Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 43
Found at i:1453992 original size:23 final size:24
Alignment explanation
Indices: 1453856--1453995 Score: 72
Period size: 24 Copynumber: 5.9 Consensus size: 24
1453846 CACCACTGCT
*
1453856 CATATAATTTG-CACTGAAGTG-CCA
1 CATAGAATTTGTCAC-GAAG-GACCA
* * * *
1453880 CGTAGAATTTTTCCCGAAGGACCG
1 CATAGAATTTGTCACGAAGGACCA
* * * * *
1453904 CGTAGAATTTTTCCCTAAGGACCG
1 CATAGAATTTGTCACGAAGGACCA
* * * *
1453928 CGTTGAATATT-TCCCGAAGGACCG
1 CATAGAAT-TTGTCACGAAGGACCA
* * *
1453952 CGTAGAATTTTTCTCGAAGGACCA
1 CATAGAATTTGTCACGAAGGACCA
1453976 CATAG-ATTTGTCACGAAGGA
1 CATAGAATTTGTCACGAAGGA
1453996 TCGCGTAGAA
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
23 16 0.16
24 78 0.80
25 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
CATAGAATTTGTCACGAAGGACCA
Found at i:1455751 original size:117 final size:117
Alignment explanation
Indices: 1455531--1455768 Score: 271
Period size: 117 Copynumber: 2.0 Consensus size: 117
1455521 ATATTACAGG
* * * * * * *
1455531 TGGATCAATATTTCCAGTAGAGAGTTCATAATGAAAAGAACTTATCTGATGAGGGAGAATAAGTT
1 TGGATCAACATTTACAGTAGAAAGTTCATAATGAAAAGAACTCATCCGACGAGGGAGAAAAAGTT
* * * * ** * *
1455596 CATAATAAGATGAACTTGTTCATCCTTGGTTCGATTCCATTACAGAAGGAGA
66 CATAATAAGAAGAAATTCTTCAACCTCAGCTCGATTCCATCACAGAAGGAGA
*
1455648 TGGATCAACATTTACAGTGGAAAGTTCATAATGAAAAGAACTCATCCGACGAGGGAGAAAAAGTT
1 TGGATCAACATTTACAGTAGAAAGTTCATAATGAAAAGAACTCATCCGACGAGGGAGAAAAAGTT
** * * *
1455713 CATAATGCGAAGAAATTCTTTAACCTCAGCTC-ATTTCCATCACATAAGGAGT
66 CATAATAAGAAGAAATTCTTCAACCTCAGCTCGA-TTCCATCACAGAAGGAGA
1455765 TGGA
1 TGGA
1455769 ACAGCACTAA
Statistics
Matches: 99, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
116 1 0.01
117 98 0.99
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (117 bp):
TGGATCAACATTTACAGTAGAAAGTTCATAATGAAAAGAACTCATCCGACGAGGGAGAAAAAGTT
CATAATAAGAAGAAATTCTTCAACCTCAGCTCGATTCCATCACAGAAGGAGA
Found at i:1455984 original size:201 final size:201
Alignment explanation
Indices: 1455615--1456132 Score: 655
Period size: 201 Copynumber: 2.6 Consensus size: 201
1455605 ATGAACTTGT
* * * *
1455615 TCATC-CTTGGTTCGATTCCATTACAGAAGGAGATGGATCAACATTTACAGTGGAAAGTTCATAA
1 TCATCACTTTGTTCGATTCCATCACAGAAGGAGATGGATCAACATTTCCAGTGGAGAGTTCATAA
* * * * *
1455679 TGAAAAGAACTCATCCGACGAGGGAGAAAAAGTTCATAATGCGAAGAAATTCTTTAACCTCAGCT
66 TG-AGA-AACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTCTTCAACCTCAGCT
* * *
1455744 CATTTCCATCACATAAGGAGTTGGAACAGCACTAATACTTGGCTT-ATCCATCGCATATGGAGTT
129 CATTTCCATCACATAAGGAGTTGGAACAACACCAATACTTGG-TTCATCCATCGCATATGAAGTT
*
1455808 GGATCAGCA
193 GGATCAACA
* * * * * *
1455817 TCATCACTTTGTTCGATTCCATCACAGAAGGAGGTGGATAAACCTTTCCAGTAGAGGGTTTATAA
1 TCATCACTTTGTTCGATTCCATCACAGAAGGAGATGGATCAACATTTCCAGTGGAGAGTTCATAA
* * * * *
1455882 TGAGAAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTATCTTG
66 TGAGAAACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTCTTCAACCTCAGC-TC
*
1455947 A-TTCCATCACATAAGGAGTTGGAATAACACCAATACTTGGTTCATCCATCGCATATGAAGTTGG
130 ATTTCCATCACATAAGGAGTTGGAACAACACCAATACTTGGTTCATCCATCGCATATGAAGTTGG
1456011 ATCAACA
195 ATCAACA
* * * * *
1456018 TCATCACTTTGTTCTATTCCATCACAGAAGGAGATGAATCAATATATCCAGTGGAGAGCTCATAA
1 TCATCACTTTGTTCGATTCCATCACAGAAGGAGATGGATCAACATTTCCAGTGGAGAGTTCATAA
* * * *
1456083 TGAGAAAAACTCATTCGATTAGGCAGAAAAAGCTCATAATGAGAAGAACT
66 TGAG--AAACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACT
1456133 CATTCGATTA
Statistics
Matches: 270, Mismatches: 41, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
200 2 0.01
201 169 0.63
202 9 0.03
203 90 0.33
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (201 bp):
TCATCACTTTGTTCGATTCCATCACAGAAGGAGATGGATCAACATTTCCAGTGGAGAGTTCATAA
TGAGAAACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTCTTCAACCTCAGCTCA
TTTCCATCACATAAGGAGTTGGAACAACACCAATACTTGGTTCATCCATCGCATATGAAGTTGGA
TCAACA
Found at i:1455996 original size:42 final size:44
Alignment explanation
Indices: 1455947--1456059 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 44
1455937 CCTTATCTTG
1455947 ATTCCATCACATAAGGAGTTGGAAT-AACACCAAT-ACTTGGTTC-
1 ATTCCATCACATAAGGAGTTGG-ATCAACACC-ATCACTTGGTTCT
* * * * *
1455990 A-TCCATCGCATATGAAGTTGGATCAACATCATCACTTTGTTCT
1 ATTCCATCACATAAGGAGTTGGATCAACACCATCACTTGGTTCT
* * *
1456033 ATTCCATCACAGAAGGAGATGAATCAA
1 ATTCCATCACATAAGGAGTTGGATCAA
1456060 TATATCCAGT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
41 4 0.07
42 30 0.55
43 2 0.04
44 19 0.35
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (44 bp):
ATTCCATCACATAAGGAGTTGGATCAACACCATCACTTGGTTCT
Found at i:1456133 original size:39 final size:39
Alignment explanation
Indices: 1456074--1456171 Score: 160
Period size: 39 Copynumber: 2.5 Consensus size: 39
1456064 TCCAGTGGAG
1456074 AGCTCATAATGAGAAAAACTCATTCGATTAGGCAGAAAA
1 AGCTCATAATGAGAAAAACTCATTCGATTAGGCAGAAAA
* *
1456113 AGCTCATAATGAGAAGAACTCATTCGATTAGGTAGAAAA
1 AGCTCATAATGAGAAAAACTCATTCGATTAGGCAGAAAA
* *
1456152 AGTTCATAATGAGAATAACT
1 AGCTCATAATGAGAAAAACT
1456172 TGTTCAACCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.23
Consensus pattern (39 bp):
AGCTCATAATGAGAAAAACTCATTCGATTAGGCAGAAAA
Found at i:1456286 original size:42 final size:42
Alignment explanation
Indices: 1456227--1456499 Score: 313
Period size: 42 Copynumber: 6.6 Consensus size: 42
1456217 ACCGACCTTA
* * *
1456227 GCTCATCCATCGCATAAGGAGTTGGATCAAGATCATTATTTT
1 GCTCGTCCATCACATAAGGAGTTGGATCAAGATCATCATTTT
* * * * * *
1456269 TCTCATCTATCATATAAGGATTTGGATCAACATCATCATTTT
1 GCTCGTCCATCACATAAGGAGTTGGATCAAGATCATCATTTT
* * * * *
1456311 GCTCGTCTATCATATAAGAAGTTGGATCAACATCATCATTTC
1 GCTCGTCCATCACATAAGGAGTTGGATCAAGATCATCATTTT
1456353 GCTCGTCCATCACATAAGGAGTTGGATC-AGCATCATCATTTT
1 GCTCGTCCATCACATAAGGAGTTGGATCAAG-ATCATCATTTT
* *
1456395 GCTCGTCCATCACATAAAGAGTTGGATC-AGCATCATCATTTC
1 GCTCGTCCATCACATAAGGAGTTGGATCAAG-ATCATCATTTT
* * * *
1456437 GCTCGTCCATCA-ATAAGGAGTTGGATCAACATTA-C-CTTA
1 GCTCGTCCATCACATAAGGAGTTGGATCAAGATCATCATTTT
1456476 GCTCGTCCATCACATAAGGAGTTG
1 GCTCGTCCATCACATAAGGAGTTG
1456500 TTTCAGCATC
Statistics
Matches: 204, Mismatches: 24, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
39 14 0.07
40 12 0.06
41 18 0.09
42 160 0.78
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (42 bp):
GCTCGTCCATCACATAAGGAGTTGGATCAAGATCATCATTTT
Found at i:1456376 original size:126 final size:123
Alignment explanation
Indices: 1456221--1456510 Score: 375
Period size: 126 Copynumber: 2.3 Consensus size: 123
1456211 AACATCACCG
* * * * * *
1456221 ACCTTAGCTCATCCATCGCATAAGGAGTTGGATCAAG-ATCATTATTTTTCTCATCTATCATATA
1 ACCTTAGCTCGTCCATCACATAAGGAGTTGGATC-AGCATCATCATTTTGCTCATCCATCACATA
* * * *
1456285 AGGATTTGGATCAACATCATCATTTTGCTCGTCTATCATATAAGAAGTTGGATCAACATC
65 AAGAGTTGGATCAACATCATCATTTCGCTCGTCCATCA-ATAAGAAGTTGGATCAACATC
* * *
1456345 ATCATTTCGCTCGTCCATCACATAAGGAGTTGGATCAGCATCATCATTTTGCTCGTCCATCACAT
1 A-C-CTTAGCTCGTCCATCACATAAGGAGTTGGATCAGCATCATCATTTTGCTCATCCATCACAT
* * *
1456410 AAAGAGTTGGATCAGCATCATCATTTCGCTCGTCCATCAATAAGGAGTTGGATCAACATT
64 AAAGAGTTGGATCAACATCATCATTTCGCTCGTCCATCAATAAGAAGTTGGATCAACATC
**
1456470 ACCTTAGCTCGTCCATCACATAAGGAGTTGTTTCAGCATCA
1 ACCTTAGCTCGTCCATCACATAAGGAGTTGGATCAGCATCA
1456511 CCTTAGGTAA
Statistics
Matches: 143, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
123 35 0.24
124 2 0.01
125 23 0.16
126 83 0.58
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (123 bp):
ACCTTAGCTCGTCCATCACATAAGGAGTTGGATCAGCATCATCATTTTGCTCATCCATCACATAA
AGAGTTGGATCAACATCATCATTTCGCTCGTCCATCAATAAGAAGTTGGATCAACATC
Found at i:1456781 original size:3 final size:3
Alignment explanation
Indices: 1456773--1456808 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1456763 AACTATTAAA
* *
1456773 TAT TAT TAT TAT TAT TAT TAT TAC TAT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1456809 AAAATTCAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1457028 original size:14 final size:14
Alignment explanation
Indices: 1457009--1457045 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1456999 CCCTTGATTA
1457009 GCTTTCATCCAAGG
1 GCTTTCATCCAAGG
1457023 GCTTTCATCCAAGG
1 GCTTTCATCCAAGG
*
1457037 GCTATCATC
1 GCTTTCATC
1457046 TCTTCAATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (14 bp):
GCTTTCATCCAAGG
Found at i:1460108 original size:21 final size:21
Alignment explanation
Indices: 1460083--1460131 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1460073 TGGTACGGGT
1460083 GGCACATGGGTCACCAGTGGC
1 GGCACATGGGTCACCAGTGGC
*
1460104 GGCACATGGGTCACCAGTGGT
1 GGCACATGGGTCACCAGTGGC
1460125 GGCACAT
1 GGCACAT
1460132 CAGTGGGCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.27, G:0.37, T:0.16
Consensus pattern (21 bp):
GGCACATGGGTCACCAGTGGC
Found at i:1469586 original size:30 final size:30
Alignment explanation
Indices: 1469552--1469616 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
