Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 43
Found at i:3237460 original size:2 final size:2
Alignment explanation
Indices: 3237448--3237571 Score: 239
Period size: 2 Copynumber: 62.0 Consensus size: 2
3237438 TATATTCATG
*
3237448 CA CA CA GA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3237490 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3237532 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3237572 TATATGTGTG
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 120 1.00
ACGTcount: A:0.50, C:0.49, G:0.01, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3237608 original size:2 final size:2
Alignment explanation
Indices: 3237603--3237628 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3237593 TGTGTGTGTG
3237603 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
3237629 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3237633 original size:2 final size:2
Alignment explanation
Indices: 3237628--3237692 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
3237618 TATATATATA
3237628 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3237670 TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG T
3237693 ATTAATGTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:3237965 original size:21 final size:19
Alignment explanation
Indices: 3237939--3237997 Score: 84
Period size: 18 Copynumber: 3.1 Consensus size: 19
3237929 TCGAGGGATT
3237939 ATAGTGGTCCTTCGGGACA
1 ATAGTGGTCCTTCGGGACA
*
3237958 TATCAGTGGTCCTTTGGGAC-
1 -AT-AGTGGTCCTTCGGGACA
3237978 ATAGTGGTCCTTCGGGACA
1 ATAGTGGTCCTTCGGGACA
3237997 A
1 A
3237998 ATATTCAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 15 0.43
19 3 0.09
20 2 0.06
21 15 0.43
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (19 bp):
ATAGTGGTCCTTCGGGACA
Found at i:3244279 original size:6 final size:6
Alignment explanation
Indices: 3244262--3244322 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
3244252 GACGCGTATT
* * * * *
3244262 ACCACG ATCACG ACCACG ACCTCG ACCATG ACCACG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
3244310 ACCTCG ACCACG A
1 ACCACG ACCACG A
3244323 GTCGAGCCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.28, C:0.46, G:0.16, T:0.10
Consensus pattern (6 bp):
ACCACG
Found at i:3244975 original size:12 final size:12
Alignment explanation
Indices: 3244958--3244982 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3244948 TCAATTCCAC
3244958 TATCATGGTCAA
1 TATCATGGTCAA
3244970 TATCATGGTCAA
1 TATCATGGTCAA
3244982 T
1 T
3244983 CCATGTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TATCATGGTCAA
Found at i:3249400 original size:10 final size:10
Alignment explanation
Indices: 3249385--3249426 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
3249375 CATATAATTG
3249385 AAATAACATA
1 AAATAACATA
3249395 AAATAACATA
1 AAATAACATA
3249405 ACAATAA-ATA
1 A-AATAACATA
* *
3249415 TAATACCATA
1 AAATAACATA
3249425 AA
1 AA
3249427 TTATAAGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 4 0.15
10 18 0.67
11 5 0.19
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAACATA
Found at i:3253437 original size:18 final size:18
Alignment explanation
Indices: 3253411--3253445 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3253401 TCGGTTTGGA
* *
3253411 AATTCAATTTTTTATTTG
1 AATTAAATTTTATATTTG
3253429 AATTAAATTTTATATTT
1 AATTAAATTTTATATTT
3253446 TTTTGAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
AATTAAATTTTATATTTG
Found at i:3253781 original size:2 final size:2
Alignment explanation
Indices: 3253769--3253807 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3253759 GTTTAAATGA
3253769 AT AT A- 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
3253808 TATGTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3263269 original size:24 final size:24
Alignment explanation
Indices: 3263236--3263287 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3263226 TCACCATCGC
*
3263236 CATCATCATTACCAACATCA-CTAT
1 CATCACCATTACCAACATCATC-AT
*
3263260 CATCACCATTATCAACATCATCAT
1 CATCACCATTACCAACATCATCAT
3263284 CATC
1 CATC
3263288 GTCATCTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (24 bp):
CATCACCATTACCAACATCATCAT
Found at i:3265178 original size:4 final size:4
Alignment explanation
Indices: 3265169--3265197 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3265159 ATACCCCTTC
3265169 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
3265198 TTACCTCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3266912 original size:72 final size:70
Alignment explanation
Indices: 3266825--3266970 Score: 265
Period size: 72 Copynumber: 2.1 Consensus size: 70
3266815 AATAAAAATT
*
3266825 TTTAAAAAAATATTTTAAAATTAATTATTTCTTATACTTTTTTTCGGTATTAAAAAGATATGAAT
1 TTTAAAAAAATATTTTAAAATTAATTAATTCTTATACTTTTTTTCGGTATTAAAAAGATATGAAT
3266890 AGATA
66 AGATA
3266895 TTTAAAAAGATATATTTTAAAATTAATTAATTCTTATACTTTTTTTCGGTATTAAAAAGATATGA
1 TTTAAAAA-A-ATATTTTAAAATTAATTAATTCTTATACTTTTTTTCGGTATTAAAAAGATATGA
3266960 ATAGATA
64 ATAGATA
3266967 TTTA
1 TTTA
3266971 TCTAAAAAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
70 8 0.11
71 1 0.01
72 64 0.88
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (70 bp):
TTTAAAAAAATATTTTAAAATTAATTAATTCTTATACTTTTTTTCGGTATTAAAAAGATATGAAT
AGATA
Found at i:3293184 original size:26 final size:26
Alignment explanation
Indices: 3293148--3293200 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3293138 TAAAAAGGTC
3293148 ACATTGAAGGAATTGGTTTCATTGGT
1 ACATTGAAGGAATTGGTTTCATTGGT
*
3293174 ACATTGAAGGAATTGGTTTTATTGGT
1 ACATTGAAGGAATTGGTTTCATTGGT
3293200 A
1 A
3293201 ACAACTCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.40
Consensus pattern (26 bp):
ACATTGAAGGAATTGGTTTCATTGGT
Found at i:3299180 original size:18 final size:18
Alignment explanation
Indices: 3299157--3299192 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3299147 GTCCCGTTTT
3299157 ATAATAATTATTATTATA
1 ATAATAATTATTATTATA
3299175 ATAATAATTATTATTATA
1 ATAATAATTATTATTATA
3299193 TTATTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAATAATTATTATTATA
Found at i:3299197 original size:11 final size:11
Alignment explanation
Indices: 3299181--3299220 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
3299171 TATAATAATA
3299181 ATTATTATTAT
1 ATTATTATTAT
*
3299192 ATTATTATTAA
1 ATTATTATTAT
* *
3299203 ATAATAATTAT
1 ATTATTATTAT
3299214 ATTATTA
1 ATTATTA
3299221 AAGCCTAGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:3304678 original size:16 final size:16
Alignment explanation
Indices: 3304657--3304723 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 16
3304647 TTTTGGTTGT
*
3304657 TTTACTATTTTTATTA
1 TTTACTATTTTAATTA
*
3304673 TTTACTGTTTTAATTA
1 TTTACTATTTTAATTA
*
3304689 TTTTAATTATTATTAAGTT-
1 -TTT-ACTATT-TTAA-TTA
3304708 TATTACTATTTTAATT
1 T-TTACTATTTTAATT
3304724 TGTTTCATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
16 16 0.39
17 7 0.17
18 10 0.24
19 6 0.15
20 2 0.05
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTACTATTTTAATTA
Found at i:3314008 original size:12 final size:12
Alignment explanation
Indices: 3313993--3314083 Score: 93
Period size: 12 Copynumber: 7.9 Consensus size: 12
3313983 TTTCATTTGG
3313993 TTTT-TTATTA-
1 TTTTATTATTAT
3314003 TTTT-TTATT-T
1 TTTTATTATTAT
*
3314013 GTTTATTA-TAT
1 TTTTATTATTAT
3314024 TATTTATTATTAT
1 T-TTTATTATTAT
*
3314037 TATTATTATTAT
1 TTTTATTATTAT
*
3314049 TATTATTATTAT
1 TTTTATTATTAT
*
3314061 TATTATTATTAT
