Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000208.1 Hibiscus syriacus cultivar Beakdansim tig00000370_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 114878
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:5513 original size:37 final size:37
Alignment explanation
Indices: 5388--5515 Score: 116
Period size: 37 Copynumber: 3.5 Consensus size: 37
5378 TCTATCGCCT
* * * * *
5388 TTGAGATTGTTTCTTTTGAAACAAAGTGTCGTCTCGC
1 TTGAGATAGTTTCTCTTAAAACAAAGTTTTGTCTCGC
* * *
5425 TAGAGACT-GTTTTTCTTAAAA-ATAAATTTTGTCTCGC
1 TTGAGA-TAGTTTCTCTTAAAACA-AAGTTTTGTCTCGC
* ** *
5462 TTGAGACAAATTCTCTTAAAACAAAGTTTTGTCTCTC
1 TTGAGATAGTTTCTCTTAAAACAAAGTTTTGTCTCGC
5499 TTGAGATAGTTTCTCTT
1 TTGAGATAGTTTCTCTT
5516 GAAATATAAA
Statistics
Matches: 70, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
36 1 0.01
37 67 0.96
38 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (37 bp):
TTGAGATAGTTTCTCTTAAAACAAAGTTTTGTCTCGC
Found at i:5577 original size:66 final size:66
Alignment explanation
Indices: 5472--5896 Score: 595
Period size: 66 Copynumber: 6.5 Consensus size: 66
5462 TTGAGACAAA
* * * * *
5472 TTCTCTTAAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAATATAAAACTTTGAGACT
1 TTCTCTTGAAACAAA-TGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGATT
5537 GT
65 GT
*
5539 TTCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGAATG
1 TTCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGATTG
5604 -
66 T
5604 TT-T-TTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGATTG
1 TTCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGATTG
5667 T
66 T
* * *
5668 TTCTCTTGAAACAAATGTTATCTCTCTTGAGACAATTTCTCTTGAAACATAAAACTTTGAGAATG
1 TTCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGATTG
5733 T
66 T
* * * *
5734 TTCTCTTAAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTTAAACATAAAAACATTAAGATT
1 TTCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAT-AAAACTTTGAGATT
5799 GT
65 GT
* * * * * * *
5801 TTCTCTTGAAACAAGTTTTTTCTCTCTTGAGATAGTTTCTCTTGAAACACAAACCTTTGAGATTA
1 TTCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGATTG
5866 T
66 T
* * * *
5867 TTCTCTTAAAACAAATTTTGTATATCTTGA
1 TTCTCTTGAAACAAATGTTGTCTCTCTTGA
5897 AACAAATTTT
Statistics
Matches: 322, Mismatches: 32, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
63 59 0.18
64 3 0.01
65 3 0.01
66 187 0.58
67 70 0.22
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (66 bp):
TTCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGATTG
T
Found at i:5663 original size:30 final size:30
Alignment explanation
Indices: 5628--5746 Score: 107
Period size: 30 Copynumber: 3.8 Consensus size: 30
5618 GTTGTCTCTC
5628 TTGAGACAGTTTCTCTTGAAACATAAAACT
1 TTGAGACAGTTTCTCTTGAAACATAAAACT
** *
5658 TTGAGATTGTTTCTCTTGAAACA-AATGTTATCTCT
1 TTGAGACAGTTTCTCTTGAAACATAA----A--ACT
*
5693 CTTGAGACAATTTCTCTTGAAACATAAAACT
1 -TTGAGACAGTTTCTCTTGAAACATAAAACT
*
5724 TTGAGA-ATGTTTCTCTTAAAACA
1 TTGAGACA-GTTTCTCTTGAAACA
5747 AATGTTGTCT
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
29 3 0.04
30 40 0.56
31 2 0.03
33 2 0.03
35 2 0.03
36 20 0.28
37 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (30 bp):
TTGAGACAGTTTCTCTTGAAACATAAAACT
Found at i:5707 original size:36 final size:36
Alignment explanation
Indices: 5529--5782 Score: 173
Period size: 36 Copynumber: 7.6 Consensus size: 36
5519 ATATAAAACT
* *
5529 TTGAGACTGTTTCTCTTGAAACAAATGTTGTCTCTC
1 TTGAGACAGTTTCTCTTGAAACAAATGTTATCTCTC
*
5565 TTGAGACAGTTTCTCTTGAAACATAA----A--ACT-
1 TTGAGACAGTTTCTCTTGAAACA-AATGTTATCTCTC
*
5595 TTGAGA-A-TGTT-T-TTGAAACAAATGTTGTCTCTC
1 TTGAGACAGT-TTCTCTTGAAACAAATGTTATCTCTC
*
5628 TTGAGACAGTTTCTCTTGAAACATAA----A--ACT-
1 TTGAGACAGTTTCTCTTGAAACA-AATGTTATCTCTC
**
5658 TTGAGATTGTTTCTCTTGAAACAAATGTTATCTCTC
1 TTGAGACAGTTTCTCTTGAAACAAATGTTATCTCTC
* *
5694 TTGAGACAATTTCTCTTGAAACATAA----A--ACT-
1 TTGAGACAGTTTCTCTTGAAACA-AATGTTATCTCTC
* *
5724 TTGAGA-ATGTTTCTCTTAAAACAAATGTTGTCTCTC
1 TTGAGACA-GTTTCTCTTGAAACAAATGTTATCTCTC
*
5760 TTGAGACAGTTTCTCTTTAAACA
1 TTGAGACAGTTTCTCTTGAAACA
5783 TAAAAACATT
Statistics
Matches: 168, Mismatches: 19, Indels: 62
0.67 0.08 0.25
Matches are distributed among these distances:
26 2 0.01
27 8 0.05
28 2 0.01
29 8 0.05
30 46 0.27
31 6 0.04
32 2 0.01
33 8 0.05
34 3 0.02
35 6 0.04
36 70 0.42
37 7 0.04
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAGACAGTTTCTCTTGAAACAAATGTTATCTCTC
Found at i:5898 original size:87 final size:87
Alignment explanation
Indices: 5804--5991 Score: 243
Period size: 87 Copynumber: 2.2 Consensus size: 87
5794 AGATTGTTTC
* * * * *
5804 TCTTGAAACAAGTTTTTTCTCTCTTGAGATAGTTTCTCTTGAAACACAAACCTTTGAGATTATTT
1 TCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACTTTGAGACTATTT
*
5869 CTCTTAAAACAAATTTTGTATA
66 CTCTTAAAACAAATGTTGTATA
* * * *
5891 TCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATATAAAACTTTGAGACTGTTT
1 TCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACTTTGAGACTATTT
* * *
5956 CTCTTGAAACAAATGTTGTCTC
66 CTCTTAAAACAAATGTTGTATA
*
5978 TCTTGAGAC-AGTTT
1 TCTTGAAACAAGTTT
5992 CTCTTGAAAC
Statistics
Matches: 86, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
86 4 0.05
87 82 0.95
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (87 bp):
TCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACTTTGAGACTATTT
CTCTTAAAACAAATGTTGTATA
Found at i:5916 original size:21 final size:21
Alignment explanation
Indices: 5875--5917 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5865 ATTTCTCTTA
*
5875 AAACAAATTTTGTATATCTTG
1 AAACAAATTTTGTATACCTTG
* *
5896 AAACAAATTTTGTCTCCCTTG
1 AAACAAATTTTGTATACCTTG
5917 A
1 A
5918 GACAGTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (21 bp):
AAACAAATTTTGTATACCTTG
Found at i:5992 original size:36 final size:35
Alignment explanation
Indices: 5891--6072 Score: 136
Period size: 36 Copynumber: 5.4 Consensus size: 35
5881 ATTTTGTATA
*
5891 TCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC
1 TCTTGAAACAAA-TTTGTCTCTCTTGAGACAGTTTC
* ** *
5927 TCTTGAAATATAA-----AACT-TTGAGACTGTTTC
1 TCTTGAAACA-AATTTGTCTCTCTTGAGACAGTTTC
5957 TCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTC
1 TCTTGAAACAAAT-TTGTCTCTCTTGAGACAGTTTC
* **
5993 TCTTGAAACATAA----AC-CT-TTGAGATTGTTTC
1 TCTTGAAACA-AATTTGTCTCTCTTGAGACAGTTTC
* * *
6023 CCTTGAAATAAATTTTGTCTCGCTTGAGACAGTTTC
1 TCTTGAAACAAA-TTTGTCTCTCTTGAGACAGTTTC
6059 TCTTGAAACAAATT
1 TCTTGAAACAAATT
6073 ATCCCTAAAG
Statistics
Matches: 110, Mismatches: 20, Indels: 33
0.67 0.12 0.20
Matches are distributed among these distances:
29 4 0.04
30 40 0.36
31 3 0.03
32 1 0.01
34 1 0.01
35 5 0.05
36 52 0.47
37 4 0.04
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (35 bp):
TCTTGAAACAAATTTGTCTCTCTTGAGACAGTTTC
Found at i:5997 original size:66 final size:66
Alignment explanation
Indices: 5891--6068 Score: 284
Period size: 66 Copynumber: 2.7 Consensus size: 66
5881 ATTTTGTATA
*
5891 TCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATATAAAACTTTGAGACTGTTT
1 TCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGACTGTTT
5956 C
66 C
* * * *
5957 TCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTT
1 TCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGACTGTTT
6022 C
66 C
* * *
6023 CCTTGAAATAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
1 TCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
6069 AATTATCCCT
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 103 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (66 bp):
TCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAACTTTGAGACTGTTT
C
Found at i:6036 original size:153 final size:154
Alignment explanation
Indices: 5737--6040 Score: 448
Period size: 153 Copynumber: 2.0 Consensus size: 154
5727 AGAATGTTTC
* * *
5737 TCTTAAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTTAAACATAAAAACATTAAGATTGTT
1 TCTTAAAACAAATGTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAAACATTAAGACTGTT
* * * *
5802 TCTCTTGAAACAAGTTTTTTCTCTCTTGAGATAGTTTCTCTTGAAACACAAACCTTTGAGATTAT
66 TCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAAACCTTTGAGATTAT
*
5867 TTCTCTTAAAACAAATTTTGTATA
131 TTCCCTTAAAACAAATTTTGTATA
* * * * *
5891 TCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATAT-AAAACTTTGAGACTGTT
1 TCTTAAAACAAATGTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAAACATTAAGACTGTT
* *
5955 TCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGT
66 TCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAAACCTTTGAGATTAT
* *
6020 TTCCCTTGAAATAAATTTTGT
131 TTCCCTTAAAACAAATTTTGT
6041 CTCGCTTGAG
Statistics
Matches: 133, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
153 91 0.68
154 42 0.32
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (154 bp):
TCTTAAAACAAATGTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAAACATTAAGACTGTT
TCTCTTGAAACAAATGTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAAACCTTTGAGATTAT
TTCCCTTAAAACAAATTTTGTATA
Found at i:6330 original size:138 final size:139
Alignment explanation
Indices: 6071--6631 Score: 608