1469542 GTTAGTACAT
**
1469552 TTGCAATAT-GGTCACTGAACTTTTAGAAAC
1 TTGCAATATAGGTCACCCAACTTTTA-AAAC
* *
1469582 TTGC-ATTTAGGTCCCCCAACTTTTAAAAC
1 TTGCAATATAGGTCACCCAACTTTTAAAAC
1469611 TTGCAA
1 TTGCAA
1469617 CATAATCCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (30 bp):
TTGCAATATAGGTCACCCAACTTTTAAAAC
Found at i:1471483 original size:31 final size:31
Alignment explanation
Indices: 1471448--1471525 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
1471438 TCAAACAGTC
1471448 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
* *
1471479 GGGGACCATTTTGCAAACAGACTAAATTTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
**
1471510 GGGGACTTTATTGCAA
1 GGGGACCATATTGCAA
1471526 GTTTTAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:1477481 original size:25 final size:25
Alignment explanation
Indices: 1477453--1477511 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
1477443 TTGTAATTGA
*
1477453 TTAATAATACGATGATTAATGATAT
1 TTAATAATACGACGATTAATGATAT
*
1477478 TTAATAATGCGACGATTAATGATAT
1 TTAATAATACGACGATTAATGATAT
*
1477503 TTGATAATA
1 TTAATAATA
1477512 ATACAATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (25 bp):
TTAATAATACGACGATTAATGATAT
Found at i:1477511 original size:28 final size:27
Alignment explanation
Indices: 1477448--1477515 Score: 86
Period size: 25 Copynumber: 2.5 Consensus size: 27
1477438 AAATGTTGTA
*
1477448 ATTGATTAATAATACGATGATTAATGAT
1 ATTGA-TAATAATACGACGATTAATGAT
*
1477476 ATT--TAATAATGCGACGATTAATGAT
1 ATTGATAATAATACGACGATTAATGAT
1477501 ATTTGATAATAATAC
1 A-TTGATAATAATAC
1477516 AATTGACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 21 0.62
26 2 0.06
28 11 0.32
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (27 bp):
ATTGATAATAATACGACGATTAATGAT
Found at i:1479077 original size:24 final size:21
Alignment explanation
Indices: 1479050--1479116 Score: 55
Period size: 24 Copynumber: 3.0 Consensus size: 21
1479040 GTCAATTCTC
1479050 GAAGTAGTATCGATACCATAGTG
1 GAAG-AGTATCGATACCATA-TG
** *
1479073 AGAAGCAACATTGATACCATATG
1 -GAAG-AGTATCGATACCATATG
*
1479096 GATGAGTATCGATACCA-ATG
1 GAAGAGTATCGATACCATATG
1479116 G
1 G
1479117 GACAAAAAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 4 0.11
21 10 0.29
22 3 0.09
23 2 0.06
24 16 0.46
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (21 bp):
GAAGAGTATCGATACCATATG
Found at i:1486961 original size:17 final size:17
Alignment explanation
Indices: 1486938--1486980 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
1486928 TTAAAATAAT
*
1486938 TAAAATAACAAATAAATA
1 TAAAATAA-AAATAAAAA
1486956 -AAAATAAAAATAAAAA
1 TAAAATAAAAATAAAAA
1486972 TAAAATAAA
1 TAAAATAAA
1486981 CATACATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (17 bp):
TAAAATAAAAATAAAAA
Found at i:1486962 original size:6 final size:6
Alignment explanation
Indices: 1486939--1486980 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
1486929 TAAAATAATT
1486939 AAAATA ACAAAT- -AAATA AAAATA AAAATA AAAAT- AAAATA AA
1 AAAATA A-AAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
1486981 CATACATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 4 0.12
5 5 0.16
6 19 0.59
7 4 0.12
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:1486969 original size:16 final size:16
Alignment explanation
Indices: 1486930--1486980 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
1486920 AAACTGAATT
*
1486930 AAAAT-AATTAAAATA
1 AAAATAAATAAAAATA
1486945 ACAAATAAATAAAAATA
1 A-AAATAAATAAAAATA
*
1486962 AAAATAAAAATAAAATA
1 AAAATAAATA-AAAATA
1486979 AA
1 AA
1486981 CATACATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 1 0.03
16 12 0.39
17 18 0.58
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAATAAATAAAAATA
Found at i:1487068 original size:24 final size:23
Alignment explanation
Indices: 1487036--1487104 Score: 68
Period size: 29 Copynumber: 2.8 Consensus size: 23
1487026 AATAGGGAAC
1487036 AAATTAAACATAAAATAAGGGCT
1 AAATTAAACATAAAATAAGGGCT
1487059 AAATTAAAACAAATTAAAATGCAAGGGCT
1 AAATT-AAAC--A-TAAAAT--AAGGGCT
*
1487088 AAATCAAA-ATAAAATAA
1 AAATTAAACATAAAATAA
1487105 TAAAAACATA
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
22 2 0.05
23 5 0.13
24 10 0.26
25 1 0.03
26 1 0.03
27 6 0.15
28 3 0.08
29 11 0.28
ACGTcount: A:0.61, C:0.09, G:0.10, T:0.20
Consensus pattern (23 bp):
AAATTAAACATAAAATAAGGGCT
Found at i:1488343 original size:3 final size:3
Alignment explanation
Indices: 1488337--1488382 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
1488327 GTAATAATTT
*
1488337 ATA ATA ATA ATA ATA ATAA ATA AT- ATA TATA ATA ATT ATA A-A ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA ATA ATA
1488382 A
1 A
1488383 ACAAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 27 0.73
4 6 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1488352 original size:19 final size:19
Alignment explanation
Indices: 1488328--1488382 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
1488318 GTCTGGTTTG
1488328 TAATAATTTATAATAATAA
1 TAATAATTTATAATAATAA
**
1488347 TAATAATAAATAAT-ATATA
1 TAATAATTTATAATAATA-A
1488366 TAATAA-TTATAA-AATAA
1 TAATAATTTATAATAATAA
1488383 ACAAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.03
18 10 0.33
19 19 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATAATTTATAATAATAA
Found at i:1488358 original size:16 final size:16
Alignment explanation
Indices: 1488339--1488371 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1488329 AATAATTTAT
1488339 AATAATA-ATAATAATA
1 AATAATATAT-ATAATA
1488355 AATAATATATATAATA
1 AATAATATATATAATA
1488371 A
1 A
1488372 TTATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATATATATAATA
Found at i:1489019 original size:22 final size:22
Alignment explanation
Indices: 1488961--1489021 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1488951 TAGTGATATG
* *
1488961 GCACTTTTGTATCAATACGAAT
1 GCACTTTTGTATCAGTGCGAAT
1488983 GCACTTTTG-ATTCAGTGCGAAT
1 GCACTTTTGTA-TCAGTGCGAAT
*
1489005 GTACTTTTGTATCAGTG
1 GCACTTTTGTATCAGTG
1489022 TTGAGGCACT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (22 bp):
GCACTTTTGTATCAGTGCGAAT
Found at i:1491045 original size:3 final size:3
Alignment explanation
Indices: 1490947--1491015 Score: 111
Period size: 3 Copynumber: 22.3 Consensus size: 3
1490937 TTGTCAGTTG
*
1490947 TTA TTA TTAA TTA TATA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TT-A TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1490994 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
1491016 ATGTATTTAA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 56 0.90
4 6 0.10
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1491078 original size:23 final size:23
Alignment explanation
Indices: 1491051--1491109 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
1491041 ATTATATTTA
1491051 CAATATTACAAA-AAC-CAAGGCC
1 CAATATTA-AAATAACTCAAGGCC
*
1491073 CAA-ATATAAAATAACTCGAGGCC
1 CAATAT-TAAAATAACTCAAGGCC
1491096 CAATATTATAAATA
1 CAATATTA-AAATA
1491110 TAACCCATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 5 0.16
22 8 0.26
23 11 0.35
24 7 0.23
ACGTcount: A:0.51, C:0.20, G:0.08, T:0.20
Consensus pattern (23 bp):
CAATATTAAAATAACTCAAGGCC
Found at i:1493265 original size:35 final size:35
Alignment explanation
Indices: 1493192--1493266 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
1493182 CGTCACGTCC
* **
1493192 AGTAAGGACCTGAGTACACAGCCGAGGAACCGGTA
1 AGTAAGGACCTGAGCACACAGCCGAGGAACCGCCA
* *
1493227 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGACCTGAGCACACAGCCGAGGAACCGCCA
1493262 AGTAA
1 AGTAA
1493267 TCTTCCTCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.35, C:0.27, G:0.28, T:0.11
Consensus pattern (35 bp):
AGTAAGGACCTGAGCACACAGCCGAGGAACCGCCA
Found at i:1493371 original size:24 final size:24
Alignment explanation
Indices: 1493344--1493434 Score: 130
Period size: 24 Copynumber: 3.8 Consensus size: 24
1493334 CATAATTCAA
1493344 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* * *
1493368 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
1493392 GTCAA-TATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
1493415 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAAT
1493435 TCAAATTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 20 0.34
24 38 0.66
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:1493414 original size:47 final size:48
Alignment explanation
Indices: 1493344--1493434 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 48
1493334 CATAATTCAA
* *
1493344 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
1493392 GTCAA-TATCATATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAGAACAGAAT
1493435 TCAAATTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 35 0.88
48 5 0.12
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:1495912 original size:13 final size:13
Alignment explanation
