Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 161 of 349
Found at i:52010954 original size:79 final size:81
Alignment explanation
Indices: 52010818--52011000 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
52010808 TCGAATGATG
* *
52010818 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
52010882 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
52010897 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
52010959 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
52010977 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
52011001 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:52011016 original size:40 final size:40
Alignment explanation
Indices: 52010819--52011002 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
52010809 CGAATGATGT
* * * *
52010819 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
52010859 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
52010899 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
52010937 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
52010978 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
52011003 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:52011024 original size:79 final size:79
Alignment explanation
Indices: 52010871--52011035 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
52010861 GGACTAAGAT
* **
52010871 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
52010936 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
52010950 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
52011013 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
52011029 CCGAAGG
1 CCGAAGG
52011036 TACGTGATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:52019041 original size:40 final size:39
Alignment explanation
Indices: 52018952--52019095 Score: 107
Period size: 40 Copynumber: 3.6 Consensus size: 39
52018942 TCGAATGATG
* * *
52018952 TCCGGGCTAAGTCCCGAAGGC-TT-GTGCTA-AGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTGGTGCGAGA-T-ACTAAA
* * *
52018991 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTGGTGCGAGATACTAAA
* * *
52019031 TCCGGGCTAAGCCCGAAGTGCATTGGTGCGTGTTACTAAA
1 TCCGGGCTAAGTCCGAAG-GCATTGGTGCGAGATACTAAA
*
52019071 T-CGGGTTAAGTCCCGAAAGGCATTG
1 TCCGGGCTAAGT-CCG-AAGGCATTG
52019096 TAGTTACTTA
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
39 32 0.38
40 43 0.51
41 9 0.11
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTGGTGCGAGATACTAAA
Found at i:52065310 original size:28 final size:28
Alignment explanation
Indices: 52065242--52065395 Score: 220
Period size: 28 Copynumber: 5.5 Consensus size: 28
52065232 CATGAGATTG
* * * *
52065242 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
52065271 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
52065299 GCACTAAGTGTGCGAGTATGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
52065327 GCACTAAGTGTGCAAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
52065355 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
52065382 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
52065396 GACTTAATAT
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
27 23 0.20
28 73 0.64
29 18 0.16
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:52068438 original size:29 final size:29
Alignment explanation
Indices: 52068405--52068466 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
52068395 AATTCTGACT
52068405 AAATTACTAAAAATT-A-CATTTTTAAAAAA
1 AAATTA-T-AAAATTAAGCATTTTTAAAAAA
* *
52068434 AAATTATCAAATTAAGCCTTTTTAAAAAA
1 AAATTATAAAATTAAGCATTTTTAAAAAA
52068463 AAAT
1 AAAT
52068467 GAGATTAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 2 0.07
29 22 0.76
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (29 bp):
AAATTATAAAATTAAGCATTTTTAAAAAA
Found at i:52069514 original size:24 final size:26
Alignment explanation
Indices: 52069478--52069531 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
52069468 AATCAAAACC
52069478 TAAAAAAACTAAAAAAAAAAACT-AT
1 TAAAAAAACTAAAAAAAAAAACTAAT
* *
52069503 TAAAAAAA-TAAAACAAAAAATTAAT
1 TAAAAAAACTAAAAAAAAAAACTAAT
52069528 TAAA
1 TAAA
52069532 GGAGAGATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.19
Consensus pattern (26 bp):
TAAAAAAACTAAAAAAAAAAACTAAT
Found at i:52080138 original size:13 final size:14
Alignment explanation
Indices: 52080120--52080152 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
52080110 ATTTTTTAAA
*
52080120 TTTAAAACAAT-AT
1 TTTAAAAAAATAAT
52080133 TTTAAAAAAATAAT
1 TTTAAAAAAATAAT
52080147 TTTAAA
1 TTTAAA
52080153 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
TTTAAAAAAATAAT
Found at i:52081586 original size:30 final size:30
Alignment explanation
Indices: 52081552--52081611 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
52081542 TATTTTATTA
*
52081552 TTAATTTTGTTATTGTTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
52081582 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
52081612 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.23, C:0.02, G:0.17, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:52083874 original size:30 final size:30
Alignment explanation
Indices: 52083815--52083874 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
52083805 TATTTTATTA
**
52083815 TTAATTTTGTTATTGTTTTAAAGGCATTTG
1 TTAATTTTGTTATTAATTTAAAGGCATTTG
* *
52083845 TTAATTTTGTTATTAATTTAGAGGTATTTG
1 TTAATTTTGTTATTAATTTAAAGGCATTTG
52083875 CTTGTTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTAATTTAAAGGCATTTG
Found at i:52086208 original size:20 final size:20
Alignment explanation
Indices: 52086180--52086226 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
52086170 TTTTCAAGGC
*
52086180 AAATGCCTTTTGAC-TTAGGA
1 AAATTCCTTTTG-CTTTAGGA
52086200 AAATTCC--TTGCTTTAGGA
1 AAATTCCTTTTGCTTTAGGA
52086218 AAATTCCTT
1 AAATTCCTT
52086227 GCTGAGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
20 6 0.26
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
AAATTCCTTTTGCTTTAGGA
Found at i:52086217 original size:18 final size:18
Alignment explanation
Indices: 52086194--52086229 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52086184 GCCTTTTGAC
52086194 TTAGGAAAATTCCTTGCT
1 TTAGGAAAATTCCTTGCT
52086212 TTAGGAAAATTCCTTGCT
1 TTAGGAAAATTCCTTGCT
52086230 GAGTTTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (18 bp):
TTAGGAAAATTCCTTGCT
Found at i:52092080 original size:21 final size:21
Alignment explanation
Indices: 52092056--52092098 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
52092046 GATACCCTTG
* * *
52092056 TAAAATATTGGTACTTTAATA
1 TAAAATATAGATAATTTAATA
*
52092077 TAAAGTATAGATAATTTAATA
1 TAAAATATAGATAATTTAATA
52092098 T
1 T
52092099 GCTATCAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (21 bp):
TAAAATATAGATAATTTAATA
Found at i:52099593 original size:17 final size:17
Alignment explanation
Indices: 52099571--52099603 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52099561 GATGATTGAG
*
52099571 TTAATAAATATTATTTC
1 TTAATAAATAATATTTC
52099588 TTAATAAATAATATTT
1 TTAATAAATAATATTT
52099604 ACAAGGTTAT
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:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATAAATAATATTTC
Found at i:52104256 original size:21 final size:21
Alignment explanation
Indices: 52104230--52104272 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
52104220 CAAAAATGAC
52104230 AATAATGATGAAAACGATAAT
1 AATAATGATGAAAACGATAAT
* * *
52104251 AATAATGTTGATAATGATAAT
1 AATAATGATGAAAACGATAAT
52104272 A
1 A
52104273 GTGGTGGTAA
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:0.53, C:0.02, G:0.14, T:0.30
Consensus pattern (21 bp):
AATAATGATGAAAACGATAAT
Found at i:52104656 original size:22 final size:22
Alignment explanation
Indices: 52104631--52104678 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
52104621 ATAAAAGAGG
* *
52104631 AAAATATAATAACAATAATAGT
1 AAAATACAACAACAATAATAGT
*
52104653 AAAATACAACAATAATAATAGT
1 AAAATACAACAACAATAATAGT
52104675 AAAA
1 AAAA
52104679 GGTGTAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (22 bp):
AAAATACAACAACAATAATAGT
Found at i:52104838 original size:14 final size:14
Alignment explanation
Indices: 52104819--52104845 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52104809 AATTACTATA
52104819 TATATACATATATC
1 TATATACATATATC
52104833 TATATACATATAT
1 TATATACATATAT
52104846 ATAAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATACATATATC
Found at i:52106337 original size:18 final size:18
Alignment explanation
Indices: 52106314--52106355 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
52106304 TCTGGGGTTA
*
52106314 TTTGGGTAGGTTATTTGT
1 TTTGGGTAGGTTATTTAT
52106332 TTTGGGTAGGTTATTTAT
1 TTTGGGTAGGTTATTTAT
52106350 TTTGGG
1 TTTGGG
52106356 CCCAAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (18 bp):
TTTGGGTAGGTTATTTAT
Found at i:52117243 original size:24 final size:24
Alignment explanation
Indices: 52117214--52117259 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
52117204 CAAAAATGAC
52117214 AATAATGATGAAAACGATAATAAT
1 AATAATGATGAAAACGATAATAAT
* * *
52117238 AATAATGTTGATAATGATAATA
1 AATAATGATGAAAACGATAATA
52117260 GTGGTGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.13, T:0.30
Consensus pattern (24 bp):
AATAATGATGAAAACGATAATAAT
Found at i:52117250 original size:18 final size:18
Alignment explanation
