Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 25
Found at i:1167059 original size:9 final size:9
Alignment explanation
Indices: 1167045--1167073 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1167035 TTGCTTCATA
1167045 ATTAGGAAG
1 ATTAGGAAG
1167054 ATTAGGAAG
1 ATTAGGAAG
1167063 ATTAGGAAG
1 ATTAGGAAG
1167072 AT
1 AT
1167074 CAATTCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (9 bp):
ATTAGGAAG
Found at i:1167533 original size:107 final size:107
Alignment explanation
Indices: 1167348--1167660 Score: 426
Period size: 107 Copynumber: 3.0 Consensus size: 107
1167338 GGTTGAGACG
1167348 GAAGAAGAAGAAGAAGAAAGATTAAAAAAAACAAAAACAAAAACCAAAAACCTAAGCTGAAGGCG
1 GAAGAAGAAGAAGAAG-AAGATTAAAAAAAACAAAAACAAAAACCAAAAACCTAAGCTGAAGGCG
*
1167413 TGAAGGAAGCTGTTGGTAGAAACCCTTAAAGCTGTTAGTTTAA
65 TGAAGGAAGCTGTTGGTAGAAACCCTAAAAGCTGTTAGTTTAA
** *
1167456 GAAGAAGAAGAAGAAGAAGATTAAAAAACCCAAAACCAAAAACCAAAAACCTAAGCTGAAGGCGT
1 GAAGAAGAAGAAGAAGAAGATTAAAAAAAACAAAAACAAAAACCAAAAACCTAAGCTGAAGGCGT
*
1167521 GAAGGATGCTGTTGGTAGAAACCCTAAAAGCTGTTAGTTTAA
66 GAAGGAAGCTGTTGGTAGAAACCCTAAAAGCTGTTAGTTTAA
* * * * ** * *
1167563 GAAGAAGAAGAAGAAGAAG------AAGAAGAAGAAGATTAA--AAGAACATAAGCTGAAGGCGT
1 GAAGAAGAAGAAGAAGAAGATTAAAAAAAACAAAAACAAAAACCAAAAACCTAAGCTGAAGGCGT
* *
1167620 GAAGGAAGCTGTTGGTAGAAACCCTAATAGCTGTGAGTTTA
66 GAAGGAAGCTGTTGGTAGAAACCCTAAAAGCTGTTAGTTTA
1167661 TATAGACAGA
Statistics
Matches: 186, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
99 57 0.31
101 8 0.04
107 105 0.56
108 16 0.09
ACGTcount: A:0.48, C:0.12, G:0.24, T:0.16
Consensus pattern (107 bp):
GAAGAAGAAGAAGAAGAAGATTAAAAAAAACAAAAACAAAAACCAAAAACCTAAGCTGAAGGCGT
GAAGGAAGCTGTTGGTAGAAACCCTAAAAGCTGTTAGTTTAA
Found at i:1167569 original size:3 final size:3
Alignment explanation
Indices: 1167561--1167594 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1167551 CTGTTAGTTT
1167561 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1167595 TTAAAAGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1167995 original size:15 final size:15
Alignment explanation
Indices: 1167969--1168021 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
1167959 TATTTTTGTA
1167969 TTTTAAATAAATTATT
1 TTTTAAA-AAATTATT
1167985 TTTTAAAAAA-TATT
1 TTTTAAAAAATTATT
*
1167999 TTATTAAAATATTATT
1 TT-TTAAAAAATTATT
1168015 ATTTTAA
1 -TTTTAA
1168022 TCATGTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.18
15 10 0.30
16 15 0.45
17 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTAAAAAATTATT
Found at i:1168277 original size:14 final size:15
Alignment explanation
Indices: 1168258--1168314 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 15
1168248 ATATATATTC
1168258 TTATTA-ATTTTTAA
1 TTATTATATTTTTAA
* *
1168272 TTATTATAATGTT-A
1 TTATTATATTTTTAA
1168286 TTATTAT-TTTTT-A
1 TTATTATATTTTTAA
1168299 TTAATTATATTTTTAA
1 TT-ATTATATTTTTAA
1168315 AAAATATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 6 0.17
14 19 0.54
15 9 0.26
16 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATTATATTTTTAA
Found at i:1168385 original size:25 final size:24
Alignment explanation
Indices: 1168353--1168409 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
1168343 TTTATTAAAC
*
1168353 TTATATTCTTAATAATTTATAATG
1 TTATATTCCTAATAATTTATAATG
* * *
1168377 TTATAATTCCTATTAATTTTTAATTA
1 TTAT-ATTCCTAATAATTTATAA-TG
1168403 TTATATT
1 TTATATT
1168410 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (24 bp):
TTATATTCCTAATAATTTATAATG
Found at i:1169591 original size:13 final size:14
Alignment explanation
Indices: 1169567--1169604 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
1169557 CGATCTATAA
1169567 AATAATAATATTTT
1 AATAATAATATTTT
1169581 AATAA-AATATTTT
1 AATAATAATATTTT
1169594 AA-AATAATATT
1 AATAATAATATT
1169605 ATTTCGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 16 0.70
14 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:1169614 original size:29 final size:29
Alignment explanation
Indices: 1169564--1169621 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1169554 CTCCGATCTA
*
1169564 TAAAATAATAATATTTTAATAAAATATTT
1 TAAAATAATAATATTTCAATAAAATATTT
* * *
1169593 TAAAATAATATTATTTCGATAATATATTT
1 TAAAATAATAATATTTCAATAAAATATTT
1169622 AAGAATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (29 bp):
TAAAATAATAATATTTCAATAAAATATTT
Found at i:1171983 original size:17 final size:18
Alignment explanation
Indices: 1171961--1171994 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1171951 TGGTATGTCC
1171961 TTTCTTTT-TTTTTTTCT
1 TTTCTTTTCTTTTTTTCT
1171978 TTTCTTTTCTTTTTTTC
1 TTTCTTTTCTTTTTTTC
1171995 CCTTAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTCTTTTCTTTTTTTCT
Found at i:1174388 original size:8 final size:8
Alignment explanation
Indices: 1174375--1174400 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1174365 AAAATCTAAA
1174375 TTAAAAAT
1 TTAAAAAT
1174383 TTAAAAAT
1 TTAAAAAT
1174391 TTAAAAAT
1 TTAAAAAT
1174399 TT
1 TT
1174401 TAAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTAAAAAT
Found at i:1174513 original size:23 final size:23
Alignment explanation
Indices: 1174478--1174531 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
1174468 ATTAATATAA
1174478 AAAAATTTTATTT-AGATATAAATT
1 AAAAA-TTTATTTAAG-TATAAATT
*
1174502 ATAAATTTATTTAAGTATAAATT
1 AAAAATTTATTTAAGTATAAATT
1174525 AAAAATT
1 AAAAATT
1174532 ACAAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
AAAAATTTATTTAAGTATAAATT
Found at i:1174538 original size:30 final size:30
Alignment explanation
Indices: 1174497--1174562 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
1174487 ATTTAGATAT
* * * *
1174497 AAATTATAAATTTATTTAAGTATAAATTAA
1 AAATTACAAATTTATCTAAATAAAAATTAA
1174527 AAATTACAAATTTATCTAAATAAAAATTAA
1 AAATTACAAATTTATCTAAATAAAAATTAA
1174557 AAATTA
1 AAATTA
1174563 TTTTATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (30 bp):
AAATTACAAATTTATCTAAATAAAAATTAA
Found at i:1174550 original size:23 final size:22
Alignment explanation
Indices: 1174519--1174613 Score: 82
Period size: 23 Copynumber: 3.9 Consensus size: 22
1174509 TATTTAAGTA
1174519 TAAATTAAAAATTACAAATTTATC
1 TAAA-TAAAAATTA-AAATTTATC
* *
1174543 TAAATAAAAATTAAAAATTATTT
1 TAAATAAAAATTAAAATTTA-TC
*
1174566 TATATAATAAAATATATAAATTTATC
1 TAAAT-A-AAAAT-TA-AAATTTATC
1174592 TAAATAAAAAAATTAAAATTTA
1 TAAAT--AAAAATTAAAATTTA
1174614 ATAATTCTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
22 6 0.10
23 14 0.24
24 12 0.20
25 7 0.12
26 12 0.20
27 8 0.14
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATAAAAATTAAAATTTATC
Found at i:1174565 original size:26 final size:24
Alignment explanation
Indices: 1174519--1174613 Score: 79
Period size: 24 Copynumber: 3.9 Consensus size: 24
1174509 TATTTAAGTA
*
1174519 TAAATTAAAAAT-TACAAATTTATC
1 TAAA-TAAAAATATAAAAATTTATC
*
1174543 TAAATAAAAAT-TAAAAA-TTATTT
1 TAAATAAAAATATAAAAATTTA-TC
* *
1174566 TATATAATAAAATATATAAATTTATC
1 TAAAT-A-AAAATATAAAAATTTATC
* *
1174592 TAAATAAAAAAATTAAAATTTA
1 TAAATAAAAATATAAAAATTTA
1174614 ATAATTCTCT
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
22 3 0.05
23 17 0.30
24 18 0.32
25 6 0.11
26 10 0.18
27 3 0.05
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAATAAAAATATAAAAATTTATC
Found at i:1174577 original size:49 final size:53
Alignment explanation
Indices: 1174497--1174601 Score: 139
Period size: 49 Copynumber: 2.1 Consensus size: 53
1174487 ATTTAGATAT
*
1174497 AAATTATAAATTTATTTAAGTATAAATTAAAA-ATTACAAATTTATCTAAATAA
1 AAATTATAAAATTATTTAAGTATAAATTAAAATA-TACAAATTTATCTAAATAA
* *
1174550 AAATTA-AAAATTATTTTA-TAT-AA-TAAAATATATAAATTTATCTAAATAA
1 AAATTATAAAATTATTTAAGTATAAATTAAAATATACAAATTTATCTAAATAA
1174599 AAA
1 AAA
1174602 AATTAAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
49 26 0.54
50 3 0.06
51 3 0.06
52 10 0.21
53 6 0.12
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (53 bp):
AAATTATAAAATTATTTAAGTATAAATTAAAATATACAAATTTATCTAAATAA
Found at i:1174726 original size:23 final size:22
Alignment explanation
Indices: 1174700--1174754 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
1174690 ACTTATTGTA
1174700 TAATTTAAAAATAATTGTTATA-T
1 TAATTTAAAAAT-ATT-TTATATT
* *
1174723 TAATATAAATATATTTTATATT
1 TAATTTAAAAATATTTTATATT
1174745 TAAATTTAAA
1 T-AATTTAAA
1174755 TAAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 5 0.19
23 17 0.63
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAATTTAAAAATATTTTATATT
Found at i:1174774 original size:16 final size:14
Alignment explanation
Indices: 1174745--1174801 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
1174735 ATTTTATATT
1174745 TAAATTTAAATAAA
1 TAAATTTAAATAAA
1174759 TAAATTTATTAATAAA
1 TAAATTTA--AATAAA
1174775 TAATAATTTAAATTAAA
1 T-A-AATTTAAA-TAAA
1174792 -AAATTTAAAT
1 TAAATTTAAAT
1174802 TAACATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
13 1 0.03
14 16 0.42
15 1 0.03
16 9 0.24
17 5 0.13
18 6 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATTTAAATAAA
Found at i:1174825 original size:16 final size:16
Alignment explanation
Indices: 1174806--1174836 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1174796 TTAAATTAAC
1174806 ATAATTTTATAAAAAA
1 ATAATTTTATAAAAAA
*
1174822 ATAATTTTTTAAAAA
1 ATAATTTTATAAAAA
1174837 TTTGATTGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATTTTATAAAAAA
Found at i:1175627 original size:6 final size:6
Alignment explanation
Indices: 1175609--1175679 Score: 72
Period size: 6 Copynumber: 11.8 Consensus size: 6
1175599 CCAACACTTT
* * * *
1175609 CAGCAA CAACAA CATCAA CAGCAA CAGCAA CAACAA CATCAA CAGCAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
* *
1175657 CCA-CTA CATCAA CAGCAA CAGCA
1 -CAGCAA CAGCAA CAGCAA CAGCA
1175680 GTGGCTCAGA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
5 2 0.04
6 50 0.93
7 2 0.04
ACGTcount: A:0.51, C:0.35, G:0.08, T:0.06
Consensus pattern (6 bp):
CAGCAA
Found at i:1175630 original size:18 final size:18
Alignment explanation
Indices: 1175612--1175676 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
1175602 ACACTTTCAG
* * *
1175612 CAACAACAACATCAACAG
1 CAACAGCAACAACAACAT
1175630 CAACAGCAACAACAACAT
1 CAACAGCAACAACAACAT
* *
1175648 CAACAGCAACCACTACAT
1 CAACAGCAACAACAACAT
1175666 CAACAGCAACA
1 CAACAGCAACA
1175677 GCAGTGGCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.52, C:0.35, G:0.06, T:0.06
Consensus pattern (18 bp):
CAACAGCAACAACAACAT
Found at i:1175636 original size:24 final size:25
Alignment explanation
Indices: 1175613--1175679 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 25
1175603 CACTTTCAGC
1175613 AACAACAACATCAACAGCAA-CAGC
1 AACAACAACATCAACAGCAACCAGC
1175637 AACAACAACATCAACAGCAACCA-C
1 AACAACAACATCAACAGCAACCAGC
* * *
1175661 TACATCAACAGCAACAGCA
1 AACAACAACATCAACAGCA
1175680 GTGGCTCAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
24 37 0.95
25 2 0.05
ACGTcount: A:0.52, C:0.34, G:0.07, T:0.06
Consensus pattern (25 bp):
AACAACAACATCAACAGCAACCAGC
Found at i:1184820 original size:2 final size:2
Alignment explanation
Indices: 1184815--1184841 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1184805 ATATATATAT
1184815 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1184842 CTACTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1185991 original size:25 final size:24
Alignment explanation
Indices: 1185963--1186019 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
1185953 AAATAAAAAT
*
1185963 TATAATTAAAAATGATATATTTAAA
1 TATAATTAAAAATAATATA-TTAAA
*
1185988 TATAATT-AATATAATATATTAAA
1 TATAATTAAAAATAATATATTAAA
1186011 TATATATTA
1 TATA-ATTA
1186020 TATTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 9 0.32
24 12 0.43
25 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TATAATTAAAAATAATATATTAAA
Found at i:1186017 original size:11 final size:11
Alignment explanation
Indices: 1185977--1186029 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
1185967 ATTAAAAATG
1185977 ATATAT-TTAA
1 ATATATATTAA
1185987 ATATA-ATTAA
1 ATATATATTAA
1185997 TATAATATATTAA
1 -AT-ATATATTAA
*
1186010 ATATATATTAT
1 ATATATATTAA
*
1186021 ATTTATATT
1 ATATATATT
1186030 TAAAAATTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 9 0.24
11 18 0.49
12 5 0.14
13 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATATATTAA
Found at i:1186017 original size:13 final size:13
Alignment explanation
Indices: 1185945--1186017 Score: 50
Period size: 13 Copynumber: 5.9 Consensus size: 13
1185935 TCTTATAGTT
*
1185945 TTAAATATAAATA
1 TTAAATATATATA
*
1185958 -AAAAT-TATA-A
1 TTAAATATATATA
*
1185968 TTAAAAATGATATA
1 TTAAATAT-ATATA
*
1185982 TTTAA-ATATA-A
1 TTAAATATATATA
1185993 TT-AATATAATATA
1 TTAAATAT-ATATA
1186006 TTAAATATATAT
1 TTAAATATATAT
1186018 TATATTTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
10 3 0.06
11 11 0.23
12 11 0.23
13 12 0.26
14 10 0.21
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (13 bp):
TTAAATATATATA
Found at i:1186022 original size:23 final size:24
Alignment explanation
Indices: 1185963--1186033 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 24
1185953 AAATAAAAAT
* *
1185963 TATAATTAAAAATGATATATTTAAA
1 TATAATT-AATATAATATATTTAAA
1185988 TATAATTAATATAATATA-TTAAA
1 TATAATTAATATAATATATTTAAA
*
1186011 TATATATT-ATAT-TTATATTTAAA
1 TATA-ATTAATATAATATATTTAAA
1186034 AATTAGAACC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.10
23 18 0.44
24 12 0.29
25 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
TATAATTAATATAATATATTTAAA
Found at i:1193028 original size:21 final size:21
Alignment explanation
Indices: 1193002--1193049 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1192992 TCCTATTTAT
* *
1193002 ATTAAATGTGATCAAAATTAC
1 ATTAAATGTCAACAAAATTAC
* *
1193023 ATTAAATTTCAACAAAATTAT
1 ATTAAATGTCAACAAAATTAC
1193044 ATTAAA
1 ATTAAA
1193050 AGCTATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.35
Consensus pattern (21 bp):
ATTAAATGTCAACAAAATTAC
Found at i:1193960 original size:7 final size:7
Alignment explanation
Indices: 1193948--1193981 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1193938 TCTTCTAGCA
1193948 AAAAAAC
1 AAAAAAC
1193955 AAAAAAC
1 AAAAAAC
*
1193962 AAAAAGC
1 AAAAAAC
1193969 AAAAAAC
1 AAAAAAC
1193976 AAAAAA
1 AAAAAA
1193982 AAATTCTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:1194114 original size:12 final size:12
Alignment explanation
Indices: 1194097--1194134 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1194087 GCGTATTGAG
*
1194097 AAATTATCATAA
1 AAATTATAATAA
*
1194109 AAATTAAAAT-A
