Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
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: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 11 of 29
Found at i:1471918 original size:27 final size:26
Alignment explanation
Indices: 1471888--1471946 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1471878 AAAAAAAGAG
1471888 AAAAATCAAAAAATAAGGAAAAATAAA
1 AAAAATCAAAAAATAA-GAAAAATAAA
* * *
1471915 AAAATTCTAAAAATTAGAAAAATAAA
1 AAAAATCAAAAAATAAGAAAAATAAA
*
1471941 ATAAAT
1 AAAAAT
1471947 AATATAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (26 bp):
AAAAATCAAAAAATAAGAAAAATAAA
Found at i:1471919 original size:18 final size:19
Alignment explanation
Indices: 1471878--1471919 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1471868 AGAAATTATT
*
1471878 AAAAA-AAGAGAAAAATCA
1 AAAAATAAGAGAAAAATAA
1471896 AAAAATAAG-GAAAAATAA
1 AAAAATAAGAGAAAAATAA
1471914 AAAAAT
1 AAAAAT
1471920 TCTAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.10
Consensus pattern (19 bp):
AAAAATAAGAGAAAAATAA
Found at i:1472094 original size:14 final size:15
Alignment explanation
Indices: 1472075--1472104 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1472065 TTTTTTGAGT
1472075 TTTTGGA-TTAAAAA
1 TTTTGGATTTAAAAA
1472089 TTTTGGATTTAAAAA
1 TTTTGGATTTAAAAA
1472104 T
1 T
1472105 AGATTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
TTTTGGATTTAAAAA
Found at i:1472534 original size:37 final size:36
Alignment explanation
Indices: 1472492--1472565 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 36
1472482 TCTTGAACTC
*
1472492 ATTTTTTTCTTT-TTTTCACTTTTTTTTTTAATTTTT
1 ATTTTTTTCTTTATTTTCA-TTTATTTTTTAATTTTT
1472528 ATTTTTTTCTTTAATTTTCATTTATTTTTTAATTTTT
1 ATTTTTTTCTTT-ATTTTCATTTATTTTTTAATTTTT
1472565 A
1 A
1472566 CAAAATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 12 0.34
37 17 0.49
38 6 0.17
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (36 bp):
ATTTTTTTCTTTATTTTCATTTATTTTTTAATTTTT
Found at i:1472545 original size:18 final size:18
Alignment explanation
Indices: 1472490--1472563 Score: 89
Period size: 18 Copynumber: 4.1 Consensus size: 18
1472480 TTTCTTGAAC
1472490 TCATTTTTTTCTTT--TTT
1 TCATTTTTTT-TTTAATTT
1472507 TCACTTTTTTTTTTAATTT
1 TCA-TTTTTTTTTTAATTT
*
1472526 TTATTTTTTTCTTTAATTT
1 TCATTTTTTT-TTTAATTT
*
1472545 TCATTTATTTTTTAATTT
1 TCATTTTTTTTTTAATTT
1472563 T
1 T
1472564 TACAAAATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
17 6 0.12
18 23 0.46
19 21 0.42
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (18 bp):
TCATTTTTTTTTTAATTT
Found at i:1472643 original size:9 final size:9
Alignment explanation
Indices: 1472609--1472728 Score: 57
Period size: 9 Copynumber: 13.1 Consensus size: 9
1472599 TTTAAATTAA
1472609 TTTTATAATT
1 TTTTAT-ATT
*
1472619 TATTGATATAT
1 T-TTTATAT-T
1472630 TTTTATATT
1 TTTTATATT
*
1472639 TTTTAGATT
1 TTTTATATT
* *
1472648 TTTTTTATC
1 TTTTATATT
1472657 TTTTATAATCT
1 TTTTAT-AT-T
* **
1472668 TTTTAAAAA
1 TTTTATATT
*
1472677 TTTTA-AAT
1 TTTTATATT
* *
1472685 TTTTAAAAT
1 TTTTATATT
1472694 TTTT-TATT
1 TTTTATATT
*
1472702 TTTTGTATT
1 TTTTATATT
* *
1472711 TTGTAAATT
1 TTTTATATT
1472720 TTTTA-ATT
1 TTTTATATT
1472728 T
1 T
1472729 AAAATTTTTT
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
8 17 0.20
9 46 0.53
10 12 0.14
11 11 0.13
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTTATATT
Found at i:1472671 original size:20 final size:20
Alignment explanation
Indices: 1472609--1472663 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
1472599 TTTAAATTAA
* * *
1472609 TTTTATAATTTATTGATATAT
1 TTTTATATTTTATAGAT-TTT
*
1472630 TTTTATATTTTTTAGATTTT
1 TTTTATATTTTATAGATTTT
*
1472650 TTTTATCTTTTATA
1 TTTTATATTTTATA
1472664 ATCTTTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTATATTTTATAGATTTT
Found at i:1472705 original size:25 final size:23
Alignment explanation
Indices: 1472675--1472737 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
1472665 TCTTTTTAAA
1472675 AATTTTAAATTTTTAAAATTTTTT
1 AATTTTAAATTTTT-AAATTTTTT
* **
1472699 ATTTTTTGTATTTTGTAAATTTTTT
1 A-ATTTTAAATTTT-TAAATTTTTT
*
1472724 AATTTAAAATTTTT
1 AATTTTAAATTTTT
1472738 TTCTTTATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
23 1 0.03
24 9 0.30
25 19 0.63
26 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (23 bp):
AATTTTAAATTTTTAAATTTTTT
Found at i:1475218 original size:20 final size:21
Alignment explanation
Indices: 1475184--1475240 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
1475174 AAATATTAAA
1475184 AATAT-TTTTATATTAATATTT
1 AATATATTTTATATT-ATATTT
1475205 -ATATATTTTA-ATTATATTT
1 AATATATTTTATATTATATTT
*
1475224 AAAATATTTTATTATTA
1 AATATATTTTA-TATTA
1475241 AATAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.19
20 16 0.52
21 5 0.16
22 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATATATTTTATATTATATTT
Found at i:1476151 original size:18 final size:17
Alignment explanation
Indices: 1476118--1476174 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
1476108 TAAAATTTAA
1476118 ATTTATATTTATATTTG
1 ATTTATATTTATATTTG
1476135 ATTTA-ATTTATAAATTTG
1 ATTTATATTTAT--ATTTG
* *
1476153 AATTATTATTTAT-TTTT
1 ATTTA-TATTTATATTTG
1476170 ATTTA
1 ATTTA
1476175 AAAATATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 6 0.18
17 12 0.36
18 9 0.27
20 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
ATTTATATTTATATTTG
Found at i:1476151 original size:36 final size:34
Alignment explanation
Indices: 1476106--1476175 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 34
1476096 TTTTAAAATG
1476106 TTTAAAATTTAAATT-TATATTTATATTTGATTTAA
1 TTTAAAATTTAAATTAT-TATTTAT-TTTGATTTAA
* *
1476141 TTTATAAATTTGAATTATTATTTATTTTTATTTAA
1 TTTA-AAATTTAAATTATTATTTATTTTGATTTAA
1476176 AAATATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 13 0.42
36 17 0.55
37 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (34 bp):
TTTAAAATTTAAATTATTATTTATTTTGATTTAA
Found at i:1476163 original size:30 final size:31
Alignment explanation
Indices: 1476136--1476203 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
1476126 TTATATTTGA
* * *
1476136 TTTAATTTATAAAT-TTGAATTATTATTTAT
1 TTTAATTTAAAAATATTAAAATATTATTTAT
*
1476166 TTTTATTTAAAAATATTAAAATATTATTTTAT
1 TTTAATTTAAAAATATTAAAATATTA-TTTAT
1476198 ATTTAA
1 -TTTAA
1476204 AATATATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 12 0.40
31 9 0.30
32 5 0.17
33 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTAATTTAAAAATATTAAAATATTATTTAT
Found at i:1476199 original size:18 final size:17
Alignment explanation
Indices: 1476178--1476223 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
1476168 TTATTTAAAA
1476178 ATATTAAAATATTATTTT
1 ATATTAAAATA-TATTTT
1476196 ATATTTAAAATATATTTT
1 ATA-TTAAAATATATTTT
*
1476214 ATAATAAAAT
1 ATATTAAAAT
1476224 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 12 0.46
19 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAAAATATATTTT
Found at i:1476904 original size:17 final size:18
Alignment explanation
Indices: 1476878--1476923 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
1476868 AATTTTAAAT
* *
1476878 AAAATTAAATAT-ATTTA
1 AAAATAAAATATAAATTA
*
1476895 AATATAAAAT-TAAATTA
1 AAAATAAAATATAAATTA
1476912 AAAATAAAATAT
1 AAAATAAAATAT
1476924 GATTATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 1 0.04
17 21 0.91
18 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATAAAATATAAATTA
Found at i:1476908 original size:32 final size:34
Alignment explanation
Indices: 1476840--1476923 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 34
1476830 TAATATGAAA
*
1476840 AAATTAAAAATTAAAT-T-TATATATATAAAATTTT
1 AAATT-AAAATTAAATATATATAAATATAAAA-TTT
*
1476874 AAA-TAAAATTAAATATATTTAAATATAAAA-TT
1 AAATTAAAATTAAATATATATAAATATAAAATTT
*
1476906 AAATTAAAAATAAA-ATAT
1 AAATTAAAATTAAATATAT
1476924 GATTATCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
32 19 0.43
33 11 0.25
34 14 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATTAAAATTAAATATATATAAATATAAAATTT
Found at i:1476911 original size:27 final size:28
Alignment explanation
Indices: 1476846--1476913 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
1476836 GAAAAAATTA
* *
1476846 AAAATTAAATT-TATATATATAAAATTT
1 AAAATTAAATTAAATATATATAAAATAT
* * *
1476873 TAAATAAAATTAAATATAT-TTAAATAT
1 AAAATTAAATTAAATATATATAAAATAT
1476900 AAAATTAAATTAAA
1 AAAATTAAATTAAA
1476914 AATAAAATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
27 27 0.82
28 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AAAATTAAATTAAATATATATAAAATAT
Found at i:1476916 original size:34 final size:34
Alignment explanation
Indices: 1476840--1476923 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 34
1476830 TAATATGAAA
*
1476840 AAATTAAAAATTAAAT-TTATATATATAAAATTTT
1 AAATTAAAAATTAAATATTATAAATATAAAA-TTT
*
1476874 AAA-T-AAAATTAAATATATTTAAATATAAAA-TT
1 AAATTAAAAATTAAATAT-TATAAATATAAAATTT
*
1476906 AAATTAAAAATAAAATAT
1 AAATTAAAAATTAAATAT
1476924 GATTATCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
32 15 0.35
33 3 0.07
34 25 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATTAAAAATTAAATATTATAAATATAAAATTT
Found at i:1477971 original size:14 final size:14
Alignment explanation
Indices: 1477954--1478010 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
1477944 AAAATATTTT
1477954 TAAATATAATTATA
1 TAAATATAATTATA
*
1477968 TAAATATAATACATA
1 TAAATATAAT-TATA
*
1477983 TAAA-ATATTTA-A
1 TAAATATAATTATA
* *
1477995 TATATATAATAATA
1 TAAATATAATTATA
1478009 TA
1 TA
1478011 GCATAAACGT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.12
13 6 0.18
14 17 0.50
15 7 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:1478001 original size:18 final size:19
Alignment explanation
Indices: 1477974--1478009 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1477964 TATATAAATA
1477974 TAATACATATAA-AATATT
1 TAATACATATAATAATATT
*
1477992 TAATATATATAATAATAT
1 TAATACATATAATAATAT
1478010 AGCATAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATACATATAATAATATT
Found at i:1478180 original size:23 final size:27
Alignment explanation
Indices: 1478114--1478186 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 27
1478104 AATAAAATAT
1478114 ATAAATA-TATAAA-TTATTATATCTA
1 ATAAATATTATAAATTTATTATATCTA
*
1478139 ATAAAATATTATAATTTTATT-TAT-TA
1 AT-AAATATTATAAATTTATTATATCTA
1478165 AT-AAT-TTATAAATTTATATATA
1 ATAAATATTATAAATTTAT-TATA
1478187 ATTATTACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 11 0.27
24 4 0.10
25 4 0.10
26 9 0.22
27 8 0.20
28 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAAATATTATAAATTTATTATATCTA
Found at i:1478811 original size:27 final size:29
Alignment explanation
Indices: 1478732--1478830 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 29
1478722 TATTAAAATA
**
1478732 AAATATAAAATATATAATGATATAA-ATATTT
1 AAATATATTATATA-AAT-ATATAATATA-TT
* *
1478763 AAATATATTTTATAATTA-ATAATATATT
1 AAATATATTATATAAATATATAATATATT
1478791 AAA-AT-TTATATAAATATATAATATATT
1 AAATATATTATATAAATATATAATATATT
1478818 AAATATAATTATA
1 AAATAT-ATTATA
