Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007915.1 Hibiscus syriacus cultivar Beakdansim tig00110318_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: 1667290
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1595315 original size:21 final size:21
Alignment explanation
Indices: 1595290--1595339 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1595280 ATAAAATGCT
1595290 AAAATAATAACAAAACAAGTA
1 AAAATAATAACAAAACAAGTA
*
1595311 AAAATAATAACAAAACATGTA
1 AAAATAATAACAAAACAAGTA
*
1595332 GAAATAAT
1 AAAATAAT
1595340 GATGTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.68, C:0.08, G:0.06, T:0.18
Consensus pattern (21 bp):
AAAATAATAACAAAACAAGTA
Found at i:1596591 original size:29 final size:29
Alignment explanation
Indices: 1596559--1596634 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 29
1596549 CAGCGATATG
1596559 GTAGGTCGCCATGCACGCCAG-GCAACATA
1 GTAGGTCGCCATGCACGCCAGCG-AACATA
* *
1596588 GTAGGTCGCCATGCACGCCCAGCGACCTTA
1 GTAGGTCGCCATGCACG-CCAGCGAACATA
1596618 -TAGGTCGCCATGCACGC
1 GTAGGTCGCCATGCACGC
1596635 TCGACGTCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 1 0.02
29 33 0.77
30 8 0.19
31 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.28, T:0.16
Consensus pattern (29 bp):
GTAGGTCGCCATGCACGCCAGCGAACATA
Found at i:1597343 original size:21 final size:21
Alignment explanation
Indices: 1597318--1597361 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1597308 AATTTAGTTA
1597318 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1597339 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1597360 AT
1 AT
1597362 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1597375 original size:28 final size:28
Alignment explanation
Indices: 1597338--1597391 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1597328 TAGTATAAAT
*
1597338 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
1597366 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
1597392 ATTTAGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:1600473 original size:10 final size:10
Alignment explanation
Indices: 1600458--1600535 Score: 56
Period size: 10 Copynumber: 7.8 Consensus size: 10
1600448 TTTATAAGAT
1600458 TTAGTAATGA
1 TTAGTAATGA
1600468 TTAGTAATGA
1 TTAGTAATGA
* *
1600478 -T-GAAATTA
1 TTAGTAATGA
*
1600486 TTATTAAT-A
1 TTAGTAATGA
*
1600495 TTTAATGATATGA
1 -TTAGT-A-ATGA
1600508 -TAGTAATGA
1 TTAGTAATGA
1600517 TTTAGTAATGA
1 -TTAGTAATGA
1600528 TTAGTAAT
1 TTAGTAAT
1600536 AATGAAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
8 5 0.09
9 7 0.13
10 26 0.48
11 13 0.24
12 2 0.04
13 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (10 bp):
TTAGTAATGA
Found at i:1600514 original size:21 final size:20
Alignment explanation
Indices: 1600485--1600596 Score: 61
Period size: 21 Copynumber: 5.5 Consensus size: 20
1600475 TGATGAAATT
*
1600485 ATTATTAATATTTAATGATATG
1 ATTAGTAATATTTAAT-A-ATG
*
1600507 A-TAGTAATGATTTAGTAATG
1 ATTAGTAAT-ATTTAATAATG
* * *
1600527 ATTAGTAATA-ATGA-AATT
1 ATTAGTAATATTTAATAATG
* *
1600545 ATTATTAATATTTAATGATTTG
1 ATTAGTAATATTTAAT-A-ATG
* *
1600567 A-TATTAATGATTTAGTAATG
1 ATTAGTAAT-ATTTAATAATG
1600587 ATTAGTAATA
1 ATTAGTAATA
1600597 ATAAAATTAT
Statistics
Matches: 68, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
18 12 0.18
19 3 0.04
20 9 0.13
21 29 0.43
22 15 0.22
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (20 bp):
ATTAGTAATATTTAATAATG
Found at i:1600526 original size:60 final size:60
Alignment explanation
Indices: 1600455--1601331 Score: 1163
Period size: 60 Copynumber: 15.2 Consensus size: 60
1600445 GTATTTATAA
* * *
1600455 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATATGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1600515 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
* *
1600575 GATTTAGTAATGATTAGTAATAATAAAATTATTATTAAT-TTTTATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
*
1600634 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
*
1600694 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--T
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
* * *
1600745 GA--TAGTAATGATTAGTAATATTGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
* * * * * * *
1600803 GA-TTAGAAAT-AAT-GAAATTAT--TATTAATTTTTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATATTAAT
1600852 GA-TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
* *
1600911 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
* * * * * *
1600971 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATATTAAT
1601020 GA-TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
*
1601079 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1601139 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
* *
1601199 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
*
1601259 GA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1601317 GATTTAGTAATGATT
1 GATTTAGTAATGATT
1601332 TGATAGTAAT
Statistics
Matches: 728, Mismatches: 47, Indels: 85
0.85 0.05 0.10
Matches are distributed among these distances:
49 69 0.09
50 7 0.01
51 17 0.02
52 21 0.03
53 10 0.01
54 10 0.01
55 8 0.01
56 23 0.03
57 12 0.02
58 41 0.06
59 125 0.17
60 385 0.53
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
Found at i:1600667 original size:119 final size:120
Alignment explanation
Indices: 1600455--1601331 Score: 1052
Period size: 119 Copynumber: 7.6 Consensus size: 120
1600445 GTATTTATAA
* * *
1600455 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATATGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
*