Period size: 138 Copynumber: 4.0 Consensus size: 139
6061 TTGAAACAAA
* * * * *
6071 TTATCCCTAAAGATGGCTAAATGTCCTCATCACGTAGAAACCGTGTCATCCTCCGACCAGATCTC
1 TTATCCCTAAAGATGGCCAAACGTCCTCATCACGTAGAATCAGTGTCATCCACCGACCAGATCTC
* * * * *
6136 CTCATCACGTAGGAGCAACGTCATCCTTTGATAGCTAGACTTCCTCATTGA-GTAGGAATCATGT
66 CTCATCACGTAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCA-TCACGTAGGAACCATGT
6200 TATCTCC-AT
130 TATCTCCAAT
** * * ** * * *
6209 TTATCCCTAAAGATGGCCAAACGTGTTCATCACGTAGGATCCGTGTCATCCACTAACTAGATTTT
1 TTATCCCTAAAGATGGCCAAACGTCCTCATCACGTAGAATCAGTGTCATCCACCGACCAGATCTC
* * * * * *
6274 CTCATCACGTATGAGCAGCGTCAACCTTAGATAACCAGACTTCATCATCACATAGGAACCGTGTT
66 CTCATCACGTAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGTT
* *
6339 GTCTCCCAAA
131 ATCT-CCAAT
* * * *
6349 TTATCCCTAAAGATGGCCAAACGTCTTCATCACATAGGAGCAGTGTCATCCACCGACCAGATCTC
1 TTATCCCTAAAGATGGCCAAACGTCCTCATCACGTAGAATCAGTGTCATCCACCGACCAGATCTC
* * * ** * * *
6414 CTTATCATGTAGGAGCAATGTCATCCTTAGATAGTCAGACTTCCTTATCGCGTAGGAACCATGAT
66 CTCATCACGTAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGTT
*
6479 ATCT-CTAT
131 ATCTCCAAT
* * *
6487 TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAAT-AGTGCCATCCACCGACCAGATCT
1 TTATCCCTAAAGATGGCCAAACGTCCTCATCACGT-AGAATCAGTGTCATCCACCGACCAGATCT
** * * * * *
6551 CCTCATCACGTAGGAGCAGTGTTACCCTTAGATAACCAGATTTCCTCATCACGTAAGAACCATAT
65 CCTCATCACGTAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
6616 TATCTCCTAAT
130 TATCTCC-AAT
6627 TTATC
1 TTATC
6632 TAAAAACGAC
Statistics
Matches: 345, Mismatches: 72, Indels: 10
0.81 0.17 0.02
Matches are distributed among these distances:
137 2 0.01
138 219 0.63
139 6 0.02
140 118 0.34
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (139 bp):
TTATCCCTAAAGATGGCCAAACGTCCTCATCACGTAGAATCAGTGTCATCCACCGACCAGATCTC
CTCATCACGTAGGAGCAACGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGTT
ATCTCCAAT
Found at i:6582 original size:278 final size:278
Alignment explanation
Indices: 6067--6611 Score: 716
Period size: 278 Copynumber: 2.0 Consensus size: 278
6057 TCTCTTGAAA
* * * * *
6067 CAAATTATCCCTAAAGATGGCTAAATGTCCTCATCACGTAGAAACCGTGTCATCCTCCGACCAGA
1 CAAATTATCCCTAAAGATGGCCAAACGTCCTCATCACATAGAAACAGTGTCATCCACCGACCAGA
* * *
6132 TCTCCTCATCACGTAGGAGCAACGTCATCCTTTGATAGCTAGACTTCCTCATTGAGTAGGAATCA
66 TCTCCTCATCACGTAGGAGCAACGTCATCCTTAGATAGCTAGACTTCCTCATCGAGTAGGAACCA
* ** * * *
6197 TGTTATCTCCATTTATCCCTAAAGATGGCCAAACGTGTTCATCACGTAGGATCCGTGTCATCCAC
131 TGATATCTCCATTTATCCCTAAAGATGGCCAAACGTCCTCATCACGTAGAATCAGTGCCATCCAC
* * * * *
6262 TAACTAGATTTTCTCATCACGTATGAGCAGCGTCAACCTTAGATAACCAGACTTCATCATCACAT
196 CAACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCATCATCACAT
*
6327 AGGAACCGTGTTGTCTCC
261 AAGAACCGTGTTGTCTCC
* * *
6345 CAAATTATCCCTAAAGATGGCCAAACGTCTTCATCACATAGGAGCAGTGTCATCCACCGACCAGA
1 CAAATTATCCCTAAAGATGGCCAAACGTCCTCATCACATAGAAACAGTGTCATCCACCGACCAGA
* * * * *
6410 TCTCCTTATCATGTAGGAGCAATGTCATCCTTAGATAG-TCAGACTTCCTTATCGCGTAGGAACC
66 TCTCCTCATCACGTAGGAGCAACGTCATCCTTAGATAGCT-AGACTTCCTCATCGAGTAGGAACC
* * *
6474 ATGATATCTCTATTTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAAT-AGTGCCATCC
130 ATGATATCTCCATTTATCCCTAAAGATGGCCAAACGTCCTCATCACGT-AGAATCAGTGCCATCC
* * * * * *
6538 ACCGACCAGATCTCCTCATCACGTAGGAGCAGTGTTACCCTTAGATAACCAGATTTCCTCATCAC
194 ACCAACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCATCATCAC
*
6603 GTAAGAACC
259 ATAAGAACC
6612 ATATTATCTC
Statistics
Matches: 227, Mismatches: 38, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
277 1 0.00
278 222 0.98
279 4 0.02
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (278 bp):
CAAATTATCCCTAAAGATGGCCAAACGTCCTCATCACATAGAAACAGTGTCATCCACCGACCAGA
TCTCCTCATCACGTAGGAGCAACGTCATCCTTAGATAGCTAGACTTCCTCATCGAGTAGGAACCA
TGATATCTCCATTTATCCCTAAAGATGGCCAAACGTCCTCATCACGTAGAATCAGTGCCATCCAC
CAACCAGATCTCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCATCATCACAT
AAGAACCGTGTTGTCTCC
Found at i:9426 original size:16 final size:18
Alignment explanation
Indices: 9399--9432 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9389 TTTTCCAATA
9399 AAATTATAATTAT-TTTT
1 AAATTATAATTATATTTT
9416 AAATT-TAATTATATTTT
1 AAATTATAATTATATTTT
9433 TTATAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AAATTATAATTATATTTT
Found at i:9602 original size:3 final size:3
Alignment explanation
Indices: 9588--9628 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
9578 TCTGAGGTAT
* *
9588 GAA GAG GAA GAA GAA GAG GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
9629 TGCCCAGTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9605 original size:12 final size:12
Alignment explanation
Indices: 9588--9628 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
9578 TCTGAGGTAT
9588 GAAGAGGAAGAA
1 GAAGAGGAAGAA
9600 GAAGAGGAAGAA
1 GAAGAGGAAGAA
*
9612 GAAGAAGAAGAA
1 GAAGAGGAAGAA
9624 GAAGA
1 GAAGA
9629 TGCCCAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
GAAGAGGAAGAA
Found at i:16546 original size:12 final size:12
Alignment explanation
Indices: 16529--16571 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
16519 TCTGAAATGA
16529 TGCTTCTCTCTC
1 TGCTTCTCTCTC
*
16541 TGCTTCTCTCAC
1 TGCTTCTCTCTC
16553 TG---CTCTCTC
1 TGCTTCTCTCTC
16562 TGCTTCTCTC
1 TGCTTCTCTC
16572 GCCGCTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 8 0.31
12 18 0.69
ACGTcount: A:0.02, C:0.42, G:0.09, T:0.47
Consensus pattern (12 bp):
TGCTTCTCTCTC
Found at i:20956 original size:21 final size:20
Alignment explanation
Indices: 20932--20975 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
20922 TTAAATGTTT
*
20932 TTAATTCAAAAAAGTTTATAA
1 TTAATTCAAAAAA-TATATAA
* *
20953 TTAATTTAAATAATATATAA
1 TTAATTCAAAAAATATATAA
20973 TTA
1 TTA
20976 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAATTCAAAAAATATATAA
Found at i:21229 original size:180 final size:183
Alignment explanation
Indices: 20929--21293 Score: 637
Period size: 180 Copynumber: 2.0 Consensus size: 183
20919 AAATTAAATG
*
20929 TTTTTAATTCAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGA
1 TTTTTAATTCAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGA
*
20994 TAATTTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATTG
66 TAATTTTTTTAATTAATTAATATTGATTTAGATTTAAAAGCTATTGGATCTTAAATTATTAATTG
* *
21059 AGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATTTAATAT
131 AGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
*
21112 TTTTTAATT-AAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTT-ATA
1 TTTTTAATTCAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGA
*
21175 TAA-TTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGCTATTGGATCTTAAATTATTAATTG
66 TAATTTTTTTAATTAATTAATATTGATTTAGATTTAAAAGCTATTGGATCTTAAATTATTAATTG
* *
21239 GGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
131 AGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
21292 TT
1 TT
21294 AAAATTTAAT
Statistics
Matches: 174, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
180 110 0.63
181 5 0.03
182 50 0.29
183 9 0.05
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (183 bp):
TTTTTAATTCAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGA
TAATTTTTTTAATTAATTAATATTGATTTAGATTTAAAAGCTATTGGATCTTAAATTATTAATTG
AGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
Found at i:29029 original size:31 final size:31
Alignment explanation
Indices: 28985--29057 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
28975 GCTAACTCTC
* *
28985 AGTGA-TAATATCTTAATTAAATAATAGCAAA
1 AGTGACTAA-ATCTTAATTAAATAAAAACAAA
29016 AGTGACTAAATCTTAATTAAATAAAAACAAA
1 AGTGACTAAATCTTAATTAAATAAAAACAAA
* *
29047 ACTGACCAAAT
1 AGTGACTAAAT
29058 ATTATTCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 34 0.92
32 3 0.08
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.27
Consensus pattern (31 bp):
AGTGACTAAATCTTAATTAAATAAAAACAAA
Found at i:32806 original size:64 final size:62
Alignment explanation
Indices: 32738--32966 Score: 255
Period size: 64 Copynumber: 3.6 Consensus size: 62
32728 TGTTTGAATG
* *
32738 TGCATCGATGCATTGGTAGTGCATCGATGCACTCTTTTAAAAGAAGAACATCGAATG-ACTTTGA
1 TGCATCGATGCATAGGTAGTGCATCGATGCA-TCTTTTAAAAGAA-AACATCGAATGCA-TTTAA
* * * * *
32802 TGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCAATCAA
1 TGCATCGATGCATAGGTAGTGCATCGATGCAT-CTTTTAAAAGAA-AACATCGAATGCATTTAA
* *
32866 TGCATCGATGCATAAGG-AGTGCATCGATGCATCTCATTAATAAGGAAACATCGAATGCATTTAA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCT-TTTAA-AAGAAAACATCGAATGCATTTAA
* * *
32930 TGCACCGATGCACAAGTAGTGCATCGATGCATACTTT
1 TGCATCGATGCATAGGTAGTGCATCGATGCAT-CTTT
32967 CATTAAAAGA
Statistics
Matches: 139, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
63 5 0.04
64 126 0.91
65 8 0.06
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (62 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCTTTTAAAAGAAAACATCGAATGCATTTAA
Found at i:33676 original size:30 final size:30
Alignment explanation
Indices: 33640--33703 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
33630 AAGGAACATA
