAAAATATAAAAAATAAAAAATTATA-TAATAGAAATAAAAATAAAA
1912051 TA
1 TA
1912053 TATAAGATTA
Statistics
Matches: 85, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
50 35 0.41
51 17 0.20
52 15 0.18
53 4 0.05
54 5 0.06
55 9 0.11
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (51 bp):
TAAAATAAAATATAAAAAATAAAAAATTATATAATAGAAATAAAAATAAAA
Found at i:1912063 original size:34 final size:33
Alignment explanation
Indices: 1912002--1912088 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
1911992 AAATAAATTA
* * *
1912002 AAATAAAATATATAATATAAAAAATTATATTAAAG
1 AAATAAAA-ATAAAATATATAAAATTATAAT-AAG
* *
1912037 AAATAAAAATAAAATATATAAGATTATAATAAT
1 AAATAAAAATAAAATATATAAAATTATAATAAG
1912070 AAATAAAAATAAAATATAT
1 AAATAAAAATAAAATATAT
1912089 GACATTCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 21 0.45
34 18 0.38
35 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAAAATTATAATAAG
Found at i:1912110 original size:33 final size:33
Alignment explanation
Indices: 1912037--1912101 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1912027 TATATTAAAG
* *
1912037 AAATAAAAATAAAATATATAAGATTATAATAAT
1 AAATAAAAATAAAATATATAACATTAAAATAAT
*
1912070 AAATAAAAATAAAATATATGACATTCAAAATA
1 AAATAAAAATAAAATATATAACATT-AAAATA
1912102 TATTTAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAACATTAAAATAAT
Found at i:1912344 original size:15 final size:15
Alignment explanation
Indices: 1912326--1912360 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1912316 GCTTGTAATT
*
1912326 ACATTACCTGCAATC
1 ACATTACCTACAATC
*
1912341 ACATTACCTATAATC
1 ACATTACCTACAATC
1912356 ACATT
1 ACATT
1912361 GCATTGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (15 bp):
ACATTACCTACAATC
Found at i:1914414 original size:15 final size:15
Alignment explanation
Indices: 1914381--1914414 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1914371 TAATTACTAT
* *
1914381 TATATATATTTTTAG
1 TATATATATTTTAAA
1914396 TATATATATTTTAAA
1 TATATATATTTTAAA
1914411 TATA
1 TATA
1914415 AACATATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TATATATATTTTAAA
Found at i:1915130 original size:16 final size:17
Alignment explanation
Indices: 1915111--1915146 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1915101 ATTTTAATAA
1915111 AATTTTTAAAT-AATTT
1 AATTTTTAAATAAATTT
1915127 AATTTTTAAATAAATTT
1 AATTTTTAAATAAATTT
1915144 AAT
1 AAT
1915147 AATTATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTTAAATAAATTT
Found at i:1921853 original size:8 final size:8
Alignment explanation
Indices: 1921840--1921865 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1921830 CAACTACCTG
1921840 AAGTAGTT
1 AAGTAGTT
1921848 AAGTAGTT
1 AAGTAGTT
1921856 AAGTAGTT
1 AAGTAGTT
1921864 AA
1 AA
1921866 CATTCTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (8 bp):
AAGTAGTT
Found at i:1924151 original size:66 final size:66
Alignment explanation
Indices: 1924023--1924152 Score: 188
Period size: 66 Copynumber: 2.0 Consensus size: 66
1924013 AAGTTATTGA
** *
1924023 TAAACTGTTACCTTAGTGATTACTACTGAAGTAGGTTTCAGTTATCAACGAATCGCTGTTCATTA
1 TAAACTGTTACCTTAGTGATTACTACCAAAGTAGGTTTCAGTTATCAACAAATCGCTGTTCATTA
