Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168456.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_667, whole genome shotgun sequence
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: 20111
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Found at i:121 original size:17 final size:18
Alignment explanation
Indices: 90--131 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
80 CACAATTATT
*
90 AATTATTAATTAAAAATA
1 AATTATTAATAAAAAATA
108 AATTA-TAATAAAAAATA
1 AATTATTAATAAAAAATA
*
125 AACTATT
1 AATTATT
132 TGTTATGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTATTAATAAAAAATA
Found at i:220 original size:17 final size:19
Alignment explanation
Indices: 198--243 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
188 ATTTATTCAT
198 AATTAATAAT-AAT-TAAA
1 AATTAATAATAAATATAAA
215 AATTAAT-ATAAATCATAAA
1 AATTAATAATAAAT-ATAAA
234 AATTAATAAT
1 AATTAATAAT
244 TATATTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 10 0.40
19 11 0.44
20 2 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAATAAATATAAA
Found at i:225 original size:26 final size:26
Alignment explanation
Indices: 196--245 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
186 AAATTTATTC
* *
196 ATAATTAATAATAATTAAAAATTAAT
1 ATAAATAATAAAAATTAAAAATTAAT
* *
222 ATAAATCATAAAAATTAATAATTA
1 ATAAATAATAAAAATTAAAAATTA
246 TATTATGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
ATAAATAATAAAAATTAAAAATTAAT
Found at i:1016 original size:16 final size:18
Alignment explanation
Indices: 985--1025 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
975 CACAATTATT
985 AATTATTAATTAAAAATA
1 AATTATTAATTAAAAATA
1003 AATTA-TAA-TAAAAATA
1 AATTATTAATTAAAAATA
*
1019 AACTATT
1 AATTATT
1026 TGTTATGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 12 0.57
17 4 0.19
18 5 0.24
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTATTAATTAAAAATA
Found at i:1321 original size:17 final size:16
Alignment explanation
Indices: 1281--1330 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 16
1271 ATCTATACAG
1281 TTATAATTAA-TTTAA
1 TTATAATTAATTTTAA
1296 TTA-AA-TAATTTTAA
1 TTATAATTAATTTTAA
1310 TTATCAATTAATTTATAA
1 TTAT-AATTAATTT-TAA
1328 TTA
1 TTA
1331 ATAAAACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.10
14 10 0.33
15 3 0.10
16 2 0.07
17 6 0.20
18 6 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATAATTAATTTTAA
Found at i:2369 original size:17 final size:18
Alignment explanation
Indices: 2338--2379 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2328 CACAATTATT
*
2338 AATTATTAATTAAAAATA
1 AATTATTAATAAAAAATA
2356 AATTA-TAATAAAAAATA
1 AATTATTAATAAAAAATA
*
2373 AACTATT
1 AATTATT
2380 TGTTATGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTATTAATAAAAAATA
Found at i:3758 original size:17 final size:18
Alignment explanation
Indices: 3727--3768 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
3717 CACAGTTATT
*
3727 AATTATTAATTAAAAATA
1 AATTATTAATAAAAAATA
3745 AATTA-TAATAAAAAATA
1 AATTATTAATAAAAAATA
*
3762 AACTATT
1 AATTATT
3769 TGTTATGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTATTAATAAAAAATA
Found at i:5007 original size:16 final size:17
Alignment explanation
