Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 55
Found at i:3589648 original size:15 final size:16
Alignment explanation
Indices: 3589628--3589657 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3589618 GGTATCAGTT
3589628 TCTTGGGCTT-TTTTC
1 TCTTGGGCTTGTTTTC
3589643 TCTTGGGCTTGTTTT
1 TCTTGGGCTTGTTTT
3589658 TATTGCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.17, G:0.23, T:0.60
Consensus pattern (16 bp):
TCTTGGGCTTGTTTTC
Found at i:3591621 original size:22 final size:22
Alignment explanation
Indices: 3591593--3591640 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
3591583 CCTTGAAGAA
*
3591593 TGTAGGCCAATAAAACTCATAT
1 TGTAGGCCAATAAAACTCAGAT
*
3591615 TGTAGGCCAATAGAACTCAGAT
1 TGTAGGCCAATAAAACTCAGAT
3591637 TGTA
1 TGTA
3591641 AGACCTTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (22 bp):
TGTAGGCCAATAAAACTCAGAT
Found at i:3596487 original size:18 final size:20
Alignment explanation
Indices: 3596464--3596512 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3596454 CCATTTTTTT
*
3596464 TATCGATACTCA-TG-AGAG
1 TATCGATACTCAGGGTAGAG
3596482 TATCGATAC-CAGGGGTAGAG
1 TATCGATACTCA-GGGTAGAG
3596502 TATCGATACTC
1 TATCGATACTC
3596513 CCAATAGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 2 0.08
18 9 0.35
19 1 0.04
20 13 0.50
21 1 0.04
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (20 bp):
TATCGATACTCAGGGTAGAG
Found at i:3604386 original size:2 final size:2
Alignment explanation
Indices: 3604375--3604410 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3604365 CCATGCCCTT
3604375 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3604411 TGCAGGTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3607977 original size:31 final size:31
Alignment explanation
Indices: 3607941--3607999 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3607931 AACTTTAAAG
* *
3607941 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
3607972 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
3608000 ACATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:3608111 original size:32 final size:32
Alignment explanation
Indices: 3608072--3608291 Score: 206
Period size: 32 Copynumber: 7.7 Consensus size: 32
3608062 CAATCGATAT
*
3608072 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3608104 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3608126 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3608158 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
3608188 --T--AATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3608216 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3608238 TTTAAAATAAATCAATCCATAATAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3608270 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
3608292 AACTAAAATA
Statistics
Matches: 155, Mismatches: 5, Indels: 56
0.72 0.02 0.26
Matches are distributed among these distances:
22 29 0.19
23 4 0.03
24 2 0.01
26 26 0.17
27 6 0.04
28 9 0.06
30 4 0.03
31 6 0.04
32 69 0.45
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:3608115 original size:54 final size:54
Alignment explanation
Indices: 3608055--3608290 Score: 364
Period size: 54 Copynumber: 4.3 Consensus size: 54
3608045 CAACTACAAT
* *
3608055 AATAAATCAATCGATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
3608109 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* **
3608163 AATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAA
*
3608221 AATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
3608275 AATAAATCAATCCATA
1 AATAAATCAATCCATA
3608291 CAACTAAAAT
Statistics
Matches: 166, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
54 112 0.67
55 4 0.02
57 4 0.02
58 46 0.28
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:3608130 original size:22 final size:22
Alignment explanation
Indices: 3608104--3608146 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3608094 TAATAAATTA
3608104 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCTATAT
3608126 TTTAAAATAAATCAATCTATA
1 TTTAAAATAAATCAATCTATA
3608147 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:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:3608155 original size:22 final size:22
Alignment explanation
Indices: 3608106--3608154 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3608096 ATAAATTATT
**
3608106 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCTATATAA
3608128 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATA-TAA
3608151 TAAA
1 TAAA
3608155 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:3608205 original size:112 final size:112
Alignment explanation
Indices: 3608077--3608311 Score: 425
Period size: 112 Copynumber: 2.1 Consensus size: 112
3608067 GATATTTTAA
* *
3608077 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAAT
1 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
* * *
3608142 CTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
66 CCATAATAATAAATTATTTAAAATAAATCAATCCATACAACTAAAAT
3608189 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
1 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
3608254 CCATAATAATAAATTATTTAAAATAAATCAATCCATACAACTAAAAT
66 CCATAATAATAAATTATTTAAAATAAATCAATCCATACAACTAAAAT
3608301 AATAAATCAAT
1 AATAAATCAAT
3608312 TCACATTTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 118 1.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (112 bp):
AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
CCATAATAATAAATTATTTAAAATAAATCAATCCATACAACTAAAAT
Found at i:3608242 original size:22 final size:22
Alignment explanation
Indices: 3608216--3608258 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3608206 TAATAAATTA
3608216 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
3608238 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
3608259 ATAATAAATT
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:3608254 original size:134 final size:140
Alignment explanation
Indices: 3608014--3608453 Score: 402
Period size: 134 Copynumber: 3.2 Consensus size: 140
3608004 ACAACTACAA
* *
3608014 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCGATATTTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA--CT--AA
* * * * *
3608079 TAAATCAATTCATACT-AATAAAT---TA-TTTAAAATAAATCAAT-C-T-AT-A-T-TTTAAAA
62 TAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATTATTTAAAA
*
3608133 TAAATCAATCTATAC
126 TAAATCAATCCATAC
3608148 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAA
1 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAA
3608213 TTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAAT
66 TTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCC---ATAAT-AATTATTTAAAAT
3608278 AAATCAATCCATAC
127 AAATCAATCCATAC
* * ** *
3608292 -AACTAAA--A--T--AATAAATCAATTC--AC-ATTTTAA-AATAAATCAATCTATACTAATAA
1 TAA-TAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAA
*
3608346 ATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTTAAA
65 ATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA-TC-CA-TAAT-AATTA-TTTAAA
* *
3608411 ATAAATCAATCTATATTTTA
125 ATAAATCAATCCATA----C
3608431 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTA-TTTAAAATAAAT
3608454 TATTTTATAA
Statistics
Matches: 258, Mismatches: 16, Indels: 52
0.79 0.05 0.16
Matches are distributed among these distances:
129 6 0.02
130 13 0.05
132 1 0.00
133 3 0.01
134 145 0.56
135 27 0.10
136 2 0.01
138 12 0.05
139 5 0.02
140 5 0.02
141 1 0.00
142 2 0.01
143 3 0.01
144 26 0.10
146 7 0.03
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (140 bp):
TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAA
TTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATTATTTAAAATAAAT
CAATCCATAC
Found at i:3608267 original size:22 final size:22
Alignment explanation
Indices: 3608218--3608266 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3608208 ATAAATTATT
**
3608218 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
3608240 TAAAATAAATCAATCCATAATAA
1 TAAAATAAATCAATCCAT-ATAA
3608263 TAAA
1 TAAA
3608267 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:3608354 original size:112 final size:110
Alignment explanation
Indices: 3608077--3608370 Score: 360
Period size: 112 Copynumber: 2.6 Consensus size: 110
3608067 GATATTTTAA
* * * *
3608077 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAAT
1 AATAAATCAATCCATACTAATAAATAATCTAAAATAAATAAATC--TATTTTAAAATAAATCAAT
* * *
3608142 CTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
64 CCATAATAATAAATTATTTAAAATAAATCAATCCATACAACTAAAAT
* * *
3608189 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
1 AATAAATCAATCCATACTAATAAATAATCTAAAATAAATAAAT-C-TATTTTAAAATAAATCAAT
3608254 CCATAATAATAAATTATTTAAAATAAATCAATCCATACAACTAAAAT
64 CCATAATAATAAATTATTTAAAATAAATCAATCCATACAACTAAAAT
** * *
3608301 AATAAATCAATTCACATTTTAAAATAAATCAATCTATACT-AATAAAT-TA-TTTAAAATAAATC
1 AATAAATCAA-TC-CATACT--AATAAAT-AATCTAAAATAAATAAATCTATTTTAAAATAAATC
3608363 AATCCATA
