Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1712
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: 71401
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:763 original size:50 final size:50
Alignment explanation
Indices: 704--959 Score: 328
Period size: 50 Copynumber: 5.2 Consensus size: 50
694 AGTTGCTTAG
*
704 AGTCAACAATTACGGTCACCTCTCTTTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGATCACCTCTCTTTATTGTCAAAGGTTGGTGAAGAAT
* * * *
754 AGTCAACAATTATGACCACCTCT-TTGTATTGTCAAAGGTTAGTAAAGAAT
1 AGTCAACAATTACGATCACCTCTCTT-TATTGTCAAAGGTTGGTGAAGAAT
* * *
804 AGTCAACAATTACGATCACCTCTCTCTATTGTCAAAAGTTGGTAAAGAAT
1 AGTCAACAATTACGATCACCTCTCTTTATTGTCAAAGGTTGGTGAAGAAT
* *
854 AGTCAACAATTAC-AGTCA-C-CTC--TATTATCAAAGGTTTGTGAAGAAT
1 AGTCAACAATTACGA-TCACCTCTCTTTATTGTCAAAGGTTGGTGAAGAAT
* *
900 AGTCAACAATTACGACCATCTCT-TTTGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGATCACCTCTCTTT-ATTGTCAAAGGTTGGTGAAGAAT
950 AGTCAACAAT
1 AGTCAACAAT
960 GACAACGCTT
Statistics
Matches: 180, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
46 35 0.19
47 2 0.01
48 5 0.03
49 5 0.03
50 132 0.73
51 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTACGATCACCTCTCTTTATTGTCAAAGGTTGGTGAAGAAT
Found at i:941 original size:96 final size:97
Alignment explanation
Indices: 704--959 Score: 347
Period size: 96 Copynumber: 2.6 Consensus size: 97
694 AGTTGCTTAG
* *
704 AGTCAACAATTACGGTCACCTCTCTTTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTATGA
1 AGTCAACAATTACGATCACCTCTCTTTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTAAGA
*
769 CCACCTCTTTGTATTGTCAAAGGTTAGTAAAGAAT
66 CCACCTC--T-TATTATCAAAGGTTAGTAAAGAAT
* * *
804 AGTCAACAATTACGATCACCTCTCTCTATTGTCAAAAGTTGGTAAAGAATAGTCAACAATTACAG
1 AGTCAACAATTACGATCACCTCTCTTTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTA-AG
* * *
869 -TCACCTC-TATTATCAAAGGTTTGTGAAGAAT
65 ACCACCTCTTATTATCAAAGGTTAGTAAAGAAT
* *
900 AGTCAACAATTACGACCATCTCT-TTTGATTGTCAAAGGTTGGTGAAGAATAGTCAACAAT
1 AGTCAACAATTACGATCACCTCTCTTT-ATTGTCAAAGGTTGGTGAAGAATAGTCAACAAT
960 GACAACGCTT
Statistics
Matches: 140, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
95 2 0.01
96 73 0.52
100 64 0.46
101 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (97 bp):
AGTCAACAATTACGATCACCTCTCTTTATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTAAGA
CCACCTCTTATTATCAAAGGTTAGTAAAGAAT
Found at i:1927 original size:23 final size:22
Alignment explanation
Indices: 1888--1936 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1878 GGAGAATCGA
*
1888 TAAAATTTTAATGAAAAAAATT
1 TAAAATTTTAATAAAAAAAATT
* *
1910 TAAATTTTATAATAAAAATAATT
1 TAAAATTT-TAATAAAAAAAATT
1933 TAAA
1 TAAA
1937 CTCAACTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAAATTTTAATAAAAAAAATT
Found at i:1959 original size:34 final size:36
Alignment explanation
Indices: 1908--1985 Score: 133
Period size: 35 Copynumber: 2.2 Consensus size: 36
1898 ATGAAAAAAA
1908 TTTAAATTTTATAATAAAAATAATTT-AAACTCAAC
1 TTTAAATTTTATAATAAAAATAATTTAAAACTCAAC
1943 TTTAAATTTTAT-ATAAAAATAATTTAAAACTCAAC
1 TTTAAATTTTATAATAAAAATAATTTAAAACTCAAC
1978 TTATAAAT
1 TT-TAAAT
1986 GTATTTTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
34 13 0.32
35 23 0.56
36 5 0.12
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (36 bp):
TTTAAATTTTATAATAAAAATAATTTAAAACTCAAC
Found at i:2053 original size:18 final size:16
Alignment explanation
Indices: 2027--2075 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 16
2017 ATCATATAAT
2027 ATATTAATAATTATTA
1 ATATTAATAATTATTA
*
2043 ATAGTTAAATAATTTTTA
1 ATA-TT-AATAATTATTA
*
2061 ATATTATTAATTATT
1 ATATTAATAATTATT
2076 TTTATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 11 0.39
17 4 0.14
18 13 0.46
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATTAATAATTATTA
Found at i:2112 original size:8 final size:8
Alignment explanation
Indices: 2095--2145 Score: 58
Period size: 7 Copynumber: 6.9 Consensus size: 8
2085 TACTATTTTA
2095 AAAATA-T
1 AAAATATT
2102 AAAATATT
1 AAAATATT
2110 AAAATATT
1 AAAATATT
2118 -AAAT-TT
1 AAAATATT
2124 AATAATA-T
1 AA-AATATT
2132 AAAA-ATT
1 AAAATATT
2139 AAAATAT
1 AAAATAT
2146 ATATTATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
6 3 0.08
7 18 0.47
8 17 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATATT
Found at i:2113 original size:15 final size:15
Alignment explanation
Indices: 2095--2146 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
2085 TACTATTTTA
2095 AAAATATAAAATATT
1 AAAATATAAAATATT
*
2110 AAAATATTAAAT-TT
1 AAAATATAAAATATT
2124 AATAATATAAAA-ATT
1 AA-AATATAAAATATT
2139 AAAATATA
1 AAAATATA
2147 TATTATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
14 10 0.30
15 23 0.70
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATATAAAATATT
Found at i:3124 original size:23 final size:22
Alignment explanation
Indices: 3097--3139 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3087 TTAATTTAAT
3097 TTTATAAAATATGTTATTATTTA
1 TTTATAAAATATGTT-TTATTTA
*
3120 TTTATAAATTATGTTTTATT
1 TTTATAAAATATGTTTTATT
3140 GTACATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTATAAAATATGTTTTATTTA
Found at i:3148 original size:23 final size:23
Alignment explanation
Indices: 3099--3148 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3089 AATTTAATTT
**
3099 TATAAAATATGTTATTATTTATT
1 TATAAAATATGTTATTATTTACA
*
3122 TATAAATTATGTT-TTATTGTACA
1 TATAAAATATGTTATTATT-TACA
3145 TATA
1 TATA
3149 TTATATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (23 bp):
TATAAAATATGTTATTATTTACA
Found at i:5078 original size:20 final size:20
Alignment explanation
Indices: 5055--5127 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
5045 ACAATTCAAA
5055 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