Indices: 1495894--1495918 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1495884 AGTCAACGGG
1495894 TCAACGGGTCGGA
1 TCAACGGGTCGGA
1495907 TCAACGGGTCGG
1 TCAACGGGTCGG
1495919 GTCGGGTCAG
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:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
TCAACGGGTCGGA
Found at i:1495921 original size:18 final size:18
Alignment explanation
Indices: 1495898--1495938 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1495888 AACGGGTCAA
*
1495898 CGGGTCGGATCAACGGGT
1 CGGGTCGGATCAACAGGT
* *
1495916 CGGGTCGGGTCAGCAGGT
1 CGGGTCGGATCAACAGGT
1495934 CGGGT
1 CGGGT
1495939 AAACGGGTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGATCAACAGGT
Found at i:1495927 original size:31 final size:31
Alignment explanation
Indices: 1495890--1495957 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1495880 CTACAGTCAA
* *
1495890 CGGGTCAACGGGTCGGATCAACGGGTCGGGT
1 CGGGTCAACAGGTCGGATAAACGGGTCGGGT
* *
1495921 CGGGTCAGCAGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACAGGTCGGATAAACGGGTCGGGT
1495952 CGGGTC
1 CGGGTC
1495958 GGGTTATGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16
Consensus pattern (31 bp):
CGGGTCAACAGGTCGGATAAACGGGTCGGGT
Found at i:1498006 original size:35 final size:35
Alignment explanation
Indices: 1497933--1498007 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1497923 TGTCACGTCC
**
1497933 AGTAAGGCCCTGAGCACACAGCCAAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCAAGGAACCGCCA
* *
1497968 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCAAGGAACCGCCA
1498003 AGTAA
1 AGTAA
1498008 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.29, G:0.27, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCAAGGAACCGCCA
Found at i:1498112 original size:24 final size:24
Alignment explanation
Indices: 1498085--1498154 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
1498075 AATAATTCAA
*
1498085 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
1498109 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
1498133 GTCAA-TATCAGATCAGAATCCA
1 GTCAAGTATCAGATCAGAATCCA
1498155 GGTTAGGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
23 17 0.40
24 26 0.60
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1498165 original size:47 final size:48
Alignment explanation
Indices: 1498085--1498175 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 48
1498075 AATAATTCAA
* * * *
1498085 GTCAAGTATCATATCAGAATCCATGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
* *
1498133 GTCAA-TATCAGATCAGAATCCAGGTTAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
1498176 TCAAATTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 32 0.86
48 5 0.14
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:1500670 original size:13 final size:13
Alignment explanation
Indices: 1500646--1500688 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1500636 GCCGGTCAAC
*
1500646 GGTCAACGGGTCG
1 GGTCAACAGGTCG
*
1500659 GGTCAGCAGGTCG
1 GGTCAACAGGTCG
* *
1500672 GGTAAACGGGTCG
1 GGTCAACAGGTCG
1500685 GGTC
1 GGTC
1500689 GGGTTATGAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.21, G:0.47, T:0.16
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:1503867 original size:14 final size:15
Alignment explanation
Indices: 1503840--1503870 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1503830 ATTATACCTT
1503840 TTGCATACATTTGCA
1 TTGCATACATTTGCA
1503855 TTGCATA-ATTTGCA
1 TTGCATACATTTGCA
1503869 TT
1 TT
1503871 CTCATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (15 bp):
TTGCATACATTTGCA
Found at i:1509477 original size:20 final size:20
Alignment explanation
Indices: 1509452--1509520 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1509442 AATTTATAAA
1509452 TCCTTCGGGTCATCTGTAAG
1 TCCTTCGGGTCATCTGTAAG
* * *
1509472 TCCTTCGAG-CATGATGTTTAAA
1 TCCTTCGGGTCAT-CTG--TAAG
*
1509494 TCCTTCGGGTCATCTGTCAG
1 TCCTTCGGGTCATCTGTAAG
*
1509514 TCTTTCG
1 TCCTTCG
1509521 AGCAAGATGA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.08
20 18 0.49
22 13 0.35
23 3 0.08
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (20 bp):
TCCTTCGGGTCATCTGTAAG
Found at i:1509507 original size:42 final size:42
Alignment explanation
Indices: 1509448--1509529 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
1509438 CACGAATTTA
*
1509448 TAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCATGATGTT
1 TAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCAAGATGTT
* *
1509490 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
1 TAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCAAGATG
1509530 ATAAGTCCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCAAGATGTT
Found at i:1509734 original size:250 final size:250
Alignment explanation
Indices: 1509286--1509826 Score: 947
Period size: 250 Copynumber: 2.2 Consensus size: 250
1509276 CCAAACACCC
1509286 CCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGA
1 CCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGA
* * *
1509351 TAGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAATGAAAGTTTTGAAAAGTAAGAAGTT
66 TAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAATGAAAGTTTTGAAAAGTAAAAAGTC
1509416 TCTTACTCAGTAAATTATTTATCACGAATTTATAAATCCTTCGGGTCATCTGTAAGTCCTTCGAG
131 TCTTACTCAGTAAATTATTTATCACGAATTTATAAATCCTTCGGGTCATCTGTAAGTCCTTCGAG
*
1509481 CATGATGTTTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGT
196 CATGATGTTTAAATCCTTCGAGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGT
*
1509536 CCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGATTTTCGCATGAAAATGATA
1 CCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGA
*
1509601 TAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAATGAAATTTTTGAAAAGTAAAAAGTC
66 TAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAATGAAAGTTTTGAAAAGTAAAAAGTC
* * * *
1509666 TCTTACTTAGTAAATTATTTATCACGAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAG
131 TCTTACTCAGTAAATTATTTATCACGAATTTATAAATCCTTCGGGTCATCTGTAAGTCCTTCGAG
* *
1509731 CATGATGTTTAAATCTTTCGAGTCATTTGTCAGTCTTTCGAGCAAGATGATAAGT
196 CATGATGTTTAAATCCTTCGAGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGT
* * *
1509786 CCTTAGGTCCATCCGTCAGACCTTTGGGCAGGATGTTTACA
1 CCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACA
1509827 CTCTTTAATT
Statistics
Matches: 276, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
250 276 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (250 bp):
CCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGATTTTCGCATGAAAATGAGA
TAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAAATGAAAGTTTTGAAAAGTAAAAAGTC
TCTTACTCAGTAAATTATTTATCACGAATTTATAAATCCTTCGGGTCATCTGTAAGTCCTTCGAG
CATGATGTTTAAATCCTTCGAGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGT
Found at i:1509766 original size:42 final size:42
Alignment explanation
Indices: 1509698--1509779 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
1509688 CACGAATTTG
* * *
1509698 TAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCATGATGTT
1 TAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATGTT
* * *
1509740 TAAATCTTTCGAGTCATTTGTCAGTCTTTCGAGCAAGATG
1 TAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATG
1509780 ATAAGTCCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (42 bp):
TAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATGTT
Found at i:1509996 original size:3 final size:3
Alignment explanation
Indices: 1509988--1510048 Score: 63
Period size: 3 Copynumber: 19.3 Consensus size: 3
1509978 TTGTCCGTTG
1509988 TTA TTA TTAA TTA -TA TTA TTA TTA TTA TT- TTA TGTA TTTA TTA TATA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA T-TA
1510035 TTA TATA TTA TTA T
1 TTA T-TA TTA TTA T
1510049 ATTTACAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
2 4 0.08
3 33 0.65
4 13 0.25
5 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1510031 original size:30 final size:29
Alignment explanation
Indices: 1509988--1510051 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
1509978 TTGTCCGTTG
1509988 TTATTATTAATTATATTATTAT-TATTATT
1 TTATTATTAATTATA-TATTATATATTATT
*
1510017 TTATGTATTTATTATATATTATATATTATT
1 TTAT-TATTAATTATATATTATATATTATT
*
1510047 ATATT
1 TTATT
1510052 TACAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (29 bp):
TTATTATTAATTATATATTATATATTATT
Found at i:1512504 original size:3 final size:3
Alignment explanation
Indices: 1512496--1512520 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1512486 CAAACATGGT
1512496 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1512521 AGAATACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1514426 original size:2 final size:2
Alignment explanation
Indices: 1514419--1514449 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1514409 AAAATGGCTT
1514419 TA TA TA 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 T
