Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 10 of 27
Found at i:1364715 original size:20 final size:20
Alignment explanation
Indices: 1364678--1364717 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1364668 TTATATTTAA
*
1364678 AATTATTAAAATATTAAATT
1 AATTATTAAAATAATAAATT
1364698 AATTATATAAAA-AATAAATT
1 AATTAT-TAAAATAATAAATT
1364718 TTTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTATTAAAATAATAAATT
Found at i:1364785 original size:20 final size:20
Alignment explanation
Indices: 1364732--1364786 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
1364722 AAAATAAATT
* **
1364732 ATATCATATATATATTTTTTA
1 ATATTATATATATA-TTTAAA
1364753 A-ATTATA-ATTATATTTAAA
1 ATATTATATA-TATATTTAAA
1364772 ATATTATATATATAT
1 ATATTATATATATAT
1364787 AAATATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 20 0.71
21 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTATATATATATTTAAA
Found at i:1364855 original size:17 final size:19
Alignment explanation
Indices: 1364834--1364875 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1364824 TAAATTTAAA
1364834 ATATTTATTTATT-TATAT
1 ATATTTATTTATTATATAT
*
1364852 -TATTTGTTTATTATATAT
1 ATATTTATTTATTATATAT
1364870 ATATTT
1 ATATTT
1364876 TTTTTCACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 11 0.52
18 5 0.24
19 5 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
ATATTTATTTATTATATAT
Found at i:1364870 original size:20 final size:20
Alignment explanation
Indices: 1364837--1364875 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1364827 ATTTAAAATA
*
1364837 TTTATTTATTTATATTATTTG
1 TTTATTTATATATA-TATTTG
1364858 TTTA-TTATATATATATTT
1 TTTATTTATATATATATTT
1364876 TTTTTCACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTATTTATATATATATTTG
Found at i:1368954 original size:22 final size:24
Alignment explanation
Indices: 1368907--1368953 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1368897 TCAATTAATG
1368907 ATATATTTTAATATTTAAATAAAA
1 ATATATTTTAATATTTAAATAAAA
1368931 ATATATTATT-ATATTT-AATAAAA
1 ATATATT-TTAATATTTAAATAAAA
1368954 TTAAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.32
24 13 0.59
25 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATATTTTAATATTTAAATAAAA
Found at i:1370572 original size:24 final size:24
Alignment explanation
Indices: 1370488--1370573 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 24
1370478 TACATCGTAA
* *
1370488 TTATATTTA-AAATATTATATATAT
1 TTATATATATAAATTTTA-ATATAT
1370512 TTATATAATTTGATAAATTATTTAATA-AT
1 TTATAT-A--T-ATAAA-T-TTTAATATAT
*
1370541 TAATTATATATAAATTTTAATATAT
1 TTA-TATATATAAATTTTAATATAT
1370566 TTATATAT
1 TTATATAT
1370574 TTATATTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
24 18 0.37
25 5 0.10
26 5 0.10
27 2 0.04
28 1 0.02
29 8 0.16
30 7 0.14
31 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
TTATATATATAAATTTTAATATAT
Found at i:1372848 original size:2 final size:2
Alignment explanation
Indices: 1372841--1372866 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1372831 CTTCGTTTGG
1372841 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1372867 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1381747 original size:19 final size:20
Alignment explanation
Indices: 1381715--1381765 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
1381705 TATAAATATC
* *
1381715 AATTATAATGTAAT-ATTAT
1 AATTATTATTTAATAATTAT
*
1381734 AATTATTATTTAATAATTTT
1 AATTATTATTTAATAATTAT
1381754 AA-TATT-TTTAAT
1 AATTATTATTTAAT
1381766 TATCGATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 16 0.57
20 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AATTATTATTTAATAATTAT
Found at i:1383695 original size:18 final size:18
Alignment explanation
Indices: 1383672--1383732 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 18
1383662 TTTACACACC
1383672 TAAAAAATGAAAAAAAAA
1 TAAAAAATGAAAAAAAAA
* *
1383690 T-AAAAATTAAAAAGAAAG
1 TAAAAAATGAAAAA-AAAA
* *
1383708 GAAAAAATG-AAAAGAAA
1 TAAAAAATGAAAAAAAAA
1383725 TAAAAAAT
1 TAAAAAAT
1383733 ATTTTTTCCA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
17 20 0.59
18 8 0.24
19 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (18 bp):
TAAAAAATGAAAAAAAAA
Found at i:1383731 original size:17 final size:17
Alignment explanation
Indices: 1383672--1383732 Score: 68
Period size: 18 Copynumber: 3.5 Consensus size: 17
1383662 TTTACACACC
*
1383672 TAAAAAATGAAAAAAAAA
1 TAAAAAATG-AAAAGAAA
* *
1383690 TAAAAATTAAAAAGAAA
1 TAAAAAATGAAAAGAAA
*
1383707 GGAAAAAATGAAAAGAAA
1 -TAAAAAATGAAAAGAAA
1383725 TAAAAAAT
1 TAAAAAAT
1383733 ATTTTTTCCA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (17 bp):
TAAAAAATGAAAAGAAA
Found at i:1384358 original size:14 final size:15
Alignment explanation
Indices: 1384307--1384358 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
1384297 GTTTTTTTAA
*
1384307 ATTAAATTAATTATT
1 ATTAAATAAATTATT
*
1384322 AATAAA-AAATTATT
1 ATTAAATAAATTATT
1384336 -TTAAAATAAATT-TT
1 ATT-AAATAAATTATT
1384350 ATTAAATAA
1 ATTAAATAA
1384359 TAATTATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 1 0.03
14 18 0.58
15 12 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAAATAAATTATT
Found at i:1385210 original size:19 final size:21
Alignment explanation
Indices: 1385186--1385232 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
1385176 ATAAAATGAT
1385186 ATAAAATACATAAAA-AATTA
1 ATAAAATACATAAAATAATTA
*
1385206 A-AAAA-ACCTAAAATAATTA
1 ATAAAATACATAAAATAATTA
1385225 ATAAAATA
1 ATAAAATA
1385233 ATATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 7 0.30
19 10 0.43
20 5 0.22
21 1 0.04
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAAAATACATAAAATAATTA
Found at i:1385332 original size:13 final size:13
Alignment explanation
Indices: 1385314--1385359 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1385304 TCTTTAAAAT
1385314 AATAAAAAATAAA
1 AATAAAAAATAAA
* **
1385327 AATAAAAATTCTA
1 AATAAAAAATAAA
*
1385340 AATAAAAAATAAC
1 AATAAAAAATAAA
1385353 AATAAAA
1 AATAAAA
1385360 TAAGAGCACA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:1385779 original size:23 final size:21
Alignment explanation
Indices: 1385743--1385787 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
1385733 AAAAATTATT
1385743 TTATATTAATATTTATATATAAA
1 TTATATTAATATTTA-A-ATAAA
1385766 TTATAATTAA-ATTTAAATAAA
1 TTAT-ATTAATATTTAAATAAA
1385787 T
1 T
1385788 ATCATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 9 0.43
24 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATATTAATATTTAAATAAA
Found at i:1387696 original size:17 final size:20
Alignment explanation
Indices: 1387674--1387712 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1387664 GAATTGAGGT
1387674 TTTGA-TTTGGA-GAA-AAG
1 TTTGATTTTGGATGAACAAG
1387691 TTTGATTTTGGATGAACAAG
1 TTTGATTTTGGATGAACAAG
1387711 TT
1 TT
1387713 CTTGATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 3 0.16
20 5 0.26
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.41
Consensus pattern (20 bp):
TTTGATTTTGGATGAACAAG