1 AAATTATAATAA
1194120 AAATTATAATAA
1 AAATTATAATAA
1194132 AAA
1 AAA
1194135 AATTAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATTATAATAA
Found at i:1194152 original size:21 final size:19
Alignment explanation
Indices: 1194114--1194152 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1194104 CATAAAAATT
1194114 AAAATAAAATTATAATAAA
1 AAAATAAAATTATAATAAA
*
1194133 AAAATTAAATATATTAATAA
1 AAAATAAAAT-TA-TAATAA
1194153 CTTTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATAAAATTATAATAAA
Found at i:1195403 original size:20 final size:19
Alignment explanation
Indices: 1195360--1195396 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1195350 TTATAAATCG
1195360 AATAACAAAATTTATATAT
1 AATAACAAAATTTATATAT
1195379 AATAA-AAAATTTATATAT
1 AATAACAAAATTTATATAT
1195397 TTAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAACAAAATTTATATAT
Found at i:1195472 original size:16 final size:17
Alignment explanation
Indices: 1195445--1195477 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1195435 ATTAAATATA
1195445 ATTTTATATTAATATTT
1 ATTTTATATTAATATTT
1195462 ATTTTAT-TTAATATTT
1 ATTTTATATTAATATTT
1195478 GATTCGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTATATTAATATTT
Found at i:1195827 original size:12 final size:12
Alignment explanation
Indices: 1195810--1195834 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1195800 AGACTTTTCC
1195810 AAAATAATAATT
1 AAAATAATAATT
1195822 AAAATAATAATT
1 AAAATAATAATT
1195834 A
1 A
1195835 TCAATATACC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:1196010 original size:19 final size:18
Alignment explanation
Indices: 1195974--1196022 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1195964 TAGCATAAAC
*
1195974 TATATTTTAATTAATTAAT
1 TATATTTT-ATAAATTAAT
1195993 TAATATTTTATAAATTAAT
1 T-ATATTTTATAAATTAAT
1196012 TATATGTTTAT
1 TATAT-TTTAT
1196023 GAAGTTGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 4 0.15
19 16 0.59
20 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TATATTTTATAAATTAAT
Found at i:1196092 original size:12 final size:13
Alignment explanation
Indices: 1196072--1196122 Score: 61
Period size: 12 Copynumber: 4.1 Consensus size: 13
1196062 TTAAAAATTC
1196072 ATTTATTTTATAA
1 ATTTATTTTATAA
*
1196085 ATTT-TTTTTTAA
1 ATTTATTTTATAA
* *
1196097 ATATATTTT-TAT
1 ATTTATTTTATAA
1196109 ATTTATTTTATAA
1 ATTTATTTTATAA
1196122 A
1 A
1196123 AAATAACTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 20 0.65
13 11 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTATTTTATAA
Found at i:1196117 original size:25 final size:25
Alignment explanation
Indices: 1196075--1196122 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1196065 AAAATTCATT
*
1196075 TATTTTATAAATTTTTTTTTAAATA
1 TATTTTATAAATTTTTTTATAAATA
*
1196100 TATTTT-TATATTTATTTTATAAA
1 TATTTTATAAATTT-TTTTATAAA
1196123 AAATAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTTTATAAATTTTTTTATAAATA
Found at i:1196679 original size:24 final size:24
Alignment explanation
Indices: 1196633--1196684 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
1196623 TTAGAACTTT
*
1196633 AATAAAACAATTATTTAATTTAGTA
1 AATAAAACAATTATTTAAATTAG-A
1196658 AATAAAACAATT-TTTAAATTAGA
1 AATAAAACAATTATTTAAATTAGA
1196681 AATA
1 AATA
1196685 TCTTGAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 5 0.19
24 9 0.35
25 12 0.46
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (24 bp):
AATAAAACAATTATTTAAATTAGA
Found at i:1197080 original size:22 final size:22
Alignment explanation
Indices: 1197045--1197101 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1197035 CATTAATAAA
* *
1197045 AAATTATTTAATTAATAATTTAT
1 AAATT-TTTTATTAATAATATAT
1197068 AAATTTTTTATTAATAATATAT
1 AAATTTTTTATTAATAATATAT
*
1197090 -TA-TTTTTATTAA
1 AAATTTTTTATTAA
1197102 ATTTAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.32
21 1 0.03
22 15 0.48
23 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATTTTTTATTAATAATATAT
Found at i:1197219 original size:21 final size:21
Alignment explanation
Indices: 1197195--1197236 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1197185 TTTTTATTGA
*
1197195 TTATA-TAAATAATGATTAAAT
1 TTATATTAAAAAAT-ATTAAAT
1197216 TTATATTAAAAAATATTAAAT
1 TTATATTAAAAAATATTAAAT
1197237 AAAAAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTATATTAAAAAATATTAAAT
Found at i:1198368 original size:29 final size:28
Alignment explanation
Indices: 1198306--1198383 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
1198296 TTTTATGTAA
* **
1198306 TAAAAAATATTTTAATTTATTATTTTAT
1 TAAAATATATTTTAATTTATTATTACAT
*
1198334 TTAAATATATTTATATATTT-TTATTACAT
1 TAAAATATATTT-TA-ATTTATTATTACAT
1198363 TAAAAT-TAATTTTTAATTTAT
1 TAAAATAT-A-TTTTAATTTAT
1198384 ATAAAAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
28 15 0.38
29 18 0.45
30 7 0.17
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
TAAAATATATTTTAATTTATTATTACAT
Found at i:1198406 original size:17 final size:17
Alignment explanation
Indices: 1198382--1198422 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
1198372 TTTTTAATTT
1198382 ATATAAAAAATTATTTAA
1 ATATAAAAAA-TATTTAA
1198400 A-ATAAAAAATATTTAA
1 ATATAAAAAATATTTAA
1198416 ATATAAA
1 ATATAAA
1198423 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 13 0.59
18 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAAAATATTTAA
Found at i:1198422 original size:6 final size:6
Alignment explanation
Indices: 1198413--1198471 Score: 51
Period size: 5 Copynumber: 10.7 Consensus size: 6
1198403 AAAAAATATT
1198413 TAAATA TAAAT- TAAA-A -AAAT- TAAACTTA TAAATA -AAATA T-AATA
1 TAAATA TAAATA TAAATA TAAATA TAAA--TA TAAATA TAAATA TAAATA
1198457 T-AATA TAAATA TAAA
1 TAAATA TAAATA TAAA
1198472 ATTATTTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
4 3 0.07
5 22 0.49
6 15 0.33
7 1 0.02
8 4 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (6 bp):
TAAATA
Found at i:1198428 original size:21 final size:21
Alignment explanation
Indices: 1198399--1198486 Score: 58
Period size: 21 Copynumber: 4.1 Consensus size: 21
1198389 AAATTATTTA
*
1198399 AAATAAAAAATATTTAAATAT
1 AAATTAAAAATATTTAAATAT
*
1198420 AAATTAAAAA-AATTAAACTTAT
1 AAATTAAAAATATTTAAA--TAT
*
1198442 AAA-T-AAAATATAATATAATAT
1 AAATTAAAAATAT-TTA-AATAT
*
1198463 AAATATAAAATTATTTTAAA-AT
1 AAAT-TAAAAATA-TTTAAATAT
1198485 AA
1 AA
1198487 TAAAATAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
20 10 0.19
21 17 0.33
22 12 0.23
23 5 0.10
24 7 0.13
25 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATTAAAAATATTTAAATAT
Found at i:1206741 original size:12 final size:12
Alignment explanation
Indices: 1206724--1206760 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1206714 GATTGTTGCA
1206724 AGTCTGGGATGC
1 AGTCTGGGATGC
*
1206736 AGTCTGGGATAAC
1 AGTCTGGGAT-GC
1206749 AGTCTGGGATGC
1 AGTCTGGGATGC
1206761 CTCCAAGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (12 bp):
AGTCTGGGATGC
Found at i:1206751 original size:13 final size:12
Alignment explanation
Indices: 1206724--1206758 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1206714 GATTGTTGCA
*
1206724 AGTCTGGGATGC
1 AGTCTGGGATAC
1206736 AGTCTGGGATAAC
1 AGTCTGGGAT-AC
1206749 AGTCTGGGAT
1 AGTCTGGGAT
