Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold7
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: 6555642
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 349864 characters in sequence are not A, C, G, or T
File 26 of 37
Found at i:4493893 original size:21 final size:21
Alignment explanation
Indices: 4493869--4493915 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4493859 TTTGATGCTG
4493869 ATTTTG-A-TGAAAAACAAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
4493889 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
4493910 ATTTTG
1 ATTTTG
4493916 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:4494054 original size:13 final size:13
Alignment explanation
Indices: 4494036--4494074 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4494026 ATAATCACCC
*
4494036 TGTATCGATACAG
1 TGTATCGATACAA
4494049 TGTATCGATACAA
1 TGTATCGATACAA
4494062 TGTATCGATACAA
1 TGTATCGATACAA
4494075 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4494085 original size:20 final size:20
Alignment explanation
Indices: 4494060--4494098 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4494050 GTATCGATAC
4494060 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
4494080 AATGTATCGATACATAGAA
1 AATGTATCGATACAAAGAA
4494099 TTTCCAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:4496162 original size:15 final size:15
Alignment explanation
Indices: 4496142--4496172 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4496132 ATTTCGTTTG
*
4496142 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
4496157 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
4496172 G
1 G
4496173 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4498005 original size:21 final size:21
Alignment explanation
Indices: 4497976--4498020 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4497966 AAGTTTTCAT
*
4497976 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
4497996 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
4498018 TTT
1 TTT
4498021 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 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:4500256 original size:13 final size:13
Alignment explanation
Indices: 4500238--4500262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4500228 CAATTTTTTG
4500238 TGTATCGATACAT
1 TGTATCGATACAT
4500251 TGTATCGATACA
1 TGTATCGATACA
4500263 AACTTGTTGT
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:4500260 original size:33 final size:32
Alignment explanation
Indices: 4500218--4500281 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
4500208 TACAAGCCAA
** *
4500218 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAAACTTGT-TGTATCGATACAT
4500251 TGTATCGATACAAACTTGTTGTATCGATACA
1 TGTATCGATACAAACTTGTTGTATCGATACA
4500282 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACAAACTTGTTGTATCGATACAT
Found at i:4503086 original size:17 final size:17
Alignment explanation
Indices: 4503063--4503101 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4503053 ATTTATCTTT
4503063 AAAATAAA-AATATAAA
1 AAAATAAAGAATATAAA
*
4503079 ATAAATAAAGAATTTAAA
1 A-AAATAAAGAATATAAA
4503097 AAAAT
1 AAAAT
4503102 CATGCACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 11 0.55
18 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAATAAAGAATATAAA
Found at i:4503302 original size:22 final size:22
Alignment explanation
Indices: 4503272--4503321 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
4503262 ATGTCATTTG
*
4503272 ACTCATAACACTAAACTTAGTT
1 ACTCATAACACTAAACTTAGTC
*
4503294 ACTCGTAACACTAAACTTAGTC
1 ACTCATAACACTAAACTTAGTC
4503316 ACTCAT
1 ACTCAT
4503322 TTTATAATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (22 bp):
ACTCATAACACTAAACTTAGTC
Found at i:4506835 original size:21 final size:20
Alignment explanation
Indices: 4506805--4506855 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
4506795 TTCTACAATT
*
4506805 TGTATTGATACAAATAGT-AA
1 TGTATCGATACAAA-AGTGAA
*
4506825 CTGTATCGATACATAAGTGAA
1 -TGTATCGATACAAAAGTGAA
4506846 TGTATCGATA
1 TGTATCGATA
4506856 AATGCCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAAAAGTGAA
Found at i:4509450 original size:80 final size:80
Alignment explanation
Indices: 4509354--4509698 Score: 257
Period size: 80 Copynumber: 4.4 Consensus size: 80
4509344 ACATCAAAAA
* *
4509354 GGGATACTCAAACCCCATTTTTATTTCAAAAATATCGATTTTTTTACCATTAGGGATACTCCAAC
1 GGGATACTCAAACCCCATTTTTATTTCAAAAATATCGAATTTTTCACCATTAGGGATACTCCAAC
*
4509419 CTCGTTATTTCCGAA
66 CTCGTTATTTCCGAG
* ** * * * *
4509434 GGGATACTCAAACCCCAGTTTTGCTTCCAAAATATCG-ATTTTTCATCA-TCGGG-GA-T---AC
1 GGGATACTCAAACCCCATTTTTATTTCAAAAATATCGAATTTTTCACCATTAGGGATACTCCAAC
* *
4509492 CTTGTTATTTTCGAG
66 CTCGTTATTTCCGAG
* * * * * *** *
4509507 GGGATACTCCAACCCTATTTCTATTTTC-AAAATGTCAAATTTTTCATTGTTAGGAATACTCCAA
1 GGGATACTCAAACCCCATTTTTA-TTTCAAAAATATCGAATTTTTCACCATTAGGGATACTCCAA
* * *
4509571 CCTTGTTATCTCTGAG
65 CCTCGTTATTTCCGAG
** * * *
4509587 GGGATACTCCGACCCCGA-TTTTATTTCCAAAATATC-AATTTTTTACTC-TTAGGGATTCTCCA
1 GGGATACTCAAACCCC-ATTTTTATTTCAAAAATATCGAATTTTTCAC-CATTAGGGATACTCCA
*
4509649 ACC-CTGTTATTTTCTGAG
64 ACCTC-GTTA-TTTCCGAG
*
4509667 GGGATACTGC-AACCCCTTTTTTATTTTCAAAA
1 GGGATACT-CAAACCCCATTTTTA-TTTCAAAA
4509699 TATTAAAATT
Statistics
Matches: 207, Mismatches: 42, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
73 39 0.19
74 12 0.06
75 3 0.01
76 2 0.01
77 2 0.01
78 4 0.02
79 39 0.19
80 97 0.47
81 9 0.04
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (80 bp):
GGGATACTCAAACCCCATTTTTATTTCAAAAATATCGAATTTTTCACCATTAGGGATACTCCAAC
CTCGTTATTTCCGAG
Found at i:4509538 original size:73 final size:74
Alignment explanation
Indices: 4509417--4509553 Score: 161
Period size: 73 Copynumber: 1.9 Consensus size: 74
4509407 GGATACTCCA
* *
4509417 ACCTCGTTATTTCCGAAGGGATACTCAAACCCCAGTTTTGCTTCCAAAATATC-GATTTTTCATC
1 ACCTCGTTATTTCCGAAGGGATACTCAAACCCCAGTTTTACTTCCAAAATATCAAATTTTTCATC
4509481 ATCGGGGAT
66 ATCGGGGAT
* * * * * * * *
4509490 ACCTTGTTATTTTCGAGGGGATACTCCAACCCTA-TTTCTATTTTCAAAATGTCAAATTTTTCAT
1 ACCTCGTTATTTCCGAAGGGATACTCAAACCCCAGTTT-TACTTCCAAAATATCAAATTTTTCAT
4509554 TGTTAGGAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
72 3 0.06
73 40 0.77
74 9 0.17
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (74 bp):
ACCTCGTTATTTCCGAAGGGATACTCAAACCCCAGTTTTACTTCCAAAATATCAAATTTTTCATC
ATCGGGGAT
Found at i:4509642 original size:153 final size:156
Alignment explanation
Indices: 4509403--4509699 Score: 345
Period size: 153 Copynumber: 1.9 Consensus size: 156
4509393 TTTTTTACCA
* * *
4509403 TTAGGGATACTCCAACCTCGTTATTTCCGAAGGGATACTCAAACCCCAGTTTTGCTTCCAAAATA
1 TTAGGAATACTCCAACCTCGTTATCTCCGAAGGGATACTCAAACCCCAGTTTTACTTCCAAAATA
* * *
4509468 TCGATTTTTCATCATCGGGGA-T-ACCTTGTTATTTTC-GAGGGGATACTCCAA-CCCTATTTCT
66 TCAATTTTTCATCATCAGGGATTCACCCTGTTATTTTCTGAGGGGATACTCCAACCCCT-TTTCT
4509529 ATTTTCAAAATGTCAAATTTTTCATTG
130 ATTTTCAAAATGTCAAATTTTTCATTG
* * * ** *
4509556 TTAGGAATACTCCAACCTTGTTATCTCTGAGGGGATACTCCGACCCC-GATTTTATTTCCAAAAT
1 TTAGGAATACTCCAACCTCGTTATCTCCGAAGGGATACTCAAACCCCAG-TTTTACTTCCAAAAT
* * *
4509620 ATCAATTTTTTACTC-TTAGGGATTCTCCAACCCTGTTATTTTCTGAGGGGATACTGCAACCCCT
65 ATCAATTTTTCA-TCATCAGGGA-T-T-C-ACCCTGTTATTTTCTGAGGGGATACTCCAACCCCT
*
4509684 TTTTTATTTTCAAAAT
125 TTTCTATTTTCAAAAT
4509700 ATTAAAATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
152 1 0.01
153 68 0.58
154 2 0.02
156 1 0.01
159 13 0.11
160 29 0.25
161 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (156 bp):
TTAGGAATACTCCAACCTCGTTATCTCCGAAGGGATACTCAAACCCCAGTTTTACTTCCAAAATA
TCAATTTTTCATCATCAGGGATTCACCCTGTTATTTTCTGAGGGGATACTCCAACCCCTTTTCTA
TTTTCAAAATGTCAAATTTTTCATTG
Found at i:4509699 original size:80 final size:81
Alignment explanation
Indices: 4509494--4509731 Score: 254
Period size: 80 Copynumber: 3.0 Consensus size: 81
4509484 GGGGATACCT
* * * *
4509494 TGTTATTTTC-GAGGGGATACTCCAA-CCCTATTTCTATTTTCAAAATGTCAAATTTTTCATTGT
1 TGTTATTTTCTGAGGGGATACTCCAACCCCT-TTTTTATTTTCAAAATATCAAATTTTTCACTCT
*
4509557 TAGGAATACTCCAACCT
65 TAGGAATACTCCAACCC
* * ** * *
4509574 TGTTA-TCTCTGAGGGGATACTCCGACCCCGATTTTATTTCCAAAATATC-AATTTTTTACTCTT
1 TGTTATTTTCTGAGGGGATACTCCAACCCCTTTTTTATTTTCAAAATATCAAATTTTTCACTCTT
* *
4509637 AGGGATTCTCCAACCC
66 AGGAATACTCCAACCC
* * * *
4509653 TGTTATTTTCTGAGGGGATACTGCAACCCCTTTTTTATTTTCAAAATATTAAAATTTT--GTCTT
1 TGTTATTTTCTGAGGGGATACTCCAACCCCTTTTTTATTTTCAAAATATCAAATTTTTCACTCTT
* *
4509716 GGGGATACTCCAACCC
66 AGGAATACTCCAACCC
4509732 CGATTTTATT
Statistics
Matches: 130, Mismatches: 24, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
79 50 0.38
80 71 0.55
81 9 0.07
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (81 bp):
TGTTATTTTCTGAGGGGATACTCCAACCCCTTTTTTATTTTCAAAATATCAAATTTTTCACTCTT
AGGAATACTCCAACCC
Found at i:4510963 original size:58 final size:57
Alignment explanation
Indices: 4510773--4510951 Score: 202
Period size: 58 Copynumber: 3.1 Consensus size: 57
4510763 AAATGAGCCC
* ** * *
4510773 AAAATTCAT-AAATTTACATAATGGTCCCTGAATCATGGGAAATGACTAAAATGGTCTT
1 AAAATGCATGAAA-TTACATAATAATCCCTAAATCAT-GAAAATGACTAAAATGGTCTT
* * * *
4510831 AAAATGCATGAAA-TAGCATAATAAGCCTTAAATGATGAAAAATGACTGAAAT-GTCTCT
1 AAAATGCATGAAATTA-CATAATAATCCCTAAATCATG-AAAATGACTAAAATGGTCT-T
4510889 AAAATGCATGAAATTACATAATAATCCCTAAATCATGAAAACTGACTAAAATGGTCTT
1 AAAATGCATGAAATTACATAATAATCCCTAAATCATGAAAA-TGACTAAAATGGTCTT
4510947 AAAAT
1 AAAAT
4510952 TTGAAAAATT
Statistics
Matches: 101, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
57 11 0.11
58 81 0.80
59 9 0.09
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.28
Consensus pattern (57 bp):
AAAATGCATGAAATTACATAATAATCCCTAAATCATGAAAATGACTAAAATGGTCTT
Found at i:4511695 original size:13 final size:13
Alignment explanation
Indices: 4511677--4511735 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
4511667 ACATTATGCT
4511677 TTGTATCGATACA
1 TTGTATCGATACA
4511690 TTGTATCGATACA
1 TTGTATCGATACA
4511703 -TGT-T---T--A
1 TTGTATCGATACA
4511709 TTGTATCGATACA
1 TTGTATCGATACA
4511722 TTGTATCGATACA
1 TTGTATCGATACA
4511735 T
1 T
4511736 GGACAATTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
6 1 0.03
7 3 0.08
8 2 0.05
11 2 0.05
12 3 0.08
13 28 0.72
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4511718 original size:32 final size:33
Alignment explanation
Indices: 4511677--4511755 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
4511667 ACATTATGCT
***
4511677 TTGTATCGATACATTGTATCGATACAT-GTTTA
1 TTGTATCGATACATTGTATCGATACATGGACAA
4511709 TTGTATCGATACATTGTATCGATACATGGACAA
1 TTGTATCGATACATTGTATCGATACATGGACAA
4511742 TTGTATCGATACAT
1 TTGTATCGATACAT
4511756 GAAACTGGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 27 0.63
33 16 0.37
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATTGTATCGATACATGGACAA
Found at i:4511820 original size:13 final size:13
Alignment explanation
Indices: 4511802--4511826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4511792 TACATGGTAC
4511802 ATTGTATCGATAT
1 ATTGTATCGATAT
4511815 ATTGTATCGATA
1 ATTGTATCGATA
4511827 CATGATGAAT
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:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:4511839 original size:33 final size:32
Alignment explanation
Indices: 4511658--4511850 Score: 141
Period size: 33 Copynumber: 6.0 Consensus size: 32
4511648 CACACCTAGA
* **
4511658 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGAT-AATTGTATCGATACAT
* *
4511691 TGTATCGATACATGTTTATTGTATCGATACAT
1 TGTATCGATACATGATAATTGTATCGATACAT
*
4511723 TGTATCGATACATGGACAATTGTATCGATACA-
1 TGTATCGATACAT-GATAATTGTATCGATACAT
