Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 125 of 290
Found at i:42529693 original size:119 final size:119
Alignment explanation
Indices: 42529482--42529716 Score: 348
Period size: 119 Copynumber: 2.0 Consensus size: 119
42529472 AATTGAAGAC
*
42529482 AGCAGATCTAGACTTCAGACATTTAAGCTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT
1 AGCAGATCTAGACTTCAGACATTTAAGCTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTCT
* * * *
42529547 ATAAGAAACAAATCGGGGACATAGCAGATTTGACTCTCAGACGTTCTCAAATAT
66 ACAAGAAACAAATCGAGGACATAGCAGATATGACTCTCAAACGTTCTCAAATAT
**
42529601 AGCAGATCTA-ACCTTCAGATGTTTATA-CTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 AGCAGATCTAGA-CTTCAGACATTTA-AGCTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
* * *
42529664 CTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAA
64 CTACAAGAAACAAATCGAGGACATAGCAGATATGACTCTCAAACGTTCTCAAA
42529717 CAAACTCAAG
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
118 1 0.01
119 102 0.98
120 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (119 bp):
AGCAGATCTAGACTTCAGACATTTAAGCTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTCT
ACAAGAAACAAATCGAGGACATAGCAGATATGACTCTCAAACGTTCTCAAATAT
Found at i:42530073 original size:37 final size:37
Alignment explanation
Indices: 42530030--42530104 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
42530020 ATCAGTACCT
*
42530030 AAAACTACCCAGCAGGCCTACTACCCAAAACCCTAAA
1 AAAACTACCCAGCAGGCCCACTACCCAAAACCCTAAA
42530067 AAAACTACCCAGCAGGCCCACTACCCAAAACCCTAAA
1 AAAACTACCCAGCAGGCCCACTACCCAAAACCCTAAA
42530104 A
1 A
42530105 TAGTCCCGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.44, C:0.39, G:0.08, T:0.09
Consensus pattern (37 bp):
AAAACTACCCAGCAGGCCCACTACCCAAAACCCTAAA
Found at i:42539966 original size:47 final size:46
Alignment explanation
Indices: 42539915--42540022 Score: 117
Period size: 47 Copynumber: 2.3 Consensus size: 46
42539905 GAATTATGAG
*
42539915 GCATCCGAACTTGTTCAGTTGCAATCTGAGTTCACCTATGGATGCAA
1 GCATCCGAACTTGTTCAGTTGCAATCCGAGTTCA-CTATGGATGCAA
* * *** *
42539962 GCATCCAAACTTGTTGAGTTGTGTTCCGAGTTCATTATGGATGCAA
1 GCATCCGAACTTGTTCAGTTGCAATCCGAGTTCACTATGGATGCAA
* * *
42540008 ACACCCGAGCTTGTT
1 GCATCCGAACTTGTT
42540023 GATTTGTGTT
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
46 22 0.44
47 28 0.56
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (46 bp):
GCATCCGAACTTGTTCAGTTGCAATCCGAGTTCACTATGGATGCAA
Found at i:42540065 original size:46 final size:46
Alignment explanation
Indices: 42539942--42540047 Score: 149
Period size: 46 Copynumber: 2.3 Consensus size: 46
42539932 GTTGCAATCT
* * * * *
42539942 GAGTTCACCTATGGATGCAAGCATCCAAACTTGTTGAGTTGTGTTCC
1 GAGTTCA-TTATGGATGCAAACACCCGAGCTTGTTGAGTTGTGTTCC
*
42539989 GAGTTCATTATGGATGCAAACACCCGAGCTTGTTGATTTGTGTTCC
1 GAGTTCATTATGGATGCAAACACCCGAGCTTGTTGAGTTGTGTTCC
42540035 GAGTTCATTATGG
1 GAGTTCATTATGG
42540048 GTGAGATTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 46 0.87
47 7 0.13
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (46 bp):
GAGTTCATTATGGATGCAAACACCCGAGCTTGTTGAGTTGTGTTCC
Found at i:42543658 original size:5 final size:5
Alignment explanation
Indices: 42543648--42543673 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42543638 TGAGCATTCG
42543648 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
42543674 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:42543974 original size:14 final size:14
Alignment explanation
Indices: 42543941--42543977 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
42543931 ACATCAACCC
*
42543941 AAATA-AACAACAA
1 AAATACAACAAAAA
42543954 AAA-ACAACAAAAA
1 AAATACAACAAAAA
42543967 AAATACAACAA
1 AAATACAACAA
42543978 GATTATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 1 0.05
13 13 0.62
14 7 0.33
ACGTcount: A:0.78, C:0.16, G:0.00, T:0.05
Consensus pattern (14 bp):
AAATACAACAAAAA
Found at i:42544289 original size:212 final size:215
Alignment explanation
Indices: 42544034--42544435 Score: 623
Period size: 212 Copynumber: 1.9 Consensus size: 215
42544024 GTCGAAGTAA
* *
42544034 ACAACGACATTATAATAAAAAAAAACATAAGAAAAAGTCCAAAATACAATAGAAACTTACACCAC
1 ACAACAACATTATAATAAAAAAAAACATAAGAAAAAGTCCAAAATACAATAGAAACCTACACCAC
* * *
42544099 TCCAAACAAAAAAA-AACACAACAAAAGTTCAATTAACCAACGACAAT-AA-CAAACCAAACCAA
66 TCCAAAAAAAAAAAGAACACAACAAAAGCTCAATTAACCAACAACAATAAACCAAACCAAACCAA
*
42544161 ACTAATAACAATAACACATAAGCTCAAAAACCATTATAGAATAGTTTAAGTTTCTTCATGAGTCC
131 ACTAATAACAATAACACATAAGCTCAAAAACCATTATAGAATAGTTTAACTTTCTTCATGAGTCC
42544226 AAATAAACAACAAAAACAAT
196 AAATAAACAACAAAAACAAT
* *
42544246 ACAACAACATTGTAATTAAAAAAAACATAAGCAAAAA-TCCAAAATACAATAGAAACCTACACCA
1 ACAACAACATTATAATAAAAAAAAACATAAG-AAAAAGTCCAAAATACAATAGAAACCTACACCA
* *
42544310 GTCCAAAAAAAAAAAGAACACAACAAAAGCTCAATTATCCAACAACAATAACAAACCAAACCAAA
65 CTCCAAAAAAAAAAAGAACACAACAAAAGCTCAATTAACCAACAACAAT---AAACCAAACCAAA
* * *
42544375 CCAAACTAATAACAATAACACATCAGTTCCAAAACCATTATAGAATAGTTTAACTTTCTTC
127 CCAAACTAATAACAATAACACATAAGCTCAAAAACCATTATAGAATAGTTTAACTTTCTTC
42544436 TTGTGCTTCA
Statistics
Matches: 170, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
212 67 0.39
213 35 0.21
217 2 0.01
218 66 0.39
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.18
Consensus pattern (215 bp):
ACAACAACATTATAATAAAAAAAAACATAAGAAAAAGTCCAAAATACAATAGAAACCTACACCAC
TCCAAAAAAAAAAAGAACACAACAAAAGCTCAATTAACCAACAACAATAAACCAAACCAAACCAA
ACTAATAACAATAACACATAAGCTCAAAAACCATTATAGAATAGTTTAACTTTCTTCATGAGTCC
AAATAAACAACAAAAACAAT
Found at i:42546855 original size:30 final size:30
Alignment explanation
Indices: 42546819--42546885 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
42546809 GTTAAATTAA
*
42546819 AAATTAATTAATATAATAGTATAATAGCAT
1 AAATTAATTAATATAATAGTACAATAGCAT
42546849 AAATTAATTAATATAATAGTACAATAGCAT
1 AAATTAATTAATATAATAGTACAATAGCAT
42546879 AAATTAA
1 AAATTAA
42546886 AAATAGATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (30 bp):
AAATTAATTAATATAATAGTACAATAGCAT
Found at i:42554550 original size:25 final size:25
Alignment explanation
Indices: 42554520--42554647 Score: 113
Period size: 24 Copynumber: 5.2 Consensus size: 25
42554510 CATCGTATTC
*
42554520 GCTCTTTTGAGCT-ATGATCAGTAA
1 GCTCTTTTGAGCTGATGAACAGTAA
* *
42554544 GCTTCTTCTAAGCTGATGAACAGTAA
1 GC-TCTTTTGAGCTGATGAACAGTAA
*
42554570 GCTCTATTGAGCTG--GAAACAGTAA
1 GCTCTTTTGAGCTGATG-AACAGTAA
**
42554594 GCTCTAATGAGCTGA-GAACAGTAA
1 GCTCTTTTGAGCTGATGAACAGTAA
**
42554618 GCTCTTAAGAGCTGAT-ATATCAGTAA
1 GCTCTTTTGAGCTGATGA-A-CAGTAA
42554644 GCTC
1 GCTC
42554648 ATACGAGTTG
Statistics
Matches: 88, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
23 1 0.01
24 45 0.51
25 20 0.23
26 22 0.25
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (25 bp):
GCTCTTTTGAGCTGATGAACAGTAA
Found at i:42555553 original size:28 final size:28
Alignment explanation
Indices: 42555516--42555572 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
42555506 AAAAAGAGAA
42555516 AGATGATCACAAAATTCATGTTGTTTTT
1 AGATGATCACAAAATTCATGTTGTTTTT
* *
42555544 AGATGGTCACAAAATTCATTTTGTTTTT
1 AGATGATCACAAAATTCATGTTGTTTTT
42555572 A
1 A
42555573 TTTAATTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (28 bp):
AGATGATCACAAAATTCATGTTGTTTTT
Found at i:42558436 original size:15 final size:15
Alignment explanation
Indices: 42558418--42558446 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42558408 TTACTTTTTT
42558418 TTGTGACATTGAGGC
1 TTGTGACATTGAGGC
42558433 TTGTGACATTGAGG
1 TTGTGACATTGAGG
42558447 GTTAATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.34
Consensus pattern (15 bp):
TTGTGACATTGAGGC
Found at i:42558803 original size:31 final size:31
Alignment explanation
Indices: 42558743--42558803 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
42558733 TAATGACCAT
* *
42558743 AAAAGAAATTTACTAATAGTAGGGTGACTAA
1 AAAAGAAATTTACTAATAGTAGAGCGACTAA
* *
42558774 AAAAGAAATTTGCTAATAGTTGAGCGACTA
1 AAAAGAAATTTACTAATAGTAGAGCGACTA
42558804 TTTTCTAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (31 bp):
AAAAGAAATTTACTAATAGTAGAGCGACTAA
Found at i:42559220 original size:17 final size:17
Alignment explanation
Indices: 42559198--42559230 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42559188 ATAAGTAAAT
*
42559198 AAATATTTAAAAAATAG
1 AAATATCTAAAAAATAG
42559215 AAATATCTAAAAAATA
1 AAATATCTAAAAAATA
42559231 AAACATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (17 bp):
AAATATCTAAAAAATAG
Found at i:42559913 original size:23 final size:23
Alignment explanation
Indices: 42559863--42559916 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
42559853 ATCTTCTAAA
42559863 AGTTTTAATAATACGTAAAATAT
1 AGTTTTAATAATACGTAAAATAT
* **
42559886 TGTTTTAATAATATTTGAAAAT-T
1 AGTTTTAATAATACGT-AAAATAT
42559909 AGTTTTAA
1 AGTTTTAA
42559917 AACAAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (23 bp):
AGTTTTAATAATACGTAAAATAT
Found at i:42561677 original size:5 final size:5
Alignment explanation
Indices: 42561667--42561698 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
42561657 TTAAATGTGA
42561667 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
42561699 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:42561690 original size:9 final size:9
Alignment explanation
Indices: 42561668--42561698 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
42561658 TAAATGTGAA
42561668 AAATAAAAT
1 AAATAAAAT
42561677 AAAATAAAAT
1 -AAATAAAAT
42561687 AAATAAAAT
1 AAATAAAAT
42561696 AAA
1 AAA
42561699 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:42566128 original size:5 final size:5
Alignment explanation
Indices: 42566118--42566149 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
42566108 CAATTTGTGA
42566118 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
