Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011692.1 Corchorus capsularis cultivar CVL-1 contig11713, 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: 108972
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:44 original size:22 final size:22
Alignment explanation
Indices: 25--97 Score: 53
Period size: 21 Copynumber: 3.4 Consensus size: 22
15 AAATGGTAAT
* *
25 CAGTAAAAAGTAAGAGGGTAAAT
1 CAGTAAAAAGTAAAAGAGT-AAT
* *
48 CA--ACAAGAGTAAAATAGTAAT
1 CAGTA-AAAAGTAAAAGAGTAAT
* *
69 CAGTATAAAGT-AAAGAATAAT
1 CAGTAAAAAGTAAAAGAGTAAT
90 CAGTAAAA
1 CAGTAAAA
98 TAGTGATGGT
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
21 21 0.55
22 14 0.37
23 3 0.08
ACGTcount: A:0.56, C:0.07, G:0.18, T:0.19
Consensus pattern (22 bp):
CAGTAAAAAGTAAAAGAGTAAT
Found at i:4690 original size:75 final size:74
Alignment explanation
Indices: 4473--4695 Score: 236
Period size: 75 Copynumber: 3.0 Consensus size: 74
4463 AAATAAATTA
* **
4473 AGAAAAGACCAAAACGGGGCGAAAATATTCTCCTATGTTAAAAGTTG-TTGGGAGCTATCAGTAC
1 AGAAAAGACCAAAACGGGACGAAAAGGTTCTCC-ATGTTAAAAGTTGATT-GGAGCTATCAGTA-
*
4537 A-TTACAGAGTG
63 ATTTCCAGAGTG
** * * * **
4548 AGAAAAGACTGAAAC-TGAGCGAAAAGGTTCTCTCACGTTAAAAGTTGATGGGAGCTATTGGTAA
1 AGAAAAGACCAAAACGGGA-CGAAAAGGTTCTC-CATGTTAAAAGTTGATTGGAGCTATCAGTAA
4612 TTTCCAGAGTG
64 TTTCCAGAGTG
* * *
4623 AGAAAAGACCAAAACGGGACAAAAAGGTTCTCACATGTTAAAAGTTGATTAGAGCTATCAATAAT
1 AGAAAAGACCAAAACGGGACGAAAAGGTTCTC-CATGTTAAAAGTTGATTGGAGCTATCAGTAAT
*
4688 TTCAAGAG
65 TTCCAGAG
4696 GGTATTCAAA
Statistics
Matches: 120, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
74 2 0.02
75 114 0.95
76 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (74 bp):
AGAAAAGACCAAAACGGGACGAAAAGGTTCTCCATGTTAAAAGTTGATTGGAGCTATCAGTAATT
TCCAGAGTG
Found at i:4729 original size:2 final size:2
Alignment explanation
Indices: 4724--4758 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4714 AGTGTGTGTG
4724 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4759 TATTTGAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5856 original size:16 final size:16
Alignment explanation
Indices: 5835--5867 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5825 GTAGCAATAA
*
5835 TACTTTTTTTTTAATT
1 TACTTTTCTTTTAATT
5851 TACTTTTCTTTTAATT
1 TACTTTTCTTTTAATT
5867 T
1 T
5868 TAGCTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (16 bp):
TACTTTTCTTTTAATT
Found at i:12777 original size:2 final size:2
Alignment explanation
Indices: 12764--12793 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12754 ATTAGTAGTA
*
12764 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12794 GGCAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12987 original size:2 final size:2
Alignment explanation
Indices: 12980--13004 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12970 AATCACCCTC
12980 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13005 GAAATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22791 original size:1 final size:1
Alignment explanation
Indices: 22743--22780 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
22733 ATTTTGGAGC
22743 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22781 AAGTTCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:23504 original size:3 final size:3
Alignment explanation
Indices: 23496--23527 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
23486 TGGTAAAGTT
23496 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23528 TAGGGGTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:23874 original size:15 final size:15
Alignment explanation
Indices: 23854--23891 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
23844 TAATTAGTAT
* *
23854 TTAATTAGTTTATGA
1 TTAATTAATTCATGA
23869 TTAATTAATTCATGA
1 TTAATTAATTCATGA
23884 TTAATTAA
1 TTAATTAA
23892 ATACTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (15 bp):
TTAATTAATTCATGA
Found at i:23899 original size:11 final size:11
Alignment explanation
Indices: 23885--23966 Score: 92
Period size: 11 Copynumber: 6.7 Consensus size: 11
23875 AATTCATGAT
23885 TAATTAAATAC
1 TAATTAAATAC
23896 TAATTAATCATAAAC
1 TAATTAA--AT--AC
23911 TAATTAAATAC
1 TAATTAAATAC
23922 TAATTAATCATAAAC
1 TAATTAA--AT--AC
23937 TAATTAAATAC
1 TAATTAAATAC
23948 TAATTAAATAC
1 TAATTAAATAC
23959 TAATTAAA
1 TAATTAAA
23967 CATAAACTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
11 37 0.59
13 8 0.13
15 18 0.29
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATTAAATAC
Found at i:23899 original size:26 final size:26
Alignment explanation
Indices: 23885--23954 Score: 140
Period size: 26 Copynumber: 2.7 Consensus size: 26
23875 AATTCATGAT
23885 TAATTAAATACTAATTAATCATAAAC
1 TAATTAAATACTAATTAATCATAAAC
23911 TAATTAAATACTAATTAATCATAAAC
1 TAATTAAATACTAATTAATCATAAAC
23937 TAATTAAATACTAATTAA
1 TAATTAAATACTAATTAA
23955 ATACTAATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (26 bp):
TAATTAAATACTAATTAATCATAAAC
Found at i:23901 original size:15 final size:15
Alignment explanation
Indices: 23883--23954 Score: 52
Period size: 15 Copynumber: 5.3 Consensus size: 15
23873 TTAATTCATG
23883 ATTAATTAAATACTA
1 ATTAATTAAATACTA
*
23898 ATTAA-T-CATA--A
1 ATTAATTAAATACTA
*
23909 ACTAATTAAATACTA
1 ATTAATTAAATACTA
*
23924 ATTAA-T-CATA--A
1 ATTAATTAAATACTA
*
23935 ACTAATTAAATACTA
1 ATTAATTAAATACTA
23950 ATTAA
1 ATTAA
23955 ATACTAATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 16
0.63 0.12 0.25
Matches are distributed among these distances:
11 10 0.24
12 2 0.05
13 12 0.29
14 2 0.05
15 15 0.37
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTAATTAAATACTA
Found at i:23926 original size:37 final size:34
Alignment explanation
Indices: 23886--23966 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 34
23876 ATTCATGATT
23886 AATTAAATACTAATTAATCATAAACTAATTAAATACT
1 AATTAAATACTAATTAA--AT-AACTAATTAAATACT
23923 AATTAATCATAAACTAATTAAAT-ACTAATTAAATACT
1 AATTAA--AT--ACTAATTAAATAACTAATTAAATACT
23960 AATTAAA
1 AATTAAA
23967 CATAAACTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
35 1 0.03
37 26 0.65
39 4 0.10
41 9 0.22
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.35
Consensus pattern (34 bp):
AATTAAATACTAATTAAATAACTAATTAAATACT
Found at i:23958 original size:63 final size:63
Alignment explanation
Indices: 23885--24007 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
23875 AATTCATGAT
* *
23885 TAATTAAATACTAATTAATCATAAACTAATTAAA-T-ACTAATTAATCATAAACTAATTAAATAC
1 TAATTAAATACTAATTAAACATAAACTAA-TAAATTAACTAATT-ATAATAAACTAATTAAATAC
* *
23948 TAATTAAATACTAATTAAACATAAACTAATAAATTAAGTAATTTTAATAAACTAATTAAA
1 TAATTAAATACTAATTAAACATAAACTAATAAATTAACTAATTATAATAAACTAATTAAA
24008 ATTAATCATA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