* * **
4511755 TG-A---A-AC-TGGTAATAGCTA-CCCTACCTATT
1 TGTATCGATACATGATAATTG-TATCGATA-C-A-T
* *
4511784 TGTATCGATACATGGTACATTGTATCGATATAT
1 TGTATCGATACATGATA-ATTGTATCGATACAT
*
4511817 TGTATCGATACATGATGAATTGTATCTATACAT
1 TGTATCGATACATGAT-AATTGTATCGATACAT
4511850 T
1 T
4511851 CCTTGTAACA
Statistics
Matches: 126, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
25 8 0.06
26 4 0.03
27 3 0.02
28 1 0.01
29 2 0.02
30 1 0.01
31 1 0.01
32 29 0.23
33 60 0.48
34 4 0.03
35 7 0.06
36 6 0.05
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATGATAATTGTATCGATACAT
Found at i:4518346 original size:13 final size:13
Alignment explanation
Indices: 4518328--4518352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4518318 CATAAAGTGT
4518328 TGTATCGATACAA
1 TGTATCGATACAA
4518341 TGTATCGATACA
1 TGTATCGATACA
4518353 TTTTTTTTTG
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:4518456 original size:52 final size:52
Alignment explanation
Indices: 4518390--4518514 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
4518380 CTACTGCTAA
*
4518390 AAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTAT
1 AAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTAT
*
4518442 AAAATGTATCGATACATGCAGGCAAATTTGCTCAGATGTATCGATACACTAT
1 AAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTAT
*
4518494 TAAATGTATCGATACATGCAG
1 AAAATGTATCGATACATGCAG
4518515 ATTTCGGGAC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
AAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTAT
Found at i:4525411 original size:12 final size:12
Alignment explanation
Indices: 4525394--4525462 Score: 84
Period size: 12 Copynumber: 5.6 Consensus size: 12
4525384 CAAAGTGATG
4525394 AAAAAAAAACAA
1 AAAAAAAAACAA
4525406 AAAAAAAAACAAA
1 AAAAAAAAAC-AA
4525419 AAAAACAAAACAA
1 AAAAA-AAAACAA
**
4525432 AACCAAAAACAA
1 AAAAAAAAACAA
* *
4525444 AAAAAAACACAG
1 AAAAAAAAACAA
4525456 AAAAAAA
1 AAAAAAA
4525463 GTGCAAAGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
12 32 0.65
13 12 0.24
14 5 0.10
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:4525428 original size:26 final size:25
Alignment explanation
Indices: 4525394--4525450 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
4525384 CAAAGTGATG
4525394 AAAAAAAAACAAAAAAAAAAACAAA
1 AAAAAAAAACAAAAAAAAAAACAAA
**
4525419 AAAAACAAAACAAAACCAAAAACAAA
1 AAAAA-AAAACAAAAAAAAAAACAAA
4525445 AAAAAA
1 AAAAAA
4525451 CACAGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (25 bp):
AAAAAAAAACAAAAAAAAAAACAAA
Found at i:4525459 original size:26 final size:22
Alignment explanation
Indices: 4525394--4525462 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 22
4525384 CAAAGTGATG
4525394 AAAAAAAAACAAAAAAAAAAAC
1 AAAAAAAAACAAAAAAAAAAAC
*
4525416 AAAAAAAACAAAACAAAACCAAAAAC
1 AAAAAAAA-ACAA-AAAA--AAAAAC
* *
4525442 AAAAAAAAACACAGAAAAAAA
1 AAAAAAAAACAAAAAAAAAAA
4525463 GTGCAAAGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 13 0.33
23 3 0.08
24 7 0.18
25 2 0.05
26 14 0.36
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (22 bp):
AAAAAAAAACAAAAAAAAAAAC
Found at i:4525462 original size:1 final size:1
Alignment explanation
Indices: 4525394--4525450 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
4525384 CAAAGTGATG
* * * * ** *
4525394 AAAAAAAAACAAAAAAAAAAACAAAAAAAACAAAACAAAACCAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4525451 CACAGAAAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4526718 original size:32 final size:32
Alignment explanation
Indices: 4526677--4526924 Score: 233
Period size: 32 Copynumber: 7.8 Consensus size: 32
4526667 GTCAAATACC
4526677 TTCTT-AAAGTCCACGACTCAGTGGCATCCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCCTT
* *
4526708 TTCTTCAAAGTCCATGACTTAGTGGCATCCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCCTT
4526740 TTCTTCAAAGTCCACGACTCAGTGGCAT--TT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCCTT
* *
4526770 TGTC-TCAAAGTCCACGGCTCAGTGGCAT-TTT
1 T-TCTTCAAAGTCCACGACTCAGTGGCATCCTT
* * *
4526801 TTCTTCAAAGCCCACAACTCCGTGGCA-CCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCCTT
* * * *
4526832 TTCCTTTAAAGCCCACAACTCCGTGGCA-CCTT
1 TT-CTTCAAAGTCCACGACTCAGTGGCATCCTT
* * * *
4526864 CTT-TTCAAAGCCCACAACTCCGTGGCACCCTTT
1 -TTCTTCAAAGTCCACGACTCAGTGGCATCC-TT
** *
4526897 TTCCTTTTAAGTCCACGACTCCGTGGCA
1 TT-CTTCAAAGTCCACGACTCAGTGGCA
4526925 CTCTTTTTAA
Statistics
Matches: 190, Mismatches: 16, Indels: 19
0.84 0.07 0.08
Matches are distributed among these distances:
30 28 0.15
31 56 0.29
32 82 0.43
33 4 0.02
34 20 0.11
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.31
Consensus pattern (32 bp):
TTCTTCAAAGTCCACGACTCAGTGGCATCCTT
Found at i:4526918 original size:34 final size:33
Alignment explanation
Indices: 4526808--4527265 Score: 409
Period size: 34 Copynumber: 13.8 Consensus size: 33
4526798 TTTTTCTTCA
*
4526808 AAGCCCACAACTCCGTGGCACC-TTTTCCTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* **
4526840 AAGCCCACAACTCCGTGGCACCTTCTT--TTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
4526871 AAGCCCACAACTCCGTGGCACCCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCA-CCTTTTTCCTTTT
* * * *
4526905 AAGTCCACGACTCCGTGGCA-C-TCTT--TTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
4526934 AAGCCCACAATTCCGTGGCAACCTATTT-CTTTT
1 AAGCCCACAACTCCGTGGC-ACCTTTTTCCTTTT
*
4526967 CAAAGCCCACCACTCCGTGGC-CCTTTTT-CTTTT
1 --AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
*
4527000 CAAAGCCCACAACTCCGTGACACTCTTTTTCCCTTTT
1 --AAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTT
* *
4527037 CAAAGCCCACAATTCCGTGGCACCTTTTTCTTTTT
1 --AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
*
4527072 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 -AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
** * *
4527106 AAAATCCACAACTCCGTGGCCCTCTTTTTCCTTCT
1 -AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
* * * **
4527141 AAGTCCACAACTCCGTGGCATCTTCTT--TTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
*
4527172 AAGCCCACAACTCCGTGGCACTTTTTTTCCCTTTT
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTT
* * *
4527207 AAAGCCCACAACTTCGTGGCACCTTGTTCTTTTT
1 -AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* * *
4527241 AAGTCCACAACTTCGTGGCATCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
4527266 CACCTTTTCT
Statistics
Matches: 359, Mismatches: 47, Indels: 39
0.81 0.11 0.09
Matches are distributed among these distances:
29 19 0.05
30 1 0.00
31 49 0.14
32 35 0.10
33 63 0.18
34 96 0.27
35 44 0.12
36 26 0.07
37 26 0.07
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
Found at i:4527088 original size:168 final size:164
Alignment explanation
Indices: 4526798--4527265 Score: 564
Period size: 168 Copynumber: 2.8 Consensus size: 164
4526788 TCAGTGGCAT
*
4526798 TTTTTCTTCAAAGCCCACAACTCCGTGGCACCTTTTCCTTT-AAAGCCCACAACTCCGTGGCAC-
1 TTTTTCTTCAAAGCCCACAACTCCGTGGC-CCTTTTCTTTTCAAAGCCCACAACTCCGTGGCACT
* * *
4526861 C---TT--CTTTTCAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGTCCACGACTCCGT
65 CTTTTTCCCTTTTCAAAGCCCACAATTCCGTGGCA-CCTTTTTCTTTTTAAGTCCACAACTCCGT
* *
4526921 GGCACTCTTTTTAAAGCCCACAATTCCGTGGCAACCTA
129 GGCACTCTTTTTAAAACCCACAACTCCGTGGC--CCTA
* *
4526959 TTTCTT-TTCAAAGCCCACCACTCCGTGGCCCTTTTTCTTTTCAAAGCCCACAACTCCGTGACAC
1 TTT-TTCTTCAAAGCCCACAACTCCGTGGCCC-TTTTCTTTTCAAAGCCCACAACTCCGTGGCAC
*
4527023 TCTTTTTCCCTTTTCAAAGCCCACAATTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCG
64 TCTTTTTCCCTTTTCAAAGCCCACAATTCCGTGGCACCTTTTTCTTTTT-AAGTCCACAACTCCG
* *
4527088 TGGCACCTTTTTCTTTTTAAAATCCACAACTCCGTGGCCCTC
128 TGGCA-C----TCTTTTTAAAACCCACAACTCCGTGGCCCTA
* * * *
4527130 TTTTTCCTTCTAAGTCCACAACTCCGTGG-CATCTTCTTTTCAAAGCCCACAACTCCGTGGCACT
1 TTTTT-CTTCAAAGCCCACAACTCCGTGGCCCTTTTCTTTTCAAAGCCCACAACTCCGTGGCACT
* * *
4527194 TTTTTTCCCTTTT-AAAGCCCACAACTT-CGTGGCACCTTGTTCTTTTTAAGTCCACAACTTCGT
65 CTTTTTCCCTTTTCAAAGCCCACAA-TTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGT
4527257 GGCA-TCTTT
129 GGCACTCTTT
4527266 CACCTTTTCT
Statistics
Matches: 268, Mismatches: 21, Indels: 35
0.83 0.06 0.11
Matches are distributed among these distances:
160 2 0.01
161 33 0.12
162 28 0.10
163 1 0.00
166 2 0.01
167 12 0.04
168 62 0.23
169 31 0.12
170 47 0.18
171 7 0.03
172 19 0.07
173 24 0.09
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (164 bp):
TTTTTCTTCAAAGCCCACAACTCCGTGGCCCTTTTCTTTTCAAAGCCCACAACTCCGTGGCACTC
TTTTTCCCTTTTCAAAGCCCACAATTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCCGTGG
CACTCTTTTTAAAACCCACAACTCCGTGGCCCTA
Found at i:4527115 original size:105 final size:104
Alignment explanation
Indices: 4526804--4527285 Score: 424
Period size: 105 Copynumber: 4.8 Consensus size: 104
4526794 GCATTTTTTC
* * *
4526804 TTCAAAGCCCACAACTCCGTGGCAC-C-TTTTCC-TTT-AAAGCCCACAACTCCGTGGCACC---
1 TTCAAAACCCACAACTCCGTGACACTCTTTTTCCTTTTCAAAGCCCACAATTCCGTGGCACCTTT
4526862 TTCTTTTCAAAGCCCACAACTCCGTGGCACCCTTTTTCCTT
66 TTCTTTTCAAAGCCCACAACTCCGTGGCA-CCTTTTT-CTT
** * * *
4526903 TT--AAGTCCACGACTCCGTGGCACTC----T--TTTT-AAAGCCCACAATTCCGTGGCAACCTA
1 TTCAAAACCCACAACTCCGTGACACTCTTTTTCCTTTTCAAAGCCCACAATTCCGTGGC-ACCTT
*
4526959 TTTCTTTTCAAAGCCCACCACTCCGTGGC-CCTTTTTCTT
65 TTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
4526998 TTCAAAGCCCACAACTCCGTGACACTCTTTTTCCCTTTTCAAAGCCCACAATTCCGTGGCACCTT
1 TTCAAAACCCACAACTCCGTGACACTCTTTTT-CCTTTTCAAAGCCCACAATTCCGTGGCACCTT
*
4527063 TTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
65 TTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* * * * * * * *
4527103 TTTAAAATCCACAACTCCGTGGCCCTCTTTTTCC--TTCTAAGTCCACAACTCCGTGGCA---TC
1 TTCAAAACCCACAACTCCGTGACACTCTTTTTCCTTTTCAAAGCCCACAATTCCGTGGCACCTTT
*
4527163 TTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTTCCCTT
66 TTCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTTT--CTT
* * * * * * *
4527205 TT-AAAGCCCACAACTTCGTGGCAC-CTTGTT-CTTTT-TAAGTCCACAACTT-CGTGGCATCTT
1 TTCAAAACCCACAACTCCGTGACACTCTTTTTCCTTTTCAAAGCCCACAA-TTCCGTGGCACCTT
**
4527265 TCACCTTTTCTAAAGCCCACA
65 T-TTCTTTTC-AAAGCCCACA
4527286 CAAGTCGGTG
Statistics
Matches: 325, Mismatches: 30, Indels: 50
0.80 0.07 0.12
Matches are distributed among these distances:
94 22 0.07
95 9 0.03
96 7 0.02
97 39 0.12
98 28 0.09
99 33 0.10
100 28 0.09
101 22 0.07
102 26 0.08
103 1 0.00
104 43 0.13
105 67 0.21
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (104 bp):
TTCAAAACCCACAACTCCGTGACACTCTTTTTCCTTTTCAAAGCCCACAATTCCGTGGCACCTTT
TTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTT
Found at i:4527183 original size:31 final size:31
Alignment explanation
Indices: 4526729--4527200 Score: 285
Period size: 34 Copynumber: 14.5 Consensus size: 31
4526719 CCATGACTTA
* * *
4526729 GTGGCATCCTT-TTCTTCAAAGTCCACGACTCA
1 GTGGCAT-CTTCTT-TTCAAAGCCCACAACTCC
* * ** *
4526761 GTGGCAT-TT-TGTCTCAAAGTCCACGGCTCA
1 GTGGCATCTTCT-TTTCAAAGCCCACAACTCC
*
4526791 GTGGCAT-TTTTTCTTCAAAGCCCACAACTCC
1 GTGGCATCTTCTT-TTCAAAGCCCACAACTCC
* *
4526822 GTGGCACCTT-TTCCTTTAAAGCCCACAACTCC
1 GTGGCATCTTCTT--TTCAAAGCCCACAACTCC
*
4526854 GTGGCACCTTCTTTTCAAAGCCCACAACTCC
1 GTGGCATCTTCTTTTCAAAGCCCACAACTCC
* * ** * *
4526885 GTGGCACCCTTTTTCCTTTTAAGTCCACGACTCC
1 GTGGCA-TCTTCTT--TTCAAAGCCCACAACTCC
* *
4526919 GTGGCA-C-TCTTTTTAAAGCCCACAATTCC
1 GTGGCATCTTCTTTTCAAAGCCCACAACTCC
* *
4526948 GTGGCAACCTATTTCTTTTCAAAGCCCACCACTCC
1 GTGGC-A--T-CTTCTTTTCAAAGCCCACAACTCC
* *
4526983 GTGGCCCTTTTTCTTTTCAAAGCCCACAACTCC
1 GTGG--CATCTTCTTTTCAAAGCCCACAACTCC
* *
4527016 GTGACACTCTTTTTCCCTTTTCAAAGCCCACAATTCC
1 GTGGCA-TC---TT--CTTTTCAAAGCCCACAACTCC
* *
4527053 GTGGCACCTTTTTCTTTTTAAAGCCCACAACTCC