42566150 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:42566143 original size:9 final size:9
Alignment explanation
Indices: 42566119--42566149 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
42566109 AATTTGTGAA
42566119 AAATAAAAT
1 AAATAAAAT
42566128 AAAATAAAAT
1 -AAATAAAAT
42566138 AAATAAAAT
1 AAATAAAAT
42566147 AAA
1 AAA
42566150 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:42571752 original size:52 final size:52
Alignment explanation
Indices: 42571685--42571785 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 52
42571675 GTATACAACC
* ** *
42571685 ATCGATGTCGTGAAAACTGCCATCCCATGTCACGACACCAAAATTTGAAGCT
1 ATCGATGTCGCGAAAACCACCATCCCATGTAACGACACCAAAATTTGAAGCT
* * * *
42571737 ATCGATGTTGCGAAAACCACCATCCCATGTAATGACACCTAACTTTGAA
1 ATCGATGTCGCGAAAACCACCATCCCATGTAACGACACCAAAATTTGAA
42571786 CCAAGAGGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (52 bp):
ATCGATGTCGCGAAAACCACCATCCCATGTAACGACACCAAAATTTGAAGCT
Found at i:42576117 original size:46 final size:46
Alignment explanation
Indices: 42576064--42576151 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 46
42576054 TTCGACATGT
*
42576064 TTATGACAATTTTCACGAAAATTCATTAAATCCTTAGAAATCCTTA
1 TTATGACAATTTTCACGAAAATTCATTAAATCCTTAAAAATCCTTA
*
42576110 TTATGACAATTTTCATGAAAATTCATTAAATCCTTAAAAATC
1 TTATGACAATTTTCACGAAAATTCATTAAATCCTTAAAAATC
42576152 GTTAACAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.38
Consensus pattern (46 bp):
TTATGACAATTTTCACGAAAATTCATTAAATCCTTAAAAATCCTTA
Found at i:42586156 original size:20 final size:20
Alignment explanation
Indices: 42586131--42586169 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42586121 TAAATTCCAA
42586131 TCCAT-ATTATAATGGTTTTG
1 TCCATAATT-TAATGGTTTTG
*
42586151 TCCATAATTTCATGGTTTT
1 TCCATAATTTAATGGTTTT
42586170 ATCTTGTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (20 bp):
TCCATAATTTAATGGTTTTG
Found at i:42586176 original size:25 final size:27
Alignment explanation
Indices: 42586148--42586206 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
42586138 TATAATGGTT
42586148 TTGTCCATA-ATTTCATGG-TTTTATC
1 TTGTCCATATATTTCATGGTTTTTATC
* * *
42586173 TTGTCTATATTTTTCATGGTTTTTGTC
1 TTGTCCATATATTTCATGGTTTTTATC
42586200 TTGTCCA
1 TTGTCCA
42586207 CTTTATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 8 0.29
26 8 0.29
27 12 0.43
ACGTcount: A:0.15, C:0.15, G:0.14, T:0.56
Consensus pattern (27 bp):
TTGTCCATATATTTCATGGTTTTTATC
Found at i:42587004 original size:8 final size:8
Alignment explanation
Indices: 42586973--42587007 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
42586963 GGAAAATAAA
42586973 AAGGAAAGG
1 AAGGAAA-G
*
42586982 AAGGAAGG
1 AAGGAAAG
42586990 AAGGAAAG
1 AAGGAAAG
42586998 AAGGAAAG
1 AAGGAAAG
42587006 AA
1 AA
42587008 CAAAGCCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 18 0.75
9 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (8 bp):
AAGGAAAG
Found at i:42588596 original size:3 final size:3
Alignment explanation
Indices: 42588588--42588624 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
42588578 TTGCTTTTCA
42588588 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42588625 CACTGTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:42589495 original size:29 final size:29
Alignment explanation
Indices: 42589453--42589513 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
42589443 AGTCTTATGC
42589453 ATCACATTCTATTAACTGACATGCAAGCA
1 ATCACATTCTATTAACTGACATGCAAGCA
42589482 ATCACATTCTATTAACTGACATGCAAGCA
1 ATCACATTCTATTAACTGACATGCAAGCA
42589511 ATC
1 ATC
42589514 TTTAATTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (29 bp):
ATCACATTCTATTAACTGACATGCAAGCA
Found at i:42590103 original size:27 final size:27
Alignment explanation
Indices: 42590073--42590127 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
42590063 AAATTAATTT
* *
42590073 TCCCTACTATCTCTTAGATTTTCCAAA
1 TCCCTACAATCACTTAGATTTTCCAAA
42590100 TCCCTACAATCACTTAGATTTTCCAAA
1 TCCCTACAATCACTTAGATTTTCCAAA
42590127 T
1 T
42590128 TAATTTTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.38
Consensus pattern (27 bp):
TCCCTACAATCACTTAGATTTTCCAAA
Found at i:42597851 original size:40 final size:40
Alignment explanation
Indices: 42597788--42598012 Score: 267
Period size: 40 Copynumber: 5.7 Consensus size: 40
42597778 TCGAAATGTT
* * * * * *
42597788 AACAGGGGCATGTAAGTGTAATCAAGGCTACCGAAGTACG
1 AACAAGGGCACGTATGTGCAATCAAGGGTACCGAAGTACA
* *
42597828 AACAAGGGCACGTATGTGCAATCAAGGGTACCAAAGTACG
1 AACAAGGGCACGTATGTGCAATCAAGGGTACCGAAGTACA
*
42597868 AACAGGGGCAC--ATGTGCAATC-AGGTGTACCGAAGTACA
1 AACAAGGGCACGTATGTGCAATCAAGG-GTACCGAAGTACA
* * *
42597906 AACAGGGGCACGTATGTGTAATCAGGGGTACCGAAGTACA
1 AACAAGGGCACGTATGTGCAATCAAGGGTACCGAAGTACA
* * **
42597946 AACAAGGGCACATATGTGCAATCAGGGGTATTGAAGTACA
1 AACAAGGGCACGTATGTGCAATCAAGGGTACCGAAGTACA
*
42597986 AATAAGGGCACGTATGTGCAATCAAGG
1 AACAAGGGCACGTATGTGCAATCAAGG
42598013 TATAATTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
37 3 0.02
38 32 0.20
40 125 0.77
41 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (40 bp):
AACAAGGGCACGTATGTGCAATCAAGGGTACCGAAGTACA
Found at i:42597919 original size:78 final size:79
Alignment explanation
Indices: 42597807--42598012 Score: 279
Period size: 78 Copynumber: 2.6 Consensus size: 79
42597797 ATGTAAGTGT
* * * *
42597807 AATCAAGGCTACCGAAGTACGAACAAGGGCACGTATGTGCAATCAAGGGTACCAAAGTACGAACA
1 AATCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCAATCAAGGGTACCAAAGTACAAACA
*
42597872 GGGGCAC-ATGTGC
66 AGGGCACAATGTGC
* * * * *
42597885 AATCAGGTGTACCGAAGTACAAACAGGGGCACGTATGTGTAATCAGGGGTACCGAAGTACAAACA
1 AATCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCAATCAAGGGTACCAAAGTACAAACA
42597950 AGGGCACATATGTGC
66 AGGGCACA-ATGTGC
** *
42597965 AATCAGGGGTATTGAAGTACAAATAAGGGCACGTATGTGCAATCAAGG
1 AATCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCAATCAAGG
42598013 TATAATTTAC
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 62 0.57
80 47 0.43
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (79 bp):
AATCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCAATCAAGGGTACCAAAGTACAAACA
AGGGCACAATGTGC
Found at i:42597996 original size:118 final size:119
Alignment explanation
Indices: 42597788--42598009 Score: 311
Period size: 118 Copynumber: 1.9 Consensus size: 119
42597778 TCGAAATGTT
* * *
42597788 AACAGGGGCATGTAAGTGTAATCAAGGCTACCGAAGTACGAACAAGGGCACGTATGTGCAATCAA
1 AACAGGGGCACGTAAGTGTAATCAAGGCTACCGAAGTACAAACAAGGGCACATATGTGCAATCAA
* *
42597853 GGGTACCAAAGTACGAACAGGGGCAC-ATGTGCAATCAGGTGTACCGAAGTACA
66 GGGTACCAAAGTACAAACAAGGGCACGATGTGCAATCAGGTGTACCGAAGTACA
* * * *
42597906 AACAGGGGCACGTATGTGTAATCAGGGGTACCGAAGTACAAACAAGGGCACATATGTGCAATCAG
1 AACAGGGGCACGTAAGTGTAATCAAGGCTACCGAAGTACAAACAAGGGCACATATGTGCAATCAA
*** *
42597971 GGGTATTGAAGTACAAATAAGGGCACGTATGTGCAATCA
66 GGGTACCAAAGTACAAACAAGGGCACG-ATGTGCAATCA
42598010 AGGTATAATT
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
118 78 0.88
120 11 0.12
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.18
Consensus pattern (119 bp):
AACAGGGGCACGTAAGTGTAATCAAGGCTACCGAAGTACAAACAAGGGCACATATGTGCAATCAA
GGGTACCAAAGTACAAACAAGGGCACGATGTGCAATCAGGTGTACCGAAGTACA
Found at i:42598188 original size:18 final size:18
Alignment explanation
Indices: 42598157--42598191 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42598147 ACTTAGTCGA
* *
42598157 TTTCTTCTTTCCCTTAGC
1 TTTCTACTTCCCCTTAGC
42598175 TTTCTACTTCCCCTTAG
1 TTTCTACTTCCCCTTAG
42598192 AGGATGAGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.34, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTCTACTTCCCCTTAGC
Found at i:42609144 original size:20 final size:20
Alignment explanation
Indices: 42609119--42609166 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
42609109 ATTTTGATAT
*
42609119 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATAC
42609139 ACATGATATGTATGATATAC
1 ACATGATATGTATGATATAC
42609159 ACATGATA
1 ACATGATA
42609167 AATTCATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATAC
Found at i:42609298 original size:25 final size:26
Alignment explanation
Indices: 42609214--42609285 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
42609204 GAGGAAGTGC
* * *
42609214 AAAAGGGC-TATGCCCCAGTTTACCG
1 AAAAGGGCTTTTGCCCCAGTTTATCA
*
42609239 AAAATGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTTGCCCCAGTTTATCA
42609265 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGCTTTTGCCCCAGTT
42609286 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 7 0.17
26 34 0.83
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCCAGTTTATCA
Found at i:42609543 original size:31 final size:31
Alignment explanation
Indices: 42609505--42609588 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
42609495 TTGTTTCAGT
42609505 AAAGGCTTCGACCCAGTGATATGAATAATGA
1 AAAGGCTTCGACCCAGTGATATGAATAATGA
*
42609536 AAAGGCTTCGACCCAGTGATATGAATAATGT
1 AAAGGCTTCGACCCAGTGATATGAATAATGA
*
42609567 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGACCCAGTGATATG
42609589 CTGAGATTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGACCCAGTGATATGAATAATGA
Found at i:42617216 original size:20 final size:20
Alignment explanation
Indices: 42617191--42617238 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
42617181 ATTTTGATAT
42617191 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
42617211 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
42617231 ACATGATA
1 ACATGATA
42617239 AATTCATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:42617218 original size:11 final size:11
Alignment explanation
Indices: 42617202--42617238 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
42617192 CATGATATGT