1924088 G
66 G
* * * * *
1924089 TAAACTGTTATCTTAGTGATTACTACCAAAGTAGGTTTCAGTTATTACCAAATTGCTTTTCATT
1 TAAACTGTTACCTTAGTGATTACTACCAAAGTAGGTTTCAGTTATCAACAAATCGCTGTTCATT
1924153 TTCTTCTCTG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (66 bp):
TAAACTGTTACCTTAGTGATTACTACCAAAGTAGGTTTCAGTTATCAACAAATCGCTGTTCATTA
G
Found at i:1926619 original size:123 final size:124
Alignment explanation
Indices: 1926394--1926641 Score: 417
Period size: 123 Copynumber: 2.0 Consensus size: 124
1926384 AACTCTGTAA
* * *
1926394 TAGGTATCTGATCACGGAATAAATGAGCTATTTTAGATGCCTGCAAACTAAATTAGAAAAGATAT
1 TAGGAATCTGATCACGGAATAAATGAGCTATTTTACATGCCTGCAAACTAAATTAGAAAAGATAC
*
1926459 TTTAGAGGTTAAACTTCTTTGAAACACCATCATAGTGTTGATTAATTCTACATGGTCTT
66 TTTAGAGGTTAAACTTCTTTGAAACACAATCATAGTGTTGATTAATTCTACATGGTCTT
*
1926518 TAGGAATCTGATCACGGAATAAATGAGGTA-TTTACATGCCTGCAAACTAAATTAGAAAAGATAC
1 TAGGAATCTGATCACGGAATAAATGAGCTATTTTACATGCCTGCAAACTAAATTAGAAAAGATAC
* * *
1926582 TTTAGAGGTTTAACTTCTTTGAAACACAATCATAGTGTTTATTAATTCTATATGGTCTT
66 TTTAGAGGTTAAACTTCTTTGAAACACAATCATAGTGTTGATTAATTCTACATGGTCTT
1926641 T
1 T
1926642 GAAACACCAT
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
123 88 0.76
124 28 0.24
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (124 bp):
TAGGAATCTGATCACGGAATAAATGAGCTATTTTACATGCCTGCAAACTAAATTAGAAAAGATAC
TTTAGAGGTTAAACTTCTTTGAAACACAATCATAGTGTTGATTAATTCTACATGGTCTT
Found at i:1965319 original size:30 final size:30
Alignment explanation
Indices: 1965256--1965319 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1965246 TTCCTATCTG
* * *
1965256 AACATGAATGCACAGCATAGCCCCTACCCA
1 AACATGAATGCACAACAGAGCCCCTACCAA
* * *
1965286 AACATGAATGCTCAACAGAGCCCTTATCAA
1 AACATGAATGCACAACAGAGCCCCTACCAA
1965316 AACA
1 AACA
1965320 GGCACCCTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.31, G:0.12, T:0.16
Consensus pattern (30 bp):
AACATGAATGCACAACAGAGCCCCTACCAA
Found at i:1967363 original size:2 final size:2
Alignment explanation
Indices: 1967358--1967386 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1967348 GCACACACAC
1967358 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 A
1967387 ACTTGTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1969648 original size:2 final size:2
Alignment explanation
Indices: 1969641--1969674 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1969631 CGGTTGACCT
*
1969641 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1969675 CACACACATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1970951 original size:3 final size:3
Alignment explanation
Indices: 1970943--1970972 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1970933 AAAATAGTAA
*
1970943 AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1970973 GTACTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1972424 original size:18 final size:18
Alignment explanation
Indices: 1972401--1972436 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1972391 TTAGTAAGAT
* *
1972401 GTCAAATAATTATGTTTG
1 GTCAAAAAATTATATTTG
1972419 GTCAAAAAATTATATTTG
1 GTCAAAAAATTATATTTG
1972437 TTCAGAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.42
