Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 64
Found at i:3685913 original size:13 final size:13
Alignment explanation
Indices: 3685895--3685919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3685885 GAAAGGAATC
3685895 TAAATTTAAAGAG
1 TAAATTTAAAGAG
3685908 TAAATTTAAAGA
1 TAAATTTAAAGA
3685920 TAAGATAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
TAAATTTAAAGAG
Found at i:3686226 original size:14 final size:14
Alignment explanation
Indices: 3686207--3686238 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3686197 ATTTAAGGAA
3686207 AAAATTGAAATAAC
1 AAAATTGAAATAAC
3686221 AAAATTGAAATAAC
1 AAAATTGAAATAAC
3686235 AAAA
1 AAAA
3686239 ATTAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAATTGAAATAAC
Found at i:3686249 original size:16 final size:14
Alignment explanation
Indices: 3686207--3686256 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
3686197 ATTTAAGGAA
*
3686207 AAAATTGAAATAAC
1 AAAATTAAAATAAC
*
3686221 AAAATTGAAATAAC
1 AAAATTAAAATAAC
3686235 AAAAATTAAAAATAAC
1 -AAAATT-AAAATAAC
3686251 GAAAAT
1 -AAAAT
3686257 AAACCAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 14 0.44
15 6 0.19
16 12 0.38
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.20
Consensus pattern (14 bp):
AAAATTAAAATAAC
Found at i:3687435 original size:75 final size:75
Alignment explanation
Indices: 3687349--3687493 Score: 281
Period size: 75 Copynumber: 1.9 Consensus size: 75
3687339 CTAAACCCAA
3687349 AACAAAGCCCTATATCAACAAGCAAGCTTCGACCGGCCAAAGAGACTCGAACGACCCCCTTAAAG
1 AACAAAGCCCTATATCAACAAGCAAGCTTCGACCGGCCAAAGAGACTCGAACGACCCCCTTAAAG
3687414 CAAGGCTTTT
66 CAAGGCTTTT
*
3687424 AACAAAGCCCTATATCAACATGCAAGCTTCGACCGGCCAAAGAGACTCGAACGACCCCCTTAAAG
1 AACAAAGCCCTATATCAACAAGCAAGCTTCGACCGGCCAAAGAGACTCGAACGACCCCCTTAAAG
3687489 CAAGG
66 CAAGG
3687494 TAAAAAAAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.37, C:0.31, G:0.18, T:0.14
Consensus pattern (75 bp):
AACAAAGCCCTATATCAACAAGCAAGCTTCGACCGGCCAAAGAGACTCGAACGACCCCCTTAAAG
CAAGGCTTTT
Found at i:3688523 original size:20 final size:20
Alignment explanation
Indices: 3688498--3688546 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
3688488 TTATATTATA
3688498 TTTTCGAGTTGTTCATGAGC
1 TTTTCGAGTTGTTCATGAGC
*
3688518 TTTTCGAGTTGTTCATGAGT
1 TTTTCGAGTTGTTCATGAGC
3688538 TTTTCGAGT
1 TTTTCGAGT
3688547 CGAATATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.49
Consensus pattern (20 bp):
TTTTCGAGTTGTTCATGAGC
Found at i:3691261 original size:103 final size:102
Alignment explanation
Indices: 3691149--3691364 Score: 317
Period size: 103 Copynumber: 2.1 Consensus size: 102
3691139 CATTTCATGA
* *
3691149 GAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAACTTTGTGTTCCAAGAGAAACTATCTCAAG
1 GAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTCCAAGAGAAAATATCTCAAG
**
3691214 CAAGATAG-AATTTGTTTTAAAAAAAAACAATCTCAAGT
66 CAAGA-AGAAATTAATTTT-AAAAAAAACAATCTCAAGT
* *
3691252 GAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGAGAAAATGTCTCAAG
1 GAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTCCAAGAGAAAATATCTCAAG
* * **
3691317 CGAGACGAAATTAATTTTATGAAAAACAATCTCAAGT
66 CAAGAAGAAATTAATTTTAAAAAAAACAATCTCAAGT
3691354 GAGATAAAATT
1 GAGATAAAATT
3691365 CATCATATTA
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
102 29 0.28
103 73 0.72
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (102 bp):
GAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTCCAAGAGAAAATATCTCAAG
CAAGAAGAAATTAATTTTAAAAAAAACAATCTCAAGT
Found at i:3693664 original size:30 final size:30
Alignment explanation
Indices: 3693628--3693685 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3693618 TATTAGTATG
3693628 TGAAAATGCTATACGAGAATATGTTCTACA
1 TGAAAATGCTATACGAGAATATGTTCTACA
* * * *
3693658 TGAAAATGTTCTATGGGAATATGTTCTA
1 TGAAAATGCTATACGAGAATATGTTCTA
3693686 TGTGAATGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (30 bp):
TGAAAATGCTATACGAGAATATGTTCTACA
Found at i:3693681 original size:15 final size:15
Alignment explanation
Indices: 3693644--3693708 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
3693634 TGCTATACGA
**
3693644 GAATATGTTCTACAT
1 GAATATGTTCTATGT
* *
3693659 GAAAATGTTCTATGG
1 GAATATGTTCTATGT
3693674 GAATATGTTCTATGT
1 GAATATGTTCTATGT
* *
3693689 GAATGTGTTTTATGT
1 GAATATGTTCTATGT
3693704 GAATA
1 GAATA
3693709 AATGATGCTT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (15 bp):
GAATATGTTCTATGT
Found at i:3699716 original size:15 final size:15
Alignment explanation
Indices: 3699694--3699769 Score: 71
Period size: 15 Copynumber: 5.1 Consensus size: 15
3699684 TAACGTGAAA
3699694 ATGTTCTATGGGAAT
1 ATGTTCTATGGGAAT
* * * *
3699709 AGGTTCTACGTGAAA
1 ATGTTCTATGGGAAT
*
3699724 ATGTTATATGGGAAT
1 ATGTTCTATGGGAAT
*
3699739 ATGTTCTATGTGAAT
1 ATGTTCTATGGGAAT
* * *
3699754 TTGTTTTATGTGAAT
1 ATGTTCTATGGGAAT
3699769 A
1 A
3699770 AATGATACTT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.42
Consensus pattern (15 bp):
ATGTTCTATGGGAAT
Found at i:3699769 original size:30 final size:30
Alignment explanation
Indices: 3699686--3699752 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
3699676 TTTTCTTATA
*
3699686 ACGTGAAAATGTTCTATGGGAATAGGTTCT
1 ACGTGAAAATGTTATATGGGAATAGGTTCT
*
3699716 ACGTGAAAATGTTATATGGGAATATGTTCT
1 ACGTGAAAATGTTATATGGGAATAGGTTCT
*
3699746 ATGTGAA
1 ACGTGAA
3699753 TTTGTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.34
Consensus pattern (30 bp):
ACGTGAAAATGTTATATGGGAATAGGTTCT
Found at i:3699899 original size:23 final size:23
Alignment explanation
Indices: 3699872--3699933 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
3699862 GAGTCGAGGG
*
3699872 TTCTACGTGATCCTTCGAGACAA
1 TTCTACGTGGTCCTTCGAGACAA
** *
3699895 TTCTATATGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGAGACAA
*
3699918 TTCTACGCGGTCCTTC
1 TTCTACGTGGTCCTTC
3699934 AGGACCAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGAGACAA
Found at i:3699938 original size:23 final size:22
Alignment explanation
Indices: 3699872--3699956 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 22
3699862 GAGTCGAGGG
*
3699872 TTCTACGTGATCCTTCGAGACAA
1 TTCTACGTGGTCCTTCG-GACAA
**
3699895 TTCTATATGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTC-GGACAA
*
3699918 TTCTACGCGGTCCTTCAGGACCAA
1 TTCTACGTGGTCCTTC-GGA-CAA
* *
3699942 -TCTATGTGGTACTTC
1 TTCTACGTGGTCCTTC
3699957 AGTGCATATT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
23 46 0.92
24 4 0.08
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (22 bp):
TTCTACGTGGTCCTTCGGACAA
Found at i:3699971 original size:24 final size:24
Alignment explanation
Indices: 3699942--3699995 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3699932 TCAGGACCAA
* * *
3699942 TCTATGTGGTACTTCAGTGCATAT
1 TCTATGTGGCACTTCACTGCAAAT
*
3699966 TCTATGTGGCACTTCACTGTAAAT
1 TCTATGTGGCACTTCACTGCAAAT
3699990 TCTATG
1 TCTATG
3699996 CGATAGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TCTATGTGGCACTTCACTGCAAAT
Found at i:3701630 original size:31 final size:30
Alignment explanation
Indices: 3701592--3701661 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
3701582 CTTTCGTTCA
3701592 TTTTTTTC-CATTTTTTCTCTT-ATTCTTTCTT
1 TTTTTTTCTC-TTTTTTCT-TTCATTCTTT-TT
3701623 TTTTTTTCTCTTTTTTCTTTCATTCTTTTT
1 TTTTTTTCTCTTTTTTCTTTCATTCTTTTT
*
3701653 TTTTCTTCT
1 TTTTTTTCT
3701662 TATTATTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 12 0.33
31 23 0.64
32 1 0.03
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTTTTCTCTTTTTTCTTTCATTCTTTTT
Found at i:3701661 original size:13 final size:13
Alignment explanation
Indices: 3701618--3701662 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
3701608 CTCTTATTCT
3701618 TTCTTTTTTTTTC
1 TTCTTTTTTTTTC
3701631 -TCTTTTTTCTTTC
1 TTCTTTTTT-TTTC
3701644 ATTCTTTTTTTTTC
1 -TTCTTTTTTTTTC
3701658 TTCTT
1 TTCTT
3701663 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.28
13 9 0.31
14 4 0.14
15 8 0.28
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Found at i:3701689 original size:16 final size:16
Alignment explanation
Indices: 3701670--3701700 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3701660 CTTATTATTT
*
3701670 TTTATTTTCTCTTTTC
1 TTTATTTTCACTTTTC
3701686 TTTATTTTCACTTTT
1 TTTATTTTCACTTTT
3701701 TTTCTCTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTTCACTTTTC
Found at i:3701690 original size:23 final size:23
Alignment explanation
Indices: 3701602--3701693 Score: 84
Period size: 23 Copynumber: 4.0 Consensus size: 23
3701592 TTTTTTTCCA
*
3701602 TTTTTTCTCTTATTCTTT-CTTT
1 TTTTTTCTCTTATTCTTTATTTT
*
3701624 TTTTTTCTCTTTTTTCTTTCATTCTT
1 TTTTTTCTC-TTATTCTTT-ATT-TT
* *
3701650 TTTTTT-TCTTCTT-ATTATTTT
1 TTTTTTCTCTTATTCTTTATTTT
3701671 TTATTTTCTCTT-TTCTTTATTTT
1 TT-TTTTCTCTTATTCTTTATTTT
3701694 CACTTTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.07
22 18 0.31
23 21 0.36
24 4 0.07
25 3 0.05
26 8 0.14
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTTCTCTTATTCTTTATTTT
Found at i:3701702 original size:50 final size:49
Alignment explanation
Indices: 3701602--3701703 Score: 111
Period size: 50 Copynumber: 2.1 Consensus size: 49
3701592 TTTTTTTCCA
* * *
3701602 TTTTTTCTCTTATTCTTTCTTTTTTTTTCTCTTTTTTCTTTCATTCTTT