42617202 ATGATATGCAC
1 ATGATATGCAC
*
42617213 ATGATATG--T
1 ATGATATGCAC
42617222 ATGATATGCAC
1 ATGATATGCAC
42617233 ATGATA
1 ATGATA
42617239 AATTCATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:42617331 original size:27 final size:26
Alignment explanation
Indices: 42617286--42617358 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
42617276 GAGGAAGTGC
*
42617286 AAAAGGGC-TATGCCCCAGTTTACCAA
1 AAAAGGGCTTTTGCCCCAGTTTACC-A
*
42617312 AAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTTGCCCCAGTTTACCA
42617338 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGCTTTTGCCCCAGTT
42617359 ATTAAAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
26 30 0.68
27 14 0.32
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCCAGTTTACCA
Found at i:42617371 original size:25 final size:26
Alignment explanation
Indices: 42617296--42617371 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 26
42617286 AAAAGGGCTA
* *
42617296 TGCCCCAGTTTACCAAAAAAGGGCTTT
1 TGCCCCAGTTTATCAAAAGA-GGCTTT
42617323 TGCCCCAGTTTATCAAAA-AGGGCTTT
1 TGCCCCAGTTTATCAAAAGA-GGCTTT
*
42617349 TGCCCCAG-TTATTAAAAGAGGCT
1 TGCCCCAGTTTATCAAAAGAGGCT
42617372 AGGCCTCCAG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.26
26 17 0.37
27 17 0.37
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (26 bp):
TGCCCCAGTTTATCAAAAGAGGCTTT
Found at i:42617616 original size:31 final size:31
Alignment explanation
Indices: 42617578--42617656 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
42617568 TTGTTTCAGT
*
42617578 AAAGGCTTCAGCCCAGTGACATGAATAATGA
1 AAAGGCTTCGGCCCAGTGACATGAATAATGA
* * * *
42617609 AAAGGCTTCGGCCTAGTTATATGAATAATGT
1 AAAGGCTTCGGCCCAGTGACATGAATAATGA
42617640 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
42617657 ATATGCTGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGACATGAATAATGA
Found at i:42621797 original size:49 final size:49
Alignment explanation
Indices: 42621734--42621864 Score: 167
Period size: 49 Copynumber: 2.7 Consensus size: 49
42621724 ACATTAAAGT
* *
42621734 CGATGCCGTGTCCTAGACAGGTTTTACACTGACTTTCATATATCAAG-GC
1 CGATGCCATGTCCTAGACAGGTCTTACACTGACTTTCATATATC-AGTGC
* * * * *
42621783 CGATGCCATCTCCTAGACAAGTCTTACACT-ATCTTTCATCTATCGGTGT
1 CGATGCCATGTCCTAGACAGGTCTTACACTGA-CTTTCATATATCAGTGC
42621832 CGATGCCATGTCCTAGACAGGTCTTACACTGAC
1 CGATGCCATGTCCTAGACAGGTCTTACACTGAC
42621865 ACACAACAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 2 0.03
49 67 0.96
50 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (49 bp):
CGATGCCATGTCCTAGACAGGTCTTACACTGACTTTCATATATCAGTGC
Found at i:42622019 original size:46 final size:47
Alignment explanation
Indices: 42621882--42622039 Score: 178
Period size: 46 Copynumber: 3.4 Consensus size: 47
42621872 AAGCTAACAC
* * * *
42621882 CATGTCCCAGACAGGTCTTACACTAGCT-TGTATATCCTGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCT-TATA-ACAGTGGCCGATG
* ** *
42621930 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAT-GCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTTATAACAGTGGCCGATG
* *
42621976 CATGTCACAGACATGTCTTACACTGGCTCTTATAAC-GTGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTTATAACAGTGGCCGATG
*
42622022 CATGTCCCAGATATGTCT
1 CATGTCCCAGACATGTCT
42622040 ACATTGGCTC
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
45 1 0.01
46 61 0.66
47 1 0.01
48 29 0.31
49 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTTATAACAGTGGCCGATG
Found at i:42631941 original size:342 final size:342
Alignment explanation
Indices: 42631316--42632001 Score: 1372
Period size: 342 Copynumber: 2.0 Consensus size: 342
42631306 TAAATGCTTT
42631316 AATATGGCATGTATGGTAAATATATATAATTTGTAACATCATGAAATAGGGCCTAGTCGGAATAA
1 AATATGGCATGTATGGTAAATATATATAATTTGTAACATCATGAAATAGGGCCTAGTCGGAATAA
42631381 TGGTTTCGGGACCACAAATCCGACGTTAAAATAATTGTTTTATGATTATTATGATTTCTAGGATA
66 TGGTTTCGGGACCACAAATCCGACGTTAAAATAATTGTTTTATGATTATTATGATTTCTAGGATA
42631446 TGAAAATAAGCATGTGTTAAAGTTTCATGAAGAAATTCTAAGTATAAGGTGTCTAATTGGAAATT
131 TGAAAATAAGCATGTGTTAAAGTTTCATGAAGAAATTCTAAGTATAAGGTGTCTAATTGGAAATT
42631511 AGGGACCAAATTGAATAAATTGCAAAACTTGGATTCTAGAAGCAATTATTACGAAATTGCTATGG
196 AGGGACCAAATTGAATAAATTGCAAAACTTGGATTCTAGAAGCAATTATTACGAAATTGCTATGG
42631576 ATTATTAATTAGGAGGTCTTAAATAGCAATTTTCCCAATTTTCACGTTTTTGGACAAAAATGGGC
261 ATTATTAATTAGGAGGTCTTAAATAGCAATTTTCCCAATTTTCACGTTTTTGGACAAAAATGGGC
42631641 ATACATGGAAATTTTTG
326 ATACATGGAAATTTTTG
42631658 AATATGGCATGTATGGTAAATATATATAATTTGTAACATCATGAAATAGGGCCTAGTCGGAATAA
1 AATATGGCATGTATGGTAAATATATATAATTTGTAACATCATGAAATAGGGCCTAGTCGGAATAA
42631723 TGGTTTCGGGACCACAAATCCGACGTTAAAATAATTGTTTTATGATTATTATGATTTCTAGGATA
66 TGGTTTCGGGACCACAAATCCGACGTTAAAATAATTGTTTTATGATTATTATGATTTCTAGGATA
42631788 TGAAAATAAGCATGTGTTAAAGTTTCATGAAGAAATTCTAAGTATAAGGTGTCTAATTGGAAATT
131 TGAAAATAAGCATGTGTTAAAGTTTCATGAAGAAATTCTAAGTATAAGGTGTCTAATTGGAAATT
42631853 AGGGACCAAATTGAATAAATTGCAAAACTTGGATTCTAGAAGCAATTATTACGAAATTGCTATGG
196 AGGGACCAAATTGAATAAATTGCAAAACTTGGATTCTAGAAGCAATTATTACGAAATTGCTATGG
42631918 ATTATTAATTAGGAGGTCTTAAATAGCAATTTTCCCAATTTTCACGTTTTTGGACAAAAATGGGC
261 ATTATTAATTAGGAGGTCTTAAATAGCAATTTTCCCAATTTTCACGTTTTTGGACAAAAATGGGC
42631983 ATACATGGAAATTTTTG
326 ATACATGGAAATTTTTG
42632000 AA
1 AA
42632002 AGGTTAGTAA
Statistics
Matches: 344, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
342 344 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (342 bp):
AATATGGCATGTATGGTAAATATATATAATTTGTAACATCATGAAATAGGGCCTAGTCGGAATAA
TGGTTTCGGGACCACAAATCCGACGTTAAAATAATTGTTTTATGATTATTATGATTTCTAGGATA
TGAAAATAAGCATGTGTTAAAGTTTCATGAAGAAATTCTAAGTATAAGGTGTCTAATTGGAAATT
AGGGACCAAATTGAATAAATTGCAAAACTTGGATTCTAGAAGCAATTATTACGAAATTGCTATGG
ATTATTAATTAGGAGGTCTTAAATAGCAATTTTCCCAATTTTCACGTTTTTGGACAAAAATGGGC
ATACATGGAAATTTTTG
Found at i:42632628 original size:171 final size:171
Alignment explanation
Indices: 42632343--42632684 Score: 675
Period size: 171 Copynumber: 2.0 Consensus size: 171
42632333 TTTTGGTCAT
42632343 TTGGTAATAAAATTAATAAAAAGGGAAAAGGAAGCAAAATTCAGCAATATTCTTCTCCATGGCTG
1 TTGGTAATAAAATTAATAAAAAGGGAAAAGGAAGCAAAATTCAGCAATATTCTTCTCCATGGCTG
42632408 CCGAAAATTGAAGGGTCTCCATAGCTAGGGTTTTCAACATTTTCAAGCTTAATAACCCCGAGGAA
66 CCGAAAATTGAAGGGTCTCCATAGCTAGGGTTTTCAACATTTTCAAGCTTAATAACCCCGAGGAA
42632473 CCAATTCCGGAGGTTGACCGTGAAAAATGAAAGGTTTCGGA
131 CCAATTCCGGAGGTTGACCGTGAAAAATGAAAGGTTTCGGA
*
42632514 TTGGTAATAAAATTAGTAAAAAGGGAAAAGGAAGCAAAATTCAGCAATATTCTTCTCCATGGCTG
1 TTGGTAATAAAATTAATAAAAAGGGAAAAGGAAGCAAAATTCAGCAATATTCTTCTCCATGGCTG
42632579 CCGAAAATTGAAGGGTCTCCATAGCTAGGGTTTTCAACATTTTCAAGCTTAATAACCCCGAGGAA
66 CCGAAAATTGAAGGGTCTCCATAGCTAGGGTTTTCAACATTTTCAAGCTTAATAACCCCGAGGAA
42632644 CCAATTCCGGAGGTTGACCGTGAAAAATGAAAGGTTTCGGA
131 CCAATTCCGGAGGTTGACCGTGAAAAATGAAAGGTTTCGGA
42632685 ATAACTGAAA
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 170 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (171 bp):
TTGGTAATAAAATTAATAAAAAGGGAAAAGGAAGCAAAATTCAGCAATATTCTTCTCCATGGCTG
CCGAAAATTGAAGGGTCTCCATAGCTAGGGTTTTCAACATTTTCAAGCTTAATAACCCCGAGGAA
CCAATTCCGGAGGTTGACCGTGAAAAATGAAAGGTTTCGGA
Found at i:42634436 original size:41 final size:41
Alignment explanation
Indices: 42634380--42634457 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
42634370 ATTTTTGGAC
* *
42634380 ACGGGCAACGACACGGGCGTGT-CTAGGCCATGTGAAGGAA
1 ACGGGCAACGACACGGGCATGTGCTAGGCAATGTGAAGGAA
* *
42634420 ACGGGCCAAGGACACGGGCATGTGCTCGGCAATGTGAA
1 ACGGG-CAACGACACGGGCATGTGCTAGGCAATGTGAA
42634458 AACCTCTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 5 0.16
41 15 0.47
42 12 0.38
ACGTcount: A:0.27, C:0.23, G:0.37, T:0.13
Consensus pattern (41 bp):
ACGGGCAACGACACGGGCATGTGCTAGGCAATGTGAAGGAA
Found at i:42636533 original size:16 final size:17
Alignment explanation
Indices: 42636501--42636533 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42636491 TCTCTCAAGT
42636501 CACACGGGCGTGTGTGAC
1 CACACGGGCG-GTGTGAC
42636519 CACACGGGC-GTGTGA
1 CACACGGGCGGTGTGA
42636534 ATCTCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.27, G:0.39, T:0.15
Consensus pattern (17 bp):
CACACGGGCGGTGTGAC
Found at i:42650087 original size:55 final size:54
Alignment explanation
Indices: 42649992--42650141 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
42649982 CTACTTTGTT
* ** * *
42649992 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
42650046 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
42650101 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
42650142 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:42650104 original size:27 final size:27
Alignment explanation
Indices: 42649964--42650141 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
42649954 TAAATTGTAC
42649964 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
42649991 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
42650017 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
42650045 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
42650073 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
42650100 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
42650127 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42650142 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:42650105 original size:82 final size:81
Alignment explanation
Indices: 42649965--42650120 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
42649955 AAATTGTACA
* * * *
42649965 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
42650030 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
42650046 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
42650109 TGTGCGAGTTGA
63 TGTGCGAATTGA
42650121 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:42652871 original size:36 final size:36
Alignment explanation
