Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold230
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: 2055625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 12 of 14
Found at i:1448999 original size:24 final size:25
Alignment explanation
Indices: 1448954--1449006 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
1448944 TATTAAAAAT
* *
1448954 AATATTAAATATATAAAATTTAA-A
1 AATAATAAATAAATAAAATTTAATA
**
1448978 AATAATAAATAAATAATGTTTAATA
1 AATAATAAATAAATAAAATTTAATA
1449003 AATA
1 AATA
1449007 TTTATGTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
AATAATAAATAAATAAAATTTAATA
Found at i:1449050 original size:20 final size:20
Alignment explanation
Indices: 1449025--1449067 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1449015 CACACTAATT
*
1449025 TATATATATTAA-AAAATATA
1 TATATATATAAATAAAATA-A
1449045 TATATATATAAATAAAATAA
1 TATATATATAAATAAAATAA
1449065 TAT
1 TAT
1449068 GTGGTGCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TATATATATAAATAAAATAA
Found at i:1451953 original size:4 final size:4
Alignment explanation
Indices: 1451944--1451970 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1451934 CTCCTTTTAT
1451944 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1451971 TACATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1451979 original size:8 final size:8
Alignment explanation
Indices: 1451941--1452012 Score: 72
Period size: 8 Copynumber: 8.8 Consensus size: 8
1451931 TTTCTCCTTT
1451941 TATATACA
1 TATATACA
*
1451949 TACATACA
1 TATATACA
*
1451957 TACATACA
1 TATATACA
1451965 TACATATACA
1 T--ATATACA
*
1451975 TATATATA
1 TATATACA
*
1451983 TATATATA
1 TATATACA
*
1451991 TATATATA
1 TATATACA
*
1451999 TATATATA
1 TATATACA
1452007 TATATA
1 TATATA
1452013 AAACTTATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
8 52 0.88
10 7 0.12
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (8 bp):
TATATACA
Found at i:1451983 original size:12 final size:12
Alignment explanation
Indices: 1451941--1452008 Score: 73
Period size: 12 Copynumber: 5.5 Consensus size: 12
1451931 TTTCTCCTTT
*
1451941 TATATACATACA
1 TATATACATATA
*
1451953 TACATACATACATA
1 TATATACAT--ATA
*
1451967 CATATACATATA
1 TATATACATATA
*
1451979 TATATATATATA
1 TATATACATATA
*
1451991 TATATATATATA
1 TATATACATATA
1452003 TATATA
1 TATATA
1452009 TATAAAACTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
12 39 0.81
14 9 0.19
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
TATATACATATA
Found at i:1452029 original size:2 final size:2
Alignment explanation
Indices: 1451968--1452012 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1451958 ACATACATAC
*
1451968 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1452010 AT A
1 AT A
1452013 AAACTTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1459404 original size:2 final size:2
Alignment explanation
Indices: 1459399--1459429 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1459389 ATTTAAACCA
1459399 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
1459430 ATTCTGCTGT
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:1459686 original size:12 final size:13
Alignment explanation
Indices: 1459662--1459691 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1459652 TCAATCAATC
1459662 AAAAGGAACAAAA
1 AAAAGGAACAAAA
1459675 AAAAGGAA-AAAA
1 AAAAGGAACAAAA
1459687 AAAAG
1 AAAAG
1459692 TAGTACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGGAACAAAA
Found at i:1460564 original size:16 final size:17
Alignment explanation
Indices: 1460486--1460566 Score: 51
Period size: 17 Copynumber: 4.6 Consensus size: 17
1460476 AAATTAAACA
*
1460486 TTAAAATTTAA-AATAT
1 TTAAAATTTAATAAAAT
* * *
1460502 AATAAATTTTAATAAAAA
1 -TTAAAATTTAATAAAAT
1460520 TTAAAATTTAATTTAATTAA-
1 TTAAAATTTAA--TAA--AAT
*
1460540 TTAATATTTAA-AAAAT
1 TTAAAATTTAATAAAAT
1460556 TTAAAATTTAA
1 TTAAAATTTAA
1460567 CTTTCAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
15 2 0.04
16 10 0.20
17 20 0.40
18 3 0.06
19 3 0.06
20 10 0.20
21 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAATTTAATAAAAT
Found at i:1460776 original size:14 final size:14
Alignment explanation
Indices: 1460757--1460783 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1460747 TTTTTTCGAC
1460757 TTATTTAAATTTTA
1 TTATTTAAATTTTA
1460771 TTATTTAAATTTT
1 TTATTTAAATTTT
1460784 TTTGAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTAAATTTTA
Found at i:1460810 original size:11 final size:11
Alignment explanation
Indices: 1460796--1460821 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1460786 TGAAATTGAA
1460796 AAAAATAAAAT
1 AAAAATAAAAT
1460807 AAAAATAAAAT
1 AAAAATAAAAT
1460818 AAAA
1 AAAA
1460822 TTTAAGTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1462466 original size:19 final size:19
Alignment explanation
Indices: 1462437--1462481 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1462427 TAATCACATA
*
1462437 TAATTTTTTAATAATTATT
1 TAATATTTTAATAATTATT
*
1462456 TATTATTTTAATAATTATT
1 TAATATTTTAATAATTATT
1462475 TAATATT
1 TAATATT
1462482 AAAATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATATTTTAATAATTATT
Found at i:1462489 original size:16 final size:18
Alignment explanation
Indices: 1462444--1462491 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
1462434 ATATAATTTT
*
1462444 TTAATAATTATTTATTATT
1 TTAATAATTATTTA-TATA
1462463 TTAATAATTATTTA-ATA
1 TTAATAATTATTTATATA
1462480 TTAA-AATTATTT
1 TTAATAATTATTT
1462492 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 8 0.29
17 6 0.21
19 14 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAATAATTATTTATATA
Found at i:1474042 original size:13 final size:13
Alignment explanation
Indices: 1474024--1474058 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1474014 ATCTAATTTA
1474024 TTAATAAAAAAAT
1 TTAATAAAAAAAT
* *
1474037 TTAATAATATAAT
1 TTAATAAAAAAAT
1474050 TTAATAAAA
1 TTAATAAAA
1474059 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TTAATAAAAAAAT
Found at i:1474670 original size:40 final size:43
Alignment explanation
Indices: 1474566--1474672 Score: 125
Period size: 44 Copynumber: 2.5 Consensus size: 43
1474556 GCATATTCCC
1474566 CAAT-TTTGTTATTAATAATATTAAAAAAATATTATAAATATAT
1 CAATATTT-TTATTAATAATATTAAAAAAATATTATAAATATAT
* *
1474609 CAATATTTTTATTTAATAATATTAAAAATA-ATTATTAAT-TAT
1 CAATATTTTTA-TTAATAATATTAAAAAAATATTATAAATATAT
*
1474651 -TATA-TTTTATATAATAATATTA
1 CAATATTTTTAT-TAATAATATTA
1474673 TTATATATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
39 1 0.02
40 16 0.28
41 3 0.05
42 3 0.05
43 15 0.26
44 20 0.34
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (43 bp):
CAATATTTTTATTAATAATATTAAAAAAATATTATAAATATAT
Found at i:1474675 original size:43 final size:44
Alignment explanation
Indices: 1474574--1474675 Score: 108
Period size: 43 Copynumber: 2.4 Consensus size: 44
1474564 CCCAATTTTG
*
1474574 TTAT-TAATAATATTA-AAAAAATATTATAAATATATCAATATT
1 TTATATAATAATATTATTAAAAATATTATAAATATATCAATATT
* * * *
1474616 TT-TAT-TTAATAATATTAAAAATAATTATTAAT-TAT-TATATT
1 TTATATAATAATATTATTAAAAAT-ATTATAAATATATCAATATT
1474657 TTATATAATAATATTATTA
1 TTATATAATAATATTATTA
1474676 TATATTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
41 15 0.31
42 15 0.31
43 18 0.38
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (44 bp):
TTATATAATAATATTATTAAAAATATTATAAATATATCAATATT
Found at i:1474713 original size:60 final size:56
Alignment explanation
Indices: 1474596--1474731 Score: 125
Period size: 60 Copynumber: 2.3 Consensus size: 56
1474586 TTAAAAAAAT
1474596 ATTATAAATATATCAATATT-TTTATTTAATAATATTAAAAATAATTATTAATTATTATA
1 ATTA-AAATA-AT-AATATTATTTATTTAATAATATTAAAAATAATTATTAA-TATTATA
* * * * *
1474655 TTTTATATAATAATATTATTATATATTAATTAATTTTAAAAATTATTACTTTAA-ATTATA
1 ATTAAAATAATAATATTATT-TAT-TTAA-TAATATTAAAAATAATTA--TTAATATTATA
1474715 ATTAAAATAAT-ATATTA
1 ATTAAAATAATAATATTA
1474732 AATATAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
56 6 0.10
57 4 0.06