1478831 GTATGTTGTA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
26 9 0.16
27 15 0.26
28 11 0.19
29 4 0.07
30 7 0.12
31 11 0.19
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
AAATATATTATATAAATATATAATATATT
Found at i:1481967 original size:19 final size:18
Alignment explanation
Indices: 1481935--1481970 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1481925 ATACACATCT
1481935 AAATTTTAAATAAATTAA
1 AAATTTTAAATAAATTAA
*
1481953 AAATATTTAATTAAATTA
1 AAAT-TTTAAATAAATTA
1481971 TTAAACCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTTTAAATAAATTAA
Found at i:1487669 original size:21 final size:21
Alignment explanation
Indices: 1487632--1487815 Score: 138
Period size: 21 Copynumber: 8.8 Consensus size: 21
1487622 TTTTGATTTT
* *
1487632 TTTTTAATATGATTTTTATAA
1 TTTTTAATATAATTTTAATAA
*
1487653 CTTTTTAATGTAATTTTAATAA
1 -TTTTTAATATAATTTTAATAA
*
1487675 TTTTTAATATAATTTTGATAA
1 TTTTTAATATAATTTTAATAA
*
1487696 TTTTTTATATAATTTTAATAA
1 TTTTTAATATAATTTTAATAA
* * * *
1487717 TCTTTCATATAATATTACTAA
1 TTTTTAATATAATTTTAATAA
* * *
1487738 TTTTTGAGATTA-TTTAATAA
1 TTTTTAATATAATTTTAATAA
* * * *
1487758 TATTTGATGTAATTTTAGTAA
1 TTTTTAATATAATTTTAATAA
** * * * *
1487779 CATTTGATACAATTGTAGTAA
1 TTTTTAATATAATTTTAATAA
1487800 TCTTTT-ATATAATTTT
1 T-TTTTAATATAATTTT
1487816 GAAAACCATT
Statistics
Matches: 130, Mismatches: 30, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
20 14 0.11
21 95 0.73
22 21 0.16
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (21 bp):
TTTTTAATATAATTTTAATAA
Found at i:1487675 original size:9 final size:9
Alignment explanation
Indices: 1487663--1487741 Score: 50
Period size: 9 Copynumber: 7.8 Consensus size: 9
1487653 CTTTTTAATG
1487663 TAATTTTAA
1 TAATTTTAA
1487672 TAATTTTTAATA
1 TAA-TTTT-A-A
*
1487684 TAATTTTGA
1 TAATTTTAA
1487693 TAATTTTTTATA
1 TAA--TTTTA-A
1487705 TAATTTTAA
1 TAATTTTAA
1487714 TAATCTTTCATA
1 TAAT-TTT-A-A
* *
1487726 TAATATTAC
1 TAATTTTAA
1487735 TAATTTT
1 TAATTTT
1487742 TGAGATTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
9 18 0.32
10 13 0.23
11 12 0.21
12 13 0.23
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (9 bp):
TAATTTTAA
Found at i:1487713 original size:42 final size:42
Alignment explanation
Indices: 1487632--1487882 Score: 158
Period size: 42 Copynumber: 6.0 Consensus size: 42
1487622 TTTTGATTTT
* * * *
1487632 TTTTTAATATGATTTTTATAACTTTTTAATGTAATTTTAATAA
1 TTTTTAATATAATTTTGATAA-TTTTTGATATAATTTTAATAA
*
1487675 TTTTTAATATAATTTTGATAATTTTTTATATAATTTTAATAA
1 TTTTTAATATAATTTTGATAATTTTTGATATAATTTTAATAA
* * * * *
1487717 TCTTTCATATAATATT-ACTAATTTTTGAGATTA-TTTAATAA
1 TTTTTAATATAATTTTGA-TAATTTTTGATATAATTTTAATAA
* * * ** * * *
1487758 TATTTGATGTAATTTT-AGTAACATTTGATACAATTGTAGTAA
1 TTTTTAATATAATTTTGA-TAATTTTTGATATAATTTTAATAA
* *** *
1487800 TCTTTT-ATATAATTTTGAAAACCATT--TATAA-TTGAAGTAA
1 T-TTTTAATATAATTTTGATAATTTTTGATATAATTTTAA-TAA
* * *
1487840 GTTTTAATATAATTTTTGATAA-TTTTGATATGATTTTATTAA
1 TTTTTAATATAA-TTTTGATAATTTTTGATATAATTTTAATAA
1487882 T
1 T
1487883 CTTTCATTAA
Statistics
Matches: 159, Mismatches: 39, Indels: 21
0.73 0.18 0.10
Matches are distributed among these distances:
39 6 0.04
40 15 0.09
41 40 0.25
42 72 0.45
43 26 0.16
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (42 bp):
TTTTTAATATAATTTTGATAATTTTTGATATAATTTTAATAA
Found at i:1487728 original size:12 final size:10
Alignment explanation
Indices: 1487663--1487729 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 10
1487653 CTTTTTAATG
1487663 TAATTTTA-A
1 TAATTTTATA
1487672 TAATTTTTAATA
1 TAA-TTTT-ATA
1487684 TAATTTTGATA
1 TAATTTT-ATA
*
1487695 -ATTTTTTATA
1 TA-ATTTTATA
1487705 TAATTTTA-A
1 TAATTTTATA
1487714 TAATCTTTCATA
1 TAAT-TTT-ATA
1487726 TAAT
1 TAAT
1487730 ATTACTAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
9 8 0.17
10 16 0.34
11 14 0.30
12 9 0.19
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (10 bp):
TAATTTTATA
Found at i:1488974 original size:16 final size:16
Alignment explanation
Indices: 1488942--1489000 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 16
1488932 AATGTGTTGT
1488942 TATTTTTTAAATTAAAA
1 TATTTTTTAAA-TAAAA
1488959 TATTTTATTAAA-AAAA
1 TATTTT-TTAAATAAAA
* *
1488975 TA-TTTTTGAAT-AAT
1 TATTTTTTAAATAAAA
1488989 TATTTTTTAAAT
1 TATTTTTTAAAT
1489001 TTAAAAGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 8 0.22
15 11 0.31
16 6 0.17
17 6 0.17
18 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TATTTTTTAAATAAAA
Found at i:1489307 original size:6 final size:6
Alignment explanation
Indices: 1489296--1489335 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
1489286 CCGACTTGAG
* *
1489296 TGCATC TGCATC TGCACC TGCACC TGCACC TGCACC TGCA
1 TGCACC TGCACC TGCACC TGCACC TGCACC TGCACC TGCA
1489336 TCATCATCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.17, C:0.42, G:0.17, T:0.23
Consensus pattern (6 bp):
TGCACC
Found at i:1490354 original size:3 final size:3
Alignment explanation
Indices: 1490346--1490375 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1490336 GAAAGCATCA
1490346 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1490376 TGCTCCCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1491066 original size:2 final size:2
Alignment explanation
Indices: 1491059--1491083 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1491049 TATGGCCACT
1491059 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1491084 CCCACAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1492716 original size:14 final size:14
Alignment explanation
Indices: 1492697--1492723 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1492687 GTTACTTGTC
1492697 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
1492711 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
1492724 CTGCAAGATG
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:1495855 original size:113 final size:113
Alignment explanation
Indices: 1495615--1495831 Score: 371
Period size: 113 Copynumber: 1.9 Consensus size: 113
1495605 TGCAACTAAA
*
1495615 AGGAAAATATAAAATGCTATTATTGATCTAAGAAAAGACAACCTTATAATCATGGTGAGGATATT
1 AGGAAACTATAAAATGCTATTATTGATCTAAGAAAAGACAACCTTATAATCATGGTGAGGATATT
1495680 AGACCCTGGCATCAACTAGAAGCCAGTAACACAAAAAGAGACTTTGCC
66 AGACCCTGGCATCAACTAGAAGCCAGTAACACAAAAAGAGACTTTGCC
* * * *
1495728 AGGAAACTATAAAATGCTGTTATTGATCTAAGAAAAGACAAGCTTGTAATCATGGTGGGGATATT
1 AGGAAACTATAAAATGCTATTATTGATCTAAGAAAAGACAACCTTATAATCATGGTGAGGATATT
* *
1495793 AGACCCTGGTATCAACTAGAAGCCAGTAATACAAAAAGA
66 AGACCCTGGCATCAACTAGAAGCCAGTAACACAAAAAGA
1495832 ATTTAGCCAT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 97 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (113 bp):
AGGAAACTATAAAATGCTATTATTGATCTAAGAAAAGACAACCTTATAATCATGGTGAGGATATT
AGACCCTGGCATCAACTAGAAGCCAGTAACACAAAAAGAGACTTTGCC
Found at i:1498298 original size:18 final size:17
Alignment explanation
Indices: 1498267--1498342 Score: 55
Period size: 18 Copynumber: 4.1 Consensus size: 17
1498257 AATAATTATA
1498267 TTTAAAATATTTAATATT
1 TTTAAAATA-TTAATATT
1498285 TTTATAAATATTAATA-T
1 TTTA-AAATATTAATATT
* *
1498302 ATTAATAATTTATATTATATAT
1 TTTAA-AA--TAT-TAATAT-T
*
1498324 TTTAAAATATTTATATT
1 TTTAAAATATTAATATT
1498341 TT
1 TT
1498343 ATATCACATT
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
16 1 0.02
17 9 0.19
18 16 0.33
19 11 0.23
20 4 0.08
21 2 0.04
22 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAAATATTAATATT
Found at i:1498321 original size:26 final size:26
Alignment explanation
Indices: 1498261--1498321 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
1498251 TAATAAAATA
*
1498261 ATTATATTTAAAATATTTAATATTTTT
1 ATTATA-TTAAAATATTTAATATTTAT
* *
1498288 ATAAATATTAATATA-TTAATAATTTAT
1 AT-TATATTAAAATATTTAAT-ATTTAT
1498315 ATTATAT
1 ATTATAT
1498322 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 9 0.32
27 16 0.57
28 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTATATTAAAATATTTAATATTTAT
Found at i:1498334 original size:30 final size:29
Alignment explanation
Indices: 1498263--1498346 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
1498253 ATAAAATAAT
1498263 TATA-TTTAAAATATT-TAATATT-T-TTA
1 TATATTTTAAAATATTATAAT-TTATATTA
* * *
1498289 TAAATATTAATATATTAATAATTTATATTA
1 TATATTTTAAAATATT-ATAATTTATATTA
*
1498319 TATATTTTAAAATATTTATATTTTATAT
1 TATATTTTAAAATA-TTATAATTTATAT
1498347 CACATTATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
26 3 0.07
27 9 0.20
28 2 0.04
29 5 0.11
30 24 0.53
31 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TATATTTTAAAATATTATAATTTATATTA
Found at i:1498339 original size:23 final size:22
Alignment explanation
Indices: 1498292--1498346 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
1498282 ATTTTTATAA
*
1498292 ATATTA-ATATATTAATAATTT
1 ATATTATATATATTAAAAATTT
*
1498313 ATATTATATATTTTAAAATATTT
1 ATATTATATATATTAAAA-ATTT
*
1498336 ATATTTTATAT
1 ATATTATATAT
1498347 CACATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTATATATATTAAAAATTT
Found at i:1498343 original size:7 final size:7
Alignment explanation
Indices: 1498310--1498385 Score: 53
Period size: 7 Copynumber: 9.7 Consensus size: 7
1498300 ATATTAATAA
1498310 TTTATAT
1 TTTATAT
*
1498317 TATATAT
1 TTTATAT
*
1498324 TTTAAAAT
1 TTT-ATAT
1498332 ATTTATAT
1 -TTTATAT
1498340 TTTATAT
1 TTTATAT
*
1498347 CACATTATAT
1 ---TTTATAT
1498357 TTTATATT
1 TTTATA-T
1498365 TTTATAATT
1 TTTAT-A-T
1498374 TTTATAT
1 TTTATAT
1498381 TTTAT
1 TTTAT
1498386 TAAATATTAC
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
7 26 0.46
8 13 0.23
9 11 0.20
10 6 0.11
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (7 bp):
TTTATAT
Found at i:1498376 original size:9 final size:8
Alignment explanation
Indices: 1498351--1498383 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1498341 TTATATCACA
1498351 TTATA-TT
1 TTATATTT
1498358 TTATATTT
1 TTATATTT
1498366 TTATAATTT
1 TTAT-ATTT
1498375 TTATATTT
1 TTATATTT
1498383 T
1 T
1498384 ATTAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 5 0.21
8 11 0.46
9 8 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTATATTT
Found at i:1498650 original size:11 final size:10
Alignment explanation
Indices: 1498612--1498651 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
1498602 AAATAAATGA
1498612 TTAATATTTT
1 TTAATATTTT
*
1498622 TTATTATTTT
1 TTAATATTTT
1498632 TT--TA-TTT
1 TTAATATTTT
1498639 TTAATATTTT
1 TTAATATTTT
1498649 TTA
1 TTA
1498652 TCCCATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
7 5 0.19
8 2 0.08
9 2 0.08
10 17 0.65
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTAATATTTT
Found at i:1498761 original size:20 final size:21
Alignment explanation
Indices: 1498738--1498780 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
1498728 AAATTAATAA
1498738 AAAAATATTGAA-ATATTTAT
1 AAAAATATTGAACATATTTAT
* *
1498758 -AAAATTTTTAACATATTTAT
1 AAAAATATTGAACATATTTAT
1498778 AAA
1 AAA
1498781 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 9 0.47
20 8 0.42
21 2 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAAATATTGAACATATTTAT
Found at i:1498785 original size:20 final size:20
Alignment explanation