Indices: 42652831--42652907 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
42652821 AACTTTACTA
*
42652831 AATATTAATATTTAATGAATTCAAATATATGACAAT
1 AATATCAATATTTAATGAATTCAAATATATGACAAT
* * *
42652867 AATATCAATATTTAATGAATTTAAATATGTGATAAT
1 AATATCAATATTTAATGAATTCAAATATATGACAAT
42652903 AATAT
1 AATAT
42652908 AATTAATTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (36 bp):
AATATCAATATTTAATGAATTCAAATATATGACAAT
Found at i:42653350 original size:29 final size:29
Alignment explanation
Indices: 42653284--42653342 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
42653274 GTCGAAACCC
42653284 TAGATCTTGAGATGAAAATAGAAAAGTTT
1 TAGATCTTGAGATGAAAATAGAAAAGTTT
42653313 TAGATCTTGAGATGAAAATAGAAAA-TTT
1 TAGATCTTGAGATGAAAATAGAAAAGTTT
42653341 TA
1 TA
42653343 ATCACTTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.32
Consensus pattern (29 bp):
TAGATCTTGAGATGAAAATAGAAAAGTTT
Found at i:42654233 original size:13 final size:13
Alignment explanation
Indices: 42654215--42654245 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42654205 ATGTGCTGTT
42654215 AATTTTAAGTTGA
1 AATTTTAAGTTGA
*
42654228 AATTTTATGTTGA
1 AATTTTAAGTTGA
42654241 AATTT
1 AATTT
42654246 ATAGAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (13 bp):
AATTTTAAGTTGA
Found at i:42656107 original size:22 final size:21
Alignment explanation
Indices: 42656054--42656107 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
42656044 TGGCCAGCAG
* *
42656054 CACAGGCGTGTCCTAGGGTCT
1 CACAGGCGTGTCCTAGGGCCA
* *
42656075 CACGGGCGTGTCCCTTGGGCCA
1 CACAGGCGTGT-CCTAGGGCCA
42656097 CACAGGCGTGT
1 CACAGGCGTGT
42656108 GTGCCCTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.13, C:0.31, G:0.35, T:0.20
Consensus pattern (21 bp):
CACAGGCGTGTCCTAGGGCCA
Found at i:42658479 original size:46 final size:48
Alignment explanation
Indices: 42658356--42658483 Score: 158
Period size: 46 Copynumber: 2.8 Consensus size: 48
42658346 CTTGTGTGAG
*
42658356 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTCAGACGAGAA
1 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATGCAGACGAGAA
* * * *
42658404 CTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGC-TGCGAGATGTG-T
1 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATGC-AGACGAGAA
*
42658449 C-AGTGTAAGACCATGTCTAGGACATGGCATCGGCA
1 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
42658484 CCCTACCCCA
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
44 9 0.13
45 15 0.22
46 21 0.30
47 13 0.19
48 11 0.16
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (48 bp):
CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATGCAGACGAGAA
Found at i:42665996 original size:46 final size:47
Alignment explanation
Indices: 42665890--42666062 Score: 182
Period size: 46 Copynumber: 3.7 Consensus size: 47
42665880 CACTTGTGTG
* * * *
42665890 AGCTAATGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGATG-A
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCCTCGAGATGTA
*
42665937 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGTGATGTA
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCCTCGAGATGTA
* *
42665984 AGCTAGTTTAAGA-CATGTCTGGGACAT-GCATCGGCTGCGAGATGT-
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGCCT-CGAGATGTA
42666029 -G-TCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGCT-AGTGTAAGACCATGTCTGGGACATGGCATCG
42666063 GTACCCTACC
Statistics
Matches: 110, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
43 1 0.01
44 9 0.08
45 17 0.15
46 57 0.52
47 14 0.13
48 12 0.11
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (47 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGCCTCGAGATGTA
Found at i:42675582 original size:42 final size:42
Alignment explanation
Indices: 42675459--42675582 Score: 115
Period size: 43 Copynumber: 2.9 Consensus size: 42
42675449 AGTACCGTAC
* ** *
42675459 CAATGTCATATCCCAGATATGGTCTTACATGTAATCTCGTAT
1 CAATGTCATATCCCATATATGGTCTTACACATAATCTCATAT
* * * * * *
42675501 CGATGCCAATAGCCCGTCTATGGTCTTACACGA-AGTCTCATAT
1 CAATGTC-ATATCCCATATATGGTCTTACAC-ATAATCTCATAT
* *
42675544 CAATGTCATATCCTATATATAGTCTTACACATAATCTCA
1 CAATGTCATATCCCATATATGGTCTTACACATAATCTCA
42675583 GTAATCCTAA
Statistics
Matches: 61, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
41 1 0.02
42 29 0.48
43 31 0.51
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (42 bp):
CAATGTCATATCCCATATATGGTCTTACACATAATCTCATAT
Found at i:42678386 original size:13 final size:14
Alignment explanation
Indices: 42678360--42678403 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
42678350 TTATTTTGAG
*
42678360 TTTTTTAAGTAAAT-
1 TTTTTTAA-AAAATA
42678374 TTTTTTAAAAAATA
1 TTTTTTAAAAAATA
*
42678388 TTTTTTAAAAACTA
1 TTTTTTAAAAAATA
42678402 TT
1 TT
42678404 AAAGTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (14 bp):
TTTTTTAAAAAATA
Found at i:42678912 original size:3 final size:3
Alignment explanation
Indices: 42678904--42678928 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42678894 TTTAACAGTG
42678904 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
42678929 TGAAAAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42682389 original size:9 final size:9
Alignment explanation
Indices: 42682358--42682399 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
42682348 AAAGATTGAG
42682358 AAAATAAGAA
1 AAAATAA-AA
*
42682368 AAAA-AAAGG
1 AAAATAAA-A
42682377 AAAATAAAA
1 AAAATAAAA
42682386 AAAATAAAA
1 AAAATAAAA
42682395 AAAAT
1 AAAAT
42682400 TATATATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 1 0.04
9 20 0.71
10 7 0.25
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (9 bp):
AAAATAAAA
Found at i:42692472 original size:46 final size:46
Alignment explanation
Indices: 42692409--42692677 Score: 340
Period size: 46 Copynumber: 5.8 Consensus size: 46
42692399 TTTGACATGA
* * * *
42692409 TGCCATAGTGTCTTTCAACCATGGTCTTGTTCATTTTATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
* * *
42692455 TGCCATGGTATCCTTCAACCATGGTCTTGTTCATTTTATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
* * *
42692501 TGCCATAGTATCCTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
* * ** *
42692547 TGCCATAGTATCTTTCAACCATGGTCCTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
* ** * *
42692593 TGCCATGGTATCTTTCAATCATGGTCTTACACATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
**
42692639 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
42692678 TTCAGAAAGC
Statistics
Matches: 201, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 201 1.00
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
Found at i:42693094 original size:24 final size:24
Alignment explanation
Indices: 42693058--42693108 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
42693048 TTCTTTCTTT
42693058 ATATATTAATAAAATAATAATAAA
1 ATATATTAATAAAATAATAATAAA
* * *
42693082 ATATCTTATTAAAATATTAATAAA
1 ATATATTAATAAAATAATAATAAA
42693106 ATA
1 ATA
42693109 ATTTTTATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATATTAATAAAATAATAATAAA
Found at i:42700119 original size:21 final size:21
Alignment explanation
Indices: 42700090--42700132 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42700080 AAAACACACT
*
42700090 AACAAAAGCTTATAAGAGCTG
1 AACAAAAGCTCATAAGAGCTG
* *
42700111 AACAGAAGCTCGTAAGAGCTG
1 AACAAAAGCTCATAAGAGCTG
42700132 A
1 A
42700133 TCTACCCAAA
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:0.44, C:0.16, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAAAAGCTCATAAGAGCTG
Found at i:42703935 original size:21 final size:21
Alignment explanation
Indices: 42703909--42703950 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42703899 ATTAATATAA
42703909 TAATAC-ATAATTATATTATTT
1 TAATACTATAATTA-ATTATTT
*
42703930 TAATACTTTAATTAATTATTT
1 TAATACTATAATTAATTATTT
42703951 ATGACCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATACTATAATTAATTATTT
Found at i:42706777 original size:30 final size:30
Alignment explanation
Indices: 42706743--42706804 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
42706733 CTTAACAAGT
*
42706743 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTATAAAATAATAACAAAATTAAC
42706773 AAATGCCTATAAAATAATAACAAAATTAAC
1 AAATGCCTATAAAATAATAACAAAATTAAC
42706803 AA
1 AA
42706805 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.60, C:0.15, G:0.03, T:0.23
Consensus pattern (30 bp):
AAATGCCTATAAAATAATAACAAAATTAAC
Found at i:42706859 original size:22 final size:22
Alignment explanation
Indices: 42706834--42706876 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42706824 TATCCAAACA
42706834 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
42706856 ATAATAGTAAAATTGTAGCAA
1 ATAACAATAAAATAGTAGCAA
42706877 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:42707156 original size:30 final size:30
Alignment explanation
Indices: 42707122--42707184 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
42707112 ACTTATTTTA
42707122 TTGTTAATTTTGTTATTATTTTAAAGATAT
1 TTGTTAATTTTGTTATTATTTTAAAGATAT
* *
42707152 TTGTTAATTTTGTTATTATTTTATAGGTAT
1 TTGTTAATTTTGTTATTATTTTAAAGATAT
42707182 TTG
1 TTG
42707185 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.00, G:0.13, T:0.62
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGATAT
Found at i:42707292 original size:18 final size:20
Alignment explanation
Indices: 42707269--42707307 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
42707259 AATATTTATA
*
42707269 TTGATGT-TTTTA-ATATTT
1 TTGATGTATTATATATATTT
42707287 TTGATGTATTATATATATTT
1 TTGATGTATTATATATATTT
42707307 T
1 T
42707308 AAAATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (20 bp):
TTGATGTATTATATATATTT
Found at i:42707329 original size:12 final size:12
Alignment explanation
