Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 15 of 297
Found at i:4942683 original size:25 final size:26
Alignment explanation
Indices: 4942655--4942703 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
4942645 CAATGATAAC
* *
4942655 CTTTATGGCGTAATATG-AAGAAAGA
1 CTTTATCGAGTAATATGAAAGAAAGA
*
4942680 CTTTGTCGAGTAATATGAAAGAAA
1 CTTTATCGAGTAATATGAAAGAAA
4942704 AACCTTTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (26 bp):
CTTTATCGAGTAATATGAAAGAAAGA
Found at i:4942721 original size:27 final size:26
Alignment explanation
Indices: 4942666--4942726 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
4942656 TTTATGGCGT
* **
4942666 AATATG-AAGAAAGACTTTGTCGAGT
1 AATATGAAAGAAAAACTTTGTCGAAA
*
4942691 AATATGAAAGAAAAACCTTTGTGGAAA
1 AATATGAAAGAAAAA-CTTTGTCGAAA
4942718 AATATGAAA
1 AATATGAAA
4942727 TGAACGCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 6 0.20
26 7 0.23
27 17 0.57
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.25
Consensus pattern (26 bp):
AATATGAAAGAAAAACTTTGTCGAAA
Found at i:4946226 original size:48 final size:46
Alignment explanation
Indices: 4946171--4946378 Score: 175
Period size: 48 Copynumber: 4.6 Consensus size: 46
4946161 ATGAGATCTC
*
4946171 GTGTAAGACCATGTCTGGGACATGGCATCGACATTAATATGTGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACA-TGATATGTGT-CCA
* * * * *
4946219 GTGTAAGACCATATCTGGGATATGGCATCGGCATCGGTATGTGATTTCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGACAT-GATATGTG--TCCA
* * * * *
4946268 -TGTAAGACCATGTCTGGGATATGGCGTTGATATGAGAT-T-T-C-
1 GTGTAAGACCATGTCTGGGACATGGCATCGACATGATATGTGTCCA
* *
4946309 GTGTAAGACCATGTTTGGGACATGGCATCG-C-T-ATGA-G-GTCCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGACATGAT-ATGTGTCCA
4946351 GTGTAAGACCATGTCTGGGACATGGCAT
1 GTGTAAGACCATGTCTGGGACATGGCAT
4946379 TGGCACCGAC
Statistics
Matches: 131, Mismatches: 20, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
39 1 0.01
40 3 0.02
41 1 0.01
42 53 0.40
43 1 0.01
46 1 0.01
47 4 0.03
48 64 0.49
49 2 0.02
50 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (46 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGACATGATATGTGTCCA
Found at i:4946320 original size:42 final size:42
Alignment explanation
Indices: 4946161--4946378 Score: 177
Period size: 42 Copynumber: 4.9 Consensus size: 42
4946151 ACCACAATTA
* *
4946161 ATGAGATCTCGTGTAAGACCATGTCTGGGACATGGCATCGAC
1 ATGAGATTTCGTGTAAGACCATGTCTGGGACATGGCATCGAT
* * * *
4946203 ATTAATATGTGTGCCAGTGTAAGACCATATCTGGGATATGGCATCGGCATCGGT
1 A-TGAGAT-T-T--C-GTGTAAGACCATGTCTGGG--A---CAT-GGCATCGAT
* * * * *
4946257 ATGTGATTTCATGTAAGACCATGTCTGGGATATGGCGTTGAT
1 ATGAGATTTCGTGTAAGACCATGTCTGGGACATGGCATCGAT
* *
4946299 ATGAGATTTCGTGTAAGACCATGTTTGGGACATGGCATCGCT
1 ATGAGATTTCGTGTAAGACCATGTCTGGGACATGGCATCGAT
* *
4946341 ATGAG-GTCCTGTGTAAGACCATGTCTGGGACATGGCAT
1 ATGAGATTTC-GTGTAAGACCATGTCTGGGACATGGCAT
4946379 TGGCACCGAC
Statistics
Matches: 138, Mismatches: 25, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
41 2 0.01
42 74 0.54
43 6 0.04
45 1 0.01
46 1 0.01
47 1 0.01
48 35 0.25
49 1 0.01
50 1 0.01
51 1 0.01
52 1 0.01
53 6 0.04
54 8 0.06
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (42 bp):
ATGAGATTTCGTGTAAGACCATGTCTGGGACATGGCATCGAT
Found at i:4949763 original size:48 final size:46
Alignment explanation
Indices: 4949662--4949873 Score: 158
Period size: 46 Copynumber: 4.6 Consensus size: 46
4949652 TTATTTGTGT
* *
4949662 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCACATTATAAGA
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGG-CACATGACAAGA
*
4949708 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACATGGAGACAAGA
1 GCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCACAT---GACAAGA
* * * *
4949756 GCTAGTGTAAGACATATCTGGGACAT-GTATCGGC-C-TCAAAATGTAA
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCACATGACAA-G--A
*
4949802 GCTAGTGTAAGACATGTCTGGGACAT-GCATTGG--C-T-ACAAGA
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCACATGACAAGA
*
4949843 TGTGTCAGTGTAAGACCATGTCTGGGACATG
1 -G-CT-AGTGTAAGA-CATGTCTGGGACATG
4949874 ACGTCAGCCT
Statistics
Matches: 138, Mismatches: 13, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 5 0.04
44 13 0.09
45 20 0.14
46 47 0.34
47 30 0.22
48 21 0.15
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCACATGACAAGA
Found at i:4951195 original size:21 final size:21
Alignment explanation
Indices: 4951169--4951229 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
4951159 GTCATAGTGG
4951169 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
*
4951190 CCACACAGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
4951211 CCACACGGGCGTG-TGCCCT
1 CCACACGGGCGTGTTGCCCT
4951230 GTTTCAAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.11, C:0.39, G:0.28, T:0.21
Consensus pattern (21 bp):
CCACACGGGCGTGTTGCCCTT
Found at i:4953070 original size:44 final size:43
Alignment explanation
Indices: 4952992--4953122 Score: 131
Period size: 42 Copynumber: 3.0 Consensus size: 43
4952982 CGTTGACATT
* ** * *
4952992 GATTTGAGATATCGTGTAAGACTGTGTCTAGGACACAGGCCTC
1 GATTTGAGATTTCGTGTAAGACCATGTCTGGGACACAGGCATC
* *
4953035 GATTTGAGATTTACGTGTAAGACCATGTATGGGACATAGGCATC
1 GATTTGAGATTT-CGTGTAAGACCATGTCTGGGACACAGGCATC
* * * *
4953079 GTATCT--GATTTTGTGTAAGACCCTGTCTGGGACAGAGGCATC
1 G-ATTTGAGATTTCGTGTAAGACCATGTCTGGGACACAGGCATC
4953121 GA
1 GA
4953123 AAATGAATTA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 28 0.38
43 16 0.22
44 26 0.35
45 3 0.04
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (43 bp):
GATTTGAGATTTCGTGTAAGACCATGTCTGGGACACAGGCATC
Found at i:4960268 original size:44 final size:41
Alignment explanation
Indices: 4960210--4960345 Score: 114
Period size: 44 Copynumber: 3.2 Consensus size: 41
4960200 TGAGATATCG
*
4960210 TGTAAGACCGTGTCTGGGACACAGGCATCGATTTGAGATTTACA
1 TGTAAGATC-TGTCTGGGACACAGGCATCGATTTGA-ATTT-CA
* * * *
4960254 TGTAAGATCATGTCTGAGACATAGACATC-ATATCT-AATTTCG
1 TGTAAGATC-TGTCTGGGACACAGGCATCGAT-T-TGAATTTCA
* * *
4960296 TGTAAGACTCTGTCTGGGAAAGAGGCATCGAAATTGAATTTCA
1 TGTAAGA-TCTGTCTGGGACACAGGCATCG-ATTTGAATTTCA
4960339 TGTAAGA
1 TGTAAGA
4960346 CCACATCCGG
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
42 24 0.32
43 22 0.30
44 27 0.36
45 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (41 bp):
TGTAAGATCTGTCTGGGACACAGGCATCGATTTGAATTTCA
Found at i:4961920 original size:21 final size:20
Alignment explanation
Indices: 4961896--4961957 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
4961886 AAAATGTTTC
4961896 AGTTTCTGAAAATTATGTATG
1 AGTTT-TGAAAATTATGTATG
* * * *
4961917 AG-TTAGAAAA-AATGTTTA
1 AGTTTTGAAAATTATGTATG
4961935 AGTTTTTGAAAATTATGTATG
1 AG-TTTTGAAAATTATGTATG
4961956 AG
1 AG
4961958 CTCGGTTTAG
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
18 7 0.23
19 5 0.17
20 9 0.30
21 9 0.30
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.40
Consensus pattern (20 bp):
AGTTTTGAAAATTATGTATG
Found at i:4961939 original size:39 final size:39
Alignment explanation
Indices: 4961880--4961957 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
4961870 CCTTTAACAC
*
4961880 TTAGAAAAAATGTTTCAGTTTCTGAAAATTATGTATGAG
1 TTAGAAAAAATGTTTAAGTTTCTGAAAATTATGTATGAG
*
4961919 TTAGAAAAAATGTTTAAGTTTTTGAAAATTATGTATGAG
1 TTAGAAAAAATGTTTAAGTTTCTGAAAATTATGTATGAG
4961958 CTCGGTTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.40
Consensus pattern (39 bp):
TTAGAAAAAATGTTTAAGTTTCTGAAAATTATGTATGAG
Found at i:4962582 original size:19 final size:19
Alignment explanation
Indices: 4962558--4962596 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4962548 ATTAATTTTG
4962558 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
4962577 ATCAAATTAATTAAAATTA
1 ATCAAATAAATTAAAATTA
4962596 A
1 A
4962597 AATGATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:4966077 original size:27 final size:27
Alignment explanation
Indices: 4966040--4966103 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
4966030 GTACATATAT
4966040 GTCA-TTTACCCTCGAGGGGTAAATTA
1 GTCATTTTACCCTCGAGGGGTAAATTA
** ** *
4966066 GTCATTTTACCCTTTAGGGGTATTTTG
1 GTCATTTTACCCTCGAGGGGTAAATTA
4966093 GTCATTTTACC
1 GTCATTTTACC
4966104 AGTCTTGGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTCGAGGGGTAAATTA
Found at i:4967873 original size:47 final size:47
Alignment explanation
Indices: 4967795--4968907 Score: 1958
Period size: 47 Copynumber: 23.6 Consensus size: 47
4967785 CCCTTCGGGA
* * * * * * *
4967795 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
* *
4967842 CCTGTCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4967889 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4967936 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4967983 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4968030 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4968077 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4968124 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4968171 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4968218 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4968265 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4968312 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4968359 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4968406 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
*
4968453 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
*
4968500 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
* *
4968547 CTTATCAAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
*
4968594 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCGATTAGGC
*
4968643 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
* *
4968690 CTTATCACATATATACATTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
* * *
4968737 CTTATCACATATATATACACTTTCACATTCATCA-ATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCGATTAGGC
*
4968785 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
* *
4968832 CTTATCACATATATATACACTTTCATATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCGATTAGGC
4968881 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
4968908 TATTCAAATA
Statistics
Matches: 1033, Mismatches: 26, Indels: 14
0.96 0.02 0.01
Matches are distributed among these distances:
46 24 0.02
47 873 0.85
48 20 0.02
49 116 0.11
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
Found at i:4976658 original size:34 final size:33
Alignment explanation
Indices: 4976603--4976678 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 33
4976593 GTGTGCTTCT
*
4976603 CTGATACTGTACTGAATTGGGCTAAGACCCACA
1 CTGATATTGTACTGAATTGGGCTAAGACCCACA
4976636 CTGATATTGTTACTGTAA-TGGGCTAAGACCCACA
1 CTGATATTG-TACTG-AATTGGGCTAAGACCCACA
*
4976670 CTGTTATTG
1 CTGATATTG
4976679 CCATTGATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
