Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_622
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: 55176
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Found at i:2269 original size:40 final size:40
Alignment explanation
Indices: 2160--2380 Score: 270
Period size: 40 Copynumber: 5.6 Consensus size: 40
2150 AATTCGGATG
* *
2160 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
2200 A-ATTCCGGGCTAAG-CCCGAAGGCAATTGTGTGAGTTATT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
2239 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
2279 ATAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
2319 ATAACCGGGTTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* **
2359 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
2381 TTCTTGGTTT
Statistics
Matches: 161, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
39 48 0.30
40 113 0.70
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:2377 original size:119 final size:119
Alignment explanation
Indices: 2160--2380 Score: 295
Period size: 119 Copynumber: 1.9 Consensus size: 119
2150 AATTCGGATG
* *
2160 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAA
* * * **
2225 TTGTGTGAGTTATTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATT
66 TTGAGCGAGTTACTATATCCGGGCTAAACCCCGAAGGCATTTGTGCGAGTTATT
* * *
2279 ATAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGTTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGC
*
2343 ATTTGAGCGAG-TAGCTATATCC-GGCTAAACCCCGAAGG
64 AATTGAGCGAGTTA-CTATATCCGGGCTAAACCCCGAAGG
2381 TTCTTGGTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
118 2 0.02
119 62 0.70
120 24 0.27
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAA
TTGAGCGAGTTACTATATCCGGGCTAAACCCCGAAGGCATTTGTGCGAGTTATT
Found at i:10457 original size:40 final size:40
Alignment explanation
Indices: 10352--10568 Score: 262
Period size: 40 Copynumber: 5.5 Consensus size: 40
10342 CGGATGATAA
* * *
10352 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACGA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* * *
10392 CCGGCCTAAG-CCCGAAGGCAATTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
10431 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTATTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
10471 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
10511 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
10551 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
10569 TACTTGGTTT
Statistics
Matches: 156, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 47 0.30
40 109 0.70
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:10568 original size:119 final size:119
Alignment explanation
Indices: 10348--10568 Score: 286
Period size: 119 Copynumber: 1.9 Consensus size: 119
10338 AATTCGGATG
* *
10348 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACGAATTCCGGCCTAAGCCCGAAGGCAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACGAATACCGGCCTAAGCCCGAAGGCAA
* * ** *
10413 TTGTGCGAGTTATTATATCCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTATT
66 TTGAGCGAGTTACTATATCCGGGCTAAACCCCGAAGGCATTTGTGCGAGTTATT
* * * *
10467 ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTAC-TATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACGAAT-ACCGGCCTAAG-CCCGAAGGC
*
10531 ATTTGAGCGAG-TAGCTATATCC-GGCTAAACCCCGAAGG
64 AATTGAGCGAGTTA-CTATATCCGGGCTAAACCCCGAAGG
10569 TACTTGGTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
118 2 0.02
119 60 0.69
120 25 0.29
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACGAATACCGGCCTAAGCCCGAAGGCAA
TTGAGCGAGTTACTATATCCGGGCTAAACCCCGAAGGCATTTGTGCGAGTTATT
Found at i:14254 original size:30 final size:29
Alignment explanation
Indices: 14220--14283 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 29
14210 ATGAATTGGA
14220 AGCTTTGGCACTAAGTGTACGATTTAAACT
1 AGCTTTGGCACTAAGTGTACGATTT-AACT
*
14250 AGCTTTGGCACTAAGTGTGCGATTTAACT
1 AGCTTTGGCACTAAGTGTACGATTTAACT
14279 AGCTT
1 AGCTT
14284 CGATTACTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (29 bp):
AGCTTTGGCACTAAGTGTACGATTTAACT
Found at i:16618 original size:65 final size:65
Alignment explanation
Indices: 16527--16677 Score: 196
Period size: 65 Copynumber: 2.3 Consensus size: 65
16517 GCAGACTACT
* * * * *
16527 GTAGCTCTTTCTGAGTGTCCTGTTATATGATCGGTTGTGATCCT-GTATATATTGCGGACACAAA
1 GTAGCTCTTTGTGAGTGTCTTATTATATGATCAGTTGTGATCCTAG-ATATATTGCAGACACAAA
16591 C
65 C
* * * *
16592 GTAGCTCTTTGTGAGCGTCTTATTATATGATCAGTTGTGATCCTAGATATGTTGTAGACACAAAT
1 GTAGCTCTTTGTGAGTGTCTTATTATATGATCAGTTGTGATCCTAGATATATTGCAGACACAAAC
*
16657 GTAGCTCTTTGTCAGTGTCTT
1 GTAGCTCTTTGTGAGTGTCTT
16678 GATATGGCTC
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 73 0.99
66 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (65 bp):
GTAGCTCTTTGTGAGTGTCTTATTATATGATCAGTTGTGATCCTAGATATATTGCAGACACAAAC
Found at i:18583 original size:40 final size:40
Alignment explanation
Indices: 18520--18708 Score: 272
Period size: 40 Copynumber: 4.7 Consensus size: 40
18510 TATTCGGATG
* * * * *
18520 ATAACTGGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
**
18560 A-ATTTCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
18600 ATAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
18640 ATAACCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
18680 ATAACCGGGCTAAGTCCCAAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
