Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3804.1
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: 101209
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.25
Warning! 17336 characters in sequence are not A, C, G, or T
Found at i:13260 original size:55 final size:54
Alignment explanation
Indices: 13125--13262 Score: 141
Period size: 55 Copynumber: 2.5 Consensus size: 54
13115 GTTTAAGGAT
* * * * ** * *
13125 ACCAAGTAAGACAATGCCAAGGCATGACATTGTTAAGTTTCACAAGGCAAGGAA
1 ACCATGTAAGACCATGCCAAGGCATGGCATTGATAAACTACACAAGGCAAAGAA
* ** * *
13179 ACCATGTAAGACCATGTCAAAACATGGCATTGATAAACTACTATAAGGCAAAGAT
1 ACCATGTAAGACCATGCCAAGGCATGGCATTGATAAACTAC-ACAAGGCAAAGAA
*
13234 CCCATGTAAGACCATGCCAAGGCATGGCA
1 ACCATGTAAGACCATGCCAAGGCATGGCA
13263 ACGGTGAGTT
Statistics
Matches: 66, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
54 31 0.47
55 35 0.53
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (54 bp):
ACCATGTAAGACCATGCCAAGGCATGGCATTGATAAACTACACAAGGCAAAGAA
Found at i:13301 original size:53 final size:53
Alignment explanation
Indices: 13122--13325 Score: 138
Period size: 53 Copynumber: 3.8 Consensus size: 53
13112 AGGGTTTAAG
* * * * ** * * *
13122 GATACCAAGTAAGACAATGCCAAGGCATGACATTGTTAAGTTTCACAAGGCAAG
1 GATACCACGTAAGACCATGCCAAGACATGGCAACGGTAAG-TTCATAAGGCAAA
* * * * ** * * *
13176 GAAACCATGTAAGACCATGTCAAAACATGGCATTGATAAACTACTATAAGGCAAA
1 GATACCACGTAAGACCATGCCAAGACATGGCAACGGT-AAGTTC-ATAAGGCAAA
* * * * **
13231 GATCCCATGTAAGACCATGCCAAGGCATGGCAACGGTGAGTTCATAAGGCAGG
1 GATACCACGTAAGACCATGCCAAGACATGGCAACGGTAAGTTCATAAGGCAAA
* * *
13284 GATACCACGTAAGACCATGTCAAGATATGGCAATGGTAAGTT
1 GATACCACGTAAGACCATGCCAAGACATGGCAACGGTAAGTT
13326 TAAAAAAGAA
Statistics
Matches: 116, Mismatches: 32, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
53 43 0.37
54 34 0.29
55 39 0.34
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (53 bp):
GATACCACGTAAGACCATGCCAAGACATGGCAACGGTAAGTTCATAAGGCAAA
Found at i:16814 original size:39 final size:39
Alignment explanation
Indices: 16771--16868 Score: 169
Period size: 39 Copynumber: 2.5 Consensus size: 39
16761 CCGGACATAT
* *
16771 TTCCAGCACGTAGCCTGCGGACCTTAAGTCCGGTTATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGGTATAA
16810 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGGTATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGGTATAA
*
16849 TTCCAGCATATAGCCTGCGG
1 TTCCAGCACATAGCCTGCGG
16869 GTCTTTAAGC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.24
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGGTATAA
Found at i:20491 original size:9 final size:9
Alignment explanation
Indices: 20477--20501 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20467 TGGATTATTT
20477 TGAATGAAA
1 TGAATGAAA
20486 TGAATGAAA
1 TGAATGAAA
20495 TGAATGA
1 TGAATGA
20502 TTGAATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (9 bp):
TGAATGAAA
Found at i:23278 original size:25 final size:25
Alignment explanation
Indices: 23162--23279 Score: 125
Period size: 26 Copynumber: 4.7 Consensus size: 25
23152 AGCTCCAAAT
* *
23162 AGCCATATATCGGGAAGTTCA-AGCG
1 AGCCATA-ATCGGGAAGCTCACAGAG
*
23187 AGCCAT-ATCGGGAAGCTC-CGGAG
1 AGCCATAATCGGGAAGCTCACAGAG
*
23210 AGCCATTAATCAGGAAGCTCACAGAG
1 AGCCA-TAATCGGGAAGCTCACAGAG
* *
23236 AGCCTTTAATCGGGAAGCTCACAAAG
1 AGCC-ATAATCGGGAAGCTCACAGAG
*
23262 AGCCATAATCGGAAAGCT
1 AGCCATAATCGGGAAGCT
23280 TAATAGAGCT
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
23 18 0.23
24 1 0.01
25 29 0.37
26 30 0.38
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (25 bp):
AGCCATAATCGGGAAGCTCACAGAG
Found at i:23288 original size:24 final size:25
Alignment explanation
Indices: 23152--23279 Score: 86
