Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 159 of 199
Found at i:47377757 original size:21 final size:21
Alignment explanation
Indices: 47377729--47377793 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
47377719 TCTATTGAGC
47377729 TTTT-GTTTAACCCTTATGGG
1 TTTTCGTTTAACCCTTATGGG
* * * *
47377749 TTTTCGTTTAGCTCTTACGAG
1 TTTTCGTTTAACCCTTATGGG
* * *
47377770 CTTTCGTTCAACCTTTATGGG
1 TTTTCGTTTAACCCTTATGGG
47377791 TTT
1 TTT
47377794 CTGTTTAGCT
Statistics
Matches: 32, Mismatches: 12, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.49
Consensus pattern (21 bp):
TTTTCGTTTAACCCTTATGGG
Found at i:47377762 original size:42 final size:42
Alignment explanation
Indices: 47377665--47377819 Score: 147
Period size: 42 Copynumber: 3.7 Consensus size: 42
47377655 TCGTGTTTAC
* * * *
47377665 TTTTCATTTAGCTCTTATGAGCTTCTGCTTAACTCATA-GGAG
1 TTTTCGTTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGG-G
* * *
47377707 TTTCCGTTCAGCTC-TATTGAGCTTTTGTTTAACCCTTATGGG
1 TTTTCGTTTAGCTCTTA-TGAGCTTCTGTTTAACCCTTATGGG
* * *
47377749 TTTTCGTTTAGCTCTTACGAGCTT-TCGTTCAACCTTTATGGG
1 TTTTCGTTTAGCTCTTATGAGCTTCT-GTTTAACCCTTATGGG
*
47377791 -TTTCTGTTTAGCTCTCATGAGCTTCTGTT
1 TTTTC-GTTTAGCTCTTATGAGCTTCTGTT
47377820 CAGCCTTCGG
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
41 7 0.08
42 81 0.87
43 5 0.05
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTTCGTTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
Found at i:47380525 original size:11 final size:11
Alignment explanation
Indices: 47380509--47380548 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
47380499 AATAGAAGTT
47380509 GAGAGAATTGA
1 GAGAGAATTGA
*
47380520 GAGAGAATTAA
1 GAGAGAATTGA
47380531 GAGAGAATTGA
1 GAGAGAATTGA
47380542 GAGAGAA
1 GAGAGAA
47380549 CTAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (11 bp):
GAGAGAATTGA
Found at i:47385592 original size:27 final size:28
Alignment explanation
Indices: 47385552--47385606 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
47385542 TTAATTTTGT
* * *
47385552 TTAAATTTTAAAATTTTAA-AAAATTAA
1 TTAAATATTAAAATGTCAATAAAATTAA
*
47385579 TTAAATATTGAAATGTCAATAAAATTAA
1 TTAAATATTAAAATGTCAATAAAATTAA
47385607 CAAATGCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (28 bp):
TTAAATATTAAAATGTCAATAAAATTAA
Found at i:47387305 original size:13 final size:14
Alignment explanation
Indices: 47387287--47387316 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
47387277 TTGAATATAT
47387287 ATACAAAAAAA-TA
1 ATACAAAAAAATTA
47387300 ATACAAAAAAATTA
1 ATACAAAAAAATTA
47387314 ATA
1 ATA
47387317 TGGGCGGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (14 bp):
ATACAAAAAAATTA
Found at i:47389221 original size:13 final size:13
Alignment explanation
Indices: 47389203--47389233 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
47389193 GCTACTACTG
47389203 GCCACTGCCACTA
1 GCCACTGCCACTA
47389216 GCCACTGCCACTA
1 GCCACTGCCACTA
47389229 GCCAC
1 GCCAC
47389234 CATTGTCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.48, G:0.16, T:0.13
Consensus pattern (13 bp):
GCCACTGCCACTA
Found at i:47392985 original size:13 final size:12
Alignment explanation
Indices: 47392967--47393017 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
47392957 AGAAAAATTC
47392967 TCTTTTCTTTCTT
1 TCTTTT-TTTCTT
*
47392980 TCTTTTTTCACTT
1 TCTTTTTT-TCTT
47392993 TCTTTTCTTTCTT
1 TCTTTT-TTTCTT
*
47393006 TATTTTTTTCTT
1 TCTTTTTTTCTT
47393018 CAGGTCAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 8 0.24
13 23 0.70
14 2 0.06
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTTTTTCTT
Found at i:47394887 original size:18 final size:18
Alignment explanation
Indices: 47394864--47394898 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47394854 TTATCTAATT
*
47394864 ATTTTAAATATTATTTAA
1 ATTTTAAAAATTATTTAA
47394882 ATTTTAAAAATTATTTA
1 ATTTTAAAAATTATTTA
47394899 TTTAAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAAAAATTATTTAA
Found at i:47395040 original size:41 final size:41
Alignment explanation
Indices: 47394994--47395106 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 41
47394984 GCAAAAGGTA
* *
47394994 AGCAATAGCGGTGTTTTTGTTCCAAATGCCGCAAAAAGTTG
1 AGCAATAGTGGTGTTTTTGTTCCAAACGCCGCAAAAAGTTG
47395035 AGCAATAGTGGTGTTTTTGGTT-CAAACGCCGCAAAAAGTTG
1 AGCAATAGTGGTGTTTTT-GTTCCAAACGCCGCAAAAAGTTG
* * * *
47395076 AGAAATAGTGGCGATTTTGGTCCAAACGCCG
1 AGCAATAGTGGTGTTTTTGTTCCAAACGCCG
47395107 TGAATATGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
40 2 0.03
41 59 0.92
42 3 0.05
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (41 bp):
AGCAATAGTGGTGTTTTTGTTCCAAACGCCGCAAAAAGTTG
Found at i:47395444 original size:25 final size:25
Alignment explanation
Indices: 47395414--47395467 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
47395404 CGACAACCCT
47395414 CTGCATCGCCGTCAACAGCCCTCTA
1 CTGCATCGCCGTCAACAGCCCTCTA
* ** *
47395439 CTGCATCTCCGTCGGCAGCCCTCTG
1 CTGCATCGCCGTCAACAGCCCTCTA
47395464 CTGC
1 CTGC
47395468 TTCGTGTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.13, C:0.44, G:0.20, T:0.22
Consensus pattern (25 bp):
CTGCATCGCCGTCAACAGCCCTCTA
Found at i:47398470 original size:11 final size:13
Alignment explanation
Indices: 47398454--47398487 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
47398444 AATTTTACGA
47398454 AAAAATTTCG-T-
1 AAAAATTTCGTTC
47398465 AAAAATTTCGTTC
1 AAAAATTTCGTTC
47398478 AAAAATTTCG
1 AAAAATTTCG
47398488 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:47404836 original size:33 final size:32
Alignment explanation
Indices: 47404685--47404983 Score: 154
Period size: 33 Copynumber: 9.0 Consensus size: 32
47404675 ATGGCAGTGC
* *
47404685 TTAT-ATGTAAGACCATGGCTGAGCTATGGCA
1 TTATGATGTAAGACCATAGCTGGGCTATGGCA
* * * *
47404716 TTCTGATGATAAGACCATAACTGGGTTATGACA
1 TTATGATG-TAAGACCATAGCTGGGCTATGGCA
* * * * * * *
47404749 CTATGAACGTAAAACCATGGTTGGACCATGGCA
1 TTATG-ATGTAAGACCATAGCTGGGCTATGGCA
* *
47404782 GTGTTTAT-ATGGAAGACCATAGTTGGGCTATGGCA
1 ----TTATGATGTAAGACCATAGCTGGGCTATGGCA
* *
47404817 TTCTGATGATAAGACCATAGCTGGGTTATGGCA
1 TTATGATG-TAAGACCATAGCTGGGCTATGGCA
* * * *
47404850 CTATGAACGTAAGACCATAACTGGGTTATGGCA
1 TTATG-ATGTAAGACCATAGCTGGGCTATGGCA
* * * * * * * *
47404883 CTATGAACGTAAGACTATGGTTGGACCATGACA
1 TTATG-ATGTAAGACCATAGCTGGGCTATGGCA
47404916 GTGTTTAT-ATGTAAGACCATAGCTGGGCTATGGCA
1 ----TTATGATGTAAGACCATAGCTGGGCTATGGCA
* * * *
47404951 TTCTAATGATAAGACCATAACTGGGTTATGGCA
1 TTATGATG-TAAGACCATAGCTGGGCTATGGCA
47404984 CTACAAATGT
Statistics
Matches: 201, Mismatches: 51, Indels: 30
0.71 0.18 0.11
Matches are distributed among these distances:
31 9 0.04
32 9 0.04
33 132 0.66
34 4 0.02
35 41 0.20
37 6 0.03
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (32 bp):
TTATGATGTAAGACCATAGCTGGGCTATGGCA
Found at i:47404868 original size:134 final size:134
Alignment explanation
Indices: 47404725--47404986 Score: 452
Period size: 134 Copynumber: 2.0 Consensus size: 134
47404715 ATTCTGATGA
*
47404725 TAAGACCATAACTGGGTTATGACACTATGAACGTAAAACCATGGTTGGACCATGGCAGTGTTTAT
1 TAAGACCATAACTGGGTTATGACACTATGAACGTAAAACCATGGTTGGACCATGACAGTGTTTAT
* * *
47404790 ATGGAAGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAGCTGGGTTATGGCACTATG
66 ATGGAAGACCATAGCTGGGCTATGGCATTCTAATGATAAGACCATAACTGGGTTATGGCACTATG
47404855 AACG
131 AACG
* * *
47404859 TAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACTATGGTTGGACCATGACAGTGTTTAT
1 TAAGACCATAACTGGGTTATGACACTATGAACGTAAAACCATGGTTGGACCATGACAGTGTTTAT
*
47404924 ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGATAAGACCATAACTGGGTTATGGCACTA
66 ATGGAAGACCATAGCTGGGCTATGGCATTCTAATGATAAGACCATAACTGGGTTATGGCACTA
47404987 CAAATGTAAA
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
134 120 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (134 bp):
TAAGACCATAACTGGGTTATGACACTATGAACGTAAAACCATGGTTGGACCATGACAGTGTTTAT
ATGGAAGACCATAGCTGGGCTATGGCATTCTAATGATAAGACCATAACTGGGTTATGGCACTATG
AACG
Found at i:47404882 original size:101 final size:101
Alignment explanation
Indices: 47404623--47404867 Score: 409
Period size: 101 Copynumber: 2.4 Consensus size: 101
47404613 GAATTGACGA
*
47404623 ATAAGACCATAACTAGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGCTTA
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGCTTA
* *
47404688 TATGTAAGACCATGGCTGAGCTATGGCATTCTGATG
66 TATGGAAGACCATAGCTGAGCTATGGCATTCTGATG
* *
47404724 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAAACCATGGTTGGACCATGGCAGTGTTTA
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGCTTA
* *
47404789 TATGGAAGACCATAGTTGGGCTATGGCATTCTGATG
66 TATGGAAGACCATAGCTGAGCTATGGCATTCTGATG
* *
47404825 ATAAGACCATAGCTGGGTTATGGCACTATGAACGTAAGACCAT
1 ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCAT
47404868 AACTGGGTTA
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 134 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (101 bp):
ATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGCTTA
TATGGAAGACCATAGCTGAGCTATGGCATTCTGATG
Found at i:47405020 original size:24 final size:24
Alignment explanation
Indices: 47404988--47405063 Score: 109
Period size: 24 Copynumber: 3.2 Consensus size: 24
47404978 ATGGCACTAC
47404988 AAATGTAAAGGATGAATTGACAGG-
1 AAATGTAAAGGATGAATTGAC-GGA
47405012 AAATGTAAAGGATGAATTGACGGA
1 AAATGTAAAGGATGAATTGACGGA
* * *
47405036 AAATATAAAAGATGAATTGACGGT
1 AAATGTAAAGGATGAATTGACGGA
47405060 AAAT
1 AAAT
47405064 TACCCAAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
23 2 0.04
24 46 0.96
ACGTcount: A:0.49, C:0.04, G:0.25, T:0.22
Consensus pattern (24 bp):
AAATGTAAAGGATGAATTGACGGA
Found at i:47407122 original size:43 final size:43
Alignment explanation
Indices: 47407075--47407177 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
47407065 GAAAAATGAA
* * *
47407075 GCTAAAAGTCATGTTCTTTATCGCCGTTTGTGGGGAAAGCGCC
1 GCTAAAAGTCATGTTCTTTAGCGACGTTTGTGGGAAAAGCGCC
*
47407118 GCT-AAAGATCATGTTCTTTAGCGACGTTTGTGGGAAAAGTGCC
1 GCTAAAAG-TCATGTTCTTTAGCGACGTTTGTGGGAAAAGCGCC
* *
47407161 GTTAAAGGTCATGTTCT
1 GCTAAAAGTCATGTTCT
47407178 ATAATGACGT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 4 0.08
