Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 111 of 211
Found at i:34997615 original size:18 final size:18
Alignment explanation
Indices: 34997589--34997628 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34997579 AAAAATAATT
*
34997589 ATTATATTATGAAAAATA
1 ATTACATTATGAAAAATA
* *
34997607 ATTACATTATTAAAATTA
1 ATTACATTATGAAAAATA
34997625 ATTA
1 ATTA
34997629 ATTCATAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTACATTATGAAAAATA
Found at i:34997617 original size:21 final size:20
Alignment explanation
Indices: 34997574--34997630 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
34997564 ATATATATAG
*
34997574 ATTATAAAAATAATTATTAT
1 ATTATAAAAATAATTAATAT
34997594 ATTATGAAAAATAATTACAT-T
1 ATTAT-AAAAATAATTA-ATAT
*
34997615 A-T-TAAAATTAATTAAT
1 ATTATAAAAATAATTAAT
34997631 TCATAAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 2 0.06
18 10 0.30
19 1 0.03
20 6 0.18
21 13 0.39
22 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTATAAAAATAATTAATAT
Found at i:34998125 original size:30 final size:30
Alignment explanation
Indices: 34998091--34998164 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
34998081 CTAGCCAGGG
* *
34998091 TCCGGACACCGGCCGATCGTCGGCCACCGC
1 TCCGGACACCGGCCGATCGTAGACCACCGC
34998121 TCCGGACACCGGCCGATCGTAGACCACCGC
1 TCCGGACACCGGCCGATCGTAGACCACCGC
* *
34998151 TCCGGCCACTGGCC
1 TCCGGACACCGGCC
34998165 TCCAGTGACG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.15, C:0.46, G:0.28, T:0.11
Consensus pattern (30 bp):
TCCGGACACCGGCCGATCGTAGACCACCGC
Found at i:34999378 original size:45 final size:45
Alignment explanation
Indices: 34999284--34999378 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 45
34999274 TTGTTTATTT
* ** *
34999284 AGTCTGCCCCACTGCAATTTCAAGGGGATAAGACTTGCTTTCTTG
1 AGTCTGCCCCACTGCAACTTCAAGGGGATAAGACTTGCCATCTTC
34999329 AGTCTGCTCCC-CTGCAACTTC-AGGGAGATAAGA-TTCGCCATCTTC
1 AGTCTGC-CCCACTGCAACTTCAAGGG-GATAAGACTT-GCCATCTTC
34999374 AGTCT
1 AGTCT
34999379 TTTAAATTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
44 6 0.14
45 34 0.79
46 3 0.07
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTCTGCCCCACTGCAACTTCAAGGGGATAAGACTTGCCATCTTC
Found at i:34999720 original size:267 final size:267
Alignment explanation
Indices: 34999370--34999862 Score: 770
Period size: 267 Copynumber: 1.8 Consensus size: 267
34999360 GATTCGCCAT
* * *
34999370 CTTCAGTCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGTCATCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGGCATCGTAGCTTCAATATGTTCCA
* * *
34999435 CTACACCGCCAGGGGAGTAAGATTCGCCATTGCGGCTTTAATCTGCTCTACTGTAATGCCAAAGA
66 CTACACCGCCAAGGGAGTAAGATTCGCCACTGCGGCTTTAATCTGCTCCACTGTAATGCCAAAGA
*** *
34999500 GATAGGATTCGCTGCCCACAGCTTCAATCTGTTCCACTTCAGCTAATCCAAGCTTTAACGCCAGG
131 GATAGGATTCGCTGCCCACAGCTTCAATCCACTCCACTTCAGCTAATCCAAGCCTTAACGCCAGG
* *
34999565 GAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAATGCCAGGGAAATAAGACTCGCC
196 GAGATAAGATTCGCCGTCGCGGCCTCAATCTGCTCCGCTACAATGCCAGGGAAATAAGACTCGCC
34999630 GTTGTGG
261 GTTGTGG
* * *
34999637 CTTCAATCTTTTAAATTGCAATGTTGGGGAAACGAGATTCGGCGTCGTAGCTTCAATATGTTCCT
1 CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGGCATCGTAGCTTCAATATGTTCCA
* * * *
34999702 TTACACCGCCAAGGGAGTAAGATTCTCCGCTGTGGCTTTAATCTGCTCCACTGTAATGCCAAAGA
66 CTACACCGCCAAGGGAGTAAGATTCGCCACTGCGGCTTTAATCTGCTCCACTGTAATGCCAAAGA
* * *
34999767 GATAGGATTCGCTGCCTATAGCTTCAATCCACTCCACTTCAGCTAATCCAAGCCTTAACGGCAGG
131 GATAGGATTCGCTGCCCACAGCTTCAATCCACTCCACTTCAGCTAATCCAAGCCTTAACGCCAGG
* *
34999832 GAGATAAGATTTGCCGTTGCGGCCTCAATCT
196 GAGATAAGATTCGCCGTCGCGGCCTCAATCT
34999863 TTTCCATTGA
Statistics
Matches: 202, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
267 202 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (267 bp):
CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGGCATCGTAGCTTCAATATGTTCCA
CTACACCGCCAAGGGAGTAAGATTCGCCACTGCGGCTTTAATCTGCTCCACTGTAATGCCAAAGA
GATAGGATTCGCTGCCCACAGCTTCAATCCACTCCACTTCAGCTAATCCAAGCCTTAACGCCAGG
GAGATAAGATTCGCCGTCGCGGCCTCAATCTGCTCCGCTACAATGCCAGGGAAATAAGACTCGCC
GTTGTGG
Found at i:35010859 original size:17 final size:18
Alignment explanation
Indices: 35010812--35010865 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
35010802 AAAAATAATG
* *
35010812 ATTATATTATGAAAAATA
1 ATTACATTATTAAAAATA
*
35010830 ATTACATTATTAAAATTA
1 ATTACATTATTAAAAATA
* *
35010848 ATTA-ATTCTTAAAGATA
1 ATTACATTATTAAAAATA
35010865 A
1 A
35010866 CAAAGAAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 11 0.37
18 19 0.63
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTACATTATTAAAAATA
Found at i:35014993 original size:20 final size:20
Alignment explanation
Indices: 35014968--35015007 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35014958 CGAAAAATGA
35014968 TTTCTGAAAAATAATTTACT
1 TTTCTGAAAAATAATTTACT
* *
35014988 TTTCTGGAAAATGATTTACT
1 TTTCTGAAAAATAATTTACT
35015008 GAAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTCTGAAAAATAATTTACT
Found at i:35019285 original size:27 final size:27
Alignment explanation
Indices: 35019250--35019571 Score: 241
Period size: 27 Copynumber: 12.1 Consensus size: 27
35019240 ATTCATGAGT
*
35019250 AAATGACCGAAATACCCTTGAAGGGTA
1 AAATTACCGAAATACCCTTGAAGGGTA
* *
35019277 AAATGACCGAAATATCCTTGAAGGGTA
1 AAATTACCGAAATACCCTTGAAGGGTA
* * *
35019304 AATATTATCTAGATACCCTTGAAGGGTA
1 AA-ATTACCGAAATACCCTTGAAGGGTA
* * * *
35019332 AATTTACCGAACTACCCTCGAA-GGTG
1 AAATTACCGAAATACCCTTGAAGGGTA
* * **
35019358 AAATTATCAAAATACCCTCAAAGGGTA
1 AAATTACCGAAATACCCTTGAAGGGTA
* ** * *
35019385 TAATTACTAAAATACCCTCGAAAGGTA
1 AAATTACCGAAATACCCTTGAAGGGTA
* * *
35019412 AAACTA-CTAAAGTACCCTCGAAGGGTA
1 AAATTACCGAAA-TACCCTTGAAGGGTA
** * *
35019439 AAATTATTGAAATACCCTCGAAAGGT-
1 AAATTACCGAAATACCCTTGAAGGGTA
* *
35019465 --A-TACTGAAATA-CCTTAAAAGGGTA
1 AAATTACCGAAATACCCTT-GAAGGGTA
*
35019489 AAATTATCGAAATACCCTT-AAGGGTA
1 AAATTACCGAAATACCCTTGAAGGGTA
* *
35019515 AAATTACTGTAATACCCTT-AAGGGTA
1 AAATTACCGAAATACCCTTGAAGGGTA
* *
35019541 AAATTACCGTAATACCCCCT-AAGGGTA
1 AAATTACCGAAATA-CCCTTGAAGGGTA
35019568 AAAT
1 AAAT
35019572 GATCTTTATA
Statistics
Matches: 240, Mismatches: 44, Indels: 22
0.78 0.14 0.07
Matches are distributed among these distances:
22 3 0.01
23 14 0.06
24 1 0.00
26 67 0.28
27 126 0.52
28 29 0.12
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (27 bp):
AAATTACCGAAATACCCTTGAAGGGTA
Found at i:35019582 original size:27 final size:25
Alignment explanation
Indices: 35019499--35019602 Score: 91
Period size: 26 Copynumber: 4.0 Consensus size: 25
35019489 AAATTATCGA
* *
35019499 AATACCCTTAAGGGTAAAATTACTGT
1 AATACCCCTAAGGGTAAAATGACT-T
* * *
35019525 AATACCCTTAAGGGTAAAATTACCGT
1 AATACCCCTAAGGGTAAAATGA-CTT
35019551 AATACCCCCTAAGGGTAAAATGATCTT
1 AATA-CCCCTAAGGGTAAAATGA-CTT
* * *
35019578 TATACCTCTAAGAGGTGAAATGACT
1 AATACCCCTAAG-GGTAAAATGACT
35019603 GTTATGGCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
26 36 0.54
27 31 0.46
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (25 bp):
AATACCCCTAAGGGTAAAATGACTT
Found at i:35020873 original size:45 final size:45
Alignment explanation
Indices: 35020822--35020910 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
35020812 GCCGGCATCA
* * *
35020822 ATCTTTCTGCCCCTGACAATTGATTGTATTAGCCACATTCTATCG
1 ATCTTTCTGCCCCTGACAATAGAATGTATCAGCCACATTCTATCG
*
35020867 ATCTTTCTGCCCTTGACAATAGAATGTATCAGCCACATTCTATC
1 ATCTTTCTGCCCCTGACAATAGAATGTATCAGCCACATTCTATC
35020911 AAGGTTGACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (45 bp):
ATCTTTCTGCCCCTGACAATAGAATGTATCAGCCACATTCTATCG
Found at i:35028975 original size:25 final size:24
Alignment explanation
Indices: 35028947--35028999 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
35028937 CAAAAAAATT
35028947 AAAATGTAAAAATTAAAATAAAAACA
1 AAAATGTAAAAA-TAAAATAAAAA-A
* *
35028973 AAAATATAAAAATAAAATAAATAA
1 AAAATGTAAAAATAAAATAAAAAA
35028997 AAA
1 AAA
35029000 TGGCTAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.16
25 10 0.40
26 11 0.44
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (24 bp):
AAAATGTAAAAATAAAATAAAAAA
Found at i:35028998 original size:34 final size:35
Alignment explanation
Indices: 35028926--35028998 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
35028916 GAACCTGCTA
* * *
35028926 AAAATAAAAAACAAAAAAATTAAAATGTAAAAATT
1 AAAATAAAAAACAAAAAAATAAAAATGAAAAAAAT
*
35028961 AAAAT-AAAAACAAAAATATAAAAAT-AAAATAAAT
1 AAAATAAAAAACAAAAAAATAAAAATGAAAA-AAAT
35028995 AAAA
1 AAAA
35028999 ATGGCTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 3 0.09
34 25 0.76
35 5 0.15
ACGTcount: A:0.78, C:0.03, G:0.01, T:0.18
Consensus pattern (35 bp):
AAAATAAAAAACAAAAAAATAAAAATGAAAAAAAT
Found at i:35029000 original size:15 final size:14
Alignment explanation
Indices: 35028924--35029000 Score: 59
Period size: 14 Copynumber: 5.5 Consensus size: 14
35028914 AAGAACCTGC
35028924 TAAAAATAAAAAACA
1 TAAAAATAAAAAA-A
* * **
35028939 AAAAAATTAAAATG
1 TAAAAATAAAAAAA
*
35028953 TAAAAAT--TAAAA
1 TAAAAATAAAAAAA
* *
35028965 TAAAAACAAAAATA
1 TAAAAATAAAAAAA
35028979 TAAAAATAAAATAAA
1 TAAAAATAAAA-AAA
35028994 TAAAAAT
1 TAAAAAT
35029001 GGCTAAATGA
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
12 8 0.17
14 19 0.41
15 19 0.41
ACGTcount: A:0.77, C:0.03, G:0.01, T:0.19
Consensus pattern (14 bp):
TAAAAATAAAAAAA
Found at i:35030489 original size:28 final size:29
Alignment explanation
Indices: 35030449--35030507 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
35030439 ATTCTTGTTG
* *
35030449 TAATTATTGTAATTT-TTTTAAGTAAGAC
1 TAATTATTCTAATTTATGTTAAGTAAGAC
*
35030477 TAATTATTCTAATTTATGTTGAGTAAGAC
1 TAATTATTCTAATTTATGTTAAGTAAGAC
