Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 5 of 199
Found at i:1572126 original size:160 final size:159
Alignment explanation
Indices: 1571949--1572464 Score: 537
Period size: 175 Copynumber: 3.1 Consensus size: 159
1571939 TACAAACAAT
* *
1571949 ATTACAATATCCATACAAAATTACAATATTCATACAAACA-A-T-ATTACAATATTCATACAA-A
1 ATTACAATATCCATACAAAATTACAATATTCATACAAA-ATACTAATT-CAAAACT-ATA-AATA
* *
1572010 CAATATTACATATTCATACAA-AATTACAA-AAT-TACAAAATTACAAAATTCATACAAAATACT
62 CAAAATT--A-ATT-ATAAAATAATTACAATAATATACAAAATTACAAAATTCATACAAAATACT
*
1572072 AATCCAAAACTATAAATACAAAATTAATTATAAAATA
123 AATCAAAAACTATAAATACAAAATTAATTATAAAATA
* * *
1572109 ATTACAATATTCATACAACATTATAATATTCATACAAAATACTAATTCAAAACTATAAATACAAA
1 ATTACAATATCCATACAAAATTACAATATTCATACAAAATACTAATTCAAAACTATAAATACAAA
* * * *
1572174 ATTAATTATAAAATAATTACAATATTCATACAACATTATAATATTCATACAAAATACTAATCAAA
66 ATTAATTATAAAATAATTACAATAAT-ATACAAAATTACAAAATTCATACAAAATACTAATCAAA
*
1572239 AACTATAAATACAAAACTATAAATATTGTAATTACA-A
130 AACTATAAATACAAAA-T-T--A-ATTATAA--A-ATA
* * *
1572276 AATACAAAATTCATACAAAATTACAAAATTACAATATTCATACAAAATACTAA-TCAAAAAATAT
1 ATTAC--AA-T-AT-C--CA-TACAAAATTACAATATTCATACAAAATACTAATTC-AAAACTAT
* * *
1572340 AAATACAAAATTAATTATAAAATAATTAAAATATTCATACAAAATTACAATATTCATACAAAATA
57 AAATACAAAATTAATTATAAAATAATTACAATAAT-ATACAAAATTACAAAATTCATACAAAATA
*
1572405 CTAATAAAAAACTATAAATACAAAATTAATTATAAAATA
121 CTAATCAAAAACTATAAATACAAAATTAATTATAAAATA
*
1572444 ATTACAATATTCATACAAAAT
1 ATTACAATATCCATACAAAAT
1572465 ACTAATAAAA
Statistics
Matches: 303, Mismatches: 27, Indels: 52
0.79 0.07 0.14
Matches are distributed among these distances:
156 5 0.02
157 11 0.04
158 3 0.01
159 3 0.01
160 103 0.34
161 8 0.03
162 4 0.01
164 3 0.01
165 7 0.02
166 2 0.01
167 7 0.02
168 7 0.02
169 2 0.01
170 7 0.02
171 3 0.01
173 1 0.00
174 4 0.01
175 123 0.41
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (159 bp):
ATTACAATATCCATACAAAATTACAATATTCATACAAAATACTAATTCAAAACTATAAATACAAA
ATTAATTATAAAATAATTACAATAATATACAAAATTACAAAATTCATACAAAATACTAATCAAAA
ACTATAAATACAAAATTAATTATAAAATA
Found at i:1572136 original size:19 final size:19
Alignment explanation
Indices: 1572109--1572145 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1572099 TTATAAAATA
1572109 ATTACAATATTCATACAAC
1 ATTACAATATTCATACAAC
*
1572128 ATTATAATATTCATACAA
1 ATTACAATATTCATACAA
1572146 AATACTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTACAATATTCATACAAC
Found at i:1572256 original size:14 final size:14
Alignment explanation
Indices: 1572237--1572263 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1572227 ATACTAATCA
1572237 AAAACTATAAATAC
1 AAAACTATAAATAC
1572251 AAAACTATAAATA
1 AAAACTATAAATA
1572264 TTGTAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAACTATAAATAC
Found at i:1572302 original size:8 final size:8
Alignment explanation
Indices: 1572268--1572309 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
1572258 TAAATATTGT
1572268 AATTACAA
1 AATTACAA
1572276 AA-TACAA
1 AATTACAA
1572283 AATTCATACAA
1 AA-T--TACAA
1572294 AATTACAA
1 AATTACAA
1572302 AATTACAA
1 AATTACAA
1572310 TATTCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
7 7 0.23
8 15 0.50
10 1 0.03
11 7 0.23
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (8 bp):
AATTACAA
Found at i:1572316 original size:27 final size:26
Alignment explanation
Indices: 1572268--1572323 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
1572258 TAAATATTGT
1572268 AATTACAAAATACAAAATTCATACAA
1 AATTACAAAATACAAAATTCATACAA
*
1572294 AATTACAAAATTACAATATTCATACAA
1 AATTACAAAA-TACAAAATTCATACAA
1572321 AAT
1 AAT
1572324 ACTAATCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (26 bp):
AATTACAAAATACAAAATTCATACAA
Found at i:1572373 original size:61 final size:61
Alignment explanation
Indices: 1572302--1572525 Score: 207
Period size: 61 Copynumber: 3.4 Consensus size: 61
1572292 AAAATTACAA
1572302 AATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACAAAATTAATTATAAAAT
* * *
1572363 AATTAAAATATTCATACAAAATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAA
1 AATTACAATATTCATACAAAA-TAC--TA---AT-CAAAA-AAT-AT-AAATAC-A-AAAT----
*
1572428 AATTAATTATAAAAT
50 TA---ATTATAAAAT
* *
1572443 AATTACAATATTCATACAAAATACTAAT-AAAAAACTATAAATATAAAACTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATCAAAAAA-TATAAATACAAAATTAATTATAAAAT
1572504 AATTACAATATTCATACAAAAT
1 AATTACAATATTCATACAAAAT
1572526 TATAATATTC
Statistics
Matches: 133, Mismatches: 10, Indels: 40
0.73 0.05 0.22
Matches are distributed among these distances:
61 52 0.39
62 3 0.02
64 3 0.02
67 2 0.02
68 8 0.06
69 3 0.02
70 6 0.05
71 8 0.06
72 6 0.05
73 4 0.03
74 2 0.02
77 3 0.02
79 3 0.02
80 30 0.23
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (61 bp):
AATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACAAAATTAATTATAAAAT
Found at i:1572391 original size:19 final size:19
Alignment explanation
Indices: 1572363--1572645 Score: 129
Period size: 19 Copynumber: 14.3 Consensus size: 19
1572353 ATTATAAAAT
*
1572363 AATTAAAATATTCATACAA
1 AATTACAATATTCATACAA
1572382 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
** *
1572401 AA-TACTAATA-AAAAACTATA
1 AATTAC-AATATTCATAC-A-A
*
1572421 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
1572442 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
** *
1572462 AA-TACTAATA-AAAAACTATA
1 AATTAC-AATATTCATAC-A-A
* *
1572482 AATATAAAACTAATT-ATAAAA
1 AAT-TACAA-T-ATTCATACAA
1572503 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
* *
1572523 AATTATAATATTCATATAA
1 AATTACAATATTCATACAA
*
1572542 AATTACAA-AAT--TACAA
1 AATTACAATATTCATACAA
* * **
1572558 TATCCATACAAAATTACAATA-TT
1 AAT---TACAATATT-C-ATACAA
1572581 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
1572600 AATTACAATATTCATACAAA
1 AATTACAATATTCATAC-AA
*
1572620 AAGTTACAATATACATACAA
1 AA-TTACAATATTCATACAA
1572640 AATTAC
1 AATTAC
1572646 TCATTGGCGC
Statistics
Matches: 201, Mismatches: 32, Indels: 62
0.68 0.11 0.21
Matches are distributed among these distances:
16 6 0.03
18 17 0.08
19 89 0.44
20 39 0.19
21 26 0.13
22 11 0.05
23 11 0.05
24 2 0.01
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:1572425 original size:27 final size:27
Alignment explanation
Indices: 1572395--1572490 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 27
1572385 TACAATATTC
1572395 ATACAAAATACTAATAAAAAACTATAA
1 ATACAAAATACTAATAAAAAACTATAA
* * **
1572422 ATACAAAATTAATTATAAAATAATTACAATATTC
1 ATACAAAA-TACTAAT-AAA-AA--AC--TATAA
1572456 ATACAAAATACTAATAAAAAACTATAA
1 ATACAAAATACTAATAAAAAACTATAA
*
1572483 ATATAAAA
1 ATACAAAA
1572491 CTAATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
27 18 0.34
28 5 0.09
29 5 0.09
30 2 0.04
31 2 0.04
32 5 0.09
33 5 0.09
34 11 0.21
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (27 bp):
ATACAAAATACTAATAAAAAACTATAA
Found at i:1572504 original size:80 final size:79
Alignment explanation
Indices: 1572443--1572620 Score: 188
Period size: 80 Copynumber: 2.3 Consensus size: 79
1572433 ATTATAAAAT
* *
1572443 AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATATAAAACTAATTATAAAATAATT
1 AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAATTAATTATAAAATAA-T
1572508 ACAATATTCATACAA
65 ACAATATTCATACAA
* * * ** * *
1572523 AATTATAATATTCATATAAAATTAC-AA-AATTACAA-TATCCATACAAAATTACAATAT-TAAT
1 AATTACAATATTCATACAAAA-TACTAATAA--AAAACTATAAATACAAAATTA-ATTATAAAAT
1572584 --TACAATATTCATACAA
62 AATACAATATTCATACAA
1572600 AATTACAATATTCATACAAAA
1 AATTACAATATTCATACAAAA
1572621 AGTTACAATA
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
77 35 0.42
79 2 0.02
80 36 0.43
81 10 0.12
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (79 bp):
AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAATTAATTATAAAATAATA
CAATATTCATACAA
Found at i:1572532 original size:61 final size:61
Alignment explanation
Indices: 1572382--1572525 Score: 270
Period size: 61 Copynumber: 2.4 Consensus size: 61
1572372 ATTCATACAA
*
1572382 AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAACTAATTATAAAAT
*
1572443 AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATATAAAACTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAACTAATTATAAAAT
1572504 AATTACAATATTCATACAAAAT
1 AATTACAATATTCATACAAAAT
1572526 TATAATATTC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 81 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (61 bp):
AATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAACTAATTATAAAAT
Found at i:1572553 original size:27 final size:27
Alignment explanation
Indices: 1572518--1572607 Score: 117
Period size: 27 Copynumber: 3.2 Consensus size: 27
1572508 ACAATATTCA
* *
1572518 TACAAAATTATAATATTCATATAAAAT
1 TACAAAATTACAATATTCATACAAAAT
*
1572545 TACAAAATTACAATATCCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
1572572 TACAATATTAATTACAATATTCATACAAAAT
1 TAC-A-A--AATTACAATATTCATACAAAAT
1572603 TACAA
1 TACAA
1572608 TATTCATACA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
27 27 0.49
28 1 0.02
29 2 0.04
30 1 0.02
31 24 0.44
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.32
Consensus pattern (27 bp):
TACAAAATTACAATATTCATACAAAAT
Found at i:1572567 original size:141 final size:138
Alignment explanation
Indices: 1572288--1572602 Score: 414
Period size: 141 Copynumber: 2.3 Consensus size: 138
1572278 TACAAAATTC
1572288 ATACAAAATTAC---AA-AATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACAAA
1 ATACAAAATTACAATAATAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACAAA
*
1572349 ATTAATTATAAAATAATTAAAATATTCATACAAAATTACAATATTCATACAAAATACTAATAAAA
66 ACTAATTATAAAATAATTAAAATATTCATACAAAATTACAATATTCATACAAAATACTAATAAAA
1572414 AACTATAA
131 AACTATAA
1572422 ATACAAAATTA-ATTATAAAATAATTACAATATTCATACAAAATACTAAT-AAAAAACTATAAAT
1 ATACAAAATTACA--AT--AATAATTACAATATTCATACAAAATACTAATCAAAAAA-TATAAAT
* * * *
1572485 ATAAAACTAATTATAAAATAATTACAATATTCATACAAAATTATAATATTCATATAAAATTAC-A
61 ACAAAACTAATTATAAAATAATTAAAATATTCATACAAAATTACAATATTCATACAAAA-TACTA
* **
1572549 A-AATTACAA-TATCC
125 ATAA--AAAACTATAA
*
1572563 ATACAAAATTACAATATTAATTACAATATTCATACAAAAT
1 ATACAAAATTACAATAATAATTACAATATTCATACAAAAT
1572603 TACAATATTC
Statistics
Matches: 159, Mismatches: 9, Indels: 22
0.84 0.05 0.12
Matches are distributed among these distances:
134 11 0.07
138 24 0.15
140 12 0.08
141 105 0.66
142 7 0.04
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.30
Consensus pattern (138 bp):
ATACAAAATTACAATAATAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACAAA
ACTAATTATAAAATAATTAAAATATTCATACAAAATTACAATATTCATACAAAATACTAATAAAA
AACTATAA
Found at i:1572588 original size:31 final size:31
Alignment explanation
Indices: 1572550--1572611 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1572540 AAAATTACAA
1572550 AATTACAATATCCATACAAAATTACAATATT
1 AATTACAATATCCATACAAAATTACAATATT
*
1572581 AATTACAATATTCATACAAAATTACAATATT
1 AATTACAATATCCATACAAAATTACAATATT
1572612 CATACAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.34
Consensus pattern (31 bp):
AATTACAATATCCATACAAAATTACAATATT
Found at i:1572697 original size:27 final size:27
Alignment explanation
Indices: 1572654--1572722 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
1572644 ACTCATTGGC
*
1572654 GCCTCCCTATGATGCACTTTTAATGGT
1 GCCTCCCTATGAGGCACTTTTAATGGT
*
1572681 GCCTCCCTATAAGGCACTTTTAATGGT
1 GCCTCCCTATGAGGCACTTTTAATGGT
1572708 GCCTCCCTATGAGGC
1 GCCTCCCTATGAGGC
1572723 GCCACCCGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (27 bp):
GCCTCCCTATGAGGCACTTTTAATGGT
Found at i:1573833 original size:3 final size:3
Alignment explanation
Indices: 1573825--1573863 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1573815 ATTTAACCCT
1573825 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1573864 TATTATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1573870 original size:3 final size:3
Alignment explanation
Indices: 1573864--1573908 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1573854 AATAATAATA
1573864 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1573909 AAATAACGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1574038 original size:40 final size:40
Alignment explanation
Indices: 1573983--1574064 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
1573973 ATTATAAAAG
*
1573983 TACAATTTTATATTAGAGTAATTGAATCAGTTCTTAAATA
1 TACAATTTTATATTAGAGTAATTGAATAAGTTCTTAAATA
1574023 TACAATTTTATATTAGAGTAATTGAATAAGTTCTTAAATA
1 TACAATTTTATATTAGAGTAATTGAATAAGTTCTTAAATA
1574063 TA
1 TA
1574065 ATAATTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (40 bp):
TACAATTTTATATTAGAGTAATTGAATAAGTTCTTAAATA
Found at i:1580480 original size:48 final size:51
Alignment explanation
Indices: 1580418--1580542 Score: 157
Period size: 48 Copynumber: 2.5 Consensus size: 51
1580408 AATATGCTTG
* **
1580418 AGATTTAATTCTTATACTTTAATTTCAATTTT-A-GTTATGCTTA-AATTA
1 AGATTTAATCCTTATACTTTAATTTCAATTTTAACAATATGCTTATAATTA
* *
1580466 AGATTTAATCCTTATAGTTTAATTTCAATTTTAACCACAATATGCTTATATTTA
1 AGATTTAATCCTTATACTTTAATTTCAATTTT-A--ACAATATGCTTATAATTA
1580520 AGATTTAATCCTTATACTTTAAT
1 AGATTTAATCCTTATACTTTAAT
1580543 CTTTTAACAT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
48 30 0.46
52 1 0.02
53 8 0.12
54 26 0.40
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (51 bp):
AGATTTAATCCTTATACTTTAATTTCAATTTTAACAATATGCTTATAATTA
Found at i:1582631 original size:2 final size:2
Alignment explanation
Indices: 1582626--1582665 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1582616 TAAACAAAAG
1582626 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
1582666 AAAGCAGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1588169 original size:107 final size:107
Alignment explanation
Indices: 1587982--1588179 Score: 238
Period size: 107 Copynumber: 1.9 Consensus size: 107
1587972 TTAGGGTGAA
* * * * *
1587982 ATATCTCTATTAATATTGAATTTTTTATCGAGTTTAGTGTTACGAGCCAATCAGATATCAGTTTA
1 ATATCTCTACTAACATTAAATTTTTTATCGAGTTTAGTGTTACGAGCCAATCAGACATCAATTTA
* * *
1588047 ATTGGATAATAACAAAAATATCCTTATTTTACAATGTAAATT
66 ATTGAAAAATAACAAAAATACCCTTATTTTACAATGTAAATT
* * **
1588089 ATATCTCTACTAACATTAAACTTTTTT-TGGAGTTTGGTGTTACGAGTTAA-CAAGACATCAATT
1 ATATCTCTACTAACATTAAA-TTTTTTATCGAGTTTAGTGTTACGAGCCAATC-AGACATCAATT
* *
1588152 TAGTTGAAAAATGACAAAAATACCCTTA
64 TAATTGAAAAATAACAAAAATACCCTTA
1588180 ACTTACAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
106 1 0.01
107 68 0.91
108 6 0.08
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (107 bp):
ATATCTCTACTAACATTAAATTTTTTATCGAGTTTAGTGTTACGAGCCAATCAGACATCAATTTA
ATTGAAAAATAACAAAAATACCCTTATTTTACAATGTAAATT
Found at i:1593650 original size:6 final size:6
Alignment explanation
Indices: 1593639--1593673 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
1593629 ATAAACCAAC
1593639 GCATAA GCATAA GCATAA GCATAA GCATAA GCATA
1 GCATAA GCATAA GCATAA GCATAA GCATAA GCATA
1593674 TAAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
GCATAA
Found at i:1597836 original size:18 final size:19
Alignment explanation
Indices: 1597795--1597837 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1597785 AAGTTTTATC
* *
1597795 TATTTTTAATTTTGAATAT
1 TATTTATAATTTTGAAAAT
1597814 T-TTTATAATTTT-AAAAT
1 TATTTATAATTTTGAAAAT
1597831 TATTTAT
1 TATTTAT
1597838 TGACATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 15 0.71
19 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTATAATTTTGAAAAT
Found at i:1603617 original size:18 final size:19
Alignment explanation
Indices: 1603577--1603622 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
1603567 CATTAATTAT
1603577 ATTTTAAATATGTATTTAG
1 ATTTTAAATATGTATTTAG
1603596 ATTTT-AATAGTGTATTTA-
1 ATTTTAAATA-TGTATTTAG
1603614 ATTTATAAA
1 ATTT-TAAA
1603623 AAAAATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.33
19 14 0.58
20 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (19 bp):
ATTTTAAATATGTATTTAG
Found at i:1604437 original size:31 final size:31
Alignment explanation
Indices: 1604343--1604440 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
1604333 ACTCATGTGC
* * * * *
1604343 CAAAGTGAACATTGAACTTAAACTTAAATAT
1 CAAATTGAACATTAAAATTAAAATTAGATAT
* *
1604374 CAAATTAGAACA-AAAAAAT-AAATT-GAAGTAT
1 CAAATT-GAACATTAAAATTAAAATTAG-A-TAT
1604405 CAAATTGAACATTAAAATTAAAATTAGATAT
1 CAAATTGAACATTAAAATTAAAATTAGATAT
1604436 CAAAT
1 CAAAT
1604441 AATATTCAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
30 10 0.19
31 30 0.58
32 11 0.21
33 1 0.02
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (31 bp):
CAAATTGAACATTAAAATTAAAATTAGATAT
Found at i:1604563 original size:34 final size:34
Alignment explanation
Indices: 1604520--1604592 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
1604510 TAAGAACAAG
1604520 TCATGATAGATATTGTATTGGACAAGTTTCACCA
1 TCATGATAGATATTGTATTGGACAAGTTTCACCA
1604554 TCATGATAGATATTGTATTGGACAAGTTTCACCA
1 TCATGATAGATATTGTATTGGACAAGTTTCACCA
1604588 TCATG
1 TCATG
1604593 GTTTGGTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Consensus pattern (34 bp):
TCATGATAGATATTGTATTGGACAAGTTTCACCA
Found at i:1615453 original size:108 final size:109
Alignment explanation
Indices: 1615282--1615568 Score: 418
Period size: 108 Copynumber: 2.6 Consensus size: 109
1615272 AATTTGGCTA
*
1615282 AACGTGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
1 AACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
*
1615347 TTA-TTTTGAAAA-TTTTTGAAAAGGATATTAAG-TCATTTGGTGG
66 TTATTTTTGAAAAGTTTTT-AAAAGGATATTAAGCT-ATTTGGTCG
* *
1615390 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCC
1 AACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
*
1615455 TTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCG
66 TTATTTTTGAAAAGTTTTTAAAAGGATATTAAGCTATTTGGTCG
* * * *
1615499 AACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCCAAATGCAAAATAT
1 AACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTT-CCAAACGCAAAATAT
1615564 TGCCT
62 TGCCT
1615569 CAAGTTGAAA
Statistics
Matches: 161, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
108 65 0.40
109 36 0.22
110 6 0.04
111 25 0.16
112 11 0.07
113 18 0.11
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (109 bp):
AACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
TTATTTTTGAAAAGTTTTTAAAAGGATATTAAGCTATTTGGTCG
Found at i:1615927 original size:10 final size:11
Alignment explanation
Indices: 1615896--1615938 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
1615886 CGTGAATTAC
*
1615896 AAAATATTTAT
1 AAAATATATAT
1615907 AAAATATATAT
1 AAAATATATAT
*
1615918 AAAAATATATTTT
1 -AAAATATA-TAT
1615931 AAAATATA
1 AAAATATA
1615939 AAGGATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
12 16 0.57
13 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATATATAT
Found at i:1615969 original size:17 final size:17
Alignment explanation
Indices: 1615949--1615982 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1615939 AAGGATAAAT
*
1615949 AAATATGTATATATATA
1 AAATATGTACATATATA
*
1615966 AAATGTGTACATATATA
1 AAATATGTACATATATA
