Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 11 of 310
Found at i:2765781 original size:26 final size:26
Alignment explanation
Indices: 2765735--2765784 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2765725 TGTTGAATAC
*
2765735 AATTAAAATATGATAACTATTTTAGT
1 AATTAAAATATGACAACTATTTTAGT
* *
2765761 AATTAAAATATTACAATTATTTTA
1 AATTAAAATATGACAACTATTTTA
2765785 ATAAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (26 bp):
AATTAAAATATGACAACTATTTTAGT
Found at i:2766192 original size:19 final size:19
Alignment explanation
Indices: 2766157--2766204 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2766147 TTGAAATTTT
2766157 ATATT-AATATTTATAATA
1 ATATTAAATATTTATAATA
*
2766175 ATATTAAATAATTT-TAATT
1 ATATTAAAT-ATTTATAATA
2766194 ATATT-AATATT
1 ATATTAAATATT
2766205 AAAAAAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.11
18 8 0.30
19 12 0.44
20 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATTAAATATTTATAATA
Found at i:2771326 original size:43 final size:43
Alignment explanation
Indices: 2771179--2771337 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 43
2771169 TATGTGTGAT
* *
2771179 CATGTAAGCCCACATCTGGGACATTGGCATCGACT-TATGATTTA
1 CATGTAAGACCACATCTGGGACATTGGCATCGA-TATTTGA-TTA
* ** * *
2771223 CATGTAAAACCACATCTAAGACGTTGGCATCG-TATTTGATTT
1 CATGTAAGACCACATCTGGGACATTGGCATCGATATTTGATTA
** * *
2771265 TGTGTAAGACC-CTATCTGGGATAATGGCATCGATATTTGATTA
1 CATGTAAGACCAC-ATCTGGGACATTGGCATCGATATTTGATTA
* *
2771308 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CATGTAAGACCACATCTGGGACATTGGCAT
2771338 TGTATGACCT
Statistics
Matches: 89, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
41 1 0.01
42 25 0.28
43 35 0.39
44 28 0.31
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (43 bp):
CATGTAAGACCACATCTGGGACATTGGCATCGATATTTGATTA
Found at i:2773380 original size:43 final size:43
Alignment explanation
Indices: 2773233--2773391 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 43
2773223 TATGTGTGAT
* *
2773233 CATGTAAGCCCACATCTGGGACATTGGCATCGACT-TATGATTTA
1 CATGTAAGACCACATCTGGGACATTGGCATCGA-TATTTGA-TTA
* ** * *
2773277 CATGTAAAACCACATCTAAGACGTTGGCATCG-TATTTGATTT
1 CATGTAAGACCACATCTGGGACATTGGCATCGATATTTGATTA
** * *
2773319 TGTGTAAGACC-CTATCTGGGATAATGGCATCGATATTTGATTA
1 CATGTAAGACCAC-ATCTGGGACATTGGCATCGATATTTGATTA
* *
2773362 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CATGTAAGACCACATCTGGGACATTGGCAT
2773392 TGTATGACCT
Statistics
Matches: 89, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
41 1 0.01
42 25 0.28
43 35 0.39
44 28 0.31
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (43 bp):
CATGTAAGACCACATCTGGGACATTGGCATCGATATTTGATTA
Found at i:2782820 original size:19 final size:19
Alignment explanation
Indices: 2782796--2782892 Score: 135
Period size: 19 Copynumber: 5.1 Consensus size: 19
2782786 ATCTTTAAGA
2782796 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
2782815 ATATGCAATCTTAAATATG
1 ATATGCAATCTTAGATATG
*
2782834 GTA--CAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
2782851 ATATGCAATCTTATATATG
1 ATATGCAATCTTAGATATG
2782870 ATATGCAATCTTGAAGATATG
1 ATATGCAATCTT--AGATATG
2782891 AT
1 AT
2782893 CTTGTAATCT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.22
19 45 0.66
21 8 0.12
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:2782825 original size:36 final size:36
Alignment explanation
Indices: 2782785--2782892 Score: 116
Period size: 36 Copynumber: 2.9 Consensus size: 36
2782775 ATGGAAATAT
2782785 AATCTTTAAGAATATGCAATCTTAGATATGATATGC
1 AATCTTTAAGAATATGCAATCTTAGATATGATATGC
2782821 AATC-TT-A-AATATGGTACAATCTTAGATATGATATGC
1 AATCTTTAAGAATAT-G--CAATCTTAGATATGATATGC
2782857 AATCTTATATATG-ATATGCAATCTTGAAGATATGAT
1 AATCTT-TA-A-GAATATGCAATCTT--AGATATGAT
2782893 CTTGTAATCT
Statistics
Matches: 61, Mismatches: 0, Indels: 18
0.77 0.00 0.23
Matches are distributed among these distances:
33 5 0.08
34 2 0.03
35 2 0.03
36 28 0.46
37 1 0.02
38 8 0.13
40 11 0.18
41 4 0.07
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (36 bp):
AATCTTTAAGAATATGCAATCTTAGATATGATATGC
Found at i:2787152 original size:22 final size:22
Alignment explanation
Indices: 2787108--2787152 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2787098 ATATAACTAT
* * *
2787108 AATGATAATAATAATATTGATC
1 AATGATAATAACAATAATAATC
*
2787130 AATGGTAATAACAATAATAATC
1 AATGATAATAACAATAATAATC
2787152 A
1 A
2787153 TAATACCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (22 bp):
AATGATAATAACAATAATAATC
Found at i:2787269 original size:12 final size:12
Alignment explanation
Indices: 2787252--2787288 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
2787242 AAAGTGCAGG
2787252 AAATAATAAAAT
1 AAATAATAAAAT
2787264 AAATAATAAAAT
1 AAATAATAAAAT
2787276 AATGATAATAAAA
1 AA--ATAATAAAA
2787289 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.61
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:2790044 original size:34 final size:34
Alignment explanation
Indices: 2790000--2790067 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2789990 GCACAGTTGA
* *
2790000 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTAT-AGTG
*
2790035 ACAGT-TTGGGCCTTAGCCCATCTCAGTATAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTATAGTG
2790068 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 4 0.13
34 21 0.70
35 5 0.17
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGTATAGTG
Found at i:2793964 original size:37 final size:37
Alignment explanation
Indices: 2793923--2794021 Score: 103
Period size: 37 Copynumber: 2.7 Consensus size: 37
2793913 TTACTTGTTG
*
2793923 ATATATCGACTAAAGCTCAACCGAGTGATATCTACTA
1 ATATATCGAATAAAGCTCAACCGAGTGATATCTACTA
* * * * *
2793960 ATATA-CTGAATAAAGCTCAACTGAGAGTTATTTACTG
1 ATATATC-GAATAAAGCTCAACCGAGTGATATCTACTA
* *
2793997 ATATGTCGAGT-AAGCTCAACCGAGT
1 ATATATCGAATAAAGCTCAACCGAGT
2794022 ATTATCCATT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
36 13 0.26
37 36 0.72
38 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (37 bp):
ATATATCGAATAAAGCTCAACCGAGTGATATCTACTA
Found at i:2794037 original size:74 final size:74
Alignment explanation
Indices: 2793901--2794043 Score: 173
Period size: 74 Copynumber: 1.9 Consensus size: 74
2793891 CTGAATGTTA
* ** *
2793901 CTCAACTGAGTGTTACTTGTTGATATATCGACTAAAGCTCAACCGAGTGATATCTACTAATATAC
1 CTCAACTGAGAGTTACTTACTGATATATCGACTAAAGCTCAACCGAGTGATATCCACTAATATAC
2793966 TGAATAAAG
66 TGAATAAAG
* * * *
2793975 CTCAACTGAGAGTTATTTACTGATATGTCGAGT-AAGCTCAACCGAGT-ATTATCCATTGAATAT
1 CTCAACTGAGAGTTACTTACTGATATATCGACTAAAGCTCAACCGAGTGA-TATCCACT-AATAT
*
2794038 ATTGAA
64 ACTGAA
2794044 CTACTGTACT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
72 1 0.02
73 20 0.34
74 37 0.64
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (74 bp):
CTCAACTGAGAGTTACTTACTGATATATCGACTAAAGCTCAACCGAGTGATATCCACTAATATAC
TGAATAAAG
Found at i:2794945 original size:24 final size:24
Alignment explanation
Indices: 2794918--2794964 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2794908 CAAATTTGAT
2794918 TGGACATTATGACCAGATCAGGCC
1 TGGACATTATGACCAGATCAGGCC
**
2794942 TGGATGTTATGACCAGATCAGGC
1 TGGACATTATGACCAGATCAGGC
2794965 GATGTCACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (24 bp):
TGGACATTATGACCAGATCAGGCC
Found at i:2803663 original size:50 final size:47
Alignment explanation
Indices: 2803599--2803764 Score: 155
Period size: 48 Copynumber: 3.5 Consensus size: 47
2803589 GGCTGACGCT
* *
2803599 ATGTCCCAGACATGGTTTTACACT-AGCTCTCACATATCCGTACCGATGTC
1 ATGTCCCAGACATGGTCTTACACTAAAC-CT-ACATAT--GTACCGATGTC
* *
2803649 ATGTCCCAGACATGGTCTTACACTGAAACCTATATATGTGCCGATGTC
1 ATGTCCCAGACATGGTCTTACACT-AAACCTACATATGTACCGATGTC
* * * *
2803697 ATGTCCCAAACATGGTCTTACA-TGAA-C-ACATCTCGTAGTCGATG-C
1 ATGTCCCAGACATGGTCTTACACTAAACCTACATAT-GTA-CCGATGTC
2803742 ATGTCCCAGACAT-GTCTTACACT
1 ATGTCCCAGACATGGTCTTACACT
2803765 TGCTTACATC
Statistics
Matches: 100, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
44 12 0.12
45 17 0.17
46 7 0.07
47 1 0.01
48 31 0.31
50 28 0.28
51 2 0.02
52 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.29
Consensus pattern (47 bp):
ATGTCCCAGACATGGTCTTACACTAAACCTACATATGTACCGATGTC
Found at i:2803865 original size:48 final size:48
Alignment explanation
Indices: 2803497--2803868 Score: 209
Period size: 46 Copynumber: 7.8 Consensus size: 48
2803487 GTATAATGTT
* * * * *
2803497 GATGCCATGTCCTAGACATGGTCTTATATTGGCTCATC-TATCAA-GTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTC-TCATATCAATGCC
* * * * *
2803544 GATGCCATGTCCTAGACATGGTCTTACACTGACTATCGAAATCAAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTC-ATATCAATGCC
* * * ** *
2803593 GACGCTATGTCCCAGACATGGTTTTACACT-AGCTCTCACATATCCGTACC
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-CTCT--CATATCAATGCC
* *
2803643 GATGTCATGTCCCAGACATGGTCTTACACTGAAAC-CT-ATAT-ATGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTG--ACTCTCATATCA-ATGCC
* * * * * * *
2803691 GATGTCATGTCCCAAACATGGTCTTACA-TGA-ACACATCTC-GTAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCAAT-GCC
* * * *
2803737 GATG-CATGTCCCAGACAT-GTCTTACACTTG-CT-TACATCTAAAGGTC
1 GATGCCATGTCCCAGACATGGTCTTACAC-TGACTCT-CATATCAATGCC
* * * * *
