Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 37 of 322
Found at i:11169745 original size:29 final size:29
Alignment explanation
Indices: 11169703--11169767 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
11169693 CCTGTTCCAT
11169703 TTGCCACCAATTAAAACATAAAAGAGCTA
1 TTGCCACCAATTAAAACATAAAAGAGCTA
11169732 TTGCCACCAATTAAAACATAAAAGAGCTA
1 TTGCCACCAATTAAAACATAAAAGAGCTA
11169761 TTGCCAC
1 TTGCCAC
11169768 ACAAAAAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.22
Consensus pattern (29 bp):
TTGCCACCAATTAAAACATAAAAGAGCTA
Found at i:11170771 original size:15 final size:15
Alignment explanation
Indices: 11170751--11170781 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11170741 GTCATGTAAG
11170751 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
11170766 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
11170781 T
1 T
11170782 ATATTGTTTT
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:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:11170971 original size:17 final size:17
Alignment explanation
Indices: 11170938--11170976 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
11170928 TAAGCTTTTG
11170938 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
11170955 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
11170972 ATTTT
1 ATTTT
11170977 CCACAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:11171742 original size:15 final size:15
Alignment explanation
Indices: 11171718--11171747 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11171708 TGGAGATCGA
*
11171718 GGAAATGGTCGTGGT
1 GGAAAAGGTCGTGGT
11171733 GGAAAAGGTCGTGGT
1 GGAAAAGGTCGTGGT
11171748 CAAGAAGGGA
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:0.23, C:0.07, G:0.47, T:0.23
Consensus pattern (15 bp):
GGAAAAGGTCGTGGT
Found at i:11175129 original size:15 final size:15
Alignment explanation
Indices: 11175109--11175139 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11175099 GTCATGTAAG
11175109 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
11175124 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
11175139 T
1 T
11175140 ATATTGTTTT
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:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:11175329 original size:17 final size:17
Alignment explanation
Indices: 11175296--11175334 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
11175286 TAAGCTTTTG
11175296 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
11175313 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
11175330 ATTTT
1 ATTTT
11175335 CCACATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:11176989 original size:17 final size:17
Alignment explanation
Indices: 11176939--11176989 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
11176929 TTGAAACATG
*
11176939 ATCTTCGAAGATATGCA
1 ATCTTAGAAGATATGCA
*
11176956 ATCTTAGATATGATATGTA
1 ATCTTAGA-A-GATATGCA
11176975 ATCTTAGAAGATATG
1 ATCTTAGAAGATATG
11176990 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
ATCTTAGAAGATATGCA
Found at i:11182146 original size:22 final size:23
Alignment explanation
Indices: 11182099--11182141 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11182089 ATGCAATCTT
* *
11182099 AGATATG-TTATGTAATCTTAAA
1 AGATATGATTTTGTAATCATAAA
11182121 AGATATGATTTTGTAATCATA
1 AGATATGATTTTGTAATCATA
11182142 GAGATTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (23 bp):
AGATATGATTTTGTAATCATAAA
Found at i:11182587 original size:36 final size:36
Alignment explanation
Indices: 11182543--11182618 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
11182533 AGTAGTCAAG
11182543 GGGCAGTGCCATCTAGCATAAGTACCAAACAACCAA
1 GGGCAGTGCCATCTAGCATAAGTACCAAACAACCAA
11182579 GGGCAGTGCCATCTAGCATAAGTACCAAACAACCAA
1 GGGCAGTGCCATCTAGCATAAGTACCAAACAACCAA
11182615 GGGC
1 GGGC
11182619 GAAGCCAACG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.37, C:0.28, G:0.22, T:0.13
Consensus pattern (36 bp):
GGGCAGTGCCATCTAGCATAAGTACCAAACAACCAA
Found at i:11184381 original size:28 final size:27
Alignment explanation
Indices: 11184316--11184373 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
11184306 GGGATTTTGG
11184316 GGGGAAAAAAAGTAAAAAGAAAAGGTT
1 GGGGAAAAAAAGTAAAAAGAAAAGGTT
11184343 GGGGAAAAAAAGTAAAGGAA-AAAAGGTT
1 GGGGAAAAAAAGTAAA--AAGAAAAGGTT
11184371 GGG
1 GGG
11184374 TTACAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 16 0.55
28 11 0.38
29 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.34, T:0.10
Consensus pattern (27 bp):
GGGGAAAAAAAGTAAAAAGAAAAGGTT
Found at i:11184662 original size:114 final size:115
Alignment explanation
Indices: 11184441--11184673 Score: 281
Period size: 114 Copynumber: 2.0 Consensus size: 115
11184431 TTTTGCGGCA
* * * *
11184441 TTTTTCACCTAGCGCCGCTGAAGCCCGACCTATTGCGGCATTTTAACAAAAACGCCACTAAAAAA
1 TTTTTCACCTAGCGCCGCTAAAGCCCGACATATTGCGGCATTTCAACAAAAACGCAACTAAAAAA
* *
11184506 TAAATAAAACGGTGTCATTTTGATTAAAACAAAATAACTTTTTGCGGTGT
66 TAAATAAAACGGCGCCATTTTGATTAAAACAAAATAACTTTTTGCGGTGT
* * * * * *
11184556 TTTTTCA-CTAGCGCCGCTAAAGCCTGACATATTGCGGCATTTCACCTAAAATGTAACTAAGAAA
1 TTTTTCACCTAGCGCCGCTAAAGCCCGACATATTGCGGCATTTCAACAAAAACGCAACTAAAAAA
* * * * * *
11184620 TCCAATAGAATGGCGCCGTTTTTATTAAAACAAAATGA-TTTTTGCGGTGT
66 T-AAATAAAACGGCGCCATTTTGATTAAAACAAAATAACTTTTTGCGGTGT
11184670 TTTT
1 TTTT
11184674 GTACCGCTAT
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
114 64 0.65
115 35 0.35
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (115 bp):
TTTTTCACCTAGCGCCGCTAAAGCCCGACATATTGCGGCATTTCAACAAAAACGCAACTAAAAAA
TAAATAAAACGGCGCCATTTTGATTAAAACAAAATAACTTTTTGCGGTGT
Found at i:11185353 original size:16 final size:16
Alignment explanation
Indices: 11185332--11185364 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11185322 ACCATTTACA
11185332 GCATATTTAGTTGGCT
1 GCATATTTAGTTGGCT
11185348 GCATATTTAGTTGGCT
1 GCATATTTAGTTGGCT
11185364 G
1 G
11185365 TAATAGCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.42
Consensus pattern (16 bp):
GCATATTTAGTTGGCT
Found at i:11188877 original size:12 final size:12
Alignment explanation
Indices: 11188860--11188886 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11188850 ACAATAATTA
11188860 TTGGGTATTGTT
1 TTGGGTATTGTT
11188872 TTGGGTATTGTT
1 TTGGGTATTGTT
11188884 TTG
1 TTG
11188887 CATAAATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.59
Consensus pattern (12 bp):
TTGGGTATTGTT
Found at i:11189129 original size:32 final size:32
Alignment explanation
Indices: 11189088--11189152 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
11189078 CAAGATGACG
11189088 AGATAGATGTAAAAGCCAAGGGCAAATATAAA
1 AGATAGATGTAAAAGCCAAGGGCAAATATAAA
* **
11189120 AGATAGATGTAAAGGGTAAGGGCAAATATAAA
1 AGATAGATGTAAAAGCCAAGGGCAAATATAAA
11189152 A
1 A
11189153 CAAATTGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.52, C:0.06, G:0.25, T:0.17
Consensus pattern (32 bp):
AGATAGATGTAAAAGCCAAGGGCAAATATAAA
Found at i:11193513 original size:46 final size:44
Alignment explanation
Indices: 11193420--11193513 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
11193410 ATTACAACAT
*
11193420 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
***
11193464 CATTCCATTCAACCAAACAGTTGAATTACTTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAGAA-TAC-TATTACAGCTCTATTC
11193510 CATT
1 CATT
11193514 ACAACTCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 22 0.50
45 3 0.07
46 19 0.43
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:11193516 original size:16 final size:16
Alignment explanation
Indices: 11193495--11193550 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
11193485 TGAATTACTT
11193495 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
11193511 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
*
11193527 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
*
11193543 ACTACAGC
1 ATTACAGC
11193551 CAACCAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:11193776 original size:15 final size:15
Alignment explanation
Indices: 11193756--11193808 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
11193746 TCATAAAACC
11193756 AAACCCTTAAACCCT
1 AAACCCTTAAACCCT
* *
11193771 AAACCCCTAACCCCT
1 AAACCCTTAAACCCT
11193786 AAA-CCTTAAACCC-
1 AAACCCTTAAACCCT
*
11193799 CAACCCTTAA
1 AAACCCTTAA
11193809 TCCATCATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 2 0.06
14 14 0.44
15 16 0.50
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACCCTTAAACCCT
Found at i:11193778 original size:43 final size:43
Alignment explanation
Indices: 11193714--11193808 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
11193704 TCTAAGCCCT
* * * * *
11193714 AAACCCCT-AACCCTTATCCCCTAACCTCTAAATCATAAAACC
1 AAACCCTTAAACCCTAAACCCCTAACCCCTAAACCATAAAACC
* *
11193756 AAACCCTTAAACCCTAAACCCCTAACCCCTAAACCTTAAACCC
1 AAACCCTTAAACCCTAAACCCCTAACCCCTAAACCATAAAACC
*
11193799 CAACCCTTAA
1 AAACCCTTAA
11193809 TCCATCATCT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 7 0.16
43 37 0.84
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (43 bp):
AAACCCTTAAACCCTAAACCCCTAACCCCTAAACCATAAAACC
Found at i:11193782 original size:14 final size:14
Alignment explanation
Indices: 11193705--11193790 Score: 59
Period size: 14 Copynumber: 5.9 Consensus size: 14
11193695 ACTAATTAAT
11193705 CTAAGCCCTAAACCC
1 CTAA-CCCTAAACCC
* *