Period size: 25 Copynumber: 5.2 Consensus size: 25
23142 TATAACGGGT
* *
23152 AGCTC-CAAATAGCCATATATCGGGA
1 AGCTCACAAAGAGCCATA-ATCGGAA
* ** *
23177 AGTTCA-AGCGAGCCAT-ATCGGGA
1 AGCTCACAAAGAGCCATAATCGGAA
**
23200 AGCTC-CGGAGAGCCATTAATCAGG-A
1 AGCTCACAAAGAGCCA-TAATC-GGAA
* * *
23225 AGCTCACAGAGAGCCTTTAATCGGGA
1 AGCTCACAAAGAGCC-ATAATCGGAA
23251 AGCTCACAAAGAGCCATAATCGGAA
1 AGCTCACAAAGAGCCATAATCGGAA
23276 AGCT
1 AGCT
23280 TAATAGAGCT
Statistics
Matches: 83, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
23 18 0.22
24 1 0.01
25 34 0.41
26 30 0.36
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.17
Consensus pattern (25 bp):
AGCTCACAAAGAGCCATAATCGGAA
Found at i:25762 original size:27 final size:26
Alignment explanation
Indices: 25694--25775 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 26
25684 AGCTGCCAAA
*
25694 AACAGTAAATGTGGCAAAGCCACCAGT
1 AACAGT-AATGTGGCATAGCCACCAGT
* *
25721 ATCACTAATTGTGGCATAGCCACCAGT
1 AACAGTAA-TGTGGCATAGCCACCAGT
* *
25748 AACAGTGAATATGGCATAGTCACCAGT
1 AACAGT-AATGTGGCATAGCCACCAGT
25775 A
1 A
25776 CAATACTTCC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
27 42 0.91
28 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (26 bp):
AACAGTAATGTGGCATAGCCACCAGT
Found at i:25968 original size:27 final size:27
Alignment explanation
Indices: 25931--26085 Score: 215
Period size: 27 Copynumber: 5.8 Consensus size: 27
25921 TGCCATGCAA
* *
25931 GGGTATCACGGTCATTTTACCTTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
25958 GGGCATTACGGTCATTTTTCCCTA-TG
1 GGGTATTACGGTCATTTTACCCTACAG
*
25984 AGGGTATTACAGTCATTTTACCCTACAG
1 -GGGTATTACGGTCATTTTACCCTACAG
*
26012 GGGTATTACGGTTATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
26039 GGGTATTACGGTCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
*
26066 GGGTATTA-GGTTATTTTACC
1 GGGTATTACGGTCATTTTACC
26086 TATTCTGGGG
Statistics
Matches: 113, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
26 12 0.11
27 100 0.88
28 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (27 bp):
GGGTATTACGGTCATTTTACCCTACAG
Found at i:26048 original size:81 final size:81
Alignment explanation
Indices: 25913--26062 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 81
25903 CCTAAGGGCT
* * * *
25913 AGTCATTTTGCCATGCAAGGGTATCACGGTCATTTTACCTTACAGGGGCATTACGGTCATTTTTC
1 AGTCATTTTACCATACAAGGGTATCACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTAC
25978 CCTATGAGGGTATTAC
66 CCTATGAGGGTATTAC
* * * * *
25994 AGTCATTTTACCCTACAGGGGTATTACGGTTATTTTACCCTACAGGGGTATTACGGTCATTTTAC
1 AGTCATTTTACCATACAAGGGTATCACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTAC
26059 CCTA
66 CCTA
26063 CAGGGGTATT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 60 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (81 bp):
AGTCATTTTACCATACAAGGGTATCACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTAC
CCTATGAGGGTATTAC
Found at i:28095 original size:28 final size:28
Alignment explanation
Indices: 28048--28124 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
28038 ATCTTTGATG
*
28048 TCTCGCACACTAAGTTCCATACTCAATA
1 TCTCGCACACTAAGTGCCATACTCAATA
* * * *
28076 TCTCGCACACCAAGCGCCATTCTTAATA
1 TCTCGCACACTAAGTGCCATACTCAATA
* *
28104 TTTTGCACACTAAGTGCCATA
1 TCTCGCACACTAAGTGCCATA
28125 TACATATATA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.30, C:0.31, G:0.10, T:0.29
Consensus pattern (28 bp):
TCTCGCACACTAAGTGCCATACTCAATA
Found at i:32512 original size:38 final size:38
Alignment explanation
Indices: 32466--32538 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
32456 CAGTTATGGT
*
32466 CTTACATGAAATCTTAT-ATCGACGCCATATCCCAGATA
1 CTTACATGAAATCTCATAAT-GACGCCATATCCCAGATA
* *