43 45 0.87
44 3 0.06
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
GCTAAAAGTCATGTTCTTTAGCGACGTTTGTGGGAAAAGCGCC
Found at i:47407187 original size:43 final size:42
Alignment explanation
Indices: 47407075--47407220 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 42
47407065 GAAAAATGAA
* * * *
47407075 GCTAAAAGTCATGTTCTTTATCGCCGTTTGTGGGGAAAGCGCC
1 GCTAAAGGTCATGTTCTTAAT-GACGTTTGTGGGAAAAGCGCC
* ** *
47407118 GCTAAAGATCATGTTCTTTAGCGACGTTTGTGGGAAAAGTGCC
1 GCTAAAGGTCATGTTC-TTAATGACGTTTGTGGGAAAAGCGCC
* * * *
47407161 GTTAAAGGTCATGTTCTATAATGACGTTTTTGTGAGAAA-CACC
1 GCTAAAGGTCATGTTCT-TAATGACGTTTGTGGGA-AAAGCGCC
* *
47407204 ACTAAATGTCATGTTCT
1 GCTAAAGGTCATGTTCT
47407221 ATAGTGGCGT
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
42 1 0.01
43 75 0.93
44 5 0.06
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (42 bp):
GCTAAAGGTCATGTTCTTAATGACGTTTGTGGGAAAAGCGCC
Found at i:47408945 original size:50 final size:50
Alignment explanation
Indices: 47408823--47409073 Score: 317
Period size: 50 Copynumber: 4.9 Consensus size: 50
47408813 GATCATAACA
* ** * *
47408823 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTATCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* *
47408874 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
47408924 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
47408974 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * *
47409029 ATACCAATGCCATGTTCCAAACATGGTCTTACATGGGA--TCTCATC
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
47409074 ACCCAAATGT
Statistics
Matches: 178, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
50 96 0.54
51 37 0.21
53 5 0.03
54 4 0.02
55 2 0.01
56 34 0.19
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:47409460 original size:29 final size:31
Alignment explanation
Indices: 47409409--47409466 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
47409399 CCTCGACTCT
*
47409409 AACTTTTCCAAAATTATGA-TTTTGCCCCTA
1 AACTTTTCCAAAATTATCATTTTTGCCCCTA
* *
47409439 AACTTTTGCATAATTA-CATTTTTGCCCC
1 AACTTTTCCAAAATTATCATTTTTGCCCC
47409467 AAGGCTCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (31 bp):
AACTTTTCCAAAATTATCATTTTTGCCCCTA
Found at i:47421072 original size:123 final size:123
Alignment explanation
Indices: 47420892--47421140 Score: 498
Period size: 123 Copynumber: 2.0 Consensus size: 123
47420882 ATTTCGCTAT
47420892 ACATGAAAAATATGAAAGACATAAGTACAAAAGACAAAACAGTGAAATGTGAAACTTATTTATTC
1 ACATGAAAAATATGAAAGACATAAGTACAAAAGACAAAACAGTGAAATGTGAAACTTATTTATTC
47420957 ATCGTTCAAATACATAGAAAATTATTACATGTTTACTACAATATTGACACATTTCCCA
66 ATCGTTCAAATACATAGAAAATTATTACATGTTTACTACAATATTGACACATTTCCCA
47421015 ACATGAAAAATATGAAAGACATAAGTACAAAAGACAAAACAGTGAAATGTGAAACTTATTTATTC
1 ACATGAAAAATATGAAAGACATAAGTACAAAAGACAAAACAGTGAAATGTGAAACTTATTTATTC
47421080 ATCGTTCAAATACATAGAAAATTATTACATGTTTACTACAATATTGACACATTTCCCA
66 ATCGTTCAAATACATAGAAAATTATTACATGTTTACTACAATATTGACACATTTCCCA
47421138 ACA
1 ACA
47421141 CTTCCATCCC
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 126 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (123 bp):
ACATGAAAAATATGAAAGACATAAGTACAAAAGACAAAACAGTGAAATGTGAAACTTATTTATTC
ATCGTTCAAATACATAGAAAATTATTACATGTTTACTACAATATTGACACATTTCCCA
Found at i:47429439 original size:12 final size:12
Alignment explanation
Indices: 47429422--47429450 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
47429412 TCTTAATTTT
47429422 CAACAGCGAATC
1 CAACAGCGAATC
47429434 CAACAGCGAATC
1 CAACAGCGAATC
47429446 CAACA
1 CAACA
47429451 ACAAACTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.34, G:0.14, T:0.07
Consensus pattern (12 bp):
CAACAGCGAATC
Found at i:47433507 original size:5 final size:5
Alignment explanation
Indices: 47433493--47433571 Score: 58
Period size: 5 Copynumber: 15.4 Consensus size: 5
47433483 GCAACCCAAT
47433493 TTTTA TTTTTA TTTT- TTGTTA -TTTA TTTATTA TTTTA TTTTA -TTT-
1 TTTTA -TTTTA TTTTA TT-TTA TTTTA -TT-TTA TTTTA TTTTA TTTTA
* *
47433538 TTTTA CTTTA TTTATTA ATTTA TTTTA TTTTA TT
1 TTTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA TT
47433572 ATTTATTACT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
4 11 0.18
5 33 0.55
6 10 0.17
7 6 0.10
ACGTcount: A:0.20, C:0.01, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:47433520 original size:4 final size:4
Alignment explanation
Indices: 47433511--47433578 Score: 59
Period size: 4 Copynumber: 16.2 Consensus size: 4
47433501 TTATTTTTTG
* *
47433511 TTAT TTAT TTA- TTATT TTATT TTAT TTTT TTACT TTAT TTAT TAAT TTATT
1 TTAT TTAT TTAT TTA-T TTA-T TTAT TTAT TTA-T TTAT TTAT TTAT TTA-T
47433562 TTAT TT-T ATTAT TTAT T
1 TTAT TTAT -TTAT TTAT T
47433579 ACTTATTACT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
3 4 0.07
4 33 0.61
5 17 0.31
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:47433527 original size:21 final size:21
Alignment explanation
Indices: 47433494--47433579 Score: 75
Period size: 17 Copynumber: 4.5 Consensus size: 21
47433484 CAACCCAATT
47433494 TTTATTT-TTATTTT-TTGTTA
1 TTTATTTATTATTTTATT-TTA
47433514 TTTATTTATTATTTTATTTTA
1 TTTATTTATTATTTTATTTTA
*
47433535 -TT-TTT-TTACTTTA-TTTA
1 TTTATTTATTATTTTATTTTA
*
47433552 TTAATTTA---TTTTATTTTA
1 TTTATTTATTATTTTATTTTA
47433570 -TTATTTATTA
1 TTTATTTATTA
47433580 CTTATTACTT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
17 14 0.26
18 12 0.23
19 6 0.11
20 9 0.17
21 10 0.19
22 2 0.04
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (21 bp):
TTTATTTATTATTTTATTTTA
Found at i:47433533 original size:38 final size:39
Alignment explanation
Indices: 47433491--47433578 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 39
47433481 AGGCAACCCA
*
47433491 ATTTTTATTTTTA-TTT-TTTGTT-ATTTATTTATTATTTT
1 ATTTTTATTTTTACTTTATTTATTAATTTA-TT-TTATTTT
*
47433529 ATTTTATTTTTTTACTTTATTTATTAATTTATTTTATTTT
1 ATTTT-TATTTTTACTTTATTTATTAATTTATTTTATTTT
47433569 ATTATTTATT
1 ATT-TTTATT
47433579 ACTTATTACT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
38 5 0.12
39 7 0.17
40 16 0.38
41 9 0.21
42 5 0.12
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (39 bp):
ATTTTTATTTTTACTTTATTTATTAATTTATTTTATTTT
Found at i:47433594 original size:35 final size:35
Alignment explanation
Indices: 47433511--47433582 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 35
47433501 TTATTTTTTG
*
47433511 TTATTTATTTA-TTATTTTATTTTATTTTTTTACT
1 TTATTTATTAATTTATTTTATTTTATTTTTTTACT
47433545 TTATTTATTAATTTATTTTATTTTATTATTTATTACT
1 TTATTTATTAATTTATTTTATTTTATT-TTT-TTACT
47433582 T
1 T
47433583 ATTACTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 10 0.29
35 15 0.44
36 3 0.09
37 6 0.18
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (35 bp):
TTATTTATTAATTTATTTTATTTTATTTTTTTACT
Found at i:47434933 original size:16 final size:15
Alignment explanation
Indices: 47434914--47434968 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 15
47434904 TTCCTAAAGC
47434914 ATAAAAAATATAAATA
1 ATAAAAAATA-AAATA
47434930 ATAAATAAATCAAAATCA
1 ATAAA-AAAT-AAAAT-A
*
47434948 A-AATAAATAAAA-A
1 ATAAAAAATAAAATA
47434961 ATAAAAAA
1 ATAAAAAA
47434969 ATATATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
13 2 0.06
14 5 0.15
15 4 0.12
16 9 0.27
17 10 0.30
18 3 0.09
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAAAAAATAAAATA
Found at i:47434938 original size:27 final size:26
Alignment explanation
Indices: 47434908--47434965 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
47434898 AGTATATTCC
*
47434908 TAAAGCATAAA-AAATATAAATAATAAA
1 TAAAGCA-AAACAAA-ATAAATAAAAAA
*
47434935 TAAATCAAAATCAAAATAAATAAAAAA
1 TAAAGCAAAA-CAAAATAAATAAAAAA
47434962 TAAA
1 TAAA
47434966 AAAATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.11
27 21 0.78
28 3 0.11
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (26 bp):
TAAAGCAAAACAAAATAAATAAAAAA
Found at i:47434944 original size:23 final size:22
Alignment explanation
Indices: 47434917--47434977 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
47434907 CTAAAGCATA
47434917 AAAAATATAAATAATAAATAAAT
1 AAAAATATAAATAATAAA-AAAT
*
47434940 CAAAATCA-AAATAAATAAAAAAT
1 AAAAAT-ATAAAT-AATAAAAAAT
* *
47434963 AAAAAAATATATAAT
1 AAAAATATAAATAAT
47434978 TTGGGGACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
22 4 0.13
23 20 0.65
24 7 0.23
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAATATAAATAATAAAAAAT
Found at i:47435550 original size:15 final size:15
Alignment explanation
Indices: 47435525--47435559 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
47435515 GACTCTATTT
*
47435525 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
47435539 TAATTAATATTAAGA
1 TAATTAATATTAAGA
47435554 TAATTA
1 TAATTA
47435560 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:47440677 original size:20 final size:21
Alignment explanation
Indices: 47440639--47440678 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
47440629 CCAAAGGAAT
*
47440639 TTTCAAAAAGAATTCTTGAAA
1 TTTCAAAAAGAAATCTTGAAA
*
47440660 TTTCAAAAGGAAAT-TTGAA
1 TTTCAAAAAGAAATCTTGAA
47440679 GCGTTCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (21 bp):
TTTCAAAAAGAAATCTTGAAA
Found at i:47449190 original size:20 final size:19
Alignment explanation
Indices: 47449144--47449204 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
47449134 GAATATGATT
*
47449144 TTACAAAAAATTATAAAAA
1 TTACAGAAAATTATAAAAA
*
47449163 TTATAGAAAATTATTAAGAAA
1 TTACAGAAAATTA-TAA-AAA
*
47449184 -TACAG-AAACTATTAAAAA
1 TTACAGAAAATTA-TAAAAA
47449202 TTA
1 TTA
47449205 ATAAAAATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 3 0.09
19 22 0.63
20 7 0.20
21 3 0.09
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
TTACAGAAAATTATAAAAA
Found at i:47449623 original size:31 final size:30
Alignment explanation
Indices: 47449585--47449666 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 30
47449575 AAGGAGGGCT
**
47449585 TAATTAATTTTTAAATTATTTTATTTGGACA
1 TAATTAATTTTTAAATTATTTT-TAAGGACA
*
47449616 TAATTAATTTTT-AATTATTTTTAAGGACT
1 TAATTAATTTTTAAATTATTTTTAAGGACA
47449645 TAATTAATTTTTAAAATTATTT
1 TAATTAATTTTT-AAATTATTT
47449667 AATTAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 17 0.37