61 AATCCATA
3608371 TTTTAAAATA
Statistics
Matches: 165, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
112 137 0.83
113 5 0.03
114 4 0.02
116 13 0.08
117 6 0.04
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (110 bp):
AATAAATCAATCCATACTAATAAATAATCTAAAATAAATAAATCTATTTTAAAATAAATCAATCC
ATAATAATAAATTATTTAAAATAAATCAATCCATACAACTAAAAT
Found at i:3608376 original size:22 final size:22
Alignment explanation
Indices: 3608350--3608392 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3608340 TAATAAATTA
3608350 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
3608372 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
3608393 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:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3608401 original size:22 final size:22
Alignment explanation
Indices: 3608352--3608400 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3608342 ATAAATTATT
**
3608352 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
3608374 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
3608397 TAAA
1 TAAA
3608401 TTATTTTAAA
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:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:3608415 original size:15 final size:15
Alignment explanation
Indices: 3608395--3608528 Score: 178
Period size: 15 Copynumber: 8.5 Consensus size: 15
3608385 AATTCATACT
3608395 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
3608410 AATAAATCAATCTATATTTTAT
1 AAT--A--AAT-TAT--TTTAA
3608432 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
3608447 AATAAATTATTTTAT
1 AATAAATTATTTTAA
3608462 AATAAATTATTTTAA
1 AATAAATTATTTTAA
3608477 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
3608492 AATAAATTATTTTAT
1 AATAAATTATTTTAA
3608507 AATAAATTATTTTAA
1 AATAAATTATTTTAA
3608522 AATAAAT
1 AATAAAT
3608529 AACCTTATTA
Statistics
Matches: 106, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
15 85 0.80
17 4 0.04
18 3 0.03
19 3 0.03
20 4 0.04
22 7 0.07
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:3608436 original size:55 final size:55
Alignment explanation
Indices: 3608301--3608468 Score: 213
Period size: 54 Copynumber: 3.1 Consensus size: 55
3608291 CAACTAAAAT
*
3608301 AATAAATCAAT-TCACATTTTAAAATAAATCAA-TCTATACTAATAAATTA-TTTAA
1 AATAAATCAATCT-ATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTTAA
*
3608355 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTTAA
* * * * *
3608410 AATAAATCAATCTATATTTTATAATAAAT-TATT-TTA-AAATAAATTATTTTAT
1 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTTAA
3608462 AATAAAT
1 AATAAAT
3608469 TATTTTAAAA
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
52 21 0.20
53 2 0.02
54 46 0.45
55 34 0.33
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.40
Consensus pattern (55 bp):
AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTTAA
Found at i:3608488 original size:45 final size:45
Alignment explanation
Indices: 3608424--3608528 Score: 201
Period size: 45 Copynumber: 2.3 Consensus size: 45
3608414 AATCAATCTA
*
3608424 TATTTTATAATAAATTATTTTAAAATAAATTATTTTATAATAAAT
1 TATTTTAAAATAAATTATTTTAAAATAAATTATTTTATAATAAAT
3608469 TATTTTAAAATAAATTATTTTAAAATAAATTATTTTATAATAAAT
1 TATTTTAAAATAAATTATTTTAAAATAAATTATTTTATAATAAAT
3608514 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
3608529 AACCTTATTA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (45 bp):
TATTTTAAAATAAATTATTTTAAAATAAATTATTTTATAATAAAT
Found at i:3609174 original size:29 final size:28
Alignment explanation
Indices: 3608997--3609175 Score: 137
Period size: 29 Copynumber: 6.2 Consensus size: 28
3608987 TCTGAAGCAG
*
3608997 AATCAGGACAGAGATATAATATCATGCAA
1 AATCAGGA-AGAGATATAATCTCATGCAA
** * *
3609026 AAAAAGGACGAGAATATAATCTCATGCAT
1 AATCAGGAAGAG-ATATAATCTCATGCAA
* *
3609055 AATCAAGACGATGATATAATCTCATGC-A
1 AATCAGGAAGA-GATATAATCTCATGCAA
* * * *
3609083 GATACAAGACATATATATAATC-CTATGCAA
1 AAT-CAGGA-AGAGATATAATCTC-ATGCAA
* *
3609113 AAACAGGACAGAGATATAATCTCATGTAA
1 AATCAGGA-AGAGATATAATCTCATGCAA
* *
3609142 AATCAGGAAGGGAATATAATCTCATGCAG
1 AATCAGGAAGAG-ATATAATCTCATGCAA
3609171 AATCA
1 AATCA
3609176 AGATGGGGAT
Statistics
Matches: 119, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
28 9 0.08
29 105 0.88
30 5 0.04
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.22
Consensus pattern (28 bp):
AATCAGGAAGAGATATAATCTCATGCAA
Found at i:3609178 original size:87 final size:87
Alignment explanation
Indices: 3608993--3609178 Score: 218
Period size: 87 Copynumber: 2.1 Consensus size: 87
3608983 AGGATCTGAA
* *
3608993 GCAGAATCAGGACAGAGATATAATATCATGCAAAAAAAGGACGAGAATATAATCTCATGCATAAT
1 GCAGAATCAAGACAGAGATATAATATCATGCAAAAAAAGGACGAGAATATAATCTCATGCAAAAT
* *
3609058 CAAGACGATGATATAATCTCAT
66 CAAGAAGAGGATATAATCTCAT
* * * * *
3609080 GCAG-ATACAAGACATATATATAAT-CCTATGCAAAAACAGGAC-AGAGATATAATCTCATGTAA
1 GCAGAAT-CAAGACAGAGATATAATATC-ATGCAAAAAAAGGACGAGA-ATATAATCTCATGCAA
*
3609142 AATCAGGAAG-GGAATATAATCTCAT
63 AATCAAGAAGAGG-ATATAATCTCAT
3609167 GCAGAATCAAGA
1 GCAGAATCAAGA
3609179 TGGGGATATA
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
86 7 0.08
87 75 0.89
88 2 0.02
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (87 bp):
GCAGAATCAAGACAGAGATATAATATCATGCAAAAAAAGGACGAGAATATAATCTCATGCAAAAT
CAAGAAGAGGATATAATCTCAT
Found at i:3609187 original size:29 final size:29
Alignment explanation
Indices: 3608997--3609204 Score: 133
Period size: 29 Copynumber: 7.2 Consensus size: 29
3608987 TCTGAAGCAG
* * *
3608997 AATCAGGACAGAGATATAATATCATGCAA
1 AATCAAGACGGAGATATAATCTCATGCAA
* *
3609026 AA-AAAGGAC-GAGAATATAATCTCATGCAT
1 AATCAA-GACGGAG-ATATAATCTCATGCAA
3609055 AATCAAGAC-GATGATATAATCTCATGC-A
1 AATCAAGACGGA-GATATAATCTCATGCAA
* ** *
3609083 GATACAAGACATATATATAATC-CTATGCAA
1 AAT-CAAGACGGAGATATAATCTC-ATGCAA
* * * *
3609113 AAACAGGACAGAGATATAATCTCATGTAA
1 AATCAAGACGGAGATATAATCTCATGCAA
* * *
3609142 AATCAGGAAGG-GAATATAATCTCATGCAG
1 AATCAAGACGGAG-ATATAATCTCATGCAA
* * * *
3609171 AATCAAGATGGGGATATAA-CTCATACAT
1 AATCAAGACGGAGATATAATCTCATGCAA
3609199 AATCAA
1 AATCAA
3609205 AACAATCATA
Statistics
Matches: 144, Mismatches: 24, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
28 21 0.15
29 115 0.80
30 8 0.06
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (29 bp):
AATCAAGACGGAGATATAATCTCATGCAA
Found at i:3612967 original size:19 final size:19
Alignment explanation
Indices: 3612927--3612968 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3612917 TTATGCACAC
* *
3612927 AAAGTTTTGAAACTCTGGG
1 AAAGTTTCGAAACTCTGCG
*
3612946 AAAGTTTCGAAACTCTTCG
1 AAAGTTTCGAAACTCTGCG
3612965 AAAG
1 AAAG
3612969 AGCCGTTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (19 bp):
AAAGTTTCGAAACTCTGCG
Found at i:3617299 original size:20 final size:20
Alignment explanation
Indices: 3617270--3617314 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3617260 TCGAGGGTTC
* *
3617270 TATGTGATCTTCGGGACATA
1 TATGTAATCTTCGGAACATA
* *
3617290 TATGTAATCTTTGGAAGATA
1 TATGTAATCTTCGGAACATA
3617310 TATGT
1 TATGT
3617315 GGTACTTCGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (20 bp):
TATGTAATCTTCGGAACATA
Found at i:3617691 original size:9 final size:9
Alignment explanation
Indices: 3617679--3617723 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
3617669 AAGAGATATG
3617679 AATGATAAT
1 AATGATAAT
*
3617688 AATGTTAAT
1 AATGATAAT
*
3617697 AATGATAAG
1 AATGATAAT
*
3617706 AATAATAAT
1 AATGATAAT
*
3617715 AAGGATAAT
1 AATGATAAT
3617724 GAGATGATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (9 bp):
AATGATAAT
Found at i:3620473 original size:18 final size:18
Alignment explanation
Indices: 3620436--3620473 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3620426 ACTATGCTTT
*
3620436 TCCGATGATCTCGACTCC
1 TCCGATGATCTCGACCCC
*
3620454 TCCGATGATCTTGACCCC
1 TCCGATGATCTCGACCCC
3620472 TC
1 TC
3620474 ATTGTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.39, G:0.16, T:0.29
Consensus pattern (18 bp):
TCCGATGATCTCGACCCC
Found at i:3632366 original size:2 final size:2
Alignment explanation
Indices: 3632359--3632435 Score: 90
Period size: 2 Copynumber: 39.5 Consensus size: 2
3632349 AACAATTTTA
3632359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AGT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
3632399 A- AGT GT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3632436 AAGCATAAGT
Statistics
Matches: 67, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
1 4 0.06
2 62 0.93
3 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3632434 original size:50 final size:50
Alignment explanation
Indices: 3632359--3632477 Score: 159
Period size: 50 Copynumber: 2.4 Consensus size: 50
3632349 AACAATTTTA
* ** * * *
3632359 ATATATATATATATATATATATATATATATTATAAGTATTAAGTGTGTAT
1 ATATATATATATATATATATATATATAAAGCATAAGTATAAAGTATATAT
3632409 ATATATATATATATATATATATATATAAAGCATAAGTATAAAGTATATAT
1 ATATATATATATATATATATATATATAAAGCATAAGTATAAAGTATATAT
*
3632459 ATAAATATATA-AGTATATA