62 4 0.07
63 44 0.81
64 6 0.11
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.35
Consensus pattern (63 bp):
TAATTAAATACTAATTAAACATAAACTAATAAATTAACTAATTATAATAAACTAATTAAATAC
Found at i:23971 original size:37 final size:36
Alignment explanation
Indices: 23909--23981 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 36
23899 TTAATCATAA
*
23909 ACTAATTAAATACTAATTAATCATAAACTAATTAAAT
1 ACTAATTAAATACTAATTAAACATAAACTAA-TAAAT
23946 ACTAATTAAATACTAATTAAACATAAACTAATAAAT
1 ACTAATTAAATACTAATTAAACATAAACTAATAAAT
23982 TAAGTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 5 0.14
37 30 0.86
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (36 bp):
ACTAATTAAATACTAATTAAACATAAACTAATAAAT
Found at i:23975 original size:26 final size:27
Alignment explanation
Indices: 23894--24012 Score: 76
Period size: 26 Copynumber: 4.5 Consensus size: 27
23884 TTAATTAAAT
*
23894 ACTAATTAATCATAAACTAATT-AAAT--
1 ACTAATTAA--ATTAACTAATTAAAATAA
*
23920 ACTAATTAATCATAAACTAATT-AAAT--
1 ACTAATTAA--ATTAACTAATTAAAATAA
23946 ACTAATTAAA-T-ACTAATTAAACATAA
1 ACTAATTAAATTAACTAATTAAA-ATAA
* **
23972 ACTAA-TAAATTAAGTAATTTTAATAA
1 ACTAATTAAATTAACTAATTAAAATAA
23998 ACTAATTAAAATTAA
1 ACTAATT-AAATTAA
24013 TCATAAACAT
Statistics
Matches: 81, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
22 7 0.09
23 2 0.02
24 3 0.04
25 4 0.05
26 50 0.62
27 8 0.10
28 7 0.09
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.34
Consensus pattern (27 bp):
ACTAATTAAATTAACTAATTAAAATAA
Found at i:24138 original size:24 final size:25
Alignment explanation
Indices: 24101--24164 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
24091 CAGCCCTAAA
24101 AACAAAAAACAAAAAACCGAA-ATTT
1 AACAAAAAA-AAAAAACCGAAGATTT
*
24126 ATCAAAAAAAAAAAACCGAAGTATTT
1 AACAAAAAAAAAAAACCGAAG-ATTT
*
24152 AACTAAAAAAAAA
1 AACAAAAAAAAAA
24165 CCGAAGTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.32
25 8 0.24
26 15 0.44
ACGTcount: A:0.69, C:0.12, G:0.05, T:0.14
Consensus pattern (25 bp):
AACAAAAAAAAAAAACCGAAGATTT
Found at i:24151 original size:26 final size:25
Alignment explanation
Indices: 24102--24171 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
24092 AGCCCTAAAA
24102 ACAAAAAACAAAAAACCGAA--ATTT
1 ACAAAAAA-AAAAAACCGAAGTATTT
24126 ATCAAAAAAAAAAAACCGAAGTATTT
1 A-CAAAAAAAAAAAACCGAAGTATTT
**
24152 A-ACTAAAAAAAAACCGAAGT
1 ACAAAAAAAAAAAACCGAAGT
24172 TTGAAGTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 29 0.71
25 7 0.17
26 5 0.12
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (25 bp):
ACAAAAAAAAAAAACCGAAGTATTT
Found at i:29080 original size:2 final size:2
Alignment explanation
Indices: 29073--29108 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29063 GTTTTATCTG
29073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29109 CAACCAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33398 original size:6 final size:6
Alignment explanation
Indices: 33389--33416 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
33379 GAAGAATAAA
33389 TCACTT TCACTT TCACTT TCACTT TCAC
1 TCACTT TCACTT TCACTT TCACTT TCAC
33417 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:35926 original size:22 final size:23
Alignment explanation
Indices: 35901--35947 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
35891 TATTAACTAA
35901 TTCTTTTTAATTAATTTA-TTTT
1 TTCTTTTTAATTAATTTAGTTTT
*
35923 TTCTTTTTATTTAATTTAGTTTT
1 TTCTTTTTAATTAATTTAGTTTT
35946 TT
1 TT
35948 TAATTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (23 bp):
TTCTTTTTAATTAATTTAGTTTT
Found at i:35947 original size:18 final size:19
Alignment explanation
Indices: 35926--35963 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
35916 TTATTTTTTC
*
35926 TTTTTATTTAA-TTTAGTT
1 TTTTTAATTAATTTTAGTT
35944 TTTTTAATTAATTTTAGTT
1 TTTTTAATTAATTTTAGTT
35963 T
1 T
35964 AATTAGGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTAATTAATTTTAGTT
Found at i:37249 original size:42 final size:42
Alignment explanation
Indices: 37190--37270 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
37180 TCAAAAATTA
* **
37190 CATTTTTCTTAAATCGTCTTCAAAATACGGCACGTTAACATC
1 CATTTTTCTTAAATCGTCATCAAAATACAACACGTTAACATC
37232 CATTTTTCTTAAATCGTCATCAAAATACAACACGTTAAC
1 CATTTTTCTTAAATCGTCATCAAAATACAACACGTTAAC
37271 GCTATTCTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (42 bp):
CATTTTTCTTAAATCGTCATCAAAATACAACACGTTAACATC
Found at i:38337 original size:21 final size:18
Alignment explanation
Indices: 38299--38339 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
38289 GGAATATTCT
38299 TGCTTCCAATGACTTCAA
1 TGCTTCCAATGACTTCAA
38317 TGCTCTCCAATTGATCTTCAA
1 TGCT-TCCAA-TGA-CTTCAA
38338 TG
1 TG
38340 GTCTTCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 3 0.15
21 8 0.40
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (18 bp):
TGCTTCCAATGACTTCAA
Found at i:38685 original size:20 final size:19
Alignment explanation
Indices: 38636--38686 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
38626 TTGGCGCATC
38636 AGATCACTTGGTAAATCAA
1 AGATCACTTGGTAAATCAA
* * *
38655 AGATTATTTGGATAAATCCAT
1 AGATCACTTGG-TAAAT-CAA
38676 AGATCA-TTGGT
1 AGATCACTTGGT
38687 CTCATATATC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 10 0.38
20 9 0.35
21 7 0.27
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (19 bp):
AGATCACTTGGTAAATCAA
Found at i:51149 original size:15 final size:15
Alignment explanation
Indices: 51119--51151 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
51109 GTAATAAAAA
51119 TTAAATATTTTAATT
1 TTAAATATTTTAATT
51134 TTAATATATTTT-ATT
1 TTAA-ATATTTTAATT
51149 TTA
1 TTA
51152 TTGAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTAAATATTTTAATT
Found at i:51372 original size:13 final size:13
Alignment explanation
Indices: 51354--51378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51344 CATACTTGTA
51354 ATCGTATATATAG
1 ATCGTATATATAG
51367 ATCGTATATATA
1 ATCGTATATATA
51379 AAGAAATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
ATCGTATATATAG
Found at i:53864 original size:2 final size:2
Alignment explanation
Indices: 53857--53885 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53847 AGAGGGTATT
53857 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 T
53886 CAGAAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55824 original size:45 final size:45
Alignment explanation
Indices: 55740--55827 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
55730 CATCGATAGC
* *
55740 AGCAGTGAGAAAACCTTCACCGACGAAAGTCATGAAACAGAAACT
1 AGCAGTGAGAAAACCTTCACCCACGAAACTCATGAAACAGAAACT
* * * *
55785 AGCAGTGAGAAAAGCTTCACCCATGAAACTCGTGCAACAGAAA
1 AGCAGTGAGAAAACCTTCACCCACGAAACTCATGAAACAGAAA