32504 CTTACATGAAGTCTCATAATGATGCCATATCCCAG
1 CTTACATGAAATCTCATAATGACGCCATATCCCAG
32539 GAATGGTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
38 29 0.94
39 2 0.06
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (38 bp):
CTTACATGAAATCTCATAATGACGCCATATCCCAGATA
Found at i:53192 original size:43 final size:42
Alignment explanation
Indices: 53145--53240 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
53135 TCCTAAATGT
* *
53145 GGTCTTACATGCAATCAAACATCGATGC-CACTGTCCCAAACAG
1 GGTCTTACACGAAATCAAACAT-GATGCTCA-TGTCCCAAACAG
* * * *
53188 GGTCTTACACGAAATCAGATATGATGCTGATGTCCCAAACAT
1 GGTCTTACACGAAATCAAACATGATGCTCATGTCCCAAACAG
53230 GGTCTTACACG
1 GGTCTTACACG
53241 TAAAATAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 27 0.59
43 19 0.41
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAACATGATGCTCATGTCCCAAACAG
Found at i:77823 original size:40 final size:40
Alignment explanation
Indices: 77749--77930 Score: 278
Period size: 40 Copynumber: 4.6 Consensus size: 40
77739 AACCCAAGTA
* *
77749 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
*
77788 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
77828 CCTTCGGGACTTGGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
77868 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAAAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
77908 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
77931 CATTCGAATA
Statistics
Matches: 133, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 12 0.09
40 118 0.89
41 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:79137 original size:40 final size:40
Alignment explanation
Indices: 79075--79314 Score: 210
Period size: 40 Copynumber: 6.0 Consensus size: 40
79065 CGGATGATAA
*
79075 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAAT-T
1 CCGGGCTAAGTCCCGAAG-GCATTTGAGCGAGT-GCTAATAT
* * *
79115 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TGCTAATAT
* * *
79155 CCAGGCTAAGTCCCGAAGGCGTTTGTGCGA--GCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGCTA--ATAT
* * *
79195 CCAGGCTAAGTCCCGAAGGCATTTGTA-CGAGTGATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTG-AGCGAGTGCTAATAT
* * * *
79234 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TGCTAATAT
*
79274 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT-GCTAATAT
79314 C
1 C
79315 TGGCTAAACT
Statistics
Matches: 166, Mismatches: 21, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
37 2 0.01
39 33 0.20
40 126 0.76
41 3 0.02
42 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGCTAATAT
Found at i:79259 original size:79 final size:80
Alignment explanation
Indices: 79118--79298 Score: 249
Period size: 79 Copynumber: 2.3 Consensus size: 80
79108 GCTAATTCCG
* * *
79118 GGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCAGGCTAAGTCCCGAAGGCGTTTGTGC
1 GGCTAAGTCCCGAAGGCATTTGTACGAGCTACTATATCCAGGCTAAGTCCCGAAGGCATTTGTGC
* * *
79183 GAGCTATTATATCCA
66 AAGCTACTATAACCA
* *
79198 GGCTAAGTCCCGAAGGCATTTGTACGAG-TGATTATA-CCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGCTAAGTCCCGAAGGCATTTGTACGAGCT-ACTATATCCAGGCTAAGTCCCGAAGGCATTTGTG
* *
79261 CAAGTTACTATAACCG
65 CAAGCTACTATAACCA
79277 GGCTAAGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
79299 AGCTAGTGGC
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
79 59 0.66
80 31 0.34
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGGCATTTGTACGAGCTACTATATCCAGGCTAAGTCCCGAAGGCATTTGTGC
AAGCTACTATAACCA
Found at i:79331 original size:79 final size:79
Alignment explanation
Indices: 79115--79321 Score: 247
Period size: 79 Copynumber: 2.6 Consensus size: 79
79105 GTGGCTAATT
* * *
