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 6 of 168
Found at i:1615865 original size:13 final size:13
Alignment explanation
Indices: 1615847--1615876 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1615837 TTTTAGTTTT
1615847 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
1615860 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
1615873 ATTG
1 ATTG
1615877 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:1620651 original size:29 final size:30
Alignment explanation
Indices: 1620598--1620657 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1620588 TCCGAGCCTT
* *
1620598 GGGGCAAAAATGTAATTATTTAAAAATTTA
1 GGGGCAAAAATGTAATTATTGAAAAAGTTA
*
1620628 GGGGCAAAATTGTAATT-TTGAAAAAGTTA
1 GGGGCAAAAATGTAATTATTGAAAAAGTTA
1620657 G
1 G
1620658 AGTCGAGGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATTGAAAAAGTTA
Found at i:1620885 original size:13 final size:13
Alignment explanation
Indices: 1620867--1620898 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1620857 TTTCCAGCAA
1620867 TTATGAATTTATT
1 TTATGAATTTATT
1620880 TTATGAATTTATT
1 TTATGAATTTATT
*
1620893 TGATGA
1 TTATGA
1620899 TGATCTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1621106 original size:50 final size:50
Alignment explanation
Indices: 1620993--1621189 Score: 250
Period size: 50 Copynumber: 3.8 Consensus size: 50
1620983 ATTTGGGTAA
* * *
1620993 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
1621049 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1621099 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1621149 AGATGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGC
1621190 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
50 83 0.65
52 1 0.01
53 3 0.02
55 2 0.02
56 39 0.30
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1621183 original size:100 final size:103
Alignment explanation
Indices: 1620993--1621189 Score: 301
Period size: 100 Copynumber: 1.9 Consensus size: 103
1620983 ATTTGGGTAA
1620993 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
*
1621058 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
1621099 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGATGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
1621161 TAAGACCATGTCTGGGACATGGCATGGGC
66 TAAGACCATGTCTGGGACATGGCATGGGC
1621190 NNNNNNNNNN
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
100 42 0.49
101 2 0.02
105 2 0.02
106 40 0.47
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1625591 original size:21 final size:21
Alignment explanation
Indices: 1625566--1625643 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 21
1625556 CAGACCCAAA
1625566 GTATAGAAACATAGATATGAG
1 GTATAGAAACATAGATATGAG
1625587 GTATA-AGAACAT-GAGTATGA-
1 GTATAGA-AACATAGA-TATGAG
* * * *
1625607 GTATCGGAACCTAGGTATGAG
1 GTATAGAAACATAGATATGAG
*
1625628 GTACT-GGAACATAGAT
1 GTA-TAGAAACATAGAT
1625644 CTATGTATCG
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
20 16 0.36
21 28 0.62
22 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.27, T:0.24
Consensus pattern (21 bp):
GTATAGAAACATAGATATGAG
Found at i:1625713 original size:20 final size:21
Alignment explanation
Indices: 1625662--1625714 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1625652 CGGAAACCCA
*
1625662 AGGTATAGGAACATAGATATG
1 AGGTATAAGAACATAGATATG
1625683 AGGTATAAGAACATA-AGTATG
1 AGGTATAAGAACATAGA-TATG
*
1625704 -GGTATCAGAAC
1 AGGTATAAGAAC
1625715 CTAGGCCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.43, C:0.08, G:0.26, T:0.23
Consensus pattern (21 bp):
AGGTATAAGAACATAGATATG
Found at i:1633873 original size:12 final size:12
Alignment explanation
Indices: 1633856--1633894 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1633846 ACTAACAATC
1633856 ATTTATTAATAT
1 ATTTATTAATAT
1633868 ATTTATATAAATAT
1 ATTTAT-T-AATAT
*
1633882 ATTTTTTAATAT
1 ATTTATTAATAT
1633894 A
1 A
1633895 AAATATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.50
13 2 0.08
14 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATTAATAT
Found at i:1641553 original size:53 final size:52
Alignment explanation
Indices: 1641492--1641597 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 52
1641482 TTTTCTATTA
*
1641492 AAAATTGATATGATTAACGGAATAATTAGATATGATTAAAAAGCAAACTGTAC
1 AAAATTGATATGATTAACGGAATAATTAGATATGATT-AAAAGCAAACTATAC
*
1641545 AAAATTGATATGATTAACTGAATAATTAGATATGATTAAAAGCAAACTATAC
1 AAAATTGATATGATTAACGGAATAATTAGATATGATTAAAAGCAAACTATAC
1641597 A
1 A
1641598 CGTGCCATGT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 15 0.29
53 36 0.71
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (52 bp):
AAAATTGATATGATTAACGGAATAATTAGATATGATTAAAAGCAAACTATAC
Found at i:1642377 original size:12 final size:12
Alignment explanation
Indices: 1642362--1642386 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1642352 TTTTGGATTA
1642362 AAATGTTATGTG
1 AAATGTTATGTG
1642374 AAATGTTATGTG
1 AAATGTTATGTG
1642386 A
1 A
1642387 TTATACATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AAATGTTATGTG
Found at i:1645035 original size:18 final size:19
Alignment explanation
Indices: 1644987--1645037 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
1644977 AAACATCATT
*
1644987 AAAATTTATAAAAATATTA
1 AAAATTAATAAAAATATTA
1645006 AATAA--AATTAAAAA-ATTA
1 AA-AATTAA-TAAAAATATTA
1645024 AAAATTAATAAAAA
1 AAAATTAATAAAAA
1645038 CCATTTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
17 2 0.07
18 13 0.48
19 10 0.37
20 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATTAATAAAAATATTA
Found at i:1645709 original size:21 final size:21
Alignment explanation
Indices: 1645685--1645742 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
1645675 AAAAAATTTG
*
1645685 AAATTTATTTAATATTTTTAT
1 AAATTTATTTAATATTTTTAA
*
1645706 AAATTT-TAATAAT-TTTTTAA
1 AAATTTAT-TTAATATTTTTAA
*
1645726 AAATTTA-TAAATATTTT
1 AAATTTATTTAATATTTT
1645743 AAGAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 3 0.10
20 17 0.57
21 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATTTATTTAATATTTTTAA
Found at i:1645763 original size:12 final size:12
Alignment explanation
Indices: 1645717--1645770 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
1645707 AATTTTAATA
1645717 ATTTTTTAAAA-
1 ATTTTTTAAAAT
*
1645728 A-TTTAT-AAAT
1 ATTTTTTAAAAT
**
1645738 ATTTTAAGAAAAT
1 ATTTT-TTAAAAT
1645751 ATTTTTTAAAAT
1 ATTTTTTAAAAT
1645763 ATTTTTTA
1 ATTTTTTA
1645771 TTTTGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 3 0.09
10 5 0.14
11 4 0.11
12 14 0.40
13 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (12 bp):
ATTTTTTAAAAT
Found at i:1666003 original size:54 final size:54
Alignment explanation
Indices: 1665866--1666017 Score: 151
Period size: 54 Copynumber: 2.8 Consensus size: 54
1665856 ACTTTCAAAG
* * * * * *
1665866 TTGGGACACACGGTTGTGTCTCAGCCCATGCCTTTGCCCGTGTAACTCACTGAC
1 TTGGGACACACGGTCGTGTCCCAGCCCGTGTCTCTGCCCGTGTAACTCACTAAC
* ** * * *
1665920 TTGAGACACACGACCATGTCCCAGCCCGTGTCTCTGCCTGTGTAACTCACTAAT
1 TTGGGACACACGGTCGTGTCCCAGCCCGTGTCTCTGCCCGTGTAACTCACTAAC
* * * **
1665974 TTGGGTCACACGGTCGTGTCGCAGGCCGTGTCTCAACCCGTGTA
1 TTGGGACACACGGTCGTGTCCCAGCCCGTGTCTCTGCCCGTGTA
1666018 GAAACTACAC
Statistics
Matches: 76, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.18, C:0.32, G:0.24, T:0.26
Consensus pattern (54 bp):
TTGGGACACACGGTCGTGTCCCAGCCCGTGTCTCTGCCCGTGTAACTCACTAAC
Found at i:1677089 original size:11 final size:11
Alignment explanation
Indices: 1677055--1677119 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 11
1677045 ATTCCGTTCA
1677055 AAAATTCTCTC
1 AAAATTCTCTC
*
1677066 -AAATTCCTTTC
1 AAAATT-CTCTC
1677077 AAAATTCTCTC
1 AAAATTCTCTC
1677088 -AAA--CTCTC
1 AAAATTCTCTC
1677096 -AAATTC-CTTCC
1 AAAATTCTC-T-C
1677107 AAAATTCTCTC
1 AAAATTCTCTC
1677118 AA
1 AA
1677120 TTTCCTTCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
8 8 0.18
9 1 0.02
10 10 0.23
11 12 0.27
12 12 0.27
13 1 0.02
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATTCTCTC
Found at i:1677090 original size:22 final size:22
Alignment explanation
Indices: 1677020--1677090 Score: 101
Period size: 22 Copynumber: 3.2 Consensus size: 22
1677010 AAATTCAATA
*
1677020 TCAATTTCCTTCAAAAATTCTC
1 TCAAATTCCTTCAAAAATTCTC
1677042 TC-AATTCCGTTCAAAAATTCTC
1 TCAAATTCC-TTCAAAAATTCTC
1677064 TCAAATTCCTTTC-AAAATTCTC
1 TCAAATTCC-TTCAAAAATTCTC
1677086 TCAAA
1 TCAAA
1677091 CTCTCAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.11
22 31 0.69
23 9 0.20
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.38
Consensus pattern (22 bp):
TCAAATTCCTTCAAAAATTCTC
Found at i:1677096 original size:30 final size:30
Alignment explanation
Indices: 1677061--1677119 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1677051 TTCAAAAATT
*
1677061 CTCTCAAATTCCTTTCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATTCTCTCAAA
1677091 CTCTCAAATTCCTTCCAAAATTCTCTCAA
1 CTCTCAAATTCCTTCCAAAATTCTCTCAA
1677120 TTTCCTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATTCTCTCAAA
Found at i:1677118 original size:22 final size:22
Alignment explanation
Indices: 1677091--1677142 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1677081 TTCTCTCAAA
* *
1677091 CTCTCAAATTCCTTCCAAAATT
1 CTCTCAAATTCCTTCAAAAAAT
*
1677113 CTCTCAATTTCCTTCAAAAAAT
1 CTCTCAAATTCCTTCAAAAAAT
1677135 CTC-CAAAT
1 CTCTCAAAT
1677143 CCATATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (22 bp):
CTCTCAAATTCCTTCAAAAAAT
Found at i:1677197 original size:27 final size:27
Alignment explanation
Indices: 1677167--1677227 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
1677157 TTTCTCCATT
1677167 AAATTTCATTA-TTTTAAGAA-AATTTTA
1 AAATTT-ATTATTTTTAA-AATAATTTTA
*
1677194 AAATTTTTTATTTTTTAAAATAATTTTA
1 AAATTTATTA-TTTTTAAAATAATTTTA
1677222 AAATTT
1 AAATTT
