Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_pilon, whole genome shotgun sequence
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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 50
Found at i:3316605 original size:3 final size:3
Alignment explanation
Indices: 3316597--3316623 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3316587 GAATTGGGTT
3316597 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
3316624 AGTGTCTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:3319512 original size:17 final size:17
Alignment explanation
Indices: 3319490--3319524 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3319480 GGTGAGTTTG
3319490 TAAATAATGTTTGGGTC
1 TAAATAATGTTTGGGTC
3319507 TAAATAATGTTTGGGTC
1 TAAATAATGTTTGGGTC
3319524 T
1 T
3319525 GGAATATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (17 bp):
TAAATAATGTTTGGGTC
Found at i:3321404 original size:17 final size:17
Alignment explanation
Indices: 3321382--3321418 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3321372 TAGGTTGATT
3321382 TGTTTGTCAATTGTACA
1 TGTTTGTCAATTGTACA
*
3321399 TGTTTGTCTATTGTACA
1 TGTTTGTCAATTGTACA
3321416 TGT
1 TGT
3321419 AAAAATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.51
Consensus pattern (17 bp):
TGTTTGTCAATTGTACA
Found at i:3325393 original size:32 final size:32
Alignment explanation
Indices: 3325357--3325441 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
3325347 GTTTCAGATC
* *
3325357 AATATTGGTTCGGTT-GACTTTTGGGTCGGATT
1 AATATTCGATCGGTTAGA-TTTTGGGTCGGATT
3325389 AATATTCGATCGGTTAGATTTTGGGTCGGATT
1 AATATTCGATCGGTTAGATTTTGGGTCGGATT
*
3325421 AATA-TCGAATCGATT-GATTTT
1 AATATTCG-ATCGGTTAGATTTT
3325442 TAATTGGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
31 9 0.19
32 37 0.77
33 2 0.04
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.42
Consensus pattern (32 bp):
AATATTCGATCGGTTAGATTTTGGGTCGGATT
Found at i:3325689 original size:16 final size:16
Alignment explanation
Indices: 3325670--3325795 Score: 58
Period size: 16 Copynumber: 7.9 Consensus size: 16
3325660 TTCGGATTAA
3325670 TTTTGGTTTGGGTTAC
1 TTTTGGTTTGGGTTAC
* * *
3325686 TTTTGGATCGGGTTAAA
1 TTTTGGTTTGGGTT-AC
** * *
3325703 TCCT-ATTCGGGTTAC
1 TTTTGGTTTGGGTTAC
* * *
3325718 TTTCGGTTCGGGTTGC
1 TTTTGGTTTGGGTTAC
*** *
3325734 TTTCAATTTAGGTTA-
1 TTTTGGTTTGGGTTAC
*
3325749 TTTTCGGTTTGAGTTAC
1 TTTT-GGTTTGGGTTAC
*
3325766 TTTTGGTTTGGGTTAA
1 TTTTGGTTTGGGTTAC
**
3325782 TTTCAGTTTGGGTT
1 TTTTGGTTTGGGTT
3325796 TTTTTTTTGG
Statistics
Matches: 79, Mismatches: 27, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
15 5 0.06
16 67 0.85
17 7 0.09
ACGTcount: A:0.13, C:0.10, G:0.27, T:0.50
Consensus pattern (16 bp):
TTTTGGTTTGGGTTAC
Found at i:3330379 original size:20 final size:20
Alignment explanation
Indices: 3330354--3330406 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3330344 AAGAACCTTC
3330354 GGTATCGATACTCTTATGGG
1 GGTATCGATACTCTTATGGG
3330374 GGTATCGATACTCTTATGGG
1 GGTATCGATACTCTTATGGG
* *
3330394 AGTATCAATACTC
1 GGTATCGATACTC
3330407 CTCTAGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (20 bp):
GGTATCGATACTCTTATGGG
Found at i:3331354 original size:20 final size:20
Alignment explanation
Indices: 3331309--3331356 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3331299 GACTAGGGTC
* * *
3331309 TTGAGACTGAGCATCCAGTC
1 TTGATACTGAGCATCCAATA
*
3331329 TCGATACTGAGCATCCAATA
1 TTGATACTGAGCATCCAATA
3331349 TTGATACT
1 TTGATACT
3331357 AAAATCCTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (20 bp):
TTGATACTGAGCATCCAATA
Found at i:3332092 original size:12 final size:12
Alignment explanation
Indices: 3332075--3332104 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3332065 AAAGGAAAAG
3332075 ACTTTTACTATA
1 ACTTTTACTATA
*
3332087 ACTTTTGCTATA
1 ACTTTTACTATA
3332099 ACTTTT
1 ACTTTT
3332105 TCTTGGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (12 bp):
ACTTTTACTATA
Found at i:3339983 original size:20 final size:19
Alignment explanation
Indices: 3339937--3339983 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3339927 ATACCGAAGT
*
3339937 GGGTATCGGTACCATAGAG
1 GGGTATCGGTACCAAAGAG
**
3339956 AAGTATCGGTACCAAAGGAG
1 GGGTATCGGTACCAAA-GAG
3339976 GGGTATCG
1 GGGTATCG
3339984 ATATTATTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.30, C:0.15, G:0.36, T:0.19
Consensus pattern (19 bp):
GGGTATCGGTACCAAAGAG
Found at i:3340501 original size:109 final size:110
Alignment explanation
Indices: 3340355--3340595 Score: 322
Period size: 109 Copynumber: 2.2 Consensus size: 110
3340345 TGTGGTTTAT
* * * * * *
3340355 CGTATTGACCCTATGTGTGAAACTCTACGAAATTCATAACGAGTTTATGAATTTCCATATTGGCA
1 CGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAACGAGTTTATGAATTTCCATATTGACA
* * * *
3340420 CTATGTGTACAACCCCACGAAATTCATAATGAGTTTATGAATTTC
66 CTATGAGTACAACCCCACAAAATTCAAAATGAGTTTATCAATTTC
* * ***
3340465 CTTATTGGCACTATGTGTGCAACCCCACG-AATTCATAATGAGTTTATGAATTTTTGTATTGACA
1 CGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAACGAGTTTATGAATTTCCATATTGACA
* *
3340529 CTATGAGTGCAACCCCACAAAATTCAAAATTAGTTTATCAATTTC
66 CTATGAGTACAACCCCACAAAATTCAAAATGAGTTTATCAATTTC
3340574 CGTATTGGCACTATGTGTGCAA
1 CGTATTGGCACTATGTGTGCAA
3340596 GTATTGGCAC
Statistics
Matches: 113, Mismatches: 18, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
109 90 0.80
110 23 0.20
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (110 bp):
CGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAACGAGTTTATGAATTTCCATATTGACA
CTATGAGTACAACCCCACAAAATTCAAAATGAGTTTATCAATTTC
Found at i:3340594 original size:55 final size:55
Alignment explanation
Indices: 3340293--3340595 Score: 324
Period size: 55 Copynumber: 5.5 Consensus size: 55
3340283 GTATATATTG
* * * * * * * * *
3340293 TGAATTACCGTATTGGCACTATGTGGGTAA-CCTAAGTAATTCATAATTAGTCTG
1 TGAATTTCCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTA
* * * * * * * *
3340347 TG-GTTTATCGTATTGACCCTATGTGTGAAACTCTACGAAATTCATAACGAGTTTA
1 TGAATTT-CCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTA
* *
3340402 TGAATTTCCATATTGGCACTATGTGTACAACCCCACGAAATTCATAATGAGTTTA
1 TGAATTTCCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTA
*
3340457 TGAATTTCCTTATTGGCACTATGTGTGCAACCCCACG-AATTCATAATGAGTTTA
1 TGAATTTCCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTA
** * * * * *
3340511 TGAATTTTTGTATTGACACTATGAGTGCAACCCCACAAAATTCAAAATTAGTTTA
1 TGAATTTCCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTA
*
3340566 TCAATTTCCGTATTGGCACTATGTGTGCAA
1 TGAATTTCCGTATTGGCACTATGTGTGCAA
3340596 GTATTGGCAC
Statistics
Matches: 206, Mismatches: 39, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
53 2 0.01
54 68 0.33
55 133 0.65
56 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (55 bp):
TGAATTTCCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTA
Found at i:3340601 original size:21 final size:21
Alignment explanation
Indices: 3340575--3340616 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3340565 ATCAATTTCC
3340575 GTATTGGCACTATGTGTGCAA
1 GTATTGGCACTATGTGTGCAA
3340596 GTATTGGCACTATGTGTGCAA
1 GTATTGGCACTATGTGTGCAA
3340617 CATACGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (21 bp):
GTATTGGCACTATGTGTGCAA
Found at i:3341120 original size:20 final size:20
Alignment explanation
Indices: 3341091--3341129 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3341081 TGAGCCCATA
*
3341091 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
3341111 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
3341130 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:3344722 original size:2 final size:2
Alignment explanation
Indices: 3344715--3344753 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3344705 AGTTTTAAGG
3344715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3344754 AAAGTCTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3345763 original size:22 final size:22
Alignment explanation
Indices: 3345730--3345781 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3345720 CTAGACTGAA
* *
3345730 TATCAATACTCTGGCGTTAGGG
1 TATCGATACTCTGGCGCTAGGG
* *
3345752 TATTGATACTCTGTCGCTAGGG
1 TATCGATACTCTGGCGCTAGGG
3345774 TATCGATA
1 TATCGATA
3345782 GTGTATTGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (22 bp):
TATCGATACTCTGGCGCTAGGG
Found at i:3345875 original size:18 final size:20
Alignment explanation
Indices: 3345830--3345880 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
3345820 CCCCTACTGA
3345830 GAGTATCGGTACTCTACCCTT
1 GAGTATCGGTAC-CTACCCTT
3345851 G-GTATCGGTA-CT-CCCTT
1 GAGTATCGGTACCTACCCTT
*
3345868 GAGTATCGATACC
1 GAGTATCGGTACC
3345881 AAAAATAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 6 0.22
18 10 0.37
19 1 0.04
20 9 0.33
21 1 0.04
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (20 bp):
GAGTATCGGTACCTACCCTT
Found at i:3350740 original size:92 final size:94
Alignment explanation
