Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003744.1 Hibiscus syriacus cultivar Beakdansim tig00008013_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: 2457414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1355787 original size:16 final size:16
Alignment explanation
Indices: 1355766--1355809 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
1355756 CTATATGTGT
1355766 GTGTGTGTGTGCTCGC
1 GTGTGTGTGTGCTCGC
1355782 GTGTGTGTGTGCTCGC
1 GTGTGTGTGTGCTCGC
1355798 GTGTGTGTGTGC
1 GTGTGTGTGTGC
1355810 ACATTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.00, C:0.16, G:0.45, T:0.39
Consensus pattern (16 bp):
GTGTGTGTGTGCTCGC
Found at i:1360040 original size:49 final size:49
Alignment explanation
Indices: 1359987--1360095 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 49
1359977 GGAATATGTA
* *
1359987 AAAATATTTATAGTTTTATCC-ATGTAAGTATACATATGAGAAATCTGTG
1 AAAATATTTATAATATTA-CCAATGTAAGTATACATATGAGAAATCTGTG
* ** * * *
1360036 AAAATATTCATAATATTACCAATGTAAGTATATGTATGTGACATTTGTG
1 AAAATATTTATAATATTACCAATGTAAGTATACATATGAGAAATCTGTG
1360085 -AAATATTTATA
1 AAAATATTTATA
1360096 TCTACATTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
48 12 0.24
49 38 0.76
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (49 bp):
AAAATATTTATAATATTACCAATGTAAGTATACATATGAGAAATCTGTG
Found at i:1360608 original size:21 final size:20
Alignment explanation
Indices: 1360584--1360628 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1360574 ACTAGGTGAC
1360584 ATTTCATGTACATCGTGTGGA
1 ATTTCATGTAC-TCGTGTGGA
* *
1360605 ATTTCGTGTGCTCGTGTGGA
1 ATTTCATGTACTCGTGTGGA
1360625 ATTT
1 ATTT
1360629 TCTTGTGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.18, C:0.13, G:0.27, T:0.42
Consensus pattern (20 bp):
ATTTCATGTACTCGTGTGGA
Found at i:1360651 original size:21 final size:21
Alignment explanation
Indices: 1360584--1360652 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
1360574 ACTAGGTGAC
*
1360584 ATTTCATGTACATCGTGTGGA
1 ATTTCATGTGCATCGTGTGGA
*
1360605 ATTTCGTGTGC-TCGTGTGGA
1 ATTTCATGTGCATCGTGTGGA
* *
1360625 ATTTTCTTGTGCATTGTGT-GA
1 A-TTTCATGTGCATCGTGTGGA
1360646 CATTTCA
1 -ATTTCA
1360653 CGTGACACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 10 0.25
21 24 0.60
22 6 0.15
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.43
Consensus pattern (21 bp):
ATTTCATGTGCATCGTGTGGA
Found at i:1362138 original size:14 final size:14
Alignment explanation
Indices: 1362119--1362170 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
1362109 CAACTACACT
1362119 AATAAATTATTTAA
1 AATAAATTATTTAA
* * *
1362133 AATAAATAATCCATACT
1 AATAAATTAT--TTA-A
1362150 AATAAATTATTTAA
1 AATAAATTATTTAA
1362164 AATAAAT
1 AATAAAT
1362171 CAATCCGTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
14 16 0.55
15 2 0.07
16 2 0.07
17 9 0.31
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:1362151 original size:31 final size:32
Alignment explanation
Indices: 1362116--1362176 Score: 115
Period size: 31 Copynumber: 1.9 Consensus size: 32
1362106 AAACAACTAC
1362116 ACTAATAAATTATTTAAAATAAAT-AATCCAT
1 ACTAATAAATTATTTAAAATAAATCAATCCAT
1362147 ACTAATAAATTATTTAAAATAAATCAATCC
1 ACTAATAAATTATTTAAAATAAATCAATCC
1362177 GTACAACTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (32 bp):
ACTAATAAATTATTTAAAATAAATCAATCCAT
Found at i:1362213 original size:48 final size:49
Alignment explanation
Indices: 1362157--1362602 Score: 255
Period size: 54 Copynumber: 8.6 Consensus size: 49
1362147 ACTAATAAAT
* * *
1362157 TATTTAAAATAAATCAATCCGTAC-AACTA-CA-ATAATAAATCAATTCA
1 TATTTAAAATAAATCAATCCATACTAA-TATCATAAAATAAATCAATCCA
*
1362204 TATTTTAAAATAAATCAATCCATACTAATATTATTTAAAATAAATCAATCCA
1 TA-TTTAAAATAAATCAATCCATACTAATATCA--TAAAATAAATCAATCCA
* *
1362256 TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTA
1 TATTTAAAATAAATCAATCCATACTAAT--ATCA--TAAAATAAATCAATCCA
* ** * * * ** **
1362309 CAACTACAATAAAATCAATCCATATTTTAAAAT-A-AATCAATCTATACTAATAAA
1 TATTTAAAAT-AAATCAATCCATA--CTAATATCATAA--AATAAAT-C-AATCCA
** * ** **
1362363 TTATTTAAAATAAATCAATCCAAATTTTAAAAT-A-AATCAATTCATACTAATAAA
1 -TATTTAAAATAAATCAATCC--ATACTAATATCATAA--AATAAAT-C-AATCCA
* * *
1362417 TTATTTAAAATAAATTAATCCATAC-AACTA-CA-ATAATAAATCAATCTA
1 -TATTTAAAATAAATCAATCCATACTAA-TATCATAAAATAAATCAATCCA
*
1362465 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
1 TA-TTTAAAATAAATCAATCCATACTAAT--ATCA--TAAAATAAATCAATCCA
*
1362519 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
1 TA-TTTAAAATAAATCAATCCATACTAAT--ATCA--TAAAATAAATCAATCCA
1362573 TAATTTAAAATAAATCAATCCATACTAATA
1 T-ATTTAAAATAAATCAATCCATACTAATA
1362603 AATTATTTAA
Statistics
Matches: 335, Mismatches: 35, Indels: 53
0.79 0.08 0.13
Matches are distributed among these distances:
47 4 0.01
48 49 0.15
49 6 0.02
50 8 0.02
51 29 0.09
52 27 0.08
53 30 0.09
54 170 0.51
55 7 0.02
56 5 0.01
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (49 bp):
TATTTAAAATAAATCAATCCATACTAATATCATAAAATAAATCAATCCA
Found at i:1362231 original size:80 final size:81
Alignment explanation
Indices: 1362128--1362520 Score: 372
Period size: 80 Copynumber: 4.7 Consensus size: 81
1362118 TAATAAATTA
* *
1362128 TTTAAAATAAAT-AATCCATACTAATAAATTATTTAAAATAAATCAATCCGTACAACTACAAT-A
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
1362191 ATAAATCAATTCATAT
66 ATAAATCAATTCATAT
**
1362207 TTTAAAATAAATCAATCCATACTAAT--ATTATTTAAAATAAATCAATCCAT--ATTTAAAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
* * *
1362268 ATCAATCCATACTAATAAATT
66 ATAAAT-CA-ATTCAT--A-T
* *
1362289 ATTTAAAATAAATCAATCTACAACTACAATAAAATCAATCCATATTTTAAAATAAATCAATCTAT
1 -TTTAAAATAAATCAATC--C-A-TAC--T--AATAAAT---TA-TTTAAAATAAATCAATCCAT
* *
1362354 ACTAA-TAAATTATTTAAAATAAATCAATCCAAAT
53 AC-AACTAAA--A--T-AAATAAATCAATTCATAT
* * *
1362388 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATTAATCCATACAACTACAAT-A
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
1362452 ATAAATCAA-TCTATAT
66 ATAAATCAATTC-ATAT
1362468 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1362521 TTTTAAAATA
Statistics
Matches: 259, Mismatches: 23, Indels: 63
0.75 0.07 0.18
Matches are distributed among these distances:
76 6 0.02
77 6 0.02
78 25 0.10
79 17 0.07
80 77 0.30
81 1 0.00
82 2 0.01
83 17 0.07
84 1 0.00
85 3 0.01
86 24 0.09
87 5 0.02
89 1 0.00
90 6 0.02
91 3 0.01
92 1 0.00
93 2 0.01
94 3 0.01
95 1 0.00
96 3 0.01
97 19 0.07
98 16 0.06
99 5 0.02
100 2 0.01
101 1 0.00
102 2 0.01
103 3 0.01
104 7 0.03
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (81 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
ATAAATCAATTCATAT
Found at i:1362260 original size:21 final size:21
Alignment explanation
Indices: 1362235--1362278 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1362225 ATACTAATAT
1362235 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
1362256 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
1362277 TA
1 TA
1362279 CTAATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCCA
Found at i:1362400 original size:76 final size:75
Alignment explanation
Indices: 1362236--1362408 Score: 260
Period size: 76 Copynumber: 2.3 Consensus size: 75
1362226 TACTAATATT
1362236 ATTTAAAATAAATCAATCCATATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
1 ATTTAAAATAAATCAATCCATATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
*
1362301 TCAATCTACA
66 TCAATCCACA
* * *
1362311 A-CTACAATAAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATA
1 ATTTAAAAT-AAATCAATCCATA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
1362375 AATCAATCCA-A
64 AATCAATCCACA
*
1362386 ATTTTAAAATAAATCAATTCATA
1 A-TTTAAAATAAATCAATCCATA
1362409 CTAATAAATT
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
74 5 0.06
75 16 0.18
76 61 0.70
77 5 0.06
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (75 bp):
ATTTAAAATAAATCAATCCATATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
TCAATCCACA
Found at i:1362498 original size:134 final size:134
Alignment explanation
Indices: 1362128--1362574 Score: 768
Period size: 134 Copynumber: 3.4 Consensus size: 134
1362118 TAATAAATTA
*
1362128 TTTAAAATAAAT-AATCCATACTAATAAATTATTTAAAATAAATCAATCCGTACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1362192 TAAATCAAT-TCATATTTTAAAATAAATCAATCCATACTAAT--ATTATTTAAAATAAATCAATC
66 TAAATCAATCT-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
1362254 CATA-
130 CATAT
1362258 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-TACAACTACAAT-A
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
* *
1362320 -AAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCC
66 TAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
*
1362384 AAAT
131 ATAT
* *
1362388 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATTAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1362453 TAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
66 TAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
1362518 ATAT
131 ATAT
1362522 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1362575 ATTTAAAATA
Statistics
