Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015373.1 Kokia drynarioides strain JFW-HI SEQ_130420, 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: 603110
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 225 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:446 original size:9 final size:9
Alignment explanation
Indices: 411--443 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
401 TGTAAATCAT
411 AAAAAATAA
1 AAAAAATAA
420 AAAAAATAA
1 AAAAAATAA
429 AAAAAA-AA
1 AAAAAATAA
437 CAAAAAA
1 -AAAAAA
444 AACTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 2 0.09
9 21 0.91
ACGTcount: A:0.91, C:0.03, G:0.00, T:0.06
Consensus pattern (9 bp):
AAAAAATAA
Found at i:2004 original size:3 final size:3
Alignment explanation
Indices: 1996--2025 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1986 TAAGGTTCTT
1996 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2026 AAGAGTACAA
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):
TAA
Found at i:3849 original size:25 final size:23
Alignment explanation
Indices: 3821--3866 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
3811 GTTGGATCCA
3821 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
3846 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
3867 CCCTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:3952 original size:13 final size:13
Alignment explanation
Indices: 3918--3964 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
3908 AAAGATAATA
*
3918 TAAATAATAAT-A
1 TAAATAATAATCC
3930 T-AATAATAATCC
1 TAAATAATAATCC
*
3942 TAAATATTAATCC
1 TAAATAATAATCC
*
3955 TAAAAAATAA
1 TAAATAATAA
3965 AGTTTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 9 0.31
12 2 0.07
13 18 0.62
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATAATAATCC
Found at i:10261 original size:17 final size:18
Alignment explanation
Indices: 10231--10264 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10221 TTTAATTAAA
10231 TGAATTATTAAAAAATAG
1 TGAATTATTAAAAAATAG
*
10249 TGAA-TATTTAAAAATA
1 TGAATTATTAAAAAATA
10265 TTAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (18 bp):
TGAATTATTAAAAAATAG
Found at i:11304 original size:26 final size:26
Alignment explanation
Indices: 11256--11308 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
11246 ATTTAACAAA
* *
11256 TATTTTTAATAATTTCTATACTTTTT
1 TATTTTTAATAAATTCTAAACTTTTT
11282 TATTTTTAATAAAATT-TAAACTTTTT
1 TATTTTTAAT-AAATTCTAAACTTTTT
11308 T
1 T
11309 TAATGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTTTTAATAAATTCTAAACTTTTT
Found at i:20703 original size:21 final size:20
Alignment explanation
Indices: 20664--20705 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
20654 CTTCCTCTTA
**
20664 ACTTTAATTTATTGGTTTTT
1 ACTTTAATTTATTAATTTTT
20684 ACTTTAATTTTATTAATTTTT
1 ACTTTAA-TTTATTAATTTTT
20705 A
1 A
20706 AAATAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
ACTTTAATTTATTAATTTTT
Found at i:24723 original size:30 final size:30
Alignment explanation
Indices: 24667--24723 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
24657 TTTGACCCCC
* *
24667 TTAAAAATGATAAAAATTTGATTTAATCCT
1 TTAAAAATAATAAAAATTTGAGTTAATCCT
*
24697 TTAAAAATAATAAAGATTT-AGGTTAAT
1 TTAAAAATAATAAAAATTTGA-GTTAAT
24724 AAAACAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.04
30 22 0.96
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.39
Consensus pattern (30 bp):
TTAAAAATAATAAAAATTTGAGTTAATCCT
Found at i:52546 original size:20 final size:20
Alignment explanation
Indices: 52517--52563 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
52507 GTTTGTAACT
52517 TTTC-TTTGGCCATATATGA
1 TTTCTTTTGGCCATATATGA
52536 TTTCTTTTGGCCATATATGA
1 TTTCTTTTGGCCATATATGA
52556 TTTCTTTT
1 TTTCTTTT
52564 CTTGCATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.55
Consensus pattern (20 bp):
TTTCTTTTGGCCATATATGA
Found at i:70012 original size:32 final size:34
Alignment explanation
Indices: 69944--70014 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 34
69934 TTTTAATGGT
* *
69944 AAAATTTCATTTTATCCTTTTTAAAAAATATGAA
1 AAAATTTCATTTAATCCTTTTTAAAAAATATAAA
* **
69978 AAAATTTGATTTAAT-C-TTTTAAAATTTATAAA
1 AAAATTTCATTTAATCCTTTTTAAAAAATATAAA
70010 AAAAT
1 AAAAT
70015 AAAAATTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 18 0.56
33 1 0.03
34 13 0.41
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (34 bp):
AAAATTTCATTTAATCCTTTTTAAAAAATATAAA
Found at i:70023 original size:17 final size:17
Alignment explanation
Indices: 69997--70041 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
69987 TTTAATCTTT
*
69997 TAAAATTTATAAAAAAA
1 TAAAAATTATAAAAAAA
* *
70014 TAAAAATTATTAAAATA
1 TAAAAATTATAAAAAAA
*
70031 TTAAAATTATA
1 TAAAAATTATA
70042 TTTTTATGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATTATAAAAAAA
Found at i:70748 original size:24 final size:25
Alignment explanation
Indices: 70706--70755 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
70696 TTGACTAGTG
70706 AGAAAAAAAAATAAAAATG-AGAAA
1 AGAAAAAAAAATAAAAATGAAGAAA
*
70730 AGAAAAAAAAA-AGAGAATGAAGAAA
1 AGAAAAAAAAATA-AAAATGAAGAAA
70755 A
1 A
70756 CATAGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 1 0.04
24 16 0.70
25 6 0.26
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (25 bp):
AGAAAAAAAAATAAAAATGAAGAAA
Found at i:70755 original size:20 final size:20
Alignment explanation
Indices: 70704--70746 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
70694 ATTTGACTAG
70704 TGAGAAAA-AAAAATAAAAA
1 TGAGAAAAGAAAAATAAAAA
70723 TGAGAAAAGAAAAA-AAAAA
1 TGAGAAAAGAAAAATAAAAA
70742 -GAGAA
1 TGAGAA
70747 TGAAGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (20 bp):
TGAGAAAAGAAAAATAAAAA
Found at i:74941 original size:22 final size:22
Alignment explanation
Indices: 74896--74941 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
74886 GAACCAATAC
*
74896 AAATCGATTGAACTGAGTTAAA
1 AAATCGATTGAACTGAGATAAA
*
74918 AAATCGATTGAATTGTAGATAAA
1 AAATCGATTGAACTG-AGATAAA
74941 A
1 A
74942 TTGTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (22 bp):
AAATCGATTGAACTGAGATAAA
Found at i:74969 original size:17 final size:18
Alignment explanation
Indices: 74947--74990 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
74937 TAAAATTGTG
74947 TTTTATAATTAT-AAATT
1 TTTTATAATTATGAAATT
*
74964 TTTTAT-TTTATGAAATT
1 TTTTATAATTATGAAATT
*
74981 TTTAATAATT
1 TTTTATAATT
74991 TATTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 16 0.73
18 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTATAATTATGAAATT
Found at i:79430 original size:30 final size:33
Alignment explanation
Indices: 79374--79433 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
79364 TGTTTGTATG
*
79374 AAATTGAAGAAAGAGGGAAGAAGGAGAAAGAAC
1 AAATTGAAGAAAGAAGGAAGAAGGAGAAAGAAC
79407 AAATTGAAGAAA-AAGG-A-AAGGAGAAAG
1 AAATTGAAGAAAGAAGGAAGAAGGAGAAAG
79434 CTAAGGTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.38
31 1 0.04
32 3 0.12
33 12 0.46
ACGTcount: A:0.60, C:0.02, G:0.32, T:0.07
Consensus pattern (33 bp):
AAATTGAAGAAAGAAGGAAGAAGGAGAAAGAAC
Found at i:80204 original size:19 final size:18
Alignment explanation
Indices: 80180--80222 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
80170 TACAACTTTG
80180 AAAATTAATATAAAAAAGA
1 AAAATTAA-ATAAAAAAGA
* * *
80199 AAAATTGAATAGAAATGA
1 AAAATTAAATAAAAAAGA
80217 AAAATT
1 AAAATT
80223 GATGTATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (18 bp):
AAAATTAAATAAAAAAGA
Found at i:83446 original size:18 final size:18
Alignment explanation
Indices: 83423--83477 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
83413 ACAAGTCATA
* *
83423 TCACTTTCAATTCCAATT
1 TCACTTTCACTTTCAATT
*
83441 TCACTTTCACTTTCACTT
1 TCACTTTCACTTTCAATT
83459 TCACTTTCACTTTCAATT
1 TCACTTTCACTTTCAATT
83477 T
1 T
83478 TGATCACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCACTTTCAATT
Found at i:83448 original size:6 final size:6
Alignment explanation
Indices: 83423--83473 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
83413 ACAAGTCATA
* * *
83423 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
83471 TCA
1 TCA
83474 ATTTTGATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:92130 original size:3 final size:3
Alignment explanation
Indices: 92122--92146 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
92112 AAAACTAAAG
92122 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
92147 TCCCAATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:94749 original size:16 final size:16
Alignment explanation
Indices: 94728--94772 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
94718 AGGCAACCTA
94728 ATTTTTGTTTTTATTT
1 ATTTTTGTTTTTATTT
*
94744 ATTTTTATTTTTATTT
1 ATTTTTGTTTTTATTT
94760 -TTTTTGTATTTTA
1 ATTTTTGT-TTTTA
94773 ATAAATTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (16 bp):
ATTTTTGTTTTTATTT
Found at i:94753 original size:22 final size:23
Alignment explanation
Indices: 94728--94771 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
94718 AGGCAACCTA
*
94728 ATTTTTGTTTTTATT-TATTTTT
1 ATTTTTATTTTTATTGTATTTTT
*
94750 ATTTTTATTTTTTTTGTATTTT
1 ATTTTTATTTTTATTGTATTTT
94772 AATAAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.82
Consensus pattern (23 bp):
ATTTTTATTTTTATTGTATTTTT
Found at i:99177 original size:26 final size:26
Alignment explanation
Indices: 99147--99198 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
99137 TTTTTGTTTG
99147 TTTAATT-GACATGATTTTAATTATTT
1 TTTAATTAG-CATGATTTTAATTATTT
99173 TTTAATTAGCATGATTTTAATTATTT