1 ATATATATATATA-TATATA
3632478 CATAAGTGTG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
49 1 0.02
50 60 0.98
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.43
Consensus pattern (50 bp):
ATATATATATATATATATATATATATAAAGCATAAGTATAAAGTATATAT
Found at i:3632737 original size:21 final size:23
Alignment explanation
Indices: 3632704--3632746 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3632694 TTCCCAAAAA
3632704 AAAAAAAATC-AAATTTTCCCTT
1 AAAAAAAATCAAAATTTTCCCTT
*
3632726 AAAAACAA-CAAAATTTTCCCT
1 AAAAAAAATCAAAATTTTCCCT
3632747 CAAAGACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAAAAATCAAAATTTTCCCTT
Found at i:3638888 original size:19 final size:19
Alignment explanation
Indices: 3638864--3638902 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3638854 TTATAAATTC
*
3638864 AAATCTTACAACTTCATCA
1 AAATCTCACAACTTCATCA
*
3638883 AAATCTCATAACTTCATCA
1 AAATCTCACAACTTCATCA
3638902 A
1 A
3638903 TCGTAAGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATCTCACAACTTCATCA
Found at i:3642522 original size:15 final size:15
Alignment explanation
Indices: 3642504--3642551 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
3642494 GAGATTGTTG
*
3642504 AGTTGGAGGTTGGAT
1 AGTTGGAGATTGGAT
3642519 AGTTGGAGATTGGAT
1 AGTTGGAGATTGGAT
* *
3642534 AGTTGAAGATTGGTT
1 AGTTGGAGATTGGAT
3642549 AGT
1 AGT
3642552 AGAACCTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (15 bp):
AGTTGGAGATTGGAT
Found at i:3653105 original size:19 final size:20
Alignment explanation
Indices: 3653078--3653115 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3653068 GCGGTATGTA
*
3653078 AATCTATGCAAGT-ATACAC
1 AATCGATGCAAGTAATACAC
3653097 AATCGATGCAAGTAATACA
1 AATCGATGCAAGTAATACA
3653116 GTAGTGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (20 bp):
AATCGATGCAAGTAATACAC
Found at i:3660737 original size:20 final size:18
Alignment explanation
Indices: 3660712--3660752 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
3660702 ATGATATCAA
*
3660712 ATAATCATATAATATTTCAT
1 ATAATCAAAT-ATA-TTCAT
3660732 ATAATCAAATATATTCAT
1 ATAATCAAATATATTCAT
3660750 ATA
1 ATA
3660753 TATAACCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATCAAATATATTCAT
Found at i:3661572 original size:9 final size:9
Alignment explanation
Indices: 3661545--3661574 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
3661535 ATAAATCATG
3661545 TAACACATA
1 TAACACATA
3661554 TAATCACATA
1 TAA-CACATA
3661564 TAACACATA
1 TAACACATA
3661573 TA
1 TA
3661575 CTCATATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (9 bp):
TAACACATA
Found at i:3665665 original size:27 final size:27
Alignment explanation
Indices: 3665611--3665666 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
3665601 AGTCCTTTCT
* *
3665611 TAAAAAAACAATGTACAATCATATTAA
1 TAAAAAAACAATGTACAATCAGACTAA
* *
3665638 TAAATAAACAGTGTACAATCAGACTAA
1 TAAAAAAACAATGTACAATCAGACTAA
3665665 TA
1 TA
3665667 TTTCTAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (27 bp):
TAAAAAAACAATGTACAATCAGACTAA
Found at i:3668138 original size:3 final size:3
Alignment explanation
Indices: 3668130--3668156 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3668120 GTGTTATCTA
3668130 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
3668157 TAAGTATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3668556 original size:25 final size:24
Alignment explanation
Indices: 3668522--3668568 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3668512 AATTTTGAAG
*
3668522 AATAAAAACAAATTATTTAATTAAA
1 AATAAAAACAAA-TACTTAATTAAA
*
3668547 AATATAAACAAATACTTAATTA
1 AATAAAAACAAATACTTAATTA
3668569 CATATAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (24 bp):
AATAAAAACAAATACTTAATTAAA
Found at i:3669382 original size:21 final size:22
Alignment explanation
Indices: 3669344--3669412 Score: 61
Period size: 26 Copynumber: 3.0 Consensus size: 22
3669334 TCTGTCTAAG
*
3669344 GTATATTTTA-TTATATTTTTAA
1 GTATTTTTTATTTA-ATTTTTAA
3669366 -TATTTTTTATTTAATTTATTTAA
1 GTATTTTTTATTTAA-TT-TTTAA
3669389 GTATTTAATTTATTTAATATTTTA
1 GTATTT--TTTATTTAAT-TTTTA
3669413 TTTAATTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 9 0.23
22 5 0.13
23 5 0.13
24 5 0.13
25 5 0.13
26 10 0.26
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (22 bp):
GTATTTTTTATTTAATTTTTAA
Found at i:3669383 original size:9 final size:9
Alignment explanation
Indices: 3669371--3669424 Score: 60
Period size: 9 Copynumber: 6.3 Consensus size: 9
3669361 TTTAATATTT
3669371 TTTATTTAA
1 TTTATTTAA
3669380 TTTATTTAA
1 TTTATTTAA
*
3669389 -GTATTTAA
1 TTTATTTAA
3669397 TTTATTTAA
1 TTTATTTAA
*
3669406 --TATTTTA
1 TTTATTTAA
*
3669413 TTTAATTAA
1 TTTATTTAA
3669422 TTT
1 TTT
3669425 TTTTGCATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
7 6 0.16
8 7 0.19
9 24 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTATTTAA
Found at i:3669395 original size:17 final size:16
Alignment explanation
Indices: 3669373--3669422 Score: 73
Period size: 17 Copynumber: 3.1 Consensus size: 16
3669363 TAATATTTTT
3669373 TATTTAATTTATTTAA
1 TATTTAATTTATTTAA
3669389 GTATTTAATTTATTTAA
1 -TATTTAATTTATTTAA
* *
3669406 TATTTTATTTAATTAA
1 TATTTAATTTATTTAA
3669422 T
1 T
3669423 TTTTTTGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 15 0.48
17 16 0.52
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATTTAATTTATTTAA
Found at i:3671650 original size:25 final size:25
Alignment explanation
Indices: 3671622--3671669 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3671612 TGTATTTAGT
* *
3671622 ACTTTTTGTTGTAGTTGTTTATTGG
1 ACTTTTTATTGTAATTGTTTATTGG
*
3671647 ACTTTTTATTGTAATTTTTTATT
1 ACTTTTTATTGTAATTGTTTATT
3671670 TATTTATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.65
Consensus pattern (25 bp):
ACTTTTTATTGTAATTGTTTATTGG
Found at i:3683700 original size:22 final size:22
Alignment explanation
Indices: 3683669--3683711 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3683659 TAATCGCGAG
3683669 TTTAGAAGATACGATTATTGGC
1 TTTAGAAGATACGATTATTGGC
* *
3683691 TTTAGCAGATACGATTTTTGG
1 TTTAGAAGATACGATTATTGG
3683712 GCTTGTTTAG
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:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (22 bp):
TTTAGAAGATACGATTATTGGC
Found at i:3686838 original size:16 final size:16
Alignment explanation
Indices: 3686817--3686848 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3686807 GATATTACCC
3686817 GACCTATTATGAACCT
1 GACCTATTATGAACCT
3686833 GACCTATTATGAACCT
1 GACCTATTATGAACCT
3686849 AAATAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (16 bp):
GACCTATTATGAACCT
Found at i:3702962 original size:40 final size:40
Alignment explanation
Indices: 3702902--3702981 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
3702892 TGATAGCGTG
* *
3702902 AGCATATGGGAATCTAAAAGCTTGAAATCAATCGCAATCA
1 AGCACATGGGAATATAAAAGCTTGAAATCAATCGCAATCA
* * *
3702942 AGCACATGGGAATATAAAAGCTTGAATTCGATTGCAATCA
1 AGCACATGGGAATATAAAAGCTTGAAATCAATCGCAATCA
3702982 CACCATCTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (40 bp):
AGCACATGGGAATATAAAAGCTTGAAATCAATCGCAATCA
Found at i:3706359 original size:11 final size:10
Alignment explanation
Indices: 3706330--3706360 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
3706320 TATATTAATC
3706330 CATTTTTTAT
1 CATTTTTTAT
3706340 CATTTTTTAT
1 CATTTTTTAT
3706350 CATTTATTTAT
1 CATTT-TTTAT
3706361 TTATCTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (10 bp):
CATTTTTTAT
Found at i:3706375 original size:16 final size:15
Alignment explanation
Indices: 3706341--3706378 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3706331 ATTTTTTATC
3706341 ATTT-TTTATCATTT
1 ATTTATTTATCATTT
3706355 ATTTATTTATCTATTT
1 ATTTATTTATC-ATTT
*
3706371 TTTTATTT
1 ATTTATTT
3706379 TAACATTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 6 0.29
16 11 0.52
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTATTTATCATTT
Found at i:3706380 original size:25 final size:23
Alignment explanation
Indices: 3706331--3706378 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
3706321 ATATTAATCC
3706331 ATTTTTTATCATTTTTTATCATTT
1 ATTTTTTATCATTTTTTAT-ATTT
3706355 ATTTATTTATCTATTTTTT-TATTT
1 ATTT-TTTATC-ATTTTTTATATTT
3706379 TAACATTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 8 0.36
25 7 0.32
26 7 0.32
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTTTTATCATTTTTTATATTT
Found at i:3706482 original size:19 final size:19
Alignment explanation
Indices: 3706458--3706506 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
3706448 CGGTTCGAAC
3706458 TTTTAAATTTCTATCTAAA
1 TTTTAAATTTCTATCTAAA
3706477 TTTTAAATTTCTATCTAAA
1 TTTTAAATTTCTATCTAAA
3706496 TTTTAAATTTC
1 TTTTAAATTTC
3706507 GCGGTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTAAATTTCTATCTAAA
Found at i:3710345 original size:46 final size:47
Alignment explanation
Indices: 3710256--3710351 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 47
