Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1083
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: 50433
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Found at i:7341 original size:9 final size:9
Alignment explanation
Indices: 7329--7405 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
7319 TTTGATAAAC
7329 ATGATATGT
1 ATGATATGT
*
7338 ATGATATGCAC
1 ATGATATG--T
7349 ATGATATGT
1 ATGATATGT
*
7358 ATGATATGCAC
1 ATGATATG--T
*
7369 ATGACATGT
1 ATGATATGT
*
7378 ATGATATGCAC
1 ATGATATG--T
7389 ATGATATGT
1 ATGATATGT
7398 ATGATATG
1 ATGATATG
7406 CACACGAGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:7354 original size:11 final size:11
Alignment explanation
Indices: 7338--7409 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
7328 CATGATATGT
7338 ATGATATGCAC
1 ATGATATGCAC
*
7349 ATGATATG--T
1 ATGATATGCAC
7358 ATGATATGCAC
1 ATGATATGCAC
* *
7369 ATGACATG--T
1 ATGATATGCAC
7378 ATGATATGCAC
1 ATGATATGCAC
*
7389 ATGATATG--T
1 ATGATATGCAC
7398 ATGATATGCAC
1 ATGATATGCAC
7409 A
1 A
7410 CGAGATGTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:7417 original size:20 final size:20
Alignment explanation
Indices: 7327--7409 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
7317 ATTTTGATAA
7327 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
7347 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
7367 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
7387 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
7407 ACA
1 ACA
7410 CGAGATGTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:7519 original size:24 final size:24
Alignment explanation
Indices: 7463--7604 Score: 202
Period size: 23 Copynumber: 6.0 Consensus size: 24
7453 GAGGAAGTGC
7463 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
7487 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
7510 AAAAGGGCTTATACCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
7534 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
7557 AAAAAGGGCTT-TGCCCTAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTATT
*
7581 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
7605 ATGATAAAGC
Statistics
Matches: 107, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
23 51 0.48
24 40 0.37
25 16 0.15
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:7532 original size:47 final size:48
Alignment explanation
Indices: 7463--7583 Score: 210
Period size: 47 Copynumber: 2.6 Consensus size: 48
7453 GAGGAAGTGC
7463 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT-
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTA
*
7510 AAAAGGGCTTATACCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTA
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTA
*
7558 AAAAGGGCTT-TGCCCTAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
7584 AGAGGCTAGG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
47 60 0.86
48 10 0.14
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTA
Found at i:7833 original size:31 final size:31
Alignment explanation
Indices: 7795--7858 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
7785 CGTTTACCGT
7795 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
7826 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
7857 AA
1 AA
7859 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:14916 original size:9 final size:9
Alignment explanation
Indices: 14904--14980 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
14894 TTTGATAAAC
14904 ATGATATGT
1 ATGATATGT
*
14913 ATGATATGCAC
1 ATGATATG--T
14924 ATGATATGT
1 ATGATATGT
*
14933 ATGATATGCAC
1 ATGATATG--T
*
14944 ATGACATGT
1 ATGATATGT
*
14953 ATGATATGCAC
1 ATGATATG--T
