Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 9 of 20
Found at i:3024032 original size:6 final size:6
Alignment explanation
Indices: 3024015--3024044 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
3024005 TTACACTTCA
3024015 ATAATAT ATAATT ATAATT ATAATT ATAAT
1 ATAAT-T ATAATT ATAATT ATAATT ATAAT
3024045 ATTTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATAATT
Found at i:3024038 original size:12 final size:13
Alignment explanation
Indices: 3024015--3024046 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
3024005 TTACACTTCA
3024015 ATAATATATAATT
1 ATAATATATAATT
3024028 ATAAT-TATAATT
1 ATAATATATAATT
3024040 ATAATAT
1 ATAATAT
3024047 TTTTTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAATATATAATT
Found at i:3024643 original size:15 final size:15
Alignment explanation
Indices: 3024619--3024657 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3024609 TAATATTATA
*
3024619 ATTAAAATAAAAGAT
1 ATTAATATAAAAGAT
*
3024634 ATTAATATAAAATAT
1 ATTAATATAAAAGAT
3024649 A-TAATATAA
1 ATTAATATAA
3024658 GAATAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
ATTAATATAAAAGAT
Found at i:3024652 original size:33 final size:33
Alignment explanation
Indices: 3024610--3024691 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 33
3024600 AATATTTTGT
*
3024610 AATATTATAAT-TAA-AATAAAAGATATTAATATAA
1 AATA-TATAATATAAGAATAAAA-A-ATTAAAATAA
3024644 AATATATAATATAAGAATAAAAAATTAAAAT-A
1 AATATATAATATAAGAATAAAAAATTAAAATAA
3024676 AA-ATATAATATAAGAA
1 AATATATAATATAAGAA
3024692 ATTAAAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 14 0.31
32 3 0.07
33 13 0.29
34 8 0.18
35 7 0.16
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (33 bp):
AATATATAATATAAGAATAAAAAATTAAAATAA
Found at i:3024699 original size:31 final size:30
Alignment explanation
Indices: 3024647--3024752 Score: 87
Period size: 31 Copynumber: 3.6 Consensus size: 30
3024637 AATATAAAAT
*
3024647 ATATAATATAAG-AATAAAAAATTAAAATAAA
1 ATATAATATAAGAAAT-TAAAATTAAAAT-AA
* *
3024678 ATATAATATAAGAAATTAAAATTTATATAA
1 ATATAATATAAGAAATTAAAATTAAAATAA
** *
3024708 CATA-GGTAAAAGAAATTAAAA-TAAAAT--
1 -ATATAATATAAGAAATTAAAATTAAAATAA
*
3024735 ATATAATATAAAAAATTA
1 ATATAATATAAGAAATTA
3024753 TATTAAAGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
26 3 0.05
27 10 0.17
29 4 0.07
30 16 0.27
31 24 0.40
32 3 0.05
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (30 bp):
ATATAATATAAGAAATTAAAATTAAAATAA
Found at i:3025871 original size:14 final size:14
Alignment explanation
Indices: 3025838--3025871 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3025828 CATATAATTA
*
3025838 TAATTTAAAAATAT
1 TAATTTAAAAAAAT
*
3025852 TTATTTAAAAAAAT
1 TAATTTAAAAAAAT
3025866 TAATTT
1 TAATTT
3025872 TTATTTTTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTTAAAAAAAT
Found at i:3041737 original size:22 final size:22
Alignment explanation
Indices: 3041690--3041733 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3041680 TTAATTATTT
*
3041690 ATATTTTATTCTTTGTAGTTTT
1 ATATTTTATTCTTTGTAGTTTA
3041712 ATATTTTATT-TTT-TAAGTTTA
1 ATATTTTATTCTTTGT-AGTTTA
3041733 A
1 A
3041734 ATATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 9 0.45
22 10 0.50
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (22 bp):
ATATTTTATTCTTTGTAGTTTA
Found at i:3051642 original size:2 final size:2
Alignment explanation
Indices: 3051637--3051673 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3051627 GAGGAAATTA
3051637 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
3051674 GATGATGATC
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:3052630 original size:2 final size:2
Alignment explanation
Indices: 3052623--3052648 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3052613 GATGGATCAT
3052623 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
3052649 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3055260 original size:23 final size:22
Alignment explanation
Indices: 3055218--3055262 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3055208 TAATAGACAC
3055218 AAAATTTAATAAATTATTATTA
1 AAAATTTAATAAATTATTATTA
*
3055240 AAAATTATACTAAACTT-TTATTA
1 AAAATT-TAATAAA-TTATTATTA
3055263 CTAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 12 0.60
24 2 0.10
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATTTAATAAATTATTATTA
Found at i:3059339 original size:2 final size:2
Alignment explanation
Indices: 3059332--3059359 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3059322 TCCTTGCTAA
3059332 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
3059360 TATTCCATAA
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):
AT
Found at i:3061100 original size:59 final size:59
Alignment explanation
Indices: 3061027--3061140 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
3061017 GATGTTTTTC
*
3061027 AAAATTATTAAACGTCAAACT-GAGATAAAATGGATTTAGACAAAAAGATATTATTTTGA
1 AAAATTATTAAACGTCAAACTGGA-ATAAAATGAATTTAGACAAAAAGATATTATTTTGA
* * *
3061086 AAAATTATTCAACGTCAAACTGGAATAAATTGAATTTGGACAAAAAGATATTATT
1 AAAATTATTAAACGTCAAACTGGAATAAAATGAATTTAGACAAAAAGATATTATT
3061141 CAAAATCATC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 48 0.96
60 2 0.04
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (59 bp):
AAAATTATTAAACGTCAAACTGGAATAAAATGAATTTAGACAAAAAGATATTATTTTGA
Found at i:3064781 original size:81 final size:78
Alignment explanation
Indices: 3064691--3064839 Score: 226
Period size: 81 Copynumber: 1.9 Consensus size: 78
3064681 GAGAAAGGGC
** * *
3064691 TTTTCTAATTTGTTGAATGATAATTGTTTGATTGATTCAAAAAAAAAAAGAGAAATGGTTTTTCC
1 TTTTCTAATTTCATGAATGATAATTGTTTGATTGATT---AAAAAAAAAGAGAAAGGGTTTTTAC
3064756 AATTTGATAAAGGTTT
63 AATTTGATAAAGGTTT
*
3064772 TTTTCTAATTTCATGAATGATTATTGTTTGATTGATTAAAAAAAAAGAGAAAGGGTTTTTACAAT
1 TTTTCTAATTTCATGAATGATAATTGTTTGATTGATTAAAAAAAAAGAGAAAGGGTTTTTACAAT
3064837 TTG
66 TTG
3064840 TTGCATAGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
78 29 0.46
81 34 0.54
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (78 bp):
TTTTCTAATTTCATGAATGATAATTGTTTGATTGATTAAAAAAAAAGAGAAAGGGTTTTTACAAT
TTGATAAAGGTTT
Found at i:3066910 original size:81 final size:81
Alignment explanation
Indices: 3066810--3067006 Score: 288
Period size: 81 Copynumber: 2.4 Consensus size: 81
3066800 TGGACTAATT
* * *
3066810 AAAATTTAATTATTGGTCATATAATTGGTCTCTAAGTAAATCAAGATAATTTAGAGATAATATTC
1 AAAATTTAATTATTGGTCATATAATTGATCTCTAAATAAATCAAGATAATTTAGAAATAATATTC
3066875 ATAGTTTTGACCAATC
66 ATAGTTTTGACCAATC
* *
3066891 AAAATTTAGTTATTGGTCATATAATTTATCTCTAAATAAATCAAGATAATTTAGAAATAATATTC
1 AAAATTTAATTATTGGTCATATAATTGATCTCTAAATAAATCAAGATAATTTAGAAATAATATTC
* *
3066956 ATATTTTTGACTAATC
66 ATAGTTTTGACCAATC
* * *
3066972 AAGATTTAATTATTGGTTATTTAAGTT-ATCTCTAA
1 AAAATTTAATTATTGGTCATATAA-TTGATCTCTAA
3067007 TAATTATTCT
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 102 0.98
82 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.42
Consensus pattern (81 bp):
AAAATTTAATTATTGGTCATATAATTGATCTCTAAATAAATCAAGATAATTTAGAAATAATATTC
ATAGTTTTGACCAATC
Found at i:3067412 original size:23 final size:25
Alignment explanation
Indices: 3067386--3067450 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
3067376 AGCAGTAGTA
* *
3067386 AAGTTCATGATCAAG-TGGC-AACG
1 AAGTTCGTGATCAAGATAGCAAACG
* *
3067409 AAGTTCGTAATCAAGATATCAAACG
1 AAGTTCGTGATCAAGATAGCAAACG
3067434 AAGTTCGTGATCAAGAT
1 AAGTTCGTGATCAAGAT
3067451 CAAGTCGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 13 0.37
24 2 0.06
25 20 0.57
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (25 bp):
AAGTTCGTGATCAAGATAGCAAACG
Found at i:3067501 original size:51 final size:51
Alignment explanation
Indices: 3067436--3067588 Score: 227
Period size: 51 Copynumber: 3.0 Consensus size: 51
3067426 ATCAAACGAA
* * *
3067436 GTTCGTGATCAAGATCAAGTCGTCAAAATCCTTGAAGTGAAAATATCAAGT
1 GTTCGTGATCAAGATCAAGTCGTCAAGACCCTTGAAGTGAAGATATCAAGT
* *
3067487 GTTCGTGATCAAGATTAAGTTGTCAAGACCCTTGAAGTGAAGATATCAAGT
1 GTTCGTGATCAAGATCAAGTCGTCAAGACCCTTGAAGTGAAGATATCAAGT
* *
3067538 GTTTGTGATCAGGATCAAGTCGT-AATGACCCTTGAAGTGAAGATATCAAGT
1 GTTCGTGATCAAGATCAAGTCGTCAA-GACCCTTGAAGTGAAGATATCAAGT
3067589 TTAGTTCATG
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
50 2 0.02
51 90 0.98
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
GTTCGTGATCAAGATCAAGTCGTCAAGACCCTTGAAGTGAAGATATCAAGT
Found at i:3081999 original size:2 final size:2
Alignment explanation
Indices: 3081992--3082020 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3081982 CCCTTTTAAC
3081992 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
3082021 AAATAAAACC
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:3086723 original size:39 final size:39
Alignment explanation
Indices: 3086599--3086734 Score: 130