Matches: 298, Mismatches: 10, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
127 37 0.12
128 1 0.00
129 36 0.12
130 59 0.20
131 36 0.12
132 12 0.04
133 1 0.00
134 116 0.39
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (134 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
TAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
ATAT
Found at i:1362515 original size:54 final size:54
Alignment explanation
Indices: 1362451--1362619 Score: 320
Period size: 54 Copynumber: 3.1 Consensus size: 54
1362441 CAACTACAAT
*
1362451 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1362505 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1362559 AATAAATCAATCCATAATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1362613 AATAAAT
1 AATAAAT
1362620 ATTTAAAATA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 113 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:1362526 original size:22 final size:22
Alignment explanation
Indices: 1362500--1362542 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1362490 TAATAAATTA
1362500 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1362522 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1362543 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1362551 original size:22 final size:22
Alignment explanation
Indices: 1362502--1362604 Score: 71
Period size: 22 Copynumber: 4.2 Consensus size: 22
1362492 ATAAATTATT
**
1362502 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1362524 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
* *
1362547 TAAATTATTTAAAATAAATCAATCCATAA
1 TAAA--A--T-AAATCAATCCAT--ATAA
1362576 TTTAAAATAAATCAATCCATACTAA
1 --TAAAATAAATCAATCCATA-TAA
1362601 TAAA
1 TAAA
1362605 TTATTTAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
22 19 0.30
23 9 0.14
24 1 0.02
25 4 0.06
26 10 0.16
27 2 0.03
28 10 0.16
29 4 0.06
30 1 0.02
31 4 0.06
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1362624 original size:13 final size:13
Alignment explanation
Indices: 1362599--1362632 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
1362589 AATCCATACT
1362599 AATAAATTATTTAA
1 AATAAA-TATTTAA
1362613 AATAAATATTTAA
1 AATAAATATTTAA
1362626 AATAAAT
1 AATAAAT
1362633 CAATCCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATAAATATTTAA
Found at i:1362646 original size:22 final size:22
Alignment explanation
Indices: 1362554--1362652 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 22
1362544 TAATAAATTA
*
1362554 TTTAAAATAAATCAATCCATAA
1 TTTAAAATAAATCAATCCATAT
1362576 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
1362599 AATAAATTATTTAAAATAAATA-
1 TTTAAAATAAAT-CAATCCATAT
1362621 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1362643 TTTATAATAA
1 TTTAAAATAA
1362653 TTTATTTTAA
Statistics
Matches: 56, Mismatches: 18, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
21 6 0.11
22 37 0.66
23 7 0.12
24 6 0.11
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1362660 original size:15 final size:15
Alignment explanation
Indices: 1362640--1362728 Score: 135
Period size: 15 Copynumber: 6.0 Consensus size: 15
1362630 AATCAATCCA
*
1362640 TATTTTATAATAATT
1 TATTTTATAATAAAT
*
1362655 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
1362670 TATTTTATAATAAAT
1 TATTTTATAATAAAT
1362685 TATTTTA-AATAAAT
1 TATTTTATAATAAAT
*
1362699 TATTTTATAATAATT
1 TATTTTATAATAAAT
*
1362714 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
1362729 AACCTTATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
14 14 0.21
15 53 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTTATAATAAAT
Found at i:1362692 original size:67 final size:65
Alignment explanation
Indices: 1362544--1362750 Score: 200
Period size: 59 Copynumber: 3.3 Consensus size: 65
1362534 CAATCCATAC
* * ** ** *
1362544 TAATAAATTATTTAAAATAAATCAATCCATAATTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTATAAT-AATTTAT-TTTA-AAATAAATTAT
1362609 TTA
63 TTA
*
1362612 AAATAAA-TATTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTA-TTT
1362676 A
65 A
* * *
1362677 TAATAAATTATTT----TAAATAAAT---TATTTTATAATAATTTATTTTAAAATAAATAACCTT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTA-TTT
1362735 A
65 A
1362736 T--TAAATTATTTAAAA
1 TAATAAATTATTTAAAA
1362751 ATTATTTTAA
Statistics
Matches: 120, Mismatches: 13, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
57 10 0.08
59 35 0.29
62 8 0.07
64 9 0.08
65 12 0.10
66 10 0.08
67 30 0.25
68 6 0.05
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (65 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTA
Found at i:1362704 original size:29 final size:30
Alignment explanation
Indices: 1362640--1362728 Score: 153
Period size: 29 Copynumber: 3.0 Consensus size: 30
1362630 AATCAATCCA
*
1362640 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
1362670 TATTTTATAATAAATTATTTT-AAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
*
1362699 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
1362729 AACCTTATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
29 28 0.50
30 28 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TATTTTATAATAAATTATTTTAAAATAAAT
Found at i:1362742 original size:29 final size:28
Alignment explanation
Indices: 1362640--1362752 Score: 111
Period size: 30 Copynumber: 3.9 Consensus size: 28
1362630 AATCAATCCA
*
1362640 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAT--TAAATTATTTTAAAATAAAT
1362670 TATTTTATAATAAATTATTTT-AAATAAAT
1 TATTTTAT--TAAATTATTTTAAAATAAAT
*
1362699 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAT--TAAATTATTTTAAAATAAAT
* ** *
1362729 AACCTTATTAAATTATTTAAAAAT
1 TATTTTATTAAATTATTTTAAAAT
1362753 TATTTTAATA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
28 14 0.19
29 28 0.37
30 33 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
TATTTTATTAAATTATTTTAAAATAAAT
Found at i:1363710 original size:23 final size:23
Alignment explanation
Indices: 1363680--1363730 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
1363670 TGTTTCTGAG
1363680 GGAATTGAAATCTGTCAGGAATT
1 GGAATTGAAATCTGTCAGGAATT
1363703 GGAATTGAAATCTGTCAGGAATT
1 GGAATTGAAATCTGTCAGGAATT
1363726 GGAAT
1 GGAAT
1363731 CTAATTCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (23 bp):
GGAATTGAAATCTGTCAGGAATT
Found at i:1364481 original size:251 final size:247
Alignment explanation
Indices: 1364085--1364692 Score: 861
Period size: 251 Copynumber: 2.4 Consensus size: 247
1364075 TCCATCCGAG
1364085 ACCCGACCCGACCAAAATAAAGTTTCACCCA-ACCCGACCCGAATATATGAATTAGAAACCCGAC
1 ACCCGACCCGACCAAAATAAAGTTTCA-CCAGACCCGACCCGAATATATGAATTAGAAA--C--C
* *
1364149 GCGACCCGAAATAATAATAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATAT
61 -CGACCCAAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATAT
*
1364214 ATAGAGAGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTGGGTC
125 ATAGAGAGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA--TATT---T-
1364279 GGGTCGGGTCGGGTATTTTTCACCCTAAACCCG-A-ACCCGACCCAAATATCACACTT-AAAAAA
184 ---TCGGGTCGGGTATTTTTCACCCTAAACCCGAACACCCGACCCAAATATCACACTTAAAAAAA
1364341 -T
246 TT
*
1364342 -CCCGACCCGACCAAAATAAAGTTTCACCTGACCCGACCCGAATATATGAATTAGAAACCCGACC
1 ACCCGACCCGACCAAAATAAAGTTTCACCAGACCCGACCCGAATATATGAATTAGAAACCCGACC
* *
1364406 CAAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATTATATATAG
66 CAAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATATATAGAG
*
1364471 AGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGGTA
131 AGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGGTA
*
1364536 TTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAATT
196 TTTTTCACCCTAAACCCGAA--C-ACCCGACCCAAATATCACACTTAAAAAAATT
1364591 GACCCGACCCGACCAAAATAAAGTTTCACCAGACCCGACCCGAATATATGAATTAGAAACCCGAT
1 -ACCCGACCCGACCAAAATAAAGTTTCACCAGACCCGACCCGAATATATGAATTAGAAACCCGA-
1364656 CCGACCTGAAAA-AATAAAAAAAATATTTTTATTCAAT
64 -C--CC--AAAATAAT-AAAAAAATATTTTTATTCAAT
1364693 GTATGAATAA
Statistics
Matches: 325, Mismatches: 9, Indels: 34
0.88 0.02 0.09
Matches are distributed among these distances:
242 30 0.09
243 1 0.00
246 1 0.00
247 21 0.06
248 6 0.02
249 4 0.01
251 174 0.54
252 1 0.00
253 1 0.00
254 1 0.00
255 4 0.01
256 56 0.17
257 25 0.08
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (247 bp):
ACCCGACCCGACCAAAATAAAGTTTCACCAGACCCGACCCGAATATATGAATTAGAAACCCGACC
CAAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATATATAGAG
AGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGGTA
TTTTTCACCCTAAACCCGAACACCCGACCCAAATATCACACTTAAAAAAATT
Found at i:1366633 original size:19 final size:19
Alignment explanation
Indices: 1366609--1366654 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1366599 ACTGCAAATG
*
1366609 CCCATGCTGGACCATGCTA
1 CCCATGCTGGACCATGCCA
*
1366628 CCCATGTTGGACCATGCCA
1 CCCATGCTGGACCATGCCA
1366647 CCC-TGCTG
1 CCCATGCTG
1366655 CAGATGTCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.22
Consensus pattern (19 bp):
CCCATGCTGGACCATGCCA
Found at i:1375227 original size:19 final size:19
Alignment explanation