1 TTTTATTATTAT
*
3314073 TATTATTATTA
1 TTTTATTATTA
3314084 CAAAAAGGCT
Statistics
Matches: 73, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
10 13 0.18
11 4 0.05
12 52 0.71
13 4 0.05
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:3314021 original size:3 final size:3
Alignment explanation
Indices: 3314015--3314083 Score: 122
Period size: 3 Copynumber: 23.0 Consensus size: 3
3314005 TTTTATTTGT
3314015 TTA TTA -TA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3314060 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
3314084 CAAAAAGGCT
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 59 0.92
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3315437 original size:15 final size:14
Alignment explanation
Indices: 3315417--3315466 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
3315407 ACTACTTAGT
3315417 TATATTGTAATTTTA
1 TATATT-TAATTTTA
3315432 TATATTT-ATTTTCAA
1 TATATTTAATTTT--A
3315447 TATATTTAATTATTA
1 TATATTTAATT-TTA
3315462 T-TATT
1 TATATT
3315467 ATTATTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 5 0.16
14 5 0.16
15 16 0.52
16 3 0.10
17 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
TATATTTAATTTTA
Found at i:3315511 original size:4 final size:4
Alignment explanation
Indices: 3315504--3315535 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
3315494 ATAATAAATA
3315504 TTAT TTAT TTAT TTAT TTAT TTAT TT-T TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
3315536 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTAT
Found at i:3318743 original size:9 final size:9
Alignment explanation
Indices: 3318731--3318810 Score: 69
Period size: 9 Copynumber: 9.0 Consensus size: 9
3318721 AAAAATCTAA
3318731 AATAAAAAT
1 AATAAAAAT
3318740 AAT-AAAAT
1 AATAAAAAT
*
3318748 ACA-ATAAAT
1 A-ATAAAAAT
3318757 AATAAATAAT
1 AATAAA-AAT
*
3318767 AATAATAAT
1 AATAAAAAT
*
3318776 AATAATAAT
1 AATAAAAAT
*
3318785 AATAATAAT
1 AATAAAAAT
3318794 AA-ACAAAA-
1 AATA-AAAAT
3318802 AATAAAAAT
1 AATAAAAAT
3318811 GGGTTGTCTC
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
8 14 0.23
9 38 0.63
10 8 0.13
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (9 bp):
AATAAAAAT
Found at i:3318760 original size:3 final size:3
Alignment explanation
Indices: 3318731--3318795 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
3318721 AAAAATCTAA
* *
3318731 AAT AAA AAT AAT AA- AAT -AC AAT AAAT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT
3318776 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
3318796 ACAAAAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 3 0.06
3 45 0.83
4 6 0.11
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3323262 original size:3 final size:3
Alignment explanation
Indices: 3323243--3323304 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
3323233 GGTTTATTTT
3323243 TTA TTA TT- TATA TTTA TTA -TA TTA TTA TTA TTAA TT- TTA TT- TTA
1 TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* *
3323287 TTA CTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
3323305 ATTTGTTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
2 7 0.15
3 35 0.73
4 5 0.10
5 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3323287 original size:17 final size:17
Alignment explanation
Indices: 3323249--3323300 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
3323239 TTTTTTATTA
* *
3323249 TTTA-TATTTATTATAT
1 TTTATTATTAATTTTAT
3323265 TATTATTATTAATTTTAT
1 T-TTATTATTAATTTTAT
* *
3323283 TTTATTACTATTTTTAT
1 TTTATTATTAATTTTAT
3323300 T
1 T
3323301 ATTAATTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 1 0.03
17 18 0.60
18 11 0.37
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATTATTAATTTTAT
Found at i:3323294 original size:29 final size:29
Alignment explanation
Indices: 3323249--3323308 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
3323239 TTTTTTATTA
3323249 TTTATATTTATTATATTATTATTATTAAT
1 TTTATATTTATTATATTATTATTATTAAT
*
3323278 TTTAT-TTTATTACTATTTTTATTATTAAT
1 TTTATATTTATTA-TATTATTATTATTAAT
3323307 TT
1 TT
3323309 GTTTGTAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
TTTATATTTATTATATTATTATTATTAAT
Found at i:3323303 original size:20 final size:20
Alignment explanation
Indices: 3323235--3323303 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
3323225 TTCATCCGGG
*
3323235 TTTATT-TTTTATTATTTATA
1 TTTATTATTTTATTA-TTATT
*
3323255 TTTATTATATTATTATTATT
1 TTTATTATTTTATTATTATT
* *
3323275 AATT-TTATTTTATTACTATT
1 -TTTATTATTTTATTATTATT
3323295 TTTATTATT
1 TTTATTATT
3323304 AATTTGTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 29 0.73
21 9 0.22
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTATTTTATTATTATT
Found at i:3323668 original size:11 final size:10
Alignment explanation
Indices: 3323647--3323672 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3323637 AATCAAGTTG
3323647 AAAAAAGAAA
1 AAAAAAGAAA
3323657 AAAAAAGAAA
1 AAAAAAGAAA
3323667 AAAAAA
1 AAAAAA
3323673 CATAGTGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:3324227 original size:35 final size:35
Alignment explanation
Indices: 3324188--3324254 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
3324178 TTTATTTACG
* *
3324188 AGCCTTAAAGTTTATTTCTTTTATATTTTAGTACA
1 AGCCTTAAAGTTTATTTCATTTATACTTTAGTACA
* *
3324223 AGCCTTAAATTTTGTTTCATTTATACTTTAGT
1 AGCCTTAAAGTTTATTTCATTTATACTTTAGT
3324255 TACCATTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (35 bp):
AGCCTTAAAGTTTATTTCATTTATACTTTAGTACA
Found at i:3326071 original size:18 final size:17
Alignment explanation
Indices: 3326048--3326088 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
3326038 AATACATATC
*
3326048 AATTTTTGTCTTAAAAAT
1 AATTTTT-TCGTAAAAAT
3326066 AA-TTTTTCGTAAAAAT
1 AATTTTTTCGTAAAAAT
3326082 AATTTTT
1 AATTTTT
3326089 CTTAAAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 11 0.52
17 8 0.38
18 2 0.10
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (17 bp):
AATTTTTTCGTAAAAAT
Found at i:3326080 original size:16 final size:16
Alignment explanation
Indices: 3326059--3326095 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3326049 ATTTTTGTCT
3326059 TAAAAATAATTTTTCG
1 TAAAAATAATTTTTCG
*
3326075 TAAAAATAATTTTTCT
1 TAAAAATAATTTTTCG
3326091 TAAAA
1 TAAAA
3326096 TTGTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (16 bp):
TAAAAATAATTTTTCG
Found at i:3339971 original size:6 final size:6
Alignment explanation
Indices: 3339960--3339994 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
3339950 ATTCCATTCC
*
3339960 ATTTTT ATTTTT ATTTTT ATTTTT TTGTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT-TTTT ATTT
3339995 GTCATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:3340002 original size:19 final size:18
Alignment explanation
Indices: 3339959--3340002 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
3339949 AATTCCATTC
3339959 CATTTTTATTTTTATTTT
1 CATTTTTATTTTTATTTT
* *
3339977 TATTTTTTTGTTTTATTTGT
1 CATTTTTAT-TTTTATTT-T
3339997 CATTTT
1 CATTTT
3340003 GATCGAGCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 7 0.33
19 8 0.38
20 6 0.29
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (18 bp):
CATTTTTATTTTTATTTT
Found at i:3345853 original size:3 final size:3
Alignment explanation
Indices: 3345847--3345885 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
3345837 AGTTTTTTTT
3345847 TTA TTA TTA TTA TTA TTA -TA TT- TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3345886 TTGTTTGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3347487 original size:5 final size:5
