Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold546
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: 102609
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:13659 original size:20 final size:19
Alignment explanation
Indices: 13622--13660 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
13612 ATTTTTTAGA
* *
13622 ATTTTTTATAAAATAAATT
1 ATTTTATATAAAACAAATT
13641 ATTTTATATCAAAACAAATT
1 ATTTTATAT-AAAACAAATT
13661 CACTTCCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTATATAAAACAAATT
Found at i:15063 original size:5 final size:5
Alignment explanation
Indices: 15053--15077 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
15043 GATTCGATAT
15053 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
15078 GAGCTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:21915 original size:13 final size:13
Alignment explanation
Indices: 21874--21953 Score: 63
Period size: 13 Copynumber: 6.1 Consensus size: 13
21864 AAATGGTAAA
*
21874 ATGAAATGTTTAG
1 ATGAAATGTTTAT
*
21887 ATGAAATGGTTAT
1 ATGAAATGTTTAT
*
21900 ATGAAATGTTTTT
1 ATGAAATGTTTAT
*
21913 ATGAATATAG-ATAT
1 ATGAA-AT-GTTTAT
* **
21927 ATGAAACGAATAT
1 ATGAAATGTTTAT
*
21940 ATGAAGTGTTTAT
1 ATGAAATGTTTAT
21953 A
1 A
21954 CAAAATACTA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
12 1 0.02
13 42 0.79
14 9 0.17
15 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.19, T:0.39
Consensus pattern (13 bp):
ATGAAATGTTTAT
Found at i:32505 original size:10 final size:10
Alignment explanation
Indices: 32486--32536 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
32476 TTTCTAAAAG
*
32486 TTTTTATGAA
1 TTTTTTTGAA
32496 TTTTTTTGAA
1 TTTTTTTGAA
* *
32506 ATTTGTTG-A
1 TTTTTTTGAA
*
32515 TTTTTTTAAA
1 TTTTTTTGAA
*
32525 TTTTTCTGAA
1 TTTTTTTGAA
32535 TT
1 TT
32537 ATTCATGAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
9 6 0.19
10 26 0.81
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.65
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:38780 original size:7 final size:7
Alignment explanation
Indices: 38768--38793 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38758 TTTTCTTGTT
38768 TTATTTA
1 TTATTTA
38775 TTATTTA
1 TTATTTA
38782 TTATTTA
1 TTATTTA
38789 TTATT
1 TTATT
38794 AAAATAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:40946 original size:17 final size:17
Alignment explanation
Indices: 40924--40956 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40914 AATCTATATA
40924 AAAATAAAAAAATTTAG
1 AAAATAAAAAAATTTAG
*
40941 AAAATAAATAAATTTA
1 AAAATAAAAAAATTTA
40957 AATTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAATAAAAAAATTTAG
Found at i:43932 original size:5 final size:5
Alignment explanation
Indices: 43922--43962 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
43912 CAACTTTAGG
* *
43922 GAAGA GAAGA GAAGAA AAAGT GAAGA GAAGA GAAGA GAAGA
1 GAAGA GAAGA GAAG-A GAAGA GAAGA GAAGA GAAGA GAAGA
43963 AAAATGATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (5 bp):
GAAGA
Found at i:48142 original size:46 final size:45
Alignment explanation
Indices: 48086--48261 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 45
48076 TGGTTGAGCA
*
48086 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
