Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2990
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: 34678
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:10702 original size:16 final size:18
Alignment explanation
Indices: 10681--10718 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
10671 ATTATAAAAA
10681 ATATAAA-A-GTACATAT
1 ATATAAATATGTACATAT
10697 ATATAAATATGTACATAT
1 ATATAAATATGTACATAT
10715 ATAT
1 ATAT
10719 GTAAGCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
ATATAAATATGTACATAT
Found at i:11985 original size:30 final size:30
Alignment explanation
Indices: 11963--12027 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
11953 TTTGTTTGTA
11963 ATTGGG-CTGAGGGTATTGGGTTTGTGGGT
1 ATTGGGTCTGAGGGTATTGGGTTTGTGGGT
* *
11992 ATTGGGTTTGTGGGTATTGGGTTTGTGGGT
1 ATTGGGTCTGAGGGTATTGGGTTTGTGGGT
12022 ATTGGG
1 ATTGGG
12028 CCGGACAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.09, C:0.02, G:0.48, T:0.42
Consensus pattern (30 bp):
ATTGGGTCTGAGGGTATTGGGTTTGTGGGT
Found at i:11993 original size:15 final size:15
Alignment explanation
Indices: 11973--12027 Score: 110
Period size: 15 Copynumber: 3.7 Consensus size: 15
11963 ATTGGGCTGA
11973 GGGTATTGGGTTTGT
1 GGGTATTGGGTTTGT
11988 GGGTATTGGGTTTGT
1 GGGTATTGGGTTTGT
12003 GGGTATTGGGTTTGT
1 GGGTATTGGGTTTGT
12018 GGGTATTGGG
1 GGGTATTGGG
12028 CCGGACAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.07, C:0.00, G:0.49, T:0.44
Consensus pattern (15 bp):
GGGTATTGGGTTTGT
Found at i:11997 original size:7 final size:7
Alignment explanation
Indices: 11973--12027 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
11963 ATTGGGCTGA
11973 GGGTATT
1 GGGTATT
*
11980 GGGTTTGT
1 GGGTAT-T
11988 GGGTATT
1 GGGTATT
*
11995 GGGTTTGT
1 GGGTAT-T
12003 GGGTATT
1 GGGTATT
*
12010 GGGTTTGT
1 GGGTAT-T
12018 GGGTATT
1 GGGTATT
12025 GGG
1 GGG
12028 CCGGACAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 21 0.54
8 18 0.46
ACGTcount: A:0.07, C:0.00, G:0.49, T:0.44
Consensus pattern (7 bp):
GGGTATT
Found at i:12005 original size:8 final size:8
Alignment explanation
Indices: 11979--12021 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
11969 CTGAGGGTAT
11979 TGGGTTTG
1 TGGGTTTG
*
11987 TGGGTAT-
1 TGGGTTTG
11994 TGGGTTTG
1 TGGGTTTG
*
12002 TGGGTAT-
1 TGGGTTTG
12009 TGGGTTTG
1 TGGGTTTG
12017 TGGGT
1 TGGGT
12022 ATTGGGCCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.05, C:0.00, G:0.49, T:0.47
Consensus pattern (8 bp):
TGGGTTTG
Found at i:16018 original size:20 final size:17
Alignment explanation
Indices: 15984--16017 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15974 CATGAAGGGT
15984 CGGAATAATATTCATCA
1 CGGAATAATATTCATCA
16001 CGGAATAATATTCATCA
1 CGGAATAATATTCATCA
16018 TTACCTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
CGGAATAATATTCATCA
Found at i:17005 original size:45 final size:45
Alignment explanation
Indices: 16607--16992 Score: 465
Period size: 45 Copynumber: 8.6 Consensus size: 45
16597 ATAAGCCGGT
* * * *
16607 GGCTTCTCCTTCTTTGGTGGTCCATACACTGGTGGTTTGGGCTCA
1 GGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCA
*
16652 GGCTTCTCTTTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGCTCA
1 GGCTTCTCCTTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCA
* * * * *
16697 GGCTTTTCCTTCTTTGGGGGTTCATATACTGGTGGTTTGGGCTCA
1 GGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCA
* *
16742 GGCTTCTCTTTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGTTCA
1 GGCTTCTCCTTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCA
* * * * *
16787 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCA
1 GGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCA
*
16832 GGCTTCTCTTTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGCTCA
1 GGCTTCTCCTTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCA
* * * * * *
16877 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGTTCA
1 GGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCA
* *
16922 GGCTTCTCTTTCTTTGGAGGTGT-ATAAACTGGTGGCTTAGGCTCA
1 GGCTTCTCCTTCTTTGGTGGT-TCATAAACTGGTGGCTTAGGCTCA
*
16967 GGCTTTTCCTTCTTTGGTGGTTCATA
1 GGCTTCTCCTTCTTTGGTGGTTCATA
16993 GACAGGGGGC
Statistics
Matches: 286, Mismatches: 47, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
44 4 0.01
45 279 0.98
46 3 0.01
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (45 bp):
GGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGCTCA
Found at i:17011 original size:90 final size:90
Alignment explanation
Indices: 16607--16992 Score: 691
Period size: 90 Copynumber: 4.3 Consensus size: 90
16597 ATAAGCCGGT
* * * *
16607 GGCTTCTCCTTCTTTGGTGGTCCATACACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGG
1 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGG
16672 TGTATAAACTGGTGGCTTAGGCTCA
66 TGTATAAACTGGTGGCTTAGGCTCA
*
16697 GGCTTTTCCTTCTTTGGGGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGG
1 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGG
*
16762 TGTATAAACTGGTGGCTTAGGTTCA
66 TGTATAAACTGGTGGCTTAGGCTCA
16787 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGG
1 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGG
16852 TGTATAAACTGGTGGCTTAGGCTCA
66 TGTATAAACTGGTGGCTTAGGCTCA
* *
16877 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGG
1 GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGG
16942 TGTATAAACTGGTGGCTTAGGCTCA
66 TGTATAAACTGGTGGCTTAGGCTCA
*
16967 GGCTTTTCCTTCTTTGGTGGTTCATA
1 GGCTTTTCCTTCTTTGGAGGTTCATA
16993 GACAGGGGGC
Statistics
Matches: 286, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 286 1.00
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (90 bp):
GGCTTTTCCTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGG
TGTATAAACTGGTGGCTTAGGCTCA
Found at i:17069 original size:45 final size:45
Alignment explanation
Indices: 17005--17095 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
16995 CAGGGGGCTT
17005 ATGTTCATAAGGTGGGGGTTTCACCTTAGGAGGTTTATAAACAGG
1 ATGTTCATAAGGTGGGGGTTTCACCTTAGGAGGTTTATAAACAGG
17050 ATGTTCATAAGGTGGGGGTTTCACCTTAGGAGGTTTATAAACAGG
1 ATGTTCATAAGGTGGGGGTTTCACCTTAGGAGGTTTATAAACAGG
17095 A
1 A
17096 GTAGGGGGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.31
Consensus pattern (45 bp):
ATGTTCATAAGGTGGGGGTTTCACCTTAGGAGGTTTATAAACAGG
Found at i:19695 original size:20 final size:20
Alignment explanation
Indices: 19656--19695 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19646 TATATATAAT
* * *
19656 TATATAATATAATATTAAAA
1 TATATAATACAACATAAAAA
19676 TATATAATACAACATAAAAA
1 TATATAATACAACATAAAAA
19696 ACATGACACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TATATAATACAACATAAAAA
Found at i:19896 original size:3 final size:3
Alignment explanation
Indices: 19881--19916 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
19871 AAGCATAAAC
* *
19881 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19917 CATTAGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:20029 original size:22 final size:23
Alignment explanation
Indices: 20012--20066 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
20002 TGTATACACG
20012 TACATAATAA-AATATATACTAA
1 TACATAATAATAATATATACTAA
**
20034 TACATAATAATAATA-ATGGTAA
1 TACATAATAATAATATATACTAA
20056 TAC-TAATAATA
1 TACATAATAATA
20067 CTAATAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 8 0.27
22 18 0.60
23 4 0.13
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
TACATAATAATAATATATACTAA
Found at i:20045 original size:3 final size:3
Alignment explanation
Indices: 20015--20084 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
20005 ATACACGTAC
* * * *
20015 ATA ATA A-A ATA TATA CTA ATA CATA ATA ATA ATA ATG GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
20061 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
20085 CAAGGATATT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
2 4 0.08
3 41 0.80
4 6 0.12
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:20572 original size:18 final size:18