Indices: 52117229--52117295 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
52117219 TGATGAAAAC
52117229 GATAATAATAATAATGTT
1 GATAATAATAATAATGTT
* * *
52117247 GATAATGATAATAGTGGT
1 GATAATAATAATAATGTT
* *
52117265 GGTAA-AACT-ATAATATT
1 GATAATAA-TAATAATGTT
*
52117282 GATGATAATAATAA
1 GATAATAATAATAA
52117296 AAATAATAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
17 10 0.28
18 26 0.72
ACGTcount: A:0.48, C:0.01, G:0.16, T:0.34
Consensus pattern (18 bp):
GATAATAATAATAATGTT
Found at i:52117645 original size:23 final size:23
Alignment explanation
Indices: 52117619--52117667 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
52117609 ATAAAAGAGG
* *
52117619 AAAATATAATAACAATAATAGTA
1 AAAATACAACAACAATAATAGTA
*
52117642 AAAATACAACAATAATAATAGTA
1 AAAATACAACAACAATAATAGTA
52117665 AAA
1 AAA
52117668 GGTGTAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAATACAACAACAATAATAGTA
Found at i:52117827 original size:14 final size:14
Alignment explanation
Indices: 52117808--52117834 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52117798 AATTACTATA
52117808 TATATACATATATC
1 TATATACATATATC
52117822 TATATACATATAT
1 TATATACATATAT
52117835 ATAAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATACATATATC
Found at i:52122173 original size:51 final size:50
Alignment explanation
Indices: 52122087--52122183 Score: 142
Period size: 49 Copynumber: 1.9 Consensus size: 50
52122077 TAATGAAGTC
* *
52122087 ATGCATTATGTAACCTCATGTTAGTTAAGTTTGCATCA-TAAATTATGAT
1 ATGCATTATATAACCCCATGTTAGTTAAGTTTGCATCATTAAATTATGAT
*
52122136 ATGCATTATATAACTCCCCTGTTAGTTAAAGTTTGCATCATTAAATTA
1 ATGCATTATATAAC-CCCATGTTAGTT-AAGTTTGCATCATTAAATTA
52122184 AGTCATGCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 13 0.31
50 10 0.24
51 12 0.29
52 7 0.17
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (50 bp):
ATGCATTATATAACCCCATGTTAGTTAAGTTTGCATCATTAAATTATGAT
Found at i:52122193 original size:52 final size:51
Alignment explanation
Indices: 52122073--52122203 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 51
52122063 ATCTGTTCTG
* * * *
52122073 CATTTAATGAAGTCATGCATTATGTAAC-CTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATATAACTCCCATGTTAGTTAAGTTTGCAT
* *
52122123 CA-TAAATTATGAT-ATGCATTATATAACTCCCCTGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAG-TCATGCATTATATAACTCCCATGTTAGTT-AAGTTTGCAT
52122174 CATTAAATTAAGTCATGCATTA-AGTAACTC
1 CATTAAATTAAGTCATGCATTATA-TAACTC
52122204 ATTTGTTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
49 19 0.28
50 13 0.19
51 14 0.21
52 22 0.32
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTATATAACTCCCATGTTAGTTAAGTTTGCAT
Found at i:52140691 original size:28 final size:28
Alignment explanation
Indices: 52140633--52140707 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
52140623 CTTTTCAAAG
* *
52140633 CTCAATTGATTGCTAACTTTAAATTAGAAA
1 CTCAATTAATTG-TAA-TTTAAATTAAAAA
*
52140663 CTCAATTAATTGTAATTTCAATTAAAAA
1 CTCAATTAATTGTAATTTAAATTAAAAA
*
52140691 CTTAATTAAATT-TAATT
1 CTCAATT-AATTGTAATT
52140708 ATTTTCTAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 22 0.55
29 7 0.17
30 11 0.28
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (28 bp):
CTCAATTAATTGTAATTTAAATTAAAAA
Found at i:52142744 original size:3 final size:3
Alignment explanation
Indices: 52142410--52142731 Score: 302
Period size: 3 Copynumber: 107.0 Consensus size: 3
52142400 ACGTAACAAC
* * *
52142410 ATA ATA ATA GATA CGATA ATA CTA ATA ACA ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA -ATA --ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
52142458 TTA ATA A-A ATA AAA ATA ATA GTA ATA A-A ATA A-A ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
52142502 GTA ATA ATA ATG ATA ATA ATG ATA ATAA ATA ATA ATA GTAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA AT-A ATA ATA
* * *
52142549 ATA A-A ATA ATA ATA ATA ATA GTA ATA ATA GTA ATA ATA ATG ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * *
52142597 ATA ATA GTA ACA ATA ATA ATA ATG ATA ATAA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* * *
52142643 GTA GTA ATA ATA ATA ATGA AT- ATAA ATA ATA GTA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA ATA
* *
52142688 ATA ATA ATG ATA ATAA ATA ATA GTA A-A A-A ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
52142732 GTAGGAATAA
Statistics
Matches: 262, Mismatches: 40, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
2 18 0.07
3 218 0.83
4 22 0.08
5 4 0.02
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:52144120 original size:45 final size:45
Alignment explanation
Indices: 52144065--52144516 Score: 227
Period size: 45 Copynumber: 9.6 Consensus size: 45
52144055 CTTTAATTTA
52144065 CTCCACTGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAGTCTG
1 CTCCACTGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAGTCTG
* * * * *
52144110 CTCTACTGCAACTTCAGGGAGATAAGATTTGTAATTTGTAGCTTCAATTTG
1 CTCCACTGCAACTTCAGGGAAATAAGATTTG----TTGT--CTTTAGTCTG
* * * * * *
52144161 CTCCACTGTAATTTCAAGGAAATGAGATTTGGTATCTTTAGTCTG
1 CTCCACTGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAGTCTG
*
52144206 CTCCACTGCAACTTCAGGGAGATAAGATTTATGACTCTTAGT-TTT-GATCTG
1 CTCCACTGCAACTTCAGGGAAATAAGA-TT-TG----TT-GTCTTTAG-TCTG
* * * *
52144257 TTCCACTGCAA-TGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTG
1 CTCCACTGCAACT-TCAGGGAAATAAGATTTGTTGTCTTTAGTCTG
* * * ** * * * * *
52144302 CTGCACTGCAACTTTAGGGAGATAAGGCTAG-TGGCTTCAATCTA
1 CTCCACTGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAGTCTG
* * * *
52144346 CTCCACTACAACTTCA-AGAAGATAAGATTCACCATAATTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAA-ATAAGATT-----T--GTTGT--CTTTAGTCTG
* * *
52144400 TTCCACTGCAACATT-AGGGAAATAAGATTCGTTGTCTTCAGTCTG
1 CTCCACTGCAAC-TTCAGGGAAATAAGATTTGTTGTCTTTAGTCTG
* * ** * * * *
52144445 CTCCGCTGCAACTTCAGGGAGATAAG-GCTGGTGGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAGTCTG
*
52144489 CTCCACTGCAACTTTA-GGAAGATAAGAT
1 CTCCACTGCAACTTCAGGGAA-ATAAGAT
52144517 CCTCCATAAT
Statistics
Matches: 303, Mismatches: 70, Indels: 68
0.69 0.16 0.15
Matches are distributed among these distances:
43 5 0.02
44 64 0.21
45 115 0.38
46 4 0.01
47 8 0.03
49 5 0.02
50 4 0.01
51 63 0.21
52 3 0.01
54 27 0.09
55 5 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAGTCTG
Found at i:52144166 original size:96 final size:95
Alignment explanation
Indices: 52144047--52144327 Score: 332
Period size: 96 Copynumber: 2.9 Consensus size: 95
52144037 GAGGTATAGG
* *
52144047 ATTTGTAGCTTTAATTTACTCCACTGCAACTTCAGGGAAATAAGATTTGTTGTCTTTAGTCTGCT
1 ATTTGTAGCTTTAATTTGCTCCACTGCAA-TTCAGGGAAATAAGATTTGCTGTCTTTAGTCTGCT
*
52144112 CTACTGCAACTTCAGGGAGATAAGATTTGT-A
65 C-ACTGCAACTTCAGGGAGATAAGATTTATGA
* * * * * *
52144143 ATTTGTAGCTTCAATTTGCTCCACTGTAATTTCAAGGAAATGAGATTTGGTATCTTTAGTCTGCT
1 ATTTGTAGCTTTAATTTGCTCCACTGCAA-TTCAGGGAAATAAGATTTGCTGTCTTTAGTCTGCT
52144208 CCACTGCAACTTCAGGGAGATAAGATTTATGA
65 -CACTGCAACTTCAGGGAGATAAGATTTATGA
* * * * * * * *
52144240 CTCT-TAGTTTTGATCTGTTCCACTGCAATGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCT
1 ATTTGTAGCTTTAATTTGCTCCACTGCAAT-TCAGGGAAATAAGATTTGCTGTCTTTAGTCTGCT
*
52144304 GCACTGCAACTTTAGGGAGATAAG
65 -CACTGCAACTTCAGGGAGATAAG
52144328 GCTAGTGGCT
Statistics
Matches: 157, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
95 1 0.01
96 152 0.97
97 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (95 bp):
ATTTGTAGCTTTAATTTGCTCCACTGCAATTCAGGGAAATAAGATTTGCTGTCTTTAGTCTGCTC
ACTGCAACTTCAGGGAGATAAGATTTATGA
Found at i:52144423 original size:143 final size:143
Alignment explanation
Indices: 52144252--52144613 Score: 499
Period size: 143 Copynumber: 2.5 Consensus size: 143
52144242 CTTAGTTTTG
** * * * *
52144252 ATCTGTTCCACTGCAATGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTGCACTGCAACTTT
1 ATCTGTTCCACTGCAACATTAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCACTGCAACTTC
*
52144317 AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAACTTCAAGAAGATAAGATTCACCATA
66 AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAACTTCAAGAAGATAAGATCCACCATA
*
52144382 ATTTGTAGCTTTA
131 ATTTGTAGCTGTA
*
52144395 ATCTGTTCCACTGCAACATTAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCGCTGCAACTTC
1 ATCTGTTCCACTGCAACATTAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCACTGCAACTTC
* * * * * *
52144460 AGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCTCCATA
66 AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAACTTCAAGAAGATAAGATCCACCATA
52144525 ATTTGTAGCTGTA
131 ATTTGTAGCTGTA
* * * * * ** *
52144538 ATTTGTTCCACTGTAACTTTAAGGAAATAAGATTCATTGTCTTCAGTCTGCTCTGCTGTAACTTC
1 ATCTGTTCCACTGCAACATTAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCACTGCAACTTC
**
52144603 AGAAAGATAAG
66 AGGGAGATAAG
52144614 ACTTGTAATT
Statistics
Matches: 195, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
143 195 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (143 bp):
ATCTGTTCCACTGCAACATTAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCACTGCAACTTC
AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAACTTCAAGAAGATAAGATCCACCATA
ATTTGTAGCTGTA
Found at i:52144627 original size:143 final size:141
Alignment explanation
Indices: 52144252--52144657 Score: 497
Period size: 143 Copynumber: 2.8 Consensus size: 141
52144242 CTTAGTTTTG
** * * * * *
52144252 ATCTGTTCCACTGCAATGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTGCACTGCAACTTT
1 ATCTGTTCCACTGCAACATTAAGGAAATAAGATTCGTTGTCTTCAGTCTGCT-CGCTGCAACTTC
* * * *
52144317 AGGGAGATAAGGCTAGTGGCTTCAATCTACTCCACTACAACTTCAAGAAGATAAGATTCACCATA
65 AGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTT-TAGAAGATAAGATCCACCATA
*
52144382 ATTTGTAGCTTTA
129 ATTTGTAGCTGTA
*
52144395 ATCTGTTCCACTGCAACATTAGGGAAATAAGATTCGTTGTCTTCAGTCTGCTCCGCTGCAACTTC
1 ATCTGTTCCACTGCAACATTAAGGAAATAAGATTCGTTGTCTTCAGTCTGCT-CGCTGCAACTTC
* *
52144460 AGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCTCCATA
65 AGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTTA-GAAGATAAGATCCACCATA
52144525 ATTTGTAGCTGTA
129 ATTTGTAGCTGTA
* * * * *
52144538 ATTTGTTCCACTGTAACTTTAAGGAAATAAGATTCATTGTCTTCAGTCTGCTCTGCTGTAACTTC
1 ATCTGTTCCACTGCAACATTAAGGAAATAAGATTCGTTGTCTTCAGTCTGCTC-GCTGCAACTTC
** * * *** * *
52144603 AGAAAGATAAGACTTGTAATTTCAACCTGCTCTACTGCAACTTTAGAGAGATAAG
65 AGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTTAGA-AGATAAG
52144658 GTTAGTGGCT
Statistics
Matches: 231, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
142 4 0.02
143 227 0.98
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (141 bp):
ATCTGTTCCACTGCAACATTAAGGAAATAAGATTCGTTGTCTTCAGTCTGCTCGCTGCAACTTCA
GGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTTAGAAGATAAGATCCACCATAAT
TTGTAGCTGTA
Found at i:52153657 original size:40 final size:40
Alignment explanation
Indices: 52153602--52153878 Score: 473
Period size: 40 Copynumber: 6.9 Consensus size: 40
52153592 GCATGAGCAT
52153602 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
52153642 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
52153682 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
52153722 TTGATATATCCGGGCTAAAACCCGAAGGCATTTGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * *
52153762 TTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
*
52153802 TTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
* * * *
52153842 TTGCTATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
52153879 TTGCGGTTAT
Statistics
Matches: 223, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 223 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (40 bp):
TTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
Found at i:52156279 original size:19 final size:19
Alignment explanation
Indices: 52156242--52156284 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
52156232 CCGTGAAATT
*
52156242 TAATGCATATGATGCAATG
1 TAATGCAAATGATGCAATG
52156261 TAATGCAAATGCATG-AATG
1 TAATGCAAATG-ATGCAATG
*
52156280 CAATG
1 TAATG
52156285 AATGCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (19 bp):
TAATGCAAATGATGCAATG
Found at i:52157016 original size:8 final size:8
Alignment explanation
Indices: 52157003--52157030 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
52156993 TTCTTTCCCT
52157003 TTCTCAGC
1 TTCTCAGC
52157011 TTCTCAGC
1 TTCTCAGC
52157019 TTCTCAGC
1 TTCTCAGC
52157027 TTCT
1 TTCT
52157031 AGTTTCTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.36, G:0.11, T:0.43
Consensus pattern (8 bp):
TTCTCAGC
Found at i:52160306 original size:3 final size:3
Alignment explanation
Indices: 52160000--52160293 Score: 263
Period size: 3 Copynumber: 97.0 Consensus size: 3
52159990 ATAAGAAATG
* *
52160000 ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA GTA ATA ATA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
* *
52160046 ATA ATA GTA ATA ATA ATA ATA ATA ATGA AT- ATAA ATA ATA GTA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA
* * * * * * *
52160091 ATA ATA ATA ATA ATA ATA ATA ATG ATG ATG ATG ATG ATG ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
52160139 ATG ATA ATAA ATT ATA ATA AAA ATA ATA ACA ATA ATA ATA GTA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
52160185 ATA ATA ATA ATA ATGA AT- ATAA ATA ATA GTA A-A ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
52160230 ATA ATA ATA ATG ATG ATG ATG ATG ATA ATG ATA ATAA ATT ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
* *
52160276 AAA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA
52160294 GTAGGAATAA
Statistics
Matches: 246, Mismatches: 34, Indels: 22
0.81 0.11 0.07
Matches are distributed among these distances:
2 8 0.03
3 219 0.89
4 19 0.08
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:52163293 original size:90 final size:90
Alignment explanation
Indices: 52163199--52163383 Score: 223
Period size: 90 Copynumber: 2.1 Consensus size: 90
52163189 TTTTACATTC
* * * * **
52163199 AATTGAGTATTTGAACTTTCAAAATGCATCAAAAAA-ACCCTTTAATTTTTTTCA-AAATAAAGC
1 AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAATACCC-TCAAAATTTTTCATAAA-AAA-C
** *
52163262 AATTAAGCTGCTTCTTTTTTTT-CACTT
63 AATTAAGCCCCTACTTTTTTTTGCACTT
* *
52163289 AATTGGGTACTTGAACTGTCAAAATGTATAAAAAAATACCCTCAAAATTTTTCATAAAAAACAAT
1 AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAATACCCTCAAAATTTTTCATAAAAAACAAT
52163354 TAAGCCCCTACTTTTTTTTGCACTT
66 TAAGCCCCTACTTTTTTTTGCACTT
52163379 AATTG
1 AATTG
52163384 TCAAAATGCA
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
89 20 0.25
90 54 0.67
91 7 0.09
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (90 bp):
AATTGAGTACTTGAACTGTCAAAATGCATAAAAAAATACCCTCAAAATTTTTCATAAAAAACAAT
TAAGCCCCTACTTTTTTTTGCACTT
Found at i:52163546 original size:27 final size:28
Alignment explanation
Indices: 52163515--52163595 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
52163505 CAAAAAAATT
*
52163515 ATAAAAA-ATAAAAACTA-TTAAATTTTA
1 ATAAAAATATAAAAA-TATTTAAAATTTA
52163542 ATAAAAATATAAAAATATTTAAAATTTA
1 ATAAAAATATAAAAATATTTAAAATTTA
* * * *
52163570 CTAAGAAT-TAGAAAAAATGTAAAATT
1 ATAAAAATATA-AAAATATTTAAAATT
52163596 GTAAAATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.24
28 35 0.76
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (28 bp):
ATAAAAATATAAAAATATTTAAAATTTA
Found at i:52163557 original size:20 final size:21
Alignment explanation
Indices: 52163521--52163563 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
52163511 AATTATAAAA
*
52163521 AATAAAAACTATTAAAT-TTT
1 AATAAAAACTATAAAATATTT
52163541 AATAAAAA-TATAAAAATATTT
1 AATAAAAACTAT-AAAATATTT
52163562 AA
1 AA
52163564 AATTTACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 12 0.60
21 5 0.25
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAAAAACTATAAAATATTT
Found at i:52163897 original size:10 final size:10
Alignment explanation
Indices: 52163884--52163926 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
52163874 GATTATAAAA
52163884 TTTTATATAT
1 TTTTATATAT
*
52163894 TTTTCTATAT
1 TTTTATATAT
*
52163904 TTCTATATA-
1 TTTTATATAT
52163913 TTTTATA-AT
1 TTTTATATAT
52163922 TTTTA
1 TTTTA
52163927 ATGACTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 1 0.04
9 11 0.39
10 16 0.57
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTATATAT
Found at i:52181164 original size:90 final size:90
Alignment explanation
Indices: 52181070--52181236 Score: 212
Period size: 90 Copynumber: 1.9 Consensus size: 90
52181060 AAGTGATTTT
* * * *
52181070 GTATAAGACCATGTTTGAGACATGGCATCGATATG-AGGTCTCGTATAAGACCATGTCT-GAGAC
1 GTATAAGACCATATCTGAGACATGACATCGATATGTAGGTC-CATATAAGACCATGTCTGGA-AC
52181133 ATGGCGTTGGCACCGATTCAAGACTTC
64 ATGGCGTTGGCACCGATTCAAGACTTC
* * * * *
52181160 GTATAAGACCATATCTGGGATATGACATCGATGTGTAGTTCCATGTAAGACCATGTCTGGAACAT
1 GTATAAGACCATATCTGAGACATGACATCGATATGTAGGTCCATATAAGACCATGTCTGGAACAT
*
52181225 GGCTTTGGCACC
66 GGCGTTGGCACC
52181237 CTATTTGGTG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
90 59 0.91
91 6 0.09
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (90 bp):
GTATAAGACCATATCTGAGACATGACATCGATATGTAGGTCCATATAAGACCATGTCTGGAACAT
GGCGTTGGCACCGATTCAAGACTTC
Found at i:52185442 original size:20 final size:22
Alignment explanation
Indices: 52185402--52185452 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
52185392 ATTTTTAGAT
52185402 TTTAATTATGTAAATATATATAA
1 TTTAATTA-GTAAATATATATAA
*
52185425 TTTAATTA-TAAA-ATATATTA
1 TTTAATTAGTAAATATATATAA
*
52185445 TTAAATTA
1 TTTAATTA
52185453 ATTAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 14 0.54
21 4 0.15
23 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTAATTAGTAAATATATATAA
Found at i:52185442 original size:24 final size:23
Alignment explanation
Indices: 52185402--52185456 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
52185392 ATTTTTAGAT
**
52185402 TTTAATTATGTAAATA-TATATAA
1 TTTAATTATAAAAATATTAT-TAA
52185425 TTTAATTATAAAATATATTATTAA
1 TTTAATTATAAAA-ATATTATTAA
*
52185449 ATTAATTA
1 TTTAATTA
52185457 ATTATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.41
24 13 0.48
25 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTAATTATAAAAATATTATTAA
Found at i:52185480 original size:25 final size:27
Alignment explanation
Indices: 52185426--52185482 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
52185416 TATATATAAT
*
52185426 TTAATTATAAAATATATTATTAAATTAA
1 TTAATTATAAAATATATTATT-AATGAA
52185454 TTAATTAT-AAATATCA-TATT-ATGAA
1 TTAATTATAAAATAT-ATTATTAATGAA
52185479 TTAA
1 TTAA
52185483 ATTAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.30
27 10 0.37
28 9 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TTAATTATAAAATATATTATTAATGAA
Found at i:52185616 original size:16 final size:16
Alignment explanation
Indices: 52185597--52185646 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
52185587 AAATAGATAT
52185597 TTATTATTTATCATTA