30 9 0.20
31 20 0.43
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (30 bp):
TAATTAATTTTTAAATTATTTTTAAGGACA
Found at i:47449637 original size:10 final size:11
Alignment explanation
Indices: 47449616--47449679 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 11
47449606 TATTTGGACA
47449616 TAATTAATTTT
1 TAATTAATTTT
47449627 TAATT-ATTTT
1 TAATTAATTTT
** *
47449637 TAA-GGA--CT
1 TAATTAATTTT
47449645 TAATTAATTTT
1 TAATTAATTTT
47449656 TAA--AATTATT
1 TAATTAATT-TT
47449666 TAATTAATTTT
1 TAATTAATTTT
47449677 TAA
1 TAA
47449680 AATTATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
8 4 0.10
9 5 0.12
10 14 0.34
11 14 0.34
12 4 0.10
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (11 bp):
TAATTAATTTT
Found at i:47449653 original size:29 final size:30
Alignment explanation
Indices: 47449583--47449658 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
47449573 ATAAGGAGGG
**
47449583 CTTAATTAATTTTTAAATTATTTTATTTGGA
1 CTTAATTAATTTTT-AATTATTTTATAAGGA
*
47449614 CATAATTAATTTTTAATTATTTT-TAAGGA
1 CTTAATTAATTTTTAATTATTTTATAAGGA
47449643 CTTAATTAATTTTTAA
1 CTTAATTAATTTTTAA
47449659 AATTATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 19 0.46
30 9 0.22
31 13 0.32
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (30 bp):
CTTAATTAATTTTTAATTATTTTATAAGGA
Found at i:47449667 original size:29 final size:29
Alignment explanation
Indices: 47449583--47449668 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 29
47449573 ATAAGGAGGG
*
47449583 CTTAATTAATTTTT-AAATTATTTTATTTGGA
1 CTTAATTAATTTTTAAAATTA-TTTA--AGGA
* *
47449614 CATAATTAATTTTTAATTATT-TTTAAGGA
1 CTTAATTAATTTTTAA-AATTATTTAAGGA
47449643 CTTAATTAATTTTTAAAATTATTTAA
1 CTTAATTAATTTTTAAAATTATTTAA
47449669 TTAATTTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
28 3 0.06
29 23 0.49
31 17 0.36
32 1 0.02
33 3 0.06
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (29 bp):
CTTAATTAATTTTTAAAATTATTTAAGGA
Found at i:47449670 original size:21 final size:21
Alignment explanation
Indices: 47449644--47449689 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
47449634 TTTTAAGGAC
47449644 TTAATTAATTTTTAAAATTAT
1 TTAATTAATTTTTAAAATTAT
47449665 TTAATTAATTTTTAAAATTAT
1 TTAATTAATTTTTAAAATTAT
47449686 TTAA
1 TTAA
47449690 GTCTAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTAATTTTTAAAATTAT
Found at i:47449740 original size:16 final size:16
Alignment explanation
Indices: 47449697--47449743 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
47449687 TAAGTCTAAA
47449697 AATTATAAAAAAGAAT
1 AATTATAAAAAAGAAT
* *
47449713 AGTTATGAAAAATAGGAT
1 AATTAT-AAAAA-AGAAT
47449731 AATTATAAAAAAG
1 AATTATAAAAAAG
47449744 TATCAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.27
17 10 0.38
18 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (16 bp):
AATTATAAAAAAGAAT
Found at i:47450091 original size:19 final size:19
Alignment explanation
Indices: 47450067--47450143 Score: 118
Period size: 19 Copynumber: 3.8 Consensus size: 19
47450057 AATTTTCGAG
47450067 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
47450086 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
47450105 GATATATGCAATCTTAGATAT
1 GATATA--CAATCTTAGATAT
47450126 GATATATACAATCTTAGA
1 G--ATATACAATCTTAGA
47450144 AGATATGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
19 25 0.46
21 24 0.44
23 5 0.09
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:47450149 original size:19 final size:21
Alignment explanation
Indices: 47450068--47450143 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
47450058 ATTTTCGAGG
47450068 ATATACAATCTTAGATATG--
1 ATATACAATCTTAGATATGAT
47450087 ATATACAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
*
47450108 ATATGCAATCTTAGATATGAT
1 ATATACAATCTTAGATATGAT
47450129 ATATACAATCTTAGA
1 ATATACAATCTTAGA
47450144 AGATATGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 19 0.36
21 34 0.64
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (21 bp):
ATATACAATCTTAGATATGAT
Found at i:47450367 original size:19 final size:21
Alignment explanation
Indices: 47450343--47450381 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
47450333 ACTGTTTTCT
*
47450343 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
47450362 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
47450382 TTAGAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:47450575 original size:3 final size:3
Alignment explanation
Indices: 47450567--47450636 Score: 108
Period size: 3 Copynumber: 23.3 Consensus size: 3
47450557 TCATTAATCT
47450567 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
47450612 TTA TTA TTA -TA TTA TATA TTA TTA T
1 TTA TTA TTA TTA TTA T-TA TTA TTA T
47450637 ACCTACATAT
Statistics
Matches: 63, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.06
3 53 0.84
4 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:47451003 original size:2 final size:2
Alignment explanation
Indices: 47450996--47451035 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
47450986 CATTATGTAT
47450996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47451036 AGTTTTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47458413 original size:29 final size:30
Alignment explanation
Indices: 47458340--47458415 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
47458330 ATAAGGAGGG
*
47458340 CTTAATTAATTTTTAAATGATTTTATGAGGA
1 CTTAATTAATTTTT-AATGATTTTATAAGGA
* * *
47458371 CATAATTAAATTTTAATTATTTT-TAAGGA
1 CTTAATTAATTTTTAATGATTTTATAAGGA
47458400 CTTAATTAATTTTTAA
1 CTTAATTAATTTTTAA
47458416 AATTATTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 19 0.49
30 8 0.21
31 12 0.31
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (30 bp):
CTTAATTAATTTTTAATGATTTTATAAGGA
Found at i:47458420 original size:31 final size:31
Alignment explanation
Indices: 47458340--47458423 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
47458330 ATAAGGAGGG
* *
47458340 CTTAATTAATTTTTAAATGATTTTATGAGGA
1 CTTAATTAATTTTTAAATTATTTTATAAGGA
* *
47458371 CATAATTAAATTTT-AATTATTTT-TAAGGA
1 CTTAATTAATTTTTAAATTATTTTATAAGGA
47458400 CTTAATTAATTTTTAAAATTATTT
1 CTTAATTAATTTTT-AAATTATTT
47458424 AAGTCTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.38
30 8 0.18
31 20 0.44
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (31 bp):
CTTAATTAATTTTTAAATTATTTTATAAGGA
Found at i:47458424 original size:29 final size:28
Alignment explanation
Indices: 47458340--47458426 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 28
47458330 ATAAGGAGGG
*
47458340 CTTAATTAATTTTTAAATGATTTTATGAGGA
1 CTTAATTAATTTTTAAA--ATTTT-TAAGGA
* * *
47458371 CATAATTAAATTTTAATTATTTTTAAGGA
1 CTTAATTAATTTTTAA-AATTTTTAAGGA
47458400 CTTAATTAATTTTTAAAATTATTTAAG
1 CTTAATTAATTTTTAAAATT-TTTAAG
47458427 TCTAAAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 3 0.06
29 25 0.53
30 5 0.11
31 14 0.30
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.49
Consensus pattern (28 bp):
CTTAATTAATTTTTAAAATTTTTAAGGA
Found at i:47458453 original size:17 final size:18
Alignment explanation
Indices: 47458433--47458479 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
47458423 TAAGTCTAAA
47458433 AATTATAAAAAAATA-AC
1 AATTATAAAAAAATAGAC
* *
47458450 AATTAT-GAAAAATAGGAT
1 AATTATAAAAAAATA-GAC
47458468 AATTATAAAAAA
1 AATTATAAAAAA
47458480 GTATCAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.29
17 6 0.25
18 7 0.29
19 4 0.17
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (18 bp):
AATTATAAAAAAATAGAC
Found at i:47458754 original size:17 final size:18
Alignment explanation
Indices: 47458732--47458789 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 18
47458722 TGAAAAAAAA
47458732 ATATTTTTTTAT-ATTTT
1 ATATTTTTTTATAATTTT
*
47458749 ATA-TTTTTTATCATTTT
1 ATATTTTTTTATAATTTT
*
47458766 AATAATTTTTATATAATTTT
1 -AT-ATTTTTTTATAATTTT
47458786 ATAT
1 ATAT
47458790 AACTCTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 8 0.23
17 8 0.23
18 4 0.11
19 3 0.09
20 12 0.34
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATTTTTTTATAATTTT
Found at i:47458774 original size:18 final size:16
Alignment explanation
Indices: 47458737--47458779 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 16
47458727 AAAAAATATT
*
47458737 TTTTTATATTTTATAT
1 TTTTTATATTTTATAA
47458753 TTTTTATCATTTTAATAA
1 TTTTTAT-ATTTT-ATAA
47458771 TTTTTATAT
1 TTTTTATAT
47458780 AATTTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 10 0.42
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATATTTTATAA
Found at i:47458798 original size:12 final size:10
Alignment explanation
Indices: 47458744--47458803 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
47458734 ATTTTTTTAT
47458744 ATTTTATAT-
1 ATTTTATATA
*
47458753 -TTTT-TATC
1 ATTTTATATA
47458761 ATTTTA-ATA
1 ATTTTATATA
47458770 ATTTTTATATA
1 A-TTTTATATA
47458781 ATTTTATATA
1 ATTTTATATA
47458791 ACTCTTTATATA
1 A-T-TTTATATA
47458803 A
1 A
47458804 AATTTATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
9 7 0.16
10 15 0.35
11 5 0.12
12 9 0.21
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTATATA
Found at i:47458807 original size:24 final size:20
Alignment explanation
Indices: 47458761--47458808 Score: 51
Period size: 24 Copynumber: 2.2 Consensus size: 20
47458751 ATTTTTTATC
*
47458761 ATTTTAATAATTTTTATATA
1 ATTTTAATAATTTTTATAAA
47458781 ATTTTATATAACTCTTTATATAAA
1 ATTTTA-ATAA-T-TTT-TATAAA
47458805 ATTT
1 ATTT
47458809 ATAAAAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 4 0.17
22 1 0.04
23 3 0.13
24 9 0.39
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTAATAATTTTTATAAA
Found at i:47459067 original size:20 final size:20
Alignment explanation
Indices: 47459042--47459146 Score: 83
Period size: 19 Copynumber: 5.2 Consensus size: 20
47459032 TCTATGATTG
47459042 TTTTTAT-ATTTTTATAACTT
1 TTTTTATAATTTTTATAA-TT
47459062 TTTTTATAATTTTTATAATTT
1 TTTTTATAATTTTTATAA-TT
* * *
47459083 TCTATTTTTTATTTTTAT-AGT
1 T-T-TTTATAATTTTTATAATT
*
47459104 TTTTTATAACTTTTATAA-T
1 TTTTTATAATTTTTATAATT
*
47459123 TTTCTA-AATTTGTTATAATAT
1 TTTTTATAATTT-TTATAAT-T
