Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 19
Found at i:3025232 original size:23 final size:26
Alignment explanation
Indices: 3025202--3025265 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
3025192 TAATACCTTC
*
3025202 ATAAAATAA-ATAAAAA-AAT-ATTA
1 ATAAAATAATATAAAAATAATAAGTA
3025225 ATAAAATAATATAAAAATAATAAGTA
1 ATAAAATAATATAAAAATAATAAGTA
*
3025251 ATAAAA-AATTTAAAA
1 ATAAAATAATATAAAA
3025266 GAAAAGAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 9 0.25
24 7 0.19
25 11 0.31
26 9 0.25
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (26 bp):
ATAAAATAATATAAAAATAATAAGTA
Found at i:3025246 original size:14 final size:13
Alignment explanation
Indices: 3025204--3025258 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 13
3025194 ATACCTTCAT
3025204 AAAATAA-ATAAA
1 AAAATAATATAAA
*
3025216 AAAAT-AT-TAAT
1 AAAATAATATAAA
3025227 AAAATAATATAAA
1 AAAATAATATAAA
3025240 AATAATAAGTAATAAA
1 AA-AATAA-T-ATAAA
3025256 AAA
1 AAA
3025259 TTTAAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
11 9 0.26
12 7 0.20
13 5 0.14
14 5 0.14
15 2 0.06
16 7 0.20
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (13 bp):
AAAATAATATAAA
Found at i:3025850 original size:14 final size:15
Alignment explanation
Indices: 3025831--3025868 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3025821 TCATAAAATA
*
3025831 AATAAAAAAAT-ATT
1 AATAAAAAAATAAGT
*
3025845 AATAAAATAATAAGT
1 AATAAAAAAATAAGT
3025860 AATAAAAAA
1 AATAAAAAA
3025869 TTTAAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAAAAAAATAAGT
Found at i:3026664 original size:2 final size:2
Alignment explanation
Indices: 3026657--3026700 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3026647 TATTATTTAT
3026657 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3026699 TA
1 TA
3026701 ATAAAATAAA
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):
TA
Found at i:3026709 original size:8 final size:8
Alignment explanation
Indices: 3026698--3026752 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
3026688 ATATATATAT
3026698 ATAATAAA
1 ATAATAAA
3026706 ATAA-AATA
1 ATAATAA-A
*
3026714 ATTAA-ATA
1 A-TAATAAA
*
3026722 ATAATTAA
1 ATAATAAA
3026730 ATAATAATA
1 ATAATAA-A
3026739 ATAATAAA
1 ATAATAAA
3026747 ATAATA
1 ATAATA
3026753 TTGCAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 5 0.13
8 22 0.56
9 12 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
ATAATAAA
Found at i:3026726 original size:3 final size:3
Alignment explanation
Indices: 3026698--3026752 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
3026688 ATATATATAT
* *
3026698 ATA ATA A-A ATA A-A ATA ATT A-A ATA ATA ATT A-A ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3026742 ATA A-A ATA ATA
1 ATA ATA ATA ATA
3026753 TTGCAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 8 0.19
3 35 0.81
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3026726 original size:11 final size:11
Alignment explanation
Indices: 3026710--3026745 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
3026700 AATAAAATAA
3026710 AATAATTAAAT
1 AATAATTAAAT
3026721 AATAATTAAAT
1 AATAATTAAAT
3026732 AATAA-T-AAT
1 AATAATTAAAT
3026741 AATAA
1 AATAA
3026746 AATAATATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 8 0.32
10 1 0.04
11 16 0.64
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAATTAAAT
Found at i:3026752 original size:11 final size:11
Alignment explanation
Indices: 3026698--3026750 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
3026688 ATATATATAT
3026698 ATAATAAAATAAA
1 ATAATAAAAT--A
*
3026711 ATAATTAAATA
1 ATAATAAAATA
*
3026722 ATAATTAAATA
1 ATAATAAAATA
3026733 ATAATAATAATA
1 ATAATAA-AATA
3026745 A-AATAA
1 ATAATAA
3026751 TATTGCAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
11 23 0.62
12 5 0.14
13 9 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATAAAATA
Found at i:3028077 original size:2 final size:2
Alignment explanation
Indices: 3028070--3028109 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3028060 GTAATTTGTA
3028070 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
3028110 TTAATAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3028136 original size:23 final size:23
Alignment explanation
Indices: 3028100--3028157 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
3028090 ATATATATAT
3028100 ATATATATATTTAATAATAATAATA
1 ATATAT-TA-TTAATAATAATAATA
*
3028125 ATATATTATTAATAATAATTATA
1 ATATATTATTAATAATAATAATA
3028148 AT-TATTATTA
1 ATATATTATTA
3028158 TGAAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 8 0.25
23 16 0.50
24 2 0.06
25 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATTATTAATAATAATAATA
Found at i:3037116 original size:9 final size:9
Alignment explanation
Indices: 3037104--3037129 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3037094 TATGCTGGTG
3037104 CTGCTGTAT
1 CTGCTGTAT
3037113 CTGCTGTAT
1 CTGCTGTAT
3037122 CTGCTGTA
1 CTGCTGTA
3037130 ACCATTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (9 bp):
CTGCTGTAT
Found at i:3041421 original size:6 final size:6
Alignment explanation
Indices: 3041395--3041435 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
3041385 TTATTTTGAA
*
3041395 TTTAATT TTTAAAT TTCAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAA-T TTT-AAT TTTAAT TTTAAT TTTAAT TTTAAT TTT
3041436 CGTAACTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 23 0.74
7 6 0.19
8 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTAAT
Found at i:3041421 original size:12 final size:12
Alignment explanation
Indices: 3041387--3041431 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
3041377 AAAGGTAATT
*
3041387 ATTTTGAATTTA
1 ATTTTAAATTTA
3041399 ATTTTTAAATTTCA
1 A-TTTTAAATTT-A
*
3041413 ATTTTAATTTTA
1 ATTTTAAATTTA
3041425 ATTTTAA
1 ATTTTAA
3041432 TTTTCGTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 9 0.31
13 18 0.62
14 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (12 bp):
ATTTTAAATTTA
Found at i:3044180 original size:20 final size:18
Alignment explanation
Indices: 3044133--3044184 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 18
3044123 CACCCTGCAG
3044133 GGGGTATCGATACAC-CA
1 GGGGTATCGATACACTCA
* *
3044150 -GTGTATGGATACACTCATA
1 GGGGTATCGATACACTC--A
3044169 GGGGTATCGATACACT
1 GGGGTATCGATACACT
3044185 TTAGCATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
19 1 0.04
20 13 0.48
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (18 bp):
GGGGTATCGATACACTCA
Found at i:3044180 original size:36 final size:37
Alignment explanation
Indices: 3044111--3044183 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
3044101 AGCAGTCATG
*
3044111 AGTGTATGGATACACCCTGCAGGGGGTATCGATACACC
1 AGTGTATGGATACA-CCTGCAAGGGGTATCGATACACC
3044149 AGTGTATGGATACA-CT-CATAGGGGTATCGATACAC
1 AGTGTATGGATACACCTGCA-AGGGGTATCGATACAC
3044184 TTTAGCATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 2 0.06
36 17 0.52
38 14 0.42
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (37 bp):
AGTGTATGGATACACCTGCAAGGGGTATCGATACACC
Found at i:3044447 original size:18 final size:18
Alignment explanation
Indices: 3044421--3044456 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3044411 CTAACAAAAG
*
3044421 GATATCAATTGTTAGAAA
1 GATACCAATTGTTAGAAA
*
3044439 GATACCAATTGTTGGAAA
1 GATACCAATTGTTAGAAA
3044457 ATATATGAAA
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:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (18 bp):
GATACCAATTGTTAGAAA
Found at i:3048978 original size:16 final size:17
Alignment explanation
Indices: 3048943--3048975 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3048933 AAACCAGAAC
3048943 CCCAGGGGGTATCGATT
1 CCCAGGGGGTATCGATT
3048960 CCCAGGGGGTATCGAT
1 CCCAGGGGGTATCGAT
3048976 CCCTCTCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.21
Consensus pattern (17 bp):
CCCAGGGGGTATCGATT
Found at i:3050908 original size:19 final size:20
Alignment explanation
Indices: 3050874--3050921 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
3050864 TCTAAATCCT
3050874 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTTCATTTTGG
*
3050894 TTTTCAAAA-TTCATTTTTG
1 TTTTCAAAATTTCATTTTGG
*
3050913 CTTTCAAAA
1 TTTTCAAAA
3050922 GAAAATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTGG
Found at i:3057811 original size:19 final size:20
Alignment explanation
Indices: 3057782--3057821 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3057772 ATATATATAT
3057782 ATATGTTTTTATTACTTTTA
1 ATATGTTTTTATTACTTTTA
*
3057802 ATAT-TTTTTATTTCTTTTA
1 ATATGTTTTTATTACTTTTA
3057821 A
1 A
3057822 CACTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (20 bp):
ATATGTTTTTATTACTTTTA
Found at i:3059201 original size:22 final size:21