Indices: 42707308--42707341 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42707298 TATATATTTT
*
42707308 AAAATTATATAA
1 AAAATAATATAA
42707320 AAAATAATATAA
1 AAAATAATATAA
*
42707332 AAATTAATAT
1 AAAATAATAT
42707342 GGACAGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:42707635 original size:17 final size:16
Alignment explanation
Indices: 42707615--42707665 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
42707605 AAAAAATTAC
42707615 AATAGAAGAAAATAAAG
1 AATAGAAGAAAA-AAAG
* *
42707632 AATAGAGGAGAAAAAG
1 AATAGAAGAAAAAAAG
*
42707648 AATTA-AAGTAAAAAAG
1 AA-TAGAAGAAAAAAAG
42707664 AA
1 AA
42707666 ATAATAGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.12
Consensus pattern (16 bp):
AATAGAAGAAAAAAAG
Found at i:42707672 original size:36 final size:36
Alignment explanation
Indices: 42707623--42707691 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
42707613 ACAATAGAAG
* *
42707623 AAAATAAAGAATAGAGGAGAAAAAGAATTAAAGTAA
1 AAAAGAAAGAATAGAAGAGAAAAAGAATTAAAGTAA
* * *
42707659 AAAAGAAATAATAGAATAGATAAAGAATTAAAG
1 AAAAGAAAGAATAGAAGAGAAAAAGAATTAAAG
42707692 GCTTCCTGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.16
Consensus pattern (36 bp):
AAAAGAAAGAATAGAAGAGAAAAAGAATTAAAGTAA
Found at i:42710345 original size:24 final size:24
Alignment explanation
Indices: 42710310--42710356 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42710300 TGGATGTTCC
42710310 TATTCCTCAGATTGTAAAAGTTTT
1 TATTCCTCAGATTGTAAAAGTTTT
*
42710334 TATT-CTCGAGATTGTGAAAGTTT
1 TATTCCTC-AGATTGTAAAAGTTT
42710357 CTGTTCTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (24 bp):
TATTCCTCAGATTGTAAAAGTTTT
Found at i:42710363 original size:24 final size:24
Alignment explanation
Indices: 42710318--42710390 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
42710308 CCTATTCCTC
* * *
42710318 AGATTGTAAAAGTTTTTATTCTCG
1 AGATTGTGAAAGTTTCTGTTCTCG
*
42710342 AGATTGTGAAAGTTTCTGTTCTTG
1 AGATTGTGAAAGTTTCTGTTCTCG
** ** *
42710366 AGGGTACGAAAGTTTCCGTTCTCG
1 AGATTGTGAAAGTTTCTGTTCTCG
42710390 A
1 A
42710391 AATAGTGGTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (24 bp):
AGATTGTGAAAGTTTCTGTTCTCG
Found at i:42710839 original size:16 final size:16
Alignment explanation
Indices: 42710818--42710872 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
42710808 GTTTGGTTCA
*
42710818 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
42710834 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
42710850 CTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
42710866 CTGTAAT
1 CTGTAAT
42710873 AAGTAGTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:42711132 original size:58 final size:58
Alignment explanation
Indices: 42711053--42711176 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 58
42711043 TTTTAATAAG
* * *
42711053 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATCATATT-TTAACATT
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAACAATTTAATAATATTCTTAACATA
* * *
42711111 ATTATTATTAAATATAATTTAATAAAATAATATACAATTTAATAATATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAACAATTTAATAATATTCTTAACATA
42711169 ATTATTAT
1 ATTATTAT
42711177 ATGAATTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 23 0.39
58 36 0.61
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAACAATTTAATAATATTCTTAACATA
Found at i:42713136 original size:35 final size:35
Alignment explanation
Indices: 42713090--42713162 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
42713080 TACAAAGATA
*
42713090 GTTAGCATTAACAAACATATAATATAAGGTAAAAT
1 GTTAGCATTAACAAACAGATAATATAAGGTAAAAT
42713125 GTTAGCATTAACAAACAGATAATATAAGGTAAAAT
1 GTTAGCATTAACAAACAGATAATATAAGGTAAAAT
42713160 GTT
1 GTT
42713163 TAACACTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (35 bp):
GTTAGCATTAACAAACAGATAATATAAGGTAAAAT
Found at i:42717313 original size:21 final size:21
Alignment explanation
Indices: 42717289--42717332 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42717279 TTTCCGATGC
42717289 CATAG-CCTAACAATGGTCTTA
1 CATAGTCC-AACAATGGTCTTA
*
42717310 CATAGTCCAACTATGGTCTTA
1 CATAGTCCAACAATGGTCTTA
42717331 CA
1 CA
42717333 CATACGTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (21 bp):
CATAGTCCAACAATGGTCTTA
Found at i:42717797 original size:43 final size:43
Alignment explanation
Indices: 42717750--42717831 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
42717740 ATCGATTAAC
* *
42717750 AATGCCAATGTCTCAGACATGGTCTTACACGTAATCACAATAG
1 AATGCCAATGCCCCAGACATGGTCTTACACGTAATCACAATAG
*
42717793 AATGCCAATGCCCCAGACATGGTCTTACATGTAATCACA
1 AATGCCAATGCCCCAGACATGGTCTTACACGTAATCACA
42717832 TCTCGATATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (43 bp):
AATGCCAATGCCCCAGACATGGTCTTACACGTAATCACAATAG
Found at i:42717811 original size:86 final size:85
Alignment explanation
Indices: 42717663--42717821 Score: 187
Period size: 86 Copynumber: 1.9 Consensus size: 85
42717653 TATAGCTCAT
* * * * * * *
42717663 ACAATGCCATATCCCAGATATGGTCTTACATGTTATCACATATCAATGTCACTGTCCTAGACA-G
1 ACAATGCCATATCCCAGACATGGTCTTACACGTAATCACATATCAATGCCAATGCCCCAGACATG
42717727 AGTCTTACACGAAATCGATTA
66 -GTCTTACACGAAATCGATTA
* * *
42717748 ACAATGCCAATGTCTCAGACATGGTCTTACACGTAATCACA-ATAGAATGCCAATGCCCCAGACA
1 ACAATGCC-ATATCCCAGACATGGTCTTACACGTAATCACATAT-CAATGCCAATGCCCCAGACA
42717812 TGGTCTTACA
64 TGGTCTTACA
42717822 TGTAATCACA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
85 10 0.16
86 50 0.82
87 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (85 bp):
ACAATGCCATATCCCAGACATGGTCTTACACGTAATCACATATCAATGCCAATGCCCCAGACATG
GTCTTACACGAAATCGATTA
Found at i:42724920 original size:93 final size:93
Alignment explanation
Indices: 42724810--42724979 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 93
42724800 CCCCTAAGTG
* *
42724810 AACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAAC
1 AACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
42724875 GAGTTCGGATGCCTGGTTACATCTCACA
66 GAGTTCGGATGCCTGGTTACATCTCACA
* * * *
42724903 AACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAAT
1 AACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
42724968 GAGTTCGGATGC
66 GAGTTCGGATGC
42724980 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
AACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTGGTTACATCTCACA
Found at i:42724976 original size:46 final size:46
Alignment explanation
Indices: 42724804--42724976 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
42724794 AACCCGCCCC
* * * *
42724804 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * * *
42724850 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTGGTTACATCTCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA--CAT--TTGCATC-CA
*
42724901 -CA---AACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* *
42724943 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
42724977 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 7 0.07
45 2 0.02
46 56 0.54
47 27 0.26
48 2 0.02
50 6 0.06
51 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:42727081 original size:4 final size:4
Alignment explanation
Indices: 42727072--42727099 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
42727062 AACTGGTACC
42727072 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
42727100 GTCCTAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:42727862 original size:12 final size:12
Alignment explanation
Indices: 42727845--42727892 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 12
42727835 CAAAAATTTG
42727845 AAATAAATCATA
1 AAATAAATCATA
42727857 AAATAAAT-A-A
1 AAATAAATCATA
*
42727867 AAATAAA-AAT-
1 AAATAAATCATA
*
42727877 AAATAATTCATA
1 AAATAAATCATA
42727889 AAAT
1 AAAT
42727893 GTAAAGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 15 0.50
11 3 0.10
12 12 0.40
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (12 bp):
AAATAAATCATA
Found at i:42727866 original size:16 final size:16
Alignment explanation
Indices: 42727845--42727892 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
42727835 CAAAAATTTG
42727845 AAATAAATCATAAAAT
1 AAATAAATCATAAAAT
*
42727861 AAATAAA-AATAAAAAT
1 AAATAAATCAT-AAAAT
*
42727877 AAATAATTCATAAAAT
1 AAATAAATCATAAAAT
42727893 GTAAAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAAATCATAAAAT
Found at i:42727952 original size:20 final size:20
Alignment explanation
Indices: 42727937--42727976 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42727927 GTATTATAAG
42727937 AAAAAAATTAAAATTAGTAC
1 AAAAAAATTAAAATTAGTAC
42727957 AAAAAAATTAAAATTAGTAC
1 AAAAAAATTAAAATTAGTAC
42727977 TATACAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (20 bp):
AAAAAAATTAAAATTAGTAC
Found at i:42728185 original size:20 final size:20
Alignment explanation
Indices: 42728148--42728185 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42728138 ATACAAAAGA
*
42728148 ATATATATGAATTACAATCT
1 ATATATATGAAATACAATCT
42728168 ATATAATATGAAAT-CAAT
1 ATAT-ATATGAAATACAAT
42728186 GATCATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (20 bp):
ATATATATGAAATACAATCT
Found at i:42730432 original size:35 final size:36
Alignment explanation
Indices: 42730366--42730437 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 36
42730356 TTCATAACAG
* **
42730366 TTCAATGACAAATAAACATATATAATTCAA-TTAAA
1 TTCAATAACAAATAAACATATATAACACAATTTAAA
* * *
42730401 TTCAATAATAAATAAGCATTTATAACACAATTTAAA
1 TTCAATAACAAATAAACATATATAACACAATTTAAA
42730437 T
1 T
42730438 ACGTTTATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
35 24 0.80
36 6 0.20
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (36 bp):
TTCAATAACAAATAAACATATATAACACAATTTAAA
Found at i:42732058 original size:12 final size:12
Alignment explanation