47459144 TTT
1 TTT
47459147 AATATAATTA
Statistics
Matches: 69, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
18 4 0.06
19 23 0.33
20 9 0.13
21 19 0.28
22 2 0.03
23 12 0.17
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTATAATTTTTATAATT
Found at i:47459074 original size:9 final size:9
Alignment explanation
Indices: 47459042--47459147 Score: 80
Period size: 9 Copynumber: 11.7 Consensus size: 9
47459032 TCTATGATTG
47459042 TTTTTAT-A
1 TTTTTATAA
47459050 TTTTTATAA
1 TTTTTATAA
47459059 CTTTTTTTATAA
1 ---TTTTTATAA
47459071 TTTTTATAA
1 TTTTTATAA
*
47459080 -TTTTCT-A
1 TTTTTATAA
47459087 TTTTT-T-A
1 TTTTTATAA
*
47459094 TTTTTATAGT
1 TTTTTATA-A
47459104 TTTTTATAA
1 TTTTTATAA
*
47459113 CTTTTATAA
1 TTTTTATAA
47459122 TTTTCTA-AA
1 TTTT-TATAA
47459131 TTTGTTATAA
1 TTT-TTATAA
47459141 TATTTTA
1 T-TTTTA
47459148 ATATAATTAA
Statistics
Matches: 81, Mismatches: 5, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
7 8 0.10
8 17 0.21
9 28 0.35
10 17 0.21
11 2 0.02
12 9 0.11
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:47459106 original size:16 final size:15
Alignment explanation
Indices: 47459062--47459110 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
47459052 TTTATAACTT
47459062 TTTTTATAATTTTTATA
1 TTTTTAT-ATTTTT-TA
* *
47459079 ATTTTCTATTTTTTA
1 TTTTTATATTTTTTA
47459094 TTTTTATAGTTTTTTA
1 TTTTTATA-TTTTTTA
47459110 T
1 T
47459111 AACTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 8 0.30
16 14 0.52
17 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTTATATTTTTTA
Found at i:47459118 original size:42 final size:45
Alignment explanation
Indices: 47459042--47459128 Score: 135
Period size: 42 Copynumber: 2.0 Consensus size: 45
47459032 TCTATGATTG
* *
47459042 TTTTTATATTTTTATAACTTTTTTTATAATTTTTATAATTTTCTA
1 TTTTTATATTTTTATAACGTTTTTTATAACTTTTATAATTTTCTA
47459087 TTTTT-TATTTTTAT-A-GTTTTTTATAACTTTTATAATTTTCTA
1 TTTTTATATTTTTATAACGTTTTTTATAACTTTTATAATTTTCTA
47459129 AATTTGTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 25 0.62
43 1 0.03
44 9 0.22
45 5 0.12
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.69
Consensus pattern (45 bp):
TTTTTATATTTTTATAACGTTTTTTATAACTTTTATAATTTTCTA
Found at i:47462324 original size:24 final size:24
Alignment explanation
Indices: 47462276--47462324 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
47462266 TATAAGTATA
* *
47462276 AGTATAAATAATCTATATAATAAT
1 AGTATAAATAATATATATAAAAAT
47462300 AGTATAATATAATATAT-TAAAAAT
1 AGTATAA-ATAATATATATAAAAAT
47462324 A
1 A
47462325 CCAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AGTATAAATAATATATATAAAAAT
Found at i:47465362 original size:26 final size:26
Alignment explanation
Indices: 47465326--47465377 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
47465316 TCTTATAGGA
47465326 TAGATTTGTGGTTTCTGAGTAATGAT
1 TAGATTTGTGGTTTCTGAGTAATGAT
47465352 TAGATTTGTGGTTTCTGAGTAATGAT
1 TAGATTTGTGGTTTCTGAGTAATGAT
47465378 CTCTCTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.04, G:0.27, T:0.46
Consensus pattern (26 bp):
TAGATTTGTGGTTTCTGAGTAATGAT
Found at i:47469316 original size:27 final size:27
Alignment explanation
Indices: 47469270--47469352 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 27
47469260 CCTCCACAAA
***
47469270 AGATGGTCCTAACAAACTTCCCACATT
1 AGATGGTCCTAACGGGCTTCCCACATT
**
47469297 AGATGGTCCTAACGGGCTTCCCACGGT
1 AGATGGTCCTAACGGGCTTCCCACATT
* *
47469324 AGATAGTCCTGACGGGCTTCCCACATT
1 AGATGGTCCTAACGGGCTTCCCACATT
47469351 AG
1 AG
47469353 TTAGGTTGGT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (27 bp):
AGATGGTCCTAACGGGCTTCCCACATT
Found at i:47472959 original size:31 final size:29
Alignment explanation
Indices: 47472895--47472963 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
47472885 CACGATAACG
*
47472895 TAAGTGAC-AAAATGTAACATTACAAAAA
1 TAAGTGACTAAAATGTAACATGACAAAAA
*
47472923 TAAGTGACTAAAATGTAACCTGAGACAAATAA
1 TAAGTGACTAAAATGTAACAT--GACAAA-AA
47472955 -AAGTGACTA
1 TAAGTGACTA
47472964 TTTTGATAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 8 0.23
29 11 0.31
31 14 0.40
32 2 0.06
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (29 bp):
TAAGTGACTAAAATGTAACATGACAAAAA
Found at i:47478820 original size:12 final size:12
Alignment explanation
Indices: 47478803--47478828 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
47478793 CTCGATGCGC
47478803 CCAAAATTGGTA
1 CCAAAATTGGTA
47478815 CCAAAATTGGTA
1 CCAAAATTGGTA
47478827 CC
1 CC
47478829 TAGTTGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (12 bp):
CCAAAATTGGTA
Found at i:47479645 original size:12 final size:12
Alignment explanation
Indices: 47479628--47479652 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47479618 CATTATAAAT
47479628 ATAATAATAGTA
1 ATAATAATAGTA
47479640 ATAATAATAGTA
1 ATAATAATAGTA
47479652 A
1 A
47479653 AAGGACAAAA
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:47482275 original size:10 final size:10
Alignment explanation
Indices: 47482262--47482302 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
47482252 ACATATATTT
47482262 ATATTTTATA
1 ATATTTTATA
47482272 ATATTTTTATA
1 ATA-TTTTATA
*
47482283 GT-TTTTA-A
1 ATATTTTATA
47482291 ATATTTTATA
1 ATATTTTATA
47482301 AT
1 AT
47482303 CCAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 2 0.08
9 10 0.38
10 6 0.23
11 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
ATATTTTATA
Found at i:47482275 original size:18 final size:18
Alignment explanation
Indices: 47482254--47482337 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 18
47482244 ATATACGTAC
47482254 ATATATTTATATTTTATA
1 ATATATTTATATTTTATA
*
47482272 ATATTTTTATAGTTTT-TA
1 ATATATTTATA-TTTTATA
* **
47482290 A-ATATTTTATAATCCA-A
1 ATATA-TTTATATTTTATA
* *
47482307 ATATATATACAGTTTTATA
1 ATATATTTATA-TTTTATA
*
47482326 ATATATATATAT
1 ATATATTTATAT
47482338 ATACATACAT
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
17 9 0.18
18 25 0.51
19 15 0.31
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (18 bp):
ATATATTTATATTTTATA
Found at i:47482497 original size:6 final size:6
Alignment explanation
Indices: 47482486--47482513 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
47482476 ATATTTTTAA
47482486 ATACCT ATACCT ATACCT ATACCT ATAC
1 ATACCT ATACCT ATACCT ATACCT ATAC
47482514 ATATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACCT
Found at i:47489265 original size:20 final size:20
Alignment explanation
Indices: 47489238--47489288 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
47489228 AGGGGCACAG
47489238 ATGTGCAATCAAGGATATCGA
1 ATGTGCAATCAAGGATA-CGA
* * *
47489259 A-GTGCAAACAGGGGTACGA
1 ATGTGCAATCAAGGATACGA
47489278 ATGTGCAATCA
1 ATGTGCAATCA
47489289 GAGATACTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 4 0.16
20 20 0.80
21 1 0.04
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (20 bp):
ATGTGCAATCAAGGATACGA
Found at i:47492566 original size:34 final size:34
Alignment explanation
Indices: 47492528--47492619 Score: 139
Period size: 34 Copynumber: 2.7 Consensus size: 34
47492518 ATTTAGGAAC
* * *
47492528 TTGTGAATGAGTAATGGTTTACTGTGGAGGAAAG
1 TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
47492562 TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
1 TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
* *
47492596 TTGTTAATGATTGATGGTTTACTC
1 TTGTGAATGAGTGATGGTTTACTC
47492620 CAGAGTCTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.27, C:0.05, G:0.30, T:0.37
Consensus pattern (34 bp):
TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
Found at i:47499680 original size:25 final size:26
Alignment explanation
Indices: 47499631--47499680 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
47499621 AAATAACCAC
*
47499631 AAAAAAAACACAATAAAGCTGTCAAAA
1 AAAAAAAACACAAT-AACCTGTCAAAA
*
47499658 AAAAAAAACACAAT-ACCTTTCAA
1 AAAAAAAACACAATAACCTGTCAA
47499681 TTTTGAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
27 14 0.67
ACGTcount: A:0.64, C:0.18, G:0.04, T:0.14
Consensus pattern (26 bp):
AAAAAAAACACAATAACCTGTCAAAA
Found at i:47507441 original size:10 final size:10
Alignment explanation
Indices: 47507426--47507454 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
47507416 GGATTTTTTG
47507426 ATTTTCGCTC
1 ATTTTCGCTC
47507436 ATTTTCGCTC
1 ATTTTCGCTC
47507446 ATTTT-GCTC
1 ATTTTCGCTC
47507455 CCAAATGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.10, C:0.28, G:0.10, T:0.52
Consensus pattern (10 bp):
ATTTTCGCTC
Found at i:47511957 original size:27 final size:27
Alignment explanation
Indices: 47511925--47511978 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
47511915 CATTCTTTTC
47511925 TCTTGTTTACATTCCCTTAATTAATTT
1 TCTTGTTTACATTCCCTTAATTAATTT
47511952 TCTTGTTTACATTCCCTTAATTAATTT
1 TCTTGTTTACATTCCCTTAATTAATTT
47511979 CAACATGTAA
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:0.22, C:0.19, G:0.04, T:0.56
Consensus pattern (27 bp):
TCTTGTTTACATTCCCTTAATTAATTT
Found at i:47513130 original size:19 final size:20
Alignment explanation
Indices: 47513104--47513149 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
47513094 ATAGAATTTT
47513104 AATT-AATA-TAAATAAACA
1 AATTAAATAGTAAATAAACA
* *
47513122 AATTAAATAGTAATTAGACA
1 AATTAAATAGTAAATAAACA
*
47513142 AATAAAAT
1 AATTAAAT
47513150 GTTTTTGCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (20 bp):
AATTAAATAGTAAATAAACA
Found at i:47513213 original size:41 final size:41
Alignment explanation
Indices: 47513156--47513427 Score: 386
Period size: 41 Copynumber: 6.7 Consensus size: 41
47513146 AAATGTTTTT
*
47513156 GCGGCGCTTTTCCAAAAATGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
**
47513197 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTTAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
* * *
47513238 GCGGCGC-TTCCCAGAAATGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
* * *
47513278 GCGGCGCTTCTCCAAAAACACCGCTAAAGCCCTA-AGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACC-AGAGCATTA
* *
47513319 GCGGCGCTTCTCCAAAAATGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
* *