Indices: 1498750--1498793 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1498740 AAATATTGAA
1498750 ATATTTATAAAATTTTTAAC
1 ATATTTATAAAATTTTTAAC
* *
1498770 ATATTTATAAATTTTTTAAT
1 ATATTTATAAAATTTTTAAC
1498790 ATAT
1 ATAT
1498794 AAAATTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTTATAAAATTTTTAAC
Found at i:1499561 original size:30 final size:31
Alignment explanation
Indices: 1499523--1499582 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1499513 TTTTTCTTTT
*
1499523 CTTTTTTTACTTTACTATAA-ATTTTTTTTAA
1 CTTTTTTAAC-TTACTATAATATTTTTTTTAA
*
1499554 CTTTTTTAACTTACTATAATCTTTTTTTT
1 CTTTTTTAACTTACTATAATATTTTTTTT
1499583 TTTCCTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (31 bp):
CTTTTTTAACTTACTATAATATTTTTTTTAA
Found at i:1499652 original size:2 final size:2
Alignment explanation
Indices: 1499645--1499676 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1499635 AAATAGGACG
1499645 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1499677 ACAAAACCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1500546 original size:21 final size:23
Alignment explanation
Indices: 1500501--1500552 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1500491 GTCATATAAT
*
1500501 AAAATATATTCAGTGAACAATTA
1 AAAATATATTCAGTAAACAATTA
* *
1500524 AAAATATATTTA-TAAACAATAA
1 AAAATATATTCAGTAAACAATTA
1500546 ACAAATA
1 A-AAATA
1500553 AATTTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.29
Consensus pattern (23 bp):
AAAATATATTCAGTAAACAATTA
Found at i:1500564 original size:4 final size:4
Alignment explanation
Indices: 1500541--1500579 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
1500531 ATTTATAAAC
*
1500541 AATA AACA AATA AATTTA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AA--TA AATA AATA AATA AATA AATA A
1500580 TATATTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 27 0.87
6 4 0.13
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1500594 original size:37 final size:36
Alignment explanation
Indices: 1500553--1500630 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 36
1500543 TAAACAAATA
*
1500553 AATTTAAATAAATAAATAA-ATAA-ATAATATATTGATT
1 AATTTAAATAAA-AAATAATAGAACATAA-ATATT-ATT
*
1500590 AATTTTAAATATAAAATAATAGAACATAAATATTATT
1 AA-TTTAAATAAAAAATAATAGAACATAAATATTATT
1500627 AATT
1 AATT
1500631 ATATTATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
36 2 0.06
37 13 0.36
38 17 0.47
39 4 0.11
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (36 bp):
AATTTAAATAAAAAATAATAGAACATAAATATTATT
Found at i:1500607 original size:41 final size:41
Alignment explanation
Indices: 1500562--1500676 Score: 116
Period size: 38 Copynumber: 2.9 Consensus size: 41
1500552 AAATTTAAAT
* *
1500562 AAATAAATAAATAAATAATATATTGATTA-ATTTTAAATATA
1 AAATAAA-AAATAAATAATATATTAATTATATTATAAATATA
*
1500603 AAATAATAGAACATAAAT-AT-TATTAATTATATTATATATATA
1 AAATAA-A-AA-ATAAATAATATATTAATTATATTATAAATATA
*
1500645 AAACAAAAAAT-AAT-A-ATATTAATTATATTATA
1 AAATAAAAAATAAATAATATATTAATTATATTATA
1500677 TTCAAATGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
38 20 0.31
39 2 0.03
40 2 0.03
41 15 0.23
42 20 0.31
43 6 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (41 bp):
AAATAAAAAATAAATAATATATTAATTATATTATAAATATA
Found at i:1501494 original size:56 final size:56
Alignment explanation
Indices: 1501425--1501560 Score: 263
Period size: 56 Copynumber: 2.4 Consensus size: 56
1501415 TATTAGTATT
*
1501425 AAATTTAAGTTTACAATTAATTTAAGCTTATTTTAAGCTCATGTTAACTTTAATTC
1 AAATTTAAATTTACAATTAATTTAAGCTTATTTTAAGCTCATGTTAACTTTAATTC
1501481 AAATTTAAATTTACAATTAATTTAAGCTTATTTTAAGCTCATGTTAACTTTAATTC
1 AAATTTAAATTTACAATTAATTTAAGCTTATTTTAAGCTCATGTTAACTTTAATTC
1501537 AAATTTAAATTTACAATTAATTTA
1 AAATTTAAATTTACAATTAATTTA
1501561 TATCTAATTT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 79 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (56 bp):
AAATTTAAATTTACAATTAATTTAAGCTTATTTTAAGCTCATGTTAACTTTAATTC
Found at i:1503455 original size:29 final size:27
Alignment explanation
Indices: 1503375--1503463 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
1503365 TTATTGATCA
* *
1503375 AAATATTTTTATATCAAATAAATAATT
1 AAATATTTTTATATAAAAAAAATAATT
*
1503402 AAAT-TTTTTTTA-AAAAAAAATTAATTT
1 AAATATTTTTATATAAAAAAAA-TAA-TT
* *
1503429 AAAATATTTTTATATTAAACAAATAATT
1 -AAATATTTTTATATAAAAAAAATAATT
1503457 AAATATT
1 AAATATT
1503464 AAATTTTAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
25 6 0.12
26 10 0.20
27 13 0.25
28 6 0.12
29 10 0.20
30 6 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATATTTTTATATAAAAAAAATAATT
Found at i:1503478 original size:42 final size:42
Alignment explanation
Indices: 1503426--1503505 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
1503416 AAAAAATTAA
1503426 TTTAAAATATTTTTATATTAAACAAATAATTAAATATTAAAT
1 TTTAAAATATTTTTATATTAAACAAATAATTAAATATTAAAT
* *
1503468 TTTAAGATATTTTTATATTAAATAAATAATTAAATATT
1 TTTAAAATATTTTTATATTAAACAAATAATTAAATATT
1503506 TTAAATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (42 bp):
TTTAAAATATTTTTATATTAAACAAATAATTAAATATTAAAT
Found at i:1511358 original size:18 final size:19
Alignment explanation
Indices: 1511335--1511372 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1511325 AAGGGTGATG
1511335 TATTGATA-TTTCACTTGA
1 TATTGATACTTTCACTTGA
1511353 TATTGATACTTTCACTTGA
1 TATTGATACTTTCACTTGA
1511372 T
1 T
1511373 GTATCAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (19 bp):
TATTGATACTTTCACTTGA
Found at i:1512988 original size:14 final size:13
Alignment explanation
Indices: 1512957--1512987 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1512947 TTAGATGAGG
*
1512957 AAAACTAAAGAAA
1 AAAAATAAAGAAA
1512970 AAAAATAAAGAAA
1 AAAAATAAAGAAA
1512983 AAAAA
1 AAAAA
1512988 AGGAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.84, C:0.03, G:0.06, T:0.06
Consensus pattern (13 bp):
AAAAATAAAGAAA
Found at i:1512996 original size:17 final size:16
Alignment explanation
Indices: 1512967--1513017 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 16
1512957 AAAACTAAAG
*
1512967 AAAAAAA-ATAAAGAA
1 AAAAAAAGAAAAAGAA
1512982 AAAAAAAGGAAAAAGGAA
1 AAAAAAA-GAAAAA-GAA
*
1513000 AAAAAAATAAAAAGAA
1 AAAAAAAGAAAAAGAA
1513016 AA
1 AA
1513018 GAGAATAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
17 9 0.29
18 10 0.32
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (16 bp):
AAAAAAAGAAAAAGAA
Found at i:1513022 original size:7 final size:6
Alignment explanation
Indices: 1512963--1513022 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
1512953 GAGGAAAACT
* * * *
1512963 AAAGAA AAAAAA TAAAGAA AAA-AA AAGGAA AAAGGA AAA-AA AAATAA
1 AAAGAA AAAGAA -AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
1513010 AAAGAA AAGAGAA
1 AAAGAA AA-AGAA
1513023 TAGGTGTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
5 8 0.19
6 26 0.60
7 9 0.21
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:1514485 original size:20 final size:20
Alignment explanation
Indices: 1514460--1514531 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
1514450 TACCCAGATG
1514460 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * *
1514480 TATCGATACATGTATGAATA
1 TATCGATACATTTTTCAATA
* * *
1514500 TATCGATATATTCTTCAATG
1 TATCGATACATTTTTCAATA
1514520 TATCGATACATT
1 TATCGATACATT
1514532 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:1514869 original size:28 final size:28
Alignment explanation
Indices: 1514829--1514884 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1514819 CTATCCCATT
1514829 ATCAACAAGAACATCATAATGTCAACAC
1 ATCAACAAGAACATCATAATGTCAACAC
*
1514857 ATCAACAAGAACATTATAATGTCAACAC
1 ATCAACAAGAACATCATAATGTCAACAC
1514885 CTTGTCTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (28 bp):
ATCAACAAGAACATCATAATGTCAACAC
Found at i:1517512 original size:57 final size:56
Alignment explanation
Indices: 1517451--1517599 Score: 167
Period size: 57 Copynumber: 2.6 Consensus size: 56
1517441 ATTTGCTATA
* *
1517451 TTTTAAGACCATTTATGCAATTAATGCATTTTAGAGCCAT-TTTAATAATTTACCATG-
1 TTTTAAGA-CATTTATGTAATTCATGCATTTTA-AG-CATATTTAATAATTTACCATGT
* * **
1517508 TTTTAAGGTCATTTATATAATTTCATGCATTTTAAGGTTATTTAATAATTTACCATGT
1 TTTTAA-GACATTTATGTAA-TTCATGCATTTTAAGCATATTTAATAATTTACCATGT
* *
1517566 TTTTAAGACTTTTATGTAATTCATTCATTTTAAG
1 TTTTAAGACATTTATGTAATTCATGCATTTTAAG
1517600 ATTATTTTAG
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
56 15 0.19
57 44 0.56
58 19 0.24
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.48
Consensus pattern (56 bp):
TTTTAAGACATTTATGTAATTCATGCATTTTAAGCATATTTAATAATTTACCATGT
Found at i:1517572 original size:29 final size:28
Alignment explanation
Indices: 1517491--1517568 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 28
1517481 TTAGAGCCAT
1517491 TTTAATAATTTACCATGTTTTAAGGTCA
1 TTTAATAATTTACCATGTTTTAAGGTCA
*
1517519 TTTATATAATTT--CATGCATTTTAAGGTTA
1 TTTA-ATAATTTACCATG--TTTTAAGGTCA
1517548 TTTAATAATTTACCATGTTTT
1 TTTAATAATTTACCATGTTTT
1517569 TAAGACTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
27 4 0.09
28 15 0.34
29 21 0.48
30 4 0.09
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (28 bp):
TTTAATAATTTACCATGTTTTAAGGTCA
Found at i:1521384 original size:23 final size:26
Alignment explanation
Indices: 1521357--1521417 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
1521347 AGTGTAAAAC
1521357 ATAAATA-C-ATGATT-TTTAAAATA
1 ATAAATACCTATGATTATTTAAAATA
* *
1521380 ATAAATTACCTTTGTTTATTTAAAATA
1 ATAAA-TACCTATGATTATTTAAAATA
1521407 ATAAATTACCT
1 ATAAA-TACCT
1521418 TTACTTAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.16
24 2 0.06
25 1 0.03
26 4 0.12
27 20 0.62
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (26 bp):
ATAAATACCTATGATTATTTAAAATA
Found at i:1521425 original size:23 final size:24
Alignment explanation
Indices: 1521372--1521426 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 24
1521362 TACATGATTT
*
1521372 TTAAAATAATAAATTACCTTTGTTTAT
1 TTAAAATAATAAATTACC--T-TTTAC
1521399 TTAAAATAATAAATTACC-TTTAC
1 TTAAAATAATAAATTACCTTTTAC
1521422 TTAAA
1 TTAAA
1521427 GTAAGAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 9 0.33
27 18 0.67
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (24 bp):
TTAAAATAATAAATTACCTTTTAC
Found at i:1522019 original size:5 final size:5
Alignment explanation
Indices: 1522006--1522063 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
1521996 GCTTCCCTTA
* * *
1522006 TTTTT TTTTC TTTTC TTTTCC TTTTC -TTTC CTATC TTTTC TTTT- TTTTCC
1 TTTTC TTTTC TTTTC TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTTT-C
1522056 TTTT- TTTT
1 TTTTC TTTT
1522064 TTCATTCCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
4 12 0.27
5 24 0.53
6 9 0.20
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:1522059 original size:35 final size:34
Alignment explanation
Indices: 1522001--1522076 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
1521991 TCTTTGCTTC
* * *
1522001 CCTTATTTTTTTTTCTTTTCTTTTCCTTTTCTTT
1 CCTTCTTTTTTTTTCTTTCCTTTTCCTTTTCATT
**
1522035 CCTATCTTTTCTTTTT-TTTCCTTTTTTTTTTCATT
1 CCT-TCTTTT-TTTTTCTTTCCTTTTCCTTTTCATT