2803783 AATG-CATGTCCCAGATAT-GTCTTATACT-AGCTCTCGTCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCATATCAATGCC
*
2803829 GATGCCATGTCCTAGACATGGTCTTACACTGACTCTCATA
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATA
2803869 ATGTGGCTGA
Statistics
Matches: 253, Mismatches: 47, Indels: 49
0.72 0.13 0.14
Matches are distributed among these distances:
44 8 0.03
45 18 0.07
46 58 0.23
47 46 0.18
48 56 0.22
49 31 0.12
50 31 0.12
51 3 0.01
52 1 0.00
53 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCAATGCC
Found at i:2817672 original size:10 final size:10
Alignment explanation
Indices: 2817657--2817722 Score: 62
Period size: 10 Copynumber: 6.4 Consensus size: 10
2817647 TCCTCCTATC
2817657 CAAATTCTCT
1 CAAATTCTCT
2817667 CAAATTCT-T
1 CAAATTCTCT
*
2817676 CCAAAAATTCTGT
1 -C--AAATTCTCT
*
2817689 CAAATTCTCC
1 CAAATTCTCT
*
2817699 CATATTCTCT
1 CAAATTCTCT
*
2817709 CAAATTTTCT
1 CAAATTCTCT
2817719 CAAA
1 CAAA
2817723 GCTCTCTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
9 1 0.02
10 36 0.78
12 8 0.17
13 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2817685 original size:22 final size:22
Alignment explanation
Indices: 2817658--2817722 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
2817648 CCTCCTATCC
2817658 AAATTCTCTCAAATTCTTCCAA
1 AAATTCTCTCAAATTCTTCCAA
* *
2817680 AAATTCTGTCAAATTC-TCC-C
1 AAATTCTCTCAAATTCTTCCAA
*
2817700 ATATTCTCTCAAATT-TTCTCAA
1 AAATTCTCTCAAATTCTTC-CAA
2817722 A
1 A
2817723 GCTCTCTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 15 0.43
21 4 0.11
22 16 0.46
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATTCTCTCAAATTCTTCCAA
Found at i:2817924 original size:48 final size:49
Alignment explanation
Indices: 2817872--2817970 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
2817862 AGTGATAATT
**
2817872 TTAATATTTCAATAGTATTTAATA-TTTTTTTAATTTATGCAATTTTAA
1 TTAATATTTCAATACAATTTAATATTTTTTTTAATTTATGCAATTTTAA
* *
2817920 TTAATTTTTCAATACAATTTAATATTTTTTTTCATTTATGCAATTTTAA
1 TTAATATTTCAATACAATTTAATATTTTTTTTAATTTATGCAATTTTAA
2817969 TT
1 TT
2817971 TTAATTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 21 0.46
49 25 0.54
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (49 bp):
TTAATATTTCAATACAATTTAATATTTTTTTTAATTTATGCAATTTTAA
Found at i:2818926 original size:7 final size:7
Alignment explanation
Indices: 2818914--2818974 Score: 86
Period size: 7 Copynumber: 8.7 Consensus size: 7
2818904 TAATCGTTTC
2818914 GTATTTA
1 GTATTTA
2818921 GTATTTA
1 GTATTTA
* *
2818928 ATATATA
1 GTATTTA
2818935 GTATTTA
1 GTATTTA
2818942 GTATTTA
1 GTATTTA
*
2818949 GTACTTA
1 GTATTTA
*
2818956 GTACTTA
1 GTATTTA
2818963 GTATTTA
1 GTATTTA
2818970 GTATT
1 GTATT
2818975 ATGTATACAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.52
Consensus pattern (7 bp):
GTATTTA
Found at i:2819615 original size:18 final size:18
Alignment explanation
Indices: 2819592--2819626 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2819582 GCCAGGTGCG
*
2819592 TATCCTAGCCCTTATATA
1 TATCCTAACCCTTATATA
2819610 TATCCTAACCCTTATAT
1 TATCCTAACCCTTATAT
2819627 GTTTCCCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.40
Consensus pattern (18 bp):
TATCCTAACCCTTATATA
Found at i:2820094 original size:27 final size:27
Alignment explanation
Indices: 2820064--2820162 Score: 78
Period size: 27 Copynumber: 3.6 Consensus size: 27
2820054 TAAAATTTGT
2820064 TTTTAATATTT-TAATTATAATTTACTC
1 TTTT-ATATTTGTAATTATAATTTACTC
* * * *
2820091 TTTTATATTTGTAATAAAATAAAAGTT-GTT
1 TTTTATATTTGTAAT----TATAATTTACTC
*
2820121 TTTTAGTATCT-TAATTATAATTTACTC
1 TTTTA-TATTTGTAATTATAATTTACTC
2820148 TTTTATATTTGTAAT
1 TTTTATATTTGTAAT
2820163 AGAATAAAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
26 16 0.30
27 18 0.33
30 10 0.19
31 10 0.19
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (27 bp):
TTTTATATTTGTAATTATAATTTACTC
Found at i:2820137 original size:57 final size:57
Alignment explanation
Indices: 2820046--2820179 Score: 225
Period size: 57 Copynumber: 2.4 Consensus size: 57
2820036 TTCTTTCATT
* *
2820046 TAATAAAATAAAATTTG-TTTTTAATATTTTAATTATAATTTACTCTTTTATATTTG
1 TAATAAAATAAAAGTTGTTTTTTAATATCTTAATTATAATTTACTCTTTTATATTTG
*
2820102 TAATAAAATAAAAGTTGTTTTTTAGTATCTTAATTATAATTTACTCTTTTATATTTG
1 TAATAAAATAAAAGTTGTTTTTTAATATCTTAATTATAATTTACTCTTTTATATTTG
*
2820159 TAATAGAATAAAAGTTGTTTT
1 TAATAAAATAAAAGTTGTTTT
2820180 GAATAAGGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
56 16 0.22
57 57 0.78
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (57 bp):
TAATAAAATAAAAGTTGTTTTTTAATATCTTAATTATAATTTACTCTTTTATATTTG
Found at i:2823417 original size:126 final size:126
Alignment explanation
Indices: 2823258--2823606 Score: 448
Period size: 126 Copynumber: 2.8 Consensus size: 126
2823248 AATAGGAACT
* * *
2823258 ACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGAAAGTGCAAACTGCA
1 ACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACTGCT
* * * *
2823323 TGAAGTGTTTTTGACACTATTTGTTCAGAAAGGTCATCTCACAATTATTTT-TTCAGATACC
66 TGAAGCGTTTTTGACACTATTTCTTCAGAAACGTCATCTCAAAATTATTTTCTT-AGATACC
** * *
2823384 ACTGTATCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATATTGCT
1 ACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACTGCT
* * * * **
2823449 TAAAGCGTTTTTTACACTATTTTTTCAAAAACGTTTTCTCAAAATTATTTTCTTAGATACC
66 TGAAGCGTTTTTGACACTATTTCTTCAGAAACGTCATCTCAAAATTATTTTCTTAGATACC
* ** * * * *
2823510 ACTGTAGAAAAAAAAAGTCCACATGAGAGCATTTTTCAGTAATTTTGCTGACAGTGCATCCTGCT
1 ACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACTGCT
* *
2823575 TGAAGCGTTTTGGATACTATTTCTTCAGAAAC
66 TGAAGCGTTTTTGACACTATTTCTTCAGAAAC
2823607 TTTTCTTAAA
Statistics
Matches: 189, Mismatches: 33, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
126 187 0.99
127 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (126 bp):
ACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACTGCT
TGAAGCGTTTTTGACACTATTTCTTCAGAAACGTCATCTCAAAATTATTTTCTTAGATACC
Found at i:2823626 original size:126 final size:124
Alignment explanation
Indices: 2823258--2823650 Score: 437
Period size: 126 Copynumber: 3.1 Consensus size: 124
2823248 AATAGGAACT
* ** * * *
2823258 ACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGAAAGTGCAAACTGCA
1 ACTGTAGAAAAAAAAAGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACTGCT
* * * ** *
2823323 TGAAGTGTTTTTGACACTATTTGTTCAGAAAGGTCATCTCACAATTATTTTTTCAGATACC
66 TGAAGCGTTTTTGACACTATTTCTTCAGAAA-CTTTTCTCAAAATT-TTTTTTCAGATACC
** * ** * *
2823384 ACTGTATCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATATTGCT
1 ACTGTAGAAAAAAAAAGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACTGCT
* * * *
2823449 TAAAGCGTTTTTTACACTATTTTTTCAAAAACGTTTTCTCAAAATTATTTTCTT-AGATACC
66 TGAAGCGTTTTTGACACTATTTCTTCAGAAAC-TTTTCTCAAAATT-TTTT-TTCAGATACC
* * * *
2823510 ACTGTAGAAAAAAAAAGTCCACATGAGAGCATTTTTCAGTAATTTTGCTGACAGTGCATCCTGCT
1 ACTGTAGAAAAAAAAAGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACTGCT
* * * *
2823575 TGAAGCGTTTTGGATACTATTTCTTCAGAAACTTTTCTTAAAATTTTTTTTCCAGATACT
66 TGAAGCGTTTTTGACACTATTTCTTCAGAAACTTTTCTCAAAATTTTTTTT-CAGATACC
*
2823635 ACTGAAGAAAAAAAAA
1 ACTGTAGAAAAAAAAA
2823651 CCAAAAAATT
Statistics
Matches: 227, Mismatches: 36, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
123 2 0.01
124 4 0.02
125 33 0.15
126 186 0.82
127 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (124 bp):
ACTGTAGAAAAAAAAAGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATACTGCT
TGAAGCGTTTTTGACACTATTTCTTCAGAAACTTTTCTCAAAATTTTTTTTCAGATACC
Found at i:2823810 original size:26 final size:26
Alignment explanation
Indices: 2823776--2823839 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
2823766 AATTAATATT
*
2823776 TAATTTAATTAATTAATTTTACACCC
1 TAATTTAATTAATTAATCTTACACCC
*
2823802 TAATTTAATTAATTAATCTTACGCCC
1 TAATTTAATTAATTAATCTTACACCC
2823828 TAATTTAATTAA
1 TAATTTAATTAA
2823840 CTAAACCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (26 bp):
TAATTTAATTAATTAATCTTACACCC
Found at i:2823873 original size:16 final size:15
Alignment explanation
Indices: 2823852--2823962 Score: 76
Period size: 16 Copynumber: 7.7 Consensus size: 15
2823842 AAACCCTTAC
2823852 AAAAACCCTAAACCCT
1 AAAAACCCT-AACCCT
2823868 AAAAACCCTAACCCT
1 AAAAACCCTAACCCT
2823883 --AAA-CC--A---T
1 AAAAACCCTAACCCT
*
2823890 AAAAACCTTAACCCAT
1 AAAAACCCTAACCC-T
*** *
2823906 CCTAACACTAACCCT
1 AAAAACCCTAACCCT
*
2823921 AAAAACCCTAAACCAT
1 AAAAACCCT-AACCCT
2823937 AAAAACCCTAACCCT
1 AAAAACCCTAACCCT
*
2823952 AAAAAACCTAA
1 AAAAACCCTAA
2823963 TCCCAACAGA
Statistics
Matches: 72, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
7 1 0.01
9 3 0.04
10 2 0.03
12 3 0.04
13 3 0.04
15 27 0.38
16 33 0.46
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAACCCTAACCCT
Found at i:2823883 original size:22 final size:22
Alignment explanation
Indices: 2823855--2823954 Score: 98
Period size: 22 Copynumber: 4.4 Consensus size: 22
2823845 CCCTTACAAA
*
2823855 AACCCTAAACCCTAAAAACCCT
1 AACCCTAAACCATAAAAACCCT
*
2823877 AACCCTAAACCATAAAAACCTT
1 AACCCTAAACCATAAAAACCCT
*
2823899 AACCC--ATCC-TAACACTAACCCT
1 AACCCTAAACCATAA-A--AACCCT
2823921 AAAAACCCTAAACCATAAAAACCCT
1 ---AACCCTAAACCATAAAAACCCT
2823946 AACCCTAAA
1 AACCCTAAA