1600520 AGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
66 AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
* *
1600575 GATTTAGTAATGATTAGTAATAATAAAATTATTATTAAT-TTTTATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
1600639 AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
66 AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
*
1600694 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA--T
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
*
1600748 AGTAATGATTAGTAATATTGAAATTATTATTAATTTTTAATGA--T-----T--T
66 AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
* * * * *
1600794 GA--TAGTAATGATTAGAAATAATGAAATTATTATTAATTTTTAATGAT--TTG-ATAGTAATGA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAA-TATT--TAATGATTTGATATTAATGA
*
1600854 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
63 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
* *
1600911 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
* * * * * ** * * *
1600975 AGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGATT--TGA-TAG-TAATGAT
66 AGTAATGATTAGTAATAATGAAATT-ATTATTAATTTTTAATGATTTGATATTAAT
* * * * * * * *
1601023 TA-GTAATGAT--TA-GTAATAATGAAATTATTATTAATATTTAATGAT--TTG-ATATTAATGA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-ATT--TAATGATTTGATATTAATGA
1601081 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
63 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
1601139 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
*
1601204 AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
66 AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
*
1601259 GA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
1601322 AGTAATGATT
66 AGTAATGATT
1601332 TGATAGTAAT
Statistics
Matches: 655, Mismatches: 56, Indels: 94
0.81 0.07 0.12
Matches are distributed among these distances:
98 33 0.05
99 1 0.00
100 5 0.01
102 2 0.00
104 1 0.00
105 2 0.00
107 4 0.01
108 74 0.11
109 57 0.09
110 3 0.00
111 17 0.03
112 16 0.02
113 8 0.01
114 6 0.01
115 8 0.01
116 20 0.03
117 18 0.03
118 57 0.09
119 194 0.30
120 129 0.20
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (120 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
Found at i:1600682 original size:35 final size:35
Alignment explanation
Indices: 1600641--1600743 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 35
1600631 AATGATTTAG
1600641 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAATTTT
* * * *
1600676 TAATGATT--TGAT-AT-TAATGA-T-TT-A---G
1 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1600701 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1600736 TAATGATT
1 TAATGATT
1600744 TGATAGTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
25 8 0.16
27 3 0.06
28 3 0.06
29 6 0.12
30 2 0.04
31 6 0.12
32 3 0.06
33 3 0.06
35 16 0.32
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTTT
Found at i:1600696 original size:168 final size:175
Alignment explanation
Indices: 1600455--1601331 Score: 1217
Period size: 168 Copynumber: 5.1 Consensus size: 175
1600445 GTATTTATAA
* * *
1600455 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATATGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGAT-TTATAG-AATGA-TT
1600520 AGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
63 A-TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
*
1600585 TGATTAGTAATAATAAAATTATTATTAATTTTTATGATTTGATATTAAT
127 TGATTAGTAATAATGAAATTATTATTAATTTTTATGATTTGATATTAAT
*
1600634 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTT-ATA-GAATGA-TT
*
1600699 AGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA--TAGTAA
63 A-TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
*
1600753 TGATTAGTAATATTGAAATTATTATTAATTTTTA--A--TG--ATT--T
127 TGATTAGTAATAATGAAATTATTATTAATTTTTATGATTTGATATTAAT
*
1600794 GA--TAGTAATGATTAGAAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTT-ATAG-AATGATTA
1600857 GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
64 -TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
1600922 GATTAGTAATAATGAAATTATTATTAATTTTTA--A--TG--ATT--T
128 GATTAGTAATAATGAAATTATTATTAATTTTTATGATTTGATATTAAT
1600962 GA--TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTT-ATAG-AATGATTA
1601025 GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
64 -TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
1601090 GATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
128 GATTAGTAATAATGAAATTATTATTAATTTTT-ATGATTTGATATTAAT
* *
1601139 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTT-ATA-GAATGA-TT
* *
1601204 AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAA
63 A-TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
* *
1601268 TGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAAT
127 TGATTAGTAATAATGAAATTATTATTAAT-TTTTATGATTTGATATTAAT
1601317 GATTTAGTAATGATT
1 GATTTAGTAATGATT
1601332 TGATAGTAAT
Statistics
Matches: 652, Mismatches: 18, Indels: 57
0.90 0.02 0.08
Matches are distributed among these distances:
157 36 0.06
158 58 0.09
160 4 0.01
161 1 0.00
162 5 0.01
164 5 0.01
166 4 0.01
168 243 0.37
169 1 0.00
170 3 0.00
171 1 0.00
172 3 0.00
173 2 0.00
174 2 0.00
175 4 0.01
176 1 0.00
177 3 0.00
178 48 0.07
179 171 0.26
180 57 0.09
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (175 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTATAGAATGATTATA
ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
TAGTAATAATGAAATTATTATTAATTTTTATGATTTGATATTAAT
Found at i:1600858 original size:10 final size:10
Alignment explanation
Indices: 1600845--1600871 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1600835 AATGATTTGA