Found at i:1388388 original size:16 final size:16
Alignment explanation
Indices: 1388367--1388401 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1388357 ACAGCCTGCC
1388367 TCTCTAAACCAGAGAT
1 TCTCTAAACCAGAGAT
1388383 TCTCTAAACCAGAGAT
1 TCTCTAAACCAGAGAT
1388399 TCT
1 TCT
1388402 GTTGAAACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (16 bp):
TCTCTAAACCAGAGAT
Found at i:1392930 original size:2 final size:2
Alignment explanation
Indices: 1392923--1392959 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1392913 GTGAATCGCT
1392923 TA 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 TA T
1392960 GAGAGATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1402116 original size:25 final size:25
Alignment explanation
Indices: 1402088--1402136 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1402078 ATATATATAT
1402088 ATATATATAAATAATA-TAATGTAAC
1 ATATA-ATAAATAATATTAATGTAAC
* *
1402113 ATATAATATATTATATTAATGTAA
1 ATATAATAAATAATATTAATGTAA
1402137 TATGATACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (25 bp):
ATATAATAAATAATATTAATGTAAC
Found at i:1402121 original size:5 final size:5
Alignment explanation
Indices: 1402075--1402177 Score: 52
Period size: 5 Copynumber: 20.0 Consensus size: 5
1402065 CTTTAAATCT
* *
1402075 TATATA TATATA TATATA TATAA -ATAA TATAA TGTAACA TATAA TATAT
1 TATA-A TATA-A TATA-A TATAA TATAA TATAA TAT-A-A TATAA TATAA
* * * * *
1402124 TAT-A T-TAA TGTAA TATGATA CAAAA TATAA TAT-G TATAA TATAA TAAAA
1 TATAA TATAA TATAA TAT-A-A TATAA TATAA TATAA TATAA TATAA TATAA
1402173 TATAA
1 TATAA
1402178 CATTATATAT
Statistics
Matches: 76, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
3 1 0.01
4 10 0.13
5 40 0.53
6 20 0.26
7 5 0.07
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:1404072 original size:23 final size:25
Alignment explanation
Indices: 1404046--1404092 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
1404036 TTAATTAATT
*
1404046 AAATTTATTATTAAA-A-ATTTTAA
1 AAATTAATTATTAAATATATTTTAA
*
1404069 AAATTAATTTTTAAATATATTTTA
1 AAATTAATTATTAAATATATTTTA
1404093 TAATTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 1 0.05
25 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATTAATTATTAAATATATTTTAA
Found at i:1404081 original size:29 final size:29
Alignment explanation
Indices: 1404009--1404079 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
1403999 TAAATTTAAA
*
1404009 TAATAAA-TAATTTTATTTATTTAAAATT
1 TAATAAATTAATTTTATTTATTAAAAATT
* *
1404037 TAATTAATTAAATTTA-TTATTAAAAATTT
1 TAATAAATTAATTTTATTTATTAAAAA-TT
1404066 TAA-AAATTAATTTT
1 TAATAAATTAATTTT
1404080 TAAATATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 24 0.67
29 12 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATAAATTAATTTTATTTATTAAAAATT
Found at i:1404386 original size:25 final size:25
Alignment explanation
Indices: 1404358--1404425 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
1404348 TAATATAAAT
*
1404358 ATATAAATATTTTAAAATTTGTAT-A
1 ATATAAA-ATTTTAAAATTTATATAA
1404383 ATAT-AAATTTTAAAATTTTTATATAA
1 ATATAAAATTTTAAAA--TTTATATAA
1404409 ATATAAAATTTTAAAAT
1 ATATAAAATTTTAAAAT
1404426 ATAATTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
23 9 0.24
24 2 0.05
25 11 0.29
26 5 0.13
27 11 0.29
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (25 bp):
ATATAAAATTTTAAAATTTATATAA
Found at i:1404396 original size:23 final size:22
Alignment explanation
Indices: 1404366--1404438 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
1404356 ATATATAAAT
1404366 ATTTTAAAATTTGTATAATATAA
1 ATTTTAAAATTT-TATAATATAA
1404389 ATTTTAAAATTTT-T-ATATAA
1 ATTTTAAAATTTTATAATATAA
* *
1404409 A-TATAAAATTTTAAAATAT-A
1 ATTTTAAAATTTTATAATATAA
1404429 ATTATTAAAA
1 ATT-TTAAAA
1404439 ATATATAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
19 10 0.23
20 9 0.21
21 6 0.14
22 6 0.14
23 12 0.28
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
ATTTTAAAATTTTATAATATAA
Found at i:1404417 original size:19 final size:19
Alignment explanation
Indices: 1404337--1404420 Score: 60
Period size: 19 Copynumber: 4.1 Consensus size: 19
1404327 AAAAATTATA
* **
1404337 TTATATAAATATAATATAA
1 TTATATAAATATAAAATTT
*
1404356 ATATATAAATATTTTAAAATTT
1 TTATATAAATA---TAAAATTT
*
1404378 GTATAATATAAATTTTAAAATTT
1 -T-T-ATATAAA-TATAAAATTT
1404401 TTATATAAATATAAAATTT
1 TTATATAAATATAAAATTT
1404420 T
1 T
1404421 AAAATATAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
19 20 0.39
20 7 0.14
21 1 0.02
22 6 0.12
23 8 0.16
24 1 0.02
25 7 0.14
26 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (19 bp):
TTATATAAATATAAAATTT
Found at i:1404921 original size:8 final size:7
Alignment explanation
Indices: 1404871--1404934 Score: 62
Period size: 7 Copynumber: 9.0 Consensus size: 7
1404861 AATTTTATGA
1404871 TATAATT
1 TATAATT
1404878 TATAATT
1 TATAATT
*
1404885 AATAATT
1 TATAATT
1404892 TATATATTT
1 TATA-A-TT
1404901 ATATAATT
1 -TATAATT
1404909 TATAATTT
1 TATAA-TT
1404917 TATAA-T
1 TATAATT
1404923 TA-AATT
1 TATAATT
1404929 TA-AATT
1 TATAATT
1404935 ATTTTATATG
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
5 2 0.04
6 10 0.20
7 21 0.42
8 10 0.20
9 3 0.06
10 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TATAATT
Found at i:1405033 original size:17 final size:17
Alignment explanation
Indices: 1404995--1405050 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
1404985 AAATTTTTAA
*
1404995 ATATT-TATTTCATATTT
1 ATATTATATTTAATA-TT
* * *
1405012 TTATTATTTTTTATATT
1 ATATTATATTTAATATT
1405029 ATATTATATTTAATATT
1 ATATTATATTTAATATT
*
1405046 TTATT
1 ATATT
1405051 TTAATTATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
17 24 0.77
18 7 0.23
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
ATATTATATTTAATATT
Found at i:1405049 original size:14 final size:14
Alignment explanation
Indices: 1405007--1405061 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
1404997 ATTTATTTCA
*
1405007 TATTTTTATTATTT
1 TATTTTAATTATTT
* *
1405021 T-TTAT-ATTATAT
1 TATTTTAATTATTT
1405033 TATATTTAA-TATTT
1 TAT-TTTAATTATTT
1405047 TATTTTAATTATTT
1 TATTTTAATTATTT
1405061 T
1 T
1405062 TAGATGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.21
13 9 0.27
14 16 0.48
15 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTTAATTATTT
Found at i:1405063 original size:23 final size:23
Alignment explanation
Indices: 1404987--1405063 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
1404977 AAGTATTGAA
*
1404987 ATTTTTAA-ATATTTA-TTTCA-T
1 ATTTTTAATAT-TTTATTTTAATT
* *
1405008 ATTTTTATTATTTTTTATATTATATT
1 ATTTTTA--ATATTTTATTTTA-ATT
*
1405034 ATATTTAATATTTTATTTTAATT
1 ATTTTTAATATTTTATTTTAATT
1405057 ATTTTTA
1 ATTTTTA
1405064 GATGATATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
21 7 0.16
23 14 0.33
24 14 0.33
25 1 0.02
26 7 0.16
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (23 bp):
ATTTTTAATATTTTATTTTAATT
Found at i:1405203 original size:273 final size:271
Alignment explanation
Indices: 1404898--1405437 Score: 866
Period size: 273 Copynumber: 2.0 Consensus size: 271