1615983 TGTAGGTACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (17 bp):
AAATATGTACATATATA
Found at i:1616186 original size:16 final size:16
Alignment explanation
Indices: 1616165--1616203 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1616155 TGAATTATAA
*
1616165 AAAAATAA-AGTAAGAT
1 AAAAATAACA-TAAAAT
1616181 AAAAATAACATAAAAT
1 AAAAATAACATAAAAT
1616197 AAAAATA
1 AAAAATA
1616204 TATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAATAACATAAAAT
Found at i:1616389 original size:3 final size:3
Alignment explanation
Indices: 1616381--1616498 Score: 109
Period size: 3 Copynumber: 39.3 Consensus size: 3
1616371 AAGCTATTAT
* *
1616381 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATG ATA AGTA ATA ATG AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* *
1616425 ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA GATG ATA AT-
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
* * *
1616471 ATA TTA AAA ATA ATGA AGA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA A
1616499 AAATGCTAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
2 8 0.08
3 80 0.83
4 8 0.08
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1616483 original size:48 final size:50
Alignment explanation
Indices: 1616381--1616498 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 50
1616371 AAGCTATTAT
1616381 ATAATAATAATAATAATAATAATAATATGATAAGTAATAATGATATAAATA
1 ATAATAATAATAATAATAATAATAATA-GATAAGTAATAATGATATAAATA
*
1616432 ATAATAATAATAATAATAATAATAATA-A-AAGATGATAAT-ATATTAAA-A
1 ATAATAATAATAATAATAATAATAATAGATAAG-TAATAATGATA-TAAATA
*
1616480 ATAATGAAGAA-AATAATAA
1 ATAAT-AATAATAATAATAA
1616499 AAATGCTAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
48 20 0.32
49 15 0.24
51 27 0.44
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (50 bp):
ATAATAATAATAATAATAATAATAATAGATAAGTAATAATGATATAAATA
Found at i:1619135 original size:16 final size:15
Alignment explanation
Indices: 1619114--1619147 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1619104 GAATTGAATA
1619114 ATTGTATGATATAGTT
1 ATTGTATGATATA-TT
*
1619130 ATTGTATGTTATATT
1 ATTGTATGATATATT
1619145 ATT
1 ATT
1619148 TTACTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (15 bp):
ATTGTATGATATATT
Found at i:1626289 original size:2 final size:2
Alignment explanation
Indices: 1626277--1626320 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1626267 GCCTAAGAGC
*
1626277 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1626319 AT
1 AT
1626321 TCTAAAGGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1631613 original size:14 final size:14
Alignment explanation
Indices: 1631594--1631620 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1631584 TTTCTAATAT
1631594 TTTTTTATAAATTA
1 TTTTTTATAAATTA
1631608 TTTTTTATAAATT
1 TTTTTTATAAATT
1631621 TGTTATGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTATAAATTA
Found at i:1632312 original size:43 final size:43
Alignment explanation
Indices: 1632250--1632337 Score: 144
Period size: 43 Copynumber: 2.0 Consensus size: 43
1632240 CTGAATTTAA
1632250 TTTAATTGTTTTATTTTTATTTT-AAAGCAAATAAGATTATATTT
1 TTTAATTGTTTTATTTTTATTTTGAAA-CAAATAAGATTAT-TTT
1632294 TTTAATTG-TTTATTTTTATTTTGAAACAAATAAGATTATTTT
1 TTTAATTGTTTTATTTTTATTTTGAAACAAATAAGATTATTTT
1632336 TT
1 TT
1632338 GAGTTTAGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
42 5 0.12
43 27 0.63
44 11 0.26
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (43 bp):
TTTAATTGTTTTATTTTTATTTTGAAACAAATAAGATTATTTT
Found at i:1636190 original size:5 final size:5
Alignment explanation
Indices: 1636180--1636204 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1636170 ACGGTCAATA
1636180 CGGGT CGGGT CGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT
1636205 GGCGCCTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
CGGGT
Found at i:1636249 original size:27 final size:27
Alignment explanation
Indices: 1636219--1636280 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
1636209 CCTATCAGGT
1636219 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
1636246 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
1636273 AGGCGCCA
1 AGGCGCCA
1636281 TTACTAGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:1636466 original size:21 final size:22
Alignment explanation
Indices: 1636424--1636483 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 22
1636414 GGCCTGGCCC
1636424 ATTTTTT-AAATAAACACCAAAAA
1 ATTTTTTAAAATAAA-A-CAAAAA
1636447 ATTTTTTAAAAT-AAA-AAAAA
1 ATTTTTTAAAATAAAACAAAAA
* *
1636467 GTATTTTAAAAATAAAA
1 AT-TTTTTAAAATAAAA
1636484 TTAAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 6 0.19
21 9 0.28
22 4 0.12
23 9 0.28
24 4 0.12
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (22 bp):
ATTTTTTAAAATAAAACAAAAA
Found at i:1636495 original size:24 final size:23
Alignment explanation
Indices: 1636443--1636530 Score: 94
Period size: 24 Copynumber: 3.9 Consensus size: 23
1636433 ATAAACACCA
*
1636443 AAAAAT-TTTTTAAAATAAAA--
1 AAAAATATTTTAAAAATAAAATT
*
1636463 AAAAGTATTTTAAAAATAAAATT
1 AAAAATATTTTAAAAATAAAATT
* *
1636486 -AAAATATATTTAAAAATATATTT
1 AAAAATAT-TTTAAAAATAAAATT
1636509 AAAAATATATTTAAAAATAAAA
1 AAAAATAT-TTTAAAAATAAAA
1636531 ATTCATACAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 5 0.09
21 13 0.23
22 6 0.11
23 13 0.23
24 19 0.34
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (23 bp):
AAAAATATTTTAAAAATAAAATT
Found at i:1636516 original size:10 final size:12
Alignment explanation
Indices: 1636462--1636527 Score: 91
Period size: 12 Copynumber: 5.6 Consensus size: 12
1636452 TTAAAATAAA
1636462 AAAAAGTAT-TTT
1 AAAAA-TATATTT
* *
1636474 AAAAATAAAATT
1 AAAAATATATTT
1636486 -AAAATATATTT
1 AAAAATATATTT
1636497 AAAAATATATTT
1 AAAAATATATTT
1636509 AAAAATATATTT
1 AAAAATATATTT
1636521 AAAAATA
1 AAAAATA
1636528 AAAATTCATA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
11 11 0.23
12 37 0.77
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (12 bp):
AAAAATATATTT
Found at i:1636650 original size:27 final size:27
Alignment explanation
Indices: 1636615--1636709 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
1636605 ATTATCTATA
1636615 TTTAGTATGAATATTGTAATATTATAAT
1 TTTA-TATGAATATTGTAATATTATAAT
*
1636643 TTTATATGAATATTG-CA-A-T-T--T
1 TTTATATGAATATTGTAATATTATAAT
*
1636664 TTTGTATGAATATTGTAATATTATAAT
1 TTTATATGAATATTGTAATATTATAAT
*
1636691 TTTGTATGAATATTGTAAT
1 TTTATATGAATATTGTAAT
1636710 GTCGGTATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
21 15 0.26
22 1 0.02
23 2 0.03
24 2 0.03
25 2 0.03
26 1 0.02
27 31 0.53
28 4 0.07
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.52
Consensus pattern (27 bp):
TTTATATGAATATTGTAATATTATAAT
Found at i:1636672 original size:48 final size:48
Alignment explanation
Indices: 1636619--1636762 Score: 186
Period size: 48 Copynumber: 3.0 Consensus size: 48
1636609 TCTATATTTA
* *
1636619 GTATGAATATTGTAATATTATAATTTTATATGAATATTGCAATTTTTT
1 GTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTT
* **
1636667 GTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAA-TGTCG
1 GTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTT
*
1636714 GTAT--ATATTGTAATATTGTAATTTTTTGTATGAATATTGTAATTATTTT
1 GTATGAATATTGTAATATTATAA--TTTTGTATGAATATTGTAATT-TTTT
1636763 ATAATTAATT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
45 16 0.19
47 25 0.30
48 41 0.49
49 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.52
Consensus pattern (48 bp):
GTATGAATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTT
Found at i:1636827 original size:19 final size:19
Alignment explanation
Indices: 1636805--1636842 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1636795 TATAAATTTA
*
1636805 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
1636824 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
1636843 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:1637090 original size:27 final size:28
Alignment explanation
Indices: 1637052--1637128 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
1637042 CCGGCCCGGC
*
1637052 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
1637079 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
1637106 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
1637129 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:1640689 original size:26 final size:27
Alignment explanation
Indices: 1640643--1640815 Score: 75
Period size: 26 Copynumber: 6.0 Consensus size: 27
1640633 TATGTTTTTA
1640643 TTAAATTATATTTAATAATTAT-TATT
1 TTAAATTATATTTAATAATTATATATT
*
1640669 TTAAATTATATTATAGT-ATTATATATT
1 TTAAATTATATT-TAATAATTATATATT
* * * * * * *
1640696 AT-AATTTTAGTAAATTCATATAAAAATAT
1 TTAAATTATATTTAA-TAAT-TATATAT-T
* *
1640725 TTAATATTAAGAATTTTATTAAATTATATATTTTT
1 TTAA-ATT-A-TA-TTTAAT-AATTATATA---TT
*
1640760 ATTAAATTATATTTAATAATAAT-TATT
1 -TTAAATTATATTTAATAATTATATATT
*
1640787 TTAAATTATATTTTATATTATTATATATT
1 TTAAATTATA-TTTA-ATAATTATATATT
1640816 ATGATTTTAG
Statistics
Matches: 106, Mismatches: 22, Indels: 35
0.65 0.13 0.21
Matches are distributed among these distances:
25 1 0.01
26 35 0.33
27 16 0.15
28 11 0.10
29 6 0.06
30 3 0.03
31 8 0.08
32 5 0.05
33 7 0.07
34 5 0.05
35 4 0.04
36 5 0.05
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (27 bp):
TTAAATTATATTTAATAATTATATATT
Found at i:1640880 original size:17 final size:16
Alignment explanation
Indices: 1640858--1640892 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1640848 ATATTAAGAA
1640858 TTTTATAAATTATATAT
1 TTTTATAAATT-TATAT
*