33 8 0.21
34 29 0.74
35 2 0.05
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (33 bp):
CTGATATTGTACTGAATTGGGCTAAGACCCACA
Found at i:4984491 original size:22 final size:22
Alignment explanation
Indices: 4984461--4984507 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
4984451 TTTGGTATTT
4984461 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
4984483 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
4984505 GGG
1 GGG
4984508 TTCAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:4984710 original size:105 final size:105
Alignment explanation
Indices: 4984578--4984787 Score: 411
Period size: 105 Copynumber: 2.0 Consensus size: 105
4984568 CCAAATTGAG
4984578 TTGGAAATGGTTGATAAGGACCTTGACCCGATACTTAGTAAAGTATGAACCAAAGGTATCAAAGG
1 TTGGAAATGGTTGATAAGGACCTTGACCCGATACTTAGTAAAGTATGAACCAAAGGTATCAAAGG
4984643 GGAACGCCACACTCGGGTTTAGGGAGTGATAAGTTCGAAA
66 GGAACGCCACACTCGGGTTTAGGGAGTGATAAGTTCGAAA
4984683 TTGGAAATGGTTGATAAGGACCTTGACCCGATACTTAGTAAAGTATGAACCAAAGGTATCAAAGG
1 TTGGAAATGGTTGATAAGGACCTTGACCCGATACTTAGTAAAGTATGAACCAAAGGTATCAAAGG
*
4984748 TGAACGCCACACTCGGGTTTAGGGAGTGATAAGTTCGAAA
66 GGAACGCCACACTCGGGTTTAGGGAGTGATAAGTTCGAAA
4984788 GAAAGACTCA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.23
Consensus pattern (105 bp):
TTGGAAATGGTTGATAAGGACCTTGACCCGATACTTAGTAAAGTATGAACCAAAGGTATCAAAGG
GGAACGCCACACTCGGGTTTAGGGAGTGATAAGTTCGAAA
Found at i:4988964 original size:16 final size:16
Alignment explanation
Indices: 4988943--4988977 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
4988933 TAAATCAAAA
*
4988943 AAATAAAGAAAGAAGG
1 AAATAAAGAAAGAAAG
4988959 AAATAAAGAAAGAAAG
1 AAATAAAGAAAGAAAG
4988975 AAA
1 AAA
4988978 AAGGAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (16 bp):
AAATAAAGAAAGAAAG
Found at i:4988968 original size:12 final size:12
Alignment explanation
Indices: 4988947--4988984 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4988937 TCAAAAAAAT
4988947 AAAGAAAGAAGG
1 AAAGAAAGAAGG
* *
4988959 AAATAAAGAAAG
1 AAAGAAAGAAGG
4988971 AAAGAAA-AAGG
1 AAAGAAAGAAGG
4988982 AAA
1 AAA
4988985 AAGAAAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (12 bp):
AAAGAAAGAAGG
Found at i:4992024 original size:22 final size:22
Alignment explanation
Indices: 4991998--4992043 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4991988 ATTATGTATA
4991998 TTAATTCATAA-TATAATTAATT
1 TTAATTCATAACTA-AATTAATT
* *
4992020 TTAATTTATAACTAATTTAATT
1 TTAATTCATAACTAAATTAATT
4992042 TT
1 TT
4992044 GGTTAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAATTCATAACTAAATTAATT
Found at i:4992035 original size:17 final size:16
Alignment explanation
Indices: 4992009--4992042 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4991999 TAATTCATAA
*
4992009 TATAATTAATTTTAATT
1 TATAACTAA-TTTAATT
4992026 TATAACTAATTTAATT
1 TATAACTAATTTAATT
4992042 T
1 T
4992043 TGGTTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TATAACTAATTTAATT
Found at i:5004437 original size:27 final size:27
Alignment explanation
Indices: 5004407--5004487 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
5004397 CGATATTGTA
**
5004407 GCAAAGCTGCCAGAAACAGTAAATGTG
1 GCAAAGCCACCAGAAACAGTAAATGTG
* * *
5004434 GCAAAGCCACCAGTATCAGTAATTGTG
1 GCAAAGCCACCAGAAACAGTAAATGTG
* * *
5004461 GCATAA-CCACCAGTAATAGTGAATGTG
1 GCA-AAGCCACCAGAAACAGTAAATGTG
5004488 ACATAGTCAC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 42 0.95
28 2 0.05
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (27 bp):
GCAAAGCCACCAGAAACAGTAAATGTG
Found at i:5004492 original size:27 final size:28
Alignment explanation
Indices: 5004423--5004502 Score: 69
Period size: 27 Copynumber: 2.9 Consensus size: 28
5004413 CTGCCAGAAA
* *
5004423 CAGTAAATGTGGCA-AAGCCACCAGT-AT
1 CAGTAATTGTGACATAA-CCACCAGTAAT
*
5004450 CAGTAATTGTGGCATAACCACCAGTAAT
1 CAGTAATTGTGACATAACCACCAGTAAT
**
5004478 -AGTGAA-TGTGACATAGTCACCAGTA
1 CAGT-AATTGTGACATAACCACCAGTA
5004503 CAGTACTTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 40 0.87
28 6 0.13
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (28 bp):
CAGTAATTGTGACATAACCACCAGTAAT
Found at i:5004661 original size:26 final size:27
Alignment explanation
Indices: 5004628--5004688 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
5004618 TCATACAGAG
5004628 CATA-AGGGCATAAT-C-GTCATTTTAC
1 CATACAGGG-ATAATACGGTCATTTTAC
* *
5004653 CATACAGGGGTATTACGGTCATTTTAC
1 CATACAGGGATAATACGGTCATTTTAC
*
5004680 CCTACAGGG
1 CATACAGGG
5004689 GTTTTACGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 7 0.23
26 5 0.17
27 18 0.60
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (27 bp):
CATACAGGGATAATACGGTCATTTTAC
Found at i:5004673 original size:27 final size:27
Alignment explanation
Indices: 5004643--5004696 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
5004633 GGGCATAATC
5004643 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
5004670 GTCATTTTACCCTACAGGGGTTTTACG
1 GTCATTTTACCATACAGGGGTATTACG
5004697 ATAATTTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:5004703 original size:27 final size:27
Alignment explanation
Indices: 5004646--5004703 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
5004636 CATAATCGTC
* *
5004646 ATTTTACCATACAGGGGTATTACGGTC
1 ATTTTACCATACAGGGGTATTACGATA
* *
5004673 ATTTTACCCTACAGGGGTTTTACGATA
1 ATTTTACCATACAGGGGTATTACGATA
5004700 ATTT
1 ATTT
5004704 CACAAATCGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (27 bp):
ATTTTACCATACAGGGGTATTACGATA
Found at i:5009579 original size:27 final size:27
Alignment explanation
Indices: 5009549--5010111 Score: 300
Period size: 27 Copynumber: 20.9 Consensus size: 27
5009539 AATGTCTTCA
* *
5009549 ATTTGTAAAATTACCAAAGTACCCTCG
1 ATTTATAAAATTACCAAATTACCCTCG
* **
5009576 ATTTATAGAATTACC-GTTTCACCCTCG
1 ATTTATAAAATTACCAAATT-ACCCTCG
* **
5009603 ATTTACAAAATTACCATTTTACCCTCG
1 ATTTATAAAATTACCAAATTACCCTCG
* **
5009630 ATTTATAGAATTACCATTTTACCCTCG
1 ATTTATAAAATTACCAAATTACCCTCG
* * *****
5009657 ATTTACAGAATTATTGTTTTACCCTCG
1 ATTTATAAAATTACCAAATTACCCTCG
* **
5009684 ATTTACAAAATTACCATTTTACCCTC-
1 ATTTATAAAATTACCAAATTACCCTCG
* ** *
5009710 AGTTTACAAAATTACCATTTTACCCTCT
1 A-TTTATAAAATTACCAAATTACCCTCG
* * * *
5009738 A-TTATGAAATTACTAAAATACCC-CC
1 ATTTATAAAATTACCAAATTACCCTCG
* * * *
5009763 AGTTGTAAAATTACCAAAGTACCCCCG
1 ATTTATAAAATTACCAAATTACCCTCG
*
5009790 GTTTATAAAATTACCCAAA-TACCCTCG
1 ATTTATAAAATTA-CCAAATTACCCTCG
* * *
5009817 ATTTGTAAAATTACTGAAA-TACCTTCG
1 ATTTATAAAATTAC-CAAATTACCCTCG
* * *
5009844 ACTTGTAAAATTACCAAAGTACCCTCG
1 ATTTATAAAATTACCAAATTACCCTCG
* * **
5009871 ATTTACAGAATTA-CAGTTTTACCCTCG
1 ATTTATAAAATTACCA-AATTACCCTCG
* * ** * *
5009898 ATTTATAGAATTACTATTTTACCTTTG
1 ATTTATAAAATTACCAAATTACCCTCG
* * ** *
5009925 ATTTATAGAATTACTATTTTACCCTTG
1 ATTTATAAAATTACCAAATTACCCTCG
* ****
5009952 ATTTATAGAATTACTGTTTTACCCTCG
1 ATTTATAAAATTACCAAATTACCCTCG
* * * *
5009979 ATTTACAAAATTACTAAAATACCC-CT
1 ATTTATAAAATTACCAAATTACCCTCG
* * *
5010005 AGTTTGTAAAATTACCAAAATACCCTTG
1 A-TTTATAAAATTACCAAATTACCCTCG
* * *
5010033 GTTTATGAAATTACCGAAA-TACCCTCA
1 ATTTATAAAATTACC-AAATTACCCTCG
* *
5010060 ATTTGTAAAATTACCAAAATACCC-CTG
1 ATTTATAAAATTACCAAATTACCCTC-G
* * * *
5010087 ATTTACAAAGTTACAAAAATACCCT
1 ATTTATAAAATTACCAAATTACCCT
5010112 TGACTTTCTA
Statistics
Matches: 439, Mismatches: 80, Indels: 33
0.80 0.14 0.06
Matches are distributed among these distances:
25 2 0.00
26 48 0.11
27 376 0.86
28 13 0.03
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (27 bp):
ATTTATAAAATTACCAAATTACCCTCG
Found at i:5009658 original size:81 final size:80
Alignment explanation
Indices: 5009568--5009993 Score: 342
Period size: 81 Copynumber: 5.3 Consensus size: 80
5009558 ATTACCAAAG
* *
5009568 TACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
1 TACCCTCGATTTATAGAATTACTGTTT-ACCCTCGATTTATAAAATTACCATTTTACCCTCGATT
5009633 TATAGAATTACCATTT
65 TATAGAATTACCATTT
* * *
5009649 TACCCTCGATTTACAGAATTATTGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTC-AGT
1 TACCCTCGATTTATAGAATTACTG-TTTACCCTCGATTTATAAAATTACCATTTTACCCTCGA-T
* *
5009713 TTACAAAATTACCATTT
64 TTATAGAATTACCATTT
* *** * * * *** * *
5009730 TACCCTCTA-TTAT-GAAATTACTAAAATACCC-CCAGTTGTAAAATTACCAAAGTACCCCCGGT
1 TACCCTCGATTTATAG-AATTACT-GTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGAT
* **
5009792 TTATAAAATTACCCA-AA
64 TTATAGAATTA-CCATTT
* * ** * * * ***
5009809 TACCCTCGATTTGTAAAATTACTGAAATACCTTCGACTTGTAAAATTACCAAAGTACCCTCGATT
1 TACCCTCGATTTATAGAATTACTG-TTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATT
*
5009874 TACAGAATTA-CAGTTT
65 TATAGAATTACCA-TTT
* * * * * *
5009890 TACCCTCGATTTATAGAATTACTATTTTACCTTTGATTTATAGAATTACTATTTTACCCTTGATT
1 TACCCTCGATTTATAGAATTACT-GTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATT
**
5009955 TATAGAATTACTGTTT
65 TATAGAATTACCATTT
* *
5009971 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTATAGAATTACT
5009994 AAAATACCCC
Statistics
Matches: 276, Mismatches: 55, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
79 42 0.15
80 34 0.12
81 197 0.71
82 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (80 bp):
TACCCTCGATTTATAGAATTACTGTTTACCCTCGATTTATAAAATTACCATTTTACCCTCGATTT
ATAGAATTACCATTT
Found at i:5009993 original size:54 final size:54
Alignment explanation
Indices: 5009568--5009994 Score: 337
Period size: 54 Copynumber: 7.9 Consensus size: 54
5009558 ATTACCAAAG
* * *
5009568 TACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACTATTT
* * *
5009622 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATTGTTT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACTATTT
* * *
5009676 TACCCTCGATTTACAAAATTACCATTTTACCCTC-AGTTTACAAAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGA-TTTACAAAATTACTATTT
* * *** * * ** * ***
5009730 TACCCTCTA-TTAT-GAAATTACTAAAATACCC-CCAGTTGTAAAATTACCAAAG
1 TACCCTCGATTTATAG-AATTACCATTTTACCCTCGATTTACAAAATTACTATTT
* * * ** ** **
5009782 TACCCCCGGTTTATAAAATTACCCA-AATACCCTCGATTTGTAAAATTACTGA-AA
1 TACCCTCGATTTATAGAATTA-CCATTTTACCCTCGATTTACAAAATTACT-ATTT
* * * * *** *
5009836 TACCTTCGACTTGTAAAATTACCAAAGTACCCTCGATTTACAGAATTAC-AGTTT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACTA-TTT
* * * * *
5009890 TACCCTCGATTTATAGAATTACTATTTTACCTTTGATTTATAGAATTACTATTT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACTATTT
* **
5009944 TACCCTTGATTTATAGAATTACTGTTTTACCCTCGATTTACAAAATTACTA
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACTA
5009995 AAATACCCCT
Statistics
Matches: 299, Mismatches: 62, Indels: 24
0.78 0.16 0.06
Matches are distributed among these distances:
52 20 0.07
53 36 0.12
54 241 0.81
55 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (54 bp):
TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACTATTT
Found at i:5010029 original size:54 final size:55
Alignment explanation
Indices: 5009971--5010194 Score: 179