1 TTTTTTCTCTTATTATTTCTTTTTTTCTCTCTTTTTTCTTTCACTCTTT
*
3701651 TTTTTTCTTCTTATTATTT-TTTATTTTCTCT-TTTCTTTATTTTCACT-TTT
1 TTTTTTC-TCTTATTATTTCTTT-TTTTCTCTCTTT-TTT-CTTTCACTCTTT
3701701 TTT
1 TTT
3701704 CTCTTCAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
49 13 0.29
50 26 0.58
51 6 0.13
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (49 bp):
TTTTTTCTCTTATTATTTCTTTTTTTCTCTCTTTTTTCTTTCACTCTTT
Found at i:3706403 original size:33 final size:32
Alignment explanation
Indices: 3706351--3706419 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
3706341 TTTTGTAAAG
*
3706351 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3706385 GGGAAAGG-TCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3706416 GGGA
1 GGGA
3706420 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 11 0.33
32 1 0.03
33 13 0.39
34 8 0.24
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3716023 original size:18 final size:18
Alignment explanation
Indices: 3715996--3716032 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3715986 ATAATTAAAA
* *
3715996 TTTTATTTAAATACTATT
1 TTTTAATTAAATAATATT
3716014 TTTTAATTAAATAATATT
1 TTTTAATTAAATAATATT
3716032 T
1 T
3716033 AAAATTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTAATTAAATAATATT
Found at i:3718861 original size:16 final size:15
Alignment explanation
Indices: 3718825--3718893 Score: 79
Period size: 15 Copynumber: 4.5 Consensus size: 15
3718815 TATTATAGTC
* *
3718825 CATATTAAATAATTT
1 CATATTATATAGTTT
3718840 CATATTATATAGTTT
1 CATATTATATAGTTT
3718855 GCATATTATATAG-TT
1 -CATATTATATAGTTT
3718870 CATATTCA-ATAGTTT
1 CATATT-ATATAGTTT
3718885 ACATATTAT
1 -CATATTAT
3718894 GGTCCATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.21
15 19 0.40
16 18 0.38
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.48
Consensus pattern (15 bp):
CATATTATATAGTTT
Found at i:3719976 original size:7 final size:7
Alignment explanation
Indices: 3719944--3719977 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3719934 CAGAGGAGCT
*
3719944 TGGTAGG
1 TGGTGGG
*
3719951 TGGTAGG
1 TGGTGGG
3719958 TGGTGGG
1 TGGTGGG
3719965 TGGTGGG
1 TGGTGGG
3719972 TGGTGG
1 TGGTGG
3719978 CTGGAGTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.06, C:0.00, G:0.65, T:0.29
Consensus pattern (7 bp):
TGGTGGG
Found at i:3722369 original size:21 final size:21
Alignment explanation
Indices: 3722345--3722384 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3722335 ACTAATATTA
* * *
3722345 AATTCAAACTTTAGCTTTTTT
1 AATTAAAACCTTAGATTTTTT
3722366 AATTAAAACCTTAGATTTT
1 AATTAAAACCTTAGATTTT
3722385 AAGTTCTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (21 bp):
AATTAAAACCTTAGATTTTTT
Found at i:3731292 original size:22 final size:22
Alignment explanation
Indices: 3731267--3731308 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3731257 ACCATATGGT
*
3731267 GCATGTTTTTCTACAAGGTGTG
1 GCATGTTTTGCTACAAGGTGTG
*
3731289 GCATGTTTTGCTGCAAGGTG
1 GCATGTTTTGCTACAAGGTG
3731309 ATACCATCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.31, T:0.38
Consensus pattern (22 bp):
GCATGTTTTGCTACAAGGTGTG
Found at i:3736335 original size:30 final size:28
Alignment explanation
Indices: 3736279--3736337 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 28
3736269 AAAAATAGAA
*
3736279 AATATAGAAAAATACAAGAAGAAAAAAG
1 AATATAGAAAAATAAAAGAAGAAAAAAG
*
3736307 AATATAGAAAAAATTAAAAGAAATAAAAAAG
1 AATATAG-AAAAA-TAAAAG-AAGAAAAAAG
3736338 GAAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.27
29 5 0.19
30 5 0.19
31 9 0.35
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.14
Consensus pattern (28 bp):
AATATAGAAAAATAAAAGAAGAAAAAAG
Found at i:3737016 original size:15 final size:15
Alignment explanation
Indices: 3736971--3737018 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
3736961 CTGCAGTTAT
3736971 AAAAG-AAAAGAAAA
1 AAAAGAAAAAGAAAA
* *
3736985 GAAAGAAAAAGAGAA
1 AAAAGAAAAAGAAAA
* *
3737000 AAAATAGAAAGAAAA
1 AAAAGAAAAAGAAAA
3737015 AAAA
1 AAAA
3737019 CCAAAATGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Found at i:3737025 original size:21 final size:21
Alignment explanation
Indices: 3736971--3737015 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3736961 CTGCAGTTAT
3736971 AAAAGA-AAAGAAA-AGAAAGA
1 AAAAGAGAAA-AAATAGAAAGA
3736991 AAAAGAGAAAAAATAGAAAGA
1 AAAAGAGAAAAAATAGAAAGA
3737012 AAAA
1 AAAA
3737016 AAACCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAGAGAAAAAATAGAAAGA
Found at i:3737169 original size:21 final size:21
Alignment explanation
Indices: 3737143--3737202 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
3737133 TGATTCCAAG
3737143 TGTGAGATGTAACCATGAAAC
1 TGTGAGATGTAACCATGAAAC
3737164 TGTGAGATGTAACCATGAAAC
1 TGTGAGATGTAACCATGAAAC
**
3737185 TGTGAGATAAAACCATGA
1 TGTGAGATGTAACCATGA
3737203 GTTGGAACCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (21 bp):
TGTGAGATGTAACCATGAAAC
Found at i:3740893 original size:2 final size:2
Alignment explanation
Indices: 3740886--3740939 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
3740876 ATTCCTCAAT
3740886 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3740927 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
3740940 TAAAACACAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3741694 original size:54 final size:54
Alignment explanation
Indices: 3741580--3742174 Score: 818
Period size: 54 Copynumber: 11.0 Consensus size: 54
3741570 GATACGATCG
* * ** ** ****
3741580 TTCATAAACATATTATGAATTTCGTGGGTTGCACAC-TTGTGCCAATACGGTCG
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* * * *
3741633 TTCATAAACTAATTATGAATTTCTTAAGCTACACACACAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* * * *
3741687 TTTATAAACTTATTATGAATTTCTTATGTTCCACACACAATGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
3741741 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* *
3741795 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCATTACAAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* * * *
3741849 TTCATAAACTTATTATTAATTTCTTAAGTTGTACA-ATTACTGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACA-CAGTGCCAATACGAAAA
*
3741903 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACAAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* * * *
3741957 TTCATAAACTTATTATTAATTTCTTAAGTTGCACA-ATTACTGCCAATACAAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACA-CAGTGCCAATACGAAAA
** *
3742011 TTCATAAACTTATTATGAATTTCTTAAGTTGCACATGCAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* *
3742065 TTCATAAACTTATTATGAATTTCTTAAGTTGCACGCACAATGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* *
3742119 TTCATAAACTTATTATGAATTTCTTAAGTTGCACGCACAATGCCAATACGGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC-GAAAA
3742174 T
1 T
3742175 ACAATACATA
Statistics
Matches: 486, Mismatches: 50, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
53 31 0.06
54 448 0.92
55 7 0.01
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (54 bp):
TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
Found at i:3743369 original size:13 final size:13
Alignment explanation
Indices: 3743349--3743382 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3743339 ATAACCCGAC
3743349 CCGACCCGTTGAT
1 CCGACCCGTTGAT
*
3743362 CTGACCCGTTGAT
1 CCGACCCGTTGAT
3743375 CCGACCCG
1 CCGACCCG
3743383 ACCCGTTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.41, G:0.24, T:0.21
Consensus pattern (13 bp):
CCGACCCGTTGAT
Found at i:3743379 original size:31 final size:31
Alignment explanation
Indices: 3743344--3743404 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
3743334 CGGTCATAAC
* *
3743344 CCGACCCGACCCGTTGATCTGACCCGTTGAT
1 CCGACCCGACCCGTTGACCCGACCCGTTGAT
3743375 CCGACCCGACCCGTTGACCCGACCCGTTGA
1 CCGACCCGACCCGTTGACCCGACCCGTTGA
3743405 CCGGCGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.43, G:0.23, T:0.18
Consensus pattern (31 bp):
CCGACCCGACCCGTTGACCCGACCCGTTGAT
Found at i:3743385 original size:18 final size:18
Alignment explanation
Indices: 3743364--3743400 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3743354 CCGTTGATCT
*
3743364 GACCCGTTGATCCGACCC
1 GACCCGTTGACCCGACCC
3743382 GACCCGTTGACCCGACCC
1 GACCCGTTGACCCGACCC
3743400 G
1 G
3743401 TTGACCGGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.46, G:0.24, T:0.14
Consensus pattern (18 bp):
GACCCGTTGACCCGACCC
Found at i:3743393 original size:13 final size:13
Alignment explanation
Indices: 3743377--3743406 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3743367 CCGTTGATCC
3743377 GACCCGACCCGTT
1 GACCCGACCCGTT
3743390 GACCCGACCCGTT
1 GACCCGACCCGTT
3743403 GACC
1 GACC
3743407 GGCGTTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3745712 original size:24 final size:24
Alignment explanation
Indices: 3745680--3745767 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
3745670 TTCTATTATA
*
3745680 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
3745704 ATATTTGACATGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
3745728 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
3745752 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
3745768 ATGTTATGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:3745783 original size:24 final size:24