2823955 AAACCTAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
19 3 0.05
20 4 0.06
22 39 0.61
25 11 0.17
27 4 0.06
28 3 0.05
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (22 bp):
AACCCTAAACCATAAAAACCCT
Found at i:2824463 original size:17 final size:17
Alignment explanation
Indices: 2824415--2824465 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
2824405 GAGGCGCGAC
2824415 ATAATATTTTAATAATA
1 ATAATATTTTAATAATA
*
2824432 A-AATTTTTTTAATAATA
1 ATAA-TATTTTAATAATA
2824449 ATAATATTATT-ATAATA
1 ATAATATT-TTAATAATA
2824466 TTTAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 2 0.07
17 23 0.79
18 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATATTTTAATAATA
Found at i:2824464 original size:20 final size:20
Alignment explanation
Indices: 2824424--2824465 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2824414 CATAATATTT
* *
2824424 TAATAATAAAATTTTTTTAA
1 TAATAATAAAATTATTATAA
*
2824444 TAATAATAATATTATTATAA
1 TAATAATAAAATTATTATAA
2824464 TA
1 TA
2824466 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATAATAAAATTATTATAA
Found at i:2824725 original size:3 final size:3
Alignment explanation
Indices: 2824719--2824743 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2824709 AAAAAAAAAG
2824719 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
2824744 AAAAGGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2825714 original size:22 final size:21
Alignment explanation
Indices: 2825666--2825716 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2825656 ATTTTGTTTC
* * *
2825666 TAAAATTTTGAAATAATTTAT
1 TAAATTTTTGAAATAATTAAA
2825687 TGAAATTTTTGAAATAAATTAAA
1 T-AAATTTTTGAAAT-AATTAAA
2825710 TAAATTT
1 TAAATTT
2825717 AATTTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (21 bp):
TAAATTTTTGAAATAATTAAA
Found at i:2827477 original size:33 final size:33
Alignment explanation
Indices: 2827425--2827592 Score: 207
Period size: 33 Copynumber: 5.1 Consensus size: 33
2827415 TATCTTCAGC
**
2827425 CCACCATC-GTACTTCGCTCCTTCCGGCTCGTAT
1 CCACCA-CAGTACTTCGCTCCTTCTAGCTCGTAT
* *
2827458 CCACTACAGTAC-TCTGCTCCTTCCAGCTCGTAT
1 CCACCACAGTACTTC-GCTCCTTCTAGCTCGTAT
2827491 CCACCACCA-TACTTCGCTCCTTCTAGCTCGTAT
1 CCACCA-CAGTACTTCGCTCCTTCTAGCTCGTAT
* * *
2827524 CCACCACCGTACTCCGCTCCTTCTAGCTCATAT
1 CCACCACAGTACTTCGCTCCTTCTAGCTCGTAT
* *
2827557 CCACCACCGTACTTCGCTCCTTCTGGCTCGTAT
1 CCACCACAGTACTTCGCTCCTTCTAGCTCGTAT
2827590 CCA
1 CCA
2827593 TCGACATTCT
Statistics
Matches: 120, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
32 4 0.03
33 112 0.93
34 4 0.03
ACGTcount: A:0.16, C:0.43, G:0.12, T:0.29
Consensus pattern (33 bp):
CCACCACAGTACTTCGCTCCTTCTAGCTCGTAT
Found at i:2827505 original size:66 final size:66
Alignment explanation
Indices: 2827425--2827592 Score: 255
Period size: 66 Copynumber: 2.5 Consensus size: 66
2827415 TATCTTCAGC
* * * * *
2827425 CCACCATCGTACTTCGCTCCTTCCGGCTCGTATCCACTACAGTACTCTGCTCCTTCCAGCTCGTA
1 CCACCACCGTACTTCGCTCCTTCTGGCTCGTATCCACCACAGTACTCCGCTCCTTCCAGCTCATA
2827490 T
66 T
* * * *
2827491 CCACCACCATACTTCGCTCCTTCTAGCTCGTATCCACCACCGTACTCCGCTCCTTCTAGCTCATA
1 CCACCACCGTACTTCGCTCCTTCTGGCTCGTATCCACCACAGTACTCCGCTCCTTCCAGCTCATA
2827556 T
66 T
2827557 CCACCACCGTACTTCGCTCCTTCTGGCTCGTATCCA
1 CCACCACCGTACTTCGCTCCTTCTGGCTCGTATCCA
2827593 TCGACATTCT
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 91 1.00
ACGTcount: A:0.16, C:0.43, G:0.12, T:0.29
Consensus pattern (66 bp):
CCACCACCGTACTTCGCTCCTTCTGGCTCGTATCCACCACAGTACTCCGCTCCTTCCAGCTCATA
T
Found at i:2827624 original size:66 final size:65
Alignment explanation
Indices: 2827425--2827635 Score: 233
Period size: 66 Copynumber: 3.2 Consensus size: 65
2827415 TATCTTCAGC
* * * *
2827425 CCACCATCGTACTTCGCTCCTTCCGGCTCGTATCCACTACAGTACTCTGCTCCTTCCAGCTCGTA
1 CCACCACCATACTTCGCTCCTTCTGGCTCGTATCCACCACA-TACTCTGCTCCTTCCAGCTCGTA
2827490 T
65 T
* * * * *
2827491 CCACCACCATACTTCGCTCCTTCTAGCTCGTATCCACCACCGTACTCCGCTCCTTCTAGCTCATA
1 CCACCACCATACTTCGCTCCTTCTGGCTCGTATCCACCA-CATACTCTGCTCCTTCCAGCTCGTA
2827556 T
65 T
* * * * * * * *
2827557 CCACCACCGTACTTCGCTCCTTCTGGCTCGTATCCATCGACATTCTCTACTTCTCCCGGCTTGTA
1 CCACCACCATACTTCGCTCCTTCTGGCTCGTATCCA-CCACATACTCTGCTCCTTCCAGCTCGTA
2827622 T
65 T
*
2827623 CCATCACCATACT
1 CCACCACCATACT
2827636 CTACTCCTCT
Statistics
Matches: 119, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
66 116 0.97
67 3 0.03
ACGTcount: A:0.17, C:0.42, G:0.11, T:0.30
Consensus pattern (65 bp):
CCACCACCATACTTCGCTCCTTCTGGCTCGTATCCACCACATACTCTGCTCCTTCCAGCTCGTAT
Found at i:2829052 original size:38 final size:38
Alignment explanation
Indices: 2828969--2829122 Score: 182
Period size: 38 Copynumber: 4.0 Consensus size: 38
2828959 GAATCCAGTC
* * ***
2828969 ACCAGCACAAAACCTGCGGGACTTTAAGCTTAGATATAAT
1 ACCAGCACGAAGCCTGCGGGA-TTTAA-CCCGGATATAAT
*
2829009 ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAAT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAAT
* * * *
2829047 ACCAGCACGAAGCTTGCGGGATTTAGCCTGGATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAAT
* *
2829085 ACCAGCACGAAGGCTGCGGGATTTAACCCGAATATAAT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAAT
2829123 TCTAGCATAT
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
38 74 0.76
39 5 0.05
40 19 0.19
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (38 bp):
ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAAT
Found at i:2829102 original size:76 final size:78
Alignment explanation
Indices: 2828969--2829122 Score: 213
Period size: 76 Copynumber: 2.0 Consensus size: 78
2828959 GAATCCAGTC
* *
2828969 ACCAGCACAAAACCTGCGGGACTTTAAGCTTAGATATAATACCAGCACTAAGCCTGCGGGATTTA
1 ACCAGCACAAAACCTGCGGGACTTTAAGCCTAGATATAATACCAGCACGAAGCCTGCGGGATTTA
*
2829034 ACCCGGATATAAT
66 ACCCGAATATAAT
* * * * * *
2829047 ACCAGCACGAAGCTTGCGGGA-TTT-AGCCTGGATATATTACCAGCACGAAGGCTGCGGGATTTA
1 ACCAGCACAAAACCTGCGGGACTTTAAGCCTAGATATAATACCAGCACGAAGCCTGCGGGATTTA
2829110 ACCCGAATATAAT
66 ACCCGAATATAAT
2829123 TCTAGCATAT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
76 46 0.69
77 3 0.04
78 18 0.27
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (78 bp):
ACCAGCACAAAACCTGCGGGACTTTAAGCCTAGATATAATACCAGCACGAAGCCTGCGGGATTTA
ACCCGAATATAAT
Found at i:2833737 original size:27 final size:27
Alignment explanation
Indices: 2833679--2833737 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
2833669 CCCTACCTGA
* *
2833679 TAGGCGCGACATGTTGAGCCTGTCAGG
1 TAGGCGCGACATGTCGAGCCTCTCAGG
*
2833706 TAGGCGCGACATGTCGTGCCTACTCAGG
1 TAGGCGCGACATGTCGAGCCT-CTCAGG
2833734 -AGGC
1 TAGGC
2833738 TCAACCCGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.19, C:0.25, G:0.36, T:0.20
Consensus pattern (27 bp):
TAGGCGCGACATGTCGAGCCTCTCAGG
Found at i:2834347 original size:7 final size:7
Alignment explanation
Indices: 2834345--2834396 Score: 56
Period size: 6 Copynumber: 7.6 Consensus size: 7
2834335 TTTTTCTTCT
2834345 TTCTTTC
1 TTCTTTC
2834352 TTCTTTC
1 TTCTTTC
2834359 TT-TTTC
1 TTCTTTC
2834365 TTC-TTC
1 TTCTTTC
*
2834371 TTTTTTC
1 TTCTTTC
2834378 TT-TTTC
1 TTCTTTC
2834384 TCTCTTTAC
1 T-TCTTT-C
2834393 TTCT
1 TTCT
2834397 GGAGTGTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
6 16 0.41
7 15 0.38
8 6 0.15
9 2 0.05
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTTC
Found at i:2834366 original size:13 final size:13
Alignment explanation
Indices: 2834335--2834384 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
2834325 AATTACTAAT
2834335 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
2834348 --TTTCTTCTTTC
1 TTTTTCTTCTTTC
2834359 TTTTTCTTC-TTC
1 TTTTTCTTCTTTC
2834371 TTTTTTCTT-TTTC
1 -TTTTTCTTCTTTC
2834384 T
1 T
2834385 CTCTTTACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 11 0.33
12 4 0.12
13 18 0.55
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:2834384 original size:16 final size:16
Alignment explanation
Indices: 2834337--2834390 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
2834327 TTACTAATTT
2834337 TTTCTTCTTTCTTTCTTC
1 TTTCTT-TTT-TTTCTTC
*
2834355 TTTCTTTTTCTTCTTC
1 TTTCTTTTTTTTCTTC
2834371 TTT-TTTCTTTTTCTCTC
1 TTTCTTT-TTTTTCT-TC
2834388 TTT
1 TTT
2834391 ACTTCTGGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 3 0.09
16 15 0.47
17 8 0.25
18 6 0.19
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTTTTTTTTCTTC
Found at i:2837210 original size:4 final size:4
Alignment explanation
Indices: 2837189--2837231 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
2837179 ATCAAATACT
*
2837189 TAAA AAAA TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
2837232 CCTCCTCGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
TAAA
Found at i:2840828 original size:16 final size:16
Alignment explanation
Indices: 2840804--2840846 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
2840794 TAAAAATAAT
*
2840804 TTAAAATATAATTTTA
1 TTAATATATAATTTTA
2840820 TTAATATATATAATTTTA
1 TT-A-ATATATAATTTTA
2840838 TTAATATAT
1 TTAATATAT
2840847 GTAAAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 2 0.08
18 14 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATATATAATTTTA
Found at i:2840832 original size:18 final size:18
Alignment explanation
Indices: 2840809--2840846 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2840799 ATAATTTAAA