5075 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
5096 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
5116 GTATCGATACAT
1 GTATCGATACAT
5128 AAAAAAGTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:5106 original size:41 final size:42
Alignment explanation
Indices: 5055--5149 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 42
5045 ACAATTCAAA
*
5055 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAG-AT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTAT
*
5096 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTAT
5138 GTATCGATACAT
1 GTATCGATACAT
5150 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 38 0.75
42 13 0.25
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTAT
Found at i:5206 original size:13 final size:13
Alignment explanation
Indices: 5188--5213 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5178 TACAGCAAGT
5188 ATGTATCGATACA
1 ATGTATCGATACA
5201 ATGTATCGATACA
1 ATGTATCGATACA
5214 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9293 original size:15 final size:15
Alignment explanation
Indices: 9273--9303 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9263 TAAAAATGTC
*
9273 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
9288 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
9303 C
1 C
9304 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:11388 original size:20 final size:21
Alignment explanation
Indices: 11309--11387 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
11299 AATGTCCAAA
*
11309 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
11329 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
11354 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
11374 TTGTATCGATACAT
1 ATGTATCGATACAT
11388 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:11392 original size:13 final size:13
Alignment explanation
Indices: 11374--11412 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
11364 ACATTTTTCT
11374 TTGTATCGATACA
1 TTGTATCGATACA
11387 TTGTATCGATACA
1 TTGTATCGATACA
*
11400 CTGTATCGATACA
1 TTGTATCGATACA
11413 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:13876 original size:20 final size:20
Alignment explanation
Indices: 13853--13925 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
13843 ACAATTCAAA
13853 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
13873 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
13894 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
13914 GTATCGATACAT
1 GTATCGATACAT
13926 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:13897 original size:21 final size:21
Alignment explanation
Indices: 13871--13946 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
13861 ACATGTTGCA
13871 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
13892 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
13912 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
13933 TTGTATCGATACAT
1 ATGTATCGATACAT
13947 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:13904 original size:41 final size:41
Alignment explanation
Indices: 13853--13946 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
13843 ACAATTCAAA
*
13853 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
13894 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
13935 GTATCGATACAT
1 GTATCGATACAT
13947 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:15236 original size:13 final size:13
Alignment explanation
Indices: 15218--15265 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
15208 AAAATTTTAT
15218 TTTCTTTTAAGAA
1 TTTCTTTTAAGAA
* *
15231 TTTCTTTTGATAA
1 TTTCTTTTAAGAA
*
15244 TTTTATTTTAAGAA
1 -TTTCTTTTAAGAA
15258 -TTCTTTTA
1 TTTCTTTTA
15266 TACATTTCGT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 7 0.25
13 11 0.39
14 10 0.36
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.60
Consensus pattern (13 bp):
TTTCTTTTAAGAA
Found at i:15259 original size:14 final size:14
Alignment explanation
Indices: 15216--15259 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
15206 GAAAAATTTT
15216 ATTTTCTTTTAAGA
1 ATTTTCTTTTAAGA
* *
15230 A-TTTCTTTTGATA
1 ATTTTCTTTTAAGA
*
15243 ATTTTATTTTAAGA
1 ATTTTCTTTTAAGA
15257 ATT
1 ATT
15260 CTTTTATACA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (14 bp):
ATTTTCTTTTAAGA
Found at i:15272 original size:26 final size:27
Alignment explanation
Indices: 15216--15272 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
15206 GAAAAATTTT
*
15216 ATTTTCTTTTAAGAATTTCTTTTGATA
1 ATTTTATTTTAAGAATTTCTTTTGATA
15243 ATTTTATTTTAAGAA-TTCTTTT-ATA
1 ATTTTATTTTAAGAATTTCTTTTGATA
15268 CATTT
1 -ATTT
15273 CGTTTTCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 3 0.11
26 11 0.39
27 14 0.50
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (27 bp):
ATTTTATTTTAAGAATTTCTTTTGATA
Found at i:15278 original size:26 final size:26
Alignment explanation
Indices: 15218--15278 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
15208 AAAATTTTAT
15218 TTTCTTTTAAGAATTTCTTTTGATAA
1 TTTCTTTTAAGAATTTCTTTTGATAA
*
15244 TTTTATTTTAAGAA-TTCTTTT-ATACA
1 -TTTCTTTTAAGAATTTCTTTTGATA-A
15270 TTTCGTTTT
1 TTTC-TTTT
15279 CATCAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 6 0.20
26 12 0.40
27 12 0.40
ACGTcount: A:0.25, C:0.08, G:0.07, T:0.61
Consensus pattern (26 bp):
TTTCTTTTAAGAATTTCTTTTGATAA
Found at i:18742 original size:19 final size:19
Alignment explanation
Indices: 18698--18753 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
18688 CTGCCAGTTT
**
18698 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
18718 CATGTATCGATGCAATGAA
1 CATGTATCGATACAATGAA
18737 CATGTATCGATACAATG
1 CATGTATCGATACAATG