Alignment explanation
Indices: 3745680--3745777 Score: 88
Period size: 24 Copynumber: 4.1 Consensus size: 24
3745670 TTCTATTATA
* * **
3745680 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTATGATATG
* * * **
3745704 ATATTTGACATGGATTCTGATCGG
1 ATACTTGACCTGGATTATGATATG
* *
3745728 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTATGATATG
*
3745752 ATACTTGACCTGGATTATGTTATG
1 ATACTTGACCTGGATTATGATATG
3745776 AT
1 AT
3745778 TTTTGATATA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTATGATATG
Found at i:3746929 original size:2 final size:2
Alignment explanation
Indices: 3746916--3746948 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3746906 ATTACTCAAT
3746916 TA TA TA -A T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3746949 TAAACACGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3747717 original size:54 final size:54
Alignment explanation
Indices: 3747686--3748062 Score: 585
Period size: 54 Copynumber: 7.0 Consensus size: 54
3747676 AATACGGTCG
* * *
3747686 TTCATAAACTAATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACTGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* *
3747740 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCTAATACAGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * * * *
3747794 TTCATAAAC-TGTTATGAATTTCTTATGTTACACACATAGTGCCAATACAGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* *
3747847 TTCATAAACTTATTATGAATTTCTTAAGTTGCTCACACAGTGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
** *
3747901 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGTAAATATGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * *
3747955 TTCATAAACTTATTATGAATTTCTTATGTTGCACACACAGTGTCAATACGTAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
3748009 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
3748063 ATACAATACA
Statistics
Matches: 294, Mismatches: 28, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
53 48 0.16
54 246 0.84
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (54 bp):
TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
Found at i:3747939 original size:161 final size:163
Alignment explanation
Indices: 3747686--3748064 Score: 615
Period size: 161 Copynumber: 2.3 Consensus size: 163
3747676 AATACGGTCG
* * *
3747686 TTCATAAACTAATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACTG-AAATTCATAAACT
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAAATTCATAAACT
*
3747750 TATTATGAATTTCTTAAGTTGCACACACAGTGCT-AATACAGAAATTCATAAAC-TGTTATGAAT
66 TATTATGAATTTCTTAAGTTGCACACACAGTG-TAAATACAGAAATTCATAAACTTATTATGAAT
*
3747813 TTCTTATGTTACACACATAGTGCCAATACAG-AAA
130 TTCTTATGTTACACACACAGTGCCAATAC-GTAAA
*
3747847 TTCATAAACTTATTATGAATTTCTTAAGTTGCTCACACAGTGCCAATAC-GAAAATTCATAAACT
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAAATTCATAAACT
**
3747911 TATTATGAATTTCTTAAGTTGCACACACAGTGTAAATATGGAAATTCATAAACTTATTATGAATT
66 TATTATGAATTTCTTAAGTTGCACACACAGTGTAAATACAGAAATTCATAAACTTATTATGAATT
* *
3747976 TCTTATGTTGCACACACAGTGTCAATACGTAAA
131 TCTTATGTTACACACACAGTGCCAATACGTAAA
3748009 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAAAT
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAAAT
3748065 ACAATACATA
Statistics
Matches: 203, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
160 2 0.01
161 109 0.54
162 86 0.42
163 6 0.03
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (163 bp):
TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAAATTCATAAACT
TATTATGAATTTCTTAAGTTGCACACACAGTGTAAATACAGAAATTCATAAACTTATTATGAATT
TCTTATGTTACACACACAGTGCCAATACGTAAA
Found at i:3754644 original size:8 final size:8
Alignment explanation
Indices: 3754633--3754715 Score: 59
Period size: 8 Copynumber: 10.5 Consensus size: 8
3754623 CCTTTTTCTA
3754633 TTTTCATT
1 TTTTCATT
3754641 TTTTCATT
1 TTTTCATT
3754649 TCTTT--TT
1 T-TTTCATT
3754656 TTAATT--TT
1 TT--TTCATT
*
3754664 TTTTCCTT
1 TTTTCATT
*
3754672 TTTTCCTT
1 TTTTCATT
3754680 TTTTCATT
1 TTTTCATT
3754688 TTTTCATCT
1 TTTTCAT-T
3754697 TTTT-ATT
1 TTTTCATT
* *
3754704 TGTTCCTT
1 TTTTCATT
3754712 TTTT
1 TTTT
3754716 TTCTTCAAGC
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
6 3 0.05
7 7 0.11
8 46 0.72
9 8 0.12
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Found at i:3754681 original size:16 final size:16
Alignment explanation
Indices: 3754662--3754715 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
3754652 TTTTTTAATT
*
3754662 TTTTTTCCTTTTTTCC
1 TTTTTTCATTTTTTCC
*
3754678 TTTTTTCATTTTTTCA
1 TTTTTTCATTTTTTCC
*
3754694 TCTTTTT-ATTTGTTCC
1 T-TTTTTCATTTTTTCC
3754710 TTTTTT
1 TTTTTT
3754716 TTCTTCAAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 5 0.15
16 23 0.70
17 5 0.15
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTTTCATTTTTTCC
Found at i:3754698 original size:26 final size:26
Alignment explanation
Indices: 3754647--3754700 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
3754637 CATTTTTTCA
* *
3754647 TTTCTTTTTTTAATTTTTTTTCCTTT
1 TTTCCTTTTTTAATTTTTTATCCTTT
*
3754673 TTTCCTTTTTTCATTTTTTCAT-CTTT
1 TTTCCTTTTTTAATTTTTT-ATCCTTT
3754699 TT
1 TT
3754701 ATTTGTTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTCCTTTTTTAATTTTTTATCCTTT
Found at i:3765475 original size:14 final size:14
Alignment explanation
Indices: 3765453--3765486 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
3765443 TAAAAACGTC
3765453 TTTT-AAAAATAAT
1 TTTTAAAAAATAAT
3765466 TTTTAGAAAAATAAT
1 TTTTA-AAAAATAAT
3765481 TTTTAA
1 TTTTAA
3765487 GACAAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 1 0.05
15 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TTTTAAAAAATAAT
Found at i:3765477 original size:15 final size:15
Alignment explanation
Indices: 3765457--3765485 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3765447 AACGTCTTTT
3765457 AAAAATAATTTTTAG
1 AAAAATAATTTTTAG
3765472 AAAAATAATTTTTA
1 AAAAATAATTTTTA
3765486 AGACAAAAGT
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:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAAAATAATTTTTAG
Found at i:3765938 original size:68 final size:69
Alignment explanation
Indices: 3765853--3765985 Score: 250
Period size: 68 Copynumber: 1.9 Consensus size: 69
3765843 AAAAATTAAC
3765853 TAAATAAAACAAATGATTATTTAACTCATGAAAATTACCATGACATTCTAATAC-AAAAATTATA
1 TAAATAAAACAAATGATTATTTAACTCATGAAAATTACCATGACATTCTAATACAAAAAATTATA
3765917 TAAT
66 TAAT
*
3765921 TAAATAAAATAAATGATTATTTAACTCATGAAAATTACCATGACATTCTAATACAAAAAATTATA
1 TAAATAAAACAAATGATTATTTAACTCATGAAAATTACCATGACATTCTAATACAAAAAATTATA
3765986 GCATTTATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
68 53 0.84
69 10 0.16
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (69 bp):
TAAATAAAACAAATGATTATTTAACTCATGAAAATTACCATGACATTCTAATACAAAAAATTATA
TAAT
Found at i:3766307 original size:23 final size:21
Alignment explanation
Indices: 3766275--3766318 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
3766265 ATGCATGGGC
3766275 TAATTAAATATAATATACTCCAA
1 TAATTAAATAT-ATATA-TCCAA
*
3766298 TAATTTAATATATATATCCAA
1 TAATTAAATATATATATCCAA
3766319 CTAAGCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
23 10 0.50
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTAAATATATATATCCAA
Found at i:3766354 original size:2 final size:2
Alignment explanation
Indices: 3766347--3766387 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3766337 AAATAAAATA
3766347 AT AT AT AT AT AT AT AT AT AT AT AT A- 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
3766388 CCAACTAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3767651 original size:3 final size:3
Alignment explanation
Indices: 3767643--3767668 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3767633 ATGATATTAG
3767643 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
3767669 TAGTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3768272 original size:15 final size:15
Alignment explanation
Indices: 3768254--3768287 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3768244 TGAGGTCCAA
*
3768254 ATTGTCCAGGTGGAT
1 ATTGTCCAGGAGGAT
*
3768269 ATTGTCCGGGAGGAT
1 ATTGTCCAGGAGGAT
3768284 ATTG
1 ATTG
3768288 GCCGTATGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.32
Consensus pattern (15 bp):
ATTGTCCAGGAGGAT
Found at i:3771058 original size:60 final size:60
Alignment explanation
Indices: 3770987--3771174 Score: 218
Period size: 60 Copynumber: 3.1 Consensus size: 60
3770977 GCATCATATG
* *
3770987 TCCTCAAACTATGATTCTCATTCTAAATTAGTCCCTAAACTTTTAAATATTTTAATTTTA
1 TCCTCAAACTATGATTCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTCAATTTTA
* * * * * *
3771047 TCCTAAAACTAT-TTTACTCATTCTAAATTAGTCCTTAAACTTCTAAACATTCCAATTTCA
1 TCCTCAAACTATGATT-CTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTCAATTTTA
** ** *
3771107 TCCTCAAACTATGACCCTCATTCTAAATT-GGGCTTCAAACTTTTAAATCTTTCAATTTTA
1 TCCTCAAACTATGATTCTCATTCTAAATTAGTCCTT-AAACTTTTAAATATTTCAATTTTA
*
3771167 TCCCCAAA
1 TCCTCAAA
3771175 TTCATACAAA
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
59 6 0.06
60 99 0.94
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (60 bp):
TCCTCAAACTATGATTCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTCAATTTTA
Found at i:3771087 original size:31 final size:31