58 7 0.11
59 12 0.19
60 30 0.48
62 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (56 bp):
ATTAAAATAATAATATTATTTATTTAATAATATTAAAAATAATTATTAATATTATA
Found at i:1474744 original size:25 final size:24
Alignment explanation
Indices: 1474675--1474744 Score: 58
Period size: 26 Copynumber: 2.9 Consensus size: 24
1474665 TAATATTATT
1474675 ATATATT-AAT-TAATTTTAAAAA
1 ATATATTAAATATAATTTTAAAAA
*
1474697 TTATTACTTTAAATTATAA--TTAAAATA
1 ATA-TA--TTAAA-TATAATTTTAAAA-A
1474724 ATATATTAAATATAATTTTAA
1 ATATATTAAATATAATTTTAA
1474745 TATTTATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 2 0.05
23 7 0.19
24 5 0.14
25 6 0.16
26 10 0.27
27 4 0.11
28 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATATTAAATATAATTTTAAAAA
Found at i:1474746 original size:23 final size:22
Alignment explanation
Indices: 1474705--1474758 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
1474695 AATTATTACT
1474705 TTAAATTATAATTAAAATAATATA
1 TTAAA-TATAATTAAAAT-ATATA
** *
1474729 TTAAATATAATTTTAATATTTA
1 TTAAATATAATTAAAATATATA
1474751 -TAAATATA
1 TTAAATATA
1474759 TCAAGTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 4 0.15
23 10 0.37
24 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAATATAATTAAAATATATA
Found at i:1474962 original size:2 final size:2
Alignment explanation
Indices: 1474955--1474981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1474945 AGACAGTGAT
1474955 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
1474982 TCAAGATACC
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:1475146 original size:25 final size:25
Alignment explanation
Indices: 1475100--1475169 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 25
1475090 TGCCGTCACG
*
1475100 ATATAAAATAATAATTAAAATATAAAA
1 ATATAAAAT-ATAA-TAATATATAAAA
*
1475127 TTAATATAAATATAATAATATATAAAA
1 AT-ATA-AAATATAATAATATATAAAA
*
1475154 ATTTAAAATATAATAA
1 ATATAAAATATAATAA
1475170 AAATATAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 11 0.30
26 2 0.05
27 13 0.35
28 7 0.19
29 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
ATATAAAATATAATAATATATAAAA
Found at i:1475153 original size:34 final size:36
Alignment explanation
Indices: 1475106--1475178 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
1475096 CACGATATAA
*
1475106 AATAATAATT-AAAATATAAAAT-TAATATAAATAT
1 AATAATAATTAAAAATATAAAATATAATAAAAATAT
*
1475140 AATAAT-ATATAAAAATTTAAAATATAATAAAAATAT
1 AATAATAAT-TAAAAATATAAAATATAATAAAAATAT
1475176 AAT
1 AAT
1475179 TTACAAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 2 0.06
34 7 0.21
35 11 0.32
36 14 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (36 bp):
AATAATAATTAAAAATATAAAATATAATAAAAATAT
Found at i:1475567 original size:15 final size:16
Alignment explanation
Indices: 1475547--1475576 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1475537 TAATAACTGA
1475547 AATAAAAAA-AATATT
1 AATAAAAAATAATATT
1475562 AATAAAAAATAATAT
1 AATAAAAAATAATAT
1475577 AATTATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAAAAAATAATATT
Found at i:1476359 original size:2 final size:2
Alignment explanation
Indices: 1476347--1476384 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1476337 CAATCAAATT
*
1476347 TA TA CA TA TA TA TA TA TA TA TA TA TA T- 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 TA T
1476385 GCAAAACAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1480616 original size:2 final size:2
Alignment explanation
Indices: 1480609--1480634 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1480599 GTTGGAGCCA
1480609 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
1480635 CTAGTTCCTA
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:1483622 original size:31 final size:30
Alignment explanation
Indices: 1483573--1483630 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
1483563 TTTTATTAAA
1483573 ATTTTTAAAAAATAAATATAATTATAATGAT
1 ATTTTTAAAAAATAAATATAATT-TAATGAT
*
1483604 ATTTTTAATAAAAT-AATATCATTTAAT
1 ATTTTTAA-AAAATAAATATAATTTAAT
1483631 TTAATATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 4 0.16
31 16 0.64
32 5 0.20
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
ATTTTTAAAAAATAAATATAATTTAATGAT
Found at i:1483638 original size:32 final size:32
Alignment explanation
Indices: 1483567--1483638 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
1483557 ATGTAATTTT
*
1483567 ATTAAAATTTTTAAAAAATAAATATAATTATA
1 ATTAATATTTTTAAAAAATAAATATAATTATA
* *
1483599 A-TGATATTTTTAATAAAAT-AATATCATT-TA
1 ATTAATATTTTTAA-AAAATAAATATAATTATA
1483629 ATTTAATATT
1 A-TTAATATT
1483639 ACTTCTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 3 0.09
31 18 0.55
32 12 0.36
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (32 bp):
ATTAATATTTTTAAAAAATAAATATAATTATA
Found at i:1484041 original size:2 final size:2
Alignment explanation
Indices: 1484036--1484065 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1484026 TTTTTTTCTC
1484036 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
1484066 TTCTAATAAC
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:1484160 original size:19 final size:19
Alignment explanation
Indices: 1484136--1484214 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 19
1484126 AATATTTAAA
*
1484136 AAATTTAAATAA-AAATATT
1 AAATTTAAAAAATAAATA-T
1484155 AAATTTAAAAAATAAATAT
1 AAATTTAAAAAATAAATAT
* *
1484174 AAA-TAAAAAAATTAGAT-T
1 AAATTTAAAAAA-TAAATAT
**
1484192 CGA-TTAAAAAATAAAT-T
1 AAATTTAAAAAATAAATAT
1484209 AAATTT
1 AAATTT
1484215 TGAATCTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
17 6 0.12
18 18 0.38
19 19 0.40
20 5 0.10
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (19 bp):
AAATTTAAAAAATAAATAT
Found at i:1484204 original size:32 final size:31
Alignment explanation
Indices: 1484131--1484204 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
1484121 TATTTAATAT
* * *
1484131 TTAAAAAATTTAAATAAAAATATTAAATTTA
1 TTAAAAAATATAAATAAAAAAATTAAATTGA
** *
1484162 AAAAATAAATATAAATAAAAAAATTAGATTCGA
1 TTAAA-AAATATAAATAAAAAAATTAAATT-GA
1484195 TTAAAAAATA
1 TTAAAAAATA
1484205 AATTAAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
31 3 0.09
32 26 0.79
33 4 0.12
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (31 bp):
TTAAAAAATATAAATAAAAAAATTAAATTGA
Found at i:1484292 original size:25 final size:25
Alignment explanation
Indices: 1484257--1484321 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 25
1484247 AATACAGTTT
1484257 ATTTTATTATTATATAATATATAT-TA
1 ATTTTA-TATTATATAATAT-TATGTA
1484283 ATTTTATATT-T-TACATATTATGTA
1 ATTTTATATTATATA-ATATTATGTA
*
1484307 ATTTT-TATAATATAA
1 ATTTTATATTATATAA
1484322 AAAATATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
23 8 0.24
24 14 0.41
25 6 0.18
26 6 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTATATTATATAATATTATGTA
Found at i:1484415 original size:15 final size:16
Alignment explanation
Indices: 1484385--1484417 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1484375 ATTTTCAAAT
1484385 TTAATAAAAAATTAAA
1 TTAATAAAAAATTAAA
*
1484401 TTAAT-AAAGATTAAA
1 TTAATAAAAAATTAAA
1484416 TT
1 TT
1484418 TTAAACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TTAATAAAAAATTAAA
Found at i:1485143 original size:26 final size:28
Alignment explanation
Indices: 1485087--1485148 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1485077 AAATTTTAGA
* *
1485087 TAATTTTATTTATATATATATGAACATT
1 TAATTTTACTTATATATATATGAACAAT
1485115 TAATTTTACTTATAT-TA-ATGTAA-AAT
1 TAATTTTACTTATATATATATG-AACAAT
1485141 TAATTTTA
1 TAATTTTA
1485149 TAATTTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 13 0.42
27 4 0.13
28 14 0.45
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (28 bp):
TAATTTTACTTATATATATATGAACAAT
Found at i:1485392 original size:2 final size:2
Alignment explanation
Indices: 1485385--1485432 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1485375 TTTTAAATAA
1485385 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
1485427 TC TC TC
