Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002346.1 Kokia drynarioides strain JFW-HI SEQ_114406, 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: 246912
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:1953 original size:26 final size:25
Alignment explanation
Indices: 1924--1973 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1914 GTATAAAATA
* *
1924 TTAACAATTTAAAATAAGTTAAAAAG
1 TTAACAAATT-AAATAAATTAAAAAG
*
1950 TTAATAAATTAAATAAATTAAAAA
1 TTAACAAATTAAATAAATTAAAAA
1974 TTAGAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (25 bp):
TTAACAAATTAAATAAATTAAAAAG
Found at i:9803 original size:26 final size:26
Alignment explanation
Indices: 9774--9828 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
9764 TCGATATTAA
9774 TTACTAAGAATTTGCATGAATTTGAG
1 TTACTAAGAATTTGCATGAATTTGAG
9800 TTACTAAGAATTTGCATGAATTTGAG
1 TTACTAAGAATTTGCATGAATTTGAG
9826 TTA
1 TTA
9829 AAAAGGGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (26 bp):
TTACTAAGAATTTGCATGAATTTGAG
Found at i:12997 original size:22 final size:19
Alignment explanation
Indices: 12954--12997 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
12944 CATTCCCATT
*
12954 ATAAAATAAATCACTTTAA
1 ATAAAATAAATCACTTCAA
12973 ATAATAATAAATCACATTCACA
1 ATAA-AATAAATCAC-TTCA-A
12995 ATA
1 ATA
12998 GCCACTTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 10 0.48
21 3 0.14
22 4 0.19
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAAATAAATCACTTCAA
Found at i:13737 original size:46 final size:45
Alignment explanation
Indices: 13644--13737 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 45
13634 TGATTACGAG
* **
13644 TTAAAAATATTATATATTTAAGCACATTAAAATTAATGTTGTCATT
1 TTAAAAATATTATATATTTAAGCACATTAAAATCAACATTG-CATT
*
13690 TTAAAAATATTATATATTTAAGCACGTTAAAATGACAACATTG-ATT
1 TTAAAAATATTATATATTTAAGCACATTAAAAT--CAACATTGCATT
13736 TT
1 TT
13738 CATTTTCTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 37 0.88
48 5 0.12
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (45 bp):
TTAAAAATATTATATATTTAAGCACATTAAAATCAACATTGCATT
Found at i:17895 original size:55 final size:55
Alignment explanation
Indices: 17829--17939 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
17819 GGTAATAAAA
*
17829 TATGCATAATACAATGAAAATGTAAAAATTGTATTAAAATAAAGTTTTGATTTAG
1 TATGCATAATACAATGAAAAAGTAAAAATTGTATTAAAATAAAGTTTTGATTTAG
17884 TATGCATAATACAATGAAAAAGTAAAAATTGTATTAAAATAAAGTTTTGATTTAG
1 TATGCATAATACAATGAAAAAGTAAAAATTGTATTAAAATAAAGTTTTGATTTAG
17939 T
1 T
17940 CATATGTTTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.36
Consensus pattern (55 bp):
TATGCATAATACAATGAAAAAGTAAAAATTGTATTAAAATAAAGTTTTGATTTAG
Found at i:18819 original size:209 final size:209
Alignment explanation
Indices: 18459--18869 Score: 759
Period size: 209 Copynumber: 2.0 Consensus size: 209
18449 TAAGAGAACT
*
18459 GAAAGTCATATCCAACACGTTAGGGCACTATGTTCTCAGACTTTCGAAACTGAAGGAGACTTTGA
1 GAAAGTCATATCCAACACGTTAGGGCACTATGTTCTCAGACTTTCGAAACTGAAGGACACTTTGA
18524 AAGACTTTAAACAGGATATTCGATTATGTGAATTATACAAAAATCACACCCAACACGTTAGGGCA
66 AAGACTTTAAACAGGATATTCGATTATGTGAATTATACAAAAATCACACCCAACACGTTAGGGCA
18589 TGTTTTTTCGAAGTCTTCACACGAAAGGATATTTCCTCGTGTTGTTTTAAAATCATTTGTATATA
131 TGTTTTTTCGAAGTCTTCACACGAAAGGATATTTCCTCGTGTTGTTTTAAAATCATTTGTATATA
18654 AATATATATATATA
196 AATATATATATATA
*
18668 GAAAGTCATATCCAACACGTTAGGGCACTATGTTCTCAGACTTTCGAAACTGAAGGACATTTTGA
1 GAAAGTCATATCCAACACGTTAGGGCACTATGTTCTCAGACTTTCGAAACTGAAGGACACTTTGA
* * *
18733 AAGACTTTAAACAGGATATTCGATTGTGTGAATTATACGAAAATCACACCCAGCACGTTAGGGCA
66 AAGACTTTAAACAGGATATTCGATTATGTGAATTATACAAAAATCACACCCAACACGTTAGGGCA
*
18798 TGTTTTTTCGAAGTCTTCACACGAAAGGATATTTCCTCGTTTTGTTTTAAAATCATTTGTATATA
131 TGTTTTTTCGAAGTCTTCACACGAAAGGATATTTCCTCGTGTTGTTTTAAAATCATTTGTATATA
*
18863 TATATAT
196 AATATAT
18870 TTGAGAACTT
Statistics
Matches: 195, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
209 195 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (209 bp):
GAAAGTCATATCCAACACGTTAGGGCACTATGTTCTCAGACTTTCGAAACTGAAGGACACTTTGA
AAGACTTTAAACAGGATATTCGATTATGTGAATTATACAAAAATCACACCCAACACGTTAGGGCA
TGTTTTTTCGAAGTCTTCACACGAAAGGATATTTCCTCGTGTTGTTTTAAAATCATTTGTATATA
AATATATATATATA
Found at i:19417 original size:29 final size:29
Alignment explanation
Indices: 19371--19435 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
19361 GATTAAATGC
* * *
19371 AATTTTTGGATGCCCGAGGGCAAAATGGT
1 AATTTTTGGAGGCACGAGGGCAAAACGGT
* **
19400 AATTTTTGGAGGTACGAGGTTAAAACGGT
1 AATTTTTGGAGGCACGAGGGCAAAACGGT
19429 AATTTTT
1 AATTTTT
19436 AGACACTTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.34
Consensus pattern (29 bp):
AATTTTTGGAGGCACGAGGGCAAAACGGT
Found at i:19512 original size:29 final size:29
Alignment explanation
Indices: 19459--19670 Score: 175
Period size: 30 Copynumber: 7.2 Consensus size: 29
19449 CGAAATGGTG
*
19459 ATTTTTGGAAAGTTCGAGGCCAAAAATGGA
1 ATTTTTGGAAAGTTCGAGG-TAAAAATGGA
* *
19489 ATTTTTGGAAA-TTTGAGG-ATAAAATGATA
1 ATTTTTGGAAAGTTCGAGGTA-AAAATG-GA
*
19518 ATTTTTGAAAAGTTCGAGGTCAAAAATGGA
1 ATTTTTGGAAAGTTCGAGGT-AAAAATGGA
* * *
19548 ATTTTTAGACA-TTCGAGGGT-AAAATGTA
1 ATTTTTGGAAAGTTCGA-GGTAAAAATGGA
*
19576 ATTTTTGGAAAGTTCGGGGTTAAAAATGGA