79115 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCT-ACTATATCCAGGCTAAGTCCCGAAGGCGTTT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TGACTATAT-CAGGCTAAGTCCCGAAGGCATTT
* * *
79179 GTGCGAGCTATTATAT
64 GTGCAAGCTACTATAA
* * * *
79195 CCAGGCTAAGTCCCGAAGGCATTTGTA-CGAGTGATTATACCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG-AGCGAGTGACTATATCAGGCTAAGTCCCGAAGGCATTTG
*
79259 TGCAAGTTACTATAA
65 TGCAAGCTACTATAA
* * *
79274 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCTGGCTAA
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATATCAGGCTAA
79322 ACTCCGAAGG
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
78 1 0.01
79 74 0.69
80 32 0.30
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATATCAGGCTAAGTCCCGAAGGCATTTGT
GCAAGCTACTATAA
Found at i:89441 original size:22 final size:22
Alignment explanation
Indices: 89413--89459 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
89403 GATGTGCACC
89413 AGGTAGGATGCCAGAAAAGAGG
1 AGGTAGGATGCCAGAAAAGAGG
89435 AGGTAGGATGCCAGAAAAGAGG
1 AGGTAGGATGCCAGAAAAGAGG
89457 AGG
1 AGG
89460 CGAGTCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.43, T:0.09
Consensus pattern (22 bp):
AGGTAGGATGCCAGAAAAGAGG
Found at i:90235 original size:27 final size:27
Alignment explanation
Indices: 90182--90295 Score: 133
Period size: 27 Copynumber: 4.3 Consensus size: 27
90172 GCATGGCTGA
* * *
90182 CAGAACAGATA-TTGTGACCGAGTCAC
1 CAGAACAGATATTTGTGGCAGAGCCAC
* *
90208 CACATACAGATA-TTATGGCAGAGCCAC
1 CAGA-ACAGATATTTGTGGCAGAGCCAC
* *
90235 CAGAACAGTTATTTGTGGCATAGCCAC
1 CAGAACAGATATTTGTGGCAGAGCCAC
*
90262 CAGAACAGATATTTGTGGCATAGCCAC
1 CAGAACAGATATTTGTGGCAGAGCCAC
90289 CAGAACA
1 CAGAACA
90296 CTTCCTCCAT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 9 0.12
27 67 0.88
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (27 bp):
CAGAACAGATATTTGTGGCAGAGCCAC
Found at i:94923 original size:39 final size:40
Alignment explanation
Indices: 94823--95007 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
94813 TTGAATGATG
* * *
94823 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
94862 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
94903 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
94942 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
94981 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
95008 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:94959 original size:79 final size:81
Alignment explanation
Indices: 94824--95007 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 81
94814 TGAATGATGT
*
94824 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
94888 GTGCGAGATACTA-ATT
66 GTGCGAGATACTATA-A
* * * * **
94904 TCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
*
94966 TGTGCGAGTTACTATAA
65 TGTGCGAGATACTATAA
*
94983 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
95008 AACGAGGAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.64
80 31 0.35
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATAA
Found at i:95029 original size:79 final size:79
Alignment explanation
Indices: 94824--95040 Score: 192
Period size: 79 Copynumber: 2.7 Consensus size: 79
94814 TGAATGATGT
** * * * **
94824 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
94887 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
* ** * *
94904 TCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
94969 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
94983 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
95041 TACGTGATTT
Statistics
Matches: 114, Mismatches: 18, Indels: 11
0.80 0.13 0.08
Matches are distributed among these distances:
78 3 0.03
79 70 0.61
80 41 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Done.