1677228 TTAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.10
27 8 0.27
28 19 0.63
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
AAATTTATTATTTTTAAAATAATTTTA
Found at i:1677237 original size:28 final size:28
Alignment explanation
Indices: 1677176--1677237 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1677166 TAAATTTCAT
*
1677176 TATTTTAAGAAAATTTTAAAATTTTTTA
1 TATTTTAAGAAAATTTTAAAATTTTTAA
*
1677204 TTTTTTAA-AATAATTTTAAAATTTTTAA
1 TATTTTAAGAA-AATTTTAAAATTTTTAA
1677232 TATTTT
1 TATTTT
1677238 CAACAATGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTTTAAGAAAATTTTAAAATTTTTAA
Found at i:1677357 original size:14 final size:15
Alignment explanation
Indices: 1677328--1677361 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1677318 AAATTTTAAA
1677328 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
1677343 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
1677357 TTTTA
1 TTTTA
1677362 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:1679623 original size:28 final size:28
Alignment explanation
Indices: 1679583--1680216 Score: 708
Period size: 28 Copynumber: 22.9 Consensus size: 28
1679573 TTTTGACATT
*
1679583 ATTTGATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1679611 ATTTAATTAAAAACCCTTACCCTAACCTA
1 ATTTAATTAAAAACCC-TAACCTAACTTA
1679640 ATTTAATTAAAAA--CT---CTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1679663 ACTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1679691 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1679719 AATTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
1679747 ATTTAATTAAAAACCCTAA-C---C-TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1679770 ATTTAATTAAAAACCCTAAACTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1679798 ATTTAATTAAAAACCCTAACATAA-TTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1679825 A-TTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1679852 ATTTAATTAAAAACCCTTACCCTAACATA
1 ATTTAATTAAAAACCC-TAACCTAACTTA
* *
1679881 ATTTAATTAAAAACTCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1679909 ATTTAATTAAAAAACC---CCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1679934 ATTTTAGTTAAAAACCCTAACCCTAACCTA
1 A-TTTAATTAAAAACCCTAA-CCTAACTTA
* * * *
1679964 TTTTACA-TGAAAACCTTAACCCTAACCTA
1 ATTTA-ATTAAAAACCCTAA-CCTAACTTA
*
1679993 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1680021 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1680049 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1680077 ATTTAATTAAAAACCCTTACCCTAACCTA
1 ATTTAATTAAAAACCC-TAACCTAACTTA
*
1680106 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1680134 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* * *** * * *
1680162 GTTAAAATTCCTAACCCGACCCTAATTTA
1 ATT-TAATTAAAAACCCTAACCTAACTTA
*
1680191 A-TTAATGTAAAAACCCTAACATAACT
1 ATTTAAT-TAAAAACCCTAACCTAACT
1680217 CAGCGGATTT
Statistics
Matches: 519, Mismatches: 63, Indels: 48
0.82 0.10 0.08
Matches are distributed among these distances:
23 40 0.08
24 1 0.00
25 10 0.02
26 35 0.07
27 13 0.03
28 283 0.55
29 129 0.25
30 8 0.02
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.33
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACTTA
Found at i:1685824 original size:11 final size:11
Alignment explanation
Indices: 1685810--1685834 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1685800 ATATAAATAT
1685810 TATATATTTAA
1 TATATATTTAA
1685821 TATATATTTAA
1 TATATATTTAA
1685832 TAT
1 TAT
1685835 GGGCTGGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATTTAA
Found at i:1692248 original size:11 final size:10
Alignment explanation
Indices: 1692235--1692287 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 10
1692225 AAATATGAAT
1692235 TTGAGAGAAA
1 TTGAGAGAAA
1692245 TTTG-GAAGGAAA
1 -TTGAG-A-GAAA
1692257 TTGAGAGCAAA
1 TTGAGAG-AAA
1692268 TTGAGAGGAAA
1 TTGAGA-GAAA
1692279 TTGAGAGAA
1 TTGAGAGAA
1692288 TAATTGAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
10 5 0.14
11 26 0.70
12 6 0.16
ACGTcount: A:0.45, C:0.02, G:0.32, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:1692260 original size:22 final size:21
Alignment explanation
Indices: 1692235--1692296 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 21
1692225 AAATATGAAT
1692235 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAA-TTGAG-AGGAAA
1692257 TTGAGAGCAAATTGAGAGGAAA
1 TTGAGAG-AAATTGAGAGGAAA
1692279 TTGAGAGAATAATTGAGA
1 TTGAGAG-A-AATTGAGA
1692297 AATGATTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 24 0.67
23 12 0.33
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.23
Consensus pattern (21 bp):
TTGAGAGAAATTGAGAGGAAA
Found at i:1695413 original size:59 final size:58
Alignment explanation
Indices: 1695307--1695418 Score: 127
Period size: 59 Copynumber: 1.9 Consensus size: 58
1695297 TATCAAAGAC
* ** * *
1695307 TAACTTGGATAAAAAAAATTCAAATCCCAATGTGGAAATAATTACCAAATTTAGGGCT
1 TAACTTGGATAAAAAAAATTCAAATCCCAATATAAAAACAATCACCAAATTTAGGGCT
* * *
1695365 TAACTTGGATAAAAAAATTTTCAAA-CCTGAATATAAAAACAATCACCAAGTTTA
1 TAACTTGGATAAAAAAA-ATTCAAATCC-CAATATAAAAACAATCACCAAATTTA
1695419 AACTAAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
58 19 0.43
59 25 0.57
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (58 bp):
TAACTTGGATAAAAAAAATTCAAATCCCAATATAAAAACAATCACCAAATTTAGGGCT
Found at i:1701081 original size:44 final size:44
Alignment explanation
Indices: 1701022--1701224 Score: 164
Period size: 44 Copynumber: 4.7 Consensus size: 44
1701012 ATCTGATGCG
* *
1701022 ATCCGCTCTACTGCAACTTCAGAGAGATGAGATCTGCGGTTTTA
1 ATCCGCTCCACTGCAACTTCAGAGAGATAAGATCTGCGGTTTTA
* * * * *
1701066 ATCCACTCCACTGCAACTTCAGGGAGATAGGATCTGC-TTTCTTCT
1 ATCCGCTCCACTGCAACTTCAGAGAGATAAGATCTGCGGTT-TT-A
* * * * * * *
1701111 GTCCGCTCCACTGTAACTTTAGGGAGATAAGA-CT--GGATGTG
1 ATCCGCTCCACTGCAACTTCAGAGAGATAAGATCTGCGGTTTTA
* * *
1701152 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
1 ATCCGCTCCACTGCAACTTCAGAGAGATAAGATCTGCGGTTTTA
* * *
1701196 ATCCACTCCATTGCAGCTTCA-AGGAGATA
1 ATCCGCTCCACTGCAACTTCAGA-GAGATA
1701225 TGATTGGTAT
Statistics
Matches: 122, Mismatches: 30, Indels: 14
0.73 0.18 0.08
Matches are distributed among these distances:
41 26 0.21
42 3 0.02
43 4 0.03
44 62 0.51
45 27 0.22
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (44 bp):
ATCCGCTCCACTGCAACTTCAGAGAGATAAGATCTGCGGTTTTA
Found at i:1701423 original size:132 final size:132
Alignment explanation
Indices: 1701267--1702421 Score: 1899
Period size: 132 Copynumber: 8.8 Consensus size: 132
1701257 ACATGAAGAC
* * * *
1701267 AAGATCTGCT-ATCTTCGATCTATTCCACTGCCGACCAGGGAGATAGAATTACTGGCTTCAATAT
1 AAGATCTG-TAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGT
* * * * *
1701331 ACTCCACTGTAACCTCAAGGAGGTAAAATCTGTCATCTTCGATCTACTCCACTACTGCCTAGGGA
65 ACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGA
1701396 GAT
130 GAT
* * *
1701399 AAGACCTGTAATCTTCAATCTATTCCACTACTGCCCAAGGAGATAGAATTACTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
* * *
1701464 CTCTACTGTAACCTCAGGGAGGTAAAATCCGTCATCTTCGATCTGCTCCACTACTGTTTAGGGAG
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1701529 AT
131 AT
* * *
1701531 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCTATGGAGATAGAATTACTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
1701596 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1701661 AT
131 AT
*
1701663 AAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
*
1701728 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTCCGATCTGCTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1701793 AT
131 AT
* *
1701795 AATATCTGTAATCTTCAATCTATTCCACTG-TCGCCCAGGGAGATAAAATTACTGGCTTCAATGT
1 AAGATCTGTAATCTTCAATCTATTCCACTGCT-GCCCAGGGAGATAGAATTACTGGCTTCAATGT
*
1701859 ACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTT-GATCTGCTCTACTACTGCTTAGGG
65 ACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT-CTTCGATCTGCTCCACTACTGCTTAGGG
1701923 AGAT
129 AGAT
*
1701927 AAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAAAATTACTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
*
1701992 TTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTT-GATCTGCTCCACTACTGCTTAGGGA
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT-CTTCGATCTGCTCCACTACTGCTTAGGGA
1702056 GAT
130 GAT
* * *
1702059 AAGATCTATAATCTTCAATCTATTGCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATATA
1 AAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
* *
1702124 CTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1702189 AT
131 AT
* * *
1702191 AAGATCTGTAATATTCAATTTATTCCACTGCTGCCCTGGGAGATAGAATTACTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
*
1702256 CTCCACTGTAACCTCATGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1702321 AT
131 AT
* * *
1702323 AAGATCTGTAATCTTCAATCTATTCCATTGCTACCCATGGAGATAGAATTACTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
1702388 CTCCACTGTAACCTCAGGGAGGT-AAA-CCGCCATC
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATC
1702422 AACCTGCTCC
Statistics
Matches: 962, Mismatches: 56, Indels: 12
0.93 0.05 0.01
Matches are distributed among these distances:
130 8 0.01
131 8 0.01
132 943 0.98
133 3 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (132 bp):
AAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
AT
Found at i:1703829 original size:14 final size:15
Alignment explanation
Indices: 1703812--1703844 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1703802 TCCATTTTAC
1703812 TTTTTCAT-TTTTCA
1 TTTTTCATCTTTTCA
1703826 -TTTTCATCTTTTCA
1 TTTTTCATCTTTTCA
1703840 TTTTT
1 TTTTT
1703845 TCACATCGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTCATCTTTTCA
Found at i:1703847 original size:8 final size:7
Alignment explanation
