Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167971.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_23, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19268551
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 68000 characters in sequence are not A, C, G, or T
File 77 of 120
Found at i:9646023 original size:46 final size:46
Alignment explanation
Indices: 9645937--9646024 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
9645927 TTTGACATTC
*
9645937 AAAGATTCTCATTGGAAAACATCTTAAAGATTTTCATTTAAGACTT
1 AAAGATTCTCATTGGAAAACATCTTAAAGATTCTCATTTAAGACTT
* **
9645983 AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTAAG
1 AAAGATTCTCATTGGAAAACATCTTAAAGATTCTCATTTAAG
9646025 GATTTCTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (46 bp):
AAAGATTCTCATTGGAAAACATCTTAAAGATTCTCATTTAAGACTT
Found at i:9646032 original size:25 final size:23
Alignment explanation
Indices: 9645958--9646033 Score: 84
Period size: 25 Copynumber: 3.2 Consensus size: 23
9645948 TTGGAAAACA
*
9645958 TCTTAAAGATTTTCATTTAAGA-
1 TCTTAAAGATTCTCATTTAAGAT
*
9645980 -CTTAAAGATTCTCATTTGAAAAT
1 TCTTAAAGATTCTCATTT-AAGAT
9646003 GTCTTAAAGATTCTCATTTAAGGATT
1 -TCTTAAAGATTCTCATTTAA-GA-T
9646029 TCTTA
1 TCTTA
9646034 TTTAAAACTC
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
21 16 0.36
22 3 0.07
24 2 0.04
25 23 0.51
26 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (23 bp):
TCTTAAAGATTCTCATTTAAGAT
Found at i:9646047 original size:107 final size:107
Alignment explanation
Indices: 9645935--9646131 Score: 295
Period size: 107 Copynumber: 1.8 Consensus size: 107
9645925 CATTTGACAT
* * *
9645935 TCAAAGATTCTCATTGGAAAACATCTTAAAGATTTTCATTTAAGACTTAAAGATTCTCATTTGAA
1 TCAAAGATTCTCATTGGAAAACATCTTAAAGATTCTCATTTAAAACTCAAAGATTCTCATTTGAA
*
9646000 AATGTCTTAAAGATTCTCATTTAAGGATTTCTTATTTAAAAC
66 AACGTCTTAAAGATTCTCATTTAAGGATTTCTTATTTAAAAC
* ** ** *
9646042 TCAAAGATTCTCATTTGAGGATTTCTTAAATATTCTCATTTAAAACTCAAAGATTCTCATTTGAA
1 TCAAAGATTCTCATTGGAAAACATCTTAAAGATTCTCATTTAAAACTCAAAGATTCTCATTTGAA
*
9646107 GACGTCTTAAAGATTCTCATTTAAG
66 AACGTCTTAAAGATTCTCATTTAAG
9646132 ACTTAAAACT
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
107 79 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (107 bp):
TCAAAGATTCTCATTGGAAAACATCTTAAAGATTCTCATTTAAAACTCAAAGATTCTCATTTGAA
AACGTCTTAAAGATTCTCATTTAAGGATTTCTTATTTAAAAC
Found at i:9646100 original size:46 final size:46
Alignment explanation
Indices: 9646028--9646130 Score: 161
Period size: 46 Copynumber: 2.2 Consensus size: 46
9646018 ATTTAAGGAT
* * ** *
9646028 TTCTTATTTAAAACTCAAAGATTCTCATTTGAGGATTTCTTAAATA
1 TTCTCATTTAAAACTCAAAGATTCTCATTTGAAGACGTCTTAAAGA
9646074 TTCTCATTTAAAACTCAAAGATTCTCATTTGAAGACGTCTTAAAGA
1 TTCTCATTTAAAACTCAAAGATTCTCATTTGAAGACGTCTTAAAGA
9646120 TTCTCATTTAA
1 TTCTCATTTAA
9646131 GACTTAAAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.41
Consensus pattern (46 bp):
TTCTCATTTAAAACTCAAAGATTCTCATTTGAAGACGTCTTAAAGA
Found at i:9646124 original size:25 final size:23
Alignment explanation
Indices: 9646028--9646134 Score: 96
Period size: 25 Copynumber: 4.7 Consensus size: 23
9646018 ATTTAAGGAT
* *
9646028 TTCTTATTTAAAACTC--AAAGA
1 TTCTCATTTAAGACTCTTAAAGA
* * *
9646049 TTCTCATTTGAGGATTTCTTAAATA
1 TTCTCATTT-AAGA-CTCTTAAAGA
*
9646074 TTCTCATTTAAAACTC--AAAGA
1 TTCTCATTTAAGACTCTTAAAGA
9646095 TTCTCATTTGAAGACGTCTTAAAGA
1 TTCTCATTT-AAGAC-TCTTAAAGA
9646120 TTCTCATTTAAGACT
1 TTCTCATTTAAGACT
9646135 TAAAACTTCA
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
21 21 0.31
22 6 0.09
23 7 0.10
24 7 0.10
25 27 0.40
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (23 bp):
TTCTCATTTAAGACTCTTAAAGA
Found at i:9647410 original size:7 final size:7
Alignment explanation
Indices: 9647400--9647462 Score: 67
Period size: 7 Copynumber: 8.6 Consensus size: 7
9647390 TCAATTTGAG
9647400 TTTTCTT
1 TTTTCTT
9647407 TTTTCTT
1 TTTTCTT
9647414 TCTTT-TT
1 T-TTTCTT
9647421 TTTTCTCT
1 TTTTCT-T
9647429 TTTTCATT
1 TTTTC-TT
9647437 TTTTC-T
1 TTTTCTT
9647443 TTTTCATTT
1 TTTTC--TT
9647452 TTTTCTT
1 TTTTCTT
9647459 TTTT
1 TTTT
9647463 TTCATCTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
6 9 0.18
7 18 0.37
8 15 0.31
9 7 0.14
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:9647438 original size:15 final size:14
Alignment explanation
Indices: 9647400--9647461 Score: 72
Period size: 15 Copynumber: 4.3 Consensus size: 14
9647390 TCAATTTGAG
9647400 TTTTC-TTTTTTCT
1 TTTTCATTTTTTCT
**
9647413 TTCTTTTTTTTTCTCT
1 TT-TTCATTTTT-TCT
9647429 TTTTCATTTTTTCT
1 TTTTCATTTTTTCT
9647443 TTTTCATTTTTTTCT
1 TTTTCA-TTTTTTCT
9647458 TTTT
1 TTTT
9647462 TTTCATCTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.05
14 11 0.26
15 24 0.57
16 5 0.12
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCATTTTTTCT
Found at i:9647868 original size:18 final size:18
Alignment explanation
Indices: 9647847--9647881 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9647837 GTTTTCCATC
9647847 TTTTTTTCCTTTTTTTGT
1 TTTTTTTCCTTTTTTTGT
**
9647865 TTTTTTTTTTTTTTTTG
1 TTTTTTTCCTTTTTTTG
9647882 CTTTAAGACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (18 bp):
TTTTTTTCCTTTTTTTGT
Found at i:9651501 original size:59 final size:59
Alignment explanation
Indices: 9651337--9651500 Score: 204
Period size: 60 Copynumber: 2.7 Consensus size: 59
9651327 GCTTTTGTAC
* * *
9651337 AAGGAAAATTGATACTTTCAACTTTTCCTTAAAATGTTTTTCTTGATAATTTTTATTTTT
1 AAGG-AAATTGATACTTTCAACTTTTCCTTAAAATGTTTTTTTTTATAATTTTTAATTTT
* * * * * * *
9651397 AAGAAAAATTGGTACTTCCAATTTTTCCTCAAAAGGCTTTTTTTTTTTAA-TTTTAATTTT
1 AAG-GAAATTGATACTTTCAACTTTTCCTTAAAATG-TTTTTTTTTATAATTTTTAATTTT
9651457 AAGGAAATTGATACTTTCAACTTTTCCTTAAAATGTTTTTTTTT
1 AAGGAAATTGATACTTTCAACTTTTCCTTAAAATGTTTTTTTTT
9651501 TATTTTAAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
58 9 0.10
59 26 0.30
60 41 0.48
61 10 0.12
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (59 bp):
AAGGAAATTGATACTTTCAACTTTTCCTTAAAATGTTTTTTTTTATAATTTTTAATTTT
Found at i:9651705 original size:13 final size:12
Alignment explanation
Indices: 9651662--9651702 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
9651652 AAAGCTAATA
9651662 AAAATACTAAAT
1 AAAATACTAAAT
*
9651674 AAAATAAATAAAT
1 AAAAT-ACTAAAT
*
9651687 AAAATACCAAAT
1 AAAATACTAAAT
9651699 AAAA
1 AAAA
9651703 ATAAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAATACTAAAT
Found at i:9651711 original size:25 final size:25
Alignment explanation
Indices: 9651662--9651711 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
9651652 AAAGCTAATA
*
9651662 AAAATACTAAATAAAATAAATAAAT
1 AAAATACCAAATAAAATAAATAAAT
9651687 AAAATACCAAATAAAAATAAA-AAAT
1 AAAATACCAAAT-AAAATAAATAAAT
9651712 TGCTCGGCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (25 bp):
AAAATACCAAATAAAATAAATAAAT
Found at i:9652650 original size:33 final size:33
Alignment explanation
Indices: 9652613--9652678 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
9652603 ATTCTAGAAA
9652613 AACAAA-AGAAAGA-AAGAAGATAAATAAATAAAT
1 AACAAATA-AAAGATAA-AAGATAAATAAATAAAT
* *
9652646 AACAAATAATATATAAAAGATAAATAAATAAAT
1 AACAAATAAAAGATAAAAGATAAATAAATAAAT
9652679 CTTTGGGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (33 bp):
AACAAATAAAAGATAAAAGATAAATAAATAAAT
Found at i:9652670 original size:18 final size:16
Alignment explanation
Indices: 9652629--9652677 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
9652619 AGAAAGAAAG
9652629 AAGATAAATAAATAAA
1 AAGATAAATAAATAAA
* *
9652645 TA-ACAAATAATATATAA
1 AAGATAAATAA-ATA-AA
9652662 AAGATAAATAAATAAA
1 AAGATAAATAAATAAA
9652678 TCTTTGGGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 7 0.27
16 6 0.23
17 6 0.23
18 7 0.27
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (16 bp):
AAGATAAATAAATAAA
Found at i:9653057 original size:3 final size:3
Alignment explanation
Indices: 9653051--9653103 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
9653041 TTAATGTCAC
* *
9653051 TAT TAT TA- TAT TAT TAT TAC TAT TAT TAT TAC TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
9653096 ATAT TAT T
1 -TAT TAT T
9653104 TTTCTTTCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:9653074 original size:12 final size:12
Alignment explanation
Indices: 9653051--9653092 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
9653041 TTAATGTCAC
9653051 TATTATTA-TAT
1 TATTATTACTAT
9653062 TATTATTACTAT
1 TATTATTACTAT
9653074 TATTATTACTAT
1 TATTATTACTAT
9653086 TATTATT
1 TATTATT
9653093 TATATATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATTACTAT
Found at i:9653663 original size:21 final size:21
Alignment explanation
Indices: 9653623--9653662 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
9653613 CTAGAAAACT
9653623 TAGAAGATATTTGGGTTTTTC
1 TAGAAGATATTTGGGTTTTTC
*
9653644 TAGAA-ATTTTTGGGTTTTT
1 TAGAAGATATTTGGGTTTTT
9653663 TTGGGTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.53
Consensus pattern (21 bp):
TAGAAGATATTTGGGTTTTTC
Found at i:9653714 original size:32 final size:31
Alignment explanation
Indices: 9653673--9653732 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
9653663 TTGGGTTAGG
9653673 ATGAATTTCCAACGA-AGGTTTGAATTTTCCA
1 ATGAATTTCCAACGATAGG-TTGAATTTTCCA
* *
9653704 ATGAAGTTTCCTACGATCGGTTGAATTTT
1 ATGAA-TTTCCAACGATAGGTTGAATTTT