Consensus pattern (18 bp):
GTCAAAAAATTATATTTG
Found at i:1974920 original size:32 final size:32
Alignment explanation
Indices: 1974863--1974924 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1974853 AATACAATCA
* *
1974863 ATAATCCTGTCACACATTAGCTAGTGCTTAGT
1 ATAATCCTATCACACATCAGCTAGTGCTTAGT
* *
1974895 ATAATCCTATCACACATCGGTTAGTGCTTA
1 ATAATCCTATCACACATCAGCTAGTGCTTA
1974925 ATAAATTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (32 bp):
ATAATCCTATCACACATCAGCTAGTGCTTAGT
Found at i:1974972 original size:95 final size:95
Alignment explanation
Indices: 1974809--1974990 Score: 337
Period size: 95 Copynumber: 1.9 Consensus size: 95
1974799 AAAAATTCTG
*
1974809 TCACACATCGGTTAGTGTTTAATAAATTGATTTAGTTAGTGCAAAATACAATCAATAATCCTGTC
1 TCACACATCGGTTAGTGCTTAATAAATTGATTTAGTTAGTGCAAAATACAATCAATAATCCTGTC
1974874 ACACATTAGCTAGTGCTTAGTATAATCCTA
66 ACACATTAGCTAGTGCTTAGTATAATCCTA
1974904 TCACACATCGGTTAGTGCTTAATAAATTGATTTAGTTAGTGCAAAATACAATCAATAATCCTGTC
1 TCACACATCGGTTAGTGCTTAATAAATTGATTTAGTTAGTGCAAAATACAATCAATAATCCTGTC
* *
1974969 ACACATTGGTTAGTGCTTAGTA
66 ACACATTAGCTAGTGCTTAGTA
1974991 AATTGATTTA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (95 bp):
TCACACATCGGTTAGTGCTTAATAAATTGATTTAGTTAGTGCAAAATACAATCAATAATCCTGTC
ACACATTAGCTAGTGCTTAGTATAATCCTA
Found at i:1974974 original size:63 final size:63
Alignment explanation
Indices: 1974895--1975022 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
1974885 AGTGCTTAGT
*
1974895 ATAATCCTATCACACATCGGTTAGTGCTTAATAAATTGATTTAGTTAGTGCAAAATACAATCA
1 ATAATCCTATCACACATCGGTTAGTGCTTAATAAATTGATTTAGTTAATGCAAAATACAATCA
* * *
1974958 ATAATCCTGTCACACATTGGTTAGTGCTTAGTAAATTGATTTAGTTAATGCAAAATACAATCA
1 ATAATCCTATCACACATCGGTTAGTGCTTAATAAATTGATTTAGTTAATGCAAAATACAATCA
1975021 AT
1 AT
1975023 CATTGAGTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (63 bp):
ATAATCCTATCACACATCGGTTAGTGCTTAATAAATTGATTTAGTTAATGCAAAATACAATCA
Found at i:1982151 original size:30 final size:29
Alignment explanation
Indices: 1982117--1982175 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
1982107 TCATTAGTCC
*
1982117 TAAAAGCGTATTTAGCTTAAAATAAAAATA
1 TAAAAACGTATTTAGC-TAAAATAAAAATA
** *
1982147 TAAAAATTTATTTAGCTCAAATAAAAATA
1 TAAAAACGTATTTAGCTAAAATAAAAATA
1982176 CAGAGGCTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (29 bp):
TAAAAACGTATTTAGCTAAAATAAAAATA
Found at i:1990772 original size:27 final size:27
Alignment explanation
Indices: 1990742--1990793 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1990732 CACAAACGGT
1990742 GAAAGCAAACGAAGTTCAAACAACGAC
1 GAAAGCAAACGAAGTTCAAACAACGAC
*
1990769 GAAAGCAAATGAAGTTCAAACAACG
1 GAAAGCAAACGAAGTTCAAACAACG
1990794 GTGGATATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.10
Consensus pattern (27 bp):
GAAAGCAAACGAAGTTCAAACAACGAC
Found at i:2003952 original size:26 final size:26
Alignment explanation
Indices: 2003914--2003965 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2003904 AAATGCATTT
2003914 AACAAAAGAGTATTCTCTACAAAAGC
1 AACAAAAGAGTATTCTCTACAAAAGC
*
2003940 AACAAAAGGGTATTCTCTACAAAAGC
1 AACAAAAGAGTATTCTCTACAAAAGC