* *
33640 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
33670 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
33700 TGGA
1 TGGA
33704 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:37650 original size:64 final size:62
Alignment explanation
Indices: 37582--37810 Score: 255
Period size: 64 Copynumber: 3.6 Consensus size: 62
37572 TGTTTGAATG
* *
37582 TGCATCGATGCATTGGTAGTGCATCGATGCACTCTTTTAAAAGAAGAACATCGAATG-ACTTTGA
1 TGCATCGATGCATAGGTAGTGCATCGATGCA-TCTTTTAAAAGAA-AACATCGAATGCA-TTTAA
* * * * *
37646 TGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCAATCAA
1 TGCATCGATGCATAGGTAGTGCATCGATGCAT-CTTTTAAAAGAA-AACATCGAATGCATTTAA
* *
37710 TGCATCGATGCATAAGG-AGTGCATCGATGCATCTCATTAATAAGGAAACATCGAATGCATTTAA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCT-TTTAA-AAGAAAACATCGAATGCATTTAA
* * *
37774 TGCACCGATGCACAAGTAGTGCATCGATGCATACTTT
1 TGCATCGATGCATAGGTAGTGCATCGATGCAT-CTTT
37811 CATTAAAGAG
Statistics
Matches: 139, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
63 5 0.04
64 126 0.91
65 8 0.06
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (62 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCTTTTAAAAGAAAACATCGAATGCATTTAA
Found at i:38534 original size:29 final size:30
Alignment explanation
Indices: 38477--38539 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
38467 AAGGAACATA
* *
38477 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* *
38507 TGGATAGTTACCG-GGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
38536 TGGA
1 TGGA
38540 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:42455 original size:64 final size:62
Alignment explanation
Indices: 42381--42608 Score: 246
Period size: 64 Copynumber: 3.6 Consensus size: 62
42371 TGTTTGAATG
* *
42381 TGCATCGATGCATTGGTAGTGCATCGATGCACTCTTTTAAAAGAAGAACATCGAATG-ACTTTGA
1 TGCATCGATGCATAGGTAGTGCATCGATGCA-TCTTTTAAAAGAA-AACATCGAATGCA-TTTAA
* * * * *
42445 TGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCAATCAA
1 TGCATCGATGCATAGGTAGTGCATCGATGCAT-CTTTTAAAAGAA-AACATCGAATGCATTTAA
* *
42509 TGCATCGATGCATAAGG-AGTGCATCGATGCATCTCATTAATAAGGAAACATCG-ATGCATTTAA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCT-TTTAA-AAGAAAACATCGAATGCATTTAA
* * *
42572 TGCACCGATGCACAAGTAGTGCATCGATGCATACTTT
1 TGCATCGATGCATAGGTAGTGCATCGATGCAT-CTTT
42609 CATTAAAAGA
Statistics
Matches: 138, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
62 2 0.01
63 38 0.28
64 92 0.67
65 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (62 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCTTTTAAAAGAAAACATCGAATGCATTTAA
Found at i:46862 original size:21 final size:21
Alignment explanation
Indices: 46836--46886 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
46826 TATGAAGTAG
46836 TATCGATACCCCTATAGGAAA
1 TATCGATACCCCTATAGGAAA
*
46857 TATCGATACCCCTATAGGGAA
1 TATCGATACCCCTATAGGAAA
46878 TATCGATAC
1 TATCGATAC
46887 TCAACCCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (21 bp):
TATCGATACCCCTATAGGAAA
Found at i:47298 original size:20 final size:21
Alignment explanation
Indices: 47273--47312 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
47263 TTTGAGATAC
47273 ATAAAT-GTAT-GGTAAGGCTT
1 ATAAATGGTATAGG-AAGGCTT
47293 ATAAATGGTATAGGAAGGCT
1 ATAAATGGTATAGGAAGGCT
47313 ACAAGGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 10 0.56
22 2 0.11
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.30
Consensus pattern (21 bp):
ATAAATGGTATAGGAAGGCTT
Found at i:48777 original size:225 final size:226
Alignment explanation
Indices: 48300--48778 Score: 858
Period size: 224 Copynumber: 2.1 Consensus size: 226
48290 GTTATATTGT
* * *
48300 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTA
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
*
48365 TCTTTGGTTAATATTGTTAAATTTAAATTCTGAATAATATTTTATAAATATCAAAACAATCAAAT
66 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAATATCAAAACAATCAAAT
48430 AATTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
131 AATTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
48495 AAATTGAAACATAAATTACATAACTTTAAAA
196 AAATTGAAACATAAATTACATAACTTTAAAA
48526 AAAGTATATATCATTTTTAT-AAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAACATATTTATTATT
*
48590 AT-TTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAATATC-AAATAATC-AA
65 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAATATCAAAACAATCAAA
*
48652 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
130 TAA-TTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
48717 AAAAATTGAAACATAAATTACATAACTTTAAAA
194 AAAAATTGAAACATAAATTACATAACTTTAAAA
48750 AAAGTATATATCATTTTTATAAAAGTGTC
1 AAAGTATATATCATTTTTATAAAAGTGTC
48779 TAGTAAAAGT
Statistics
Matches: 244, Mismatches: 6, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
223 5 0.02
224 120 0.49
225 82 0.34
226 37 0.15
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (226 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAATATCAAAACAATCAAAT
AATTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
AAATTGAAACATAAATTACATAACTTTAAAA
Found at i:49177 original size:178 final size:178
Alignment explanation
Indices: 48847--49315 Score: 665
Period size: 178 Copynumber: 2.6 Consensus size: 178
48837 TCGATCCAAA
* * * *
48847 TAAAAAATGTGTCGATCCAAAACGATATAACA-GTAAAACTATGACAAAACCGGTATA-GAAATG
1 TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGT-TACAAAATG
* * * * *
48910 ATAAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTAATATAAGGATCGACACT
65 ATAAAACCGGTAAAACGATACCGGAT--ATTGAAAGTGTCGATACTTTATATAAGGATCGACACT
*
48975 TCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTT
128 TCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTT
* *
49026 TTAAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTTACAAAATGA
1 TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTACAAAATGA
* * *
49091 TAAAACCGGTAAAACGTTACCGGATATTGAAAGTGTCGATACTTTATATGAGGATCGACACTTTG
66 TAAAACCGGTAAAACGATACCGGATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
** *
49156 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTT
131 TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTT
* * *
49204 TAAAAAATATATCGATTCACAACGATATAACAGGTAAAAATATGATAAAACCGG-TATCAAAATG
1 TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTA-CAAAATG
*
49268 ATAAAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
65 ATAAAACCGGTAAAACGATACCGG--ATATTGAAAGTGTCGATACTTT
49316 TGTAAGTACG
Statistics
Matches: 261, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
177 2 0.01
178 157 0.60
179 31 0.12
180 71 0.27
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (178 bp):
TAAAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTTACAAAATGA
TAAAACCGGTAAAACGATACCGGATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTT
Found at i:49259 original size:20 final size:19
Alignment explanation
Indices: 49236--49282 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
49226 CGATATAACA
49236 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
49256 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
49276 GGTAAAA
1 GGTAAAA
49283 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:49284 original size:17 final size:19
Alignment explanation
Indices: 49245--49287 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
49235 AGGTAAAAAT
49245 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
49265 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
49282 ATGATA
1 ATGATA
49288 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:51513 original size:21 final size:21
Alignment explanation
Indices: 51489--51532 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
51479 AAGACAATCA
51489 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
51510 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
51531 AG
1 AG
51533 GTCACTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:56104 original size:32 final size:32
Alignment explanation
Indices: 56062--56150 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
56052 GAGGCAATAG
* *
56062 AGGGCATCTTTGAAGATTCAACATCAAATGTT
1 AGGGCATCTTTGGAGATTCAACATCAAATATT
* *
56094 GGGGCATCTTTGGAGATTCAACATTAAATATT
1 AGGGCATCTTTGGAGATTCAACATCAAATATT
* *
56126 AGGTCATCTTTGGGGATTCAACATC
1 AGGGCATCTTTGGAGATTCAACATC
56151 CTGATACGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (32 bp):
AGGGCATCTTTGGAGATTCAACATCAAATATT
Found at i:56728 original size:36 final size:36
Alignment explanation
Indices: 56688--56783 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 36
56678 TTGAAAAATA
*
56688 AAATTTTGTCTCGCTTGAGACAATTTCAATCAAAAC
1 AAATTTTGTCTCCCTTGAGACAATTTCAATCAAAAC
* * * ** **
56724 AAA--TTGTCTCTCTTGAGACAGTTGCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAATTTCAATCAAAAC
*
56758 AAGTTTTGTCTCCCTTGAGACAATTT
1 AAATTTTGTCTCCCTTGAGACAATTT
56784 TTCTTAAAAC
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
34 26 0.55
36 21 0.45
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (36 bp):
AAATTTTGTCTCCCTTGAGACAATTTCAATCAAAAC