9653733 TCAACCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.20
32 18 0.72
33 2 0.08
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (31 bp):
ATGAATTTCCAACGATAGGTTGAATTTTCCA
Found at i:9655094 original size:39 final size:39
Alignment explanation
Indices: 9655051--9655136 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
9655041 TTGTCTTTCC
* * *
9655051 TATTTCTTTCTTTTCATTATCTATATTTGACTAATTATT
1 TATTTATTTCTTATCATTATCTATATTTGACTAATTACT
* * **
9655090 TATTTATTTCTTATCATTGTTTATATTTGTTTAATTACT
1 TATTTATTTCTTATCATTATCTATATTTGACTAATTACT
9655129 TATTTATT
1 TATTTATT
9655137 GTATATATAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.64
Consensus pattern (39 bp):
TATTTATTTCTTATCATTATCTATATTTGACTAATTACT
Found at i:9661156 original size:42 final size:42
Alignment explanation
Indices: 9661093--9661174 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
9661083 ACCTATATAT
* * *
9661093 GAATTACAAAATTAAAAGGTTATCTAGATGTCTATTGTTTCA
1 GAATTACAAAATTAAAAGGTTATATAAATGCCTATTGTTTCA
*
9661135 GAATTACAAAATTAAAGGGTTATATAAATGCCTATTGTTT
1 GAATTACAAAATTAAAAGGTTATATAAATGCCTATTGTTT
9661175 ATGATTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.38
Consensus pattern (42 bp):
GAATTACAAAATTAAAAGGTTATATAAATGCCTATTGTTTCA
Found at i:9664886 original size:23 final size:23
Alignment explanation
Indices: 9664860--9664921 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
9664850 AAATAAATAA
* *
9664860 TAAATAATAATTAAAATTAAAAT
1 TAAAAAATAATAAAAATTAAAAT
9664883 TAAAAAATTAA-AAAAATTAAAAT
1 TAAAAAA-TAATAAAAATTAAAAT
9664906 TAAAAAATAATAAAAA
1 TAAAAAATAATAAAAA
9664922 ATAAGAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 3 0.09
23 29 0.83
24 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAAAATAATAAAAATTAAAAT
Found at i:9664891 original size:8 final size:8
Alignment explanation
Indices: 9664878--9664923 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
9664868 AATTAAAATT
9664878 AAAATTAA
1 AAAATTAA
9664886 AAAATTAAA
1 AAAATT-AA
9664895 AAAATT--
1 AAAATTAA
9664901 AAAATTAA
1 AAAATTAA
9664909 AAAATAATAA
1 AAAAT--TAA
9664919 AAAAT
1 AAAAT
9664924 AAGAGAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.18
8 11 0.33
9 8 0.24
10 8 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:9664898 original size:17 final size:17
Alignment explanation
Indices: 9664878--9664923 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
9664868 AATTAAAATT
9664878 AAAATTAAAAAATTAAA
1 AAAATTAAAAAATTAAA
9664895 AAAATT--AAAATTAAA
1 AAAATTAAAAAATTAAA
*
9664910 AAATAATAAAAAAT
1 AAA-ATTAAAAAAT
9664924 AAGAGAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 12 0.48
16 2 0.08
17 6 0.24
18 5 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATTAAAAAATTAAA
Found at i:9665741 original size:59 final size:59
Alignment explanation
Indices: 9665667--9665792 Score: 137
Period size: 59 Copynumber: 2.1 Consensus size: 59
9665657 TGATTCGTGC
* * * *
9665667 TTTTATCTCGGTCATTTTCGATCTCGAC-TCAGTCCTAGTCGTTTAATTTTAACTCATGA
1 TTTTATCCCGATCATTTTCGACCTCGACAT-AATCCTAGTCGTTTAATTTTAACTCATGA
** * * * *
9665726 TTTTATCCCGATCATTTTTTACCTCGACATAATCCTGGTCGTTTTATTTTGACTCGTGA
1 TTTTATCCCGATCATTTTCGACCTCGACATAATCCTAGTCGTTTAATTTTAACTCATGA
*
9665785 TTTCATCC
1 TTTTATCC
9665793 TAGTCATCTG
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 54 0.98
60 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (59 bp):
TTTTATCCCGATCATTTTCGACCTCGACATAATCCTAGTCGTTTAATTTTAACTCATGA
Found at i:9665858 original size:115 final size:114
Alignment explanation
Indices: 9665734--9666099 Score: 382
Period size: 115 Copynumber: 3.2 Consensus size: 114
9665724 GATTTTATCC
* * *
9665734 CGATCATTTTTTACCTCGACAT-AATCCTGGTCGTTTTATTTTGACTCGTGATTTCATCCTAGTC
1 CGATCATTTTTTACCTCAAC-TCGATCCTGGTCGTTTTATTTTGACTCATG-TTTCATCCTAGTC
*
9665798 ATCTGATCTTGGCTCAGTCCAAATCATTTCTTATGATT-TGTGGTTTCGTCA
64 ATCTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTAT-TGGTTTCATCA
* * * * ** * * *
9665849 TGGTCATTTTTTACATCAACTCGATCTTGGTCACTTCATTTTGACTCATGGTTCATCCTGGTCAT
1 CGATCATTTTTTACCTCAACTCGATCCTGGTCGTTTTATTTTGACTCATGTTTCATCCTAGTCAT
* * * * *
9665914 CTAATCTTGGCTCAGTCTAGATCATTTCTTATGATTATTGGTTTTATCC
66 CTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTATTGGTTTCATCA
* * * * *
9665963 CGATTACTTTTTACCTCAACTCGATCCTGATCGTTTTATTTTGAGTCATGGTTTCATCC-CGTTC
1 CGATCATTTTTTACCTCAACTCGATCCTGGTCGTTTTATTTTGACTCAT-GTTTCATCCTAG-TC
* * *
9666027 ATCTGATCTTGGCTCAATCCATATCATTTCTTATGATTCA-TGGTTTTATC-
64 ATCTGATCTTGGCTCAGTCCAAATCATTTCTTATGATT-ATTGGTTTCATCA
*
9666077 CTGATCATTTTTCAACCTCAACT
1 C-GATCATTTTT-TACCTCAACT
9666100 TGGTCCTAAT
Statistics
Matches: 206, Mismatches: 38, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
114 95 0.46
115 101 0.49
116 10 0.05
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (114 bp):
CGATCATTTTTTACCTCAACTCGATCCTGGTCGTTTTATTTTGACTCATGTTTCATCCTAGTCAT
CTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTATTGGTTTCATCA
Found at i:9665922 original size:114 final size:114
Alignment explanation
Indices: 9665771--9666180 Score: 344
Period size: 114 Copynumber: 3.6 Consensus size: 114
9665761 TGGTCGTTTT
* * *
9665771 ATTTTGACTCGTGATTTCATCCTAGTCATCTGATCTTGGCTCAGTCCAAATCATTTCTTATGATT
1 ATTTTGACTCATG-GTTCATCCTGGTCATCTGATCTTGGCTCAGTCCAAATCATTTCTTATGATT
* * * * * *
9665836 -TGTGGTTTCGTCATGGTCATTTTTTACATCAACTCGATCTTGGTCACTTC
65 AT-TGGTTTCATCACGATCACTTTTTACATCAACTCGATCCTGATCACTTC
* * *
9665886 ATTTTGACTCATGGTTCATCCTGGTCATCTAATCTTGGCTCAGTCTAGATCATTTCTTATGATTA
1 ATTTTGACTCATGGTTCATCCTGGTCATCTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTA
* * * * ** *
9665951 TTGGTTTTATCCCGATTACTTTTTACCTCAACTCGATCCTGATCGTTTT
66 TTGGTTTCATCACGATCACTTTTTACATCAACTCGATCCTGATCACTTC
* * * * *
9666000 ATTTTGAGTCATGGTTTCATCCCGTTCATCTGATCTTGGCTCAATCCATATCATTTCTTATGATT
1 ATTTTGACTCATGG-TTCATCCTGGTCATCTGATCTTGGCTCAGTCCAAATCATTTCTTATGATT
* * * * * *
9666065 CA-TGGTTTTATC-CTGATCA-TTTTTCAACCTCAACTTGGTCCTAATCGCTTC
65 -ATTGGTTTCATCAC-GATCACTTTTT--ACATCAACTCGATCCTGATCACTTC
* ** * * * * * * *
9666116 ATTTTAACTTGTGGTTTTAT-CTCGATCATTTGGTCTTGGCTTAATCTAAATCATTTCTTATGAT
1 ATTTTGACTCATGG-TTCATCCT-GGTCATCTGATCTTGGCTCAGTCCAAATCATTTCTTATGAT
9666180 T
64 T
9666181 CGTGATTTTG
Statistics
Matches: 244, Mismatches: 44, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
114 100 0.41
115 72 0.30
116 72 0.30
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (114 bp):
ATTTTGACTCATGGTTCATCCTGGTCATCTGATCTTGGCTCAGTCCAAATCATTTCTTATGATTA
TTGGTTTCATCACGATCACTTTTTACATCAACTCGATCCTGATCACTTC
Found at i:9666169 original size:116 final size:116
Alignment explanation
Indices: 9665726--9666181 Score: 370
Period size: 115 Copynumber: 4.0 Consensus size: 116
9665716 TAACTCATGA
* * * ** * * * * *
9665726 TTTTATCCCGATCATTTTTTACCTCGACAT-AATCCTGGTCGTTTTATTTTGACTCGTGATTTCA
1 TTTTATCCCGATCACTTTTTACCTCAAC-TCGATCCTAATCGCTTCATTTTAACTCATGGTTTCA
* * *
9665790 T-CCTAGTCATCTGATCTTGGCTCAGTCCAAATCATTTCTTATGATT--TGTGG
65 TCCCGA-TCATCTGATCTTGGCTCAATCTAAATCATTTCTTATGATTCAT-TGG
** ** * * * * ** * *
9665841 TTTCGTCATGGTCATTTTTTACATCAACTCGATCTTGGTCACTTCATTTTGACTCATGG-TTCAT
1 TTTTATCCCGATCACTTTTTACCTCAACTCGATCCTAATCGCTTCATTTTAACTCATGGTTTCAT
* * * * *
9665905 CCTGGTCATCTAATCTTGGCTCAGTCTAGATCATTTCTTATGATT-ATTGG
66 CCCGATCATCTGATCTTGGCTCAATCTAAATCATTTCTTATGATTCATTGG
* * * * * *
9665955 TTTTATCCCGATTACTTTTTACCTCAACTCGATCCTGATCGTTTTATTTTGAGTCATGGTTTCAT
1 TTTTATCCCGATCACTTTTTACCTCAACTCGATCCTAATCGCTTCATTTTAACTCATGGTTTCAT
* * *
9666020 CCCGTTCATCTGATCTTGGCTCAATCCATATCATTTCTTATGATTCA-TGG
66 CCCGATCATCTGATCTTGGCTCAATCTAAATCATTTCTTATGATTCATTGG
* * * ** *
9666070 TTTTATCCTGATCA-TTTTTCAACCTCAACTTGGTCCTAATCGCTTCATTTTAACTTGTGGTTTT
1 TTTTATCCCGATCACTTTTT--ACCTCAACTCGATCCTAATCGCTTCATTTTAACTCATGGTTTC
* * * *
9666134 ATCTCGATCATTTGGTCTTGGCTTAATCTAAATCATTTCTTATGATTC
64 ATCCCGATCATCTGATCTTGGCTCAATCTAAATCATTTCTTATGATTC
9666182 GTGATTTTGT
Statistics
Matches: 275, Mismatches: 59, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
114 96 0.35
115 104 0.38
116 75 0.27
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.45
Consensus pattern (116 bp):
TTTTATCCCGATCACTTTTTACCTCAACTCGATCCTAATCGCTTCATTTTAACTCATGGTTTCAT
CCCGATCATCTGATCTTGGCTCAATCTAAATCATTTCTTATGATTCATTGG
Found at i:9666209 original size:56 final size:56
Alignment explanation
Indices: 9666130--9666255 Score: 164
Period size: 56 Copynumber: 2.2 Consensus size: 56
9666120 TAACTTGTGG
* * *
9666130 TTTTATCTCGATCATTTGGTCTTGGCTTAATCTAAATCATTTCTTATGATTCGTGA
1 TTTTATCTCGATCATCTGATCTTGGCTCAATCTAAATCATTTCTTATGATTCGTGA
* * * *
9666186 TTTTGTCTCGATCATCTGATCTTGGCTCAGTCTAGATCATTTCTTATGATTTGT-A
1 TTTTATCTCGATCATCTGATCTTGGCTCAATCTAAATCATTTCTTATGATTCGTGA
*
9666241 GTTTCATCTCGATCA
1 -TTTTATCTCGATCA
9666256 ATTTTTGACC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
55 1 0.02
56 59 0.98
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (56 bp):
TTTTATCTCGATCATCTGATCTTGGCTCAATCTAAATCATTTCTTATGATTCGTGA
Found at i:9666604 original size:3 final size:3
Alignment explanation
Indices: 9666596--9666918 Score: 246
Period size: 3 Copynumber: 108.3 Consensus size: 3
9666586 TTAATGTCAC
* * *
9666596 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TGT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * **
9666644 TAT T-T TAT T-T TCCT T-T TCT T-T CT-T TGG TAT T-T T-T GTAT ATAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT -TAT TAT TAT TAT TAT -TAT -TAT
* * * * * * *
9666686 TAT AAT ATAG TAT TAT TAA TGT CAC CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * * *
9666732 TAT TAT TAT TGT TGT TGT TGT TGT TGT TGT TGT TGT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9666780 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * *
9666828 TAT TAT TGT TGT TGT TGT TGT TGT TGT TGT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
9666876 TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9666919 TTCGCTTCTT
Statistics
Matches: 283, Mismatches: 28, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
2 11 0.04
3 265 0.94
4 7 0.02
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:9666941 original size:11 final size:11
Alignment explanation
Indices: 9666917--9666972 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
9666907 ATTATTATTA
* *
9666917 TTTTCGCTTCT
1 TTTTCTCTTTT
9666928 TTTTCTCTTTT
1 TTTTCTCTTTT
9666939 TTTTCT-TTTT
1 TTTTCTCTTTT
*
9666949 TTTTCTTTTCTT
1 TTTTCTCTT-TT
9666961 TTTTC-CTTTT
1 TTTTCTCTTTT
9666971 TT
1 TT
9666973 ATACCAATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
10 14 0.35
11 19 0.47
12 7 0.17
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:9667829 original size:19 final size:19
Alignment explanation
Indices: 9667807--9667844 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
9667797 AGGTTTTTCT
9667807 TTTTTTCATTTTATTTTTA
1 TTTTTTCATTTTATTTTTA
*
9667826 TTTTTTGATTTTATTTTTA
1 TTTTTTCATTTTATTTTTA
9667845 CTTTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTTTCATTTTATTTTTA
Found at i:9667979 original size:20 final size:19
Alignment explanation
Indices: 9667954--9667991 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
9667944 TTCTATAAAA
9667954 AAAAAAAACCCTTTTCAAAC
1 AAAAAAAA-CCTTTTCAAAC
*
9667974 AAAAAAAATCTTTTCAAA
1 AAAAAAAACCTTTTCAAA
9667992 TAAGGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAAAACCTTTTCAAAC
Found at i:9668098 original size:22 final size:22
Alignment explanation
Indices: 9668042--9668105 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
9668032 TTTAAGTTTC
* *
9668042 AAAAAAAT-ATTT-ATATATAT
1 AAAAAAATCATTTCAAATAAAT
9668062 ATAAAAAATCATTTC-AATAAAT
1 A-AAAAAATCATTTCAAATAAAT
*
9668084 AAAAAAATCTTTTTCAAATAAA
1 AAAAAAATC-ATTTCAAATAAA
9668106 AATCCTTACA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 1 0.03
21 15 0.42
22 14 0.39
23 6 0.17
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAAAATCATTTCAAATAAAT
Found at i:9670763 original size:10 final size:10
Alignment explanation
Indices: 9670750--9670779 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
9670740 ATTGAGCTTT
9670750 TATATTTTAA
1 TATATTTTAA
9670760 TATATTTTAA
1 TATATTTTAA
9670770 T-TATTTTAA
1 TATATTTTAA
9670779 T
1 T
9670780 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:9670776 original size:9 final size:9
Alignment explanation
Indices: 9670752--9670781 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
9670742 TGAGCTTTTA
9670752 TATTTTAAT
1 TATTTTAAT
9670761 ATATTTTAAT
1 -TATTTTAAT
9670771 TATTTTAAT
1 TATTTTAAT
9670780 TA
1 TA
9670782 ATAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:9671869 original size:14 final size:14
Alignment explanation
Indices: 9671842--9671877 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
9671832 TTTTTTGTGC
9671842 TTTTTATTTCTTTT
1 TTTTTATTTCTTTT
*
9671856 TTTTTGTTT-TTTT
1 TTTTTATTTCTTTT
9671869 TTTTTATTT
1 TTTTTATTT
9671878 GGGTCATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.06, C:0.03, G:0.03, T:0.89
Consensus pattern (14 bp):
TTTTTATTTCTTTT
Found at i:9671995 original size:26 final size:27
Alignment explanation
Indices: 9671957--9672087 Score: 132
Period size: 25 Copynumber: 5.1 Consensus size: 27
9671947 CTTTTGGTAG
*
9671957 GATTTTTATTATGAGATTTATTTGCAT
1 GATTTTTATTATGATATTTATTTGCAT
*
9671984 GATTTTT-TTATGAT-TTTATTTGTAT
1 GATTTTTATTATGATATTTATTTGCAT
* *
9672009 AATTTTT-TTATGATATTTAGTTGCAT
1 GATTTTTATTATGATATTTATTTGCAT
*
9672035 AATTTTTATTATGATA-TT-TTTGCAT
1 GATTTTTATTATGATATTTATTTGCAT
* * * *
9672060 GA--ATGATTATAATATATATTTGCAT
1 GATTTTTATTATGATATTTATTTGCAT
9672085 GAT
1 GAT
9672088 ACTTTTCATG
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
23 9 0.10
24 1 0.01
25 39 0.44
26 24 0.27
27 15 0.17
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.56
Consensus pattern (27 bp):
GATTTTTATTATGATATTTATTTGCAT
Found at i:9682531 original size:2 final size:2
Alignment explanation
Indices: 9682526--9682552 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9682516 GCCTGCATTA
9682526 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 A
9682553 GCTGTCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9683624 original size:25 final size:24
Alignment explanation
Indices: 9683581--9683627 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
9683571 AAAACTCGAT
*
9683581 CGAGTTTGAGTCGATATCGAGTCA
1 CGAGTTTGAGTCGAGATCGAGTCA
*
9683605 CGAGTTGTGAGTGGAGATCGAGT
1 CGAGTT-TGAGTCGAGATCGAGT
9683628 TCGAGCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (24 bp):
CGAGTTTGAGTCGAGATCGAGTCA
Found at i:9690210 original size:2 final size:2
Alignment explanation
Indices: 9690205--9690236 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9690195 GCCTCACACA
9690205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9690237 TGTGTTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9691180 original size:16 final size:16
Alignment explanation
Indices: 9691156--9691219 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
9691146 TCAGACAATC
* *
9691156 AAATGATTTCAAATTT
1 AAATTATTTTAAATTT
*
9691172 AAATTATTTTGAATTCT
1 AAATTATTTTAAATT-T
9691189 -AATTATTTTAAATTT
1 AAATTATTTTAAATTT
* *
9691204 GAGTTATTTTTAAATT
1 AAATTA-TTTTAAATT
9691220 CAAGACATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 29 0.73
17 10 0.25
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
AAATTATTTTAAATTT
Found at i:9699909 original size:10 final size:10
Alignment explanation
Indices: 9699894--9699923 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
9699884 ATCGAGTTTT
9699894 TATATTTTAA
1 TATATTTTAA
9699904 TATATTTTAA
1 TATATTTTAA
9699914 T-TATTTTAA
1 TATATTTTAA
9699923 T
1 T
9699924 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:9699920 original size:9 final size:9
Alignment explanation
Indices: 9699896--9699925 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
9699886 CGAGTTTTTA
9699896 TATTTTAAT
1 TATTTTAAT
9699905 ATATTTTAAT
1 -TATTTTAAT
9699915 TATTTTAAT
1 TATTTTAAT
9699924 TA
1 TA
9699926 ATAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:9702188 original size:22 final size:24
Alignment explanation
Indices: 9702141--9702186 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
9702131 CTTCACTTAG
9702141 TACCATCATCTCAAATCATTTTTTA
1 TACCATCATCTCAAATCA-TTTTTA
9702166 TACCATCATCTC-AATCATTTT
1 TACCATCATCTCAAATCATTTT
9702187 ATTAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
25 12 0.57
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.43
Consensus pattern (24 bp):
TACCATCATCTCAAATCATTTTTA
Found at i:9702742 original size:20 final size:20
Alignment explanation
Indices: 9702705--9702742 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9702695 TTAATTTAAT
*
9702705 TTAAATAAAAAATAAAAAGC
1 TTAAATAAAAAAAAAAAAGC
9702725 TTAAA-AAACAAAAAAAAA
1 TTAAATAAA-AAAAAAAAA
9702743 AAGAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (20 bp):
TTAAATAAAAAAAAAAAAGC
Found at i:9702779 original size:20 final size:20
Alignment explanation
Indices: 9702726--9702783 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
9702716 ATAAAAAGCT
* *
9702726 TAAAAAACAAAAAAAAAAAG
1 TAAAAAACAAATAAAATAAG
**
9702746 -AAAAAATC-TTTAAAATAAG
1 TAAAAAA-CAAATAAAATAAG
9702765 TAAAAAACAAATAAAATAA
1 TAAAAAACAAATAAAATAA
9702784 AAAGAAAGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (20 bp):
TAAAAAACAAATAAAATAAG
Found at i:9703285 original size:61 final size:65
Alignment explanation
Indices: 9703220--9703360 Score: 175
Period size: 61 Copynumber: 2.2 Consensus size: 65
9703210 ATAACAAACA
* * * *
9703220 CCTTGAATAATCTTCTTC-AATTTTTAT-GAGGGGATTATTAAAGGTGTTTT-GGC-AAAAAATG
1 CCTTGAATAATCTCCTTCTAATTTTTATAGAAGGGATAATTAAAGGTGTTTTAGGCAAAAAAAGG
* * *
9703281 CCTTGAATAATC-CCTTCTAATTTTTTTAGAAGGGATAATTCAAGGTGTTTTATGCAAAAAAAGG
1 CCTTGAATAATCTCCTTCTAATTTTTATAGAAGGGATAATTAAAGGTGTTTTAGGCAAAAAAAGG
*
9703345 CCTTCAATAATCTCCT
1 CCTTGAATAATCTCCT
9703361 CCCTTTTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
60 4 0.06
61 20 0.30
62 20 0.30
63 2 0.03
64 18 0.27
65 3 0.04
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (65 bp):
CCTTGAATAATCTCCTTCTAATTTTTATAGAAGGGATAATTAAAGGTGTTTTAGGCAAAAAAAGG
Found at i:9705218 original size:19 final size:19
Alignment explanation
Indices: 9705194--9705230 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9705184 AGAAAGCAAA
9705194 AAAAAAAAAAAAAAAAATC
1 AAAAAAAAAAAAAAAAATC
**
9705213 AAAAAAACCAAAAAAAAT
1 AAAAAAAAAAAAAAAAAT
9705231 GGTAAACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.05
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAATC
Found at i:9711936 original size:30 final size:30
Alignment explanation
Indices: 9711840--9711960 Score: 122
Period size: 30 Copynumber: 4.0 Consensus size: 30
9711830 ACTTTTATAT
* * *
9711840 CATTTAAAGAAATTTTTAATTTTTAATTTA
1 CATTCAAATAAATTCTTAATTTTTAATTTA
* *
9711870 CACTT-AAAT-AATCTATTAATCTTTAATTTA
1 CA-TTCAAATAAAT-TCTTAATTTTTAATTTA
*
9711900 CGTTCAAATAAATTCTTAATTTTTAATTTGA
1 CATTCAAATAAATTCTTAATTTTTAATTT-A
*
9711931 -ATTCAAATAAACTCTTATATTTTTAATTTA
1 CATTCAAATAAATTCTTA-ATTTTTAATTTA
9711961 TGCATAACAA
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
29 5 0.06
30 55 0.71
31 17 0.22
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (30 bp):
CATTCAAATAAATTCTTAATTTTTAATTTA
Found at i:9713688 original size:13 final size:13
Alignment explanation
Indices: 9713660--9713692 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
9713650 ATATATTATT
9713660 TTATTT-TTTGGA
1 TTATTTATTTGGA
*
9713672 TTATTTATTTTGA
1 TTATTTATTTGGA
9713685 TTATTTAT
1 TTATTTAT
9713693 GTCATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (13 bp):
TTATTTATTTGGA
Found at i:9715540 original size:27 final size:27
Alignment explanation
Indices: 9715510--9715562 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
9715500 AAGATATGAA
* *
9715510 ATTTTAAATTTTGAAAATTTTAATTTG
1 ATTTTAAATTTTGAAAAGTATAATTTG
* *
9715537 ATTTTAATTTTTTAAAAGTATAATTT
1 ATTTTAAATTTTGAAAAGTATAATTT
9715563 TTTATTAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (27 bp):
ATTTTAAATTTTGAAAAGTATAATTTG
Found at i:9716281 original size:20 final size:18
Alignment explanation
Indices: 9716241--9716276 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
9716231 ATAGGTGATC
*
9716241 GATCACACCTGGCCAAAA
1 GATCACACCTAGCCAAAA
9716259 GATCACACCTAGCCAAAA
1 GATCACACCTAGCCAAAA
9716277 AAGATTGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.14, T:0.11
Consensus pattern (18 bp):
GATCACACCTAGCCAAAA
Found at i:9717018 original size:2 final size:2
Alignment explanation
Indices: 9717011--9717079 Score: 65
Period size: 2 Copynumber: 36.0 Consensus size: 2
9717001 CAATACAATA
* * *
9717011 AT AT AT AT AT TT AT A- AT TT AT AT -T AT AT AA AT -T AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
9717051 AT AT AT AT AT AT AT AA AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9717080 TATCAATACT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
1 4 0.07
2 48 0.89
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9717045 original size:14 final size:13
Alignment explanation
Indices: 9717015--9717078 Score: 69
Period size: 13 Copynumber: 4.9 Consensus size: 13
9717005 ACAATAATAT
9717015 ATATATT-TATAA
1 ATATATTATATAA
*
9717027 TTTATATTATATAA
1 -ATATATTATATAA
* *
9717041 ATTATATGATATAT
1 A-TATATTATATAA
9717055 ATATA-TATATAA
1 ATATATTATATAA
9717067 ATATATTATATA
1 ATATATTATATA
9717079 TTATCAATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 10 0.24
13 16 0.38
14 16 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
ATATATTATATAA
Found at i:9717071 original size:25 final size:25
Alignment explanation
Indices: 9717029--9717079 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
9717019 ATTTATAATT
9717029 TATATTATATAAATTATATGATATA
1 TATATTATATAAATTATATGATATA
*
9717054 TATATATATATAAA-TATATTATATA
1 TATAT-TATATAAATTATATGATATA
9717079 T
1 T
9717080 TATCAATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TATATTATATAAATTATATGATATA
Found at i:9717197 original size:11 final size:12
Alignment explanation
Indices: 9717162--9717204 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
9717152 ATTTAGGGTT
9717162 AAAATT-GGAAA
1 AAAATTGGGAAA
* **
9717173 AATATTAAGAAA
1 AAAATTGGGAAA
9717185 AAAATTGGGAAA
1 AAAATTGGGAAA
9717197 AAAATTGG
1 AAAATTGG
9717205 CATGTATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 5 0.19
12 21 0.81
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (12 bp):
AAAATTGGGAAA
Found at i:9720409 original size:22 final size:22
Alignment explanation
Indices: 9720369--9720412 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
9720359 TGTGTGCTAA
9720369 ATTTGGAGTTTAGACTTTTAGG
1 ATTTGGAGTTTAGACTTTTAGG
*
9720391 ATTTGGGAGTTTGGA-TTTTAGG
1 ATTT-GGAGTTTAGACTTTTAGG
9720413 GTTTCACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.45
Consensus pattern (22 bp):
ATTTGGAGTTTAGACTTTTAGG
Found at i:9720485 original size:36 final size:36
Alignment explanation
Indices: 9720444--9720520 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
9720434 GGTTTTAGGG
* *
9720444 TTTAGT-TTTAAGATTTGAAGGGTTT-AGGGTTTTGAT
1 TTTAGTGTTTAAGATTT--AGGATTTAAGGGTTTGGAT
* *
9720480 TTTAGTGTTTGAGGTTTAGGATTTAAGGGTTTGGAT
1 TTTAGTGTTTAAGATTTAGGATTTAAGGGTTTGGAT
9720516 TTTAG
1 TTTAG
9720521 GGCTAAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 6 0.17
36 21 0.60
37 8 0.23
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (36 bp):
TTTAGTGTTTAAGATTTAGGATTTAAGGGTTTGGAT
Found at i:9722118 original size:27 final size:28
Alignment explanation
Indices: 9722088--9722152 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
9722078 TGGGCTTCGG
* *
9722088 GCCCAGTTGGA-TCAAATTGGGCCTAAA
1 GCCCAGTTGAAGTCAAATCGGGCCTAAA
* **
9722115 GCCCAATT-AAGTCAAATCGGGCCTGGA
1 GCCCAGTTGAAGTCAAATCGGGCCTAAA
9722142 GCCCAGTTGAA
1 GCCCAGTTGAA
9722153 CCGAAATCGG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.03
27 27 0.90
28 2 0.07
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (28 bp):
GCCCAGTTGAAGTCAAATCGGGCCTAAA
Found at i:9722874 original size:35 final size:35
Alignment explanation
Indices: 9722835--9723001 Score: 89
Period size: 35 Copynumber: 4.8 Consensus size: 35
9722825 AGATGACGAT
9722835 GATTGAACTACGAGTCAAAGAATAACGATGATTGG
1 GATTGAACTACGAGTCAAAGAATAACGATGATTGG
*
9722870 GATTGAA-T-CGTAAGTC-AAGTAATAATGATGATTGGG
1 GATTGAACTACG--AGTCAAAG-AATAACGATGATT-GG
* * * * **
9722906 GA-TGAGCCACAAGTCATAA-AATAATGA-GAACCGG
1 GATTGAACTACGAGTCA-AAGAATAACGATG-ATTGG
* ** * *
9722940 GATTAAACCGCGAGTCAAAGAATAA-TAAGATTGG
1 GATTGAACTACGAGTCAAAGAATAACGATGATTGG
**
9722974 GATTGAACTGTGAGTCATAA-AATAACGA
1 GATTGAACTACGAGTCA-AAGAATAACGA
9723002 CGACCAGGAT
Statistics
Matches: 101, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
33 2 0.02
34 34 0.34
35 58 0.57
36 4 0.04
37 3 0.03
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (35 bp):
GATTGAACTACGAGTCAAAGAATAACGATGATTGG
Found at i:9722989 original size:34 final size:34
Alignment explanation
Indices: 9722937--9723205 Score: 118
Period size: 34 Copynumber: 7.8 Consensus size: 34
9722927 TAATGAGAAC
* * *
9722937 CGGGATTAAACCGCGAGTCAAAGAATAATAAGAT
1 CGGGATTGAACTGTGAGTCAAAGAATAATAAGAT
* * * *
9722971 TGGGATTGAACTGTGAGTCATAA-AATAACGACGAC
1 CGGGATTGAACTGTGAGTCA-AAGAATAA-TAAGAT
* * * * *
9723006 CAGGATT-AAATCATGAGTCAGAGAATAATGAGAT
1 CGGGATTGAACT-GTGAGTCAAAGAATAATAAGAT
* * * * *
9723040 CGTGATTGAACCGTGTGTCAGAGAATAATGATGAT
1 CGGGATTGAACTGTGAGTCAAAGAATAAT-AAGAT
* * * * * * *
9723075 TGGGATTAAACCGTGAGTTAGAGAATAATGAGGT
1 CGGGATTGAACTGTGAGTCAAAGAATAATAAGAT
* ** * * *
9723109 TGGGATTGAACCATTAGTCATAA-AATAACGACGAT
1 CGGGATTGAACTGTGAGTCA-AAGAATAA-TAAGAT
* * *
9723144 CGGGATT-AAATCGTGAGTCAGAGAATAATGAGAT
1 CGGGATTGAACT-GTGAGTCAAAGAATAATAAGAT
9723178 CGGGATTGAA-TCGTGAGTCATAA-AATAA
1 CGGGATTGAACT-GTGAGTCA-AAGAATAA
9723206 CGTCGACAGG
Statistics
Matches: 172, Mismatches: 51, Indels: 24
0.70 0.21 0.10
Matches are distributed among these distances:
34 98 0.57
35 74 0.43
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (34 bp):
CGGGATTGAACTGTGAGTCAAAGAATAATAAGAT
Found at i:9723012 original size:69 final size:69
Alignment explanation
Indices: 9722917--9723240 Score: 380
Period size: 69 Copynumber: 4.7 Consensus size: 69
9722907 ATGAGCCACA
* * * * * *
9722917 AGTCATAAAATAATGA-GAACCGGGATTAAACCGCGAGTCAAAGAATAATAAGATTGGGATTGAA
1 AGTCATAAAATAACGACG-ACCGGGATTAAATCGTGAGTCAGAGAATAATGAGATCGGGATTGAA
*
9722981 CTGTG
65 CCGTG
* * *
9722986 AGTCATAAAATAACGACGACCAGGATTAAATCATGAGTCAGAGAATAATGAGATCGTGATTGAAC
1 AGTCATAAAATAACGACGACCGGGATTAAATCGTGAGTCAGAGAATAATGAGATCGGGATTGAAC
9723051 CGTG
66 CGTG
* * * * * ** * * * *
9723055 TGTCAGAGAATAATGATGATTGGGATTAAACCGTGAGTTAGAGAATAATGAGGTTGGGATTGAAC
1 AGTCATAAAATAACGACGACCGGGATTAAATCGTGAGTCAGAGAATAATGAGATCGGGATTGAAC
* *
9723120 CATT
66 CGTG
* *
9723124 AGTCATAAAATAACGACGATCGGGATTAAATCGTGAGTCAGAGAATAATGAGATCGGGATTGAAT
1 AGTCATAAAATAACGACGACCGGGATTAAATCGTGAGTCAGAGAATAATGAGATCGGGATTGAAC
9723189 CGTG
66 CGTG
* * *
9723193 AGTCATAAAATAACGTCGACAGGGATTAAATCGTGAATCAGAGAATAA
1 AGTCATAAAATAACGACGACCGGGATTAAATCGTGAGTCAGAGAATAA
9723241 ATGTGACCAA
Statistics
Matches: 211, Mismatches: 43, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
69 210 1.00
70 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.23
Consensus pattern (69 bp):
AGTCATAAAATAACGACGACCGGGATTAAATCGTGAGTCAGAGAATAATGAGATCGGGATTGAAC
CGTG
Found at i:9723033 original size:35 final size:34
Alignment explanation
Indices: 9722925--9723240 Score: 240
Period size: 35 Copynumber: 9.1 Consensus size: 34
9722915 CAAGTCATAA
* * * *
9722925 AATAATGAGAACCGGGATTAAACCGCGAGTCAAAG
1 AATAATGAG-ATCGGGATTAAATCGTGAGTCAGAG
* * * * *
9722960 AATAATAAGATTGGGATTGAA-CTGTGAGTCATAA
1 AATAATGAGATCGGGATTAAATC-GTGAGTCAGAG
* * * *
9722994 AATAACGACGACCAGGATTAAATCATGAGTCAGAG