Alignment explanation
Indices: 3059172--3059216 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3059162 TAGGGATTTT
*
3059172 TATTTTTATATTATT-AAAATA
1 TATTTTTA-ATCATTAAAAATA
3059193 TATTCTTTAATCATTAAAAATA
1 TATT-TTTAATCATTAAAAATA
3059215 TA
1 TA
3059217 AAAATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTTTTAATCATTAAAAATA
Found at i:3059244 original size:42 final size:42
Alignment explanation
Indices: 3059190--3059271 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
3059180 TATTATTAAA
* *
3059190 ATATATTCTTTAATCATTAAAAATATAA-AAATTATTATATG
1 ATATATTCTTTAATAATTAAAAATATAATAAATAATTATATG
* *
3059231 ATATATTATTTTAATAATTTAAAATATAATAAATAATTATA
1 ATATATT-CTTTAATAATTAAAAATATAATAAATAATTATA
3059272 AAATATTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 7 0.20
42 18 0.51
43 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (42 bp):
ATATATTCTTTAATAATTAAAAATATAATAAATAATTATATG
Found at i:3063253 original size:6 final size:6
Alignment explanation
Indices: 3063242--3063268 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3063232 GCTCAAAAAG
3063242 AAAGGA AAAGGA AAAGGA AAAGGA AAA
1 AAAGGA AAAGGA AAAGGA AAAGGA AAA
3063269 TTACCAGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:3064779 original size:42 final size:40
Alignment explanation
Indices: 3064690--3064785 Score: 117
Period size: 39 Copynumber: 2.4 Consensus size: 40
3064680 TTTTTATATT
* *
3064690 ATTA-AAATATATT-CTTTAATTATTAAAAATATAAAAAA
1 ATTATAAATATATTATTTTAATAATTAAAAATATAAAAAA
* *
3064728 ATTAT-AATATATTATTTTAATAATTTAAATTATAATAAATA
1 ATTATAAATATATTATTTTAATAATTAAAAATATAA-AAA-A
3064769 ATTATAAATATATTATT
1 ATTATAAATATATTATT
3064786 ATAAAATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
38 12 0.24
39 17 0.35
40 3 0.06
41 6 0.12
42 11 0.22
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (40 bp):
ATTATAAATATATTATTTTAATAATTAAAAATATAAAAAA
Found at i:3064794 original size:13 final size:13
Alignment explanation
Indices: 3064728--3064816 Score: 56
Period size: 13 Copynumber: 6.5 Consensus size: 13
3064718 ATATAAAAAA
*
3064728 ATTATAATATATT
1 ATTATAAAATATT
*
3064741 ATTTTAATAAT-TT
1 ATTATAA-AATATT
*
3064754 AAATTATAATAA-ATA
1 --ATTATAA-AATATT
3064769 ATTATAAATATATT
1 ATTATAAA-ATATT
3064783 ATTATAAAATATATT
1 ATTAT-AAA-ATATT
*
3064798 ATTTTAAAATATT
1 ATTATAAAATATT
*
3064811 AATATA
1 ATTATA
3064817 TTCATGCCAG
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
12 1 0.02
13 25 0.41
14 12 0.20
15 23 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTATAAAATATT
Found at i:3064794 original size:15 final size:15
Alignment explanation
Indices: 3064769--3064809 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
3064759 ATAATAAATA
3064769 ATTAT-AAATATATT
1 ATTATAAAATATATT
3064783 ATTATAAAATATATT
1 ATTATAAAATATATT
*
3064798 ATTTTAAAATAT
1 ATTATAAAATAT
3064810 TAATATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:3064799 original size:39 final size:38
Alignment explanation
Indices: 3064690--3064789 Score: 103
Period size: 38 Copynumber: 2.5 Consensus size: 38
3064680 TTTTTATATT
* * * *
3064690 ATTAAAATATATTCTT-TAATTATTAAAAATATAAAAAA
1 ATTATAATATATTATTATAATAATT-AAATTATAAAAAA
*
3064728 ATTATAATATATTATTTTAATAATTTAAATTATAATAAATA
1 ATTATAATATATTATTATAATAA-TTAAATTATAA-AAA-A
3064769 ATTATAAATATATTATTATAA
1 ATTAT-AATATATTATTATAA
3064790 AATATATTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
38 14 0.27
39 13 0.25
40 5 0.10
41 6 0.12
42 14 0.27
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (38 bp):
ATTATAATATATTATTATAATAATTAAATTATAAAAAA
Found at i:3066273 original size:15 final size:14
Alignment explanation
Indices: 3066234--3066263 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3066224 TACTATTGTG
*
3066234 ATAAATTTAATTTT
1 ATAAAATTAATTTT
3066248 ATAAAATTAATTTT
1 ATAAAATTAATTTT
3066262 AT
1 AT
3066264 CACTATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAAAATTAATTTT
Found at i:3067494 original size:33 final size:32
Alignment explanation
Indices: 3067427--3067515 Score: 81
Period size: 32 Copynumber: 2.7 Consensus size: 32
3067417 AATTTATAAC
* * * *
3067427 AAATATTAATTTCTCATTATAAAAATTGTGACAA
1 AAATATT-ATTTCACAATA-AAAAACTGTAACAA
3067461 ATAATATTATTTCACAATAAAAAACTGTAACAA
1 A-AATATTATTTCACAATAAAAAACTGTAACAA
* *
3067494 AATTATT-TAGTCACAATAAAAA
1 AAATATTAT-TTCACAATAAAAA
3067516 GTTATAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
31 1 0.02
32 17 0.36
33 13 0.28
34 10 0.21
35 6 0.13
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.34
Consensus pattern (32 bp):
AAATATTATTTCACAATAAAAAACTGTAACAA
Found at i:3067532 original size:31 final size:32
Alignment explanation
Indices: 3067472--3067540 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
3067462 TAATATTATT
* *
3067472 TCACAATAAAAAACTGTAACAAAATTATTTAG
1 TCACAATAAAAAACTATAACAAAAATATTTAG
**
3067504 TCACAATAAAAAGTTATAA-AAAAATATTTAG
1 TCACAATAAAAAACTATAACAAAAATATTTAG
*
3067535 TGACAA
1 TCACAA
3067541 AATAAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 16 0.50
32 16 0.50
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (32 bp):
TCACAATAAAAAACTATAACAAAAATATTTAG
Found at i:3075801 original size:13 final size:13
Alignment explanation
Indices: 3075785--3075824 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
3075775 AATAAGATGT
3075785 ATAATATAATTAA
1 ATAATATAATTAA
*
3075798 ATAATATAAAGTAA
1 ATAATAT-AATTAA
*
3075812 ATAATTTAATTAA
1 ATAATATAATTAA
3075825 CTATTTACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
ATAATATAATTAA
Found at i:3076217 original size:36 final size:37
Alignment explanation
Indices: 3076161--3076235 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 37
3076151 TCTCTCTGAG
*
3076161 TCCAAATCTCTCCCATTCTCAACCTTTCTGTGAATTC
1 TCCAAATCTCTCCCATTCTCAACCTTTCTATGAATTC
3076198 TCCAAATCTC-CCCATTCTCAACCTTTCTATGAATTC
1 TCCAAATCTCTCCCATTCTCAACCTTTCTATGAATTC
3076234 TC
1 TC
3076236 TCCAAGTCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 27 0.73
37 10 0.27
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.37
Consensus pattern (37 bp):
TCCAAATCTCTCCCATTCTCAACCTTTCTATGAATTC
Found at i:3076857 original size:39 final size:40
Alignment explanation
Indices: 3076767--3076858 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 40
3076757 CTATTATTTC
*
3076767 CTACACAAGCTAAAAAGAAGATAAGAAAGTGAAAATTTTAT
1 CTACACAAGCTAAAAAGAAGATAAAAAAGTG-AAATTTTAT
*
3076808 CTACAAAAGCTAAAAAGAAGATAAAAAAGTG-AATTTTAT
1 CTACACAAGCTAAAAAGAAGATAAAAAAGTGAAATTTTAT
*
3076847 CTGCACAAGCTA
1 CTACACAAGCTA
3076859 TGCTACTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
39 18 0.38
41 29 0.62
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (40 bp):
CTACACAAGCTAAAAAGAAGATAAAAAAGTGAAATTTTAT
Found at i:3081984 original size:26 final size:26
Alignment explanation
Indices: 3081938--3081989 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
3081928 AAAATTGATA
*
3081938 TAATTTTATATTTTTTAATTATATTT
1 TAATTTTATATTTTTTAATTAAATTT
3081964 TAATTTTA-ATTTAATTT-ATTAAATTT
1 TAATTTTATATTT--TTTAATTAAATTT
3081990 AATCCTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
26 16 0.70
27 3 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TAATTTTATATTTTTTAATTAAATTT
Found at i:3082589 original size:17 final size:18
Alignment explanation
Indices: 3082567--3082606 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3082557 ATATATATTT
3082567 AATTATAT-AGAAAATTA
1 AATTATATAAGAAAATTA
* *
3082584 AATTATTTAATAAAATTA
1 AATTATATAAGAAAATTA
3082602 AATTA
1 AATTA
3082607 CTTTATTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AATTATATAAGAAAATTA
Found at i:3082600 original size:18 final size:18
Alignment explanation
Indices: 3082577--3082630 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
3082567 AATTATATAG
3082577 AAAATTAAATTATTTAAT
1 AAAATTAAATTATTTAAT
3082595 AAAATTAAATTACTTT-AT
1 AAAATTAAATTA-TTTAAT
* * *
3082613 TAAGTTAAAATATTTAAT
1 AAAATTAAATTATTTAAT
3082631 TCCATGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 3 0.10
18 25 0.81
19 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAATTAAATTATTTAAT
Found at i:3082762 original size:19 final size:17
Alignment explanation
Indices: 3082683--3082753 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
3082673 ATTTTGTAAA
* *
3082683 TAATTAAATAAATATATT
1 TAATAAAAT-AATTTATT
* *
3082701 AAATAAAAGTAATTGATT
1 TAATAAAA-TAATTTATT
*
3082719 TAA-ATATATAATTTATT
1 TAATA-AAATAATTTATT
3082736 TAATAAAATAATTTATT
1 TAATAAAATAATTTATT
3082753 T
1 T
3082754 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
17 24 0.57
18 17 0.40
19 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TAATAAAATAATTTATT