1 TTTAATTAGCATGATTTTAATTATTT
99199 AGCTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTAATTAGCATGATTTTAATTATTT
Found at i:101922 original size:3 final size:3
Alignment explanation
Indices: 101914--101957 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
101904 ATCTAGTGAA
101914 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
101958 AACTTGTGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:103165 original size:25 final size:25
Alignment explanation
Indices: 103137--103188 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
103127 AAAGGAAAGG
*
103137 AAATCAAATCTCCAAACAAGATTGT
1 AAATCAAATCTCCAAAAAAGATTGT
* *
103162 AAATCAAATCTGCAAAAAATATTGT
1 AAATCAAATCTCCAAAAAAGATTGT
103187 AA
1 AA
103189 TTTCGTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (25 bp):
AAATCAAATCTCCAAAAAAGATTGT
Found at i:106862 original size:26 final size:28
Alignment explanation
Indices: 106798--106862 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 28
106788 TGCACCTAGA
*
106798 TATGTCACTGCAGGAACTTGTCCAGAAG
1 TATGTCACTGCATGAACTTGTCCAGAAG
* *
106826 TAT-TGAC-GCATGAAGTTGTCCAG-AG
1 TATGTCACTGCATGAACTTGTCCAGAAG
106851 T-TGTCACTGCAT
1 TATGTCACTGCAT
106863 AAGAGGATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
24 1 0.03
25 6 0.19
26 18 0.58
27 3 0.10
28 3 0.10
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (28 bp):
TATGTCACTGCATGAACTTGTCCAGAAG
Found at i:118647 original size:16 final size:16
Alignment explanation
Indices: 118619--118658 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
118609 TACCTTTCTT
118619 GCATATGCA-TTCATTA
1 GCAT-TGCATTTCATTA
118635 GCATTGCATTTCATTA
1 GCATTGCATTTCATTA
118651 -CA-TGCATT
1 GCATTGCATT
118659 AAATTTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.26
15 6 0.26
16 11 0.48
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (16 bp):
GCATTGCATTTCATTA
Found at i:118709 original size:3 final size:3
Alignment explanation
Indices: 118694--118729 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
118684 ATTATAAAAA
118694 AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
118730 GATGATGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:118734 original size:3 final size:3
Alignment explanation
Indices: 118728--118783 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
118718 AATAATAATA
*
118728 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATT ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
118776 ATG ATG AT
1 ATG ATG AT
118784 AATAATAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (3 bp):
ATG
Found at i:118788 original size:3 final size:3
Alignment explanation
Indices: 118782--118830 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
118772 GATGATGATG
118782 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
118830 A
1 A
118831 AGATCCTCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:123925 original size:49 final size:49
Alignment explanation
Indices: 123847--124215 Score: 192
Period size: 49 Copynumber: 7.6 Consensus size: 49
123837 GCCACAATGG
* * * *
123847 CGGACCTAACA-TTCTAAAATTGAAA-AGGGATAGGTTGAAGTTGTAATGA
1 CGGACCTAACACCT-TAAAA-TCAAAGAGGGATAGGTTGAAGTCGTAACGA
* ** *
123896 CGGACCTAACACCTTAAAATCAAAGAGGGAT-GGATTGAAGCCACAACGG
1 CGGACCTAACACCTTAAAATCAAAGAGGGATAGG-TTGAAGTCGTAACGA
* * * * * * * *
123945 TGGATCTAACACCTTAAAACCGAAGAGGGAAAGATTGAAGCCGCAACGA
1 CGGACCTAACACCTTAAAATCAAAGAGGGATAGGTTGAAGTCGTAACGA
* * ** * *
123994 CGGA--TCAGACCTTAAAATTGAAGAGGAATAGGTTGAAGTCGTAACGG
1 CGGACCTAACACCTTAAAATCAAAGAGGGATAGGTTGAAGTCGTAACGA
** * ** * * * * * *
124041 TTGAGCTAACACCCAAAAACCAAAAAAGGAAAGATTAAAGTCGTAACGA
1 CGGACCTAACACCTTAAAATCAAAGAGGGATAGGTTGAAGTCGTAACGA
** * * * **
124090 CGGGTCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGCCGCGACGA
1 CGGACCTAACACCTTAAAATCAAAGAGGGATAGGTTGAAGTCGTAACGA
* * * * * * * * *
124139 TGGACGTAATACCTTTAAACCAAAGAGGGATAGATTGAAGCCATGAA-GG
1 CGGACCTAACACCTTAAAATCAAAGAGGGATAGGTTGAAGTCGT-AACGA
* * *
124188 CAGATCTAACACCTTAAAACCAAAGAGG
1 CGGACCTAACACCTTAAAATCAAAGAGG
124216 AAACAAATTG
Statistics
Matches: 233, Mismatches: 80, Indels: 14
0.71 0.24 0.04
Matches are distributed among these distances:
47 35 0.15
48 6 0.03
49 189 0.81
50 3 0.01
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (49 bp):
CGGACCTAACACCTTAAAATCAAAGAGGGATAGGTTGAAGTCGTAACGA
Found at i:123996 original size:98 final size:96
Alignment explanation
Indices: 123894--124281 Score: 307
Period size: 98 Copynumber: 4.0 Consensus size: 96
123884 AAGTTGTAAT
* *
123894 GACGGACCTAACACCTTAAAATCAAAGAGGGAT-GGATTGAAGCCACAACGGTGGATCTAACACC
1 GACGGATCTAACACCTTAAAATCAAAGAGGGATAGG-TTGAAGCCGCAACGGTGGA-CTAACACC
*
123958 TTAAAACCGAAGAGGGAAAGATTGAAGCCGCAAC
64 TTAAAACCAAAGAGGGAAAGATTGAAGCCG-AAC
* ** * * * * *
123992 GACGGATC--AGACCTTAAAATTGAAGAGGAATAGGTTGAAGTCGTAACGGTTGAGCTAACACCC
1 GACGGATCTAACACCTTAAAATCAAAGAGGGATAGGTTGAAGCCGCAACGGTGGA-CTAACACCT
* * * * *
124055 AAAAACCAAAAAAGGAAAGATTAAAGTCGTAAC
65 TAAAACCAAAGAGGGAAAGATTGAAGCCG-AAC
* * * * * *
124088 GACGGGTCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGCCGCGACGATGGACGTAATACCT
1 GACGGATCTAACACCTTAAAATCAAAGAGGGATAGGTTGAAGCCGCAACGGTGGAC-TAACACCT
* *
124153 TTAAACCAAAGAGGGATAGATTGAAGCCATGAA-
65 TAAAACCAAAGAGGGAAAGATTGAAGCC--GAAC
* * * * * ** * ** *
124186 GGCAGATCTAACACCTTAAAACCAAAGAGGAAACAAATTGAAGCTGTGACGGCGGATCTAACACC
1 GACGGATCTAACACCTTAAAATCAAAGAGG-GATAGGTTGAAGCCGCAACGGTGGA-CTAACACC
* * *
124251 TTAAAGCCAAAGAGGAAACAAATTGAAGCCG
64 TTAAAACCAAAGAGGGAA-AGATTGAAGCCG
124282 CGATGGCGAA
Statistics
Matches: 225, Mismatches: 56, Indels: 18
0.75 0.19 0.06
Matches are distributed among these distances:
96 75 0.33
97 3 0.01
98 96 0.43
99 39 0.17
100 12 0.05
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.16
Consensus pattern (96 bp):
GACGGATCTAACACCTTAAAATCAAAGAGGGATAGGTTGAAGCCGCAACGGTGGACTAACACCTT
AAAACCAAAGAGGGAAAGATTGAAGCCGAAC
Found at i:124244 original size:50 final size:50
Alignment explanation
Indices: 124149--124280 Score: 176
Period size: 50 Copynumber: 2.7 Consensus size: 50
124139 TGGACGTAAT
* * * *
124149 ACCTTTAAACCAAAGAGG-GATAGATTGAAGCCATGAAGGCAGATCTAAC
1 ACCTTAAAACCAAAGAGGAAACAAATTGAAGCCATGAAGGCAGATCTAAC
** * *
124198 ACCTTAAAACCAAAGAGGAAACAAATTGAAGCTGTGACGGCGGATCTAAC
1 ACCTTAAAACCAAAGAGGAAACAAATTGAAGCCATGAAGGCAGATCTAAC
*
124248 ACCTTAAAGCCAAAGAGGAAACAAATTGAAGCC
1 ACCTTAAAACCAAAGAGGAAACAAATTGAAGCC
124281 GCGATGGCGA
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 17 0.24
50 55 0.76
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (50 bp):
ACCTTAAAACCAAAGAGGAAACAAATTGAAGCCATGAAGGCAGATCTAAC
Found at i:124300 original size:50 final size:50
Alignment explanation
Indices: 124194--124301 Score: 153
Period size: 50 Copynumber: 2.2 Consensus size: 50
124184 AAGGCAGATC
* * * *
124194 TAACACCTTAAAACCAAAGAGGAAACAAATTGAAGCTGTGACGGCGGATC
1 TAACACCTTAAAACCAAAGAGGAAACAAATTGAAGCCGCGACGGCGAATA
* *
124244 TAACACCTTAAAGCCAAAGAGGAAACAAATTGAAGCCGCGATGGCGAATA
1 TAACACCTTAAAACCAAAGAGGAAACAAATTGAAGCCGCGACGGCGAATA
*
124294 TTACACCT
1 TAACACCT
124302 CTTGAAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (50 bp):
TAACACCTTAAAACCAAAGAGGAAACAAATTGAAGCCGCGACGGCGAATA
Found at i:125018 original size:25 final size:25
Alignment explanation
Indices: 124973--125024 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
124963 AAAGGAAAGA
* *
124973 AAATCAAATCTCGGAACAAGATTGT
1 AAATCAAATCTCGAAAAAAGATTGT
124998 AAATCAAATCT-GCAAAAAAGATTGT
1 AAATCAAATCTCG-AAAAAAGATTGT
125023 AA
1 AA
125025 TTTCGTGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.23
Consensus pattern (25 bp):
AAATCAAATCTCGAAAAAAGATTGT
Found at i:125943 original size:21 final size:19
Alignment explanation
Indices: 125906--125944 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
125896 CATTATTCAA
*
125906 TTTTTATTTTTAGTTATTT
1 TTTTTATTTTTACTTATTT
125925 TTTTTAATTTTTAACTTATT
1 TTTTT-ATTTTT-ACTTATT
125945 AATTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTTTATTTTTACTTATTT
Found at i:126079 original size:3 final size:3
Alignment explanation
Indices: 126073--126154 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
126063 GGGTTTATGC
126073 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
126121 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
126155 TTCTATTTTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:128256 original size:19 final size:19
Alignment explanation
Indices: 128234--128272 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
128224 CCGAGTTGAC
128234 TGACCCGACCCGTTGACTT
1 TGACCCGACCCGTTGACTT
* **
128253 TGACCTGACCTTTTGACTT
1 TGACCCGACCCGTTGACTT
128272 T
1 T
128273 TACTTGATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.36
Consensus pattern (19 bp):
TGACCCGACCCGTTGACTT
Found at i:128304 original size:19 final size:18
Alignment explanation
Indices: 128245--128315 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
128235 GACCCGACCC
*
128245 GTTGACTTTGACCTGACCT
1 GTTGACTTTGACTTGA-CT
* *
128264 TTTGACTTTTACTTGA-T
1 GTTGACTTTGACTTGACT
128281 AGTTGACTTTGACTTTGACT
1 -GTTGACTTTGAC-TTGACT
*
128301 GTTGGCTGTTGACTT
1 GTTGACT-TTGACTT
128316 TTTTTATCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 1 0.02
18 10 0.24
19 25 0.60
20 6 0.14
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.46
Consensus pattern (18 bp):
GTTGACTTTGACTTGACT
Found at i:131625 original size:46 final size:46
Alignment explanation
Indices: 131559--131649 Score: 121
Period size: 48 Copynumber: 2.0 Consensus size: 46
131549 ACCAGCACAC