Indices: 4986--5018 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4976 TATTGATTTC
4986 AAATAG-ATAATTATTG
1 AAATAGCATAATTATTG
5002 AAATAGCCATAATTATT
1 AAATAG-CATAATTATT
5019 TGAACTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (17 bp):
AAATAGCATAATTATTG
Found at i:5275 original size:180 final size:175
Alignment explanation
Indices: 4890--5382 Score: 533
Period size: 180 Copynumber: 2.8 Consensus size: 175
4880 ACTTACTAAC
** * * *** *
4890 TTTTGAAAGGTTAATAAATTAGTGTTATTTTATTT-AGAAGCTTGTATGATAAAAAAACAATTAT
1 TTTTGAAATATTAATAAATTAGTATTATTTTATTTGATAAGCTTGTATGA-ACTGAAACAATTGT
* ** * * * * *
4954 TATATGACCGAACAAAAGGTAATATTGATTTCAAATAGATAATTATTGAAATAGCCATAATTATT
65 TTTATGACAAAACAAAAGGTCATAATGATTTTAAATAGATAATTATTCAAATAGCCATAACTATT
* * * *
5019 TGAACTAATTCAGTAAACAAAATCATTTTTTAAATCACTTGTTAAT
130 TAAACTAATTAAATAAACAAAATAATTTTTTAAATCACTTGTTAAT
*
5065 TTTTGAAATATTAATAAATTACTATTATTTTATTTCGAATAAGCTTGTATGAACTGAAACAATTG
1 TTTTGAAATATTAATAAATTAGTATTATTTTATTT-G-ATAAGCTTGTATGAACTGAAACAATTG
* *
5130 TTTTATGACAAAACCAAAGATCATAATGATTTTAAATAGATAA-TATTCAAATAGCCATAACTAT
64 TTTTATGACAAAACAAAAGGTCATAATGATTTTAAATAGATAATTATTCAAATAGCCATAACTAT
* ** * *
5194 TTAAATTTGTTAAATAAACAAATTAATTTTTTTAAA-CTCTTGCTCATTAAT
129 TTAAACTAATTAAATAAACAAAATAA-TTTTTTAAATCACTTG----TTAAT
* *
5245 TTTTGAAATATTAAGAAATTAGTATTATTTTATCTTGGATAAGCTTTTATGAACTGAAACAATTG
1 TTTTGAAATATTAATAAATTAGTATTATTTTAT-TT-GATAAGCTTGTATGAACTGAAACAATTG
* * * * * *
5310 TTTTTTTGTCAAAACAAAAGGTCATAATGATTTTAAATAAATAATTGTTCAAATAGTCACAACTA
64 -TTTTATGACAAAACAAAAGGTCATAATGATTTTAAATAGATAATTATTCAAATAGCCATAACTA
*
5375 TTTGAACT
128 TTTAAACT
5383 TGATTGGTAA
Statistics
Matches: 265, Mismatches: 42, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
175 31 0.12
176 42 0.16
177 53 0.20
178 13 0.05
180 62 0.23
181 41 0.15
182 23 0.09
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (175 bp):
TTTTGAAATATTAATAAATTAGTATTATTTTATTTGATAAGCTTGTATGAACTGAAACAATTGTT
TTATGACAAAACAAAAGGTCATAATGATTTTAAATAGATAATTATTCAAATAGCCATAACTATTT
AAACTAATTAAATAAACAAAATAATTTTTTAAATCACTTGTTAAT
Found at i:5481 original size:22 final size:22
Alignment explanation
Indices: 5443--5484 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5433 GAATGTTAAT
*
5443 AATTAAAAGTTTTAAATATTTA
1 AATTAAAAGTTTAAAATATTTA
5465 AATTAAAA-TATTAAAATATT
1 AATTAAAAGT-TTAAAATATT
5485 ATTAGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTAAAAGTTTAAAATATTTA
Found at i:6069 original size:20 final size:20
Alignment explanation
Indices: 6041--6078 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6031 TTTTATTAAT
* *
6041 ATTTCAAAAATTAATAAGAG
1 ATTTAAAAAATAAATAAGAG
6061 ATTTAAAAAATAAATAAG
1 ATTTAAAAAATAAATAAG
6079 CTTGCCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (20 bp):
ATTTAAAAAATAAATAAGAG
Found at i:6194 original size:173 final size:176
Alignment explanation
Indices: 5762--6196 Score: 425
Period size: 173 Copynumber: 2.5 Consensus size: 176
5752 CTATTTGACC
* * **
5762 AATTGTCTATTTAAAATTGTTATGACCTTTCG-TTTGTCATAAAACAATTGTTTT-AATTCATAC
1 AATTATCTATTTCAAATCATTATGACCTTTCGTTTTGTCATAAAACAATTGTTTTCAA--CATAC
*
5825 AAGCTTATTCAAAATAAAATAAAACTAATTTATTAATATTCCAAAAATTAATAACTAAGTGATTT
64 AAGCTTATT--AAATAAAATAAAACTAATTTATTAATATTCCAAAAATT-ATAACTAAGAGATTT
