Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007725.1 Hibiscus syriacus cultivar Beakdansim tig00109972_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: 3026330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 14
Found at i:609925 original size:27 final size:27
Alignment explanation
Indices: 609895--609956 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
609885 ATTCCCTTTA
*
609895 AATTTCTCAAT-TTCCCTCCAAA-TTCTC
1 AATTTCTCAATATT--CTCAAAATTTCTC
*
609922 AATTTCTCTATATTCTCAAAATTTCTC
1 AATTTCTCAATATTCTCAAAATTTCTC
609949 AATTTCTC
1 AATTTCTC
609957 TCTAAGTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 6 0.19
27 23 0.74
28 2 0.06
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.45
Consensus pattern (27 bp):
AATTTCTCAATATTCTCAAAATTTCTC
Found at i:610117 original size:15 final size:14
Alignment explanation
Indices: 610094--610175 Score: 59
Period size: 13 Copynumber: 6.0 Consensus size: 14
610084 ATAAACTTTT
610094 TATAGTTTATACATA
1 TATAGTTTATA-ATA
*
610109 TATAATTTAT-ATA
1 TATAGTTTATAATA
610122 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
610135 TATA-TTTGATGTAACA
1 TATAGTTT-A--TAATA
610151 TA-A-TTTAT-ATA
1 TATAGTTTATAATA
*
610162 TATAGCTTATAATA
1 TATAGTTTATAATA
610176 ATTGTATGGT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
11 4 0.07
12 5 0.09
13 24 0.44
14 4 0.07
15 14 0.25
16 4 0.07
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:610122 original size:13 final size:13
Alignment explanation
Indices: 610106--610254 Score: 96
Period size: 13 Copynumber: 11.5 Consensus size: 13
610096 TAGTTTATAC
610106 ATATATAATTTAT
1 ATATATAATTTAT
*
610119 ATATATAGTTTAT
1 ATATATAATTTAT
610132 ATATAT-ATTTGAT
1 ATATATAATTT-AT
* *
610145 GTAACATAATTTAT
1 AT-ATATAATTTAT
**
610159 ATATAT-AGCT-T
1 ATATATAATTTAT
610170 ATA-ATAATTGTAT
1 ATATATAATT-TAT
* *
610183 GGTTTATAA--TAT
1 -ATATATAATTTAT
* *
610195 AAATATAGTTTAT
1 ATATATAATTTAT
610208 ATATATAATTTAT
1 ATATATAATTTAT
*
610221 ATATA-AACTTAT
1 ATATATAATTTAT
*
610233 ATTATATATATATAT
1 A-TATATA-ATTTAT
610248 ATATATA
1 ATATATA
610255 TTAATTTTTT
Statistics
Matches: 102, Mismatches: 21, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
10 2 0.02
11 9 0.09
12 16 0.16
13 48 0.47
14 14 0.14
15 13 0.13
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (13 bp):
ATATATAATTTAT
Found at i:610192 original size:38 final size:40
Alignment explanation
Indices: 610108--610253 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 40
610098 GTTTATACAT
610108 ATATAATTTATATATATAGTTTATATATATATTTGATGTA
1 ATATAATTTATATATATAGTTTATATATATATTTGATGTA
* *
610148 ACATAATTTATATATATAGCTTATA-ATA-A-TTGTATGGT-
1 ATATAATTTATATATATAGTTTATATATATATTTG-AT-GTA
* * *
610186 TTATAA--TATAAATATAGTTTATATATATAATTT-ATAT-
1 ATATAATTTATATATATAGTTTATATATAT-ATTTGATGTA
* *
610223 ATA-AACTTATATTATATA-TATATATATATAT
1 ATATAATTTATA-TATATAGTTTATATATATAT
610254 ATTAATTTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
36 17 0.20
37 11 0.13
38 23 0.26
39 11 0.13
40 25 0.29
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (40 bp):
ATATAATTTATATATATAGTTTATATATATATTTGATGTA
Found at i:610212 original size:2 final size:2
Alignment explanation
Indices: 610187--610255 Score: 56
Period size: 2 Copynumber: 35.5 Consensus size: 2
610177 TTGTATGGTT
* * * *
610187 TA TA -A TA TA AA TA TA GTT TA TA TA TA TA -A TT TA TA TA TA AA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
610228 CT- TA TA T- 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
610256 TAATTTTTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
1 4 0.08
2 48 0.91
3 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:610225 original size:17 final size:19
Alignment explanation
Indices: 610205--610253 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
610195 AAATATAGTT
610205 TATATATATA-ATT-TATA
1 TATATATATATATTATATA
*
610222 TATAAACT-TATATTATATA
1 TATATA-TATATATTATATA
610241 TATATATATATAT
1 TATATATATATAT
610254 ATTAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 7 0.27
18 5 0.19
19 14 0.54
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATATATATATTATATA
Found at i:616315 original size:24 final size:24
Alignment explanation
Indices: 616287--616332 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
616277 GAATTTATAT
*
616287 TAAAATTTTAAGGATGTAAAATTA
1 TAAAATTTTAAAGATGTAAAATTA
*
616311 TAAAATTTTAAAGATGTTAAAT
1 TAAAATTTTAAAGATGTAAAAT
616333 CCAATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (24 bp):
TAAAATTTTAAAGATGTAAAATTA
Found at i:619853 original size:20 final size:20
Alignment explanation
Indices: 619828--619865 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
619818 AGTTTAATTT
619828 TTATATAATATAATATAATA
1 TTATATAATATAATATAATA
* *
619848 TTATATTATATATTATAA
1 TTATATAATATAATATAA
619866 ACTTACAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATAATATAATATAATA
Found at i:620147 original size:2 final size:2
Alignment explanation
Indices: 620142--620176 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
620132 ACACACATAC
*
620142 AT AT AT AC 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
620177 ATACCCCTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:620149 original size:8 final size:8
Alignment explanation
Indices: 620138--620172 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
620128 ACACACACAC
620138 ATACATAT
1 ATACATAT
620146 ATACATAT
1 ATACATAT
*
620154 ATATATAT
1 ATACATAT
*
620162 ATATATAT
1 ATACATAT
620170 ATA
1 ATA
620173 TATAATACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (8 bp):
ATACATAT
Found at i:621277 original size:67 final size:67
Alignment explanation
Indices: 621133--621286 Score: 220
Period size: 67 Copynumber: 2.3 Consensus size: 67
621123 ATTCGACTTC
* * * *
621133 TTGCTCGTTAAGCTCGTTAAAATTTTGTTTGACTCGTGCTCGTTAAGAAAATTTATTACTCGAAT
1 TTGCTCGTTAAGCTCGTTAAAATTTTGCTCGACTCATACTCGTTAAGAAAATTTATTACTCGAAT
621198 CA
66 CA
* *
621200 TTGATTGTTAAGCTCGTTAAAATTTTGCTCGACTCATACTCGTTAAGAAAATTTATTACTC-AAT
1 TTGCTCGTTAAGCTCGTTAAAATTTTGCTCGACTCATACTCGTTAAGAAAATTTATTACTCGAA-
621264 TCA
65 TCA
* *
621267 TTGCTCGTTAATCTCATTAA
1 TTGCTCGTTAAGCTCGTTAA
621287 GCTCGTTACA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
66 2 0.03
67 74 0.97
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (67 bp):
TTGCTCGTTAAGCTCGTTAAAATTTTGCTCGACTCATACTCGTTAAGAAAATTTATTACTCGAAT
CA
Found at i:622734 original size:21 final size:21
Alignment explanation
Indices: 622695--622737 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
622685 TACATGCCGG
622695 TGTTTTTTTCTTTCTTTTTTA
1 TGTTTTTTTCTTTCTTTTTTA
622716 TGTTTGTTTTCTTTCTTTTTTA
1 TGTTT-TTTTCTTTCTTTTTTA
622738 GCATGAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.05, C:0.09, G:0.07, T:0.79
Consensus pattern (21 bp):
TGTTTTTTTCTTTCTTTTTTA
Found at i:623301 original size:3 final size:3
Alignment explanation
Indices: 623293--623333 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
623283 CTCCTAATTG
623293 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
623334 TATTTAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:623459 original size:4 final size:4
Alignment explanation
Indices: 623450--623476 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
623440 ACAACTAATT
623450 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
623477 TATGTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:623752 original size:2 final size:2
Alignment explanation
Indices: 623745--623770 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
623735 TGTCCCATGA
623745 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
623771 GCATGTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:630704 original size:45 final size:44
Alignment explanation
Indices: 630638--630759 Score: 136
Period size: 45 Copynumber: 2.7 Consensus size: 44
630628 TAGCTTGACA
* * *
630638 AGATGTCGATATTGTTGACCCGGATCTAGCCTGAGGTAATTAGG
1 AGATGTCAATGTTGTTGACCCGGATCTAGCCTGAGGTAATAAGG
* * *
630682 AGGTGTCAATGTTGTATGACCCGAACCTAGCCTGAGGTAATAAGG
1 AGATGTCAATGTTGT-TGACCCGGATCTAGCCTGAGGTAATAAGG
* * * *
630727 AGATGTTAATTTTGTGTGACCCAGATCTCGCCT
1 AGATGTCAATGTTGT-TGACCCGGATCTAGCCT
630760 AAGTTTCCTA
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
44 12 0.19
45 51 0.81
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (44 bp):
AGATGTCAATGTTGTTGACCCGGATCTAGCCTGAGGTAATAAGG
Found at i:637305 original size:20 final size:21
Alignment explanation
Indices: 637266--637305 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
637256 CCATGGTGAT
637266 GGTATCGATACCCTAAATAAG
1 GGTATCGATACCCTAAATAAG
*
637287 GGTATCGATACTC-AAATAA
1 GGTATCGATACCCTAAATAA
637306 TTTTTCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (21 bp):
GGTATCGATACCCTAAATAAG
Found at i:642762 original size:182 final size:182
Alignment explanation
Indices: 642452--643085 Score: 939
Period size: 182 Copynumber: 3.5 Consensus size: 182
642442 TTACTATCGA
** * * * * *
642452 TTTTGTCATTTCGAGATCGATTTTATCATATTTTTACCTGTTATATTGTTATAGATCGATATATT
1 TTTTGTCATTTATAGACCGTTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
642517 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGA
*
642582 TACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAGCGCTTTACCTG
131 TACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
* * *
642634 TTCTGTCATTTATAGACCGTTTTTGTCATTTTTTTACCTATTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTATAGACCGTTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
* *
642699 TTTATAAAGTATCGACACTTTATTGGCGTTATAACTTCTTTTATTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGA
* * *
642764 TACTTATAATAAAGTATCAACACTTTTAACATATCCGGTAGCTCTTTACC-G
131 TACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