3710246 ATCATTTTTG
*
3710256 AAATCAAGTTTTGAAATTACTCCCCCTTACTCTTATACTTTGAAAAT
1 AAATCAAGTTTTGAAATTACTCCCCCTTACTCTAATACTTTGAAAAT
3710303 AAATCAAGTTTTGAAATTACT-CCCCTTACTCTAATACTTTGAAAAT
1 AAATCAAGTTTTGAAATTACTCCCCCTTACTCTAATACTTTGAAAAT
3710349 AAA
1 AAA
3710352 CTCTCTAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 27 0.56
47 21 0.44
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (47 bp):
AAATCAAGTTTTGAAATTACTCCCCCTTACTCTAATACTTTGAAAAT
Found at i:3716361 original size:20 final size:21
Alignment explanation
Indices: 3716322--3716361 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3716312 AAAGCTTTAA
* *
3716322 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
3716343 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
3716362 AAGTAAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:3716512 original size:22 final size:21
Alignment explanation
Indices: 3716470--3716509 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3716460 AAGACTATTT
3716470 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
3716491 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
3716510 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:3720054 original size:11 final size:11
Alignment explanation
Indices: 3720038--3720062 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3720028 AGATTTAGGT
3720038 AAAAAATTTTA
1 AAAAAATTTTA
3720049 AAAAAATTTTA
1 AAAAAATTTTA
3720060 AAA
1 AAA
3720063 TCAAAGCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAAAATTTTA
Found at i:3722441 original size:16 final size:15
Alignment explanation
Indices: 3722412--3722445 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3722402 ATTATTTTTC
3722412 ATAAAAGTAATTTAT
1 ATAAAAGTAATTTAT
3722427 ATAAAAGTAATTT-T
1 ATAAAAGTAATTTAT
3722441 ATAAA
1 ATAAA
3722446 TAGGATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (15 bp):
ATAAAAGTAATTTAT
Found at i:3722445 original size:14 final size:14
Alignment explanation
Indices: 3722407--3722445 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 14
3722397 ATATGATTAT
3722407 TTTTCATAAAAGTAA
1 TTTT-ATAAAAGTAA
3722422 TTTATATAAAAGTAA
1 TTT-TATAAAAGTAA
3722437 TTTTATAAA
1 TTTTATAAA
3722446 TAGGATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.26
15 16 0.70
16 1 0.04
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (14 bp):
TTTTATAAAAGTAA
Found at i:3723982 original size:3 final size:3
Alignment explanation
Indices: 3723976--3724081 Score: 81
Period size: 3 Copynumber: 36.0 Consensus size: 3
3723966 ATTTATTATT
* * *
3723976 TAA TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAA TAT TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * * *
3724022 TAT TAT TAT TAA TAT TAT TAA TAT TAT TAT TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3724070 TAA TAC TAA TAA
1 TAA TAA TAA TAA
3724082 AAATGATATA
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
2 3 0.03
3 84 0.97
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:3724341 original size:17 final size:17
Alignment explanation
Indices: 3724319--3724378 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
3724309 GTTGAACAAA
3724319 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
** *
3724336 TTCTTCTTTTTCA-GATGAG
1 TTCTTCTCATT-ATGA--AC
3724355 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
3724372 TCCTTCT
1 TTCTTCT
3724379 GGAAATGTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
17 18 0.56
18 2 0.06
19 12 0.38
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:3724494 original size:124 final size:122
Alignment explanation
Indices: 3724278--3724857 Score: 706
Period size: 123 Copynumber: 4.8 Consensus size: 122
3724268 GATGACAATT
* * * *
3724278 TATCTCCTTCTGTGAT-GTAATCTAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTC
1 TATCTCCTTCTGTGATAG-AGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
* *
3724342 TT--T-TTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGATGCTGATC
65 TTCCTCTTCAGATAAGTTCTTCTCATTATGAACT-CTTCTGGAAAAGTTGATGCTGATC
* * * * * *
3724398 TATCTTCTTCTGTGATAGCGTCATGCAAAAAGGTTGAACAAGCTCTTTTCTTTATGAACTTCTTC
1 TATCTCCTTCTGTGATAGAGTCAAGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
* *
3724463 TTCCTCTTCAGATAAGTTTTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATC
65 TTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-TCTTCTGGAAAAGTTGATGCTGATC
* *
3724522 TATCTCCTTCTGTGATATAGTCACGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* *
3724587 TCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAATC
66 TCCTCTTCAGATAAGTTCTTCTCATTATGAACTCT-TCTGGAAAAGTTGATGCTGATC
3724645 TATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* *
3724710 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGG-AAA--TG-T--TGATC
66 TCC-TCTTCAGATAAGTTCTTCTCATTATGAACTCTTCTGGAAAAGTTGATGCTGATC
* ** * * * * * *
3724762 CA--T-C--GAGTGAT-GAATACGAGCAAAAGTTTGAACAAATTCTTCTCATTATGAACTTATTT
1 TATCTCCTTCTGTGATAGAGT-CAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
*
3724821 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
65 TTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTCT
3724858 ACCTGGCAAT
Statistics
Matches: 413, Mismatches: 38, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
111 3 0.01
112 80 0.19
114 1 0.00
115 1 0.00
117 5 0.01
119 1 0.00
120 21 0.05
121 36 0.09
122 6 0.01
123 159 0.38
124 99 0.24
125 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (122 bp):
TATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
TCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTTCTGGAAAAGTTGATGCTGATC
Found at i:3724720 original size:247 final size:240
Alignment explanation
Indices: 3724278--3724855 Score: 730
Period size: 247 Copynumber: 2.4 Consensus size: 240
3724268 GATGACAATT
* * *
3724278 TATCTCCTTCTGTGATGTAATCTAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTGTGATAT-ATCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
* * *
3724343 T--T-TTCAGATGAGTTCTTCTCATTATGAAC-TCCTTCTGGAAATGTTGATGCTGATCTATCTT
65 TCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGGAAAAGTTGATGCTAATCTATCTC
* * * *
3724404 CTTCTGTGATAGCGTCATGCAAAAAGGTTGAACAAGCTCTTTTCTTTATGAACTTCTTCTTCCTC
130 CTTCTGTGATAGAGTCAAGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTC
* * *
3724469 TTCAGATAAGTTTTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGCTGATC
195 TTCAGATAAGTTCTTCTCATTATGAAC-TCTACTGG-AAA--TG-T--TGATC
*
3724522 TATCTCCTTCTGTGATATAGTC-ACGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
1 TATCTCCTTCTGTGATATA-TCGA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
* *
3724586 TTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGTTGATGCTAATCTATCT
64 TTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGGAAAAGTTGATGCTAATCTATCT
*
3724650 CCTTCTGTGATAGAGTCAAGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
129 CCTTCTGTGATAGAGTCAAGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-
*
3724714 TCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAATGTTGATC
193 TCTTCAGATAAGTTCTTCTCATTATGAACTCTACTGGAAATGTTGATC
* *** * * *
3724762 CA--T-CGAGTGATGA-ATA-CGAGCAAAAGTTTGAACAAATTCTTCTCATTATGAACTTATTTT
1 TATCTCCTTCTG-TGATATATCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
3724822 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
65 TCC-TCTTCAGATGAGTTCTTCTCATTATGAACT
3724856 CTACCTGGCA
Statistics
Matches: 298, Mismatches: 26, Indels: 28
0.85 0.07 0.08
Matches are distributed among these distances:
235 41 0.14
236 30 0.10
237 6 0.02
238 4 0.01
240 6 0.02
242 1 0.00
243 4 0.01
244 59 0.20
245 3 0.01
246 46 0.15
247 96 0.32
248 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.40
Consensus pattern (240 bp):
TATCTCCTTCTGTGATATATCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
CCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGGAAAAGTTGATGCTAATCTATCTCC
TTCTGTGATAGAGTCAAGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCT
TCAGATAAGTTCTTCTCATTATGAACTCTACTGGAAATGTTGATC
Found at i:3724793 original size:112 final size:113
Alignment explanation
Indices: 3724668--3724886 Score: 368
Period size: 112 Copynumber: 1.9 Consensus size: 113
3724658 GATAGAGTCA
* *
3724668 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCT
* *
3724733 CATTATGAACTCTA-CTGGAAATGTTGATCCATCGAGTGATGAATACG
66 CATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATACG
* *
3724780 AGCAAAAGTTTGAACAAATTCTTCTCATTATGAACTTATTTTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCT
*
3724845 CATTATGAACTCTACCTGGCAATGCTGATCCATCGAATGATG
66 CATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATG
3724887 GATCCGAATC
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
112 75 0.76
113 24 0.24
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (113 bp):
AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATACG
Found at i:3732622 original size:14 final size:14
Alignment explanation
Indices: 3732600--3732677 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