Indices: 1703812--1703844 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1703802 TCCATTTTAC
1703812 TTTTTCA
1 TTTTTCA
1703819 TTTTTCA
1 TTTTTCA
1703826 -TTTTCA
1 TTTTTCA
1703832 TCTTTTCA
1 T-TTTTCA
1703840 TTTTT
1 TTTTT
1703845 TCACATCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:1704826 original size:19 final size:19
Alignment explanation
Indices: 1704802--1704841 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1704792 GGTTTGGCAG
1704802 AAAAAATCCAAAAGAATGA
1 AAAAAATCCAAAAGAATGA
**
1704821 AAAAAATCGTAAAGAATGA
1 AAAAAATCCAAAAGAATGA
1704840 AA
1 AA
1704842 GAACATTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.07, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAAATCCAAAAGAATGA
Found at i:1706710 original size:19 final size:20
Alignment explanation
Indices: 1706686--1706725 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1706676 AACTGTGTTT
* *
1706686 AATGCATATG-ATGTAATGA
1 AATGCAAATGCATGAAATGA
1706705 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
1706725 A
1 A
1706726 TTCGAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:1708898 original size:2 final size:2
Alignment explanation
Indices: 1708893--1708920 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1708883 ATACAAAACA
1708893 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
1708921 TACATAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1708959 original size:6 final size:6
Alignment explanation
Indices: 1708950--1708991 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
1708940 GCATATGGAT
*
1708950 ATAAAA ATAATAAA ATGAAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAAAA AT-A-AAA ATAAAA ATAAAA ATAAAA ATAAAA ATAA
1708992 GTAATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.81
7 1 0.03
8 5 0.16
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:1711148 original size:19 final size:19
Alignment explanation
Indices: 1711124--1711161 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1711114 GACTGAATTG
1711124 CTTATCCATTCATCTACAA
1 CTTATCCATTCATCTACAA
1711143 CTTATCCATTCATCTACAA
1 CTTATCCATTCATCTACAA
1711162 ACTAACTCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.37
Consensus pattern (19 bp):
CTTATCCATTCATCTACAA
Found at i:1714130 original size:20 final size:20
Alignment explanation
Indices: 1714107--1714151 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1714097 AAAAAATTAG
1714107 AAAATTAAAAAAAGTATTTT
1 AAAATTAAAAAAAGTATTTT
*
1714127 AAAAATAAAAAAAGTATTTT
1 AAAATTAAAAAAAGTATTTT
1714147 AAAAT
1 AAAAT
1714152 ATTTCTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAATTAAAAAAAGTATTTT
Found at i:1714637 original size:20 final size:20
Alignment explanation
Indices: 1714607--1714658 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1714597 GGCCTTCTGC
*
1714607 CACCGCCGCCAAC-GTCACGT
1 CACCACCGCC-ACGGTCACGT
*
1714627 CGCCACCGCCACGGTCACGT
1 CACCACCGCCACGGTCACGT
*
1714647 CACCACCACCAC
1 CACCACCGCCAC
1714659 TTGCGCCGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.21, C:0.54, G:0.17, T:0.08
Consensus pattern (20 bp):
CACCACCGCCACGGTCACGT
Found at i:1715525 original size:3 final size:3
Alignment explanation
Indices: 1715508--1715570 Score: 108
Period size: 3 Copynumber: 20.3 Consensus size: 3
1715498 CTTGGCAATT
1715508 TTA TTA TTTA GTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1715555 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
1715571 CATCTACTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
3 52 0.90
4 6 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1718048 original size:19 final size:19
Alignment explanation
Indices: 1718008--1718050 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1717998 ATCTCTTTAG
* *
1718008 GCATTCATTTCATGCATGT
1 GCATTCATTGCATGCATAT
1718027 GCATTGCATTGCAT-CATAT
1 GCATT-CATTGCATGCATAT
1718046 GCATT
1 GCATT
1718051 AAATTTTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (19 bp):
GCATTCATTGCATGCATAT
Found at i:1720301 original size:15 final size:14
Alignment explanation
Indices: 1720281--1720336 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1720271 ATTTTCAAAA
1720281 AAAAAGAAGAAGAAG
1 AAAAAGAA-AAGAAG
*
1720296 AAAAAGAAAA-AAA
1 AAAAAGAAAAGAAG
1720309 AGAAAAGAAAA-AAGG
1 A-AAAAGAAAAGAA-G
1720324 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
1720337 AATGAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
13 3 0.08
14 22 0.61
15 11 0.31
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGAAG
Found at i:1720310 original size:24 final size:24
Alignment explanation
Indices: 1720278--1720345 Score: 81
Period size: 22 Copynumber: 3.0 Consensus size: 24
1720268 AGAATTTTCA
1720278 AAAAAAAAGAAGAAGAAGAAAAAG
1 AAAAAAAAGAAGAAGAAGAAAAAG
*
1720302 AAAAAAAAGAA-AAGAA-AAAAGG
1 AAAAAAAAGAAGAAGAAGAAAAAG
*
1720324 AAAAAGAA-AAGAA-AATGAAAAA
1 AAAAAAAAGAAGAAGAA-GAAAAA
1720346 AGGAGAGGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.11
22 14 0.37
23 9 0.24
24 11 0.29
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (24 bp):
AAAAAAAAGAAGAAGAAGAAAAAG
Found at i:1720319 original size:19 final size:19
Alignment explanation
Indices: 1720280--1720346 Score: 73
Period size: 19 Copynumber: 3.3 Consensus size: 19
1720270 AATTTTCAAA
1720280 AAAAAAGAAGAAGAAGAAAAAG
1 AAAAAA-AAGAA-AAG-AAAAG
1720302 AAAAAAAAGAAAAGAAAA-
1 AAAAAAAAGAAAAGAAAAG
*
1720320 AAGGAAAAAGAAAAGAAAATG
1 AA-AAAAAAGAAAAGAAAA-G
1720341 AAAAAA
1 AAAAAA
1720347 GGAGAGGCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 2 0.05
19 19 0.47
20 6 0.15
21 7 0.17
22 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (19 bp):
AAAAAAAAGAAAAGAAAAG
Found at i:1720320 original size:6 final size:6
Alignment explanation
Indices: 1720277--1720345 Score: 50
Period size: 7 Copynumber: 10.8 Consensus size: 6
1720267 AAGAATTTTC
* * *
1720277 AAAAAA AAAGAAG AAGAAG AAAAAG AAAAAAA AGAAAAG AAAAAAGG AAAAAG
1 AAAAAG AAA-AAG AAAAAG AAAAAG -AAAAAG A-AAAAG -AAAAA-G AAAAAG
*
1720330 -AAAAG AAAATG AAAAA
1 AAAAAG AAAAAG AAAAA
1720346 AGGAGAGGCC
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
5 5 0.10
6 21 0.42
7 22 0.44
8 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:1720795 original size:97 final size:97
Alignment explanation
Indices: 1720629--1721013 Score: 590
Period size: 97 Copynumber: 4.0 Consensus size: 97
1720619 ATTCATTTCG
*
1720629 TATCTTAGCAAAATTTGCTAACTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
*
1720694 CATCTTATTCATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
* *
1720726 TATCTTAGCAGAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTTTCAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
*
1720791 CATCTTATCTATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
* * *
1720823 TATCTTAGCAGAATTTGCTATCTTGATTAATTTATTCATTTTGAGCTGTGCTCTGAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
*
1720888 CATCTTATCCATTGTGATAATCGTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
** ** * * * *
1720920 TATCTTAGCAAAATTTGCTATCTTGATTGGTTTATTTGTTTAGAGCTTTCCTCTCAACAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
* * *
1720985 CATTTTGTCCATTTTGATAATCTTTTTCA
66 CATCTTATCCATTGTGATAATCTTTTTCA
1721014 AGCATTTTTC
Statistics
Matches: 264, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 264 1.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.48
Consensus pattern (97 bp):
TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
CATCTTATCCATTGTGATAATCTTTTTCATCT
Found at i:1721702 original size:15 final size:16
Alignment explanation
Indices: 1721682--1721717 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1721672 TGACATTCTG
1721682 CATTC-ATGCAAATAT
1 CATTCAATGCAAATAT
1721697 CATTCAATGCAAATAT
1 CATTCAATGCAAATAT
1721713 CATTC
1 CATTC
1721718 CTACACACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (16 bp):
CATTCAATGCAAATAT
Found at i:1721983 original size:46 final size:46
Alignment explanation
Indices: 1721927--1722790 Score: 1361
Period size: 46 Copynumber: 18.6 Consensus size: 46
1721917 GACTAGAAGC
*
1721927 AGCAGATCTTGTCTTTCTGTATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * *
1721973 AGTAGATCTTGTCTTCCTGTATTTAGCAGCGAAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * * *
1722019 AACAGATCTTGTCTTCCTATATTTAGCAGCGGAAGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
**
1722065 AGCAGATCTTGTCTTCCTGTATTTGAAAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * *
1722111 AGCAGATCTTGTCTTCATGTATTTGGTAGCGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
1722157 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
1722203 AGCAGATCTTGTCTTCCTGTATTTGGCAGGGGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
1722249 AGCAGATCTTGTCTTCCTGTATTTGGCAG-GGAAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGG-AGGAGATCGAAGAT
*
1722295 AGCAGATCTTGTCTTCCTGTATTTGGCAGGGGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
1722341 AGCAGATCTTGTCTTCTTGTATTTGGTAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
1722387 AGAAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
1722433 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCAAAGATAGCAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATC---G--A--AGAT
* *
1722486 AGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGGAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
**
1722532 AGCAGATCTTGTCTTCCTGTATTTGGCAGTAGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* **
1722578 AGCAGATCTTGTATTCCTGTATTTGGCAGTAGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * *
1722624 AGCAGATCTTGTATTCCTGTATTTGGCAGCGAAGGAGATCGAAAAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
1722670 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
1722716 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
1722762 AGCAGATCTTGTCTTCCTGTATCTGGCAG
1 AGCAGATCTTGTCTTCCTGTATTTGGCAG