47513360 GCGGCGCTTCTCCAAAAACGCCGCTAAAGACCCGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
**
47513401 GCGGCGCTTTTATAAAAACGCCGCTAA
1 GCGGCGCTTTTCCAAAAACGCCGCTAA
47513428 GCCCCGAAAG
Statistics
Matches: 206, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
40 36 0.17
41 169 0.82
42 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
Found at i:47514028 original size:110 final size:110
Alignment explanation
Indices: 47513829--47514234 Score: 588
Period size: 108 Copynumber: 3.7 Consensus size: 110
47513819 AAAATTGAAG
* * * *
47513829 AGGATATTTAGCAATTTGG-CTAAACGTGAAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGA
1 AGGATATTTAGCTATTTGGTC-GAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGA
*
47513893 ATTTCCAAACGCAAAACATTACCTTATTTTTGAAAAGTTTTTTAAA
65 ATTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTTAAA
*
47513939 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAA
* * * *
47514004 TTTCTAAACGCAAAATATTGCCTTA-TTTT-AAAAATTTTTGAAA
66 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTTAAA
* * *
47514047 AGGATATTAAG-TCATTTGGTGGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1 AGGATATTTAGCT-ATTTGGTCGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGA
*
47514111 ATTTCCAAACTCAAAACATTGCCTTATTTTTGAAAAG-TTTTTAAA
65 ATTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTTAAA
* *
47514156 AGGATATTTAGCTATTTGGTCGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTCGAACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTC
47514221 GAATTTCCAAACGC
63 GAATTTCCAAACGC
47514235 TAAATGTTGC
Statistics
Matches: 265, Mismatches: 23, Indels: 14
0.88 0.08 0.05
Matches are distributed among these distances:
107 1 0.00
108 95 0.36
109 39 0.15
110 85 0.32
111 27 0.10
112 18 0.07
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (110 bp):
AGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTTAAA
Found at i:47514653 original size:2 final size:2
Alignment explanation
Indices: 47514646--47514682 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
47514636 ATATGAAAAG
**
47514646 TA TA TA TA TA TA TA TA GG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47514683 GAATCATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:47514793 original size:2 final size:2
Alignment explanation
Indices: 47514745--47514774 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47514735 GAATATGTAA
47514745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47514775 GAAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47514919 original size:3 final size:3
Alignment explanation
Indices: 47514911--47514956 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
47514901 TATAAAAGCG
47514911 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
47514957 CGCTAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:47517981 original size:114 final size:113
Alignment explanation
Indices: 47517805--47518248 Score: 676
Period size: 114 Copynumber: 3.9 Consensus size: 113
47517795 AAAATAAGCA
* * *
47517805 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGTCGTTTCCCGAGCTT
1 TTAGCGGCGTTTTTG-GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
47517869 TCGGGGATTTAGCAGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
65 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
47517918 TTAGCGGCATTTTTCGGAAAGCGCCGCAAAAAAACCTCAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTT-GGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
47517983 TCGGGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGAT
65 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* ** *
47518032 TTAACGGCGTTTTTGGAAAAGTACCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGG-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
47518097 TCGAGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGACT
65 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
*
47518146 TTAGCGGCGTTTTTCGGAAAGCGCTGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTT-GGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
47518211 TCGGGGATTTAGCGGCGTTTTT-GGAAAAGCGCCGCTAA
65 TCGGGGATTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAA
47518249 AAATATTTTA
Statistics
Matches: 300, Mismatches: 26, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
113 27 0.09
114 271 0.90
115 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:47518515 original size:15 final size:15
Alignment explanation
Indices: 47518495--47518525 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47518485 CATATTTTAA
47518495 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
47518510 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
47518525 G
1 G
47518526 ATTAGGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:47518830 original size:21 final size:21
Alignment explanation
Indices: 47518758--47518832 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
47518748 GAGTTCATAT
47518758 TTTAAGGTTTAAGGAGTAT-GGA
1 TTTAAGGTTTAAGGA-T-TGGGA
* * * *
47518780 TTTAGGGATTATGAATTAGGGA
1 TTTAAGGTTTAAGGATT-GGGA
* *
47518802 -CTATGGTTTAAGGATTGGGA
1 TTTAAGGTTTAAGGATTGGGA
47518822 TTTAAGGTTTA
1 TTTAAGGTTTA
47518833 GGAGTTAGGG
Statistics
Matches: 39, Mismatches: 11, Indels: 7
0.68 0.19 0.12
Matches are distributed among these distances:
20 5 0.13
21 20 0.51
22 14 0.36
ACGTcount: A:0.29, C:0.01, G:0.31, T:0.39
Consensus pattern (21 bp):
TTTAAGGTTTAAGGATTGGGA
Found at i:47518891 original size:15 final size:15
Alignment explanation
Indices: 47518808--47518896 Score: 55
Period size: 14 Copynumber: 6.1 Consensus size: 15
47518798 GGGACTATGG
*
47518808 TTTAAGGATT-GGGA
1 TTTAAGGTTTAGGGA
47518822 TTTAAGGTTTA-GGA
1 TTTAAGGTTTAGGGA
* *
47518836 GTTAGGGGTTTAGGG-
1 TTTA-AGGTTTAGGGA
* *
47518851 GTT-AGATGTTAGGG-
1 TTTAAGGT-TTAGGGA
*
47518865 GTTAAGAG-TTAGGGA
1 TTTAAG-GTTTAGGGA
47518880 TTTAAGGTTTAGGGA
1 TTTAAGGTTTAGGGA
47518895 TT
1 TT
47518897 CAGGGGTCGA
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
13 2 0.03
14 31 0.52
15 25 0.42
16 2 0.03
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.37
Consensus pattern (15 bp):
TTTAAGGTTTAGGGA
Found at i:47519983 original size:84 final size:85
Alignment explanation
Indices: 47519895--47520059 Score: 260
Period size: 85 Copynumber: 2.0 Consensus size: 85
47519885 ATAAAAACGT
* * **
47519895 CGCAAAAAATAAATCAATTTAT-AAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGTGTCA
1 CGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGGCATCA
47519959 TTTTGTTCAAAATGAAATAG
66 TTTTGTTCAAAATGAAATAG
* **
47519979 CGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAACTTTTTAGAATAGCAAAACGGCATTG
1 CGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGGCATCA
47520044 TTTTGTTCAAAATGAA
66 TTTTGTTCAAAATGAA
47520060 TAAAATTTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
84 22 0.30
85 51 0.70
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (85 bp):
CGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGGCATCA
TTTTGTTCAAAATGAAATAG
Found at i:47526871 original size:5 final size:5
Alignment explanation
Indices: 47526825--47526855 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
47526815 TCAAATTTAA
47526825 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
47526856 TTTATCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:47526981 original size:41 final size:43
Alignment explanation
Indices: 47526912--47527050 Score: 124
Period size: 42 Copynumber: 3.3 Consensus size: 43
47526902 GTTATGTTTT
* * *
47526912 TAGTGGCGTTTTTGCAAGAAGCGTCGCTAAAGGT-TTGTTCTA
1 TAGTGGCGTTTTTGCAAAAAGCGCCGCTAAAGGTCTTGATCTA
47526954 TAGTGGCG-TTTTG-ATAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGTGGCGTTTTTGCA-AAAAGCGCCGCTAAAGGTCTTGATCTA
* * ** * ** * *
47526996 CAGTGGCGCTTAAGGAAAAA-CGCCGCTAAAGAACATGATCTT
1 TAGTGGCGTTTTTGCAAAAAGCGCCGCTAAAGGTCTTGATCTA
*
47527038 TAGCGGCGTTTTT
1 TAGTGGCGTTTTT
47527051 CTCTAAGCGC
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
40 1 0.01
41 21 0.27
42 48 0.62
43 7 0.09
44 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
TAGTGGCGTTTTTGCAAAAAGCGCCGCTAAAGGTCTTGATCTA
Found at i:47527067 original size:42 final size:42
Alignment explanation
Indices: 47527016--47527134 Score: 195
Period size: 42 Copynumber: 2.8 Consensus size: 42
47527006 TAAGGAAAAA
*
47527016 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTCTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTC-CTAAG
*
47527058 CGCCTCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCCTAAG
*
47527100 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
47527135 GTTTGTAAAC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
42 66 0.92
43 6 0.08
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCCTAAG
Found at i:47532557 original size:17 final size:17
Alignment explanation
Indices: 47532535--47532569 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
47532525 CCGTGTGTGC
47532535 ACCTAAAAGTACTTTAA
1 ACCTAAAAGTACTTTAA
47532552 ACCTAAAAGTACTTTAA
1 ACCTAAAAGTACTTTAA
47532569 A
1 A
47532570 ACTCAAGTTT
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:0.17, G:0.06, T:0.29
Consensus pattern (17 bp):
ACCTAAAAGTACTTTAA
Found at i:47533436 original size:43 final size:42
Alignment explanation
Indices: 47533382--47533466 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 42
47533372 TTCATATCTC
47533382 ATTTCTCATCTCATAATCATTTCTCATATTTGT-CATTTCAAT
1 ATTTCTCATCTCATAATCATTTCTCATATTT-TCCATTTCAAT
* *
47533424 ATTTCCTCATCTCATATTCATTTCTCATCTTTTCCATTTCAAT
1 ATTT-CTCATCTCATAATCATTTCTCATATTTTCCATTTCAAT
47533467 TAGATAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
42 5 0.13
43 34 0.87
ACGTcount: A:0.24, C:0.25, G:0.01, T:0.51
Consensus pattern (42 bp):
ATTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAAT
Found at i:47534722 original size:2 final size:2
Alignment explanation
Indices: 47534717--47534747 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47534707 TATATTAAAA
47534717 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47534748 CTGTCGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47536485 original size:21 final size:21
Alignment explanation