1 TC TC TC
1485433 CATATATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1487824 original size:16 final size:17
Alignment explanation
Indices: 1487801--1487836 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1487791 TAAATATCTT
*
1487801 TAAAAATTAAAATTTAA
1 TAAAATTTAAAATTTAA
*
1487818 TAAAATTTAAATTTTAA
1 TAAAATTTAAAATTTAA
1487835 TA
1 TA
1487837 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTAAAATTTAA
Found at i:1488272 original size:3 final size:3
Alignment explanation
Indices: 1488264--1488290 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1488254 TAAAGGGTTG
1488264 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1488291 TCTTAAAGTG
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:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1504370 original size:38 final size:39
Alignment explanation
Indices: 1504304--1504403 Score: 141
Period size: 38 Copynumber: 2.6 Consensus size: 39
1504294 GCCCTAACCG
* * *
1504304 ACTCCTTCTTTATGAAGCAAA-AATTAAAGTCAAAGCCC
1 ACTCCTTCCTTATCAAGTAAATAATTAAAGTCAAAGCCC
*
1504342 ACTCCTTCCTTATCAAGTAAATAA-TAAAGTCAAGGCCC
1 ACTCCTTCCTTATCAAGTAAATAATTAAAGTCAAAGCCC
*
1504380 ACTCCTTCCTTATCGAGTAAATAA
1 ACTCCTTCCTTATCAAGTAAATAA
1504404 CAATGTTAGG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 54 0.96
39 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (39 bp):
ACTCCTTCCTTATCAAGTAAATAATTAAAGTCAAAGCCC
Found at i:1506827 original size:26 final size:27
Alignment explanation
Indices: 1506789--1506841 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1506779 TGATAAAAAA
1506789 TTAAAATAATATA-AATATATAAATATT
1 TTAAAATAATATATAATATA-AAATATT
*
1506816 TTAAAAT-TTATATAATATAAAATATT
1 TTAAAATAATATATAATATAAAATATT
1506842 AATATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TTAAAATAATATATAATATAAAATATT
Found at i:1506831 original size:33 final size:33
Alignment explanation
Indices: 1506785--1506885 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 33
1506775 GAGATGATAA
* * *
1506785 AAAATTAAAATAATATAAATATATAAATATTTT
1 AAAATTTATATAATATAAATATATAAATATATT
*
1506818 AAAATTTATATAATATAAA-ATATTAATATATT
1 AAAATTTATATAATATAAATATATAAATATATT
* * *
1506850 AAAA-TTATATAATTATGAAATAAATATATAAATT
1 AAAATTTATATAA-TAT-AAATATATAAATATATT
1506884 AA
1 AA
1506886 CATATTATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
31 8 0.14
32 18 0.32
33 20 0.35
34 11 0.19
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (33 bp):
AAAATTTATATAATATAAATATATAAATATATT
Found at i:1506852 original size:32 final size:31
Alignment explanation
Indices: 1506785--1506878 Score: 102
Period size: 32 Copynumber: 3.0 Consensus size: 31
1506775 GAGATGATAA
* * *
1506785 AAAATTAAAATAATATAAATATATAAATATTTT
1 AAAATTTATATAATATAAA-ATAT-AATATATT
1506818 AAAATTTATATAATATAAAATATTAATATATT
1 AAAATTTATATAATATAAAATA-TAATATATT
*
1506850 AAAA-TTATATAATTATGAAATA-AATATAT
1 AAAATTTATATAA-TATAAAATATAATATAT
1506879 AAATTAACAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
30 7 0.13
31 8 0.15
32 22 0.40
33 18 0.33
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAATTTATATAATATAAAATATAATATATT
Found at i:1507861 original size:14 final size:14
Alignment explanation
Indices: 1507846--1507915 Score: 67
Period size: 14 Copynumber: 5.1 Consensus size: 14
1507836 ATTAATTAAT
1507846 TTAATATATAT-AA
1 TTAATATATATAAA
*
1507859 TTTATAT-TAATAAA
1 TTAATATAT-ATAAA
*
1507873 TTAATAAATATAAA
1 TTAATATATATAAA
*
1507887 TT-ATATA-AAAAA
1 TTAATATATATAAA
1507899 TTATATATATATAAA
1 TTA-ATATATATAAA
1507914 TT
1 TT
1507916 TAAAATAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 7 0.16
13 12 0.27
14 19 0.42
15 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATATATATAAA
Found at i:1507876 original size:27 final size:27
Alignment explanation
Indices: 1507836--1507917 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
1507826 ATAATAAAAA
*
1507836 ATTAATTAATTTAATATATATAATTTAT
1 ATTAA-TAAATTAATATATATAATTTAT
* *
1507864 ATTAATAAATTAATAAATATAAATTAT
1 ATTAATAAATTAATATATATAATTTAT
*
1507891 A-TAAAAAATTATATATATATAAATTTA
1 ATTAATAAATTA-ATATATAT-AATTTA
1507918 AAATAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 9 0.20
27 27 0.59
28 10 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
ATTAATAAATTAATATATATAATTTAT
Found at i:1507925 original size:27 final size:26
Alignment explanation
Indices: 1507846--1507930 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 26
1507836 ATTAATTAAT
1507846 TTAATATATAT-AATTTATATTAAT-AAA
1 TTAATATATATAAATTTA-A--AATAAAA
* *
1507873 TTAATAAATATAAATTATATAA-AAAA
1 TTAATATATATAAATT-TAAAATAAAA
1507899 TTATATATATATAAATTTAAAATAAAA
1 TTA-ATATATATAAATTTAAAATAAAA
1507926 TTAAT
1 TTAAT
1507931 TTTACAATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
26 14 0.29
27 29 0.59
28 4 0.08
29 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TTAATATATATAAATTTAAAATAAAA
Found at i:1509035 original size:14 final size:15
Alignment explanation
Indices: 1509004--1509040 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1508994 TATATAAATT
1509004 TTTATATTTTAATAA
1 TTTATATTTTAATAA
1509019 TTTATA-TTT-ATATA
1 TTTATATTTTAATA-A
1509033 TTTATATT
1 TTTATATT
1509041 AATTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 10 0.50
15 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATATTTTAATAA
Found at i:1509036 original size:29 final size:28
Alignment explanation
Indices: 1508952--1509040 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
1508942 AAATAAATTA
1508952 ATTTTAAAAATTTATA-TTATATTATTAT
1 ATTTTAAAAATTTATATTTATATT-TTAT
* * * *
1508980 A-ATTAAAAATTATTTATATAAATTTTTAT
1 ATTTTAAAAATT-TATATTTATA-TTTTAT
*
1509009 ATTTTAATAATTTATATTTATATATTTAT
1 ATTTTAAAAATTTATATTTATAT-TTTAT
1509038 ATT
1 ATT
1509041 AATTTTAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
27 9 0.19
28 5 0.11
29 23 0.49
30 10 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTTTAAAAATTTATATTTATATTTTAT
Found at i:1509559 original size:24 final size:22
Alignment explanation
Indices: 1509532--1509576 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1509522 TCTTGTACGA
*
1509532 AATTATTATTATTTATAATAATAT
1 AATTATT-TAATTTATAA-AATAT
1509556 AATTATTTAATTTATAAAATA
1 AATTATTTAATTTATAAAATA
1509577 ATTAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTATTTAATTTATAAAATAT
Found at i:1509581 original size:16 final size:17
Alignment explanation
Indices: 1509562--1509594 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1509552 ATATAATTAT
1509562 TTAA-TTTATAAAATAA
1 TTAATTTTATAAAATAA
*
1509578 TTAATTTTTTAAAATAA
1 TTAATTTTATAAAATAA
1509595 ATTTAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATTTTATAAAATAA
Found at i:1509582 original size:24 final size:23
Alignment explanation
Indices: 1509532--1509690 Score: 65
Period size: 24 Copynumber: 6.4 Consensus size: 23
1509522 TCTTGTACGA
*
1509532 AATTATTATTATTTATAATAATAT
1 AATTATT-TAATTTATAATAATAT
1509556 AATTATTTAATTTATAA-AATAATT
1 AATTATTTAATTTATAATAAT-A-T
* ** *
1509580 AATTTTTTAAAATA-AATTTAAAAT
1 AATTATTTAATTTATAA--TAATAT
* *
1509604 AATTAATTAATATTTTTTAATTAA-AT
1 AATT-ATT--TAATTTATAA-TAATAT
* *
1509630 GATTATTTTAATTTTATATTTTAATA-
1 AATTA-TTTAA-TTTATA--ATAATAT
1509656 AATTATTTAATGAATTATAATAATAT
1 AATTATTTAAT---TTATAATAATAT
1509682 AATTATTTA
1 AATTATTTA
1509691 TTTTTATTTT
Statistics
Matches: 101, Mismatches: 16, Indels: 34
0.67 0.11 0.23
Matches are distributed among these distances:
22 3 0.03
23 12 0.12
24 27 0.27
25 19 0.19
26 25 0.25
27 13 0.13
28 2 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
AATTATTTAATTTATAATAATAT
Found at i:1509623 original size:14 final size:17
Alignment explanation
Indices: 1509606--1509642 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1509596 TTTAAAATAA
1509606 TTAATT-AAT-ATT-TT
1 TTAATTAAATGATTATT
1509620 TTAATTAAATGATTATT
1 TTAATTAAATGATTATT
1509637 TTAATT
1 TTAATT
1509643 TTATATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.30
15 3 0.15