1722791 TGAAGCAGAT
Statistics
Matches: 761, Mismatches: 48, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
45 2 0.00
46 711 0.93
47 2 0.00
48 1 0.00
49 1 0.00
51 1 0.00
53 43 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (46 bp):
AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
Found at i:1723070 original size:44 final size:43
Alignment explanation
Indices: 1723026--1723145 Score: 109
Period size: 42 Copynumber: 2.8 Consensus size: 43
1723016 AGGTAAAAGA
* *
1723026 TATAAGTCTTATTTCCATGAAGTTGCAGTGGAGTAGACTGAAG
1 TATAAGTCTTATTTCCATGAAGTTGCAGTGGAGCAAACTGAAG
* * * * *
1723069 -ATGAGTCTCATTTCCTTGAAGTTGCAGAGGAGCAAATTGAAG
1 TATAAGTCTTATTTCCATGAAGTTGCAGTGGAGCAAACTGAAG
* * * *
1723111 CTACTAA-TCCTATCTCCCTGAAGTTGTAGTGGAGC
1 -TA-TAAGTCTTATTTCCATGAAGTTGCAGTGGAGC
1723146 GGATTAAAAC
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
42 35 0.58
44 23 0.38
45 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
TATAAGTCTTATTTCCATGAAGTTGCAGTGGAGCAAACTGAAG
Found at i:1723734 original size:20 final size:20
Alignment explanation
Indices: 1723711--1723748 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1723701 GCCGCCAACA
* *
1723711 TCACGTCGCCACCGCCACGG
1 TCACGTCACCACCACCACGG
1723731 TCACGTCACCACCACCAC
1 TCACGTCACCACCACCAC
1723749 TTGCGCCGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.53, G:0.16, T:0.11
Consensus pattern (20 bp):
TCACGTCACCACCACCACGG
Found at i:1724631 original size:3 final size:3
Alignment explanation
Indices: 1724614--1724667 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
1724604 CTTGGCAATT
* *
1724614 TTA TTA TTTA GTTA TTA TTA TTA TTA TTG TTA TTA TTA TCA TTA TTA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1724661 TTA TTA T
1 TTA TTA T
1724668 CTACTTATCT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1726737 original size:26 final size:27
Alignment explanation
Indices: 1726689--1726739 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1726679 CACATTTGTA
* * *
1726689 TTTTTTTTATTTTATGTTGTTTTAAGT
1 TTTTTTTTAATTAATATTGTTTTAAGT
1726716 TTTTTTTTAATTAATATT-TTTTAA
1 TTTTTTTTAATTAATATTGTTTTAA
1726740 TATATCAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.73
Consensus pattern (27 bp):
TTTTTTTTAATTAATATTGTTTTAAGT
Found at i:1739353 original size:32 final size:30
Alignment explanation
Indices: 1739301--1739359 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
1739291 CAACCAAGTA
*
1739301 AATTAATTGATTTTTTAATTAAATAAATTT
1 AATTAATTGATTTTTAAATTAAATAAATTT
* *
1739331 AATTAGTTGAATTTTCTAAATTAATTAAA
1 AATTAATTG-ATTTT-TAAATTAAATAAA
1739360 GGAAAATGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.33
31 5 0.21
32 11 0.46
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (30 bp):
AATTAATTGATTTTTAAATTAAATAAATTT
Found at i:1741187 original size:25 final size:25
Alignment explanation
Indices: 1741158--1741212 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1741148 TACCAATTTT
*
1741158 AGCTCTTATGAGCTTACCGATACTC
1 AGCTCGTATGAGCTTACCGATACTC
* * *
1741183 AGCTCGTATGAGCTTATCGTTATTC
1 AGCTCGTATGAGCTTACCGATACTC
1741208 AGCTC
1 AGCTC
1741213 CAAGAAGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATACTC
Found at i:1745323 original size:12 final size:12
Alignment explanation
Indices: 1745303--1745337 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1745293 TCACGAACAA
1745303 GCTCGTTTATTG
1 GCTCGTTTATTG
*
1745315 GCTCATTTATTG
1 GCTCGTTTATTG
*
1745327 ACTCGTTTATT
1 GCTCGTTTATT
1745338 TATTAATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.51
Consensus pattern (12 bp):
GCTCGTTTATTG
Found at i:1745581 original size:24 final size:23
Alignment explanation
Indices: 1745554--1745623 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
1745544 TTATTAACAT
1745554 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* **
1745578 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
1745601 TGTTTGTGAACATGTTCAATTAA
1 TGTTCGTGAACATGTTCAATTAA
1745624 GTTAAATGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:1745633 original size:23 final size:23
Alignment explanation
Indices: 1745560--1745639 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
1745550 ACATTGTTCG
*
1745560 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCAATTA-ATGTTAA
** **
1745584 TGAACATGTTCGTTTAATGTTTG
1 TGAACATGTTCAATTAATGTTAA
1745607 TGAACATGTTCAATTAA-GTTAAA
1 TGAACATGTTCAATTAATGTT-AA
1745630 TGAACATGTT
1 TGAACATGTT
1745640 TGTGAACATT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.06
23 30 0.64
24 14 0.30
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (23 bp):
TGAACATGTTCAATTAATGTTAA
Found at i:1747346 original size:26 final size:26
Alignment explanation
Indices: 1747296--1747347 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1747286 TTTAGTTTCA
*
1747296 TTAATTGTAGTTTCTTATTCCACAAG
1 TTAATTGTAGTTTCTTATGCCACAAG
*
1747322 TTAATTTTAGTTTCTTA-GCCTACAAG
1 TTAATTGTAGTTTCTTATGCC-ACAAG
1747348 AATAAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (26 bp):
TTAATTGTAGTTTCTTATGCCACAAG
Found at i:1748403 original size:9 final size:9
Alignment explanation
Indices: 1748389--1748439 Score: 84
Period size: 9 Copynumber: 5.7 Consensus size: 9
1748379 TTTGGTTAAA
1748389 AATTAACCG
1 AATTAACCG
1748398 AATTAACCG
1 AATTAACCG
1748407 AATTAACCG
1 AATTAACCG
* *
1748416 GATTACCCG
1 AATTAACCG
1748425 AATTAACCG
1 AATTAACCG
1748434 AATTAA
1 AATTAA
1748440 ATCACTACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:1749347 original size:14 final size:15
Alignment explanation
Indices: 1749328--1749357 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1749318 ATAAAAGCAC
1749328 TTAATT-TAGTTTCT
1 TTAATTATAGTTTCT
1749342 TTAATTATAGTTTCT
1 TTAATTATAGTTTCT
1749357 T
1 T
1749358 ATTCTACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (15 bp):
TTAATTATAGTTTCT
Found at i:1749371 original size:26 final size:26
Alignment explanation
Indices: 1749342--1749393 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1749332 TTTAGTTTCT
*
1749342 TTAATTATAGTTTCTTATTCTACAAG
1 TTAATTATAGTTTCTTAGTCTACAAG
*
1749368 TTAATTTTAGTTTCTTAGTCTACAAG
1 TTAATTATAGTTTCTTAGTCTACAAG
1749394 AATAAAACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.50
Consensus pattern (26 bp):
TTAATTATAGTTTCTTAGTCTACAAG
Found at i:1752277 original size:30 final size:30
Alignment explanation
Indices: 1752243--1752299 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1752233 CAATAAAAAA
1752243 ATATAAGAAA-ATAATATTATT-AATATTTTG
1 ATATAAGAAATATAA-ATT-TTAAATATTTTG
*
1752273 ATATATGAAATATAAATTTTAAATATT
1 ATATAAGAAATATAAATTTTAAATATT
1752300 CTTTAAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.08
30 18 0.75
31 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (30 bp):
ATATAAGAAATATAAATTTTAAATATTTTG
Found at i:1755294 original size:21 final size:20
Alignment explanation
Indices: 1755256--1755294 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1755246 AATATATAAT
* *
1755256 AATTTTTTAATTTTAATTAG
1 AATTTTTTAAATTAAATTAG
1755276 AATTTTTATAAATTAAATT
1 AATTTTT-TAAATTAAATT
1755295 TAAATAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
AATTTTTTAAATTAAATTAG
Found at i:1758539 original size:100 final size:100
Alignment explanation
Indices: 1758410--1758617 Score: 371
Period size: 100 Copynumber: 2.1 Consensus size: 100
1758400 GAAGATTTTT
*
1758410 TTTTAAAATAATAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCAAACGTATTG
1 TTTT-AAATAATAAAGGAAATATTCCGAGTTAGGGATTTTAAAGGAATTGTGCCCAAACGTATTG
1758475 GGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTC
65 GGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTC
* * *
1758511 TTTTAAATAATAAAGTAAATATTTCGAGTTAGGGATTTTAAAGGAATTGTGCCCTAACGTATTGG
1 TTTTAAATAATAAAGGAAATATTCCGAGTTAGGGATTTTAAAGGAATTGTGCCCAAACGTATTGG
1758576 GTGTGATTTCTTAAATCTTGGATAAGTGGATGTTC
66 GTGTGATTTCTTAAATCTTGGATAAGTGGATGTTC
1758611 TTTTAAA
1 TTTTAAA
1758618 GTTTTATTGC
Statistics
Matches: 103, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
100 99 0.96
101 4 0.04
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (100 bp):
TTTTAAATAATAAAGGAAATATTCCGAGTTAGGGATTTTAAAGGAATTGTGCCCAAACGTATTGG
GTGTGATTTCTTAAATCTTGGATAAGTGGATGTTC
Found at i:1762136 original size:12 final size:12
Alignment explanation
Indices: 1762119--1762146 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1762109 CCTCTTTGAA
1762119 GATAAAAATTTT
1 GATAAAAATTTT
1762131 GATAAAAATTTT
1 GATAAAAATTTT
1762143 GATA
1 GATA
1762147 TATCGCATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (12 bp):
GATAAAAATTTT
Found at i:1764138 original size:6 final size:6
Alignment explanation
Indices: 1764127--1764151 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1764117 ATTCATTTCC
1764127 TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT T
1764152 GAGAAAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCATTT
Found at i:1765734 original size:45 final size:46
Alignment explanation
Indices: 1765666--1765789 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
1765656 CATATGACCT
*
1765666 CTTATCAC-TTGTCA-TTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
1765709 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
1765755 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
1765790 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 5 0.07
45 20 0.27
46 41 0.55
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:1765793 original size:37 final size:37
Alignment explanation
Indices: 1765751--1765883 Score: 221
Period size: 37 Copynumber: 3.6 Consensus size: 37
1765741 AGCTGAAGCT
* **
1765751 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
1765788 GCCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1765825 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