1600845 TAGTAATGAT
1 TAGTAATGAT
1600855 TAGTAATGAT
1 TAGTAATGAT
1600865 TAGTAAT
1 TAGTAAT
1600872 AATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:1600980 original size:24 final size:24
Alignment explanation
Indices: 1600953--1601033 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
1600943 TATTAATTTT
1600953 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
* *** * * * **
1600977 TAATAATGAAATTATTATTAATTTT
1 TAATGATTTGA-TAGTAATGATTAG
1601002 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
1601026 TAATGATT
1 TAATGATT
1601034 AGTAATAATG
Statistics
Matches: 38, Mismatches: 18, Indels: 2
0.66 0.31 0.03
Matches are distributed among these distances:
24 23 0.61
25 15 0.39
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (24 bp):
TAATGATTTGATAGTAATGATTAG
Found at i:1601026 original size:10 final size:10
Alignment explanation
Indices: 1601013--1601039 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1601003 AATGATTTGA
1601013 TAGTAATGAT
1 TAGTAATGAT
1601023 TAGTAATGAT
1 TAGTAATGAT
1601033 TAGTAAT
1 TAGTAAT
1601040 AATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:1601075 original size:21 final size:20
Alignment explanation
Indices: 1601051--1601204 Score: 63
Period size: 21 Copynumber: 7.6 Consensus size: 20
1601041 ATGAAATTAT
1601051 TATTAATATTTAATGATTTGA
1 TATTAATATTTAAT-ATTTGA
* *
1601072 TATTAATGATTTAGTA-ATGA
1 TATTAAT-ATTTAATATTTGA
* * *
1601092 TTAGTAATAATGAA-A-TT-A
1 -TATTAATATTTAATATTTGA
*
1601110 TTATTAATTTTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
* *
1601132 TATTAATGATTTAGTA-ATGA
1 TATTAAT-ATTTAATATTTGA
* * *
1601152 TTAGTAATAATGAA-A-TT-A
1 -TATTAATATTTAATATTTGA
1601170 TTATTAATATTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
1601192 TATTAATGATTTA
1 TATTAAT-ATTTA
1601205 GTAATGATTA
Statistics
Matches: 98, Mismatches: 22, Indels: 25
0.68 0.15 0.17
Matches are distributed among these distances:
18 23 0.23
19 4 0.04
20 14 0.14
21 39 0.40
22 18 0.18
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (20 bp):
TATTAATATTTAATATTTGA
Found at i:1601265 original size:10 final size:10
Alignment explanation
Indices: 1601252--1601278 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1601242 AATGATTTGA
1601252 TAGTAATGAT
1 TAGTAATGAT
1601262 TAGTAATGAT
1 TAGTAATGAT
1601272 TAGTAAT
1 TAGTAAT
1601279 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:1601302 original size:21 final size:22
Alignment explanation
Indices: 1601278--1601347 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 22
1601268 TGATTAGTAA
1601278 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
1601299 TAATGATTTGATATTAATGATTT
1 TAATAATTTGATATTAATGA-TT
* *
1601322 AGTAATGATTTGATAGTAATGATT
1 --TAATAATTTGATATTAATGATT
1601346 TA
1 TA
1601348 CGACTTGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 15 0.36
22 4 0.10
23 2 0.05
24 2 0.05
25 19 0.45
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:1601315 original size:14 final size:14
Alignment explanation
Indices: 1601299--1601346 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1601289 TATTAATATT
*
1601299 TAATGATTTGATAT
1 TAATGATTTGATAG
1601313 TAATGA-TT--TAG
1 TAATGATTTGATAG
1601324 TAATGATTTGATAG
1 TAATGATTTGATAG
1601338 TAATGATTT
1 TAATGATTT
1601347 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:1601328 original size:25 final size:25
Alignment explanation
Indices: 1601299--1601347 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1601289 TATTAATATT
*
1601299 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
1601324 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
1601348 CGACTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:1603579 original size:8 final size:8
Alignment explanation
Indices: 1603566--1603598 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
1603556 AATTTTAATA
1603566 TAATAAAC
1 TAATAAAC
1603574 TAATAAAC
1 TAATAAAC
1603582 TAATAAAC
1 TAATAAAC
*
1603590 TAACAAAC
1 TAATAAAC
1603598 T
1 T
1603599 GAACTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (8 bp):
TAATAAAC
Found at i:1603939 original size:22 final size:21
Alignment explanation
Indices: 1603901--1603941 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1603891 TTTATGTATA
*
1603901 ATATAACTTAAACTAACAATC
1 ATATAACCTAAACTAACAATC
*
1603922 ATATAACCCTAAATTAACAA
1 ATATAA-CCTAAACTAACAA
1603942 ACTAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
ATATAACCTAAACTAACAATC
Found at i:1604079 original size:13 final size:13
Alignment explanation
Indices: 1604040--1604086 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1604030 CTCACAAGAG
1604040 CCTTGTCTCCCTTT
1 CCTT-TCTCCCTTT
* *
1604054 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
1604068 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
1604081 -CTTTCT
1 CCTTTCT
1604087 TTCTCGGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 12 0.43
15 1 0.04
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.57
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:1604144 original size:26 final size:28
Alignment explanation
Indices: 1604081--1604144 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 28
1604071 TTCTCCCTTT
*
1604081 CTTTCTTTCTCGGCTGCAATTTCTTCTCC
1 CTTTCTTTCTC-GCTGCAATCTCTTCTCC
1604110 CTTTC-TTCT-GCTGCAATCTCTTCT-C
1 CTTTCTTTCTCGCTGCAATCTCTTCTCC
1604135 CTTTCTTTCT
1 CTTTCTTTCT
1604145 TTTATGTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 6 0.18
26 18 0.55
28 4 0.12
29 5 0.15
ACGTcount: A:0.06, C:0.34, G:0.08, T:0.52
Consensus pattern (28 bp):
CTTTCTTTCTCGCTGCAATCTCTTCTCC