11193720 CTAACCCTTATCCC
1 CTAACCCTAAACCC
*
11193734 CTAACCTCTAAA-TC
1 CTAACC-CTAAACCC
* *
11193748 ATAAAACC-AAACCC
1 CT-AACCCTAAACCC
*
11193762 TTAAACCCTAAACCC
1 CT-AACCCTAAACCC
11193777 CTAACCCCTAAACC
1 CTAA-CCCTAAACC
11193791 TTAAACCCCA
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
13 3 0.05
14 26 0.47
15 26 0.47
ACGTcount: A:0.37, C:0.43, G:0.01, T:0.19
Consensus pattern (14 bp):
CTAACCCTAAACCC
Found at i:11193788 original size:22 final size:22
Alignment explanation
Indices: 11193722--11193804 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 22
11193712 CTAAACCCCT
* * *
11193722 AACCCTTATCCCCTAACCTCTA
1 AACCCTAAACCCCTAACCCCTA
* * * * *
11193744 AATCATAAA-ACCAAACCCTTA
1 AACCCTAAACCCCTAACCCCTA
11193765 AACCCTAAACCCCTAACCCCTA
1 AACCCTAAACCCCTAACCCCTA
*
11193787 AACCTTAAACCCC-AACCC
1 AACCCTAAACCCCTAACCC
11193805 TTAATCCATC
Statistics
Matches: 46, Mismatches: 14, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
21 20 0.43
22 26 0.57
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCCTAAACCCCTAACCCCTA
Found at i:11193795 original size:7 final size:7
Alignment explanation
Indices: 11193756--11193798 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
11193746 TCATAAAACC
11193756 AAACCCTT
1 AAACCC-T
11193764 AAACCCT
1 AAACCCT
11193771 AAACCCCT
1 AAA-CCCT
*
11193779 AACCCCT
1 AAACCCT
*
11193786 AAACCTT
1 AAACCCT
11193793 AAACCC
1 AAACCC
11193799 CAACCCTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 18 0.60
8 12 0.40
ACGTcount: A:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:11193861 original size:14 final size:14
Alignment explanation
Indices: 11193842--11193888 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
11193832 TAGTAACTCC
*
11193842 TAAACCTTAAACCT
1 TAAACCATAAACCT
*
11193856 TAAACCATATA-CT
1 TAAACCATAAACCT
*
11193869 CTAAACCATAAACCC
1 -TAAACCATAAACCT
11193884 TAAAC
1 TAAAC
11193889 TATGTGATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.89
15 1 0.04
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:11193881 original size:28 final size:30
Alignment explanation
Indices: 11193819--11193888 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 30
11193809 TCCATCATCT
11193819 ATAAACCTTAAA-ATAGTAACTCCTAAACC
1 ATAAACCTTAAACATAGTAACTCCTAAACC
*
11193848 TTAAACCTTAAACCATA-T-ACT-CTAAACC
1 ATAAACCTTAAA-CATAGTAACTCCTAAACC
*
11193876 ATAAACCCTAAAC
1 ATAAACCTTAAAC
11193889 TATGTGATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 1 0.03
28 17 0.47
29 14 0.39
30 1 0.03
31 3 0.08
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.24
Consensus pattern (30 bp):
ATAAACCTTAAACATAGTAACTCCTAAACC
Found at i:11194391 original size:114 final size:114
Alignment explanation
Indices: 11194191--11194402 Score: 279
Period size: 114 Copynumber: 1.9 Consensus size: 114
11194181 AGATAAAAAT
* * * **
11194191 ATTTTTTGCGGCGTTTTTAATAAAGCGCCGCTAAAGCTTGATCTATAGCGGCGTTTTTCAAAAAG
1 ATTTTTTGCGGCGTTTTTAATAAACCGCCACTAAAGCTCGATCTATAGCGGCAATTTTCAAAAAG
**
11194256 CGTCTCTAATGTCACTAAAGCTCAACATAAAACTACTGCGCCTTATTGA
66 CGTCTCTAATACCACTAAAGCTCAACATAAAACTACTGCGCCTTATTGA
* *
11194305 ATTTTTTGCTGCGTTTTTCAA-AAACCGCCACTAATA-CTCGATCTATAGCGGTAATTTTCAAAA
1 ATTTTTTGCGGCGTTTTT-AATAAACCGCCACTAA-AGCTCGATCTATAGCGGCAATTTTCAAAA
11194368 AGCG-CTCCTAGA-ACCACTAAAGCTCAACATAAAAC
64 AGCGTCT-CTA-ATACCACTAAAGCTCAACATAAAAC
11194403 GGCAGCATTG
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
113 2 0.02
114 79 0.93
115 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (114 bp):
ATTTTTTGCGGCGTTTTTAATAAACCGCCACTAAAGCTCGATCTATAGCGGCAATTTTCAAAAAG
CGTCTCTAATACCACTAAAGCTCAACATAAAACTACTGCGCCTTATTGA
Found at i:11194539 original size:40 final size:40
Alignment explanation
Indices: 11194429--11194556 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
11194419 CTTTTTTTGC
* *
11194429 GGCGTTTTTCAAAAAGCGTCGCTAATGATCGACCTATAGT
1 GGCGTTTTTCAAAAAGCGTCGCTAATGCTCGATCTATAGT
* * * *
11194469 GGTGTTTCTT--AAAAGTGTCACTAATTCTCGATCTATAGT
1 GGCGTTT-TTCAAAAAGCGTCGCTAATGCTCGATCTATAGT
* * * *
11194508 GGCGTTTTTCAAAAAGCGCCGCTAGTGCTCGATCTGTAGC
1 GGCGTTTTTCAAAAAGCGTCGCTAATGCTCGATCTATAGT
11194548 GGCGTTTTT
1 GGCGTTTTT
11194557 TATCCAAACG
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.03
39 30 0.42
40 37 0.52
41 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (40 bp):
GGCGTTTTTCAAAAAGCGTCGCTAATGCTCGATCTATAGT
Found at i:11196609 original size:3 final size:3
Alignment explanation
Indices: 11196601--11196627 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11196591 ATAGCCTCAA
11196601 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
11196628 TTTTGAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11198734 original size:17 final size:17
Alignment explanation
Indices: 11198712--11198760 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
11198702 AAATTAAAAT
11198712 ATCAATTTTAAGGATAA
1 ATCAATTTTAAGGATAA
*
11198729 ATCAA-TTTAA--A-AT
1 ATCAATTTTAAGGATAA
11198742 ATCAATTTTAAGGATAA
1 ATCAATTTTAAGGATAA
11198759 AT
1 AT
11198761 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
13 6 0.23
14 6 0.23
16 6 0.23
17 8 0.31
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
ATCAATTTTAAGGATAA
Found at i:11198892 original size:15 final size:15
Alignment explanation
Indices: 11198851--11198897 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
11198841 TCCCTTCTTT
11198851 AATTAAAAGATAAATAA
1 AATTAAAAG-T-AATAA
11198868 AATT-AAAGTAATAA
1 AATTAAAAGTAATAA
*
11198882 ATTTAAAAGTAA-AA
1 AATTAAAAGTAATAA
11198896 AA
1 AA
11198898 AAAGATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 11 0.41
15 8 0.30
16 4 0.15
17 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
AATTAAAAGTAATAA
Found at i:11203158 original size:90 final size:90
Alignment explanation
Indices: 11203020--11203324 Score: 303
Period size: 89 Copynumber: 3.4 Consensus size: 90
11203010 CACAACAAAT
* * * ** * * *
11203020 TTTTTTTTACATATACAAGAA-AATACGAACATACTACAAAACTAATATACGAAATTATATAATT
1 TTTTATTTACAGATACAAAAATAATACGAACATTTTACAAAACTGATATACGAAAATATAAAATT
** * * *
11203084 CAACCAACAAATAAAACCGGCTAAA
66 TGACCAACAAATAATACTGACTAAA
* * * ** *
11203109 TTTTATTTACATATAAAAAAATAATACGAACATTTTAGAAATTTGATATACAAAAATATAAAATT
1 TTTTATTTACAGATACAAAAATAATACGAACATTTTACAAAACTGATATACGAAAATATAAAATT
*
11203174 TGACCGACAAATAATA-TGAACTAAAA
66 TGACCAACAAATAATACTG-ACT-AAA
* * * *
11203200 TATT-TTT-CAGATCCAAAAATAATACAAACATTTTACAAAACTGATATACGAAAGTATAAAATT
1 TTTTATTTACAGATACAAAAATAATACGAACATTTTACAAAACTGATATACGAAAATATAAAATT
*
11203263 TGACCAATAAATAATACTGACTAAA
66 TGACCAACAAATAATACTGACTAAA
* * * *
11203288 ATTGATTTACGGATACAAAAATAATACGAATATTTTA
1 TTTTATTTACAGATACAAAAATAATACGAACATTTTA
11203325 AATAGTAGTT
Statistics
Matches: 173, Mismatches: 37, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
88 4 0.02
89 86 0.50
90 77 0.45
91 6 0.03
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.30
Consensus pattern (90 bp):
TTTTATTTACAGATACAAAAATAATACGAACATTTTACAAAACTGATATACGAAAATATAAAATT
TGACCAACAAATAATACTGACTAAA
Found at i:11205140 original size:16 final size:17
Alignment explanation
Indices: 11205119--11205153 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
11205109 TTATATAAGA
*
11205119 TAAATAAAACTAT-TTT
1 TAAATAAAAATATATTT
11205135 TAAATAAAAATATATTT
1 TAAATAAAAATATATTT
11205152 TA
1 TA
11205154 TTTGAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATAAAAATATATTT
Found at i:11205905 original size:97 final size:92
Alignment explanation
Indices: 11205777--11206006 Score: 237
Period size: 97 Copynumber: 2.4 Consensus size: 92
11205767 TTTTTTTTGG
* * * * * *
11205777 TTTTTTAAATTTAAAATTTTTAAAAACTATATTTTATTTGATGGAGTCATTAATAATGGCGCCAA
1 TTTTTTAAATTT-AAA-TATAAAAAATTATATTTTATTTG-TGGAGTCATTAAGAATGACACCAA
* * * *
11205842 CAGTGTATTGTACTTGTTTTTTTTTTAAATGCGT
63 CAATGTA-AGTACCTG---TTTTTTAAAATGCGT
* *
11205876 TTTTTT-AATTTAAATATAAAAAAATTATATTTTATTTTGTGGAGTCATTAAGAATGATACCACC
1 TTTTTTAAATTTAAATAT-AAAAAATTATATTTTA-TTTGTGGAGTCATTAAGAATGACACCAAC
*
11205940 AATGTAAGTACCTGTTTTTTAAAATGTGT
64 AATGTAAGTACCTGTTTTTTAAAATGCGT
* *
11205969 TTTTTTAAATTTAAATATAAAAAATAAAATTTTATTTG
1 TTTTTTAAATTTAAATATAAAAAATTATATTTTATTTG
11206007 GTGAAGCCAT
Statistics
Matches: 113, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
92 4 0.04
93 33 0.29
94 11 0.10
96 8 0.07
97 42 0.37
98 9 0.08
99 6 0.05
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (92 bp):
TTTTTTAAATTTAAATATAAAAAATTATATTTTATTTGTGGAGTCATTAAGAATGACACCAACAA
TGTAAGTACCTGTTTTTTAAAATGCGT
Found at i:11207257 original size:17 final size:17
Alignment explanation
Indices: 11207231--11207270 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
11207221 TTAGAATTGG
* *
11207231 ATTAAAAAATTTATTTA
1 ATTAATAAATTAATTTA
11207248 ATTAATAAATTAATTTA
1 ATTAATAAATTAATTTA
*
11207265 GTTAAT
1 ATTAAT
11207271 TCAATCAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTAATAAATTAATTTA
Found at i:11207283 original size:22 final size:21
Alignment explanation
Indices: 11207238--11207295 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
11207228 TGGATTAAAA
*
11207238 AATTTATTTAATTAATAAATT
1 AATTTAATTAATTAATAAATT
* *
11207259 AATTTAGTTAATTCAATCAATT
1 AATTTAATTAATT-AATAAATT
11207281 AATTTAATTAATTAA
1 AATTTAATTAATTAA
11207296 ATAGATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (21 bp):
AATTTAATTAATTAATAAATT