1514450 TTGATACTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1517511 original size:31 final size:32
Alignment explanation
Indices: 1517473--1517532 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
1517463 CTTATTGGAA
**
1517473 ATAGAAAATTAAAAGAAAATAAA-AATATGAT
1 ATAGAAAAGGAAAAGAAAATAAATAATATGAT
1517504 ATAGAAAAGGAAAAGAAAATAAATAATAT
1 ATAGAAAAGGAAAAGAAAATAAATAATAT
1517533 CGACGGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (32 bp):
ATAGAAAAGGAAAAGAAAATAAATAATATGAT
Found at i:1520606 original size:16 final size:16
Alignment explanation
Indices: 1520587--1520622 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1520577 ATTTAACTAT
*
1520587 AATAAATTAAAATTAA
1 AATAAATTAAAAGTAA
*
1520603 AATAAATTTAAAGTAA
1 AATAAATTAAAAGTAA
1520619 AATA
1 AATA
1520623 TTATAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAAATTAAAAGTAA
Found at i:1522376 original size:13 final size:14
Alignment explanation
Indices: 1522333--1522377 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
1522323 TTTGCTTCAA
1522333 TATACATAATCAGT
1 TATACATAATCAGT
* *
1522347 TATAAAGTAATCGGT
1 TATACA-TAATCAGT
1522362 TAT-CATAATCAGT
1 TATACATAATCAGT
1522375 TAT
1 TAT
1522378 TATATCAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 10 0.38
14 6 0.23
15 10 0.38
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (14 bp):
TATACATAATCAGT
Found at i:1524117 original size:95 final size:94
Alignment explanation
Indices: 1523947--1524168 Score: 284
Period size: 95 Copynumber: 2.3 Consensus size: 94
1523937 CCGAACGATG
* *
1523947 TAGTATCGATACCATAGTAAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATTGATG
1 TAGTATCGATACCATAGT-AGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATC
* * *
1524012 TCGGATGGGGGTATCTATACCATAATATAA
65 TCGGAAGGGGGTATCGATACCATAATAGAA
* * ** *
1524042 TAGTATCGATACCATGGTGAGAGTATCGATACCAGGCTACATCGAAGCTAATTTTGGTATCGATA
1 TAGTATCGATACCATAGT-AGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGAT-
* **
1524107 CT-GGAAGGGGGTATCGATACCATATTAGGG
64 CTCGGAAGGGGGTATCGATACCATAATAGAA
1524137 TAGTATCGATACCATAGTAGGGGTATCGATAC
1 TAGTATCGATACCATAGTA-GGGTATCGATAC
1524169 TGAAGATCCA
Statistics
Matches: 109, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
94 1 0.01
95 107 0.98
96 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (94 bp):
TAGTATCGATACCATAGTAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATCT
CGGAAGGGGGTATCGATACCATAATAGAA
Found at i:1524164 original size:20 final size:20
Alignment explanation
Indices: 1524114--1524168 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 20
1524104 ATACTGGAAG
*
1524114 GGGGTATCGATACCATATTA
1 GGGGTATCGATACCATAGTA
1524134 GGGTAGTATCGATACCATAGTA
1 GGG--GTATCGATACCATAGTA
1524156 GGGGTATCGATAC
1 GGGGTATCGATAC
1524169 TGAAGATCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 13 0.41
22 19 0.59
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (20 bp):
GGGGTATCGATACCATAGTA
Found at i:1524553 original size:59 final size:59
Alignment explanation
Indices: 1524490--1524955 Score: 788
Period size: 59 Copynumber: 7.9 Consensus size: 59
1524480 ATTACTGAAT
1524490 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
1524549 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* **
1524608 GGCACTTTGTGTACTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTTTAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
1524667 GGAACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATTG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
*
1524726 GACACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
1524785 GGCACTTTGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* * * *
1524844 GCCACTTTGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTAAGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* * * *
1524903 GGCACTTTGTGTGCTAAAATGATAAGGAAATCATAATAATTATATGAATTTCC
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCC
1524956 TAGTGAATTT
Statistics
Matches: 385, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 385 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (59 bp):
GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
Found at i:1526601 original size:19 final size:20
Alignment explanation
Indices: 1526577--1526616 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1526567 AATTTAATCA
*
1526577 AATATATAAT-TAAAAATTC
1 AATATAAAATCTAAAAATTC
*
1526596 AATATAAAATCTTAAAATTC
1 AATATAAAATCTAAAAATTC
1526616 A
1 A
1526617 TTAACACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
AATATAAAATCTAAAAATTC
Found at i:1528365 original size:15 final size:14
Alignment explanation
Indices: 1528339--1528388 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
1528329 TACCTCCTCA
1528339 TCCTTCTTCTTCTTCT
1 TCCTT-TTCTTC-TCT
**
1528355 TGTTTTTCTTCTCT
1 TCCTTTTCTTCTCT
1528369 TCCTTTTCTTCATCT
1 TCCTTTTCTTC-TCT
1528384 TCCTT
1 TCCTT
1528389 CACCATCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 12 0.41
15 14 0.48
16 3 0.10
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64
Consensus pattern (14 bp):
TCCTTTTCTTCTCT
Found at i:1530000 original size:19 final size:20
Alignment explanation
Indices: 1529976--1530015 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1529966 AATTTAATCG
*
1529976 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
1529995 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
1530015 A
1 A
1530016 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:1539425 original size:19 final size:19
Alignment explanation
Indices: 1539401--1539439 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1539391 TCGAATGCAT
1539401 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1539420 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1539439 T
1 T
1539440 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1539564 original size:64 final size:65
Alignment explanation
Indices: 1539387--1539549 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
1539377 GAATTAATTG
* * * *
1539387 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
1539452 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
1539515 A
65 A
1539516 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
1539550 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1543100 original size:20 final size:21
Alignment explanation
Indices: 1543075--1543133 Score: 84
Period size: 20 Copynumber: 2.8 Consensus size: 21
1543065 TTTGGTGCAG
1543075 AGGGAATCGATTCCCCCTTT-
1 AGGGAATCGATTCCCCCTTTA
*
1543095 AGGGAACCGATTCCCCCTTTAA
1 AGGGAATCGATTCCCCCTTT-A
1543117 AGGGGAATCGATTCCCC
1 A-GGGAATCGATTCCCC
1543134 TCACAGGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 19 0.56
22 1 0.03
23 14 0.41
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.24
Consensus pattern (21 bp):
AGGGAATCGATTCCCCCTTTA
Found at i:1548530 original size:23 final size:23
Alignment explanation
Indices: 1548504--1548559 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
1548494 CACGAAAATA
1548504 CTGACTGGACCTTTTAGAAGGTG
1 CTGACTGGACCTTTTAGAAGGTG
1548527 CTGACTGGACCTTTTAGAAGGTG
1 CTGACTGGACCTTTTAGAAGGTG
1548550 CTGACTGGAC
1 CTGACTGGAC
1548560 GCCACATCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (23 bp):
CTGACTGGACCTTTTAGAAGGTG
Found at i:1551268 original size:30 final size:30
Alignment explanation
Indices: 1551234--1551298 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
1551224 ATTATGTTAA
1551234 TCTTTTTATGATCAACCCAAAACTTTATGC
1 TCTTTTTATGATCAACCCAAAACTTTATGC
1551264 TCTTTTTATGATCAACCCAAAACTTTATGC
1 TCTTTTTATGATCAACCCAAAACTTTATGC
1551294 TCTTT
1 TCTTT
1551299 GACTGTTGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (30 bp):
TCTTTTTATGATCAACCCAAAACTTTATGC
Found at i:1553467 original size:37 final size:37
Alignment explanation
Indices: 1553426--1553500 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
1553416 AAAAGTCCGA
* * * *
1553426 TCGGGTGGAGGGTATATATTTTTCGGGTCAGGTCGGG
1 TCGGGTGAAGGATATAAAATTTTCGGGTCAGGTCGGG
*
1553463 TCGGGTGAAGGATATAAAATTTTCGGGTCGGGTCGGG
1 TCGGGTGAAGGATATAAAATTTTCGGGTCAGGTCGGG
1553500 T
1 T
1553501 TGGCCGAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.17, C:0.11, G:0.41, T:0.31
Consensus pattern (37 bp):
TCGGGTGAAGGATATAAAATTTTCGGGTCAGGTCGGG
Found at i:1553816 original size:15 final size:14
Alignment explanation
Indices: 1553789--1553818 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1553779 AAAATATTAA
1553789 ATATTTAATATATT
1 ATATTTAATATATT
1553803 ATATTTATATATATT
1 ATATTTA-ATATATT
1553818 A
1 A
1553819 AATACATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATTTAATATATT
Found at i:1555396 original size:12 final size:12
Alignment explanation
Indices: 1555379--1555403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1555369 TGTAATTAGT
1555379 CTTATAAATAGA
1 CTTATAAATAGA
1555391 CTTATAAATAGA
1 CTTATAAATAGA
