Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 86 of 206
Found at i:24628569 original size:27 final size:26
Alignment explanation
Indices: 24628530--24628727 Score: 130
Period size: 27 Copynumber: 7.3 Consensus size: 26
24628520 TCCTCATGGT
*
24628530 CTTCCACAAAAGATAGTCCTGGCAGA
1 CTTCCACAAAAGATAGTCCTGACAGA
* *
24628556 CTTTCCACATAAGATAGTCTTGATCA-A
1 C-TTCCACAAAAGATAGTCCTGA-CAGA
* * *
24628583 CCTTCCGCATTTCAA-ATAGTCCTAACAGA
1 -CTTCCACA---AAAGATAGTCCTGACAGA
* *
24628612 CTTCCACAAAAGATAGTCTTGACGGA
1 CTTCCACAAAAGATAGTCCTGACAGA
* *
24628638 CTTCCACAAAAGATAGCCCTAACAGA
1 CTTCCACAAAAGATAGTCCTGACAGA
* * **
24628664 CCTTTCACATAAGATAGTCCTGATGGA
1 -CTTCCACAAAAGATAGTCCTGACAGA
** * *
24628691 CTTCCCACATTTCAGATAGTCCTTACGGA
1 CTT-CCACA--AAAGATAGTCCTGACAGA
24628720 CTTCCACA
1 CTTCCACA
24628728 TATTCGGTAT
Statistics
Matches: 134, Mismatches: 26, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
25 2 0.01
26 37 0.28
27 49 0.37
28 17 0.13
29 27 0.20
30 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (26 bp):
CTTCCACAAAAGATAGTCCTGACAGA
Found at i:24628703 original size:108 final size:108
Alignment explanation
Indices: 24628530--24628727 Score: 274
Period size: 108 Copynumber: 1.8 Consensus size: 108
24628520 TCCTCATGGT
* ** * *
24628530 CTTCCACAAAAGATAGTCCTGGCAGACTTTCCACATAAGATAGTCTTGATCAACCTTCCGCATTT
1 CTTCCACAAAAGATAGCCCTAACAGACTTTCCACATAAGATAGTCCTGATCAACCTTCCACATTT
24628595 CAAATAGTCCTAACAGACTTCCACAAAAGATAGTCTTGACGGA
66 CAAATAGTCCTAACAGACTTCCACAAAAGATAGTCTTGACGGA
**
24628638 CTTCCACAAAAGATAGCCCTAACAGACCTTT-CACATAAGATAGTCCTGATGGA-CTTCCCACAT
1 CTTCCACAAAAGATAGCCCTAACAGA-CTTTCCACATAAGATAGTCCTGATCAACCTT-CCACAT
* * *
24628701 TTCAGATAGTCCTTACGGACTTCCACA
64 TTCAAATAGTCCTAACAGACTTCCACA
24628728 TATTCGGTAT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 3 0.04
108 71 0.91
109 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (108 bp):
CTTCCACAAAAGATAGCCCTAACAGACTTTCCACATAAGATAGTCCTGATCAACCTTCCACATTT
CAAATAGTCCTAACAGACTTCCACAAAAGATAGTCTTGACGGA
Found at i:24632193 original size:30 final size:32
Alignment explanation
Indices: 24632142--24632210 Score: 97
Period size: 30 Copynumber: 2.2 Consensus size: 32
24632132 ACGAACGTCC
* **
24632142 TTCTTTGCTCTCTACTCTCTGCCCTCTGCTGG
1 TTCTTTGCCCTCTACTCTCTGCCCTCTGCCAG
24632174 TTCTTTGCCCTC-A-TCTCTGCCCTCTGCCAG
1 TTCTTTGCCCTCTACTCTCTGCCCTCTGCCAG
24632204 TTCTTTG
1 TTCTTTG
24632211 TCCTGCCCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 22 0.65
31 1 0.03
32 11 0.32
ACGTcount: A:0.04, C:0.38, G:0.14, T:0.43
Consensus pattern (32 bp):
TTCTTTGCCCTCTACTCTCTGCCCTCTGCCAG
Found at i:24632220 original size:23 final size:26
Alignment explanation
Indices: 24632188--24632250 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 26
24632178 TTGCCCTCAT
24632188 CTCTGCCCTCTGCCAGTTCTTTG-T-
1 CTCTGCCCTCTGCCAGTTCTTTGTTC
*
24632212 C-CTGCCCTCTGCCGGTTCTTTGTTC
1 CTCTGCCCTCTGCCAGTTCTTTGTTC
24632237 CTCTGCCCTCTGCC
1 CTCTGCCCTCTGCC
24632251 GGCGAGTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
23 20 0.57
24 2 0.06
25 1 0.03
26 12 0.34
ACGTcount: A:0.02, C:0.43, G:0.17, T:0.38
Consensus pattern (26 bp):
CTCTGCCCTCTGCCAGTTCTTTGTTC
Found at i:24632222 original size:30 final size:30
Alignment explanation
Indices: 24632142--24632224 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
24632132 ACGAACGTCC
* **
24632142 TTCTTTGCTCTCTACTCTCTGCCCTCTGCTGG
1 TTCTTTGCCCTC-AC-CTCTGCCCTCTGCCAG
*
24632174 TTCTTTGCCCTCATCTCTGCCCTCTGCCAG
1 TTCTTTGCCCTCACCTCTGCCCTCTGCCAG
*
24632204 TTCTTTGTCCTGC-CCTCTGCC
1 TTCTTTGCCCT-CACCTCTGCC
24632225 GGTTCTTTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
30 31 0.70
31 2 0.05
32 11 0.25
ACGTcount: A:0.04, C:0.41, G:0.14, T:0.41
Consensus pattern (30 bp):
TTCTTTGCCCTCACCTCTGCCCTCTGCCAG
Found at i:24632352 original size:8 final size:8
Alignment explanation
Indices: 24632339--24632376 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
24632329 GGATAGGAGA
24632339 TAAACCAT
1 TAAACCAT
24632347 TAAACCAT
1 TAAACCAT
24632355 TAAACCAT
1 TAAACCAT
24632363 TAAACCAT
1 TAAACCAT
24632371 TAAACC
1 TAAACC
24632377 CAAGTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (8 bp):
TAAACCAT
Found at i:24639166 original size:117 final size:117
Alignment explanation
Indices: 24638960--24639194 Score: 470
Period size: 117 Copynumber: 2.0 Consensus size: 117
24638950 TGCAAATAGT
24638960 TGAAAAAGAGAAATAGCAGATCATATAGGTTGTTTAGAAGATTTGCATGATCGTGAGCTCCTTTC
1 TGAAAAAGAGAAATAGCAGATCATATAGGTTGTTTAGAAGATTTGCATGATCGTGAGCTCCTTTC
24639025 CCTACATATTTGAATTATCATGGCTGGATGGCTTCTTCTCTCTGGTAATTGC
66 CCTACATATTTGAATTATCATGGCTGGATGGCTTCTTCTCTCTGGTAATTGC
24639077 TGAAAAAGAGAAATAGCAGATCATATAGGTTGTTTAGAAGATTTGCATGATCGTGAGCTCCTTTC
1 TGAAAAAGAGAAATAGCAGATCATATAGGTTGTTTAGAAGATTTGCATGATCGTGAGCTCCTTTC
24639142 CCTACATATTTGAATTATCATGGCTGGATGGCTTCTTCTCTCTGGTAATTGC
66 CCTACATATTTGAATTATCATGGCTGGATGGCTTCTTCTCTCTGGTAATTGC
24639194 T
1 T
24639195 TCTTCTATTA
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (117 bp):
TGAAAAAGAGAAATAGCAGATCATATAGGTTGTTTAGAAGATTTGCATGATCGTGAGCTCCTTTC
CCTACATATTTGAATTATCATGGCTGGATGGCTTCTTCTCTCTGGTAATTGC
Found at i:24645138 original size:18 final size:18
Alignment explanation
Indices: 24645110--24645152 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
24645100 CCCAATCTTC
* *
24645110 TCCCTTTTCCCCTTCTCCT
1 TCCC-TTTCCCCTACCCCT
24645129 TCCCTTTCCCCTACCCCT
1 TCCCTTTCCCCTACCCCT
24645147 TCCCTT
1 TCCCTT
24645153 CCCGTTTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.02, C:0.56, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCCTTTCCCCTACCCCT
Found at i:24646618 original size:30 final size:30
Alignment explanation
Indices: 24646582--24646639 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
24646572 GCATTTGTAC
24646582 AAGACCATAAGTACCAATTTGCTATGACAT
1 AAGACCATAAGTACCAATTTGCTATGACAT
*
24646612 AAGACCATAAGTACTAATTTGCTATGAC
1 AAGACCATAAGTACCAATTTGCTATGAC
24646640 TGGCATGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (30 bp):
AAGACCATAAGTACCAATTTGCTATGACAT
Found at i:24647641 original size:31 final size:31
Alignment explanation
Indices: 24647606--24647668 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
24647596 ATTTGATTTA
24647606 TTTAATTATAAATAAATCATTGCAATATATG
1 TTTAATTATAAATAAATCATTGCAATATATG
24647637 TTTAATTATAAATAAATCATTGCAATATATG
1 TTTAATTATAAATAAATCATTGCAATATATG
24647668 T
1 T
24647669 AAAAATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (31 bp):
TTTAATTATAAATAAATCATTGCAATATATG
Found at i:24647872 original size:14 final size:14
Alignment explanation
Indices: 24647834--24647873 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
24647824 ACAAAAAAGT
*
24647834 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
24647848 AAATCATTTTACGG
1 AAAACATTTTACAG
24647862 AAAACATTTTAC
1 AAAACATTTTAC
24647874 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:24676126 original size:20 final size:20
Alignment explanation
Indices: 24676088--24676141 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
24676078 TACTCTTTTT
**
24676088 TTATAAAAAAAATCATAAAAA
1 TTAT-AAAAAAATTTTAAAAA
*
24676109 TTATAAAATAATTTTAAAAA
1 TTATAAAAAAATTTTAAAAA
24676129 TTATAAAAAAATT
1 TTATAAAAAAATT
24676142 AAATATTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TTATAAAAAAATTTTAAAAA
Found at i:24676191 original size:9 final size:9
Alignment explanation
Indices: 24676095--24676230 Score: 53
Period size: 9 Copynumber: 14.6 Consensus size: 9
24676085 TTTTTATAAA
*
24676095 AAAAATCAT
1 AAAAATTAT
24676104 AAAAATTAT
1 AAAAATTAT
*
24676113 AAAATAATTTT
1 -AAA-AATTAT
24676124 AAAAATTAT
1 AAAAATTAT
*
24676133 AAAAA-AAT
1 AAAAATTAT
*
24676141 -TAAA-TATT
1 AAAAATTA-T
*
24676149 AGAAATTAT
1 AAAAATTAT
* *
24676158 TAAAATTTT
1 AAAAATTAT
*
24676167 ATAAACTTATT
1 A-AAAATTA-T
24676178 AAAAAATTAT
1 -AAAAATTAT
* *
24676188 AAAACTAAT
1 AAAAATTAT
*
24676197 AAAACTTATT
1 AAAAATTA-T
* *
24676207 TAAAATTAA
1 AAAAATTAT
*
24676216 AAACAATTTT
1 AAA-AATTAT
24676226 AAAAA
1 AAAAA
24676231 ACTTGAACTG
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
7 4 0.04
8 3 0.03
9 46 0.49
10 28 0.30
11 12 0.13
12 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:24676199 original size:19 final size:18
Alignment explanation
Indices: 24676104--24676200 Score: 59
Period size: 18 Copynumber: 5.2 Consensus size: 18
24676094 AAAAAATCAT
*
24676104 AAAAATTATAAAATAATTTT
1 AAAAATTATAAAATAA--TA
* *
24676124 AAAAATTATAAAAAAATT
1 AAAAATTATAAAATAATA
* * * *
24676142 AAATATTAGAAATTATTA
1 AAAAATTATAAAATAATA
** * *
24676160 AAATTTTATAAACTTATTA
1 AAAAATTATAAA-ATAATA
24676179 AAAAATTATAAAACTAATA
1 AAAAATTATAAAA-TAATA
24676198 AAA
1 AAA
24676201 CTTATTTAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
18 24 0.39
19 23 0.37
20 15 0.24
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (18 bp):
AAAAATTATAAAATAATA
Found at i:24676228 original size:29 final size:32
Alignment explanation
Indices: 24676161--24676229 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 32
24676151 AAATTATTAA
24676161 AATTTTATAAACTTATTAAAAAATTATAAAACT
1 AATTTTA-AAACTTATTAAAAAATTATAAAACT
*
24676194 AA---TAAAACTTATT-TAAAATTA-AAAAC-
1 AATTTTAAAACTTATTAAAAAATTATAAAACT
24676220 AATTTTAAAA
1 AATTTTAAAA
24676230 AACTTGAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
26 2 0.06
27 5 0.16
28 7 0.22
29 14 0.44
30 2 0.06
33 2 0.06
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (32 bp):
AATTTTAAAACTTATTAAAAAATTATAAAACT
Found at i:24676869 original size:19 final size:19
Alignment explanation
Indices: 24676841--24676883 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
24676831 CTTTAAATTA
24676841 TTTT-TAATATTTAATAAT
1 TTTTATAATATTTAATAAT
*
24676859 TTTTATAATATTTAATCAT
1 TTTTATAATATTTAATAAT
24676878 TTTTAT
1 TTTTAT
24676884 GGAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTATAATATTTAATAAT
Found at i:24678289 original size:5 final size:5
Alignment explanation
Indices: 24678281--24678306 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
24678271 AATTTTTGTA
24678281 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