* *
131559 CAAATTGTGAACAGTGTCACA-AACGCATATAAACTGCCATATAAT
1 CAAATTGTGAACAATGTCACATAACGCAGATAAACTGCCATATAAT
* *
131604 CAAATTCGTGAACAATGTCACATTAATGCAGATAAATTGCCATATA
1 CAAATT-GTGAACAATGTCACA-TAACGCAGATAAACTGCCATATA
131650 CTCCCACCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
45 6 0.15
46 14 0.36
48 19 0.49
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (46 bp):
CAAATTGTGAACAATGTCACATAACGCAGATAAACTGCCATATAAT
Found at i:132411 original size:17 final size:17
Alignment explanation
Indices: 132389--132436 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
132379 TATTATAAGG
132389 GTATAATAGTAAATGAA
1 GTATAATAGTAAATGAA
* *
132406 GTATAAAAGTAAATTAA
1 GTATAATAGTAAATGAA
*
132423 GTAAAATAAGTAAA
1 GTATAAT-AGTAAA
132437 CAAATCATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (17 bp):
GTATAATAGTAAATGAA
Found at i:136089 original size:25 final size:21
Alignment explanation
Indices: 136044--136084 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
136034 CTATGTAAAG
136044 AATGTGTAAATAAATACAAGA
1 AATGTGTAAATAAATACAAGA
136065 AATGTGTAAATAAATACAAG
1 AATGTGTAAATAAATACAAG
136085 TAAGATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.24
Consensus pattern (21 bp):
AATGTGTAAATAAATACAAGA
Found at i:137644 original size:22 final size:22
Alignment explanation
Indices: 137616--137661 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
137606 TGATTTGTTT
137616 ACTGGACTGTTGCAGAATGTCG
1 ACTGGACTGTTGCAGAATGTCG
137638 ACTGGACTGTTGCAGAATGTCG
1 ACTGGACTGTTGCAGAATGTCG
137660 AC
1 AC
137662 GCAATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (22 bp):
ACTGGACTGTTGCAGAATGTCG
Found at i:140014 original size:30 final size:29
Alignment explanation
Indices: 139989--140415 Score: 395
Period size: 30 Copynumber: 14.5 Consensus size: 29
139979 TAAACTGTTT
*
139989 AAAAATTACATTTTAACTCCCAAACTTTTC
1 AAAAATTACATTTTAAC-CCCAAACTTTCC
*
140019 AAAAATTACATTTGT-ACCCACGAACTTTCC
1 AAAAATTACATTT-TAACCC-CAAACTTTCC
*
140049 AAAAATTA-ATTTTTTACCCTCAAACTTTCC
1 AAAAATTACA-TTTTAACCC-CAAACTTTCC
* * *
140079 AAAAAGTATATTTTAACCCCTAAAATTTCC
1 AAAAATTACATTTTAACCCC-AAACTTTCC
*
140109 AAAAATTACATTTTAACCCCTAAACTTTCT
1 AAAAATTACATTTTAACCCC-AAACTTTCC
*
140139 AAAAATTACATTTTAACCCTCAAACATTCC
1 AAAAATTACATTTTAACCC-CAAACTTTCC
*
140169 AAAAATTACATTTTAACTCCCAAACTTTCT
1 AAAAATTACATTTTAAC-CCCAAACTTTCC
*
140199 AAAAATAACATTTTAACCCTCAAACTTTCC
1 AAAAATTACATTTTAACCC-CAAACTTTCC
* * * * *
140229 AAAAATTATATATTGACCCTAAACTTTCT
1 AAAAATTACATTTTAACCCCAAACTTTCC
*
140258 AAAAATTACATTTTAACCCCTGAACTTT-C
1 AAAAATTACATTTTAACCCC-AAACTTTCC
* *
140287 -AAAATTACATTTTTACCTCTAAACTTT-C
1 AAAAATTACATTTTAACC-CCAAACTTTCC
**
140315 AAAAATTACAATTTTTGCCCCTAAA-TTTCC
1 AAAAATTAC-ATTTTAACCCC-AAACTTTCC
* * *
140345 AAAAAGTACCATTTT-ACCCACAGA-TGTCC
1 AAAAATTA-CATTTTAACCC-CAAACTTTCC
** * * *
140374 AAAAATTACATTTTGTCCTC-GAGTTTCC
1 AAAAATTACATTTTAACCCCAAACTTTCC
140402 AAAAATTACATTTT
1 AAAAATTACATTTT
140416 GTCCTCGAGT
Statistics
Matches: 336, Mismatches: 42, Indels: 40
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.01
28 48 0.14
29 62 0.18
30 218 0.65
31 6 0.02
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCCAAACTTTCC
Found at i:140386 original size:28 final size:29
Alignment explanation
Indices: 140340--140451 Score: 131
Period size: 28 Copynumber: 3.9 Consensus size: 29
140330 TGCCCCTAAA
* *
140340 TTTCCAAAAAGTACCATTTTACCCAC-AG
1 TTTCCAAAAATTACCATTTTACCCTCGAG
* **
140368 ATGTCCAAAAATTA-CATTTTGTCCTCGAG
1 -TTTCCAAAAATTACCATTTTACCCTCGAG
**
140397 TTTCCAAAAATTA-CATTTTGTCCTCGAG
1 TTTCCAAAAATTACCATTTTACCCTCGAG
140425 TTTCCAAAAATTACCATTTTACCCTCG
1 TTTCCAAAAATTACCATTTTACCCTCG
140452 GACATCCAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
28 49 0.67
29 24 0.33
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.35
Consensus pattern (29 bp):
TTTCCAAAAATTACCATTTTACCCTCGAG
Found at i:140406 original size:29 final size:28
Alignment explanation
Indices: 140371--140444 Score: 139
Period size: 28 Copynumber: 2.6 Consensus size: 28
140361 CCCACAGATG
140371 TCCAAAAATTACATTTTGTCCTCGAGTT
1 TCCAAAAATTACATTTTGTCCTCGAGTT
140399 TCCAAAAATTACATTTTGTCCTCGAGTT
1 TCCAAAAATTACATTTTGTCCTCGAGTT
140427 TCCAAAAATTACCATTTT
1 TCCAAAAATTA-CATTTT
140445 ACCCTCGGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 39 0.87
29 6 0.13
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (28 bp):
TCCAAAAATTACATTTTGTCCTCGAGTT
Found at i:149354 original size:209 final size:208
Alignment explanation
Indices: 148992--149598 Score: 944
Period size: 209 Copynumber: 2.9 Consensus size: 208
148982 ACAACAAGCT
* * * * * *
148992 GGTCATCTTCCTGATGAGTTACAGAGAAGTATACCAACTCAATGAAGCTAAGCTCAAAGTGAGCA
1 GGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGC-AAGCTCAAAGTGAGCA
* *
149057 AATCTTCGAACCCCAACTTCCTGATGAGATATTGAGAAGCAGGTCGAAACAATAAAATGGTTAGC
65 AATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAACCAATAAAATGGTTAGC
* *
149122 TTCCTGATGAGATACTAAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGGATT
130 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
*
149187 GAAATAAGTGATGC
195 GAAACAAGTGATGC
*
149201 GGTCATCTTCTTGATGAAATACTGAGAAGAAGACCAAATCAATGAAGTCAAGCTCAAAGTGAGCA
1 GGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAATGAAG-CAAGCTCAAAGTGAGCA
* *
149266 AATCTTCGAACCCCAGTTTCTTGATGAGATATTGAGAAGCAGGTCGAACCAATAAAATGGTTAGC
65 AATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAACCAATAAAATGGTTAGC
* * *
149331 TTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCTTGATGAGATACAGAGAAGTGGATT
130 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
149396 GAAACAAGTGATGC
195 GAAACAAGTGATGC
* * *
149410 GGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCGATGCGAGCA
1 GGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAATGAAG-CAAGCTCAAAGTGAGCA
* * ** *
149475 AACCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTAAACCAATTAAATGGTTAGC
65 AATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAACCAATAAAATGGTTAGC
* *
149540 TTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACTGAGAAG
130 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
149599 AAGACCAAAT
Statistics
Matches: 364, Mismatches: 33, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
209 363 1.00
210 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (208 bp):
GGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCAAGCTCAAAGTGAGCAA
ATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAACCAATAAAATGGTTAGCT
TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTG
AAACAAGTGATGC
Found at i:149605 original size:160 final size:159
Alignment explanation
Indices: 149415--149757 Score: 551
Period size: 160 Copynumber: 2.2 Consensus size: 159
149405 GATGCGGTCA
149415 TCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCGATGCGAGCAAACCT
1 TCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCGATGCGAGCAAACCT
* * * * *
149480 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTAAACCAATTAAATGGTTAGCTTCTT
66 TCGAACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGTCAAACCAATAAAATGATTAGCTTC-T
* *
149545 GATGAGATACTGAGAAGTGGACCAAATTCG
130 GATGAGATACTAAGAAGTAGACCAAATTCG
* * *
149575 TCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAATCTCGATGCGAGCGAACCT
1 TCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCGATGCGAGCAAACCT
* * *
149640 TCGAACCCCAGCTTCCTGATAAGACATTGAGAAGCAGGTCGAAGCAATAAAATGATTAGCTTCTG
66 TCGAACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGTCAAACCAATAAAATGATTAGCTTCTG
149705 ATGAGATACTAAGAAGTAGACCAAATTCG
131 ATGAGATACTAAGAAGTAGACCAAATTCG
*
149734 TCTTCTTGATGAGATACAGAGAAG
1 TCTTCTTGATGAGATACTGAGAAG
149758 CGGATTGAAA
Statistics
Matches: 168, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
159 51 0.30
160 117 0.70
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (159 bp):
TCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCGATGCGAGCAAACCT
TCGAACCCCAGCTTCCTGATAAGACACTGAGAAGCAGGTCAAACCAATAAAATGATTAGCTTCTG
ATGAGATACTAAGAAGTAGACCAAATTCG
Found at i:150175 original size:6 final size:6
Alignment explanation
Indices: 150156--150237 Score: 64
Period size: 6 Copynumber: 14.0 Consensus size: 6
150146 CATTTTAAGA
* ** *
150156 TTAAAT TT-ATT TTAAAT TTAAAT TT-GTT TTAAAAT TTAAGT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT
* *
150203 TTATAT TTAAAT TTAAAA TT--AT TCTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT
150238 AAATAAAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
4 2 0.03
5 8 0.14
6 42 0.72
7 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:150193 original size:24 final size:24
Alignment explanation
Indices: 150166--150219 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
150156 TTAAATTTAT
*
150166 TTTAAATTTAAATTTGT-TTTAAAA
1 TTTAAATTTAAATTTATATTT-AAA
*
150190 TTTAAGTTTAAATTTATATTTAAA
1 TTTAAATTTAAATTTATATTTAAA
150214 TTTAAA
1 TTTAAA
150220 ATTATTCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTAAATTTAAATTTATATTTAAA
Found at i:150219 original size:18 final size:17
Alignment explanation
Indices: 150147--150217 Score: 72
Period size: 18 Copynumber: 4.1 Consensus size: 17
150137 AACTAAACCC
150147 ATTTTAAGA-TTAAATTT
1 ATTTTAA-ATTTAAATTT
150164 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
* *
150181 GTTTTAAAATTTAAGTTT
1 ATTTT-AAATTTAAATTT
* *
150199 AAATTTATATTTAAATTT
1 -ATTTTAAATTTAAATTT
150217 A
1 A
150218 AAATTATTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
16 1 0.02
17 20 0.44
18 21 0.47