1765862 ACCACTTATCACTTTGTCTCTT
1 ACCACTTATCACTTTGTTTCTT
1765884 NNNNNNNNNN
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 90 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:1769907 original size:41 final size:41
Alignment explanation
Indices: 1769849--1769960 Score: 138
Period size: 41 Copynumber: 2.7 Consensus size: 41
1769839 ACTGGCTTTT
* *
1769849 AGCCTGCTAGACTTATAGTCCG-A-AATGTATCACCGGCATTA
1 AGCCTGCTAGACATATAGTCCGAATAAT-T-TCACCGGCATCA
*
1769890 AGCCTGCTAGACATATAGTCTGAATAATTTCACCGGCATCA
1 AGCCTGCTAGACATATAGTCCGAATAATTTCACCGGCATCA
* * *
1769931 AGCCTGCTAGACATAAAGTCTGAATTATTT
1 AGCCTGCTAGACATATAGTCCGAATAATTT
1769961 TACTGACATT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 59 0.92
42 2 0.03
43 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACATATAGTCCGAATAATTTCACCGGCATCA
Found at i:1776108 original size:21 final size:21
Alignment explanation
Indices: 1776082--1776121 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1776072 CAAAACAATG
*
1776082 TAGTTTTGCCTTTTAACTTGA
1 TAGTTTTGACTTTTAACTTGA
1776103 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
1776122 TAGATAAGGT
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:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTGA
Found at i:1776475 original size:17 final size:18
Alignment explanation
Indices: 1776444--1776481 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1776434 ATTTTTTAGA
**
1776444 TTTTTTAAATTTAT-AAT
1 TTTTTTAAAAATATAAAT
1776461 TTTTTTAAAAATATAAAT
1 TTTTTTAAAAATATAAAT
1776479 TTT
1 TTT
1776482 AGGATTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTTAAAAATATAAAT
Found at i:1776518 original size:19 final size:18
Alignment explanation
Indices: 1776496--1776546 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
1776486 TTTCTATAAA
1776496 TATTTTGAATTTTAAAAAT
1 TATTTT-AATTTTAAAAAT
*
1776515 TATTTTCAAATTTTGAAAAT
1 TATTTT--AATTTTAAAAAT
*
1776535 TAGTTTAATTTT
1 TATTTTAATTTT
1776547 TTTTGTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 16 0.57
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (18 bp):
TATTTTAATTTTAAAAAT
Found at i:1776709 original size:9 final size:9
Alignment explanation
Indices: 1776695--1776725 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1776685 TTGCGTTGAC
1776695 TCGAATAAT
1 TCGAATAAT
1776704 TCGAATAAT
1 TCGAATAAT
*
1776713 TCGAATAAC
1 TCGAATAAT
1776722 TCGA
1 TCGA
1776726 TTCGATTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (9 bp):
TCGAATAAT
Found at i:1782927 original size:35 final size:36
Alignment explanation
Indices: 1782871--1782943 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 36
1782861 ATAAATACAC
1782871 ATTTAAAAATAAATATAATATAA-TTTAAAATTATT
1 ATTTAAAAATAAATATAATATAATTTTAAAATTATT
** * *
1782906 ATTTAAAAATACTTATTATATAATTTTTAAATTATT
1 ATTTAAAAATAAATATAATATAATTTTAAAATTATT
1782942 AT
1 AT
1782944 AAAAATGACT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 20 0.61
36 13 0.39
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (36 bp):
ATTTAAAAATAAATATAATATAATTTTAAAATTATT
Found at i:1785132 original size:17 final size:18
Alignment explanation
Indices: 1785086--1785139 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
1785076 TTTTACATTA
1785086 TTATTTTTATTAATATTG
1 TTATTTTTATTAATATTG
* *
1785104 TTAAATTGTTATTATTATTG
1 TT--ATTTTTATTAATATTG
*
1785124 TT-TTTTTATTAGTATT
1 TTATTTTTATTAATATT
1785140 ATTTATTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 12 0.40
18 2 0.07
20 16 0.53
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (18 bp):
TTATTTTTATTAATATTG
Found at i:1788981 original size:13 final size:13
Alignment explanation
Indices: 1788963--1788990 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1788953 TGTTCACATC
1788963 AATGTCATAGATG
1 AATGTCATAGATG
1788976 AATGTCATAGATG
1 AATGTCATAGATG
1788989 AA
1 AA
1788991 GACACAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (13 bp):
AATGTCATAGATG
Found at i:1789702 original size:13 final size:13
Alignment explanation
Indices: 1789686--1789745 Score: 86
Period size: 13 Copynumber: 4.6 Consensus size: 13
1789676 GTAATCTGAG
1789686 CAAAAGCA-TTTCT
1 CAAAAGCACTTT-T
1789699 CAAAAGCACTTTT
1 CAAAAGCACTTTT
* *
1789712 CTACAGCACTTTT
1 CAAAAGCACTTTT
1789725 CAAAAGCACTTTT
1 CAAAAGCACTTTT
1789738 CAAAAGCA
1 CAAAAGCA
1789746 ATGAAGAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
13 39 0.93
14 3 0.07
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.28
Consensus pattern (13 bp):
CAAAAGCACTTTT
Found at i:1791449 original size:42 final size:42
Alignment explanation
Indices: 1791381--1791460 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
1791371 ACAGTGAGTT
**
1791381 ACACGGCCTGGACACACGCCTGTGTCCCT-GCTCGTGTGACTC
1 ACACGGCCTGGACACACGCCCATGTCCCTGGC-CGTGTGACTC
* *
1791423 ACACGGCCTGGGCACATGCCCATGTCCCTGGCCGTGTG
1 ACACGGCCTGGACACACGCCCATGTCCCTGGCCGTGTG
1791461 GTCTTAAGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.14, C:0.38, G:0.29, T:0.20
Consensus pattern (42 bp):
ACACGGCCTGGACACACGCCCATGTCCCTGGCCGTGTGACTC
Found at i:1795121 original size:31 final size:26
Alignment explanation
Indices: 1795058--1795128 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 26
1795048 AAATTTGTAT
1795058 ATTA-TTTTAATAATTTATTTATTTTC
1 ATTATTTTTAA-AATTTATTTATTTTC
1795084 ATTATTTTTAAAATATTATTTTAATCTTTC
1 ATTATTTTTAAAAT-TTA-TTT-AT-TTTC
1795114 AATTATTTTTCAAAA
1 -ATTATTTTT-AAAA
1795129 CTAATTCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
26 7 0.18
27 9 0.24
28 3 0.08
29 2 0.05
30 4 0.11
31 9 0.24
32 4 0.11
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (26 bp):
ATTATTTTTAAAATTTATTTATTTTC
Found at i:1798172 original size:20 final size:21
Alignment explanation
Indices: 1798143--1798182 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1798133 TTAAAACTTT
*
1798143 TTTTATTAAA-CTCTTAAAAG
1 TTTTACTAAATCTCTTAAAAG
*
1798163 TTTTACTAAATTTCTTAAAA
1 TTTTACTAAATCTCTTAAAA
1798183 TTTAATCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (21 bp):
TTTTACTAAATCTCTTAAAAG
Found at i:1799744 original size:11 final size:11
Alignment explanation
Indices: 1799730--1799808 Score: 80
Period size: 11 Copynumber: 7.5 Consensus size: 11
1799720 ATTTTTTTAA
1799730 TTTTAAAATAT
1 TTTTAAAATAT
1799741 TTTTAAAATACT
1 TTTTAAAATA-T
*
1799753 TTTT-TAAT-T
1 TTTTAAAATAT
1799762 TTTT--AA-A-
1 TTTTAAAATAT
1799769 TTTTAAAATAT
1 TTTTAAAATAT
1799780 TTTTAAAATACT
1 TTTTAAAATA-T
*
1799792 TTTTAAAATTT
1 TTTTAAAATAT
1799803 TTTTAA
1 TTTTAA
1799809 TTTTAAGATA
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
7 4 0.07
8 2 0.03
9 7 0.12
10 1 0.02
11 30 0.51
12 15 0.25
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1799758 original size:30 final size:27
Alignment explanation
Indices: 1799722--1799783 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 27
1799712 TTTTTTTAAT
1799722 TTTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTTAATTTTAAAA-A-TTTTAAAATA
**
1799751 CTTTTTTAATTTTTTAAATTTTAAAATA
1 -TTTTTTAATTTTAAAAATTTTAAAATA
1799779 TTTTT
1 TTTTT
1799784 AAAATACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 5 0.17
28 10 0.33
29 1 0.03
30 14 0.47
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTTTTAATTTTAAAAATTTTAAAATA
Found at i:1799765 original size:8 final size:9
Alignment explanation
Indices: 1799711--1799812 Score: 55
Period size: 9 Copynumber: 10.6 Consensus size: 9
1799701 AAAGATATTT
*
1799711 ATTTTTTTA
1 ATTTTTTAA
*
1799720 ATTTTTTTA
1 ATTTTTTAA
*
1799729 A-TTTTAAA
1 ATTTTTTAA
1799737 ATATTTTTAAA
1 AT-TTTTT-AA
*
1799748 ATACTTTTTTA
1 AT--TTTTTAA
1799759 ATTTTTTAA
1 ATTTTTTAA
*
1799768 A-TTTTAAA
1 ATTTTTTAA
1799776 ATATTTTTAAA
1 AT-TTTTT-AA
1799787 ATACTTTTTAAA
1 AT--TTTTT-AA
*
1799799 ATTTTTTTA
1 ATTTTTTAA
1799808 ATTTT
1 ATTTT
1799813 AAGATACTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
8 13 0.17
9 23 0.31
10 13 0.17
11 11 0.15
12 15 0.20
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:1799771 original size:39 final size:39
Alignment explanation
Indices: 1799713--1799824 Score: 179
Period size: 39 Copynumber: 2.8 Consensus size: 39
1799703 AGATATTTAT
1799713 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
*
1799752 TTTTTTAATTTTTTAAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
* *
1799791 TTTTTAAAATTTTTTTAATTTTAAGATACTTTTT
1 TTTTT-TAATTTTTTTAATTTTAAAATA-TTTTT
1799825 TAATTTTAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 43 0.64
40 19 0.28
41 5 0.07
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (39 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:1802716 original size:60 final size:60
Alignment explanation
Indices: 1802634--1802767 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 60
1802624 AACAAAATTG
* * * * *
1802634 AATAGTTGAGTGACCATCTTGTAATTTTTCATAATTAGGTGACCGAAAAAGAAATTTACT
1 AATAGTTGAGTGACCATCTTGTAACTTCTCATAATTAGGTGAACAAAAAAGAAATTCACT
* * * *
1802694 AATAGTT-AGGTGATCATTTTGTAACTTCTCATAGTTGGGTGAACAAAAAAGAAATTCACT
1 AATAGTTGA-GTGACCATCTTGTAACTTCTCATAATTAGGTGAACAAAAAAGAAATTCACT
1802754 AATAGTTGAGTGAC
1 AATAGTTGAGTGAC
1802768 TACTAGTGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.02
60 60 0.97
61 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.34
Consensus pattern (60 bp):
AATAGTTGAGTGACCATCTTGTAACTTCTCATAATTAGGTGAACAAAAAAGAAATTCACT
Found at i:1803364 original size:7 final size:7
Alignment explanation
Indices: 1803352--1803402 Score: 75
Period size: 7 Copynumber: 7.3 Consensus size: 7
1803342 AAAAAAATTC
1803352 AAACCCT
1 AAACCCT
1803359 AAACCCT
1 AAACCCT
1803366 AAACCCT
1 AAACCCT
* *
1803373 AAATCTT
1 AAACCCT
1803380 AAACCCT
1 AAACCCT
1803387 AAACCCT
1 AAACCCT
*
1803394 AAAACCT
1 AAACCCT
1803401 AA
1 AA
1803403 GCCACAATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:1810173 original size:14 final size:15