1 GTGGCA---TCTTCTTTTCAAAGCCCACAACTCC
* * **
4527087 GTGGCACCTTTTTCTTTTTAAAATCCACAACTCC
1 GTGGCA---TCTTCTTTTCAAAGCCCACAACTCC
* * * *
4527121 GTGGCCCTCTTTTTCCTTCTAAGTCCACAACTCC
1 GTGG-CATCTTCTT--TTCAAAGCCCACAACTCC
4527155 GTGGCATCTTCTTTTCAAAGCCCACAACTCC
1 GTGGCATCTTCTTTTCAAAGCCCACAACTCC
*
4527186 GTGGCA-CTTTTTTTC
1 GTGGCATCTTCTTTTC
4527201 CCTTTTAAAG
Statistics
Matches: 364, Mismatches: 48, Indels: 58
0.77 0.10 0.12
Matches are distributed among these distances:
29 19 0.05
30 38 0.10
31 72 0.20
32 50 0.14
33 35 0.10
34 95 0.26
35 26 0.07
36 2 0.01
37 26 0.07
39 1 0.00
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (31 bp):
GTGGCATCTTCTTTTCAAAGCCCACAACTCC
Found at i:4527260 original size:202 final size:196
Alignment explanation
Indices: 4526804--4527285 Score: 541
Period size: 202 Copynumber: 2.4 Consensus size: 196
4526794 GCATTTTTTC
* *
4526804 TTCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTAAAGCCCACAACTCCGTGGCACC---TTCT
1 TTCAAAGCCCACAACTCCGTGGCACCTTTTCTTTTAAAGCCCACAACTTCGTGGCACCTTTTTCT
* * *
4526866 TTTCAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGTCCACGACTCCGTGGCACTCTTT
66 TTTTAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAATCCACAACTCCGTGGCACTCTTT
* * *
4526931 TTAAAGCCCACAATTCCGTGGCAACCTATTTCTTTTCAAAGCCCACCACTCCGTGGCCCTTTTTC
131 TTAAAGCCCACAACTCCGTGGCAA-CTACTTCTTTTCAAAGCCCACAACTCCGTGGCCCTTTTTC
4526996 TT
195 TT
*
4526998 TTCAAAGCCCACAACTCCGTGACACTCTTTTTCCCTTTTCAAAGCCCACAA-TTCCGTGGCACCT
1 TTCAAAGCCCACAACTCCGTGGCAC-C-TTTT--CTTTT-AAAGCCCACAACTT-CGTGGCACCT
*
4527062 TTTTCTTTTTAAAGCCCACAACTCCGTGGCA-CCTTTTTCTTTTTAAAATCCACAACTCCGTGGC
60 TTTTCTTTTTAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTT-AAATCCACAACTCCGTGGC
* * *
4527126 CCTCTTTTTCCTTCTAAGTCCACAACTCCGTGGC-A-T-CTTCTTTTCAAAGCCCACAACTCCGT
124 ACTC--TTT--TT-AAAGCCCACAACTCCGTGGCAACTACTTCTTTTCAAAGCCCACAACTCCGT
*
4527188 GGCACTTTTTTTCCCTT
184 GGC-C-CTTTTT--CTT
* * * * **
4527205 TT-AAAGCCCACAACTTCGTGGCACCTTGTTCTTTTTAAGTCCACAACTTCGTGGCATCTTTCAC
1 TTCAAAGCCCACAACTCCGTGGCACCTT-TTCTTTTAAAGCCCACAACTTCGTGGCACCTTT-TT
4527269 CTTTTCTAAAGCCCACA
64 CTTTT-TAAAGCCCACA
4527286 CAAGTCGGTG
Statistics
Matches: 244, Mismatches: 21, Indels: 36
0.81 0.07 0.12
Matches are distributed among these distances:
194 24 0.10
195 1 0.00
196 4 0.02
198 5 0.02
199 20 0.08
201 12 0.05
202 68 0.28
203 39 0.16
204 18 0.07
205 8 0.03
206 23 0.09
207 22 0.09
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (196 bp):
TTCAAAGCCCACAACTCCGTGGCACCTTTTCTTTTAAAGCCCACAACTTCGTGGCACCTTTTTCT
TTTTAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAATCCACAACTCCGTGGCACTCTTT
TTAAAGCCCACAACTCCGTGGCAACTACTTCTTTTCAAAGCCCACAACTCCGTGGCCCTTTTTCT
T
Found at i:4527277 original size:135 final size:133
Alignment explanation
Indices: 4526807--4527271 Score: 382
Period size: 139 Copynumber: 3.5 Consensus size: 133
4526797 TTTTTTCTTC
* ** * **
4526807 AAAGCCCACAACTCCGTGGCACCTT-TTC-CTTTAAAGCCCACAACTCCGTGG-CA-CCTTC-TT
1 AAAGCCCACAACTCCGTGGCACCTTGTTCTTTTTAAAATCCACAACTCCGTGGCCATCTTTCACC
* * * * ** * *
4526867 TTCAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGTCCACGACTCCGTGGCA-C----T
66 TTCTAAGTCCACAACTCCGTGGCA-TCTTCTT--TTCAAAGCCCACAACTCCGTGGCACCTTTTT
*
4526927 CTTTTT
128 CCTTTT
* * ** * * *
4526933 AAAGCCCACAATTCCGTGGCAACCTAT-TTCTTTTCAAAGCCCACCACTCCGTGGCCCTTTTTC-
1 AAAGCCCACAACTCCGTGGC-ACCT-TGTTCTTTTTAAAATCCACAACTCCGTGGCCATCTTTCA
** * * * *
4526996 TTTTCAAAGCCCACAACTCCGTGACACTCTTTTTCCCTTTTCAAAGCCCACAATTCCGTGGCACC
64 CCTTCTAAGTCCACAACTCCGTGGCA-TC---TT--CTTTTCAAAGCCCACAACTCCGTGGCACC
*
4527061 TTTTTCTTTTT
123 TTTTTCCTTTT
* * **
4527072 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAATCCACAACTCCGTGGCCCTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTGTTCTTTTTAAAATCCACAACTCCGTGGCCATCTTTCACC
*
4527137 TTCTAAGTCCACAACTCCGTGGCATCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTTCC
66 TTCTAAGTCCACAACTCCGTGGCATCTTCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTTT-C
4527202 CTTTT
129 CTTTT
* * *
4527207 AAAGCCCACAACTTCGTGGCACCTTGTTCTTTTT-AAGTCCACAACTTCGTGG-CATCTTTCACC
1 AAAGCCCACAACTCCGTGGCACCTTGTTCTTTTTAAAATCCACAACTCCGTGGCCATCTTTCACC
4527270 TT
66 TT
4527272 TTCTAAAGCC
Statistics
Matches: 283, Mismatches: 37, Indels: 31
0.81 0.11 0.09
Matches are distributed among these distances:
126 19 0.07
127 4 0.01
128 4 0.01
129 20 0.07
130 1 0.00
131 30 0.11
133 37 0.13
134 42 0.15
135 40 0.14
136 2 0.01
137 1 0.00
138 36 0.13
139 47 0.17
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (133 bp):
AAAGCCCACAACTCCGTGGCACCTTGTTCTTTTTAAAATCCACAACTCCGTGGCCATCTTTCACC
TTCTAAGTCCACAACTCCGTGGCATCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCT
TTT
Found at i:4527310 original size:33 final size:33
Alignment explanation
Indices: 4527268--4527339 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
4527258 GCATCTTTCA
*
4527268 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
*
4527301 CCTTCTCTAAAGCCCACATAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
4527334 CCTTCT
1 CCTTCT
4527340 AAGCCCAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.24
Consensus pattern (33 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:4527451 original size:49 final size:48
Alignment explanation
Indices: 4527339--4528032 Score: 801
Period size: 49 Copynumber: 14.8 Consensus size: 48
4527329 GCAACCCTTC
* *
4527339 TAAGCCCAATGTAGCTGGCCTTGAATCAGTACATTGGC-A---C-CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTCTCTT
* *
4527382 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAACTTCTTCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTC-TCTT
*
4527431 TAAGTCCAATGTAGCTGGCCTTGAATCAGTACATTGGC-A---C-CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTCTCTT
* * *
4527474 TAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCAACTTCTTCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTC-TCTT
4527523 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC-A---C-CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTCTCTT
* * *
4527566 TAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCAACTTCTTCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTC-TCTT
4527615 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC-A---C-CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTCTCTT
* * *
4527658 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTC-TCTT
* * * * *
4527707 TAAGTCCAATATAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTC-TCTT
* * * *
4527756 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAAC-TTCTCTT
* * *
4527805 TAAGTCCAATGTAGCTAGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTC-TCTT
* *
4527854 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC-ACCTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTC-TCTT
4527902 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC-A---C-CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTCTCTT
* * *
4527945 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAAC--TT-C-TCTT
* *
4527997 TAAGTTCAAAGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
4528033 ACATCCTTTT
Statistics
Matches: 566, Mismatches: 50, Indels: 61
0.84 0.07 0.09
Matches are distributed among these distances:
43 187 0.33
44 3 0.01
45 4 0.01
47 4 0.01
48 51 0.09
49 279 0.49
50 3 0.01
52 35 0.06
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (48 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTTCTCTT
Found at i:4527495 original size:22 final size:22
Alignment explanation
Indices: 4527428--4527495 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
4527418 GCAACTTCTT
*
4527428 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
* * * *
4527450 CTTGAA-T-CAGTACA-TTGGCAC
1 CTTTAAGTCCAATATAGCTGG--C
4527471 CTTTAAGTCCAATATAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
4527493 CTT
1 CTT
4527496 GAATCAACAT
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 10 0.31
23 5 0.16
24 3 0.09
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (22 bp):
CTTTAAGTCCAATATAGCTGGC
Found at i:4527501 original size:92 final size:92
Alignment explanation
Indices: 4527339--4528041 Score: 1050
Period size: 92 Copynumber: 7.5 Consensus size: 92
4527329 GCAACCCTTC
* *
4527339 TAAGCCCAATGTAGCTGGCCTTGAATCAGTACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
4527404 GAATCAGCATATTGGCAACTTCTTCTT
66 GAATCAGCATATTGGCAACTTCTTCTT
*
4527431 TAAGTCCAATGTAGCTGGCCTTGAATCAGTACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
*
4527496 GAATCAACATATTGGCAACTTCTTCTT
66 GAATCAGCATATTGGCAACTTCTTCTT
*
4527523 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGTTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
4527588 GAATCAGCATATTGGCAACTTCTTCTT
66 GAATCAGCATATTGGCAACTTCTTCTT
4527615 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
*
4527680 GAATCAGCATATTGGCACCTTCTTCTT
66 GAATCAGCATATTGGCAACTTCTTCTT
* *
4527707 TAAGTCCAATATAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-T-----TTAAGTCCAATATAGCT
*
4527772 GGCCTTGAATCAGCATATTGGCACCTT-TATCTT
60 GGCCTTGAATCAGCATATTGGCAACTTCT-TCTT
* * *
4527805 TAAGTCCAATGTAGCTAGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCT
* * **
4527870 GGCCTTGAATCAGCACATTGGC-ACCTCACCTT
60 GGCCTTGAATCAGCATATTGGCAACTTCTTCTT
4527902 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
* *
4527967 GAATCAGCATATTGGCACCTTTTCCATCTT
66 GAATCAGCATATTGGCAAC--TT-CTTCTT
* * *
4527997 TAAGTTCAAAGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTT
4528042 TTCTCATCTT
Statistics
Matches: 565, Mismatches: 27, Indels: 34
0.90 0.04 0.05
Matches are distributed among these distances:
91 39 0.07
92 309 0.55
93 2 0.00
94 1 0.00
95 41 0.07
96 5 0.01
97 43 0.08
98 122 0.22
102 1 0.00
103 1 0.00
104 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (92 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
GAATCAGCATATTGGCAACTTCTTCTT
Found at i:4528020 original size:52 final size:53
Alignment explanation
Indices: 4527942--4528095 Score: 177
Period size: 52 Copynumber: 2.9 Consensus size: 53
4527932 ACATTGGCAC
4527942 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * *
4527994 CTTTAAGTTCAA-AGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATA-TAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * * * *
4528049 CTTCAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
4528096 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
51 1 0.01
52 37 0.44
53 5 0.06
54 6 0.07
55 34 0.40
56 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:4528984 original size:13 final size:13
Alignment explanation
Indices: 4528966--4528990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4528956 CATAAAGTGT
4528966 TGTATCGATACAA
1 TGTATCGATACAA
4528979 TGTATCGATACA
1 TGTATCGATACA
4528991 TTTTTTTTTT
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:4529070 original size:13 final size:13
Alignment explanation
Indices: 4529052--4529111 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
4529042 ACATTACTCA
4529052 AATGTATCGATAC
1 AATGTATCGATAC
4529065 AATGTATCGATAC
1 AATGTATCGATAC
4529078 AA---A--GAT-C
1 AATGTATCGATAC
*
4529085 AGTGTATCGATAC
1 AATGTATCGATAC
4529098 AATGTATCGATAC
1 AATGTATCGATAC
4529111 A
1 A
4529112 CTGATCTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
10 2 0.05
12 3 0.08
13 29 0.74
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:4529096 original size:33 final size:33
Alignment explanation
Indices: 4529054--4529168 Score: 178
Period size: 33 Copynumber: 3.5 Consensus size: 33
4529044 ATTACTCAAA
** **
4529054 TGTATCGATACAATGTATCGATACAAAGATCAG