19 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:150232 original size:41 final size:41
Alignment explanation
Indices: 150149--150235 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
150139 CTAAACCCAT
* * *
150149 TTTAAGATTAAATTTATTTTAAATTTAAATTTGTTTTAAAA
1 TTTAAGATTAAATTTATTTTAAATTTAAAATTATTCTAAAA
*
150190 TTTAAGTTTAAATTTATATTTAAATTTAAAATTATTCT-AAA
1 TTTAAGATTAAATTTAT-TTTAAATTTAAAATTATTCTAAAA
150231 TTTAA
1 TTTAA
150236 ATAAATAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 24 0.59
42 17 0.41
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (41 bp):
TTTAAGATTAAATTTATTTTAAATTTAAAATTATTCTAAAA
Found at i:151952 original size:30 final size:30
Alignment explanation
Indices: 151877--152105 Score: 234
Period size: 30 Copynumber: 7.7 Consensus size: 30
151867 CCCAGAAGAT
*
151877 CCTTAAACTAT-TAAGAAATTATATTTTGAC
1 CCTTAAACTTTCTAA-AAATTATATTTTGAC
* * *
151907 TC-TAAACTTTTTAAAAATTATATTTTAAC
1 CCTTAAACTTTCTAAAAATTATATTTTGAC
* * * *
151936 CTTTAAACGTTCTAAAAATTATATTTTTAA
1 CCTTAAACTTTCTAAAAATTATATTTTGAC
* *
151966 CCTCAAACATTCTAAAAATTATATTTTGAC
1 CCTTAAACTTTCTAAAAATTATATTTTGAC
*
151996 CCTCAAACTTT-TAAAAAATTATATTTTGAC
1 CCTTAAACTTTCT-AAAAATTATATTTTGAC
* * *
152026 CCCTAAACTTTCCAAAAATTACATTTTGAC
1 CCTTAAACTTTCTAAAAATTATATTTTGAC
* * *
152056 CCTTAAA-TTTTTCAAAAATTACATTTTTAC
1 CCTTAAACTTTCT-AAAAATTATATTTTGAC
*
152086 CCCTAAACTTTC-AAAAATTA
1 CCTTAAACTTTCTAAAAATTA
152106 CCATTTCTAC
Statistics
Matches: 168, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
29 33 0.20
30 132 0.79
31 3 0.02
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.41
Consensus pattern (30 bp):
CCTTAAACTTTCTAAAAATTATATTTTGAC
Found at i:152013 original size:60 final size:60
Alignment explanation
Indices: 151877--152105 Score: 259
Period size: 60 Copynumber: 3.9 Consensus size: 60
151867 CCCAGAAGAT
* * * * *
151877 CCTTAAACTATTAAGAAATTATATTTTGA-CTCTAAACTTTTTAAAAATTATATTTTAAC
1 CCTTAAACTTTTAAAAAATTATATTTTGACCCCTAAACTTTCTAAAAATTATATTTTGAC
* * * * *
151936 CTTTAAACGTTCT-AAAAATTATATTTTTA-ACCTCAAACATTCTAAAAATTATATTTTGAC
1 CCTTAAAC-TTTTAAAAAATTATATTTTGACCCCT-AAACTTTCTAAAAATTATATTTTGAC
* * *
151996 CCTCAAACTTTTAAAAAATTATATTTTGACCCCTAAACTTTCCAAAAATTACATTTTGAC
1 CCTTAAACTTTTAAAAAATTATATTTTGACCCCTAAACTTTCTAAAAATTATATTTTGAC
* * * *
152056 CCTTAAATTTTTCAAAAATTACATTTTTACCCCTAAACTTTC-AAAAATTA
1 CCTTAAACTTTTAAAAAATTATATTTTGACCCCTAAACTTTCTAAAAATTA
152106 CCATTTCTAC
Statistics
Matches: 143, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
59 34 0.24
60 106 0.74
61 3 0.02
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.41
Consensus pattern (60 bp):
CCTTAAACTTTTAAAAAATTATATTTTGACCCCTAAACTTTCTAAAAATTATATTTTGAC
Found at i:152126 original size:29 final size:30
Alignment explanation
Indices: 152024--152147 Score: 114
Period size: 30 Copynumber: 4.2 Consensus size: 30
152014 TTATATTTTG
152024 ACCCCTAAACTTTCCAAAAATTA-CATTT-T
1 ACCCCTAAACTTT-CAAAAATTACCATTTCT
* * *
152053 GACCCTTAAATTTTTCAAAAATTA-CATTTTT
1 -ACCCCTAAA-CTTTCAAAAATTACCATTTCT
152084 ACCCCTAAACTTTCAAAAATTACCATTTCT
1 ACCCCTAAACTTTCAAAAATTACCATTTCT
* * * *
152114 A-CGCTCAAGTTTCCAAAAATTACTATTT-T
1 ACCCCTAAACTTT-CAAAAATTACCATTTCT
152143 ACCCC
1 ACCCC
152148 GAATGCCCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
29 22 0.28
30 53 0.67
31 4 0.05
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (30 bp):
ACCCCTAAACTTTCAAAAATTACCATTTCT
Found at i:152142 original size:60 final size:61
Alignment explanation
Indices: 151892--152147 Score: 210
Period size: 60 Copynumber: 4.3 Consensus size: 61
151882 AACTATTAAG
* * ** * * * *
151892 AAATTA-TATTTTGA-CTCTAAACTTTTTAAAAATTATATTTTAACCTTTAAACG-TTCTAA
1 AAATTACTATTTTTACCCCTAAACTTTCCAAAAATTACATTTTGACCCTTAAA-GTTTCCAA
* * * * * * **
151951 AAATTA-TATTTTTA-ACCTCAAACATTCTAAAAATTATATTTTGACCCTCAAACTTTTAAA
1 AAATTACTATTTTTACCCCT-AAACTTTCCAAAAATTACATTTTGACCCTTAAAGTTTCCAA
* * *
152011 AAATTA-TATTTTGACCCCTAAACTTTCCAAAAATTACATTTTGACCCTTAAATTTTTCAA
1 AAATTACTATTTTTACCCCTAAACTTTCCAAAAATTACATTTTGACCCTTAAAGTTTCCAA
* *
152071 AAATTAC-ATTTTTACCCCTAAACTTT-CAAAAATTACCATTTCT-ACGC-TCAAGTTTCCAA
1 AAATTACTATTTTTACCCCTAAACTTTCCAAAAATTA-CATTT-TGACCCTTAAAGTTTCCAA
152130 AAATTACTA-TTTTACCCC
1 AAATTACTATTTTTACCCC
152148 GAATGCCCAA
Statistics
Matches: 166, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
59 49 0.30
60 113 0.68
61 4 0.02
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (61 bp):
AAATTACTATTTTTACCCCTAAACTTTCCAAAAATTACATTTTGACCCTTAAAGTTTCCAA
Found at i:152163 original size:28 final size:29
Alignment explanation
Indices: 152126--152198 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
152116 GCTCAAGTTT
152126 CCAAAAATTACTATTTTACCCCGA-ATGC
1 CCAAAAATTACTATTTTACCCCGATATGC
** * *
152154 CCAAAAATTA-TATTTTTGCCCTATATGT
1 CCAAAAATTACTATTTTACCCCGATATGC
*
152182 CTAAAAATTACTATTTT
1 CCAAAAATTACTATTTT
152199 CCCTCGAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 10 0.26
28 22 0.58
29 6 0.16
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (29 bp):
CCAAAAATTACTATTTTACCCCGATATGC
Found at i:161475 original size:209 final size:209
Alignment explanation
Indices: 160811--161493 Score: 933
Period size: 209 Copynumber: 3.3 Consensus size: 209
160801 AACGAGCTGT
* * * * * *
160811 TCATCTTCCTGATGAGATACAGAGAAGTATACTAACTCAATGAAGCAAAGCTCAAAGTGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAA
* * * *
160876 TCTTTGAACCCTATCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
*
160941 CCTGATGAGATATTGAGAAGTGGACCAAATTCGTC-TTCTTGATGAGATACAGAGAAGCGGATTG
131 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTTC-TGATGAGATACAGAGAAGCGGATTG
161005 AAACAAGTGATGCGG
195 AAACAAGTGATGCGG
* * * * *
161020 TCATCTTCCTAATGAAATACTGAGAAGAAGACCATATCAATGAAGTCAAGCTCAAAGTGAACAAA
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAA
* * * *
161085 TCTTCGAACCTCGGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAACGGTTAG-TT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
* * *
161149 CCTGATGAGATACTAAGAAGTGGACCAAATTAGTCTTCCTGATGAGATACAGAGAAGCGGATTGA
131 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCGGATTGA
*
161214 AACAAGTGGTGCGG
196 AACAAGTGATGCGG
* * * * * *
161228 TCATCTTCCTGATGAGATACTAAGAAAAAGACCAAATCAATAAAGCCAAGCTCGATGCGAGCAAA
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAA
* * * *
161293 CCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGATTAGCTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
*
161358 CC-GAATGAGATACTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCGGATCG
131 CCTG-ATGAGATACTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCGGATTG
161422 AAACAAGTGATGCGG
195 AAACAAGTGATGCGG
* * * * ** *
161437 TCAACATCCTGATGAGATATTGAGAAGTAGGTCAAATCAATGAAACCATA-CTCAAAG
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCA-AGCTCAAAG
161494 ACTACAGTGA
Statistics
Matches: 410, Mismatches: 60, Indels: 8
0.86 0.13 0.02
Matches are distributed among these distances:
208 182 0.44
209 227 0.55
210 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (209 bp):
TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAA
TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCGGATTGA
AACAAGTGATGCGG
Found at i:161818 original size:11 final size:11
Alignment explanation
Indices: 161806--161931 Score: 69
Period size: 11 Copynumber: 11.0 Consensus size: 11
161796 CTAAACCCAT
*
161806 TTTAAATTTAT
1 TTTAAATTTAA
*
161817 TTTAAGATTAAA
1 TTTAA-ATTTAA
*
161829 TTT-ATTTTAAA
1 TTTAAATTT-AA
*
161840 TTTAAATTTATT
1 TTTAAATTTA-A
*
161852 TTTAATTTTAAA
1 TTTAAATTT-AA
**
161864 TTT-GTTTTAAAA
1 TTTAAATTT--AA
161876 TTTAAATTTAA
1 TTTAAATTTAA
*
161887 TTTAAGTTTAA
1 TTTAAATTTAA
*
161898 TTTATATTTAAA
1 TTTAAATTT-AA
*
161910 TTTAAAATT-A
1 TTTAAATTTAA
161920 TTCTAAATTTAA
1 TT-TAAATTTAA
161932 ATAAATAAAA
Statistics
Matches: 88, Mismatches: 17, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
10 5 0.06
11 41 0.47
12 38 0.43
13 4 0.05
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:161829 original size:17 final size:17
Alignment explanation
Indices: 161806--161933 Score: 152
Period size: 17 Copynumber: 7.4 Consensus size: 17
161796 CTAAACCCAT
161806 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
161824 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
161840 TTTAAATTTATTTTTAAT
1 TTTAAATTTA-TTTTAAA
*
161858 TTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
* *
161876 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
161893 TTT-AATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
161910 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
161927 TTTAAAT
1 TTTAAAT
161934 AAATAAAAAT
Statistics
Matches: 94, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.07
17 52 0.55
18 35 0.37
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:161843 original size:6 final size:6
Alignment explanation
Indices: 161806--161933 Score: 83
Period size: 6 Copynumber: 22.2 Consensus size: 6
161796 CTAAACCCAT
* * **
161806 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTAAA TTTATT
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
161852 TTTAAT TTTAAA TTT-GT TTTAAAA TTTAAA TTT-AA TTTAAG TTT-AA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
161898 TTTATA TTTAAA TTTAAA ATT--A TTCTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA T
161934 AAATAAAAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 22
0.70 0.14 0.17
Matches are distributed among these distances:
4 2 0.02
5 22 0.24
6 63 0.68
7 6 0.06
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:163588 original size:29 final size:29