Found at i:11215544 original size:72 final size:70
Alignment explanation
Indices: 11215399--11215537 Score: 208
Period size: 72 Copynumber: 2.0 Consensus size: 70
11215389 ACTCCATTTG
* *
11215399 AAGTAAATTGATTCGAAATCTATCAGATAATTTAAATTTTGCCATCTCATTTAAATAAAATCATC
1 AAGTAAATTGATTCGAAATCTATCAGACAATTTAAATTTT--CATCTCATTCAAATAAAATCATC
11215464 ATAATAA
64 ATAATAA
* * *
11215471 AAGTGAATTGATTCGAAATCTATCAGACAATTTAAATTTT-ATCTCGTTCAAATAAAATCATCGT
1 AAGTAAATTGATTCGAAATCTATCAGACAATTTAAATTTTCATCTCATTCAAATAAAATCATCAT
11215535 AAT
66 AAT
11215538 GATAAAAAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
69 24 0.39
72 38 0.61
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (70 bp):
AAGTAAATTGATTCGAAATCTATCAGACAATTTAAATTTTCATCTCATTCAAATAAAATCATCAT
AATAA
Found at i:11215927 original size:31 final size:31
Alignment explanation
Indices: 11215863--11215927 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
11215853 AGTTTATATC
** * **
11215863 TTTATAATTTTTAAAGGATTAAATTATTTTT
1 TTTATAATTTTTAAAGGAGCAAAGTATAATT
*
11215894 TTTATCATTTTTAAAGGAGCAAAGTATAATT
1 TTTATAATTTTTAAAGGAGCAAAGTATAATT
11215925 TTT
1 TTT
11215928 CATTACTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.52
Consensus pattern (31 bp):
TTTATAATTTTTAAAGGAGCAAAGTATAATT
Found at i:11225897 original size:2 final size:2
Alignment explanation
Indices: 11225890--11225915 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11225880 TTACTCACCA
11225890 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
11225916 AATGCAGGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:11231489 original size:27 final size:27
Alignment explanation
Indices: 11231451--11231505 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
11231441 GCGAATAGAA
11231451 AACGTTGTAGACTGAGTACCATCATCT
1 AACGTTGTAGACTGAGTACCATCATCT
11231478 AACGTTGTAGACTGAGTACCATCATCT
1 AACGTTGTAGACTGAGTACCATCATCT
11231505 A
1 A
11231506 TGTTGTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (27 bp):
AACGTTGTAGACTGAGTACCATCATCT
Found at i:11240144 original size:23 final size:23
Alignment explanation
Indices: 11240118--11240162 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11240108 GAGTTTAATA
*
11240118 TTAAGAGTTAAATCAACAATTAT
1 TTAAAAGTTAAATCAACAATTAT
* *
11240141 TTAAAATTTAAATCAACTATTA
1 TTAAAAGTTAAATCAACAATTA
11240163 AATTAAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (23 bp):
TTAAAAGTTAAATCAACAATTAT
Found at i:11240170 original size:23 final size:23
Alignment explanation
Indices: 11240125--11240169 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
11240115 ATATTAAGAG
*
11240125 TTAAATCAACAATTATTTAAAAT
1 TTAAATCAACAATTAATTAAAAT
*
11240148 TTAAATCAACTATTAAATTAAA
1 TTAAATCAACAATT-AATTAAA
11240170 TAGATTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAAATCAACAATTAATTAAAAT
Found at i:11240238 original size:8 final size:8
Alignment explanation
Indices: 11240222--11240272 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
11240212 TTAATTAACT
11240222 AATTA-AA
1 AATTATAA
11240229 AATTATAA
1 AATTATAA
*
11240237 AATATTTAA
1 AAT-TATAA
*
11240246 AA-TAAAA
1 AATTATAA
11240253 ACATTATAA
1 A-ATTATAA
11240262 AATTATAA
1 AATTATAA
11240270 AAT
1 AAT
11240273 ATTGATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
7 9 0.25
8 16 0.44
9 11 0.31
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (8 bp):
AATTATAA
Found at i:11240260 original size:25 final size:23
Alignment explanation
Indices: 11240226--11240273 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
11240216 TTAACTAATT
*
11240226 AAAAATTATAAAATATTTAAAATA
1 AAAAATTATAAAAT-TATAAAATA
11240250 AAAACATTATAAAATTATAAAATA
1 AAAA-ATTATAAAATTATAAAATA
11240274 TTGATTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAATTATAAAATTATAAAATA
Found at i:11242388 original size:22 final size:22
Alignment explanation
Indices: 11242363--11242427 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
11242353 AAATTTTATT
11242363 TATTTCTATTATTTAAAACTAA
1 TATTTCTATTATTTAAAACTAA
*
11242385 TATTTGTA-TA-TT--AA-T-A
1 TATTTCTATTATTTAAAACTAA
11242401 TATTTCTATTATTTAAAACTAA
1 TATTTCTATTATTTAAAACTAA
11242423 TATTT
1 TATTT
11242428 GTATATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
16 8 0.23
17 3 0.09
18 4 0.11
20 4 0.11
21 3 0.09
22 13 0.37
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (22 bp):
TATTTCTATTATTTAAAACTAA
Found at i:11242414 original size:38 final size:38
Alignment explanation
Indices: 11242363--11242439 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
11242353 AAATTTTATT
11242363 TATTTCTATTATTTAAAACTAATATTTGTATATTAATA
1 TATTTCTATTATTTAAAACTAATATTTGTATATTAATA
11242401 TATTTCTATTATTTAAAACTAATATTTGTATATTAATA
1 TATTTCTATTATTTAAAACTAATATTTGTATATTAATA
11242439 T
1 T
11242440 GAAGTATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (38 bp):
TATTTCTATTATTTAAAACTAATATTTGTATATTAATA
Found at i:11246427 original size:21 final size:21
Alignment explanation
Indices: 11246401--11246444 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
11246391 AGACGAGCAA
* *
11246401 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
11246422 TACTCCAAAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
11246443 TA
1 TA
11246445 ACAGCCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:11251521 original size:16 final size:16
Alignment explanation
Indices: 11251500--11251549 Score: 73
Period size: 16 Copynumber: 3.0 Consensus size: 16
11251490 TTTATTTTTT
11251500 ATATAAAAAATTAAAA
1 ATATAAAAAATTAAAA
*
11251516 ATATAATAAATTAAAA
1 ATATAAAAAATTAAAA
11251532 ATACTAAAAACATTAAAA
1 ATA-TAAAAA-ATTAAAA
11251550 TAAATGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 18 0.60
17 5 0.17
18 7 0.23
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (16 bp):
ATATAAAAAATTAAAA
Found at i:11253420 original size:17 final size:17
Alignment explanation
Indices: 11253398--11253433 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
11253388 TAATATTGGA
11253398 GAATTTGATCA-ATACTT
1 GAATTTG-TCAGATACTT
11253415 GAATTTGTCAGATACTT
1 GAATTTGTCAGATACTT
11253432 GA
1 GA
11253434 TTCTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (17 bp):
GAATTTGTCAGATACTT
Found at i:11254320 original size:28 final size:30
Alignment explanation
Indices: 11254256--11254319 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
11254246 TTCAATGCGG
*
11254256 ATTTTTAAAAGAATTAAATATATATTTTTT
1 ATTTTTAAAAGAATAAAATATATATTTTTT
*
11254286 ATTTTTAAAA-AATAAAATGTAT-TTTTATT
1 ATTTTTAAAAGAATAAAATATATATTTT-TT
11254315 ATTTT
1 ATTTT
11254320 ATAGAGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 4 0.13
29 17 0.55
30 10 0.32
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
ATTTTTAAAAGAATAAAATATATATTTTTT
Found at i:11260973 original size:75 final size:75
Alignment explanation
Indices: 11260892--11261038 Score: 222
Period size: 75 Copynumber: 2.0 Consensus size: 75
11260882 TAAGATCTAT
* * * *
11260892 TTTTCTTGAGTTTGAATTTTAGATTCAGAGTAATTATAATTGCAATAATCTAGCTATTATATTTC
1 TTTTCTTGAGTTTGAATTCTAGATTCAGAGTAACTATAATTGCAATAATATAGCTATTATAATTC
11260957 AAATCTAGAA
66 AAATCTAGAA
** * *
11260967 TTTTCTTGAGTTTGAATTCTAGATTTGGAGTAACTATAATTGCAATAATATAGTTGTTATAATTC
1 TTTTCTTGAGTTTGAATTCTAGATTCAGAGTAACTATAATTGCAATAATATAGCTATTATAATTC
11261032 AAATCTA
66 AAATCTA
11261039 AAAGTTGAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (75 bp):
TTTTCTTGAGTTTGAATTCTAGATTCAGAGTAACTATAATTGCAATAATATAGCTATTATAATTC
AAATCTAGAA
Found at i:11262989 original size:30 final size:31
Alignment explanation
Indices: 11262947--11263004 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
11262937 AATAGTTCAT
*
11262947 TTCTTTTATAATT-TGTCCCTTTTATTTTAG
1 TTCTTTTATAATTAAGTCCCTTTTATTTTAG
*
11262977 TTCTTTCT-TAATTAAGTCCTTTTTATTT
1 TTCTTT-TATAATTAAGTCCCTTTTATTT
11263005 ATTCATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.17, C:0.14, G:0.05, T:0.64
Consensus pattern (31 bp):
TTCTTTTATAATTAAGTCCCTTTTATTTTAG
Found at i:11264473 original size:135 final size:133
Alignment explanation
Indices: 11264200--11264578 Score: 390
Period size: 135 Copynumber: 2.8 Consensus size: 133
11264190 ACAACTATAA
* * *
11264200 AAAAAAAAATCTTTAAAACGAAGGCTAGATTCGATATTTGGCAATTCACGGAATAGTACCCTAAC
1 AAAAAAAATTCTTTAAAACGAAGGC--GATTCGATATTTGGCAATTCACGGAATCGTGCCCTAAC
* * * * *
11264265 GTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCAAATATCCCTTCACAATTTCACTCATGC
64 GTGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCAAATATCCCTTCACAATTTCACGCAGGC
*
11264330 CTTTT
129 CTTCT
*
11264335 AAAAAAAATTCTTTAAAACGAAGGCGATGTGCGATATTTGGCAATTCATGGAATCGTGCCCTAAC
1 AAAAAAAATTCTTTAAAACGAAGGCGAT-T-CGATATTTGGCAATTCACGGAATCGTGCCCTAAC
* * * *
11264400 GTGCTGGGTTGCAACTTCTCGTTTGTTTAAAATAATCAAATATCCC-TCTATATTTTCACGCAGG
64 GTGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCAAATATCCCTTC-ACAATTTCACGCAGG
*
11264464 TCTTCT
128 CCTTCT
* * ** * * * * * * *
11264470 ---AAAAATCCTTTCAAACGAAGGTAATACTCGGTGTTTGACAGTTC-GGGAATCATGCCCTATC
1 AAAAAAAATTCTTTAAAACGAAGGCGAT--TCGATATTTGGCAATTCACGGAATCGTGCCCTAAC
** * *
11264531 GTGCTGGGTTGTGATTTCTCGTTTGTTCAAAATAATCGAATATTCCTT
64 GTGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCAAATATCCCTT
11264579 TAGGTTTTCA
Statistics
Matches: 206, Mismatches: 33, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
131 54 0.26
132 34 0.17
133 4 0.02
134 3 0.01
135 111 0.54