Indices: 1375200--1375236 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1375190 GCACTGCAAA
*
1375200 TGCCCATGCTGAACCATGC
1 TGCCAATGCTGAACCATGC
*
1375219 TGCCAATGCTGGACCATG
1 TGCCAATGCTGAACCATG
1375237 TCGCCCTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (19 bp):
TGCCAATGCTGAACCATGC
Found at i:1376471 original size:22 final size:20
Alignment explanation
Indices: 1376430--1376472 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
1376420 ACACTACCAC
*
1376430 CATTCCATTTTCACATCATT
1 CATTCCATTTTCACAACATT
1376450 CATTCCATTTTGCCACAACATT
1 CATTCCATTTT--CACAACATT
1376472 C
1 C
1376473 TCATTTGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.40
Consensus pattern (20 bp):
CATTCCATTTTCACAACATT
Found at i:1379534 original size:66 final size:66
Alignment explanation
Indices: 1379444--1379661 Score: 357
Period size: 66 Copynumber: 3.3 Consensus size: 66
1379434 GAGAGTTATA
* * *
1379444 GGTGCATT-TTGGCATAAAAGGTGCCACTAATAAAAATTATTGATCGATTTTGATTAATGCATAA
1 GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAA
1379508 C
66 C
* *
1379509 GGTGCATTATCGGTATAAAATGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAA
1 GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAA
1379574 C
66 C
* *
1379575 GGTGCATTATCGGCATAAAAGGTGCTACTAATGAAAATTATCGATCGATTTTGATTAACGCATAA
1 GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAA
1379640 C
66 C
*
1379641 GGTGCATTATCGACATAAAAG
1 GGTGCATTATCGGCATAAAAG
1379662 ATGTCACTCA
Statistics
Matches: 142, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
65 8 0.06
66 134 0.94
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (66 bp):
GGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAA
C
Found at i:1382196 original size:20 final size:20
Alignment explanation
Indices: 1382171--1382213 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1382161 CCATTTTCGT
1382171 AACGCGAATCTGTAAATCGC
1 AACGCGAATCTGTAAATCGC
*
1382191 AACGCGAATTTGTAAATCGC
1 AACGCGAATCTGTAAATCGC
1382211 AAC
1 AAC
1382214 ACAGAAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
AACGCGAATCTGTAAATCGC
Found at i:1382230 original size:20 final size:19
Alignment explanation
Indices: 1382207--1382277 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
1382197 AATTTGTAAA
1382207 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
1382227 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
* * *
1382247 TCACAAC-TGAATTTCAAAT
1 TCGCAACACGAA-GTCAAAT
1382266 TCGCAACACGAA
1 TCGCAACACGAA
1382278 TTTAGTTTCG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.02
19 16 0.38
20 25 0.60
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:1382280 original size:20 final size:20
Alignment explanation
Indices: 1382187--1382293 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
1382177 AATCTGTAAA
* *
1382187 TCGCAACGCGAATTTGTAAA-
1 TCGCAACACGAATTT-CAAAT
*
1382207 TCGCAACACAGAA-GTCAAAT
1 TCGCAACAC-GAATTTCAAAT
* *
1382227 TCGCAACGCG-ATAGTCAAAT
1 TCGCAACACGAAT-TTCAAAT
* *
1382247 TCACAAC-TGAATTTCAAAT
1 TCGCAACACGAATTTCAAAT
**
1382266 TCGCAACACGAATTT-AGTT
1 TCGCAACACGAATTTCAAAT
1382285 TCGCAACAC
1 TCGCAACAC
1382294 AAATATTTTG
Statistics
Matches: 70, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.01
19 28 0.40
20 38 0.54
21 3 0.04
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.23
Consensus pattern (20 bp):
TCGCAACACGAATTTCAAAT
Found at i:1382449 original size:14 final size:15
Alignment explanation
Indices: 1382430--1382467 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1382420 TCCCCATCTC
1382430 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1382444 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1382460 TAATTTTT
1 TAATTTTT
1382468 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1383193 original size:24 final size:24
Alignment explanation
Indices: 1383166--1383219 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1383156 GTATTCGAAA
1383166 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1383190 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1383214 TTTGAT
1 TTTGAT
1383220 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1385517 original size:18 final size:18
Alignment explanation
Indices: 1385484--1385519 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1385474 AAGCAAAAGG
**
1385484 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
1385502 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1385520 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1386103 original size:61 final size:63
Alignment explanation
Indices: 1385966--1386088 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 63
1385956 TTTTAGAAAC
* *
1385966 AACATATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACACATCAAATT
1386031 A
63 A
* * *
1386032 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATCAA
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACACATCAA
1386089 TAATCAACTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
61 24 0.46
62 3 0.06
66 25 0.48
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACACATCAAATTA
Found at i:1387405 original size:21 final size:21
Alignment explanation
Indices: 1387381--1387433 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1387371 ATGAATCGGG
1387381 CTCTTGAACGGCG-AGCGGGAC
1 CTCTTGAACGGCGAAG-GGGAC
* ** *
1387402 CTCTTAAACGATGAAGGGGGC
1 CTCTTGAACGGCGAAGGGGAC
1387423 CTCTTGAACGG
1 CTCTTGAACGG
1387434 TGGGAGGGGC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.23, C:0.25, G:0.34, T:0.19
Consensus pattern (21 bp):
CTCTTGAACGGCGAAGGGGAC
Found at i:1387442 original size:21 final size:21
Alignment explanation
Indices: 1387401--1387498 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 21
1387391 GCGAGCGGGA
* *
1387401 CCTCTTAAACGAT-GAAGGGGG
1 CCTCTTGAACGATGGGA-GGGG
*
1387422 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGGGAGGGG
* * * *
1387443 CTTATTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGGGAGGGG
* **
1387464 CCTCTTGAACGATAGGAGACG
1 CCTCTTGAACGATGGGAGGGG
*
1387485 CCTCTTGAATGATG
1 CCTCTTGAACGATG
1387499 ATAGGTGCAT
Statistics
Matches: 57, Mismatches: 17, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
20 1 0.02
21 53 0.93
22 3 0.05
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGGGAGGGG
Found at i:1387947 original size:42 final size:41
Alignment explanation
Indices: 1387851--1387950 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
1387841 CGTGAAAAAT
* * *
1387851 CCACCTCACCACGTAAAGATCGAACCTCATCACGCCATGCA
1 CCACCTCATCACGTAAAGATCGAACCTCATCACGCAAAGCA
** * *
1387892 CCATTATCTTCACGTAAAGTATCG-ACCTCATGACGCAAAGCA
1 CCA-CCTCATCACGTAAAG-ATCGAACCTCATCACGCAAAGCA
1387934 CCGACCTCATCACGTAA
1 CC-ACCTCATCACGTAA
1387951 TTCCCCTAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
41 3 0.07
42 38 0.83
43 5 0.11
ACGTcount: A:0.32, C:0.36, G:0.13, T:0.19
Consensus pattern (41 bp):
CCACCTCATCACGTAAAGATCGAACCTCATCACGCAAAGCA
Found at i:1389590 original size:20 final size:20
Alignment explanation
Indices: 1389565--1389635 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
1389555 AAACTTAAAT
*
1389565 TCGCAACGTAAAAATGAAAA
1 TCGCAACGTGAAAATGAAAA
* *
1389585 TCGCAATGGGAAAATGAAAA
1 TCGCAACGTGAAAATGAAAA
* *
1389605 TCGCAATGCGAAAATGAAAA
1 TCGCAACGTGAAAATGAAAA
1389625 TCGCAACGTGA
1 TCGCAACGTGA
1389636 TTTTCGTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGTGAAAATGAAAA
Found at i:1390172 original size:40 final size:39
Alignment explanation
Indices: 1390127--1390285 Score: 164
Period size: 40 Copynumber: 4.0 Consensus size: 39
1390117 GTAAAAATAG
* *
1390127 TTGACTTTCGCGTTGCGAATTTGACGATCGCGTTGCGAAT
1 TTGACTTT-GTGTTGCGAATTTGACAATCGCGTTGCGAAT
* * *
1390167 TTGACTTATGTGTTGCG-ATTT-ATAAATTTGCGTCGCGAAT
1 TTGACTT-TGTGTTGCGAATTTGA-CAA-TCGCGTTGCGAAT
*
1390207 TTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAAT
1 TTGAC-TTTGTGTTGCGAATTTGACAATCGCGTTGCGAAT
1390247 TTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGAA
1 TTGACTT-TGTGTTGCGAATTTGAC-AA-TCGCGTTGCGAA
1390286 ATTGGAAACT
Statistics
Matches: 100, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
38 3 0.03
39 12 0.12
40 76 0.76
41 8 0.08
42 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (39 bp):
TTGACTTTGTGTTGCGAATTTGACAATCGCGTTGCGAAT
Found at i:1390223 original size:80 final size:80
Alignment explanation
Indices: 1390127--1390285 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 80
1390117 GTAAAAATAG
*
1390127 TTGACTTTCGCGTTGCGAATTTGACGATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTATAA
1 TTGACTTTCGCGTTGCGAATTTGACGATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAA
*
1390192 ATTTGCGTCGCGAAT
66 ATTCGCGTCGCGAAT
* * * *
1390207 TTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAA
1 TTGACTTTCGCGTTGCGAATTTGACGATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAA
*
1390272 ATTCGCGTTGCGAA
66 ATTCGCGTCGCGAA
1390286 ATTGGAAACT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (80 bp):
TTGACTTTCGCGTTGCGAATTTGACGATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAA
ATTCGCGTCGCGAAT