18754 TATTGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:25116 original size:13 final size:13
Alignment explanation
Indices: 25098--25124 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25088 ACATAAAGTG
25098 TTGTATCGATACA
1 TTGTATCGATACA
25111 TTGTATCGATACA
1 TTGTATCGATACA
25124 T
1 T
25125 AAGTGTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:25134 original size:32 final size:32
Alignment explanation
Indices: 25079--25179 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
25069 TTCAACGATT
*
25079 TGTATCGATACATAAAGTGTTGTATCGATACAT
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
25112 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
25144 TGTATCAATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
25176 TGTA
1 TGTA
25180 AGCTACTGCC
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 52 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:25135 original size:19 final size:18
Alignment explanation
Indices: 25077--25174 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
25067 ATTTCAACGA
25077 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
25096 TGTTGTATCGATAC---A-
1 T-TTGTATCGATACATAAG
25111 -TTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
25128 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
25144 --TGTATCAATACATAAG
1 TTTGTATCGATACATAAG
25160 TTTTGTATCGATACA
1 -TTTGTATCGATACA
25175 ATGTAAGCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 22 0.34
15 2 0.03
16 2 0.03
17 2 0.03
19 24 0.38
20 12 0.19
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:25294 original size:52 final size:52
Alignment explanation
Indices: 25250--25378 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
25240 CACTGATCTT
25250 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
25302 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
25354 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
25379 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:28901 original size:13 final size:13
Alignment explanation
Indices: 28883--28908 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28873 TACAGCAAGT
28883 ATGTATCGATACA
1 ATGTATCGATACA
28896 ATGTATCGATACA
1 ATGTATCGATACA
28909 CAACAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:34699 original size:32 final size:31
Alignment explanation
Indices: 34639--34857 Score: 191
Period size: 32 Copynumber: 7.0 Consensus size: 31
34629 GGTGCCATAA
* **** *
34639 ACTTGTGTGGGCTTTGAAAAAAAATGCCACAA
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCAC-G
*
34671 ACTTGTGTGGGCTTTGAAGGGGGTTGCCAGCG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCA-CG
* *
34703 ACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCA-CG
*
34735 ACTTGTGTGGGCTTTGAATG-GGGTTGCTAGCG
1 ACTTGTGTGGGCTTTGAA-GAGGGTTGCCA-CG
* *
34767 ACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCA-CG
34799 ACTTGTGTGGGCTTT-AGAGAAGGG-TGCCACTG
1 ACTTGTGTGGGCTTTGA-AG-AGGGTTGCCAC-G
*
34831 AC-T-TGTGGGTTTTGAA-AGGG-TGCCACG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCACG
34858 GAGTTGTGGA
Statistics
Matches: 158, Mismatches: 22, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
27 1 0.01
28 10 0.06
30 10 0.06
31 4 0.03
32 127 0.80
33 6 0.04
ACGTcount: A:0.19, C:0.16, G:0.37, T:0.29
Consensus pattern (31 bp):
ACTTGTGTGGGCTTTGAAGAGGGTTGCCACG
Found at i:34837 original size:64 final size:64
Alignment explanation
Indices: 34671--34813 Score: 268
Period size: 64 Copynumber: 2.2 Consensus size: 64
34661 AATGCCACAA
34671 ACTTGTGTGGGCTTTGAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
* *
34735 ACTTGTGTGGGCTTTGAATGGGGTTGCTAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
34799 ACTTGTGTGGGCTTT
1 ACTTGTGTGGGCTTT
34814 AGAGAAGGGT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 77 1.00
ACGTcount: A:0.13, C:0.16, G:0.39, T:0.31
Consensus pattern (64 bp):
ACTTGTGTGGGCTTTGAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
Found at i:34851 original size:28 final size:28
Alignment explanation
Indices: 34676--36749 Score: 361
Period size: 27 Copynumber: 74.9 Consensus size: 28
34666 CACAAACTTG
*
34676 TGTGGGCTTTGAAGGGGGTTGCCAGC-GACT
1 TGTGGGCTTTGAA-AGGG-TGCCA-CTGACT
* *
34706 TGTGTGGACTTTGGAGAGGGTTGCCACCGACTT
1 TGTG-GG-CTTT-GAAAGGG-TGCCACTGAC-T
* *
34739 GTGTGGGCTTTGAATGGGGTTGCTAGC-GACT
1 -TGTGGGCTTTGAA-AGGG-TGCCA-CTGACT
* *
34770 TGTGTGGACTTTGGAGAGGGTTGCCACCGACTT
1 TGTG-GG-CTTT-GAAAGGG-TGCCACTGAC-T
34803 GTGTGGGCTTTAGAGAAGGGTGCCACTGACT
1 -TGTGGGCTTT-GA-AAGGGTGCCACTGACT
* * *
34834 TGTGGGTTTTGAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
34862 TGTGGAC-TTAAAACGGATGCCACTAACT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACT
* * * *
34890 TGTGGACTTTAAAAGGGTGTCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * *
34918 TGTGGGCTCTAAAAAAGAAGATGCCACTAACT
1 TGTGGGCT-T-TGAAAG--GGTGCCACTGACT
* * * *
34950 TGTGGGCTTTTGAAAAGATACCATTGACT
1 TGTGGGC-TTTGAAAGGGTGCCACTGACT
* *
34979 TGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
35007 TGTGGGCTTTGAAAGGGTGTCACT-AAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
35034 TCGTGGGCTTTGAAAGGATGTCACTGAC-
1 T-GTGGGCTTTGAAAGGGTGCCACTGACT
*
35062 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
35090 TGTGGGCTTTGCAAA-GGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * ** *
35118 TGTGAGC-TTAAAAGAATGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * * * *
35145 TGTGGTC-ATGAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
35172 TGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** * * *
35199 TATAGAATTT-AAAAGATGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * *
35226 TGTGGAC-TTAAAAGGGTGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * *
35253 TGTGGAC-TTAAAAGGGTGCCA-TGAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * **
35280 TGTGGACTTTAAAAGGGTGCCACGGGGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
35308 TATGGAC-TTAAAAAGATGCCACGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** *
35335 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
35362 TGTGGAC-TTAAAAGGATGCCAC-GAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * ** *
35389 TGTGGACTTTAAAAGGGTACCACAAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
35417 TTTGGAC-TTAAAAGGATACCACAGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
35444 TCT-GGATTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
35471 TGTGGAC-TTAAAAAGATGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
35498 TGTGGAG--TTAAAAGGGTGCCAC-GAAGT
1 TGTGG-GCTTTGAAAGGGTGCCACTG-ACT
* * * * *
35525 TGTGGACTTTAAAAGGGTGTCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
35553 TGTGGACTTTAAAAGGGTGCCAC-GAACT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * * *
35581 TGTGGAC-TTAAAAGGATGCTACGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
35608 TGTGGAC-TTAAAAGAGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
35635 TGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
35662 TATGGACCTTAAAAGGGTGCCAC-GAACT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * * * *
35690 TCTGGAC-TTAAAAGGATGCTACGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
35717 TGTGGAC-TTAAAAGAGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
35744 TGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
35771 TGTGGACTTTAAAAGGGTGCCAC-GAACT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * * * **
35799 TCTGGAC-TTAAAAGGATGCCACGGTGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
35826 TGTGGAC-TTAAAAGGATACCACGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** * *
35853 TGTGGAC-TTAAAAGAATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
35880 TGTGGAC-TTGAAAGGATGCCAC-GCACT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * *
35907 TGTGGAC-TT-AATAGGATGCCACGGAGT
1 TGTGGGCTTTGAA-AGGGTGCCACTGACT
* * * * *
35934 TGTGGTC-ATGAAAGGCTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
35961 TATGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** * * * *
35988 TATAGAATTT-AAAAGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
36015 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * * * *
36042 TGTGAAC-TTAAAAGAGCGCCAC-GAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* *
36069 TGTGGACTTTAAAAGGGTGCCAC-GAACT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * * * **
36097 TCTGGAC-TTAAAAGGATGCCACGGTGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** *
36124 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
36151 TGTGGAC-TTAAAAGGGTGTCA-TGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * * *
36178 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
36206 TATGGAC-TTAAAAGGATGCCACAGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** *
36233 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** *
36260 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
36287 TGTGGAC-TTAAAAGGGTACCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
36314 TGTGGACTTTAAAAGGGTACCACAGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
36342 TGTGGAC-TTAAAAGGATGCCACAGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
36369 TATGGAC-TTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
36396 TGTGGAC-TTAAAAGGATGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
36423 TGTGGAG--TTAAAAGGGTGCCAC-GAAGT
1 TGTGG-GCTTTGAAAGGGTGCCACTG-ACT
* * * * *
36450 TGTGGACTTTAAAAGGGTGTCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** *
36478 TGTGGACTTTAAAAGGGTGTTACGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * **
36506 TGTGGAC-TTAAAAGAGTGCCACAGAGG
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
36533 TGTGGAC-TTAAAAGGATGCCA-TAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* *
36560 TGTGGACTTTAAAAGGGTGCCAC-GCACT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * * *
36588 TATGGAC-TTAAAAGGATGCCAC-GAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * * * *
36615 TGTGGAC-TTAAAAGGATACCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
36642 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
36669 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
36696 TGTGGAC-TTAAAAGGATACCACGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
36723 TATGGACTTTAAAAGGAATGCCACTGA
1 TGTGGGCTTTGAAAGG-GTGCCACTGA
36750 ATCGTAGACT
Statistics
Matches: 1721, Mismatches: 245, Indels: 157
0.81 0.12 0.07
Matches are distributed among these distances:
26 16 0.01
27 1082 0.63
28 444 0.26
29 40 0.02
30 22 0.01
31 13 0.01
32 80 0.05
33 16 0.01
34 8 0.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:34979 original size:29 final size:28
Alignment explanation
Indices: 34935--35126 Score: 154
Period size: 28 Copynumber: 6.9 Consensus size: 28
34925 TCTAAAAAAG
* *
34935 AAGATGCCACTAACTTGTGGGCTTTTGAA
1 AAGATACCACTGACTTGTGGGC-TTTGAA
* *
34964 AAGATACCATTGACTTGTGGACTTTGAA
1 AAGATACCACTGACTTGTGGGCTTTGAA
* *
34992 AGGATGCCACTGACTTGTGGGCTTTGAA
1 AAGATACCACTGACTTGTGGGCTTTGAA
* * ** *
35020 AGGGTGTCACT-AATTCGTGGGCTTTGAA
1 AAGATACCACTGACTT-GTGGGCTTTGAA
* **
35048 AGGATGTCACTGAC-TGTGGGCTTTGAA
1 AAGATACCACTGACTTGTGGGCTTTGAA
* * * * *
35075 AGGGTGCCACTAACTTGTGGGCTTTGCA
1 AAGATACCACTGACTTGTGGGCTTTGAA
* * *
35103 AAGGTGCCACTGACTTGTGAGCTT
1 AAGATACCACTGACTTGTGGGCTT
35127 AAAAGAATGC
Statistics
Matches: 140, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
27 26 0.19
28 95 0.68
29 19 0.14
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
AAGATACCACTGACTTGTGGGCTTTGAA
Found at i:34982 original size:117 final size:116