Indices: 3350633--3350831 Score: 267
Period size: 95 Copynumber: 2.1 Consensus size: 94
3350623 ACTTCTGTGG
* * * *
3350633 GTATCGATACCAAGAGAAAGGTATCGATACCAGGAATTCCA-GA-TAAAAATGGTATCGTTACTG
1 GTATCGATACCAAGAGAAAGGTATCGATACCAGGAATTACATAAGTAAAAATAGTATCGATACTG
3350696 AAAGGAAGTATCGATACCATAGTATAGAA
66 AAAGGAAGTATCGATACCATAGTATAGAA
* ** * *
3350725 GTATCGATACTAAGAGAAAGGTATCGATACCTTGAATTACATAATGTAGAAATAGTATTGATACT
1 GTATCGATACCAAGAGAAAGGTATCGATACCAGGAATTACATAA-GTAAAAATAGTATCGATACT
* *
3350790 GGAAGGGAGTATCGATACCATAGTATAGAA
65 GAAAGGAAGTATCGATACCATAGTATAGAA
*
3350820 GTACCGATACCA
1 GTATCGATACCA
3350832 TGGTAGGGGT
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
92 37 0.41
93 1 0.01
95 53 0.58
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.25
Consensus pattern (94 bp):
GTATCGATACCAAGAGAAAGGTATCGATACCAGGAATTACATAAGTAAAAATAGTATCGATACTG
AAAGGAAGTATCGATACCATAGTATAGAA
Found at i:3351303 original size:45 final size:45
Alignment explanation
Indices: 3351252--3351577 Score: 413
Period size: 45 Copynumber: 7.2 Consensus size: 45
3351242 AAATGAATTA
* * **
3351252 ATAAATGAAATGTATAACGATGCATTATCGATATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * * * *
3351297 ATAAATGAAATGAATAATGGTTCA-TATTGGGCATGAAAGGATACA
1 ATAAATGAAATGCATAACGGTGCATTA-TCGGCATGAAAGGATGCC
*
3351342 ATAAATGAAATGCATAACAGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
3351387 ATAAATGAAATGCATAACGGTTCATTATCAGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
3351432 ATAATTGAAATTCATAACGATGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
3351477 ATAAATGAAATGCATAACGGTGCA-TATTCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTA-TCGGCATGAAAGGATGCC
* ** * *
3351522 ATAAATGAAAATGCATAATGGTGCATTATAAGCATGAAATGATGCT
1 ATAAATG-AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
3351568 ATAAATGAAA
1 ATAAATGAAA
3351578 ATAAAGGATA
Statistics
Matches: 242, Mismatches: 34, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
44 4 0.02
45 197 0.81
46 39 0.16
47 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:3357893 original size:17 final size:17
Alignment explanation
Indices: 3357868--3357907 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3357858 GTATGTTGTT
*
3357868 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
3357885 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
3357902 CATTTA
1 CATTTA
3357908 GGGAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:3358006 original size:18 final size:18
Alignment explanation
Indices: 3357961--3358008 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
3357951 TCATTCATGC
3357961 ATTTAGTTCATTGAATAA
1 ATTTAGTTCATTGAATAA
*
3357979 AGTTAGTTCATTGAATAA
1 ATTTAGTTCATTGAATAA
* *
3357997 TTTTATTTCATT
1 ATTTAGTTCATT
3358009 AATCAAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.50
Consensus pattern (18 bp):
ATTTAGTTCATTGAATAA
Found at i:3376206 original size:13 final size:13
Alignment explanation
Indices: 3376188--3376286 Score: 53
Period size: 13 Copynumber: 7.4 Consensus size: 13
3376178 CCTGAAGAAT
*
3376188 GAAAAATGAAAAA
1 GAAAAAAGAAAAA
3376201 GAAAAAAGAAAATA
1 GAAAAAAGAAAA-A
* *
3376215 AATAAATACAGAAAAT
1 GA-AAA-A-AGAAAAA
* *
3376231 GAAAAGAG-GAAA
1 GAAAAAAGAAAAA
*
3376243 GAAAAATGAAATAA
1 GAAAAAAGAAA-AA
3376257 GAGAAAAAG--AAA
1 GA-AAAAAGAAAAA
3376269 GAAAATAAGAAAAA
1 GAAAA-AAGAAAAA
3376283 -AAAA
1 GAAAA
3376287 TAAAAGGAGA
Statistics
Matches: 65, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
11 3 0.05
12 15 0.23
13 19 0.29
14 9 0.14
15 11 0.17
16 2 0.03
17 6 0.09
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (13 bp):
GAAAAAAGAAAAA
Found at i:3376287 original size:57 final size:54
Alignment explanation
Indices: 3376188--3376292 Score: 133
Period size: 57 Copynumber: 1.9 Consensus size: 54
3376178 CCTGAAGAAT
* *
3376188 GAAAAATGAAAAAGAAAAAAGAAAATAAATAAATACAGAAAATGAAAAGAGGAAA
1 GAAAAATGAAAAAGAAAAAAGAAAATAAATAAATAAAAAAAAT-AAAAGAGGAAA
3376243 GAAAAATGAAATAAGAGAAAAAGAAAGA-AAATAAGA-AAAAAAAATAAAAG
1 GAAAAATGAAA-AAGA-AAAAAGAAA-ATAAATAA-ATAAAAAAAATAAAAG
3376293 GAGAACAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
55 11 0.25
56 9 0.20
57 22 0.50
58 2 0.05
ACGTcount: A:0.74, C:0.01, G:0.16, T:0.09
Consensus pattern (54 bp):
GAAAAATGAAAAAGAAAAAAGAAAATAAATAAATAAAAAAAATAAAAGAGGAAA
Found at i:3376291 original size:18 final size:18
Alignment explanation
Indices: 3376239--3376291 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
3376229 ATGAAAAGAG
* *
3376239 GAAAGAAAAATGAAATAA
1 GAAAAAAAAATAAAATAA
*
3376257 GAGAAAAAGAAAGAAAATAA
1 GA-AAAAA-AAATAAAATAA
3376277 GAAAAAAAAATAAAA
1 GAAAAAAAAATAAAA
3376292 GGAGAACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 9 0.31
19 9 0.31
20 11 0.38
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (18 bp):
GAAAAAAAAATAAAATAA
Found at i:3376297 original size:18 final size:18
Alignment explanation
Indices: 3376226--3376297 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
3376216 ATAAATACAG
*
3376226 AAAATGAAAAGAGGAAAGA
1 AAAATGAAAAGA-GAAAAA
3376245 AAAATGAAATAAGAGAAAAA
1 AAAATG-AA-AAGAGAAAAA
* *
3376265 GAAA-GAAAATAAGAAAAA
1 AAAATGAAAA-GAGAAAAA
3376283 AAAAT-AAAAGGAGAA
1 AAAATGAAAA-GAGAA
3376298 CAAACAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
17 2 0.05
18 20 0.47
19 7 0.16
20 10 0.23
21 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (18 bp):
AAAATGAAAAGAGAAAAA
Found at i:3377772 original size:133 final size:133
Alignment explanation
Indices: 3377540--3377978 Score: 478
Period size: 133 Copynumber: 3.3 Consensus size: 133
3377530 GAAAATCGAA
* ** *
3377540 CTCAATTCAGTCTTCCCTGACTAACAGTGGAATGAATCAACGA-CCCCATATCTAATTTTTCCCT
1 CTCAATTCAATCTTCCCTGAAGAACAGTGGAATGAATC-AC-ATCCCCAGATCTAA-TTTTCCCT
* * * * * * *
3377604 CATA-AAGAAG-TAGATCAGATGCATTTCTTTCAAGATTTGATATTCCCTCAGTAAAATTGGAAT
63 CA-AGAAGAAGCAAAAT-ATATCCATTTCTTTCAAGATTTGATATTCCCTCAGTAACAGTGGAAC
*
3377667 AAGTCTTC
126 AAGTCTGC
* *
3377675 CTCAATTCAATCTTCCCTGAAGAATAGT-GAATGAATCGACATCCCTAGATCTAATTTTCCCTCA
1 CTCAATTCAATCTTCCCTGAAGAACAGTGGAATGAATC-ACATCCCCAGATCTAATTTTCCCTCA
*
3377739 AGAAGAAGCAAAATATATCCATTTCTTTCAAGATTTGATCTTCCC-CGAGTAACAGTGGAACAAG
65 AGAAGAAGCAAAATATATCCATTTCTTTCAAGATTTGATATTCCCTC-AGTAACAGTGGAACAAG
*
3377803 CCTGC
129 TCTGC
* * * * *
3377808 CTCGATTCAATCTTCCCTAAAGAAGAGTGGAATCAATCA-AGTCCCCAGATCTGATTTTCCCTCA
1 CTCAATTCAATCTTCCCTGAAGAACAGTGGAATGAATCACA-TCCCCAGATCTAATTTTCCCTCA
** * * * * *
3377872 AGAAGAAGCGTAACATATCCATCTCTTTCAAGATTTCATATTCCATGAGTAACAGTGGAACAAGT
65 AGAAGAAGCAAAATATATCCATTTCTTTCAAGATTTGATATTCCCTCAGTAACAGTGGAACAAGT
*
3377937 ATGC
130 CTGC
**
3377941 CTTGATTCAATCTTCCCTGAAGAACAGTGGAAT-AATCA
1 CTCAATTCAATCTTCCCTGAAGAACAGTGGAATGAATCA
3377979 ATGTTTCTCG
Statistics
Matches: 261, Mismatches: 36, Indels: 17
0.83 0.11 0.05
Matches are distributed among these distances:
132 8 0.03
133 197 0.75
134 32 0.12
135 24 0.09
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (133 bp):
CTCAATTCAATCTTCCCTGAAGAACAGTGGAATGAATCACATCCCCAGATCTAATTTTCCCTCAA
GAAGAAGCAAAATATATCCATTTCTTTCAAGATTTGATATTCCCTCAGTAACAGTGGAACAAGTC
TGC
Found at i:3378165 original size:3 final size:3
Alignment explanation
Indices: 3378157--3378204 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
3378147 CAACTTTCTT
3378157 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3378204 T
1 T
3378205 GCAGGATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3378747 original size:1 final size:1
Alignment explanation
Indices: 3378741--3378801 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
3378731 GAAGAAAATG
* * * * * * *
3378741 AAAAAAAAAAAAAAAGAGAGAAAAAAAACAAAAAAAAGAAAAAAAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3378802 GAGACCAACC
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.89, C:0.02, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:3378765 original size:20 final size:20
Alignment explanation
Indices: 3378740--3378797 Score: 84
Period size: 19 Copynumber: 2.9 Consensus size: 20
3378730 GGAAGAAAAT
3378740 GAAAAAAAAAAAAAAAGAGA
1 GAAAAAAAAAAAAAAAGAGA
3378760 GAAAAAAAACAAAAAAA-AGA
1 GAAAAAAAA-AAAAAAAGAGA
3378780 -AAAAAAAAAAGAAAAAGA
1 GAAAAAAAAAA-AAAAAGA
3378798 AAAAGAGACC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.06
19 13 0.37
20 13 0.37
21 7 0.20
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAAAAAAAAGAGA
Found at i:3378794 original size:18 final size:18
Alignment explanation
Indices: 3378732--3378801 Score: 88
Period size: 18 Copynumber: 3.8 Consensus size: 18
3378722 CATTAGCAGG
*
3378732 AAGAAAATGAAAAAAAAA
1 AAGAAAAAGAAAAAAAAA
3378750 AA-AAAAGAGAGAAAAAAAA
1 AAGAAAA-AGA-AAAAAAAA
*
3378769 CAAAAAAAAGAAAAAAAAA
1 -AAGAAAAAGAAAAAAAAA
3378788 AAGAAAAAGAAAAA
1 AAGAAAAAGAAAAA
3378802 GAGACCAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.09
18 17 0.37
19 16 0.35
20 5 0.11
21 4 0.09
ACGTcount: A:0.86, C:0.01, G:0.11, T:0.01
Consensus pattern (18 bp):