35030506 TA
1 TA
35030508 CTTCACAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (29 bp):
TAATTATTCTAATTTATGTTAAGTAAGAC
Found at i:35031251 original size:22 final size:22
Alignment explanation
Indices: 35031226--35031282 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
35031216 CCAAATCACC
*
35031226 ATACCACCACTCTAGCACCATT
1 ATACCACCACCCTAGCACCATT
**
35031248 ATACCACCACCCTAGCACCACC
1 ATACCACCACCCTAGCACCATT
*
35031270 ATATCACCACCCT
1 ATACCACCACCCT
35031283 TGTACCACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.47, G:0.04, T:0.18
Consensus pattern (22 bp):
ATACCACCACCCTAGCACCATT
Found at i:35037556 original size:50 final size:50
Alignment explanation
Indices: 35037498--35037621 Score: 167
Period size: 50 Copynumber: 2.5 Consensus size: 50
35037488 CATTGATGTT
* *
35037498 ATGAGAGGTCCCATGTAAGACCATGTCCAGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATGTCCAGGACATGGCATGGGCACCAAG
** * * *
35037548 ATGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCCAGGACATGGCATGGGCACCAAG
**
35037598 ATGAGAACTCCCATGTAAGACCAT
1 ATGAGAGGTCCCATGTAAGACCAT
35037622 ATCTGGGATA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCCAGGACATGGCATGGGCACCAAG
Found at i:35038040 original size:14 final size:15
Alignment explanation
Indices: 35038013--35038046 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
35038003 CTTACTAAGC
35038013 TTTATGCTTACTTCT
1 TTTATGCTTACTTCT
*
35038028 TTTATG-TTCCTTCT
1 TTTATGCTTACTTCT
35038042 TTTAT
1 TTTAT
35038047 AGTATTGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.12, C:0.18, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTATGCTTACTTCT
Found at i:35043812 original size:26 final size:27
Alignment explanation
Indices: 35043777--35043840 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
35043767 CGACAACTTA
*
35043777 TATGAGCAT-ATATGAAAAAGGATGGT
1 TATGACCATAATATGAAAAAGGATGGT
*
35043803 TATGACCATAGAATATGAAAAGGGATGGT
1 TATGACCAT--AATATGAAAAAGGATGGT
35043832 T-TCGACCAT
1 TAT-GACCAT
35043841 CGTTTAGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 8 0.25
28 1 0.03
29 23 0.72
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (27 bp):
TATGACCATAATATGAAAAAGGATGGT
Found at i:35058092 original size:29 final size:30
Alignment explanation
Indices: 35058017--35058098 Score: 116
Period size: 29 Copynumber: 2.8 Consensus size: 30
35058007 TATGAGCATC
*
35058017 TATGAAAAGGGATGGTTACGAA-C-ATAGAA
1 TATGAAAAGGGATGGTTTC-AACCAATAGAA
35058046 TATGAAAAGGGATGGTTTCAACCAAT-GAA
1 TATGAAAAGGGATGGTTTCAACCAATAGAA
*
35058075 TATGAAAAGGGATGGTTTCGACCA
1 TATGAAAAGGGATGGTTTCAACCA
35058099 TCGTTTAGCA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.04
29 45 0.92
30 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (30 bp):
TATGAAAAGGGATGGTTTCAACCAATAGAA
Found at i:35061933 original size:50 final size:50
Alignment explanation
Indices: 35061829--35062007 Score: 178
Period size: 50 Copynumber: 3.5 Consensus size: 50
35061819 GGTAAAGATA
* * * *
35061829 TCCCATGTAAGACCATGTATGGGACATGACATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATGAGAGG
35061885 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
** ** * * **
35061935 TCCCCCGTAAGACCATGTCCAGGACATGGCGTTGGCACCGATATAAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
* *
35061985 TCCTATGTAAGACCATATCTGGG
1 TCCCATGTAAGACCATGTCTGGG
35062008 GTATGGAATT
Statistics
Matches: 105, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
50 67 0.64
53 3 0.03
55 1 0.01
56 34 0.32
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
Found at i:35062287 original size:12 final size:12
Alignment explanation
Indices: 35062270--35062308 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35062260 ATGAGTTATT
35062270 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
35062282 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
35062294 TAAGTGAGTAAG
1 TAAGTAAGCAAG
35062306 TAA
1 TAA
35062309 AGAAGGGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:35063026 original size:181 final size:179
Alignment explanation
Indices: 35062796--35063174 Score: 679
Period size: 181 Copynumber: 2.1 Consensus size: 179
35062786 AAATCCTATC
*
35062796 GAGTCTATTTTC-GTAGAAAAATAATGGTGTGGGTAAAGGAATTTTATATTCTGATATATTTAAT
1 GAGTTTATTTTCTGTAGAAAAATAATGGTGTGGGTAAAGGAATTTTATATTCTGATATATTTAAT
* *
35062860 TTTTGTTAGACAGGATCAGAATGGTTTTTGGAGTCCCCTGTTCTGACTTTTTAAAATCATTAAAA
66 TTTAGTTAGACAGGATCAGAATGGTTTTTGGAGTCCCCTGTTCTGACTTTATAAAATCATT--AA
35062925 ATTGTACAAACATAATTATGAGTTATAATTTATATTTATAGATTACTTAGT
129 ATTGTACAAACATAATTATGAGTTATAATTTATATTTATAGATTACTTAGT
*
35062976 GAGTTTATTTTCTGTAGAAAAATAATGGTGTGGGTAAATGAATTTTATATTCTGATATATTTAAT
1 GAGTTTATTTTCTGTAGAAAAATAATGGTGTGGGTAAAGGAATTTTATATTCTGATATATTTAAT
* *
35063041 TTTAGTTAGACAGGATCAGAATGGTTTTTGGAGTCTCCTGTTTTGACTTTATAAAATCATTAAAT
66 TTTAGTTAGACAGGATCAGAATGGTTTTTGGAGTCCCCTGTTCTGACTTTATAAAATCATTAAAT
35063106 TGTACAAACATAATTATGAGTTATAATTTATATTTATAGATTACTTAGT
131 TGTACAAACATAATTATGAGTTATAATTTATATTTATAGATTACTTAGT
35063155 GAGTTTATTTTCTGTAGAAA
1 GAGTTTATTTTCTGTAGAAA
35063175 CAAGAGAAAA
Statistics
Matches: 192, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
179 73 0.38
180 11 0.06
181 108 0.56
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (179 bp):
GAGTTTATTTTCTGTAGAAAAATAATGGTGTGGGTAAAGGAATTTTATATTCTGATATATTTAAT
TTTAGTTAGACAGGATCAGAATGGTTTTTGGAGTCCCCTGTTCTGACTTTATAAAATCATTAAAT
TGTACAAACATAATTATGAGTTATAATTTATATTTATAGATTACTTAGT
Found at i:35063225 original size:179 final size:180
Alignment explanation
Indices: 35062853--35063225 Score: 484
Period size: 179 Copynumber: 2.1 Consensus size: 180
35062843 ATTCTGATAT
*
35062853 ATTTAATTTTT-GTTAGACAGGATCAGAATGGTTTTTGGAGTCCCCTGTTCTGACTTTTTAAAAT
1 ATTT-ATTTTTAGTTAGACAGGATCAGAATGGTTTTTGGAGTCCCCTGTTCTGACTTTATAAAAT
35062917 CATTAAAAATTGTACAAACATAATTATGAGTTATAATTTATATTTATAGATTACTTAGTGAGTTT
65 CATT-AAAATTGTACAAACATAATTATGAGTTATAATTTATATTTATAGATTACTTAGTGAGTTT
******** ** * *** * *
35062982 ATTTTCTGTAGAAAAATAATGGTGTGGGTAAATGAATTTTATATTCTGATAT
129 ATTTTCTGTAGAAAAATAATGAAAACACCAAATGAAAATCATACGATGAGAA
* * *
35063034 ATTTAATTTTAGTTAGACAGGATCAGAATGGTTTTTGGAGTCTCCTGTTTTGACTTTATAAAATC
1 ATTTATTTTTAGTTAGACAGGATCAGAATGGTTTTTGGAGTCCCCTGTTCTGACTTTATAAAATC
35063099 ATT-AAATTGTACAAACATAATTATGAGTTATAATTTATATTTATAGATTACTTAGTGAGTTTAT
66 ATTAAAATTGTACAAACATAATTATGAGTTATAATTTATATTTATAGATTACTTAGTGAGTTTAT
* *
35063163 TTTCTGTAGAAACAA-GA-GAAAACACCATATGAAAATCATACGATGAGAA
131 TTTCTGTAGAAA-AATAATGAAAACACCAAATGAAAATCATACGATGAGAA
35063212 ATTTGATTTTTAGT
1 ATTT-ATTTTTAGT
35063226 GAATAAAGGC
Statistics
Matches: 166, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
178 19 0.11
179 82 0.49
180 7 0.04
181 58 0.35
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (180 bp):
ATTTATTTTTAGTTAGACAGGATCAGAATGGTTTTTGGAGTCCCCTGTTCTGACTTTATAAAATC
ATTAAAATTGTACAAACATAATTATGAGTTATAATTTATATTTATAGATTACTTAGTGAGTTTAT
TTTCTGTAGAAAAATAATGAAAACACCAAATGAAAATCATACGATGAGAA
Found at i:35069694 original size:50 final size:50
Alignment explanation
Indices: 35069640--35069756 Score: 144
Period size: 50 Copynumber: 2.3 Consensus size: 50
35069630 ATTATGAGTT
* * *
35069640 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAA
** * * * *
35069690 GTCCCCCGTAAAACTATGTTTGGGACATGGCATGGGCACCGATATGAGAA
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAA
*
35069740 CTCCCATGTAAGACCAT
1 GTCCCATGTAAGACCAT
35069757 ATCTAGGGTA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.21
Consensus pattern (50 bp):
GTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAA
Found at i:35070043 original size:12 final size:12
Alignment explanation
Indices: 35070026--35070076 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
35070016 ATGAGTTATT
35070026 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
35070038 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
35070050 TAAGTGAGTAAG
1 TAAGTAAGCAAG
*
35070062 TTAAG-AAGCGAG
1 -TAAGTAAGCAAG
35070074 TAA
1 TAA
35070077 AGATTCTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
11 3 0.10
12 24 0.77
13 4 0.13
ACGTcount: A:0.49, C:0.06, G:0.25, T:0.20
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:35078263 original size:3 final size:3
Alignment explanation
Indices: 35078255--35078279 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35078245 CAAAGGCACC
35078255 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
35078280 ATGATTTCAT
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:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:35084386 original size:50 final size:50
Alignment explanation
Indices: 35084319--35084547 Score: 264
Period size: 50 Copynumber: 4.6 Consensus size: 50
35084309 GGGAATGAGA
*
35084319 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGGGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
35084369 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGAACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
35084419 TCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * **
35084469 TCCCATGTAAGACCATATCTGGGACATGGAATTGGTA--GTACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
*
35084518 TCCCATATAAGACCATGTCTGGGACATGGC
1 TCCCATGTAAGACCATGTCTGGGACATGGC
35084548 TTTCGCATGT
Statistics
Matches: 151, Mismatches: 27, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
48 1 0.01
49 32 0.21
50 118 0.78
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:35091748 original size:50 final size:50
Alignment explanation
Indices: 35091681--35091910 Score: 327
Period size: 50 Copynumber: 4.6 Consensus size: 50
35091671 GGGAATGAGA