Found at i:56775 original size:70 final size:69
Alignment explanation
Indices: 56689--57040 Score: 320
Period size: 73 Copynumber: 5.0 Consensus size: 69
56679 TGAAAAATAA
* * ** ** *
56689 AATTTTGTCTCGCTTGAGACAATTTCAATCAAAACAAATTGTCTCTCTTGAGACAGTTGCCCTTG
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTGTCTCTCTTGAGACAGTTTCCCTTG
56754 AAAC
66 AAAC
* * * * * * * *
56758 AAGTTTTGTCTCCCTTGAGACAATTTTTCTTAAAACCAGATTTTATCTCGCTTGAGATAGTTTCT
1 AA-TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA-CA-A-ATTGTCTCTCTTGAGACAGTTTCC
56823 CTTGAAAC
62 CTTGAAAC
* ** * **
56831 AATTTTTATCTCTTTTGAGATAGTTTCTCTTGAAAC--A-TG-AACT-TTGAGA-ACGTTTCCCT
1 AA-TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTGTCTCTCTTGAGACA-GTTTCCCT
56890 TGAAAC
64 TGAAAC
* * * *
56896 GAATCTTGTCTACCTTGAGACAGTTTCCCTTGAAACAAATTGTCTCCCTTGAGACAGTTTCCCTT
1 -AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTGTCTCTCTTGAGACAGTTTCCCTT
*
56961 GAAATA
65 GAAA-C
*
56967 AATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCC
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAA---TTGTCTCTCTTGAGACAGTTTCCC
57032 TTGAAAC
63 TTGAAAC
57039 AA
1 AA
57041 AATCGTTCAA
Statistics
Matches: 225, Mismatches: 42, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
64 1 0.00
65 45 0.20
66 3 0.01
67 2 0.01
68 2 0.01
69 3 0.01
70 80 0.36
71 3 0.01
72 4 0.02
73 82 0.36
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (69 bp):
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTGTCTCTCTTGAGACAGTTTCCCTTG
AAAC
Found at i:56928 original size:15 final size:15
Alignment explanation
Indices: 56908--56962 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
56898 ATCTTGTCTA
56908 CCTTGAGACAGTTTC
1 CCTTGAGACAGTTTC
* *
56923 CCTTGAAACAAATTGTCTC
1 CCTTGAGAC--A--GTTTC
56942 CCTTGAGACAGTTTC
1 CCTTGAGACAGTTTC
56957 CCTTGA
1 CCTTGA
56963 AATAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 18 0.56
17 2 0.06
19 12 0.38
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (15 bp):
CCTTGAGACAGTTTC
Found at i:57091 original size:102 final size:106
Alignment explanation
Indices: 56874--57354 Score: 476
Period size: 106 Copynumber: 4.6 Consensus size: 106
56864 AACATGAACT
* * * *
56874 TTGAGA-ACGTTTCCCTTGAAACGAA-TCTTGTCTAC-CTTGAGACAGTTTCCCTTGAAACAAAT
1 TTGAGACA-GTTTCTCTTGAAACAAAGTTTTGTCT-CTCTTGAGACAGTTTCTCTTGAAACAAAT
* * *
56936 -T-GTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTC
64 ATCG-CTCTC-T-AGACAATTTCCCTTGAAACAAATTTTGTCTCTC
*
56980 TTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-AT
1 TTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATAT
* * *
57044 CG-T-TC-A-ATATTTTTCCCTTGAAACAAAGTTTGTCTCTC
66 CGCTCTCTAGACA-ATTTCCCTTGAAACAAATTTTGTCTCTC
* * *
57082 TTGAGACAGTTTCT-TTTAGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATT
1 TTGAGACAGTTTCTCTTGA-AACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATA
*
57146 TCGTCTCTCTTGAGACAATTTCCCTTAAAACAAATTTTGTCTCTC
65 TCG-CTCTC-T-AGACAATTTCCCTTGAAACAAATTTTGTCTCTC
* * *
57191 TTGAGACAGTTT-TCTTGAAACAAA-TTTTGTCTCTCTTGAAACA-TTTTTCTTGAAACAAATTT
1 TTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATAT
* * * *
57253 TGTCTCTCTTGAGACAGTTTCCCTTGAAACATATTTTGTCTCAC
66 CG-CTCTC-T-AGACAATTTCCCTTGAAACAAATTTTGTCTCTC
* * *
57297 TTGAGACCGTTTCTCTTGAAAC-AA-TTTTGTCTCCCTCT-AGACAATTTCT-TATGAAACA
1 TTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCT-TGAGACAGTTTCTCT-TGAAACA
57355 CCAAACTTTG
Statistics
Matches: 326, Mismatches: 29, Indels: 39
0.83 0.07 0.10
Matches are distributed among these distances:
101 5 0.02
102 81 0.25
103 3 0.01
105 2 0.01
106 111 0.34
107 74 0.23
108 7 0.02
109 41 0.13
110 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (106 bp):
TTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATAT
CGCTCTCTAGACAATTTCCCTTGAAACAAATTTTGTCTCTC
Found at i:57159 original size:36 final size:36
Alignment explanation
Indices: 57055--57354 Score: 378
Period size: 36 Copynumber: 8.4 Consensus size: 36
57045 GTTCAATATT
* *
57055 TTTCCCTTGAAACAAAGTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
57091 TTTCT-TTTAGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGA-AAC-AAATTTTGTCTCTCTTGAGACAG
* *
57128 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
57164 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
57200 TTT-TCTTGAAACAAATTTTGTCTCTCTTGAAACA-
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
57234 TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
57270 TTTCCCTTGAAACATATTTTGTCTCACTTGAGACCG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
57306 TTTCTCTTGAAAC-AATTTTGTCTCCCTCT-AGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCT-TGAGACAG
57341 TTTCT-TATGAAACA
1 TTTCTCT-TGAAACA
57355 CCAAACTTTG
Statistics
Matches: 230, Mismatches: 26, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
34 4 0.02
35 88 0.38
36 106 0.46
37 29 0.13
38 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:57223 original size:71 final size:72
Alignment explanation
Indices: 57055--57354 Score: 367
Period size: 71 Copynumber: 4.2 Consensus size: 72
57045 GTTCAATATT
* * * * * *
57055 TTTCCCTTGAAACAAAGTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAAC-AAATTTTGTCTCTCT
57120 TGAGACAG
65 TGAGACAG
* *
57128 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTAAAACAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTT
57193 GAGACAG
66 GAGACAG
* * *
57200 TTT-TCTTGAAACAAATTTTGTCTCTCTTGAAAC-ATTTTTCTTGAAACAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTT
57263 GAGACAG
66 GAGACAG
* * * ** * *
57270 TTTCCCTTGAAACATATTTTGTCTCACTTGAGACCGTTTCTCTTGAAAC-AATTTTGTCTCCCTC
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCT-
*
57334 T-AGACAA
65 TGAGACAG
57341 TTTCT-TATGAAACA
1 TTTCTCT-TGAAACA
57355 CCAAACTTTG
Statistics
Matches: 201, Mismatches: 22, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
70 38 0.19
71 83 0.41
72 38 0.19
73 42 0.21
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (72 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTT
GAGACAG
Found at i:57283 original size:106 final size:106
Alignment explanation
Indices: 56924--57329 Score: 433
Period size: 102 Copynumber: 3.9 Consensus size: 106
56914 GACAGTTTCC
* * * *
56924 CTTGAAACAAATTGTC-TC-C-CTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGA
1 CTTGAAACAAATT-TCGTCTCTCTTGAGACAATTTCCCTTAAAACAAATTTTGTCTCACTTGAGA
* **
56986 CAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCC
65 CAGTTTCTCTTGAAAC-AA-TTTTGTCTCTCTTGAAACA-TTTTT
* * * * * *
57031 CTTGAAACAAA-ATCG--T-TC---A-ATATTTTTCCCTTGAAACAAAGTTTGTCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCTCTTGAGACA-ATTTCCCTTAAAACAAATTTTGTCTCACTTGAGA
* * *
57088 CAGTTTCT-TTTAGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCT
65 CAGTTTCTCTTGA-AAC-AA-TTTTGTCTCTCTTGAAACA-TTTTT
*
57133 CTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTAAAACAAATTTTGTCTCTCTTGAGAC
1 CTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTAAAACAAATTTTGTCTCACTTGAGAC
57198 AGTTT-TCTTGAAACAAATTTTGTCTCTCTTGAAACATTTTT
66 AGTTTCTCTTGAAAC-AATTTTGTCTCTCTTGAAACATTTTT
* * * *
57239 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACATATTTTGTCTCACTTGAGAC
1 CTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTAAAACAAATTTTGTCTCACTTGAGAC
*
57304 CGTTTCTCTTGAAACAATTTTGTCTC
66 AGTTTCTCTTGAAACAATTTTGTCTC
57330 CCTCTAGACA
Statistics
Matches: 261, Mismatches: 23, Indels: 31
0.83 0.07 0.10
Matches are distributed among these distances:
101 5 0.02
102 81 0.31
103 3 0.01
105 4 0.02
106 81 0.31
107 38 0.15
108 6 0.02
109 41 0.16
110 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (106 bp):
CTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTAAAACAAATTTTGTCTCACTTGAGAC
AGTTTCTCTTGAAACAATTTTGTCTCTCTTGAAACATTTTT
Found at i:57345 original size:35 final size:36
Alignment explanation
Indices: 56688--57041 Score: 311
Period size: 36 Copynumber: 10.1 Consensus size: 36
56678 TTGAAAAATA
* * ** **
56688 AAATTTTGTCTCGCTTGAGACAATTTCAATCAAAAC
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
*
56724 AAA--TTGTCTCTCTTGAGACAGTTGCCCTTGAAAC
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * ** *
56758 AAGTTTTGTCTCCCTTGAGACAATTTTTCTTAAAACC
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-C
* * * * *
56795 AGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * * *
56831 AATTTTTATCTCTTTTGAGATAGTTTCTCTTGAAAC
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
**
56867 --A---TG-AACT-TTGAGA-ACGTTTCCCTTGAAAC
1 AAATTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAAC
* *
56896 GAATCTTGTCTAC-CTTGAGACAGTTTCCCTTGAAAC
1 AAATTTTGTCT-CTCTTGAGACAGTTTCCCTTGAAAC
* *
56932 AAA--TTGTCTCCCTTGAGACAGTTTCCCTTGAAAT
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
*
56966 AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
57002 AAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 AAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
57039 AAA
1 AAA
57042 ATCGTTCAAT
Statistics