Found at i:3082779 original size:2 final size:2
Alignment explanation
Indices: 3082772--3082800 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3082762 AATTGGGTTA
3082772 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 A
3082801 AATTATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3088499 original size:54 final size:54
Alignment explanation
Indices: 3088417--3088524 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
3088407 AGTGCATCCG
3088417 GTGAAACATAACTAATGTATCCAAACAACTCGATAATTGGATCCTTGAATTCAT
1 GTGAAACATAACTAATGTATCCAAACAACTCGATAATTGGATCCTTGAATTCAT
3088471 GTGAAACATAACTAATGTATCCAAACAACTCGATAATTGGATCCTTGAATTCAT
1 GTGAAACATAACTAATGTATCCAAACAACTCGATAATTGGATCCTTGAATTCAT
3088525 CCACTAAACT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (54 bp):
GTGAAACATAACTAATGTATCCAAACAACTCGATAATTGGATCCTTGAATTCAT
Found at i:3091014 original size:25 final size:25
Alignment explanation
Indices: 3090986--3091040 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
3090976 ATACTTGTAT
*
3090986 ATTCTATTAATTTGGTCTTAATTTA
1 ATTCTATTAATTTAGTCTTAATTTA
*
3091011 ATTCTATTAATTTAGTTTTAATTTA
1 ATTCTATTAATTTAGTCTTAATTTA
3091036 ATTCT
1 ATTCT
3091041 GATTGAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.58
Consensus pattern (25 bp):
ATTCTATTAATTTAGTCTTAATTTA
Found at i:3101320 original size:25 final size:24
Alignment explanation
Indices: 3101292--3101346 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
3101282 TTTTTTGAAA
3101292 TTTTGGCTTTTTTGTTTT-TTTTGTT
1 TTTTGGCTTTTTT-TTTTGTTTT-TT
*
3101317 TTTTGCCTTTTTTTTTTGTTTTTT
1 TTTTGGCTTTTTTTTTTGTTTTTT
3101341 TTTTGG
1 TTTTGG
3101347 AAAAAATAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.80
Consensus pattern (24 bp):
TTTTGGCTTTTTTTTTTGTTTTTT
Found at i:3101333 original size:13 final size:11
Alignment explanation
Indices: 3101299--3101345 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 11
3101289 AAATTTTGGC
3101299 TTTTTTGTTTT-
1 TTTTTT-TTTTG
3101310 TTTTGTTTTTTG
1 TTTT-TTTTTTG
3101322 CCTTTTTTTTTTG
1 --TTTTTTTTTTG
3101335 TTTTTTTTTTG
1 TTTTTTTTTTG
3101346 GAAAAAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 19 0.59
12 2 0.06
13 7 0.22
14 4 0.12
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:3101338 original size:9 final size:9
Alignment explanation
Indices: 3101299--3101342 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
3101289 AAATTTTGGC
3101299 TTTTTTGTT
1 TTTTTTGTT
3101308 TTTTTTGTT
1 TTTTTTGTT
3101317 TTTTGCCTT-TT
1 TTTT---TTGTT
3101328 TTTTTTGTT
1 TTTTTTGTT
3101337 TTTTTT
1 TTTTTT
3101343 TTGGAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 2 0.06
9 21 0.68
11 6 0.19
12 2 0.06
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:3105301 original size:14 final size:14
Alignment explanation
Indices: 3105284--3105342 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
3105274 GTAATTGATT
*
3105284 TTCTGGAAATTGAA
1 TTCTGGAAAATGAA
3105298 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
* **
3105312 TTACTAGAATTTGAA
1 TT-CTGGAAAATGAA
*
3105327 TTATGGAAAATGAA
1 TTCTGGAAAATGAA
3105341 TT
1 TT
3105343 ATATTTCTGG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.36
Consensus pattern (14 bp):
TTCTGGAAAATGAA
Found at i:3105529 original size:22 final size:23
Alignment explanation
Indices: 3105504--3105572 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 23
3105494 ATACAATAAA
*
3105504 TAATATTATTTATTATAAAA-CT
1 TAATATTATTTATTATAAAATAT
*
3105526 TAATATTA-TTATTTTAAAATAT
1 TAATATTATTTATTATAAAATAT
* * *
3105548 TAAAATAATTTATTATTAAATAT
1 TAATATTATTTATTATAAAATAT
3105571 TA
1 TA
3105573 TTTTTATAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
21 10 0.26
22 15 0.38
23 14 0.36
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATATTATTTATTATAAAATAT
Found at i:3105722 original size:35 final size:35
Alignment explanation
Indices: 3105674--3105741 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
3105664 TTATATTATA
3105674 TTTTAAAAATATTAATTAG--TATATTTTAAATATCT
1 TTTTAAAAATATT-ATTAGATTA-ATTTTAAATATCT
*
3105709 TTTTTAAAATATTATTAGATTAATTTTAAATAT
1 TTTTAAAAATATTATTAGATTAATTTTAAATAT
3105742 ATAAATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 5 0.17
35 23 0.77
36 2 0.07
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTTAAAAATATTATTAGATTAATTTTAAATATCT
Found at i:3105870 original size:22 final size:20
Alignment explanation
Indices: 3105845--3105893 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
3105835 ATTAAAATAA
*
3105845 AAATATAATATTATATTATTAT
1 AAATATAATA-AATA-TATTAT
*
3105867 AAATATTAATAAATATATTTT
1 AAATA-TAATAAATATATTAT
3105888 AAATAT
1 AAATAT
3105894 TTTAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
22 8 0.33
23 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATAATAAATATATTAT
Found at i:3105884 original size:29 final size:29
Alignment explanation
Indices: 3105813--3105885 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 29
3105803 ATATAAATTG
*
3105813 TATTAAT-AATTTATTATATATTATTAAA
1 TATTAATAAATATATTATATATTATTAAA
*
3105841 -A-TAA-AAATATAATATTATATTATTATAAA
1 TATTAATAAATATATTA-TATATTA-T-TAAA
3105870 TATTAATAAATATATT
1 TATTAATAAATATATT
3105886 TTAAATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
26 10 0.29
27 8 0.23
28 1 0.03
29 4 0.11
30 1 0.03
31 3 0.09
32 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TATTAATAAATATATTATATATTATTAAA
Found at i:3116192 original size:31 final size:31
Alignment explanation
Indices: 3116157--3116235 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
3116147 AGTTTTAAAA
* * * *
3116157 ATAATAAATTATTCACTAATATTATCGATTT
1 ATAATAAAATAGTCACTAATATTATCAATTC
3116188 ATAATAAAATAGTCACTAATATTATCAATTC
1 ATAATAAAATAGTCACTAATATTATCAATTC
* *
3116219 ATAACAAAATGGTCACT
1 ATAATAAAATAGTCACT
3116236 CTAACATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.37
Consensus pattern (31 bp):
ATAATAAAATAGTCACTAATATTATCAATTC
Found at i:3122259 original size:173 final size:173
Alignment explanation
Indices: 3121970--3122315 Score: 692
Period size: 173 Copynumber: 2.0 Consensus size: 173
3121960 AGCAAAGTTC
3121970 CGAACCTTCAGAAGGCCTTGCCGGGCTTTCAGATGATGTCGGGGCTGGCTTCATATCTGGACACA
1 CGAACCTTCAGAAGGCCTTGCCGGGCTTTCAGATGATGTCGGGGCTGGCTTCATATCTGGACACA
3122035 ACCAGCCTACCTCAAATTCTGATTTGAATGTAGATAGATCGGTCGACTTGCCAGCACAAGATGAA
66 ACCAGCCTACCTCAAATTCTGATTTGAATGTAGATAGATCGGTCGACTTGCCAGCACAAGATGAA
3122100 ATCGGTAACATGGGGGTTTCAAAGGTGATCAGAGCTGATCAGA
131 ATCGGTAACATGGGGGTTTCAAAGGTGATCAGAGCTGATCAGA
3122143 CGAACCTTCAGAAGGCCTTGCCGGGCTTTCAGATGATGTCGGGGCTGGCTTCATATCTGGACACA
1 CGAACCTTCAGAAGGCCTTGCCGGGCTTTCAGATGATGTCGGGGCTGGCTTCATATCTGGACACA
3122208 ACCAGCCTACCTCAAATTCTGATTTGAATGTAGATAGATCGGTCGACTTGCCAGCACAAGATGAA
66 ACCAGCCTACCTCAAATTCTGATTTGAATGTAGATAGATCGGTCGACTTGCCAGCACAAGATGAA
3122273 ATCGGTAACATGGGGGTTTCAAAGGTGATCAGAGCTGATCAGA
131 ATCGGTAACATGGGGGTTTCAAAGGTGATCAGAGCTGATCAGA
3122316 AGAGGTTTTT
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 173 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (173 bp):
CGAACCTTCAGAAGGCCTTGCCGGGCTTTCAGATGATGTCGGGGCTGGCTTCATATCTGGACACA
ACCAGCCTACCTCAAATTCTGATTTGAATGTAGATAGATCGGTCGACTTGCCAGCACAAGATGAA
ATCGGTAACATGGGGGTTTCAAAGGTGATCAGAGCTGATCAGA
Found at i:3122953 original size:32 final size:32
Alignment explanation
Indices: 3122912--3122975 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
3122902 AGGCTTGGAT
3122912 ATATTGTAATTTGACCCTTTCAATAATGCTTA
1 ATATTGTAATTTGACCCTTTCAATAATGCTTA
3122944 ATATTGTAATTTGACCCTTTCAATAATGCTTA
1 ATATTGTAATTTGACCCTTTCAATAATGCTTA
3122976 CTTATTTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (32 bp):
ATATTGTAATTTGACCCTTTCAATAATGCTTA
Found at i:3123453 original size:32 final size:32
Alignment explanation
Indices: 3123410--3123501 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 32
3123400 TCATACCTAA
3123410 CGTTTACTTTTTATTTCATTTTAGTAC-CCAG
1 CGTTTACTTTTTATTTCATTTTAGTACTCCAG
*
3123441 CGTTTACTTTTTTATTTCATTTTAGTACTCCAT
1 CGTTTAC-TTTTTATTTCATTTTAGTACTCCAG
* * *
3123474 TGTTAACTTTTTGTTTCATTTTAGTACT
1 CGTTTACTTTTTATTTCATTTTAGTACT
3123502 AAATTTTTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
31 7 0.13
32 40 0.73
33 8 0.15
ACGTcount: A:0.18, C:0.16, G:0.09, T:0.57
Consensus pattern (32 bp):
CGTTTACTTTTTATTTCATTTTAGTACTCCAG
Found at i:3123512 original size:32 final size:32
Alignment explanation
Indices: 3123415--3123512 Score: 99
Period size: 32 Copynumber: 3.1 Consensus size: 32
3123405 CCTAACGTTT
** ** *
3123415 ACTTTTTATTTCATTTTAGTAC-CCAGCGTTT
1 ACTTTTTATTTCATTTTAGTACTAAATTGTTA
**
3123446 ACTTTTTTATTTCATTTTAGTACTCCATTGTTA
1 AC-TTTTTATTTCATTTTAGTACTAAATTGTTA
* *
3123479 ACTTTTTGTTTCATTTTAGTACTAAATTTTTA