Found at i:1604451 original size:29 final size:29
Alignment explanation
Indices: 1604392--1604474 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 29
1604382 GTGAAGCTTG
* *
1604392 GTCGCCGGGATTGCTTGGCGACCTACAAA
1 GTCGCTGGGAGTGCTTGGCGACCTACAAA
* ***
1604421 GTCGCTGGGAGTGCATGGCGACCTTGTAA
1 GTCGCTGGGAGTGCTTGGCGACCTACAAA
* *
1604450 GTCGTTGAGAGTGCTTGGCGACCTA
1 GTCGCTGGGAGTGCTTGGCGACCTA
1604475 TGGTTGGGTT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.18, C:0.23, G:0.35, T:0.24
Consensus pattern (29 bp):
GTCGCTGGGAGTGCTTGGCGACCTACAAA
Found at i:1614024 original size:16 final size:18
Alignment explanation
Indices: 1614003--1614042 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1613993 ATCTGCAATG
1614003 TAAAAAA-AACAAAG-CA
1 TAAAAAAGAACAAAGACA
*
1614019 TAAAAAAGAACAAGGACA
1 TAAAAAAGAACAAAGACA
1614037 TAAAAA
1 TAAAAA
1614043 TCAGCTAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 6 0.29
18 8 0.38
ACGTcount: A:0.72, C:0.10, G:0.10, T:0.07
Consensus pattern (18 bp):
TAAAAAAGAACAAAGACA
Found at i:1616990 original size:21 final size:21
Alignment explanation
Indices: 1616966--1617012 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1616956 ACTAATCAGA
1616966 TAAAATTA-ATTAATTATTATT
1 TAAAATTAGATTAATTA-TATT
* **
1616987 TAAATTTAGATTTTTTATATT
1 TAAAATTAGATTAATTATATT
1617008 TAAAA
1 TAAAA
1617013 AATATTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TAAAATTAGATTAATTATATT
Found at i:1617242 original size:2 final size:2
Alignment explanation
Indices: 1617235--1617271 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1617225 AGCAATATTA
1617235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1617272 ACTTTTTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1618297 original size:12 final size:12
Alignment explanation
Indices: 1618280--1618310 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1618270 ATTTATCTAA
1618280 AAATTAAGATTT
1 AAATTAAGATTT
1618292 AAATTAAGATTT
1 AAATTAAGATTT
*
1618304 AATTTAA
1 AAATTAA
1618311 AGTTTAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (12 bp):
AAATTAAGATTT
Found at i:1618830 original size:27 final size:26
Alignment explanation
Indices: 1618775--1618830 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
1618765 AACCGAATCA
* *
1618775 AAAAAATGAAGCCTTTAAACCGAATC
1 AAAAAATGAAGCCTTTAAACCAAACC
*
1618801 AAAAACTGAA-CCGTTTAAAACCAAACC
1 AAAAAATGAAGCC-TTT-AAACCAAACC
1618828 AAA
1 AAA
1618831 TCAAATCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 2 0.08
26 12 0.48
27 11 0.44
ACGTcount: A:0.54, C:0.21, G:0.09, T:0.16
Consensus pattern (26 bp):
AAAAAATGAAGCCTTTAAACCAAACC
Found at i:1625947 original size:15 final size:16
Alignment explanation
Indices: 1625927--1625956 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1625917 TACTGTGAAC
1625927 TGCA-TTTTTATTTTT
1 TGCATTTTTTATTTTT
1625942 TGCATTTTTTATTTT
1 TGCATTTTTTATTTT
1625957 GTGACAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (16 bp):
TGCATTTTTTATTTTT
Found at i:1631510 original size:82 final size:84
Alignment explanation
Indices: 1631371--1631531 Score: 195
Period size: 82 Copynumber: 1.9 Consensus size: 84
1631361 CGAAAGCCAT
* ** *
1631371 ATATATAGTGGCGCTTTTTGTGAAAACTCTGCTAAAAATGCATACTTATGTGGCGTTTATGTAAA
1 ATATATAGTGACGCTTTTTGTGAAAACTCTGCTAAAAACACATACTTATGTGGCGTTTATATAAA
*
1631436 AAAAA-TCGCGATAACAAG
66 AAAAAGCCGCGATAACAAG
* * * *
1631454 ATATATAGTGACG-TTTTTGTGAAAACATC-GTTAAACACACGTACTT-TAGTGTCGTTTATATA
1 ATATATAGTGACGCTTTTTGTGAAAAC-TCTGCTAAAAACACATACTTAT-GTGGCGTTTATATA
1631516 AAAAAAAGCCGCGATA
64 AAAAAAAGCCGCGATA
1631532 GCCCAATATA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
81 1 0.02
82 44 0.67
83 21 0.32
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (84 bp):
ATATATAGTGACGCTTTTTGTGAAAACTCTGCTAAAAACACATACTTATGTGGCGTTTATATAAA
AAAAAGCCGCGATAACAAG
Found at i:1632506 original size:30 final size:30
Alignment explanation
Indices: 1632458--1632537 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
1632448 GACCTACCAA
1632458 CCAACGACCTCCAT----GCCCATGCACGC
1 CCAACGACCTCCATGCACGCCCATGCACGC
*
1632484 CCAACGACCTCCATGCACGCCCATGCATGC
1 CCAACGACCTCCATGCACGCCCATGCACGC
1632514 CCAACGACCTCCATGCACGCCCAT
1 CCAACGACCTCCATGCACGCCCAT
1632538 CTCGCCAAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
26 14 0.29
30 35 0.71
ACGTcount: A:0.24, C:0.49, G:0.15, T:0.12
Consensus pattern (30 bp):
CCAACGACCTCCATGCACGCCCATGCACGC
Found at i:1632556 original size:28 final size:30
Alignment explanation
Indices: 1632524--1632591 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 30
1632514 CCAACGACCT
*
1632524 CCATGCACGC-C-CATCTCGCCAAAGGTCA
1 CCATGCACGCACTCAGCTCGCCAAAGGTCA
*
1632552 CCATGCAATGCACGTTCAGCTCGCCAAAGGTCA
1 CCATGC-ACGCAC--TCAGCTCGCCAAAGGTCA
1632585 CCATGCA
1 CCATGCA
1632592 GTCCATGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 6 0.18
29 3 0.09
30 1 0.03
32 1 0.03
33 22 0.67
ACGTcount: A:0.26, C:0.38, G:0.19, T:0.16
Consensus pattern (30 bp):
CCATGCACGCACTCAGCTCGCCAAAGGTCA
Found at i:1632802 original size:12 final size:11
Alignment explanation
Indices: 1632782--1632817 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1632772 GAAATCAACT
1632782 GCATTATTGCA
1 GCATTATTGCA
*
1632793 GCACTTATTGCT
1 GCA-TTATTGCA
1632805 GCATTATTGCA
1 GCATTATTGCA
1632816 GC
1 GC
1632818 CCGTGAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:1633017 original size:8 final size:9
Alignment explanation
Indices: 1632987--1633024 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1632977 GTAAGTTTTT
1632987 TTTTAATTA
1 TTTTAATTA
1632996 TTTTAATTA