35091681 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
35091731 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGATATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
35091781 TCCCATGTAAGATCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * **
35091831 TTCCC-CGTAAGACCATGTATAGGACATGGCATGGGCACCGATATGAGAAC
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
35091881 TCCCATGTAAGACCATATCTGGGATATGGC
1 TCCCATGTAAGACCATGTCTGGGACATGGC
35091911 GCAGTAAAAG
Statistics
Matches: 160, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 4 0.03
50 152 0.95
51 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:35105296 original size:29 final size:28
Alignment explanation
Indices: 35105262--35105322 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
35105252 TCAAAGATAT
35105262 TTATTTGTACTTGTTT-TTCTCCTTTTTTA
1 TTATTTGTACTT-TTTCTTCT-CTTTTTTA
* *
35105291 TTATTTTTTCTTTTTCTTCTCTTTTTTA
1 TTATTTGTACTTTTTCTTCTCTTTTTTA
35105319 TTAT
1 TTAT
35105323 ATTAGGGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (28 bp):
TTATTTGTACTTTTTCTTCTCTTTTTTA
Found at i:35111885 original size:62 final size:62
Alignment explanation
Indices: 35111789--35111910 Score: 244
Period size: 62 Copynumber: 2.0 Consensus size: 62
35111779 TTCATCATAC
35111789 CATAAAATACACTTTTCATTTCATCACCAAAAGATTGTAGAACTAATGCCCTTTAACTTATT
1 CATAAAATACACTTTTCATTTCATCACCAAAAGATTGTAGAACTAATGCCCTTTAACTTATT
35111851 CATAAAATACACTTTTCATTTCATCACCAAAAGATTGTAGAACTAATGCCCTTTAACTTA
1 CATAAAATACACTTTTCATTTCATCACCAAAAGATTGTAGAACTAATGCCCTTTAACTTA
35111911 CTCCTGGGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (62 bp):
CATAAAATACACTTTTCATTTCATCACCAAAAGATTGTAGAACTAATGCCCTTTAACTTATT
Found at i:35113676 original size:20 final size:20
Alignment explanation
Indices: 35113659--35113697 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35113649 GAAATGCAGA
35113659 CAGAGGCA-CGAATGTGCAAT
1 CAGAGGCACCGAA-GTGCAAT
35113679 CAGAGGCACCGAAGTGCAA
1 CAGAGGCACCGAAGTGCAA
35113698 ACCCATACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.23, G:0.31, T:0.10
Consensus pattern (20 bp):
CAGAGGCACCGAAGTGCAAT
Found at i:35115150 original size:28 final size:27
Alignment explanation
Indices: 35115087--35115238 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
35115077 ATATTAAGTC
* * *
35115087 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
35115114 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
35115142 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
35115169 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
35115197 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
35115224 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35115239 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:35115171 original size:55 final size:55
Alignment explanation
Indices: 35115087--35115238 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
35115077 ATATTAAGTC
* * *
35115087 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
35115142 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
35115197 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
35115239 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:35123810 original size:19 final size:17
Alignment explanation
Indices: 35123786--35123828 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
35123776 TAATAAAAAA
35123786 TAAAATAAATGAAAAATTT
1 TAAAATAAA--AAAAATTT
*
35123805 TAAAATAAAACAAATTT
1 TAAAATAAAAAAAATTT
35123822 TAAAATA
1 TAAAATA
35123829 GGAAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.61
19 9 0.39
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAATAAAAAAAATTT
Found at i:35129154 original size:15 final size:15
Alignment explanation
Indices: 35129134--35129163 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35129124 TCATATGAGT
*
35129134 ACTCATTATCTTCAC
1 ACTCATTATCATCAC
35129149 ACTCATTATCATCAC
1 ACTCATTATCATCAC
35129164 TCCATTGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (15 bp):
ACTCATTATCATCAC
Found at i:35142401 original size:29 final size:30
Alignment explanation
Indices: 35142366--35142434 Score: 122
Period size: 29 Copynumber: 2.3 Consensus size: 30
35142356 AGATAATTGA
35142366 GATTGATTACAGTATATGATATGTAAATAT
1 GATTGATTACAGTATATGATATGTAAATAT
35142396 G-TTGATTACAGTATATGATATGTAAATAT
1 GATTGATTACAGTATATGATATGTAAATAT
*
35142425 GAATGATTAC
1 GATTGATTAC
35142435 CAAAAGCGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
29 29 0.78
30 8 0.22
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (30 bp):
GATTGATTACAGTATATGATATGTAAATAT
Found at i:35155261 original size:128 final size:128
Alignment explanation
Indices: 35155100--35155362 Score: 481
Period size: 128 Copynumber: 2.1 Consensus size: 128
35155090 GAATCATATT
35155100 TATATATGAGAATGTGTTAGAAAGGGGGTTCTTCTTTCTCTTTCTCTTTCTCTTCCTTAAGTAGA
1 TATATATGAGAATGTGTTAGAAAGGGGGTTCTTCTTTCTCTTTCTCTTTCTCTTCCTTAAGTAGA
35155165 ATTTACTGATACTCTTTTTAAGTCTGAATGTATCTATAAACTTGAAATTATATAGGGTTTTTC
66 ATTTACTGATACTCTTTTTAAGTCTGAATGTATCTATAAACTTGAAATTATATAGGGTTTTTC
* * * *
35155228 TGTATATGAGAGTGTGTTAGAAAGGGGGTTCTTCTTTCTCTTTCTCTTTCTTTTCCTTAAGTGGA
1 TATATATGAGAATGTGTTAGAAAGGGGGTTCTTCTTTCTCTTTCTCTTTCTCTTCCTTAAGTAGA
*
35155293 ATTTACTGATACTCTTTTTAAGTCTGAATGTATCTATAAGCTTGAAATTATATAGGGTTTTTC
66 ATTTACTGATACTCTTTTTAAGTCTGAATGTATCTATAAACTTGAAATTATATAGGGTTTTTC
35155356 TATATAT
1 TATATAT
35155363 TTTTACCACC
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 129 1.00
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.46
Consensus pattern (128 bp):
TATATATGAGAATGTGTTAGAAAGGGGGTTCTTCTTTCTCTTTCTCTTTCTCTTCCTTAAGTAGA
ATTTACTGATACTCTTTTTAAGTCTGAATGTATCTATAAACTTGAAATTATATAGGGTTTTTC
Found at i:35157764 original size:37 final size:37
Alignment explanation
Indices: 35157723--35157795 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
35157713 ATAGCTAGTG
35157723 TGACTGAAAATGCAATGAGGTTAAAATTGTTTCCATT
1 TGACTGAAAATGCAATGAGGTTAAAATTGTTTCCATT
* *
35157760 TGACTGAAGATGCACTGAGGTTAAAATTGTTTCCAT
1 TGACTGAAAATGCAATGAGGTTAAAATTGTTTCCAT
35157796 ACTCATTGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (37 bp):
TGACTGAAAATGCAATGAGGTTAAAATTGTTTCCATT
Found at i:35163061 original size:36 final size:38
Alignment explanation
Indices: 35162987--35163100 Score: 105
Period size: 36 Copynumber: 3.1 Consensus size: 38
35162977 TTCGAATTCG
* * * *
35162987 TTTTAATCTTT-TC-TTAGTTTTATTTTTA-TTTCTCAT
1 TTTTAGTCTTTATCTTTAATTTTAATTTTAGTTTC-AAT
*
35163023 TTTTA-TCTTTGTCTTTAATTTTAA-TTTAGTTTCAA-
1 TTTTAGTCTTTATCTTTAATTTTAATTTTAGTTTCAAT
* * *
35163058 TTTTAGTCTTTATTTTTAATTTTAATTTTAGTTTTATT
1 TTTTAGTCTTTATCTTTAATTTTAATTTTAGTTTCAAT
35163096 TTTTA
1 TTTTA
35163101 ATAAAGGGGT
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
35 10 0.15
36 29 0.45
37 21 0.32
38 5 0.08
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.68
Consensus pattern (38 bp):
TTTTAGTCTTTATCTTTAATTTTAATTTTAGTTTCAAT
Found at i:35163098 original size:12 final size:12
Alignment explanation
Indices: 35163000--35163098 Score: 69
Period size: 12 Copynumber: 8.2 Consensus size: 12
35162990 TAATCTTTTC
35163000 TTAGTTTTATTT
1 TTAGTTTTATTT
35163012 TTA-TTTCTCATTT
1 TTAGTTT-T-ATTT
* *
35163025 TTA-TCTTTGTCT
1 TTAGT-TTTATTT
* *
35163037 TTAATTTTA-AT
1 TTAGTTTTATTT
* *
35163048 TTAGTTTCAATT
1 TTAGTTTTATTT
35163060 TTAGTCTTTATTT
1 TTAGT-TTTATTT
* *
35163073 TTAATTTTAATT
1 TTAGTTTTATTT
35163085 TTAGTTTTATTT
1 TTAGTTTTATTT
35163097 TT
1 TT
35163099 TAATAAAGGG
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
11 11 0.16
12 36 0.53
13 19 0.28
14 2 0.03
ACGTcount: A:0.20, C:0.06, G:0.05, T:0.69
Consensus pattern (12 bp):
TTAGTTTTATTT
Found at i:35163102 original size:25 final size:25
Alignment explanation
Indices: 35163047--35163098 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
35163037 TTAATTTTAA
*
35163047 TTTAGTTTCAATTTTAGTCTTTATT
1 TTTAATTTCAATTTTAGTCTTTATT
*
35163072 TTTAATTTTAATTTTAGT-TTTATT
1 TTTAATTTCAATTTTAGTCTTTATT
35163096 TTT
1 TTT
35163099 TAATAAAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (25 bp):
TTTAATTTCAATTTTAGTCTTTATT
Found at i:35165376 original size:25 final size:25
Alignment explanation
Indices: 35165348--35165398 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
35165338 TTAAAGGGGG
**
35165348 ATAAAAGATTTTTCATGAATTTTTA
1 ATAAAAGATTTCGCATGAATTTTTA
**
35165373 ATAAGGGATTTCGCATGAATTTTTA
1 ATAAAAGATTTCGCATGAATTTTTA
35165398 A
1 A
35165399 GTATGTTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (25 bp):
ATAAAAGATTTCGCATGAATTTTTA
Found at i:35169155 original size:50 final size:50
Alignment explanation
Indices: 35169027--35169212 Score: 225
Period size: 50 Copynumber: 3.7 Consensus size: 50
35169017 GATAATAACA
* *
35169027 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* * *
35169076 TGCCAATGCTATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* ** ** *
35169126 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
*
35169176 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
35169213 TCTCATTCCC
Statistics
Matches: 116, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
48 4 0.03
49 38 0.33
50 74 0.64
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:35188368 original size:22 final size:23
Alignment explanation
Indices: 35188345--35188386 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35188335 ACTCTTACTA
35188345 AAATT-AATCGA-TTGATTAACT
1 AAATTAAATCGATTTGATTAACT
*
35188366 AAATTAAATTGATTTGATTAA
1 AAATTAAATCGATTTGATTAA
35188387 TTAATTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 5 0.28
23 8 0.44
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (23 bp):