1 TGTATCGATACAATGTATCGATACACTGATCTT
4529087 TGTATCGATACAATGTATCGATACACTGATCTT
1 TGTATCGATACAATGTATCGATACACTGATCTT
*
4529120 TGTATCGATACATTGTATCGATACACTGATCTT
1 TGTATCGATACAATGTATCGATACACTGATCTT
4529153 TGTATCGATAC-ATGTA
1 TGTATCGATACAATGTA
4529169 GGCAAATTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 4 0.05
33 72 0.95
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATACACTGATCTT
Found at i:4529125 original size:20 final size:20
Alignment explanation
Indices: 4529100--4529164 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
4529090 ATCGATACAA
4529100 TGTATCGATACACTGATCTT
1 TGTATCGATACACTGATCTT
4529120 TGTATCGAT--AC--A---T
1 TGTATCGATACACTGATCTT
4529133 TGTATCGATACACTGATCTT
1 TGTATCGATACACTGATCTT
4529153 TGTATCGATACA
1 TGTATCGATACA
4529165 TGTAGGCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 22 0.58
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACACTGATCTT
Found at i:4529137 original size:13 final size:13
Alignment explanation
Indices: 4529087--4529144 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
4529077 CAAAGATCAG
*
4529087 TGTATCGATACAA
1 TGTATCGATACAT
*
4529100 TGTATCGATACAC
1 TGTATCGATACAT
4529113 TG-ATC--T---T
1 TGTATCGATACAT
4529120 TGTATCGATACAT
1 TGTATCGATACAT
4529133 TGTATCGATACA
1 TGTATCGATACA
4529145 CTGATCTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
10 2 0.05
12 3 0.08
13 27 0.73
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4529196 original size:52 final size:53
Alignment explanation
Indices: 4529133--4529273 Score: 198
Period size: 52 Copynumber: 2.7 Consensus size: 53
4529123 ATCGATACAT
*** *
4529133 TGTATCGATACACTGAT-CTTTGTATCGATACATGTAGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
4529185 TGTATCGATACA-TTATAAAATGTATCGATACATGCGGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
4529237 TGTATCGATACACT-ATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTGATAAAATGTATCGATACATGCAG
4529274 ATTTCGGGAC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 3 0.04
52 75 0.95
53 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (53 bp):
TGTATCGATACACTGATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:4533842 original size:21 final size:21
Alignment explanation
Indices: 4533799--4533875 Score: 91
Period size: 22 Copynumber: 3.6 Consensus size: 21
4533789 AGATTTGACA
* *
4533799 AAGGGGGAGAAATGCTTTGATT
1 AAGGGGGAGAAAT-TTTTAATT
*
4533821 AAGGGGGAGAAATTTTTCATT
1 AAGGGGGAGAAATTTTTAATT
* *
4533842 AAAGGGGAGAAATTCTTTAATA
1 AAGGGGGAGAAATT-TTTAATT
4533864 AAGGGGGAGAAA
1 AAGGGGGAGAAA
4533876 CATGAAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 19 0.40
22 29 0.60
ACGTcount: A:0.39, C:0.04, G:0.32, T:0.25
Consensus pattern (21 bp):
AAGGGGGAGAAATTTTTAATT
Found at i:4534445 original size:19 final size:20
Alignment explanation
Indices: 4534421--4534472 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
4534411 CATTATGCTT
**
4534421 TGTATCGATACATGTTC-AC
1 TGTATCGATACATGGACAAC
*
4534440 TGTATCGATACATGGACAAT
1 TGTATCGATACATGGACAAC
4534460 TGTATCGATACAT
1 TGTATCGATACAT
4534473 AAGATTGGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATGGACAAC
Found at i:4534539 original size:13 final size:13
Alignment explanation
Indices: 4534518--4534570 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
4534508 TGATACATGG
*
4534518 TACAATGTATCGA
1 TACATTGTATCGA
4534531 TACATTGTATCGA
1 TACATTGTATCGA
4534544 TACA-TG-AT-G-
1 TACATTGTATCGA
4534553 -A-ATTGTATCGA
1 TACATTGTATCGA
4534564 TACATTG
1 TACATTG
4534571 CTTGTAATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:4537419 original size:142 final size:141
Alignment explanation
Indices: 4537126--4537642 Score: 621
Period size: 142 Copynumber: 3.6 Consensus size: 141
4537116 TTTTGTCACT
* * **
4537126 AAATAAAAATTATTTTCTTAATTTTTCTAA-ATTTCTAATATTCTTAT-AGTTTTTTGTAGGAGT
1 AAATAAAAATTATTATCTTAATTTTT-TAAGATTTCTAATATTCCTATGA-TTTTCCGTAGGAGT
* * * *
4537189 ATAGAAATCTTCAAAA-TTTTT-CATTTTTTTGGTTCTCCATTAAGGTATA-AAATAAATTTTCT
64 ATAAAAATCTTCAAAACTTTTTGTATCTTTTTGGTTCTCCATTAAGGTA-AGAAATGAATTTTCT
4537251 TAAAAATTAAAAATC
128 T-AAAATTAAAAATC
* * * * *
4537266 AAACAAAAATTATTATCCTAATTTTTTGAGATTTCTAATATTCCTATGGTTTTCCGTATGAGTAT
1 AAATAAAAATTATTATCTTAATTTTTTAAGATTTCTAATATTCCTATGATTTTCCGTAGGAGTAT
*
4537331 AAAAATCTTCAAAATTTTTTGTATCTTTTTGGTTCTCCATTAAGGTAAGAAATGAATTTTCTTAA
66 AAAAATCTTCAAAACTTTTTGTATCTTTTTGGTTCTCCATTAAGGTAAGAAATGAATTTTCTTAA
4537396 AACTTAAAAATC
131 AA-TTAAAAATC
* *
4537408 AAATAAAAATTATTATCTTAATTTTTTAAGATTTCTAATATTCTTATGATTTTCCGTAGGGGTAT
1 AAATAAAAATTATTATCTTAATTTTTTAAGATTTCTAATATTCCTATGATTTTCCGTAGGAGTAT
* * * * * * * *
4537473 AAAAATCTTCAAAACCTTTCGTATCTTTTTGATTTTCTATTTAGGTATGAAATGAATTTTTTTTG
66 AAAAATCTTCAAAACTTTTTGTATCTTTTTGGTTCTCCATTAAGGTAAGAAATGAA-TTTTCTT-
* *
4537538 AAAATAAAAAAGTTT
129 AAAATTAAAAA--TC
* * * * *
4537553 AATTAAAAATTAATATCTTAATTTTTCAAGATTTATAATATTCCTATGATTTTCCGTAAGAGTAT
1 AAATAAAAATTATTATCTTAATTTTTTAAGATTTCTAATATTCCTATGATTTTCCGTAGGAGTAT
* *
4537618 AGAAATTTTCAAAACTTTTTGTATC
66 AAAAATCTTCAAAACTTTTTGTATC
4537643 CCCTAATTTT
Statistics
Matches: 325, Mismatches: 42, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
139 2 0.01
140 65 0.20
141 10 0.03
142 152 0.47
143 12 0.04
144 4 0.01
145 80 0.25
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (141 bp):
AAATAAAAATTATTATCTTAATTTTTTAAGATTTCTAATATTCCTATGATTTTCCGTAGGAGTAT
AAAAATCTTCAAAACTTTTTGTATCTTTTTGGTTCTCCATTAAGGTAAGAAATGAATTTTCTTAA
AATTAAAAATC
Found at i:4537639 original size:287 final size:282
Alignment explanation
Indices: 4537126--4537642 Score: 687
Period size: 287 Copynumber: 1.8 Consensus size: 282
4537116 TTTTGTCACT
* **
4537126 AAATAAAAATTATTTTCTTAATTTTTCTAAATTTCTAATATTCTTATAGTTTTTTGTAGGAGTAT
1 AAATAAAAATTATTATCTTAATTTTTCTAAATTTCTAATATTCTTATAGTTTTCCGTAGGAGTAT
* ** * *
4537191 AGAAATCTTCAAAATTTTTCATTTTTTTGGTTCTCCATTAAGGTATAAAATAAATTTTCTTAAAA
66 AAAAATCTTCAAAACCTTTCATCTTTTTGATTCTCCATTAAGGTATAAAATAAATTTTCTTAAAA
* * ** * *
4537256 ATTAAAAATCAAACAAAAATTATTATCCTAATTTTTTGAGATTTCTAATATTCCTATGGTTTTCC
131 ATAAAAAATCAAACAAAAATTAATATCCTAATTTTTCAAGATTTATAATATTCCTATGATTTTCC
* *
4537321 GTATGAGTATAAAAATCTTCAAAATTTTTTGTATCTTTTTGGTTCTCCATTAAGGTAAGAAATGA
196 GTAAGAGTATAAAAATCTTCAAAACTTTTTGTATCTTTTTGGTTCTCCATTAAGGTAAGAAATGA
4537386 ATTTTCTTAAAACTTAAAAATC
261 ATTTTCTTAAAACTTAAAAATC
*
4537408 AAATAAAAATTATTATCTTAATTTTT-TAAGATTTCTAATATTCTTAT-GATTTTCCGTAGGGGT
1 AAATAAAAATTATTATCTTAATTTTTCTAA-ATTTCTAATATTCTTATAG-TTTTCCGTAGGAGT
* * * * * *
4537471 ATAAAAATCTTCAAAACCTTTCGTATCTTTTTGATTTTCTATTTAGGTATGAAATGAATTTTTTT
64 ATAAAAATCTTCAAAACCTTTC--ATCTTTTTGATTCTCCATTAAGGTATAAAAT-AAATTTTCT
* * ** *
4537536 TGAAAATAAAAAAGTTTAATTAAAAATTAATATCTTAATTTTTCAAGATTTATAATATTCCTATG
126 TAAAAATAAAAAA--TCAAACAAAAATTAATATCCTAATTTTTCAAGATTTATAATATTCCTATG
* *
4537601 ATTTTCCGTAAGAGTATAGAAATTTTCAAAACTTTTTGTATC
189 ATTTTCCGTAAGAGTATAAAAATCTTCAAAACTTTTTGTATC
4537643 CCCTAATTTT
Statistics
Matches: 198, Mismatches: 30, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
281 4 0.02
282 72 0.36
284 25 0.13
285 18 0.09
287 79 0.40
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (282 bp):
AAATAAAAATTATTATCTTAATTTTTCTAAATTTCTAATATTCTTATAGTTTTCCGTAGGAGTAT
AAAAATCTTCAAAACCTTTCATCTTTTTGATTCTCCATTAAGGTATAAAATAAATTTTCTTAAAA
ATAAAAAATCAAACAAAAATTAATATCCTAATTTTTCAAGATTTATAATATTCCTATGATTTTCC
GTAAGAGTATAAAAATCTTCAAAACTTTTTGTATCTTTTTGGTTCTCCATTAAGGTAAGAAATGA
ATTTTCTTAAAACTTAAAAATC
Found at i:4541356 original size:159 final size:159
Alignment explanation
Indices: 4541062--4541426 Score: 441
Period size: 159 Copynumber: 2.3 Consensus size: 159
4541052 ATAAAAATGA
* * * *
4541062 GGTTGGAGTA-TCCTCGATGATGGAAAATTGGTGTTTTGGAAATAAAATCGAGGTTGGAGTATCC
1 GGTTGGAGTACTCC-CGATGGTAGAAAATCGATGTTTTGGAAATAAAATCGAGGTTGGAGTATCC
* * * * *
4541126 CCTCGAAAATAATGGGGTTGGAGTATCCTCGATTATAAAAAATCGATGTTTTAGAAATAAAACCG
65 CCTCGAAAATAACGGGGTTGAAATATCCCCGATTATAAAAAATCGATGTTTTAAAAATAAAACCG
*
4541191 AAGGTTAGAGTATCCCCTCAGAAATAACAG
130 AAGGTTAGAGTATCCCCTCAAAAATAACAG
* * * * *
4541221 GGTTGGAGTA-TCCCTTATTGTAGAGAATCGATGTTTTAGAAATAAAA-CTGGGGTTGGAGTATC
1 GGTTGGAGTACTCCC-GATGGTAGAAAATCGATGTTTTGGAAATAAAATC-GAGGTTGGAGTATC
* * * * * * *
4541284 CCTCTTGGAAATAACGGGGTTGAAATATCCCCTATTGTGAAAAATCGGTGTTTTAAAAATAAAAT
64 CC-CTCGAAAATAACGGGGTTGAAATATCCCCGATTATAAAAAATCGATGTTTTAAAAATAAAAC
* *
4541349 TG-GGGTTAGAGTATCCCCTCAAAAATAACAG
128 CGAAGGTTAGAGTATCCCCTCAAAAATAACAG
*
4541380 GGTTGGAGTACTCCCGATGGTGGAAAATCGATGTTTTGGAAATAAAA
1 GGTTGGAGTACTCCCGATGGTAGAAAATCGATGTTTTGGAAATAAAA
4541427 ATATCAATGA
Statistics
Matches: 173, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
158 2 0.01
159 116 0.67
160 55 0.32
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (159 bp):
GGTTGGAGTACTCCCGATGGTAGAAAATCGATGTTTTGGAAATAAAATCGAGGTTGGAGTATCCC
CTCGAAAATAACGGGGTTGAAATATCCCCGATTATAAAAAATCGATGTTTTAAAAATAAAACCGA
AGGTTAGAGTATCCCCTCAAAAATAACAG
Found at i:4541423 original size:79 final size:78
Alignment explanation
Indices: 4541062--4541426 Score: 354
Period size: 80 Copynumber: 4.6 Consensus size: 78
4541052 ATAAAAATGA
* * * * *
4541062 GGTTGGAGTATCCTCGA-TGATGGAAAATTGGTGTTTTGGAAATAAAATCGAGGTTGGAGTATCC
1 GGTTGGAGTATCC-CGATTG-TGGAAAATCGATGTTTTAGAAATAAAACCGAGGTTAGAGTATCC
* **
4541126 CCTCGAAAATAATGG
64 CCTCAAAAATAACAG
* **
4541141 GGTTGGAGTATCCTCGATTATAAAAAATCGATGTTTTAGAAATAAAACCGAAGGTTAGAGTATCC
1 GGTTGGAGTATCC-CGATTGTGGAAAATCGATGTTTTAGAAATAAAACCG-AGGTTAGAGTATCC
*
4541206 CCTCAGAAATAACAG
64 CCTCAAAAATAACAG
* * * * * *
4541221 GGTTGGAGTATCCCTTATTGTAGAGAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCC-GATTGTGGAAAATCGATGTTTTAGAAATAAAACCGAGGTTAGAGTATCCC
*** *
4541286 TCTTGGAAATAACGG
65 -CTCAAAAATAACAG
* * * * * * ** *
4541301 GGTTGAAATATCCCCTATTGTGAAAAATCGGTGTTTTAAAAATAAAATTGGGGTTAGAGTATCCC
1 GGTTGGAGTAT-CCCGATTGTGGAAAATCGATGTTTTAGAAATAAAACCGAGGTTAGAGTATCCC
4541366 CTCAAAAATAACAG
65 CTCAAAAATAACAG
* *
4541380 GGTTGGAGTACTCCCGATGGTGGAAAATCGATGTTTTGGAAATAAAA
1 GGTTGGAGTA-TCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAA
4541427 ATATCAATGA
Statistics
Matches: 237, Mismatches: 43, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
79 102 0.43
80 132 0.56
81 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (78 bp):
GGTTGGAGTATCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAACCGAGGTTAGAGTATCCCC
TCAAAAATAACAG
Found at i:4545179 original size:6 final size:6
Alignment explanation
Indices: 4545168--4545209 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
4545158 ATTTTCTTCC
*
4545168 TTTTCT TTTTCT TTTT-T TTCTTCT TTTTCT TCTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TT-TTCT TTTTCT TTTTCT TTTTCT
4545210 CAAGGCATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 3 0.09
6 26 0.81
7 3 0.09
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:4545190 original size:24 final size:24
Alignment explanation
Indices: 4545159--4545207 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
4545149 CTTTCCTTCA
*
4545159 TTTTCTTCCTTTTCTTTTTCTTTT
1 TTTTCTTCCTTTTCTTCTTCTTTT
*
4545183 TTTTCTTCTTTTTCTTCTTCTTTT
1 TTTTCTTCCTTTTCTTCTTCTTTT
4545207 T
1 T
4545208 CTCAAGGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTCTTCCTTTTCTTCTTCTTTT
Found at i:4545208 original size:12 final size:12
Alignment explanation
Indices: 4545161--4545209 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
4545151 TTCCTTCATT
*
4545161 TTCTTCCTTTTC
1 TTCTTCTTTTTC
* *
4545173 TTTTTCTTTTTT
1 TTCTTCTTTTTC
4545185 TTCTTCTTTTTC
1 TTCTTCTTTTTC
4545197 TTCTTCTTTTTC
1 TTCTTCTTTTTC
4545209 T
1 T
4545210 CAAGGCATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTCTTCTTTTTC
Found at i:4545209 original size:9 final size:9
Alignment explanation
Indices: 4545170--4545201 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
4545160 TTTCTTCCTT
4545170 TTCTTTTTC
1 TTCTTTTTC
*
4545179 TTTTTTTTC
1 TTCTTTTTC
4545188 TTCTTTTTC
1 TTCTTTTTC
4545197 TTCTT
1 TTCTT
4545202 CTTTTTCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:4548080 original size:13 final size:13
Alignment explanation
Indices: 4548062--4548087 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4548052 TACAGCAAGT
4548062 ATGTATCGATACA
1 ATGTATCGATACA
4548075 ATGTATCGATACA
1 ATGTATCGATACA
4548088 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:4550336 original size:21 final size:21
Alignment explanation
Indices: 4550303--4550347 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4550293 TTGCAAATTG
*
4550303 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
4550325 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
4550345 AAA
1 AAA
4550348 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:4552170 original size:15 final size:15
Alignment explanation
Indices: 4552150--4552180 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4552140 TAAAAATGTC
*
4552150 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4552165 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4552180 C
1 C
4552181 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:4553916 original size:20 final size:20
Alignment explanation
Indices: 4553873--4553918 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
4553863 AAATCTTTTG
4553873 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
4553894 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
4553914 CAAAA
1 CAAAA
4553919 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:4555959 original size:20 final size:20
Alignment explanation
Indices: 4555929--4555980 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
4555919 AACCAGAAAT
* *
4555929 TATTTTGAAAATAACAATAA
1 TATTTTAAAAATAAAAATAA
* *
4555949 TATTTTAAAAACAAAAATAG
1 TATTTTAAAAATAAAAATAA
*
4555969 TTTTTTAAAAAT
1 TATTTTAAAAAT
4555981 TGAGAAAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
TATTTTAAAAATAAAAATAA
Found at i:4558400 original size:3 final size:3
Alignment explanation
Indices: 4558386--4558419 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
4558376 TAAAATCCTA
* *
4558386 TAT TAC TAT TAT TAT TGT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4558420 GTTTGAGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4558752 original size:21 final size:19
Alignment explanation
Indices: 4558728--4558792 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 19
4558718 AATTAATTAT
4558728 TATTATTATTATTACTATAAA
1 TATT-TTATTATTA-TATAAA
*
4558749 TATTTTTTATTATTAAATAAA
1 TA--TTTTATTATTATATAAA
4558770 -ATTTTATT-TTAT-TAAAA
1 TATTTTATTATTATAT-AAA
4558787 TATTTT
1 TATTTT
4558793 TGTTCAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
16 1 0.03
17 6 0.16
18 12 0.32
20 1 0.03
21 7 0.18
22 9 0.24
23 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTATTATTATATAAA
Found at i:4558761 original size:22 final size:21
Alignment explanation
Indices: 4558730--4558785 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
4558720 TTAATTATTA
*
4558730 TTATTATTATTACTATAAATATT
1 TTATTATTATTA-AATAAA-ATT
4558753 TT-TTATTATTAAATAAAATT
1 TTATTATTATTAAATAAAATT
4558773 TTATT-TTATTAAA
1 TTATTATTATTAAA
4558786 ATATTTTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 13 0.42
21 7 0.23
22 9 0.29
23 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTATTATTAAATAAAATT
Found at i:4562616 original size:20 final size:20
Alignment explanation
Indices: 4562566--4562619 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
4562556 TTCAACAATT
4562566 TATATTGATACAATAAGGTAA
1 TATATTGATAC-ATAAGGTAA
*
4562587 TGTATTGATACATAA-GTGAA
1 TATATTGATACATAAGGT-AA
*
4562607 TATATCGATACAT
1 TATATTGATACAT
4562620 GCTTGAAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 17 0.59
21 10 0.34
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (20 bp):
TATATTGATACATAAGGTAA
Found at i:4562807 original size:52 final size:52
Alignment explanation
Indices: 4562675--4562807 Score: 151
Period size: 52 Copynumber: 2.5 Consensus size: 52
4562665 TCTAGAAAGA
* * *
4562675 AAATGTATCAAATACATTTTTCATTATATCGATATATTCTGAGTTTTTGAACC
1 AAATGTATC-AATACATTTTTCATTGTATCGATACATTCTGAATTTTTGAACC
* ** * *
4562728 AAATATATTGATACATTTTTCGTTGTATCGATACATTTTGAATTTTT-AACCC
1 AAATGTATCAATACATTTTTCATTGTATCGATACATTCTGAATTTTTGAA-CC
* *
4562780 AAATGTATCAATACATTCTTCAATGTAT
1 AAATGTATCAATACATTTTTCATTGTAT
4562808 TGATTCATGC
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
51 2 0.03
52 56 0.86
53 7 0.11
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.44
Consensus pattern (52 bp):
AAATGTATCAATACATTTTTCATTGTATCGATACATTCTGAATTTTTGAACC
Found at i:4573539 original size:24 final size:24
Alignment explanation
Indices: 4573512--4573557 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
4573502 TAAGTCTAAT
4573512 TAAAAA-TATTTTAAAATTTTAAAG
1 TAAAAAGTA-TTTAAAATTTTAAAG
4573536 TAAAAAGTATTTAAAATTTTAA
1 TAAAAAGTATTTAAAATTTTAA
4573558 TTTTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
TAAAAAGTATTTAAAATTTTAAAG
Found at i:4573716 original size:18 final size:19
Alignment explanation
Indices: 4573679--4573720 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
4573669 AAAATATTGT
4573679 TATTTGAATAATTCTTTAA
1 TATTTGAATAATTCTTTAA
4573698 TATTGTGAAT-ATT-TTTAA
1 TATT-TGAATAATTCTTTAA
4573716 TATTT
1 TATTT
4573721 TAAAGATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.05
18 9 0.41
19 7 0.32
20 5 0.23
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (19 bp):
TATTTGAATAATTCTTTAA
Found at i:4577687 original size:20 final size:20
Alignment explanation
Indices: 4577662--4577707 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
4577652 TATCGATACA
4577662 ATGTATCAATACAAAGCATG
1 ATGTATCAATACAAAGCATG
* *
4577682 ATGTATCGATACAAGGCATG
1 ATGTATCAATACAAAGCATG
*
4577702 ACGTAT
1 ATGTAT
4577708 TGATATGTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (20 bp):
ATGTATCAATACAAAGCATG
Found at i:4577712 original size:20 final size:20
Alignment explanation
Indices: 4577664--4577712 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
4577654 TCGATACAAT
* *
4577664 GTATCAATACAAAGCATGAT
1 GTATCGATACAAAGCATGAC
*
4577684 GTATCGATACAAGGCATGAC
1 GTATCGATACAAAGCATGAC
*
4577704 GTATTGATA
1 GTATCGATA
4577713 TGTCTGGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (20 bp):
GTATCGATACAAAGCATGAC
Found at i:4579250 original size:13 final size:13
Alignment explanation
Indices: 4579232--4579257 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4579222 AATTTTTTGG
4579232 TGTATCGATACAT
1 TGTATCGATACAT
4579245 TGTATCGATACAT
1 TGTATCGATACAT
4579258 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:4581397 original size:13 final size:13
Alignment explanation
Indices: 4581375--4581437 Score: 90
Period size: 13 Copynumber: 4.8 Consensus size: 13
4581365 GTAACCCATA
*
4581375 TATCGATACATTG
1 TATCGATACAATG
*
4581388 TATTGATACAATG
1 TATCGATACAATG
*
4581401 TATCGATACATTG
1 TATCGATACAATG
*
4581414 TATTGATACAATG
1 TATCGATACAATG
4581427 TATCGATACAA
1 TATCGATACAA
4581438 AGAACATTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:4581404 original size:26 final size:26
Alignment explanation
Indices: 4581375--4581436 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
4581365 GTAACCCATA
4581375 TATCGATACATTGTATTGATACAATG
1 TATCGATACATTGTATTGATACAATG
4581401 TATCGATACATTGTATTGATACAATG
1 TATCGATACATTGTATTGATACAATG
4581427 TATCGATACA
1 TATCGATACA
4581437 AAGAACATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (26 bp):
TATCGATACATTGTATTGATACAATG
Found at i:4584405 original size:13 final size:13
Alignment explanation
Indices: 4584387--4584412 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4584377 CAATTTTTTG
4584387 TGTATCGATACAT
1 TGTATCGATACAT
4584400 TGTATCGATACAT
1 TGTATCGATACAT
4584413 ACTTGCTGTA
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:4584477 original size:21 final size:21
Alignment explanation
Indices: 4584451--4584526 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
4584441 CTGCCAAGAA
*
4584451 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
4584472 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
4584492 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
4584513 ATGTATCGATACAT
1 ATGTATCGATACAT
4584527 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:4584497 original size:20 final size:20
Alignment explanation
Indices: 4584472--4584544 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4584462 CATCTTTTTT
4584472 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
4584492 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
4584513 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
4584533 ATGTATCGATAC
1 ATGTATCGATAC
4584545 TTTGAATTGT
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:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:4584508 original size:41 final size:41
Alignment explanation
Indices: 4584451--4584544 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
4584441 CTGCCAAGAA
*
4584451 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
4584492 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
4584533 ATGTATCGATAC
1 ATGTATCGATAC
4584545 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:4587003 original size:13 final size:13
Alignment explanation
Indices: 4586985--4587023 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4586975 ATAATCACCC
*
4586985 TGTATCGATACAG
1 TGTATCGATACAA
4586998 TGTATCGATACAA
1 TGTATCGATACAA
4587011 TGTATCGATACAA
1 TGTATCGATACAA
4587024 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4587034 original size:20 final size:20
Alignment explanation
Indices: 4587009--4587087 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
4586999 GTATCGATAC
4587009 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
4587029 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
4587054 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
4587074 CATGTATCGATACA
1 AATGTATCGATACA
4587088 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:4592372 original size:13 final size:13
Alignment explanation
Indices: 4592354--4592379 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4592344 CAATTTTTTG
4592354 TGTATCGATACAT
1 TGTATCGATACAT
4592367 TGTATCGATACAT
1 TGTATCGATACAT
4592380 ACTTGCTGTA
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:4592444 original size:21 final size:21
Alignment explanation
Indices: 4592418--4592493 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
4592408 CTGCCAAGAA
*
4592418 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
4592439 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
4592459 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
4592480 ATGTATCGATACAT
1 ATGTATCGATACAT
4592494 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:4592464 original size:20 final size:20
Alignment explanation
Indices: 4592439--4592511 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4592429 CATCTTTTTT
4592439 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
4592459 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
4592480 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
4592500 ATGTATCGATAC
1 ATGTATCGATAC
4592512 TTTGAATTGT