Matches: 262, Mismatches: 39, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
28 1 0.00
29 19 0.07
30 2 0.01
31 2 0.01
33 1 0.00
34 59 0.23
36 114 0.44
37 64 0.24
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (36 bp):
AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
Found at i:57487 original size:69 final size:68
Alignment explanation
Indices: 57407--57570 Score: 199
Period size: 69 Copynumber: 2.4 Consensus size: 68
57397 CTTGAGATCA
*
57407 TTTGAGATGTTTCTCTTGAAACAAATACC-ATT-TTCTTTAAGATCGTTTCTCATGAAACAACAA
1 TTTGAGATGTTTCTCTTGAAATAAAT-CCTATTATT-TTTAAGATCGTTTCTCATGAAACAACAA
57470 CCA-AAC
64 --ATAAC
* * * *
57476 TTTGAGATGTTTTTCTTTAGATAAATCCTATTATTTTTTAGATCGTTTCTCATGAAACAACAAAT
1 TTTGAGATGTTTCTCTTGAAATAAATCCTATTATTTTTAAGATCGTTTCTCATGAAACAACAAAT
*
57541 ATC
66 AAC
*
57544 TTTGAGATCGTTTCCCTTGAAATAAAT
1 TTTGAGAT-GTTTCTCTTGAAATAAAT
57571 TTTGTCTCTT
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
67 1 0.01
68 12 0.15
69 66 0.81
70 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.40
Consensus pattern (68 bp):
TTTGAGATGTTTCTCTTGAAATAAATCCTATTATTTTTAAGATCGTTTCTCATGAAACAACAAAT
AAC
Found at i:57709 original size:40 final size:42
Alignment explanation
Indices: 57656--57839 Score: 108
Period size: 40 Copynumber: 4.3 Consensus size: 42
57646 TGGCATGTCG
* * * *
57656 TCCTTATCTCGTAGAAACTGTGTCATCCCTCGACCA-GATC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCACGATCA
* * * * * ** *
57696 TCCTCATCACGTAGGAGCCGTGTTAACCTTAGATAACGAGTCG
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCACGA-TCA
* * * *
57739 TCCTCATCACGTAGGAACTGTGTTATCATCCCTAATGATGGCATG-TCA
1 TCCTCATCACGTAGGAACCGTG---TCATCCCT--CGA--CCACGATCA
*
57787 TCCTCATCACGTAGGAACCATGTCATCCCTCGACCA-GATC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCACGATCA
57827 TCCTCATCACGTA
1 TCCTCATCACGTA
57840 AAAGCCGTAT
Statistics
Matches: 108, Mismatches: 25, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
40 39 0.36
41 6 0.06
42 2 0.02
43 22 0.20
45 8 0.07
46 5 0.05
48 24 0.22
50 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (42 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCACGATCA
Found at i:57905 original size:112 final size:112
Alignment explanation
Indices: 57758--57978 Score: 388
Period size: 112 Copynumber: 2.0 Consensus size: 112
57748 CGTAGGAACT
57758 GTGTTATCATCCCTAATGATGGCATGTCATCCTCATCACGTAGGAACCATGTCATCCCTCGACCA
1 GTGTTATCATCCCTAATGATGGCATGTCATCCTCATCACGTAGGAACCATGTCATCCCTCGACCA
* *
57823 GATCTCCTCATCACGTAAAAGCCGTATCAACCTTAGATAACCAGACC
66 GATCTCCTCATCACGTAAAAGCAGTATCAACCATAGATAACCAGACC
* **
57870 GTGTTATCATCCCTAATGATGGCATGTCGTCCTCATCACGTAGGAACTGTGTCATCCCTCGACCA
1 GTGTTATCATCCCTAATGATGGCATGTCATCCTCATCACGTAGGAACCATGTCATCCCTCGACCA
*
57935 GATCTCCTCATCACGTAAGAGCAGTATCAACCATAGATAACCAG
66 GATCTCCTCATCACGTAAAAGCAGTATCAACCATAGATAACCAG
57979 TCGTCCTCAT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 103 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (112 bp):
GTGTTATCATCCCTAATGATGGCATGTCATCCTCATCACGTAGGAACCATGTCATCCCTCGACCA
GATCTCCTCATCACGTAAAAGCAGTATCAACCATAGATAACCAGACC
Found at i:58321 original size:17 final size:18
Alignment explanation
Indices: 58291--58324 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
58281 TTAAAATAAC
58291 CTACCACTAACCCATTAT
1 CTACCACTAACCCATTAT
58309 CTACCAC-AACCCATTA
1 CTACCACTAACCCATTA
58325 AATAAATCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (18 bp):
CTACCACTAACCCATTAT
Found at i:59143 original size:30 final size:29
Alignment explanation
Indices: 59058--59151 Score: 104
Period size: 29 Copynumber: 3.2 Consensus size: 29
59048 TGAATCTTTG
*
59058 TGTTTTTCTTATTTTGACACTTT-AGTTTC
1 TGTTTTT-TTATTTTGTCACTTTAAGTTTC
* *
59087 TGTTATTTTATTTTAGTCAC-TGAAGTTTC
1 TGTTTTTTTATTTT-GTCACTTTAAGTTTC
59116 TGTTTTTGTTATTTATGTC-CTTTAAGTTTC
1 TGTTTTT-TTATTT-TGTCACTTTAAGTTTC
59146 TGTTTT
1 TGTTTT
59152 AGCTCTTTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
28 8 0.15
29 23 0.42
30 23 0.42
31 1 0.02
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.62
Consensus pattern (29 bp):
TGTTTTTTTATTTTGTCACTTTAAGTTTC
Found at i:62589 original size:19 final size:19
Alignment explanation
Indices: 62547--62588 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
62537 TAATCAGAAC
*
62547 AAAAGGAGAAAATAAGCAA
1 AAAAGGAGAAAAAAAGCAA
*
62566 AAAAGAGAGAAAAAAAGGAA
1 AAAAG-GAGAAAAAAAGCAA
62586 AAA
1 AAA
62589 GTGAGGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (19 bp):
AAAAGGAGAAAAAAAGCAA
Found at i:63412 original size:32 final size:32
Alignment explanation
Indices: 63371--63458 Score: 131
Period size: 32 Copynumber: 2.8 Consensus size: 32
63361 AAGCAATAGA
* *
63371 GGGCATCTTTGAAGATTTAACATCAAATGTTG
1 GGGCATCTTTGAAGATTCAACATCAAATATTG
*
63403 GGGCATCTTTGGAGATTCAACATCAAATATTG
1 GGGCATCTTTGAAGATTCAACATCAAATATTG
**
63435 GGGCATCTTTGGGGATTCAACATC
1 GGGCATCTTTGAAGATTCAACATC
63459 CTGATGTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (32 bp):
GGGCATCTTTGAAGATTCAACATCAAATATTG
Found at i:64244 original size:21 final size:21
Alignment explanation
Indices: 64196--64281 Score: 76
Period size: 21 Copynumber: 4.4 Consensus size: 21
64186 TGAGAACTTT
* * *
64196 TCCCTTAAAACGAATTGTGTC
1 TCCCTTGAAACAAATTTTGTC
64217 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* *
64238 TCCCTTGAGAC--A----GTT
1 TCCCTTGAAACAAATTTTGTC
64253 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
64274 TCTCTTGA
1 TCCCTTGA
64282 GACAGTTTCT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
15 12 0.24
17 1 0.02
19 1 0.02
21 37 0.73
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:64317 original size:37 final size:36
Alignment explanation
Indices: 64217--64339 Score: 219
Period size: 36 Copynumber: 3.4 Consensus size: 36
64207 GAATTGTGTC
*
64217 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
1 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
64253 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
1 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
*
64289 TCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTT
1 TCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTT
64326 TCCCTTGAAACAAA
1 TCCCTTGAAACAAA
64340 ATCGTTGAAT
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
36 48 0.58
37 35 0.42
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (36 bp):
TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
Found at i:64367 original size:102 final size:104
Alignment explanation
Indices: 64241--64546 Score: 388
Period size: 102 Copynumber: 2.9 Consensus size: 104
64231 TTTTGTCTCC
* * *
64241 CTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTT
1 CTTGAGATAATTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTT
*
64306 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-ATCG
66 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATATCG
* * * * * * *
64344 -TTGA-ATATGTTTCTATTGAAACAAAGTTTGTCTCTCTTGAGATAGTTTCTTTTGGAACTAAGT
1 CTTGAGATA-ATTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGT
*
64407 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCG
65 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATATCG
* *
64447 TCTCTCTTGAGATAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-TTTTTCTTGAAACA
1 -----CTTGAGATAATTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
*
64511 AA-TTTTGTCTCTCTTGAGACATTTTCTCTTGAAACA
61 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
64547 TATTTTGTCT
Statistics
Matches: 174, Mismatches: 20, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
101 2 0.01
102 86 0.49
103 3 0.02
107 33 0.19
108 12 0.07
109 35 0.20
110 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (104 bp):
CTTGAGATAATTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTT
TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATATCG
Found at i:64407 original size:36 final size:36
Alignment explanation
Indices: 64352--64593 Score: 333
Period size: 36 Copynumber: 6.7 Consensus size: 36
64342 CGTTGAATAT
* * *
64352 GTTTCTATTGAAACAAAGTTTGTCTCTCTTGAGATA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
64388 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
* *
64425 GTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGATA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
64461 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
64497 -TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * * *
64532 TTTTCTCTTGAAACATATTTTGTCTCACTTGAGACC
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
64568 GTTTCTCTTGAAACAAATTTTGTCTC
1 GTTTCTCTTGAAACAAATTTTGTCTC
64594 CCTCGAGATG
Statistics
Matches: 182, Mismatches: 22, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
35 33 0.18
36 118 0.65
37 31 0.17
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:64515 original size:71 final size:71
Alignment explanation
Indices: 64353--64602 Score: 329
Period size: 71 Copynumber: 3.5 Consensus size: 71
64343 GTTGAATATG
* * * * * *
64353 TTTCTATTGAAACAAAGTTTGTCTCTCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAATTTCTCTTGAAAC-AAATTTTGTCTCTCT