Alignment explanation
Indices: 163528--163708 Score: 127
Period size: 30 Copynumber: 6.1 Consensus size: 29
163518 AACTATATAG
* * * *
163528 AAAA-TATATTTTAACCTCTAAACGTTCT
1 AAAATTATATTTTAACCCCTAACCTTTCA
163556 AAAATTATATTTTAACCCCTAACCTTTCAA
1 AAAATTATATTTTAACCCCTAACCTTTC-A
* **
163586 AAAAATATATTTTGGCCCCTTAA-CTTTCCA
1 AAAATTATATTTTAACCCC-TAACCTTT-CA
* *
163616 AAAATTAT-TGTTTGACCCCTAAACTTTCCA
1 AAAATTATAT-TTTAACCCCTAACCTTT-CA
* * *
163646 AAAATTAT-TGTTTGACCCCTAAACTTTTTA
1 AAAATTATAT-TTTAACCCCT-AACCTTTCA
* * *
163676 AAAATTACATTTTAACCCTTAAACTTTTCA
1 AAAATTATATTTTAACCCCT-AACCTTTCA
163706 AAA
1 AAA
163709 TAAATATTTT
Statistics
Matches: 129, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
28 4 0.03
29 24 0.19
30 91 0.71
31 10 0.08
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAATTATATTTTAACCCCTAACCTTTCA
Found at i:163597 original size:30 final size:30
Alignment explanation
Indices: 163528--163771 Score: 120
Period size: 30 Copynumber: 8.1 Consensus size: 30
163518 AACTATATAG
* * * *
163528 AAAATATATTTTAACCTCTAAACGTTC-TA
1 AAAATATATTTTAACCCCTAACCTTTCAAA
*
163557 AAATTATATTTTAACCCCTAACCTTTCAAA
1 AAAATATATTTTAACCCCTAACCTTTCAAA
** *
163587 AAAATATATTTTGGCCCCTTAA-CTTTCCAA
1 AAAATATATTTTAACCCC-TAACCTTTCAAA
* * * *
163617 AAATTAT-TGTTTGACCCCTAAACTTTCCAA
1 AAAATATAT-TTTAACCCCTAACCTTTCAAA
* * * **
163647 AAATTAT-TGTTTGACCCCTAAACTTTTTAA
1 AAAATATAT-TTTAACCCCTAACCTTTCAAA
* * * *
163677 AAATTACATTTTAACCCTTAAACTTTTCAAA
1 AAAATATATTTTAACCCCT-AACCTTTCAAA
* * * * *
163708 ATAAATAT-TTTGACCCCCAAACTTTTTATAA
1 A-AAATATATTTTAACCCCTAACCTTTCA-AA
* * * *
163739 AAAATACATTTTGACCCTTAAACTTTTCAAA
1 AAAATATATTTTAACCCCT-AACCTTTCAAA
163770 AA
1 AA
163772 TTACATTTTT
Statistics
Matches: 171, Mismatches: 34, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
29 27 0.16
30 100 0.58
31 32 0.19
32 12 0.07
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (30 bp):
AAAATATATTTTAACCCCTAACCTTTCAAA
Found at i:163762 original size:62 final size:61
Alignment explanation
Indices: 163626--163830 Score: 192
Period size: 62 Copynumber: 3.4 Consensus size: 61
163616 AAAATTATTG
* * * * *
163626 TTTGACCCCTAAAC-TTTCCAAAAATTATTGTTTGACCCCTAAACTTTTTAAAAATTACAT
1 TTTGACCCTTAAACTTTTCAAAAAAATATTGTTTGACCCCCAAACTTTTTAAAAAATACAT
*
163686 TTTAACCCTTAAACTTTTCAAAATAAATA-T-TTTGACCCCCAAACTTTTTATAAAAAATACAT
1 TTTGACCCTTAAACTTTTCAAAA-AAATATTGTTTGACCCCCAAAC-TTTT-TAAAAAATACAT
* * *
163748 TTTGACCCTTAAACTTTTCAAAAATTACATT-TTT--CCCCTCAAAC-TTTTAAAAATTACCAT
1 TTTGACCCTTAAACTTTTCAAAAA-AATATTGTTTGACCCC-CAAACTTTTTAAAAAATA-CAT
* * *
163808 TTTTACCCTCAAA-TTTCCAAAAA
1 TTTGACCCTTAAACTTTTCAAAAA
163831 TTACCATTTT
Statistics
Matches: 124, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
59 17 0.14
60 42 0.34
61 17 0.14
62 44 0.35
63 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (61 bp):
TTTGACCCTTAAACTTTTCAAAAAAATATTGTTTGACCCCCAAACTTTTTAAAAAATACAT
Found at i:163777 original size:30 final size:30
Alignment explanation
Indices: 163556--163902 Score: 243
Period size: 30 Copynumber: 11.6 Consensus size: 30
163546 TAAACGTTCT
* * *
163556 AAAATTATATTTTAACCCCT-AACCTTTCAA
1 AAAATTACATTTTGACCCCTAAACTTTTC-A
* * * * *
163586 AAAAATATATTTTGGCCCCTTAACTTTCCA
1 AAAATTACATTTTGACCCCTAAACTTTTCA
* *
163616 AAAATTA-TTGTTTGACCCCTAAACTTTCCA
1 AAAATTACAT-TTTGACCCCTAAACTTTTCA
* *
163646 AAAATTA-TTGTTTGACCCCTAAACTTTTTA
1 AAAATTACAT-TTTGACCCCTAAACTTTTCA
* *
163676 AAAATTACATTTTAACCCTTAAACTTTTC-
1 AAAATTACATTTTGACCCCTAAACTTTTCA
* * * *
163705 AAAATAAATATTTTGACCCCCAAACTTTTTATA
1 AAAAT-TACATTTTGACCCCTAAAC-TTTT-CA
* *
163738 AAAAATACATTTTGACCCTTAAACTTTTCA
1 AAAATTACATTTTGACCCCTAAACTTTTCA
*
163768 AAAATTACATTTT-TCCCCTCAAACTTTT-A
1 AAAATTACATTTTGACCCCT-AAACTTTTCA
* *
163797 AAAATTACCATTTTTA-CCCTCAAA-TTTCCA
1 AAAATTA-CATTTTGACCCCT-AAACTTTTCA
** * *
163827 AAAATTACCATTTT-ACCCCCGAA-TGTCCA
1 AAAATTA-CATTTTGACCCCTAAACTTTTCA
* *
163856 AAAATTACATTTTG-TCCCT-AAGTTTTCA
1 AAAATTACATTTTGACCCCTAAACTTTTCA
163884 AAAATTACTATTTT-ACCCC
1 AAAATTAC-ATTTTGACCCC
163903 CGAATGTCTA
Statistics
Matches: 261, Mismatches: 40, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
27 2 0.01
28 21 0.08
29 44 0.17
30 160 0.61
31 15 0.06
32 15 0.06
33 4 0.02
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAACTTTTCA
Found at i:163842 original size:29 final size:29
Alignment explanation
Indices: 163737--163987 Score: 181
Period size: 29 Copynumber: 8.7 Consensus size: 29
163727 AACTTTTTAT
* * *
163737 AAAAAATA-CATTTTGACCCTTAAACTTTTC
1 AAAAATTACCATTTT-ACCCTCAAA-TTTCC
* *
163767 AAAAATTA-CATTTTTCCCCTCAAACTTT-T
1 AAAAATTACCA-TTTTACCCTCAAA-TTTCC
163796 AAAAATTACCATTTTTACCCTCAAATTTCC
1 AAAAATTACCA-TTTTACCCTCAAATTTCC
* * *
163826 AAAAATTACCATTTTACCCCCGAATGTCC
1 AAAAATTACCATTTTACCCTCAAATTTCC
* * *
163855 AAAAATTA-CATTTTGTCCCT-AAGTTTTC
1 AAAAATTACCATTTT-ACCCTCAAATTTCC
* * * * *
163883 AAAAATTACTATTTTACCCCCGAATGTCT
1 AAAAATTACCATTTTACCCTCAAATTTCC
** * *
163912 AAAAATTA-CATTTTTGCCTTAAATGTCC
1 AAAAATTACCATTTTACCCTCAAATTTCC
** ** *
163940 AAAAATTACCGGTTTACCCTTGAGTTTCC
1 AAAAATTACCATTTTACCCTCAAATTTCC
163969 AAAAATTACCATTTTACCC
1 AAAAATTACCATTTTACCC
163988 CTGTACATCA
Statistics
Matches: 175, Mismatches: 39, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
28 42 0.24
29 83 0.47
30 46 0.26
31 4 0.02
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCAAATTTCC
Found at i:163919 original size:86 final size:84
Alignment explanation
Indices: 163766--163988 Score: 223
Period size: 86 Copynumber: 2.6 Consensus size: 84
163756 TTAAACTTTT
* * *
163766 CAAAAATTACATTTTTCCCCTCAAACTTTT-AAAAATTACCATTTTTACCCTCAAATTTCCAAAA
1 CAAAAATTACATTTTT-CCCT--AAGTTTTCAAAAATTACCA-TTTTACCCCCAAATGTCCAAAA
*
163830 ATTACCATTTTACCCCCGAATGTC
62 ATTA-CATTTTACCCCCAAATGTC
* * *
163854 CAAAAATTACATTTTGTCCCTAAGTTTTCAAAAATTACTATTTTACCCCCGAATGTCTAAAAATT
1 CAAAAATTACATTTT-TCCCTAAGTTTTCAAAAATTACCATTTTACCCCCAAATGTCCAAAAATT
** **
163919 ACATTTTTGCCTTAAATGTC
65 ACATTTTACCCCCAAATGTC
** * * *
163939 CAAAAATTACCGGTTTACCCTTGAGTTTCCAAAAATTACCATTTTACCCC
1 CAAAAATTA-CATTTTTCCC-TAAGTTTTCAAAAATTACCATTTTACCCC
163989 TGTACATCAA
Statistics
Matches: 114, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
85 26 0.23
86 58 0.51
87 10 0.09
88 19 0.17
89 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (84 bp):
CAAAAATTACATTTTTCCCTAAGTTTTCAAAAATTACCATTTTACCCCCAAATGTCCAAAAATTA
CATTTTACCCCCAAATGTC
Found at i:163956 original size:57 final size:57
Alignment explanation
Indices: 163736--163958 Score: 211
Period size: 57 Copynumber: 3.8 Consensus size: 57
163726 AAACTTTTTA
* * * * *
163736 TAAAAAATACA-TTTTGACCCTTAAACTTTTCAAAAATTA-CATTTTTCCCCTCAAACT-TT
1 TAAAAATTACATTTTTG--CCTTAAA-TTTCCAAAAATTACCATTTTACCCC-CGAA-TGTC
* *
163795 TAAAAATTACCATTTTTACCCTCAAATTTCCAAAAATTACCATTTTACCCCCGAATGTC
1 TAAAAATTA-CATTTTT-GCCTTAAATTTCCAAAAATTACCATTTTACCCCCGAATGTC
* * * * *
163854 CAAAAATTACA-TTTTGTCCCTAAGTTTTCAAAAATTACTATTTTACCCCCGAATGTC
1 TAAAAATTACATTTTTG-CCTTAAATTTCCAAAAATTACCATTTTACCCCCGAATGTC
* **
163911 TAAAAATTACATTTTTGCCTTAAATGTCCAAAAATTACCGGTTTACCC
1 TAAAAATTACATTTTTGCCTTAAATTTCCAAAAATTACCATTTTACCC
163959 TTGAGTTTCC
Statistics
Matches: 135, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
57 73 0.54
58 8 0.06
59 32 0.24
60 18 0.13
61 4 0.03
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.36
Consensus pattern (57 bp):
TAAAAATTACATTTTTGCCTTAAATTTCCAAAAATTACCATTTTACCCCCGAATGTC
Found at i:163973 original size:57 final size:58
Alignment explanation
Indices: 163796--163983 Score: 211
Period size: 57 Copynumber: 3.3 Consensus size: 58
163786 TCAAACTTTT
* *
163796 AAAAATTACCATTTTTACCCTCAAATTTCCAAAAATTACCATTTTACCCCCGAATGTCC
1 AAAAATTACCATTTTT-GCCTTAAATTTCCAAAAATTACCATTTTACCCCCGAATGTCC
* * * * *
163855 AAAAATTA-CA-TTTTGTCCCTAAGTTTTCAAAAATTACTATTTTACCCCCGAATGTCT
1 AAAAATTACCATTTTTG-CCTTAAATTTCCAAAAATTACCATTTTACCCCCGAATGTCC
* ** ** * *
163912 AAAAATTA-CATTTTTGCCTTAAATGTCCAAAAATTACCGGTTTACCCTTGAGTTTCC
1 AAAAATTACCATTTTTGCCTTAAATTTCCAAAAATTACCATTTTACCCCCGAATGTCC
163969 AAAAATTACCATTTT
1 AAAAATTACCATTTT
163984 ACCCCTGTAC
Statistics
Matches: 107, Mismatches: 19, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
57 86 0.80
58 13 0.12
59 8 0.07
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (58 bp):
AAAAATTACCATTTTTGCCTTAAATTTCCAAAAATTACCATTTTACCCCCGAATGTCC
Found at i:165682 original size:17 final size:17
Alignment explanation
Indices: 165657--165723 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
165647 TATATATATG
*
165657 AAAATGCAATGACAATG
1 AAAATGCAATGACAATA
* * *
165674 TAGATGCAACGACAATA
1 AAAATGCAATGACAATA
*
165691 AAAATGCAATGACATTA
1 AAAATGCAATGACAATA
* *
165708 ATAATGCAAGGACAAT
1 AAAATGCAATGACAAT
165724 TATACTACAG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.51, C:0.13, G:0.16, T:0.19
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:165715 original size:34 final size:34
Alignment explanation
Indices: 165657--165723 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
165647 TATATATATG
*
165657 AAAATGCAATGACAATGTAGATGCAACGACAATA
1 AAAATGCAATGACAATATAGATGCAACGACAATA
* *
165691 AAAATGCAATGACATTAATA-ATGCAAGGACAAT
1 AAAATGCAATGACAAT-ATAGATGCAACGACAAT
165724 TATACTACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.51, C:0.13, G:0.16, T:0.19
Consensus pattern (34 bp):
AAAATGCAATGACAATATAGATGCAACGACAATA
Found at i:166360 original size:30 final size:30
Alignment explanation
Indices: 166324--166385 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