1 ATTTTTGGAAAGTTCGAGG-TAAAAATGGA
* * *
19606 ATTTTT-GAAAATCCAAAGGT-AAAATGGTA
1 ATTTTTGGAAAGTTC-GAGGTAAAAATGG-A
* * *
19635 ATTTTTGGAAAGTTTGGGGTCAAAAATAGA
1 ATTTTTGGAAAGTTCGAGGT-AAAAATGGA
19665 ATTTTT
1 ATTTTT
19671 TAGAAGTTTG
Statistics
Matches: 145, Mismatches: 23, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.01
28 31 0.21
29 44 0.30
30 56 0.39
31 12 0.08
32 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (29 bp):
ATTTTTGGAAAGTTCGAGGTAAAAATGGA
Found at i:19580 original size:117 final size:117
Alignment explanation
Indices: 19459--19670 Score: 300
Period size: 117 Copynumber: 1.8 Consensus size: 117
19449 CGAAATGGTG
* ***
19459 ATTTTTGGAAAGTTCGAGGCCAAAAATGGAATTTTTGGAAAT-TTGAGGATAAAATGATAATTTT
1 ATTTTTGGAAAGTTCGAGGCCAAAAATGGAATTTTTGAAAATCCAAAGG-TAAAATGATAATTTT
*
19523 TGAAAAGTTCGAGGTCAAAAATGGAATTTTTAGACATTCGAGGGTAAAATGTA
65 TGAAAAGTTCGAGGTCAAAAATAGAATTTTTAGACATTCGAGGGTAAAATGTA
* ** *
19576 ATTTTTGGAAAGTTCGGGGTTAAAAATGGAATTTTTGAAAATCCAAAGGTAAAATGGTAATTTTT
1 ATTTTTGGAAAGTTCGAGGCCAAAAATGGAATTTTTGAAAATCCAAAGGTAAAATGATAATTTTT
* * *
19641 GGAAAGTTTGGGGTCAAAAATAGAATTTTT
66 GAAAAGTTCGAGGTCAAAAATAGAATTTTT
19671 TAGAAGTTTG
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
117 79 0.96
118 3 0.04
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (117 bp):
ATTTTTGGAAAGTTCGAGGCCAAAAATGGAATTTTTGAAAATCCAAAGGTAAAATGATAATTTTT
GAAAAGTTCGAGGTCAAAAATAGAATTTTTAGACATTCGAGGGTAAAATGTA
Found at i:19690 original size:29 final size:29
Alignment explanation
Indices: 19634--19878 Score: 80
Period size: 30 Copynumber: 8.2 Consensus size: 29
19624 GTAAAATGGT
19634 AATTTTTG-GAAAGTTTGGGGTCAAAAATAG
1 AATTTTTGTG-AAGTTTGGGGT-AAAAATAG
*
19664 AATTTTT-TAGAAGTTTGGGGGT-AAAATGG
1 AATTTTTGT-GAAGTTT-GGGGTAAAAATAG
* ** ** *
19693 ACTTTTTGTGAAGTTCAAGGGTCGAAATAT
1 AATTTTTGTGAAGTT-TGGGGTAAAAATAG
* * * *
19723 AATTTTTAGAT-AA-TTCGGGATAAAAAAACAT
1 AATTTTT-G-TGAAGTTTGGGGT--AAAAATAG
*
19754 AATTTTTG-GAAGTTTGGGGGTCAAAAA-AT
1 AATTTTTGTGAAGTTT-GGGGT-AAAAATAG
* **
19783 AATTTTTG-GAAAGTTCGAGGGT-TGAAT-G
1 AATTTTTGTG-AAGTTTG-GGGTAAAAATAG
* * *
19811 TAATTTTTGAGAAGTTTGAGGGTCAAAATAT
1 -AATTTTTGTGAAGTTTG-GGGTAAAAATAG
* *
19842 AATTTTTG-GAAAGTTTAGGGGTTAAAATAT
1 AATTTTTGTG-AAGTTT-GGGGTAAAAATAG
19872 AATTTTT
1 AATTTTT
19879 AGACAGTTCA
Statistics
Matches: 167, Mismatches: 26, Indels: 44
0.70 0.11 0.19
Matches are distributed among these distances:
28 2 0.01
29 59 0.35
30 79 0.47
31 26 0.16
32 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (29 bp):
AATTTTTGTGAAGTTTGGGGTAAAAATAG
Found at i:19699 original size:59 final size:58
Alignment explanation
Indices: 19385--19747 Score: 265
Period size: 59 Copynumber: 6.2 Consensus size: 58
19375 TTTGGATGCC
* * * * * *
19385 CGAGGGCAAAATGGTAATTTTTGG-AGGTACGAGGT-TAAAACGGTAATTTTTAGACACTT
1 CGAGGGTAAAATGG-AATTTTTGGAAAGTTCGAGGTCAAAAATGG-AATTTTTAGA-AATT
* ** * * *
19444 -GGGGGCGAAATGGTGATTTTTGGAAAGTTCGAGGCCAAAAATGGAATTTTTGGAAATT
1 CGAGGGTAAAATGG-AATTTTTGGAAAGTTCGAGGTCAAAAATGGAATTTTTAGAAATT
* * * * *
19502 TGAGGATAAAATGATAATTTTTGAAAAGTTCGAGGTCAAAAATGGAATTTTTAGACATT
1 CGAGGGTAAAATG-GAATTTTTGGAAAGTTCGAGGTCAAAAATGGAATTTTTAGAAATT
* * * *
19561 CGAGGGTAAAATGTAATTTTTGGAAAGTTCGGGGTTAAAAATGGAATTTTT-GAAAATC
1 CGAGGGTAAAATGGAATTTTTGGAAAGTTCGAGGTCAAAAATGGAATTTTTAG-AAATT
* * * * * *
19619 CAAAGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATAGAATTTTTTAGAAGTT
1 CGAGGGTAAAATGG-AATTTTTGGAAAGTTCGAGGTCAAAAATGGAA-TTTTTAGAAATT
* * * * *
19679 TGGGGGTAAAATGGACTTTTTGTG-AAGTTCAAGGGTCGAAATAT--AATTTTTAGATAATT
1 CGAGGGTAAAATGGAATTTTTG-GAAAGTTCGA-GGTC-AAAAATGGAATTTTTAGA-AATT
*
19738 CG-GGATAAAA
1 CGAGGGTAAAA
19748 AAACATAATT
Statistics
Matches: 245, Mismatches: 47, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
57 1 0.00
58 87 0.36
59 122 0.50
60 29 0.12
61 6 0.02
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.33
Consensus pattern (58 bp):
CGAGGGTAAAATGGAATTTTTGGAAAGTTCGAGGTCAAAAATGGAATTTTTAGAAATT
Found at i:19797 original size:30 final size:30
Alignment explanation
Indices: 19488--19878 Score: 159
Period size: 29 Copynumber: 13.2 Consensus size: 30
19478 CCAAAAATGG
* *
19488 AATTTTTGGAAA-TTTGAGGAT-AAAATGAT
1 AATTTTTGGAAAGTTTGGGGGTCAAAAT-AT
* * *
19517 AATTTTTGAAAAG-TTCGAGGTCAAAA-AT
1 AATTTTTGGAAAGTTTGGGGGTCAAAATAT
* * * * *
19545 GGAATTTTTAGACA-TTCGAGGGT-AAAATGT
1 --AATTTTTGGAAAGTTTGGGGGTCAAAATAT
* * * **
19575 AATTTTTGGAAAGTTCGGGGTTAAAAATGG
1 AATTTTTGGAAAGTTTGGGGGTCAAAATAT
* ***** *
19605 AATTTTT-GAAAATCCAAAGGT-AAAATGGT
1 AATTTTTGGAAAGTTTGGGGGTCAAAAT-AT
*
19634 AATTTTTGGAAAGTTT-GGGGTCAAAAATAG
1 AATTTTTGGAAAGTTTGGGGGTC-AAAATAT
* **
19664 AATTTTT-TAGAAGTTTGGGGGT-AAAATGG
1 AATTTTTGGA-AAGTTTGGGGGTCAAAATAT
* *** *
19693 ACTTTTTGTG-AAGTTCAAGGGTCGAAATAT
1 AATTTTTG-GAAAGTTTGGGGGTCAAAATAT
* * * * *
19723 AATTTTTAGATAA--TTCGGGATAAAAAAACAT
1 AATTTTTGGA-AAGTTTGGGGGT--CAAAATAT
*
19754 AATTTTTGG-AAGTTTGGGGGTCAAAAAAT
1 AATTTTTGGAAAGTTTGGGGGTCAAAATAT
* * ** *
19783 AATTTTTGGAAAGTTCGAGGGT-TGAATGT
1 AATTTTTGGAAAGTTTGGGGGTCAAAATAT
*
19812 AATTTTT-GAGAAGTTTGAGGGTCAAAATAT
1 AATTTTTGGA-AAGTTTGGGGGTCAAAATAT
* *
19842 AATTTTTGGAAAGTTTAGGGGTTAAAATAT
1 AATTTTTGGAAAGTTTGGGGGTCAAAATAT