2840809 ATATAATTTTATTAATAT
1 ATATAATTTTATTAATAT
2840827 ATATAATTTTATTAATAT
1 ATATAATTTTATTAATAT
2840845 AT
1 AT
2840847 GTAAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATAATTTTATTAATAT
Found at i:2840951 original size:19 final size:20
Alignment explanation
Indices: 2840927--2840972 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
2840917 CATCCAAACA
2840927 CCAGAAAAGTAAATCA-TTT
1 CCAGAAAAGTAAATCATTTT
*
2840946 CCAGAAAAGTAAATTATTTT
1 CCAGAAAAGTAAATCATTTT
2840966 CCAGAAA
1 CCAGAAA
2840973 TCATTTTCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:2846078 original size:19 final size:19
Alignment explanation
Indices: 2846026--2846071 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2846016 TTTAATTTTA
*
2846026 ATTTTATGTA-TACTATTAT
1 ATTTTAT-TACTATTATTAT
2846045 ATTTTATTACTATTATTAT
1 ATTTTATTACTATTATTAT
2846064 A-TTTATTA
1 ATTTTATTA
2846072 TTTATTAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTTTATTACTATTATTAT
Found at i:2846170 original size:15 final size:15
Alignment explanation
Indices: 2846006--2846172 Score: 54
Period size: 15 Copynumber: 10.3 Consensus size: 15
2845996 ACTTTTTCTC
*
2846006 ATTATTTTATTTTAAT
1 ATTATTTT-TATTAAT
* *
2846022 TTTAATTTTATGTATACT
1 ATTATTTTTAT-TA-A-T
*
2846040 ATTATATTTTATTACT
1 ATTAT-TTTTATTAAT
*
2846056 ATTA-TTATATT--T
1 ATTATTTTTATTAAT
*
2846068 ATTATTTATTAGCATTAGT
1 ATTATTT-TT---ATTAAT
2846087 ATTATTTTTACTTAAT
1 ATTATTTTTA-TTAAT
*
2846103 ACTTATATGTATATATAAT
1 A-TTAT-T-TTTAT-TAAT
* *
2846122 A-TAATATTATTAAT
1 ATTATTTTTATTAAT
* *
2846136 AGTTTTTTTTTATTATT
1 A--TTATTTTTATTAAT
*
2846153 ATTATTTTTCTTAAT
1 ATTATTTTTATTAAT
2846168 ATTAT
1 ATTAT
2846173 ATTATGTATA
Statistics
Matches: 112, Mismatches: 20, Indels: 39
0.65 0.12 0.23
Matches are distributed among these distances:
12 5 0.04
13 2 0.02
14 12 0.11
15 22 0.20
16 19 0.17
17 20 0.18
18 10 0.09
19 22 0.20
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTATTTTTATTAAT
Found at i:2846195 original size:27 final size:26
Alignment explanation
Indices: 2846146--2846196 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
2846136 AGTTTTTTTT
*
2846146 TATTATTATTATTTTTCTTAATATTA
1 TATTATTATTATTCTTCTTAATATTA
2846172 TATTATGTATATATTCTT-TTAATAT
1 TATTAT-TAT-TATTCTTCTTAATAT
2846197 ATTAGGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 6 0.27
27 10 0.45
28 6 0.27
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TATTATTATTATTCTTCTTAATATTA
Found at i:2846445 original size:21 final size:18
Alignment explanation
Indices: 2846419--2846461 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 18
2846409 TAATACTATG
2846419 TATATATGTTTTCAATGTATA
1 TATATATG-TTT--ATGTATA
2846440 TATATATGTTTATGTATA
1 TATATATGTTTATGTATA
2846458 TATA
1 TATA
2846462 GCGTTACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.50
20 3 0.14
21 8 0.36
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (18 bp):
TATATATGTTTATGTATA
Found at i:2846532 original size:3 final size:3
Alignment explanation
Indices: 2846524--2846582 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
2846514 TTATATGTTC
* * *
2846524 TTA TTA TTA TTA -TA TCTA TTA TTTA TTA GTA TT- TTA CTA TTA CTA
1 TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
*
2846569 TTA TTA GTA TTA TT
1 TTA TTA TTA TTA TT
2846583 TTTTAATCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2846657 original size:27 final size:26
Alignment explanation
Indices: 2846626--2846699 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 26
2846616 TTTTTAATAC
2846626 TATATTTTTAATACCATATATATTG-TG
1 TATATTTTTAATA-C-TATATATTGATG
*
2846653 TATATTCTTAATACTATATATTGTATG
1 TATATTTTTAATACTATATATTG-ATG
*
2846680 TATTTTTTTAATAACTATAT
1 TATATTTTTAAT-ACTATAT
2846700 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:2846758 original size:15 final size:16
Alignment explanation
Indices: 2846732--2846765 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2846722 GTATTTTTAA
*
2846732 TATTATTATATATTTT
1 TATTATTATATATGTT
2846748 TATTA-TATATATGTT
1 TATTATTATATATGTT
2846763 TAT
1 TAT
2846766 ATTTATGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TATTATTATATATGTT
Found at i:2846804 original size:53 final size:56
Alignment explanation
Indices: 2846695--2846806 Score: 133
Period size: 53 Copynumber: 2.1 Consensus size: 56
2846685 TTTTAATAAC
* * *
2846695 TATATTATATGTATATATATTATGTACGTATTTTTAATATTATTATATATTTTTAT
1 TATATTATATGTATATATATTATGTACGTATTATTAATATTATTATATAATATTAT
* * *
2846751 TATA-TATATGTTTATAT-TTATGTA-GTATTATTAATAGTTGTT-TTTAATATTAT
1 TATATTATATGTATATATATTATGTACGTATTATTAATA-TTATTATATAATATTAT
2846804 TAT
1 TAT
2846807 TTTTTCTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
53 22 0.45
54 11 0.22
55 12 0.24
56 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (56 bp):
TATATTATATGTATATATATTATGTACGTATTATTAATATTATTATATAATATTAT
Found at i:2846861 original size:21 final size:20
Alignment explanation
Indices: 2846826--2846869 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
2846816 ATGTATATAT
2846826 TATGTATATATTTTTAATAC
1 TATGTATATATTTTTAATAC
2846846 TATGTATATACTTTTTAATAC
1 TATGTATATA-TTTTTAATAC
2846867 TAT
1 TAT
2846870 TATTATGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TATGTATATATTTTTAATAC
Found at i:2855586 original size:31 final size:31
Alignment explanation
Indices: 2855548--2855606 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
2855538 GAATATGGAG
2855548 AAAACTACTTTCGTAACGTTGTGGGGAACAT
1 AAAACTACTTTCGTAACGTTGTGGGGAACAT
2855579 AAAACTACTTTCGTAACGTTGTGGGGAA
1 AAAACTACTTTCGTAACGTTGTGGGGAA
2855607 TATTTTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (31 bp):
AAAACTACTTTCGTAACGTTGTGGGGAACAT
Found at i:2859271 original size:91 final size:89
Alignment explanation
Indices: 2859118--2859304 Score: 275
Period size: 91 Copynumber: 2.1 Consensus size: 89
2859108 GGTATCCAGA
* *
2859118 TATTTTTATTTTTGTTGTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCC
1 TATTTTTATTTCTGTTGTCCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCC
* *
2859183 ACATGCCGAGATATTTTCAATTTC
66 ACACGCCGAGATATTTTCAATTCC
2859207 TATTTTTAATTTCTGTTGTCCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTT-ATTTCTGTTGTCC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * * * *
2859272 TCACACGCTGAGGTATTTTTAGTTCC
64 CCACACGCCGAGATATTTTCAATTCC
2859298 TATTTTT
1 TATTTTT
2859305 CAAAAAATCA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
89 7 0.08
90 11 0.13
91 69 0.79
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (89 bp):
TATTTTTATTTCTGTTGTCCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCC
ACACGCCGAGATATTTTCAATTCC
Found at i:2859335 original size:76 final size:76
Alignment explanation
Indices: 2859230--2859599 Score: 560
Period size: 76 Copynumber: 4.8 Consensus size: 76
2859220 TGTTGTCCAA
2859230 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAGT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAGT
2859295 TCCTATTTTTC
66 TCCTATTTTTC
2859306 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAGT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAGT
2859371 TCCTATTTTTC
66 TCCTATTTTTC
* * *
2859382 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACAAGCCGAGGTATTTTTAGT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAGT
2859447 TCCTATTTTTC
66 TCCTATTTTTC
* * *
2859458 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAA
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAG
* *
2859523 TTCCTCTTTTTTTT
65 TT-C-CTATTTTTC
* * * * * * * * *
2859537 TAAAAGTCAACTCGTATTACAAGAGGTGAGTTGAACCTCGGCTCACACACTGAGGTAATTTTA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTA
2859600 ATTTCTGTTA
Statistics
Matches: 269, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
76 149 0.55
77 60 0.22
78 53 0.20
79 7 0.03
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (76 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAGT
TCCTATTTTTC
Found at i:2859829 original size:88 final size:86
Alignment explanation
Indices: 2859533--2859835 Score: 247
Period size: 88 Copynumber: 3.5 Consensus size: 86
2859523 TTCCTCTTTT
* * * * * * * *
2859533 TTTTTAAAAGTCAACTCGTATTACAAGAGGTGAGTTGAACCTCGGCTCACACACTGAGGTAATTT
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACACGCTGAGGT-ATTT
*
2859598 T-AATTTCTGTTATTCAATT-TA
65 TCAATTTCTGTT-TTTAATTCTA
* * * * *
2859619 TGTTCCAAAAAATCAGCTTATATTGCGAGATGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAA
1 T-TTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCTCACACGCTGAGGTAT
* * **
2859681 TTTCAAGTTCTATTTTTCAATTTCCG
63 TTTCAATTTCTGTTTTT-AA-TTCTA
* * * *
2859707 TTTGTCAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTTGGCTCACATGCTGAGCTATTT
1 TTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACACGCTGAGGTATTT
2859772 TCAATTTCTGTTTTTAATATCTA
65 TCAATTTCTGTTTTTAAT-TCTA
* * * *
2859795 TTTTTAAAGAGTCAACTTATATTGCGAGAAGTGAGTTGAGC
1 TTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGC
2859836 TCAGGATCAC
Statistics
Matches: 168, Mismatches: 36, Indels: 24
0.74 0.16 0.11
Matches are distributed among these distances:
85 6 0.04
86 24 0.14
87 44 0.26
88 66 0.39
89 28 0.17
