Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005518.1 Hibiscus syriacus cultivar Beakdansim tig00012750_pilon, 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: 63133
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2996 original size:2 final size:2
Alignment explanation
Indices: 2989--3033 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
2979 AATGTTTTTA
2989 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3029 AT AT A
1 AT AT A
3034 AGTTTTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8229 original size:17 final size:17
Alignment explanation
Indices: 8209--8264 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
8199 GAAAGTCAAC
8209 GGTCAACGGTCCGGTCG
1 GGTCAACGGTCCGGTCG
*
8226 GGTC--GGGTCAACGGTCG
1 GGTCAACGGTC--CGGTCG
**
8243 GGTCAACGGTTGGGTCG
1 GGTCAACGGTCCGGTCG
8260 GGTCA
1 GGTCA
8265 GACCGGTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 4 0.13
17 24 0.77
19 3 0.10
ACGTcount: A:0.12, C:0.23, G:0.45, T:0.20
Consensus pattern (17 bp):
GGTCAACGGTCCGGTCG
Found at i:8241 original size:12 final size:12
Alignment explanation
Indices: 8209--8258 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
8199 GAAAGTCAAC
*
8209 GGTCAACGGTCC
1 GGTCAACGGTCG
*
8221 GGTC--GGGTCG
1 GGTCAACGGTCG
8231 GGTCAACGGTCG
1 GGTCAACGGTCG
*
8243 GGTCAACGGTTG
1 GGTCAACGGTCG
8255 GGTC
1 GGTC
8259 GGGTCAGACC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 8 0.25
12 24 0.75
ACGTcount: A:0.12, C:0.24, G:0.44, T:0.20
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:8316 original size:10 final size:10
Alignment explanation
Indices: 8266--8359 Score: 81
Period size: 9 Copynumber: 9.7 Consensus size: 10
8256 GTCGGGTCAG
8266 ACCGG-TCAA
1 ACCGGTTCAA
* *
8275 ATCGGTTCAG
1 ACCGGTTCAA
8285 ACCGG-TCAA
1 ACCGGTTCAA
* *
8294 ACCGATTCGA
1 ACCGGTTCAA
*
8304 ACCGGTTGAA
1 ACCGGTTCAA
8314 ACCGG-TCAA
1 ACCGGTTCAA
8323 ACCGG-TCAGA
1 ACCGGTTCA-A
*
8333 ACCGGTTGAAA
1 ACCGGTT-CAA
8344 ACCGGTT-AA
1 ACCGGTTCAA
8353 ACCGGTT
1 ACCGGTT
8360 TCCAGCAGCG
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
9 31 0.45
10 28 0.41
11 9 0.13
12 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.18
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:8337 original size:19 final size:19
Alignment explanation
Indices: 8260--8358 Score: 71
Period size: 19 Copynumber: 5.2 Consensus size: 19
8250 GGTTGGGTCG
*
8260 GGTCAG-ACCGGTCAAATC
1 GGTCAGAACCGGTCAAACC
8278 GGTTCAG-ACCGGTCAAACC
1 GG-TCAGAACCGGTCAAACC
* *
8297 GATTC-GAACCGGTTGAAACC
1 G-GTCAGAACCGG-TCAAACC
8317 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
8336 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
8356 GGT
1 GGT
8359 TTCCAGCAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.08
19 38 0.58
20 15 0.23
21 8 0.12
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.17
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:15543 original size:22 final size:22
Alignment explanation
Indices: 15518--15582 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
15508 GAAAGTCAAC
15518 GGTCAACGGTCCGGTCGGGTCG
1 GGTCAACGGTCCGGTCGGGTCG
15540 GGTCAACGGTCCGGTCGGGTCG
1 GGTCAACGGTCCGGTCGGGTCG
*
15562 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCCGGTCGGGTC
15583 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.09, C:0.26, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCCGGTCGGGTCG
Found at i:15571 original size:17 final size:17
Alignment explanation
Indices: 15551--15583 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
15541 GTCAACGGTC
15551 CGGTCGGGTCGGGTCAA
1 CGGTCGGGTCGGGTCAA
15568 CGGTCGGGTCGGGTCA
1 CGGTCGGGTCGGGTCA
15584 GACCGGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.24, G:0.48, T:0.18
Consensus pattern (17 bp):
CGGTCGGGTCGGGTCAA
Found at i:15603 original size:19 final size:19
Alignment explanation
Indices: 15581--15695 Score: 160
Period size: 19 Copynumber: 6.1 Consensus size: 19
15571 TCGGGTCGGG
15581 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
15600 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* * *
15619 TGAAACCGGTCAAACCAGT
1 TCAGACCGGTCAAACCGGT
15638 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
15657 TGAAACCGGTCAAACCGG-
1 TCAGACCGGTCAAACCGGT
*
15675 TCAGAACCGGTTAAACCGGT
1 TCAG-ACCGGTCAAACCGGT
15695 T
1 T
15696 TCCAGCAGCC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
18 2 0.02
19 80 0.96
20 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:15627 original size:38 final size:38
Alignment explanation
Indices: 15585--15695 Score: 188
Period size: 38 Copynumber: 2.9 Consensus size: 38
15575 GTCGGGTCAG
15585 ACCGGTCAAACCGGTTCAGACCGGTCAAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAGACCGGTCAAACCGGTTGAA
*
15623 ACCGGTCAAACCAGTTCAGACCGGTCAAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAGACCGGTCAAACCGGTTGAA
*
15661 ACCGGTCAAACCGG-TCAGAACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTTCAG-ACCGGTCAAACCGGTT
15696 TCCAGCAGCC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
37 4 0.06
38 65 0.94
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (38 bp):
ACCGGTCAAACCGGTTCAGACCGGTCAAACCGGTTGAA
Found at i:19780 original size:15 final size:16
Alignment explanation
Indices: 19749--19781 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19739 CATGTGTAAA
19749 TATTAAATATCAAAGT
1 TATTAAATATCAAAGT
*
19765 TATTATATAT-AAAGT
1 TATTAAATATCAAAGT
19780 TA
1 TA
19782 AACAATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (16 bp):
TATTAAATATCAAAGT
Found at i:21391 original size:18 final size:18
Alignment explanation
Indices: 21360--21409 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
21350 AAGTTATTTG
21360 TATATAAATTTTATTAAATA
1 TATATAAA-TTTA-TAAATA
21380 TATATAAA-TTATAAATA
1 TATATAAATTTATAAATA
* *
21397 -ATAGAAACTTATA
1 TATATAAATTTATA
21410 TGAATTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.21
17 11 0.39
18 3 0.11
20 8 0.29
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TATATAAATTTATAAATA
Found at i:21397 original size:62 final size:63
Alignment explanation
Indices: 21330--21458 Score: 147
Period size: 62 Copynumber: 2.1 Consensus size: 63
21320 AAAGATTAAA
* * * * *
21330 AAATAATA-AAAATATATATTAAGTTATTTGTATATAAATTTTATTAAA-TATATATA-AATTAT
1 AAATAATAGAAAAT-TATATGAAGTTATTTGTATA-AAAATATAATAAATTATAAATATAATTAT
* * *
21392 AAATAATAGAAACTTATATGAATTTATTTGTGTAAAAATATAATAAATTATAAATATAATTAT
1 AAATAATAGAAAATTATATGAAGTTATTTGTATAAAAATATAATAAATTATAAATATAATTAT
21455 AAAT
1 AAAT
21459 TTAATTTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
61 10 0.18
62 32 0.57
63 14 0.25
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.42
Consensus pattern (63 bp):
AAATAATAGAAAATTATATGAAGTTATTTGTATAAAAATATAATAAATTATAAATATAATTAT
Found at i:21975 original size:18 final size:18