2003966 CATATTTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (26 bp):
AACAAAAGAGTATTCTCTACAAAAGC
Found at i:2006064 original size:20 final size:20
Alignment explanation
Indices: 2006024--2006067 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2006014 CTTGATCCAT
**
2006024 TTTGAGTTGATTTGGGCTAA
1 TTTGAGTTGATTTGAACTAA
*
2006044 TTTGAGTTGATTTGAATTAA
1 TTTGAGTTGATTTGAACTAA
2006064 TTTG
1 TTTG
2006068 GGTTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.50
Consensus pattern (20 bp):
TTTGAGTTGATTTGAACTAA
Found at i:2006242 original size:25 final size:25
Alignment explanation
Indices: 2006214--2006262 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2006204 AGTTAATAAT
*
2006214 ATTAAT-TTTCATGTAATAAATAAAC
1 ATTAATCTTT-ATATAATAAATAAAC
2006239 ATTAATCTTTATATAATAAATAAA
1 ATTAATCTTTATATAATAAATAAA
2006263 TAGTAGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (25 bp):
ATTAATCTTTATATAATAAATAAAC
Found at i:2006578 original size:13 final size:13
Alignment explanation
Indices: 2006560--2006584 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2006550 TTACCTGAAA
2006560 AATACAAATAACC
1 AATACAAATAACC
2006573 AATACAAATAAC
1 AATACAAATAAC
2006585 ATGTTAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (13 bp):
AATACAAATAACC
Found at i:2008717 original size:16 final size:16
Alignment explanation
Indices: 2008698--2008735 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2008688 AAATAGTGAT
2008698 TTATTTATT-TTAATTA
1 TTATTTATTATT-ATTA
*
2008714 TTATTTATTATTATTT
1 TTATTTATTATTATTA
2008730 TTATTT
1 TTATTT
2008736 GAGAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTATTATTATTA
Found at i:2009720 original size:21 final size:20
Alignment explanation
Indices: 2009678--2009744 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
2009668 TTGAATGGAG
* *
2009678 GCATCAATCTTAGTCATAAAT
1 GCATCAATCTT-GTTATGAAT
2009699 GCATCAATCTCTGTTATGAAT
1 GCATCAATCT-TGTTATGAAT
* *
2009720 GTATCAATATTTGTTATGAACT
1 GCATCAAT-CTTGTTATGAA-T
2009742 GCA
1 GCA
2009745 CGAATATATC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 33 0.87
22 5 0.13
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (20 bp):
GCATCAATCTTGTTATGAAT
Found at i:2013106 original size:64 final size:64
Alignment explanation
Indices: 2013005--2013134 Score: 172
Period size: 64 Copynumber: 2.0 Consensus size: 64
2012995 TCATCTTTTA
* * * *
2013005 TTGATGTGAGATTCATAACATTTTACCTCACTCAATTATGCAACG-CTCTCATTGCACTGGCTTT
1 TTGATATGAGATTCATAACATTTTACCACACCCAATTATGCAACGCCT-TCATTACACTGGCTTT
* * * *
2013069 TTGATATGAGATTCATGACATTTTTCCAGACCCAATTATGCAACGCCTTCATTACATTGGCTTT
1 TTGATATGAGATTCATAACATTTTACCACACCCAATTATGCAACGCCTTCATTACACTGGCTTT
2013133 TT
1 TT
2013135 ACCCACATCA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 55 0.96
65 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (64 bp):
TTGATATGAGATTCATAACATTTTACCACACCCAATTATGCAACGCCTTCATTACACTGGCTTT
Found at i:2013238 original size:54 final size:54
Alignment explanation
Indices: 2013139--2013247 Score: 130
Period size: 54 Copynumber: 2.0 Consensus size: 54
2013129 CTTTTTACCC
* ** * * *