Alignment explanation
Indices: 3347467--3347540 Score: 56
Period size: 4 Copynumber: 16.4 Consensus size: 5
3347457 ATAAGTTTTC
* *
3347467 TTTAT TTCAA TTTAT TTTAT TTTA- TTTA- TTTA- TTTA- TTTA- TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
* *
3347512 TTTA- TTT-T TTTAT CTCAT TTTA- TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
3347541 AAACAATTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
4 30 0.53
5 27 0.47
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:3347494 original size:4 final size:4
Alignment explanation
Indices: 3347476--3347541 Score: 69
Period size: 4 Copynumber: 15.2 Consensus size: 4
3347466 CTTTATTTCA
* *
3347476 ATTT ATTTT ATTTT ATTT ATTT ATTT ATTT ATTT ATTTT ATTT TTTT ATCTC
1 ATTT A-TTT A-TTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT AT-TT
3347528 ATTTT ATTT ATTT A
1 A-TTT ATTT ATTT A
3347542 AACAATTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
4 36 0.67
5 17 0.31
6 1 0.02
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:3347518 original size:35 final size:36
Alignment explanation
Indices: 3347467--3347541 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
3347457 ATAAGTTTTC
*
3347467 TTTATTTCAATTTATTTTATTTTAT-TTA-TTTATTTA
1 TTTATTTCAATTTA-TTT-TTTTATCTCATTTTATTTA
*
3347503 TTTATTT-ATTTTATTTTTTTATCTCATTTTATTTA
1 TTTATTTCAATTTATTTTTTTATCTCATTTTATTTA
3347538 TTTA
1 TTTA
3347542 AACAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 6 0.17
34 5 0.14
35 17 0.49
36 7 0.20
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (36 bp):
TTTATTTCAATTTATTTTTTTATCTCATTTTATTTA
Found at i:3347678 original size:19 final size:19
Alignment explanation
Indices: 3347602--3347692 Score: 57
Period size: 19 Copynumber: 4.9 Consensus size: 19
3347592 ATTTATTTAT
*
3347602 TTATTTTATTATTTTATCC
1 TTATTTTATTATTTTATTC
** *
3347621 TTATTTT-CCATTTTAATC
1 TTATTTTATTATTTTATTC
* * *
3347639 --AATTTATT-TTTAATTAT
1 TTATTTTATTATTTTATT-C
3347656 TTATTTTATTATTTTATTC
1 TTATTTTATTATTTTATTC
3347675 TTATCTTT-TTATCTTTAT
1 TTAT-TTTATTAT-TTTAT
3347693 CTGAAATTAT
Statistics
Matches: 52, Mismatches: 13, Indels: 13
0.67 0.17 0.17
Matches are distributed among these distances:
16 9 0.17
18 7 0.13
19 22 0.42
20 14 0.27
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTTATTATTTTATTC
Found at i:3347684 original size:14 final size:13
Alignment explanation
Indices: 3347601--3347692 Score: 55
Period size: 14 Copynumber: 6.8 Consensus size: 13
3347591 TATTTATTTA
3347601 TTTATTTTATTAT
1 TTTATTTTATTAT
*
3347614 TTTATCCTTATT-T
1 TTTAT-TTTATTAT
** * *
3347627 TCCATTTTAATCAA
1 TTTATTTT-ATTAT
3347641 TTTATTTTTAATTA-
1 TTTA-TTTT-ATTAT
3347655 TTTATTTTATTAT
1 TTTATTTTATTAT
3347668 TTTATTCTTATCT-T
1 TTTATT-TTAT-TAT
3347682 TTTATCTTTAT
1 TTTAT-TTTAT
3347693 CTGAAATTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
12 6 0.10
13 21 0.34
14 25 0.40
15 10 0.16
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATTTTATTAT
Found at i:3348200 original size:2 final size:2
Alignment explanation
Indices: 3348193--3348224 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3348183 TTGGTTTTAG
3348193 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
3348225 GTGTGTGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3348721 original size:21 final size:19
Alignment explanation
Indices: 3348688--3348729 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
3348678 ACCATATATT
3348688 ATTTTTATAGATACCTTTTAA
1 ATTTTTATAGATA-C-TTTAA
3348709 ATTTATTAT-GATACTTTAA
1 ATTT-TTATAGATACTTTAA
3348728 AT
1 AT
3348730 AATTTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 8 0.40
22 4 0.20
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (19 bp):
ATTTTTATAGATACTTTAA
Found at i:3349483 original size:18 final size:19
Alignment explanation
Indices: 3349450--3349486 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3349440 TGTTAATGAA
*
3349450 TTTTAAGATTTTATATTCG
1 TTTTAAGATATTATATTCG
3349469 TTTTAA-ATATTATATTCG
1 TTTTAAGATATTATATTCG
3349487 ATTCAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (19 bp):
TTTTAAGATATTATATTCG
Found at i:3349873 original size:24 final size:24
Alignment explanation
Indices: 3349841--3349963 Score: 106
Period size: 24 Copynumber: 5.5 Consensus size: 24
3349831 ACCATGTTAT
**
3349841 GTATCGATACTACTTTACATAGTA
1 GTATCGATACTACTGCACATAGTA
*
3349865 GTATCGATACTCACTGGAC---G--
1 GTATCGATACT-ACTGCACATAGTA
3349885 GTATCGATACTACTGCACATAGTA
1 GTATCGATACTACTGCACATAGTA
3349909 GTATCG--A-TACT-CAC-TAG-A
1 GTATCGATACTACTGCACATAGTA
*
3349927 GGGTATCGATACTACTGCATATAGTA
1 --GTATCGATACTACTGCACATAGTA
3349953 GTATCGATACT
1 GTATCGATACT
3349964 CCCTGGACAG
Statistics
Matches: 81, Mismatches: 4, Indels: 28
0.72 0.04 0.25
Matches are distributed among these distances:
18 1 0.01
19 9 0.11
20 20 0.25
21 4 0.05
22 4 0.05
23 4 0.05
24 30 0.37
25 8 0.10
26 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (24 bp):
GTATCGATACTACTGCACATAGTA
Found at i:3349890 original size:20 final size:19
Alignment explanation
Indices: 3349865--3349943 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 19
3349855 TTACATAGTA
3349865 GTATCGATACTCACTGGACG
1 GTATCGATACT-ACTGGACG
*
3349885 GTATCGATACTACTGCACATAG
1 GTATCGATACTACTGGAC---G
* *
3349907 TAGTATCGATACTCACTAGAGG
1 --GTATCGATACT-ACTGGACG
3349929 GTATCGATACTACTG
1 GTATCGATACTACTG
3349944 CATATAGTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
19 9 0.19
20 22 0.46
22 2 0.04
24 11 0.23
25 4 0.08
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (19 bp):
GTATCGATACTACTGGACG
Found at i:3349905 original size:44 final size:44
Alignment explanation
Indices: 3349841--3349977 Score: 211
Period size: 44 Copynumber: 3.1 Consensus size: 44
3349831 ACCATGTTAT
**
3349841 GTATCGATACTACTTTACATAGTAGTATCGATACTCACTGGACG
1 GTATCGATACTACTGCACATAGTAGTATCGATACTCACTGGACG
* *
3349885 GTATCGATACTACTGCACATAGTAGTATCGATACTCACTAGAGG
1 GTATCGATACTACTGCACATAGTAGTATCGATACTCACTGGACG
* * *
3349929 GTATCGATACTACTGCATATAGTAGTATCGATACTCCCTGGACA
1 GTATCGATACTACTGCACATAGTAGTATCGATACTCACTGGACG
3349973 GTATC
1 GTATC
3349978 AATATCGTTG
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 84 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (44 bp):
GTATCGATACTACTGCACATAGTAGTATCGATACTCACTGGACG
Found at i:3357459 original size:21 final size:22
Alignment explanation
Indices: 3357435--3357477 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3357425 AACAAAAAGG
3357435 GGGGGAG-AAATCTCAAAGTAA
1 GGGGGAGTAAATCTCAAAGTAA
*
3357456 GGGGGAGTAAATTTCAAAGTAA
1 GGGGGAGTAAATCTCAAAGTAA
3357478 TTTTTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.42, C:0.07, G:0.33, T:0.19
Consensus pattern (22 bp):
GGGGGAGTAAATCTCAAAGTAA
Found at i:3360596 original size:2 final size:2
Alignment explanation
Indices: 3360589--3360619 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3360579 TTAGTAAGTA
3360589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3360620 ATTAAAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3370720 original size:2 final size:2
Alignment explanation
Indices: 3370713--3370738 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3370703 TAGATATTAT
3370713 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
3370739 ATTTATAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3376061 original size:3 final size:3
Alignment explanation
Indices: 3376053--3376158 Score: 166
