Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 121 of 279
Found at i:38344750 original size:89 final size:90
Alignment explanation
Indices: 38344599--38345274 Score: 729
Period size: 80 Copynumber: 7.8 Consensus size: 90
38344589 CGCTGAGACG
* ** *
38344599 TTTTCAATTTCTGCTTTTC-AAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
38344663 ATGCTGAGGTATTTTCAATTTCTAC
66 ATGCTGAGGTATTTTCAATTTCTAC
*
38344688 TTTTCAATTTATATTTTTC-AAAAATCAACTCATATTGCGAGGGGTGAGTTGAGCCTCGGCTCAC
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
38344752 ATGCTGAGGTATTTTCAATTTCTAC
66 ATGCTGAGGTATTTTCAATTTCTAC
38344777 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---A
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCA
* *
38344839 CACGCTAAGGTAATTTT-AA-TT-T-C
65 CATGCTGAGGT-ATTTTCAATTTCTAC
*
38344862 ---T--GTTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---A
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCA
* *
38344919 CACGCTAAGGTAATTTT-AA-TT-T-C
65 CATGCTGAGGT-ATTTTCAATTTCTAC
* * * **
38344942 ---T--GTTTATATTTTTCAAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCATCGGGGCAC
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
*
38345002 --GCTGAGGTATTTTCAATTTCTGC
66 ATGCTGAGGTATTTTCAATTTCTAC
*
38345025 TTTTCAATTTATATTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTC
1 TTTTCAATTTATATTTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTC
**
38345090 AC--GCTGAGGTATTTTCAATTTCTGT
64 ACATGCTGAGGTATTTTCAATTTCTAC
* * *
38345115 TTTTCAATCTATATTTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCAC
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
* *
38345179 CTGCTGAGCTATTTTCAATTTCTA-
66 ATGCTGAGGTATTTTCAATTTCTAC
* * * * * * ** *
38345203 TTTTTAATGTT-TAGTTTT-AAAGAGTCAATTCATATCGCGAGAAATGAGTTGAG-CTCAGGATC
1 TTTTCAAT-TTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTC
*
38345265 AGATGCTGAG
64 ACATGCTGAG
38345275 TAAAGAATAA
Statistics
Matches: 528, Mismatches: 37, Indels: 45
0.87 0.06 0.07
Matches are distributed among these distances:
79 7 0.01
80 138 0.26
81 2 0.00
82 4 0.01
83 1 0.00
85 1 0.00
86 2 0.00
87 46 0.09
88 78 0.15
89 129 0.24
90 118 0.22
91 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (90 bp):
TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
ATGCTGAGGTATTTTCAATTTCTAC
Found at i:38344782 original size:14 final size:14
Alignment explanation
Indices: 38344763--38344797 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
38344753 TGCTGAGGTA
*
38344763 TTTTCAATTTCTAC
1 TTTTCAATTTATAC
*
38344777 TTTTCAATTTATAT
1 TTTTCAATTTATAC
38344791 TTTTCAA
1 TTTTCAA
38344798 AAAATCAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTATAC
Found at i:38345095 original size:90 final size:88
Alignment explanation
Indices: 38344599--38345201 Score: 748
Period size: 80 Copynumber: 7.0 Consensus size: 88
38344589 CGCTGAGACG
* ** *
38344599 TTTTCAATTTCTGCTTTTC-AAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
*
38344663 ATGCTGAGGTATTTTCAATTTCTAC
66 --GCTGAGGTATTTTCAATTTCTGC
*
38344688 TTTTCAATTTATATTTTTC-AAAAATCAACTCATATTGCGAGGGGTGAGTTGAGCCTCGGCTCAC
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
*
38344752 ATGCTGAGGTATTTTCAATTTCTAC
66 --GCTGAGGTATTTTCAATTTCTGC
*
38344777 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACA
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCA
*
38344841 CGCTAAGGTAATTTT-AATTTCTG-
65 CGCTGAGGT-ATTTTCAATTTCTGC
*
38344864 -------TTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACA
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCA
*
38344921 CGCTAAGGTAATTTT-AATTTCTG-
65 CGCTGAGGT-ATTTTCAATTTCTGC
* * **
38344944 -------TTTATATTTTTCAAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCATCGGGGCAC
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
38345002 GCTGAGGTATTTTCAATTTCTGC
66 GCTGAGGTATTTTCAATTTCTGC
*
38345025 TTTTCAATTTATATTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTC
1 TTTTCAATTTATATTTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTC
*
38345090 ACGCTGAGGTATTTTCAATTTCTGT
64 ACGCTGAGGTATTTTCAATTTCTGC
* * *
38345115 TTTTCAATCTATATTTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCAC
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCA-
*
38345179 CTGCTGAGCTATTTTCAATTTCT
65 C-GCTGAGGTATTTTCAATTTCT
38345202 ATTTTTAATG
Statistics
Matches: 473, Mismatches: 24, Indels: 34
0.89 0.05 0.06
Matches are distributed among these distances:
79 7 0.01
80 147 0.31
87 41 0.09
88 27 0.06
89 128 0.27
90 121 0.26
91 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (88 bp):
TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAC
GCTGAGGTATTTTCAATTTCTGC
Found at i:38351036 original size:3 final size:3
Alignment explanation
Indices: 38351008--38351051 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
38350998 CCAATAAGCG
* * *
38351008 CCA CCA CAA CCA CAA CCA CAA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
38351052 GTCTCCTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.39, C:0.61, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:38351051 original size:12 final size:12
Alignment explanation
Indices: 38351008--38351050 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
38350998 CCAATAAGCG
38351008 CCACCACAACCA
1 CCACCACAACCA
*
38351020 CAACCACAACCA
1 CCACCACAACCA
*
38351032 CCACCACCACCA
1 CCACCACAACCA
38351044 CCACCAC
1 CCACCAC
38351051 CGTCTCCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (12 bp):
CCACCACAACCA
Found at i:38353521 original size:51 final size:51
Alignment explanation
Indices: 38353461--38353563 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
38353451 ACATGTTTAT
38353461 ATGTTTGATTAAAATCATGTTTAAGGTTATTCATTCATTAATCATTTGGTC
1 ATGTTTGATTAAAATCATGTTTAAGGTTATTCATTCATTAATCATTTGGTC
38353512 ATGTTTGATTAAAATCATGTTTAAGGTTATTCATTCATTAATCATTTGGTC
1 ATGTTTGATTAAAATCATGTTTAAGGTTATTCATTCATTAATCATTTGGTC
38353563 A
1 A
38353564 AGCAACCTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (51 bp):
ATGTTTGATTAAAATCATGTTTAAGGTTATTCATTCATTAATCATTTGGTC
Found at i:38354709 original size:19 final size:18
Alignment explanation
Indices: 38354687--38354729 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
38354677 TTCCAATTAA
*
38354687 ATAAATATATTTTTTATGT
1 ATAAATATA-ATTTTATGT
*
38354706 ATAAGTATAATTTTATGT
1 ATAAATATAATTTTATGT
38354724 -TAAATA
1 ATAAATA
38354730 CAATAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
ATAAATATAATTTTATGT
Found at i:38355730 original size:46 final size:47
Alignment explanation
Indices: 38355670--38355837 Score: 234
Period size: 46 Copynumber: 3.6 Consensus size: 47
38355660 TTTGACGTGA
* * * *
38355670 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGTCACGT
*
38355716 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGTCACGT
* * * *
38355762 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGTCACGT
38355808 TGCCATGGTATCTTTCAACCATGGTCTTAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC
38355838 ACACAGGTTG
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
45 5 0.05
46 105 0.95
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.40
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATGTCACGT
Found at i:38355838 original size:46 final size:46
Alignment explanation
Indices: 38355670--38355888 Score: 233
Period size: 46 Copynumber: 5.0 Consensus size: 46
38355660 TTTGACGTGA
* * * * * *
38355670 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
38355716 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
38355762 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
38355808 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
38355846 TGCCATGGTATCTATCAACTAT-GTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
38355889 AGAGCACACT
Statistics
Matches: 150, Mismatches: 14, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
37 5 0.03
38 25 0.17
39 4 0.03
41 1 0.01
42 1 0.01
44 4 0.03
45 7 0.05
46 103 0.69
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:38355854 original size:38 final size:37
Alignment explanation
Indices: 38355803--38355877 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 37
38355793 CATCTCATAT
*
38355803 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTATCAACCAT-GTCTTACACA
*
38355841 CAGGTTGCCATGGTATCTATCAACTATGTCTTACACA
1 CAGGTTGCCATGGTATCTATCAACCATGTCTTACACA
38355878 TTTCATATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 10 0.29
38 25 0.71
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (37 bp):
CAGGTTGCCATGGTATCTATCAACCATGTCTTACACA
Found at i:38356176 original size:62 final size:62
Alignment explanation
Indices: 38356085--38356225 Score: 210
Period size: 62 Copynumber: 2.3 Consensus size: 62
38356075 TTACCGTCCG
* * * * *
38356085 GGCTAAATCCATTTTACACGTATTTTTCGGGAGGGCTATATCAGAATAGGATCACCCGTCCA
1 GGCTAGATCCTTTTTACACATATTCTTCGGGAGGGCTATATCAGAATAGGATCACCCATCCA
* * *