1 ACTTTTTATTTCATTTTAGTACTAAATTGTTA
3123511 AC
1 AC
3123513 GGCGAGTACT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
31 2 0.03
32 48 0.83
33 8 0.14
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.55
Consensus pattern (32 bp):
ACTTTTTATTTCATTTTAGTACTAAATTGTTA
Found at i:3129285 original size:20 final size:20
Alignment explanation
Indices: 3129262--3129308 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3129252 AATATGTAAA
* *
3129262 TCGCAACATAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
3129282 TCGCAACGCAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
3129302 TCGCAAC
1 TCGCAAC
3129309 GCGAAACACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.17
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:3129309 original size:20 final size:20
Alignment explanation
Indices: 3129273--3129310 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3129263 CGCAACATAG
3129273 AAGTCAAATTCGCAACGCAA
1 AAGTCAAATTCGCAACGCAA
3129293 AAGTCAAATTCGCAACGC
1 AAGTCAAATTCGCAACGC
3129311 GAAACACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCAA
Found at i:3129449 original size:22 final size:22
Alignment explanation
Indices: 3129424--3129474 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3129414 CTACGGCGAC
*
3129424 ATCCGTCCCCATCTTCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
3129446 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
3129468 ATCCGTC
1 ATCCGTC
3129475 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:3129865 original size:20 final size:20
Alignment explanation
Indices: 3129815--3129865 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
3129805 AAACTTAAAT
*
3129815 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
3129835 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
3129855 TCGCAACGCGA
1 TCGCAACGCGA
3129866 TTTTAGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:3129925 original size:21 final size:20
Alignment explanation
Indices: 3129862--3129913 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
3129852 AAATCGCAAC
3129862 GCGATTTT-AGTTT-CGCGTT
1 GCGATTTTCA-TTTCCGCGTT
3129881 GCGATTTTCATTTCCGCGTT
1 GCGATTTTCATTTCCGCGTT
3129901 GCGATTTTCATTT
1 GCGATTTTCATTT
3129914 TTTGCGTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (20 bp):
GCGATTTTCATTTCCGCGTT
Found at i:3131362 original size:16 final size:16
Alignment explanation
Indices: 3131341--3131375 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3131331 TTACAAAGGT
3131341 TGACACCCACAGAGGC
1 TGACACCCACAGAGGC
3131357 TGACACCCACAGAGGC
1 TGACACCCACAGAGGC
3131373 TGA
1 TGA
3131376 GCTTGCCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.34, G:0.26, T:0.09
Consensus pattern (16 bp):
TGACACCCACAGAGGC
Found at i:3131893 original size:21 final size:20
Alignment explanation
Indices: 3131817--3131909 Score: 60
Period size: 21 Copynumber: 4.5 Consensus size: 20
3131807 CCTATCATCA
* *
3131817 TTCAAGAGGCGCCTCCTATAG
1 TTCAAGAGGCCCCTCCCAT-G
* *
3131838 TTCAAGAGGCCCCTCTCATA
1 TTCAAGAGGCCCCTCCCATG
* * * *
3131858 ATCGAAAAAGTCCCTCCCACTG
1 TTC-AAGAGGCCCCTCCCA-TG
**
3131880 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCCCAT-G
3131901 TTCAAGAGG
1 TTCAAGAGG
3131910 TCCCGCCCGC
Statistics
Matches: 53, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
20 3 0.06
21 47 0.89
22 3 0.06
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (20 bp):
TTCAAGAGGCCCCTCCCATG
Found at i:3131913 original size:42 final size:42
Alignment explanation
Indices: 3131811--3131913 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 42
3131801 GATGCACCTA
*
3131811 TCATCATTCAAGAGG-CGCCTCCTATAGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGTC-CCTCCCATAGTTCAAGAGGCCCCTC
* * * *
3131853 TCAT-AATCGAAAAAGTCCCTCCCACT-GTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGTCCCTCCCA-TAGTTCAAGAGGCCCCTC
*
3131895 TCATCGTTCAAGAGGTCCC
1 TCATCATTCAAGAGGTCCC
3131914 GCCCGCCATT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
41 3 0.06
42 41 0.85
43 4 0.08
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAGGTCCCTCCCATAGTTCAAGAGGCCCCTC
Found at i:3133400 original size:65 final size:65
Alignment explanation
Indices: 3133258--3133435 Score: 234
Period size: 66 Copynumber: 2.6 Consensus size: 65
3133248 TTTAGGGTAC
*
3133258 ATTTGTTTTGCTTGTTTAATTGAATTTTACTTTGAAAGTTGATTTGTTTAATTGATGAGGAAATA
1 ATTT-TTTTGCTTGTTTAATTG-A--TT--TTTAAAAGTTGATTTGTTTAATTGATGAGGAAATA
3133323 AGAATT
60 AGAATT
*
3133329 A-TTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTTTAATTTGATGTA-TAAATAAGAA
1 ATTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTTTAA-TTGATG-AGGAAATAAGAA
3133392 TT
64 TT
* *
3133394 ATTTTTTTACTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 ATTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTT
3133436 GTTTTAAATT
Statistics
Matches: 100, Mismatches: 4, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
64 20 0.20
65 18 0.18
66 41 0.41
68 1 0.01
69 17 0.17
70 2 0.02
71 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (65 bp):
ATTTTTTTGCTTGTTTAATTGATTTTTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATT
Found at i:3133547 original size:13 final size:14
Alignment explanation
Indices: 3133511--3133549 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
3133501 GAAAGTCAAA
3133511 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
3133525 TTCG-GTTTGCGA-T
1 TTCGCG-TTGCGATT
3133538 TTCGCGTTGCGA
1 TTCGCGTTGCGA
3133550 ATTTGACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.08, C:0.21, G:0.31, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:3133553 original size:14 final size:14
Alignment explanation
Indices: 3133511--3133553 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3133501 GAAAGTCAAA
*
3133511 TTCGCGTTGCGATT
1 TTCGCGTTGCGAAT
3133525 TTCG-GTTTGCG-AT
1 TTCGCG-TTGCGAAT
3133538 TTCGCGTTGCGAAT
1 TTCGCGTTGCGAAT
3133552 TT
1 TT
3133554 GACTTTCGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (14 bp):
TTCGCGTTGCGAAT
Found at i:3133875 original size:18 final size:18
Alignment explanation
Indices: 3133852--3133887 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3133842 AAGCCGGTTG
*
3133852 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3133870 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
3133888 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3134858 original size:18 final size:18
Alignment explanation
Indices: 3134837--3134873 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3134827 CGAAATTTAT
3134837 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
3134855 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
3134873 A
1 A
3134874 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:3138064 original size:24 final size:24
Alignment explanation
Indices: 3138030--3138083 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3138020 CCATCACATC
3138030 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3138054 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3138078 ATCAAA
1 ATCAAA
3138084 TTTCGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3138097 original size:24 final size:24
Alignment explanation
Indices: 3138030--3138097 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
3138020 CCATCACATC
* * *
3138030 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
3138054 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
3138078 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
3138098 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:3138862 original size:14 final size:15
Alignment explanation
Indices: 3138826--3138863 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3138816 GAAATCATTG
3138826 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
3138841 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
3138856 AAAAATTA
1 AAAAATTA
3138864 GAGATGAGGA
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:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:3139083 original size:20 final size:20
Alignment explanation
Indices: 3139058--3139207 Score: 135
Period size: 20 Copynumber: 7.5 Consensus size: 20
3139048 TTGAAATTCA
3139058 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* *
3139078 GTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGACTTTTGT
* *
3139098 GTTGCAAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
3139118 GTTGCG-ATAT-ACAAATTCGC
1 GTTGCGAATTTGAC--TTTTGT
3139138 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* ***
3139158 GTTGCGAATTTGACTATCAC
1 GTTGCGAATTTGACTTTTGT
*
3139178 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
*
3139198 TTTGC-AATTT
1 GTTGCGAATTT
3139208 ACAAATTCGC
Statistics