Period size: 3 Copynumber: 36.7 Consensus size: 3
3376043 CCAAGTTTAT
3376053 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3376101 TTA TTA -TA TTT TTA TTA TTA TTA -TA TT- TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3376145 TTT TTA TTA TTA TT
1 TTA TTA TTA TTA TT
3376159 TTGTTTGTAG
Statistics
Matches: 95, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
2 8 0.08
3 87 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3377668 original size:4 final size:4
Alignment explanation
Indices: 3377654--3377711 Score: 57
Period size: 4 Copynumber: 14.0 Consensus size: 4
3377644 TTTATATCAG
*
3377654 TTTA TTTTA TTTA TTTA TTTA TTTTA TTTA TTTA -TT- TTTA TCTCA TTTTA
1 TTTA -TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA T-TTA -TTTA
3377704 TTTA TTTA
1 TTTA TTTA
3377712 AACAATTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
3 4 0.09
4 29 0.63
5 12 0.26
6 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:3377672 original size:13 final size:13
Alignment explanation
Indices: 3377654--3377711 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
3377644 TTTATATCAG
3377654 TTTATTTTATTTA
1 TTTATTTTATTTA
3377667 TTTA-TTTATTTTA
1 TTTATTTTA-TTTA
*
3377680 TTTATTTATTTTTA
1 TTTATTT-TATTTA
*
3377694 TCTCATTTTATTTA
1 T-TTATTTTATTTA
3377708 TTTA
1 TTTA
3377712 AACAATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.11
13 14 0.38
14 13 0.35
15 6 0.16
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:3377676 original size:17 final size:17
Alignment explanation
Indices: 3377654--3377690 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3377644 TTTATATCAG
3377654 TTTATTTTATTTATTTA
1 TTTATTTTATTTATTTA
3377671 TTTATTTTATTTATTTA
1 TTTATTTTATTTATTTA
3377688 TTT
1 TTT
3377691 TTATCTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTATTTATTTA
Found at i:3378557 original size:27 final size:27
Alignment explanation
Indices: 3378527--3378586 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
3378517 TTCTATTTAT
3378527 TTAATGTAT-TTATATT-TTTATCATTAC
1 TTAAT-TATCTTAT-TTATTTATCATTAC
* *
3378554 TTAATTATCTTATTTATTTATCTTTTC
1 TTAATTATCTTATTTATTTATCATTAC
3378581 TTAATT
1 TTAATT
3378587 TTATTTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (27 bp):
TTAATTATCTTATTTATTTATCATTAC
Found at i:3378697 original size:18 final size:19
Alignment explanation
Indices: 3378663--3378699 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3378653 GTGTTAATGA
*
3378663 ATTTTAAGATTTTATATTC
1 ATTTTAAGATATTATATTC
3378682 ATTTTAA-ATATTATATTC
1 ATTTTAAGATATTATATTC
3378700 GATTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTTTAAGATATTATATTC
Found at i:3379104 original size:20 final size:19
Alignment explanation
Indices: 3379079--3379157 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 19
3379069 ATGTGTAGTA
3379079 GTATCGATACTCACTGGACG
1 GTATCGATACT-ACTGGACG
*
3379099 GTATCGATACTACTGCACATAG
1 GTATCGATACTACTGGAC---G
* *
3379121 TAGTATCGATACTCATTGGAGG
1 --GTATCGATACT-ACTGGACG
3379143 GTATCGATACTACTG
1 GTATCGATACTACTG
3379158 CACATAGTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
19 9 0.19
20 22 0.46
22 2 0.04
24 11 0.23
25 4 0.08
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (19 bp):
GTATCGATACTACTGGACG
Found at i:3379106 original size:44 final size:44
Alignment explanation
Indices: 3379074--3379195 Score: 199
Period size: 44 Copynumber: 2.8 Consensus size: 44
3379064 TTACTATGTG
3379074 TAGTAGTATCGATACTCACTGGACGGTATCGATACTACTGCACA
1 TAGTAGTATCGATACTCACTGGACGGTATCGATACTACTGCACA
* *
3379118 TAGTAGTATCGATACTCATTGGAGGGTATCGATACTACTGCACA
1 TAGTAGTATCGATACTCACTGGACGGTATCGATACTACTGCACA
* * *
3379162 TAGTAGTATCGATACTCCCAGGACAGTATCGATA
1 TAGTAGTATCGATACTCACTGGACGGTATCGATA
3379196 TCGTTGAGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
TAGTAGTATCGATACTCACTGGACGGTATCGATACTACTGCACA
Found at i:3379126 original size:24 final size:24
Alignment explanation
Indices: 3379099--3379177 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
3379089 TCACTGGACG
3379099 GTATCGATACTACTGCACATAGTA
1 GTATCGATACTACTGCACATAGTA
* * *
3379123 GTATCGATACTCATTG----GAG-G
1 GTATCGATACT-ACTGCACATAGTA
3379143 GTATCGATACTACTGCACATAGTA
1 GTATCGATACTACTGCACATAGTA
3379167 GTATCGATACT
1 GTATCGATACT
3379178 CCCAGGACAG
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 3 0.07
20 11 0.26
21 2 0.05
23 2 0.05
24 22 0.51
25 3 0.07
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (24 bp):
GTATCGATACTACTGCACATAGTA
Found at i:3386789 original size:18 final size:19
Alignment explanation
Indices: 3386755--3386791 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3386745 GTGTTAATGA
*
3386755 ATTTTAAGATTTTATATTC
1 ATTTTAAGATATTATATTC
3386774 ATTTTAA-ATATTATATTC
1 ATTTTAAGATATTATATTC
3386792 GATTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTTTAAGATATTATATTC
Found at i:3387195 original size:44 final size:44
Alignment explanation
Indices: 3387145--3387244 Score: 137
Period size: 44 Copynumber: 2.3 Consensus size: 44
3387135 ATACCATGTT
**
3387145 CGGTATCGATACTAATTTACATAGTAGTATCGATACTCACTAGA
1 CGGTATCGATACTAATACACATAGTAGTATCGATACTCACTAGA
* * * *
3387189 GGGTATCGATACTACTACACATAGTAGTATCGATACTCCCTTGA
1 CGGTATCGATACTAATACACATAGTAGTATCGATACTCACTAGA
*
3387233 CAGTATCGATAC
1 CGGTATCGATAC
3387245 CGTTTAGTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (44 bp):
CGGTATCGATACTAATACACATAGTAGTATCGATACTCACTAGA
Found at i:3387218 original size:24 final size:24
Alignment explanation
Indices: 3387147--3387225 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 24
3387137 ACCATGTTCG
* **
3387147 GTATCGATACTAATTTACATAGTA
1 GTATCGATACTACTACACATAGTA
* * *
3387171 GTATCGATACT-C-AC-TAGAG-G
1 GTATCGATACTACTACACATAGTA
3387191 GTATCGATACTACTACACATAGTA
1 GTATCGATACTACTACACATAGTA
3387215 GTATCGATACT
1 GTATCGATACT
3387226 CCCTTGACAG
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
20 11 0.26
21 4 0.10
22 2 0.05
23 3 0.07
24 22 0.52
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (24 bp):
GTATCGATACTACTACACATAGTA
Found at i:3402048 original size:73 final size:73
Alignment explanation
Indices: 3401959--3402326 Score: 610
Period size: 73 Copynumber: 5.0 Consensus size: 73
3401949 GGTCTTATGA
* * *
3401959 ATGACCCTTAGACTTTAAAATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGG
*
3402024 TCTTATAG
66 TCTTACAG
** * *
3402032 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCTTAAGGATTTTTGAAAACATCATGCATTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGG
3402097 TCTTACAG
66 TCTTACAG
3402105 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGG
3402170 TCTTACAG
66 TCTTACAG
* *
3402178 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGG
3402243 TCTTACAG
66 TCTTACAG
* * * *
3402251 ATGACCCTGAGGCTTTAGGATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATAATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGG
3402316 TCTTACAG
66 TCTTACAG
3402324 ATG
1 ATG
3402327 TGGGAAATAA
Statistics
Matches: 279, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 279 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (73 bp):
ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGG
TCTTACAG
Found at i:3403010 original size:22 final size:20
Alignment explanation
Indices: 3402985--3403038 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 20
3402975 AATAAAGCTT
*
3402985 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTG--AAGAAAATCTA
3403007 TCATCTTTG--GAAAATCTA