Indices: 42732041--42732070 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
42732031 AATCACATGG
42732041 TCGTGTCCTACC
1 TCGTGTCCTACC
42732053 TCGTGTCCTACC
1 TCGTGTCCTACC
42732065 TCGTGT
1 TCGTGT
42732071 AACTCTCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.37, G:0.20, T:0.37
Consensus pattern (12 bp):
TCGTGTCCTACC
Found at i:42738234 original size:6 final size:6
Alignment explanation
Indices: 42738223--42739106 Score: 1768
Period size: 6 Copynumber: 147.3 Consensus size: 6
42738213 GAGAATAACC
42738223 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738271 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738319 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738367 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738415 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738463 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738511 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738559 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738607 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738655 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738703 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738751 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738799 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738847 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738895 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738943 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42738991 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42739039 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
42739087 ACATAT ACATAT ACATAT AC
1 ACATAT ACATAT ACATAT AC
42739107 CAACATATGC
Statistics
Matches: 878, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 878 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:42746973 original size:28 final size:29
Alignment explanation
Indices: 42746948--42747013 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
42746938 GGTTTTTCAT
42746948 ATTTTACAAATT-TGCCACTGATTTTCTAG
1 ATTTTAC-AATTCTGCCACTGATTTTCTAG
42746977 ATTTTACAATTCTGCCACT-ATTTTCTAG
1 ATTTTACAATTCTGCCACTGATTTTCTAG
42747005 AATTTTACA
1 -ATTTTACA
42747014 GTTTTACCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
28 13 0.37
29 22 0.63
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (29 bp):
ATTTTACAATTCTGCCACTGATTTTCTAG
Found at i:42752576 original size:94 final size:95
Alignment explanation
Indices: 42752459--42752775 Score: 323
Period size: 94 Copynumber: 3.3 Consensus size: 95
42752449 TTTGTGTGCC
* * * *
42752459 AGTGTAAGA-CATGTCTAGGACAT-GCATCAGCTACATTATGAGAGCCAATGTAAGACCA-GTTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACATTATGAGAGTCAGTGTAAGACCATG-TT
42752521 TGGGACATGGCATCGACATTGAGACGAGAGCT
65 TGGGACATGGCATCGACATTGAGA-GAGAGCT
* *
42752553 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACA--A-GATGTGTCAGTGTATGACCATGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACATTATGA-GAGTCAGTGTAAGACCATGTT
** *
42752613 TGGGACATGGCATCGACACAGATATGTGAGAGCT
65 TGGGACATGGCATCGACATTG--A-GAGAGAGCT
* * * *
42752647 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCCT-CGATTTTGATAGTTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CTAC-ATTATGAGAGTCAGTGTAAGACCATGT
* *
42752711 TTGGGAAATGGCATCGAC-TTGATG-GATGAGCC
64 TTGGGACATGGCATCGACATTGA-GAGA-GAGCT
*
42752743 AGCGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
42752776 ATTATACCCT
Statistics
Matches: 189, Mismatches: 21, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
91 2 0.01
92 35 0.19
93 1 0.01
94 50 0.26
95 18 0.10
96 44 0.23
97 3 0.02
98 1 0.01
99 33 0.17
100 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (95 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACATTATGAGAGTCAGTGTAAGACCATGTTT
GGGACATGGCATCGACATTGAGAGAGAGCT
Found at i:42752711 original size:99 final size:95
Alignment explanation
Indices: 42752507--42752775 Score: 302
Period size: 96 Copynumber: 2.8 Consensus size: 95
42752497 TGAGAGCCAA
*
42752507 TGTAAGACCA-GTTTTGGGACATGGCATCGACATTGAGA-CGAGAGCTAGTGTAAGA-CATGTCT
1 TGTAAGACCATG-TTTGGGACATGGCATCGACATTGA-ATGGAGAGCTAGTGTAAGACCATGTCT
42752569 GGGACAT-GCATCGG-CTACAAGATGTGTCAG
64 GGGACATGGCATCGGCCTACAAGATGTGTCAG
* **
42752599 TGTATGACCATGTTTGGGACATGGCATCGACACAGATATGTGAGAGCTAGTGTAAGACCATGTCT
1 TGTAAGACCATGTTTGGGACATGGCATCGACATTGA-ATG-GAGAGCTAGTGTAAGACCATGTCT
* *** *
42752664 GGGACATGGCGTCGGCCT-CGATTTTGATAGTTAG
64 GGGACATGGCATCGGCCTAC-AAGATG-T-GTCAG
* * *
42752698 TGTAAGACCATGTTTGGGAAATGGCATCGAC-TTG-ATGGATGAGCCAGCGTAAGACCATGTCTG
1 TGTAAGACCATGTTTGGGACATGGCATCGACATTGAATGGA-GAGCTAGTGTAAGACCATGTCTG
42752761 GGACATGGCATCGGC
65 GGACATGGCATCGGC
42752776 ATTATACCCT
Statistics
Matches: 150, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
92 32 0.21
93 1 0.01
94 16 0.11
95 16 0.11
96 45 0.30
97 5 0.03
98 2 0.01
99 33 0.22
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (95 bp):
TGTAAGACCATGTTTGGGACATGGCATCGACATTGAATGGAGAGCTAGTGTAAGACCATGTCTGG
GACATGGCATCGGCCTACAAGATGTGTCAG
Found at i:42752716 original size:49 final size:50
Alignment explanation
Indices: 42752497--42752773 Score: 190
Period size: 47 Copynumber: 5.8 Consensus size: 50
42752487 AGCTACATTA
* * ** *
42752497 TGAGAGCCAATGTAAGACCA-GTTTTGGGACATGGCATCGACATTGAGA--
1 TGAGAGCTAGTGTAAGACCATG-TTTGGGACATGGCATCGACACAGATATG
* * * *
42752545 CGAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACA-AGATG
1 TGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGAC-ACAGATATG
* *
42752593 T--G-TC-AGTGTATGACCATGTTTGGGACATGGCATCGACACAGATATG
1 TGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACACAGATATG
* * * * *
42752639 TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGC-CTCGAT-TT
1 TGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACAC-AGATATG
* * * **
42752688 TGATAGTTAGTGTAAGACCATGTTTGGGAAATGGCATCGAC-TTG--ATG
1 TGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACACAGATATG
* * *
42752735 -GATGAGCCAGCGTAAGACCATGTCTGGGACATGGCATCG
1 TGA-GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCG
42752774 GCATTATACC
Statistics
Matches: 180, Mismatches: 35, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
44 8 0.04
45 17 0.09
46 25 0.14
47 43 0.24
48 17 0.09
49 38 0.21
50 32 0.18
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.25
Consensus pattern (50 bp):
TGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACACAGATATG
Found at i:42756770 original size:43 final size:43
Alignment explanation
Indices: 42756689--42756846 Score: 110
Period size: 43 Copynumber: 3.7 Consensus size: 43
42756679 AAGCTCCTAC
* * * * * *
42756689 AATGCCAACGTCTCAGACGTGGTCTTACATGT-AGTCAAATAT
1 AATGCCAACATCCCAGACATGGTCCTACACGTAAATCAAATAT
* *
42756731 CAATGCC-ACTGTCCCAGACA-GGATCTTACACG-AAATCAAATAT
1 -AATGCCAAC-ATCCCAGACATGG-TCCTACACGTAAATCAAATAT
* **
42756774 GATGCCAACATCCCAGACATGGTCCTACACGTAAATCATAAGTCG
1 AATGCCAACATCCCAGACATGGTCCTACACGTAAATCA-AA-TAT
* * *
42756819 AA-GCCAACATCCCAAACGTGGTCTTACA
1 AATGCCAACATCCCAGACATGGTCCTACA
42756847 TGAGAACACA
Statistics
Matches: 94, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
42 26 0.28
43 41 0.44
44 25 0.27
45 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (43 bp):
AATGCCAACATCCCAGACATGGTCCTACACGTAAATCAAATAT
Found at i:42761009 original size:68 final size:68
Alignment explanation
Indices: 42760898--42761053 Score: 267
Period size: 68 Copynumber: 2.3 Consensus size: 68
42760888 CAAGCATCCT
* * *
42760898 GATCGGTAGTGATCCTGCATGTGTTGCACACTACCGCAGCTCTTTGTGAGCCTCCTGTTACATGA
1 GATCGGTTGTGATCCTGCATGTGTTGCACACTACCGCAACTCTTTGTGAGCCTCCTGTTACACGA
42760963 TTC
66 TTC
42760966 GATCGGTTGTGATCCTGCATGTGTTGCACACTACCGCAACTCTTTGTGAGCCTCCTGTTACACGA
1 GATCGGTTGTGATCCTGCATGTGTTGCACACTACCGCAACTCTTTGTGAGCCTCCTGTTACACGA
42761031 TTC
66 TTC
* *
42761034 GATTGGTTGTGATCCAGCAT
1 GATCGGTTGTGATCCTGCAT
42761054 TTACTACGAA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 83 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.33
Consensus pattern (68 bp):
GATCGGTTGTGATCCTGCATGTGTTGCACACTACCGCAACTCTTTGTGAGCCTCCTGTTACACGA
TTC
Found at i:42778427 original size:53 final size:54
Alignment explanation
Indices: 42778364--42778471 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
42778354 TAGTTCTTAT
*
42778364 TTACAAACCATAATCACTAAA-CCCACAACCTACTTATCCATGATCGAACCATG
1 TTACAAACCATAATCACTAAACCCCAAAACCTACTTATCCATGATCGAACCATG
*
42778417 TTACAAACCATAATCACTAAACCCCAAAACTTACTTATCCATGATCGAACCATG
1 TTACAAACCATAATCACTAAACCCCAAAACCTACTTATCCATGATCGAACCATG
42778471 T
1 T
42778472 CCCTAAAAGC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
53 21 0.40
54 31 0.60
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.24
Consensus pattern (54 bp):
TTACAAACCATAATCACTAAACCCCAAAACCTACTTATCCATGATCGAACCATG
Found at i:42782601 original size:46 final size:46
Alignment explanation
Indices: 42782434--42782721 Score: 240
Period size: 46 Copynumber: 6.1 Consensus size: 46
42782424 GAAATCTTAC
* * * * *
42782434 ACATATCGATGCCGATGCCATATCCCGAATATGGTCTTACACTGGCTC
1 ACATATCGATGCCGATG-CATGTCCCAAACAT-GTCTTACACTAGCTT
* * * *
42782482 ACATATATCCATGCCAATGCATGTACCAGACATGTCTTACACTAGCTCT
1 AC--ATATCGATGCCGATGCATGTCCCAAACATGTCTTACACTAGCT-T
* *
42782531 CATATATCCG-TGCCGATGCATGTCCCAAACATGTCTTACACTGGCTT
1 -ACATAT-CGATGCCGATGCATGTCCCAAACATGTCTTACACTAGCTT
* *
42782578 ACATCTCGAGGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCT
1 ACATATCGATGCCGATGCATGTCCCAAACATGTCTTACACTAGCT-T
* * ** * * * *
42782625 -CGTCTTAATGCCAATCCATGTCCCAGACATGTCTGACACTAGCATT
1 ACATATCGATGCCGATGCATGTCCCAAACATGTCTTACACTAGC-TT
* * * *
42782671 TCATAACG-TGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
1 ACATATCGAT-GCCGATGCATGTCCCAAACATGTCTTACACTAGCTT