16 3 0.15
17 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTAATTAAATGATTATT
Found at i:1511657 original size:13 final size:13
Alignment explanation
Indices: 1511639--1511664 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1511629 TTTAAAAATA
1511639 TTTATAAATATTT
1 TTTATAAATATTT
1511652 TTTATAAATATTT
1 TTTATAAATATTT
1511665 CATTATCTTA
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:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATAAATATTT
Found at i:1511660 original size:23 final size:22
Alignment explanation
Indices: 1511619--1511664 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1511609 AATTAATTAA
*
1511619 TATAATTATTTTTAAAAATATT
1 TATAAATATTTTTAAAAATATT
*
1511641 TATAAATATTTTTTATAAATATT
1 TATAAATA-TTTTTAAAAATATT
1511664 T
1 T
1511665 CATTATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATAAATATTTTTAAAAATATT
Found at i:1521629 original size:2 final size:2
Alignment explanation
Indices: 1521622--1521662 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1521612 TCTGGTTTAC
1521622 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1521663 GATTTTGCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1522123 original size:2 final size:2
Alignment explanation
Indices: 1522116--1522155 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1522106 AGTGCTCTAC
1522116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1522156 GTTTCAGTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1522882 original size:26 final size:27
Alignment explanation
Indices: 1522833--1522887 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 27
1522823 AAGTTTATTA
1522833 ATACATTATATTATTTTTCATATATAAT
1 ATACATTATATTATTTTT-ATATATAAT
1522861 ATACATTATATTATTTTT-TATATAAT
1 ATACATTATATTATTTTTATATATAAT
1522887 A
1 A
1522888 AAAAGCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (27 bp):
ATACATTATATTATTTTTATATATAAT
Found at i:1527144 original size:2 final size:2
Alignment explanation
Indices: 1527137--1527164 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1527127 CATATCGTAT
1527137 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
1527165 GCTTCGAATT
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):
TA
Found at i:1528698 original size:2 final size:2
Alignment explanation
Indices: 1528693--1528727 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1528683 AGACAAAGTT
1528693 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1528728 TAAGGTAGCA
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:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1529649 original size:2 final size:2
Alignment explanation
Indices: 1529636--1529668 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1529626 TCTTCCAATA
*
1529636 AT AT AT AC 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
1529669 GGAAAGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1535764 original size:22 final size:23
Alignment explanation
Indices: 1535726--1535778 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1535716 GTTATTTTTT
1535726 TTAAAATATTTAAATA-TAAAAA
1 TTAAAATATTTAAATATTAAAAA
* *
1535748 TTAAAATATATT-TATATTAAATA
1 TTAAAATAT-TTAAATATTAAAAA
*
1535771 TAAAAATA
1 TTAAAATA
1535779 AAAGATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAAAATATTTAAATATTAAAAA
Found at i:1535774 original size:29 final size:30
Alignment explanation
Indices: 1535735--1535805 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
1535725 TTTAAAATAT
*
1535735 TTAAATATAAAAATTAAA-ATATATTTATA
1 TTAAATATAAAAATAAAAGATATATTTATA
1535764 TTAAATATAAAAATAAAAGATATATTTATA
1 TTAAATATAAAAATAAAAGATATATTTATA
*
1535794 TCAAATATAAAA
1 TTAAATATAAAA
1535806 CGAGGGAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 17 0.44
30 22 0.56
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (30 bp):
TTAAATATAAAAATAAAAGATATATTTATA
Found at i:1536397 original size:22 final size:22
Alignment explanation
Indices: 1536360--1536413 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1536350 TACTCAATAA
* *
1536360 TATTTATTAAAATTTTTATA-AT
1 TATTTAAT-AAATTTTAATATAT
1536382 TAATTTAATAAATTTTAATATAT
1 T-ATTTAATAAATTTTAATATAT
1536405 TATTTAATA
1 TATTTAATA
1536414 TAAAAGCCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTTAATAAATTTTAATATAT
Found at i:1548234 original size:22 final size:22
Alignment explanation
Indices: 1548189--1548234 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1548179 GATGCATTGG
**
1548189 TTGGATGAAAAAAATACATTTT
1 TTGGATGAAAAAAATACAACTT
1548211 TTGGATGAAAAAAATACAACTT
1 TTGGATGAAAAAAATACAACTT
1548233 TT
1 TT
1548235 AATAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (22 bp):
TTGGATGAAAAAAATACAACTT
Found at i:1551473 original size:13 final size:15
Alignment explanation
Indices: 1551455--1551488 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
1551445 AGCCTGGACT
1551455 GCTATGCT-TGCA-G
1 GCTATGCTGTGCATG
1551468 GCTATGCTGTGCATG
1 GCTATGCTGTGCATG
1551483 GCTATG
1 GCTATG
1551489 GGAAAGATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 4 0.21
15 7 0.37
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
GCTATGCTGTGCATG
Found at i:1555133 original size:26 final size:24
Alignment explanation
Indices: 1555103--1555156 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 24
1555093 AATTAATAAA
1555103 TTAATTTAATAATTTTAAAAAATTAT
1 TTAATTTAATAATTTT-AAAAA-TAT
*
1555129 TTAATTTTATAATTTTAAAAATAT
1 TTAATTTAATAATTTTAAAAATAT
1555153 TTAA
1 TTAA
1555157 ATATTGATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 7 0.26
25 5 0.19
26 15 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAATTTAATAATTTTAAAAATAT
Found at i:1556002 original size:11 final size:9
Alignment explanation
Indices: 1555974--1556011 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
1555964 TATTAAAATT
1555974 AAAATTTTA
1 AAAATTTTA
1555983 AAAATTTTA
1 AAAATTTTA
1555992 AAACGATTTT-
1 AAA--ATTTTA
1556002 AAAATTTTA
1 AAAATTTTA
1556011 A
1 A
1556012 GTAGACCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 5 0.19
9 13 0.50
10 3 0.12
11 5 0.19
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (9 bp):
AAAATTTTA
Found at i:1562190 original size:2 final size:2
Alignment explanation
Indices: 1562183--1562210 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1562173 ATGAACCTTT
1562183 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
1562211 AAAGCTGAGA
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):
TA
Found at i:1562763 original size:16 final size:17
Alignment explanation
Indices: 1562721--1562763 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1562711 ATTTAATTTA
1562721 AATATAAAATTATAACT
1 AATATAAAATTATAACT
*
1562738 AATTTAAAATT-TAA-T
1 AATATAAAATTATAACT
1562753 AGATATAAAAT
1 A-ATATAAAAT
1562764 AACTACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 11 0.48
17 10 0.43
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AATATAAAATTATAACT
Found at i:1564605 original size:13 final size:13
Alignment explanation
Indices: 1564571--1564654 Score: 68
Period size: 13 Copynumber: 6.5 Consensus size: 13
1564561 TATGATTAGG
1564571 TATTATAATTATT
1 TATTATAATTATT
* *
1564584 ATTTTATAATTTTT
1 -TATTATAATTATT
*
1564598 TATTATAAATATT
1 TATTATAATTATT
*
1564611 TATGATTAA-TATT
1 TATTA-TAATTATT
1564624 TATTATAATTAATT
1 TATTATAATT-ATT
*
1564638 T-TAATAA-TA-T
1 TATTATAATTATT
1564648 TATTATA
1 TATTATA
1564655 TAATTAGAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
10 2 0.04
11 5 0.09
12 4 0.07
13 28 0.49
14 18 0.32
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (13 bp):
TATTATAATTATT
Found at i:1568915 original size:20 final size:21
Alignment explanation
Indices: 1568877--1568915 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1568867 AGGTATTTCG
*
1568877 AATTCAAAATATTATATAACA
1 AATTCAAAATATTAGATAACA
*
1568898 AATTC-AAATCTTAGATAA
1 AATTCAAAATATTAGATAA
1568916 AGTAATGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (21 bp):