Matches: 100, Mismatches: 26, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
18 2 0.02
19 8 0.08
20 85 0.85
21 3 0.03
22 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:3139113 original size:40 final size:40
Alignment explanation
Indices: 3139037--3139227 Score: 207
Period size: 40 Copynumber: 4.8 Consensus size: 40
3139027 AATTAAATTA
*
3139037 GTGTTGCGAATTTGA-AATT-CAGTTGCGAATTTGACTTTT
1 GTGTTGCGAATTTGACAATTGC-GTTGCGAATTTGACTTCT
* *
3139076 GTGTTGCGAATTTGACTATTGCGTTGCAAATTTGACTTCT
1 GTGTTGCGAATTTGACAATTGCGTTGCGAATTTGACTTCT
* *
3139116 GTGTTGCG-ATAT-ACAAATTCGCGTTGCGAATTTGACTTTT
1 GTGTTGCGAATTTGAC-AATT-GCGTTGCGAATTTGACTTCT
* **
3139156 GTGTTGCGAATTTGACTATCACGTTGCGAATTTGACTTCT
1 GTGTTGCGAATTTGACAATTGCGTTGCGAATTTGACTTCT
*
3139196 GTTTTGC-AATTT-ACAAATTCGCGTTGC-AATTT
1 GTGTTGCGAATTTGAC-AATT-GCGTTGCGAATTT
3139228 ATATATTCAC
Statistics
Matches: 128, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
38 4 0.03
39 33 0.26
40 83 0.65
41 6 0.05
42 2 0.02
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (40 bp):
GTGTTGCGAATTTGACAATTGCGTTGCGAATTTGACTTCT
Found at i:3139152 original size:80 final size:80
Alignment explanation
Indices: 3139058--3139227 Score: 279
Period size: 80 Copynumber: 2.1 Consensus size: 80
3139048 TTGAAATTCA
**
3139058 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATTGCGTTGCAAATTTGACTTCTGTGTTGC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCAAATTTGACTTCTGTGTTGC
*
3139123 GATATACAAATTCGC
66 AATATACAAATTCGC
* *
3139138 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCGAATTTGACTTCTGTTTTGC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCAAATTTGACTTCTGTGTTGC
*
3139203 AATTTACAAATTCGC
66 AATATACAAATTCGC
3139218 GTTGC-AATTT
1 GTTGCGAATTT
3139228 ATATATTCAC
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 5 0.06
80 79 0.94
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (80 bp):
GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCAAATTTGACTTCTGTGTTGC
AATATACAAATTCGC
Found at i:3139264 original size:20 final size:20
Alignment explanation
Indices: 3139199--3139262 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
3139189 GACTTCTGTT
*
3139199 TTGCAATTTACAAATTCGCG
1 TTGCAATTTACATATTCGCG
* *
3139219 TTGCAATTTATATATTCACG
1 TTGCAATTTACATATTCGCG
* *
3139239 TTGCGATTTACATATTCGTG
1 TTGCAATTTACATATTCGCG
3139259 TTGC
1 TTGC
3139263 GAAATTGGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (20 bp):
TTGCAATTTACATATTCGCG
Found at i:3140385 original size:43 final size:41
Alignment explanation
Indices: 3140338--3140653 Score: 210
Period size: 43 Copynumber: 7.3 Consensus size: 41
3140328 GGGCTTAAAC
*
3140338 TATAAAAGTAAAAAGTATGATTGAAAAAATTACAGATCTCAAT
1 TATAAAGGTAAAAAGTA-GATTGAAAAAATTA-AGATCTCAAT
*
3140381 TATAAAGGTAAAAAGTGAGATT-AAAATAATTAGGGGA-CTCAAT
1 TATAAAGGTAAAAAGT-AGATTGAAAA-AATTA--AGATCTCAAT
* * *
3140424 TTTAAAGGTAAAAAGTGAGATTAAAAAAAATTAGAGAACTCAAT
1 TATAAAGGTAAAAAGT-AGATT-GAAAAAATTA-AGATCTCAAT
* * * * *
3140468 TATAAAGGTAGAAAGCGAGATTGAAAAAATCAGGAGCTCAAT
1 TATAAAGGTAAAAAG-TAGATTGAAAAAATTAAGATCTCAAT
* * * *
3140510 TATAAAGGTACAAAA-TGGGATTG-AAAAACTAAGGTCATCAGT
1 TATAAAGGTA-AAAAGT-AGATTGAAAAAATTAAGATC-TCAAT
* **
3140552 TATAAATGTAAAAAAGTGAGATTGAAAAAAATTAAGGGCCTCAAT
1 TATAAAGGT-AAAAAGT-AGATTG-AAAAAATTAA-GATCTCAAT
* * * * *
3140597 TATAAAGATAAAAAATAGGATT-ACAAAAATTAGGAACCTCATT
1 TATAAAGGTAAAAAGTA-GATTGA-AAAAATTAAG-ATCTCAAT
*
3140640 TATAAAGATAAAAA
1 TATAAAGGTAAAAA
3140654 TAAAAAATAA
Statistics
Matches: 223, Mismatches: 32, Indels: 36
0.77 0.11 0.12
Matches are distributed among these distances:
41 8 0.04
42 45 0.20
43 102 0.46
44 42 0.19
45 23 0.10
46 3 0.01
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (41 bp):
TATAAAGGTAAAAAGTAGATTGAAAAAATTAAGATCTCAAT
Found at i:3140472 original size:87 final size:85
Alignment explanation
Indices: 3140338--3140653 Score: 293
Period size: 87 Copynumber: 3.7 Consensus size: 85
3140328 GGGCTTAAAC
* * * * *
3140338 TATAAAAGTAAAAAGTATGATTGAAAAAATTACAGATCTCAATTATAAAGGTAAAAAGTGAGATT
1 TATAAAGGTAAAAAGTAGGATTAAAAAAATTAGAGAACTCAATTATAAAGGTAAAAAGTGAGATT
3140403 -AAAATAATTAGGGGACTCAAT
66 GAAAA-AATTAGGGG-CTCAAT
* * *
3140424 TTTAAAGGTAAAAAGT-GAGATTAAAAAAAATTAGAGAACTCAATTATAAAGGTAGAAAGCGAGA
1 TATAAAGGTAAAAAGTAG-GATT-AAAAAAATTAGAGAACTCAATTATAAAGGTAAAAAGTGAGA
* *
3140488 TTGAAAAAATCAGGAGCTCAAT
64 TTGAAAAAATTAGGGGCTCAAT
* * * ** * *
3140510 TATAAAGGTACAAAA-TGGGATT-GAAAAACTA-AGGTCATCAGTTATAAATGTAAAAAAGTGAG
1 TATAAAGGTA-AAAAGTAGGATTAAAAAAATTAGAGAAC-TCAATTATAAAGGT-AAAAAGTGAG
*
3140572 ATTGAAAAAAATTAAGGGCCTCAAT
63 ATTG-AAAAAATT-AGGGGCTCAAT
* * * * *
3140597 TATAAAGATAAAAAATAGGATTACAAAAATTAG-GAACCTCATTTATAAAGATAAAAA
1 TATAAAGGTAAAAAGTAGGATTAAAAAAATTAGAGAA-CTCAATTATAAAGGTAAAAA
3140654 TAAAAAATAA
Statistics
Matches: 186, Mismatches: 31, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
83 3 0.02
84 19 0.10
85 12 0.06
86 49 0.26
87 79 0.42
88 23 0.12
89 1 0.01
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (85 bp):
TATAAAGGTAAAAAGTAGGATTAAAAAAATTAGAGAACTCAATTATAAAGGTAAAAAGTGAGATT
GAAAAAATTAGGGGCTCAAT
Found at i:3140566 original size:129 final size:130
Alignment explanation
Indices: 3140356--3140603 Score: 301
Period size: 129 Copynumber: 1.9 Consensus size: 130
3140346 TAAAAAGTAT
* * *
3140356 GATTGAAAAAATTACAGATCTCAATTATAAAGGTAAAAAGTGAGATTAAAATAATTAGGGGACTC
1 GATTGAAAAAATTACAGAGCTCAATTATAAAGGTAAAAAGTGAGATTAAAATAATAAGGGCACTC
*
3140421 AATTTTAAAGGTAAAAAGTGAGATTAAAAAAAATT-AGAGAACTCAATTATAAAGGTAGAAAGCG
66 AATTATAAAGGTAAAAAGTGAGATTAAAAAAAATTAAG-GAACTCAATTATAAAGGTAGAAAGCG
3140485 A
130 A
* * *
3140486 GATTGAAAAAA-T-CAGGAGCTCAATTATAAAGGTACAAAA-TGGGATTGAAAA-ACTAAGGTCA
1 GATTGAAAAAATTACA-GAGCTCAATTATAAAGGTA-AAAAGTGAGATT-AAAATAATAAGGGCA
* * * **
3140547 -TCAGTTATAAATGTAAAAAAGTGAGATTGAAAAAAATTAAGGGCCTCAATTATAAAG
63 CTCAATTATAAAGGT-AAAAAGTGAGATTAAAAAAAATTAAGGAACTCAATTATAAAG
3140604 ATAAAAAATA
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
128 13 0.13
129 67 0.66
130 21 0.21
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.24
Consensus pattern (130 bp):
GATTGAAAAAATTACAGAGCTCAATTATAAAGGTAAAAAGTGAGATTAAAATAATAAGGGCACTC
AATTATAAAGGTAAAAAGTGAGATTAAAAAAAATTAAGGAACTCAATTATAAAGGTAGAAAGCGA
Found at i:3140950 original size:31 final size:30
Alignment explanation
Indices: 3140866--3140970 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 30
3140856 TCAAGGGAGT
* * * *
3140866 AAAATGTAATTAACTATAGAAAATGATGGG
1 AAAATATAATTAACCATAGAAAATGAAGGA
*
3140896 ACAATATAATTAACCATAGAAAATGAAGGA
1 AAAATATAATTAACCATAGAAAATGAAGGA
* * * * *
3140926 AAAAGTATTATTAATCATATAAAATGAGGGT
1 AAAA-TATAATTAACCATAGAAAATGAAGGA
3140957 AAAATATAATTAAC
1 AAAATATAATTAAC
3140971 TGTTGAAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
30 36 0.59
31 25 0.41
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.27
Consensus pattern (30 bp):
AAAATATAATTAACCATAGAAAATGAAGGA
Found at i:3141416 original size:30 final size:32
Alignment explanation
Indices: 3141361--3141420 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
3141351 AATTTAAGGC
3141361 AAAATGGTTTCTGGACTTGAATTGAATTTACA
1 AAAATGGTTTCTGGACTTGAATTGAATTTACA
*
3141393 AAAAT-GTTTTTGGACTT-AATTGAATTTA
1 AAAATGGTTTCTGGACTTGAATTGAATTTA
3141421 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 11 0.41
31 11 0.41
32 5 0.19
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (32 bp):
AAAATGGTTTCTGGACTTGAATTGAATTTACA
Found at i:3141525 original size:21 final size:21
Alignment explanation
Indices: 3141499--3141597 Score: 105
Period size: 21 Copynumber: 4.7 Consensus size: 21
3141489 AGGGTGTCAA
* *
3141499 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCCATGC
*
3141520 AGTGCATCTATGCATCCC-TGC
1 AGTGCATCCATGCA-CCCATGC
*
3141541 AGTGCATCCATGCACCTGCAT-T
1 AGTGCATCCATGCACC--CATGC
*
3141563 AGTGCATCGATGCA-CCATGC
1 AGTGCATCCATGCACCCATGC
3141583 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3141598 TCAAACACCG
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
19 3 0.05
20 15 0.23
21 29 0.45
22 17 0.26
23 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATGC
Found at i:3141584 original size:42 final size:42
Alignment explanation
Indices: 3141499--3141597 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
3141489 AGGGTGTCAA
* * *
3141499 AGTGCATCCATGCACCCCTGTAGTGCATCTATGCATCCCTGC
1 AGTGCATCCATGCACCCATGTAGTGCATCGATGCATCCATGC
3141541 AGTGCATCCATGCACCTGCAT-TAGTGCATCGATGCA-CCATGC
1 AGTGCATCCATGCACC--CATGTAGTGCATCGATGCATCCATGC
3141583 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3141598 TCAAACACCG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
42 36 0.69
43 14 0.27
44 2 0.04
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.24
