Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 22 of 27
Found at i:3573101 original size:13 final size:13
Alignment explanation
Indices: 3573083--3573107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3573073 ACAAAAAATA
3573083 TGTATCGATACAT
1 TGTATCGATACAT
3573096 TGTATCGATACA
1 TGTATCGATACA
3573108 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3573102 original size:32 final size:33
Alignment explanation
Indices: 3573062--3573127 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
3573052 AGTAGCTTAA
3573062 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
3573094 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
3573127 A
1 A
3573128 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:3573671 original size:77 final size:77
Alignment explanation
Indices: 3573397--3573695 Score: 352
Period size: 79 Copynumber: 3.8 Consensus size: 77
3573387 TTTTTGAGTA
* * *
3573397 GATACTCCAACCCCAACTTTATTTCTAAAATATCAATTTTTCATAATCGGGGATACTCCAACCTC
1 GATACTCCAACCCCAATTTTATTTCAAAAACATCAATTTTTCATAATCGGGGATACTCCAACC-C
* *
3573462 GTTATTTCCGAAGG
65 G-TATTTTCGAGGG
* * * * *
3573476 GATACTCCAACCCCAGTATTATTTCAAAAACATCGATTTTTCACAATCGGAGATACTCCAACCCC
1 GATACTCCAACCCCAATTTTATTTCAAAAACATCAATTTTTCATAATCGGGGATACTCCAA-CCC
*
3573541 GTTATTTTCAAGGG
65 G-TATTTTCGAGGG
* *
3573555 GATACTCCAACCCCAATTTTATTTCAAAAACATCGATTTTTCACT-ATCGAGGATAC-CCTAACC
1 GATACTCCAACCCCAATTTTATTTCAAAAACATCAATTTTTCA-TAATCGGGGATACTCC-AACC
3573618 C-TATTTTCTGAGGG
64 CGTATTTTC-GAGGG
* * * * *
3573632 GATACTCCAACCTCGATTTTATTTCTAAAACATCAATTTTCCATAATCGGGGATACTCTAACCC
1 GATACTCCAACCCCAATTTTATTTCAAAAACATCAATTTTTCATAATCGGGGATACTCCAACCC
3573696 CGATTTTATT
Statistics
Matches: 190, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
76 8 0.04
77 57 0.30
78 6 0.03
79 117 0.62
80 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (77 bp):
GATACTCCAACCCCAATTTTATTTCAAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCG
TATTTTCGAGGG
Found at i:3573695 original size:156 final size:158
Alignment explanation
Indices: 3573397--3573697 Score: 389
Period size: 156 Copynumber: 1.9 Consensus size: 158
3573387 TTTTTGAGTA
* * *
3573397 GATACTCCAACCCCAACTTTATTTCTAAAATATCAATTTTTCATAATCGGGGATACTCCAACCTC
1 GATACTCCAACCCCAACTTTATTTCAAAAACATCAATTTTTCATAATCGAGGATACTCCAACCTC
* *
3573462 GTTATTTCCGAAGGGATACTCCAACCCCAGTATTATTTCAAAAACATCGATTTTTCACAATCGGA
66 GTTATTTCCGAAGGGATACTCCAACCCCAGTATTATTTCAAAAACATCAATTTTCCACAATCGGA
3573527 GATACTCCAACCCCGTTATTTTCAAGGG
131 GATACTCCAACCCCGTTATTTTCAAGGG
* *
3573555 GATACTCCAACCCCAATTTTATTTCAAAAACATCGATTTTTCACT-ATCGAGGATAC-CCTAACC
1 GATACTCCAACCCCAACTTTATTTCAAAAACATCAATTTTTCA-TAATCGAGGATACTCC-AACC
* * * * * *
3573618 -C--TATTTTCTGAGGGGATACTCCAACCTC-GATTTTATTTCTAAAACATCAATTTTCCATAAT
64 TCGTTA-TTTCCGAAGGGATACTCCAACCCCAG-TATTATTTCAAAAACATCAATTTTCCACAAT
* *
3573679 CGGGGATACTCTAACCCCG
127 CGGAGATACTCCAACCCCG
3573698 ATTTTATTTT
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
155 3 0.02
156 64 0.52
157 3 0.02
158 53 0.43
159 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (158 bp):
GATACTCCAACCCCAACTTTATTTCAAAAACATCAATTTTTCATAATCGAGGATACTCCAACCTC
GTTATTTCCGAAGGGATACTCCAACCCCAGTATTATTTCAAAAACATCAATTTTCCACAATCGGA
GATACTCCAACCCCGTTATTTTCAAGGG
Found at i:3573700 original size:51 final size:51
Alignment explanation
Indices: 3573629--3573758 Score: 178
Period size: 51 Copynumber: 2.6 Consensus size: 51
3573619 TATTTTCTGA
* * *
3573629 GGGGATACTCCAACCTCGATTTTATTTCTAAAACATCAATTTTCCATAATC
1 GGGGATACTCTAACCCCGATTTTATTTCTAAAACACCAATTTTCCATAATC
* * *
3573680 GGGGATACTCTAACCCCGATTTTATTTTTAAAATACCAATTTTTCATAATC
1 GGGGATACTCTAACCCCGATTTTATTTCTAAAACACCAATTTTCCATAATC
3573731 -GGGATACTCTAACCCCG---TTATTTCTAAA
1 GGGGATACTCTAACCCCGATTTTATTTCTAAA
3573759 GGGATACTCC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
47 10 0.14
50 17 0.24
51 45 0.62
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (51 bp):
GGGGATACTCTAACCCCGATTTTATTTCTAAAACACCAATTTTCCATAATC
Found at i:3576594 original size:21 final size:21
Alignment explanation
Indices: 3576561--3576601 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3576551 CTAAGTAAAA
3576561 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
3576582 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
3576602 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:3576764 original size:53 final size:53
Alignment explanation
Indices: 3576681--3576817 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
3576671 AGATTGCATA
3576681 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
3576735 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
3576788 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
3576818 TTGGAAGTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.83
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:3576915 original size:24 final size:22
Alignment explanation
Indices: 3576862--3576916 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
3576852 CACTATTCAT
* *
3576862 ACTGTTCATGTATCGATACATC
1 ACTGTTCATGTATCGAAAAATC
*
3576884 ACTATTCATGTATCGTTAAAAATC
1 ACTGTTCATGTATCG--AAAAATC
3576908 ACTGTTCAT
1 ACTGTTCAT
3576917 CACTATTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 14 0.52
24 13 0.48
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (22 bp):
ACTGTTCATGTATCGAAAAATC
Found at i:3576944 original size:13 final size:13
Alignment explanation
Indices: 3576926--3576964 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3576916 TCACTATTCA
3576926 TGTATCGATACAT
1 TGTATCGATACAT
*
3576939 TGTATCGATACAG
1 TGTATCGATACAT
3576952 TGTATCGATACAT
1 TGTATCGATACAT
3576965 CATAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3576979 original size:14 final size:14
Alignment explanation
Indices: 3576960--3576989 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3576950 AGTGTATCGA
3576960 TACATCATAAATAG
1 TACATCATAAATAG
3576974 TACATCATAAATAG
1 TACATCATAAATAG
3576988 TA
1 TA
3576990 TCGATACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (14 bp):
TACATCATAAATAG
Found at i:3580058 original size:12 final size:13
Alignment explanation
Indices: 3580030--3580071 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
3580020 TAAAAGCCAA
3580030 AAAAATGAGAAAC
1 AAAAATGAGAAAC
3580043 -AAAA-GAGAAAC
1 AAAAATGAGAAAC
*
3580054 AAAAATGA-AAAA
1 AAAAATGAGAAAC
3580066 AAAAAT
1 AAAAAT
3580072 CAAAAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 7 0.27
12 17 0.65
13 2 0.08
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (13 bp):
AAAAATGAGAAAC
Found at i:3580088 original size:11 final size:12
Alignment explanation
Indices: 3580031--3580098 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
3580021 AAAAGCCAAA
*
3580031 AAAATGAGAAAC
1 AAAATGAAAAAC
*
3580043 AAAA-GAGAAAC
1 AAAATGAAAAAC
*
3580054 AAAAATGAAAAAA
1 -AAAATGAAAAAC
*
3580067 AAAATCAAAAAAC
1 AAAAT-GAAAAAC
3580080 AAAA-GAAAAA-
1 AAAATGAAAAAC
3580090 AAGAATGAA
1 AA-AATGAA
3580099 TAAAAGTGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
10 2 0.04
11 14 0.30
12 16 0.35
13 14 0.30
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (12 bp):
AAAATGAAAAAC
Found at i:3581508 original size:62 final size:61
Alignment explanation
Indices: 3581376--3582011 Score: 670
Period size: 61 Copynumber: 10.3 Consensus size: 61
3581366 ATGGGAGCCC
* * * * * *
3581376 TTTAGTCCTCAAAGAGTAAGACGCCTTTTTCTTTTAAAGCCTACACGAGTTGGTGGTACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* ** * *
3581437 TTTAGTCCTCAAAGAGTAGGATACATTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCT
* * * *
3581499 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCTATACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACCT
* * * * *
3581561 TTTAGTCCTCAAAGAGCATGACGTCTTTTCTTTTTTAAAG-CCACACAAATTGGTGGCATCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTT-TCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* * * * *
3581622 CTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCTCACACAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* * * * *
3581683 TTCAGTCCTCAAAGAGTAGGACGCCTTTTTCTTTTAAGGCCCATATAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* * * *
3581744 TTCAGTCCTCAAAGAGCAGGACGTC-TTTTCTTTTTAAAGCCTACACAAGTTGGTGGTACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTC-TTTTAAAGCCCACACAAGTTGGTGGCACCT
** * * * * * *
3581805 TCCAGTCCTTAAAGAGTAGGAC-AC-TTTCCTTTCAAAACCCACACAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* * **
3581864 TCTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTGCAAAGCCCACACAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* * * **
3581925 TCTAGTTCC-CAAAGAGCATGACACTTTCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGTGC
1 TTTAG-TCCTCAAAGAGCA-G-GAC--GCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCAC
3581989 CT
60 CT
* *
3581991 TTTAATCCTCAAAGAGTAGGA
1 TTTAGTCCTCAAAGAGCAGGA
3582012 TGCACTTCAT
Statistics
Matches: 486, Mismatches: 76, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
59 45 0.09
60 18 0.04
61 254 0.52
62 113 0.23
63 7 0.01
64 1 0.00
65 10 0.02
66 38 0.08
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (61 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCT
Found at i:3582103 original size:41 final size:41
Alignment explanation
Indices: 3581996--3582306 Score: 309
Period size: 41 Copynumber: 7.4 Consensus size: 41
3581986 TGCCTTTTAA
* * *
3581996 TCCTCAAAGAGTAGGATGCACTTCATTTCTTTCTTTTCCCTTTTG
1 TCCTCAAAGAGCAGGACGCACTTTATTTC---CTTTTCCC-TTTG
*
3582041 TCCTCAAAGAGCAGGATGCACTTTATTTCCTTTTCCCTTTG
1 TCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTCCCTTTG
* * * *
3582082 TCCTAAAAGAGTAGGACGCACTTCATTTCTTTTTCCCTTTG
1 TCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTCCCTTTG
* * *
3582123 TCCTCAAAAAGCAGGACGTACTTTGTTTCCTTTTCCCTTTG
1 TCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTCCCTTTG
* * *
3582164 TCTTTAAAGAGTAGGACGCACTTTATTTCCTTTTCTCCTTTG
1 TCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTC-CCTTTG
* * * *
3582206 TCCTCAAAGAGCATGACACA-TTTAATTTCCTTATTTTCCTTTA
1 TCCTCAAAGAGCAGGACGCACTTT-ATTTCC-T-TTTCCCTTTG
* * * * * *
3582249 TCCTCAAAGAGCAAGACACATTTTATTTTCGTTTTTCTTTTG
1 TCCTCAAAGAGCAGGACGCACTTTA-TTTCCTTTTCCCTTTG
*
3582291 TCCTCAAAGAGTAGGA
1 TCCTCAAAGAGCAGGA
3582307 TGTATTCATT
Statistics
Matches: 227, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
41 106 0.47
42 57 0.25
43 27 0.12
44 10 0.04
45 27 0.12
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (41 bp):
TCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTCCCTTTG
Found at i:3582404 original size:34 final size:34
Alignment explanation
Indices: 3582280--3582417 Score: 132
Period size: 34 Copynumber: 3.9 Consensus size: 34
3582270 TTTATTTTCG
*
3582280 TTTTTCTTTTGTCCTCAAAGAGTAGGATGTATTC
1 TTTTTCTTTTGTCCTCAAAGAGCAGGATGTATTC
* * * *
3582314 ATTTTTCTTTTGTCCTCAAGGAGTAAGACCCATTTCATTC
1 -TTTTTCTTTTGTCCTCAAAGAG-CAG---GATGT-ATTC
* * * *
3582354 TCTTTTCCTTTATCCTCGAAGAGCAGGATGTACTC
1 T-TTTTCTTTTGTCCTCAAAGAGCAGGATGTATTC
3582389 TTTTTCTTTTGTCCTCAAAGAGCAGGATG
1 TTTTTCTTTTGTCCTCAAAGAGCAGGATG
3582418 CCTCTTCCTT
Statistics
Matches: 82, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
34 25 0.30
35 25 0.30
36 5 0.06
39 6 0.07
40 21 0.26
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (34 bp):
TTTTTCTTTTGTCCTCAAAGAGCAGGATGTATTC
Found at i:3582433 original size:75 final size:75
Alignment explanation
Indices: 3582239--3582412 Score: 215
Period size: 77 Copynumber: 2.3 Consensus size: 75
3582229 AATTTCCTTA
* * * * * * * *
3582239 TTTTCCTTTATCCTCAAAGAGCAAGACACATTTTATTTTCGTTTTTCTTTTGTCCTCAAAGAGTA
1 TTTTCTTTTGTCCTCAAAGAGCAAGACCCATTTCATTCTC--TTTTCCTTTATCCTCAAAGAGCA
*
3582304 GGATGTATTCAT
64 GGATGTACTCAT
* * *
3582316 TTTTCTTTTGTCCTCAAGGAGTAAGACCCATTTCATTCTCTTTTCCTTTATCCTCGAAGAGCAGG
1 TTTTCTTTTGTCCTCAAAGAGCAAGACCCATTTCATTCTCTTTTCCTTTATCCTCAAAGAGCAGG
3582381 ATGTACTC-T
66 ATGTACTCAT
3582390 TTTTCTTTTGTCCTCAAAGAGCA
1 TTTTCTTTTGTCCTCAAAGAGCA
3582413 GGATGCCTCT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
74 22 0.27
75 28 0.34
77 33 0.40
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (75 bp):