AATTCAAAATATTAGATAACA
Found at i:1569622 original size:2 final size:2
Alignment explanation
Indices: 1569615--1569648 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1569605 TTCCTTAACC
1569615 AG AG AG AG 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 AG AG AG AG
1569649 GTGGGGGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1572030 original size:338 final size:334
Alignment explanation
Indices: 1571411--1572574 Score: 1303
Period size: 337 Copynumber: 3.5 Consensus size: 334
1571401 TAACACCTCG
* * ** * *
1571411 TGCATTCATTACTATATTGGTGTTGATCTTTAAGAGAGTGCCCAACTGATTTCCAACAAGTTGTA
1 TGCATTCATCACTGTATTGGTGTCAATCTTCAAGAGAGTGCCCAACTGATTTCCAACACGTTGTA
* * * * * *
1571476 ATTCATATTTATCAAAATATTCAATGGGTA-GCTCAGGTAATTTGA-CCACACTGCAGTTATAGT
66 ATCCATATTTATCAAAATATTCAATGGGTAGGC-CAAGTAATCTGACCCACACTACAATTGTAGT
* * *
1571539 AAAGGCTGCCAGTGATGGCTTGAATCCTAGTTCCCCCAATCTCATAGGTAAGTAATAGGGTCCAA
130 AAAGTCTGCTAGTGATGGCTTGAATCCTAGTT-CCCAAATCTCATA-GTAAGTAATAGGGTCCAA
*
1571604 CAAACCAAGGTCCTCCACGCAAAACTCTTTGAAAATTCCATGCATCATGAAAACGAAAAAGGGAA
193 CAAACCAAGGTCCTCCACGCAAAACCCTTTGAAAATTCCATGCATCATGAAAACGAAAAA-GGAA
* **
1571669 AAATCCATT-CTTCAATCTATTTAGGAATCAAGGGACGGTCAAGATAAACCTGGGCACAAATACA
257 AAATCCATTCCCT-AATCTATTTAGGAATCAAGGGACGGTCAAGATAAACCTGGATACAAATACA
*
1571733 CACATAACGCCTTC
321 CACATAATGCCTTC
* * * *
1571747 ATGCATTCATCACTTTATTGGTTTTAATCTTCAAGAGAGTGCCCAACTGATTTCCATCACGTTGT
1 -TGCATTCATCACTGTATTGGTGTCAATCTTCAAGAGAGTGCCCAACTGATTTCCAACACGTTGT
* *
1571812 AATCTATATTTATCAAAATATTCAATGGGTAGGCCAAGTAATGTGACCCACACTACAATTGTAGT
65 AATCCATATTTATCAAAATATTCAATGGGTAGGCCAAGTAATCTGACCCACACTACAATTGTAGT
*
1571877 AAAGTCTGCTAGTGATGGCTTGAATCCTGGTTCCCATAATCTCATAGTCAAGTAATAGGGTCCAA
130 AAAGTCTGCTAGTGATGGCTTGAATCCTAGTTCCCA-AATCTCATAGT-AAGTAATAGGGTCCAA
* * * *
1571942 CAAACTAAGGTCCTCCATGCAAAACCCTTTAAAAATCCCATGCATCATGAAAACGAAAAAGGAAA
193 CAAACCAAGGTCCTCCACGCAAAACCCTTTGAAAATTCCATGCATCATGAAAACGAAAAAGGAAA
* * ** *
1572007 ATATCCATTCCCTAATTTATTTAGGAATCTAGGGACGGTCAAGATCAAA-CTAAATACAAATATA
258 A-ATCCATTCCCTAATCTATTTAGGAATCAAGGGACGGTCAAGAT-AAACCTGGATACAAATACA
*
1572071 TCA-AAAATGCC--C
321 -CACATAATGCCTTC
* * * *
1572083 T-CGTGCAT---TGTA----T-TCAATCTTCGAGAGAGTGCCCAATTGATTTCCAACACGTTGTA
1 TGCATTCATCACTGTATTGGTGTCAATCTTCAAGAGAGTGCCCAACTGATTTCCAACACGTTGTA
* * *
1572139 ATCCATATTTATCAAAATATTCAATGGGTAGGCCAGGTAATCTAACCCACA--GCAATTGTAGTA
66 ATCCATATTTATCAAAATATTCAATGGGTAGGCCAAGTAATCTGACCCACACTACAATTGTAGTA
* * * * * * * * *
1572202 GAGGT-TGCTAGTGAT-GCTTTGAATCTTAATACCCACAT-TCATATTAAGCAATAGGGCCCAGC
131 -AAGTCTGCTAGTGATGGC-TTGAATCCTAGTTCCCAAATCTCATAGTAAGTAATAGGGTCCAAC
* * * *
1572264 AAACCCAGGTCCCCCACACAAAACCTTTTGAAAATTCCATGCAATCATGAAAAACGACAAAAGGA
194 AAACCAAGGTCCTCCACGCAAAACCCTTTGAAAATTCCATGC-ATCATG-AAAACGA-AAAAGG-
* * * * *
1572329 AAAAATCAATTCCCAAAATCTATTTAGGAATCAAGGGAAGGTCAAGATAAACTTGGATACATATA
255 AAAAATCCATTCCC-TAATCTATTTAGGAATCAAGGGACGGTCAAGATAAACCTGGATACAAATA
*
1572394 CACGCATAATGCCTTC
319 CACACATAATGCCTTC
* * * **
1572410 GTGCGTCCATCACTGTATTGGTGTCAATCTTCAAGAGAGTGGCCAACTGATTTCCTTCACGTTGT
1 -TGCATTCATCACTGTATTGGTGTCAATCTTCAAGAGAGTGCCCAACTGATTTCCAACACGTTGT
* * ** * *
1572475 AATCCATATTTATCAAAATATTCCATGGG-AGGACCAAGAAATCTGACCCACGGTACAGTTGTCG
65 AATCCATATTTATCAAAATATTCAATGGGTAGG-CCAAGTAATCTGACCCACACTACAATTGTAG
*
1572539 TAAA-TGCTGCTAGTGATGGCTTGAACCCTAGTTCCC
129 TAAAGT-CTGCTAGTGATGGCTTGAATCCTAGTTCCC
1572575 GCAATTTCAT
Statistics
Matches: 698, Mismatches: 94, Indels: 68
0.81 0.11 0.08
Matches are distributed among these distances:
321 48 0.07
322 12 0.02
323 11 0.02
324 53 0.08
325 53 0.08
326 86 0.12
327 2 0.00
328 1 0.00
329 6 0.01
331 3 0.00
332 4 0.01
334 5 0.01
335 1 0.00
336 5 0.01
337 188 0.27
338 180 0.26
339 38 0.05
340 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (334 bp):
TGCATTCATCACTGTATTGGTGTCAATCTTCAAGAGAGTGCCCAACTGATTTCCAACACGTTGTA
ATCCATATTTATCAAAATATTCAATGGGTAGGCCAAGTAATCTGACCCACACTACAATTGTAGTA
AAGTCTGCTAGTGATGGCTTGAATCCTAGTTCCCAAATCTCATAGTAAGTAATAGGGTCCAACAA
ACCAAGGTCCTCCACGCAAAACCCTTTGAAAATTCCATGCATCATGAAAACGAAAAAGGAAAAAT
CCATTCCCTAATCTATTTAGGAATCAAGGGACGGTCAAGATAAACCTGGATACAAATACACACAT
AATGCCTTC
Found at i:1572480 original size:337 final size:330
Alignment explanation
Indices: 1571425--1572588 Score: 1255
Period size: 338 Copynumber: 3.5 Consensus size: 330
1571415 TTCATTACTA
** * * *
1571425 TATTGGTGTTGATCTTTAAGAGAGTGCCCAACTGATTTCCAACAAGTTGTAATTCATATTTATCA
1 TATTGGTGTCAATCTTCAAGAGAGTGCCCAACTGATTTCCAACACGTTGTAATCCATATTTATCA
* * * * * * *
1571490 AAATATTCAATGGGTA-GCTCAGGTAATTTGACCACACTGCAGTTATAGTAAAGGCTGCCAGTGA
66 AAATATTCAATGGGTAGGC-CAAGTAATCTGACC-CACAGCAATTGTAGT-AAGGTTGCTAGTGA
* *
1571554 TGGCTTGAATCCTAGTTCCCCCAATCTCATAGGTAAGTAATAGGGTCCAACAAACCAAGGTCCTC
128 TGGCTTGAATCCTAGTTCCCAC-ATCTCATAGTTAAGTAATAGGGTCCAACAAACCAAGGTCCTC
* *
1571619 CACGCAAAA-CTCTTTGAAAATTCCATGCATCATGAAAACGAAAAAGGGAAAAATCCATTCTTCA
192 CACGCAAAACCT-TTTGAAAATTCCATGCATCATGAAAACGAAAAAGGAAAAAATCCATTC-CCA
** *
1571683 ATCTATTTAGGAATCAAGGGACGGTCAAGATAAACCTGGGCACAAATACACACATAACGCCTTCA
255 ATCTATTTAGGAATCAAGGGACGGTCAAGATAAA-CTGGATACAAATACAC-CATAATGCCTTC-
* * *
1571748 TGCATTCATCACTT
317 TGCGTCCATCACTG
* * * *
1571762 TATTGGTTTTAATCTTCAAGAGAGTGCCCAACTGATTTCCATCACGTTGTAATCTATATTTATCA
1 TATTGGTGTCAATCTTCAAGAGAGTGCCCAACTGATTTCCAACACGTTGTAATCCATATTTATCA
* * *
1571827 AAATATTCAATGGGTAGGCCAAGTAATGTGACCCACACTACAATTGTAGTAAAGTCTGCTAGTGA
66 AAATATTCAATGGGTAGGCCAAGTAATCTGACCCACA--GCAATTGTAGTAAGGT-TGCTAGTGA
* * * *
1571892 TGGCTTGAATCCTGGTTCCCATAATCTCATAGTCAAGTAATAGGGTCCAACAAACTAAGGTCCTC
128 TGGCTTGAATCCTAGTTCCCA-CATCTCATAGTTAAGTAATAGGGTCCAACAAACCAAGGTCCTC
* * * * *
1571957 CATGCAAAACCCTTTAAAAATCCCATGCATCATGAAAACGAAAAAGGAAAATATCCATTCCCTAA
192 CACGCAAAACCTTTTGAAAATTCCATGCATCATGAAAACGAAAAAGGAAAAAATCCATTCCC-AA
* * ** * * *
1572022 TTTATTTAGGAATCTAGGGACGGTCAAGATCAAACTAAATACAAATATATCAAAAATGCC--CT-
256 TCTATTTAGGAATCAAGGGACGGTCAAGAT-AAACTGGATACAAATACA-CCATAATGCCTTCTG
*
1572084 CGTGCAT---TG
319 CGTCCATCACTG
* *
1572093 TA----T-TCAATCTTCGAGAGAGTGCCCAATTGATTTCCAACACGTTGTAATCCATATTTATCA
1 TATTGGTGTCAATCTTCAAGAGAGTGCCCAACTGATTTCCAACACGTTGTAATCCATATTTATCA
* *
1572153 AAATATTCAATGGGTAGGCCAGGTAATCTAACCCACAGCAATTGTAGTAGAGGTTGCTAGTGAT-
66 AAATATTCAATGGGTAGGCCAAGTAATCTGACCCACAGCAATTGTAGTA-AGGTTGCTAGTGATG
* * * * * * * *
1572217 GCTTTGAATCTTAATACCCACAT-TCATA-TTAAGCAATAGGGCCCAGCAAACCCAGGTCCCCCA
130 GC-TTGAATCCTAGTTCCCACATCTCATAGTTAAGTAATAGGGTCCAACAAACCAAGGTCCTCCA
* *
1572280 CACAAAACCTTTTGAAAATTCCATGCAATCATGAAAAACGACAAAAGGAAAAAATCAATTCCCAA
194 CGCAAAACCTTTTGAAAATTCCATGC-ATCATG-AAAACGA-AAAAGGAAAAAATCCATTCCC--
* *
1572345 AATCTATTTAGGAATCAAGGGAAGGTCAAGATAAACTTGGATACATATACACGCATAATGCCTTC
254 AATCTATTTAGGAATCAAGGGACGGTCAAGATAAAC-TGGATACAAATACAC-CATAATGCCTTC
1572410 GTGCGTCCATCACTG
317 -TGCGTCCATCACTG
* **
1572425 TATTGGTGTCAATCTTCAAGAGAGTGGCCAACTGATTTCCTTCACGTTGTAATCCATATTTATCA
1 TATTGGTGTCAATCTTCAAGAGAGTGCCCAACTGATTTCCAACACGTTGTAATCCATATTTATCA
* * * * * * *
1572490 AAATATTCCATGGG-AGGACCAAGAAATCTGACCCACGGTACAGTTGTCGTAAATGCTGCTAGTG
66 AAATATTCAATGGGTAGG-CCAAGTAATCTGACCCACAG--CAATTGTAGT-AAGGTTGCTAGTG
* * *
1572554 ATGGCTTGAACCCTAGTTCCCGCAATTTCATAGTT
127 ATGGCTTGAATCCTAGTTCCCAC-ATCTCATAGTT
1572589 GTAGTAAATA
Statistics
Matches: 689, Mismatches: 101, Indels: 69
0.80 0.12 0.08
Matches are distributed among these distances:
321 49 0.07
322 11 0.02
323 11 0.02
324 58 0.08
325 49 0.07
326 86 0.12
327 2 0.00
328 1 0.00
329 6 0.01
331 3 0.00
332 4 0.01
334 5 0.01
335 1 0.00
336 8 0.01
337 171 0.25
338 174 0.25
339 38 0.06
340 5 0.01
341 5 0.01
342 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (330 bp):
TATTGGTGTCAATCTTCAAGAGAGTGCCCAACTGATTTCCAACACGTTGTAATCCATATTTATCA
AAATATTCAATGGGTAGGCCAAGTAATCTGACCCACAGCAATTGTAGTAAGGTTGCTAGTGATGG
CTTGAATCCTAGTTCCCACATCTCATAGTTAAGTAATAGGGTCCAACAAACCAAGGTCCTCCACG
CAAAACCTTTTGAAAATTCCATGCATCATGAAAACGAAAAAGGAAAAAATCCATTCCCAATCTAT
TTAGGAATCAAGGGACGGTCAAGATAAACTGGATACAAATACACCATAATGCCTTCTGCGTCCAT