Alignment explanation
Indices: 21952--21987 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21942 TTAATATATA
21952 AATAAATAAACTAAAATT
1 AATAAATAAACTAAAATT
21970 AATAAATAAACTAAAATT
1 AATAAATAAACTAAAATT
21988 GATAGTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAATAAACTAAAATT
Found at i:22261 original size:16 final size:16
Alignment explanation
Indices: 22240--22270 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22230 TACAAAATTT
22240 AATAATTCATAATATA
1 AATAATTCATAATATA
*
22256 AATAATTCATTATAT
1 AATAATTCATAATAT
22271 TTTATATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:22983 original size:45 final size:45
Alignment explanation
Indices: 22955--23044 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
22945 GATAAATTTG
* *
22955 AAAATATAATATACTATTTTATTATTATAATTATATTATTATTAT
1 AAAATATAATATAATATTTTATTATTATAATTATATTATAATTAT
*
23000 AAAATATAATATAATATTTTATT-TTAGTAA-TATATAATAAATTAT
1 AAAATATAATATAATATTTTATTATTA-TAATTATATTAT-AATTAT
23045 TAATAAAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
44 10 0.25
45 30 0.75
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (45 bp):
AAAATATAATATAATATTTTATTATTATAATTATATTATAATTAT
Found at i:23039 original size:26 final size:26
Alignment explanation
Indices: 22980--23053 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 26
22970 ATTTTATTAT
*
22980 TATAATTATATTATTATTATAAAATA
1 TATAATAATATTATTATTATAAAATA
* *
23006 TA-ATATAATATT-TTATTTTAGTAATA
1 TATA-ATAATATTATTATTATA-AAATA
23032 TATAATAA-ATTATTA--ATAAAAT
1 TATAATAATATTATTATTATAAAAT
23054 CAATATTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
23 3 0.08
24 2 0.05
25 11 0.28
26 22 0.56
27 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TATAATAATATTATTATTATAAAATA
Found at i:23045 original size:28 final size:29
Alignment explanation
Indices: 22980--23045 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
22970 ATTTTATTAT
*
22980 TATAATTATATTATTATTATAAAATATAA
1 TATAATTATTTTATTATTATAAAATATAA
*
23009 TATAA-TATTTTATT-TTAGTAATATATAA
1 TATAATTATTTTATTATTA-TAAAATATAA
23037 TA-AATTATT
1 TATAATTATT
23046 AATAAAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 5 0.15
28 23 0.70
29 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TATAATTATTTTATTATTATAAAATATAA
Found at i:23221 original size:39 final size:41
Alignment explanation
Indices: 23159--23241 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 41
23149 TAATTCATTA
23159 TTATTTTAATAAATAACTAATATAATTAAT-ATATATTTT-T
1 TTATTTTAATAAATAACTAATATAATTAATAATA-ATTTTAT
* *
23199 TTATTTTAAT-AATAAGTAATATAATTTATAATAATTTTAT
1 TTATTTTAATAAATAACTAATATAATTAATAATAATTTTAT
23239 TTA
1 TTA
23242 ATAAATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 22 0.56
40 17 0.44
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (41 bp):
TTATTTTAATAAATAACTAATATAATTAATAATAATTTTAT
Found at i:25409 original size:14 final size:15
Alignment explanation
Indices: 25379--25410 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
25369 ATCTTTTAAT
25379 AATAATATTAAAATA
1 AATAATATTAAAATA
25394 AATAATA-TAAAATA
1 AATAATATTAAAATA
25408 AAT
1 AAT
25411 TCTTCTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAATATTAAAATA
Found at i:34867 original size:19 final size:19
Alignment explanation
Indices: 34843--34884 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
34833 TTAATGTGAA
34843 AATTTAATAATATATTGAC
1 AATTTAATAATATATTGAC