1404888 AATTTATATA
* *
1404898 TTTATATAATTTATAATTTTATAATTAAATTTAAATTATTTTATATGATGATACATTAATAATTA
1 TTTATATAATTTATAATCTCATAATTAAATTTAAATTATTTTATATGATGATACATTAATAATTA
* *
1404963 ATATTATATTATATAAGTATTGAAATTTTTAAATATTTATTTCATATTTTTATTATTTTTTATAT
66 ATATTATATTATATAAGTATTGAAACTTTCAAATATTTATTTCATATTTTTATTATTTTTTATAT
* *
1405028 TATATTATATTTAATATTTTATTTTAATTATTTTTAGATGATATTTATATAATTGTATGGAGCAT
131 TATATTATATTT--TATTTTATTTTAATTATTTTTAGATAATATTGATATAATTGTATGGAGCAT
*
1405093 ATAATTAC-ATTTATTATATTTTCGTCTGTATTATTGTAAATTAATTTAAGAGAGGAAACTTAAA
194 ATAATT-CTATTTATTACATTTTCGTCTGTATTATTGTAAATTAATTTAAGAGAGGAAACTTAAA
*
1405157 AAATGATATATCAT
258 AAACGATATATCAT
* *
1405171 TTTATATAATTTATAATCTCATAATTAAATTTAAATTATTTTATATGTTGATACATTAATCATTA
1 TTTATATAATTTATAATCTCATAATTAAATTTAAATTATTTTATATGATGATACATTAATAATTA
* * *
1405236 ATATTATATTATATAAGTATTGAAACTTTCGAATATTTATTTTATGTTTTTATTATTTTTTATAT
66 ATATTATATTATATAAGTATTGAAACTTTCAAATATTTATTTCATATTTTTATTATTTTTTATAT
** *
1405301 TATATTATATTTTATTTTATTTTAATTATTTTTTTATAATATTGATATAATTGTATTGAGCATAT
131 TATATTATATTTTATTTTATTTTAATTATTTTTAGATAATATTGATATAATTGTATGGAGCATAT
* * * *
1405366 AATTCTATTTATTACATTTTCGTGTGTATTATTGTAAATTAATTTCAGGGAGGAAACTTGAAAAA
196 AATTCTATTTATTACATTTTCGTCTGTATTATTGTAAATTAATTTAAGAGAGGAAACTTAAAAAA
1405431 CGATATA
261 CGATATA
1405438 CGTACGAGCA
Statistics
Matches: 246, Mismatches: 20, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
270 1 0.00
271 112 0.46
273 133 0.54
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (271 bp):
TTTATATAATTTATAATCTCATAATTAAATTTAAATTATTTTATATGATGATACATTAATAATTA
ATATTATATTATATAAGTATTGAAACTTTCAAATATTTATTTCATATTTTTATTATTTTTTATAT
TATATTATATTTTATTTTATTTTAATTATTTTTAGATAATATTGATATAATTGTATGGAGCATAT
AATTCTATTTATTACATTTTCGTCTGTATTATTGTAAATTAATTTAAGAGAGGAAACTTAAAAAA
CGATATATCAT
Found at i:1405306 original size:17 final size:17
Alignment explanation
Indices: 1405268--1405320 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1405258 AAACTTTCGA
*
1405268 ATATT-TATTTTATGTTT
1 ATATTATATTTTAT-ATT
* *
1405285 TTATTATTTTTTATATT
1 ATATTATATTTTATATT
*
1405302 ATATTATATTTTATTTT
1 ATATTATATTTTATATT
1405319 AT
1 AT
1405321 TTTAATTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 22 0.76
18 7 0.24
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:1413216 original size:22 final size:22
Alignment explanation
Indices: 1413161--1413223 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
1413151 CACACATGTT
*
1413161 ATTTACTTAATATAAAAATTATA
1 ATTT-CTTAAGATAAAAATTATA
*
1413184 ATTT-TAAAAGATAAAAA-TATA
1 ATTTCT-TAAGATAAAAATTATA
1413205 ATGTTCTTAAGAGTAAAAA
1 AT-TTCTTAAGA-TAAAAA
1413224 AGAATGTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 7 0.21
22 15 0.45
23 11 0.33
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (22 bp):
ATTTCTTAAGATAAAAATTATA
Found at i:1413829 original size:12 final size:12
Alignment explanation
Indices: 1413814--1413872 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
1413804 GAATACACTT
* *
1413814 AATAATATTAGA
1 AATAATATAAAA
1413826 AATAATATAAAA
1 AATAATATAAAA
1413838 AATAAT-TAAAA
1 AATAATATAAAA
*
1413849 TATAAATATAATATA
1 AAT-AATATAA-A-A
1413864 AAT-ATATAA
1 AATAATATAA
1413873 TTATATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 7 0.18
12 19 0.49
13 9 0.23
14 1 0.03
15 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
AATAATATAAAA
Found at i:1413857 original size:6 final size:6
Alignment explanation
Indices: 1413846--1413933 Score: 55
Period size: 6 Copynumber: 15.2 Consensus size: 6
1413836 AAAATAATTA
* **
1413846 AAATAT AAATAT -AATAT AAATAT ATAAT-T ATAT-T AAA-AT TTATAT
1 AAATAT AAATAT AAATAT AAATAT A-AATAT AAATAT AAATAT AAATAT
*
1413891 -AATAT AAATATT AAAATAT AAAAAAT AAA-AT -AATAT AAATAT A
1 AAATAT AAATA-T -AAATAT -AAATAT AAATAT AAATAT AAATAT A
1413934 GGAATTAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
4 2 0.03
5 20 0.30
6 29 0.43
7 11 0.16
8 5 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AAATAT
Found at i:1413866 original size:17 final size:17
Alignment explanation
Indices: 1413846--1413933 Score: 73
Period size: 16 Copynumber: 5.4 Consensus size: 17
1413836 AAAATAATTA
1413846 AAATATAAATATAATAT
1 AAATATAAATATAATAT
1413863 AAATATATAAT-T-ATATT
1 AAATATA-AATATAATA-T
**
1413880 AAA-ATTTATATAATAT
1 AAATATAAATATAATAT
1413896 AAATATTAAA-AT-ATA-
1 AAATA-TAAATATAATAT
*
1413911 AAAAATAAA-ATAATAT
1 AAATATAAATATAATAT
1413927 AAATATA
1 AAATATA
1413934 GGAATTAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 17
0.71 0.08 0.21
Matches are distributed among these distances:
14 6 0.11
15 9 0.16
16 19 0.33
17 18 0.32
18 5 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAAATATAATAT
Found at i:1414519 original size:3 final size:3
Alignment explanation
Indices: 1414513--1414544 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1414503 TCACGCCTCC
*
1414513 TCT TCT TCT TCT TCT TCT TCT TCT GCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1414545 ATGGTCGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:1418199 original size:30 final size:30
Alignment explanation
Indices: 1418163--1418220 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1418153 CAAAATATTA
*
1418163 AAAATTTTT-ATAAATATAAATGAACAAATT
1 AAAATTTTTCAAAAAT-TAAATGAACAAATT
*
1418193 AAAATTTTTCAAAAATTAAATGATCAAA
1 AAAATTTTTCAAAAATTAAATGAACAAA
1418221 ATGCAAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAATTTTTCAAAAATTAAATGAACAAATT
Found at i:1421103 original size:2 final size:2
Alignment explanation
Indices: 1421096--1421130 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1421086 TCAAACTGTA
1421096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1421131 ACCTCTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1421213 original size:22 final size:20
Alignment explanation
Indices: 1421173--1421227 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
1421163 GGTTCATTAG
*
1421173 TTTTTAAAATTTTTAAAATAT
1 TTTTTATAATTTTTAAAAT-T
1421194 ATTTTTATAATATTTT-AAATT
1 -TTTTTATAAT-TTTTAAAATT
1421215 TTTTTATTAATTT
1 TTTTTA-TAATTT
1421228 AAAAAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 8 0.27
21 5 0.17
22 13 0.43
23 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTATAATTTTTAAAATT
Found at i:1422877 original size:18 final size:18
Alignment explanation
Indices: 1422854--1422901 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
1422844 GATTTTTATA
1422854 TTTTATAT-TTATATAATT
1 TTTTATATATTA-ATAATT
1422872 TTTTATATATTAATAATT
1 TTTTATATATTAATAATT
1422890 TATCTTATATAT
1 T-T-TTATATAT
1422902 AAATTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 15 0.56
19 4 0.15
20 8 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATATATTAATAATT
Found at i:1422882 original size:20 final size:21
Alignment explanation
Indices: 1422848--1422901 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
1422838 TACTTTGATT
* *
1422848 TTTATATTTTATATTTATATAA
1 TTTATCTTATATATTTA-ATAA
1422870 TTT-T-TTATATA-TTAATAA