64418 TGAGACA
65 TGAGACA
* *
64425 GTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAACAAATTTTGTCTCTCT
1 -TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAATTTCTCTTGAAACAAATTTTGTCTCTCT
64490 TGAGACA
65 TGAGACA
* * * * *
64497 TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTGAAACATATTTTGTCTCACTT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAATTTCTCTTGAAACAAATTTTGTCTCTCTT
*
64562 GAGACCG
66 GAGA-CA
* *
64569 TTTCTCTTGAAACAAATTTTGTCTCCCTCGAGAT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAT
64603 GGTTTCTTAT
Statistics
Matches: 156, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
71 62 0.40
72 52 0.33
73 42 0.27
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (71 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAATTTCTCTTGAAACAAATTTTGTCTCTCTT
GAGACA
Found at i:64562 original size:21 final size:19
Alignment explanation
Indices: 64466--64563 Score: 61
Period size: 21 Copynumber: 5.3 Consensus size: 19
64456 AGATAATTTC
64466 CCTTGAAACAAATTTTGTCT
1 CCTTGAAAC-AATTTTGTCT
*
64486 CTCTTGAGAC-A-TTT-T-T
1 C-CTTGAAACAATTTTGTCT
64502 -CTTGAAACAAATTTTGTCT
1 CCTTGAAAC-AATTTTGTCT
*
64521 CTCTTGAGAC-A-TTT-TCT
1 C-CTTGAAACAATTTTGTCT
64538 -CTTGAAACATATTTTGTCT
1 CCTTGAAACA-ATTTTGTCT
64557 CACTTGA
1 C-CTTGA
64564 GACCGTTTCT
Statistics
Matches: 60, Mismatches: 4, Indels: 27
0.66 0.04 0.30
Matches are distributed among these distances:
14 7 0.12
15 7 0.12
16 2 0.03
17 8 0.13
18 10 0.17
19 6 0.10
20 1 0.02
21 19 0.32
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (19 bp):
CCTTGAAACAATTTTGTCT
Found at i:64714 original size:45 final size:46
Alignment explanation
Indices: 64625--64714 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 46
64615 AACACCAAAC
* * * *
64625 TTTGAGATTGTTTCCTTTGAAACAAGTTTTAGTTTCCTTGAGATCA
1 TTTGAGATTGTTTCCTTTGAAACAAATCTCAGTTTCCTTAAGATCA
* *
64671 TTTGAGA-TGTTT-CTCTTGAAACAAATCTCATTTTCTTTAAGATC
1 TTTGAGATTGTTTCCT-TTGAAACAAATCTCAGTTTCCTTAAGATC
64715 GTTTCTCATG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
44 2 0.05
45 28 0.76
46 7 0.19
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (46 bp):
TTTGAGATTGTTTCCTTTGAAACAAATCTCAGTTTCCTTAAGATCA
Found at i:64756 original size:70 final size:67
Alignment explanation
Indices: 64674--64834 Score: 184
Period size: 70 Copynumber: 2.3 Consensus size: 67
64664 GAGATCATTT
64674 GAGATGTTTCTCTTGAAACAAAT-CTCATT-TTCTTTAAGATCGTTTCTCATGAAA-AAAACAAC
1 GAGATGTTTCTCTTGAAACAAATCCT-ATTATT-TTT-AGATCGTTTCTCATGAAACAAAA-AA-
64736 CAAACTTA
61 -AAACTTA
* * * *
64744 GAGATGTTTCTCTTGAGATAAATCCTATTATTTTTAGATCGTTTCTCATGAAACAAAAAATATCT
1 GAGATGTTTCTCTTGAAACAAATCCTATTATTTTTAGATCGTTTCTCATGAAACAAAAAAAAACT
*
64809 TT
66 TA
*
64811 GAGATCGTTTCCCTTGAAACAAAT
1 GAGAT-GTTTCTCTTGAAACAAAT
64835 TTTGTCTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
67 9 0.11
68 15 0.19
69 20 0.25
70 31 0.39
71 4 0.05
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (67 bp):
GAGATGTTTCTCTTGAAACAAATCCTATTATTTTTAGATCGTTTCTCATGAAACAAAAAAAAACT
TA
Found at i:65013 original size:43 final size:43
Alignment explanation
Indices: 64953--65097 Score: 131
Period size: 43 Copynumber: 3.4 Consensus size: 43
64943 TCATCCCTCG
64953 ACCAGATCTCCTCATCACGTAAGAGCCGTGTCAACCTTAGATA
1 ACCAGATCTCCTCATCACGTAAGAGCCGTGTCAACCTTAGATA
*** * * *
64996 ACCAG-TCGTCCTCATCACGT-AGAAATTGTGTCATCCCTCG---
1 ACCAGATC-TCCTCATCACGTAAG-AGCCGTGTCAACCTTAGATA
* * *
65036 ACCAGATCTCCTCATCGCATAGGAGCCGTGTCAACCTTAGATA
1 ACCAGATCTCCTCATCACGTAAGAGCCGTGTCAACCTTAGATA
*
65079 ATCAG-TCATCCTCATCACG
1 ACCAGATC-TCCTCATCACG
65098 CAGGAATCGT
Statistics
Matches: 76, Mismatches: 18, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
40 26 0.34
41 3 0.04
42 6 0.08
43 41 0.54
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (43 bp):
ACCAGATCTCCTCATCACGTAAGAGCCGTGTCAACCTTAGATA
Found at i:65062 original size:83 final size:83
Alignment explanation
Indices: 64918--65097 Score: 297
Period size: 83 Copynumber: 2.2 Consensus size: 83
64908 AGATGGCTTA
* *
64918 TCATCCTCATCACGTAGGAACTGTGTCATCCCTCGACCAGATCTCCTCATCACGTAAGAGCCGTG
1 TCATCCTCATCACGTAGAAACTGTGTCATCCCTCGACCAGATCTCCTCATCACATAAGAGCCGTG
64983 TCAACCTTAGATAACCAG
66 TCAACCTTAGATAACCAG
* * * *
65001 TCGTCCTCATCACGTAGAAATTGTGTCATCCCTCGACCAGATCTCCTCATCGCATAGGAGCCGTG
1 TCATCCTCATCACGTAGAAACTGTGTCATCCCTCGACCAGATCTCCTCATCACATAAGAGCCGTG
*
65066 TCAACCTTAGATAATCAG
66 TCAACCTTAGATAACCAG
65084 TCATCCTCATCACG
1 TCATCCTCATCACG
65098 CAGGAATCGT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 89 1.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (83 bp):
TCATCCTCATCACGTAGAAACTGTGTCATCCCTCGACCAGATCTCCTCATCACATAAGAGCCGTG
TCAACCTTAGATAACCAG
Found at i:65109 original size:43 final size:42
Alignment explanation
Indices: 64921--65233 Score: 160
Period size: 40 Copynumber: 7.4 Consensus size: 42
64911 TGGCTTATCA
* * * *
64921 TCCTCATCACGTAGGAACTGTGTCATCCCTCG---ACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAG-TC
* *
64961 TCCTCATCACGTAAGAGCCGTGTCAACCTTAGATAACCAGTC
1 TCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAGTC
* ** * * *
65003 GTCCTCATCACGTAGAAATTGTGTCATCCCTCG---ACCAGATC
1 -TCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAG-TC
* * * *
65044 TCCTCATCGCATAGGAGCCGTGTCAACCTTAGATAATCAGTC
1 TCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAGTC
* * * * ***
65086 ATCCTCATCACGCAGGAATCGTGTTATCATCCCTA-ATAATGGTTGTC
1 -TCCTCATCACGTAGGAACCGTG---TCAACCTTAGATAA--CCAGTC
* * *
65133 GTCCTCATCACGTAGGAACCGTGTCATCCCTCG---ACCAGATC
1 -TCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAG-TC
* * * * **
65174 TCCTCATCACGTAGGAGCAGTGTCAACTTTAGATAATCAACC
1 TCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAGTC
65216 TTCCTCATCACGTAGGAA
1 -TCCTCATCACGTAGGAA
65234 TTGTGTTATC
Statistics
Matches: 202, Mismatches: 51, Indels: 37
0.70 0.18 0.13
Matches are distributed among these distances:
40 81 0.40
41 4 0.02
42 6 0.03
43 69 0.34
44 8 0.04
45 4 0.02
46 7 0.03
47 23 0.11
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (42 bp):
TCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAGTC
Found at i:65157 original size:130 final size:130
Alignment explanation
Indices: 65000--65247 Score: 388
Period size: 130 Copynumber: 1.9 Consensus size: 130
64990 TAGATAACCA
** * *
65000 GTCGTCCTCATCACGTAGAAATTGTGTCATCCCTCGACCAGATCTCCTCATCGCATAGGAGCCGT
1 GTCGTCCTCATCACGTAGAAACCGTGTCATCCCTCGACCAGATCTCCTCATCACATAGGAGCAGT
**
65065 GTCAACCTTAGATAATCAGTCATCCTCATCACGCAGGAATCGTGTTATCATCCCTAATAATGGTT
66 GTCAACCTTAGATAATCAACCATCCTCATCACGCAGGAATCGTGTTATCATCCCTAATAATGGTT
* *
65130 GTCGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCTCCTCATCACGTAGGAGCAGT
1 GTCGTCCTCATCACGTAGAAACCGTGTCATCCCTCGACCAGATCTCCTCATCACATAGGAGCAGT
* * * *
65195 GTCAACTTTAGATAATCAACCTTCCTCATCACGTAGGAATTGTGTTATCATCC
66 GTCAACCTTAGATAATCAACCATCCTCATCACGCAGGAATCGTGTTATCATCC
65248 TTAGACGATC
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 106 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (130 bp):
GTCGTCCTCATCACGTAGAAACCGTGTCATCCCTCGACCAGATCTCCTCATCACATAGGAGCAGT
GTCAACCTTAGATAATCAACCATCCTCATCACGCAGGAATCGTGTTATCATCCCTAATAATGGTT
Found at i:65187 original size:40 final size:41
Alignment explanation
Indices: 64921--65198 Score: 172
Period size: 40 Copynumber: 6.6 Consensus size: 41
64911 TGGCTTATCA
*
64921 TCCTCATCACGTAGGAACTGTGTCATCCCTCGACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCG
* * * * *
64961 TCCTCATCACGTAAGAGCCGTGTCAACCTTAGATAACCAG-TCG
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCG---ACCAGATCG
* **
65004 TCCTCATCACGTAGAAATTGTGTCATCCCTCGACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCG
* * * * * * * *
65044 TCCTCATCGCATAGGAGCCGTGTCAACCTTAGATAATCAG-TCA
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCG---ACCAGATCG
* * * ** *
65087 TCCTCATCACGCAGGAATCGTGTTATCATCCCT-AATAATGGTTGTCG
1 TCCTCATCACGTAGGAACCGTG---TCATCCCTCGACCA--G--ATCG
65134 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCG
* *
65174 TCCTCATCACGTAGGAGCAGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
65199 ACTTTAGATA
Statistics
Matches: 178, Mismatches: 42, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
40 77 0.43
41 4 0.02
42 7 0.04
43 51 0.29
44 9 0.05
45 2 0.01
46 6 0.03
47 22 0.12
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (41 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCG
Found at i:66955 original size:7 final size:7
Alignment explanation
Indices: 66943--66968 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
66933 AAAATTTAAT
66943 AAATTCA
1 AAATTCA
66950 AAATTCA
1 AAATTCA
66957 AAATTCA
1 AAATTCA
66964 AAATT
1 AAATT
66969 TAATGTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATTCA
Found at i:71376 original size:2 final size:2
Alignment explanation
Indices: 71371--71406 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
71361 AAAATTCAAA
71371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71407 TTAAAAACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72195 original size:8 final size:8