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:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:4592475 original size:41 final size:41
Alignment explanation
Indices: 4592418--4592511 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
4592408 CTGCCAAGAA
*
4592418 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
4592459 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
4592500 ATGTATCGATAC
1 ATGTATCGATAC
4592512 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:4597654 original size:32 final size:31
Alignment explanation
Indices: 4597604--4597815 Score: 147
Period size: 32 Copynumber: 6.9 Consensus size: 31
4597594 TGAAAAGGGT
* **
4597604 TGCCATTGACTTGCGTGGGCTTTAAAAAATGG
1 TGCCACTGACTTATGTGGGCTTTAAAAAA-GG
* *
4597636 TGCCACTAACTTATGTGGGCTTTGAAAAAAGT
1 TGCCACTGACTTATGTGGGCTTT-AAAAAAGG
* * *
4597668 TGCCATTGACTTGTGTGGGCTTT-GAAAAGG
1 TGCCACTGACTTATGTGGGCTTTAAAAAAGG
* * *
4597698 TGCCACTGAC-T-TGTAGGCTTGGAAAAAATAGT
1 TGCCACTGACTTATGTGGGCTT--TAAAAA-AGG
* *
4597730 TGCCA-TCGACTTGTGTGGGCTTT-GAAAAGG
1 TGCCACT-GACTTATGTGGGCTTTAAAAAAGG
* *
4597760 TGCCACTGACTTA--TGGGCTTTTAAAAAGA
1 TGCCACTGACTTATGTGGGCTTTAAAAAAGG
*
4597789 TGCCA-TCGAC-T-TGTGGGCTTTTAAAAA
1 TGCCACT-GACTTATGTGGGCTTTAAAAAA
4597816 TGTGGGCTTT
Statistics
Matches: 145, Mismatches: 22, Indels: 29
0.74 0.11 0.15
Matches are distributed among these distances:
28 18 0.12
29 28 0.19
30 26 0.18
31 8 0.06
32 50 0.34
33 7 0.05
34 8 0.06
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (31 bp):
TGCCACTGACTTATGTGGGCTTTAAAAAAGG
Found at i:4597741 original size:62 final size:60
Alignment explanation
Indices: 4597602--4597803 Score: 235
Period size: 62 Copynumber: 3.3 Consensus size: 60
4597592 TTTGAAAAGG
* * * * *
4597602 GTTGCCATTGACTTGCGTGGGCTTTAAAAAATGGTGCCACTAACTTATGTGGGCTTTGAAAAAA
1 GTTGCCATTGACTTGTGTGGGCTTT-GAAAA-GGTGCCACTGAC-T-TGTAGGCTTGGAAAAAA
4597666 GTTGCCATTGACTTGTGTGGGCTTTGAAAAGGTGCCACTGACTTGTAGGCTTGGAAAAAATA
1 GTTGCCATTGACTTGTGTGGGCTTTGAAAAGGTGCCACTGACTTGTAGGCTTGG-AAAAA-A
* * * **
4597728 GTTGCCATCGACTTGTGTGGGCTTTGAAAAGGTGCCACTGACTTATGGGCTT-TTAAAAA
1 GTTGCCATTGACTTGTGTGGGCTTTGAAAAGGTGCCACTGACTTGTAGGCTTGGAAAAAA
* *
4597787 GATGCCATCGACTTGTG
1 GTTGCCATTGACTTGTG
4597804 GGCTTTTAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
59 17 0.14
60 13 0.10
61 6 0.05
62 61 0.49
63 4 0.03
64 24 0.19
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (60 bp):
GTTGCCATTGACTTGTGTGGGCTTTGAAAAGGTGCCACTGACTTGTAGGCTTGGAAAAAA
Found at i:4597799 original size:29 final size:29
Alignment explanation
Indices: 4597649--4597815 Score: 108
Period size: 29 Copynumber: 5.6 Consensus size: 29
4597639 CACTAACTTA
* * *
4597649 TGTGGGCTTTGAAAAAAGTTGCCATTGACTT
1 TGTGGGCTTT-TAAAAAGATGCCATCGAC-T
* *
4597680 GTGTGGGC-TTTGAAAAGGTGCCA-CTGACT
1 -TGTGGGCTTTTAAAAAGATGCCATC-GACT
* ** *
4597709 TGTAGGCTTGGAAAAAATAGTTGCCATCGACTT
1 TGTGGGCTT--TTAAAA-AGATGCCATCGAC-T
* *
4597742 GTGTGGGC-TTTGAAAAGGTGCCA-CTGACT
1 -TGTGGGCTTTTAAAAAGATGCCATC-GACT
*
4597771 TATGGGCTTTTAAAAAGATGCCATCGACT
1 TGTGGGCTTTTAAAAAGATGCCATCGACT
4597800 TGTGGGCTTTTAAAAA
1 TGTGGGCTTTTAAAAA
4597816 TGTGGGCTTT
Statistics
Matches: 106, Mismatches: 18, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
28 12 0.11
29 36 0.34
30 24 0.23
31 8 0.08
32 17 0.16
33 3 0.03
34 6 0.06
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (29 bp):
TGTGGGCTTTTAAAAAGATGCCATCGACT
Found at i:4597821 original size:16 final size:16
Alignment explanation
Indices: 4597800--4597830 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4597790 GCCATCGACT
4597800 TGTGGGCTTTTAAAAA
1 TGTGGGCTTTTAAAAA
4597816 TGTGGGCTTTTAAAA
1 TGTGGGCTTTTAAAA
4597831 GGATGCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (16 bp):
TGTGGGCTTTTAAAAA
Found at i:4597837 original size:45 final size:45
Alignment explanation
Indices: 4597773--4597859 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
4597763 CACTGACTTA
*
4597773 TGGGCTTTTAAAAAGATGCCATCGACTTGTGGGCTTTTAAAAATG
1 TGGGCTTTTAAAAAGATGCCATCAACTTGTGGGCTTTTAAAAATG
* *
4597818 TGGGCTTTTAAAAGGATGCCATTAACTTGTGGGCTTTTAAAA
1 TGGGCTTTTAAAAAGATGCCATCAACTTGTGGGCTTTTAAAA
4597860 GTATGCCACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (45 bp):
TGGGCTTTTAAAAAGATGCCATCAACTTGTGGGCTTTTAAAAATG
Found at i:4597882 original size:74 final size:73
Alignment explanation
Indices: 4597743--4597888 Score: 179
Period size: 74 Copynumber: 2.0 Consensus size: 73
4597733 CATCGACTTG
* * *
4597743 TGTGGGCTTTGAAAAGGTGCCACTGACTTATGGGCTTTTAAAAAGATGCCATCGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGGTGCCACTAACTTATGGGCTTTTAAAAAGATGCCATCAACTTATGGGCT
*
4597808 TTTAAAAA
66 TTGAAAAA
* * * *
4597816 TGTGGGCTTTTAAAAGGATGCCATTAACTTGTGGGCTTTT-AAAAGTATGCCA-CTAACTTATTG
1 TGTGGGCTTTGAAAAGG-TGCCACTAACTTATGGGCTTTTAAAAAG-ATGCCATC-AACTTATGG
4597879 GCTTTGAAAA
63 GCTTTGAAAA
4597889 TATGCCATTG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
73 22 0.35
74 40 0.65
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (73 bp):
TGTGGGCTTTGAAAAGGTGCCACTAACTTATGGGCTTTTAAAAAGATGCCATCAACTTATGGGCT
TTGAAAAA
Found at i:4598015 original size:32 final size:32
Alignment explanation
Indices: 4597977--4598277 Score: 152
Period size: 32 Copynumber: 9.9 Consensus size: 32
4597967 TTTGGAAGGG
*
4597977 TGCCACCGATTTGTGTAGG-CTTTGAAAAAAGT
1 TGCCACCGACTTGTGT-GGACTTTGAAAAAAGT
*
4598009 TGCCACCGACTTGTGTGGACTTTGAAAAGAGT
1 TGCCACCGACTTGTGTGGACTTTGAAAAAAGT
** * *
4598041 TGCCACTAACTTGTG-GG-CTTTG-AAAAGGG
1 TGCCACCGACTTGTGTGGACTTTGAAAAAAGT
*** **
4598070 TGCCGTTGACTTGTG-GG-CTTTG-AAAGGGT
1 TGCCACCGACTTGTGTGGACTTTGAAAAAAGT
** * *
4598099 ATGCCACTAACTTGTG-GG-CTTTG--AAAGGG
1 -TGCCACCGACTTGTGTGGACTTTGAAAAAAGT
* * * * * * *
4598128 GGCCGCTGACTTATG-GG-CTTTG--GAAGGG
1 TGCCACCGACTTGTGTGGACTTTGAAAAAAGT
* * **
4598156 TGCC-CTCGATTTGTGTGGGCTTTGAAAAGGGT
1 TGCCAC-CGACTTGTGTGGACTTTGAAAAAAGT
* *
4598188 TGCCACCAACTTGTGTGGACTTTGAAAATAGT
1 TGCCACCGACTTGTGTGGACTTTGAAAAAAGT
* * *
4598220 TGCCATCGACTTGTGTAGACTTTGAAAAGAGT
1 TGCCACCGACTTGTGTGGACTTTGAAAAAAGT
* *
4598252 TGCCACTGACTTGT-AGG-CTTTGAAAA
1 TGCCACCGACTTGTGTGGACTTTGAAAA
4598278 GGGTGCCACT
Statistics
Matches: 219, Mismatches: 42, Indels: 18
0.78 0.15 0.06
Matches are distributed among these distances:
27 1 0.00
28 32 0.15
29 34 0.16
30 38 0.17
31 5 0.02
32 108 0.49
33 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGACTTTGAAAAAAGT
Found at i:4598168 original size:179 final size:179
Alignment explanation
Indices: 4597863--4598328 Score: 602
Period size: 179 Copynumber: 2.6 Consensus size: 179
4597853 TTTAAAAGTA
* * * * * *
4597863 TGCCACTAACTTATTGGCTTTGAAAA-TATGCCATTGTCTTATGGGATTTGAAAGGGTATGCCAC
1 TGCCACTAACTTGTGGGCTTTGAAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGGTATGCCAC
*
4597927 TAACTTGTGGGCTTTGAAAGGGTGCCAATGACTTATGGGCTTTGGAAGGGTGCCACCGATTTGTG
66 TAACTTGTGGGCTTTGAAAGGGGGCCAATGACTTATGGGCTTTGGAAGGGTGCCACCGATTTGTG
*
4597992 TAGGCTTTGAAAAAAGTTGCCACCGACTTGTGTGGACTTTGAAAAGAGT
131 TAGGCTTTGAAAAAAGTTGCCACCAACTTGTGTGGACTTTGAAAAGAGT
* *
4598041 TGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCGTTGACTTGTGGGCTTTGAAAGGGTATGCCAC
1 TGCCACTAACTTGTGGGCTTTGAAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGGTATGCCAC
**
4598106 TAACTTGTGGGCTTTGAAAGGGGGCCGCTGACTTATGGGCTTTGGAAGGGTGCC-CTCGATTTGT
66 TAACTTGTGGGCTTTGAAAGGGGGCCAATGACTTATGGGCTTTGGAAGGGTGCCAC-CGATTTGT
* ** *
4598170 GTGGGCTTTGAAAAGGGTTGCCACCAACTTGTGTGGACTTTGAAAATAGT
130 GTAGGCTTTGAAAAAAGTTGCCACCAACTTGTGTGGACTTTGAAAAGAGT
* * * * *
4598220 TGCCA-TCGACTTGTGTAGACTTTGAAAAGAGTTGCCACTGACTTGTAGGCTTTGAAAAGGG--T
1 TGCCACT-AACTTGTG--GGCTTTGAAAAG-GATGCCATTGACTTGTGGGCTTTG-AAAGGGTAT
* * * **
4598282 GCCACTAACTTATGGGCTTTG-AAGGGTGCCATTGACTCGTGGGCTTT
61 GCCACTAACTTGTGGGCTTTGAAAGGGGGCCAATGACTTATGGGCTTT
4598329 AAAAGGGTAC
Statistics
Matches: 253, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
178 26 0.10
179 148 0.58
180 21 0.08
181 32 0.13
182 20 0.08
183 6 0.02
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.31
Consensus pattern (179 bp):
TGCCACTAACTTGTGGGCTTTGAAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGGTATGCCAC
TAACTTGTGGGCTTTGAAAGGGGGCCAATGACTTATGGGCTTTGGAAGGGTGCCACCGATTTGTG
TAGGCTTTGAAAAAAGTTGCCACCAACTTGTGTGGACTTTGAAAAGAGT
Found at i:4598245 original size:211 final size:206
Alignment explanation
Indices: 4597923--4598357 Score: 554
Period size: 211 Copynumber: 2.1 Consensus size: 206
4597913 AAAGGGTATG
* * * * * * *
4597923 CCACTAACTTGTGGGCTTTGAAAGGGTGCCAAT-GA-CT-TATGGGCTTTGGAAGGGTGCCACCG
1 CCACTAACTTATGGGCTTTGGAAGGGTGCC-CTCGATTTGTGTGGGCTTTGAAAGGGTGCCACCA
* *
4597985 ATTTGTGTAGGCTTTGAAAAAAGTTGCCACCGACTTGTGTGGACTTTGAAAAGAGTTGCCACTAA
65 ACTTGTGTAGGCTTTGAAAAAAGTTGCCACCGACTTGTGTAGACTTTGAAAAGAGTTGCCACTAA
* ** * * *
4598050 CTTGTGGGCTTTGAAAAGGGTGCCGTTGACTTGTGGGCTTTGAAAGGGTATGCCACTAACTTGTG
130 CTTGTAGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTG-AAGGG--TGCCACTAACTCGTG
* *
4598115 GGCTTTGAAAGGGGG
192 GGCTTTAAAAGGGGA
* *
4598130 CCGCTGACTTATGGGCTTTGGAAGGGTGCCCTCGATTTGTGTGGGCTTTGAAAAGGGTTGCCACC
1 CCACTAACTTATGGGCTTTGGAAGGGTGCCCTCGATTTGTGTGGGCTTTG-AAAGGG-TGCCACC
* *
4598195 AACTTGTGT-GGACTTTGAAAATAGTTGCCATCGACTTGTGTAGACTTTGAAAAGAGTTGCCACT
64 AACTTGTGTAGG-CTTTGAAAAAAGTTGCCACCGACTTGTGTAGACTTTGAAAAGAGTTGCCACT
* * *
4598259 GACTTGTAGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTGAAGGGTGCCATTGACTCGTGG
128 AACTTGTAGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTGAAGGGTGCCACTAACTCGTGG
*
4598324 GCTTTAAAAGGGTA
193 GCTTTAAAAGGGGA
4598338 CCACTAACTTATGGGCTTTG
1 CCACTAACTTATGGGCTTTG
4598358 AAAATGGTGC
Statistics
Matches: 195, Mismatches: 27, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
206 1 0.01
207 28 0.14
208 43 0.22
209 10 0.05
210 12 0.06
211 101 0.52
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (206 bp):
CCACTAACTTATGGGCTTTGGAAGGGTGCCCTCGATTTGTGTGGGCTTTGAAAGGGTGCCACCAA
CTTGTGTAGGCTTTGAAAAAAGTTGCCACCGACTTGTGTAGACTTTGAAAAGAGTTGCCACTAAC
TTGTAGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTGAAGGGTGCCACTAACTCGTGGGCT
TTAAAAGGGGA
Found at i:4598536 original size:111 final size:112
Alignment explanation
Indices: 4598252--4598593 Score: 269
Period size: 111 Copynumber: 3.1 Consensus size: 112
4598242 TGAAAAGAGT
* * * * * * ** * * *
4598252 TGCCACTGACTTGTAGGCTTTGAAAAGGGTGCCACTAACTTATGGGC-TTTGAAGGGTGCCATTG
1 TGCCACTGACTCGTAAGCTTT-AAAAGGATGCCACTGACTCATGGCCATTAAAAGGATGCCACTA
* * * * * * *
4598316 ACTCGTGGGCTTTAAAAGGGTACCACTAACTTATGGGCTTTGAAAATGG
65 ACTTGTGGGATTAAAAAAGTTGCCACTAACTTGTGGGCTTTG-AAATGG
** * ** **
4598365 TGCCACTGACTCGTAAGCTTTGGAAGGATGCCACTGACTTATGGGGATTGGAAGGATGCCACTAA
1 TGCCACTGACTCGTAAGCTTTAAAAGGATGCCACTGACTCATGGCCATTAAAAGGATGCCACTAA
* *
4598430 CTTGTGGGATTAAAAAAGTTGCCATTGA-TTGGTGGGCTTTGAAA-GG
66 CTTGTGGGATTAAAAAAGTTGCCACTAACTT-GTGGGCTTTGAAATGG
* * * * * *
4598476 T-CTCATTGACTCGTGAGCTTTAAAAGGATGCCACTGACTCGTGGCCTTTAAAAGGTTGCCACTG
1 TGC-CACTGACTCGTAAGCTTTAAAAGGATGCCACTGACTCATGGCCATTAAAAGGATGCCACTA
* * ** * *
4598540 ACTTGTGGGCTTTAAAGGGTTGCCACTAACTTGTGGGCTTTGAAAAGT
65 ACTTGTGGGATTAAAAAAGTTGCCACTAACTTGTGGGCTTTGAAATGG
4598588 TGCCAC
1 TGCCAC
4598594 CAACTTGTGT
Statistics
Matches: 182, Mismatches: 41, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
110 1 0.01
111 87 0.48
112 31 0.17
113 63 0.35
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (112 bp):
TGCCACTGACTCGTAAGCTTTAAAAGGATGCCACTGACTCATGGCCATTAAAAGGATGCCACTAA
CTTGTGGGATTAAAAAAGTTGCCACTAACTTGTGGGCTTTGAAATGG
Found at i:4598600 original size:28 final size:28
Alignment explanation
Indices: 4597816--4598666 Score: 410
Period size: 28 Copynumber: 29.1 Consensus size: 28
4597806 CTTTTAAAAA