1206759 GCCTCCAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.23, C:0.14, G:0.37, T:0.26
Consensus pattern (12 bp):
AGTCTGGGATAC
Found at i:1210374 original size:18 final size:19
Alignment explanation
Indices: 1210351--1210387 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1210341 GTTGGCACAT
*
1210351 TTTTTAAA-ATATTATTAA
1 TTTTTAAATAAATTATTAA
1210369 TTTTTAAATAAATTATTAA
1 TTTTTAAATAAATTATTAA
1210388 AATATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTAAATAAATTATTAA
Found at i:1210388 original size:30 final size:30
Alignment explanation
Indices: 1210354--1210432 Score: 126
Period size: 29 Copynumber: 2.7 Consensus size: 30
1210344 GGCACATTTT
*
1210354 TTAAAATATTATTAATTTTTAAATAAATTA
1 TTAAAATATTATTAATTTTAAAATAAATTA
1210384 TTAAAATATTATTAA-TTTAAAATAAATTA
1 TTAAAATATTATTAATTTTAAAATAAATTA
*
1210413 TAAAAATATTATT-ATTTTAA
1 TTAAAATATTATTAATTTTAA
1210433 TACATAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
28 1 0.02
29 30 0.65
30 15 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAAAATATTATTAATTTTAAAATAAATTA
Found at i:1210902 original size:17 final size:16
Alignment explanation
Indices: 1210865--1210904 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1210855 ATTGTAAGTT
1210865 TTTTATTTAAATTTAA
1 TTTTATTTAAATTTAA
* *
1210881 ATTTATTTGAAATTTTA
1 TTTTATTT-AAATTTAA
1210898 TTTTATT
1 TTTTATT
1210905 ATTAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTATTTAAATTTAA
Found at i:1212701 original size:21 final size:22
Alignment explanation
Indices: 1212671--1212715 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
1212661 TTAATTATAT
1212671 TTAATTATAAAATATTTAAATA
1 TTAATTATAAAATATTTAAATA
*
1212693 TTAA-TATAAAATTTTTAAATA
1 TTAATTATAAAATATTTAAATA
1212714 TT
1 TT
1212716 TTTACATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATTATAAAATATTTAAATA
Found at i:1214197 original size:2 final size:2
Alignment explanation
Indices: 1214190--1214224 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1214180 ATTAATAAGG
1214190 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
1214225 GGAGTCAAAT
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:1222141 original size:5 final size:5
Alignment explanation
Indices: 1222131--1222175 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
1222121 AGCTGCTTAT
* *
1222131 TTTTC TTTTC TTTCC TTTTC TTTTC TTTTC TTTTC TTTTT TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
1222176 CTCCCTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:1222328 original size:17 final size:16
Alignment explanation
Indices: 1222306--1222338 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1222296 AGTGTGCAAA
1222306 TATAAAATAATTAAAAT
1 TATAAAATAA-TAAAAT
1222323 TATAAAATAATAAAAT
1 TATAAAATAATAAAAT
1222339 ATTATCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATAAAATAATAAAAT
Found at i:1223512 original size:33 final size:34
Alignment explanation
Indices: 1223461--1223526 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 34
1223451 ATAATATAAT
*
1223461 TAATATTTAAATATTTTATGTTTATAAAAATTTTA
1 TAATATTTAAATAATTTAT-TTTATAAAAATTTTA
*
1223496 TAATA-TT-AATAATTTATTTTATATAAATTTT
1 TAATATTTAAATAATTTATTTTATAAAAATTTT
1223527 CATTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.45
33 9 0.31
34 2 0.07
35 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (34 bp):
TAATATTTAAATAATTTATTTTATAAAAATTTTA
Found at i:1223551 original size:49 final size:45
Alignment explanation
Indices: 1223430--1223590 Score: 125
Period size: 49 Copynumber: 3.5 Consensus size: 45
1223420 ACTTTAATAA
* **
1223430 TTATTATATTTTATATTTTA-TATAATATAATTAATATTTAAAT-ATT
1 TTATTATATTATATATTTTATTAT-AT-TAA-TAATATTTTTATAATT
* * * *
1223476 TTATGTTTA-TAAAAATTTTATAATATTAATAATTTATTTTATATAAATT
1 TTAT-TATATTATATATTTTATTATATTAATAA--TATTTT-TAT-AATT
* *
1223525 TTCATTAT-TTATATATTTTATTATATTCATAATATTTTTATTATT
1 TT-ATTATATTATATATTTTATTATATTAATAATATTTTTATAATT
1223570 TTATTATATTATAT-TTTTATT
1 TTATTATATTATATATTTTATT
1223591 TTTTTATCAT
Statistics
Matches: 92, Mismatches: 13, Indels: 22
0.72 0.10 0.17
Matches are distributed among these distances:
44 15 0.16
45 14 0.15
46 22 0.24
47 13 0.14
49 26 0.28
50 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (45 bp):
TTATTATATTATATATTTTATTATATTAATAATATTTTTATAATT
Found at i:1223578 original size:19 final size:19
Alignment explanation
Indices: 1223509--1223579 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
1223499 TATTAATAAT
* *
1223509 TTATTTTATATAAATTTTCA
1 TTATTTTAT-TATATTTTTA
1223529 TTA-TTTA-TATA-TTTTA
1 TTATTTTATTATATTTTTA
* *
1223545 TTATATTCATAATATTTTTA
1 TTAT-TTTATTATATTTTTA
1223565 TTATTTTATTATATT
1 TTATTTTATTATATT
1223580 ATATTTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.17
17 3 0.07
18 3 0.07
19 16 0.39
20 12 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTTATTATATTTTTA
Found at i:1224129 original size:28 final size:28
Alignment explanation
Indices: 1224065--1224129 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
1224055 ATTTTAAATA
* * *
1224065 TATTAGATTTATTATATTATTTTTTATT
1 TATTAAATATATTATATTATTATTTATT
1224093 TATTAAATATATTATATT-TATATTT-TT
1 TATTAAATATATTATATTAT-TATTTATT
1224120 TATTACAATA
1 TATTA-AATA
1224130 AAATTTATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 8 0.25
28 24 0.75
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
TATTAAATATATTATATTATTATTTATT
Found at i:1224600 original size:3 final size:3
Alignment explanation
Indices: 1224592--1224626 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1224582 TATACATTAC
1224592 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1224627 AATTTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1225188 original size:15 final size:16
Alignment explanation
Indices: 1225168--1225200 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1225158 TACATTTTAT
1225168 AATTAAATT-AAATTA
1 AATTAAATTAAAATTA
*
1225183 AATTAATTTAAAATTA
1 AATTAAATTAAAATTA
1225199 AA
1 AA
1225201 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTAAATTAAAATTA
Found at i:1225197 original size:21 final size:21
Alignment explanation
Indices: 1225172--1225226 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1225162 TTTTATAATT
1225172 AAATTAAATTAAATTAATTTA
1 AAATTAAATTAAATTAATTTA
* ** *
1225193 AAATTAAAATATTTTTATTTA
1 AAATTAAATTAAATTAATTTA
1225214 AAATTTAAATTAA
1 AAA-TTAAATTAA
1225227 TTCATATCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTAAATTAAATTAATTTA
Found at i:1225946 original size:16 final size:15
Alignment explanation
Indices: 1225925--1225959 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1225915 ATGTTATGAA
*
1225925 TTAATTAAATATTAAT
1 TTAATTAAAAATT-AT
1225941 TTAATTAAAAATTAT
1 TTAATTAAAAATTAT
1225956 TTAA
1 TTAA
1225960 AATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAATTAAAAATTAT
Found at i:1231840 original size:50 final size:50
Alignment explanation
Indices: 1231758--1231963 Score: 294
Period size: 50 Copynumber: 4.2 Consensus size: 50
1231748 GAAAAGTACA
* * *
1231758 TTTGACAATAGA-A-AAGTGATCATAATTGTTGACGATTCTTCATCAACC
1 TTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACC
* * * *
1231806 TTTGATAATAGAGAGAGGTGGTCGTAATTGTTGACGATTCTTTACCAACT
1 TTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACC
* *
1231856 TTTGACAATAGAGGGAGGTGGTTATAATTGTTGACGATTCTTCACCAACC
1 TTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACC
*
1231906 -TTGACAATAGAGAGAGGT-GCCATAATTGTTGACGATTCTTCACCAACC
1 TTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACC
1231954 TTTGACAATA
1 TTTGACAATA
1231964 AAAAAAAGTG
Statistics
Matches: 139, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
48 39 0.28
49 27 0.19
50 73 0.53
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (50 bp):
TTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACC
Found at i:1231943 original size:98 final size:100
Alignment explanation
Indices: 1231779--1231963 Score: 302
Period size: 98 Copynumber: 1.9 Consensus size: 100
1231769 AAAAGTGATC
* * * *
1231779 ATAATTGTTGACGATTCTTCATCAACCTTTGATAATAGAGAGAGGTGGTCGTAATTGTTGACGAT
1 ATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGAT
* *
1231844 TCTTTACCAACTTTTGACAATAGAGGGAGGTGGTT
66 TCTTCACCAACCTTTGACAATAGAGGGAGGTGGTT
1231879 ATAATTGTTGACGATTCTTCACCAACC-TTGACAATAGAGAGAGGT-GCCATAATTGTTGACGAT
1 ATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGAT
1231942 TCTTCACCAACCTTTGACAATA
66 TCTTCACCAACCTTTGACAATA
1231964 AAAAAAAGTG
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
98 36 0.46
99 17 0.22
100 26 0.33
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (100 bp):
ATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGAT
TCTTCACCAACCTTTGACAATAGAGGGAGGTGGTT
Found at i:1231981 original size:98 final size:100
Alignment explanation
Indices: 1231769--1231988 Score: 300
Period size: 98 Copynumber: 2.2 Consensus size: 100
1231759 TTGACAATAG
* * * *
1231769 AAAAGTGATCATAATTGTTGACGATTCTTCATCAACCTTTGATAATAGAGAGAGGTGGTCGTAAT
1 AAAAGTGATCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAAT
* * * *
1231834 TGTTGACGATTCTTTACCAACTTTTGACAATAGAG
66 TGTTGACGATTCTTCACCAACCTTTGACAATAAAA
** * * *
1231869 GGAGGTGGTTATAATTGTTGACGATTCTTCACCAACC-TTGACAATAGAGAGAGGT-GCCATAAT
1 AAAAGTGATCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAAT
1231932 TGTTGACGATTCTTCACCAACCTTTGACAATAAAA
66 TGTTGACGATTCTTCACCAACCTTTGACAATAAAA
*
1231967 AAAAGTGACCATAATTGTTGAC
1 AAAAGTGATCATAATTGTTGAC
1231989 TCTAAATATG
Statistics
Matches: 101, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
98 53 0.52
99 17 0.17
100 31 0.31
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (100 bp):
AAAAGTGATCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAAT
TGTTGACGATTCTTCACCAACCTTTGACAATAAAA
Found at i:1232507 original size:13 final size:13
Alignment explanation
Indices: 1232491--1232516 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1232481 ATTTTTTTTA
1232491 AATATTTATATTC
1 AATATTTATATTC
1232504 AATATTTATATTC
1 AATATTTATATTC
1232517 GACGTATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTTATATTC
Found at i:1232724 original size:49 final size:48
Alignment explanation
Indices: 1232658--1232755 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 48
1232648 AAAAAACTAT
* * * *
1232658 ATTTATCATACAAATATTTATATTTAATATTTATTTAAGTGTAAAATAA
1 ATTTATCATACAAATATTCATATTTAATACTTATTCAAGTCT-AAATAA
* *
1232707 ATTTATCATACACATATTCATATTTTATACTTATTCAAGTCTAAATAA
1 ATTTATCATACAAATATTCATATTTAATACTTATTCAAGTCTAAATAA
1232755 A
1 A
1232756 AAAAATTACA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
48 7 0.16
49 36 0.84
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (48 bp):
ATTTATCATACAAATATTCATATTTAATACTTATTCAAGTCTAAATAA
Found at i:1234122 original size:97 final size:97
Alignment explanation
Indices: 1233956--1234243 Score: 576
Period size: 97 Copynumber: 3.0 Consensus size: 97
1233946 TAATAGACAC
1233956 TTTGTAATTTAACATAAAAGAACCAAAGTTAATCATAGCTAATAGATGGAAAACAAACTAATAAG
1 TTTGTAATTTAACATAAAAGAACCAAAGTTAATCATAGCTAATAGATGGAAAACAAACTAATAAG
1234021 ATGCTAGTCCTTTTCTTTTCCTACAGGCTTAT
66 ATGCTAGTCCTTTTCTTTTCCTACAGGCTTAT
1234053 TTTGTAATTTAACATAAAAGAACCAAAGTTAATCATAGCTAATAGATGGAAAACAAACTAATAAG
1 TTTGTAATTTAACATAAAAGAACCAAAGTTAATCATAGCTAATAGATGGAAAACAAACTAATAAG
1234118 ATGCTAGTCCTTTTCTTTTCCTACAGGCTTAT
66 ATGCTAGTCCTTTTCTTTTCCTACAGGCTTAT
1234150 TTTGTAATTTAACATAAAAGAACCAAAGTTAATCATAGCTAATAGATGGAAAACAAACTAATAAG
1 TTTGTAATTTAACATAAAAGAACCAAAGTTAATCATAGCTAATAGATGGAAAACAAACTAATAAG
1234215 ATGCTAGTCCTTTTCTTTTCCTACAGGCT
66 ATGCTAGTCCTTTTCTTTTCCTACAGGCT
1234244 ACGCCAGTAG
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 191 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (97 bp):
TTTGTAATTTAACATAAAAGAACCAAAGTTAATCATAGCTAATAGATGGAAAACAAACTAATAAG
ATGCTAGTCCTTTTCTTTTCCTACAGGCTTAT
Found at i:1241289 original size:167 final size:167
Alignment explanation
Indices: 1241013--1241345 Score: 605
Period size: 167 Copynumber: 2.0 Consensus size: 167
1241003 CTCACTCTGG
*
1241013 AGACCAAACTTAATCCATTGATTTATTTTCTTTGATTTCACTTACCATTCCAGTTTGTCAGTTCC
1 AGACCAAACTTAATCCATTGATTTATTGTCTTTGATTTCACTTACCATTCCAGTTTGTCAGTTCC
* *
1241078 TTCAGTACGCTCAAAAATCATACATTTTACAAGTGAAGACAAATGGATAAAAAAGAGAGTAGGGG
66 TTCAGTACGCTCAAAAATCATACAATTTACAAGTGAAGACAAATGGATAAAAAAGAGAATAGGGG
*
1241143 TTAGCTCAGCATGAGGCTGCCCGGCCTGAGGATGAAT
131 TTAGCTCAGCATGAGGCTGCCCAGCCTGAGGATGAAT
1241180 AGACCAAACTTAATCCATTGATTTATTGTCTTTGATTTCACTTACCATTCCAGTTTGTCAGTTCC
1 AGACCAAACTTAATCCATTGATTTATTGTCTTTGATTTCACTTACCATTCCAGTTTGTCAGTTCC
*
1241245 TTCATTACGCT-AGAAAATCATACAATTTACAAGTGAAGACAAATGGATAAAAAAGAGAATAGGG
66 TTCAGTACGCTCA-AAAATCATACAATTTACAAGTGAAGACAAATGGATAAAAAAGAGAATAGGG
1241309 GTTAGCTCAGCATGAGGCTGCCCAGCCTGAGGATGAA
130 GTTAGCTCAGCATGAGGCTGCCCAGCCTGAGGATGAA
1241346 ATCCTTAACC
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
166 1 0.01
167 159 0.99
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (167 bp):
AGACCAAACTTAATCCATTGATTTATTGTCTTTGATTTCACTTACCATTCCAGTTTGTCAGTTCC
TTCAGTACGCTCAAAAATCATACAATTTACAAGTGAAGACAAATGGATAAAAAAGAGAATAGGGG
TTAGCTCAGCATGAGGCTGCCCAGCCTGAGGATGAAT
Found at i:1243835 original size:1 final size:1
Alignment explanation
Indices: 1243829--1243860 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
1243819 AAATCTTCAC
*
1243829 TTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1243861 CCAATTGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:1256217 original size:4 final size:4
Alignment explanation
Indices: 1256208--1256233 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1256198 AATTTCTGAT
1256208 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
1256234 CTTGTTGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1256332 original size:3 final size:3
Alignment explanation
Indices: 1256318--1256353 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1256308 GTTTTCTCAA
*
1256318 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1256354 TAAGATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1257510 original size:2 final size:2
Alignment explanation
Indices: 1257503--1257545 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1257493 TTAATAATGT
* *
1257503 TA TA TA TA CA TA CA 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
1257545 T
1 T
1257546 GTGGGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1261378 original size:2 final size:2
Alignment explanation
Indices: 1261373--1261407 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1261363 TATATATATA