38356147 TGCTAGATCCTTTTTACACATATTCTTCGGGAGGGCTATATCAGGATAGGATCACCCATCCG
1 GGCTAGATCCTTTTTACACATATTCTTCGGGAGGGCTATATCAGAATAGGATCACCCATCCA
38356209 GGCTAGATCCTTTTTAC
1 GGCTAGATCCTTTTTAC
38356226 CGTCAATTCN
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (62 bp):
GGCTAGATCCTTTTTACACATATTCTTCGGGAGGGCTATATCAGAATAGGATCACCCATCCA
Found at i:38358743 original size:51 final size:51
Alignment explanation
Indices: 38358584--38358740 Score: 262
Period size: 51 Copynumber: 3.1 Consensus size: 51
38358574 ACTTCTGATC
* *
38358584 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
38358635 AGTGACAAATGATAAGTGGTAGCTT-AGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
*
38358685 AGTGATAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
38358736 AGTGA
1 AGTGA
38358741 TAAATGTGAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
50 46 0.47
51 52 0.53
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:38362261 original size:31 final size:31
Alignment explanation
Indices: 38362226--38362305 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
38362216 CAACCTATTG
* *
38362226 ACTTAATTAAAAACTTTTGAATAGTTTAATT
1 ACTTAATTAAAATCTTTTGAATAATTTAATT
* *
38362257 ACTTAAATAAAATTTTTTGAATAATTTAATT
1 ACTTAATTAAAATCTTTTGAATAATTTAATT
* * *
38362288 CCTAAATTATAATCTTTT
1 ACTTAATTAAAATCTTTT
38362306 TAATTAAGTG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.47
Consensus pattern (31 bp):
ACTTAATTAAAATCTTTTGAATAATTTAATT
Found at i:38365131 original size:47 final size:44
Alignment explanation
Indices: 38365038--38365131 Score: 102
Period size: 47 Copynumber: 2.0 Consensus size: 44
38365028 TTAATATGAA
* *
38365038 ATTTTTTAAAATAATTTTAAATTTAATAAATTCATATTTTTATAT
1 ATTTTTTAAAATAATATTAAATTTAATAAATT-ATATTTATATAT
38365083 ATTTTTTAATATATAATATTAAATTTTAACT-AATT-TATTTATACTAT
1 ATTTTTTAA-A-ATAATATTAAA-TTTAA-TAAATTATATTTATA-TAT
38365130 AT
1 AT
38365132 GGACTTCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
45 9 0.21
46 8 0.19
47 15 0.36
48 9 0.21
49 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (44 bp):
ATTTTTTAAAATAATATTAAATTTAATAAATTATATTTATATAT
Found at i:38379328 original size:28 final size:29
Alignment explanation
Indices: 38379296--38379351 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
38379286 CCGAAATACT
* *
38379296 GATA-TCATAGCCTGAAGCCAAATCAGTC
1 GATATTCATAGCCCGAACCCAAATCAGTC
38379324 GATATTCATAGCCCGAACCCAAATCAGT
1 GATATTCATAGCCCGAACCCAAATCAGT
38379352 ATAACTCGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (29 bp):
GATATTCATAGCCCGAACCCAAATCAGTC
Found at i:38381685 original size:17 final size:17
Alignment explanation
Indices: 38381663--38381713 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
38381653 GACTAATCCC
*
38381663 TATACATCACTTAGGTA
1 TATACATTACTTAGGTA
*
38381680 TATACATTACCTAGGTA
1 TATACATTACTTAGGTA
*
38381697 TGTACATTACTTAGGTA
1 TATACATTACTTAGGTA
38381714 CATGCCACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (17 bp):
TATACATTACTTAGGTA
Found at i:38382498 original size:41 final size:40
Alignment explanation
Indices: 38382391--38382501 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 40
38382381 TCGGATAGTT
* *
38382391 CGAAGCAATAGTTGACACCCAGTGTCTCATCG-GCCAAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
** ** * * *
38382430 CGAAGT-A-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
38382468 CGAAGTAATAGTATGACACCCAGTGTCTCATCGA
1 CGAAGTAATAGT-TGACACCCAGTGTCTCATCGA
38382502 CTCAAGGTCG
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
37 19 0.35
38 10 0.18
39 6 0.11
40 3 0.05
41 17 0.31
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCAAGC
Found at i:38384295 original size:120 final size:120
Alignment explanation
Indices: 38384082--38384323 Score: 398
Period size: 120 Copynumber: 2.0 Consensus size: 120
38384072 GGGGTTTTGT
*
38384082 GGAAGAGGTGGAGAACTTGTTCGTTGAGAATTCTTTTCAAGGAGAAGATTGTTAGAGTTGTATGA
1 GGAAGAGGTGGAGAACTTGTTCGTTGAGAATTCTGTTCAAGGAGAAGATTGTTAGAGTTGTATGA
* *
38384147 CCCAAATTCCAGTTAAAGAAATAAAATACAGTGGCAAAATAGGGGGATCTGTGGG
66 CCCAAATTCCAGTTAAAGAAATAAAATACAGTGACAAAATAAGGGGATCTGTGGG
* *
38384202 GGAAGGGGTGGAGAACTTGTTCGTTGAGAATTCGTGTT-AAGGAGGAA-ATTGTTAGAGTTGTGT
1 GGAAGAGGTGGAGAACTTGTTCGTTGAGAATTC-TGTTCAAGGA-GAAGATTGTTAGAGTTGTAT
*
38384265 GACCCAAATTCCTGTTAAAGAAATAAAATACAGTGACAAAATAAGGGGATCTGTGGG
64 GACCCAAATTCCAGTTAAAGAAATAAAATACAGTGACAAAATAAGGGGATCTGTGGG
38384322 GG
1 GG
38384324 CGAAGGCCAA
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
120 108 0.95
121 6 0.05
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (120 bp):
GGAAGAGGTGGAGAACTTGTTCGTTGAGAATTCTGTTCAAGGAGAAGATTGTTAGAGTTGTATGA
CCCAAATTCCAGTTAAAGAAATAAAATACAGTGACAAAATAAGGGGATCTGTGGG
Found at i:38384432 original size:48 final size:49
Alignment explanation
Indices: 38384361--38384454 Score: 138
Period size: 48 Copynumber: 1.9 Consensus size: 49
38384351 CGTATAGAAG
* *
38384361 TACACTCTTTTTATTTGATATTGATTAGAA-AA-GGTGTTTCAACCTTAT
1 TACACTCTTTCTATTTGACATTGATTAGAATAAGGGT-TTTCAACCTTAT
*
38384409 TACACTGTTTCTATTTGACATTGATTAGAATAAGGGTTTTCAACCT
1 TACACTCTTTCTATTTGACATTGATTAGAATAAGGGTTTTCAACCT
38384455 ATAAATATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
48 27 0.66
49 11 0.27
50 3 0.07
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (49 bp):
TACACTCTTTCTATTTGACATTGATTAGAATAAGGGTTTTCAACCTTAT
Found at i:38387806 original size:38 final size:40
Alignment explanation
Indices: 38387760--38387857 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 40
38387750 AATTTTACTA
38387760 ATAATTTATATTAATTATTTAAAAAATATTTAAA-ATT-T
1 ATAATTTATATTAATTATTTAAAAAATATTTAAATATTAT
* * * * * *
38387798 ATACTTTATGTATCATTATAT-CAAATTATTTAAATATTAT
1 ATAATTTATAT-TAATTATTTAAAAAATATTTAAATATTAT
38387838 ATAATTTA-ATTAATT-TTTAA
1 ATAATTTATATTAATTATTTAA
38387858 CTTTCCACTA
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
37 2 0.04
38 24 0.53
39 11 0.24
40 8 0.18
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (40 bp):
ATAATTTATATTAATTATTTAAAAAATATTTAAATATTAT
Found at i:38388387 original size:66 final size:65
Alignment explanation
Indices: 38388251--38388377 Score: 184
Period size: 66 Copynumber: 1.9 Consensus size: 65
38388241 CTTTCAACCC
* * *
38388251 AAAATTCTAAAATATGTAATTATAAATTTAAAAAATCAAAATATTACATAAAAATTGAAAAAATA
1 AAAATTCTAAAATATATAAATATAAATTTAAAAAATCAAAAGATTACATAAAAATTGAAAAAATA
* *
38388316 AAAATTCTAAAATATATAAATATAGATTTTAAAAAAAT-AAAAGATTATATAAAAATTGAAAA
1 AAAATTCTAAAATATATAAATATA-AATTT-AAAAAATCAAAAGATTACATAAAAATTGAAAA
38388378 TGGTCAAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
65 22 0.40
66 26 0.47
67 7 0.13
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (65 bp):
AAAATTCTAAAATATATAAATATAAATTTAAAAAATCAAAAGATTACATAAAAATTGAAAAAATA
Found at i:38388658 original size:16 final size:18
Alignment explanation
Indices: 38388615--38388653 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
38388605 TAATTACATA
38388615 TTTTAAAATTTTATATTT
1 TTTTAAAATTTTATATTT
38388633 TTTTAAAATTTTATATTT
1 TTTTAAAATTTTATATTT
38388651 TTT
1 TTT
38388654 GAATTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTAAAATTTTATATTT
Found at i:38388667 original size:20 final size:18
Alignment explanation
Indices: 38388615--38388671 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
38388605 TAATTACATA
38388615 TTTT-AAAATTTTATATT
1 TTTTGAAAATTTTATATT
*
38388632 TTTTTAAAATTTTATATT
1 TTTTGAAAATTTTATATT
*
38388650 TTTTGAATTATTTATATATT
1 TTTTGAA-AATTT-TATATT
38388670 TT
1 TT
38388672 ATATATAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
17 4 0.11
18 19 0.54
19 4 0.11
20 8 0.23
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTGAAAATTTTATATT
Found at i:38389779 original size:20 final size:18
Alignment explanation
Indices: 38389754--38389795 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
38389744 TGAGTTGAGA
*
38389754 AATTTATTTAATTGAAAATT
1 AATTTATCTAATT--AAATT
38389774 AATTTATCTAATTAAATT
1 AATTTATCTAATTAAATT
38389792 AATT
1 AATT
38389796 AATTAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
AATTTATCTAATTAAATT
Found at i:38390159 original size:18 final size:20
Alignment explanation
Indices: 38390125--38390161 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
38390115 TCACCAATTC
38390125 TCCTTCATCCATTCTTCATT
1 TCCTTCATCCATTCTTCATT
38390145 TCCTTC-TCC-TTCTTCAT
1 TCCTTCATCCATTCTTCAT
38390162 GCAGCTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.11, C:0.38, G:0.00, T:0.51
Consensus pattern (20 bp):
TCCTTCATCCATTCTTCATT
Found at i:38395832 original size:26 final size:26
Alignment explanation
Indices: 38395795--38395878 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
38395785 CATGAAATTC
38395795 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
38395821 TTATCATAAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
38395847 TTACCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
38395873 TTATCA
1 TTATCA