1 TTTATCTTATATATTTAATAA
1422888 TTTATCTTATATAT
1 TTTATCTTATATAT
1422902 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.25
19 4 0.14
20 13 0.46
21 1 0.04
22 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATCTTATATATTTAATAA
Found at i:1422903 original size:34 final size:35
Alignment explanation
Indices: 1422855--1422933 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 35
1422845 ATTTTTATAT
* * *
1422855 TTTATATT-TATATAATTTTTTATATATTAA-TAA
1 TTTATATTATATATAAATTTTAAAATATTAATTAA
*
1422888 TTTATCTTATATATAAATTTTAAAATATTAATTAA
1 TTTATATTATATATAAATTTTAAAATATTAATTAA
*
1422923 TTTATTTTATA
1 TTTATATTATA
1422934 ATTTTATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 7 0.18
34 19 0.49
35 13 0.33
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (35 bp):
TTTATATTATATATAAATTTTAAAATATTAATTAA
Found at i:1424303 original size:17 final size:16
Alignment explanation
Indices: 1424265--1424295 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1424255 AATTTTTAAT
*
1424265 AAATATTTATATTTTA
1 AAATAATTATATTTTA
1424281 AAATAATTATATTTT
1 AAATAATTATATTTT
1424296 TAACATAAAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATAATTATATTTTA
Found at i:1425348 original size:3 final size:3
Alignment explanation
Indices: 1425340--1425373 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1425330 ATTTAAGAAC
1425340 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1425374 TTACGAATAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1434648 original size:17 final size:19
Alignment explanation
Indices: 1434626--1434663 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1434616 CTCTATCTTC
1434626 TTTTTC-CCTTTT-TTTTT
1 TTTTTCTCCTTTTATTTTT
*
1434643 TTTTTCTTCTTTTATTTTT
1 TTTTTCTCCTTTTATTTTT
1434662 TT
1 TT
1434664 AATTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTCTCCTTTTATTTTT
Found at i:1435150 original size:16 final size:16
Alignment explanation
Indices: 1435125--1435155 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1435115 TTATGTCAAA
*
1435125 TCAATTAAATCAATTC
1 TCAATCAAATCAATTC
1435141 TCAATCAAATCAATT
1 TCAATCAAATCAATT
1435156 ACTTTAATTC
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:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (16 bp):
TCAATCAAATCAATTC
Found at i:1436239 original size:7 final size:7
Alignment explanation
Indices: 1436227--1436251 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1436217 TATTATTTAA
1436227 TTATTTT
1 TTATTTT
1436234 TTATTTT
1 TTATTTT
1436241 TTATTTT
1 TTATTTT
1436248 TTAT
1 TTAT
1436252 GTATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTATTTT
Found at i:1436304 original size:18 final size:18
Alignment explanation
Indices: 1436265--1436311 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1436255 TTTTTATAAT
* *
1436265 ATTTTAATTTTATTTTAC
1 ATTTTAATTTAATTTTAA
1436283 ATTTTAA-TTAATTTTAAA
1 ATTTTAATTTAATTTT-AA
*
1436301 ATTTTTATTTA
1 ATTTTAATTTA
1436312 CTCAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.29
18 14 0.58
19 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTAATTTAATTTTAA
Found at i:1437324 original size:16 final size:17
Alignment explanation
Indices: 1437283--1437321 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1437273 TAAATTTTTT
*
1437283 ATCTAATTTATCTTTAA
1 ATCTAAATTATCTTTAA
1437300 ATCTAAATTAT-TTTAA
1 ATCTAAATTATCTTTAA
1437316 AT-TAAA
1 ATCTAAA
1437322 ATTGAGTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 7 0.33
17 10 0.48
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (17 bp):
ATCTAAATTATCTTTAA
Found at i:1439719 original size:12 final size:13
Alignment explanation
Indices: 1439702--1439733 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1439692 TGTGAGAATA
1439702 TATTTTTA-TTTT
1 TATTTTTATTTTT
1439714 TATTTTTATTTTT
1 TATTTTTATTTTT
1439727 TATTTTT
1 TATTTTT
1439734 TTGTAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:1439734 original size:7 final size:6
Alignment explanation
Indices: 1439702--1439733 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
1439692 TGTGAGAATA
1439702 TATTTT TATTTT TATTTT TATTTTT TATTTT T
1 TATTTT TATTTT TATTTT TA-TTTT TATTTT T
1439734 TTGTAGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:1440108 original size:41 final size:42
Alignment explanation
Indices: 1440062--1440161 Score: 100
Period size: 43 Copynumber: 2.4 Consensus size: 42
1440052 ATTTTATGAG
*
1440062 TAAAATTAAAAAATTATTATATA-TTTTTATAATATAT-TTTA-A
1 TAAAATTAAAAAATTATAATA-ACTTTTTA-AAT-TATCTTTATA
* *
1440104 -AAAATAAATAAAATATATAATAACTTTTTAAATTCTCTTTATA
1 TAAAATTAA-AAAAT-TATAATAACTTTTTAAATTATCTTTATA
1440147 TAAAATTAAAAAATT
1 TAAAATTAAAAAATT
1440162 TACCATCTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
41 9 0.19
42 14 0.29
43 18 0.38
44 7 0.15
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (42 bp):
TAAAATTAAAAAATTATAATAACTTTTTAAATTATCTTTATA
Found at i:1441409 original size:19 final size:19
Alignment explanation
Indices: 1441386--1441431 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1441376 TATTAAACCA
1441386 AATATTTAT-TAATATATAT
1 AATATTTATATAATA-ATAT
* *
1441405 GATATTAATATAATAATAT
1 AATATTTATATAATAATAT
1441424 AATATTTA
1 AATATTTA
1441432 AACTCAGTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AATATTTATATAATAATAT
Found at i:1441426 original size:13 final size:15
Alignment explanation
Indices: 1441392--1441428 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1441382 ACCAAATATT
*
1441392 TATTAATATATATGA
1 TATTAATATATATAA
1441407 TATTAATATA-ATAA
1 TATTAATATATATAA
1441421 TA-TAATAT
1 TATTAATAT
1441429 TTAAACTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.29
14 5 0.24
15 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
TATTAATATATATAA
Found at i:1442550 original size:36 final size:35
Alignment explanation
Indices: 1442481--1442552 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 35
1442471 TTTGTTTTAA
*
1442481 TTTTTTTTATTATTTTAAATTAAATTAATTTAAAT
1 TTTTTTTTATTATTATAAATTAAATTAATTTAAAT
1442516 TTTTATTTTATTATTAT-AA-TAATATTAATATTAAAT
1 TTTT-TTTTATTATTATAAATTAA-ATTAAT-TTAAAT
1442552 T
1 T
1442553 ATTGTAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
34 3 0.09
35 12 0.36
36 18 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (35 bp):
TTTTTTTTATTATTATAAATTAAATTAATTTAAAT
Found at i:1443111 original size:15 final size:16
Alignment explanation
Indices: 1443089--1443213 Score: 62
Period size: 15 Copynumber: 7.6 Consensus size: 16
1443079 CTTATTAAAA
1443089 AATTAAATTATTATTT
1 AATTAAATTATTATTT
* *
1443105 -TTTAAATT-TAATTT
1 AATTAAATTATTATTT
1443119 AATTAAATTATT-TTT
1 AATTAAATTATTATTT
*
1443134 AATTATATTGA--ATTT
1 AATTAAATT-ATTATTT
* *
1443149 GAAATAGTATATTTTTATTT
1 --AAT--TAAATTATTATTT
* *
1443169 AAATAAATTTTTAATTT
1 AATTAAATTATT-ATTT
* *
1443186 GATTTAAATTATTATTA
1 -AATTAAATTATTATTT
1443203 AATTAATATTA
1 AATTAA-ATTA
1443214 ATGTATATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 25
0.69 0.11 0.21
Matches are distributed among these distances:
14 5 0.06