Alignment explanation
Indices: 72179--72274 Score: 67
Period size: 7 Copynumber: 11.9 Consensus size: 8
72169 CAGAAAAGAT
72179 AAAGAAAA
1 AAAGAAAA
72187 AAAGGAAAA
1 AAA-GAAAA
72196 GAGAAG-AAA
1 -A-AAGAAAA
*
72205 AAAG-ATA
1 AAAGAAAA
*
72212 AAA-AAAT
1 AAAGAAAA
72219 AAAGAAAA
1 AAAGAAAA
72227 AAGAGAGAAA
1 AA-AGA-AAA
*
72237 AAA-ACAA
1 AAAGAAAA
72244 AAAGAAAA
1 AAAGAAAA
*
72252 AGAG-AAA
1 AAAGAAAA
72259 AAAGAAAA
1 AAAGAAAA
72267 AGAAGAAA
1 A-AAGAAA
72275 GAGAACAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
7 23 0.33
8 20 0.29
9 18 0.26
10 7 0.10
11 2 0.03
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAGAAAA
Found at i:72196 original size:20 final size:21
Alignment explanation
Indices: 72171--72237 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 21
72161 TTCATATTCA
72171 GAAAAGATAAAGAAAAAA-AG
1 GAAAAGATAAAGAAAAAAGAG
* *
72191 GAAAAGA-GAAGAAAAAAGAT
1 GAAAAGATAAAGAAAAAAGAG
* *
72211 AAAAAAATAAAGAAAAAAGAG
1 GAAAAGATAAAGAAAAAAGAG
72232 AGAAAA
1 -GAAAA
72238 AAACAAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 9 0.24
20 13 0.35
21 11 0.30
22 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (21 bp):
GAAAAGATAAAGAAAAAAGAG
Found at i:72209 original size:32 final size:31
Alignment explanation
Indices: 72172--72272 Score: 109
Period size: 31 Copynumber: 3.2 Consensus size: 31
72162 TCATATTCAG
*
72172 AAAAGATAAAGAAAAAAAGGAAAAGAGAAGAA
1 AAAAGATAAA-AAAAAAAGGAAAAAAGAAGAA
72204 AAAAGATAAAAAAATAAA-GAAAAAAGAGAGAA
1 AAAAGATAAAAAAA-AAAGGAAAAAAGA-AGAA
*
72236 AAAA-ACAAAAAGAAAAAGAGAAAAAAGAA-AA
1 AAAAGATAAAAA-AAAAAG-GAAAAAAGAAGAA
*
72267 AGAAGA
1 AAAAGA
72273 AAGAGAACAA
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
31 26 0.43
32 25 0.42
33 9 0.15
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (31 bp):
AAAAGATAAAAAAAAAAGGAAAAAAGAAGAA
Found at i:72227 original size:11 final size:10
Alignment explanation
Indices: 72179--72267 Score: 51
Period size: 10 Copynumber: 8.9 Consensus size: 10
72169 CAGAAAAGAT
72179 AAAG-AAAAA
1 AAAGAAAAAA
* *
72188 AAGGAAAAGA
1 AAAGAAAAAA
*
72198 GAAGAAAAAA
1 AAAGAAAAAA
*
72208 GATAA-AAAAAT
1 -A-AAGAAAAAA
72219 AAAGAAAAAA
1 AAAGAAAAAA
*
72229 GAGAGAAAAAA
1 -AAAGAAAAAA
*
72240 ACAA-AAAGAA
1 A-AAGAAAAAA
*
72250 AAAG-AGAAA
1 AAAGAAAAAA
72259 AAAGAAAAA
1 AAAGAAAAA
72268 GAAGAAAGAG
Statistics
Matches: 58, Mismatches: 14, Indels: 15
0.67 0.16 0.17
Matches are distributed among these distances:
9 14 0.24
10 27 0.47
11 15 0.26
12 2 0.03
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.02
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:72227 original size:22 final size:22
Alignment explanation
Indices: 72202--72279 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
72192 AAAAGAGAAG
* *
72202 AAAAAAGATAAAAAAATAAAGA
1 AAAAAAGAGAAAAAAAAAAAGA
72224 AAAAAGAGAGAAAAAAACAAAA-A
1 AAAAA-AGAGAAAAAAA-AAAAGA
*
72247 GAAAAAGAGAAAAAAGAAAAAG-
1 AAAAAAGAGAAAAAA-AAAAAGA
*
72269 AAGAAAGAGAA
1 AAAAAAGAGAA
72280 CAAATCAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
22 28 0.60
23 16 0.34
24 3 0.06
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (22 bp):
AAAAAAGAGAAAAAAAAAAAGA
Found at i:72237 original size:10 final size:11
Alignment explanation
Indices: 72181--72263 Score: 59
Period size: 11 Copynumber: 7.9 Consensus size: 11
72171 GAAAAGATAA
72181 AGAAAAAA-AG
1 AGAAAAAAGAG
*
72191 -GAAAAGAGA-
1 AGAAAAAAGAG
*
72200 AGAAAAAAGAT
1 AGAAAAAAGAG
* *
72211 A-AAAAAATAA
1 AGAAAAAAGAG
72221 AGAAAAAAGAG
1 AGAAAAAAGAG
*
72232 AGAAAAAA-AC
1 AGAAAAAAGAG
* *
72242 AAAAAGAAAAAG
1 AGAAA-AAAGAG
72254 AGAAAAAAGA
1 AGAAAAAAGA
72264 AAAAGAAGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
9 6 0.11
10 22 0.39
11 23 0.41
12 5 0.09
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.02
Consensus pattern (11 bp):
AGAAAAAAGAG
Found at i:72238 original size:24 final size:22
Alignment explanation
Indices: 72199--72279 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
72189 AGGAAAAGAG
* *
72199 AAGAAAAAAGA-TAAAAAAATA
1 AAGAAAAAAGAGAAAAAAAAAA
72220 AAGAAAAAAGAGAGAAAAAAACAA
1 AAGAAAAAAGAGA-AAAAAAA-AA
*
72244 AA-AGAAAAAGAGAAAAAAGAAA
1 AAGA-AAAAAGAGAAAAAAAAAA
*
72266 AAGAAGAAAGAGAA
1 AAGAAAAAAGAGAA
72280 CAAATCAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
21 11 0.22
22 13 0.25
23 15 0.29
24 12 0.24
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.02
Consensus pattern (22 bp):
AAGAAAAAAGAGAAAAAAAAAA
Found at i:72239 original size:33 final size:32
Alignment explanation
Indices: 72172--72272 Score: 104
Period size: 32 Copynumber: 3.2 Consensus size: 32
72162 TCATATTCAG
*
72172 AAAAGATAAAGAAAAAAAG-GAAAAGAGAAGAA
1 AAAAGATAAA-AAAAAAAGAAAAAAGAGAAGAA
72204 AAAAGATAAAAAAATAAAGAAAAAAGAG-AGAA
1 AAAAGATAAAAAAA-AAAGAAAAAAGAGAAGAA
*
72236 AAAA-ACAAAAAGAAAAAGAGAAAAA-AGAA-AA
1 AAAAGATAAAAA-AAAAAGA-AAAAAGAGAAGAA
*
72267 AGAAGA
1 AAAAGA
72273 AAGAGAACAA
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
31 22 0.37
32 31 0.52
33 7 0.12
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (32 bp):
AAAAGATAAAAAAAAAAGAAAAAAGAGAAGAA
Found at i:72246 original size:40 final size:39
Alignment explanation
Indices: 72172--72283 Score: 99
Period size: 40 Copynumber: 2.8 Consensus size: 39
72162 TCATATTCAG
* *
72172 AAAAGATAAAGAAAAAA-AG-GAAAAGAGAAGAAAAAAGATA
1 AAAAAATAAAGAAAAAAGAGAGAAAA-A-AACAAAAAAGA-A
72212 AAAAAATAAAGAAAAAAGAGAGAAAAAAAC-AAAAAGAA
1 AAAAAATAAAGAAAAAAGAGAGAAAAAAACAAAAAAGAA
* *
72250 AAAGAGAAAAAAG-AAAAAGA-AGAAAGAGAACAAA
1 AAA-A-AATAAAGAAAAAAGAGAGAAA-AAAACAAA
72284 TCAAATACTT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
38 9 0.15
39 19 0.31
40 26 0.42
41 3 0.05
42 5 0.08
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.03
Consensus pattern (39 bp):
AAAAAATAAAGAAAAAAGAGAGAAAAAAACAAAAAAGAA
Found at i:72261 original size:21 final size:21
Alignment explanation
Indices: 72199--72288 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 21
72189 AGGAAAAGAG
72199 AAGAAAAA-AGATAAAAA-AATA
1 AAGAAAAAGAGA-AAAAACAA-A
72220 AAGAAAAAAGAGAGAAAAAAACAAA
1 AAG--AAAA-AGAG-AAAAAACAAA
*
72245 AAGAAAAAGAGAAAAAAGAAA
1 AAGAAAAAGAGAAAAAACAAA
*
72266 AAGAAGAAAGAGAACAAATCAAA
1 AAGAA-AAAGAGAA-AAAACAAA
72289 TACTTCAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
21 17 0.29
22 12 0.21
23 14 0.24
24 1 0.02
25 11 0.19
26 3 0.05
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (21 bp):
AAGAAAAAGAGAAAAAACAAA
Found at i:74453 original size:41 final size:43
Alignment explanation
Indices: 74352--74463 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 43
74342 CCAAAATTAG
* * * *
74352 TAAGTCCTTCGGGCCATC-AGTAAGCCTTTCGAGTATGATGAT
1 TAAGTCTTTCGGGCCATCTAGTAAGCCTTTAGAGCAAGATGAT
* * * *
74394 TAAATCTTTCGGGTCATCTA-TCAGTCTTTAGAGCAAGATGA-
1 TAAGTCTTTCGGGCCATCTAGTAAGCCTTTAGAGCAAGATGAT
74435 TAAGTCTTTCGGGCCATCT-GTAAGACCTT
1 TAAGTCTTTCGGGCCATCTAGTAAG-CCTT
74464 CAGGCATGAT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
41 20 0.36
42 34 0.62
43 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (43 bp):
TAAGTCTTTCGGGCCATCTAGTAAGCCTTTAGAGCAAGATGAT
Found at i:74786 original size:150 final size:152
Alignment explanation
Indices: 74485--74757 Score: 401
Period size: 150 Copynumber: 1.8 Consensus size: 152
74475 TTTTCACATG
* ** *
74485 ATTTTCGAGAAAATGAGAAGGCGATTTCCAAAGCTTCTCATTTAATGTTTTCAGAAAATAAAATT
1 ATTTTCGAGAAAATGAGAAAGCGATTTCCAAAGCTTCTCATTTAAAATTTTCAGAAAATAAAATC
* *
74550 TTTGAAAAGTAAAAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATCTATAAG
66 TTTGAAAAGTAAAAAAGCGATTTCCAAAGTTTCTTAACTAGTAAACTATTTCCAAAATCTATAAG
74615 AACTTCAGACCATCAGTAAGTC
131 AACTTCAGACCATCAGTAAGTC
* * * *
74637 ATTTT-GA-AAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATTTTTAGAAAATGAAATC
1 ATTTTCGAGAAAATGAGAAAGCGATTTCCAAAGCTTCTCATTTAAAATTTTCAGAAAATAAAATC
*
74700 TTTGAAAAGTAAGAAAA-CGATTTCCAAAGTTT-TTAAACTAGTCAACTATTTCCAAAAT
66 TTTGAAAAGTAA-AAAAGCGATTTCCAAAGTTTCTT-AACTAGTAAACTATTTCCAAAAT
74758 TGGTAAGTCA
Statistics
Matches: 108, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
149 2 0.02
150 95 0.88
151 6 0.06
152 5 0.05
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (152 bp):
ATTTTCGAGAAAATGAGAAAGCGATTTCCAAAGCTTCTCATTTAAAATTTTCAGAAAATAAAATC
TTTGAAAAGTAAAAAAGCGATTTCCAAAGTTTCTTAACTAGTAAACTATTTCCAAAATCTATAAG
AACTTCAGACCATCAGTAAGTC
Found at i:74844 original size:20 final size:20
Alignment explanation
Indices: 74783--74845 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
74773 ACCATCAGTA
*
74783 AGTCTTTCGAGCATGATGATT
1 AGTCTTTCGAGCAAGATG-TT
* * *
74804 AAATCTTTCGGATCAA-CTGTT
1 -AGTCTTTC-GAGCAAGATGTT
74825 AGTCTTTCGAGCAAGATGTT
1 AGTCTTTCGAGCAAGATGTT
74845 A
1 A
74846 AGTTCTTCAG
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 5 0.16
20 12 0.38
21 2 0.06
22 9 0.28
23 4 0.12
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTCTTTCGAGCAAGATGTT
Found at i:78327 original size:20 final size:20
Alignment explanation
Indices: 78277--78327 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
