Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 57 of 168
Found at i:16200522 original size:13 final size:13
Alignment explanation
Indices: 16200488--16200524 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
16200478 ACATTAATCA
16200488 AAAGAAAAGAAAG
1 AAAGAAAAGAAAG
16200501 AAA-ATAAAGAAAG
1 AAAGA-AAAGAAAG
16200514 AAAGAAAAGAA
1 AAAGAAAAGAA
16200525 GTTTAACGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.05
13 20 0.91
14 1 0.05
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (13 bp):
AAAGAAAAGAAAG
Found at i:16203557 original size:2 final size:2
Alignment explanation
Indices: 16203550--16203574 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16203540 CAATAATAAA
16203550 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
16203575 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16205083 original size:8 final size:8
Alignment explanation
Indices: 16205070--16205097 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
16205060 TATACTAAAC
16205070 AATAAAAT
1 AATAAAAT
16205078 AATAAAAT
1 AATAAAAT
16205086 AATAAAAT
1 AATAAAAT
16205094 AATA
1 AATA
16205098 TTTAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AATAAAAT
Found at i:16207176 original size:29 final size:29
Alignment explanation
Indices: 16207143--16207204 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
16207133 TCGCGTAGAC
*
16207143 CTCGCAAAAATGAGGTTGCAAGAGGAAAG
1 CTCGCAAAAATGAGGCTGCAAGAGGAAAG
* *
16207172 CTCGCAGAAATGAGGCTGCAAGAGGAGAG
1 CTCGCAAAAATGAGGCTGCAAGAGGAAAG
16207201 CTCG
1 CTCG
16207205 AATAAACCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.34, T:0.13
Consensus pattern (29 bp):
CTCGCAAAAATGAGGCTGCAAGAGGAAAG
Found at i:16208224 original size:22 final size:22
Alignment explanation
Indices: 16208168--16208226 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
16208158 TCTTCCGTTG
**
16208168 TAAGCTCTCATGGCTAACGTAC
1 TAAGCTCTCATGTTTAACGTAC
*
16208190 TAAGCTCTCATGTTTCACGTAC
1 TAAGCTCTCATGTTTAACGTAC
16208212 TAAGCTCTCATGTTT
1 TAAGCTCTCATGTTT
16208227 GAACAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (22 bp):
TAAGCTCTCATGTTTAACGTAC
Found at i:16215066 original size:23 final size:23
Alignment explanation
Indices: 16215021--16215066 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
16215011 TATCTTTAGG
* *
16215021 ATTTACAATAATTACCTTGATAA
1 ATTTACAATAATTACCCTAATAA
16215044 ATTTACAATAATTACCCTAATAA
1 ATTTACAATAATTACCCTAATAA
16215067 CTCTAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTTACAATAATTACCCTAATAA
Found at i:16217935 original size:25 final size:26
Alignment explanation
Indices: 16217848--16217937 Score: 105
Period size: 26 Copynumber: 3.5 Consensus size: 26
16217838 GCAACACATA
*
16217848 TGAGCGTCCTG-TTATATGGCTCTTTG
1 TGAGCTTCCTGATTA-ATGGCTCTTTG
* *
16217874 TGAGCTT-CTCGGTTAAAGGCTCTTTG
1 TGAGCTTCCT-GATTAATGGCTCTTTG
*
16217900 TGAGCTTCCTGATTAATGGCTCTCTG
1 TGAGCTTCCTGATTAATGGCTCTTTG
16217926 -GAGCTTCCTGAT
1 TGAGCTTCCTGAT
16217938 ATGGCTTGCT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
25 14 0.25
26 37 0.66
27 5 0.09
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.39
Consensus pattern (26 bp):
TGAGCTTCCTGATTAATGGCTCTTTG
Found at i:16222183 original size:24 final size:25
Alignment explanation
Indices: 16222120--16222183 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
16222110 TTATCGATAC
* *
16222120 TCAGCTTGTATGAGCTTACCATTTT
1 TCAGCTCGTATGAGCTTACCATTTA
* * * *
16222145 TCAACTCGGAGGAGCTTACCGTTTA
1 TCAGCTCGTATGAGCTTACCATTTA
16222170 T-AGCTCGTATGAGC
1 TCAGCTCGTATGAGC
16222184 ATACATGTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (25 bp):
TCAGCTCGTATGAGCTTACCATTTA
Found at i:16223891 original size:21 final size:21
Alignment explanation
Indices: 16223861--16223900 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16223851 ACTGTATGGT
*
16223861 GATATTTGATAGAAAGTCTGC
1 GATATCTGATAGAAAGTCTGC
16223882 GATATCTGATAGAAAGTCT
1 GATATCTGATAGAAAGTCT
16223901 CGTTTCCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (21 bp):
GATATCTGATAGAAAGTCTGC
Found at i:16224285 original size:76 final size:76
Alignment explanation
Indices: 16224199--16224352 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
16224189 GTAAATCTCT
16224199 TTTTAAACTTAGTTTTCCAGGAACATGCAGAACCCTTAAAATGGTTTTGGAAACTCTTAACTTTG
1 TTTTAAACTTAGTTTTCCAGGAACATGCAGAACCCTTAAAATGGTTTTGGAAACTCTTAACTTTG
16224264 TTTTCTGAATC
66 TTTTCTGAATC
16224275 TTTTAAACTTAGTTTTCCAGGAACATGCAGAACCCTTAAAATGGTTTTGGAAACTCTTAACTTTG
1 TTTTAAACTTAGTTTTCCAGGAACATGCAGAACCCTTAAAATGGTTTTGGAAACTCTTAACTTTG
16224340 TTTTCTGAATC
66 TTTTCTGAATC
16224351 TT
1 TT
16224353 ACATACACCA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (76 bp):
TTTTAAACTTAGTTTTCCAGGAACATGCAGAACCCTTAAAATGGTTTTGGAAACTCTTAACTTTG
TTTTCTGAATC
Found at i:16226548 original size:15 final size:16
Alignment explanation
Indices: 16226528--16226560 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16226518 TGATACTGAT
16226528 TTGAGACAGGC-CATA
1 TTGAGACAGGCGCATA
*
16226543 TTGAGAGAGGCGCATA
1 TTGAGACAGGCGCATA
16226559 TT
1 TT
16226561 AGCCCTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (16 bp):
TTGAGACAGGCGCATA
Found at i:16238025 original size:22 final size:22
Alignment explanation
Indices: 16237995--16238037 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16237985 ACATCAAAAC
* * *
16237995 AGGCTTTTAGCGGCGTTTTTTT
1 AGGCCTTTAGCAGCGCTTTTTT
16238017 AGGCCTTTAGCAGCGCTTTTT
1 AGGCCTTTAGCAGCGCTTTTT
16238038 AGCGCTGCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCAGCGCTTTTTT
Found at i:16238179 original size:43 final size:43
Alignment explanation
Indices: 16238131--16238296 Score: 260
Period size: 43 Copynumber: 3.9 Consensus size: 43
16238121 TTATGAGGCA
* * * *
16238131 AAACGCCACTAAAGATCATGTTCTTTAGCGGCACTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* *
16238174 AAACGCCGCTAAAGAACATGATCTTTAGTGGCGCCTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
*
16238217 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTAACCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
*
16238260 AAACGCTGCTAAAGAACATGATCTTTAGCGGCGCTTT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTT
16238297 TGATAAAAGC
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 113 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
Found at i:16238315 original size:86 final size:85
Alignment explanation
Indices: 16238129--16238316 Score: 250
Period size: 86 Copynumber: 2.2 Consensus size: 85
16238119 GTTTATGAGG
* * *
16238129 CAAAACGCCACTAAAGATCATGTTCTTTAGCGGCACTTTACCCACAAACGCCGCTAAAGAACATG
1 CAAAACGCCACTAAAGAACATGATCTTTAGCGGCACTTTAACCACAAACGCCGCTAAAGAACATG
* *
16238194 ATCTTTAGTGGCGCCTTACC
66 ATCTTTAGCGGCGCCTTACA
* * *
16238214 CACAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTAACCACAAACGCTGCTAAAGAACAT
1 CA-AAACGCCACTAAAGAACATGATCTTTAGCGGCACTTTAACCACAAACGCCGCTAAAGAACAT
* **
16238279 GATCTTTAGCGGCGCTTTTGA
65 GATCTTTAGCGGCGCCTTACA
*
16238300 TAAAAGCGCCACTAAAG
1 CAAAA-CGCCACTAAAG
16238317 GTCATAAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
85 5 0.06
86 83 0.94
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.22
Consensus pattern (85 bp):
CAAAACGCCACTAAAGAACATGATCTTTAGCGGCACTTTAACCACAAACGCCGCTAAAGAACATG
ATCTTTAGCGGCGCCTTACA
Found at i:16238666 original size:2 final size:2
Alignment explanation
Indices: 16238659--16238688 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16238649 CCATTCAGTG
16238659 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
16238689 ATAACACAAC
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):
TA
Found at i:16243101 original size:47 final size:48
Alignment explanation
Indices: 16243043--16243141 Score: 173
Period size: 47 Copynumber: 2.1 Consensus size: 48
16243033 CATAGTTTTG
*
16243043 TTTAAGTAATATTTATAAAAATTAGATAAAATTATAAATTTTAGT-TT
1 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
*
16243090 TTTAAGTAATATTTATAATAATTAGATAAAATTAAAAATTTTAGTGTT
1 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
16243138 TTTA
1 TTTA
16243142 TTTCATTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 43 0.88
48 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (48 bp):
TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
Found at i:16243155 original size:25 final size:26
Alignment explanation
Indices: 16243127--16243179 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
16243117 AAAATTAAAA
* *
16243127 ATTTTAGTGTTTTTATTTCATTT-TT
1 ATTTTAGTATTTTAATTTCATTTCTT
* *
16243152 ATTTTTGTATTTTAATTTTATTTCTT
1 ATTTTAGTATTTTAATTTCATTTCTT
16243178 AT
1 AT
16243180 AATTTGGTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72
Consensus pattern (26 bp):
ATTTTAGTATTTTAATTTCATTTCTT
Found at i:16243162 original size:19 final size:18
Alignment explanation
Indices: 16243126--16243179 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
16243116 TAAAATTAAA
16243126 AATTTTAGTGTTTTTATTTC
1 AATTTTA-T-TTTTTATTTC
* *
16243146 ATTTTTATTTTTGTATTTT
1 AATTTTATTTTT-TATTTC
*
16243165 AATTTTATTTCTTAT
1 AATTTTATTTTTTAT
16243180 AATTTGGTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (18 bp):
AATTTTATTTTTTATTTC
Found at i:16243538 original size:14 final size:14
Alignment explanation
Indices: 16243496--16243551 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
16243486 AATCTTTATG
*