* **
642815 ATTTTATCATTTCGAGACCGATTTTT-TCATATTTTTACCTGTTATATTGTTATGGATCGATACA
1 -TTTTGTCATTTATAGACCG-TTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
* * * * *
642879 TTTTTATAAAGTATCGACACTTAATTAGCGCTATAATTTCTTCTCTTTTAAATTCCAAAAGTGTT
64 TTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTC
* * *
642944 GATACTTATAATAAAGTATCGACACTATCAACATATCCGATAGCGCTTTACTTG
129 GATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
* * * *
642998 TTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTTTACATGTTATATTGTTATGAATCGATACA
1 TTTTGTCATTTATAGACCGTTTTTGTCA--TATTTTTACCTGTTATATTGTTATGGATCGATACA
643063 TTTTTATAAAGTATCGACACTTT
64 TTTTTATAAAGTATCGACACTTT
643086 CAATATAACC
Statistics
Matches: 403, Mismatches: 43, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
181 5 0.01
182 338 0.84
183 6 0.01
184 54 0.13
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (182 bp):
TTTTGTCATTTATAGACCGTTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
Found at i:643124 original size:94 final size:94
Alignment explanation
Indices: 643017--643215 Score: 339
Period size: 93 Copynumber: 2.1 Consensus size: 94
643007 TTATAGACCG
*
643017 GTTTTGTCATTTTTTTTTACATGTTATATTGTTAT-GAATCGATACATTTTTATAAAGTATCGAC
1 GTTTTGTCATTTTTTTTTACATGCTATATTGTTATAG-ATCGATACATTTTTATAAAGTATCGAC
643081 ACTTTCAATATAACCGGTAGCGCTTTACCT
65 ACTTTCAATATAACCGGTAGCGCTTTACCT
* *
643111 GTTTTGTCA-TTTTTTTTACCTGCTATATTGTTATAGATCGATACCTTTTTATAAAGTATCGACA
1 GTTTTGTCATTTTTTTTTACATGCTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACA
*
643175 CTTTCAATATATCCGGTAGCGCTTTACCT
66 CTTTCAATATAACCGGTAGCGCTTTACCT
643204 GTTTTGTCATTT
1 GTTTTGTCATTT
643216 ATAGACCGGT
Statistics
Matches: 99, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
93 87 0.88
94 12 0.12
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (94 bp):
GTTTTGTCATTTTTTTTTACATGCTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACA
CTTTCAATATAACCGGTAGCGCTTTACCT
Found at i:643273 original size:113 final size:113
Alignment explanation
Indices: 643111--643400 Score: 483
Period size: 113 Copynumber: 2.6 Consensus size: 113
643101 CGCTTTACCT
* * * * **
643111 GTTTTGTCATTTTTTTTACCTGCTATATTGTTATAGATCGATACCTTTTTATAAAGTATCGACAC
1 GTTTTGTCATTTTTTTTACCTGTTATATTATTATGGATCAATATATTTTTATAAAGTATCGACAC
*
643176 TTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
66 TTTCAATATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCG
*
643224 GTTTTGTCATTTTTTTTACATGTTATATTATTATGGATCAATATATTTTTATAAAGTATCGACAC
1 GTTTTGTCATTTTTTTTACCTGTTATATTATTATGGATCAATATATTTTTATAAAGTATCGACAC
643289 TTTCAATATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCG
66 TTTCAATATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCG
* *
643337 ATTTTGTCA-TTTTTTTACCTGTTATATTATTATGGATAAATATATTTTTATAAAGTATCGACAC
1 GTTTTGTCATTTTTTTTACCTGTTATATTATTATGGATCAATATATTTTTATAAAGTATCGACAC
643401 AAACTGACAA
Statistics
Matches: 166, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
112 53 0.32
113 113 0.68
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.47
Consensus pattern (113 bp):
GTTTTGTCATTTTTTTTACCTGTTATATTATTATGGATCAATATATTTTTATAAAGTATCGACAC
TTTCAATATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCG
Found at i:643327 original size:206 final size:207
Alignment explanation
Indices: 642954--643328 Score: 653
Period size: 206 Copynumber: 1.8 Consensus size: 207
642944 GATACTTATA
*
642954 ATAAAGTATCGACACTATCAACATATCCGATAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
643019 TTTGTCATTTTTTTTTACATGTTATATTGTTATGAATCGATACATTTTTATAAAGTATCGACACT
66 TTTGTCATTTTTTTTTACATGTTATATTATTATGAATCAATACATTTTTATAAAGTATCGACACT
*
643084 TTCAATATAACCGGTAGCGCTTTACCTGTTTTGTCATTTTTTTTACCTGCTATATTGTTATAGAT
131 TTCAATATAACCGGTAACGCTTTACCTGTTTTGTCATTTTTTTTACCTGCTATATTGTTATAGAT
643149 CGATACCTTTTT
196 CGATACCTTTTT
* * *
643161 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
643226 TTTGTCA-TTTTTTTTACATGTTATATTATTATGGATCAATATATTTTTATAAAGTATCGACACT
66 TTTGTCATTTTTTTTTACATGTTATATTATTATGAATCAATACATTTTTATAAAGTATCGACACT
*
643290 TTCAATATATCCGGTAACGCTTTACCTGTTTTGTCATTT
131 TTCAATATAACCGGTAACGCTTTACCTGTTTTGTCATTT
643329 ATAGACCGAT
Statistics
Matches: 158, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
206 90 0.57
207 68 0.43
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (207 bp):
ATAAAGTATCGACACTATCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTTTACATGTTATATTATTATGAATCAATACATTTTTATAAAGTATCGACACT
TTCAATATAACCGGTAACGCTTTACCTGTTTTGTCATTTTTTTTACCTGCTATATTGTTATAGAT
CGATACCTTTTT
Found at i:644850 original size:20 final size:20
Alignment explanation
Indices: 644825--644874 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
644815 ATCTATATTG
*
644825 TAATTTAATCTACTTCAATT
1 TAATTTAATCTACTTCAATC
644845 TAATTTAATCTACTTCAATC
1 TAATTTAATCTACTTCAATC
*
644865 TACTTTAATC
1 TAATTTAATC
644875 ATTAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATTTAATCTACTTCAATC
Found at i:644866 original size:10 final size:10
Alignment explanation
Indices: 644831--644874 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
644821 ATTGTAATTT
644831 AATCTACTTC
1 AATCTACTTC
* * *
644841 AATTTAATTT
1 AATCTACTTC
644851 AATCTACTTC
1 AATCTACTTC
*
644861 AATCTACTTT
1 AATCTACTTC
644871 AATC
1 AATC
644875 ATTAATTTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.45
Consensus pattern (10 bp):
AATCTACTTC
Found at i:645731 original size:40 final size:40
Alignment explanation
Indices: 645676--645751 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
645666 CTTCATTAGT
*
645676 TCATTCCTGACCATATATACACGTATGTATGAACGAATGA
1 TCATTCCTGACCATATATACACGTATGTACGAACGAATGA
645716 TCATTCCTGTA-CATATATACACGTATGTACGAACGA
1 TCATTCCTG-ACCATATATACACGTATGTACGAACGA
645752 CTGTCTAGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (40 bp):
TCATTCCTGACCATATATACACGTATGTACGAACGAATGA
Found at i:646035 original size:14 final size:14
Alignment explanation
Indices: 645982--646026 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
645972 GTTCATTTAT
645982 GTTCGTTTATGTGC
1 GTTCGTTTATGTGC
*
645996 GTTCGTTTATGCGC
1 GTTCGTTTATGTGC
646010 GTTCGTTTATGTGC
1 GTTCGTTTATGTGC
646024 GTT
1 GTT
646027 TATTTATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.07, C:0.16, G:0.29, T:0.49
Consensus pattern (14 bp):
GTTCGTTTATGTGC
Found at i:646237 original size:23 final size:23
Alignment explanation
Indices: 646207--646250 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
646197 TTTTCATTTA
*
646207 TGTTTGTTTATGTTCATTTATTG
1 TGTTTGTTTACGTTCATTTATTG
646230 TGTTTGTTTACGTTCATTTAT
1 TGTTTGTTTACGTTCATTTAT
646251 GTTCGTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.14, C:0.07, G:0.16, T:0.64
Consensus pattern (23 bp):
TGTTTGTTTACGTTCATTTATTG
Found at i:646321 original size:10 final size:10
Alignment explanation
Indices: 646306--646331 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
646296 TATCATTTAA
646306 ATGAACGAAC
1 ATGAACGAAC
646316 ATGAACGAAC
1 ATGAACGAAC
646326 ATGAAC
1 ATGAAC
646332 AAGCTACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (10 bp):
ATGAACGAAC
Found at i:648588 original size:27 final size:23
Alignment explanation
Indices: 648528--648583 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
648518 TGTACTTCTG
*
648528 TGCTGAATCATTCAACATTGTTT
1 TGCTGAATCAGTCAACATTGTTT
648551 TGCTGAATCAGTCAACATTGTTT
1 TGCTGAATCAGTCAACATTGTTT
*
648574 TGTTGAATCA
1 TGCTGAATCA
648584 ATCAGCACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (23 bp):
TGCTGAATCAGTCAACATTGTTT
Found at i:652713 original size:29 final size:30
Alignment explanation
Indices: 652671--652742 Score: 119
Period size: 29 Copynumber: 2.4 Consensus size: 30
652661 GTCCCCATAT
652671 AGGTCGCCATGCACGCCCAGCGACCTA-CC
1 AGGTCGCCATGCACGCCCAGCGACCTAGCC
**
652700 AGGTCGCCATGCACGCCCAGCGACCTAGGT
1 AGGTCGCCATGCACGCCCAGCGACCTAGCC
652730 AGGTCGCCATGCA
1 AGGTCGCCATGCA
652743 ATCCATGCAG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.21, C:0.39, G:0.28, T:0.12
Consensus pattern (30 bp):
AGGTCGCCATGCACGCCCAGCGACCTAGCC
Found at i:652803 original size:10 final size:10
Alignment explanation
Indices: 652790--652844 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
652780 ACACGCTGGG
652790 CATCCGAGGC
1 CATCCGAGGC
*
652800 CATCCGAAAG-
1 CATCCG-AGGC
652810 CATCCGAGGC
1 CATCCGAGGC
*
652820 CATCCGAAAG-
1 CATCCG-AGGC
652830 CATCCGAGGC
1 CATCCGAGGC
652840 CATCC
1 CATCC
652845 AAATGAGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 4 0.11
10 29 0.78
11 4 0.11
ACGTcount: A:0.27, C:0.38, G:0.24, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:652814 original size:20 final size:20
Alignment explanation
Indices: 652789--652844 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
652779 AACACGCTGG
652789 GCATCCGAGGCCATCCGAAA
1 GCATCCGAGGCCATCCGAAA
652809 GCATCCGAGGCCATCCGAAA
1 GCATCCGAGGCCATCCGAAA
652829 GCATCCGAGGCCATCC
1 GCATCCGAGGCCATCC
652845 AAATGAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.27, C:0.38, G:0.25, T:0.11
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAAA
Found at i:652915 original size:31 final size:32
Alignment explanation
Indices: 652849--652915 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
652839 CCATCCAAAT
* *
652849 GAGCTATGTGAGGGCATCCGAGGGCAAACGAGC
1 GAGCTATGCGAGGGAATCCGA-GGCAAACGAGC
*
652882 GAGCTATGCGAGGGAATCCGA-GCAACCGAGC
1 GAGCTATGCGAGGGAATCCGAGGCAAACGAGC
652913 GAG
1 GAG
652916 GGTAGGTCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 12 0.39
33 19 0.61
ACGTcount: A:0.28, C:0.22, G:0.39, T:0.10
Consensus pattern (32 bp):
GAGCTATGCGAGGGAATCCGAGGCAAACGAGC
Found at i:653006 original size:33 final size:32
Alignment explanation
Indices: 652948--653037 Score: 108