15 28 0.34
16 15 0.18
17 14 0.17
18 11 0.13
19 6 0.07
20 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTAAATTATTATTT
Found at i:1443148 original size:30 final size:30
Alignment explanation
Indices: 1443089--1443148 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1443079 CTTATTAAAA
* *
1443089 AATTAAATTATTATTTTTTAAATTTAATTT
1 AATTAAATTATTATTTATTAAATTGAATTT
*
1443119 AATTAAATTATT-TTTAATTATATTGAATTT
1 AATTAAATTATTATTT-ATTAAATTGAATTT
1443149 GAAATAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
AATTAAATTATTATTTATTAAATTGAATTT
Found at i:1444003 original size:17 final size:19
Alignment explanation
Indices: 1443968--1444004 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1443958 ATCAATTTAT
*
1443968 AAATATATATATATAATAA
1 AAATATATATAAATAATAA
1443987 AAATATAT-TAAAT-ATAA
1 AAATATATATAAATAATAA
1444004 A
1 A
1444005 TTTTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATATATAAATAATAA
Found at i:1444519 original size:21 final size:21
Alignment explanation
Indices: 1444495--1444534 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1444485 TATTTTTTTT
1444495 AAAAT-TTAATTATAAAATATG
1 AAAATATTAA-TATAAAATATG
1444516 AAAATATTAATATAAAATA
1 AAAATATTAATATAAAATA
1444535 ATTTATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAATATTAATATAAAATATG
Found at i:1444989 original size:28 final size:30
Alignment explanation
Indices: 1444949--1445006 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
1444939 TTTTCTTATT
*
1444949 TATTAATATTTTAAATA-TGTAAAAATTAAA
1 TATTAATATTTT-AATAGTATAAAAATTAAA
1444979 TATTAA-A-TTTAATAGTATAAAAATTAAA
1 TATTAATATTTTAATAGTATAAAAATTAAA
1445007 ATAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.15
28 15 0.58
29 1 0.04
30 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (30 bp):
TATTAATATTTTAATAGTATAAAAATTAAA
Found at i:1449603 original size:2 final size:2
Alignment explanation
Indices: 1449596--1449628 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1449586 CCACAACCAC
1449596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1449629 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1449633 original size:2 final size:2
Alignment explanation
Indices: 1449628--1449653 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1449618 ATATATATAT
1449628 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
1449654 TGGAAAACCA
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:1457478 original size:19 final size:19
Alignment explanation
Indices: 1457456--1457492 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1457446 AAAATAATAA
1457456 TAAAATATTTAATATTTTT
1 TAAAATATTTAATATTTTT
* *
1457475 TAAATTTTTTAATATTTT
1 TAAAATATTTAATATTTT
1457493 ATTCTTGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAAAATATTTAATATTTTT
Found at i:1457491 original size:10 final size:10
Alignment explanation
Indices: 1457463--1457492 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1457453 TAATAAAATA
1457463 TTTAATATTT
1 TTTAATATTT
1457473 TTTAA-ATTT
1 TTTAATATTT
1457482 TTTAATATTT
1 TTTAATATTT
1457492 T
1 T
1457493 ATTCTTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTAATATTT
Found at i:1457678 original size:2 final size:2
Alignment explanation
Indices: 1457671--1457707 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1457661 CTAAGGAAAG
1457671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1457708 ATAATTGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1458885 original size:14 final size:15
Alignment explanation
Indices: 1458859--1458903 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1458849 ACGATTTAAA
1458859 AAAATTATAAATATT
1 AAAATTATAAATATT
1458874 AAAATT-TAAATA-T
1 AAAATTATAAATATT
*
1458887 AAATTTATTAAATATT
1 AAAATTA-TAAATATT
1458903 A
1 A
1458904 TTTTTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.23
14 6 0.23
15 12 0.46
16 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:1458900 original size:29 final size:25
Alignment explanation
Indices: 1458852--1458903 Score: 68
Period size: 29 Copynumber: 1.9 Consensus size: 25
1458842 AAAGCTTACG
1458852 ATTTAAAAAAATTATAAATATTAAA
1 ATTTAAAAAAATTATAAATATTAAA
1458877 ATTTAAATATAAATTTATTAAATATTA
1 ATTTAAA-A-AAA-TTA-TAAATATTA
1458904 TTTTTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.30
26 1 0.04
27 3 0.13
28 3 0.13
29 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAAAAAATTATAAATATTAAA
Found at i:1460471 original size:16 final size:16
Alignment explanation
Indices: 1460452--1460494 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1460442 TTGTGTACGC
1460452 AATTTATTAATTAATT
1 AATTTATTAATTAATT
* * *
1460468 AATTTGTTATTTATTT
1 AATTTATTAATTAATT
*
1460484 AATTAATTAAT
1 AATTTATTAAT
1460495 ATTTTATATG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
AATTTATTAATTAATT
Found at i:1461327 original size:22 final size:22
Alignment explanation
Indices: 1461302--1461344 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1461292 ATTAATTTAA
* * *
1461302 TTAATTTTATTTATAAAATTTG
1 TTAATTATATTAAAAAAATTTG
1461324 TTAATTATATTAAAAAAATTT
1 TTAATTATATTAAAAAAATTT
1461345 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTATATTAAAAAAATTTG
Found at i:1461531 original size:15 final size:16
Alignment explanation
Indices: 1461511--1461541 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1461501 TTCAATTAAA
1461511 TTTTTAAA-TTAAAAT
1 TTTTTAAATTTAAAAT
1461526 TTTTTAAATTTAAAAT
1 TTTTTAAATTTAAAAT
1461542 AAATACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTTAAATTTAAAAT
Found at i:1462135 original size:5 final size:5
Alignment explanation
Indices: 1462127--1462153 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1462117 TAAAATATAT
1462127 TTAAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TT
1462154 TATAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:1462282 original size:2 final size:2
Alignment explanation
Indices: 1462275--1462304 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1462265 TTATCAACTC
1462275 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
1462305 GCTGAAATGA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1462684 original size:22 final size:21
Alignment explanation
Indices: 1462635--1462685 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1462625 ATCGGTTAAA
*
1462635 TTAAAT-TATTTAATTAAATAT
1 TTAAATAT-TTTAAATAAATAT
1462656 TTAAATATTTTAAATAAATAAT
1 TTAAATATTTTAAATAAAT-AT
*
1462678 TTTAATAT
1 TTAAATAT
1462686 CAACCGAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAATATTTTAAATAAATAT
Found at i:1463515 original size:93 final size:93
Alignment explanation
Indices: 1463299--1463576 Score: 407
Period size: 94 Copynumber: 3.0 Consensus size: 93
1463289 GCTAAAAAAA
* *
1463299 AATGATGCAAACTTTTAAAGATTTTTTTTTTTTTAGTTTGAAAGCAACTTAACTTTAGA-AGGTT
1 AATGATGCAAACTTTTAAAG---TTTTTTTTTTTGGTTTGAAAGCAACTTAATTTTAGAGA-GTT
1463363 TTAATAAAATAGAATGGCTTTAAAATCCAATG
62 TTAATAAAATAGAATGGCTTTAAAATCCAATG
* * *
1463395 AATCATTCAAACTTTTAGAGTTTTTTTTTTTGGTTTGAAAGCAACTTAATTTTTAGAGAGTTTTA