1555403 C
1 C
1555404 ATAATGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (12 bp):
CTTATAAATAGA
Found at i:1557170 original size:33 final size:34
Alignment explanation
Indices: 1557132--1557197 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
1557122 TTATAGTATT
1557132 TTTATATTTGATATATT-AATATCTTAATAATTA
1 TTTATATTTGATATATTAAATATCTTAATAATTA
* * * *
1557165 TTTATATTTTATATTTTAAATATTTTCATAATT
1 TTTATATTTGATATATTAAATATCTTAATAATT
1557198 TTTTCTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (34 bp):
TTTATATTTGATATATTAAATATCTTAATAATTA
Found at i:1557737 original size:14 final size:14
Alignment explanation
Indices: 1557720--1557761 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1557710 TAAATATTTT
1557720 AATAATTATATTAAA
1 AATAATTAT-TTAAA
1557735 ATATAATTATTTAAA
1 A-ATAATTATTTAAA
1557750 AACT-ATTATTTA
1 AA-TAATTATTTA
1557762 TCTCTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.36
15 8 0.32
16 8 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
AATAATTATTTAAA
Found at i:1557751 original size:16 final size:16
Alignment explanation
Indices: 1557721--1557750 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1557711 AAATATTTTA
1557721 ATAATTATATTAAAAT
1 ATAATTATATTAAAAT
1557737 ATAATTAT-TTAAAA
1 ATAATTATATTAAAA
1557751 ACTATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAATTATATTAAAAT
Found at i:1560662 original size:22 final size:22
Alignment explanation
Indices: 1560636--1560685 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
1560626 GAACAATATT
1560636 GATACCATATG-GAAGAGGTATC
1 GATACCATATGTGAAG-GGTATC
*
1560658 GATACC-TATGTGGAGGGTATC
1 GATACCATATGTGAAGGGTATC
1560679 GATACCA
1 GATACCA
1560686 GGGAACATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (22 bp):
GATACCATATGTGAAGGGTATC
Found at i:1560768 original size:24 final size:19
Alignment explanation
Indices: 1560707--1560756 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1560697 ATCTAATTTT
*
1560707 GGTATCGATACCTAAGAGG
1 GGTATCGGTACCTAAGAGG
1560726 GGTATCGGTACCTAAGAGG
1 GGTATCGGTACCTAAGAGG
1560745 GGTATCGGTACC
1 GGTATCGGTACC
1560757 CTAGAGTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (19 bp):
GGTATCGGTACCTAAGAGG
Found at i:1564011 original size:15 final size:15
Alignment explanation
Indices: 1563991--1564021 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1563981 GGGTTTTATT
1563991 ATTTCAAATTAATTA
1 ATTTCAAATTAATTA
1564006 ATTTCAAATTAATTA
1 ATTTCAAATTAATTA
1564021 A
1 A
1564022 ATCTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTCAAATTAATTA
Found at i:1568270 original size:24 final size:22
Alignment explanation
Indices: 1568226--1568285 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 22
1568216 CGAAGAGAGG
*
1568226 AAAAAATAAATAAATTGAGAA-A
1 AAAAAATAAA-AAATTAAGAAGA
1568248 ATAAAAATAAAAAATGTTAAGAAGGA
1 A-AAAAATAAAAAA--TTAAGAA-GA
1568274 AAAAAATAAAAA
1 AAAAAATAAAAA
1568286 TAAAAATGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 4 0.12
23 9 0.28
24 6 0.19
25 11 0.34
26 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAAATAAAAAATTAAGAAGA
Found at i:1572569 original size:20 final size:20
Alignment explanation
Indices: 1572496--1572572 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 20
1572486 TCTAGAGAGT
***
1572496 TCTACAATTCTCTAGAGTTC
1 TCTACAATTCTCTAGAAAAC
** * *
1572516 TCTGGAATGCTCTAGAAAAT
1 TCTACAATTCTCTAGAAAAC
*
1572536 TCTACACTTCTCTAGAAAAC
1 TCTACAATTCTCTAGAAAAC
* *
1572556 TCTAGAATTTTCTAGAA
1 TCTACAATTCTCTAGAA
1572573 TCTCTCCAAT
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (20 bp):
TCTACAATTCTCTAGAAAAC
Found at i:1572570 original size:40 final size:40
Alignment explanation
Indices: 1572485--1572572 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 40
1572475 TTCCACAAGC
* * *** *
1572485 TTCTAGAGAGTTCTACAATTCTCTAGAGTTCTCTGGAATG
1 TTCTAGAAAATTCTACAATTCTCTAGAAAACTCTAGAATG
* * *
1572525 CTCTAGAAAATTCTACACTTCTCTAGAAAACTCTAGAATT
1 TTCTAGAAAATTCTACAATTCTCTAGAAAACTCTAGAATG
1572565 TTCTAGAA
1 TTCTAGAA
1572573 TCTCTCCAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (40 bp):
TTCTAGAAAATTCTACAATTCTCTAGAAAACTCTAGAATG
Found at i:1575753 original size:3 final size:3
Alignment explanation
Indices: 1575738--1575769 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1575728 TACTAAGGAA
*
1575738 GAC GAC AAC GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
1575770 TGATGGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.31, G:0.31, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:1583771 original size:16 final size:16
Alignment explanation
Indices: 1583750--1583807 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
1583740 AATTTTTTAA
1583750 TAATTTTTAATTTGTT
1 TAATTTTTAATTTGTT
* * *
1583766 TAATTTAATATTTTTTT
1 TAATTT-TTAATTTGTT
1583783 CTAAAATTTTTAATTTGTT
1 -T--AATTTTTAATTTGTT
1583802 TAATTT
1 TAATTT
1583808 AATATTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 11 0.34
17 7 0.22
18 2 0.06
19 7 0.22
20 5 0.16
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (16 bp):
TAATTTTTAATTTGTT
Found at i:1583791 original size:36 final size:37
Alignment explanation
Indices: 1583742--1583821 Score: 146
Period size: 36 Copynumber: 2.2 Consensus size: 37
1583732 TATACATAAA
1583742 TTTTT-TAATAATTTTTAATTTGTTTAATTTAATATT
1 TTTTTCTAATAATTTTTAATTTGTTTAATTTAATATT
1583778 TTTTTCTAA-AATTTTTAATTTGTTTAATTTAATATT
1 TTTTTCTAATAATTTTTAATTTGTTTAATTTAATATT
1583814 TTTTTCTA
1 TTTTTCTA
1583822 CTTAGAAGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
36 40 0.93
37 3 0.07
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (37 bp):
TTTTTCTAATAATTTTTAATTTGTTTAATTTAATATT
Found at i:1584575 original size:20 final size:19
Alignment explanation
Indices: 1584548--1584587 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1584538 TAAATATTAT
1584548 TTTAATAAAAATAATAATA
1 TTTAATAAAAATAATAATA
* *
1584567 TTTACATAAATATATTAATA
1 TTTA-ATAAAAATAATAATA
1584587 T
1 T
1584588 AAAATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATAAAAATAATAATA
Found at i:1584576 original size:35 final size:34
Alignment explanation
Indices: 1584520--1584628 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 34
1584510 TAATAATTCT
* * *
1584520 AAATAAATAATAATTATATAAATATTATT-TTAATAA
1 AAAT-AATAATATTTACATAAATA-TATTAAT-ATAA
1584556 AAATAATAATATTTACATAAATATATTAATATAA
1 AAATAATAATATTTACATAAATATATTAATATAA
* *
1584590 AATATAATAACTATTTA-A-AAA-ATACTAACATAA
1 AA-ATAATAA-TATTTACATAAATATATTAATATAA
1584623 AAATAA
1 AAATAA
1584629 ATTTCTTACC
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
32 4 0.06
33 12 0.18
34 13 0.20
35 26 0.40
36 10 0.15
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (34 bp):
AAATAATAATATTTACATAAATATATTAATATAA
Found at i:1585665 original size:124 final size:124
Alignment explanation
Indices: 1585485--1585734 Score: 473
Period size: 124 Copynumber: 2.0 Consensus size: 124
1585475 ATCATTTCTC
* *
1585485 TAACAGATAAGTTGATGGGGGTGTCCTTGTCTTATGTTATCAATCAAAAATAGGATAAACTATCT
1 TAACAAATAAGTTAATGGGGGTGTCCTTGTCTTATGTTATCAATCAAAAATAGGATAAACTATCT
1585550 CCCTGATGACCCGTTAATATTTAATAGAATGATTGATGTGGCAGTTAAATAAATTAGTA
66 CCCTGATGACCCGTTAATATTTAATAGAATGATTGATGTGGCAGTTAAATAAATTAGTA
1585609 TAACAAATAAGTTAATGGGGGTGTCCTTGTCTTATGTTATCAATCAAAAATAGGATAAACTATCT
1 TAACAAATAAGTTAATGGGGGTGTCCTTGTCTTATGTTATCAATCAAAAATAGGATAAACTATCT
*
1585674 CCCTGATGACTCGTTAATATTTAATAGAATGATTGATGTGGCAGTTAAATAAATTAGTA
66 CCCTGATGACCCGTTAATATTTAATAGAATGATTGATGTGGCAGTTAAATAAATTAGTA
1585733 TA
1 TA
1585735 TTTATATATT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (124 bp):
TAACAAATAAGTTAATGGGGGTGTCCTTGTCTTATGTTATCAATCAAAAATAGGATAAACTATCT
CCCTGATGACCCGTTAATATTTAATAGAATGATTGATGTGGCAGTTAAATAAATTAGTA
Found at i:1586436 original size:26 final size:26
Alignment explanation
Indices: 1586402--1586455 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
1586392 ATCAATTAAT
* *
1586402 TAACTGAATTAACCAAAATTATCAAA
1 TAACCGAATCAACCAAAATTATCAAA
1586428 TAACCGAATCAACCAAAATTATCAAA
1 TAACCGAATCAACCAAAATTATCAAA
1586454 TA
1 TA
1586456 TTAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.19, G:0.04, T:0.24
Consensus pattern (26 bp):
TAACCGAATCAACCAAAATTATCAAA
Found at i:1586831 original size:21 final size:21
Alignment explanation
Indices: 1586803--1586842 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1586793 CTTAAATAAT
*
1586803 TTAAAAAATATAAT-TTTTAG
1 TTAAAAAAAATAATATTTTAG
1586823 TTAATAAAAAATAATATTTT
1 TTAA-AAAAAATAATATTTT
1586843 TTATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TTAAAAAAAATAATATTTTAG
Found at i:1586834 original size:23 final size:23
Alignment explanation
Indices: 1586804--1586853 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1586794 TTAAATAATT
1586804 TAAAAAAT-ATAATTTTTAGTTAA
1 TAAAAAATAATAATTTTTA-TTAA
*
1586827 TAAAAAATAATATTTTTTATTAA
1 TAAAAAATAATAATTTTTATTAA