Period size: 33 Copynumber: 2.8 Consensus size: 32
652938 GCGACCTACC
* *
652948 CTCGCTCGGTGTCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTGCCCTCGGATGCCCTCGCATAG
*
652980 CTCGCTCGGTTGCCCTCGGATGCCCTCGTATAG
1 CTCGCTCGG-TGCCCTCGGATGCCCTCGCATAG
* **
653013 CTCGTTCGGATGGTCTCGGATGCCC
1 CTCGCTCGG-TGCCCTCGGATGCCC
653038 AGCGTGTTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 9 0.18
33 41 0.82
ACGTcount: A:0.09, C:0.36, G:0.28, T:0.28
Consensus pattern (32 bp):
CTCGCTCGGTGCCCTCGGATGCCCTCGCATAG
Found at i:653089 original size:29 final size:29
Alignment explanation
Indices: 653047--653122 Score: 152
Period size: 29 Copynumber: 2.6 Consensus size: 29
653037 CAGCGTGTTA
653047 GGGCGTGCATGGCGACCTGGTAGGTCGCT
1 GGGCGTGCATGGCGACCTGGTAGGTCGCT
653076 GGGCGTGCATGGCGACCTGGTAGGTCGCT
1 GGGCGTGCATGGCGACCTGGTAGGTCGCT
653105 GGGCGTGCATGGCGACCT
1 GGGCGTGCATGGCGACCT
653123 ACCCCCAGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.11, C:0.25, G:0.45, T:0.20
Consensus pattern (29 bp):
GGGCGTGCATGGCGACCTGGTAGGTCGCT
Found at i:658645 original size:19 final size:19
Alignment explanation
Indices: 658602--658645 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
658592 AAATGACCAA
*
658602 CAAATTCACAACGCGATCT
1 CAAATTCACAACGCGAACT
*
658621 CAAATTCGCAACGCGAACT
1 CAAATTCACAACGCGAACT
*
658640 CTAATT
1 CAAATT
658646 TCCAATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (19 bp):
CAAATTCACAACGCGAACT
Found at i:658739 original size:20 final size:19
Alignment explanation
Indices: 658690--658818 Score: 113
Period size: 20 Copynumber: 6.6 Consensus size: 19
658680 GCGATTTTCT
658690 AAATTCGCAACACGAA-TC
1 AAATTCGCAACACGAAGTC
658708 TGTAAATT-GCAACACAGAAGTC
1 ---AAATTCGCAACAC-GAAGTC
*
658730 AAATTCGCAACGCGATAG-C
1 AAATTCGCAACACGA-AGTC
* *
658749 -AATCCGCAACACAAAGTC
1 AAATTCGCAACACGAAGTC
*
658767 AAATTCGCAAACACAAAAGTC
1 AAATTCGC-AACAC-GAAGTC
*
658788 AAATTCGCAACACGAATTTC
1 AAATTCGCAACACGAA-GTC
658808 AAATTCGCAAC
1 AAATTCGCAAC
658819 GCAAACACAA
Statistics
Matches: 92, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
17 2 0.02
18 12 0.13
19 16 0.17
20 38 0.41
21 22 0.24
22 2 0.02
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.18
Consensus pattern (19 bp):
AAATTCGCAACACGAAGTC
Found at i:658966 original size:22 final size:21
Alignment explanation
Indices: 658932--658980 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
658922 CTACGGCGAC
658932 ATCCGT-CCCATCTCCGACGAA
1 ATCCGTCCCCATCT-CGACGAA
*
658953 ATCCGTCCCCATCTCGGCGAA
1 ATCCGTCCCCATCTCGACGAA
658974 ATCCGTC
1 ATCCGTC
658981 TATCTCCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (21 bp):
ATCCGTCCCCATCTCGACGAA
Found at i:661473 original size:21 final size:21
Alignment explanation
Indices: 661449--661518 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
661439 CCTATCATTA
*
661449 TTCAAGAGGCACCTCCTATCG
1 TTCAAGAGGCCCCTCCTATCG
* *
661470 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCTATCG
*
661491 TTCAAGAGGCCCCT-GTCATCG
1 TTCAAGAGGCCCCTCCT-ATCG
661512 TTCAAGA
1 TTCAAGA
661519 TGTCCCGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCTATCG
Found at i:661512 original size:42 final size:42
Alignment explanation
Indices: 661449--661540 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
661439 CCTATCATTA
*
661449 TTCAAGAGGCACCTCCTATCGTTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCACCTCCTATCGTTCAAGAGGCCCCGCCCACCG
* * * * *
661491 TTCAAGAGGCCCCT-GTCATCGTTCAAGATGTCCCGCCCGCCG
1 TTCAAGAGGCACCTCCT-ATCGTTCAAGAGGCCCCGCCCACCG
661533 TTCAAGAG
1 TTCAAGAG
661541 CCCGATTCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.21, C:0.37, G:0.22, T:0.21
Consensus pattern (42 bp):
TTCAAGAGGCACCTCCTATCGTTCAAGAGGCCCCGCCCACCG
Found at i:662958 original size:50 final size:51
Alignment explanation
Indices: 662904--663011 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 51
662894 ACATTGAAAG
*
662904 TTGATTTGTTTAA-TTGATGAGGAAATAATAATTATTTTGTGCTTGTTTAA
1 TTGATTTGTTTAATTTGATGAGGAAATAAGAATTATTTTGTGCTTGTTTAA
* * * *
662954 TTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTGCTTGTTTAT
1 TTGATTTGTTTAATTTGATGAGGAAATAAGAATTATTTTGTGCTTGTTTAA
663005 TTGATTT
1 TTGATTT
663012 ATTGTTTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
50 13 0.25
51 39 0.75
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.55
Consensus pattern (51 bp):
TTGATTTGTTTAATTTGATGAGGAAATAAGAATTATTTTGTGCTTGTTTAA
Found at i:663094 original size:20 final size:20
Alignment explanation
Indices: 663069--663141 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
663059 TTGAAGGTAC
663069 AAATTCGCAACGCGAAAGGT
1 AAATTCGCAACGCGAAAGGT
*
663089 AAATTCGTAACGCGAAAGGT
1 AAATTCGCAACGCGAAAGGT
*
663109 AAATTCACAACGCGAAA-GT
1 AAATTCGCAACGCGAAAGGT
663128 CAAATTCGCAACGC
1 -AAATTCGCAACGC
663142 AAAATAAGCG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 2 0.04
20 46 0.96
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGGT
Found at i:663514 original size:18 final size:18
Alignment explanation
Indices: 663488--663528 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
663478 AGGTGAAGCC
* *
663488 GATTGTGATTGGGATTTT
1 GATTTTGATTGCGATTTT
663506 GATTTTGATTGCGATTTT
1 GATTTTGATTGCGATTTT
663524 GATTT
1 GATTT
663529 CCTTTTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.02, G:0.27, T:0.54
Consensus pattern (18 bp):
GATTTTGATTGCGATTTT
Found at i:665845 original size:24 final size:24
Alignment explanation
Indices: 665794--665845 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
665784 ATCCGAGTAT
* * * *
665794 TGACCAAGATTAAAGTTCGAGTAT
1 TGACCAAGATCAAAGTTCAAATAC
*
665818 TGACCAAGATCAAATTTCAAATAC
1 TGACCAAGATCAAAGTTCAAATAC
665842 TGAC
1 TGAC
665846 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCAAATAC
Found at i:665978 original size:12 final size:12
Alignment explanation
Indices: 665957--665990 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
665947 GGTTGTGGGT
*
665957 TTTGAGATTGTG
1 TTTGATATTGTG
665969 TTTGATATTGTG
1 TTTGATATTGTG
*
665981 TTTGGTATTG
1 TTTGATATTG
665991 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:666607 original size:16 final size:15
Alignment explanation
Indices: 666585--666623 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
666575 GAAATCATTG
666585 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
666601 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
666616 AAAAATTA
1 AAAAATTA
666624 GGGATGGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:666803 original size:19 final size:19
Alignment explanation
Indices: 666760--666806 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
666750 CAAAACATTT
666760 GTGTTGCGAAATTAAAATC
1 GTGTTGCGAAATTAAAATC
*
666779 -TGTTGCGAAATTAAATTC
1 GTGTTGCGAAATTAAAATC
666797 GTGTTGCGAA
1 GTGTTGCGAA
666807 TTCAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:666844 original size:21 final size:20
Alignment explanation
Indices: 666760--666947 Score: 97
Period size: 20 Copynumber: 9.4 Consensus size: 20
666750 CAAAACATTT
* *
666760 GTGTTGCGAAATT-AAAATC
1 GTGTTGCGAATTTGAAATTC
*
666779 -TGTTGCGAAATT-AAATTC
1 GTGTTGCGAATTTGAAATTC
** *
666797 GTGTTGCGAATTCAAAAAATC
1 GTGTTGCGAATT-TGAAATTC
666818 -TAGTTGCGAATTTGAAATTC
1 GT-GTTGCGAATTTGAAATTC
*
666838 AGTGTTGCGAATTTG-ACTTC
1 -GTGTTGCGAATTTGAAATTC
* *
666858 TGTGTTGCG-ATTTACAAATTT
1 -GTGTTGCGAATTT-GAAATTC
*
666879 GCGTTGCG-ATTT-ACAGATTC
1 GTGTTGCGAATTTGA-A-ATTC
* *
666899 GCGTTGCGAATTTG-ACTATC
1 GTGTTGCGAATTTGAAAT-TC
* ** *
666919 GCGTTGCGAATTTGACTTTT
1 GTGTTGCGAATTTGAAATTC
666939 GTGTTGCGA
1 GTGTTGCGA
666948 TTTACAGATT
Statistics
Matches: 136, Mismatches: 19, Indels: 27
0.75 0.10 0.15
Matches are distributed among these distances:
18 18 0.13
19 16 0.12
20 66 0.49
21 35 0.26
22 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (20 bp):
GTGTTGCGAATTTGAAATTC
Found at i:666846 original size:42 final size:39
Alignment explanation
Indices: 666773--666850 Score: 120
Period size: 42 Copynumber: 1.9 Consensus size: 39
666763 TTGCGAAATT
666773 AAAATCTGTTGCGAAATTAAATTCGTGTTGCGAATTCAA
1 AAAATCTGTTGCGAAATTAAATTCGTGTTGCGAATTCAA
*
666812 AAAATCTAGTTGCGAATTTGAAATTCAGTGTTGCGAATT
1 AAAATCT-GTTGCGAAATT-AAATTC-GTGTTGCGAATT
666851 TGACTTCTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 7 0.20
40 10 0.29
41 6 0.17
42 12 0.34
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (39 bp):
AAAATCTGTTGCGAAATTAAATTCGTGTTGCGAATTCAA
Found at i:666909 original size:60 final size:60
Alignment explanation
Indices: 666841--667051 Score: 177
Period size: 60 Copynumber: 3.5 Consensus size: 60
666831 GAAATTCAGT
*
666841 GTTGCGAATTTGACT-TCTGTGTTGCG-ATTT-ACAAATTTGCGTTGCGATTTACAGATTCGC
1 GTTGCGAATTTGACTATC-GCGTTGCGAATTTGAC--ATTTGCGTTGCGATTTACAGATTCGC
* *
666901 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTACAGATTCGC
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACATTTGCGTTGCGATTTACAGATTCGC
* * * * * * **
666961 TTTTCG-ATTT-ACATATTCGCGTTGCGAAATTGGAAACTTG-GTTGCGAAATTGGAG-TTCGC
1 GTTGCGAATTTGAC-TA-TCGCGTTGCG-AATTTGACATTTGCGTTGCG-ATTTACAGATTCGC
* * *
667021 GTTGCAAATTTGA-GATTGCGTTGCGAATTTG
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTG
667052 TTGGTCATTT
Statistics
Matches: 124, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
58 7 0.06
59 15 0.12
60 75 0.60
61 24 0.19
62 3 0.02
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (60 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACATTTGCGTTGCGATTTACAGATTCGC
Found at i:666942 original size:80 final size:80
Alignment explanation
Indices: 666841--666988 Score: 242
Period size: 80 Copynumber: 1.9 Consensus size: 80
666831 GAAATTCAGT
*
666841 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTTGCGTTGCGATTTACAGATTCGCGTTGC