166314 TTAGAGTATG
* * *
166324 CACCTCTTTAACCATAGCTGCTCGTTCTAC
1 CACCTCTTCAACCATAGCTGCCCGCTCTAC
166354 CACCTCTTCAACCATAGCTGCCCGCTCTAC
1 CACCTCTTCAACCATAGCTGCCCGCTCTAC
166384 CA
1 CA
166386 TATTAAACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.21, C:0.42, G:0.10, T:0.27
Consensus pattern (30 bp):
CACCTCTTCAACCATAGCTGCCCGCTCTAC
Found at i:174168 original size:23 final size:23
Alignment explanation
Indices: 174142--174201 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
174132 AAGTTTGTTG
* *
174142 TTAGTAGTTAATGAAGTCTATTA
1 TTAGCAGTTAATGAAGTCCATTA
* *
174165 TTAGCAGTTAATGGAGTCCGTTA
1 TTAGCAGTTAATGAAGTCCATTA
*
174188 TTAGCAGTTGATGA
1 TTAGCAGTTAATGA
174202 GGTTGGTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (23 bp):
TTAGCAGTTAATGAAGTCCATTA
Found at i:175431 original size:6 final size:6
Alignment explanation
Indices: 175422--175447 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
175412 AATATGACAC
175422 AATATT AATATT AATATT AATATT AA
1 AATATT AATATT AATATT AATATT AA
175448 CTAAATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATATT
Found at i:177435 original size:29 final size:29
Alignment explanation
Indices: 177402--177457 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
177392 CAAATAGAGT
*
177402 AACTAAA-TTCATGAAATTAAAAGTATAAG
1 AACTAAATTTCA-AAAATTAAAAGTATAAG
*
177431 AACTAAATTTCAAAAATTCAAAGTATA
1 AACTAAATTTCAAAAATTAAAAGTATA
177458 TGGACCAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (29 bp):
AACTAAATTTCAAAAATTAAAAGTATAAG
Found at i:181793 original size:15 final size:16
Alignment explanation
Indices: 181761--181793 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
181751 TAAAGTTAAA
181761 AACATATATTTAAAAT
1 AACATATATTTAAAAT
*
181777 AACATAT-TTTAATAT
1 AACATATATTTAAAAT
181792 AA
1 AA
181794 AAATTTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
AACATATATTTAAAAT
Found at i:182959 original size:21 final size:21
Alignment explanation
Indices: 182935--182974 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
182925 ATTTAAAATC
*
182935 ATATCTAAATAATT-TAATAAA
1 ATATC-AAAAAATTATAATAAA
182956 ATATCAAAAAATTATAATA
1 ATATCAAAAAATTATAATA
182975 TCAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
ATATCAAAAAATTATAATAAA
Found at i:186507 original size:97 final size:97
Alignment explanation
Indices: 186394--186584 Score: 346
Period size: 97 Copynumber: 2.0 Consensus size: 97
186384 AAATAAATAG
* * *
186394 AGTTTAACTAAAAGATTATTTTTCAAATTTGACTAAAATATGAGTCATACTCAACAATTATTGTG
1 AGTTTAACTAAAAGATTATTTCTCAAATTTAACTAAAATATGAGTCATACTAAACAATTATTGTG
186459 GAAGAACAAACTATTAACTAATAAGGAGACAA
66 GAAGAACAAACTATTAACTAATAAGGAGACAA
*
186491 AGTTTAACTAAAAGATTATTTCTCAAATTTAACTGAAATATGAGTCATACTAAACAATTATTGTG
1 AGTTTAACTAAAAGATTATTTCTCAAATTTAACTAAAATATGAGTCATACTAAACAATTATTGTG
186556 GAAGAACAAACTATTAACTAATAAGGAGA
66 GAAGAACAAACTATTAACTAATAAGGAGA
186585 GACTTAGAAG
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.31
Consensus pattern (97 bp):
AGTTTAACTAAAAGATTATTTCTCAAATTTAACTAAAATATGAGTCATACTAAACAATTATTGTG
GAAGAACAAACTATTAACTAATAAGGAGACAA
Found at i:188238 original size:183 final size:183
Alignment explanation
Indices: 187930--188298 Score: 702
Period size: 183 Copynumber: 2.0 Consensus size: 183
187920 TGAAGATAGA
*
187930 AATTTTTTAAGGGTCGAAATTAAATTATAATTTTTACGATAGTAAAAATGTAATTTTTGAAAGAT
1 AATTTTTTAAGGGTCGAAATTAAATTATAATTTTTACGATAGTAAAAATGTAATTTTTAAAAGAT
*
187995 TAAATCAAAATTTTATTATTTTTAAAGGGGTAAAGTGCAATTTAACATTTATTAATTTAAACTTT
66 TAAATCAAAATTTTATTATTTTTAAAGGGGTAAAGTACAATTTAACATTTATTAATTTAAACTTT
188060 TAAATTTTTAAAAAATGTAAACGGAAAAAATTTCATTTTAAGAGTGACCTCCT
131 TAAATTTTTAAAAAATGTAAACGGAAAAAATTTCATTTTAAGAGTGACCTCCT
*
188113 AATTTTTTAAGGGTCGAAATTAAATTATAATTTTTACTATAGTAAAAATGTAATTTTTAAAAGAT
1 AATTTTTTAAGGGTCGAAATTAAATTATAATTTTTACGATAGTAAAAATGTAATTTTTAAAAGAT
*
188178 TAAATCAAAATTTTATTATTTTTAAAGGGGTAAAGTATAATTTAACATTTATTAATTTAAACTTT
66 TAAATCAAAATTTTATTATTTTTAAAGGGGTAAAGTACAATTTAACATTTATTAATTTAAACTTT
188243 TAAATTTTTAAAAAATGTAAACGGAAAAAATTTCATTTTAAGAGTGACCTCCT
131 TAAATTTTTAAAAAATGTAAACGGAAAAAATTTCATTTTAAGAGTGACCTCCT
188296 AAT
1 AAT
188299 CCAAAATTTG
Statistics
Matches: 182, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 182 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (183 bp):
AATTTTTTAAGGGTCGAAATTAAATTATAATTTTTACGATAGTAAAAATGTAATTTTTAAAAGAT
TAAATCAAAATTTTATTATTTTTAAAGGGGTAAAGTACAATTTAACATTTATTAATTTAAACTTT
TAAATTTTTAAAAAATGTAAACGGAAAAAATTTCATTTTAAGAGTGACCTCCT
Found at i:191256 original size:51 final size:49
Alignment explanation
Indices: 191190--191314 Score: 139
Period size: 49 Copynumber: 2.5 Consensus size: 49
191180 CATGTCAACA
* *
191190 TTTAATTAATTTTTAAAATTTAAAAATA-TTAAAAATATATATTTATATATTT
1 TTTAA-TAATTTTTAAATTTTAAAAATAGTT---AATATATATATATATATTT
*
191242 TTTAATAATTTTT-AATTTGTAAAAATAGTTTATATATATATATATATTT
1 TTTAATAATTTTTAAATTT-TAAAAATAGTTAATATATATATATATATTT
**
191291 TTTTTTAA-TTTTAAATTTTAAAAA
1 TTTAATAATTTTTAAATTTTAAAAA
191315 ATCAATTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
48 10 0.15
49 28 0.43
50 4 0.06
51 16 0.25
52 7 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (49 bp):
TTTAATAATTTTTAAATTTTAAAAATAGTTAATATATATATATATATTT
Found at i:191706 original size:19 final size:20
Alignment explanation
Indices: 191682--191732 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 20
191672 TGATTTAATG
191682 TTTAATTGTATAA-ATAAAT
1 TTTAATTGTATAATATAAAT
*
191701 TTTAATTTGGTGTAATTATAAAT
1 TTTAA-TT-GTATAA-TATAAAT
191724 TTTAATTGT
1 TTTAATTGT
191733 GGTTCAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.19
20 2 0.07
21 7 0.26
22 2 0.07
23 11 0.41
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTAATTGTATAATATAAAT
Found at i:191955 original size:29 final size:30
Alignment explanation
Indices: 191902--191981 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
191892 AATTGGATCT
* *
191902 AATCAAAATTTTATGTATAAAATT-ACATAA
1 AATCAAAA-TTCATATATAAAATTAACATAA
*
191932 AATCAAAATTCATATATAAAATTACACATTA
1 AATCAAAATTCATATATAAAATTA-ACATAA
* *
191963 AACCATAATTCATATATAA
1 AATCAAAATTCATATATAA
191982 TTTTAAGATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.30
30 8 0.19
31 22 0.51
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (30 bp):
AATCAAAATTCATATATAAAATTAACATAA
Found at i:200985 original size:4 final size:4
Alignment explanation
Indices: 200976--201022 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
200966 GGTGTTAAAC
200976 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
201023 AAGAAAAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:202922 original size:45 final size:45
Alignment explanation
Indices: 202821--202911 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
202811 TATGGTTTCA
202821 ACCTAAATTTTCGATACAAATATTTAACTATCTAATAAAAAGATT
1 ACCTAAATTTTCGATACAAATATTTAACTATCTAATAAAAAGATT
*
202866 ACCTAAATTTTCGATACAAATATTTAACTATCTAATAGAAAGATT
1 ACCTAAATTTTCGATACAAATATTTAACTATCTAATAAAAAGATT
202911 A
1 A
202912 TTTGTTTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.35
Consensus pattern (45 bp):
ACCTAAATTTTCGATACAAATATTTAACTATCTAATAAAAAGATT
Found at i:205078 original size:80 final size:80
Alignment explanation
Indices: 204908--205133 Score: 253
Period size: 80 Copynumber: 2.8 Consensus size: 80
204898 TAACCAGTAT
* * * * * *
204908 ACGATGCTGCTCATACAAGCTATCAAGAATCCGTAACAAATTCC-GACCTCAGCCATC-GATACG
1 ACGATGCTGCTCACACAAGCTATCAAGAATCCGCAACATATGCCGGATCTTAGCCATCGGA-A-G
*
204971 G-CCCTTTTATCCACTC
64 GTCCATTTTATCCACTC
*
204987 ACGATGTTGCTCACACAAGCTATCAAGAATCCGCAACATATGCCGGATCTTAGCCATCGGAAGGT
1 ACGATGCTGCTCACACAAGCTATCAAGAATCCGCAACATATGCCGGATCTTAGCCATCGGAAGGT
*
205052 CCATATT-TCTCACTC
66 CCATTTTATC-CACTC
* *** ** *
205067 ACGATACTGCTCACACAAGCTATCAAGAAAATGCAACATATGTAGGATCTTAGCCATCGGAGGGT
1 ACGATGCTGCTCACACAAGCTATCAAGAATCCGCAACATATGCCGGATCTTAGCCATCGGAAGGT
205132 CC
66 CC
205134 TTACATCAAT
Statistics
Matches: 126, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
79 43 0.34
80 81 0.64
81 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (80 bp):
ACGATGCTGCTCACACAAGCTATCAAGAATCCGCAACATATGCCGGATCTTAGCCATCGGAAGGT
CCATTTTATCCACTC
Found at i:205383 original size:3 final size:3
Alignment explanation
Indices: 205375--205414 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
205365 AAGGGCTCAA
* *
205375 ATT ATT ATT ATC ATT ACT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
205415 GGGTTCATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:205950 original size:151 final size:151
Alignment explanation
Indices: 205790--206362 Score: 527
Period size: 151 Copynumber: 3.7 Consensus size: 151
205780 TAAAGGGTTT
* * *** * * *
205790 TTTTAAAGAAAAATAGCTTGATTTGGGAA-ATAGTTTTGGTTTTTTTAAACAATTTCGAAATAAA
1 TTTTAAAGAAAAATAACTTAATTTTTAAACAAAGTTTTGATTTTTTTAAACTATTTCGAAATAAA
205854 AGTTTTGATTTTTATGAAAATTAGTGATTTTCTTTAAAAAAAAAAAGAAAGTTTATATTTTTAAA
66 AGTTTTGATTTTTATGAAAA-TAGTGATTTTCTTTAAAAAAAAAAAGAAAGTTTATATTTTTAAA
* *
205919 AATAAAAATCTATTTTTAGTTA
130 AATAAAAATATATTTTTAGTCA
** * *
205941 TTTTAAAGAAAAATTTC-AAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAA
1 TTTTAAAGAAAAATAACTTAATTTTTAAACAAAGTTTTGATTTTTTTAAACTATTTCGAAATAAA
* * * * * *
206005 AATTTAGATTTTTAAAT-AAAATAGTAAATTTCTTT---AAAAAAGAGAAAGTTTAGATTTTTAA
66 AGTTTTGATTTTT--ATGAAAATAGTGATTTTCTTTAAAAAAAAAAAGAAAGTTTATATTTTTAA
* *
206066 AATTAAAAATTTATTTTTTAGTCA
129 AAATAAAAATATA-TTTTTAGTCA
* * * * *
206090 TTTTAAAGAAAAAAAAATTAAGTTTTTAAACAAAATTTTGATTTTTTTTTAAACTATTTTGTAAT