Found at i:1390261 original size:20 final size:20
Alignment explanation
Indices: 1390127--1390264 Score: 122
Period size: 20 Copynumber: 6.9 Consensus size: 20
1390117 GTAAAAATAG
1390127 TTGACTT-TCGCGTTGCGAAT
1 TTGACTTCT-GCGTTGCGAAT
*
1390147 TTGACGATC-GCGTTGCGAAT
1 TTGAC-TTCTGCGTTGCGAAT
* * *
1390167 TTGACTTATGTGTTGCGATT
1 TTGACTTCTGCGTTGCGAAT
* * *
1390187 TATAAATT-TGCGTCGCGAAT
1 T-TGACTTCTGCGTTGCGAAT
* *
1390207 TTGACTTTTGTGTTGCGAAT
1 TTGACTTCTGCGTTGCGAAT
1390227 TTGACTATC-GCGTTGCGAAT
1 TTGACT-TCTGCGTTGCGAAT
*
1390247 TTGACTTCTGTGTTGCGA
1 TTGACTTCTGCGTTGCGA
1390265 TTTACAAATT
Statistics
Matches: 94, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
19 7 0.07
20 81 0.86
21 6 0.06
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (20 bp):
TTGACTTCTGCGTTGCGAAT
Found at i:1390305 original size:80 final size:80
Alignment explanation
Indices: 1390141--1390329 Score: 220
Period size: 80 Copynumber: 2.4 Consensus size: 80
1390131 CTTTCGCGTT
* * *
1390141 GCGAATTTGACGATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTATAAATTTGCGTCGCGAA
1 GCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTCGCGAA
* *** * *
1390206 TTTGACTTTTGTGTT
66 TTGGACAACTGGGTA
* *
1390221 GCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAA
1 GCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTCGCG-A
1390286 ATTGGA-AACTGGGTA
65 ATTGGACAACTGGGTA
* * *
1390301 GCGAAATTGGAGT-TCGCATTGCGAATTTG
1 GCG-AATTTGACTATCGCGTTGCGAATTTG
1390330 TTGGTTATTT
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
80 80 0.86
81 13 0.14
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (80 bp):
GCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCGTCGCGAA
TTGGACAACTGGGTA
Found at i:1390873 original size:29 final size:31
Alignment explanation
Indices: 1390822--1390881 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
1390812 AATTATATAA
** *
1390822 TTTTTAAATTTGACACATTAAAATAACTTTT
1 TTTTTAAATTTGACACACCAAAATAAATTTT
1390853 TTTTTAAA-TTGACAC-CCAAAATAAATTTT
1 TTTTTAAATTTGACACACCAAAATAAATTTT
1390882 ATAGCCCAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 11 0.42
30 7 0.27
31 8 0.31
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (31 bp):
TTTTTAAATTTGACACACCAAAATAAATTTT
Found at i:1393332 original size:29 final size:29
Alignment explanation
Indices: 1393297--1393378 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1393287 AAACTAAATT
*
1393297 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1393326 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1393355 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1393379 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1398103 original size:29 final size:29
Alignment explanation
Indices: 1398068--1398149 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1398058 AAACTAAATT
*
1398068 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1398097 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1398126 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1398150 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1399316 original size:31 final size:31
Alignment explanation
Indices: 1399278--1399336 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1399268 ATACAATCAA
*
1399278 TTTCGTTTTTATTTAATTAAGGTATGATTAT
1 TTTCGTTTTTATTTAATTAAGATATGATTAT
1399309 TTTCGTTTTTATTTAATTAAGATATGAT
1 TTTCGTTTTTATTTAATTAAGATATGAT
1399337 CACCACCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (31 bp):
TTTCGTTTTTATTTAATTAAGATATGATTAT
Found at i:1400508 original size:18 final size:19
Alignment explanation
Indices: 1400485--1400530 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
1400475 ATATATATTT
*
1400485 TTTCTTA-TTGAAAGCATG
1 TTTCTTATTTAAAAGCATG
1400503 TTTCTTAATTTTAAAAGCATG
1 TTTCTT-A-TTTAAAAGCATG
1400524 TTTCTTA
1 TTTCTTA
1400531 CTATTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 1 0.04
20 1 0.04
21 16 0.67
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTCTTATTTAAAAGCATG
Found at i:1400521 original size:21 final size:21
Alignment explanation
Indices: 1400490--1400539 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1400480 TATTTTTTCT
*
1400490 TATTGAAAGCATGTTTCTTAA
1 TATTAAAAGCATGTTTCTTAA
* *
1400511 TTTTAAAAGCATGTTTCTTAC
1 TATTAAAAGCATGTTTCTTAA
1400532 TATTAAAA
1 TATTAAAA
1400540 TTTTTGTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
TATTAAAAGCATGTTTCTTAA
Found at i:1404023 original size:2 final size:2
Alignment explanation
Indices: 1403971--1404005 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1403961 GTGCTAGAGG
1403971 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
1404006 ACAACCTATC
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:1409041 original size:26 final size:26
Alignment explanation
Indices: 1409004--1409063 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
1408994 CCTGAGACAT
1409004 TACTT-AACGATATCAAGATGTTTAC
1 TACTTAAACGATATCAAGATGTTTAC
1409029 TACTTAAACGATATCAAGATGTTTAC
1 TACTTAAACGATATCAAGATGTTTAC
1409055 TACTTAAAC
1 TACTTAAAC
1409064 CAACCCGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 5 0.15
26 29 0.85
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (26 bp):
TACTTAAACGATATCAAGATGTTTAC
Found at i:1409129 original size:21 final size:22
Alignment explanation
Indices: 1409087--1409132 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1409077 CAGTGATTAC
*
1409087 ATATTTAAAAAGTTATACTTAA
1 ATATTTAAAAAGTAATACTTAA
*
1409109 ATATTTAAAAA-TAATATTTAA
1 ATATTTAAAAAGTAATACTTAA
1409130 ATA
1 ATA
1409133 ATGTATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
ATATTTAAAAAGTAATACTTAA
Found at i:1410414 original size:20 final size:20
Alignment explanation
Indices: 1410389--1410449 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
1410379 GTCCCGGAGG
1410389 ACCACTGATTGTTCCGAAGA
1 ACCACTGATTGTTCCGAAGA
*
1410409 ACCACT-A-TG-TCCGAAGG
1 ACCACTGATTGTTCCGAAGA
*
1410426 ACCACTGTTTGTTCCGAAGA
1 ACCACTGATTGTTCCGAAGA
1410446 ACCA
1 ACCA
1410450 TTATGTCCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 13 0.37
18 2 0.06
19 3 0.09
20 17 0.49
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (20 bp):
ACCACTGATTGTTCCGAAGA
Found at i:1410423 original size:17 final size:17
Alignment explanation
Indices: 1410361--1410468 Score: 90
Period size: 17 Copynumber: 5.9 Consensus size: 17
1410351 GTTCAGTATT
*
1410361 TGTCCGGAGGACCACTA
1 TGTCCGAAGGACCACTA
*
1410378 TGTCCCGGAGGACCACTGA
1 TGT-CCGAAGGACCACT-A
*
1410397 TTGTTCCGAAGAACCACTA
1 -TG-TCCGAAGGACCACTA
*
1410416 TGTCCGAAGGACCACTGTT
1 TGTCCGAAGGACCAC--TA
* *
1410435 TGTTCCGAAGAACCATTA
1 TG-TCCGAAGGACCACTA
*
1410453 TGTCCGAAGGATCACT
1 TGTCCGAAGGACCACT
1410469 GTTCATCCCT
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
17 26 0.35
18 18 0.24
19 5 0.07
20 24 0.32
21 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (17 bp):
TGTCCGAAGGACCACTA
Found at i:1410438 original size:37 final size:37
Alignment explanation
Indices: 1410371--1410471 Score: 157
Period size: 37 Copynumber: 2.7 Consensus size: 37
1410361 TGTCCGGAGG
* *
1410371 ACCACTATGTCCCGGAGGACCACTGATTGTTCCGAAGA
1 ACCACTATGT-CCGAAGGACCACTGTTTGTTCCGAAGA
1410409 ACCACTATGTCCGAAGGACCACTGTTTGTTCCGAAGA
1 ACCACTATGTCCGAAGGACCACTGTTTGTTCCGAAGA
* *
1410446 ACCATTATGTCCGAAGGATCACTGTT
1 ACCACTATGTCCGAAGGACCACTGTT
1410472 CATCCCTCGA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 49 0.83
38 10 0.17
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (37 bp):
ACCACTATGTCCGAAGGACCACTGTTTGTTCCGAAGA
Found at i:1415499 original size:20 final size:20
Alignment explanation
Indices: 1415476--1415540 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
1415466 GTCCCGGAGG
1415476 ACCACTGATTGTTCCGAAGA
1 ACCACTGATTGTTCCGAAGA
*
1415496 ACCACTGTTTGTTCCGAAGA
1 ACCACTGATTGTTCCGAAGA
* * *
1415516 ACCA-TTA-TGTCCCGAAGG
1 ACCACTGATTGTTCCGAAGA
1415534 ACCACTG
1 ACCACTG
1415541 TTCATCCCTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 13 0.34
19 2 0.05
20 23 0.61
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (20 bp):
ACCACTGATTGTTCCGAAGA
Found at i:1415532 original size:18 final size:20
Alignment explanation
Indices: 1415465--1415541 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
1415455 GTTCAGTATT
* *
1415465 TGTCCCGGAGGACCACTG-A
1 TGTCCCGAAGAACCACTGTA
* *
1415484 TTGTTCCGAAGAACCACTGTT
1 -TGTCCCGAAGAACCACTGTA
*
1415505 TGTTCCGAAGAACCA-T-TA
1 TGTCCCGAAGAACCACTGTA
*
1415523 TGTCCCGAAGGACCACTGT
1 TGTCCCGAAGAACCACTGT
1415542 TCATCCCTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 14 0.30
19 2 0.04
20 31 0.66
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (20 bp):
TGTCCCGAAGAACCACTGTA
Found at i:1418913 original size:17 final size:16
Alignment explanation
Indices: 1418891--1418925 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 16
1418881 TAAATTCAAC
1418891 AAAATAATATTTATCTA
1 AAAATAA-ATTTATCTA
1418908 AAAATAAATTTATCTA
1 AAAATAAATTTATCTA
1418924 AA
1 AA
1418926 TTTTCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATAAATTTATCTA
Found at i:1419119 original size:3 final size:3
Alignment explanation
Indices: 1419111--1419239 Score: 190
Period size: 3 Copynumber: 43.7 Consensus size: 3
1419101 TTTTTATCCA
*
1419111 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
1419158 TAT TAG TAT TAT TAG TAT TAT TAT TAT TAT TAG TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1419205 TAT TAT CAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1419240 AATATATATT
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
2 4 0.04
3 108 0.96
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1419251 original size:11 final size:11
Alignment explanation
Indices: 1419235--1419266 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1419225 TTATTATTAT
1419235 TATTAAATATA
1 TATTAAATATA
1419246 TATTAAATATA
1 TATTAAATATA
1419257 TATATAAATA
1 TAT-TAAATA
1419267 ATAAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1420515 original size:19 final size:18
Alignment explanation
Indices: 1420483--1420531 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1420473 TAGATTTTTA
1420483 ATTTTATT-TTTTCAGTT
1 ATTTTATTGTTTTCAGTT
*
1420500 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCAGTT
1420519 ATTTTATTGTTTT
1 ATTTTATTGTTTT
1420532 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.71
Consensus pattern (18 bp):
ATTTTATTGTTTTCAGTT
Found at i:1420585 original size:11 final size:11
Alignment explanation
Indices: 1420571--1420613 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1420561 TTTTATTATA
1420571 TTATTAAATAT
1 TTATTAAATAT
1420582 TTATTAAATAT
1 TTATTAAATAT
1420593 TT-TATAAATAT
1 TTAT-TAAATAT
* *
1420604 ATAATAAATA
1 TTATTAAATA
1420614 GTATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 1 0.04
11 27 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TTATTAAATAT
Found at i:1422392 original size:22 final size:22
Alignment explanation
Indices: 1422367--1422415 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1422357 CTTACTTTCA
1422367 CCCAAAATCCTAAATCT-AAATT
1 CCCAAAATCC-AAATCTCAAATT
* *
1422389 CCCAATATCCAAATCTCTAATT
1 CCCAAAATCCAAATCTCAAATT
1422411 CCCAA
1 CCCAA
1422416 CTTCAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.27
Consensus pattern (22 bp):
CCCAAAATCCAAATCTCAAATT
Found at i:1422556 original size:6 final size:6
Alignment explanation
Indices: 1422492--1422545 Score: 81
Period size: 6 Copynumber: 8.7 Consensus size: 6
1422482 GGAAAAGCAC
*
1422492 AGGGAA AGGGAA AGGAGGAA AGGGAA AGGGAA AGGGAA AGGGAA AGAGAA
1 AGGGAA AGGGAA A-G-GGAA AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA
1422542 AGGG
1 AGGG
1422546 GGAAGGGGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 37 0.84
7 2 0.05
8 5 0.11
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGGAA
Found at i:1422604 original size:15 final size:14
Alignment explanation
Indices: 1422584--1422611 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1422574 TGCTGTGTTG
1422584 TTTTTTTTTAAATA
1 TTTTTTTTTAAATA
1422598 TTTTTTTTTAAATA
1 TTTTTTTTTAAATA
1422612 AAATCTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTTTAAATA
Found at i:1422896 original size:23 final size:22
Alignment explanation
Indices: 1422870--1422916 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1422860 TTTTTAACAG
* *
1422870 TAAATTAAATAAAAATCAACTTT
1 TAAATCAAAT-AAAATCAAATTT
*
1422893 TAAATCAAATCAAATCAAATTT
1 TAAATCAAATAAAATCAAATTT
1422915 TA
1 TA
1422917 TTCACCTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATCAAATAAAATCAAATTT
Found at i:1424174 original size:267 final size:272
Alignment explanation
Indices: 1423879--1424423 Score: 746
Period size: 276 Copynumber: 2.0 Consensus size: 272
1423869 GAAATATTTT
*
1423879 TTATAAAACAATATATTTTAATTAATTAATAAAAACATTTTTATAATATTATATAATCAAA-T-T
1 TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
* * *
1423942 ATTTTTATAC-ATGACCCTCAAACTCATAAAAAA-TTAATATGATAC-CTTGATCAAC-TGTTTC
66 ATTTTTATACTATGACCCTCAAACTCAGAAAAAACTCAATATGAT-CTCTTAATCAACAT-TTTC
* * ** ** * *
1424003 TATCATTAG-CATTACAATACCAACACGACATTTCATGATGCTGACGTGA-TGATTCACGATAAC
129 TATCATTAGTCAATACAATACCAACACGACAATTCACAACACTAACGTGATTG-TTCAAGATAAC
* * *
1424066 TAATGACATATTCACATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAGTTTATAATT
193 TAATAACATATTCAAATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAATTTATAATT
*
1424131 AATATACTTTTATTG
258 AATACACTTTTATTG
1424146 TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
1 TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
* **
1424211 TTTTTTATACTTAATATGGTCCTCAAACTCAGAAAAAACTCAATATGATCTCTTAATCAACATTT
66 ATTTTTATAC----TATGACCCTCAAACTCAGAAAAAACTCAATATGATCTCTTAATCAACATTT
* * * * *
1424276 TCTATCATTAGTCAATACAATATCAGCATGATAATTCACAACACTAACGTGATTGTTCAAGATGA
127 TCTATCATTAGTCAATACAATACCAACACGACAATTCACAACACTAACGTGATTGTTCAAGATAA
*
1424341 CTAATAACATATTCAAATTATCTTTTTAATTAATTAATAAAAACATATTCCCTTGAATTTATAAT
192 CTAATAACATATTCAAATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAATTTATAAT
1424406 TAATACACTTTTATTG
257 TAATACACTTTTATTG
1424422 TT
1 TT
1424424 TTTCCTCTAC
Statistics
Matches: 241, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
267 60 0.25
268 1 0.00
269 10 0.04
274 21 0.09
275 31 0.13
276 116 0.48
277 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (272 bp):
TTATAAAACAATATATTTTAATTAATTAATAAAAACATTATTATAATATTATATAATCAAACTAT
ATTTTTATACTATGACCCTCAAACTCAGAAAAAACTCAATATGATCTCTTAATCAACATTTTCTA
TCATTAGTCAATACAATACCAACACGACAATTCACAACACTAACGTGATTGTTCAAGATAACTAA
TAACATATTCAAATTATCTTTCTAATTAATTAATAAAAACATATTCCCTTGAATTTATAATTAAT
ACACTTTTATTG
Found at i:1434342 original size:49 final size:49
Alignment explanation
Indices: 1434289--1434397 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 49
1434279 GGAATATGTA
* *
1434289 AAAATATTTATAGTTTTATCC-ATGTAAGTATACATATGAGAAATCTGTG
1 AAAATATTTATAATATTA-CCAATGTAAGTATACATATGAGAAATCTGTG
* ** * * *
1434338 AAAATATTCATAATATTACCAATGTAAGTATATGTATGTGACATTTGTG
1 AAAATATTTATAATATTACCAATGTAAGTATACATATGAGAAATCTGTG
1434387 -AAATATTTATA
1 AAAATATTTATA
1434398 TCTACATTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
48 12 0.24
49 38 0.76
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (49 bp):
AAAATATTTATAATATTACCAATGTAAGTATACATATGAGAAATCTGTG
Found at i:1434523 original size:50 final size:49
Alignment explanation
Indices: 1434469--1434682 Score: 139
Period size: 50 Copynumber: 4.3 Consensus size: 49
1434459 TAGTTATAGC
* *
1434469 TTATATGAAATCTGTGAAATTAATCATGTTTATAACAGTGTAATTATGAA
1 TTATATGAAATATGTGAAATTAATCATGTTTA-AACAGTGTAAATATGAA
* * * *
1434519 TTATATAAAATATGTAAAATTAATCACG-ATAACACTAGTGTAAAATAT-AA
1 TTATATGAAATATGTGAAATTAATCATGTTTAA-AC-AGTGT-AAATATGAA
* ** * * * *
1434569 TTATATGAAATTTGTGATGTTGATCATGTTTACAACAATATAAGTATG-A
1 TTATATGAAATATGTGAAATTAATCATGTTTA-AACAGTGTAAATATGAA
* * * * * ** * * *
1434618 TTATATGATATGTTTCAAGTTGGTCATGTTTACACAATATAAATATG-A
1 TTATATGAAATATGTGAAATTAATCATGTTTAAACAGTGTAAATATGAA
*
1434666 TCATATGAAATATGTGA
1 TTATATGAAATATGTGA
1434683 TGATGTTCAT
Statistics
Matches: 128, Mismatches: 30, Indels: 14
0.74 0.17 0.08
Matches are distributed among these distances:
48 27 0.21
49 36 0.28
50 55 0.43
51 9 0.07
52 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (49 bp):
TTATATGAAATATGTGAAATTAATCATGTTTAAACAGTGTAAATATGAA
Found at i:1434894 original size:21 final size:21
Alignment explanation
Indices: 1434868--1434919 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1434858 CAAGTTTAAT
*
1434868 ATTTCGTGTGCACCAG-GTGAC
1 ATTTCGTGTGCACC-GTGTGAA
* *
1434889 ATTTCGTGTACATCGTGTGAA
1 ATTTCGTGTGCACCGTGTGAA
1434910 ATTTCGTGTG
1 ATTTCGTGTG
1434920 TTCGTGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (21 bp):
ATTTCGTGTGCACCGTGTGAA
Found at i:1436506 original size:21 final size:21
Alignment explanation
Indices: 1436464--1436506 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1436454 TTTCTGGGTT
* * *
1436464 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1436485 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1436506 A
1 A
1436507 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1436566 original size:66 final size:67
Alignment explanation
Indices: 1436486--1436635 Score: 223
Period size: 67 Copynumber: 2.3 Consensus size: 67
1436476 ACCCATTCAA
*
1436486 GGGGAACCGATACCCCCTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
1436550 -GG
65 GGG
* * * *
1436552 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAG
1436617 GG
66 GG
*
1436619 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1436636 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
66 32 0.42
67 44 0.58
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAG
GG
Found at i:1436971 original size:29 final size:29
Alignment explanation
Indices: 1436937--1437008 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1436927 CATATTATGA
* *
1436937 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
1436966 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
1436995 TGCATGACATGAAT
1 TACATGACATGAAT