Alignment explanation
Indices: 34823--35042 Score: 300
Period size: 117 Copynumber: 1.9 Consensus size: 116
34813 TAGAGAAGGG
* * * * *
34823 TGCCACTGACTTGTGGGTTTTGAAAGGGTGCCACGGAGTTGTGGAC-TTAAAACGGATGCCACTA
1 TGCCACTAACTTGTGGGTTTTGAAAAGATACCACGGACTTGTGGACTTTAAAA-GGATGCCACTA
34887 ACTTGTGGACTTTAAAAGGGTGTCACTAACTT-GTGGGCTCTAAAAAAGAAGA
65 ACTTGTGGACTTTAAAAGGGTGTCACTAA-TTCGTGGGCTCTAAAAAAGAAGA
** * *
34939 TGCCACTAACTTGTGGGCTTTTGAAAAGATACCATTGACTTGTGGACTTTGAAAGGATGCCACTG
1 TGCCACTAACTTGTGGG-TTTTGAAAAGATACCACGGACTTGTGGACTTTAAAAGGATGCCACTA
* *
35004 ACTTGTGGGCTTTGAAAGGGTGTCACTAATTCGTGGGCT
65 ACTTGTGGACTTTAAAAGGGTGTCACTAATTCGTGGGCT
35043 TTGAAAGGAT
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
116 18 0.20
117 67 0.74
118 5 0.06
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (116 bp):
TGCCACTAACTTGTGGGTTTTGAAAAGATACCACGGACTTGTGGACTTTAAAAGGATGCCACTAA
CTTGTGGACTTTAAAAGGGTGTCACTAATTCGTGGGCTCTAAAAAAGAAGA
Found at i:35138 original size:55 final size:56
Alignment explanation
Indices: 34804--35955 Score: 400
Period size: 54 Copynumber: 20.9 Consensus size: 56
34794 CACCGACTTG
* * ** *
34804 TGTGGGCTTTAGAGAAGGGTGCCACTGACTTGTGGGTTTTGAAAGGGTGCCACGGAGT
1 TGTGGGCTTT-GA-AAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * * *
34862 TGTGGAC-TTAAAACGGATGCCACTAACTTGTGGACTTTAAAAGGGTGTCACTAACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
** * * * * * *
34918 TGTGGGCTCTAAAAAAGAAGATGCCACTAACTTGTGGGCTTTTGAAAAGATACCATTGACT
1 TGTGGGCT-T-TGAAAG--GATGCCACTGACTTGTGGGC-TTTGAAAGGGTGCCACTAACT
* *
34979 TGTGGACTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGTCACTAA-T
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
*
35034 TCGTGGGCTTTGAAAGGATGTCACTGAC-TGTGGGCTTTGAAAGGGTGCCACTAACT
1 T-GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * ** * *
35090 TGTGGGCTTTGCAAAGG-TGCCACTGACTTGTGAGC-TTAAAAGAATGCCA-TGGAGT
1 TGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT-AACT
* * * * * * * ** *
35145 TGTGGTC-ATGAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * ** * * * * * *
35199 TATAGAATTT-AAAAGATGCCA-TGGAGTTGTGGAC-TTAAAAGGGTGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGATGCCACT-GACTTGTGGGCTTTGAAAGGGTGCCACT-AACT
* * * * * * ****
35253 TGTGGAC-TTAAAAGGGTGCCA-TGAAGTTGTGGACTTTAAAAGGGTGCCACGGGGT
1 TGTGGGCTTTGAAAGGATGCCACTG-ACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * * * * * *
35308 TATGGAC-TTAAAAAGATGCCACGGACTTGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * * * * *
35362 TGTGGAC-TTAAAAGGATGCCAC-GAAGTTGTGGACTTTAAAAGGGTACCACAAAGT
1 TGTGGGCTTTGAAAGGATGCCACTG-ACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * * * * * ** *
35417 TTTGGAC-TTAAAAGGATACCACAGACTTCT-GGATTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * * * * *
35471 TGTGGAC-TTAAAAAGATGCCACAGAGTTGTGGAG--TTAAAAGGGTGCCACGAAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGG-GCTTTGAAAGGGTGCCACTAACT
* * * * * * * * *
35525 TGTGGACTTTAAAAGGGTGTCACGGAGTTGTGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * * * * *
35581 TGTGGAC-TTAAAAGGATGCTACGGACTTGTGGAC-TTAAAAGAGTGCCAC-AGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTA-ACT
* * * * * * * * *
35635 TGTGGAC-TTAAAAGGATGCCACGGAGTTATGGACCTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * * * * * *
35690 TCTGGAC-TTAAAAGGATGCTACGGACTTGTGGAC-TTAAAAGAGTGCCAC-AGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTA-ACT
* * * * * * *
35744 TGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * ** * * * * **
35799 TCTGGAC-TTAAAAGGATGCCACGGTGTTGTGGAC-TTAAAAGGATACCACGGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * * * * **
35853 TGTGGAC-TTAAAAGAATGCCACGGAGTTGTGGAC-TTGAAAGGATGCCACGCACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
* * * * * *
35907 TGTGGAC-TT-AATAGGATGCCACGGAGTTGTGGTC-ATGAAAGGCTGCCAC
1 TGTGGGCTTTGAA-AGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
35956 GGAGTTATGG
Statistics
Matches: 922, Mismatches: 135, Indels: 78
0.81 0.12 0.07
Matches are distributed among these distances:
53 13 0.01
54 416 0.45
55 294 0.32
56 121 0.13
57 21 0.02
58 8 0.01
59 8 0.01
60 20 0.02
61 21 0.02
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACT
Found at i:35147 original size:27 final size:27
Alignment explanation
Indices: 35102--36746 Score: 1794
Period size: 27 Copynumber: 60.4 Consensus size: 27
35092 TGGGCTTTGC
* *
35102 AAAGG-TGCCACTGACTTGT-GAGCTTA
1 AAAGGATGCCACGGAGTTGTGGA-CTTA
* * * * *
35128 AAAGAATGCCATGGAGTTGTGGTCATG
1 AAAGGATGCCACGGAGTTGTGGACTTA
35155 AAAGGATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
35182 AAAGGATGCCACGGAGTTATAGAATTTA
1 AAAGGATGCCACGGAGTTGT-GGACTTA
*
35210 AAA-GATGCCATGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
35236 AAAGGGTGCCATGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
35263 AAAGGGTGCCATGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
35291 AAAGGGTGCCACGGGGTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
35318 AAAAGATGCCACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* **
35345 AAAGGGTGCCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
35372 AAAGGATGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * ** *
35400 AAAGGGTACCACAAAGTTTTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * * * *
35427 AAAGGATACCACAGACTTCTGGATTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
35454 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
35481 AAAAGATGCCACAGAGTTGTGGAGTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
35508 AAAGGGTGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* *
35536 AAAGGGTGTCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
35564 AAAGGGTGCCACGAACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