Period size: 39 Copynumber: 3.4 Consensus size: 39
3086589 TTATTTTCTA
* *
3086599 TTTTCGGTTTATTTATATGATAAACCA-TGATTTATGAATG
1 TTTT-GGTTTATTCATATGATAAA-AATTGATTTATGAATG
* * * * *
3086639 TTGTAGTTTATTCATATGACAAAAATTTTATTTATGAGTG
1 TTTTGGTTTATTCATATGATAAAAA-TTGATTTATGAATG
* * * *
3086679 ATTTGGTTTATTTATATGATGAATATTGATTTATGAATG
1 TTTTGGTTTATTCATATGATAAAAATTGATTTATGAATG
*
3086718 TTTTGGTGTATTCATAT
1 TTTTGGTTTATTCATAT
3086735 AACAATTGTC
Statistics
Matches: 75, Mismatches: 19, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
38 1 0.01
39 42 0.56
40 32 0.43
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.50
Consensus pattern (39 bp):
TTTTGGTTTATTCATATGATAAAAATTGATTTATGAATG
Found at i:3090178 original size:87 final size:87
Alignment explanation
Indices: 3090024--3090199 Score: 307
Period size: 87 Copynumber: 2.0 Consensus size: 87
3090014 AATTTTTTAT
* *
3090024 ACCTATCTGACGAAGTTCTCTACCTCACTCACAACACACCAAAACCTCATTCCCTCTATCATGCT
1 ACCTATCTGACGAAGTTCTCTACCTCACTCACAACACACCAAAACCTCATTCCCTCTACCATACT
3090089 GATGACTCTTGATTTTGCTACA
66 GATGACTCTTGATTTTGCTACA
* * *
3090111 ACCTATGTGACGAAGTTCTCTACCTCACTCACAACACACCAAAGCCTTATTCCCTCTACCATACT
1 ACCTATCTGACGAAGTTCTCTACCTCACTCACAACACACCAAAACCTCATTCCCTCTACCATACT
3090176 GATGACTCTTGATTTTGCTACA
66 GATGACTCTTGATTTTGCTACA
3090198 AC
1 AC
3090200 GTATACCTGA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.28, C:0.33, G:0.10, T:0.30
Consensus pattern (87 bp):
ACCTATCTGACGAAGTTCTCTACCTCACTCACAACACACCAAAACCTCATTCCCTCTACCATACT
GATGACTCTTGATTTTGCTACA
Found at i:3090277 original size:14 final size:14
Alignment explanation
Indices: 3090260--3090304 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
3090250 CATGCTACCT
3090260 CACTCACAACACAC
1 CACTCACAACACAC
3090274 CACTCACAACTAC-C
1 CACTCACAAC-ACAC
3090288 TCACTCACAACACAC
1 -CACTCACAACACAC
3090303 CA
1 CA
3090305 AAGCCTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.40, C:0.49, G:0.00, T:0.11
Consensus pattern (14 bp):
CACTCACAACACAC
Found at i:3090294 original size:15 final size:15
Alignment explanation
Indices: 3090254--3090358 Score: 74
Period size: 15 Copynumber: 6.8 Consensus size: 15
3090244 CTCTACCATG
3090254 CTACCTCACTCACAA
1 CTACCTCACTCACAA
3090269 C-ACAC-CACTCACAA
1 CTAC-CTCACTCACAA
3090283 CTACCTCACTCACAA
1 CTACCTCACTCACAA
* ** *
3090298 CACACCAAAGCCTCATTC-C
1 C-TACCTCA--CTCA--CAA
3090317 CTACAC-CACTCACAA
1 CTAC-CTCACTCACAA
*
3090332 TTACCTCACTCACAA
1 CTACCTCACTCACAA
3090347 CTACCTCACTCA
1 CTACCTCACTCA
3090359 TAACACACCA
Statistics
Matches: 70, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
14 15 0.21
15 37 0.53
16 8 0.11
18 7 0.10
19 2 0.03
20 1 0.01
ACGTcount: A:0.34, C:0.47, G:0.01, T:0.18
Consensus pattern (15 bp):
CTACCTCACTCACAA
Found at i:3090548 original size:124 final size:124
Alignment explanation
Indices: 3090347--3090572 Score: 375
Period size: 124 Copynumber: 1.8 Consensus size: 124
3090337 TCACTCACAA
*
3090347 CTACCTCACTCATAACACACCAAAGCCATCATTCCCTCTACCACGCTGATGACTCTTGATTTTGC
1 CTACCTCACTCACAACACACCAAAGCCATCATTCCCTCTACCACGCTGATGACTCTTGATTTTGC
* * *
3090412 TACAACTGTATACTTGACTAAGTATATATGCTACATGCTGAGGACTATCCTTTACCATG
66 TACAACTATATACCTGACTAAGTATACATGCTACATGCTGAGGACTATCCTTTACCATG
*
3090471 CTACCTCACTCACAACACACCAAAGCC-TCATTCCCTCTACCATGCTGATGACTCTCCTGATTTT
1 CTACCTCACTCACAACACACCAAAGCCATCATTCCCTCTACCACGCTGATGACTCT--TGATTTT
3090535 GCTACAA-TATATACCTGACTAAGTATACATGCTACATG
64 GCTACAACTATATACCTGACTAAGTATACATGCTACATG
3090573 TTGATAACTC
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
123 27 0.28
124 54 0.57
125 14 0.15
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.30
Consensus pattern (124 bp):
CTACCTCACTCACAACACACCAAAGCCATCATTCCCTCTACCACGCTGATGACTCTTGATTTTGC
TACAACTATATACCTGACTAAGTATACATGCTACATGCTGAGGACTATCCTTTACCATG
Found at i:3090690 original size:33 final size:33
Alignment explanation
Indices: 3090648--3090747 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 33
3090638 ACCAAGTTTC
*
3090648 CAAGTACTCTACCATGTTACCTCACTCACAACA
1 CAAGTACTCTACCATGCTACCTCACTCACAACA
* *
3090681 CAAGTACTCTATCATGCTACCCTCACTC-CACACG
1 CAAGTACTCTACCATGCTA-CCTCACTCACA-ACA
*
3090715 CAAGTACTCTACCATGCTACCTTACTCACAACA
1 CAAGTACTCTACCATGCTACCTCACTCACAACA
3090748 ACCTCACTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
33 28 0.48
34 30 0.52
ACGTcount: A:0.31, C:0.38, G:0.07, T:0.24
Consensus pattern (33 bp):
CAAGTACTCTACCATGCTACCTCACTCACAACA
Found at i:3090756 original size:15 final size:15
Alignment explanation
Indices: 3090733--3090762 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3090723 CTACCATGCT
*
3090733 ACCTTACTCACAACA
1 ACCTCACTCACAACA
3090748 ACCTCACTCACAACA
1 ACCTCACTCACAACA
3090763 CACCAAAGCC
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:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (15 bp):
ACCTCACTCACAACA
Found at i:3090941 original size:31 final size:31
Alignment explanation
Indices: 3090899--3090991 Score: 86
Period size: 31 Copynumber: 3.0 Consensus size: 31
3090889 CGTATACTTG
*
3090899 ACTAAGAATACATGCTAGCCAAGTTTCTCTC
1 ACTAAGTATACATGCTAGCCAAGTTTCTCTC
* * *
3090930 ACTAAGTATACATGTTA--CAATGTATACT-TG
1 ACTAAGTATACATGCTAGCCAA-GT-TTCTCTC
*
3090960 ACTAAGTATACATGCT-GACCAAGTTTGTCTC
1 ACTAAGTATACATGCTAG-CCAAGTTTCTCTC
3090991 A
1 A
3090992 ACTCTCTGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
29 3 0.06
30 20 0.42
31 22 0.46
32 3 0.06
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (31 bp):
ACTAAGTATACATGCTAGCCAAGTTTCTCTC
Found at i:3090966 original size:30 final size:29
Alignment explanation
Indices: 3090883--3090975 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 29
3090873 CTTGATTTTA
*
3090883 CTACAACGTATACTTGACTAAGAATACATG
1 CTACAA-GTATACTTGACTAAGTATACATG
* *
3090913 CTAGCCAAGT-TTCTCTCACTAAGTATACATG
1 CTA--CAAGTATACT-TGACTAAGTATACATG
*
3090944 TTACAATGTATACTTGACTAAGTATACATG
1 CTACAA-GTATACTTGACTAAGTATACATG
3090974 CT
1 CT
3090976 GACCAAGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
29 3 0.06
30 24 0.47
31 21 0.41
32 3 0.06
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.32
Consensus pattern (29 bp):
CTACAAGTATACTTGACTAAGTATACATG
Found at i:3091010 original size:61 final size:60
Alignment explanation
Indices: 3090868--3091013 Score: 143
Period size: 61 Copynumber: 2.4 Consensus size: 60
3090858 CTTGCTGATG
*
3090868 ACTCTCTTGATTTTACTACAACGTATACTTGACTAAGAATACATGCTAGCCAAGTTTCTCTC
1 ACTCTC-TGATTTGA-TACAACGTATACTTGACTAAGAATACATGCTAGCCAAGTTTCTCTC
* * ** * * * *
3090930 ACTAAGTAT-ACATGTTACAATGTATACTTGACTAAGTATACATGCT-GACCAAGTTTGTCTC
1 ACT--CTCTGATTTGATACAACGTATACTTGACTAAGAATACATGCTAG-CCAAGTTTCTCTC
3090991 AACTCTCTGATTTGATACAACGT
1 -ACTCTCTGATTTGATACAACGT
3091014 TCATCTTATT
Statistics
Matches: 64, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
60 3 0.05
61 51 0.80
62 8 0.12
63 1 0.02
64 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (60 bp):
ACTCTCTGATTTGATACAACGTATACTTGACTAAGAATACATGCTAGCCAAGTTTCTCTC
Found at i:3098819 original size:20 final size:20
Alignment explanation
Indices: 3098796--3098836 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
3098786 CCTTAAAAGT
3098796 TGGAAATTAATCTT-ATATTG
1 TGGAAATTAAT-TTGATATTG
3098816 TGGAAATTAATTTGATATTG
1 TGGAAATTAATTTGATATTG
3098836 T
1 T
3098837 ATGCAACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.46
Consensus pattern (20 bp):
TGGAAATTAATTTGATATTG
Found at i:3104029 original size:19 final size:20
Alignment explanation
Indices: 3104007--3104049 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
3103997 CGACGATAGG
3104007 TAAAAAGAATATTTT-TAAA
1 TAAAAAGAATATTTTATAAA
* *
3104026 T-AAAATAATATTTTATGAA
1 TAAAAAGAATATTTTATAAA
3104045 TAAAA
1 TAAAA
3104050 TAATATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.60
19 5 0.25
20 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
TAAAAAGAATATTTTATAAA
Found at i:3104035 original size:18 final size:19
Alignment explanation
Indices: 3104009--3104056 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
3103999 ACGATAGGTA
*
3104009 AAAAGAATATTTT-TAAAT
1 AAAATAATATTTTATAAAT
*
3104027 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATAAAT
3104046 AAAATAATATT
1 AAAATAATATT
3104057 AAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:3117885 original size:446 final size:444
Alignment explanation
Indices: 3117047--3117940 Score: 1355
Period size: 446 Copynumber: 2.0 Consensus size: 444
3117037 CTTACATTTT
*
3117047 TTTAATGTAAAATTTTAACTTTTCAACTTTATCCCTTAAAATAATAAATAATAACATGACCAAAA
1 TTTAATGTAAAATTTTAACTTTTCAACTTTATCCCTTAAAATAATAAATAATAACATGACAAAAA
*
3117112 TAACATAATATTTTAATATTAATTATTTAAATATTAAAACATATAAAATTATTAAATATTTATTT
66 TAACATAATATTTAAATATTAATTATTTAAATATTAAAACATATAAAATTATTAAATATTTATTT
* * * *
3117177 TTACTAAATATTCAGCTTGAAATAAATATGTTTGTCTAACCCATACTCTTGACTTTCCCTCTTAC