55828 TGGTTAGGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (45 bp):
AGCAGTGAGAAAACCTTCACCCACGAAACTCATGAAACAGAAACT
Found at i:56358 original size:14 final size:14
Alignment explanation
Indices: 56339--56386 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
56329 TTTCACCCCC
56339 TATGCACTTGCACA
1 TATGCACTTGCACA
* *
56353 TATGCAC-T-AACC
1 TATGCACTTGCACA
*
56365 TATTCACTTGCACA
1 TATGCACTTGCACA
56379 TATGCACT
1 TATGCACT
56387 AAATTTGCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 8 0.31
13 2 0.08
14 16 0.62
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.31
Consensus pattern (14 bp):
TATGCACTTGCACA
Found at i:56373 original size:26 final size:26
Alignment explanation
Indices: 56337--56388 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
56327 ATTTTCACCC
56337 CCTATGCACTTGCACATATGCACTAA
1 CCTATGCACTTGCACATATGCACTAA
*
56363 CCTATTCACTTGCACATATGCACTAA
1 CCTATGCACTTGCACATATGCACTAA
56389 ATTTGCTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (26 bp):
CCTATGCACTTGCACATATGCACTAA
Found at i:63955 original size:22 final size:22
Alignment explanation
Indices: 63880--64148 Score: 143
Period size: 22 Copynumber: 12.5 Consensus size: 22
63870 AGCATCACTA
*
63880 TTTTACTGATTA-TTCTTTACT
1 TTTTACTGATTACCTCTTTACT
* *
63901 TTGTACTGATTA-CTATTTTACT
1 TTTTACTGATTACCT-CTTTACT
* *
63923 CTTGT--TGATTACCTCCTTACT
1 -TTTTACTGATTACCTCTTTACT
*
63944 TTTTACTGATTATCAT-TTTACT
1 TTTTACTGATTA-CCTCTTTACT
63966 CTTTTACTGATTA-CTCTTTACT
1 -TTTTACTGATTACCTCTTTACT
* **
63988 ATTTT-CTG-CT-CC-CATTTTTT
1 -TTTTACTGATTACCTC-TTTACT
64008 TTTTACTGATTA-CTCTTTTACT
1 TTTTACTGATTACCTC-TTTACT
* * *
64030 TTTTACTGATTGCCT-TTTGCC
1 TTTTACTGATTACCTCTTTACT
* *
64051 TTGTACTGATTACCTTTTTACT
1 TTTTACTGATTACCTCTTTACT
* * * *
64073 TCTTGCTGATTAGCTTTTTACT
1 TTTTACTGATTACCTCTTTACT
* * *
64095 CTTTACTGATCACCTTTTTAC-
1 TTTTACTGATTACCTCTTTACT
* * *
64116 TCTTACCGATTTCCT-TTTACT
1 TTTTACTGATTACCTCTTTACT
* *
64137 TCTTACTTATTA
1 TTTTACTGATTA
64149 TTTTTTTACT
Statistics
Matches: 190, Mismatches: 41, Indels: 34
0.72 0.15 0.13
Matches are distributed among these distances:
19 5 0.03
20 17 0.09
21 65 0.34
22 83 0.44
23 20 0.11
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTTACTGATTACCTCTTTACT
Found at i:64032 original size:21 final size:21
Alignment explanation
Indices: 63880--64222 Score: 148
Period size: 21 Copynumber: 16.3 Consensus size: 21
63870 AGCATCACTA
*
63880 TTTTACTGATTATTC-TTTAC
1 TTTTACTGATTACTCTTTTAC
*
63900 TTTGTACTGATTACTATTTTAC
1 TTT-TACTGATTACTCTTTTAC
* ** *
63922 TCTTGTTGATTAC-CTCCTTAC
1 TTTTACTGATTACTCT-TTTAC
63943 TTTTTACTGATTA-TCATTTTACTC
1 -TTTTACTGATTACTC-TTTTA--C
63967 TTTTACTGATTACTC-TTTAC
1 TTTTACTGATTACTCTTTTAC
* * * **
63987 TATTTTCTG-CT-CCCATTTTTT
1 T-TTTACTGATTACTC-TTTTAC
64008 TTTTACTGATTACTCTTTTAC
1 TTTTACTGATTACTCTTTTAC
* *
64029 TTTTTACTGATTGC-CTTTTGCC
1 -TTTTACTGATTACTCTTTT-AC
*
64051 TTGTACTGATTAC-CTTTTTAC
1 TTTTACTGATTACTC-TTTTAC
*
64072 TTCTTGCTGATTAGCT-TTTTAC
1 TT-TTACTGATTA-CTCTTTTAC
*
64094 TCTTTACTGATCAC-CTTTTTAC
1 T-TTTACTGATTACTC-TTTTAC
* * *
64116 TCTTACCGATTTC-CTTTTAC
1 TTTTACTGATTACTCTTTTAC
*
64136 TTCTTACTTATTA----TTT--
1 TT-TTACTGATTACTCTTTTAC
*
64152 TTTTACTGATTACT-ATTTAC
1 TTTTACTGATTACTCTTTTAC
* *
64172 TTTTTACTGACTACTATTTTAC
1 -TTTTACTGATTACTCTTTTAC
* **
64194 TCTTGTTGATTAC-CTTCTTAC
1 TTTTACTGATTACTCTT-TTAC
64215 TTCTTACT
1 TT-TTACT
64223 TTTTACTGAT
Statistics
Matches: 241, Mismatches: 49, Indels: 64
0.68 0.14 0.18
Matches are distributed among these distances:
15 9 0.04
16 2 0.01
18 6 0.02
19 2 0.01
20 22 0.09
21 101 0.42
22 81 0.34
23 15 0.06
24 3 0.01
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTACTGATTACTCTTTTAC
Found at i:64070 original size:43 final size:43
Alignment explanation
Indices: 63881--64158 Score: 150
Period size: 43 Copynumber: 6.5 Consensus size: 43
63871 GCATCACTAT
* *
63881 TTTACTGATTA--TTCTTTACTT-TGTACTGATTACTATTTTACTC
1 TTTACTGATTACCTT-TTTACTTCT-TACTGATTGC-CTTTTACTC
** * * *
63924 TTGT--TGATTACCTCCTTACTTTTTACTGATTATCATTTTACTC
1 TT-TACTGATTACCTTTTTACTTCTTACTGATT-GCCTTTTACTC
* * * * * *
63967 TTTTACTGATTA-CTCTTTACTAT-TTTCTG-CTCCCATTTT-TTT
1 -TTTACTGATTACCTTTTTACT-TCTTACTGATTGCC-TTTTACTC
* *
64009 TTTACTGATTA-CTCTTTTACTTTTTACTGATTGCCTTTTGC-C
1 TTTACTGATTACCT-TTTTACTTCTTACTGATTGCCTTTTACTC
* *
64051 TTGTACTGATTACCTTTTTACTTCTTGCTGATTAGCTTTTTACTC
1 TT-TACTGATTACCTTTTTACTTCTTACTGATT-GCCTTTTACTC
* * *
64096 TTTACTGATCACCTTTTTAC-TCTTACCGATTTCCTTTTACT-
1 TTTACTGATTACCTTTTTACTTCTTACTGATTGCCTTTTACTC
* **
64137 TCTTACTTATTATTTTTTTACT
1 T-TTACTGATTACCTTTTTACT
64159 GATTACTATT
Statistics
Matches: 186, Mismatches: 29, Indels: 40
0.73 0.11 0.16
Matches are distributed among these distances:
41 15 0.08
42 48 0.26
43 68 0.37
44 45 0.24
45 10 0.05
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.56
Consensus pattern (43 bp):
TTTACTGATTACCTTTTTACTTCTTACTGATTGCCTTTTACTC
Found at i:64116 original size:129 final size:128
Alignment explanation
Indices: 63880--64111 Score: 301
Period size: 129 Copynumber: 1.8 Consensus size: 128
63870 AGCATCACTA
*
63880 TTTTACTGATTATTCTTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCTCCTTACTT
1 TTTTACTGATTACTCTTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCTCCTTACTT
* * *
63945 TTTACTGATTATCATTTTACTCTTTTACTGATTACTCTTTACTATTTTCTGCTCCCATTTTTT
66 CTTACTGATTAGCATTTTACTCTTTTACTGATCACTCTTTACTATTTTCTGCTCCCATTTTTT
* * * * **
64008 TTTTACTGATTACTCTTTTACTTTTTACTGATTGC-CTTTTGC-CTTGTACTGATTACCTTTTTA
1 TTTTACTGATTACTC-TTTACTTTGTACTGATTACTATTTTACTCTTGT--TGATTACCTCCTTA
* *
64071 CTTCTTGCTGATTAGCTTTTTACTC-TTTACTGATCAC-CTTT
63 CTTCTTACTGATTAGCATTTTACTCTTTTACTGATCACTCTTT
64112 TTACTCTTAC
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
127 9 0.10
128 30 0.34
129 50 0.56
ACGTcount: A:0.17, C:0.20, G:0.08, T:0.55
Consensus pattern (128 bp):
TTTTACTGATTACTCTTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCTCCTTACTT
CTTACTGATTAGCATTTTACTCTTTTACTGATCACTCTTTACTATTTTCTGCTCCCATTTTTT
Found at i:64164 original size:22 final size:22
Alignment explanation
Indices: 64151--64278 Score: 65
Period size: 21 Copynumber: 5.6 Consensus size: 22
64141 ACTTATTATT
64151 TTTTTACTGATTAC-TATTTAC
1 TTTTTACTGATTACTTATTTAC
*
64172 TTTTTACTGACTAC-TATTTTAC
1 TTTTTACTGATTACTTA-TTTAC
*
64194 TCTTGT--TGATTACCTTCTTACTTCTTAC
1 T-TTTTACTGATTA----CTTA--T-TTAC
*
64222 TTTTTACTGATTA-TTGTTTTA-
1 TTTTTACTGATTACTT-ATTTAC
64243 TTCTTTACTGATTACCTT-TTTAC
1 TT-TTTACTGATTA-CTTATTTAC
64266 -TTTTACTGATTAC
1 TTTTTACTGATTAC
64279 CCTTTTACTC
Statistics
Matches: 86, Mismatches: 5, Indels: 33
0.69 0.04 0.27
Matches are distributed among these distances:
20 1 0.01
21 33 0.38
22 25 0.29
23 4 0.05
24 4 0.05
25 1 0.01