16243496 TCCTAACCCCTAAAT
1 TCCTAACCCCT-AAC
* *
16243511 TCCTAACTCTTAAC
1 TCCTAACCCCTAAC
*
16243525 CCCTAACCCCTAAC
1 TCCTAACCCCTAAC
*
16243539 TACTAACCCCTAA
1 TCCTAACCCCTAA
16243552 ACCTTAAATC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
14 24 0.73
15 9 0.27
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.25
Consensus pattern (14 bp):
TCCTAACCCCTAAC
Found at i:16243538 original size:21 final size:21
Alignment explanation
Indices: 16243498--16243551 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
16243488 TCTTTATGTC
**
16243498 CTAACCCCTAAATTCCTAACT-
1 CTAACCCCT-AACCCCTAACTA
16243519 CTTAACCCCTAACCCCTAACTA
1 C-TAACCCCTAACCCCTAACTA
16243541 CTAACCCCTAA
1 CTAACCCCTAA
16243552 ACCTTAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.33, C:0.43, G:0.00, T:0.24
Consensus pattern (21 bp):
CTAACCCCTAACCCCTAACTA
Found at i:16243700 original size:7 final size:7
Alignment explanation
Indices: 16243688--16243771 Score: 71
Period size: 7 Copynumber: 11.7 Consensus size: 7
16243678 ACTAGTTAAT
16243688 CTAAACC
1 CTAAACC
16243695 CTAAACC
1 CTAAACC
*
16243702 ATAAA-C
1 CTAAACC
*
16243708 TTAAACC
1 CTAAACC
16243715 CTAAAACC
1 CT-AAACC
16243723 CTAAACC
1 CTAAACC
16243730 CATAAACC
1 C-TAAACC
*
16243738 CTTAACC
1 CTAAACC
*
16243745 ATAAACC
1 CTAAACC
*
16243752 CATAATCC
1 C-TAAACC
*
16243760 ATAAACC
1 CTAAACC
*
16243767 TTAAA
1 CTAAA
16243772 ATGGTAACAC
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
6 5 0.08
7 38 0.61
8 19 0.31
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:16243750 original size:29 final size:27
Alignment explanation
Indices: 16243689--16243770 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 27
16243679 CTAGTTAATC
*
16243689 TAAACCCTAAACCATAAA-CTTAAACCC
1 TAAACCCTAAACCATAAACCTT-AACCA
16243716 TAAAACCCTAAACCCATAAACCCTTAACCA
1 T-AAACCCTAAA-CCATAAA-CCTTAACCA
*
16243746 TAAACCCATAATCCATAAACCTTAA
1 TAAACCC-TAAACCATAAACCTTAA
16243771 AATGGTAACA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
27 1 0.02
28 16 0.33
29 20 0.42
30 8 0.17
31 3 0.06
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.20
Consensus pattern (27 bp):
TAAACCCTAAACCATAAACCTTAACCA
Found at i:16243766 original size:22 final size:22
Alignment explanation
Indices: 16243696--16243771 Score: 52
Period size: 22 Copynumber: 3.5 Consensus size: 22
16243686 ATCTAAACCC
*
16243696 TAAACCATAAA-CTTAAACCC-
1 TAAACCATAAACCATAAACCCA
*
16243716 TAAAACCCTAAACCCATAAACCC-
1 T-AAACCATAAA-CCATAAACCCA
* *
16243739 TTAACCATAAACCCAT-AATCCA
1 TAAACCATAAA-CCATAAACCCA
*
16243761 TAAACCTTAAA
1 TAAACCATAAA
16243772 ATGGTAACAC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 13 0.29
22 22 0.49
23 9 0.20
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.20
Consensus pattern (22 bp):
TAAACCATAAACCATAAACCCA
Found at i:16244054 original size:41 final size:41
Alignment explanation
Indices: 16243997--16244075 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
16243987 TTTTAAATCC
*
16243997 CTGAGCATTAGCGGCGCTTTCTCAAAAACGCCACTAAAGCA
1 CTGAGCATTAGCGGCGCTTTATCAAAAACGCCACTAAAGCA
* *
16244038 CTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAA
1 CTGAGCATTAGCGGCGCTTTATCAAAAACGCCACTAAA
16244076 TCCTCGAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCTTTATCAAAAACGCCACTAAAGCA
Found at i:16244215 original size:114 final size:114
Alignment explanation
Indices: 16244007--16244686 Score: 929
Period size: 114 Copynumber: 6.0 Consensus size: 114
16243997 CTGAGCATTA
* *
16244007 GCGGCGCTTTCTCAAAAACGCCACTAAAGCACTGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
* * *
16244072 TAAATCCTCGAAAGCTCAGAAAATGGCGTCGTTGAGCTTAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * * * ** *
16244121 GCAGCGCTTTCCCAAAAACGCCGCTAAAGCCATGAGCATTAGCAGCGCTTTCCTAAAAATGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
*
16244186 TAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * *
16244235 GCGGCGCTTT-TCCAAAAATGCCGCTAAAAGCCCTGAGCATTAGCAGCGCTTTCTTAAAAACGCC
1 GCGGCGCTTTCT-CAAAAACGCCGCT-AAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCC
* * *
16244299 GCTAAATCCCCAAAAGCTCAGAAAACGGTGTTGTTGGGCTTAGG-TTTTTT
64 GCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * * * *
16244349 GAGGCGCTTTCTAAAAAAAGCCGCTAAAGCCCTGAACATTAGCGGCGCTTTATTAAAAAAGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
* * * *
16244414 TAAATCCTCGGAAGCTCAGAAAACGACGTCGTTGGACTTAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * * *
16244463 ACGGCGCTTTCTCAAAAACGCCGCTAAAGCCTTGAACATTAGCGGCGCTTTATTAATAACGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
* *
16244528 CAAATCCCCGAAAGCTCAGAAAACGGAGTCGTTGGGAC-TAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG-CTTAGGTTTTTTT
* * * * *
16244577 GCGGCGCTTTCTAAAAAACGCAGCTAAAGCCCTGAGCATTAGCGGC-CTTTCTT-CAAACGCTGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
**
16244640 TAAATCCCCGAAAGCTTGGAAAACGGCGTCGTTGGGCTTAGGTTTTT
66 TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTT
16244687 AGTGGCGCTG
Statistics
Matches: 497, Mismatches: 63, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
111 1 0.00
112 48 0.10
113 77 0.15
114 294 0.59
115 77 0.15
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
Found at i:16246514 original size:21 final size:21
Alignment explanation
Indices: 16246490--16246539 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
16246480 CATTATTTCT
* *
16246490 AATCTCACCGCTACAATATCC
1 AATCTCACAGCTACAATAACC
* *
16246511 AATCTCACAGCTACAGTAACT
1 AATCTCACAGCTACAATAACC
16246532 AATCTCAC
1 AATCTCAC
16246540 TGCCACCGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.34, G:0.06, T:0.24
Consensus pattern (21 bp):
AATCTCACAGCTACAATAACC
Found at i:16250635 original size:31 final size:30
Alignment explanation
Indices: 16250600--16250659 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
16250590 GGAGGTGGGA
*
16250600 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* *
16250631 TGGGAGGGAATAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
16250660 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:16250891 original size:9 final size:9
Alignment explanation
Indices: 16250873--16250909 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
16250863 TATAGTTTGA
*
16250873 TATTCAAAT
1 TATTCGAAT
16250882 TATTCGAAT
1 TATTCGAAT
*
16250891 TATTCGAGT
1 TATTCGAAT
16250900 TATTCGAAT
1 TATTCGAAT
16250909 T
1 T
16250910 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:16253082 original size:50 final size:50
Alignment explanation
Indices: 16252967--16253159 Score: 271
Period size: 50 Copynumber: 3.8 Consensus size: 50
16252957 GATAATAACA
* ** *
16252967 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTTGG
* * *
16253018 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATCTTGG
* *
16253068 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
*
16253118 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
16253160 TTACCCAAAT
Statistics
Matches: 127, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
50 94 0.74
51 33 0.26
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
Found at i:16253531 original size:30 final size:29
Alignment explanation
Indices: 16253497--16253563 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
16253487 CCTCGACTCT
16253497 AACTTTGGCAAAATTATGATTTTGCCCCTA
1 AACTTTGGCAAAATTATGATTTTGCCCC-A
** * *
16253527 AACTTTTACATAATTATGCTTTTGCCCCA
1 AACTTTGGCAAAATTATGATTTTGCCCCA
*
16253556 AAGTTTGG
1 AACTTTGG
16253564 AAATTAAACT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (29 bp):
AACTTTGGCAAAATTATGATTTTGCCCCA
Found at i:16255617 original size:235 final size:235
Alignment explanation
Indices: 16255108--16255770 Score: 1096
Period size: 235 Copynumber: 2.8 Consensus size: 235
16255098 TCATTTGATA
* * * *
16255108 AAAAGTTTCCAAGTTTTGCAAGAAATCCTAAGAATGTAAGGCTTGGGCTTGCATCTGATGGCTTT
1 AAAAGTTTCCAAGTTTTGCAAGCAATCCTAAGAATGTGAGGCTTGGGCTTACATCTGATGGCCTT
* *
16255173 AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCTTGTTGTGATTGTT-TCTTACAATT
66 AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCCTGTTGTGCTTGTTCT-TTACAATT
* * * *
16255237 TCCCTTCATGAATTTGCATGAAACAATCTTC-TTTATCTTATCTATGATAATCCTTGGGGAGAAA
130 TGCCTCCATGGATTTGCATGAAACAATATTCTTTTATCTTATCTATGATAATCCTTGGGGAGAAA
*
16255301 GGTCTAAAGAACAATATTGGCATTTATATGCAGTCGCTTAT
195 GGTCTAAAGAACAATATTGGCATTTATATGCAGTCACTTAT
* * *
16255342 AAAAGTTTCCAAGTTTTGCAAGCAATCCTAAGAGTGTGAGGCTTGGGTTTACATCTAATGGCCTT
1 AAAAGTTTCCAAGTTTTGCAAGCAATCCTAAGAATGTGAGGCTTGGGCTTACATCTGATGGCCTT
16255407 AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCCTGTTGTGCTTGTTCTTTACAATTT
66 AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCCTGTTGTGCTTGTTCTTTACAATTT
*
16255472 GCCTCCATGGATTTGCATGAAACAATATTCTTTTATTTTATCTATGATAATCCTTGGGGAGAAAG
131 GCCTCCATGGATTTGCATGAAACAATATTCTTTTATCTTATCTATGATAATCCTTGGGGAGAAAG
**
16255537 GTCTAAAGAATGATATTGGCATTTATATGCAGTCACTTAT
196 GTCTAAAGAACAATATTGGCATTTATATGCAGTCACTTAT
* *
16255577 AAAAGTTTCCAAGTTTTGCAAGCAATCTTAAGAATGTGAGGCTTGGGCCTACATCTGATGGCCTT
1 AAAAGTTTCCAAGTTTTGCAAGCAATCCTAAGAATGTGAGGCTTGGGCTTACATCTGATGGCCTT
* *
16255642 AATCCTTTTAAAATCATGAGTCATTCATATAGTACTTGGCCTGTTGTGCTTGTTCCTTACAATTT
66 AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCCTGTTGTGCTTGTTCTTTACAATTT
* *
16255707 GCCTCCATGGATTTGCATGAAACAATGTTCTTTTATCTTATCTATGATAATCATTGGGGAGAAA