42782717 ACATA
1 ACATA
42782722 ACAGTAGTGT
Statistics
Matches: 193, Mismatches: 37, Indels: 22
0.77 0.15 0.09
Matches are distributed among these distances:
45 2 0.01
46 81 0.42
47 35 0.18
48 51 0.26
49 10 0.05
50 14 0.07
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (46 bp):
ACATATCGATGCCGATGCATGTCCCAAACATGTCTTACACTAGCTT
Found at i:42782702 original size:93 final size:94
Alignment explanation
Indices: 42782498--42782711 Score: 270
Period size: 93 Copynumber: 2.3 Consensus size: 94
42782488 ATCCATGCCA
* ** * *
42782498 ATGCATGTACCAGACATGTCTTACACTAGCTCTCATATATCCGTGCCGATGCATGTCCCAAACAT
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATATCAATGCCAATCCATGTCCCAAACAT
* * **
42782563 GTCTTACACTGGCTTACATCTCGAGGCCG
66 GTCTGACACTAGCTTACATAACGAGGCCG
* * * *
42782592 ATGCATGTCCCAAACATGTCTTACACTAGCTCTCGTCT-T-AATGCCAATCCATGTCCCAGACAT
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATATCAATGCCAATCCATGTCCCAAACAT
* *
42782655 GTCTGACACTAGCATTTCATAACGTGGCCG
66 GTCTGACACTAGC-TTACATAACGAGGCCG
42782685 ATGCATGTCCCAGACATGTCTTACACT
1 ATGCATGTCCCAGACATGTCTTACACT
42782712 GGCTTACATA
Statistics
Matches: 103, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
92 30 0.29
93 39 0.38
94 34 0.33
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (94 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATATCAATGCCAATCCATGTCCCAAACAT
GTCTGACACTAGCTTACATAACGAGGCCG
Found at i:42788295 original size:48 final size:48
Alignment explanation
Indices: 42788195--42788395 Score: 177
Period size: 48 Copynumber: 4.3 Consensus size: 48
42788185 TAGATATGGT
* * ** *
42788195 CTTACATTGGCTCTCATATATTCGTGCCGATGCATGTCCCAGGCATGT
1 CTTACACTAGCTCTCATATATTCGTGCCGATGCATGTCCCAAACATGC
*
42788243 CTTACACTAGCTCTCATATATTTGTGCCGATGCATGTCCCAAACATGC
1 CTTACACTAGCTCTCATATATTCGTGCCGATGCATGTCCCAAACATGC
* *
42788291 CTTACACTAG----CACAT-CTCGTAGCCGATGCATGTCCCAAACAT-C
1 CTTACACTAGCTCTCATATATTCGT-GCCGATGCATGTCCCAAACATGC
* * * * * *
42788334 TCTTACACTGGCT-T-ACAT-CTCGAGGCCGATGCATGTCCCAGACATGT
1 -CTTACACTAGCTCTCATATATTCG-TGCCGATGCATGTCCCAAACATGC
*
42788381 CTTACACTAACTCTC
1 CTTACACTAGCTCTC
42788396 GTCTCAATGC
Statistics
Matches: 129, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
43 4 0.03
44 34 0.26
46 38 0.29
47 1 0.01
48 52 0.40
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.29
Consensus pattern (48 bp):
CTTACACTAGCTCTCATATATTCGTGCCGATGCATGTCCCAAACATGC
Found at i:42788325 original size:92 final size:87
Alignment explanation
Indices: 42788216--42788476 Score: 251
Period size: 92 Copynumber: 2.9 Consensus size: 87
42788206 TCTCATATAT
* *
42788216 TCGT-GCCGATGCATGTCCCAGGCATGTCTTACACTAGCTCTCATATATTTGTGCCGATGCATGT
1 TCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCT-TCATATATTTG-GCCGATGCATGT
*
42788280 CCCAAACATGCCTTACACTAGCACATC
64 CCCAAACATGTCTTACACTA--AC-TC
* * * ***
42788307 TCGTAGCCGATGCATGTCCCAAACATCTCTTACACTGGCTTACATCT-CGAGGCCGATGCATGTC
1 TCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CATATATTTGGCCGATGCATGTC
*
42788371 CCAGACATGTCTTACACTAACTC
65 CCAAACATGTCTTACACTAACTC
* * *
42788394 TCGTCTCAATGCCGATGCATGTCCTAGACATGTCTTGCACTGGCATTTCATA-ATGTGGCCGATG
1 TCG--T--A-GCCGATGCATGTCCCAGACATGTCTTACACTGGC--TTCATATATTTGGCCGATG
*
42788458 CATG-CCCACACATGTCTTA
59 CATGTCCCAAACATGTCTTA
42788477 AATTGGCTCA
Statistics
Matches: 142, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
87 5 0.04
88 2 0.01
89 1 0.01
90 30 0.21
91 7 0.05
92 79 0.56
93 16 0.11
94 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.28
Consensus pattern (87 bp):
TCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTCATATATTTGGCCGATGCATGTCC
CAAACATGTCTTACACTAACTC
Found at i:42788369 original size:46 final size:46
Alignment explanation
Indices: 42788220--42788476 Score: 204
Period size: 46 Copynumber: 5.6 Consensus size: 46
42788210 ATATATTCGT
** * * * *
42788220 GCCGATGCATGTCCCAGGCATGTCTTACACTAGCTCTCATATATTTG-T
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCT-T-ACAT-CTCGAG
*
42788268 GCCGATGCATGTCCCAAACATGCCTTACACTAGC--ACATCTCGTA-
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCTTACATCTCG-AG
* *
42788312 GCCGATGCATGTCCCAAACATCTCTTACACTGGCTTACATCTCGAG
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCTTACATCTCGAG
* * * * *
42788358 GCCGATGCATGTCCCAGACATGTCTTACACTAACTCT-CGTCTCAAT
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCT-TACATCTCGAG
* * * * * * *
42788404 GCCGATGCATGTCCTAGACATGTCTTGCACTGGCATTTCATAAT-GTG
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGC-TTACAT-CTCGAG
*
42788451 GCCGATGCATG-CCCACACATGTCTTA
1 GCCGATGCATGTCCCAAACATGTCTTA
42788477 AATTGGCTCA
Statistics
Matches: 172, Mismatches: 28, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
43 2 0.01
44 34 0.20
45 1 0.01
46 88 0.51
47 15 0.09
48 32 0.19
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTAGCTTACATCTCGAG
Found at i:42788484 original size:138 final size:136
Alignment explanation
Indices: 42788220--42788489 Score: 303
Period size: 138 Copynumber: 2.0 Consensus size: 136
42788210 ATATATTCGT
* * *
42788220 GCCGATGCATGTCCCAGGCATGTCTTACACTAGCTCTCATATATTTGTGCCGATGCATGTCCCAA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAACTCTCATATA--TATGCCGATGCATGTCCCAA
* * *
42788285 ACATGCCTTACACTAGCACATCTCGTAGCCGATGCATGTCCCAAACATCTCTTACACTGGCTTAC
64 ACATGCCTTACACTAGCACATATCGTAGCCGATGCATGTCCCAAACATCTCTTAAACTGGCTCAC
42788350 ATCTCGAG
129 ATCTCGAG
* * * *
42788358 GCCGATGCATGTCCCAGACATGTCTTACACTAACTCTCGTCTCA-ATGCCGATGCATGTCCTAGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAACTCTCATAT-ATATGCCGATGCATGTCCCAAA
* * * * * * *
42788422 CATGTCTTGCACTGGCATTTCATAAT-GTGGCCGATGCATG-CCCACACATGTCTTAAATTGGCT
65 CATGCCTTACACTAGCA---CAT-ATCGTAGCCGATGCATGTCCCAAACATCTCTTAAACTGGCT
42788485 CACAT
126 CACAT
42788490 AACAGCAGTG
Statistics
Matches: 110, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
136 31 0.28
138 61 0.55
139 17 0.15
140 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (136 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAACTCTCATATATATGCCGATGCATGTCCCAAAC
ATGCCTTACACTAGCACATATCGTAGCCGATGCATGTCCCAAACATCTCTTAAACTGGCTCACAT
CTCGAG
Found at i:42802032 original size:30 final size:30
Alignment explanation
Indices: 42801997--42802054 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
42801987 GAATTATTTT
* *
42801997 TAAAATTTAGTTG-CTCTTTTCGTAAATAA
1 TAAAAATTAGGTGCCTCTTTTCGTAAATAA
*
42802026 TAAAAATTAGGTGCCTCTTTTTGTAAATA
1 TAAAAATTAGGTGCCTCTTTTCGTAAATA
42802055 TTTTTAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (30 bp):
TAAAAATTAGGTGCCTCTTTTCGTAAATAA
Found at i:42802893 original size:25 final size:27
Alignment explanation
Indices: 42802838--42802893 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
42802828 TTTCTCTTAA
*
42802838 ATTTTAATTTTATTCTAATATCTAATT
1 ATTTTAATTTTATTCGAATATCTAATT
42802865 -TTTTAA-TTTATT-GAATCAT-TAATT
1 ATTTTAATTTTATTCGAAT-ATCTAATT
42802889 ATTTT
1 ATTTT
42802894 TATTAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 8 0.31
25 12 0.46
26 6 0.23
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (27 bp):
ATTTTAATTTTATTCGAATATCTAATT
Found at i:42807964 original size:15 final size:15
Alignment explanation
Indices: 42807941--42807975 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
42807931 GCTCAGTAAA
*
42807941 GAGAAAAGACAAGCT
1 GAGATAAGACAAGCT
42807956 GAGATAAGACAAGCT
1 GAGATAAGACAAGCT
42807971 GAGAT
1 GAGAT
42807976 GGATACTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.29, T:0.11
Consensus pattern (15 bp):
GAGATAAGACAAGCT
Found at i:42811410 original size:47 final size:45
Alignment explanation
Indices: 42811372--42811475 Score: 127
Period size: 47 Copynumber: 2.2 Consensus size: 45
42811362 AATCCGTATA
*
42811372 TGATTTCTGATGATCTAACGCTGTTTTCAGACTTTCAAAGATCACTT
1 TGATTTCTGATGATCTAACGCTGTTTTCAAACTTTC-AA-ATCACTT
* *
42811419 TTATTTCTGATGATCTAACGTTGTTTTCAAACTTTCAAAGATCACTT
1 TGATTTCTGATGATCTAACGCTGTTTTCAAACTTTC-AA-ATCACTT
*
42811466 TTACTTTCTG
1 TGA-TTTCTG
42811476 TTCAGTCTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
47 47 0.89
48 6 0.11
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.44
Consensus pattern (45 bp):
TGATTTCTGATGATCTAACGCTGTTTTCAAACTTTCAAATCACTT
Found at i:42817168 original size:27 final size:29
Alignment explanation
Indices: 42817138--42817222 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
42817128 TACCTGTATC
*
42817138 TGGCACATTAAG-CC-AATCATATTCATA
1 TGGCACATTAAGCCCAAATCACATTCATA
* * *
42817165 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCACATTAAGCCCAAATCACATTCATA
* * *
42817194 TGGCCCGTT-AGACCC-AGTCACATTCATA
1 TGGCACATTAAG-CCCAAATCACATTCATA
42817222 T
1 T
42817223 TCATGCTCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
27 10 0.21
28 15 0.32
29 22 0.47
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (29 bp):
TGGCACATTAAGCCCAAATCACATTCATA
Found at i:42817185 original size:29 final size:28
Alignment explanation
Indices: 42817150--42817222 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 28
42817140 GCACATTAAG
* *
42817150 CCAATCATATTCATATGGCCCATTAGGC
1 CCAATCACATTCATATGGCCCATTAGAC
* *
42817178 CCAAATCACATTTATATGGCCCGTTAGAC
1 CC-AATCACATTCATATGGCCCATTAGAC
*
42817207 CCAGTCACATTCATAT
1 CCAATCACATTCATAT
42817223 TCATGCTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 14 0.37
29 24 0.63
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.29
Consensus pattern (28 bp):
CCAATCACATTCATATGGCCCATTAGAC
Found at i:42817466 original size:8 final size:8
Alignment explanation
Indices: 42817433--42817475 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
42817423 GTAGCCAAAC
*
42817433 TTTCAACT
1 TTTCGACT
*
42817441 TTTCGACA
1 TTTCGACT
42817449 TTTCGACT