131 TTACTAAATATTCAGCTCGAAAGAAATATATTTGTCCAACCCATACTCTTGACTTTCCCTCTTAC
* * * * *
3117242 ATGGGAAGGTCATTTTCCCTCTAGCCCAAGAGGGAATCATGTTGCAATGTCATTATGTTGAGAAA
196 ATGGAAAAGTCACTTTCCCTCTAGCCCAAGAGGGAAT-ATGTTGCAATGTCAGTACGTTGAGAAA
* *
3117307 GTACCATACCAAACATGATAAAGTGATTCAATCCAATTAAAATCCCTGTAAAATGCTTAACTTCC
260 GTACCATACCAAACATGATAAAGTGATTAAATCCAATTAAAATCCCTATAAAATGCTTAACTTCC
* **
3117372 TCAATACCAAATAGGACCTTAGTTCTCATAAATAATATGTGAACTGAAATTTCAAGGTTGCGAGT
325 TCAATACCAAATAGGACCTTAGTTCTCATAAATAATATGTGAACTGAAATTTCAAAGTTAAGAGT
*
3117437 TGACATTTTTATCTTTTCCCGATGTATGCTTTGTAAGAGATCAGTAAAACTTTATA
390 TGACATTTTTATCTTTTCCC-ATGTATGCTTTGTAAGAGATCAATAAAACTTTATA
*
3117493 TTTAATGTAAAATTTTAACTTTTCAATTTTATCCCTTAAAATAATAAATAATAACA-GAACAAAA
1 TTTAATGTAAAATTTTAACTTTTCAACTTTATCCCTTAAAATAATAAATAATAACATG-ACAAAA
* *
3117557 ATAACATAATATTTAAATATTAATTATTTAAATCTTAAAATATATAAAATTATTAAATATTTATT
65 ATAACATAATATTTAAATATTAATTATTTAAATATTAAAACATATAAAATTATTAAATATTTATT
*** * * * *
3117622 TTTACTAAATATTCAGCTCGAAAGGGGTATATTTGTCCAATCTATTCTCTTGACTTTCCCTCTTC
130 TTTACTAAATATTCAGCTCGAAAGAAATATATTTGTCCAACCCATACTCTTGACTTTCCCTCTTA
* *
3117687 CATGGAAAAGTCACTTTCCCTCTAGCCCTAGAGGGAGT-TGCCTTGCAATGTCAGTACGTTGAGA
195 CATGGAAAAGTCACTTTCCCTCTAGCCCAAGAGGGAATATG--TTGCAATGTCAGTACGTTGAGA
* * ** *
3117751 AAGTATCATACTAAATGTGGTAAAGTGATTAAAAT-CAATTAAAATCCCTATAAAATGCTTAACT
258 AAGTACCATACCAAACATGATAAAGTGATT-AAATCCAATTAAAATCCCTATAAAATGCTTAACT
*
3117815 TCCTCAATACCAAATGGGACCTTAGTTCTCATAAATAATATGTGAA-TGGAAATTTCAAAGTTAA
322 TCCTCAATACCAAATAGGACCTTAGTTCTCATAAATAATATGTGAACT-GAAATTTCAAAGTTAA
* * *
3117879 GAGTTGACATTTTTATCTTTTCCCCTTTATGCTTTGTAAGAGATCAATAAAACTTTGTA
386 GAGTTGACATTTTTATCTTTTCCCATGTATGCTTTGTAAGAGATCAATAAAACTTTATA
3117938 TTT
1 TTT
3117941 TTATATTAAA
Statistics
Matches: 405, Mismatches: 38, Indels: 11
0.89 0.08 0.02
Matches are distributed among these distances:
444 2 0.00
445 36 0.09
446 364 0.90
447 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (444 bp):
TTTAATGTAAAATTTTAACTTTTCAACTTTATCCCTTAAAATAATAAATAATAACATGACAAAAA
TAACATAATATTTAAATATTAATTATTTAAATATTAAAACATATAAAATTATTAAATATTTATTT
TTACTAAATATTCAGCTCGAAAGAAATATATTTGTCCAACCCATACTCTTGACTTTCCCTCTTAC
ATGGAAAAGTCACTTTCCCTCTAGCCCAAGAGGGAATATGTTGCAATGTCAGTACGTTGAGAAAG
TACCATACCAAACATGATAAAGTGATTAAATCCAATTAAAATCCCTATAAAATGCTTAACTTCCT
CAATACCAAATAGGACCTTAGTTCTCATAAATAATATGTGAACTGAAATTTCAAAGTTAAGAGTT
GACATTTTTATCTTTTCCCATGTATGCTTTGTAAGAGATCAATAAAACTTTATA
Found at i:3135081 original size:2 final size:2
Alignment explanation
Indices: 3135074--3135175 Score: 87
Period size: 2 Copynumber: 51.0 Consensus size: 2
3135064 ATACTTTTCA
* * * * *
3135074 AT AT AT AT AA AT AT AT AT GT AC AT AT AT AT AT GT AC 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
* * * * * * * *
3135116 AT GT GT AC AC AT AT AT GT GT GT GT 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
3135158 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
3135176 GCACTATGGT
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3135091 original size:14 final size:14
Alignment explanation
Indices: 3135074--3135176 Score: 98
Period size: 14 Copynumber: 7.4 Consensus size: 14
3135064 ATACTTTTCA
* *
3135074 ATATATATAAATAT
1 ATATGTATATATAT
*
3135088 ATATGTACATATAT
1 ATATGTATATATAT
*
3135102 ATATGTACATATAT
1 ATATGTATATATAT
* * *
3135116 ATGTGTACACATAT
1 ATATGTATATATAT
* * *
3135130 ATGTGTGTGTATAT
1 ATATGTATATATAT
*
3135144 ATATATATATATAT
1 ATATGTATATATAT
*
3135158 ATATATATATATAT
1 ATATGTATATATAT
3135172 ATATG
1 ATATG
3135177 CACTATGGTA
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 75 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:3142464 original size:2 final size:2
Alignment explanation
Indices: 3142457--3142482 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3142447 TAGCAAGTAA
3142457 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
3142483 TTACTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3147697 original size:80 final size:80
Alignment explanation
Indices: 3147559--3147718 Score: 275
Period size: 80 Copynumber: 2.0 Consensus size: 80
3147549 NNNNNNNNNN
*
3147559 ATAATTTAGATTTATTTAGAGATAAATTGAATGACCAATAGCTAATATTTGATCGGTCAAAATAT
1 ATAAGTTAGATTTATTTAGAGATAAATTGAATGACCAATAGCTAATATTTGATCGGTCAAAATAT
3147624 AAATATTATCTCTAA
66 AAATATTATCTCTAA
* * *
3147639 ATAAGTTAGATTTATTTAGAGATAAATTGGATGACCAATAGTTAATATTTGATTGGTCAAAATAT
1 ATAAGTTAGATTTATTTAGAGATAAATTGAATGACCAATAGCTAATATTTGATCGGTCAAAATAT
*
3147704 GAATATTATCTCTAA
66 AAATATTATCTCTAA
3147719 TTTATTTTGA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.38
Consensus pattern (80 bp):
ATAAGTTAGATTTATTTAGAGATAAATTGAATGACCAATAGCTAATATTTGATCGGTCAAAATAT
AAATATTATCTCTAA
Found at i:3148379 original size:21 final size:20
Alignment explanation
Indices: 3148340--3148379 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3148330 AAGTGAGTTA
* *
3148340 TTTTAATTTTATGTTATTTC
1 TTTTAATTTGATATTATTTC
3148360 TTTTAATTTGATTATTATTT
1 TTTTAATTTGA-TATTATTT
3148380 ATTAGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTAATTTGATATTATTTC
Found at i:3151046 original size:22 final size:23
Alignment explanation
Indices: 3151001--3151044 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3150991 AAGTCAAGAA
3151001 TAATTTTTAAAAAATCTAAAAAT
1 TAATTTTTAAAAAATCTAAAAAT
* *
3151024 TAATTTTTATAAATTCTAAAA
1 TAATTTTTAAAAAATCTAAAA
3151045 TTTCAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATTTTTAAAAAATCTAAAAAT
Found at i:3156155 original size:15 final size:15
Alignment explanation
Indices: 3156135--3156168 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3156125 TTCCTTGGCC
3156135 AAGCTGTAAAGAAAT
1 AAGCTGTAAAGAAAT
*
3156150 AAGCTGTAAAGAATT
1 AAGCTGTAAAGAAAT
3156165 AAGC
1 AAGC
3156169 GCAGATGAGN
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.21
Consensus pattern (15 bp):
AAGCTGTAAAGAAAT
Found at i:3162670 original size:36 final size:38
Alignment explanation
Indices: 3162602--3162673 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 38
3162592 CTGCCTTTTA
*
3162602 AAGATTCAAGCATAATCATTACACATTACCTTTTCAAG
1 AAGATTCAAGCATAATCATCACACATTACCTTTTCAAG
* *
3162640 AAGATT-AAGCATAA-CCTCACACATTGCCTTTTCA
1 AAGATTCAAGCATAATCATCACACATTACCTTTTCA
3162674 CAGGAGCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 17 0.55
37 8 0.26
38 6 0.19
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.31
Consensus pattern (38 bp):
AAGATTCAAGCATAATCATCACACATTACCTTTTCAAG
Found at i:3163294 original size:63 final size:63
Alignment explanation
Indices: 3163219--3163431 Score: 157
Period size: 63 Copynumber: 3.4 Consensus size: 63
3163209 AATTAAGCAG
* * *
3163219 TGCATT-TATGAGAAGTCGATTCTTTGTGTTTCTAGAAC-TTTCTATTTTG-AAGGAATCAAACA
1 TGCATTCT-TGAGAAGTTGATTCTTTGTATCTCTAGAACATTTC-ATTTTGTAA-GAATCAAACA
3163281 T
63 T
* * * * * * * *
3163282 TGCATTCTTGAGAAGTTGATTTTTTTTATCTGTGGAGCATTTCGTTTTGTAAGAATCGAGCAT
1 TGCATTCTTGAGAAGTTGATTCTTTGTATCTCTAGAACATTTCATTTTGTAAGAATCAAACAT
* * ** * * *
3163345 TGCATTCTTGAGAAGTTGATTCTTTTTA-CACTTAGAGTA-TTCTATTTTCTAAGAATCGAGCAT
1 TGCATTCTTGAGAAGTTGATTCTTTGTATCTC-TAGAACATTTC-ATTTTGTAAGAATCAAACAT
* * *
3163408 TCCTTTTTTGAGAAGTTGATTCTT
1 TGCATTCTTGAGAAGTTGATTCTT
3163432 GATGCCAATT
Statistics
Matches: 124, Mismatches: 21, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
62 4 0.03
63 113 0.91
64 7 0.06
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (63 bp):
TGCATTCTTGAGAAGTTGATTCTTTGTATCTCTAGAACATTTCATTTTGTAAGAATCAAACAT
Found at i:3177328 original size:2 final size:2
Alignment explanation
Indices: 3177321--3177351 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3177311 TAATTTTGAC
*
3177321 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
3177352 CCAAACAATT
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:3186131 original size:2 final size:2
Alignment explanation
Indices: 3186124--3186156 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3186114 ATGAAGGTTT
3186124 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3186157 GAGATTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3186994 original size:16 final size:17
Alignment explanation
Indices: 3186962--3186994 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3186952 TTTATAAAAA
*
3186962 AAAATCTATAGAGATTT
1 AAAATATATAGAGATTT
3186979 AAAATATATA-AGATTT
1 AAAATATATAGAGATTT
3186995 CACATAAGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (17 bp):
AAAATATATAGAGATTT
Found at i:3190235 original size:12 final size:12
Alignment explanation
Indices: 3190218--3190242 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3190208 TTGTTAAATG
3190218 TTATAGAAGTAT
1 TTATAGAAGTAT
3190230 TTATAGAAGTAT
1 TTATAGAAGTAT
3190242 T
1 T
3190243 CTCATGTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TTATAGAAGTAT