19872 AATTTTT
1 AATTTTT
19879 AGACAGTTCA
Statistics
Matches: 266, Mismatches: 69, Indels: 53
0.69 0.18 0.14
Matches are distributed among these distances:
28 19 0.07
29 110 0.41
30 104 0.39
31 33 0.12
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTGGGGGTCAAAATAT
Found at i:19818 original size:119 final size:120
Alignment explanation
Indices: 19515--19848 Score: 287
Period size: 119 Copynumber: 2.8 Consensus size: 120
19505 GGATAAAATG
* * * * *
19515 ATAATTTTTGAAAAGTTCGAGGTCAAAAATGGAATTTTT-AGACA-TTCGAGGGTAAAATGTAAT
1 ATAATTTTTGGAAAGTTTGGGGTCAAAAATAGAATTTTTGAGA-AGTTCGAGGGTAAAATGGAAT
* * * * * **
19578 TTTTG-GAAAGTTC-GGGGTTAAAA-ATGGAATTTTT-GAAAATCCAAAGG-T--AAAATG
65 TTTTGAG-AAGTTCAAGGGTCAAAATAT--AATTTTTAGATAATTC--GGGATAAAAAAAC
* * * * *
19632 GTAATTTTTGGAAAGTTTGGGGTCAAAAATAGAATTTTTTAGAAGTTTGGGGGTAAAATGGACTT
1 ATAATTTTTGGAAAGTTTGGGGTCAAAAATAGAATTTTTGAGAAGTTCGAGGGTAAAATGGAATT
* *
19697 TTTGTGAAGTTCAAGGGTCGAAATATAATTTTTAGATAATTCGGGATAAAAAAAC
66 TTTGAGAAGTTCAAGGGTCAAAATATAATTTTTAGATAATTCGGGATAAAAAAAC
* ** *
19752 ATAATTTTTGG-AAGTTTGGGGGTCAAAAA-ATAATTTTTG-GAAAGTTCGAGGGTTGAATGTAA
1 ATAATTTTTGGAAAGTTT-GGGGTCAAAAATAGAATTTTTGAG-AAGTTCGAGGGTAAAATGGAA
**
19814 TTTTTGAGAAGTTTGAGGGTCAAAATATAATTTTT
64 TTTTTGAGAAGTTCAAGGGTCAAAATATAATTTTT
19849 GGAAAGTTTA
Statistics
Matches: 176, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
117 37 0.21
118 38 0.22
119 74 0.42
120 27 0.15
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (120 bp):
ATAATTTTTGGAAAGTTTGGGGTCAAAAATAGAATTTTTGAGAAGTTCGAGGGTAAAATGGAATT
TTTGAGAAGTTCAAGGGTCAAAATATAATTTTTAGATAATTCGGGATAAAAAAAC
Found at i:19864 original size:59 final size:60
Alignment explanation
Indices: 19747--19886 Score: 180
Period size: 59 Copynumber: 2.4 Consensus size: 60
19737 TCGGGATAAA
* * *
19747 AAAACATAATTTTTG-GAAGTTTGGGGGTCAAAAAATAATTTTTGGAAAGTTCGAGGGTT
1 AAAATATAATTTTTGAGAAGTTTGAGGGTCAAAAAATAATTTTTGGAAAGTTAGAGGGTT
* * *
19806 -GAATGTAATTTTTGAGAAGTTTGAGGGTCAAAATATAATTTTTGGAAAGTTTAG-GGGTT
1 AAAATATAATTTTTGAGAAGTTTGAGGGTCAAAAAATAATTTTTGGAAAG-TTAGAGGGTT
19865 AAAATATAATTTTT-AGACAGTT
1 AAAATATAATTTTTGAGA-AGTT
19887 CAGGGACCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
58 11 0.16
59 40 0.58
60 18 0.26
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (60 bp):
AAAATATAATTTTTGAGAAGTTTGAGGGTCAAAAAATAATTTTTGGAAAGTTAGAGGGTT
Found at i:21656 original size:17 final size:19
Alignment explanation
Indices: 21634--21675 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
21624 ACTTTTTAAG
21634 TAAATTTTAA-TTCT-AAA
1 TAAATTTTAAGTTCTAAAA
*
21651 TAAA-TTTAAGTTTTAAAA
1 TAAATTTTAAGTTCTAAAA
21669 TAAATTT
1 TAAATTT
21676 AAACTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 7 0.33
19 2 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TAAATTTTAAGTTCTAAAA
Found at i:21685 original size:17 final size:18
Alignment explanation
Indices: 21665--21713 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
21655 TTTAAGTTTT
21665 AAAATAAATTTAAACTAA
1 AAAATAAATTTAAACTAA
* **
21683 AAAATAAGTTTAAA-TTT
1 AAAATAAATTTAAACTAA
21700 AAAATAAATTTAAA
1 AAAATAAATTTAAA
21714 TTGAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAATAAATTTAAACTAA
Found at i:21714 original size:17 final size:17
Alignment explanation
Indices: 21634--21737 Score: 95
Period size: 18 Copynumber: 6.0 Consensus size: 17
21624 ACTTTTTAAG
*
21634 TAAATTTTAATTCT-AAA
1 TAAATTTAAATT-TAAAA
*
21651 TAAATTTAAGTTTTAAAA
1 TAAATTTAA-ATTTAAAA
**
21669 TAAATTTAAACTAAAAAA
1 TAAATTTAAA-TTTAAAA
*
21687 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
21704 TAAATTTAAA-TTGAAA
1 TAAATTTAAATTTAAAA
*
21720 TAAATTAAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
21738 ATTCCAGAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
16 14 0.20
17 23 0.33
18 33 0.47
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:21739 original size:35 final size:34
Alignment explanation
Indices: 21634--21737 Score: 111
Period size: 35 Copynumber: 3.0 Consensus size: 34
21624 ACTTTTTAAG
* * *
21634 TAAATTTTAATTCTAAATAAATTTAAGTTTTAAAA
1 TAAATTTAAATT-AAAATAAATTTAAATTTTAAAA
* *
21669 TAAATTTAAACTAAAAAATAAGTTTAAA-TTTAAAA
1 TAAATTTAAA-T-TAAAATAAATTTAAATTTTAAAA
* *
21704 TAAATTTAAATTGAAATAAATTAAAATTTTAAAA
1 TAAATTTAAATTAAAATAAATTTAAATTTTAAAA
21738 ATTCCAGAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
33 11 0.19
34 8 0.14
35 26 0.46
36 12 0.21
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (34 bp):
TAAATTTAAATTAAAATAAATTTAAATTTTAAAA
Found at i:22068 original size:149 final size:149
Alignment explanation
Indices: 21798--22096 Score: 535
Period size: 149 Copynumber: 2.0 Consensus size: 149
21788 CTTTAACAGT
* **
21798 TGCCCCTCTTTGCTTGTTGTTGTGTAATAGGAACGGAGCAAAGACCAAAAGAAGGCCCAATTTTG
1 TGCCCCTCTTTGCTCGTTGTTGTGTAATAGGAACAAAGCAAAGACCAAAAGAAGGCCCAATTTTG
*
21863 TCAAGTTTCATTTCTTTAACTGGTCCACACTTCGCTTTATCGGTCATTCGATTTCACTGCCTCCG
66 TCAAGTTTCATTTCTTCAACTGGTCCACACTTCGCTTTATCGGTCATTCGATTTCACTGCCTCCG
*
21928 TTTCTCTACGTCTTTGGTG
131 CTTCTCTACGTCTTTGGTG
*
21947 TGCCCCTCTTTGCTCGTTGTTGTGTAATAGGAATAAAGCAAAGACCAAAAGAAGGCCCAATTTTG
1 TGCCCCTCTTTGCTCGTTGTTGTGTAATAGGAACAAAGCAAAGACCAAAAGAAGGCCCAATTTTG