1586850 -AAAA
1 TAAAA
1586854 TCATATAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 4 0.16
23 12 0.48
24 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAAAAATAATAATTTTTATTAA
Found at i:1601179 original size:21 final size:21
Alignment explanation
Indices: 1601150--1601191 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1601140 GAGACGATAA
* *
1601150 AGCATAAGTGTTCGACAAATT
1 AGCACAAGTATTCGACAAATT
1601171 AGCACAAGTATTCGACAAATT
1 AGCACAAGTATTCGACAAATT
1601192 GTCCCACTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (21 bp):
AGCACAAGTATTCGACAAATT
Found at i:1601939 original size:20 final size:20
Alignment explanation
Indices: 1601902--1601958 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1601892 ATTAATTATT
1601902 ATTATTATTAAATATTTGAAG
1 ATTATT-TTAAATATTTGAAG
*
1601923 ATTATTTTAAGAT-TTTGATG
1 ATTATTTTAA-ATATTTGAAG
* *
1601943 ATTTTTTTAATTATTT
1 ATTATTTTAAATATTT
1601959 AATTACATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 22 0.71
21 8 0.26
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (20 bp):
ATTATTTTAAATATTTGAAG
Found at i:1604589 original size:64 final size:64
Alignment explanation
Indices: 1604485--1604663 Score: 180
Period size: 64 Copynumber: 2.8 Consensus size: 64
1604475 GAATAAATTG
* *** * * * * *
1604485 AACATCTAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACT-TGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATT-TTAA
* *
1604549 AACATCGGATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATTTTAA
* * * ** **
1604613 AACATCGAATGCATTTTATGCATCAATGTACACTCGGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACT
1604664 AAGTGTTCCA
Statistics
Matches: 95, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 90 0.95
65 5 0.05
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATTTTAA
Found at i:1610493 original size:44 final size:44
Alignment explanation
Indices: 1610440--1610543 Score: 122
Period size: 44 Copynumber: 2.3 Consensus size: 44
1610430 CACTTAACAG
* * * *
1610440 TGCACCGATGCATCCCTTTGAATGTGCATCGAT-ACATCAGCTGA
1 TGCATCGATGCATCCCCTTGAATGTGCATCGATCACAACAGC-CA
*
1610484 TGCATCGATGCA-CGCCCTTGAATGTGCATCGATGCACAAGAGCCA
1 TGCATCGATGCATC-CCCTTGAATGTGCATCGAT-CACAACAGCCA
1610529 TGCATCGATGCATCC
1 TGCATCGATGCATCC
1610544 GTCAGGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
43 1 0.02
44 29 0.57
45 14 0.27
46 7 0.14
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (44 bp):
TGCATCGATGCATCCCCTTGAATGTGCATCGATCACAACAGCCA
Found at i:1613190 original size:64 final size:65
Alignment explanation
Indices: 1613115--1613320 Score: 208
Period size: 64 Copynumber: 3.2 Consensus size: 65
1613105 GCATCAATCC
* * * * *
1613115 ATGCATCGATGCACCATTGAATAAATT-GAACATCGAATGCATTTCATGCATCGATGCACTCTCT
1 ATGCACCGATGCACCATTGGATATATTAAAACATCGAATGCATTTCATGCATCGATGCACACTCT
* * * **
1613179 ATGCAACGATGCA-C-TTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGC
1 ATGCACCGATGCACCATT-GGATATATTAAAACATCGAATGCATTTCATGCATCGATGCACACTC
*
1613242 A
65 T
* * * *
1613243 ATGCACCGATGCACTCA--GGCTATTTTCAAACATCGAATGCATTTTATGCATCGATGCACACT-
1 ATGCACCGATGCAC-CATTGGATATATTAAAACATCGAATGCATTTCATGCATCGATGCACACTC
1613305 T
65 T
1613306 AGTGCACCGATGCAC
1 A-TGCACCGATGCAC
1613321 TAAGTGTTCC
Statistics
Matches: 117, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
62 2 0.02
63 7 0.06
64 107 0.91
66 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (65 bp):
ATGCACCGATGCACCATTGGATATATTAAAACATCGAATGCATTTCATGCATCGATGCACACTCT
Found at i:1613321 original size:64 final size:63
Alignment explanation
Indices: 1613143--1613322 Score: 229
Period size: 64 Copynumber: 2.8 Consensus size: 63
1613133 GAATAAATTG
* * * * *
1613143 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCAACGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* *
1613207 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
1613270 A
63 A
*
1613271 AACATCGAATGCATTTTATGCATCGATGCACACTTAGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTTA-TGCACCGATGCACTA
1613323 AGTGTTCCAA
Statistics
Matches: 102, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 92 0.90
65 5 0.05
66 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:1614872 original size:33 final size:33
Alignment explanation
Indices: 1614811--1614894 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
1614801 AAAAATTATC
1614811 AAACTAACAAAACTAATTTATTTAAATATAACTT
1 AAACTAAC-AAACTAATTTATTTAAATATAACTT
* * * *
1614845 CAATTAATAAACTACTTT-TTTATAATATAACTT
1 AAACTAACAAACTAATTTATTTA-AATATAACTT
1614878 AAACTAACAAACTAATT
1 AAACTAACAAACTAATT
1614895 AACAAAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 4 0.10
33 32 0.78
34 5 0.12
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (33 bp):
AAACTAACAAACTAATTTATTTAAATATAACTT
Found at i:1615632 original size:14 final size:14
Alignment explanation
Indices: 1615615--1615642 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1615605 TGAAATCTGT
1615615 AAAACATTTTCCAG
1 AAAACATTTTCCAG
1615629 AAAACATTTTCCAG
1 AAAACATTTTCCAG
1615643 TGTTTGGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAACATTTTCCAG
Found at i:1620781 original size:28 final size:28
Alignment explanation
Indices: 1620745--1620831 Score: 77
Period size: 34 Copynumber: 2.9 Consensus size: 28
1620735 AATAACCACT
1620745 ATAAACAAAATCAGAAATCGAAGAAACC
1 ATAAACAAAATCAGAAATCGAAGAAACC
** *
1620773 ATAAACAAACCCAGATTGAAATTTC-ACAGAAACT
1 ATAAACAAAATC--A--GAAA--TCGA-AGAAACC
1620807 ATAAACAAAATCAGAAATCGAAGAA
1 ATAAACAAAATCAGAAATCGAAGAA
1620832 GTTAAATAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
28 16 0.35
29 1 0.02
30 5 0.11
32 5 0.11
33 1 0.02
34 18 0.39
ACGTcount: A:0.57, C:0.17, G:0.10, T:0.15
Consensus pattern (28 bp):
ATAAACAAAATCAGAAATCGAAGAAACC
Found at i:1627376 original size:24 final size:24
Alignment explanation
Indices: 1627344--1627397 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1627334 GTATTCAAAA
*
1627344 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTAGTCAATACCCGGAC
* *
1627368 TTTGATCTTAGTCAATACTCGGAT
1 TTTGATCTTAGTCAATACCCGGAC
1627392 TTTGAT
1 TTTGAT
1627398 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTAGTCAATACCCGGAC
Found at i:1628719 original size:20 final size:20
Alignment explanation
Indices: 1628694--1628735 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1628684 GTTGGTATAA
1628694 AAAATGAATATCGCAACGCG
1 AAAATGAATATCGCAACGCG
*
1628714 AAAATGACTATCGCAACGCG
1 AAAATGAATATCGCAACGCG
1628734 AA
1 AA
1628736 TTTGACTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.14
Consensus pattern (20 bp):
AAAATGAATATCGCAACGCG
Found at i:1628741 original size:20 final size:20
Alignment explanation
Indices: 1628702--1628771 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
1628692 AAAAAATGAA
**
1628702 TATCGCAACGCGAAAATGAC
1 TATCGCAACGCGAATTTGAC
1628722 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTTGAC
* **
1628742 TATTGCAACTTGAATTTGAC
1 TATCGCAACGCGAATTTGAC
1628762 TATCGCAACG
1 TATCGCAACG
1628772 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (20 bp):
TATCGCAACGCGAATTTGAC
Found at i:1628839 original size:20 final size:20
Alignment explanation
Indices: 1628814--1628861 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1628804 GCGATTCTTT
1628814 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1628834 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
1628854 GGTTGCGA
1 CGTTGCGA
1628862 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1630787 original size:20 final size:20
Alignment explanation
Indices: 1630764--1630814 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1630754 TCTGAAACTT
*
1630764 AAAATCGCAATAAGAAAATG
1 AAAATCGCAACAAGAAAATG
*
1630784 AAAATCGCAACACGAAAATG
1 AAAATCGCAACAAGAAAATG
**
1630804 ACTATCGCAAC
1 AAAATCGCAAC
1630815 GCGAATTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.53, C:0.20, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACAAGAAAATG
Found at i:1630819 original size:20 final size:20
Alignment explanation
Indices: 1630777--1630859 Score: 96
Period size: 20 Copynumber: 4.2 Consensus size: 20
1630767 ATCGCAATAA
*
1630777 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
1630797 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
1630817 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
1630837 G-AAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACGC
1630856 GAAA
1 GAAA
1630860 CTAAAATCAC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.28
20 38 0.72
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:1631275 original size:22 final size:22
Alignment explanation
Indices: 1631244--1631300 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1631234 GATGGAGATA
1631244 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
1631266 GACTGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1631288 GACGGATGTCGCC