Alignment explanation
Indices: 3770986--3771087 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 31
3770976 TGCATCATAT
* *
3770986 GTCCTCAAACTATGATT-CTCATTCTAAATTA
1 GTCCTTAAACTAT-TTTACTCATTCTAAATTA
* * * * *
3771017 GTCCCTAAACT-TTTAAAT-ATTTTAATTTTA
1 GTCCTTAAACTATTTTACTCATTCTAA-ATTA
*
3771047 -TCCTAAAACTATTTTACTCATTCTAAATTA
1 GTCCTTAAACTATTTTACTCATTCTAAATTA
3771077 GTCCTTAAACT
1 GTCCTTAAACT
3771088 TCTAAACATT
Statistics
Matches: 52, Mismatches: 14, Indels: 10
0.68 0.18 0.13
Matches are distributed among these distances:
29 15 0.29
30 13 0.25
31 24 0.46
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (31 bp):
GTCCTTAAACTATTTTACTCATTCTAAATTA
Found at i:3771098 original size:29 final size:29
Alignment explanation
Indices: 3771005--3771098 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
3770995 CTATGATTCT
*
3771005 CATTCTAAATTAGTCCCTAAACTTTTAAA
1 CATTCTAAATTAGTCCTTAAACTTTTAAA
* * * * **
3771034 TATTTTAATTTTA-TCCTAAAACTATTTTACT
1 CATTCTAA-ATTAGTCCTTAAAC--TTTTAAA
*
3771065 CATTCTAAATTAGTCCTTAAACTTCTAAA
1 CATTCTAAATTAGTCCTTAAACTTTTAAA
3771094 CATTC
1 CATTC
3771099 CAATTTCATC
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
29 22 0.47
30 6 0.13
31 19 0.40
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (29 bp):
CATTCTAAATTAGTCCTTAAACTTTTAAA
Found at i:3771391 original size:60 final size:60
Alignment explanation
Indices: 3771296--3771412 Score: 168
Period size: 60 Copynumber: 1.9 Consensus size: 60
3771286 TAGTATATAC
3771296 ATATAATTTGGGATGAAATTAAAATGTTGAAAAAGTTTGAGGACT-AATTTAGAATGAAGG
1 ATATAATTTGGGATGAAATTAAAATGTTGAAAAAGTTTGAGGA-TAAATTTAGAATGAAGG
* *
3771356 ATATAGTTTGGGGATG-AATATAAAATGTT-TAAAAGTTTGAGGATAAATTTAGAATGA
1 ATATAATTT-GGGATGAAAT-TAAAATGTTGAAAAAGTTTGAGGATAAATTTAGAATGA
3771413 TAATCATATT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
59 1 0.02
60 36 0.69
61 15 0.29
ACGTcount: A:0.43, C:0.01, G:0.23, T:0.33
Consensus pattern (60 bp):
ATATAATTTGGGATGAAATTAAAATGTTGAAAAAGTTTGAGGATAAATTTAGAATGAAGG
Found at i:3771430 original size:60 final size:60
Alignment explanation
Indices: 3771296--3771436 Score: 166
Period size: 60 Copynumber: 2.4 Consensus size: 60
3771286 TAGTATATAC
*
3771296 ATATAATTT-GGGATGAAATTAAAATGTTGAAAAAGTTTGAGGACTAATTTAGAATGAAGG
1 ATATAGTTTAGGGATGAAATTAAAATGTTGAAAAAGTTTGAGGACTAATTTAGAATGAA-G
* *
3771356 ATATAGTTTGGGGATG-AATATAAAATGTT-TAAAAGTTTGAGGA-TAAATTTAGAATGATA-
1 ATATAGTTTAGGGATGAAAT-TAAAATGTTGAAAAAGTTTGAGGACT-AATTTAGAATGA-AG
*
3771415 ATCATATTTTAGGGATGAAATT
1 AT-ATAGTTTAGGGATGAAATT
3771437 GAAGTATTTA
Statistics
Matches: 71, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
59 3 0.04
60 49 0.69
61 19 0.27
ACGTcount: A:0.42, C:0.01, G:0.22, T:0.35
Consensus pattern (60 bp):
ATATAGTTTAGGGATGAAATTAAAATGTTGAAAAAGTTTGAGGACTAATTTAGAATGAAG
Found at i:3771447 original size:60 final size:59
Alignment explanation
Indices: 3771296--3771466 Score: 147
Period size: 60 Copynumber: 2.9 Consensus size: 59
3771286 TAGTATATAC
* * *
3771296 ATATAATTT-GGGATGAA-ATTAAAATGTTGAAAAAGTTTGAGGACT-AATTTAGAATGAAGG
1 ATATAGTTTAGGGATGAATA-TAAAATATT-TAAAAGTTTGAGGA-TAAATTTAGAATGAA-G
* *
3771356 ATATAGTTTGGGGATGAATATAAAATGTTTAAAAGTTTGAGGATAAATTTAGAATGATA-
1 ATATAGTTTAGGGATGAATATAAAATATTTAAAAGTTTGAGGATAAATTTAGAATGA-AG
* * * *
3771415 ATCATATTTTAGGGATGAA-ATTGAAGTATTTAAAAGTTT-ATGAATAAATTTA
1 AT-ATAGTTTAGGGATGAATA-TAAAATATTTAAAAGTTTGA-GGATAAATTTA
3771467 AAAAGAGTAT
Statistics
Matches: 96, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
59 5 0.05
60 72 0.75
61 18 0.19
62 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.20, T:0.36
Consensus pattern (59 bp):
ATATAGTTTAGGGATGAATATAAAATATTTAAAAGTTTGAGGATAAATTTAGAATGAAG
Found at i:3773625 original size:262 final size:262
Alignment explanation
Indices: 3773160--3773685 Score: 1052
Period size: 262 Copynumber: 2.0 Consensus size: 262
3773150 ACATTAATTT
3773160 AAACTGACAAATATTCATTATTAATCATTAATTAGTGACATGCAAAATTTTAGCTTAAAAGGAAA
1 AAACTGACAAATATTCATTATTAATCATTAATTAGTGACATGCAAAATTTTAGCTTAAAAGGAAA
3773225 TCAAACAGGGACCTAATTGAACATGCAAGTCTATGGACCACAATGTAAACGATTCAAAAGCTACA
66 TCAAACAGGGACCTAATTGAACATGCAAGTCTATGGACCACAATGTAAACGATTCAAAAGCTACA
3773290 AACGTACATAAAATATGCAATTAACATTCCCATTATAAAACTTAGTTTATTAGAGAGTGAAAAAA
131 AACGTACATAAAATATGCAATTAACATTCCCATTATAAAACTTAGTTTATTAGAGAGTGAAAAAA
3773355 TAGATCTCATCAAATTTTGAGTTAAGGCCAAGTATTAATTTAGTAATTCAATTTCTGGACCATTT
196 TAGATCTCATCAAATTTTGAGTTAAGGCCAAGTATTAATTTAGTAATTCAATTTCTGGACCATTT
3773420 TG
261 TG
3773422 AAACTGACAAATATTCATTATTAATCATTAATTAGTGACATGCAAAATTTTAGCTTAAAAGGAAA
1 AAACTGACAAATATTCATTATTAATCATTAATTAGTGACATGCAAAATTTTAGCTTAAAAGGAAA
3773487 TCAAACAGGGACCTAATTGAACATGCAAGTCTATGGACCACAATGTAAACGATTCAAAAGCTACA
66 TCAAACAGGGACCTAATTGAACATGCAAGTCTATGGACCACAATGTAAACGATTCAAAAGCTACA
3773552 AACGTACATAAAATATGCAATTAACATTCCCATTATAAAACTTAGTTTATTAGAGAGTGAAAAAA
131 AACGTACATAAAATATGCAATTAACATTCCCATTATAAAACTTAGTTTATTAGAGAGTGAAAAAA
3773617 TAGATCTCATCAAATTTTGAGTTAAGGCCAAGTATTAATTTAGTAATTCAATTTCTGGACCATTT
196 TAGATCTCATCAAATTTTGAGTTAAGGCCAAGTATTAATTTAGTAATTCAATTTCTGGACCATTT
3773682 TG
261 TG
3773684 AA
1 AA
3773686 CTTACACTAA
Statistics
Matches: 264, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
262 264 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (262 bp):
AAACTGACAAATATTCATTATTAATCATTAATTAGTGACATGCAAAATTTTAGCTTAAAAGGAAA
TCAAACAGGGACCTAATTGAACATGCAAGTCTATGGACCACAATGTAAACGATTCAAAAGCTACA
AACGTACATAAAATATGCAATTAACATTCCCATTATAAAACTTAGTTTATTAGAGAGTGAAAAAA
TAGATCTCATCAAATTTTGAGTTAAGGCCAAGTATTAATTTAGTAATTCAATTTCTGGACCATTT
TG
Found at i:3777898 original size:23 final size:22
Alignment explanation
Indices: 3777856--3777899 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3777846 ATAAAAATAT
* *
3777856 TATTTTTTTAATGTATAAAATC
1 TATTTTTTTAATATACAAAATC
3777878 TATTTTTTTAATAATACAAAAT
1 TATTTTTTTAAT-ATACAAAAT
3777900 TAGATATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTTTTTTAATATACAAAATC
Found at i:3779282 original size:20 final size:21
Alignment explanation
Indices: 3779257--3779372 Score: 74
Period size: 20 Copynumber: 5.8 Consensus size: 21
3779247 GTTATAATAT
3779257 TATTAA-ATATATTAATAAAC
1 TATTAACATATATTAATAAAC
3779277 TATTAACA-ATATTAA-ACAA-
1 TATTAACATATATTAATA-AAC
*
3779296 TATTTTATACAT-TATTAATATAC
1 TA--TTA-ACATATATTAATAAAC
* *
3779319 TA--AA-ATAT-TGTTATAATAT
1 TATTAACATATAT-TAATAA-AC
3779338 TATTAA-ATATATTAATAAAC
1 TATTAACATATATTAATAAAC
3779358 TATTAACA-ATATTAA
1 TATTAACATATATTAA
3779373 ACAATATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 30
0.68 0.05 0.27
Matches are distributed among these distances:
17 3 0.04
18 6 0.08
19 7 0.09
20 29 0.39
21 16 0.21
22 11 0.15
23 3 0.04
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (21 bp):
TATTAACATATATTAATAAAC
Found at i:3779312 original size:42 final size:42
Alignment explanation
Indices: 3779266--3779396 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 42
3779256 TTATTAAATA
3779266 TATTAATAAACTATTAACAATATTAAACAATATTTTATACAT
1 TATTAATAAACTATTAACAATATTAAACAATATTTTATACAT
* ** *
3779308 TATTAAT--A-TACTAA-AATATTGTTATAATATTATTA-A-AT
1 TATTAATAAACTATTAACAATATT-AAACAATATT-TTATACAT
3779346 ATATTAATAAACTATTAACAATATTAAACAATATTTTATACAT
1 -TATTAATAAACTATTAACAATATTAAACAATATTTTATACAT
3779389 TATTAATA
1 TATTAATA
3779397 TATTTAATAA
Statistics
Matches: 72, Mismatches: 8, Indels: 18
0.73 0.08 0.18
Matches are distributed among these distances:
38 8 0.11
39 20 0.28
40 4 0.06
41 4 0.06
42 28 0.39
43 8 0.11
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.43
Consensus pattern (42 bp):
TATTAATAAACTATTAACAATATTAAACAATATTTTATACAT
Found at i:3779351 original size:39 final size:40
Alignment explanation
Indices: 3779222--3779354 Score: 130
Period size: 39 Copynumber: 3.3 Consensus size: 40
3779212 TAAATCTAAG
* *
3779222 ATATATTAATAGTTTCTAAAATATTGTTATAATATTATTAA
1 ATATATTAATA-CTACTAAAATATTGTTATAATATTATTAA
* ** *
3779263 ATATATTAATAAACTATTAACAATATT-AAACAATATT-TTATA
1 ATATATTAAT--ACTACTAA-AATATTGTTATAATATTATTA-A
3779305 CAT-TATTAATA-TACTAAAATATTGTTATAATATTATTAA
1 -ATATATTAATACTACTAAAATATTGTTATAATATTATTAA
3779344 ATATATTAATA
1 ATATATTAATA
3779355 AACTATTAAC
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
38 8 0.11
39 21 0.28
40 4 0.05
41 13 0.18
42 19 0.26
43 9 0.12
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (40 bp):
ATATATTAATACTACTAAAATATTGTTATAATATTATTAA
Found at i:3779372 original size:81 final size:82
Alignment explanation
Indices: 3779225--3779453 Score: 351
Period size: 81 Copynumber: 2.8 Consensus size: 82
3779215 ATCTAAGATA
*
3779225 TATTAATAGTTTCTAAAATATTGTTATAATATTATTAAATATATTAATAAACTATTAACAATATT
1 TATTAATA-TATCTAAAATATTGTTATAATATTATTAAATATATTAATAAACTATTAACAATATT
3779290 AAACAATATTTTATACAT
65 AAACAATATTTTATACAT
3779308 TATTAATATA-CTAAAATATTGTTATAATATTATTAAATATATTAATAAACTATTAACAATATTA
1 TATTAATATATCTAAAATATTGTTATAATATTATTAAATATATTAATAAACTATTAACAATATTA
3779372 AACAATATTTTATACAT
66 AACAATATTTTATACAT
* * * *
3779389 TATTAATATATTTAATAATATTATTAATAAT-TTATT--ATATA-CAATAAACTATTAATAATAT
1 TATTAATATATCTAA-AATATTGTT-ATAATATTATTAAATATATTAATAAACTATTAACAATAT
3779450 TAAA
64 TAAA
3779454 TGATATTATA
Statistics
Matches: 138, Mismatches: 5, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