Alignment explanation
Indices: 20545--20582 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20535 AGAAAAAAAA
*
20545 AGAAGAGAGAGGGAAGAG
1 AGAAGAGAGAGAGAAGAG
*
20563 AGAAGGGAGAGAGAAGAG
1 AGAAGAGAGAGAGAAGAG
20581 AG
1 AG
20583 GGGAATCCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (18 bp):
AGAAGAGAGAGAGAAGAG
Found at i:20577 original size:11 final size:12
Alignment explanation
Indices: 20546--20578 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
20536 GAAAAAAAAA
20546 GAAGAGAG-AGG
1 GAAGAGAGAAGG
20557 GAAGAGAGAAGG
1 GAAGAGAGAAGG
20569 G-AGAGAGAAG
1 GAAGAGAGAAG
20579 AGAGGGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:21871 original size:74 final size:75
Alignment explanation
Indices: 21613--21847 Score: 359
Period size: 75 Copynumber: 3.2 Consensus size: 75
21603 CATGTGAACC
** *
21613 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAAGCAGAAATTGAAAATACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATACCTC
21676 AACGTGTCTT
66 AACGTGTCTT
*
21686 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATACCTC
*
21751 AATGTGTCTT
66 AACGTGTCTT
* * *
21761 GAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGACAA-CAGAAATTGAAATTACCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATACCTC
* *
21825 AGCGTGTCCT
66 AACGTGTCTT
21835 GAGGCTCAACTCA
1 GAGGCTCAACTCA
21848 TTTATTGCAA
Statistics
Matches: 148, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
73 31 0.21
74 38 0.26
75 79 0.53
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (75 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATACCTC
AACGTGTCTT
Found at i:22148 original size:173 final size:177
Alignment explanation
Indices: 21760--22168 Score: 458
Period size: 173 Copynumber: 2.3 Consensus size: 177
21750 CAATGTGTCT
* *
21760 TGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGACAACAGAAATTGAAATTACCTC
1 TGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGAAAACAGAAATTGAAAATACCTC
* * * **
21825 AGCGTGTCCTGAGGCTCAACTCATTTATTGCAATAAGAGCTGATTTTGGAAATGTAGAATTTGAA
66 AACGTGTCCTGAGGCTCAACTCATTTATCGCAAT-A-A-CTGATGTTAAAAATGTAGAATTTGAA
* * *
21890 AAGCATAAATTGAAAAAGCGAAAAATTGAAAATACCTCAGCGTGCGAGCC
128 AAGCAGAAATTGAAAAAACGAAAAATTGAAAATACCTCAGCGTACGAGCC
* *
21940 -GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAACTTGAAAATACCT
1 TGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGAAAA-CAGAAATTGAAAATACCT
* * **** *
22004 CAACGTGTCTTGAGGCTCAACTCATTTCTCGCAAT-A-TGA-GTTAAAAAT-TTTTTTTTGAGAA
65 CAACGTGTCCTGAGGCTCAACTCATTTATCGCAATAACTGATGTTAAAAATGTAGAATTTGAAAA
*** * *
22065 GCAGAAATTGGAAAAAAC-ATCTATTGAAAATACCTCGGCGTATGA-CC
130 GCAGAAATT-GAAAAAACGAAAAATTGAAAATACCTCAGCGTACGAGCC
* * * *
22112 TGAGGCTCCATTCACCTCTAGCAATATGAATTGA--TTTTTGAAAACATAAATTGAAAA
1 TGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGAAAACAGAAATTGAAAA
22169 ACAGAAATGG
Statistics
Matches: 196, Mismatches: 30, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
170 11 0.06
171 10 0.05
172 2 0.01
173 66 0.34
174 13 0.07
175 3 0.02
177 1 0.01
179 43 0.22
180 47 0.24
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (177 bp):
TGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGAAAACAGAAATTGAAAATACCTC
AACGTGTCCTGAGGCTCAACTCATTTATCGCAATAACTGATGTTAAAAATGTAGAATTTGAAAAG
CAGAAATTGAAAAAACGAAAAATTGAAAATACCTCAGCGTACGAGCC
Found at i:22225 original size:86 final size:83
Alignment explanation
Indices: 22110--22264 Score: 193
Period size: 86 Copynumber: 1.8 Consensus size: 83
22100 CGGCGTATGA
* * * *
22110 CCTGAGGCTCCATTCACCTCTAGCAATATGAATTGATTTTTGAAAACATAAATTGAAAAACAGAA
1 CCTGAGGCTCAACTCACCTCTAGCAATATGAATTGA-TTTAGAAAACAGAAA-T-AAAAACAGAA
22175 ATGGAAAATACCCCAGCATGT
63 ATGGAAAATACCCCAGCATGT
* * * * * *
22196 CCTGAGGCTCAACTCACTTCTTGTAATATGAGTTGATTTAGAAAACAGACATAAAAACAGAAATT
1 CCTGAGGCTCAACTCACCTCTAGCAATATGAATTGATTTAGAAAACAGAAATAAAAACAGAAATG
22261 GAAA
66 GAAA
22265 GTGACTCAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
83 16 0.27