24678307 GATAGTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:24679116 original size:7 final size:7
Alignment explanation
Indices: 24679091--24679162 Score: 72
Period size: 7 Copynumber: 10.3 Consensus size: 7
24679081 TCCATCCTAT
24679091 ATTTTCA
1 ATTTTCA
* *
24679098 ATCTTAA
1 ATTTTCA
24679105 ATTTTCA
1 ATTTTCA
24679112 ATTTTCA
1 ATTTTCA
24679119 ATTTTCA
1 ATTTTCA
*
24679126 AATTTCA
1 ATTTTCA
*
24679133 AATTTCA
1 ATTTTCA
**
24679140 ATCCTCA
1 ATTTTCA
**
24679147 ATCCTCA
1 ATTTTCA
24679154 ATTTTCA
1 ATTTTCA
24679161 AT
1 AT
24679163 CCTCAATCCT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (7 bp):
ATTTTCA
Found at i:24679164 original size:21 final size:21
Alignment explanation
Indices: 24679130--24679177 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
24679120 TTTTCAAATT
*
24679130 TCAAATTTCAATCCTCAATCC
1 TCAATTTTCAATCCTCAATCC
24679151 TCAATTTTCAATCCTCAATCC
1 TCAATTTTCAATCCTCAATCC
*
24679172 TTAATT
1 TCAATT
24679178 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (21 bp):
TCAATTTTCAATCCTCAATCC
Found at i:24679168 original size:7 final size:7
Alignment explanation
Indices: 24679137--24679172 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
24679127 ATTTCAAATT
24679137 TCAATCC
1 TCAATCC
24679144 TCAATCC
1 TCAATCC
**
24679151 TCAATTT
1 TCAATCC
24679158 TCAATCC
1 TCAATCC
24679165 TCAATCC
1 TCAATCC
24679172 T
1 T
24679173 TAATTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (7 bp):
TCAATCC
Found at i:24684407 original size:3 final size:3
Alignment explanation
Indices: 24684399--24684424 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
24684389 AGAGCGCGAA
24684399 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
24684425 AAGCCTGGCT
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:24684737 original size:19 final size:19
Alignment explanation
Indices: 24684684--24684741 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
24684674 CCATTTGTTC
*
24684684 ATCTCCGTTTCAATTTTTT
1 ATCTCCATTTCAATTTTTT
*
24684703 -CCTTCCGGATTT-AATTTTTT
1 ATC-TCC--ATTTCAATTTTTT
24684723 ATCTCCATTTCAATTTTTT
1 ATCTCCATTTCAATTTTTT
24684742 CTATACCGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 11 0.35
21 4 0.13
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
ATCTCCATTTCAATTTTTT
Found at i:24687220 original size:84 final size:86
Alignment explanation
Indices: 24687073--24687242 Score: 211
Period size: 84 Copynumber: 2.0 Consensus size: 86
24687063 CTCTCAAGTG
* * * *
24687073 TTTGAGCTTAGTTCTAAAACATTAATGTAAAGGTTTTACTTGAGCAGATCAAACAAAATTATTCT
1 TTTGAGCTTAGTTCTAAAACATCAATGGAAAGGTCTTACTTGAGCAGACCAAACAAAATTATTCT
*
24687138 CAGACAGT-AAAACAAAAGCA
66 AAGACAGTAAAAACAAAAGCA
* * * *
24687158 TTTGA-CTTAGTTCTATAACATCAATGGACAGGTCTTATTTTG-GCGGACCAAACAAAATTATTC
1 TTTGAGCTTAGTTCTAAAACATCAATGGAAAGGTCTTA-CTTGAGCAGACCAAACAAAATTATTC
* *
24687221 TAAGACGGTAAAAACAGAAGCA
65 TAAGACAGTAAAAACAAAAGCA
24687243 GATAAGGTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
84 53 0.74
85 19 0.26
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (86 bp):
TTTGAGCTTAGTTCTAAAACATCAATGGAAAGGTCTTACTTGAGCAGACCAAACAAAATTATTCT
AAGACAGTAAAAACAAAAGCA
Found at i:24687607 original size:9 final size:9
Alignment explanation
Indices: 24687595--24687628 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
24687585 GAGGAAGAAC
24687595 AAGAAGATG
1 AAGAAGATG
* *
24687604 AAGAACAAG
1 AAGAAGATG
24687613 AAGAAGATG
1 AAGAAGATG
24687622 AAGAAGA
1 AAGAAGA
24687629 GGCAGGAGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.62, C:0.03, G:0.29, T:0.06
Consensus pattern (9 bp):
AAGAAGATG
Found at i:24687608 original size:15 final size:15
Alignment explanation
Indices: 24687588--24687616 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24687578 AAAGGGAGAG
24687588 GAAGAACAAGAAGAT
1 GAAGAACAAGAAGAT
24687603 GAAGAACAAGAAGA
1 GAAGAACAAGAAGA
24687617 AGATGAAGAA
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:0.62, C:0.07, G:0.28, T:0.03
Consensus pattern (15 bp):
GAAGAACAAGAAGAT
Found at i:24688633 original size:18 final size:18
Alignment explanation
Indices: 24688589--24688634 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
24688579 ATTTAATTGG
*
24688589 GACCAAATTAAAATTTAA
1 GACCAAATTAAAATTGAA
24688607 GTACCAAATTAAACATTGAA
1 G-ACCAAATTAAA-ATTGAA
24688627 G-CCAAATT
1 GACCAAATT
24688635 TAAGTGCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 8 0.32
19 11 0.44
20 6 0.24
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (18 bp):
GACCAAATTAAAATTGAA
Found at i:24688699 original size:22 final size:23
Alignment explanation
Indices: 24688654--24688700 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
24688644 AATTGGAACA
*
24688654 AAAAATACTCAAGTATCAAATTG
1 AAAAATACTCAAGTACCAAATTG
* *
24688677 AAAAA-ACTCAAGTCCCAATTTG
1 AAAAATACTCAAGTACCAAATTG
24688699 AA
1 AA
24688701 TATTGAAGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (23 bp):
AAAAATACTCAAGTACCAAATTG
Found at i:24708637 original size:67 final size:68
Alignment explanation
Indices: 24708521--24708655 Score: 218
Period size: 67 Copynumber: 2.0 Consensus size: 68
24708511 GAGAAGATAA
* *
24708521 AGTTAAAATGGAATATTCAGAACATATAGAGACAATAAGCCCAAGAAACATTTAGGA-TTTATCC
1 AGTTAAAATGGAATATTCAAAACATATAAAGACAATAAGCCCAAGAAACATTTAGGATTTTATCC
24708585 TAT
66 TAT
* **
24708588 AGTTAAAATGGAATATTCAAAACATATAAAGACAATAAGCCTATTAAACATTTAGGATTTTATCC
1 AGTTAAAATGGAATATTCAAAACATATAAAGACAATAAGCCCAAGAAACATTTAGGATTTTATCC
24708653 TAT
66 TAT
24708656 GTCTCTTGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
67 52 0.84
68 10 0.16
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (68 bp):
AGTTAAAATGGAATATTCAAAACATATAAAGACAATAAGCCCAAGAAACATTTAGGATTTTATCC
TAT
Found at i:24711402 original size:3 final size:3
Alignment explanation
Indices: 24711394--24711447 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
24711384 CAAACGAAAC
24711394 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24711442 ATA ATA
1 ATA ATA
24711448 TGCTGAGAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:24715259 original size:16 final size:16
Alignment explanation
Indices: 24715238--24715269 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24715228 GTTTTGTTGC
*
24715238 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
24715254 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
24715270 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:24715561 original size:51 final size:50
Alignment explanation
Indices: 24715503--24715674 Score: 195
Period size: 51 Copynumber: 3.4 Consensus size: 50
24715493 CACATAATAA
*
24715503 CCTGCACATAGTACTACACATGTGACAATCACTATCCGATACACGTAGTAG
1 CCTGCACATAGTACTACACATGTGACAAT-ACTATCCGGTACACGTAGTAG
* * * *
24715554 CCTGCACATAGTACTACACACGTGATCGAA-GCTATCCGGTACGCATAGTAG
1 CCTGCACATAGTACTACACATGTGA-C-AATACTATCCGGTACACGTAGTAG
* * * * **
24715605 CCTGCACATAGTATTACACATGCGAC-CTACCATTTTGGTACACGTAGTAG
1 CCTGCACATAGTACTACACATGTGACAATACTA-TCCGGTACACGTAGTAG
24715655 CCTGCACATAGTACTACACA
1 CCTGCACATAGTACTACACA
24715675 CATGACCATC
Statistics
Matches: 101, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.02
50 33 0.33
51 63 0.62
52 1 0.01
53 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CCTGCACATAGTACTACACATGTGACAATACTATCCGGTACACGTAGTAG
Found at i:24716454 original size:196 final size:195
Alignment explanation
Indices: 24716120--24716503 Score: 741
Period size: 196 Copynumber: 2.0 Consensus size: 195
24716110 CTTGTTTTCA
24716120 CTTAAAATCGGCTAGCAAAAGTTATTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATC
1 CTTAAAATCGGCTAGCAAAAGTTATTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATC
*
24716185 AAAATAGACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTCAGTTAAATTATTGCTAG
66 AAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTCAGTTAAATTATTGCTAG
24716250 AATAAGCTAAATCAAGTTACCCGGACTCTAAAAACGTAAAGAACATTGGAATCACTTACCCGGAC
131 AATAAGCTAAATCAAGTTACCCGGACTCTAAAAACGTAAAGAACATT-GAATCACTTACCCGGAC
24716315 T
195 T
24716316 CTTAAAATCGGCTAGCAAAAGTTATTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATC
1 CTTAAAATCGGCTAGCAAAAGTTATTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATC
24716381 AAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTCAGTTAAATTATTGCTAG
66 AAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTCAGTTAAATTATTGCTAG
*
24716446 AATAAGCTAAATCAAGTTACCCGGACTCTAAAAACGTAAAGAATATTGAATCACTTAC
131 AATAAGCTAAATCAAGTTACCCGGACTCTAAAAACGTAAAGAACATTGAATCACTTAC
24716504 TATGGAGCTT
Statistics
Matches: 186, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
195 11 0.06
196 175 0.94
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.30
Consensus pattern (195 bp):
CTTAAAATCGGCTAGCAAAAGTTATTTAACATAATTTCAAGCTTCATATTCTACCATAAAACATC
AAAATAAACACATTTCACCTATGGGTATTTTTCCAAATATGAACCCTCAGTTAAATTATTGCTAG
AATAAGCTAAATCAAGTTACCCGGACTCTAAAAACGTAAAGAACATTGAATCACTTACCCGGACT
Found at i:24720257 original size:90 final size:90
Alignment explanation
Indices: 24720104--24720281 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
24720094 AATTTGATAT
* * * *
24720104 TTTATTATGTTTTTTGGATTATTGGGGTAAAAAGGTCAAGAAATGATGAATGGTACAATATTTTT
1 TTTATTATATTTTTTGGATTATTGGGGTAAAAAGGTCAAAAAACGATGAATGGTACAACATTTTT
24720169 ACCTAAATAATATAAAAAATAATGC
66 ACCTAAATAATATAAAAAATAATGC
*
24720194 TTTATTATATTTTTTGGATTATTGGGGTAAAAAGGTCAAAAAACGATGTATGGTACAACATTTTT
1 TTTATTATATTTTTTGGATTATTGGGGTAAAAAGGTCAAAAAACGATGAATGGTACAACATTTTT
*
24720259 ACCTAAATAATATAAAAATTAAT
66 ACCTAAATAATATAAAAAATAAT
24720282 TAAATACAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (90 bp):
TTTATTATATTTTTTGGATTATTGGGGTAAAAAGGTCAAAAAACGATGAATGGTACAACATTTTT
ACCTAAATAATATAAAAAATAATGC
Found at i:24722803 original size:30 final size:31
Alignment explanation
Indices: 24722764--24722823 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
24722754 GGAGGTGGGA
*
24722764 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
24722795 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
24722824 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:24723148 original size:9 final size:9