TTTTCTTTTGTCCTCAAAGAGCAAGACCCATTTCATTCTCTTTTCCTTTATCCTCAAAGAGCAGG
ATGTACTCAT
Found at i:3585514 original size:79 final size:78
Alignment explanation
Indices: 3585413--3585818 Score: 363
Period size: 79 Copynumber: 5.2 Consensus size: 78
3585403 CTACCATCGA
* * * * * * * * * *
3585413 GGATACTCTAACCTCGGCTTTATTTCTAAAATATTAATTTTATATAATCAAGGATACTCTAGCCC
1 GGATACTCCAACCCCAGTTTTATTTCCAAAACACTAATTTT-TATAATCGAGGATACTCCAACCC
**
3585478 CATTATTTTCAAGG
65 CATTATTTTTGAGG
* * *
3585492 GGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCTAACCC
1 GGATACTCCAACCCCAGTTTTATTTCCAAAACACTAATTTTT-ATAATCGAGGATACTCCAACCC
* *
3585557 TATTATTTTTGAGA
65 CATTATTTTTGAGG
* * * ** *
3585571 GGATACTCCAACCCC-GATTTTATTTCTAAAACACTGATTTTCCACCATCGGGGATAC-CCAACC
1 GGATACTCCAACCCCAG-TTTTATTTCCAAAACACTAATTTT-TATAATCGAGGATACTCCAACC
***
3585634 GTGTTATTTTTGA-G
64 CCATTATTTTTGAGG
* * * * **
3585648 GGATACTGCAACCGCGGTTTTATTTCCAAAACA-TCGATTTTCTATAAGGGAGGATACTCCAACC
1 GGATACTCCAACCCCAGTTTTATTTCCAAAACACT-AATTTT-TATAATCGAGGATACTCCAACC
*
3585712 TCATTATTTTTGAGG
64 CCATTATTTTTGAGG
** *
3585727 GGATACTCCAACCCCAGTTTTATTTTTAAAACACTAATTTTTCACAATCGA-GATACTCCAACCC
1 GGATACTCCAACCCCAGTTTTATTTCCAAAACACTAATTTTT-ATAATCGAGGATACTCCAACCC
* * *
3585791 CGTTATTTTCGTGG
65 CATTATTTTTGAGG
3585805 GGATACTCCAACCC
1 GGATACTCCAACCC
3585819 TTTTTTATCT
Statistics
Matches: 268, Mismatches: 50, Indels: 19
0.80 0.15 0.06
Matches are distributed among these distances:
76 1 0.00
77 44 0.16
78 73 0.27
79 149 0.56
80 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (78 bp):
GGATACTCCAACCCCAGTTTTATTTCCAAAACACTAATTTTTATAATCGAGGATACTCCAACCCC
ATTATTTTTGAGG
Found at i:3585703 original size:156 final size:155
Alignment explanation
Indices: 3585411--3585834 Score: 428
Period size: 156 Copynumber: 2.7 Consensus size: 155
3585401 TTCTACCATC
* * * * * * ** * * * *
3585411 GAGGATACTCTAACCTCGGCTTTATTTCTAAAATATTAATTTTATATAATCAAGGATACTCTAGC
1 GAGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTCCACAATCGA-GATACTCCAAC
* *
3585476 CCCATTATTTTCAAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTTCATAATC
65 CCCGTTATTTTC-TGGGGATACTCCAA-CCCAGTTTTATTTCCAAAACACCAATTTTTCATAATC
*
3585541 GGGGATACTCTAACC-CTATTATTTTTGA
128 GGGGATACTCCAACCTC-ATTATTTTTGA
* * *
3585569 GAGGATACTCCAACCCC-GATTTTATTTCTAAAACACTGATTTTCCACCATCGGGGATAC-CCAA
1 GAGGATACTCCAACCCCAG-TTTTATTTCTAAAACACTAATTTTCCACAATC-GAGATACTCCAA
** * * * *
3585632 CCGTGTTATTTT-TGAGGGATACTGCAACCGCGGTTTTATTTCCAAAACATCGA-TTTTCTATAA
64 CCCCGTTATTTTCTG-GGGATACTCCAACC-CAGTTTTATTTCCAAAACACCAATTTTTC-ATAA
*
3585695 -GGGAGGATACTCCAACCTCATTATTTTTGA
126 TCGG-GGATACTCCAACCTCATTATTTTTGA
* * *
3585725 GGGGATACTCCAACCCCAGTTTTATTTTTAAAACACTAATTTTTCACAATCGAGATACTCCAACC
1 GAGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTCCACAATCGAGATACTCCAACC
** *
3585790 CCGTTATTTTCGTGGGGATACTCCAACCCTTTTTTATCTCCAAAA
66 CCGTTATTTTC-TGGGGATACTCCAACCCAGTTTTATTTCCAAAA
3585835 TATTAAAATT
Statistics
Matches: 219, Mismatches: 36, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
155 16 0.07
156 130 0.59
157 27 0.12
158 46 0.21
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (155 bp):
GAGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTCCACAATCGAGATACTCCAACC
CCGTTATTTTCTGGGGATACTCCAACCCAGTTTTATTTCCAAAACACCAATTTTTCATAATCGGG
GATACTCCAACCTCATTATTTTTGA
Found at i:3588056 original size:21 final size:21
Alignment explanation
Indices: 3588031--3588090 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
3588021 TTTTTATTAG
3588031 CCAACTCA-TCATTTTCATTTT
1 CCAACTCATTCATTTTC-TTTT
*
3588052 GCAAC-CTATTTC-TTTTCTTTT
1 CCAACTC-A-TTCATTTTCTTTT
3588073 CCAACTCATTCATTTTCT
1 CCAACTCATTCATTTTCT
3588091 CTTCTAGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
20 4 0.12
21 20 0.62
22 6 0.19
23 2 0.06
ACGTcount: A:0.20, C:0.28, G:0.02, T:0.50
Consensus pattern (21 bp):
CCAACTCATTCATTTTCTTTT
Found at i:3588579 original size:24 final size:24
Alignment explanation
Indices: 3588534--3588579 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3588524 CATAGCTATT
*
3588534 TCATCATTTTCATCAACCTCTTGA
1 TCATCATTTTCATCAACATCTTGA
*
3588558 TCATC-TTTATCATCATCATCTT
1 TCATCATTT-TCATCAACATCTT
3588580 TAACGGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.24, C:0.28, G:0.02, T:0.46
Consensus pattern (24 bp):
TCATCATTTTCATCAACATCTTGA
Found at i:3589764 original size:36 final size:34
Alignment explanation
Indices: 3589682--3589914 Score: 207
Period size: 36 Copynumber: 6.9 Consensus size: 34
3589672 CTTACAACAC
* *
3589682 TATC-TTTC-AAGGCTAAGATAGAAAC-C-TCAT
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTTCCT
**
3589712 TATCTTTTCACGGGCTAAGATAGAACCTCTGTCCT
1 TATCTTTTCAAAGGCTAAGATAGAACCTCT-TCCT
3589747 TATCTTTTTCAAAGGCTAAGATAGAAACCTC-T-C-
1 TATC-TTTTCAAAGGCTAAGATAG-AACCTCTTCCT
* * * *
3589780 TATCTTTTCACAGTCTAAGATAGAACCTTTCTCCC
1 TATCTTTTCAAAGGCTAAGATAGAACCTCT-TCCT
* *
3589815 TATCTTTTTCAAAAGCTAAGGTAGAAACCTC--CC-
1 TATC-TTTTCAAAGGCTAAGATAG-AACCTCTTCCT
** *
3589848 TATCTTTTCATGGGCTAATATAGAACCTCTCTCCT
1 TATCTTTTCAAAGGCTAAGATAGAACCTCT-TCCT
3589883 TATCTTTTACAAAGGCTAAGATAGAACCTCTT
1 TATCTTTT-CAAAGGCTAAGATAGAACCTCTT
3589915 AATCACTTAG
Statistics
Matches: 163, Mismatches: 22, Indels: 31
0.75 0.10 0.14
Matches are distributed among these distances:
30 4 0.02
31 15 0.09
32 45 0.28
33 10 0.06
34 6 0.04
35 21 0.13
36 51 0.31
37 11 0.07
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (34 bp):
TATCTTTTCAAAGGCTAAGATAGAACCTCTTCCT
Found at i:3589774 original size:68 final size:67
Alignment explanation
Indices: 3589686--3589915 Score: 320
Period size: 68 Copynumber: 3.4 Consensus size: 67
3589676 CAACACTATC
*
3589686 TTTC-AAGGCTAAGATAGAAACCTCATTATCTTTTCACGGGCTAAGATAGAACCTCTGTCCTTAT
1 TTTCAAAGGCTAAGATAGAAACCTC-TTATCTTTTCACGGGCTAAGATAGAACCTCTCTCCTTAT
3589750 CTT
65 CTT
* * * *
3589753 TTTCAAAGGCTAAGATAGAAACCTCTCTATCTTTTCACAGTCTAAGATAGAACCTTTCTCCCTAT
1 TTTCAAAGGCTAAGATAGAAACCTCT-TATCTTTTCACGGGCTAAGATAGAACCTCTCTCCTTAT
3589818 CTT
65 CTT
* * * * *
3589821 TTTCAAAAGCTAAGGTAGAAACCTCCCTATCTTTTCATGGGCTAATATAGAACCTCTCTCCTTAT
1 TTTCAAAGGCTAAGATAGAAACCT-CTTATCTTTTCACGGGCTAAGATAGAACCTCTCTCCTTAT
3589886 CTT
65 CTT
*
3589889 TTACAAAGGCTAAGATAG-AACCTCTTA
1 TTTCAAAGGCTAAGATAGAAACCTCTTA
3589916 ATCACTTAGA
Statistics
Matches: 142, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
66 3 0.02
67 10 0.07
68 128 0.90
69 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (67 bp):
TTTCAAAGGCTAAGATAGAAACCTCTTATCTTTTCACGGGCTAAGATAGAACCTCTCTCCTTATC
TT
Found at i:3590394 original size:13 final size:13
Alignment explanation
Indices: 3590362--3590396 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3590352 ATATTTAACT
3590362 ATGTATCGATACA
1 ATGTATCGATACA
* *
3590375 CTATATCGATACA
1 ATGTATCGATACA
3590388 ATGTATCGA
1 ATGTATCGA
3590397 GACTGAGTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3590632 original size:20 final size:21
Alignment explanation
Indices: 3590607--3590650 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
3590597 GAGACTTTGG
3590607 ATTATTTTTA-CTTGAAAAAC
1 ATTATTTTTAGCTTGAAAAAC
*
3590627 ATTATTTTTATGCTTGAAAGAC
1 ATTATTTTTA-GCTTGAAAAAC
3590649 AT
1 AT
3590651 CTATACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (21 bp):
ATTATTTTTAGCTTGAAAAAC
Found at i:3594074 original size:79 final size:79
Alignment explanation
Indices: 3593986--3594157 Score: 236
Period size: 79 Copynumber: 2.2 Consensus size: 79
3593976 ATAAAAATGA
* * *
3593986 GGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGTTTGTGGAAAATCAGTGTTTT
1 GGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATGGTGGAAAATCAGTGTTTT
3594051 AGAAATAAAACCAG
66 AGAAATAAAACCAG
* ** * **
3594065 GGTTCGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATCCCCGATGGTGGAAACTTGGTGTTTT
1 GGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATGGTGGAAAATCAGTGTTTT
* **
3594130 GGAAATAAAACTGG
66 AGAAATAAAACCAG
3594144 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
3594158 TAATTATGAA
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATGGTGGAAAATCAGTGTTTT
AGAAATAAAACCAG
Found at i:3594157 original size:51 final size:50
Alignment explanation
Indices: 3594088--3594209 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 50
3594078 CCTCAAAAAT
* * * * * * *
3594088 AATGGGGTTGGAGTATCCCCGATGGTGGAAACTTGGTGTTTTGGAAATAA
1 AATGGGGTTGGAGTATCCCCAATGATGAAAAATCGGTATTTTAGAAATAA
* *
3594138 AACTGGGGTTGGAGTATCCCTAATTATGAAAAATCGGTATTTTAGAAATAA
1 AA-TGGGGTTGGAGTATCCCCAATGATGAAAAATCGGTATTTTAGAAATAA
3594189 AATCGGGGTTGGAGTATCCCC
1 AAT-GGGGTTGGAGTATCCCC
3594210 TCAGAAATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
50 3 0.05
51 57 0.95
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.30
Consensus pattern (50 bp):
AATGGGGTTGGAGTATCCCCAATGATGAAAAATCGGTATTTTAGAAATAA
Found at i:3594181 original size:130 final size:129
Alignment explanation
Indices: 3594013--3594285 Score: 321
Period size: 130 Copynumber: 2.1 Consensus size: 129
3594003 GAAAATAACA
** * * *
3594013 GGGTTGGAGTATCCCCGTTTGTGGAAAATCAGTGTTTTAGAAATAAAACCAGGGTTCGAGTATCC
1 GGGTTGGAGTATCCCCAATTATGAAAAATCAGTATTTTAGAAATAAAACCAGGGTTCGAGTATCC
**** * * * *
3594078 CCTCAAAAATAATGGGGTTGGAGTATCCCCGATGGTGGAAACTTGGTGTTTTGGAAATAAAACTG
66 CCTCAAAAATAACAACGTTGGAGTATCCCCGATGATGGAAAATCGATGTTTTGGAAATAAAAC-G
* * * * *
3594143 GGGTTGGAGTATCCCTAATTATGAAAAATCGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATTATGAAAAATCAGTATTTTAGAAATAAAACCAGGGTTCGAGTATCC
* * * *
3594208 CCTCAGAAATAACAACGTTGGAGTATCCTCGATTATGGAAAATCGATGTTTTGGAAATAAATCG
66 CCTCAAAAATAACAACGTTGGAGTATCCCCGATGATGGAAAATCGATGTTTTGGAAATAAAACG
* *
3594272 AGGTTTGAGTATCC
1 GGGTTGGAGTATCC
3594286 TTTCAAAAAT
Statistics
Matches: 119, Mismatches: 24, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
129 13 0.11
130 106 0.89
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (129 bp):
GGGTTGGAGTATCCCCAATTATGAAAAATCAGTATTTTAGAAATAAAACCAGGGTTCGAGTATCC
CCTCAAAAATAACAACGTTGGAGTATCCCCGATGATGGAAAATCGATGTTTTGGAAATAAAACG
Found at i:3594229 original size:79 final size:79
Alignment explanation
Indices: 3594144--3594473 Score: 338
Period size: 79 Copynumber: 4.2 Consensus size: 79
3594134 ATAAAACTGG
** * * * *
3594144 GGTTGGAGTATCCCTAATTATGAAAAATCGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCC
*
3594209 CTCAGAAATAACAA
66 CTCAAAAATAACAA
* * * * * * *
3594223 CGTTGGAGTATCCTCGATTATGGAAAATCGATGTTTTGGAAAT-AAATCGAGGTTTGAGTATCCT
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCC
* *
3594287 TTCAAAAATAACGA
66 CTCAAAAATAACAA
** * * * * *
3594301 GGTTGGAGTATCCCCGATGGTGAAAAATCGATGTCTTAGAAATAGAACCGGGGTTAGAGTATTCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCC
*
3594366 CTCAAAAATAACAG
66 CTCAAAAATAACAA
* * * * *
3594380 GGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCGAGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCC
*** **
3594445 CTTGGAAATAACGG
66 CTCAAAAATAACAA
*
3594459 GGTTGGACTATCCCC
1 GGTTGGAGTATCCCC
3594474 TCAAAAATAA
Statistics
Matches: 204, Mismatches: 46, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
78 65 0.32
79 139 0.68
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCC
CTCAAAAATAACAA
Found at i:3594475 original size:107 final size:107
Alignment explanation
Indices: 3594349--3594591 Score: 378
Period size: 107 Copynumber: 2.3 Consensus size: 107
3594339 GAAATAGAAC
* *
3594349 CGGGGTTAGAGTATTCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGT
1 CGGGGTTAGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATTGTGAAAAATTAGTGT
***
3594414 TTTGGAAATAAAACCGAGGTTGGAGTATCCCCTTGGAAATAA
66 TTTGGAAATAAAACCGAGGTTGGAGTATCCCCTAAAAAATAA
* * * * *
3594456 CGGGGTTGGACTATCCCCTCAAAAATAATAGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGT
1 CGGGGTTAGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATTGTGAAAAATTAGTGT
*
3594521 TTTGGAAATAAAACCGAGGTTGGAGTATCCTCTAAAAAATAA
66 TTTGGAAATAAAACCGAGGTTGGAGTATCCCCTAAAAAATAA
*
3594563 CGGGGTTAGAGTATCCCCTAAAAAATAAC
1 CGGGGTTAGAGTATCCCCTCAAAAATAAC
3594592 GGAGTATCCT
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 121 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (107 bp):
CGGGGTTAGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATTGTGAAAAATTAGTGT
TTTGGAAATAAAACCGAGGTTGGAGTATCCCCTAAAAAATAA
Found at i:3594481 original size:28 final size:28
Alignment explanation
Indices: 3594431--3594499 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
3594421 ATAAAACCGA
*** *
3594431 GGTTGGAGTATCCCCTTGGAAATAACGG
1 GGTTGGAGTATCCCCTCAAAAATAACAG
* *
3594459 GGTTGGACTATCCCCTCAAAAATAATAG
1 GGTTGGAGTATCCCCTCAAAAATAACAG
3594487 GGTTGGAGTATCC
1 GGTTGGAGTATCC
3594500 TCGATTGTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCAAAAATAACAG
Found at i:3594574 original size:28 final size:28
Alignment explanation
Indices: 3594538--3594593 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
3594528 ATAAAACCGA
* *
3594538 GGTTGGAGTATCCTCTAAAAAATAACGG
1 GGTTAGAGTATCCCCTAAAAAATAACGG
3594566 GGTTAGAGTATCCCCTAAAAAATAACGG
1 GGTTAGAGTATCCCCTAAAAAATAACGG
3594594 AGTATCCTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (28 bp):
GGTTAGAGTATCCCCTAAAAAATAACGG
Found at i:3598305 original size:13 final size:13
Alignment explanation
Indices: 3598287--3598312 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3598277 CAATTTTTGG
3598287 TGTATCGATACAT
1 TGTATCGATACAT
3598300 TGTATCGATACAT
1 TGTATCGATACAT
3598313 ACTTGGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3598324 original size:32 final size:33
Alignment explanation
Indices: 3598267--3598330 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3598257 TACAAGCCAA
**
3598267 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
3598300 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
3598331 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:3598337 original size:19 final size:18
Alignment explanation
Indices: 3598267--3598337 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
3598257 TACAAGCCAA
3598267 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
3598287 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
3598300 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
3598319 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
3598338 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:3602036 original size:13 final size:13
Alignment explanation
Indices: 3602018--3602056 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
3602008 ATAATCACCC
3602018 TGTATCGATACAA
1 TGTATCGATACAA
3602031 TGTATCGATACAA
1 TGTATCGATACAA
3602044 TGTATCGATACAA
1 TGTATCGATACAA
3602057 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3605982 original size:21 final size:21
Alignment explanation
Indices: 3605953--3605997 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3605943 AAGTTTTTAT
*
3605953 TTTTCTTAGCTAA-TTCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3605973 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3605995 TTT
1 TTT
3605998 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3605997 original size:22 final size:20
Alignment explanation
Indices: 3605948--3605997 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
3605938 TATACAAGTT
*
3605948 TTTATTTTTCTTAGCTAATTC
1 TTTA-TTTTCTTAGCCAATTC
*
3605969 ATTATTTTCATTAGCCAACTTC
1 TTTATTTTC-TTAGCCAA-TTC
3605991 TTTATTT
1 TTTATTT
3605998 CAACTTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 10 0.42
22 9 0.38
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTATTTTCTTAGCCAATTC
Found at i:3606948 original size:59 final size:59
Alignment explanation
Indices: 3606856--3606973 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
3606846 TTTAGCCCAT
*
3606856 TAACAATATCGGTGAACCGATCGGACATTTCTTTGATATTCTCATCGGTTTTCATTTTA
1 TAACAATATCGGTGAACCGATCAGACATTTCTTTGATATTCTCATCGGTTTTCATTTTA
3606915 TAACAATATCGGTGAACCGATCAGACATTTCTTTGATATTCTCATCGGTTTTCATTTTA
1 TAACAATATCGGTGAACCGATCAGACATTTCTTTGATATTCTCATCGGTTTTCATTTTA
3606974 AATAATTCAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (59 bp):
TAACAATATCGGTGAACCGATCAGACATTTCTTTGATATTCTCATCGGTTTTCATTTTA
Found at i:3608295 original size:13 final size:13
Alignment explanation
Indices: 3608277--3608302 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3608267 CAATTTTTGG
3608277 TGTATCGATACAT
1 TGTATCGATACAT
3608290 TGTATCGATACAT
1 TGTATCGATACAT
3608303 ACTTGGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3608314 original size:32 final size:33
Alignment explanation
Indices: 3608257--3608320 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3608247 TACAAGCCAA
**
3608257 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
3608290 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
3608321 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:3608327 original size:19 final size:18
Alignment explanation
Indices: 3608257--3608327 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
3608247 TACAAGCCAA
3608257 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
3608277 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
3608290 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
3608309 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
3608328 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:3609178 original size:79 final size:77
Alignment explanation
Indices: 3609004--3609426 Score: 406
Period size: 79 Copynumber: 5.4 Consensus size: 77
3608994 CATTCCCCGA
* * ** *
3609004 TGAAAAATTGATATTTTGGAAATAAAACCGGGGTTGGAGTATCCCCTTAGAAATAACAGGGG-TG
1 TGAAAAATCGATATTTTTGAAATAAAAATGGGGTTGGAGTAT-CCTTTAGAAATAAC-GGGGTTG
*
3609068 GAGTATCTCGATGG
64 GAGTATCCCGATGG
* * * *
3609082 TGAAAAA-CTAATATTTTTGAAATAAAAATGGGGTTGGAGTATCCTTTCAAAAATAACGGGTTTA
1 TGAAAAATC-GATATTTTTGAAATAAAAATGGGGTTGGAGTATCCTTT-AGAAATAACGGGGTTG
3609146 GAGTATCCTCGATGG
64 GAGTATCC-CGATGG
* * * *
3609161 TGAAAAATCGATATTTTTGAAATAAAAATGAGGTTGAAGTATCCCTTGAGAAATAATGGGGTTGG
1 TGAAAAATCGATATTTTTGAAATAAAAATGGGGTTGGAGTAT-CCTTTAGAAATAACGGGGTTGG
*
3609226 AGTATCCCTAATGG
65 AGTATCCC-GATGG
* * * * * *
3609240 TAAAAAATCGATA-TTTTGAAAATAAAATTAGAGTTAGAGTAT-CTGCTCAGAAATAACGGGGTT
1 TGAAAAATCGATATTTTTG-AAATAAAAATGGGGTTGGAGTATCCT--TTAGAAATAACGGGGTT
*
3609303 GGAGTAACCCCGATGG
63 GGAGT-ATCCCGATGG
* * * * * * *
3609319 TGGAAAATTGATATTTTAGAAATAAAACTGGGATTTGAGTATCCATTTAGAAATAAGGGGGTTGG
1 TGAAAAATCGATATTTTTGAAATAAAAATGGGGTTGGAGTATCC-TTTAGAAATAACGGGGTTGG
3609384 AGTATCCCTGATGG
65 AGTATCCC-GATGG
*
3609398 TGAAGAAAATC-ATATTTTGGAAATAAAAA
1 TG-A-AAAATCGATATTTTTGAAATAAAAA
3609427 AAATCAATGA
Statistics
Matches: 282, Mismatches: 46, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
77 9 0.03
78 62 0.22
79 175 0.62
80 30 0.11
81 6 0.02
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.29
Consensus pattern (77 bp):
TGAAAAATCGATATTTTTGAAATAAAAATGGGGTTGGAGTATCCTTTAGAAATAACGGGGTTGGA
GTATCCCGATGG
Found at i:3609326 original size:158 final size:153
Alignment explanation
Indices: 3609004--3609426 Score: 456
Period size: 158 Copynumber: 2.7 Consensus size: 153
3608994 CATTCCCCGA
* *
3609004 TGAAAAATTGATATTTTGGAAATAAAACCGGGGTTGGAGTATCCCCTTAGAAATAACAGGGG-TG
1 TGAAAAATTGATATTTTAGAAATAAAA-CTGGGTT-GAGTAT-CCCTTAGAAATAA-AGGGGTTG
* * * * * * *
3609068 GAGTATCTC-GATGGTGAAAAACTAATATTTTTGAAATAAAAATGGGGTTGGAGTATCCTTTCAA
62 GAGTATCCCTGATGGT-AAAAAATCATA-TTTTGAAATAAAAATAGAGTTAGAGTATCCTCTCAA
* * *
3609132 AAATAACGGGTTTAGAGTATCCTCGATGG
125 AAATAACGGGGTTAGAGTAACCCCGATGG
* * * *
3609161 TGAAAAATCGATATTTTTGAAATAAAAATGAGGTTGAAGTATCCCTTGAGAAATAATGGGGTTGG
1 TGAAAAATTGATATTTTAGAAATAAAACTG-GGTTG-AGTATCCCTT-AGAAATAAAGGGGTTGG
* * *
3609226 AGTATCCCTAATGGTAAAAAATCGATATTTTGAAAATAAAATTAGAGTTAGAGTAT-CTGCTCAG
63 AGTATCCCTGATGGTAAAAAATC-ATATTTTG-AAATAAAAATAGAGTTAGAGTATCCT-CTCAA
*
3609290 AAATAACGGGGTTGGAGTAACCCCGATGG
125 AAATAACGGGGTTAGAGTAACCCCGATGG
* * *
3609319 TGGAAAATTGATATTTTAGAAATAAAACTGGGATTTGAGTATCCATTTAGAAATAAGGGGGTTGG
1 TGAAAAATTGATATTTTAGAAATAAAACTGGG--TTGAGTATCC-CTTAGAAATAAAGGGGTTGG
3609384 AGTATCCCTGATGGTGAAGAAAATCATATTTTGGAAATAAAAA
63 AGTATCCCTGATGGT-AA-AAAATCATATTTT-GAAATAAAAA
3609427 AAATCAATGA
Statistics
Matches: 225, Mismatches: 27, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
156 11 0.05
157 67 0.30
158 118 0.52
159 22 0.10
160 7 0.03
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.29
Consensus pattern (153 bp):
TGAAAAATTGATATTTTAGAAATAAAACTGGGTTGAGTATCCCTTAGAAATAAAGGGGTTGGAGT
ATCCCTGATGGTAAAAAATCATATTTTGAAATAAAAATAGAGTTAGAGTATCCTCTCAAAAATAA
CGGGGTTAGAGTAACCCCGATGG
Found at i:3613300 original size:16 final size:16
Alignment explanation
Indices: 3613253--3613341 Score: 70
Period size: 16 Copynumber: 5.4 Consensus size: 16
3613243 GTCAAAAGAA
*
3613253 ATTTAAATTATTTTTG
1 ATTTAAATTATTTTAG
***
3613269 AGTTTGGGTTATTTTTAG
1 A-TTTAAATTA-TTTTAG
3613287 ATTTAAATTATTTTAG
1 ATTTAAATTATTTTAG
* * *
3613303 ATTTGATTTGTTTTAG
1 ATTTAAATTATTTTAG
**
3613319 ATTTTGATTATTTTAG
1 ATTTAAATTATTTTAG
*
3613335 ATCTAAA
1 ATTTAAA
3613342 AATTTCAAGT
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
16 36 0.67
17 12 0.22
18 6 0.11
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.57
Consensus pattern (16 bp):
ATTTAAATTATTTTAG
Found at i:3613322 original size:32 final size:33
Alignment explanation
Indices: 3613253--3613336 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 33
3613243 GTCAAAAGAA
* *
3613253 ATTTAAATTATTTTTGAGTTTGGGTTATTTTTAG
1 ATTTAAATTATTTTAGA-TTTGGATTATTTTTAG
3613287 ATTTAAATTATTTTAGATTT-GATT-TGTTTTAG
1 ATTTAAATTATTTTAGATTTGGATTAT-TTTTAG
**
3613319 ATTTTGATTATTTTAGAT
1 ATTTAAATTATTTTAGAT
3613337 CTAAAAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
31 1 0.02
32 25 0.56
33 3 0.07
34 16 0.36
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (33 bp):
ATTTAAATTATTTTAGATTTGGATTATTTTTAG
Found at i:3617268 original size:25 final size:25
Alignment explanation
Indices: 3617232--3617282 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3617222 GCTCAGTGAG
*
3617232 CTTGTTTTTATAAAACAAGTATCCA
1 CTTGTTTCTATAAAACAAGTATCCA
3617257 CTTGTTTCTATAAAACAAGTATCCA
1 CTTGTTTCTATAAAACAAGTATCCA
3617282 C
1 C
3617283 ATGCCATCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (25 bp):
CTTGTTTCTATAAAACAAGTATCCA
Found at i:3618940 original size:13 final size:13
Alignment explanation
Indices: 3618922--3618947 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3618912 AATTTGGTCA
3618922 TGTATCGATACAT
1 TGTATCGATACAT
3618935 TGTATCGATACAT
1 TGTATCGATACAT
3618948 CTTGTCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3618944 original size:34 final size:32
Alignment explanation
Indices: 3618901--3618965 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 32
3618891 TACAAGCCAA
3618901 TGTATCGATACAAT-TTGGTCATGTATCGATACAT
1 TGTATCGATAC-ATCTT-GTC-TGTATCGATACAT
3618935 TGTATCGATACATCTTGTCTGTATCGATACA
1 TGTATCGATACATCTTGTCTGTATCGATACA
3618966 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 12 0.40
33 5 0.17
34 13 0.43
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATCTTGTCTGTATCGATACAT
Found at i:3619900 original size:5 final size:5
Alignment explanation
Indices: 3619890--3619920 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
3619880 GGTGGCAATT
3619890 TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA T
3619921 CCAGCTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:3623478 original size:20 final size:20
Alignment explanation
Indices: 3623454--3623506 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3623444 TACAATTGTG
3623454 TATGTATCGATACA-AAGCA
1 TATGTATCGATACATAAGCA
* *
3623473 TGATGTATCGATACATCAGGA
1 T-ATGTATCGATACATAAGCA
3623494 TATGTATCGATAC
1 TATGTATCGATAC
3623507 TTTCAAGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 25 0.83
21 4 0.13
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
TATGTATCGATACATAAGCA
Found at i:3630597 original size:79 final size:80
Alignment explanation
Indices: 3630463--3630669 Score: 292
Period size: 79 Copynumber: 2.6 Consensus size: 80
3630453 TCTTCATCTC
* *
3630463 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCA-TAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACAAATCGGGGATACTCCAA
* * * *
3630527 TCTCGTTATTTCCGA
66 CCCCGTCATTTCCAA
* * * *
3630542 GGGGATACTCCAACCCTGATTTTATTCCCAAAACACCAGTTTTTCACAAAT-GGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACAAATCGGGGATACTCCAA
*
3630606 CCCCGTCATTTCTAA