84 1 0.02
85 12 0.20
86 30 0.51
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (83 bp):
CCTGAGGCTCAACTCACCTCTAGCAATATGAATTGATTTAGAAAACAGAAATAAAAACAGAAATG
GAAAATACCCCAGCATGT
Found at i:22413 original size:74 final size:73
Alignment explanation
Indices: 22285--22859 Score: 682
Period size: 74 Copynumber: 7.8 Consensus size: 73
22275 ACGTGAGCCA
* ** * * *
22285 AGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTG-AAAGTAGAATTTGAAAATACCTCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAAAAATTGAAAATACCTCA
* * *
22349 GCATGCCCCG
64 GCGTGTCCTG
*
22359 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAAAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAAAAATTGAAAATACCTCAG
22424 CGTGTCCTG
65 CGTGTCCTG
22433 AGGCTCAACTCACCTCTCG-AATATGAGTTGA-TTTTGAAAAACAAATTGAACAGGAATTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC------AA-A--AATTGAAAA
* *
22496 TACCTCAACGTGTCTTG
57 TACCTCAGCGTGTCCTG
* *
22513 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-TTGAAAAACAAAAATTGAAAATACCTCA
** *
22578 ATGTGTCTTG
64 GCGTGTCCTG
* * *
22588 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-ACAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAAAAATTGAAAATACCTCAG
22652 CGTGTCCTG
65 CGTGTCCTG
* *
22661 AGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAAAATACCTCAGC
22725 GTGTCCTG
66 GTGTCCTG
** * * *
22733 A-GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTG-ACAACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAAAAATTGAAAATACCTCA
22796 GCGTGTCCTG
64 GCGTGTCCTG
*
22806 AGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATT-AAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAAAA
22860 GGCTTAACTC
Statistics
Matches: 444, Mismatches: 36, Indels: 45
0.85 0.07 0.09
Matches are distributed among these distances:
71 46 0.10
72 54 0.12
73 104 0.23
74 110 0.25
75 61 0.14
77 3 0.01
78 2 0.00
80 42 0.09
81 12 0.03
83 2 0.00
84 8 0.02
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (73 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAAAATACCTCAGC
GTGTCCTG
Found at i:22677 original size:73 final size:73
Alignment explanation
Indices: 22481--22841 Score: 530
Period size: 73 Copynumber: 4.9 Consensus size: 73
22471 AAACAAATTG
* * * *
22481 AACAGGAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
22546 TTTCTTGAA
66 TTT-TTGAA
* ** *
22555 AAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AA-CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
22620 TTTTTTGAC
65 TTTTTTGAA
*
22629 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-
1 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
22693 -TTTTGAAA
66 TTTTTG-AA
* **
22701 AACAAAAATTGAAATTACCTCAGCGTGTCCTGA-GCTCAACTCATTTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
22765 TTTTTTGAC
65 TTTTTTGAA
*
22774 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
22839 TTT
66 TTT
22842 GAAAAACAAA
Statistics
Matches: 263, Mismatches: 18, Indels: 13
0.89 0.06 0.04
Matches are distributed among these distances:
71 32 0.12
72 33 0.13
73 94 0.36
74 40 0.15
75 64 0.24
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (73 bp):
AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTGAA
Found at i:22790 original size:145 final size:147
Alignment explanation
Indices: 22285--22855 Score: 767
Period size: 145 Copynumber: 3.9 Consensus size: 147
22275 ACGTGAGCCA
* * * *
22285 AGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGA-AAGTAGAATTTGAAAATACCTCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAA-CAGAAATTGAAAATACCTCA
* * * *
22349 GCATGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAAAAATTGAA
65 GCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTG-AAAAACAAAAATTGAA
22414 ATTACCTCAGCGTGTCCTG
129 ATTACCTCAGCGTGTCCTG
**** *
22433 AGGCTCAACTCACCTCTCG-AATATGAGTTGATTTTGAAAAACAAATTGAACAGGAATTGAAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTTGAC------AACAGAAATTGAAAAT
* * * * *