1 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTACAGATTCGCGTTGC
666906 GAATTTGACTATCGC
66 GAATTTGACTATCGC
* * * * *
666921 GTTGCGAATTTGACTTTTGTGTTGCGATTTACAGATTCGCTTTTCGATTTACATATTCGCGTTGC
1 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTACAGATTCGCGTTGC
666986 GAA
66 GAA
666989 ATTGGAAACT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.41
Consensus pattern (80 bp):
GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTACAGATTCGCGTTGC
GAATTTGACTATCGC
Found at i:667025 original size:80 final size:80
Alignment explanation
Indices: 666841--667025 Score: 182
Period size: 80 Copynumber: 2.3 Consensus size: 80
666831 GAAATTCAGT
* * *
666841 GTTGCGAATTTGAC-TTCTGTGTTGCGATTTACAAATTTGCGTTGCGATTTACAGATTCGCGTTG
1 GTTGCGAATTGGACGTTC-GCGTTGCGATTTACAAATTCGCGTTGCGATTTACAGATTCGCGTTG
*
666905 CGAATTTGACTATCGC
65 CGAATTGGACTATCGC
* * * * * * * *
666921 GTTGCGAATTTGACTTTTGTGTTGCGATTTACAGATTCGCTTTTCGATTTACATATTCGCGTTGC
1 GTTGCGAATTGGACGTTCGCGTTGCGATTTACAAATTCGCGTTGCGATTTACAGATTCGCGTTGC
666986 GAAATTGGAAACT-T-G-
66 G-AATTGG--ACTATCGC
667001 GTTGCGAAATTGGA-GTTCGCGTTGC
1 GTTGCG-AATTGGACGTTCGCGTTGC
667026 AAATTTGAGA
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
80 71 0.80
81 14 0.16
82 1 0.01
83 3 0.03
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (80 bp):
GTTGCGAATTGGACGTTCGCGTTGCGATTTACAAATTCGCGTTGCGATTTACAGATTCGCGTTGC
GAATTGGACTATCGC
Found at i:667041 original size:19 final size:20
Alignment explanation
Indices: 666979--667047 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
666969 TTACATATTC
*
666979 GCGTTGCGAAATTGGAAACTT
1 GCGTTGCGAAATTGGAGA-TT
667000 G-GTTGCGAAATTGGAG-TT
1 GCGTTGCGAAATTGGAGATT
*
667018 CGCGTTGC-AAATTTGAGATT
1 -GCGTTGCGAAATTGGAGATT
667038 GCGTTGCGAA
1 GCGTTGCGAA
667048 TTTGTTGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 2 0.05
19 16 0.38
20 23 0.55
21 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.32, T:0.30
Consensus pattern (20 bp):
GCGTTGCGAAATTGGAGATT
Found at i:668072 original size:24 final size:24
Alignment explanation
Indices: 668023--668073 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
668013 CGTTCGATAA
* *
668023 TATATTCATTTATGTTCTTTAGTT
1 TATATTCATTTATGTGCTTCAGTT
*
668047 TATATTCGTTTATGTGCGTTCA-TT
1 TATATTCATTTATGTGC-TTCAGTT
668071 TAT
1 TAT
668074 GTTTAGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.59
Consensus pattern (24 bp):
TATATTCATTTATGTGCTTCAGTT
Found at i:668262 original size:24 final size:24
Alignment explanation
Indices: 668235--668325 Score: 87
Period size: 24 Copynumber: 3.8 Consensus size: 24
668225 AAAAATTATT
*
668235 TTCATTTATGTTCGTTTATGTTCA
1 TTCATTTGTGTTCGTTTATGTTCA
* * *
668259 TTCATTTGTTTTCGTTTACGTTCGT
1 TTCATTTGTGTTCGTTTATGTTC-A
* *
668284 TTACA-TT-CGTTCGTTTATGTTCG
1 TT-CATTTGTGTTCGTTTATGTTCA
*
668307 TTCATTTGTGTCCGTTTAT
1 TTCATTTGTGTTCGTTTAT
668326 CATTTATGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
22 2 0.04
23 4 0.08
24 41 0.77
25 4 0.08
26 2 0.04
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.57
Consensus pattern (24 bp):
TTCATTTGTGTTCGTTTATGTTCA
Found at i:671599 original size:16 final size:16
Alignment explanation
Indices: 671578--671612 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
671568 ATTAAGTTCA
671578 CATAAGTAGCTATTTG
1 CATAAGTAGCTATTTG
671594 CATAAGTAGCTATTTG
1 CATAAGTAGCTATTTG
671610 CAT
1 CAT
671613 TCTAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (16 bp):
CATAAGTAGCTATTTG
Found at i:675170 original size:30 final size:29
Alignment explanation
Indices: 675096--675185 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
675086 AAAATGAATG
*
675096 TTTTAGGTATCTA-TTTGATCAAAAAATA
1 TTTTAGGTACCTATTTTGATCAAAAAATA
* * *
675124 CTTTAGATACCTATTTTGATCAAAAATTAA
1 TTTTAGGTACCTATTTTGATCAAAAAAT-A
*
675154 TTTTAGGTA-CTAATTTT-AACAAGAAAATA
1 TTTTAGGTACCT-ATTTTGATCAA-AAAATA
675183 TTT
1 TTT
675186 AAAATACTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
28 10 0.20
29 23 0.46
30 17 0.34
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (29 bp):
TTTTAGGTACCTATTTTGATCAAAAAATA
Found at i:676750 original size:28 final size:29
Alignment explanation
Indices: 676714--676780 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
676704 TTAAGTGGTC
* * *
676714 AAAAAATAAAT-TATGAAGTTTAGTGAC-
1 AAAACATAAATCTATAAAGTTAAGTGACT
*
676741 AAAAGCATAAATCTTTAAAGTTAAGTGACT
1 AAAA-CATAAATCTATAAAGTTAAGTGACT
676771 AAAACATAAA
1 AAAACATAAA
676781 CATAGTACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.12
28 6 0.18
29 19 0.58
30 4 0.12
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (29 bp):
AAAACATAAATCTATAAAGTTAAGTGACT
Found at i:681572 original size:52 final size:50
Alignment explanation
Indices: 681463--681576 Score: 120
Period size: 52 Copynumber: 2.2 Consensus size: 50
681453 TCGAGGTGAT
* * * ** * *
681463 GAGTTTTAATAAAAAATATTTTTTATTCTAACTTTTTACTTCGATGTGAT
1 GAGTTTTAATAAAAAATATTTTTTATTCTAACTTATCACGTCGACATAAC
* * *
681513 AAATTTTAATAAAAAATATATATTTTATTGTAACTTATCACGTCGACATAAC
1 GAGTTTTAATAAAAAATAT-T-TTTTATTCTAACTTATCACGTCGACATAAC
681565 GAGTTTTAATAA
1 GAGTTTTAATAA
681577 CACTGTAGAA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
50 17 0.34
51 1 0.02
52 32 0.64
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (50 bp):
GAGTTTTAATAAAAAATATTTTTTATTCTAACTTATCACGTCGACATAAC
Found at i:682806 original size:27 final size:25
Alignment explanation
Indices: 682752--682825 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
682742 TTAAATTTAT
*
682752 AATATTTTATTTA-TATTAATTTAGA
1 AATATTTT-TTTATTATTAACTTAGA
*
682777 AATATTTTTTATATTATTAACTTATTA
1 AATATTTTTT-TATTATTAACTTA-GA
*
682804 AATA-TATTTTATTATTAACTTA
1 AATATTTTTTTATTATTAACTTA
682826 ATCTAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
24 2 0.05
25 23 0.53
26 13 0.30
27 5 0.12
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (25 bp):
AATATTTTTTTATTATTAACTTAGA
Found at i:682822 original size:25 final size:28
Alignment explanation
Indices: 682788--682844 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
682778 ATATTTTTTA
*
682788 TATTATTAACTT-AT-T-AAATATATTT
1 TATTATTAACTTAATCTAAAAAATATTT
682813 TATTATTAACTTAATCTAAAAAATATTT
1 TATTATTAACTTAATCTAAAAAATATTT
682841 TATT
1 TATT
682845 TCTATTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 12 0.43
26 2 0.07
27 1 0.04
28 13 0.46
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (28 bp):
TATTATTAACTTAATCTAAAAAATATTT
Found at i:687944 original size:131 final size:131
Alignment explanation
Indices: 687710--688067 Score: 477
Period size: 131 Copynumber: 2.7 Consensus size: 131
687700 AGACAATACA
* * *
687710 ATAATATCTAATTATTTCCAATTGAGAATAAATGACATCTCATACCTTAAAACAATCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTA
* ** * * *
687775 CT-TCAATCGAAATGAAGAGATGTCACTATTCTGTCTTAAAATTCAATATTGATTCAAGTGAAAA
66 CTCT-AATCGAAATGAAGAGATATCACTATTCCCTCTTAAAAATCAATATTAATTCAAGAGAAAA
687839 CG
130 CG
* * *
687841 ATAATATCTAATGATTTCCAATCGAGAATAAATGACCTTTCATACCTTAAAGCAATCATTTATTG
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTA
** *
687906 CTCTAATCGAAATGAAGAGATATCACTATTCCCTCTTAAAAATCAATATTAATTTGAGAGAAAAT
66 CTCTAATCGAAATGAAGAGATATCACTATTCCCTCTTAAAAATCAATATTAATTCAAGAGAAAAC
687971 G
131 G
* * * * *
687972 GTAATATCGAATTATTTCCAATCGAGAATAAATGACCTCCCATGCCTTAAAGCAGTCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTA
* * *
688037 CTCCAA-CTGAAATGAAAAGATATTACTATTC
66 CTCTAATC-GAAATGAAGAGATATCACTATTC
688068 TCAATATCGA
Statistics
Matches: 199, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
130 1 0.01
131 197 0.99
132 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (131 bp):
ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTATTA
CTCTAATCGAAATGAAGAGATATCACTATTCCCTCTTAAAAATCAATATTAATTCAAGAGAAAAC
G
Found at i:690010 original size:3 final size:3
Alignment explanation
Indices: 690002--690029 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
689992 TAAAAAACAA
690002 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
690030 TTATTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:690501 original size:4 final size:4
Alignment explanation
Indices: 690492--690518 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
690482 TTTTATTCCA
690492 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
690519 ATTGTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:691312 original size:43 final size:43
Alignment explanation
Indices: 691265--691357 Score: 114
Period size: 43 Copynumber: 2.2 Consensus size: 43
691255 ATATCTCTCG
** * * *
691265 AGATATTTCTCCGTGAATGATAACTCAATTGTTATACCTTTAA
1 AGATATTTCTCAATGAATGACAACTCAATTGTCATACCTCTAA
** *
691308 AGATATTTCTCAATGTGTGACAACTCAATTGTCATACCTCTAG
1 AGATATTTCTCAATGAATGACAACTCAATTGTCATACCTCTAA
691351 AGATATT
1 AGATATT
691358 CCACCATGAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (43 bp):
AGATATTTCTCAATGAATGACAACTCAATTGTCATACCTCTAA
Found at i:691373 original size:43 final size:43
Alignment explanation
Indices: 691286--691375 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 43
691276 CGTGAATGAT
* * * * * *
691286 AACTCAATTGTTATACCTTTAAAGATATTTCTCAATGTGTGAC
1 AACTCAATTGTCATACCTCTAAAGATATTCCACAATGAGCGAC
* *
691329 AACTCAATTGTCATACCTCTAGAGATATTCCACCATGAGCGAC
1 AACTCAATTGTCATACCTCTAAAGATATTCCACAATGAGCGAC
691372 AACT
1 AACT
691376 TCGTCTACCA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.32
Consensus pattern (43 bp):
AACTCAATTGTCATACCTCTAAAGATATTCCACAATGAGCGAC
Found at i:692990 original size:40 final size:40
Alignment explanation
Indices: 692944--693048 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 40
692934 CTTAACACTA
692944 ATACTAAAATGAAACAAAAACTAAAGTTTTTAACAGTGAGG
1 ATACTAAAATGAAACAAAAACTAAAGTTTTTAACAGTG-GG