48132 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGAAG
* *
48179 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
48225 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
48262 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
44 3 0.03
45 2 0.02
46 68 0.62
47 31 0.28
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:48242 original size:93 final size:93
Alignment explanation
Indices: 48083--48253 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
48073 GGATGGTTGA
* * * *
48083 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
48148 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
48176 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
48241 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
48254 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:50144 original size:32 final size:33
Alignment explanation
Indices: 50103--50196 Score: 91
Period size: 32 Copynumber: 2.8 Consensus size: 33
50093 GGTACATGAC
*
50103 TTGAGAAGGTCATGAACTTTGAAAAGTTGTG-T
1 TTGAGAAGGTCACGAACTTTGAAAAGTTGTGAT
* * * * * *
50135 TTGAAAAGGTAAGGTACTTTAAAAAGTACGTGAT
1 TTGAGAAGGTCACGAACTTTGAAAAGT-TGTGAT
* *
50169 TTGGGAAGGTCACAAACTTTGAAAAGTT
1 TTGAGAAGGTCACGAACTTTGAAAAGTT
50197 AAGTGCTTAA
Statistics
Matches: 46, Mismatches: 14, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
32 22 0.48
33 3 0.07
34 21 0.46
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (33 bp):
TTGAGAAGGTCACGAACTTTGAAAAGTTGTGAT
Found at i:50242 original size:68 final size:66
Alignment explanation
Indices: 50079--50249 Score: 166
Period size: 68 Copynumber: 2.6 Consensus size: 66
50069 CTAAGAAGAC
* * * * ** *
50079 AAGGTAC-CAAAAAAGGTACATGACTTGAGAAGGTCATGAACTTTGAAAAGTTGTGTTTGAAAAG
1 AAGGTACTCTAAAAA-GTACGTGACCTGGGAAGGTCACAAACTTTGAAAAGTTGTGCTTGAAAAG
50143 GT
65 GT
* **
50145 AAGGTACTTTAAAAAGTACGTGATTTGGGAAGGTCACAAACTTTGAAAAGTTAAGTGCTT-AAGA
1 AAGGTACTCTAAAAAGTACGTGACCTGGGAAGGTCACAAACTTTGAAAAGTT--GTGCTTGAA-A
50209 AGGT
63 AGGT
* * * *
50213 GAGGTACTCTAAGAAGTATGTGACCTGGGAAGATCAC
1 AAGGTACTCTAAAAAGTACGTGACCTGGGAAGGTCAC
50250 GTTATAACGC
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
66 39 0.45
67 7 0.08
68 40 0.47
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (66 bp):
AAGGTACTCTAAAAAGTACGTGACCTGGGAAGGTCACAAACTTTGAAAAGTTGTGCTTGAAAAGG
T
Found at i:51991 original size:42 final size:42
Alignment explanation
Indices: 51915--52033 Score: 152
Period size: 42 Copynumber: 2.8 Consensus size: 42
51905 TCGGACCAAT
* *
51915 GCCATATCCTAGATATGGTCTTACATATAATCTCATATCGAA
1 GCCAAATCCCAGATATGGTCTTACATATAATCTCATATCGAA
* * *
51957 GCC-AATACCCAGCTATGGTCTTACATGA-AGTCTCATATCGAT
1 GCCAAAT-CCCAGATATGGTCTTACAT-ATAATCTCATATCGAA
*
51999 GCCAAATCCCAGATATGGTCTTACACATAATCTCA
1 GCCAAATCCCAGATATGGTCTTACATATAATCTCA
52034 GTAATCCTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
41 3 0.05
42 58 0.89
43 4 0.06
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (42 bp):
GCCAAATCCCAGATATGGTCTTACATATAATCTCATATCGAA
Found at i:53697 original size:87 final size:87
Alignment explanation
Indices: 53575--53745 Score: 245
Period size: 87 Copynumber: 2.0 Consensus size: 87
53565 AAGTTAAGAG