* * * **** * * * * *
5890 TAAAAGTTAATTTTTTTATCGAATCAGTTCAAATAGTCATGTCCATTTGAAT
126 AAAAAATAAATAAGCTTACCAAATCAGATCAAATAATCATGGCCA-TTGAAT
* * * * * ** *
5942 AGTTATCTATTTCAAATCGTTATGACCTTTTGTTTTTTCATAAAATAATTG-TTTCAGTATAAAA
1 AATTATCTATTTCAAATCATTATGACCTTTCGTTTTGTCATAAAACAATTGTTTTCAACATACAA
* * * *
6006 GCTTATGCAAAATAAAATAATACTATTTTATTAATATTTCAAAAA-T-TAA-TAAGAGATTTAAA
66 GCTTAT--TAAATAAAATAAAACTAATTTATTAATATTCCAAAAATTATAACTAAGAGATTTAAA
* * *
6068 AAATAAATAAGCTTGCCAAATTAGATCAAATAATTATGGCC-TTGAAT
129 AAATAAATAAGCTTACCAAATCAGATCAAATAATCATGGCCATTGAAT
** *
6115 AATTATCTATTTTTAATCATTATTACCTTTCGTTTTGTCATAAAACAATTGTTTTCCAACATACA
1 AATTATCTATTTCAAATCATTATGACCTTTCGTTTTGTCATAAAACAATTGTTTT-CAACATACA
6180 AGCTTATTAAATAAAAT
65 AGCTTATTAAATAAAAT
6197 TGTTATTACC
Statistics
Matches: 207, Mismatches: 42, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
173 58 0.28
174 3 0.01
175 51 0.25
176 3 0.01
178 1 0.00
179 44 0.21
180 30 0.14
181 17 0.08
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (176 bp):
AATTATCTATTTCAAATCATTATGACCTTTCGTTTTGTCATAAAACAATTGTTTTCAACATACAA
GCTTATTAAATAAAATAAAACTAATTTATTAATATTCCAAAAATTATAACTAAGAGATTTAAAAA
ATAAATAAGCTTACCAAATCAGATCAAATAATCATGGCCATTGAAT
Found at i:6833 original size:17 final size:18
Alignment explanation
Indices: 6802--6843 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
6792 CACAGTTATT
*
6802 AATTATTAATTAAAAATA
1 AATTATTAATAAAAAATA
6820 AATTA-TAATAAAAAATA
1 AATTATTAATAAAAAATA
*
6837 AACTATT
1 AATTATT
6844 TGTTATGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTATTAATAAAAAATA
Found at i:7775 original size:16 final size:18
Alignment explanation
Indices: 7744--7779 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
7734 AACAATTATT
7744 AATTATGAATTAAAAATA
1 AATTATGAATTAAAAATA
7762 AATTAT-AA-TAAAAATA
1 AATTATGAATTAAAAATA
7778 AA
1 AA
7780 CTATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AATTATGAATTAAAAATA
Found at i:8440 original size:16 final size:17
Alignment explanation
Indices: 8407--8442 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
8397 AAAAAAGGTC
*
8407 ATAATTAGTTGAAGTAA
1 ATAATTAGTTGAAATAA
8424 ATAATTA-TTGAAATAA
1 ATAATTAGTTGAAATAA
8440 ATA
1 ATA
8443 TAATTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (17 bp):
ATAATTAGTTGAAATAA
Found at i:8990 original size:16 final size:17
Alignment explanation
Indices: 8969--9001 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
8959 TATTGATTTC
8969 AAATAG-ATAATTATTG
1 AAATAGCATAATTATTG
8985 AAATAGCCATAATTATT
1 AAATAG-CATAATTATT
9002 TGAACTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (17 bp):
AAATAGCATAATTATTG
Found at i:9210 original size:177 final size:178
Alignment explanation
Indices: 8847--9365 Score: 553
Period size: 180 Copynumber: 2.9 Consensus size: 178
8837 AAATAAATTT
* * * ** * *
8847 ATTTTTTAAATTTCTTACTTACTAACTTTTGAAAGGTTAATAAATTAGTGTTATTTTA-TTC-AG
1 ATTTTTTAAA-CTC-TACTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTTCGAT
*** * * ** * * *
8910 AAGCTTGTATGATAAAAAAACAATTATTATATGACCGAACAAAAGGTAATATTGATTTCAAATAG
64 AAGCTTGTATGA-ACTGAAACAATTGTTTTATGACAAAACAAAAGGTCATAATGATTTTAAATAG
* * * * * *