1 AATAATGA-GATCGGGATTAAATCGTGAGTCAGAG
* * * *
9723029 AATAATGAGATCGTGATTGAACCGTGTGTCAGAG
1 AATAATGAGATCGGGATTAAATCGTGAGTCAGAG
* * *
9723063 AATAATGATGATTGGGATTAAACCGTGAGTTAGAG
1 AATAATGA-GATCGGGATTAAATCGTGAGTCAGAG
* * * * * * * *
9723098 AATAATGAGGTTGGGATTGAACCATTAGTCATAA
1 AATAATGAGATCGGGATTAAATCGTGAGTCAGAG
*
9723132 AATAACGACGATCGGGATTAAATCGTGAGTCAGAG
1 AATAATGA-GATCGGGATTAAATCGTGAGTCAGAG
* * *
9723167 AATAATGAGATCGGGATTGAATCGTGAGTCATAA
1 AATAATGAGATCGGGATTAAATCGTGAGTCAGAG
* * *
9723201 AATAACGTCGA-CAGGGATTAAATCGTGAATCAGAG
1 AATAATG-AGATC-GGGATTAAATCGTGAGTCAGAG
9723236 AATAA
1 AATAA
9723241 ATGTGACCAA
Statistics
Matches: 219, Mismatches: 55, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
33 1 0.00
34 106 0.48
35 111 0.51
36 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (34 bp):
AATAATGAGATCGGGATTAAATCGTGAGTCAGAG
Found at i:9735790 original size:22 final size:22
Alignment explanation
Indices: 9735739--9735793 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
9735729 GGGTTTAGAC
* *
9735739 TTTTAGGATTTGGGATTTTGGA
1 TTTTAGGGTTTGGAATTTTGGA
9735761 TTTTAGGGTTTGGAATTTTGGA
1 TTTTAGGGTTTGGAATTTTGGA
9735783 TTTTAGGGTTT
1 TTTTAGGGTTT
9735794 TGATTTCGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (22 bp):
TTTTAGGGTTTGGAATTTTGGA
Found at i:9735830 original size:22 final size:22
Alignment explanation
Indices: 9735805--9735847 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9735795 GATTTCGGGG
9735805 TTTAAAGGTTTG-AGGGTTTAGT
1 TTTAAA-GTTTGAAGGGTTTAGT
9735827 TTTAAAGTTTGAAGGGTTTAG
1 TTTAAAGTTTGAAGGGTTTAG
9735848 GGTTTTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (22 bp):
TTTAAAGTTTGAAGGGTTTAGT
Found at i:9735860 original size:30 final size:29
Alignment explanation
Indices: 9735784--9735876 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 29
9735774 AATTTTGGAT
** * *
9735784 TTTAGGGTTTTGATTTCGGGGTTTAAAGG
1 TTTAGGGTTTTGATTTTAGAGTTTGAAGG
* *
9735813 TTTGAGGGTTTAG-TTTTAAAGTTTGAAGGG
1 TTT-AGGGTTTTGATTTTAGAGTTTGAA-GG
*
9735843 TTTAGGGTTTTGATTTTAGTGTTTG-AGG
1 TTTAGGGTTTTGATTTTAGAGTTTGAAGG
9735871 TTTAGG
1 TTTAGG
9735877 ATTTAAGGGT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
28 8 0.15
29 21 0.40
30 23 0.44
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.47
Consensus pattern (29 bp):
TTTAGGGTTTTGATTTTAGAGTTTGAAGG
Found at i:9735888 original size:22 final size:22
Alignment explanation
Indices: 9735838--9735889 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
9735828 TTAAAGTTTG
*
9735838 AAGGGTTT-AGGGTTTTGATTT
1 AAGGGTTTGAGGGTTTGGATTT
* *
9735859 TAGTGTTTGA-GGTTTAGGATTT
1 AAGGGTTTGAGGGTTT-GGATTT
9735881 AAGGGTTTG
1 AAGGGTTTG
9735890 TATTTTAGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (22 bp):
AAGGGTTTGAGGGTTTGGATTT
Found at i:9735997 original size:3 final size:3
Alignment explanation
Indices: 9735989--9736019 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
9735979 AAAAATTAAC
9735989 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9736020 AAAGAGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9740061 original size:22 final size:22
Alignment explanation
Indices: 9740015--9740061 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
9740005 TAATTTCAAC
*
9740015 AAAAATCTATTTTTTTTTCTTA
1 AAAAATCTATTTTTTTTTCTGA
*
9740037 AAAAATCTGTTTTTTTTGT-TGA
1 AAAAATCTATTTTTTTT-TCTGA
9740059 AAA
1 AAA
9740062 TTTATTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (22 bp):
AAAAATCTATTTTTTTTTCTGA
Found at i:9740702 original size:13 final size:13
Alignment explanation
Indices: 9740684--9740709 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9740674 AATAATATAA
9740684 TAAATAATTTTAT
1 TAAATAATTTTAT
9740697 TAAATAATTTTAT
1 TAAATAATTTTAT
9740710 ATTCCTCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAATAATTTTAT
Found at i:9742654 original size:2 final size:2
Alignment explanation
Indices: 9742647--9742685 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9742637 CTTTCGATCG
9742647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9742686 GATTAACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9745157 original size:7 final size:6
Alignment explanation
Indices: 9745145--9745191 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
9745135 TTGACTTTGG
* *
9745145 TTTTAA TTTTTAA TTTTGA TTTTAGT TTTTAA TTTTAA TTTT-A TTTT
1 TTTTAA -TTTTAA TTTTAA TTTTA-A TTTTAA TTTTAA TTTTAA TTTT
9745192 TGGTCAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 5 0.14
6 19 0.54
7 11 0.31
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (6 bp):
TTTTAA
Found at i:9745162 original size:19 final size:19
Alignment explanation
Indices: 9745140--9745192 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
9745130 TGATTTTGAC
*
9745140 TTTGGTTTTAATTTTTAAT
1 TTTGATTTTAATTTTTAAT
*
9745159 TTTGATTTTAGTTTTTAAT
1 TTTGATTTTAATTTTTAAT
*
9745178 TTTAATTTT-ATTTTT
1 TTTGATTTTAATTTTT
9745193 GGTCAAAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 5 0.17
19 25 0.83
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTGATTTTAATTTTTAAT
Found at i:9745172 original size:25 final size:25
Alignment explanation
Indices: 9745122--9745191 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
9745112 AACTCCAAAA
* * *
9745122 TTTTAA-TTTGATTTTGACTTT-GG
1 TTTTAATTTTAATTTTGATTTTAGT
9745145 TTTTAATTTTTAATTTTGATTTTAGT
1 TTTTAA-TTTTAATTTTGATTTTAGT
9745171 TTTTAATTTTAATTTT-ATTTT
1 TTTTAATTTTAATTTTGATTTT
9745192 TGGTCAAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 6 0.15
24 5 0.12
25 23 0.56
26 7 0.17
ACGTcount: A:0.21, C:0.01, G:0.09, T:0.69
Consensus pattern (25 bp):
TTTTAATTTTAATTTTGATTTTAGT
Found at i:9746293 original size:12 final size:13
Alignment explanation
Indices: 9746265--9746297 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
9746255 TTTATTTTAT
9746265 TTTATTTTTGGGA
1 TTTATTTTTGGGA
*
9746278 TTTATTTTT-GGC
1 TTTATTTTTGGGA
9746290 TTTATTTT
1 TTTATTTT
9746298 ATTTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.70
Consensus pattern (13 bp):
TTTATTTTTGGGA
Found at i:9752506 original size:23 final size:23
Alignment explanation
Indices: 9752480--9752525 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
9752470 GAGATTACTT
* *
9752480 GATAGTATATGATATCCCATATG
1 GATAGTACATGATAACCCATATG
9752503 GATAGTACATGATAACCCATATG
1 GATAGTACATGATAACCCATATG
9752526 ATATGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (23 bp):
GATAGTACATGATAACCCATATG
Found at i:9752865 original size:13 final size:13
Alignment explanation
Indices: 9752847--9752871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9752837 AAAATCTTTT
9752847 CATTCATTACATG
1 CATTCATTACATG
9752860 CATTCATTACAT
1 CATTCATTACAT
9752872 ACGTTTGGAA
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:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (13 bp):
CATTCATTACATG
Found at i:9753443 original size:6 final size:6
Alignment explanation
Indices: 9753434--9753511 Score: 66
Period size: 6 Copynumber: 12.5 Consensus size: 6
9753424 AAAATTTTAA
* * * * *
9753434 TTTGAT TTTGAT TTTGAT CTTAAT TTTAAT TTTGATT TTTAATT TTTAAT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGA-T TTTGA-T TTTGAT
* *
9753484 TTTGAT TTTGGT TTTAAAT TTTGAT TTT
1 TTTGAT TTTGAT TTT-GAT TTTGAT TTT
9753512 AGTTTTGGTC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
6 44 0.73
7 16 0.27
ACGTcount: A:0.22, C:0.01, G:0.10, T:0.67
Consensus pattern (6 bp):
TTTGAT
Found at i:9753475 original size:13 final size:13
Alignment explanation
Indices: 9753457--9753511 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
9753447 TTGATCTTAA
9753457 TTTTAATTTTGAT
1 TTTTAATTTTGAT
* *
9753470 TTTTAATTTTTAA
1 TTTTAATTTTGAT
* *
9753483 TTTTGATTTTGGT
1 TTTTAATTTTGAT
*
9753496 TTTAAATTTTGAT
1 TTTTAATTTTGAT
9753509 TTT
1 TTT
9753512 AGTTTTGGTC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (13 bp):
TTTTAATTTTGAT
Found at i:9753477 original size:19 final size:18
Alignment explanation
Indices: 9753438--9753517 Score: 88
Period size: 19 Copynumber: 4.3 Consensus size: 18
9753428 TTTTAATTTG
* *
9753438 ATTTTGATTTTGATCTTA
1 ATTTTAATTTTGATTTTA
9753456 ATTTTAATTTTGATTTTTA
1 ATTTTAATTTTGA-TTTTA
*
9753475 ATTTTTAATTTTGATTTTG
1 A-TTTTAATTTTGATTTTA
*
9753494 GTTTTAAATTTTGATTTTA
1 ATTTT-AATTTTGATTTTA
*
9753513 GTTTT
1 ATTTT
9753518 GGTCAAAGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.30
19 26 0.48
20 12 0.22
ACGTcount: A:0.23, C:0.01, G:0.10, T:0.66
Consensus pattern (18 bp):
ATTTTAATTTTGATTTTA
Found at i:9753505 original size:7 final size:6
Alignment explanation
Indices: 9753426--9753517 Score: 60
Period size: 6 Copynumber: 15.0 Consensus size: 6
9753416 AAAGCTCGAA
* * * * *
9753426 AATTTT AA-TTT GATTTT GATTTT GATCTT AATTTT AATTTT GATTTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT -AATTTT
* ** * *
9753474 AATTTTT AATTTT GATTTT GGTTTT AAATTTT GATTTT AGTTTT
1 AA-TTTT AATTTT AATTTT AATTTT -AATTTT AATTTT AATTTT
9753518 GGTCAAAGTA
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
5 4 0.06
6 50 0.72
7 15 0.22
ACGTcount: A:0.24, C:0.01, G:0.10, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:9753547 original size:12 final size:11
Alignment explanation