Consensus pattern (42 bp):
AGTGCATCCATGCACCCATGTAGTGCATCGATGCATCCATGC
Found at i:3141643 original size:20 final size:20
Alignment explanation
Indices: 3141614--3141690 Score: 122
Period size: 20 Copynumber: 3.9 Consensus size: 20
3141604 ACCGAATGCA
3141614 CTTA-GTGCATCGATGCATC
1 CTTATGTGCATCGATGCATC
3141633 CTTATGTGCATCGATGCATC
1 CTTATGTGCATCGATGCATC
3141653 CTTATGTGCATCGATGCATC
1 CTTATGTGCATCGATGCATC
*
3141673 CTGT-TGTGCATCCATGCA
1 CT-TATGTGCATCGATGCA
3141691 CGAAGGCTGC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
19 4 0.07
20 50 0.91
21 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (20 bp):
CTTATGTGCATCGATGCATC
Found at i:3142668 original size:23 final size:24
Alignment explanation
Indices: 3142642--3142691 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3142632 ATTTTGGAAA
* *
3142642 TTTTA-TTTAAATAAAATATTTTT
1 TTTTATTTTAAACAAAATAATTTT
*
3142665 TTTTATTTTAAACAACATAATTTT
1 TTTTATTTTAAACAAAATAATTTT
3142689 TTT
1 TTT
3142692 AAATCTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATTTTAAACAAAATAATTTT
Found at i:3143703 original size:65 final size:65
Alignment explanation
Indices: 3143567--3143726 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
3143557 TGCACTAAGA
* * *
3143567 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCTTGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
3143631 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
3143694 AT
65 -G
*
3143696 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
3143727 CAATTTAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 29 0.34
65 53 0.62
66 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:3143765 original size:65 final size:64
Alignment explanation
Indices: 3143567--3143776 Score: 182
Period size: 65 Copynumber: 3.2 Consensus size: 64
3143557 TGCACTAAGA
* * * * *
3143567 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCTTGG-C
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCAATGCATGGTA
3143629 TG
63 TG
**
3143631 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCAATGCATGGTAT
3143696 -
64 G
* ** *
3143696 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGTATCAATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCAATGCATGGTA
3143758 TTG
63 -TG
*
3143761 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
3143777 CTCTGAAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 4 0.03
64 47 0.38
65 63 0.51
66 5 0.04
67 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCAATGCATGGTATG
Found at i:3144249 original size:2 final size:2
Alignment explanation
Indices: 3144242--3144266 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3144232 AATTGATTAA
3144242 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 A
3144267 GCTTAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3150320 original size:22 final size:21
Alignment explanation
Indices: 3150278--3150317 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3150268 GAGTTTATTT
*
3150278 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3150299 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3150318 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3151442 original size:20 final size:20
Alignment explanation
Indices: 3151417--3151483 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
3151407 ATTTATTTTG
3151417 ATTTTTGAAAGCTCTAAATT
1 ATTTTTGAAAGCTCTAAATT
* * * **
3151437 ATTTTTCAAA-ATTTCATTTT
1 ATTTTTGAAAGCTCT-AAATT
3151457 GATTTTTGAAAGCTCTAAATT
1 -ATTTTTGAAAGCTCTAAATT
3151478 ATTTTT
1 ATTTTT
3151484 AAAAATTTCA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 2 0.06
20 18 0.53
21 12 0.35
22 2 0.06
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTTTGAAAGCTCTAAATT
Found at i:3151461 original size:21 final size:21
Alignment explanation
Indices: 3151437--3151509 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 21
3151427 GCTCTAAATT
3151437 ATTTTTCAAAATTTCATTTTG
1 ATTTTTCAAAATTTCATTTTG
* ** **
3151458 ATTTTT-GAAAGCTCTAAATT-
1 ATTTTTCAAAATTTC-ATTTTG
*
3151478 ATTTTTAAAAATTTCATTTTG
1 ATTTTTCAAAATTTCATTTTG
3151499 A-TTTTCAAAAT
1 ATTTTTCAAAAT
3151510 CAACTTTTGC
Statistics
Matches: 38, Mismatches: 11, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.52
Consensus pattern (21 bp):
ATTTTTCAAAATTTCATTTTG
Found at i:3151462 original size:41 final size:41
Alignment explanation
Indices: 3151407--3151503 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
3151397 TTTCTAAATC
*
3151407 ATTT-ATTTTGATTTTTGAAAGCTCTAAATTATTTTTCAAA
1 ATTTCATTTTGATTTTTGAAAGCTCTAAATTATTTTTAAAA
3151447 ATTTCATTTTGATTTTTGAAAGCTCTAAATTATTTTTAAAA
1 ATTTCATTTTGATTTTTGAAAGCTCTAAATTATTTTTAAAA
3151488 ATTTCATTTTGATTTT
1 ATTTCATTTTGATTTT
3151504 CAAAATCAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 4 0.07
41 51 0.93
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (41 bp):
ATTTCATTTTGATTTTTGAAAGCTCTAAATTATTTTTAAAA
Found at i:3153503 original size:17 final size:19
Alignment explanation
Indices: 3153462--3153511 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
3153452 TTGGACTCTC
* *
3153462 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGTACTAAG
3153481 AGTGCATCGATGTA-TAA-
1 AGTGCATCGATGTACTAAG
3153498 AGTGCATTCGATGT
1 AGTGCA-TCGATGT
3153512 TTCAAAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 10 0.36
19 12 0.43
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (19 bp):
AGTGCATCGATGTACTAAG
Found at i:3153607 original size:65 final size:64
Alignment explanation
Indices: 3153482--3153641 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 64
3153472 TGCACTAAGA
* * *
3153482 GTGCATCGATGTATAAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT-
1 GTGCATCAATGCATAAA-TGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGG-TA
3153545 G
64 G
* * *
3153546 GTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTA
1 GTGCATCAATGCAT-AAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGTA
*
3153610 T
64 G
*
3153611 GTGCATCAATGCATGAAATGCATTCCATGTT
1 GTGCATCAATGCAT-AAATGCATTCGATGTT
3153642 CAATTTAATT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 24 0.29
65 56 0.67
66 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCAATGCATAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGTAG
Found at i:3153680 original size:65 final size:63
Alignment explanation
Indices: 3153526--3153691 Score: 185
Period size: 65 Copynumber: 2.6 Consensus size: 63
3153516 AAATAGCCAG
* *
3153526 AGTGCATCGATGCATGGCTGGTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATCAATGCATCAAATGCATTCCATG-TTTCATAAAAT-CTC
* * **
3153591 AGTGCATCGGTGCATGGTAT-GTGCATCAATGCATGAAATGCATTCCATG-TTCAATTTAAT-TC
1 AGTGCATCGATGCATGGT-TGGTGCATCAATGCATCAAATGCATTCCATGTTTC-ATAAAATCTC
*
3153653 ATGGTGCATCGATGCATGGATTGGTGCATCAGTGCATCA
1 A--GTGCATCGATGCATGG-TTGGTGCATCAATGCATCA
3153692 CTATGAAAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 21 0.24
65 58 0.67
66 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTTGGTGCATCAATGCATCAAATGCATTCCATGTTTCATAAAATCTC
Found at i:3154565 original size:29 final size:30
Alignment explanation
Indices: 3154532--3154593 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
3154522 TATGCCTTTG
3154532 GTTCCAGTTTAGTGTC-TAAAGTTT-ATTTT
1 GTTCCAGTTTAGTG-CATAAAGTTTCATTTT
* *
3154561 GTTCCAGTTTGGTGCATAACGTTTCATTTT
1 GTTCCAGTTTAGTGCATAAAGTTTCATTTT
3154591 GTT
1 GTT
3154594 ACTCAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.03
29 20 0.69
30 8 0.28
ACGTcount: A:0.18, C:0.13, G:0.19, T:0.50
Consensus pattern (30 bp):
GTTCCAGTTTAGTGCATAAAGTTTCATTTT
Found at i:3156375 original size:3 final size:3
Alignment explanation
Indices: 3156362--3156402 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
3156352 ATTTATTTAT
*
3156362 TTA TT- TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3156403 GAAAATACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3157578 original size:394 final size:391
Alignment explanation
Indices: 3156946--3157662 Score: 1060
Period size: 394 Copynumber: 1.8 Consensus size: 391
3156936 AACCATTGAG
* *
3156946 AGGGAGAGAAGACACCGATGAACCAAATACTGAAAAATCATCTCGATCCAACAGCGGCCGAAGAT
1 AGGGAGAGAAGACACCGATGAACCAAATACTGAAAAATCATCTCAATCCAACAGCGGCCGAAGAC
* * * **
3157011 GATCAGAGCCTTGAAAGCTGAAGGGTTTTAGCTTATTTCACGACAAAAGAGGCTGAATCTCGCTA
66 GATCAGAGCCTTAAAAACTGAAGGGTTTTAGCTTATTTCACGACAAAAGAGACCAAATCTCGCTA
** * * ** * *
3157076 ATCTGACGTTGGATCCGTGCTCCCGTGCTGAGATGAATCTCATTTGAAAGTTTGGTGGCCAACTC
131 AAATGACGTCGGATCCGTGCTCACGTGCCAAGACGAATCTCACTTGAAAGTTTGGTGGCCAACTC
* * * *
3157141 GGTAGCCAACAGGTGGCGCGGACACTAGACACTCCCAGTTAGAGAGAAGGTAGAGAAATATG-AG
196 GGTAGCCAACAGGTGGCGCAGACACCAGACACTCCCAGTTAGAGAGAAGGCAGAGAAA-AGGAAG
* *