** * * * *
53575 ATACCTTAAGAGATATGTGACCTGAAAAGGTCAAAAGCTTTGGAAAGCTCGACACTTGAGAATGC
1 ATACCTTAAGAGATATGTGACCTGAAAAGACCAAAAGCTTTAGAAAACTCAACACTTGAGAAGGC
*
53640 AAGGTGTATCTTAAGAGATGCA
66 AAGGTGTATCTTAAAAGATGCA
*
53662 ATACCTTAA-ACGATATGTGACCTGAAAAGACCAAAAGCTTTAGAAAACTCAACCCTTGAGAAGG
1 ATACCTTAAGA-GATATGTGACCTGAAAAGACCAAAAGCTTTAGAAAACTCAACACTTGAGAAGG
*
53726 CGAGGTGTATCTTAAAAGAT
65 CAAGGTGTATCTTAAAAGAT
53746 ATGAGGTGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 1 0.01
87 73 0.99
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (87 bp):
ATACCTTAAGAGATATGTGACCTGAAAAGACCAAAAGCTTTAGAAAACTCAACACTTGAGAAGGC
AAGGTGTATCTTAAAAGATGCA
Found at i:53753 original size:21 final size:21
Alignment explanation
Indices: 53727--53767 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53717 TTGAGAAGGC
53727 GAGGTGTATCTTAAAAGATAT
1 GAGGTGTATCTTAAAAGATAT
* *
53748 GAGGTGTATTTTAAGAGATA
1 GAGGTGTATCTTAAAAGATA
53768 CAATACCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (21 bp):
GAGGTGTATCTTAAAAGATAT
Found at i:53830 original size:108 final size:108
Alignment explanation
Indices: 53641--53857 Score: 292
Period size: 108 Copynumber: 2.0 Consensus size: 108
53631 TGAGAATGCA
* *
53641 AGGTGTATCTTAAGAGATGCAATACCTTAAACGATATGTGACCTGAAAAGACCAAAAGCTTTAGA
1 AGGTGTATCTTAAGAGATACAATACCTTAAAAGATATGTGACCTGAAAAGACCAAAAGCTTTAGA
53706 AAACTCAACCCTTGAGAAGGCGAGGTGTATCTTAAAAGATATG
66 AAACTCAACCCTTGAGAAGGCGAGGTGTATCTTAAAAGATATG
* * * * * *
53749 AGGTGTATTTTAAGAGATACAATACCTTAAAAGGTATGTGACTTGAAAA-AGCTAACAGCTTTCG
1 AGGTGTATCTTAAGAGATACAATACCTTAAAAGATATGTGACCTGAAAAGA-CCAAAAGCTTTAG
* ** ** *
53813 AAAGCTTGATGCTTGAGAAGGCGAGGTGTATCTTAAGAGATATG
65 AAAACTCAACCCTTGAGAAGGCGAGGTGTATCTTAAAAGATATG
53857 A
1 A
53858 TACCTTAAGA
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
107 1 0.01
108 93 0.99
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.26
Consensus pattern (108 bp):
AGGTGTATCTTAAGAGATACAATACCTTAAAAGATATGTGACCTGAAAAGACCAAAAGCTTTAGA
AAACTCAACCCTTGAGAAGGCGAGGTGTATCTTAAAAGATATG
Found at i:53885 original size:195 final size:195
Alignment explanation
Indices: 53575--53944 Score: 451
Period size: 195 Copynumber: 1.9 Consensus size: 195
53565 AAGTTAAGAG
* * * *
53575 ATACCTTAAGAGATATGTGACCTGAAAAGGTCAAAAGCTTTGGAAAGCTCGACACTTGAGAATGC
1 ATACCTTAAAAGATATGTGACCTGAAAAGCTCAAAAGCTTTCGAAAGCTCGACACTTGAGAAGGC
* *
53640 AAGGTGTATCTTAAGAGATGCAATACCTTAAACGATATGTGACCTGAAAAGACCAAAAGCTTTAG
66 AAGGTGTATCTTAAGAGATACAATACCTTAAACGATATGTGAACTGAAAAGACCAAAAGCTTTA-
* *
53705 A-AAACTCAA-CCCTTGAGAAGGCGAGGTGTATCTTAAAAGATATGAGGTGTATTTTAAGAGATA
130 ACAAACTCAATCCC-TGAAAAGGCAAGGTGTATCTTAAAAGATATGAGGTGTATTTTAAGAGATA
53768 CA
194 CA
* * * * **
53770 ATACCTTAAAAGGTATGTGACTTGAAAAAGCT-AACAGCTTTCGAAAGCTTGATGCTTGAGAAGG
1 ATACCTTAAAAGATATGTGACCTG-AAAAGCTCAAAAGCTTTCGAAAGCTCGACACTTGAGAAGG
* ** * * * *
53834 CGAGGTGTATCTTAAGAGATATGATACCTTAAGA-GGTATGTGAATTGAAAAGGCTAAAAGCTTT
65 CAAGGTGTATCTTAAGAGATACAATACCTTAA-ACGATATGTGAACTGAAAAGACCAAAAGCTTT
* * * *
53898 AACAAGCTTAATGCCTGAAAAGGCAATGTGTATCTTAAAAGATATGA
129 AACAAACTCAATCCCTGAAAAGGCAAGGTGTATCTTAAAAGATATGA
53945 TACCTTAATA
Statistics
Matches: 146, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
194 1 0.01
195 136 0.93
196 9 0.06