Indices: 9753522--9753546 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9753512 AGTTTTGGTC
9753522 AAAGTAAAAAA
1 AAAGTAAAAAA
9753533 AAAGTAAAAAA
1 AAAGTAAAAAA
9753544 AAA
1 AAA
9753547 AAGAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGTAAAAAA
Found at i:9754704 original size:19 final size:19
Alignment explanation
Indices: 9754691--9754787 Score: 131
Period size: 19 Copynumber: 5.1 Consensus size: 19
9754681 GATTTGCATA
*
9754691 ATTATTTATTATTTACATG
1 ATTAATTATTATTTACATG
*
9754710 ATTAATTATTAATTACATG
1 ATTAATTATTATTTACATG
*
9754729 ATTAATTATTATCTACATG
1 ATTAATTATTATTTACATG
*
9754748 ATTAATTATTATTTGCATG
1 ATTAATTATTATTTACATG
* * *
9754767 ATTATTTATTAATTGCATG
1 ATTAATTATTATTTACATG
9754786 AT
1 AT
9754788 ATTTTATATT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 70 1.00
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (19 bp):
ATTAATTATTATTTACATG
Found at i:9754794 original size:19 final size:19
Alignment explanation
Indices: 9754684--9754791 Score: 112
Period size: 19 Copynumber: 5.7 Consensus size: 19
9754674 ATTGCATGAT
* *
9754684 TTGCATAATTATTTATTAT
1 TTGCATGATTATTTATTAA
* *
9754703 TTACATGATTAATTATTAA
1 TTGCATGATTATTTATTAA
* *
9754722 TTACATGATTAATTATT-A
1 TTGCATGATTATTTATTAA
* * *
9754740 TCTACATGATTAATTATTAT
1 T-TGCATGATTATTTATTAA
9754760 TTGCATGATTATTTATTAA
1 TTGCATGATTATTTATTAA
9754779 TTGCATGA-TATTT
1 TTGCATGATTATTT
9754792 TATATTATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.09
19 71 0.90
20 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.52
Consensus pattern (19 bp):
TTGCATGATTATTTATTAA
Found at i:9763674 original size:30 final size:30
Alignment explanation
Indices: 9763638--9763698 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
9763628 TTAAAGACAA
9763638 AAATTCATATACTCTAATAAATTATTAAAT
1 AAATTCATATACTCTAATAAATTATTAAAT
*
9763668 AAATTCATATATTCTAATAAATTATTAAAT
1 AAATTCATATACTCTAATAAATTATTAAAT
9763698 A
1 A
9763699 TTTTATGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATTCATATACTCTAATAAATTATTAAAT
Found at i:9763688 original size:18 final size:17
Alignment explanation
Indices: 9763638--9763690 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
9763628 TTAAAGACAA
9763638 AAATTCATATACTCTAAT
1 AAATTCATATA-TCTAAT
9763656 AAATT-AT-TA---AAT
1 AAATTCATATATCTAAT
9763668 AAATTCATATATTCTAAT
1 AAATTCATATA-TCTAAT
9763686 AAATT
1 AAATT
9763691 ATTAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
12 8 0.28
13 2 0.07
14 2 0.07
16 2 0.07
17 2 0.07
18 13 0.45
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTCATATATCTAAT
Found at i:9764862 original size:127 final size:127
Alignment explanation
Indices: 9764636--9764896 Score: 522
Period size: 127 Copynumber: 2.1 Consensus size: 127
9764626 TTGGCAAAAT
9764636 GAAAATGGTAAAAGCTAAAACCTTATGGCAAGTTAATTAAGGTTGTAATCAAAACATTATGAGTG
1 GAAAATGGTAAAAGCTAAAACCTTATGGCAAGTTAATTAAGGTTGTAATCAAAACATTATGAGTG
9764701 GAGACTATTATTGCATCTCTAATTGGTTTATGGATTAGTGTTGTAGCGGCATAATCACCTAA
66 GAGACTATTATTGCATCTCTAATTGGTTTATGGATTAGTGTTGTAGCGGCATAATCACCTAA
9764763 GAAAATGGTAAAAGCTAAAACCTTATGGCAAGTTAATTAAGGTTGTAATCAAAACATTATGAGTG
1 GAAAATGGTAAAAGCTAAAACCTTATGGCAAGTTAATTAAGGTTGTAATCAAAACATTATGAGTG
9764828 GAGACTATTATTGCATCTCTAATTGGTTTATGGATTAGTGTTGTAGCGGCATAATCACCTAA
66 GAGACTATTATTGCATCTCTAATTGGTTTATGGATTAGTGTTGTAGCGGCATAATCACCTAA
9764890 GAAAATG
1 GAAAATG
9764897 TCCTTTGACT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 134 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (127 bp):
GAAAATGGTAAAAGCTAAAACCTTATGGCAAGTTAATTAAGGTTGTAATCAAAACATTATGAGTG
GAGACTATTATTGCATCTCTAATTGGTTTATGGATTAGTGTTGTAGCGGCATAATCACCTAA
Found at i:9767235 original size:82 final size:81
Alignment explanation
Indices: 9767086--9767235 Score: 214
Period size: 82 Copynumber: 1.8 Consensus size: 81
9767076 TTGCATCATA
* * * *
9767086 AAAACATCAGCTATTCTGCTTGAACTAAAATGAAACTGTTCTAGTTGAAATGCTGTAGTAATGCC
1 AAAACATCAGCTATTCTGCTTGAACTAAAATAAAACTGTTCTAGCTGAAATGCTGTACTAATCCC
9767151 CATATTTACACTACTT
66 CATATTTACACTACTT
*
9767167 AAAACATCAGCTATTCTGC-TGAAACTAATATAAAAACTGTTCTAGCTGAAATGCTGTAACT-AT
1 AAAACATCAGCTATTCTGCTTG-AACTAAAAT-AAAACTGTTCTAGCTGAAATGCTGT-ACTAAT
9767230 CCCCAT
63 CCCCAT
9767236 GCATAAGCAT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
80 2 0.03
81 27 0.44
82 30 0.49
83 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (81 bp):
AAAACATCAGCTATTCTGCTTGAACTAAAATAAAACTGTTCTAGCTGAAATGCTGTACTAATCCC
CATATTTACACTACTT
Found at i:9771250 original size:22 final size:24
Alignment explanation
Indices: 9771222--9771265 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9771212 AAATTTTTAA
9771222 TATAAAT-T-ATATTTTAATTATG
1 TATAAATATAATATTTTAATTATG
*
9771244 TATAAATATAATATTTTTATTA
1 TATAAATATAATATTTTAATTA
9771266 AATTAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TATAAATATAATATTTTAATTATG
Found at i:9772057 original size:121 final size:121
Alignment explanation
Indices: 9771783--9772059 Score: 322
Period size: 121 Copynumber: 2.3 Consensus size: 121
9771773 GTTTGGCATG
* * * *
9771783 AAAAACACCTTAAATAATCTTGTTCAATTTTTTGAGAGATTATTTAAGGTGTTTTTTTATCAGAA
1 AAAAACGCCTTAAATAATCTTGTTCAA-TTTTTGAGAGATTATTTAAGGTG-TTTATGACCAGAA
* * * * * *
9771848 AATACCTTAAATAATCTCTTAAATAAAGTAATTAATATTATTTAAGGCTTTTTCTAAT
64 AACACCTTAAATAATCTCCTAAATAAAGTAACTAACATTATTTAAGCCGTTTTCTAAT
* * * * * *
9771906 AAAAATGCCTTAAATAATTTTATTCAAATTTTTGTGAGATTATTTAAGGTG-TTATGGCCAGATA
1 AAAAACGCCTTAAATAATCTTGTTC-AATTTTTGAGAGATTATTTAAGGTGTTTATGACCAGAAA
* * * *
9771970 ACACCTTAAATAATCTCCTAAATAAATTGACTAGCATTATTTAAGCCGTTTTCTGAT
65 ACACCTTAAATAATCTCCTAAATAAAGTAACTAACATTATTTAAGCCGTTTTCTAAT
*
9772027 CAAAAACGCCTTAAATAATCTCGTTCAATTTTT
1 -AAAAACGCCTTAAATAATCTTGTTCAATTTTT
9772060 TTTAGTCAAA
Statistics
Matches: 128, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
121 62 0.48
122 21 0.16
123 43 0.34
124 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (121 bp):
AAAAACGCCTTAAATAATCTTGTTCAATTTTTGAGAGATTATTTAAGGTGTTTATGACCAGAAAA
CACCTTAAATAATCTCCTAAATAAAGTAACTAACATTATTTAAGCCGTTTTCTAAT
Found at i:9772363 original size:127 final size:125
Alignment explanation
Indices: 9772078--9772472 Score: 311
Period size: 127 Copynumber: 3.1 Consensus size: 125
9772068 AAAATATCTT
* * * *
9772078 AAATAATCTTTTATAAAAAA-TTGTACGATGATTATTTAAGGT-TTTTTTGCTAGAAAATGCATT
1 AAATAATCATTTA-AAAAAATTTATACGAAGATTATTTAAGGTATTTTTTGCTAGAAAACGCATT
* * *
9772141 GAATAATCCTATTTAATTTTTTAAATGATTATTTAAGGCATATTTTACCCAAAAAGGCCTA
65 GAATAATCCTATTCAATTTTTTAAATGATTACTTAAGGCATATTTTACCAAAAAAGGCCTA
* * * * *
9772202 AAATAATCTTTTAAAAAAATTTGTACGAAAATTATTTATGGTATTTTTTG-TCAGAAAACGCTTT
1 AAATAATCATTTAAAAAAATTTATACGAAGATTATTTAAGGTATTTTTTGCT-AGAAAACGCATT
* * * *
9772266 GAATAAT-CTCATTCAATTTTTTTAAA-GATTTACTTAAGG-TTGTTTTTCACTAAAAAATGCCT
65 GAATAATCCT-ATTCAA-TTTTTTAAATGA-TTACTTAAGGCAT-ATTTT-ACCAAAAAAGGCCT
*
9772328 T
125 A
* * ** * ** * * *
9772329 AAATAATCATTTGAAAAAATTTATGCGGGGATTATTTAAGATATTTTCAGCTAGAAAACACTTTA
1 AAATAATCATTTAAAAAAATTTATACGAAGATTATTTAAGGTATTTTTTGCTAGAAAACGCATTG
* * * * * * * * *
9772394 AATACTCCCATTAAATTTTTTGAGAGGATTATTTAAGGCATTATTTAACCTAAAATA--CCTT
66 AATAATCCTATTCAATTTTTT-AAATGATTACTTAAGGCA-TATTTTACC-AAAAAAGGCCTA
*
9772455 AAATAATCCTTTAAAAAA
1 AAATAATCATTTAAAAAA
9772473 TTTTTAATAT
Statistics
Matches: 218, Mismatches: 38, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
123 6 0.03
124 35 0.16
125 32 0.15
126 48 0.22
127 84 0.39
128 12 0.06
129 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (125 bp):
AAATAATCATTTAAAAAAATTTATACGAAGATTATTTAAGGTATTTTTTGCTAGAAAACGCATTG
AATAATCCTATTCAATTTTTTAAATGATTACTTAAGGCATATTTTACCAAAAAAGGCCTA
Found at i:9772520 original size:189 final size:189
Alignment explanation
Indices: 9772317--9772713 Score: 437
Period size: 189 Copynumber: 2.1 Consensus size: 189
9772307 GTTTTTCACT
* * * * *
9772317 AAAAAATGCCTTAAATAATCATTTGAAAAAATTTATGCGGGGATTATTTAA-G-ATATTTTCAGC
1 AAAAAATACCTTAAATAATCATTTAAAAAAATTTATACAGGGATTATTGAATGTAT-TTTTCAGC
* * * * * * *
9772380 TAGAAAACACTTTAAATACTCCCATTAAATTTTTTG-AGAGGATTATTTAAGGCATTATT-TAAC
65 CAAAAAACACATTAAATAATCCCATTAAATTTTTTGAAG-GGATTACTGAAAGCATT-TTCTAA-
*
9772443 CT-AAAATACCTTAAATAATCCTTTAAAAAATTTTT-AATATGATTATTTAAGACATTTTCTATC
127 -TAAAAATACCTTAAATAATCCTTT-AAAAATTTTTGAATAGGATTATTTAAGACATTTTCTATC
* * * **
9772506 CAAAAATACCTTAAATAATCTTTTAAAAAAATTTGTACAGGGATTATTGAATGTATTTTTTGGCC
1 AAAAAATACCTTAAATAATCATTTAAAAAAATTTATACAGGGATTATTGAATGTATTTTTCAGCC
* * * * *
9772571 AAAAAACACATTGAATAATCTCATTCAATTTTTTGAAGGGATTACTGAAAGTATTTTCTGATAAA
66 AAAAAACACATTAAATAATCCCATTAAATTTTTTGAAGGGATTACTGAAAGCATTTTCTAATAAA
** * * * *
9772636 AATGTCTTAAATAATCCTTTAAAAATTTTTGTATAGGATTATTTAAGACGTTTTTTATT
131 AATACCTTAAATAATCCTTTAAAAATTTTTGAATAGGATTATTTAAGACATTTTCTATC
9772695 AAAAAATACCTTAAATAAT
1 AAAAAATACCTTAAATAAT
9772714 TCTTTTTAAT
Statistics
Matches: 172, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
188 11 0.06
189 106 0.62
190 51 0.30
191 4 0.02
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (189 bp):
AAAAAATACCTTAAATAATCATTTAAAAAAATTTATACAGGGATTATTGAATGTATTTTTCAGCC
AAAAAACACATTAAATAATCCCATTAAATTTTTTGAAGGGATTACTGAAAGCATTTTCTAATAAA
AATACCTTAAATAATCCTTTAAAAATTTTTGAATAGGATTATTTAAGACATTTTCTATC
Found at i:9772573 original size:64 final size:63
Alignment explanation