38395879 ATTTGTATCA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:38411550 original size:34 final size:34
Alignment explanation
Indices: 38411507--38411574 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
38411497 AAGGGTCCAG
38411507 TACAAAGATCAAAACTCAAATAAAAATGCCTTAA
1 TACAAAGATCAAAACTCAAATAAAAATGCCTTAA
38411541 TACAAAGATCAAAACTCAAATAAAAATGCCTTAA
1 TACAAAGATCAAAACTCAAATAAAAATGCCTTAA
38411575 AGACTAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.56, C:0.18, G:0.06, T:0.21
Consensus pattern (34 bp):
TACAAAGATCAAAACTCAAATAAAAATGCCTTAA
Found at i:38414408 original size:3 final size:3
Alignment explanation
Indices: 38414400--38414430 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
38414390 AAATGATTAC
*
38414400 ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38414431 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:38419725 original size:25 final size:25
Alignment explanation
Indices: 38419697--38419748 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
38419687 TTTGGCTTGA
**
38419697 CATTTACTAAGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
38419722 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
38419747 CA
1 CA
38419749 AATTATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:38421014 original size:11 final size:11
Alignment explanation
Indices: 38420998--38421030 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
38420988 TTCAGCAGAT
38420998 GAAAATG-AGAA
1 GAAAATGAAG-A
38421009 GAAAATGAAGA
1 GAAAATGAAGA
38421020 GAAAATGAAGA
1 GAAAATGAAGA
38421031 AAACTCTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 19 0.90
12 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:38444043 original size:7 final size:6
Alignment explanation
Indices: 38444015--38444064 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
38444005 CTTTCCTTTC
* *
38444015 CTTTTT -TTTTT CTTTTT CTTTTT CATTTT CTTCTATT C-TATT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTT-T-TT CTTTTT CTTTTT
38444063 CT
1 CT
38444065 CTTCTCCTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
5 8 0.22
6 23 0.64
7 2 0.06
8 3 0.08
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (6 bp):
CTTTTT
Found at i:38447686 original size:32 final size:32
Alignment explanation
Indices: 38447650--38447714 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
38447640 TGTCTTTTCT
**
38447650 TAATTTATTTCATAAT-ATAATAATAATTAATA
1 TAATTTATAGCATAATAATAATAATAA-TAATA
*
38447682 TAATTTATAGCTTAATAATAATAATAATAATA
1 TAATTTATAGCATAATAATAATAATAATAATA
38447714 T
1 T
38447715 CTTTTTACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (32 bp):
TAATTTATAGCATAATAATAATAATAATAATA
Found at i:38447891 original size:16 final size:16
Alignment explanation
Indices: 38447853--38447902 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
38447843 TCTATAATTC
*
38447853 ATATTATAATTTAAATA
1 ATATAATAA-TTAAATA
* *
38447870 AAATAATAATTATATA
1 ATATAATAATTAAATA
*
38447886 ATATAATAATTTAATA
1 ATATAATAATTAAATA
38447902 A
1 A
38447903 AGTAAGAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAATAATTAAATA
Found at i:38454724 original size:3 final size:3
Alignment explanation
Indices: 38454718--38454788 Score: 58
Period size: 3 Copynumber: 24.0 Consensus size: 3
38454708 CATCATCATC
* *
38454718 ATT ATT ATT GA-T ATT ATT ATT ATT ATT AAT ATT ATT ATT GTT ACTT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* * *
38454764 -TT GTC ATT ATT A-T ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
38454789 GGTATTATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 5 0.09
3 46 0.85
4 3 0.06
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:38454736 original size:15 final size:15
Alignment explanation
Indices: 38454718--38454796 Score: 63
Period size: 15 Copynumber: 5.1 Consensus size: 15
38454708 CATCATCATC
38454718 ATTATTATTGATATT
1 ATTATTATTGATATT
*
38454733 ATTATTATT-ATTAAT
1 ATTATTATTGA-TATT
*
38454748 ATTATTATTGTTACTT
1 ATTATTATTGATA-TT
*
38454764 TTGTCATTATT-ATATT
1 AT-T-ATTATTGATATT
* *
38454780 ATTACTATTGGTATT
1 ATTATTATTGATATT
38454795 AT
1 AT
38454797 ATTTATATTC
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
14 6 0.12
15 30 0.60
16 5 0.10
17 3 0.06
18 6 0.12
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.59
Consensus pattern (15 bp):
ATTATTATTGATATT
Found at i:38456189 original size:32 final size:32
Alignment explanation
Indices: 38456148--38456208 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
38456138 AGTCCTTAAC
38456148 ATCCGTTTTAATTTATTCAATCATTTTTTTTT
1 ATCCGTTTTAATTTATTCAATCATTTTTTTTT
38456180 ATCCGTTTTAATTTATTCAATCATTTTTT
1 ATCCGTTTTAATTTATTCAATCATTTTTT
38456209 ATAAATTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (32 bp):
ATCCGTTTTAATTTATTCAATCATTTTTTTTT
Found at i:38459480 original size:4 final size:4
Alignment explanation
Indices: 38459471--38459495 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
38459461 AACTTGAGCC
38459471 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
38459496 GTACACAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:38459524 original size:19 final size:20
Alignment explanation
Indices: 38459488--38459533 Score: 76
Period size: 19 Copynumber: 2.3 Consensus size: 20
38459478 ATTTATTTAT
38459488 TTATTTATGTACACAAGCAAA
1 TTATTTATGTA-ACAAGCAAA
38459509 TTATTTATGT-ACAAGCAAA
1 TTATTTATGTAACAAGCAAA
38459528 TTATTT
1 TTATTT
38459534 TTCAAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 15 0.60
21 10 0.40
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (20 bp):
TTATTTATGTAACAAGCAAA
Found at i:38465986 original size:93 final size:93
Alignment explanation
Indices: 38465874--38466042 Score: 311
Period size: 93 Copynumber: 1.8 Consensus size: 93
38465864 CGCCCATAAG
* *
38465874 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38465939 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
38465967 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
38466032 ACGAGTTCGGA
66 ACGAGTTCGGA
38466043 CGCTCAAATA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:38466042 original size:46 final size:46
Alignment explanation
Indices: 38465867--38466043 Score: 218
Period size: 46 Copynumber: 3.8 Consensus size: 46
38465857 TGTAACCCGC
* * *
38465867 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
38465913 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
38465963 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
38466006 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAC
38466044 GCTCAAATAT
Statistics
Matches: 112, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:38472964 original size:31 final size:31
Alignment explanation
Indices: 38472905--38472980 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
38472895 ACACACATAT
*
38472905 ATATACTAAATAAAATAATAAAATAATAATAA
1 ATAT-CTAATTAAAATAATAAAATAATAATAA
* *
38472937 ATATCTTATTAAAAT-ATTAAATAAATAATAA
1 ATATCTAATTAAAATAATAAAAT-AATAATAA
*
38472968 TTATCTAATTAAA
1 ATATCTAATTAAA
38472981 TAACTATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 6 0.16
31 28 0.74
32 4 0.11
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (31 bp):
ATATCTAATTAAAATAATAAAATAATAATAA
Found at i:38472970 original size:23 final size:23
Alignment explanation
Indices: 38472911--38472970 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
38472901 ATATATATAC
38472911 TAAAT-AA-AATAA-TAAAATAA
1 TAAATAAATAATAATTAAAATAA
* * *
38472931 T-AATAAATATCTTATTAAAATAT
1 TAAATAAATA-ATAATTAAAATAA
38472954 TAAATAAATAATAATTA
1 TAAATAAATAATAATTA
38472971 TCTAATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.10
20 3 0.10
21 1 0.03
22 2 0.07
23 13 0.43
24 8 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATAAATAATAATTAAAATAA
Found at i:38473238 original size:30 final size:31
Alignment explanation
Indices: 38473191--38473249 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
38473181 CACCCTTGAA
* * *
38473191 ATATTTGCACTATTAGTCCTTCAACTTTTTC
1 ATATTTACACTATTAGTCCCTCAAATTTTTC
38473222 ATATTTACACT-TTAGTCCCTCAAATTTT
1 ATATTTACACTATTAGTCCCTCAAATTTT
38473250 AAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.47
Consensus pattern (31 bp):
ATATTTACACTATTAGTCCCTCAAATTTTTC
Found at i:38473257 original size:30 final size:31
Alignment explanation
Indices: 38473190--38473259 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
38473180 CCACCCTTGA
* * *
38473190 AATATTTGCACTATTAGTCCTTCAACTTTTT
1 AATATTTACACTATTAGTCCCTCAACATTTT
*
38473221 CATATTTACACT-TTAGTCCCTCAA-ATTTT
1 AATATTTACACTATTAGTCCCTCAACATTTT
38473250 AAGTATTTAC
1 AA-TATTTAC
38473260 TCTTGGACCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 5 0.15
30 18 0.55
31 10 0.30
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.46
Consensus pattern (31 bp):
AATATTTACACTATTAGTCCCTCAACATTTT
Found at i:38475334 original size:14 final size:14
Alignment explanation
Indices: 38475315--38475344 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38475305 TAAAATTTTC