3732590 ATGTAAATGT
*
3732600 AAATACAAATATAA
1 AAATGCAAATATAA
* **
3732614 AAATGCAAAGATGC
1 AAATGCAAATATAA
*
3732628 AAATGCAAATACAA
1 AAATGCAAATATAA
* *
3732642 AGATGTAAATATAGA
1 AAATGCAAATATA-A
*
3732657 AAA---AAAAATAA
1 AAATGCAAATATAA
3732668 AAATGCAAAT
1 AAATGCAAAT
3732678 TGTGCAATAC
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
11 4 0.09
12 6 0.13
14 33 0.72
15 3 0.07
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (14 bp):
AAATGCAAATATAA
Found at i:3732631 original size:28 final size:28
Alignment explanation
Indices: 3732600--3732676 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
3732590 ATGTAAATGT
3732600 AAATACAAATATAAAAATGCAAAGAT-G
1 AAATACAAATATAAAAATGCAAAGATAG
* * * * *
3732627 CAAATGCAAATACAAAGATGTAAATATAG
1 -AAATACAAATATAAAAATGCAAAGATAG
*
3732656 AAA-A-AAAAATAAAAATGCAAA
1 AAATACAAATATAAAAATGCAAA
3732677 TTGTGCAATA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
26 13 0.34
28 24 0.63
29 1 0.03
ACGTcount: A:0.65, C:0.08, G:0.10, T:0.17
Consensus pattern (28 bp):
AAATACAAATATAAAAATGCAAAGATAG
Found at i:3732637 original size:20 final size:20
Alignment explanation
Indices: 3732614--3732651 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3732604 ACAAATATAA
*
3732614 AAATGCAAAGATGCAAATGC
1 AAATACAAAGATGCAAATGC
*
3732634 AAATACAAAGATGTAAAT
1 AAATACAAAGATGCAAAT
3732652 ATAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.18
Consensus pattern (20 bp):
AAATACAAAGATGCAAATGC
Found at i:3733417 original size:36 final size:36
Alignment explanation
Indices: 3733357--3733428 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
3733347 TCTTGCCGTA
* *
3733357 GAATGCTTTTGGTATCAATCTAACAAGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAAGATCTTTGTG
* * *
3733393 GAATACTTTTTGTATTAATATAACATGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAAGATCTTTGTG
3733429 TGCATAGCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAAGATCTTTGTG
Found at i:3735016 original size:25 final size:27
Alignment explanation
Indices: 3734975--3735032 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
3734965 AAAAATAAAT
*
3734975 AAAT-ATTAATAAAAAATT-TCTATAA
1 AAATAATTAATAAAAAATTATATATAA
*
3735000 AAATAATTAA-AATAAATTAATATATAA
1 AAATAATTAATAAAAAATT-ATATATAA
3735027 AAATAA
1 AAATAA
3735033 GATATTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 11 0.39
26 5 0.18
27 12 0.43
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATAATTAATAAAAAATTATATATAA
Found at i:3735252 original size:3 final size:3
Alignment explanation
Indices: 3735244--3735281 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3735234 ATATGACTAC
3735244 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3735282 TAAATATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3736403 original size:87 final size:87
Alignment explanation
Indices: 3736304--3736478 Score: 305
Period size: 87 Copynumber: 2.0 Consensus size: 87
3736294 CTTCGACGTG
* *
3736304 GGCTGCCATCTGGTGTTCTGGAATCTACGGTGGCGAGGTGGCATGGCCAAAGGAGTCGATCGTGG
1 GGCTGCCATCTGGTGTTCTGGAATCTACAGCGGCGAGGTGGCATGGCCAAAGGAGTCGATCGTGG
3736369 TGGTGGCAGCAAGGGAGGCGGC
66 TGGTGGCAGCAAGGGAGGCGGC
* * *
3736391 GGCTGCCATCTGGTGTTCTGGAATCTACAGCGGCGAGGTGGCATGGCTAAAGGAGTCGGTTGTGG
1 GGCTGCCATCTGGTGTTCTGGAATCTACAGCGGCGAGGTGGCATGGCCAAAGGAGTCGATCGTGG
3736456 TGGTGGCAGCAAGGGAGGCGGC
66 TGGTGGCAGCAAGGGAGGCGGC
3736478 G
1 G
3736479 ACGTGGTCCT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.17, C:0.19, G:0.44, T:0.20
Consensus pattern (87 bp):
GGCTGCCATCTGGTGTTCTGGAATCTACAGCGGCGAGGTGGCATGGCCAAAGGAGTCGATCGTGG
TGGTGGCAGCAAGGGAGGCGGC
Found at i:3736697 original size:3 final size:3
Alignment explanation
Indices: 3736691--3736760 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
3736681 ATTTATTATT
* * * *
3736691 TAA TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAT TAT TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3736737 TAA TAA AAA TAA TAA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
3736761 AAATGATATA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
2 3 0.05
3 54 0.95
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3738479 original size:34 final size:34
Alignment explanation
Indices: 3738417--3738531 Score: 132
Period size: 34 Copynumber: 3.5 Consensus size: 34
3738407 AGTAACTTTT
*
3738417 TTTTATCTATATCCATAGTTAATGTATGGGTTAAC
1 TTTTATCTATATCCTTAG-TAATGTATGGGTTAAC
3738452 TTTTATCTATATCCTTAGTAATGTATGGGTTAAC
1 TTTTATCTATATCCTTAGTAATGTATGGGTTAAC
* *
3738486 TTTCATCTA-AGTCC-T--T-ATGTATAGGTTAAC
1 TTTTATCTATA-TCCTTAGTAATGTATGGGTTAAC
* *
3738516 TTTTAGCTATACCCTT
1 TTTTATCTATATCCTT
3738532 CTTCCTATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
30 22 0.31
31 3 0.04
33 2 0.03
34 27 0.38
35 17 0.24
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (34 bp):
TTTTATCTATATCCTTAGTAATGTATGGGTTAAC
Found at i:3739998 original size:30 final size:31
Alignment explanation
Indices: 3739957--3740016 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 31
3739947 TTGCTAATTA
3739957 CTTATTTTAAAAAAAAATATTGCAGCGTTTG
1 CTTATTTTAAAAAAAAATATTGCAGCGTTTG
3739988 CTTA-TTTAAAAAAAAATATTGCAGCGTTT
1 CTTATTTTAAAAAAAAATATTGCAGCGTTT
3740017 ACTAGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (31 bp):
CTTATTTTAAAAAAAAATATTGCAGCGTTTG
Found at i:3741891 original size:231 final size:229
Alignment explanation
Indices: 3741423--3741924 Score: 683
Period size: 231 Copynumber: 2.2 Consensus size: 229
3741413 TGAATTAGAA
3741423 ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
1 ACCCGACCCGAAATAATAAAAAAA-TATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
* *
3741488 ATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATATTTT
65 ATTATATATAGAGAGGTATGATTGTAATTATTCCTAAATATATAAGATAAAATTATATATATTTT
*
3741553 GGGTCGGGTCGGGTATTTTTCACCCTAACCCTCAACCCGACCCGACCTGAATATCACACTTAAAA
130 --GTCGGGTCGGGTATTTTTCACCCTAACCCTCAACCCGACCCGACCTCAATATCACACTTAAAA
* * * ***
3741618 AAACCGACCCGACTCGACCAAAATAAAGTTTCACCTG
193 AAACCGACCCGACCCAAACAAAATAAAGACCCACCTG
* *
3741655 ACCCGACCCGAAATAATTAAAAAATATTTTTATTCAATAAAAATAGTGACTTAATTGAAAAAAAA
1 ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAA
*
3741720 TTATATATAGAGAGGTATGATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATA-TTT-
66 TTATATATAGAGAGGTATGATTGTAATTATTCCTAAATATATAAGATAAAATTATATATATTTTG
* * * * ** *
3741783 TCGGGTTGGGTATTTTTCACCCTAAACCC-GATCTCGACCTTACCCTCAA-ATCACACTTTAAAA
131 TCGGGTCGGGTATTTTTCACCCT-AACCCTCAACCCGACCCGA-CCTCAATATCACACTTAAAAA
*
3741846 AACCGACCCGACCCAAATATATGAATTAGAA-ACCCGACC-G
194 AACCGACCCGACCCAAACA-A--AA-TA-AAGACCC-ACCTG
3741886 ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
1 ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
3741925 TATGAATAAG
Statistics
Matches: 241, Mismatches: 21, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
227 58 0.24
228 11 0.05
230 5 0.02
231 139 0.58
232 28 0.12
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (229 bp):
ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAA
TTATATATAGAGAGGTATGATTGTAATTATTCCTAAATATATAAGATAAAATTATATATATTTTG
TCGGGTCGGGTATTTTTCACCCTAACCCTCAACCCGACCCGACCTCAATATCACACTTAAAAAAA
CCGACCCGACCCAAACAAAATAAAGACCCACCTG
Found at i:3744801 original size:16 final size:16
Alignment explanation
Indices: 3744780--3744838 Score: 100
Period size: 16 Copynumber: 3.7 Consensus size: 16
3744770 CATTTAATAA
3744780 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
3744796 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
* *
3744812 ATAAATGAATACGAAC
1 ATAAACGAACACGAAC
3744828 ATAAACGAACA
1 ATAAACGAACA
3744839 TAAACGAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:3744805 original size:10 final size:10
Alignment explanation
Indices: 3744790--3744854 Score: 69
Period size: 10 Copynumber: 6.3 Consensus size: 10
3744780 ATAAACGAAC
3744790 ACGAACATAA
1 ACGAACATAA
**
3744800 ACGAACACGA
1 ACGAACATAA
*
3744810 AC-ATAAATGAA
1 ACGA-ACAT-AA
3744821 TACGAACATAA
1 -ACGAACATAA
3744832 ACGAACATAA
1 ACGAACATAA
3744842 ACGAACATAA
1 ACGAACATAA
3744852 ACG
1 ACG
3744855 TTGGAGACCT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
9 1 0.02
10 35 0.78
11 3 0.07
12 5 0.11
13 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (10 bp):
ACGAACATAA
Found at i:3745926 original size:14 final size:14
Alignment explanation
Indices: 3745909--3745959 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
3745899 GATTGGGTTA
3745909 AACATAATCGAACG
1 AACATAATCGAACG
3745923 AACATAAT----CG
1 AACATAATCGAACG
3745933 AACATAATCGAACG
1 AACATAATCGAACG
3745947 AACATAATCGAAC
1 AACATAATCGAAC
3745960 ATTCACGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.30
14 23 0.70
ACGTcount: A:0.51, C:0.22, G:0.12, T:0.16
Consensus pattern (14 bp):
AACATAATCGAACG
Found at i:3745961 original size:10 final size:10
Alignment explanation
Indices: 3745921--3745945 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3745911 CATAATCGAA