1522070 CCTTCTT
1 CCTTCTT
1522077 CATAAATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 7 0.20
35 23 0.66
36 5 0.14
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (34 bp):
CCTTCTTTTTTTTTCTTTCCTTTTCCTTTTCATT
Found at i:1522212 original size:66 final size:66
Alignment explanation
Indices: 1522081--1522214 Score: 173
Period size: 66 Copynumber: 2.0 Consensus size: 66
1522071 CTTCTTCATA
*** * *
1522081 AATAAAAAAATAAAATACTATAACTACTTTTATCAAACTTTTTATTCCCTCGTATCCTTATCAAG
1 AATAAAAAAATAAAATACTATAACTACTCCCATCAAACTTTTTAATCCCTCGTATCCTTAGCAAG
1522146 G
66 G
* *
1522147 AATAAAAAAATTAAAATACTGTAACTA-TCCCATCAAACTTTTTAATCCCTCGTAT-ATCTAGCA
1 AATAAAAAAA-TAAAATACTATAACTACTCCCATCAAACTTTTTAATCCCTCGTATCCT-TAGCA
1522210 AGG
64 AGG
1522213 AA
1 AA
1522215 GTCAAATTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 1 0.02
66 43 0.73
67 15 0.25
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.33
Consensus pattern (66 bp):
AATAAAAAAATAAAATACTATAACTACTCCCATCAAACTTTTTAATCCCTCGTATCCTTAGCAAG
G
Found at i:1522557 original size:26 final size:26
Alignment explanation
Indices: 1522509--1522558 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1522499 AATTATTATT
* * **
1522509 ATAATTATTTTATTTTATTTTTATAA
1 ATAATTATTTCATTATAAGTTTATAA
1522535 ATAATTATTTCATTATAAGTTTAT
1 ATAATTATTTCATTATAAGTTTAT
1522559 TTCATTTCAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
ATAATTATTTCATTATAAGTTTATAA
Found at i:1526207 original size:24 final size:24
Alignment explanation
Indices: 1526175--1526222 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1526165 CTTTGGTAGG
1526175 GAATAATATCGAATATAAGAAACT
1 GAATAATATCGAATATAAGAAACT
1526199 GAATAATATCGAATATAAGAAACT
1 GAATAATATCGAATATAAGAAACT
1526223 TATTCTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.25
Consensus pattern (24 bp):
GAATAATATCGAATATAAGAAACT
Found at i:1526631 original size:22 final size:21
Alignment explanation
Indices: 1526603--1526644 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1526593 CTTAACTAAA
1526603 ACAAAAGGATGTTGTAGCCCTC
1 ACAAAA-GATGTTGTAGCCCTC
* *
1526625 ACAAAAGTTTTTGTAGCCCT
1 ACAAAAGATGTTGTAGCCCT
1526645 TAAGAGTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (21 bp):
ACAAAAGATGTTGTAGCCCTC
Found at i:1528014 original size:14 final size:14
Alignment explanation
Indices: 1527995--1528023 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1527985 CAGACATGCC
1527995 TCTCTCTCTCTCTT
1 TCTCTCTCTCTCTT
1528009 TCTCTCTCTCTCTT
1 TCTCTCTCTCTCTT
1528023 T
1 T
1528024 TTGTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TCTCTCTCTCTCTT
Found at i:1543466 original size:21 final size:20
Alignment explanation
Indices: 1543437--1543482 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1543427 AAATTTATTG
1543437 ATTAATTAATAA-TAAAAATA
1 ATTAATTAA-AATTAAAAATA
*
1543457 TATTATTTAAAATTAAAAATA
1 -ATTAATTAAAATTAAAAATA
1543478 ATTAA
1 ATTAA
1543483 AAATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAATTAAAATTAAAAATA
Found at i:1545134 original size:35 final size:34
Alignment explanation
Indices: 1545060--1545142 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 34
1545050 TTCAAAACTG
* * *
1545060 CAATTTCTTTA-AAATTTTGAGAATCTTAAAGCT
1 CAATTTCTTGAGAATTTTTGAAAATCTTAAAGCT
* *
1545093 CGATTTCTTGAGAATTTGTTGAAAATCTTAAGGCT
1 CAATTTCTTGAGAATTT-TTGAAAATCTTAAAGCT
1545128 CAATTTCTTGAGAAT
1 CAATTTCTTGAGAAT
1545143 CTAGCTATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 9 0.21
34 4 0.10
35 29 0.69
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (34 bp):
CAATTTCTTGAGAATTTTTGAAAATCTTAAAGCT
Found at i:1545185 original size:23 final size:20
Alignment explanation
Indices: 1545131--1545186 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 20
1545121 TAAGGCTCAA
*
1545131 TTTCTTGAGAATCTAGCTAT
1 TTTCTTGAGAATCTAGCTAG
1545151 TATTCTCT-AGAATCTTGAGCTTAG
1 T-TTCT-TGAGAATC-T-AGC-TAG
1545175 TTTCTTGAGAAT
1 TTTCTTGAGAAT
1545187 TTATAAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
20 1 0.03
21 10 0.34
22 3 0.10
23 12 0.41
24 3 0.10
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (20 bp):
TTTCTTGAGAATCTAGCTAG
Found at i:1546001 original size:26 final size:26
Alignment explanation
Indices: 1545950--1546002 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1545940 CTAAAATCTC
**
1545950 AAATAAAGTTGAACTTTATCGGTCCT
1 AAATAAAGTTGAACTTTATCAATCCT
*
1545976 AAATAAAGTTGAATTTTATCAATCCT
1 AAATAAAGTTGAACTTTATCAATCCT
1546002 A
1 A
1546003 TATCTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (26 bp):
AAATAAAGTTGAACTTTATCAATCCT
Found at i:1547650 original size:21 final size:21
Alignment explanation
Indices: 1547625--1547696 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
1547615 GCCAATGACT
1547625 TGTATCGATACTTTCACATAA
1 TGTATCGATACTTTCACATAA
* **
1547646 TGTATCGATACATTGCA-A-GG
1 TGTATCGATAC-TTTCACATAA
* *
1547666 TGTATTGATACTTTTACATAA
1 TGTATCGATACTTTCACATAA
1547687 TGTATCGATA
1 TGTATCGATA
1547697 TATTGCAAGG
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 3 0.08
20 11 0.28
21 21 0.54
22 4 0.10
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (21 bp):
TGTATCGATACTTTCACATAA
Found at i:1547675 original size:20 final size:20
Alignment explanation
Indices: 1547646--1547753 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
1547636 TTTCACATAA
1547646 TGTATCGATACATTGCAAGG
1 TGTATCGATACATTGCAAGG
* * * *
1547666 TGTATTGATACTTTTACATA-A
1 TGTATCGATAC-ATTGCA-AGG
*
1547687 TGTATCGATATATTGCAAGG
1 TGTATCGATACATTGCAAGG
1547707 TGTATCGAT--A---CAA--
1 TGTATCGATACATTGCAAGG
**
1547720 TGTATCGATACATTGCAATA
1 TGTATCGATACATTGCAAGG
1547740 TGTATCGATACATT
1 TGTATCGATACATT
1547754 TTTATGTGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 20
0.70 0.09 0.20
Matches are distributed among these distances:
13 9 0.13
15 4 0.06
18 4 0.06
19 1 0.01
20 37 0.54
21 13 0.19
22 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTGCAAGG
Found at i:1547685 original size:41 final size:41
Alignment explanation
Indices: 1547625--1547717 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
1547615 GCCAATGACT
1547625 TGTATCGATACTTTCACATAATGTATCGATACATTGCAAGG
1 TGTATCGATACTTTCACATAATGTATCGATACATTGCAAGG
* * *
1547666 TGTATTGATACTTTTACATAATGTATCGATATATTGCAAGG
1 TGTATCGATACTTTCACATAATGTATCGATACATTGCAAGG
1547707 TGTATCGATAC
1 TGTATCGATAC
1547718 AATGTATCGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (41 bp):
TGTATCGATACTTTCACATAATGTATCGATACATTGCAAGG
Found at i:1547722 original size:33 final size:33
Alignment explanation
Indices: 1547685--1547751 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1547675 ACTTTTACAT
* *
1547685 AATGTATCGATATATTGCAAGGTGTATCGATAC
1 AATGTATCGATACATTGCAAGATGTATCGATAC
*
1547718 AATGTATCGATACATTGCAATATGTATCGATAC
1 AATGTATCGATACATTGCAAGATGTATCGATAC
1547751 A
1 A
1547752 TTTTTATGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (33 bp):
AATGTATCGATACATTGCAAGATGTATCGATAC
Found at i:1547725 original size:13 final size:13
Alignment explanation
Indices: 1547707--1547731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1547697 TATTGCAAGG
1547707 TGTATCGATACAA
1 TGTATCGATACAA
1547720 TGTATCGATACA
1 TGTATCGATACA
1547732 TTGCAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1547769 original size:20 final size:20
Alignment explanation
Indices: 1547625--1547753 Score: 78
Period size: 20 Copynumber: 6.7 Consensus size: 20
1547615 GCCAATGACT
*
1547625 TGTATCGATAC-TTTCACATAA
1 TGTATCGATACATTGCA-AT-A
**
1547646 TGTATCGATACATTGCAAGG
1 TGTATCGATACATTGCAATA
* **
1547666 TGTATTGATAC-TTTTACATAA
1 TGTATCGATACATTGCA-AT-A
* **
1547687 TGTATCGATATATTGCAAGG
1 TGTATCGATACATTGCAATA
1547707 TGTATCGAT--A---C-A-A
1 TGTATCGATACATTGCAATA
1547720 TGTATCGATACATTGCAATA
1 TGTATCGATACATTGCAATA
1547740 TGTATCGATACATT
1 TGTATCGATACATT
1547754 TTTATGTGTA
Statistics
Matches: 82, Mismatches: 15, Indels: 23
0.68 0.12 0.19
Matches are distributed among these distances:
13 9 0.11
14 1 0.01
15 2 0.02
18 2 0.02
19 4 0.05
20 35 0.43
21 22 0.27
22 7 0.09
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATTGCAATA
Found at i:1550453 original size:23 final size:21
Alignment explanation
Indices: 1550425--1550468 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
1550415 TATCAAATTA
*
1550425 AAGATCATTCAATCATAAATCAC
1 AAGATCAATCAAT-AT-AATCAC
1550448 AAGATCAATCAATATAATCAC
1 AAGATCAATCAATATAATCAC
1550469 TAAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 2 0.10
23 12 0.60
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (21 bp):
AAGATCAATCAATATAATCAC
Found at i:1556292 original size:72 final size:72
Alignment explanation
Indices: 1556175--1556311 Score: 229
Period size: 72 Copynumber: 1.9 Consensus size: 72
1556165 GCATGTTCTT
* * *
1556175 CATTCCCACGTCATTGTATCGATACATTACTTAAAGTATTGATACATTGCATTTGAAAATCTAGT
1 CATTCCCACGTCATTGTATCGATACATTACTTAAAGTATCGATACATTACATTTAAAAATCTAGT
1556240 TGTTGGG
66 TGTTGGG
* *
1556247 CATTCCCGCGTCATTGTATCGATACATTATTTAAAGTATCGATACATTACATTTAAAAATCTAGT
1 CATTCCCACGTCATTGTATCGATACATTACTTAAAGTATCGATACATTACATTTAAAAATCTAGT
1556312 CATTGGGCTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (72 bp):
CATTCCCACGTCATTGTATCGATACATTACTTAAAGTATCGATACATTACATTTAAAAATCTAGT
TGTTGGG
Found at i:1556396 original size:22 final size:22
Alignment explanation
Indices: 1556343--1556404 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
1556333 ATAATTATGG
1556343 ATGTATCGATACATTCTGAAAT
1 ATGTATCGATACATTCTGAAAT
*
1556365 -TGTATCGATACATTCCT-ATAT
1 ATGTATCGATACATT-CTGAAAT
*
1556386 ATGTATTGATACATT-TGAA
1 ATGTATCGATACATTCTGAA
1556405 GGGTAGTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 1 0.03
21 18 0.53
22 15 0.44
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
ATGTATCGATACATTCTGAAAT
Found at i:1556472 original size:20 final size:20
Alignment explanation
Indices: 1556446--1556496 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1556436 CTTTCACATA
1556446 ATGTATCGATACATTGCAAG
1 ATGTATCGATACATTGCAAG
* *
1556466 GTGTATCGATACATTGCAAT
1 ATGTATCGATACATTGCAAG
1556486 ATGTATCGATA
1 ATGTATCGATA
1556497 TATTTTCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAG
Found at i:1561115 original size:13 final size:13
Alignment explanation
Indices: 1561099--1561127 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1561089 AAAATATTTA
1561099 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1561112 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1561125 AAA
1 AAA
1561128 TAATTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:1562556 original size:5 final size:5
Alignment explanation
Indices: 1562546--1562573 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1562536 TTTCCTTACC
1562546 AAGGA AAGGA AAGGA AAGGA AAGGA AAG
1 AAGGA AAGGA AAGGA AAGGA AAGGA AAG
1562574 TAGTGAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
AAGGA
Found at i:1562792 original size:2 final size:2
Alignment explanation
Indices: 1562785--1562815 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1562775 ATAAATTCTT
1562785 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 T