AAATTAAATCGATTTGATTAACT
Found at i:35188403 original size:80 final size:80
Alignment explanation
Indices: 35188266--35188414 Score: 244
Period size: 80 Copynumber: 1.9 Consensus size: 80
35188256 AAATTAGATC
* * *
35188266 AATTAATCGACTGATTAACTAAATTAGATTGGTTTGATTGATTAATTTAGTTCTAATCAAAATTT
1 AATTAATCGACTGATTAACTAAATTAAATTGATTTGATTAATTAATTTAGTTCTAATCAAAATTT
35188331 AAACACTCTTACTAA
66 AAACACTCTTACTAA
* * *
35188346 AATTAATCGATTGATTAACTAAATTAAATTGATTTGATTAATTAATTTAGTTTTAATCGAAATTT
1 AATTAATCGACTGATTAACTAAATTAAATTGATTTGATTAATTAATTTAGTTCTAATCAAAATTT
35188411 AAAC
66 AAAC
35188415 CCTCATTATA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 63 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (80 bp):
AATTAATCGACTGATTAACTAAATTAAATTGATTTGATTAATTAATTTAGTTCTAATCAAAATTT
AAACACTCTTACTAA
Found at i:35196262 original size:46 final size:46
Alignment explanation
Indices: 35196221--35196308 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
35196211 TATTAATTCA
*
35196221 CATCCATTTACGTTCTTGCAATTAACTAAAA-TAATCAATTAAGTT
1 CATCCAATTACGTTCTTGCAATTAACTAAAACTAATCAATTAAGTT
** ** *
35196266 TTTTTAATTACGTTCTTTCAATTAACTAAAACTAATCAATTAA
1 CATCCAATTACGTTCTTGCAATTAACTAAAACTAATCAATTAA
35196309 ACCTTTCCGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 25 0.69
46 11 0.31
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (46 bp):
CATCCAATTACGTTCTTGCAATTAACTAAAACTAATCAATTAAGTT
Found at i:35196449 original size:19 final size:20
Alignment explanation
Indices: 35196425--35196465 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
35196415 TAAAAATATT
35196425 AAAAATCA-CAAATATTAAA
1 AAAAATCATCAAATATTAAA
*
35196444 AAAAATGATCAAATATTAAA
1 AAAAATCATCAAATATTAAA
35196464 AA
1 AA
35196466 TATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAAATCATCAAATATTAAA
Found at i:35196512 original size:9 final size:9
Alignment explanation
Indices: 35196495--35196566 Score: 60
Period size: 9 Copynumber: 8.0 Consensus size: 9
35196485 TGATATGAAC
*
35196495 TTATGAAAA
1 TTATAAAAA
35196504 TTATAAAAA
1 TTATAAAAA
35196513 -TATAAAATA
1 TTATAAAA-A
*
35196522 TTATAAATA
1 TTATAAAAA
35196531 TTATAAAAA
1 TTATAAAAA
*
35196540 TCTA-ATAAA
1 T-TATAAAAA
*
35196549 TCTA-ATAAA
1 T-TATAAAAA
35196558 TTATAAAAA
1 TTATAAAAA
35196567 AAATAAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
8 9 0.17
9 37 0.69
10 8 0.15
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:35196560 original size:27 final size:26
Alignment explanation
Indices: 35196495--35196566 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
35196485 TGATATGAAC
35196495 TTATGAAAATTATAAAAATATAAAATA
1 TTAT-AAAATTATAAAAATATAAAATA
*
35196522 TTATAAATATTATAAAAATCTAATAA-A
1 TTATAAA-ATTATAAAAATATAA-AATA
35196549 TCTA-ATAAATTATAAAAA
1 T-TATA-AAATTATAAAAA
35196567 AAATAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
26 3 0.08
27 31 0.77
28 6 0.15
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (26 bp):
TTATAAAATTATAAAAATATAAAATA
Found at i:35201864 original size:59 final size:59
Alignment explanation
Indices: 35201746--35201904 Score: 259
Period size: 59 Copynumber: 2.7 Consensus size: 59
35201736 TATATACCTA
* *
35201746 TTATATACCTATGCACTTTCACATAACAAATT--AACAGATTAACAAATACGAACCATT
1 TTATATACCTATGCACTTTCACATAACAAGTTAAAACAAATTAACAAATACGAACCATT
* * *
35201803 TTATATACATGTGTACTTTCACATAACAAGTTAAAACAAATTAACAAATACGAACCATT
1 TTATATACCTATGCACTTTCACATAACAAGTTAAAACAAATTAACAAATACGAACCATT
35201862 TTATATACCTATGCACTTTCACATAACAAGTTAAAACAAATTA
1 TTATATACCTATGCACTTTCACATAACAAGTTAAAACAAATTA
35201905 TATTATACCA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
57 28 0.30
59 64 0.70
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.31
Consensus pattern (59 bp):
TTATATACCTATGCACTTTCACATAACAAGTTAAAACAAATTAACAAATACGAACCATT
Found at i:35203504 original size:43 final size:41
Alignment explanation
Indices: 35203434--35203552 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 41
35203424 TACTCGGATA
* * * * ** *
35203434 GATGCCATATCCCAGATATGGTATTACATGTTATAATATATT
1 GATGCCATGTCCCAGAAATGGTCTTACACGAAATAATATA-C
* *
35203476 GATGCCACTGTCCCAGAAAGGGTCTTACACGAAATCATATAC
1 GATGCCA-TGTCCCAGAAATGGTCTTACACGAAATAATATAC
*
35203518 GATGCCAATGTCCCAGACATGGTCTTACACGAAAT
1 GATGCC-ATGTCCCAGAAATGGTCTTACACGAAAT
35203553 CATACCTCAG
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 38 0.59
43 26 0.41
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (41 bp):
GATGCCATGTCCCAGAAATGGTCTTACACGAAATAATATAC
Found at i:35203522 original size:42 final size:42
Alignment explanation
Indices: 35203476--35203556 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
35203466 ATAATATATT
*
35203476 GATGCCACTGTCCCAGAAAGGGTCTTACACGAAATCATATAC
1 GATGCCAATGTCCCAGAAAGGGTCTTACACGAAATCATATAC
* *
35203518 GATGCCAATGTCCCAGACATGGTCTTACACGAAATCATA
1 GATGCCAATGTCCCAGAAAGGGTCTTACACGAAATCATA
35203557 CCTCAGAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (42 bp):
GATGCCAATGTCCCAGAAAGGGTCTTACACGAAATCATATAC
Found at i:35209680 original size:23 final size:23
Alignment explanation
Indices: 35209660--35209705 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
35209650 CCACAGCTTG
*
35209660 TATGAGCTTACCGTTTTAGCTCT
1 TATGAGCTTACCGTTTCAGCTCT
*
35209683 TATGAGCTTACTGTTTCAGCTCT
1 TATGAGCTTACCGTTTCAGCTCT
35209706 ACAGACCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (23 bp):
TATGAGCTTACCGTTTCAGCTCT
Found at i:35223232 original size:16 final size:16
Alignment explanation
Indices: 35223206--35223250 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
35223196 TAGAATCGAG
*
35223206 TTGAGAAAATTATTTAA
1 TTGA-AAAATTAATTAA
35223223 TTGAAAAATTAATTAA
1 TTGAAAAATTAATTAA
35223239 TT--AAAATTAATT
1 TTGAAAAATTAATT
35223251 TATAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 10 0.37
16 13 0.48
17 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (16 bp):
TTGAAAAATTAATTAA
Found at i:35226832 original size:12 final size:13
Alignment explanation
Indices: 35226808--35226834 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35226798 AAAAAACAAC
35226808 GAAACCAAAAAAA
1 GAAACCAAAAAAA
35226821 GAAACCAAAAAAA
1 GAAACCAAAAAAA
35226834 G
1 G
35226835 GAAAAAAAAT
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:0.74, C:0.15, G:0.11, T:0.00
Consensus pattern (13 bp):
GAAACCAAAAAAA
Found at i:35226843 original size:13 final size:14
Alignment explanation
Indices: 35226785--35226843 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 14
35226775 CATTTTGCCT
*
35226785 AAAAAAGGAGAATAA
1 AAAAAAGGA-AACAA
* *
35226800 AAAACAACGAAACCA
1 AAAA-AAGGAAACAA
*
35226815 AAAAAA-GAAACCA
1 AAAAAAGGAAACAA
35226828 AAAAAAGGAAA-AA
1 AAAAAAGGAAACAA
35226841 AAA
1 AAA
35226844 TAGAGAGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
13 17 0.45
14 6 0.16
15 11 0.29
16 4 0.11
ACGTcount: A:0.76, C:0.10, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAAAAGGAAACAA
Found at i:35227326 original size:42 final size:41
Alignment explanation
Indices: 35227251--35227387 Score: 184
Period size: 42 Copynumber: 3.3 Consensus size: 41
35227241 AAGGAAAGCA
* * *
35227251 TTCATTGCACTTAGAGGCCTAGGTGTGGCGGTCCATTTACAT
1 TTCATTGCATTTAGAGGCC-AGGTGTAGAGGTCCATTTACAT
* *
35227293 TTCATTGCATTTAGAGGTCCAGATGTAGAGGTCCATTTACCT
1 TTCATTGCATTTAGAGG-CCAGGTGTAGAGGTCCATTTACAT
* *
35227335 TTCATTGCATTTAGAGGCCCAGGTGGAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGG-CCAGGTGTAGAGGTCCATTTACAT
35227377 TTCATTGCATT
1 TTCATTGCATT
35227388 GTATATGAAG
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 83 0.98
43 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
TTCATTGCATTTAGAGGCCAGGTGTAGAGGTCCATTTACAT
Found at i:35227838 original size:3 final size:3
Alignment explanation
Indices: 35227832--35227878 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
35227822 TTATTATCAT
35227832 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
35227879 AATATTATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:35228004 original size:3 final size:3
Alignment explanation
Indices: 35227998--35228026 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
35227988 AAAAAGAGTA
35227998 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
35228027 GAAGCATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:35228324 original size:77 final size:78
Alignment explanation
Indices: 35228212--35228386 Score: 318
Period size: 77 Copynumber: 2.2 Consensus size: 78
35228202 CTTGATCTTG
35228212 GGAAAAGTTTTGAT-TTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAATAAAATTATGTTT
1 GGAAAA-TTTT-ATATTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAATAAAATTATGTTT
35228276 TTTAGTCATTTTAAA
64 TTTAGTCATTTTAAA
35228291 GGAAAATTTTATATTTTTTTT-AAAAAAGAGAAAGTTTAGATTTTTAAAATAAAATTATGTTTTT
1 GGAAAATTTTATATTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAATAAAATTATGTTTTT
35228355 TAGTCATTTTAAA
66 TAGTCATTTTAAA
35228368 GGAAAATTTTATATTTTTT
1 GGAAAATTTTATATTTTTT
35228387 AAAACAAAGT
Statistics
Matches: 95, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
77 77 0.81
78 12 0.13
79 6 0.06
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.47
Consensus pattern (78 bp):
GGAAAATTTTATATTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAATAAAATTATGTTTTT
TAGTCATTTTAAA
Found at i:35228609 original size:21 final size:20
Alignment explanation
Indices: 35228576--35228632 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
35228566 AAAGCTTTGA
*
35228576 TTTTTAAGAAAAATAGTGAT
1 TTTTTAAAAAAAATAGTGAT
**
35228596 TTTTTAAAAGAAAATTTTGAT
1 TTTTTAAAA-AAAATAGTGAT
*
35228617 TTTTCAAAACAAAATA
1 TTTTTAAAA-AAAATA