CACTG
Found at i:1575375 original size:13 final size:13
Alignment explanation
Indices: 1575357--1575383 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1575347 CAAGCAACTG
1575357 TACTAATTGTACA
1 TACTAATTGTACA
1575370 TACTAATTGTACA
1 TACTAATTGTACA
1575383 T
1 T
1575384 TTTGATGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TACTAATTGTACA
Found at i:1588530 original size:20 final size:20
Alignment explanation
Indices: 1588498--1588540 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1588488 TATTACAAAA
*
1588498 AAAATTAATTTAAAAT-TTT
1 AAAATTAAATTAAAATATTT
1588517 AAAATTAAAATTAAAATATTT
1 AAAATT-AAATTAAAATATTT
1588538 AAA
1 AAA
1588541 TATAATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 9 0.43
21 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATTAAATTAAAATATTT
Found at i:1589021 original size:13 final size:13
Alignment explanation
Indices: 1588991--1589073 Score: 60
Period size: 13 Copynumber: 6.0 Consensus size: 13
1588981 TTTTTTAAAA
*
1588991 AAATTATAAATATT
1 AAATTAAAAAT-TT
1589005 AAATTAAAAATTT
1 AAATTAAAAATTT
1589018 AAATTTAATAAATATT
1 AAA-TTAA-AAAT-TT
** *
1589034 -AATTAATTATAT
1 AAATTAAAAATTT
1589046 AAATTAATTAAATTT
1 AAATTAA--AAATTT
*
1589061 AAATTTAAAATTT
1 AAATTAAAAATTT
1589074 TCAATAAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
12 1 0.02
13 19 0.35
14 18 0.33
15 15 0.27
16 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATTAAAAATTT
Found at i:1589025 original size:37 final size:41
Alignment explanation
Indices: 1588984--1589070 Score: 110
Period size: 43 Copynumber: 2.2 Consensus size: 41
1588974 ATTCTATTTT
1588984 TTTAAAAAAATT-A-TAAATAT-TAAATTAA-AAATTTAAA
1 TTTAAAAAAATTAATTAAATATATAAATTAATAAATTTAAA
* *
1589021 TTTAATAAATATTAATTAATTATATAAATTAATTAAATTTAAA
1 TTTAA-AAAAATTAATTAAATATATAAATTAA-TAAATTTAAA
1589064 TTTAAAA
1 TTTAAAA
1589071 TTTTCAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
37 5 0.12
38 6 0.14
39 1 0.02
40 6 0.14
41 8 0.19
42 2 0.05
43 14 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (41 bp):
TTTAAAAAAATTAATTAAATATATAAATTAATAAATTTAAA
Found at i:1589048 original size:28 final size:27
Alignment explanation
Indices: 1588991--1589071 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 27
1588981 TTTTTTAAAA
*
1588991 AAATT-ATAAATATTAAATTAAAAATTT
1 AAATTAATAAATATT-AATTAAAAATAT
**
1589018 AAATTTAATAAATATTAATTAATTATAT
1 AAA-TTAATAAATATTAATTAAAAATAT
*
1589046 AAATTAATTAAAT-TTAAATTTAAAAT
1 AAATTAA-TAAATATT-AATTAAAAAT
1589072 TTTCAATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 9 0.20
28 26 0.59
29 9 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AAATTAATAAATATTAATTAAAAATAT
Found at i:1589090 original size:50 final size:47
Alignment explanation
Indices: 1588995--1589091 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 47
1588985 TTAAAAAAAT
1588995 TATAAATATTAAATTAAAAATTTAAATTTAATAAATATTAATTAATTA
1 TATAAATATTAAATTAAAAATTTAAATTTAATAAATATT-ATTAATTA
*
1589043 TATAAATTAATTAAATT-TAAATTTAAAATTTTCAATAAATATT-TTAATT
1 TATAAA-T-ATTAAATTAAAAATTT-AAA-TTT-AATAAATATTATTAATT
1589092 TAATCTAGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
48 6 0.14
49 7 0.16
50 17 0.40
51 3 0.07
52 10 0.23
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (47 bp):
TATAAATATTAAATTAAAAATTTAAATTTAATAAATATTATTAATTA
Found at i:1589261 original size:25 final size:23
Alignment explanation
Indices: 1589199--1589273 Score: 75
Period size: 25 Copynumber: 3.2 Consensus size: 23
1589189 ATTTATAATA
1589199 ATTATGA-ATATAAT-AAATATT
1 ATTATGATATATAATAAAATATT
*
1589220 ATTATAATTAATTATAATAAAATATGT
1 ATTATGA-T-A-TATAATAAAATAT-T
1589247 ATTATGATATAATAATAAAATA-T
1 ATTATGATAT-ATAATAAAATATT
1589270 ATTA
1 ATTA
1589274 AAATTATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
21 6 0.13
23 5 0.11
24 2 0.04
25 18 0.40
26 7 0.16
27 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
ATTATGATATATAATAAAATATT
Found at i:1591019 original size:14 final size:14
Alignment explanation
Indices: 1591000--1591044 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
1590990 TTGATAAAAT
1591000 TAAATATAATTATA
1 TAAATATAATTATA
1591014 TAAATATAA-TATA
1 TAAATATAATTATA
*
1591027 AAAATATAAATTAT-
1 TAAATAT-AATTATA
1591041 TAAA
1 TAAA
1591045 CTTATCAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 10 0.37
14 14 0.52
15 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:1591961 original size:23 final size:25
Alignment explanation
Indices: 1591917--1591966 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
1591907 GAGTATGTTG
1591917 AAAAAAAATATTTACTTATTTC-TT
1 AAAAAAAATATTTACTTATTTCATT
* *
1591941 AAAAAAATTATTTA-TTTTTTCATT
1 AAAAAAAATATTTACTTATTTCATT
1591965 AA
1 AA
1591967 GTTAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (25 bp):
AAAAAAAATATTTACTTATTTCATT
Found at i:1592069 original size:22 final size:24
Alignment explanation
Indices: 1592038--1592084 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1592028 AAATTTTATC
* *
1592038 TTTTGATTT-ATAATTAAATAAAA
1 TTTTGATTTAAAAATAAAATAAAA
1592061 TTTT-ATTTAAAAATAAAATAAAA
1 TTTTGATTTAAAAATAAAATAAAA
1592084 T
1 T
1592085 ATTAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTTGATTTAAAAATAAAATAAAA
Found at i:1592121 original size:23 final size:22
Alignment explanation
Indices: 1592043--1592121 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
1592033 TTATCTTTTG
* *
1592043 ATTTATAATTAAATAAAATTTT
1 ATTTAAAATTAAATAAAATTTA
*
1592065 ATTTAAAAATAAAATAAAATATTA
1 ATTT-AAAATTAAATAAAAT-TTA
* *
1592089 ATATTAAAATTAATATATAATTAA
1 AT-TTAAAATTAA-ATAAAATTTA
1592113 ATTTAAAAT
1 ATTTAAAAT
1592122 ATTTTTGTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
22 4 0.09
23 20 0.43
24 15 0.32
25 8 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTAAAATTAAATAAAATTTA
Found at i:1592549 original size:32 final size:30
Alignment explanation
Indices: 1592473--1592571 Score: 116
Period size: 30 Copynumber: 3.3 Consensus size: 30
1592463 ATATTTTGTT
*
1592473 TAAA-AATATATTT-AGATACAAATTAAAAG
1 TAAATAATTTATTTAAG-TACAAATTAAAAG
* *
1592502 TTAATAATTTATTTAAGTATAAATTAAAAG
1 TAAATAATTTATTTAAGTACAAATTAAAAG
1592532 TAAATATGATTTATTTAAGTACAAATTAAAA-
1 TAAATA--ATTTATTTAAGTACAAATTAAAAG
1592563 -AAATAATTT
1 TAAATAATTT
1592572 TTTTTATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
28 4 0.07
29 3 0.05
30 30 0.49
31 2 0.03
32 22 0.36
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (30 bp):
TAAATAATTTATTTAAGTACAAATTAAAAG
Found at i:1592778 original size:19 final size:20
Alignment explanation
Indices: 1592728--1592772 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1592718 ATATCATTAC
*
1592728 TTTGATGTAATTTTTTTTTTG
1 TTTGGTGTAA-TTTTTTTTTG
1592749 TTTGGTGTAATTTTTTTTT-
1 TTTGGTGTAATTTTTTTTTG
1592768 TTTGG
1 TTTGG
1592773 ATTAATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 9 0.39
21 9 0.39
ACGTcount: A:0.11, C:0.00, G:0.18, T:0.71
Consensus pattern (20 bp):
TTTGGTGTAATTTTTTTTTG
Found at i:1592783 original size:19 final size:20
Alignment explanation
Indices: 1592741--1592783 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1592731 GATGTAATTT
1592741 TTTTTTTGTTTGGTGTAAT-
1 TTTTTTTGTTTGGTGTAATG
*
1592760 TTTTTTTTTTTGGAT-TAATG
1 TTTTTTTGTTTGG-TGTAATG
1592780 TTTT
1 TTTT
1592784 ACAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (20 bp):
TTTTTTTGTTTGGTGTAATG
Found at i:1592783 original size:21 final size:21
Alignment explanation
Indices: 1592728--1592768 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1592718 ATATCATTAC
*
1592728 TTTGATGTAATTTTTTTTTTG
1 TTTGGTGTAATTTTTTTTTTG
1592749 TTTGGTGTAATTTTTTTTTT
1 TTTGGTGTAATTTTTTTTTT
1592769 TTGGATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.73
Consensus pattern (21 bp):
TTTGGTGTAATTTTTTTTTTG
Found at i:1597481 original size:16 final size:17
Alignment explanation
Indices: 1597460--1597492 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1597450 TTTTTTTAAA