66 CCCCGTCATTTCCAA
*
3630621 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCACAA
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACAA
3630670 TCGAGGACAC
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 108 0.97
80 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACAAATCGGGGATACTCCAA
CCCCGTCATTTCCAA
Found at i:3630716 original size:51 final size:51
Alignment explanation
Indices: 3630627--3630738 Score: 170
Period size: 51 Copynumber: 2.2 Consensus size: 51
3630617 CTAAGGGGAT
* * *
3630627 ACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCACAATCGAGGAC
1 ACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAGGAC
* * *
3630678 ACTTCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGAT
1 ACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAGGAC
3630729 ACTCCAACTC
1 ACTCCAACTC
3630739 TGTTATTTCC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.30
Consensus pattern (51 bp):
ACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAGGAC
Found at i:3630762 original size:29 final size:28
Alignment explanation
Indices: 3630726--3630797 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
3630716 CACAATCGGG
* *
3630726 GATACTCCAACTCTGTTATTTCCATCGAA
1 GATACTCCAACCCCGTTATTT-CATCGAA
**
3630755 GATACTCCAACCCCGTTATTTCATCGGG
1 GATACTCCAACCCCGTTATTTCATCGAA
*
3630783 GATACTCTAACCCCG
1 GATACTCCAACCCCG
3630798 GCTTTATTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 19 0.50
29 19 0.50
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (28 bp):
GATACTCCAACCCCGTTATTTCATCGAA
Found at i:3630788 original size:28 final size:29
Alignment explanation
Indices: 3630720--3630797 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
3630710 ATTTTTCACA
* *
3630720 ATCGGGGATACTCCAACTCTGTTATTTCC
1 ATCGGGGATACTCCAACCCCGTTATTTCC
**
3630749 ATCGAAGATACTCCAACCCCGTTATTT-C
1 ATCGGGGATACTCCAACCCCGTTATTTCC
*
3630777 ATCGGGGATACTCTAACCCCG
1 ATCGGGGATACTCCAACCCCG
3630798 GCTTTATTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 19 0.45
29 23 0.55
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTATTTCC
Found at i:3630806 original size:159 final size:159
Alignment explanation
Indices: 3630596--3630905 Score: 381
Period size: 159 Copynumber: 1.9 Consensus size: 159
3630586 CACAAATGGG
* *
3630596 GATACTCCAACCCCGTCATTTCTAAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAAT
1 GATACTCCAACCCCGTCATTTCTAAGGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAAT
* * **
3630661 TTTTCACAATCGAGGACACTTCAACTC-CGATTTTATTTCCAAAACACCAATTTTTCACAATCGG
66 TTCTCACAATCGAGGACACTTCAACCCTCG-CCTTATTTCCAAAACACCAATTTTTCACAATCGG
* * *
3630725 GGATACTCCAACTCTGTTATTTCCATCGAA
130 AGATACTCCAACCCCGTTATTTCCATCGAA
* * * * ***
3630755 GATACTCCAACCCCGTTATTTC-ATCGGGGATACTCTAACCCCGGCTTTATTTCCAAAATATTGA
1 GATACTCCAACCCCGTCATTTCTA-AGGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAA
* * * * * *
3630819 TTTCTCACAATCGGGGATACTTCAACCCTCGCCTTATTTCTAAATCATCGATTTTTCACAATCGG
65 TTTCTCACAATCGAGGACACTTCAACCCTCGCCTTATTTCCAAAACACCAATTTTTCACAATCGG
*
3630884 AGATACTCTAACCCCGTTATTT
130 AGATACTCCAACCCCGTTATTT
3630906 TCGAAATGAT
Statistics
Matches: 126, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
158 1 0.01
159 123 0.98
160 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (159 bp):
GATACTCCAACCCCGTCATTTCTAAGGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAAT
TTCTCACAATCGAGGACACTTCAACCCTCGCCTTATTTCCAAAACACCAATTTTTCACAATCGGA
GATACTCCAACCCCGTTATTTCCATCGAA
Found at i:3630832 original size:51 final size:51
Alignment explanation
Indices: 3630777--3630899 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 51
3630767 CCGTTATTTC
* *
3630777 ATCGGGGATACTCTAACCCCGGCTTTATTTCCAAAAT-ATTGATTTCTCACA
1 ATCGGGGATACTCTAACCCCGGCCTTATTT-CAAAATCATCGATTTCTCACA
* *
3630828 ATCGGGGATACT-TCAACCCTC-GCCTTATTTCTAAATCATCGATTTTTCACA
1 ATCGGGGATACTCT-AACCC-CGGCCTTATTTCAAAATCATCGATTTCTCACA
*
3630879 ATCGGAGATACTCTAACCCCG
1 ATCGGGGATACTCTAACCCCG
3630900 TTATTTTCGA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
50 7 0.11
51 53 0.85
52 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.32
Consensus pattern (51 bp):
ATCGGGGATACTCTAACCCCGGCCTTATTTCAAAATCATCGATTTCTCACA
Found at i:3630967 original size:78 final size:77
Alignment explanation
Indices: 3630855--3631058 Score: 171
Period size: 79 Copynumber: 2.6 Consensus size: 77
3630845 CCTCGCCTTA
* * * *
3630855 TTTCTAAATCATCGATTTT-TCACAATCGGAGATACTCTAACCCCGTTATTTTCGAA-ATGATAC
1 TTTCAAAAT-ATCGATTTTCT-ATAATCGG-GATACTCTAACCCCGTTA-TTTCCAAGAGGATAC
**
3630918 TCCAA-CCTGATTTTAT
62 TCCAACCCCAATTTT-T
* ** *
3630934 TTTCAAAATATCGATTTTCTATAATCAGGGATACTCCAACCATGTTATTTCCAAGGGGATACTCC
1 TTTCAAAATATCGATTTTCTATAATC-GGGATACTCTAACCCCGTTATTTCCAAGAGGATACTCC
3630999 AACCCCAATTTTT
65 AACCCCAATTTTT
* * * * * *
3631012 TTTCCAGAACACCGATTTTCCATAATTGGGGATACTCTAGCCCCGTT
1 TTT-CAAAATATCGATTTTCTATAA-TCGGGATACTCTAACCCCGTT
3631059 GTTATCTCCA
Statistics
Matches: 100, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
77 6 0.06
78 43 0.43
79 50 0.50
80 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (77 bp):
TTTCAAAATATCGATTTTCTATAATCGGGATACTCTAACCCCGTTATTTCCAAGAGGATACTCCA
ACCCCAATTTTT
Found at i:3634594 original size:3 final size:3
Alignment explanation
Indices: 3634580--3634620 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
3634570 CGAGTTAACT
* * *
3634580 TCA TCA TTA TCA TCA TCA TCA TCA TCA TTA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
3634621 TTTGATGGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (3 bp):
TCA
Found at i:3635396 original size:165 final size:165
Alignment explanation
Indices: 3635123--3635465 Score: 442
Period size: 165 Copynumber: 2.1 Consensus size: 165
3635113 TTGTTCATGC
* * *
3635123 ATTTTTCATTTTTCTTTAAAATTTCTCTATTTTCGAAATACAGAGTTTTCTACTCCGTAAATGTT
1 ATTTTTCATTTTTCTTTAAAATTTCCCTATTTTCGAAAAACAGAGTTTTATACTCCGTAAATGTT
* * * * * * *
3635188 TTCGAGGGAATTTTTCTTAGTTTATAATTTTTACAATTCATCAAATATTATCATTTAATTTATAG
66 TTCGAGGGAATTTTTCTCAATTTAAAAATTTTAAAATTCATCAAATATTATCATTAAATTCATAG
3635253 TAAATTAGTTTTGA-AAAATTT-ATTTATTTTCATAA
131 TAAATTAG-TTTGAGAAAATTTAATTTATTTT-ATAA
* * * *
3635288 CTTTTTCATTTTTCTTTGAAA-TTCCCT-TGTTTATGAAAAACTGAGTTTTATACTCCGTAAATG
1 ATTTTTCATTTTTCTTTAAAATTTCCCTAT-TTT-CGAAAAACAGAGTTTTATACTCCGTAAATG
* * * *
3635351 TTTTCGAGGGGATTTTTCTCAATTTAAAAATTTTAAAATTCATCAAATATTGTTATTAAATTCCT
64 TTTTCGAGGGAATTTTTCTCAATTTAAAAATTTTAAAATTCATCAAATATTATCATTAAATTCAT
*
3635416 ATTAAATTAGTTTGAGAAAATTTAATTTATTTTATAA
129 AGTAAATTAGTTTGAGAAAATTTAATTTATTTTATAA
*
3635453 ATTTTACATTTTT
1 ATTTTTCATTTTT
3635466 TCATATAAGA
Statistics
Matches: 153, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
163 1 0.01
164 13 0.08
165 130 0.85
166 9 0.06
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (165 bp):
ATTTTTCATTTTTCTTTAAAATTTCCCTATTTTCGAAAAACAGAGTTTTATACTCCGTAAATGTT
TTCGAGGGAATTTTTCTCAATTTAAAAATTTTAAAATTCATCAAATATTATCATTAAATTCATAG
TAAATTAGTTTGAGAAAATTTAATTTATTTTATAA
Found at i:3635815 original size:20 final size:19
Alignment explanation
Indices: 3635781--3635824 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
3635771 AAGAAAAATA
*
3635781 AAAAAATTAAAAAAAGTCAT
1 AAAAAATGAAAAAAA-TCAT
* *
3635801 AAAAAATGAATAAAATGAT
1 AAAAAATGAAAAAAATCAT
3635820 AAAAA
1 AAAAA
3635825 GAAAGCATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (19 bp):
AAAAAATGAAAAAAATCAT
Found at i:3637731 original size:148 final size:146
Alignment explanation
Indices: 3637408--3637924 Score: 569
Period size: 149 Copynumber: 3.5 Consensus size: 146
3637398 TAAGTAAAAG
* * * *
3637408 GTATCGCC-TAAGGGTATTTTCATTATTTTTCTAAAATCGAGTCCTAATTTGTCACCTAGTCGCT
1 GTATAGCCATAAGGGTATTTTCATAATTTTTCAAAAATCGAGTCCTAATTTGTCACCGAGTCGCT
* **
3637472 TTTATGCCAAGGGTACATATTAGGTGTAGGTTTGCTTTCTTTTTTTAAGTCCTTTAGGGTTATCG
66 TCTATGCCAAGGGTACATATTAGG-G-AGGTTTGCTTT-TCCTTTTAAGTCCTTTAGGGTTA-CG
*
3637537 -GGATACTTTCATGTTGAAA
127 AGAATACTTTCATGTTGAAA
* * * * * *
3637556 GTATACCCATAAGGGTATTTTTATAATTTTTCTAGAATCGAGTCCTAATTAGTCACCGAGTCACT
1 GTATAGCCATAAGGGTATTTTCATAATTTTTCAAAAATCGAGTCCTAATTTGTCACCGAGTCGCT
* * * *
3637621 TCTATGCCGACGATACATATTAGGCAGAGGTTTGCTTTTCCTTTTAAATCCTTTAGGGTTACGAG
66 TCTATGCCAAGGGTACATATTAGG--GAGGTTTGCTTTTCCTTTTAAGTCCTTTAGGGTTACGAG
* *
3637686 AATACTTTCATATGGAAA
129 AATACTTTCATGTTGAAA
* * * * *
3637704 GTATAGCCATAAGGGCATTTTCATAATTTTTTCAAAAATTGATTCCTAATTTGTCACCAAGTTGC
1 GTATAGCCATAAGGGTATTTTCATAA-TTTTTCAAAAATCGAGTCCTAATTTGTCACCGAGTCGC
* * * * * *
3637769 TTCTATGCCAAGGGTACGTA-TA-GTAGGTTCGCTTTTTCCTTTTAAGTCTTTTAAGGTTACTA-
65 TTCTATGCCAAGGGTACATATTAGGGAGGTTTGC-TTTTCCTTTTAAGTCCTTTAGGGTTACGAG
*
3637831 AGATACTTTCATGTTGAAG
129 A-ATACTTTCATGTTGAAA
* * * *
3637850 GTATA-TCTTAAGGGTATTTTCATAATTTTTCAAAAATCGAGTCCTAAATTGTCACCGGGTCCGC
1 GTATAGCCATAAGGGTATTTTCATAATTTTTCAAAAATCGAGTCCTAATTTGTCACCGAGT-CGC
*
3637914 TTTTATGCCAA
65 TTCTATGCCAA
3637925 AGATGGGTAT
Statistics
Matches: 309, Mismatches: 53, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
144 30 0.10
145 37 0.12
146 44 0.14
147 3 0.01
148 67 0.22
149 127 0.41
150 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (146 bp):
GTATAGCCATAAGGGTATTTTCATAATTTTTCAAAAATCGAGTCCTAATTTGTCACCGAGTCGCT
TCTATGCCAAGGGTACATATTAGGGAGGTTTGCTTTTCCTTTTAAGTCCTTTAGGGTTACGAGAA
TACTTTCATGTTGAAA
Found at i:3639382 original size:28 final size:28
Alignment explanation
Indices: 3639338--3639400 Score: 110
Period size: 28 Copynumber: 2.2 Consensus size: 28
3639328 ATCCATTTAG
3639338 AACTCGCTTTCTTGGTGAGCGAGTTCGA
1 AACTCGCTTTCTTGGTGAGCGAGTTCGA
3639366 AACTCGCTTT-TTGGGTGAGCGAGTTCGA
1 AACTCGCTTTCTT-GGTGAGCGAGTTCGA
3639394 AACTCGC
1 AACTCGC
3639401 CCCTTGAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 2 0.06
28 32 0.94
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (28 bp):
AACTCGCTTTCTTGGTGAGCGAGTTCGA
Found at i:3639415 original size:28 final size:28
Alignment explanation
Indices: 3639354--3639419 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
3639344 CTTTCTTGGT
*** * *
3639354 GAGCGAGTTCGAAACTCGCTTTTTGGGT
1 GAGCGAGTTCGAAACTCGCCCCTTGAGA
3639382 GAGCGAGTTCGAAACTCGCCCCTTGAGA
1 GAGCGAGTTCGAAACTCGCCCCTTGAGA
*
3639410 GGGCGAGTTC
1 GAGCGAGTTC
3639420 ATTTATCTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (28 bp):
GAGCGAGTTCGAAACTCGCCCCTTGAGA
Found at i:3639519 original size:14 final size:16
Alignment explanation
Indices: 3639502--3639541 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
3639492 TGAAAGTCTT
3639502 TTTTTTAT-TC-ATAA
1 TTTTTTATGTCTATAA
3639516 TTTTTT-TGTCTATAA
1 TTTTTTATGTCTATAA
3639531 TTGTTTTATGT
1 TT-TTTTATGT
3639542 TTTCTAGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 8 0.36
15 6 0.27
16 4 0.18
17 3 0.14
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (16 bp):
TTTTTTATGTCTATAA
Found at i:3644627 original size:130 final size:130
Alignment explanation
Indices: 3644376--3644646 Score: 327
Period size: 130 Copynumber: 2.1 Consensus size: 130
3644366 ATTTTTCATT
** * * *
3644376 TCGGGGATAC-TCTAACCCCGGTTTTATTTCCAAAACATCAATTTTTCATAATCGAGGATACTCT
1 TCGGGGATACTTCTAACCCCAATTTTATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCC
* * **
3644440 AATCCCGTTATTTTCGAGGAGATATCCAACCCTGACTTTATTTCTAAAATATTGATTTCTCACAA
66 AACCCCGTTATTTTCGAGGAGATATCCAACCCTGACTTTATTTCTAAAACACCGATTTCTCACAA
* *
3644505 TCGGGGATACTTC-AACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATCGGGGATACTC
1 TCGGGGATACTTCTAACCCCAATTTTATTTCCAAAACACCAAT-TTTTCACAATCGAGGATACTC
* * * *
3644569 CAACCCCGTTATTTTCGAGG-GATACTCCAATCCT-AGTTTTATTT-TCAGAACACCGATTTTTC
65 CAACCCCGTTATTTTCGAGGAGATA-TCCAACCCTGA-CTTTATTTCT-AAAACACCGATTTCTC
3644631 ACAA
127 ACAA
*
3644635 TTGGGGATACTT
1 TCGGGGATACTT
3644647 AAATCCCGTT
Statistics
Matches: 121, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
129 41 0.34
130 80 0.66
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (130 bp):
TCGGGGATACTTCTAACCCCAATTTTATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCC
AACCCCGTTATTTTCGAGGAGATATCCAACCCTGACTTTATTTCTAAAACACCGATTTCTCACAA
Found at i:3644655 original size:78 final size:79
Alignment explanation
Indices: 3644507--3644736 Score: 243
Period size: 79 Copynumber: 2.9 Consensus size: 79