3745921 CGAACATAAT
1 CGAACATAAT
3745931 CGAACATAAT
1 CGAACATAAT
3745941 CGAAC
1 CGAAC
3745946 GAACATAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.16
Consensus pattern (10 bp):
CGAACATAAT
Found at i:3745970 original size:24 final size:24
Alignment explanation
Indices: 3745909--3745961 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
3745899 GATTGGGTTA
3745909 AACATAATCGAACGAACATAATCG
1 AACATAATCGAACGAACATAATCG
3745933 AACATAATCGAACGAACATAATCG
1 AACATAATCGAACGAACATAATCG
3745957 AACAT
1 AACAT
3745962 TCACGAACGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.21, G:0.11, T:0.17
Consensus pattern (24 bp):
AACATAATCGAACGAACATAATCG
Found at i:3746541 original size:35 final size:37
Alignment explanation
Indices: 3746480--3746549 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 37
3746470 CCGAGGTTTT
*
3746480 TATAATATATAGTTTTAGAAAACGATTTTTGAAAACA
1 TATAATATATAGCTTTAGAAAACGATTTTTGAAAACA
*
3746517 TATAATATATA-CTTTA-AAATCGATTTTTGAAAA
1 TATAATATATAGCTTTAGAAAACGATTTTTGAAAA
3746550 TATGTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 16 0.52
36 4 0.13
37 11 0.35
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (37 bp):
TATAATATATAGCTTTAGAAAACGATTTTTGAAAACA
Found at i:3746635 original size:37 final size:35
Alignment explanation
Indices: 3746539--3746635 Score: 133
Period size: 35 Copynumber: 2.7 Consensus size: 35
3746529 TTTAAAATCG
* *
3746539 ATTTTTG-AAAATATGTATATTATATAGTTTTGAA
1 ATTTTTGAAAAATATATATATTATATAATTTTGAA
* *
3746573 ATTTTTTAAAAATATATATAATATATAATTTTGAAA
1 ATTTTTGAAAAATATATATATTATATAATTTTG-AA
3746609 ATTTTTGAAAAAATATATATATTATAT
1 ATTTTTG-AAAAATATATATATTATAT
3746636 TTAAAAACAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
34 6 0.11
35 22 0.41
36 8 0.15
37 18 0.33
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (35 bp):
ATTTTTGAAAAATATATATATTATATAATTTTGAA
Found at i:3748157 original size:31 final size:31
Alignment explanation
Indices: 3748055--3748163 Score: 82
Period size: 31 Copynumber: 3.4 Consensus size: 31
3748045 GAAATTTAAC
*
3748055 ATTTATATATTTTT-T-TATTTTT-TTTTCTAA
1 ATTTA-ATATTTTTATCT-TTTTTATTTTCTTA
* * *
3748085 AGTTTAAGATTTTCTTCATCTTATTTTATTTTCCTC
1 A-TTTAATA-TTT-TT-ATCTT-TTTTATTTTCTTA
*
3748121 TTTTAATATTTTTATCTTTTTTATTTTCTTA
1 ATTTAATATTTTTATCTTTTTTATTTTCTTA
3748152 ATTTAAT-TTTTT
1 ATTTAATATTTTT
3748164 CTTTCTTTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
30 8 0.13
31 24 0.39
32 7 0.11
33 2 0.03
34 5 0.08
35 11 0.18
36 5 0.08
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (31 bp):
ATTTAATATTTTTATCTTTTTTATTTTCTTA
Found at i:3750263 original size:31 final size:31
Alignment explanation
Indices: 3750199--3750269 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 31
3750189 AAAGTTTAAG
**
3750199 ATTTTCTTCATCTTATTTTATTTTCCTCTTTTA
1 ATTTT-TT-ATCTTATTTTATTTTCCTAATTTA
*
3750232 ATATTTTTATCTT-TTTTATTTTCTTAATTTA
1 AT-TTTTTATCTTATTTTATTTTCCTAATTTA
3750263 ATTTTTT
1 ATTTTTT
3750270 CTTTCTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 5 0.15
31 17 0.50
32 5 0.15
33 4 0.12
34 3 0.09
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.70
Consensus pattern (31 bp):
ATTTTTTATCTTATTTTATTTTCCTAATTTA
Found at i:3755256 original size:22 final size:22
Alignment explanation
Indices: 3755228--3755271 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3755218 AAAAGAAAGG
*
3755228 AAAAAAACATTTTCAAATAGGA
1 AAAAAAACATTTTCAAACAGGA
*
3755250 AAAAAAATATTTTCAAACAGGA
1 AAAAAAACATTTTCAAACAGGA
3755272 CAATATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.23
Consensus pattern (22 bp):
AAAAAAACATTTTCAAACAGGA
Found at i:3756908 original size:97 final size:97
Alignment explanation
Indices: 3756737--3756931 Score: 282
Period size: 97 Copynumber: 2.0 Consensus size: 97
3756727 ATATGGAACT
* * * *
3756737 ATATCCCAGTCAAATTTACAGCATAGCTCAAGGTGAAAAGGGTTATATGTCAACAAAAACCTTCA
1 ATATCCCAGTCAAATTCACAACATAGCTCAAGGCGAAAAGGGTTATATATCAACAAAAACCTTCA
* *
3756802 AGTTTGATTCCAATCTGCTCAAGGGCATATCA
66 AGTTCGATTCCAATCAGCTCAAGGGCATATCA
* * * *
3756834 ATATCCCAGTCAAATTCGCAACATAGCTCAAGGCGAGAAGGGTTATCTATCAACAAAAACCTTCG
1 ATATCCCAGTCAAATTCACAACATAGCTCAAGGCGAAAAGGGTTATATATCAACAAAAACCTTCA
* *
3756899 AGTTCGATTCCATTCAGCTCGAGGGCATATCA
66 AGTTCGATTCCAATCAGCTCAAGGGCATATCA
3756931 A
1 A
3756932 CCACATGGTA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 86 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (97 bp):
ATATCCCAGTCAAATTCACAACATAGCTCAAGGCGAAAAGGGTTATATATCAACAAAAACCTTCA
AGTTCGATTCCAATCAGCTCAAGGGCATATCA
Found at i:3757427 original size:37 final size:36
Alignment explanation
Indices: 3757325--3757550 Score: 158
Period size: 35 Copynumber: 6.4 Consensus size: 36
3757315 GTTTATGTAA
*
3757325 TATATAGTTTTTAGAAAACGGTTTTTGAAAA-CGTATAA
1 TATATAG-TTTT-GAAAACGGTTTTTGAAAATC-TATAT
* *
3757363 TATATA-CTTT-AAAATCGATTTTTGAAAATCTATAT
1 TATATAGTTTTGAAAA-CGGTTTTTGAAAATCTATAT
*
3757398 TATATAGTTTTGAAAACGGTTTTTCGAAAATATATATAT
1 TATATAGTTTTGAAAACGGTTTTT-G-AAA-ATCTATAT
3757437 TATATAGTTTTGAAAA---TTTTTGAAAA-C-ATA-
1 TATATAGTTTTGAAAACGGTTTTTGAAAATCTATAT
* * * *
3757467 TATATA-ATAT--ATA--GTTTTTGAAAATATATATAT
1 TATATAGTTTTGAAAACGGTTTTTG-AAA-ATCTATAT
* *
3757500 TATATAGTTTTGAAAAC-ATTTTTGAAAATATATAT
1 TATATAGTTTTGAAAACGGTTTTTGAAAATCTATAT
3757535 AATATATAGTTTTGAA
1 --TATATAGTTTTGAA
3757551 TTTTTTTGAA
Statistics
Matches: 154, Mismatches: 15, Indels: 39
0.74 0.07 0.19
Matches are distributed among these distances:
27 2 0.01
28 6 0.04
29 5 0.03
30 7 0.05
31 3 0.02
32 3 0.02
33 7 0.05
34 9 0.06
35 31 0.20
36 24 0.16
37 25 0.16
38 9 0.06
39 23 0.15
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (36 bp):
TATATAGTTTTGAAAACGGTTTTTGAAAATCTATAT
Found at i:3757484 original size:28 final size:28
Alignment explanation
Indices: 3757453--3757518 Score: 102
Period size: 26 Copynumber: 2.5 Consensus size: 28
3757443 GTTTTGAAAA
3757453 TTTTTGAAAACATATATATAATATATAG
1 TTTTTGAAAACATATATATAATATATAG
*
3757481 TTTTTG-AAA-ATATATATATTATATAG
1 TTTTTGAAAACATATATATAATATATAG
3757507 -TTTTGAAAACAT
1 TTTTTGAAAACAT
3757519 TTTTGAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 5 0.14
26 19 0.54
27 5 0.14
28 6 0.17
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (28 bp):
TTTTTGAAAACATATATATAATATATAG
Found at i:3757493 original size:63 final size:64
Alignment explanation
Indices: 3757416--3757547 Score: 225
Period size: 63 Copynumber: 2.1 Consensus size: 64
3757406 TTTGAAAACG
3757416 GTTTTTCGAAAATATATATATTATATAGTTTTG-AAA-ATTTTTGAAAACATATATATAATATAT
1 GTTTTTCGAAAATATATATATTATATAGTTTTGAAAACATTTTTG-AAA-ATATATATAATATAT
3757479 A
64 A
3757480 GTTTTT-GAAAATATATATATTATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATA
1 GTTTTTCGAAAATATATATATTATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATA
3757543 GTTTT
1 GTTTT
3757548 GAATTTTTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
63 47 0.71
64 12 0.18
65 7 0.11
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (64 bp):
GTTTTTCGAAAATATATATATTATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATA
Found at i:3757578 original size:38 final size:35
Alignment explanation
Indices: 3757380--3757588 Score: 184
Period size: 37 Copynumber: 6.0 Consensus size: 35
3757370 TTTAAAATCG
*
3757380 ATTTTTGAAAATCTATAT--TATATAGTTTTGAAAAC
1 ATTTTTGAAAATATATATAATATATAGTTTTG--AAC
* * *
3757415 GGTTTTTCGAAAATATATATATTATATAGTTTTGAAA
1 -ATTTTT-GAAAATATATATAATATATAGTTTTGAAC
* *
3757452 ATTTTTGAAAACATATAT-ATA-ATA--TAT--A-
1 ATTTTTGAAAATATATATAATATATAGTTTTGAAC
* *
3757480 GTTTTTGAAAATATATATATTATATAGTTTTGAAAAC
1 ATTTTTGAAAATATATATAATATATAGTTTTG--AAC
*
3757517 ATTTTTGAAAATATATATAATATATAGTTTTGAAT
1 ATTTTTGAAAATATATATAATATATAGTTTTGAAC
*
3757552 TTTTTTGAAAAACATATATATAATATATAGTTTTGAA
1 ATTTTTG--AAA-ATATATATAATATATAGTTTTGAA
3757589 AATGATTTTT
Statistics
Matches: 143, Mismatches: 15, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
28 16 0.11
29 3 0.02
30 3 0.02
31 2 0.01
32 2 0.01
33 3 0.02
34 2 0.01
35 19 0.13
36 11 0.08
37 46 0.32
38 24 0.17
39 12 0.08
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (35 bp):
ATTTTTGAAAATATATATAATATATAGTTTTGAAC
Found at i:3757607 original size:38 final size:37
Alignment explanation
Indices: 3757481--3757616 Score: 170
Period size: 37 Copynumber: 3.6 Consensus size: 37
3757471 TAATATATAG
* *
3757481 TTTTTGAAAATATATATATTATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAATA
*
3757518 TTTTTGAAAATATATATAATATATAGTTTTG--AATT
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAATA
3757553 TTTTTGAAAAACATATATATAATATATAGTTTTGAAAATGA
1 TTTTTG--AAA-ATATATATAATATATAGTTTTGAAAAT-A
* *
3757594 TTTTTGCATATATATAT-ATATAT
1 TTTTTGAAAATATATATAATATAT
3757617 TATATTTGAA
Statistics
Matches: 87, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
35 8 0.09
37 39 0.45
38 30 0.34
39 1 0.01
40 3 0.03
41 6 0.07
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAATA
Found at i:3757635 original size:38 final size:36
Alignment explanation