8975 ATAATTATTGAAATAGCCATAATTATTTGAACTAATTCAGTAAACAAAATC
128 ATAATTATTCAAATAGCCATAACTATTTAAACTAATTAAATAAACAAAATA
*
9026 ATTTTTTAAA-TC-ACTTATTAATTTTTGAAATATTAATAAATTACTATTATTTTATTTCGAATA
1 ATTTTTTAAACTCTACTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTTCG-ATA
*
9089 AGCTTGTATGAACTGAAACAATTGTTTTATGACAAAACAAAAGATCATAATGATTTTAAATAGAT
65 AGCTTGTATGAACTGAAACAATTGTTTTATGACAAAACAAAAGGTCATAATGATTTTAAATAGAT
* * ** *
9154 AA-TATTCAAATAGCCCTAACTATTTAAATTTGTTAAATAAACAAATTA
130 AATTATTCAAATAGCCATAACTATTTAAACTAATTAAATAAACAAAATA
* * * *
9202 ATTTTTTTAAACTCTTGCTCATTAATTTTTGAAATATTAAGAAATTAGTATTATTTTATCTTGGA
1 A-TTTTTTAAACTC-TACTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTAT-TTCGA
* * *
9267 TAAGCTTTTATGAACTGAAACAATTGTTTTTTTGTCAAAACAAAAGGTCATAATGATTTTAAATA
63 TAAGCTTGTATGAACTGAAACAATTG-TTTTATGACAAAACAAAAGGTCATAATGATTTTAAATA
* * * * *
9332 AATAATTGTTCAAATAGTCACAACTATTTGAACT
127 GATAATTATTCAAATAGCCATAACTATTTAAACT
9366 TGATTGGTAA
Statistics
Matches: 285, Mismatches: 45, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
175 36 0.13
176 39 0.14
177 56 0.20
178 15 0.05
179 10 0.04
180 65 0.23
181 42 0.15
182 22 0.08
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (178 bp):
ATTTTTTAAACTCTACTTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTTCGATAA
GCTTGTATGAACTGAAACAATTGTTTTATGACAAAACAAAAGGTCATAATGATTTTAAATAGATA
ATTATTCAAATAGCCATAACTATTTAAACTAATTAAATAAACAAAATA
Found at i:9464 original size:22 final size:22
Alignment explanation
Indices: 9426--9467 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9416 GAATGTTAAT
*
9426 AATTAAAAGTTTTAAATATTTA
1 AATTAAAAGTTTAAAATATTTA
9448 AATTAAAA-TATTAAAATATT
1 AATTAAAAGT-TTAAAATATT
9468 ATTAGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTAAAAGTTTAAAATATTTA
Found at i:9515 original size:19 final size:20
Alignment explanation
Indices: 9491--9528 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9481 TGATATTTAT
9491 TAATAA-ATAAGTTATGAAA
1 TAATAATATAAGTTATGAAA
*
9510 TAATAATATAATTTATGAA
1 TAATAATATAAGTTATGAA
9529 TTTTGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (20 bp):
TAATAATATAAGTTATGAAA
Found at i:10803 original size:16 final size:17
Alignment explanation
Indices: 10773--10812 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
10763 CACAGTTATT
*
10773 AATTATTAATTAAAATA
1 AATTATTAATAAAAATA
10790 AATTA-TAATAAAAATA
1 AATTATTAATAAAAATA
*
10806 AACTATT
1 AATTATT
10813 TGTTATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTATTAATAAAAATA
Found at i:11135 original size:17 final size:16
Alignment explanation
Indices: 11095--11144 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 16
11085 ATCTATACAG
11095 TTATAATTAA-TTTAA
1 TTATAATTAATTTTAA
11110 TTA-AA-TAATTTTAA
1 TTATAATTAATTTTAA
11124 TTATCAATTAATTTATAA
1 TTAT-AATTAATTT-TAA
11142 TTA
1 TTA
11145 ATAAAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.10
14 10 0.33
15 3 0.10
16 2 0.07
17 6 0.20
18 6 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATAATTAATTTTAA
Found at i:12052 original size:16 final size:17
Alignment explanation
Indices: 12031--12063 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12021 TATTGATTTC
12031 AAATAG-ATAATTATTG
1 AAATAGCATAATTATTG
12047 AAATAGCTATAATTATT