Alignment explanation
Indices: 24723131--24723161 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
24723121 TCGAGTTGAT
24723131 TCGAATAAC
1 TCGAATAAC
*
24723140 TCGATTAAC
1 TCGAATAAC
24723149 TCGAATAAC
1 TCGAATAAC
24723158 TCGA
1 TCGA
24723162 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:24736369 original size:26 final size:26
Alignment explanation
Indices: 24736340--24736393 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
24736330 TAATTAGTAT
*
24736340 AAAATATT-AATAATTCAAT-AAATTG
1 AAAA-ATTAAATAATTAAATAAAATTG
*
24736365 AAAAATTAAATACTTAAATAAAATTG
1 AAAAATTAAATAATTAAATAAAATTG
24736391 AAA
1 AAA
24736394 TTTAGGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (26 bp):
AAAAATTAAATAATTAAATAAAATTG
Found at i:24737158 original size:16 final size:15
Alignment explanation
Indices: 24737133--24737166 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
24737123 AAACTTGATA
*
24737133 ATAATTAATATATATT
1 ATAATAAATATA-ATT
24737149 ATAATAAATATAATT
1 ATAATAAATATAATT
24737164 ATA
1 ATA
24737167 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:24748024 original size:11 final size:11
Alignment explanation
Indices: 24748008--24748037 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
24747998 ATTAGATCTC
*
24748008 TACTTCTTTTA
1 TACTTCTTCTA
24748019 TACTTCTTCTA
1 TACTTCTTCTA
24748030 TACTTCTT
1 TACTTCTT
24748038 ATGCCTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (11 bp):
TACTTCTTCTA
Found at i:24748755 original size:2 final size:2
Alignment explanation
Indices: 24748748--24748774 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24748738 AACTAAGTAA
24748748 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 A
24748775 AATACAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24749294 original size:18 final size:18
Alignment explanation
Indices: 24749255--24749307 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
24749245 TCTAAAAATT
* *
24749255 AAATTTAAAATTATTA-AT
1 AAATTTAAAAATA-TACAA
24749273 AAATTTAAAAATATACAA
1 AAATTTAAAAATATACAA
24749291 AAATTATAAAAATATAC
1 AAATT-TAAAAATATAC
24749308 TCCCCCTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 2 0.06
18 18 0.58
19 11 0.35
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTTAAAAATATACAA
Found at i:24760828 original size:55 final size:55
Alignment explanation
Indices: 24760744--24760853 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
24760734 AAATAGGCTC
*
24760744 TGTCAACACATGTTATAGATACTTTTTCATTTTGCATAATTTTCTCCTTAGATCT
1 TGTCAACACATGTTATAGACACTTTTTCATTTTGCATAATTTTCTCCTTAGATCT
24760799 TGTCAACACATGTTATAGACACTTTTTCATTTTGCATAATTTTCTCCTTAGATCT
1 TGTCAACACATGTTATAGACACTTTTTCATTTTGCATAATTTTCTCCTTAGATCT
24760854 AGGCTTTAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.46
Consensus pattern (55 bp):
TGTCAACACATGTTATAGACACTTTTTCATTTTGCATAATTTTCTCCTTAGATCT
Found at i:24773172 original size:13 final size:13
Alignment explanation
Indices: 24773154--24773178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24773144 AGTTTGGTAC
24773154 GTTATTGTTGCTT
1 GTTATTGTTGCTT
24773167 GTTATTGTTGCT
1 GTTATTGTTGCT
24773179 GGTTTATTGA
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:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (13 bp):
GTTATTGTTGCTT
Found at i:24783531 original size:69 final size:69
Alignment explanation
Indices: 24783420--24783548 Score: 204
Period size: 69 Copynumber: 1.9 Consensus size: 69
24783410 TGTAGTAAAA
* * ** * *
24783420 TAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGGAAACTAATACCAAAGTTTAAGTGTG
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGCAGGAAACTAAAAACAAAGTTTAAGTGTG
24783485 AAAC
66 AAAC
24783489 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGCAGGAAACTAAAAACAAAGTTTAA
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGCAGGAAACTAAAAACAAAGTTTAA
24783549 CTGGGAGAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (69 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTTAAGCAGGAAACTAAAAACAAAGTTTAAGTGTG
AAAC
Found at i:24786319 original size:8 final size:8
Alignment explanation
Indices: 24786306--24786333 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
24786296 CTTCCTTCAC
24786306 AAAAAAGA
1 AAAAAAGA
24786314 AAAAAAGA
1 AAAAAAGA
24786322 AAAAAAGA
1 AAAAAAGA
24786330 AAAA
1 AAAA
24786334 CTTATACAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:24789389 original size:14 final size:14
Alignment explanation
Indices: 24789367--24789397 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
24789357 TTTTTAGTAA
24789367 AATAAGTAAAATAT
1 AATAAGTAAAATAT
*
24789381 AATAGGTAAAATAT
1 AATAAGTAAAATAT
24789395 AAT
1 AAT
24789398 TTAATTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (14 bp):
AATAAGTAAAATAT
Found at i:24797555 original size:2 final size:2
Alignment explanation
Indices: 24797509--24797537 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24797499 AACGTATACG
24797509 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 T
24797538 TAGAATCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24799135 original size:50 final size:49
Alignment explanation
Indices: 24799058--24799219 Score: 171
Period size: 50 Copynumber: 3.2 Consensus size: 49
24799048 TGTGATGTCA
* * *
24799058 GGGAAGCAAGATTCGCCGCTGTGGCTTTAATCTGTTCCACCGCACTATCT
1 GGGAAGTAAGATTCGCCGATGTGGCTTTAATCTGTTCCACTGCA-TATCT
* * * * ** *
24799108 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAATATCA
1 GGGAAGTAAGATTCGCCGATGTGGCTTTAATCTGTTCCACTGC-ATATCT
* * * *
24799158 GGGAAATAAGATTCACCGATGTGGTTTTAATCTGTTCCACTGCATCACCT
1 GGGAAGTAAGATTCGCCGATGTGGCTTTAATCTGTTCCACTGCAT-ATCT
24799208 GGGAAGTAAGAT
1 GGGAAGTAAGAT
24799220 CTAAAATTCT
Statistics
Matches: 89, Mismatches: 21, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
49 2 0.02
50 86 0.97
51 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (49 bp):
GGGAAGTAAGATTCGCCGATGTGGCTTTAATCTGTTCCACTGCATATCT
Found at i:24799376 original size:44 final size:44
Alignment explanation
Indices: 24799318--24799537 Score: 147
Period size: 44 Copynumber: 4.8 Consensus size: 44
24799308 CTTTATTTTG
* *
24799318 ATCTGCTCCACTGTAACCTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTACTCCACTGTAACCTCAGGGAGATAAGATTACTAGCTTCA
* * * *
24799362 ATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
1 ATCTACTCCACTGTAACCTCAGGGAGATAAGATTACTAGCTTCA
* * * *
24799406 ATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATTA-CTTTA
1 ATC---T---A-CT-C-C-ACTGTAACCTCAGGGAGATAAGAT-TACTAGCTTCA
* ** * * * *
24799460 ATCTGCTCCACTACAACTTCAGGGAGATAGGATTA-TTGAATTCA
1 ATCTACTCCACTGTAACCTCAGGGAGATAAGATTACTAG-CTTCA
* *
24799504 ATCTACTCCACTGCAACCTCAGGGATATAAGATT
1 ATCTACTCCACTGTAACCTCAGGGAGATAAGATT
24799538 TGCTTCTTCA
Statistics
Matches: 136, Mismatches: 27, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 93 0.68
45 1 0.01
46 1 0.01
47 3 0.02
50 1 0.01
51 3 0.02
52 1 0.01
53 1 0.01
54 27 0.20
55 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTACTCCACTGTAACCTCAGGGAGATAAGATTACTAGCTTCA
Found at i:24799547 original size:142 final size:142
Alignment explanation
Indices: 24799266--24799538 Score: 415
Period size: 142 Copynumber: 1.9 Consensus size: 142
24799256 GAGATAAGAC
* * *
24799266 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTGATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTACTTTAATCTGCTCCACTA
* * * * *
24799331 TAACCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
66 CAACCTCAGGGAGATAGGATTACTAGATTCAATCTACTCCACTGCAACCTCAGGGAGATAAGATT
24799396 TCTGGCTTCAAT
131 TCTGGCTTCAAT
24799408 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTATTACTTTAATCTGCTCCACT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTACTTTAATCTGCTCCACT
* * *
24799472 ACAACTTCAGGGAGATAGGATTA-TTGAATTCAATCTACTCCACTGCAACCTCAGGGATATAAGA
65 ACAACCTCAGGGAGATAGGATTACTAG-ATTCAATCTACTCCACTGCAACCTCAGGGAGATAAGA
24799536 TTT
129 TTT
24799539 GCTTCTTCAG
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
141 4 0.03
142 114 0.97
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTACTTTAATCTGCTCCACTA
CAACCTCAGGGAGATAGGATTACTAGATTCAATCTACTCCACTGCAACCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:24799819 original size:84 final size:84
Alignment explanation
Indices: 24799563--24799879 Score: 248
Period size: 84 Copynumber: 3.7 Consensus size: 84
24799553 CCCCACTGTG
* * ** * *
24799563 ACTTTAGGGGGATAAGACTTGT-TGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGA
1 ACTTCAGGGAGATAAGACCCGTATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTG-
*
24799627 TTTTAATCCACTCCACTGCA
65 TTTTAATCCGCTCCACTGCA
* * * *** * * *
24799647 ATTTTAGGGAGATAGGATTGGTTTTTTTTTCG-TCTGCTTCACTACTGCTTAGGGAGATAAGA-C
1 ACTTCAGGGAGATAAGACCCG-----TATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC
* * * *
24799710 TTGTTTTCTTAGTCTGCTCCGCTGCA
61 TT-TGTT-TTAATCCGCTCCACTGCA
24799736 ACTTCAGGGAGATAAGACCCG-ATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTG
1 ACTTCAGGGAGATAAGACCCGTATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-TTG
*
24799800 TTTTAATCCGCTTCACTGCA
65 TTTTAATCCGCTCCACTGCA
* ** * * *
24799820 ACTTCAGGGAGATAAAATTTACTTCTTCTG-TCTGCTCCACTACTGCTTAGGGAGATAAGA
1 ACTTCAGGGAGATAAGA--CCCGTATGC-GATCTGCTCCACTACTGCTTAGGGAGATAAGA
24799880 CTTGATGCGA
Statistics
Matches: 184, Mismatches: 34, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
83 3 0.02
84 75 0.41
85 5 0.03
86 2 0.01
87 32 0.17
88 5 0.03
89 59 0.32
90 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (84 bp):
ACTTCAGGGAGATAAGACCCGTATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTGT
TTTAATCCGCTCCACTGCA
Found at i:24799877 original size:43 final size:43
Alignment explanation
Indices: 24799762--24799917 Score: 122
Period size: 40 Copynumber: 3.7 Consensus size: 43
24799752 ACCCGATGCG
* * *
24799762 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAAATCTATTCTTCTA
* * * ** *
24799805 ATCCGCTTCACTGCAACTTCAGGGAGATAAAATTTACTTCTTCT-
1 ATCTGCTCCACTACTGCTT-AGGGAGATAAAATCTA-TTCTTCTA
* * ** * *
24799849 GTCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGC-G