1 TCATCTTTGAAGAAAATCTA
3403025 TCATCTTTGAAGAA
1 TCATCTTTGAAGAA
3403039 TGTAGATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 17 0.59
20 3 0.10
22 9 0.31
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
TCATCTTTGAAGAAAATCTA
Found at i:3404373 original size:74 final size:75
Alignment explanation
Indices: 3404247--3404414 Score: 230
Period size: 74 Copynumber: 2.3 Consensus size: 75
3404237 TATATGGATC
* * *
3404247 TTCATCATGCCCCATCATTGGCTAATACAAACGTTCAAAATACATCAACATTCTTGATTCTGATT
1 TTCAGCATGCCCCATCATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATTATGATT
*
3404312 GAAA-GGGCT
66 GAAATAGGCT
* * *** *
3404321 TTCAGCATGCCCCAGCATTGGCTAATACAAATGTTCAAAATGTGTTAACATTCCTGATTATGATT
1 TTCAGCATGCCCCATCATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATTATGATT
3404386 GAAATAGGCT
66 GAAATAGGCT
*
3404396 TTCAGCATGCTCCATCATT
1 TTCAGCATGCCCCATCATT
3404415 TGCTTCTTGT
Statistics
Matches: 81, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 60 0.74
75 21 0.26
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (75 bp):
TTCAGCATGCCCCATCATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTGATTATGATT
GAAATAGGCT
Found at i:3407894 original size:11 final size:10
Alignment explanation
Indices: 3407878--3407937 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
3407868 ATTTCTCATC
*
3407878 TTTTCCTTTT
1 TTTTTCTTTT
3407888 TTTTTCCTTTT
1 TTTTT-CTTTT
3407899 TTTTTC-TTT
1 TTTTTCTTTT
*
3407908 TTTTTCTTTG
1 TTTTTCTTTT
3407918 TTTTTCTTTT
1 TTTTTCTTTT
3407928 TGTTTT-TTTT
1 T-TTTTCTTTT
3407938 CTTCTGATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.20
10 21 0.48
11 14 0.32
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:3407898 original size:9 final size:9
Alignment explanation
Indices: 3407885--3407942 Score: 64
Period size: 9 Copynumber: 6.1 Consensus size: 9
3407875 ATCTTTTCCT
3407885 TTTTTTTTCC
1 TTTTTTTT-C
3407895 TTTTTTTTTC
1 -TTTTTTTTC
3407905 TTTTTTTTC
1 TTTTTTTTC
3407914 TTTGTTTTTC
1 TTT-TTTTTC
3407924 TTTTTGTTT-
1 TTTTT-TTTC
*
3407933 TTTTTCTTC
1 TTTTTTTTC
3407942 T
1 T
3407943 GATGAATGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
8 2 0.05
9 20 0.47
10 13 0.30
11 8 0.19
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.84
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:3407908 original size:19 final size:19
Alignment explanation
Indices: 3407886--3407928 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3407876 TCTTTTCCTT
*
3407886 TTTTTTTCCTTTTTTTTTC
1 TTTTTTTCCTTTGTTTTTC
*
3407905 TTTTTTTTCTTTGTTTTTC
1 TTTTTTTCCTTTGTTTTTC
3407924 TTTTT
1 TTTTT
3407929 GTTTTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (19 bp):
TTTTTTTCCTTTGTTTTTC
Found at i:3413400 original size:2 final size:2
Alignment explanation
Indices: 3413393--3413428 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3413383 TCTATTAATT
3413393 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
3413429 AGATATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3413918 original size:16 final size:16
Alignment explanation
Indices: 3413897--3413930 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3413887 TAAAAGTAAT
3413897 AATAAT-ATTGAAAATA
1 AATAATGATT-AAAATA
3413913 AATAATGATTAAAATA
1 AATAATGATTAAAATA
3413929 AA
1 AA
3413931 AGAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AATAATGATTAAAATA
Found at i:3415198 original size:3 final size:3
Alignment explanation
Indices: 3415186--3415242 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
3415176 GTGTAATTAT
* * *
3415186 TAA TAA -AA TAA TAA TAC T-A TTA TAA TAA TAA TAA TAA TAA T-A TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3415231 TAT TAA TAA TAA
1 TAA TAA TAA TAA
3415243 AAAAAATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 5 0.11
3 40 0.89
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3415215 original size:20 final size:20
Alignment explanation
Indices: 3415183--3415242 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
3415173 TTGGTGTAAT
*
3415183 TATTAATAA-AATAATAATAC
1 TATT-ATAATAATAATAATAA
3415203 TATTATAATAATAATAATAA
1 TATTATAATAATAATAATAA
* * *
3415223 TAATATGATATTAATAATAA
1 TATTATAATAATAATAATAA
3415243 AAAAAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TATTATAATAATAATAATAA
Found at i:3415218 original size:23 final size:23
Alignment explanation
Indices: 3415181--3415242 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
3415171 GTTTGGTGTA
*
3415181 ATTATTAATAA-AATAATAATACT
1 ATTA-TAATAATAATAATAATAAT
3415204 ATTATAATAATAATAATAATAAT
1 ATTATAATAATAATAATAATAAT
* *
3415227 ATGATATTAATAATAA
1 ATTATAATAATAATAA
3415243 AAAAAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 6 0.17
23 29 0.83
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
ATTATAATAATAATAATAATAAT
Found at i:3417252 original size:21 final size:21
Alignment explanation
Indices: 3417228--3417271 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3417218 GGTAGTAAAT
3417228 TAGCAAGGTAGAATAAGTAGC
1 TAGCAAGGTAGAATAAGTAGC
* **
3417249 TAGCTAGGTAGTGTAAGTAGC
1 TAGCAAGGTAGAATAAGTAGC
3417270 TA
1 TA
3417272 CTAGATACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.30, T:0.25
Consensus pattern (21 bp):
TAGCAAGGTAGAATAAGTAGC
Found at i:3429589 original size:38 final size:38
Alignment explanation
Indices: 3429533--3429612 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
3429523 TTCATTTGTG
*
3429533 TTATTCATATTTCTAATTCTTTGATGCAATC-TGCCAT
1 TTATTCATATTTCCAATTCTTTGATGCAATCATGCCAT
* * *
3429570 TTATTCGTAATTTCCAATTCTTTGATGTAGTCATGCCAT
1 TTATTCAT-ATTTCCAATTCTTTGATGCAATCATGCCAT
3429609 TTAT
1 TTAT
3429613 ATGTTCCATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 7 0.19
38 20 0.54
39 10 0.27
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (38 bp):
TTATTCATATTTCCAATTCTTTGATGCAATCATGCCAT
Found at i:3435439 original size:30 final size:28
Alignment explanation
Indices: 3435395--3435455 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 28
3435385 AGTTGTTTTT
*
3435395 TTTCTAAAACATGTTAATTGTATGACGA
1 TTTCTAAAACATGTTAATTGTATAACGA
*
3435423 TTTCTAGAAAGCATGTTGATTGTATAACGA
1 TTTCTA-AAA-CATGTTAATTGTATAACGA
3435453 TTT
1 TTT
3435456 TCTCATGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 6 0.21
29 3 0.10
30 20 0.69
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (28 bp):
TTTCTAAAACATGTTAATTGTATAACGA
Found at i:3436447 original size:2 final size:2
Alignment explanation
Indices: 3436406--3436436 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3436396 TATAATCAAA
3436406 AT AT -T 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
3436437 TGTGGATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3441176 original size:5 final size:5
Alignment explanation
Indices: 3441166--3441190 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3441156 ACAAATAGAT
3441166 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
3441191 CAAGAGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3443451 original size:21 final size:20
Alignment explanation
Indices: 3443426--3443506 Score: 57
Period size: 21 Copynumber: 4.2 Consensus size: 20
3443416 AATTGAAAAT
3443426 ATTAAAATTATATAAT-TTTAA
1 ATTAAAA-TA-ATAATATTTAA
*
3443447 GTTAAACATAATAATATTTAA
1 ATTAAA-ATAATAATATTTAA
*
3443468 ATT-AAA-AATAAT-CTTAA
1 ATTAAAATAATAATATTTAA
*
3443485 ATTAATATAACT-AT-TTTAA
1 ATTAAAATAA-TAATATTTAA
3443504 ATT
1 ATT
3443507 TTTAAATATA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
17 7 0.14
18 8 0.16
19 12 0.24