* *
34862 AATTTAATAATATGTTGTC
1 AATTTAATAATATATTGAC
34881 AATT
1 AATT
34885 GGATGGACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (19 bp):
AATTTAATAATATATTGAC
Found at i:35208 original size:19 final size:20
Alignment explanation
Indices: 35184--35231 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
35174 TTTATTTTTT
35184 TAAAATTAGAAAATA-AAAA
1 TAAAATTAGAAAATACAAAA
* **
35203 TAAAATTTGTGAATACAAAA
1 TAAAATTAGAAAATACAAAA
35223 -AAAATTAGA
1 TAAAATTAGA
35232 CGAAACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (20 bp):
TAAAATTAGAAAATACAAAA
Found at i:35337 original size:14 final size:15
Alignment explanation
Indices: 35309--35340 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
35299 GTCAAAATAC
35309 AAATAAAATTTTTAA
1 AAATAAAATTTTTAA
35324 AAATAAAA-TTTTAA
1 AAATAAAATTTTTAA
35338 AAA
1 AAA
35341 AATGAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATAAAATTTTTAA
Found at i:35341 original size:15 final size:15
Alignment explanation
Indices: 35309--35341 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35299 GTCAAAATAC
*
35309 AAATAAAATTTTTAA
1 AAATAAAATTTTAAA
35324 AAATAAAATTTTAAA
1 AAATAAAATTTTAAA
35339 AAA
1 AAA
35342 ATGAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATAAAATTTTAAA
Found at i:38128 original size:11 final size:11
Alignment explanation
Indices: 38112--38137 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38102 ATCCATCTTT
38112 AAAAGATTCAC
1 AAAAGATTCAC
38123 AAAAGATTCAC
1 AAAAGATTCAC
38134 AAAA
1 AAAA
38138 CTGTTGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAGATTCAC
Found at i:39041 original size:11 final size:11
Alignment explanation
Indices: 39025--39050 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39015 ATCCATCTTT
39025 AAAAGATTCAC
1 AAAAGATTCAC
39036 AAAAGATTCAC
1 AAAAGATTCAC
39047 AAAA
1 AAAA
39051 CTGTTGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAGATTCAC
Found at i:39949 original size:11 final size:11
Alignment explanation
Indices: 39933--39958 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39923 ATCCATCTTT
39933 AAAAGATTCAC
1 AAAAGATTCAC
39944 AAAAGATTCAC
1 AAAAGATTCAC
39955 AAAA
1 AAAA
39959 CTGTTGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAGATTCAC
Found at i:40102 original size:910 final size:912
Alignment explanation
Indices: 37655--40395 Score: 5418
Period size: 913 Copynumber: 3.0 Consensus size: 912
37645 AATGACCTAC
37655 ATAAGGCCCACTACTCAGGAACCATTTAAAAATAATATTCGAGTTTAATATATATATACTGTAGC
1 ATAAGGCCCACTACTCAGGAACCATTTAAAAATAATATTCGAGTTTAATATATATATACTGTAGC
37720 AATTGTCGTGTTGTCACTATGTACACTGTAGCAATTGTCGTAATTTTCAAAATAAAAATTTGAGA
66 AATTGTCGTGTTGTCACTATGTACACTGTAGCAATTGTCGTAATTTTCAAAATAAAAATTTGAGA
37785 GGCCCAATAACATAAATAATTGATCCGCTTGGGGTATTGTACCAAAAAAACCCAGTAACTTTTGA
131 GGCCCAATAACATAAATAATTGATCCGCTTGGGGTATTGTACCAAAAAAACCCAGTAACTTTTGA
37850 TATGCTAAATATAAGATTTAAAATTTTGAGTTAAAATCAATTTGTAGCAAACGTTTTAGATAAAA
196 TATGCTAAATATAAGATTTAAAATTTTGAGTTAAAATCAATTTGTAGCAAACGTTTTAGATAAAA
37915 ATTGTTTTATATTCAAATCAATTGAGTTTGAGGAGATTTGAATACGTAGACAGTTAAGACATTTT
261 ATTGTTTTATATTCAAATCAATTGAGTTTGAGGAGATTTGAATACGTAGACAGTTAAGACATTTT
37980 ATAATAAATTCTTGGGTAAATTTTATATTTAGTTATCAAACTATCACTTTGATTCTATTTTGATC
326 ATAATAAATTCTTGGGTAAATTTTATATTTAGTTATCAAACTATCACTTTGATTCTATTTTGATC
38045 ATCCAACTATTATTTTTTAAAGTATCATTAACTTCACATTTTAATTTCATTTTAGTTATCCATCT