1261373 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1261408 CTAGAATATG
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1263123 original size:13 final size:13
Alignment explanation
Indices: 1263107--1263138 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1263097 AGTAACAAAT
1263107 AACAAAATTAACA
1 AACAAAATTAACA
1263120 AACAAAATTAACA
1 AACAAAATTAACA
*
1263133 AGCAAA
1 AACAAA
1263139 CGGAGCCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.69, C:0.16, G:0.03, T:0.12
Consensus pattern (13 bp):
AACAAAATTAACA
Found at i:1264897 original size:20 final size:20
Alignment explanation
Indices: 1264872--1264910 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1264862 AGATTAAATT
1264872 TATTA-TAATATTTTTATAAC
1 TATTATTAATA-TTTTATAAC
*
1264892 TATTATTAGTATTTTATAA
1 TATTATTAATATTTTATAA
1264911 GTTTCCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
TATTATTAATATTTTATAAC
Found at i:1265182 original size:2 final size:2
Alignment explanation
Indices: 1265175--1265200 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1265165 GAAGCATTTT
1265175 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1265201 TGAGGGGTGC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1265453 original size:6 final size:6
Alignment explanation
Indices: 1265428--1265475 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
1265418 TTTATTTTAA
* *
1265428 TAATATT TAGTTT ATAATTT TAATTT TAATTT TAATTT TATTTT TAAT
1 TAAT-TT TAATTT -TAATTT TAATTT TAATTT TAATTT TAATTT TAAT
1265476 ATATTGAGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 28 0.78
7 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (6 bp):
TAATTT
Found at i:1265729 original size:6 final size:6
Alignment explanation
Indices: 1265703--1265732 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1265693 AATAAAAATT
*
1265703 AATATA AAGATA AATATA AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA
1265733 GAAGCAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (6 bp):
AATATA
Found at i:1266252 original size:1 final size:1
Alignment explanation
Indices: 1266246--1266283 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
1266236 TCTATAACAT
1266246 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1266284 AAGTTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1268119 original size:19 final size:19
Alignment explanation
Indices: 1268091--1268131 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1268081 GACAAACGTT
*
1268091 AAGAATCTTAATTAGCTTC
1 AAGAACCTTAATTAGCTTC
1268110 AAGAACCTTAATTAGCTTC
1 AAGAACCTTAATTAGCTTC
1268129 AAG
1 AAG
1268132 GGTTTTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (19 bp):
AAGAACCTTAATTAGCTTC
Found at i:1270033 original size:21 final size:21
Alignment explanation
Indices: 1270004--1270049 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1269994 AGCAATTAAG
*
1270004 AGAAGGAAAAAAAAAAAAAAA
1 AGAAAGAAAAAAAAAAAAAAA
* * *
1270025 AGAAAGAAAGAAAGAAAGAAA
1 AGAAAGAAAAAAAAAAAAAAA
1270046 AGAA
1 AGAA
1270050 TACTACATAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AGAAAGAAAAAAAAAAAAAAA
Found at i:1273808 original size:68 final size:68
Alignment explanation
Indices: 1273699--1273838 Score: 244
Period size: 68 Copynumber: 2.1 Consensus size: 68
1273689 GTTTCAAAGA
* *
1273699 ATAATTTCATGAGCCAATATAAATATAGAGAAAGAAGTTTGAATTAGAAAACTCACTGGTAGCAT
1 ATAATTTCATGAGCCAATACAAATATAGAGAAAGAAGTTTGAATTAGAAAACTCACGGGTAGCAT
*
1273764 TAC
66 AAC
*
1273767 ATAATTTTATGAGCCAATACAAATATAGAGAAAGAAGTTTGAATTAGAAAACTCACGGGTAGCAT
1 ATAATTTCATGAGCCAATACAAATATAGAGAAAGAAGTTTGAATTAGAAAACTCACGGGTAGCAT
1273832 AAC
66 AAC
1273835 ATAA
1 ATAA
1273839 ACTGGAACAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.26
Consensus pattern (68 bp):
ATAATTTCATGAGCCAATACAAATATAGAGAAAGAAGTTTGAATTAGAAAACTCACGGGTAGCAT
AAC
Found at i:1276650 original size:3 final size:3
Alignment explanation
Indices: 1276642--1276673 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1276632 TATCTTTTCT
1276642 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1276674 GAAGAGGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1281266 original size:11 final size:12
Alignment explanation
Indices: 1281243--1281278 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1281233 TAATTTTTTT
1281243 AATATTAATTAA
1 AATATTAATTAA
1281255 AATATT-ATTAA
1 AATATTAATTAA
*
1281266 AATTTTAATTAA
1 AATATTAATTAA
1281278 A
1 A
1281279 TTTAAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATATTAATTAA
Found at i:1281899 original size:2 final size:2
Alignment explanation
Indices: 1281892--1281922 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1281882 AGCTCAAGGA
1281892 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
1281923 AGCATCAAAG
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:1282467 original size:42 final size:45
Alignment explanation
Indices: 1282371--1282469 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 45
1282361 TTTAATTTGA
1282371 TATAAAATAAAAAATATTAATATATGTTTATAATATTTATTAAATAT
1 TATAAAATAAAAAATATTAATATA--TTTATAATATTTATTAAATAT
* *
1282418 TAAAAAATAAAAAATA-TAAT-TA-TTATAATATTTTTTAAAT-T
1 TATAAAATAAAAAATATTAATATATTTATAATATTTATTAAATAT
1282459 TCATAAAATAA
1 T-ATAAAATAA
1282470 TTGATTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
41 2 0.04
42 25 0.52
45 2 0.04
46 4 0.08
47 15 0.31
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (45 bp):
TATAAAATAAAAAATATTAATATATTTATAATATTTATTAAATAT
Found at i:1282927 original size:18 final size:18
Alignment explanation
Indices: 1282881--1282930 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1282871 GAAATGCACG
1282881 TTTAAGATTTAATTATTTTA
1 TTTAA-ATTT-ATTATTTTA
** *
1282901 AATATATTTATTATTTTA
1 TTTAAATTTATTATTTTA
1282919 TTTAAATTTATT
1 TTTAAATTTATT
1282931 TTTAAATTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 18 0.75
19 4 0.17
20 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTAAATTTATTATTTTA
Found at i:1282940 original size:22 final size:22
Alignment explanation
Indices: 1282889--1282940 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1282879 CGTTTAAGAT
1282889 TTAA-TTATTTTAAATATATTTA
1 TTAATTTA-TTTAAATATATTTA
* *
1282911 TTATTTTATTTAAATTTATTT-
1 TTAATTTATTTAAATATATTTA
1282932 TTAAATTTA
1 TT-AATTTA
1282941 ATATTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 2 0.08
22 20 0.80
23 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTAATTTATTTAAATATATTTA
Found at i:1283580 original size:13 final size:13
Alignment explanation
Indices: 1283545--1283614 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 13
1283535 TTATTTTTTA
*
1283545 ATTTAAAAAT-AT
1 ATTTTAAAATAAT
*
1283557 ATATTATAAATAAT
1 ATTTTA-AAATAAT
1283571 ATTTTAAAATAAT
1 ATTTTAAAATAAT
*
1283584 A-ATT-AAATAAT
1 ATTTTAAAATAAT
*
1283595 -TTTT-AATTAAT
1 ATTTTAAAATAAT
1283606 ATTTATAAA
1 ATTT-TAAA
1283615 TTTTAAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 15 0.33
12 9 0.20
13 13 0.28
14 9 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTAAAATAAT
Found at i:1283590 original size:24 final size:26
Alignment explanation
Indices: 1283545--1283600 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
1283535 TTATTTTTTA
* *