*
22012 TCAAGTTTCATTTCTTCAACTGGTCCACACTTCGCTTTATCGGTCATTTGATTTCACTGCCTCCG
66 TCAAGTTTCATTTCTTCAACTGGTCCACACTTCGCTTTATCGGTCATTCGATTTCACTGCCTCCG
22077 CTTCTCTACGTCTTTGGTG
131 CTTCTCTACGTCTTTGGTG
22096 T
1 T
22097 TGTGATTCCC
Statistics
Matches: 143, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 143 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (149 bp):
TGCCCCTCTTTGCTCGTTGTTGTGTAATAGGAACAAAGCAAAGACCAAAAGAAGGCCCAATTTTG
TCAAGTTTCATTTCTTCAACTGGTCCACACTTCGCTTTATCGGTCATTCGATTTCACTGCCTCCG
CTTCTCTACGTCTTTGGTG
Found at i:22786 original size:209 final size:209
Alignment explanation
Indices: 22412--22808 Score: 609
Period size: 209 Copynumber: 1.9 Consensus size: 209
22402 GAGTTAGCAT
*
22412 ACTTCTCTATGTCTCATCAGGAAGACGAATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTAA
1 ACTTCTCTATGTCTCATCAAGAAGACGAATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTAA
* *
22477 CCGCTTTATTGCTTCGACCTTCTTCTCAGTATCTCATCAGGAAGCAAGGGTTCAAAGATTCGCTC
66 CCGCTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAAGAAGCAAGGGTTCAAAGATTCGCTC
* **
22542 ACATTGAGCTTTGTTTCATTGAATTGGTATACTTCTTTGTATCTCATCAGGAAGATGACTGCATC
131 ACATTGAGCTTGGTTTCATTGAATTGGTATACTTCTCAGTATCTCATCAGGAAGATGACTGCATC
22607 ACTTGTTTTGATCC
196 ACTTGTTTTGATCC
* * *
22621 ACTTCTCTGTGTCTCATCAAGATGAC-AGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTA
1 ACTTCTCTATGTCTCATCAAGAAGACGA-ATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTA
* ** * *
22685 ACCGCTTTATTGCTTCGACCTACTTCTTAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCT
65 ACCGCTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAAGAAGCAAGGGTTCAAAGATTCGCT
* * *
22750 CACTTTGAGCTTGGTTTC-TTCGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGA
130 CACATTGAGCTTGGTTTCATT-GAATTGGTATACTTCTCAGTATCTCATCAGGAAGATGA
22809 TCGCCTCGTT
Statistics
Matches: 169, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
208 3 0.02
209 166 0.98
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (209 bp):
ACTTCTCTATGTCTCATCAAGAAGACGAATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTAA
CCGCTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAAGAAGCAAGGGTTCAAAGATTCGCTC
ACATTGAGCTTGGTTTCATTGAATTGGTATACTTCTCAGTATCTCATCAGGAAGATGACTGCATC
ACTTGTTTTGATCC
Found at i:50912 original size:51 final size:51
Alignment explanation
Indices: 50851--50951 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
50841 CAGGAAATCA
50851 CATAGATTTAAAAACATTAAATGTAACCTGATCATCCTGAACACGCACGTT
1 CATAGATTTAAAAACATTAAATGTAACCTGATCATCCTGAACACGCACGTT
50902 CATAGATTTAAAAACATTAAATGTAACCTGATCATCCTGAACACGCACGT
1 CATAGATTTAAAAACATTAAATGTAACCTGATCATCCTGAACACGCACGT
50952 AAGCACGCCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.27
Consensus pattern (51 bp):
CATAGATTTAAAAACATTAAATGTAACCTGATCATCCTGAACACGCACGTT
Found at i:57051 original size:30 final size:30
Alignment explanation
Indices: 57017--57079 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
57007 TTTTACAATA
* * *
57017 AAATTTTAATAAGAGTTC-AATTTGGTCCTT
1 AAATTTCAATAA-AATTCTAATTTAGTCCTT
*
57047 AAATTTCACTAAAATTCTAATTTAGTCCTT
1 AAATTTCAATAAAATTCTAATTTAGTCCTT
57077 AAA
1 AAA
57080 ATCCATCGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (30 bp):
AAATTTCAATAAAATTCTAATTTAGTCCTT
Found at i:57129 original size:30 final size:30
Alignment explanation
Indices: 57046--57130 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
57036 ATTTGGTCCT
* * * *
57046 TAAATTTCACTAAAATTCTAATTTAGTCCT
1 TAAAATTCACTAAAATTCAAATTTAGCCCC
* * *
57076 TAAAATCCA-TCGAACTT-ACAATTTAGCCCC
1 TAAAATTCACT-AAAATTCA-AATTTAGCCCC
57106 TAAAATTCACTAAAATTCAAATTTA
1 TAAAATTCACTAAAATTCAAATTTA
57131 ATCCTTAAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
29 1 0.02
30 38 0.93
31 2 0.05
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (30 bp):
TAAAATTCACTAAAATTCAAATTTAGCCCC
Found at i:59748 original size:17 final size:17
Alignment explanation
Indices: 59728--59765 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
59718 AAATGTGAGA
* *
59728 ACAATTAAACTGTAGTG
1 ACAATTAAAATGTAATG
59745 ACAATTAAAATGTAATG
1 ACAATTAAAATGTAATG
59762 ACAA
1 ACAA
59766 CTAGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (17 bp):
ACAATTAAAATGTAATG
Found at i:60187 original size:9 final size:9
Alignment explanation
Indices: 60173--60226 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
60163 AGGCAACGTC
60173 TTCTTCTTT
1 TTCTTCTTT
*
60182 TTCTTCCTT
1 TTCTTCTTT
*
60191 CTCTTCTTT
1 TTCTTCTTT
60200 TTCTTCTTT
1 TTCTTCTTT
*
60209 AT-TTCTTT
1 TTCTTCTTT
60217 CCTTCTTCTT
1 --TTCTTCTT
60227 CTGCTTCAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 6 0.17
9 24 0.67
10 1 0.03
11 5 0.14
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (9 bp):
TTCTTCTTT
Found at i:60207 original size:30 final size:31
Alignment explanation
Indices: 60171--60228 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
60161 CGAGGCAACG
*
60171 TCTTCTTCTTTTTC-TTCCTTC-TCTTCTTTT
1 TCTTCTT-TATTTCTTTCCTTCTTCTTCTTTT
60201 TCTTCTTTATTTCTTTCCTTCTTCTTCT
1 TCTTCTTTATTTCTTTCCTTCTTCTTCT
60229 GCTTCAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 5 0.20
30 14 0.56
31 6 0.24