1 TTTTAATTA
*
1633005 GTTT-ATTA
1 TTTTAATTA
1633013 TTTTAAATTA
1 TTTT-AATTA
1633023 TT
1 TT
1633025 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:1633065 original size:38 final size:41
Alignment explanation
Indices: 1633017--1633117 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 41
1633007 TTATTATTTT
*
1633017 AAATTATTAGTTTGTTAGTTT-ATGGTT-TA-AGTTAAAACA
1 AAATTATTAGTTTGTTAGTTTGATGGTTATATA-TTAAAAAA
*
1633056 AAATT-TTAGTTTGTTTGTTTGATGGTTATATATTAAAAAA
1 AAATTATTAGTTTGTTAGTTTGATGGTTATATATTAAAAAA
*
1633096 ATAATTAATTAGTGTGTTAGTT
1 A-AATT-ATTAGTTTGTTAGTT
1633118 AGTCTAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
38 14 0.27
39 11 0.21
40 10 0.19
41 5 0.10
43 12 0.23
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.49
Consensus pattern (41 bp):
AAATTATTAGTTTGTTAGTTTGATGGTTATATATTAAAAAA
Found at i:1633134 original size:28 final size:27
Alignment explanation
Indices: 1633095--1633147 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1633085 ATATTAAAAA
1633095 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
1633123 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
1633148 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:1633153 original size:27 final size:29
Alignment explanation
Indices: 1633094--1633158 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
1633084 TATATTAAAA
1633094 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
1633123 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
1633149 AAATAGTTAA
1 AAATAATTAA
1633159 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:1633373 original size:21 final size:21
Alignment explanation
Indices: 1633348--1633387 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1633338 GTTAATTAGT
1633348 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
1633369 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
1633388 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:1633627 original size:30 final size:30
Alignment explanation
Indices: 1633559--1633632 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
1633549 ATTAGTTAAT
* *
1633559 TAGTTTTTTAGTAGTAAATTATAATTAAAAA
1 TAGTTTATTAGT-TTAAATTATAATTAAAAA
*
1633590 TCA-TTTATTAGTTTAATTTAT-ATTAAAGAA
1 T-AGTTTATTAGTTTAAATTATAATTAAA-AA
1633620 TAGTTTATTAGTT
1 TAGTTTATTAGTT
1633633 GTTTAAGGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 7 0.19
30 20 0.54
31 9 0.24
32 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.50
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAATTATAATTAAAAA
Found at i:1634936 original size:22 final size:21
Alignment explanation
Indices: 1634886--1634936 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1634876 AATCTGTTAT
*
1634886 TTTTAATTATTATTTAAATTAA
1 TTTT-ATTATTATTTAAATAAA
* *
1634908 CTATATTATTGATTTAAATAAA
1 TTTTATTATT-ATTTAAATAAA
1634930 TTTTATT
1 TTTTATT
1634937 GTTTTTGTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTATTATTATTTAAATAAA
Found at i:1635951 original size:14 final size:14
Alignment explanation
Indices: 1635932--1636021 Score: 82
Period size: 14 Copynumber: 6.6 Consensus size: 14
1635922 TTCAAGTCGT
1635932 AAATCATTACTATC
1 AAATCATTACTATC
1635946 AAATCATTAC--T-
1 AAATCATTACTATC
*
1635957 AAATCATTAATATC
1 AAATCATTACTATC
*
1635971 AAATCATTAAATAAT-
1 AAATCATT-ACT-ATC
* *
1635986 AAATTATTATTA-C
1 AAATCATTACTATC
*
1635999 TAATCATTACTATC
1 AAATCATTACTATC
1636013 AAATCATTA
1 AAATCATTA
1636022 AAAATTAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
11 9 0.15
12 1 0.02
13 11 0.18
14 29 0.47
15 10 0.16
16 2 0.03
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:1635959 original size:25 final size:25
Alignment explanation
Indices: 1635931--1635979 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1635921 GTTCAAGTCG
*
1635931 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
1635956 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
1635980 AATAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:1636013 original size:42 final size:48
Alignment explanation
Indices: 1635951--1636178 Score: 164
Period size: 60 Copynumber: 4.4 Consensus size: 48
1635941 CTATCAAATC
*
1635951 ATTACTAAATCATTAATATCAAATCATT-AAA-TAAT-A-AA-TT-ATT
1 ATTACT-AATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
1635994 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATT
1636043 ATTACTAATCATTACTAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATT
1 ATTACTAATCATTACT--ATCA--A--ATC--AT--TA-A-AATTAATAATAATTTCATT
1636103 ATTACTAATCATTAGTAAATCATTACTATCAAATCATTAAAAATTAATAAT-ATTTCATT
1 A-T--T-A-C-----T-AATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATT
1636162 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1636179 AATCATTAAT
Statistics
Matches: 153, Mismatches: 1, Indels: 57
0.73 0.00 0.27
Matches are distributed among these distances:
42 20 0.13
43 6 0.04
44 3 0.02
45 4 0.03
46 1 0.01
47 2 0.01
48 13 0.08
49 20 0.13
51 4 0.03
53 1 0.01
54 1 0.01
55 4 0.03
56 1 0.01
57 2 0.01
58 2 0.01
59 11 0.07
60 30 0.20
61 3 0.02
62 1 0.01
63 3 0.02
64 1 0.01
65 4 0.03
67 1 0.01
69 4 0.03
70 1 0.01
71 10 0.07
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
Found at i:1636069 original size:60 final size:60
Alignment explanation
Indices: 1635994--1636361 Score: 588
Period size: 60 Copynumber: 6.2 Consensus size: 60
1635984 ATAAATTATT
1635994 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
1636053 ATTACTAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATC
*
1636113 ATTAGTAAATCATTACTATCAAATCATTAAAAATTAATAAT-ATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