1283545 ATTTAAAAATATATATTATAAATAAT
1 ATTTTAAAATATATAATATAAATAAT
1283571 ATTTTAAAATA-ATAAT-TAAATAAT
1 ATTTTAAAATATATAATATAAATAAT
1283595 -TTTTAA
1 ATTTTAA
1283601 TTAATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 8 0.29
25 4 0.14
26 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTTAAAATATATAATATAAATAAT
Found at i:1283614 original size:24 final size:23
Alignment explanation
Indices: 1283555--1283615 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
1283545 ATTTAAAAAT
1283555 ATATATTATAAATAATATTTTAAA
1 ATAT-TTATAAATAATATTTTAAA
* *
1283579 ATAATAATTAAATAAT-TTTTAATTA
1 ATATTTA-TAAATAATATTTTAA--A
1283604 ATATTTATAAAT
1 ATATTTATAAAT
1283616 TTTAAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
23 8 0.27
24 16 0.53
25 6 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTTATAAATAATATTTTAAA
Found at i:1291192 original size:6 final size:6
Alignment explanation
Indices: 1291183--1291212 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1291173 TCAAAACTAA
1291183 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1291213 TGAGAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:1291735 original size:2 final size:2
Alignment explanation
Indices: 1291728--1291769 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1291718 CTTACCAGTA
1291728 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1291770 CCCCTGCTGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1298750 original size:69 final size:69
Alignment explanation
Indices: 1298635--1298767 Score: 205
Period size: 69 Copynumber: 1.9 Consensus size: 69
1298625 ATGGAATCGT
* * * *
1298635 AGAAGAAAGTAGAGATGAGTGCAATAGTGACTATGAAAAGAGAAGTGAATGCATATGGTTCGAAC
1 AGAAGAAAGTAAAGATGAGTACAATAGAGACTATGAAAAGAAAAGTGAATGCATATGGTTCGAAC
1298700 TACC
66 TACC
*
1298704 AGAAGAAAGTAAAGATGAGTACAATAGAGA-TGATGAAAATAAAAGTGAATGCATATGGTTCGAA
1 AGAAGAAAGTAAAGATGAGTACAATAGAGACT-ATGAAAAGAAAAGTGAATGCATATGGTTCGAA
1298768 ACTTACAAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 1 0.02
69 57 0.98
ACGTcount: A:0.46, C:0.08, G:0.26, T:0.20
Consensus pattern (69 bp):
AGAAGAAAGTAAAGATGAGTACAATAGAGACTATGAAAAGAAAAGTGAATGCATATGGTTCGAAC
TACC
Found at i:1313202 original size:2 final size:2
Alignment explanation
Indices: 1313195--1313225 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1313185 AAGAAAACCA
*
1313195 AT AT AT AT GT 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
1313226 CATTTGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1313630 original size:12 final size:12
Alignment explanation
Indices: 1313611--1313655 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1313601 AAAATTTAAA
1313611 AAATTTAT-ATT
1 AAATTTATAATT
1313622 AATATTTATAATT
1 AA-ATTTATAATT
1313635 AAATTTA-AA-T
1 AAATTTATAATT
*
1313645 AAATATATAAT
1 AAATTTATAAT
1313656 ATTTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 7 0.24
11 6 0.21
12 11 0.38
13 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AAATTTATAATT
Found at i:1313662 original size:32 final size:32
Alignment explanation
Indices: 1313602--1313664 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 32
1313592 AATATTATTA
1313602 AAATTTAAAAAATTTATATTAATATTTATAATT
1 AAATTTAAAAAA-TTATATTAATATTTATAATT
1313635 AAATTTAAATAAA-TATA-TAATATTTTATAA
1 AAATTTAAA-AAATTATATTAATA-TTTATAA
1313665 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 5 0.18
32 11 0.39
33 9 0.32
34 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
AAATTTAAAAAATTATATTAATATTTATAATT
Found at i:1313908 original size:121 final size:123
Alignment explanation
Indices: 1313759--1314001 Score: 330
Period size: 125 Copynumber: 2.0 Consensus size: 123
1313749 ATGTGAATAG
** *
1313759 GTATACTTTAAACATATTATGTATATAAATATATGTGCTCATT-ACA-ATATATATAT-TTTTTA
1 GTATACTTTAAACATACCATGTATATAAATATATGTGCTCATTAACATATATATATATATATTT-
* * *
1313821 AGATAATGTGGGCTTGGATATTCCTCCAATTAAGTCGAAAAGTCTATTTGCAAATATAT
65 AGATAATGTAGGCTTGGATATGCCTCCAATTAAGTCGAAAAGTCCATTTGCAAATATAT
* * *
1313880 GTATACTTTTAACATACCGTGTGTATAAATATATGTGCTCATTGCAACATATATATATATATATT
1 GTATACTTTAAACATACCATGTATATAAATATATGTGCTCATT--AACATATATATATATATATT
* * *
1313945 TAGATAATGTAGGTTTGGATATGCCTCCAATTAGGTCGAAAGGTCCATTTGCAAATA
64 TAGATAATGTAGGCTTGGATATGCCTCCAATTAAGTCGAAAAGTCCATTTGCAAATA
1314002 AATGACATTG
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
121 38 0.36
124 3 0.03
125 60 0.57
126 4 0.04
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (123 bp):
GTATACTTTAAACATACCATGTATATAAATATATGTGCTCATTAACATATATATATATATATTTA
GATAATGTAGGCTTGGATATGCCTCCAATTAAGTCGAAAAGTCCATTTGCAAATATAT
Found at i:1324274 original size:30 final size:30
Alignment explanation
Indices: 1324218--1324275 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
1324208 TAGACTAATA
1324218 ATCTTAATAGTTATTTTCATTTTTATTTTT
1 ATCTTAATAGTTATTTTCATTTTTATTTTT
*
1324248 ATCTTATTA-TTACTTTT-ATTTATTATTT
1 ATCTTAATAGTTA-TTTTCATTT-TTATTT
1324276 AAAAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (30 bp):
ATCTTAATAGTTATTTTCATTTTTATTTTT
Found at i:1324738 original size:2 final size:2
Alignment explanation
Indices: 1324731--1324760 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1324721 CGCCGGAAGG
1324731 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1324761 AACTGATCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1330231 original size:1 final size:1
Alignment explanation
Indices: 1330225--1330256 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
1330215 TATTACAAAG
*
1330225 TTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1330257 GGCCACTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:1331128 original size:6 final size:6
Alignment explanation
Indices: 1331108--1331147 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
1331098 CTCAAGATTG
1331108 AAAT-A AAAT-A AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1331148 TATATTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.26
6 25 0.74
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:1331166 original size:19 final size:18
Alignment explanation
Indices: 1331142--1331199 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 18
1331132 ATAAAAATAA
1331142 AAATAATATATTTTAAAAT
1 AAATAAT-TATTTTAAAAT
1331161 AAATAATCTATTGATATAAAAT
1 AAATAAT-TATT--T-TAAAAT
1331183 ATAGATAATTATTTTAA
1 A-A-ATAATTATTTTAA
1331200 TGAAAGATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 11 0.33
20 3 0.09
21 2 0.06
22 7 0.21
23 5 0.15
24 5 0.15
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATAATTATTTTAAAAT
Found at i:1344231 original size:26 final size:26
Alignment explanation
Indices: 1344184--1344253 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
1344174 ATTTTTATCT
* *
1344184 TAATATTTTTATAATTATATTTAAAATA
1 TAATATATTTAT-A-TAAATTTAAAATA
*
1344212 TAATATATTTATATAAATTTTAAATA
1 TAATATATTTATATAAATTTAAAATA
* *
1344238 TATTAAATTTTATATA
1 TAATATA-TTTATATA
1344254 TTTTTATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 16 0.44
27 9 0.25
28 11 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TAATATATTTATATAAATTTAAAATA
Found at i:1344246 original size:16 final size:15
Alignment explanation
Indices: 1344221--1344254 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1344211 ATAATATATT