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (133 bp):
AAAAAAAATTCTTTAAAACGAAGGCGATTCGATATTTGGCAATTCACGGAATCGTGCCCTAACGT
GCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCAAATATCCCTTCACAATTTCACGCAGGCCT
TCT
Found at i:11264622 original size:131 final size:131
Alignment explanation
Indices: 11264384--11264622 Score: 302
Period size: 131 Copynumber: 1.8 Consensus size: 131
11264374 GGCAATTCAT
* *
11264384 GGAATCGTGCCCTAACGTGCTGGGTTGCAACTTCTCGTTTGTTTAAAATAATCAAATATCCCTCT
1 GGAATCATGCCCTAACGTGCTGGGTTGCAACTTCTCGTTTGTTCAAAATAATCAAATATCCCTCT
* *
11264449 ATATTTTCACGCAGGTCTTCTAAAAATCCTTTCAAACGAAGGTAATACTCGGTGTTTGACAGTTC
66 AGATTTTCACGCAGGTCTTCTAAAAATCCTTTCAAACAAAGGTAATACTCGGTGTTTGACAGTTC
11264514 G
131 G
* ** * * * *
11264515 GGAATCATGCCCTATCGTGCTGGGTTGTGATTTCTCGTTTGTTCAAAATAATCGAATATTCCTTT
1 GGAATCATGCCCTAACGTGCTGGGTTGCAACTTCTCGTTTGTTCAAAATAATCAAATATCCCTCT
* ** * *
11264580 AGGTTTTCATTCATGT-TTATTAAAAA-CCTTTCAAAACAAAGGT
66 AGATTTTCACGCAGGTCTT-CTAAAAATCCTTTC-AAACAAAGGT
11264623 GATGTTTGAT
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
130 8 0.09
131 82 0.91
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (131 bp):
GGAATCATGCCCTAACGTGCTGGGTTGCAACTTCTCGTTTGTTCAAAATAATCAAATATCCCTCT
AGATTTTCACGCAGGTCTTCTAAAAATCCTTTCAAACAAAGGTAATACTCGGTGTTTGACAGTTC
G
Found at i:11282121 original size:40 final size:40
Alignment explanation
Indices: 11282050--11282145 Score: 106
Period size: 40 Copynumber: 2.5 Consensus size: 40
11282040 CCATCTCCGT
* *
11282050 CCAACCCAACACACC--ATGTGGGGATAAAATCGACCCAG
1 CCAACCCTACACACCATATATGGGGATAAAATCGACCCAG
* ** * * *
11282088 CCATCCCTGTACACCATATATGGGGTTATAATCGACCCAT
1 CCAACCCTACACACCATATATGGGGATAAAATCGACCCAG
11282128 CCAACCCTACACACCATA
1 CCAACCCTACACACCATA
11282146 AAGTATCGCA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
38 11 0.24
40 34 0.76
ACGTcount: A:0.33, C:0.35, G:0.14, T:0.18
Consensus pattern (40 bp):
CCAACCCTACACACCATATATGGGGATAAAATCGACCCAG
Found at i:11286899 original size:25 final size:24
Alignment explanation
Indices: 11286833--11286899 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
11286823 TATTATTTTG
* *
11286833 TTAATTATCTATTTAAAATATTATT
1 TTAATTAT-AATTTTAAATATTATT
* * * *
11286858 TTAAATAAAATTATAAATTTTATTT
1 TTAATTATAATTTTAAATATTA-TT
11286883 TTAATTATAATTTTAAA
1 TTAATTATAATTTTAAA
11286900 AATATTTGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATTATAATTTTAAATATTATT
Found at i:11294059 original size:26 final size:26
Alignment explanation
Indices: 11294008--11294061 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
11293998 AATATGAAAT
* *
11294008 AAATAGATGATGTACTATATTGATCA
1 AAATAGATGATGTACAATATTCATCA
*
11294034 AAATGGATGAT-TACAATATTTCATCA
1 AAATAGATGATGTACAATA-TTCATCA
11294060 AA
1 AA
11294062 GTTTCTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (26 bp):
AAATAGATGATGTACAATATTCATCA
Found at i:11294663 original size:14 final size:13
Alignment explanation
Indices: 11294644--11294707 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 13
11294634 TTATATTAAC
*
11294644 TTAATATTTAAGTA
1 TTAATATATAA-TA
11294658 TTAATATATAATA
1 TTAATATATAATA
11294671 -TAATATATTATTATA
1 TTAATATA-TA--ATA
*
11294686 TT-ATACATAATA
1 TTAATATATAATA
11294698 -TAATATATAA
1 TTAATATATAA
11294708 AACATAAGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.02
12 17 0.40
13 4 0.10
14 12 0.29
15 7 0.17
16 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (13 bp):
TTAATATATAATA
Found at i:11295027 original size:17 final size:17
Alignment explanation
Indices: 11295005--11295039 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11294995 ATTCAAATTA
11295005 GAATTGAGAAAAAGATT
1 GAATTGAGAAAAAGATT
* *
11295022 GAATTGTGAAATAGATT
1 GAATTGAGAAAAAGATT
11295039 G
1 G
11295040 CAATAAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.29
Consensus pattern (17 bp):
GAATTGAGAAAAAGATT
Found at i:11295906 original size:22 final size:22
Alignment explanation
Indices: 11295877--11295933 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
11295867 TAGCACGTTA
11295877 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCAC-TCT
* * *
11295900 -GTGCTCTCAGTATAGCACTTT
1 AGTGCTCTCTGTTTAGCACTCT
11295921 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
11295934 CGTTTGTGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTCT
Found at i:11299891 original size:3 final size:3
Alignment explanation
Indices: 11299885--11299928 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
11299875 CTATGATGAT
* * * *
11299885 GAG GAG GAG GAG GAG GAG GCG GAG GTG GAG GTG GAG GTG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
11299929 TTCTCAGCTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.25, C:0.02, G:0.66, T:0.07
Consensus pattern (3 bp):
GAG
Found at i:11300395 original size:5 final size:5
Alignment explanation
Indices: 11300378--11300408 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
11300368 TCTATCTATT
*
11300378 AGAAA AGAGA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
11300409 CATGAAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:11302984 original size:42 final size:42
Alignment explanation
Indices: 11302937--11303022 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
11302927 GTTTTCTCAA
11302937 AGATAATAAAGTGGGCTTGCATGCATGCATGTATTATGTATG
1 AGATAATAAAGTGGGCTTGCATGCATGCATGTATTATGTATG
11302979 AGATAATAAAGTGGGCTTGCATGCATGCATGTATTATGTATG
1 AGATAATAAAGTGGGCTTGCATGCATGCATGTATTATGTATG
11303021 AG
1 AG
11303023 TTTTCACAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.33
Consensus pattern (42 bp):
AGATAATAAAGTGGGCTTGCATGCATGCATGTATTATGTATG
Found at i:11307586 original size:20 final size:21
Alignment explanation
Indices: 11307544--11307585 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
11307534 CTACACAGAA
11307544 TCAATTTTTTTTTCTTTTTTT
1 TCAATTTTTTTTTCTTTTTTT
11307565 TCAATTTTTTTTTCTTTTTTT
1 TCAATTTTTTTTTCTTTTTTT
11307586 CTTTTTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (21 bp):
TCAATTTTTTTTTCTTTTTTT
Found at i:11307592 original size:10 final size:10
Alignment explanation
Indices: 11307548--11307585 Score: 51
Period size: 9 Copynumber: 3.7 Consensus size: 10
11307538 ACAGAATCAA
11307548 TTTTTTTTTC
1 TTTTTTTTTC
11307558 -TTTTTTTTC
1 TTTTTTTTTC
11307567 AATTTTTTTTTC
1 --TTTTTTTTTC
11307579 TTTTTTT
1 TTTTTTT
11307586 CTTTTTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 9 0.36
10 7 0.28
12 9 0.36
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:11312649 original size:21 final size:19
Alignment explanation
Indices: 11312625--11312668 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
11312615 TCGACTTTCG
11312625 TTCTTTTCCCTTTTCTAATTT
1 TTCTTTTCCCTTTTCT--TTT
* *
11312646 TTCTTTTTCTTTTTCTTTT
1 TTCTTTTCCCTTTTCTTTT
11312665 TTCT
1 TTCT
11312669 AATAAAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (19 bp):
TTCTTTTCCCTTTTCTTTT
Found at i:11331679 original size:31 final size:31
Alignment explanation
Indices: 11331641--11331701 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
11331631 ATAGCAACGC
*
11331641 TTATAAACGCCACTAAAACTATTTGTGGCGT
1 TTATAAACGCCACTAAAACTATTTGCGGCGT
*
11331672 TTATAAACGCCATTAAAACTATTTGCGGCG
1 TTATAAACGCCACTAAAACTATTTGCGGCG
11331702 CTTTTACAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (31 bp):
TTATAAACGCCACTAAAACTATTTGCGGCGT
Found at i:11331839 original size:42 final size:42
Alignment explanation
Indices: 11331771--11331932 Score: 182
Period size: 42 Copynumber: 3.9 Consensus size: 42
11331761 TTATGTAAAA
* *
11331771 AAACGCCGCTAAAGGTCATTACCTTTAGCGGCACTTCCCCAC
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTCCCCAC
* * * * *
11331813 AAACGCCGCTAAAGATCATGATCTTTAACGGTGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGC-TTCCCCAC
* * *
11331856 AAACGCCGTTAAAGGTCATGACCTTTAGCAGCGCTTCCCCAA
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTCCCCAC
** * *
11331898 AAACATCGCTAAAGGTCATG-CTTTTAGCGACGCTT
1 AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTT
11331933 TCCTTAAAAA
Statistics
Matches: 98, Mismatches: 21, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
41 12 0.12
42 51 0.52
43 35 0.36
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTCCCCAC
Found at i:11331942 original size:42 final size:42
Alignment explanation
Indices: 11331769--11331957 Score: 123
Period size: 42 Copynumber: 4.5 Consensus size: 42
11331759 GTTTATGTAA
* * * * *
11331769 AAAAACGCCGCTAAAGGTCATTACCTTTAGCGGCACTTCCCC
1 AAAAACACTGCTAAAGGTCATGACCTTTAGCAGCGCTTCCCC
* * * * * * * * *
11331811 ACAAACGCCGCTAAAGATCATGATCTTTAACGGTGCTTTTCCC
1 AAAAACACTGCTAAAGGTCATGACCTTTAGCAGCGC-TTCCCC
* * * *
11331854 ACAAACGCCGTTAAAGGTCATGACCTTTAGCAGCGCTTCCCC
1 AAAAACACTGCTAAAGGTCATGACCTTTAGCAGCGCTTCCCC
* **
11331896 AAAAACA-TCGCTAAAGGTCATG-CTTTTAGC-GACGCTTTCCTT
1 AAAAACACT-GCTAAAGGTCATGACCTTTAGCAG-CGC-TTCCCC
*
11331938 AAAAACACTGCTAAAAGTCA
1 AAAAACACTGCTAAAGGTCA
11331958 CCACTATCCC
Statistics
Matches: 119, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
40 1 0.01
41 10 0.08
42 72 0.61
43 36 0.30
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (42 bp):
AAAAACACTGCTAAAGGTCATGACCTTTAGCAGCGCTTCCCC
Found at i:11337046 original size:37 final size:37
Alignment explanation
Indices: 11337004--11337078 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
11336994 AAAAAGTAGC
* *