Found at i:3193129 original size:23 final size:23
Alignment explanation
Indices: 3193099--3193185 Score: 120
Period size: 23 Copynumber: 3.8 Consensus size: 23
3193089 TGGACTTTAT
3193099 CTTGATCACGAACTTCGCTATTG
1 CTTGATCACGAACTTCGCTATTG
* * *
3193122 CTTGATCACAAATTTCGCCATTG
1 CTTGATCACGAACTTCGCTATTG
* * *
3193145 CTTTATCACGAACTTCACTGTTG
1 CTTGATCACGAACTTCGCTATTG
3193168 CTTGATCACGAACTTCGC
1 CTTGATCACGAACTTCGC
3193186 CGTCGCTTGA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (23 bp):
CTTGATCACGAACTTCGCTATTG
Found at i:3193193 original size:23 final size:23
Alignment explanation
Indices: 3193099--3193197 Score: 117
Period size: 23 Copynumber: 4.3 Consensus size: 23
3193089 TGGACTTTAT
*
3193099 CTTGATCACGAACTTCGCTATTG
1 CTTGATCACGAACTTCGCCATTG
* *
3193122 CTTGATCACAAATTTCGCCATTG
1 CTTGATCACGAACTTCGCCATTG
* * **
3193145 CTTTATCACGAACTTCACTGTTG
1 CTTGATCACGAACTTCGCCATTG
* *
3193168 CTTGATCACGAACTTCGCCGTCG
1 CTTGATCACGAACTTCGCCATTG
3193191 CTTGATC
1 CTTGATC
3193198 TTCACCCCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.34
Consensus pattern (23 bp):
CTTGATCACGAACTTCGCCATTG
Found at i:3193663 original size:42 final size:41
Alignment explanation
Indices: 3193617--3193744 Score: 100
Period size: 42 Copynumber: 3.1 Consensus size: 41
3193607 TTATTTAGAG
*
3193617 ATAAATTAGATGATCAATAGCTAATATTTGATTGGTCAAAAT
1 ATAAATT-GATGATCAATAGCTAATATTTGATTGGTAAAAAT
* ** ** * * ** * *
3193659 ATAAA-T-ATTATCTCTAATTTAT-TTTGATTTGTTTAGAG
1 ATAAATTGATGATCAATAGCTAATATTTGATTGGTAAAAAT
*
3193697 ATAAATTGGATGACCAATAGCTAATATTTGATTGGTAAAAAT
1 ATAAATT-GATGATCAATAGCTAATATTTGATTGGTAAAAAT
3193739 ATAAAT
1 ATAAAT
3193745 ATTATCTCTA
Statistics
Matches: 59, Mismatches: 23, Indels: 8
0.66 0.26 0.09
Matches are distributed among these distances:
38 16 0.27
39 11 0.19
41 10 0.17
42 22 0.37
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (41 bp):
ATAAATTGATGATCAATAGCTAATATTTGATTGGTAAAAAT
Found at i:3193694 original size:80 final size:80
Alignment explanation
Indices: 3193531--3193839 Score: 408
Period size: 80 Copynumber: 3.9 Consensus size: 80
3193521 ATATAATTAA
* * * * * *
3193531 TAGAGATAATTTAAATGACCAATAATTAA-ATTTTGATTGGTCAAAAATATGAAGATTATCTCCA
1 TAGAGATAAATTAGATGACCAATAACTAATA-TTTGATTGGTC-AAAATATAAATATTATCTCTA
*
3193595 AATTATTTTGATTTATT
64 AATTATTTTGATTTGTT
* * *
3193612 TAGAGATAAATTAGATGATCAATAGCTAATATTTGATTGGTCAAAATATAAATATTATCTCTAAT
1 TAGAGATAAATTAGATGACCAATAACTAATATTTGATTGGTCAAAATATAAATATTATCTCTAAA
3193677 TTATTTTGATTTGTT
66 TTATTTTGATTTGTT
* * *
3193692 TAGAGATAAATTGGATGACCAATAGCTAATATTTGATTGGTAAAAATATAAATATTATCTCTAAA
1 TAGAGATAAATTAGATGACCAATAACTAATATTTGATTGGTCAAAATATAAATATTATCTCTAAA
3193757 TTATTTTGATTTGTT
66 TTATTTTGATTTGTT
* * * * *
3193772 TAGAGATAAATTTGATGACCAATAACTAATTTTTAATTGGTC-CAATTTAAATATTATCT-TCAA
1 TAGAGATAAATTAGATGACCAATAACTAATATTTGATTGGTCAAAATATAAATATTATCTCT-AA
3193835 ATTAT
65 ATTAT
3193840 CTCAAGAGAT
Statistics
Matches: 205, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
78 1 0.00
79 22 0.11
80 146 0.71
81 35 0.17
82 1 0.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (80 bp):
TAGAGATAAATTAGATGACCAATAACTAATATTTGATTGGTCAAAATATAAATATTATCTCTAAA
TTATTTTGATTTGTT
Found at i:3193701 original size:38 final size:38
Alignment explanation
Indices: 3193659--3193782 Score: 97
Period size: 38 Copynumber: 3.2 Consensus size: 38
3193649 TGGTCAAAAT
3193659 ATAAATATTATCTCTAATTTATTTTGATTTGTTTAGAG
1 ATAAATATTATCTCTAATTTATTTTGATTTGTTTAGAG
* ** * * * ** * *
3193697 ATAAAT-TGGATGACCAATAGCTAATATTTGATTGGTAAAAAT
1 ATAAATAT-TATCTCTAAT---TTAT-TTTGATTTGTTTAGAG
*
3193739 ATAAATATTATCTCTAAATTATTTTGATTTGTTTAGAG
1 ATAAATATTATCTCTAATTTATTTTGATTTGTTTAGAG
3193777 ATAAAT
1 ATAAAT
3193783 TTGATGACCA
Statistics
Matches: 59, Mismatches: 21, Indels: 12
0.64 0.23 0.13
Matches are distributed among these distances:
37 1 0.02
38 29 0.49
39 3 0.05
41 3 0.05
42 22 0.37
43 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (38 bp):
ATAAATATTATCTCTAATTTATTTTGATTTGTTTAGAG
Found at i:3211953 original size:24 final size:25
Alignment explanation
Indices: 3211904--3211963 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
3211894 AAATTTTAAA
*
3211904 TTAATCAAAATTATACTATTTCA-T
1 TTAATCAAATTTATACTATTTCATT
* *
3211928 TTAATCAAATTTTTA-TATTTTTATT
1 TTAATCAAATTTATACTA-TTTCATT
3211953 TTAAATCAAAT
1 TT-AATCAAAT
3211964 AAGTCATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 2 0.07
24 17 0.57
25 3 0.10
26 8 0.27
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAATCAAATTTATACTATTTCATT
Found at i:3214463 original size:15 final size:17
Alignment explanation
Indices: 3214435--3214467 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3214425 TATTTTATAT
3214435 TAACATTATAAAAATTA
1 TAACATTATAAAAATTA
3214452 TAAC-TTAT-AAAATTA
1 TAACATTATAAAAATTA
3214467 T
1 T
3214468 TAGTGAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACATTATAAAAATTA
Found at i:3215618 original size:214 final size:214
Alignment explanation
Indices: 3215249--3215656 Score: 656
Period size: 214 Copynumber: 1.9 Consensus size: 214
3215239 AAATATATTG
* *
3215249 TATATACATATATTTAATTTATACATAAGCATTACTATAATTTATAATAAACTTTATTTATATGA
1 TATATACATACATTTAATTTATACATAAGCATTACTATAACTTATAATAAACTTTATTTATATGA
** ** *
3215314 ATACACTTAATAACTTTATTAGTTATCATGTTAGATTTTATAACATATTGTTTATAATTAGTTAT
66 ATACACTTAATAACTTTATTAGCCATCACCTTAGATTTTATAACATATTCTTTATAATTAGTTAT
* * * *
3215379 TATTTATACAAACTTTGATATAAAACATTTTATCATATAATTTGTATCATTAATTAT-ATATATA
131 CATTTATACAAACTTTGATATAAAACATTTTAACATATAAGTTATATCATTAATT-TCATATATA
3215443 TAACAAAGTAATATTATATA
195 TAACAAAGTAATATTATATA
* *
3215463 TATATACATACATTTAATTTATACATAAGTATTACTATAACTTATAATAAATTTTATTTATATGA
1 TATATACATACATTTAATTTATACATAAGCATTACTATAACTTATAATAAACTTTATTTATATGA
* *
3215528 CTACACTTAATAAGTTTATTAGCCATCACCTTAGATTTTATAACATATTCTTTATAATTAGTTAT
66 ATACACTTAATAACTTTATTAGCCATCACCTTAGATTTTATAACATATTCTTTATAATTAGTTAT
*
3215593 CATTTATACAAACTTTGATATAAAACATTTTAACATATAAGTTATATTATTAATTTCATATATA
131 CATTTATACAAACTTTGATATAAAACATTTTAACATATAAGTTATATCATTAATTTCATATATA
3215657 CATATAATTA
Statistics
Matches: 177, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
213 1 0.01
214 176 0.99
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (214 bp):
TATATACATACATTTAATTTATACATAAGCATTACTATAACTTATAATAAACTTTATTTATATGA
ATACACTTAATAACTTTATTAGCCATCACCTTAGATTTTATAACATATTCTTTATAATTAGTTAT
CATTTATACAAACTTTGATATAAAACATTTTAACATATAAGTTATATCATTAATTTCATATATAT
AACAAAGTAATATTATATA
Found at i:3216060 original size:7 final size:7
Alignment explanation
Indices: 3216048--3216072 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3216038 AGCGCTTCAG
3216048 CATTTGT
1 CATTTGT
3216055 CATTTGT
1 CATTTGT
3216062 CATTTGT
1 CATTTGT
3216069 CATT
1 CATT
3216073 AAGATCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.56
Consensus pattern (7 bp):
CATTTGT
Found at i:3219035 original size:18 final size:18
Alignment explanation
Indices: 3219012--3219049 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3219002 GCTTGATTCT
3219012 TTCTTCTCCTAATT-TTTC
1 TTCTTCTCC-AATTCTTTC
*
3219030 TTCTTCTTCAATTCTTTC
1 TTCTTCTCCAATTCTTTC
3219048 TT
1 TT
3219050 AGCTGTGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (18 bp):
TTCTTCTCCAATTCTTTC
Found at i:3219048 original size:15 final size:16
Alignment explanation
Indices: 3219007--3219049 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
3218997 ACCTTGCTTG
3219007 ATTCTTTCTTCTCCTA
1 ATTCTTTCTTCTCCTA
*
3219023 ATT-TTTCTTCTTCTTCA
1 ATTCTTTCTTC-TCCT-A
3219040 ATTCTTTCTT
1 ATTCTTTCTT
3219050 AGCTGTGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.30
16 6 0.26
17 4 0.17
18 6 0.26
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTCTTTCTTCTCCTA
Found at i:3223942 original size:8 final size:9
Alignment explanation
Indices: 3223922--3223946 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3223912 GTTACTTTTA
3223922 TTTTATTCT
1 TTTTATTCT
3223931 TTTTATTCT
1 TTTTATTCT
3223940 TTTTATT
1 TTTTATT
3223947 TGTTCCCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTATTCT
Found at i:3226968 original size:2 final size:2
Alignment explanation
Indices: 3226955--3226984 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3226945 ACAAGTGGAA
*
3226955 AT AT AC 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
3226985 TATCAGGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3228557 original size:21 final size:21
Alignment explanation
Indices: 3228522--3228571 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
3228512 AAAAATATTT
* *
3228522 TAAAATTACATAATATTATAAA
1 TAAAAATACATAATAAT-TAAA
3228544 TAAAAATA-ATAATAATTAAA
1 TAAAAATACATAATAATTAAA
*
3228564 GAAAAATA
1 TAAAAATA
3228572 GTTTTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.44
21 7 0.28