3644497 TCTCACAATC
* * * *
3644507 GGGGATACTTCAACCCCA-ATTTTATTTCTAAAACACCAATCTTTTCACAATCGGGGATACTCCA
1 GGGGATAC-TCAAACCTAGATTTTATTTCTAGAACACCAAT-TTTTCACAATCGGGGATACTCAA
*
3644571 ACCCCGTTATTTTCGA
64 ACCCCGTTATTTTCAA
* * * *
3644587 -GGGATACTCCAATCCTAG-TTTTATTT-TCAGAACACCGATTTTTCACAATTGGGGATACTTAA
1 GGGGATACT-CAAACCTAGATTTTATTTCT-AGAACACCAATTTTTCACAATCGGGGATACTCAA
*
3644649 ATCCCGTTATTTTCAA
64 ACCCCGTTATTTTCAA
* * * * * *
3644665 GGGGATACTCAAACCTTGATTTTATTTCTAGAACACCCATTTTCCATAGTCAGGGGATACTCCAA
1 GGGGATACTCAAACCTAGATTTTATTTCTAGAACACCAATTTTTCACAATC-GGGGATACTCAAA
3644730 CCCCGTT
65 CCCCGTT
3644737 GTCATCTCCA
Statistics
Matches: 124, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
78 43 0.35
79 63 0.51
80 18 0.15
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
GGGGATACTCAAACCTAGATTTTATTTCTAGAACACCAATTTTTCACAATCGGGGATACTCAAAC
CCCGTTATTTTCAA
Found at i:3655338 original size:7 final size:7
Alignment explanation
Indices: 3655326--3655356 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3655316 GTGTTTTTTA
3655326 AAAAAAT
1 AAAAAAT
3655333 AAAAAAT
1 AAAAAAT
3655340 AAAAAAT
1 AAAAAAT
3655347 AAAAAA-
1 AAAAAAT
3655353 AAAA
1 AAAA
3655357 TTCCAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:3655435 original size:19 final size:19
Alignment explanation
Indices: 3655411--3655478 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3655401 AATTCAACAA
3655411 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3655430 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3655445 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3655462 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3655479 TTGGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3655450 original size:13 final size:13
Alignment explanation
Indices: 3655432--3655456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3655422 ACATAAGTTT
3655432 TGTATCGATACAA
1 TGTATCGATACAA
3655445 TGTATCGATACA
1 TGTATCGATACA
3655457 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3655454 original size:32 final size:32
Alignment explanation
Indices: 3655413--3655475 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3655403 TTCAACAATT
*
3655413 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3655445 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3655476 TAATTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3655536 original size:13 final size:13
Alignment explanation
Indices: 3655518--3655543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3655508 CATTTTTCTG
3655518 TGTATCGATACAT
1 TGTATCGATACAT
3655531 TGTATCGATACAT
1 TGTATCGATACAT
3655544 GGATCTTTGT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3655540 original size:33 final size:33
Alignment explanation
Indices: 3655498--3655564 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3655488 GCCAAGGAAA
***
3655498 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3655531 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3655564 T
1 T
3655565 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3658013 original size:52 final size:52
Alignment explanation
Indices: 3657912--3658247 Score: 200
Period size: 53 Copynumber: 6.4 Consensus size: 52
3657902 AATTCTCCAC
* * * **
3657912 AATCGAGGATATTCCAACTCCGATTTTACTTT-CAAAAACATTAATTT-TCTAT
1 AATCGGGGATACTCCAACCCCGATTTTA-TTTCCAAAAACACCAATTTCTC-AT
* *
3657964 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAAACACCAATTTC-TCAT
* * * *** * * *** *
3658018 AATCGGGGACACTCCAACCCCG--TTAATCATCGGGGACACTCCAACCCCGTTAT
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC-CAAAAACACCAATTTC-TCAT
* * * * * * *
3658071 -TTCTGAGGGGATACTCCAACCCCGACTTTATTTTC-AAAATATCGATTTTTCAT
1 AATC---GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCTCAT
* * *
3658124 AATCGGGGATACTCCAACCCCGATTTTATTTTC-ACAACACCAATTTCTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCT-C-AT
** * * *
3658177 AATCGGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCTCAT
*
3658229 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
3658248 TCGTTATTTC
Statistics
Matches: 213, Mismatches: 56, Indels: 30
0.71 0.19 0.10
Matches are distributed among these distances:
51 41 0.19
52 50 0.23
53 59 0.28
54 39 0.18
55 19 0.09
56 1 0.00
57 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (52 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTCTCAT
Found at i:3658089 original size:28 final size:27
Alignment explanation
Indices: 3658022--3658094 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
3658012 CTTCACAATC
*
3658022 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGACACTCCAACCCCGTTAATCATA
*
3658049 GGGGACACTCCAACCCCGTTATTTC-TGA
1 GGGGACACTCCAACCCCGTTA-ATCAT-A
*
3658077 GGGGATACTCCAACCCCG
1 GGGGACACTCCAACCCCG
3658095 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.23, C:0.36, G:0.22, T:0.19
Consensus pattern (27 bp):
GGGGACACTCCAACCCCGTTAATCATA
Found at i:3658139 original size:51 final size:51
Alignment explanation
Indices: 3658077--3658247 Score: 207
Period size: 51 Copynumber: 3.3 Consensus size: 51
3658067 TTATTTCTGA
* * *
3658077 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * *
3658128 GGGGATACTCCAACCCCGATTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
3658181 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
3658233 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3658248 TCGTTATTTC
Statistics
Matches: 99, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
51 37 0.37
52 18 0.18
53 33 0.33
54 11 0.11
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:3658266 original size:28 final size:28
Alignment explanation
Indices: 3658230--3658311 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
3658220 ATTTTTCACA
*
3658230 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3658258 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
3658286 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
3658312 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:3658301 original size:212 final size:212
Alignment explanation
Indices: 3657912--3658303 Score: 565
Period size: 212 Copynumber: 1.8 Consensus size: 212
3657902 AATTCTCCAC
* * **
3657912 AATCGAGGATATTCCAACTCCGATTTTACTTTCAAAAACATTAATTTTCTATAATCGGGGATACT
1 AATCGAGGATACTCCAACCCCGATTTTACTTTCAAAAACACCAATTTTCTATAATCGGGGATACT
*
3657977 CCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTT
66 CCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTT
* * * *
3658042 AATCATCGGGGACACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTTTCA
131 AATCATCGGGGACACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTTCA
3658107 AAATATCGATTTTTCAT
196 AAATATCGATTTTTCAT
* * * *
3658124 AATCGGGGATACTCCAACCCCGATTTTATTTTC-ACAACACCAATTTCTCCTTTAATCGGGGATA
1 AATCGAGGATACTCCAACCCCGATTTTACTTTCAAAAACACCAATTT-T-CTATAATCGGGGATA
* * * *
3658188 CTCCAATTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCG
64 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCG
* *
3658251 TTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACC
129 TTA-ATCATCGGGGACACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACC
3658304 TCGTTATTAT
Statistics
Matches: 158, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
211 37 0.23
212 86 0.54
213 35 0.22
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.30
Consensus pattern (212 bp):
AATCGAGGATACTCCAACCCCGATTTTACTTTCAAAAACACCAATTTTCTATAATCGGGGATACT
CCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTT
AATCATCGGGGACACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTTCA
AAATATCGATTTTTCAT
Found at i:3660659 original size:13 final size:13
Alignment explanation
Indices: 3660641--3660667 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3660631 TAGAAAGATT
3660641 AATGTATCGATAC
1 AATGTATCGATAC
3660654 AATGTATCGATAC
1 AATGTATCGATAC
3660667 A
1 A
3660668 TTGAATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:3660664 original size:33 final size:33
Alignment explanation
Indices: 3660622--3660687 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3660612 AAATTCCTAG
* *
3660622 ATGTATCGATAGAAAGATTAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
**
3660655 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
3660688 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:3661612 original size:52 final size:51
Alignment explanation
Indices: 3661556--3662188 Score: 268
Period size: 48 Copynumber: 13.5 Consensus size: 51
3661546 GTACTCAGAT
* ** *
3661556 AAGGCCAGCGACATTGGACTTAGGAATGTTAAAGATGCCAATATGCTGATTC
1 AAGGCCAGCGACATTGGACTTA-AAATGACAAAGGTGCCAATATGCTGATTC
* * ** * * *
3661608 AAGGCCAACGATATCAGACTTAAAGATG---AAGATGCCAATGTGCTAATTC
1 AAGGCCAGCGACATTGGACTTAAA-ATGACAAAGGTGCCAATATGCTGATTC
* * * **
3661657 AAGGCCAGCGGCATTGGTCTTAAAGATGACGAAGGCACCAATATGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAA-ATGACAAAGGTGCCAATATGCTGATTC
* * *
3661709 AAGGCCAGCGATATTGGACTTAAAAATG---AAGGTGCCAATGTGTTGATTC
1 AAGGCCAGCGACATTGGACTT-AAAATGACAAAGGTGCCAATATGCTGATTC
* *
3661758 AAGGCTAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAA-ATGACAAAGGTGCCAATATGCTGATTC
* * * *
3661810 AAGACCAGCGATATTGGGC-T----T-------GTGCCAATGTGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAAATGACAAAGGTGCCAATATGCTGATTC
* * * *
3661849 AAGGCCAGCGACATTGGTCTTAGAA--AC-AAGGTGCTAATATGCTAATTC
1 AAGGCCAGCGACATTGGACTTAAAATGACAAAGGTGCCAATATGCTGATTC
* * * * *
3661897 AAGGTCAGCGATATTGGGC-T----T-------GTGCCAATGTGTTGATTC
1 AAGGCCAGCGACATTGGACTTAAAATGACAAAGGTGCCAATATGCTGATTC
* * * * * * * *
3661936 AAGGTCAGTGGCATTGGTCTT-AGA-GAC-AAGATGCTAATATGCTAATTC
1 AAGGCCAGCGACATTGGACTTAAAATGACAAAGGTGCCAATATGCTGATTC
* * * *
3661984 AAGGCCAGCGATATTGGGC-T----T-----A--TGCCAATGTGCTAATTC
1 AAGGCCAGCGACATTGGACTTAAAATGACAAAGGTGCCAATATGCTGATTC
* * *
3662023 AAGGTCAGCGACATTGGTCTT-AGA-GAC-AAGGTGCCAATATGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAAATGACAAAGGTGCCAATATGCTGATTC
* * * ** * *
3662071 AAGGCCAGCGATATTGGACTCAAGATGGTAAAGGTACCGATATGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAAATGACAAAGGTGCCAATATGCTGATTC
* * *
3662122 AAGGCCAGCGATATTAGAC-T----T-A-AAA-GTGCCAATATGCTGATGC
1 AAGGCCAGCGACATTGGACTTAAAATGACAAAGGTGCCAATATGCTGATTC
*
3662165 AAGGCCAGCGACATTGGTCTTAAA
1 AAGGCCAGCGACATTGGACTTAAA
3662189 GGTGCCAATG
Statistics
Matches: 446, Mismatches: 87, Indels: 101
0.70 0.14 0.16
Matches are distributed among these distances:
39 92 0.21
40 3 0.01
41 1 0.00
43 31 0.07
44 4 0.01
46 3 0.01
47 2 0.00
48 93 0.21
49 83 0.19
50 1 0.00
51 39 0.09
52 91 0.20
53 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (51 bp):
AAGGCCAGCGACATTGGACTTAAAATGACAAAGGTGCCAATATGCTGATTC
Found at i:3661657 original size:49 final size:49
Alignment explanation
Indices: 3661556--3662235 Score: 338
Period size: 39 Copynumber: 14.6 Consensus size: 49
3661546 GTACTCAGAT
* *
3661556 AAGGCCAGCGACATTGGACTTAGGAATGTTAAAGATGCCAATATGCTGATTC
1 AAGGCCAGCGACATTGGACTTA--AA-GATGAAGATGCCAATATGCTGATTC
* * ** * *
3661608 AAGGCCAACGATATCAGACTTAAAGATGAAGATGCCAATGTGCTAATTC
1 AAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
* * * *
3661657 AAGGCCAGCGGCATTGGTCTTAAAGATGACGAAGGCACCAATATGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAAGATGAAG-ATG--CCAATATGCTGATTC
* * * * *
3661709 AAGGCCAGCGATATTGGACTTAAAAATGAAGGTGCCAATGTGTTGATTC
1 AAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
* **
3661758 AAGGCTAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAAGATG---AAGATGCCAATATGCTGATTC
* * * *
3661810 AAGACCAGCGATATTGGGC-T-----T---G-TGCCAATGTGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
* * * * *
3661849 AAGGCCAGCGACATTGGTCTTAGAA-A-CAAGGTGCTAATATGCTAATTC
1 AAGGCCAGCGACATTGGACTTA-AAGATGAAGATGCCAATATGCTGATTC
* * * * *
3661897 AAGGTCAGCGATATTGGGC-T-----T---G-TGCCAATGTGTTGATTC
1 AAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
* * * * * * * *
3661936 AAGGTCAGTGGCATTGGTCTTAGAGA-CAAGATGCTAATATGCTAATTC
1 AAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
* * * *
3661984 AAGGCCAGCGATATTGGGC-T-----T----ATGCCAATGTGCTAATTC
1 AAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
* * * * *