AAGAAAAAGAAAAAAAAA
Found at i:3380153 original size:15 final size:15
Alignment explanation
Indices: 3380129--3380158 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3380119 TTTTTATCTT
3380129 TTAAAATTATTTTAA
1 TTAAAATTATTTTAA
*
3380144 TTAAATTTATTTTAA
1 TTAAAATTATTTTAA
3380159 AAGATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAAAATTATTTTAA
Found at i:3391712 original size:13 final size:13
Alignment explanation
Indices: 3391694--3391719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3391684 CCCATGTATC
3391694 ATTCTTCTTGAGA
1 ATTCTTCTTGAGA
3391707 ATTCTTCTTGAGA
1 ATTCTTCTTGAGA
3391720 GCCTTTAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTCTTCTTGAGA
Found at i:3391933 original size:35 final size:35
Alignment explanation
Indices: 3391887--3391954 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
3391877 TGATATTTAA
*
3391887 AATAAGTCATGTCAGTTGGCAAATAAACTTATTAT
1 AATAAGTCATGTCACTTGGCAAATAAACTTATTAT
*
3391922 AATAAGTCATGTCACTTGGCAAATATACTTATT
1 AATAAGTCATGTCACTTGGCAAATAAACTTATT
3391955 TTTTAGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (35 bp):
AATAAGTCATGTCACTTGGCAAATAAACTTATTAT
Found at i:3395328 original size:20 final size:20
Alignment explanation
Indices: 3395305--3395378 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
3395295 AAAAGTAAAT
*
3395305 CCTTTTATGAAAAGGTTAAG
1 CCTTTTATCAAAAGGTTAAG
* * **
3395325 CCTTTCATCAAAGGGAGAAG
1 CCTTTTATCAAAAGGTTAAG
*
3395345 TCTTTTAATCAAAAGGTTAAG
1 CCTTTT-ATCAAAAGGTTAAG
*
3395366 TCCTTTCATCAAA
1 -CCTTTTATCAAA
3395379 TGATCTTAAC
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
20 19 0.47
21 17 0.43
22 4 0.10
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
CCTTTTATCAAAAGGTTAAG
Found at i:3395366 original size:21 final size:21
Alignment explanation
Indices: 3395304--3395378 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
3395294 AAAAAGTAAA
* *
3395304 TCCTTTTATGAAAAGGTTAAG
1 TCCTTTCATCAAAAGGTTAAG
* **
3395325 -CCTTTCATCAAAGGGAGAAG
1 TCCTTTCATCAAAAGGTTAAG
* *
3395345 TCTTTTAATCAAAAGGTTAAG
1 TCCTTTCATCAAAAGGTTAAG
3395366 TCCTTTCATCAAA
1 TCCTTTCATCAAA
3395379 TGATCTTAAC
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
TCCTTTCATCAAAAGGTTAAG
Found at i:3398035 original size:2 final size:2
Alignment explanation
Indices: 3398028--3398055 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3398018 AAAATATAAT
3398028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3398056 AATTTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3401992 original size:21 final size:20
Alignment explanation
Indices: 3401962--3402001 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3401952 TTAGGGTTCG
*
3401962 AATATTGATACAAAGATGAAC
1 AATATCGATAC-AAGATGAAC
*
3401983 AATATCGATACTAGATGAA
1 AATATCGATACAAGATGAA
3402002 TTGAAGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (20 bp):
AATATCGATACAAGATGAAC
Found at i:3405744 original size:18 final size:19
Alignment explanation
Indices: 3405698--3405745 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
3405688 ACTATTTTTG
*
3405698 GTATCGATACTCAGGGTGA
1 GTATCGATACTCAAGGTGA
* *
3405717 GTATCAATACTCAAGGT-T
1 GTATCGATACTCAAGGTGA
3405735 GTATCGATACT
1 GTATCGATACT
3405746 ACTGGTACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (19 bp):
GTATCGATACTCAAGGTGA
Found at i:3416543 original size:21 final size:21
Alignment explanation
Indices: 3416491--3416544 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
3416481 AGGGTTCGAG
*
3416491 TATCGATACTAGGATAAACAA
1 TATCGATACTGGGATAAACAA
*
3416512 TATCGATACTGGGATAAATAA
1 TATCGATACTGGGATAAACAA
3416533 TATCGATACTGG
1 TATCGATACTGG
3416545 TAAAATTAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (21 bp):
TATCGATACTGGGATAAACAA
Found at i:3417765 original size:32 final size:32
Alignment explanation
Indices: 3417711--3417835 Score: 173
Period size: 32 Copynumber: 4.0 Consensus size: 32
3417701 TAGTAGAATC
* * *
3417711 AGTATGGCATTC-TATAATGCATAGCAGAGTT
1 AGTATTGCATTCAGATAATGCATAACAGAGTT
* *
3417742 AGTATTGCATTCAGATAATGCATAACAAAGCT
1 AGTATTGCATTCAGATAATGCATAACAGAGTT
3417774 AGTATTGCATTCAGATAATGCATAACA-AGTT
1 AGTATTGCATTCAGATAATGCATAACAGAGTT
* *
3417805 AGTATTGAATTCAGATAATGCATAAGAGAGT
1 AGTATTGCATTCAGATAATGCATAACAGAGT
3417836 CAGTGTTGTA
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
31 39 0.46
32 45 0.54
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (32 bp):
AGTATTGCATTCAGATAATGCATAACAGAGTT
Found at i:3417805 original size:63 final size:63
Alignment explanation
Indices: 3417711--3417829 Score: 186
Period size: 63 Copynumber: 1.9 Consensus size: 63
3417701 TAGTAGAATC
* * *
3417711 AGTATGGCATTCTATAATGCATAGCAGAGTTAGTATTGCATTCAGATAATGCATAACAAAGCT
1 AGTATGGCATTCGATAATGCATAACAGAGTTAGTATTGAATTCAGATAATGCATAACAAAGCT
*
3417774 AGTATTGCATTCAGATAATGCATAACA-AGTTAGTATTGAATTCAGATAATGCATAA
1 AGTATGGCATTC-GATAATGCATAACAGAGTTAGTATTGAATTCAGATAATGCATAA
3417830 GAGAGTCAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
63 39 0.76
64 12 0.24
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (63 bp):
AGTATGGCATTCGATAATGCATAACAGAGTTAGTATTGAATTCAGATAATGCATAACAAAGCT
Found at i:3423231 original size:42 final size:42
Alignment explanation
Indices: 3423163--3423290 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
3423153 TACCACCTTC
*
3423163 TTTGGGAACTTTTATGGTCAAATGATAATTCGGGAAGCAAGTTT
1 TTTGGGAA-TTTTATGGTCAAATGATAATTCGAGAAGCAA-TTT
* * *
3423207 TTT-TGAATTTTATGGTGAAATGATAATTTGAGAAGCAATTT
1 TTTGGGAATTTTATGGTCAAATGATAATTCGAGAAGCAATTT
* *
3423248 TTTGGGAATTTTATGATCAAATGATAATTCGAGTAG-AATTT
1 TTTGGGAATTTTATGGTCAAATGATAATTCGAGAAGCAATTT
3423289 TT
1 TT
3423291 GTGTGTAAGC
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
41 13 0.18
42 55 0.74
43 3 0.04
44 3 0.04
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.41
Consensus pattern (42 bp):
TTTGGGAATTTTATGGTCAAATGATAATTCGAGAAGCAATTT
Found at i:3426947 original size:22 final size:22
Alignment explanation
Indices: 3426922--3427002 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
3426912 TTAATCATGG
*
3426922 AAGTGCCTTAGCACTAATACCA
1 AAGTGCCTTAGCACTGATACCA
*
3426944 AAGTGCCTTAGCACGGATA-CA
1 AAGTGCCTTAGCACTGATACCA
* * *
3426965 AAGTGCATTCGCACTGATACAA
1 AAGTGCCTTAGCACTGATACCA
* *
3426987 AAGTGCCATAGAACTG
1 AAGTGCCTTAGCACTG
3427003 TGGAAGAGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
21 18 0.38
22 30 0.62
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGATACCA
Found at i:3437163 original size:19 final size:20
Alignment explanation
Indices: 3437128--3437165 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3437118 TAGAAATTAG
3437128 TGTTAGAATGTTGAAATTGA
1 TGTTAGAATGTTGAAATTGA
*
3437148 TGTTATAATG-TGAAATTG
1 TGTTAGAATGTTGAAATTG
3437166 GGCTATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (20 bp):
TGTTAGAATGTTGAAATTGA
Found at i:3438426 original size:2 final size:2
Alignment explanation
Indices: 3438419--3438450 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3438409 TGCATTGATC
3438419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3438451 GATGTTATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3441110 original size:431 final size:434
Alignment explanation
Indices: 3440302--3441140 Score: 1596
Period size: 431 Copynumber: 1.9 Consensus size: 434
3440292 TGATTTTACT
3440302 TGGTTTTGATTTGATTCAAGCATGGAATCAACTTTGATTCAACCTTATAAAATCTCTACAATCAA
1 TGGTTTTGATTTGATTCAAGCATGGAATCAACTTTGATTCAACCTTATAAAATCTCTACAATCAA
*
3440367 AACCCTAACTTAATTTCATCAAAACACATCTTCCTCCCAAGATTAGGGTTAGGTCAAAGCTTCTT
66 AACCCTAACTTAATTTCATCAAAACACATCTTCCTCCCAAGATTAGGGTTAGGTCAAAGCTTCAT
3440432 ATGTTCATATGATAATGTACAAGTGATTTTATCATCAATCATGCTTGTAAATGATTCTACAACCT
131 ATGTTCATATGATAATGTACAAGTGATTTTATCATCAATCATGCTTGTAAATGATTCTACAACCT
*
3440497 CAACAACATCAAAATCTTTTATCTATTTCATAAACCCTAATATGAATATAAACCCTAGAATTTTG
196 -AACAACATCAAAATCTTTTATCTATTTCATAAACCCTAATATGAACATAAACCCTAGAATTTTG
3440562 GATCCTTGAACACAAAACAAATTAGCAAACAATAATGGTACCAAATGATAGCAATTTTCGAATAG
260 GATCCTTGAACACAAAACAAATTAGCAAACAATAATGGTACCAAATGATAGCAATTTTCGAATAG
3440627 AACAATTTTATATTTCACGACATGATCCAAAAATCCAAAGGAAATTTCTCAAAAATGAAAAAAAT
325 AACAATTTTATATTTCACGACATGATCCAAAAATCCAAAGGAAATTTCTCAAAAATG-AAAAAAT
3440692 AAAATTTCTCTTACCTTGGTCATGGGAGTACAAAATGGAGCTGAAA
389 AAAATTTCTCTTACCTTGGTCATGGGAGTACAAAATGGAGCTGAAA
3440738 TGGTTTTGATTTGATTCAAGCATGGAATCAACTTTGATTCAACCTTATAAAATCTCTACAATCAA
1 TGGTTTTGATTTGATTCAAGCATGGAATCAACTTTGATTCAACCTTATAAAATCTCTACAATCAA
*
3440803 AACCCTAACTTAATTT-ATCAAAACACATCTTCCTTCCAAGATTAGGGTTAGGTCAAAGCTTCAT
66 AACCCTAACTTAATTTCATCAAAACACATCTTCCTCCCAAGATTAGGGTTAGGTCAAAGCTTCAT
3440867 ATGTTCATATGATAATGTACAAGTGATTTTATCATCAATCATGCTTGTAAATGATTCTACAA-CT
131 ATGTTCATATGATAATGTACAAGTGATTTTATCATCAATCATGCTTGTAAATGATTCTACAACCT
*
3440931 -TCAACATCAAAATCTTTTATCTATTTCATAAACCCTAATATGAACATAAACCCTAGAATTTTGG
196 AACAACATCAAAATCTTTTATCTATTTCATAAACCCTAATATGAACATAAACCCTAGAATTTTGG
