Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3540
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: 60714
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Found at i:11346 original size:26 final size:26
Alignment explanation
Indices: 11248--11399 Score: 198
Period size: 27 Copynumber: 5.7 Consensus size: 26
11238 AAAACTTTCA
*
11248 ATTTGTAAAATTACCAGAAGA-CCCTCA
1 ATTTGTAAAATTACC-GAA-ACCCCTCG
* *
11275 ATTTGTAAAATTATCGAAACACCTCG
1 ATTTGTAAAATTACCGAAACCCCTCG
11301 ATTTGGTAAAATTACCGAAACCCCTCG
1 ATTT-GTAAAATTACCGAAACCCCTCG
* *
11328 ATTTGTAAAATTACTGAAATACCCTCG
1 ATTTGTAAAATTACCGAAA-CCCCTCG
*
11355 ATTTGTAAAATTACCGAAACCCCCCG
1 ATTTGTAAAATTACCGAAACCCCTCG
*
11381 ATTTGTAAAATTATCGAAA
1 ATTTGTAAAATTACCGAAA
11400 TTCCCTTGTA
Statistics
Matches: 111, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
25 1 0.01
26 48 0.43
27 62 0.56
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (26 bp):
ATTTGTAAAATTACCGAAACCCCTCG
Found at i:11400 original size:53 final size:53
Alignment explanation
Indices: 11248--11405 Score: 223
Period size: 53 Copynumber: 3.0 Consensus size: 53
11238 AAAACTTTCA
* *
11248 ATTTGTAAAATTACCAGAAGA-CCCTCAATTTGTAAAATTATCGAAACA-CCTCG
1 ATTTGTAAAATTACC-GAA-ACCCCTCGATTTGTAAAATTATCGAAATACCCTCG
11301 ATTTGGTAAAATTACCGAAACCCCTCGATTTGTAAAATTA-CTGAAATACCCTCG
1 ATTT-GTAAAATTACCGAAACCCCTCGATTTGTAAAATTATC-GAAATACCCTCG
* *
11355 ATTTGTAAAATTACCGAAACCCCCCGATTTGTAAAATTATCGAAATTCCCT
1 ATTTGTAAAATTACCGAAACCCCTCGATTTGTAAAATTATCGAAATACCCT
11406 TGTAGTGTAA
Statistics
Matches: 96, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
52 2 0.02
53 73 0.76
54 21 0.22
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (53 bp):
ATTTGTAAAATTACCGAAACCCCTCGATTTGTAAAATTATCGAAATACCCTCG
Found at i:11415 original size:80 final size:80
Alignment explanation
Indices: 11251--11432 Score: 208
Period size: 80 Copynumber: 2.3 Consensus size: 80
11241 ACTTTCAATT
* * * *
11251 TGTAAAATTAC-CAGAAGACCCTCAATTTGTAAAATTATCGAAACACCTCGATTTGGTAAAATTA
1 TGTAAAATTACTGA-AATACCCTCAATTTGTAAAATTACCGAAACACCCCGATTTGGTAAAATTA
*
11315 CCGAAACCCCTCGATT
65 CCGAAACCCCTCGATG
* * *
11331 TGTAAAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAACCCCCCGATTT-GTAAAATTAT
1 TGTAAAATTACTGAAATACCCTCAATTTGTAAAATTACCGAAACACCCCGATTTGGTAAAATTAC
* *
11395 CGAAATTCCCTTG-TAG
66 CGAAA-CCCCTCGAT-G
*
11411 TGTAAAATTGACTGACATACCC
1 TGTAAAATT-ACTGAAATACCC
11433 CTGTAGGGTA
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
79 15 0.17
80 60 0.69
81 12 0.14
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (80 bp):
TGTAAAATTACTGAAATACCCTCAATTTGTAAAATTACCGAAACACCCCGATTTGGTAAAATTAC
CGAAACCCCTCGATG
Found at i:11922 original size:11 final size:11
Alignment explanation
Indices: 11906--11931 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11896 ATTGCATGTA
11906 TGATATTATTG
1 TGATATTATTG
11917 TGATATTATTG
1 TGATATTATTG
11928 TGAT
1 TGAT
11932 GTGGGCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (11 bp):
TGATATTATTG
Found at i:20783 original size:17 final size:18
Alignment explanation
Indices: 20761--20803 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
20751 TGCTTTGAAG
20761 ATTTGG-CGCCACTATCT
1 ATTTGGACGCCACTATCT
20778 ATTTGGTGACGCCACTATCT
1 ATTT-G-GACGCCACTATCT
20798 ATTTGG
1 ATTTGG
20804 TGAGAAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.17
18 2 0.09
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (18 bp):
ATTTGGACGCCACTATCT
Found at i:20792 original size:20 final size:20
Alignment explanation
Indices: 20767--20806 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20757 GAAGATTTGG
20767 CGCCACTATCTATTTGGTGA
1 CGCCACTATCTATTTGGTGA
20787 CGCCACTATCTATTTGGTGA
1 CGCCACTATCTATTTGGTGA
20807 GAAATGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (20 bp):
CGCCACTATCTATTTGGTGA
Found at i:22635 original size:49 final size:47
Alignment explanation
Indices: 22577--22958 Score: 638
Period size: 47 Copynumber: 8.0 Consensus size: 47
22567 GATAATTGTG
*
22577 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
22624 ATGTGAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTG-AAA-GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
22673 ATGTGAAAGTGTATATACATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
22722 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
22771 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
22818 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
22865 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
22912 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
22959 GGCCTAATGG
Statistics
Matches: 325, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
47 181 0.56