391 ATCCAACTATTATTTTTTAAAGTATCATTAACTTCACATTTTAATTTCATTTTAGTTATCCATCT
38110 TTAAAAGATTCACAAAAGATTCACAAAACTGTTGGCCTGAATTTTATTATTATTTTTAATGATGA
456 TTAAAAGATTCACAAAAGATTCACAAAACTGTTGGCCTGAATTTTATTATTATTTTTAATGATGA
38175 CATGATATTACCTTATGATGACACATAAAAAACACCATTAATTTTTTAACGACTGGTGACTAAAA
521 CATGATATTACCTTATGATGACACATAAAAAACACCATTAATTTTTTAACGACTGGTGACTAAAA
38240 TGAAATCAAAATTTAATGATAGTGATGATTTTGAAAAAAAAAATTGACCACAACAGAACCAAAAT
586 TGAAATCAAAATTTAATGATAGTGATGATTTTGAAAAAAAAAATTGACCACAACAGAACCAAAAT
38305 GATAGTTGGGTGGGTGACTAAATAAGTAGACTACTCTAAATACTTTAAAGACGCATGTTTTCCAG
651 GATAGTTGGGTGGGTGACTAAATAAGTA-ACTACTCTAAATACTTTAAAGACGCATGTTTTCCAG
38370 AACTGAAAACCCAACAGCATACATTGCAACACAGTCATGGAGAACTTATTATTACCATTTTCGTC
715 AACTGAAAACCCAACAGCATACATTGCAACACAGTCATGGAGAACTTATTATTACCATTTTCGTC
38435 CCTCTAACTTGTTAAAGTTCTATAGTTTCATTGTCTTTTTTCCCTTCTGAATTTCATCCGCAATC
780 CCTCTAACTTGTTAAAGTTCTATAGTTTCATTGTCTTTTTTCCCTTCTGAATTTCATCCGCAATC
38500 CAATCAGACTTTTCCTACAACTACCCATTTTCAGGCCATCTCAATGATCCAGTAACAGCAGCTGT
845 CAATCAGACTTTTCCTACAACTACCCATTTTCAGGCCATCTCAATGATCCAGTAACAGCAGCTGT
38565 GGA
910 GGA
38568 ATAAGGCCCACTACTCAGGAACCATTTAAAAATAATATTCGAGTTTAATATATATATACTGTAGC
1 ATAAGGCCCACTACTCAGGAACCATTTAAAAATAATATTCGAGTTTAATATATATATACTGTAGC
38633 AATTGTCGTGTTGTCACTATGTACACTGTAGCAATTGTCGTAATTTTCAAAATAAAAATTTGAGA
66 AATTGTCGTGTTGTCACTATGTACACTGTAGCAATTGTCGTAATTTTCAAAATAAAAATTTGAGA
38698 GGCCCAATAACATAAATAATTGATCCGCTTGGGGTATTGTACCAAAAAAACCCAGTAACTTTTGA
131 GGCCCAATAACATAAATAATTGATCCGCTTGGGGTATTGTACCAAAAAAACCCAGTAACTTTTGA
38763 TATGCTAAATATAAGATTTAAAATTTTGAGTTAAAATCAATTTGTAGCAAACGTTTTAGATAAAA
196 TATGCTAAATATAAGATTTAAAATTTTGAGTTAAAATCAATTTGTAGCAAACGTTTTAGATAAAA
38828 ATTGTTTTATATTCAAATCAATTGAGTTTGAGGAGATTTGAATACGTAGACAGTTAAGACATTTT
261 ATTGTTTTATATTCAAATCAATTGAGTTTGAGGAGATTTGAATACGTAGACAGTTAAGACATTTT
38893 ATAATAAATTCTTGGGTAAATTTTATATTTAGTTATCAAACTATCACTTTGATTCTATTTTGATC
326 ATAATAAATTCTTGGGTAAATTTTATATTTAGTTATCAAACTATCACTTTGATTCTATTTTGATC
38958 ATCCAACTATTATTTTTTAAAGTATCATTAACTTCACATTTTAATTTCATTTTAGTTATCCATCT
391 ATCCAACTATTATTTTTTAAAGTATCATTAACTTCACATTTTAATTTCATTTTAGTTATCCATCT
39023 TTAAAAGATTCACAAAAGATTCACAAAACTGTTGGCCTGAATTTTATTATTATTTTTAATGATGA
456 TTAAAAGATTCACAAAAGATTCACAAAACTGTTGGCCTGAATTTTATTATTATTTTTAATGATGA
39088 CATGATATTACCTTATGATGACACATAAAAAACACCATTAATTTTTTAACGACTGGTGACTAAAA
521 CATGATATTACCTTATGATGACACATAAAAAACACCATTAATTTTTTAACGACTGGTGACTAAAA
39153 TGAAATCAAAATTTAATGATAGTGATGATTTTGAAAAAAAAAATTGACCACAACAGAACCAAAAT
586 TGAAATCAAAATTTAATGATAGTGATGATTTTGAAAAAAAAAATTGACCACAACAGAACCAAAAT
39218 GATAGTTGGGTGGGTGACTAAATAAGT-A-TACTCTAAATACTTTAAAGACGCATGTTTTCCAGA
651 GATAGTTGGGTGGGTGACTAAATAAGTAACTACTCTAAATACTTTAAAGACGCATGTTTTCCAGA
39281 ACTGAAAACCCAACAGCATACATTGCAACACAGTCATGGAGAACTTATTATTACCATTTTCGTCC
716 ACTGAAAACCCAACAGCATACATTGCAACACAGTCATGGAGAACTTATTATTACCATTTTCGTCC
39346 CTCTAACTTGTTAAAGTTCTATAGTTTCATTGTCTTTTTTCCCTTCTGAATTTCATCCGCAATCC
781 CTCTAACTTGTTAAAGTTCTATAGTTTCATTGTCTTTTTTCCCTTCTGAATTTCATCCGCAATCC
39411 AATCAGACTTTTCCTACAACTACCCATTTTCAGGCCATCTCAATGATCCAGTAACAGCAGCTGTG
846 AATCAGACTTTTCCTACAACTACCCATTTTCAGGCCATCTCAATGATCCAGTAACAGCAGCTGTG
39476 GA
911 GA
39478 ATAAGGCCCACTACTCAGGAACCATTTAAAAATAATATTCGAGTTTAATATATATATACTGTAGC
1 ATAAGGCCCACTACTCAGGAACCATTTAAAAATAATATTCGAGTTTAATATATATATACTGTAGC
39543 AATTGTCGTGTTGTCACTATGTACACTGTAGCAATTGTCGTAATTTTCAAAATAAAAATTTGAGA
66 AATTGTCGTGTTGTCACTATGTACACTGTAGCAATTGTCGTAATTTTCAAAATAAAAATTTGAGA