20 8 0.16
21 14 0.28
22 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (20 bp):
ATTAAAATAATAATATTTAA
Found at i:3445227 original size:31 final size:28
Alignment explanation
Indices: 3445186--3445266 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 28
3445176 AGTTGGATTT
* *
3445186 AAATTGATATTTTATCTAAACTTCAGAGGTC
1 AAATTAATATTTTATCTAAAC-T-ACA-GTC
3445217 AAATTAATATTTTATCTGAAAACTACAGTC
1 AAATTAATATTTTATCT--AAACTACAGTC
*
3445247 AAATTAATATTCTATCTAAA
1 AAATTAATATTTTATCTAAA
3445267 ATTTAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
28 3 0.07
30 19 0.42
31 18 0.40
32 1 0.02
33 4 0.09
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (28 bp):
AAATTAATATTTTATCTAAACTACAGTC
Found at i:3450105 original size:19 final size:19
Alignment explanation
Indices: 3450064--3450106 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3450054 GAATAATTTT
* *
3450064 ATTTT-TATTATATAATTA
1 ATTTTATATTATAAAAATA
3450082 ATTTTATATTATAAAAATA
1 ATTTTATATTATAAAAATA
*
3450101 TTTTTA
1 ATTTTA
3450107 AATATATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTATATTATAAAAATA
Found at i:3456888 original size:20 final size:20
Alignment explanation
Indices: 3456865--3456903 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3456855 CGATACTGAA
*
3456865 GTGGTAGTATCGGTACCATG
1 GTGGAAGTATCGGTACCATG
3456885 GTGGAAGTATCGGTACCAT
1 GTGGAAGTATCGGTACCAT
3456904 TTTTACAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.28
Consensus pattern (20 bp):
GTGGAAGTATCGGTACCATG
Found at i:3457736 original size:21 final size:21
Alignment explanation
Indices: 3457710--3457895 Score: 113
Period size: 21 Copynumber: 8.7 Consensus size: 21
3457700 GGTTCTACGC
*
3457710 GGTCCTTCGGGACATATATGT
1 GGTCATTCGGGACATATATGT
* * * *
3457731 GGTCCTTTGGAACATATATGC
1 GGTCATTCGGGACATATATGT
* * * * *
3457752 GATCCTTCGGTATATATATTT
1 GGTCATTCGGGACATATATGT
* ** * *
3457773 GTTCATTTAGAACATATATGC
1 GGTCATTCGGGACATATATGT
* *
3457794 GGTCATTAGGGACAATTCTATGT
1 GGTCATTCGGGAC-A-TATATGT
* * *
3457817 GGTCATTCGAGATATTTATGT
1 GGTCATTCGGGACATATATGT
*
3457838 GGTCATTTGGGACATA-ATGT
1 GGTCATTCGGGACATATATGT
* *
3457858 GGTCATTCGGGACATTTCTACGT
1 GGTCATTCGGGACA--TATATGT
*
3457881 GGTCTTTCGGGACAT
1 GGTCATTCGGGACAT
3457896 TTTATATGGT
Statistics
Matches: 125, Mismatches: 35, Indels: 10
0.74 0.21 0.06
Matches are distributed among these distances:
20 17 0.14
21 74 0.59
22 3 0.02
23 31 0.25
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (21 bp):
GGTCATTCGGGACATATATGT
Found at i:3457820 original size:23 final size:22
Alignment explanation
Indices: 3457789--3457905 Score: 96
Period size: 23 Copynumber: 5.4 Consensus size: 22
3457779 TTAGAACATA
* *
3457789 TATGCGGTCATTAGGGACAATT
1 TATGTGGTCATTCGGGACAATT
* *
3457811 CTATGTGGTCATTCGAGA-TATT
1 -TATGTGGTCATTCGGGACAATT
*
3457833 TATGTGGTCATTTGGGAC-A-T
1 TATGTGGTCATTCGGGACAATT
* *
3457853 AATGTGGTCATTCGGGACATTT
1 TATGTGGTCATTCGGGACAATT
* * *
3457875 CTACGTGGTCTTTCGGGACATTT
1 -TATGTGGTCATTCGGGACAATT
*
3457898 TATATGGT
1 TATGTGGT
3457906 ACTTAGTGCA
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
20 17 0.22
21 16 0.21
22 10 0.13
23 33 0.43
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.38
Consensus pattern (22 bp):
TATGTGGTCATTCGGGACAATT
Found at i:3457859 original size:20 final size:20
Alignment explanation
Indices: 3457813--3457872 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
3457803 GGACAATTCT
* * *
3457813 ATGTGGTCATTCGAGATATTT
1 ATGTGGTCATTCGGGACA-TA
*
3457834 ATGTGGTCATTTGGGACATA
1 ATGTGGTCATTCGGGACATA
3457854 ATGTGGTCATTCGGGACAT
1 ATGTGGTCATTCGGGACAT
3457873 TTCTACGTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (20 bp):
ATGTGGTCATTCGGGACATA
Found at i:3457895 original size:43 final size:41
Alignment explanation
Indices: 3457813--3457895 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
3457803 GGACAATTCT
* *
3457813 ATGTGGTCATTCGAGATATTTATGTGGTCATTTGGGACATA
1 ATGTGGTCATTCGAGACATTTACGTGGTCATTTGGGACATA
*
3457854 ATGTGGTCATTCGGGACATTTCTACGTGGTC-TTTCGGGACAT
1 ATGTGGTCATTCGAGACA-TT-TACGTGGTCATTT-GGGACAT
3457896 TTTATATGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 16 0.44
42 5 0.14
43 15 0.42
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.37
Consensus pattern (41 bp):
ATGTGGTCATTCGAGACATTTACGTGGTCATTTGGGACATA
Found at i:3458131 original size:23 final size:23
Alignment explanation
Indices: 3458104--3458163 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
3458094 CAGGTAAGAG
* *
3458104 ATGAAAGTATGTGATTGTATGAT
1 ATGAAAGTATGTAAATGTATGAT
* *
3458127 ATGAAAGTATGTAAATGTGTGTT
1 ATGAAAGTATGTAAATGTATGAT
3458150 ATGAAAGTATGTAA
1 ATGAAAGTATGTAA
3458164 CTTTATGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.37
Consensus pattern (23 bp):
ATGAAAGTATGTAAATGTATGAT
Found at i:3458172 original size:23 final size:22
Alignment explanation
Indices: 3458104--3458172 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
3458094 CAGGTAAGAG
* *
3458104 ATGAAAGTATGTGATTGTATGAT
1 ATGAAAGTATGTAATT-TATGTT
* *
3458127 ATGAAAGTATGTAAATGTGTGTT
1 ATGAAAGTATGT-AATTTATGTT
3458150 ATGAAAGTATGTAACTTTATGTT
1 ATGAAAGTATGTAA-TTTATGTT
3458173 TCCTTAGTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 2 0.05
23 34 0.89
24 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (22 bp):
ATGAAAGTATGTAATTTATGTT
Found at i:3464412 original size:42 final size:42
Alignment explanation
Indices: 3464352--3464442 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
3464342 GGTTCTACGC
* *
3464352 GGTCCTTCGGGACATATATATGGTCATTTGGAACATATATGT
1 GGTCCTTCGAGACATATATATGGTCATTTAGAACATATATGT
* * * *
3464394 TGTCCTTCGAGATATATATTTGGTCCTTTAGAACATATATGT
1 GGTCCTTCGAGACATATATATGGTCATTTAGAACATATATGT
3464436 GGTCCTT
1 GGTCCTT
3464443 AGGGACAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (42 bp):
GGTCCTTCGAGACATATATATGGTCATTTAGAACATATATGT
Found at i:3464431 original size:21 final size:21
Alignment explanation
Indices: 3464363--3464442 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
3464353 GTCCTTCGGG
* * *
3464363 ACATATATATGGTCATTTGGA
1 ACATATATTTGGTCCTTTAGA
*
3464384 ACATATATGTT-GTCC-TTCGA
1 ACATATAT-TTGGTCCTTTAGA
*
3464404 GATATATATTTGGTCCTTTAGA
1 -ACATATATTTGGTCCTTTAGA
*
3464426 ACATATATGTGGTCCTT
1 ACATATATTTGGTCCTT
3464443 AGGGACAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
20 6 0.12
21 37 0.77
22 5 0.10
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (21 bp):
ACATATATTTGGTCCTTTAGA
Found at i:3488598 original size:42 final size:44
Alignment explanation
Indices: 3488552--3488636 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
3488542 ATCACAATTC
*
3488552 TATGTGGTCCTTAGAGACA-TT-TATGTGGTCCTTCAGGACATA
1 TATGTGGTCCTTAGAGACATTTCTAGGTGGTCCTTCAGGACATA
* * *
3488594 TATGTGGTCCTTCGGGACATTTCTAGGTGGTCCTTCGGGACAT
1 TATGTGGTCCTTAGAGACATTTCTAGGTGGTCCTTCAGGACAT
3488637 TTTTTATGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 17 0.46
43 2 0.05
44 18 0.49
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (44 bp):
TATGTGGTCCTTAGAGACATTTCTAGGTGGTCCTTCAGGACATA
Found at i:3488638 original size:23 final size:22
Alignment explanation
Indices: 3488548--3488637 Score: 112
Period size: 21 Copynumber: 4.1 Consensus size: 22
3488538 AGCGATCACA
* *
3488548 ATTCTATGTGGTCCTTAGAGAC
1 ATTCTATGTGGTCCTTCGGGAC
*
3488570 ATT-TATGTGGTCCTTCAGGAC
1 ATTCTATGTGGTCCTTCGGGAC
*
3488591 A-TATATGTGGTCCTTCGGGAC
1 ATTCTATGTGGTCCTTCGGGAC
*
3488612 ATTTCTAGGTGGTCCTTCGGGAC
1 A-TTCTATGTGGTCCTTCGGGAC