1 AATGATGCAAACTTTTAAAGTTTTTTTTTTTGGTTTGAAAGCAACTTAA-TTTTAGAGAGTTTTA
1463460 ATAAAATAGAATGGCTTTAAAATCCAATG
65 ATAAAATAGAATGGCTTTAAAATCCAATG
* * *
1463489 AATGATGCAAACTTTTATAG-TTTTTTTTTTGGTTTGAAAGCAACTTAATTTTAAAGGGTTTTAA
1 AATGATGCAAACTTTTAAAGTTTTTTTTTTTGGTTTGAAAGCAACTTAATTTTAGAGAGTTTTAA
* *
1463553 TAAAATATAATAGCTTTAAAATCC
66 TAAAATAGAATGGCTTTAAAATCC
1463577 CCATAAAAGA
Statistics
Matches: 168, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
92 36 0.21
93 56 0.33
94 58 0.35
95 1 0.01
96 17 0.10
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (93 bp):
AATGATGCAAACTTTTAAAGTTTTTTTTTTTGGTTTGAAAGCAACTTAATTTTAGAGAGTTTTAA
TAAAATAGAATGGCTTTAAAATCCAATG
Found at i:1472614 original size:6 final size:7
Alignment explanation
Indices: 1472596--1472627 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1472586 CTAAACTATG
1472596 ATTTTTT
1 ATTTTTT
1472603 ATTTTTT
1 ATTTTTT
1472610 ATTTTTT
1 ATTTTTT
*
1472617 ATTTTTC
1 ATTTTTT
1472624 ATTT
1 ATTT
1472628 GTAGGTGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (7 bp):
ATTTTTT
Found at i:1473688 original size:3 final size:3
Alignment explanation
Indices: 1473674--1473712 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1473664 TACTTAAGAC
* *
1473674 ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1473713 TGTTTTAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1474075 original size:3 final size:3
Alignment explanation
Indices: 1474067--1474097 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1474057 TAGAAGGAGG
1474067 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1474098 AATTTGTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1474643 original size:30 final size:30
Alignment explanation
Indices: 1474585--1474646 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1474575 ATTGATGTAA
* *
1474585 ATTAATTTAATTTAATTTATTGTAATTTTT
1 ATTAATTTAATTTAATTTAATCTAATTTTT
*
1474615 ATTAATTTATATTT-ATTTAATCTGATTTTT
1 ATTAATTTA-ATTTAATTTAATCTAATTTTT
1474645 AT
1 AT
1474647 ATTATATGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (30 bp):
ATTAATTTAATTTAATTTAATCTAATTTTT
Found at i:1475319 original size:21 final size:23
Alignment explanation
Indices: 1475282--1475324 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
1475272 TTAAAAATAA
1475282 TTTATATATTAATATTTATATAT
1 TTTATATATTAATATTTATATAT
1475305 TTTATA-ATTAA-ATTTATATA
1 TTTATATATTAATATTTATATA
1475325 AAAATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 5 0.25
23 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTATATATTAATATTTATATAT
Found at i:1475320 original size:35 final size:32
Alignment explanation
Indices: 1475280--1475344 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
1475270 ATTTAAAAAT
* *
1475280 AATTTATATATTAATATTTATATATTTTATAATTA
1 AATTTATATA--AAAATTTATAT-TTATATAATTA
1475315 AATTTATATAAAAATTTATATTTATATAAT
1 AATTTATATAAAAATTTATATTTATATAAT
1475345 AATTCAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 8 0.29
33 10 0.36
35 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
AATTTATATAAAAATTTATATTTATATAATTA
Found at i:1476300 original size:11 final size:11
Alignment explanation
Indices: 1476279--1476341 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
1476269 ATGTTAAATA
1476279 ATTAT-TTTAT
1 ATTATATTTAT
1476289 ATTATATTTAT
1 ATTATATTTAT
1476300 A-T-TATTT-T
1 ATTATATTTAT
*
1476308 -TTAT-GTTAT
1 ATTATATTTAT
1476317 AATTATATTTAT
1 -ATTATATTTAT
*
1476329 AATATATTTAT
1 ATTATATTTAT
1476340 AT
1 AT
1476342 ATTTTAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
8 4 0.10
9 7 0.17
10 6 0.14
11 21 0.50
12 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:1476362 original size:18 final size:19
Alignment explanation
Indices: 1476320--1476355 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1476310 ATGTTATAAT
*
1476320 TATATTTATAATATATTTA
1 TATATTTATAAAATATTTA
1476339 TATATTT-TAAAATATTT
1 TATATTTATAAAATATTT
1476356 GTGTATTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTTATAAAATATTTA
Found at i:1477307 original size:9 final size:10
Alignment explanation
Indices: 1477283--1477315 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
1477273 AAAATAATAA
1477283 ATTTATATTAT
1 ATTTATA-TAT
1477294 ATTTATAT-T
1 ATTTATATAT
1477303 ATTTATATAT
1 ATTTATATAT
1477313 ATT
1 ATT
1477316 ATTTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 5 0.24
11 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTATATAT
Found at i:1478221 original size:21 final size:21
Alignment explanation
Indices: 1478173--1478223 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1478163 CGTTATTTTT
*
1478173 TAATAATTATTTTATATTATAT
1 TAAT-ATTATTTTATATTATAA
* * *
1478195 TTATATTTTTTTATGTTATAA
1 TAATATTATTTTATATTATAA
1478216 TAATATTA
1 TAATATTA
1478224 ATAATATTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TAATATTATTTTATATTATAA
Found at i:1478968 original size:8 final size:8
Alignment explanation
Indices: 1478955--1478979 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1478945 TATCTAAAGT
1478955 ATTATATA
1 ATTATATA
1478963 ATTATATA
1 ATTATATA
1478971 ATTATATA
1 ATTATATA
1478979 A
1 A
1478980 ATTTTGGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTATATA
Found at i:1479995 original size:6 final size:6
Alignment explanation
Indices: 1479986--1480012 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1479976 AGATTAAAAT
1479986 AAAACC AAAACC AAAACC AAAACC AAA
1 AAAACC AAAACC AAAACC AAAACC AAA
1480013 TCCCTACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:1481585 original size:2 final size:2
Alignment explanation
Indices: 1481578--1481611 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1481568 AATTTTGGCT
1481578 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1481612 GGATTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1481985 original size:2 final size:2
Alignment explanation
Indices: 1481980--1482006 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1481970 TGTGTGTGTG
1481980 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 T
1482007 GACTGAAATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1487155 original size:20 final size:20
Alignment explanation
Indices: 1487122--1487167 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
1487112 CAAAAATATG
* *
1487122 TTTTTATATAAAATTTTAA-
1 TTTTTATAAAAAATCTTAAC
1487141 TTTTTATAAATAAATCTTAAC
1 TTTTTATAAA-AAATCTTAAC
1487162 TTTTTA
1 TTTTTA
1487168 ATCATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 8 0.35
21 6 0.26
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTTATAAAAAATCTTAAC
Found at i:1488369 original size:23 final size:24
Alignment explanation
Indices: 1488341--1488386 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1488331 ATATTTTTTA
*
1488341 ATTAATTATTTAT-TATATTTAAT
1 ATTAATTATTTATAAATATTTAAT
*
1488364 ATTAATTTTTTATAAATATTTAA
1 ATTAATTATTTATAAATATTTAA
1488387 AATTTGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTAATTATTTATAAATATTTAAT
Found at i:1494782 original size:10 final size:10