80 22 0.16
81 86 0.62
82 4 0.03
83 21 0.15
84 5 0.04
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (82 bp):
TATTAATATATCTAAAATATTGTTATAATATTATTAAATATATTAATAAACTATTAACAATATTA
AACAATATTTTATACAT
Found at i:3779427 original size:42 final size:42
Alignment explanation
Indices: 3779225--3779427 Score: 139
Period size: 42 Copynumber: 4.9 Consensus size: 42
3779215 ATCTAAGATA
*
3779225 TATTAATAGT-TTCTAAAATATTGTT-ATAATATTATTA-A-AT
1 TATTAATA-TATT-TAAAATATTATTAATAATATTATTATACAT
* *
3779265 ATATTAATAAACTATTAACAATATTA--AACAATATT-TTATACAT
1 -TATTAATATA-T-TTAA-AATATTATTAATAATATTATTATACAT
* *
3779308 TATTAATATA-CTAAAATATTGTT-ATAATATTATTA-A-AT
1 TATTAATATATTTAAAATATTATTAATAATATTATTATACAT
* *
3779346 ATATTAATAAACTATTAACAATATTA--AACAATATT-TTATACAT
1 -TATTAATATA-T-TTAA-AATATTATTAATAATATTATTATACAT
3779389 TATTAATATATTTAATAATATTATTAATAAT-TTATTATA
1 TATTAATATATTTAA-AATATTATTAATAATATTATTATA
3779428 TACAATAAAC
Statistics
Matches: 127, Mismatches: 14, Indels: 41
0.70 0.08 0.23
Matches are distributed among these distances:
38 8 0.06
39 20 0.16
40 14 0.11
41 17 0.13
42 51 0.40
43 17 0.13
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (42 bp):
TATTAATATATTTAAAATATTATTAATAATATTATTATACAT
Found at i:3780308 original size:60 final size:61
Alignment explanation
Indices: 3780257--3780383 Score: 156
Period size: 60 Copynumber: 2.1 Consensus size: 61
3780247 TTTGACTCTT
*
3780257 AAACTATGA-CTATCATTCTAAATT-AGTC-CTTAAACTTTTGGAA-ATTTCAATTTTATCCCC
1 AAACTATGACCT-TCATTCTAAATTGA-TCTC-TAAACTTTTGGAATATTTCAATTTGATCCCC
* * *
3780317 AAACTATGACCTTCATTCTAAATTGATCTCTAAACTTTTTGAATATTCCAATTTCA-CCCC
1 AAACTATGACCTTCATTCTAAATTGATCTCTAAACTTTTGGAATATTTCAATTTGATCCCC
3780377 AAACTAT
1 AAACTAT
3780384 ACGCATATAC
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
60 46 0.77
61 14 0.23
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.39
Consensus pattern (61 bp):
AAACTATGACCTTCATTCTAAATTGATCTCTAAACTTTTGGAATATTTCAATTTGATCCCC
Found at i:3780542 original size:29 final size:29
Alignment explanation
Indices: 3780509--3780588 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 29
3780499 TTTGGATGAA
3780509 TTTAGGGATGAAATTGGAATAT-TCAAAAG
1 TTTAGGGATGAAATTGGAATATGTC-AAAG
* * *
3780538 TTTAGGGACT-AATTTAGAAATATGGTCATAG
1 TTTAGGGA-TGAAATT-GGAATAT-GTCAAAG
*
3780569 TTTAGGGATGAAATTAGAAT
1 TTTAGGGATGAAATTGGAAT
3780589 GTTTAACAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
29 12 0.30
30 11 0.28
31 15 0.38
32 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.34
Consensus pattern (29 bp):
TTTAGGGATGAAATTGGAATATGTCAAAG
Found at i:3780586 original size:31 final size:30
Alignment explanation
Indices: 3780509--3780660 Score: 88
Period size: 29 Copynumber: 5.1 Consensus size: 30
3780499 TTTGGATGAA
*
3780509 TTTAGGGATGAAATT-GGAATATTCAAAAG
1 TTTAGGGATGAAATTAGAAATATTCAAAAG
* *
3780538 TTTAGGGACT-AATTTAGAAATATGGTC-ATAG
1 TTTAGGGA-TGAAATTAGAAATAT--TCAAAAG
* * *
3780569 TTTAGGGATGAAATTAG-AATGTTTAACAG
1 TTTAGGGATGAAATTAGAAATATTCAAAAG
* * *
3780598 TTTAAGGGCT-AATTTAGAATGAAATTGC--AA-
1 TTT-AGGGATGAAATTAGAA--ATATT-CAAAAG
*
3780628 TTTAAGGATGAAATTAG-AATATTCAAAAG
1 TTTAGGGATGAAATTAGAAATATTCAAAAG
3780657 TTTA
1 TTTA
3780661 AAGACTATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 30
0.66 0.12 0.22
Matches are distributed among these distances:
26 1 0.01
27 4 0.04
28 3 0.03
29 33 0.36
30 27 0.30
31 18 0.20
32 5 0.05
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (30 bp):
TTTAGGGATGAAATTAGAAATATTCAAAAG
Found at i:3780659 original size:59 final size:59
Alignment explanation
Indices: 3780507--3780661 Score: 190
Period size: 60 Copynumber: 2.6 Consensus size: 59
3780497 TATTTGGATG
* *
3780507 AATTTAGGGATGAAATTGGAATATTCAAAAGTTT-AGGGACTAATTTAGAAATATGGTC
1 AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGGACTAATTTAGAAAAATGGTC
* * * *
3780565 ATAGTTTAGGGATGAAATTAGAATGTTTAACAGTTTAAGGG-CTAATTTAGAATGAAATTG-C
1 A-A-TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGGACTAATTTAGAA--AAATGGTC
*
3780626 AATTTAAGGATGAAATTAGAATATTCAAAAGTTTAA
1 AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAA
3780662 AGACTATTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
58 1 0.01
59 31 0.38
60 40 0.49
61 6 0.07
62 4 0.05
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.34
Consensus pattern (59 bp):
AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGGACTAATTTAGAAAAATGGTC
Found at i:3780678 original size:59 final size:60
Alignment explanation
Indices: 3780507--3780683 Score: 191
Period size: 59 Copynumber: 3.0 Consensus size: 60
3780497 TATTTGGATG
* * *
3780507 AATTTAGGGATGAAATTGGAATATTCAAAAGTTTAGGGACTAATTTAGAAAT---ATGGTC
1 AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA-AAATGAAATTGTC
* * * * *
3780565 ATAGTTTAGGGATGAAATTAGAATGTTTAACAGTTTAAGGGCTAATTTAGAATGAAATTG-C
1 A-A-TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAATTGTC
* * *
3780626 AATTTAAGGATGAAATTAGAATATTCAAAAGTTTAAAGACTATTTTAAAATGAGAATT
1 AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGA-AATT
3780684 ATAATTTGAG
Statistics
Matches: 97, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
58 1 0.01
59 47 0.48
60 44 0.45
61 2 0.02
62 3 0.03
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.34
Consensus pattern (60 bp):
AATTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAATTGTC
Found at i:3781360 original size:60 final size:60
Alignment explanation
Indices: 3781264--3781390 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
3781254 TAGTTATAGA
* *** ** * *
3781264 ACCATTTTGTAACTTTTAATAGTTGGTGGACACAACAAAGTAATGCCCTATAGTCAGATG
1 ACCATTTTATAACTTTTAATAGTTGGAAAACACAACAAAACAATACCCTATAGTCAGAGG
* * *
3781324 ACCATTTTATAACTTTTAATAGTTGGAAAACTCAACAAAACAATATCCTATAGTCAGGGG
1 ACCATTTTATAACTTTTAATAGTTGGAAAACACAACAAAACAATACCCTATAGTCAGAGG
3781384 ACCATTT
1 ACCATTT
3781391 GTGTGCTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (60 bp):
ACCATTTTATAACTTTTAATAGTTGGAAAACACAACAAAACAATACCCTATAGTCAGAGG
Found at i:3781627 original size:17 final size:17
Alignment explanation
Indices: 3781596--3781628 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3781586 TTCATTATCA
3781596 TTAAATATAAAAATAAT
1 TTAAATATAAAAATAAT
3781613 TTAAA-ATAAATAATAA
1 TTAAATATAAA-AATAA
3781629 AATAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAATATAAAAATAAT
Found at i:3788762 original size:15 final size:15
Alignment explanation
Indices: 3788733--3788761 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3788723 TATTAAGAAG
3788733 ACACGTGGTTTTTTT
1 ACACGTGGTTTTTTT
3788748 ACACGT-GTTTTTTT
1 ACACGTGGTTTTTTT
3788762 TGGTTGCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (15 bp):
ACACGTGGTTTTTTT
Found at i:3790287 original size:17 final size:19
Alignment explanation
Indices: 3790251--3790287 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3790241 TTTTTTAACA
*
3790251 TTTTATTCATTTTGTTTAT
1 TTTTATTCATTATGTTTAT
3790270 TTTTATT-ATTAT-TTTAT
1 TTTTATTCATTATGTTTAT
3790287 T
1 T
3790288 ATTTTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 4 0.24
19 7 0.41
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTATTCATTATGTTTAT
Found at i:3790291 original size:20 final size:20
Alignment explanation
Indices: 3790266--3790313 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3790256 TTCATTTTGT
*
3790266 TTATTTTTATTA-TTATTTTA
1 TTATTTTT-TTACGTATTTTA
*
3790286 TTATTTTTTTACGTATTTTG
1 TTATTTTTTTACGTATTTTA
3790306 TTATTTTT
1 TTATTTTT
3790314 CATTTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (20 bp):
TTATTTTTTTACGTATTTTA
Found at i:3791158 original size:27 final size:27
Alignment explanation
Indices: 3791120--3791173 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3791110 GGTTTAGGAC
3791120 TAAGGGTCTGGCAAGCCCAACAGGGCA
1 TAAGGGTCTGGCAAGCCCAACAGGGCA
3791147 TAAGGGTCTGGCAAGCCCAACAGGGCA
1 TAAGGGTCTGGCAAGCCCAACAGGGCA
3791174 CCGGCAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.33, T:0.11
Consensus pattern (27 bp):
TAAGGGTCTGGCAAGCCCAACAGGGCA
Found at i:3793342 original size:13 final size:13
Alignment explanation
Indices: 3793326--3793360 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3793316 AGAAAAAAGT
3793326 AAAGAGAAAATAA
1 AAAGAGAAAATAA
3793339 AAAGAGAAAA-AA
1 AAAGAGAAAATAA
3793351 AAAGA-AAAAT
1 AAAGAGAAAAT
3793361 TGAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 7 0.33
13 10 0.48
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (13 bp):
AAAGAGAAAATAA
Found at i:3793516 original size:65 final size:68
Alignment explanation
Indices: 3793432--3793569 Score: 203
Period size: 65 Copynumber: 2.1 Consensus size: 68
3793422 GATTCAAACT
* * *
3793432 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCA-TCGAAGATCATA-AGCA
1 ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCAATTCACTCGAAAATCATAGAGCA
3793495 TCA
66 TCA
* *
3793498 ATGAGA-TGATCAAGCACAATCATTTCTAAATCACTGAATCAATTCACTCGAAAATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCAATTCACTCGAAAATCATAGAGCA
3793562 TCA
66 TCA
3793565 A-GAGA
1 ATGAGA
3793570 GAGACACATA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
65 36 0.55
66 21 0.32
67 8 0.12
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (68 bp):