Indices: 47536459--47536555 Score: 144
Period size: 21 Copynumber: 4.7 Consensus size: 21
47536449 AATCATATCT
*
47536459 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
*
47536480 TCTAAGATTACATATATCATA
1 TCTAAGATTGCATATATCATA
*
47536501 TCTAATATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
47536522 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
47536541 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
47536556 CCTCGAAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.26
21 50 0.74
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:47536941 original size:44 final size:44
Alignment explanation
Indices: 47536866--47537844 Score: 403
Period size: 44 Copynumber: 22.5 Consensus size: 44
47536856 CTCTAACCCA
* * * *
47536866 CTCCACTACAACTT-AGGGAGATAGGATTTGTTTATTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
* *
47536909 C-CTCACTTCAACTTTA-GGAGGATAAGACTTGTTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTG
* ** *
47536953 CTCCACTGCAACTTCAGGGAGATAAGACTAG-ACAC-GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
* * ** * *
47536994 CT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTT--TT-GATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA--CTTGTTTACTTAG-TCTG
* * * *** *
47537037 CTCCACTACAACTTCAGGGAGATAGGA-TTATCGGCTCTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACT-TAGTCTG
* *
47537081 CTCCACTGCAACTTCAGGGAGATAAGA-TT-TTCCATCTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTT-TA-CTT-AGTCTG
* * * *
47537126 C-CTCACTACAACTTCA-GGAGGATAAGACTTGCTTGCTGAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTG
* * *** *
47537170 CTCCACTGCAACTTCAGGGAGATAGGA-TTATCGGCTCTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACT-TAGTCTG
* ** *
47537214 CTCCACTGCAACTTCAGGGAGATAAGATTTG-CCATCTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTA-CTT-AGTCTG
* * * *
47537259 C-CTCACTACAACTTCA-GGAGGATAAGACTTGCTTGCTGAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTG
* * * *
47537303 CTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
* * * * ** * * *
47537344 AT-CTCTGCAACTTCAGAGAGATACGATCCAAGGTT--TTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA--CTTGTTTACTTAGTCTG
* * * * * * ** *
47537387 CTCAACTGCAACTTTAAGAAGATAGGA-TTATCGACTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTAC-TTAGTCTG
* * **
47537431 CTCCACTGCAACTTTAGGGAGATAAGATTTG-CCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTA-CTT-AGTCTG
*
47537476 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTG
* * * *
47537520 CTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
* * * * ** * * *
47537561 CT-CTCTACAAATTCAGAGAGATAAGATCCAAGGTT--TTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA--CTTGTTTACTTAGTCTG
* * * ** *
47537604 CTCCACTGCAACTTTAGGGAGATATGA-TTATCGACTCTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACT-TAGTCTG
* **
47537648 CTCCACTGCAACTTCAGGGAGAT-AGAATTTGCCGT-CTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAG-ACTTG-TTTACTT-AGTCTG
*
47537693 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTG
* * * *
47537737 CTCTACTGCAACTTCAGGGAGATAAGACTAG-ATAC-GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
* * * * * *
47537778 CT-CTCTGCAACTTCAGAGAGATAAGATTTAAGGTT--TTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT--GTTTACTTAGTCTG
*
47537821 CTCCACTGCAACTTCAAGGAGATA
1 CTCCACTGCAACTTCAGGGAGATA
47537845 GGATTATCGG
Statistics
Matches: 711, Mismatches: 149, Indels: 151
0.70 0.15 0.15
Matches are distributed among these distances:
40 85 0.12
41 23 0.03
42 19 0.03
43 55 0.08
44 375 0.53
45 148 0.21
46 5 0.01
47 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
Found at i:47537182 original size:133 final size:133
Alignment explanation
Indices: 47537036--47537326 Score: 564
Period size: 133 Copynumber: 2.2 Consensus size: 133
47537026 GTTTTGATCC
*
47537036 GCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTCTAATCTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTCTAATCTGCTCCACTGCAACTTCAGGGA
*
47537101 GATAAGATTTTCCATCTTCAGTCTACCTCACTACAACTTCAGGAGGATAAGACTTGCTTGCTGAG
66 GATAAGATTTGCCATCTTCAGTCTACCTCACTACAACTTCAGGAGGATAAGACTTGCTTGCTGAG
47537166 TCT
131 TCT
47537169 GCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTCTAATCTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTCTAATCTGCTCCACTGCAACTTCAGGGA
47537234 GATAAGATTTGCCATCTTCAGTCTACCTCACTACAACTTCAGGAGGATAAGACTTGCTTGCTGAG
66 GATAAGATTTGCCATCTTCAGTCTACCTCACTACAACTTCAGGAGGATAAGACTTGCTTGCTGAG
47537299 TCT
131 TCT
47537302 GCTCCACTGCAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
47537327 AGACTAGATG
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 156 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (133 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTCTAATCTGCTCCACTGCAACTTCAGGGA
GATAAGATTTGCCATCTTCAGTCTACCTCACTACAACTTCAGGAGGATAAGACTTGCTTGCTGAG
TCT
Found at i:47537357 original size:217 final size:216
Alignment explanation
Indices: 47537169--47537853 Score: 1120
Period size: 217 Copynumber: 3.2 Consensus size: 216
47537159 TGCTGAGTCT
* *
47537169 GCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTCTAATCTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAAGGAGATAGGATTATCGACTCTAATCTGCTCCACTGCAACTTCAGGGA
* * * *
47537234 GATAAGATTTGCCATCTTCAGTCTACCTCACTACAACTTCAGGAGGATAAGACTTGCTTGCTGAG
66 GATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAG
*
47537299 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGATCTCTGCAACTTCAGAGAG
131 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
*
47537364 ATACGATCCAAGGTTTTAATCC
196 ATAAGA-CCAAGGTTTTAATCC
* * * * *
47537386 GCTCAACTGCAACTTTAAGAAGATAGGATTATCGACTTTAATCTGCTCCACTGCAACTTTAGGGA
1 GCTCCACTGCAACTTCAAGGAGATAGGATTATCGACTCTAATCTGCTCCACTGCAACTTCAGGGA
47537451 GATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAG
66 GATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAG
* *
47537516 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTACAAATTCAGAGAG
131 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
47537581 ATAAGATCCAAGGTTTTAATCC
196 ATAAGA-CCAAGGTTTTAATCC
* * *
47537603 GCTCCACTGCAACTTTAGGGAGATATGATTATCGACTCTAATCTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAAGGAGATAGGATTATCGACTCTAATCTGCTCCACTGCAACTTCAGGGA
*
47537668 GAT-AGAATTTGCCGTCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTA
66 GATAAG-ATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTA
* *
47537732 GTCTGCTCTACTGCAACTTCAGGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCAGAGA
130 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGA
**
47537797 GATAAGATTTAAGGTTTTAATCC
195 GATAAGA-CCAAGGTTTTAATCC
47537820 GCTCCACTGCAACTTCAAGGAGATAGGATTATCG
1 GCTCCACTGCAACTTCAAGGAGATAGGATTATCG
47537854 GCCACCGATC
Statistics
Matches: 436, Mismatches: 31, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
216 2 0.00
217 434 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (216 bp):
GCTCCACTGCAACTTCAAGGAGATAGGATTATCGACTCTAATCTGCTCCACTGCAACTTCAGGGA
GATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAG
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
ATAAGACCAAGGTTTTAATCC
Found at i:47539112 original size:22 final size:20
Alignment explanation
Indices: 47539086--47539135 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
47539076 TCCATTTTCC
47539086 TTTTCTTTTTCTTTTTATCACT
1 TTTTCTTTTT-TTTTT-TCACT
* *
47539108 TTTTCTTCTTTTTTTTCTCT
1 TTTTCTTTTTTTTTTTCACT
47539128 TTTT-TTTT
1 TTTTCTTTT
47539136 ATATTTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 8 0.32
21 5 0.20
22 9 0.36
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCTTTTTTTTTTTCACT
Found at i:47543520 original size:12 final size:12
Alignment explanation
Indices: 47543490--47543523 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
47543480 ATAATGACAT
47543490 AAAAATAATATAA
1 AAAAATAA-ATAA
*
47543503 ACAAATAAATAA
1 AAAAATAAATAA
47543515 AAAAATAAA
1 AAAAATAAA
47543524 AGATANNNNN
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAATAAATAA
Found at i:47544421 original size:21 final size:21
Alignment explanation
Indices: 47544395--47544491 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
47544385 AATCATATCT
*
47544395 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
*
47544416 TCTAAGATTACATATATCATA
1 TCTAAGATTGCATATATCATA
47544437 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
47544458 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
47544477 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
47544492 CCTCGAAAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.26
21 52 0.74
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:47545625 original size:9 final size:9
Alignment explanation
Indices: 47545611--47545702 Score: 134
Period size: 9 Copynumber: 10.4 Consensus size: 9
47545601 TGGTTAAAAA
47545611 TTAACCGAT
1 TTAACCGAT
*
47545620 TTAACCTAT
1 TTAACCGAT
47545629 TTAACCGA-
1 TTAACCGAT
47545637 TTAACCGAT
1 TTAACCGAT
*
47545646 TTAACCTAT
1 TTAACCGAT
47545655 TTAACCGA-
1 TTAACCGAT
* *
47545663 TTAACTGAC
1 TTAACCGAT
47545672 TTAACCGAT
1 TTAACCGAT
47545681 TTAACCGAT
1 TTAACCGAT
47545690 TTAACCGAT
1 TTAACCGAT
47545699 TTAA
1 TTAA
47545703 ATCACTATAT
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
8 15 0.20
9 59 0.80
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (9 bp):
TTAACCGAT
Found at i:47545640 original size:26 final size:26
Alignment explanation
Indices: 47545610--47545702 Score: 150
Period size: 26 Copynumber: 3.5 Consensus size: 26
47545600 TTGGTTAAAA
47545610 ATTAACCGATTTAACCTATTTAACCG
1 ATTAACCGATTTAACCTATTTAACCG
47545636 ATTAACCGATTTAACCTATTTAACCG
1 ATTAACCGATTTAACCTATTTAACCG
* * *
47545662 ATTAACTGACTTAACCGATTTAACCG
1 ATTAACCGATTTAACCTATTTAACCG
47545688 ATTTAACCGATTTAA
1 A-TTAACCGATTTAA
47545703 ATCACTATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
26 50 0.82
27 11 0.18
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (26 bp):
ATTAACCGATTTAACCTATTTAACCG
Found at i:47545650 original size:35 final size:36
Alignment explanation
Indices: 47545611--47545702 Score: 143