Period size: 54 Copynumber: 4.1 Consensus size: 55
5009961 ATTACTGTTT
5009971 TACCCTCGATTTACAAAATTACTAAAATACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAATACCCCTCAGTTTGTAAAATTACCAAAA
* * ** ** *
5010025 TACCCTTGGTTTATGAAATTACCGAAATA-CCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAATACCCCTCAGTTTGTAAAATTACCAAAA
* * * * * * *
5010079 TACCC-CTGATTTACAAAGTTACAAAAATACCCTTGACTTTCTAAAAATTA-TAGAAA
1 TACCCTC-GATTTACAAAATTACTAAAATACCCCTCAGTTTGT-AAAATTACCA-AAA
* * * * ** * *
5010135 TACCATTGGTTTACAAAATTACTGAAATA-CCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAATACCCCTCAGTTTGTAAAATTACCAAAA
*
5010189 CACCCT
1 TACCCT
5010195 TGTAGGATGA
Statistics
Matches: 128, Mismatches: 35, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
53 4 0.03
54 75 0.59
55 17 0.13
56 32 0.25
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.31
Consensus pattern (55 bp):
TACCCTCGATTTACAAAATTACTAAAATACCCCTCAGTTTGTAAAATTACCAAAA
Found at i:5010084 original size:81 final size:81
Alignment explanation
Indices: 5009730--5010196 Score: 300
Period size: 81 Copynumber: 5.8 Consensus size: 81
5009720 ATTACCATTT
* * * * ** *
5009730 TACCCTCTA-TTATGAAATTACTAAAATACCCCCAG-TTGTAAAATTACCAAAGTACCCCCGGTT
1 TACCCTCGATTTATAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGATT
* *
5009793 TATAAAATTACCCAAA
66 TATAGAATTACCGAAA
* * * * * * *
5009809 TACCCTCGATTTGTAAAATTACTGAAATA-CCTTCGACTTGTAAAATTACCAAAGTACCCTCGAT
1 TACCCTCGATTTATAAAATTACTAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCTTGAT
* * ***
5009873 TTACAGAATTACAGTTT
65 TTATAGAATTACCGAAA
* *** * * * * * ***
5009890 TACCCTCGATTTATAGAATTACTATTTTA-CCTTTGATTTATAGAATTACTATTTTACCCTTGAT
1 TACCCTCGATTTATAAAATTACTAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCTTGAT
* ***
5009954 TTATAGAATTACTGTTT
65 TTATAGAATTACCGAAA
* *
5009971 TACCCTCGATTTACAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTT
1 TACCCTCGATTTATAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGATT
5010036 TAT-GAAATTACCGAAA
66 TATAG-AATTACCGAAA
* * * * *
5010052 TACCCTCAATTTGTAAAATTACCAAAATACCCCT-GATT-TACAAAGTTACAAAAATACCCTTGA
1 TACCCTCGATTTATAAAATTACTAAAATACCCCTAGTTTGTA-AAA-TTACCAAAATACCCTTGA
* * **
5010115 CTTTCTAAAAATTATAGAAA
64 -TTTAT-AGAATTACCGAAA
* * * * * * * * * *
5010135 TACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTTGTAGATTTACCAAAACACCCTTG
1 TACCCTCGATTTATAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTG
5010197 TAGGATGAAA
Statistics
Matches: 300, Mismatches: 76, Indels: 20
0.76 0.19 0.05
Matches are distributed among these distances:
79 13 0.04
80 23 0.08
81 201 0.67
82 8 0.03
83 49 0.16
84 4 0.01
85 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (81 bp):
TACCCTCGATTTATAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGATT
TATAGAATTACCGAAA
Found at i:5010155 original size:27 final size:27
Alignment explanation
Indices: 5010122--5010173 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
5010112 TGACTTTCTA
5010122 AAAATTA-TAGAAATACCATTGGTTTAC
1 AAAATTACT-GAAATACCATTGGTTTAC
*
5010149 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCATTGGTTT
5010174 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTACTGAAATACCATTGGTTTAC
Found at i:5010175 original size:110 final size:109
Alignment explanation
Indices: 5009973--5010193 Score: 257
Period size: 110 Copynumber: 2.0 Consensus size: 109
5009963 TACTGTTTTA
* * * *
5009973 CCCTCGATTTACAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTA
1 CCCTCGATTTACAAAATTACAAAAATACCCCTACTTTCTAAAATTACCAAAATACCATTGGTTTA
** *
5010038 TGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATAC
66 CAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAACAC
* * *
5010082 CCCT-GATTTACAAAGTTACAAAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGT
1 CCCTCGATTTACAAAATTACAAAAATACCCCT-ACTTTCT-AAAATTACCA-AAATACCATTGGT
* *** * *
5010145 TTACAAAATTACTGAAATACCCTTGGTTTGTAGATTTACCAAAACAC
63 TTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAACAC
5010192 CC
1 CC
5010194 TTGTAGGATG
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
108 24 0.26
109 10 0.11
110 59 0.63
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (109 bp):
CCCTCGATTTACAAAATTACAAAAATACCCCTACTTTCTAAAATTACCAAAATACCATTGGTTTA
CAAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAACAC
Found at i:5010291 original size:27 final size:26
Alignment explanation
Indices: 5010214--5010291 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 26
5010204 AAATGACTAA
*
5010214 AATACCCCTATCAGGTAAAAAGACCGT
1 AATACCCCTAT-AGGTAAAATGACCGT
* *
5010241 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTATA-GGTAAAATGACCGT
5010268 AATACCCCTATATGGTAAAATGAC
1 AATACCCCTATA-GGTAAAATGAC
5010292 GAATATGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.05
27 39 0.93
28 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (26 bp):
AATACCCCTATAGGTAAAATGACCGT
Found at i:5011498 original size:25 final size:25
Alignment explanation
Indices: 5011451--5011498 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5011441 TTATAACATG
* * *
5011451 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
*
5011476 AAAATGACCATTATACCCGTAGG
1 AAAATGACCATTATACCCCTAGG
5011499 GTTTATGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:5011601 original size:20 final size:20
Alignment explanation
Indices: 5011535--5011601 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
5011525 ATTTTGATAA
*
5011535 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
5011555 ACATGACATGTATGATACGC
1 ACATGATATGTATGATATGC
5011575 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
5011595 ACATGAT
1 ACATGAT
5011602 GTAATCATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:5011708 original size:24 final size:24
Alignment explanation
Indices: 5011651--5011816 Score: 232
Period size: 24 Copynumber: 7.0 Consensus size: 24
5011641 GAGGAAGTGA
5011651 AAAAGGGCTTATGCCCCAGTTATTC
1 AAAAGGGCTTATGCCCCAGTTA-TC
5011676 --AAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
5011698 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
5011722 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
* *
5011745 TAAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATC
* *
5011769 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
5011793 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
5011817 ATGATAAAGC
Statistics
Matches: 130, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.02
23 42 0.32
24 75 0.58
25 11 0.08
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:5011720 original size:47 final size:46
Alignment explanation
Indices: 5011651--5011816 Score: 210
Period size: 47 Copynumber: 3.5 Consensus size: 46
5011641 GAGGAAGTGA
5011651 AAAAGGGCTTATGCCCCAGTTATTCAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTCAAGGGCTTATGCCCCAGTTAT
5011697 CAAAAGGGCTTATGCCCCAGTTA-TCAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATTC--AAGGGCTTATGCCCCAGTTAT
* ** *
5011745 TAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTAT-TCAAGGGCTTATGCCCCAGTTA-T
*
5011793 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
5011817 ATGATAAAGC
Statistics
Matches: 106, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
46 2 0.02
47 62 0.58
48 31 0.29
49 11 0.10
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATTCAAGGGCTTATGCCCCAGTTAT
Found at i:5011767 original size:71 final size:71
Alignment explanation
Indices: 5011651--5011816 Score: 262
Period size: 71 Copynumber: 2.3 Consensus size: 71
5011641 GAGGAAGTGA
* *
5011651 AAAAGGGCTTATGCCCCAGTTATTCAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
5011716 GTTATC
66 GTTATC
*
5011722 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
*
5011787 GTTATT
66 GTTATC
*
5011793 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
5011817 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
71 77 0.88
72 11 0.12
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
GTTATC
Found at i:5012045 original size:31 final size:31
Alignment explanation
Indices: 5012010--5012073 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
5012000 CATTTACAGT
* *
5012010 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
**
5012041 AAAGGCTTCAGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
5012072 AA
1 AA
5012074 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTAATATGAAATATGA
Found at i:5018677 original size:50 final size:50
Alignment explanation
Indices: 5018597--5018726 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
5018587 CTAATAGAGT
*
5018597 CATGGATTATGTAACT-TCTATGTTAGTTAAG-TATGCATCATAAATAATGA
1 CATGCATTATGTAACTCTC-ATGTTAGTTAAGAT-TGCATCATAAATAATGA
* *
5018647 CATGCATTATGTAACTCTCATGTTAGTTAAGATTGCATCATAAATTATGT
1 CATGCATTATGTAACTCTCATGTTAGTTAAGATTGCATCATAAATAATGA
* *
5018697 CGTGCATTATGTAACTCCCATGTTAGTTAA
1 CATGCATTATGTAACTCTCATGTTAGTTAA
5018727 AGTTTGCAAC
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 70 0.96
51 3 0.04
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (50 bp):
CATGCATTATGTAACTCTCATGTTAGTTAAGATTGCATCATAAATAATGA
Found at i:5020002 original size:16 final size:16
Alignment explanation
Indices: 5019981--5020014 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5019971 AAAAAAATAG
5019981 TTATTTGTGTAAACCA
1 TTATTTGTGTAAACCA
* *
5019997 TTATTTTTGTAAATCA
1 TTATTTGTGTAAACCA
5020013 TT
1 TT
5020015 TTGTTAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (16 bp):
TTATTTGTGTAAACCA
Found at i:5021535 original size:16 final size:17
Alignment explanation
Indices: 5021514--5021552 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
5021504 GTGGGAAAAG
*
5021514 AAAATAAAAATTTTAA-
1 AAAATAAAAATTTCAAT
*
5021530 AAAATAAATATTTCAAT
1 AAAATAAAAATTTCAAT
5021547 AAAATA
1 AAAATA
5021553 TCCCTATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATAAAAATTTCAAT
Found at i:5023987 original size:43 final size:42
Alignment explanation
Indices: 5023927--5024037 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 42
5023917 TGTGTATTCG
* * * *
5023927 TGTAACACCACGTCTGGGACGTTGGCATCGTTATGTGATTACG
1 TGTAAGACCACG-CTGGGACGTTGGCATCGATATGTGACTACA
5023970 TGTAAGACCCTAC-CTGGGACAG-TGGCATCGATATGTGACTACA
1 TGTAAGA-CC-ACGCTGGGAC-GTTGGCATCGATATGTGACTACA
5024013 TGTAAGACCACGTCTGGGACGTTGG
1 TGTAAGACCACG-CTGGGACGTTGG
5024038 TATTGTATGA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
41 2 0.03
42 3 0.05
43 48 0.83
44 3 0.05
45 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (42 bp):
TGTAAGACCACGCTGGGACGTTGGCATCGATATGTGACTACA
Found at i:5034110 original size:27 final size:27
Alignment explanation
Indices: 5034080--5034672 Score: 603
Period size: 27 Copynumber: 22.1 Consensus size: 27
5034070 TATGTTGGTC
*
5034080 ATTTTAC-AATACAAGGGTATTTCGGTA
1 ATTTTACAAAT-CGAGGGTATTTCGGTA
* * *