3440995 AT-CTTGAACACAAAACAAATTAGCAAACAATAATGGTACCAAATGATAGCAATTTTCGAATAGA
261 ATCCTTGAACACAAAACAAATTAGCAAACAATAATGGTACCAAATGATAGCAATTTTCGAATAGA
3441059 ACAATTTTATATTTCACGACATGATCCAAAAATCCAAAGGAAATTTCTCAAAAATGAAAAAATAA
326 ACAATTTTATATTTCACGACATGATCCAAAAATCCAAAGGAAATTTCTCAAAAATGAAAAAATAA
3441124 AATTTCTCTTACCTTGG
391 AATTTCTCTTACCTTGG
3441141 CTAAGTTTTT
Statistics
Matches: 399, Mismatches: 4, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
430 26 0.07
431 118 0.30
432 64 0.16
434 2 0.01
435 108 0.27
436 81 0.20
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (434 bp):
TGGTTTTGATTTGATTCAAGCATGGAATCAACTTTGATTCAACCTTATAAAATCTCTACAATCAA
AACCCTAACTTAATTTCATCAAAACACATCTTCCTCCCAAGATTAGGGTTAGGTCAAAGCTTCAT
ATGTTCATATGATAATGTACAAGTGATTTTATCATCAATCATGCTTGTAAATGATTCTACAACCT
AACAACATCAAAATCTTTTATCTATTTCATAAACCCTAATATGAACATAAACCCTAGAATTTTGG
ATCCTTGAACACAAAACAAATTAGCAAACAATAATGGTACCAAATGATAGCAATTTTCGAATAGA
ACAATTTTATATTTCACGACATGATCCAAAAATCCAAAGGAAATTTCTCAAAAATGAAAAAATAA
AATTTCTCTTACCTTGGTCATGGGAGTACAAAATGGAGCTGAAA
Found at i:3446990 original size:11 final size:11
Alignment explanation
Indices: 3446958--3446992 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3446948 AGATGATAAC
*
3446958 TAAGCTTAAGG
1 TAAGCTTAAGT
*
3446969 AAAGCTTAAGT
1 TAAGCTTAAGT
3446980 TAAGCTTAAGT
1 TAAGCTTAAGT
3446991 TA
1 TA
3446993 TCATAAAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (11 bp):
TAAGCTTAAGT
Found at i:3448051 original size:37 final size:36
Alignment explanation
Indices: 3447979--3448052 Score: 87
Period size: 38 Copynumber: 2.0 Consensus size: 36
3447969 GTTGGAAAAT
* *
3447979 ATTTATATATTTTCTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTAAAAAATTGAAAATCATAAA
* *
3448015 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-A-TTTTCTTAAAAAATTGAAAATCATAAA
3448052 A
1 A
3448053 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 8 0.25
37 7 0.22
38 17 0.53
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (36 bp):
ATTTATATATTTTCTTAAAAAATTGAAAATCATAAA
Found at i:3456587 original size:20 final size:20
Alignment explanation
Indices: 3456566--3456634 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
3456556 AAGACTACTG
*
3456566 GTCTCTATACCCAAAAACTG
1 GTCTCTATACCCAAAAACTA
*
3456586 GTCTCTATA-CCAAAGGACTA
1 GTCTCTATACCCAAA-AACTA
* *
3456606 GTCTCCATACCAAAAAACTA
1 GTCTCTATACCCAAAAACTA
3456626 GTCTCTATA
1 GTCTCTATA
3456635 GTGTAGACTG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 5 0.12
20 32 0.78
21 4 0.10
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (20 bp):
GTCTCTATACCCAAAAACTA
Found at i:3457502 original size:28 final size:28
Alignment explanation
Indices: 3457471--3457525 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
3457461 TTCATTTCGA
*
3457471 AGCTTGAGGGTAAATTTGATTATTTTGG
1 AGCTTGAGAGTAAATTTGATTATTTTGG
* *
3457499 AGCTTGAGAGTAATTTTGGTTATTTTG
1 AGCTTGAGAGTAAATTTGATTATTTTG
3457526 AACAATTCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.27, T:0.45
Consensus pattern (28 bp):
AGCTTGAGAGTAAATTTGATTATTTTGG
Found at i:3462711 original size:86 final size:87
Alignment explanation
Indices: 3462604--3462764 Score: 263
Period size: 86 Copynumber: 1.9 Consensus size: 87
3462594 TAATCCTGAA
* * *
3462604 TATTTAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAA-AATCCCTAATATGATTA-
1 TATTAAATTCAATTAAATAAATATAGATTTAATTAATTTGAAATAATAAACCCTAATATGATTAG
3462667 GGTAACTTGAATATAAGAGTAT
66 GGTAACTTGAATATAAGAGTAT
3462689 TATTAAATTCCAATTAAATAAATATAGATTTAATTAATTTGAAATAATTAAACCCTAATATGATT
1 TATTAAATT-CAATTAAATAAATATAGATTTAATTAATTTGAAATAA-TAAACCCTAATATGATT
3462754 AGGGTAACTTG
64 AGGGTAACTTG
3462765 GCTATAAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
85 8 0.12
86 36 0.52
88 16 0.23
89 9 0.13
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (87 bp):
TATTAAATTCAATTAAATAAATATAGATTTAATTAATTTGAAATAATAAACCCTAATATGATTAG
GGTAACTTGAATATAAGAGTAT
Found at i:3463556 original size:2 final size:2
Alignment explanation
Indices: 3463549--3463580 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3463539 CGTAACAATG
3463549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3463581 AGATATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3483804 original size:20 final size:20
Alignment explanation
Indices: 3483741--3483804 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
3483731 TTAATCTTAA
* * *
3483741 GGTATCGAGACTAGTTTTTC
1 GGTATGGAGACCAATTTTTC
*
3483761 GGTATGGAGACCAATCTTTC
1 GGTATGGAGACCAATTTTTC
*
3483781 GGTATGGAGACCAATTTTTG
1 GGTATGGAGACCAATTTTTC
3483801 GGTA
1 GGTA
3483805 GGGATACTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.34
Consensus pattern (20 bp):
GGTATGGAGACCAATTTTTC
Found at i:3495101 original size:21 final size:21
Alignment explanation
Indices: 3495077--3495128 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
3495067 CTCTAACACT
3495077 CTTTGTAATAGAGTTGCTTCA
1 CTTTGTAATAGAGTTGCTTCA
* **
3495098 CTTTGTAATAGAGTTGTTTTG
1 CTTTGTAATAGAGTTGCTTCA
3495119 CTTTGTAATA
1 CTTTGTAATA
3495129 ACGCACCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (21 bp):
CTTTGTAATAGAGTTGCTTCA
Found at i:3504583 original size:32 final size:31
Alignment explanation
Indices: 3504540--3504615 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 31
3504530 TTGGGCCTGT
* *
3504540 GAGCCTACCCAAGAATAATCTCGGGGCCACA
1 GAGCCTACCCAAGAAAAATCTCAGGGCCACA
*
3504571 GAGGCCTACCCAAGAAAAATCTCAGGGCCGCA
1 GA-GCCTACCCAAGAAAAATCTCAGGGCCACA
*
3504603 TAGCCTACCCAAG
1 GAGCCTACCCAAG
3504616 GTCACCTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 13 0.32
32 27 0.68
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.12
Consensus pattern (31 bp):
GAGCCTACCCAAGAAAAATCTCAGGGCCACA
Found at i:3504790 original size:24 final size:24
Alignment explanation
Indices: 3504758--3504815 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
3504748 TGGAGAAATA
*
3504758 AGAAATCAGAGCAA-AAATCATAAC
1 AGAAATCAGAG-AAGAAATCAGAAC
*
3504782 AGAATTCAGAGAAGAAATCAGAAC
1 AGAAATCAGAGAAGAAATCAGAAC
*
3504806 AGATATCAGA
1 AGAAATCAGA
3504816 TAAAATATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (24 bp):
AGAAATCAGAGAAGAAATCAGAAC
Found at i:3506321 original size:20 final size:20
Alignment explanation
Indices: 3506291--3506328 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3506281 AAATAATCTT
3506291 ATTCAAACTAT-TAGAAAAC
1 ATTCAAACTATATAGAAAAC
3506310 ATTCATAACTATATAGAAA
1 ATTCA-AACTATATAGAAA
3506329 CTAGAAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (20 bp):
ATTCAAACTATATAGAAAAC
Found at i:3519717 original size:20 final size:20
Alignment explanation
Indices: 3519689--3519746 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
3519679 AGTTTTCCAG
* *
3519689 AAAATGGATTGATCCCTTTT
1 AAAAAGGATCGATCCCTTTT
**
3519709 AAAAAGGATCGATCCCTTAACC
1 AAAAAGGATCGATCCCTT--TT
3519731 AAAAAGGATCGATCCC
1 AAAAAGGATCGATCCC
3519747 AAAGTTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 16 0.50
22 16 0.50
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
AAAAAGGATCGATCCCTTTT
Found at i:3521057 original size:26 final size:26
Alignment explanation
Indices: 3521027--3521085 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
3521017 ATTCTAAATT
3521027 AATTAAATATAAATTTAATTATTTTG
1 AATTAAATATAAATTTAATTATTTTG
3521053 AATTAAATATAAATTTAATTATTTTG
1 AATTAAATATAAATTTAATTATTTTG
3521079 AATTAAA
1 AATTAAA
3521086 ATATTCCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (26 bp):
AATTAAATATAAATTTAATTATTTTG
Found at i:3521178 original size:2 final size:2
Alignment explanation
Indices: 3521171--3521220 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3521161 GGTACGATTA
3521171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3521213 AT AT AT AT
1 AT AT AT AT
3521221 TGGTACACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3521412 original size:2 final size:2
Alignment explanation
Indices: 3521405--3521482 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
3521395 ACTCGTTGGC
3521405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3521447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3521483 CAATTTTAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3522642 original size:32 final size:32
Alignment explanation
Indices: 3522596--3522664 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
3522586 CCTAAGGTGA
* * * *
3522596 CCCTTGGGTTGGCTCTTAGGCCTCAAAGTACT
1 CCCTTGGGTAGGCTCTAAGGCCCCAAAGCACT
*
3522628 CCCTTGGGTAGGCTCTAAGGCCCCAAGGCACT
1 CCCTTGGGTAGGCTCTAAGGCCCCAAAGCACT
3522660 CCCTT
1 CCCTT
3522665 AATTTGGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.16, C:0.33, G:0.25, T:0.26
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTAAGGCCCCAAAGCACT
Found at i:3525923 original size:15 final size:15
Alignment explanation
Indices: 3525905--3525933 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3525895 ATATATTAAA