35228633 TTTTTAGCCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTTTAAAAAAAATAGTGAT
Found at i:35228913 original size:43 final size:43
Alignment explanation
Indices: 35228852--35228941 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
35228842 ACAAAAAGTA
*
35228852 ACCCATTTCTTGCAGCGCCGCCCTCGCTCTCTGGCGTACTTAC
1 ACCCATTTCTTGCAGCGCCGCCCTCACTCTCTGGCGTACTTAC
*
35228895 ACCCATTTCTTGTAGCGCCGCCCTCACTCTCTGGCGTACTTAC
1 ACCCATTTCTTGCAGCGCCGCCCTCACTCTCTGGCGTACTTAC
35228938 ACCC
1 ACCC
35228942 GTAACCCTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.13, C:0.42, G:0.17, T:0.28
Consensus pattern (43 bp):
ACCCATTTCTTGCAGCGCCGCCCTCACTCTCTGGCGTACTTAC
Found at i:35239992 original size:25 final size:26
Alignment explanation
Indices: 35239939--35240010 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
35239929 AAATTTATCG
* *
35239939 AAATTTTATCGGGGGT-AAATTCGTTA
1 AAATTTTATC-GAGGTAAAATTCGTGA
35239965 AAATTTTATCGAGGTAAAATT-GTGA
1 AAATTTTATCGAGGTAAAATTCGTGA
* *
35239990 AAAATTTA-CTAGGGTAAAATT
1 AAATTTTATCGA-GGTAAAATT
35240011 AGGGTTAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 2 0.05
25 23 0.57
26 15 0.38
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (26 bp):
AAATTTTATCGAGGTAAAATTCGTGA
Found at i:35248290 original size:21 final size:21
Alignment explanation
Indices: 35248223--35248291 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
35248213 GCATTGAAGA
* *
35248223 GTGTTGTGGCTGCATCTGATT
1 GTGTTGTGGATGCATCTGAGT
* *
35248244 CTGGTGTGGATGCATCTG-GCT
1 GTGTTGTGGATGCATCTGAG-T
*
35248265 TTGTTGTGGATGCATCTGAGT
1 GTGTTGTGGATGCATCTGAGT
35248286 GTGTTG
1 GTGTTG
35248292 ATTATAGTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.10, C:0.13, G:0.36, T:0.41
Consensus pattern (21 bp):
GTGTTGTGGATGCATCTGAGT
Found at i:35261558 original size:50 final size:50
Alignment explanation
Indices: 35261437--35261629 Score: 287
Period size: 50 Copynumber: 3.8 Consensus size: 50
35261427 AACAAGAACA
* * ** *
35261437 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * ** *
35261488 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTATCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
35261538 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
35261588 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
35261630 TTACCCAAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
50 96 0.75
51 32 0.25
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:35262475 original size:20 final size:20
Alignment explanation
Indices: 35262450--35262487 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
35262440 GAAGAAGATG
35262450 ATCAAAAATTGGCTTCTATT
1 ATCAAAAATTGGCTTCTATT
35262470 ATCAAAAATTGGCTTCTA
1 ATCAAAAATTGGCTTCTA
35262488 ATTTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
ATCAAAAATTGGCTTCTATT
Found at i:35263505 original size:26 final size:26
Alignment explanation
Indices: 35263474--35263898 Score: 390
Period size: 26 Copynumber: 16.2 Consensus size: 26
35263464 GTAATGGGCC
*
35263474 TAAATTACCGAAATACCCTCGATGGG
1 TAAATTATCGAAATACCCTCGATGGG
* * **
35263500 TAAATTACCAAAATA-CCTTTATTGGG
1 TAAATTATCGAAATACCCTCGA-TGGG
35263526 TAAATTATCGAAATACCCTCGATGGG
1 TAAATTATCGAAATACCCTCGATGGG
* *
35263552 TAAATTA-CTGAAATACCTTTGATGGG
1 TAAATTATC-GAAATACCCTCGATGGG
* *
35263578 TAAATTACCGAAATACCCTCAATGGG
1 TAAATTATCGAAATACCCTCGATGGG
*
35263604 TAAATTA-CTGAAATACCCTCGACGGG
1 TAAATTATC-GAAATACCCTCGATGGG
*
35263630 TAAATTATCGAAATACCCACGATGGG
1 TAAATTATCGAAATACCCTCGATGGG
*
35263656 TAAATTCTCGAAATACCCTCGATGGG
1 TAAATTATCGAAATACCCTCGATGGG
*
35263682 TAAATTATCGAAATACCCTCGACGGG
1 TAAATTATCGAAATACCCTCGATGGG
* * * * *
35263708 TAAAATTACCAAAATA-CCTTGAAGAG
1 T-AAATTATCGAAATACCCTCGATGGG
* *
35263734 TAAAATTATCGAAATACCCCCGAGGGG
1 T-AAATTATCGAAATACCCTCGATGGG
* * *
35263761 TAAAATTATTGAAATACCCTCGAAGTG
1 T-AAATTATCGAAATACCCTCGATGGG
* * ** *
35263788 TAAAATGATAGAAATACCCTTAAAGGG
1 T-AAATTATCGAAATACCCTCGATGGG
* * **
35263815 TAAAATGATCGAAATATCCTCGAAAGG
1 T-AAATTATCGAAATACCCTCGATGGG
* *
35263842 TAAAATGATCGAAATACCCTCGAAGGG
1 T-AAATTATCGAAATACCCTCGATGGG
* * * * *
35263869 TAAAATGTCGATATACCCCCGAAGGG
1 TAAATTATCGAAATACCCTCGATGGG
35263895 TAAA
1 TAAA
35263899 ATGATTGTTA
Statistics
Matches: 339, Mismatches: 52, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
25 6 0.02
26 216 0.64
27 117 0.35
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (26 bp):
TAAATTATCGAAATACCCTCGATGGG
Found at i:35277336 original size:15 final size:15
Alignment explanation
Indices: 35277316--35277346 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35277306 ATAGGGTTAC
35277316 ATTGTGTAAGACCAT
1 ATTGTGTAAGACCAT
35277331 ATTGTGTAAGACCAT
1 ATTGTGTAAGACCAT
35277346 A
1 A
35277347 GTTGGGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (15 bp):
ATTGTGTAAGACCAT
Found at i:35279614 original size:13 final size:13
Alignment explanation
Indices: 35279596--35279620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35279586 AGGAGAAAAA
35279596 GAAGGAAGTGAAT
1 GAAGGAAGTGAAT
35279609 GAAGGAAGTGAA
1 GAAGGAAGTGAA
35279621 ATATTTCCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.40, T:0.12
Consensus pattern (13 bp):
GAAGGAAGTGAAT
Found at i:35279669 original size:22 final size:21
Alignment explanation
Indices: 35279644--35279686 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
35279634 AAAAGGTTAG
35279644 ATGG-ATTGCCAACACAAATGCC
1 ATGGAATT-CCAACA-AAATGCC
35279666 ATGGCAATTCCAACAAAATGC
1 ATGG-AATTCCAACAAAATGC
35279687 TGACGTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.53
23 6 0.32
24 3 0.16
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.19
Consensus pattern (21 bp):
ATGGAATTCCAACAAAATGCC
Found at i:35279841 original size:13 final size:13
Alignment explanation
Indices: 35279825--35279851 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35279815 TAAAGAAAGA
35279825 ATGAGGATTTTGG
1 ATGAGGATTTTGG
35279838 ATGAGGATTTTGG
1 ATGAGGATTTTGG
35279851 A
1 A
35279852 GGGGGATTTG
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:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (13 bp):
ATGAGGATTTTGG
Found at i:35279858 original size:13 final size:13
Alignment explanation
Indices: 35279827--35279864 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
35279817 AAGAAAGAAT
*
35279827 GAGGATTTTGGAT
1 GAGGATTTTGGAG
35279840 GAGGATTTTGGAG
1 GAGGATTTTGGAG
*
35279853 GGGGA-TTTGGAG
1 GAGGATTTTGGAG
35279865 AACAATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (13 bp):
GAGGATTTTGGAG
Found at i:35281568 original size:27 final size:27
Alignment explanation
Indices: 35281530--35281583 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
35281520 ACTGTGGTTC
35281530 GCAATGATGACAACGAACTCATTCCAA
1 GCAATGATGACAACGAACTCATTCCAA
35281557 GCAATGATGACAACGAACTCATTCCAA
1 GCAATGATGACAACGAACTCATTCCAA
35281584 CTCGTACTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.19
Consensus pattern (27 bp):
GCAATGATGACAACGAACTCATTCCAA
Found at i:35287607 original size:13 final size:13
Alignment explanation
Indices: 35287574--35287609 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
35287564 AGAAAGAAAA
35287574 AAGAGGATTTTGG
1 AAGAGGATTTTGG
*
35287587 ATGAGGATTTTGG
1 AAGAGGATTTTGG
*
35287600 AAGGGGATTT
1 AAGAGGATTT
35287610 GGAGAGCAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.39, T:0.33
Consensus pattern (13 bp):
AAGAGGATTTTGG
Found at i:35290133 original size:49 final size:49
Alignment explanation
Indices: 35290073--35290318 Score: 201
Period size: 49 Copynumber: 4.9 Consensus size: 49
35290063 GATAATAACT
* ** *
35290073 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTTTCATGTAC-
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATGT-CG
* * ** *
35290122 TGCCAATGCCATATCCCAAATATGGTCTTA-ATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATGTC-G
* * ** *
35290171 TGCCCATGCCATGT-CCAAGACATGATCTTACGGGGGACCTCTCATCTCG
1 TGCCAATGCCATGTCCCAA-ACATGGTCTTACATGGGACCTCTCATGTCG
* * *
35290220 ATGCCAACGCCATGCCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 -TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATG---TC---G
* *
35290276 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
35290319 TTACCCAAAT
Statistics
Matches: 158, Mismatches: 27, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
47 1 0.01
48 16 0.10
49 49 0.31
50 46 0.29
51 3 0.02
53 2 0.01
56 41 0.26
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATGTCG
Found at i:35297347 original size:49 final size:49
Alignment explanation
Indices: 35297275--35297374 Score: 184
Period size: 49 Copynumber: 2.0 Consensus size: 49
35297265 AATTTGATTA
35297275 ATGTACTACCAGTGCCATATCCCAGATATGGTCTTACATGGGATGTT-TC
1 ATGTACTACCAGTGCCATATCCCAGATATGGTCTTACATGGGA-GTTCTC
35297324 ATGTACTACCAGTGCCATATCCCAGATATGGTCTTACATGGGAGTTCTC
1 ATGTACTACCAGTGCCATATCCCAGATATGGTCTTACATGGGAGTTCTC
35297373 AT
1 AT
35297375 ATCGGTGTCC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 3 0.06
49 47 0.94
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (49 bp):
ATGTACTACCAGTGCCATATCCCAGATATGGTCTTACATGGGAGTTCTC
Found at i:35297545 original size:101 final size:105
Alignment explanation
Indices: 35297387--35297628 Score: 291
Period size: 101 Copynumber: 2.3 Consensus size: 105
35297377 CGGTGTCCAT
** *
35297387 GCCATGTCCCAGAC-TTGGTCTTACGA-GGGACCTCTCATCTTGGTGCCAACGCTATGTCCCAAA
1 GCCATGTCCCAGACATTGGTCTTAC-ATGGGACCTCTCATCTCCGTGCCAACGCCATGTCCCAAA
* *
35297450 CATGGCCTTATATGGGACCTCT-TGA-CT-CGG-TGCCAAC
65 CATGACCTTACATGGGACCTCTATGATCTACGGATGCCAAC
* *
35297487 GCCATGTCCCAGACATTGGTCTTACATGGGACCTCTCGTCTCCGTGCCAACGCCATGTCTCAAAC
1 GCCATGTCCCAGACATTGGTCTTACATGGGACCTCTCATCTCCGTGCCAACGCCATGTCCCAAAC