5034107 ATTTTACACTAT-AAGGGTATTTCGATA
1 ATTTTACA-AATCGAGGGTATTTCGGTA
*
5034134 ATTTTACAAATCGAGGGTGTTTCGGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
**
5034161 ATTTTACAAATCGAGGGTATTTTAGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
* *
5034188 ATTTTACAAATCGAGGGTGTTTCAGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
* * *
5034215 ATTTTACAAATTGAGGGTGTTTCGATA
1 ATTTTACAAATCGAGGGTATTTCGGTA
* * *
5034242 ATTTTACAAATCCAGGGTGTTTCGATA
1 ATTTTACAAATCGAGGGTATTTCGGTA
* * **
5034269 ATTTCACAAATCGAGAGTATTTTAGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
* **
5034296 ATTTTTCAAATCGAGGGTATTTTTGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
* * *
5034323 ATTTCAC-AATTGAGGGTATTTTGGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
*
5034349 ATTTTACAAATCGGGGGTATTTCAGG-A
1 ATTTTACAAATCGAGGGTATTTC-GGTA
* *
5034376 ATTTTACAAATCGAGGGTGTTTCGATA
1 ATTTTACAAATCGAGGGTATTTCGGTA
* * * *
5034403 ATTTCACAAATTG-GGAGTATTTTGATA
1 ATTTTACAAATCGAGG-GTATTTCGGTA
* **
5034430 ATTTTACAAATTGAGGGTATTTCAATA
1 ATTTTACAAATCGAGGGTATTTCGGTA
* * *
5034457 ATTTCAC-AATCGAGGTTATTTCAGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
*
5034483 ATTTTACAAATCGAGGGTATTTCAGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
* *
5034510 ATTTCAC-AATCGAGGGTATTTTGGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
*
5034536 ATTTTACAAATCGAGGGTGTTTCGGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
*
5034563 ATTTCACAAATCGAGGGTATTTCGGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
* *
5034590 ATTTTACAAATCAAAGGTATTTCAGG-A
1 ATTTTACAAATCGAGGGTATTTC-GGTA
* * * *
5034617 ATTTCAC-AA-CGAGGGTGTTTTGATA
1 ATTTTACAAATCGAGGGTATTTCGGTA
** *
5034642 ATTTTTTAAATCGAGGGTATTTCAGTA
1 ATTTTACAAATCGAGGGTATTTCGGTA
5034669 ATTT
1 ATTT
5034673 CACTTTATTA
Statistics
Matches: 477, Mismatches: 75, Indels: 28
0.82 0.13 0.05
Matches are distributed among these distances:
24 1 0.00
25 13 0.03
26 77 0.16
27 378 0.79
28 6 0.01
29 2 0.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
ATTTTACAAATCGAGGGTATTTCGGTA
Found at i:5034609 original size:107 final size:107
Alignment explanation
Indices: 5034093--5034675 Score: 653
Period size: 107 Copynumber: 5.4 Consensus size: 107
5034083 TTACAATACA
* * * * *
5034093 AGGGTATTTCGGTAATTTTAC-ACTATAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTC
1 AGGGTATTTTGGTAATTTTACAAAT-TGAGGGTATTTCGATAATTTCACAAATCGAGGGTATTTC
* *
5034157 GGTAATTTTACAAATCGAGGGTATTTTAGTAATTTTACAAATCG
65 GGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCAC-AATCG
* ** * * * *
5034201 AGGGTGTTTCAGTAATTTTACAAATTGAGGGTGTTTCGATAATTTTACAAATCCAGGGTGTTTCG
1 AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAATCGAGGGTATTTCG
* * * *
5034266 ATAATTTCACAAATCGAGAGTATTTTAGTAATTTTTCA-AATCG
66 GTAATTTTACAAATCGAGGGTATTTCAGTAA--TTTCACAATCG
* * * * * *
5034309 AGGGTATTTTTGTAATTTCAC-AATTGAGGGTATTTTGGTAATTTTACAAATCGGGGGTATTTCA
1 AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAATCGAGGGTATTTC-
* *
5034373 GG-AATTTTACAAATCGAGGGTGTTTC-GATAATTTCACAAATTG
65 GGTAATTTTACAAATCGAGGGTATTTCAG-TAATTTCAC-AATCG
* * *
5034416 -GGAGTATTTTGATAATTTTACAAATTGAGGGTATTTCAATAATTTCAC-AATCGAGGTTATTTC
1 AGG-GTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAATCGAGGGTATTTC
*
5034479 AGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAATCG
65 GGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAATCG
* * *
5034522 AGGGTATTTTGGTAATTTTACAAATCGAGGGTGTTTCGGTAATTTCACAAATCGAGGGTATTTCG
1 AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAATCGAGGGTATTTCG
* * *
5034587 GTAATTTTACAAATCAAAGGTATTTCAGGAATTTCACAA-CG
66 GTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAATCG
* * ** *
5034628 AGGGTGTTTTGATAATTTTTTAAATCGAGGGTATTTC-AGTAATTTCAC
1 AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGA-TAATTTCAC
5034676 TTTATTATGG
Statistics
Matches: 407, Mismatches: 54, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
105 5 0.01
106 91 0.22
107 175 0.43
108 130 0.32
109 2 0.00
110 4 0.01
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (107 bp):
AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAATCGAGGGTATTTCG
GTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAATCG
Found at i:5049533 original size:26 final size:26
Alignment explanation
Indices: 5049503--5049584 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
5049493 TGAAATGCCC
5049503 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5049529 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
5049555 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5049581 ATCA
1 ATCA
5049585 ATTTTTATCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:5055070 original size:49 final size:49
Alignment explanation
Indices: 5055015--5055239 Score: 218
Period size: 49 Copynumber: 4.5 Consensus size: 49
5055005 TTGGTATGCA
5055015 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATAC-GGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTAT-CGGGTACACG
* * ** * *
5055064 TAGTAGCCTGCACCTAGTACTACACATGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCGGGTACACG
* ** * * ** ** *
5055114 TAGTAGACTATACTTAGTACTACACACGTGATTGAAGTTATCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCGGGTACACG
* * *
5055165 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGCACATG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCGGGTACACG
* *
5055214 TAGTAGCTTACACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
5055240 CGTGACCTTA
Statistics
Matches: 138, Mismatches: 34, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
49 64 0.46
50 41 0.30
51 33 0.24
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCGGGTACACG
Found at i:5055132 original size:50 final size:49
Alignment explanation
Indices: 5055015--5055144 Score: 136
Period size: 50 Copynumber: 2.6 Consensus size: 49
5055005 TTGGTATGCA
* * * ** *
5055015 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATACGGTACACG
1 TAGTAGACTACACTTAGTACTACACATGTGACCAACCATACGATACACG
* * *
5055064 TAGTAGCCTGCACCTAGTACTACACATGTGACCTAACCAT-CTGATACACG
1 TAGTAGACTACACTTAGTACTACACATGTGACC-AACCATAC-GATACACG
* *
5055114 TAGTAGACTATACTTAGTACTACACACGTGA
1 TAGTAGACTACACTTAGTACTACACATGTGA
5055145 TTGAAGTTAT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 32 0.46
50 37 0.54
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (49 bp):
TAGTAGACTACACTTAGTACTACACATGTGACCAACCATACGATACACG
Found at i:5055244 original size:100 final size:101
Alignment explanation
Indices: 5055064--5055244 Score: 258
Period size: 100 Copynumber: 1.8 Consensus size: 101
5055054 ACGGTACACG
* * * *
5055064 TAGTAGCCTGCACCTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGACTATACTT
1 TAGTAGCCTGCACCTAGTACTACACATGCGACCTAACCATCCGACACACGTAGTAGACTACACTT
5055129 AGTACTACACACGTGATTGAAGTTATCGGGTATGCA
66 AGTACTACACACGTGATTGAAGTTATCGGGTATGCA
* ** * *
5055165 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGGCACATGTAGTAG-CTTACACT
1 TAGTAGCCTGCACCTAGTACTACACATGCGACCTAACCATCCGACACACGTAGTAGAC-TACACT
5055228 TAGTACTACACACGTGA
65 TAGTACTACACACGTGA
5055245 CCTTACAATA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
99 1 0.01
100 38 0.54
101 31 0.44
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (101 bp):
TAGTAGCCTGCACCTAGTACTACACATGCGACCTAACCATCCGACACACGTAGTAGACTACACTT
AGTACTACACACGTGATTGAAGTTATCGGGTATGCA
Found at i:5062132 original size:48 final size:49
Alignment explanation
Indices: 5062060--5062279 Score: 232
Period size: 48 Copynumber: 4.6 Consensus size: 49
5062050 GTTTCATAAT
* *
5062060 GATGCCATGTCCCAGACATAGTCTTACACGA-AATCACATATCGATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACGAGGATCACATATCGATGCC
* * * ** * *
5062108 GATGCCATGTCCCAGACATGGTCTTATAC-TGGCTCACACGTCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACGAGGATCACATATCGATGCC
* * * **
5062156 GATGCCATGTCCCAGACATGGTCTTACACTAGCA-CACATATCAATATC
1 GATGCCATGTCCCAGACATGGTCTTACACGAGGATCACATATCGATGCC
* * * *
5062204 GATGCCATGTCCTAGACATGGTCTTATAC-AGGATCTCATCTCGATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACGAGGATCACATATCGATGCC
* *
5062252 AATGCCATGTCCCAGACATAGTCTTACA
1 GATGCCATGTCCCAGACATGGTCTTACA
5062280 TGGGATCTCA
Statistics
Matches: 137, Mismatches: 32, Indels: 6
0.78 0.18 0.03
Matches are distributed among these distances:
47 3 0.02
48 133 0.97
49 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACGAGGATCACATATCGATGCC
Found at i:5062223 original size:96 final size:96
Alignment explanation
Indices: 5062059--5062279 Score: 293
Period size: 96 Copynumber: 2.3 Consensus size: 96
5062049 TGTTTCATAA
* *
5062059 TGATGCCATGTCCCAGACATAGTCTTACACGAAATCACATATCGATGCCGATGCCATGTCCCAGA
1 TGATGCCATGTCCCAGACATAGTCTTACACGAAATCACATATCAATACCGATGCCATGTCCCAGA
* *
5062124 CATGGTCTTATACTGGCTCACA-CGTCGAGGC
66 CATGGTCTTATACAGGATCACATC-TCGAGGC
* * * * *
5062155 TGATGCCATGTCCCAGACATGGTCTTACACTAGCA-CACATATCAATATCGATGCCATGTCCTAG
1 TGATGCCATGTCCCAGACATAGTCTTACACGA-AATCACATATCAATACCGATGCCATGTCCCAG
* *
5062219 ACATGGTCTTATACAGGATCTCATCTCGATGC
65 ACATGGTCTTATACAGGATCACATCTCGAGGC
**
5062251 CAATGCCATGTCCCAGACATAGTCTTACA
1 TGATGCCATGTCCCAGACATAGTCTTACA
5062280 TGGGATCTCA
Statistics
Matches: 109, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
96 107 0.98
97 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.26
Consensus pattern (96 bp):
TGATGCCATGTCCCAGACATAGTCTTACACGAAATCACATATCAATACCGATGCCATGTCCCAGA
CATGGTCTTATACAGGATCACATCTCGAGGC
Found at i:5070163 original size:39 final size:39
Alignment explanation
Indices: 5070119--5070550 Score: 711
Period size: 39 Copynumber: 11.1 Consensus size: 39
5070109 ATTATATTAT
* *
5070119 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
5070158 CAGCACGAAGCCTGCGGGACTTTGGCCCAGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
5070197 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* * *
5070236 CAGCACAAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
5070275 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
5070314 CAGCACGAAGCCTGCGGGACTTTAGCCCAGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
5070353 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
5070392 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATATATATC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
5070431 CAGCACGAAACCTGCGGGACTTTAGCCCAGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
5070470 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
5070509 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
5070548 CAG
1 CAG
5070551 TGTCTTGCAT
Statistics
Matches: 365, Mismatches: 28, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 365 1.00
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:5081629 original size:50 final size:50
Alignment explanation
Indices: 5081566--5081666 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