131 GCCTCCATGGATTTGCATGAAACAATATTCTTTTATCTTATCTATGATAATCCTTGGGGAGAAA
16255771 AGTAAAAAAG
Statistics
Matches: 400, Mismatches: 27, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
234 145 0.36
235 255 0.64
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (235 bp):
AAAAGTTTCCAAGTTTTGCAAGCAATCCTAAGAATGTGAGGCTTGGGCTTACATCTGATGGCCTT
AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCCTGTTGTGCTTGTTCTTTACAATTT
GCCTCCATGGATTTGCATGAAACAATATTCTTTTATCTTATCTATGATAATCCTTGGGGAGAAAG
GTCTAAAGAACAATATTGGCATTTATATGCAGTCACTTAT
Found at i:16264692 original size:56 final size:50
Alignment explanation
Indices: 16264611--16264801 Score: 220
Period size: 50 Copynumber: 3.7 Consensus size: 50
16264601 GGGAATGAGA
* *
16264611 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGATATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CG--A-TATGAGAGG
* * *
16264667 TCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
* * **
16264717 TCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
* * *
16264767 TCTCATGTAAGACCATATCTGGGATATGGCATTGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
16264802 TCATACAGAA
Statistics
Matches: 118, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 81 0.69
51 1 0.01
53 1 0.01
55 1 0.01
56 34 0.29
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
Found at i:16265083 original size:16 final size:16
Alignment explanation
Indices: 16265057--16265098 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
16265047 TTATTTAAGT
*
16265057 AAGCAAGTAAGTAAAA
1 AAGCGAGTAAGTAAAA
* *
16265073 AAGTGAGTAAGTAAAG
1 AAGCGAGTAAGTAAAA
16265089 AAGCGAGTAA
1 AAGCGAGTAA
16265099 AGATTCTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.26, T:0.14
Consensus pattern (16 bp):
AAGCGAGTAAGTAAAA
Found at i:16266878 original size:29 final size:30
Alignment explanation
Indices: 16266845--16266908 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
16266835 CTTTTAAAAA
16266845 AAAAACCTT-AACAACATAGTAACTTAAAT
1 AAAAACCTTGAACAACATAGTAACTTAAAT
* * ** *
16266874 AAAAACTTTGAATAATTTAGTGACTTAAAT
1 AAAAACCTTGAACAACATAGTAACTTAAAT
16266904 AAAAA
1 AAAAA
16266909 TTTTCGAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (30 bp):
AAAAACCTTGAACAACATAGTAACTTAAAT
Found at i:16266900 original size:30 final size:31
Alignment explanation
Indices: 16266861--16266921 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
16266851 CTTAACAACA
16266861 TAGTAACTTAAATAAAAACTTT-GAATAATT
1 TAGTAACTTAAATAAAAACTTTCGAATAATT
* *
16266891 TAGTGACTTAAATAAAAATTTTCGAATAATT
1 TAGTAACTTAAATAAAAACTTTCGAATAATT
16266922 CAATGACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.38
Consensus pattern (31 bp):
TAGTAACTTAAATAAAAACTTTCGAATAATT
Found at i:16266933 original size:30 final size:30
Alignment explanation
Indices: 16266866--16266933 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
16266856 CAACATAGTA
* *
16266866 ACTTAAATAAAAACTTTGAATAATTTAGTG
1 ACTTAAATAAAAACTTTGAATAATTCAATG
*
16266896 ACTTAAATAAAAATTTTCGAATAATTCAATG
1 ACTTAAATAAAAACTTT-GAATAATTCAATG
16266927 AC-TAAAT
1 ACTTAAAT
16266934 TCCAACTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 21 0.62
31 13 0.38
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (30 bp):
ACTTAAATAAAAACTTTGAATAATTCAATG
Found at i:16267786 original size:9 final size:9
Alignment explanation
Indices: 16267757--16267793 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
16267747 TGAGTTTTCA
16267757 AATTCGAAT
1 AATTCGAAT
*
16267766 AACTCGAAT
1 AATTCGAAT
16267775 AATTCGAAT
1 AATTCGAAT
*
16267784 AATTCAAAT
1 AATTCGAAT
16267793 A
1 A
16267794 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16268039 original size:30 final size:31
Alignment explanation
Indices: 16268005--16268064 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
16267995 AAACCTTTTA
*
16268005 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
16268035 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
16268065 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:16274754 original size:42 final size:42
Alignment explanation
Indices: 16274660--16274754 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
16274650 TCTTATTCTA
* * * *
16274660 GGAA-TATTTTATTTTATGTTTTAGTAGTTTATTAGAATAAG
1 GGAATTATTTTCTCTTATATTTTAATAGTTTATTAGAATAAG
*
16274701 GGAATTATTTTCTCTTATATTTTAATAGTTTATTAGAGTAAG
1 GGAATTATTTTCTCTTATATTTTAATAGTTTATTAGAATAAG
16274743 GGAATTATTTTC
1 GGAATTATTTTC
16274755 CCAACTAGGA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.51
Consensus pattern (42 bp):
GGAATTATTTTCTCTTATATTTTAATAGTTTATTAGAATAAG
Found at i:16276364 original size:15 final size:15
Alignment explanation
Indices: 16276340--16276381 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
16276330 TTGGCAGTGC
16276340 TTTA-TCTGGTGAAA
1 TTTACTCTGGTGAAA
*
16276354 TTTACTCTGGTGGAA
1 TTTACTCTGGTGAAA
*
16276369 TTTACTCTCGTGA
1 TTTACTCTGGTGA
16276382 CGACAACCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (15 bp):
TTTACTCTGGTGAAA
Found at i:16279417 original size:42 final size:42
Alignment explanation
Indices: 16279371--16279460 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
16279361 ATTCTAGGAA
**
16279371 TATTTTATTTTATCTTTTAGTAGTTTATTAAAATAAGGAAAT
1 TATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAGGAAAT
** * * * *
16279413 TATTTCCCCTTATGTTTTAGTAGTTTATTAGAGTAAGGGAAT
1 TATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAGGAAAT
16279455 TATTTT
1 TATTTT
16279461 CCCAATTAGG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (42 bp):
TATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAGGAAAT
Found at i:16280832 original size:13 final size:13
Alignment explanation
Indices: 16280816--16280845 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16280806 AGACTGAAAA
*
16280816 GCAAAACTGCAAT
1 GCAAAACCGCAAT
16280829 GCAAAACCGCAAT
1 GCAAAACCGCAAT
16280842 GCAA
1 GCAA
16280846 TTTTCATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.10
Consensus pattern (13 bp):
GCAAAACCGCAAT
Found at i:16295343 original size:12 final size:12
Alignment explanation
Indices: 16295328--16295357 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
16295318 TCTCATCTTC
16295328 ATTTTCATTTTT
1 ATTTTCATTTTT
16295340 ATTTTCATTTTT
1 ATTTTCATTTTT
16295352 AGTTTT
1 A-TTTT
16295358 GAGAAACCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (12 bp):
ATTTTCATTTTT
Found at i:16309857 original size:6 final size:6
Alignment explanation
Indices: 16309848--16309901 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
16309838 GTGTGAATGA
** *
16309848 AATAAT AATAAT AATGTT AATAAT AATAAC AATAAAT AA-AAT AA-AAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AAT-AAT AATAAT AATAAT
16309895 AA-AAT AA
1 AATAAT AA
16309902 AGTGCTAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
5 15 0.37
6 22 0.54
7 4 0.10
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (6 bp):
AATAAT
Found at i:16309862 original size:9 final size:9
Alignment explanation
Indices: 16309848--16309901 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
16309838 GTGTGAATGA
16309848 AATAATAAT
1 AATAATAAT
**
16309857 AATAATGTT
1 AATAATAAT
16309866 AATAATAAT
1 AATAATAAT
*
16309875 AACAATAAAT
1 AATAAT-AAT
16309885 AA-AATAA-
1 AATAATAAT
16309892 AATAA-AAT
1 AATAATAAT
16309900 AA
1 AA
16309902 AGTGCTAACA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
7 4 0.11
8 6 0.16
9 22 0.59
10 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (9 bp):
AATAATAAT
Found at i:16311505 original size:45 final size:44
Alignment explanation
Indices: 16311455--16311548 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
16311445 CTTGTATCTT
* **
16311455 CGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTTTC
1 CGATCTACTTCA-CACCAATACAGGAAGACAAGATCTGCTTTTTC
* * * *
16311500 CGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTTTT
1 CGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTTTTTC
16311544 CGATC
1 CGATC
16311549 GATTCCACTG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 30 0.71
45 12 0.29
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (44 bp):
CGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTTTTTC
Found at i:16311858 original size:221 final size:220
Alignment explanation
Indices: 16311501--16311898 Score: 609
Period size: 221 Copynumber: 1.8 Consensus size: 220
16311491 TGCTTTTTCC
* * **
16311501 GATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTTTTCGATCGATTCCACTGCCGACCA
1 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCGATTCCACCACCGACCA
* * **
16311566 GGGGAATTGAATTACTGGCTTCAATATACTCTACTGGAACCTCAGGGAGGTAAAATCTACCATAT
66 GGGGAATAGAATTACTGGCTTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTACCATAT
*
16311631 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCACTCTACTTGCCGCCAGTA
131 TTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCACTCTACTTGCCGCCAGTA
16311696 TGGGAGGATAAAATATGTTGTATTT
196 TGGGAGGATAAAATATGTTGTATTT
** ** * **
16311721 GATCTACTTCACGCTGATACATGAAGACAAGATCTGCTTTCTTCGATTTATTCCACCATC-AGTA
1 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCGATTCCACCACCGACCA
*
16311785 TGGGGAGATAGAATTACTGGCTTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTGCCAT
66 -GGGGA-ATAGAATTACTGGCTTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTACCAT
*
16311850 CTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