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (31 bp):
TCTTCTTTATTTCTTTCCTTCTTCTTCTTTT
Found at i:82760 original size:42 final size:42
Alignment explanation
Indices: 82643--82821 Score: 175
Period size: 43 Copynumber: 4.2 Consensus size: 42
82633 TGATGTATAA
* * * * * *
82643 AAAGGAAGACTCGTGTCTCGAGTTGAGCATGGGAATTTG-TAT
1 AAAGGAAGACTCATGTCTCAAGATGAGAATGAGAATATGAT-T
* * * *
82685 AAATGAAAGACTCGTGACTC-AGAGTGAGCATGAGAATATGATT
1 AAA-GGAAGACTCATGTCTCAAGA-TGAGAATGAGAATATGATT
*
82728 AAAGGAAGACTCATGTCTCAAGATGAGAATGAGATTTAT-ATTT
1 AAAGGAAGACTCATGTCTCAAGATGAGAATGAGA-ATATGA-TT
*
82771 AAAGGAAGACTCATGTCTCAGGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCAAGATGAGAATGAGAATATGATT
*
82813 TAAGGAAGA
1 AAAGGAAGA
82822 ATTATGACTC
Statistics
Matches: 117, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
42 42 0.36
43 74 0.63
44 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCAAGATGAGAATGAGAATATGATT
Found at i:82803 original size:85 final size:85
Alignment explanation
Indices: 82643--82821 Score: 211
Period size: 85 Copynumber: 2.1 Consensus size: 85
82633 TGATGTATAA
* * * * * * *
82643 AAAGGAAGACTCGTGTCTCGAGTTGAGCATGGGAATTTGTATAAATGAAAGACTCGTGACTCAGA
1 AAAGGAAGACTCATGTCTCAAGATGAGAATGAGAATTTATATAAATGAAAGACTCATGACTCAGA
*
82708 GTGAGCATGAGAATATGATT
66 GTGAGAATGAGAATATGATT
* *
82728 AAAGGAAGACTCATGTCTCAAGATGAGAATGAG-ATTTATATTTAAA-GGAAGACTCATGTCTCA
1 AAAGGAAGACTCATGTCTCAAGATGAGAATGAGAATTTATA--TAAATGAAAGACTCATGACTCA
82791 G-GATGAGAATGAGAATATGATT
64 GAG-TGAGAATGAGAATATGATT
*
82813 TAAGGAAGA
1 AAAGGAAGA
82822 ATTATGACTC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
84 7 0.09
85 69 0.86
86 4 0.05
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (85 bp):
AAAGGAAGACTCATGTCTCAAGATGAGAATGAGAATTTATATAAATGAAAGACTCATGACTCAGA
GTGAGAATGAGAATATGATT
Found at i:84326 original size:9 final size:10
Alignment explanation
Indices: 84303--84332 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
84293 TTTTTGGTTT
84303 GAAAGAAAAA
1 GAAAGAAAAA
84313 GAAAGAAAAA
1 GAAAGAAAAA
84323 -AAAGAAAAA
1 GAAAGAAAAA
84332 G
1 G
84333 GAGGTGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAA
Found at i:87964 original size:164 final size:161
Alignment explanation
Indices: 87696--88006 Score: 516
Period size: 164 Copynumber: 1.9 Consensus size: 161
87686 TCTAATAATC
* * *
87696 GCCCTCTTCTTTTGCAAACTAATAAGTTTTTTATACTTAGAGGAATACCTTTTCGTTTCTTGGTA
1 GCCCTCTTCTTTTGCAAACTAATAAGTTTTTTATACTTAGAGGAAGACCTTTTCATTTCTTGGCA
**
87761 GGGTGGACTGAGCATCCTGATTTCAATAATTTTATGAAGAACAAGTGGTTTTTCTTGGGGAACAT
66 AAGTGGACTGAGCATCCTGATTTCAATAATTTTATGAAGAACAAGTGGTTTTTCTTGGGGAACAT
* *
87826 GGCTGACTCCTTGCTTTAGCTTACTTAGATA
131 GGATGACTCCTTACTTTAGCTTACTTAGATA
87857 GCCCTCTTCTTTTGCAAACTAATCCGAAGTTTTTTATACTTAGAGGAAGACC-TTTCTATTTCTT
1 GCCCTCTTCTTTTGCAAACTAAT---AAGTTTTTTATACTTAGAGGAAGACCTTTTC-ATTTCTT
87921 GGCAAAGTGGACTGAGCATCCTGATTTCAATAATTTTATGAAGAACAAGTGGTTTTTCTTGGGGA
62 GGCAAAGTGGACTGAGCATCCTGATTTCAATAATTTTATGAAGAACAAGTGGTTTTTCTTGGGGA
87986 ACATGGATGACTCCTTACTTT
127 ACATGGATGACTCCTTACTTT
88007 TCCTTACTCA
Statistics
Matches: 139, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
161 23 0.17
163 4 0.03
164 112 0.81
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (161 bp):
GCCCTCTTCTTTTGCAAACTAATAAGTTTTTTATACTTAGAGGAAGACCTTTTCATTTCTTGGCA
AAGTGGACTGAGCATCCTGATTTCAATAATTTTATGAAGAACAAGTGGTTTTTCTTGGGGAACAT
GGATGACTCCTTACTTTAGCTTACTTAGATA
Found at i:110734 original size:20 final size:19
Alignment explanation
Indices: 110705--110742 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
110695 TTAAATTCAA
110705 ATCTAATCTTATAAGATTC
1 ATCTAATCTTATAAGATTC
*
110724 ATCTAAATCTTCTAAGATT
1 ATCT-AATCTTATAAGATT
110743 AGTTTCCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (19 bp):
ATCTAATCTTATAAGATTC
Found at i:112783 original size:230 final size:229
Alignment explanation
Indices: 112376--112833 Score: 763
Period size: 230 Copynumber: 2.0 Consensus size: 229
112366 AAATGGACAG
*
112376 CTTCTTCCGGGTCCCCTGTGAATATTTTGAATCAAATTTTGTTAGAACAGAGAAACCTGGAATAA
1 CTTCTTCCGGGTCCCCTGTGAATATTTTGAATAAAATTTTGTTAGAACAGAGAAACCTGGAATAA
* ** * *
112441 TTTCACAGGGTTTGGATGTGAATCTTGTGGAGTTTCTACTTTAATTAACTTTATCATGTAAGATT
66 TTTCACAGGGTTTGGATGTGAATCTTGTGGAGTTTCTACTTAAAGAAACTTTATAATGTAAGATG
* * * *
112506 TCCTTTACTGAATGACTGCTCTACTTGGCTCTGGATGTGATATGTAAATGTTTCCATTTGCCTCC
131 TCCTTTACTGAATGACTGCTCTACTCGGATCTGGATGTGAGATGTAAATGTTTCCATTTACCTCC
* * *
112571 TTGTTAGCCAATCAAAATATTAGTTATTTTTCAA
196 TTGCTAGCCAATCAAAATATTAGTGAATTTTCAA
*
112605 CTTCTTCTGGGTCCCCTGTGAATATTTTGAATAAAATTTTGTTAGAACAGAGAAACCTGGAATAA
1 CTTCTTCCGGGTCCCCTGTGAATATTTTGAATAAAATTTTGTTAGAACAGAGAAACCTGGAATAA
*
112670 TATTCACAGGGTTTGGATGTGAATCTTGTGGAGTTTCTGCTTAAAGAAACTTTATAATGTAAGAT
66 T-TTCACAGGGTTTGGATGTGAATCTTGTGGAGTTTCTACTTAAAGAAACTTTATAATGTAAGAT
*
112735 GTCCTTTACTGAATGACTGCTCTACTCGGATTTGGATGTGAGATGTAAATGTTTCCATTTACCTC
130 GTCCTTTACTGAATGACTGCTCTACTCGGATCTGGATGTGAGATGTAAATGTTTCCATTTACCTC
112800 CTTGCTAGCCAATCAAAATATTAGTGAATTTTCA
195 CTTGCTAGCCAATCAAAATATTAGTGAATTTTCA
112834 GCTTATTCGC
Statistics
Matches: 212, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