1437009 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:1437064 original size:30 final size:30
Alignment explanation
Indices: 1437022--1437098 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
1437012 CAGAAAAGTT
* *
1437022 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
1437053 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
1437083 ATATGACTACGTGATA
1 ATATGACTATGTGATA
1437099 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:1437375 original size:23 final size:23
Alignment explanation
Indices: 1437309--1437367 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
1437299 ATCATTATAT
*
1437309 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
1437331 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
1437354 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1437368 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:1443447 original size:21 final size:21
Alignment explanation
Indices: 1443405--1443447 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1443395 TTTCTGGGTT
* * *
1443405 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1443426 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1443447 A
1 A
1443448 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1443507 original size:66 final size:67
Alignment explanation
Indices: 1443427--1443576 Score: 223
Period size: 67 Copynumber: 2.3 Consensus size: 67
1443417 ACCCATTCAA
*
1443427 GGGGAACCGATACCCCCTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
1443491 -GG
65 GGG
* * * *
1443493 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAG
1443558 GG
66 GG
*
1443560 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1443577 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
66 32 0.42
67 44 0.58
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAG
GG
Found at i:1443912 original size:29 final size:29
Alignment explanation
Indices: 1443878--1443949 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1443868 CATATTATGA
* *
1443878 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
1443907 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
1443936 TGCATGACATGAAT
1 TACATGACATGAAT
1443950 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:1444005 original size:30 final size:30
Alignment explanation
Indices: 1443963--1444039 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
1443953 CAGAAAAGTT
* *
1443963 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
1443994 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
1444024 ATATGACTACGTGATA
1 ATATGACTATGTGATA
1444040 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:1444316 original size:23 final size:23
Alignment explanation
Indices: 1444250--1444308 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
1444240 ATCATTATAT
*
1444250 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
1444272 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
1444295 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1444309 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:1445563 original size:31 final size:31
Alignment explanation
Indices: 1445527--1445585 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1445517 AACTTAAAAG
*
1445527 AGTTTTACAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1445558 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1445586 CCAAACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1445636 original size:22 final size:22
Alignment explanation
Indices: 1445610--1445652 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1445600 TAATAAATTA
*
1445610 TTTAAAATAAATCAATGCATAT
1 TTTAAAATAAATCAATCCATAT
1445632 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1445653 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1445661 original size:22 final size:22
Alignment explanation
Indices: 1445612--1445660 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1445602 ATAAATTATT
* **
1445612 TAAAATAAATCAATGCATATTT
1 TAAAATAAATCAATCCATATAA
1445634 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1445657 TAAA
1 TAAA
1445661 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1445670 original size:32 final size:31
Alignment explanation
Indices: 1445632--1445819 Score: 136
Period size: 32 Copynumber: 6.7 Consensus size: 31
1445622 CAATGCATAT
1445632 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
1445664 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
1445694 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
1445712 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
1445744 TTTAAAATAAATCAAT---T-C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
1445766 TTTAAAATAGATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
1445798 TTTAAAATAAATCAATCTATAC
1 TTTAAAATAAATCAATCCATAC
1445820 AACTATAATA
Statistics
Matches: 125, Mismatches: 5, Indels: 52
0.69 0.03 0.29
Matches are distributed among these distances:
20 1 0.01
22 28 0.22
23 2 0.02
24 3 0.02
25 2 0.02
26 18 0.14
28 4 0.03
29 1 0.01
30 2 0.02
31 3 0.02
32 61 0.49
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.35
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:1445705 original size:80 final size:80
Alignment explanation
Indices: 1445615--1445924 Score: 377
Period size: 80 Copynumber: 3.9 Consensus size: 80
1445605 AATTATTTAA
1445615 AATAAATCAATGC-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAAT-CTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1445679 TCCATACAACTACAAT
65 TCCATACAACTACAAT
* *
1445695 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *** *
1445760 TCATA-TTTTAAAAT
66 CCATACAACTACAAT
* * * *
1445774 AGATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATAC-AACT--A-TA---ATAAT
1 A-ATAAATCAAT-CT-AT--A-T-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAAT
1445832 AAATCAATCCATACAACTACAAT
58 AAATCAATCCATACAACTACAAT
1445855 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1445920 CCATA
66 CCATA
1445925 TTTTATAATA
Statistics
Matches: 192, Mismatches: 21, Indels: 34
0.78 0.09 0.14
Matches are distributed among these distances:
74 22 0.11
75 3 0.02
76 2 0.01
77 2 0.01
78 2 0.01
79 9 0.05
80 115 0.60
81 7 0.04
82 2 0.01
83 2 0.01
84 2 0.01
85 3 0.02
86 21 0.11
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:1445751 original size:134 final size:134
Alignment explanation
Indices: 1445600--1445844 Score: 454
Period size: 134 Copynumber: 1.8 Consensus size: 134
1445590 ACAACTACAA
1445600 TAATAAATTATTTAAAATAAATCAATGCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATGCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1445665 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
1445730 ATAC
131 ATAC
* *
1445734 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAGATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATGCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* *
1445799 TTAAAATAAATCAATCTATACAACTATAATAATAAATCAATCCATA
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA
1445845 CAACTACAAT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
134 107 1.00
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (134 bp):
TAATAAATTATTTAAAATAAATCAATGCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
ATAC
Found at i:1445765 original size:54 final size:54
Alignment explanation
Indices: 1445695--1445935 Score: 284
Period size: 54 Copynumber: 4.5 Consensus size: 54
1445685 CAACTACAAT
* *
1445695 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1445749 AATAAATCAATTCATATTTTAAAATAGATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
1445803 AATAAATCAA-TCTATACAACTATAATAATAAATCAATCCATAC-AACTACA--A--T--
1 AATAAATCAATTC-AT---ATTTTAA-AATAAATCAATCCATACTAA-TAAATTATTTAA
1445855 AATAAATCAA-TCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATTC-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
1445909 AATAAATCAATCCATATTTTATAATAA
1 AATAAATCAATTCATATTTTAAAATAA
1445936 TTTATTTTAA
Statistics
Matches: 161, Mismatches: 12, Indels: 28
0.80 0.06 0.14
Matches are distributed among these distances:
48 20 0.12
49 7 0.04
50 1 0.01
52 16 0.10
53 2 0.01
54 87 0.54
55 1 0.01
56 1 0.01
57 7 0.04
58 19 0.12
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:1445770 original size:22 final size:22
Alignment explanation
Indices: 1445744--1445786 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1445734 TAATAAATTA
*
1445744 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
*
1445766 TTTAAAATAGATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1445787 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1445836 original size:26 final size:26
Alignment explanation
Indices: 1445803--1445870 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
1445793 AATTATTTAA
*
1445803 AATAAATCAATCTATACAACTATAAT
1 AATAAATCAATCTATACAACTACAAT
*
1445829 AATAAATCAATCCATACAACTACAAT
1 AATAAATCAATCTATACAACTACAAT
1445855 AATAAATCAATCTATA
1 AATAAATCAATCTATA
1445871 TTTTAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (26 bp):
AATAAATCAATCTATACAACTACAAT
Found at i:1445901 original size:22 final size:23