38475315 TAACAAAACTTTAA
1 TAACAAAACTTTAA
38475329 TAACAAAACTTTAA
1 TAACAAAACTTTAA
38475343 TA
1 TA
38475345 CTAACTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (14 bp):
TAACAAAACTTTAA
Found at i:38482421 original size:31 final size:31
Alignment explanation
Indices: 38482383--38482452 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
38482373 ATAAAAAAAC
38482383 TTAATAACCTTGTCACTTAAATAAAAACTTT
1 TTAATAACCTTGTCACTTAAATAAAAACTTT
* *
38482414 TTAATAACCTTGTCACTTATATAAAAATTTT
1 TTAATAACCTTGTCACTTAAATAAAAACTTT
38482445 TTGAATAA
1 TT-AATAA
38482453 TCCAATCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 31 0.86
32 5 0.14
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.41
Consensus pattern (31 bp):
TTAATAACCTTGTCACTTAAATAAAAACTTT
Found at i:38482462 original size:32 final size:31
Alignment explanation
Indices: 38482383--38482468 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
38482373 ATAAAAAAAC
**
38482383 TTAATAACCTTGTCACTTAAATAAAAACTTT
1 TTAATAACCTAATCACTTAAATAAAAACTTT
** * *
38482414 TTAATAACCTTGTCACTTATATAAAAATTTT
1 TTAATAACCTAATCACTTAAATAAAAACTTT
38482445 TTGAATAATCC-AATCACTTTAAAT
1 TT-AATAA-CCTAATCAC-TTAAAT
38482469 TTCTAAATCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 31 0.66
32 9 0.19
33 7 0.15
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (31 bp):
TTAATAACCTAATCACTTAAATAAAAACTTT
Found at i:38485176 original size:25 final size:25
Alignment explanation
Indices: 38485147--38485202 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
38485137 AAGTTATAAG
38485147 TTGAT-TACAATATTTTGTATAGCA
1 TTGATGTACAATATTTTGTATAGCA
*
38485171 TATGATGTTCAATATTTTGTATAGCA
1 T-TGATGTACAATATTTTGTATAGCA
38485197 TTGATG
1 TTGATG
38485203 GCTTAGGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 1 0.03
25 9 0.31
26 19 0.66
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.46
Consensus pattern (25 bp):
TTGATGTACAATATTTTGTATAGCA
Found at i:38485183 original size:26 final size:25
Alignment explanation
Indices: 38485154--38485202 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
38485144 AAGTTGATTA
38485154 CAATATTTTGTATAGCATATGATGTT
1 CAATATTTTGTATAGCAT-TGATGTT
38485180 CAATATTTTGTATAGCATTGATG
1 CAATATTTTGTATAGCATTGATG
38485203 GCTTAGGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (25 bp):
CAATATTTTGTATAGCATTGATGTT
Found at i:38502086 original size:21 final size:21
Alignment explanation
Indices: 38502062--38502101 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38502052 CATAAATTCG
38502062 AAAATTGAT-AATAGTAAAAAT
1 AAAATT-ATAAATAGTAAAAAT
*
38502083 AAAATTATAAATATTAAAA
1 AAAATTATAAATAGTAAAA
38502102 TGAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAATTATAAATAGTAAAAAT
Found at i:38503178 original size:20 final size:18
Alignment explanation
Indices: 38503153--38503197 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
38503143 ATAGCAATAT
*
38503153 AGAAAGATTGCAAAGTAAAA
1 AGAAAGAATG-AAAG-AAAA
38503173 AGAAAGAATGAAAGAAAA
1 AGAAAGAATGAAAGAAAA
38503191 A-AAAGAA
1 AGAAAGAA
38503198 CACACAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 5 0.21
19 4 0.17
20 9 0.38
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
AGAAAGAATGAAAGAAAA
Found at i:38503191 original size:19 final size:20
Alignment explanation
Indices: 38503153--38503192 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
38503143 ATAGCAATAT
* *
38503153 AGAAAGATTGCAAAGTAAAA
1 AGAAAGAATGCAAAGAAAAA
38503173 AGAAAGAATG-AAAGAAAAA
1 AGAAAGAATGCAAAGAAAAA
38503192 A
1 A
38503193 AAGAACACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.68, C:0.03, G:0.20, T:0.10
Consensus pattern (20 bp):
AGAAAGAATGCAAAGAAAAA
Found at i:38506891 original size:3 final size:3
Alignment explanation
Indices: 38506883--38506918 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
38506873 ATTGATTGGC
38506883 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
38506919 CTTTGGAGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:38513074 original size:21 final size:21
Alignment explanation
Indices: 38513034--38513075 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38513024 GCAGGGGAAG
*
38513034 GAAAGAAAGAAAAAGAGAAAA
1 GAAAGAAAAAAAAAGAGAAAA
38513055 GAAAGAAGAAAAAAAG-GAAAA
1 GAAAGAA-AAAAAAAGAGAAAA
38513076 TTCAAGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
GAAAGAAAAAAAAAGAGAAAA
Found at i:38514143 original size:54 final size:57
Alignment explanation
Indices: 38514018--38514143 Score: 156
Period size: 54 Copynumber: 2.2 Consensus size: 57
38514008 TAAGTGTCAA
*
38514018 TTACTGTTACTGTTTCTGGATTCGTTCCGAAGAGGTACTCTGTACCTGACTATGACTG
1 TTACTGTTACTGTTTCTGGATTCGTTCCGAAGAGGTACTATGTACCTGAC-ATGACTG
*
38514076 TTACTGTTACTGTTTC-GGATTTGTTCC-AATGAGGTACTTTATGTACC-G-C-T-ACTG
1 TTACTGTTACTGTTTCTGGATTCGTTCCGAA-GAGGTAC--TATGTACCTGACATGACTG
38514130 TTACTGTTACTGTT
1 TTACTGTTACTGTT
38514144 ACTATTACCC
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
54 18 0.29
55 1 0.02
56 2 0.03
57 18 0.29
58 17 0.27
59 7 0.11
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (57 bp):
TTACTGTTACTGTTTCTGGATTCGTTCCGAAGAGGTACTATGTACCTGACATGACTG
Found at i:38524060 original size:10 final size:10
Alignment explanation
Indices: 38524044--38524100 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
38524034 AGTAATTTTA
38524044 ATTAAAAAGTT
1 ATTAAAAA-TT
38524055 -TTAAAAATT
1 ATTAAAAATT
*
38524064 ATTAAAAA-A
1 ATTAAAAATT
38524073 ATTTAGAAAATT
1 A-TTA-AAAATT
*
38524085 ATAAAAAATT
1 ATTAAAAATT
38524095 ATTAAA
1 ATTAAA
38524101 TATTGTAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
9 3 0.08
10 28 0.74
11 6 0.16
12 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:38524069 original size:20 final size:21
Alignment explanation
Indices: 38524044--38524092 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
38524034 AGTAATTTTA
**
38524044 ATTAAAAAGTTTTA-AAAATT
1 ATTAAAAAAATTTAGAAAATT
38524064 ATTAAAAAAATTTAGAAAATT
1 ATTAAAAAAATTTAGAAAATT
38524085 A-TAAAAAA
1 ATTAAAAAA
38524093 TTATTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
ATTAAAAAAATTTAGAAAATT
Found at i:38525997 original size:19 final size:19
Alignment explanation
Indices: 38525975--38526011 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
38525965 GCTTAGGATT
38525975 AATAATAT-ATATTAATAAC
1 AATAATATAAT-TTAATAAC
38525994 AATAATATAATTTAATAA
1 AATAATATAATTTAATAA
38526012 TATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAATATAATTTAATAAC
Found at i:38528999 original size:38 final size:38
Alignment explanation
Indices: 38528916--38529062 Score: 204
Period size: 39 Copynumber: 3.8 Consensus size: 38
38528906 AATCTATTAT
* *
38528916 AGATTCTAAGGTAATATAATGAGATCTAGCATTTGTTGC
1 AGATTCTAGGGTAATATAATGAGATCTAGC-CTTGTTGC
* * *
38528955 AGATTCTCGAGTAATATAACGAGATCTAGCCTTGTTGC
1 AGATTCTAGGGTAATATAATGAGATCTAGCCTTGTTGC
* *
38528993 AGATTCTAGGGGTAATATAATGAGATTTAGCCTTATTGC
1 AGATTCTA-GGGTAATATAATGAGATCTAGCCTTGTTGC
*
38529032 AGATACTAGGGTAATATAATGAGATCTAGCC
1 AGATTCTAGGGTAATATAATGAGATCTAGCC
38529063 CTTGCCGTGG
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
38 36 0.38
39 59 0.62
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (38 bp):
AGATTCTAGGGTAATATAATGAGATCTAGCCTTGTTGC
Found at i:38529056 original size:77 final size:77
Alignment explanation
Indices: 38528916--38529062 Score: 206
Period size: 77 Copynumber: 1.9 Consensus size: 77
38528906 AATCTATTAT
* * * *
38528916 AGATTCTAAGGTAATATAATGAGATCTAGCATTTGTTGCAGATTCTCGAGTAATATAACGAGATC
1 AGATTCTAAGGTAATATAATGAGATCTAGCACTTATTGCAGATACTAGAGTAATATAACGAGATC
38528981 TAGCCTTGTTGC
66 TAGCCTTGTTGC
* * * *
38528993 AGATTCTAGGGGTAATATAATGAGATTTAGC-CTTATTGCAGATACTAGGGTAATATAATGAGAT
1 AGATTCTA-AGGTAATATAATGAGATCTAGCACTTATTGCAGATACTAGAGTAATATAACGAGAT
38529057 CTAGCC
65 CTAGCC
38529063 CTTGCCGTGG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 41 0.67
78 20 0.33
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (77 bp):
AGATTCTAAGGTAATATAATGAGATCTAGCACTTATTGCAGATACTAGAGTAATATAACGAGATC
TAGCCTTGTTGC
Found at i:38529083 original size:77 final size:78
Alignment explanation
Indices: 38528916--38529088 Score: 199
Period size: 77 Copynumber: 2.2 Consensus size: 78
38528906 AATCTATTAT
* * * * *
38528916 AGATTCTA-AGGTAATATAATGAGATCTAGCATTTGTTGCAGATTCTCGAGTAATATAACGAGAT
1 AGATTCTAGGGGTAATATAATGAGATCTAGCACTTATTGCAGATACTAGAGTAATATAACGAGAT
**
38528980 CTAGCCTTGTTGC
66 CTAGCCTTGCCGC
* * *
38528993 AGATTCTAGGGGTAATATAATGAGATTTAGC-CTTATTGCAGATACTAGGGTAATATAATGAGAT
1 AGATTCTAGGGGTAATATAATGAGATCTAGCACTTATTGCAGATACTAGAGTAATATAACGAGAT
*
38529057 CTAGCCCTTGCCGT
66 CTAG-CCTTGCCGC
* *
38529071 GGATTCT-TGGGTAATATA
1 AGATTCTAGGGGTAATATA
38529089 TGACATAGGT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
77 49 0.60
78 32 0.40
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.34
Consensus pattern (78 bp):