Alignment explanation
Indices: 1494764--1494801 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1494754 TTGATAATTT
*
1494764 TAATGAAATA
1 TAATAAAATA
1494774 TAATAAAAT-
1 TAATAAAATA
*
1494783 TATTAAAATA
1 TAATAAAATA
1494793 TAATAAAAT
1 TAATAAAAT
1494802 TATAGTGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (10 bp):
TAATAAAATA
Found at i:1494849 original size:25 final size:27
Alignment explanation
Indices: 1494819--1494868 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
1494809 TGAAATAAAA
1494819 ATAATAT-AAATATTATA-AATATATG
1 ATAATATCAAATATTATATAATATATG
*
1494844 ATAATATCAAATTTTATATAATATA
1 ATAATATCAAATATTATATAATATA
1494869 AATTAGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 9 0.41
27 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
ATAATATCAAATATTATATAATATATG
Found at i:1494878 original size:17 final size:16
Alignment explanation
Indices: 1494832--1494901 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
1494822 ATATAAATAT
1494832 TATAAA-TATATGATAA
1 TATAAATTATAT-ATAA
*
1494848 TATCAAATTTTATATAA
1 TAT-AAATTATATATAA
*
1494865 TATAAATTAGTATAATAT
1 TATAAATTA-TAT-ATAA
* *
1494883 TGTAATTTATATA-AA
1 TATAAATTATATATAA
1494898 TATA
1 TATA
1494902 TTAAGCATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
15 4 0.09
16 9 0.21
17 16 0.37
18 14 0.33
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (16 bp):
TATAAATTATATATAA
Found at i:1495972 original size:14 final size:13
Alignment explanation
Indices: 1495930--1495973 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1495920 ATAATAGTTG
1495930 TAAATATAAAAATT
1 TAAATAT-AAAATT
1495944 TAAATGATAAAATT
1 TAAAT-ATAAAATT
*
1495958 TAAATTTAAATATT
1 TAAATATAAA-ATT
1495972 TA
1 TA
1495974 TTAAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 4 0.15
14 21 0.78
15 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
TAAATATAAAATT
Found at i:1495991 original size:31 final size:32
Alignment explanation
Indices: 1495956--1496021 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 32
1495946 AATGATAAAA
*
1495956 TTTAAATTTAAATATT-TATTAA-ATATTATTT
1 TTTAAAGTTAAAT-TTATATTAATATATTATTT
* *
1495987 TTT-AAGTTAAGTTTATATTAATTTATTATTT
1 TTTAAAGTTAAATTTATATTAATATATTATTT
1496018 TTTA
1 TTTA
1496022 TGCAATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
29 2 0.07
30 13 0.45
31 14 0.48
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (32 bp):
TTTAAAGTTAAATTTATATTAATATATTATTT
Found at i:1496803 original size:20 final size:20
Alignment explanation
Indices: 1496778--1496827 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1496768 GGGCATAATG
*
1496778 TATCGATACAAT-TCTTCATA
1 TATCGATACAATGTC-CCATA
1496798 TATCGATACAATGTCCCATA
1 TATCGATACAATGTCCCATA
1496818 TATCGATACA
1 TATCGATACA
1496828 TTTCACTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (20 bp):
TATCGATACAATGTCCCATA
Found at i:1496882 original size:20 final size:20
Alignment explanation
Indices: 1496856--1496911 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
1496846 CTGTCAGTTT
1496856 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
1496876 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
*
1496895 CATGTATCAATACAATT
1 CATGTATCGATACAATT
1496912 ATCGATACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:1499177 original size:21 final size:19
Alignment explanation
Indices: 1499130--1499177 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
1499120 TTTATTGATG
1499130 ATTTTGATGAAAAACAGAA
1 ATTTTGATGAAAAACAGAA
1499149 AGTTTTGATGTAAATAACA-AGA
1 A-TTTTGATG-AAA-AACAGA-A
1499171 ATTTTGA
1 ATTTTGA
1499178 AAAGAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.04
20 8 0.32
21 10 0.40
22 6 0.24
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (19 bp):
ATTTTGATGAAAAACAGAA
Found at i:1499308 original size:13 final size:13
Alignment explanation
Indices: 1499290--1499338 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
1499280 GTAACTCATA
*
1499290 TATCGATACATTG
1 TATCGATACAGTG
1499303 TATCGATACAGTG
1 TATCGATACAGTG
*
1499316 TATCGATATAGTG
1 TATCGATACAGTG
*
1499329 TATCAATACA
1 TATCGATACA
1499339 AAAAACCTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:1505494 original size:12 final size:12
Alignment explanation
Indices: 1505477--1505502 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1505467 TATAATTCTT
1505477 CATGTATCGATA
1 CATGTATCGATA
1505489 CATGTATCGATA
1 CATGTATCGATA
1505501 CA
1 CA
1505503 ATGTCTCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:1505499 original size:32 final size:32
Alignment explanation
Indices: 1505458--1505520 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
1505448 GTTGGGCATA
*
1505458 ATGTATCGATATAAT-TCTTCATGTATCGATAC
1 ATGTATCGATACAATGTC-TCATGTATCGATAC
1505490 ATGTATCGATACAATGTCTCATGTATCGATA
1 ATGTATCGATACAATGTCTCATGTATCGATA
1505521 TATTTCACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACAATGTCTCATGTATCGATAC
Found at i:1505701 original size:185 final size:179
Alignment explanation
Indices: 1505395--1505754 Score: 639
Period size: 185 Copynumber: 2.0 Consensus size: 179
1505385 CGTTACTATG
1505395 TTTTGATACATTTCATAATGTTTTGATACATGCATTTGAAGCCATTTATAACCGTTGGGCATAAT
1 TTTTGATACATTTCATAATGTTTTGATACATGCATTTGAAGCCATTTATAACCGTTGGGCATAAT
*
1505460 GTATCGATATAATTCTTCATGTATCGATACATGTATCGATACAATGTCTCATGTATCGATATATT
66 GTATCGATATAATTCTTCATGTATCGATACATATATCGATACAATGTCTCATGTATCGATATATT
*
1505525 TCACTTAGGGTAGCTATTGCCAGTTTCATGTATCAATACAATTGATATA
131 TCACTTAGGGTAGCTACTGCCAGTTTCATGTATCAATACAATTGATATA
*
1505574 TTTTGATACATTTCATAATGTTTTGATACATGCATTTGAAATTAAAGCCATTTATAGCCGTTGGG
1 TTTTGATACATTTCATAATGTTTTGATACATGCATTTG------AAGCCATTTATAACCGTTGGG
1505639 CATAATGTATCGATATAATTCTTCATGTATCGATACATATATCGATACAATGTCTCATGTATCGA
60 CATAATGTATCGATATAATTCTTCATGTATCGATACATATATCGATACAATGTCTCATGTATCGA
1505704 TATATTTCACTTAGGGTAGCTACTGCCAGTTTCATGTATCAATACAATTGA
125 TATATTTCACTTAGGGTAGCTACTGCCAGTTTCATGTATCAATACAATTGA
1505755 GTATGTATCG
Statistics
Matches: 172, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
179 38 0.22
185 134 0.78
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (179 bp):
TTTTGATACATTTCATAATGTTTTGATACATGCATTTGAAGCCATTTATAACCGTTGGGCATAAT
GTATCGATATAATTCTTCATGTATCGATACATATATCGATACAATGTCTCATGTATCGATATATT
TCACTTAGGGTAGCTACTGCCAGTTTCATGTATCAATACAATTGATATA
Found at i:1505762 original size:20 final size:19
Alignment explanation
Indices: 1505736--1505782 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1505726 CTGCCAGTTT
1505736 CATGTATCAATACAATTGAG
1 CATGTATCAATACAA-TGAG
* * *
1505756 TATGTATCGATATAATGAG
1 CATGTATCAATACAATGAG
1505775 CATGTATC
1 CATGTATC
1505783 GATATAATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (19 bp):
CATGTATCAATACAATGAG
Found at i:1505779 original size:19 final size:19
Alignment explanation
Indices: 1505736--1505791 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1505726 CTGCCAGTTT
* *
1505736 CATGTATCAATACAATTGAG
1 CATGTATCGATATAA-TGAG
*
1505756 TATGTATCGATATAATGAG