3157205 TGAGGAGAGAAAGCGTTATATGCAAAATGAAAAAAAAATCAGCCTATTTATAAGTATTACAAAAC
260 TGAGGAGAGAAAGAGTTATATGCAAAATG-AAAAAAAATCAGCCTATTTATAAGCATTACAAAAC
3157270 AGTGCAAAGGAACGAAAAAAACCGAAGAGAGAAAGGAGGGGACTCTACCTCTCAGCTGGAGGGAG
324 AGTGCAAAGGAACGAAAAAAACCGAAGAGAGAAAGGAGGGGACTCTACCTCTCAGCTGGAGGGAG
3157335 AGA
389 AGA
* *
3157338 AGGGAGAGAAGACACCGGTGAACCAAATACTGAAAAATCATCTCAATCCAAC-GACGGCCGAAGG
1 AGGGAGAGAAGACACCGATGAACCAAATACTGAAAAATCATCTCAATCCAACAG-CGGCCGAAGA
* *
3157402 CGAATCAGAGCCTTAAAAACTGAAGGGTTTTGGCTTATTTCACGACAGAAGAGACCAAATCTCGC
65 CG-ATCAGAGCCTTAAAAACTGAAGGGTTTTAGCTTATTTCACGACAAAAGAGACCAAATCTCGC
* * *
3157467 TAAAATTACGTCGGATCCGTGCTTCATGTGCCAAGACGAATCTCCCTTGAAAGTTTGGTGGCCAA
129 TAAAATGACGTCGGATCCGTGC-TCACGTGCCAAGACGAATCTCACTTGAAAGTTTGGTGGCCAA
* * * *
3157532 CTCGGTAGTCGACGGGTGGCGCAGACACCAGACACTCCCAGTTAGAGAGAAGGCAGAGAAACGGA
193 CTCGGTAGCCAACAGGTGGCGCAGACACCAGACACTCCCAGTTAGAGAGAAGGCAGAGAAAAGGA
* * *
3157597 AGTGAGGAGAGAAAGAGTTCTGTGCAAAATGAAAAAAAATCGGCCTATTTATAAGCATTACAAAA
258 AGTGAGGAGAGAAAGAGTTATATGCAAAATGAAAAAAAATCAGCCTATTTATAAGCATTACAAAA
3157662 C
323 C
3157663 GGTGTTGTTT
Statistics
Matches: 286, Mismatches: 35, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
391 1 0.00
392 60 0.21
393 107 0.37
394 118 0.41
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.19
Consensus pattern (391 bp):
AGGGAGAGAAGACACCGATGAACCAAATACTGAAAAATCATCTCAATCCAACAGCGGCCGAAGAC
GATCAGAGCCTTAAAAACTGAAGGGTTTTAGCTTATTTCACGACAAAAGAGACCAAATCTCGCTA
AAATGACGTCGGATCCGTGCTCACGTGCCAAGACGAATCTCACTTGAAAGTTTGGTGGCCAACTC
GGTAGCCAACAGGTGGCGCAGACACCAGACACTCCCAGTTAGAGAGAAGGCAGAGAAAAGGAAGT
GAGGAGAGAAAGAGTTATATGCAAAATGAAAAAAAATCAGCCTATTTATAAGCATTACAAAACAG
TGCAAAGGAACGAAAAAAACCGAAGAGAGAAAGGAGGGGACTCTACCTCTCAGCTGGAGGGAGAG
A
Found at i:3158254 original size:30 final size:29
Alignment explanation
Indices: 3158155--3158275 Score: 115
Period size: 29 Copynumber: 4.1 Consensus size: 29
3158145 CCCTCTAGGA
* * *
3158155 TTAGATTTTTCACAGTTAGGTACCTA-AACT
1 TTAG-TTTTTTACACTTAGGTCCCTAGAA-T
**
3158185 TTAGATTTTTTACAAATAGG-CCCTAGAAT
1 TTAG-TTTTTTACACTTAGGTCCCTAGAAT
3158214 TTAG-TTTTTACACTTAGGTCCCCTAGAAT
1 TTAGTTTTTTACACTTAGGT-CCCTAGAAT
*
3158243 TTAGTTTTTTACACTTTA-GTCCCTAGACT
1 TTAGTTTTTTACAC-TTAGGTCCCTAGAAT
3158272 TTAG
1 TTAG
3158276 AGTTCTCACA
Statistics
Matches: 79, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
27 12 0.15
29 34 0.43
30 30 0.38
31 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (29 bp):
TTAGTTTTTTACACTTAGGTCCCTAGAAT
Found at i:3161258 original size:14 final size:14
Alignment explanation
Indices: 3161239--3161265 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3161229 ACATTAAGGG
3161239 GTGTATCGATACCT
1 GTGTATCGATACCT
3161253 GTGTATCGATACC
1 GTGTATCGATACC
3161266 CATAGACAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (14 bp):
GTGTATCGATACCT
Found at i:3164570 original size:41 final size:41
Alignment explanation
Indices: 3164481--3164595 Score: 194
Period size: 41 Copynumber: 2.8 Consensus size: 41
3164471 TTCCACGAAA
* *
3164481 TCCCGTGTTTGTTTCATGTAATTCGTTTTCTGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTC-CGAAAATGTTT
3164523 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAATGTTT
*
3164564 TCCCGTGTTTATTTCACGTAATTCGTTTTCCG
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCG
3164596 GAATGTAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 41 0.59
42 29 0.41
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.48
Consensus pattern (41 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAATGTTT
Found at i:3164823 original size:21 final size:22
Alignment explanation
Indices: 3164770--3164847 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 22
3164760 CATTTTCATC
*
3164770 AATATATTATTTATTAAAATATTT
1 AATATA-TATTTATTAATAT-TTT
*
3164794 AAGATATATTTATTAATATTTT
1 AATATATATTTATTAATATTTT
*
3164816 AATA-ATA-TAATATAATATTTTT
1 AATATATATTTAT-TAATA-TTTT
3164838 AATATTATAT
1 AATA-TATAT
3164848 AAAATAATCA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
20 3 0.07
21 8 0.18
22 14 0.31
23 12 0.27
24 8 0.18
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
AATATATATTTATTAATATTTT
Found at i:3164842 original size:19 final size:20
Alignment explanation
Indices: 3164807--3164849 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
3164797 ATATATTTAT
3164807 TAATATTTTAATAATATAATA
1 TAATATTTT-ATAATATAATA
*
3164828 TAATATTTT-TAATATTATA
1 TAATATTTTATAATATAATA
3164847 TAA
1 TAA
3164850 AATAATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATATTTTATAATATAATA
Found at i:3164853 original size:21 final size:21
Alignment explanation
Indices: 3164808--3164853 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3164798 TATATTTATT
*
3164808 AATATTTTAATAATATAATAT
1 AATATTTTAATAATATAATAA
*
3164829 AATATTTTTAATATTAT-ATAA
1 AATA-TTTTAATAATATAATAA
3164850 AATA
1 AATA
3164854 ATCAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATTTTAATAATATAATAA
Found at i:3164930 original size:30 final size:28
Alignment explanation
Indices: 3164860--3164963 Score: 88
Period size: 29 Copynumber: 3.5 Consensus size: 28
3164850 AATAATCAAT
* *
3164860 TATATTATAATAAAATA-AGATATTATAGTTT
1 TATATT-TAATAATATATA-ATATTAT--TTA
*
3164891 TAT-TTTAATAATATATAATAAATTTTTTA
1 TATATTTAATAATATATAAT--ATTATTTA
3164920 TATATTTAATAATGA-ATAATATTATTTA
1 TATATTTAATAAT-ATATAATATTATTTA
3164948 TATATTTAAATAATAT
1 TATATTT-AATAATAT
3164964 TTTAGTAAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
28 15 0.24
29 22 0.35
30 17 0.27
31 8 0.13
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
TATATTTAATAATATATAATATTATTTA
Found at i:3165187 original size:19 final size:17
Alignment explanation
Indices: 3165164--3165218 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 17
3165154 TAATATTAAG
3165164 TTTTATGATAAATAATAT
1 TTTTAT-ATAAATAATAT
**
3165182 TATTTATTATATTTAATAT
1 T-TTTA-TATAAATAATAT
3165201 TTTTA-ATAAATAAT-T
1 TTTTATATAAATAATAT
3165216 TTT
1 TTT
3165219 AAAAAACTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 4 0.13
16 7 0.23
18 5 0.16
19 14 0.45
20 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTTATATAAATAATAT
Found at i:3165323 original size:20 final size:20
Alignment explanation
Indices: 3165298--3165356 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
3165288 TGTTTACCAG
3165298 AAATGTAATTCATTTTCCAA
1 AAATGTAATTCATTTTCCAA
*
3165318 AAATGTAATTCATTTTTCAA
1 AAATGTAATTCATTTTCCAA
3165338 AAATGTAATTCATTTTCCA
1 AAATGTAATTCATTTTCCA
3165357 GAATTCAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (20 bp):
AAATGTAATTCATTTTCCAA
Found at i:3165394 original size:30 final size:29
Alignment explanation
Indices: 3165342--3165444 Score: 145
Period size: 30 Copynumber: 3.5 Consensus size: 29
3165332 TTTCAAAAAT
3165342 GTAATTCATTTTCCAG-AATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTC-A
*
3165371 ATAATTCATTTTCCAGTAATTCAAATTACA
1 GTAATTCATTTTCCAGTAATTCAAATT-CA
**
3165401 GTAATTCAAATTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATT-CA
3165431 GTAATTCATTTTCC
1 GTAATTCATTTTCC
3165445 GGAAAACCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
29 15 0.23
30 49 0.75
31 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.40
Consensus pattern (29 bp):
GTAATTCATTTTCCAGTAATTCAAATTCA
Found at i:3165444 original size:15 final size:15
Alignment explanation
Indices: 3165342--3165438 Score: 124
Period size: 15 Copynumber: 6.5 Consensus size: 15
3165332 TTTCAAAAAT
**
3165342 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
3165357 G-AATTCAAATTCTA
1 GTAATTCAAATTCCA
* **
3165371 ATAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
3165386 GTAATTCAAATTACA
1 GTAATTCAAATTCCA
3165401 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
3165416 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
3165431 GTAATTCA
1 GTAATTCA
3165439 TTTTCCGGAA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
14 10 0.14
15 59 0.86
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:3167730 original size:2 final size:2
Alignment explanation
Indices: 3167723--3167804 Score: 55
Period size: 2 Copynumber: 43.0 Consensus size: 2
3167713 TCGGGCCGGG
* * * *
3167723 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
3167763 TA TA TA TT TA AA T- TA AA TT TA TA AA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3167803 TA
1 TA
3167805 ATAATTATTT
Statistics
Matches: 58, Mismatches: 18, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
1 4 0.07
2 54 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3167746 original size:17 final size:17
Alignment explanation
Indices: 3167724--3167785 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
3167714 CGGGCCGGGT