Indices: 3757490--3757635 Score: 113
Period size: 38 Copynumber: 3.9 Consensus size: 36
3757480 GTTTTTGAAA
* *
3757490 ATATATATATTATATAGTTTTGAAAAC-ATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACAATTTTTG--C
**
3757527 ATATATATAATATATAGTTTTG--AA-TTTTTTTGAAAAAC
1 ATATATATAATATATAGTTTTGAAAACAATTTTTG-----C
**
3757565 ATATATATAATATATAGTTTTGAAAATGATTTTTGC
1 ATATATATAATATATAGTTTTGAAAACAATTTTTGC
3757601 ATATATATATATATATTA-TATTTGAAAACAATTTT
1 ATATATATA-ATATA-TAGT-TTTGAAAACAATTTT
3757636 CTTGAAAACA
Statistics
Matches: 92, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
35 8 0.09
36 10 0.11
37 27 0.29
38 39 0.42
40 2 0.02
41 6 0.07
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTGAAAACAATTTTTGC
Found at i:3759161 original size:35 final size:36
Alignment explanation
Indices: 3759102--3759185 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 36
3759092 CTGCATCTTA
*
3759102 TTTTATTTTATTTTTCTCTTTTTAACATTTTTCTCT-
1 TTTTATTTTA-TTTTCTCTATTTAACATTTTTCTCTC
**
3759138 TTTTATTTTATTTTCT-TAATTTAATTTTTTTCTCTC
1 TTTTATTTTATTTTCTCT-ATTTAACATTTTTCTCTC
*
3759174 TTTGA-TTTATTT
1 TTTTATTTTATTT
3759186 AATATTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 1 0.02
35 27 0.64
36 14 0.33
ACGTcount: A:0.15, C:0.11, G:0.01, T:0.73
Consensus pattern (36 bp):
TTTTATTTTATTTTCTCTATTTAACATTTTTCTCTC
Found at i:3768622 original size:20 final size:22
Alignment explanation
Indices: 3768597--3768636 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3768587 TATTGGTTGA
3768597 AATTA-TT-AAAAAATTAATAT
1 AATTATTTAAAAAAATTAATAT
3768617 AATTATTTAAAAAAATTAAT
1 AATTATTTAAAAAAATTAAT
3768637 TTTTGCTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTATTTAAAAAAATTAATAT
Found at i:3769281 original size:8 final size:8
Alignment explanation
Indices: 3769230--3769322 Score: 79
Period size: 8 Copynumber: 12.0 Consensus size: 8
3769220 TCTACTACAC
3769230 CTCTCAAA
1 CTCTCAAA
3769238 CTTCTCAAA
1 C-TCTCAAA
*
3769247 -TCGTCTAA
1 CTC-TCAAA
*
3769255 CTCTCAAT
1 CTCTCAAA
* *
3769263 CTTTGAAA
1 CTCTCAAA
3769271 CTCTCAAA
1 CTCTCAAA
3769279 CTCT-AAA
1 CTCTCAAA
*
3769286 -TCTCAAG
1 CTCTCAAA
3769293 CTCTCAAA
1 CTCTCAAA
3769301 CTCT-AAA
1 CTCTCAAA
*
3769308 -TCTCAAG
1 CTCTCAAA
3769315 CTCTCAAA
1 CTCTCAAA
3769323 ATGAGGCGTA
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
6 6 0.09
7 12 0.18
8 39 0.59
9 9 0.14
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.30
Consensus pattern (8 bp):
CTCTCAAA
Found at i:3769299 original size:22 final size:22
Alignment explanation
Indices: 3769271--3769322 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
3769261 ATCTTTGAAA
3769271 CTCTCAAACTCTAAATCTCAAG
1 CTCTCAAACTCTAAATCTCAAG
3769293 CTCTCAAACTCTAAATCTCAAG
1 CTCTCAAACTCTAAATCTCAAG
3769315 CTCTCAAA
1 CTCTCAAA
3769323 ATGAGGCGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.27
Consensus pattern (22 bp):
CTCTCAAACTCTAAATCTCAAG
Found at i:3769302 original size:30 final size:32
Alignment explanation
Indices: 3769230--3769309 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 32
3769220 TCTACTACAC
* *
3769230 CTCTCAAACTTCTCAAATCGTCTAACTCTCAAT
1 CTCTCAAAC-TCTCAAATCGTCTAAATCTCAAG
* *
3769263 CTTTGAAACTCTCAAA-C-TCTAAATCTCAAG
1 CTCTCAAACTCTCAAATCGTCTAAATCTCAAG
3769293 CTCTCAAACTCT-AAATC
1 CTCTCAAACTCTCAAATC
3769310 TCAAGCTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 3 0.08
30 22 0.55
31 1 0.03
32 7 0.17
33 7 0.17
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (32 bp):
CTCTCAAACTCTCAAATCGTCTAAATCTCAAG
Found at i:3771004 original size:20 final size:21
Alignment explanation
Indices: 3770970--3771011 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3770960 CTTTTTATCT
*
3770970 AACCCTTAAACTATTAAAATA
1 AACCCTTAAAATATTAAAATA
*
3770991 AACCC-TAAAATATTTAAATA
1 AACCCTTAAAATATTAAAATA
3771011 A
1 A
3771012 TATAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.29
Consensus pattern (21 bp):
AACCCTTAAAATATTAAAATA
Found at i:3772151 original size:2 final size:2
Alignment explanation
Indices: 3772144--3772187 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3772134 ACTAAAACAA
3772144 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
3772186 AT
1 AT
3772188 TTCTTATCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3772383 original size:20 final size:20
Alignment explanation
Indices: 3772358--3772395 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3772348 TCAATGTAAA
3772358 AAAAAATTCA-TTATATACTC
1 AAAAAATT-ATTTATATACTC
3772378 AAAAAATTATTTATATAC
1 AAAAAATTATTTATATAC
3772396 AACTCAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAAATTATTTATATACTC
Found at i:3773266 original size:64 final size:65
Alignment explanation
Indices: 3773143--3773267 Score: 166
Period size: 64 Copynumber: 1.9 Consensus size: 65
3773133 GAATGCATTT
*
3773143 CATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTCATGCATCGATGCACCAGC
1 CATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCACTTCATGCATCGATGCACCAGC
* * * *
3773208 CATGCATCGATGCACT-ATGGCTATTT-TG-AAACATCGAATGTACTTGATGTATCGATGCAC
1 CATGCATCGATGCACTGA-GGAT-TTTATGAAAACATCGAATGCACTTCATGCATCGATGCAC
3773268 TCTTAGTGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
64 29 0.55
65 21 0.40
66 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (65 bp):
CATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCACTTCATGCATCGATGCACCAGC
Found at i:3779068 original size:44 final size:42
Alignment explanation
Indices: 3778979--3779070 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 42
3778969 TGCTTAATGT
* *
3778979 ATCGATACACCTAACAGTGCATCGATGCATCCTTGAATGTAC
1 ATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATGTAC
* *
3779021 ATCGATACACCATGAA-GGTGCACCGATGCACGCCTTGAATGTGC
1 ATCGATACACC-T-AACAGTGCACCGATGCA-GCCTTGAATGTAC
3779065 ATCGAT
1 ATCGAT
3779071 GTACAAGGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 11 0.26
43 13 0.30
44 19 0.44
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (42 bp):
ATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATGTAC
Found at i:3780612 original size:21 final size:21
Alignment explanation
Indices: 3780586--3780630 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3780576 ACCCCGGGAG
*
3780586 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
3780607 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
3780628 CTA
1 CTA
3780631 CTCCTTCGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.40, G:0.16, T:0.33
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:3781012 original size:29 final size:28
Alignment explanation
Indices: 3780980--3781036 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
3780970 TGGATGTTTA
3780980 AATTTGATGGTTCT-TGGATGTTTTGAACT
1 AATTTG-TGGTTCTATGGAT-TTTTGAACT
* *
3781009 AATTTGTTGTTTTATGGATTTTTGAACT
1 AATTTGTGGTTCTATGGATTTTTGAACT
3781037 TAATATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (28 bp):
AATTTGTGGTTCTATGGATTTTTGAACT
Found at i:3781799 original size:65 final size:65
Alignment explanation
Indices: 3781728--3781888 Score: 304
Period size: 65 Copynumber: 2.5 Consensus size: 65
3781718 AATTAAATTG
* *
3781728 AACATCGAATGCATTTCATTCATCGATGCACATACCATGCATTGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCATTGATGCACTGAGGATTTTATGAA
3781793 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCATTGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCATTGATGCACTGAGGATTTTATGAA
3781858 AACATCGAATGCATTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
3781889 TCTGACTATT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 94 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATGCATTGATGCACTGAGGATTTTATGAA
Found at i:3781886 original size:46 final size:45
Alignment explanation
Indices: 3781829--3781934 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 45
3781819 TGCACATACC
* * *
3781829 ATGCATTGATGCACTGAGGA-T-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACT-AGGACTATTT-TG-AAACATCAAATGCACTTG
**
3781875 ATGCATCGATGCACTCTGACTATTTTGAAACATCAAATGCACTTG
1 ATGCATCGATGCACTAGGACTATTTTGAAACATCAAATGCACTTG
3781920 ATGCATCGATGCACT
1 ATGCATCGATGCACT
3781935 CTTAGTGCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
45 33 0.62
46 17 0.32
47 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (45 bp):
ATGCATCGATGCACTAGGACTATTTTGAAACATCAAATGCACTTG
Found at i:3781933 original size:17 final size:19
Alignment explanation
Indices: 3781911--3781953 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3781901 GAAACATCAA
*
3781911 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
3781928 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
3781947 ATGCACT
1 ATGCACT
3781954 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:3783869 original size:28 final size:28
Alignment explanation
Indices: 3783808--3783873 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
3783798 CGAAACCCAA
* * *
3783808 TTTAGAGTTAATGTTTTAAAGTTTAGAG
1 TTTAGGGTTTATGTTTTAAAATTTAGAG