3525905 CAATTTGATATCTTT
1 CAATTTGATATCTTT
3525920 CAATTTGATATCTT
1 CAATTTGATATCTT
3525934 CTTATAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (15 bp):
CAATTTGATATCTTT
Found at i:3527968 original size:16 final size:16
Alignment explanation
Indices: 3527949--3528014 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 16
3527939 GTTAAAAGAG
3527949 AAAATAAAAATAAAAC
1 AAAATAAAAATAAAAC
*
3527965 AAAATAAAAA-AAGAATTGGG
1 AAAATAAAAATAA-AA----C
*
3527985 AAAATAAAGATAAAAC
1 AAAATAAAAATAAAAC
3528001 AAAAT-AAAATAAAA
1 AAAATAAAAATAAAA
3528015 AGTTAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
15 10 0.25
16 17 0.43
20 11 0.28
21 2 0.05
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.14
Consensus pattern (16 bp):
AAAATAAAAATAAAAC
Found at i:3528163 original size:19 final size:18
Alignment explanation
Indices: 3528144--3528187 Score: 79
Period size: 19 Copynumber: 2.4 Consensus size: 18
3528134 GTTATTTTTA
3528144 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
3528162 AAATAAAAAGATAAGAATT
1 AAAT-AAAAGATAAGAATT
3528181 AAATAAA
1 AAATAAA
3528188 TAATCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:3529471 original size:270 final size:269
Alignment explanation
Indices: 3528978--3529589 Score: 865
Period size: 270 Copynumber: 2.3 Consensus size: 269
3528968 ACACAAATTT
* * * *
3528978 TCATTCGG-ACGATATCATTC-TTCGTGAAGTTGAAATCAT-GAGTGGCTCCTTTGTTGTGAAGT
1 TCATTGGGTACGATATCCTTCGTT-GTGAAGTCGAAATCATAG-GTGGCTCCTTCGTTGTGAAGT
* **
3529040 TGAGCTTTGAACTGAAAAATCCTGAGCACAATATCCTTCGTCGTGAAGTTGAAACCGGGCTCAAA
64 TGAGCTTTGAACTGAAAAATCCTGAGCACAATATCCTTCGTCGTGAAGTTAAAACAAGGCTCAAA
* *
3529105 GCATTGGAAAGTCACTCATGTATCGTCTTCTAGCCCAATATACTTCATCGTGAAGCTGAAATTTG
129 GAATTGGAAAGTCACTCATGTATCGTCTTATAGCCCAATATACTTCATCGTGAAGCTGAAATTTG
* ** *
3529170 ACCTGAAGACTTTGGTATGAAACTGGTTTTTCATT-TTTATGTTACAGATGACTTC-TTTGTCGT
194 ACCTGAAGACTTTGGTATAAAACTGGTTTTTCATTGTTT-TGTTACAGATGAC-TCATTCATCAT
3529233 GAAGTTGGGTCAA
257 GAAGTTGGGTCAA
* * * *
3529246 TCTTTTGGGTACGATATCCTTCGTTGTGAAGTCAAAATCATAGGTGGCTTCTTCGTTGTGATGTT
1 TC-ATTGGGTACGATATCCTTCGTTGTGAAGTCGAAATCATAGGTGGCTCCTTCGTTGTGAAGTT
* * *
3529311 GAGCTTTGAACTGAAAAATCCTGAGCACTATATCCTTTGTCGTGAAGTTAAAATAAGGCTCAAAG
65 GAGCTTTGAACTGAAAAATCCTGAGCACAATATCCTTCGTCGTGAAGTTAAAACAAGGCTCAAAG
* * *
3529376 AATTGGAAAGTCGCTCATGTATTGTCTTATAGCCCAATATACTTCGTCGTGAAGCTGAAATTTGA
130 AATTGGAAAGTCACTCATGTATCGTCTTATAGCCCAATATACTTCATCGTGAAGCTGAAATTTGA
* * *
3529441 CCTGAATACTTTGGTATAAAATTTGTTTTTCATTGTTTTGTTACAGATGACTCATTCATCATGAA
195 CCTGAAGACTTTGGTATAAAACTGGTTTTTCATTGTTTTGTTACAGATGACTCATTCATCATGAA
3529506 GTTGGGTCAA
260 GTTGGGTCAA
* * ** *
3529516 TCATTGGGTACGATATCCTTCGTTGTGGAGTCGAAATCGTAGGTGAATCCTTCGTTATGAAGTTG
1 TCATTGGGTACGATATCCTTCGTTGTGAAGTCGAAATCATAGGTGGCTCCTTCGTTGTGAAGTTG
3529581 AGCTTTGAA
66 AGCTTTGAA
3529590 TTGGATATCC
Statistics
Matches: 303, Mismatches: 35, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
268 2 0.01
269 69 0.23
270 226 0.75
271 6 0.02
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (269 bp):
TCATTGGGTACGATATCCTTCGTTGTGAAGTCGAAATCATAGGTGGCTCCTTCGTTGTGAAGTTG
AGCTTTGAACTGAAAAATCCTGAGCACAATATCCTTCGTCGTGAAGTTAAAACAAGGCTCAAAGA
ATTGGAAAGTCACTCATGTATCGTCTTATAGCCCAATATACTTCATCGTGAAGCTGAAATTTGAC
CTGAAGACTTTGGTATAAAACTGGTTTTTCATTGTTTTGTTACAGATGACTCATTCATCATGAAG
TTGGGTCAA
Found at i:3529747 original size:123 final size:123
Alignment explanation
Indices: 3529563--3529785 Score: 349
Period size: 123 Copynumber: 1.8 Consensus size: 123
3529553 CGTAGGTGAA
* *
3529563 TCCTTCGTTATGAAGTTGAGCTTTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAATCTTG
1 TCCTTCGCTATGAAGTTGAGCTTTGAATTGGATATCATTCATTGTGAAGTTGAAATCCAATCTTG
* *
3529628 TAAATTGAATT-GCTTTGAGATTAATATCTTTCGCTGTGAAGTTGAAATTGTGGATGGC
66 AAAATTGAATTGGC-TCGAGATTAATATCTTTCGCTGTGAAGTTGAAATTGTGGATGGC
* * *
3529686 TCCTTCGCTGTGAAGTTGAGTTTTGAATTGGATGTCATTCATTGTGAAGTTGAAATCCAATCTTG
1 TCCTTCGCTATGAAGTTGAGCTTTGAATTGGATATCATTCATTGTGAAGTTGAAATCCAATCTTG
* *
3529751 AAAATTGCATTGGCTCGAGTTTAATATCTTTCGCT
66 AAAATTGAATTGGCTCGAGATTAATATCTTTCGCT
3529786 ATAAGGATGA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
123 88 0.98
124 2 0.02
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (123 bp):
TCCTTCGCTATGAAGTTGAGCTTTGAATTGGATATCATTCATTGTGAAGTTGAAATCCAATCTTG
AAAATTGAATTGGCTCGAGATTAATATCTTTCGCTGTGAAGTTGAAATTGTGGATGGC
Found at i:3533032 original size:6 final size:6
Alignment explanation
Indices: 3533021--3533049 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3533011 CTTAATTACG
3533021 AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAAT
3533050 ATTTGATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:3533405 original size:12 final size:12
Alignment explanation
Indices: 3533385--3533436 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
3533375 GGAAAGAAAA
3533385 AAAAT-AAAGGT
1 AAAATAAAAGGT
3533396 AAAATAAAAGGT
1 AAAATAAAAGGT
* *
3533408 ATAACAAAA--T
1 AAAATAAAAGGT
*
3533418 AAAATAAAAGAT
1 AAAATAAAAGGT
3533430 AAAATAA
1 AAAATAA
3533437 TAAATAATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.24
11 5 0.15
12 21 0.62
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (12 bp):
AAAATAAAAGGT
Found at i:3533480 original size:13 final size:13
Alignment explanation
Indices: 3533458--3533487 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3533448 AGTAAAGCTA
3533458 AAAAGGGGTTTTT
1 AAAAGGGGTTTTT
*
3533471 AAAAGTGGTTTTT
1 AAAAGGGGTTTTT
3533484 AAAA
1 AAAA
3533488 TAAAAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (13 bp):
AAAAGGGGTTTTT
Found at i:3533506 original size:18 final size:18
Alignment explanation
Indices: 3533485--3533531 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
3533475 GTGGTTTTTA
3533485 AAATAAA-AGATAAGAATT
1 AAATAAATA-ATAAGAATT
*
3533503 AAATAAATAATAATAATT
1 AAATAAATAATAAGAATT
3533521 AAATAAATAAT
1 AAATAAATAAT
3533532 CTGAAGAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (18 bp):
AAATAAATAATAAGAATT
Found at i:3537139 original size:12 final size:12
Alignment explanation
Indices: 3537121--3537152 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3537111 GTACTAAAAG
3537121 ATTAAAATCAAA
1 ATTAAAATCAAA
*
3537133 TTTAAAATCAAA
1 ATTAAAATCAAA
3537145 ATTAAAAT
1 ATTAAAAT
3537153 TATACAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (12 bp):
ATTAAAATCAAA
Found at i:3541439 original size:22 final size:21
Alignment explanation
Indices: 3541411--3541453 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
3541401 ATAGCGGAAG
3541411 TGCCTTAGCACTAATACTAAAA
1 TGCCTTAGCACTAATAC-AAAA
*
3541433 TGCCTTAGCACTAGTACAAAA
1 TGCCTTAGCACTAATACAAAA
3541454 GTGCATCGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (21 bp):
TGCCTTAGCACTAATACAAAA
Found at i:3550257 original size:21 final size:22
Alignment explanation
Indices: 3550231--3550272 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3550221 TGTTTTGTTA
* *
3550231 TTAATTATAATTATAT-TATTG
1 TTAATTAGAAGTATATATATTG
3550252 TTAATTAGAAGTATATATATT
1 TTAATTAGAAGTATATATATT
3550273 CTTATAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
TTAATTAGAAGTATATATATTG
Found at i:3551199 original size:28 final size:30
Alignment explanation
Indices: 3551139--3551199 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
3551129 TCTATTATTC
3551139 TTTTAAATTTACTTAAATTTATATTTTAAT
1 TTTTAAATTTACTTAAATTTATATTTTAAT
* * *
3551169 TTTTAAA-TT-CTTGAATTTTTATTTTTAT
1 TTTTAAATTTACTTAAATTTATATTTTAAT
3551197 TTT
1 TTT
3551200 AGTGAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.68
29 2 0.07
30 7 0.25
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (30 bp):
TTTTAAATTTACTTAAATTTATATTTTAAT
Found at i:3555439 original size:17 final size:17
Alignment explanation
Indices: 3555417--3555453 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3555407 ATTAGTATAT
*
3555417 TTTTATTTTATGATCAC
1 TTTTATTTTAGGATCAC
*
3555434 TTTTATTTTGGGATCAC
1 TTTTATTTTAGGATCAC
3555451 TTT
1 TTT
3555454 CTACTAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (17 bp):
TTTTATTTTAGGATCAC
Found at i:3555694 original size:13 final size:13
Alignment explanation
Indices: 3555669--3555703 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
3555659 CATATATTAC
3555669 AATATTATTATTTA
1 AATATT-TTATTTA
3555683 AATATTTTATTTA
1 AATATTTTATTTA
3555696 AATTATTT
1 AA-TATTT
3555704 AATTATGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTTATTTA
Found at i:3556885 original size:21 final size:21
Alignment explanation
Indices: 3556861--3556903 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3556851 GTTGATAATT
* *
3556861 TTGAAAATTTGAATTTTTTTA
1 TTGAAAATTTAAATATTTTTA
*
3556882 TTGAAATTTTAAATATTTTTA
1 TTGAAAATTTAAATATTTTTA
3556903 T
1 T
3556904 GATTCCTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
TTGAAAATTTAAATATTTTTA
Found at i:3590140 original size:20 final size:20
Alignment explanation