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (86 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACACGCTGAGGTATTTT
CAATTTCTGTTTTTAATTCTA
Found at i:2859950 original size:21 final size:21
Alignment explanation
Indices: 2859900--2859953 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
2859890 TCTTGCCTCC
**
2859900 TTGAAGTTGCAGTAGAGCTGA
1 TTGAAGTTGCAGTAGAGCACA
* * *
2859921 TCGAGGTTGCAGTGGAGCACA
1 TTGAAGTTGCAGTAGAGCACA
2859942 TTGAAGTTGCAG
1 TTGAAGTTGCAG
2859954 ATCTTATCTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.13, G:0.35, T:0.26
Consensus pattern (21 bp):
TTGAAGTTGCAGTAGAGCACA
Found at i:2861463 original size:22 final size:22
Alignment explanation
Indices: 2861438--2861492 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2861428 TTAATTTTAA
*
2861438 TATTATGTA-TACTATTATATTT
1 TATTATCTATTACTATTATA-TT
*
2861460 TATTA-CTATTATTATTATATT
1 TATTATCTATTACTATTATATT
*
2861481 TATTATTTATTA
1 TATTATCTATTA
2861493 GCATTAGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTATCTATTACTATTATATT
Found at i:2861498 original size:22 final size:22
Alignment explanation
Indices: 2861451--2861510 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
2861441 TATGTATACT
* **
2861451 ATTATATTTTATTA-CTATTATT
1 ATTATA-TTTATTATTTATTAGC
2861473 ATTATATTTATTATTTATTAGC
1 ATTATATTTATTATTTATTAGC
2861495 ATTAGTA-TTATT-TTTA
1 ATTA-TATTTATTATTTA
2861511 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:2861831 original size:28 final size:28
Alignment explanation
Indices: 2861800--2861853 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
2861790 ATTTTTCTTA
*
2861800 AATATTATAT-TATATGTATTTAAATACT
1 AATACTATATATATATGT-TTTAAATACT
* *
2861828 AATACTATGTATATATGTTTTCAATA
1 AATACTATATATATATGTTTTAAATA
2861854 TATATATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (28 bp):
AATACTATATATATATGTTTTAAATACT
Found at i:2862038 original size:13 final size:15
Alignment explanation
Indices: 2862019--2862054 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2862009 TACTTATATG
2862019 TATATATTAT-TTTT
1 TATATATTATATTTT
2862033 TA-ATATTATATTTT
1 TATATATTATATTTT
2862047 TATATATT
1 TATATATT
2862055 GTGTATATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.35
14 8 0.40
15 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATATTATATTTT
Found at i:2862050 original size:26 final size:27
Alignment explanation
Indices: 2861971--2862051 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 27
2861961 TTTATTAGTA
* *
2861971 TTTTACTATTACTATTATTAGTATTATTT
1 TTTTAATATTA-TATTTTTA-TATTATTT
* *
2862000 TTTAATCAATACTTATATGTATATATTA-TT
1 TTT--T-AATA-TTATATTTTTATATTATTT
2862030 TTTTAATATTATATTTTTATAT
1 TTTTAATATTATATTTTTATAT
2862052 ATTGTGTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
26 12 0.29
27 4 0.10
28 1 0.02
29 3 0.07
30 5 0.12
31 6 0.14
32 8 0.19
33 3 0.07
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTAATATTATATTTTTATATTATTT
Found at i:2862086 original size:27 final size:28
Alignment explanation
Indices: 2862047--2862120 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
2862037 ATTATATTTT
2862047 TATATATTG--TGTATATTCTTAAT-AC
1 TATATATTGTATGTATATTCTTAATAAC
* *
2862072 TATATATTGTATGTATTTTTTTAATAAC
1 TATATATTGTATGTATATTCTTAATAAC
*
2862100 TATATTATATGTATATATATT
1 TATA-TAT-TGTATGTATATT
2862121 ATGTACGTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 9 0.22
27 12 0.30
28 6 0.15
29 3 0.08
30 10 0.25
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (28 bp):
TATATATTGTATGTATATTCTTAATAAC
Found at i:2862166 original size:20 final size:20
Alignment explanation
Indices: 2862116--2862210 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 20
2862106 ATATGTATAT
*
2862116 ATATTATGTACGTA-TTTTTA
1 ATATTAT-TATGTATTTTTTA
2862136 ATATTATTATGTATTTTTTA
1 ATATTATTATGTATTTTTTA
2862156 ATA-TATATATGTATATTTATGTA
1 ATATTAT-TATGTAT-TTT-T-TA
*
2862179 GTATTATTAATAGT-TGTTTTTA
1 ATATTATT-AT-GTAT-TTTTTA
2862201 ATATTATTAT
1 ATATTATTAT
2862211 TTTTCTAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
19 8 0.13
20 23 0.37
21 5 0.08
22 10 0.16
23 6 0.10
24 9 0.14
25 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.08, T:0.58
Consensus pattern (20 bp):
ATATTATTATGTATTTTTTA
Found at i:2862171 original size:62 final size:63
Alignment explanation
Indices: 2862081--2862248 Score: 158
Period size: 62 Copynumber: 2.7 Consensus size: 63
2862071 CTATATATTG
*
2862081 TATGTATTTTTTTAATA-ACTATATTATATGTATATATATTATGT-A-CG-TATTTTTAATATTA
1 TATGTA-TTTTTTAATATA-TATATTATATGTATATATATTAT-TAATAGTTATTTTTAATATTA
2862142 T
63 T
* * *
2862143 TATGTATTTTTTAATATATATATGTATATTTATGTAGTATTATTAATAGTTGTTTTTAATATTAT
1 TATGTATTTTTTAATATATATAT-TATATGTATATA-TATTATTAATAGTTATTTTTAATATTAT
* *
2862208 TA--T-TTTTCTAATATGTATA-TATTATGTATATAT-TT-TTAATA
1 TATGTATTTTTTAATATATATATTA-TATGTATATATATTATTAATA
2862249 CTATGTATAT
Statistics
Matches: 91, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
58 6 0.07
59 2 0.02
60 3 0.03
61 23 0.25
62 32 0.35
63 8 0.09
64 1 0.01
65 16 0.18
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (63 bp):
TATGTATTTTTTAATATATATATTATATGTATATATATTATTAATAGTTATTTTTAATATTAT
Found at i:2862184 original size:43 final size:45
Alignment explanation
Indices: 2862112--2862210 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 45
2862102 TATTATATGT
2862112 ATATATATTATGTACGTATTTTTAATATTATT-AT-GTAT-TTTTTA
1 ATATATATTATGTAC-TATTTTTAATATTATTAATAGT-TGTTTTTA
*
2862156 ATATATA-TATGTA-TATTTATGTAGTATTATTAATAGTTGTTTTTA
1 ATATATATTATGTACTATTT-T-TAATATTATTAATAGTTGTTTTTA
2862201 ATAT-TATTAT
1 ATATATATTAT
2862211 TTTTCTAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
41 5 0.10
42 1 0.02
43 15 0.31
44 12 0.25
45 15 0.31
ACGTcount: A:0.33, C:0.01, G:0.08, T:0.58
Consensus pattern (45 bp):
ATATATATTATGTACTATTTTTAATATTATTAATAGTTGTTTTTA
Found at i:2862235 original size:11 final size:11
Alignment explanation
Indices: 2862219--2862259 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2862209 ATTTTTCTAA
2862219 TATGTATATAT
1 TATGTATATAT
2862230 TATGTATATAT
1 TATGTATATAT
* *
2862241 T-TTTA-ATAC
1 TATGTATATAT
2862250 TATGTATATA
1 TATGTATATA
2862260 CTTTTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
9 4 0.16
10 6 0.24
11 15 0.60
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (11 bp):
TATGTATATAT
Found at i:2862255 original size:20 final size:21
Alignment explanation
Indices: 2862230--2862273 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2862220 ATGTATATAT
2862230 TATGTATATA-TTTTTAATAC
1 TATGTATATACTTTTTAATAC
2862250 TATGTATATACTTTTTAATAC
1 TATGTATATACTTTTTAATAC
2862271 TAT
1 TAT
2862274 TATTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TATGTATATACTTTTTAATAC
Found at i:2864559 original size:15 final size:13
Alignment explanation
Indices: 2864532--2864557 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2864522 GTAGAAATTA
2864532 CGTATATAATTTT
1 CGTATATAATTTT
2864545 CGTATATAATTTT
1 CGTATATAATTTT
2864558 TTTCAAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
CGTATATAATTTT
Found at i:2865584 original size:61 final size:57
Alignment explanation
Indices: 2865504--2865625 Score: 190
Period size: 61 Copynumber: 2.1 Consensus size: 57
2865494 CCGTAAGACA
2865504 TTTTCCATCACCTTCTTCATCCAGGTAAGTCTTCTTCTTCTTCTTATTCCGTTCTTCAACT
1 TTTTCCATCACCTTCTTCATCCAGGTAAGTC-T-TT-TTCTTC-TATTCCGTTCTTCAACT
* *
2865565 TTTTCCATCTCCTTCTTCATCCAGGTAAGTCTTTTTCTTCTCTTCCGTTCTTCAACT
1 TTTTCCATCACCTTCTTCATCCAGGTAAGTCTTTTTCTTCTATTCCGTTCTTCAACT
2865622 TTTT
1 TTTT
2865626 AAATATTTCT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
57 20 0.34
58 6 0.10
59 2 0.03
60 1 0.02
61 30 0.51
ACGTcount: A:0.13, C:0.30, G:0.07, T:0.50
Consensus pattern (57 bp):
TTTTCCATCACCTTCTTCATCCAGGTAAGTCTTTTTCTTCTATTCCGTTCTTCAACT
Found at i:2868874 original size:16 final size:18
Alignment explanation
Indices: 2868846--2868882 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2868836 CAAACAATGA
2868846 AAATATAATAAA-TTCTT
1 AAATATAATAAATTTCTT
2868863 AAATAT-ATAAATTTCTT
1 AAATATAATAAATTTCTT
2868880 AAA
1 AAA
2868883 ACAGCTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATAATAAATTTCTT
Found at i:2873391 original size:28 final size:29
Alignment explanation
Indices: 2873339--2873395 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
2873329 ATTTAAACTA
* *
2873339 TAATCAAAATTTCATATATATAATTACAC
1 TAATCAAAATTTCATAAATAAAATTACAC
*
2873368 TAATTAAAA-TTCATAAATAAAATTACAC
1 TAATCAAAATTTCATAAATAAAATTACAC
2873396 ATGATAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (29 bp):
TAATCAAAATTTCATAAATAAAATTACAC
Found at i:2879035 original size:21 final size:21
Alignment explanation
Indices: 2879005--2879093 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
2878995 CTCACAAAGA
* *
2879005 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
2879025 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
2879046 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
2879067 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
2879091 AAA
1 AAA
2879094 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:2879086 original size:24 final size:21
Alignment explanation
Indices: 2879005--2879073 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