1562816 TTTCAATCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1563517 original size:19 final size:19
Alignment explanation
Indices: 1563493--1563531 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1563483 TTTTTGATTA
1563493 AATAGA-AGAATTAGATTGG
1 AATAGATAGAATTA-ATTGG
*
1563512 AATAGATTGAATTAATTGG
1 AATAGATAGAATTAATTGG
1563531 A
1 A
1563532 TTTTTATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (19 bp):
AATAGATAGAATTAATTGG
Found at i:1564239 original size:21 final size:23
Alignment explanation
Indices: 1564203--1564249 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1564193 TTAAACGAGC
1564203 TTTATTTTTATGTAAATATAT-T
1 TTTATTTTTATGTAAATATATAT
* *
1564225 TTTATTTTT-TTTAAATCTATAT
1 TTTATTTTTATGTAAATATATAT
1564247 TTT
1 TTT
1564250 CATCAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTATTTTTATGTAAATATATAT
Found at i:1565813 original size:36 final size:36
Alignment explanation
Indices: 1565773--1565854 Score: 146
Period size: 36 Copynumber: 2.3 Consensus size: 36
1565763 ATCTTAACCA
* *
1565773 TAAAAGATAAAATAAATATTGCTATCTTAGCTTAGG
1 TAAAAGATAAAATAAATATTACTATCTTAGCCTAGG
1565809 TAAAAGATAAAATAAATATTACTATCTTAGCCTAGG
1 TAAAAGATAAAATAAATATTACTATCTTAGCCTAGG
1565845 TAAAAGATAA
1 TAAAAGATAA
1565855 GAGTTGTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (36 bp):
TAAAAGATAAAATAAATATTACTATCTTAGCCTAGG
Found at i:1567973 original size:33 final size:33
Alignment explanation
Indices: 1567936--1568005 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
1567926 AATAAATTTA
*
1567936 ATCTAATCA-AATTTATTTGACTTATTTATCATG
1 ATCTAAT-ATAATCTATTTGACTTATTTATCATG
* *
1567969 ATCTAATATAATCTATTTGATTTGTTTATCATG
1 ATCTAATATAATCTATTTGACTTATTTATCATG
1568002 ATCT
1 ATCT
1568006 TGATAAGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.50
Consensus pattern (33 bp):
ATCTAATATAATCTATTTGACTTATTTATCATG
Found at i:1570440 original size:155 final size:154
Alignment explanation
Indices: 1570244--1570789 Score: 602
Period size: 154 Copynumber: 3.5 Consensus size: 154
1570234 GCCCCTATAG
* ** *
1570244 GATATCTTC-AGCGTAGAAGTACCCAATACCCCTAAAGGACTTAAAAAGGATTTTAAATGGGATG
1 GATATCTTCGA-CGTAAAAGTACCTGATACCCCTAAAAGACTTAAAAAGGATTTTAAATGGGATG
*
1570308 AACCTATCCTAAATATCTACCTTTGGCATAAAAGTAGACCTAGTGACAATCTAAGACTCGGTTCT
65 AACCTATCCTAAATATCTACCTTTGGCATAAAAGTAGA-CTAGTGACAACCTAAGACTCGGTTCT
* *
1570373 AAAAAATTAATAAAATGCCTTTAGGA
129 TAAAAATTAATAAAATACCTTTAGGA
* * * *
1570399 GATATCTTCGATGTAAAAGTGCCTGATACCACTAAAAGACTT--AAAGGATTTATAGATGGGATG
1 GATATCTTCGACGTAAAAGTACCTGATACCCCTAAAAGACTTAAAAAGGATTT-TAAATGGGATG
* * * *
1570462 AACCTATCCTAAACATCTACCTTTGGCATAAAAGT-GAACTCGATGACAACCTAAGACTCGATTT
65 AACCTATCCTAAATATCTACCTTTGGCATAAAAGTAG-ACTAG-TGACAACCTAAGACTCGGTTC
*
1570526 TTAAAAATT-ATGAAAATACC-CTAGGA
128 TTAAAAATTAAT-AAAATACCTTTAGGA
* ** * *
1570552 GATATCTTCGACGTAAAAGTACTTGATACCCCTAAGGGATTTAAAAAGGATTTTAAAAGGGATGA
1 GATATCTTCGACGTAAAAGTACCTGATACCCCTAAAAGACTTAAAAAGGATTTTAAATGGGATGA
* * * * ** ** * * **
1570617 ACCTATCCTAAATATCTACCTTCGACATAAAAGCAGATTCACCGATGACCTAGGAGTTAGTTCTT
66 ACCTATCCTAAATATCTACCTTTGGCATAAAAGTAGACT-AGTGACAACCTAAGACTCGGTTCTT
** *
1570682 AAAAATTACGAAAATACCTCTAAGG-
130 AAAAATTAATAAAATACCT-TTAGGA
* * * *
1570707 GATACCTTCGACGTAAAAGTACCTGATACCCCTAAAAGATTTAAAGAGGATTTTAAAGGGGATGA
1 GATATCTTCGACGTAAAAGTACCTGATACCCCTAAAAGACTTAAAAAGGATTTTAAATGGGATGA
*
1570772 ACTTATCCTAAATATCTA
66 ACCTATCCTAAATATCTA
1570790 TCTTCAGCAT
Statistics
Matches: 327, Mismatches: 52, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
153 55 0.17
154 149 0.46
155 119 0.36
156 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (154 bp):
GATATCTTCGACGTAAAAGTACCTGATACCCCTAAAAGACTTAAAAAGGATTTTAAATGGGATGA
ACCTATCCTAAATATCTACCTTTGGCATAAAAGTAGACTAGTGACAACCTAAGACTCGGTTCTTA
AAAATTAATAAAATACCTTTAGGA
Found at i:1570838 original size:308 final size:310
Alignment explanation
Indices: 1570244--1570908 Score: 738
Period size: 308 Copynumber: 2.2 Consensus size: 310
1570234 GCCCCTATAG
* ** * * *
1570244 GATATCTTC-AGCGTAGAAGTACCCAATACCCCTAAAGGACTTAAAAAGGATTTTAAATGGGATG
1 GATATCTTCGA-CGTAAAAGTACCTGATACCCCTAAGGGATTTAAAAAGGATTTTAAAAGGGATG
* * * ** * *
1570308 AACCTATCCTAAATATCTACCTTTGGCATAAAAGTAGACCTAGTGACAATCTAAGACTCGGTTCT
65 AACCTATCCTAAATATCTACCTTCGACATAAAAGCAGACCTACCGACAACCTAAGACTCAGTTCT
* * * * * *
1570373 AAAAAATTAATAAAATGCCTTTAGGAGATATCTTCGATGTAAAAGTGCCTGATACCACTAAAAGA
130 AAAAAATTAAGAAAATACCTTAAGGAGATACCTTCGACGTAAAAGTACCTGATACCACTAAAAGA
* * **
1570438 CTTAAAGGATTTATAGATGGGATGAACCTATCCTAAACATCTACCTTTGGCATAAAAGTGAACTC
195 CTTAAAGGATTTATAAAGGGGATGAACCTATCCTAAACATCTACCTTCAGCATAAAAGTGAACTC
* *
1570503 GATGACAACCTAAGACTCGA-TTTTTAAAAATTATGAAAATAC-CCTAGGA
260 GATAACAACCTAAGACTCGAGTTTTAAAAAATTATGAAAATACGCCTAGGA
*
1570552 GATATCTTCGACGTAAAAGTACTTGATACCCCTAAGGGATTTAAAAAGGATTTTAAAAGGGATGA
1 GATATCTTCGACGTAAAAGTACCTGATACCCCTAAGGGATTTAAAAAGGATTTTAAAAGGGATGA
* ** * * *
1570617 ACCTATCCTAAATATCTACCTTCGACATAAAAGCAGA-TTCACCGATGACCTAGGAGTTAGTTCT
66 ACCTATCCTAAATATCTACCTTCGACATAAAAGCAGACCT-ACCGACAACCTAAGACTCAGTTCT
* * *
1570681 TAAAAATTACGAAAATACCTCTAAGG-GATACCTTCGACGTAAAAGTACCTGATACCCCTAAAAG
130 AAAAAATTAAGAAAATACCT-TAAGGAGATACCTTCGACGTAAAAGTACCTGATACCACTAAAAG
* * * *
1570745 ATTTAAAGAGGATTT-TAAAGGGGATGAACTTATCCTAAATATCTATCTTCAGCATGAAAACG-G
194 ACTT-AA-AGGATTTATAAAGGGGATGAACCTATCCTAAACATCTACCTTCAGCAT-AAAA-GTG
* * * * *
1570808 -ACTC-AGTAACGACCTAAGAGTTG-GTTTTAAAAAATTATGAAAATGCGCCTAGGG
255 AACTCGA-TAACAACCTAAGACTCGAGTTTTAAAAAATTATGAAAATACGCCTAGGA
* * * ** *
1570862 GTTATCTTTGATGTAAAAGTACCTGATACCTTTGAGGGATTTAAAAA
1 GATATCTTCGACGTAAAAGTACCTGATACCCCTAAGGGATTTAAAAA
1570909 CATAAGGGAA
Statistics
Matches: 296, Mismatches: 51, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
307 1 0.00
308 159 0.54
309 77 0.26
310 58 0.20
311 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (310 bp):
GATATCTTCGACGTAAAAGTACCTGATACCCCTAAGGGATTTAAAAAGGATTTTAAAAGGGATGA
ACCTATCCTAAATATCTACCTTCGACATAAAAGCAGACCTACCGACAACCTAAGACTCAGTTCTA
AAAAATTAAGAAAATACCTTAAGGAGATACCTTCGACGTAAAAGTACCTGATACCACTAAAAGAC
TTAAAGGATTTATAAAGGGGATGAACCTATCCTAAACATCTACCTTCAGCATAAAAGTGAACTCG
ATAACAACCTAAGACTCGAGTTTTAAAAAATTATGAAAATACGCCTAGGA
Found at i:1570906 original size:155 final size:154
Alignment explanation
Indices: 1570244--1570891 Score: 652
Period size: 155 Copynumber: 4.2 Consensus size: 154
1570234 GCCCCTATAG
* ** * *
1570244 GATATCTTC-AGCGTAGAAGTACCCAATACCCCTAAAGGACTTAAAAAGGATTTTAAATGGGATG
1 GATATCTTCGA-CGTAAAAGTACCTGATACCCCTAAAAGATTTAAAAAGGATTTTAAATGGGATG
* * *
1570308 AACCTATCCTAAATATCTACCTTTGGCATAAAAGTAGAC-CTAGTGACAATCTAAGACTCGGTTC
65 AACCTATCCTAAATATCTACCTTCGGCATAAAAGT-GACTC-AGTGACAACCTAAGACTCGGTTT
* *
1570372 TAAAAAATTAAT-AAAATGCCTTTAGGA
128 TAAAAAATT-ATGAAAATACCTCTAGGA
* * * * *
1570399 GATATCTTCGATGTAAAAGTGCCTGATACCACTAAAAGACTT--AAAGGATTTATAGATGGGATG
1 GATATCTTCGACGTAAAAGTACCTGATACCCCTAAAAGATTTAAAAAGGATTT-TAAATGGGATG
* * *
1570462 AACCTATCCTAAACATCTACCTTTGGCATAAAAGTGAACTC-GATGACAACCTAAGACTCGATTT
65 AACCTATCCTAAATATCTACCTTCGGCATAAAAGTG-ACTCAG-TGACAACCTAAGACTCGGTTT
*
1570526 TTAAAAATTATGAAAATACC-CTAGGA
128 TAAAAAATTATGAAAATACCTCTAGGA
* ** *
1570552 GATATCTTCGACGTAAAAGTACTTGATACCCCTAAGGGATTTAAAAAGGATTTTAAAAGGGATGA
1 GATATCTTCGACGTAAAAGTACCTGATACCCCTAAAAGATTTAAAAAGGATTTTAAATGGGATGA
* * * ** ** * * **
1570617 ACCTATCCTAAATATCTACCTTCGACATAAAAGCAGATTCACCGATGACCTAGGAGTTAGTTCTT
66 ACCTATCCTAAATATCTACCTTCGGCATAAAAG-TGACTCAGTGACAACCTAAGACTCGGTT-TT
*
1570682 -AAAAATTACGAAAATACCTCTAAGG-
129 AAAAAATTATGAAAATACCTCT-AGGA
* * *
1570707 GATACCTTCGACGTAAAAGTACCTGATACCCCTAAAAGATTTAAAGAGGATTTTAAAGGGGATGA
1 GATATCTTCGACGTAAAAGTACCTGATACCCCTAAAAGATTTAAAAAGGATTTTAAATGGGATGA
* * * * * * *
1570772 ACTTATCCTAAATATCTATCTTCAGCATGAAAACG-GACTCAGTAACGACCTAAGAGTTGGTTTT
66 ACCTATCCTAAATATCTACCTTCGGCAT-AAAA-GTGACTCAGTGACAACCTAAGACTCGGTTTT
* *
1570836 AAAAAATTATGAAAATGCGC-CTAGGG
129 AAAAAATTATGAAAATAC-CTCTAGGA
* * *
1570862 GTTATCTTTGATGTAAAAGTACCTGATACC
1 GATATCTTCGACGTAAAAGTACCTGATACC
1570892 TTTGAGGGAT
Statistics
Matches: 413, Mismatches: 62, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
153 53 0.13
154 156 0.38
155 194 0.47
156 9 0.02
157 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (154 bp):
GATATCTTCGACGTAAAAGTACCTGATACCCCTAAAAGATTTAAAAAGGATTTTAAATGGGATGA
ACCTATCCTAAATATCTACCTTCGGCATAAAAGTGACTCAGTGACAACCTAAGACTCGGTTTTAA
AAAATTATGAAAATACCTCTAGGA
Found at i:1571465 original size:133 final size:135
Alignment explanation
Indices: 1571295--1571565 Score: 449
Period size: 133 Copynumber: 2.0 Consensus size: 135
1571285 ATTTTATTTT
1571295 ATTTGTTTCCAAAAAATACAATTTCAAACCTTAATAGAAACCTGCAAAGATACGAAAAGTTTTTG
1 ATTTGTTTCCAAAAAATACAATTTCAAACCTTAATAGAAACCTGCAAAGATACGAAAAGTTTTTG
* *
1571360 AAATTTTTTATACTCCTAAGGACCTTATAAGAA-TAT-AAA-AGTAAGAAAACTAATTAATTTTT
66 AAATTTTTTATACTCCTAAGGACCCTATAA-AATTATCAAAGAGTAAGAAAACTAATTAATATTT
1571422 ATGTCA
130 ATGTCA
* *
1571428 ATTTGTTTCCAAAAAATACCATTTCATACCTTAATAGAAACCTGCAAAGATACGAAAAGTTTTTG
1 ATTTGTTTCCAAAAAATACAATTTCAAACCTTAATAGAAACCTGCAAAGATACGAAAAGTTTTTG
* * *
1571493 AAATTTTTTATACTCCTATGGACCCTATAAAATTATCAAAGATTAAGAAAATTAATTAATATTTA
66 AAATTTTTTATACTCCTAAGGACCCTATAAAATTATCAAAGAGTAAGAAAACTAATTAATATTTA
1571558 TGTCA
131 TGTCA
1571563 ATT
1 ATT
1571566 ATGAAGGTGT
Statistics
Matches: 128, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
132 2 0.02
133 94 0.73
134 3 0.02
135 29 0.23
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.35
Consensus pattern (135 bp):
ATTTGTTTCCAAAAAATACAATTTCAAACCTTAATAGAAACCTGCAAAGATACGAAAAGTTTTTG
AAATTTTTTATACTCCTAAGGACCCTATAAAATTATCAAAGAGTAAGAAAACTAATTAATATTTA
TGTCA
Found at i:1579620 original size:20 final size:20
Alignment explanation
Indices: 1579591--1579664 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
1579581 TATCTAGATA
*
1579591 TATCGATACATTTTTCAATG
1 TATCGATACATTCTTCAATG
* * * *
1579611 TATTGATACATGCATGAATG
1 TATCGATACATTCTTCAATG
1579631 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
1579651 TATCGATACATTCT
1 TATCGATACATTCT
1579665 GTCTTTTTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:1581197 original size:24 final size:26
Alignment explanation
Indices: 1581169--1581220 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1581159 TCAAAATTTT
1581169 TATTCATT-AGGG-ATACTCCAACCC
1 TATTCATTCAGGGTATACTCCAACCC
* *
1581193 TATTCCTTCGAGGGTCTACTCCAACCC
1 TATTCATTC-AGGGTATACTCCAACCC
1581220 T
1 T
1581221 GCTTTTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.23, C:0.33, G:0.13, T:0.31
Consensus pattern (26 bp):
TATTCATTCAGGGTATACTCCAACCC
Found at i:1586095 original size:22 final size:23
Alignment explanation
Indices: 1586059--1586129 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 23
1586049 CAAAATGACA
* *
1586059 AAAAAAAGTTCAAAAGCAAAAAT
1 AAAAAAAGTGCAAAAGCAAAAAC
*
1586082 ACAAAATA-TG-AAAAG-AAAAAC
1 A-AAAAAAGTGCAAAAGCAAAAAC
1586103 AAAAAAAGTGCAAAAGCAAAAA-
1 AAAAAAAGTGCAAAAGCAAAAAC
1586125 AAAAA
1 AAAAA
1586130 GGAACAACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 5 0.12
21 8 0.20
22 15 0.38
23 7 0.17