1 ATCTGCTCCACTACTGCTTAGGGAGATAAAATCTATTCTTCTA
*
24799889 ATCTGCTCTACTACTGCTTAGGGAGATAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAA
24799918 GATTTGTTGT
Statistics
Matches: 88, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
40 30 0.34
42 1 0.01
43 25 0.28
44 27 0.31
45 5 0.06
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (43 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAAATCTATTCTTCTA
Found at i:24800008 original size:127 final size:127
Alignment explanation
Indices: 24799741--24800010 Score: 416
Period size: 127 Copynumber: 2.1 Consensus size: 127
24799731 CTGCAACTTC
**
24799741 AGGGAGATAAGACCCGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTAA
1 AGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTAA
*
24799806 TCCGCTTCACTGCAACTTCAGGGAGATAAAATTTACTTCTTCTGTCTGCTCCACTACTGCTT
66 TCCGCTTCACTGCAACTTCAGGGAGATAAAATTGACTTCTTCTGTCTGCTCCACTACTGCTT
* * *
24799868 AGGGAGATAAGACTTGATGCGATCTGCTCTACTACTGCTTAGGGAGATAAGATTTGTTGTTTTAA
1 AGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTAA
* * *** *
24799933 TCCGC-TCTATTGCAACTTTAGGGAGATTGGATTGATTTCTTCTGTCTGCTCCACTACTGCTT
66 TCCGCTTC-ACTGCAACTTCAGGGAGATAAAATTGACTTCTTCTGTCTGCTCCACTACTGCTT
24799995 AGGGAGATAAGACTTG
1 AGGGAGATAAGACTTG
24800011 TAATTTCCAA
Statistics
Matches: 130, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
126 2 0.02
127 128 0.98
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (127 bp):
AGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTAA
TCCGCTTCACTGCAACTTCAGGGAGATAAAATTGACTTCTTCTGTCTGCTCCACTACTGCTT
Found at i:24801438 original size:21 final size:21
Alignment explanation
Indices: 24801414--24801454 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24801404 TTAGCCTCTC
24801414 CATTTTAC-TCTTTCATTTTTT
1 CATTTTACAT-TTTCATTTTTT
*
24801435 CATTTTTCATTTTCATTTTT
1 CATTTTACATTTTCATTTTT
24801455 CATCTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (21 bp):
CATTTTACATTTTCATTTTTT
Found at i:24801442 original size:7 final size:7
Alignment explanation
Indices: 24801424--24801457 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
24801414 CATTTTACTC
24801424 TTTCATTT
1 TTTCA-TT
24801432 TTTCATT
1 TTTCATT
24801439 TTTCA-T
1 TTTCATT
24801445 TTTCATT
1 TTTCATT
24801452 TTTCAT
1 TTTCAT
24801458 CTATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 14 0.56
8 5 0.20
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTCATT
Found at i:24801447 original size:13 final size:13
Alignment explanation
Indices: 24801431--24801457 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24801421 CTCTTTCATT
24801431 TTTTCATTTTTCA
1 TTTTCATTTTTCA
24801444 TTTTCATTTTTCA
1 TTTTCATTTTTCA
24801457 T
1 T
24801458 CTATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:24801902 original size:26 final size:25
Alignment explanation
Indices: 24801839--24801915 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 25
24801829 TCTTTTCATA
**
24801839 TTTGTTTTGACTTTGATTGATTTCTTTT
1 TTTGTTTTGACTTTGATT--TTT-TCCT
24801867 TTTGCTTTTGACTTTGATTTTTTCCT
1 TTTG-TTTTGACTTTGATTTTTTCCT
*
24801893 TTTGATTTTGATTTTGATTTTTT
1 TTTG-TTTTGACTTTGATTTTTT
24801916 TTTTGAATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 23 0.52
27 3 0.07
28 4 0.09
29 14 0.32
ACGTcount: A:0.10, C:0.08, G:0.13, T:0.69
Consensus pattern (25 bp):
TTTGTTTTGACTTTGATTTTTTCCT
Found at i:24801915 original size:20 final size:20
Alignment explanation
Indices: 24801864--24801907 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
24801854 ATTGATTTCT
*
24801864 TTTTTTGCTTTTGACTTTGA
1 TTTTTTCCTTTTGACTTTGA
*
24801884 TTTTTTCCTTTTGATTTTGA
1 TTTTTTCCTTTTGACTTTGA
24801904 TTTT
1 TTTT
24801908 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.09, G:0.11, T:0.70
Consensus pattern (20 bp):
TTTTTTCCTTTTGACTTTGA
Found at i:24805830 original size:17 final size:18
Alignment explanation
Indices: 24805808--24805849 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
24805798 CTAATGAACA
24805808 CAAATAATCAAT-CAATG
1 CAAATAATCAATACAATG
*
24805825 CAAATAATTAATACAATG
1 CAAATAATCAATACAATG
*
24805843 CACATAA
1 CAAATAA
24805850 GAGCAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.24
Consensus pattern (18 bp):
CAAATAATCAATACAATG
Found at i:24807947 original size:82 final size:82
Alignment explanation
Indices: 24807810--24807963 Score: 299
Period size: 82 Copynumber: 1.9 Consensus size: 82
24807800 AGGAAAAATC
*
24807810 AAATTGAAGTGGAGTGAGAGGGGTGATGATGGGTGCATCCAATATTCATGAGGTGGTAGTGGTTT
1 AAATTGAAGTGGAGTGAGAGGGGTGAGGATGGGTGCATCCAATATTCATGAGGTGGTAGTGGTTT
24807875 TCAAGATTATAAAATTT
66 TCAAGATTATAAAATTT
24807892 AAATTGAAGTGGAGTGAGAGGGGTGAGGATGGGTGCATCCAATATTCATGAGGTGGTAGTGGTTT
1 AAATTGAAGTGGAGTGAGAGGGGTGAGGATGGGTGCATCCAATATTCATGAGGTGGTAGTGGTTT
24807957 TCAAGAT
66 TCAAGAT
24807964 GATACATTCA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.29, C:0.06, G:0.34, T:0.30
Consensus pattern (82 bp):
AAATTGAAGTGGAGTGAGAGGGGTGAGGATGGGTGCATCCAATATTCATGAGGTGGTAGTGGTTT
TCAAGATTATAAAATTT
Found at i:24809610 original size:22 final size:22
Alignment explanation
Indices: 24809584--24809627 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
24809574 AGAATGCCTG
*
24809584 ATATTGATGTAGCCCTGAACAT
1 ATATTGATGCAGCCCTGAACAT
*
24809606 ATATTGATGCAGTCCTGAACAT
1 ATATTGATGCAGCCCTGAACAT
24809628 TGTACAGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (22 bp):
ATATTGATGCAGCCCTGAACAT
Found at i:24814383 original size:2 final size:2
Alignment explanation
Indices: 24814376--24814411 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24814366 GCATGGCTAA
24814376 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24814412 CATCAAAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24815332 original size:42 final size:43
Alignment explanation
Indices: 24815240--24815384 Score: 136
Period size: 42 Copynumber: 3.4 Consensus size: 43
24815230 AGTCTTGTAT
* * * * * **
24815240 ATCACATA-CAATGCC-ATATCCCGAATATGGTCTTACATGTT
1 ATCACATATCGATGCCAATAGCCCAAACATGGTCTTACACGAA
* **
24815281 ATCACATATCGATGCCAATAGCCC-AGCAATTTTCTTACACG-A
1 ATCACATATCGATGCCAATAGCCCAAAC-ATGGTCTTACACGAA
* *
24815323 ATCATATATCGATGCCAATATCCCAAACATGGTCTTACACGAA
1 ATCACATATCGATGCCAATAGCCCAAACATGGTCTTACACGAA
*
24815366 ATCACATAACGATGCCAAT
1 ATCACATATCGATGCCAAT
24815385 GTCCCAGACA
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
41 8 0.10
42 40 0.48
43 36 0.43
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (43 bp):
ATCACATATCGATGCCAATAGCCCAAACATGGTCTTACACGAA
Found at i:24815383 original size:43 final size:42
Alignment explanation
Indices: 24815240--24815395 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 42
24815230 AGTCTTGTAT
* * * * *
24815240 ATCACAT-ACAATGCC-ATATCCCGAATATGGTCTTACATGTT
1 ATCACATAACGATGCCAATATCCCAAACATGGTCTTACACG-A
* * * **
24815281 ATCACATATCGATGCCAATAGCCC-AGCAATTTTCTTACACGA
1 ATCACATAACGATGCCAATATCCCAAAC-ATGGTCTTACACGA
* *
24815323 ATCATATATCGATGCCAATATCCCAAACATGGTCTTACACGAA
1 ATCACATAACGATGCCAATATCCCAAACATGGTCTTACACG-A
* *
24815366 ATCACATAACGATGCCAATGTCCCAGACAT
1 ATCACATAACGATGCCAATATCCCAAACAT
24815396 ATATCCCAGA
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
41 7 0.08
42 40 0.43
43 45 0.49
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (42 bp):
ATCACATAACGATGCCAATATCCCAAACATGGTCTTACACGA
Found at i:24820334 original size:6 final size:6
Alignment explanation
Indices: 24820323--24820374 Score: 61
Period size: 6 Copynumber: 8.7 Consensus size: 6
24820313 ACGAAGGAAT
* * *
24820323 AAGATG AAGATG AAGATG AAGGTG AAGGTG AATG-TG GAGATG AAGATG
1 AAGATG AAGATG AAGATG AAGATG AAGATG AA-GATG AAGATG AAGATG
24820371 AAGA
1 AAGA
24820375 AGATGGGGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
5 1 0.02
6 39 0.95
7 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.17
Consensus pattern (6 bp):
AAGATG
Found at i:24821922 original size:12 final size:12
Alignment explanation
Indices: 24821907--24821950 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
24821897 CCCCCAGCTC
*
24821907 CTCCCGCTGGTT
1 CTCCCGCTGGCT
24821919 CTCCCGCTGGCT
1 CTCCCGCTGGCT
*
24821931 CTCCCTCTGGCT
1 CTCCCGCTGGCT
*
24821943 CCCCCGCT
1 CTCCCGCT
24821951 AGCGCTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.00, C:0.52, G:0.20, T:0.27
Consensus pattern (12 bp):
CTCCCGCTGGCT
Found at i:24832447 original size:25 final size:25
Alignment explanation
Indices: 24832419--24832466 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
24832409 CTGTCTTTGA
*
24832419 TAGTATATCCTGAAACTACTATATG
1 TAGTATATACTGAAACTACTATATG
* *
24832444 TAGTATATATTGAGACTACTATA
1 TAGTATATACTGAAACTACTATA
24832467 GATAGATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATATG
Found at i:24836915 original size:22 final size:22
Alignment explanation
Indices: 24836890--24836943 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
24836880 AAAGAGTCAT
* *
24836890 TTTTCACTCCATCTTTCTAATG
1 TTTTCTCTCCATCTTTCTAACG
* *
24836912 TTTTCTCTCTATCTTTCTGACG
1 TTTTCTCTCCATCTTTCTAACG
24836934 TTTTCTCTCC
1 TTTTCTCTCC
24836944 CCCATCTCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.11, C:0.30, G:0.06, T:0.54
Consensus pattern (22 bp):
TTTTCTCTCCATCTTTCTAACG
Found at i:24844779 original size:51 final size:49
Alignment explanation
Indices: 24844659--24844944 Score: 234
Period size: 51 Copynumber: 5.7 Consensus size: 49
24844649 AAAGTGATGG
* * * * * * * *
24844659 TCACGTGTGTAGTATTATGTGTAGGCTACTACGTGTACCATA-ATGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA-G-TTGA
*
24844709 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAG-TT-GA
** * * * * *
24844760 TCATGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-ATGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA-G-TTGA
* * *
24844810 TCATATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTTAA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAG--TTGA
* * * * * *
24844861 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGT--TGA
*
24844912 TCACATGTGTAGTACTATGTGCATGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
24844945 TGAATCCGCA