1 GACGGATTTCGCC
1631301 TTAGAGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1631500 original size:20 final size:20
Alignment explanation
Indices: 1631472--1631558 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
1631462 GAAAATCACA
* *
1631472 TTGCAATAGTCAGCATCGCG
1 TTGCGATAGTCAGAATCGCG
*
1631492 TTGCGATAGTCAGCATCGCG
1 TTGCGATAGTCAGAATCGCG
*
1631512 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1631532 TTGCGATAGTCAGAATCGTG
1 TTGCGATAGTCAGAATCGCG
1631552 TTGCGAT
1 TTGCGAT
1631559 TTACATATTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1631575 original size:20 final size:20
Alignment explanation
Indices: 1631552--1631598 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1631542 CAGAATCGTG
1631552 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
1631572 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
1631592 TTGCGAT
1 TTGCGAT
1631599 AGTCGGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCA
Found at i:1634312 original size:18 final size:18
Alignment explanation
Indices: 1634289--1634390 Score: 58
Period size: 18 Copynumber: 5.7 Consensus size: 18
1634279 ATTGAAAAAA
1634289 ATATAATATATATATAAT
1 ATATAATATATATATAAT
*
1634307 ATATAAAATTATATATAA-
1 ATATAATA-TATATATAAT
*
1634325 ACTAT-ATTTATATTATAAACT
1 A-TATAATATATA-TAT-AA-T
1634346 ATATAAT-TAT-TATAAACT
1 ATATAATATATATAT-AA-T
1634364 ATATAAT-TAT-TATAA-
1 ATATAATATATATATAAT
1634379 ACTAT-ATATATA
1 A-TATAATATATA
1634391 AATTATATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 21
0.75 0.03 0.22
Matches are distributed among these distances:
15 3 0.04
16 6 0.08
17 6 0.08
18 33 0.46
19 14 0.20
20 6 0.08
21 3 0.04
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATATATATATAAT
Found at i:1634392 original size:13 final size:13
Alignment explanation
Indices: 1634374--1634538 Score: 64
Period size: 13 Copynumber: 11.8 Consensus size: 13
1634364 ATATAATTAT
1634374 TATAAACTATATA
1 TATAAACTATATA
*
1634387 TATAAATTATATTTA
1 TATAAACTATA--TA
* * *
1634402 TGTGAATTATATA
1 TATAAACTATATA
*
1634415 TATAAAAACTATGTA
1 TAT--AAACTATATA
*
1634430 TATAAAAT-TATA
1 TATAAACTATATA
* * *
1634442 AACTATA-TTTATA
1 TA-TAAACTATATA
1634455 TTATAAACTATATAA
1 -TATAAACTATAT-A
1634470 TTATTATAAGCTATATA
1 -TA-TA-AA-CTATATA
* * *
1634487 TAAAAATTATGTTTA
1 TATAAACTA--TATA
* *
1634502 TGTGAACTATATA
1 TATAAACTATATA
*
1634515 TATAAACTATGTA
1 TATAAACTATATA
1634528 TATAAACTATA
1 TATAAACTATA
1634539 AAAAGTATAT
Statistics
Matches: 112, Mismatches: 26, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
12 5 0.04
13 53 0.47
14 7 0.06
15 34 0.30
16 4 0.04
17 3 0.03
18 6 0.05
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (13 bp):
TATAAACTATATA
Found at i:1634398 original size:9 final size:9
Alignment explanation
Indices: 1634318--1634386 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
1634308 TATAAAATTA
1634318 TATATAAAC
1 TATATAAAC
**
1634327 TATATTTA-
1 TATATAAAC
1634335 TATTATAAAC
1 TA-TATAAAC
*
1634345 TATAT-AAT
1 TATATAAAC
1634353 TATTATAAAC
1 TA-TATAAAC
*
1634363 TATAT-AAT
1 TATATAAAC
1634371 TATTATAAAC
1 TA-TATAAAC
1634381 TATATA
1 TATATA
1634387 TATAAATTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
8 10 0.22
9 26 0.57
10 10 0.22
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (9 bp):
TATATAAAC
Found at i:1634454 original size:21 final size:18
Alignment explanation
Indices: 1634409--1634488 Score: 74
Period size: 18 Copynumber: 4.3 Consensus size: 18
1634399 TTATGTGAAT
*
1634409 TATATATA-TAAAAACTA
1 TATATATATTATAAACTA
*
1634426 TGTATATAAAATTATAAACTA
1 --TATAT-ATATTATAAACTA
*
1634447 TATTTATATTATAAACTA
1 TATATATATTATAAACTA
*
1634465 TATA-ATTATTATAAGCTA
1 TATATA-TATTATAAACTA
1634483 TATATA
1 TATATA
1634489 AAAATTATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
17 1 0.02
18 30 0.59
19 10 0.20
20 2 0.04
21 8 0.16
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (18 bp):
TATATATATTATAAACTA
Found at i:1634468 original size:100 final size:98
Alignment explanation
Indices: 1634316--1634533 Score: 318
Period size: 100 Copynumber: 2.2 Consensus size: 98
1634306 TATATAAAAT
* *
1634316 TATATATAAACTA--TAT-TTATATTATAAACTATATAATTATTATAAACTATATAATTATTATA
1 TATATATAAACTATGTATATAAAATTATAAACTATATAATTATTATAAACTATATAATTATTATA
* *
1634378 AACTATATATATAAATTATATTTATGTGAATTA
66 AACTATATATAAAAATTATATTTATGTGAACTA
*
1634411 TATATATAAAAACTATGTATATAAAATTATAAACTATAT-TTATATTATAAACTATATAATTATT
1 TATATAT--AAACTATGTATATAAAATTATAAACTATATAAT-TATTATAAACTATATAATTATT
* *
1634475 ATAAGCTATATATAAAAATTATGTTTATGTGAACTA
63 ATAAACTATATATAAAAATTATATTTATGTGAACTA
1634511 TATATATAAACTATGTATATAAA
1 TATATATAAACTATGTATATAAA
1634534 CTATAAAAAG
Statistics
Matches: 110, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
95 7 0.06
97 6 0.05
98 16 0.15
99 4 0.04
100 77 0.70
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (98 bp):
TATATATAAACTATGTATATAAAATTATAAACTATATAATTATTATAAACTATATAATTATTATA
AACTATATATAAAAATTATATTTATGTGAACTA
Found at i:1634597 original size:10 final size:11
Alignment explanation
Indices: 1634574--1634638 Score: 52
Period size: 10 Copynumber: 6.5 Consensus size: 11
1634564 ATTTATATTA
1634574 ATATAGTATAT
1 ATATAGTATAT
*
1634585 ATAT-GTATGT
1 ATATAGTATAT
*
1634595 ATA-ACTA-AT
1 ATATAGTATAT
*
1634604 ATA-ACTA-AT
1 ATATAGTATAT
*
1634613 ATATAGAATAT
1 ATATAGTATAT
1634624 ATATA-TATAT
1 ATATAGTATAT
1634634 ATATA
1 ATATA
1634639 TTAAAGAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
9 13 0.29
10 21 0.47
11 11 0.24
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (11 bp):
ATATAGTATAT
Found at i:1635265 original size:20 final size:20
Alignment explanation
Indices: 1635240--1635282 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1635230 CATTTCTCCT
1635240 CTTCCTCGCAATAGTAAGTA
1 CTTCCTCGCAATAGTAAGTA
*
1635260 CTTCCTCGCAATATTAAGTA
1 CTTCCTCGCAATAGTAAGTA
1635280 CTT
1 CTT
1635283 TCATATAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (20 bp):
CTTCCTCGCAATAGTAAGTA
Found at i:1635394 original size:23 final size:24
Alignment explanation
Indices: 1635368--1635417 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
1635358 TTATTTTTTC
1635368 TTTATATAAATTAAACTACA-TAA
1 TTTATATAAATTAAACTACATTAA
*
1635391 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTACATTAA
1635415 TTT
1 TTT
1635418 TCCTTTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTATATAAATTAAACTACATTAA
Found at i:1635707 original size:32 final size:32
Alignment explanation
Indices: 1635671--1635741 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
1635661 CGGATCATTT
*
1635671 ACAGGTTAGGTTAAAAAC-AGATCAGATTAAAA
1 ACAGGTCAGGTTAAAAACAAG-TCAGATTAAAA
* * *
1635703 ACAGGTCAGGTTGAAAACAAGTCAGGTTTAAA
1 ACAGGTCAGGTTAAAAACAAGTCAGATTAAAA
1635735 ACAGGTC
1 ACAGGTC
1635742 GGGTAATACC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (32 bp):
ACAGGTCAGGTTAAAAACAAGTCAGATTAAAA
Found at i:1635726 original size:16 final size:16
Alignment explanation
Indices: 1635678--1635737 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
1635668 TTTACAGGTT
1635678 AGGTTAAAAAC-AGATC
1 AGGTTAAAAACAAG-TC
* *
1635694 AGATTAAAAACAGGTC
1 AGGTTAAAAACAAGTC
*
1635710 AGGTTGAAAACAAGTC
1 AGGTTAAAAACAAGTC
*
1635726 AGGTTTAAAACA
1 AGGTTAAAAACA
1635738 GGTCGGGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
16 36 0.97
17 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20
Consensus pattern (16 bp):
AGGTTAAAAACAAGTC
Found at i:1638267 original size:16 final size:17
Alignment explanation
Indices: 1638237--1638295 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 17
1638227 TGTCAAAGAA
*
1638237 TATATATATTTTTTATT
1 TATATATATTATTTATT
1638254 TATA-ATATTATTTA-T
1 TATATATATTATTTATT
*
1638269 T-TAT-TATTCTTTATAT
1 TATATATATTATTTAT-T
1638285 TATATATATTA
1 TATATATATTA
1638296 GATAAAACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 10 0.29
15 2 0.06
16 11 0.32
17 7 0.21
18 4 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATATATTATTTATT
Found at i:1638492 original size:16 final size:16
Alignment explanation
Indices: 1638471--1638505 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1638461 ATATGATAAA
1638471 AAATTAATTTAAATTT
1 AAATTAATTTAAATTT
*
1638487 AAATTAATTTAATTTT
1 AAATTAATTTAAATTT
1638503 AAA
1 AAA
1638506 ATAACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATTAATTTAAATTT
Found at i:1639810 original size:10 final size:10
Alignment explanation
Indices: 1639795--1639819 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1639785 TATTACTTGG
1639795 ATTAAACCGA
1 ATTAAACCGA
1639805 ATTAAACCGA
1 ATTAAACCGA
1639815 ATTAA
1 ATTAA
1639820 TTAATCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (10 bp):
ATTAAACCGA
Found at i:1642198 original size:56 final size:57
Alignment explanation
Indices: 1641678--1642616 Score: 1359