** *
35297552 ATGATTTTACATGGGACCTCTCATGATCTCACGGATGCCAAT
66 ATGACCTTACATGGGACCTCT-ATGATCT-ACGGATGCCAAC
** *
35297594 GCCATGTCTTAGACA-TGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATTGGTCTTACATGGGACCTCT
35297629 TTACCCAAAT
Statistics
Matches: 121, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
100 15 0.12
101 60 0.50
103 3 0.02
104 2 0.02
106 22 0.18
107 19 0.16
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (105 bp):
GCCATGTCCCAGACATTGGTCTTACATGGGACCTCTCATCTCCGTGCCAACGCCATGTCCCAAAC
ATGACCTTACATGGGACCTCTATGATCTACGGATGCCAAC
Found at i:35297618 original size:56 final size:53
Alignment explanation
Indices: 35297337--35297628 Score: 234
Period size: 50 Copynumber: 5.7 Consensus size: 53
35297327 TACTACCAGT
* * * * * * *
35297337 GCCATATCCCAGATATGGTCTTACATGGGA-GT-TCTCATAT-CGGTGTCC-AT
1 GCCATGTCTCAGACATGGTCTTACATGGGACCTCTCTGATCTCCGGTG-CCAAC
* * *
35297387 GCCATGTCCCAGACTTGGTCTTACGA-GGGACCTCTC--ATCT-TGGTGCCAAC
1 GCCATGTCTCAGACATGGTCTTAC-ATGGGACCTCTCTGATCTCCGGTGCCAAC
* * * * *
35297437 GCTATGTCCCAAACATGGCCTTATATGGGACCTCT-TGA-CT-CGGTGCCAAC
1 GCCATGTCTCAGACATGGTCTTACATGGGACCTCTCTGATCTCCGGTGCCAAC
*
35297487 GCCATGTCCCAGACATTGGTCTTACATGGGACCTCTC-G-TCTCC-GTGCCAAC
1 GCCATGTCTCAGACA-TGGTCTTACATGGGACCTCTCTGATCTCCGGTGCCAAC
* * * *
35297538 GCCATGTCTCAAACATGATTTTACATGGGACCTCTCATGATCTCACGGATGCCAAT
1 GCCATGTCTCAGACATGGTCTTACATGGGACCTCTC-TGATCTC-CGG-TGCCAAC
* *
35297594 GCCATGTCTTAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCTCAGACATGGTCTTACATGGGACCTCT
35297629 TTACCCAAAT
Statistics
Matches: 198, Mismatches: 27, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
49 3 0.02
50 104 0.53
51 45 0.23
52 4 0.02
53 4 0.02
54 1 0.01
55 1 0.01
56 36 0.18
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (53 bp):
GCCATGTCTCAGACATGGTCTTACATGGGACCTCTCTGATCTCCGGTGCCAAC
Found at i:35305581 original size:6 final size:6
Alignment explanation
Indices: 35305572--35305614 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
35305562 GCTAGGGTTA
* *
35305572 GTTAAG GTTAGG GTT-A- GTTAAG GTTAAG GTTAGG GTTAAG GTT
1 GTTAAG GTTAAG GTTAAG GTTAAG GTTAAG GTTAAG GTTAAG GTT
35305615 TTTGTTAGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 3 0.10
5 1 0.03
6 27 0.87
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (6 bp):
GTTAAG
Found at i:35305583 original size:16 final size:16
Alignment explanation
Indices: 35305564--35305614 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
35305554 GGGTTAGGGC
35305564 TAGGGTTAGTTAAGGT
1 TAGGGTTAGTTAAGGT
35305580 TAGGGTTAGTTAAGGT
1 TAGGGTTAGTTAAGGT
*
35305596 TAAGGTTAGGGTTAAGGT
1 TAGGGTTA--GTTAAGGT
35305614 T
1 T
35305615 TTTGTTAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 23 0.72
18 9 0.28
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
TAGGGTTAGTTAAGGT
Found at i:35305607 original size:22 final size:22
Alignment explanation
Indices: 35305516--35305609 Score: 92
Period size: 22 Copynumber: 4.4 Consensus size: 22
35305506 ATAAATTAGT
35305516 TTAGGGTT--TTAAGTTAAGGG
1 TTAGGGTTAGTTAAGTTAAGGG
* *
35305536 TTAGAGTT-TTTAAGTTAAGGG
1 TTAGGGTTAGTTAAGTTAAGGG
*
35305557 TTAGGGCTAGGGTT-AGTTAA-GG
1 TTAGGGTTA--GTTAAGTTAAGGG
35305579 TTAGGGTTAGTTAAGGTTAA-GG
1 TTAGGGTTAGTTAA-GTTAAGGG
35305601 TTAGGGTTA
1 TTAGGGTTA
35305610 AGGTTTTTGT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
20 10 0.16
21 19 0.30
22 26 0.41
23 6 0.10
24 2 0.03
ACGTcount: A:0.26, C:0.01, G:0.35, T:0.38
Consensus pattern (22 bp):
TTAGGGTTAGTTAAGTTAAGGG
Found at i:35307935 original size:19 final size:20
Alignment explanation
Indices: 35307913--35307956 Score: 74
Period size: 18 Copynumber: 2.3 Consensus size: 20
35307903 TTTTTACGAT
35307913 TTAAAATTTTTTTAAAA-AA
1 TTAAAATTTTTTTAAAATAA
35307932 TT-AAATTTTTTTAAAATAA
1 TTAAAATTTTTTTAAAATAA
35307951 TTAAAA
1 TTAAAA
35307957 ATAGGGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 14 0.61
19 6 0.26
20 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAATTTTTTTAAAATAA
Found at i:35308413 original size:28 final size:28
Alignment explanation
Indices: 35308347--35308411 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
35308337 GCGTTTTCGG
35308347 AAAAAAGGGCCCATTCAGGTAAATAATA
1 AAAAAAGGGCCCATTCAGGTAAATAATA
** *
35308375 AAATACCGGGCCCATTTC-GGTAAAT-TTA
1 AAA-AAAGGGCCCA-TTCAGGTAAATAATA
35308403 AAAAAAGGG
1 AAAAAAGGG
35308412 GCTTTTTTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
27 4 0.13
28 8 0.27
29 15 0.50
30 3 0.10
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (28 bp):
AAAAAAGGGCCCATTCAGGTAAATAATA
Found at i:35317103 original size:3 final size:3
Alignment explanation
Indices: 35317095--35317184 Score: 180
Period size: 3 Copynumber: 30.0 Consensus size: 3
35317085 CGATCTTAAC
35317095 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
35317143 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
35317185 AATGTTCAGG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35319696 original size:17 final size:18
Alignment explanation
Indices: 35319674--35319714 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
35319664 GATACAGGGG
35319674 ACACACGA-CCGTGTGTC
1 ACACACGAGCCGTGTGTC
35319691 ACACAC-AGCCGTGTGTC
1 ACACACGAGCCGTGTGTC
35319708 ACACACG
1 ACACACG
35319715 GCTGAGACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.27, C:0.37, G:0.22, T:0.15
Consensus pattern (18 bp):
ACACACGAGCCGTGTGTC
Found at i:35325914 original size:21 final size:21
Alignment explanation
Indices: 35325889--35325928 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35325879 TGTCATAATC
35325889 TAAAATATA-TATTAAAAATAA
1 TAAAA-ATAGTATTAAAAATAA
*
35325910 TAAAAATAGTTTTAAAAAT
1 TAAAAATAGTATTAAAAAT
35325929 TATTTCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAAAATAGTATTAAAAATAA
Found at i:35325962 original size:17 final size:18
Alignment explanation
Indices: 35325928--35325962 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35325918 GTTTTAAAAA
*
35325928 TTATTTCCATTTTTTTTC
1 TTATTTCCATTCTTTTTC
35325946 TTATTTCC-TTCTTTTTC
1 TTATTTCCATTCTTTTTC
35325963 CCAATATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTCCATTCTTTTTC
Found at i:35327648 original size:28 final size:28
Alignment explanation
Indices: 35327574--35327648 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
35327564 TCCTCATAAC
35327574 GATAGTCCTGACAGACTTTCTCCATATTA
1 GATAGTCCTGA-AGACTTTCTCCATATTA
* *
35327603 GACAGTCCTAAAGAACTTTC-CACAT-TTA
1 GATAGTCCTGAAG-ACTTTCTC-CATATTA
35327631 GATAGTCCTGGAAGACTT
1 GATAGTCCT-GAAGACTT
35327649 CCCAATATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 18 0.46
29 21 0.54
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (28 bp):
GATAGTCCTGAAGACTTTCTCCATATTA
Found at i:35329100 original size:30 final size:29
Alignment explanation
Indices: 35329060--35329118 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
35329050 TAAAAAATCC
*
35329060 AAAAAATTAACATCACAAAAAAAACCCAT
1 AAAAAATTAACATAACAAAAAAAACCCAT
* *
35329089 AAAAAAGTTAACATAATAAACAAAACCCAT
1 AAAAAA-TTAACATAACAAAAAAAACCCAT
35329119 CAATCCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.64, C:0.19, G:0.02, T:0.15
Consensus pattern (29 bp):
AAAAAATTAACATAACAAAAAAAACCCAT
Found at i:35332582 original size:43 final size:43
Alignment explanation
Indices: 35332545--35332636 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
35332535 CTTACATGTT
* *
35332545 ATCACATATCGATGCCACTGTCCCAGACAAGGCCTTACACATA
1 ATCACATATCGATGCCAATGTCCAAGACAAGGCCTTACACATA
* * *
35332588 ATCTCATATCGATGCCAATGTCCAAGACATGGTCTTACACGA-A
1 ATCACATATCGATGCCAATGTCCAAGACAAGGCCTTACAC-ATA
35332631 ATCACA
1 ATCACA
35332637 CCTCGGGAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 41 0.98
44 1 0.02
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (43 bp):
ATCACATATCGATGCCAATGTCCAAGACAAGGCCTTACACATA
Found at i:35334868 original size:75 final size:76
Alignment explanation
Indices: 35334718--35334898 Score: 247
Period size: 75 Copynumber: 2.4 Consensus size: 76
35334708 GTTATCCGTT
* * *
35334718 ATCGGTGGATTCAACACTTAGCAACCCCTTTCACATTCAAAAATACTGTGGAATCAGCACTTAGA
1 ATCGG-GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGA
35334783 AACCACCAATGA
65 AACCACCAATGA
* * * * ** *
35334795 ATCGGGGAATTAGCACTTAGCAACTCCTTTCACATT-TAAGATACGGTGGGGTCAGCACTTAGCA
1 ATCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGAA
35334859 ACCACCAATGA
66 ACCACCAATGA
*
35334870 TTCGGGGAATCAGCACTTAGCAACCCCTT
1 ATCGGGGAATCAGCACTTAGCAACCCCTT
35334899 GGGGGAATCA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 59 0.65
76 27 0.30
77 5 0.05
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (76 bp):
ATCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGAA
ACCACCAATGA
Found at i:35334888 original size:33 final size:33
Alignment explanation
Indices: 35334846--35334996 Score: 116
Period size: 33 Copynumber: 4.5 Consensus size: 33
35334836 TACGGTGGGG
35334846 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
*
35334879 TCAGCACTTAGCAACC-CC-----TTGGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
* * * *
35334906 TCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAA
1 TCAGCACTTAGCAA-CCAC--CA-A--T--GATTCGG-GGAA
* *
35334948 TCAACACTTAGCAACCACCAATGAATCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
35334981 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
35334997 CCTTGGGGGA
Statistics
Matches: 94, Mismatches: 9, Indels: 30
0.71 0.07 0.23
Matches are distributed among these distances:
27 21 0.22
28 2 0.02
29 1 0.01
31 1 0.01
32 2 0.02
33 35 0.37
34 4 0.04
36 1 0.01
38 1 0.01
39 2 0.02
41 6 0.06