*
39608 GGCCCAATAACATAAATAATTGATCCGCTTGGGGTATTGTACCAAAAAAACCCAGTAAATTTTGA
131 GGCCCAATAACATAAATAATTGATCCGCTTGGGGTATTGTACCAAAAAAACCCAGTAACTTTTGA
39673 TATGCTAAATATAAGATTTAAAATTTTGAGTTAAAATCAATTTGTAGCAAACGTTTTAGATAAAA
196 TATGCTAAATATAAGATTTAAAATTTTGAGTTAAAATCAATTTGTAGCAAACGTTTTAGATAAAA
39738 ATTGTTTTATATTCAAATCAATTGAGTTTGAGGAGATTTGAATACGTAGACAGTTAAGACATTTT
261 ATTGTTTTATATTCAAATCAATTGAGTTTGAGGAGATTTGAATACGTAGACAGTTAAGACATTTT
39803 ATAATAAATTCTTGGGTAAATTTTATATTTAGTTATCAAACTATCACTTTGATTCTATTTTGATC
326 ATAATAAATTCTTGGGTAAATTTTATATTTAGTTATCAAACTATCACTTTGATTCTATTTTGATC
39868 ATCCAACTATTATTTTTTAAAGTATCATTAACTTCACA-TTTAATTTCA-TTTAGTTATCCATCT
391 ATCCAACTATTATTTTTTAAAGTATCATTAACTTCACATTTTAATTTCATTTTAGTTATCCATCT
39931 TTAAAAGATTCACAAAAGATTCACAAAACTGTTGGCCTGAATTTTATTATTATTTTTAATGATGA
456 TTAAAAGATTCACAAAAGATTCACAAAACTGTTGGCCTGAATTTTATTATTATTTTTAATGATGA
39996 CATGATATTACCTTATGATGACACATAAAAAACACCATTAATTTTTTAACGACTGGTGACTAAAA
521 CATGATATTACCTTATGATGACACATAAAAAACACCATTAATTTTTTAACGACTGGTGACTAAAA
*
40061 TGAAATCAAAATTTAATGATAGTGATGATTTTGGAAAAAAAAATTGACCACAACAGAACCAAAAT
586 TGAAATCAAAATTTAATGATAGTGATGATTTTGAAAAAAAAAATTGACCACAACAGAACCAAAAT
40126 GATAGTTGGGTGGGTGACTAAATAAGTAGACTACTCTAAATACTTTAAAGACGCATGTTTTCCAG
651 GATAGTTGGGTGGGTGACTAAATAAGTA-ACTACTCTAAATACTTTAAAGACGCATGTTTTCCAG
40191 AACTGAAAACCCAACAGCATACATTGCAACACAGTCATGGAGAACTTATTATTACCATTTTCGTC
715 AACTGAAAACCCAACAGCATACATTGCAACACAGTCATGGAGAACTTATTATTACCATTTTCGTC
40256 CCTCTAACTTGTTAAAGTTCTATAGTTTCATTGTCTTTTTTCCCTTCTGAATTTCATCCGCAATC
780 CCTCTAACTTGTTAAAGTTCTATAGTTTCATTGTCTTTTTTCCCTTCTGAATTTCATCCGCAATC
40321 CAATCAGACTTTTCCTACAACTACCCATTTTCAGGCCATCTCAATGATCCAGTAACAGCAGCTGT
845 CAATCAGACTTTTCCTACAACTACCCATTTTCAGGCCATCTCAATGATCCAGTAACAGCAGCTGT
40386 GGA
910 GGA
40389 ATAAGGC
1 ATAAGGC
40396 TTCCCCCCCC
Statistics
Matches: 1823, Mismatches: 2, Indels: 8
0.99 0.00 0.00
Matches are distributed among these distances:
908 236 0.13
909 10 0.01
910 660 0.36
911 240 0.13
913 677 0.37
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (912 bp):
ATAAGGCCCACTACTCAGGAACCATTTAAAAATAATATTCGAGTTTAATATATATATACTGTAGC
AATTGTCGTGTTGTCACTATGTACACTGTAGCAATTGTCGTAATTTTCAAAATAAAAATTTGAGA
GGCCCAATAACATAAATAATTGATCCGCTTGGGGTATTGTACCAAAAAAACCCAGTAACTTTTGA
TATGCTAAATATAAGATTTAAAATTTTGAGTTAAAATCAATTTGTAGCAAACGTTTTAGATAAAA
ATTGTTTTATATTCAAATCAATTGAGTTTGAGGAGATTTGAATACGTAGACAGTTAAGACATTTT
ATAATAAATTCTTGGGTAAATTTTATATTTAGTTATCAAACTATCACTTTGATTCTATTTTGATC
ATCCAACTATTATTTTTTAAAGTATCATTAACTTCACATTTTAATTTCATTTTAGTTATCCATCT
TTAAAAGATTCACAAAAGATTCACAAAACTGTTGGCCTGAATTTTATTATTATTTTTAATGATGA
CATGATATTACCTTATGATGACACATAAAAAACACCATTAATTTTTTAACGACTGGTGACTAAAA
TGAAATCAAAATTTAATGATAGTGATGATTTTGAAAAAAAAAATTGACCACAACAGAACCAAAAT
GATAGTTGGGTGGGTGACTAAATAAGTAACTACTCTAAATACTTTAAAGACGCATGTTTTCCAGA
ACTGAAAACCCAACAGCATACATTGCAACACAGTCATGGAGAACTTATTATTACCATTTTCGTCC
CTCTAACTTGTTAAAGTTCTATAGTTTCATTGTCTTTTTTCCCTTCTGAATTTCATCCGCAATCC
AATCAGACTTTTCCTACAACTACCCATTTTCAGGCCATCTCAATGATCCAGTAACAGCAGCTGTG
GA
Found at i:44733 original size:4 final size:4
Alignment explanation
Indices: 44724--44787 Score: 55
Period size: 4 Copynumber: 16.8 Consensus size: 4
44714 GATAGACCTA
* * * *
44724 AAAT AAAT AAAT AAAT AAAT AAAC GAGT AAAT -AAT -AAT AAAC AAGA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT
44770 AAAT AAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAA
44788 ATACTATATA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
3 10 0.20
4 38 0.78
5 1 0.02
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:44764 original size:18 final size:19
Alignment explanation
Indices: 44731--44780 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
44721 CTAAAATAAA
*
44731 TAAATAAATAAATAAACGAG
1 TAAAT-AATAAATAAACAAG
44751 TAAATAAT-AATAAACAAG
1 TAAATAATAAATAAACAAG
*
44769 AAAATAAATAAA
1 TAAAT-AATAAA
44781 AAATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 13 0.50
19 6 0.23
20 7 0.27
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.20
Consensus pattern (19 bp):
TAAATAATAAATAAACAAG
Found at i:44830 original size:34 final size:34
Alignment explanation
Indices: 44790--44931 Score: 102
Period size: 33 Copynumber: 4.4 Consensus size: 34
44780 AAAATAAAAT
44790 ACTATATAATATATATTTAAAAAAATGTTTTAAA
1 ACTATATAATATATATTTAAAAAAATGTTTTAAA
* * *
44824 AC--TAT-ATATAT-TTCAAAAATAT-TTTCAAA
1 ACTATATAATATATATTTAAAAAAATGTTTTAAA
* * *
44853 ACCATATACTATATAATTT-TAAAAATGTTTTAAA
1 ACTATATAATATAT-ATTTAAAAAAATGTTTTAAA
** ** *
44887 ACTATA-CGT-TATAGTTTTCAAAAACGTTTTAAA
1 ACTATATAATATATA-TTTAAAAAAATGTTTTAAA
*
44920 ACTATATTATAT
1 ACTATATAATAT
44932 GTTTCAACTA
Statistics
Matches: 83, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
29 8 0.10
30 9 0.11
31 10 0.12
32 14 0.17
33 25 0.30
34 16 0.19
35 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (34 bp):
ACTATATAATATATATTTAAAAAAATGTTTTAAA
Found at i:45009 original size:37 final size:37
Alignment explanation
Indices: 44937--45250 Score: 256
Period size: 38 Copynumber: 8.4 Consensus size: 37
44927 TATATGTTTC
*
44937 AACTATATATTATATAA-ATTTC-AAAATGATTTT-AA
1 AACTATATATTATATAAGTTTTCAAAAAT-ATTTTAAA
* *
44972 AACTATTTATTATATAAGTTTTCAAAAATGGTTTTAAA
1 AACTATATATTATATAAGTTTTCAAAAAT-ATTTTAAA
* * * *
45010 AACTATATAATATATATGGTTTCAAAAATATCTTCAAA
1 AACTATATATTATATAAGTTTTCAAAAATAT-TTTAAA
* * * *
45048 AACTATATAATATATATGTTTTCAAAAAAATGTTTTCAA
1 AACTATATATTATATAAGTTTTC--AAAAATATTTTAAA
* * *
45087 AACTATA-A-TATATATGTTTTTAAAAATGTTTTCAAA
1 AACTATATATTATATAAGTTTTCAAAAATATTTT-AAA
*
45123 AACTATATA-TATATAATTTTTC-AAAATGATTTTAAA
1 AACTATATATTATATAAGTTTTCAAAAAT-ATTTTAAA
* * *
45159 AATTATATATTATATATA-TTTTCTAAAATATTTTTTTTAA
1 AACTATATATTATATA-AGTTTTC-AAAA-A-TATTTTAAA
45199 AACTATATATTATAT-AGTTTT-AAAAACTA--TTAAA
1 AACTATATATTATATAAGTTTTCAAAAA-TATTTTAAA
45233 AACTCTATATATTATATA
1 AA--CTATATATTATATA
45251 CGTAGTTTCA
Statistics
Matches: 234, Mismatches: 26, Indels: 36
0.79 0.09 0.12
Matches are distributed among these distances:
34 6 0.03
35 27 0.12
36 44 0.19
37 53 0.23
38 57 0.24
39 18 0.08
40 28 0.12
41 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
AACTATATATTATATAAGTTTTCAAAAATATTTTAAA
Found at i:48171 original size:17 final size:17
Alignment explanation
Indices: 48149--48185 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
48139 CGATTTTGAG
48149 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
48166 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
48183 CTC
1 CTC
48186 AAACTCGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:50589 original size:158 final size:158
Alignment explanation
Indices: 50244--50559 Score: 596
Period size: 158 Copynumber: 2.0 Consensus size: 158
50234 GTGTCTCGTT
*
50244 GAGGAGAGATGAGGAAATGATTTAGGTTAAGCGTTTCACCCTAATCTTCCAATATATTCCAACGA