2013139 ACATCAATAAAGATTGGGGTCTGTTGGAACTTAAGCCTAATCTCGTGTTGCCTT
1 ACATCAATAAAGATCGGGGTCTGCCGAAACTTAAGCCTAACCTCGTGCTGCCTT
* *
2013193 ACATCAATAAAGATCGGGGTTTGCCGAAACTTAAGCCCT-CCCTCGTGCTGCCTT
1 ACATCAATAAAGATCGGGGTCTGCCGAAACTTAAG-CCTAACCTCGTGCTGCCTT
2013247 A
1 A
2013248 AACTCTAAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 43 0.93
55 3 0.07
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (54 bp):
ACATCAATAAAGATCGGGGTCTGCCGAAACTTAAGCCTAACCTCGTGCTGCCTT
Found at i:2013257 original size:29 final size:29
Alignment explanation
Indices: 2013219--2013285 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
2013209 GGGTTTGCCG
** *
2013219 AAACT-TAAGCCCTCCCTCGTGCTGCCTT
1 AAACTCTAAGCCCAACCTCATGCTGCCTT
*
2013247 AAACTCTAAGCCCAACTTCATGCTGCCTT
1 AAACTCTAAGCCCAACCTCATGCTGCCTT
2013276 AAACTCTAAG
1 AAACTCTAAG
2013286 AGTTTAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.27, C:0.34, G:0.12, T:0.27
Consensus pattern (29 bp):
AAACTCTAAGCCCAACCTCATGCTGCCTT
Found at i:2022392 original size:2 final size:2
Alignment explanation
Indices: 2022385--2022415 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2022375 ATGTTTTTCT
*
2022385 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2022416 GTTAAAAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2030128 original size:51 final size:51
Alignment explanation
Indices: 2030072--2030172 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
2030062 TTAGAGCAGC
2030072 ACCATCCATCAACCGTGGCGGTCTGAACGTCCTACCAAATACAAGGACAGG
1 ACCATCCATCAACCGTGGCGGTCTGAACGTCCTACCAAATACAAGGACAGG
* * * * *
2030123 ACCATCCATCAACGGTGGTGGTCTGAACGTCTTACTAAGTACAAGGACAG
1 ACCATCCATCAACCGTGGCGGTCTGAACGTCCTACCAAATACAAGGACAG
2030173 CTGTGGTCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.19
Consensus pattern (51 bp):
ACCATCCATCAACCGTGGCGGTCTGAACGTCCTACCAAATACAAGGACAGG
Found at i:2030883 original size:17 final size:17
Alignment explanation
Indices: 2030863--2030930 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
2030853 TCATAATTAA
*
2030863 AATAATTAATAAATTTT
1 AATAAATAATAAATTTT
*
2030880 AATAAATATTAAATTTAT
1 AATAAATAATAAATTT-T
*
2030898 AAATAAAAAATAATATATTT
1 -AATAAATAATAA-AT-TTT
2030918 AA-AAATAA-AAATT
1 AATAAATAATAAATT
2030931 ATTATCTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
15 1 0.02
16 2 0.05
17 16 0.38
18 6 0.14
19 12 0.29
20 3 0.07
21 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAATAATAAATTTT
Found at i:2030892 original size:41 final size:37
Alignment explanation
Indices: 2030842--2030924 Score: 87
Period size: 41 Copynumber: 2.2 Consensus size: 37
2030832 AAATTAAGTT
*
2030842 AAAAT-TTAAAATCATAATTAAAATAATTAATAAATTTTA
1 AAAATATTAAAATCATAAATAAAA-AA-TAATAAA-TTTA
* * *
2030881 ATAAATATTAAATTTATAAATAAAAAATAATATATTTA
1 A-AAATATTAAAATCATAAATAAAAAATAATAAATTTA
2030919 AAAATA
1 AAAATA
2030925 AAAATTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
37 5 0.13
38 5 0.13
39 7 0.18
40 6 0.16
41 15 0.39
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (37 bp):
AAAATATTAAAATCATAAATAAAAAATAATAAATTTA
Found at i:2030917 original size:22 final size:22