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (195 bp):
ATACCTTAAAAGATATGTGACCTGAAAAGCTCAAAAGCTTTCGAAAGCTCGACACTTGAGAAGGC
AAGGTGTATCTTAAGAGATACAATACCTTAAACGATATGTGAACTGAAAAGACCAAAAGCTTTAA
CAAACTCAATCCCTGAAAAGGCAAGGTGTATCTTAAAAGATATGAGGTGTATTTTAAGAGATACA
Found at i:53896 original size:87 final size:86
Alignment explanation
Indices: 53749--54093 Score: 322
Period size: 87 Copynumber: 4.0 Consensus size: 86
53739 AAAAGATATG
* * * * * *
53749 AGGTGTATTTTAAGAGATACAATACCTTAAAAGGTATGTGACTTGAAAAAGCT-AACAGCTTTCG
1 AGGTGTATCTTAAAAGATACGATACCTT-AAAGGTATGTGAATTGAAAAGGCTCAAGAGCTTT-G
* * *
53813 AAAGCTTGATGCTTGAGAAGGCG
64 AAAGCTCGATGCTTGAAAAGGCA
* * * *
53836 AGGTGTATCTTAAGAGATATGATACCTTAAGAGGTATGTGAATTGAAAAGGCT-AAAAGCTTTAA
1 AGGTGTATCTTAAAAGATACGATACCTTAA-AGGTATGTGAATTGAAAAGGCTCAAGAGCTTTGA
** *
53900 CAAGCTTAATGCCTGAAAAGGCA
65 -AAGCTCGATGCTTGAAAAGGCA
* * * *
53923 ATGTGTATCTTAAAAGATATGATACCTTAATAGGTATGTGTCA-T-AAAAGGGTCAAGAGCTTTG
1 AGGTGTATCTTAAAAGATACGATACCTTAA-AGGTATGTG-AATTGAAAAGGCTCAAGAGCTTTG
*
53986 AAAAGCTCGACGCTTGAAAAGGCA
64 -AAAGCTCGATGCTTGAAAAGGCA
* * * * * * *
54010 ATGTATATTTTAAAAGATACGATACCTTAAAAGCATGTGACTTGAAAATG-TCAAGAGCTTTGAA
1 AGGTGTATCTTAAAAGATACGATACCTTAAAGGTATGTGAATTGAAAAGGCTCAAGAGCTTTGAA
54074 AGGCTCGATGCTTGAGAAAG
66 A-GCTCGATGCTTGA-AAAG
54094 TGAGGTATCT
Statistics
Matches: 218, Mismatches: 31, Indels: 18
0.82 0.12 0.07
Matches are distributed among these distances:
85 3 0.01
86 42 0.19
87 171 0.78
88 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (86 bp):
AGGTGTATCTTAAAAGATACGATACCTTAAAGGTATGTGAATTGAAAAGGCTCAAGAGCTTTGAA
AGCTCGATGCTTGAAAAGGCA
Found at i:57079 original size:21 final size:21
Alignment explanation
Indices: 57053--57098 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
57043 TTTTTATTTA
*
57053 TATATTATTCAT-TATATTATT
1 TATATTA-TCATACATATTATT
*
57074 TATATTATCATACATTTTATT
1 TATATTATCATACATATTATT
57095 TATA
1 TATA
57099 AATTTAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TATATTATCATACATATTATT
Found at i:57094 original size:24 final size:23
Alignment explanation
Indices: 57046--57094 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
57036 TATATAATTT
* *
57046 TTATTTATATATTATTCATTATA
1 TTATTTATATATCATACATTATA
*
57069 TTATTTATATTATCATACATTTTA
1 TTATTTATA-TATCATACATTATA
57093 TT
1 TT
57095 TATAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATTTATATATCATACATTATA
Found at i:68867 original size:9 final size:9
Alignment explanation
Indices: 68809--69162 Score: 90
Period size: 10 Copynumber: 37.3 Consensus size: 9
68799 ATTCTCAATA
68809 AAAATATTAT
1 AAAA-ATTAT
*
68819 AAAATTATAT
1 AAAAAT-TAT
68829 AAAAATTAT
1 AAAAATTAT
*
68838 -TAAATTGATT
1 AAAAATT-A-T
* *
68848 TAAACTTAT
1 AAAAATTAT
68857 AAAAATTAT
1 AAAAATTAT
*
68866 AAAATATAAT
1 AAAA-ATTAT
68876 AAAAA-TAT
1 AAAAATTAT
*
68884 AATAAATTCT
1 AA-AAATTAT
68894 AATAAATTTAT
1 AA-AAA-TTAT
*
68905 AAATTTAA-TAA
1 AAA---AATTAT
68916 AACAAATT-T
1 AA-AAATTAT
68925 -AAAATATAT
1 AAAAAT-TAT
* *
68934 AAAATTGTAC
1 AAAAAT-TAT
68944 AAAAATGTA-
1 AAAAAT-TAT
*
68953 AAACAAATACTT
1 AAA-AATTA--T
*
68965 GAAAACTTAT
1 -AAAAATTAT
68975 AAAAATTATT
1 AAAAATTA-T
68985 AAAAA-TAT
1 AAAAATTAT
*
68993 AAAAATGAT
1 AAAAATTAT