22 7 0.28
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAAAATACATAATAATTAAA
Found at i:3229117 original size:13 final size:13
Alignment explanation
Indices: 3229099--3229123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3229089 ATCAACCTAA
3229099 ATATTTTATTTTT
1 ATATTTTATTTTT
3229112 ATATTTTATTTT
1 ATATTTTATTTT
3229124 ATAAAAATAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATATTTTATTTTT
Found at i:3230161 original size:16 final size:15
Alignment explanation
Indices: 3230152--3230180 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3230142 AAAACCTTAT
3230152 TAAGAAAAAACTTCA
1 TAAGAAAAAACTTCA
3230167 TAAGAAAAAA-TTCA
1 TAAGAAAAAACTTCA
3230181 AGTGAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (15 bp):
TAAGAAAAAACTTCA
Found at i:3233753 original size:54 final size:53
Alignment explanation
Indices: 3233691--3233793 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 53
3233681 CTAGTGGGTA
* * * *
3233691 AAAGTATCCATCCA-CTTCTGATGGGTAAAGTTATCTATCCATTTTTGGTTGGT
1 AAAGTATCCATCCACCTT-TGATAGGTAAAGATATCCATCCATCTTTGGTTGGT
*
3233744 AAAGTTATCCATCCACCTTTGGTAGGTAAAGATATCCATCCATCTTTGGT
1 AAAG-TATCCATCCACCTTTGATAGGTAAAGATATCCATCCATCTTTGGT
3233794 ATGTTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 4 0.09
54 36 0.84
55 3 0.07
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (53 bp):
AAAGTATCCATCCACCTTTGATAGGTAAAGATATCCATCCATCTTTGGTTGGT
Found at i:3233794 original size:27 final size:27
Alignment explanation
Indices: 3233691--3233794 Score: 122
Period size: 27 Copynumber: 3.9 Consensus size: 27
3233681 CTAGTGGGTA
* *
3233691 AAAG-TATCCATCCA-CTTCTGATGGGT
1 AAAGTTATCCATCCATCTT-TGGTAGGT
* * *
3233717 AAAGTTATCTATCCATTTTTGGTTGGT
1 AAAGTTATCCATCCATCTTTGGTAGGT
*
3233744 AAAGTTATCCATCCACCTTTGGTAGGT
1 AAAGTTATCCATCCATCTTTGGTAGGT
*
3233771 AAAGATATCCATCCATCTTTGGTA
1 AAAGTTATCCATCCATCTTTGGTA
3233795 TGTTTTAAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
26 4 0.06
27 60 0.91
28 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (27 bp):
AAAGTTATCCATCCATCTTTGGTAGGT
Found at i:3237113 original size:66 final size:66
Alignment explanation
Indices: 3237007--3237141 Score: 243
Period size: 66 Copynumber: 2.0 Consensus size: 66
3236997 ATGTTTTTAC
*
3237007 ACTAAATTCTCTCATTTAACAAAATCTCACTGTTTTCAATGACACATTACTAATAATCCGAAATC
1 ACTAAATTCTCTCACTTAACAAAATCTCACTGTTTTCAATGACACATTACTAATAATCCGAAATC
3237072 A
66 A
* *
3237073 ACTAAGTTCTCTTACTTAACAAAATCTCACTGTTTTCAATGACACATTACTAATAATCCGAAATC
1 ACTAAATTCTCTCACTTAACAAAATCTCACTGTTTTCAATGACACATTACTAATAATCCGAAATC
3237138 A
66 A
3237139 ACT
1 ACT
3237142 TTGATACCAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (66 bp):
ACTAAATTCTCTCACTTAACAAAATCTCACTGTTTTCAATGACACATTACTAATAATCCGAAATC
A
Found at i:3242107 original size:57 final size:57
Alignment explanation
Indices: 3242019--3242133 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
3242009 TGATGACATA
* *
3242019 GACAAATTATATATGGAATCTGAACCTTTCAACAAAGGAAGGTGATTGATTTCTGTG
1 GACAAATTATATATGGAATCTGAACCTTTCAACAAAGGAAGATGATTAATTTCTGTG
*
3242076 GACAAATTATATATGGAATCTGAACCTTTCAACAAAGGAAGATGATTAATTTTTGTG
1 GACAAATTATATATGGAATCTGAACCTTTCAACAAAGGAAGATGATTAATTTCTGTG
3242133 G
1 G
3242134 TTTGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (57 bp):
GACAAATTATATATGGAATCTGAACCTTTCAACAAAGGAAGATGATTAATTTCTGTG
Found at i:3242977 original size:31 final size:31
Alignment explanation
Indices: 3242882--3242982 Score: 121
Period size: 31 Copynumber: 3.3 Consensus size: 31
3242872 ATACAAAAAT
*
3242882 TAAATTGAACAAAACTCTATAATACATGGAT
1 TAAATTGAACAAAACTCTATAATACATGGAC
* ** * *
3242913 TATATTGAACAAAGTTTTATAATACATGAAC
1 TAAATTGAACAAAACTCTATAATACATGGAC
* * *
3242944 TAAATTTAACAAAACTCTATAATATACGGAC
1 TAAATTGAACAAAACTCTATAATACATGGAC
3242975 TAAATTGA
1 TAAATTGA
3242983 TTGCTTTTAT
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.32
Consensus pattern (31 bp):
TAAATTGAACAAAACTCTATAATACATGGAC
Found at i:3244486 original size:22 final size:22
Alignment explanation
Indices: 3244461--3244621 Score: 105
Period size: 22 Copynumber: 7.5 Consensus size: 22
3244451 GTTTTTGGAC
3244461 ATTGCGTGACTAATTTTTAGGT
1 ATTGCGTGACTAATTTTTAGGT
* * **
3244483 ATTGCGTGACTGA-CTTTAGAC
1 ATTGCGTGACTAATTTTTAGGT
* * * *
3244504 ATTGTGTGATTAA-CTTT-GGC
1 ATTGCGTGACTAATTTTTAGGT
** * * * *
3244524 ATTATGTGATTAGTTTTTAAGC
1 ATTGCGTGACTAATTTTTAGGT
3244546 ATTGCGTGACTAATTTTTAGGT
1 ATTGCGTGACTAATTTTTAGGT
* * * *
3244568 ATTGCGTGATTGACTTTGA-GT
1 ATTGCGTGACTAATTTTTAGGT
* * *
3244589 ATTACGTGACTAGTTTTTAAGT
1 ATTGCGTGACTAATTTTTAGGT
3244611 ATTGCGTGACT
1 ATTGCGTGACT
3244622 GGTTGATATG
Statistics
Matches: 107, Mismatches: 29, Indels: 6
0.75 0.20 0.04
Matches are distributed among these distances:
20 13 0.12
21 37 0.35
22 57 0.53
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (22 bp):
ATTGCGTGACTAATTTTTAGGT
Found at i:3244598 original size:43 final size:42
Alignment explanation
Indices: 3244460--3244619 Score: 153
Period size: 43 Copynumber: 3.8 Consensus size: 42
3244450 GGTTTTTGGA
*
3244460 CATTGCGTGACTAATTTTTAGGTATTGCGTGACTGACTTTAG
1 CATTGCGTGACTAATTTTTAGGTATTGCGTGATTGACTTTAG
* * * * ** **
3244502 ACATTGTGTGATTAA-CTTT-GGCATTATGTGATTAGTTTTTAAG
1 -CATTGCGTGACTAATTTTTAGGTATTGCGTGATT-GACTTT-AG
3244545 CATTGCGTGACTAATTTTTAGGTATTGCGTGATTGACTTTGAG
1 CATTGCGTGACTAATTTTTAGGTATTGCGTGATTGACTTT-AG
* * * *
3244588 TATTACGTGACTAGTTTTTAAGTATTGCGTGA
1 CATTGCGTGACTAATTTTTAGGTATTGCGTGA
3244620 CTGGTTGATA
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 10 0.11
42 19 0.21
43 51 0.56
44 11 0.12
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (42 bp):
CATTGCGTGACTAATTTTTAGGTATTGCGTGATTGACTTTAG
Found at i:3244642 original size:23 final size:23
Alignment explanation
Indices: 3244594--3244667 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
3244584 TGAGTATTAC
** *
3244594 GTGACTAGTTTTTAA-GTATTGC
1 GTGACTAGTTAGTAAGGTATTGT
* *
3244616 GTGACTGGTT-GATATGGTATTGT
1 GTGACTAGTTAG-TAAGGTATTGT
*
3244639 GTGATTAGTTAGTAAGGTATTGT
1 GTGACTAGTTAGTAAGGTATTGT
3244662 GTGACT
1 GTGACT
3244668 TAGGCGTTGC
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
22 11 0.27
23 29 0.71
24 1 0.02
ACGTcount: A:0.22, C:0.05, G:0.30, T:0.43
Consensus pattern (23 bp):
GTGACTAGTTAGTAAGGTATTGT
Found at i:3244729 original size:21 final size:21
Alignment explanation
Indices: 3244705--3244745 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3244695 AATACTTAAA
3244705 AACTAATCACGAAATGTCTAT
1 AACTAATCACGAAATGTCTAT
* *
3244726 AACTAATCATGTAATGTCTA
1 AACTAATCACGAAATGTCTA
3244746 AAAACCAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (21 bp):
AACTAATCACGAAATGTCTAT
Found at i:3245823 original size:21 final size:22
Alignment explanation
Indices: 3245783--3245866 Score: 89
Period size: 22 Copynumber: 3.9 Consensus size: 22
3245773 TTAATTAGTG
3245783 CATGACTAGTTTTTAAGCATTA
1 CATGACTAGTTTTTAAGCATTA
* *
3245805 CATGATTAG-TTTTAGGCATTA
1 CATGACTAGTTTTTAAGCATTA
* * * *
3245826 CGTAACTGGTTTTTAGGCATTA
1 CATGACTAGTTTTTAAGCATTA
* *
3245848 TATGACTAATTTTTAAGCA
1 CATGACTAGTTTTTAAGCA
3245867 ATACCTAAGT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 16 0.33
22 33 0.67
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.42
Consensus pattern (22 bp):
CATGACTAGTTTTTAAGCATTA
Found at i:3245914 original size:23 final size:23
Alignment explanation
Indices: 3245888--3245955 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
3245878 ACACAATACA
3245888 TTACTAACTAGTCACGCAATGTC
1 TTACTAACTAGTCACGCAATGTC
* *
3245911 TTACTAA-TAAATCATGCAATG-C
1 TTACTAACT-AGTCACGCAATGTC
* *
3245933 CTA-TCATCTAGTCACGCAATGTC
1 TTACT-AACTAGTCACGCAATGTC
3245956 ATATCAATCA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
21 1 0.03
22 15 0.43
23 19 0.54
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (23 bp):
TTACTAACTAGTCACGCAATGTC
Found at i:3247297 original size:31 final size:31
Alignment explanation
Indices: 3247183--3247297 Score: 101
Period size: 31 Copynumber: 3.7 Consensus size: 31
3247173 AATGTAAAAG
* * *
3247183 TATTTAATTTAGT-TTCTATATCATAGAATTT
1 TATTTAATTTAATCTT-TATATTATAAAATTT
* * * * *
3247214 TGTTCAA-TTAAGTTTTTATATAACAAAATTT
1 TATTTAATTTAA-TCTTTATATTATAAAATTT
3247245 TATTTAATTTAATCTTTATATTATAAAATTT
1 TATTTAATTTAATCTTTATATTATAAAATTT
*
3247276 TATTTATTTTAAT-TTTCATATT
1 TATTTAATTTAATCTTT-ATATT
3247298 TTATATAATT
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
30 6 0.09
31 56 0.82
32 6 0.09
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (31 bp):
TATTTAATTTAATCTTTATATTATAAAATTT
Found at i:3252250 original size:2 final size:2
Alignment explanation
Indices: 3252243--3252270 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3252233 CTAGCAGTCT
3252243 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