78267 GAATTTATAT
78277 AAATTTAAAAAACATAAACG
1 AAATTTAAAAAACATAAACG
*
78297 AAATGTTAAAAACCATATAA-G
1 AAAT-TTAAAAAACATA-AACG
78318 -AATTTAAAAA
1 AAATTTAAAAA
78328 TTTTAAATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 7 0.25
20 7 0.25
21 12 0.43
22 2 0.07
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.24
Consensus pattern (20 bp):
AAATTTAAAAAACATAAACG
Found at i:80887 original size:75 final size:78
Alignment explanation
Indices: 80714--80912 Score: 266
Period size: 76 Copynumber: 2.6 Consensus size: 78
80704 AATTATGGAT
* * **
80714 TGCTCAGAGGGAACTGATTCCCCCCCATAGGAGGAACCGATT--CCCCTAAATGGTTTTGGCCCC
1 TGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCC
*
80777 GAGATTTCCAGAA
66 GAGAATTCCAGAA
*
80790 TGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTT-GCTCC
1 TGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCC
*
80853 GAGAATTCCAGTA
66 GAGAATTCCAGAA
* * *
80866 TGCTCGGAGGGAACCGA-TCCCCCCCAAAGG-GGTACTGATTCCCCCCT
1 TGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCT
80913 TGTACAACGG
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
75 38 0.35
76 59 0.54
77 13 0.12
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (78 bp):
TGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCC
GAGAATTCCAGAA
Found at i:88701 original size:17 final size:17
Alignment explanation
Indices: 88679--88726 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
88669 TTTCAACATT
88679 TTTGATATTTTGGATTG
1 TTTGATATTTTGGATTG
88696 TTTGAT-TTTGTGGATTG
1 TTTGATATTT-TGGATTG
*
88713 -TTG-GATTTTGGATT
1 TTTGATATTTTGGATT
88727 TATGAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
TTTGATATTTTGGATTG
Found at i:88993 original size:29 final size:29
Alignment explanation
Indices: 88960--89029 Score: 106
Period size: 29 Copynumber: 2.3 Consensus size: 29
88950 GGAGAAGAAT
88960 AGGTGTTAAATG-TTTACATAATAAATTGA
1 AGGTGTTAAATGTTTTACATAAT-AATTGA
88989 AGGTGTTAAATGTTTTACATAATAATTGA
1 AGGTGTTAAATGTTTTACATAATAATTGA
89018 AGAAGTGTTAAA
1 AG--GTGTTAAA
89030 GTAAGGGGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 20 0.53
30 10 0.26
31 8 0.21
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.37
Consensus pattern (29 bp):
AGGTGTTAAATGTTTTACATAATAATTGA
Found at i:89520 original size:75 final size:77
Alignment explanation
Indices: 89354--89545 Score: 266
Period size: 75 Copynumber: 2.5 Consensus size: 77
89344 AGATTGCTTA
** * *
89354 GAGGGAACCGATTCCCCCCATAGGAGGAACCGATT--CCCCTAAATGGTTTTGGCCCCGAGATTT
1 GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGACCCCGAGAATT
89417 CCAGAATGCTCG
66 CCAGAATGCTCG
* *
89429 GAGGGAACCGATTCCCCCTATAGGAGGAACCGATTCCCCCCTAAACAGTTTT-ACTCCGAGAATT
1 GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGACCCCGAGAATT
*
89493 CCAGTATGCTCG
66 CCAGAATGCTCG
* * *
89505 GAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
89546 TGTACAACGG
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
75 53 0.51
76 38 0.37
77 13 0.12
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (77 bp):
GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGACCCCGAGAATT
CCAGAATGCTCG
Found at i:94456 original size:7 final size:7
Alignment explanation
Indices: 94444--94476 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
94434 AATATGAACA
94444 TGCTTCG
1 TGCTTCG
94451 TGCTTCG
1 TGCTTCG
94458 TGCTTCG
1 TGCTTCG
94465 TGCTTCG
1 TGCTTCG
94472 TGCTT
1 TGCTT
94477 ACGCTCGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.27, G:0.27, T:0.45
Consensus pattern (7 bp):
TGCTTCG
Found at i:98704 original size:20 final size:21
Alignment explanation
Indices: 98661--98705 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
98651 TTAGTTCTTA
*
98661 AATTTTTAAAATTTATAATAT
1 AATTATTAAAATTTATAATAT
*
98682 AATTATTAAAATTT-TAATTT
1 AATTATTAAAATTTATAATAT
98702 AATT
1 AATT
98706 TAATTGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTATTAAAATTTATAATAT
Found at i:99466 original size:9 final size:9
Alignment explanation
Indices: 99452--99493 Score: 84
Period size: 9 Copynumber: 4.7 Consensus size: 9
99442 TTCTCTACTT
99452 ATTTTCTTC
1 ATTTTCTTC
99461 ATTTTCTTC
1 ATTTTCTTC
99470 ATTTTCTTC
1 ATTTTCTTC
99479 ATTTTCTTC
1 ATTTTCTTC
99488 ATTTTC
1 ATTTTC
99494 CTTTCTTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTTCTTC
Found at i:103951 original size:17 final size:16
Alignment explanation
Indices: 103929--103960 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
103919 TAATATACAT
103929 TATATACTTTATATAAG
1 TATATAC-TTATATAAG
103946 TATATACTTATATAA
1 TATATACTTATATAA
103961 AATATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
TATATACTTATATAAG
Found at i:103966 original size:17 final size:17
Alignment explanation
Indices: 103929--103968 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
103919 TAATATACAT
*
103929 TATATACTTTATATAAG
1 TATATACTTTATATAAA
103946 TATATAC-TTATATAAAA
1 TATATACTTTATAT-AAA
103963 TATATA
1 TATATA
103969 ATGTATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
TATATACTTTATATAAA
Found at i:104035 original size:13 final size:13
Alignment explanation
Indices: 104017--104042 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
104007 GTATATACTT
104017 ATATAAGTATATA
1 ATATAAGTATATA
104030 ATATAAGTATATA
1 ATATAAGTATATA
104043 TAAGTATAAA
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
ATATAAGTATATA
Found at i:104055 original size:17 final size:15
Alignment explanation
Indices: 104002--104051 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
103992 ATGCATTCAT
* *
104002 TATATGTATATACTTA
1 TATAAGTATATA-TAA
104018 TATAAG--TATATAA
1 TATAAGTATATATAA
104031 TATAAGTATATATAA
1 TATAAGTATATATAA
104046 GTATAA
1 -TATAA
104052 AGTACAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 8 0.28
14 4 0.14
15 7 0.24
16 10 0.34
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (15 bp):
TATAAGTATATATAA
Found at i:104739 original size:15 final size:14
Alignment explanation
Indices: 104709--104748 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
104699 TTAATTTAAT
104709 GATTATAAT-T-AA
1 GATTATAATATAAA
104721 GATTTATAATATAAA
1 GA-TTATAATATAAA
104736 GATTATAA-ATAAA
1 GATTATAATATAAA
104749 AAGTAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 12 0.48
14 7 0.28
15 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
GATTATAATATAAA
Found at i:104900 original size:16 final size:16
Alignment explanation
Indices: 104876--104925 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
104866 AACTTGTAAC
*
104876 TCAGGTAAATATCAAG
1 TCAGTTAAATATCAAG
104892 TCAGTTAAATATCATA-
1 TCAGTTAAATATCA-AG
* *
104908 TCAGTTCAATAACAAG
1 TCAGTTAAATATCAAG
104924 TC
1 TC
104926 GAATCATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (16 bp):
TCAGTTAAATATCAAG
Found at i:110027 original size:22 final size:22
Alignment explanation
Indices: 109999--110119 Score: 163
Period size: 22 Copynumber: 5.5 Consensus size: 22
109989 TTCAATATTT
*
109999 GTCCTGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
* * *
110021 GTCCTGAAAGACCACTGGATTC
1 GTCCCGAAGGACCACTGGATAC
* *
110043 GTCCCGAATGACTACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
110065 GTCCCGAAGGACTACTGGATA-
1 GTCCCGAAGGACCACTGGATAC
*
110086 GTCCCGAATGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
110108 GTCCCGAAGGAC
1 GTCCCGAAGGAC
110120 TAATATACCC
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
21 19 0.22
22 69 0.78
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:110104 original size:43 final size:44
Alignment explanation
Indices: 109999--110121 Score: 176
Period size: 43 Copynumber: 2.8 Consensus size: 44
109989 TTCAATATTT
* * * * * *
109999 GTCCTGAAGGACCACTGGATACGTCCTGAAAGACCACTGGATTC
1 GTCCCGAATGACCACTGGATACGTCCCGAAGGACTACTGGATTA
*
110043 GTCCCGAATGACTACTGGATACGTCCCGAAGGACTACTGGA-TA
1 GTCCCGAATGACCACTGGATACGTCCCGAAGGACTACTGGATTA
110086 GTCCCGAATGACCACTGGATACGTCCCGAAGGACTA
1 GTCCCGAATGACCACTGGATACGTCCCGAAGGACTA
110122 ATATACCCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 36 0.51
44 35 0.49
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (44 bp):
GTCCCGAATGACCACTGGATACGTCCCGAAGGACTACTGGATTA
Found at i:110773 original size:64 final size:64
Alignment explanation
Indices: 110664--110822 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 64
110654 ATCCCTTGAC
* * *
110664 GGTGCATCGATGCACTTCCCATGCATCGGTGCATAAATCAGATTCGATGTT-TGTATTTTAA-GC
1 GGTGCATCGATGCAC-TCCTATGCATCGATGCATAAATCAGATTCGATGTTATGTATTTAAATG-
110727 A
64 A
* *
110728 GGTGCATCGATGCACTCCTTATGCATCGATGCACT-AAT-GGCATTCGATGTTCATTTATTTAAA
1 GGTGCATCGATGCACTCC-TATGCATCGATGCA-TAAATCAG-ATTCGATGTT-ATGTATTTAAA
110791 TGA
62 TGA
* *
110794 -GTGCATCGATACACTCCATGTGCATCGAT
1 GGTGCATCGATGCACTCC-TATGCATCGAT
110823 ATACCTTCAA
Statistics
Matches: 81, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
63 4 0.05
64 40 0.49
65 27 0.33
66 9 0.11
67 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (64 bp):
GGTGCATCGATGCACTCCTATGCATCGATGCATAAATCAGATTCGATGTTATGTATTTAAATGA
Done.