129 ATTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
16311899 ATTTGTTCAA
Statistics
Matches: 158, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
219 2 0.01
220 56 0.35
221 100 0.63
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (220 bp):
GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCGATTCCACCACCGACCA
GGGGAATAGAATTACTGGCTTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTACCATAT
TTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCACTCTACTTGCCGCCAGTA
TGGGAGGATAAAATATGTTGTATTT
Found at i:16311956 original size:50 final size:50
Alignment explanation
Indices: 16311894--16312102 Score: 184
Period size: 50 Copynumber: 4.2 Consensus size: 50
16311884 GATCTGTAAT
* *
16311894 CTTCAATTTGTTCAACTGCAATGTTGGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
* * * * *** * **
16311944 CTTCAATCTGTTCCACCGCACTGTCAGGGAAGTAAGATCCGCCGTTGTTT
1 CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
* * * *
16311994 CTTCAATCTTTTTAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
** * * * * *** *
16312044 CTTCAATCTGTTCCGCTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTAG
1 CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
16312094 CTTCAATCT
1 CTTCAATCT
16312103 TTTTAATTGC
Statistics
Matches: 119, Mismatches: 40, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 119 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (50 bp):
CTTCAATCTGTTCAACTGCAATGTTAGGGAAACCAGATCCGCCGTCGTAG
Found at i:16312042 original size:100 final size:100
Alignment explanation
Indices: 16311892--16312122 Score: 331
Period size: 100 Copynumber: 2.3 Consensus size: 100
16311882 AAGATCTGTA
* * * *
16311892 ATCTTCAAT-TTGTTCAACTGCAATGTTGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTT
1 ATCTTCAATCTT-TTTAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTT
*
16311956 CCACCGCACTG-TCAGGGAAGTAAGATCCGCCGTTGT
65 CCACCGCACTGCT-AAGGAAGTAAGATCCGCCGTTGT
*
16311992 TTCTTCAATCTTTTTAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTC
1 ATCTTCAATCTTTTTAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTC
* * *
16312057 CGCTGTACTGCTAAGGAAGTAAGATCCGCCGTTGT
66 CACCGCACTGCTAAGGAAGTAAGATCCGCCGTTGT
* *
16312092 AGCTTCAATCTTTTTAATTGCAATATCAGGG
1 ATCTTCAATCTTTTTAATTGCAATATTAGGG
16312123 GGATAAGACT
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
100 114 0.97
101 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (100 bp):
ATCTTCAATCTTTTTAATTGCAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTC
CACCGCACTGCTAAGGAAGTAAGATCCGCCGTTGT
Found at i:16312130 original size:50 final size:50
Alignment explanation
Indices: 16311976--16312130 Score: 132
Period size: 50 Copynumber: 3.1 Consensus size: 50
16311966 GTCAGGGAAG
** * *
16311976 TAAGATCCGCCGTTGTTTCTTCAATCTTTTTAATTGCAATATTAGGGAAA
1 TAAGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATATAAGGGAGA
** * * **** * * * *
16312026 CCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGTACTGCTAAGGAAG-
1 TAAGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAAT-ATAAGGGAGA
* *
16312076 TAAGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATATCAGGGGGA
1 TAAGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATATAAGGGAGA
16312126 TAAGA
1 TAAGA
16312131 CTTTATGATT
Statistics
Matches: 73, Mismatches: 30, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
49 5 0.07
50 63 0.86
51 5 0.07
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (50 bp):
TAAGATCCGCCGTTGTAGCTTCAATCTTTTTAATTGCAATATAAGGGAGA
Found at i:16334888 original size:15 final size:16
Alignment explanation
Indices: 16334868--16334898 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16334858 GAGTATGGTA
16334868 AAATA-TTAAAAAAAT
1 AAATATTTAAAAAAAT
16334883 AAATATTTAAAAAAAT
1 AAATATTTAAAAAAAT
16334899 TACTAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATTTAAAAAAAT
Found at i:16336424 original size:22 final size:23
Alignment explanation
Indices: 16336385--16336434 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
16336375 AATTGAATAT
16336385 ATTAAAATATGAAAAATAAAAAA
1 ATTAAAATATGAAAAATAAAAAA
* *
16336408 ATTAAAAT-TTAAAAATACAAAA
1 ATTAAAATATGAAAAATAAAAAA
16336430 ATTAA
1 ATTAA
16336435 GTTCTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
ATTAAAATATGAAAAATAAAAAA
Found at i:16342278 original size:39 final size:37
Alignment explanation
Indices: 16342159--16342307 Score: 133
Period size: 38 Copynumber: 3.9 Consensus size: 37
16342149 AGTTTAAGTC
* * *
16342159 TTTAATTATGTCATAATTTGAACATCATTAATATGAGT
1 TTTAATTATGTCATACTTAGAACATCTTTAATAT-AGT
16342197 TTTAATTATGTCATACTCT-GAACATCTTTAATA-AGGGTT
1 TTTAATTATGTCATACT-TAGAACATCTTTAATATA--G-T
* *
16342236 TTTAATTATGTCATAGCTTAGGACATCTTAAATATATGT
1 TTTAATTATGTCATA-CTTAGAACATCTTTAATATA-GT
* * *
16342275 TTTAAATATGTCCTAGTTTAG-ACATCTTTAATA
1 TTTAATTATGTCATA-CTTAGAACATCTTTAATA
16342308 CAAGTCTTTA
Statistics
Matches: 95, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
36 1 0.01
38 41 0.43
39 37 0.39
40 15 0.16
41 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTAATTATGTCATACTTAGAACATCTTTAATATAGT
Found at i:16345006 original size:32 final size:32
Alignment explanation
Indices: 16344970--16345041 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
16344960 AAGAAGAGAA
16344970 AGAAGATGAACTCGAAGCACTCGCCGAAAAGG
1 AGAAGATGAACTCGAAGCACTCGCCGAAAAGG
16345002 AGAAGATGAACTCGAAGCACTCGCCGAAAAGG
1 AGAAGATGAACTCGAAGCACTCGCCGAAAAGG
16345034 AGGAAGAT
1 A-GAAGAT
16345042 CTCGAGTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 33 0.85
33 6 0.15
ACGTcount: A:0.42, C:0.19, G:0.29, T:0.10
Consensus pattern (32 bp):
AGAAGATGAACTCGAAGCACTCGCCGAAAAGG
Found at i:16348470 original size:38 final size:39
Alignment explanation
Indices: 16348419--16348510 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 39
16348409 AGTTTAAGTC
* * *
16348419 TTTAATTATGTCATAATTTGAACAT-TATTAATATGAG-T
1 TTTAATTATGTCATAATCTAAACATCT-TTAATAGGAGTT
*
16348457 TTTAATTATGTCATAATCTAAACATCTTTAATAGGGGTT
1 TTTAATTATGTCATAATCTAAACATCTTTAATAGGAGTT
16348496 TTTAATTATGTCATA
1 TTTAATTATGTCATA
16348511 TTTTAGGATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
38 31 0.65
39 17 0.35
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.47
Consensus pattern (39 bp):
TTTAATTATGTCATAATCTAAACATCTTTAATAGGAGTT
Found at i:16348577 original size:39 final size:40
Alignment explanation
Indices: 16348419--16348577 Score: 102
Period size: 39 Copynumber: 4.1 Consensus size: 40
16348409 AGTTTAAGTC
* * *
16348419 TTTAATTATGTCATAATTT-GAACAT-TATTAAT--ATGAGT
1 TTTAATTATGTCATAGTTTAGGACATCT-TTAATACATG-TT
* * * ***
16348457 TTTAATTATGTCATAATCTA-AACATCTTTAATAGGGGTT
1 TTTAATTATGTCATAGTTTAGGACATCTTTAATACATGTT
* * *
16348496 TTTAATTATGTCATATTTTAGGATATC-TTAACTATATG-T
1 TTTAATTATGTCATAGTTTAGGACATCTTTAA-TACATGTT
*
16348535 TTT-ATATATGTCCTAGTTTA-GACATCTTTAATACATGTT
1 TTTAAT-TATGTCATAGTTTAGGACATCTTTAATACATGTT
16348574 TTTA
1 TTTA
16348578 GTTCAGACCA
Statistics
Matches: 96, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
38 40 0.42
39 48 0.50
40 8 0.08
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (40 bp):
TTTAATTATGTCATAGTTTAGGACATCTTTAATACATGTT
Found at i:16350549 original size:2 final size:2
Alignment explanation
Indices: 16350542--16350577 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16350532 AAATATAGGA
16350542 AT AT AT 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 AT AT AT
16350578 GATCAAACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16350894 original size:13 final size:13
Alignment explanation
Indices: 16350876--16350900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16350866 TGGTTGAAAA
16350876 TTTTAAAAATAAT
1 TTTTAAAAATAAT
16350889 TTTTAAAAATAA
1 TTTTAAAAATAA
16350901 AAATTAGAAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTAAAAATAAT
Found at i:16351405 original size:19 final size:19
Alignment explanation
Indices: 16351372--16351446 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
16351362 TATCTAACCA
*
16351372 AAAAATAATTTAAAAACTAT
1 AAAAATAATTCAAAAA-TAT
16351392 AAAAAT-ATTC-AAAA-AT
1 AAAAATAATTCAAAAATAT
**
16351408 AATCATAATTCAAAAAAATAT
1 AAAAATAATTC--AAAAATAT
16351429 ATAAAAT-ATTCAAAAATA
1 A-AAAATAATTCAAAAATA
16351447 ACATAATTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
16 6 0.14
17 4 0.09
18 4 0.09
19 10 0.23
20 10 0.23
21 7 0.16
22 3 0.07
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATAATTCAAAAATAT
Found at i:16351420 original size:17 final size:17
Alignment explanation
Indices: 16351398--16351454 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
16351388 CTATAAAAAT
16351398 ATTCAAAAATAATCATA
1 ATTCAAAAATAATCATA
* *
16351415 ATTCAAAAAAATATATAAAA
1 ATTC--AAAAATA-ATCATA
16351435 TATTCAAAAATAA-CATA
1 -ATTCAAAAATAATCATA
16351452 ATT
1 ATT
16351455 ACATGTGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
16 3 0.09
17 6 0.19
18 1 0.03
19 14 0.44
20 4 0.12
21 4 0.12
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTCAAAAATAATCATA
Found at i:16351452 original size:37 final size:37
Alignment explanation
Indices: 16351383--16351454 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
16351373 AAAATAATTT
*
16351383 AAAAACTATAAAAATATTCAAAAATAATCATAATTCA
1 AAAAAATATAAAAATATTCAAAAATAATCATAATTCA
16351420 AAAAAATATATAAAATATTCAAAAATAA-CATAATT