3252271 AGTTTCTCAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3262042 original size:27 final size:28
Alignment explanation
Indices: 3262004--3262082 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 28
3261994 GTTTTGGGCT
* *
3262004 CTTCCTCTTCTTCTTCAGACGAAGAC-C
1 CTTCTTCTTCTTCTTCAGATGAAGACTC
*
3262031 CTTCTTCTTCTTCTTCAGATGAAGTCTC
1 CTTCTTCTTCTTCTTCAGATGAAGACTC
*
3262059 C-TCTTTTTCTTCTTCAGATGAAGA
1 CTTCTTCTTCTTCTTCAGATGAAGA
3262083 AGCAGTGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 44 0.96
28 2 0.04
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (28 bp):
CTTCTTCTTCTTCTTCAGATGAAGACTC
Found at i:3269443 original size:39 final size:39
Alignment explanation
Indices: 3269401--3269672 Score: 237
Period size: 39 Copynumber: 7.0 Consensus size: 39
3269391 GAAATCTGAG
* * * **
3269401 GAGTCTTTTGATTTTCTCTTTGGCCCTGAGTTAACACTG
1 GAGTCTTCTGATTTTCTCTTTGGCCCTGAGATATCACAA
* * * * * *
3269440 GAGTCTGT-TGGTTTTGTCATTGGACCTGAGTTATCGCAA
1 GAGTCT-TCTGATTTTCTCTTTGGCCCTGAGATATCACAA
* * * *
3269479 GAGTCTTCCGATTTTCTATTTGGTCCTGAAATATCACAA
1 GAGTCTTCTGATTTTCTCTTTGGCCCTGAGATATCACAA
** * *
3269518 GAGGGTTCTGATTTTCTCTTTGGCGCTGAGATAACACAA
1 GAGTCTTCTGATTTTCTCTTTGGCCCTGAGATATCACAA
* *
3269557 GAATCTTCTGATTTTCGCTTTGGCCCTGCAG-TATCACAA
1 GAGTCTTCTGATTTTCTCTTTGGCCCTG-AGATATCACAA
* *
3269596 GAATCTTCTGATTTTCTCTTTGGCCCTGAAATATCACAA
1 GAGTCTTCTGATTTTCTCTTTGGCCCTGAGATATCACAA
* ** *
3269635 GAGAT-TTCTGAATTTT-TCCTCCGCCCTGAGTTATCACA
1 GAG-TCTTCTG-ATTTTCTCTTTGGCCCTGAGATATCACA
3269673 GGCATCAACA
Statistics
Matches: 188, Mismatches: 39, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
38 2 0.01
39 177 0.94
40 9 0.05
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (39 bp):
GAGTCTTCTGATTTTCTCTTTGGCCCTGAGATATCACAA
Found at i:3269618 original size:117 final size:117
Alignment explanation
Indices: 3269409--3269637 Score: 293
Period size: 117 Copynumber: 2.0 Consensus size: 117
3269399 AGGAGTCTTT
* ** * *
3269409 TGATTTTCTCTTTGGCCCTGAGTTAACACTGGAGTCTGTTGGTTTTGTCATTGGACCTGAGTTAT
1 TGATTTTCTCTTTGGCCCTGAGATAACACAAGAATCTGTTGATTTTGTCATTGGACCTGAGTTAT
* * *
3269474 CGCAAGAGTCTTCCGATTTTCTATTTGGTCCTGAAATATCACAAGAGGGTTC
66 CACAAGAATCTTCCGATTTTCTATTTGGCCCTGAAATATCACAAGAGGGTTC
* * *
3269526 TGATTTTCTCTTTGGCGCTGAGATAACACAAGAATCT-TCTGATTTTCG-CTTTGGCCCTGCAG-
1 TGATTTTCTCTTTGGCCCTGAGATAACACAAGAATCTGT-TGATTTT-GTCATTGGACCTG-AGT
* *
3269588 TATCACAAGAATCTTCTGATTTTCTCTTTGGCCCTGAAATATCACAAGAG
63 TATCACAAGAATCTTCCGATTTTCTATTTGGCCCTGAAATATCACAAGAG
3269638 ATTTCTGAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
116 1 0.01
117 92 0.96
118 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (117 bp):
TGATTTTCTCTTTGGCCCTGAGATAACACAAGAATCTGTTGATTTTGTCATTGGACCTGAGTTAT
CACAAGAATCTTCCGATTTTCTATTTGGCCCTGAAATATCACAAGAGGGTTC
Found at i:3271383 original size:35 final size:35
Alignment explanation
Indices: 3271322--3271390 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
3271312 CATGGGCAAA
* *
3271322 AAACAGGTATATGTCTGTTTTACTTTTAATTGCAC
1 AAACAAGTATATGCCTGTTTTACTTTTAATTGCAC
* *
3271357 AAACAAGTATATGCCT-TCTTTGCTTTTGATTGCA
1 AAACAAGTATATGCCTGT-TTTACTTTTAATTGCA
3271391 TAGGTTAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.03
35 28 0.97
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (35 bp):
AAACAAGTATATGCCTGTTTTACTTTTAATTGCAC
Found at i:3282005 original size:25 final size:25
Alignment explanation
Indices: 3281941--3282012 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
3281931 TGAAAAGGTT
* **
3281941 CTTTTCCCCTCTTTTGCTCTCTTTC
1 CTTTTCCCCTATTTCACTCTCTTTC
* * *
3281966 CTATTCACCTATTTCACTTTCTTTC
1 CTTTTCCCCTATTTCACTCTCTTTC
*
3281991 CTTTTCCCCTGTTTCACTCTCT
1 CTTTTCCCCTATTTCACTCTCT
3282013 ATTTGCTTTG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.07, C:0.38, G:0.03, T:0.53
Consensus pattern (25 bp):
CTTTTCCCCTATTTCACTCTCTTTC
Found at i:3285292 original size:12 final size:12
Alignment explanation
Indices: 3285277--3285302 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3285267 TTGTTTGGTA
3285277 AATTTTTTTTAT
1 AATTTTTTTTAT
3285289 AATTTTTTTTAT
1 AATTTTTTTTAT
3285301 AA
1 AA
3285303 GTTATAATTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
AATTTTTTTTAT
Found at i:3292926 original size:29 final size:28
Alignment explanation
Indices: 3292826--3292926 Score: 78
Period size: 29 Copynumber: 3.5 Consensus size: 28
3292816 ACGCATAATA
* * *
3292826 AAATAAATGACGT-AACAAAATACATTAC
1 AAATAAATGACATGAA-AAAACATATTAC
* * * **
3292854 AAAATAAATTACGTGACAAAACATATTGT
1 -AAATAAATGACATGAAAAAACATATTAC
* *
3292883 AAACAAATGATATGAAAAAACATATTAC
1 AAATAAATGACATGAAAAAACATATTAC
3292911 ATAATAAATGACATGA
1 A-AATAAATGACATGA
3292927 TAGAAGACAT
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
28 22 0.40
29 32 0.58
30 1 0.02
ACGTcount: A:0.56, C:0.11, G:0.09, T:0.24
Consensus pattern (28 bp):
AAATAAATGACATGAAAAAACATATTAC
Found at i:3293374 original size:2 final size:2
Alignment explanation
Indices: 3293361--3293394 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3293351 TTTATGTAGC
*
3293361 AT AT AC 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
3293395 CAGATGAAGA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3297454 original size:15 final size:15
Alignment explanation
Indices: 3297413--3297455 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
3297403 TCTTATGTTT
*
3297413 TTTTATTTATTTAAA
1 TTTTATTTATTTTAA
3297428 TTTT-TTTAATTTTAA
1 TTTTATTT-ATTTTAA
3297443 TTTTATTTATTTT
1 TTTTATTTATTTT
3297456 TAGATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 19 0.76
16 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTTATTTTAA
Found at i:3299037 original size:6 final size:6
Alignment explanation
Indices: 3299026--3299050 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3299016 TGCCTCCCTG
3299026 GTGGCA GTGGCA GTGGCA GTGGCA G
1 GTGGCA GTGGCA GTGGCA GTGGCA G
3299051 CCCTCTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GTGGCA
Found at i:3306379 original size:21 final size:22
Alignment explanation
Indices: 3306339--3306379 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3306329 TTTTTTTTTT
**
3306339 AATTATTTGTTTCGATTAAAAA
1 AATTATTTAATTCGATTAAAAA
3306361 AATTATTTAATTC-ATTAAA
1 AATTATTTAATTCGATTAAA
3306380 TGTTTAGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (22 bp):
AATTATTTAATTCGATTAAAAA
Found at i:3311581 original size:22 final size:22
Alignment explanation
Indices: 3311547--3311591 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3311537 TAAAATTGAG
* *
3311547 ATAATCAATAGAAAATTATTTA
1 ATAATCAAGAGAAAAATATTTA
*
3311569 ATAATTAAGAGAAAAATATTTA
1 ATAATCAAGAGAAAAATATTTA
3311591 A
1 A
3311592 AACATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (22 bp):
ATAATCAAGAGAAAAATATTTA
Found at i:3315140 original size:7 final size:7
Alignment explanation
Indices: 3315128--3315156 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3315118 ATGACACAAA
3315128 AAAAAAG
1 AAAAAAG
3315135 AAAAAAG
1 AAAAAAG
3315142 AAAAAAG
1 AAAAAAG
3315149 AAAAAAG
1 AAAAAAG
3315156 A
1 A
3315157 CGTGTGTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:3316385 original size:3 final size:3
Alignment explanation
Indices: 3316377--3316402 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3316367 ATTGACTAAA
3316377 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
3316403 GCTTAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3317608 original size:19 final size:19
Alignment explanation
Indices: 3317584--3317631 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
3317574 ACTATAATTT
3317584 TAATTTTAATAATATTAAA
1 TAATTTTAATAATATTAAA
* *
3317603 TAATTTATATAATAATATTTAT
1 TAA-TT-T-TAATAATATTAAA
3317625 TAATTTT
1 TAATTTT
3317632 TTAATACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 4 0.17
20 3 0.12
21 3 0.12
22 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTTTAATAATATTAAA
Found at i:3320674 original size:309 final size:312
Alignment explanation
Indices: 3320108--3320726 Score: 1163
Period size: 309 Copynumber: 2.0 Consensus size: 312
3320098 TTTTTTAGTC
3320108 AAAAGTAATGCAACTTTTTAGGGTAAAATAAAAATATTTTTTTTAAGTAAAATGCATTTTCCAAT
1 AAAAGTAATGCAACTTTTTAGGGTAAAATAAAAATATTTTTTTTAAGTAAAATGCATTTTCCAAT
*
3320173 CTCATGGGATGAAATACTTCTTTCCTTTTCAATAGGACTGATTTGTTCTATACTAGGAGGATCAC
66 CTCATGGGATGAAATACTTCTTTCCTTGTCAATAGGACTGATTTGTTCTATACTAGGAGGATCAC
3320238 TCATCCAATTTCACATCCTGTATTTTCTCCAAGTAAATACCAAATGTGATTATTATAATTCTACC
131 TCATCCAATTTCACATCCTGTATTTTCTCCAAGTAAATACCAAATGTGATTATTATAATTCTACC
*
3320303 CTCTCTATTATCTCATGAACCAAATGAGTTTGTGAAATGATTATATGCTCGTGAATGGTTGGTAG
196 CTCTCTATTATCTCATGAACCAAATGAGTTTGTGAAATGATTATATGCTCCTGAATGGTTGGTAG
3320368 TTGATGTACTTTTACCTTTCAGGTATATGAAGAGGAAGTGAGGGCTTAGGGT
261 TTGATGTACTTTTACCTTTCAGGTATATGAAGAGGAAGTGAGGGCTTAGGGT