Indices: 9772418--9772718 Score: 152
Period size: 63 Copynumber: 4.8 Consensus size: 63
9772408 ATTTTTTGAG
* * * * *
9772418 AGGATTATTTAAGGCATTATT-TAACCTAAAATACCTTAAATAATCCTTTAAAAAATTTTTAAT
1 AGGATTATTGAAGACATT-TTCTAGCCAAAAATACCTTAAATAATCCTTTAAAAAATTTGTAAT
* * * *
9772481 ATGATTATTTAAGACATTTTCTATCCAAAAATACCTTAAATAATCTTTTAAAAAAATTTGTACA-
1 AGGATTATTGAAGACATTTTCTAGCCAAAAATACCTTAAATAATCCTTT-AAAAAATTTGTA-AT
* * * * * * * ***
9772545 GGGATTATTGAATG-TATTTTTTGGCCAAAAA-ACACATTGAATAATCTCATTCAATTTTTTG-A
1 AGGATTATTGAA-GACATTTTCTAGCCAAAAATAC-C-TTAAATAATC-CTTTAAAAAATTTGTA
9772607 A-
62 AT
* * * ** ** *
9772608 GGGATTACTGAA-AGTATTTTCT-GATAAAAATGTCTTAAATAATCCTTTAAAAATTTTTGT-AT
1 AGGATTATTGAAGA-CATTTTCTAGCCAAAAATACCTTAAATAATCCTTTAAAAA-ATTTGTAAT
* * * *** *
9772670 AGGATTATTTAAGACGTTTTTTATTAAAAAATACCTTAAATAATTCTTT
1 AGGATTATTGAAGACATTTTCTAGCCAAAAATACCTTAAATAATCCTTT
9772719 TTAATTTTTA
Statistics
Matches: 180, Mismatches: 43, Indels: 30
0.71 0.17 0.12
Matches are distributed among these distances:
60 5 0.03
61 15 0.08
62 23 0.13
63 83 0.46
64 35 0.19
65 17 0.09
66 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (63 bp):
AGGATTATTGAAGACATTTTCTAGCCAAAAATACCTTAAATAATCCTTTAAAAAATTTGTAAT
Found at i:9772885 original size:61 final size:61
Alignment explanation
Indices: 9772797--9772913 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 61
9772787 TTTTTTAAAA
* *
9772797 GATTATTCAAGGCTTTTTTGACAAAAAATCGTCTTAAATAATC-AAAAAAAAAATTGAATGG
1 GATTATTCAAGGCTTTTCTGACAAAAAAT-GCCTTAAATAATCTAAAAAAAAAATTGAATGG
* *
9772858 GATTATTTAAGGCATTTTCTGACAAAAAATGCCTTAAATAATCTAATAAAAAAATT
1 GATTATTCAAGGC-TTTTCTGACAAAAAATGCCTTAAATAATCTAAAAAAAAAATT
9772914 CATCAATGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
61 24 0.48
62 26 0.52
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.32
Consensus pattern (61 bp):
GATTATTCAAGGCTTTTCTGACAAAAAATGCCTTAAATAATCTAAAAAAAAAATTGAATGG
Found at i:9773813 original size:16 final size:17
Alignment explanation
Indices: 9773784--9773822 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
9773774 AAAAATTTAA
*
9773784 TAAAAACAATTAAAAAT
1 TAAAAACAACTAAAAAT
*
9773801 TAAAAA-AACTAAAACT
1 TAAAAACAACTAAAAAT
9773817 TAAAAA
1 TAAAAA
9773823 TTAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAACAACTAAAAAT
Found at i:9773835 original size:21 final size:20
Alignment explanation
Indices: 9773772--9773835 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 20
9773762 CCATACATAG
* *
9773772 TTAAAAATTTAATAAAAACAA
1 TTAAAAA-TTAAAAAAAAAAA
9773793 TTAAAAATTAAAAAAACTAAAA
1 TTAAAAATTAAAAAAA--AAAA
9773815 CTTAAAAATTAAAAAAAAAAA
1 -TTAAAAATTAAAAAAAAAAA
9773836 ACCTAAGCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.21
21 11 0.29
22 3 0.08
23 16 0.42
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (20 bp):
TTAAAAATTAAAAAAAAAAA
Found at i:9774236 original size:11 final size:11
Alignment explanation
Indices: 9774220--9774244 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9774210 TATCTTATTA
9774220 AAAAAAAAAAG
1 AAAAAAAAAAG
9774231 AAAAAAAAAAG
1 AAAAAAAAAAG
9774242 AAA
1 AAA
9774245 TAGAGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:9779940 original size:34 final size:34
Alignment explanation
Indices: 9779850--9779929 Score: 108
Period size: 33 Copynumber: 2.3 Consensus size: 34
9779840 TGATATGATA
*
9779850 AAAATTTTTATAAAAATTTATAAAAATAATATAATTT
1 AAAATTTTAATAAAAA--TA-AAAAATAATATAATTT
*
9779887 AAAATTTTAATAAAAATAAAAAAT-ATATATTTT
1 AAAATTTTAATAAAAATAAAAAATAATATAATTT
9779920 AAAATTTTAA
1 AAAATTTTAA
9779930 ATCAATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
33 18 0.44
34 6 0.15
35 2 0.05
37 15 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAAATTTTAATAAAAATAAAAAATAATATAATTT
Found at i:9788819 original size:19 final size:20
Alignment explanation
Indices: 9788781--9788824 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
9788771 AATAAATTTA
*
9788781 TGAAAAGTTATAAATTTTTT
1 TGAAAAGTCATAAATTTTTT
*
9788801 TGAAAAGTCA-AACTTTTTT
1 TGAAAAGTCATAAATTTTTT
*
9788820 GGAAA
1 TGAAA
9788825 TAGGTTTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (20 bp):
TGAAAAGTCATAAATTTTTT
Found at i:9789544 original size:34 final size:35
Alignment explanation
Indices: 9789495--9789570 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
9789485 AATCTTCCAG
9789495 AAATCCATTTATGAAAAA-TTATATGACTTTTTAA
1 AAATCCATTTATGAAAAAGTTATATGACTTTTTAA
* * * * **
9789529 AAATTCATTTTTGAAAAAGTTTTATTACTTTTTGT
1 AAATCCATTTATGAAAAAGTTATATGACTTTTTAA
9789564 AAATCCA
1 AAATCCA
9789571 ATTTCAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
34 16 0.47
35 18 0.53
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (35 bp):
AAATCCATTTATGAAAAAGTTATATGACTTTTTAA
Found at i:9789926 original size:9 final size:9
Alignment explanation
Indices: 9789914--9789970 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 9
9789904 AACATTAATT
9789914 TAATAAAAA
1 TAATAAAAA
9789923 TAAT--AAA
1 TAATAAAAA
9789930 T-ATAACAAA
1 TAATAA-AAA
9789939 -AATAAAAA
1 TAATAAAAA
*
9789947 TAATAAATA
1 TAATAAAAA
**
9789956 TAGCAAAAA
1 TAATAAAAA
9789965 TAATAA
1 TAATAA
9789971 CTTATTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
6 2 0.05
7 4 0.11
8 3 0.08
9 28 0.76
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (9 bp):
TAATAAAAA
Found at i:9789947 original size:24 final size:24
Alignment explanation
Indices: 9789915--9789967 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
9789905 ACATTAATTT
9789915 AATAAAAATAATAAATATAACAAA
1 AATAAAAATAATAAATATAACAAA
*
9789939 AATAAAAATAATAAATATAGCAAA
1 AATAAAAATAATAAATATAACAAA
9789963 AATAA
1 AATAA
9789968 TAACTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (24 bp):
AATAAAAATAATAAATATAACAAA
Found at i:9790628 original size:17 final size:17
Alignment explanation
Indices: 9790606--9790645 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
9790596 TTTCATGTCT
9790606 AATATGTGTACTCATAC
1 AATATGTGTACTCATAC
*
9790623 AATATGTGTACTCGTAC
1 AATATGTGTACTCATAC
9790640 AATATG
1 AATATG
9790646 ATTTAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (17 bp):
AATATGTGTACTCATAC
Found at i:9791058 original size:26 final size:25
Alignment explanation
Indices: 9790998--9791059 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
9790988 TATGAGTTTA
* * *
9790998 ATTTAATTTTATATTGGATTTGTTT
1 ATTTAATTTTAAATTGGAGTTGATT
* *
9791023 AGTTATATTTTAAATTGTTAGTTGATT
1 ATTTA-ATTTTAAATTG-GAGTTGATT
9791050 ATTTAATTTT
1 ATTTAATTTT
9791060 CTTTTATTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 4 0.14
26 15 0.52
27 10 0.34
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.61
Consensus pattern (25 bp):
ATTTAATTTTAAATTGGAGTTGATT
Found at i:9793013 original size:15 final size:16
Alignment explanation
Indices: 9792987--9793016 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9792977 TGTTTACTAG
9792987 AAAAGTAAAATGTAGT
1 AAAAGTAAAATGTAGT
9793003 AAAAG-AAAATGTAG
1 AAAAGTAAAATGTAG
9793017 AAACTAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (16 bp):
AAAAGTAAAATGTAGT
Found at i:9799855 original size:15 final size:15
Alignment explanation
Indices: 9799821--9799849 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9799811 TTCTATAACA
9799821 ATTTAAAAGTTTTTT
1 ATTTAAAAGTTTTTT
9799836 ATTTAAAA-TTTTTT
1 ATTTAAAAGTTTTTT
9799850 CCTTTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTAAAAGTTTTTT
Found at i:9800686 original size:16 final size:14
Alignment explanation
Indices: 9800637--9800679 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
9800627 AAGTTATCCA
9800637 ACAAGAAAATCCAAC
1 ACAAGAAAAT-CAAC
*
9800652 ACCAAAAAAATCAAC
1 A-CAAGAAAATCAAC
9800667 -CAAGAAAATCAAC
1 ACAAGAAAATCAAC
9800680 CATCAAGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.48
15 5 0.20
16 8 0.32
ACGTcount: A:0.63, C:0.26, G:0.05, T:0.07
Consensus pattern (14 bp):
ACAAGAAAATCAAC
Found at i:9803503 original size:2 final size:2
Alignment explanation
Indices: 9803496--9803523 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9803486 AGTTCACACT
9803496 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
9803524 ATAAATAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9803903 original size:2 final size:2
Alignment explanation
Indices: 9803892--9803932 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
9803882 CGAGCTTATC
9803892 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9803933 TTGGCGAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9804216 original size:2 final size:2
Alignment explanation
Indices: 9804209--9804233 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9804199 TGCATGCACC
9804209 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9804234 CATGTGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9808041 original size:17 final size:18
Alignment explanation
Indices: 9808004--9808041 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9807994 TTAATTTTTT
9808004 TTTGTAAAAAAAATTTCA
1 TTTGTAAAAAAAATTTCA
* *
9808022 TTTGTGAAAAGAATTT-A
1 TTTGTAAAAAAAATTTCA
9808039 TTT
1 TTT
9808042 TTAGAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTGTAAAAAAAATTTCA
Found at i:9808479 original size:362 final size:361
Alignment explanation
Indices: 9807815--9808547 Score: 1380