69002 AAAAAATTATT
1 -AAAAATTA-T
*
69013 AAATATT-T
1 AAAAATTAT
* *
69021 TAACA-T-T
1 AAAAATTAT
*
69028 -AAAATCAT
1 AAAAATTAT
*
69036 ATAAACTTAT
1 A-AAAATTAT
69046 AAAAATTAT
1 AAAAATTAT
69055 AATAAA-TAT
1 AA-AAATTAT
*
69064 AAAAAATAT
1 AAAAATTAT
69073 AAAAA-TAT
1 AAAAATTAT
69081 AATAAATTATTTT
1 AA-AAATTA---T
69094 AAAAATATAT
1 AAAAAT-TAT
*
69104 AAAATATTTT
1 AAAA-ATTAT
***
69114 AATTCTTAT
1 AAAAATTAT
*
69123 AAAAACTAAT
1 AAAAA-TTAT
69133 AAATAA-TAT
1 AAA-AATTAT
*
69142 -AAAAGTATT
1 AAAAATTA-T
69151 AAAAATTAT
1 AAAAATTAT
69160 AAA
1 AAA
69163 TATCATTTAA
Statistics
Matches: 259, Mismatches: 42, Indels: 87
0.67 0.11 0.22
Matches are distributed among these distances:
6 3 0.01
7 8 0.03
8 34 0.13
9 77 0.30
10 101 0.39
11 18 0.07
12 8 0.03
13 10 0.04
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:68896 original size:21 final size:19
Alignment explanation
Indices: 68855--68917 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 19
68845 ATTTAAACTT
68855 ATAAAAATTATAAAATATA
1 ATAAAAATTATAAAATATA
* *
68874 ATAAAAATATAATAAATTCTA
1 ATAAAAAT-T-ATAAAATATA
* *
68895 AT-AAATTTAT-AAATTTA
1 ATAAAAATTATAAAATATA
68912 ATAAAA
1 ATAAAA
68918 CAAATTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.19
18 5 0.14
19 9 0.25
20 5 0.14
21 10 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAAATTATAAAATATA
Found at i:68908 original size:8 final size:9
Alignment explanation
Indices: 68878--68916 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
68868 AATATAATAA
*
68878 AAATATAAT
1 AAATTTAAT
68887 AAATTCTAAT
1 AAATT-TAAT
68897 AAATTT-AT
1 AAATTTAAT
68905 AAATTTAAT
1 AAATTTAAT
68914 AAA
1 AAA
68917 ACAAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
8 8 0.30
9 10 0.37
10 9 0.33
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
AAATTTAAT
Found at i:69067 original size:17 final size:17
Alignment explanation
Indices: 68972--69110 Score: 66
Period size: 18 Copynumber: 7.7 Consensus size: 17
68962 CTTGAAAACT
*
68972 TATAAAAATTATTAAAAA
1 TATAAAAAATA-TAAAAA
68990 TAT-AAAAATGATAAAAAA
1 TATAAAAAAT-AT-AAAAA
* * * * *
69008 TTATTAAATATTTTAACA
1 -TATAAAAAATATAAAAA
* **
69026 T-TAAAATCATATAAACT
1 TATAAAA-AATATAAAAA
*
69043 TATAAAAATTATAATAAA
1 TATAAAAAATATAA-AAA
69061 TATAAAAAATATAAAAA
1 TATAAAAAATATAAAAA
*
69078 TATAATAAATTATTTTAAAAA
1 TATAA-AAA--A-TATAAAAA
*
69099 TATATAAAATAT
1 TATAAAAAATAT
69111 TTTAATTCTT
Statistics
Matches: 92, Mismatches: 18, Indels: 23
0.69 0.14 0.17
Matches are distributed among these distances:
16 4 0.04
17 29 0.32
18 35 0.38
19 4 0.04
20 9 0.10
21 11 0.12
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (17 bp):
TATAAAAAATATAAAAA
Found at i:69098 original size:29 final size:26
Alignment explanation
Indices: 69043--69110 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 26
69033 CATATAAACT
69043 TATAAAAATTATAATAAATATAAAAAA
1 TATAAAAA-TATAATAAATATAAAAAA
*
69070 TATAAAAATATAATAAATTATTTTAAAAA
1 TATAAAAATATAATAAA-TA--TAAAAAA
69099 TATATAAAATAT
1 TATA-AAAATAT
69111 TTTAATTCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
26 9 0.25
27 10 0.28
29 10 0.28
30 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
TATAAAAATATAATAAATATAAAAAA
Found at i:69117 original size:29 final size:30