1 TTTCGACT
*
42817457 TTTCGGCT
1 TTTCGACT
*
42817465 TTTCGGCT
1 TTTCGACT
42817473 TTT
1 TTT
42817476 GCCGATACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.12, C:0.23, G:0.14, T:0.51
Consensus pattern (8 bp):
TTTCGACT
Found at i:42828040 original size:40 final size:40
Alignment explanation
Indices: 42827979--42828200 Score: 306
Period size: 40 Copynumber: 5.6 Consensus size: 40
42827969 AACCCAAGTA
* *
42827979 CCTTCGGGAATTAG-CCGGATATAG-CAACTCGCAGAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCAGAAATG
* * *
42828018 CCTTCGGGTCTTGGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAGAAATG
* *
42828058 CCTTCGGGACTTAGCTCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAGAAATG
*
42828098 CCTTCGGGACTTAGCCCGGATATAGTCACTAGC-GCAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAG-AAATG
** *
42828138 CCTTCGGGACTTAGCTGGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAGAAATG
42828178 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
42828201 CATCCGAATA
Statistics
Matches: 161, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
39 11 0.07
40 149 0.93
41 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAGAAATG
Found at i:42828115 original size:80 final size:80
Alignment explanation
Indices: 42827979--42828200 Score: 349
Period size: 80 Copynumber: 2.8 Consensus size: 80
42827969 AACCCAAGTA
* * * * *
42827979 CCTTCGGGAATTAGC-CGGATATAG-CAACTCGCAGAAATGCCTTCGGGTCTTGGCCCGGATATA
1 CCTTCGGGACTTAGCTCGGATATAGTC-ACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATA
*
42828042 GTCACTAGCACAAATG
65 GTCACTAGCACAAAGG
42828058 CCTTCGGGACTTAGCTCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCTCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAG
*
42828123 TCACTAGCGCAAAGG
66 TCACTAGCACAAAGG
*
42828138 CCTTCGGGACTTAGCTGGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCTCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATAT
42828201 CATCCGAATA
Statistics
Matches: 133, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
79 14 0.11
80 118 0.89
81 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTAGCTCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATATAG
TCACTAGCACAAAGG
Found at i:42832210 original size:17 final size:18
Alignment explanation
Indices: 42832188--42832221 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42832178 TTACATTGAA
42832188 GTGTTTT-AGTGAAAACT
1 GTGTTTTCAGTGAAAACT
*
42832205 GTGTTTTCATTGAAAAC
1 GTGTTTTCAGTGAAAAC
42832222 CCTTCTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACT
Found at i:42832795 original size:13 final size:13
Alignment explanation
Indices: 42832777--42832803 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42832767 GAACTACCTT
42832777 CATATACCCGTTG
1 CATATACCCGTTG
42832790 CATATACCCGTTG
1 CATATACCCGTTG
42832803 C
1 C
42832804 CACATCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.30
Consensus pattern (13 bp):
CATATACCCGTTG
Found at i:42833939 original size:29 final size:29
Alignment explanation
Indices: 42833873--42834505 Score: 1171
Period size: 29 Copynumber: 21.9 Consensus size: 29
42833863 AATTTCACAT
* *
42833873 ACCTGTATCTGGCCCATTAAGCCC-AATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
**
42833901 ATAT-TCATATGGCCCATTAGGCCCAAATC
1 ACCTGT-ATATGGCCCATTAGGCCCAAATC
42833930 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42833959 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42833988 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834017 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834046 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834075 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834104 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834133 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834162 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834191 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834220 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834249 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834278 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834307 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834336 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834365 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834394 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
42834423 ACCTGTATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
*
42834452 ACCTGTATATGGCCCATTAGGCACAAATC
1 ACCTGTATATGGCCCATTAGGCCCAAATC
* * *
42834481 ACATTTATATGGCCCGTTAGGCCCA
1 ACCTGTATATGGCCCATTAGGCCCA
42834506 GTCACATTCA
Statistics
Matches: 591, Mismatches: 11, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
27 1 0.00
28 18 0.03
29 571 0.97
30 1 0.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (29 bp):
ACCTGTATATGGCCCATTAGGCCCAAATC
Found at i:42835606 original size:37 final size:37
Alignment explanation
Indices: 42835564--42835635 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
42835554 TGAACCTTGG
42835564 ATCTCCTTGCTAGCTACTAACACCACCTCCCTACTTA
1 ATCTCCTTGCTAGCTACTAACACCACCTCCCTACTTA
* *
42835601 ATCTCCTTGCTAGCTACTAACGCCACCTCTCTACT
1 ATCTCCTTGCTAGCTACTAACACCACCTCCCTACT
42835636 CCCTAAGTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.22, C:0.40, G:0.07, T:0.31
Consensus pattern (37 bp):
ATCTCCTTGCTAGCTACTAACACCACCTCCCTACTTA
Found at i:42836503 original size:18 final size:18
Alignment explanation
Indices: 42836482--42836516 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42836472 GCTCAGTGCG
42836482 CTTTACCTCCTCCACTAT
1 CTTTACCTCCTCCACTAT
* *
42836500 CTTTTCCTTCTCCACTA
1 CTTTACCTCCTCCACTA
42836517 ACTCTGAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (18 bp):
CTTTACCTCCTCCACTAT
Found at i:42837721 original size:15 final size:15
Alignment explanation
Indices: 42837701--42837736 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
42837691 GTTATCATTG
**
42837701 AAAACCCTTCTTAAA
1 AAAACCCTAATTAAA
42837716 AAAACCCTAATTAAA
1 AAAACCCTAATTAAA
42837731 AAAACC
1 AAAACC
42837737 TTTCAGTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAACCCTAATTAAA
Found at i:42838846 original size:28 final size:28
Alignment explanation
Indices: 42838751--42838849 Score: 119
Period size: 29 Copynumber: 3.5 Consensus size: 28
42838741 TACTTGTATC
* *
42838751 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATT-ATA
*
42838779 TGGCCCATTAGGCCCAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACAT-TATA
*
42838808 TGGCCTATTAGGCCCAAATCACATTATA
1 TGGCCCATTAGGCCCAAATCACATTATA
* *
42838836 AGGCCCGTTAGGCC
1 TGGCCCATTAGGCC
42838850 TAGTCACATT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 29 0.48
29 31 0.51
30 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAAATCACATTATA
Found at i:42839823 original size:29 final size:28
Alignment explanation
Indices: 42839763--42839847 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
42839753 GCCTATATCT
* * *
42839763 GGCCCATTAAGCCCAATCATATTCATAT
1 GGCCCATTAGGCCCAATCACATTCATAA
*
42839791 GGCCCATTAGGCCCAAATCACATTTATAA
1 GGCCCATTAGGCCC-AATCACATTCATAA
** *
42839820 GGCCTGTTAGGCCCAGTCACATTCATAA
1 GGCCCATTAGGCCCAATCACATTCATAA
42839848 TCATGCTCAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 25 0.52
29 23 0.48
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (28 bp):
GGCCCATTAGGCCCAATCACATTCATAA
Found at i:42839928 original size:17 final size:18
Alignment explanation
Indices: 42839906--42839939 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42839896 TGCCTATTAT
42839906 GGGCCCA-ATAGCCCATC
1 GGGCCCATATAGCCCATC
*
42839923 GGGCCCATTTAGCCCAT
1 GGGCCCATATAGCCCAT
42839940 TCTAGCCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.18
Consensus pattern (18 bp):
GGGCCCATATAGCCCATC
Found at i:42840846 original size:29 final size:29
Alignment explanation
Indices: 42840749--42840848 Score: 139
Period size: 29 Copynumber: 3.5 Consensus size: 29
42840739 TACCTGTATC
* *
42840749 TGGCCCATTAAGCCC-AATCATATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* * *
42840777 TGGCCCATTAGACCCAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
42840806 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
*
42840835 TGGCCCGTTAGGCC
1 TGGCCCATTAGGCC
42840849 TAGTCACATT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
28 13 0.21
29 49 0.79
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:42841798 original size:28 final size:29
Alignment explanation
Indices: 42841754--42841867 Score: 119
Period size: 29 Copynumber: 4.0 Consensus size: 29
42841744 TACCTATATC
*
42841754 TGGCCCATTAAGG-CC-AATCATATTCATA
1 TGGCCCATT-AGGCCCAAATCACATTCATA
*
42841782 TGGCCCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
*
42841811 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* * * *
42841840 TCGCCCGTTAGG-CCTAGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
42841868 ATAATGCTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.04
28 25 0.34
29 45 0.61
30 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:42841818 original size:57 final size:58
Alignment explanation
Indices: 42841745--42841853 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 58
42841735 AATTTCTCAT
* * *
42841745 ACCTATATCTGGCCCATTAAGG-CC-AATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATT-AGGCCCAAATCACATTCATATCGCCCATTAGGCCCAAATC
* * *
42841802 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATCGCCCGTTAGGCC
1 ACCTATATATGGCCCATTAGGCCCAAATCACATTCATATCGCCCATTAGGCC
42841854 TAGTCACATT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
56 3 0.07
57 18 0.41
58 23 0.52
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (58 bp):
ACCTATATATGGCCCATTAGGCCCAAATCACATTCATATCGCCCATTAGGCCCAAATC
Done.