Period size: 362 Copynumber: 2.0 Consensus size: 361
9807805 GTATTAGTTT
9807815 GATTTTAAATTATCTATCTCTTAAAACATATTTATAATTTACCAAATAACGTAATATTGAAAGTT
1 GATTTTAAATTATCTATCTCTTAAAACATATTTATAATTTACCAAATAACGTAATATTGAAAGTT
9807880 TTTCTTAAATTACTCCAATATTGGTAATAATTTAAAAATATTTTCTCATTTCAGGAGTATTCAAT
66 TTTCTTAAATTACTCCAATATTGGTAATAATTTAAAAATATTTTCTCATTTCAGGAGTATTCAAT
*
9807945 GCGACTATTTGTCACGTTTTGAAGAGGCTCCATCGTTAAATTCATTTAATTAATTTTTTTTTGTA
131 GAGACTATTTGTCACGTTTTGAAGAGGCTCCATCGTTAAATTCATTTAATTAATTTTTTTTTGTA
9808010 AAAAAAATTTCATTTGTGAAAAGAATTTATTTTTAGAAATATTTTTCAATATGTCGGTAAGATTT
196 AAAAAAATTTCATTTGTGAAAAGAATTTATTTTTAGAAATATTTTTCAATATGTCGGTAAGATTT
*
9808075 TCTGTCAAAGATTATCTTCCAATATATTGGTAGGATTGAAAAATTATTTGTTTCGAAAAAATTTA
261 TCTGTCAAAGATTATCTTCCAATATATTGGTAGGATTGAAAAATTATTTGTTTCAAAAAAATTTA
9808140 TTAAGTCCTTTAATAGTTTGGTAAGACTTAATTTAA
326 TTAAGTCCTTTAATAGTTTGGTAAGACTTAATTTAA
9808176 GATTTTAAATTATCTATCTCTTAAAACATATTTATAATTTACCAAATAACGTAATATTGAAAGTT
1 GATTTTAAATTATCTATCTCTTAAAACATATTTATAATTTACCAAATAACGTAATATTGAAAGTT
9808241 TTTCTTAAATTACTCCAATATATTGGTAATAATTTAAAAATATTTTCTCATTTCAGGAGTATTCA
66 TTTCTTAAATTACTCC-A-ATATTGGTAATAATTTAAAAATATTTTCTCATTTCAGGAGTATTCA
*
9808306 ATGAGACTATTTGTCACGTTTTGAAGATGCTCCATCGTTAAATTCATTTAATTAA-TTTTTTTTG
129 ATGAGACTATTTGTCACGTTTTGAAGAGGCTCCATCGTTAAATTCATTTAATTAATTTTTTTTTG
* *
9808370 TAAAAAATATTTCATTTGTGAAAAGAATTTATTTTTAGAAATATTTTTCAATATGTTGGTAAGAT
194 TAAAAAAAATTTCATTTGTGAAAAGAATTTATTTTTAGAAATATTTTTCAATATGTCGGTAAGAT
*
9808435 TTTTTGTCAAAGATTATCTTCCAATATATTGGTAGGATTGAAAAATTATTTGTTTCAAAAAAATT
259 TTTCTGTCAAAGATTATCTTCCAATATATTGGTAGGATTGAAAAATTATTTGTTTCAAAAAAATT
9808500 TATTAAGTCCTTTAATAGTTTGGTAAGACTTAATTTAA
324 TATTAAGTCCTTTAATAGTTTGGTAAGACTTAATTTAA
9808538 GA-TTTAAATT
1 GATTTTAAATT
9808548 CTTCAATATT
Statistics
Matches: 364, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
361 89 0.24
362 176 0.48
363 99 0.27
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (361 bp):
GATTTTAAATTATCTATCTCTTAAAACATATTTATAATTTACCAAATAACGTAATATTGAAAGTT
TTTCTTAAATTACTCCAATATTGGTAATAATTTAAAAATATTTTCTCATTTCAGGAGTATTCAAT
GAGACTATTTGTCACGTTTTGAAGAGGCTCCATCGTTAAATTCATTTAATTAATTTTTTTTTGTA
AAAAAAATTTCATTTGTGAAAAGAATTTATTTTTAGAAATATTTTTCAATATGTCGGTAAGATTT
TCTGTCAAAGATTATCTTCCAATATATTGGTAGGATTGAAAAATTATTTGTTTCAAAAAAATTTA
TTAAGTCCTTTAATAGTTTGGTAAGACTTAATTTAA
Found at i:9808646 original size:23 final size:22
Alignment explanation
Indices: 9808620--9808699 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
9808610 AAAATCAATT
9808620 AAAATAAGTAAAA-ATTATCATGC
1 AAAATAA-TAAAATA-TATCATGC
*
9808643 AAAATAATATAATATATCATGC
1 AAAATAATAAAATATATCATGC
* * * *
9808665 AATTATGATATATTATATCATGC
1 AA-AATAATAAAATATATCATGC
9808688 AATAATAATAAA
1 AA-AATAATAAA
9808700 CTATCATGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 14 0.29
23 34 0.71
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.33
Consensus pattern (22 bp):
AAAATAATAAAATATATCATGC
Found at i:9809923 original size:187 final size:187
Alignment explanation
Indices: 9809607--9809943 Score: 470
Period size: 187 Copynumber: 1.8 Consensus size: 187
9809597 AAAAGAATAC
**
9809607 AATTATTTATATTGAAATTTCATCTAAATTATTCCACAATTTGGGTTAAATTTAGAAAAAATTTC
1 AATTATTTATATTGAAATTTCATCTAAATTATTCCACAATTTGGGACAAATTTAGAAAAAATTTC
* * * *
9809672 TCACTTAGAGATTTCTTAGAAAATTTACCATTTGAAATTTCTATGAATCTCATCCTTAGATAATT
66 TCACCTAGAGAATTCTTAGAAAATTTACCATTTGAAATTTCTATAAATCTCATCATTAGATAATT
**
9809737 TGTATTTAATTCC-AAAATTTTTTATTTTTTAATTTTTTTTGTTTGAAAATAAACATT
131 AATATTT-ATTCCTAAAATTTTTTATTTTTTAATTTTTTTTGTTTGAAAATAAACATT
*
9809794 AATTATTGT-TATTGAAACTTT-ATCTAAATTATTCCATAATTTGGGACAAATTTAGACAAAAAT
1 AATTATT-TATATTGAAA-TTTCATCTAAATTATTCCACAATTTGGGACAAATTTAGA-AAAAAT
* * *
9809857 TTCTCACCTAG-GAATT-TTATAAAGATTTACCATTTGAAATTTTTATAAAT-TCTATCATTGGA
63 TTCTCACCTAGAGAATTCTTAGAAA-ATTTACCATTTGAAATTTCTATAAATCTC-ATCATTAGA
9809919 TAATTAATATTTATTCCTAAAATTT
126 TAATTAATATTTATTCCTAAAATTT
9809944 ATTTTATTAT
Statistics
Matches: 132, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
186 13 0.10
187 99 0.75
188 20 0.15
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.45
Consensus pattern (187 bp):
AATTATTTATATTGAAATTTCATCTAAATTATTCCACAATTTGGGACAAATTTAGAAAAAATTTC
TCACCTAGAGAATTCTTAGAAAATTTACCATTTGAAATTTCTATAAATCTCATCATTAGATAATT
AATATTTATTCCTAAAATTTTTTATTTTTTAATTTTTTTTGTTTGAAAATAAACATT
Found at i:9810771 original size:42 final size:42
Alignment explanation
Indices: 9810726--9811076 Score: 431
Period size: 42 Copynumber: 8.4 Consensus size: 42
9810716 GAGGCTTAAT
* * *
9810726 GACTTTGAAAAAAATAAAT-GCTTCTCTAAATAGAGGC-ACCG
1 GACTTTG-GAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
* * *
9810767 TGACTTTGGAAAAATAAATTGCTCCTCTAAATAGAGGCACCAT
1 -GACTTTGGAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
* * * *
9810810 GACTTTGAAAAAATAAATGGCTCTTCTAAATAAAGGCAATAG
1 GACTTTGGAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
* *
9810852 GAC-TTGGAAAAATAAATAGCTCCTATAAATAGAGGCAACAG
1 GACTTTGGAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
* * * *
9810893 AACTTTAGAAAAATAAATGGCTCTTATAAATAGAGGCAACAG
1 GACTTTGGAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
* * *
9810935 GACTTT-GAAAACAAAAATGTCTCCTCTAAATAAAGGCAACAG
1 GACTTTGGAAAA-ATAAATGGCTCCTCTAAATAGAGGCAACAG
* * * *
9810977 GACTTTGGAAAAATAAATGACTACTCTAAATAAAGGCAACAA
1 GACTTTGGAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
*
9811019 AACTTTGGAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
1 GACTTTGGAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
9811061 GACTTTGGAAAAATAA
1 GACTTTGGAAAAATAA
9811077 TTGAAAAAAT
Statistics
Matches: 266, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
41 49 0.18
42 211 0.79
43 6 0.02
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (42 bp):
GACTTTGGAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
Found at i:9810926 original size:125 final size:125
Alignment explanation
Indices: 9810726--9811076 Score: 474
Period size: 125 Copynumber: 2.8 Consensus size: 125
9810716 GAGGCTTAAT
* * * * *
9810726 GACTTTGAAAAAAATAAATGCTTCTCTAAATAGAGGC-ACCGTGACTTTGGAAAAATAAATTGCT
1 GACTTTG-GAAAAATAAATGCTACTCTAAATAGAGGCAACAG-AACTTTGGAAAAATAAATGGCT
* * * *
9810790 CCTCTAAATAGAGGCACCATGACTTTGAAAAAATAAATGGCTCTTCTAAATAAAGGCAATAG
64 CCTCTAAATAGAGGCAACAGGACTTTGAAAAAATAAATGGCTCCTCTAAATAAAGGCAACAG
* * *
9810852 GAC-TTGGAAAAATAAATAGCTCCTATAAATAGAGGCAACAGAACTTTAGAAAAATAAATGGCTC
1 GACTTTGGAAAAATAAAT-GCTACTCTAAATAGAGGCAACAGAACTTTGGAAAAATAAATGGCTC
* * *
9810916 TTATAAATAGAGGCAACAGGACTTTGAAAACAA-AAATGTCTCCTCTAAATAAAGGCAACAG
65 CTCTAAATAGAGGCAACAGGACTTTGAAAA-AATAAATGGCTCCTCTAAATAAAGGCAACAG
* *
9810977 GACTTTGGAAAAATAAATGACTACTCTAAATAAAGGCAACAAAACTTTGGAAAAATAAATGGCTC
1 GACTTTGGAAAAATAAATG-CTACTCTAAATAGAGGCAACAGAACTTTGGAAAAATAAATGGCTC
*
9811042 CTCTAAATAGAGGCAACAGGACTTTGGAAAAATAA
65 CTCTAAATAGAGGCAACAGGACTTTGAAAAAATAA
9811077 TTGAAAAAAT
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
124 10 0.05
125 96 0.49
126 91 0.46
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (125 bp):
GACTTTGGAAAAATAAATGCTACTCTAAATAGAGGCAACAGAACTTTGGAAAAATAAATGGCTCC
TCTAAATAGAGGCAACAGGACTTTGAAAAAATAAATGGCTCCTCTAAATAAAGGCAACAG
Found at i:9811541 original size:21 final size:21
Alignment explanation
Indices: 9811540--9811584 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
9811530 TTGAAACTCA
9811540 AAACTCAAAGATTCTTCTTTG
1 AAACTCAAAGATTCTTCTTTG
*
9811561 AAATTCAAAGATTC-TCATTTG
1 AAACTCAAAGATTCTTC-TTTG
9811582 AAA
1 AAA
9811585 AAAAAATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (21 bp):
AAACTCAAAGATTCTTCTTTG
Found at i:9811560 original size:28 final size:28
Alignment explanation
Indices: 9811515--9811569 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
9811505 AGTTTCATAT
9811515 CTCAAAGATTCTCATTTGAAACTCAAAA
1 CTCAAAGATTCTCATTTGAAACTCAAAA
*
9811543 CTCAAAGATTCTTC-TTTGAAATTCAAA
1 CTCAAAGATTC-TCATTTGAAACTCAAA
9811570 GATTCTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (28 bp):
CTCAAAGATTCTCATTTGAAACTCAAAA
Found at i:9813646 original size:19 final size:20
Alignment explanation
Indices: 9813622--9813672 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 20
9813612 GATAACAAAT
9813622 GAAATCCTATTAC-CTAAAA
1 GAAATCCTATTACTCTAAAA
9813641 GAAATCCTAACATTACTCTAAAA
1 GAAATCCT---ATTACTCTAAAA
9813664 GAAATCCTA
1 GAAATCCTA
9813673 AAATGACAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 8 0.29
20 1 0.04
22 5 0.18
23 14 0.50
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (20 bp):
GAAATCCTATTACTCTAAAA
Found at i:9813662 original size:23 final size:22
Alignment explanation
Indices: 9813630--9813673 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
9813620 ATGAAATCCT
9813630 ATTACCTAAAAGAAATCCTAAC
1 ATTACCTAAAAGAAATCCTAAC
9813652 ATTACTCTAAAAGAAATCCTAA
1 ATTAC-CTAAAAGAAATCCTAA
9813674 AATGACAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (22 bp):
ATTACCTAAAAGAAATCCTAAC
Found at i:9817757 original size:4 final size:4
Alignment explanation
Indices: 9817748--9817774 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
9817738 AATAAAGAGG
9817748 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
9817775 TAAAAATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Done.