24 5 0.12
ACGTcount: A:0.73, C:0.08, G:0.10, T:0.08
Consensus pattern (23 bp):
AAAAAAAGTGCAAAAGCAAAAAC
Found at i:1587487 original size:29 final size:29
Alignment explanation
Indices: 1587400--1588517 Score: 769
Period size: 28 Copynumber: 37.7 Consensus size: 29
1587390 AGTCCATGAT
* *
1587400 TCAGTGGCATTTCATTTCAAAGCCCACAAG
1 TCAGTGGCA-TCCTTTTCAAAGCCCACAAG
1587430 TCAGTGGCATCC-TTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* * *
1587458 TTAGTGACATCCTTTTCAAAGCCCATAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
*
1587487 TTAGTGGCAT-CTTTCTCAAAGCCCACAAG
1 TCAGTGGCATCCTTT-TCAAAGCCCACAAG
* * *
1587516 TCAGTGGCATCATTCTCAAAGCCCACACAAA
1 TCAGTGGCATCCTTTTCAAAG-CC-CACAAG
* *
1587547 TCGGTGGCAACCTATTTCAAAGCCCACATAAG
1 TCAGTGGCATCCT-TTTCAAAGCCCAC--AAG
*
1587579 TC-GATGGCAACCTATTTCAAAGCCCACACAAG
1 TCAG-TGGCATCCT-TTTCAAAG-CC-CACAAG
* * *
1587611 TCTGTGGCAACCCATTTCAAAGCCCACAAG
1 TCAGTGGC-ATCCTTTTCAAAGCCCACAAG
**
1587641 TCAGTGGCAT-CAGTTCAAAGCCTACACAAG
1 TCAGTGGCATCCTTTTCAAAGCC--CACAAG
* * * * *
1587671 TCGGTGGCAACTCATTTCAACGCCTACATAAG
1 TCAGTGGCATC-CTTTTCAAAGCC--CACAAG
*
1587703 TC-GATGGCAACCTATTTCAAAGCCCACACAAG
1 TCAG-TGGCATCCT-TTTCAAAG-CC-CACAAG
** *
1587735 TTGGTGGC-TACCAATTTCAAAGCCCACACAAG
1 TCAGTGGCAT-CC-TTTTCAAAG-CC-CACAAG
* *
1587767 TCGGTGGCAACTCTTTTCAAAGCCCACAAG
1 TCAGTGGCATC-CTTTTCAAAGCCCACAAG
* *
1587797 TCAGTGGCAT-CTCTTCAAAAGACCACAAG
1 TCAGTGGCATCCTTTTC-AAAGCCCACAAG
* *
1587826 TTAGTGGCATCC-TTTCAAAGCCCGCAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* *
1587854 TTAGTGGCATACCCTTTCAAAGCCCACAAG
1 TCAGTGGCAT-CCTTTTCAAAGCCCACAAG
* * *
1587884 TCAATGGCA-CCCTTCCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
*
1587912 TCAGTGGCA-CCTTTTCAAAGCCCACAAT
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
*
1587940 TCAGTGGCA-CCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
*
1587968 TCAGTGGCATACCCTTTCAAAGCCCACAAG
1 TCAGTGGCAT-CCTTTTCAAAGCCCACAAG
* * * **
1587998 TCGGTGGCA-CCCTTCCAAAATCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* * * *
1588026 TCAGTGGCACCCCTTTT-TAAGCTCGCAAG
1 TCAGTGGCA-TCCTTTTCAAAGCCCACAAG
* *
1588055 TCAATGGC--CTTATTTCAAAGCCTACACAAG
1 TCAGTGGCATCCT-TTTCAAAGCC--CACAAG
* * * *
1588085 TCGGTGGCAACTCATTTGAAAGCCCACACAAG
1 TCAGTGGCATC-CTTTTCAAAG-CC-CACAAG
* * *
1588117 TCGGTGGAAACCTATTTCAAAGCCCACACAAG
1 TCAGTGGCATCCT-TTTCAAAG-CC-CACAAG
* *
1588149 TC-GATGGCAACCCATTTCAAAGCCCACAAG
1 TCAG-TGGC-ATCCTTTTCAAAGCCCACAAG
* * **
1588179 TCAATGGTAT-CAGTTCAAAGCCTACACAAG
1 TCAGTGGCATCCTTTTCAAAGCC--CACAAG
** * *
1588209 TTGGTGGCAACCCATTTCAAAGCCCACATAAG
1 TCAGTGGC-ATCCTTTTCAAAGCCCAC--AAG
* * * * * *
1588241 TCGGTGGTAACCTATTTCAAAGCTCATAAA
1 TCAGTGGCATCCT-TTTCAAAGCCCACAAG
*
1588271 TCAGTGGCA-CCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
*
1588299 TCAGTGGCATCC-TTTCAAAGCCCATAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
*
1588327 -CTAGTGGCATCCTTTT-AAAGTCCACAAG
1 TC-AGTGGCATCCTTTTCAAAGCCCACAAG
* *
1588355 TCGGTGGCATCCTTTTCAAAGCCTACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* * *
1588384 TCGGTGGCAT-TTTTTCAAAGCCCACAAA
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
*
1588412 TCAGTGGCA-CATTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* * * *
1588440 TCAATAGCAT--TCTTCAAAGTCCACAAG
1 TCAGTGGCATCCTTTTCAAAGCCCACAAG
* *
1588467 TCAGTGACAACC-TTTCAAAGCCCACGCAAG
1 TCAGTGGCATCCTTTTCAAAGCCCA--CAAG
*
1588497 TC-GATGGCAACCCTTTTCAAA
1 TCAG-TGGC-ATCCTTTTCAAA
1588518 TCACCACTTT
Statistics
Matches: 895, Mismatches: 127, Indels: 130
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.00
27 25 0.03
28 308 0.34
29 124 0.14
30 164 0.18
31 35 0.04
32 219 0.24
33 15 0.02
34 3 0.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (29 bp):
TCAGTGGCATCCTTTTCAAAGCCCACAAG
Found at i:1588193 original size:538 final size:529
Alignment explanation
Indices: 1587414--1588517 Score: 1379
Period size: 538 Copynumber: 2.1 Consensus size: 529
1587404 TGGCATTTCA
* * *
1587414 TTTCAAAGCCCACAAGTCAGTGGCAT--CCTTTCAAAGCCCACAAGTTAGTGACATCCTTTTCAA
1 TTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACAAGTCAGTGACATCCCTTCCAA
* * * * *
1587477 AGCCCATAAGTTAGTGGCATCTTTCTCAAAGCCCACAAGTCAGTGGCATCATTCTCAAAGCCCAC
66 AACCCACAAGTCAGTGGCACCTTTCTCAAAGCCCACAAGTCAATGGCATCATTCTCAAAGCCCAC
* *
1587542 ACAAATCGGTGGCAACCTATTTCAAAGCCCACATAAGTCGATGGCAACCTATTTCAAAGCCCACA
131 ACAAATCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGATGGAAACCTATTTCAAAGCCCACA
*
1587607 CAAGTCTGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGCATCAGTTCAAAGCCTACACAAGT
196 CAAGTCTGTGGCAACCCATTTCAAAGCCCACAAGTCAATGGCATCAGTTCAAAGCCTACACAAGT
* * * *
1587672 CGGTGGCAACTCATTTCAACGCCTACATAAGTCGATGGCAACCTATTTCAAAGCCCACACAAGTT
261 CGGTGGCAACCCATTTCAAAGCCCACATAAGTCGATGGCAACCTATTTCAAAGCCCACA-AA-TC
* * *
1587737 GGTGGCTACCAATTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAG-TCAG
324 AGTGGC-ACC-ATTTCAAAG-CC-CACAAGTCAGTGGC-A-TCCTTTCAAAGCCCACAAGCT-AG
* * *
1587801 TGGCATCTCTTCAAAAGACCACAAGTTAGTGGCATCC-TTTCAAAGCCCGCAAGTTAGTGGCATA
382 TGGCATC-CTTCAAAAGACCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCAT-
* * * *
1587865 CCCTTTCAAAGCCCACAAGTCAATGGCACCCTTCCAAAGCCCACAAGTCAGTGGCACCTT-TTCA
445 -CCTTTCAAAGCCCACAAATCAATGGCACACTTCCAAAGCCCACAAGTCAATAGCA--TTCTTCA
* * *
1587929 AAGCCCACAATTCAGTGGCACCC
507 AAGCCCACAAGTCAGTGACAACC
* *
1587952 TTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACAAGTCGGTGGCA-CCCTTCCAA
1 TTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACAAGTCAGTGACATCCCTTCCAA
* * * * * * *
1588016 AATCCACAAGTCAGTGGCACCCCTTT-T-TAAGCTCGCAAGTCAATGGCCTTATT-TCAAAGCCT
66 AACCCACAAGTCAGTGGCA--CCTTTCTCAAAGCCCACAAGTCAATGGCATCATTCTCAAAGCCC
* * *
1588078 ACACAAGTCGGTGGCAA-CTCATTTGAAAGCCCACACAAGTCGGTGGAAACCTATTTCAAAGCCC
129 ACACAAATCGGTGGCAACCT-ATTTCAAAGCCCACACAAGTCGATGGAAACCTATTTCAAAGCCC
*
1588142 ACACAAGTC-GATGGCAACCCATTTCAAAGCCCACAAGTCAATGGTATCAGTTCAAAGCCTACAC
193 ACACAAGTCTG-TGGCAACCCATTTCAAAGCCCACAAGTCAATGGCATCAGTTCAAAGCCTACAC
* * * * *
1588206 AAGTTGGTGGCAACCCATTTCAAAGCCCACATAAGTCGGTGGTAACCTATTTCAAAGCTCATAAA
257 AAGTCGGTGGCAACCCATTTCAAAGCCCACATAAGTCGATGGCAACCTATTTCAAAGCCCACAAA
* *
1588271 TCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGCTAGTGGCA
322 TCAGTGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGCTAGTGGCA
** * * * * **
1588336 TCCTTTTAAAGTCCACAAGTCGGTGGCATCCTTTTCAAAGCCTACAAGTCGGTGGCATTTTTTCA
387 TCCTTCAAAAGACCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCA
* * * *
1588401 AAGCCCACAAATCAGTGGCACATTTTCAAAGCCCACAAGTCAATAGCATTCTTCAAAGTCCACAA
452 AAGCCCACAAATCAATGGCACACTTCCAAAGCCCACAAGTCAATAGCATTCTTCAAAGCCCACAA
1588466 GTCAGTGACAACC
517 GTCAGTGACAACC
1588479 TTTCAAAGCCCACGCAAGTC-GATGGCA-ACCCTTTTCAAA
1 TTTCAAAGCCCA--CAAGTCAG-TGGCATACCC-TTTCAAA
1588518 TCACCACTTT
Statistics
Matches: 493, Mismatches: 60, Indels: 35
0.84 0.10 0.06
Matches are distributed among these distances:
526 2 0.00
527 35 0.07
528 51 0.10
529 42 0.09
530 48 0.10
531 2 0.00
532 13 0.03
533 2 0.00
534 8 0.02
535 3 0.01
536 6 0.01
537 5 0.01
538 205 0.42
539 42 0.09
540 25 0.05
541 4 0.01
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (529 bp):
TTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACAAGTCAGTGACATCCCTTCCAA
AACCCACAAGTCAGTGGCACCTTTCTCAAAGCCCACAAGTCAATGGCATCATTCTCAAAGCCCAC
ACAAATCGGTGGCAACCTATTTCAAAGCCCACACAAGTCGATGGAAACCTATTTCAAAGCCCACA
CAAGTCTGTGGCAACCCATTTCAAAGCCCACAAGTCAATGGCATCAGTTCAAAGCCTACACAAGT
CGGTGGCAACCCATTTCAAAGCCCACATAAGTCGATGGCAACCTATTTCAAAGCCCACAAATCAG
TGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGCTAGTGGCATCCT
TCAAAAGACCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
CCACAAATCAATGGCACACTTCCAAAGCCCACAAGTCAATAGCATTCTTCAAAGCCCACAAGTCA
GTGACAACC
Found at i:1588642 original size:48 final size:48
Alignment explanation
Indices: 1588582--1588795 Score: 356
Period size: 48 Copynumber: 4.5 Consensus size: 48
1588572 GGCACCTTTA
*
1588582 TTAGCTCAATGTCGCTGGCCTTGAATCAGTACATTATCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
* *
1588630 TTAGCTCAATGTCGCTGACCTTGAATCAGCGCATTATCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
* *
1588678 TTAGCTTAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
* *
1588726 TTAGCTCAATGTCGCTGGCCTTAAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
*
1588774 TTAGCTCAATGTCGTTGGCCTT
1 TTAGCTCAATGTCGCTGGCCTT
1588796 CAATTGGCAT
Statistics
Matches: 156, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 156 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
Found at i:1589532 original size:20 final size:20
Alignment explanation
Indices: 1589507--1589603 Score: 106
Period size: 20 Copynumber: 4.8 Consensus size: 20
1589497 TTTTACCCAG
*
1589507 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1589527 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1589547 ATCTATCGATACA-TGTACGA
1 ATGTATCGATACATTTTTC-A
*
1589567 ATCTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
1589587 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
1589604 ATCTTTTTAC
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 59 0.95
21 3 0.05
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1594981 original size:33 final size:33
Alignment explanation
Indices: 1594944--1595011 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
1594934 ATTTAAATAA
*
1594944 ATTTAATCTAATCTGCTTGACTTGTTTATCATG
1 ATTTAATCTAATCTGCTTGACTTGTTAATCATG
* * *
1594977 ATTTAATTTAATTTGTTTGACTTGTTAATCATG
1 ATTTAATCTAATCTGCTTGACTTGTTAATCATG
1595010 AT
1 AT
1595012 CTTGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.51
Consensus pattern (33 bp):
ATTTAATCTAATCTGCTTGACTTGTTAATCATG
Found at i:1596396 original size:16 final size:16
Alignment explanation
Indices: 1596340--1596397 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
1596330 TCATGATTTT
1596340 TTTTTAATTTTTTCTAA
1 TTTTTAATTTTTT-TAA
* *
1596357 -TTATAATTGTTTTTCA
1 TTTTTAATT-TTTTTAA
1596373 TTCATTTAATTTTTTTAA
1 TT--TTTAATTTTTTTAA
1596391 TTTTTAA
1 TTTTTAA
1596398 AAATTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
16 14 0.42
17 5 0.15
18 8 0.24
19 6 0.18
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTTAATTTTTTTAA
Found at i:1596806 original size:15 final size:14
Alignment explanation
Indices: 1596786--1596819 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1596776 AATTTTGTTC
1596786 ATAAATAATAAACAA
1 ATAAAT-ATAAACAA
*
1596801 ATAAATCTAAACAA
1 ATAAATATAAACAA
1596815 ATAAA
1 ATAAA
1596820 CATGGTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAATATAAACAA
Found at i:1597372 original size:2 final size:2
Alignment explanation
Indices: 1597365--1597399 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1597355 ACCTCCCTAC
1597365 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
1597400 GTTTTCACCT
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:1599208 original size:14 final size:14
Alignment explanation
Indices: 1599179--1599216 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1599169 TATTAATTAT
*
1599179 TATATAAAAGTAAAA
1 TATATTAAA-TAAAA
1599194 TATATTAAATAAAA
1 TATATTAAATAAAA