* **
692985 -TACTAAAAAGAAACAAAAACTAAAGTTTTTAATGGTGGG
1 ATACTAAAATGAAACAAAAACTAAAGTTTTTAACAGTGGG
* *
693024 ATATTAAAATGAAATAAAAACTAAA
1 ATACTAAAATGAAACAAAAACTAAA
693049 CTTTAAGTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.04
40 55 0.96
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.25
Consensus pattern (40 bp):
ATACTAAAATGAAACAAAAACTAAAGTTTTTAACAGTGGG
Found at i:693402 original size:21 final size:21
Alignment explanation
Indices: 693372--693412 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
693362 AAATGTTAAA
*
693372 AAATATTAATGTTTTAGATAG
1 AAATAATAATGTTTTAGATAG
693393 AAATAATAATGTTTTAGATA
1 AAATAATAATGTTTTAGATA
693413 ATTTTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.41
Consensus pattern (21 bp):
AAATAATAATGTTTTAGATAG
Found at i:693806 original size:21 final size:21
Alignment explanation
Indices: 693755--693807 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
693745 CGTTTACAAA
693755 ATTATAAATTTACATTTTAAC
1 ATTATAAATTTACATTTTAAC
* * *
693776 A-AAGTTAATTTACATTTTAAT
1 ATTA-TAAATTTACATTTTAAC
693797 ATTATAAATTT
1 ATTATAAATTT
693808 CATCGTGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTATAAATTTACATTTTAAC
Found at i:696707 original size:137 final size:136
Alignment explanation
Indices: 696461--696739 Score: 513
Period size: 137 Copynumber: 2.0 Consensus size: 136
696451 TTAAAGTGGT
* *
696461 TCAAGTACTTCTTCAATGAAGTCTACATCCACTATCTTAGTTTCCATACTAAGGATTTCGACAAA
1 TCAAGTACTTATTCAATGAAGTCTACATCCACTACCTTAGTTTCCATACTAAGGATTTCGACAAA
696526 TTCACTAATTTATTCTAACATTTTAGGACAAGGTGTAACCTTACAACACACTTAGACTTGTACCC
66 TTCACTAATTTATTCTAACATTTTAGGACAAGGTGTAACCTTACAACACACTTAGACTTGTA-CC
696591 CAAAGTC
130 CAAAGTC
696598 TCAAGTACTTATTCAATGAAGTCTACATCCACTACCTTAGTTTCCATACTAAGGATTTCGACAAA
1 TCAAGTACTTATTCAATGAAGTCTACATCCACTACCTTAGTTTCCATACTAAGGATTTCGACAAA
* *
696663 TTCACTAATTTATTCTAACCTTTTAGGACAATGTGTAACCTTACAACACACTTAGACTTGTACCC
66 TTCACTAATTTATTCTAACATTTTAGGACAAGGTGTAACCTTACAACACACTTAGACTTGTACCC
696728 AAAGTC
131 AAAGTC
696734 TCAAGT
1 TCAAGT
696740 GCACAACCCT
Statistics
Matches: 138, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
136 15 0.11
137 123 0.89
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (136 bp):
TCAAGTACTTATTCAATGAAGTCTACATCCACTACCTTAGTTTCCATACTAAGGATTTCGACAAA
TTCACTAATTTATTCTAACATTTTAGGACAAGGTGTAACCTTACAACACACTTAGACTTGTACCC
AAAGTC
Found at i:697137 original size:20 final size:20
Alignment explanation
Indices: 697114--697159 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
697104 CCAAAGTATT
697114 GAAACT-TTAATGAAAGTTTC
1 GAAACTCTTAA-GAAAGTTTC
* *
697134 GAAACTCTTGAGATAGTTTC
1 GAAACTCTTAAGAAAGTTTC
697154 GAAACT
1 GAAACT
697160 ATAAAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (20 bp):
GAAACTCTTAAGAAAGTTTC
Found at i:700543 original size:18 final size:18
Alignment explanation
Indices: 700517--700552 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
700507 TCGAAAGGAC
*
700517 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
700535 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
700553 CGGATGGTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:701777 original size:24 final size:24
Alignment explanation
Indices: 701688--701782 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 24
701678 TTATCTAATT
* * *
701688 TCTGATTTGAATTCTGTTTTGACA
1 TCTGATCTGAATTCTGTTCTGATA
*
701712 TCTGATCTGAAATCTGTTCTGAT-
1 TCTGATCTGAATTCTGTTCTGATA
* *
701735 TCCT-AACATGGATTCTGTTCTGATA
1 T-CTGATC-TGAATTCTGTTCTGATA
* *
701760 TCTGATCTGAATTATGTTTTGAT
1 TCTGATCTGAATTCTGTTCTGAT
701783 TTTTGATATC
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
23 3 0.05
24 50 0.89
25 3 0.05
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (24 bp):
TCTGATCTGAATTCTGTTCTGATA
Found at i:705187 original size:18 final size:18
Alignment explanation
Indices: 705161--705196 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
705151 TCGAAAGGAC
*
705161 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
705179 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
705197 CGGATGGTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:707064 original size:3 final size:3
Alignment explanation
Indices: 707052--707094 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
707042 AATCTATGAT
707052 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
707095 GGAGAGGGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:711960 original size:3 final size:3
Alignment explanation
Indices: 711952--711979 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
711942 GAATTGGGTT
711952 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
711980 ATTTATGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:724377 original size:34 final size:34
Alignment explanation
Indices: 724312--724378 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
724302 AATCAAACCA
**
724312 AATATCTTTTAATTTTCAACATTAAACAGATAAC
1 AATATCTTTTAATTTGAAACATTAAACAGATAAC
*
724346 AATATCTTTTAATTTGAAATATTCAAA-AGATAA
1 AATATCTTTTAATTTGAAACATT-AAACAGATAA
724379 AACTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.39
Consensus pattern (34 bp):
AATATCTTTTAATTTGAAACATTAAACAGATAAC
Found at i:724705 original size:190 final size:192
Alignment explanation
Indices: 724352--724757 Score: 565
Period size: 190 Copynumber: 2.1 Consensus size: 192
724342 TAACAATATC
* * ** *
724352 TTTTAATTTGA-AATATTCAAAAGATAAAACTCATTTTATCATTTAAACTTAAATATGTATTATT
1 TTTTAATTT-ACAATAGTCAAAAGGTAAAACTCATTTTATCATTTAAACTTAAATAAATATCATT
* *
724416 TTAATTTGAAATAAACAAAAGTATATAATTATCTTTAATATTCAAAGTTAAAAAATGTAACAACT
65 TTAATTTGAAATAAACAAAAGTATATAATTATCTTTAATATTCAAAATTAAAAAATGTAACAAAT
** * *
724481 ATTTTTTTAAGTTAACATATTCAAAGAGTAATTATCCTACTAATATTCAAATTAAATAA-TATA
130 ACCTTTTTAAATTAACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAA-AATTATA
*
724544 -TTTAATTTACAATGGTCAAAAGGT-AAACTCATTTTA-CTATTTAAACTTAAATAAATATCATT
1 TTTTAATTTACAATAGTCAAAAGGTAAAACTCATTTTATC-ATTTAAACTTAAATAAATATCATT
*
724606 TTAATTTGAAATATACAAAAGTATATAATTATCTTTTAATATTCAAAATTAAAAAA-GATAACAA
65 TTAATTTGAAATAAACAAAAGTATATAATTATC-TTTAATATTCAAAATTAAAAAATG-TAACAA
* * *
724670 ATACCTTTTTAAATTGACTTATTAAAATA-TAATTATCCTACTAATATTCAAATTAAAAATTATA
128 ATACCTTTTTAAATTAACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAAAATTATA
*
724734 TTTTAATTTGCAATAGTCAAAAGG
1 TTTTAATTTACAATAGTCAAAAGG
724758 ACTATGAATT
Statistics
Matches: 190, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
189 3 0.02
190 99 0.52
191 88 0.46
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (192 bp):
TTTTAATTTACAATAGTCAAAAGGTAAAACTCATTTTATCATTTAAACTTAAATAAATATCATTT
TAATTTGAAATAAACAAAAGTATATAATTATCTTTAATATTCAAAATTAAAAAATGTAACAAATA
CCTTTTTAAATTAACATATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAAAATTATA
Found at i:728450 original size:190 final size:188
Alignment explanation
Indices: 728151--728651 Score: 711
Period size: 188 Copynumber: 2.7 Consensus size: 188
728141 TAACAATATC
* * * *
728151 TTTTAATTTGAAATAAACAAAATTATATAATTATC-TTTAATATTCAAAGTTAAAAAGGTAACAA
1 TTTTAATTTGAAATATACAAAAATATATAATTATCTTTTAATATTCAAAATTAAAAAGATAACAA
* * * *
728215 ATACATTTTTAAGTTGACATATTCAAAGATTAATTATCCTACTAATATTAAAATTAAATAATATA
66 ATACATTTTTAAATTGACTTATTCAAAGAGTAATTATCCTACTAATATTTAAATTAAATAATATA
* *
728280 TTTGATTTACAAT-GATCAAAAGGTAAACTCATTTTACTATTCAAACTTAAACAGATATTA
131 TTTAATTTACAATAG-TCAAAA-ATAAACTCATTTTACTATTCAAACTT-AACAGATATTA
* * * *
728340 TTTTAATTTAAAATATACAAAAGTATATAGTTACCTTTTAATATTCAAAATTAAAAAGATAACAA
1 TTTTAATTTGAAATATACAAAAATATATAATTATCTTTTAATATTCAAAATTAAAAAGATAACAA
728405 ATACATTTTTAAATTGACTTATTCAAAGAGTAATTATCCTACTAATATTTAAATTAAATAATATA
66 ATACATTTTTAAATTGACTTATTCAAAGAGTAATTATCCTACTAATATTTAAATTAAATAATATA
* * * ** *
728470 TTTAATTTGCAATAGTCAAAAATAAATTCCTTTTACTATTCAAACTTAATTGATTTTA
131 TTTAATTTACAATAGTCAAAAATAAACTCATTTTACTATTCAAACTTAACAGATATTA
* * *
728528 TTTTAATTTGAAATATACAAAAATATATAATTATATTTTAATATTTAAAATTATAAAGATAACAA
1 TTTTAATTTGAAATATACAAAAATATATAATTATCTTTTAATATTCAAAATTAAAAAGATAACAA
* * *
728593 ATACATTTTTAAAATT-AATTATTAAAAGAGTAATTATTCTACTAATATTTAAATTAAAT
66 ATACATTTTT-AAATTGACTTATTCAAAGAGTAATTATCCTACTAATATTTAAATTAAAT
728652 CCATCAATTA
Statistics
Matches: 280, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
188 116 0.41
189 58 0.21
190 105 0.38
191 1 0.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (188 bp):
TTTTAATTTGAAATATACAAAAATATATAATTATCTTTTAATATTCAAAATTAAAAAGATAACAA
ATACATTTTTAAATTGACTTATTCAAAGAGTAATTATCCTACTAATATTTAAATTAAATAATATA
TTTAATTTACAATAGTCAAAAATAAACTCATTTTACTATTCAAACTTAACAGATATTA
Found at i:728662 original size:13 final size:13
Alignment explanation
Indices: 728644--728688 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
728634 CTAATATTTA
728644 AATTAAATCCATC
1 AATTAAATCCATC
**
728657 AATTAAA-AGAT-
1 AATTAAATCCATC
728668 AATTAAATCCATC
1 AATTAAATCCATC
728681 AATTAAAT
1 AATTAAAT
728689 TCACCATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 7 0.27
12 4 0.15
13 15 0.58
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (13 bp):
AATTAAATCCATC
Found at i:731926 original size:28 final size:28
Alignment explanation
Indices: 731888--731968 Score: 119
Period size: 28 Copynumber: 2.9 Consensus size: 28
731878 TATTAAAAGG
* *
731888 AAGACCGGGTGAACAGGTTAAGAGGACA
1 AAGACCTGGTGAACAGGTTACGAGGACA
*
731916 AAGACCTGGTGAAC-GCGTTACGAGGACT
1 AAGACCTGGTGAACAG-GTTACGAGGACA
731944 AAGACCTGGTGAACAGGTTACGAGG
1 AAGACCTGGTGAACAGGTTACGAGG
731969 TTTGAATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
27 1 0.02
28 46 0.96
29 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.35, T:0.15
Consensus pattern (28 bp):
AAGACCTGGTGAACAGGTTACGAGGACA
Found at i:736409 original size:19 final size:17
Alignment explanation