1636172 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
1636232 ATTACTAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATC
* * *
1636292 ATTACT--ATCAAATTACTATTAAATCATT-AATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1636351 ATTACTAAATC
1 ATTACTAAATC
1636362 TTTAAATACA
Statistics
Matches: 288, Mismatches: 11, Indels: 18
0.91 0.03 0.06
Matches are distributed among these distances:
58 3 0.01
59 101 0.35
60 178 0.62
61 6 0.02
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:1636204 original size:179 final size:178
Alignment explanation
Indices: 1635994--1636366 Score: 635
Period size: 179 Copynumber: 2.1 Consensus size: 178
1635984 ATAAATTATT
*
1635994 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
1636058 TAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATTAGTAAAT
66 TAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATTACT--AT
*
1636123 C-ATTACTATCAAATCATTAAAAATTAATAAT-ATTTCATTATTACTAATC
129 CAATTACTATCAAATCATT-AAAATTAATAATAATTTCATCATTACTAATC
1636172 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1636237 TAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATTACTATCA
66 TAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATTACTATC-
* *
1636302 AATTACTATTAAATCATTAATATTAATAATAATTTCATCATTACTAATC
130 AATTACTATCAAATCATTAAAATTAATAATAATTTCATCATTACTAATC
*
1636351 ATTACTAAATCTTTAA
1 ATTACTAAATCATTAA
1636367 ATACATAGAA
Statistics
Matches: 185, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
177 3 0.02
178 17 0.09
179 165 0.89
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (178 bp):
ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
TAAATCATTACTATCAAATCATACATAATTAATAATAATTTCATTATTACTAATCATTACTATCA
ATTACTATCAAATCATTAAAATTAATAATAATTTCATCATTACTAATC
Found at i:1636212 original size:119 final size:120
Alignment explanation
Indices: 1635994--1636361 Score: 588
Period size: 119 Copynumber: 3.1 Consensus size: 120
1635984 ATAAATTATT
1635994 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
1636058 TAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATC
66 TAAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATC
*
1636113 ATTAGTAAATCATTACTATCAAATCATTAAAAATTAATAAT-ATTTCATTATTACTAATCATTAC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
*
1636177 TAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
66 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
1636232 ATTACTAAATCATTACTATCAAATCA-TACATAATTAATAATAATTTCATTATTACTAATCATTA
1 ATTACTAAATCATTACTATCAAATCATTA-AAAATTAATAATAATTTCATTATTACTAATCATTA
* * *
1636296 CT--ATCAAATTACTATTAAATCATT-AATATTAATAATAATTTCATCATTACTAATC
65 CTAAATC--ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1636351 ATTACTAAATC
1 ATTACTAAATC
1636362 TTTAAATACA
Statistics
Matches: 234, Mismatches: 9, Indels: 12
0.92 0.04 0.05
Matches are distributed among these distances:
118 5 0.02
119 154 0.66
120 75 0.32
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (120 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:1639476 original size:28 final size:28
Alignment explanation
Indices: 1639424--1639477 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1639414 ATAATCTAAT
**
1639424 ATATAACTTAAACTAACAATTTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
1639452 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
1639478 ATTTATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:1639484 original size:28 final size:28
Alignment explanation
Indices: 1639420--1639484 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
1639410 TTATATAATC
**
1639420 TAATATATAACTTAAACTAACAATTTAA
1 TAATATATAACTTAAACTAACAAACTAA
1639448 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
1639476 TAATTTATA
1 TAATATATA
1639485 CTAACAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 28 0.88
29 2 0.06
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:1639487 original size:21 final size:21
Alignment explanation
Indices: 1639454--1639502 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1639444 TTAATATAAT
1639454 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1639475 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1639496 ATTAACT
1 A-TAACT
1639503 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1640170 original size:20 final size:20
Alignment explanation
Indices: 1640145--1640193 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1640135 TTTGGCGAGC
1640145 TGGGCGTGCATGGAGGTCGT
1 TGGGCGTGCATGGAGGTCGT
1640165 TGGGCGTGCATGGAGGTCGT
1 TGGGCGTGCATGGAGGTCGT
1640185 TGGGCGTGC
1 TGGGCGTGC
1640194 CTGGGCGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.08, C:0.16, G:0.51, T:0.24
Consensus pattern (20 bp):
TGGGCGTGCATGGAGGTCGT
Found at i:1640201 original size:30 final size:30
Alignment explanation
Indices: 1640165--1640241 Score: 136
Period size: 30 Copynumber: 2.6 Consensus size: 30
1640155 TGGAGGTCGT
*
1640165 TGGGCGTGCATGGAGGTCGTTGGGCGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1640195 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
*
1640225 TAGGCGTGCATGGAGGT
1 TGGGCGTGCATGGAGGT
1640242 GCTGGTAGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.10, C:0.17, G:0.49, T:0.23
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
Found at i:1640280 original size:49 final size:49
Alignment explanation
Indices: 1640203--1640301 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
1640193 CCTGGGCGTG
1640203 CATGGAGGTCGTTGGGCGTGCATAGGCGTGCATGGAGGTGCTGGTAGGT
1 CATGGAGGTCGTTGGGCGTGCATAGGCGTGCATGGAGGTGCTGGTAGGT
* *
1640252 CATGGAGGTCGTTGGGCGTGCCTGGGCGTGCATGGAGGTGCTGGTAGGT