1640875 TTTTATTAATTTATAT
1 TTTTATAAATTTATAT
1640891 TT
1 TT
1640893 AATAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATAAATTTATAT
Found at i:1640928 original size:119 final size:120
Alignment explanation
Indices: 1640557--1641030 Score: 809
Period size: 119 Copynumber: 4.0 Consensus size: 120
1640547 TAGATTATAT
* *
1640557 ATTAT-TTTTATAGTATTATATATTGTGATTTTAGTAAATTCATATAAGAATAATT-ATATT--G
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* *
1640618 AATTTTATTAAATTATATGTTTTTATTAAATTATATTTAATAATTATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
* *
1640673 ATTATA--TTATAGTATTATATATTATAATTTTAGTAAATTCATATAAAAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1640736 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
*
1640791 ATTATATTTTATATTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* *
1640856 AATTTTA-TAAATTATATATTTTTATTAATTTATATTTAATAATAAATATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
1640910 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
1640975 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
1641030 A
1 A
1641031 ATATGATTAA
Statistics
Matches: 336, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
115 44 0.13
116 10 0.03
118 60 0.18
119 116 0.35
120 106 0.32
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (120 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
Found at i:1640977 original size:239 final size:234
Alignment explanation
Indices: 1640557--1641030 Score: 797
Period size: 239 Copynumber: 2.0 Consensus size: 234
1640547 TAGATTATAT
*
1640557 ATTATTTTTATAGTATTATATATTGTGATTTTAGTAAATTCATATAAGAATAATTATATTGAATT
1 ATTATTTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATTATATTGAATT
* * *
1640622 TTATTAAATTATATGTTTTTATTAAATTATATTTAATAATTATTATTTTAAATTATATTATAGTA
66 TTATTAAATTATATATTTTTATTAAATTATATTTAATAATAAATATTTTAAATTATATTATAGTA
1640687 TTATATATTATAATTTTAGTAAATTCATATAAAAATATTTAATATTAAGAATTTTATTAAATTAT
131 TTATATATTATAATTTTAGTAAATTCATATAAAAATATTTAATATTAAGAATTTTATTAAATTAT
*
1640752 ATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
196 ATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
* *
1640791 ATTATATTTTATATTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATT-ATATT--G
*
1640856 AATTTTA-TAAATTATATATTTTTATTAATTTATATTTAATAATAAATATTTTAAATTATATTTT
62 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAAATATTTTAAATTATA--TT
* *
1640920 ATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
125 ATAGTATTATATATTATAATTTTAGTAAATTCATATAAAAATATTTAATATTAAGAATTTTATTA
1640985 AATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
190 AATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
1641030 A
1 A
1641031 ATATGATTAA
Statistics
Matches: 224, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
234 5 0.02
235 47 0.21
236 5 0.02
237 49 0.22
238 8 0.04
239 110 0.49
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (234 bp):
ATTATTTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATTATATTGAATT
TTATTAAATTATATATTTTTATTAAATTATATTTAATAATAAATATTTTAAATTATATTATAGTA
TTATATATTATAATTTTAGTAAATTCATATAAAAATATTTAATATTAAGAATTTTATTAAATTAT
ATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
Found at i:1645357 original size:3 final size:3
Alignment explanation
Indices: 1645349--1645377 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1645339 TTTCATATCT
1645349 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1645378 TTCTTCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:1647814 original size:7 final size:7
Alignment explanation
Indices: 1647794--1647822 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1647784 AAAAAAAATA
1647794 TAATAAT
1 TAATAAT
1647801 T-ATAAT
1 TAATAAT
1647807 TAATAAT
1 TAATAAT
1647814 TAATAAT
1 TAATAAT
1647821 TA
1 TA
1647823 TATGTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAATAAT
Found at i:1651581 original size:25 final size:26
Alignment explanation
Indices: 1651541--1651589 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
1651531 AAATAACATA
*
1651541 ATACTACAATATTGTTCATACCAATG
1 ATACTACAATATTGTTCAAACCAATG
1651567 ATACTAC-ATATTGTTCAAACCAA
1 ATACTACAATATTGTTCAAACCAA
1651590 ATAATCATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (26 bp):
ATACTACAATATTGTTCAAACCAATG
Found at i:1651827 original size:13 final size:13
Alignment explanation
Indices: 1651809--1651835 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1651799 ACTTTTTTTG
1651809 TTTAAAAATTGTT
1 TTTAAAAATTGTT
1651822 TTTAAAAATTGTT
1 TTTAAAAATTGTT
1651835 T
1 T
1651836 ATACTTCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TTTAAAAATTGTT
Found at i:1654741 original size:16 final size:16
Alignment explanation
Indices: 1654712--1654781 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
1654702 TTTGGTTCGC
* *
1654712 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
1654728 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
1654744 TGTAATGGATTAGAGG
1 TGTAATGGAATAGAGG
1654760 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
1654776 TGTAAT
1 TGTAAT
1654782 AGCAAATCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:1654758 original size:32 final size:32
Alignment explanation
Indices: 1654712--1654781 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
1654702 TTTGGTTCGC
*
1654712 TGTATTGGATTAGAGGCGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATGGAATAGAGG
*
1654744 TGTAATGGATTAGAGGTGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATGGAATAGAGG
1654776 TGTAAT
1 TGTAAT
1654782 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.30
Consensus pattern (32 bp):
TGTAATGGATTAGAGGCGTAATGGAATAGAGG
Found at i:1655014 original size:16 final size:16
Alignment explanation
Indices: 1654995--1655035 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1654985 TTAATCATAT
*
1654995 TTAAATATAATTATTA
1 TTAAATATAATTATAA
1655011 TTAAATAT-ATTATAA
1 TTAAATATAATTATAA
1655026 TTAAAATATA
1 TT-AAATATA
1655036 TAATTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAATATAATTATAA
Found at i:1655043 original size:14 final size:15
Alignment explanation
Indices: 1654995--1655045 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1654985 TTAATCATAT
*
1654995 TTAAATATAATTATTA
1 TTAAATAT-ATTATAA
1655011 TTAAATATATTATAA
1 TTAAATATATTATAA
1655026 TTAAA-ATA-TATAA
1 TTAAATATATTATAA
*
1655039 TTTAATA
1 TTAAATA
1655046 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 9 0.28
14 4 0.12
15 11 0.34
16 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAATATATTATAA
Found at i:1655096 original size:61 final size:60
Alignment explanation
Indices: 1655030--1655216 Score: 177
Period size: 61 Copynumber: 3.1 Consensus size: 60
1655020 TTATAATTAA
1655030 AATATATAATTTAATAAAATTCTTAATAATCAAGATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAA-ATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * *
1655091 AATATATGATACT-ATAAAATT-TAAATTAA-CATAATTATTAT-TAAATATA-TTATAGTTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCA-AATTCTTATATGAATTTACTCA-AATCAT
*
1655150 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAA-ATTCTTATATGAATTTACTCAAATCAT
*
1655211 CATATA
1 AATATA
1655217 AAATCGTGTT
Statistics
Matches: 94, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.32
60 23 0.24
61 35 0.37
62 3 0.03
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATAATCAAATTCTTATATGAATTTACTCAAATCAT
Found at i:1655136 original size:120 final size:120
Alignment explanation
Indices: 1655001--1655216 Score: 396
Period size: 120 Copynumber: 1.8 Consensus size: 120
1654991 ATATTTAAAT
1655001 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAAGAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAAGAT
1655066 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATTAAC
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATTAAC
* * *
1655121 ATAATTATTATTAAATATATTATAGTTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAAGAT
*
1655186 TCTTATATGAATTTACTCAAATCATCATATA
66 TCTTATATGAATTTACTCAAATCATAATATA
1655217 AAATCGTGTT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 92 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAAGAT
TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATTAAC
Found at i:1655216 original size:59 final size:58
Alignment explanation
Indices: 1655031--1655217 Score: 168
Period size: 59 Copynumber: 3.1 Consensus size: 58
1655021 TATAATTAAA
* *
1655031 ATATATAATTTAATAAAATTCTTAATAATCAAGATTCTTATATGAATTTACTCAAATC
1 ATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
* * * * * * *
1655089 ATA-ATATATGATACTATAAAATT-TAAATTAACATAATTATTATTAAAT-ATATTATAGTTAAA
1 ATATATA-AT-TTA--ATAAAATTCTTAA-TAA-TTAA-TATTCTTATATGA-ATT-TACTCAAA
1655151 --
57 TC
1655151 ATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1655209 ATCATATAA
1 AT-ATATAA
1655218 AATCGTGTTA
Statistics
Matches: 98, Mismatches: 16, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
56 6 0.06
57 15 0.15
58 11 0.11
59 19 0.19
60 6 0.06
61 13 0.13
62 8 0.08
63 14 0.14
64 6 0.06
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (58 bp):
ATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
Found at i:1656544 original size:11 final size:11
Alignment explanation
Indices: 1656537--1656564 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1656527 TAAGCACGCG
1656537 CAAAGCACACA
1 CAAAGCACACA
1656548 CAAAGCACACA
1 CAAAGCACACA
1656559 CAAAGC
1 CAAAGC
1656565 CATAACATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.36, G:0.11, T:0.00