Alignment explanation
Indices: 69043--69135 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 30
69033 CATATAAACT
69043 TATA-AAAATTATAATAAA-TA-TA-AAAAA
1 TATATAAAA-TATAATAAATTATTATAAAAA
*
69070 TATA-AAAATATAATAAATTATTTTAAAAA
1 TATATAAAATATAATAAATTATTATAAAAA
* * *
69099 TATATAAAATAT-TTTAATTCTTATAAAAA
1 TATATAAAATATAATAAATTATTATAAAAA
69128 CTA-ATAAA
1 -TATATAAA
69136 TAATATAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
26 9 0.16
27 10 0.18
28 1 0.02
29 27 0.48
30 9 0.16
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (30 bp):
TATATAAAATATAATAAATTATTATAAAAA
Found at i:69491 original size:16 final size:16
Alignment explanation
Indices: 69470--69502 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
69460 CGTTAATTTG
69470 ATTCGTTTAAAAATAT
1 ATTCGTTTAAAAATAT
69486 ATTCGTTTAAAAATAT
1 ATTCGTTTAAAAATAT
69502 A
1 A
69503 GTTTAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTCGTTTAAAAATAT
Found at i:72042 original size:11 final size:10
Alignment explanation
Indices: 72016--72207 Score: 54
Period size: 10 Copynumber: 19.8 Consensus size: 10
72006 TTTTATTTTT
72016 TAATTTT-TA
1 TAATTTTATA
72025 TAATTTTATA
1 TAATTTTATA
72035 TCAATTTTA-A
1 T-AATTTTATA
72045 T-ATTTT-TA
1 TAATTTTATA
* *
72053 TGATTTTTTA
1 TAATTTTATA
72063 TAAGTTTT-TAA
1 TAA-TTTTAT-A
* *
72074 GAACTTTAATA
1 TAA-TTTTATA
**
72085 TTTTTTTATA
1 TAATTTTATA
* *
72095 AAATTTTAAA
1 TAATTTTATA
72105 T-ATTTT-TA
1 TAATTTTATA
72113 TAA-TTTATTA
1 TAATTTTA-TA
*
72123 GAATTTTA-A
1 TAATTTTATA
*
72132 -GATATTTA-A
1 TAAT-TTTATA
72141 TAATATTTATA
1 TAAT-TTTATA
**
72152 TGGTTTTAT-
1 TAATTTTATA
72161 T-ATTTTATTA
1 TAATTTTA-TA
* *
72171 CAATTTT-CA
1 TAATTTTATA
*
72180 TAAGTTTATA
1 TAATTTTATA
72190 TCAATTTTA-A
1 T-AATTTTATA
*
72200 TATTTTTA
1 TAATTTTA
72208 AAACTATTTT
Statistics
Matches: 136, Mismatches: 27, Indels: 40
0.67 0.13 0.20
Matches are distributed among these distances:
8 19 0.14
9 38 0.28
10 42 0.31
11 36 0.26
12 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (10 bp):
TAATTTTATA
Found at i:72070 original size:10 final size:9
Alignment explanation
Indices: 72010--72129 Score: 64
Period size: 10 Copynumber: 12.6 Consensus size: 9
72000 TCAAGTTTTT
72010 ATTTTT-TA
1 ATTTTTATA
72018 ATTTTTATA
1 ATTTTTATA
72027 ATTTTATATCA
1 ATTTT-TAT-A
*
72038 ATTTTAAT-
1 ATTTTTATA
72046 ATTTTTATGA
1 ATTTTTAT-A
*
72056 TTTTTTATA
1 ATTTTTATA
*
72065 AGTTTTTAAGA
1 A-TTTTT-ATA
* *
72076 ACTTTAATA
1 ATTTTTATA
*
72085 TTTTTTTATAA
1 -ATTTTTAT-A
* *
72096 AATTTTAAA
1 ATTTTTATA
72105 TATTTTTATA
1 -ATTTTTATA
*
72115 ATTTATTAGA
1 ATTT-TTATA
72125 ATTTT
1 ATTTT
72130 AAGATATTTA
Statistics
Matches: 84, Mismatches: 17, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
8 13 0.15
9 16 0.19
10 45 0.54
11 10 0.12
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:72090 original size:20 final size:22
Alignment explanation
Indices: 72067--72111 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
72057 TTTTTATAAG
*
72067 TTTTTA-AGAACTTT-AATATT
1 TTTTTATAAAACTTTAAATATT
*
72087 TTTTTATAAAATTTTAAATATT
1 TTTTTATAAAACTTTAAATATT
72109 TTT
1 TTT
72112 ATAATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 6 0.29
22 9 0.43