3662023 AAGGTCAGCGACATTGGTCTTAGAGA-CAAGGTGCCAATATGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
* * * * *
3662071 AAGGCCAGCGATATTGGAC-TCAAGATGGTAAAGGTACCGATATGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAAGAT-G--AAGATGCCAATATGCTGATTC
* * *
3662122 AAGGCCAGCGATATTAGACTT--A-A--AAG-TGCCAATATGCTGATGC
1 AAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
* *
3662165 AAGGCCAGCGACATTGGTCTT-AA-A-G--G-TGCCAATGTGCTGATTC
1 AAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
* **
3662208 AAGGCCAGAGACATTGGTTTTAAAGATG
1 AAGGCCAGCGACATTGGACTTAAAGATG
3662236 CCACAGAGTT
Statistics
Matches: 488, Mismatches: 92, Indels: 102
0.72 0.13 0.15
Matches are distributed among these distances:
39 91 0.19
40 5 0.01
43 67 0.14
44 7 0.01
45 1 0.00
46 2 0.00
47 8 0.02
48 88 0.18
49 84 0.17
50 5 0.01
51 39 0.08
52 91 0.19
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
AAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
Found at i:3661698 original size:101 final size:101
Alignment explanation
Indices: 3661500--3661823 Score: 354
Period size: 101 Copynumber: 3.2 Consensus size: 101
3661490 AATGAGAATG
* * * * *
3661500 TGCTGATTCATGGCCAGCGATATTAGA-TT-TAAA-GAAGAATACCAATGTACTCAGA-T-AAGG
1 TGCTGATTCAAGGCCAGCGATATCAGACTTAAAAATGAAG-ATGCCAATGTGCT-A-ATTCAAGG
* ** ***
3661560 CCAGCGACATTGGACTT-AGGAATGTTAAAGATGCCAATA
63 CCAGCGACATTGGACTTAAAG-ATGACAAAGGCACCAATA
* *
3661599 TGCTGATTCAAGGCCAACGATATCAGACTTAAAGATGAAGATGCCAATGTGCTAATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATCAGACTTAAAAATGAAGATGCCAATGTGCTAATTCAAGGCCA
* * *
3661664 GCGGCATTGGTCTTAAAGATGACGAAGGCACCAATA
66 GCGACATTGGACTTAAAGATGACAAAGGCACCAATA
** * * * *
3661700 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGGTGCCAATGTGTTGATTCAAGGCTA
1 TGCTGATTCAAGGCCAGCGATATCAGACTTAAAAATGAAGATGCCAATGTGCTAATTCAAGGCCA
*
3661765 GCGACATTGGACTTAAAGATGACAAAGGCGCCAATA
66 GCGACATTGGACTTAAAGATGACAAAGGCACCAATA
*
3661801 TGCTGATTCAAGACCAGCGATAT
1 TGCTGATTCAAGGCCAGCGATAT
3661824 TGGGCTTGTG
Statistics
Matches: 190, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
99 25 0.13
100 4 0.02
101 155 0.82
102 6 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (101 bp):
TGCTGATTCAAGGCCAGCGATATCAGACTTAAAAATGAAGATGCCAATGTGCTAATTCAAGGCCA
GCGACATTGGACTTAAAGATGACAAAGGCACCAATA
Found at i:3661824 original size:101 final size:101
Alignment explanation
Indices: 3661500--3662090 Score: 396
Period size: 87 Copynumber: 6.3 Consensus size: 101
3661490 AATGAGAATG
* * * * *
3661500 TGCTGATTCATGGCCAGCGATATTAGA-TT-TAAA-GAAGAATACCAATGTACTCAGA-T-AAGG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAG-ATGCCAATGTGCT-A-ATTCAAGG
* ** **
3661560 CCAGCGACATTGGACTT-AGGAATGTTAAAGATGCCAATA
63 CCAGCGACATTGGACTTAAAG-ATGACAAAGGCGCCAATA
* ** *
3661599 TGCTGATTCAAGGCCAACGATATCAGACTTAAAGATGAAGATGCCAATGTGCTAATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGCCAATGTGCTAATTCAAGGCCA
* * * *
3661664 GCGGCATTGGTCTTAAAGATGACGAAGGCACCAATA
66 GCGACATTGGACTTAAAGATGACAAAGGCGCCAATA
* * * *
3661700 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGGTGCCAATGTGTTGATTCAAGGCTA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGCCAATGTGCTAATTCAAGGCCA
3661765 GCGACATTGGACTTAAAGATGACAAAGGCGCCAATA
66 GCGACATTGGACTTAAAGATGACAAAGGCGCCAATA
* * *
3661801 TGCTGATTCAAGACCAGCGATATTGGGC-T-----T---G-TGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGCCAATGTGCTAATTCAAGGCCA
* * * *
3661856 GCGACATTGGTCTT--AGA-AAC-AAGGTGCTAATA
66 GCGACATTGGACTTAAAGATGACAAAGGCGCCAATA
* * * * * *
3661888 TGCTAATTCAAGGTCAGCGATATTGGGC-T-----T---G-TGCCAATGTGTTGATTCAAGGTCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGCCAATGTGCTAATTCAAGGCCA
* * * ** *
3661943 GTGGCATTGGTCTT--AGA-GAC-AAGATGCTAATA
66 GCGACATTGGACTTAAAGATGACAAAGGCGCCAATA
* * *
3661975 TGCTAATTCAAGGCCAGCGATATTGGGC-T-----T----ATGCCAATGTGCTAATTCAAGGTCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGCCAATGTGCTAATTCAAGGCCA
* *
3662030 GCGACATTGGTCTT--AGA-GAC-AAGGTGCCAATA
66 GCGACATTGGACTTAAAGATGACAAAGGCGCCAATA
3662062 TGCTGATTCAAGGCCAGCGATATTGGACT
1 TGCTGATTCAAGGCCAGCGATATTGGACT
3662091 CAAGATGGTA
Statistics
Matches: 430, Mismatches: 54, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
87 193 0.45
88 2 0.00
89 3 0.01
91 35 0.08
92 1 0.00
95 1 0.00
99 25 0.06
100 5 0.01
101 159 0.37
102 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (101 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGCCAATGTGCTAATTCAAGGCCA
GCGACATTGGACTTAAAGATGACAAAGGCGCCAATA
Found at i:3661919 original size:87 final size:87
Alignment explanation
Indices: 3661740--3662087 Score: 489
Period size: 87 Copynumber: 4.0 Consensus size: 87
3661730 AAAAATGAAG
* * * *
3661740 GTGCCAATGTGTTGATTCAAGGCTAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT--AGA-GAC-AAGGTGCCAATATGCT
* *
3661805 GATTCAAGACCAGCGATATTGGGCTT
62 AATTCAAGGCCAGCGATATTGGGCTT
* *
3661831 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAAACAAGGTGCTAATATGCTAATT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTAATT
*
3661896 CAAGGTCAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
* * * * * *
3661918 GTGCCAATGTGTTGATTCAAGGTCAGTGGCATTGGTCTTAGAGACAAGATGCTAATATGCTAATT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTAATT
3661983 CAAGGCCAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
* * * *
3662005 ATGCCAATGTGCTAATTCAAGGTCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTAATT
3662070 CAAGGCCAGCGATATTGG
66 CAAGGCCAGCGATATTGG
3662088 ACTCAAGATG
Statistics
Matches: 233, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
87 192 0.82
88 2 0.01
89 3 0.01
91 36 0.15
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (87 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTAATT
CAAGGCCAGCGATATTGGGCTT
Found at i:3662223 original size:43 final size:43
Alignment explanation
Indices: 3662099--3662238 Score: 181
Period size: 43 Copynumber: 3.3 Consensus size: 43
3662089 CTCAAGATGG
* * * * *
3662099 TAAAGGTACCGATATGCTGATTCAAGGCCAGCGATATTAGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCT
* *
3662142 TAAAAGTGCCAATATGCTGATGCAAGGCCAGCGACATTGGTCT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCT
* * *
3662185 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGAGACATTGGTTT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCT
*
3662228 TAAAGATGCCA
1 TAAAGGTGCCA
3662239 CAGAGTTATG
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCT
Found at i:3662279 original size:34 final size:34
Alignment explanation
Indices: 3662234--3662859 Score: 429
Period size: 34 Copynumber: 19.8 Consensus size: 34
3662224 GTTTTAAAGA
* *
3662234 TGCCACAGAGTTATGGACTTAAAAGGAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
* *
3662268 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
*
3662302 TGCCACGGAGTTGTGGACTTAAAAAG-AAAAGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGG-G
* * *
3662336 TGCCATGGAGTTGTGGGCTT-------AAAAGGT
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
* *
3662363 TGCCACGAAGTTGTGGACTTAAAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
3662397 TGCCACGGAGTTGTGGACTT-------AAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
*
3662424 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
* * **
3662458 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGGG
* *
3662493 TGCCACTGAGTTATGGACTT-------AAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
* *
3662520 TACCACGGAGTTGAGGACTT------AAAAA-GG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
* * * *
3662547 TGTCACAGAGTTGTAGACTTAAAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
* * *
3662581 TGCCACGAAGTTGTAGG-CTTTAAAAAGAAAAAAGG
1 TGCCACGGAGTTGT-GGAC-TTAAAAGGAAAAAGGG
**
3662616 TGCCACTAAGTTGTGGACTT-------AAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
3662643 TGCCACGGAGTTGTGGACTT-------AAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
**
3662670 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
* * * *
3662704 TGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAAGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGGG
* *
3662739 TGCAACAGAGTTGTGGACTT-------AAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
* * *
3662766 TGCCACGGAGTTGTGAACTTAAAAGAAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
* * * *
3662800 TGCCACAGAGTTGTGGGCTTTAAAAAGAAGAA-GG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGGG
* *
3662834 TGCTACGAAGTTGTGGACTTAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGG
3662860 GTGCCATGGA
Statistics
Matches: 475, Mismatches: 74, Indels: 87
0.75 0.12 0.14
Matches are distributed among these distances:
27 155 0.33
28 10 0.02
33 17 0.04
34 198 0.42
35 95 0.20
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (34 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
Found at i:3662369 original size:61 final size:60
Alignment explanation
Indices: 3662296--3662728 Score: 381
Period size: 61 Copynumber: 7.1 Consensus size: 60
3662286 TTAAAAGGAA
* * *
3662296 AAAAGGTGCCACGGAGTTGTGGACTTAAAAAGAAAAGGAGTGCCATGGAGTTGTGGGCTT
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
3662356 AAAAGGTTGCCACGAAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
1 AAAAGG-TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
3662417 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAA-GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT
* * * * *
3662479 AAAAAGAAAAAAAGTGCCACTGAGTTATGGACTTAAAA-G-----G-GTACCACGGAGTTGAGGA
1 -AAAAG-------GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGG
3662537 CTT
58 CTT
* * * * *
3662540 AAAAAGGTGTCACAGAGTTGTAGACTTAAAAGGAAAAAGAGTGCCACGAAGTTGTAGGCTTT
1 -AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT
** *
3662602 AAAAAGAAAAAAGGTGCCACTAAGTTGTGGACTTAAAA-G-----G-GTGCCACGGAGTTGTGGA
1 --------AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGG
3662660 CTT
58 CTT
* *
3662663 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAAAGTGCCACGAAGTTGTGGGCTTT
1 AAAA-GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT
3662725 AAAA
1 AAAA
3662729 AGAAAAAAGG
Statistics
Matches: 305, Mismatches: 33, Indels: 68
0.75 0.08 0.17
Matches are distributed among these distances:
53 4 0.01
54 45 0.15
55 2 0.01
60 7 0.02
61 144 0.47
62 45 0.15
63 6 0.02
68 2 0.01
69 50 0.16
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (60 bp):
AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:3662374 original size:27 final size:27
Alignment explanation
Indices: 3662295--3662880 Score: 247
Period size: 27 Copynumber: 19.0 Consensus size: 27
3662285 CTTAAAAGGA
*
3662295 AAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
3662322 AAAAAGAAAAGGAGTGCCATGGAGTTGTGGGCTT
1 ------AAAAGG-GTGCCACGGAGTTGTGGACTT
* *
3662356 AAAAGGTTGCCACGAAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
3662383 AAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
1 AAAA-G-----G-GTGCCACGGAGTTGTGGACTT
3662417 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
3662444 AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAA-G-----G-GTGCCACGGAGTTGTGGAC-TT
* * *
3662479 AAAAAGAAAAAAAGTGCCACTGAGTTATGGACTT
1 -AAAAG------GGTGCCACGGAGTTGTGGACTT
* *
3662513 AAAAGGGTACCACGGAGTTGAGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * * *
3662540 AAAAAGGTGTCACAGAGTTGTAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
3662567 AAAAGGAAAAAGAGTGCCACGAAGTTGTAGG-CTTT
1 AAAA-G-----G-GTGCCACGGAGTTGT-GGAC-TT
**
3662602 AAAAAGAAAAAAGGTGCCACTAAGTTGTGGACTT
1 -AAAAG------GGTGCCACGGAGTTGTGGACTT
3662636 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
3662663 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
3662690 AAAAGGAAAAAAAGTGCCACGAAGTTGTGGGCTTT
1 AAAAGG-------GTGCCACGGAGTTGTGGAC-TT
* *
3662725 AAAAAGAAAAAAGGTGCAACAGAGTTGTGGACTT
1 -AAAAG------GGTGCCACGGAGTTGTGGACTT
*
3662759 AAAAGGGTGCCACGGAGTTGTGAACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
3662786 AAAAGAAAAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAAG------G-GTGCCACGGAGTTGTGGAC-TT
* *
3662821 AAAAAGAAGAAGGTGCTACGAAGTTGTGGACTT
1 ---AA-AAG--GGTGCCACGGAGTTGTGGACTT
*
3662854 AAAAGGGTGCCATGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
3662881 TGAGAAGAGA
Statistics