229 64 0.30
230 148 0.70
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (229 bp):
CTTCTTCCGGGTCCCCTGTGAATATTTTGAATAAAATTTTGTTAGAACAGAGAAACCTGGAATAA
TTTCACAGGGTTTGGATGTGAATCTTGTGGAGTTTCTACTTAAAGAAACTTTATAATGTAAGATG
TCCTTTACTGAATGACTGCTCTACTCGGATCTGGATGTGAGATGTAAATGTTTCCATTTACCTCC
TTGCTAGCCAATCAAAATATTAGTGAATTTTCAA
Found at i:117273 original size:40 final size:40
Alignment explanation
Indices: 117229--117312 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
117219 ATGGGCTAAT
117229 TATAGTTCGTGGCCTGAAGTTTTGATTTTTGCATCACATG
1 TATAGTTCGTGGCCTGAAGTTTTGATTTTTGCATCACATG
117269 TATAGTTCGTGGCCTGAAGTTTTGATTTTTGCATCACATG
1 TATAGTTCGTGGCCTGAAGTTTTGATTTTTGCATCACATG
117309 TATA
1 TATA
117313 ATGGAAGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (40 bp):
TATAGTTCGTGGCCTGAAGTTTTGATTTTTGCATCACATG
Found at i:130960 original size:30 final size:30
Alignment explanation
Indices: 130924--130983 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
130914 GGTGGTGGTA
130924 AATCTTGTGGAGCACTAGAAAAATATTATC
1 AATCTTGTGGAGCACTAGAAAAATATTATC
130954 AATCTTGTGGAGCACTAGAAAAATATTATC
1 AATCTTGTGGAGCACTAGAAAAATATTATC
130984 CTGTGACAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (30 bp):
AATCTTGTGGAGCACTAGAAAAATATTATC
Found at i:135382 original size:27 final size:28
Alignment explanation
Indices: 135347--135400 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
135337 AAGTAAAAAT
* *
135347 TATTAAAATATTGTTAT-TTATATTAAC
1 TATTAAAATATTATTATCTTAAATTAAC
*
135374 TATTTAAATATTATTATCTTAAATTAA
1 TATTAAAATATTATTATCTTAAATTAA
135401 TTAAATATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (28 bp):
TATTAAAATATTATTATCTTAAATTAAC
Found at i:136479 original size:42 final size:42
Alignment explanation
Indices: 136420--136503 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
136410 GGACGTTGTC
136420 GCGATGTGACTGATTGTTTCCAAATGGTATAAATTGACACCA
1 GCGATGTGACTGATTGTTTCCAAATGGTATAAATTGACACCA
136462 GCGATGTGACTGATTGTTTCCAAATGGTATAAATTGACACCA
1 GCGATGTGACTGATTGTTTCCAAATGGTATAAATTGACACCA
136504 ACCTGCAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (42 bp):
GCGATGTGACTGATTGTTTCCAAATGGTATAAATTGACACCA
Found at i:137554 original size:13 final size:13
Alignment explanation
Indices: 137538--137563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
137528 ATTGAAATGT
137538 AAGTTGAAAATAA
1 AAGTTGAAAATAA
137551 AAGTTGAAAATAA
1 AAGTTGAAAATAA
137564 GGTCATTAAT
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:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
AAGTTGAAAATAA
Found at i:137681 original size:20 final size:21
Alignment explanation
Indices: 137658--137696 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
137648 TTCTAAAGTT
137658 ATTT-TGAAGTTTCGTTAAAA
1 ATTTCTGAAGTTTCGTTAAAA
*
137678 ATTTCTTAAGTTTCGTTAA
1 ATTTCTGAAGTTTCGTTAA
137697 TTTTTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.49
Consensus pattern (21 bp):
ATTTCTGAAGTTTCGTTAAAA
Found at i:138218 original size:15 final size:15
Alignment explanation
Indices: 138198--138227 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
138188 ATATGTTTGC
138198 TTGTGAAATTGTGAA
1 TTGTGAAATTGTGAA
*
138213 TTGTGAATTTGTGAA
1 TTGTGAAATTGTGAA
138228 CATATATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (15 bp):
TTGTGAAATTGTGAA
Found at i:138713 original size:66 final size:66
Alignment explanation
Indices: 138608--138738 Score: 174
Period size: 66 Copynumber: 2.0 Consensus size: 66
138598 GAAATAAGGA
* * * *
138608 GTGTTAGCTTTACGCTTCACTTTCGGGACATGTTTGACTCTATGACTCTTTTGGTGTGTTTGGAG
1 GTGTTAGCTATACGCTTCACTTTCGGGACATGTTCGACTCTATGACTCATTTGGTGTATTTGGAG
138673 T
66 T
* * * *
138674 GTGTTAGCTATATGCTTCACTTAT-GGGATATGTTCGACTCTGTGAGTCATTTGGTGTATTTGGA
1 GTGTTAGCTATACGCTTCACTT-TCGGGACATGTTCGACTCTATGACTCATTTGGTGTATTTGGA
138738 G
65 G
138739 ATCCGTGTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 55 0.98
67 1 0.02
ACGTcount: A:0.16, C:0.15, G:0.27, T:0.43
Consensus pattern (66 bp):
GTGTTAGCTATACGCTTCACTTTCGGGACATGTTCGACTCTATGACTCATTTGGTGTATTTGGAG
T
Found at i:138836 original size:10 final size:11
Alignment explanation
Indices: 138821--139040 Score: 68
Period size: 10 Copynumber: 19.5 Consensus size: 11
138811 ATATGACTGA
138821 ATGTGATT-AT
1 ATGTGATTAAT
138831 ATGTGATTAAT
1 ATGTGATTAAT
* *
138842 ATGTGACGTGAT
1 ATGTGA-TTAAT
* *
138854 AATGCTGAAATATT
1 -ATG-TG-ATTAAT
138868 CATGTGATTAA-
1 -ATGTGATTAAT
*
138879 ATGTGACTAA-
1 ATGTGATTAAT
*
138889 ATGTTATTAAT
1 ATGTGATTAAT
*
138900 ATGTGATGTGATAA
1 ATGTGAT-T-A-AT
* * *
138914 ATGCTAAAATATT
1 ATG-T-GATTAAT
138927 CATGTGATT-A-
1 -ATGTGATTAAT
138937 ATGTGATTAA-
1 ATGTGATTAAT
138947 ATGTGATTAAT
1 ATGTGATTAAT
138958 ATGTGAGGTGTTAA-
1 ATGTGA----TTAAT
* *
138972 ATGTTGAAATATT
1 ATG-TG-ATTAAT
*
138985 CATGTGACT-A-
1 -ATGTGATTAAT
138995 ATGTGATTAA-
1 ATGTGATTAAT
139005 ATGTGATT-AT
1 ATGTGATTAAT
*
139015 ATGTGATCAA-
1 ATGTGATTAAT
139025 ATGTGATTAAT
1 ATGTGATTAAT
139036 ATGTG
1 ATGTG
139041 TTGTGTTAAA
Statistics
Matches: 157, Mismatches: 27, Indels: 51
0.67 0.11 0.22
Matches are distributed among these distances:
9 16 0.10
10 61 0.39
11 26 0.17
12 13 0.08
13 9 0.06
14 21 0.13
15 9 0.06