3167724 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
**
3167741 ATATATAAATAATATATATA
1 ATATATATTTAA-AT-TA-A
3167761 TATATATATTTAAATTAA
1 -ATATATATTTAAATTAA
*
3167779 ATTTATA
1 ATATATA
3167786 AATATTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 16 0.44
18 3 0.08
19 4 0.11
20 3 0.08
21 10 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:3167769 original size:38 final size:38
Alignment explanation
Indices: 3167723--3167804 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
3167713 TCGGGCCGGG
3167723 TATATATATTTAAATTAAATATATAAATAATATATATA
1 TATATATATTTAAATTAAATATATAAATAATATATATA
* *
3167761 TATATATATTTAAATTAAATTTATAAATATTATATATA
1 TATATATATTTAAATTAAATATATAAATAATATATATA
3167799 TATATA
1 TATATA
3167805 ATAATTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
TATATATATTTAAATTAAATATATAAATAATATATATA
Found at i:3171376 original size:21 final size:21
Alignment explanation
Indices: 3171346--3171422 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
3171336 GCTCTAAAAG
*
3171346 AATTGTAAGAGTTGAAGAATC
1 AATTGCAAGAGTTGAAGAATC
3171367 AATTGCAAGAGTTGAAGAATC
1 AATTGCAAGAGTTGAAGAATC
*
3171388 TATTGCAAGAGTTGAAGAATC
1 AATTGCAAGAGTTGAAGAATC
*
3171409 TATTGCAAGAGTTG
1 AATTGCAAGAGTTG
3171423 CTAGAGAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.29
Consensus pattern (21 bp):
AATTGCAAGAGTTGAAGAATC
Found at i:3177536 original size:21 final size:17
Alignment explanation
Indices: 3177508--3177571 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
3177498 ACATAGAAAT
3177508 AAAAAAGAGAAAATATAA
1 AAAAAAGAGAAAATAT-A
* *
3177526 CAACAAGAAGAAAAAACATA
1 -AA-AA-AAGAGAAAATATA
*
3177546 AAAAAAGAGAAAATAAA
1 AAAAAAGAGAAAATATA
3177563 GAAAAAAGA
1 -AAAAAAGA
3177572 TAGAGAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 10 0.27
18 10 0.27
19 4 0.11
20 3 0.08
21 10 0.27
ACGTcount: A:0.77, C:0.05, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAAGAGAAAATATA
Found at i:3177553 original size:20 final size:18
Alignment explanation
Indices: 3177508--3177622 Score: 83
Period size: 19 Copynumber: 6.1 Consensus size: 18
3177498 ACATAGAAAT
*
3177508 AAAAAAG-AGAAAATATAA
1 AAAAAAGAAGAAAA-AAAA
* *
3177526 CAACAAGAAGAAAAAACATA
1 AAAAAAGAAGAAAAAA-A-A
*
3177546 AAAAAAG-AGAAAATAAAG
1 AAAAAAGAAGAAAA-AAAA
3177564 AAAAAAGATAGAGAAAAAAA
1 AAAAAAGA-AGA-AAAAAAA
*
3177584 AGAAAA-AAGAAAAAAAA
1 AAAAAAGAAGAAAAAAAA
*
3177601 AAAAGAAAAAGAAAAAAGAA
1 AAAA-AAGAAGAAAAAA-AA
3177621 AA
1 AA
3177623 CAAATCAAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
17 10 0.13
18 18 0.23
19 24 0.31
20 23 0.29
21 3 0.04
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.04
Consensus pattern (18 bp):
AAAAAAGAAGAAAAAAAA
Found at i:3177563 original size:11 final size:10
Alignment explanation
Indices: 3177545--3177617 Score: 61
Period size: 9 Copynumber: 7.6 Consensus size: 10
3177535 GAAAAAACAT
3177545 AAAAAAAGAG
1 AAAAAAAGAG
3177555 AAAATAAAGA-
1 AAAA-AAAGAG
3177565 AAAAAGATAGAG
1 AAAAA-A-AGAG
3177577 AAAAAAA-AG
1 AAAAAAAGAG
3177586 -AAAAAAGA-
1 AAAAAAAGAG
3177594 AAAAAAA-A-
1 AAAAAAAGAG
3177602 AAAGAAAA-AG
1 AAA-AAAAGAG
3177612 AAAAAA
1 AAAAAA
3177618 GAAAACAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
8 10 0.18
9 18 0.33
10 13 0.24
11 9 0.16
12 5 0.09
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:3177570 original size:7 final size:7
Alignment explanation
Indices: 3177560--3177622 Score: 78
Period size: 7 Copynumber: 9.1 Consensus size: 7
3177550 AAGAGAAAAT
3177560 AAAGAAA
1 AAAGAAA
3177567 AAAGATAGA
1 AAAGA-A-A
*
3177576 GAA-AAA
1 AAAGAAA
3177582 AAAGAAA
1 AAAGAAA
3177589 AAAGAAA
1 AAAGAAA
3177596 AAA-AAA
1 AAAGAAA
3177602 AAAG-AA
1 AAAGAAA
3177608 AAAGAAA
1 AAAGAAA
3177615 AAAGAAA
1 AAAGAAA
3177622 A
1 A
3177623 CAAATCAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
6 15 0.31
7 29 0.59
8 2 0.04
9 3 0.06
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:3177576 original size:22 final size:21
Alignment explanation
Indices: 3177531--3177610 Score: 90
Period size: 22 Copynumber: 3.8 Consensus size: 21
3177521 TATAACAACA
* * *
3177531 AGAAGAAAAAACATAAAAAAAG
1 AGAA-AAAAAAGAAAAAAGAAG
*
3177553 AGAAAATAAAGAAAAAAGATAG
1 AGAAAAAAAAGAAAAAAGA-AG
3177575 AGAAAAAAAAGAAAAAAGAA-
1 AGAAAAAAAAGAAAAAAGAAG
*
3177595 AAAAAAAAAAGAAAAA
1 AGAAAAAAAAGAAAAA
3177611 GAAAAAAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
20 15 0.29
21 12 0.24
22 24 0.47
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.04
Consensus pattern (21 bp):
AGAAAAAAAAGAAAAAAGAAG
Found at i:3177580 original size:13 final size:13
Alignment explanation
Indices: 3177580--3177622 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
3177570 GATAGAGAAA
3177580 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
*
3177593 AAAAAAAAAAAAG
1 AAAAAGAAAAAAG
3177606 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
3177619 AAAA
1 AAAA
3177623 CAAATCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:3177584 original size:15 final size:16
Alignment explanation
Indices: 3177533--3177622 Score: 69
Period size: 16 Copynumber: 5.4 Consensus size: 16
3177523 TAACAACAAG
*
3177533 AAGAAAAAACATAAAAA
1 AAGAAAAAAGA-AAAAA
3177550 AAGAGAAAATA-AAGAAAA
1 AAGA-AAAA-AGAA-AAAA
* *
3177568 AAG-ATAGAGAAAAAA
1 AAGAAAAAAGAAAAAA
3177583 AAGAAAAAAGAAAAAA
1 AAGAAAAAAGAAAAAA
*
3177599 AA-AAAAGAAAAAGAAAA
1 AAGAAAA-AAGAA-AAAA
3177616 AAGAAAA
1 AAGAAAA
3177623 CAAATCAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
15 12 0.20
16 20 0.33
17 11 0.18
18 16 0.27
19 1 0.02
ACGTcount: A:0.82, C:0.01, G:0.13, T:0.03
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAA
Found at i:3177622 original size:22 final size:21
Alignment explanation
Indices: 3177530--3177622 Score: 89
Period size: 22 Copynumber: 4.3 Consensus size: 21
3177520 ATATAACAAC
* *
3177530 AAGAAGAAAAAACATAAAAAAA
1 AAGAA-AAAAAAGAAAAAAAAA
* * *
3177552 GAGAAAATAAAGAAAAAAGATA
1 AAGAAAAAAAAGAAAAAA-AAA
* *
3177574 GAGAAAAAAAAGAAAAAAGAA
1 AAGAAAAAAAAGAAAAAAAAA
3177595 AA-AAAAAAAAGAAAAAGAAAA
1 AAGAAAAAAAAGAAAAA-AAAA
3177616 AAGAAAA
1 AAGAAAA
3177623 CAAATCAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 14 0.24
21 17 0.29
22 27 0.47
ACGTcount: A:0.82, C:0.01, G:0.14, T:0.03
Consensus pattern (21 bp):
AAGAAAAAAAAGAAAAAAAAA
Found at i:3178414 original size:28 final size:28
Alignment explanation
Indices: 3178365--3178423 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3178355 ACCAAAAAAC
* * *
3178365 CAACCTGAAACACATTATCTCCCCAAAT
1 CAACATGAAACACATTACCTCCACAAAT
*
3178393 CAACATGAAACAC-TCTACCTCCACAAGT
1 CAACATGAAACACAT-TACCTCCACAAAT
3178421 CAA
1 CAA
3178424 TCTAACCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.41, C:0.36, G:0.05, T:0.19
Consensus pattern (28 bp):
CAACATGAAACACATTACCTCCACAAAT
Found at i:3179952 original size:58 final size:58
Alignment explanation
Indices: 3179804--3180013 Score: 201
Period size: 57 Copynumber: 3.6 Consensus size: 58
3179794 GATTTTTTTT
* * * * *
3179804 AGAAACT-AGTCTGACTTTCAGAGGTTTTTTAATTGAGATGAGGTTTTCAAATGAATTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAGG---TTT-CTTGACATGATGTATTCAAATGAATTTT-AA
* *
3179866 AGAAACTAAGTCTGGTTTTCAGAGGTTTCTTGACATGATGTCTTCAAATGAATTTTAA
1 AGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGATGTATTCAAATGAATTTTAA
* ** * * * *
3179924 AGAAACTACGTCTGATTTTTGGAAGTTTCTT--TATGATTTATTCAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGATGTATTCAAATGA-ATTTTAA
**
3179981 AGAAGTTAAGTCTGATTTTCAGAGGTTTCTTGA
1 AGAAACTAAGTCTGATTTTCAGAGGTTTCTTGA
3180014 TGATTGCTCA
Statistics
Matches: 123, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
56 15 0.12
57 31 0.25
58 28 0.23
59 24 0.20
60 3 0.02
62 7 0.06
63 15 0.12
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.40
Consensus pattern (58 bp):
AGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGATGTATTCAAATGAATTTTAA
Found at i:3180191 original size:41 final size:41
Alignment explanation
Indices: 3180082--3180235 Score: 161
Period size: 41 Copynumber: 3.7 Consensus size: 41
3180072 AGGGTTTCTT
* *
3180082 GATGAGTAAGTCCCTCGGGTCATC-AGTAAGTCTTTCGAGCATTA
1 GATG-GTAAGTCCTTCAGGTCATCTA-TAAGTCTTTCGAGCA--A
* * *
3180126 TAT-TTAAATCCTTC-GAGTCATCTATAAGTCTTTCGAGCAA
1 GATGGTAAGTCCTTCAG-GTCATCTATAAGTCTTTCGAGCAA
*
3180166 GATGGTAAGTCCTTCAGGTCATCTATAAGTCTTTTGAGCAA
1 GATGGTAAGTCCTTCAGGTCATCTATAAGTCTTTCGAGCAA
** *
3180207 GATATTAAGTCCTTCAGGCCATCTATAAG
1 GATGGTAAGTCCTTCAGGTCATCTATAAG
3180236 ACCTTCCGAC
Statistics
Matches: 95, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
40 3 0.03
41 59 0.62
42 30 0.32
43 1 0.01
44 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (41 bp):
GATGGTAAGTCCTTCAGGTCATCTATAAGTCTTTCGAGCAA
Done.