5081556 TTTATTACTC
5081566 ATCATTAAACAACAAGATACTCAAACATTCAATAATGGCATCATCCAAAT
1 ATCATTAAACAACAAGATACTCAAACATTCAATAATGGCATCATCCAAAT
5081616 ATCATTAAACAACAAGATACTCAAACATTCAATAATGGCATCATCCAAAT
1 ATCATTAAACAACAAGATACTCAAACATTCAATAATGGCATCATCCAAAT
5081666 A
1 A
5081667 CTTTAACCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.49, C:0.22, G:0.06, T:0.24
Consensus pattern (50 bp):
ATCATTAAACAACAAGATACTCAAACATTCAATAATGGCATCATCCAAAT
Found at i:5084360 original size:79 final size:79
Alignment explanation
Indices: 5084229--5084386 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
5084219 ACGCACTGAT
5084229 CAATAACCAAATGAATAGTAACTTGTACAATGATAAATCATGAAATAGTATGTGTTTTGATGTGA
1 CAATAACCAAATGAATAGTAACTTGTACAATGATAAATCATGAAATAGTATGTGTTTTGATGTGA
5084294 AGTATAGGTGTCCA
66 AGTATAGGTGTCCA
*
5084308 CAATAACCTAATGAATAGTAACTTGTACAATGATAAATCATGAAATAGTATGTGTTTTGATGTGA
1 CAATAACCAAATGAATAGTAACTTGTACAATGATAAATCATGAAATAGTATGTGTTTTGATGTGA
5084373 AGTATAGGTGTCCA
66 AGTATAGGTGTCCA
5084387 AATTGATATT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (79 bp):
CAATAACCAAATGAATAGTAACTTGTACAATGATAAATCATGAAATAGTATGTGTTTTGATGTGA
AGTATAGGTGTCCA
Found at i:5085582 original size:50 final size:50
Alignment explanation
Indices: 5085489--5085627 Score: 169
Period size: 50 Copynumber: 2.8 Consensus size: 50
5085479 TTTAATAAAG
*
5085489 TCATGCATTATGTAACTTTCA--TTAGTTAAGCA-TGCATCATAAATAATGA
1 TCATGCATTATGTAACTCTCATGTTAGTTAAG-ATTGCATCATAAATAAT-A
*
5085538 -CATGCATTATGTAACTCTCATGTTAGTTAAGATTGCATCATAAATTATA
1 TCATGCATTATGTAACTCTCATGTTAGTTAAGATTGCATCATAAATAATA
* * * *
5085587 TCGTGCATTATGTAACTCCCATGGTAGTTAAAGTTTGCATC
1 TCATGCATTATGTAACTCTCATGTTAGTT-AAGATTGCATC
5085628 TTTTAATGAA
Statistics
Matches: 79, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
48 19 0.24
49 2 0.03
50 48 0.61
51 10 0.13
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (50 bp):
TCATGCATTATGTAACTCTCATGTTAGTTAAGATTGCATCATAAATAATA
Found at i:5090237 original size:43 final size:43
Alignment explanation
Indices: 5090176--5090512 Score: 554
Period size: 43 Copynumber: 7.9 Consensus size: 43
5090166 GAATATTCAG
5090176 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
5090219 ATGATAACCGGGCCAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
5090262 ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
5090305 ATGATAACCGGGCCAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
5090348 ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
5090391 ATGATAACCGGGCCAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
5090434 ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
5090477 AT-AT--CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGT
1 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
5090513 AGCTATATCC
Statistics
Matches: 274, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
40 29 0.11
42 2 0.01
43 243 0.89
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (43 bp):
ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:5090321 original size:86 final size:86
Alignment explanation
Indices: 5090176--5090501 Score: 613
Period size: 86 Copynumber: 3.8 Consensus size: 86
5090166 GAATATTCAG
*
5090176 ATGATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGATAACCGGGCCAAGTCCCG
1 ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGATAACCGGGCCAAGTCCCG
5090241 AAGGCATTTGTGTGAGTTACT
66 AAGGCATTTGTGTGAGTTACT
5090262 ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGATAACCGGGCCAAGTCCCG
1 ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGATAACCGGGCCAAGTCCCG
5090327 AAGGCATTTGTGTGAGTTACT
66 AAGGCATTTGTGTGAGTTACT
5090348 ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGATAACCGGGCCAAGTCCCG
1 ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGATAACCGGGCCAAGTCCCG
5090413 AAGGCATTTGTGTGAGTTACT
66 AAGGCATTTGTGTGAGTTACT
*
5090434 ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT--CCGGGCTAAGTCCCG
1 ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGATAACCGGGCCAAGTCCCG
5090496 AAGGCA
66 AAGGCA
5090502 GTTGAGCGAG
Statistics
Matches: 238, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
83 20 0.08
85 2 0.01
86 216 0.91
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (86 bp):
ATGATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGATAACCGGGCCAAGTCCCG
AAGGCATTTGTGTGAGTTACT
Found at i:5093439 original size:37 final size:37
Alignment explanation
Indices: 5093389--5093467 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
5093379 TTATTACGAA
* * *
5093389 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
5093426 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
5093463 GTCTT
1 GTCTT
5093468 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:5096231 original size:40 final size:41
Alignment explanation
Indices: 5096161--5096344 Score: 232
Period size: 43 Copynumber: 4.5 Consensus size: 41
5096151 AAACCAAGTA
* * * *
5096161 CCTTTGGGATTTAG-CCGGAT-ATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATCATAG-TAACTCGCACAAATG
5096200 CCTTCGGGACTTAGCCCGGAT-ATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATCATAGTAACTCGCACAAATG
* *
5096240 CCTTCGGGACTTAGCCCGATTATCATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCG--GATCATAGTAACTCGCACAAATG
*
5096283 CCTTCGGGACTTGGCCCGGTTATCATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGG--ATCATAGTAACTCGCACAAATG
5096326 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
5096345 TTATCATCTG
Statistics
Matches: 128, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
39 13 0.10
40 39 0.30
42 2 0.02
43 74 0.58
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (41 bp):
CCTTCGGGACTTAGCCCGGATCATAGTAACTCGCACAAATG
Found at i:5096282 original size:43 final size:43
Alignment explanation
Indices: 5096187--5096351 Score: 264
Period size: 43 Copynumber: 3.9 Consensus size: 43
5096177 GGATATAGCT
* *
5096187 ACTCGCTCAACTGCCTTCGGGACTTAGCCCGG--AT-ATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATCATAGTA
*
5096227 ACTCGCACAAATGCCTTCGGGACTTAGCCCGATTATCATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATCATAGTA
* *
5096270 ACTCACACAAATGCCTTCGGGACTTGGCCCGGTTATCATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATCATAGTA
5096313 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATCAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATCAT
5096352 CTGAATATTC
Statistics
Matches: 114, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
40 29 0.25
42 2 0.02
43 83 0.73
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (43 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATCATAGTA
Found at i:5101744 original size:21 final size:21
Alignment explanation
Indices: 5101715--5101754 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5101705 GTGTACTGTG
*
5101715 CTGGAAGCTCTGCTGCAATTA
1 CTGGAAGCTCTGCTACAATTA
*
5101736 CTGGCAGCTCTGCTACAAT
1 CTGGAAGCTCTGCTACAAT
5101755 CACTAATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.28
Consensus pattern (21 bp):
CTGGAAGCTCTGCTACAATTA
Found at i:5101935 original size:34 final size:34
Alignment explanation
Indices: 5101888--5101964 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
5101878 GTTGCATTTT
*
5101888 CTGATACTATTATTGTAATGGGCTAAAGCCCACA
1 CTGATACTGTTATTGTAATGGGCTAAAGCCCACA
* *
5101922 CTGATACTGTTATTGTAATGGGCTAAGGCCTACA
1 CTGATACTGTTATTGTAATGGGCTAAAGCCCACA
*
5101956 CTGGTACTG
1 CTGATACTG
5101965 GACTGTAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (34 bp):
CTGATACTGTTATTGTAATGGGCTAAAGCCCACA
Found at i:5104011 original size:21 final size:21
Alignment explanation
Indices: 5103981--5104033 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5103971 TACTGTCCAC
*
5103981 CCACCTAGAGGTGTTCAGCAG
1 CCACCGAGAGGTGTTCAGCAG
*
5104002 CCACTGAGAGGTGTTCAGCAG
1 CCACCGAGAGGTGTTCAGCAG
5104023 CCACCGAGAGG
1 CCACCGAGAGG
5104034 CCATGGTCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.28, G:0.32, T:0.15
Consensus pattern (21 bp):
CCACCGAGAGGTGTTCAGCAG
Found at i:5107596 original size:30 final size:31
Alignment explanation
Indices: 5107548--5107605 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
5107538 TTTTCGAGCC
5107548 TAGGGGAAAAATCATAATTCTG-CAAAGGTT
1 TAGGGGAAAAATCATAATTCTGCCAAAGGTT
* ** *
5107578 TAGGGGCAAAATTGTAATTTTGCCAAAG
1 TAGGGGAAAAATCATAATTCTGCCAAAG
5107606 TTTGAGTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (31 bp):
TAGGGGAAAAATCATAATTCTGCCAAAGGTT
Found at i:5108218 original size:44 final size:44
Alignment explanation
Indices: 5108145--5108229 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
5108135 TTGATGTCTC
* *
5108145 AAAGTCCATGGTTGTACCACGGCAATTAAGGAAGAATTGACAGA
1 AAAGTCCATGGTTATAACACGGCAATTAAGGAAGAATTGACAGA
* * * *
5108189 AAAGTCCATGTTTATAACATGGCATTTAAGGAGGAATTGAC
1 AAAGTCCATGGTTATAACACGGCAATTAAGGAAGAATTGAC
5108230 GGTTAAGGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACACGGCAATTAAGGAAGAATTGACAGA
Found at i:5108430 original size:47 final size:47
Alignment explanation
Indices: 5108368--5108489 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
5108358 GCATTGGCAC
5108368 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
5108415 TCAGACAAGAATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
5108462 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
5108490 CCAAGGCATG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:5110021 original size:4 final size:4
Alignment explanation
Indices: 5109999--5110051 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
5109989 TTTTCTTGCA
* * *
5109999 ATTT AATTT AATT -TTT ATTT ATTT ATTT ATTT TTATT ATTT ATTA ATTT
1 ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT
5110048 ATTT
1 ATTT
5110052 TTTTCCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
3 2 0.05
4 31 0.77
5 7 0.17
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:5110037 original size:17 final size:18
Alignment explanation
Indices: 5109999--5110047 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
5109989 TTTTCTTGCA
5109999 ATTTAATTTAATTTTTATTT
1 ATTT-ATTT-ATTTTTATTT
5110019 ATTTATTTATTTTTA-TT
1 ATTTATTTATTTTTATTT
*
5110036 ATTTATTAATTT
1 ATTTATTTATTT
5110048 ATTTTTTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 13 0.46
18 7 0.25
19 4 0.14
20 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATTTATTTTTATTT
Found at i:5110039 original size:21 final size:21
Alignment explanation
Indices: 5110001--5110053 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
5109991 TTCTTGCAAT
*
5110001 TTAATTTA-ATTT-TTATTTA
1 TTAATTTATTTTTATTATTTA
*
5110020 TTTATTTATTTTTATTATTTA
1 TTAATTTATTTTTATTATTTA
5110041 TTAATTTATTTTT
1 TTAATTTATTTTT
5110054 TTCCTTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.24
20 3 0.10
21 19 0.66
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTAATTTATTTTTATTATTTA
Found at i:5110040 original size:25 final size:24
Alignment explanation
Indices: 5109999--5110055 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
5109989 TTTTCTTGCA
* *
5109999 ATTTAATTTAATTTTTATTTATTT
1 ATTTATTTTAATTTTTATTAATTT
*
5110023 ATTTATTTTTATTATTTATTAATTT
1 ATTTATTTTAATT-TTTATTAATTT
5110048 ATTT-TTTT
1 ATTTATTTT
5110056 CCTTCTCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (24 bp):
ATTTATTTTAATTTTTATTAATTT
Found at i:5110237 original size:102 final size:102
Alignment explanation
Indices: 5110061--5110264 Score: 408
Period size: 102 Copynumber: 2.0 Consensus size: 102
5110051 TTTTTCCTTC
5110061 TCTTAGCAGGTTTTTATAGTTTATGACTAGAAGAAACCCGTCGGGACCATTACTTTTTGAAGAAG
1 TCTTAGCAGGTTTTTATAGTTTATGACTAGAAGAAACCCGTCGGGACCATTACTTTTTGAAGAAG
5110126 AAATTGATCGCACAGTTCATAGAAACCAAAGAGAAAT
66 AAATTGATCGCACAGTTCATAGAAACCAAAGAGAAAT
5110163 TCTTAGCAGGTTTTTATAGTTTATGACTAGAAGAAACCCGTCGGGACCATTACTTTTTGAAGAAG
1 TCTTAGCAGGTTTTTATAGTTTATGACTAGAAGAAACCCGTCGGGACCATTACTTTTTGAAGAAG
5110228 AAATTGATCGCACAGTTCATAGAAACCAAAGAGAAAT
66 AAATTGATCGCACAGTTCATAGAAACCAAAGAGAAAT
5110265 AAGGCATAGC
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (102 bp):
TCTTAGCAGGTTTTTATAGTTTATGACTAGAAGAAACCCGTCGGGACCATTACTTTTTGAAGAAG
AAATTGATCGCACAGTTCATAGAAACCAAAGAGAAAT
Found at i:5113919 original size:13 final size:13
Alignment explanation
Indices: 5113901--5113925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5113891 TTCAAACTAC
5113901 TTTTTATTTTTTA
1 TTTTTATTTTTTA
5113914 TTTTTATTTTTT
1 TTTTTATTTTTT
5113926 TAAAGATTTA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:5121158 original size:46 final size:46
Alignment explanation
Indices: 5121099--5121458 Score: 449
Period size: 46 Copynumber: 7.8 Consensus size: 46
5121089 TTGACATGAA
* * *
5121099 GCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCATGTT
* *
5121145 GCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCATGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTT
* * *
5121191 GCCATGGTATCTTTCAACCATGGTTTTATTCATTTCATGTCACGCTT
1 GCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATG-TT
*
5121238 -CCATGGTATCTTTCAACCATGGTCTTATTCATTTC-TCGTCATGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT-GTCATGTT
* * * * *
5121283 GTCATGGTATCTTTCAACCATTGTCTTATTCTTTTCATGTCACGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTT
* * * *
5121329 TCCATGGTATCTTTCAACCATGGTTTTACACATTTCATATCATGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTT
* * * *
5121375 GCCATGATATCTTTCAACCATGGTCTTACACCTTTCATATCATGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTT
*
5121421 GTCATGGTATCTTTCAACCATGGTCTTACAT-ATTTCAT
1 GCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTCAT
5121459 TTCAGAGAGC
Statistics
Matches: 277, Mismatches: 31, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
45 7 0.03
46 267 0.96
47 3 0.01
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (46 bp):
GCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTT
Found at i:5121356 original size:138 final size:138
Alignment explanation
Indices: 5121108--5121448 Score: 508
Period size: 138 Copynumber: 2.5 Consensus size: 138
5121098 AGCCATAGTG
* *
5121108 TCTTTCAACTATGGTCTTACTCATTT-TCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTT
1 TCTTTCAACCATGGTCTTACTCATTTCTC-GTCATGTTGTCATGGTATCTTTCAACCATGGTCTT
* ** *
5121172 ATTCTTTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTTTTATTCATTTCATGTCACGCT
65 ATTCTTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTTTTACACATTTCATATCACG-T
*
5121237 T-CCATGGTA
129 TGCCATGATA
* *
5121246 TCTTTCAACCATGGTCTTATTCATTTCTCGTCATGTTGTCATGGTATCTTTCAACCATTGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCTCGTCATGTTGTCATGGTATCTTTCAACCATGGTCTTA
* *
5121311 TTCTTTTCATGTCACGTTTCCATGGTATCTTTCAACCATGGTTTTACACATTTCATATCATGTTG
66 TTCTTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTTTTACACATTTCATATCACGTTG
5121376 CCATGATA
131 CCATGATA
* * *
5121384 TCTTTCAACCATGGTCTTACACCTTTCAT-ATCATGTTGTCATGGTATCTTTCAACCATGGTCTT
1 TCTTTCAACCATGGTCTTACTCATTTC-TCGTCATGTTGTCATGGTATCTTTCAACCATGGTCTT
5121448 A
65 A
5121449 CATATTTCAT
Statistics
Matches: 184, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
137 2 0.01
138 179 0.97
139 3 0.02
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (138 bp):
TCTTTCAACCATGGTCTTACTCATTTCTCGTCATGTTGTCATGGTATCTTTCAACCATGGTCTTA
TTCTTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTTTTACACATTTCATATCACGTTG
CCATGATA
Found at i:5121389 original size:25 final size:25
Alignment explanation
Indices: 5121361--5121436 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
5121351 GTTTTACACA
*
5121361 TTTCATATCATGTTGCCATGATATC
1 TTTCATATCATGTTGTCATGATATC
* * * *
5121386 TTTCA-ACCATG--GTC-TTACACC
1 TTTCATATCATGTTGTCATGATATC
*
5121407 TTTCATATCATGTTGTCATGGTATC
1 TTTCATATCATGTTGTCATGATATC
5121432 TTTCA
1 TTTCA
5121437 ACCATGGTCT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 9 0.24
22 7 0.19
24 8 0.22
25 13 0.35
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (25 bp):
TTTCATATCATGTTGTCATGATATC
Found at i:5129270 original size:81 final size:81
Alignment explanation
Indices: 5129175--5129337 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
5129165 TGTTTTATAT
5129175 ACTGTTGATAATTTTAGTACGAGCTTACTAAGCTTTGGAAAGCTTACTTTGTGTGTATTTGCATT
1 ACTGTTGATAATTTTAGTACGAGCTTACTAAGCTTTGGAAAGCTTACTTTGTGTGTATTTGCATT
5129240 GTTTTATAGATATCAA
66 GTTTTATAGATATCAA
*
5129256 ACTGTTGATGATTTTAGTACGAGCTTACTAAGCTTTGGAAAGCTTACTTTGTGTGTATTTGCATT
1 ACTGTTGATAATTTTAGTACGAGCTTACTAAGCTTTGGAAAGCTTACTTTGTGTGTATTTGCATT
5129321 GTTTTATAGATATCAA
66 GTTTTATAGATATCAA
5129337 A
1 A
5129338 GCTGCTAAAA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (81 bp):
ACTGTTGATAATTTTAGTACGAGCTTACTAAGCTTTGGAAAGCTTACTTTGTGTGTATTTGCATT
GTTTTATAGATATCAA
Found at i:5130987 original size:10 final size:10
Alignment explanation
Indices: 5130972--5131003 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
5130962 GTTATGGGAA
5130972 AAAATCAAAT
1 AAAATCAAAT
5130982 AAAATCAAAT
1 AAAATCAAAT
*
5130992 AAAATCCAAT
1 AAAATCAAAT
5131002 AA
1 AA
5131004 TCCCTTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATCAAAT
Found at i:5131662 original size:14 final size:14
Alignment explanation
Indices: 5131643--5131671 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5131633 ATTATTAGTC
5131643 GGGATCCTTGAGTT
1 GGGATCCTTGAGTT
5131657 GGGATCCTTGAGTT
1 GGGATCCTTGAGTT
5131671 G
1 G
5131672 AAAGAGTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.38, T:0.34
Consensus pattern (14 bp):
GGGATCCTTGAGTT
Found at i:5131689 original size:24 final size:24
Alignment explanation
Indices: 5131661--5131713 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
5131651 TGAGTTGGGA
5131661 TCCTTGAGTTGAAAGAGTTCGTTG
1 TCCTTGAGTTGAAAGAGTTCGTTG
5131685 TCCTTGAGTTGAAAGAGTTCGTTG
1 TCCTTGAGTTGAAAGAGTTCGTTG
5131709 TCCTT
1 TCCTT
5131714 AAATGAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.40
Consensus pattern (24 bp):
TCCTTGAGTTGAAAGAGTTCGTTG
Found at i:5141767 original size:17 final size:18
Alignment explanation
Indices: 5141742--5141787 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
5141732 TATAAGAATA
*
5141742 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
5141759 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
5141777 ATTAAATTATA
1 ATTAAATTATA
5141788 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:5141880 original size:120 final size:120
Alignment explanation
Indices: 5141688--5142082 Score: 722
Period size: 120 Copynumber: 3.3 Consensus size: 120
5141678 TAGATTATAT
* * *
5141688 ATTAT-TTTTATAGTATTATATATATTATGATTTTAGTAAATTCATATAAGAATAATT-ATATTA
1 ATTATATTTTATAGTA-T-TATATATTATGATTTTAGCAAATTCATTTAAGAATATTTAATATTA
5141751 AGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAG
64 AGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAG
5141808 ATTATATTTTATAGTATTATATATTATGATTTTAGCAAATTCATTTAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGCAAATTCATTTAAGAATATTTAATATTAAG
5141873 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAG
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAG
5141928 ATTATATTTTATAGTATTATATATTATGATTTTAGCAAATTCATTTAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGCAAATTCATTTAAGAATATTTAATATTAAG
*
5141993 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAG
5142048 ATTATATTTTATAGTATTATATATTATGATTTTAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAG
5142083 NNNNNNNNNN
Statistics
Matches: 269, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
119 36 0.13
120 223 0.83
121 10 0.04
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (120 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGCAAATTCATTTAAGAATATTTAATATTAAG
AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAG
Found at i:5155027 original size:23 final size:23
Alignment explanation
Indices: 5155001--5155048 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5154991 GGGATGAAAT
5155001 GTTCAGAGCCGTTGCTGGAATGA
1 GTTCAGAGCCGTTGCTGGAATGA
* *
5155024 GTTCAGAGCTGTTGTTGGAATGA
1 GTTCAGAGCCGTTGCTGGAATGA
5155047 GT
1 GT
5155049 CCCACTGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.31
Consensus pattern (23 bp):
GTTCAGAGCCGTTGCTGGAATGA
Found at i:5156572 original size:26 final size:26
Alignment explanation
Indices: 5156503--5156573 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
5156493 TTTACATCAT
**
5156503 TGCTCACACGAGCTGTGAAATGGGCC
1 TGCTCACACGAGCTGTGGGATGGGCC
* * *
5156529 TGTTCACATGAGTTGTGGGATGGGCC
1 TGCTCACACGAGCTGTGGGATGGGCC
*
5156555 TGCTCACACAAGCTGTGGG
1 TGCTCACACGAGCTGTGGG
5156574 TCAGAATGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.24
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGGGATGGGCC
Found at i:5158322 original size:5 final size:5
Alignment explanation
Indices: 5158303--5158337 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
5158293 TTTAACTAAG
5158303 TAAAA T-AAA TAAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA
5158338 GTTCCAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 20 0.71
6 4 0.14
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:5160568 original size:42 final size:42
Alignment explanation
Indices: 5160501--5160615 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
5160491 GTGCTAAACA
* * ** *
5160501 GAAACCCGTAAGGGTTGAAGAGAAGCTCATAGGAGCTGAA-T
1 GAAACCCATAAGGGTTAAATTGAAGCTCATAAGAGCTGAATT
* *
5160542 GAAAACCCATAAGGGTTAAATTGAAGCTCAGAAGAGTTGAATT
1 G-AAACCCATAAGGGTTAAATTGAAGCTCATAAGAGCTGAATT
* * *
5160585 GAAACCTAGAAGGGTTAAATTGAAACTCATA
1 GAAACCCATAAGGGTTAAATTGAAGCTCATA
5160616 TGAGTTAACT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.02
42 58 0.95
43 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAATTGAAGCTCATAAGAGCTGAATT
Found at i:5160584 original size:21 final size:20