2878995 CTCACAAAGA
* * *
2879005 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
2879025 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
2879046 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
2879067 AAAAAGA
1 AAAAAGA
2879074 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:2883734 original size:32 final size:30
Alignment explanation
Indices: 2883674--2883743 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 30
2883664 TAATATAATA
* *
2883674 ATATAATATATAACTATTACTAAAATTATT
1 ATATTATATATAACTATTAATAAAATTATT
* **
2883704 AATATGTATATATAATTATTAATATTATTATT
1 -ATAT-TATATATAACTATTAATAAAATTATT
2883736 ATATTATA
1 ATATTATA
2883744 GATTATAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 4 0.12
31 8 0.24
32 21 0.64
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (30 bp):
ATATTATATATAACTATTAATAAAATTATT
Found at i:2884179 original size:23 final size:24
Alignment explanation
Indices: 2884142--2884198 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
2884132 AACATTACTT
*
2884142 CAAAAAAATAGTAACAACATAATAG
1 CAAAAAAA-AGTAACAACAAAATAG
* *
2884167 GAAAAAAAA-TAACAATAAAATAG
1 CAAAAAAAAGTAACAACAAAATAG
2884190 CAAAAAAAA
1 CAAAAAAAA
2884199 AAGAGAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 20 0.71
24 1 0.04
25 7 0.25
ACGTcount: A:0.72, C:0.09, G:0.07, T:0.12
Consensus pattern (24 bp):
CAAAAAAAAGTAACAACAAAATAG
Found at i:2893137 original size:17 final size:17
Alignment explanation
Indices: 2893115--2893148 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2893105 ATCCACTAAT
*
2893115 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2893132 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2893149 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:2897776 original size:17 final size:17
Alignment explanation
Indices: 2897754--2897787 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2897744 ATCCACTAAT
*
2897754 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2897771 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2897788 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:2902415 original size:17 final size:17
Alignment explanation
Indices: 2902393--2902426 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2902383 ATCCACTAAT
*
2902393 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2902410 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2902427 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:2903813 original size:23 final size:24
Alignment explanation
Indices: 2903773--2903869 Score: 78
Period size: 23 Copynumber: 4.2 Consensus size: 24
2903763 ATTTTTTTAA
2903773 AAAAATTATATTAT--AAAT-ATT
1 AAAAATTATATTATAAAAATAATT
2903794 AAAAATTATATTATAAAAATAATT
1 AAAAATTATATTATAAAAATAATT
* * * *
2903818 -TATATTATTTTATAAAATCATAATA
1 AAAAATTATATTATAAAA--ATAATT
* **
2903843 AAAAAATATATTATTTAAAT-ATT
1 AAAAATTATATTATAAAAATAATT
2903866 AAAA
1 AAAA
2903870 TAATTTAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
21 14 0.24
23 24 0.41
24 5 0.08
25 5 0.08
26 11 0.19
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAAATTATATTATAAAAATAATT
Found at i:2905992 original size:29 final size:29
Alignment explanation
Indices: 2905955--2906015 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
2905945 TTTTTATTAG
* *
2905955 TAAATGTTTTATCGACTATTTTCTTGGGC
1 TAAATGTTTTATCGACTACTTTCTTGGAC
2905984 TAAATGTTTTATCGACTACTTTCTTGGAC
1 TAAATGTTTTATCGACTACTTTCTTGGAC
2906013 TAA
1 TAA
2906016 CAATATTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (29 bp):
TAAATGTTTTATCGACTACTTTCTTGGAC
Found at i:2909825 original size:17 final size:17
Alignment explanation
Indices: 2909800--2909832 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2909790 CTTGGATTGA
2909800 GAAAATAATTTAATTAG
1 GAAAATAATTTAATTAG
*
2909817 GAAATTAATTTAATTA
1 GAAAATAATTTAATTA
2909833 ATTAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
GAAAATAATTTAATTAG
Found at i:2909833 original size:4 final size:4
Alignment explanation
Indices: 2909819--2909851 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
2909809 TTAATTAGGA
2909819 AATT AATTT AATT AATT AATT AATT AATT AATT
1 AATT AA-TT AATT AATT AATT AATT AATT AATT
2909852 GATAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
AATT
Found at i:2916284 original size:26 final size:26
Alignment explanation
Indices: 2916247--2916330 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
2916237 TGATACAAAT
* *
2916247 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2916273 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2916299 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2916325 TGATAA
1 TGATAA
2916331 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:2920387 original size:3 final size:3
Alignment explanation
Indices: 2920379--2920557 Score: 98
Period size: 3 Copynumber: 59.7 Consensus size: 3
2920369 TAAAAATTTT
* * * * * *
2920379 TAA TAA TAA TAA TAA TAG TAA CAA TAG CAA TAA TAA T-A TAT TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
2920426 TAAA TAA -AA GGAA TAA AAA TAA TAG TAA TAA AAA TAT TAA CAA TAG
1 T-AA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * *
2920472 TAA TAA TAA CGA TAA T-A TAAA TAC TAA TATA TACA CAA -AA -AA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA-A TA-A TAA TAA TAA TAA
* * *
2920517 TAA TAA TAA TAG TAA TAG TAA TAA TAA TAA TAA TAA CAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2920558 CATTAATATA
Statistics
Matches: 129, Mismatches: 39, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
2 10 0.08
3 107 0.83
4 12 0.09
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:2920629 original size:20 final size:20
Alignment explanation
Indices: 2920604--2920661 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2920594 AAAAAAGGGG
2920604 AATAATAATAGTATAGTAAA
1 AATAATAATAGTATAGTAAA
* *
2920624 AATAATAATAATAT-GTTAAT
1 AATAATAATAGTATAG-TAAA
*
2920644 AAGAATAATAGTAGTAGT
1 AATAATAATAGTA-TAGT
2920662 TGTAGACACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 1 0.03
20 27 0.87
21 2 0.06
22 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (20 bp):
AATAATAATAGTATAGTAAA
Found at i:2920634 original size:23 final size:23
Alignment explanation
Indices: 2920604--2920653 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2920594 AAAAAAGGGG
*
2920604 AATAATAATA-GTATAGTAAAAAT
1 AATAATAATATGT-TAATAAAAAT
*
2920627 AATAATAATATGTTAATAAGAAT
1 AATAATAATATGTTAATAAAAAT
2920650 AATA
1 AATA
2920654 GTAGTAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (23 bp):
AATAATAATATGTTAATAAAAAT
Found at i:2920868 original size:19 final size:19
Alignment explanation
Indices: 2920844--2920941 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
2920834 AATCTTTAAG
2920844 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2920863 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2920882 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
2920899 GATATGCAGTCTTAGATAT
1 GATATGCAATCTTAGATAT
2920918 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
2920939 GAT
1 GAT
2920942 CTTGTAATCT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
17 17 0.23
19 47 0.64
21 9 0.12
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2920890 original size:36 final size:37
Alignment explanation
Indices: 2920844--2920941 Score: 144
Period size: 36 Copynumber: 2.6 Consensus size: 37
2920834 AATCTTTAAG
2920844 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
1 GATA-GCAATCTTAGATATGATATGCAATCTTAGATAT
*
2920882 GATA-CAATCTTAGATATGATATGCAGTCTTAGATAT
1 GATAGCAATCTTAGATATGATATGCAATCTTAGATAT
2920918 GATATGCAATCTTGAAGATATGAT
1 GATA-GCAATCTT--AGATATGAT
2920942 CTTGTAATCT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
36 35 0.64
38 11 0.20
40 9 0.16
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (37 bp):
GATAGCAATCTTAGATATGATATGCAATCTTAGATAT
Found at i:2929850 original size:13 final size:13
Alignment explanation
Indices: 2929828--2929876 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
2929818 TCTATTTCAA
*
2929828 AAAAAAAGAAAAG
1 AAAAAGAGAAAAG
*
2929841 AAAAAGAGAAAAA
1 AAAAAGAGAAAAG
2929854 AATAAAGAGAAAAAAG
1 AA-AAAGAG--AAAAG
2929870 AAAAAGA
1 AAAAAGA
2929877 TGGAGAGGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 13 0.43
14 6 0.20
15 5 0.17
16 6 0.20
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAAGAGAAAAG
Found at i:2929853 original size:14 final size:15
Alignment explanation
Indices: 2929836--2929876 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
2929826 AAAAAAAAAG
2929836 AAAAGAAAAAGAGAA
1 AAAAGAAAAAGAGAA
*
2929851 AAAA-ATAAAGAGAA
1 AAAAGAAAAAGAGAA
2929865 AAAAGAAAAAGA
1 AAAAGAAAAAGA
2929877 TGGAGAGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAAGAGAA
Found at i:2929854 original size:21 final size:21
Alignment explanation
Indices: 2929828--2929874 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
2929818 TCTATTTCAA
2929828 AAAAAAAGAAA-AGAAAAAGAG
1 AAAAAAAGAAAGAGAAAAA-AG
*
2929849 AAAAAAATAAAGAGAAAAAAG
1 AAAAAAAGAAAGAGAAAAAAG
2929870 AAAAA
1 AAAAA
2929875 GATGGAGAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAGAGAAAAAAG
Found at i:2929855 original size:22 final size:21