ATGAGATTGATCAAGCACAATCATTTCCAAATCACTGAACCAATTCACTCGAAAATCATAGAGCA
TCA
Found at i:3794528 original size:32 final size:32
Alignment explanation
Indices: 3794483--3794571 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
3794473 AGGAACATTA
3794483 GGGGC-TTTCTTGGAGATTCAACATCGAATATT
1 GGGGCATTT-TTGGAGATTCAACATCGAATATT
*
3794515 GGGGCATTTTTGGAGATTCAACATTGAATATT
1 GGGGCATTTTTGGAGATTCAACATCGAATATT
* * *
3794547 GGGGTATCTTTGGGGATTCAACATC
1 GGGGCATTTTTGGAGATTCAACATC
3794572 CTGATACGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 48 0.94
33 3 0.06
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (32 bp):
GGGGCATTTTTGGAGATTCAACATCGAATATT
Found at i:3795358 original size:106 final size:106
Alignment explanation
Indices: 3795201--3795523 Score: 405
Period size: 106 Copynumber: 3.0 Consensus size: 106
3795191 ATATCATGCC
* * * *
3795201 ACTCGAGACAACACAAGTTCAACTTCACAACAAAGGGATGACTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
* *
3795266 AATTTCAGAGCCAATTTCAACTTCATAGA-TAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACA-ACGAAGGATATTGG
* * *
3795307 ACTTGAGACAACACAAGTTCAACTTCATAACGAAGGGACGGTTGGTTGTCAACAAACAATTTCCT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
** *
3795372 AATTTTGGAGCCAATTTCAACTTGACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
3795413 ACTCGAGACAACACAAGCTCAACTTCACAGCGTAGGGACGGCAGGCTGTCAACAAATAATTTCCT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
* * * *** *
3795478 AGTTCCAGAGCCAATTTTAACTTCACGGTGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3795519 ACTCG
1 ACTCG
3795524 GAACAATACA
Statistics
Matches: 185, Mismatches: 31, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
105 1 0.01
106 184 0.99
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:3795858 original size:102 final size:102
Alignment explanation
Indices: 3795752--3796121 Score: 573
Period size: 102 Copynumber: 3.6 Consensus size: 102
3795742 TTTTAGAACT
* *
3795752 AAATTTTGTCTCTCTTAAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* *
3795817 GAAATTTATCTCGATTGAGATAGTTTCCCTTGAAACG
66 GAAATTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
*
3795854 AAATTTTGTCTCCCCTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* *
3795919 -AAATTTTATCTCGCTTGGGGTAGTTTCCCTTGAAACA
66 GAAA-TTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
*
3795956 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCTTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* * * *
3796021 GAATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAGCA
66 GAAATTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
* * *
3796058 AAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAATATAAACCA-TGAAAACGTTTCCCTTGAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAACATTTCCCTTGAAA
3796122 CACAAAATAT
Statistics
Matches: 246, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
101 3 0.01
102 239 0.97
103 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (102 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
GAAATTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
Found at i:3795981 original size:37 final size:37
Alignment explanation
Indices: 3795906--3796092 Score: 119
Period size: 37 Copynumber: 5.3 Consensus size: 37
3795896 ATTGAAAACA
* * * * *
3795906 TTTCCCTTGAAA-TAAATTTTATCTCGCTTGGGGTAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
3795942 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
* * * *
3795979 TTTCTCTTGAAACATAAA---------CATTGA-AAACA
1 TTTCCCTTGAAACA-AAATTTTGTCTCCCTTGAGATA-G
* ** * *
3796008 TTTCCTTTGAAA-TGAATTTTTTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
3796044 TTTCCCTTGAAGCAAAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
3796081 TTTCTCTTGAAA
1 TTTCCCTTGAAA
3796093 TATAAACCAT
Statistics
Matches: 111, Mismatches: 26, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
27 2 0.02
28 2 0.02
29 15 0.14
36 26 0.23
37 63 0.57
38 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
Found at i:3796206 original size:37 final size:37
Alignment explanation
Indices: 3796156--3796258 Score: 181
Period size: 36 Copynumber: 2.8 Consensus size: 37
3796146 TTAAACGAGT
*
3796156 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTATCTCTC
*
3796193 TTGAGACAGTTTCCCTTGAAAC-AAATTTTATCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTATCTCTC
3796229 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
3796259 TGAATATATT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 34 0.55
37 28 0.45
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTATCTCTC
Found at i:3796278 original size:102 final size:102
Alignment explanation
Indices: 3796169--3796355 Score: 254
Period size: 102 Copynumber: 1.8 Consensus size: 102
3796159 AGACAGTTTC
* *
3796169 CCTTGAAACAAAATCTT-GTCTCTCTTGAGACAGTTTCCCTTGA-AAC-AAATTTTATCTCTCTT
1 CCTTGAAAC-AAAT-TTCATCTCCCTTGAGACAGTTT-CCTTGAGAACTAAATTTTATCTCTCTT
3796231 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTT
63 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTT
* * * *
3796271 CCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTAGAACTAAGTTTTGTCTCTCTTGAG
1 CCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCTTGAGAACTAAATTTTATCTCTCTTGAG
**
3796336 ACAGTTTCTTTTGAAACAAA
66 ACAGTTTCCCTTGAAACAAA
3796356 TTTTGTCCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 6 0.08
101 24 0.32
102 44 0.59
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (102 bp):
CCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCTTGAGAACTAAATTTTATCTCTCTTGAG
ACAGTTTCCCTTGAAACAAAATCTTTGAATATATTTT
Found at i:3796343 original size:37 final size:36
Alignment explanation
Indices: 3796273--3796389 Score: 137
Period size: 36 Copynumber: 3.2 Consensus size: 36
3796263 TATATTTTCC
** *
3796273 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
*
3796309 TT-AGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTT
1 TTGA-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
* * * *
3796346 TTGAAACAAATTTTGTCCCTCTTAAGACAGTTTATC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
3796382 TTGAAACA
1 TTGAAACA
3796390 CAAAAAAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 1 0.01
36 37 0.54
37 30 0.43
38 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:3796424 original size:37 final size:39
Alignment explanation
Indices: 3796375--3796466 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
3796365 TCTTAAGACA
* *
3796375 GTTTATCTTGAAACACA-A-AAAAAAACCCCTCGAAATT
1 GTTTCTCTTGAAACACACACAAAAAAACCCCTCGAAAAT
* * *
3796412 GTTTCTCTTGAAACACACACACAAAAACCCTTTGAAAAT
1 GTTTCTCTTGAAACACACACAAAAAAACCCCTCGAAAAT
*
3796451 GTTTCTCTTAAAACAC
1 GTTTCTCTTGAAACAC
3796467 CAAACCCTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 16 0.34
38 1 0.02
39 30 0.64
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (39 bp):
GTTTCTCTTGAAACACACACAAAAAAACCCCTCGAAAAT
Found at i:3796631 original size:84 final size:85
Alignment explanation
Indices: 3796474--3796631 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 85
3796464 CACCAAACCC
* * * *
3796474 TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGC
*
3796539 TATTTGTCACCAAAAGACCT
66 TATCTGTCACCAAAAGACCT
** * * *
3796559 TCGAGTTCGACTATGCTCAGC-TCTAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAATGGC
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGC
3796623 TATCTGTCA
66 TATCTGTCA
3796632 ATAAAATCGT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
84 45 0.71
85 18 0.29
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (85 bp):
TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGGCAAGAAGGGC
TATCTGTCACCAAAAGACCT
Found at i:3797579 original size:2 final size:2
Alignment explanation
Indices: 3797572--3797596 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3797562 TTTCGTCCCT
3797572 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3797597 TTTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3797664 original size:2 final size:2
Alignment explanation
Indices: 3797657--3797699 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
3797647 TTATTTTTAT
*
3797657 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
3797698 TA
1 TA
3797700 AATGTATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3797670 original size:14 final size:15
Alignment explanation
Indices: 3797638--3797699 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 15
3797628 CTCTTTTTTT
*
3797638 TATATTATAT-TATT
1 TATATTATATATATA
* *
3797652 TTTATTATATATATCT
1 TATATTATATATAT-A
*
3797668 TATATCAT-TATATA
1 TATATTATATATATA
3797682 TATA-TATATATATA
1 TATATTATATATATA
3797696 TATA
1 TATA
3797700 AATGTATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 2 0.05
14 23 0.57
15 8 0.20
16 7 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:3797770 original size:37 final size:34
Alignment explanation
Indices: 3797729--3797825 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 34
3797719 ATTTATGATG
*
3797729 TATATATTTTTTCTTAATATTATATTTTATATGTTTT
1 TATATATTTATTCTTAATATTATA-TTT-T-TGTTTT
* *
3797766 TATATATATATTCTTAATATTCTATTTTTGTTTT
1 TATATATTTATTCTTAATATTATATTTTTGTTTT
* *
3797800 TATTTATTTA-T-AT-ATATTATATTTTT
1 TATATATTTATTCTTAATATTATATTTTT
3797826 ACTTTATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