35591 AAAGGATGCTACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
35618 AAA-GAGTGCCACAGAGTTGTGGACTTA
1 AAAGGA-TGCCACGGAGTTGTGGACTTA
*
35645 AAAGGATGCCACGGAGTTATGGACCTTA
1 AAAGGATGCCACGGAGTTGTGGA-CTTA
* * * *
35673 AAAGGGTGCCACGAACTTCTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
35700 AAAGGATGCTACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
35727 AAA-GAGTGCCACAGAGTTGTGGACTTA
1 AAAGGA-TGCCACGGAGTTGTGGACTTA
35754 AAAGGATGCCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
35782 AAAGGGTGCCACGAACTTCTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
35809 AAAGGATGCCACGGTGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
35836 AAAGGATACCACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
35863 AAAGAATGCCACGGAGTTGTGGACTTG
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
35890 AAAGGATGCCACGCACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * * *
35917 ATAGGATGCCACGGAGTTGTGGTCATG
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
35944 AAAGGCTGCCACGGAGTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
35971 AAAGGATGCCACGGAGTTATAGAATTTA
1 AAAGGATGCCACGGAGTTGT-GGACTTA
35999 AAA-GATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
36025 AAAGGGTGCCACGGAGTTGTGAACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
36052 AAA-GAGCGCCACGAAGTTGTGGACTTTA
1 AAAGGA-TGCCACGGAGTTGTGGAC-TTA
* * * *
36080 AAAGGGTGCCACGAACTTCTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
36107 AAAGGATGCCACGGTGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* **
36134 AAAGGGTGCCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
36161 AAAGGGTGTCATGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* *
36189 AAAGGGTGCCACGGAGTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
36216 AAAGGATGCCACAGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* **
36243 AAAGGGTGCCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* **
36270 AAAGGGTGCCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
36297 AAAGGGTACCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
36325 AAAGGGTACCACAGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
36352 AAAGGATGCCACAGACTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
36379 AAAGGGTGCCACAGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
36406 AAAGGATGCCACAGAGTTGTGGAGTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
36433 AAAGGGTGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
36461 AAAGGGTGTCACAGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* ** *
36489 AAAGGGTGTTACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
36516 AAA-GAGTGCCACAGAGGTGTGGACTTA
1 AAAGGA-TGCCACGGAGTTGTGGACTTA
**
36543 AAAGGATGCCATAGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
36571 AAAGGGTGCCACGCACTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
36598 AAAGGATGCCACGAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
36625 AAAGGATACCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
36652 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
36679 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
36706 AAAGGATACCACGGACTTATGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
36734 AAAGGAATGCCAC
1 AAAGG-ATGCCAC
36747 TGAATCGTAG
Statistics
Matches: 1386, Mismatches: 207, Indels: 49
0.84 0.13 0.03
Matches are distributed among these distances:
26 26 0.02
27 1040 0.75
28 313 0.23
29 7 0.01
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (27 bp):
AAAGGATGCCACGGAGTTGTGGACTTA
Found at i:35347 original size:109 final size:108
Alignment explanation
Indices: 34845--36746 Score: 1876
Period size: 109 Copynumber: 17.4 Consensus size: 108
34835 GTGGGTTTTG
** * *
34845 AAAGGGTGCCACGGAGTTGTGGACTTAAAACGGATGCCACTAACTTGTGGACTTTAAAAGGGTGT
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAA-GGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
** * * ** * *
34910 CACTAACTTGTGGGCTCTAAAAAAGAAGATGCCACTAACTTGTGGGCTTTTGA
64 CACGGAGTTGTGGACT-T--AAAAG--GATGCCACGGAGTTGTGGAC--TT-A
* * ** * * * * * * *
34963 AAA-GATACCATTGACTTGTGGACTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGT
1 AAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
* * * * * * * * *
35027 CAC-TAATTCGTGGGCTTTGAAAGGATGTCACTGA-CTGTGGGCTTTG
64 CACGGAGTT-GTGGAC-TTAAAAGGATGCCACGGAGTTGTGGAC-TTA
** * * * * * **
35073 AAAGGGTGCCACTAACTTGTGGGCTTTGCAAAGG-TGCCACTGACTTGT-GAGCTTAAAAGAATG
1 AAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGATGCCACGGAGTTGTGGA-CTTAAAAGGGTG
* * * *
35136 CCATGGAGTTGTGGTCATGAAAGGATGCCACGGAGTTGTGGACTTA
63 CCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * *
35182 AAAGGATGCCACGGAGTTATAGAATTTAAAA-GATGCCATGGAGTTGTGGACTTAAAAGGGTGCC
1 AAAGGGTGCCACGGAGTTGT-GGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * * *
35246 ATGGAGTTGTGGACTTAAAAGGGTGCCATGAAGTTGTGGACTTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
35291 AAAGGGTGCCACGGGGTTATGGACTTAAAAAGATGCCACGGACTTGTGGACTTAAAAGGGTGCCA
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
** *
35356 CAAAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* ** * * * * * *
35400 AAAGGGTACCACAAAGTTTTGGACTTAAAAGGATACCACAGACTTCTGGATTTAAAAGGGTGCCA
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * *
35465 CGGAGTTGTGGACTTAAAAAGATGCCACAGAGTTGTGGAGTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * *
35508 AAAGGGTGCCACGAAGTTGTGGACTTTAAAAGGGTGTCACGGAGTTGTGGACTTTAAAAGGGTGC
1 AAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
* * * *
35573 CACGAACTTGTGGACTTAAAAGGATGCTACGGACTTGTGGACTTA
64 CACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * *
35618 AAAGAGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACCTTAAAAGGGTGCC
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGA-CTTAAAAGGGTGCC
* * * * *
35683 ACGAACTTCTGGACTTAAAAGGATGCTACGGACTTGTGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* *
35727 AAAGAGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGCC
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCC
* * * *
35792 ACGAACTTCTGGACTTAAAAGGATGCCACGGTGTTGTGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * * *
35836 AAAGGATACCACGGACTTGTGGACTTAAAAGAATGCCACGGAGTTGTGGACTTGAAAGGATGCCA
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * * * *
35901 CGCACTTGTGGACTTAATAGGATGCCACGGAGTTGTGGTCATG
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * * *
35944 AAAGGCTGCCACGGAGTTATGGACTTAAAAGGATGCCACGGAGTTATAGAATTTAAAA-GATGCC
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT-GGACTTAAAAGGGTGCC
* *
36008 ACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGAACTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * * * * *
36052 AAAGAGCGCCACGAAGTTGTGGACTTTAAAAGGGTGCCACGAACTTCTGGACTTAAAAGGATGCC
1 AAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * **
36117 ACGGTGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * *
36161 AAAGGGTGTCATGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGGATGCC
1 AAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * * **
36226 ACAGACTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
** * * *
36270 AAAGGGTGCCACAAAGTTGTGGACTTAAAAGGGTACCACGGAGTTGTGGACTTTAAAAGGGTACC
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCC
* * * * *
36335 ACAGACTTGTGGACTTAAAAGGATGCCACAGACTTATGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * *
36379 AAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGAGTTAAAAGGGTGCCA
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * *
36444 CGAAGTTGTGGACTTTAAAAGGGTGTCACAGAGTTGTGGACTTTA
66 CGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGAC-TTA
** * * * *
36489 AAAGGGTGTTACGGACTTGTGGACTTAAAA-GAGTGCCACAGAGGTGTGGACTTAAAAGGATGCC
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA-TGCCACGGAGTTGTGGACTTAAAAGGGTGCC
** * * * *
36553 ATAGAGTTGTGGACTTTAAAAGGGTGCCACGCACTTATGGACTTA
65 ACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTA
* * *
36598 AAAGGATGCCACGAAGTTGTGGACTTAAAAGGATACCACGGAGTTGTGGACTTAAAAGGGTGCCA
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
*
36663 CGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * *
36706 AAAGGATACCACGGACTTATGGACTTTAAAAGGAATGCCAC
1 AAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGG-ATGCCAC
36747 TGAATCGTAG
Statistics
Matches: 1528, Mismatches: 229, Indels: 62
0.84 0.13 0.03
Matches are distributed among these distances:
107 1 0.00
108 347 0.23
109 851 0.56
110 197 0.13
111 39 0.03
112 12 0.01
113 9 0.01
115 4 0.00
116 3 0.00
117 56 0.04
118 9 0.01
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (108 bp):
AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
Found at i:38093 original size:20 final size:18
Alignment explanation
Indices: 38068--38130 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 18
38058 TGTCCTTGTT
38068 TTTTTATTTTTGTTGTTCCA
1 TTTTTATTTTTGTT-TT-CA
38088 TTTTTA-TTTTGTTTTTGCA
1 TTTTTATTTTTG-TTTT-CA
*
38107 CTTTTTATTTTTCTTTTCA
1 -TTTTTATTTTTGTTTTCA
38126 TTTTT
1 TTTTT
38131 TGTGCTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 5 0.13
19 11 0.29
20 18 0.47
21 4 0.11
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTTATTTTTGTTTTCA
Found at i:38097 original size:19 final size:20
Alignment explanation
Indices: 38068--38117 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
38058 TGTCCTTGTT
38068 TTTTTATTTTTGTTGTTCCA-
1 TTTTTA-TTTTGTTGTTCCAC
* *
38088 TTTTTATTTTGTTTTTGCAC
1 TTTTTATTTTGTTGTTCCAC
38108 TTTTTATTTT
1 TTTTTATTTT
38118 TCTTTTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.74
Consensus pattern (20 bp):
TTTTTATTTTGTTGTTCCAC
Found at i:44742 original size:22 final size:22
Alignment explanation
Indices: 44716--44770 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
44706 TTTTTCTTTG
44716 TTTCT-ATTTCTTCTCTCTTTTT
1 TTTCTCATTT-TTCTCTCTTTTT
* *
44738 TTTCTCCTTTTTTTCTCTTTTT
1 TTTCTCATTTTTCTCTCTTTTT
*
44760 TTT-TCTTTTTT
1 TTTCTCATTTTT
44771 TTAGTTGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.24
22 19 0.66
23 3 0.10
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTCTCATTTTTCTCTCTTTTT
Found at i:44771 original size:22 final size:24
Alignment explanation
Indices: 44726--44772 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
44716 TTTCTATTTC
44726 TTCTCTCTTTTTTTTCTCCTTTTT
1 TTCTCTCTTTTTTTTCTCCTTTTT
44750 TTCTCT-TTTTTTTTCT--TTTTT
1 TTCTCTCTTTTTTTTCTCCTTTTT
44771 TT
1 TT
44773 AGTTGAACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.30
23 10 0.43
24 6 0.26
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTCTCTCTTTTTTTTCTCCTTTTT
Found at i:44772 original size:10 final size:10
Alignment explanation
Indices: 44731--44772 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
44721 ATTTCTTCTC
44731 TCTTTTTTTT
1 TCTTTTTTTT
*
44741 CTCCTTTTTTTC
1 -T-CTTTTTTTT
44753 TCTTTTTTTT
1 TCTTTTTTTT
44763 TCTTTTTTTT
1 TCTTTTTTTT
44773 AGTTGAACCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 18 0.64
11 2 0.07
12 8 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:44772 original size:11 final size:11
Alignment explanation
Indices: 44733--44772 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
44723 TTCTTCTCTC
*
44733 TTTTTTTTCTC
1 TTTTTTTTCTT
*
44744 CTTTTTTTCTCT
1 TTTTTTTTCT-T
44756 TTTTTTTTCTT
1 TTTTTTTTCTT
44767 TTTTTT
1 TTTTTT
44773 AGTTGAACCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:46658 original size:20 final size:21
Alignment explanation
Indices: 46633--46681 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