14964 ATGATATGT
1 ATGATATGT
14973 ATGATATG
1 ATGATATG
14981 CACACGAGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:14929 original size:11 final size:11
Alignment explanation
Indices: 14913--14984 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
14903 CATGATATGT
14913 ATGATATGCAC
1 ATGATATGCAC
*
14924 ATGATATG--T
1 ATGATATGCAC
14933 ATGATATGCAC
1 ATGATATGCAC
* *
14944 ATGACATG--T
1 ATGATATGCAC
14953 ATGATATGCAC
1 ATGATATGCAC
*
14964 ATGATATG--T
1 ATGATATGCAC
14973 ATGATATGCAC
1 ATGATATGCAC
14984 A
1 A
14985 CGAGATGTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:14992 original size:20 final size:20
Alignment explanation
Indices: 14902--14984 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
14892 ATTTTGATAA
14902 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
14922 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
14942 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
14962 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
14982 ACA
1 ACA
14985 CGAGATGTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:15071 original size:23 final size:24
Alignment explanation
Indices: 15038--15133 Score: 117
Period size: 23 Copynumber: 4.0 Consensus size: 24
15028 GAAGAAGTGC
15038 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
15062 AAAA-GGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
15085 AAAAATGGGCTT-TGCCCCAATTATT
1 -AAAA-GGGCTTATGCCCCAGTTATT
*
15110 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
15134 ATGATAAAGC
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
23 21 0.33
24 18 0.29
25 19 0.30
26 5 0.08
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:15133 original size:25 final size:23
Alignment explanation
Indices: 15038--15133 Score: 95
Period size: 25 Copynumber: 4.0 Consensus size: 23
15028 GAAGAAGTGC
*
15038 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAAGGC-TATGCCCCAGTTATT
15062 -AAAAGGCTTATGCCCCAGTTATT
1 AAAAAGGC-TATGCCCCAGTTATT
* *
15085 AAAAATGGGCTTTGCCCCAATTATT
1 AAAAA--GGCTATGCCCCAGTTATT
*
15110 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAA-AGGCTATGCC-CCAGTTAT
15134 ATGATAAAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
23 22 0.36
24 11 0.18
25 24 0.39
26 4 0.07
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (23 bp):
AAAAAGGCTATGCCCCAGTTATT
Found at i:22534 original size:48 final size:48
Alignment explanation
Indices: 22463--22760 Score: 280
Period size: 48 Copynumber: 6.2 Consensus size: 48
22453 TGACACCTGT
*
22463 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGA
** * * *
22511 GCCAGTGTAAGAATATGTTTGGGACATGGCATCGTCATTGATATGTGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGA
* * * ** **
22559 GCTAGTGTAAAACCATGTCTGGGACATAGCATC-G-ATCACATCATAAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGAT-ATGTGA
* * * * *
22607 GCCAATGTAAGACCATGTTTGGAACATGGCATTGGCAAT-AT-TGTGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGT--GA
* * *
22655 GCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGATGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGA
* * * * * *
22703 GCTAGTATAAGACCATGTCTGGGACATGGCATCGACCTCGACATGTGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGA
*
22751 GCCAATGTAA
1 GCCAGTGTAA
22761 TTGGAACATG
Statistics
Matches: 196, Mismatches: 46, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
46 3 0.02
47 2 0.01
48 186 0.95
49 2 0.01
50 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.26
Consensus pattern (48 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGA
Found at i:22728 original size:144 final size:144
Alignment explanation
Indices: 22463--22737 Score: 365
Period size: 144 Copynumber: 1.9 Consensus size: 144