3488635 ATT
1 ATT
3488638 TTTTATGGCA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.02
21 34 0.58
22 5 0.08
23 19 0.32
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (22 bp):
ATTCTATGTGGTCCTTCGGGAC
Found at i:3488918 original size:23 final size:23
Alignment explanation
Indices: 3488853--3488918 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
3488843 GTAAGAGATT
* * *
3488853 AAAGTATGTGATTGTATGATATG
1 AAAGTATGTAAATGTATGTTATG
*
3488876 AAAGTATGTAAATGTGTGTTATG
1 AAAGTATGTAAATGTATGTTATG
*
3488899 AAAGTATGTAACTGTATGTT
1 AAAGTATGTAAATGTATGTT
3488919 TCCTTAGTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (23 bp):
AAAGTATGTAAATGTATGTTATG
Found at i:3489501 original size:22 final size:22
Alignment explanation
Indices: 3489476--3489517 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3489466 TCTAAAGAAA
*
3489476 AATTTAAAGCTATTTAAAATAG
1 AATTAAAAGCTATTTAAAATAG
*
3489498 AATTAAAAGGTATTTAAAAT
1 AATTAAAAGCTATTTAAAAT
3489518 GAGTTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (22 bp):
AATTAAAAGCTATTTAAAATAG
Found at i:3491370 original size:22 final size:21
Alignment explanation
Indices: 3491336--3491376 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3491326 ATAATTATTT
3491336 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
3491357 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
3491377 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:3492707 original size:37 final size:37
Alignment explanation
Indices: 3492628--3492708 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
3492618 GTAACTAAAT
* * *
3492628 AACCGACTGGTTAAACCATTAGGATGATAAATCCAAT
1 AACCGACTAGTTAAACCATTAAGATGATAAATCCAAC
* *
3492665 TACCGACTAGTTTAACC-TCTAAGATGATAAATCCAAC
1 AACCGACTAGTTAAACCAT-TAAGATGATAAATCCAAC
3492702 AACCGAC
1 AACCGAC
3492709 CGGTTCATCC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (37 bp):
AACCGACTAGTTAAACCATTAAGATGATAAATCCAAC
Found at i:3496112 original size:11 final size:11
Alignment explanation
Indices: 3496096--3496123 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3496086 TTACATTTTT
3496096 TATTATTTTAA
1 TATTATTTTAA
3496107 TATTATTTTAA
1 TATTATTTTAA
3496118 TATTAT
1 TATTAT
3496124 CTATGTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATTTTAA
Found at i:3496163 original size:23 final size:23
Alignment explanation
Indices: 3496137--3496184 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3496127 TGTAGTTTTA
3496137 TTATATAAATATAT-TATTATAGT
1 TTATATAAATATATATATTAT-GT
*
3496160 TTATATATATATATATATTATGT
1 TTATATAAATATATATATTATGT
3496183 TT
1 TT
3496185 TGAAAACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTATATAAATATATATATTATGT
Found at i:3496258 original size:2 final size:2
Alignment explanation
Indices: 3496253--3496283 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3496243 ATAGTTTTCA
3496253 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3496284 TTTTTAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3496275 original size:56 final size:54
Alignment explanation
Indices: 3496205--3496325 Score: 136
Period size: 58 Copynumber: 2.2 Consensus size: 54
3496195 TAATTTTGAA
* * *
3496205 ATATACATATATATAAAATATTTTTAAAGAATATATGTATAGTTTTCAATATATATAT
1 ATATATATATATATATAATATTTTTAAA-AACATATGTA-A-TTTTCAA-ATATATAT
* * * *
3496263 ATATATATATATATATTATATTTTTTAAAACATATGTAATTTTGAAATATGTAT
1 ATATATATATATATATAATATTTTTAAAAACATATGTAATTTTCAAATATATAT
3496317 AT-TATATAT
1 ATATATATAT
3496326 TTTAAATTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
53 7 0.12
54 9 0.16
55 6 0.11
56 1 0.02
57 9 0.16
58 24 0.43
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (54 bp):
ATATATATATATATATAATATTTTTAAAAACATATGTAATTTTCAAATATATAT
Found at i:3496327 original size:23 final size:24
Alignment explanation
Indices: 3496301--3496349 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
3496291 AACATATGTA
*
3496301 ATTTTGAAA-TATGTATAT-TATAT
1 ATTTT-AAATTATATATATATATAT
3496324 ATTTTAAATTATATATATATATAT
1 ATTTTAAATTATATATATATATAT
3496348 AT
1 AT
3496350 ATATAGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 3 0.13
23 13 0.57
24 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTTTAAATTATATATATATATAT
Found at i:3496360 original size:31 final size:31
Alignment explanation
Indices: 3496309--3496382 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 31
3496299 TAATTTTGAA
* **
3496309 ATATGTATAT-TATATATTTTA-AATTATAT
1 ATATATATATATATATATTTTAGAAAAATAT
3496338 ATATATATATATATATAGTTTTATGAAAAATAT
1 ATATATATATATATATA-TTTTA-GAAAAATAT
3496371 ATA-ATATATATA
1 ATATATATATATA
3496383 GCTTAAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 9 0.24
30 6 0.16
31 5 0.13
32 9 0.24
33 9 0.24
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (31 bp):
ATATATATATATATATATTTTAGAAAAATAT
Found at i:3496422 original size:18 final size:16
Alignment explanation
Indices: 3496399--3496443 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
3496389 AAGAATTTAT
3496399 TTATTTATTATTACACTA
1 TTATTTATTATTA-A-TA
3496417 TTATTTATTATTAATA
1 TTATTTATTATTAATA
3496433 TTA-TTATTATT
1 TTATTTATTATT
3496444 GTATTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 1 0.04
18 13 0.48
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTTATTATTAATA
Found at i:3497861 original size:15 final size:15
Alignment explanation
Indices: 3497791--3497861 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 15
3497781 TTTTGAAACA
*
3497791 TTTTTTATTATTTAAT
1 TTTTTTACTA-TTAAT
3497807 TTTTATTATCTACTTAAT
1 TTTT-TTA-CTA-TTAAT
**
3497825 TTTTTTACTATTTCT
1 TTTTTTACTATTAAT
3497840 TTTTTTAC-ATTAAT
1 TTTTTTACTATTAAT
3497854 TTTATTTA
1 TTT-TTTA
3497862 TTTATTTTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
14 7 0.15
15 15 0.33
16 7 0.15
17 6 0.13
18 11 0.24
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTACTATTAAT
Found at i:3500175 original size:84 final size:83
Alignment explanation
Indices: 3500038--3500192 Score: 283
Period size: 84 Copynumber: 1.9 Consensus size: 83
3500028 TTTCCTTTCA
*
3500038 CACTAATTAGTATTAACCAATCACTCAAAATATAGAAACTTTCATTCTCAAATAAAAATAAAAAA
1 CACTAATTAGTATTAACCAATCACTCAAAATATAGAAACTTTCATTCACAAATAAAAAT-AAAAA
3500103 GTTAAATGTATAACACTAT
65 GTTAAATGTATAACACTAT
*
3500122 CACTAATTAGTATTAACCAATCACTCAAAATATAGAAACTTTCTTTCACAAATAAAAATAAAAAG
1 CACTAATTAGTATTAACCAATCACTCAAAATATAGAAACTTTCATTCACAAATAAAAATAAAAAG
3500187 TTAAAT
66 TTAAAT
3500193 ACATATTATT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 12 0.17
84 57 0.83
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (83 bp):
CACTAATTAGTATTAACCAATCACTCAAAATATAGAAACTTTCATTCACAAATAAAAATAAAAAG
TTAAATGTATAACACTAT
Found at i:3502304 original size:29 final size:29
Alignment explanation
Indices: 3502190--3502294 Score: 192
Period size: 29 Copynumber: 3.6 Consensus size: 29
3502180 CAAGTTAACT
3502190 ACTAACTTTAATTTTATTACATATTAATC
1 ACTAACTTTAATTTTATTACATATTAATC
3502219 ACTAACTTTAATTTTATTACATATTAATC
1 ACTAACTTTAATTTTATTACATATTAATC
*
3502248 ACTAACTTTTATTTTATTACATATTAATC
1 ACTAACTTTAATTTTATTACATATTAATC
*
3502277 ACTAACTTTTATTTTATT
1 ACTAACTTTAATTTTATT
3502295 GCATTCTAAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.51
Consensus pattern (29 bp):
ACTAACTTTAATTTTATTACATATTAATC
Found at i:3502823 original size:2 final size:2
Alignment explanation
Indices: 3502816--3502875 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
3502806 AGTCCCATGA
3502816 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