42 18 0.19
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (33 bp):
TCAGCACTTAGCAACCACCAATGATTCGGGGAA
Found at i:35334956 original size:102 final size:102
Alignment explanation
Indices: 35334798--35335028 Score: 381
Period size: 102 Copynumber: 2.3 Consensus size: 102
35334788 CCAATGAATC
* * * * * ** *
35334798 GGGGAATTAGCACTTAGCAACTCCTTTCACATTTAAGATACGGTGGGGTCAGCACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
*
35334863 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
35334900 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
35334965 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
35335002 GGGGAATCAACACTTAGCAACCCCCTT
1 GGGGAATCAACACTTAGCAACCCCCTT
35335029 TATATTCATT
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 120 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (102 bp):
GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAACACTTAGCAACCA
CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:35336737 original size:17 final size:19
Alignment explanation
Indices: 35336716--35336757 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
35336706 TATTATTTTA
35336716 ATAAATTTAATA-TTATAT
1 ATAAATTTAATATTTATAT
35336734 -TAAATTTAATATTTATAT
1 ATAAATTTAATATTTATAT
35336752 ATAAAT
1 ATAAAT
35336758 ATTCTATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
18 6 0.27
19 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAAATTTAATATTTATAT
Found at i:35337652 original size:18 final size:19
Alignment explanation
Indices: 35337631--35337677 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
35337621 GGGAAAGAAT
35337631 AAAAGAAAAGGAAAAAG-G
1 AAAAGAAAAGGAAAAAGTG
*
35337649 AAAAAAAAAGGAAAAAGTG
1 AAAAGAAAAGGAAAAAGTG
35337668 AAATAGAAAA
1 AAA-AGAAAA
35337678 ATATATTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.64
19 4 0.16
20 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (19 bp):
AAAAGAAAAGGAAAAAGTG
Found at i:35341018 original size:43 final size:43
Alignment explanation
Indices: 35340956--35341333 Score: 472
Period size: 43 Copynumber: 8.8 Consensus size: 43
35340946 TTTTAGAAAT
* * * * *
35340956 AAACGCCGTTATAGACCATGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCACTTCTCCCAC
*
35340999 AAACGCCGCTATAGGCCATGACCTTTAGTGGCACTTCTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCACTTCTCCCAC
* ** * * *
35341042 AAATG-C-CTATAGAACATGATCTTTAGCGACGCTTCTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCACTTCTCCCAC
* * * * *
35341083 AAACGCCGCTATAGACCATGATCTTTAGCGGCACTTTTCCAAT
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCACTTCTCCCAC
* *
35341126 AAACGCCGTTATAGGCCATGACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCACTTCTCCCAC
*
35341169 AAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCACTTCTCCCAC
* * ** *
35341212 AAATGCCGCTATAGGCCATGACCTTTAGTGGTGCTTCTCCTAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCACTTCTCCCAC
* * *
35341255 AAACGCCGCTATAGGCTATGACCTTTAGCGGTACTTTTCCCAC
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCACTTCTCCCAC
* *
35341298 AAACGCCGCTATAGGCCATAACTTTTAGCGGCACTT
1 AAACGCCGCTATAGGCCATGACCTTTAGCGGCACTT
35341334 GGTTTAAAAA
Statistics
Matches: 291, Mismatches: 42, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
41 33 0.11
42 2 0.01
43 256 0.88
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGGCCATGACCTTTAGCGGCACTTCTCCCAC
Found at i:35341259 original size:129 final size:129
Alignment explanation
Indices: 35340956--35341329 Score: 527
Period size: 129 Copynumber: 2.9 Consensus size: 129
35340946 TTTTAGAAAT
* *
35340956 AAACGCCGTTATAGACCATGATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGGCCATGAC
1 AAACGCCGCTATAGACCATGATCTTTAGCGGCGCTTTTCCAACAAACGCCGCTATAGGCCATGAC
* * * ** * *
35341021 CTTTAGTGGCACTTCTCCCACAAATG-C-CTATAGAACATGATCTTTAGCGACGCTTCTCCCAC
66 CTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTCTCCCAC
* * *
35341083 AAACGCCGCTATAGACCATGATCTTTAGCGGCACTTTTCCAATAAACGCCGTTATAGGCCATGAC
1 AAACGCCGCTATAGACCATGATCTTTAGCGGCGCTTTTCCAACAAACGCCGCTATAGGCCATGAC
35341148 CTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTCTCCCAC
66 CTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTCTCCCAC
* * * * * * * *
35341212 AAATGCCGCTATAGGCCATGACCTTTAGTGGTGCTTCTCCTACAAACGCCGCTATAGGCTATGAC
1 AAACGCCGCTATAGACCATGATCTTTAGCGGCGCTTTTCCAACAAACGCCGCTATAGGCCATGAC
* * *
35341277 CTTTAGCGGTACTTTTCCCACAAACGCCGCTATAGGCCATAACTTTTAGCGGC
66 CTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGCCATGACCTTTAGCGGC
35341330 ACTTGGTTTA
Statistics
Matches: 219, Mismatches: 26, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
127 83 0.38
128 1 0.00
129 135 0.62
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (129 bp):
AAACGCCGCTATAGACCATGATCTTTAGCGGCGCTTTTCCAACAAACGCCGCTATAGGCCATGAC
CTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTCTCCCAC
Found at i:35341749 original size:87 final size:87
Alignment explanation
Indices: 35341658--35341830 Score: 240
Period size: 87 Copynumber: 2.0 Consensus size: 87
35341648 TCTGCTCTGC
* * ** * *
35341658 TCTGCTTCCCTCGTTGCAGCCTCTGCTTCTCTCGATGTCGCAC-CTGCTTTAAGTTGTAGCTGGA
1 TCTGCTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATACCGC-CTCTGCTTTAAGCTGTAGATGGA
*
35341722 GTTCTTCATATTTCTTTTGAACA
65 GTTCTTCATATTTCCTTTGAACA
* * *
35341745 TCTGCTTCTCTCGCTGCAGCCTCTGCTTCCCTCGCTACCGCCTTTGCTTTAAGCTGTAGATGGAG
1 TCTGCTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATACCGCCTCTGCTTTAAGCTGTAGATGGAG
35341810 TTCTTCATATTTCCTTTGAAC
66 TTCTTCATATTTCCTTTGAAC
35341831 CTCAACTGTG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
86 1 0.01
87 74 0.99
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.39
Consensus pattern (87 bp):
TCTGCTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATACCGCCTCTGCTTTAAGCTGTAGATGGAG
TTCTTCATATTTCCTTTGAACA
Found at i:35341787 original size:21 final size:21
Alignment explanation
Indices: 35341745--35341793 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
35341735 CTTTTGAACA
* *
35341745 TCTGCTTCTCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTACAGCC
*
35341766 TCTGCTTCCCTCGCTACCGCC
1 TCTGCTTCCCTCGCTACAGCC
*
35341787 TTTGCTT
1 TCTGCTT
35341794 TAAGCTGTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.43, G:0.16, T:0.37
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTACAGCC
Found at i:35341961 original size:34 final size:32
Alignment explanation
Indices: 35341910--35342001 Score: 95
Period size: 34 Copynumber: 2.9 Consensus size: 32
35341900 CCCCGAAGGC
*
35341910 ATGTAAGTTATGCAAGTTTATATATAAGTTTCT
1 ATGTAAGTTATGTAAGTTTATATATAAGTTT-T
* *
35341943 ATATTAAGTTATGTAAG-TTATTATGTAAG--TT
1 AT-GTAAGTTATGTAAGTTTA-TATATAAGTTTT
35341974 ATGT-A-TTATGTAAGTTTATATATAAGTT
1 ATGTAAGTTATGTAAGTTTATATATAAGTT
35342002 ATGATATGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
28 16 0.33
29 4 0.08
30 1 0.02
31 3 0.06
32 1 0.02
33 5 0.10
34 19 0.39
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (32 bp):
ATGTAAGTTATGTAAGTTTATATATAAGTTTT
Found at i:35341968 original size:12 final size:12
Alignment explanation
Indices: 35341951--35341975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35341941 CTATATTAAG
35341951 TTATGTAAGTTA
1 TTATGTAAGTTA
35341963 TTATGTAAGTTA
1 TTATGTAAGTTA
35341975 T
1 T
35341976 GTATTATGTA
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:35341999 original size:28 final size:28
Alignment explanation
Indices: 35341951--35342004 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
35341941 CTATATTAAG
*
35341951 TTATGTAAGTTATTATGTAAGTTATGTA
1 TTATGTAAGTTATTATATAAGTTATGTA
35341979 TTATGTAAGTT-TATATATAAGTTATG
1 TTATGTAAGTTAT-TATATAAGTTATG
35342005 ATATGATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (28 bp):
TTATGTAAGTTATTATATAAGTTATGTA
Found at i:35342205 original size:69 final size:69
Alignment explanation
Indices: 35342085--35342227 Score: 225
Period size: 69 Copynumber: 2.1 Consensus size: 69
35342075 TGGGGTGATA
* *
35342085 TATTAAAAATATAGGTGTTAATCTTTAGAAAATAACATTTTCAATTATTTTTAAAATTATAAAAT
1 TATTAAAAATATAGGTGTTAATATTTAGAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
35342150 TTAT
66 TTAT
* * *
35342154 TATTGAAATTATAGGTTTTAATATTTA-AAGAATAACATTTACAATTATTTTTAAAATTATAAAA
1 TATTAAAAATATAGGTGTTAATATTTAGAA-AATAACATTTACAATTATTTTTAAAATTATAAAA
35342218 TTTAT
65 TTTAT
35342223 TATTA
1 TATTA
35342228 TTAAAATTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 2 0.03
69 65 0.97
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (69 bp):
TATTAAAAATATAGGTGTTAATATTTAGAAAATAACATTTACAATTATTTTTAAAATTATAAAAT
TTAT
Found at i:35342248 original size:24 final size:24
Alignment explanation
Indices: 35342197--35342249 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
35342187 AACATTTACA
* **
35342197 ATTATTTTTAAAATTATAAAATTT
1 ATTATTATTAAAATTATAAAATAG
35342221 ATTATTATTAAAATT-TAAATATAG
1 ATTATTATTAAAATTATAAA-ATAG
35342245 ATTAT
1 ATTAT
35342250 ATATCCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTATTATTAAAATTATAAAATAG
Found at i:35344941 original size:15 final size:14
Alignment explanation
Indices: 35344903--35344943 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
35344893 AAACTTAAAT
*
35344903 TAAACCCTAAACCC
1 TAAACCATAAACCC
*
35344917 TAAACTATAAACCC
1 TAAACCATAAACCC
35344931 GTAAACCATAAAC
1 -TAAACCATAAAC
35344944 ACAAACCACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.49, C:0.32, G:0.02, T:0.17
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:35344942 original size:22 final size:21
Alignment explanation
Indices: 35344903--35344943 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