Consensus pattern (11 bp):
CAAAGCACACA
Found at i:1661384 original size:25 final size:25
Alignment explanation
Indices: 1661350--1661401 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1661340 GCTGATTATC
1661350 CTCCTATTTATGGGTTGAAGAGGAG
1 CTCCTATTTATGGGTTGAAGAGGAG
1661375 CTCCTATTTATGGGTTGAAGAGGAG
1 CTCCTATTTATGGGTTGAAGAGGAG
1661400 CT
1 CT
1661402 ATGGATAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (25 bp):
CTCCTATTTATGGGTTGAAGAGGAG
Found at i:1665918 original size:154 final size:154
Alignment explanation
Indices: 1665566--1666560 Score: 1560
Period size: 154 Copynumber: 6.5 Consensus size: 154
1665556 TATTAAAAAT
* * *
1665566 TCAACGGGGTCTATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACTGGTTCGAAC
1 TCAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
* * * *
1665631 CCGGTTGGGCCCT-TTGTTTA-TATATTTTTGCCGAGTCCGTCC---A--TCCTTAGTTTATACA
66 CCGGTTGGGCCCTGCT-TTTACT-TAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACA
* **** * *
1665689 TCTAGCGGTCAAAGTAACATTGCATC
129 TGTAGTAACCAAAGTAAAATTGCTTC
*
1665715 TCAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTTGAAC
1 TCAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
** * *
1665780 CCGGTTGGGCCCTAATTTTACCTATTTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATG
66 CCGGTTGGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATG
* *
1665845 TACTAACCAAAGTAGAATTGCTTC
131 TAGTAACCAAAGTAAAATTGCTTC
*
1665869 TGAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
1 TCAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
*
1665934 CCGGTTGGGCCCTGC--TTACTTAATTTTGCCAAGTCCGTCCTAAACTTCCATAGTTTATACATG
66 CCGGTTGGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATG
*
1665997 TAGTAACCAAAGCAAAATTGCTTC
131 TAGTAACCAAAGTAAAATTGCTTC
* *
1666021 TCAACGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGATGTCACCGGTTCGAAC
1 TCAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
* ** *
1666086 CCGGTTGGGCCCTGCTTTCACTTGCTTTTGCCAAGTCCGTCCAAAACTTCCATAATTTATACATG
66 CCGGTTGGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATG
*
1666151 TAGTAACCAAAGGAAAATTGCTTC
131 TAGTAACCAAAGTAAAATTGCTTC
*
1666175 TCAATGCGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
1 TCAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
**
1666240 CCGGTTGGGCCCTGCTTTTACTTGCTTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATG
66 CCGGTTGGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATG
1666305 TAGTAACCAAAGTGAAAA-TGCTTC
131 TAGTAACCAAAGT-AAAATTGCTTC
*
1666329 ACAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
1 TCAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
*
1666394 CCGGTTGGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCTAAACTTCCATAGTTTATACATG
66 CCGGTTGGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATG
*
1666459 TAGTAACCAAAGTAAAACTGCTTC
131 TAGTAACCAAAGTAAAATTGCTTC
1666483 TCAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
1 TCAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
1666548 CCGGTTGGGCCCT
66 CCGGTTGGGCCCT
1666561 CTATATTTTT
Statistics
Matches: 787, Mismatches: 48, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
149 97 0.12
150 1 0.00
152 144 0.18
153 4 0.01
154 537 0.68
155 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (154 bp):
TCAATGGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAAC
CCGGTTGGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATG
TAGTAACCAAAGTAAAATTGCTTC
Found at i:1668717 original size:20 final size:22
Alignment explanation
Indices: 1668694--1668747 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
1668684 AATGTTATAG
1668694 TAAATATATATTT-ATTATCA-
1 TAAATATATATTTAATTATCAT
* *
1668714 TAAATATATTTTTAATTATTAT
1 TAAATATATATTTAATTATCAT
*
1668736 TTAATATATATT
1 TAAATATATATT
1668748 ATAAACTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 12 0.43
21 6 0.21
22 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TAAATATATATTTAATTATCAT
Found at i:1668943 original size:17 final size:17
Alignment explanation
Indices: 1668903--1668944 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1668893 CAACCACGGA
1668903 AAAAAAG-AACTTTACT
1 AAAAAAGCAACTTTACT
*
1668919 AAATAAGCAA-TTTATCT
1 AAAAAAGCAACTTTA-CT
1668936 AAAAAAGCA
1 AAAAAAGCA
1668945 CAAGATGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (17 bp):
AAAAAAGCAACTTTACT
Found at i:1673028 original size:18 final size:17
Alignment explanation
Indices: 1673005--1673038 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1672995 AATTTGGTAC
*
1673005 TTTCCTTTTTCTCTTTTT
1 TTTCCTTATTCT-TTTTT
1673023 TTTCCTTATTCTTTTT
1 TTTCCTTATTCTTTTT
1673039 CTTGCTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCCTTATTCTTTTTT
Found at i:1681742 original size:10 final size:10
Alignment explanation
Indices: 1681727--1681771 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
1681717 ACATTTAATT
*
1681727 AATTTTTTAA
1 AATTTTTAAA
1681737 AA-TTTTAAA
1 AATTTTTAAA
1681746 AATTTTTAAAA
1 AATTTTT-AAA
1681757 AATATTTTAAA
1 AAT-TTTTAAA
1681768 AATT
1 AATT
1681772 AAAAATCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
9 8 0.26
10 7 0.23
11 12 0.39
12 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:1681764 original size:12 final size:12
Alignment explanation
Indices: 1681738--1681769 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1681728 ATTTTTTAAA
1681738 ATTTT-AAAAAT
1 ATTTTAAAAAAT
1681749 -TTTTAAAAAAT
1 ATTTTAAAAAAT
1681760 ATTTTAAAAA
1 ATTTTAAAAA
1681770 TTAAAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.21
11 6 0.32
12 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTTTAAAAAAT
Found at i:1684739 original size:14 final size:15
Alignment explanation
Indices: 1684715--1684744 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1684705 CTTTAGAGTT
1684715 TTTTTAGAATTTTTA
1 TTTTTAGAATTTTTA
1684730 TTTTTA-AATTTTTA
1 TTTTTAGAATTTTTA
1684744 T
1 T
1684745 AATTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTTAGAATTTTTA
Found at i:1684779 original size:19 final size:18
Alignment explanation
Indices: 1684754--1684828 Score: 78
Period size: 19 Copynumber: 4.0 Consensus size: 18
1684744 TAATTTAAAA
1684754 AAAATATTTGAAATTTTT
1 AAAATATTTGAAATTTTT
* *
1684772 ATAAATATTTGGATTTTTT
1 A-AAATATTTGAAATTTTT
*
1684791 AAAATTATTTTGAATTTTTT
1 AAAA-TA-TTTGAAATTTTT
* *
1684811 AAAATTTTTAAAATTTTT
1 AAAATATTTGAAATTTTT
1684829 TGTTGATTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
18 14 0.29
19 19 0.40
20 15 0.31
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
AAAATATTTGAAATTTTT
Found at i:1684816 original size:10 final size:10
Alignment explanation
Indices: 1684784--1684829 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
1684774 AAATATTTGG
1684784 ATTTTTTAAA
1 ATTTTTTAAA
*
1684794 ATTATTTT-GA
1 ATT-TTTTAAA
1684804 ATTTTTTAAA
1 ATTTTTTAAA
1684814 A-TTTTTAAA
1 ATTTTTTAAA
1684823 ATTTTTT
1 ATTTTTT
1684830 GTTGATTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 13 0.42
10 14 0.45
11 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:1684818 original size:8 final size:9
Alignment explanation
Indices: 1684754--1684828 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
1684744 TAATTTAAAA
*
1684754 AAAATATTT
1 AAAATTTTT
*
1684763 GAAATTTTT
1 AAAATTTTT
*
1684772 ATAAATATTT
1 A-AAATTTTT
** *
1684782 GGATTTTTT
1 AAAATTTTT
1684791 AAAATTATTTT
1 AAAA-T-TTTT
* *
1684802 GAATTTTTT
1 AAAATTTTT
1684811 AAAATTTTT
1 AAAATTTTT
1684820 AAAATTTTT
1 AAAATTTTT
1684829 TGTTGATTAG
Statistics
Matches: 48, Mismatches: 15, Indels: 6
0.70 0.22 0.09
Matches are distributed among these distances:
9 33 0.69
10 9 0.19
11 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (9 bp):
AAAATTTTT
Found at i:1686718 original size:7 final size:7
Alignment explanation
Indices: 1686706--1686730 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1686696 TTTTATATGA
1686706 ATTTAAT
1 ATTTAAT
1686713 ATTTAAT
1 ATTTAAT
1686720 ATTTAAT
1 ATTTAAT
1686727 ATTT
1 ATTT
1686731 TATTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTAAT
Found at i:1686978 original size:4 final size:4
Alignment explanation
Indices: 1686947--1686971 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1686937 CATAATAATC
1686947 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
1686972 AATAAATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1687782 original size:19 final size:19
Alignment explanation
Indices: 1687760--1687803 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1687750 TTCTAATACT
*
1687760 TTTTTAAATTTTATTA-AAA
1 TTTTCAAATTTT-TTAGAAA
*
1687779 TTTTCATATTTTTTAGAAA
1 TTTTCAAATTTTTTAGAAA
1687798 TTTTCA
1 TTTTCA
1687804 TTTTTGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTCAAATTTTTTAGAAA
Found at i:1687804 original size:19 final size:19
Alignment explanation
Indices: 1687767--1687808 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1687757 ACTTTTTTAA
1687767 ATTTTATTAAAATTTTCAT
1 ATTTTATTAAAATTTTCAT
1687786 ATTTT-TTAGAAATTTTCAT
1 ATTTTATTA-AAATTTTCAT
1687805 -TTTT
1 ATTTT
1687809 GGAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTATTAAAATTTTCAT
Found at i:1688995 original size:2 final size:2
Alignment explanation
Indices: 1688988--1689015 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1688978 TAGCTAAGGT
1688988 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
1689016 ACATATTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1710915 original size:20 final size:20
Alignment explanation