Indices: 736373--736412 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
736363 CAAAAAAAAT
736373 ATTTTAAAACTTTATAA
1 ATTTTAAAACTTTATAA
*
736390 ATTTTAACAACATTTTTAA
1 ATTTTAA-AAC-TTTATAA
736409 ATTT
1 ATTT
736413 ATTTTTGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 3 0.15
19 10 0.50
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTAAAACTTTATAA
Found at i:736888 original size:14 final size:14
Alignment explanation
Indices: 736869--736902 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
736859 AGTATGCTAG
736869 AAATATCCAACAAA
1 AAATATCCAACAAA
* *
736883 AAATATCCATCATA
1 AAATATCCAACAAA
736897 AAATAT
1 AAATAT
736903 AAAAGCATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATATCCAACAAA
Found at i:738438 original size:62 final size:64
Alignment explanation
Indices: 738310--738452 Score: 166
Period size: 62 Copynumber: 2.3 Consensus size: 64
738300 AACCTGTTAT
* * * * *
738310 AGGGGGTTTCAAAATCTTTAGTCCGAGAAAAGTATTCTACCCGACCGGTTTCAAAACCACATGG
1 AGGGGGTTTCAAAACCTTTAGTCCCAGAAAAGCATTATACCCGACCAGTTTCAAAACCACATGG
* * * *
738374 AGGGGGTTTCAAAACCTTTAG-CCCA-AAAAGCATTATGCCCTACTAGTTTCAAAACCTCGA-GG
1 AGGGGGTTTCAAAACCTTTAGTCCCAGAAAAGCATTATACCCGACCAGTTTCAAAACCAC-ATGG
*
738436 AGGGGGATTCAAAACCT
1 AGGGGGTTTCAAAACCT
738453 CTGTTCTTGA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
62 44 0.65
63 4 0.06
64 20 0.29
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (64 bp):
AGGGGGTTTCAAAACCTTTAGTCCCAGAAAAGCATTATACCCGACCAGTTTCAAAACCACATGG
Found at i:741477 original size:9 final size:8
Alignment explanation
Indices: 741457--741516 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
741447 ACTAAACAAT
741457 TAATAAACA
1 TAATAAA-A
741466 TAATTAAAA
1 TAA-TAAAA
741475 TAATAAAA
1 TAATAAAA
* *
741483 TAACATTAA
1 TAATA-AAA
741492 TAA-AAAA
1 TAATAAAA
*
741499 TAGTAAAA
1 TAATAAAA
741507 -AATAAAA
1 TAATAAAA
741514 TAA
1 TAA
741517 ACATAAACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
7 10 0.24
8 16 0.38
9 12 0.29
10 4 0.10
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (8 bp):
TAATAAAA
Found at i:741530 original size:16 final size:15
Alignment explanation
Indices: 741510--741549 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
741500 AGTAAAAAAT
741510 AAAATAAACATAAAC
1 AAAATAAACATAAAC
* *
741525 ATAAATAAAAATAAAT
1 A-AAATAAACATAAAC
741541 AAAATAAAC
1 AAAATAAAC
741550 TTGCATTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATAAACATAAAC
Found at i:741531 original size:31 final size:30
Alignment explanation
Indices: 741459--741549 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 30
741449 TAAACAATTA
741459 ATAAACAT-AAT-TAAAATAATAAAAT-AAC
1 ATAAACATAAATATAAAA-AATAAAATAAAC
*
741487 ATTAATA-AAAAATAGTAAAAAATAAAATAAAC
1 A-TAA-ACATAAATA-TAAAAAATAAAATAAAC
*
741519 ATAAACATAAATAAAAATAAATAAAATAAAC
1 ATAAACATAAATATAAA-AAATAAAATAAAC
741550 TTGCATTGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
28 1 0.02
29 4 0.08
30 8 0.15
31 30 0.58
32 9 0.17
ACGTcount: A:0.71, C:0.05, G:0.01, T:0.22
Consensus pattern (30 bp):
ATAAACATAAATATAAAAAATAAAATAAAC
Found at i:741538 original size:10 final size:9
Alignment explanation
Indices: 741458--741548 Score: 60
Period size: 10 Copynumber: 9.2 Consensus size: 9
741448 CTAAACAATT
741458 AATAAACATA
1 AATAAA-ATA
*
741468 ATTAAAAT-
1 AATAAAATA
741476 AATAAAATA
1 AATAAAATA
*
741485 ACATTAATAAAA
1 A-A-TAA-AATA
741497 AATAGTAAA-A
1 AATA--AAATA
741507 AATAAAATAA
1 AATAAAAT-A
741517 ACATAAACATA
1 A-ATAAA-ATA
741528 AATAAAAATA
1 AAT-AAAATA
741538 AATAAAATA
1 AATAAAATA
741547 AA
1 AA
741549 CTTGCATTGG
Statistics
Matches: 67, Mismatches: 3, Indels: 23
0.72 0.03 0.25
Matches are distributed among these distances:
8 10 0.15
9 11 0.16
10 23 0.34
11 16 0.24
12 7 0.10
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.22
Consensus pattern (9 bp):
AATAAAATA
Found at i:741664 original size:5 final size:5
Alignment explanation
Indices: 741654--741680 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
741644 TGTTTTCATG
741654 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
741681 CATATAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:753347 original size:12 final size:13
Alignment explanation
Indices: 753322--753350 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
753312 ATATTTATTT
753322 ATATAAAAATATA
1 ATATAAAAATATA
753335 ATATAAAAA-ATA
1 ATATAAAAATATA
753347 ATAT
1 ATAT
753351 TATGGTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAAATATA
Found at i:753388 original size:16 final size:17
Alignment explanation
Indices: 753369--753405 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
753359 TAAAATATTA
753369 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
753385 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
753402 TTTT
1 TTTT
753406 TTCATTCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:762066 original size:4 final size:4
Alignment explanation
Indices: 762057--762086 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
762047 CACATAGTGA
762057 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
762087 GAGAGATAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:769126 original size:3 final size:3
Alignment explanation
Indices: 769120--769160 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
769110 ACTACTACTA
* *
769120 CTG CTG CTG CTG CTG CTG CTA CTG CTG CTG CTG CTA CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
769161 AATCTCTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.05, C:0.34, G:0.27, T:0.34
Consensus pattern (3 bp):
CTG
Found at i:776804 original size:20 final size:19
Alignment explanation
Indices: 776753--776828 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 19
776743 CGCGTTGCGA
* * *
776753 ATTTTATTTTTGCAACTCG
1 ATTTTAATTTCGCAACACG
776772 ATTTTCGAA-TTCGCAACACG
1 ATTTT--AATTTCGCAACACG
776792 AATTTTAATTTCGCAACA-G
1 -ATTTTAATTTCGCAACACG
* *
776811 GTTTTATTTTCGCAACAC
1 ATTTTAATTTCGCAACAC
776829 AAATGTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 15 0.32
19 8 0.17
20 18 0.38
21 6 0.13
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (19 bp):
ATTTTAATTTCGCAACACG
Found at i:777789 original size:24 final size:24
Alignment explanation
Indices: 777731--777776 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
777721 AGTCAGTATT
*
777731 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
777755 CGAACTTTGATCTTGGTCAATA
1 CGAACTTTGATCTTGGTCAATA
777777 GTCGGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:780356 original size:19 final size:20
Alignment explanation
Indices: 780327--780375 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
780317 ATTGTTGCGA
780327 AAGTCAAATTTGCAACGCGG
1 AAGTCAAATTTGCAACGCGG
* *
780347 AAGT-AAATTTGTAACGCGA
1 AAGTCAAATTTGCAACGCGG
*
780366 AAATCAAATT
1 AAGTCAAATT
780376 CGCGTTACGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (20 bp):
AAGTCAAATTTGCAACGCGG
Found at i:780389 original size:81 final size:83
Alignment explanation
Indices: 780276--780454 Score: 227
Period size: 82 Copynumber: 2.2 Consensus size: 83
780266 CCTTGAGTTT
* * ** * *
780276 ACAACGCGAAAGTCAAATTCACGTTGCAATTTT-TTGTTGCGATTGTTGCGAAAGTCAAATTTGC
1 ACAACGCGAAAATCAAATTCACGTTACAATTTTCGCGTTGCGATTGTTGCAAAAGTCAAATTTGA
* *
780340 AACGCGGAAGT-AAATTT
66 AACGCGAAAGTAAAATTC
** * * *
780357 GTAACGCGAAAATCAAATTCGCGTTACGATTTTCGCGTTGCGATTGTTGCAAAAGTCAACTTTGA
1 ACAACGCGAAAATCAAATTCACGTTACAATTTTCGCGTTGCGATTGTTGCAAAAGTCAAATTTGA
780422 AACGCGAAAGTAAAATTC
66 AACGCGAAAGTAAAATTC
780440 ACAACGCGAAAATCA
1 ACAACGCGAAAATCA
780455 CATTGCGAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
81 27 0.33
82 36 0.44
83 18 0.22
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (83 bp):
ACAACGCGAAAATCAAATTCACGTTACAATTTTCGCGTTGCGATTGTTGCAAAAGTCAAATTTGA
AACGCGAAAGTAAAATTC
Found at i:781076 original size:207 final size:207
Alignment explanation
Indices: 780718--781120 Score: 677
Period size: 207 Copynumber: 1.9 Consensus size: 207
780708 TCCAAATACA
* *
780718 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
1 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACAATTTATAC
780783 ACATCTAAAACCAACAAACAACAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
66 ACATCTAAAACCAACAAACAACAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
* *
780848 AACAAGTATATAACAGTTAACAATACTTGCACAAACTTACCAATAACAACTGGTTGTTTATGCAC
131 AACAAGTATATAACAGTTAACAACACTTGCACAAACTTACCAATAACAAATGGTTGTTTATGCAC
780913 AAATACATCAAT
196 AAATACATCAAT
* *
780925 TTCACGCAGCTTACTTCAGGATTAACCTGCATAAACCAAACATTTGCTCAAACAACAATTTATAC
1 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACAATTTATAC
780990 ACATCTAAAACCAACAAACAACAAATTATTGAATTCTAGGTACTT-AACCAAACATTTTCAAACC
66 ACATCTAAAACCAACAAACAACAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
* * *
781054 AACAAAG-AGTGTATA-TGTTAACAACACTTGCTCAAACTTACCAATAACAAATGGTTGTTTATG
131 AAC-AAGTA-TATA-ACAGTTAACAACACTTGCACAAACTTACCAATAACAAATGGTTGTTTATG
781117 CACA
193 CACA
781121 CTTTCAGCAC
Statistics
Matches: 184, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
206 23 0.12
207 160 0.87
208 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (207 bp):
TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACAATTTATAC
ACATCTAAAACCAACAAACAACAAATTATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACC
AACAAGTATATAACAGTTAACAACACTTGCACAAACTTACCAATAACAAATGGTTGTTTATGCAC
AAATACATCAAT
Found at i:782250 original size:21 final size:21
Alignment explanation
Indices: 782226--782360 Score: 153
Period size: 21 Copynumber: 6.4 Consensus size: 21
782216 GTGAATTGGG
782226 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* *
782247 CTCTCGAATGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* *
782268 CTCTCGAACGGTAGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
782289 CTCTTGAATGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
** *
782310 CTCTTGAACAATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* ** **
782331 CCCTTGAACAATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
782352 CTCTTGAAC
1 CTCTTGAAC
782361 AATGACAGGT
Statistics
Matches: 100, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 100 1.00
ACGTcount: A:0.20, C:0.21, G:0.39, T:0.19
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:782361 original size:21 final size:21
Alignment explanation
Indices: 782304--782375 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
782294 GAATGGTGGG
*
782304 AGGGGCCTCTTGAACAATGAG
1 AGGGGCCTCTTGAACAATGAC
*
782325 AGGGGCCCCTTGAACAATGAC
1 AGGGGCCTCTTGAACAATGAC
782346 AGGGGCCTCTTGAACAATGAC
1 AGGGGCCTCTTGAACAATGAC
*
782367 AGGTGCCTC
1 AGGGGCCTC
782376 GGGCTTCTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.26, C:0.25, G:0.31, T:0.18
Consensus pattern (21 bp):
AGGGGCCTCTTGAACAATGAC
Found at i:782796 original size:21 final size:21
Alignment explanation
Indices: 782772--782821 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
782762 ACCATTGTCG
* *
782772 TCACGTAAAGTACCGACCTCA
1 TCACGCAAAGCACCGACCTCA
*
782793 TCACGCAAAGCACTGACCTCA
1 TCACGCAAAGCACCGACCTCA
782814 TCACGCAA
1 TCACGCAA
782822 CTCCCCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.36, G:0.14, T:0.16
Consensus pattern (21 bp):
TCACGCAAAGCACCGACCTCA
Found at i:782983 original size:42 final size:42
Alignment explanation
Indices: 782936--783033 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
782926 GTGATGGAAT
** * *
782936 AGGTGATGGCTCTCTTTGTAGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTAGAGCTGTAGAATCGGCTCGATC
* *
782978 AGGTGATGGCTCTGGGTGTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTAGAGCTGTAGAATCGGCTCGATC
783020 AGGTGAT-GCTCTCG
1 AGGTGATGGCTCTCG
783034 AAGTGGGGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 6 0.12
42 43 0.88
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.30
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTAGAGCTGTAGAATCGGCTCGATC
Found at i:784577 original size:20 final size:20
Alignment explanation
Indices: 784534--784578 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
784524 TCGCAACGTG
* *
784534 AAAATGAAAATCATAACACG
1 AAAATGAAAATCACAACACA
*
784554 AAAATGAAAATCACAACGCA
1 AAAATGAAAATCACAACACA
784574 AAAAT
1 AAAAT
784579 CGCAACGCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.16, G:0.09, T:0.13
Consensus pattern (20 bp):
AAAATGAAAATCACAACACA
Found at i:785212 original size:20 final size:20
Alignment explanation
Indices: 785189--785233 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
785179 GAATTTGACT
*
785189 TTTGTGTTGCGAATTATAAA
1 TTTGTGTTGCGAATTACAAA
* *
785209 TTTGCGTTGCGATTTACAAA
1 TTTGTGTTGCGAATTACAAA
785229 TTTGT
1 TTTGT
785234 AACGCGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (20 bp):
TTTGTGTTGCGAATTACAAA
Found at i:790112 original size:13 final size:14
Alignment explanation
Indices: 790089--790127 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
790079 AGAGGGGTAC
*
790089 TTTATTTATTTTAT
1 TTTATTTATTTGAT
790103 TTTA-TTATTTGATT
1 TTTATTTATTTGA-T
790117 TTTATTTATTT
1 TTTATTTATTT
790128 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 9 0.41
15 6 0.27
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTATTTATTTGAT
Found at i:790600 original size:15 final size:14
Alignment explanation
Indices: 790570--790620 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
790560 TATATAGTTA
*
790570 ATATATATTTAAAAT
1 ATATATATTT-TAAT
790585 ATATATATTGTTAAT
1 ATATATATT-TTAAT
*
790600 ACATA-ATTTTAAT
1 ATATATATTTTAAT
*
790613 ATACATAT
1 ATATATAT
790621 ATACTCTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 8 0.27
14 5 0.17
15 16 0.53
16 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (14 bp):
ATATATATTTTAAT
Found at i:790613 original size:28 final size:28
Alignment explanation
Indices: 790559--790623 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
790549 ATTAGGCTTA
*
790559 ATATATAGTTAATATATATTTAAAATAT
1 ATATATAGTTAATACATATTTAAAATAT
* * *
790587 ATATATTGTTAATACATAATTTTAATATAC
1 ATATATAGTTAATACAT-A-TTTAAAATAT
790617 ATATATA
1 ATATATA
790624 CTCTGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 15 0.50
29 1 0.03
30 14 0.47
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (28 bp):
ATATATAGTTAATACATATTTAAAATAT
Found at i:790730 original size:16 final size:16
Alignment explanation
Indices: 790705--790759 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
790695 TAATAACCCT
*
790705 AATAAGAATATATTAA
1 AATAATAATATATTAA
*
790721 AATAATAATATTTTAA
1 AATAATAATATATTAA
*
790737 AACTATATATATATATTAT
1 AA-TA-ATA-ATATATTAA
790756 AATA
1 AATA
790760 TTATTATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 16 0.50
17 2 0.06
18 5 0.16
19 9 0.28
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
AATAATAATATATTAA
Found at i:790762 original size:43 final size:43
Alignment explanation
Indices: 790714--790795 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
790704 TAATAAGAAT
790714 ATATTA-AAATAATAATATTTTAAAACTATATATATATATTATA
1 ATATTATAAATAATAATATTTT-AAACTATATATATATATTATA
* * * * *
790757 ATATTATTATTATTATTATTTTAAACTTTATATATATAT
1 ATATTATAAATAATAATATTTTAAACTATATATATATAT
790796 ATTCACTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 22 0.67
44 11 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (43 bp):
ATATTATAAATAATAATATTTTAAACTATATATATATATTATA
Found at i:800353 original size:27 final size:27
Alignment explanation
Indices: 800322--800389 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
800312 TATATTTACA
800322 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
800349 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
800376 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
800390 ATTCCTACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:808404 original size:47 final size:46
Alignment explanation
Indices: 808330--808422 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 46
808320 GGTTAAAATA
* *
808330 CTAACACTACTAACCGCTAACTCCTAACTTTTATTTTGTTTTTATTT
1 CTAACACTACTAACCGCTAACTACTAACTTTTATTTT-ATTTTATTT
* * *
808377 CTAACAGTACTAACCTCTGACTACTAACTTTTATTTTATTTTATTT
1 CTAACACTACTAACCGCTAACTACTAACTTTTATTTTATTTTATTT
808423 TTATGCTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
46 8 0.20
47 33 0.80
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (46 bp):
CTAACACTACTAACCGCTAACTACTAACTTTTATTTTATTTTATTT
Found at i:833603 original size:23 final size:23
Alignment explanation
Indices: 833584--833630 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
833574 CTGAAATATT
833584 TTTTATATT-TTATTAAAAATTTA
1 TTTTA-ATTCTTATTAAAAATTTA
* *
833607 TTTTAATTCTTCTTAAAATTTTA
1 TTTTAATTCTTATTAAAAATTTA
833630 T
1 T
833631 AAGTTCATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAATTCTTATTAAAAATTTA
Found at i:839712 original size:20 final size:20
Alignment explanation
Indices: 839689--839752 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
839679 TATTTTGTTT
839689 ACAAATAATCATTTGATGGA
1 ACAAATAATCATTTGATGGA
* * ***
839709 ACAAA-ACTCATCTT-TTTTT
1 ACAAATAATCAT-TTGATGGA
839728 ACAAATAATCATTTGATGGA
1 ACAAATAATCATTTGATGGA
839748 ACAAA
1 ACAAA
839753 ACGACCTCGT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (20 bp):
ACAAATAATCATTTGATGGA
Found at i:843695 original size:2 final size:2
Alignment explanation
Indices: 843690--843722 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
843680 ATTATTCGAA
843690 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 A
843723 GCAAGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:847442 original size:22 final size:21
Alignment explanation
Indices: 847413--847469 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
847403 CAATATCGTA
*
847413 ATAGAGTATCGGTACCATGGT
1 ATAGAGTATCGATACCATGGT
*
847434 ATAGTAGTATCGATACCATGTT
1 ATAG-AGTATCGATACCATGGT
*
847456 A-AGGGTATCGATAC
1 ATAGAGTATCGATAC
847470 TATTAAGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.31
21 6 0.19
22 16 0.50
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (21 bp):
ATAGAGTATCGATACCATGGT
Found at i:847842 original size:57 final size:56
Alignment explanation
Indices: 847769--847879 Score: 204
Period size: 57 Copynumber: 2.0 Consensus size: 56
847759 TTGATTACCA
*
847769 CATGGAACTTTTTGTGCAAGAAAATAATAAATTCATAATAAGTTTATGAATTTCAG
1 CATGGAACTTTGTGTGCAAGAAAATAATAAATTCATAATAAGTTTATGAATTTCAG
847825 CATGGACACTTTGTGTGCAAGAAAATAATAAATTCATAATAAGTTTATGAATTTC
1 CATGGA-ACTTTGTGTGCAAGAAAATAATAAATTCATAATAAGTTTATGAATTTC
847880 TGTATTGGTA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
56 6 0.11
57 47 0.89
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (56 bp):
CATGGAACTTTGTGTGCAAGAAAATAATAAATTCATAATAAGTTTATGAATTTCAG
Found at i:848144 original size:81 final size:81
Alignment explanation
Indices: 848005--848905 Score: 1311
Period size: 81 Copynumber: 11.1 Consensus size: 81
847995 AATAATTATA
* * *
848005 TGAGTAAAATATTAATGGCCTAGTTGTGTATTTGACAGAAATGTGTCAATTATGCTAGTTAGATG
1 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
*
848070 AAATGTTAAATACCTT
66 AAAGGTTAAATACCTT
* * * * * * *
848086 TGAGTAAAAGATTAATGGCCTAGCTATGGATTTGATAGAAATGTGTCAATTATACTAG-TAAATG
1 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
848150 AAAGGTTAAATACCTT
66 AAAGGTTAAATACCTT
* * * *
848166 TGAATAAAAGATTTAATGGCCTAGTTGTGCATTTGACATAAAGGTGTAAATTATGCCAGTTAGAT
1 TGAGTAAAAGA-TTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGAT
848231 GAAAGGTTAAATACCTT
65 GAAAGGTTAAATACCTT
* * * * * * *