Alignment explanation
Indices: 2929826--2929874 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
2929816 CTTCTATTTC
*
2929826 AAAAAAAAAGAAAAGAAAAAGAG
1 AAAAAAATA-AAAAGAAAAA-AG
*
2929849 AAAAAAATAAAGAGAAAAAAG
1 AAAAAAATAAAAAGAAAAAAG
2929870 AAAAA
1 AAAAA
2929875 GATGGAGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
22 9 0.38
23 8 0.33
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAAAAATAAAAAGAAAAAAG
Found at i:2930895 original size:44 final size:44
Alignment explanation
Indices: 2930754--2930933 Score: 179
Period size: 44 Copynumber: 4.1 Consensus size: 44
2930744 CAAAGAAACA
* *
2930754 AGATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* * * * * * * * **
2930798 AGATCTGACATTCCTGTGCTCTCT-GCGAAGTAGATTGAAGATTTC
1 AGATTTGGCATCCCTGTG-TTTATAGGGAA-CAGATCGAAGATAGC
*
2930843 AGCA--TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
2930886 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
2930930 AGAT
1 AGAT
2930934 CTAACCTTCA
Statistics
Matches: 107, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
42 2 0.02
43 15 0.14
44 73 0.68
45 16 0.15
46 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
Found at i:2931136 original size:119 final size:119
Alignment explanation
Indices: 2930925--2931399 Score: 869
Period size: 119 Copynumber: 4.0 Consensus size: 119
2930915 CAGATCGAAG
2930925 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
2930990 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
*
2931044 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
2931109 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
*
2931163 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
2931228 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
* * *
2931282 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGC
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
* * * *
2931347 TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAA
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAA
2931400 CAGACTCAAG
Statistics
Matches: 347, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 347 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (119 bp):
ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGT
TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
Found at i:2931589 original size:18 final size:18
Alignment explanation
Indices: 2931541--2931738 Score: 353
Period size: 18 Copynumber: 10.9 Consensus size: 18
2931531 ATAATCTTCA
2931541 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
2931560 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
2931577 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
2931595 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
2931613 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
2931631 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
2931649 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
2931667 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
2931685 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
2931703 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
2931721 ATGATATACAATCTTAGA
1 ATGAT-TGCAATCTTAGA
2931739 AGATATGATT
Statistics
Matches: 174, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
17 16 0.09
18 143 0.82
19 15 0.09
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:2932245 original size:18 final size:18
Alignment explanation
Indices: 2932224--2932280 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 18
2932214 ATATATTTTA
2932224 TATTTTTTATATAATTAT
1 TATTTTTTATATAATTAT
*
2932242 TA-TTCTTATA-AA-TAT
1 TATTTTTTATATAATTAT
2932257 T-TTTTTTATTATATATTA-
1 TATTTTTTA-TATA-ATTAT
2932275 TATTTT
1 TATTTT
2932281 AAATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
15 9 0.29
16 4 0.13
17 8 0.26
18 4 0.13
19 6 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTTTTATATAATTAT
Found at i:2933181 original size:3 final size:3
Alignment explanation
Indices: 2933175--2933453 Score: 168
Period size: 3 Copynumber: 93.7 Consensus size: 3
2933165 TCGACAGTAG
* * * * *
2933175 TAA TAA TAA CAA TAG TAA GAA TAA TAA TGA TAA T-A TAA CAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* **
2933219 TAA TAA T-A TAA TCAA TAA -AA T-A TAA TAG TAA TGAA -AA TAA TGC
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*** * * *
2933262 TAA CCG TAA TAA TAA TAA TAA TAA TGA TAA TGA TAG TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2933309 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TGA TAA TGAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
* * *
2933354 -AA GTAA TAA TAA TAA TACA TTAA GTTA CAA TAA TAA -AA TAA TAA TAG
1 TAA -TAA TAA TAA TAA TA-A -TAA -TAA TAA TAA TAA TAA TAA TAA TAA
** * * *
2933401 CGA TAA TGA TAA T-A TAT TAGA TAA TAA TAG TAA -AA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA -TAA
2933446 TAA TAA TA
1 TAA TAA TA
2933454 GGTTAAATTG
Statistics
Matches: 207, Mismatches: 48, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
2 23 0.11
3 163 0.79
4 19 0.09
5 2 0.01
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:2948235 original size:51 final size:51
Alignment explanation
Indices: 2948157--2948256 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
2948147 GGCAACTCAA
*
2948157 ATACTTGCCCATTGAATCAAACATTTAACGGATGTTCTTAATCAAGCCAAT
1 ATACTTACCCATTGAATCAAACATTTAACGGATGTTCTTAATCAAGCCAAT
*
2948208 ATACTTACCCATTGAATCAAACGTTTAACGGATGTTCTTAATCAAGCCA
1 ATACTTACCCATTGAATCAAACATTTAACGGATGTTCTTAATCAAGCCA
2948257 TCGTTCAGGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (51 bp):
ATACTTACCCATTGAATCAAACATTTAACGGATGTTCTTAATCAAGCCAAT
Found at i:2953321 original size:3 final size:3
Alignment explanation
Indices: 2953313--2953338 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2953303 TTTTTATAAT
2953313 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2953339 CATATAAAAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2957143 original size:21 final size:21
Alignment explanation
Indices: 2957117--2957157 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2957107 ATCTGCTCAA
* *
2957117 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2957138 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2957158 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2975099 original size:23 final size:23
Alignment explanation
Indices: 2975073--2975118 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2975063 AATGATAGTC
*
2975073 TAAATA-CTAAAATAAAATAAATT
1 TAAATATC-AAAATAAAAGAAATT
*
2975096 TAAATATCAAAGTAAAAGAAATT
1 TAAATATCAAAATAAAAGAAATT
2975119 ATATAGTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (23 bp):
TAAATATCAAAATAAAAGAAATT
Found at i:2981830 original size:30 final size:31
Alignment explanation
Indices: 2981777--2981841 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
2981767 CTAATAATTG
*
2981777 TTTAGTTATTTAAATAAAAAATTTCAAATAA
1 TTTAGTAATTTAAATAAAAAATTTCAAATAA
* * *
2981808 TTTAGTAATTTAAAT-GAAAATTTTAAATAG
1 TTTAGTAATTTAAATAAAAAATTTCAAATAA
2981838 TTTA
1 TTTA
2981842 ATGATGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.45
Consensus pattern (31 bp):
TTTAGTAATTTAAATAAAAAATTTCAAATAA
Found at i:2982183 original size:20 final size:20
Alignment explanation
Indices: 2982151--2982195 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2982141 TCTTTTTTAT
*
2982151 ATTTTTGAATTTT-GGTGAA
1 ATTTTTGAATTTTGGGGGAA
*
2982170 ATTTTTGGATTTTTGGGGGAA
1 ATTTTT-GAATTTTGGGGGAA
2982191 ATTTT
1 ATTTT
2982196 ACTGCTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 6 0.27
21 10 0.45
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.53
Consensus pattern (20 bp):
ATTTTTGAATTTTGGGGGAA
Found at i:2984443 original size:55 final size:55
Alignment explanation
Indices: 2984361--2984471 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
2984351 TGATGACTGA
*
2984361 TATTTATTCATTGTATAGCATTCCTTGATGAAAATACTGCAGAACCATGTATTTT
1 TATTTATTCATTGTATAGCATTCCTTGATGAAAATACTGAAGAACCATGTATTTT
* * *
2984416 TATTTATTCATTGTATAGCATTTCTTGATGAAAATGCTGAAGAACTATGTATTTT
1 TATTTATTCATTGTATAGCATTCCTTGATGAAAATACTGAAGAACCATGTATTTT
2984471 T
1 T
2984472 TACCTACAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (55 bp):
TATTTATTCATTGTATAGCATTCCTTGATGAAAATACTGAAGAACCATGTATTTT
Found at i:2997421 original size:20 final size:20
Alignment explanation
Indices: 2997378--2997422 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2997368 AAAAAATCAG
*
2997378 AAAATATAAAATCTAGAAAA
1 AAAATATAAAATATAGAAAA
*
2997398 AAAATATAAATTATA-AAAA
1 AAAATATAAAATATAGAAAA
2997417 TAAAAT
1 -AAAAT
2997423 TTACAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATATAAAATATAGAAAA
Found at i:2997449 original size:33 final size:34
Alignment explanation
Indices: 2997377--2997449 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 34
2997367 AAAAAAATCA
2997377 GAAAATATAAAATCTAGAAAAAAAATATAAATTAT
1 GAAAA-ATAAAATCTAGAAAAAAAATATAAATTAT
* * *
2997412 -AAAAATAAAATTTA-CAAAAAAATA-CAATTATT
1 GAAAAATAAAATCTAGAAAAAAAATATAAATTA-T
2997444 GAAAAA
1 GAAAAA
2997450 AATTAGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
31 5 0.15
32 10 0.30
33 14 0.42
34 4 0.12
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (34 bp):