48 5 0.02
49 139 0.43
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:22956 original size:22 final size:22
Alignment explanation
Indices: 22928--22980 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
22918 AAGTGTATAT
22928 ATGTGATGAGGCCTAATGGCCG
1 ATGTGATGAGGCCTAATGGCCG
22950 ATGTGATGAGGCCTAATGGCCG
1 ATGTGATGAGGCCTAATGGCCG
22972 ATGTGATGA
1 ATGTGATGA
22981 ATGTGAAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.36, T:0.25
Consensus pattern (22 bp):
ATGTGATGAGGCCTAATGGCCG
Found at i:22967 original size:116 final size:116
Alignment explanation
Indices: 22834--23050 Score: 337
Period size: 116 Copynumber: 1.9 Consensus size: 116
22824 AAGTGTATAT
*
22834 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG-GCCTAAT
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA-AAGAGCCGAAT
* * *
22898 AGCCGATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCG
65 AGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATGAGGCCTAATGGCCG
* * * *
22950 ATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGAGCCGAGTG
1 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAAAGAGCCGAATA
*
23015 GCCAACGTGATGGATGTGAAAGTGTATAAATGTGAT
66 GCCAACGTGATGAATGTGAAAGTGTATAAATGTGAT
23051 AAGTCCCGAA
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
115 2 0.02
116 89 0.98
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (116 bp):
ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAAAGAGCCGAATA
GCCAACGTGATGAATGTGAAAGTGTATAAATGTGATGAGGCCTAATGGCCG
Found at i:23001 original size:47 final size:48
Alignment explanation
Indices: 22950--23050 Score: 125
Period size: 47 Copynumber: 2.1 Consensus size: 48
22940 CTAATGGCCG
* * * * *
22950 ATGTGATGAG-GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATCAGAGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAA
* *
22997 ATGTGA-CAGAGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAA
1 ATGTGATCAGAGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAA
23044 ATGTGAT
1 ATGTGAT
23051 AAGTCCCGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
46 2 0.04
47 43 0.96
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.27
Consensus pattern (48 bp):
ATGTGATCAGAGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAA
Found at i:23017 original size:69 final size:69
Alignment explanation
Indices: 22881--23026 Score: 213
Period size: 69 Copynumber: 2.1 Consensus size: 69
22871 AAGTGTATAT
* * *
22881 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTAATG
1 ATGTGATGAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGAAGAGGCCGAATG
*
22946 GCCG
66 GCCA
* *
22950 ATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGA-GCCGAGT
1 ATGTGATGAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA-AGAGGCCGAAT
23014 GGCCA
65 GGCCA
*
23019 ACGTGATG
1 ATGTGATG
23027 GATGTGAAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 67 0.97
70 2 0.03
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.26
Consensus pattern (69 bp):
ATGTGATGAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGAAGAGGCCGAATG
GCCA
Found at i:25159 original size:43 final size:43
Alignment explanation
Indices: 25109--25254 Score: 256
Period size: 43 Copynumber: 3.4 Consensus size: 43
25099 TTGGTTTTCA
25109 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
* *
25152 GAACTAAGTGTGCGGGTAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
* *
25195 GCACTAAGTGTGCGGGTAATAAGTGTTCACGGTTGTGAGGTTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
25238 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
25255 TTGAAATGCA
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 98 1.00
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:25271 original size:29 final size:29
Alignment explanation
Indices: 25236--25309 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
25226 GTTGTGAGGT
* *
25236 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
25265 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
25294 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
25310 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:25741 original size:40 final size:40
Alignment explanation
Indices: 25697--25973 Score: 482
Period size: 40 Copynumber: 6.9 Consensus size: 40
25687 GAGTTACTAA
25697 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
25737 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
25777 ATCCTGGCTAAGTCTCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
25817 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
25857 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
25897 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * * *
25937 ATCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
25974 CGTGTATTCG
Statistics
Matches: 226, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 226 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:25755 original size:80 final size:80
Alignment explanation
Indices: 25618--25973 Score: 477
Period size: 80 Copynumber: 4.5 Consensus size: 80
25608 TCGAATGATG
** ** *
25618 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAG-GC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TGTATCCGGGCTAAG-TCCCGAAGAGC
** * * *
25679 ATTGGTGCGAGTTACTAAA
63 ATTCATGCTAGTGA-TATA
25698 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
*
25763 CATGCTAGTGATGTA
66 CATGCTAGTGATATA
* *
25778 TCCTGGCTAAGTCTCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
*
25843 CATGCTAGTGATGTA
66 CATGCTAGTGATATA
*
25858 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
25923 CATGCTAGTGATATA
66 CATGCTAGTGATATA
* * * *
25938 TCCGTGCTAAATCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
25974 CGTGTATTCG
Statistics
Matches: 250, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
79 1 0.00
80 224 0.90
81 19 0.08
82 6 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATT
CATGCTAGTGATATA
Found at i:27325 original size:17 final size:17
Alignment explanation
Indices: 27303--27335 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27293 ATAAATATAC
*
27303 ATTGTCATTGCATTTTT
1 ATTGTCATTACATTTTT
27320 ATTGTCATTACATTTT
1 ATTGTCATTACATTTT
27336 CATTTTAGTG
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:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (17 bp):
ATTGTCATTACATTTTT
Found at i:29722 original size:13 final size:13
Alignment explanation
Indices: 29704--29740 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
29694 TAAGTTTTGG
29704 TCATGAAATTGAA
1 TCATGAAATTGAA
29717 TCATGAAATTGAA
1 TCATGAAATTGAA
*
29730 TGATGTAAATT
1 TCATG-AAATT
29741 TAAATATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.35
Consensus pattern (13 bp):
TCATGAAATTGAA
Found at i:32042 original size:27 final size:27
Alignment explanation
Indices: 32005--32209 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
31995 TAAATTGTAC
32005 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
32032 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
32059 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
32085 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
32113 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
32141 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
32168 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
32195 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
32210 GACTCAATAT
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:32144 original size:109 final size:108
Alignment explanation
Indices: 32006--32209 Score: 320
Period size: 109 Copynumber: 1.9 Consensus size: 108
31996 AAATTGTACA
* *
32006 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
32071 GCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
66 GCGAAATGAATAT-ATAGCACTAAGTGTGCGAATTGACCATGCG
*
32114 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTG
** * *
32179 TGCGAGTTGATTATATAGCACTGAGTGTGCG
65 TGCGAAATGAATATATAGCACTAAGTGTGCG
32210 GACTCAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 17 0.20
109 70 0.80
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (108 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
GCGAAATGAATATATAGCACTAAGTGTGCGAATTGACCATGCG
Found at i:40117 original size:27 final size:27
Alignment explanation
Indices: 40080--40280 Score: 251
Period size: 27 Copynumber: 7.4 Consensus size: 27
40070 TAAATTGTAC
40080 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
40107 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40134 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40160 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40188 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40216 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40243 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40270 AGCACTGAGTG
1 AGCACTAAGTG
40281 AGCGGACTCA
Statistics
Matches: 152, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 129 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:60226 original size:14 final size:15
Alignment explanation
Indices: 60195--60227 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
60185 GTAGAAGCGA
60195 CTGCTCGTGGAGATT
1 CTGCTCGTGGAGATT
*
60210 CTGCTCGT-GATATT
1 CTGCTCGTGGAGATT
60224 CTGC
1 CTGC
60228 AGGCGCGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.12, C:0.24, G:0.27, T:0.36
Consensus pattern (15 bp):
CTGCTCGTGGAGATT
Done.