Alignment explanation
Indices: 5160560--5160633 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
5160550 ATAAGGGTTA
*
5160560 AATTGAAGCTCAGAAGAGTT
1 AATTGAAACTCAGAAGAGTT
*
5160580 GAATTGAAAC-CTAGAAGGGTT
1 -AATTGAAACTC-AGAAGAGTT
* *
5160601 AAATTGAAACTCATATGAGTT
1 -AATTGAAACTCAGAAGAGTT
* *
5160622 AACTGAAGCTCA
1 AATTGAAACTCA
5160634 TGAGAGCTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 11 0.26
21 31 0.72
22 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (20 bp):
AATTGAAACTCAGAAGAGTT
Found at i:5163728 original size:24 final size:24
Alignment explanation
Indices: 5163691--5163763 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
5163681 GGTAAGACAT
5163691 TTTCCACAGCTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
* * *
5163715 TTTCCACTGTTCCTCTCTTTACCC
1 TTTCCACAGCTCCTCTCTTCACCC
*
5163739 TTTCCACAGCTCCTCTATTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
5163763 T
1 T
5163764 ATCGATTGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.12, C:0.45, G:0.04, T:0.38
Consensus pattern (24 bp):
TTTCCACAGCTCCTCTCTTCACCC
Found at i:5164577 original size:8 final size:8
Alignment explanation
Indices: 5164564--5164588 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5164554 AATGCCGTTC
5164564 CTGTTGTT
1 CTGTTGTT
5164572 CTGTTGTT
1 CTGTTGTT
5164580 CTGTTGTT
1 CTGTTGTT
5164588 C
1 C
5164589 CTGGTAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.24, T:0.60
Consensus pattern (8 bp):
CTGTTGTT
Found at i:5168207 original size:34 final size:35
Alignment explanation
Indices: 5168149--5168215 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
5168139 CAAACACCAG
* * *
5168149 AAAATATTTTCCTGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
5168184 AAAACATTTTCCAG-AAATCATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
5168216 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5179808 original size:15 final size:15
Alignment explanation
Indices: 5179788--5179818 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5179778 CGAGAATTTG
5179788 AGGGATCATGTTCTA
1 AGGGATCATGTTCTA
5179803 AGGGATCATGTTCTA
1 AGGGATCATGTTCTA
5179818 A
1 A
5179819 CTTACGGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (15 bp):
AGGGATCATGTTCTA
Found at i:5195142 original size:15 final size:15
Alignment explanation
Indices: 5195122--5195154 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
5195112 TCTGGGTTCT
5195122 TTTACTTCATTT-TTA
1 TTTACTT-ATTTATTA
5195137 TTTACTTATTTATTA
1 TTTACTTATTTATTA
5195152 TTT
1 TTT
5195155 TTATTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTACTTATTTATTA
Found at i:5195718 original size:14 final size:14
Alignment explanation
Indices: 5195699--5195726 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5195689 TATATTAGTA
5195699 TTTTCTATTCTATT
1 TTTTCTATTCTATT
5195713 TTTTCTATTCTATT
1 TTTTCTATTCTATT
5195727 AGTATTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:5195734 original size:6 final size:6
Alignment explanation
Indices: 5195723--5195796 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
5195713 TTTTCTATTC
*
5195723 TATTAG TATTAGAG TATTAG -ATTAG TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATT--AG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
5195770 TATTAG --TTAG -ATTAG -ATTAG TATTAG T
1 TATTAG TATTAG TATTAG TATTAG TATTAG T
5195797 TAGTGATCCC
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
4 4 0.07
5 23 0.39
6 26 0.44
8 6 0.10
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (6 bp):
TATTAG
Found at i:5195749 original size:11 final size:11
Alignment explanation
Indices: 5195724--5195800 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
5195714 TTTCTATTCT
5195724 ATTAGTATTAG
1 ATTAGTATTAG
5195735 ---AGTATTAG
1 ATTAGTATTAG
**
5195743 ATTAGTATTCT
1 ATTAGTATTAG
5195754 ATTAGTATTAG
1 ATTAGTATTAG
5195765 ATTAGTATTAG
1 ATTAGTATTAG
5195776 -TTAG-ATTAG
1 ATTAGTATTAG
5195785 ATTAGTATTAG
1 ATTAGTATTAG
5195796 -TTAGT
1 ATTAGT
5195801 GATCCCGGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (11 bp):
ATTAGTATTAG
Found at i:5195754 original size:30 final size:30
Alignment explanation
Indices: 5195718--5195796 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
5195708 CTATTTTTTC
5195718 TATTCTATTAGTATTAG-AGTATTAGATTAG
1 TATTCTATTAGTATTAGTAGTATTAG-TTAG
5195748 TATTCTATTAGTATTAGATTAGTATTAGTTAG
1 TATTCTATTAGTATTAG--TAGTATTAGTTAG
**
5195780 -ATTAGATTAGTATTAGT
1 TATTCTATTAGTATTAGT
5195797 TAGTGATCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 1 0.02
30 17 0.39
31 14 0.32
32 4 0.09
33 8 0.18
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (30 bp):
TATTCTATTAGTATTAGTAGTATTAGTTAG
Found at i:5195768 original size:5 final size:5
Alignment explanation
Indices: 5195738--5195799 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
5195728 GTATTAGAGT
**
5195738 ATTAG ATTAG TATTCT ATTAG TATTAG ATTAG TATTAG -TTAG ATTAG
1 ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG -ATTAG ATTAG ATTAG
5195785 ATTAG TATTAG -TTAG
1 ATTAG -ATTAG ATTAG
5195800 TGATCCCGGC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.47
Consensus pattern (5 bp):
ATTAG
Found at i:5195785 original size:20 final size:21
Alignment explanation
Indices: 5195724--5195800 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
5195714 TTTCTATTCT
5195724 ATTAGTATTAG--AGTATTAG
1 ATTAGTATTAGTTAGTATTAG
5195743 ATTAGTATTCTA-TTAGTATTAG
1 ATTAGTA-T-TAGTTAGTATTAG
5195765 ATTAGTATTAGTTAG-ATTAG
1 ATTAGTATTAGTTAGTATTAG
5195785 ATTAGTATTAGTTAGT
1 ATTAGTATTAGTTAGT
5195801 GATCCCGGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.13
20 23 0.44
21 7 0.13
22 15 0.29
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (21 bp):
ATTAGTATTAGTTAGTATTAG
Found at i:5210551 original size:34 final size:34
Alignment explanation
Indices: 5210498--5210584 Score: 95
Period size: 34 Copynumber: 2.6 Consensus size: 34
5210488 TGTATTGAAT
* * * *
5210498 TGGGCTAAGGCTCATACTGATACTGCTACT-ATAA
1 TGGGCTAAGGCCCACACTGATAATGCGACTGAT-A
*
5210532 TGGGCTAATGCCCACACTGATAATGCGACTGATA
1 TGGGCTAAGGCCCACACTGATAATGCGACTGATA
* *
5210566 TGGGCTTAGGCCCAGACTG
1 TGGGCTAAGGCCCACACTG
5210585 TTCAACACTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 42 0.95
35 2 0.05
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.25
Consensus pattern (34 bp):
TGGGCTAAGGCCCACACTGATAATGCGACTGATA
Found at i:5214136 original size:3 final size:3
Alignment explanation
Indices: 5214128--5214164 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5214118 ATTCTTTCTT
5214128 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5214165 ATAACATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5215819 original size:28 final size:28
Alignment explanation
Indices: 5215788--5215848 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
5215778 CAAAGGCATT
5215788 CTTTAAGGGGTTCGCCACAAAAGCTCAC
1 CTTTAAGGGGTTCGCCACAAAAGCTCAC
* * * * *
5215816 CTTTTTAGGGTTTTGCCAGAAAGGCTCAC
1 C-TTTAAGGGGTTCGCCACAAAAGCTCAC
5215845 CTTT
1 CTTT
5215849 CTAGAGTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (28 bp):
CTTTAAGGGGTTCGCCACAAAAGCTCAC
Found at i:5215842 original size:29 final size:29
Alignment explanation
Indices: 5215801--5215982 Score: 104
Period size: 29 Copynumber: 6.3 Consensus size: 29
5215791 TAAGGGGTTC
* * *
5215801 GCCACAAAAGCTCACCTTTTTAGGGTTTT
1 GCCACAAAGGCTCACCTTTCTAGAGTTTT
*
5215830 GCCAGAAAGGCTCACCTTTCTAGAGTTTT
1 GCCACAAAGGCTCACCTTTCTAGAGTTTT
* ** * * *
5215859 GCCACAAAGGTTGTCCTGT-AACAGTTTT
1 GCCACAAAGGCTCACCTTTCTAGAGTTTT
* * * * *
5215887 TCCACAATGGCTTACCTTTCCAAAGTTTT
1 GCCACAAAGGCTCACCTTTCTAGAGTTTT
* * * * *
5215916 TCCATAAAGGCT-ATCCTTT-AACAG-GTT
1 GCCACAAAGGCTCA-CCTTTCTAGAGTTTT
* *
5215943 -CCTAGCAAAGGCTTACCTTTCTAGATTTTT
1 GCC-A-CAAAGGCTCACCTTTCTAGAGTTTT
5215973 GCCACAAAGG
1 GCCACAAAGG
5215983 TTATCCTTTA
Statistics
Matches: 116, Mismatches: 29, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
26 2 0.02
27 3 0.03
28 36 0.31
29 70 0.60
30 3 0.03
31 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (29 bp):
GCCACAAAGGCTCACCTTTCTAGAGTTTT
Found at i:5215904 original size:57 final size:57
Alignment explanation
Indices: 5215835--5216084 Score: 267
Period size: 57 Copynumber: 4.4 Consensus size: 57
5215825 GTTTTGCCAG
* * * * **
5215835 AAAGGCTCACCTTTCTAGAGTTTTGCCACAAAGGTTGTCCTGTAACAGTTTTTCCAC
1 AAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTATCCTTTAACAGGTTCACCAC
* * * * * * *
5215892 AATGGCTTACCTTTCCAAAGTTTTTCCATAAAGGCTATCCTTTAACAGGTTC-CTAGC
1 AAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTATCCTTTAACAGGTTCACCA-C
*
5215949 AAAGGCTTACCTTTCTAGATTTTTGCCACAAAGGTTATCCTTTAACAGGTTCACCAC
1 AAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTATCCTTTAACAGGTTCACCAC
* * * * *
5216006 AAAGGCTTACCTTTCCA-AGGTTTTACAAAAAAGGTTGTCCTTTAACAGGTTCACCAC
1 AAAGGCTTACCTTTCTAGA-GTTTTGCCACAAAGGTTATCCTTTAACAGGTTCACCAC
*
5216063 AATGGCTT---TTTCTAGAGTTTTG
1 AAAGGCTTACCTTTCTAGAGTTTTG
5216085 TAAAACCCCA
Statistics
Matches: 160, Mismatches: 29, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
54 10 0.06
55 1 0.01
56 3 0.02
57 144 0.90
58 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (57 bp):
AAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTATCCTTTAACAGGTTCACCAC
Found at i:5216018 original size:28 final size:28
Alignment explanation
Indices: 5215921--5216070 Score: 85
Period size: 28 Copynumber: 5.3 Consensus size: 28
5215911 GTTTTTCCAT
*
5215921 AAAGGC-TATCCTTTAACAGGTTC-CTAGC
1 AAAGGCTTA-CCTTTAACAGGTTCACCA-C
* * ** **
5215949 AAAGGCTTACCTTTCTAGATTTTTGCCAC
1 AAAGGCTTACCTTT-AACAGGTTCACCAC
5215978 AAAGG-TTATCCTTTAACAGGTTCACCAC
1 AAAGGCTTA-CCTTTAACAGGTTCACCAC
* * * *
5216006 AAAGGCTTACCTTT-CCAAGGTTTTACAAA
1 AAAGGCTTACCTTTAAC-AGG-TTCACCAC
*
5216035 AAAGG-TTGTCCTTTAACAGGTTCACCAC
1 AAAGGCTT-ACCTTTAACAGGTTCACCAC
*
5216063 AATGGCTT
1 AAAGGCTT
5216071 TTTCTAGAGT
Statistics
Matches: 90, Mismatches: 22, Indels: 19
0.69 0.17 0.15
Matches are distributed among these distances:
27 1 0.01
28 46 0.51
29 40 0.44
30 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (28 bp):
AAAGGCTTACCTTTAACAGGTTCACCAC
Found at i:5216070 original size:114 final size:114
Alignment explanation
Indices: 5215831--5216084 Score: 320
Period size: 114 Copynumber: 2.3 Consensus size: 114
5215821 TAGGGTTTTG
* * * ** *
5215831 CCAG-AAAGGCTCACCTTTCTAGAGTTTTGCCACAAAGGTTGTCCTGTAACAGTTTTTCCACAAT
1 CCAGCAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTATCCTGTAACAGGTTCACCACAAA
* * *
5215895 GGCTTACCTTTCCAAAGTTTTTCCATAAAGGCTATCCTTTAACAGGTTC
66 GGCTTACCTTTCCAAAGTTTTACAAAAAAGGCTATCCTTTAACAGGTTC
* * *
5215944 CTAGCAAAGGCTTACCTTTCTAGATTTTTGCCACAAAGGTTATCCTTTAACAGGTTCACCACAAA
1 CCAGCAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTATCCTGTAACAGGTTCACCACAAA
* * *