Alignment explanation
Indices: 1810142--1810175 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1810132 CACAATTTAT
1810142 AAATATTAAAAATCA
1 AAATATTAAAAATCA
*
1810157 AAATTTTAAAAAT-A
1 AAATATTAAAAATCA
1810171 AAATA
1 AAATA
1810176 AAATAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATATTAAAAATCA
Found at i:1815438 original size:204 final size:204
Alignment explanation
Indices: 1815088--1815491 Score: 596
Period size: 204 Copynumber: 2.0 Consensus size: 204
1815078 AATTTGATTG
* * *
1815088 GATATTTCCCGTTAAAAGTTTTTGTGTGGACAAGAACACTCTTGGCTTATTAATTGGCTTCATCA
1 GATATTTCCCGTTAAAAGTTGTTGTGTGGACAAGAACACTCTTGGCTCATTAATTGGCCTCATCA
* * * * * *
1815153 CATCGGTTTCGCAACATTGATGGCAATCTACTAGTCTTAGGCATGTTTTCAAGGTTGTGTTGCGA
66 CATCAGTGTCGCAACATTGATGGCAATCTACTAGTATTAGGCATGTCTTCAAGGTTATGTCGCGA
1815218 CACTGGAAGCAGACTACCCCTATTAAGTACTCTGTTCACTGTGTTGCGACATCGAAGCTCCGTGT
131 CACTGGAAGCAGACTACCCCTATTAAGTACTCTGTTCACTGTGTTGCGACATCGAAGCTCCGTGT
1815283 TGCAAAATT
196 TGCAAAATT
* *
1815292 GATATTTCCCGTTAAAAGTTGTTGTGTGGACGAA-AATACTCTTGGCTCATTAATTGGCCTCATT
1 GATATTTCCCGTTAAAAGTTGTTGTGTGGAC-AAGAACACTCTTGGCTCATTAATTGGCCTCATC
* * **
1815356 ACATCAGTGTCGCAACATTGATGGCAGTTTACTAGTATTTTGCATGTCTTCAAGGTTATGTCGCG
65 ACATCAGTGTCGCAACATTGATGGCAATCTACTAGTATTAGGCATGTCTTCAAGGTTATGTCGCG
* * * * *
1815421 ACACT-GAAGGTAGACTACTCCTTTTGAGTACTCTGTTCACTGTGTTGCGACATTGAAGCTCCGT
130 ACACTGGAA-GCAGACTACCCCTATTAAGTACTCTGTTCACTGTGTTGCGACATCGAAGCTCCGT
1815485 GTTGCAA
194 GTTGCAA
1815492 CATCGCAGGT
Statistics
Matches: 178, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
203 3 0.02
204 173 0.97
205 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (204 bp):
GATATTTCCCGTTAAAAGTTGTTGTGTGGACAAGAACACTCTTGGCTCATTAATTGGCCTCATCA
CATCAGTGTCGCAACATTGATGGCAATCTACTAGTATTAGGCATGTCTTCAAGGTTATGTCGCGA
CACTGGAAGCAGACTACCCCTATTAAGTACTCTGTTCACTGTGTTGCGACATCGAAGCTCCGTGT
TGCAAAATT
Found at i:1817622 original size:12 final size:12
Alignment explanation
Indices: 1817605--1817634 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1817595 TCAGACAATT
1817605 ACACGGCCTAGC
1 ACACGGCCTAGC
*
1817617 ACACGGCCTGGC
1 ACACGGCCTAGC
1817629 ACACGG
1 ACACGG
1817635 GTGTGTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:1819073 original size:26 final size:26
Alignment explanation
Indices: 1819044--1819104 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
1819034 GAGTTGGTAT
*
1819044 TCACCAATGGACCTGGTAAGCTAAGA
1 TCACCAATGGACCTGGCAAGCTAAGA
* * *
1819070 TCA-CAAGTGGGCTTGGCGAGCTAAGA
1 TCACCAA-TGGACCTGGCAAGCTAAGA
*
1819096 TCGCCAATG
1 TCACCAATG
1819105 AGCTTGATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 3 0.11
26 22 0.79
27 3 0.11
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (26 bp):
TCACCAATGGACCTGGCAAGCTAAGA
Found at i:1819454 original size:20 final size:21
Alignment explanation
Indices: 1819429--1819470 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1819419 GGACTAATCT
1819429 GATCAAAAC-ATAAAATTTTG
1 GATCAAAACTATAAAATTTTG
*
1819449 GATCAAAACTATAAATTTTTG
1 GATCAAAACTATAAAATTTTG
1819470 G
1 G
1819471 TTCTAGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (21 bp):
GATCAAAACTATAAAATTTTG
Found at i:1820082 original size:24 final size:24
Alignment explanation
Indices: 1820055--1820106 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1820045 ATTATCGATG
*
1820055 ATAGATTCGACGGTTGATGAAGAA
1 ATAGATTCGACGATTGATGAAGAA
1820079 ATAGATTCGACGATTGATGAAGAA
1 ATAGATTCGACGATTGATGAAGAA
1820103 ATAG
1 ATAG
1820107 GTGGAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.27, T:0.25
Consensus pattern (24 bp):
ATAGATTCGACGATTGATGAAGAA
Found at i:1821765 original size:22 final size:22
Alignment explanation
Indices: 1821740--1821783 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1821730 TAAGAAAACT
1821740 GTTTTCAAACTGAGATTTTTCC
1 GTTTTCAAACTGAGATTTTTCC
1821762 GTTTTCAAACTGAGATTTTTCC
1 GTTTTCAAACTGAGATTTTTCC
1821784 AACAAGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (22 bp):
GTTTTCAAACTGAGATTTTTCC
Found at i:1824769 original size:12 final size:12
Alignment explanation
Indices: 1824752--1824778 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1824742 TATTGAATGC
1824752 CAGGCTTAACTG
1 CAGGCTTAACTG
1824764 CAGGCTTAACTG
1 CAGGCTTAACTG
1824776 CAG
1 CAG
1824779 ACTTGTTGAT
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:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (12 bp):
CAGGCTTAACTG
Found at i:1827546 original size:91 final size:90
Alignment explanation
Indices: 1827345--1827643 Score: 459
Period size: 87 Copynumber: 3.4 Consensus size: 90
1827335 TGATTTTAGT
* * *
1827345 AAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATGTCATTATTAAATTATA-
1 AAATTCATATAAGAAAATTTATTA-TAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
1827409 TT--TAATAATTATTTTAAATTATAC
65 TTAATAATAATTATTTTAAATTATAC
*
1827433 AAATTCATAGAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTAT-AAGAATTTTATGAAATTATATATTATTATTAAATTATAT
1827498 TTAATAATAATTATTTTAAATTATAC
65 TTAATAATAATTATTTTAAATTATAC
*
1827524 AAATTCATATAAGAAAATTTATTAGTAAGAGTTTTATGAAA-T-TATA-TATTATT-AATTATAT
1 AAATTCATATAAGAAAATTTATTA-TAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
1827585 TTAATAATAATTATTTTAAATTATAC
65 TTAATAATAATTATTTTAAATTATAC
*
1827611 AAATTCATATAAGAAAATTTATTAGTAATAATT
1 AAATTCATATAAGAAAATTTATTA-TAAGAATT
1827644 ATTTTAAATT
Statistics
Matches: 198, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
87 66 0.33
88 65 0.33
89 6 0.03
90 1 0.01
91 59 0.30
92 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (90 bp):
AAATTCATATAAGAAAATTTATTATAAGAATTTTATGAAATTATATATTATTATTAAATTATATT
TAATAATAATTATTTTAAATTATAC
Found at i:1827707 original size:54 final size:54
Alignment explanation
Indices: 1827636--1827845 Score: 149
Period size: 54 Copynumber: 3.6 Consensus size: 54
1827626 AATTTATTAG
*
1827636 TAATAATTAT-TTTAAATTTCATTAAATTATATATTTTAATTAAAATATATTTAA
1 TAATAATTATATTAAAATTT-ATTAAATTATATATTTTAATTAAAATATATTTAA
* * * * *
1827690 TAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAAT-TCATATAA
1 TAATAATTATATTAAAATT-TA--TTA-A--ATTATATATT-TTA-ATTA--AAATAT-ATTTAA
*
1827753 GAAT-ATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
1 TAATAATT-A-TATTAA-AA-TTTATTAAATTATATATTTTAATTAAAATATATTTAA
* * *
1827810 TAATAATTATGTTAAAATATGATTAAATTATTTATT
1 TAATAATTATATTAAAAT-TTATTAAATTATATATT
1827846 ATTGATATTA
Statistics
Matches: 122, Mismatches: 15, Indels: 37
0.70 0.09 0.21
Matches are distributed among these distances:
54 19 0.16
55 18 0.15
56 8 0.07
57 14 0.11
58 4 0.03
59 12 0.10
60 4 0.03
61 12 0.10
62 4 0.03
63 14 0.11
64 4 0.03
65 3 0.02
66 4 0.03
67 2 0.02
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (54 bp):
TAATAATTATATTAAAATTTATTAAATTATATATTTTAATTAAAATATATTTAA
Found at i:1827799 original size:18 final size:17
Alignment explanation
Indices: 1827771--1827805 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1827761 ATTATTAAGA
*
1827771 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1827788 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1827806 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1828025 original size:44 final size:46
Alignment explanation
Indices: 1827962--1828057 Score: 169
Period size: 44 Copynumber: 2.1 Consensus size: 46
1827952 CTATTACACC
*
1827962 TCCATTCCATTCAACCAAACACAAGAA-TA-CTATTACGCCTCTAT
1 TCCATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
1828006 TCCATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
1 TCCATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
1828052 TCCATT
1 TCCATT
1828058 ACACCTCTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 26 0.53
45 2 0.04
46 21 0.43
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.29
Consensus pattern (46 bp):
TCCATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
Found at i:1828064 original size:16 final size:16
Alignment explanation
Indices: 1828039--1828076 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1828029 AGAATTACCT
*
1828039 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
1828055 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
1828071 ATTACA
1 ATTACA
1828077 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:1839233 original size:13 final size:13
Alignment explanation
Indices: 1839215--1839239 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1839205 AGAAATTTGA
1839215 AACACGAAAAATT
1 AACACGAAAAATT
1839228 AACACGAAAAAT
1 AACACGAAAAAT
1839240 CAAAACATTA
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:0.64, C:0.16, G:0.08, T:0.12
Consensus pattern (13 bp):
AACACGAAAAATT
Found at i:1839983 original size:23 final size:23
Alignment explanation
Indices: 1839956--1840030 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 23
1839946 TATCTCTAAC
1839956 CCTAAACGCTTAAAAATAAAAAA
1 CCTAAACGCTTAAAAATAAAAAA
*
1839979 CCTAAAC-CCTAAAAATTAAATAAAA
1 CCTAAACGCTTAAAAA-T-AA-AAAA
*
1840004 CCCTAAA-GACTAAAAAATAAAAAA
1 -CCTAAACG-CTTAAAAATAAAAAA
1840028 CCT
1 CCT
1840031 TAAATCCTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
22 7 0.16
23 11 0.26
24 6 0.14
25 6 0.14
26 7 0.16
27 6 0.14
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (23 bp):
CCTAAACGCTTAAAAATAAAAAA
Found at i:1840085 original size:114 final size:115
Alignment explanation
Indices: 1839855--1840069 Score: 247
Period size: 120 Copynumber: 1.8 Consensus size: 115
1839845 ATTTTTTCAT
* * *
1839855 AAAACCTAAACTCTAAAAATTAAATAAAACCTTAAACCCTTGACCCTAAAAAATTAAAACATTAA
1 AAAACCTAAACCCTAAAAATTAAATAAAACCCTAAA--C--GA-CCTAAAAAATAAAAACATTAA
* * * ** **
1839920 ACCCTAATTTCATAAACTTTAAACCCTATCTCTAACCCTAAACGCTTAAAAATAA
61 ACCCTAATTTCATAAACTATAAACCCTAACCCTAAAACTAAACAATTAAAAATAA
* *