1 TTATTATTTATCATTA
*
52185613 TTATTATTCTATCA-AA
1 TTATTATT-TATCATTA
*
52185629 TTATAATTTAT-ATTA
1 TTATTATTTATCATTA
52185644 TTA
1 TTA
52185647 AATTATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 16 0.55
17 5 0.17
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTATTTATCATTA
Found at i:52185775 original size:20 final size:20
Alignment explanation
Indices: 52185750--52185787 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52185740 TATTTAATTA
52185750 ATTTTTATT-TAATTAAAAAG
1 ATTTTTATTAT-ATTAAAAAG
52185770 ATTTTTATTATATTAAAA
1 ATTTTTATTATATTAAAA
52185788 TATTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTTTTATTATATTAAAAAG
Found at i:52185903 original size:19 final size:18
Alignment explanation
Indices: 52185874--52185929 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
52185864 CTCCAATTGT
*
52185874 AATATATATTTATTATTA
1 AATAAATATTTATTATTA
*
52185892 AATAAGATATTTATTATAA
1 AATAA-ATATTTATTATTA
*
52185911 TAATAATTA-TTATTATTA
1 -AATAAATATTTATTATTA
52185929 A
1 A
52185930 GTTAATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 1 0.03
18 12 0.38
19 14 0.44
20 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATAAATATTTATTATTA
Found at i:52185951 original size:13 final size:14
Alignment explanation
Indices: 52185933--52185979 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 14
52185923 TTATTAAGTT
52185933 AATAAAATAAAAG-
1 AATAAAATAAAAGA
*
52185946 AATAAAATAAATGA
1 AATAAAATAAAAGA
52185960 AATAAAAT-AAAGA
1 AATAAAATAAAAGA
*
52185973 AACAAAA
1 AATAAAA
52185980 CAAAGTAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 22 0.73
14 8 0.27
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:52186819 original size:40 final size:40
Alignment explanation
Indices: 52186737--52186843 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 40
52186727 TTGAGACTGA
* * * * *
52186737 TACTGAACTGAATTATGGAA-TACTGAATATTGTTTTGAG
1 TACTGAATTGAATTGTGAAATTACTGAATATTATTATGAG
* *
52186776 TACTGAATTGAATTGTGAACTTACTGAATATTATTATGTG
1 TACTGAATTGAATTGTGAAATTACTGAATATTATTATGAG
*
52186816 TACTGCATTGAATTGTGAAATTACTGAA
1 TACTGAATTGAATTGTGAAATTACTGAA
52186844 GTAATGAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
39 16 0.28
40 42 0.72
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (40 bp):
TACTGAATTGAATTGTGAAATTACTGAATATTATTATGAG
Found at i:52187064 original size:12 final size:12
Alignment explanation
Indices: 52187047--52187071 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52187037 GCCGACTATT
52187047 GTTACTGTTACC
1 GTTACTGTTACC
52187059 GTTACTGTTACC
1 GTTACTGTTACC
52187071 G
1 G
52187072 ATTCGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:52187097 original size:43 final size:45
Alignment explanation
Indices: 52187049--52187157 Score: 143
Period size: 43 Copynumber: 2.5 Consensus size: 45
52187039 CGACTATTGT
* *
52187049 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTG-CAT-AA
1 TACTGTTACCGTTACTGTTACAGAGTCAG-CACTTTGTGTCATGAA
**
52187092 TACTGTTACCGTTACTGTTACAGAGTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGAGTCAGCACTTTGTGTCATGAA
*
52187137 TACTGTTACTGTTACTGTTAC
1 TACTGTTACCGTTACTGTTAC
52187158 TGTTGTCGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
43 34 0.59
44 2 0.03
45 22 0.38
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGAGTCAGCACTTTGTGTCATGAA
Found at i:52187148 original size:6 final size:6
Alignment explanation
Indices: 52187137--52187180 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
52187127 GTGTGTTGAA
*
52187137 TACTGT TACTGT TACTGT TACTGT T-GTCGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACT-GT TACTG-T TACTGT T
52187181 TAAGTACTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 1 0.03
6 25 0.76
7 7 0.21
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.50
Consensus pattern (6 bp):
TACTGT
Found at i:52188474 original size:18 final size:18
Alignment explanation
Indices: 52188447--52188490 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
52188437 AGGGGAATTG
*
52188447 TACCTGCTACTAAATCAA
1 TACCTACTACTAAATCAA
* *
52188465 TACCTACTACTACATCAG
1 TACCTACTACTAAATCAA
52188483 TACCTACT
1 TACCTACT
52188491 GTCAGACGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.30
Consensus pattern (18 bp):
TACCTACTACTAAATCAA
Found at i:52193231 original size:20 final size:22
Alignment explanation
Indices: 52193191--52193241 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
52193181 ATTTTTAGAT
52193191 TTTAATTATGTAAATATATATAA
1 TTTAATTA-GTAAATATATATAA
*
52193214 TTTAATTA-TAAA-ATATATTA
1 TTTAATTAGTAAATATATATAA
*
52193234 TTAAATTA
1 TTTAATTA
52193242 ATTAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 14 0.54
21 4 0.15
23 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTAATTAGTAAATATATATAA
Found at i:52193231 original size:24 final size:23
Alignment explanation
Indices: 52193191--52193245 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
52193181 ATTTTTAGAT
**
52193191 TTTAATTATGTAAATA-TATATAA
1 TTTAATTATAAAAATATTAT-TAA
52193214 TTTAATTATAAAATATATTATTAA
1 TTTAATTATAAAA-ATATTATTAA
*
52193238 ATTAATTA
1 TTTAATTA
52193246 ATTATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.41
24 13 0.48
25 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTAATTATAAAAATATTATTAA
Found at i:52193269 original size:25 final size:27
Alignment explanation
Indices: 52193215--52193271 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
52193205 TATATATAAT
*
52193215 TTAATTATAAAATATATTATTAAATTAA
1 TTAATTATAAAATATATTATT-AATGAA
52193243 TTAATTAT-AAATATCA-TATT-ATGAA
1 TTAATTATAAAATAT-ATTATTAATGAA
52193268 TTAA
1 TTAA
52193272 ATTAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.30
27 10 0.37
28 9 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TTAATTATAAAATATATTATTAATGAA
Found at i:52193422 original size:16 final size:16
Alignment explanation
Indices: 52193401--52193450 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
52193391 TATTTATGAT
52193401 TTATTATTTATCATTA
1 TTATTATTTATCATTA
*
52193417 TTATTATTCTATCA-AA
1 TTATTATT-TATCATTA
*
52193433 TTATAATTTAT-ATTA
1 TTATTATTTATCATTA
52193448 TTA
1 TTA
52193451 AATTATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 16 0.55
17 5 0.17
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTATTTATCATTA
Found at i:52193710 original size:19 final size:18
Alignment explanation
Indices: 52193681--52193736 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
52193671 CACCAACTGT
*
52193681 AATATATATTTATTATTA
1 AATAAATATTTATTATTA
*
52193699 AATAAGATATTTATTATAA
1 AATAA-ATATTTATTATTA
*
52193718 TAATAATTA-TTATTATTA
1 -AATAAATATTTATTATTA
52193736 A
1 A
52193737 GTTAATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 1 0.03
18 12 0.38
19 14 0.44
20 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATAAATATTTATTATTA
Found at i:52193758 original size:13 final size:14
Alignment explanation
Indices: 52193740--52193786 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
52193730 TTATTAAGTT
52193740 AATAAAATAAAAG-
1 AATAAAATAAAAGA
* *
52193753 AATAAAAGAAATGA
1 AATAAAATAAAAGA
52193767 AATAAAAT-AAAGA
1 AATAAAATAAAAGA
*
52193780 AACAAAA
1 AATAAAA
52193787 CAAAGTAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:52194652 original size:40 final size:40
Alignment explanation
Indices: 52194576--52194662 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
52194566 AATTATGGAA
* * * *
52194576 TACTGAATATTGTTTTGAGTACTAAATTGCATTGTGAAGT
1 TACTGAATATTGTTATGAGTACTAAATTGAACTGTGAAAT
* * **
52194616 TACTTAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGAGTACTAAATTGAACTGTGAAAT
52194656 TACTGAA
1 TACTGAA
52194663 GTAATGAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.41
Consensus pattern (40 bp):
TACTGAATATTGTTATGAGTACTAAATTGAACTGTGAAAT
Found at i:52194972 original size:6 final size:6
Alignment explanation
Indices: 52194961--52195001 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
52194951 TGTTGAATAT
* *
52194961 TGTTAC TGTTAC TGTTAC TGCTAC TGTTAC TAATTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC T-GTTAC TGTT
52195002 TAGGTACTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
TGTTAC
Found at i:52201063 original size:19 final size:19
Alignment explanation
Indices: 52201041--52201086 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
52201031 CGTGTCCTAA
* *
52201041 CCACATGGGTGTGTAAAAT
1 CCACACGGGCGTGTAAAAT
*
52201060 CCACACGGGCGTGTGAAAT
1 CCACACGGGCGTGTAAAAT
52201079 CCACACGG
1 CCACACGG
52201087 CCTACCCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.17
Consensus pattern (19 bp):
CCACACGGGCGTGTAAAAT
Found at i:52210809 original size:16 final size:16
Alignment explanation
Indices: 52210790--52210823 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
52210780 AAAGTGATTT
52210790 AATCTAA-AAGCACTAA
1 AATCTAACAA-CACTAA
52210806 AATCTAACAACACTAA
1 AATCTAACAACACTAA
52210822 AA
1 AA
52210824 GTGATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.18
Consensus pattern (16 bp):
AATCTAACAACACTAA
Found at i:52210833 original size:41 final size:41
Alignment explanation
Indices: 52210776--52210858 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
52210766 TGCCTTGTGA
52210776 ACTAAAAGTGATTTAATCTAAAAGCACTAAAATCTAACAAC
1 ACTAAAAGTGATTTAATCTAAAAGCACTAAAATCTAACAAC
52210817 ACTAAAAGTGATTTAATCTAAAAGCACTAAAATCTAACAAC
1 ACTAAAAGTGATTTAATCTAAAAGCACTAAAATCTAACAAC
52210858 A
1 A