46623 GCACTCGTTA
46633 GATGAAAAGACATACTT-TTG
1 GATGAAAAGACATACTTGTTG
**
46653 GATGAAAAGATGTACTTGTTG
1 GATGAAAAGACATACTTGTTG
*
46674 GACGAAAA
1 GATGAAAA
46682 AAATTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (21 bp):
GATGAAAAGACATACTTGTTG
Found at i:52249 original size:20 final size:20
Alignment explanation
Indices: 52224--52277 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
52214 CTACCACTGT
* *
52224 TTGTATCGATACATGGTCCA
1 TTGTATCGATACATGATCAA
*
52244 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATCAA
52264 TTGTATCGATACAT
1 TTGTATCGATACAT
52278 TGCTTGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATCAA
Found at i:54525 original size:21 final size:20
Alignment explanation
Indices: 54491--54533 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
54481 TATTAAAAAG
*
54491 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
54512 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
54532 TT
1 TT
54534 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:54532 original size:20 final size:21
Alignment explanation
Indices: 54491--54533 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
54481 TATTAAAAAG
*
54491 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
54512 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
54532 TT
1 TT
54534 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:56886 original size:33 final size:34
Alignment explanation
Indices: 56823--56888 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
56813 TATTACAAGC
*
56823 AATGTATCGATACAATTTCATCATGTATCGATAT
1 AATGTATCGATACAATTTCACCATGTATCGATAT
56857 AATGTATCGATAC-ATTGTC-CCATGTATCGATA
1 AATGTATCGATACAATT-TCACCATGTATCGATA
56889 CAAACAGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (34 bp):
AATGTATCGATACAATTTCACCATGTATCGATAT
Found at i:59485 original size:13 final size:13
Alignment explanation
Indices: 59466--59507 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
59456 AAATAGTACC
59466 CAATGTATCGATA
1 CAATGTATCGATA
* *
59479 TAATGTATTGATA
1 CAATGTATCGATA
*
59492 CATTGTATCGATA
1 CAATGTATCGATA
59505 CAA
1 CAA
59508 GGAATGTTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:65014 original size:13 final size:13
Alignment explanation
Indices: 64996--65052 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
64986 CATAAAGTGT
64996 TGTATCGATACAA
1 TGTATCGATACAA
65009 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
65024 GTGTTGTACCGATACAA
1 ----TGTATCGATACAA
65041 TGTATCGATACA
1 TGTATCGATACA
65053 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:65031 original size:32 final size:32
Alignment explanation
Indices: 64978--65073 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
64968 CAATGATTTA
64978 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACAT-AAGTGTTGTATCGATACAATG
*
65011 TATCGATACATAAGTGTTGTACCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
*
65043 TATCGATACATAAGTTTTGTATCGATACAAT
1 TATCGATACATAAGTGTTGTATCGATACAAT
65074 TTAAGCTACT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 49 0.82
33 11 0.18
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATG
Found at i:65065 original size:19 final size:18
Alignment explanation
Indices: 64978--65071 Score: 73
Period size: 19 Copynumber: 5.6 Consensus size: 18
64968 CAATGATTTA
64978 TATCGATACATAAAGTGTTG
1 TATCGATACAT-AAGT-TTG
64998 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
65011 TATCGATACATAAGTGTTG
1 TATCGATACATAAGT-TTG
*
65030 TACCGATAC--AA---TG
1 TATCGATACATAAGTTTG
65043 TATCGATACATAAGTTTTG
1 TATCGATACATAAG-TTTG
65062 TATCGATACA
1 TATCGATACA
65072 ATTTAAGCTA
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
13 21 0.35
15 4 0.07
17 4 0.07
19 22 0.37
20 9 0.15
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
TATCGATACATAAGTTTG
Found at i:65132 original size:13 final size:13
Alignment explanation
Indices: 65114--65138 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65104 ATTACTCAAA
65114 TGTATCGATACAT
1 TGTATCGATACAT
65127 TGTATCGATACA
1 TGTATCGATACA
65139 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:65191 original size:52 final size:51
Alignment explanation
Indices: 65127--65275 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
65117 ATCGATACAT
**
65127 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
65179 TGTATCGATACACTA-CAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATC--AATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
65231 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTT
65276 TCATATTTCG
Statistics
Matches: 90, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 88 0.98
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:69390 original size:13 final size:13
Alignment explanation
Indices: 69349--69397 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
69339 CCGTTACAAG
69349 CAATGTATCGATA
1 CAATGTATCGATA
69362 CAAT-T-TC-AT-
1 CAATGTATCGATA
69371 C-ATGTATCGATA
1 CAATGTATCGATA
69383 CAATGTATCGATA
1 CAATGTATCGATA
69396 CA
1 CA
69398 TTGTCCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 4 0.13
12 2 0.06
13 17 0.55
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:69413 original size:33 final size:34
Alignment explanation
Indices: 69349--69418 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
69339 CCGTTACAAG
*
69349 CAATGTATCGATACAATTTCATCATGTATCGATA
1 CAATGTATCGATACAATTTCACCATGTATCGATA
69383 CAATGTATCGATAC-ATTGTC-CCATGTATCGATA
1 CAATGTATCGATACAATT-TCACCATGTATCGATA
69416 CAA
1 CAA
69419 ACAGTGGTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 18 0.53
34 16 0.47
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (34 bp):
CAATGTATCGATACAATTTCACCATGTATCGATA
Done.