11337004 ACGAACAACAAAAATAAGTGCAATAAGCATGATTGCA
1 ACGAACAAAAAAAATAAGGGCAATAAGCATGATTGCA
11337041 ACGAACAAAAAAAATAAGGGCAATAAGCATGATTGCA
1 ACGAACAAAAAAAATAAGGGCAATAAGCATGATTGCA
11337078 A
1 A
11337079 GTAAACAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.53, C:0.15, G:0.17, T:0.15
Consensus pattern (37 bp):
ACGAACAAAAAAAATAAGGGCAATAAGCATGATTGCA
Found at i:11338643 original size:14 final size:14
Alignment explanation
Indices: 11338624--11338653 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11338614 AAATCAAAGG
11338624 GATGGAGATTTAGA
1 GATGGAGATTTAGA
11338638 GATGGAGATTTAGA
1 GATGGAGATTTAGA
11338652 GA
1 GA
11338654 AACAGGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (14 bp):
GATGGAGATTTAGA
Found at i:11338738 original size:14 final size:14
Alignment explanation
Indices: 11338721--11338751 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
11338711 AATGATGGAA
11338721 GGATTTTGATTTGG
1 GGATTTTGATTTGG
11338735 GGATTTTGATTTGG
1 GGATTTTGATTTGG
11338749 GGA
1 GGA
11338752 AAAATTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (14 bp):
GGATTTTGATTTGG
Found at i:11339812 original size:22 final size:21
Alignment explanation
Indices: 11339787--11339850 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
11339777 GATTTAGGCC
**
11339787 TAAATCCCTAACCCTTAGCCCT
1 TAAA-CCCTAACCCTTAAACCT
*
11339809 TAAACCCCTAACCCCTAAACCT
1 TAAA-CCCTAACCCTTAAACCT
11339831 TAAACCCTAACCCTTAAACC
1 TAAACCCTAACCCTTAAACC
11339851 ATAATTCAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 15 0.41
22 22 0.59
ACGTcount: A:0.34, C:0.42, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAACCCTAACCCTTAAACCT
Found at i:11339840 original size:14 final size:14
Alignment explanation
Indices: 11339821--11339850 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11339811 AACCCCTAAC
11339821 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
*
11339835 CCCTAACCCTTAAA
1 CCCTAAACCTTAAA
11339849 CC
1 CC
11339851 ATAATTCAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (14 bp):
CCCTAAACCTTAAA
Found at i:11339914 original size:14 final size:14
Alignment explanation
Indices: 11339895--11339933 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
11339885 ATAGTAACTT
* *
11339895 CTAAACCATATACC
1 CTAAACCATAAACA
11339909 CTAAACCATAAACA
1 CTAAACCATAAACA
*
11339923 CTAAACTATAA
1 CTAAACCATAA
11339934 TGATAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAAACCATAAACA
Found at i:11340372 original size:40 final size:40
Alignment explanation
Indices: 11340267--11340382 Score: 171
Period size: 40 Copynumber: 2.9 Consensus size: 40
11340257 AGTGGCTTTG
* * *
11340267 TCTATAGTGGCGTTTTTCAAAAAGCACCACTAATGCTTGA
1 TCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTTGA
11340307 TCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCT-A
1 TCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCT-TGA
* *
11340347 TCTATAGCGGCGTTTTGCAAAAAGCGCCGCAAATGC
1 TCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGC
11340383 AACTAAAGCT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 69 0.99
41 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (40 bp):
TCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTTGA
Found at i:11340558 original size:81 final size:80
Alignment explanation
Indices: 11340413--11340586 Score: 215
Period size: 81 Copynumber: 2.1 Consensus size: 80
11340403 TTAATTTTTT
* * *
11340413 GCGGCGTTTTTTTATAAAGCGCCACTAATAGTCGACCTATAGCGGCGTTTTCCCAAAAGTGCCGC
1 GCGGCG-TTTTTTAAAAAGCGCCACTAATAGTCGACCTATAGCAGCGTTTTCCCAAAAGCGCCGC
* * *
11340478 TAATGCTCGATCTATA
65 TAATACTCAATCTACA
* * **
11340494 GCGGCGTTATTTTAAAAAGCGCCGCTAATGGTCGACCTATAGCAGCGTTTT-TTAAGAAGCGCCG
1 GCGGCGTT-TTTTAAAAAGCGCCACTAATAGTCGACCTATAGCAGCGTTTTCCCAA-AAGCGCCG
11340558 CTAATACTCAATCTACA
64 CTAATACTCAATCTACA
*
11340575 GTGGCGTTTTTT
1 GCGGCGTTTTTT
11340587 GTTCAAGTAC
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
80 8 0.10
81 72 0.90
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (80 bp):
GCGGCGTTTTTTAAAAAGCGCCACTAATAGTCGACCTATAGCAGCGTTTTCCCAAAAGCGCCGCT
AATACTCAATCTACA
Found at i:11340586 original size:40 final size:40
Alignment explanation
Indices: 11340413--11340586 Score: 179
Period size: 40 Copynumber: 4.3 Consensus size: 40
11340403 TTAATTTTTT
* * *
11340413 GCGGCGTTTTTTTATAAAGCGCCACTAATAG-TCGACCTATA
1 GCGGCG-TTTTTTAAAAAGCGCCGCTAAT-GCTCGATCTATA
*** *
11340454 GCGGCGTTTTCCCAAAAGTGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
* *
11340494 GCGGCGTTATTTTAAAAAGCGCCGCTAATGGTCGACCTATA
1 GCGGCGTT-TTTTAAAAAGCGCCGCTAATGCTCGATCTATA
* * * * *
11340535 GCAGCGTTTTTTAAGAAGCGCCGCTAATACTCAATCTACA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
*
11340575 GTGGCGTTTTTT
1 GCGGCGTTTTTT
11340587 GTTCAAGTAC
Statistics
Matches: 109, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.01
40 69 0.63
41 39 0.36
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (40 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
Found at i:11342422 original size:22 final size:22
Alignment explanation
Indices: 11342392--11342433 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11342382 AGATTATTAT
*
11342392 GATTTTATTTAGATTTATTTCA
1 GATTATATTTAGATTTATTTCA
**
11342414 GATTATATTTTTATTTATTT
1 GATTATATTTAGATTTATTT
11342434 TTTAGAGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (22 bp):
GATTATATTTAGATTTATTTCA
Found at i:11344071 original size:41 final size:41
Alignment explanation
Indices: 11344002--11344136 Score: 164
Period size: 41 Copynumber: 3.3 Consensus size: 41
11343992 TTTGAGATAA
* * * *
11344002 TATATCAAGCTTTGTGCCTAGCAAGCTTCATGCCGGTGATT
1 TATATCAGGCTTTGTACCTAGTAGGCTTCATGCCGGTGATT
* * *
11344043 TATATCAGGCTTTGTAACTAGTAGGCTTCGTGCTGGTGATT
1 TATATCAGGCTTTGTACCTAGTAGGCTTCATGCCGGTGATT
* *
11344084 TATATCAGGCTTTGTACCTA-TCAGGTTTCATGTCGGTGATT
1 TATATCAGGCTTTGTACCTAGT-AGGCTTCATGCCGGTGATT
*
11344125 TTTATCAGGCTT
1 TATATCAGGCTT
11344137 CGAGCCTAGC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 1 0.01
41 79 0.99
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (41 bp):
TATATCAGGCTTTGTACCTAGTAGGCTTCATGCCGGTGATT
Found at i:11348249 original size:45 final size:45
Alignment explanation
Indices: 11348185--11348271 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
11348175 TCGATCTATG
*
11348185 GACTCCCTCATTAGGTTTCACCCTAATCCGGCAAAATCTTGTATA
1 GACTCCCTCATTAGGTTTCACCCTAATCCGACAAAATCTTGTATA
11348230 GACTCCCTCATTAGGTTTCACCCTAATCCGACAAAATCTTGT
1 GACTCCCTCATTAGGTTTCACCCTAATCCGACAAAATCTTGT
11348272 CACCCTATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (45 bp):
GACTCCCTCATTAGGTTTCACCCTAATCCGACAAAATCTTGTATA
Found at i:11349627 original size:21 final size:20
Alignment explanation
Indices: 11349599--11349638 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
11349589 CTCTTGAAAT
* *
11349599 AGGGAACACGCCTGTGTGGA
1 AGGGAACACACCCGTGTGGA
11349619 AGGGCAACACACCCGTGTGG
1 AGGG-AACACACCCGTGTGG
11349639 TCATTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (20 bp):
AGGGAACACACCCGTGTGGA
Found at i:11350847 original size:47 final size:47
Alignment explanation
Indices: 11350778--11351142 Score: 198
Period size: 47 Copynumber: 7.6 Consensus size: 47
11350768 GGTATAATGC
* *
11350778 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAAT
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAAGT
** * * *
11350825 CGATGCCATGTCCCAAACATGGTCTTACACTTACT-ATCGAAATCGAGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATC--CATC-AAGT
* * ****
11350874 CAAAGCCATGTCCTGGGCATGGTCTTACACTGGCTCATCCATCAAGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAAGT
* * * * *
11350921 CGATGCCATGTTCCAAGCATGGTCTTACACTGACT-ATCGAAATCTAGGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATC--CATC-AAGT
* * * *
11350970 CGACT-TCATGT-CCAGACATGGTCTTACACTAGCTC-TCACAT-ATCCGT
1 CGA-TGCCATGTCCCAAACATGGTCTTACACTGGCTCATC-CATCA--AGT
* ** *
11351017 GCCGATGCCATGTCCCAGACATGGTCTTACACAAGTTC-T-CAT-AATGT
1 --CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAA-GT
* * *
11351064 GGCCGATG-CATGTCTCAGACAT-GTCTTACACTGGCTC-TCGTC-TCAATGC
1 ---CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATC--CATCAA-GT
*
11351113 CGATGCCATGTCCCAGACATGGTCTTACAC
1 CGATGCCATGTCCCAAACATGGTCTTACAC
11351143 AAGTTCTCAT
Statistics
Matches: 251, Mismatches: 44, Indels: 45
0.74 0.13 0.13
Matches are distributed among these distances:
45 1 0.00
46 24 0.10
47 95 0.38
48 52 0.21
49 52 0.21
50 27 0.11
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATCAAGT
Found at i:11350980 original size:96 final size:95
Alignment explanation
Indices: 11350782--11351142 Score: 319
Period size: 96 Copynumber: 3.8 Consensus size: 95
11350772 TAATGCCGAT
11350782 GCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAAATCGATGCCATGTCCCAAACATGG
1 GCCATGT-CCAGACATGGTCTTACACTGGCTCATCCATCAAATCGATGCCATGTCCCAAACATGG
*
11350847 TCTTACACTTACTATCGAAATCGAGGCCAAA
65 TCTTACACTGACTATCGAAATCGAGGCCAAA
* * * * *
11350878 GCCATGTCCTGGGCATGGTCTTACACTGGCTCATCCATCAAGTCGATGCCATGTTCCAAGCATGG
1 GCCATGTCC-AGACATGGTCTTACACTGGCTCATCCATCAAATCGATGCCATGTCCCAAACATGG
* * * *
11350943 TCTTACACTGACTATCGAAATCTAGGTCGAC
65 TCTTACACTGACTATCGAAATCGAGGCCAAA
** * ** *
11350974 TTCATGTCCAGACATGGTCTTACACTAGCTC-TCACAT-ATCCGTGCCGATGCCATGTCCCAGAC
1 GCCATGTCCAGACATGGTCTTACACTGGCTCATC-CATCA--AAT--CGATGCCATGTCCCAAAC
* * * * * *