52210859 TTCTTAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (41 bp):
ACTAAAAGTGATTTAATCTAAAAGCACTAAAATCTAACAAC
Found at i:52213861 original size:237 final size:236
Alignment explanation
Indices: 52213440--52213877 Score: 655
Period size: 237 Copynumber: 1.9 Consensus size: 236
52213430 GAGGGCTGAA
* * *
52213440 TTCAAACAGAAATCAATGATAGACTGGATACAAAGGGCAACTTAACACGAAATTGGTTCATATGA
1 TTCAAACAGAAATCAATAATAGACTGGATACAAAGGGCAACTCAACACAAAATTGGTTCATATGA
* * *
52213505 TGGTCAAAAGCAAGCACTGTAGGGCCACTATAAGGATATTAACTGATTTGGTGGGGAATAAATTG
66 TGGTCAAAAGCAAGCACTGTAGGGCCACTATAAGCATATTAACTGATTTGGAGGGAAATAAATTG
* * *
52213570 GAAACTTCGCAGCAGATTTCAAGGGAAGTCACAATGTTCTTCAAGCAGTTGTTGGCTATTGCAGA
131 GAAACTTCCCAGCAGATTTCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGGCTACTGCAGA
*
52213635 TGGCCACATTCAAAGAGTTGCAGCTGGCCGAGGAATGTTTC
196 CGGCCACATTCAAAGAGTTGCAGCTGGCCGAGGAATGTTTC
* * *
52213676 TTCAGACAGAAATCAATAATAGACTGGATACAAATGGGCAACTCAACACAAAATTGTTTCGTATG
1 TTCAAACAGAAATCAATAATAGACTGGATACAAA-GGGCAACTCAACACAAAATTGGTTCATATG
* * ** *
52213741 ATGGTCAAAAGCAAGCACTTTAGGGACC-CTATAA-CATTTTTTTCTGATTTGGAGGTAAATAAA
65 ATGGTCAAAAGCAAGCACTGTAGGG-CCACTATAAGCA-TATTAACTGATTTGGAGGGAAATAAA
* *
52213804 TTGGAAACTTCCCAGTAGATTTTAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGGCTACTGC
128 TTGGAAACTTCCCAGCAGATTTCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGGCTACTGC
52213869 AGACGGCCA
193 AGACGGCCA
52213878 GATTACAGGA
Statistics
Matches: 179, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
236 33 0.18
237 144 0.80
238 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (236 bp):
TTCAAACAGAAATCAATAATAGACTGGATACAAAGGGCAACTCAACACAAAATTGGTTCATATGA
TGGTCAAAAGCAAGCACTGTAGGGCCACTATAAGCATATTAACTGATTTGGAGGGAAATAAATTG
GAAACTTCCCAGCAGATTTCAAGGGAAGTCACAATGTTCTTCAAGCAATTGTTGGCTACTGCAGA
CGGCCACATTCAAAGAGTTGCAGCTGGCCGAGGAATGTTTC
Found at i:52216726 original size:25 final size:25
Alignment explanation
Indices: 52216668--52216718 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
52216658 TTTGGATAAA
52216668 TGAAACCAACTTATCCAAAAAATCC
1 TGAAACCAACTTATCCAAAAAATCC
52216693 TGAAACCAACTTATCCAAAAAATCC
1 TGAAACCAACTTATCCAAAAAATCC
52216718 T
1 T
52216719 CGGACCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.27, G:0.04, T:0.22
Consensus pattern (25 bp):
TGAAACCAACTTATCCAAAAAATCC
Found at i:52218902 original size:27 final size:27
Alignment explanation
Indices: 52218871--52218925 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
52218861 AGTAGCAGAA
*
52218871 CAAACATTATACGCAATCTCTCAGTTT
1 CAAACATTATACGCAATCGCTCAGTTT
* *
52218898 CAAACATTATATGCAATCGCTCGGTTT
1 CAAACATTATACGCAATCGCTCAGTTT
52218925 C
1 C
52218926 TCTCATAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (27 bp):
CAAACATTATACGCAATCGCTCAGTTT
Found at i:52220165 original size:14 final size:14
Alignment explanation
Indices: 52220146--52220173 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52220136 AAGATTCAAA
52220146 TTCCTAACTTTCTT
1 TTCCTAACTTTCTT
52220160 TTCCTAACTTTCTT
1 TTCCTAACTTTCTT
52220174 ATGATTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (14 bp):
TTCCTAACTTTCTT
Found at i:52220772 original size:16 final size:18
Alignment explanation
Indices: 52220748--52220784 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
52220738 AATTTTATCA
*
52220748 TTATTAATT-TAAAAT-T
1 TTATAAATTATAAAATGT
52220764 TTATAAATTATAAAATGT
1 TTATAAATTATAAAATGT
52220782 TTA
1 TTA
52220785 AATGAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTATAAATTATAAAATGT
Found at i:52236815 original size:19 final size:19
Alignment explanation
Indices: 52236765--52236834 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
52236755 CAACTTATTT
*
52236765 ATTAATCTAAGATGAA-T-T
1 ATTAA-CTAAGATGAACTCA
*
52236783 ATTAAATAAGATGAACTCA
1 ATTAACTAAGATGAACTCA
*
52236802 ATTAACTAAAATGAACTCA
1 ATTAACTAAGATGAACTCA
52236821 ATTAACTAAGATGA
1 ATTAACTAAGATGA
52236835 GTAATTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
17 9 0.20
18 6 0.13
19 30 0.67
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (19 bp):
ATTAACTAAGATGAACTCA
Found at i:52239082 original size:26 final size:26
Alignment explanation
Indices: 52239032--52239084 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
52239022 CTCATTTTGC
* *
52239032 TTTCTCTCATTCTTTTTCATTTTCTT
1 TTTCTCGCATTCTTTTTCATCTTCTT
52239058 TTTCTCGCATCTCTTTTTC-TCTTCTT
1 TTTCTCGCAT-TCTTTTTCATCTTCTT
52239084 T
1 T
52239085 CGATTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTCTCGCATTCTTTTTCATCTTCTT
Found at i:52241394 original size:17 final size:18
Alignment explanation
Indices: 52241364--52241397 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
52241354 AGCAACTCAT
52241364 TTATTAATCTAAGATGAG
1 TTATTAATCTAAGATGAG
52241382 TTATTAA-CTAAGATGA
1 TTATTAATCTAAGATGA
52241398 ACTCAATTAA
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:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (18 bp):
TTATTAATCTAAGATGAG
Found at i:52241408 original size:19 final size:19
Alignment explanation
Indices: 52241384--52241436 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
52241374 AAGATGAGTT
52241384 ATTAACTAAGATGAACTCA
1 ATTAACTAAGATGAACTCA
52241403 ATTAACTCAA-ATGAACTCA
1 ATTAACT-AAGATGAACTCA
52241422 ATTAACTAAGATGAA
1 ATTAACTAAGATGAA
52241437 TAATTTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.06
19 28 0.88
20 2 0.06
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.26
Consensus pattern (19 bp):
ATTAACTAAGATGAACTCA
Found at i:52245818 original size:42 final size:41
Alignment explanation
Indices: 52245760--52245838 Score: 140
Period size: 42 Copynumber: 1.9 Consensus size: 41
52245750 AAGGGAGTTG
*
52245760 TTATTTTAAAGGCATTTGTTAATTTTATTATTAATTTTGTTA
1 TTATTTTAAAGACATTTGTTAATTTTATTATT-ATTTTGTTA
52245802 TTATTTTAAAGACATTTGTTAATTTTATTATTATTTT
1 TTATTTTAAAGACATTTGTTAATTTTATTATTATTTT
52245839 AGAGGTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 5 0.14
42 31 0.86
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (41 bp):
TTATTTTAAAGACATTTGTTAATTTTATTATTATTTTGTTA
Found at i:52245966 original size:15 final size:15
Alignment explanation
Indices: 52245948--52245998 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 15
52245938 TTTATTTTAG
52245948 TATTTTTTAAATATT
1 TATTTTTTAAATATT
*
52245963 TATTTTTAAAAAATATT
1 TATTTTT--TAAATATT
*
52245980 TA-TTTTTAAA-ACT
1 TATTTTTTAAATATT
52245993 TATTTT
1 TATTTT
52245999 AAAAAGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 4 0.13
14 6 0.20
15 7 0.23
16 4 0.13
17 9 0.30
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTTTTAAATATT
Found at i:52245997 original size:17 final size:17
Alignment explanation
Indices: 52245956--52245990 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
52245946 AGTATTTTTT
52245956 AAATATTTATTTTTAAA
1 AAATATTTATTTTTAAA
52245973 AAATATTTATTTTTAAA
1 AAATATTTATTTTTAAA
52245990 A
1 A
52245991 CTTATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATATTTATTTTTAAA
Found at i:52248423 original size:30 final size:31
Alignment explanation
Indices: 52248387--52248466 Score: 128
Period size: 30 Copynumber: 2.6 Consensus size: 31
52248377 TTCATGTATC
52248387 ATTATATTAAATTATTTAAATATT-TTTATT
1 ATTATATTAAATTATTTAAATATTATTTATT
*
52248417 ATTATATTAAATTATTTAAATCTTATTTATT
1 ATTATATTAAATTATTTAAATATTATTTATT
*
52248448 ATTATATTTAATT-TTTAAA
1 ATTATATTAAATTATTTAAA
52248467 ATAGTTTATG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 29 0.62
31 18 0.38
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
ATTATATTAAATTATTTAAATATTATTTATT
Found at i:52251614 original size:20 final size:20
Alignment explanation
Indices: 52251577--52251614 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52251567 TTAATAAGTA
*
52251577 AAATTTCTTTTCTATTTTTC
1 AAATTTCTTTGCTATTTTTC
52251597 AAATTTCTTATGCT-TTTT
1 AAATTTCTT-TGCTATTTT
52251615 ATCTTTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.63
Consensus pattern (20 bp):
AAATTTCTTTGCTATTTTTC
Found at i:52251727 original size:43 final size:43
Alignment explanation
Indices: 52251679--52251764 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
52251669 TATTATATTG
* * *
52251679 TTATTACCATAATATAAATGACCTAATTTGATAAGTGCTAAAA
1 TTATTACAATAATATAAATAACCTAAATTGATAAGTGCTAAAA
52251722 TTATTACAATAATATAAATAACCTAAATTGATAAGTGCTAAAA
1 TTATTACAATAATATAAATAACCTAAATTGATAAGTGCTAAAA
52251765 GAAACATGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (43 bp):
TTATTACAATAATATAAATAACCTAAATTGATAAGTGCTAAAA
Found at i:52254218 original size:39 final size:39
Alignment explanation
Indices: 52254164--52254239 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
52254154 GAATGTTTAC
52254164 TCTTTGGTTTTAATATAGAGCACAAGCAAGTCAACTTAT
1 TCTTTGGTTTTAATATAGAGCACAAGCAAGTCAACTTAT
52254203 TCTTTGGTTTTAATATAGAGCACAAGCAAGTCAACTT
1 TCTTTGGTTTTAATATAGAGCACAAGCAAGTCAACTT
52254240 TATGGGTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (39 bp):
TCTTTGGTTTTAATATAGAGCACAAGCAAGTCAACTTAT
Found at i:52262160 original size:26 final size:26
Alignment explanation
Indices: 52262130--52262211 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
52262120 TGAAATTCCC
52262130 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
52262156 ATCATGGAACATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
52262182 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
52262208 ATCA
1 ATCA