1 CATGGAGGTCGTTGGGCGTGCATAGGCGTGCATGGAGGTGCTGGTAGGT
1640301 C
1 C
1640302 GCAGGGCATG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.12, C:0.16, G:0.47, T:0.24
Consensus pattern (49 bp):
CATGGAGGTCGTTGGGCGTGCATAGGCGTGCATGGAGGTGCTGGTAGGT
Found at i:1640332 original size:29 final size:29
Alignment explanation
Indices: 1640297--1640383 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
1640287 AGGTGCTGGT
*
1640297 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* **
1640326 AGGTCGCTGGGCGTGCATGGCGACCTAGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* *
1640355 AGGTCGCCGGACGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
1640384 CCCGGGACTG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.17, C:0.30, G:0.37, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:1648735 original size:2 final size:2
Alignment explanation
Indices: 1648730--1648772 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1648720 TATGTGTGTG
1648730 TA 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
1648772 T
1 T
1648773 TACACGGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1652121 original size:27 final size:27
Alignment explanation
Indices: 1652083--1652151 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
1652073 TCTAATAAAC
1652083 ATATTCCAATTAAATAATTTTCAACTA
1 ATATTCCAATTAAATAATTTTCAACTA
*
1652110 ATATTCCAATTAAATAATTTTTAACTA
1 ATATTCCAATTAAATAATTTTCAACTA
1652137 ATATTCCAATTAAAT
1 ATATTCCAATTAAAT
1652152 CTTAATTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATTCCAATTAAATAATTTTCAACTA
Found at i:1653362 original size:199 final size:200
Alignment explanation
Indices: 1652879--1653425 Score: 564
Period size: 199 Copynumber: 2.7 Consensus size: 200
1652869 AAATTATTTT
* * *
1652879 AAAAACAAAACGAGGCT-AAACCGGT-AAAA-TATCGAAACTTTTTATATAGAATGTATTCGAAT
1 AAAAACAAAACGAGGCTGAAACCGATAAAAAGTATCGAAACTTTTTATATAAAATGTA-TGGAAT
* *
1652941 AAATATCGATACTTTTCCACAAATATAGATACTTTCAAATTTAAAAAAAATATATATGGAAAATG
65 AAGTATCGATACTTTTCCACAAATATAGATACTTTCAAATTT---TAAAA-A-A-ATGGAAAATG
** * * *
1653006 AGAATGCTGCAAAGTATCGATACTTTTATTTCTTTGCTTCCTTATAAATAATCGTTATTGTTTTA
124 AG-ATGCTGCAAAGTATCGATACTTCAATTTCTATGCTTCCTTATAAACAATCGTTA-T-TTATA
1653071 CTAAGGTAACCAATA
186 CTAAGGTAACCAATA
* * * *
1653086 AAAAATAAAACAAGGC-GAAACCAGA-AAAAAGTACCGAAACTTTTTATATAAAATGCATGTGAA
1 AAAAACAAAACGAGGCTGAAACC-GATAAAAAGTATCGAAACTTTTTATATAAAATGTATG-GAA
*
1653149 T-AGTATCGATACTTTTCCACAAATATCGATACTTTCAAATTTTAAAAAAATGGAAAATGAGATG
64 TAAGTATCGATACTTTTCCACAAATATAGATACTTTCAAATTTTAAAAAAATGGAAAATGAGAT-
* * *
1653213 GCTGCAAA-TATTGATACTTCAATTTCTCATGCTTCCTTATAAGCAA-CTGTTA-TTATATTAAG
128 GCTGCAAAGTATCGATACTTCAATTTCT-ATGCTTCCTTATAAACAATC-GTTATTTATACTAAG
**
1653275 GTAACTGATA
191 GTAACCAATA
* * * *
1653285 TAAAACAAAACGA-GCTGATACCGATAAAAAGTATTGAAAATTTTTATATAAAATGTA-GGAAAT
1 AAAAACAAAACGAGGCTGAAACCGATAAAAAGTATCGAAACTTTTTATATAAAATGTATGG-AAT
* ** * *
1653348 AAGTATCGATACTTTTACACAAATATTA-ATACTTTTGAA--TTAAAAAAATAGAAAATGAGAAG
65 AAGTATCGATACTTTTCCACAAATA-TAGATACTTTCAAATTTTAAAAAAATGGAAAATGAGATG
* *
1653410 TTGCAAAATATCGATA
129 CTGCAAAGTATCGATA
1653426 TTTTCTACAA
Statistics
Matches: 290, Mismatches: 36, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
196 7 0.02
197 28 0.10
198 8 0.03
199 91 0.31
200 1 0.00
201 19 0.07
202 39 0.13
203 1 0.00
204 1 0.00
205 4 0.01
207 19 0.07
208 45 0.16
209 27 0.09
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (200 bp):
AAAAACAAAACGAGGCTGAAACCGATAAAAAGTATCGAAACTTTTTATATAAAATGTATGGAATA
AGTATCGATACTTTTCCACAAATATAGATACTTTCAAATTTTAAAAAAATGGAAAATGAGATGCT
GCAAAGTATCGATACTTCAATTTCTATGCTTCCTTATAAACAATCGTTATTTATACTAAGGTAAC
CAATA
Found at i:1653535 original size:72 final size:72
Alignment explanation
Indices: 1653398--1653535 Score: 172
Period size: 73 Copynumber: 1.9 Consensus size: 72
1653388 TAAAAAAATA
* * *
1653398 GAAAATGAGAAGTTGCAAAATATCGATATTTTCTACAAGTATTAAGACTTTCGAATTTAAAAAAA
1 GAAAATAAGAAGTTGCAAAATATCGATATTTTCCACAAGTATCAAGACTTTCGAATTTAAAAAAA
1653463 AACATGG
66 AACATGG
* * * * *
1653470 GAAAATAAGAAGGTTGCAAAGTATTGATACTTTTCCACAAGTATCGATAC-TTCGAA-TTAATAA
1 GAAAATAAGAA-GTTGCAAAATATCGATA-TTTTCCACAAGTATCAAGACTTTCGAATTTAAAAA
1653533 AAA
64 AAA
1653536 TCTTTTCAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
72 19 0.34
73 21 0.38
74 16 0.29
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (72 bp):
GAAAATAAGAAGTTGCAAAATATCGATATTTTCCACAAGTATCAAGACTTTCGAATTTAAAAAAA
AACATGG
Found at i:1653771 original size:100 final size:100
Alignment explanation
Indices: 1653548--1653963 Score: 474
Period size: 99 Copynumber: 4.2 Consensus size: 100
1653538 TTTTCAACGA
** *
1653548 TTAAGTTGT-AATATTTTATTGTTTACATTATTATTATA-CTTATAAACAAATTGGTAGC-AAGT
1 TTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTT-TAAACAAACTGGTAGCTAA-T
* * * * * * * *
1653610 TT-ATGTAATAGGTGGCGCATAATTT-TTTTAATCAG
64 TTAACGTAATATGTTGCACCTATTTTATTTTAACCGG
*
1653645 TTAAG-TGTAAATATTTTATCGTTTACATTATTATGTTATACCTTTAAACAAACTGGTAGCTAAT
1 TTAAGTTGTAAATATTTTACCGTTTACATTATTA--TTATACCTTTAAACAAACTGGTAGCTAAT
* *
1653709 TTAACGTAATAAGTTGCATCT-TTTTATTTTAACCGG
64 TTAACGTAATATGTTGCACCTATTTTATTTTAACCGG
* * * *
1653745 TTAAGTTGTAAATATTTTACCG-TTACATTATTATTATATCGTTAAACAAACAT-GTAGTTAGTT
1 TTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAAC-TGGTAGCTAATT
* *
1653808 TAACGTAATATGTTACACCTATTTTATTTTAACAGG
65 TAACGTAATATGTTGCACCTATTTTATTTTAACCGG
* *
1653844 TTAAGTTGTAAATATTTTACAGTTTACATTATTATTATACATTTAAACAAACTGGTAGCT-ATTT
1 TTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACTGGTAGCTAATTT
* * *
1653908 AACGTAATATGTTGCGCCTACTTTATTTTAATCGG