18709 AGCAAGTAGC
Statistics
Matches: 133, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 131 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:18722 original size:80 final size:79
Alignment explanation
Indices: 18520--18731 Score: 284
Period size: 80 Copynumber: 2.7 Consensus size: 79
18510 TATTCGGATG
* * * *
18520 ATAACTGGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACCA-ATTTCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCAAAGGCATTTGTGCAAGT-ACTATA-TCCGGGCTAAGTCCCGAAGGC
18584 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGTTACT
* * * * *
18600 ATAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCG
1 ATAACCGGGCTAAGTCCCAAAGGCATTTGTGCAAG-TACTATATCCGGGCTAAGTCCCGAAGGCA
18665 TTTGTGCGAGTTACT
65 TTTGTGCGAGTTACT
*
18680 ATAACCGGGCTAAGTCCCAAAGGCATTTGAGCAAGTAGCTATATCC-GGCTAA
1 ATAACCGGGCTAAGTCCCAAAGGCATTTGTGCAAGTA-CTATATCCGGGCTAA
18732 ATTCCAAAGG
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
79 8 0.07
80 106 0.91
81 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCAAAGGCATTTGTGCAAGTACTATATCCGGGCTAAGTCCCGAAGGCAT
TTGTGCGAGTTACT
Found at i:25018 original size:46 final size:46
Alignment explanation
Indices: 24853--25025 Score: 163
Period size: 46 Copynumber: 3.7 Consensus size: 46
24843 TGTAACCCGC
* * * * * *
24853 CCATAAGTGAACTCGGACTCAGCTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
** * * * *
24899 CCACGAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC--A-GAC-ATTTGCAT
* *
24949 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
24992 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
25026 GGATGCTCAA
Statistics
Matches: 100, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 3 0.03
46 55 0.55
47 25 0.25
48 1 0.01
49 3 0.03
50 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
Found at i:25020 original size:93 final size:93
Alignment explanation
Indices: 24861--25031 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
24851 GCCCATAAGT
* * * * *
24861 GAACTCGGACTCAGCTCAACGAGCTCGGGCGTTCGCATCCACGAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCACAAGTGAACTCAGACTCAACTCAA
24926 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
24954 GAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCACAAGTGAACTCAGACTCAACTCAA
25019 CGAGTTCGGATGC
66 CGAGTTCGGATGC
25032 TCAACCATCC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCACAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:25047 original size:46 final size:45
Alignment explanation
Indices: 24858--25047 Score: 122
Period size: 46 Copynumber: 4.1 Consensus size: 45
24848 CCCGCCCATA
* * * * * * *
24858 AGTGAACTCGGACTCAGCTCAACGAGCTCGGGCGTTCGCATCCA-CG
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GG-ATGCTCAACCATCT
*
24904 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT
* * * * *
24951 CA-CGAACTCGGACTCAACTCAACGAGTTCAGACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTC-G-GATGCT-CAACCATCT
24997 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
25043 AGTGA
1 AGTGA
25048 CATGTCACTT
Statistics
Matches: 111, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
43 1 0.01
44 11 0.10
45 5 0.05
46 59 0.53
47 29 0.26
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Found at i:29273 original size:40 final size:40
Alignment explanation
Indices: 29111--29259 Score: 237
Period size: 40 Copynumber: 3.7 Consensus size: 40
29101 TATTTGGATG
* * *
29111 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
29151 A-ATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
29191 ATAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
29231 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
29260 AGCAAGTAGC
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.01
40 98 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:29273 original size:80 final size:80
Alignment explanation
Indices: 29111--29292 Score: 235
Period size: 80 Copynumber: 2.3 Consensus size: 80
29101 TATTTGGATG
* *
29111 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACCAATTCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAATACCGGGCTAAGTCCCGAAGGCA
* *
29176 TTTGTGCGAGTTACT
66 TTTGAGCAAGTTACT
* * *
29191 ATAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAT-ACCGGGCTAAGTCCCGAAGGC
29255 ATTTGAGCAAG-TAGCT
65 ATTTGAGCAAGTTA-CT
* * *
29271 ATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
29293 TACTTGGTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
79 18 0.20
80 71 0.80
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAATACCGGGCTAAGTCCCGAAGGCA
TTTGAGCAAGTTACT
Found at i:34000 original size:48 final size:48
Alignment explanation
Indices: 33927--34107 Score: 195
Period size: 48 Copynumber: 3.8 Consensus size: 48
33917 CATTAGGGGA
* *
33927 TACTTTGATTTGGCTTCCGGCCATGATATCGGCACTTCGGGTGCGAGT
1 TACTTTGATTTGGCTTCGGGCCATGATATCGGCACTTCGAGTGCGAGT
* * *
33975 TACTTTGATTTGGCTTCGGGTCATGATATCGACACTTTGAGTGCGAGCT
1 TACTTTGATTTGGCTTCGGGCCATGATATCGGCACTTCGAGTGCGAG-T
** * ** * * *
34024 T-CAATGATTTGGCTACGGGCCATGATATTAGCACTTCGCGTGTGAGA
1 TACTTTGATTTGGCTTCGGGCCATGATATCGGCACTTCGAGTGCGAGT
* *
34071 TA-TATTGAGTTGGCTTCGGGCCATGATATTGGCACTT
1 TACT-TTGATTTGGCTTCGGGCCATGATATCGGCACTT
34108 AGTGTGTGAG
Statistics
Matches: 109, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
47 1 0.01
48 106 0.97