Alignment explanation
Indices: 2030883--2030928 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2030873 AAATTTTAAT
* *
2030883 AAATATTAAATTTATAAATAAA
1 AAATAATAAATTTAAAAATAAA
*
2030905 AAATAATATATTTAAAAATAAA
1 AAATAATAAATTTAAAAATAAA
2030927 AA
1 AA
2030929 TTATTATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATAATAAATTTAAAAATAAA
Found at i:2035306 original size:34 final size:32
Alignment explanation
Indices: 2035268--2035339 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
2035258 GATAATGAAG
2035268 AATA-TTTTCTATAAGTTGATCCAAACAATCAAAA
1 AATATTTTTC-ATAA-TTGATCCAAACAAT-AAAA
* * *
2035302 AATATTTTTCATAATTTATCTAAATAATAAAA
1 AATATTTTTCATAATTGATCCAAACAATAAAA
2035334 AATATT
1 AATATT
2035340 AAATTTTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 10 0.29
33 11 0.32
34 8 0.24
35 5 0.15
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.39
Consensus pattern (32 bp):
AATATTTTTCATAATTGATCCAAACAATAAAA
Found at i:2035572 original size:10 final size:10
Alignment explanation
Indices: 2035557--2035619 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
2035547 AGTTATAAGA
2035557 AAATAAAAAT
1 AAATAAAAAT
*
2035567 AAATAAGAAT
1 AAATAAAAAT
*
2035577 AAATAGAAA-
1 AAATAAAAAT
*
2035586 AATTAAAAATT
1 AAATAAAAA-T
* *
2035597 AAATGAAATT
1 AAATAAAAAT
*
2035607 AAAAAAAAAT
1 AAATAAAAAT
2035617 AAA
1 AAA
2035620 AAGTCATTAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
9 7 0.17
10 27 0.68
11 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:2037448 original size:24 final size:24
Alignment explanation
Indices: 2037421--2037480 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2037411 TTGATTCGTA
* *
2037421 GTTTTGATTGTTTGAATATTTGAG
1 GTTTTGATTATTTGAATATTTAAG
** *
2037445 GTTTTTTTTATTTGAGTATTTAAG
1 GTTTTGATTATTTGAATATTTAAG
*
2037469 GTTTTGTTTATT
1 GTTTTGATTATT
2037481 GTGCATTTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.20, T:0.62
Consensus pattern (24 bp):
GTTTTGATTATTTGAATATTTAAG
Found at i:2037488 original size:23 final size:24
Alignment explanation
Indices: 2037438--2037489 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2037428 TTGTTTGAAT
* * *
2037438 ATTTGAGGTTTTTTTTATTTGAGT
1 ATTTAAGGTTTTGTTTATTTGAGC
*
2037462 ATTTAAGGTTTTGTTTA-TTGTGC
1 ATTTAAGGTTTTGTTTATTTGAGC
2037485 ATTTA
1 ATTTA
2037490 GGATTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.19, C:0.02, G:0.19, T:0.60
Consensus pattern (24 bp):
ATTTAAGGTTTTGTTTATTTGAGC
Found at i:2043315 original size:26 final size:26
Alignment explanation
Indices: 2043286--2043340 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
2043276 AAGAAAGTTA
2043286 TAAGTGA-AAAATTTTTTGAAAATTTT
1 TAAGTGAGAAAATTTTTT-AAAATTTT
*
2043312 TAAGTGAGGAAATTTTTTAAAATTTT
1 TAAGTGAGAAAATTTTTTAAAATTTT
2043338 TAA
1 TAA
2043341 AAAAAATGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (26 bp):
TAAGTGAGAAAATTTTTTAAAATTTT
Found at i:2050268 original size:1 final size:1
Alignment explanation
Indices: 2050262--2050288 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2050252 CCTCCCCGAA
2050262 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