22453 TGACACCTGT
* * * * *
22463 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGTGCCAGTGTAAGAATATG
1 GCCAATGTAAGACCATGTCTGGAACATGGCATCGGCAATGATATGTGAGCCAGTGTAAGAACATG
* * * * * * *
22528 TTTGGGACATGGCATCGTCATTGATATGTGTGCTAGTGTAAAACCATGTCTGGGACATAGCATCG
66 TCTAGGACATGGCATCGGCATTGAGATGAGAGCTAGTATAAAACCATGTCTGGGACATAGCATCG
22593 ATCACATCATAAGA
131 ATCACATCATAAGA
* * *
22607 GCCAATGTAAGACCATGTTTGGAACATGGCATTGGCAAT-AT-TGTGAGAGCCAGTGTAAGACCA
1 GCCAATGTAAGACCATGTCTGGAACATGGCATCGGCAATGATATGT--GAGCCAGTGTAAGAACA
* *
22670 TGTCTAGGACATGGCATCGGCATTGAGATGAGAGCTAGTATAAGACCATGTCTGGGACATGGCAT
64 TGTCTAGGACATGGCATCGGCATTGAGATGAGAGCTAGTATAAAACCATGTCTGGGACATAGCAT
22735 CGA
129 CGA
22738 CCTCGACATG
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
142 3 0.03
143 2 0.02
144 107 0.96
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (144 bp):
GCCAATGTAAGACCATGTCTGGAACATGGCATCGGCAATGATATGTGAGCCAGTGTAAGAACATG
TCTAGGACATGGCATCGGCATTGAGATGAGAGCTAGTATAAAACCATGTCTGGGACATAGCATCG
ATCACATCATAAGA
Found at i:25187 original size:42 final size:42
Alignment explanation
Indices: 25140--25227 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
25130 TGAATTATAC
25140 ATGTTTCATTGAAATATGTAAATATATCTATGTATTAGCCAA
1 ATGTTTCATTGAAATATGTAAATATATCTATGTATTAGCCAA
*
25182 ATGTTTCATTGAAATATGTAAATATATCTATGTATTAGCCAC
1 ATGTTTCATTGAAATATGTAAATATATCTATGTATTAGCCAA
25224 ATGT
1 ATGT
25228 GAATAAGTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (42 bp):
ATGTTTCATTGAAATATGTAAATATATCTATGTATTAGCCAA
Found at i:31802 original size:64 final size:64
Alignment explanation
Indices: 31723--31905 Score: 194
Period size: 66 Copynumber: 2.8 Consensus size: 64
31713 AGACATTATG
* *
31723 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
31787 ATGTAGCTAGGTCGCATGCGG-GTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATG-GGTGATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
31851 AA
63 AA
* * * *
31853 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
31906 CGAACTATAT
Statistics
Matches: 98, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.26
65 20 0.20
66 31 0.32
67 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:44351 original size:202 final size:200
Alignment explanation
Indices: 43966--44368 Score: 702
Period size: 202 Copynumber: 2.0 Consensus size: 200
43956 TACGGCTAAT
43966 GTAGCCGATGCACTGAGGCCATAGGGTTGTTACTGACTGAGGCAATGTTTGCTCGTCTCAGCTTA
1 GTAGCCGATGCACTGAGGCCATAGGGTTGTTACTGACTGAGGCAATGTTTGCTCGTCTCAGCTTA
*
44031 TACGACATGGTAGTCACTTGCCTGAACTTCAGGTTAAACTGAGGTGGATTGAGTAGATTATGGAT
66 TACGACATGGCAGTCACTTGCCTGAACTTCAGGTTAAACTGAGGTGGATTGAGTAGATTATGGAT
44096 AAGTAGATGAGGATAAGTCACTAAAGTCCTCGATTTCGTCAGGTAGAGAGTGGTGAAATTTCAAA
131 AAGTAGATGAGGATAAGTCACTAAAGTCCTCGATTTCGTCAGGTAGAGAGTGGTGAAATTTCAAA
44161 ATTTG
196 ATTTG
44166 GTAGCCGATGCACTGA-GCCATAGGGTTGTTACTGATCTGAGGGCAATGTTTGCTCGTCTCAGCT
1 GTAGCCGATGCACTGAGGCCATAGGGTTGTTACTGA-CTGA-GGCAATGTTTGCTCGTCTCAGCT
* *
44230 TATTCGACGATGGCAGTCTCTTGCCTGAACTTCAGGTTAAACTGAGGTGGATTGAGTAGATTATG
64 TATACGAC-ATGGCAGTCACTTGCCTGAACTTCAGGTTAAACTGAGGTGGATTGAGTAGATTATG
* *
44295 GATAAGTAGATGGAGGATGAGTCACT-AAGTCCTCGATTTCGTTAGGTAGAGAGTGGTGAAATTT
128 GATAAGTAGAT-GAGGATAAGTCACTAAAGTCCTCGATTTCGTCAGGTAGAGAGTGGTGAAATTT
*
44359 CAAATTTTG
192 CAAAATTTG
44368 G
1 G
44369 ACTGAATAGT
Statistics
Matches: 193, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
199 19 0.10
200 20 0.10
201 30 0.16
202 111 0.58
203 13 0.07
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (200 bp):
GTAGCCGATGCACTGAGGCCATAGGGTTGTTACTGACTGAGGCAATGTTTGCTCGTCTCAGCTTA
TACGACATGGCAGTCACTTGCCTGAACTTCAGGTTAAACTGAGGTGGATTGAGTAGATTATGGAT