AGATTCTAGGGGTAATATAATGAGATCTAGCACTTATTGCAGATACTAGAGTAATATAACGAGAT
CTAGCCTTGCCGC
Found at i:38530309 original size:22 final size:22
Alignment explanation
Indices: 38530253--38530300 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
38530243 ATCATAATCA
*
38530253 ATCCCTTAAAATC-TCATAAAAT
1 ATCCCATAAAATCGT-ATAAAAT
38530275 ATCCCATAAAATCGTATAAAAT
1 ATCCCATAAAATCGTATAAAAT
38530297 ATCC
1 ATCC
38530301 TAATCAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (22 bp):
ATCCCATAAAATCGTATAAAAT
Found at i:38535766 original size:17 final size:17
Alignment explanation
Indices: 38535744--38535777 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38535734 ATCCACTAAT
*
38535744 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
38535761 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
38535778 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:38540405 original size:17 final size:17
Alignment explanation
Indices: 38540383--38540416 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38540373 ATCCACTAAT
*
38540383 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
38540400 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
38540417 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:38541200 original size:2 final size:2
Alignment explanation
Indices: 38541193--38541223 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38541183 ATCCATTTGA
38541193 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38541224 TAAAAGACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38541545 original size:4 final size:4
Alignment explanation
Indices: 38541523--38541557 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
38541513 ACATTCAGGT
* *
38541523 ATAC AGAC ATAC ATGC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
38541558 ATATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:38545017 original size:21 final size:21
Alignment explanation
Indices: 38545004--38545057 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
38544994 AACAATAAAT
38545004 AATCGATTTAAAACAGAAAAG
1 AATCGATTTAAAACAGAAAAG
*
38545025 AATCGATTT-AAACAGAAAAC
1 AATCGATTTAAAACAGAAAAG
* *
38545045 AATCCATTCAAAA
1 AATCGATTTAAAA
38545058 TAAAGAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.20
Consensus pattern (21 bp):
AATCGATTTAAAACAGAAAAG
Found at i:38545043 original size:20 final size:19
Alignment explanation
Indices: 38544962--38545048 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 19
38544952 TAATCTATAG
*
38544962 AGAATCGATTTAAATCAAGA
1 AGAATCGATTTAAA-CAAAA
* * *
38544982 TGAATCAATTCAAACAATAA
1 AGAATCGATTTAAACAA-AA
*
38545002 ATAATCGATTTAAAACAGAAA
1 AGAATCGATTT-AAACA-AAA
38545023 AGAATCGATTTAAACAGAAA
1 AGAATCGATTTAAACA-AAA
*
38545043 ACAATC
1 AGAATC
38545049 CATTCAAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.06
20 33 0.61
21 17 0.31
22 1 0.02
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.23
Consensus pattern (19 bp):
AGAATCGATTTAAACAAAA
Found at i:38545670 original size:11 final size:11
Alignment explanation
Indices: 38545650--38545691 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
38545640 TAGAATATAC
* *
38545650 CCCATTCCTTT
1 CCCATACCTTA
*
38545661 CCCATACCTTG
1 CCCATACCTTA
38545672 CCCATACC-TA
1 CCCATACCTTA
38545682 CCCATACCTT
1 CCCATACCTT
38545692 GGAAAGGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.19, C:0.48, G:0.02, T:0.31
Consensus pattern (11 bp):
CCCATACCTTA
Found at i:38548972 original size:87 final size:88
Alignment explanation
Indices: 38548844--38549017 Score: 226
Period size: 87 Copynumber: 2.0 Consensus size: 88
38548834 TCAAGCCATT
* * ** * * * * *
38548844 GAATGGGATGAATATGAAGAACGTACATCTTGCTTGCCTAGCGTGGTT-AGATTACTATAGTTGG
1 GAATGGGATGAATATGAAGAACCTACACCCCGCTTACCTAGCATAGTTGA-ATCACTATAGTTAG
38548908 AT-ATAGAAGAATAAGATCACAAC
65 ATCATAGAAGAATAAGATCACAAC
* *
38548931 GAATGGGATGAATATGAAGAACCTACACCCCGCTTATCTAGCATAGTTGAATCATTATAGTTAGA
1 GAATGGGATGAATATGAAGAACCTACACCCCGCTTACCTAGCATAGTTGAATCACTATAGTTAGA
38548996 TCATAGAAGAATAAGATCACAA
66 TCATAGAAGAATAAGATCACAA
38549018 TGAAATCAGG
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
87 53 0.72
88 21 0.28
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (88 bp):
GAATGGGATGAATATGAAGAACCTACACCCCGCTTACCTAGCATAGTTGAATCACTATAGTTAGA
TCATAGAAGAATAAGATCACAAC
Found at i:38550575 original size:20 final size:20
Alignment explanation
Indices: 38550550--38550599 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
38550540 TGGCTTAAAA
38550550 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
38550570 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
38550587 GTGGTAGTGGATT
1 TTGGTAGTGGATT
38550600 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:38555619 original size:62 final size:62
Alignment explanation
Indices: 38555545--38555667 Score: 228
Period size: 62 Copynumber: 2.0 Consensus size: 62
38555535 ATAATAAAGG
38555545 CAACGACAACAAAGAAAAAAGCATAGCAATACTAGTTTCTGCTTGATTTTTCCTAGGAGGAT
1 CAACGACAACAAAGAAAAAAGCATAGCAATACTAGTTTCTGCTTGATTTTTCCTAGGAGGAT
* *
38555607 CAACGACAACAAAGAACAATGCATAGCAATACTAGTTTCTGCTTGATTTTTCCTAGGAGGA
1 CAACGACAACAAAGAAAAAAGCATAGCAATACTAGTTTCTGCTTGATTTTTCCTAGGAGGA
38555668 GGAAGAAATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (62 bp):
CAACGACAACAAAGAAAAAAGCATAGCAATACTAGTTTCTGCTTGATTTTTCCTAGGAGGAT
Found at i:38575864 original size:75 final size:75
Alignment explanation
Indices: 38575741--38575890 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
38575731 TTCCCTAAGG
* *
38575741 TAGTTGTTTTCAACATGATGTTCTCAAAGGTAGTTGTTTTAAAAAATACTCCTACTGATAGCAAT
1 TAGTTGTTTCCAACATGATGTTCTCAAAGGTAATTGTTTTAAAAAATACTCCTACTGATAGCAAT
*
38575806 ATTTTTTAGA
66 ATTTTATAGA
*
38575816 TAGTTGTTTCCAACGTGATGTTCTCAAAGGTAATTGTTTTAAAAAATACTCCTACTGATAGCAAT
1 TAGTTGTTTCCAACATGATGTTCTCAAAGGTAATTGTTTTAAAAAATACTCCTACTGATAGCAAT
38575881 ATTTTATAGA
66 ATTTTATAGA
38575891 ACTACCATTG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (75 bp):
TAGTTGTTTCCAACATGATGTTCTCAAAGGTAATTGTTTTAAAAAATACTCCTACTGATAGCAAT
ATTTTATAGA
Found at i:38576357 original size:7 final size:7
Alignment explanation
Indices: 38576345--38576370 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38576335 TGAACTTTTT
38576345 AATTTAA
1 AATTTAA
38576352 AATTTAA
1 AATTTAA
38576359 AATTTAA
1 AATTTAA
38576366 AATTT
1 AATTT
38576371 GTTTCATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AATTTAA
Found at i:38577743 original size:34 final size:34
Alignment explanation
Indices: 38577705--38577795 Score: 130
Period size: 34 Copynumber: 2.7 Consensus size: 34
38577695 AATATAAACT
*
38577705 TCATAATTCATATAAAAAGTTTTAACAATAACCA
1 TCATAATTCATATAAAAAATTTTAACAATAACCA
38577739 TCATAATTCATATAAAAAATTTTAACAATAACCA
1 TCATAATTCATATAAAAAATTTTAACAATAACCA
* * * *
38577773 TTA-AATACATATCAAATATTTTA
1 TCATAATTCATATAAAAAATTTTA
38577796 TAAACTGCTA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
33 17 0.33
34 35 0.67
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.35
Consensus pattern (34 bp):
TCATAATTCATATAAAAAATTTTAACAATAACCA
Found at i:38577851 original size:30 final size:30
Alignment explanation
Indices: 38577806--38577871 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
38577796 TAAACTGCTA
* *
38577806 CATTAATATAGTATCTAAATGTTATTA-CATT
1 CATT-ATATAATATCTAAATGATA-TAGCATT
38577837 CATTATATAATATCTAAATGATATAGCATT
1 CATTATATAATATCTAAATGATATAGCATT
38577867 CATTA
1 CATTA
38577872 CAAGACGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 2 0.06
30 26 0.81
31 4 0.12
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (30 bp):
CATTATATAATATCTAAATGATATAGCATT
Found at i:38580090 original size:18 final size:18
Alignment explanation
Indices: 38580063--38580155 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
38580053 TACGACCGTT
38580063 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
38580081 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
38580099 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
38580117 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
38580135 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
38580153 TAC
1 TAC
38580156 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:38588446 original size:10 final size:10
Alignment explanation
Indices: 38588427--38588458 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
38588417 TTTTAGGATT
38588427 TTAT-TTTAA
1 TTATCTTTAA
38588436 TTATCTTTAA
1 TTATCTTTAA
38588446 TTATCTTTAA
1 TTATCTTTAA
38588456 TTA
1 TTA
38588459 ATTGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:38592187 original size:5 final size:5
Alignment explanation
Indices: 38592177--38592226 Score: 59
Period size: 5 Copynumber: 10.4 Consensus size: 5
38592167 GCAACCCAAT
* * *
38592177 TTTTA TTTTA TTTTA TTTTT TTTTT TTTTA TTTTA TCTTA --TTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
38592225 TT
1 TT
38592227 ATTTATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