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTATAAAACTTTAAATATT
Found at i:72207 original size:48 final size:45
Alignment explanation
Indices: 72096--72207 Score: 102
Period size: 48 Copynumber: 2.4 Consensus size: 45
72086 TTTTTTATAA
*
72096 AATTTTAAATATTTTTATAATTTATTAGAATTTTAAGATATTTAAT
1 AATTTT-AATATTTTTATAATTTATTACAATTTTAAGATATTTAAT
* * *
72142 AATATTT-ATATGGTTTTATTATTTTATTACAATTTTCATA-AGTTTATAT
1 AAT-TTTAATAT--TTTTA-TAATTTATTACAATTTTAAGATA-TTTA-AT
72191 CAATTTTAATATTTTTA
1 -AATTTTAATATTTTTA
72208 AAACTATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
45 4 0.07
46 3 0.06
47 9 0.17
48 26 0.48
49 5 0.09
50 7 0.13
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (45 bp):
AATTTTAATATTTTTATAATTTATTACAATTTTAAGATATTTAAT
Found at i:72794 original size:7 final size:7
Alignment explanation
Indices: 72778--72806 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
72768 ATAATTATAT
72778 TAAA-AA
1 TAAATAA
72784 TAAATAA
1 TAAATAA
72791 TAAATAA
1 TAAATAA
72798 TAAATAA
1 TAAATAA
72805 TA
1 TA
72807 TTATTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAATAA
Found at i:72799 original size:14 final size:13
Alignment explanation
Indices: 72764--72806 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
72754 TAATAAGTTC
*
72764 AAAAATAATTATATT
1 AAAAATAA--ATAAT
72779 AAAAATAAATAAT
1 AAAAATAAATAAT
72792 AAATAATAAATAAT
1 AAA-AATAAATAAT
72806 A
1 A
72807 TTATTATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 7 0.27
14 11 0.42
15 8 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAAATAAATAAT
Found at i:88570 original size:14 final size:14
Alignment explanation
Indices: 88551--88582 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
88541 AAATAAGTCT
*
88551 TTTTCCAGAAATCA
1 TTTTCCAGAAACCA
88565 TTTTCCAGAAACCA
1 TTTTCCAGAAACCA
88579 TTTT
1 TTTT
88583 TAATGAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (14 bp):
TTTTCCAGAAACCA
Found at i:93168 original size:12 final size:13
Alignment explanation
Indices: 93151--93179 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
93141 TAATGTTGAA
93151 TTTTATTTTT-AT
1 TTTTATTTTTCAT
93163 TTTTATTTTTCAT
1 TTTTATTTTTCAT
93176 TTTT
1 TTTT
93180 TAAAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTTTTCAT
Found at i:93191 original size:2 final size:2
Alignment explanation
Indices: 93186--93219 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
93176 TTTTTAAAAT
* *
93186 TA TA TA TA TA CA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
93220 AATTTCTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:98081 original size:18 final size:18
Alignment explanation
Indices: 98058--98093 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
98048 TTTGAAAAAA
98058 ATGATTTTTTAAATTTAT
1 ATGATTTTTTAAATTTAT
98076 ATGATTTTTTAAATTTAT
1 ATGATTTTTTAAATTTAT
98094 TCTGGTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
ATGATTTTTTAAATTTAT
Found at i:102149 original size:2 final size:2
Alignment explanation
Indices: 102144--102177 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
102134 TTTTTTAAAT
* *
102144 TA TA TA TA TA CA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
102178 ATTTCTAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Done.