AAGTAGATGAGGATAAGTCACTAAAGTCCTCGATTTCGTCAGGTAGAGAGTGGTGAAATTTCAAA
ATTTG
Found at i:46732 original size:25 final size:25
Alignment explanation
Indices: 46703--46750 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
46693 TTATAATATG
* * *
46703 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
46728 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
46751 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:46801 original size:9 final size:9
Alignment explanation
Indices: 46789--46865 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
46779 TTTGATAAAC
46789 ATGATATGT
1 ATGATATGT
*
46798 ATGATATGCAC
1 ATGATATG--T
46809 ATGATATGT
1 ATGATATGT
*
46818 ATGATATGCAC
1 ATGATATG--T
*
46829 ATGACATGT
1 ATGATATGT
*
46838 ATGATATGCAC
1 ATGATATG--T
46849 ATGATATGT
1 ATGATATGT
46858 ATGATATG
1 ATGATATG
46866 CACACGAGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:46814 original size:11 final size:11
Alignment explanation
Indices: 46798--46869 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
46788 CATGATATGT
46798 ATGATATGCAC
1 ATGATATGCAC
*
46809 ATGATATG--T
1 ATGATATGCAC
46818 ATGATATGCAC
1 ATGATATGCAC
* *
46829 ATGACATG--T
1 ATGATATGCAC
46838 ATGATATGCAC
1 ATGATATGCAC
*
46849 ATGATATG--T
1 ATGATATGCAC
46858 ATGATATGCAC
1 ATGATATGCAC
46869 A
1 A
46870 CGAGATGTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:46877 original size:20 final size:20
Alignment explanation
Indices: 46787--46869 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
46777 ATTTTGATAA
46787 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
46807 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
46827 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
46847 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
46867 ACA
1 ACA
46870 CGAGATGTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:46987 original size:45 final size:48
Alignment explanation
Indices: 46923--47042 Score: 203
Period size: 45 Copynumber: 2.6 Consensus size: 48
46913 GAGGAAGTGC
46923 AAAAGGGCTTATGCCCCAGTTATTAAA-GGCTTATG-CCCAGTTATT-
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTA
46968 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAA
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT-A
47017 AAAAGGGCTT-TGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
47043 AGAGGCTAGG
Statistics
Matches: 71, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
45 27 0.38
46 8 0.11
47 10 0.14
48 16 0.23
49 10 0.14
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTA
Found at i:47059 original size:25 final size:24
Alignment explanation
Indices: 46923--47063 Score: 195
Period size: 23 Copynumber: 6.0 Consensus size: 24
46913 GAGGAAGTGC
46923 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
46947 -AAA-GGCTTATG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
46968 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
46992 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
47015 AAAAAAGGGCTT-TGCCCCAGTTATT
1 --AAAAGGGCTTATGCCCCAGTTATT
*
47040 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
47064 ATGATAAAGC
Statistics
Matches: 107, Mismatches: 1, Indels: 17
0.86 0.01 0.14
Matches are distributed among these distances:
21 10 0.09
22 11 0.10
23 40 0.37
24 16 0.15
25 21 0.20
26 9 0.08
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:47298 original size:31 final size:31
Alignment explanation
Indices: 47260--47323 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
47250 CGTTTACCGT
47260 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
47291 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
47322 AA
1 AA
47324 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Done.