5216009 GGCTTACCTTTCCAAGGTTTTACAAAAAAGGTTGTCCTTTAACAGGTTC
66 GGCTTACCTTTCCAAAGTTTTACAAAAAAGGCTATCCTTTAACAGGTTC
*
5216058 ACCA-CAATGGCTT---TTTCTAGAGTTTTG
1 -CCAGCAAAGGCTTACCTTTCTAGAGTTTTG
5216085 TAAAACCCCA
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
111 13 0.11
113 3 0.02
114 103 0.85
115 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (114 bp):
CCAGCAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTATCCTGTAACAGGTTCACCACAAA
GGCTTACCTTTCCAAAGTTTTACAAAAAAGGCTATCCTTTAACAGGTTC
Found at i:5217207 original size:34 final size:30
Alignment explanation
Indices: 5217168--5217226 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
5217158 ACGGTATTAA
5217168 TTAATTAATTAAGTTTTATGTAGTCATCAG
1 TTAATTAATTAAGTTTTATGTAGTCATCAG
5217198 TTAATTAATTAAGTTTTATGTAGTCATCA
1 TTAATTAATTAAGTTTTATGTAGTCATCA
5217227 TATATTAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (30 bp):
TTAATTAATTAAGTTTTATGTAGTCATCAG
Found at i:5217337 original size:29 final size:30
Alignment explanation
Indices: 5217258--5217371 Score: 96
Period size: 29 Copynumber: 3.9 Consensus size: 30
5217248 ACATACATGC
* *
5217258 ATATGGCCCACTGGGCCCAA-TC-TCATTC-
1 ATATGGCCCAATAGGCCCAATTCAT-ATTCT
* *
5217286 ATATGGCCC-ATCTGGCCCGATTCATATTCT
1 ATATGGCCCAAT-AGGCCCAATTCATATTCT
* *
5217316 -TATGGCCCAATAGTCCCAATTCACA-TCT
1 ATATGGCCCAATAGGCCCAATTCATATTCT
* *
5217344 ATATGGCCCATTAGGCCCAAATCATATT
1 ATATGGCCCAATAGGCCCAATTCATATT
5217372 ATACTCATGC
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.01
28 18 0.26
29 45 0.66
30 4 0.06
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (30 bp):
ATATGGCCCAATAGGCCCAATTCATATTCT
Found at i:5217568 original size:16 final size:15
Alignment explanation
Indices: 5217541--5217577 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
5217531 CCGTAGCCCA
*
5217541 ACTTTCAGCTTTTCG
1 ACTTTTAGCTTTTCG
5217556 ACATTTTAGCTTTTCG
1 AC-TTTTAGCTTTTCG
5217572 ACTTTT
1 ACTTTT
5217578 TGGCATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.16, C:0.22, G:0.11, T:0.51
Consensus pattern (15 bp):
ACTTTTAGCTTTTCG
Found at i:5218901 original size:28 final size:27
Alignment explanation
Indices: 5218851--5218918 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
5218841 ATTACAAGTT
* *
5218851 TTTCCACAAAGGTTTTCCCTTAATAGG
1 TTTCCACAAAGGTTGTCCCTTAACAGG
* *
5218878 TTCTCCACAATGGTTGTCCTTTAACAGG
1 TT-TCCACAAAGGTTGTCCCTTAACAGG
5218906 TTTGCCACAAAGG
1 TTT-CCACAAAGG
5218919 CTTTCCTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 3 0.09
28 31 0.91
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (27 bp):
TTTCCACAAAGGTTGTCCCTTAACAGG
Found at i:5218925 original size:28 final size:27
Alignment explanation
Indices: 5218853--5218926 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 27
5218843 TACAAGTTTT
* *
5218853 TCCACAAAGGTTTTCCCTTAATAGGTTC
1 TCCACAAAGG-TTTCCTTTAACAGGTTC
*
5218881 TCCACAATGGTTGTCCTTTAACAGGTT-
1 TCCACAAAGGTT-TCCTTTAACAGGTTC
5218908 TGCCACAAAGGCTTTCCTT
1 T-CCACAAAGG-TTTCCTT
5218927 AATGGTGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.08
28 34 0.87
29 2 0.05
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (27 bp):
TCCACAAAGGTTTCCTTTAACAGGTTC
Found at i:5219297 original size:15 final size:15
Alignment explanation
Indices: 5219279--5219323 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
5219269 CTTTCATAAA
*
5219279 AGACTTATTCATATT
1 AGACTCATTCATATT
* * *
5219294 AGACTCCTTTATGTT
1 AGACTCATTCATATT
5219309 AGACTCATTCATATT
1 AGACTCATTCATATT
5219324 TTCTAAACAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (15 bp):
AGACTCATTCATATT
Found at i:5225902 original size:26 final size:26
Alignment explanation
Indices: 5225864--5225924 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
5225854 CTTCTTACCA
5225864 AAAATATATGGAAACCCTGAGAAAAAG
1 AAAATA-ATGGAAACCCTGAGAAAAAG
* *
5225891 AAAATAATGGAAACTCTGAGAAAGAG
1 AAAATAATGGAAACCCTGAGAAAAAG
5225917 AAAATAAT
1 AAAATAAT
5225925 CTTTCTTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 26 0.81
27 6 0.19
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.16
Consensus pattern (26 bp):
AAAATAATGGAAACCCTGAGAAAAAG
Found at i:5226860 original size:58 final size:57
Alignment explanation
Indices: 5226756--5226902 Score: 147
Period size: 58 Copynumber: 2.6 Consensus size: 57
5226746 ATTGACCTCA
* * * * *
5226756 TTACAGATAGGATTTAGCCTGGAC-AGGTAATCCTGTTATAATTCTTCTCGAGCATATG
1 TTACAGATAGGATTTAGCCTGGACTA-GTAATCCTATTAGAACTCTTCT-GAACACATG
* * *
5226814 TTATA-ATTAGGATTTAGCCTGGACTAGTAATCCTAATT-GAGCTCTTCTTAACACATG
1 TTACAGA-TAGGATTTAGCCTGGACTAGTAATCCT-ATTAGAACTCTTCTGAACACATG
* *
5226871 TTACAGAAAGGATTTAGCCTGGACTGGTAATC
1 TTACAGATAGGATTTAGCCTGGACTAGTAATC
5226903 GTTATATATG
Statistics
Matches: 74, Mismatches: 11, Indels: 9
0.79 0.12 0.10
Matches are distributed among these distances:
57 34 0.46
58 37 0.50
59 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (57 bp):
TTACAGATAGGATTTAGCCTGGACTAGTAATCCTATTAGAACTCTTCTGAACACATG
Found at i:5230993 original size:12 final size:12
Alignment explanation
Indices: 5230976--5231001 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5230966 CATTCCGAAG
5230976 TATATATATACA
1 TATATATATACA
5230988 TATATATATACA
1 TATATATATACA
5231000 TA
1 TA
5231002 AGTATGCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:5231492 original size:29 final size:28
Alignment explanation
Indices: 5231450--5231547 Score: 108
Period size: 27 Copynumber: 3.5 Consensus size: 28
5231440 CATGAGATTG
* * *
5231450 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTAT-AATTATACA
* *
5231479 GCACTAAGTGTGCGAGTATGATTATATA
1 GCACTAAGTGTGCGAGTATAATTATACA
* *
5231507 GCACTAAGTGTGCGAGT-TGATTATATA
1 GCACTAAGTGTGCGAGTATAATTATACA
*
5231534 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
5231548 GACTTAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 23 0.37
28 23 0.37
29 17 0.27
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTATAATTATACA
Found at i:5231535 original size:27 final size:27
Alignment explanation
Indices: 5231450--5231547 Score: 124
Period size: 28 Copynumber: 3.5 Consensus size: 27
5231440 CATGAGATTG
* * * *
5231450 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAG-TT-GATTATATA
5231479 GCACTAAGTGTGCGAGTATGATTATATA
1 GCACTAAGTGTGCGAGT-TGATTATATA
5231507 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGTTGATTATATA
*
5231534 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
5231548 GACTTAATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
27 23 0.37
28 24 0.38
29 16 0.25
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGTTGATTATATA
Found at i:5231558 original size:27 final size:27
Alignment explanation
Indices: 5231478--5231560 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
5231468 TAAATTGTAC
* *
5231478 AGCACTAAGTGTGCGAGTATGATTATAT
1 AGCACTAAGTGTGCGACT-TGAATATAT
* *
5231506 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
5231533 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
5231560 A
1 A
5231561 CTTTTGAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
27 29 0.57
28 22 0.43
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:5238810 original size:25 final size:25
Alignment explanation
Indices: 5238775--5238936 Score: 218
Period size: 25 Copynumber: 6.5 Consensus size: 25
5238765 TAAGCTTGTT
*
5238775 AATTTGTTCTTAATAATTCTGGTTA
1 AATTTGCTCTTAATAATTCTGGTTA
* *
5238800 AATTTACTCTTAATAATTCCGGTTA
1 AATTTGCTCTTAATAATTCTGGTTA
*
5238825 AATTTGCTCTTAATAATTTTGGTTA
1 AATTTGCTCTTAATAATTCTGGTTA
* *
5238850 AATTTGTTCTTAATAATTCCGGTTA
1 AATTTGCTCTTAATAATTCTGGTTA
* *
5238875 AATTTTCTCTTAAT-ATTTTCGGTTA
1 AATTTGCTCTTAATAATTCT-GGTTA
*
5238900 AATTTGCTCTTAATATTTCTGGTTA
1 AATTTGCTCTTAATAATTCTGGTTA
*
5238925 AATTTGCCCTTA
1 AATTTGCTCTTA
5238937 TTATTTCCGA
Statistics
Matches: 118, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
24 3 0.03
25 112 0.95
26 3 0.03
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.50
Consensus pattern (25 bp):
AATTTGCTCTTAATAATTCTGGTTA
Found at i:5238857 original size:75 final size:75
Alignment explanation
Indices: 5238775--5238930 Score: 260
Period size: 75 Copynumber: 2.1 Consensus size: 75
5238765 TAAGCTTGTT
*
5238775 AATTTGTTCTTAATAATTCTGGTTAAATTTACTCTTAATAATTCCGGTTAAATTTGCTCTTAATA
1 AATTTGTTCTTAATAATTCCGGTTAAATTTACTCTTAATAATTCCGGTTAAATTTGCTCTTAAT-
5238840 ATTT-TGGTTA
65 ATTTCTGGTTA
* * *
5238850 AATTTGTTCTTAATAATTCCGGTTAAATTTTCTCTTAATATTTTCGGTTAAATTTGCTCTTAATA
1 AATTTGTTCTTAATAATTCCGGTTAAATTTACTCTTAATAATTCCGGTTAAATTTGCTCTTAATA
5238915 TTTCTGGTTA
66 TTTCTGGTTA
5238925 AATTTG
1 AATTTG
5238931 CCCTTATTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
74 4 0.05
75 72 0.95
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51
Consensus pattern (75 bp):
AATTTGTTCTTAATAATTCCGGTTAAATTTACTCTTAATAATTCCGGTTAAATTTGCTCTTAATA
TTTCTGGTTA
Found at i:5239831 original size:45 final size:45
Alignment explanation
Indices: 5239763--5239981 Score: 313
Period size: 45 Copynumber: 5.0 Consensus size: 45
5239753 TATCGTACAG
*
5239763 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGATA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
5239808 TACCATTCGGGCCTTTGAGCCTAG-AGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
5239852 TACGATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * *
5239897 TACTATTCAGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
** *
5239942 TGA-TATT-GGG-CTTCAAGCCTAGCAGGCGA-AATGCCGGTGA
1 T-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
5239982 ATGAATTCGG
Statistics
Matches: 162, Mismatches: 10, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
42 11 0.07
43 17 0.10
44 44 0.27
45 89 0.55
46 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:5239918 original size:89 final size:88
Alignment explanation
Indices: 5239767--5239981 Score: 301
Period size: 89 Copynumber: 2.4 Consensus size: 88
5239757 GTACAGTACT
* * *
5239767 ATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGATATACCATTCGGGCCTTTGAGCCTAG
1 ATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATACCATTCAGGCCTTCGAGCCTAG
5239832 -AGGCTATAATGCCGGTGAGATACG
66 CAGGCTATAATGCCGGTGA-A-ACG
*
5239856 ATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATACTATTCAGGCCTTCGAGCCTAG
1 ATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATACCATTCAGGCCTTCGAGCCTAG
*
5239921 CAGGCTATAATGCCGGTGAAATG
66 CAGGCTATAATGCCGGTGAAACG
* ** *
5239944 ATATTGGG-CTTCAAGCCTAGCAGGCGA-AATGCCGGTGA
1 AT-TCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
5239982 ATGAATTCGG
Statistics
Matches: 115, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
87 11 0.10
88 20 0.17
89 66 0.57
90 18 0.16
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (88 bp):
ATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATACCATTCAGGCCTTCGAGCCTAG
CAGGCTATAATGCCGGTGAAACG
Done.