Statistics
Matches: 191, Mismatches: 38, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
49 1 0.01
50 77 0.40
51 113 0.59
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGTTGA
Found at i:24844779 original size:101 final size:101
Alignment explanation
Indices: 24844659--24844944 Score: 439
Period size: 101 Copynumber: 2.8 Consensus size: 101
24844649 AAAGTGATGG
* *
24844659 TCACGTGTGTAGTATTATGTGTAGGCTACTACGTGTACCATAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCATAATGATAGGTCACATGTGTAGTAC
*
24844724 TATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCAGATAGCTTCAA
* * *
24844760 TCATGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCATATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCATAATGATAGGTCACATGTGTAGTAC
* *
24844825 TATGTGCAGGCTACTATGCGTACCGGATAGCTTTAA
66 TATGTGCAGGCTACTATGCGTACCAGATAGCTTCAA
* * *
24844861 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTA-C-CATAATGATAGGTCACATGTGTAGT
*
24844925 ACTATGTGCATGCTACTATG
64 ACTATGTGCAGGCTACTATG
24844945 TGAATCCGCA
Statistics
Matches: 168, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
101 128 0.76
102 34 0.20
103 6 0.04
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCATAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCAGATAGCTTCAA
Found at i:24844946 original size:26 final size:26
Alignment explanation
Indices: 24844866--24844946 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
24844856 TTTAATCACG
*
24844866 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
* * *
24844892 CGTGTA-T-CGGATAGTG-ATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCATGCT-ACTA
24844917 TGTGTAGTACTATGTGCATGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
24844943 TGTG
1 TGTG
24844947 AATCCGCATC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCATGCTACTA
Found at i:24845069 original size:41 final size:42
Alignment explanation
Indices: 24844955--24845082 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 42
24844945 TGAATCCGCA
* * * *
24844955 TCATTGAATATAAAGGTGGTTGCTAAGTGCTGACTCCACCATA
1 TCATTGATTAT-AAGGTGGTTGCTAAGTGCTGATTCCACCGTG
* *
24844998 TCCTTGACTGTGA-AAGG-GGTTGCTATGTGCTGATTCC-CCGTG
1 TCATTGA-T-T-ATAAGGTGGTTGCTAAGTGCTGATTCCACCGTG
24845040 TCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTG
1 TCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTG
24845082 T
1 T
24845083 AACGGTTAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
39 1 0.01
40 5 0.07
41 20 0.28
42 15 0.21
43 24 0.34
44 4 0.06
45 1 0.01
46 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (42 bp):
TCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTG
Found at i:24848757 original size:18 final size:18
Alignment explanation
Indices: 24848723--24848758 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
24848713 GTAAATTGAC
24848723 ATTTAGAAACTTAAAAAG
1 ATTTAGAAACTTAAAAAG
24848741 ATTTAAGAAACTTAAAAA
1 ATTT-AGAAACTTAAAAA
24848759 TTCAACATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (18 bp):
ATTTAGAAACTTAAAAAG
Found at i:24851759 original size:18 final size:18
Alignment explanation
Indices: 24851736--24851770 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24851726 AGGAATCTTC
24851736 TTTTC-TTTCTTTCTTTCT
1 TTTTCTTTTCTTT-TTTCT
24851754 TTTTCTTTTCTTTTTTC
1 TTTTCTTTTCTTTTTTC
24851771 CCTCACTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTTCT
Found at i:24855435 original size:37 final size:37
Alignment explanation
Indices: 24855393--24855467 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
24855383 TTAACCTCGT
* *
24855393 TAATAAATGGTCGAATTACCATCTAAGTCTACTAACA
1 TAATAAATGGTCCAATTACCATCTAAGTCCACTAACA
*
24855430 TAATAAATGGTCCAATTACCATCTAAGTCCACTCACA
1 TAATAAATGGTCCAATTACCATCTAAGTCCACTAACA
24855467 T
1 T
24855468 TGTAACACCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (37 bp):
TAATAAATGGTCCAATTACCATCTAAGTCCACTAACA
Found at i:24857098 original size:27 final size:27
Alignment explanation
Indices: 24857067--24857220 Score: 181
Period size: 27 Copynumber: 5.7 Consensus size: 27
24857057 CTGCATCAAG
24857067 ACCCCCATAGGGTAAAATGATCGAAAT
1 ACCCCCATAGGGTAAAATGATCGAAAT
* *
24857094 ACCCCTATAGGATAAAATGA-CAGAAAT
1 ACCCCCATAGGGTAAAATGATC-GAAAT
* *
24857121 ACCCTCATAGGGTAAAAT-AACTGAAAT
1 ACCCCCATAGGGTAAAATGATC-GAAAT
24857148 ACCCCCATAGGGTAAAATGAAT-GAAAT
1 ACCCCCATAGGGTAAAATG-ATCGAAAT
* * *
24857175 ACCCCCATAGGGGAAAATTACCGAAAT
1 ACCCCCATAGGGTAAAATGATCGAAAT
*
24857202 ACCCCTA-AGGGTAAAATGA
1 ACCCCCATAGGGTAAAATGA
24857221 CTATTATACC
Statistics
Matches: 108, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
26 13 0.12
27 94 0.87
29 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (27 bp):
ACCCCCATAGGGTAAAATGATCGAAAT
Found at i:24857136 original size:54 final size:54
Alignment explanation
Indices: 24857067--24857221 Score: 208
Period size: 54 Copynumber: 2.9 Consensus size: 54
24857057 CTGCATCAAG
* *
24857067 ACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGGATAAAATGACA-GAAAT
1 ACCCCCATAGGGTAAAAT-AACGAAATACCCCTATAGGGTAAAATGACATGAAAT
* *
24857121 ACCCTCATAGGGTAAAATAACTGAAATACCCCCATAGGGTAAAATGA-ATGAAAT
1 ACCCCCATAGGGTAAAATAAC-GAAATACCCCTATAGGGTAAAATGACATGAAAT
* *
24857175 ACCCCCATAGGGGAAAATTACCGAAATACCCCTA-AGGGTAAAATGAC
1 ACCCCCATAGGGTAAAA-TAACGAAATACCCCTATAGGGTAAAATGAC
24857222 TATTATACCC
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
53 15 0.17
54 71 0.80
55 3 0.03
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18
Consensus pattern (54 bp):
ACCCCCATAGGGTAAAATAACGAAATACCCCTATAGGGTAAAATGACATGAAAT
Found at i:24857202 original size:81 final size:80
Alignment explanation
Indices: 24857067--24857218 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 80
24857057 CTGCATCAAG
* *
24857067 ACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGGATAAAATGACAGAAATA-CCCTCATAG
1 ACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGAGAAAATGACAGAAATACCCCT-A-AG
24857131 GGTAAAATAACTGAAAT
64 GGTAAAATAACTGAAAT
* * *
24857148 ACCCCCATAGGGTAAAATGAAT-GAAATACCCCCATAGGGGAAAATTACCGAAATACCCCTAAGG
1 ACCCCCATAGGGTAAAATG-ATCGAAATACCCCCATAGGAGAAAATGACAGAAATACCCCTAAGG
24857212 GTAAAAT
65 GTAAAAT
24857219 GACTATTATA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
80 10 0.16
81 48 0.75
82 6 0.09
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18
Consensus pattern (80 bp):
ACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGAGAAAATGACAGAAATACCCCTAAGGG
TAAAATAACTGAAAT
Found at i:24866114 original size:84 final size:86
Alignment explanation
Indices: 24865958--24866190 Score: 283
Period size: 84 Copynumber: 2.7 Consensus size: 86
24865948 GATTTCCACA
* * * *
24865958 TATAACATAAAACAGCCACAAATGCTTCAACTTATCAGAGAACAACCATAGAGGCTTCCACATAT
1 TATAATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGAACAACCATAGAGGCTTCCACATAT
*
24866023 AACATATTTTTCCATTAA-GG-
66 AACATATTTCTCCA-TAAGGGC
* * * * **
24866043 T-TCATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGTACAACTACAGAGGCTTCGGCATAT
1 TATAATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGAACAACCATAGAGGCTTCCACATAT
*
24866107 AATATATTTCTCCATAAGGGCTCAC
66 AACATATTTCTCCATAAGGG----C
24866132 ATATAATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGAACAACCATAGAGGCTTC
1 -TATAATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGAACAACCATAGAGGCTTC
24866191 TATATTTGAG
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
83 3 0.02
84 67 0.54
85 1 0.01
90 1 0.01
91 52 0.42
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (86 bp):
TATAATATAGAACAGCCACAAAGGCTTCCACTTATCAGAGAACAACCATAGAGGCTTCCACATAT
AACATATTTCTCCATAAGGGC
Found at i:24877547 original size:131 final size:131
Alignment explanation
Indices: 24877305--24878249 Score: 1287
Period size: 131 Copynumber: 7.3 Consensus size: 131
24877295 TCGGTGAAAT
* * * **
24877305 CACAAGTCCTATGTCCCTGACCAGCAATGGAATGGGTTGGAAATTGTAGATCTTGTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
24877370 CAATAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
24877435 C
131 C
*
24877436 CACACGTCCTATGTCCCTGACCATCAGTGGAATAGGTTGGAAATTGA-AGATCTTGTCTCCCTAA
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATT-ACAGATCTTGTCTCCCTAA
* * * *
24877500 GCAGTAGCGAAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGAGTAGGGAAATAGATTTAA
65 GCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAA
24877565 GC
130 GC
* * * *
24877567 CACACGTCCTATGTCCCTGACCAACAATGGAATAGGTTGGAAATCACAGATCTTTTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * *
24877632 CAGTAGCGGAGTAGATCAAAGACGGTGAATCTTATCTTTCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
24877697 C
131 C
* * *
24877698 CGCACGTCCTATGTCCCTGACCAGCAATGGAATAGGTTTGAAATTACAGATCTTGTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
24877763 CAGTAGCGGAGCATATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAAGGAAACATAATTAAG
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
24877828 C
131 C
24877829 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
24877894 CAATAGCAGAGCAAATCAAAGACGGTGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
24877959 C
131 C
*
24877960 CACACGTCCTATGTCCCTGACTAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
24878025 CAGTAGCGGAGTAGATCAAAGATGACGAATCTTATTTTCCCC------A--G-----GATTTAAG
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
24878077 C
131 C
* * * *
24878078 CACACGTCCTCTGTCCCTGACCAGCAGTGGAATTGGTTGGAAATTGCAGATCTCGTCTCCCTAAG
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * * * * * *
24878143 TAGTAACGGAGCAGATCGAAGACGACGAATCTTATCTT---CAAGTGTA-AGAAAGCAAATTTAA
66 CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAA-CAGATTTAA
24878204 GC
130 GC
* *
24878206 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAAT
1 CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAAT
24878250 CAGATTGAAG
Statistics
Matches: 730, Mismatches: 69, Indels: 33
0.88 0.08 0.04
Matches are distributed among these distances:
115 1 0.00
118 101 0.14
121 1 0.00
122 1 0.00
123 1 0.00
125 1 0.00
128 48 0.07
130 1 0.00
131 575 0.79
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (131 bp):
CACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
CAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
C
Found at i:24878159 original size:118 final size:118
Alignment explanation
Indices: 24877951--24878249 Score: 364
Period size: 118 Copynumber: 2.4 Consensus size: 118
24877941 TAGGGAAACA
* *
24877951 GATTTAAGCCACACGTCCTATGTCCCTGACTAGCAGTGGAATAGGTTGGAAATTACAGATCTTGT
1 GATTTAAGCCACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTCGT
* * *
24878016 CTCCCTAAGCAGTAGCGGAGTAGATCAAAGATGACGAATCTTATTTTCCCCAG
66 CTCCCTAAGCAGTAACGGAGCAGATCAAAGACGACGAATCTTATTTTCCCCAG
* * *
24878069 GATTTAAGCCACACGTCCTCTGTCCCTGACCAGCAGTGGAATTGGTTGGAAATTGCAGATCTCGT
1 GATTTAAGCCACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTCGT
* * * ***
24878134 CTCCCTAAGTAGTAACGGAGCAGATCGAAGACGACGAATCTTATCTTCAAGTGTAAG
66 CTCCCTAAGCAGTAACGGAGCAGATCAAAGACGACGAATCTTATTTTC----CCCAG
* *
24878191 AAAGCAAATTTAAGCCACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAAT
1 ---G---ATTTAAGCCACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAAT
24878250 CAGATTGAAG
Statistics
Matches: 153, Mismatches: 18, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
118 102 0.67
122 2 0.01
125 1 0.01
128 48 0.31
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (118 bp):
GATTTAAGCCACACGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTCGT
CTCCCTAAGCAGTAACGGAGCAGATCAAAGACGACGAATCTTATTTTCCCCAG
Found at i:24878318 original size:44 final size:44
Alignment explanation
Indices: 24878250--24878485 Score: 172
Period size: 44 Copynumber: 5.1 Consensus size: 44
24878240 GGTTGGAAAT
* *
24878250 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAG
* *
24878294 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAG
* ** * *
24878338 CGGATT-AAAATAAAGT-ATCTTATCTCTCTGA-AGTTACAGTAGAGCAGATCGCAT
1 CAGATTGAAGCT--AGTAATCTTATCTCCCTGAGA-TTAC-----AGC-G---G-AG
* *
24878392 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAG
* * * * * *
24878436 CAGATGGAAGTTAATAACCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAG
*
24878480 CTGATT
1 CAGATT
24878486 AAAATAAAGG
Statistics
Matches: 148, Mismatches: 28, Indels: 32
0.71 0.13 0.15
Matches are distributed among these distances:
43 4 0.03
44 103 0.70
45 4 0.03
48 1 0.01
49 5 0.03
50 1 0.01
53 3 0.02
54 24 0.16
55 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (44 bp):
CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGCGGAG
Found at i:24878473 original size:98 final size:98
Alignment explanation
Indices: 24878294--24878480 Score: 225
Period size: 98 Copynumber: 1.9 Consensus size: 98
24878284 TACAGCGGAG
* * * * * * *
24878294 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGTATCTT
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATGAAAATAAAGTACCCT
*
24878359 ATCTCTCTGAAGTTACAGTAGAGCAGATCGCAT
66 ATCTCCCTGAAGTTACAGTAGAGCAGATCGCAT
* * * *
24878392 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGTTAA-TAACCC
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATGAAAATAAAGT-ACCC
*
24878456 TATCTCCCTG-AGATTACAGTGGAGC
65 TATCTCCCTGAAG-TTACAGTAGAGC
24878481 TGATTAAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
97 3 0.04
98 71 0.96
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (98 bp):
CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATGAAAATAAAGTACCCT
ATCTCCCTGAAGTTACAGTAGAGCAGATCGCAT
Found at i:24878509 original size:142 final size:142
Alignment explanation
Indices: 24878248--24878536 Score: 497
Period size: 142 Copynumber: 2.0 Consensus size: 142
24878238 TAGGTTGGAA
* * *
24878248 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATC
1 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGCTAATAACC
* * *
24878313 CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGTATCTTATCTCTCTGAAGTTACAGT
66 CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCACTCTGAAGTTACAAT
24878378 AGAGCAGATCGC
131 AGAGCAGATCGC
*
24878390 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGTTAATAACC
1 ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGCTAATAACC
*
24878455 CTATCTCCCTGAGATTACAGTGGAGCTGATTAAAATAAAGGATCTTATCACTCTGAAGTTACAAT
66 CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCACTCTGAAGTTACAAT
*
24878520 AGAGTAGATCGC
131 AGAGCAGATCGC
24878532 ATCAG
1 ATCAG
24878537 GTCTTATCTC
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 138 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (142 bp):
ATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGCTAATAACC
CTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCACTCTGAAGTTACAAT
AGAGCAGATCGC
Found at i:24886720 original size:17 final size:18
Alignment explanation
Indices: 24886700--24886736 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
24886690 GGATTCACCA
24886700 TTTGGCAAACTCT-AGGT
1 TTTGGCAAACTCTAAGGT
24886717 TTTGGCAAACTCTAAGGT
1 TTTGGCAAACTCTAAGGT
24886735 TT
1 TT
24886737 GACAGACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (18 bp):
TTTGGCAAACTCTAAGGT
Found at i:24892528 original size:50 final size:50
Alignment explanation
Indices: 24892466--24892567 Score: 152
Period size: 50 Copynumber: 2.0 Consensus size: 50
24892456 TTTATCTAGA
* *
24892466 TGAAAAAGTAATTTC-CTCGCCTATCATCAATGAAATCATTTTCATTTGTT
1 TGAAAAAGTAATTTCTC-CACCCATCATCAATGAAATCATTTTCATTTGTT
* *
24892516 TGAAAAAGTAATTTCTCCACCCATTATCAATGGAATCATTTTCATTTGTT
1 TGAAAAAGTAATTTCTCCACCCATCATCAATGAAATCATTTTCATTTGTT
24892566 TG
1 TG
24892568 TGGCAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
50 46 0.98
51 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (50 bp):
TGAAAAAGTAATTTCTCCACCCATCATCAATGAAATCATTTTCATTTGTT
Found at i:24893489 original size:25 final size:25
Alignment explanation
Indices: 24893460--24893508 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
24893450 TGATGCATGT
* * *
24893460 ATATAACCTATTATTATATTATATG
1 ATATAACATATCATTATATAATATG
*
24893485 ATATAATATATCATTATATAATAT
1 ATATAACATATCATTATATAATAT
24893509 AGTGGGAGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (25 bp):
ATATAACATATCATTATATAATATG
Found at i:24893955 original size:16 final size:16
Alignment explanation
Indices: 24893922--24893959 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
24893912 CTCTAATTAT
24893922 TTTATATAAAAATAAA
1 TTTATATAAAAATAAA
*
24893938 TTTAT-TAAATATATAA
1 TTTATATAAAAATA-AA
24893954 TTTATA
1 TTTATA
24893960 CTTTTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTATATAAAAATAAA
Found at i:24894511 original size:15 final size:15
Alignment explanation
Indices: 24894491--24894547 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
24894481 TTTGACAAAC
24894491 TGAAAAATTAAGTGT
1 TGAAAAATTAAGTGT
*
24894506 TGAAAAAATAAGTGT
1 TGAAAAATTAAGTGT
*
24894521 TG-AAAATTAAGTAT
1 TGAAAAATTAAGTGT
*
24894535 TGAAAATTTAAGT
1 TGAAAAATTAAGT
24894548 ACTAAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
14 12 0.32
15 25 0.68
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (15 bp):
TGAAAAATTAAGTGT
Found at i:24894526 original size:14 final size:14
Alignment explanation
Indices: 24894491--24894540 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
24894481 TTTGACAAAC
24894491 TGAAAAATTAAGTGT
1 TGAAAAA-TAAGTGT
24894506 TGAAAAAATAAGTGT
1 TG-AAAAATAAGTGT
* *
24894521 TGAAAATTAAGTAT
1 TGAAAAATAAGTGT
24894535 TGAAAA
1 TGAAAA
24894541 TTTAAGTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 16 0.50
15 11 0.34
16 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (14 bp):
TGAAAAATAAGTGT
Found at i:24897546 original size:3 final size:3
Alignment explanation
Indices: 24897538--24897574 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
24897528 TTTCGAAAAC
24897538 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
24897575 GTTTTGCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:24903938 original size:626 final size:626
Alignment explanation
Indices: 24902747--24904004 Score: 2246
Period size: 626 Copynumber: 2.0 Consensus size: 626
24902737 CCTTTTAAAT
*
24902747 TTTATTGTTGTTGTTATGAACATGTCCATGAATAATTGTGATGTTTATATGTTTAATTTAATTAA
1 TTTATTGTTGTTGTTATGAACATGTCCATGAATAATTGTGATGTTAATATGTTTAATTTAATTAA
* **
24902812 TATGGCTTAAATTTAATTCGTGTTAGGTTGATTGCATTTCATCTACTTGAGTTATTAAAATTGTG
66 TATGGCTTAAATTTAATTCCTGTTAGGTCAATTGCATTTCATCTACTTGAGTTATTAAAATTGTG
*
24902877 TTTGTGTTGTTATAGGCCTCGGCAAGATGTTTGATTAAGTAAAACCATGACTAATTTATTCTTGC
131 TTTGTGTTGTTATAGGCCTCGGCAAGATGTTTGATTAAGTAAAACCATGACTAAGTTATTCTTGC
24902942 ATTACAATTGTAAGGTAACTAATGAATTAATTATTTAAACGGCTTGAAATTATAATTAATTGACA
196 ATTACAATTGTAAGGTAACTAATGAATTAATTATTTAAACGGCTTGAAATTATAATTAATTGACA
* * *
24903007 TGAGATTTAATCAGTGCATGTTTAATCATCTAAGGTAGCTGAGGGTTAAATTAGCAACGGTATCT
261 AGAGATTTAATCAGTCCAAGTTTAATCATCTAAGGTAGCTGAGGGTTAAATTAGCAACGGTATCT
*
24903072 AACGATACATTAGCCTTGTATAACTTGCAAGAGTATTGTGATTAAACTGTTTCAAGGTAGAAATA
326 AACGATACATTAGCCTTGCATAACTTGCAAGAGTATTGTGATTAAACTGTTTCAAGGTAGAAATA
* * *
24903137 CATTGTTACCTTAAGTAATCTTTTATGTGCTTCTGAGATTGAATTAATTGTTTGAATTGGCATAG
391 CATTGTTACCTCAAGTAATCTTTTATGTGCTTATGAGATTGAATTAATTGTTTGAATTGGAATAG
*
24903202 AGACATGTACAAGAGATTATTTTAATTTCATAAGTATGTATGTGCATTAACACATTTATTTATTA
456 AGACATGTACAAGAGATTATTTTAATTTCATAAGTATGTATGTGCATTAACACATTTACTTATTA
*
24903267 AAATTTGTTTAATCTATTGAATTGACATAGAGATATAGTCAAGAGATAAATGGATTTTGGTAGGT
521 AAATTTGTTTAATCGATTGAATTGACATAGAGATATAGTCAAGAGATAAATGGATTTTGGTAGGT
*
24903332 AAGTATGTTCATAAGTTAGCAAATTACCGAGTTGCCATGAA
586 AAGTATGTTCATAAGTTAGCAAATTACCGAATTGCCATGAA
24903373 TTTATTGTTGTTGTTATGAACATGTCCATGAATAATTGTGATGTTAATATGTTTAATTTAATTAA
1 TTTATTGTTGTTGTTATGAACATGTCCATGAATAATTGTGATGTTAATATGTTTAATTTAATTAA
*
24903438 TATGGCTTAAATTTAATTCCTGTTTGGTCAATTGCATTTCATCTACTTGAGTTATTAAAATTGTG
66 TATGGCTTAAATTTAATTCCTGTTAGGTCAATTGCATTTCATCTACTTGAGTTATTAAAATTGTG
*
24903503 TTTGTGTTGTTATAGGCCTCGGTAAGATGTTTGATTAAGTAAAACCATGACTAAGTTATTCTTGC
131 TTTGTGTTGTTATAGGCCTCGGCAAGATGTTTGATTAAGTAAAACCATGACTAAGTTATTCTTGC
* *
24903568 ATTACAATTGTAAGGTAACTAATGAATTAATTATTTAAACGGGTTGAAATTGTAATTAATTGACA
196 ATTACAATTGTAAGGTAACTAATGAATTAATTATTTAAACGGCTTGAAATTATAATTAATTGACA
* * ** *
24903633 AGATATTTAATCAGTCCAAGTTTAATCATCTAAGGTAGGTGAGTTTTAAATTAGCAATGGTATCT