26 2 0.02
27 5 0.06
28 5 0.06
29 6 0.07
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTTACTGATTACTTATTTAC
Found at i:64222 original size:50 final size:49
Alignment explanation
Indices: 64161--64272 Score: 136
Period size: 50 Copynumber: 2.2 Consensus size: 49
64151 TTTTTACTGA
64161 TTACTATTTACTTTTTACTGACTACTATTTTACTCTTGT-TGATTACCTTC
1 TTACT-TTTACTTTTTACTGACTACTATTTTACTCTT-TATGATTACCTTC
* * * * *
64211 TTACTTCTTACTTTTTACTGATTATTGTTTTATTCTTTACTGATTACCTTT
1 TTACTT-TTACTTTTTACTGACTACTATTTTACTCTTTA-TGATTACCTTC
64262 TTACTTTTACT
1 TTACTTTTACT
64273 GATTACCCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
49 2 0.04
50 36 0.67
51 16 0.30
ACGTcount: A:0.19, C:0.18, G:0.05, T:0.58
Consensus pattern (49 bp):
TTACTTTTACTTTTTACTGACTACTATTTTACTCTTTATGATTACCTTC
Found at i:64270 original size:21 final size:22
Alignment explanation
Indices: 64218--64292 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
64208 TTCTTACTTC
* *
64218 TTACTTTTTACTGATTA-TTGTT
1 TTACTCTTTACTGATTACCT-TT
*
64240 TTATTCTTTACTGATTACCTTT
1 TTACTCTTTACTGATTACCTTT
*
64262 TTACT-TTTACTGATTACCCTT
1 TTACTCTTTACTGATTACCTTT
64283 TTACTCTTTA
1 TTACTCTTTA
64293 TCATTCTTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 20 0.43
22 25 0.54
23 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.05, T:0.59
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCTTT
Found at i:64276 original size:72 final size:73
Alignment explanation
Indices: 64135--64287 Score: 172
Period size: 72 Copynumber: 2.1 Consensus size: 73
64125 TTTCCTTTTA
* **
64135 CTTCTTACTTATTATTTTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTTGT
1 CTTCTTACTTATTATCTTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTTAC
64200 TGATTA-C
66 TGATTACC
* * * * *
64207 CTTCTTACTTCTTA-CTTTTTACTGATTATTGTTTTA-TTCTTTACTGATTACCT-TTTTACTTT
1 CTTCTTACTTATTATCTTTTTACTGATTACT-ATTTACTT-TTTACTGACTA-CTATTTTACTCT
64269 TACTGATTACC
63 TACTGATTACC
64280 CTT-TTACT
1 CTTCTTACT
64288 CTTTATCATT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
71 16 0.23
72 47 0.68
73 6 0.09
ACGTcount: A:0.19, C:0.18, G:0.05, T:0.58
Consensus pattern (73 bp):
CTTCTTACTTATTATCTTTTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTTAC
TGATTACC
Found at i:64327 original size:93 final size:92
Alignment explanation
Indices: 64153--64327 Score: 196
Period size: 93 Copynumber: 1.9 Consensus size: 92
64143 TTATTATTTT
* *
64153 TTTACTGATTACTATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTCTTACTTC
1 TTTACTGATTACTATTTACTTTTTACTGACTACCATTTTACTCTTGTTCATTA-CTTCTTACTTC
* *
64218 TTACTTTTTACTGATTATTGTTTTATTC
65 TTACTCTTTACCGATTATTGTTTTATTC
* * *
64246 TTTACTGATTACCTTTTTAC-TTTTACTGATTACCCTTTTACTCTT-TATCATT-CTTCCTTTAC
1 TTTACTGATTA-CTATTTACTTTTTACTGACTACCATTTTACTCTTGT-TCATTACTT-C-TTAC
*
64308 -TCATTACTCTTTGCCGATTA
62 TTC-TTACTCTTTACCGATTA
64328 CTTTTACCTG
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
91 3 0.04
92 4 0.06
93 55 0.80
94 7 0.10
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.55
Consensus pattern (92 bp):
TTTACTGATTACTATTTACTTTTTACTGACTACCATTTTACTCTTGTTCATTACTTCTTACTTCT
TACTCTTTACCGATTATTGTTTTATTC
Found at i:65403 original size:101 final size:100
Alignment explanation
Indices: 65276--65533 Score: 322
Period size: 101 Copynumber: 2.5 Consensus size: 100
65266 AAGGGTGACA
* * *
65276 TTTTATTTACTAATTACTTAAGAAATTCAATCTTTTATTCAATGGTTTAATCTTTATTTATTAAC
1 TTTTATCTACCAATTACTTAA-AAATTCAATCTTTTATTCAA-GGTTTAATCTTTATTTACTAAC
*
65341 TACCCTAAAAATTCAAACTTTTACTCAAAGATAACAT
64 TACCCTAAAAATTCAAACTTTTACTCAAAGACAACAT
* * * * *
65378 TTTTGTCTACCGATTACTTAAAAATTCAATCTTTTGTTCGAAGGTTAAATCTTTATTTACTAATT
1 TTTTATCTACCAATTACTTAAAAATTCAATCTTTTATTC-AAGGTTTAATCTTTATTTACTAACT
* *
65443 ACCCTAAAAATTCAATCTTTTACTCAAAGACAATAT
65 ACCCTAAAAATTCAAACTTTTACTCAAAGACAACAT
* *
65479 TTTTATTTATCAATTTACTTAAAAATTCAAT-TTTTCATTCAAAGG-TTACATCTTT
1 TTTTATCTACCAA-TTACTTAAAAATTCAATCTTTT-ATTC-AAGGTTTA-ATCTTT
65534 TAGCAAAAGG
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
101 85 0.63
102 49 0.37
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (100 bp):
TTTTATCTACCAATTACTTAAAAATTCAATCTTTTATTCAAGGTTTAATCTTTATTTACTAACTA
CCCTAAAAATTCAAACTTTTACTCAAAGACAACAT
Found at i:65484 original size:51 final size:50
Alignment explanation
Indices: 65276--65522 Score: 205
Period size: 51 Copynumber: 4.9 Consensus size: 50
65266 AAGGGTGACA
* * *
65276 TTTTATTTACTAATTACTTAAGAAATTCAATCTTTTATTCAATGGT-TTAAT
1 TTTTATTTACTAATTACTTAA-AAATTCAATCTTTTATTCAAAGATAAT-AT
* * * * * * *
65327 CTTTATTTATTAACTACCCTAAAAATTCAAACTTTTACTCAAAGATAACAT
1 TTTTATTTACTAATTA-CTTAAAAATTCAATCTTTTATTCAAAGATAATAT
* * ** * * *
65378 TTTTGTCTACCGATTACTTAAAAATTCAATCTTTTGTTCGAAGGTTAA-AT
1 TTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTC-AAAGATAATAT
* * * *
65428 CTTTATTTACTAATTACCCTAAAAATTCAATCTTTTACTCAAAGACAATAT
1 TTTTATTTACTAATTA-CTTAAAAATTCAATCTTTTATTCAAAGATAATAT
65479 TTTTATTTA-TCAATTTACTTAAAAATTCAAT-TTTTCATTCAAAG
1 TTTTATTTACT-AA-TTACTTAAAAATTCAATCTTTT-ATTCAAAG
65523 GTTACATCTT
Statistics
Matches: 151, Mismatches: 37, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
50 42 0.28
51 102 0.68
52 7 0.05
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (50 bp):
TTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGATAATAT
Found at i:65544 original size:20 final size:20
Alignment explanation
Indices: 65519--65557 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
65509 TTTTTCATTC
65519 AAAGGTTACATCTTTTAGCA
1 AAAGGTTACATCTTTTAGCA
65539 AAAGGTTACATCTTTTAGC
1 AAAGGTTACATCTTTTAGC
65558 CAAATATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
AAAGGTTACATCTTTTAGCA
Found at i:68046 original size:27 final size:27
Alignment explanation
Indices: 68016--68085 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
68006 AAGGTGAACC
*
68016 CAAAAATGACTAAAATGCCCCTGAGTA
1 CAAAAATGACCAAAATGCCCCTGAGTA
* *
68043 CAAAAATGACCAAAATGCCCCTGGGTG
1 CAAAAATGACCAAAATGCCCCTGAGTA
68070 CAAAAATGACCAAAAT
1 CAAAAATGACCAAAAT
68086 ACCCTTGGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.16
Consensus pattern (27 bp):
CAAAAATGACCAAAATGCCCCTGAGTA
Found at i:78582 original size:25 final size:27
Alignment explanation
Indices: 78554--78625 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
78544 TAGGGTCACT
*
78554 TAGGGGGATTTTGGTCATTTG-CA-TC
1 TAGGGGCATTTTGGTCATTTGTCATTC
*
78579 TAGGGGCATTTTGGTCATTTGTGATTC
1 TAGGGGCATTTTGGTCATTTGTCATTC
78606 TAGGGGCATTTTGGTCATTT
1 TAGGGGCATTTTGGTCATTT
78626 ACTAATTACT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 20 0.47
26 1 0.02
27 22 0.51
ACGTcount: A:0.15, C:0.11, G:0.31, T:0.43
Consensus pattern (27 bp):
TAGGGGCATTTTGGTCATTTGTCATTC