Matches: 444, Mismatches: 52, Indels: 120
0.72 0.08 0.19
Matches are distributed among these distances:
27 184 0.41
28 9 0.02
29 3 0.01
30 2 0.00
33 27 0.06
34 129 0.29
35 60 0.14
36 24 0.05
38 2 0.00
39 3 0.01
42 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:3662567 original size:123 final size:123
Alignment explanation
Indices: 3662390--3662790 Score: 658
Period size: 123 Copynumber: 3.3 Consensus size: 123
3662380 CTTAAAAGGA
*
3662390 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* * *
3662455 GAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAAGTGCCACTGAGTTATGGACTT
66 GAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCCACTGAGTTGTGGACTT
* * * * * *
3662513 AAAAGGGTACCACGGAGTTGAGGACTTAAAAAGGTGTCACAGAGTTGTAGACTTAAAAGGAAAAA
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* *
3662578 GAGTGCCACGAAGTTGTAGGCTTTAAAAAGAAAAAAGGTGCCACTAAGTTGTGGACTT
66 GAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCCACTGAGTTGTGGACTT
3662636 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* * *
3662701 AAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCAACAGAGTTGTGGACTT
66 GAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCCACTGAGTTGTGGACTT
*
3662759 AAAAGGGTGCCACGGAGTTGTGAACTTAAAAG
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
3662791 AAAAAAGAGT
Statistics
Matches: 254, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
123 254 1.00
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (123 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
GAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCCACTGAGTTGTGGACTT
Found at i:3662702 original size:96 final size:94
Alignment explanation
Indices: 3662602--3662880 Score: 283
Period size: 96 Copynumber: 2.9 Consensus size: 94
3662592 TGTAGGCTTT
* *
3662602 AAAAAGAAAAAAGGTGCCACTAAGTTGTGGAC-TT-AAAAG-GGTGCCACGGAGTTGTGGACTTA
1 AAAAAGAAAAAA-GTGCCAC-AAGTTGTGGGCTTTAAAAAGAGGTGCAACGGAGTTGTGGACTTA
3662664 AAAGGGTGCCACGGAGTTGTGGACTTAAAAG
64 AAAGGGTGCCACGGAGTTGTGGACTTAAAAG
* *
3662695 ---GA-AAAAAAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCAACAGAGTTGTGGA
1 AAAAAGAAAAAAGTGCCAC-AAGTTGTGGGCTTTAAAAAG-----AGGTGCAACGGAGTTGTGGA
*
3662756 CTTAAAAGGGTGCCACGGAGTTGTGAACTTAAAAG
60 CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
* * *
3662791 ---AA-AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCTACGAAGTTGTGGAC
1 AAAAAGAAAAAAGTGCCACA-AGTTGTGGGCTTT--AAA-AAG-AGGTGCAACGGAGTTGTGGAC
*
3662852 TTAAAAGGGTGCCATGGAGTTGTGGACTT
61 TTAAAAGGGTGCCACGGAGTTGTGGACTT
3662881 TGAGAAGAGA
Statistics
Matches: 161, Mismatches: 13, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
88 17 0.11
89 8 0.05
90 6 0.04
95 47 0.29
96 77 0.48
98 3 0.02
99 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.21
Consensus pattern (94 bp):
AAAAAGAAAAAAGTGCCACAAGTTGTGGGCTTTAAAAAGAGGTGCAACGGAGTTGTGGACTTAAA
AGGGTGCCACGGAGTTGTGGACTTAAAAG
Found at i:3662809 original size:61 final size:63
Alignment explanation
Indices: 3662703--3662824 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 63
3662693 AGGAAAAAAA
**
3662703 GTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCAACAGAGTTGTGGAC-TTAAAAGG
1 GTGCCACGAAGTTGTGAACTTTAAAAAGAAAAAAGGTGCAACAGAGTTGTGGACTTTAAAAGG
* * *
3662765 GTGCCACGGAGTTGTGAAC-TT-AAAAGAAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAA
1 GTGCCACGAAGTTGTGAACTTTAAAAAGAAAAAAG-GTGCAACAGAGTTGTGGACTTTAAAA
3662825 AGAAGAAGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
60 12 0.23
61 19 0.36
62 22 0.42
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (63 bp):
GTGCCACGAAGTTGTGAACTTTAAAAAGAAAAAAGGTGCAACAGAGTTGTGGACTTTAAAAGG
Found at i:3663000 original size:32 final size:31
Alignment explanation
Indices: 3662868--3663206 Score: 296
Period size: 31 Copynumber: 10.7 Consensus size: 31
3662858 GGGTGCCATG
* * *
3662868 GAGTTGTGGACTTTG-AGAAGAGATTGTCACT
1 GAGTCGTGGACTTTGAAGAAAAGA-TGCCACT
* * *
3662899 AAGTTGTGGACTTTG-AGAAGAGATGCCACT
1 GAGTCGTGGACTTTGAAGAAAAGATGCCACT
*
3662929 GAGTCATGGACTTTGAAGAAAAACGATGCCACT
1 GAGTCGTGGACTTTGAAG-AAAA-GATGCCACT
* *
3662962 AAGTCGTGGACTTAGAAGCAAAAGATGCCACT
1 GAGTCGTGGACTTTGAAG-AAAAGATGCCACT
* * * *
3662994 GGGTCGTGGACTTAGAA-AAGAGATGCCATT
1 GAGTCGTGGACTTTGAAGAAAAGATGCCACT
* *
3663024 AAGTTGTGGACTTTGAAGAAAAGATGCCACT
1 GAGTCGTGGACTTTGAAGAAAAGATGCCACT
* * * *
3663055 GAGTTGTGGGCTTTG-GGAAGAGATGCCACT
1 GAGTCGTGGACTTTGAAGAAAAGATGCCACT
*
3663085 GAGTCGTGGACATTGAAAGAAAAAAAAAGATGCCACT
1 GAGTCGTGGACTTTG-AAG-----AAAAGATGCCACT
*
3663122 GAGTCGTGGACTTTG-GGACAAGAGATGCCACT
1 GAGTCGTGGACTTTGAAGA-AA-AGATGCCACT
* *
3663154 GAGTCATGGACTTTGAAGAGAAA-ATGCCACC
1 GAGTCGTGGACTTTGAAGA-AAAGATGCCACT
*
3663185 GAGTCATGGACTTTG-AGAAAAG
1 GAGTCGTGGACTTTGAAGAAAAG
3663207 GGATTTGAAG
Statistics
Matches: 258, Mismatches: 35, Indels: 31
0.80 0.11 0.10
Matches are distributed among these distances:
29 3 0.01
30 71 0.28
31 72 0.28
32 53 0.21
33 32 0.12
35 1 0.00
37 26 0.10
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (31 bp):
GAGTCGTGGACTTTGAAGAAAAGATGCCACT
Found at i:3663029 original size:156 final size:158
Alignment explanation
Indices: 3662869--3663166 Score: 406
Period size: 156 Copynumber: 1.9 Consensus size: 158
3662859 GGTGCCATGG
* *
3662869 AGTTGTGGACTTTG-AGAAGAGATTGTCACTAAGTTGTGGACTTTGAGAAGAGATGCCACTGAGT
1 AGTTGTGGACTTTGAAGAAAAGA-TGCCACTAAGTTGTGGACTTTGAGAAGAGATGCCACTGAGT
* *
3662933 CATGGACTTTG-AAG-AAAAACGATGCCACTAAGTCGTGGACTTAGA-AGCAAAAGATGCCACTG
65 CATGGACATTGAAAGAAAAAAAGATGCCACTAAGTCGTGGACTTAGAGA-CAAAAGATGCCACTG
* *
3662995 GGTCGTGGACTTAGAAAAGAGATGCCATTA
129 AGTCATGGACTTAGAAAAGAGATGCCATTA
* * *
3663025 AGTTGTGGACTTTGAAGAAAAGATGCCACTGAGTTGTGGGCTTTGGGAAGAGATGCCACTGAGTC
1 AGTTGTGGACTTTGAAGAAAAGATGCCACTAAGTTGTGGACTTTGAGAAGAGATGCCACTGAGTC
* * * * *
3663090 GTGGACATTGAAAGAAAAAAAAAGATGCCACTGAGTCGTGGACTTTGGGACAAGAGATGCCACTG
66 ATGGACATTGAAAG--AAAAAAAGATGCCACTAAGTCGTGGACTTAGAGACAAAAGATGCCACTG
3663155 AGTCATGGACTT
129 AGTCATGGACTT
3663167 TGAAGAGAAA
Statistics
Matches: 122, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
156 60 0.49
157 10 0.08
160 51 0.42
161 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.24
Consensus pattern (158 bp):
AGTTGTGGACTTTGAAGAAAAGATGCCACTAAGTTGTGGACTTTGAGAAGAGATGCCACTGAGTC
ATGGACATTGAAAGAAAAAAAGATGCCACTAAGTCGTGGACTTAGAGACAAAAGATGCCACTGAG
TCATGGACTTAGAAAAGAGATGCCATTA
Found at i:3671507 original size:20 final size:20
Alignment explanation
Indices: 3671482--3671558 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
3671472 GTAAAAAGAC
3671482 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
3671502 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
3671522 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
3671542 AAAATGTATTGATACAT
1 AGAATGTATCGATACAT
3671559 CTAGGTACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:3672508 original size:1 final size:1
Alignment explanation
Indices: 3672504--3672564 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
3672494 TCTTCTTTTT
* * * * * * * *
3672504 AAAAAAAAACAAAAAACACAAAAAAAATAAAAAAAAATAAAAAAAAAGAAAGAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3672565 GAACATGTTT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.05, G:0.05, T:0.03
Consensus pattern (1 bp):
A
Found at i:3672528 original size:11 final size:10
Alignment explanation
Indices: 3672504--3672550 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
3672494 TCTTCTTTTT
3672504 AAAAAAA-AA
1 AAAAAAATAA
* *
3672513 CAAAAAACACA
1 AAAAAAATA-A
3672524 AAAAAAATAA
1 AAAAAAATAA
3672534 AAAAAAATAA
1 AAAAAAATAA
3672544 AAAAAAA
1 AAAAAAA
3672551 GAAAGAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 6 0.18
10 19 0.58
11 8 0.24
ACGTcount: A:0.89, C:0.06, G:0.00, T:0.04
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:3673680 original size:94 final size:97
Alignment explanation
Indices: 3673492--3673680 Score: 260
Period size: 100 Copynumber: 1.9 Consensus size: 97
3673482 GGTATCTAAA
**
3673492 CTTTCTCCTTTCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAG
1 CTTTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTCTCC---TAAAGCCCACACAAG
*
3673557 TTGGTGGCACTTCTCAATCCTCAAAGAGCAGGACG
63 TTAGTGGCACTTCTCAATCCTCAAAGAGCAGGACG
*
3673592 CTTTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGATGCCTT-T-C-AAAGCCCACACAAGTTA
1 CTTTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTAAAGCCCACACAAGTTA
* *
3673654 GTGGCA-TTTTCCAGTCCTCAAAGAGCA
66 GTGGCACTTCT-CAATCCTCAAAGAGCA
3673681 AGACACCTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
93 3 0.04
94 37 0.45
98 1 0.01
99 1 0.01
100 40 0.49
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (97 bp):
CTTTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTAAAGCCCACACAAGTTA
GTGGCACTTCTCAATCCTCAAAGAGCAGGACG
Found at i:3673817 original size:62 final size:62
Alignment explanation
Indices: 3673631--3674427 Score: 846
Period size: 61 Copynumber: 13.1 Consensus size: 62
3673621 GAGCAGGATG
* * * * * *
3673631 CCTTTCAAAGCCCACACAAGTTAGTGGCA-TTTTCCAGTCCTCAAAGAGCA--A-GAC---A
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
3673686 CCTTTTAAAGCCCACACAAGCTGGTGGCACC-TTC-AGTCCTCAAAGAGTAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* *
3673746 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
3673808 CCTTTTAAAGCCCATACAAATTGGTGGCACC-TTCTAGTCCTTAAAGAGC-GAGATGTCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAG-GACGCCTTTT
* * * *
3673869 CTTTTTAAAGCCCACACAAGTTGGTGGCA-CTTT-TTGATCCTTAAGGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAG-TCCTCAAAGAGCAGGACGCCTTTT
* * *
3673930 CCTTTTAAAGACCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAAGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
3673991 CCTTTTAAAGCCAACACAAGTTGGTGGCACC-TTCTACTCCTCAAAGAGCAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTT-T
** * * * * *
3674052 CCTTGCAAAACCCATACAAGTTGGTGGCACCCTT-GAGTCCTCAAAGAGCAAGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * ** * *
3674113 TCTTTTCAAGCCCACATGAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAAGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
3674175 TCTTTCCAAAGCCCACACAAGTTGGTGGCACCTCT-TAGTCTTCAAAGAGTAGGACGCCTTTT
1 CCTTT-TAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
3674237 TCTTTTCAAAGCCCACACGAGTTGGCGGCACCTCT-TAGTCCTCAAAGAGCAGGACACCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
3674299 TCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT-TAGTCTTCAAAGAGCAGGATGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * * *
3674361 -TTTTTCAAAGCCTACACAAGTTGGTGGC-CCTTTTTAGTCTTCAAAGAGCATGATGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
3674422 CCTTTT
1 CCTTTT
3674428 CTCTTTTGCC
Statistics
Matches: 634, Mismatches: 84, Indels: 41
0.84 0.11 0.05
Matches are distributed among these distances:
54 14 0.02
55 29 0.05
56 1 0.00
57 2 0.00
60 45 0.07
61 288 0.45
62 231 0.36
63 24 0.04
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (62 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:3674546 original size:42 final size:42
Alignment explanation
Indices: 3674418--3674749 Score: 273
Period size: 42 Copynumber: 7.8 Consensus size: 42
3674408 GCATGATGCC
* * * *
3674418 TTTTCCTTTTCTCTTTTGCCCTCAAAGAGCAAGA--CACATTTCA
1 TTTT-CTTTTTTCCTTTGTCCTCAAAGAGCAGGATGCAC-TTT-A
* * *
3674461 TTTCCTTTTTTTCCCTTTTGTCCTCATAGAGCAGGATG--CTTTT
1 TTTTC-TTTTTT-CC-TTTGTCCTCAAAGAGCAGGATGCACTTTA
* *
3674504 TTTTCTTTTTTCCTCTTGTCCTCAAAGAGCAGGATGC-TTTTT
1 TTTTCTTTTTTCCT-TTGTCCTCAAAGAGCAGGATGCACTTTA
* *
3674546 TTTTCCTTTTTCCTTTGTCCTCAAAGAGCAAGATGCACTTTA
1 TTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGATGCACTTTA
* * *
3674588 TTTTCTTCTTTTCCCTTCTAGTTCTTAAAGAGCAGGACGCACTTTA
1 TTTTCTT-TTTT-CCTT-T-GTCCTCAAAGAGCAGGATGCACTTTA
* * *
3674634 TTCTCCTTTTTCCTTTGTCCTCAAAAAGCAGGA--CACATTTA
1 TTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGATGCAC-TTTA
* * * * * * *
3674675 ATTTCCTTTTCCCTTTGTCTTCAAAGGGTAGGATGCATTTTA
1 TTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGATGCACTTTA
* *
3674717 TTTCCTTTTTTCCTTTGTCCTCAAGGAGCAGGA
1 TTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGA
3674750 CCCATTTCAT
Statistics