66 AACGTAATATGTTGCACCTATTTTATTTTAACCGG
*
1653943 TTAAGTTGTAATTATTATTAC
1 TTAAGTTGTAAATATT-TTAC
1653964 ATTATCTATA
Statistics
Matches: 274, Mismatches: 32, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
96 3 0.01
97 28 0.10
98 41 0.15
99 111 0.41
100 76 0.28
101 15 0.05
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.44
Consensus pattern (100 bp):
TTAAGTTGTAAATATTTTACCGTTTACATTATTATTATACCTTTAAACAAACTGGTAGCTAATTT
AACGTAATATGTTGCACCTATTTTATTTTAACCGG
Found at i:1654118 original size:21 final size:21
Alignment explanation
Indices: 1654092--1654143 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1654082 CTCAAATGTT
1654092 AAAGTATCGAACATAATAGAA
1 AAAGTATCGAACATAATAGAA
1654113 AAAGTATCGAACATAATAGAA
1 AAAGTATCGAACATAATAGAA
1654134 AAAGTATCGA
1 AAAGTATCGA
1654144 TATTTTACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (21 bp):
AAAGTATCGAACATAATAGAA
Found at i:1654389 original size:68 final size:69
Alignment explanation
Indices: 1654217--1654391 Score: 176
Period size: 68 Copynumber: 2.5 Consensus size: 69
1654207 AAAAAAGTTC
* * *
1654217 GATACTTTGCAGTCTTCTCATTTTCTATATTTTTTAATTCGAAAGTATTAATATTTGTGGAAAAT
1 GATACTTTGCAAT-TTCTCATTTTC-ATATTTTTAAATTCGAAAGTATCAATATTTGTGGAAAAT
*
1654282 ATTATT
64 AGTATT
* * * * * * * *
1654288 GAAACATTGCAGCTTTCTTATTTTTCAT-TTTTTAAATTTGAAAGTATCGATATTTGT-GTATA-
1 GATACTTTGCA-ATTTCTCA-TTTTCATATTTTTAAATTCGAAAGTATCAATATTTGTGGAAAAT
1654350 AGTATT
64 AGTATT
1654356 GATACTTTGCAATATTCTCATTTTCATATTTTTAAA
1 GATACTTTGCAAT-TTCTCATTTTCATATTTTTAAA
1654392 ATTTTAAGTA
Statistics
Matches: 85, Mismatches: 15, Indels: 11
0.77 0.14 0.10
Matches are distributed among these distances:
67 8 0.09
68 27 0.32
69 3 0.04
70 25 0.29
71 16 0.19
72 6 0.07
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (69 bp):
GATACTTTGCAATTTCTCATTTTCATATTTTTAAATTCGAAAGTATCAATATTTGTGGAAAATAG
TATT
Found at i:1655476 original size:15 final size:15
Alignment explanation
Indices: 1655456--1655495 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1655446 CATGATCACT
1655456 TCACATAGCTTCTTA
1 TCACATAGCTTCTTA
1655471 TCACATAGCTTCTTA
1 TCACATAGCTTCTTA
*
1655486 TCACGTAGCT
1 TCACATAGCT
1655496 CATATAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (15 bp):
TCACATAGCTTCTTA
Found at i:1659250 original size:21 final size:21
Alignment explanation
Indices: 1659206--1659280 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 21
1659196 TGAATTTGTT
*
1659206 CCGAATGACCGCATAGAAATGTC
1 CCGAATGACCACATAG--ATGTC
1659229 CCGAATGACCACATAGATGTC
1 CCGAATGACCACATAGATGTC
* *
1659250 CCGAATGA-C-CATATATATC
1 CCGAATGACCACATAGATGTC
1659269 CCGAATGACCAC
1 CCGAATGACCAC
1659281 TCTTTAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.34
20 2 0.04
21 14 0.30
23 15 0.32
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
CCGAATGACCACATAGATGTC
Found at i:1662640 original size:7 final size:7
Alignment explanation
Indices: 1662628--1662668 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
1662618 TGCTAATATT
1662628 AAAAAAG
1 AAAAAAG
1662635 AAAAAAG
1 AAAAAAG
1662642 AAAAAA-
1 AAAAAAG
1662648 AGAAAAAG
1 A-AAAAAG
1662656 AAAAAAG
1 AAAAAAG
1662663 AAAAAA
1 AAAAAA
1662669 ACCAAAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 1 0.03
7 30 0.94
8 1 0.03
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1662653 original size:13 final size:13
Alignment explanation
Indices: 1662628--1662667 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 13
1662618 TGCTAATATT
1662628 AAAAAAGAAAAAAG
1 AAAAAAG-AAAAAG
1662642 AAAAAAAGAAAAAG
1 -AAAAAAGAAAAAG
1662656 AAAAAAGAAAAA
1 AAAAAAGAAAAA
1662668 AACCAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 12 0.48
14 6 0.24
15 7 0.28
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:1662655 original size:21 final size:21
Alignment explanation
Indices: 1662629--1662669 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1662619 GCTAATATTA
1662629 AAAAAGAAAAAAGAAAAAAAG
1 AAAAAGAAAAAAGAAAAAAAG
1662650 AAAAAGAAAAAAGAAAAAAA
1 AAAAAGAAAAAAGAAAAAAA
1662670 CCAAAAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAAGAAAAAAAG
Found at i:1662675 original size:21 final size:21
Alignment explanation
Indices: 1662629--1662676 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1662619 GCTAATATTA
*
1662629 AAAAAGAAAAAAGAAAAAAAG
1 AAAAAGAAAAAAGAAAAAAAC
1662650 AAAAAGAAAAAAGAAAAAAAC
1 AAAAAGAAAAAAGAAAAAAAC
*
1662671 CAAAAG
1 AAAAAG
1662677 TTAGCTACAT
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:0.83, C:0.04, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAAGAAAAAAAC
Found at i:1663362 original size:21 final size:21
Alignment explanation
Indices: 1663324--1663369 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1663314 AAAACAAAAA
*
1663324 AAAAGAAAAAACATGCAA-GT
1 AAAAGAAAAAACAAGCAAGGT
*
1663344 AAAATAAAAAACAAAGCAAGGT
1 AAAAGAAAAAAC-AAGCAAGGT
1663366 AAAA
1 AAAA
1663370 ATGATACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 5 0.23
22 6 0.27
ACGTcount: A:0.70, C:0.09, G:0.13, T:0.09
Consensus pattern (21 bp):
AAAAGAAAAAACAAGCAAGGT
Found at i:1663929 original size:2 final size:2
Alignment explanation
Indices: 1663919--1663984 Score: 50
Period size: 2 Copynumber: 34.5 Consensus size: 2
1663909 GATAAAAAAA
* *
1663919 AT AT A- AT AT AT AT AT AT AT AT GT TT A- AT ACT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * *
1663959 AA AC AT TT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1663985 ACAGTATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
1 4 0.08
2 45 0.88
3 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Done.