Found at i:78983 original size:1 final size:1
Alignment explanation
Indices: 78979--79003 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
78969 AAAAAATTAC
78979 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
79004 GAGTTTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:86583 original size:165 final size:166
Alignment explanation
Indices: 86302--86621 Score: 452
Period size: 165 Copynumber: 1.9 Consensus size: 166
86292 TTCTTACTCT
* * *
86302 TTTTACTGATTACTCTTTTCTCTTTGAATTTAATTACTGACTATCATTTTACTCTTTACTGATTA
1 TTTTACTGACTACTCTTTTCTCTTTGAACTAAATTACTGACTATCATTTTACTCTTTACTGATTA
* * *
86367 TTTTTTTTACTTTTTATTGATTACTATTTCACACTTATTGATTACCATTAC-TTTTTGAACTTGA
66 TTTTCTTTACTTTTTATTAATTACTATTTCACACTTACTGATTACCATTACTTTTTTGAACTTGA
86431 ACACTGATTA-CCTTTTTACTTTTCTTCTTTTTCTC
131 ACACTGATTACCCTTTTTACTTTTCTTCTTTTTCTC
86466 TTTTACTGACTAC-CATTTTACTCTTTGAACTAAATTACTGACTATCATTTTACTCTTTACTGAT
1 TTTTACTGACTACTC-TTTT-CTCTTTGAACTAAATTACTGACTATCATTTTACTCTTTACTGAT
* *
86530 TA-TTTCTTTACTTTTTTATTAATTACTACTTT-ACTCTTACTGATTATCATTACTTTTTTTGAA
64 TATTTTCTTTAC-TTTTTATTAATTACTA-TTTCACACTTACTGATTACCATTAC-TTTTTTGAA
*** *
86593 CTTGGTTACTTATTACCCTTTTTACTTTT
126 CTTGAACACTGATTACCCTTTTTACTTTT
86622 ACTGTTTACT
Statistics
Matches: 137, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
163 1 0.01
164 24 0.18
165 77 0.56
166 3 0.02
167 19 0.14
168 13 0.09
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.55
Consensus pattern (166 bp):
TTTTACTGACTACTCTTTTCTCTTTGAACTAAATTACTGACTATCATTTTACTCTTTACTGATTA
TTTTCTTTACTTTTTATTAATTACTATTTCACACTTACTGATTACCATTACTTTTTTGAACTTGA
ACACTGATTACCCTTTTTACTTTTCTTCTTTTTCTC
Found at i:86655 original size:20 final size:19
Alignment explanation
Indices: 86614--86926 Score: 96
Period size: 20 Copynumber: 15.1 Consensus size: 19
86604 ATTACCCTTT
* *
86614 TTACTTTTACTGTTTACTA
1 TTACTTTTACTGATTACCA
*
86633 TTACTTCTTATTGATTACCA
1 TTACTT-TTACTGATTACCA
*
86653 TTACTCTTTA-TGATTATCACT
1 TTACT-TTTACTGATTA-C-CA
*
86674 TTACTCTTTACTAATTACCA
1 TTACT-TTTACTGATTACCA
* * *
86694 TTTTACCCTTT-CAGA-TACCTTT
1 --TTA-CTTTTACTGATTACC--A
* *
86716 TTACTTTTTACTGTTTACTA
1 TTAC-TTTTACTGATTACCA
* *
86736 TTACTTCTTACTGATTTCTA
1 TTACTT-TTACTGATTACCA
*
86756 TTACTCTTTACTGATTATCACT
1 TTACT-TTTACTGATTA-C-CA
*
86778 TTACTCTTTACTAATTACCA
1 TTACT-TTTACTGATTACCA
* * *
86798 TTTTACCCTTT-CAGA-TACCTTT
1 --TTA-CTTTTACTGATTACC--A
*
86820 TTACTTTTTACTGATTACCTTT
1 TTAC-TTTTACTGATTACC--A
* *
86842 TTACTTTTTTACTGTTTACTA
1 TTAC--TTTTACTGATTACCA
* *
86863 TTACTTCTTACTGATTTCTA
1 TTACTT-TTACTGATTACCA
*
86883 TTACTCTTTACTGATTATCACT
1 TTACT-TTTACTGATTA-C-CA
*
86905 TTACTCTTTACTAATTACCA
1 TTACT-TTTACTGATTACCA
86925 TT
1 TT
86927 TTACCCTTTA
Statistics
Matches: 226, Mismatches: 38, Indels: 59
0.70 0.12 0.18
Matches are distributed among these distances:
19 18 0.08
20 98 0.43
21 32 0.14
22 63 0.28
23 15 0.07
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (19 bp):
TTACTTTTACTGATTACCA
Found at i:86698 original size:22 final size:22
Alignment explanation
Indices: 86598--86980 Score: 216
Period size: 22 Copynumber: 18.1 Consensus size: 22
86588 TTGAACTTGG
* *
86598 TTACTTATTACCCTTTTTACT-T
1 TTACTGATTA-CCATTTTACTCT
* *
86620 TTACTGTTTA-C-TATTACT-T
1 TTACTGATTACCATTTTACTCT
*
86639 CTTATTGATTACCA--TTACTCT
1 -TTACTGATTACCATTTTACTCT
* *
86660 TTA-TGATTATCACTTTACTCT
1 TTACTGATTACCATTTTACTCT
* *
86681 TTACTAATTACCATTTTACCCT
1 TTACTGATTACCATTTTACTCT
* * *
86703 TT-CAGA-TACCTTTTTACTTT
1 TTACTGATTACCATTTTACTCT
* *
86723 TTACTGTTTA-C-TATTACT-T
1 TTACTGATTACCATTTTACTCT
* *
86742 CTTACTGATT-TC-TATTACTCT
1 -TTACTGATTACCATTTTACTCT
* *
86763 TTACTGATTATCACTTTACTCT
1 TTACTGATTACCATTTTACTCT
* *
86785 TTACTAATTACCATTTTACCCT
1 TTACTGATTACCATTTTACTCT
* * *
86807 TT-CAGA-TACCTTTTTACTTT
1 TTACTGATTACCATTTTACTCT
* *
86827 TTACTGATTACCTTTTTACTTTT
1 TTACTGATTACCATTTTAC-TCT
* *
86850 TTACTGTTTA-C-TATTACT-T
1 TTACTGATTACCATTTTACTCT
* *
86869 CTTACTGATT-TC-TATTACTCT
1 -TTACTGATTACCATTTTACTCT
* *
86890 TTACTGATTATCACTTTACTCT
1 TTACTGATTACCATTTTACTCT
* *
86912 TTACTAATTACCATTTTACCCT
1 TTACTGATTACCATTTTACTCT
* * *
86934 TTACAGA-TACCCTTTTTACTTT
1 TTACTGATTA-CCATTTTACTCT
*
86956 TTACTGATTACCTTTTTACTTCT
1 TTACTGATTACCATTTTAC-TCT
86979 TT
1 TT
86981 TGACTTACCC
Statistics
Matches: 289, Mismatches: 47, Indels: 49
0.75 0.12 0.13
Matches are distributed among these distances:
19 17 0.06
20 100 0.35
21 35 0.12
22 119 0.41
23 18 0.06
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.53
Consensus pattern (22 bp):
TTACTGATTACCATTTTACTCT
Found at i:86807 original size:104 final size:104
Alignment explanation
Indices: 86609--86913 Score: 417
Period size: 104 Copynumber: 2.9 Consensus size: 104
86599 TACTTATTAC
* * *
86609 CCTTTTTAC-TTTTACTGTTTACTATTACTTCTTATTGATTACCATTACTCTTTA-TGATTATCA
1 CCTTTTTACTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTACTGATTATCA
86672 CTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATA
66 CTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATA
86711 CCTTTTTACTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTACTGATTATCA
1 CCTTTTTACTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTACTGATTATCA
86776 CTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATA
66 CTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATA
* * *
86815 CCTTTTTACTTTTTACTGATTACCTTTTTACTTTTTTACTG-TTTACTATTACT-TCTTACTGAT
1 CCTTTTTACTTTTTACTGTTTA-C-TATTAC-TTCTTACTGATTT-CTATTACTCT-TTACTGAT
* * * *
86878 T-T--CTATTACTCTTTACTGATTATCACTTTACTCTTT
61 TATCACT-TTACTCTTTACTAATTACCATTTTACCCTTT
86914 ACTAATTACC
Statistics
Matches: 185, Mismatches: 10, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
102 9 0.05
103 42 0.23
104 71 0.38
105 28 0.15
106 10 0.05
107 25 0.14
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.53
Consensus pattern (104 bp):
CCTTTTTACTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTACTGATTATCA
CTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATA
Found at i:86867 original size:127 final size:129
Alignment explanation
Indices: 86709--86981 Score: 516
Period size: 127 Copynumber: 2.1 Consensus size: 129
86699 CCCTTTCAGA
86709 TACCTTTTTAC-TTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTACTGATTA
1 TACCTTTTTACTTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTACTGATTA
86773 TCACTTTACTCTTTACTAATTACCATTTTACCCTTT-CAGATA-CCTTTTTACTTTTTACTGAT
66 TCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCCTTTTTACTTTTTACTGAT
86835 TACCTTTTTACTTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTACTGATTA
1 TACCTTTTTACTTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTACTGATTA
86900 TCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCCTTTTTACTTTTTACTGAT
66 TCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCCTTTTTACTTTTTACTGAT
86964 TACCTTTTTACTTCTTTT
1 TACCTTTTTACTT-TTTT
86982 GACTTACCCC
Statistics
Matches: 143, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
126 11 0.08
127 89 0.62
128 6 0.04
129 33 0.23
130 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.54
Consensus pattern (129 bp):
TACCTTTTTACTTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTACTGATTA
TCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCCTTTTTACTTTTTACTGAT
Found at i:87723 original size:24 final size:24
Alignment explanation
Indices: 87696--87751 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 24
87686 TTTATCCTGA
*
87696 TTTTTATTTTTTAATCTCCACATG
1 TTTTGATTTTTTAATCTCCACATG
87720 TTTTGA-TTTTTAATCTCCACATG
1 TTTTGATTTTTTAATCTCCACATG
87743 TTTTGATTT
1 TTTTGATTT
87752 ACTTAACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (24 bp):
TTTTGATTTTTTAATCTCCACATG
Found at i:87729 original size:23 final size:23
Alignment explanation
Indices: 87703--87751 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
87693 TGATTTTTAT
87703 TTTTTAATCTCCACATGTTTTGA
1 TTTTTAATCTCCACATGTTTTGA
87726 TTTTTAATCTCCACATGTTTTGA
1 TTTTTAATCTCCACATGTTTTGA
87749 TTT
1 TTT
87752 ACTTAACTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.55
Consensus pattern (23 bp):
TTTTTAATCTCCACATGTTTTGA
Found at i:92183 original size:35 final size:34
Alignment explanation
Indices: 92137--92220 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 34
92127 CAAATGAGCT
* *
92137 CATGAGAAAATTAAAAGTTAGAATCGGGCCTATCC
1 CATGAGAAAATTAAAA-TTAGAATCGGGCCAAGCC
* *
92172 CATGAGAAAATTTAGAATTAGAATCGGTCCAAGCC
1 CATGAGAAAA-TTAAAATTAGAATCGGGCCAAGCC
*
92207 CATGAGATAATTAA
1 CATGAGAAAATTAA
92221 GCACCGATAG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
34 3 0.07
35 34 0.81
36 5 0.12
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (34 bp):
CATGAGAAAATTAAAATTAGAATCGGGCCAAGCC
Found at i:92623 original size:26 final size:26
Alignment explanation
Indices: 92589--92638 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
92579 TGAACATATG
*
92589 ATATGATTTAATTAAATAATTGTAAT
1 ATATAATTTAATTAAATAATTGTAAT
* *
92615 ATATAATTTGATTAAATACTTGTA
1 ATATAATTTAATTAAATAATTGTA
92639 GATGCTATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (26 bp):
ATATAATTTAATTAAATAATTGTAAT
Found at i:93164 original size:11 final size:11
Alignment explanation
Indices: 93150--93182 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
93140 ATTCATAACA
93150 AATTTATAATT
1 AATTTATAATT
93161 AATTTATAATT
1 AATTTATAATT
93172 -ATTTGATAATT
1 AATTT-ATAATT
93183 TAGATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:95691 original size:20 final size:20
Alignment explanation
Indices: 95666--95704 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
95656 AAAAAGAGCA
*
95666 CCAATTTGCAAATCAAATGT
1 CCAATTCGCAAATCAAATGT
*
95686 CCAATTCGTAAATCAAATG
1 CCAATTCGCAAATCAAATG
95705 CCTTGTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (20 bp):
CCAATTCGCAAATCAAATGT
Found at i:95863 original size:14 final size:14
Alignment explanation
Indices: 95844--95878 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
95834 TTAACTATGA
*
95844 GACTAATCTAAATG
1 GACTAAACTAAATG
95858 GACTAAACTAAATG
1 GACTAAACTAAATG
95872 GACTAAA
1 GACTAAA
95879 GTTAATATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (14 bp):
GACTAAACTAAATG
Found at i:96262 original size:27 final size:27
Alignment explanation
Indices: 96194--96265 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
96184 AAGTGAACTT
* *
96194 AAAATGACCAAAATACCCCTAAATGCA
1 AAAATGACCAAAATGCCCCTAAACGCA
* **
96221 AAAATGACCAAAATGCCCCTGAACGTG
1 AAAATGACCAAAATGCCCCTAAACGCA
96248 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
96266 TATGTGACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.47, C:0.26, G:0.12, T:0.14
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAACGCA
Found at i:96808 original size:33 final size:34
Alignment explanation
Indices: 96745--96814 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 34
96735 TTGGAATAGT
96745 AGAGAGTCATGGTTTTCAAAAAAATATTTTTCAAA
1 AGAGAGTCATGGTTTTC-AAAAAATATTTTTCAAA
*
96780 AGAGAGTCATGGTTTTC-AAAAATGTTTTTCAAA
1 AGAGAGTCATGGTTTTCAAAAAATATTTTTCAAA
96813 AG
1 AG
96815 TAATTTTCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 17 0.50
35 17 0.50
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (34 bp):
AGAGAGTCATGGTTTTCAAAAAATATTTTTCAAA
Found at i:97425 original size:25 final size:26
Alignment explanation
Indices: 97396--97454 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
97386 TTTGTAAAAT
97396 GTTTT-AGTCAAAACTCTTGAAAAGA
1 GTTTTCAGTCAAAACTCTTGAAAAGA
*
97421 GTTTTCGAGTCAAAACTTTTGAAAAGA
1 GTTTTC-AGTCAAAACTCTTGAAAAGA
97448 GTTTTCA
1 GTTTTCA
97455 AGTAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 5 0.16
26 1 0.03
27 25 0.81
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (26 bp):
GTTTTCAGTCAAAACTCTTGAAAAGA
Found at i:97432 original size:27 final size:27
Alignment explanation
Indices: 97401--97453 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
97391 AAAATGTTTT
97401 AGTCAAAACTCTTGAAAAGAGTTTTCG
1 AGTCAAAACTCTTGAAAAGAGTTTTCG
*
97428 AGTCAAAACTTTTGAAAAGAGTTTTC
1 AGTCAAAACTCTTGAAAAGAGTTTTC
97454 AAGTAAATTA
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:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (27 bp):
AGTCAAAACTCTTGAAAAGAGTTTTCG
Found at i:97502 original size:7 final size:8
Alignment explanation
Indices: 97483--97533 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
97473 GAGTGCAATA
97483 AAAAAATG
1 AAAAAATG
97491 AAAAAATG
1 AAAAAATG
*
97499 AAAAAA-A
1 AAAAAATG
97506 AAGAAAATG
1 AA-AAAATG
97515 AAAAAGA-G
1 AAAAA-ATG
*
97523 AAAAAAAG
1 AAAAAATG
97531 AAA
1 AAA
97534 GAAAAAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 3 0.08
8 31 0.84
9 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (8 bp):
AAAAAATG
Found at i:97504 original size:16 final size:15
Alignment explanation
Indices: 97483--97556 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 15
97473 GAGTGCAATA
97483 AAAAAATGAAAAAATG
1 AAAAAA-GAAAAAATG
*
97499 AAAAAAAAAGAAAATG
1 AAAAAAGAA-AAAATG
*
97515 AAAAAGAGAAAAAAAG
1 AAAAA-AGAAAAAATG
*
97531 AAAGAAA-AAAGAAACG
1 AAA-AAAGAAA-AAATG
97547 -AAAAAGAAAA
1 AAAAAAGAAAA
97557 GCAGCTCTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
14 4 0.08
15 10 0.20
16 30 0.61
17 5 0.10
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (15 bp):
AAAAAAGAAAAAATG
Found at i:97513 original size:24 final size:23
Alignment explanation
Indices: 97485--97556 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 23