1 AAATAGC-ATAATTATT
12064 TGAACTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (17 bp):
AAATAGCATAATTATTG
Found at i:13231 original size:173 final size:177
Alignment explanation
Indices: 12799--13233 Score: 420
Period size: 173 Copynumber: 2.5 Consensus size: 177
12789 CTATTTGACC
* * ** *
12799 AATTGTCTATTTAAAATTGTTATGACCTTTCG-TTTGTCATAAAACAATTGTTTT-AGTTCATAC
1 AATTATCTATTTCAAATCATTATGACCTTTCGTTTTGTCATAAAACAATTGTTTTCA--ACATAC
*
12862 AAGCTTATTCAAAATAAAATAAAACTAATTTACTAATATTCCAAAAATTAATAACTAAGTGATTT
64 AAGCTTATT--AAATAAAATAAAACTAATTTACTAATATTCCAAAAATT-ATAACTAAGAGATTT
* * **** * * * *
12927 AAAAAGTTAATTTTTTTATCGAATCAGTTCAAATAGTCATGTCCATTTGAAT
126 AAAAAATAAATCAGCTTACCAAATCAGTTCAAATAATCATGGCCATTTGAAT
* * * * * ** *
12979 AGTTATCTATTTCAAATCGTTATGACCTTTTGTTTTTTCATAAAATAATTG-TTTCAGTATAAAA
1 AATTATCTATTTCAAATCATTATGACCTTTCGTTTTGTCATAAAACAATTGTTTTCAACATACAA
* * * * *
13043 GCTTATGCAAAATAAAATAATACTACTTTATTAATATTTCAAAAA-T-TAA-TAAGAGATTTAAA
66 GCTTAT--TAAATAAAATAAAACTAATTTACTAATATTCCAAAAATTATAACTAAGAGATTTAAA
* * *
13105 AAATAAATCAGCTTGCCAAATTA-TATCAAATAATTATGGCC-TTT-AAT
129 AAATAAATCAGCTTACCAAATCAGT-TCAAATAATCATGGCCATTTGAAT
* *
13152 AATTATCTATTTCCAATCATTATTACCTTTCGTTTTGTCATAAAACAATTGTTTTCCAACATACA
1 AATTATCTATTTCAAATCATTATGACCTTTCGTTTTGTCATAAAACAATTGTTTT-CAACATACA
13217 AGCTTATTAAATAAAAT
65 AGCTTATTAAATAAAAT
13234 TGTTATTACC
Statistics
Matches: 208, Mismatches: 40, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
173 56 0.27
174 7 0.03
175 51 0.25
176 3 0.01
178 1 0.00
179 43 0.21
180 30 0.14
181 17 0.08
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (177 bp):
AATTATCTATTTCAAATCATTATGACCTTTCGTTTTGTCATAAAACAATTGTTTTCAACATACAA
GCTTATTAAATAAAATAAAACTAATTTACTAATATTCCAAAAATTATAACTAAGAGATTTAAAAA
ATAAATCAGCTTACCAAATCAGTTCAAATAATCATGGCCATTTGAAT
Found at i:13961 original size:18 final size:18
Alignment explanation
Indices: 13938--13982 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
13928 ATTTATTCAT
13938 AATTAATAAATAAT-TAAA
1 AATTAATAAA-AATATAAA
*
13956 AATTAATATAAATATAAA
1 AATTAATAAAAATATAAA
13974 AATTAATAA
1 AATTAATAA
13983 TTATATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTAATAAAAATATAAA
Found at i:13988 original size:18 final size:18
Alignment explanation
Indices: 13938--13988 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
13928 ATTTATTCAT
*
13938 AATTAATAAATA-ATTAAA
1 AATTAATAATTATA-TAAA
*
13956 AATTAAT-ATAAATATAAA
1 AATTAATAAT-TATATAAA
13974 AATTAATAATTATAT
1 AATTAATAATTATAT
13989 TATGAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.04
18 23 0.85
19 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTAATAATTATATAAA
Found at i:14170 original size:17 final size:16
Alignment explanation
Indices: 14130--14179 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 16
14120 ATCTATACAG
14130 TTATAATTAA-TTTAA
1 TTATAATTAATTTTAA
14145 TTA-AA-TAATTTTAA
1 TTATAATTAATTTTAA
14159 TTATCAATTAATTTATAA
1 TTAT-AATTAATTT-TAA
14177 TTA
1 TTA
14180 ATAAAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.10
14 10 0.33
15 3 0.10
16 2 0.07
17 6 0.20
18 6 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATAATTAATTTTAA
Found at i:16997 original size:14 final size:14