Period size: 35 Copynumber: 2.6 Consensus size: 36
47545601 TGGTTAAAAA
*
47545611 TTAACCGATTTAACCTATTTAACCGA-TTAACCGAT
1 TTAACCGATTTAACCGATTTAACCGACTTAACCGAT
* *
47545646 TTAACCTATTTAACCGA-TTAACTGACTTAACCGAT
1 TTAACCGATTTAACCGATTTAACCGACTTAACCGAT
47545681 TTAACCGATTTAACCGATTTAA
1 TTAACCGATTTAACCGATTTAA
47545703 ATCACTATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 7 0.14
35 40 0.78
36 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (36 bp):
TTAACCGATTTAACCGATTTAACCGACTTAACCGAT
Found at i:47547323 original size:18 final size:19
Alignment explanation
Indices: 47547302--47547338 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
47547292 CCAAATTCGG
47547302 TCGG-TTAACCGAATTTTT
1 TCGGTTTAACCGAATTTTT
47547320 TCGGTTTTAACCGAATTTT
1 TCGG-TTTAACCGAATTTT
47547339 GCACACCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (19 bp):
TCGGTTTAACCGAATTTTT
Found at i:47549179 original size:35 final size:35
Alignment explanation
Indices: 47549139--47549207 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
47549129 ACGATAGCGG
* *
47549139 AAACCCAACTCTAAACTGATAAAATCCTCCATATT
1 AAACCCAACTCAAAACCGATAAAATCCTCCATATT
* *
47549174 AAACCCAGCTCAAAACCGATAAAATCCTTCATAT
1 AAACCCAACTCAAAACCGATAAAATCCTCCATAT
47549208 CAACCCCTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.43, C:0.29, G:0.04, T:0.23
Consensus pattern (35 bp):
AAACCCAACTCAAAACCGATAAAATCCTCCATATT
Found at i:47552406 original size:11 final size:11
Alignment explanation
Indices: 47552386--47552483 Score: 61
Period size: 11 Copynumber: 9.4 Consensus size: 11
47552376 CAAAAATTAA
47552386 AAAAAGTATTTT
1 AAAAA-TATTTT
47552398 AAAAATATTTT
1 AAAAATATTTT
*
47552409 --AAA-A-TTA
1 AAAAATATTTT
47552416 AAAAAGTATTTT
1 AAAAA-TATTTT
* *
47552428 AAAAAAAATTT
1 AAAAATATTTT
47552439 --AAA-A-TTT
1 AAAAATATTTT
47552446 AAAAA-ATTTT
1 AAAAATATTTT
47552456 AAAAAAGTATTTT
1 -AAAAA-TATTTT
*
47552469 AAAAGTATTTT
1 AAAAATATTTT
47552480 AAAA
1 AAAA
47552484 TTAAAAAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 23
0.71 0.05 0.23
Matches are distributed among these distances:
7 5 0.07
8 2 0.03
9 13 0.19
10 3 0.04
11 26 0.37
12 16 0.23
13 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:47552421 original size:30 final size:30
Alignment explanation
Indices: 47552378--47552472 Score: 122
Period size: 30 Copynumber: 3.1 Consensus size: 30
47552368 AATTAAAACA
47552378 AAAATTAAAAAAAGTATTTTAAAAATATTTT
1 AAAATT-AAAAAAGTATTTTAAAAATATTTT
* *
47552409 AAAATTAAAAAAGTATTTTAAAAAAAATTT
1 AAAATTAAAAAAGTATTTTAAAAATATTTT
*
47552439 AAAATTTAAAAAA-T-TTTAAAAAAGTATTTT
1 AAAA-TTAAAAAAGTATTTTAAAAA-TATTTT
47552469 AAAA
1 AAAA
47552473 GTATTTTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
29 8 0.14
30 35 0.61
31 14 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTAAAAAAGTATTTTAAAAATATTTT
Found at i:47552458 original size:41 final size:41
Alignment explanation
Indices: 47552413--47552492 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
47552403 TATTTTAAAA
*
47552413 TTAAAAAAGTATTTTAAAAAAAATTTAAAATTTAAAAAATT
1 TTAAAAAAGTATTTTAAAAAAAATTTAAAATTAAAAAAATT
** *
47552454 TTAAAAAAGTATTTTAAAAGTATTTTAAAATTAAAAAAA
1 TTAAAAAAGTATTTTAAAAAAAATTTAAAATTAAAAAAA
47552493 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (41 bp):
TTAAAAAAGTATTTTAAAAAAAATTTAAAATTAAAAAAATT
Found at i:47560179 original size:2 final size:2
Alignment explanation
Indices: 47560168--47560230 Score: 74
Period size: 2 Copynumber: 32.0 Consensus size: 2
47560158 CGTGCGTTTT
* * * * *
47560168 TA TA -A TA TA TA TG TA TA TA TA CA TA TG CA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47560209 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
47560231 CGAACCTACA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:47566403 original size:10 final size:11
Alignment explanation
Indices: 47566388--47566413 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47566378 AAAGATTTTT
47566388 AAAAAAGGGAA
1 AAAAAAGGGAA
47566399 AAAAAAGGGAA
1 AAAAAAGGGAA
47566410 AAAA
1 AAAA
47566414 GAAAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAAAGGGAA
Found at i:47566420 original size:6 final size:6
Alignment explanation
Indices: 47566409--47566470 Score: 56
Period size: 6 Copynumber: 10.0 Consensus size: 6
47566399 AAAAAAGGGA
* *
47566409 AAAAAG AAAAAG AAAGAA- AAAGAAG AAAAA- AGAAAG AAGAAG ATGAAAAG
1 AAAAAG AAAAAG AAA-AAG AAA-AAG AAAAAG AAAAAG AAAAAG A--AAAAG
47566459 AAAAAG AAAAAG
1 AAAAAG AAAAAG
47566471 GAGAGACCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
5 4 0.09
6 33 0.70
7 5 0.11
8 5 0.11
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:47566424 original size:10 final size:10
Alignment explanation
Indices: 47566411--47566467 Score: 62
Period size: 10 Copynumber: 5.3 Consensus size: 10
47566401 AAAAGGGAAA
47566411 AAAGAAAAAG
1 AAAGAAAAAG
47566421 AAAGAAAAAG
1 AAAGAAAAAG
47566431 -AAGAAAAAAG
1 AAAG-AAAAAG
47566441 AAAGAAGAAGATG
1 AAAGAA-AA-A-G
47566454 AAAAGAAAAAG
1 -AAAGAAAAAG
47566465 AAA
1 AAA
47566468 AAGGAGAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 3 0.07
10 21 0.51
11 6 0.15
12 2 0.05
13 3 0.07
14 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:47566440 original size:20 final size:20
Alignment explanation
Indices: 47566415--47566470 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
47566405 GGGAAAAAAG
47566415 AAAAAGAAAGAAAAAGAAGA
1 AAAAAGAAAGAAAAAGAAGA
* *
47566435 AAAAAGAAAGAAGAAGATGA
1 AAAAAGAAAGAAAAAGAAGA
47566455 AAAGAA-AAAGAAAAAG
1 AAA-AAGAAAGAAAAAG
47566471 GAGAGACCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAGAAAAAGAAGA
Found at i:47567803 original size:44 final size:44
Alignment explanation
Indices: 47567733--47567952 Score: 151
Period size: 44 Copynumber: 5.0 Consensus size: 44
47567723 GATAGCAGAT
* *
47567733 CTTGCCTTTCTGTACTGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGTACTCACAGCGAAGCAGATCGAAGACACCAGC
* * * * *
47567777 CTTGCCTTCCTATACTCACAGTGAAGCAGA-CTGAAGATAACAGAT
1 CTTGCCTTCCTGTACTCACAGCGAAGCAGATC-GAAGACACCAG-C
* ** * *
47567822 CATGCCTTCCTGTA-TCGGTAGCGAAGTAGATCGAAGACACCTGC
1 CTTGCCTTCCTGTACTC-ACAGCGAAGCAGATCGAAGACACCAGC
* * * * * * **
47567866 CTTGCCTTTCTGTACTAATAGC-AGAGCA-AACTGAAGATAGCAAAT
1 CTTGCCTTCCTGTACTCACAGCGA-AGCAGATC-GAAGACA-CCAGC
* * *
47567911 CTTGCCTTCCTGTACTGACAGTGAAGCAGATTGAAGACACCA
1 CTTGCCTTCCTGTACTCACAGCGAAGCAGATCGAAGACACCA
47567953 TAGTTTGCAA
Statistics
Matches: 130, Mismatches: 36, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
43 4 0.03
44 64 0.49
45 59 0.45
46 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (44 bp):
CTTGCCTTCCTGTACTCACAGCGAAGCAGATCGAAGACACCAGC
Found at i:47567845 original size:89 final size:89
Alignment explanation
Indices: 47567688--47567952 Score: 309
Period size: 89 Copynumber: 3.0 Consensus size: 89
47567678 AGTTACAGAT
* * * * * *
47567688 CTTGTCTTCCTGTACTGACTGCAGAGTAGACTGAAGATAGCAGATCTTGCCTTTCTGTACTGACA
1 CTTGCCTTCCTATACTAACAGCAGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
47567753 GCGAAGCAGATCGAAGACACCAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * * * *
47567777 CTTGCCTTCCTATACTCACAG-TGAAGCAGACTGAAGATAACAGATCATGCCTTCCTGTA-TCGG
1 CTTGCCTTCCTATACTAACAGCAG-AGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACT-GA
* * *
47567840 TAGCGAAGTAGATCGAAGACACCTGC
64 CAGCGAAGCAGATCGAAGACACCAGC
* * * * *
47567866 CTTGCCTTTCTGTACTAATAGCAGAGCAAACTGAAGATAGCAAATCTTGCCTTCCTGTACTGACA
1 CTTGCCTTCCTATACTAACAGCAGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* *
47567931 GTGAAGCAGATTGAAGACACCA
66 GCGAAGCAGATCGAAGACACCA
47567953 TAGTTTGCAA
Statistics
Matches: 144, Mismatches: 28, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
88 2 0.01
89 140 0.97
90 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (89 bp):
CTTGCCTTCCTATACTAACAGCAGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
GCGAAGCAGATCGAAGACACCAGC
Found at i:47567946 original size:45 final size:44
Alignment explanation
Indices: 47567681--47567947 Score: 150
Period size: 45 Copynumber: 6.0 Consensus size: 44
47567671 TCAATAAAGT
* * *
47567681 TACAGATCTTGTCTTCCTGTACTGAC--TGCAGAGTAGACTGAAGA
1 TACAAATCTTGCCTTCCTGTACTGACAGTG-A-AGCAGACTGAAGA
* * *
47567725 TAGCAGATCTTGCCTTTCTGTACTGACAGCGAAGCAGA-TCGAAGA
1 TA-CAAATCTTGCCTTCCTGTACTGACAGTGAAGCAGACT-GAAGA
* * ** * *
47567770 CACCAGCCTTGCCTTCCTATACTCACAGTGAAGCAGACTGAAGA
1 TACAAATCTTGCCTTCCTGTACTGACAGTGAAGCAGACTGAAGA
* * ** * *
47567814 TAACAGATCATGCCTTCCTGTA-TCGGTAGCGAAGTAGA-TCGAAGA
1 T-ACAAATCTTGCCTTCCTGTACT-GACAGTGAAGCAGACT-GAAGA
* **** * * * * *
47567859 CACCTGCCTTGCCTTTCTGTACTAATAG-CAGAGCAAACTGAAGA
1 TACAAATCTTGCCTTCCTGTACTGACAGTGA-AGCAGACTGAAGA
*
47567903 TAGCAAATCTTGCCTTCCTGTACTGACAGTGAAGCAGATTGAAGA
1 TA-CAAATCTTGCCTTCCTGTACTGACAGTGAAGCAGACTGAAGA
47567948 CACCATAGTT
Statistics
Matches: 162, Mismatches: 48, Indels: 25
0.69 0.20 0.11
Matches are distributed among these distances:
43 1 0.01
44 64 0.40
45 94 0.58
46 2 0.01
47 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (44 bp):
TACAAATCTTGCCTTCCTGTACTGACAGTGAAGCAGACTGAAGA
Found at i:47568225 original size:44 final size:44
Alignment explanation
Indices: 47568158--47568561 Score: 301
Period size: 44 Copynumber: 9.4 Consensus size: 44
47568148 AACCAACAAA
* * *
47568158 TCTTATCTCCCTGAAGTTCCAGTAGAGCAGATTGAAGTTACTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* * * * * *
47568202 TCCTATCTCCCTGAAGTTGCAGTAGAGCAGA-TCACA--T-CCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGA-AGTTACTAG
*
47568243 TCTTATCTCCCTGATGTTGCAGTGGAGTAGATTGAAGTTACTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* * * * * ***
47568287 TCCTATCTTCCTGAAGTTGCACTGGAGTGGATTAAAACCAC-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* * *** * *
47568330 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCCCA--T-CCAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* **
47568372 TCTTATCTCCCTAAAGTTTTAGTGGAGTAGATTGAAGTTACTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* * * * ***
47568416 TCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCAC-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* * * * * * *