1839975 AAAACCTAAACCCTAAAAATTAAATAAAACCCTAAA-GA-CTAAAAAATAAAAAACCTTAAATCC
1 AAAACCTAAACCCTAAAAATTAAATAAAACCCTAAACGACCTAAAAAAT-AAAAACATTAAACCC
1840038 TAATTTCATAAACTAT-AACCCTAACCCTAAAA
65 TAATTTCATAAACTATAAACCCTAACCCTAAAA
1840070 AATTAAAAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
113 21 0.25
114 27 0.32
115 2 0.02
120 34 0.40
ACGTcount: A:0.52, C:0.23, G:0.01, T:0.24
Consensus pattern (115 bp):
AAAACCTAAACCCTAAAAATTAAATAAAACCCTAAACGACCTAAAAAATAAAAACATTAAACCCT
AATTTCATAAACTATAAACCCTAACCCTAAAACTAAACAATTAAAAATAA
Found at i:1840719 original size:52 final size:50
Alignment explanation
Indices: 1840630--1840727 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 50
1840620 TCAATTTAGT
* * * *
1840630 CCTCAATTTTTACATATTGTGTCAATTTGTTTATAATTTCTAATAAAACTTA
1 CCTCAATATTTACATATTATCTCAATTTATTTATAA-TTCTAA-AAAACTTA
1840682 CCTCAATATTTACATATTATCTCAATTTAATTT-TAATTCTAAAAAA
1 CCTCAATATTTACATATTATCTCAATTT-ATTTATAATTCTAAAAAA
1840728 TTTAAAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 4 0.10
51 6 0.15
52 28 0.68
53 3 0.07
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (50 bp):
CCTCAATATTTACATATTATCTCAATTTATTTATAATTCTAAAAAACTTA
Found at i:1840891 original size:16 final size:17
Alignment explanation
Indices: 1840870--1840910 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1840860 TGTCCCGTAC
*
1840870 AATAAAATAT-TTAAAA
1 AATAAAATATATAAAAA
1840886 AAT-AAATATATAAAAA
1 AATAAAATATATAAAAA
1840902 AATAAAATA
1 AATAAAATA
1840911 CACTAGAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAAAATATATAAAAA
Found at i:1849585 original size:23 final size:24
Alignment explanation
Indices: 1849529--1849586 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
1849519 ACTAGCGTAC
1849529 AAAGACTAA-TTTTAACAAAACAA
1 AAAGACTAATTTTTAACAAAACAA
*
1849552 ATAGA-TAAATTTTTAACAAAA-AA
1 AAAGACT-AATTTTTAACAAAACAA
1849575 AAAGACTAATTT
1 AAAGACTAATTT
1849587 ACTTTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 17 0.57
24 12 0.40
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.28
Consensus pattern (24 bp):
AAAGACTAATTTTTAACAAAACAA
Found at i:1851211 original size:15 final size:15
Alignment explanation
Indices: 1851191--1851220 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1851181 GTCAGAGCGT
*
1851191 GTTGTTCTCTTTCGA
1 GTTGTTCTATTTCGA
1851206 GTTGTTCTATTTCGA
1 GTTGTTCTATTTCGA
1851221 CTTATATCTG
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:0.10, C:0.17, G:0.20, T:0.53
Consensus pattern (15 bp):
GTTGTTCTATTTCGA
Found at i:1853059 original size:55 final size:56
Alignment explanation
Indices: 1852972--1853200 Score: 239
Period size: 55 Copynumber: 4.1 Consensus size: 56
1852962 TAGACGTGCT
* * *
1852972 ACATAACAATCAATTTAAATATATAAACAATCGATTCAAAAAAAG-CAACATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGATTCAAAAAAAGACAATATTCCA
*
1853027 ACATAACAATCGATTTAAACATATAAAAAATCGATTCAAAAGAAGAAGAAACAATATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGATTC-AAA-AA-AAG--ACAATATTCCA
* * * * * *
1853088 CCATAAAAATCGATTTAAACATATAAACAGTCGAATCAAAAGAAGTC-ATATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGATTCAAAAAAAGACAATATTCCA
* * * * * * *
1853143 ACATGATAATTGATTTAAACATATAAACAATTGATTTAAAAGAAG-CAGTATTCCA
1 ACATAACAATCGATTTAAACATATAAACAATCGATTCAAAAAAAGACAATATTCCA
1853198 ACA
1 ACA
1853201 ATTAAGAAGA
Statistics
Matches: 147, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.01
55 89 0.61
56 4 0.03
57 2 0.01
58 6 0.04
59 1 0.01
60 3 0.02
61 41 0.28
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (56 bp):
ACATAACAATCGATTTAAACATATAAACAATCGATTCAAAAAAAGACAATATTCCA
Found at i:1853184 original size:116 final size:116
Alignment explanation
Indices: 1852973--1853187 Score: 297
Period size: 116 Copynumber: 1.9 Consensus size: 116
1852963 AGACGTGCTA
* * *
1852973 CATAACAATCAATTTAAATATATAAACAATCGATTCAAAAAAAGCAACATTCCAACATAACAATC
1 CATAAAAATCAATTTAAACATATAAACAATCGAATCAAAAAAAGCAACATTCCAACATAACAATC
1853038 GATTTAAACATATAAAAAATCGATTCAAAAGAAGAAGAAACAATATTCCAC
66 GATTTAAACATATAAAAAATCGATTCAAAAGAAGAAGAAACAATATTCCAC
* * * * * *
1853089 CATAAAAATCGATTTAAACATATAAACAGTCGAATCAAAAGAAGTC-ATATTCCAACATGATAAT
1 CATAAAAATCAATTTAAACATATAAACAATCGAATCAAAAAAAG-CAACATTCCAACATAACAAT
* * * *
1853153 TGATTTAAACATATAAACAATTGATTTAAAAGAAG
65 CGATTTAAACATATAAAAAATCGATTCAAAAGAAG
1853188 CAGTATTCCA
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
116 84 0.99
117 1 0.01
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.25
Consensus pattern (116 bp):
CATAAAAATCAATTTAAACATATAAACAATCGAATCAAAAAAAGCAACATTCCAACATAACAATC
GATTTAAACATATAAAAAATCGATTCAAAAGAAGAAGAAACAATATTCCAC
Found at i:1855891 original size:11 final size:11
Alignment explanation
Indices: 1855866--1855917 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
1855856 TTCTATAATC
1855866 CATTTT-ATTT
1 CATTTTCATTT
*
1855876 CCATTTTCATAT
1 -CATTTTCATTT
*
1855888 CATTCTCATTT
1 CATTTTCATTT
*
1855899 CAATTTCATTT
1 CATTTTCATTT
*
1855910 CATATTCA
1 CATTTTCA
1855918 AATTTTACTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
11 30 0.91
12 3 0.09
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (11 bp):
CATTTTCATTT
Found at i:1856566 original size:13 final size:13
Alignment explanation
Indices: 1856548--1856574 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1856538 AACTGTCTCC
1856548 TAATCATTTTCCA
1 TAATCATTTTCCA
1856561 TAATCATTTTCCA
1 TAATCATTTTCCA
1856574 T
1 T
1856575 CCAAAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATCATTTTCCA
Found at i:1860630 original size:50 final size:50
Alignment explanation
Indices: 1860515--1860757 Score: 396
Period size: 50 Copynumber: 4.8 Consensus size: 50
1860505 GATAATAACA
* ** *
1860515 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
1860566 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
1860616 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
1860666 TGCCAATGCCATGTCCCAGACATGATCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1860716 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1860758 TTACCCAAAT
Statistics
Matches: 178, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 145 0.81
51 33 0.19
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:1860873 original size:13 final size:13
Alignment explanation
Indices: 1860852--1860882 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1860842 GCTTAGATCA
*
1860852 TCATCAAATAAAT
1 TCATAAAATAAAT
1860865 TCATAAAATAAAT
1 TCATAAAATAAAT
1860878 TCATA
1 TCATA
1860883 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1864334 original size:10 final size:10
Alignment explanation
Indices: 1864321--1864345 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1864311 AGATTATATG
1864321 TATATTGTGA
1 TATATTGTGA
1864331 TATATTGTGA
1 TATATTGTGA
1864341 TATAT
1 TATAT
1864346 GCTTAAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (10 bp):
TATATTGTGA
Found at i:1866175 original size:17 final size:18
Alignment explanation
Indices: 1866155--1866188 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1866145 ACATTTTTTG
1866155 TATAT-ACATTATTTTAC
1 TATATAACATTATTTTAC
*
1866172 TATATAATATTATTTTA
1 TATATAACATTATTTTA
1866189 AGTGTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATAACATTATTTTAC
Found at i:1872351 original size:53 final size:53
Alignment explanation
Indices: 1872288--1872391 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
1872278 TCTCCTAGAA
*
1872288 GACGACTATTGTGAGTGATTAGCTTGCCAGGGTGTTGAGGCAGAGGCATTGAC
1 GACGACTATTGTGAGGGATTAGCTTGCCAGGGTGTTGAGGCAGAGGCATTGAC
1872341 GACGACTATTGTGAGGGATTAGCTTGCCAGGGTGTTGAGGCAGAGGCATTG
1 GACGACTATTGTGAGGGATTAGCTTGCCAGGGTGTTGAGGCAGAGGCATTG
1872392 GCACTAACTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.26
Consensus pattern (53 bp):
GACGACTATTGTGAGGGATTAGCTTGCCAGGGTGTTGAGGCAGAGGCATTGAC
Found at i:1876587 original size:41 final size:42
Alignment explanation
Indices: 1876494--1876587 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 42
1876484 TCCAAGATAT
* * **
1876494 TCAGGCTCTATGTGCCTAGCAGGCTTGATGCCGGTGAAATATT
1 TCAGGCTTTATGT-CCTAGCAGGCTTCATGCCGGTGAAATAAA
* * *
1876537 TCAGACTTTATGT-CTAGCAGGCTTCATGCCGGTGTATTAAA
1 TCAGGCTTTATGTCCTAGCAGGCTTCATGCCGGTGAAATAAA
1876578 TCAGGCTTTA
1 TCAGGCTTTA
1876588 AGCCTAGTAG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 32 0.74
43 11 0.26
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (42 bp):
TCAGGCTTTATGTCCTAGCAGGCTTCATGCCGGTGAAATAAA
Found at i:1877004 original size:20 final size:20
Alignment explanation
Indices: 1876979--1877019 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1876969 CTAAGTTAGC
1876979 TTACTTTGTATTTTTATTTA
1 TTACTTTGTATTTTTATTTA
1876999 TTACTTTGTATTTTTATTTA
1 TTACTTTGTATTTTTATTTA
1877019 T
1 T
1877020 CTTTGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (20 bp):
TTACTTTGTATTTTTATTTA
Found at i:1887418 original size:22 final size:22
Alignment explanation
Indices: 1887355--1887420 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1887345 TAAGATCTCC
**
1887355 AACGTACTAAGCTCTCATGGCT
1 AACGTACTAAGCTCTCATGTTT
1887377 AACGTACTAAGCTCTCATGTTT
1 AACGTACTAAGCTCTCATGTTT
*
1887399 CACGTACTAAGCTCTCATGTTT
1 AACGTACTAAGCTCTCATGTTT
1887421 GAACAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (22 bp):
AACGTACTAAGCTCTCATGTTT
Found at i:1891637 original size:110 final size:109
Alignment explanation
Indices: 1891399--1891692 Score: 468
Period size: 110 Copynumber: 2.7 Consensus size: 109
1891389 ATATTTGGCA
* * * *
1891399 ATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
* *
1891461 CAAAACATTGCCTTATTTTAAAATTTTTGAAAGGATATTTAGCC
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
* * *
1891505 ATTTAGTTGAAAGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTAGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