49 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (48 bp):
TACTTTGATTTGGCTTCGGGCCATGATATCGGCACTTCGAGTGCGAGT
Found at i:37467 original size:12 final size:12
Alignment explanation
Indices: 37447--37478 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
37437 TTTATCATTA
*
37447 TCAAGCATTTCC
1 TCAACCATTTCC
37459 TCAACCATTTCC
1 TCAACCATTTCC
37471 TCAACCAT
1 TCAACCAT
37479 ACCATTACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.38, G:0.03, T:0.31
Consensus pattern (12 bp):
TCAACCATTTCC
Found at i:38143 original size:93 final size:93
Alignment explanation
Indices: 37984--38153 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
37974 CCCATAAGCA
*
37984 AACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAACTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAACTGAACTCGGACTCAACTCAAC
38049 GAGTTCGGATGCCTAGTTACATCTCACG
66 GAGTTCGGATGCCTAGTTACATCTCACG
* *
38077 AACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 AACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAACTGAACTCGGACTCAACTCAA
38141 CGAGTTCGGATGC
65 CGAGTTCGGATGC
38154 TCAACCATCC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAACTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCACG
Found at i:38148 original size:46 final size:46
Alignment explanation
Indices: 37975--38150 Score: 193
Period size: 46 Copynumber: 3.8 Consensus size: 46
37965 TGTAACCCGC
* * *
37975 CCATAAGCAAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
*
38021 CCATAA-CTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGC-GAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
38071 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
38114 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
38151 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 8, Indels: 22
0.79 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 5 0.05
46 59 0.53
47 29 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:38169 original size:46 final size:44
Alignment explanation
Indices: 37984--38169 Score: 137
Period size: 46 Copynumber: 4.0 Consensus size: 44
37974 CCCATAAGCA
* * * * * *
37984 AACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCAT-AACTG
1 AACTCGGACTCAACTCAACGAGTTC-GG-ATGC-CAACCATCTAGTG
*
38030 AACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTCA-CG
1 AACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT-AGTG
* * *
38077 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AAGTG
1 AACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTAGTG
38123 AACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGTG
1 AACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CTAGTG
38169 A
1 A
38170 CATGTCACTT
Statistics
Matches: 113, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
43 1 0.01
44 12 0.11
45 3 0.03
46 60 0.53
47 31 0.27
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (44 bp):
AACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTAGTG
Found at i:53119 original size:28 final size:28
Alignment explanation
Indices: 53062--53241 Score: 267
Period size: 28 Copynumber: 6.5 Consensus size: 28
53052 TAAATTGTGC
*
53062 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
53089 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
53117 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
53145 AGCACTAAGTGTGCGAG-TTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* * *
53172 AGCACTAAGTGTTCAAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* * *
53200 AGCACTAACTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
53227 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53242 GACTTAATAT
Statistics
Matches: 141, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 63 0.45
28 78 0.55
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:53126 original size:55 final size:54
Alignment explanation
Indices: 53062--53241 Score: 254
Period size: 55 Copynumber: 3.3 Consensus size: 54
53052 TAAATTGTGC
53062 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAG-TTGACTATGT
*
53117 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
* * * * *
53172 AGCACTAAGTGTTC-AAGTTTGATTATGTAGCACTAACTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAA--TTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
*
53227 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53242 GACTTAATAT
Statistics
Matches: 112, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
54 1 0.01
55 84 0.75
56 27 0.24
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (54 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGT
Found at i:53201 original size:83 final size:82
Alignment explanation
Indices: 53062--53241 Score: 279
Period size: 83 Copynumber: 2.2 Consensus size: 82
53052 TAAATTGTGC
* *
53062 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCAAGTTTGACTATGTAGCACTAACT
*
53127 GTGCGAGTTTGACTATGT
66 GTGCGAG-TTGACTATAT
* * *
53145 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTTCAAGTTTGATTATGTAGCACTAACT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCAAGTTTGACTATGTAGCACTAACT
*
53210 GTGCGAGTTGATTATAT
66 GTGCGAGTTGACTATAT
*
53227 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
53242 GACTTAATAT
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 22 0.25
83 67 0.75
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCAAGTTTGACTATGTAGCACTAACT
GTGCGAGTTGACTATAT
Done.