31 12 0.23
32 1 0.02
33 1 0.02
34 14 0.26
35 1 0.02
36 3 0.06
37 21 0.40
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (34 bp):
TATATATTTATTCTTAATATTATATTTTTGTTTT
Found at i:3797819 original size:17 final size:16
Alignment explanation
Indices: 3797799--3797857 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
3797789 ATTTTTGTTT
3797799 TTATTTATTTATATATA
1 TTATTT-TTTATATATA
* *
3797816 TTATATTTTTACTTTATT
1 TTAT-TTTTTA-TATATA
*
3797834 TTATTTTTTCTAT-TA
1 TTATTTTTTATATATA
3797849 TTATTTTTT
1 TTATTTTTT
3797858 CTTAATATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 10 0.29
16 2 0.06
17 13 0.37
18 10 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTTTATATATA
Found at i:3797834 original size:30 final size:31
Alignment explanation
Indices: 3797798--3797856 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
3797788 TATTTTTGTT
3797798 TTTA-TTTATTTATATATATTA-TATTTTTAC
1 TTTATTTTATTT-TATATATTATTATTTTTAC
* *
3797828 TTTATTTTATTTTTTCTATTATTATTTTT
1 TTTATTTTATTTTATATATTATTATTTTT
3797857 TCTTAATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (31 bp):
TTTATTTTATTTTATATATTATTATTTTTAC
Found at i:3797842 original size:42 final size:41
Alignment explanation
Indices: 3797719--3797842 Score: 99
Period size: 44 Copynumber: 2.9 Consensus size: 41
3797709 ATGTTTCTCC
* * * * *
3797719 ATTTATGATGTATATATTTTTTCTTAATATTATATTTTATAT
1 ATTTAT-ATATATATATTTTTACTTTATTTTATTTTTTATAT
* * *
3797761 GTTTTTATATATATATTCTTAATA-TTCTATTTT-TGTTTTTATTT
1 ATTTATATATATATATT-TT--TACTT-TATTTTAT-TTTTTATAT
3797805 ATTTATATATATTATATTTTTACTTTATTTTATTTTTT
1 ATTTATATATA-TATATTTTTACTTTATTTTATTTTTT
3797843 CTATTATTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
41 10 0.16
42 19 0.30
43 6 0.09
44 23 0.36
45 6 0.09
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (41 bp):
ATTTATATATATATATTTTTACTTTATTTTATTTTTTATAT
Found at i:3797852 original size:15 final size:14
Alignment explanation
Indices: 3797830--3797859 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3797820 ATTTTTACTT
3797830 TATTTTATTTTTTC
1 TATTTTATTTTTTC
3797844 TATTATTATTTTTTC
1 TATT-TTATTTTTTC
3797859 T
1 T
3797860 TAATATCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTTATTTTTTC
Found at i:3797856 original size:16 final size:17
Alignment explanation
Indices: 3797800--3797857 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
3797790 TTTTTGTTTT
*
3797800 TATTTATTTATATATATTA
1 TATTT-TTTCTAT-TATTA
* *
3797819 TATTTTTACT-TTATTT
1 TATTTTTTCTATTATTA
3797835 TATTTTTTCTATTATTA
1 TATTTTTTCTATTATTA
3797852 T-TTTTT
1 TATTTTT
3797858 CTTAATATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 18 0.55
17 7 0.21
18 3 0.09
19 5 0.15
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTTTTCTATTATTA
Found at i:3798103 original size:18 final size:17
Alignment explanation
Indices: 3798053--3798104 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
3798043 CATTTTATTC
*
3798053 ATTTTGTTTATTTTTATT
1 ATTTTG-TTATTTTTAGT
*
3798071 ATTTTTATTATTTTTTACGT
1 A-TTTTGTTA-TTTTTA-GT
3798091 ATTTTGTTATTTTT
1 ATTTTGTTATTTTT
3798105 CATTTTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 9 0.32
19 17 0.61
20 2 0.07
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (17 bp):
ATTTTGTTATTTTTAGT
Found at i:3798104 original size:9 final size:9
Alignment explanation
Indices: 3798045--3798085 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
3798035 TTTTTTAACA
3798045 TTTTATTCAT
1 TTTTATT-AT
3798055 TTTGT-TTAT
1 TTT-TATTAT
3798064 TTTTATTAT
1 TTTTATTAT
3798073 TTTTATTAT
1 TTTTATTAT
3798082 TTTT
1 TTTT
3798086 TACGTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.03
9 22 0.76
10 5 0.17
11 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (9 bp):
TTTTATTAT
Found at i:3800150 original size:11 final size:11
Alignment explanation
Indices: 3800134--3800164 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3800124 TCGATAAGTT
3800134 TGAAGTTATAA
1 TGAAGTTATAA
3800145 TGAAGTTATAA
1 TGAAGTTATAA
*
3800156 TGGAGTTAT
1 TGAAGTTAT
3800165 GAGTTTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (11 bp):
TGAAGTTATAA
Found at i:3801099 original size:17 final size:18
Alignment explanation
Indices: 3801067--3801106 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3801057 CATTCTGTTT
*
3801067 TATTTTAATGATTTTATA
1 TATTTCAATGATTTTATA
*
3801085 TATTTCAAT-ATTTTATT
1 TATTTCAATGATTTTATA
3801102 TATTT
1 TATTT
3801107 GTTATCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
TATTTCAATGATTTTATA
Found at i:3808392 original size:17 final size:18
Alignment explanation
Indices: 3808360--3808399 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3808350 CAGTCTGTTT
3808360 TATTTTAAAGATTTTATA
1 TATTTTAAAGATTTTATA
* *
3808378 TATTTT-AATATTTTATT
1 TATTTTAAAGATTTTATA
3808395 TATTT
1 TATTT
3808400 GTTCTCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TATTTTAAAGATTTTATA
Found at i:3809389 original size:30 final size:31
Alignment explanation
Indices: 3809345--3809404 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3809335 ATTTTTTAAA
* *
3809345 TTAAATTATTAAAAAA-ACCCAAAATATTTT
1 TTAAAATATCAAAAAATACCCAAAATATTTT
* *
3809375 TTAAAATATCAAAAAATTCCCTAAATATTT
1 TTAAAATATCAAAAAATACCCAAAATATTT
3809405 ATTCAATCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.37
Consensus pattern (31 bp):
TTAAAATATCAAAAAATACCCAAAATATTTT
Found at i:3811129 original size:78 final size:78
Alignment explanation
Indices: 3811045--3811190 Score: 197
Period size: 78 Copynumber: 1.9 Consensus size: 78
3811035 AGTGAACACA
*
3811045 GTGTGTAAGTAACCCGTCTTAACTGTTGAAACA-AATTTT-TAATTAAAAAAAATTAAAGACGGT
1 GTGTGTAAGCAACCCGTCTTAACTGTTGAAACATAATTTTGTAATT--AAAAAATTAAAGACGGT
3811108 ATATTTATAAAGTAG
64 ATATTTATAAAGTAG
* * ** * *
3811123 GTGTGTAAGCAATCCGTCTTCACTGTTGAAACATTTTTTTGTAATTAAAAAATTAAAGTCGTTAT
1 GTGTGTAAGCAACCCGTCTTAACTGTTGAAACATAATTTTGTAATTAAAAAATTAAAGACGGTAT
3811188 ATT
66 ATT
3811191 CACATATCGT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
78 50 0.85
79 4 0.07
80 5 0.08
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (78 bp):
GTGTGTAAGCAACCCGTCTTAACTGTTGAAACATAATTTTGTAATTAAAAAATTAAAGACGGTAT
ATTTATAAAGTAG
Found at i:3811249 original size:60 final size:60
Alignment explanation
Indices: 3811160--3811364 Score: 297
Period size: 60 Copynumber: 3.4 Consensus size: 60
3811150 GAAACATTTT
* *
3811160 TTTGTAATT-AAAAAATTAAAG-TCGTTATATTCACATATCGTCTACACTGTTTACTTTTCA
1 TTTG-AATTAAAAAAATTAAAGAT-GGTATATTTACATATCGTCTACACTGTTTACTTTTCA
*
3811220 TTTGAATTAAAAAAATTAAAGATGGTATATTTACATATCGTCTACACTGTTTAATTTTCA
1 TTTGAATTAAAAAAATTAAAGATGGTATATTTACATATCGTCTACACTGTTTACTTTTCA
* * * *
3811280 TTTGAATTAAAAAAATTAAAGATGGTATATTTACATATCATCTACACTATTCACTATTTCT
1 TTTGAATTAAAAAAATTAAAGATGGTATATTTACATATCGTCTACACTGTTTACT-TTTCA
*
3811341 TTTGAATAAAAAAAATTAAAGATG
1 TTTGAATTAAAAAAATTAAAGATG
3811365 ATAGTATATT
Statistics
Matches: 133, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
59 4 0.03
60 101 0.76
61 28 0.21
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (60 bp):
TTTGAATTAAAAAAATTAAAGATGGTATATTTACATATCGTCTACACTGTTTACTTTTCA
Found at i:3813203 original size:38 final size:37
Alignment explanation
Indices: 3813147--3813259 Score: 194
Period size: 38 Copynumber: 3.1 Consensus size: 37
3813137 TAAAAATCGG
3813147 TATTTT-AAAAATATATATAATATATAGTTTTTAAAA
1 TATTTTGAAAAATATATATAATATATAGTTTTTAAAA
3813183 TATTTTGAAAAAATATATATAATATATAGTTTTTAAAA
1 TATTTTG-AAAAATATATATAATATATAGTTTTTAAAA
*
3813221 TATTTTGAAAAA-ATATATAATATATAGTTTCTAAAA
1 TATTTTGAAAAATATATATAATATATAGTTTTTAAAA
3813257 TAT
1 TAT
3813260 AATATATAGT
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
36 32 0.43
37 5 0.07
38 37 0.50
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
TATTTTGAAAAATATATATAATATATAGTTTTTAAAA
Found at i:3813261 original size:21 final size:20
Alignment explanation
Indices: 3813235--3813279 Score: 81
Period size: 21 Copynumber: 2.2 Consensus size: 20
3813225 TTGAAAAAAT
3813235 ATATAATATATAGTTTCTAAA
1 ATATAATATATAGTTT-TAAA
3813256 ATATAATATATAGTTTTAAA
1 ATATAATATATAGTTTTAAA
3813276 ATAT
1 ATAT
3813280 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
ATATAATATATAGTTTTAAA
Found at i:3813368 original size:3 final size:3
Alignment explanation
Indices: 3813362--3813409 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
3813352 AAAAAAATAT
* * *
3813362 TTA TTA TTA TTA TTA -TA TTA -TA TTA ATA TTA TTT TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3813408 TT
1 TT
3813410 TAATTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3813392 original size:25 final size:25
Alignment explanation
Indices: 3813363--3813436 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 25
3813353 AAAAAATATT
3813363 TATTATTATTA-TTATATTATATTAA
1 TATTATTATTATTTATATTAT-TTAA
* *
3813388 TATTATTTTTATTTTTATTATTTAA
1 TATTATTATTATTTATATTATTTAA
3813413 TTAATT-TTATTTATTTA-ATTATTT
1 -T-ATTATTA-TTATTTATATTATTT
3813437 TTCTTTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
25 14 0.34
26 18 0.44
27 9 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TATTATTATTATTTATATTATTTAA
Found at i:3813419 original size:18 final size:18
Alignment explanation