261 AGAGATTTAATCAGTCCAAGTTTAATCATCTAAGGTAGCTGAGGGTTAAATTAGCAACGGTATCT
* *
24903698 AACGTTACATTAGCCTTGCATAACTTGCAAGATTATTGTGATTAAACTGTTTCAAGGTAGAAATA
326 AACGATACATTAGCCTTGCATAACTTGCAAGAGTATTGTGATTAAACTGTTTCAAGGTAGAAATA
*
24903763 CATTGTTACCTCACGTAATCTTTTATGTGCTTATGAGATTGAATTAATTGTTTGAATTGGAATAG
391 CATTGTTACCTCAAGTAATCTTTTATGTGCTTATGAGATTGAATTAATTGTTTGAATTGGAATAG
* *
24903828 AGATATGTTCAAGAGATTATTTTAATTTCATAAGTATGTATGTGCATTAACACATTTACTTATTA
456 AGACATGTACAAGAGATTATTTTAATTTCATAAGTATGTATGTGCATTAACACATTTACTTATTA
*
24903893 AAATTTGTTTAATCGGTTGAATTGACATAGAGATATAGTCAAGAGATAAATGGATTTTGGTAGGT
521 AAATTTGTTTAATCGATTGAATTGACATAGAGATATAGTCAAGAGATAAATGGATTTTGGTAGGT
24903958 AAGTATGTTCATAAGTTAGCAAATTACCGAATTGCCATGAA
586 AAGTATGTTCATAAGTTAGCAAATTACCGAATTGCCATGAA
24903999 TTTATT
1 TTTATT
24904005 CGTAACAACA
Statistics
Matches: 602, Mismatches: 30, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
626 602 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (626 bp):
TTTATTGTTGTTGTTATGAACATGTCCATGAATAATTGTGATGTTAATATGTTTAATTTAATTAA
TATGGCTTAAATTTAATTCCTGTTAGGTCAATTGCATTTCATCTACTTGAGTTATTAAAATTGTG
TTTGTGTTGTTATAGGCCTCGGCAAGATGTTTGATTAAGTAAAACCATGACTAAGTTATTCTTGC
ATTACAATTGTAAGGTAACTAATGAATTAATTATTTAAACGGCTTGAAATTATAATTAATTGACA
AGAGATTTAATCAGTCCAAGTTTAATCATCTAAGGTAGCTGAGGGTTAAATTAGCAACGGTATCT
AACGATACATTAGCCTTGCATAACTTGCAAGAGTATTGTGATTAAACTGTTTCAAGGTAGAAATA
CATTGTTACCTCAAGTAATCTTTTATGTGCTTATGAGATTGAATTAATTGTTTGAATTGGAATAG
AGACATGTACAAGAGATTATTTTAATTTCATAAGTATGTATGTGCATTAACACATTTACTTATTA
AAATTTGTTTAATCGATTGAATTGACATAGAGATATAGTCAAGAGATAAATGGATTTTGGTAGGT
AAGTATGTTCATAAGTTAGCAAATTACCGAATTGCCATGAA
Found at i:24911291 original size:66 final size:66
Alignment explanation
Indices: 24911178--24911308 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
24911168 GGTTCTTATC
* **
24911178 CAGACAGCTGTCAGGTGCGGTGACAATTCTGAACACAATCTGTAATTAACCCATGCAGCGACATT
1 CAGACAGCTGTCAGATGCGACGACAATTCTGAACACAATCTGTAATTAACCCATGCAGCGACATT
24911243 G
66 G
* * * *
24911244 CAGACATCTGTCAGATGCGACGACAATTCTGGACACCATCTAG-AATTAACTCATGCAGCGACAT
1 CAGACAGCTGTCAGATGCGACGACAATTCTGAACACAATCT-GTAATTAACCCATGCAGCGACAT
24911308 T
65 T
24911309 AATGTAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 56 0.98
67 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (66 bp):
CAGACAGCTGTCAGATGCGACGACAATTCTGAACACAATCTGTAATTAACCCATGCAGCGACATT
G
Found at i:24912250 original size:21 final size:21
Alignment explanation
Indices: 24912224--24912292 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
24912214 TCATTTTTAG
24912224 CAACTTCCTCTTCTTCAGCAA
1 CAACTTCCTCTTCTTCAGCAA
24912245 CAACTTCCTCTT-TT--GCAA
1 CAACTTCCTCTTCTTCAGCAA
* * *
24912263 CAACTT-TTGCTTCTGCAGCAT
1 CAACTTCCT-CTTCTTCAGCAA
24912284 CAACTTCCT
1 CAACTTCCT
24912293 TCTAAACAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.03
18 13 0.33
19 1 0.03
20 2 0.05
21 21 0.54
22 1 0.03
ACGTcount: A:0.22, C:0.35, G:0.07, T:0.36
Consensus pattern (21 bp):
CAACTTCCTCTTCTTCAGCAA
Found at i:24931053 original size:6 final size:6
Alignment explanation
Indices: 24931042--24931071 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
24931032 TGAATCTTGG
*
24931042 TGTGTA TGTGTA TGTGTA TGTGTG TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
24931072 ACATGACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (6 bp):
TGTGTA
Found at i:24932219 original size:28 final size:26
Alignment explanation
Indices: 24932173--24932294 Score: 145
Period size: 26 Copynumber: 4.6 Consensus size: 26
24932163 AACAGATAAG
24932173 GAAAACCTTTGTGGCGTAATATGAAAA
1 GAAAACCTTTGTGGCGTAATATG-AAA
*
24932200 GAATAACCTTTGTGGAGTAATATGAAA
1 GAA-AACCTTTGTGGCGTAATATGAAA
* * **
24932227 GAAAGCCTTTGTGTCGCCATATGAAA
1 GAAAACCTTTGTGGCGTAATATGAAA
* *
24932253 GAAAACCTTTGTGGCGTAAAATGAATT
1 GAAAACCTTTGTGGCGTAATATGAA-A
*
24932280 GAAAGCCTTTGTGGC
1 GAAAACCTTTGTGGC
24932295 AAACCATGAA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
26 38 0.47
27 23 0.29
28 19 0.24
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (26 bp):
GAAAACCTTTGTGGCGTAATATGAAA
Found at i:24932304 original size:53 final size:52
Alignment explanation
Indices: 24932173--24932310 Score: 136
Period size: 54 Copynumber: 2.6 Consensus size: 52
24932163 AACAGATAAG
* * * *
24932173 GAAAACCTTTGTGGCGTAATATGAAAAGAATAACCTTTGTGGAGTAATATGAAA
1 GAAAGCCTTTGT-GCGCAACATGAAAAGAA-AACCTTTGTGGAGTAAAATGAAA
* * * *
24932227 GAAAGCCTTTGTGTCGCCATATG-AAAGAAAACCTTTGTGGCGTAAAATGAATT
1 GAAAGCCTTTGTG-CGCAACATGAAAAGAAAACCTTTGTGGAGTAAAATGAA-A
24932280 GAAAGCCTTTGTG-GCAAACCATGAAAAGAAA
1 GAAAGCCTTTGTGCGC-AA-CATGAAAAGAAA
24932311 GCCTCTATGA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
51 2 0.03
52 21 0.30
53 23 0.32
54 25 0.35
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.25
Consensus pattern (52 bp):
GAAAGCCTTTGTGCGCAACATGAAAAGAAAACCTTTGTGGAGTAAAATGAAA
Found at i:24932630 original size:13 final size:13
Alignment explanation
Indices: 24932596--24932628 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
24932586 AAAGGCATAG
24932596 TTGTATTTACTCA
1 TTGTATTTACTCA
*
24932609 TTGTATTTACTTA
1 TTGTATTTACTCA
24932622 -TGTATTT
1 TTGTATTT
24932629 TAGTTTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.61
Consensus pattern (13 bp):
TTGTATTTACTCA
Found at i:24932973 original size:32 final size:32
Alignment explanation
Indices: 24932936--24932997 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
24932926 TTGCAATTTC
24932936 CATTCATAAATATAGAGAATTTGAGTAGTTCA
1 CATTCATAAATATAGAGAATTTGAGTAGTTCA
* * *
24932968 CATTCATGAATCTAGAGAGTTTGAGTAGTT
1 CATTCATAAATATAGAGAATTTGAGTAGTT
24932998 GGTTTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (32 bp):
CATTCATAAATATAGAGAATTTGAGTAGTTCA
Found at i:24938424 original size:13 final size:13
Alignment explanation
Indices: 24938406--24938430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24938396 CTGTCGAGGG
24938406 AGCCTTACATTAC
1 AGCCTTACATTAC
24938419 AGCCTTACATTA
1 AGCCTTACATTA
24938431 TTGCACTGTC
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:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (13 bp):
AGCCTTACATTAC
Found at i:24938832 original size:41 final size:41
Alignment explanation
Indices: 24938775--24938856 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
24938765 TTGTGCATTT
24938775 ATGCTAATGCTAGCAATAATGTAAGAGTTTTTCGTGGGAAA
1 ATGCTAATGCTAGCAATAATGTAAGAGTTTTTCGTGGGAAA
24938816 ATGCTAATGCTAGCAATAATGTAAGAGTTTTTCGTGGGAAA
1 ATGCTAATGCTAGCAATAATGTAAGAGTTTTTCGTGGGAAA
24938857 TTCAACTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (41 bp):
ATGCTAATGCTAGCAATAATGTAAGAGTTTTTCGTGGGAAA
Found at i:24940294 original size:21 final size:21
Alignment explanation
Indices: 24940253--24940295 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
24940243 AATAAAGTAG
*
24940253 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
*
24940274 ATTATATTTTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
24940295 A
1 A
24940296 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:24940322 original size:12 final size:12
Alignment explanation
Indices: 24940302--24940348 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
24940292 AGTAAATTCA
*
24940302 TATAATAATAAT
1 TATATTAATAAT
24940314 TATATTAATAAT
1 TATATTAATAAT
*
24940326 TTTATT-A-AAT
1 TATATTAATAAT
24940336 TATATTTAATAAT
1 TATA-TTAATAAT
24940349 AATTATGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 6 0.21
11 3 0.10
12 17 0.59
13 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATTAATAAT
Found at i:24940346 original size:38 final size:37
Alignment explanation
Indices: 24940287--24940359 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
24940277 ATATTTTATG
24940287 ATTTTAGTAAATTCATATAATAATAATTATATTAATA
1 ATTTTAGTAAATTCATATAATAATAATTATATTAATA
* *
24940324 ATTTTATTAAATT-ATATTTAATAATAATTATGTTAA
1 ATTTTAGTAAATTCATA--TAATAATAATTATATTAA
24940360 AATATGGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 3 0.09
37 12 0.38
38 17 0.53
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
ATTTTAGTAAATTCATATAATAATAATTATATTAATA
Found at i:24940573 original size:44 final size:46
Alignment explanation
Indices: 24940510--24940604 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 46
24940500 TATTAAAACA
*
24940510 TCATTCCATTCAACCAAACAAAAGAA-TGCT-ATTACAGCTCTATT
1 TCATTCCATTCAACCAAACAAAAGAATTACTGATTACAGCTCTATT
**
24940554 TCATTCCATTCAACCAAACAATTGAATTACTGATTACAGCTCTATT
1 TCATTCCATTCAACCAAACAAAAGAATTACTGATTACAGCTCTATT
*
24940600 CCATT
1 TCATT
24940605 ACAGCTCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 24 0.53
45 3 0.07
46 18 0.40
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (46 bp):
TCATTCCATTCAACCAAACAAAAGAATTACTGATTACAGCTCTATT
Found at i:24940607 original size:16 final size:16
Alignment explanation
Indices: 24940586--24940656 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
24940576 TGAATTACTG
*
24940586 ATTACAGCTCTATTCC
1 ATTACAGCCCTATTCC
*
24940602 ATTACAGCTCTATTCC
1 ATTACAGCCCTATTCC
* *
24940618 CTTACAGCCCTATTCA
1 ATTACAGCCCTATTCC
* *
24940634 ATTACAACCCTATTCG
1 ATTACAGCCCTATTCC
24940650 ATTACAG
1 ATTACAG
24940657 TGAACCAAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:24945646 original size:3 final size:3
Alignment explanation
Indices: 24945633--24945671 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
24945623 CATCATTGTT
*
24945633 ATC AAC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
24945672 GCCTTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:24960369 original size:47 final size:47
Alignment explanation
Indices: 24960318--24960426 Score: 173
Period size: 47 Copynumber: 2.3 Consensus size: 47
24960308 AGTAACGTAG
** *
24960318 ATAAACTGCCAATAATCAATATTGTGGACAAGCCACCAAAATCGCAA
1 ATAAACTGCCAATAATCAATATCATGGACAAGCCACCAAAATCACAA
* *
24960365 ATAAACTGCCAATAATCAATATCATGGACAAGCCACCAAAATCATAG
1 ATAAACTGCCAATAATCAATATCATGGACAAGCCACCAAAATCACAA
24960412 ATAAACTGCCAATAA
1 ATAAACTGCCAATAA
24960427 ATTCCACCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (47 bp):