97475 GTGCAATAAA
97485 AAAATGAAAAAATGAAAAAAAAAG
1 AAAATGAAAAAA-GAAAAAAAAAG
*
97509 AAAATG-AAAAAGAGAAAAAAAG
1 AAAATGAAAAAAGAAAAAAAAAG
*
97531 -AAA-GAAAAAAGAAACGAAAAAG
1 AAAATGAAAAAAGAAA-AAAAAAG
97553 AAAA
1 AAAA
97557 GCAGCTCTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.02
21 11 0.26
22 16 0.38
23 8 0.19
24 6 0.14
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.04
Consensus pattern (23 bp):
AAAATGAAAAAAGAAAAAAAAAG
Found at i:97518 original size:14 final size:12
Alignment explanation
Indices: 97499--97556 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
97489 TGAAAAAATG
97499 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
97511 AATGAAAAAGAGAA
1 AA--AAAAAAAGAA
*
97525 AAAAAGAAAGAA
1 AAAAAAAAAGAA
* *
97537 AAAAGAAACGAA
1 AAAAAAAAAGAA
97549 AAAGAAAA
1 AAA-AAAA
97557 GCAGCTCTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
12 22 0.61
13 3 0.08
14 11 0.31
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:97526 original size:32 final size:32
Alignment explanation
Indices: 97490--97553 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
97480 ATAAAAAAAT
* *
97490 GAAAAAATGAAA-AAAAAAGAAAATGAAAAAGA
1 GAAAAAAAGAAAGAAAAAAG-AAACGAAAAAGA
97522 GAAAAAAAGAAAGAAAAAAGAAACGAAAAAGA
1 GAAAAAAAGAAAGAAAAAAGAAACGAAAAAGA
97554 AAAGCAGCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (32 bp):
GAAAAAAAGAAAGAAAAAAGAAACGAAAAAGA
Found at i:97550 original size:11 final size:10
Alignment explanation
Indices: 97492--97555 Score: 58
Period size: 11 Copynumber: 5.9 Consensus size: 10
97482 AAAAAAATGA
*
97492 AAAAATGAAAA
1 AAAAA-GAAAG
97503 AAAAAGAAAATG
1 AAAAAG-AAA-G
97515 AAAAAGAGAA-
1 AAAAAGA-AAG
97525 AAAAAGAAAG
1 AAAAAGAAAG
97535 AAAAAAGAAACG
1 -AAAAAGAAA-G
97547 AAAAAGAAA
1 AAAAAGAAA
97556 AGCAGCTCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
9 2 0.04
10 8 0.17
11 27 0.59
12 9 0.20
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:98680 original size:40 final size:39
Alignment explanation
Indices: 98588--98732 Score: 204
Period size: 38 Copynumber: 3.7 Consensus size: 39
98578 AAGAAGTCCC
* * *
98588 AAAGTTGATTGGAAACAAGTCATCTTTCAACAATCATCG
1 AAAGTTGACTGGAAACAGGTCATCTTTCAGCAATCATCG
* *
98627 -AAGTTGACTGGAAACAGGTCACCTTTCAGCAATAATCG
1 AAAGTTGACTGGAAACAGGTCATCTTTCAGCAATCATCG
*
98665 AAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATCGTC-
1 -AAAGTTGACTGGAAACAGGTCATCTTTCAGCAATCATCG
*
98704 AAAGTGGACTGGAAACAGGTCATCTTTCA
1 AAAGTTGACTGGAAACAGGTCATCTTTCA
98733 AATTATCAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
38 61 0.64
40 34 0.36
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (39 bp):
AAAGTTGACTGGAAACAGGTCATCTTTCAGCAATCATCG
Found at i:98717 original size:78 final size:78
Alignment explanation
Indices: 98588--98732 Score: 227
Period size: 78 Copynumber: 1.9 Consensus size: 78
98578 AAGAAGTCCC
* * *
98588 AAAGTTGATTGGAAACAAGTCATCTTTCAACAATCATCGAAGTTGACTGGAAACAGGTCACCTTT
1 AAAGTTGACTGGAAACAAGTCATCTTTCAACAATCATCAAAGTGGACTGGAAACAGGTCACCTTT
98653 CAGCAATAATCGA
66 CAGCAATAATCGA
* * * *
98666 AAAGTTGACTGGAAACAGGTCATCTTTCAGCAATCGTCAAAGTGGACTGGAAACAGGTCATCTTT
1 AAAGTTGACTGGAAACAAGTCATCTTTCAACAATCATCAAAGTGGACTGGAAACAGGTCACCTTT
98731 CA
66 CA
98733 AATTATCAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 60 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (78 bp):
AAAGTTGACTGGAAACAAGTCATCTTTCAACAATCATCAAAGTGGACTGGAAACAGGTCACCTTT
CAGCAATAATCGA
Found at i:98791 original size:38 final size:38
Alignment explanation
Indices: 98744--98871 Score: 166
Period size: 38 Copynumber: 3.3 Consensus size: 38
98734 ATTATCAAAA
* *
98744 GTCATCTTTCAACAATCATCGAAGTTGATTGGAAACAG
1 GTCATCTTTCAACAATAATCGAAGTTGACTGGAAACAG
* * *
98782 GTCACCTTTCAGCAATAATTGAAAAGTTGACTGGAAACAG
1 GTCATCTTTCAACAATAATCG--AAGTTGACTGGAAACAG
* * *
98822 GTCATCTTTCAGCAATAATCAAAGTTGACTCGAAACAG
1 GTCATCTTTCAACAATAATCGAAGTTGACTGGAAACAG
98860 GTCATCTTTCAA
1 GTCATCTTTCAA
98872 GTTATCAGAG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
38 44 0.56
40 34 0.44
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (38 bp):
GTCATCTTTCAACAATAATCGAAGTTGACTGGAAACAG
Found at i:98823 original size:100 final size:99
Alignment explanation
Indices: 98644--98832 Score: 263
Period size: 100 Copynumber: 1.9 Consensus size: 99
98634 CTGGAAACAG
* * * *
98644 GTCACCTTTCAGCAATAATCGAAAAGTTGACTGGAAACAGGTCATCTTTCAGCAATCGTCAAAGT
1 GTCACCTTTCAACAATAATCG-AAAGTTGACTGGAAACAGGTCACCTTTCAGCAATAGTAAAAGT
98709 GGACTGGAAACAGGTCATCTTTCAAATTATCAAAA
65 GGACTGGAAACAGGTCATCTTTCAAATTATCAAAA
* * * *
98744 GTCATCTTTCAACAATCATCG-AAGTTGATTGGAAACAGGTCACCTTTCAGCAATAATTGAAAAG
1 GTCACCTTTCAACAATAATCGAAAGTTGACTGGAAACAGGTCACCTTTCAGCAAT-AGT-AAAAG
*
98808 TTGACTGGAAACAGGTCATCTTTCA
64 TGGACTGGAAACAGGTCATCTTTCA
98833 GCAATAATCA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
98 31 0.40
99 1 0.01
100 46 0.59
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (99 bp):
GTCACCTTTCAACAATAATCGAAAGTTGACTGGAAACAGGTCACCTTTCAGCAATAGTAAAAGTG
GACTGGAAACAGGTCATCTTTCAAATTATCAAAA
Found at i:98857 original size:138 final size:137
Alignment explanation
Indices: 98604--98972 Score: 521
Period size: 138 Copynumber: 2.7 Consensus size: 137
98594 GATTGGAAAC
*
98604 AAGTCATCTTTCAACAATCATCGAAGTTGACTGGAAACAGGTCACCTTTCAGCAATAATCGAAAA
1 AAGTCATCTTTCAACAATCATCGAAGTTGACTGGAAACAGGTCACCTTTCAGCAATAATTGAAAA
** *
98669 GTTGACTGGAAACAGGTCATCTTTCAGCAATCGTCAAAGTGGACTGGAAACAGGTCATCTTTCAA
66 GTTGACTGGAAACAGGTCATCTTTCAGCAATAATCAAAGTGGACTCGAAACAGGTCATCTTTCAA
98734 ATTATCAA
131 ATTATC-A
*
98742 AAGTCATCTTTCAACAATCATCGAAGTTGATTGGAAACAGGTCACCTTTCAGCAATAATTGAAAA
1 AAGTCATCTTTCAACAATCATCGAAGTTGACTGGAAACAGGTCACCTTTCAGCAATAATTGAAAA
*
98807 GTTGACTGGAAACAGGTCATCTTTCAGCAATAATCAAAGTTGACTCGAAACAGGTCATCTTTCAA
66 GTTGACTGGAAACAGGTCATCTTTCAGCAATAATCAAAGTGGACTCGAAACAGGTCATCTTTCAA
*
98872 GTTATCA
131 ATTATCA
* * * * * * * *
98879 GAGATCATC-TTCCA-AATTATCAAAGTTGACTGGAAACAGGTCATCTTTCAACAAGTTA-TCAA
1 AAG-TCATCTTTCAACAATCATCGAAGTTGACTGGAAACAGGTCACCTTTCAGCAA-TAATTGAA
* * *
98941 GA-TCGACTGGAAACAAGTCATCTTTCAGCAAT
64 AAGTTGACTGGAAACAGGTCATCTTTCAGCAAT
98973 TATCTTACGA
Statistics
Matches: 210, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
135 28 0.13
136 39 0.19
137 9 0.04
138 134 0.64
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (137 bp):
AAGTCATCTTTCAACAATCATCGAAGTTGACTGGAAACAGGTCACCTTTCAGCAATAATTGAAAA
GTTGACTGGAAACAGGTCATCTTTCAGCAATAATCAAAGTGGACTCGAAACAGGTCATCTTTCAA
ATTATCA
Found at i:98940 original size:39 final size:39
Alignment explanation
Indices: 98893--99044 Score: 163
Period size: 38 Copynumber: 4.0 Consensus size: 39
98883 TCATCTTCCA
* * *
98893 AATTATCAAAG-TTGACTGGAAACAGGTCATCTTTCAAC
1 AATTATCTAAGATCGACTGGAAACAGGTCATCTTTCAGC