1344221 TATATAAATTTTAAA
1 TATATAAATTTTAAA
*
1344236 TATATTAAATTTTATA
1 TATA-TAAATTTTAAA
1344252 TAT
1 TAT
1344255 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATAAATTTTAAA
Found at i:1344267 original size:17 final size:17
Alignment explanation
Indices: 1344245--1344304 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
1344235 ATATATTAAA
1344245 TTTTATATATTTTTATT
1 TTTTATATATTTTTATT
1344262 TTTTATATATTATATTATAT
1 TTTTATATATT-T-TTAT-T
* *
1344282 TTTAATTAATATTTTAATT
1 TTTTA-T-ATATTTTTATT
1344301 TTTT
1 TTTT
1344305 TGTATTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 11 0.31
18 1 0.03
19 8 0.23
20 8 0.23
21 2 0.06
22 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATATATTTTTATT
Found at i:1351866 original size:15 final size:15
Alignment explanation
Indices: 1351846--1351878 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1351836 GAAAAAAACA
1351846 AAGAAAGAATGATTC
1 AAGAAAGAATGATTC
*
1351861 AAGAAAGAATTATTC
1 AAGAAAGAATGATTC
1351876 AAG
1 AAG
1351879 GAAGTGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.21
Consensus pattern (15 bp):
AAGAAAGAATGATTC
Found at i:1352544 original size:26 final size:26
Alignment explanation
Indices: 1352508--1352558 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1352498 TTAAAATTAT
*
1352508 ATTTAACATATT-TTATATTTATATAA
1 ATTTAACATATTAATA-ATTTATATAA
*
1352534 ATTTAATATATTAATAATTTATATA
1 ATTTAACATATTAATAATTTATATA
1352559 CTAACGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTAACATATTAATAATTTATATAA
Found at i:1352607 original size:35 final size:35
Alignment explanation
Indices: 1352568--1352638 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 35
1352558 ACTAACGTAA
* * *
1352568 TATTTATATAATT-TTTTATTAAATTATATTTTAAT
1 TATTTATAT-ATTATATAATTAAATTATATTTAAAT
* *
1352603 TATTTTTATATTATATAATTATATTATATTTAAAT
1 TATTTATATATTATATAATTAAATTATATTTAAAT
1352638 T
1 T
1352639 TATTAATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 3 0.10
35 27 0.90
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (35 bp):
TATTTATATATTATATAATTAAATTATATTTAAAT
Found at i:1352618 original size:22 final size:23
Alignment explanation
Indices: 1352576--1352618 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1352566 AATATTTATA
*
1352576 TAATTTTTTATTAAATTATATTT
1 TAATTATTTATTAAATTATATTT
*
1352599 TAATTATTT-TTATATTATAT
1 TAATTATTTATTAAATTATAT
1352619 AATTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TAATTATTTATTAAATTATATTT
Found at i:1352649 original size:19 final size:17
Alignment explanation
Indices: 1352590--1352661 Score: 65
Period size: 19 Copynumber: 4.0 Consensus size: 17
1352580 TTTTTATTAA
*
1352590 ATTATATTTTAATTATT
1 ATTATATTTAAATTATT
*
1352607 TTTATATTATATAATTA-T
1 ATTATATT-TA-AATTATT
1352625 ATTATATTTAAATTTATT
1 ATTATATTTAAA-TTATT
*
1352643 AATTATACTTAAAATTATT
1 -ATTATA-TTTAAATTATT
1352662 TATTTTTACT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
16 2 0.04
17 12 0.27
18 10 0.22
19 16 0.36
20 5 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATATTTAAATTATT
Found at i:1352657 original size:20 final size:20
Alignment explanation
Indices: 1352620--1352658 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1352610 ATATTATATA
*
1352620 ATTATATTATATTTAAATTT
1 ATTATATTATATTAAAATTT
1352640 ATTA-ATTATACTTAAAATT
1 ATTATATTATA-TTAAAATT
1352659 ATTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTATATTATATTAAAATTT
Found at i:1353116 original size:25 final size:25
Alignment explanation
Indices: 1353088--1353135 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1353078 AATATAAAAA
1353088 TTTATAAA-ATTTATATAAATAATTT
1 TTTATAAATA-TTATATAAATAATTT
**
1353113 TTTATTTATATTATATAAATAAT
1 TTTATAAATATTATATAAATAAT
1353136 ATAAAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTATAAATATTATATAAATAATTT
Found at i:1357012 original size:2 final size:2
Alignment explanation
Indices: 1357005--1357029 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1356995 AGATTGTTGG
1357005 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 T
1357030 GTAACTCGCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1358481 original size:30 final size:32
Alignment explanation
Indices: 1358447--1358511 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 32
1358437 AGATTATGCC
1358447 AAAGTTATCAAAAGA-TA-A-CAAAACTAATCA
1 AAAGTTATCAAAAGATTATACCAAAACTAAT-A
*
1358477 AAAGTTATCAAAATATTATACCAAAACTAATA
1 AAAGTTATCAAAAGATTATACCAAAACTAATA
1358509 AAA
1 AAA
1358512 TTTTTATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 14 0.45
31 2 0.06
32 5 0.16
33 10 0.32
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (32 bp):
AAAGTTATCAAAAGATTATACCAAAACTAATA
Found at i:1358676 original size:20 final size:20
Alignment explanation
Indices: 1358616--1358677 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
1358606 AAGTTACTAA
*
1358616 AAAAATTATTAAAATTATGCT
1 AAAAATTATTAAAATTAT-AT
* * *
1358637 AAAAAATATTAATATCATAT
1 AAAAATTATTAAAATTATAT
1358657 GAAAAATTA-TAAAATTATAT
1 -AAAAATTATTAAAATTATAT
1358677 A
1 A
1358678 TTTTATAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 10 0.30
21 22 0.67
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAAATTATTAAAATTATAT
Found at i:1358899 original size:37 final size:34
Alignment explanation
Indices: 1358866--1358930 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1358856 TAATTTATAT
1358866 TATTTTTAAATAATATTTAAA-AATAAATTA-TTTA
1 TATTTTTAAATAA-ATTTAAATAA-AAATTATTTTA
*
1358900 TATTTTTAATTAAATTTAAATAAAAATTATT
1 TATTTTTAAATAAATTTAAATAAAAATTATT
1358931 AAATAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATTTTTAAATAAATTTAAATAAAAATTATTTTA
Found at i:1358927 original size:33 final size:34
Alignment explanation
Indices: 1358866--1358930 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
1358856 TAATTTATAT
1358866 TATTTTTAAATAATATTTAAAAATAAATTATTTA
1 TATTTTTAAATAATATTTAAAAATAAATTATTTA
*
1358900 TATTTTTAATTAA-ATTTAAATAA-AAATTATT
1 TATTTTTAAATAATATTTAAA-AATAAATTATT
1358931 AAATAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATTTTTAAATAATATTTAAAAATAAATTATTTA
Found at i:1359304 original size:19 final size:20
Alignment explanation
Indices: 1359276--1359315 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1359266 TACCCTCACC
*
1359276 CCCCACCCCCCACC-CCCCT
1 CCCCACCCCCAACCGCCCCT
*
1359295 CCCCATCCCCAACCGCCCCT
1 CCCCACCCCCAACCGCCCCT
1359315 C
1 C
1359316 TATTTTTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.12, C:0.78, G:0.03, T:0.07
Consensus pattern (20 bp):
CCCCACCCCCAACCGCCCCT
Found at i:1359844 original size:21 final size:21
Alignment explanation
Indices: 1359815--1359858 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1359805 CTTAAAATTT
*
1359815 TTATTTAAAT-TTAATTATAAA
1 TTATATAAATATTAA-TATAAA
1359836 TTATATAAATATTAATATAAA
1 TTATATAAATATTAATATAAA
1359857 TT
1 TT
1359859 TAATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATATAAATATTAATATAAA
Found at i:1359979 original size:2 final size:2
Alignment explanation
Indices: 1359972--1359999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1359962 ACGTAATCAA
1359972 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
1360000 TTTTGGTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.