52262212 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:52264185 original size:19 final size:19
Alignment explanation
Indices: 52264137--52264175 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
52264127 GTGACCCCTG
*
52264137 TTTCGAAAATTTTCTAATT
1 TTTCTAAAATTTTCTAATT
52264156 TTTCTAAAATTTTCT-ATT
1 TTTCTAAAATTTTCTAATT
52264174 TT
1 TT
52264176 GTTTCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTCTAAAATTTTCTAATT
Found at i:52264509 original size:18 final size:18
Alignment explanation
Indices: 52264486--52264523 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
52264476 TACCCGAGAC
52264486 CGTTGCCGGAGTCGAACA
1 CGTTGCCGGAGTCGAACA
52264504 CGTTGCCGGAGTCGAACA
1 CGTTGCCGGAGTCGAACA
52264522 CG
1 CG
52264524 AGGTGGTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.16
Consensus pattern (18 bp):
CGTTGCCGGAGTCGAACA
Found at i:52265903 original size:93 final size:93
Alignment explanation
Indices: 52265791--52265962 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
52265781 CGCCCATAAG
* *
52265791 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
52265856 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
* *
52265884 CGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
52265949 ACGAGTTTGGATGC
66 ACGAGCTCGGATGC
52265963 TCAACAATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:52265959 original size:46 final size:46
Alignment explanation
Indices: 52265784--52265953 Score: 193
Period size: 46 Copynumber: 3.7 Consensus size: 46
52265774 TGTAACCCGC
* * *
52265784 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
52265830 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** * *
52265876 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
52265923 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
52265954 TTTGGATGCT
Statistics
Matches: 103, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 63 0.61
47 31 0.30
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:52270557 original size:28 final size:28
Alignment explanation
Indices: 52270494--52270616 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
52270484 ATATTAAGTC
*
52270494 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
52270521 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
52270549 CGAACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
52270577 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
52270606 CGCACACTTAG
1 CGCACACTTAG
52270617 CACCAATCTC
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 22 0.26
28 47 0.55
29 16 0.19
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:52272281 original size:40 final size:39
Alignment explanation
Indices: 52272159--52272416 Score: 249
Period size: 40 Copynumber: 6.6 Consensus size: 39
52272149 TTGAATGCTG
* * * * *
52272159 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAG-TGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTG-TTAAA
*
52272199 TCCGGATTAAGAT-CCGAAGGCATTGTGCGA---GTTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTGTGCGAGTTGTTAAA
52272235 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTGTTAAA
*
52272275 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTGTTAAA
* * * **
52272315 TCCGGGATATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTGTTAAA
* * * **
52272354 TCCGGGATATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTGTTAAA
* *
52272393 ACCGGGCTATA-TCCCGAAGGCATT
1 TCCGGGTTA-AGTCCCGAAGGCATT
52272417 TGAACGAGGA
Statistics
Matches: 193, Mismatches: 17, Indels: 17
0.85 0.07 0.07
Matches are distributed among these distances:
35 1 0.01
36 24 0.12
37 7 0.04
39 73 0.38
40 86 0.45
41 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTGTTAAA
Found at i:52272332 original size:80 final size:78
Alignment explanation
Indices: 52272159--52272416 Score: 254
Period size: 76 Copynumber: 3.3 Consensus size: 78
52272149 TTGAATGCTG
* * * * * * * *
52272159 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCATT
1 TCCGGGATATGTCCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
52272223 GTGCGA---GTTAAA
64 GTGCGAGTTGTTAAA
* * ** *
52272235 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCAGTC
1 TCCGGGATATGTCCCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCA-TT
52272300 GTGCGAGTTGTTAAA
64 GTGCGAGTTGTTAAA
* * *
52272315 TCCGGGATATGTCCCGAAGGCATTGTGTGAGTTACTAAATCCGGGATATGTCCCGAAGGCATTGT
1 TCCGGGATATGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTGT
* **
52272380 GTGAGTTACTAAA
66 GCGAGTTGTTAAA
* * *
52272393 ACCGGGCTATATCCCGAAGGCATT
1 TCCGGGATATGTCCCGAAGGCATT
52272417 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
75 1 0.01
76 47 0.31
77 11 0.07
78 34 0.22
79 32 0.21
80 28 0.18
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (78 bp):
TCCGGGATATGTCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTGT
GCGAGTTGTTAAA
Found at i:52272358 original size:39 final size:39
Alignment explanation
Indices: 52272212--52272416 Score: 245
Period size: 39 Copynumber: 5.3 Consensus size: 39
52272202 GGATTAAGAT
* *
52272212 CCGAAGGCATTGTGCGAG-T--TAAATCCGGGTTAAGTC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGATATGTC
** * *
52272248 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATT-GTGCGAGTTACTAAATCCGGGATATGTC
* **
52272288 CCGAAGGCAGTCGTGCGAGTTGTTAAATCCGGGATATGTC
1 CCGAAGGCA-TTGTGCGAGTTACTAAATCCGGGATATGTC
*
52272328 CCGAAGGCATTGTGTGAGTTACTAAATCCGGGATATGTC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGATATGTC
* * * *
52272367 CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATATC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGATATGTC
52272406 CCGAAGGCATT
1 CCGAAGGCATT
52272417 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
36 11 0.07
37 7 0.05
38 1 0.01
39 73 0.47
40 61 0.40
41 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAGTTACTAAATCCGGGATATGTC
Found at i:52272437 original size:79 final size:79
Alignment explanation
Indices: 52272170--52272416 Score: 206
Period size: 78 Copynumber: 3.2 Consensus size: 79
52272160 CCGGGCTAAG
* * * * *
52272170 TCCCGAAGGCTTTGTGCTAAGTGAATATATCC-GGATTAAGAT-CCGAAGGCA-TTGTGCGAG-T
1 TCCCGAAGGCATTGTGC-GAGTGACTAAATCCGGGA-TAAG-TCCCGAAGGCAGTCGTGCGAGTT
* *
52272231 --TAAATCCGGGTTA-A
63 ACTAAAACCGGGATATA
* *
52272245 GTCCCGAAGGCATTCGTGCGAGTTG-TTAAATCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTT
1 -TCCCGAAGGCATT-GTGCGAG-TGACTAAATCCGGGATAAGTCCCGAAGGCAGTCGTGCGAGTT
** * *
52272309 GTTAAATCCGGGATATG
63 ACTAAAACCGGGATATA
* * * * *
52272326 TCCCGAAGGCATTGTGTGAGTTACTAAATCCGGGATATGTCCCGAAGGCA-TTGTGTGAGTTACT
1 TCCCGAAGGCATTGTGCGAGTGACTAAATCCGGGATAAGTCCCGAAGGCAGTCGTGCGAGTTACT
*
52272390 AAAACCGGGCTATA
66 AAAACCGGGATATA
52272404 TCCCGAAGGCATT
1 TCCCGAAGGCATT
52272417 TGAACGAGGA
Statistics
Matches: 141, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
75 1 0.01
76 33 0.23
77 16 0.11
78 36 0.26
79 30 0.21
80 25 0.18
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCCGAAGGCATTGTGCGAGTGACTAAATCCGGGATAAGTCCCGAAGGCAGTCGTGCGAGTTACT
AAAACCGGGATATA
Found at i:52280187 original size:40 final size:40
Alignment explanation
Indices: 52280060--52280279 Score: 254
Period size: 40 Copynumber: 5.6 Consensus size: 40
52280050 TTGAATGCTG
* * * * * *
52280060 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* *
52280100 TCCGGATTAAGAT-CCGAAGGCATTTGTGCGAG---TTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
52280137 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
52280177 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
52280217 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
52280256 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
52280280 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
36 1 0.01
37 31 0.19
39 35 0.22
40 86 0.53
41 8 0.05
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:52280187 original size:77 final size:77
Alignment explanation
Indices: 52280060--52280281 Score: 268
Period size: 77 Copynumber: 2.8 Consensus size: 77
52280050 TTGAATGCTG
* * * * * *
52280060 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGTTAAG-TCCCGAAGGCATT
52280124 TGTGCGA-GTTAAA
64 TGTGCGATGTTAAA
* *
52280137 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGTTAAGTCCCGAAGGCATTT
52280202 GTGCGAGTTGTTAAA
65 GTGCGA--TGTTAAA
* * * * *
52280217 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGTTAAGTCCCGAAGGCATTTG
52280282 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
76 1 0.01
77 56 0.44
78 4 0.03
79 36 0.29
80 29 0.23
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (77 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGTTAAGTCCCGAAGGCATTTG
TGCGATGTTAAA
Found at i:52280299 original size:79 final size:80
Alignment explanation
Indices: 52280133--52280314 Score: 233
Period size: 79 Copynumber: 2.3 Consensus size: 80
52280123 TTGTGCGAGT
* *
52280133 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGC
** ** *
52280198 ATTCGTGCGAGTTGT
66 ATTCGAACGAGGAGC
* * *
52280213 TAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGC
*
52280277 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
* *
52280292 TATATCC-GGTTAAATCCCGAAGG
1 TAAATCCGGGTTAAGTCCCGAAGG
52280315 TACGTGATTT
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 14 0.16
79 47 0.53
80 27 0.31
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:52291584 original size:21 final size:21
Alignment explanation