Indices: 1710878--1710916 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1710868 AGAAAACGCA
*
1710878 CAAAAATCAACACCAAACAG
1 CAAAAATCAACACAAAACAG
1710898 CAAAAA-CAACAACAAAACA
1 CAAAAATCAAC-ACAAAACA
1710917 TCAGGAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.67, C:0.28, G:0.03, T:0.03
Consensus pattern (20 bp):
CAAAAATCAACACAAAACAG
Found at i:1710916 original size:11 final size:10
Alignment explanation
Indices: 1710849--1710916 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 10
1710839 AATAATATTA
1710849 AAAACAACAGC
1 AAAACAACA-C
*
1710860 AAAACAACAG
1 AAAACAACAC
*
1710870 AAAAC-GCAC
1 AAAACAACAC
1710879 AAAAATCAACAC
1 -AAAA-CAACAC
* *
1710891 CAAACAGCA-
1 AAAACAACAC
1710900 AAAACAACAAC
1 AAAACAAC-AC
1710911 AAAACA
1 AAAACA
1710917 TCAGGAACAA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
9 8 0.18
10 14 0.32
11 19 0.43
12 3 0.07
ACGTcount: A:0.66, C:0.26, G:0.06, T:0.01
Consensus pattern (10 bp):
AAAACAACAC
Found at i:1716505 original size:24 final size:23
Alignment explanation
Indices: 1716459--1716507 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1716449 AAAAAATTAA
* **
1716459 AAAAATATTTTTATAATCTTTTT
1 AAAAATATTTTTACAATAATTTT
1716482 AAAAATATTTTTACCAATAATTTT
1 AAAAATATTTTTA-CAATAATTTT
1716506 AA
1 AA
1716508 TATAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAAATATTTTTACAATAATTTT
Found at i:1718969 original size:2 final size:2
Alignment explanation
Indices: 1718962--1719003 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1718952 ATTGAGAAAT
1718962 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
1719004 GCATGAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1719431 original size:22 final size:22
Alignment explanation
Indices: 1719406--1719450 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1719396 TCTACCATTG
1719406 TCCTTCAGATCTCAAAACTTGC
1 TCCTTCAGATCTCAAAACTTGC
1719428 TCCTTCAGATCTCAAAACTTGC
1 TCCTTCAGATCTCAAAACTTGC
1719450 T
1 T
1719451 GGACACTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (22 bp):
TCCTTCAGATCTCAAAACTTGC
Found at i:1739211 original size:9 final size:9
Alignment explanation
Indices: 1739197--1739234 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
1739187 ACTAAAGGGG
1739197 AAGAAAAAA
1 AAGAAAAAA
1739206 AAGAAAAAA
1 AAGAAAAAA
*
1739215 AAGAGATAAA
1 AAGA-AAAAA
1739225 AAGAAAAAA
1 AAGAAAAAA
1739234 A
1 A
1739235 TTAAATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:1739658 original size:13 final size:13
Alignment explanation
Indices: 1739640--1739664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1739630 AAAGAGGATA
1739640 ATTTTATTTATTT
1 ATTTTATTTATTT
1739653 ATTTTATTTATT
1 ATTTTATTTATT
1739665 AGTATATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:1742946 original size:110 final size:109
Alignment explanation
Indices: 1742765--1743074 Score: 498
Period size: 110 Copynumber: 2.8 Consensus size: 109
1742755 ATATTTGGCA
* * * * *
1742765 ATTTGGTTAAACGAG-AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTTCCAAACTC
1 ATTTGGTTGAACGAGAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGC
1742828 AAAACATTGCCTTATTTTGAAATTTTTAAGAAGGATATTAAGCC
66 AAAACATTGCCTTATTTTGAAATTTTTAAGAAGGATATTAAGCC
* *
1742872 ATTTGGTTGAACGAGAAAAATCGACACCCAACACCTTAAGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAG-AAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
*
1742937 CAAAACATTGCCCTATTTTGAAATTTTTAAGAAGGATATTAAGCC
65 CAAAACATTGCCTTATTTTGAAATTTTTAAGAAGGATATTAAGCC
1742982 ATTTGGTTGAACGAGGAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTGAACGA-GAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
*
1743047 CAAAACATTGCCTTATTTATAAAATTTT
65 CAAAACATTGCCTTATTT-TGAAATTTT
1743075 GTTTTTTTTT
Statistics
Matches: 186, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
107 14 0.08
109 24 0.13
110 139 0.75
111 9 0.05
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (109 bp):
ATTTGGTTGAACGAGAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGC
AAAACATTGCCTTATTTTGAAATTTTTAAGAAGGATATTAAGCC
Found at i:1743567 original size:2 final size:2
Alignment explanation
Indices: 1743497--1743548 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1743487 ATAAAAGAAG
1743497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1743539 AT AT AT AT AT
1 AT AT AT AT AT
1743549 TCATAAGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1745869 original size:114 final size:114
Alignment explanation
Indices: 1745667--1745894 Score: 429
Period size: 114 Copynumber: 2.0 Consensus size: 114
1745657 ACCAAAGACA
*
1745667 ACATGGCCAAAAAGAGCAAGGCATAAAGACTCAAGGTGCTCGAGGTGGTGTAATGGAAACAAAAC
1 ACATGGCCAAAAAGAACAAGGCATAAAGACTCAAGGTGCTCGAGGTGGTGTAATGGAAACAAAAC
*
1745732 CGTTGAACATGTCTTGTTATTTTGTCCATTTGCAAGTGTAGTGTGGGAG
66 CATTGAACATGTCTTGTTATTTTGTCCATTTGCAAGTGTAGTGTGGGAG
1745781 ACATGGCCAAAAAGAACAAGGCATAAAGACTCAAGGTGCTCGAGGTGGTGTAATGGAAACAAAAC
1 ACATGGCCAAAAAGAACAAGGCATAAAGACTCAAGGTGCTCGAGGTGGTGTAATGGAAACAAAAC
*
1745846 CATTGAACATGTCTTGTTCTTTTGTCCATTTGCAAGTGTAGTGTGGGAG
66 CATTGAACATGTCTTGTTATTTTGTCCATTTGCAAGTGTAGTGTGGGAG
1745895 GCTTGTAGTC
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.25
Consensus pattern (114 bp):
ACATGGCCAAAAAGAACAAGGCATAAAGACTCAAGGTGCTCGAGGTGGTGTAATGGAAACAAAAC
CATTGAACATGTCTTGTTATTTTGTCCATTTGCAAGTGTAGTGTGGGAG
Found at i:1750788 original size:17 final size:16
Alignment explanation
Indices: 1750744--1750788 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
1750734 AAAAAAATTA
1750744 AAATATATATATTTTT
1 AAATATATATATTTTT
*
1750760 AAAT-TCTCATATGTTTT
1 AAATATAT-ATAT-TTTT
1750777 AAATATATATAT
1 AAATATATATAT
1750789 ATATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 2 0.08
16 8 0.33
17 12 0.50
18 2 0.08
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (16 bp):
AAATATATATATTTTT
Found at i:1755946 original size:31 final size:29
Alignment explanation
Indices: 1755905--1755980 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 29
1755895 CCCTTGAAAC
**
1755905 TTTTAGAAAATTTTAACTAAGCTCTCTTA-AA
1 TTTTA-AAAATTTTAACTAA--TCTCACAGAA
* *
1755936 TTTTTAAAAATTATCACTAATCTCACAGAA
1 -TTTTAAAAATTTTAACTAATCTCACAGAA
1755966 TTTTAAAAATTTTAA
1 TTTTAAAAATTTTAA
1755981 TTAGACCCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
29 18 0.49
30 2 0.05
31 12 0.32
32 5 0.14
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTTAAAAATTTTAACTAATCTCACAGAA
Found at i:1758750 original size:21 final size:21
Alignment explanation
Indices: 1758722--1758763 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1758712 GGCAAAAATT
1758722 ATAATATA-TATTTGTTATAA
1 ATAATATATTATTTGTTATAA
*
1758742 ATAAGTATATTATTTTTTATAA
1 ATAA-TATATTATTTGTTATAA
1758764 TATATAGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 11 0.58
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (21 bp):
ATAATATATTATTTGTTATAA
Found at i:1762770 original size:46 final size:40
Alignment explanation
Indices: 1762717--1763018 Score: 230
Period size: 37 Copynumber: 7.7 Consensus size: 40
1762707 TTTGAGTACT
1762717 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGT-GT-GC--TA--TACACTTA
* *
1762763 TCTGATCACG-AAACAAAGTGATAAGTG-G-T-TACACTTA
1 TCTGATCAAGTGAA-AAAGTGATAAGTGTGCTATACACTTA
*
1762800 TCTGATCAAG-AAACAAAGTGATAAGTG-G-T-TACACTTA
1 TCTGATCAAGTGAA-AAAGTGATAAGTGTGCTATACACTTA
*
1762837 TCTGATCAAGTGACAAAGTGATAA--GTGCTA-A-ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGTGCTATACACTTA
* * *
1762873 TCTGATCAAGAGACAAAGGGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGT-GT-GC--TA--TACACTTA
*
1762919 TCTGATCAAGTGACAAAGTGATAA--GTGC--TACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGTGCTATACACTTA
**
1762955 TCTGATCAAGTGGCAAAGTGATAAGTG-G-T-TACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGTGCTATACACTTA
*
1762992 TCTGATCAAG-AAACAAAGTGATAAGTG
1 TCTGATCAAGTGAA-AAAGTGATAAGTG
1763019 ATCATACGTA
Statistics
Matches: 224, Mismatches: 13, Indels: 47
0.79 0.05 0.17
Matches are distributed among these distances:
35 1 0.00
36 59 0.26
37 98 0.44
38 2 0.01
39 2 0.01
40 3 0.01
42 4 0.02
43 3 0.01
45 4 0.02
46 48 0.21
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (40 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGTGCTATACACTTA
Found at i:1762796 original size:37 final size:37
Alignment explanation
Indices: 1762755--1763018 Score: 325
Period size: 37 Copynumber: 6.9 Consensus size: 37
1762745 TAGCTTTAGC
* *
1762755 TACACTTATCTGATCACGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
*
1762792 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
* *
1762829 TACACTTATCTGATCAAGTGACAAAGTGATAAGT-GC
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
* *
1762865 TAAACTTATCTGATCAAGAGACAAAGGGATAAGTGGTAGCTTT
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGT-G--G---T
* *
1762908 AGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT-GC
1 ---TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
* *
1762947 TACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
*
1762984 TACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1763019 ATCATACGTA
Statistics
Matches: 199, Mismatches: 17, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
36 65 0.33
37 101 0.51
40 1 0.01
42 1 0.01
46 31 0.16
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (37 bp):
TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
Found at i:1762972 original size:82 final size:82
Alignment explanation
Indices: 1762829--1762983 Score: 274
Period size: 82 Copynumber: 1.9 Consensus size: 82