1 TTTTAAAGAAAAATAACTTAA-TTTTTAAACAAAGTTTTGA--TTTTTTTAAACTATTTCGAAAT
* * * * *
206155 AAAAG-TTTGAATTTTTAAGTAAAGTGGTGATTTTCATTAAAAAAAAAAAAGAAAGTTTAGATTT
63 AAAAGTTTTG-ATTTTTATG-AAAATAGTGATTTTC-TTTAAAAAAAAAAAGAAAGTTT--A-TA
* *
206219 TTTTTAAAAATAAAAATATGTTTTTTAGTGA
122 TTTTTAAAAATAAAAATAT-ATTTTTAGTCA
* * ** *
206250 TTTTAAAGAAAAAGT-TC-AAAAATTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAA
1 TTTTAAAGAAAAA-TAACTTAATTTTTAAACAAAGTTTTGATTTTTTTAAACTATTTCGAAATAA
* * * *
206313 AAGTTTTGATTTTGAAAT-AAAATAGTGATTTTGTTTTAAACAAAAGAAGA
65 AAGTTTTGATTTT--TATGAAAATAGTGATTTT-CTTTAAAAAAAAAAAGA
206363 CTTTTGATTT
Statistics
Matches: 336, Mismatches: 62, Indels: 43
0.76 0.14 0.10
Matches are distributed among these distances:
148 35 0.10
149 22 0.07
150 8 0.02
151 88 0.26
152 7 0.02
153 42 0.12
154 2 0.01
156 54 0.16
157 19 0.06
158 17 0.05
159 3 0.01
160 39 0.12
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (151 bp):
TTTTAAAGAAAAATAACTTAATTTTTAAACAAAGTTTTGATTTTTTTAAACTATTTCGAAATAAA
AGTTTTGATTTTTATGAAAATAGTGATTTTCTTTAAAAAAAAAAAGAAAGTTTATATTTTTAAAA
ATAAAAATATATTTTTAGTCA
Found at i:207487 original size:18 final size:17
Alignment explanation
Indices: 207448--207483 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
207438 TTTAATTTTT
207448 AATTTATTTAAAGTTTA
1 AATTTATTTAAAGTTTA
207465 AATTTATTTCAAA-TTTA
1 AATTTATTT-AAAGTTTA
207482 AA
1 AA
207484 ATTTGAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
AATTTATTTAAAGTTTA
Found at i:208112 original size:3 final size:3
Alignment explanation
Indices: 208099--208136 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
208089 ATATTAAATA
*
208099 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
208137 AGGAACTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:209242 original size:30 final size:30
Alignment explanation
Indices: 209208--209338 Score: 169
Period size: 30 Copynumber: 4.4 Consensus size: 30
209198 AAACTCTTCC
*
209208 AAAATTGCATTTTAACCCTTAAAATTTTCT
1 AAAATTACATTTTAACCCTTAAAATTTTCT
* *
209238 AAAATTACATTTTAACCC--AAATTTTTTT
1 AAAATTACATTTTAACCCTTAAAATTTTCT
*
209266 AAAATTACATTTTAACCCTTAAACTTTTCCT
1 AAAATTACATTTTAACCCTTAAAATTTT-CT
* * *
209297 -AAATTACATTTTGACCCCTAAAATTTTCC
1 AAAATTACATTTTAACCCTTAAAATTTTCT
209326 AAAATTACATTTT
1 AAAATTACATTTT
209339 GCCTCAAACT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
28 26 0.30
29 1 0.01
30 60 0.68
31 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAAATTTTCT
Found at i:209279 original size:58 final size:60
Alignment explanation
Indices: 209204--209338 Score: 186
Period size: 58 Copynumber: 2.3 Consensus size: 60
209194 TTCTAAACTC
* *
209204 TTCCAAAATTGCATTTTAACCCTTAAAATTTT-CTAAAATTACATTTT-AACCC-AAATTT
1 TTCCAAAATTACATTTTAACCCTTAAAATTTTCCT-AAATTACATTTTGAACCCTAAAATT
** * *
209262 TTTTAAAATTACATTTTAACCCTTAAACTTTTCCTAAATTACATTTTGACCCCTAAAATT
1 TTCCAAAATTACATTTTAACCCTTAAAATTTTCCTAAATTACATTTTGAACCCTAAAATT
209322 TTCCAAAATTACATTTT
1 TTCCAAAATTACATTTT
209339 GCCTCAAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 40 0.61
59 6 0.09
60 20 0.30
ACGTcount: A:0.36, C:0.19, G:0.01, T:0.43
Consensus pattern (60 bp):
TTCCAAAATTACATTTTAACCCTTAAAATTTTCCTAAATTACATTTTGAACCCTAAAATT
Found at i:209339 original size:30 final size:30
Alignment explanation
Indices: 209172--209338 Score: 167
Period size: 30 Copynumber: 5.6 Consensus size: 30
209162 GTCCCTGAAC
* * ** *
209172 TTTCCAAAAATCATATTTTAACTTCTAAACT
1 TTTCC-AAAATTACATTTTAACCCCTAAAAT
* * *
209203 CTTCCAAAATTGCATTTTAACCCTTAAAAT
1 TTTCCAAAATTACATTTTAACCCCTAAAAT
* *
209233 TTTCTAAAATTACATTTTAA-CCC-AAATT
1 TTTCCAAAATTACATTTTAACCCCTAAAAT
** * *
209261 TTTTTAAAATTACATTTTAACCCTTAAACT
1 TTTCCAAAATTACATTTTAACCCCTAAAAT
* *
209291 TTTCCTAAATTACATTTTGACCCCTAAAAT
1 TTTCCAAAATTACATTTTAACCCCTAAAAT
209321 TTTCCAAAATTACATTTT
1 TTTCCAAAATTACATTTT
209339 GCCTCAAACT
Statistics
Matches: 111, Mismatches: 23, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
28 23 0.21
29 4 0.04
30 80 0.72
31 4 0.04
ACGTcount: A:0.37, C:0.20, G:0.01, T:0.43
Consensus pattern (30 bp):
TTTCCAAAATTACATTTTAACCCCTAAAAT
Found at i:209409 original size:29 final size:28
Alignment explanation
Indices: 209297--209535 Score: 134
Period size: 29 Copynumber: 8.4 Consensus size: 28
209287 AACTTTTCCT
* * * *
209297 AAATTACATTTTGACCCCTAAAATTTTCCA
1 AAATCACATTTTTACCCC--AAACTTTCAA
* * * *
209327 AAATTACA-TTTTGCCTCAAACTTCCAA
1 AAATCACATTTTTACCCCAAACTTTCAA
* * *
209354 AAATCACA--TTTCCCCCGAACTTCCAA
1 AAATCACATTTTTACCCCAAACTTTCAA
*
209380 AAATCATATTTTTACCCCTAAACTTTCAA
1 AAATCACATTTTTACCCC-AAACTTTCAA
*
209409 AAATCACATTTTCACTCCCAAACTTCTCAA
1 AAATCACATTTTTAC-CCCAAACTT-TCAA
**
209439 AAATCACA-TTTTACCCTCGAATTTTTCAA
1 AAATCACATTTTTACCC-C-AAACTTTCAA
* * * *
209468 AAATTACCA--TTTCCCCCGAACATTCAA
1 AAATCA-CATTTTTACCCCAAACTTTCAA
*
209495 AAATTACCA-TTTTACCCTCAAA-TTTCTAA
1 AAATCA-CATTTTTACCC-CAAACTTTC-AA
*
209524 AAATTACATTTT
1 AAATCACATTTT
209536 CGACCTTAAA
Statistics
Matches: 169, Mismatches: 28, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
26 22 0.13
27 29 0.17
28 21 0.12
29 68 0.40
30 29 0.17
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (28 bp):
AAATCACATTTTTACCCCAAACTTTCAA
Found at i:209441 original size:30 final size:28
Alignment explanation
Indices: 209322--209536 Score: 142
Period size: 29 Copynumber: 7.7 Consensus size: 28
209312 CCCTAAAATT
* * *
209322 TTCC-AAAATTACATTTT-GCCTCAAAC
1 TTCCAAAAATCACATTTTCACCCCAAAC
*
209348 TTCCAAAAATCACA-TTTC-CCCCGAAC
1 TTCCAAAAATCACATTTTCACCCCAAAC
* *
209374 TTCCAAAAATCATATTTTTACCCCTAAAC
1 TTCCAAAAATCACATTTTCACCCC-AAAC
*
209403 TTTCAAAAATCACATTTTCACTCCCAAAC
1 TTCCAAAAATCACATTTTCAC-CCCAAAC
**
209432 TTCTCAAAAATCACATTTT-ACCCTCGAATT
1 TTC-CAAAAATCACATTTTCACCC-C-AAAC
* * *
209462 TTTCAAAAATTACCA-TTTC-CCCCGAAC
1 TTCCAAAAATCA-CATTTTCACCCCAAAC
* *
209489 ATT-CAAAAATTACCATTTT-ACCCTCAAAT
1 -TTCCAAAAATCA-CATTTTCACCC-CAAAC
* *
209518 TTCTAAAAATTACATTTTC
1 TTCCAAAAATCACATTTTC
209537 GACCTTAAAT
Statistics
Matches: 152, Mismatches: 20, Indels: 31
0.75 0.10 0.15
Matches are distributed among these distances:
26 26 0.17
27 24 0.16
28 23 0.15
29 55 0.36
30 24 0.16
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.33
Consensus pattern (28 bp):
TTCCAAAAATCACATTTTCACCCCAAAC
Found at i:216823 original size:21 final size:23
Alignment explanation
Indices: 216799--216840 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
216789 CCAAGCATAA
*
216799 GGTGTTTTG-AAGA-AGAAAAAT
1 GGTGTTTGGCAAGAGAGAAAAAT
216820 GGTGTTTGGCAAGAGAGAAAA
1 GGTGTTTGGCAAGAGAGAAAA
216841 TCAGGGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.40, C:0.02, G:0.33, T:0.24
Consensus pattern (23 bp):
GGTGTTTGGCAAGAGAGAAAAAT
Found at i:225271 original size:24 final size:24
Alignment explanation
Indices: 225242--225287 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
225232 TAAGGATTCG
225242 AAATTAAATTATAAATTTTTATAA
1 AAATTAAATTATAAATTTTTATAA
*
225266 AAATTAAATTATAATTTTTTAT
1 AAATTAAATTATAAATTTTTAT
225288 TGTTTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATTAAATTATAAATTTTTATAA
Found at i:226182 original size:13 final size:14
Alignment explanation
Indices: 226163--226195 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
226153 TTAAAATACT
*
226163 TAATAATTATAAAA
1 TAATAATAATAAAA
226177 -AATAATAATAAAA
1 TAATAATAATAAAA
226190 TAATAA
1 TAATAA
226196 GAGCTGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:229980 original size:45 final size:45
Alignment explanation
Indices: 229896--229984 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
229886 TTGATCCTTA
*
229896 TTCTCCAAAAGAACATCTTTTTCACCCTTCTCTCCCACAGTTTCT
1 TTCTCCAAAAGAACATCTTTTTCACCCTTATCTCCCACAGTTTCT
** **
229941 TTCTCCAAAAGAACA-CTTTTTTCTGCCTTATCTGTCACAGTTTC
1 TTCTCCAAAAGAACATC-TTTTTCACCCTTATCTCCCACAGTTTC
229985 ATCTTTTTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.22, C:0.31, G:0.07, T:0.39
Consensus pattern (45 bp):
TTCTCCAAAAGAACATCTTTTTCACCCTTATCTCCCACAGTTTCT
Found at i:234755 original size:7 final size:7
Alignment explanation
Indices: 234743--234789 Score: 58
Period size: 7 Copynumber: 6.3 Consensus size: 7
234733 ATTTTTTCTC
234743 CTTTTTT
1 CTTTTTT
234750 CTTTTTT
1 CTTTTTT
234757 CTTTTTT
1 CTTTTTT
234764 CTTTTTTT
1 C-TTTTTT
234772 CTTCCTTTT
1 CTT--TTTT
*
234781 TTTTTTT
1 CTTTTTT
234788 CT
1 CT
234790 CTTGGTGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 22 0.63
8 7 0.20
9 6 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
CTTTTTT
Found at i:234762 original size:14 final size:14
Alignment explanation
Indices: 234743--234789 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
234733 ATTTTTTCTC
234743 CTTTTTTCTTTTTT
1 CTTTTTTCTTTTTT
234757 CTTTTTTCTTTTTTT
1 CTTTTTTC-TTTTTT
*
234772 CTTCCTTTTTTTTTTT
1 CTT--TTTTCTTTTTT
234788 CT
1 CT
234790 CTTGGTGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 8 0.28
15 9 0.31
16 8 0.28
17 4 0.14
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
CTTTTTTCTTTTTT
Found at i:234765 original size:24 final size:24
Alignment explanation
Indices: 234734--234792 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
234724 TTTTGGTTCA
234734 TTTTTTCTCCTTTTTTCTT-TTTTC
1 TTTTTTCT-CTTTTTTCTTCTTTTC
*
234758 TTTTTTCT-TTTTTTCTTCCTTTTT
1 TTTTTTCTCTTTTTTCTT-CTTTTC
234782 TTTTTTCTCTT
1 TTTTTTCTCTT
234793 GGTGTGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 9 0.29
24 20 0.65
25 2 0.06
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTTTCTCTTTTTTCTTCTTTTC
Found at i:241915 original size:19 final size:19