*
1597460 AATATATAAAT-ATTTT
1 AATATAAAAATAATTTT
1597476 AATATAAAAATAATTTT
1 AATATAAAAATAATTTT
1597493 TATTATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATAAAAATAATTTT
Found at i:1599968 original size:28 final size:27
Alignment explanation
Indices: 1599915--1599980 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1599905 GTCACTCATT
* * *
1599915 TGTTTGTAAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGATGGTTATTTTA
*
1599942 TGTTTGTCAAAAATGATGGTTTCTTTTA
1 TGTTTGTCAAAAATGATGG-TTATTTTA
*
1599970 TATTTGTCAAA
1 TGTTTGTCAAA
1599981 TATTGAGGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 17 0.52
28 16 0.48
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATGATGGTTATTTTA
Found at i:1604835 original size:2 final size:2
Alignment explanation
Indices: 1604828--1604854 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1604818 CTGATTTCAC
1604828 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
1604855 GTAGATGATA
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:1605291 original size:27 final size:25
Alignment explanation
Indices: 1605236--1605291 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
1605226 GATTACTACT
*
1605236 TAATTAAAATATATATATTTAAATT
1 TAATTAAAATATATATATTTAAATA
* *
1605261 TAATTATAATATATGTATATTTTAATA
1 TAATTA-AA-ATATATATATTTAAATA
1605288 TAAT
1 TAAT
1605292 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 6 0.23
26 2 0.08
27 18 0.69
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TAATTAAAATATATATATTTAAATA
Found at i:1605304 original size:21 final size:21
Alignment explanation
Indices: 1605243--1605304 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1605233 ACTTAATTAA
*
1605243 AATAT-ATATATTTA-AATTT
1 AATATAATATATTTATATTTT
*
1605262 AATTATAATATATGTATATTTT
1 AA-TATAATATATTTATATTTT
*
1605284 AATATAATATTTTTATATTTT
1 AATATAATATATTTATATTTT
1605305 TAAATAGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.06
20 3 0.08
21 25 0.69
22 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AATATAATATATTTATATTTT
Found at i:1609403 original size:189 final size:189
Alignment explanation
Indices: 1609083--1609463 Score: 762
Period size: 189 Copynumber: 2.0 Consensus size: 189
1609073 CCTTTAAAGA
1609083 AATGGGTTTTAGTTGAAATAAAAATGATTAAATAATTAACTATTATTACTATTTACTCATTTAAA
1 AATGGGTTTTAGTTGAAATAAAAATGATTAAATAATTAACTATTATTACTATTTACTCATTTAAA
1609148 TACCCTACAAAACATAATGGACAGCAGTGGAGATGACGTCAATAGCAATCAATGCATCGTTTTTT
66 TACCCTACAAAACATAATGGACAGCAGTGGAGATGACGTCAATAGCAATCAATGCATCGTTTTTT
1609213 AATTAGATTTCGTGTCTCATCTCCCATCAACCAAATTTTCACAAAGCAATAACATTAAG
131 AATTAGATTTCGTGTCTCATCTCCCATCAACCAAATTTTCACAAAGCAATAACATTAAG
1609272 AATGGGTTTTAGTTGAAATAAAAATGATTAAATAATTAACTATTATTACTATTTACTCATTTAAA
1 AATGGGTTTTAGTTGAAATAAAAATGATTAAATAATTAACTATTATTACTATTTACTCATTTAAA
1609337 TACCCTACAAAACATAATGGACAGCAGTGGAGATGACGTCAATAGCAATCAATGCATCGTTTTTT
66 TACCCTACAAAACATAATGGACAGCAGTGGAGATGACGTCAATAGCAATCAATGCATCGTTTTTT
1609402 AATTAGATTTCGTGTCTCATCTCCCATCAACCAAATTTTCACAAAGCAATAACATTAAG
131 AATTAGATTTCGTGTCTCATCTCCCATCAACCAAATTTTCACAAAGCAATAACATTAAG
1609461 AAT
1 AAT
1609464 TCAATAAAAA
Statistics
Matches: 192, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 192 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (189 bp):
AATGGGTTTTAGTTGAAATAAAAATGATTAAATAATTAACTATTATTACTATTTACTCATTTAAA
TACCCTACAAAACATAATGGACAGCAGTGGAGATGACGTCAATAGCAATCAATGCATCGTTTTTT
AATTAGATTTCGTGTCTCATCTCCCATCAACCAAATTTTCACAAAGCAATAACATTAAG
Found at i:1609749 original size:15 final size:15
Alignment explanation
Indices: 1609729--1609804 Score: 73
Period size: 15 Copynumber: 5.0 Consensus size: 15
1609719 ATAATTTTAT
*
1609729 AAATAAATTTAAATA
1 AAATTAATTTAAATA
1609744 AAA-TAATTTAAATA
1 AAATTAATTTAAATA
* *
1609758 ATAATTATTTTAAATT
1 A-AATTAATTTAAATA
*
1609774 TAATTAATTTAAATA
1 AAATTAATTTAAATA
**
1609789 ATTTTAATATTAAATA
1 AAATTAAT-TTAAATA
1609805 TATCTCATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
14 11 0.22
15 22 0.45
16 16 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTAATTTAAATA
Found at i:1614032 original size:23 final size:22
Alignment explanation
Indices: 1614005--1614054 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1613995 GTCATTTAGG
*
1614005 TCTTTGGAT-GTTAACATTCATA
1 TCTTT-GATGGTTAACAGTCATA
*
1614027 TGCTTTGCTGGTTAACAGTCATA
1 T-CTTTGATGGTTAACAGTCATA
1614050 TCTTT
1 TCTTT
1614055 TGCCCCCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (22 bp):
TCTTTGATGGTTAACAGTCATA
Found at i:1616642 original size:13 final size:12
Alignment explanation
Indices: 1616626--1616669 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1616616 TTTTAAAAAT
1616626 ATTTATATTTTAA
1 ATTTATA-TTTAA
*
1616639 ATTTATATTT-G
1 ATTTATATTTAA
*
1616650 ATATATATTTAA
1 ATTTATATTTAA
1616662 ATTTATAT
1 ATTTATAT
1616670 AAAAATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 9 0.35
12 10 0.38
13 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
ATTTATATTTAA
Found at i:1616728 original size:15 final size:15
Alignment explanation
Indices: 1616710--1616741 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1616700 ATTTAAAAGA
*
1616710 ATTAAATATATTTAT
1 ATTAAATATATATAT
1616725 ATTAAATATATATAT
1 ATTAAATATATATAT
1616740 AT
1 AT
1616742 ATATTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAAATATATATAT
Found at i:1619700 original size:2 final size:2
Alignment explanation
Indices: 1619693--1619717 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1619683 AGCAGTGAAG
1619693 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1619718 ATGATATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1622106 original size:25 final size:26
Alignment explanation
Indices: 1622063--1622134 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
1622053 TAATGTATAA
*
1622063 ATATAT-A-TTATTAATAAATTACATT
1 ATATATAATTTATTAA-AAATTAAATT
*
1622088 ATAT-TAATTTATTAAAAATAAAATT
1 ATATATAATTTATTAAAAATTAAATT
* *
1622113 ATTTATAATTATTTTAAAAATT
1 ATATATAATT-TATTAAAAATT
1622135 CTTTAATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 1 0.03
25 16 0.42
26 12 0.32
27 9 0.24
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATATAATTTATTAAAAATTAAATT
Found at i:1622121 original size:26 final size:25
Alignment explanation
Indices: 1622070--1622133 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
1622060 TAAATATATA
* *
1622070 TTATTAATAAATTACATTATATTAAT
1 TTATTAA-AAATAAAATTATATTAAT
*
1622096 TTATTAAAAATAAAATTATTTATAAT
1 TTATTAAAAATAAAATTATAT-TAAT
*
1622122 TATTTTAAAAAT
1 T-TATTAAAAAT
1622134 TCTTTAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 11 0.34
26 12 0.38
27 9 0.28
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TTATTAAAAATAAAATTATATTAAT
Found at i:1624315 original size:2 final size:2
Alignment explanation
Indices: 1624310--1624351 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1624300 TCTTTTTTTA
*
1624310 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1624352 TCATGTGCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1630662 original size:21 final size:21
Alignment explanation
Indices: 1630636--1630685 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1630626 GTGCCACACA
*
1630636 CATCCAATAGCCCAAGTGATC
1 CATCCAACAGCCCAAGTGATC
*
1630657 CATCCAACAGTCCAAGTGATC
1 CATCCAACAGCCCAAGTGATC
1630678 CATCCAAC
1 CATCCAAC
1630686 GCATCCTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.36, G:0.12, T:0.18
Consensus pattern (21 bp):
CATCCAACAGCCCAAGTGATC
Found at i:1641103 original size:46 final size:45
Alignment explanation
Indices: 1641036--1641127 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 45
1641026 TACAGAACCC
1641036 TACTGCTCAAACAATGGGAACACAAAGTGCTTTTATCCCCCTGATT
1 TACTGCTCAAACAATGGGAACACAAAGTGC-TTTATCCCCCTGATT
1641082 TACTGCTCAAACAATGGGAACACAAAGTGCTTTATCCCCCTGATT
1 TACTGCTCAAACAATGGGAACACAAAGTGCTTTATCCCCCTGATT
1641127 T
1 T
1641128 TTTAAATTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 16 0.35