1 AAAAAATATA-AAAATATTCAAAAATAATCATAATT
16351455 ACATGTGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 16 0.48
38 17 0.52
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (37 bp):
AAAAAATATAAAAATATTCAAAAATAATCATAATTCA
Found at i:16353948 original size:87 final size:87
Alignment explanation
Indices: 16353802--16353975 Score: 323
Period size: 87 Copynumber: 2.0 Consensus size: 87
16353792 ATCCCACACT
*
16353802 CAGCTTCCCAGCAGCAACCTTTTCTCTAACAAAATAAAAGTCCAATTCAACATACTTAAACTTCA
1 CAGCTTCCCAGCAGCAACCTTTTCTCTAACAAAATAAAAGTCCAACTCAACATACTTAAACTTCA
16353867 AGTGCATCATTGGATTAGCAGA
66 AGTGCATCATTGGATTAGCAGA
16353889 CAGCTTCCCAGCAGCAACCTTTTCTCTAACAAAATATAAA-TCCAACTCAACATACTTAAACTTC
1 CAGCTTCCCAGCAGCAACCTTTTCTCTAACAAAATA-AAAGTCCAACTCAACATACTTAAACTTC
16353953 AAGTGCATCATTGGATTAGCAGA
65 AAGTGCATCATTGGATTAGCAGA
16353976 AACTGCAACA
Statistics
Matches: 85, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
87 82 0.96
88 3 0.04
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (87 bp):
CAGCTTCCCAGCAGCAACCTTTTCTCTAACAAAATAAAAGTCCAACTCAACATACTTAAACTTCA
AGTGCATCATTGGATTAGCAGA
Found at i:16376744 original size:21 final size:21
Alignment explanation
Indices: 16376718--16376773 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
16376708 AACAGCGGTG
*
16376718 GCGGTGAGATTAGTTACTATA
1 GCGGTGAGATTAGATACTATA
* *
16376739 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTATA
*
16376760 GCGATGAGATTAGA
1 GCGGTGAGATTAGA
16376774 AACAATGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTATA
Found at i:16380889 original size:26 final size:27
Alignment explanation
Indices: 16380850--16380909 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
16380840 TCAGGACCGT
16380850 AAACACGGGGTAGTCT-CCGAGACAAC
1 AAACACGGGGTAGTCTGCCGAGACAAC
* * * * *
16380876 AAACATGGGTTAGTTTGCCGGGACAAT
1 AAACACGGGGTAGTCTGCCGAGACAAC
16380903 AAACACG
1 AAACACG
16380910 AAGTAGTCCA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.17
Consensus pattern (27 bp):
AAACACGGGGTAGTCTGCCGAGACAAC
Found at i:16385158 original size:5 final size:5
Alignment explanation
Indices: 16385148--16385181 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
16385138 CCCAAAATCT
16385148 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
16385182 TCCTCATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:16385403 original size:20 final size:21
Alignment explanation
Indices: 16385357--16385403 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
16385347 CATGGAAATA
* *
16385357 TTTCACTTCTTTCATTTTCTT
1 TTTCATTTCTCTCATTTTCTT
* *
16385378 TCTCATTTCTCTC-TTTTTTT
1 TTTCATTTCTCTCATTTTCTT
16385398 TTTCAT
1 TTTCAT
16385404 CATGCACCTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCATTTCTCTCATTTTCTT
Found at i:16387168 original size:3 final size:3
Alignment explanation
Indices: 16387162--16387210 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
16387152 TTCTCCAGCT
16387162 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T-A TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
16387209 TC
1 TC
16387211 TTCTGGCTCC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:16393407 original size:2 final size:2
Alignment explanation
Indices: 16393400--16393435 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16393390 TGCTACTAGC
16393400 AT AT AT 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 AT AT AT
16393436 CTTATAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16394041 original size:23 final size:23
Alignment explanation
Indices: 16394011--16394064 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
16394001 CAAACTCAAA
16394011 ACTCGAATTACTTATTCGAGTTG
1 ACTCGAATTACTTATTCGAGTTG
16394034 ACTCGAATTACTTATTCGAGTTG
1 ACTCGAATTACTTATTCGAGTTG
16394057 ACTCGAAT
1 ACTCGAAT
16394065 AACTCGATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (23 bp):
ACTCGAATTACTTATTCGAGTTG
Found at i:16395799 original size:17 final size:17
Alignment explanation
Indices: 16395777--16395809 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16395767 GGAGTACATG
*
16395777 AAAAAAGAAATTAAAAA
1 AAAAAAGAAAATAAAAA
16395794 AAAAAAGAAAATAAAA
1 AAAAAAGAAAATAAAA
16395810 GAAAGAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAAAAGAAAATAAAAA
Found at i:16399885 original size:42 final size:42
Alignment explanation
Indices: 16399832--16399920 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
16399822 GAACTTCCAT
16399832 TACTTATGTACAAGCCACACTAATTCTATAATTTAAATTACA
1 TACTTATGTACAAGCCACACTAATTCTATAATTTAAATTACA
16399874 TACTTATGTACAAGCCACACTAATTCTATAATTTAAATTACA
1 TACTTATGTACAAGCCACACTAATTCTATAATTTAAATTACA
16399916 TACTT
1 TACTT
16399921 CACAAGTCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.37
Consensus pattern (42 bp):
TACTTATGTACAAGCCACACTAATTCTATAATTTAAATTACA
Found at i:16401227 original size:25 final size:26
Alignment explanation
Indices: 16401183--16401236 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
16401173 ATTAGAAATT
16401183 AAATAATAAAAATAAATAAACA-ATA
1 AAATAATAAAAATAAATAAACAGATA
* * * *
16401208 AAATAATCAAAATGACTAAATAGATA
1 AAATAATAAAAATAAATAAACAGATA
16401234 AAA
1 AAA
16401237 CCAATTAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (26 bp):
AAATAATAAAAATAAATAAACAGATA
Found at i:16411492 original size:21 final size:21
Alignment explanation
Indices: 16411468--16411508 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16411458 AGATTGATTA
* *
16411468 TATAGATATATCCAACTTTTC
1 TATAGAGATATACAACTTTTC
*
16411489 TATAGAGATATAGAACTTTT
1 TATAGAGATATACAACTTTT
16411509 ATCAGTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (21 bp):
TATAGAGATATACAACTTTTC
Found at i:16413794 original size:21 final size:22
Alignment explanation
Indices: 16413762--16413822 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
16413752 TAAAATGTAA
16413762 AAATTAAATTAAAAACAAAATT
1 AAATTAAATTAAAAACAAAATT
16413784 AAATT-AATTAAAAACAAAATT
1 AAATTAAATTAAAAACAAAATT
* *
16413805 --ATTAAAATAAAAATAAAA
1 AAATTAAATTAAAAACAAAA
16413823 ATGGCTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.08
20 12 0.33
21 16 0.44
22 5 0.14
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATTAAATTAAAAACAAAATT
Found at i:16429651 original size:120 final size:121
Alignment explanation
Indices: 16429519--16429809 Score: 505
Period size: 120 Copynumber: 2.4 Consensus size: 121
16429509 CAAACTTTAG
* *
16429519 ATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAAATTATATTTTATAGTT
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
* *
16429584 TTATATATTATGATTTTAGTAAATTCATA-TAAGAATATTTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
16429639 ATTAAATTATATATATTTT-TTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
1 ATTAAATTATATAT-TTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT
*
16429703 ATTATATATTATGATTTTAGTAATTTAATATTAAGAATATCTAATATTAAGAATTTT
65 ATTATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
*
16429760 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
16429810 ATATGATTAA
Statistics
Matches: 162, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
120 89 0.55
121 73 0.45
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (121 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
TTATATATTATGATTTTAGTAAATTAATATTAAGAATATCTAATATTAAGAATTTT
Found at i:16429733 original size:22 final size:20
Alignment explanation
Indices: 16429683--16429735 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
16429673 TAATAATTAT
*
16429683 TTTAA-ATTATATTTTATAG
1 TTTAATATTATATTTTATAA
16429702 TATTATATATTATGATTTTAGTAA
1 T-TTA-ATATTAT-ATTTTA-TAA
16429726 TTTAATATTA
1 TTTAATATTA
16429736 AGAATATCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 3 0.11
21 1 0.04
22 11 0.39
23 9 0.32
24 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TTTAATATTATATTTTATAA
Found at i:16430080 original size:16 final size:16
Alignment explanation
Indices: 16430016--16430072 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
16430006 TTGATTTGCT
*
16430016 ATTATGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
16430032 ATTACGCCTCTATTAC
1 ATTACGCCTCTATTCC
*
16430048 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
16430064 ATTACGCCT
1 ATTACGCCT
16430073 TTCTTCCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.23, C:0.33, G:0.05, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:16432152 original size:43 final size:42
Alignment explanation
Indices: 16432002--16432207 Score: 299
Period size: 42 Copynumber: 4.8 Consensus size: 42
16431992 GTTTTCAAAT
* *
16432002 AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
16432044 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
16432086 CAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
16432128 AAGAAACGCCGCTAAAGAAAATGTTCTTTAGCGGCGCTTTA-AA
1 AA-AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TTAGAA
* *
16432171 AAGAAATGCCGCTAAAG-ACAATGCTCTTTTAGCGGCG
1 AA-AAACGCCGCTAAAGAAC-ATGTTC-TTTAGCGGCG
16432208 TTTATTCTTA
Statistics
Matches: 152, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
42 83 0.55
43 56 0.37
44 13 0.09
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:16432595 original size:21 final size:21
Alignment explanation
Indices: 16432569--16432626 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
16432559 TTTGGCCTGC
*
16432569 TCTGCTTCTCTTGCTGCAGCT