Indices: 3590115--3590182 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
3590105 ACGTGAACAA
3590115 TATCGATATTGTTCATGCAG
1 TATCGATATTGTTCATGCAG
* * * *
3590135 TATCGAAACTG-T-AAGAACAA
1 TATCGATATTGTTCATG--CAG
3590155 TATCGATATTGTTCATGCAG
1 TATCGATATTGTTCATGCAG
3590175 TATCGATA
1 TATCGATA
3590183 CTGTAAGAAC
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 30 0.83
21 1 0.03
22 2 0.06
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (20 bp):
TATCGATATTGTTCATGCAG
Found at i:3590153 original size:40 final size:40
Alignment explanation
Indices: 3590109--3590202 Score: 179
Period size: 40 Copynumber: 2.4 Consensus size: 40
3590099 TGTACTACGT
3590109 GAACAATATCGATATTGTTCATGCAGTATCGAAACTGTAA
1 GAACAATATCGATATTGTTCATGCAGTATCGAAACTGTAA
*
3590149 GAACAATATCGATATTGTTCATGCAGTATCGATACTGTAA
1 GAACAATATCGATATTGTTCATGCAGTATCGAAACTGTAA
3590189 GAACAATATCGATA
1 GAACAATATCGATA
3590203 CTATGTACCC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (40 bp):
GAACAATATCGATATTGTTCATGCAGTATCGAAACTGTAA
Found at i:3590198 original size:20 final size:20
Alignment explanation
Indices: 3590135--3590204 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
3590125 GTTCATGCAG
*
3590135 TATCGAAACTGTAAGAACAA
1 TATCGATACTGTAAGAACAA
* * *
3590155 TATCGATATTGTTCATG--CAG
1 TATCGATACTG-T-AAGAACAA
3590175 TATCGATACTGTAAGAACAA
1 TATCGATACTGTAAGAACAA
3590195 TATCGATACT
1 TATCGATACT
3590205 ATGTACCCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 2 0.05
19 1 0.03
20 33 0.85
21 1 0.03
22 2 0.05
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
TATCGATACTGTAAGAACAA
Found at i:3591595 original size:3 final size:3
Alignment explanation
Indices: 3591587--3591630 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
3591577 CTTGGCAATC
* *
3591587 TCT TCT TCT TCT TCT TCT TCT TCT TCA TCT TCT TCT TCA TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
3591631 ATCCACTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:3618769 original size:145 final size:145
Alignment explanation
Indices: 3618506--3618793 Score: 576
Period size: 145 Copynumber: 2.0 Consensus size: 145
3618496 CTCGCATCAC
3618506 TACATGATAGTAGTAGTGAAATAAATATGCCATGACATTAGTAAATGTTTGAATAGTTTTTGGAA
1 TACATGATAGTAGTAGTGAAATAAATATGCCATGACATTAGTAAATGTTTGAATAGTTTTTGGAA
3618571 TTAGTTAAGGATACCCGATGATGATGATGATTTTGATGGCTAGGATAGAATGTACATGACTGGTT
66 TTAGTTAAGGATACCCGATGATGATGATGATTTTGATGGCTAGGATAGAATGTACATGACTGGTT
3618636 GAGGATGATAGAATG
131 GAGGATGATAGAATG
3618651 TACATGATAGTAGTAGTGAAATAAATATGCCATGACATTAGTAAATGTTTGAATAGTTTTTGGAA
1 TACATGATAGTAGTAGTGAAATAAATATGCCATGACATTAGTAAATGTTTGAATAGTTTTTGGAA
3618716 TTAGTTAAGGATACCCGATGATGATGATGATTTTGATGGCTAGGATAGAATGTACATGACTGGTT
66 TTAGTTAAGGATACCCGATGATGATGATGATTTTGATGGCTAGGATAGAATGTACATGACTGGTT
3618781 GAGGATGATAGAA
131 GAGGATGATAGAA
3618794 CCAACTCTAG
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 143 1.00
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (145 bp):
TACATGATAGTAGTAGTGAAATAAATATGCCATGACATTAGTAAATGTTTGAATAGTTTTTGGAA
TTAGTTAAGGATACCCGATGATGATGATGATTTTGATGGCTAGGATAGAATGTACATGACTGGTT
GAGGATGATAGAATG
Found at i:3622222 original size:116 final size:116
Alignment explanation
Indices: 3622033--3622402 Score: 481
Period size: 116 Copynumber: 3.2 Consensus size: 116
3622023 TGTTGTACTA
* * * *
3622033 TGGCACTTAGGTGCTTATTGGGTGCACTTTGTGTGAAAGGATGGTATTCATAATGAATTACCACT
1 TGGCACTCAAGTGCTTATT-AGTGCACTTTGTGTGCAAGGATGGTATTCATAATGAATTACCACT
* * *
3622098 CCATAATTGTTAGTATAGTGTCGTTATATACTACAGTACATATACATCATTG
65 CCATAATTGTTAGTATAGTATCGTTGTATACTACAGTACCTATACATCATTG
* * * * *
3622150 TGGCACTCAAGTTCTTATTCGTGCACTTTGTGTGCAAGGTTGGTATTCATAATGAATTATCACTT
1 TGGCACTCAAGTGCTTATTAGTGCACTTTGTGTGCAAGGATGGTATTCATAATGAATTACCACTC
*** * *
3622215 TGGAATTGTTAGTATAGTATCATTGTATACTACAGTACCTCA-ACGTCATTG
66 CATAATTGTTAGTATAGTATCGTTGTATACTACAGTACCT-ATACATCATTG
* * *
3622266 TGGTACTTAGGTGCTTATTAGTGCACTTTGTGTGCAAGGATGGTATTCATAATGAATTACCACTC
1 TGGCACTCAAGTGCTTATTAGTGCACTTTGTGTGCAAGGATGGTATTCATAATGAATTACCACTC
* * *
3622331 CATAATTGTTAGTATATTATTGTTGTATACTACAGAACCTATACATCATTG
66 CATAATTGTTAGTATAGTATCGTTGTATACTACAGTACCTATACATCATTG
* * *
3622382 TGCCACTTAGGTGCTTATTAG
1 TGGCACTCAAGTGCTTATTAG
3622403 GTACATTGCA
Statistics
Matches: 217, Mismatches: 34, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
115 1 0.00
116 199 0.92
117 17 0.08
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (116 bp):
TGGCACTCAAGTGCTTATTAGTGCACTTTGTGTGCAAGGATGGTATTCATAATGAATTACCACTC
CATAATTGTTAGTATAGTATCGTTGTATACTACAGTACCTATACATCATTG
Found at i:3623789 original size:54 final size:54
Alignment explanation
Indices: 3623481--3623841 Score: 304
Period size: 54 Copynumber: 6.7 Consensus size: 54
3623471 CATTTTAGAT
* * * * * * **
3623481 ACCGAGT-AGCTCTAGTGTTCCTTTATTATTGAGGAGTGGACCCATACTTTTTTAAG
1 ACCGAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGA-GCA-A-ATTTCCAAG
* * * *
3623537 ACCAAGTAAGCTTTAGC-ATCTCTTTGTTAT---GGAGTAGAGCAAACTTCCAAG
1 ACCGAGTAAGCTCTAGCGTTC-CTTTGTTATGGAGGAGTAGAGCAAATTTCCAAG
* * *
3623588 ACCGACTAAGCTCTAGCGTTCCTTTGTTA--GTGGAGTAGAGCATATTTCCAAG
1 ACCGAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGCAAATTTCCAAG
* * * * *
3623640 ACAGAGTAAGCTCTAGCGTTCCTTTGTTATGGAGAAGTAGAACCATTTTCCAAG
1 ACCGAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGCAAATTTCCAAG
* * *
3623694 ACTGAGTAAGCTCTAGCGTTCCTTTGTCATGGAGGAGTAGAGGAAATTTCCAAG
1 ACCGAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGCAAATTTCCAAG
* ** * ** *
3623748 ACCGAGTAAACTCTATTGTTCCTTCGTTATGGAGGAGTAGAGCAAATTTTTATG
1 ACCGAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGCAAATTTCCAAG
* ** * * *
3623802 ACCAAGCGAGCTCTAGTGTTCCTTTTTTTATAGAGGAGTA
1 ACCGAGTAAGCTCTAGCGTTCC-TTTGTTATGGAGGAGTA
3623842 AATCACGTTA
Statistics
Matches: 247, Mismatches: 50, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
51 27 0.11
52 49 0.20
53 2 0.01
54 132 0.53
55 14 0.06
56 8 0.03
57 15 0.06
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (54 bp):
ACCGAGTAAGCTCTAGCGTTCCTTTGTTATGGAGGAGTAGAGCAAATTTCCAAG
Found at i:3640201 original size:21 final size:22
Alignment explanation
Indices: 3640177--3640217 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3640167 TTGGGATTTT
* *
3640177 TTTTCT-TCTCTTTGTGCTTTA
1 TTTTCTATCTATTTGAGCTTTA
3640198 TTTTCTATCTATTTGAGCTT
1 TTTTCTATCTATTTGAGCTT
3640218 GTACTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.10, C:0.17, G:0.10, T:0.63
Consensus pattern (22 bp):
TTTTCTATCTATTTGAGCTTTA
Found at i:3642619 original size:5 final size:5
Alignment explanation
Indices: 3642611--3642639 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3642601 TGAATCAATG
3642611 TAGTA TAGTA TAGTA TAGTA TAGTA TAGT
1 TAGTA TAGTA TAGTA TAGTA TAGTA TAGT
3642640 TATTATGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (5 bp):
TAGTA
Found at i:3644452 original size:14 final size:14
Alignment explanation
Indices: 3644435--3644461 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3644425 GCTTGTTTAT
3644435 GTTCATTTATGTTC
1 GTTCATTTATGTTC
3644449 GTTCATTTATGTT
1 GTTCATTTATGTT
3644462 AGGTTATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.15, T:0.59
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:3644457 original size:24 final size:24
Alignment explanation
Indices: 3644416--3644461 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3644406 TTAACAAGAT
*
3644416 TTTATGTTCGCTTGTTTATGTTCA
1 TTTATGTTCGCTTATTTATGTTCA
3644440 TTTATGTTCG-TTCATTTATGTT
1 TTTATGTTCGCTT-ATTTATGTT
3644462 AGGTTATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.13, C:0.11, G:0.15, T:0.61
Consensus pattern (24 bp):
TTTATGTTCGCTTATTTATGTTCA
Found at i:3648266 original size:22 final size:22
Alignment explanation
Indices: 3648241--3648282 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3648231 ATTTAGGTCC
*
3648241 TTATAT-TTATGTTTATTTTATT
1 TTATATGTTATATTT-TTTTATT
3648263 TTATATGTTATATTTTTTTA
1 TTATATGTTATATTTTTTTA
3648283 ACTGTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (22 bp):
TTATATGTTATATTTTTTTATT
Found at i:3648273 original size:17 final size:17
Alignment explanation
Indices: 3648248--3648297 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
3648238 TCCTTATATT
3648248 TATGTTTATTTTATTTTA
1 TATG-TTATTTTATTTTA
3648266 TATGTTATATTT-TTTTA
1 TATGTTAT-TTTATTTTA
*
3648283 -ACTGTTCTTTTATTT
1 TA-TGTTATTTTATTT
3648298 GTTCTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.14
17 17 0.61
18 7 0.25
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (17 bp):
TATGTTATTTTATTTTA
Found at i:3651845 original size:13 final size:13
Alignment explanation
Indices: 3651827--3651853 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3651817 CAAAGCTAGG
3651827 AGACTCCACACAC
1 AGACTCCACACAC
3651840 AGACTCCACACAC
1 AGACTCCACACAC
3651853 A
1 A
3651854 AACACTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.44, G:0.07, T:0.07
Consensus pattern (13 bp):