Indices: 52291533--52291614 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 21
52291523 CCTGATCAAT
*
52291533 ATACGACACATAA-GTGCCTA
1 ATACGACACACAAGGTGCCTA
* * *
52291553 AAACGATACACGAGGTGCCTA
1 ATACGACACACAAGGTGCCTA
* * *
52291574 ATATGACACACAAGGTGCTTG
1 ATACGACACACAAGGTGCCTA
* *
52291595 ATACGACACATAAAGTGCCT
1 ATACGACACACAAGGTGCCT
52291615 GATATATGAC
Statistics
Matches: 47, Mismatches: 14, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
20 9 0.19
21 38 0.81
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (21 bp):
ATACGACACACAAGGTGCCTA
Found at i:52291617 original size:21 final size:21
Alignment explanation
Indices: 52291533--52291640 Score: 74
Period size: 21 Copynumber: 5.1 Consensus size: 21
52291523 CCTGATCAAT
*
52291533 ATACGACACAT-AAGTGCCTA
1 ATACGACACATAAAGTGCCTG
* * ** * *
52291553 AAACGATACACGAGGTGCCTA
1 ATACGACACATAAAGTGCCTG
* * * *
52291574 ATATGACACACAAGGTGCTTG
1 ATACGACACATAAAGTGCCTG
52291595 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* *
52291616 ATATATGACACATAAAGTTCCTG
1 --ATACGACACATAAAGTGCCTG
52291639 AT
1 AT
52291641 CGGCAAAGCC
Statistics
Matches: 69, Mismatches: 16, Indels: 5
0.77 0.18 0.06
Matches are distributed among these distances:
20 8 0.12
21 42 0.61
23 19 0.28
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:52291629 original size:23 final size:22
Alignment explanation
Indices: 52291567--52291639 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 22
52291557 GATACACGAG
* *
52291567 GTGCCT-AATATGACACACAAG
1 GTGCCTGAATATGACACATAAA
* *
52291588 GTGCTTG-ATACGACACATAAA
1 GTGCCTGAATATGACACATAAA
52291609 GTGCCTGATATATGACACATAAA
1 GTGCCTGA-ATATGACACATAAA
*
52291632 GTTCCTGA
1 GTGCCTGA
52291640 TCGGCAAAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 22 0.52
23 20 0.48
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (22 bp):
GTGCCTGAATATGACACATAAA
Found at i:52293282 original size:19 final size:20
Alignment explanation
Indices: 52293247--52293284 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
52293237 ATTACAAACG
52293247 TATGTATAATATTTATTACA
1 TATGTATAATATTTATTACA
*
52293267 TATGTAT-ATTTTTATTAC
1 TATGTATAATATTTATTAC
52293285 TACACATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TATGTATAATATTTATTACA
Found at i:52301278 original size:67 final size:67
Alignment explanation
Indices: 52301164--52301365 Score: 269
Period size: 67 Copynumber: 3.0 Consensus size: 67
52301154 CACGGCTGAG
* * *
52301164 ACACACACCAGTGTAAGCTTCGAATTAGGGCACACGACTGTGCCCCAGCTTGTGTCCTTACCCGT
1 ACACAC-CCA-TGTAAGCTTCGAACTAGGGCACACGACCGTGTCCCAGCTTGTGTCCTTACCCGT
52301229 GTGC
64 GTGC
** * * *
52301233 ACACATTCATGTAAGCTTCGAACTAGGGCACACGGCCGTGTCCCAGCTTGTGTCCTCACCCGCGT
1 ACACACCCATGTAAGCTTCGAACTAGGGCACACGACCGTGTCCCAGCTTGTGTCCTTACCCGTGT
*
52301298 GT
66 GC
* * * *
52301300 ACACACCCATGTAAGCTTCAAACTAGGGCACACAACCGTGTCCTAGCTTGTATCCTTACCCGTGT
1 ACACACCCATGTAAGCTTCGAACTAGGGCACACGACCGTGTCCCAGCTTGTGTCCTTACCCGTGT
52301365 G
66 G
52301366 ACTTTTTGAG
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
67 108 0.94
68 2 0.02
69 5 0.04
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (67 bp):
ACACACCCATGTAAGCTTCGAACTAGGGCACACGACCGTGTCCCAGCTTGTGTCCTTACCCGTGT
GC
Found at i:52312725 original size:3 final size:3
Alignment explanation
Indices: 52312666--52312706 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
52312656 TAATGTATAT
52312666 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
52312707 GAAAATGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:52313520 original size:25 final size:25
Alignment explanation
Indices: 52313472--52313520 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
52313462 CACAATTGAA
* * *
52313472 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
52313497 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
52313521 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:52318793 original size:48 final size:48
Alignment explanation
Indices: 52318726--52319155 Score: 743
Period size: 48 Copynumber: 9.0 Consensus size: 48
52318716 ATAAATATAG
*
52318726 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAG
1 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
52318774 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
1 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
52318822 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
1 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
* *
52318870 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGGGATAT
1 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
* *
52318918 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGCATGGGATAT
1 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
* * * *
52318966 GTATATATGGTAAAGCCAAATGGCTAATGTGAAATATGCATGGGATAT
1 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
52319014 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
1 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
*
52319062 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAC
1 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
* * *
52319110 GTATATGTGGTAAAGCCGAAGGGCTAGTGTGAAATATGTAGGAGAT
1 GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
52319156 GTGTGTATAT
Statistics
Matches: 369, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 369 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (48 bp):
GTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATAT
Found at i:52319441 original size:37 final size:37
Alignment explanation
Indices: 52319298--52319440 Score: 241
Period size: 37 Copynumber: 3.9 Consensus size: 37
52319288 AAATATATTT
52319298 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
52319335 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
*
52319372 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
* * * *
52319409 CGGTTAAGACCCGATAACTTCGTGTAGAGATT
1 CGGGTAAGACCCGATGACTACGTGTGGAGATT
52319441 TCATCTGAGC
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 101 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
Found at i:52335992 original size:49 final size:48
Alignment explanation
Indices: 52335890--52336152 Score: 204
Period size: 49 Copynumber: 5.5 Consensus size: 48
52335880 ATACCCGACA
* * *
52335890 CCATGTCCTAGACATGGTCTTACACTGGC-T-ATTATGTCAAGGTCGATG
1 CCATGTCCCAGACA-GGTCTTACACTGACTTCA-TATATCAAGGTCGATG
* *
52335938 CCATGTCCCAGATAGGTCTTACACTGACTTTCATATATCAAGG-CTGATT
1 CCATGTCCCAGACAGGTCTTACACTGAC-TTCATATATCAAGGTC-GATG
* * * * *
52335987 CCATGTCCCAGACAGGTGTTACACTGGCTCTCATCTATCAATGTCCATG
1 CCATGTCCCAGACAGGTCTTACACTGACT-TCATATATCAAGGTCGATG
* * * * * *
52336036 CCATGTCCCAGATAGCTCTTACACTGAC-ACACA-A-CAAGCT-GACG
1 CCATGTCCCAGACAGGTCTTACACTGACTTCATATATCAAGGTCGATG
* * *
52336080 CCATGTCCCAGACAGGTCTTACACT-AGC-TCGTATATCTTGAGGCCGATG
1 CCATGTCCCAGACAGGTCTTACACTGA-CTTCATATATC--AAGGTCGATG
*
52336129 -CATGTCCCAGACATGTCTTACACT
1 CCATGTCCCAGACAGGTCTTACACT
52336153 AGCTCTCGTC
Statistics
Matches: 170, Mismatches: 33, Indels: 24
0.75 0.15 0.11
Matches are distributed among these distances:
43 1 0.01
44 28 0.16
45 5 0.03
46 2 0.01
47 15 0.09
48 39 0.23
49 78 0.46
50 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (48 bp):
CCATGTCCCAGACAGGTCTTACACTGACTTCATATATCAAGGTCGATG
Found at i:52336102 original size:93 final size:95
Alignment explanation
Indices: 52335890--52336116 Score: 264
Period size: 98 Copynumber: 2.4 Consensus size: 95
52335880 ATACCCGACA
* * * * *
52335890 CCATGTCCTAGACATGGTCTTACACTGGCTATTATGTCAAGGTCGATGCCATGTCCCAGATAGGT
1 CCATGTCCCAGACA-GGTCTTACACTGGCTCTTATATCAAGGTCCATGCCATGTCCCAGATAGCT
* * **
52335955 CTTACACTGACTTTCATATATCAAGGCTGATT
65 CTTACACTGAC-TACACATATCAAGGCTGACG
* * *
52335987 CCATGTCCCAGACAGGTGTTACACTGGCTCTCATCTATCAATGTCCATGCCATGTCCCAGATAGC
1 CCATGTCCCAGACAGGTCTTACACTGGCTCT--TATATCAAGGTCCATGCCATGTCCCAGATAGC
52336052 TCTTACACTGAC-ACACA-A-CAA-GCTGACG
64 TCTTACACTGACTACACATATCAAGGCTGACG
* *
52336080 CCATGTCCCAGACAGGTCTTACACTAGCTCGTATATC
1 CCATGTCCCAGACAGGTCTTACACTGGCTCTTATATC
52336117 TTGAGGCCGA
Statistics
Matches: 112, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
91 5 0.04
93 33 0.29
94 3 0.03
95 1 0.01
96 18 0.16
97 13 0.12
98 39 0.35
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.28
Consensus pattern (95 bp):
CCATGTCCCAGACAGGTCTTACACTGGCTCTTATATCAAGGTCCATGCCATGTCCCAGATAGCTC
TTACACTGACTACACATATCAAGGCTGACG
Found at i:52336189 original size:46 final size:48
Alignment explanation
Indices: 52336081--52336198 Score: 159
Period size: 46 Copynumber: 2.5 Consensus size: 48
52336071 AAGCTGACGC
* * ** *
52336081 CATGTCCCAGACAGGTCTTACACTAGCTCGTATATCTTGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCGTACATCTCAAGACCGATG
* *
52336129 CATGTCCCAGACATGTCTTACACTAGCTC-T-CGTCTCAATACCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCGTACATCTCAAGACCGATG
52336175 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
52336199 GACACACATA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
46 34 0.54
47 1 0.02
48 28 0.44
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.28
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTCGTACATCTCAAGACCGATG
Found at i:52343770 original size:42 final size:42
Alignment explanation
Indices: 52343705--52343790 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
52343695 TATGTGATTT
*
52343705 ATATTGAAATGGAAAAAACGAGAAATGAATATGAGATGAGAA
1 ATATTGAAATGGAAAAAACGAGAAATGAATATGAGATAAGAA