3 3 0.08
5 37 0.93
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:38592231 original size:20 final size:19
Alignment explanation
Indices: 38592175--38592233 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 19
38592165 AGGCAACCCA
38592175 ATTT-TTATTTTA-T-TTT
1 ATTTATTATTTTATTATTT
* * *
38592191 ATTTTTTTTTTTTTTATTTT
1 ATTTATTATTTTATTA-TTT
38592211 ATCTTATTATTTTATTATTT
1 AT-TTATTATTTTATTATTT
38592231 ATT
1 ATT
38592234 ATTTTCAGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.12
17 6 0.18
18 1 0.03
19 1 0.03
20 10 0.30
21 11 0.33
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.80
Consensus pattern (19 bp):
ATTTATTATTTTATTATTT
Found at i:38595884 original size:41 final size:42
Alignment explanation
Indices: 38595839--38595918 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
38595829 GTGCAGGGGA
*
38595839 CACACGGCCTAA-CAACATGCCCGTGTG-CAAGCCGTGTGTTT
1 CACACGGCCTAATC-ACACGCCCGTGTGCCAAGCCGTGTGTTT
* *
38595880 CACACGGTCTAATCACACGCCCGTGTGCCAGGCCGTGTG
1 CACACGGCCTAATCACACGCCCGTGTGCCAAGCCGTGTG
38595919 GACTCAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 23 0.68
42 11 0.32
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.20
Consensus pattern (42 bp):
CACACGGCCTAATCACACGCCCGTGTGCCAAGCCGTGTGTTT
Found at i:38598743 original size:48 final size:48
Alignment explanation
Indices: 38598679--38598826 Score: 224
Period size: 48 Copynumber: 3.1 Consensus size: 48
38598669 TTGATGTACA
*
38598679 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTAAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
38598727 AGATATATATATGTGGTAAAGTCGAAAGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
** ** *
38598775 AGCCATGCATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
38598823 AGAT
1 AGAT
38598827 GTGTATATAT
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (48 bp):
AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:38609710 original size:29 final size:30
Alignment explanation
Indices: 38609658--38609715 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
38609648 TGATGAATAG
*
38609658 ATATGTCCCTTCGAAATTAATGCATGTGCA
1 ATATGTCCCTTAGAAATTAATGCATGTGCA
*
38609688 ATATGTCCC-TAGGAATTAATGCATGTGC
1 ATATGTCCCTTAGAAATTAATGCATGTGC
38609716 CATGTGCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (30 bp):
ATATGTCCCTTAGAAATTAATGCATGTGCA
Found at i:38611176 original size:17 final size:17
Alignment explanation
Indices: 38611154--38611189 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
38611144 TAAATTTGGG
38611154 TTGAGACAA-TAATTTAA
1 TTGAGA-AATTAATTTAA
38611171 TTGAGAAATTAATTTAA
1 TTGAGAAATTAATTTAA
38611188 TT
1 TT
38611190 AAGTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (17 bp):
TTGAGAAATTAATTTAA
Found at i:38611191 original size:9 final size:9
Alignment explanation
Indices: 38611177--38611209 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
38611167 TTAATTGAGA
38611177 AATTAATTT
1 AATTAATTT
*
38611186 AATTAAGTT
1 AATTAATTT
38611195 AATTAA-TT
1 AATTAATTT
38611203 AATTAAT
1 AATTAAT
38611210 ATTTTGGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (9 bp):
AATTAATTT
Found at i:38615365 original size:131 final size:131
Alignment explanation
Indices: 38615185--38615427 Score: 371
Period size: 131 Copynumber: 1.9 Consensus size: 131
38615175 AAATTCTTTA
* *
38615185 AAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGAAATCGTACCCTATCGTGCT-GAGTTGCA
1 AAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGAAATAGTACCCTATCATGCTAG-GTTGCA
*
38615249 ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTCGAAATTTCACTCATGTCTCTAAAGATTTT
65 ATTTCCCGTTTGTTCAAAATAATCAAATATTCCTTCGAAATTTCACTCATGTCTCTAAAGATTTT
38615314 TC
130 TC
** * * * * *
38615316 AAAACGAAGGTGATGTTTGATGTTTGGCAATTCGGGGAATAGTGCCCTATCATGCTAGGTTTCGA
1 AAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGAAATAGTACCCTATCATGCTAGGTTGCAA
*
38615381 TTTCCCGTTTGTTCAAAATAATCAAATATTCCTTTGAAATTTCACTC
66 TTTCCCGTTTGTTCAAAATAATCAAATATTCCTTCGAAATTTCACTC
38615428 GTGTTTTCTA
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
131 99 0.99
132 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (131 bp):
AAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGAAATAGTACCCTATCATGCTAGGTTGCAA
TTTCCCGTTTGTTCAAAATAATCAAATATTCCTTCGAAATTTCACTCATGTCTCTAAAGATTTTT
C
Found at i:38627697 original size:3 final size:3
Alignment explanation
Indices: 38627673--38627816 Score: 50
Period size: 3 Copynumber: 48.0 Consensus size: 3
38627663 ATATGTATAC
* *
38627673 TAT TA- TAT T-T TAT TAC TAT TAT TAT TA- TATT TAT TATT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT
* * * * * *
38627717 CAT TAG TAT TAG TAT TAT TTT TACT TAA TACT TA- TAT ATAT TAT ATAG
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT -TAT TAT -TAT
* * * * * *
38627765 TAT TAT TAA TAGT T-T T-T TTT TGT TAT TAT TAT TTT TCT TAA TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38627809 TA- TAT TAT
1 TAT TAT TAT
38627817 GTATATATTC
Statistics
Matches: 103, Mismatches: 25, Indels: 26
0.67 0.16 0.17
Matches are distributed among these distances:
2 14 0.14
3 73 0.71
4 16 0.16
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:38627700 original size:22 final size:19
Alignment explanation
Indices: 38627673--38627715 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 19
38627663 ATATGTATAC
38627673 TATTATATTTTATTACTATTAT
1 TATTATA-TTTATTA-T-TTAT
38627695 TATTATATTTATTATTTAT
1 TATTATATTTATTATTTAT
38627714 TA
1 TA
38627716 GCATTAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 7 0.33
22 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTATATTTATTATTTAT
Found at i:38627721 original size:22 final size:22
Alignment explanation
Indices: 38627674--38627736 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 22
38627664 TATGTATACT
* **
38627674 ATTATATTTTATTA-CTATTATT
1 ATTATA-TTTATTATTTATTAGC
38627696 ATTATATTTATTATTTATTAGC
1 ATTATATTTATTATTTATTAGC
38627718 ATTAGTATTAGTATTATTT
1 ATTA-TATT--TATTATTT
38627737 TTACTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 7 0.21
22 15 0.44
23 4 0.12
25 8 0.24
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTATATTTATTATTTATTAGC
Found at i:38628269 original size:15 final size:15
Alignment explanation
Indices: 38628249--38628282 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
38628239 TACTTATATG
38628249 TATATTTTTTAATAC
1 TATATTTTTTAATAC
38628264 TATA-TTTTTAATAC
1 TATATTTTTTAATAC
*
38628278 CATAT
1 TATAT
38628283 ATATTGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATTTTTTAATAC
Found at i:38628294 original size:27 final size:26
Alignment explanation
Indices: 38628264--38628337 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 26
38628254 TTTTTAATAC
38628264 TATATTTTTAATACCATATATATTG-TG
1 TATATTTTTAATA-C-TATATATTGATG
*
38628291 TATATTCTTAATACTATATATTGTATG
1 TATATTTTTAATACTATATATTG-ATG
*
38628318 TATTTTTTTAATAACTATAT
1 TATATTTTTAAT-ACTATAT
38628338 TATATGTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 9 0.22
26 1 0.02
27 24 0.59
28 7 0.17
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (26 bp):
TATATTTTTAATACTATATATTGATG
Found at i:38628374 original size:20 final size:19
Alignment explanation
Indices: 38628349--38628386 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
38628339 ATATGTATAT
38628349 ATATTATGTACGTATTTTTA
1 ATATTAT-TACGTATTTTTA
*
38628369 ATATTATTATGTATTTTT
1 ATATTATTACGTATTTTT
38628387 TAAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (19 bp):
ATATTATTACGTATTTTTA
Found at i:38628387 original size:20 final size:20
Alignment explanation
Indices: 38628349--38628511 Score: 73
Period size: 21 Copynumber: 7.5 Consensus size: 20
38628339 ATATGTATAT
*
38628349 ATATTATGTACGTA-TTTTTA
1 ATATTAT-TATGTATTTTTTA
38628369 ATATTATTATGTATTTTTTA
1 ATATTATTATGTATTTTTTA
*
38628389 A-ATATATATGTGTATATTTATGTA
1 ATAT-TAT-TATGTAT-TTT-T-TA
*
38628413 GTATTATTAATAGT-TGTTTTTA
1 ATATTATT-AT-GTAT-TTTTTA
*
38628435 ATATTATTAT-TATTTCTAATA
1 ATATTATTATGTATTT-T-TTA
*
38628456 TGTATATATTATGTATATATTTTTA
1 -ATAT-TATTATG--TAT-TTTTTA
* *
38628481 ATACTATGTATATATTTTTTA
1 ATATTAT-TATGTATTTTTTA
*
38628502 ATACTATTAT
1 ATATTATTAT
38628512 TATGTTTATA
Statistics
Matches: 112, Mismatches: 12, Indels: 38
0.69 0.07 0.23
Matches are distributed among these distances:
19 10 0.09
20 22 0.20
21 23 0.21
22 18 0.16
23 12 0.11
24 15 0.13
25 6 0.05
26 4 0.04
27 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (20 bp):
ATATTATTATGTATTTTTTA
Found at i:38628470 original size:11 final size:11
Alignment explanation
Indices: 38628454--38628496 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
38628444 TTATTTCTAA
38628454 TATGTATATAT
1 TATGTATATAT
38628465 TATGTATATAT
1 TATGTATATAT
* *
38628476 T-TTTA-ATAC
1 TATGTATATAT
38628485 TATGTATATAT
1 TATGTATATAT
38628496 T
1 T
38628497 TTTTAATACT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 4 0.15