Alignment explanation
Indices: 1445800--1445900 Score: 80
Period size: 26 Copynumber: 4.2 Consensus size: 23
1445790 ATAAATTATT
* *
1445800 TAAAATAAATCAATCTATACAACTA
1 TAAAATAAATCAATCCATACTA--A
1445825 TAATAATAAATCAATCCATAC-AA
1 TAA-AATAAATCAATCCATACTAA
* **
1445848 CTACAATAATAAATCAATCTATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
1445874 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
1445897 TAAA
1 TAAA
1445901 TTATTTAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
22 15 0.24
23 8 0.13
24 1 0.02
25 5 0.08
26 34 0.54
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:1445941 original size:36 final size:33
Alignment explanation
Indices: 1445869--1446011 Score: 122
Period size: 29 Copynumber: 4.5 Consensus size: 33
1445859 AATCAATCTA
*
1445869 TATTTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAAT
*
1445902 TA-TTTAAAATAAATCAATCCATATTTTATAATAATT
1 TATTTTAAAATAAATCAATCCATA----ATAATAAAT
* * *
1445938 TATTTTAAAATAAAT-TAT--TTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAAT
* * *
1445968 TATTTT-AAATAAAT-TAT--TTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAAT
1445997 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
1446012 AACCTTATTA
Statistics
Matches: 98, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
29 29 0.30
30 22 0.22
32 21 0.21
33 2 0.02
34 1 0.01
36 11 0.11
37 12 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (33 bp):
TATTTTAAAATAAATCAATCCATAATAATAAAT
Found at i:1445943 original size:15 final size:15
Alignment explanation
Indices: 1445923--1446011 Score: 144
Period size: 15 Copynumber: 6.0 Consensus size: 15
1445913 AATCAATCCA
*
1445923 TATTTTATAATAATT
1 TATTTTATAATAAAT
*
1445938 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
1445953 TATTTTATAATAAAT
1 TATTTTATAATAAAT
1445968 TATTTTA-AATAAAT
1 TATTTTATAATAAAT
1445982 TATTTTATAATAAAT
1 TATTTTATAATAAAT
*
1445997 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
1446012 AACCTTATTA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
14 14 0.20
15 55 0.80
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTATAATAAAT
Found at i:1445987 original size:29 final size:30
Alignment explanation
Indices: 1445923--1446011 Score: 162
Period size: 29 Copynumber: 3.0 Consensus size: 30
1445913 AATCAATCCA
*
1445923 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
1445953 TATTTTATAATAAATTATTTT-AAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
1445982 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
1446012 AACCTTATTA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 29 0.51
30 28 0.49
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTTTATAATAAATTATTTTAAAATAAAT
Found at i:1445987 original size:44 final size:45
Alignment explanation
Indices: 1445923--1446011 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 45
1445913 AATCAATCCA
* *
1445923 TATTTTATAATAATTTATTTTAAAATAAATTATTTTATAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT
*
1445968 TATTTTA-AATAAATTATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT
1446012 AACCTTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 34 0.83
45 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (45 bp):
TATTTTATAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT
Found at i:1458433 original size:19 final size:19
Alignment explanation
Indices: 1458406--1458442 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1458396 GCACTGCAAA
*
1458406 TGCCCATGCTGAACCATGC
1 TGCCAATGCTGAACCATGC
*
1458425 TGCCAATGCTGGACCATG
1 TGCCAATGCTGAACCATG
1458443 TCGCCCTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (19 bp):
TGCCAATGCTGAACCATGC
Found at i:1462014 original size:16 final size:17
Alignment explanation
Indices: 1461993--1462036 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
1461983 CGATGAACAA
1461993 TATCGATACTGA-TGAG
1 TATCGATACTGAGTGAG
* *
1462009 TATCGATACAGATGTGTG
1 TATCGATACTGA-GTGAG
1462027 TATCGATACT
1 TATCGATACT
1462037 AAGAAGAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 11 0.48
18 12 0.52
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (17 bp):
TATCGATACTGAGTGAG
Found at i:1462748 original size:66 final size:66
Alignment explanation
Indices: 1462671--1462883 Score: 336
Period size: 66 Copynumber: 3.2 Consensus size: 66
1462661 GCATTTTGGC
* * *
1462671 ATAAAAGGTGCCACTAATAAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCGG
1 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATAGG
1462736 T
66 T
* *
1462737 ATAAAATGTGCCACTAATGGAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATAGG
1 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATAGG
*
1462802 C
66 T
* * *
1462803 ATAAAAGGTGCTACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATTGA
1 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATAGG
1462868 T
66 T
*
1462869 ATAAAAGATGCCACT
1 ATAAAAGGTGCCACT
1462884 CATGGTATTC
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 133 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (66 bp):
ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATAGG
T
Found at i:1469878 original size:66 final size:65
Alignment explanation
Indices: 1469786--1469998 Score: 345
Period size: 66 Copynumber: 3.2 Consensus size: 65
1469776 GCATTTTGGT
*
1469786 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAATGGTGCATTATCAT
1 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCA-
1469851 C
65 C
* * *
1469852 ATAAAAGGTGCCACTAATGAAAATTATAGATCGATTTTGATTAATGCATGACGGTGTATTATCGA
1 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATC-A
1469917 C
65 C
* *
1469918 ATAAAAGGTGCTACTAATGAAAATTATCAATCGATTTTGATTAATGCATAACGGTGCATTATCAG
1 ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCA-
1469983 C
65 C
1469984 ATAAAAGGTGCCACT
1 ATAAAAGGTGCCACT
1469999 CATGGTATTC
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
65 1 0.01
66 133 0.99
67 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (65 bp):
ATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCAC
Found at i:1475325 original size:2 final size:2
Alignment explanation
Indices: 1475320--1475367 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1475310 CTTTTCTAGG
1475320 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1475362 TC TC TC
1 TC TC TC
1475368 CTAAGTTCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1477742 original size:17 final size:17
Alignment explanation
Indices: 1477720--1477757 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1477710 AACGATCAAC
1477720 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1477737 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1477754 GGTC
1 GGTC
1477758 GGGTCAGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1477783 original size:19 final size:19
Alignment explanation
Indices: 1477761--1477858 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
1477751 TCGGGTCGGG
1477761 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* **
1477780 TCAGATCGGTCAAAATGGT
1 TCAGACCGGTCAAACCGGT
1477799 TC-GAACCGGTCGAAACCGG-
1 TCAG-ACCGGTC-AAACCGGT
* * *
1477818 TCAAATCGGTCAAAACTGGT
1 TCAGACCGGTC-AAACCGGT
* *
1477838 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
1477858 T
1 T
1477859 TCCAGCAGCG
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.02
19 38 0.62
20 14 0.23
21 8 0.13
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1477817 original size:10 final size:9
Alignment explanation
Indices: 1477759--1477857 Score: 63
Period size: 9 Copynumber: 10.3 Consensus size: 9
1477749 GGTCGGGTCG
*
1477759 GGTCAGACC
1 GGTCAAACC
1477768 GGTCAAACC
1 GGTCAAACC
* *
1477777 GGTTCAGATC
1 GG-TCAAACC
**
1477787 GGTCAAAAT
1 GGTCAAACC
*
1477796 GGTTCGAACC
1 GG-TCAAACC
1477806 GGTCGAAACC
1 GGTC-AAACC
*
1477816 GGTCAAATC
1 GGTCAAACC
*
1477825 GGTCAAAACT
1 GGTC-AAACC
*
1477835 GGTTGAAAACC
1 GG-T-CAAACC
1477846 GGTCAAACC
1 GGTCAAACC
1477855 GGT
1 GGT
1477858 TTCCAGCAGC
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
9 34 0.50
10 27 0.40
11 7 0.10
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1485154 original size:19 final size:19
Alignment explanation
Indices: 1485132--1485200 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
1485122 GTCGGGTCAG
*
1485132 ACCGGTCAAAACGGTTCGA
1 ACCGGTCAAAACGGTTCAA
*
1485151 ACCGGTCGAAACCGG-TCAA
1 ACCGGTC-AAAACGGTTCAA
* *
1485170 ACCTGTCAAAACCGGTTGAAA
1 ACCGGTCAAAA-CGGTT-CAA
*
1485191 ACTGGTCAAA
1 ACCGGTCAAA
1485201 CCGATTTCCA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
18 3 0.08
19 19 0.49
20 7 0.18
21 10 0.26
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACGGTTCAA
Found at i:1485163 original size:10 final size:9
Alignment explanation
Indices: 1485126--1485185 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
1485116 GGTCAGGTCG
*
1485126 GGTCAGACC
1 GGTCAAACC
*
1485135 GGTCAAAAC
1 GGTCAAACC
*
1485144 GGTTCGAACC
1 GG-TCAAACC
1485154 GGTCGAAACC
1 GGTC-AAACC
1485164 GGTCAAACC
1 GGTCAAACC
*
1485173 TGTCAAAACC
1 GGTC-AAACC
1485183 GGT
1 GGT