2050289 TCTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2055334 original size:35 final size:35
Alignment explanation
Indices: 2055288--2055356 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
2055278 CCAATAAAGC
2055288 TAAGTAGAGAGGAGG-AAGAAAAGAGAATTGAGGTA
1 TAAGTAGAGAGGAGGAAAG-AAAGAGAATTGAGGTA
* *
2055323 TAAGTATAGAGGAGGAAAGAGAGAGAATTGAGGT
1 TAAGTAGAGAGGAGGAAAGAAAGAGAATTGAGGT
2055357 GTGGTGTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 28 0.90
36 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.38, T:0.16
Consensus pattern (35 bp):
TAAGTAGAGAGGAGGAAAGAAAGAGAATTGAGGTA
Found at i:2060666 original size:21 final size:21
Alignment explanation
Indices: 2060624--2060662 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2060614 TAAATAATAG
*
2060624 ATAATAAAAAAGAAATGAATT
1 ATAATAAAAAAGAAATAAATT
*
2060645 ATAAT-AAGAAGAAATAAA
1 ATAATAAAAAAGAAATAAA
2060663 ATTAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (21 bp):
ATAATAAAAAAGAAATAAATT
Found at i:2060673 original size:12 final size:12
Alignment explanation
Indices: 2060656--2060681 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2060646 TAATAAGAAG
2060656 AAATAAAATTAA
1 AAATAAAATTAA
2060668 AAATAAAATTAA
1 AAATAAAATTAA
2060680 AA
1 AA
2060682 TGTTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATAAAATTAA
Found at i:2063130 original size:15 final size:15
Alignment explanation
Indices: 2063110--2063146 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2063100 TAATAAAAAA
2063110 TTTAAAAAATATTTT
1 TTTAAAAAATATTTT
2063125 TTTAAAAAATATTTT
1 TTTAAAAAATATTTT
2063140 TTTAAAA
1 TTTAAAA
2063147 TTATTTTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTAAAAAATATTTT
Found at i:2063139 original size:14 final size:14
Alignment explanation
Indices: 2063110--2063153 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
2063100 TAATAAAAAA
2063110 TTTAAAAAATATTTT
1 TTTAAAAAATA-TTT
2063125 TTTAAAAAATATTT
1 TTTAAAAAATATTT
* *
2063139 TTTTAAAATTATTT
1 TTTAAAAAATATTT
2063153 T
1 T
2063154 CGTATGGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAAAAAATATTT
Found at i:2067468 original size:15 final size:15
Alignment explanation
Indices: 2067448--2067477 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2067438 TTCCACAGTG
*
2067448 ATGCTTTTCTGCACC
1 ATGCTTTTCAGCACC
2067463 ATGCTTTTCAGCACC
1 ATGCTTTTCAGCACC
2067478 TGCAACCCAA
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:0.17, C:0.33, G:0.13, T:0.37
Consensus pattern (15 bp):
ATGCTTTTCAGCACC
Found at i:2075137 original size:19 final size:19
Alignment explanation
Indices: 2075113--2075156 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2075103 AACTTTACAC
2075113 TTATTTAGGCTATTTTAGA
1 TTATTTAGGCTATTTTAGA
* *
2075132 TTATTTAGGTTATTTTATA
1 TTATTTAGGCTATTTTAGA
2075151 TTATTT
1 TTATTT
2075157 TACTTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.25, C:0.02, G:0.11, T:0.61
Consensus pattern (19 bp):
TTATTTAGGCTATTTTAGA
Found at i:2084251 original size:46 final size:46
Alignment explanation
Indices: 2084178--2084270 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