46 30 0.65
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (45 bp):
TACTGCTCAAACAATGGGAACACAAAGTGCTTTATCCCCCTGATT
Found at i:1641478 original size:2 final size:2
Alignment explanation
Indices: 1641471--1641498 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1641461 ATTCTTTTAC
1641471 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
1641499 GAGAGCTAAT
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
Found at i:1642292 original size:21 final size:22
Alignment explanation
Indices: 1642266--1642310 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1642256 TCAAAGTAAT
* *
1642266 ATTAAATTTAATTATTTTA-AA
1 ATTAAATTAAATTATATTATAA
1642287 ATTAAATTAAATTATATTATAA
1 ATTAAATTAAATTATATTATAA
1642309 AT
1 AT
1642311 AAAAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAAATTAAATTATATTATAA
Found at i:1647137 original size:22 final size:21
Alignment explanation
Indices: 1647111--1647158 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1647101 TAAGAAGCCA
1647111 ATTAATACAAATAATTTAATTT
1 ATTAATACAAATAA-TTAATTT
* *
1647133 ATTAATATAAATTATTAATTT
1 ATTAATACAAATAATTAATTT
1647154 ATTAA
1 ATTAA
1647159 ATTTTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAATACAAATAATTAATTT
Found at i:1647501 original size:25 final size:25
Alignment explanation
Indices: 1647467--1647514 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1647457 ATTGGCAACA
*
1647467 AACAAACAAACTGCTGTTTTAAGCC
1 AACAAACAAACTGATGTTTTAAGCC
1647492 AACAAACAAACTGATGTTTTAAG
1 AACAAACAAACTGATGTTTTAAG
1647515 GAGCTTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (25 bp):
AACAAACAAACTGATGTTTTAAGCC
Found at i:1653414 original size:2 final size:2
Alignment explanation
Indices: 1653407--1653437 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1653397 AGTGCTCATG
1653407 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
1653438 GTTAGAGAGA
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:1656614 original size:2 final size:2
Alignment explanation
Indices: 1656607--1656645 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1656597 TAATTCTGAT
* *
1656607 TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC TA TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1656646 GTGTAACTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1658122 original size:51 final size:52
Alignment explanation
Indices: 1658061--1658179 Score: 195
Period size: 52 Copynumber: 2.3 Consensus size: 52
1658051 CAAGGATGGG
*
1658061 ATTTGAGTGAATGATT-AAAATACGTATGTGATTTTGCAAGGGATTATTGGC
1 ATTTGAGTGAATGATTAAAAATACGTATGTGATTTTGCAAGGGATTATTAGC
** *
1658112 ATTTGAGTGAATGATTAAAAATGTGTATTTGATTTTGCAAGGGATTATTAGC
1 ATTTGAGTGAATGATTAAAAATACGTATGTGATTTTGCAAGGGATTATTAGC
1658164 ATTTGAGTGAATGATT
1 ATTTGAGTGAATGATT
1658180 GATTAATTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 16 0.25
52 47 0.75
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.39
Consensus pattern (52 bp):
ATTTGAGTGAATGATTAAAAATACGTATGTGATTTTGCAAGGGATTATTAGC
Found at i:1663716 original size:68 final size:68
Alignment explanation
Indices: 1663607--1663745 Score: 233
Period size: 68 Copynumber: 2.0 Consensus size: 68
1663597 ACCATTCAAG
* *
1663607 ATTAGGCCTCGTAGGCTAACAGTGGACCTAAGAGGTCAACCGTTTGGTCCAATCTTAAGCCTTGG
1 ATTAGGCCTCGTAGACAAACAGTGGACCTAAGAGGTCAACCGTTTGGTCCAATCTTAAGCCTTGG
*
1663672 TCA
66 CCA
* *
1663675 ATTAGGCCTCGTAGACAAACAGTGGACCTAAGAGGTCAACCGTTTGGTTCAATCTTCAGCCTTGG
1 ATTAGGCCTCGTAGACAAACAGTGGACCTAAGAGGTCAACCGTTTGGTCCAATCTTAAGCCTTGG
1663740 CCA
66 CCA
1663743 ATT
1 ATT
1663746 CGGCATTGGG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.27
Consensus pattern (68 bp):
ATTAGGCCTCGTAGACAAACAGTGGACCTAAGAGGTCAACCGTTTGGTCCAATCTTAAGCCTTGG
CCA
Found at i:1664401 original size:15 final size:15
Alignment explanation
Indices: 1664377--1664412 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1664367 AACTGAAGCC
*
1664377 AAAAAGAAAAAAAAG
1 AAAAAAAAAAAAAAG
1664392 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
1664407 AAAAAA
1 AAAAAA
1664413 GGAACTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:1664412 original size:9 final size:9
Alignment explanation
Indices: 1664377--1664405 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1664367 AACTGAAGCC
1664377 AAAAAGAAA
1 AAAAAGAAA
1664386 AAAAAGAAA
1 AAAAAGAAA
1664395 AAAAA-AAA
1 AAAAAGAAA
1664403 AAA
1 AAA
1664406 GAAAAAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:1670481 original size:3 final size:3
Alignment explanation
Indices: 1670320--1670461 Score: 82
Period size: 3 Copynumber: 48.7 Consensus size: 3
1670310 CGATTAAATC
* * *
1670320 ATA ATA TATT ATA ATA ATA ATA ATA AT- ATT ATT ATA ATA ATA A-A
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
1670364 AT- TTA AAA ATA ATA AT- ACA ATT A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
1670409 ATA A-A ATT TTA AAA ACCCA CTC ACA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1670454 ATA ATA AT
1 ATA ATA AT
1670462 TATTTTGCTT
Statistics
Matches: 105, Mismatches: 24, Indels: 20
0.70 0.16 0.13
Matches are distributed among these distances:
2 11 0.10
3 91 0.87
4 2 0.02
5 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1671110 original size:2 final size:2
Alignment explanation
Indices: 1671105--1671143 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1671095 TCTGGTATTG
1671105 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1671144 GTGGGTGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1675287 original size:2 final size:2
Alignment explanation
Indices: 1675282--1675311 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1675272 TATGTGTGTG
1675282 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1675312 GAGAGAGAGA
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):
TA
Found at i:1675316 original size:2 final size:2
Alignment explanation
Indices: 1675311--1675337 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1675301 ATATATATAT
1675311 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
1675338 AGAATACCTT
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:1690749 original size:15 final size:14
Alignment explanation
Indices: 1690731--1690765 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1690721 AGTATAACAA
1690731 ATTAAATTATATAAT
1 ATTAAATTATA-AAT
*
1690746 ATTATATTATAAAT
1 ATTAAATTATAAAT
1690760 ATTAAA
1 ATTAAA
1690766 ATATTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTAAATTATAAAT
Found at i:1690763 original size:29 final size:30
Alignment explanation
Indices: 1690699--1690775 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 30
1690689 ATGTGATTTT
1690699 TTAAATATCATATAATTTATATAGTATAACAAA
1 TTAAAT-T-ATATAATTTATATA-TATAACAAA
*
1690732 TTAAATTATATAATATTATAT-TATAA-ATA
1 TTAAATTATATAAT-TTATATATATAACAAA
* *
1690761 TTAAAATATTTAATT
1 TTAAATTATATAATT
1690776 ATTTGATCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 1 0.03
29 14 0.35
30 5 0.12
31 7 0.17
32 7 0.17
33 6 0.15
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (30 bp):
TTAAATTATATAATTTATATATATAACAAA
Found at i:1691143 original size:13 final size:12
Alignment explanation
Indices: 1691108--1691149 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
1691098 TCTGATAAAA
1691108 AAATAAAAA-AT
1 AAATAAAAATAT
*
1691119 CAATAAAAATAT
1 AAATAAAAATAT
*
1691131 AATATAAATATAT
1 AA-ATAAAAATAT
1691144 AAATAA
1 AAATAA
1691150 TTAAAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 8 0.31
12 7 0.27
13 11 0.42
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATAAAAATAT
Found at i:1710383 original size:15 final size:15
Alignment explanation
Indices: 1710363--1710393 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1710353 GAAGCCAGAA
1710363 ATAAGAAAAACTAGG
1 ATAAGAAAAACTAGG
*
1710378 ATAAGAGAAACTAGG
1 ATAAGAAAAACTAGG
1710393 A
1 A
1710394 ATAGAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.23, T:0.13
Consensus pattern (15 bp):
ATAAGAAAAACTAGG
Done.