1 CATGTATCGATATAATGAG
1505775 CATGTATCGATATAATG
1 CATGTATCGATATAATG
1505792 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATCGATATAATGAG
Found at i:1506037 original size:21 final size:20
Alignment explanation
Indices: 1506013--1506055 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
1506003 TTTTTAAAAA
1506013 ATAAAATTTATTTATAAATTT
1 ATAAAATTTATTT-TAAATTT
*
1506034 ATAAAATTTATTTTAATTTT
1 ATAAAATTTATTTTAAATTT
1506054 AT
1 AT
1506056 TCATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAAAATTTATTTTAAATTT
Found at i:1507928 original size:17 final size:17
Alignment explanation
Indices: 1507906--1507942 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1507896 TACATTTATA
*
1507906 TTTATTTTTTATAATAT
1 TTTATTTTATATAATAT
*
1507923 TTTATTTTATATTATAT
1 TTTATTTTATATAATAT
1507940 TTT
1 TTT
1507943 TTACGATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTTATATAATAT
Found at i:1509475 original size:3 final size:3
Alignment explanation
Indices: 1509467--1509493 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1509457 TTTGTTTATA
1509467 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1509494 CATATGACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:1515619 original size:19 final size:18
Alignment explanation
Indices: 1515588--1515631 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
1515578 TAAAATTATA
1515588 TATTTAAATTTAAAAATT
1 TATTTAAATTTAAAAATT
1515606 TATTTAATATTTAAAAA--
1 TATTTAA-ATTTAAAAATT
1515623 TATTTAAAT
1 TATTTAAAT
1515632 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 7 0.28
18 7 0.28
19 9 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTAAATTTAAAAATT
Found at i:1515645 original size:27 final size:27
Alignment explanation
Indices: 1515615--1515670 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1515605 TTATTTAATA
1515615 TTTAAAAAT-ATTTAAATAAAATAAAAT
1 TTTAAAAATAATTTAAATAAAA-AAAAT
**
1515642 TTTAAAAATAATTTGGATAAAAAAAAT
1 TTTAAAAATAATTTAAATAAAAAAAAT
1515669 TT
1 TT
1515671 ATTTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
TTTAAAAATAATTTAAATAAAAAAAAT
Found at i:1515678 original size:14 final size:15
Alignment explanation
Indices: 1515661--1515689 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1515651 AATTTGGATA
1515661 AAAAAAATT-TATTT
1 AAAAAAATTATATTT
1515675 AAAAAAATTATATTT
1 AAAAAAATTATATTT
1515690 TAAATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAAAATTATATTT
Found at i:1516073 original size:22 final size:23
Alignment explanation
Indices: 1516034--1516086 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
1516024 ATAAGTTTAC
1516034 AATAAATTATAAACCTATAATTT
1 AATAAATTATAAACCTATAATTT
*
1516057 AATAAATTAT-AACCTATGATTT
1 AATAAATTATAAACCTATAATTT
*
1516079 AAAAAATT
1 AATAAATT
1516087 CACATCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.38
Consensus pattern (23 bp):
AATAAATTATAAACCTATAATTT
Found at i:1519401 original size:22 final size:20
Alignment explanation
Indices: 1519354--1519401 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
1519344 ATTAATATAA
*
1519354 AAAATATAATTTTTAATATT
1 AAAATATAATTTTTAATACT
**
1519374 TTAATATATATTTTTAAATACT
1 AAAATATA-ATTTTT-AATACT
1519396 AAAATA
1 AAAATA
1519402 AAAATACCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 6 0.29
21 6 0.29
22 9 0.43
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAATATAATTTTTAATACT
Found at i:1522420 original size:24 final size:23
Alignment explanation
Indices: 1522359--1522422 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 23
1522349 TCTGCTGCTG
*
1522359 CTGTTGCTGTTGCTGCGGTTGAA
1 CTGTTGCTGTTGCTGCTGTTGAA
*
1522382 C--TTGCTGCTGCTGCTGTTGAA
1 CTGTTGCTGTTGCTGCTGTTGAA
1522403 CTTGTTGCTGTTGCTGCTGT
1 C-TGTTGCTGTTGCTGCTGT
1522423 GTCTGGCTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 19 0.54
23 1 0.03
24 15 0.43
ACGTcount: A:0.06, C:0.20, G:0.31, T:0.42
Consensus pattern (23 bp):
CTGTTGCTGTTGCTGCTGTTGAA
Found at i:1525050 original size:2 final size:2
Alignment explanation
Indices: 1525043--1525071 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1525033 ACTTTAAACC
1525043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1525072 GTTATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1525712 original size:2 final size:2
Alignment explanation
Indices: 1525705--1525737 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1525695 CGACAAATTT
1525705 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 T
1525738 TTCTTGGCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1528414 original size:10 final size:10
Alignment explanation
Indices: 1528391--1528448 Score: 70
Period size: 9 Copynumber: 6.1 Consensus size: 10
1528381 AATTAAATAA
*
1528391 ATATAAATTAT
1 ATATAAAAT-T
1528402 ATATAAAATT
1 ATATAAAATT
1528412 ATA-AAAATT
1 ATATAAAATT
1528421 -TATAAAATT
1 ATATAAAATT
1528430 ATA-AAAATT
1 ATATAAAATT
1528439 -TATAAAATT
1 ATATAAAATT
1528448 A
1 A
1528449 ATTTAATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
8 4 0.10
9 24 0.57
10 6 0.14
11 8 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATAAAATT
Found at i:1528461 original size:19 final size:18
Alignment explanation
Indices: 1528403--1528471 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
1528393 ATAAATTATA
1528403 TATAAAATTATAAAAATT
1 TATAAAATTATAAAAATT
1528421 TATAAAATTATAAAAATT
1 TATAAAATTATAAAAATT
** *
1528439 TATAAAATTAATTTAATTT
1 TATAAAATT-ATAAAAATT
*
1528458 TATAAAAATATAAA
1 TATAAAATTATAAA
1528472 TAAATCCATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
18 30 0.68
19 14 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAAATTATAAAAATT
Found at i:1528678 original size:22 final size:21
Alignment explanation
Indices: 1528625--1528685 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1528615 ATTATAAAAA
*
1528625 TATATAAA-ATTAATTAAATTT
1 TATATAAATA-TAAATAAATTT
1528646 TATATAAATATAAATAAATTT
1 TATATAAATATAAATAAATTT
* * *
1528667 TTTCATATATATACATAAA
1 TAT-ATAAATATAAATAAA
1528686 AATATGCGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
TATATAAATATAAATAAATTT
Found at i:1531230 original size:17 final size:18
Alignment explanation
Indices: 1531208--1531241 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1531198 ATTATGATCG
1531208 TTATTTTAT-ATTTTTAA
1 TTATTTTATAATTTTTAA
*
1531225 TTATTTTTTAATTTTTA
1 TTATTTTATAATTTTTA
1531242 CAATTGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTATAATTTTTAA
Found at i:1531409 original size:2 final size:2
Alignment explanation
Indices: 1531398--1531437 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1531388 AACAAAATGG
*
1531398 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1531438 TTATTCAGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1537418 original size:2 final size:2
Alignment explanation
Indices: 1537411--1537439 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1537401 TTGAAAAGAA
1537411 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1537440 GTATGTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.