Indices: 3813396--3813446 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
3813386 AATATTATTT
3813396 TTATTTTTA-TTATTTAA
1 TTATTTTTATTTATTTAA
*
3813413 TTAATTTTATTTATTTAA
1 TTATTTTTATTTATTTAA
*
3813431 TTATTTTTCTTTATTT
1 TTATTTTTATTTATTT
3813447 TTTTTGGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 8 0.27
18 22 0.73
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTTTTATTTATTTAA
Found at i:3813434 original size:29 final size:32
Alignment explanation
Indices: 3813358--3813435 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 32
3813348 TTTTAAAAAA
3813358 ATATTTATTATTATTATTATATTATATTAATATT
1 ATATTTA-T-TTATTATTATATTATATTAATATT
*
3813392 ATTTTTATTT-TTATTAT-TTA-ATTAAT-TT
1 ATATTTATTTATTATTATATTATATTAATATT
3813420 -TATTTATTTAATTATT
1 ATATTTATTT-ATTATT
3813436 TTTCTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 8 0.20
28 2 0.05
29 11 0.28
30 3 0.08
31 7 0.17
32 2 0.05
33 1 0.03
34 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (32 bp):
ATATTTATTTATTATTATATTATATTAATATT
Found at i:3814583 original size:6 final size:6
Alignment explanation
Indices: 3814572--3814615 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
3814562 TTTCCTTCGA
*
3814572 TTTATT TTTA-- TTTATT TTCTATC TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TT-TATT TTTATT TTTATT TTTATT TTT
3814616 TCCTCTGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.12
6 24 0.73
7 5 0.15
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:3814584 original size:23 final size:22
Alignment explanation
Indices: 3814558--3814609 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
3814548 ATTTTTTCTC
3814558 ATTTTTTCCT-TCGATTTATTTTT
1 ATTTTTTCCTATC--TTTATTTTT
*
3814581 ATTTATTTTCTATCTTTATTTTT
1 ATTT-TTTCCTATCTTTATTTTT
3814604 ATTTTT
1 ATTTTT
3814610 ATTTTTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 17 0.65
24 5 0.19
25 2 0.08
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTTTTCCTATCTTTATTTTT
Found at i:3814682 original size:45 final size:46
Alignment explanation
Indices: 3814578--3814689 Score: 126
Period size: 45 Copynumber: 2.5 Consensus size: 46
3814568 TCGATTTATT
* *
3814578 TTTATTTA-TTTTC--TATCTTTATTTTTATTTTTATTTTTTCCTCTGG
1 TTTATTTATTTTTCTTTTTCTTTATTTTTATTTTTATGTTTT-CTC--G
*
3814624 TTTATTTCTTTTTCTTTTTCTTTAATTTTTATTTTTATGTTTT-TC-
1 TTTATTTATTTTTCTTTTTCTTT-ATTTTTATTTTTATGTTTTCTCG
3814669 TTTATTTATTTTTCTTTTTCT
1 TTTATTTATTTTTCTTTTTCT
3814690 CTTTGATTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
45 20 0.34
46 7 0.12
47 5 0.09
48 2 0.03
49 6 0.10
50 18 0.31
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.76
Consensus pattern (46 bp):
TTTATTTATTTTTCTTTTTCTTTATTTTTATTTTTATGTTTTCTCG
Found at i:3817498 original size:20 final size:19
Alignment explanation
Indices: 3817475--3817536 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
3817465 TTTTTGTTAT
3817475 TAAAGTTTTAATTTTATGCG
1 TAAAGTTTTAATTTTATG-G
* **
3817495 TAAACTTTTGTTTGTTAT--
1 TAAAGTTTTAATT-TTATGG
3817513 TAAAGTTTTAATTTTATGTG
1 TAAAGTTTTAATTTTATG-G
3817533 TAAA
1 TAAA
3817537 CTACGCGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 4 0.12
18 10 0.31
20 14 0.44
21 4 0.12
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.53
Consensus pattern (19 bp):
TAAAGTTTTAATTTTATGG
Found at i:3817667 original size:17 final size:18
Alignment explanation
Indices: 3817645--3817744 Score: 59
Period size: 20 Copynumber: 5.6 Consensus size: 18
3817635 TTTTTATTTA
*
3817645 AAATTTAAA-ATTTAAAT
1 AAATTTAAATAATTAAAT
3817662 AAATTTAAATAATTAAAT
1 AAATTTAAATAATTAAAT
* ** **
3817680 ATATTTTTAAATCTTTAGTTT
1 A-A-ATTTAAATAATTA-AAT
3817701 AAATTTTAAATAATTAAAT
1 AAA-TTTAAATAATTAAAT
3817720 --ATTT--ATAATTTAAAT
1 AAATTTAAATAA-TTAAAT
3817735 AAA-TTAAATA
1 AAATTTAAATA
3817745 TATATTTTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 19
0.67 0.12 0.21
Matches are distributed among these distances:
14 4 0.06
15 6 0.10
16 5 0.08
17 11 0.18
18 11 0.18
19 2 0.03
20 21 0.34
21 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (18 bp):
AAATTTAAATAATTAAAT
Found at i:3817690 original size:20 final size:20
Alignment explanation
Indices: 3817665--3817780 Score: 67
Period size: 20 Copynumber: 5.5 Consensus size: 20
3817655 TTTAAATAAA
3817665 TTTAAATAATTAAATATATT
1 TTTAAATAATTAAATATATT
* * * * *
3817685 TTTAAAT-CTTTAGTTTAAAT
1 TTTAAATAATTAAATAT-ATT
*
3817705 TTTAAATAATTAAATATTTATAA
1 TTTAAATAATTAAATA--TAT-T
3817728 TTTAAATAAATTAAATATATAT
1 TTTAAAT-AATTAAATATAT-T
* *
3817750 TTTATAAT-ATT-TATTTATT
1 TTTA-AATAATTAAATATATT
3817769 TTTAAAATAATT
1 TTT-AAATAATT
3817781 TAAAATTTGT
Statistics
Matches: 73, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
19 12 0.16
20 25 0.34
21 7 0.10
22 9 0.12
23 11 0.15
24 9 0.12
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.53
Consensus pattern (20 bp):
TTTAAATAATTAAATATATT
Found at i:3817709 original size:64 final size:63
Alignment explanation
Indices: 3817641--3817776 Score: 163
Period size: 64 Copynumber: 2.1 Consensus size: 63
3817631 GAAATTTTTA
*
3817641 TTTAAAATTTAAA-ATTTAAATAAATTTAAAT-AATTAAATATAT-TTTTA-AATCTTTAGTTTA
1 TTTAAAATTTAAATATTT--AT-AATTTAAATAAATTAAATATATATTTTATAATATTTA-TTT-
3817702 AAT
61 AAT
* *
3817705 TTTAAATAATTAAATATTTATAATTTAAATAAATTAAATATATATTTTATAATATTTATTTATT
1 TTTAAA-ATTTAAATATTTATAATTTAAATAAATTAAATATATATTTTATAATATTTATTTAAT
3817769 TTTAAAAT
1 TTTAAAAT
3817777 AATTTAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
63 10 0.16
64 28 0.44
65 14 0.22
66 11 0.17
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (63 bp):
TTTAAAATTTAAATATTTATAATTTAAATAAATTAAATATATATTTTATAATATTTATTTAAT
Found at i:3817758 original size:23 final size:23
Alignment explanation
Indices: 3817703--3817758 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
3817693 TTTAGTTTAA
3817703 ATTTTAAAT-AATTAAATATTTAT
1 ATTTTAAATAAATTAAATA-TTAT
*
3817726 AATTTAAATAAATTAAATA-TAT
1 ATTTTAAATAAATTAAATATTAT
3817748 ATTTTATAATA
1 ATTTTA-AATA
3817759 TTTATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 8 0.28
23 12 0.41
24 9 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTTAAATAAATTAAATATTAT
Found at i:3817784 original size:66 final size:65
Alignment explanation
Indices: 3817646--3817788 Score: 179
Period size: 65 Copynumber: 2.2 Consensus size: 65
3817636 TTTTATTTAA
*
3817646 AATTTAAAATTTAAATAAATTTAAATAATTAAATATATTTTTAAATCTTTAGTTTAAATTTTAAA
1 AATTTAAAATTT-AATAAATTTAAATAATTAAATATATTTTTAAATATTTAGTTTAAATTTTAAA
3817711 T
65 T
*
3817712 AA-TTAAATATTT-AT-AATTTAAATAAATTAAATATATATTTTATAATATTTA-TTT-ATTTTT
1 AATTTAAA-ATTTAATAAATTTAAAT-AATTAAATATAT-TTTTA-AATATTTAGTTTAAATTTT
3817772 AAAAT
62 -AAAT
3817777 AATTTAAAATTT
1 AATTTAAAATTT
3817789 GTATTTCACT
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
63 9 0.13
64 19 0.28
65 23 0.33
66 18 0.26
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (65 bp):
AATTTAAAATTTAATAAATTTAAATAATTAAATATATTTTTAAATATTTAGTTTAAATTTTAAAT
Found at i:3817810 original size:65 final size:63
Alignment explanation
Indices: 3817663--3817810 Score: 160
Period size: 65 Copynumber: 2.3 Consensus size: 63
3817653 AATTTAAATA
* *
3817663 AATTTAAATAATTAAATATATTTTTAAATCTTTAGTTTAAATTTTAAATAATTAAATATTTAT
1 AATTTAAATAAATAAATATATTTTTAAATATTTAGTTTAAATTTTAAATAATTAAATATTTAT
*
3817726 AATTTAAATAAATTAAATATATATTTTATAATATTTA-TTT-ATTTTTAAAATAATTTAAA-ATT
1 AATTTAAATAAA-TAAATATAT-TTTTA-AATATTTAGTTTAAATTTT-AAATAA-TTAAATATT
*
3817788 TGT
61 TAT
*
3817791 -ATTTCACTATAAATAAATAT
1 AATTT-A-AATAAATAAATAT
3817811 CATAAATTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
63 11 0.15
64 18 0.25
65 27 0.37
66 17 0.23
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (63 bp):
AATTTAAATAAATAAATATATTTTTAAATATTTAGTTTAAATTTTAAATAATTAAATATTTAT
Found at i:3817870 original size:25 final size:25
Alignment explanation
Indices: 3817805--3817866 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
3817795 CACTATAAAT
*
3817805 AAATATCATAAAT-TTAATATTTTTA
1 AAATAT-ATAAATATTAATATTTATA
* *
3817830 AAATAAATTAATATTAAT-TTTATA
1 AAATATATAAATATTAATATTTATA
3817854 AAATATATAAATA
1 AAATATATAAATA
3817867 ATTATTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 21 0.68
25 10 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATATATAAATATTAATATTTATA
Found at i:3817873 original size:24 final size:23
Alignment explanation
Indices: 3817805--3817873 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 23
3817795 CACTATAAAT
3817805 AAATATCATAAATTTAA-TATTTTTA
1 AAATAT-ATAAA--TAATTATTTTTA
* *
3817830 AAATAAATTAAT-ATTAATTTTATA
1 AAATATATAAATAATT-ATTTT-TA
3817854 AAATATATAAATAATTATTT
1 AAATATATAAATAATTATTT
3817874 AATTTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
21 1 0.03
22 2 0.06
23 5 0.14
24 20 0.56
25 8 0.22
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATATAAATAATTATTTTTA
Found at i:3821515 original size:21 final size:22
Alignment explanation
Indices: 3821473--3821516 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3821463 GGTTGAATAT
**
3821473 TCTAGATCATTTTGGGGATGAA
1 TCTAGATCATTTTGAAGATGAA
*
3821495 TCTAGAT-ATTTTGAAGCTGAA
1 TCTAGATCATTTTGAAGATGAA
3821516 T
1 T
3821517 ATGGCCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.39
Consensus pattern (22 bp):
TCTAGATCATTTTGAAGATGAA
Done.