* * * *
52343747 ATATTGAAATGGAAAATATGAGAAATGATTGTGAGATAAGAA
1 ATATTGAAATGGAAAAAACGAGAAATGAATATGAGATAAGAA
52343789 AT
1 AT
52343791 GAAATATGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.52, C:0.01, G:0.23, T:0.23
Consensus pattern (42 bp):
ATATTGAAATGGAAAAAACGAGAAATGAATATGAGATAAGAA
Found at i:52347020 original size:40 final size:40
Alignment explanation
Indices: 52346838--52347060 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
52346828 TCCTCGTTCA
* * * * *
52346838 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
52346877 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52346917 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
52346957 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
52346997 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
52347037 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
52347061 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:52347069 original size:41 final size:41
Alignment explanation
Indices: 52346992--52347069 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
52346982 TTAGTATCTC
* * *
52346992 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
52347033 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
52347070 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:52354924 original size:40 final size:40
Alignment explanation
Indices: 52354742--52354964 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
52354732 TCCTCGTTCA
* * * * *
52354742 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
52354781 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52354821 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
52354861 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
52354901 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
52354941 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
52354965 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:52354973 original size:41 final size:41
Alignment explanation
Indices: 52354896--52354973 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
52354886 TTAGTATCTC
* * *
52354896 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
52354937 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
52354974 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:52356671 original size:16 final size:16
Alignment explanation
Indices: 52356650--52356683 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52356640 AGAAAAATAT
52356650 TTGTTTGCGTAAACCA
1 TTGTTTGCGTAAACCA
* *
52356666 TTGTTTTCGTAAATCA
1 TTGTTTGCGTAAACCA
52356682 TT
1 TT
52356684 TTGTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.47
Consensus pattern (16 bp):
TTGTTTGCGTAAACCA
Found at i:52358152 original size:14 final size:14
Alignment explanation
Indices: 52358135--52358162 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52358125 AATTGAGAAA
52358135 GAAAAAGAAGAGAT
1 GAAAAAGAAGAGAT
52358149 GAAAAAGAAGAGAT
1 GAAAAAGAAGAGAT
52358163 AGAAGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
GAAAAAGAAGAGAT
Found at i:52359600 original size:17 final size:17
Alignment explanation
Indices: 52359558--52359593 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
52359548 ATCTCAAGAT
52359558 TACCACTTATTCATTCA
1 TACCACTTATTCATTCA
52359575 TACCACTTATTCATTCA
1 TACCACTTATTCATTCA
52359592 TA
1 TA
52359594 GTGCTTACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.42
Consensus pattern (17 bp):
TACCACTTATTCATTCA
Found at i:52364058 original size:16 final size:16
Alignment explanation
Indices: 52364021--52364060 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
52364011 TGCATATCAG
*
52364021 ACAG-ACAAATTTATC
1 ACAGAACAAATTTATA
52364036 A-AGAACAAATTTATA
1 ACAGAACAAATTTATA
52364051 ACAGAACAAA
1 ACAGAACAAA
52364061 ACAGATACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 12 0.55
16 8 0.36
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.20
Consensus pattern (16 bp):
ACAGAACAAATTTATA
Found at i:52369037 original size:40 final size:39
Alignment explanation
Indices: 52369000--52369091 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
52368990 GCTACTCGTT
*
52369000 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
52369040 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
52369079 CAAATGCCTTCGG
1 CAAATGCCTTCGG
52369092 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:52369071 original size:39 final size:40
Alignment explanation
Indices: 52368981--52369144 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
52368971 CGGAATTTAA
** *
52368981 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
52369021 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52369060 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
52369100 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
52369140 CCGGA
1 CCGGA
52369145 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:52383260 original size:36 final size:36
Alignment explanation
Indices: 52383213--52383283 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
52383203 CACACACAAT
*
52383213 CCTTGGCCCAGCACCGGTTGAACATTTGAGTGACAC
1 CCTTGGCCCAGCACCGGTTGAACATTTGAATGACAC
*
52383249 CCTTGGCCCAGCACCGGTTGACCATTTGAATGACA
1 CCTTGGCCCAGCACCGGTTGAACATTTGAATGACA
52383284 GCTGATGTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.23, C:0.31, G:0.24, T:0.23
Consensus pattern (36 bp):
CCTTGGCCCAGCACCGGTTGAACATTTGAATGACAC
Found at i:52396318 original size:39 final size:39
Alignment explanation
Indices: 52396263--52396460 Score: 180
Period size: 39 Copynumber: 5.0 Consensus size: 39
52396253 GTTCGATTTT
* * *
52396263 CAAATACTCAAATTCCTATTGGAAACCCAACTTTGTATC
1 CAAATACTCAAATTCCTAGTGGAAACCCAAATTTGTAAC
* * **
52396302 CAAATACTCAACTTCCTAGTGAAAAAACATAATTTTGTAAC
1 CAAATACTCAAATTCCTAGTGGAAACCCA-AA-TTTGTAAC
* * * * * *
52396343 CAAATACTCAAAGTCCTAATGGAAATCCAACTTCGTGAC
1 CAAATACTCAAATTCCTAGTGGAAACCCAAATTTGTAAC
* * **
52396382 CAAATACTCAAATTCCTAGCGAAATAACATAAATTTGTAAC
1 CAAATACTCAAATTCCTAGTG-GA-AACCCAAATTTGTAAC
* * *
52396423 CAAATACTCAAATACCTATTAGAAACCCAAATTTGTAA
1 CAAATACTCAAATTCCTAGTGGAAACCCAAATTTGTAA
52396461 ATTCTTTAAA
Statistics
Matches: 122, Mismatches: 33, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
39 61 0.50
40 4 0.03
41 57 0.47
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.27
Consensus pattern (39 bp):
CAAATACTCAAATTCCTAGTGGAAACCCAAATTTGTAAC
Found at i:52396351 original size:41 final size:41
Alignment explanation
Indices: 52396263--52396440 Score: 157
Period size: 41 Copynumber: 4.4 Consensus size: 41
52396253 GTTCGATTTT
* * ** * *
52396263 CAAATACTCAAATTCCTATTG--GAAACCCAACTTTGTATC
1 CAAATACTCAAATTCCTAGTGAAAAAACATAAATTTGTAAC
* *
52396302 CAAATACTCAACTTCCTAGTGAAAAAACATAATTTTGTAAC
1 CAAATACTCAAATTCCTAGTGAAAAAACATAAATTTGTAAC
* * * * * * * *
52396343 CAAATACTCAAAGTCCTAATG-GAAATC-CAACTTCGTGAC
1 CAAATACTCAAATTCCTAGTGAAAAAACATAAATTTGTAAC
* *
52396382 CAAATACTCAAATTCCTAGCGAAATAACATAAATTTGTAAC
1 CAAATACTCAAATTCCTAGTGAAAAAACATAAATTTGTAAC
*
52396423 CAAATACTCAAATACCTA
1 CAAATACTCAAATTCCTA
52396441 TTAGAAACCC
Statistics
Matches: 108, Mismatches: 27, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
39 45 0.42
40 7 0.06
41 56 0.52
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (41 bp):
CAAATACTCAAATTCCTAGTGAAAAAACATAAATTTGTAAC
Found at i:52396366 original size:80 final size:78
Alignment explanation
Indices: 52396263--52396459 Score: 268
Period size: 80 Copynumber: 2.5 Consensus size: 78
52396253 GTTCGATTTT
* *
52396263 CAAATACTCAAATTCCTATTGGAAACCCAACTTTGTATCCAAATACTCAACTTCCTAGTGAAAAA
1 CAAATACTCAAA-TCCTATTGGAAACCCAACTTTGTA-CCAAATACTCAAATTCCTAGCGAAAAA
*
52396328 ACATAATTTTGTAAC
64 ACATAAATTTGTAAC
* * * *
52396343 CAAATACTCAAAGTCCTAATGGAAATCCAACTTCGTGACCAAATACTCAAATTCCTAGCGAAATA
1 CAAATACTCAAA-TCCTATTGGAAACCCAACTTTGT-ACCAAATACTCAAATTCCTAGCGAAAAA
52396408 ACATAAATTTGTAAC
64 ACATAAATTTGTAAC
* *
52396423 CAAATACTCAAATACCTATTAGAAACCCAAATTTGTA
1 CAAATACTCAAAT-CCTATTGGAAACCCAACTTTGTA
52396460 AATTCTTTAA
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
79 2 0.02
80 99 0.97
81 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.27
Consensus pattern (78 bp):
CAAATACTCAAATCCTATTGGAAACCCAACTTTGTACCAAATACTCAAATTCCTAGCGAAAAAAC
ATAAATTTGTAAC
Found at i:52398457 original size:39 final size:40
Alignment explanation
Indices: 52398407--52398486 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
52398397 TGAATCAAAG
52398407 TTAATTGGTTCAGGTAA-C-AAAGAAACAAAAAAGAATTAA
1 TTAATTGGTTCAGGTAACCAAAAGAAA-AAAAAAGAATTAA
* *
52398446 TTAATTGGTTCATGTAACCAAAAGAAAAAAAAAGAGTTAA
1 TTAATTGGTTCAGGTAACCAAAAGAAAAAAAAAGAATTAA
52398486 T
1 T
52398487 GGTTTCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 16 0.43
40 14 0.38
41 7 0.19
ACGTcount: A:0.53, C:0.07, G:0.15, T:0.25
Consensus pattern (40 bp):
TTAATTGGTTCAGGTAACCAAAAGAAAAAAAAAGAATTAA
Found at i:52400653 original size:22 final size:21
Alignment explanation
Indices: 52400627--52400681 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
52400617 TTTTTGCTTC
52400627 TTTTTGTCCTAAAACTAACATT
1 TTTTTGT-CTAAAACTAACATT
*
52400649 TTTTTGT-TAAAACTAACTTT
1 TTTTTGTCTAAAACTAACATT
52400669 TTTTTGTC-AAAAC
1 TTTTTGTCTAAAAC
52400682 ACCCAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 24 0.77
22 7 0.23
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (21 bp):
TTTTTGTCTAAAACTAACATT
Done.