Matches: 234, Mismatches: 40, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
40 4 0.02
41 73 0.31
42 76 0.32
43 19 0.08
44 12 0.05
45 23 0.10
46 27 0.12
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (42 bp):
TTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGATGCACTTTA
Found at i:3674680 original size:129 final size:126
Alignment explanation
Indices: 3674419--3674773 Score: 355
Period size: 129 Copynumber: 2.8 Consensus size: 126
3674409 CATGATGCCT
* *
3674419 TTTCCTTTTCTCTTTTGCCCTCAAAGAGCAAGA--CACATTTCATTTCCTTTTTTTCCCTTTTGT
1 TTTCCTTTT-TCCTTTGTCCTCAAAGAGCAAGATGCAC-TTT-ATTTCC-TTTTTTCCC-TTTGT
* * * * * * ** *
3674482 CCTCATAGAGCAGGATG--CTTTTTTTTCTTTTTTCCTCTTGTCCTCAAAGAGCAGGATGCTTTT
61 CCTCAAAGAGCAGGACGCACTTTATTCTCCTTTTTCCT-TTGTCCTCAAAAAGCAGGACACATTT
**
3674545 TT
125 AA
* *
3674547 TTTCCTTTTTCCTTTGTCCTCAAAGAGCAAGATGCACTTTATTTTCTTCTTTTCCCTTCTAGTTC
1 TTTCCTTTTTCCTTTGTCCTCAAAGAGCAAGATGCACTTTATTTCCTT-TTTTCCCTT-T-GTCC
*
3674612 TTAAAGAGCAGGACGCACTTTATTCTCCTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTAA
63 TCAAAGAGCAGGACGCACTTTATTCTCCTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTAA
* * * * * *
3674676 TTTCCTTTTCCCTTTGTCTTCAAAGGGTAGGATGCATTTTATTTCCTTTTTT-CCTTTGTCCTCA
1 TTTCCTTTTTCCTTTGTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTTTCCCTTTGTCCTCA
* *
3674740 AGGAGCAGGACCCA-TTTCATTCTCC-TTTTCCTTT
66 AAGAGCAGGACGCACTTT-ATTCTCCTTTTTCCTTT
3674774 ATCTTTAAAG
Statistics
Matches: 192, Mismatches: 27, Indels: 20
0.80 0.11 0.08
Matches are distributed among these distances:
124 12 0.06
125 24 0.12
126 5 0.03
127 38 0.20
128 31 0.16
129 66 0.34
130 16 0.08
ACGTcount: A:0.18, C:0.25, G:0.12, T:0.45
Consensus pattern (126 bp):
TTTCCTTTTTCCTTTGTCCTCAAAGAGCAAGATGCACTTTATTTCCTTTTTTCCCTTTGTCCTCA
AAGAGCAGGACGCACTTTATTCTCCTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTAA
Found at i:3674738 original size:83 final size:81
Alignment explanation
Indices: 3674419--3674793 Score: 304
Period size: 83 Copynumber: 4.4 Consensus size: 81
3674409 CATGATGCCT
* * * * ** *
3674419 TTTCCTTTTCTCTTTTGCCCTCAAAGAGCAAGACACATTTCATTTCCTTTTTTTCCCTTTTGTCC
1 TTTCCTTTTC-CCTTTGTCTTCAAAGAGCAGGATGCATTTTATTTCC--TTTTT-CC-TTTGTCC
* ** **
3674484 TCATAGAGCAGGATGCTTTTT
61 TCAAAGAGCAGGACACTTTAA
* * * * *
3674505 TTTCTTTTTTCCTCTTGTCCTCAAAGAGCAGGATGCTTTTTTTTTCCTTTTTCCTTTGTCCTCAA
1 TTTCCTTTTCCCT-TTGTCTTCAAAGAGCAGGATGCATTTTATTTCCTTTTTCCTTTGTCCTCAA
* *
3674570 AGAGCAAGATGCACTTTAT
65 AGAGCAGGA--CACTTTAA
* *
3674589 TTTCTTCTTTTCCCTTCTAGTTCTT-AAAGAGCAGGACGCACTTTATTCTCCTTTTTCCTTTGTC
1 TTTC--CTTTTCCCTT-T-G-TCTTCAAAGAGCAGGATGCATTTTATT-TCCTTTTTCCTTTGTC
*
3674653 CTCAAAAAGCAGGACACATTTAA
60 CTCAAAGAGCAGGACAC-TTTAA
* *
3674676 TTTCCTTTTCCCTTTGTCTTCAAAGGGTAGGATGCATTTTATTTCCTTTTTTCCTTTGTCCTCAA
1 TTTCCTTTTCCCTTTGTCTTCAAAGAGCAGGATGCATTTTATTTCC-TTTTTCCTTTGTCCTCAA
* * *
3674741 GGAGCAGGACCCATTTCA
65 AGAGCAGGACAC-TTTAA
* * *
3674759 TTCTCCTTTT-CCTTTATCTTTAAAGAGTAGGATGC
1 TT-TCCTTTTCCCTTTGTCTTCAAAGAGCAGGATGC
3674794 CCCCTCCTTT
Statistics
Matches: 240, Mismatches: 36, Indels: 29
0.79 0.12 0.10
Matches are distributed among these distances:
82 25 0.10
83 77 0.32
84 22 0.09
85 13 0.05
86 45 0.19
87 27 0.11
88 31 0.13
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (81 bp):
TTTCCTTTTCCCTTTGTCTTCAAAGAGCAGGATGCATTTTATTTCCTTTTTCCTTTGTCCTCAAA
GAGCAGGACACTTTAA
Found at i:3674756 original size:42 final size:42
Alignment explanation
Indices: 3674419--3674768 Score: 305
Period size: 41 Copynumber: 8.2 Consensus size: 42
3674409 CATGATGCCT
* * * * * *
3674419 TTTCCTTTTCTCTTTTGCCCTCAAAGAGCAAGACACATTTCA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTA
* *
3674461 TTTCCTTTTTTTCCCTTTTGTCCTCATAGAGCAGGATGC-TTTT-
1 TTTCC-TTTTTT-CC-TTTGTCCTCAAAGAGCAGGACGCATTTTA
* * * *
3674504 TTTTCTTTTTTCCTCTTGTCCTCAAAGAGCAGGATGCTTTTTT
1 TTTCCTTTTTTCCT-TTGTCCTCAAAGAGCAGGACGCATTTTA
* * *
3674547 TTTCC-TTTTTCCTTTGTCCTCAAAGAGCAAGATGCACTTTA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTA
* * * *
3674588 TTTTCTTCTTTTCCCTTCTAGTTCTTAAAGAGCAGGACGCACTTTA
1 TTTCCTT-TTTT-CCTT-T-GTCCTCAAAGAGCAGGACGCATTTTA
* * *
3674634 TTCTCC-TTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTAA
1 TT-TCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTA
* * * * *
3674676 TTTCC-TTTTCCCTTTGTCTTCAAAGGGTAGGATGCATTTTA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTA
* * *
3674717 TTTCCTTTTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTA
3674759 TTCTCCTTTT
1 TT-TCCTTTT
3674769 CCTTTATCTT
Statistics
Matches: 251, Mismatches: 43, Indels: 27
0.78 0.13 0.08
Matches are distributed among these distances:
40 1 0.00
41 87 0.35
42 76 0.30
43 25 0.10
44 12 0.05
45 23 0.09
46 25 0.10
47 2 0.01
ACGTcount: A:0.18, C:0.25, G:0.13, T:0.45
Consensus pattern (42 bp):
TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTTA
Found at i:3675974 original size:13 final size:13
Alignment explanation
Indices: 3675956--3675981 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3675946 TACAGCAAGT
3675956 ATGTATCGATACA
1 ATGTATCGATACA
3675969 ATGTATCGATACA
1 ATGTATCGATACA
3675982 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3679698 original size:13 final size:13
Alignment explanation
Indices: 3679680--3679704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3679670 TTTTCCAGAT
3679680 TGTATCGATACAA
1 TGTATCGATACAA
3679693 TGTATCGATACA
1 TGTATCGATACA
3679705 TTACTTCAGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3681541 original size:13 final size:13
Alignment explanation
Indices: 3681523--3681548 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3681513 TACAGCAAGT
3681523 ATGTATCGATACA
1 ATGTATCGATACA
3681536 ATGTATCGATACA
1 ATGTATCGATACA
3681549 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3684624 original size:52 final size:52
Alignment explanation
Indices: 3684553--3684731 Score: 238
Period size: 52 Copynumber: 3.5 Consensus size: 52
3684543 TATTGATTTC
*
3684553 TCACAATCGGGGATACTCCAACCCTAATTTTATTTCTAAAACACCAATTTTT
1 TCACAATCGGGGATACTCCAACCCTAATTTTATTTCTAGAACACCAATTTTT
* * *
3684605 TCACAATCGAGGATACTCCAACCCCAGTTTTATTT-TCAGAACACCAA-TTTT
1 TCACAATCGGGGATACTCCAACCCTAATTTTATTTCT-AGAACACCAATTTTT
* *
3684656 TCACAATCGGGGATACTCCAACCCTGATTTTATTTCTAGAACACCCA-TTTT
1 TCACAATCGGGGATACTCCAACCCTAATTTTATTTCTAGAACACCAATTTTT
* * *
3684707 TCATAGTCAGGGGATACTTCAACCC
1 TCACAATC-GGGGATACTCCAACCC
3684732 CGTTGTCATC
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
51 55 0.49
52 57 0.51
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (52 bp):
TCACAATCGGGGATACTCCAACCCTAATTTTATTTCTAGAACACCAATTTTT
Found at i:3687303 original size:20 final size:19
Alignment explanation
Indices: 3687280--3687334 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
3687270 ACATAAGTAA
3687280 ATGTATCGATACATTCCCT
1 ATGTATCGATACATTCCCT
* **
3687299 GATGTATCAATACCATTTGCT
1 -ATGTATCGATA-CATTCCCT
*
3687320 TTGTATCGATACATT
1 ATGTATCGATACATT
3687335 TTGAGTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.14
20 19 0.66
21 6 0.21
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTCCCT
Found at i:3689609 original size:20 final size:21
Alignment explanation
Indices: 3689576--3689617 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
3689566 TTGGGAAATT
3689576 TTACCCAGATGTATCGATACA
1 TTACCCAGATGTATCGATACA
3689597 TTACCCA-ATGTATCGATACA
1 TTACCCAGATGTATCGATACA
3689617 T
1 T
3689618 GCAGGCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (21 bp):
TTACCCAGATGTATCGATACA
Found at i:3690283 original size:20 final size:20
Alignment explanation
Indices: 3690260--3690332 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3690250 ACAATTCAAA
3690260 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3690280 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3690301 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3690321 GTATCGATACAT
1 GTATCGATACAT
3690333 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3690304 original size:21 final size:21
Alignment explanation
Indices: 3690278--3690353 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3690268 ACATGTTGCA
3690278 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3690299 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3690319 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
3690340 TTGTATCGATACAT
1 ATGTATCGATACAT
3690354 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3690311 original size:41 final size:41
Alignment explanation
Indices: 3690260--3690353 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3690250 ACAATTCAAA
*
3690260 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
3690301 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3690342 GTATCGATACAT
1 GTATCGATACAT
3690354 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3690410 original size:13 final size:13
Alignment explanation
Indices: 3690392--3690417 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3690382 TACAGCAAGT
3690392 ATGTATCGATACA
1 ATGTATCGATACA
3690405 ATGTATCGATACA
1 ATGTATCGATACA
3690418 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3692479 original size:15 final size:16
Alignment explanation
Indices: 3692459--3692492 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3692449 AAACTAAAAG
3692459 AAAATAAT-AAATTGA
1 AAAATAATGAAATTGA
*
3692474 AAAATATTGAAATTGA
1 AAAATAATGAAATTGA
3692490 AAA
1 AAA
3692493 TCTAGAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
AAAATAATGAAATTGA
Found at i:3692666 original size:21 final size:21
Alignment explanation
Indices: 3692633--3692677 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3692623 TTGCAAGTTG
*
3692633 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3692655 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3692675 AAA
1 AAA
3692678 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3694501 original size:15 final size:15
Alignment explanation
Indices: 3694481--3694511 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3694471 TAAAAATGTC
*
3694481 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3694496 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3694511 C
1 C
3694512 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3696609 original size:13 final size:13
Alignment explanation
Indices: 3696591--3696628 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3696581 CATTTTTATT
3696591 TGTATCGATACAA
1 TGTATCGATACAA
*
3696604 TGTATCGATACAC
1 TGTATCGATACAA
3696617 TGTATCGATACA
1 TGTATCGATACA
3696629 GGGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3699080 original size:20 final size:20
Alignment explanation
Indices: 3699057--3699129 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3699047 ACAATTCAAA
3699057 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3699077 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3699098 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3699118 GTATCGATACAT
1 GTATCGATACAT
3699130 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3699101 original size:21 final size:21
Alignment explanation
Indices: 3699075--3699150 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3699065 ACATGTTGCA
3699075 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3699096 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3699116 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
3699137 TTGTATCGATACAT
1 ATGTATCGATACAT
3699151 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3699108 original size:41 final size:41
Alignment explanation
Indices: 3699057--3699150 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3699047 ACAATTCAAA
*
3699057 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
3699098 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3699139 GTATCGATACAT
1 GTATCGATACAT
3699151 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3699207 original size:13 final size:13
Alignment explanation
Indices: 3699189--3699214 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3699179 TACAGCAAGT
3699189 ATGTATCGATACA
1 ATGTATCGATACA
3699202 ATGTATCGATACA
1 ATGTATCGATACA
3699215 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.