*
3783836 TTTAGGGTTTATGTTTTAAAATTTAGGG
1 TTTAGGGTTTATGTTTTAAAATTTAGAG
3783864 TTTAGGGTTT
1 TTTAGGGTTT
3783874 CTATAAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (28 bp):
TTTAGGGTTTATGTTTTAAAATTTAGAG
Found at i:3783966 original size:13 final size:13
Alignment explanation
Indices: 3783948--3783995 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
3783938 TAATTTACTT
3783948 TATATAGTTTTTA
1 TATATAGTTTTTA
3783961 TATATAAGTTATATATA
1 TATAT-AGTT-T-T-TA
*
3783978 TATATAGTTTATA
1 TATATAGTTTTTA
3783991 TATAT
1 TATAT
3783996 TATACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 12 0.40
14 4 0.13
15 2 0.07
16 5 0.17
17 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (13 bp):
TATATAGTTTTTA
Found at i:3783981 original size:17 final size:15
Alignment explanation
Indices: 3783948--3783995 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
3783938 TAATTTACTT
*
3783948 TATATAGTTTTTATA
1 TATATAGTTTATATA
3783963 TATA-AGTTATATATA
1 TATATAGTT-TATATA
3783978 TATATAGTTTATATA
1 TATATAGTTTATATA
3783993 TAT
1 TAT
3783996 TATACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 4 0.13
15 22 0.73
16 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:3784067 original size:21 final size:21
Alignment explanation
Indices: 3784045--3784083 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3784035 TATAATTCAG
3784045 GGGTT-AGGGTTAAGAGTTGA
1 GGGTTAAGGGTTAAGAGTTGA
*
3784065 GGGTTAAGGGTTTAGAGTT
1 GGGTTAAGGGTTAAGAGTT
3784084 CATAGTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.44, T:0.33
Consensus pattern (21 bp):
GGGTTAAGGGTTAAGAGTTGA
Found at i:3784095 original size:21 final size:21
Alignment explanation
Indices: 3784048--3784100 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3784038 AATTCAGGGG
* * *
3784048 TTAGGGTTAAGAGTTGAGGGT
1 TTAGGGTTTAGAGTTCAGAGT
* *
3784069 TAAGGGTTTAGAGTTCATAGT
1 TTAGGGTTTAGAGTTCAGAGT
3784090 TTAGGGTTTAG
1 TTAGGGTTTAG
3784101 GGTTTCTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
TTAGGGTTTAGAGTTCAGAGT
Found at i:3784105 original size:14 final size:14
Alignment explanation
Indices: 3784043--3784105 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
3784033 TATATAATTC
*
3784043 AGGGGTTAGGGTTA
1 AGGGTTTAGGGTTA
* *
3784057 AGAGTTGAGGGTTA
1 AGGGTTTAGGGTTA
* *
3784071 AGGGTTTAGAGTTC
1 AGGGTTTAGGGTTA
** *
3784085 ATAGTTTAGGGTTT
1 AGGGTTTAGGGTTA
3784099 AGGGTTT
1 AGGGTTT
3784106 CTATAAACTA
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.22, C:0.02, G:0.40, T:0.37
Consensus pattern (14 bp):
AGGGTTTAGGGTTA
Found at i:3784166 original size:2 final size:2
Alignment explanation
Indices: 3784155--3784311 Score: 91
Period size: 2 Copynumber: 81.0 Consensus size: 2
3784145 ATAGTATTTC
*
3784155 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
3784195 TA GA T- TA CA TA GA T- TA GT- TA TA TA TA CA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
3784236 T- TA -A TA TA AA T- TA TA AA T- TA TA AA CTA TA TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
3784274 TA GTT TA TA CA TA TA TA GTT 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
3784312 GAGAGAGAGA
Statistics
Matches: 117, Mismatches: 23, Indels: 30
0.69 0.14 0.18
Matches are distributed among these distances:
1 10 0.09
2 101 0.86
3 6 0.05
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3784299 original size:17 final size:15
Alignment explanation
Indices: 3784270--3784305 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3784260 CTATATATTT
3784270 TATATAGTTTATACA
1 TATATAGTTTATACA
*
3784285 TATATAGTTTATATA
1 TATATAGTTTATACA
3784300 TATATA
1 TATATA
3784306 TATATAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:3784557 original size:20 final size:20
Alignment explanation
Indices: 3784532--3784588 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
3784522 AATTTTTCTA
3784532 TTCCCTCTAAATTTCTCAAT
1 TTCCCTCTAAATTTCTCAAT
*
3784552 TTCCCTCTAAA-TTCCCAAT
1 TTCCCTCTAAATTTCTCAAT
*
3784571 TTCCCTCCAAATTT-TCAA
1 TTCCCTCTAAATTTCTCAA
3784589 ATAAAATCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.40
Consensus pattern (20 bp):
TTCCCTCTAAATTTCTCAAT
Found at i:3784728 original size:24 final size:25
Alignment explanation
Indices: 3784679--3784732 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
3784669 TTAATATAAA
3784679 TTATAGTTTATAAACTATATAATTT
1 TTATAGTTTATAAACTATATAATTT
* *
3784704 TTATAGTTTATACA-TATATAGTTT
1 TTATAGTTTATAAACTATATAATTT
3784728 TTATA
1 TTATA
3784733 TATAGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (25 bp):
TTATAGTTTATAAACTATATAATTT
Found at i:3784733 original size:13 final size:15
Alignment explanation
Indices: 3784705--3784843 Score: 83
Period size: 15 Copynumber: 9.3 Consensus size: 15
3784695 ATATAATTTT
*
3784705 TATAGTTTATACATA
1 TATAGTTTATATATA
3784720 TATAGTTT-T-TATA
1 TATAGTTTATATATA
*
3784733 TATAGTTTATATGTA
1 TATAGTTTATATATA
* *
3784748 TATAGTTCATATAAA
1 TATAGTTTATATATA
* * *
3784763 CATA-ATT-TATGTA
1 TATAGTTTATATATA
* *
3784776 CATAGCTTATAATAATTA
1 TATAGTTTAT-AT-A-TA
*
3784794 TATAGTATATATATAAA
1 TATAGT-T-TATATATA
3784811 TATAGTTTATATATA
1 TATAGTTTATATATA
*
3784826 -A-ACTTATATATATA
1 TATAGTT-TATATATA
3784840 TATA
1 TATA
3784844 TATTATATTT
Statistics
Matches: 95, Mismatches: 17, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
13 22 0.23
14 14 0.15
15 35 0.37
16 4 0.04
17 7 0.07
18 7 0.07
19 3 0.03
20 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (15 bp):
TATAGTTTATATATA
Found at i:3784760 original size:28 final size:28
Alignment explanation
Indices: 3784705--3784760 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3784695 ATATAATTTT
**
3784705 TATAGTTTATACATATATAGTTTTTATA
1 TATAGTTTATACATATATAGTTCATATA
**
3784733 TATAGTTTATATGTATATAGTTCATATA
1 TATAGTTTATACATATATAGTTCATATA
3784761 AACATAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.52
Consensus pattern (28 bp):
TATAGTTTATACATATATAGTTCATATA
Found at i:3784804 original size:2 final size:2
Alignment explanation
Indices: 3784792--3784851 Score: 52
Period size: 2 Copynumber: 29.5 Consensus size: 2
3784782 TTATAATAAT
* * *
3784792 TA TA TA GTA TA TA TA TA AA TA TA GTT TA TA TA TA AA CT- TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
3784834 TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA T
3784852 TTTTTCAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
1 2 0.04
2 42 0.89
3 3 0.06
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3784815 original size:17 final size:17
Alignment explanation
Indices: 3784793--3784843 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
3784783 TATAATAATT
3784793 ATATAGTATATATATAA
1 ATATAGTATATATATAA
*
3784810 ATATAGTTTATATATAA
1 ATATAGTATATATATAA
3784827 ACTTATA-TATATATATA
1 A--TATAGTATATATATA
3784844 TATTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 17 0.57
18 9 0.30
19 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (17 bp):
ATATAGTATATATATAA
Found at i:3784821 original size:35 final size:37
Alignment explanation
Indices: 3784777--3784845 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
3784767 ATTTATGTAC
3784777 ATAGCTTATA-AT-AA-TTATATAGTATATATATAAAT
1 ATAGCTTATATATAAACTTATATA-TATATATATAAAT
*
3784812 ATAGTTTATATATAAACTTATATATATATATATA
1 ATAGCTTATATATAAACTTATATATATATATATA
3784846 TTATATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 9 0.30
36 2 0.07
37 12 0.40
38 7 0.23
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (37 bp):
ATAGCTTATATATAAACTTATATATATATATATAAAT
Found at i:3784851 original size:17 final size:17
Alignment explanation
Indices: 3784790--3784851 Score: 61
Period size: 19 Copynumber: 3.4 Consensus size: 17
3784780 GCTTATAATA
3784790 ATTATATAGTATATATAT
1 ATTATATA-TATATATAT
* * *
3784808 AAATATAGTTTATATATAA
1 -ATTATA-TATATATATAT
3784827 ACTTATATATATATATAT
1 A-TTATATATATATATAT
3784845 ATTATAT
1 ATTATAT
3784852 TTTTTCAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 6 0.17
18 11 0.31
19 17 0.49
20 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (17 bp):
ATTATATATATATATAT
Found at i:3785817 original size:31 final size:32
Alignment explanation
Indices: 3785757--3785819 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
3785747 AAAGAAGCGA
3785757 TTACTTTATGTGTCTTGTAATAAAAATCATTT
1 TTACTTTATGTGTCTTGTAATAAAAATCATTT
* *
3785789 TTACTTTTTGTGTTTTGTAAT-AAAATCATTT
1 TTACTTTATGTGTCTTGTAATAAAAATCATTT
3785820 AGATTTGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 10 0.34
32 19 0.66
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.54
Consensus pattern (32 bp):
TTACTTTATGTGTCTTGTAATAAAAATCATTT
Found at i:3786640 original size:15 final size:15
Alignment explanation
Indices: 3786604--3786634 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3786594 CATAATTAAG
3786604 TAATTTAATTTTCTT
1 TAATTTAATTTTCTT
3786619 TAATTTAATTTT-TT
1 TAATTTAATTTTCTT
3786633 TA
1 TA
3786635 TCTTTAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTTAATTTTCTT
Done.