* * * *
4597816 TGTGGGCTTTTAAAAGGATGCCATTAACT
1 TGTGGGCTTTGAAAA-GTTGCCACTGACT
* *
4597845 TGTGGGCTTTTAAAAGTATGCCACTAACT
1 TGTGGGCTTTGAAAAGT-TGCCACTGACT
* * * *
4597874 TATTGGCTTTGAAAA-TATGCCATTGTCT
1 TGTGGGCTTTGAAAAGT-TGCCACTGACT
* * * *
4597902 TATGGGATTTGAAAGGGTATGCCACTAACT
1 TGTGGGCTTTGAAA-AGT-TGCCACTGACT
* * *
4597932 TGTGGGCTTTGAAAGGGTGCCAATGACT
1 TGTGGGCTTTGAAAAGTTGCCACTGACT
* * * * * *
4597960 TATGGGCTTTGGAAGGGTGCCACCGATT
1 TGTGGGCTTTGAAAAGTTGCCACTGACT
*
4597988 TGTGTAGGCTTTGAAAAAAGTTGCCACCGACT
1 TGTG--GGCTTTG--AAAAGTTGCCACTGACT
*
4598020 TGTGTGGACTTTGAAAAGAGTTGCCACTAACT
1 TGTG-GG-CTTTG-AAA-AGTTGCCACTGACT
* **
4598052 TGTGGGCTTTGAAAAGGGTGCCGTTGACT
1 TGTGGGCTTTGAAAA-GTTGCCACTGACT
* *
4598081 TGTGGGCTTTGAAAGGGTATGCCACTAACT
1 TGTGGGCTTTGAAA-AGT-TGCCACTGACT
* ** *
4598111 TGTGGGCTTTGAAAGGGGGCCGCTGACT
1 TGTGGGCTTTGAAAAGTTGCCACTGACT
* * * * *
4598139 TATGGGCTTTGGAAGGGTGCC-CTCGATTT
1 TGTGGGCTTTGAAAAGTTGCCACT-GA-CT
**
4598168 GTGTGGGCTTTGAAAAGGGTTGCCACCAACT
1 -TGTGGGCTTTGAAAA--GTTGCCACTGACT
4598199 TGTGTGGACTTTGAAAATAGTTGCCA-TCGACT
1 TGTG-GG-CTTTG-AAA-AGTTGCCACT-GACT
*
4598231 TGTGTAGACTTTGAAAAGAGTTGCCACTGACT
1 TGTG--GGCTTTG-AAA-AGTTGCCACTGACT
* * *
4598263 TGTAGGCTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAA-GTTGCCACTGACT
* * * *
4598292 TATGGGCTTTG-AAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAAGTTGCCACTGACT
* * * *
4598319 CGTGGGCTTT-AAAAGGGTACCACTAACT
1 TGTGGGCTTTGAAAA-GTTGCCACTGACT
* *
4598347 TATGGGCTTTGAAAATGGTGCCACTGACT
1 TGTGGGCTTTGAAAA-GTTGCCACTGACT
* ** * * *
4598376 CGTAAGCTTTGGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGTTGCCACTGACT
* ** * * * *
4598404 TATGGGGATTGGAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGTTGCCACTGACT
* ** *
4598432 TGTGGGATTAAAAAAGTTGCCATTGA-T
1 TGTGGGCTTTGAAAAGTTGCCACTGACT
* *
4598459 TGGTGGGCTTTG-AAAGGT-CTCATTGACT
1 T-GTGGGCTTTGAAAAGTTGC-CACTGACT
* * *
4598487 CGTGAGCTTT-AAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAA-GTTGCCACTGACT
* *
4598515 CGTGGCCTTT-AAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAA-GTTGCCACTGACT
* *
4598543 TGTGGGCTTT-AAAGGGTTGCCACTAACT
1 TGTGGGCTTTGAAA-AGTTGCCACTGACT
**
4598571 TGTGGGCTTTGAAAAGTTGCCACCAACT
1 TGTGGGCTTTGAAAAGTTGCCACTGACT
* **
4598599 TGTGTAGGCTTTAGAGAAGGTTGCCACCAACT
1 TGTG--GGCTTT-GA-AAAGTTGCCACTGACT
* **
4598631 TGTGTGGTCTTTAGAGAAGGTTGCCACCAACT
1 TGTG-GG-CTTT-GA-AAAGTTGCCACTGACT
4598663 TGTG
1 TGTG
4598667 TGGACCTTAG
Statistics
Matches: 656, Mismatches: 124, Indels: 81
0.76 0.14 0.09
Matches are distributed among these distances:
26 1 0.00
27 47 0.07
28 248 0.38
29 120 0.18
30 84 0.13
31 15 0.02
32 134 0.20
33 6 0.01
34 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGTTGCCACTGACT
Found at i:4598625 original size:32 final size:31
Alignment explanation
Indices: 4598527--4598684 Score: 193
Period size: 32 Copynumber: 5.2 Consensus size: 31
4598517 TGGCCTTTAA
**
4598527 AAGGTTGCCACTGACTTGTG-GGCTTTA-A-
1 AAGGTTGCCACCAACTTGTGTGGCTTTAGAG
* *
4598555 AGGGTTGCCACTAACTTGTG-GGCTTT-GA-
1 AAGGTTGCCACCAACTTGTGTGGCTTTAGAG
*
4598583 AAAGTTGCCACCAACTTGTGTAGGCTTTAGAG
1 AAGGTTGCCACCAACTTGTGT-GGCTTTAGAG
4598615 AAGGTTGCCACCAACTTGTGTGGTCTTTAGAG
1 AAGGTTGCCACCAACTTGTGTGG-CTTTAGAG
*
4598647 AAGGTTGCCACCAACTTGTGTGGACCTTAGAG
1 AAGGTTGCCACCAACTTGTGTGG-CTTTAGAG
4598679 AAGGTT
1 AAGGTT
4598685 TCTCCACTAG
Statistics
Matches: 116, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
28 42 0.36
30 6 0.05
31 4 0.03
32 64 0.55
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (31 bp):
AAGGTTGCCACCAACTTGTGTGGCTTTAGAG
Found at i:4603771 original size:12 final size:12
Alignment explanation
Indices: 4603749--4603800 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
4603739 CCTTTTCTTA
4603749 TTTAT-TGTTTT
1 TTTATGTGTTTT
*
4603760 TTTGTGTGTTTT
1 TTTATGTGTTTT
*
4603772 TTGTATTTGTTTT
1 TT-TATGTGTTTT
*
4603785 TTTTTGTGTTTGT
1 TTTATGTGTTT-T
4603798 TTT
1 TTT
4603801 TTTTTCATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
11 4 0.12
12 15 0.45
13 14 0.42
ACGTcount: A:0.04, C:0.00, G:0.17, T:0.79
Consensus pattern (12 bp):
TTTATGTGTTTT
Found at i:4603771 original size:27 final size:27
Alignment explanation
Indices: 4603741--4603793 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4603731 TTCTTCCCCC
4603741 TTTTCT-TATTTATTGTTTTTTTGTGTG
1 TTTTCTGTATTTATT-TTTTTTTGTGTG
* *
4603768 TTTTTTGTATTTGTTTTTTTTTGTGT
1 TTTTCTGTATTTATTTTTTTTTGTGT
4603794 TTGTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.06, C:0.02, G:0.15, T:0.77
Consensus pattern (27 bp):
TTTTCTGTATTTATTTTTTTTTGTGTG
Found at i:4603789 original size:16 final size:16
Alignment explanation
Indices: 4603768--4603805 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
4603758 TTTTTGTGTG
4603768 TTTTTTGTATTTGTTT
1 TTTTTTGTATTTGTTT
*
4603784 TTTTTTGTGTTTGTTT
1 TTTTTTGTATTTGTTT
4603800 TTTTTT
1 TTTTTT
4603806 CATGAAGGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.84
Consensus pattern (16 bp):
TTTTTTGTATTTGTTT
Found at i:4603800 original size:27 final size:28
Alignment explanation
Indices: 4603747--4603802 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
4603737 CCCCTTTTCT
4603747 TATTTATTGTTTTTTTGTGTGTTTTTTG
1 TATTTATTGTTTTTTTGTGTGTTTTTTG
*
4603775 TATTTGTT-TTTTTTTGTGTTTGTTTTTT
1 TATTTATTGTTTTTTTGTG--TGTTTTTT
4603803 TTTCATGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 10 0.40
28 7 0.28
29 8 0.32
ACGTcount: A:0.05, C:0.00, G:0.16, T:0.79
Consensus pattern (28 bp):
TATTTATTGTTTTTTTGTGTGTTTTTTG
Found at i:4606843 original size:33 final size:34
Alignment explanation
Indices: 4606796--4606865 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 34
4606786 AATTTTCATA
*
4606796 ATTTGTATCGATACATTGTTCATTGTATCGATAC
1 ATTTGTATCGATACATTGTTCAATGTATCGATAC
*
4606830 ATTT-TATCGATACATTTTTCAATGTATCGATAC
1 ATTTGTATCGATACATTGTTCAATGTATCGATAC
4606863 ATT
1 ATT
4606866 CAGGAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 30 0.88
34 4 0.12
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (34 bp):
ATTTGTATCGATACATTGTTCAATGTATCGATAC
Found at i:4606846 original size:13 final size:13
Alignment explanation
Indices: 4606816--4606847 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4606806 ATACATTGTT
*
4606816 CATTGTATCGATA
1 CATTTTATCGATA
4606829 CATTTTATCGATA
1 CATTTTATCGATA
4606842 CATTTT
1 CATTTT
4606848 TCAATGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (13 bp):
CATTTTATCGATA
Found at i:4606859 original size:20 final size:18
Alignment explanation
Indices: 4606799--4606865 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 18
4606789 TTTCATAATT
4606799 TGTATCGATACATTGTTCA
1 TGTATCGATACATT-TTCA
4606818 TTGTATCGATACA--TT--
1 -TGTATCGATACATTTTCA
4606833 T-TATCGATACATTTTTCAA
1 TGTATCGATACA-TTTTC-A
4606852 TGTATCGATACATT
1 TGTATCGATACATT
4606866 CAGGAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.25
14 1 0.03
16 2 0.05
17 2 0.05
19 3 0.08
20 22 0.55
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (18 bp):
TGTATCGATACATTTTCA
Found at i:4609304 original size:51 final size:51
Alignment explanation
Indices: 4609230--4609351 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 51
4609220 TTATTTCCGA
* ** *
4609230 GGGGATACTCCAACCCCTGTTTTATTTCTAAAACAGTAATTTTCCATAATC
1 GGGGATACTCCAACCCCTGTTTTATTTCCAAAACACCAATTTTCCACAATC
** *
4609281 GGGGATACTCCAACTTC-GATTTTATTTCCAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCTG-TTTTATTTCCAAAACACCAATTTTCCACAATC
*
4609332 GAGGATACTCCAA-CCCTGTT
1 GGGGATACTCCAACCCCTGTT
4609352 ATTTCATCGA
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
50 4 0.07
51 55 0.93
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCTGTTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:4609361 original size:28 final size:28
Alignment explanation
Indices: 4609329--4609383 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
4609319 ATTTTTCACA
4609329 ATCGAGGATACTCCAACCCTGTTATTTC
1 ATCGAGGATACTCCAACCCTGTTATTTC
4609357 ATCGAGGATACTCCAACCCTGTTATTT
1 ATCGAGGATACTCCAACCCTGTTATTT
4609384 TCAAGGGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCTGTTATTTC
Found at i:4609393 original size:28 final size:28
Alignment explanation
Indices: 4609332--4609403 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
4609322 TTTCACAATC
*
4609332 GAGGATACTCCAACCCTGTTATTTCATC
1 GAGGATACTCCAACCCTGTTATTTCATA
4609360 GAGGATACTCCAACCCTGTTATTTTCA-A
1 GAGGATACTCCAACCCTGTTA-TTTCATA
* *
4609388 GGGGATACTCTAACCC
1 GAGGATACTCCAACCC
4609404 CGGCCTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 35 0.88
29 5 0.12
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (28 bp):
GAGGATACTCCAACCCTGTTATTTCATA
Found at i:4609445 original size:79 final size:79
Alignment explanation
Indices: 4609357--4609607 Score: 247
Period size: 79 Copynumber: 3.2 Consensus size: 79
4609347 CTGTTATTTC
* * ** *
4609357 ATCGAGGATACTCCAACCCTGTTATTTTCAAGGGGATACTCTAACCCCGGCCTTA-TTTCTAAAG
1 ATCGGGGATACTCTAACCCTGTTATTTTCAAGGGGATACTCTAACCCCAACCTTATTTTC-AAAA
4609421 CATCAATTTTTCACA
65 CATCAATTTTTCACA
**
4609436 ATCGGGGATACTCTAACCCTGTTATTTTCAAGGGGATACT-TCAACCCCAATTTTATTTTCAAAA
1 ATCGGGGATACTCTAACCCTGTTATTTTCAAGGGGATACTCT-AACCCCAACCTTATTTTCAAAA
* * *
4609500 CATCGATTTTTTATA
65 CATCAATTTTTCACA
** * * * * ** **
4609515 ATTAGGGATACTCTGACCCTGTTATTTCCGAGGGGATACTCCAACCCTGATTTTATTTTCAAAAC
1 ATCGGGGATACTCTAACCCTGTTATTTTCAAGGGGATACTCTAACCCCAACCTTATTTTCAAAAC
* * *
4609580 ATCGATTTTCCATA
66 ATCAATTTTTCACA
*
4609594 AT-TGGGATACTCTA
1 ATCGGGGATACTCTA
4609608 GCCTTGTTGT
Statistics
Matches: 147, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
78 11 0.07
79 132 0.90
80 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (79 bp):
ATCGGGGATACTCTAACCCTGTTATTTTCAAGGGGATACTCTAACCCCAACCTTATTTTCAAAAC
ATCAATTTTTCACA
Found at i:4613540 original size:28 final size:28
Alignment explanation
Indices: 4613507--4613561 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
4613497 ATTTTTCATA
*
4613507 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCATTATTTC
4613535 ATCGGGGATACTCCAACCCCATTATTT
1 ATCGGGGATACTCCAACCCCATTATTT
4613562 TCGAGAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCATTATTTC
Found at i:4613571 original size:28 final size:27
Alignment explanation
Indices: 4613507--4613574 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 27
4613497 ATTTTTCATA
*
4613507 ATCGGGGATACTCCAACCCCGTTATTT
1 ATCGGGGATACTCCAACCCCATTATTT
4613534 CATCGGGGATACTCCAACCCCATTATTT
1 -ATCGGGGATACTCCAACCCCATTATTT
4613562 -TCGAGAGGATACT
1 ATCG-G-GGATACT
4613575 TTTGAATGCC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 3 0.08
27 1 0.03
28 33 0.89
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCATTATTT
Found at i:4620631 original size:39 final size:36
Alignment explanation
Indices: 4620561--4620632 Score: 99
Period size: 39 Copynumber: 1.9 Consensus size: 36
4620551 AGAAGCTAGA
* *
4620561 AAAGGCTCGAGCTGCTAGTTCGTGGATGCTGCTGCT
1 AAAGGCTCGAGCTGCAAGTTCGTGGAAGCTGCTGCT
4620597 AAAGTGCTCGAGCTGCAAGTGTTCGTGGAAGCTGCT
1 AAAG-GCTCGAGCTGCAA--GTTCGTGGAAGCTGCT
4620633 ACTACCATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 4 0.13
37 12 0.39
39 15 0.48
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.26
Consensus pattern (36 bp):
AAAGGCTCGAGCTGCAAGTTCGTGGAAGCTGCTGCT
Found at i:4620910 original size:33 final size:33
Alignment explanation
Indices: 4620837--4620973 Score: 127
Period size: 33 Copynumber: 4.2 Consensus size: 33
4620827 ATTCCCTTCT
* * *
4620837 TTTTTTCTCATCTCCTACTTGCTGTGAGTT-GC
1 TTTTTTCTCCTCTCCTACTTGCCGTGAGTTACC
*
4620869 TTTATTTCTCCTCTCCTACTTGCCGGGAGTTACC