*
98931 AAGTTATC-AAGATCGACTGGAAACAAGTCATCTTTCAGC
1 AA-TTATCTAAGATCGACTGGAAACAGGTCATCTTTCAGC
* *
98970 AATTATCT--TA-CGACTGGAAACAGGTCGTCTTTCAGC
1 AATTATCTAAGATCGACTGGAAACAGGTCATCTTTCAGC
* * * *
99006 ACTTAT-TAGGTTTGACTGGAAACAGGTCATCTTTCAGC
1 AATTATCTAAGATCGACTGGAAACAGGTCATCTTTCAGC
99044 A
1 A
99045 GTTTTCGGTT
Statistics
Matches: 97, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
35 1 0.01
36 29 0.30
37 1 0.01
38 35 0.36
39 31 0.32
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (39 bp):
AATTATCTAAGATCGACTGGAAACAGGTCATCTTTCAGC
Found at i:99041 original size:74 final size:75
Alignment explanation
Indices: 98906--99044 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 75
98896 TATCAAAGTT
*
98906 GACTGGAAACAGGTCATCTTTCAACAAGTTATCAAGATCGACTGGAAACAAGTCATCTTTCAGCA
1 GACTGGAAACAGGTCATCTTTCAACAACTTATCAAGATCGACTGGAAACAAGTCATCTTTCAGCA
98971 ATTATCTTAC
66 ATTATCTTAC
* * * * * * *
98981 GACTGGAAACAGGTCGTCTTTCAGC-ACTTATTAGGTTTGACTGGAAACAGGTCATCTTTCAGCA
1 GACTGGAAACAGGTCATCTTTCAACAACTTATCAAGATCGACTGGAAACAAGTCATCTTTCAGCA
99045 GTTTTCGGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
74 33 0.59
75 23 0.41
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (75 bp):
GACTGGAAACAGGTCATCTTTCAACAACTTATCAAGATCGACTGGAAACAAGTCATCTTTCAGCA
ATTATCTTAC
Found at i:99146 original size:34 final size:34
Alignment explanation
Indices: 99092--99331 Score: 363
Period size: 34 Copynumber: 6.9 Consensus size: 34
99082 TTTCAATTTG
99092 CAACTTTTCAGAATTTACAACTTTACAGCATTTCAA
1 CAACTTTTC--AATTTACAACTTTACAGCATTTCAA
* *
99128 CAACTTTTCAATTTACAACTGTATAGCATTTCAA
1 CAACTTTTCAATTTACAACTTTACAGCATTTCAA
*
99162 CAACTTTTTCAGAATTTACAACTCTACAGCATTTCAA
1 CAAC-TTTTC--AATTTACAACTTTACAGCATTTCAA
99199 CAACTTTTCAATTTACAACTTTACAGCATTTCAA
1 CAACTTTTCAATTTACAACTTTACAGCATTTCAA
* *
99233 TAACTTTTCAATTTACAACTTTTCAGCATTTCAA
1 CAACTTTTCAATTTACAACTTTACAGCATTTCAA
*
99267 CAACTTTTGAATTTACAACTTTACAGCATTTCAA
1 CAACTTTTCAATTTACAACTTTACAGCATTTCAA
* *
99301 CAACTTTTCAATTTACAACTTTTCAGAATTT
1 CAACTTTTCAATTTACAACTTTACAGCATTT
99332 ACAATTTTAC
Statistics
Matches: 188, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
34 142 0.76
35 5 0.03
36 14 0.07
37 27 0.14
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.39
Consensus pattern (34 bp):
CAACTTTTCAATTTACAACTTTACAGCATTTCAA
Found at i:99348 original size:85 final size:85
Alignment explanation
Indices: 99092--99416 Score: 328
Period size: 85 Copynumber: 3.8 Consensus size: 85
99082 TTTCAATTTG
* *
99092 CAACTTTTCAGAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTGTAT-AGCA
1 CAACTTTT--GAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACT-TTTCAGAA
*
99156 TTTCAACAACTTTTTCAGAATTT--A
63 TTT--ACAAC-TTTTCAGCATTTCAA
** * * * *
99180 CAACTCTACAGCATTTCAACAACTTTTCA--ATTT--ACAACTTTACAGCATTTCAATAACTTTT
1 CAACT-T-TTGAATTT--ACAACTTTACAGCATTTCAACAACTTTTCA--ATTT--ACAACTTTT
99241 C--AATTTACAACTTTTCAGCATTTCAA
58 CAGAATTTACAACTTTTCAGCATTTCAA
99267 CAACTTTTGAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTT
1 CAACTTTTGAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTT
99332 ACAA-TTTTACAGCATTTCAA
66 ACAACTTTT-CAGCATTTCAA
** * *
99352 CAACTTTTCTATTTACAATTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTTCAGTATTT
1 CAACTTTTGAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTT
99417 CAATTCACAA
Statistics
Matches: 200, Mismatches: 19, Indels: 39
0.78 0.07 0.15
Matches are distributed among these distances:
83 19 0.09
84 4 0.02
85 105 0.52
86 16 0.08
87 16 0.08
88 22 0.11
89 3 0.01
90 15 0.08
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.40
Consensus pattern (85 bp):
CAACTTTTGAATTTACAACTTTACAGCATTTCAACAACTTTTCAATTTACAACTTTTCAGAATTT
ACAACTTTTCAGCATTTCAA
Found at i:99371 original size:34 final size:34
Alignment explanation
Indices: 99315--99419 Score: 158
Period size: 34 Copynumber: 3.0 Consensus size: 34
99305 TTTTCAATTT
99315 ACAACTTTTCAGAATTTACAATTTTACAGCATTTCA
1 ACAACTTTTC--AATTTACAATTTTACAGCATTTCA
*
99351 ACAACTTTTCTATTTACAATTTTACAGCATTTCA
1 ACAACTTTTCAATTTACAATTTTACAGCATTTCA
*
99385 ACAACTTTTCAATTTACAACTTTT-CAGTATTTCA
1 ACAACTTTTCAATTTACAA-TTTTACAGCATTTCA
99419 A
1 A
99420 TTCACAACTT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 51 0.78
35 4 0.06
36 10 0.15
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (34 bp):
ACAACTTTTCAATTTACAATTTTACAGCATTTCA
Found at i:99480 original size:42 final size:39
Alignment explanation
Indices: 99434--99516 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 39
99424 CAACTTTTGA
* *
99434 GCATTCCAACAACTTTACAGTTTTCGGTTGCTCACAAAGCGG
1 GCATTCCAACAACTTT-CA-TTGTCAGTTGCTCACAAAG-GG
* *
99476 GCATTCTAACAACTTTCATTGTCAGTTGCTCTCAAAGGG
1 GCATTCCAACAACTTTCATTGTCAGTTGCTCACAAAGGG
99515 GC
1 GC
99517 CTTATAGCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 4 0.11
40 16 0.43
41 2 0.05
42 15 0.41
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (39 bp):
GCATTCCAACAACTTTCATTGTCAGTTGCTCACAAAGGG
Found at i:101001 original size:30 final size:30
Alignment explanation
Indices: 100933--101010 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
100923 ATGGAGAGGA
*
100933 TGCCAA-CGCACAAGACCGGCCATTGCATG
1 TGCCAATCGCACAAGACCGGCCATGGCATG
*** *
100962 -GAGGGATCGCACATGACCGGCCATGGCATG
1 TG-CCAATCGCACAAGACCGGCCATGGCATG
100992 TGCCAATCGCACAAGACCG
1 TGCCAATCGCACAAGACCG
101011 AGCACAACCA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
28 1 0.03
29 1 0.03
30 34 0.92
31 1 0.03
ACGTcount: A:0.27, C:0.32, G:0.28, T:0.13
Consensus pattern (30 bp):
TGCCAATCGCACAAGACCGGCCATGGCATG
Found at i:102059 original size:11 final size:10
Alignment explanation
Indices: 102043--102079 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
102033 AGTTATATCG
102043 AAAAATATCAA
1 AAAAATAT-AA
102054 AAAAATA-AA
1 AAAAATATAA
102063 AAAAA-ATAA
1 AAAAATATAA
102072 AAAAATAT
1 AAAAATAT
102080 TTCGACCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 1 0.04
9 14 0.58
10 2 0.08
11 7 0.29
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATATAA
Found at i:102064 original size:9 final size:10
Alignment explanation
Indices: 102052--102076 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
102042 GAAAAATATC
102052 AAAAAAATAA
1 AAAAAAATAA
102062 AAAAAAATAA
1 AAAAAAATAA
102072 AAAAA
1 AAAAA
102077 TATTTCGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:102633 original size:12 final size:12
Alignment explanation
Indices: 102616--102641 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
102606 AGGTCACGAG
102616 AATTTTGCTACT
1 AATTTTGCTACT
102628 AATTTTGCTACT
1 AATTTTGCTACT
102640 AA
1 AA
102642 AAGTCAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (12 bp):
AATTTTGCTACT
Done.