1762819 GATAAGTGGT
1762829 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGGGA
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGGGA
1762894 TAAGTGGTAGCTTTAGC
66 TAAGTGGTAGCTTTAGC
* * * *
1762911 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTACACTTATCTGATCAAGTGGCAAAGTGA
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGGGA
1762976 TAAGTGGT
66 TAAGTGGT
1762984 TACACTTATC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (82 bp):
TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGGGA
TAAGTGGTAGCTTTAGC
Found at i:1763011 original size:155 final size:156
Alignment explanation
Indices: 1762717--1763018 Score: 489
Period size: 155 Copynumber: 1.9 Consensus size: 156
1762707 TTTGAGTACT
* * *
1762717 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCACGAAACAAAGT
1 TCTGATCAAGAGAAAAAGGGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGAAACAAAGT
*
1762782 GATAAGTGGTTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTATCTGATCAAG
66 GATAAGTGGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTATCTGATCAAG
**
1762847 TGACAAAGTGATAAGTGCTAAACTTA
131 AAACAAAGTGATAAGTGCTAAACTTA
* **
1762873 TCTGATCAAGAGACAAAGGGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGAAAAAGGGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGAAACAAAGT
***
1762938 GATAAGT-GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTTACACTTATCTGATCAAG
66 GATAAGTGGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTATCTGATCAAG
1763002 AAACAAAGTGATAAGTG
131 AAACAAAGTGATAAGTG
1763019 ATCATACGTA
Statistics
Matches: 134, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
155 68 0.51
156 66 0.49
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (156 bp):
TCTGATCAAGAGAAAAAGGGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGAAACAAAGT
GATAAGTGGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTATCTGATCAAG
AAACAAAGTGATAAGTGCTAAACTTA
Found at i:1764555 original size:24 final size:24
Alignment explanation
Indices: 1764527--1764578 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1764517 TTAGTAGGTC
* *
1764527 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1764551 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1764575 AAAT
1 AAAT
1764579 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1765110 original size:13 final size:13
Alignment explanation
Indices: 1765092--1765117 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1765082 AAATAAACCA
1765092 TTAATAGAATCAG
1 TTAATAGAATCAG
1765105 TTAATAGAATCAG
1 TTAATAGAATCAG
1765118 ACACTGCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
TTAATAGAATCAG
Found at i:1770102 original size:24 final size:24
Alignment explanation
Indices: 1770075--1770126 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 24
1770065 AGTTGGATTT
1770075 GAAATTTTCAGGAGGAAAAAGTTG
1 GAAATTTTCAGGAGGAAAAAGTTG
1770099 GAAA---TCAGGAGGAAAAAGTTG
1 GAAATTTTCAGGAGGAAAAAGTTG
*
1770120 AAAATTT
1 GAAATTT
1770127 GATTTTTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 20 0.83
24 4 0.17
ACGTcount: A:0.46, C:0.04, G:0.27, T:0.23
Consensus pattern (24 bp):
GAAATTTTCAGGAGGAAAAAGTTG
Found at i:1770122 original size:20 final size:21
Alignment explanation
Indices: 1770082--1770124 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1770072 TTTGAAATTT
1770082 TCAGGAGGAAAAAGTTGGAAA
1 TCAGGAGGAAAAAGTTGGAAA
*
1770103 TCAGGAGGAAAAAGTTGAAAA
1 TCAGGAGGAAAAAGTTGGAAA
1770124 T
1 T
1770125 TTGATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.30, T:0.16
Consensus pattern (21 bp):
TCAGGAGGAAAAAGTTGGAAA
Found at i:1777441 original size:6 final size:6
Alignment explanation
Indices: 1777432--1777466 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1777422 GTGGCTGTGG
* *
1777432 CGGTCA CGGTCA CGGTTA CGGTTA CGGTTA CGGTT
1 CGGTTA CGGTTA CGGTTA CGGTTA CGGTTA CGGTT
1777467 CGCACTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (6 bp):
CGGTTA
Found at i:1778174 original size:13 final size:13
Alignment explanation
Indices: 1778156--1778181 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1778146 CTCGTCTCGA
1778156 ATTTTATTTTATT
1 ATTTTATTTTATT
1778169 ATTTTATTTTATT
1 ATTTTATTTTATT
1778182 TTGAAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTATTTTATT
Found at i:1788406 original size:2 final size:2
Alignment explanation
Indices: 1788399--1788432 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1788389 ACTTGAATTT
1788399 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
1788433 GTACTCCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1789073 original size:20 final size:20
Alignment explanation
Indices: 1789048--1789087 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1789038 AAATTGTAGT
1789048 TCTTGATTCAATTATTTGTA
1 TCTTGATTCAATTATTTGTA
1789068 TCTTGATTCAATTATTTGTA
1 TCTTGATTCAATTATTTGTA
1789088 CAGATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
TCTTGATTCAATTATTTGTA
Found at i:1792774 original size:19 final size:19
Alignment explanation
Indices: 1792750--1792787 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1792740 GTGATTTCAA
*
1792750 CTTTTATTTCTCTGTTTCT
1 CTTTTATTTCTCAGTTTCT
*
1792769 CTTTTATTTTTCAGTTTCT
1 CTTTTATTTCTCAGTTTCT
1792788 TTAGTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.18, G:0.05, T:0.68
Consensus pattern (19 bp):
CTTTTATTTCTCAGTTTCT
Found at i:1793570 original size:3 final size:3
Alignment explanation
Indices: 1793553--1793596 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
1793543 TTAGTTTCCT
*
1793553 TTA TTA TTTA GTTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1793597 ATGTTATTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1793834 original size:16 final size:16
Alignment explanation
Indices: 1793803--1793847 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1793793 TGAATATATG
1793803 TATATATACTTATATTT
1 TATATAT-CTTATATTT
*
1793820 TATATATCTTGTATTT
1 TATATATCTTATATTT
1793836 TATA-ATC-TATAT
1 TATATATCTTATAT
1793848 ACATATACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 4 0.15
15 3 0.12
16 12 0.46
17 7 0.27
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (16 bp):
TATATATCTTATATTT
Found at i:1793901 original size:30 final size:31
Alignment explanation
Indices: 1793867--1793932 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 31
1793857 TGTAAATACT
1793867 TATATT-TTT-ATATCTT-ATAATTTATATATA
1 TATATTCTTTCATAT-TTAATAATTT-TATATA
*
1793897 TATATTCTTTCATATTTACATAATTTTATGTA
1 TATATTCTTTCATATTTA-ATAATTTTATATA
1793929 TATA
1 TATA
1793933 CATACATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
30 6 0.19
31 5 0.16
32 13 0.42
33 7 0.23
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (31 bp):
TATATTCTTTCATATTTAATAATTTTATATA
Found at i:1794967 original size:10 final size:9
Alignment explanation
Indices: 1794930--1794978 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
1794920 GTAATTTTAT
1794930 TTTTAAAAA
1 TTTTAAAAA
1794939 --TTAAAAA
1 TTTTAAAAA
1794946 TTTTAAAAA
1 TTTTAAAAA
1794955 TTTTAAAAGA
1 TTTTAAAA-A
*
1794965 TTTAAATAAA
1 TTTTAA-AAA
1794975 TTTT
1 TTTT
1794979 GCACTTGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
7 7 0.21
9 15 0.44
10 10 0.29
11 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:1795047 original size:2 final size:2
Alignment explanation
Indices: 1795040--1795074 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1795030 CTGTATACTA
1795040 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1795075 AAGCTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1795577 original size:18 final size:17
Alignment explanation
Indices: 1795535--1795582 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1795525 TTGGCCCCCC
1795535 TAAAATGATAGAAATTA
1 TAAAATGATAGAAATTA
1795552 TAAAGAT-ATAG--ATTA
1 TAAA-ATGATAGAAATTA
1795567 TTAAAATGATA-AAATT
1 -TAAAATGATAGAAATT
1795583 GTATTTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
15 6 0.23
16 7 0.27
17 11 0.42
18 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (17 bp):
TAAAATGATAGAAATTA
Found at i:1798454 original size:88 final size:88
Alignment explanation
Indices: 1798305--1798481 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
1798295 TTGTATTGTT
1798305 AAAATTTGACAAGGTTGATGGAATAACTAGACAGTGAAATGTGGCGTGTCATGAGTAACTCATAT
1 AAAATTTGACAAGGTTGATGGAATAACTAGACAGTGAAATGTGGCGTGTCATGAGTAACTCATAT
1798370 TGATTTACAGGAATCAATTTTTA
66 TGATTTACAGGAATCAATTTTTA
1798393 AAAATTTGACAAGGTTGATGGAATAACTAGACAGTGAAATGTGGCGTGTCATGAGTAACTCATAT
1 AAAATTTGACAAGGTTGATGGAATAACTAGACAGTGAAATGTGGCGTGTCATGAGTAACTCATAT
1798458 TGATTTACAGGAATCAATTTTTA
66 TGATTTACAGGAATCAATTTTTA
1798481 A
1 A
1798482 CAGAAAGACC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (88 bp):
AAAATTTGACAAGGTTGATGGAATAACTAGACAGTGAAATGTGGCGTGTCATGAGTAACTCATAT
TGATTTACAGGAATCAATTTTTA
Found at i:1799942 original size:44 final size:44
Alignment explanation
Indices: 1799868--1799954 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
1799858 AAAAAATTGT
*
1799868 AATATATAATATATAAATTAATAAAAAATTAAAAATTTACAAAA
1 AATATATAATATATAAATTAATAAAAAATTAAAAAATTACAAAA
*
1799912 AATATAT-ATATATATA-TATATAAAAGAATTAAAAAATTACAAA
1 AATATATAATATATAAATTA-ATAAAA-AATTAAAAAATTACAAA
1799955 TTTATAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 2 0.05
43 14 0.36
44 23 0.59
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.32
Consensus pattern (44 bp):
AATATATAATATATAAATTAATAAAAAATTAAAAAATTACAAAA
Found at i:1799949 original size:52 final size:50
Alignment explanation