11351037 ATGGTCTTACAC-AAGT-TCTCATAAT-GTGGCCGAT
61 ATGGTCTTACACTGACTATC-GA-AATCGAGGCCAAA
*
11351071 G-CATGTCTCAGACAT-GTCTTACACTGGCTC-TCGTC-TC-AATGCCGATGCCATGTCCCAGAC
1 GCCATGTC-CAGACATGGTCTTACACTGGCTCATC--CATCAAAT--CGATGCCATGTCCCAAAC
11351131 ATGGTCTTACAC
61 ATGGTCTTACAC
11351143 AAGTTCTCAT
Statistics
Matches: 223, Mismatches: 31, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
94 36 0.16
95 24 0.11
96 117 0.52
97 16 0.07
98 30 0.13
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (95 bp):
GCCATGTCCAGACATGGTCTTACACTGGCTCATCCATCAAATCGATGCCATGTCCCAAACATGGT
CTTACACTGACTATCGAAATCGAGGCCAAA
Found at i:11351131 original size:94 final size:95
Alignment explanation
Indices: 11350976--11351192 Score: 357
Period size: 94 Copynumber: 2.3 Consensus size: 95
11350966 AGGTCGACTT
**
11350976 CATGTC-CAGACATGGTCTTACACTAGCTCTCACATATCCGTGCCGATGCCATGTCCCAGACATG
1 CATGTCTCAGACAT-GTCTTACACTAGCTCT-ACATATCAATGCCGATGCCATGTCCCAGACATG
11351040 GTCTTACACAAGTTCTCATAATGTGGCCGATG
64 GTCTTACACAAGTTCTCATAATGTGGCCGATG
* * *
11351072 CATGTCTCAGACATGTCTTACACTGGCTCT-CGTCTCAATGCCGATGCCATGTCCCAGACATGGT
1 CATGTCTCAGACATGTCTTACACTAGCTCTACATATCAATGCCGATGCCATGTCCCAGACATGGT
11351136 CTTACACAAGTTCTCATAATGTGGCCGATG
66 CTTACACAAGTTCTCATAATGTGGCCGATG
11351166 CATGTCTCAGACATGTCTTACACTAGC
1 CATGTCTCAGACATGTCTTACACTAGC
11351193 ACACAAACAA
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
94 86 0.75
96 21 0.18
97 7 0.06
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (95 bp):
CATGTCTCAGACATGTCTTACACTAGCTCTACATATCAATGCCGATGCCATGTCCCAGACATGGT
CTTACACAAGTTCTCATAATGTGGCCGATG
Found at i:11351170 original size:47 final size:47
Alignment explanation
Indices: 11350976--11351188 Score: 226
Period size: 47 Copynumber: 4.5 Consensus size: 47
11350966 AGGTCGACTT
* * *
11350976 CATGT-CCAGACATGGTCTTACACTAGCTCTCACATATCCGTGCCGATGC
1 CATGTCCCAGACATGGTCTTACACAAGTTCTCATA-AT--GTGCCGATGC
11351025 CATGTCCCAGACATGGTCTTACACAAGTTCTCATAATGTGGCCGATG-
1 CATGTCCCAGACATGGTCTTACACAAGTTCTCATAATGT-GCCGATGC
* **
11351072 CATGTCTCAGACAT-GTCTTACACTGGCTCTCGTC-TCAA--TGCCGATGC
1 CATGTCCCAGACATGGTCTTACACAAG-T-TC-TCAT-AATGTGCCGATGC
11351119 CATGTCCCAGACATGGTCTTACACAAGTTCTCATAATGTGGCCGATG-
1 CATGTCCCAGACATGGTCTTACACAAGTTCTCATAATGT-GCCGATGC
*
11351166 CATGTCTCAGACAT-GTCTTACAC
1 CATGTCCCAGACATGGTCTTACAC
11351189 TAGCACACAA
Statistics
Matches: 142, Mismatches: 10, Indels: 27
0.79 0.06 0.15
Matches are distributed among these distances:
45 4 0.03
46 29 0.20
47 45 0.32
48 27 0.19
49 11 0.08
50 26 0.18
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
CATGTCCCAGACATGGTCTTACACAAGTTCTCATAATGTGCCGATGC
Found at i:11353854 original size:13 final size:12
Alignment explanation
Indices: 11353822--11353871 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
11353812 AACCATATAT
11353822 AAATAA-TAA-A
1 AAATAATTAATA
11353832 AAATAA-TAATA
1 AAATAATTAATA
*
11353843 ATAGTAATTAATA
1 A-AATAATTAATA
11353856 GAAATAATTAATA
1 -AAATAATTAATA
11353869 AAA
1 AAA
11353872 CAACAGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.26
11 2 0.06
12 7 0.21
13 15 0.44
14 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (12 bp):
AAATAATTAATA
Found at i:11354198 original size:14 final size:14
Alignment explanation
Indices: 11354179--11354209 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11354169 ATATATTTAC
*
11354179 ATAATAAATATATA
1 ATAATAAATAAATA
11354193 ATAATAAATAAATA
1 ATAATAAATAAATA
11354207 ATA
1 ATA
11354210 TAATAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAAATAAATA
Found at i:11354210 original size:19 final size:18
Alignment explanation
Indices: 11354181--11354217 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
11354171 ATATTTACAT
11354181 AATAAATATATAATAATA
1 AATAAATATATAATAATA
11354199 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
11354218 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:11354255 original size:67 final size:64
Alignment explanation
Indices: 11354192--11354326 Score: 163
Period size: 63 Copynumber: 2.2 Consensus size: 64
11354182 ATAAATATAT
* * * *
11354192 AATAATAAATAAA-TAATATAATAAT-ATGAAACAT-AA-CTCAAATTAATTAAATTAATAG-AA
1 AATAATAAAAAAACAAATATAAAAATAATGAAA-ATAAAGCTCAAATTAATTAAATTAACAGTAA
* *
11354252 AATAATAAAAAAACAAATATAAAAATAATGAGAATAAAGCTCAAATTAATTAATTTAACAGTAA
1 AATAATAAAAAAACAAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAA
*
11354316 AATAACAAAAA
1 AATAATAAAAA
11354327 TAAAAAAAGG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
60 12 0.19
61 12 0.19
62 7 0.11
63 20 0.32
64 12 0.19
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (64 bp):
AATAATAAAAAAACAAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAA
Found at i:11356105 original size:18 final size:18
Alignment explanation
Indices: 11356082--11356154 Score: 60
Period size: 18 Copynumber: 4.0 Consensus size: 18
11356072 ATAACAAGTA
* *
11356082 GGGTGATGGAGTTAGTGG
1 GGGTGATAGAGGTAGTGG
11356100 GGGTGATAGAGGTAGTGG
1 GGGTGATAGAGGTAGTGG
* *
11356118 ATGGT-TTAGTAGGGT-GTGG
1 -GGGTGATAG-A-GGTAGTGG
*
11356137 GGGTGATGGAGGTAGTGG
1 GGGTGATAGAGGTAGTGG
11356155 ATAGTTTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
17 3 0.07
18 27 0.63
19 10 0.23
20 3 0.07
ACGTcount: A:0.18, C:0.00, G:0.55, T:0.27
Consensus pattern (18 bp):
GGGTGATAGAGGTAGTGG
Found at i:11356133 original size:29 final size:30
Alignment explanation
Indices: 11356093--11356183 Score: 76
Period size: 37 Copynumber: 2.8 Consensus size: 30
11356083 GGTGATGGAG
* *
11356093 TTAGTGGGGGTGATAGAGGTAGTGGATGGT
1 TTAGTAGGGGTGATAGAGGTAGTGGATAGT
*
11356123 TTAGTAGGGTGTGGGGGTGATGGAGGTAGTGGATAGT
1 TTAGTA-------GGGGTGATAGAGGTAGTGGATAGT
*
11356160 TTAGTA-GGGTGATAGAGTTAGTGG
1 TTAGTAGGGGTGATAGAGGTAGTGG
11356184 GGGTGATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
29 16 0.33
30 5 0.10
37 28 0.57
ACGTcount: A:0.21, C:0.00, G:0.48, T:0.31
Consensus pattern (30 bp):
TTAGTAGGGGTGATAGAGGTAGTGGATAGT
Found at i:11356149 original size:37 final size:37
Alignment explanation
Indices: 11356096--11356170 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
11356086 GATGGAGTTA
*
11356096 GTGGGGGTGATAGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATAGAGGTAGTGGATAGTTTAGTAGGGT
*
11356133 GTGGGGGTGATGGAGGTAGTGGATAGTTTAGTAGGGT
1 GTGGGGGTGATAGAGGTAGTGGATAGTTTAGTAGGGT
11356170 G
1 G
11356171 ATAGAGTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.29
Consensus pattern (37 bp):
GTGGGGGTGATAGAGGTAGTGGATAGTTTAGTAGGGT
Found at i:11356698 original size:133 final size:133
Alignment explanation
Indices: 11356460--11356897 Score: 615
Period size: 133 Copynumber: 3.3 Consensus size: 133
11356450 GATCTGCTGT
** ** * *
11356460 AATTTGATCTGCTTTACTCCTGCTCAGTAAAGATAAGATCTTGTATGTTTAGCTTGCTCCACTCC
1 AATTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGTA--TTTAGCCTGCTCCACTCC
* ** ** *
11356525 TGCTCAGTGAATATAAGGCTAATGATTGGAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
64 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
*
11356590 ATCAA
129 ACCAA
* ** * *
11356595 ATTTTGATCTGCTTTACTCCTGCTCTGCGAAGATAAGATCTAGTATATAGCCTGCTCCACTCCTG
1 AATTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
*
11356660 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCGGATACATGGAGATAAGATTCAC
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
11356725 CAA
131 CAA
* * *
11356728 AACTTGATCTGCTCCGCTCTTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
1 AATTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
* * *
11356793 CTCAATGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGTCGATACATAGAGATAAGATTCAC
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
11356858 CAA
131 CAA
* *
11356861 AATTTAATCTGCTCCACTCCTGCTCAGTGAAGATAAG
1 AATTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAG
11356898 GCTGGTGGCT
Statistics
Matches: 271, Mismatches: 32, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
133 231 0.85
135 40 0.15
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (133 bp):
AATTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
CAA
Found at i:11356881 original size:90 final size:90
Alignment explanation
Indices: 11356779--11356987 Score: 330
Period size: 90 Copynumber: 2.3 Consensus size: 90
11356769 AGTATTTAGC
* *
11356779 CTGCTCCACTCCTGCTCAATGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGTCGATACATA
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATA
11356844 GAGATAAGA-TTCACCAAAATTTAAT
66 GAGATAAGACTT-ACCAAAATTTAAT
* * *
11356869 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATTTGTTCCATTGCCGATACATG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATA
* *
11356934 GAGATAAGACTTGCCAAAATTTGAT
66 GAGATAAGACTTACCAAAATTTAAT
*
11356959 CTGCTTCACTCCTGCTCAGTGAAGATAAG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAG
11356988 ATCTAGTATG
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
90 108 0.98
91 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (90 bp):
CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATA
GAGATAAGACTTACCAAAATTTAAT
Found at i:11356892 original size:223 final size:224
Alignment explanation
Indices: 11356646--11357122 Score: 744
Period size: 223 Copynumber: 2.1 Consensus size: 224
11356636 AGTATATAGC
*
11356646 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCGGATACATG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATG
* *
11356711 GAGATAAGA-TTCACCAAAACTTGATCTGCTCCGCTCTTGCTCAGCGAAGATAAGATCTAGTA-T
66 GAGATAAGACTT-ACCAAAACTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGTAGT
* *
11356774 TTAGCCTGCTCCACTCCTGCTCAATGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGTCGAT
130 TTAGCCTGCCCCACTCCTGCTCAATGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGAT
11356839 ACATAGAGATAAGA-TTCACCAAAATTTAAT
195 ACATAGAGATAAGACTT-ACCAAAATTTAAT
* *
11356869 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATTTGTTCCATTGCCGATACATG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATG
* * * *
11356934 GAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATGT
66 GAGATAAGACTTACCAAAACTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGTA-GT
* * *
11356999 TTAGCCTGCCCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATTTGTTCCATTGCCGAT
130 TTAGCCTGCCCCACTCCTGCTCAATGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGAT
* * *
11357064 ACATGGAGATAAGACTTGCCAAAATTTGAT
195 ACATAGAGATAAGACTTACCAAAATTTAAT
*
11357094 CTGCTTCACTCCTGCTCAGTGAAGATAAG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAG
11357123 ATCTAGTATG
Statistics
Matches: 232, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
223 115 0.50
224 2 0.01
225 113 0.49
226 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (224 bp):
CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATG
GAGATAAGACTTACCAAAACTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATCTAGTAGTT
TAGCCTGCCCCACTCCTGCTCAATGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATA
CATAGAGATAAGACTTACCAAAATTTAAT
Found at i:11357027 original size:135 final size:135
Alignment explanation
Indices: 11356869--11357302 Score: 687
Period size: 135 Copynumber: 3.2 Consensus size: 135
11356859 AAAATTTAAT
11356869 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATTTGTTCCATTGCCGATACATG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATTTGTTCCATTGCCGATACATG
11356934 GAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATGT
66 GAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATGT
11356999 TTAGC
131 TTAGC
*
11357004 CTGCCCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATTTGTTCCATTGCCGATACATG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATTTGTTCCATTGCCGATACATG
11357069 GAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATGT
66 GAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATGT
11357134 TTAGC
131 TTAGC
* * * *
11357139 CTGCTCCACTCCTGCTCAGTGAATATAAGACTGGTGGCTGAAATCTGCTCCATTGCCGATACATG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATTTGTTCCATTGCCGATACATG
* * * * * * * *
11357204 GAGATAATA-TTCACCAAAATTTAATCTACTCCGCTCCTGCTCAGCGAAGATAAGATTTAGTA--
66 GAGATAAGACTT-GCCAAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATG
11357266 TTTAGC
130 TTTAGC
* * *
11357272 CTGCTCTACTTCTGCTCAGTG-GGATAAGGCT
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCT
11357303 TGCCAAAATC
Statistics
Matches: 279, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
132 7 0.03
133 25 0.09
134 2 0.01
135 245 0.88
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (135 bp):
CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATTTGTTCCATTGCCGATACATG
GAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATGT
TTAGC
Found at i:11358612 original size:25 final size:25
Alignment explanation
Indices: 11358574--11358648 Score: 91
Period size: 25 Copynumber: 2.9 Consensus size: 25
11358564 TTGCTTTGCT
11358574 TTTCTTTTT-CTTTTTTATTTTTCTC
1 TTTCTTTTTCCTTTTTT-TTTTTCTC
11358599 -TTCTTTTTCCTTTTTCTTTTTTCTC
1 TTTCTTTTTCCTTTTT-TTTTTTCTC
11358624 TTTCCTTTTTCTCTTCTTTTTTTTT
1 TTT-CTTTTTC-CTT-TTTTTTTTT
11358649 GAAAGTGAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
24 8 0.18
25 14 0.32
26 3 0.07
27 7 0.16
28 9 0.20
29 3 0.07
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTCTTTTTCCTTTTTTTTTTTCTC
Found at i:11358615 original size:13 final size:13
Alignment explanation
Indices: 11358573--11358647 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
11358563 TTTGCTTTGC
*
11358573 TTTTCTTTTTCTT
1 TTTTCTTTTTCCT
*
11358586 TTTTATTTTT-C-
1 TTTTCTTTTTCCT
*
11358597 TCTTCTTTTTCCT
1 TTTTCTTTTTCCT
*
11358610 TTTTCTTTTTTCT
1 TTTTCTTTTTCCT
*
11358623 CTTTCCTTTTTCTCT
1 -TTTTCTTTTTC-CT
11358638 TCTTT-TTTTT
1 T-TTTCTTTTT
11358648 TGAAAGTGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
11 8 0.17
12 1 0.02
13 20 0.42
14 15 0.31
15 4 0.08
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTTCCT
Found at i:11358633 original size:38 final size:37
Alignment explanation
Indices: 11358573--11358644 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
11358563 TTTGCTTTGC
* *
11358573 TTTTCTTTTTCTTTTTTATTTTTCTCTTCTTTTTCCT
1 TTTTCTTTTTCTCTTTCATTTTTCTCTTCTTTTTCCT
*
11358610 TTTTCTTTTTTCTCTTTCCTTTTTCTCTTCTTTTT
1 TTTTC-TTTTTCTCTTTCATTTTTCTCTTCTTTTT
11358645 TTTTGAAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 5 0.16
38 26 0.84
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (37 bp):
TTTTCTTTTTCTCTTTCATTTTTCTCTTCTTTTTCCT
Found at i:11361191 original size:21 final size:21
Alignment explanation
Indices: 11361165--11361209 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11361155 GCTGGCTCAT
*
11361165 CATGTTGTTCTGTGACTCAAG
1 CATGTTGTTCTGGGACTCAAG
* *
11361186 CATGTTTTTCTGGGACTCTAG
1 CATGTTGTTCTGGGACTCAAG
11361207 CAT
1 CAT
11361210 TTAATCCCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCAAG
Found at i:11364982 original size:21 final size:21
Alignment explanation
Indices: 11364942--11364993 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
11364932 CTTCGCTTAA
** *
11364942 AAATATATATATTTACATAAT
1 AAATATATATAAATAAATAAT
11364963 AAATATATATAAATAAATAAT
1 AAATATATATAAATAAATAAT
11364984 ATAATA-ATAT
1 A-AATATATAT
11364994 GAAACATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATATATATAAATAAATAAT
Found at i:11365397 original size:18 final size:18
Alignment explanation
Indices: 11365374--11365446 Score: 69
Period size: 18 Copynumber: 4.0 Consensus size: 18
11365364 ATAACAAGTA
*
11365374 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
11365392 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
* * *
11365410 ATGGTTTAATAG-GGT-GTGG
1 --GG-GTGATGGAGGTAGTGG
11365429 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
11365447 ATAGTTTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
16 4 0.09
17 5 0.12
18 21 0.49
19 4 0.09
20 5 0.12
21 4 0.09
ACGTcount: A:0.18, C:0.00, G:0.55, T:0.27
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:11365425 original size:29 final size:30
Alignment explanation
Indices: 11365391--11365476 Score: 75
Period size: 37 Copynumber: 2.7 Consensus size: 30
11365381 GGAGTTAGTG
*
11365391 GGGGTGATGGAGGTAGTGGATGGTTTAATA
1 GGGGTGATGGAGGTAGTGGATAGTTTAATA
*
11365421 GGGTGTGGGGGTGATGGAGGTAGTGGATAGTTTAGTA
1 -------GGGGTGATGGAGGTAGTGGATAGTTTAATA
*
11365458 -GGGTGATGGAGTTAGTGGA
1 GGGGTGATGGAGGTAGTGGA
11365477 GGTGGAGGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 18 0.39
37 28 0.61
ACGTcount: A:0.21, C:0.00, G:0.50, T:0.29
Consensus pattern (30 bp):
GGGGTGATGGAGGTAGTGGATAGTTTAATA
Found at i:11365438 original size:37 final size:37
Alignment explanation
Indices: 11365388--11365462 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
11365378 GATGGAGTTA
*
11365388 GTGGGGGTGATGGAGGTAGTGGATGGTTTAATAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATAGTTTAATAGGGT
*
11365425 GTGGGGGTGATGGAGGTAGTGGATAGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATAGTTTAATAGGGT
11365462 G
1 G
11365463 ATGGAGTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.29
Consensus pattern (37 bp):
GTGGGGGTGATGGAGGTAGTGGATAGTTTAATAGGGT
Found at i:11369874 original size:23 final size:23
Alignment explanation
Indices: 11369848--11369893 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
11369838 TTCATAGAAA
11369848 ATTTAA-TTAAATAATATATTTTT
1 ATTTAACTTAAA-AATATATTTTT
11369871 ATTTAACTTTAAAAATATATTTT
1 ATTTAAC-TTAAAAATATATTTT
11369894 AAAGTATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.29
24 10 0.48
25 5 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTAACTTAAAAATATATTTTT
Found at i:11370023 original size:23 final size:26
Alignment explanation
Indices: 11370000--11370057 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
11369990 TAAATTCAAA
11370000 ATTT-ATTATCATAAAAATAAAAAAATT
1 ATTTAATTATCATAAAAAT-AAAAAA-T
* *
11370027 ATTTAATTATCATAAAAATAAATATT
1 ATTTAATTATCATAAAAATAAAAAAT
11370053 ATTTA
1 ATTTA
11370058 TCTTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 8 0.29
28 14 0.50
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (26 bp):
ATTTAATTATCATAAAAATAAAAAAT
Found at i:11377355 original size:145 final size:145
Alignment explanation
Indices: 11377092--11377382 Score: 555
Period size: 145 Copynumber: 2.0 Consensus size: 145
11377082 TAGTTTCAGG
11377092 GAAAATTAACGGATCTTAATTTCAAGTTCTGTAGCTAAAGATATAAATAATTTAGTGACTATGAC
1 GAAAATTAACGGATCTTAATTTCAAGTTCTGTAGCTAAAGATATAAATAATTTAGTGACTATGAC
11377157 GCAAATGGACAGTTTTGAATATACATAAGTAAATAGTGAAATTATTGATAATGTTACTTGTTGCA
66 GCAAATGGACAGTTTTGAATATACATAAGTAAATAGTGAAATTATTGATAATGTTACTTGTTGCA
11377222 TGTTATATAAATTAA
131 TGTTATATAAATTAA
* * *
11377237 GAAAATTAGCGGATCTTAATTTCGAGTTCTGTAGCTTAAGATATAAATAATTTAGTGACTATGAC