ATAAACTGCCAATAATCAATATCATGGACAAGCCACCAAAATCACAA
Found at i:24969597 original size:29 final size:28
Alignment explanation
Indices: 24969563--24969774 Score: 186
Period size: 29 Copynumber: 7.4 Consensus size: 28
24969553 AAGAAGTTGA
24969563 CCACAAAGGCTTACCTTTCTAGAGCTTTT
1 CCACAAAGGCTTACCTTTCTAGAG-TTTT
* * *
24969592 CCAC-AAGGGTTATCCTTTAATAG-GTTTG
1 CCACAAAGGCTTA-CCTTT-CTAGAGTTTT
24969620 CCACAAAGGCTTACCTTT-TAAGAGTTTTT
1 CCACAAAGGCTTACCTTTCT-AGAG-TTTT
* * **
24969649 CCACAAAGG-TTGTCCTTTAATAG-GTTCA
1 CCACAAAGGCTT-ACCTTT-CTAGAGTTTT
*
24969677 CCACAAAGGCTTACCTTTCCAGAGTTTT
1 CCACAAAGGCTTACCTTTCTAGAGTTTT
**
24969705 ACCACAAAGGCTTACCTTTAAC-AG-GTTCG
1 -CCACAAAGGCTTACCTTT--CTAGAGTTTT
24969734 CCACAAAGGCTTACCTTTCTAGAGTTTT
1 CCACAAAGGCTTACCTTTCTAGAGTTTT
24969762 GCCACAAAGGCTT
1 -CCACAAAGGCTT
24969775 TTTTTCTCCT
Statistics
Matches: 149, Mismatches: 17, Indels: 34
0.75 0.09 0.17
Matches are distributed among these distances:
26 2 0.01
27 6 0.04
28 62 0.42
29 70 0.47
30 7 0.05
31 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (28 bp):
CCACAAAGGCTTACCTTTCTAGAGTTTT
Found at i:24969654 original size:114 final size:115
Alignment explanation
Indices: 24969520--24969769 Score: 334
Period size: 114 Copynumber: 2.2 Consensus size: 115
24969510 GAAGGAATTT
* *
24969520 CCTTTC-AGAGATTTTT-CACAAAAGG-TGTTCTTTAAGAAGTTGACCACAAAGGCTTACCTTTC
1 CCTTTCTAGAG-TTTTTCCACAAAAGGTTGTCCTTTAAGAAGTTCACCACAAAGGCTTACCTTTC
* * * *
24969582 TAGAGCTTTT-CCAC-AAGGGTTATCCTTTAATAGGTTTGCCACAAAGGCTTA
65 CAGAG-TTTTACCACAAAGGCTTA-CCTTTAACAGGTTCGCCACAAAGGCTTA
* *
24969633 CCTTT-TAAGAGTTTTTCCAC-AAAGGTTGTCCTTTAATAGGTTCACCACAAAGGCTTACCTTTC
1 CCTTTCT-AGAGTTTTTCCACAAAAGGTTGTCCTTTAAGAAGTTCACCACAAAGGCTTACCTTTC
24969696 CAGAGTTTTACCACAAAGGCTTACCTTTAACAGGTTCGCCACAAAGGCTTA
65 CAGAGTTTTACCACAAAGGCTTACCTTTAACAGGTTCGCCACAAAGGCTTA
*
24969747 CCTTTCTAGAGTTTTGCCACAAA
1 CCTTTCTAGAGTTTTTCCACAAA
24969770 GGCTTTTTTT
Statistics
Matches: 120, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
113 19 0.16
114 91 0.76
115 10 0.08
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (115 bp):
CCTTTCTAGAGTTTTTCCACAAAAGGTTGTCCTTTAAGAAGTTCACCACAAAGGCTTACCTTTCC
AGAGTTTTACCACAAAGGCTTACCTTTAACAGGTTCGCCACAAAGGCTTA
Found at i:24969769 original size:57 final size:56
Alignment explanation
Indices: 24969563--24969774 Score: 286
Period size: 57 Copynumber: 3.7 Consensus size: 56
24969553 AAGAAGTTGA
* *
24969563 CCACAAAGGCTTACCTTTCTAGAGCTTTTCCAC-AAGGGTTATCCTTTAATAGGTTTG
1 CCACAAAGGCTTACCTTTCTAGAG-TTTTCCACAAAGGCTTA-CCTTTAATAGGTTCG
* *
24969620 CCACAAAGGCTTACCTTT-TAAGAGTTTTTCCACAAAGG-TTGTCCTTTAATAGGTTCA
1 CCACAAAGGCTTACCTTTCT-AGAG-TTTTCCACAAAGGCTT-ACCTTTAATAGGTTCG
* *
24969677 CCACAAAGGCTTACCTTTCCAGAGTTTTACCACAAAGGCTTACCTTTAACAGGTTCG
1 CCACAAAGGCTTACCTTTCTAGAGTTTT-CCACAAAGGCTTACCTTTAATAGGTTCG
24969734 CCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTT
1 CCACAAAGGCTTACCTTTCTAGAGTTTT-CCACAAAGGCTT
24969775 TTTTTCTCCT
Statistics
Matches: 139, Mismatches: 10, Indels: 12
0.86 0.06 0.07
Matches are distributed among these distances:
56 5 0.04
57 128 0.92
58 6 0.04
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (56 bp):
CCACAAAGGCTTACCTTTCTAGAGTTTTCCACAAAGGCTTACCTTTAATAGGTTCG
Found at i:24995887 original size:65 final size:65
Alignment explanation
Indices: 24995783--24995918 Score: 245
Period size: 65 Copynumber: 2.1 Consensus size: 65
24995773 TTAATCTAGT
24995783 TTGAAAATGACTGGGTTTTGTGAATTGATAATGGGTAGGAACTAATTTTGCTTGTCGTTGATGAA
1 TTGAAAATGACTGGGTTTTGTGAATTGATAATGGGTAGGAACTAATTTTGCTTGTCGTTGATGAA
* * *
24995848 TTGAAAATGATTGGGTTTTGTGAATTGATAATGGGTAGGAACTAATTTTGCTTGTGGTTGATTAA
1 TTGAAAATGACTGGGTTTTGTGAATTGATAATGGGTAGGAACTAATTTTGCTTGTCGTTGATGAA
24995913 TTGAAA
1 TTGAAA
24995919 TGTTCATTGG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (65 bp):
TTGAAAATGACTGGGTTTTGTGAATTGATAATGGGTAGGAACTAATTTTGCTTGTCGTTGATGAA
Found at i:25012952 original size:22 final size:22
Alignment explanation
Indices: 25012926--25012970 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
25012916 ATTATGTGTA
25012926 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
* *
25012948 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
25012970 T
1 T
25012971 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:25018693 original size:14 final size:12
Alignment explanation
Indices: 25018672--25018714 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
25018662 AATGCTAGTG
25018672 AAAAAAAGAACA
1 AAAAAAAGAACA
25018684 AAAAGCAAAGAA-A
1 AAAA--AAAGAACA
*
25018697 AGAAAAAGAACA
1 AAAAAAAGAACA
25018709 AAAAAA
1 AAAAAA
25018715 GAGAGCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.23
12 10 0.38
13 4 0.15
14 6 0.23
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAACA
Found at i:25018699 original size:19 final size:17
Alignment explanation
Indices: 25018672--25018716 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
25018662 AATGCTAGTG
25018672 AAAAAAAGAACAAA-AAGC
1 AAAAAAAGAA-AAAGAA-C
25018690 AAAGAAAAGAAAAAGAAC
1 AAA-AAAAGAAAAAGAAC
25018708 AAAAAAAGA
1 AAAAAAAGA
25018717 GAGCATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAGAAC
Found at i:25021324 original size:17 final size:14
Alignment explanation
Indices: 25021278--25021328 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
25021268 AATATTTATT
25021278 TCTAAAAAAACAAG
1 TCTAAAAAAACAAG
25021292 TCTAAAAAACACAAG
1 TCTAAAAAA-ACAAG
25021307 TCTAAATTGAAAACAAG
1 TCTAAA---AAAACAAG
25021324 TCTAA
1 TCTAA
25021329 GAAAGTCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.27
15 11 0.33
17 10 0.30
18 3 0.09
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.20
Consensus pattern (14 bp):
TCTAAAAAAACAAG
Found at i:25021900 original size:15 final size:15
Alignment explanation
Indices: 25021876--25021905 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25021866 GAAACTAGAC
*
25021876 TCATATATTTTTTTA
1 TCATAAATTTTTTTA
25021891 TCATAAATTTTTTTA
1 TCATAAATTTTTTTA
25021906 GAATTTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TCATAAATTTTTTTA
Found at i:25023094 original size:50 final size:50
Alignment explanation
Indices: 25022977--25023273 Score: 328
Period size: 50 Copynumber: 5.8 Consensus size: 50
25022967 GAATATAACA
* * * ** * *
25022977 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTATAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* **
25023026 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
25023076 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
25023126 TGCCAACGCCATGTCCCTGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
25023176 TGCCAACGCCATGTCCCAGACATAGTCTTACATGGGACCTCTCATAGTCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA---TC---GG
* *
25023232 TGCCAATGCCATGTCCCATACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
25023274 TTACCCAAAT
Statistics
Matches: 215, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
48 1 0.00
49 40 0.19
50 133 0.62
53 2 0.01
56 39 0.18
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:25032987 original size:27 final size:27
Alignment explanation
Indices: 25032947--25033397 Score: 441
Period size: 27 Copynumber: 16.7 Consensus size: 27
25032937 GTAATGGGCC
*
25032947 TAAAATGATTGAAATACCCTCAAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* * * *
25032974 TAAAACGACCGAAATATCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* * * * * *
25033001 TAAAATGATTAAAATTCCTTCGAAGGA
1 TAAAATGACTGAAATACCCTCAAAGGG
* * *
25033028 TAAAATGACCGAAATACCCTCGAAGGT
1 TAAAATGACTGAAATACCCTCAAAGGG
25033055 TAAAATGACTGAAATACCCTCAAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
** *
25033082 TAAAATGACCAAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* *
25033109 TAAAATAACTGAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* *
25033136 TAAAATGATTGAAATACCCTTGAAA-GG
1 TAAAATGACTGAAATACCC-TCAAAGGG
* *
25033163 TAAAATGACCGAAATACCCCTGACAA--G
1 TAAAATGACTGAAATA-CCCTCA-AAGGG
* * *
25033190 TAAAATAATTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
* ** *
25033217 TAAAATAACTGAAATATGCTCAAAAGG
1 TAAAATGACTGAAATACCCTCAAAGGG
25033244 TAAAATGACTGAAATAGCCC-CAAAGGG
1 TAAAATGACTGAAATA-CCCTCAAAGGG
* * *
25033271 TAAAATAACCGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCAAAGGG
*
25033298 TAAAATGACTGAAATACCC-CTAAAGGT
1 TAAAATGACTGAAATACCCTC-AAAGGG
*
25033325 TAAAATGACTGACATAACCC-C-AAGGG
1 TAAAATGACTGAAAT-ACCCTCAAAGGG
*
25033351 TAAAATGACTGAAATA-CCTCTGAAGGG
1 TAAAATGACTGAAATACCCTC-AAAGGG
**
25033378 TAAAATGACTGTTATACCCT
1 TAAAATGACTGAAATACCCT
25033398 TAGGAGTTGA
Statistics
Matches: 349, Mismatches: 62, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
24 2 0.01
25 4 0.01
26 26 0.07
27 300 0.86
28 17 0.05
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCAAAGGG
Found at i:25033578 original size:27 final size:26
Alignment explanation
Indices: 25033548--25033604 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
25033538 TGTATTGGTG
25033548 GCTTTGCCACATATACCGTTACTAGCA
1 GCTTTGCCACAT-TACCGTTACTAGCA
** * *
25033575 GCTTTGCTGCATTACTGTTACTGGCA
1 GCTTTGCCACATTACCGTTACTAGCA
25033601 GCTT
1 GCTT
25033605 CGCTGCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.35
Consensus pattern (26 bp):
GCTTTGCCACATTACCGTTACTAGCA
Found at i:25041396 original size:51 final size:50
Alignment explanation
Indices: 25041341--25041525 Score: 196
Period size: 51 Copynumber: 3.7 Consensus size: 50
25041331 CCGGTTCACA
* *
25041341 TAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCATCCGATACACG
* * * *
25041392 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCC-AGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATATC-ATCCGA-TACACG
* * * * **
25041443 TAGTAGCCTACACATAGTACTACACATGTGGCC-TATCATTCTGGCACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATATCA-TCCGATACACG
25041493 TAGTAGCCTGCACATAGTACTACACACGTGACC
1 TAGTAGCCTGCACATAGTACTACACACGTGACC
25041526 TAGCAACTTC
Statistics
Matches: 109, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
49 1 0.01
50 40 0.37
51 66 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATATCATCCGATACACG
Done.