3502858 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
3502876 GCATATTTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3507885 original size:20 final size:20
Alignment explanation
Indices: 3507862--3507900 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3507852 TTCCCATTTT
*
3507862 TGCATCTTTGCATTTGCATG
1 TGCATCTTTGCATTAGCATG
3507882 TGCATCTTTGCATTAGCAT
1 TGCATCTTTGCATTAGCAT
3507901 CTATACATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (20 bp):
TGCATCTTTGCATTAGCATG
Found at i:3508975 original size:2 final size:2
Alignment explanation
Indices: 3508968--3509010 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3508958 ATTTATCCTT
*
3508968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT 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
3509010 T
1 T
3509011 CCCTTGTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3509303 original size:22 final size:22
Alignment explanation
Indices: 3509278--3509322 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3509268 AGAGAAAAAT
* *
3509278 AAGAGATATAAAAGAAAAGAAA
1 AAGAGAGAGAAAAGAAAAGAAA
*
3509300 AAGAGAGAGAAAAGAAAGGAAA
1 AAGAGAGAGAAAAGAAAAGAAA
3509322 A
1 A
3509323 CAAAAAGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.04
Consensus pattern (22 bp):
AAGAGAGAGAAAAGAAAAGAAA
Found at i:3518184 original size:12 final size:12
Alignment explanation
Indices: 3518169--3518193 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3518159 ACAAAGTATT
3518169 TCGAACCAAAAA
1 TCGAACCAAAAA
3518181 TCGAACCAAAAA
1 TCGAACCAAAAA
3518193 T
1 T
3518194 TAAATTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.24, G:0.08, T:0.12
Consensus pattern (12 bp):
TCGAACCAAAAA
Found at i:3522251 original size:2 final size:2
Alignment explanation
Indices: 3522244--3522269 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3522234 AATCCTATGC
3522244 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
3522270 TGAAAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3527711 original size:2 final size:2
Alignment explanation
Indices: 3527704--3527754 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
3527694 AATCTTATGC
*
3527704 AT AT AT AT AT AT GT 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
3527746 AT AT AT AT A
1 AT AT AT AT A
3527755 AAAGTACACA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3528179 original size:2 final size:2
Alignment explanation
Indices: 3528172--3528206 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3528162 AAAATACCTT
3528172 TA TA 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 T
3528207 TAATGTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3529155 original size:75 final size:75
Alignment explanation
Indices: 3529066--3529229 Score: 206
Period size: 76 Copynumber: 2.2 Consensus size: 75
3529056 TAAACTCAAG
*
3529066 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTT-GTATTTTAGTTTAAATAGGTTTTAGTA
1 TTTAGGATATTATTTT-AACATTATATCTTTAT-TTTAGTATTTTAGTTTAAATAGGTTTTAGTA
*
3529129 TTTTAATTAAGT
64 TTTTAATTAAGA
* * * * *
3529141 TTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTAT
1 TTTAGGATATTATTTTAACATTATATCTTTATTTTA-GTATTTTAGTTTAAATAGGTTTTAGTAT
*
3529206 TTTAATTAGGA
65 TTTAATTAAGA
*
3529217 TTTAGAATATTAT
1 TTTAGGATATTAT
3529230 ATTATTTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
74 10 0.13
75 19 0.25
76 48 0.62
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.57
Consensus pattern (75 bp):
TTTAGGATATTATTTTAACATTATATCTTTATTTTAGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGA
Found at i:3529304 original size:20 final size:19
Alignment explanation
Indices: 3529252--3529295 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
3529242 GGTATTTTAG
*
3529252 TTTAAATAGTTTTAAGTGT
1 TTTAATTAGTTTTAAGTGT
3529271 TTTAATTAGATTTTAAGATGT
1 TTTAATTAG-TTTTAAG-TGT
3529292 TTTA
1 TTTA
3529296 GCTTGTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 7 0.32
21 7 0.32
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (19 bp):
TTTAATTAGTTTTAAGTGT
Found at i:3529919 original size:19 final size:19
Alignment explanation
Indices: 3529856--3529923 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 19
3529846 TAAGTTTTCC
*
3529856 TTTATCTTAATCTCTTTAATTT
1 TTTAT-TTAAT-TATTTAA-TT
*
3529878 GTTTATTTAATTATTT-TTCT
1 -TTTATTTAATTATTTAAT-T
3529898 TTTATTTAATTATTTAATT
1 TTTATTTAATTATTTAATT
3529917 TTTATTT
1 TTTATTT
3529924 TAAAAAAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 24 0.60
20 2 0.05
21 4 0.10
22 5 0.12
23 5 0.12
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.69
Consensus pattern (19 bp):
TTTATTTAATTATTTAATT
Found at i:3537926 original size:4 final size:4
Alignment explanation
Indices: 3537917--3537965 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
3537907 AATATCTTTA
*
3537917 ATTT ATTT ATTT AATT ATTT -TTCT -TTT ATTT ATTT -TTT ATTT -TTT
1 ATTT ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT
3537962 ATTT
1 ATTT
3537966 TAAAAATAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 9 0.23
4 30 0.77
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (4 bp):
ATTT
Found at i:3537944 original size:23 final size:22
Alignment explanation
Indices: 3537918--3537960 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3537908 ATATCTTTAA
3537918 TTTATTTATTTAATTATTTTTCT
1 TTTATTTATTT-ATTATTTTTCT
*
3537941 TTTATTTATTTTTTATTTTT
1 TTTATTTATTTATTATTTTT
3537961 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTATTTATTTATTATTTTTCT
Found at i:3537949 original size:15 final size:15
Alignment explanation
Indices: 3537917--3537966 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
3537907 AATATCTTTA
*
3537917 ATTTATTTATTTAATT
1 ATTT-TTTATTTATTT
3537933 ATTTTTCT-TTTATTT
1 ATTTTT-TATTTATTT
3537948 ATTTTTTATTT-TTT
1 ATTTTTTATTTATTT
3537962 ATTTT
1 ATTTT
3537967 AAAAATAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 9 0.29
15 17 0.55
16 5 0.16
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (15 bp):
ATTTTTTATTTATTT
Found at i:3537961 original size:23 final size:23
Alignment explanation
Indices: 3537913--3537967 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3537903 TCTCAATATC
*
3537913 TTTAATTTATTTATTTAATTATT
1 TTTATTTTATTTATTTAATTATT
* *
3537936 TTTCTTTTATTTATTT-TTTATTT
1 TTTATTTTATTTATTTAATTA-TT
3537959 TTTATTTTA
1 TTTATTTTA
3537968 AAAATAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTATTTTATTTATTTAATTATT
Found at i:3537963 original size:18 final size:20
Alignment explanation
Indices: 3537917--3537965 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
3537907 AATATCTTTA
3537917 ATTTATTTATTTAATTATTTT
1 ATTT-TTTATTTAATTATTTT
*
3537938 -TCTTTTATTT-ATT-TTTT
1 ATTTTTTATTTAATTATTTT
3537955 ATTTTTTATTT
1 ATTTTTTATTT
3537966 TAAAAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.16
18 12 0.48
19 7 0.28
20 2 0.08
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (20 bp):
ATTTTTTATTTAATTATTTT
Found at i:3538033 original size:14 final size:14
Alignment explanation
Indices: 3537993--3538043 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
3537983 AATCCTCTTT
*
3537993 TTATATTTATTACTA
1 TTATTTTTATTA-TA
3538008 TTAATTTATTATTATA
1 TT-ATTT-TTATTATA
3538024 TTATTTTTATT-TA
1 TTATTTTTATTATA
3538037 TTTATTT
1 -TTATTT
3538044 ATTTATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 2 0.06
14 11 0.34
15 6 0.19
16 7 0.22
17 6 0.19
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTTTATTATA
Done.