Indices: 1799869--1799965 Score: 140
Period size: 52 Copynumber: 1.9 Consensus size: 50
1799859 AAAAATTGTA
**
1799869 ATATATAATATATAAATTAATAAAAAATTAAAAATTTACAAAAAATATAT
1 ATATATAATATATAAAAGAATAAAAAATTAAAAATTTACAAAAAATATAT
* *
1799919 ATATATATATATATAAAAGAATTAAAAAATTACAAATTTATAAAAAA
1 ATATATA-ATATATAAAAGAA-TAAAAAATTAAAAATTTACAAAAAA
1799966 CAATTAAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 7 0.17
51 11 0.27
52 23 0.56
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (50 bp):
ATATATAATATATAAAAGAATAAAAAATTAAAAATTTACAAAAAATATAT
Found at i:1801574 original size:20 final size:19
Alignment explanation
Indices: 1801521--1801574 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
1801511 CATATAATAA
1801521 AATTCATATAAAT-TATA-
1 AATTCATATAAATATATAT
1801538 AA--CATATAAA-ATAATAT
1 AATTCATATAAATAT-ATAT
1801555 ATATTCATATAAATATATAT
1 A-ATTCATATAAATATATAT
1801575 GTGTCAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
15 9 0.30
16 3 0.10
17 3 0.10
18 1 0.03
20 12 0.40
21 2 0.07
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCATATAAATATATAT
Found at i:1802381 original size:14 final size:15
Alignment explanation
Indices: 1802354--1802384 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1802344 TCCAATCCAC
1802354 ATTAATATTTTTTAT
1 ATTAATATTTTTTAT
1802369 ATTAATA-TTTTTAT
1 ATTAATATTTTTTAT
1802383 AT
1 AT
1802385 AAAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTAATATTTTTTAT
Found at i:1807365 original size:304 final size:299
Alignment explanation
Indices: 1806786--1807415 Score: 994
Period size: 304 Copynumber: 2.1 Consensus size: 299
1806776 TATTATCACC
* **
1806786 ATTTTCCGCTCAATTTGGACAAATATCACACGGGGTTCCATGAAACTTTTTTTTCTCAATGAAAG
1 ATTTTCCACTCAATTTGGACAAATATCACACCAGGTTCCATGAAACTTTTTTTTCTCAATGAAAG
* *
1806851 ATCACAAACTTCAAACAACGTTCTCATAAAAATAAATAAAAAAATTAAATCGCTAGCAACCAGAT
66 ATCACAAACTTCAAACAACGTTCTCATAAAAACAAACAAAAAAATTAAATCGCTAGCAACCAGAT
1806916 AGCACAATCCTCGATTACTAAACCAAACCGTGATGAAATTCAATAAGATCTTGATCACAAAAAAA
131 AGCACAATCCTCGATTACTAAACCAAACCGTGATGAAATTCAATAAGATCTTGAT---------A
* *
1806981 AAAAAAAAATCATCAAACTAAAAATGAAAATTTCAATGAAAATGGAGCTTGAATATACCTGAAAT
187 AAAAAAAAATCATCAAAATAAAAATGAAAATTTCAATGAAAATGGAGCTCGAATATACCTGAAAT
1807046 CGGCATCCGAAGATTGCCGAGTTACGGTAGAAAACAAC-CTATGCTCAT
252 CGGCATCCGAAGATTGCCGAGTTACGGTAGAAAACAACAC-ATGCTCAT
* *
1807094 ATTTTCCACTCAATTTGGACAAATGTCACACCAGGTTCCATGAAACTTCTTTTTTCTCTATGAAA
1 ATTTTCCACTCAATTTGGACAAATATCACACCAGGTTCCATGAAACTT-TTTTTTCTCAATGAAA
1807159 GATCACAAACTTCAAACAACGTTCTCATAAAAACAAACAAACAAACAAAATTAAATCGCTAGCAA
65 GATCACAAACTTCAAACAACGTTCTCAT---AA-AAACAAACAAA-AAAATTAAATCGCTAGCAA
*
1807224 CCAGATAGCACAATCCTCGATTACTAAACCAACCCGTGATGAAATTCAATAAGATCTTGAT-AAA
125 CCAGATAGCACAATCCTCGATTACTAAACCAAACCGTGATGAAATTCAATAAGATCTTGATAAAA
1807288 AAAAAATCATCAAAATAAAAATGAAAATTTCAATGAAAATGGAGCTCGAATATACCTGAAATCGG
190 AAAAAATCATCAAAATAAAAATGAAAATTTCAATGAAAATGGAGCTCGAATATACCTGAAATCGG
1807353 CATCCGAAGATTGCCGAGTTACGGTAGAAAACAACACATGCTCAT
255 CATCCGAAGATTGCCGAGTTACGGTAGAAAACAACACATGCTCAT
*
1807398 ATTTGCCACTCAAATTTG
1 ATTTTCCACTC-AATTTG
1807416 TTTTCAAAAG
Statistics
Matches: 303, Mismatches: 11, Indels: 19
0.91 0.03 0.06
Matches are distributed among these distances:
304 119 0.39
305 7 0.02
308 44 0.15
309 43 0.14
312 2 0.01
313 9 0.03
314 79 0.26
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (299 bp):
ATTTTCCACTCAATTTGGACAAATATCACACCAGGTTCCATGAAACTTTTTTTTCTCAATGAAAG
ATCACAAACTTCAAACAACGTTCTCATAAAAACAAACAAAAAAATTAAATCGCTAGCAACCAGAT
AGCACAATCCTCGATTACTAAACCAAACCGTGATGAAATTCAATAAGATCTTGATAAAAAAAAAA
TCATCAAAATAAAAATGAAAATTTCAATGAAAATGGAGCTCGAATATACCTGAAATCGGCATCCG
AAGATTGCCGAGTTACGGTAGAAAACAACACATGCTCAT
Found at i:1813284 original size:17 final size:18
Alignment explanation
Indices: 1813262--1813303 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
1813252 ATGATAAGGG
1813262 TTCATACATA-TTTGACT
1 TTCATACATATTTTGACT
*
1813279 TTCATATATATATTTTGACT
1 TTC--ATACATATTTTGACT
1813299 TTCAT
1 TTCAT
1813304 TTTCCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 3 0.14
18 2 0.10
19 6 0.29
20 10 0.48
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (18 bp):
TTCATACATATTTTGACT
Found at i:1818503 original size:20 final size:20
Alignment explanation
Indices: 1818463--1818503 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1818453 TATATATTAT
*
1818463 ATTTATGATTTCAAATTAAA
1 ATTTATGATTTCAAATAAAA
1818483 ATTTATGA-TTCAATATAAAA
1 ATTTATGATTTCAA-ATAAAA
1818503 A
1 A
1818504 AAACATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (20 bp):
ATTTATGATTTCAAATAAAA
Found at i:1833230 original size:12 final size:12
Alignment explanation
Indices: 1833213--1833254 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1833203 AGATGAGAGC
1833213 TTGATTTATGAA
1 TTGATTTATGAA
* * *
1833225 TTGATTCAAGAC
1 TTGATTTATGAA
1833237 TTGATTTATGAA
1 TTGATTTATGAA
1833249 TTGATT
1 TTGATT
1833255 CAAGACTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (12 bp):
TTGATTTATGAA
Found at i:1833239 original size:24 final size:24
Alignment explanation
Indices: 1833212--1833265 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1833202 AAGATGAGAG
1833212 CTTGATTTATGAATTGATTCAAGA
1 CTTGATTTATGAATTGATTCAAGA
1833236 CTTGATTTATGAATTGATTCAAGA
1 CTTGATTTATGAATTGATTCAAGA
1833260 CTTGAT
1 CTTGAT
1833266 GGTTAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (24 bp):
CTTGATTTATGAATTGATTCAAGA
Found at i:1833264 original size:12 final size:12
Alignment explanation
Indices: 1833225--1833265 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1833215 GATTTATGAA
1833225 TTGATTCAAGAC
1 TTGATTCAAGAC
* * *
1833237 TTGATTTATGAA
1 TTGATTCAAGAC
1833249 TTGATTCAAGAC
1 TTGATTCAAGAC
1833261 TTGAT
1 TTGAT
1833266 GGTTAAAATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (12 bp):
TTGATTCAAGAC
Found at i:1840529 original size:408 final size:407
Alignment explanation
Indices: 1839475--1840670 Score: 2101
Period size: 409 Copynumber: 2.9 Consensus size: 407
1839465 TTGAACATGG
1839475 TAGCAAAGTTAACAATTCCATCTATA-TTATTTTGGGGTGATTTGAC--AAAAAATGCAATTTCA
1 TAGCAAAGTTAACAATTCCATCTATATTTATTTTGGGGTGATTTGACAAAAAAAATGCAATTTCA
* * *
1839537 ATGGCTAAAATAGGCGAAAAATTAAGTGGGATGCTAAAATGACTTCTTCTTTTTTTATAAAGTTA
66 AGGGCTAAAATAGGTGAAAATTTAAGTGGGATGCTAAAATGA---CTTCTTTTTTTATAAAGTTA
*
1839602 AAGGGTCAAAAAAATAATTATACATTTTAAAAATTAGTAATGAGAAAGTATTTGTAACACATTTT
128 GAGGGTCAAAAAAATAATTATACATTTTAAAAATTAGTAATGAGAAAGTATTTGTAACACATTTT
* *
1839667 ACCATTTATATATCATTAAACAATTTTCCAAGACACTCCTTATTAGGGATGGCAAAACCCGTACC
193 ACCATTTATATATCATTAAACAATTTTCCAAGACACTCCTTATTAGGGATGGCAAAACTCGAACC
* * *
1839732 GGCGGATGGATTTTGAATTGGTTCACTCCTTATTAGAGATGAGTAAAATTCGATTCAATGCGAAA
258 GCCTGATGGATTTTGAATTGGTTCACTCCTTATTAGAGATGAGTAAAATTCGATTCAATTCGAAA
* *
1839797 AATTCGATAAAAAATTAATTTTTTAATTAAATAGTTCGAGTTAATCGAGTGATCTGACAAAAAAA
323 AATTCGATAAAAAATTAAATTTTTAATTAAATAGTTCGAGTTAATCGAGTGATTTGACAAAAAAA
*
1839862 TACAATTTTAAGGGCTAAAA
388 TACAATTTCAAGGGCTAAAA
1839882 TAGCAAAGTTAACAATTCCATCTATATTTATTTTGGGGTGATTTGACCAAAAAAAAATGCAATTT
1 TAGCAAAGTTAACAATTCCATCTATATTTATTTTGGGGTGATTTGA-C-AAAAAAAATGCAATTT
*
1839947 CAAGGACTAAAATAGGTGAAAATTTAAGTGGGATGCTAAAATGACTTCTTTTTTTATAAAGTTAG
64 CAAGGGCTAAAATAGGTGAAAATTTAAGTGGGATGCTAAAATGACTTCTTTTTTTATAAAGTTAG
* * *
1840012 AGGGTCAAAAAAGTAATTATACATTTTAAAAATTAGTAATGAGAAAGTATCTATAACACATTTTA
129 AGGGTCAAAAAAATAATTATACATTTTAAAAATTAGTAATGAGAAAGTATTTGTAACACATTTTA
*
1840077 CCATTTATATATCATTAAACAATTTTCCAAGACACTCATTATTAGGGATGGCAAAACTCGAACCG
194 CCATTTATATATCATTAAACAATTTTCCAAGACACTCCTTATTAGGGATGGCAAAACTCGAACCG
1840142 CCTGATGGATTTTGAATTGGTTCACTCCTTATTAGAGATGAGTAAAATTCGATTCAATTCGAAAA
259 CCTGATGGATTTTGAATTGGTTCACTCCTTATTAGAGATGAGTAAAATTCGATTCAATTCGAAAA
1840207 ATTCGATAAAAAATTAAATTTTTAATTAAATAGTTCGAGTTAATCGAGTGATTTGACAAAAAAAA
324 ATTCGATAAAAAATTAAATTTTTAATTAAATAGTTCGAGTTAATCGAGTGATTTGAC-AAAAAAA
1840272 TACAATTTCAAGGGCTAAAA
388 TACAATTTCAAGGGCTAAAA
1840292 TAGCAAAGTTAACAATTCCATCTATATTTATTTTGGGGTGATTTGACAAAAAAAATGCAATTTCA
1 TAGCAAAGTTAACAATTCCATCTATATTTATTTTGGGGTGATTTGACAAAAAAAATGCAATTTCA
1840357 AGGGCTAAAATAGGTGAAAATTTAAGTGGGATGCTAAAATGACTTCTTTTTTTATAAAGTTAGAG
66 AGGGCTAAAATAGGTGAAAATTTAAGTGGGATGCTAAAATGACTTCTTTTTTTATAAAGTTAGAG
1840422 GGTCAAAAAAATAATTATACATTTTAAAAATTAGTAATGAGAAAGTATTTGTAACACATTTTACC
131 GGTCAAAAAAATAATTATACATTTTAAAAATTAGTAATGAGAAAGTATTTGTAACACATTTTACC
1840487 ATTTATATATCATTAAACAATTTTCCAAGACACTCCTTATTAGGGATGGCAAAACTCGAACCGCC
196 ATTTATATATCATTAAACAATTTTCCAAGACACTCCTTATTAGGGATGGCAAAACTCGAACCGCC
* * ** *
1840552 TGATGGATTTTGAATTGGTTCACTCCTTATTAGATATGAGTAAAATTCTATTTGATTTGAAAAAT
261 TGATGGATTTTGAATTGGTTCACTCCTTATTAGAGATGAGTAAAATTCGATTCAATTCGAAAAAT
*
1840617 TCGATAAAAAATTTAAATTTTTAATTAAATAGTTCGAGTTAATCGAGTTATTTG
326 TCGATAAAAAA-TTAAATTTTTAATTAAATAGTTCGAGTTAATCGAGTGATTTG
1840671 GATCAACTCA
Statistics
Matches: 754, Mismatches: 28, Indels: 12
0.95 0.04 0.02
Matches are distributed among these distances:
407 26 0.03
408 298 0.40
409 304 0.40
410 72 0.10
412 54 0.07
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (407 bp):
TAGCAAAGTTAACAATTCCATCTATATTTATTTTGGGGTGATTTGACAAAAAAAATGCAATTTCA
AGGGCTAAAATAGGTGAAAATTTAAGTGGGATGCTAAAATGACTTCTTTTTTTATAAAGTTAGAG
GGTCAAAAAAATAATTATACATTTTAAAAATTAGTAATGAGAAAGTATTTGTAACACATTTTACC
ATTTATATATCATTAAACAATTTTCCAAGACACTCCTTATTAGGGATGGCAAAACTCGAACCGCC
TGATGGATTTTGAATTGGTTCACTCCTTATTAGAGATGAGTAAAATTCGATTCAATTCGAAAAAT
TCGATAAAAAATTAAATTTTTAATTAAATAGTTCGAGTTAATCGAGTGATTTGACAAAAAAATAC
AATTTCAAGGGCTAAAA
Done.