1 TCTGCTTCTCTCGCTGCAGCT
16432590 TCTGCTTCTCTCGCTGCAGCT
1 TCTGCTTCTCTCGCTGCAGCT
*
16432611 TCTGCTTCTCGCGCTG
1 TCTGCTTCTCTCGCTG
16432627 TCGCCTCTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.03, C:0.36, G:0.21, T:0.40
Consensus pattern (21 bp):
TCTGCTTCTCTCGCTGCAGCT
Found at i:16432635 original size:21 final size:21
Alignment explanation
Indices: 16432568--16432638 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
16432558 TTTTGGCCTG
*
16432568 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
*
16432589 TTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
* *
16432610 TTCTGCTTCTCGCGCTGTC-GC
1 CTCTGCTTCTCTCGCTG-CAGC
16432631 CTCTGCTT
1 CTCTGCTT
16432639 TAAGTTGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 44 0.98
22 1 0.02
ACGTcount: A:0.03, C:0.38, G:0.20, T:0.39
Consensus pattern (21 bp):
CTCTGCTTCTCTCGCTGCAGC
Found at i:16436932 original size:9 final size:9
Alignment explanation
Indices: 16436920--16437127 Score: 121
Period size: 9 Copynumber: 23.8 Consensus size: 9
16436910 TGTACATGTA
16436920 TAAGTTATG
1 TAAGTTATG
16436929 TAAGTTATG
1 TAAGTTATG
*
16436938 T-A-TTAAG
1 TAAGTTATG
* *
16436945 TAAGCTATT
1 TAAGTTATG
*
16436954 TAAGTTGTG
1 TAAGTTATG
*
16436963 T-CG-TATG
1 TAAGTTATG
16436970 TAAGTTATG
1 TAAGTTATG
* *
16436979 TAAGTTTTC
1 TAAGTTATG
* *
16436988 AAAGTAATG
1 TAAGTTATG
*
16436997 TATGTTATG
1 TAAGTTATG
16437006 TAAG-T-TG
1 TAAGTTATG
16437013 TAAGTTAT-
1 TAAGTTATG
*
16437021 TATGTATTATG
1 TAAG--TTATG
*
16437032 TAGGTTATG
1 TAAGTTATG
16437041 TAAGTTATG
1 TAAGTTATG
*
16437050 TAAGTTTTG
1 TAAGTTATG
*
16437059 T-A-TTATT
1 TAAGTTATG
*
16437066 TAAGTTGTG
1 TAAGTTATG
16437075 TAAGTTATG
1 TAAGTTATG
* * *
16437084 GATGCTATG
1 TAAGTTATG
*
16437093 TAAGTAATG
1 TAAGTTATG
*
16437102 TGTA-TTATG
1 T-AAGTTATG
*
16437111 TAAGCTTATA
1 TAAG-TTATG
16437121 TAAGTTA
1 TAAGTTA
16437128 ATATGTAACT
Statistics
Matches: 145, Mismatches: 40, Indels: 28
0.68 0.19 0.13
Matches are distributed among these distances:
7 19 0.13
8 12 0.08
9 98 0.68
10 13 0.09
11 3 0.02
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:16437069 original size:16 final size:16
Alignment explanation
Indices: 16437023--16437076 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
16437013 TAAGTTATTA
* *
16437023 TGTATTATGTAGGTTA
1 TGTATTATGTAAGTTG
*
16437039 TGTAAGTTATGTAAGTTT
1 TGT-A-TTATGTAAGTTG
*
16437057 TGTATTATTTAAGTTG
1 TGTATTATGTAAGTTG
16437073 TGTA
1 TGTA
16437077 AGTTATGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 17 0.53
17 2 0.06
18 13 0.41
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (16 bp):
TGTATTATGTAAGTTG
Found at i:16437424 original size:57 final size:57
Alignment explanation
Indices: 16437357--16437475 Score: 222
Period size: 57 Copynumber: 2.1 Consensus size: 57
16437347 TTTTAAAATA
16437357 ATAT-ATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAG
1 ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAG
*
16437413 ATATCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAG
1 ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAG
16437470 ATATCA
1 ATATCA
16437476 ATTTTAAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 4 0.07
57 57 0.93
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (57 bp):
ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAG
Found at i:16437503 original size:76 final size:76
Alignment explanation
Indices: 16437416--16437728 Score: 587
Period size: 76 Copynumber: 4.2 Consensus size: 76
16437406 ATGTAAGATA
16437416 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
1 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
16437481 AAAATATATAT
66 AAAATATATAT
*
16437492 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAACGTAAGATATCAATTTT
1 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
16437557 AAAATA-ATA-
66 AAAATATATAT
*
16437566 T-ATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
1 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
16437630 AAAATATATAT
66 AAAATATATAT
16437641 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
1 TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
16437706 AAAATATATAT
66 AAAATATATAT
16437717 TCATTAATAAGT
1 TCATTAATAAGT
16437729 TAAATGAAAT
Statistics
Matches: 230, Mismatches: 4, Indels: 6
0.96 0.02 0.03
Matches are distributed among these distances:
73 67 0.29
74 4 0.02
75 4 0.02
76 155 0.67
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (76 bp):
TCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAATTTT
AAAATATATAT
Found at i:16437688 original size:149 final size:151
Alignment explanation
Indices: 16437413--16437728 Score: 591
Period size: 149 Copynumber: 2.1 Consensus size: 151
16437403 GTAATGTAAG
*
16437413 ATATCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAAT
1 ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAAT
16437478 TTTAAAATATATATTCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAACGT
66 TTTAAAATATATATTCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAACGT
16437543 AAGATATCAATTTTAAAATA-
131 AAGATATCAATTTTAAAATAT
16437563 ATAT-ATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAAT
1 ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAAT
*
16437627 TTTAAAATATATATTCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAATGT
66 TTTAAAATATATATTCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAACGT
16437692 AAGATATCAATTTTAAAATAT
131 AAGATATCAATTTTAAAATAT
16437713 ATATTCATTAATAAGT
1 ATA-TCATTAATAAGT
16437729 TAAATGAAAT
Statistics
Matches: 161, Mismatches: 2, Indels: 4
0.96 0.01 0.02
Matches are distributed among these distances:
149 143 0.89
150 7 0.04
151 1 0.01
152 10 0.06
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (151 bp):
ATATCATTAATAAGTCATGTAAAATATACTTAATAATATATATTTAAGTAATGTAAGATATCAAT
TTTAAAATATATATTCATTAATAAGTCGTGTAAAATATACTTAATAATATATATTTAAGTAACGT
AAGATATCAATTTTAAAATAT
Found at i:16437925 original size:67 final size:67
Alignment explanation
Indices: 16437853--16437991 Score: 253
Period size: 67 Copynumber: 2.1 Consensus size: 67
16437843 TTTGTTGAGA
*
16437853 ATTCATTATATAATGAATTTATTAAACATTCAATCAATTA-ACTAACCAAAATTGATAATTCATT
1 ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACA-TAACCAAAATTGATAATTCATT
16437917 GAC
65 GAC
16437920 ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
1 ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
16437985 AC
66 AC
16437987 ATTCA
1 ATTCA
16437992 ATCAATTAAT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 69 0.99
68 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (67 bp):
ATTCATTATATAATGAATTTATAAAACATTCAATCAATTACATAACCAAAATTGATAATTCATTG
AC
Found at i:16438072 original size:16 final size:16
Alignment explanation
Indices: 16438051--16438086 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
16438041 ATTAATTGAA
*
16438051 ATAAAATTGTAAATCG
1 ATAAAATTGCAAATCG
16438067 ATAAAATTGCAAATCG
1 ATAAAATTGCAAATCG
16438083 ATAA
1 ATAA
16438087 TTATAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAAAATTGCAAATCG
Found at i:16440155 original size:44 final size:44
Alignment explanation
Indices: 16440071--16440156 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
16440061 ACATATCCAA
* **
16440071 TTGCGGCGTTTTAAGCAAAGCGCCACAAAATGGAGGTCAAAAAT
1 TTGCGGCGTTTTAAGCAAAGCGCCACAAAATAGAACTCAAAAAT
* * *
16440115 TTGCGGCGTTTTATA-CTAAGCGCCACTAAATATAACTCAAAA
1 TTGCGGCGTTTTA-AGCAAAGCGCCACAAAATAGAACTCAAAA
16440157 CGCGGTCGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 34 0.97
45 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (44 bp):
TTGCGGCGTTTTAAGCAAAGCGCCACAAAATAGAACTCAAAAAT
Found at i:16440765 original size:7 final size:7
Alignment explanation
Indices: 16440703--16440768 Score: 87
Period size: 7 Copynumber: 9.4 Consensus size: 7
16440693 CTCAAAAACC
*
16440703 AAACCCC
1 AAACCCT
*
16440710 AAACCCA
1 AAACCCT
*
16440717 AAACCCC
1 AAACCCT
*
16440724 AATCCCT
1 AAACCCT
*
16440731 AAACCCC
1 AAACCCT
16440738 AAACCCT
1 AAACCCT
16440745 AAACCCT
1 AAACCCT
16440752 AAACCCT
1 AAACCCT
16440759 AAACCCT
1 AAACCCT
16440766 AAA
1 AAA
16440769 ACCCCGAGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.45, C:0.45, G:0.00, T:0.09
Consensus pattern (7 bp):
AAACCCT
Found at i:16440768 original size:14 final size:14
Alignment explanation
Indices: 16440703--16440764 Score: 97
Period size: 14 Copynumber: 4.4 Consensus size: 14
16440693 CTCAAAAACC
*
16440703 AAACCCCAAACCCA
1 AAACCCCAAACCCT
*
16440717 AAACCCCAATCCCT
1 AAACCCCAAACCCT
16440731 AAACCCCAAACCCT
1 AAACCCCAAACCCT
*
16440745 AAACCCTAAACCCT
1 AAACCCCAAACCCT
16440759 AAACCC
1 AAACCC
16440765 TAAAACCCCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 44 1.00
ACGTcount: A:0.44, C:0.48, G:0.00, T:0.08
Consensus pattern (14 bp):
AAACCCCAAACCCT
Found at i:16441715 original size:18 final size:18
Alignment explanation
Indices: 16441692--16441727 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
16441682 ATTGAATTTT
16441692 AATT-AATATAAATAAACA
1 AATTAAATATAAA-AAACA
16441710 AATTAAATATAAAAAACA
1 AATTAAATATAAAAAACA
16441728 TATAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AATTAAATATAAAAAACA
Found at i:16441735 original size:18 final size:19
Alignment explanation
Indices: 16441696--16441735 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
16441686 AATTTTAATT
*