10 6 0.23
11 16 0.62
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (11 bp):
TATGTATATAT
Found at i:38628479 original size:46 final size:47
Alignment explanation
Indices: 38628429--38628530 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 47
38628419 TTAATAGTTG
*
38628429 TTTTTAATATTAT-TAT-TA-TTTCTAATATGTATATATTATGTATATA
1 TTTTTAATATTATGTATATATTTTCTAATA-CTAT-TATTATGTATATA
* * *
38628475 TTTTTAATACTATGTATATATTTTTTAATACTATTATTATGTTTATA
1 TTTTTAATATTATGTATATATTTTCTAATACTATTATTATGTATATA
38628522 -TTTTAATAT
1 TTTTTAATAT
38628531 ATATACCTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
46 20 0.42
47 15 0.31
48 5 0.10
49 8 0.17
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (47 bp):
TTTTTAATATTATGTATATATTTTCTAATACTATTATTATGTATATA
Found at i:38639415 original size:55 final size:55
Alignment explanation
Indices: 38639349--38639459 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
38639339 ATAGGTTCAA
*
38639349 ACTCGATATGACCAGCTAAACCTTATCGAAGAAAAACGTTTGAAGACAATCTGTC
1 ACTCGATATGACCAGCTAAACCTTATCAAAGAAAAACGTTTGAAGACAATCTGTC
38639404 ACTCGATATGACCAGCTAAACCTTATCAAAGAAAAACGTTTGAAGACAATCTGTC
1 ACTCGATATGACCAGCTAAACCTTATCAAAGAAAAACGTTTGAAGACAATCTGTC
38639459 A
1 A
38639460 TGGACAGATG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (55 bp):
ACTCGATATGACCAGCTAAACCTTATCAAAGAAAAACGTTTGAAGACAATCTGTC
Found at i:38640900 original size:161 final size:156
Alignment explanation
Indices: 38640588--38640901 Score: 459
Period size: 161 Copynumber: 2.0 Consensus size: 156
38640578 TCTGTCTTTC
*
38640588 AAAAATCAACTCATATTGCGAGAGGTGATTTGAACCTCGGACATGCTGAGGTATTTTCAATTTCT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCTGAGGTATTTTCAATTTCT
** * * *
38640653 ATTTTTTATTTTTGTTTTCAAAAATCAACTCATATTGCGAGGGTGAGTTGAGCCTCAAGACATGT
66 ATTTTTTATTTCCGTTGTCAAAAATCAACTCATATTGCGAAGGTGAGTTGAGCCTCAAGACACGT
38640718 TGAAGTAATTTTAATTTCTGTTCAAA
131 TGAAGTAATTTTAATTTCTGTTCAAA
* *
38640744 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGGTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGG---ACATGCTGAGGTATTTTCAATT
* *
38640809 TCTGTTTTTTAATTTCCGTTCGTC-AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGG
63 TCTATTTTTT-ATTTCCGTT-GTCAAAAATCAACTCATATTGCG-AAGGTGAGTTGAGCCTCAAG
* *
38640873 ACGCGTTGAGGTAATTTTAATTTCTGTTC
125 ACACGTTGAAGTAATTTTAATTTCTGTTC
38640902 TTCAAATTAT
Statistics
Matches: 140, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
156 38 0.27
159 30 0.21
160 26 0.19
161 46 0.33
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (156 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCGGACATGCTGAGGTATTTTCAATTTCT
ATTTTTTATTTCCGTTGTCAAAAATCAACTCATATTGCGAAGGTGAGTTGAGCCTCAAGACACGT
TGAAGTAATTTTAATTTCTGTTCAAA
Found at i:38640925 original size:88 final size:87
Alignment explanation
Indices: 38640737--38640993 Score: 304
Period size: 88 Copynumber: 2.9 Consensus size: 87
38640727 TTTAATTTCT
* *
38640737 GTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGGTGAGGT-A
1 GTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAA
* * *
38640800 TTTTCAATTTCTGTTTTTTAATTTCC
63 TTTT-AATTTCTGTTTTTCAAATTAC
*** * * *
38640826 GTTC-GTCAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGACGCGTTGAGGTAATTT
1 GTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
* *
38640890 TAATTTCTGTTCTTCAAATTAT
66 TAATTTCTGTTTTTCAAATTAC
* * *
38640912 GTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACACGCTAAGGTATTT
1 G-TTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT
38640977 TTAATTTCTGTTTTTCA
65 TTAATTTCTGTTTTTCA
38640994 TCAAAATCAA
Statistics
Matches: 142, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
86 26 0.18
87 8 0.06
88 102 0.72
89 6 0.04
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (87 bp):
GTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
TAATTTCTGTTTTTCAAATTAC
Found at i:38642173 original size:7 final size:8
Alignment explanation
Indices: 38642156--38642184 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
38642146 TTATTTAACT
38642156 AAAAATAA
1 AAAAATAA
38642164 AAAAATAA
1 AAAAATAA
38642172 AAAAATAA
1 AAAAATAA
38642180 AAAAA
1 AAAAA
38642185 GTTTTACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAATAA
Found at i:38642750 original size:3 final size:3
Alignment explanation
Indices: 38642726--38642862 Score: 50
Period size: 3 Copynumber: 45.0 Consensus size: 3
38642716 ATATGTATAC
* *
38642726 TAT TA- TAT T-T TAT TAC TAT TAT TAT TA- TATT TAT TATT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT
* * * * *
38642770 CAT TAG TAT TAT TTT TACT TAA TACT TA- TAT ATAT TAT ATAG TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT -TAT TAT -TAT TAT TAT
* * * * * * *
38642818 TAA TAGT TTT TTT TGT TAT TAT TAT TTT TCT TAA TAT TA- TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38642863 GTATATATTC
Statistics
Matches: 98, Mismatches: 24, Indels: 24
0.67 0.16 0.16
Matches are distributed among these distances:
2 10 0.10
3 72 0.73
4 16 0.16
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:38642753 original size:22 final size:19
Alignment explanation
Indices: 38642726--38642768 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 19
38642716 ATATGTATAC
38642726 TATTATATTTTATTACTATTAT
1 TATTATA-TTTATTA-T-TTAT
38642748 TATTATATTTATTATTTAT
1 TATTATATTTATTATTTAT
38642767 TA
1 TA
38642769 GCATTAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 7 0.33
22 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTATATTTATTATTTAT
Found at i:38642774 original size:22 final size:22
Alignment explanation
Indices: 38642727--38642786 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
38642717 TATGTATACT
* **
38642727 ATTATATTTTATTA-CTATTATT
1 ATTATA-TTTATTATTTATTAGC
38642749 ATTATATTTATTATTTATTAGC
1 ATTATATTTATTATTTATTAGC
38642771 ATTAGTA-TTATT-TTTA
1 ATTA-TATTTATTATTTA
38642787 CTTAATACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 11 0.33
22 20 0.61
23 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (22 bp):
ATTATATTTATTATTTATTAGC
Found at i:38642962 original size:24 final size:25
Alignment explanation
Indices: 38642917--38642979 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
38642907 TACGTATATA
*
38642917 TATACATTTCTTATACTATATTATG
1 TATACATTTCTTATAATATATTATG
38642942 TATACA-TTCTTA-AATATTATTA-G
1 TATACATTTCTTATAATA-TATTATG
*
38642965 TTATATATTT-TTATA
1 -TATACATTTCTTATA
38642980 TTATCATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
23 4 0.12
24 19 0.59
25 9 0.28
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (25 bp):
TATACATTTCTTATAATATATTATG
Found at i:38643317 original size:15 final size:15
Alignment explanation
Indices: 38643297--38643330 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
38643287 TACTTATATG
38643297 TATATTTTTTAATAC
1 TATATTTTTTAATAC
38643312 TATA-TTTTTAATAC
1 TATATTTTTTAATAC
*
38643326 CATAT
1 TATAT
38643331 ATATTGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATTTTTTAATAC
Found at i:38643431 original size:20 final size:21
Alignment explanation
Indices: 38643406--38643457 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
38643396 ATATGTATAT
38643406 ATATTATGTACGTA-TTTTTA
1 ATATTATGTACGTATTTTTTA
*
38643426 ATATTAT-TATGTATTTTTTA
1 ATATTATGTACGTATTTTTTA
38643446 ATATATATGTAC
1 ATAT-TATGTAC
38643458 ATTTATGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 17 0.63
21 3 0.11
22 2 0.07
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (21 bp):
ATATTATGTACGTATTTTTTA
Found at i:38643454 original size:18 final size:20
Alignment explanation
Indices: 38643406--38643503 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 20
38643396 ATATGTATAT
*
38643406 ATATTATGTACGTA-TTTTTA
1 ATATTAT-TATGTATTTTTTA
38643426 ATATTATTATGTATTTTTTA
1 ATATTATTATGTATTTTTTA
*
38643446 ATA-TA-TATGTACATTTATGTA
1 ATATTATTATGT--ATTT-TTTA
*
38643467 GTATTATTAATAGT-TGTTTTTA
1 ATATTATT-AT-GTAT-TTTTTA
38643489 ATATTATTAT-TATTT
1 ATATTATTATGTATTT
38643504 CTAATATGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
18 5 0.08
19 10 0.16
20 21 0.33
21 7 0.11
22 13 0.21
23 3 0.05
24 2 0.03
25 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (20 bp):
ATATTATTATGTATTTTTTA
Found at i:38643510 original size:18 final size:17
Alignment explanation
Indices: 38643484--38643546 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 17
38643474 TAATAGTTGT
38643484 TTTTAATATTATTATTA
1 TTTTAATATTATTATTA
38643501 TTTCTAATATGTA-TA-TA
1 TTT-TAATAT-TATTATTA
*
38643518 TTTTTAATACTATGTATATA
1 -TTTTAATATTAT-TAT-TA
38643538 TTTTAATAT
1 TTTTAATAT
38643547 ATATACGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
16 2 0.05
17 10 0.27
18 13 0.35
19 10 0.27
20 2 0.05
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTAATATTATTATTA
Found at i:38643531 original size:20 final size:19
Alignment explanation
Indices: 38643508--38643545 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