*
1891570 CAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATATTAAGCC
66 CAAAACATTGCCTTATTTT-AAAATTTTTAAAAGGATATTAAGCC
1891615 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
1891680 CAAAACATTGCCT
66 CAAAACATTGCCT
1891693 CAATTAGAAA
Statistics
Matches: 171, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
106 12 0.07
108 26 0.15
109 36 0.21
110 97 0.57
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (109 bp):
ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
Found at i:1892081 original size:50 final size:50
Alignment explanation
Indices: 1892022--1893005 Score: 612
Period size: 50 Copynumber: 19.7 Consensus size: 50
1892012 GCAGCGGAGC
* * *
1892022 AGATTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTCAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* * * * * *** *
1892072 AGATCGAAGCCACAACGGCGAATCTTATTTCCCAGGCAGTGCAGCGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* * * * * *
1892122 ATATTGAAGCTACGATGGCGAATCTTGCTTCCCCGACATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* * * * * * * *
1892172 AGATTGAGGCCACAACAGCGGATCTTACTTCCCAGGCGA-TGCAGTGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGAC-ATTGCAATTGAAA
* * * *
1892222 AGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* * * * * *** *
1892272 AGATTGAGGCCACAACAGCGGATCTTACTTCCCAGGCGA-TGCAGCGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGAC-ATTGCAATTGAAA
* * * *
1892322 AGATTGAAGCTACAACAGCGAATCTCACTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* * *** *
1892372 AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGCGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGAC-ATTGCAATTGAAA
* * * *
1892422 AGATTGAAGTCACAACGGCGAATCTTGCGTCCCCGACATTGCAATTCAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* * * * * * *** *
1892472 AGATCGAAGCCACAATGGTGAATCTTACTT-CCAGGCAATGCAGCGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* * * * * * * *
1892521 AGATTAAAGCTACGACGGTGAATCTTGCTTCCTCGACATTGCAATTCAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* * *** *
1892571 AGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGCGGAAT
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGAC-ATTGCAATTGAAA
* * * *
1892621 AGATTGAAGCTACGACGGCGAATCTCACTTCCCCGACATTGCAATTCAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
** * ** * *
1892671 AGATCAAAGCCACAACGGCGAATCTTACTTCCCAGGTGA-TGCAGTGGAACA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCC-CGACATTGCAATTGAA-A
* * * * * * * * *
1892722 A-ATTAAAGCTACGATGGCGAATCCTGCTTCCTCGACATTGCAGTTTAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* * ** * *
1892771 AGATTGAGGCCACAATGGCGAATCTTACTTCCAAG-CTATATAGC---GGAAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGAC-AT-T-GCAATTGAAA
* * *
1892820 AGATTGAAGCCACAATGGCGAATCTTCCTTCCCCGACATTGCAA-TCAAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* ** * * * * *
1892869 TAGATTGAAGCTACAACAACGAATCTTA-TCTCCCTGGCGA-TGCAGTGGAAC
1 -AGATTGAAGCCACAACGGCGAATCTTACT-TCCCCGAC-ATTGCAATTGAAA
* * * * * * * * * * *
1892920 ATATTGAAGCTACGATGGTGAATTTTGCTTTCCTGATATTGCAACT-AAA
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
* *
1892969 AGATTGAAGCCACAACGGCGAATCTTATTTCCTCGAC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGAC
1893006 GAGACCGGGC
Statistics
Matches: 682, Mismatches: 227, Indels: 51
0.71 0.24 0.05
Matches are distributed among these distances:
47 2 0.00
48 1 0.00
49 110 0.16
50 554 0.81
51 13 0.02
52 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCAATTGAAA
Found at i:1892164 original size:100 final size:100
Alignment explanation
Indices: 1891991--1893000 Score: 1260
Period size: 100 Copynumber: 10.1 Consensus size: 100
1891981 TATGAAAAAT
* * **
1891991 GAATCTTACTTCCTAGGCGATGCAGCGGAGCAGATTGAAGCTACAACGGCGAATCTCACTTCCCC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCC
*
1892056 GACATTGCAATTCAAAAGATCGAAGCCACAACGGC
66 GACATTGCAATTCAAAAGATTGAAGCCACAACGGC
* * * *
1892091 GAATCTTATTTCCCAGGC-AGTGCAGCGGAACATATTGAAGCTACGATGGCGAATCTTGCTTCCC
1 GAATCTTACTTCCCAGGCGA-TGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCC
* * *
1892155 CGACATTGCAATTTAAAAGATTGAGGCCACAACAGC
65 CGACATTGCAATTCAAAAGATTGAAGCCACAACGGC
* * **
1892191 GGATCTTACTTCCCAGGCGATGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCC
* * * *
1892256 AACATTGCAATTTAAAAGATTGAGGCCACAACAGC
66 GACATTGCAATTCAAAAGATTGAAGCCACAACGGC
* * **
1892291 GGATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCC
*
1892356 GACATTGCAATTAAAAAGATTGAAGCCACAACGGC
66 GACATTGCAATTCAAAAGATTGAAGCCACAACGGC
*
1892391 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAG-TCACAACGGCGAATCTTGCGTCCC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCT-ACAACGGCGAATCTTGCTTCCC
* * *
1892455 CGACATTGCAATTCAAAAGATCGAAGCCACAATGGT
65 CGACATTGCAATTCAAAAGATTGAAGCCACAACGGC
* * * * *
1892491 GAATCTTACTT-CCAGGCAATGCAGCGGAACAGATTAAAGCTACGACGGTGAATCTTGCTTCCTC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCC
*
1892555 GACATTGCAATTCAACAGATTGAAGCCACAACGGC
66 GACATTGCAATTCAAAAGATTGAAGCCACAACGGC
* * **
1892590 GAATCTTACTTCCCAGGCGATGCAGCGGAATAGATTGAAGCTACGACGGCGAATCTCACTTCCCC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCC
**
1892655 GACATTGCAATTCAAAAGATCAAAGCCACAACGGC
66 GACATTGCAATTCAAAAGATTGAAGCCACAACGGC
* * * * * * * *
1892690 GAATCTTACTTCCCAGGTGATGCAGTGGAACAAATTAAAGCTACGATGGCGAATCCTGCTTCCTC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCC
* * * *
1892755 GACATTGCAGTTTAAAAGATTGAGGCCACAATGGC
66 GACATTGCAATTCAAAAGATTGAAGCCACAACGGC
* * ** * * *
1892790 GAATCTTACTT-CCAAGCTATATAGCGGAACAGATTGAAGCCACAATGGCGAATCTTCCTTCCCC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCC
* **
1892854 GACATTGCAA-TCAAATAGATTGAAGCTACAACAAC
66 GACATTGCAATTCAAA-AGATTGAAGCCACAACGGC
* * * * * * * *
1892889 GAATCTTA-TCTCCCTGGCGATGCAGTGGAACATATTGAAGCTACGATGGTGAATTTTGCTTTCC
1 GAATCTTACT-TCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCC
* * *
1892953 TGATATTGCAACT-AAAAGATTGAAGCCACAACGGC
65 CGACATTGCAATTCAAAAGATTGAAGCCACAACGGC
*
1892988 GAATCTTATTTCC
1 GAATCTTACTTCC
1893001 TCGACGAGAC
Statistics
Matches: 790, Mismatches: 110, Indels: 21
0.86 0.12 0.02
Matches are distributed among these distances:
98 5 0.01
99 188 0.24
100 595 0.75
101 2 0.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.22
Consensus pattern (100 bp):
GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCC
GACATTGCAATTCAAAAGATTGAAGCCACAACGGC
Found at i:1892674 original size:299 final size:299
Alignment explanation
Indices: 1891991--1893000 Score: 1355
Period size: 299 Copynumber: 3.4 Consensus size: 299
1891981 TATGAAAAAT
* *
1891991 GAATCTTACTTCCTAGGCGATGCAGCGGAGCAGATTGAAGCTACAACGGCGAATCTCACTTCCCC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCC
*
1892056 GACATTGCAATTCAAAAGATCGAAGCCACAACGGCGAATCTTATTTCCCAGGC-AGTGCAGCGGA
66 GACATTGCAATTCAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGCGGA
*
1892120 ACATATTGAAGCTACGATGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAGGCCAC
130 ACAAATTGAAGCTACGATGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAGGCCAC
** * * * *
1892185 AACAGCGGATCTTACTTCCCAGGCGATGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCAC
195 AATGGCGAATCTTACTT-CCAGGCAATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTAC
* * *
1892250 TTCCCCAACATTGCAATTTAAAAGATTGAGGCCACAACAGC
259 TTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACAGC
* *
1892291 GGATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCC
* *
1892356 GACATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAA
66 GACATTGCAATTCAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAA
* * * * * * *
1892421 CAGATTGAAG-TCACAACGGCGAATCTTGCGTCCCCGACATTGCAATTCAAAAGATCGAAGCCAC
131 CAAATTGAAGCT-ACGATGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAGGCCAC
* * * * *
1892485 AATGGTGAATCTTACTTCCAGGCAATGCAGCGGAACAGATTAAAGCTACGACGGTGAATCTTGCT
195 AATGGCGAATCTTACTTCCAGGCAATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTACT
* * *
1892550 TCCTCGACATTGCAATTCAACAGATTGAAGCCACAACGGC
260 TCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACAGC
* *
1892590 GAATCTTACTTCCCAGGCGATGCAGCGGAATAGATTGAAGCTACGACGGCGAATCTCACTTCCCC
1 GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCC
* * *
1892655 GACATTGCAATTCAAAAGATCAAAGCCACAACGGCGAATCTTACTTCCCAGGTGATGCAGTGGAA
66 GACATTGCAATTCAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAA
* * * *
1892720 CAAATTAAAGCTACGATGGCGAATCCTGCTTCCTCGACATTGCAGTTTAAAAGATTGAGGCCACA
131 CAAATTGAAGCTACGATGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAGGCCACA
* * ** * * *
1892785 ATGGCGAATCTTACTTCCAAGCTATATAGCGGAACAGATTGAAGCCACAATGGCGAATCTTCCTT
196 ATGGCGAATCTTACTTCCAGGCAATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTACTT
* *
1892850 CCCCGACATTGCAA-TCAAATAGATTGAAGCTACAACAAC
261 CCCCGACATTGCAATTCAAA-AGATTGAAGCCACAACAGC
* * * * * * * ** *
1892889 GAATCTTA-TCTCCCTGGCGATGCAGTGGAACATATTGAAGCTACGATGGTGAATTTTGCTTTCC
1 GAATCTTACT-TCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCC
* * * * *
1892953 TGATATTGCAACT-AAAAGATTGAAGCCACAACGGCGAATCTTATTTCC
65 CGACATTGCAATTCAAAAGATCGAAGCCACAACGGCGAATCTTACTTCC
1893001 TCGACGAGAC
Statistics
Matches: 622, Mismatches: 83, Indels: 12
0.87 0.12 0.02
Matches are distributed among these distances:
298 37 0.06
299 394 0.63
300 190 0.31
301 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.22
Consensus pattern (299 bp):
GAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCC
GACATTGCAATTCAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAA
CAAATTGAAGCTACGATGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAGGCCACA
ATGGCGAATCTTACTTCCAGGCAATGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTACTT
CCCCGACATTGCAATTCAAAAGATTGAAGCCACAACAGC
Done.