16441696 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
16441715 AATATAAA-AAACATATAA
1 AATATAAATAAACAAATAA
16441733 AAT
1 AAT
16441736 GATTTGTGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:16441972 original size:114 final size:114
Alignment explanation
Indices: 16441844--16442265 Score: 772
Period size: 114 Copynumber: 3.7 Consensus size: 114
16441834 CTGCTAATAC
* *
16441844 TATACTTCAGCGGCGTTTTTAACCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
*
16441909 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAATGCCGCTGATGA
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
16441958 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
* *
16442023 CGTTTTGGTTAAGATGATTTGCGGCGCATCAGACAAACGCCACTGATGA
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
16442072 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
16442137 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
66 CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
* * *
16442186 TATACTTTAGCGGCATTTTTTATCAAGTGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
1 TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
16442251 CGTTTTGGTTAAGAT
66 CGTTTTGGTTAAGAT
16442266 ATCTGGAGGC
Statistics
Matches: 298, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 298 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (114 bp):
TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACCAAAACTCTG
CGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCCGCTGATGA
Found at i:16442474 original size:116 final size:113
Alignment explanation
Indices: 16442327--16442596 Score: 278
Period size: 114 Copynumber: 2.4 Consensus size: 113
16442317 TTTCCTTAAA
** * * *
16442327 CGCCACTAATTATAGTATACATCAAGACCAAAACGGAGCGTTTTGATTAGGATATC-TTGCGGCG
1 CGCCACTAATTGCAATATACATCAAGACCAAAACGCAGCGTTTTGATTA--ACATCGTTGCGGCG
* ** * * *
16442391 TTTAATGC-TATGCGCCGCTAATACTATACATTAGCGGCGTTTTATTTATAAG
64 CTT--CCCATAAGCGCCGCTAATACTATACATTACCGGCGTTTT-TTCATAAG
* * *
16442443 CGCCACTAATTGCAATATACATCAAGACC-AAACTCTGCGTTTTGGTTAACATCGTTTGCGGCGC
1 CGCCACTAATTGCAATATACATCAAGACCAAAACGCAGCGTTTTGATTAACATCG-TTGCGGCGC
*
16442507 TTCCCATAAGCGCCGCTAATACTATACATTACCGGCGTTTTTTCGTAAG
65 TTCCCATAAGCGCCGCTAATACTATACATTACCGGCGTTTTTTCATAAG
* * * *
16442556 AGCCAC-AAATGCCAATATACATCAAGACCAGAACGCTGCGT
1 CGCCACTAATTG-CAATATACATCAAGACCAAAACGCAGCGT
16442597 GTTGGTCTTG
Statistics
Matches: 130, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
112 4 0.03
113 33 0.25
114 42 0.32
115 25 0.19
116 26 0.20
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (113 bp):
CGCCACTAATTGCAATATACATCAAGACCAAAACGCAGCGTTTTGATTAACATCGTTGCGGCGCT
TCCCATAAGCGCCGCTAATACTATACATTACCGGCGTTTTTTCATAAG
Found at i:16442530 original size:114 final size:114
Alignment explanation
Indices: 16441836--16442548 Score: 718
Period size: 114 Copynumber: 6.3 Consensus size: 114
16441826 TAAAAGCGCT
* *
16441836 GCTAAT-ACTATACTTCAGCGGCGTTTTTAACCAAGCGCCACTAATTCTAATACTCCTAAAGACC
1 GCTAATGACTATACTTTAGCGGCGTTTTTAA-TAAGCGCCACTAATTCTAATACTCCTAAAGACC
* *
16441900 AAAACTCTGCGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAATGCC
65 AAAACTCTGCGTTTTGGTTAAGATGATTTGCGGCGCATCCCACAAACGCC
*
16441950 GCTGATGA-TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACC
1 GCTAATGACTATACTTTAGCGGCGTTTTTAAT-AAGCGCCACTAATTCTAATACTCCTAAAGACC
**
16442014 AAAACTCTGCGTTTTGGTTAAGATGATTTGCGGCGCATCAGACAAACGCC
65 AAAACTCTGCGTTTTGGTTAAGATGATTTGCGGCGCATCCCACAAACGCC
* *
16442064 ACTGATGA-TATACTTTAGCGGCGTTTTTAATCAAGCGCCACTAATTCTAATACTCCTAAAGACC
1 GCTAATGACTATACTTTAGCGGCGTTTTTAAT-AAGCGCCACTAATTCTAATACTCCTAAAGACC
*
16442128 AAAACTCTGCGTTTTGGTTAAGATGATTTGCGGCGCATCCGACAAACGCC
65 AAAACTCTGCGTTTTGGTTAAGATGATTTGCGGCGCATCCCACAAACGCC
* * * *
16442178 GCTGATGA-TATACTTTAGCGGCATTTTTTATCAAGTGCCACTAATTCTAATACTCCTAAAGACC
1 GCTAATGACTATACTTTAGCGGCGTTTTTAAT-AAGCGCCACTAATTCTAATACTCCTAAAGACC
* * * * *
16442242 AAAACTCTGCGTTTTGGTTAAGAT-ATCTGGAGGCCCTTCCCACCAAACGCT
65 AAAACTCTGCGTTTTGGTTAAGATGAT-TTGCGGCGCATCCCA-CAAACGCC
* * *** * * * * *
16442293 GCT-ATAACTATCCTTTA-CTGGCGTTTTCCTTAAACGCCACTAATTATAGTA-TACATCAAGAC
1 GCTAATGACTATACTTTAGC-GGCGTTTTTAATAAGCGCCACTAATTCTAATACT-CCTAAAGAC
*** * * ** **** **
16442355 CAAAACGGAGCGTTTTGATTAGGAT-ATCTTGCGGCGTTTAATGCTATGCGCC
64 CAAAACTCTGCGTTTTGGTTAAGATGAT-TTGCGGCGCATCCCAC-AAACGCC
* * * *
16442407 GCTAAT-ACTATACATTAGCGGCGTTTTATTTATAAGCGCCACTAATTGC-AATA-TACATCAAG
1 GCTAATGACTATACTTTAGCGGCG-TTT-TTAATAAGCGCCACTAATT-CTAATACT-CCTAAAG
* * * *
16442469 ACC-AAACTCTGCGTTTTGGTTAACATCG-TTTGCGGCGCTTCCCATAAGCGCC
62 ACCAAAACTCTGCGTTTTGGTTAAGAT-GATTTGCGGCGCATCCCACAAACGCC
* *
16442521 GCTAAT-ACTATACATTACCGGCGTTTTT
1 GCTAATGACTATACTTTAGCGGCGTTTTT
16442549 TCGTAAGAGC
Statistics
Matches: 517, Mismatches: 67, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
112 2 0.00
113 7 0.01
114 417 0.81
115 60 0.12
116 31 0.06
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (114 bp):
GCTAATGACTATACTTTAGCGGCGTTTTTAATAAGCGCCACTAATTCTAATACTCCTAAAGACCA
AAACTCTGCGTTTTGGTTAAGATGATTTGCGGCGCATCCCACAAACGCC
Found at i:16445949 original size:29 final size:29
Alignment explanation
Indices: 16445916--16445972 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
16445906 ATTTAAAACT
16445916 ATGTAATTATCGATACAATTTCAAAAGTG
1 ATGTAATTATCGATACAATTTCAAAAGTG
16445945 ATGTAATTATCGATACAATTTCAAAAGT
1 ATGTAATTATCGATACAATTTCAAAAGT
16445973 ATCTATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (29 bp):
ATGTAATTATCGATACAATTTCAAAAGTG
Found at i:16452577 original size:23 final size:23
Alignment explanation
Indices: 16452551--16452606 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
16452541 ATTGTTGTGG
16452551 CCAACGAGAAGAACGAGTTGATT
1 CCAACGAGAAGAACGAGTTGATT
*
16452574 CCAACGGGAAGAACGAGTTGATT
1 CCAACGAGAAGAACGAGTTGATT
*
16452597 CCAACAAGAA
1 CCAACGAGAA
16452607 CAACCACGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (23 bp):
CCAACGAGAAGAACGAGTTGATT
Found at i:16461912 original size:25 final size:25
Alignment explanation
Indices: 16461884--16461958 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
16461874 GAGAGCTTAT
**
16461884 CGATTCTCAGCTTGTATGAGGTTAC
1 CGATTCTCAGCTTGTATGAGCATAC
16461909 CGATT-TACAGCTTGTGA-GAGCATAC
1 CGATTCT-CAGCTTGT-ATGAGCATAC
*
16461934 CGATTCAT-AGCTCGTATGAGCATAC
1 CGATTC-TCAGCTTGTATGAGCATAC
16461959 ATGTACAGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
24 2 0.05
25 38 0.90
26 1 0.02
27 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (25 bp):
CGATTCTCAGCTTGTATGAGCATAC
Found at i:16461927 original size:50 final size:51
Alignment explanation
Indices: 16461841--16461954 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 51
16461831 AGACACACCA
** * *
16461841 CAGCTTGTATGAGCTTACCGATTTGTAGATCATGAGAGCTTATCGATTC-T
1 CAGCTTGTATGAGCTTACCGATTTACAGATCATGAGAGCATACCGATTCAT
* * **
16461891 CAGCTTGTATGAGGTTACCGATTTACAGCTTGTGAGAGCATACCGATTCAT
1 CAGCTTGTATGAGCTTACCGATTTACAGATCATGAGAGCATACCGATTCAT
*
16461942 -AGCTCGTATGAGC
1 CAGCTTGTATGAGC
16461955 ATACATGTAC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 52 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (51 bp):
CAGCTTGTATGAGCTTACCGATTTACAGATCATGAGAGCATACCGATTCAT
Found at i:16463190 original size:13 final size:13
Alignment explanation
Indices: 16463149--16463182 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16463139 ACAGTGAGTT
* *
16463149 ACATGGCTTGGCG
1 ACATGGCCTGGGG
16463162 ACATGGCCTGGGG
1 ACATGGCCTGGGG
16463175 ACATGGCC
1 ACATGGCC
16463183 GTGTGACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.26, G:0.38, T:0.18
Consensus pattern (13 bp):
ACATGGCCTGGGG
Found at i:16465869 original size:6 final size:6
Alignment explanation
Indices: 16465860--16465912 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
16465850 GTTTTATTTT
* *
16465860 TTTATG TTTATG TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
16465908 TTTAT
1 TTTAT
16465913 TTTTTATTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:16473729 original size:21 final size:21
Alignment explanation
Indices: 16473699--16473741 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
16473689 GTATTATGCA
*
16473699 TTATACATATGTGCCCATAAT
1 TTATACATATGTGCCCACAAT
*
16473720 TTATATATATGTGCCCACAAT
1 TTATACATATGTGCCCACAAT
16473741 T
1 T
16473742 ATCCAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (21 bp):
TTATACATATGTGCCCACAAT
Found at i:16475153 original size:127 final size:127
Alignment explanation
Indices: 16474927--16475181 Score: 456
Period size: 127 Copynumber: 2.0 Consensus size: 127
16474917 TATATATAAG
16474927 TAAATGAGGAAACATAAAACCTAGTTCTAAAACTCCATGTTTCCTCTTTTTTTAACTTGATGTTT
1 TAAATGAGGAAACATAAAACCTAGTTCTAAAACTCCATGTTTCCTCTTTTTTTAACTTGATGTTT
*
16474992 AACTCCTCAGCCAACTTTTTCAAATGTTGTAAGGTTCCATTGTCGGTATTATACCATCTTGA
66 AACTCCTCAGCCAACTTTTTCAAATGTTGTAAGGTTCCACTGTCGGTATTATACCATCTTGA
* * *
16475054 TAAATGAGTAAACATAAAACCTGGTTCTAAAACTCCCTGTTTCCTCTTTTTTTAACTTGATGTTT
1 TAAATGAGGAAACATAAAACCTAGTTCTAAAACTCCATGTTTCCTCTTTTTTTAACTTGATGTTT
* *
16475119 AACTTCTCAGCCAAGTTTTTCAAATGTTGTAAGGTTCCACTGTCGGTATTATACCATCTTGA
66 AACTCCTCAGCCAACTTTTTCAAATGTTGTAAGGTTCCACTGTCGGTATTATACCATCTTGA
16475181 T
1 T
16475182 CTCCACTATA
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 122 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (127 bp):
TAAATGAGGAAACATAAAACCTAGTTCTAAAACTCCATGTTTCCTCTTTTTTTAACTTGATGTTT