22497 ACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGA
59 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTT-TTGAAAAACAAA
* ** *
22562 AATTGAAAATACCTCAATGTGTCTTG
122 AATTGAAATTACCTCAGCGTGTCCTG
*
22588 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGACAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAAATACCTCAG
22652 CGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATTGAAAT
66 CGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAAAT
22716 TACCTCAGCGTGTCCTG
131 TACCTCAGCGTGTCCTG
** *
22733 A-GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAAATACCTCAG
22797 CGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATT
66 CGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAACAAAAATT
22856 AAAAGGCTTA
Statistics
Matches: 374, Mismatches: 37, Indels: 27
0.85 0.08 0.06
Matches are distributed among these distances:
144 28 0.07
145 124 0.33
146 2 0.01
147 16 0.04
148 78 0.21
154 55 0.15
155 56 0.15
156 15 0.04
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (147 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAAATACCTCAG
CGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAACAAAAATTGAAAT
TACCTCAGCGTGTCCTG
Found at i:23005 original size:68 final size:70
Alignment explanation
Indices: 22859--23031 Score: 219
Period size: 68 Copynumber: 2.5 Consensus size: 70
22849 AAAAATTAAA
* * * **
22859 AGGCTTAACTCACTTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
22923 CCTCG
66 CCTCG
** *
22928 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTAA-A-AAATTAAAAATACCTCAACGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
* *
22991 TCTTG
66 CCTCG
22996 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
23032 CCTTGGAAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
67 1 0.01
68 56 0.61
69 28 0.30
70 7 0.08
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.31
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
CCTCG
Found at i:23027 original size:190 final size:195
Alignment explanation
Indices: 22661--23031 Score: 495
Period size: 190 Copynumber: 1.9 Consensus size: 195
22651 GCGTGTCCTG
* * * * *
22661 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTGAAATTACCTCAGCG
1 AGGCTCAACTCACCTCTAGCAATATGAGTTCAATTT-AAAAACAAAAACTAAAAATACCTCAGCG
* * *
22726 TGTCCTGAGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTA
65 TGTCCTGAGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTT-A-AACAGAAATTAAAAATA
*
22791 CCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATT
128 CCTCAACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATT
22856 AAA
193 AAA
* * * * *
22859 AGGCTTAACTCACTTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCGGCGT
1 AGGCTCAACTCACCTCTAGCAATATGAGTTCAATTTAAAAACAAAAACTAAAAATACCTCAGCGT
22922 G-CCTCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTT-AA-A-AAATTAAAAATAC
66 GTCCT-GA-GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAACAGAAATTAAAAATAC
* * *
22982 CTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
129 CTCAACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
23032 CCTTGGAAAG
Statistics
Matches: 154, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
190 57 0.37
191 1 0.01
192 2 0.01
194 3 0.02
195 32 0.21
196 29 0.19
197 5 0.03
198 25 0.16
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (195 bp):
AGGCTCAACTCACCTCTAGCAATATGAGTTCAATTTAAAAACAAAAACTAAAAATACCTCAGCGT
GTCCTGAGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAACAGAAATTAAAAATACCT
CAACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
Found at i:31291 original size:12 final size:13
Alignment explanation
Indices: 31260--31297 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
31250 AGTATGGGAT
*
31260 ATGCAATGAATGTG
1 ATGC-ATGAATGTA
31274 ATGCATGAATG-A
1 ATGCATGAATGTA
31286 ATGCATGAATGT
1 ATGCATGAATGT
31298 CAAATGAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 7 0.32
14 4 0.18
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (13 bp):
ATGCATGAATGTA
Done.