1 GAAAATTAACGGATCTTAATTTCAAGTTCTGTAGCTAAAGATATAAATAATTTAGTGACTATGAC
11377302 GCAAATGGACAGTTTTGAATATACATAAGTAAATAGTGAAATTATTGATAATGTTACTTGTTGCA
66 GCAAATGGACAGTTTTGAATATACATAAGTAAATAGTGAAATTATTGATAATGTTACTTGTTGCA
11377367 TGTTATATAAATTAA
131 TGTTATATAAATTAA
11377382 G
1 G
11377383 GATGTGGAAT
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 143 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (145 bp):
GAAAATTAACGGATCTTAATTTCAAGTTCTGTAGCTAAAGATATAAATAATTTAGTGACTATGAC
GCAAATGGACAGTTTTGAATATACATAAGTAAATAGTGAAATTATTGATAATGTTACTTGTTGCA
TGTTATATAAATTAA
Found at i:11383907 original size:17 final size:17
Alignment explanation
Indices: 11383887--11383920 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11383877 AGATTTAGGT
11383887 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
11383904 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
11383921 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:11384069 original size:31 final size:29
Alignment explanation
Indices: 11384034--11384098 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
11384024 GTCATCACTT
11384034 CGTAATAAAATAGTAATATAAGTGACTAAAA
1 CGTAATAAAATA--AATATAAGTGACTAAAA
***
11384065 CGTAATATTTTAAATATAAGTGACTAAAA
1 CGTAATAAAATAAATATAAGTGACTAAAA
*
11384094 TGTAA
1 CGTAA
11384099 CATGAGACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 21 0.70
31 9 0.30
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (29 bp):
CGTAATAAAATAAATATAAGTGACTAAAA
Found at i:11389257 original size:26 final size:26
Alignment explanation
Indices: 11389181--11389624 Score: 323
Period size: 26 Copynumber: 16.7 Consensus size: 26
11389171 AAGACAAATG
*
11389181 AAATAAAATAATATACAAAAACAATTTA
1 AAAT-AAATAATATA-TAAAACAATTTA
* * **
11389209 GAGTAAAT-A-ATATAAAA-GGTTTA
1 AAATAAATAATATATAAAACAATTTA
* * *
11389232 AAATAGATAATAAATAAAATAATTTA
1 AAATAAATAATATATAAAACAATTTA
*
11389258 AAATTTAAAATAA-ATAATTCAAAAAAATGGTTCA
1 AAA--T-AAATAATAT-A-T-AAAACAAT--TT-A
* **
11389292 AAATAAACAATATATGAAAATGATTTA
1 AAATAAATAATATAT-AAAACAATTTA
* *
11389319 ACATAAATAA-AGTATAAAACAATTTG
1 AAATAAATAATA-TATAAAACAATTTA
**
11389345 AAATAAATAAT-T-TAATGCAATTTA
1 AAATAAATAATATATAAAACAATTTA
* * *
11389369 AAATAAACAATACATAAAACAATCTA
1 AAATAAATAATATATAAAACAATTTA
* * * *
11389395 AAAGAAATAATATGTGGAAAAAAATCTA
1 AAATAAATAATATAT--AAAACAATTTA
*
11389423 AAATAAATAATATATATAAATCAGTTTA
1 AAATAAATAATATATA-AAA-CAATTTA
* *
11389451 AAATAAAATAATATATAAAGCAATTCA
1 AAAT-AAATAATATATAAAACAATTTA
11389478 AAATAAATAATATATAAAACAATTTA
1 AAATAAATAATATATAAAACAATTTA
* **
11389504 AAATAAATAATAATCTAAAATGATTTA
1 AAATAAATAAT-ATATAAAACAATTTA
11389531 AAATAAAT-A-ATATAAAACAATTTA
1 AAATAAATAATATATAAAACAATTTA
* * *
11389555 ATATAAATAATATATAAGA-ATTTTA
1 AAATAAATAATATATAAAACAATTTA
* **
11389580 AAATAAATAAAATATAAAACTGTTTA
1 AAATAAATAATATATAAAACAATTTA
*
11389606 AAATAAATAATGTATAAAA
1 AAATAAATAATATATAAAA
11389625 AATGAATAAA
Statistics
Matches: 327, Mismatches: 63, Indels: 54
0.74 0.14 0.12
Matches are distributed among these distances:
23 9 0.03
24 43 0.13
25 33 0.10
26 107 0.33
27 48 0.15
28 39 0.12
29 18 0.06
30 8 0.02
31 13 0.04
32 3 0.01
33 2 0.01
34 4 0.01
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (26 bp):
AAATAAATAATATATAAAACAATTTA
Found at i:11389622 original size:51 final size:51
Alignment explanation
Indices: 11389291--11389622 Score: 266
Period size: 51 Copynumber: 6.4 Consensus size: 51
11389281 AAAATGGTTC
* * *
11389291 AAAATAAACAATATATGAA-AATGATTTAACATAAATAAAGTATAAAACAATTT
1 AAAATAAATAATATAT-AAGAAT--TTTAAAATAAATAAAATATAAAACAATTT
* * * * *
11389344 GAAATAAATAAT-T-TAATGCAA-TTTAAAATAAACAATACATAAAACAATCT
1 AAAATAAATAATATATAA-G-AATTTTAAAATAAATAAAATATAAAACAATTT
* * * * * * *
11389394 AAAAGAAATAATATGTGGAAAAAAATCTAAAATAAATAATATATATAAATCAGTTT
1 AAAATAAATAATATAT---AAGAATTTTAAAATAAATAA-A-ATATAAAACAATTT
* *
11389450 AAAATAAAATAATATATAAAGCAA-TTCAAAATAAATAATATATAAAACAATTT
1 AAAAT-AAATAATATAT-AAG-AATTTTAAAATAAATAAAATATAAAACAATTT
*
11389503 AAAATAAATAATAATCTAA-AATGATTTAAAATAAAT--AATATAAAACAATTT
1 AAAATAAATAAT-ATATAAGAAT--TTTAAAATAAATAAAATATAAAACAATTT
* **
11389554 AATATAAATAATATATAAGAATTTTAAAATAAATAAAATATAAAACTGTTT
1 AAAATAAATAATATATAAGAATTTTAAAATAAATAAAATATAAAACAATTT
*
11389605 AAAATAAATAATGTATAA
1 AAAATAAATAATATATAA
11389623 AAAATGAATA
Statistics
Matches: 224, Mismatches: 35, Indels: 42
0.74 0.12 0.14
Matches are distributed among these distances:
49 12 0.05
50 42 0.19
51 59 0.26
52 11 0.05
53 45 0.20
54 12 0.05
55 17 0.08
56 16 0.07
57 10 0.04
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (51 bp):
AAAATAAATAATATATAAGAATTTTAAAATAAATAAAATATAAAACAATTT
Found at i:11389632 original size:18 final size:19
Alignment explanation
Indices: 11389605--11389646 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
11389595 AAAACTGTTT
*
11389605 AAAATAAAT-AATGTATAA
1 AAAATAAATAAATATATAA
*
11389623 AAAATGAATAAATATATAA
1 AAAATAAATAAATATATAA
11389642 AAAAT
1 AAAAT
11389647 TTAAAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAATAAATAAATATATAA
Found at i:11392440 original size:18 final size:18
Alignment explanation
Indices: 11392405--11392441 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11392395 AGTGAGTGGA
*
11392405 ACAAAAGCATGGTTAGTG
1 ACAAAAGCATGGTGAGTG
*
11392423 ACAAAAGCATTGTGAGTG
1 ACAAAAGCATGGTGAGTG
11392441 A
1 A
11392442 AAATTATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.22
Consensus pattern (18 bp):
ACAAAAGCATGGTGAGTG
Found at i:11396094 original size:22 final size:22
Alignment explanation
Indices: 11396066--11396108 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
11396056 GAATTGCATC
11396066 GCAATGAGCAAGCCCCGAAGTT
1 GCAATGAGCAAGCCCCGAAGTT
11396088 GCAATGAGCAAGCCCCGAAGT
1 GCAATGAGCAAGCCCCGAAGT
11396109 CGTGATGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.12
Consensus pattern (22 bp):
GCAATGAGCAAGCCCCGAAGTT
Found at i:11396618 original size:17 final size:18
Alignment explanation
Indices: 11396585--11396621 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11396575 TCAAAACCGG
11396585 TCGGTTAACCGAAAAAAT
1 TCGGTTAACCGAAAAAAT
* *
11396603 TCGGTTAATCAAAAAAAT
1 TCGGTTAACCGAAAAAAT
11396621 T
1 T
11396622 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (18 bp):
TCGGTTAACCGAAAAAAT
Found at i:11396741 original size:13 final size:13
Alignment explanation
Indices: 11396723--11396747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11396713 CAAGTACCCA
11396723 ACCCAACCCAATT
1 ACCCAACCCAATT
11396736 ACCCAACCCAAT
1 ACCCAACCCAAT
11396748 CATAAAAATT
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:11396811 original size:5 final size:6
Alignment explanation
Indices: 11396772--11396815 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
11396762 ATAATTTATT
*
11396772 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA
11396816 GAAACATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 29 0.85
8 5 0.15
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:11396856 original size:9 final size:9
Alignment explanation
Indices: 11396838--11396914 Score: 100
Period size: 9 Copynumber: 8.6 Consensus size: 9
11396828 TTTATACAAA
11396838 TAATTCGGT
1 TAATTCGGT
*
11396847 TAATTTGGT
1 TAATTCGGT
*
11396856 TAATTCGAT
1 TAATTCGGT
* *
11396865 TAATTTGGG
1 TAATTCGGT
*
11396874 TAATTCGGG
1 TAATTCGGT
11396883 TAATTCGGT
1 TAATTCGGT
*
11396892 TAATTCGAT
1 TAATTCGGT
11396901 TAATTCGGT
1 TAATTCGGT
11396910 TAATT
1 TAATT
11396915 TTATACTTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (9 bp):
TAATTCGGT
Found at i:11396878 original size:36 final size:36
Alignment explanation
Indices: 11396838--11396914 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
11396828 TTTATACAAA
* * *
11396838 TAATTCGGTTAATTTGGTTAATTCGATTAATTTGGG
1 TAATTCGGGTAATTCGGTTAATTCGATTAATTCGGG
*
11396874 TAATTCGGGTAATTCGGTTAATTCGATTAATTCGGT
1 TAATTCGGGTAATTCGGTTAATTCGATTAATTCGGG
11396910 TAATT
1 TAATT
11396915 TTATACTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (36 bp):
TAATTCGGGTAATTCGGTTAATTCGATTAATTCGGG
Found at i:11397868 original size:18 final size:18
Alignment explanation
Indices: 11397845--11397895 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
11397835 TAATAGTCAG
*
11397845 TTATTCAGTAACGAT-ATA
1 TTATTCAGTAACAATCA-A
11397863 TTATTCAGTAACAATCAA
1 TTATTCAGTAACAATCAA
*
11397881 TTATTCAATAACAAT
1 TTATTCAGTAACAAT
11397896 TTTTTTTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 29 0.97
19 1 0.03
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:11397933 original size:18 final size:18
Alignment explanation
Indices: 11397912--11397964 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
11397902 TATGCAATAG
11397912 CAGTTAGTTA-TCTAGTAA
1 CAGTTAGTTATTC-AGTAA
*
11397930 CAGTCAGTTATTCAGTAA
1 CAGTTAGTTATTCAGTAA
*
11397948 CAGTTAATTATTCAGTA
1 CAGTTAGTTATTCAGTA
11397965 CCTTTATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 29 0.94
19 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (18 bp):
CAGTTAGTTATTCAGTAA
Found at i:11399259 original size:15 final size:16
Alignment explanation
Indices: 11399239--11399268 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11399229 TTCTTCCTCC
11399239 TTTCTTT-TTCTTTTG
1 TTTCTTTATTCTTTTG
11399254 TTTCTTTATTCTTTT
1 TTTCTTTATTCTTTT
11399269 ATAACATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTCTTTATTCTTTTG
Done.