AGACTCCACACAC
Found at i:3663205 original size:18 final size:18
Alignment explanation
Indices: 3663182--3663216 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3663172 TCTCTGCTCT
3663182 TATTTTTCAAAATCAAAA
1 TATTTTTCAAAATCAAAA
3663200 TATTTTTCAAAATCAAA
1 TATTTTTCAAAATCAAA
3663217 GATCGACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
TATTTTTCAAAATCAAAA
Found at i:3666351 original size:12 final size:11
Alignment explanation
Indices: 3666327--3666367 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
3666317 AATTCCGTTA
*
3666327 TATTTTTATTT
1 TATTTTTTTTT
3666338 TATTTTTTTGTT
1 TATTTTTTT-TT
3666350 TATTTTTTATTT
1 TATTTTTT-TTT
3666362 TATTTT
1 TATTTT
3666368 ATTTCAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 8 0.30
12 18 0.67
13 1 0.04
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (11 bp):
TATTTTTTTTT
Found at i:3666362 original size:17 final size:17
Alignment explanation
Indices: 3666330--3666371 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3666320 TCCGTTATAT
3666330 TTTTATTTTATTTTTT-
1 TTTTATTTTATTTTTTA
3666346 TGTTTATTTT-TTATTTTA
1 T-TTTATTTTATT-TTTTA
3666364 TTTTATTT
1 TTTTATTT
3666372 CAATTAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTATTTTATTTTTTA
Found at i:3668504 original size:7 final size:7
Alignment explanation
Indices: 3668492--3668516 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3668482 TTGAGTGATT
3668492 TGAGTAA
1 TGAGTAA
3668499 TGAGTAA
1 TGAGTAA
3668506 TGAGTAA
1 TGAGTAA
3668513 TGAG
1 TGAG
3668517 CATTGAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (7 bp):
TGAGTAA
Found at i:3671331 original size:26 final size:26
Alignment explanation
Indices: 3671292--3671359 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
3671282 TCAAGTTGAC
* * *
3671292 AAAACAGAAAAGAAACATAAAAAAGG
1 AAAAAAGAAGAGAAACAGAAAAAAGG
*
3671318 AAAAAAGAAGAGAAAGAGAAAAAAGG
1 AAAAAAGAAGAGAAACAGAAAAAAGG
* *
3671344 GAAGAAGATAGAGAAA
1 AAAAAAGA-AGAGAAA
3671360 AAGAGAAAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
26 28 0.80
27 7 0.20
ACGTcount: A:0.71, C:0.03, G:0.24, T:0.03
Consensus pattern (26 bp):
AAAAAAGAAGAGAAACAGAAAAAAGG
Found at i:3671340 original size:27 final size:28
Alignment explanation
Indices: 3671310--3671416 Score: 85
Period size: 29 Copynumber: 3.7 Consensus size: 28
3671300 AAAGAAACAT
3671310 AAAAAAGGAAAA-AAGAAGAGAAAGAGA
1 AAAAAAGGAAAAGAAGAAGAGAAAGAGA
* *
3671337 AAAAAGGGAAGAAGATAG-AGAAAAAGAGA
1 AAAAAAGGAA-AAGA-AGAAGAGAAAGAGA
* * *
3671366 AAGCAACA-GAAAAGAAAGAAAAAGAAAAAGA
1 AA--AAAAGGAAAAG-AAG-AAGAGAAAGAGA
*
3671397 AAGAAAGGAAAAGAAGAAGA
1 AAAAAAGGAAAAGAAGAAGA
3671417 AATAAAACAA
Statistics
Matches: 61, Mismatches: 10, Indels: 17
0.69 0.11 0.19
Matches are distributed among these distances:
27 9 0.15
28 5 0.08
29 23 0.38
30 12 0.20
31 12 0.20
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.01
Consensus pattern (28 bp):
AAAAAAGGAAAAGAAGAAGAGAAAGAGA
Found at i:3671341 original size:20 final size:20
Alignment explanation
Indices: 3671318--3671418 Score: 53
Period size: 21 Copynumber: 4.8 Consensus size: 20
3671308 ATAAAAAAGG
3671318 AAAAAAGAAGAGAAAGAGAA
1 AAAAAAGAAGAGAAAGAGAA
** *
3671338 AAAAGGGAAGAAGATAGAGAAA
1 AAAAAAGAAG-AGAAAGAG-AA
*
3671360 AAGAGAAAGCAACAGAAA-AGAA
1 AA-A-AAAG-AAGAGAAAGAGAA
*
3671382 AGAAAAAGAAAAAGAAAGA-AA
1 A-AAAAAG-AAGAGAAAGAGAA
**
3671403 GGAAAAGAAGAAGAAA
1 AAAAAAGAAG-AGAAA
3671419 TAAAACAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
19 2 0.03
20 18 0.30
21 20 0.33
22 9 0.15
23 4 0.07
24 6 0.10
25 2 0.03
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.01
Consensus pattern (20 bp):
AAAAAAGAAGAGAAAGAGAA
Found at i:3671358 original size:21 final size:18
Alignment explanation
Indices: 3671313--3671416 Score: 71
Period size: 16 Copynumber: 5.9 Consensus size: 18
3671303 GAAACATAAA
3671313 AAAG-GAAAAAAGAAGAG
1 AAAGAGAAAAAAGAAGAG
3671330 AAAGAGAAAAAAGGGAAGAAG
1 AAAGAGAAAAAA--GAAG-AG
*
3671351 ATAGAGAAAAAGAGAA-AG
1 AAAGAGAAAAA-AGAAGAG
* *
3671369 CAACAG--AAAAGAA-AG
1 AAAGAGAAAAAAGAAGAG
*
3671384 AAAAAG-AAAAAGAA-AG
1 AAAGAGAAAAAAGAAGAG
3671400 AAAG-GAAAAGAAGAAGA
1 AAAGAGAAAA-AAGAAGA
3671417 AATAAAACAA
Statistics
Matches: 71, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
15 11 0.15
16 18 0.25
17 9 0.13
18 13 0.18
20 7 0.10
21 12 0.17
22 1 0.01
ACGTcount: A:0.70, C:0.02, G:0.27, T:0.01
Consensus pattern (18 bp):
AAAGAGAAAAAAGAAGAG
Found at i:3673709 original size:42 final size:41
Alignment explanation
Indices: 3673649--3673759 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 41
3673639 TTCAAGGGTT
*
3673649 TCATGATGAGTAAGTCCTTCGGGCCATC-AGTAAATCTTTCGA
1 TCATGATGA-TAAGTCCTTCGGGCCATCTA-TAAATCTTTCAA
* * * * *
3673691 TCATGATGTTTAAATCCTTCGAGTCATCTATAAGTCTTTCAA
1 TCATGATG-ATAAGTCCTTCGGGCCATCTATAAATCTTTCAA
*
3673733 GCATGATGATAAGTCCTTCGGGCCATC
1 TCATGATGATAAGTCCTTCGGGCCATC
3673760 CATAGGACCT
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
41 15 0.27
42 40 0.71
43 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (41 bp):
TCATGATGATAAGTCCTTCGGGCCATCTATAAATCTTTCAA
Found at i:3674048 original size:59 final size:59
Alignment explanation
Indices: 3673954--3674065 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 59
3673944 ACGAGCAATG
* *
3673954 CCCACCAGAGGCGATAACATTTCCTTCACTCGATTCACATCATTTCGAATCAGTGAAGC
1 CCCACCAGAGGCGATAACATTTCCTTCACTCGATTCACAACATTTCAAATCAGTGAAGC
* * * * ** *
3674013 CCCACCAGAGGGGTTAACTTTTTCTTTGCTCGATTCATAACATTTCAAATCAG
1 CCCACCAGAGGCGATAACATTTCCTTCACTCGATTCACAACATTTCAAATCAG
3674066 CGATGCCTCA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 44 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (59 bp):
CCCACCAGAGGCGATAACATTTCCTTCACTCGATTCACAACATTTCAAATCAGTGAAGC
Found at i:3674272 original size:59 final size:59
Alignment explanation
Indices: 3674197--3674343 Score: 190
Period size: 59 Copynumber: 2.5 Consensus size: 59
3674187 TTCTTTATTT
* *
3674197 GATTCATAACACTTCGAATTAGCAATGCCCCACCAGAGAGGATAACATTT-CTATTCCTC
1 GATTCACAACACTTCGAATCAGCAATGCCCCACCAGAGAGGATAACATTTACT-TTCCTC
* * *
3674256 GATTCACAACACTTCGAATCATCAATGCCCCACCAGAGGGGATAACATTTACTTTGCTC
1 GATTCACAACACTTCGAATCAGCAATGCCCCACCAGAGAGGATAACATTTACTTTCCTC
* * *
3674315 GATTCA-AGACATTTTGAATCAGTAATGCC
1 GATTCACA-ACACTTCGAATCAGCAATGCC
3674344 TCACTTGAGG
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
58 1 0.01
59 74 0.96
60 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (59 bp):
GATTCACAACACTTCGAATCAGCAATGCCCCACCAGAGAGGATAACATTTACTTTCCTC
Found at i:3674403 original size:39 final size:39
Alignment explanation
Indices: 3674360--3674514 Score: 265
Period size: 39 Copynumber: 4.0 Consensus size: 39
3674350 GAGGGATCAA
* * *
3674360 TATCTCGTTTGAGATAGTTTCACTCGAAATAGAAGATTT
1 TATCTCGCTTGAGATAGGTTCACTCGAAACAGAAGATTT
* *
3674399 TATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTT
1 TATCTCGCTTGAGATAGGTTCACTCGAAACAGAAGATTT
3674438 TATCTCGCTTGAGATAGGTTCACTCGAAACAGAAGATTT
1 TATCTCGCTTGAGATAGGTTCACTCGAAACAGAAGATTT
3674477 TATCTCGCTTGAGATAGGTTCACTCGAAACAGAAGATT
1 TATCTCGCTTGAGATAGGTTCACTCGAAACAGAAGATT
3674515 GATTTCACTT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 112 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (39 bp):
TATCTCGCTTGAGATAGGTTCACTCGAAACAGAAGATTT
Found at i:3674643 original size:59 final size:58
Alignment explanation
Indices: 3674551--3674694 Score: 191
Period size: 59 Copynumber: 2.4 Consensus size: 58
3674541 AAACAAAATG
* * * *
3674551 TGCCTCACTTGAGGGATTAACATTTACTTTGCTCGATTCATAATA-TTTCGAATCAGTGA
1 TGCCTCACATGAGGGATCAACATTT-CTTTGCTCGATTCATAACACTTT-GAATCAGCGA
3674610 TGCCTCACATGAGGGATCAACATTTCGTTTGCTCGATTCATAACACTTTGAATCAGCGA
1 TGCCTCACATGAGGGATCAACATTTC-TTTGCTCGATTCATAACACTTTGAATCAGCGA
* * *
3674669 CGCCTCACATGAGGGACCAATATTTC
1 TGCCTCACATGAGGGATCAACATTTC
3674695 CAGTAGAGAA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
58 1 0.01
59 72 0.95
60 3 0.04
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (58 bp):
TGCCTCACATGAGGGATCAACATTTCTTTGCTCGATTCATAACACTTTGAATCAGCGA
Found at i:3676239 original size:15 final size:13
Alignment explanation
Indices: 3676214--3676278 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
3676204 GGTCCTTGTA
3676214 TTTATGTT-TTTT
1 TTTATGTTATTTT
* *
3676226 TTATTTTTTATTTT
1 TT-TATGTTATTTT
3676240 TTTATGTTATTTT
1 TTTATGTTATTTT
*
3676253 TTTACTGTTCTTTT
1 TTTA-TGTTATTTT
*
3676267 ATT-TGTTATTTT
1 TTTATGTTATTTT
3676279 AATTATTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
12 10 0.23
13 17 0.40
14 16 0.37
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.78
Consensus pattern (13 bp):
TTTATGTTATTTT
Found at i:3677072 original size:20 final size:20
Alignment explanation
Indices: 3677043--3677094 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3677033 AGGTAAGGGA
3677043 AGTATCGATACTCACTGGGT
1 AGTATCGATACTCACTGGGT
*
3677063 AGTTTCGATACTCACTGGGT
1 AGTATCGATACTCACTGGGT