*
3320420 AAAA-TAATGCAACTTTTTAGGGTAAAATAAAAATA-TTTTTTTAAGTAAAATGCTTTTTCCAAT
1 AAAAGTAATGCAACTTTTTAGGGTAAAATAAAAATATTTTTTTTAAGTAAAATGCATTTTCCAAT
* *
3320483 CTCAT-GGATGAAATACTTGTTTCCTTGTCAATAGGACTGATTTGTTCTATGCTAGGAGGATCAC
66 CTCATGGGATGAAATACTTCTTTCCTTGTCAATAGGACTGATTTGTTCTATACTAGGAGGATCAC
*
3320547 TCATCCAATTTCACATCCTGTATTTTCTCCATGTAAATACCAAATGTGATTATTATAATTCTACC
131 TCATCCAATTTCACATCCTGTATTTTCTCCAAGTAAATACCAAATGTGATTATTATAATTCTACC
3320612 CTCTCTATTATCTCATGAACCAAATGAGTTTGTGAAATGATTATATGCTCCTGAATGGTTGGTAG
196 CTCTCTATTATCTCATGAACCAAATGAGTTTGTGAAATGATTATATGCTCCTGAATGGTTGGTAG
3320677 TTGATGTACTTTTACCTTTCAGGTATATGAAGAGGAAGTGAGGGCTTAGG
261 TTGATGTACTTTTACCTTTCAGGTATATGAAGAGGAAGTGAGGGCTTAGG
3320727 TAATTCAGTC
Statistics
Matches: 301, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
309 234 0.78
310 32 0.11
311 31 0.10
312 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (312 bp):
AAAAGTAATGCAACTTTTTAGGGTAAAATAAAAATATTTTTTTTAAGTAAAATGCATTTTCCAAT
CTCATGGGATGAAATACTTCTTTCCTTGTCAATAGGACTGATTTGTTCTATACTAGGAGGATCAC
TCATCCAATTTCACATCCTGTATTTTCTCCAAGTAAATACCAAATGTGATTATTATAATTCTACC
CTCTCTATTATCTCATGAACCAAATGAGTTTGTGAAATGATTATATGCTCCTGAATGGTTGGTAG
TTGATGTACTTTTACCTTTCAGGTATATGAAGAGGAAGTGAGGGCTTAGGGT
Found at i:3331906 original size:13 final size:14
Alignment explanation
Indices: 3331871--3331900 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3331861 TCATGGAGTT
*
3331871 AAAAGGAGAAAAGA
1 AAAAGGAAAAAAGA
3331885 AAAAGGAAAAAAGA
1 AAAAGGAAAAAAGA
3331899 AA
1 AA
3331901 TGGAAATTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAAGGAAAAAAGA
Found at i:3334050 original size:62 final size:58
Alignment explanation
Indices: 3333984--3334098 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 58
3333974 TAAAATTATA
* * *
3333984 AATAAATTATCAAAAACATTCATACTTCAAAATAAATAATCATATAAATTATTAATACCTTT
1 AATAAATTAT-AAAAAAATTAATACTTCAAAATAAA-AA-AATATAAATT-TTAATACCTTT
* *
3334046 AATAAATTATAAAAAAATTAATATTTCAAATTAAAAAAATATAAATTTTAATA
1 AATAAATTATAAAAAAATTAATACTTCAAAATAAAAAAATATAAATTTTAATA
3334099 AAAAATATGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 6 0.12
59 9 0.19
60 2 0.04
61 21 0.44
62 10 0.21
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.36
Consensus pattern (58 bp):
AATAAATTATAAAAAAATTAATACTTCAAAATAAAAAAATATAAATTTTAATACCTTT
Found at i:3334102 original size:21 final size:22
Alignment explanation
Indices: 3334056--3334103 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
3334046 AATAAATTAT
*
3334056 AAAAAAATTAATATTTCAAATT
1 AAAAAAATTAATATTTCAAATA
*
3334078 AAAAAAATATAA-ATTT-TAATA
1 AAAAAAAT-TAATATTTCAAATA
3334099 AAAAA
1 AAAAA
3334104 TATGTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 12 0.52
23 3 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAAAATTAATATTTCAAATA
Found at i:3335931 original size:2 final size:2
Alignment explanation
Indices: 3335924--3335956 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3335914 GTTTCACCAT
3335924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3335957 TAATCGAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3337438 original size:14 final size:16
Alignment explanation
Indices: 3337419--3337451 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3337409 TTATTATTAT
3337419 AAAAAT-AAAGA-AAG
1 AAAAATAAAAGATAAG
3337433 AAAAATAAAAGATAAG
1 AAAAATAAAAGATAAG
3337449 AAA
1 AAA
3337452 TATGGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 5 0.29
16 6 0.35
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (16 bp):
AAAAATAAAAGATAAG
Found at i:3346043 original size:22 final size:22
Alignment explanation
Indices: 3346018--3346069 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
3346008 AAATAGATTA
*
3346018 GACTAGTTTTTA-AGTATTACGT
1 GACTAGTTTTTAGA-TATTACAT
3346040 GACT-GATTTTTAGATATTACAT
1 GACTAG-TTTTTAGATATTACAT
*
3346062 GATTAGTT
1 GACTAGTT
3346070 ATAGGCTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 1 0.04
22 22 0.88
23 2 0.08
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (22 bp):
GACTAGTTTTTAGATATTACAT
Found at i:3346150 original size:22 final size:23
Alignment explanation
Indices: 3346119--3346167 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
3346109 GATTTTTAAA
*
3346119 CAATATCTTACTAACTAGTCA-G
1 CAATACCTTACTAACTAGTCACG
3346141 CAATACCTTACTAACTAGTCACG
1 CAATACCTTACTAACTAGTCACG
3346164 CAAT
1 CAAT
3346168 GTTTACCGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.29
Consensus pattern (23 bp):
CAATACCTTACTAACTAGTCACG
Found at i:3346254 original size:21 final size:21
Alignment explanation
Indices: 3346228--3346298 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
3346218 AAAACTAGTC
* *
3346228 ACGCAATGCTGAAAGTCAATT
1 ACGCAATACTAAAAGTCAATT
* * *
3346249 ACGCAATACTTAAAA-ACTAGTC
1 ACGCAATAC-TAAAAGTC-AATT
3346271 ACGCAATACTAAAAGTCAATT
1 ACGCAATACTAAAAGTCAATT
3346292 ACGCAAT
1 ACGCAAT
3346299 GCTTAAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 23 0.59
22 16 0.41
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.23
Consensus pattern (21 bp):
ACGCAATACTAAAAGTCAATT
Found at i:3346257 original size:43 final size:43
Alignment explanation
Indices: 3346204--3346328 Score: 187
Period size: 43 Copynumber: 2.9 Consensus size: 43
3346194 TATCAACCAG
* *
3346204 TTACGTAATACTTAAAAACTAGTCACGCAATGCTGAAAGTCAA
1 TTACGCAATACTTAAAAACTAGTCACGCAATGCTAAAAGTCAA
*
3346247 TTACGCAATACTTAAAAACTAGTCACGCAATACTAAAAGTCAA
1 TTACGCAATACTTAAAAACTAGTCACGCAATGCTAAAAGTCAA
* * *
3346290 TTACGCAATGCTTAAAAATTAATCACGCAATGCTTAAAA
1 TTACGCAATACTTAAAAACTAGTCACGCAATGC-TAAAA
3346329 ACTAGACACG
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 69 0.93
44 5 0.07
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (43 bp):
TTACGCAATACTTAAAAACTAGTCACGCAATGCTAAAAGTCAA
Found at i:3346277 original size:22 final size:22
Alignment explanation
Indices: 3346210--3346364 Score: 111
Period size: 22 Copynumber: 7.2 Consensus size: 22
3346200 CCAGTTACGT
3346210 AATACTTAAAAACTAGTCACGC
1 AATACTTAAAAACTAGTCACGC
* * ** * *
3346232 AATGCTGAAAGTC-AATTACGC
1 AATACTTAAAAACTAGTCACGC
3346253 AATACTTAAAAACTAGTCACGC
1 AATACTTAAAAACTAGTCACGC
* * *
3346275 AATAC-T-AAAAGTCAATTACGC
1 AATACTTAAAAACT-AGTCACGC
* * *
3346296 AATGCTTAAAAATTAATCACGC
1 AATACTTAAAAACTAGTCACGC
* *
3346318 AATGCTTAAAAACTAGACACGC
1 AATACTTAAAAACTAGTCACGC
* * * *
3346340 AATGCCTAAAATC-AGTCACGT
1 AATACTTAAAAACTAGTCACGC
3346361 AATA
1 AATA
3346365 TCCAAAGTCA
Statistics
Matches: 103, Mismatches: 26, Indels: 9
0.75 0.19 0.07
Matches are distributed among these distances:
20 5 0.05
21 35 0.34
22 58 0.56
23 5 0.05
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.23
Consensus pattern (22 bp):
AATACTTAAAAACTAGTCACGC
Found at i:3352347 original size:44 final size:44
Alignment explanation
Indices: 3352292--3352376 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
3352282 GCATAAAATA
* * * * *
3352292 ATTATTTTATAAGAATATAAT-AAGATATGAATATTTATTATTTG
1 ATTATTCTATAAAAATAAAATAAAG-TAAGAATACTTATTATTTG
3352336 ATTATTCTATAAAAATAAAATAAAGTAAGAATACTTATTAT
1 ATTATTCTATAAAAATAAAATAAAGTAAGAATACTTATTAT
3352377 GTAATTTGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 32 0.91
45 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.42
Consensus pattern (44 bp):
ATTATTCTATAAAAATAAAATAAAGTAAGAATACTTATTATTTG
Found at i:3352713 original size:19 final size:19
Alignment explanation
Indices: 3352691--3352751 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
3352681 AAATATTAAC
3352691 AAATTTATAATATAATTTT
1 AAATTTATAATATAATTTT
* *
3352710 AAATTCA-AAAATTAATTTTT
1 AAATTTATAATA-TAA-TTTT
* *
3352730 ATAATTTATATTAAAATTTT
1 A-AATTTATAATATAATTTT
3352750 AA
1 AA
3352752 TTTTTTATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 3 0.09
19 10 0.31
20 10 0.31
21 7 0.22
22 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTATAATATAATTTT
Found at i:3352779 original size:28 final size:27
Alignment explanation
Indices: 3352701--3352779 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
3352691 AAATTTATAA
3352701 TATAATTT-TAAATTCAAAAATTAATTTT
1 TATAATTTAT-AATT-AAAAATTAATTTT
*
3352729 TATAATTTAT-ATTAAAATTTTAATTTTT
1 TATAATTTATAATTAAAA-ATTAA-TTTT
*
3352757 TATAATTTATAATTAAAACTTAA
1 TATAATTTATAATTAAAAATTAA
3352780 AACTTTTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
26 4 0.09
27 7 0.16
28 26 0.58
29 8 0.18
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
TATAATTTATAATTAAAAATTAATTTT
Found at i:3352786 original size:29 final size:28
Alignment explanation
Indices: 3352726--3352788 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
3352716 AAAAATTAAT
* * **
3352726 TTTTATAATTTATATTAAAATTTTAATT
1 TTTTATAATTTATATTAAAACTTAAAAC
3352754 TTTTATAATTTATAATTAAAACTTAAAAC
1 TTTTATAATTTAT-ATTAAAACTTAAAAC