848248 TGAGTAAAAGATTAATGTCCTAGCTATGCATTTGATAGAAAGGTGTCAATTATACCAGCTAGATG
1 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
848313 AAAGGTTAAATACCTT
66 AAAGGTTAAATACCTT
* * * * * *
848329 TGAGTAAAATATTAATAGCCTAGCTGTGCATTTGACAGAATTATGTCAATTATGCTAGTTAGATG
1 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
848394 AAAGGTTAAATACCTT
66 AAAGGTTAAATACCTT
* * * *
848410 TGAGTAAATGATTAATGGTCTAGTTGTGCATTTGAAAAAAATGTGTCAATTATGCCAGTTAGATG
1 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
848475 AAAGGTTAAATACCTT
66 AAAGGTTAAATACCTT
* *
848491 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATG-CAGTTAGATG
1 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
* *
848555 AAATGTTAAATCCCTT
66 AAAGGTTAAATACCTT
*
848571 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTAACAGAAATGTGTCAATTATGCCAGTTAGATG
1 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
848636 AAAGGTTAAATACCTT
66 AAAGGTTAAATACCTT
*
848652 TGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
1 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
*
848717 AAAGGTTAAATACATT
66 AAAGGTTAAATACCTT
* * * *
848733 TGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATA
1 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
848798 AAAGGTTAAATACCTT
66 AAAGGTTAAATACCTT
* ** * * * *
848814 TGATTAAAAGATTAATGGTTTAGCTGTGTATTTGACAGAAATGTGTCAATTATGTCGGTTAGATG
1 TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
*
848879 AAAGGTTAAATGCCTT
66 AAAGGTTAAATACCTT
*
848895 TGGGTAAAAGA
1 TGAGTAAAAGA
848906 CTAAATGTTT
Statistics
Matches: 735, Mismatches: 82, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
80 105 0.14
81 599 0.81
82 31 0.04
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (81 bp):
TGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATG
AAAGGTTAAATACCTT
Found at i:849604 original size:2 final size:2
Alignment explanation
Indices: 849594--850566 Score: 297
Period size: 2 Copynumber: 490.0 Consensus size: 2
849584 TTATATACTT
*
849594 TA TA T- TA TA TA TA TA TA TA T- TA TA TA -A GTA TA TA TA CTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
* *
849635 TA TT TA -A TA CT- TA TA TA -A TT TA TA T- TA TA TA CT- TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
849674 CTT TA TA T- TA T- TA TT TA CA TG TG TA TA TA TA TA TA CT- TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
849715 CTT TA TA T- TA T- TA TA TA TG TA TA TA TA CTT TA TA CTA -A AA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
849755 CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
849798 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * * *
849840 CA TA CTT TA TA TT TA -A TGC T- TA TA TT TA -A TGC T- TA CA TA
1 TA TA -TA TA TA TA TA TA T-A TA TA TA TA TA TA T-A TA TA TA TA
* *
849879 CTT TA TA T- TA TA TA CT- TA TA TA T- TT TA TA T- TA T- TA TA TA
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** * * * *
849918 CG TA TA TA TA CTT TA TA TT TA TA TA CT- TA TA TA -A TT TA GTC
1 TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
* * * *
849959 TT TA TA -A T- TA TA CTT TT TA TA TA TA TA -A TA TA CT- TA TA CTT
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
*
850000 TA TA T- TA T- TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
850040 CTT TA TA CTA -A AA CTT TA TA TA TA TA CT- TA TA TT TG TA CTT TA
1 -TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* * *
850083 TA TG TA TA AA TA CT- TA TA TA T- TT TA TA T- TA -A T- TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** * * * *
850121 CG TA TA TA TA TT TA TA CTA -A AA CTT TA TA TA TA TA TA TA TA CTT
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * *
850165 TA TA GTT TA TA TA TA TA GT- TA TA TA CTT TA TA TT TA -A TA CT-
1 TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA
* * *
850206 TA CA TA CT- TA TA CT- TA -A TA TT TA TA TA CTT TA TA T- TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * *
850245 TA CT- TA TA TA CTT TA TA -A T- TA TA CTT TT TA TA TA TA GA GA
1 TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
850285 GA GTA TA CT- TA TA CTT TA TA T- TA T- TA TA TA TG TA TA TA TA
1 TA -TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
850325 T- TT TA TA CTA -A AA CTT TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
850367 TA TA TA TA TA 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 TA TA TA TA TA TA
* * * * *
850408 TA TA AA GT- TT TA GTA TA -A AA TA TA TA TA CTT TA TA GTT TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
850450 TA TA TA CT- TA TA CTT TA TA GTT TA TA TA TA TA TA TA TA CA CA
1 TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * *
850492 T- TA TA TA TA TA TA -A GTG TA TA TA TA TT TA TA TA TT TA TA TG
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
850533 TA TA TA CT- TT TA TA TT TA TA TA TA AA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
850567 ATTGTATACT
Statistics
Matches: 720, Mismatches: 134, Indels: 234
0.66 0.12 0.22
Matches are distributed among these distances:
1 62 0.09
2 603 0.84
3 55 0.08
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:851021 original size:24 final size:24
Alignment explanation
Indices: 850976--851021 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
850966 TAGTCAACTT
*
850976 TTTTATATTAATATCAGCTTCACA
1 TTTTATATTAATATCAACTTCACA
*
851000 TTTTATAATTAAT-TCAATTTCA
1 TTTTAT-ATTAATATCAACTTCA
851022 TCCCTCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTATATTAATATCAACTTCACA
Found at i:851582 original size:547 final size:544
Alignment explanation
Indices: 850667--851685 Score: 1709
Period size: 547 Copynumber: 1.9 Consensus size: 544
850657 ACATACATAC
*
850667 ATATATTATAATTGTTTTAATTTTCCCCAACTTTTGAAATTAATGCAATTTAGTCCATTTTACAA
1 ATATATTATAATTGTTTTAATTTTCCCCAACTTTTGAAATTAATGCAATTCAGTCCATTTTACAA
*
850732 TTTGTCCTCACATTTTACAATTTTTTGATTTGATCATTTTATGTTGTTTATTGTATTTTAATTTT
66 TTTGTCCTCACATTTTACAATTTTTTGATTTGATCATTTTATGTTGTTTATTGTAATTTAATTTT
*
850797 AATTTGTAATTTCATATTTGTTCAATTTAGTCATTCAAATCATATTTGTATATGAAATTAACCCA
131 AATTTGTAATTTCATATTTGTTCAATTTAGTCATTCAAATCATATTTGTATATAAAATTAACCCA
*
850862 TACTTATTTATATTTTGTAATTTACTTAAAACCCTATAAAATGTAAATCACATAATAACTTTCTT
196 TACTTATTTATATTTTGTAATTTACTTAAAACCCTATAAAATGTAAATCACATAATAAATTTCTT
* *
850927 TTCAAATTATGTTCACCAACTTTTTAAATGTATGCAATTTAGTCAACTTTTTTATATTAATATCA
261 TTCAAATTATGTTCACCAACTTTTTAAATCTATGCAATTTAGTCAACTTTTTTATATTAATACCA
*
850992 GCTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGCTTAATTTATTCAAT
326 ACTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGCTTAATTTATTCAA-
* * *
851057 TTTTTTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATATATAAAGTATAAAGT
390 ATTTTTATTTCCAATTTCATATTTGTTCAATTTGGTACTTTATATACATATATAAACTATAAAGT
* *
851122 ATAAGTATATATGTATATGTATAATGTACATTATATATATATGCATCATATTATCATAACATTCA
455 ACAAGTATATATATATATGTATAATGTACATTATATATATATGCATCATATTATCATAACATTCA
851187 TTATACATATTATATATATATATAT
520 TTATACATATTATATATATATATAT
* * *
851212 ATATATTGTAATTGTTTTAATTTTTCTCCAACTTTTGAAATTAATGCAATTCAGTCCATTTTATA
1 ATATATTATAATTGTTTTAA-TTTTCCCCAACTTTTGAAATTAATGCAATTCAGTCCATTTTACA
* * * *
851277 ATTTTTTCTCAGATTTTACAATTTTTTTGATTTGATCCTTTTATGTTGTTTATTGTAATTTAATT
65 ATTTGTCCTCACATTTTACAA-TTTTTTGATTTGATCATTTTATGTTGTTTATTGTAATTTAATT
* * * * *
851342 TTAATTTGTGATTTCATATTTGTTCAATTTAGTCCTTCAAATTATATTTGTATCTAAAATTTACC
129 TTAATTTGTAATTTCATATTTGTTCAATTTAGTCATTCAAATCATATTTGTATATAAAATTAACC
*
851407 CATACTTATTTATATTTTTGTAATTTACTTAAAACCTTATAAAATGTAAATCACATAATAAATTT
194 CATACTTATTTATA-TTTTGTAATTTACTTAAAACCCTATAAAATGTAAATCACATAATAAATTT
*
851472 CTTTTCAAATTATGTTCACCAACTTTTTAAATCTATGCAATTTAGTCCA-TTTTTTATATTAATA
258 CTTTTCAAATTATGTTCACCAACTTTTTAAATCTATGCAATTTAGTCAACTTTTTTATATTAATA
* * *
851536 CCAACTTTACATTTTATAATTAATTCAGTTTCA-CTCCTCATCAATGTGTGTTGTTTAATTTATT
323 CCAACTTCACATTTTATAATTAATTCAATTTCATC-CCTCATCAATGTGTGTTGCTTAATTTATT
*
851600 CAAATTTTTATTTCCAATTTCATATTTGTTCAATTTGGTACTTTATATTCATATATAAACTATAA
387 CAAATTTTTATTTCCAATTTCATATTTGTTCAATTTGGTACTTTATATACATATATAAACTATAA
851665 AGTACAAGTATATATATATAT
452 AGTACAAGTATATATATATAT
851686 AATATAATAT
Statistics
Matches: 440, Mismatches: 30, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
545 19 0.04
546 137 0.31
547 189 0.43
548 95 0.22
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (544 bp):
ATATATTATAATTGTTTTAATTTTCCCCAACTTTTGAAATTAATGCAATTCAGTCCATTTTACAA
TTTGTCCTCACATTTTACAATTTTTTGATTTGATCATTTTATGTTGTTTATTGTAATTTAATTTT
AATTTGTAATTTCATATTTGTTCAATTTAGTCATTCAAATCATATTTGTATATAAAATTAACCCA
TACTTATTTATATTTTGTAATTTACTTAAAACCCTATAAAATGTAAATCACATAATAAATTTCTT
TTCAAATTATGTTCACCAACTTTTTAAATCTATGCAATTTAGTCAACTTTTTTATATTAATACCA
ACTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGCTTAATTTATTCAAA
TTTTTATTTCCAATTTCATATTTGTTCAATTTGGTACTTTATATACATATATAAACTATAAAGTA
CAAGTATATATATATATGTATAATGTACATTATATATATATGCATCATATTATCATAACATTCAT
TATACATATTATATATATATATAT
Found at i:851730 original size:22 final size:22
Alignment explanation
Indices: 851715--851865 Score: 124
Period size: 22 Copynumber: 6.9 Consensus size: 22
851705 AAGTGTTTGG
851715 ATATAAGTATTAAAGTATATAA
1 ATATAAGTATTAAAGTATATAA
851737 ATATAAGTATTAAA-TATA-AA
1 ATATAAGTATTAAAGTATATAA
*
851757 GTATATAAGTA-CATAAGTACTA-AA
1 --ATATAAGTATTA-AAGTA-TATAA
851781 ATAT-A-TAATGTAAAGTAT-TAA
1 ATATAAGT-AT-TAAAGTATATAA
* *
851802 ACTATATAATA-TCAAGTAT-TAA
1 A-TATA-AGTATTAAAGTATATAA
851824 ATATCAAGTATTAAAGTATATAA
1 ATAT-AAGTATTAAAGTATATAA
851847 ATATAAGTATTAAA-TATAT
1 ATATAAGTATTAAAGTATAT
851866 TTAATAATCA
Statistics
Matches: 108, Mismatches: 5, Indels: 33
0.74 0.03 0.23
Matches are distributed among these distances:
20 3 0.03
21 22 0.20
22 66 0.61
23 10 0.09
24 6 0.06
25 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (22 bp):
ATATAAGTATTAAAGTATATAA
Done.