Alignment explanation
Indices: 241887--241930 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
241877 TGCTTGAATT
241887 TTTGTTGCA-GTTTATTTA
1 TTTGTTGCAGGTTTATTTA
*
241905 TTTGCTTGCAGGTTTTTTTA
1 TTTG-TTGCAGGTTTATTTA
241925 -TTGTTG
1 TTTGTTG
241931 GGATAGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 8 0.35
20 8 0.35
ACGTcount: A:0.11, C:0.07, G:0.20, T:0.61
Consensus pattern (19 bp):
TTTGTTGCAGGTTTATTTA
Found at i:242216 original size:22 final size:23
Alignment explanation
Indices: 242154--242219 Score: 62
Period size: 28 Copynumber: 2.7 Consensus size: 23
242144 TTTTAAAAAT
*
242154 TTAATTTAAAATTTTATTATTTT
1 TTAATTTAAAATTTTATTATTTA
*
242177 TTAGATTAAAATATAATTTTATT-TTTA
1 TTA-ATT----TAAAATTTTATTATTTA
242204 TTAATTTAAAATTTTA
1 TTAATTTAAAATTTTA
242220 AAAAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
22 9 0.26
23 3 0.09
24 3 0.09
26 3 0.09
27 6 0.17
28 11 0.31
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTAATTTAAAATTTTATTATTTA
Found at i:242318 original size:21 final size:21
Alignment explanation
Indices: 242294--242333 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
242284 TTGCAGTGGT
*
242294 GACAGGAGAGA-TGATAGGTAC
1 GACAAGAGAGACTG-TAGGTAC
242315 GACAAGAGAGACTGTAGGT
1 GACAAGAGAGACTGTAGGT
242334 TAAGGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.38, C:0.10, G:0.38, T:0.15
Consensus pattern (21 bp):
GACAAGAGAGACTGTAGGTAC
Found at i:258033 original size:24 final size:25
Alignment explanation
Indices: 258000--258049 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
257990 GACTCATTTA
* *
258000 AAAATTATAAAAATATATA-TTATT
1 AAAATAATAAAAATACATATTTATT
*
258024 AAAATAATAAAATTACATATTTATT
1 AAAATAATAAAAATACATATTTATT
258049 A
1 A
258050 TTGTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAATAATAAAAATACATATTTATT
Found at i:261347 original size:2 final size:2
Alignment explanation
Indices: 261340--261370 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
261330 CCGAAGAAGG
261340 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
261371 GGGATCAGCG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:268148 original size:18 final size:19
Alignment explanation
Indices: 268113--268154 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
268103 AAATTCGAAA
*
268113 AAAT-ATTCGAGTTTACTC
1 AAATAATTCGAGTTAACTC
268131 AAATAATTCGA-TTAACTC
1 AAATAATTCGAGTTAACTC
*
268149 GAATAA
1 AAATAA
268155 CTAGATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (19 bp):
AAATAATTCGAGTTAACTC
Found at i:268753 original size:2 final size:2
Alignment explanation
Indices: 268748--268780 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
268738 TCTCTCTCTC
268748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
268781 GAAGTAGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:272782 original size:41 final size:41
Alignment explanation
Indices: 272720--272899 Score: 227
Period size: 41 Copynumber: 4.3 Consensus size: 41
272710 ACTTGATGAA
272720 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGTCTCGGGATGAGCATGAGATTATAT
*
272762 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGTATAT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATAT
* *
272803 TAAAGAAAGACTCATGTCTCGAGG-TGAGCATGAGATTATTTT
1 TAAAGGAAGACTCATGTCTCG-GGATGAGCATGAGATTA-TAT
* ** * **
272845 TAAAGGGAAAACTTGTGACTCGGGATGAGCATGAGATTACGT
1 TAAA-GGAAGACTCATGTCTCGGGATGAGCATGAGATTATAT
272887 GTAAAGGAAGACT
1 -TAAAGGAAGACT
272900 TATGATACGA
Statistics
Matches: 121, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
41 69 0.57
42 22 0.18
43 30 0.25
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (41 bp):
TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATAT
Found at i:273522 original size:21 final size:21
Alignment explanation
Indices: 273481--273534 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
273471 CGCATAATAA
273481 GTATCGGTAGAAGCATAACTT
1 GTATCGGTAGAAGCATAACTT
* *
273502 GTTTCGGTAGAAG-TTACACTT
1 GTATCGGTAGAAGCATA-ACTT
*
273523 GTACCGGTAGAA
1 GTATCGGTAGAA
273535 CTATCACAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAGCATAACTT
Found at i:279819 original size:41 final size:40
Alignment explanation
Indices: 279757--279872 Score: 128
Period size: 39 Copynumber: 2.9 Consensus size: 40
279747 GAATAAATGG
*
279757 AAGACTCATGTCTCGGAATGAGCATGAGATTATATTAAAGA
1 AAGACTAATGTCTCGG-ATGAGCATGAGATTATATTAAAGA
* * *
279798 AAGACTTATGTCTCTGGATGAGCATGAG--TATATTAATGG
1 AAGACTAATGTCTC-GGATGAGCATGAGATTATATTAAAGA
* * *
279837 AAGGCTAATTTCTCGGGGTGAGCATGAGATTATATT
1 AAGACTAATGTCTC-GGATGAGCATGAGATTATATT
279873 TAAAAGGAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 32 0.50
41 30 0.47
42 2 0.03
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (40 bp):
AAGACTAATGTCTCGGATGAGCATGAGATTATATTAAAGA
Found at i:279859 original size:39 final size:40
Alignment explanation
Indices: 279752--279872 Score: 136
Period size: 41 Copynumber: 3.0 Consensus size: 40
279742 TTAATGAATA
* *
279752 AATGGAAGACTCATGTCTCGGAATGAGCATGAGATTATATT
1 AATGGAAGACTAATGTCTCGGGATGAGCATGAGA-TATATT
* * * *
279793 AAAGAAAGACTTATGTCTCTGGATGAGCATGAG-TATATT
1 AATGGAAGACTAATGTCTCGGGATGAGCATGAGATATATT
* * *
279832 AATGGAAGGCTAATTTCTCGGGGTGAGCATGAGATTATATT
1 AATGGAAGACTAATGTCTCGGGATGAGCATGAGA-TATATT
279873 TAAAAGGAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
39 32 0.48
41 34 0.52
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.31
Consensus pattern (40 bp):
AATGGAAGACTAATGTCTCGGGATGAGCATGAGATATATT
Found at i:279934 original size:42 final size:41
Alignment explanation
Indices: 279855--279969 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 41
279845 TTTCTCGGGG
* *
279855 TGAGCATGAGATTATATTTAAAAGGAAGATTCGTGACTC-AA
1 TGAGCATGAGATTATGTTT-AAAGGAAGACTCGTGACTCGAA
* * *
279896 CTAGAGCATGAGATTATGTTTTAAGGAATACTCGTGACTCGGGA
1 -T-GAGCATGAGATTATGTTTAAAGGAAGACTCGTGACTC-GAA
*
279940 TGAGCATGAGATTATGTGTAAAGGAAGACT
1 TGAGCATGAGATTATGTTTAAAGGAAGACT
279970 TATGTTTCAG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
42 43 0.69
43 18 0.29
44 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (41 bp):
TGAGCATGAGATTATGTTTAAAGGAAGACTCGTGACTCGAA
Found at i:286842 original size:43 final size:42
Alignment explanation
Indices: 286693--286904 Score: 215
Period size: 41 Copynumber: 5.2 Consensus size: 42
286683 TGAATAAATA
* * *
286693 GAAGACTCATGTCTCGGGATGAACATGAGATTAT-ATTAAAG
1 GAAGACTCATGACTCGGGATGAGCATGAGATTATGTTTAAAG
* * * *
286734 GAAGACTCATGTCTTGGGATGAGCATGAGAGTAT-ATTAAAG
1 GAAGACTCATGACTCGGGATGAGCATGAGATTATGTTTAAAG
**
286775 GAAGACTCAT-ATCTCTAGATGAGCATGAGATTATGTTTAAAAG
1 GAAGACTCATGA-CTCGGGATGAGCATGAGATTATGTTT-AAAG
*
286818 GAAGACTCGTGACTC-GGATAGAGCATGAGATTATGTTT----
1 GAAGACTCATGACTCGGGAT-GAGCATGAGATTATGTTTAAAG
* * * *
286856 TAAGACTCGTGACTCGGGATGAGCATGAGATTACGTGTAAAG
1 GAAGACTCATGACTCGGGATGAGCATGAGATTATGTTTAAAG
286898 GAAGACT
1 GAAGACT
286905 TACGATTCGG
Statistics
Matches: 146, Mismatches: 15, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
38 30 0.21
39 4 0.03
41 66 0.45
42 11 0.08
43 34 0.23
44 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (42 bp):
GAAGACTCATGACTCGGGATGAGCATGAGATTATGTTTAAAG
Found at i:289195 original size:3 final size:3
Alignment explanation
Indices: 289187--289213 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
289177 TCAACTTGCA
289187 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
289214 TAATCTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:292300 original size:23 final size:23
Alignment explanation
Indices: 292249--292293 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
292239 TACTTGAATT
292249 TTAAAATTTGAAAAATAAAAAAA
1 TTAAAATTTGAAAAATAAAAAAA
*
292272 TTAAAATTTTAAAAATAAAAAA
1 TTAAAATTTGAAAAATAAAAAA
292294 TATAAAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
TTAAAATTTGAAAAATAAAAAAA
Found at i:293385 original size:31 final size:31
Alignment explanation
Indices: 293347--293410 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
293337 GTATTTATAC
* * * *
293347 TTTAATTTGGTTATTTTTAGTCATTATACTT
1 TTTAATTTAGTCAATTTTAGTCATTATAATT
*
293378 TTTAATTTAGTCAATTTTAGTCCTTATAATT
1 TTTAATTTAGTCAATTTTAGTCATTATAATT
293409 TT
1 TT
293411 CAAAATCTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.59
Consensus pattern (31 bp):
TTTAATTTAGTCAATTTTAGTCATTATAATT
Found at i:300134 original size:21 final size:21
Alignment explanation
Indices: 300110--300154 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
300100 TGAGTAAAAA
300110 ATATTGTGATA-ATATTTTTAT
1 ATATTGTGA-AGATATTTTTAT
* *
300131 ATATTTTTAAGATATTTTTAT
1 ATATTGTGAAGATATTTTTAT
300152 ATA
1 ATA
300155 AAAAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATATTGTGAAGATATTTTTAT
Found at i:300138 original size:11 final size:10
Alignment explanation
Indices: 300121--300154 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
300111 TATTGTGATA
300121 ATATTTTTAT
1 ATATTTTTAT
*
300131 ATATTTTTAAG
1 ATATTTTT-AT
300142 ATATTTTTAT
1 ATATTTTTAT
300152 ATA
1 ATA
300155 AAAAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (10 bp):
ATATTTTTAT
Found at i:300163 original size:24 final size:24
Alignment explanation
Indices: 300136--300185 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
300126 TTTATATATT
300136 TTTAAGATATT-TTTATATAAAAAA
1 TTTAAGA-ATTATTTATATAAAAAA
** *
300160 TTTATTAATTATTTATATAATAAA
1 TTTAAGAATTATTTATATAAAAAA
300184 TT
1 TT
300186 AATAAAATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAGAATTATTTATATAAAAAA
Done.