3352783 TTTTAT
1 TTTTAT
3352789 TTTAGTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTATAATTTATATTAAAACTTAAAAC
Found at i:3358599 original size:21 final size:23
Alignment explanation
Indices: 3358575--3358627 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 23
3358565 ATTATAAAAA
3358575 AAAATAAAATTCAT-ATAA-CAG
1 AAAATAAAATTCATGATAAGCAG
*
3358596 AAAA-AAAA-ACATGATAAGCAG
1 AAAATAAAATTCATGATAAGCAG
3358617 AAAATAAAATT
1 AAAATAAAATT
3358628 TACATATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 3 0.12
20 8 0.31
21 11 0.42
22 4 0.15
ACGTcount: A:0.66, C:0.08, G:0.08, T:0.19
Consensus pattern (23 bp):
AAAATAAAATTCATGATAAGCAG
Found at i:3358908 original size:10 final size:10
Alignment explanation
Indices: 3358879--3358914 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3358869 TGAGAGGCCA
*
3358879 TTAAAGAAAT
1 TTAAAAAAAT
3358889 TTATAAAAAAT
1 TTA-AAAAAAT
3358900 TTAAAAAAAT
1 TTAAAAAAAT
3358910 TTAAA
1 TTAAA
3358915 TTTTGGAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:3361549 original size:1 final size:1
Alignment explanation
Indices: 3361543--3361572 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3361533 TCTTAGCTTC
3361543 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3361573 ATCTTTGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3364186 original size:71 final size:71
Alignment explanation
Indices: 3364104--3364244 Score: 273
Period size: 71 Copynumber: 2.0 Consensus size: 71
3364094 ATAATGTCTG
*
3364104 GTTAACTTTTATATTGCTGTGAACCTCTATTTCTGTGGGCATGAAAGAATGATGTCTTTCTGTTG
1 GTTAACTTTTATATTGCTGTGAACCTCTATTTCTGTGGGCATAAAAGAATGATGTCTTTCTGTTG
3364169 GTTAAA
66 GTTAAA
3364175 GTTAACTTTTATATTGCTGTGAACCTCTATTTCTGTGGGCATAAAAGAATGATGTCTTTCTGTTG
1 GTTAACTTTTATATTGCTGTGAACCTCTATTTCTGTGGGCATAAAAGAATGATGTCTTTCTGTTG
3364240 GTTAA
66 GTTAA
3364245 CTTTTATATC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.43
Consensus pattern (71 bp):
GTTAACTTTTATATTGCTGTGAACCTCTATTTCTGTGGGCATAAAAGAATGATGTCTTTCTGTTG
GTTAAA
Found at i:3365564 original size:4 final size:4
Alignment explanation
Indices: 3365555--3365580 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3365545 TTAGAAGGAA
3365555 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
3365581 CTTTGACAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3372154 original size:20 final size:20
Alignment explanation
Indices: 3372127--3372182 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
3372117 ATAAAATCTA
**
3372127 TAAAAAAATGTATTTATTAAT
1 TAAAAAAAT-TATTTACAAAT
3372148 TAAAAAAAATTATTTACAAAT
1 T-AAAAAAATTATTTACAAAT
*
3372169 TAAAAAATTTATTT
1 TAAAAAAATTATTT
3372183 TGTCTCTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.39
21 11 0.35
22 8 0.26
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAAAAAATTATTTACAAAT
Found at i:3374080 original size:34 final size:34
Alignment explanation
Indices: 3374016--3374080 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
3374006 CTTTTACTTG
* * *
3374016 CCTTTTTTCTCCTTCCTTTTTCTTATTCTCTTAC
1 CCTTTCTTCTCCTTCCTTTTCCTCATTCTCTTAC
*
3374050 CCTTTCTTCTCTTCTCCTTTTCCTCA-TCTCT
1 CCTTTCTTCTCCT-TCCTTTTCCTCATTCTCT
3374081 GGACCACCGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
34 16 0.62
35 10 0.38
ACGTcount: A:0.05, C:0.37, G:0.00, T:0.58
Consensus pattern (34 bp):
CCTTTCTTCTCCTTCCTTTTCCTCATTCTCTTAC
Found at i:3385518 original size:3 final size:3
Alignment explanation
Indices: 3385512--3385542 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3385502 GCTTAAGGAG
3385512 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
3385543 GGTGGCCAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3391691 original size:7 final size:8
Alignment explanation
Indices: 3391674--3391698 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3391664 TGTCGACATC
3391674 TTTTTATT
1 TTTTTATT
3391682 TTTTTATT
1 TTTTTATT
3391690 TTTTTATT
1 TTTTTATT
3391698 T
1 T
3391699 CAATAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:3395577 original size:23 final size:23
Alignment explanation
Indices: 3395551--3395598 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3395541 CATAATACTT
3395551 TACTAACCGGTCACGCAATGTCC
1 TACTAACCGGTCACGCAATGTCC
3395574 TACTAACCGGTCACGCAATGTCC
1 TACTAACCGGTCACGCAATGTCC
3395597 TA
1 TA
3395599 AAAATTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (23 bp):
TACTAACCGGTCACGCAATGTCC
Found at i:3395637 original size:22 final size:22
Alignment explanation
Indices: 3395590--3395646 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
3395580 CCGGTCACGC
*
3395590 AATGTCCTAAAAATTAGAAACGT
1 AATGTCC-AAAAATTAGAAACAT
*
3395613 AATGTCCAAAAA-TAGATTACAT
1 AATGTCCAAAAATTAGA-AACAT
3395635 AATG-CACAAAAA
1 AATGTC-CAAAAA
3395647 CCACAAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 5 0.17
22 18 0.60
23 7 0.23
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.23
Consensus pattern (22 bp):
AATGTCCAAAAATTAGAAACAT
Found at i:3395852 original size:60 final size:60
Alignment explanation
Indices: 3395747--3395862 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
3395737 TATTTGACGA
* * * *
3395747 AAAATATTCCAAAGTTTTTCTTCATGTATCAAAGATCACTCCAAAAAGTTTAAAATGCTC
1 AAAATACTCCAAAGTTTTTCTTCATGTATCAAAAACCACTCCAAAAAGTTCAAAATGCTC
** * * *
3395807 AAAATACT-CAAACGTTTTTCTTTGTGTATCAAAAACCATTTCAAAATGTTCAAAAT
1 AAAATACTCCAAA-GTTTTTCTTCATGTATCAAAAACCACTCCAAAAAGTTCAAAAT
3395863 ACTTAAAGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
59 4 0.09
60 42 0.91
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (60 bp):
AAAATACTCCAAAGTTTTTCTTCATGTATCAAAAACCACTCCAAAAAGTTCAAAATGCTC
Found at i:3407070 original size:27 final size:28
Alignment explanation
Indices: 3407040--3407100 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
3407030 TTTACAATTA
*
3407040 GAACACCT-TTGGGTGTTTCCGCACTTG
1 GAACACCTCTTGGGTGTTTCCACACTTG
* *
3407067 GAACA-CTCTTGGGTGTTTTCATACTTG
1 GAACACCTCTTGGGTGTTTCCACACTTG
3407094 GAACACC
1 GAACACC
3407101 CCTAACACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 26 0.90
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.33
Consensus pattern (28 bp):
GAACACCTCTTGGGTGTTTCCACACTTG
Found at i:3407175 original size:54 final size:54
Alignment explanation
Indices: 3407105--3407222 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 54
3407095 AACACCCCTA
** * * *
3407105 ACACTTCCGCACTTGTAACGACCTTGAACGTTTTTGCGCTTAAAACACCCTTGG
1 ACACTTCCGTGCTTGTAACGACCCTGAACGTTTCTACGCTTAAAACACCCTTGG
* * * * *
3407159 A-AGCTTCCGTGCTTGTAATGACCCTGAGCGTTTCTACGCTTGAAATACTCTTGG
1 ACA-CTTCCGTGCTTGTAACGACCCTGAACGTTTCTACGCTTAAAACACCCTTGG
3407213 ACACTTCCGT
1 ACACTTCCGT
3407223 ACTTAGAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
53 1 0.02
54 50 0.96
55 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (54 bp):
ACACTTCCGTGCTTGTAACGACCCTGAACGTTTCTACGCTTAAAACACCCTTGG
Found at i:3410925 original size:103 final size:101
Alignment explanation
Indices: 3410785--3410986 Score: 350
Period size: 103 Copynumber: 2.0 Consensus size: 101
3410775 ATTATTCTAC
*
3410785 ATACCAATGCTTGATTAATCATCTTGCAGAAAATCATGAATCACCTCGAAGATGGAAGAAAATCA
1 ATACCAATGCTTGATCAATCATCTTGCAGAAAATCATGAATCACCTCGAAGATGGAA-AAAATCA
3410850 AATGAGCATGAGCTGTATTCATTATTTCCATAATCAAT
65 AATGAGCATGAGCTGTATTCATTA-TTCCATAATCAAT
* *
3410888 ATACCAATGCTTGATCAATCATCTTGCAGAAAATCATGAATCTCCTCGATGATGGAAAAAATCAA
1 ATACCAATGCTTGATCAATCATCTTGCAGAAAATCATGAATCACCTCGAAGATGGAAAAAATCAA
*
3410953 ATGAGTATGAGCTGTATTCATTATTCCATAATCA
66 ATGAGCATGAGCTGTATTCATTATTCCATAATCA
3410987 CATGAATAAT
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
101 11 0.12
102 30 0.32
103 54 0.57
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (101 bp):
ATACCAATGCTTGATCAATCATCTTGCAGAAAATCATGAATCACCTCGAAGATGGAAAAAATCAA
ATGAGCATGAGCTGTATTCATTATTCCATAATCAAT
Found at i:3414067 original size:16 final size:17
Alignment explanation
Indices: 3414043--3414084 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3414033 ATCTGCAAAG
*
3414043 AAAAA-ATAA-ATAAAT
1 AAAAATATAAGATAAAA
3414058 AAAAATATAAGATAAAA
1 AAAAATATAAGATAAAA
3414075 AAAAAGTATA
1 AAAAA-TATA
3414085 GGAAATACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 4 0.17
17 10 0.43
18 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAAATATAAGATAAAA
Found at i:3416891 original size:28 final size:28
Alignment explanation
Indices: 3416856--3416913 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
3416846 TTTTAAAAAA
*
3416856 TTATTTTTTATTAT-ATTTAATTAAATT
1 TTATTTTTTATTATAATTTAAATAAATT
* *
3416883 TTATATTTTTATTTTAATTTAAATAATTT
1 TTAT-TTTTTATTATAATTTAAATAAATT
3416912 TT
1 TT
3416914 TATAATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.15
28 9 0.35
29 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TTATTTTTTATTATAATTTAAATAAATT
Done.