16 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.40
Consensus pattern (11 bp):
ATGTGATTAAT
Found at i:138911 original size:58 final size:58
Alignment explanation
Indices: 138820--139021 Score: 300
Period size: 58 Copynumber: 3.5 Consensus size: 58
138810 AATATGACTG
* *
138820 AATGTGATTATATGTGATTAATATGTGACGTGAT-AATGCTGAAATATTCATGTGATT
1 AATGTGATTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGATT
* * *
138877 AAATGTGACTAAATGTTATTAATATGTGATGTGATAAATGCTAAAATATTCATGTGATT
1 -AATGTGATTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGATT
* * * *
138936 AATGTGATTAAATGTGATTAATATGTGAGGTGTTAAATGTTGAAATATTCATGTGACT
1 AATGTGATTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGATT
138994 AATGTGATTAAATGTGATT-ATATGTGAT
1 AATGTGATTAAATGTGATTAATATGTGAT
139022 CAAATGTGAT
Statistics
Matches: 130, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
57 8 0.06
58 100 0.77
59 22 0.17
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (58 bp):
AATGTGATTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGATT
Found at i:138942 original size:9 final size:9
Alignment explanation
Indices: 138928--138957 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
138918 TAAAATATTC
138928 ATGTGATTA
1 ATGTGATTA
138937 ATGTGATTAA
1 ATGTGATT-A
138947 ATGTGATTA
1 ATGTGATTA
138956 AT
1 AT
138958 ATGTGAGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (9 bp):
ATGTGATTA
Found at i:139019 original size:78 final size:76
Alignment explanation
Indices: 138928--139086 Score: 212
Period size: 78 Copynumber: 2.1 Consensus size: 76
138918 TAAAATATTC
* *
138928 ATGTGATTAATGTGATTAAATGTGATTAATATGTGAGGTGTTAAATG-TTGAAATATTCATGTGA
1 ATGTGATTAATGTGATCAAATGTGATTAATATGTGAGGTGTTAAATGCTT-AAATACTCATGTGA
*
138992 CTAATGTGATTAA
65 CTAATGAGATT-A
** * *
139005 ATGTGATTATATGTGATCAAATGTGATTAATATGTGTTGTGTTAAATGCTTAAGTACTCATGTTA
1 ATGTGATTA-ATGTGATCAAATGTGATTAATATGTGAGGTGTTAAATGCTTAAATACTCATGTGA
*
139070 TTAATGAGATTA
65 CTAATGAGATTA
139082 ATGTG
1 ATGTG
139087 TAAAAGAATG
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
77 15 0.21
78 55 0.76
79 2 0.03
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (76 bp):
ATGTGATTAATGTGATCAAATGTGATTAATATGTGAGGTGTTAAATGCTTAAATACTCATGTGAC
TAATGAGATTA
Found at i:139020 original size:20 final size:20
Alignment explanation
Indices: 138986--139040 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
138976 TGAAATATTC
* *
138986 ATGTGACTA-ATGTGATTAA
1 ATGTGATTATATGTGATCAA
139005 ATGTGATTATATGTGATCAA
1 ATGTGATTATATGTGATCAA
139025 ATGTGATTAATATGTG
1 ATGTGATT-ATATGTG
139041 TTGTGTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.25
20 17 0.53
21 7 0.22
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.40
Consensus pattern (20 bp):
ATGTGATTATATGTGATCAA
Found at i:144452 original size:12 final size:14
Alignment explanation
Indices: 144428--144475 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 14
144418 GCACAAAATC
*
144428 CTCTTCATTTTCTT
1 CTCTTCCTTTTCTT
144442 -T-TTCCTTTTCTT
1 CTCTTCCTTTTCTT
144454 CTCTTCCTTCTTCTT
1 CTCTTCCTT-TTCTT
144469 CTTCTTC
1 C-TCTTC
144476 TCTATTCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 10 0.34
13 2 0.07
14 6 0.21
15 6 0.21
16 5 0.17
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (14 bp):
CTCTTCCTTTTCTT
Found at i:154458 original size:34 final size:34
Alignment explanation
Indices: 154420--154502 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
154410 ACATGCTTTT
154420 ATGCAAATTCTA-TTTAAGTCTGATAATCTTTTGC
1 ATGCAAATT-TATTTTAAGTCTGATAATCTTTTGC
** *
154454 ATGCATGTTTATTTTAAGTTTGATAATCTTTTGC
1 ATGCAAATTTATTTTAAGTCTGATAATCTTTTGC
**
154488 ATGCATGTTTATTTT
1 ATGCAAATTTATTTT
154503 GTTTGCGAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 2 0.04
34 43 0.96
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (34 bp):
ATGCAAATTTATTTTAAGTCTGATAATCTTTTGC
Found at i:154467 original size:33 final size:33
Alignment explanation
Indices: 154430--154501 Score: 126
Period size: 34 Copynumber: 2.2 Consensus size: 33
154420 ATGCAAATTC
154430 TATTTAAGTCTGATAATCTTTTGCATGCATGTT
1 TATTTAAGTCTGATAATCTTTTGCATGCATGTT
*
154463 TATTTTAAGTTTGATAATCTTTTGCATGCATGTT
1 TA-TTTAAGTCTGATAATCTTTTGCATGCATGTT
154497 TATTT
1 TATTT
154502 TGTTTGCGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
33 5 0.14
34 32 0.86
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (33 bp):
TATTTAAGTCTGATAATCTTTTGCATGCATGTT
Found at i:166393 original size:15 final size:15
Alignment explanation
Indices: 166373--166407 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
166363 TTCACATTTT
*
166373 CTTTTATTTGTTTCA
1 CTTTTACTTGTTTCA
166388 CTTTTACTTGTTTCA
1 CTTTTACTTGTTTCA
166403 -TTTTA
1 CTTTTA
166408 ATTTCTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.66
Consensus pattern (15 bp):
CTTTTACTTGTTTCA
Found at i:168751 original size:19 final size:18
Alignment explanation
Indices: 168727--168767 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
168717 ATGCATTTTA
168727 TTGTCATTGCATTTCTATT
1 TTGTCATTGCATTTCT-TT
168746 TTGTCATTGCATTTCTTT
1 TTGTCATTGCATTTCTTT
168764 TTGT
1 TTGT
168768 TAATAGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.61