38643498 TTATTTCTAA
38643508 TATGTATATATTTTTAATAC
1 TATGTATATA-TTTTAATAC
38643528 TATGTATATATTTTAATA
1 TATGTATATATTTTAATA
38643546 TATATACGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
TATGTATATATTTTAATAC
Found at i:38643634 original size:116 final size:115
Alignment explanation
Indices: 38643507--38643866 Score: 321
Period size: 113 Copynumber: 3.1 Consensus size: 115
38643497 ATTATTTCTA
38643507 ATATGTATATATTTTTAATACTATGTATATATTTTAATATATATACGTATGTATATAGATAAAAT
1 ATATGTATATA-TTTTAATACTATGTATATATTTTAATATATATACGTATGTATATAGATAAAAT
38643572 TATTAGTGATTTTTTTAATATCATGTTTCCGTCACTTTACTAACTATTATT
65 TATTAGTGATTTTTTTAATATCATGTTTCCGTCACTTTACTAACTATTATT
* * * * * *** *
38643623 ATATGTATATATATTATGTACGTATTTTTAATATTATT-ATGTAT-TTTTTA-ATATATATG-TA
1 ATATGTATATATTTTA-ATAC-TATGTAT-ATATT-TTAATATATATACGTATGTATATA-GATA
* * * *** * * * ** *
38643684 CATTTATGTAGT-A--TTATTAATAGT--TGTTTTTAAT-ATTATTA-TTATTTCTAAT
61 AAATTAT-TAGTGATTTTTTTAATA-TCATG-TTTCCGTCACT-TTACTAACTATTATT
* * *
38643736 ATGTATATATT-TTTAATACTATGTATATATTTTAATATATATACGTATGTATATAGATAAAATT
1 ATATGTATATATTTTAATACTATGTATATATTTTAATATATATACGTATGTATATAGATAAAATT
38643800 ATTAGTGATTTTTTTAATATCATGTTTCCGTCACTTTACTAACTATTATT
66 ATTAGTGATTTTTTTAATATCATGTTTCCGTCACTTTACTAACTATTATT
38643850 ATATGTATATATATTTA
1 ATATGTATATAT-TTTA
38643867 TTGTTTTTAT
Statistics
Matches: 174, Mismatches: 48, Indels: 44
0.65 0.18 0.17
Matches are distributed among these distances:
108 2 0.01
109 10 0.06
110 13 0.07
111 17 0.10
112 4 0.02
113 33 0.19
114 33 0.19
115 5 0.03
116 32 0.18
117 13 0.07
118 10 0.06
119 2 0.01
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (115 bp):
ATATGTATATATTTTAATACTATGTATATATTTTAATATATATACGTATGTATATAGATAAAATT
ATTAGTGATTTTTTTAATATCATGTTTCCGTCACTTTACTAACTATTATT
Found at i:38643635 original size:227 final size:227
Alignment explanation
Indices: 38643381--38643864 Score: 952
Period size: 227 Copynumber: 2.1 Consensus size: 227
38643371 TATGTATTTT
*
38643381 TTTAATAACTA-TATTATATGTATATATATTATGTACGTATTTTTAATATTATTATGTATTTTTT
1 TTTACTAACTATTATTATATGTATATATATTATGTACGTATTTTTAATATTATTATGTATTTTTT
38643445 AATATATATGTACATTTATGTAGTATTATTAATAGTTGTTTTTAATATTATTATTATTTCTAATA
66 AATATATATGTACATTTATGTAGTATTATTAATAGTTGTTTTTAATATTATTATTATTTCTAATA
38643510 TGTATATATTTTTAATACTATGTATATATTTTAATATATATACGTATGTATATAGATAAAATTAT
131 TGTATATATTTTTAATACTATGTATATATTTTAATATATATACGTATGTATATAGATAAAATTAT
38643575 TAGTGATTTTTTTAATATCATGTTTCCGTCAC
196 TAGTGATTTTTTTAATATCATGTTTCCGTCAC
38643607 TTTACTAACTATTATTATATGTATATATATTATGTACGTATTTTTAATATTATTATGTATTTTTT
1 TTTACTAACTATTATTATATGTATATATATTATGTACGTATTTTTAATATTATTATGTATTTTTT
38643672 AATATATATGTACATTTATGTAGTATTATTAATAGTTGTTTTTAATATTATTATTATTTCTAATA
66 AATATATATGTACATTTATGTAGTATTATTAATAGTTGTTTTTAATATTATTATTATTTCTAATA
38643737 TGTATATATTTTTAATACTATGTATATATTTTAATATATATACGTATGTATATAGATAAAATTAT
131 TGTATATATTTTTAATACTATGTATATATTTTAATATATATACGTATGTATATAGATAAAATTAT
38643802 TAGTGATTTTTTTAATATCATGTTTCCGTCAC
196 TAGTGATTTTTTTAATATCATGTTTCCGTCAC
38643834 TTTACTAACTATTATTATATGTATATATATT
1 TTTACTAACTATTATTATATGTATATATATT
38643865 TATTGTTTTT
Statistics
Matches: 256, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
226 10 0.04
227 246 0.96
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (227 bp):
TTTACTAACTATTATTATATGTATATATATTATGTACGTATTTTTAATATTATTATGTATTTTTT
AATATATATGTACATTTATGTAGTATTATTAATAGTTGTTTTTAATATTATTATTATTTCTAATA
TGTATATATTTTTAATACTATGTATATATTTTAATATATATACGTATGTATATAGATAAAATTAT
TAGTGATTTTTTTAATATCATGTTTCCGTCAC
Found at i:38643658 original size:20 final size:21
Alignment explanation
Indices: 38643633--38643684 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
38643623 ATATGTATAT
38643633 ATATTATGTACGTA-TTTTTA
1 ATATTATGTACGTATTTTTTA
*
38643653 ATATTAT-TATGTATTTTTTA
1 ATATTATGTACGTATTTTTTA
38643673 ATATATATGTAC
1 ATAT-TATGTAC
38643685 ATTTATGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 17 0.63
21 3 0.11
22 2 0.07
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (21 bp):
ATATTATGTACGTATTTTTTA
Found at i:38643681 original size:18 final size:20
Alignment explanation
Indices: 38643633--38643730 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 20
38643623 ATATGTATAT
*
38643633 ATATTATGTACGTA-TTTTTA
1 ATATTAT-TATGTATTTTTTA
38643653 ATATTATTATGTATTTTTTA
1 ATATTATTATGTATTTTTTA
*
38643673 ATA-TA-TATGTACATTTATGTA
1 ATATTATTATGT--ATTT-TTTA
*
38643694 GTATTATTAATAGT-TGTTTTTA
1 ATATTATT-AT-GTAT-TTTTTA
38643716 ATATTATTAT-TATTT
1 ATATTATTATGTATTT
38643731 CTAATATGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
18 5 0.08
19 10 0.16
20 21 0.33
21 7 0.11
22 13 0.21
23 3 0.05
24 2 0.03
25 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (20 bp):
ATATTATTATGTATTTTTTA
Found at i:38643737 original size:18 final size:17
Alignment explanation
Indices: 38643711--38643773 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 17
38643701 TAATAGTTGT
38643711 TTTTAATATTATTATTA
1 TTTTAATATTATTATTA
38643728 TTTCTAATATGTA-TA-TA
1 TTT-TAATAT-TATTATTA
*
38643745 TTTTTAATACTATGTATATA
1 -TTTTAATATTAT-TAT-TA
38643765 TTTTAATAT
1 TTTTAATAT
38643774 ATATACGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
16 2 0.05
17 10 0.27
18 13 0.35
19 10 0.27
20 2 0.05
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTAATATTATTATTA
Found at i:38643758 original size:20 final size:19
Alignment explanation
Indices: 38643735--38643772 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
38643725 TTATTTCTAA
38643735 TATGTATATATTTTTAATAC
1 TATGTATATA-TTTTAATAC
38643755 TATGTATATATTTTAATA
1 TATGTATATATTTTAATA
38643773 TATATACGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
TATGTATATATTTTAATAC
Found at i:38645358 original size:3 final size:3
Alignment explanation
Indices: 38645346--38645418 Score: 73
Period size: 3 Copynumber: 25.7 Consensus size: 3
38645336 GCATCTCCAT
* * *
38645346 TTC TTC -TC TTC TTT TTC -TC TTC TTC TTC -TC TTC TTC TTC TAC TTG
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
38645391 TTT TTC ATC TTC TT- TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
38645419 TTACTATTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
2 8 0.14
3 49 0.86
ACGTcount: A:0.03, C:0.29, G:0.01, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:38645363 original size:11 final size:11
Alignment explanation
Indices: 38645349--38645415 Score: 73
Period size: 11 Copynumber: 5.9 Consensus size: 11
38645339 TCTCCATTTC
38645349 TTCTCTTCTTT
1 TTCTCTTCTTT
*
38645360 TTCTCTTCTTC
1 TTCTCTTCTTT
*
38645371 TTCTCTTCTTC
1 TTCTCTTCTTT
*
38645382 TTCTACTTGTTT
1 TTCT-CTTCTTT
38645394 TTCATCTTC-TT
1 TTC-TCTTCTTT
38645405 TTCTTCTTCTT
1 TTC-TCTTCTT
38645416 CTTTTACTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
11 35 0.73
12 12 0.25
13 1 0.02
ACGTcount: A:0.03, C:0.28, G:0.01, T:0.67
Consensus pattern (11 bp):
TTCTCTTCTTT
Found at i:38645369 original size:14 final size:15
Alignment explanation
Indices: 38645345--38645420 Score: 79
Period size: 14 Copynumber: 5.1 Consensus size: 15
38645335 GGCATCTCCA
38645345 TTTCTTC-TCTTCTT
1 TTTCTTCTTCTTCTT
38645359 TTTC-TCTTCTTCTT
1 TTTCTTCTTCTTCTT
*
38645373 CTCTTCTTCTTCTACTT
1 -T-TTCTTCTTCTTCTT
*
38645390 GTTT-TTCATCTTC-T
1 -TTTCTTCTTCTTCTT
38645404 TTTCTTCTTCTTCTT
1 TTTCTTCTTCTTCTT
38645419 TT
1 TT
38645421 ACTATTTTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
13 5 0.10
14 20 0.39
15 11 0.22
16 5 0.10
17 10 0.20
ACGTcount: A:0.03, C:0.28, G:0.01, T:0.68
Consensus pattern (15 bp):
TTTCTTCTTCTTCTT
Found at i:38646523 original size:29 final size:30
Alignment explanation
Indices: 38646491--38646551 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
38646481 AAGTTATAAC
*
38646491 AAATA-TTAAATTTTAATAAAAATATAAAA
1 AAATATTTAAATTTTAATAAAAAAATAAAA
* *
38646520 AAATATTTAAATTTTATTAAAAAAATTAAA
1 AAATATTTAAATTTTAATAAAAAAATAAAA
38646550 AA
1 AA
38646552 TAAAAACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATATTTAAATTTTAATAAAAAAATAAAA
Found at i:38646583 original size:20 final size:19
Alignment explanation
Indices: 38646551--38646606 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
38646541 AAAATTAAAA
*
38646551 ATAAAAA-CATAAAATTTT
1 ATAAAAATCATAAAAATTT
38646569 ATAAAAATCATTAAAAATTT
1 ATAAAAATCA-TAAAAATTT
38646589 ATAAAAATGCATCAAAAA
1 ATAAAAAT-CAT-AAAAA
38646607 GGCCTTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 7 0.21
19 2 0.06
20 17 0.52
21 7 0.21
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAAAATCATAAAAATTT
Found at i:38650203 original size:16 final size:17
Alignment explanation
Indices: 38650182--38650214 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38650172 ATGATGGTGC
38650182 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
38650198 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
38650215 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Done.