1599208 TATA-TAAAT
1 TATATTAAAT
1599217 TCAACCCGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.23
14 9 0.41
15 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
TATATTAAATAAAA
Found at i:1607372 original size:131 final size:131
Alignment explanation
Indices: 1607138--1607399 Score: 506
Period size: 131 Copynumber: 2.0 Consensus size: 131
1607128 CCAGCTTGGA
1607138 AATACCATCTTGGAATTGTGCATTACTCAACCCCTTTGTGAACATGTTCACTAATTGGTTTCCAG
1 AATACCATCTTGGAATTGTGCATTACTCAACCCCTTTGTGAACATGTTCACTAATTGGTTTCCAG
1607203 TTGTTACATATGGAGTACAAATAACTCCACCATCTAGCTTCTCCTCTATAATGTGTCTGTCCACC
66 TTGTTACATATGGAGTACAAATAACTCCACCATCTAGCTTCTCCTCTATAATGTGTCTGTCCACC
1607268 T
131 T
1607269 AATACCATCTTGGAATTGTGCATTACTCAACCCCTTTGTGAACATGTTCACTAATTGGTTTCCAG
1 AATACCATCTTGGAATTGTGCATTACTCAACCCCTTTGTGAACATGTTCACTAATTGGTTTCCAG
* *
1607334 TTGTTACATATGGAGTACAAATAACTCCGCTATCTAGCTTCTCCTCTATAATGTGTCTGTCCACC
66 TTGTTACATATGGAGTACAAATAACTCCACCATCTAGCTTCTCCTCTATAATGTGTCTGTCCACC
1607399 T
131 T
1607400 CTATATTTTT
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 129 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (131 bp):
AATACCATCTTGGAATTGTGCATTACTCAACCCCTTTGTGAACATGTTCACTAATTGGTTTCCAG
TTGTTACATATGGAGTACAAATAACTCCACCATCTAGCTTCTCCTCTATAATGTGTCTGTCCACC
T
Found at i:1636096 original size:20 final size:20
Alignment explanation
Indices: 1636044--1636097 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
1636034 AAAACCTAAA
* * *
1636044 ATGTATCGATACTTTTTTTC
1 ATGTATTGATACCTTATTTC
*
1636064 AAGTATT-AGTACCTTATTTC
1 ATGTATTGA-TACCTTATTTC
1636084 ATGTATTGATACCT
1 ATGTATTGATACCT
1636098 AACCTACCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (20 bp):
ATGTATTGATACCTTATTTC
Found at i:1638435 original size:27 final size:27
Alignment explanation
Indices: 1638392--1640310 Score: 2895
Period size: 27 Copynumber: 70.3 Consensus size: 27
1638382 GTGGCATTTT
* *
1638392 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1638420 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1638447 CTTTTAAAGTCTACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1638475 CTTTTAAGTCCACAACTCTGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1638502 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1638530 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1638557 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1638584 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1638611 CTTTTAAGTCCACAACTCCGTGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
1638639 CTTTTAAGACCACAACTCCGTGGAATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1638667 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1638694 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1638722 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1638749 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* **
1638777 CTTTTTAGTCCACAACTTTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1638804 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1638831 CTTTTAAGACCACAACTCCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1638858 CTTTTAAGTCCACGACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1638885 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1638913 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1638940 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1638967 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1638994 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1639021 CTTTTAAGTCCACAACTCCGTGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1639049 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639076 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1639103 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1639131 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639158 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1639186 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1639213 CTTTTAAGTCCACAACTCCGTGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1639241 CTTTTAAGACCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639268 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1639295 CTTTTAAGTCCATAACTCCGTGGCATCTC
1 CTTTTAAGTCCACAACTCCGTGGCA-C-C
*
1639324 C-TTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639350 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1639378 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1639405 ATTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1639432 CTTTTAAGACCACAACTCCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1639459 CTTTTAAGTCCACGACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1639486 CTTTTAAAGTCCACAACTTCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1639514 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639541 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639568 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1639595 ATTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
1639622 TTTTTAAGACCACAACTCCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1639649 CTTTTAAGTCCACGACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1639676 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1639704 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639731 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639758 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639785 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1639812 TTTTTAAGTCCACAACTCCGTGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1639840 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639867 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1639894 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1639922 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1639949 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* ** *
1639977 CTTTTTAGTCCACAACTCTATAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1640004 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
1640031 CTTTTAAGACCACAACTCCATGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1640058 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1640085 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1640113 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1640140 CTCTTAAAGTCCACAACTCCGTGGCACC
1 CT-TTTAAGTCCACAACTCCGTGGCACC
* *
1640168 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1640195 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1640222 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1640249 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1640276 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1640303 CATTTTAA
1 C-TTTTAA
1640311 AGCCCACACA
Statistics
Matches: 1726, Mismatches: 143, Indels: 44
0.90 0.07 0.02
Matches are distributed among these distances:
26 2 0.00
27 1218 0.71
28 504 0.29
29 2 0.00
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1638492 original size:82 final size:81
Alignment explanation
Indices: 1638392--1640310 Score: 2895
Period size: 82 Copynumber: 23.4 Consensus size: 81
1638382 GTGGCATTTT
* * *
1638392 CTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
* *
1638457 CTACAACTCCGTGGTACC
64 CCACAACTCCGTGGCACC
* * * *
1638475 CTTTTAAGTCCACAACTCTGTGGTACCCTTTTAAAGTCCACAACTCCGTGGTACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1638540 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
1638557 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
1638622 ACAACTCCGTGGCATTC
66 ACAACTCCGTGGCA-CC
* * * *
1638639 CTTTTAAGACCACAACTCCGTGGAATTCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
1638704 CATAACTCCGTGGCATCT
65 CACAACTCCGTGGCA-CC
* *
1638722 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
**
1638787 CACAACTTTGTGGCACC
65 CACAACTCCGTGGCACC
* *
1638804 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGACCACAACTCCGTGGTACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
1638869 ACGACTCTGTGGCACC
66 ACAACTCCGTGGCACC
* * *
1638885 CTTTTAAAGTCCACAACTCCGTGGTACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1638950 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
1638967 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
1639032 ACAACTCCGTGGCATTC
66 ACAACTCCGTGGCA-CC
*
1639049 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
1639114 ATAACTCCGTGGCATCT
66 ACAACTCCGTGGCA-CC
* *
1639131 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1639196 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
* * *
1639213 CTTTTAAGTCCACAACTCCGTGGCATTCCTTTTAAGACCACAACTCCGTGGCATCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1639278 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
1639295 CTTTTAAGTCCATAACTCCGTGGCATCTCC-TTTAAGTCCACAACTCTGTGGCACCCTTTTAAAG
1 CTTTTAAGTCCACAACTCCGTGGCA-C-CCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAG
1639359 TCCACAACTCCGTGGCACC
63 TCCACAACTCCGTGGCACC
* * *
1639378 CTTTTTAGTCCACAACTCCGTGGCACCATTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
1639443 ACAACTCCGTGGTACC
66 ACAACTCCGTGGCACC
* * * * *
1639459 CTTTTAAGTCCACGACTCTGTGGCACCCTTTTAAAGTCCACAACTTCGTGGTACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1639524 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
*
1639541 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCATTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1639606 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
* * * * *
1639622 TTTTTAAGACCACAACTCCGTGGTACCCTTTTAAGTCCACGACTCTGTGGCACCCTTTTAAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
*
1639687 CACAACTCCGTGGTACC
65 CACAACTCCGTGGCACC
* *
1639704 CTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1639769 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
* * *
1639785 CTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGCATTCCTTTTAAGAC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
1639850 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
1639867 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
1639932 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
* ** *
1639949 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTATAGCACCCTTTTAAGTC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1640014 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* * *
1640031 CTTTTAAGACCACAACTCCATGGTACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
1640096 ATAACTCCGTGGCATCT
66 ACAACTCCGTGGCA-CC
* * *
1640113 CTTTTAAGTCCACAACTCTGTGGCACCCTCTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCT-TTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
1640178 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
*
1640195 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
1640260 ACAACTCCGTGGCATC
66 ACAACTCCGTGGCACC
* *
1640276 CTTTTAAATCCACAACTCTGTGGCACCCATTTTAA
1 CTTTTAAGTCCACAACTCCGTGGCACCC-TTTTAA
1640311 AGCCCACACA
Statistics
Matches: 1672, Mismatches: 146, Indels: 37
0.90 0.08 0.02
Matches are distributed among these distances:
81 522 0.31
82 819 0.49
83 331 0.20