Consensus pattern (18 bp):
TTGTCATTGCATTTCTTT
Found at i:172432 original size:17 final size:17
Alignment explanation
Indices: 172410--172451 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
172400 TATGACAATA
172410 TTTTTCT-TTCTTTTCTC
1 TTTTTCTCTTC-TTTCTC
*
172427 TTTTTCTCTTCTTTCTT
1 TTTTTCTCTTCTTTCTC
172444 TTTTTCTC
1 TTTTTCTC
172452 ATTCATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTCTTCTTTCTC
Found at i:177347 original size:15 final size:14
Alignment explanation
Indices: 177321--177356 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
177311 CTATTGATGA
*
177321 TTGCTGTAACTCCT
1 TTGCTATAACTCCT
177335 TTGTCTATAACTCCT
1 TTG-CTATAACTCCT
177350 TTGCTAT
1 TTGCTAT
177357 GAGGAATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (14 bp):
TTGCTATAACTCCT
Found at i:187656 original size:14 final size:14
Alignment explanation
Indices: 187637--187667 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
187627 AACATATGAA
187637 AAAGGAGGCCAATC
1 AAAGGAGGCCAATC
187651 AAAGGAGGCCAATC
1 AAAGGAGGCCAATC
187665 AAA
1 AAA
187668 CTTGATCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.19, G:0.26, T:0.06
Consensus pattern (14 bp):
AAAGGAGGCCAATC
Found at i:190794 original size:26 final size:26
Alignment explanation
Indices: 190760--190830 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
190750 AGACCATTTA
*
190760 TAGTTTACCATTTATTTTTCAGCAAT
1 TAGTTTACCATTTATTTTCCAGCAAT
**
190786 TAGTTTACCATTTATTTTCCATTAAT
1 TAGTTTACCATTTATTTTCCAGCAAT
*
190812 TAGTTTATCATTTATTTTC
1 TAGTTTACCATTTATTTTC
190831 TCATTAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.55
Consensus pattern (26 bp):
TAGTTTACCATTTATTTTCCAGCAAT
Found at i:192542 original size:15 final size:14
Alignment explanation
Indices: 192499--192542 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
192489 TTTTGCTACA
192499 ATTTACTTTCTTGC
1 ATTTACTTTCTTGC
*
192513 ATTTAAATTTC-TGC
1 ATTT-ACTTTCTTGC
192527 ATTTACTTTCCTTGC
1 ATTTACTTT-CTTGC
192542 A
1 A
192543 CCGAAGCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 4 0.16
14 12 0.48
15 9 0.36
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.52
Consensus pattern (14 bp):
ATTTACTTTCTTGC
Found at i:213456 original size:18 final size:16
Alignment explanation
Indices: 213435--213474 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
213425 ACATATGCTC
* *
213435 TTTTTTTCTTTTTCTCC
1 TTTTTTTCATTTT-TCA
213452 TTTTTTTCATTTTTCA
1 TTTTTTTCATTTTTCA
213468 TTTTTTT
1 TTTTTTT
213475 TTCTAAGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTCATTTTTCA
Found at i:213472 original size:17 final size:16
Alignment explanation
Indices: 213432--213478 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
213422 AGTACATATG
213432 CTCTTTTTTTCTTTTT
1 CTCTTTTTTTCTTTTT
213448 CTCCTTTTTTTCATTTTT
1 CT-CTTTTTTTC-TTTTT
*
213466 CATTTTTTTTTCT
1 C-TCTTTTTTTCT
213479 AAGCATCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 2 0.07
17 10 0.37
18 14 0.52
19 1 0.04
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
CTCTTTTTTTCTTTTT
Found at i:219476 original size:33 final size:33
Alignment explanation
Indices: 219437--219502 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
219427 AGTCTGCTGA
*
219437 CTATCCACGTTGGGGACCCCATTTCATTATTAT
1 CTATCCACATTGGGGACCCCATTTCATTATTAT
219470 CTATCCACATTGGGGACCCCATTTCATTATTAT
1 CTATCCACATTGGGGACCCCATTTCATTATTAT
219503 ATCATTTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (33 bp):
CTATCCACATTGGGGACCCCATTTCATTATTAT
Found at i:239341 original size:27 final size:27
Alignment explanation
Indices: 239311--239363 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
239301 ATCTGATTTG
239311 TTCATTAGGTAGTTGCAGATTGTCGCA
1 TTCATTAGGTAGTTGCAGATTGTCGCA
*
239338 TTCATTAGGTAGTTGTAGATTGTCGC
1 TTCATTAGGTAGTTGCAGATTGTCGC
239364 GACATTGCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (27 bp):
TTCATTAGGTAGTTGCAGATTGTCGCA
Found at i:239698 original size:14 final size:14
Alignment explanation
Indices: 239681--239722 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
239671 TAGAAATTGC
*
239681 AAATACTAAATATG
1 AAATGCTAAATATG
*
239695 AAATGCTAAAAATG
1 AAATGCTAAATATG
*
239709 -TATGCTAAATATG
1 AAATGCTAAATATG
239722 A
1 A
239723 TGCACCCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (14 bp):
AAATGCTAAATATG
Found at i:243051 original size:81 final size:81
Alignment explanation
Indices: 242916--243080 Score: 296
Period size: 81 Copynumber: 2.0 Consensus size: 81
242906 TTGCCTCGAT
* *
242916 CCACTTGGAGACATAGTCAACAGCAACCTGATTATACACGTTCCCAAAGGAATTTGGAAATGGTC
1 CCACTTGGAGACATAGTCAACAGCAACCTGAATATACACATTCCCAAAGGAATTTGGAAATGGTC
242981 CCATAAAATCTATACC
66 CCATAAAATCTATACC
242997 CCACTTGGAGACATAGTCAACAGCAA-CTAGAATATACACATTCCCAAAGGAATTTGGAAATGGT
1 CCACTTGGAGACATAGTCAACAGCAACCT-GAATATACACATTCCCAAAGGAATTTGGAAATGGT
243061 CCCATAAAATCTATACC
65 CCCATAAAATCTATACC
243078 CCA
1 CCA
243081 AACATCAAAT
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
80 2 0.02
81 79 0.98
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (81 bp):
CCACTTGGAGACATAGTCAACAGCAACCTGAATATACACATTCCCAAAGGAATTTGGAAATGGTC
CCATAAAATCTATACC
Done.