AACTCCTCAGCCAACTTTTTCAAATGTTGTAAGGTTCCACTGTCGGTATTATACCATCTTGA
Found at i:16503350 original size:26 final size:26
Alignment explanation
Indices: 16503320--16503380 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
16503310 TAGGTTAATT
* *
16503320 TTAAAATAAGTAATATGTAAAATAAC
1 TTAAAATAAATAATATATAAAATAAC
*
16503346 TTAAAATAAATAATATATAAAGTAAC
1 TTAAAATAAATAATATATAAAATAAC
16503372 TTAAAATAA
1 TTAAAATAA
16503381 TTAGTCTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:16503428 original size:21 final size:21
Alignment explanation
Indices: 16503399--16503438 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16503389 ATAGGTTATG
16503399 TTAAAATAATAAATAAAAGGT
1 TTAAAATAATAAATAAAAGGT
* **
16503420 TTAATATAATCTATAAAAG
1 TTAAAATAATAAATAAAAG
16503439 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAAATAATAAATAAAAGGT
Found at i:16504625 original size:21 final size:20
Alignment explanation
Indices: 16504592--16504631 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
16504582 AATCGGGTTT
16504592 GGGTTAGGCTAATTTGGGCTG
1 GGGTTAGGCTAA-TTGGGCTG
16504613 GGGTT-GGCTTAATTGGGCT
1 GGGTTAGGC-TAATTGGGCT
16504632 TAGTTCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.12, C:0.10, G:0.42, T:0.35
Consensus pattern (20 bp):
GGGTTAGGCTAATTGGGCTG
Found at i:16504723 original size:14 final size:15
Alignment explanation
Indices: 16504699--16504733 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
16504689 TTTTGGTTTG
16504699 TTATATGGACTGTTA
1 TTATATGGACTGTTA
*
16504714 TTAT-TGGACTTTTA
1 TTATATGGACTGTTA
16504728 TTATAT
1 TTATAT
16504734 ATATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (15 bp):
TTATATGGACTGTTA
Found at i:16508530 original size:251 final size:251
Alignment explanation
Indices: 16508087--16508595 Score: 946
Period size: 251 Copynumber: 2.0 Consensus size: 251
16508077 TAAAATTTTA
*
16508087 GATTTTTGTTGAGTAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGA
1 GATTTTTGCTGAGTAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGA
16508152 AGTAGTTTTAACAATCTTTTTCATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTCTTCTTC
66 AGTAGTTTTAACAATCTTTTTCATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTCTTCTTC
** *
16508217 ATTGGAGGGGAGATTAGAGTTGTTTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGCTTCTT
131 ATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAGTTGTGAAATATTTCTCGATTTCAAGGCTTCTT
16508282 AGGACTTTATCTTTATTTTCTTGCTGTTCAATCTCTTTTAAATTTCTGCTTGTGTC
196 AGGACTTTATCTTTATTTTCTTGCTGTTCAATCTCTTTTAAATTTCTGCTTGTGTC
16508338 GATTTTTGCTGAGTAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGA
1 GATTTTTGCTGAGTAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGA
* *
16508403 AGTAGTTTTAACAATCTTTTTCATTGTGGGAGCCATCTTTAGCCTTCTTCTTGCCATTGTTCTTC
66 AGTAGTTTTAACAATCTTTTTCATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTCTTCTTC
*
16508468 ATTGGAGGGGAGGTTAGAGCCGTTTGAAGGGAGTTGTGAAATATTTCTCGATTTCAAGGCTTCTT
131 ATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAGTTGTGAAATATTTCTCGATTTCAAGGCTTCTT
*
16508533 AGGACTTTATCTTTATTTTCTTGTTGTTCAATCTCTTTTAAATTTCTGCTTGTGTC
196 AGGACTTTATCTTTATTTTCTTGCTGTTCAATCTCTTTTAAATTTCTGCTTGTGTC
16508589 GATTTTT
1 GATTTTT
16508596 ATTAGCTAAT
Statistics
Matches: 250, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
251 250 1.00
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (251 bp):
GATTTTTGCTGAGTAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGA
AGTAGTTTTAACAATCTTTTTCATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTCTTCTTC
ATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAGTTGTGAAATATTTCTCGATTTCAAGGCTTCTT
AGGACTTTATCTTTATTTTCTTGCTGTTCAATCTCTTTTAAATTTCTGCTTGTGTC
Found at i:16514470 original size:17 final size:17
Alignment explanation
Indices: 16514437--16514474 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
16514427 CAAGTCCACA
*
16514437 ACCAATTTACTTAGCAT
1 ACCAATTTACATAGCAT
16514454 ACCAATTTACCAT-GCAT
1 ACCAATTTA-CATAGCAT
16514471 ACCA
1 ACCA
16514475 TCCATTAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (17 bp):
ACCAATTTACATAGCAT
Found at i:16516275 original size:15 final size:15
Alignment explanation
Indices: 16516232--16516279 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
16516222 TAGGGTTGTA
*
16516232 GTAAATAAAATATAT
1 GTAAGTAAAATATAT
*
16516247 ATAAGTAAATAATATAT
1 GTAAGT-AA-AATATAT
*
16516264 GTATGTAAAATATAT
1 GTAAGTAAAATATAT
16516279 G
1 G
16516280 CGATGTTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.35
Consensus pattern (15 bp):
GTAAGTAAAATATAT
Found at i:16517031 original size:16 final size:17
Alignment explanation
Indices: 16516998--16517037 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
16516988 TGCTTGGGAA
16516998 ATTATTTTGGACTTTGG
1 ATTATTTTGGACTTTGG
*
16517015 ATTATTTT-GATTTTGG
1 ATTATTTTGGACTTTGG
16517031 ATT-TTTT
1 ATTATTTT
16517038 TACATGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 10 0.45
17 8 0.36
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.62
Consensus pattern (17 bp):
ATTATTTTGGACTTTGG
Found at i:16517735 original size:16 final size:16
Alignment explanation
Indices: 16517714--16517745 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16517704 ATATATTGTG
*
16517714 AAACTCTAGATTCTGA
1 AAACTCTAGATACTGA
16517730 AAACTCTAGATACTGA
1 AAACTCTAGATACTGA
16517746 TACAATAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (16 bp):
AAACTCTAGATACTGA
Found at i:16521358 original size:22 final size:22
Alignment explanation
Indices: 16521330--16521374 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
16521320 ATTATGATGA
16521330 TTGATATG-ATGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
16521352 TTGATATGTATGTGATTATATT
1 TTGATATGTATGAGATTATATT
16521374 T
1 T
16521375 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:16522529 original size:15 final size:15
Alignment explanation
Indices: 16522509--16522537 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16522499 TATGCATACA
16522509 AAATATAAAAGACAG
1 AAATATAAAAGACAG
16522524 AAATATAAAAGACA
1 AAATATAAAAGACA
16522538 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (15 bp):
AAATATAAAAGACAG
Found at i:16538672 original size:51 final size:50
Alignment explanation
Indices: 16538544--16538731 Score: 209
Period size: 51 Copynumber: 3.7 Consensus size: 50
16538534 TACCATTCGA
* **
16538544 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTCCGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAACCCTCCGG
* *
16538594 TTCACGTAGTAGCCTACACATAGTACTACACACGTGA-CTAAATCCCTCTGG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGATC-AAA-CCCTCCGG
* * * * * *
16538645 TACACATAGTAGCCTGCACATAGTACTACACATGTGATCATTA-TCTACCGA
1 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCA-AACCCT-CCGG
* *
16538696 TACACGTAGTAGCCTACACTTATTACTACACACGTG
1 TACACGTAGTAGCCTACACATAGTACTACACACGTG
16538732 TCCACAAACA
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 40 0.35
51 72 0.63
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (50 bp):
TACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAACCCTCCGG
Found at i:16540274 original size:24 final size:24
Alignment explanation
Indices: 16540250--16540296 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
16540240 AAACTCCTTC
16540250 TAAAGAAAACTCAAGAAAGAATTCT
1 TAAAGAAAACTCAA-AAAGAATTCT
** *
16540275 TGGAGAAAACTCAAAGAGAATT
1 TAAAGAAAACTCAAAAAGAATT
16540297 TTTCACTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (24 bp):
TAAAGAAAACTCAAAAAGAATTCT
Found at i:16553873 original size:12 final size:12
Alignment explanation
Indices: 16553856--16553926 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 12
16553846 TCACTCTCAT
16553856 TTTCTTTTTCAA
1 TTTCTTTTTCAA
16553868 TTTCTTGTTTTC--
1 TTTC-T-TTTTCAA
* * *
16553880 TTTCATGTTCAT
1 TTTCTTTTTCAA
16553892 TTTCTTTTTCAA
1 TTTCTTTTTCAA
***
16553904 TTTCTTTTTGTT
1 TTTCTTTTTCAA
16553916 TTTCTTTTTCA
1 TTTCTTTTTCA
16553927 CATGCTGTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
10 4 0.09
12 35 0.78
13 1 0.02
14 5 0.11
ACGTcount: A:0.10, C:0.15, G:0.04, T:0.70
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:16554970 original size:13 final size:12
Alignment explanation
Indices: 16554938--16554969 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
16554928 AACGCAACCA
16554938 TTTTTTTTGAAC
1 TTTTTTTTGAAC
16554950 TTTTTTTTGAAC
1 TTTTTTTTGAAC
16554962 TTTTTTTT
1 TTTTTTTT
16554970 TCAATTCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (12 bp):
TTTTTTTTGAAC
Found at i:16556190 original size:20 final size:20
Alignment explanation
Indices: 16556165--16556209 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
16556155 TAAATTCACA
16556165 TAATTAAAAC-AAGACAC-AAT
1 TAATT-AAACTAAGAC-CTAAT
16556185 TAATTAAACTAAGACCTAAT
1 TAATTAAACTAAGACCTAAT
16556205 TAATT
1 TAATT
16556210 CTGTTAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (20 bp):
TAATTAAACTAAGACCTAAT
Found at i:16557903 original size:18 final size:19
Alignment explanation
Indices: 16557880--16557918 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16557870 CTTGGCCCAT
* *
16557880 TACAGTATC-GATATTCAG
1 TACAGTAACTGATATACAG
16557898 TACAGTAACTGATATACAG
1 TACAGTAACTGATATACAG
16557917 TA
1 TA
16557919 TCAAATCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
TACAGTAACTGATATACAG
Done.