1 TTT-TTTCTCCTCTCCTACTTGCCGTGAGTTACC
* * *
4620903 TTTTTTCT--TTTTCTTCTTGCCGTGAGTTACC
1 TTTTTTCTCCTCTCCTACTTGCCGTGAGTTACC
* * * * *
4620934 TTTTTTTTCCTCACCTTCTTACCGTAAGTTACCC
1 TTTTTTCTCCTCTCCTACTTGCCGTGAGTTA-CC
4620968 TTTTTT
1 TTTTTT
4620974 TTCTCCCCCT
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
31 26 0.30
32 3 0.03
33 45 0.52
34 12 0.14
ACGTcount: A:0.10, C:0.27, G:0.12, T:0.51
Consensus pattern (33 bp):
TTTTTTCTCCTCTCCTACTTGCCGTGAGTTACC
Found at i:4621471 original size:9 final size:9
Alignment explanation
Indices: 4621459--4621488 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4621449 TCATGAAGAT
4621459 TTTTTTTAC
1 TTTTTTTAC
4621468 TTTTTTTA-
1 TTTTTTTAC
4621476 TTTTTTTAC
1 TTTTTTTAC
4621485 TTTT
1 TTTT
4621489 ATTTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:4621481 original size:17 final size:19
Alignment explanation
Indices: 4621459--4621498 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
4621449 TCATGAAGAT
4621459 TTTTTTTAC-TTT-TTTTA
1 TTTTTTTACTTTTATTTTA
4621476 TTTTTTTACTTTTATTTTA
1 TTTTTTTACTTTTATTTTA
4621495 TTTT
1 TTTT
4621499 ATATCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.43
18 3 0.14
19 9 0.43
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTACTTTTATTTTA
Found at i:4621500 original size:10 final size:9
Alignment explanation
Indices: 4621457--4621498 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
4621447 TTTCATGAAG
4621457 ATTTTTTTT
1 ATTTTTTTT
*
4621466 ACTTTTTTT
1 ATTTTTTTT
4621475 A-TTTTTTT
1 ATTTTTTTT
4621483 ACTTTTATTTT
1 A-TTTT-TTTT
4621494 ATTTT
1 ATTTT
4621499 ATATCAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.28
9 9 0.31
10 7 0.24
11 5 0.17
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:4624484 original size:155 final size:154
Alignment explanation
Indices: 4624052--4624561 Score: 526
Period size: 155 Copynumber: 3.3 Consensus size: 154
4624042 AACTCTAATG
* * * * ** *
4624052 GACTCAAAAATGATTATTAAAGGGTGAACCTATATTAAATGCACATCTTTGACATAAAAGCATCC
1 GACTCAAAAATAATCATAAAAGGGTGAACATATCCTAAATGCACATCTTTAACATAAAAGCATCC
* * * * * *
4624117 TAGTGACTACAT---CGAGCTTCTAAGAAAATTATCAAAATGTTTTTGGGGTGTACCTTTGATAT
66 TAGTGACTACATAGACTAGATTCTAGGAAAATTACCAAAATGCTTTTGGGGTATACCTTTGATAT
*
4624179 AAAAGTATTTCGATAACCCTAAAA
131 AAAAGTATCTCGATAACCCTAAAA
* * * * * * **
4624203 GACTGAAAAATTACCACAAAAAAGGTGAACATATCCTAAATGCACATTTTTTTTGCATAAAAGCA
1 GACTCAAAAATAATCA-TAAAAGGGTGAACATATCCTAAATGCACA--TCTTTAACATAAAAGCA
*
4624268 TCCTAGCGACTACATCAGACTCA-ATTCTAGGAAAATTACCAAAATGCTTTTGGGGTATACCTTT
63 TCCTAGTGACTACAT-AGACT-AGATTCTAGGAAAATTACCAAAATGCTTTTGGGGTATACCTTT
* *
4624332 AATATTAAAGTATCTCGATAACCCTAAAA
126 GATATAAAAGTATCTCGATAACCCTAAAA
*
4624361 GACTCAAAAATAATCATAAAAGGGTGAACATATCCTAAATGCACACCTTTAACATAAAAGCAT-C
1 GACTCAAAAATAATCATAAAAGGGTGAACATATCCTAAATGCACATCTTTAACATAAAAGCATCC
* * * * ** * *
4624425 TCGATAACTACATAGAACTAGGTTTTAGGAAAATTACCAAAACACTTTTGGGGTTTACCTTTGAC
66 TAG-TGACTACATAG-ACTAGATTCTAGGAAAATTACCAAAATGCTTTTGGGGTATACCTTTGAT
* ** * *
4624490 ATGAAAGTATCTTAATAAACTTAAAA
129 ATAAAAGTATCTCGATAACCCTAAAA
* * * * *
4624516 AACTCAAAAATAATAATAAAAGGATGAACCTATCCTCAATGCACAT
1 GACTCAAAAATAATCATAAAAGGGTGAACATATCCTAAATGCACAT
4624562 TGTTGGCATA
Statistics
Matches: 295, Mismatches: 53, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
151 12 0.04
152 23 0.08
154 34 0.12
155 122 0.41
157 27 0.09
158 76 0.26
159 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (154 bp):
GACTCAAAAATAATCATAAAAGGGTGAACATATCCTAAATGCACATCTTTAACATAAAAGCATCC
TAGTGACTACATAGACTAGATTCTAGGAAAATTACCAAAATGCTTTTGGGGTATACCTTTGATAT
AAAAGTATCTCGATAACCCTAAAA
Found at i:4624572 original size:155 final size:155
Alignment explanation
Indices: 4624295--4624677 Score: 391
Period size: 155 Copynumber: 2.5 Consensus size: 155
4624285 GACTCAATTC
** * * * *
4624295 TAGGAAAATTACCAAAATGCTTTTGGGGTATACCTTTAATATTAAAGTATCTCGATAACCCTAAA
1 TAGGAAAATTACCAAAACACTTTTGGGGTATACCTTTAACATGAAAGTATCTCAATAAACCTAAA
* * *
4624360 AGACTCAAAAATAATCATAAAAGGGTGAACATATCCTAAATGCACACCTTTAACATAAAAGCATC
66 AAACTCAAAAATAATAATAAAAGGATGAACATATCCTAAATGCACACCTTTAACATAAAAGCATC
*
4624425 TCGATAACTACATAGAACTAGGTTT
131 CCGATAACTACATAGAACTAGGTTT
* * * *
4624450 TAGGAAAATTACCAAAACACTTTTGGGGTTTACCTTTGACATGAAAGTATCTTAATAAACTTAAA
1 TAGGAAAATTACCAAAACACTTTTGGGGTATACCTTTAACATGAAAGTATCTCAATAAACCTAAA
* * * ** *
4624515 AAACTCAAAAATAATAATAAAAGGATGAACCTATCCTCAATGCACA-TTGTTGGCATAAAAGTAT
66 AAACTCAAAAATAATAATAAAAGGATGAACATATCCTAAATGCACACCT-TTAACATAAAAGCAT
* * * *
4624579 CCCGATGACTACATCGAATTTA-GTTA
130 CCCGATAACTACATAGAA-CTAGGTTT
* * * * * * * *
4624605 TA-AAAAATTATCAAAATA-TCCTT-GGGTATACTTTTAACATAAAAGTATCACAGT-AACCTTA
1 TAGGAAAATTACCAAAACACT-TTTGGGGTATACCTTTAACATGAAAGTATCTCAATAAACC-TA
*
4624666 AAAGACTCAAAA
64 AAAAACTCAAAA
4624678 TGCTAAGAAA
Statistics
Matches: 187, Mismatches: 37, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
152 3 0.02
153 38 0.20
154 16 0.09
155 128 0.68
156 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.28
Consensus pattern (155 bp):
TAGGAAAATTACCAAAACACTTTTGGGGTATACCTTTAACATGAAAGTATCTCAATAAACCTAAA
AAACTCAAAAATAATAATAAAAGGATGAACATATCCTAAATGCACACCTTTAACATAAAAGCATC
CCGATAACTACATAGAACTAGGTTT
Found at i:4625298 original size:29 final size:29
Alignment explanation
Indices: 4625248--4625304 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
4625238 GGAACAAAAT
*
4625248 TTTTTAATATTTTCAAATAAACCTCTAAAC
1 TTTTTAATATTTTCAAAAAAACC-CTAAAC
4625278 TTTTTAA-ATTTAT-AAAAAAACCCTAAA
1 TTTTTAATATTT-TCAAAAAAACCCTAAA
4625305 AAGATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 12 0.48
30 8 0.32
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (29 bp):
TTTTTAATATTTTCAAAAAAACCCTAAAC
Found at i:4625882 original size:34 final size:34
Alignment explanation
Indices: 4625844--4625915 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
4625834 ATGACAAAAT
4625844 CAAAATCATATCACAAAGATTACCACCTTATCAA
1 CAAAATCATATCACAAAGATTACCACCTTATCAA
4625878 CAAAATCATATCACAAAGATTACCACCTTATCAA
1 CAAAATCATATCACAAAGATTACCACCTTATCAA
4625912 CAAA
1 CAAA
4625916 CAATATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.49, C:0.26, G:0.03, T:0.22
Consensus pattern (34 bp):
CAAAATCATATCACAAAGATTACCACCTTATCAA
Found at i:4626373 original size:20 final size:20
Alignment explanation
Indices: 4626350--4626413 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
4626340 ACACCTAGAT
*
4626350 GTATCGATACAAATTGCTAA
1 GTATCAATACAAATTGCTAA
4626370 GTATCAATAC--ATTGC---
1 GTATCAATACAAATTGCTAA
4626385 --ATCAATACAAATTGCTAA
1 GTATCAATACAAATTGCTAA
*
4626403 GTATCGATACA
1 GTATCAATACA
4626414 TTCTATCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 8 0.23
15 5 0.14
18 5 0.14
20 17 0.49
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (20 bp):
GTATCAATACAAATTGCTAA
Found at i:4626446 original size:33 final size:34
Alignment explanation
Indices: 4626351--4626433 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 34
4626341 CACCTAGATG
* *
4626351 TATCGATACAAATTGCTAAGTATCAATACATTGC
1 TATCAATACAAATTGCTAAGTATCGATACATTGC
4626385 -ATCAATACAAATTGCTAAGTATCGATACATT-C
1 TATCAATACAAATTGCTAAGTATCGATACATTGC
4626417 TATCAATACAAATTGCT
1 TATCAATACAAATTGCT
4626434 TTGTGTCGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 1 0.02
33 45 0.98
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (34 bp):
TATCAATACAAATTGCTAAGTATCGATACATTGC
Found at i:4627385 original size:20 final size:19
Alignment explanation
Indices: 4627350--4627392 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
4627340 TCATCCATTT
*
4627350 TTTTATTTTTATTTATT-C
1 TTTTATTTTTAATTATTAC
4627368 TTTTAGTTTTGTAATTATTAC
1 TTTTA-TTTT-TAATTATTAC
4627389 TTTT
1 TTTT
4627393 GTTATCACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 4 0.19
20 7 0.33
21 5 0.24
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTTATTTTTAATTATTAC
Found at i:4629129 original size:527 final size:527
Alignment explanation
Indices: 4628147--4629137 Score: 1797
Period size: 527 Copynumber: 1.9 Consensus size: 527
4628137 AGTATTCTTG
4628147 ATAGTGAAAAATCGATGCTTCTAGAAGGAAAATTTTAAAAATTTGACAAAAATACTTTGGGTTTA
1 ATAGTGAAAAATCGATGCTTCTAGAAGGAAAATTTTAAAAATTTGACAAAAATACTTTGGGTTTA
4628212 GCCTTGGTTTGAGCCTAGGGGGTTAGGTTGTGAGAGAGCCAACCGAATACTCTTCGAGATATTCG
66 GCCTTGGTTTGAGCCTAGGGGGTTAGGTTGTGAGAGAGCCAACCGAATACTCTTCGAGATATTCG
*
4628277 AAAGTCTCAAATTGAGCATTTTGAGAGATTGGGCTTGAAATAGGGGACAACATTGTGTCGCCTTT
131 AAAGTCTCAAATTGAGCATTTTGAGAGATTGGGCTTGAAATAGGGGACAACATTGTGTCACCTTT
*
4628342 CTTTCTGAATTTATTTCGAGTTCATTCAAAAGTTTTAAGGGGTAAACAAAGTACCATTGGAAAGA
196 CTTTCTGAATTTATTTCGAGTTCATTCAAAAGTTTTAAAGGGTAAACAAAGTACCATTGGAAAGA
4628407 TAAACTCAACAAGGATTAATGTAAAAATATTCCAAAAACCTTAGACAATAACCTTATAGGGAGAC
261 TAAACTCAACAAGGATTAATGTAAAAATATTCCAAAAACCTTAGACAATAACCTTATAGGGAGAC
* *
4628472 TTAATTTTTGAACTCGACCCTATCTTGACACTAACAGCATGTATAGGGTAAAGGTGTGATGGACT
326 TTAATTTTTAAACTCGAACCTATCTTGACACTAACAGCATGTATAGGGTAAAGGTGTGATGGACT
*
4628537 TCAAAAAATCATTTTGGATTTAGCTAGAATCATTAAATGAGAATAATACCTTTTCGAAAAGAGAA
391 TCAAAAAATCATTTTGGATTTAGCTAGAATCATTAAATGAGAATAATACCTTTTCAAAAAGAGAA
4628602 TTTCATGCAGTTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTTGGAAATGATGGGGTTAGAGT
456 TTTCATGCAGTTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTTGGAAATGATGGGGTTAGAGT
4628667 ATTCCCA
521 ATTCCCA
*
4628674 ATAGTGAAAAATCGATGCTTCTAGAAGGAAAATTTTAAAAATTTGACAAAAATACTTTGGGTTTG
1 ATAGTGAAAAATCGATGCTTCTAGAAGGAAAATTTTAAAAATTTGACAAAAATACTTTGGGTTTA
*
4628739 GCTTTGGTTTGAGCCTAGGGGGTTAGGTTGTGAGAGAGCCAACCGAATACTCTTCGAGATATTCG
66 GCCTTGGTTTGAGCCTAGGGGGTTAGGTTGTGAGAGAGCCAACCGAATACTCTTCGAGATATTCG
*
4628804 AAAGTCTCAAATTGAGCATTTTGAGAGATTGGGCTTGAAATAGGGGACAACATTGTGTTACCTTT
131 AAAGTCTCAAATTGAGCATTTTGAGAGATTGGGCTTGAAATAGGGGACAACATTGTGTCACCTTT
* ***
4628869 TTTTCTGAATTTATTTC-ATGTTCATTTGGAAGTTTTAAAGGGTAAACAAAGTACCATTGGAAAG
196 CTTTCTGAATTTATTTCGA-GTTCATTCAAAAGTTTTAAAGGGTAAACAAAGTACCATTGGAAAG
* *
4628933 AT-GACTCAACGAGGATTAATGTAAAAATATTCCAAAAACCTTAGACAATAACCTTATAGGGAGA
260 ATAAACTCAACAAGGATTAATGTAAAAATATTCCAAAAACCTTAGACAATAACCTTATAGGGAGA
* * *
4628997 CTTAATTTTTAAACTTGAACCTATCTTGACATTAGCAGCATGTATAGGGTAAAGGTGTGATGGAC
325 CTTAATTTTTAAACTCGAACCTATCTTGACACTAACAGCATGTATAGGGTAAAGGTGTGATGGAC
4629062 TTCAAAAAATCATTTTGGATTTAGCTAGAATCATTAAAATGAGAATAATACCTTTTCAAAAAGAG
390 TTCAAAAAATCATTTTGGATTTAGCTAGAATCATT-AAATGAGAATAATACCTTTTCAAAAAGAG
4629127 AATTTCATGCA
454 AATTTCATGCA
4629138 ATTTCTTGGA
Statistics
Matches: 445, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
526 156 0.35
527 289 0.65
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (527 bp):
ATAGTGAAAAATCGATGCTTCTAGAAGGAAAATTTTAAAAATTTGACAAAAATACTTTGGGTTTA
GCCTTGGTTTGAGCCTAGGGGGTTAGGTTGTGAGAGAGCCAACCGAATACTCTTCGAGATATTCG
AAAGTCTCAAATTGAGCATTTTGAGAGATTGGGCTTGAAATAGGGGACAACATTGTGTCACCTTT
CTTTCTGAATTTATTTCGAGTTCATTCAAAAGTTTTAAAGGGTAAACAAAGTACCATTGGAAAGA
TAAACTCAACAAGGATTAATGTAAAAATATTCCAAAAACCTTAGACAATAACCTTATAGGGAGAC
TTAATTTTTAAACTCGAACCTATCTTGACACTAACAGCATGTATAGGGTAAAGGTGTGATGGACT
TCAAAAAATCATTTTGGATTTAGCTAGAATCATTAAATGAGAATAATACCTTTTCAAAAAGAGAA
TTTCATGCAGTTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTTGGAAATGATGGGGTTAGAGT
ATTCCCA
Found at i:4631082 original size:20 final size:21
Alignment explanation
Indices: 4631057--4631109 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
4631047 TACATGGTCC
4631057 TGTATCGATACATT-CACTTA-
1 TGTATCGATACATTAC-CTTAT
4631077 TGTATCGATACATTACCTTAT
1 TGTATCGATACATTACCTTAT
*
4631098 TATATCGATACA
1 TGTATCGATACA
4631110 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTACCTTAT
Done.