2084168 TGGAGAAGAG
* *
2084178 TTTTAAGTGAAACAAAGAAAACCAAACACCAAACAACATAGTATAA
1 TTTTAAATGAAACAAAGAAAACCAAACACCAAACAACATAGGATAA
* **
2084224 TTTTAAATGAAACAAAGATAATTAAACACCAAACAACATAGGATAA
1 TTTTAAATGAAACAAAGAAAACCAAACACCAAACAACATAGGATAA
2084270 T
1 T
2084271 CTTACCTGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.20
Consensus pattern (46 bp):
TTTTAAATGAAACAAAGAAAACCAAACACCAAACAACATAGGATAA
Found at i:2085948 original size:16 final size:16
Alignment explanation
Indices: 2085929--2085962 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2085919 AAACAAAAAG
*
2085929 GAAAGAGAGAGTGAGA
1 GAAAGAGAGAGAGAGA
2085945 GAAAGAGAGAGAGAGA
1 GAAAGAGAGAGAGAGA
2085961 GA
1 GA
2085963 TCAGTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (16 bp):
GAAAGAGAGAGAGAGA
Found at i:2097770 original size:29 final size:29
Alignment explanation
Indices: 2097728--2097793 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
2097718 ATTGAAAGTG
2097728 CCAACACATACTGATATAGTACACACGTA
1 CCAACACATACTGATATAGTACACACGTA
2097757 CCAACACATACTGATATAGTACACACGTA
1 CCAACACATACTGATATAGTACACACGTA
*
2097786 CCGACACA
1 CCAACACA
2097794 CACAAAAGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.18
Consensus pattern (29 bp):
CCAACACATACTGATATAGTACACACGTA
Found at i:2112117 original size:17 final size:16
Alignment explanation
Indices: 2112094--2112139 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
2112084 TTATTTCTAC
2112094 ATAAAAGACAATTGTA-
1 ATAAAAGACAATT-TAT
*
2112110 ATTAAAAGACAAATTAT
1 A-TAAAAGACAATTTAT
2112127 ATAAAAGACAATT
1 ATAAAAGACAATT
2112140 AATGTCTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.26
Consensus pattern (16 bp):
ATAAAAGACAATTTAT
Found at i:2126910 original size:23 final size:24
Alignment explanation
Indices: 2126884--2126934 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
2126874 TTAAGATTTT
*
2126884 AATAAATAATTTGAATTT-AATA-A
1 AATAAATAA-TTAAATTTAAATATA
*
2126907 AATATATAATTAAATTTAAATATA
1 AATAAATAATTAAATTTAAATATA
2126931 AATA
1 AATA
2126935 TTCATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 12 0.50
24 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
AATAAATAATTAAATTTAAATATA
Found at i:2126976 original size:15 final size:15
Alignment explanation
Indices: 2126956--2127006 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2126946 TTATCATTAA
2126956 TTATTAATATTTATT
1 TTATTAATATTTATT
2126971 TTATTAA-ATATTATT
1 TTATTAATAT-TTATT
* * *
2126986 TGATCAATTATTTTTT
1 TTATTAA-TATTTATT
2127002 TTATT
1 TTATT
2127007 TTATTTTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 2 0.07
15 17 0.61
16 7 0.25
17 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATTAATATTTATT
Found at i:2127417 original size:22 final size:21
Alignment explanation
Indices: 2127378--2127434 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
2127368 AAAAATTAAT
* *
2127378 TTAATATAATATTATTTATAA-T
1 TTAATAT-TTATTATTTA-AACA
*
2127400 TTAATTTTTATTATTTTAAACA
1 TTAATATTTATTA-TTTAAACA
2127422 TTAATATTTATTA
1 TTAATATTTATTA
2127435 AAAGTTGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATATTTATTATTTAAACA
Done.