35344893 AAACTTAAAT
*
35344903 TAAACCCTAAACCCTAAACTA
1 TAAACCCTAAACCATAAACTA
35344924 TAAACCCGTAAACCATAAAC
1 TAAACCC-TAAACCATAAAC
35344944 ACAAACCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.49, C:0.32, G:0.02, T:0.17
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACTA
Found at i:35344949 original size:21 final size:21
Alignment explanation
Indices: 35344904--35344950 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
35344894 AACTTAAATT
* *
35344904 AAACCCTAAACCCTAAACTAT
1 AAACCCTAAACCATAAACTAC
35344925 AAACCCGTAAACCATAAAC-AC
1 AAACCC-TAAACCATAAACTAC
35344946 AAACC
1 AAACC
35344951 ACCAAACCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.51, C:0.34, G:0.02, T:0.13
Consensus pattern (21 bp):
AAACCCTAAACCATAAACTAC
Found at i:35353915 original size:19 final size:19
Alignment explanation
Indices: 35353887--35353927 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
35353877 ATAAATGGGA
35353887 AAAATAAAATTAGATAACC
1 AAAATAAAATTAGATAACC
* *
35353906 AAAATTAAATTAGATAATC
1 AAAATAAAATTAGATAACC
35353925 AAA
1 AAA
35353928 TATGAGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAATAAAATTAGATAACC
Found at i:35356575 original size:76 final size:78
Alignment explanation
Indices: 35356412--35356587 Score: 221
Period size: 76 Copynumber: 2.3 Consensus size: 78
35356402 AAAGTATATA
* * * *
35356412 AATTAAATTAAAGGTATGAATTTTATATACGTATATGTGAGGTTCGAAGATATATGTATATACAT
1 AATTAAATTAAAGGTATGAATTTTACATACGTATATGTGAGATTAGAAGATAGATGTATATACAT
* * *
35356477 GTATAAGTTCTTG
66 ATAGAAGTACTTG
* * *
35356490 AATTAAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTAG-A-ATAGATGTATATACAT
1 AATTAAATTAAAGGTATGAATTTTACATACGTATATGTGAGATTAGAAGATAGATGTATATACAT
35356553 ATAGAAGTACTTG
66 ATAGAAGTACTTG
* * *
35356566 AGTTGAATTAAAAGTATGAATT
1 AATTAAATTAAAGGTATGAATT
35356588 GTAAATACTT
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
76 44 0.52
77 1 0.01
78 40 0.47
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (78 bp):
AATTAAATTAAAGGTATGAATTTTACATACGTATATGTGAGATTAGAAGATAGATGTATATACAT
ATAGAAGTACTTG
Found at i:35356982 original size:31 final size:31
Alignment explanation
Indices: 35356947--35357157 Score: 151
Period size: 31 Copynumber: 6.6 Consensus size: 31
35356937 GATAAGTATT
*
35356947 TATATGCATTCGGTTATATACCTTTGAAGTG
1 TATATGCATTCGGTTATATACATTTGAAGTG
* * * *
35356978 TATATGCTTTCGATTATA-AGTATTTGATAGGTATA
1 TATATGCATTCGGTTATATA-CATTTGA-A-G--TG
* * *
35357013 TATATGCATTTGGTTATATACCTTTGATGTG
1 TATATGCATTCGGTTATATACATTTGAAGTG
* * *
35357044 TATATGCATTCGATTATA-AGAATTTGATAGGTA
1 TATATGCATTCGGTTATATA-CATTTGA-A-GTG
*
35357077 TATATGCATTCGGTT-TATACATTTGATGTG
1 TATATGCATTCGGTTATATACATTTGAAGTG
* * * *
35357107 TATATGCATCCGGTTATA-AGTAGTTGATAAGTA
1 TATATGCATTCGGTTATATA-CATTTG--AAGTG
35357140 TATATGCATTCGGTTATA
1 TATATGCATTCGGTTATA
35357158 AGTATTTGAT
Statistics
Matches: 138, Mismatches: 28, Indels: 26
0.72 0.15 0.14
Matches are distributed among these distances:
30 19 0.14
31 49 0.36
32 9 0.07
33 39 0.28
35 21 0.15
36 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (31 bp):
TATATGCATTCGGTTATATACATTTGAAGTG
Found at i:35357086 original size:33 final size:32
Alignment explanation
Indices: 35356932--35357176 Score: 193
Period size: 33 Copynumber: 7.5 Consensus size: 32
35356922 ATTTATATAT
35356932 TATTTGATAAGTATTTATATGCATTCGGTTAT-A-
1 TATTTGAT-AGTA--TATATGCATTCGGTTATAAG
* * *
35356965 TACCTTTGA-AGTGTATATGCTTTCGATTATAAG
1 TA--TTTGATAGTATATATGCATTCGGTTATAAG
*
35356998 TATTTGATAGGTATATATATGCATTTGGTTAT-A-
1 TATTTGATA-G--TATATATGCATTCGGTTATAAG
* *
35357031 TACCTTTGAT-GTGTATATGCATTCGATTATAAG
1 TA--TTTGATAGTATATATGCATTCGGTTATAAG
*
35357064 AATTTGATAGGTATATATGCATTCGGTT-TATA-
1 TATTTGATA-GTATATATGCATTCGGTTATA-AG
* * *
35357096 CATTTGAT-GTGTATATGCATCCGGTTATAAG
1 TATTTGATAGTATATATGCATTCGGTTATAAG
*
35357127 TAGTTGATAAGTATATATGCATTCGGTTATAAG
1 TATTTGAT-AGTATATATGCATTCGGTTATAAG
*
35357160 TATTTGATGAGTCTATA
1 TATTTGAT-AGTATATA
35357177 CATACATTTG
Statistics
Matches: 170, Mismatches: 23, Indels: 38
0.74 0.10 0.16
Matches are distributed among these distances:
30 17 0.10
31 50 0.29
32 12 0.07
33 64 0.38
34 1 0.01
35 26 0.15
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (32 bp):
TATTTGATAGTATATATGCATTCGGTTATAAG
Found at i:35357125 original size:63 final size:64
Alignment explanation
Indices: 35356932--35357157 Score: 319
Period size: 66 Copynumber: 3.5 Consensus size: 64
35356922 ATTTATATAT
* *
35356932 TATTTGATAAGTATTTATATGCATTCGGTTATATACCTTTGAAGTGTATATGCTTTCGATTATAA
1 TATTTGATAAGTA--TATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
35356997 G
64 G
* *
35356998 TATTTGATAGGTATATATATGCATTTGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
1 TATTTGATAAG--TATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
35357063 G
64 G
* * * * *
35357064 AATTTGATAGGTATATATGCATTCGGTT-TATACATTTGATGTGTATATGCATCCGGTTATAAG
1 TATTTGATAAGTATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAAG
*
35357127 TAGTTGATAAGTATATATGCATTCGGTTATA
1 TATTTGATAAGTATATATGCATTCGGTTATA
35357158 AGTATTTGAT
Statistics
Matches: 145, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
63 57 0.39
64 18 0.12
66 68 0.47
68 2 0.01
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (64 bp):
TATTTGATAAGTATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAAG
Found at i:35357762 original size:23 final size:23
Alignment explanation
Indices: 35357732--35357778 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
35357722 TAGTGTTCGA
35357732 GATTTTTATTATGAAAAAGCTAT
1 GATTTTTATTATGAAAAAGCTAT
35357755 GATTTTTATTATGAAAAAGCTAT
1 GATTTTTATTATGAAAAAGCTAT
35357778 G
1 G
35357779 TAAGCTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (23 bp):
GATTTTTATTATGAAAAAGCTAT
Found at i:35359798 original size:14 final size:14
Alignment explanation
Indices: 35359779--35359806 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35359769 TTTTCAGTTG
35359779 CAGAAAATCTATTT
1 CAGAAAATCTATTT
35359793 CAGAAAATCTATTT
1 CAGAAAATCTATTT
35359807 TTTAACTGTT
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:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
CAGAAAATCTATTT
Found at i:35364301 original size:86 final size:86
Alignment explanation
Indices: 35364185--35364347 Score: 211
Period size: 86 Copynumber: 1.9 Consensus size: 86
35364175 TACATGCATA
* * ** **
35364185 AGGTTGAGTTCTTACTCTTAATAAATTCATATCCTAGGGTTTGGGTGCTCCTATTGAAACGGACT
1 AGGTTGAGTTCTTACTCTTAATAAAGTCATATCCAAAAGTTTGGGTGCTCCTATTGAAACAAACT
*
35364250 TGATGAATTCACCAACATGTG
66 TGATGAACTCACCAACATGTG
* * * *
35364271 AGGTTGAGTTTCTTACTCTTAAT-GAGTCATATCCAAAATTTTGGGTGGTCCTATTGAGACAAAC
1 AGGTTGAG-TTCTTACTCTTAATAAAGTCATATCCAAAAGTTTGGGTGCTCCTATTGAAACAAAC
35364335 TTGATGAACTCAC
65 TTGATGAACTCAC
35364348 TGAATTTAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
86 51 0.78
87 14 0.22
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (86 bp):
AGGTTGAGTTCTTACTCTTAATAAAGTCATATCCAAAAGTTTGGGTGCTCCTATTGAAACAAACT
TGATGAACTCACCAACATGTG
Found at i:35365311 original size:93 final size:93
Alignment explanation
Indices: 35365147--35365334 Score: 277
Period size: 93 Copynumber: 2.0 Consensus size: 93
35365137 TCTCCTCATT
* * * ** *
35365147 TTACACTACAAGGAAAGCAACAATCTTTTATCCCACAGCTCACCTGTTCCTTTTTCAGTTTTTTC
1 TTACACAACAAGGAAAACAACAATCTTTTATCCCACAGCTCACATGTTCCTTTTTCAAATTTTCC
** *
35365212 GTTTCCTTTTTTAGAAGAGCAATACCAC
66 AATTCCTTTTCTAGAAGAGCAATACCAC
*
35365240 TTACACAACAAGGAAAACAACAATCTTTTATCCCATAGCTCACATGTTCCTTTTTCAAATTTTCC
1 TTACACAACAAGGAAAACAACAATCTTTTATCCCACAGCTCACATGTTCCTTTTTCAAATTTTCC
*
35365305 AATTCCTTTTCTAGAAGAGCAATATCAC
66 AATTCCTTTTCTAGAAGAGCAATACCAC
35365333 TT
1 TT
35365335 GTGTTCCACA
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (93 bp):
TTACACAACAAGGAAAACAACAATCTTTTATCCCACAGCTCACATGTTCCTTTTTCAAATTTTCC
AATTCCTTTTCTAGAAGAGCAATACCAC
Found at i:35367361 original size:10 final size:10
Alignment explanation
Indices: 35367346--35367381 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
35367336 ATTTATATTT
35367346 TAAAAATATA
1 TAAAAATATA
35367356 TAAAAAT-TA
1 TAAAAATATA
35367365 TAAAAATATA
1 TAAAAATATA
35367375 TATAAAA
1 TA-AAAA
35367382 AGTTAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 11 0.46
11 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TAAAAATATA
Found at i:35375754 original size:5 final size:5
Alignment explanation
Indices: 35375734--35375768 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
35375724 AATTTGTATT
35375734 TTAATA TTATAA TTAAA TTAAA TTAAA TTAAA TTA
1 TTAA-A TTA-AA TTAAA TTAAA TTAAA TTAAA TTA
35375769 TTGAAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 20 0.71
6 7 0.25
7 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (5 bp):
TTAAA
Found at i:35380608 original size:32 final size:32
Alignment explanation
Indices: 35380572--35380637 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
35380562 CCTTAGGAAT
*
35380572 GTAAGTATACTACATCAAATAAATTGGAATGG
1 GTAAGTATACTACATCAAATAAAGTGGAATGG
*
35380604 GTAAGTATACTGCATCAAATAAAGTGGAATGG
1 GTAAGTATACTACATCAAATAAAGTGGAATGG
35380636 GT
1 GT
35380638 TTTACAACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (32 bp):
GTAAGTATACTACATCAAATAAAGTGGAATGG
Found at i:35381168 original size:24 final size:24
Alignment explanation
Indices: 35381140--35381187 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35381130 TCTAATCCTT
35381140 CCAGTGGGTACATAGAAATCAATC
1 CCAGTGGGTACATAGAAATCAATC
35381164 CCAGTGGGTACATAGAAATCAATC
1 CCAGTGGGTACATAGAAATCAATC
35381188 ATACTTCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
CCAGTGGGTACATAGAAATCAATC
Done.