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.29
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:1640345 original size:32 final size:32
Alignment explanation
Indices: 1640286--1640567 Score: 440
Period size: 32 Copynumber: 8.8 Consensus size: 32
1640276 CTTTTAAATC
* * *
1640286 CACAACTCTGTGGC-ACCCATTTTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1640317 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1640349 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1640381 CACAAGTCGATGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1640413 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1640445 CACAAGTCGGTGGCAACCCATTTCAGAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1640477 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
1640509 CGCAAGTCGATGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
1640541 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
1640568 TCACCATTTT
Statistics
Matches: 234, Mismatches: 16, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
31 12 0.05
32 222 0.95
ACGTcount: A:0.32, C:0.34, G:0.18, T:0.17
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:1641823 original size:17 final size:15
Alignment explanation
Indices: 1641803--1641852 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
1641793 TTAGGTAAAA
1641803 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
1641820 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
*
1641834 AA-AAAGAAA-AAAA
1 AAGAAAGAAAGAAAG
1641847 AAGAAA
1 AAGAAA
1641853 AAAATATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.17
14 12 0.40
15 1 0.03
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:1641841 original size:10 final size:10
Alignment explanation
Indices: 1641800--1641856 Score: 62
Period size: 10 Copynumber: 5.4 Consensus size: 10
1641790 AAGTTAGGTA
1641800 AAAAAGAAAG
1 AAAAAGAAAG
1641810 AAAGAAGATGAAG
1 AAA-AAGA--AAG
1641823 AAGAAAGAAAG
1 AA-AAAGAAAG
*
1641834 AAAAAGAAAA
1 AAAAAGAAAG
1641844 AAAAAGAAA-
1 AAAAAGAAAG
1641853 AAAA
1 AAAA
1641857 TATGAAATGG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
9 4 0.10
10 19 0.45
11 9 0.21
13 9 0.21
14 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:1645805 original size:29 final size:29
Alignment explanation
Indices: 1645772--1645831 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1645762 AGTCAAAATG
*
1645772 ATATCATAGACTTATT-GAGAAATTAAACT
1 ATATCATAAACTTATTAG-GAAATTAAACT
*
1645801 ATATCATAAACTTATTAGGAACTTAAACT
1 ATATCATAAACTTATTAGGAAATTAAACT
1645830 AT
1 AT
1645832 CATACAGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (29 bp):
ATATCATAAACTTATTAGGAAATTAAACT
Found at i:1652353 original size:16 final size:15
Alignment explanation
Indices: 1652311--1652353 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1652301 TTTTAAAGAT
*
1652311 TATCATATTATTTTG
1 TATCATATTATGTTG
*
1652326 TA-CATATCATGTTG
1 TATCATATTATGTTG
1652340 TATCTATATTATGT
1 TATC-ATATTATGT
1652354 ATTGCATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 12 0.52
15 3 0.13
16 8 0.35
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (15 bp):
TATCATATTATGTTG
Found at i:1661145 original size:16 final size:16
Alignment explanation
Indices: 1661124--1661184 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
1661114 AGATTCAAGT
* *
1661124 TTATTTTGAGTTTAAA
1 TTATTTTAAATTTAAA
1661140 TTATTTTAAATTTAAA
1 TTATTTTAAATTTAAA
* * *
1661156 TATTTTTTGAATTTGAA
1 T-TATTTTAAATTTAAA
*
1661173 TAATTTTAAATT
1 TTATTTTAAATT
1661185 CAATTTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
16 23 0.64
17 13 0.36
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
TTATTTTAAATTTAAA
Found at i:1661168 original size:17 final size:17
Alignment explanation
Indices: 1661127--1661179 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1661117 TTCAAGTTTA
* *
1661127 TTTTGAGTTTAAAT-TA
1 TTTTGAATTTAAATATT
*
1661143 TTTTAAATTTAAATATT
1 TTTTGAATTTAAATATT
*
1661160 TTTTGAATTTGAATAATT
1 TTTTGAATTTAAAT-ATT
1661178 TT
1 TT
1661180 AAATTCAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 12 0.40
17 13 0.43
18 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
TTTTGAATTTAAATATT
Found at i:1661196 original size:33 final size:33
Alignment explanation
Indices: 1661110--1661196 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
1661100 AATTTGAACT
* * * * *
1661110 TTTTAGATTCAAGTTTATTTTGAGTTTAAATTA
1 TTTTAAATTCAAATTTTTTTTGAATTTAAATAA
* * *
1661143 TTTTAAATTTAAATATTTTTTGAATTTGAATAA
1 TTTTAAATTCAAATTTTTTTTGAATTTAAATAA
*
1661176 TTTTAAATTCAATTTTTTTTT
1 TTTTAAATTCAAATTTTTTTT
1661197 ATATTCAAAG
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (33 bp):
TTTTAAATTCAAATTTTTTTTGAATTTAAATAA
Found at i:1671358 original size:59 final size:59
Alignment explanation
Indices: 1671212--1671557 Score: 249
Period size: 59 Copynumber: 5.9 Consensus size: 59
1671202 TACAAAGTAT
** *
1671212 AAAAATAATCCT-AATGA-CTCTAAAATGCACAAAAATTGCT-CTATGGTCTTTAGATAATG
1 AAAAATAAT-CTAAATGACCT-TAAAATGCATGAAAATTGCTAC-ATGGTCTTTAGATTATG
* * * * *
1671271 GAAAATAA-CTTAAATGATCC-CAATATGTATGAAAATTGCTACATGGTCTATAGATTATG
1 AAAAATAATC-TAAATGA-CCTTAAAATGCATGAAAATTGCTACATGGTCTTTAGATTATG
* ** ** * *
1671330 AAAAATAATCTAAATGACCTTAAAATGTAAAAAAATTGCTGA-ATAATCTCTAGGTTATG
1 AAAAATAATCTAAATGACCTTAAAATGCATGAAAATTGCT-ACATGGTCTTTAGATTATG
* * * * ** *
1671389 AAAAATGACCTGAATAACCTCCAAATGCGA-GGAAATTGCTACATGGTCTTTAGATTATG
1 AAAAATAATCTAAATGACCTTAAAATGC-ATGAAAATTGCTACATGGTCTTTAGATTATG
* * * * * * * *
1671448 GAAGATAATCTAAATGACTTTAAAATGAATGGAAATTGCTATATGGTCCTTGGATTATG
1 AAAAATAATCTAAATGACCTTAAAATGCATGAAAATTGCTACATGGTCTTTAGATTATG
* * * * *
1671507 AAAAATAACCTAAATGA-CTTCGACATGCATGGAAATTGCTAAATGGTCTTT
1 AAAAATAATCTAAATGACCTT-AAAATGCATGAAAATTGCTACATGGTCTTT
1671558 TATATGCATG
Statistics
Matches: 223, Mismatches: 52, Indels: 24
0.75 0.17 0.08
Matches are distributed among these distances:
57 1 0.00
58 7 0.03
59 210 0.94
60 4 0.02
61 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (59 bp):
AAAAATAATCTAAATGACCTTAAAATGCATGAAAATTGCTACATGGTCTTTAGATTATG
Found at i:1671484 original size:118 final size:118
Alignment explanation
Indices: 1671212--1671557 Score: 303
Period size: 118 Copynumber: 2.9 Consensus size: 118
1671202 TACAAAGTAT
* * * ** * * *
1671212 AAAAATAATCCT-AATGA-CTCTAAAATGCACAAAAATTGCTCTATGGTCTTTA-GATAATGGAA
1 AAAAATAAT-CTAAATGACCT-TAAAATGTAAAAAAATTGCTATATAATC-CTAGGATTATGAAA
* * * * * *
1671274 AATAACTTAAATGATC-CCAATATGTATGAAAATTGCTACATGGTCTATAGATTATG
63 AATAACCTAAATAACCTCCAA-ATGCATGGAAATTGCTACATGGTCTTTAGATTATG
1671330 AAAAATAATCTAAATGACCTTAAAATGTAAAAAAATTGCTGA-ATAATCTCTAGG-TTATGAAAA
1 AAAAATAATCTAAATGACCTTAAAATGTAAAAAAATTGCT-ATATAATC-CTAGGATTATGAAAA
* *
1671393 ATGACCTGAATAACCTCCAAATGCGA-GGAAATTGCTACATGGTCTTTAGATTATG
64 ATAACCTAAATAACCTCCAAATGC-ATGGAAATTGCTACATGGTCTTTAGATTATG
* * * ** ** *
1671448 GAAGATAATCTAAATGACTTTAAAATG-AATGGAAATTGCTATATGGTCCTTGGATTATGAAAAA
1 AAAAATAATCTAAATGACCTTAAAATGTAA-AAAAATTGCTATATAATCCTAGGATTATGAAAAA
* * * * *
1671512 TAACCTAAATGACTTCGACATGCATGGAAATTGCTAAATGGTCTTT
65 TAACCTAAATAACCTCCAAATGCATGGAAATTGCTACATGGTCTTT
1671558 TATATGCATG
Statistics
Matches: 187, Mismatches: 31, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
117 10 0.05
118 169 0.90
119 8 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (118 bp):
AAAAATAATCTAAATGACCTTAAAATGTAAAAAAATTGCTATATAATCCTAGGATTATGAAAAAT
AACCTAAATAACCTCCAAATGCATGGAAATTGCTACATGGTCTTTAGATTATG
Found at i:1676821 original size:237 final size:238
Alignment explanation
Indices: 1676399--1676890 Score: 616
Period size: 237 Copynumber: 2.1 Consensus size: 238
1676389 AAAAATTTAA
* * * * * *
1676399 TATTTTGGAGATAAAAA-CGAGGTTGGAGTATCTCCTTGGAAATAACAAGGTTGGAGTATCCCTG
1 TATTTTAGAAATAAAAACCGAGGTTAGAGTATCTCCTTAGAAATAACAAGGTAGGAGTATCCCCG
** * *
1676463 ATGGTAAAAAATCGATGTTTTGGAAATAAAACTAAGGTTGGAGTATCCCTTCGAAAATAACGGGG
66 ATGGTAAAAAATCGATGTTTCAGAAATAAAACTAAGGTTGGAGTATCCCCTCGAAAATAACAGGG
* * * * * *
1676528 TTGGAGTATCCTCGATTGTGAAAAATTAATGTTTTAAAAATAAAGCTAGAGTTGGAGTATCCCCT
131 TTAGAATATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACCAGAGTTGGAGTATCCCCT
* ** *
1676593 AAAAAATAACGGGGTTGGAGTAT-CTCCGATTATGAAAAATCGG
196 AAAAAATAACGGGATTAAAGTATCCT-CGATGATGAAAAATCGG
*
1676636 TGTTTTAGAAATAAAAACCGAGGTTAGAGTATC-CCTTCAGAAATAAC-AGGATAGGAGTATCCC
1 TATTTTAGAAATAAAAACCGAGGTTAGAGTATCTCCTT-AGAAATAACAAGG-TAGGAGTATCCC
* * **
1676699 CGATGGTGAAAAATCGGTGTTTCAGAAATAAAAC-GGGGTTGGAGTATCCCCTCGAAAATAACAG
64 CGATGGTAAAAAATCGATGTTTCAGAAATAAAACTAAGGTTGGAGTATCCCCTCGAAAATAACAG
* * *
1676763 GGTTAGAATATCCCCGATTGTGGAAAATCAATGTTTTGAAAATAAAACCAGGGTTGGAGTATCCC
129 GGTTAGAATATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACCAGAGTTGGAGTATCCC
*** * * *
1676828 CTCGGAAATAATGGGATTAAAGTATCCTCGATGGTGGAAAATCGG
194 CTAAAAAATAACGGGATTAAAGTATCCTCGATGATGAAAAATCGG
1676873 TATTTTAGAAATAAAAAC
1 TATTTTAGAAATAAAAAC
1676891 ATGAATAAAA
Statistics
Matches: 216, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
237 152 0.70
238 64 0.30
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (238 bp):
TATTTTAGAAATAAAAACCGAGGTTAGAGTATCTCCTTAGAAATAACAAGGTAGGAGTATCCCCG
ATGGTAAAAAATCGATGTTTCAGAAATAAAACTAAGGTTGGAGTATCCCCTCGAAAATAACAGGG
TTAGAATATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAACCAGAGTTGGAGTATCCCCT
AAAAAATAACGGGATTAAAGTATCCTCGATGATGAAAAATCGG
Found at i:1676854 original size:79 final size:79
Alignment explanation
Indices: 1676419--1676888 Score: 382
Period size: 79 Copynumber: 5.9 Consensus size: 79
1676409 ATAAAAACGA
* * * * * * * *
1676419 GGTTGGAGTATCTCCTTGGAAATAACAAGG-TTGGAGTATCCCTGATGGTAAAAAATCGATGTTT
1 GGTTGGAGTATCCCCTCGAAAATAAC-GGGATTAGAGTATCCCCGATTGTGAAAAATCGATGTTT
* * *
1676483 TGGAAATAAAACTAA
65 TGAAAATAAAACCAG
* * * * **
1676498 GGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTAATGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGTATCCCCGATTGTGAAAAATCGATGTTTT
* * *
1676563 AAAAATAAAGCTAG
66 GAAAATAAAACCAG
* ** * * * * *
1676577 AGTTGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCTCCGATTATGAAAAATCGGTGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGTATCCCCGATTGTGAAAAATCGATGTTTT
1676642 -AGAAATAAAAACC-G
66 GA-AAAT-AAAACCAG
* * * * *
1676656 AGGTTAGAGTATCCCTTC-AGAAATAACAGGA-TAGGAGTATCCCCGATGGTGAAAAATCGGTG-
1 -GGTTGGAGTATCCCCTCGA-AAATAACGGGATTA-GAGTATCCCCGATTGTGAAAAATCGATGT
* *
1676718 TTTCAGAAATAAAA-CGG
63 TTTGA-AAATAAAACCAG
* * *
1676735 GGTTGGAGTATCCCCTCGAAAATAACAGGG-TTAGAATATCCCCGATTGTGGAAAATCAATGTTT
1 GGTTGGAGTATCCCCTCGAAAATAAC-GGGATTAGAGTATCCCCGATTGTGAAAAATCGATGTTT
1676799 TGAAAATAAAACCAG
65 TGAAAATAAAACCAG
* * * * * * * *
1676814 GGTTGGAGTATCCCCTCGGAAATAATGGGATTAAAGTATCCTCGATGGTGGAAAATCGGTATTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGTATCCCCGATTGTGAAAAATCGATGTTTT
1676879 -AGAAATAAAA
66 GA-AAATAAAA
1676889 ACATGAATAA
Statistics
Matches: 320, Mismatches: 56, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
78 61 0.19
79 202 0.63
80 57 0.18
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGTATCCCCGATTGTGAAAAATCGATGTTTT
GAAAATAAAACCAG
Done.