47568459 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCA--T-CCAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
47568501 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
* *
47568545 TCCTATCTTCCTGAAGT
1 TCTTATCTCCCTGAAGT
47568562 AGAGCAGATC
Statistics
Matches: 273, Mismatches: 72, Indels: 30
0.73 0.19 0.08
Matches are distributed among these distances:
41 91 0.33
42 5 0.02
43 9 0.03
44 168 0.62
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG
Found at i:47568275 original size:85 final size:86
Alignment explanation
Indices: 47568156--47568561 Score: 358
Period size: 85 Copynumber: 4.7 Consensus size: 86
47568146 AAAACCAACA
* * *
47568156 AATCTTATCTCCCTGAAGTTCCAGTAGAGCAGATTGAAGTTACTAGTCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAGTCCTATCTCCCTGAAGTTG
47568221 CAGTAGAGCAGA-TCACATCC
66 CAGTAGAGCAGATTCACATCC
* *
47568241 AATCTTATCTCCCTGATGTTGCAGTGGAGTAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAGTCCTATCTCCCTGAAGTTG
* * ** * * *
47568306 CACTGGAGTGGATTAAAACCAC
66 CAGTAGAGCAGATTCACATC-C
* * *** * * * *
47568328 AGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCCCA--T-CCAATCTTATCTCCCTAAAGTT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAGTCCTATCTCCCTGAAGTT
** * * * *
47568390 TTAGTGGAGTAGATTGA-AGTTACT
65 GCAGTAGAGCAGATTCACA--T-CC
* * * * * *** * *
47568414 AGTCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCAC-AGATCTTATCTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAG-TCCTATCTCCCTGAAGTT
*
47568478 GCAGTAGAGCAGA-TCGCATCC
65 GCAGTAGAGCAGATTCACATCC
*
47568499 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAGTCCTATCTTCCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAGTCCTATCTCCCTGAAGT
47568562 AGAGCAGATC
Statistics
Matches: 248, Mismatches: 61, Indels: 24
0.74 0.18 0.07
Matches are distributed among these distances:
84 1 0.00
85 175 0.71
86 9 0.04
87 5 0.02
88 58 0.23
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (86 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACTAGTCCTATCTCCCTGAAGTTG
CAGTAGAGCAGATTCACATCC
Found at i:47568346 original size:129 final size:129
Alignment explanation
Indices: 47568205--47568561 Score: 633
Period size: 129 Copynumber: 2.8 Consensus size: 129
47568195 TTACTAGTCC
* *
47568205 TATCTCCCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGATGTTGCAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGCAGTGGAG
47568270 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTGCACTGGAGTGGATTAAAACCACAGATCT
66 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTGCACTGGAGTGGATTAAAACCACAGATCT
* * * **
47568334 TATCTCTCTGAAGTTGCAGTAGAGTAGATCCCATCCAATCTTATCTCCCTAAAGTTTTAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGCAGTGGAG
*
47568399 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCT
66 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTGCACTGGAGTGGATTAAAACCACAGATCT
*
47568463 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGCAGTGGAG
47568528 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGT
66 TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGT
47568562 AGAGCAGATC
Statistics
Matches: 215, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 215 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (129 bp):
TATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGCAGTGGAG
TAGATTGAAGTTACTAGTCCTATCTTCCTGAAGTTGCACTGGAGTGGATTAAAACCACAGATCT
Found at i:47569995 original size:20 final size:20
Alignment explanation
Indices: 47569970--47570017 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
47569960 AATTGAAATG
47569970 AATGTGATATTGAGTTATGA
1 AATGTGATATTGAGTTATGA
*
47569990 AATGTGATATTGGGTTATGA
1 AATGTGATATTGAGTTATGA
47570010 AATGTGAT
1 AATGTGAT
47570018 TTTATGGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (20 bp):
AATGTGATATTGAGTTATGA
Found at i:47570064 original size:35 final size:35
Alignment explanation
Indices: 47570024--47570267 Score: 176
Period size: 35 Copynumber: 7.1 Consensus size: 35
47570014 TGATTTTATG
**
47570024 GACTAGCATTGGGCACAACTTCTGTCAGTTTATCT
1 GACTAGCGCTGGGCACAACTTCTGTCAGTTTATCT
* * * * *
47570059 GACTAGTGCTGGGCACAACCATC-GT-TGGTTATTT
1 GACTAGCGCTGGGCACAA-CTTCTGTCAGTTTATCT
** ** *
47570093 GACTAGCATTGGGTGCAACTTCTGTCAATTTATCT
1 GACTAGCGCTGGGCACAACTTCTGTCAGTTTATCT
* * * *
47570128 GACTAGTGCTGGGCACAACCATC-GTC-GGTTATCC
1 GACTAGCGCTGGGCACAA-CTTCTGTCAGTTTATCT
* * *
47570162 GAGTAGCACTGGGCGCAACTTCTGTCAGTTTATCT
1 GACTAGCGCTGGGCACAACTTCTGTCAGTTTATCT
* * * * * *
47570197 AACTAGTGTTAGACACAACCATC-GTCAG-TTATCT
1 GACTAGCGCTGGGCACAA-CTTCTGTCAGTTTATCT
* *
47570231 GACTACCGCTGGGCGCAACTTCTGTCAGTTTATCT
1 GACTAGCGCTGGGCACAACTTCTGTCAGTTTATCT
47570266 GA
1 GA
47570268 GTAGTGCTAG
Statistics
Matches: 150, Mismatches: 50, Indels: 18
0.69 0.23 0.08
Matches are distributed among these distances:
33 9 0.06
34 65 0.43
35 67 0.45
36 9 0.06
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (35 bp):
GACTAGCGCTGGGCACAACTTCTGTCAGTTTATCT
Found at i:47570135 original size:69 final size:69
Alignment explanation
Indices: 47570024--47570287 Score: 357
Period size: 69 Copynumber: 3.8 Consensus size: 69
47570014 TGATTTTATG
* * * *
47570024 GACTAGCATTGGGCACAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTTGGTT
1 GACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTT
*
47570089 ATTT
66 ATCT
* * * *
47570093 GACTAGCATTGGGTGCAACTTCTGTCAATTTATCTGACTAGTGCTGGGCACAACCATCGTCGGTT
1 GACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTT
*
47570158 ATCC
66 ATCT
* * * * *
47570162 GAGTAGCACTGGGCGCAACTTCTGTCAGTTTATCTAACTAGTGTTAGACACAACCATCGTCAGTT
1 GACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTT
47570227 ATCT
66 ATCT
* * * *
47570231 GACTACCGCTGGGCGCAACTTCTGTCAGTTTATCTGAGTAGTGCTAGGAACAACCAT
1 GACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCAT
47570288 TGTCAATTAT
Statistics
Matches: 171, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 171 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (69 bp):
GACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTAGGCACAACCATCGTCGGTT
ATCT
Found at i:47570292 original size:35 final size:35
Alignment explanation
Indices: 47570184--47570292 Score: 89
Period size: 35 Copynumber: 3.1 Consensus size: 35
47570174 GCGCAACTTC
* *
47570184 TGTCAGTTTATCTAACTAGTGTTA-GACACAACCAT
1 TGTCAGTTTATCTGACTAGTGCTAGGA-ACAACCAT
* ** * ** *
47570219 CGTCAG-TTATCTGACTACCGCTGGGCGCAA-CTT
1 TGTCAGTTTATCTGACTAGTGCTAGGAACAACCAT
*
47570252 CTGTCAGTTTATCTGAGTAGTGCTAGGAACAACCAT
1 -TGTCAGTTTATCTGACTAGTGCTAGGAACAACCAT
47570288 TGTCA
1 TGTCA
47570293 ATTATCTTGA
Statistics
Matches: 53, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
33 2 0.04
34 20 0.38
35 29 0.55
36 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (35 bp):
TGTCAGTTTATCTGACTAGTGCTAGGAACAACCAT
Found at i:47570832 original size:20 final size:20
Alignment explanation
Indices: 47570807--47570854 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
47570797 AACTGAAATG
47570807 AATGTGATATTAAGTTATGA
1 AATGTGATATTAAGTTATGA
**
47570827 AATGTGATATTGGGTTATGA
1 AATGTGATATTAAGTTATGA
47570847 AATGTGAT
1 AATGTGAT
47570855 TTTATGGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
AATGTGATATTAAGTTATGA
Found at i:47570902 original size:35 final size:35
Alignment explanation
Indices: 47570863--47571117 Score: 157
Period size: 35 Copynumber: 7.4 Consensus size: 35
47570853 ATTTTATGGT
*
47570863 CTAGTGCTGGGCGCAACTTCTGTCAGTTTATCTGA
1 CTAGTGCTGGGCACAACTTCTGTCAGTTTATCTGA
* * * *
47570898 CTAGTGCTGGGCACAACCATC-GT-TGGTTATTTGA
1 CTAGTGCTGGGCACAA-CTTCTGTCAGTTTATCTGA
* ** * *
47570932 CTAGTGTTGGGTGCAACTTTTGTCAATTTATCTGA
1 CTAGTGCTGGGCACAACTTCTGTCAGTTTATCTGA
* * *
47570967 CTA--GCTAGGCACAACCAT-TGTC-GGTTATCTGA
1 CTAGTGCTGGGCACAA-CTTCTGTCAGTTTATCTGA
* ** *** * *
47570999 GTAGCACTGGGGTTAACTTCTATCAGTCTATCTGA
1 CTAGTGCTGGGCACAACTTCTGTCAGTTTATCTGA
* * *
47571034 CTAGTGTTGGGCACAACCATC-GTCAG-TTATCCGA
1 CTAGTGCTGGGCACAA-CTTCTGTCAGTTTATCTGA
* * * *
47571068 CTAGCGTTGGGCACAACTTCTGTTAGTTTATTTGA
1 CTAGTGCTGGGCACAACTTCTGTCAGTTTATCTGA
* *
47571103 CCAGTGTTGGGCACA
1 CTAGTGCTGGGCACA
47571118 CTTTTTATAT
Statistics
Matches: 160, Mismatches: 49, Indels: 22
0.69 0.21 0.10
Matches are distributed among these distances:
32 10 0.06
33 18 0.11
34 59 0.37
35 67 0.42
36 6 0.04
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (35 bp):
CTAGTGCTGGGCACAACTTCTGTCAGTTTATCTGA
Found at i:47571063 original size:69 final size:69
Alignment explanation
Indices: 47570875--47571117 Score: 233
Period size: 69 Copynumber: 3.6 Consensus size: 69
47570865 AGTGCTGGGC
* * ** *
47570875 GCAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTTGGTTATTTGACTAGTGTT
1 GCAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTCGGTTATCTGACTAGACTG
47570940 GGGT
66 GGGT
* * * * *
47570944 GCAACTTTTGTCAATTTATCTGACTA--GCTAGGCACAACCATTGTCGGTTATCTGAGTAGCACT
1 GCAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTCGGTTATCTGACTAG-ACT
47571007 GGGGT
65 GGGGT
* * * * * *
47571012 -TAACTTCTATCAGTCTATCTGACTAGTGTTGGGCACAACCATCGTCAGTTATCCGACTAG-CGT
1 GCAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTCGGTTATCTGACTAGAC-T
* *
47571075 TGGGC
65 GGGGT
* * * * *
47571080 ACAACTTCTGTTAGTTTATTTGACCAGTGTTGGGCACA
1 GCAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACA
47571118 CTTTTTATAT
Statistics
Matches: 140, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
67 49 0.35
68 9 0.06
69 82 0.59
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (69 bp):
GCAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACAACCATCGTCGGTTATCTGACTAGACTG
GGGT
Found at i:47572201 original size:23 final size:23
Alignment explanation
Indices: 47572175--47572232 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
47572165 AATTTTCCCA
*
47572175 ACTGTAAAAAAT-GATTTGTAATT
1 ACTGGAAAAAATAG-TTTGTAATT
* *
47572198 ACTGGAAATAATAGTTTGTAACT
1 ACTGGAAAAAATAGTTTGTAATT
* *
47572221 GCTGGAATAAAT
1 ACTGGAAAAAAT
47572233 TTGCAATATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (23 bp):
ACTGGAAAAAATAGTTTGTAATT
Done.