Period size: 57 Copynumber: 16.5 Consensus size: 57
1641668 GTCCAATATA
* * * ** *
1641678 GAAATTCATACACTTAGTATGAATTTCTTATCATGTTAACACAC-AAAGTGCCCTATCT
1 GAAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCGTACGAAA-CGCCCTATCT
* *
1641736 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCGTACGAAATGCCCTATCT
1 -GAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACGAAACGCCCTATCT
*
1641795 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTGTCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * *
1641852 TAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAAAGCCCTCTCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
1641909 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* *
1641966 GAAATTTATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATAT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
*
1642023 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAATGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
1642080 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGTGTATGAAACGCCCTATAT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * *
1642137 GAAATTTATACACTTAGTATGATTTCTT-ATATTTTAGTGTACGAAACGCCCTATCC
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * * *
1642193 AAAATTCATACACTTAGTATGATTTCTT-ATATTTTAGCGTACGAAATGTCCTATCC
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
1642249 GAAATCCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCAATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
1642306 AAAACTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAATGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* ** *
1642363 GAAATTCATACACTTAGTATGATTTCTT-ATATTTTAGCGTATAAAATGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
1642419 GAAATTCATACACTTTGTATGATTTCTTAATATTTTAGCGTACGAAACGCTCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * *
1642476 AAAATTCATACACTTAGTATGATTTCTT-ATATTTTAGCATACGAAACACCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
1642532 AAAATTCATACACTTAGTATGATTTCTT-ATATTTTAGTGTACGAAACGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
*
1642588 GAAATTCATACACTTAATATGATTTCTTA
1 GAAATTCATACACTTAGTATGATTTCTTA
1642617 TATTTTGTAC
Statistics
Matches: 807, Mismatches: 68, Indels: 12
0.91 0.08 0.01
Matches are distributed among these distances:
56 257 0.32
57 473 0.59
58 29 0.04
59 45 0.06
60 3 0.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (57 bp):
GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
Found at i:1643081 original size:95 final size:95
Alignment explanation
Indices: 1642957--1643181 Score: 254
Period size: 96 Copynumber: 2.3 Consensus size: 95
1642947 TGGCTCTATA
* * * * *
1642957 GTATCGATACCCCTATCATGGTATCGATACTAC-TCTACTATGGTACCGATACCCCCTTCTAGTA
1 GTATCGATACCCTTACCATGGTATCGATACTACATATACTATGGTACCAATA-CCCCTTCCAGTA
* * * * * **
1643021 TCGATACCAATTTTTGATTTGATGTTGTTTG
65 TCAATACCAATTTTAGATTCGATATAGACTG
* * * * *
1643052 GTATCGATACCCTTACCATAGAATAGATACTACTATATATTATGGTACCAATACTCCTTCCAGTA
1 GTATCGATACCCTTACCATGGTATCGATACTAC-ATATACTATGGTACCAATACCCCTTCCAGTA
*
1643117 TCAATACCCATTTTAGATTCGATATAGACTG
65 TCAATACCAATTTTAGATTCGATATAGACTG
1643148 GTATCGATACCCTCTACCATGGTATCGATACTAC
1 GTATCGATACCCT-TACCATGGTATCGATACTAC
1643182 CTTATTGGTA
Statistics
Matches: 106, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
95 28 0.26
96 46 0.43
97 32 0.30
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACATATACTATGGTACCAATACCCCTTCCAGTAT
CAATACCAATTTTAGATTCGATATAGACTG
Found at i:1645097 original size:101 final size:101
Alignment explanation
Indices: 1644934--1645183 Score: 259
Period size: 101 Copynumber: 2.5 Consensus size: 101
1644924 CATCGCCTCT
* * * * *
1644934 AGTTCAAGGGGAAGGCATTCATCTGCCAATTTCTTTGACCTGAATATGGAGATGCCCTCGACACA
1 AGTTCAAGGGG-AGGCATTCAACTACCAGTTTCTTCGACCTAAATATGGAGATGCCCTCGACACA
* ** *
1644999 ACAATCTATTCAGTACCCATTTGACACGATGCCTACA
65 ACAATCAATTCAAAACCCATATGACACGATGCCTACA
* * * *
1645036 AGTTCCAGGGGAGGCATTCAACTACGAGTTTCTTCGACCTCAATATGGAGATG-TCTGCGACACA
1 AGTTCAAGGGGAGGCATTCAACTACCAGTTTCTTCGACCTAAATATGGAGATGCCCT-CGACACA
* ** *
1645100 ACACTCAATTCAAAACCTGTATGACACGATGCCTTCA
65 ACAATCAATTCAAAACCCATATGACACGATGCCTACA
* * * * * *
1645137 AGTTCAAAGAGAAGACATTCAACTACTAGCTTGTTCGACCTAAATAT
1 AGTTC-AAGGGGAGGCATTCAACTACCAGTTTCTTCGACCTAAATAT
1645184 CGACATCACA
Statistics
Matches: 122, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
100 2 0.02
101 77 0.63
102 43 0.35
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (101 bp):
AGTTCAAGGGGAGGCATTCAACTACCAGTTTCTTCGACCTAAATATGGAGATGCCCTCGACACAA
CAATCAATTCAAAACCCATATGACACGATGCCTACA
Found at i:1647619 original size:93 final size:90
Alignment explanation
Indices: 1647507--1647731 Score: 348
Period size: 91 Copynumber: 2.5 Consensus size: 90
1647497 TATAATTCAA
*
1647507 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAATTCCATAATTAAATAATAAAAAC
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAATCCATAATT--A-AATAAAAAC
*
1647572 ATTAAAAAACAAAATAAATAAAAAGTTT
63 ATTAAAAAACAAAATAAATAAAAAGTTC
* *
1647600 ATAATTAAATAATAAAAACATTAAGAAATAAAATAAATAAAAAATCCATAATTAAATAAAAATAT
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAAT-AAAAATCCATAATTAAATAAAAACAT
*
1647665 TAAAAAACAATATAAATAAAAAGTTC
65 TAAAAAACAAAATAAATAAAAAGTTC
1647691 ATAATT--A-AATAAAAACATTAAGAAACAAAATAAATAAAAAT
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAT
1647732 AAGTCTATCG
Statistics
Matches: 125, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
87 6 0.05
88 27 0.22
89 1 0.01
91 40 0.32
92 1 0.01
93 37 0.30
94 13 0.10
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (90 bp):
ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAATCCATAATTAAATAAAAACATT
AAAAAACAAAATAAATAAAAAGTTC
Found at i:1647622 original size:47 final size:47
Alignment explanation
Indices: 1647507--1647730 Score: 311
Period size: 44 Copynumber: 4.9 Consensus size: 47
1647497 TATAATTCAA
1647507 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAAT-AAAA-TTCC
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTT-C
* *
1647553 ATAATTAAATAATAAAAACATTAAAAAACAAAATAAATAAAAAGTTT
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTTC
* * *
1647600 ATAATTAAATAATAAAAACATTAAGAAATAAAATAAATAAAAAATCC
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTTC
* * *
1647647 ATAATT--A-AATAAAAATATTAAAAAACAATATAAATAAAAAGTTC
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTTC
1647691 ATAATT--A-AATAAAAACATTAAGAAACAAAATAAATAAAAA
1 ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAA
1647731 TAAGTCTATC
Statistics
Matches: 160, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
44 68 0.43
45 1 0.01
46 37 0.23
47 52 0.32
48 2 0.01
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (47 bp):
ATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGTTC
Found at i:1647668 original size:13 final size:13
Alignment explanation
Indices: 1647650--1647686 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1647640 AAAATCCATA
1647650 ATTAAATAAAAAT
1 ATTAAATAAAAAT
1647663 ATTAAA-AAACAAT
1 ATTAAATAAA-AAT
1647676 A-TAAATAAAAA
1 ATTAAATAAAAA
1647687 GTTCATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
ATTAAATAAAAAT
Found at i:1648144 original size:21 final size:21
Alignment explanation
Indices: 1648120--1648194 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
1648110 TACGATGGAA
*
1648120 GCATCTGAAACGGCTGTGGTG
1 GCATCTGAAACGGCTATGGTG
*
1648141 GCATC-GAAAATGGCTATGGTG
1 GCATCTG-AAACGGCTATGGTG
* * ** * *
1648162 TCATTTGAAAAAGCTACGATG
1 GCATCTGAAACGGCTATGGTG
1648183 GCATCTGAAACG
1 GCATCTGAAACG
1648195 ACTGCAAAAT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (21 bp):
GCATCTGAAACGGCTATGGTG
Found at i:1649575 original size:23 final size:23
Alignment explanation
Indices: 1649525--1649576 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1649515 CAGCTCGTAT
* *
1649525 AAATTGCACCGAAGTGCCACGTA
1 AAATTGAACCGAAGTGCCACATA
* * *
1649548 GAATTGAACCGTAGTGCCATATA
1 AAATTGAACCGAAGTGCCACATA
1649571 AAATTG
1 AAATTG
1649577 TCCATAAGGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (23 bp):
AAATTGAACCGAAGTGCCACATA
Found at i:1656850 original size:23 final size:23
Alignment explanation
Indices: 1656820--1656886 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
1656810 AATACATATA
1656820 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
1656843 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
* *
1656866 TGTCCCGAATGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
1656887 CCCTATACTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:1659116 original size:2 final size:2
Alignment explanation
Indices: 1659109--1659143 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1659099 TCATACATAC
1659109 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 A
1659144 GTTGAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.