3677083 AGTATCGATACT
1 AGTATCGATACT
3677095 ACCAGCAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTCACTGGGT
Found at i:3679079 original size:19 final size:19
Alignment explanation
Indices: 3679045--3679092 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
3679035 AATGATTTGG
3679045 TTTTGAAAACAAAAATTG-A
1 TTTTGAAAACAAAAA-TGAA
3679064 TTTTGAAAATC-AAAATGAAA
1 TTTTGAAAA-CAAAAATG-AA
3679084 TTTTGAAAA
1 TTTTGAAAA
3679093 ATGATTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 11 0.42
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.33
Consensus pattern (19 bp):
TTTTGAAAACAAAAATGAA
Found at i:3680494 original size:40 final size:40
Alignment explanation
Indices: 3680434--3680517 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
3680424 AAGTAGTACC
*
3680434 GATAATGTTCTTATAGTATCGATACCTCA-TGAACAGTATT
1 GATAATGTTCATATAGTATCGATA-CTCACTGAACAGTATT
* * **
3680474 GATATTGTTCATATGGTATCGATACTCACTGAGTAGTATT
1 GATAATGTTCATATAGTATCGATACTCACTGAACAGTATT
3680514 GATA
1 GATA
3680518 CTACCAGCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 4 0.11
40 34 0.89
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (40 bp):
GATAATGTTCATATAGTATCGATACTCACTGAACAGTATT
Found at i:3680860 original size:18 final size:18
Alignment explanation
Indices: 3680834--3680877 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3680824 GTGAAGTATG
*
3680834 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGTCGTGGCA
*
3680852 AATGTTGTTGTCGTGGTA
1 AATGTTGTTGTCGTGGCA
*
3680870 AGTGTTGT
1 AATGTTGT
3680878 AAGGTAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.41
Consensus pattern (18 bp):
AATGTTGTTGTCGTGGCA
Found at i:3687263 original size:18 final size:18
Alignment explanation
Indices: 3687237--3687280 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3687227 GTGAAGTTAT
* *
3687237 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGTCATGGCA
*
3687255 AATGTTGTTGTCATGGTA
1 AATGTTGTTGTCATGGCA
*
3687273 AGTGTTGT
1 AATGTTGT
3687281 AAGGTTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.07, G:0.34, T:0.41
Consensus pattern (18 bp):
AATGTTGTTGTCATGGCA
Found at i:3687970 original size:12 final size:12
Alignment explanation
Indices: 3687949--3687978 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3687939 ACATGCATAA
*
3687949 AATTCGCGTAAC
1 AATTCCCGTAAC
3687961 AATTCCCGTAAC
1 AATTCCCGTAAC
3687973 AATTCC
1 AATTCC
3687979 AGCCTGCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.27
Consensus pattern (12 bp):
AATTCCCGTAAC
Found at i:3691204 original size:57 final size:57
Alignment explanation
Indices: 3691118--3691230 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 57
3691108 TGATTGGGAT
** * * *
3691118 TTAAAGGCCTAAGTTGGTTGCAAATACATATGATGATTTTTTGTTGATTTTTATATA
1 TTAAAGGCCTAAGTTAATTGCAAACACATATGATGATTTTGTGTTGATTTCTATATA
* *
3691175 TTAAAGGTCTAAGTTAATTGTAAACACATATGATGATTTTGTGTTGATTTCTATAT
1 TTAAAGGCCTAAGTTAATTGCAAACACATATGATGATTTTGTGTTGATTTCTATAT
3691231 TCATATATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (57 bp):
TTAAAGGCCTAAGTTAATTGCAAACACATATGATGATTTTGTGTTGATTTCTATATA
Found at i:3692343 original size:32 final size:31
Alignment explanation
Indices: 3692307--3692379 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 31
3692297 ATCGGGTCAC
3692307 TTTTCAGGTTGGGTGATTATCGAATCAGTTGT
1 TTTTC-GGTTGGGTGATTATCGAATCAGTTGT
*
3692339 TTTTCGGGTTGGGTGATTATCGAATTAGTTGT
1 TTTTC-GGTTGGGTGATTATCGAATCAGTTGT
3692371 TTTTCGGTT
1 TTTTCGGTT
3692380 CAGATCAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 4 0.10
32 35 0.90
ACGTcount: A:0.15, C:0.08, G:0.29, T:0.48
Consensus pattern (31 bp):
TTTTCGGTTGGGTGATTATCGAATCAGTTGT
Found at i:3692520 original size:32 final size:32
Alignment explanation
Indices: 3692429--3692521 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 32
3692419 ATATCAGGTT
* * *
3692429 GGGTCAATATCGGATAGGTTGATTTTTGGGTC
1 GGGTCAATATCGGATCGATTGATTTTCGGGTC
* * * * * *
3692461 AGGTTAACACCGAATCGTTTAGA-TTTCGGGTC
1 GGGTCAATATCGGATCGATT-GATTTTCGGGTC
3692493 GGGTCAATATCGGATCGATTGATTTTCGG
1 GGGTCAATATCGGATCGATTGATTTTCGG
3692522 TTTGAGTCAA
Statistics
Matches: 45, Mismatches: 14, Indels: 4
0.71 0.22 0.06
Matches are distributed among these distances:
31 2 0.04
32 41 0.91
33 2 0.04
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (32 bp):
GGGTCAATATCGGATCGATTGATTTTCGGGTC
Found at i:3693236 original size:130 final size:130
Alignment explanation
Indices: 3692973--3693207 Score: 382
Period size: 130 Copynumber: 1.8 Consensus size: 130
3692963 TTTTAGTTGT
3692973 TTTCTATTATTTTTATTATAAATCTAATATTTTTTATTACAAGTAAGATAAGTAAACTTTATTTG
1 TTTCTATTATTTTTATTATAAATCTAATATTTTTTATTACAAGTAAGATAAGTAAACTTTATTTG
* * * * ** *
3693038 TTATTGTTTTTAATCTTACAATAAGATTCTTATTTTTATATTCCTCTAATCTAACACAAGTAAAC
66 TTACTATTTTCAATCTTACAATAAGATCCTTATTTCGATATTCCTCTAATCTAACACAAGGAAAC
3693103 TTTCTATTATTTTTTATTATAAATCTAATA-TTTTTATTACAAGTAAGATAAGTAAACTTTATTT
1 TTTCTATTA-TTTTTATTATAAATCTAATATTTTTTATTACAAGTAAGATAAGTAAACTTTATTT
3693167 GTTACTATTTTCAATCTTACAATAAGATCCTTAATTTCGAT
65 GTTACTATTTTCAATCTTACAATAAGATCCTT-ATTTCGAT
3693208 TTGGGTTAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
130 71 0.73
131 26 0.27
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (130 bp):
TTTCTATTATTTTTATTATAAATCTAATATTTTTTATTACAAGTAAGATAAGTAAACTTTATTTG
TTACTATTTTCAATCTTACAATAAGATCCTTATTTCGATATTCCTCTAATCTAACACAAGGAAAC
Found at i:3693315 original size:33 final size:32
Alignment explanation
Indices: 3693278--3693378 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 32
3693268 CAGATCAGGA
3693278 TAAAATTCAATTCATATTTCTTTTGGTTCGGGT
1 TAAAATTCAATTCA-ATTTCTTTTGGTTCGGGT
* * *
3693311 TAAAATTCAGTTCAGATTTCTTTAGGTTTGGGT
1 TAAAATTCAATTCA-ATTTCTTTTGGTTCGGGT
* * * *
3693344 T-AATTTCGATTCGAATTTCTTTTGATTCAGGT
1 TAAAATTCAATTC-AATTTCTTTTGGTTCGGGT
3693376 TAA
1 TAA
3693379 TTTCGGTTCG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
32 23 0.42
33 32 0.58
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.48
Consensus pattern (32 bp):
TAAAATTCAATTCAATTTCTTTTGGTTCGGGT
Found at i:3693398 original size:16 final size:16
Alignment explanation
Indices: 3693379--3693462 Score: 78
Period size: 16 Copynumber: 5.2 Consensus size: 16
3693369 TTCAGGTTAA
3693379 TTTCGGTTCGGGTTGC
1 TTTCGGTTCGGGTTGC
* * * **
3693395 TTTCGATTTGGATTAA
1 TTTCGGTTCGGGTTGC
**
3693411 TTTCAATTCGGGTTGC
1 TTTCGGTTCGGGTTGC
* **
3693427 TTTCGGTTAGGGTTAA
1 TTTCGGTTCGGGTTGC
3693443 TTTCGGTTCGGGTTGC
1 TTTCGGTTCGGGTTGC
3693459 TTTC
1 TTTC
3693463 AGTTTCGCTA
Statistics
Matches: 50, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.11, C:0.14, G:0.29, T:0.46
Consensus pattern (16 bp):
TTTCGGTTCGGGTTGC
Found at i:3693411 original size:32 final size:32
Alignment explanation
Indices: 3693343--3693462 Score: 134
Period size: 32 Copynumber: 3.8 Consensus size: 32
3693333 TAGGTTTGGG
* ** * *
3693343 TTAATTTCGATTCGAATTTCTTTTGATTCAGG-
1 TTAATTTCGGTTCGGGTTGCTTTCGATT-AGGA
*
3693375 TTAATTTCGGTTCGGGTTGCTTTCGATTTGGA
1 TTAATTTCGGTTCGGGTTGCTTTCGATTAGGA
** * *
3693407 TTAATTTCAATTCGGGTTGCTTTCGGTTAGGG
1 TTAATTTCGGTTCGGGTTGCTTTCGATTAGGA
3693439 TTAATTTCGGTTCGGGTTGCTTTC
1 TTAATTTCGGTTCGGGTTGCTTTC
3693463 AGTTTCGCTA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
31 2 0.03
32 72 0.97
ACGTcount: A:0.15, C:0.13, G:0.24, T:0.47
Consensus pattern (32 bp):
TTAATTTCGGTTCGGGTTGCTTTCGATTAGGA
Found at i:3693420 original size:64 final size:64
Alignment explanation
Indices: 3693201--3693462 Score: 208
Period size: 64 Copynumber: 4.1 Consensus size: 64
3693191 AGATCCTTAA
* * * * * *
3693201 TTTCGATTTGGGTTAATTTTC-ATTCGGATTGCTTTCAGG-TCGGGTTAAATTCGGTTCTGGTTG
1 TTTCGATTTGGATTAA-TTTCAATTCGAATTTCTTT-TGGTTCAGGTTAAATTCGGTTCGGGTTG
3693264 C
64 C
** * * * * * *
3693265 TTTCAGATCAGGATAAAATTCAATTC-ATATTTCTTTTGGTTCGGGTTAAAATTCAGTTCAGATT
1 TTTC-GATTTGGATTAATTTCAATTCGA-ATTTCTTTTGGTTCAGGTT-AAATTCGGTTCGGGTT
*
3693329 TC
63 GC
* * * * * *
3693331 TTTAGGTTTGGGTTAATTTCGATTCGAATTTCTTTTGATTCAGGTTAATTTCGGTTCGGGTTGC
1 TTTCGATTTGGATTAATTTCAATTCGAATTTCTTTTGGTTCAGGTTAAATTCGGTTCGGGTTGC
** * * *
3693395 TTTCGATTTGGATTAATTTCAATTCGGGTTGCTTTCGGTT-AGGGTTAATTTCGGTTCGGGTTGC
1 TTTCGATTTGGATTAATTTCAATTCGAATTTCTTTTGGTTCA-GGTTAAATTCGGTTCGGGTTGC
3693459 TTTC
1 TTTC
3693463 AGTTTCGCTA
Statistics
Matches: 155, Mismatches: 36, Indels: 14
0.76 0.18 0.07
Matches are distributed among these distances:
63 1 0.01
64 79 0.51
65 57 0.37
66 18 0.12
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (64 bp):
TTTCGATTTGGATTAATTTCAATTCGAATTTCTTTTGGTTCAGGTTAAATTCGGTTCGGGTTGC
Found at i:3699419 original size:4 final size:4
Alignment explanation
Indices: 3699399--3699433 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
3699389 TTGGATTTGA
* *
3699399 AAAT GAAT AATT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3699434 ACTTTTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
AAAT
Done.