1485186 TGAAAACTGG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
9 19 0.46
10 22 0.54
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1487029 original size:19 final size:19
Alignment explanation
Indices: 1487005--1487042 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1486995 TTGAGAAAGT
1487005 TAAAGAAAGATGACAAGGG
1 TAAAGAAAGATGACAAGGG
1487024 TAAAGAAAGATGACAAGGG
1 TAAAGAAAGATGACAAGGG
1487043 ATCCCGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.32, T:0.11
Consensus pattern (19 bp):
TAAAGAAAGATGACAAGGG
Found at i:1488020 original size:30 final size:30
Alignment explanation
Indices: 1487943--1488036 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
1487933 TGTTTATTTG
* * *
1487943 TTTATTTTTGAAGGTGTTCATATTCGTTTAA
1 TTTATTTTTTAAGGTGTTTATGTTCGTTT-A
** **
1487974 TTT-TTTAGTATTGTGTTTATGTTCGTTTA
1 TTTATTTTTTAAGGTGTTTATGTTCGTTTA
* *
1488003 TTTATTTTTTAAGGTGTTTGTGTTTGTTTA
1 TTTATTTTTTAAGGTGTTTATGTTCGTTTA
1488033 TTTA
1 TTTA
1488037 ACGTTCACGA
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
29 4 0.08
30 42 0.86
31 3 0.06
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (30 bp):
TTTATTTTTTAAGGTGTTTATGTTCGTTTA
Found at i:1488053 original size:23 final size:23
Alignment explanation
Indices: 1488027--1488082 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1488017 TGTTTGTGTT
* *
1488027 TGTTTATTTAACGTTCACGAACG
1 TGTTCATTTAACATTCACGAACG
* *
1488050 TGTTCGTTTAATATTCACGAACG
1 TGTTCATTTAACATTCACGAACG
*
1488073 TGTTCGTTTA
1 TGTTCATTTA
1488083 GGGATCGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (23 bp):
TGTTCATTTAACATTCACGAACG
Found at i:1488117 original size:34 final size:34
Alignment explanation
Indices: 1488053--1488117 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
1488043 ACGAACGTGT
* *
1488053 TCGTTTAATATTCACGAACGTGTTCGTTTAGGGA
1 TCGTTTAATATTCACGAACATATTCGTTTAGGGA
* *
1488087 TCGTTT-ATCATTCACGAATATATTCTTTTAG
1 TCGTTTAAT-ATTCACGAACATATTCGTTTAG
1488118 CATTCGTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 2 0.08
34 24 0.92
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (34 bp):
TCGTTTAATATTCACGAACATATTCGTTTAGGGA
Found at i:1490416 original size:50 final size:50
Alignment explanation
Indices: 1490341--1490504 Score: 179
Period size: 50 Copynumber: 3.3 Consensus size: 50
1490331 ATCCATAGAA
* * * *
1490341 TTGATCATATTTACACTAATGTAATTATAGATTATATGAAATCTGTGAAG
1 TTGATCATGTTTACACTAGTGTAATTATAGATTATATAAAATATGTGAAG
* * * *
1490391 TTGATCATGTTTATAATAGTGTAATTAT-GAATTATATAAAATATGTAAAA
1 TTGATCATGTTTACACTAGTGTAATTATAG-ATTATATAAAATATGTGAAG
* * * * * *
1490441 TTAATTATGGTAACACTAGTGTAAATATA-ATCATATAAAATATGTGAAG
1 TTGATCATGTTTACACTAGTGTAATTATAGATTATATAAAATATGTGAAG
1490490 TTGATCATGTTTACA
1 TTGATCATGTTTACA
1490505 ACAATATGAG
Statistics
Matches: 90, Mismatches: 22, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
49 29 0.32
50 61 0.68
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (50 bp):
TTGATCATGTTTACACTAGTGTAATTATAGATTATATAAAATATGTGAAG
Found at i:1490519 original size:49 final size:48
Alignment explanation
Indices: 1490466--1490583 Score: 137
Period size: 49 Copynumber: 2.4 Consensus size: 48
1490456 CTAGTGTAAA
*
1490466 TATAATCATATAAAATATGTGAAGTTGATCATGTTTACAACAATATGAG
1 TATAATCATATGAAATATGTGAAGTTGATCATGTTTAC-ACAATATGAG
* * * * * * * *
1490515 TATAATTATATGATATCTTTCAAGTTGGTTATGTTTACACAATCTGAG
1 TATAATCATATGAAATATGTGAAGTTGATCATGTTTACACAATATGAG
*
1490563 TATGATCATATGAAATATGTG
1 TATAATCATATGAAATATGTG
1490584 GAGATATTCA
Statistics
Matches: 54, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
48 24 0.44
49 30 0.56
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (48 bp):
TATAATCATATGAAATATGTGAAGTTGATCATGTTTACACAATATGAG
Found at i:1490806 original size:21 final size:21
Alignment explanation
Indices: 1490768--1490808 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1490758 AAAGTTTAAT
*
1490768 ATTTCCTGTGCATCGTGTGAC
1 ATTTCCTGTACATCGTGTGAC
* *
1490789 ATTTCGTGTACATTGTGTGA
1 ATTTCCTGTACATCGTGTGA
1490809 ATCGTGTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.41
Consensus pattern (21 bp):
ATTTCCTGTACATCGTGTGAC
Found at i:1494787 original size:15 final size:15
Alignment explanation
Indices: 1494769--1494821 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
1494759 CCTGTTTCGG
1494769 TTTTAAAAAAACCGA
1 TTTTAAAAAAACCGA
* *
1494784 TTTTTTTAAAAAACCGG
1 --TTTTAAAAAAACCGA
*
1494801 TTATAAAAAAACCGA
1 TTTTAAAAAAACCGA
1494816 TTTTAA
1 TTTTAA
1494822 TATTCCAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 17 0.57
17 13 0.43
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (15 bp):
TTTTAAAAAAACCGA
Found at i:1495013 original size:21 final size:21
Alignment explanation
Indices: 1494989--1495041 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1494979 ACACTTAGGG
1494989 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
1495010 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
1495031 TACCGATTCCC
1 AACCGATTCCC
1495042 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:1495258 original size:13 final size:13
Alignment explanation
Indices: 1495237--1495291 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1495227 AAGTTCGATA
*
1495237 AATTCAAATACTT
1 AATTGAAATACTT
1495250 AATTGAAATACTT
1 AATTGAAATACTT
* *
1495263 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1495277 AATTGAAATACTT
1 AATTGAAATACTT
1495290 AA
1 AA
1495292 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1495347 original size:33 final size:33
Alignment explanation
Indices: 1495277--1495374 Score: 164
Period size: 32 Copynumber: 3.0 Consensus size: 33
1495267 AACTCAACAT
* *
1495277 AATTGAAATACTTAAATACTTCCAAGTT-GATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1495309 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1495342 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1495374 A
1 A
1495375 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 38 0.60
33 25 0.40
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1495393 original size:21 final size:21
Alignment explanation
Indices: 1495369--1495408 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1495359 ACTTCAAGTT
1495369 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1495390 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
1495409 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1510780 original size:17 final size:17
Alignment explanation
Indices: 1510758--1510799 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
1510748 ATAAAGGTAA
1510758 AGATTTATTAGTAGTTC
1 AGATTTATTAGTAGTTC
1510775 AGATTTATTAGTAGTTC
1 AGATTTATTAGTAGTTC
1510792 AGATTTAT
1 AGATTTAT
1510800 GTTGATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (17 bp):
AGATTTATTAGTAGTTC
Found at i:1515350 original size:35 final size:37
Alignment explanation
Indices: 1515279--1515351 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 37
1515269 GTTGGAAAAT
* *
1515279 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAATTTAAAATCATAAA
*
1515316 ATTTATATAATTT-TTT-ACAAATTTGAAAAT-ATAAA
1 ATTTATATAATTTCTTTAAAAAATTT-AAAATCATAAA
1515351 A
1 A
1515352 AATATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 13 0.41
36 7 0.22
37 12 0.38
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATAATTTCTTTAAAAAATTTAAAATCATAAA
Found at i:1518931 original size:24 final size:24
Alignment explanation
Indices: 1518898--1518947 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1518888 AGTCTTCCTG
*
1518898 ATGATGTATAAAACATCTATGTAC
1 ATGATATATAAAACATCTATGTAC
1518922 ATGATATATAAAACATCTATGTAC
1 ATGATATATAAAACATCTATGTAC
1518946 AT
1 AT
1518948 TATCATGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (24 bp):
ATGATATATAAAACATCTATGTAC
Found at i:1520537 original size:30 final size:31
Alignment explanation
Indices: 1520503--1520562 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
1520493 TTTGGTCTCT
** *
1520503 AAACTTTTTAAAAT-TTATACTTTAGTCACC
1 AAACTTTACAAAATCTTATAATTTAGTCACC
*
1520533 AAACTTTACAAAATCTTATAATTTGGTCAC
1 AAACTTTACAAAATCTTATAATTTAGTCAC
1520563 TCACTAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (31 bp):
AAACTTTACAAAATCTTATAATTTAGTCACC
Found at i:1520562 original size:31 final size:30
Alignment explanation
Indices: 1520493--1520562 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
1520483 AAACTACCAT
* * ** *
1520493 TTTGGTCTCTAAACTTTTTAAAATTTATAC
1 TTTGGTCACCAAACTTTACAAAATTTATAA
*
1520523 TTTAGTCACCAAACTTTACAAAATCTTATAA
1 TTTGGTCACCAAACTTTACAAAAT-TTATAA
1520554 TTTGGTCAC
1 TTTGGTCAC
1520563 TCACTAAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (30 bp):
TTTGGTCACCAAACTTTACAAAATTTATAA
Found at i:1522444 original size:18 final size:18
Alignment explanation
Indices: 1522423--1522463 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1522413 GTATCTCTCA
*
1522423 TTTTTTTTTCTTTTTTCT
1 TTTTTTTTTCTTCTTTCT
1522441 TTTTTTTTTCTTCTTTCT
1 TTTTTTTTTCTTCTTTCT
1522459 TTTTT
1 TTTTT
1522464 AGCTCTCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTTTTTCTTCTTTCT
Done.