GAAAAATAAAATCTAGAAAAAAAATATAAATTAT
Found at i:2997717 original size:22 final size:23
Alignment explanation
Indices: 2997692--2997753 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
2997682 TTTTTTGACT
* *
2997692 TTTTCAAATTTATA-ATTATATA
1 TTTTCAAATTTATATATAAAATA
2997714 TTTT-AGAATTT-TATATAAAATA
1 TTTTCA-AATTTATATATAAAATA
2997736 TATTTCAAATTTAT-TATA
1 T-TTTCAAATTTATATATA
2997754 CATTATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 3 0.09
22 16 0.48
23 12 0.36
24 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTTCAAATTTATATATAAAATA
Found at i:2997753 original size:23 final size:23
Alignment explanation
Indices: 2997693--2997753 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
2997683 TTTTTGACTT
**
2997693 TTTCAAATTTA-TA-ATTATATA
1 TTTCAAATTTATTATAAAATATA
*
2997714 TTTTAGAATTT-TATATAAAATATA
1 TTTCA-AATTTAT-TATAAAATATA
2997738 TTTCAAATTTATTATA
1 TTTCAAATTTATTATA
2997754 CATTATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
21 4 0.13
22 5 0.16
23 11 0.35
24 11 0.35
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTCAAATTTATTATAAAATATA
Found at i:3007189 original size:29 final size:28
Alignment explanation
Indices: 3007107--3007189 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 28
3007097 TTTTAAAGAT
* *
3007107 AAAATTATATTATCATATTTG-AAAAGT
1 AAAATGATATTATCATATTTGTAAAAGC
* * *
3007134 AAATTGAT-TGATCATTCAATTTTTAAAAGGC
1 AAAATGATATTATCA-T--ATTTGTAAAA-GC
3007165 AAAATGATATTATCATATTTGTAAA
1 AAAATGATATTATCATATTTGTAAA
3007190 GTAAATTGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
26 5 0.12
27 7 0.17
29 12 0.29
30 4 0.10
31 9 0.21
32 5 0.12
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.40
Consensus pattern (28 bp):
AAAATGATATTATCATATTTGTAAAAGC
Found at i:3012445 original size:39 final size:39
Alignment explanation
Indices: 3012362--3012455 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
3012352 TGAAACCAAT
*
3012362 TACCAGCAC-AAGCCTGCGGGAATTTAAACCCGGTATAA
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGGCATAA
* * * *
3012400 TACCAGCTCGAAGCCTGCGGGACTTT-AGCCCGGACATAT
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGG-CATAA
* *
3012439 TTCCAGCACGTAGCCTG
1 TACCAGCACGAAGCCTG
3012456 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 14 0.30
39 32 0.70
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (39 bp):
TACCAGCACGAAGCCTGCGGGAATTTAAACCCGGCATAA
Found at i:3015592 original size:31 final size:31
Alignment explanation
Indices: 3015557--3015616 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
3015547 AGGTATATCT
3015557 GAGTCTCGAACTCGCAACTGATAATAACCCC
1 GAGTCTCGAACTCGCAACTGATAATAACCCC
*
3015588 GAGTCTCGAACTCGCAATTGATAATAACC
1 GAGTCTCGAACTCGCAACTGATAATAACC
3015617 TGATCTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (31 bp):
GAGTCTCGAACTCGCAACTGATAATAACCCC
Found at i:3038532 original size:26 final size:26
Alignment explanation
Indices: 3038492--3038558 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
3038482 GCCATATCGA
*
3038492 AAAGCTC-CGAAGAGCCATTAATCAGG
1 AAAGCTCACAAAGAGCCATTAATCA-G
*
3038518 AAA-CTCACAAAGAGCCTTTAATCAG
1 AAAGCTCACAAAGAGCCATTAATCAG
*
3038543 AAAGCTCACGAAGAGC
1 AAAGCTCACAAAGAGC
3038559 TATATAACGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 7 0.19
26 29 0.81
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.15
Consensus pattern (26 bp):
AAAGCTCACAAAGAGCCATTAATCAG
Found at i:3041228 original size:11 final size:12
Alignment explanation
Indices: 3041198--3041227 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3041188 TGTATAAATA
3041198 TTTTTTTT-TAG
1 TTTTTTTTGTAG
3041209 TTTTTTTTGTAG
1 TTTTTTTTGTAG
3041221 TTTTTTT
1 TTTTTTT
3041228 GGGACATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (12 bp):
TTTTTTTTGTAG
Found at i:3042567 original size:22 final size:22
Alignment explanation
Indices: 3042526--3042567 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3042516 ATTTATTGTA
*
3042526 TTTCATATTATCTTTATGTTTT
1 TTTCATATTATATTTATGTTTT
3042548 TTTCATATGTATATTT-TGTT
1 TTTCATAT-TATATTTATGTT
3042568 ACTTATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (22 bp):
TTTCATATTATATTTATGTTTT
Found at i:3053534 original size:54 final size:53
Alignment explanation
Indices: 3053415--3053571 Score: 183
Period size: 54 Copynumber: 2.9 Consensus size: 53
3053405 CAAGGGAAGT
* ** **
3053415 CAAAGTGAAAACCCGCAAAGGGCATTTTGAGACTTTAAA-AAAAA-AAGGAGGC
1 CAAAGTGAAAACCCGCAAAGGGCACTTTGAGAC-CCAAATAAAAAGAAAAAGGC
* *
3053467 TAAAGTGAAAACCCGTAAAGGGCACTTTGAGACCCAAATAAAAATGAAAAAGGC
1 CAAAGTGAAAACCCGCAAAGGGCACTTTGAGACCCAAATAAAAA-GAAAAAGGC
*
3053521 CAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACCCAATATTAAAAAAGAAA
1 CAAAGTGAAAACCCGCAAAGGGCACTTTGAGACCCAA-A-T-AAAAAGAAA
3053572 GAAAAAGAGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
51 3 0.03
52 35 0.39
54 40 0.45
55 1 0.01
56 5 0.06
57 5 0.06
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
CAAAGTGAAAACCCGCAAAGGGCACTTTGAGACCCAAATAAAAAGAAAAAGGC
Found at i:3054613 original size:64 final size:64
Alignment explanation
Indices: 3054503--3054628 Score: 191
Period size: 64 Copynumber: 2.0 Consensus size: 64
3054493 CTACATATAT
* *
3054503 CATTTAGTTAGGAGTATTTGATTAATTTCGATCATAGCACTCTAATTATTTGACATAAGCATCA
1 CATTTAGTTAGGAGCACTTGATTAATTTCGATCATAGCACTCTAATTATTTGACATAAGCATCA
* * *
3054567 CATTTAGTTAGGAGCACTTGATTCATTTCGATCATAGGA-TCTTAATTATTTGGCATAAGCAT
1 CATTTAGTTAGGAGCACTTGATTAATTTCGATCATAGCACTC-TAATTATTTGACATAAGCAT
3054629 GTGCATATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 2 0.04
64 54 0.96
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (64 bp):
CATTTAGTTAGGAGCACTTGATTAATTTCGATCATAGCACTCTAATTATTTGACATAAGCATCA
Found at i:3055158 original size:180 final size:180
Alignment explanation
Indices: 3054693--3055458 Score: 952
Period size: 180 Copynumber: 4.3 Consensus size: 180
3054683 ATTGGTAAAG
* ** * * * *
3054693 ATTGAAGATTTTATCTCCCTGAAGTTGCAG-GGAGTAAATCTTTGCAGATGGTGAATCTTATCCC
1 ATTGAAGATTTTATCTCCCTAAAGTTGCAGCGGAACAGATCTTCGCAAATGGTGAATCTTATCTC
*
3054757 CATGTATTGGCAATGGAGTAGATTTTACTACCAAGCCTTATCTCTCTGAAGTAGCA-GAAGAGCA
66 CATGTATTGGCAATGGAGCAGATTTTACTACCAAGCCTTATCTCTCTGAAGTAGCAGGAA-AGCA
* * *
3054821 GGTTGAAGAATGAGTCTTATCTTCCTAAGGTAGCAAAGGAAGTAGACTGAGA
130 GGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGC-AAGGAAGCAGACTAAGA
* * * *
3054873 ATTGAAGATTTTATCTCCCTAAAGTTGTAGCGGAGCAGATATTCACAAATGGTGAATCTTATCTC
1 ATTGAAGATTTTATCTCCCTAAAGTTGCAGCGGAACAGATCTTCGCAAATGGTGAATCTTATCTC
* * *
3054938 CATGTATCGGCAATGGAGCAGATTTTACTACCAAGCCTTATCTCTTTGAAGTAGCAGGAAAGCGG
66 CATGTATTGGCAATGGAGCAGATTTTACTACCAAGCCTTATCTCTCTGAAGTAGCAGGAAAGCAG
* *
3055003 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCATACTAAAA
131 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAGA
* * *
3055053 ATTGAAGATTTTATCTCCCTGAAGTTGCAGCGGAACAGATCTTCGCAAATGGTGAATTTTATCTT
1 ATTGAAGATTTTATCTCCCTAAAGTTGCAGCGGAACAGATCTTCGCAAATGGTGAATCTTATCTC
* * * *
3055118 CATGT-TTCAGCAATTGAGCAGATTTTACTACTAAGCCTTATCTCTCTGAAGTAGCAGGAGAGCA
66 CATGTATT-GGCAATGGAGCAGATTTTACTACCAAGCCTTATCTCTCTGAAGTAGCAGGAAAGCA
3055182 GGTTGAAGAATGAGTCTTATCTT-CTCGAGGTAGCAAGGAAGCAGACTAAGA
130 GGTTGAAGAATGAGTCTTATCTTCCT-GAGGTAGCAAGGAAGCAGACTAAGA
* * * * * * * ** * *
3055233 ATTGAAGATTTTATTTCCCTAAAGTTGTAGCGAAACAAATTTTCACAGATAATAAATCTTATTTC
1 ATTGAAGATTTTATCTCCCTAAAGTTGCAGCGGAACAGATCTTCGCAAATGGTGAATCTTATCTC
* * * * * * * *
3055298 CATGTATTGGCAATGGAGTAAATTTTACCA-CGAGCCTCATCACTCTGAGGTAGCAGGAGAGCAG
66 CATGTATTGGCAATGGAGCAGATTTTACTACCAAGCCTTATCTCTCTGAAGTAGCAGGAAAGCAG
* * * *
3055362 GTTAAAGAATGAGTCTTATCTTCTTGAGGTAGCAAAGAAGCAGACTGAGA
131 GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAGA
* * *
3055412 ATTGAAGATTTTATCCCCCT-AAGTTTGCAG-TGAAGCAGATCTCCGCA
1 ATTGAAGATTTTATCTCCCTAAAG-TTGCAGCGGAA-CAGATCTTCGCA
3055459 GATACAAGGA
Statistics
Matches: 507, Mismatches: 71, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
178 5 0.01
179 107 0.21
180 274 0.54
181 118 0.23
182 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (180 bp):
ATTGAAGATTTTATCTCCCTAAAGTTGCAGCGGAACAGATCTTCGCAAATGGTGAATCTTATCTC
CATGTATTGGCAATGGAGCAGATTTTACTACCAAGCCTTATCTCTCTGAAGTAGCAGGAAAGCAG
GTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAAGA
Found at i:3061958 original size:30 final size:30
Alignment explanation
Indices: 3061924--3061986 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
3061914 AGTCGAGTTC
*
3061924 CCATATATAAAATTCTTATTGTGACTATTT
1 CCATATATAAAATTCTTATTGTGACCATTT
* *
3061954 CCATATATAGAATTCTTATTTTGACCATTT
1 CCATATATAAAATTCTTATTGTGACCATTT
3061984 CCA
1 CCA
3061987 CGTATAGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.44
Consensus pattern (30 bp):
CCATATATAAAATTCTTATTGTGACCATTT
Found at i:3061993 original size:30 final size:30
Alignment explanation
Indices: 3061928--3061997 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
3061918 GAGTTCCCAT
* * *
3061928 ATATAAAATTCTTATTGTGACTATTTCCAT
1 ATATAGAATTCTTATTGTGACCATTTCCAC
*
3061958 ATATAGAATTCTTATTTTGACCATTTCCAC
1 ATATAGAATTCTTATTGTGACCATTTCCAC
*
3061988 GTATAGAATT
1 ATATAGAATT
3061998 GACGGCTAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (30 bp):
ATATAGAATTCTTATTGTGACCATTTCCAC
Done.