Alignment explanation
Indices: 16975--17013 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
16965 TATTCGTAAT
16975 TAATAAATAATTAA
1 TAATAAATAATTAA
*
16989 TAATTAATAATTATA
1 TAATAAATAATTA-A
*
17004 TTATAAATAA
1 TAATAAATAA
17014 AAGCTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATAAATAATTAA
Found at i:17158 original size:17 final size:16
Alignment explanation
Indices: 17118--17160 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
17108 ATCTATACAG
17118 TTATAATTAA-TTTAA
1 TTATAATTAATTTTAA
17133 TTA-AA-TAATTTTAA
1 TTATAATTAATTTTAA
17147 TTATCAATTAATTT
1 TTAT-AATTAATTT
17161 ATAACTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.12
14 10 0.42
15 3 0.12
16 2 0.08
17 6 0.25
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATAATTAATTTTAA
Found at i:17516 original size:18 final size:19
Alignment explanation
Indices: 17493--17537 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
17483 AAAAAGGTCT
*
17493 TAATTATTTGAAATAA-AA
1 TAATTATTTCAAATAATAA
*
17511 TAATTA-TTCAAATAATTA
1 TAATTATTTCAAATAATAA
17529 TAATTATTT
1 TAATTATTT
17538 AACTGGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 13 0.57
19 2 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TAATTATTTCAAATAATAA
Found at i:18149 original size:138 final size:141
Alignment explanation
Indices: 18007--18280 Score: 369
Period size: 142 Copynumber: 2.0 Consensus size: 141
17997 ATAATTATTG
* * * * *
18007 AAATAGCCATAATTATTTAAATTAATTCAATAAACAAAATCA-TTTTTTAAA-TC-ACTTATTAA
1 AAATACCCATAACTATTTAAATTAATTAAATAAACAAAATAATTTTTTTAAACTCTACTCATTAA
* *
18069 TTTTTGAAATATTAATAAATTACTATTATTTTAT-TTCGAATAAGCTTGTT-TGAACTGAAACAA
66 TTTTGGAAATATTAAGAAATTACTATTATTTTATCTT-GAATAAGCTT-TTATGAACTGAAACAA
18132 TTGTTTTACGACA
129 TTGTTTTACGACA
** * *
18145 AAATACCCATAACTATTTAAATTTGTTAAATAAACAAATTAATTTTTTTAAACTCTTGCTCATTA
1 AAATACCCATAACTATTTAAATTAATTAAATAAACAAAATAATTTTTTTAAACTC-TACTCATTA
* *
18210 ATTTTGGAAATATTAAGAAATTAGTATTATTTTATCTTGGATAAGCTTTTATGAACTGAAACAAT
65 ATTTTGGAAATATTAAGAAATTACTATTATTTTATCTTGAATAAGCTTTTATGAACTGAAACAAT
18275 TGTTTT
130 TGTTTT
18281 TTTGTCAAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
138 35 0.30
139 9 0.08
140 2 0.02
141 2 0.02
142 67 0.57
143 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43
Consensus pattern (141 bp):
AAATACCCATAACTATTTAAATTAATTAAATAAACAAAATAATTTTTTTAAACTCTACTCATTAA
TTTTGGAAATATTAAGAAATTACTATTATTTTATCTTGAATAAGCTTTTATGAACTGAAACAATT
GTTTTACGACA
Found at i:18448 original size:22 final size:22
Alignment explanation
Indices: 18410--18451 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
18400 GAATGTTAAT
*
18410 AATTAAAAGTTTTAAATATTTA
1 AATTAAAAGTTTAAAATATTTA
18432 AATTAAAA-TATTAAAATATT
1 AATTAAAAGT-TTAAAATATT
18452 ATTAGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTAAAAGTTTAAAATATTTA
Found at i:19799 original size:18 final size:18
Alignment explanation
Indices: 19776--19819 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
19766 CACAGTTATT
*
19776 AATTATTAATTAAAAATA
1 AATTATTAATAAAAAATA
*
19794 AATTATCAAATAAAAAATA
1 AATTAT-TAATAAAAAATA
*
19813 AACTATT
1 AATTATT
19820 TGTTATGTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTATTAATAAAAAATA
Done.