1 GAGGATAGATGAGGAAATGATTTAGGTTAAGCGTTTCACCCTAATCTTCCAATATATTCCAACGA
*
50309 CCAAAACGACGTAACTTTAATCAGCACCAAAACGAATTATTAGCATTTTAGGACCTGTTATATTT
66 CCAAAACGACGTAACTTTAATCAACACCAAAACGAATTATTAGCATTTTAGGACCTGTTATATTT
50374 GTAATCTTCTGATTTCGTCATTAATCAA
131 GTAATCTTCTGATTTCGTCATTAATCAA
*
50402 GAGGATAGATGAGGAAATGATTTAGGTTAAGCGTTTCACCCTAATTTTCCAATATATTCCAACGA
1 GAGGATAGATGAGGAAATGATTTAGGTTAAGCGTTTCACCCTAATCTTCCAATATATTCCAACGA
*
50467 CCAAAACGACGTAACTTTAATCAACACCAAAATGAATTATTAGCATTTTAGGACCTGTTATATTT
66 CCAAAACGACGTAACTTTAATCAACACCAAAACGAATTATTAGCATTTTAGGACCTGTTATATTT
50532 GTAATCTTCTGATTTCGTCATTAATCAA
131 GTAATCTTCTGATTTCGTCATTAATCAA
50560 TGTTTATGTT
Statistics
Matches: 154, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 154 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (158 bp):
GAGGATAGATGAGGAAATGATTTAGGTTAAGCGTTTCACCCTAATCTTCCAATATATTCCAACGA
CCAAAACGACGTAACTTTAATCAACACCAAAACGAATTATTAGCATTTTAGGACCTGTTATATTT
GTAATCTTCTGATTTCGTCATTAATCAA
Found at i:50846 original size:21 final size:21
Alignment explanation
Indices: 50822--50870 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
50812 TTTGGGGTTT
*
50822 GAGTTTAAGGTTTATAATTTA
1 GAGTTTAAAGTTTATAATTTA
50843 GAGTTTAAAGTTTATAATTTA
1 GAGTTTAAAGTTTATAATTTA
*
50864 GGGTTTA
1 GAGTTTA
50871 GGGTGTAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (21 bp):
GAGTTTAAAGTTTATAATTTA
Found at i:50908 original size:14 final size:14
Alignment explanation
Indices: 50891--50920 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
50881 TAACATGTGT
*
50891 TTAATTAAATGAGC
1 TTAATTAAACGAGC
50905 TTAATTAAACGAGC
1 TTAATTAAACGAGC
50919 TT
1 TT
50921 TTATTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (14 bp):
TTAATTAAACGAGC
Found at i:51137 original size:7 final size:7
Alignment explanation
Indices: 51122--51221 Score: 80
Period size: 7 Copynumber: 14.7 Consensus size: 7
51112 GATTAGATTA
51122 AGGGTTT
1 AGGGTTT
*
51129 AGGGCTT
1 AGGGTTT
51136 AGGGTTT
1 AGGGTTT
*
51143 AGTGTTT
1 AGGGTTT
*
51150 ATGGTTT
1 AGGGTTT
*
51157 -GAGTTT
1 AGGGTTT
*
51163 GGGGTTT
1 AGGGTTT
51170 A-GGTTT
1 AGGGTTT
51176 A-GGTTT
1 AGGGTTT
*
51182 AGAGTTT
1 AGGGTTT
*
51189 AGAGTTT
1 AGGGTTT
* *
51196 AGAGATT
1 AGGGTTT
*
51203 AGAGTTT
1 AGGGTTT
*
51210 AGGGTGT
1 AGGGTTT
51217 AGGGT
1 AGGGT
51222 GTAATCAACA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
6 16 0.21
7 61 0.79
ACGTcount: A:0.19, C:0.01, G:0.38, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:51139 original size:163 final size:165
Alignment explanation
Indices: 50903--51267 Score: 479
Period size: 163 Copynumber: 2.2 Consensus size: 165
50893 AATTAAATGA
* * *
50903 GCTTAATTAAACGAGCTTTTATTTTTCTTTTAGTACCCTATTACATAATTAGATTAAGGGTTTAG
1 GCTTAATTAAATGAGCTTTTATTTTTCTTTTAGAACCCTATCACATAATTAGATTAAGGGTTTAG
* * * *
50968 GACTTAGGGCTTAGTGCTTATGGTTTGGGGTTT-GGGTTT-GAGTTTGGGTTTGGAGATTATAGT
66 GACTTAGGGCTTAGTGCTTATGGTTT-GAGTTTGGGGTTTAG-GTTTAGGTTTAGAGATTAGAGT
* *
51031 TTAGGGTTTAG-GTTTAGGG-GTA-TAATCTAACATGT
129 TTAGAGATTAGAGTTTAGGGTGTAGTAATC-AACATGT
* * *
51066 GCTTAATTAAATGAGCTTTTATTTTTCTTTTAGAACCTTATCACGTGATTAGATTAAGGGTTTAG
1 GCTTAATTAAATGAGCTTTTATTTTTCTTTTAGAACCCTATCACATAATTAGATTAAGGGTTTAG
* * * *
51131 GGCTTAGGGTTTAGTGTTTATGGTTTGAGTTTGGGGTTTAGGTTTAGGTTTAGAGTTTAGAGTTT
66 GACTTAGGGCTTAGTGCTTATGGTTTGAGTTTGGGGTTTAGGTTTAGGTTTAGAGATTAGAGTTT
51196 AGAGATTAGAGTTTAGGGTGTAGGGTGTAATCAACATGT
131 AGAGATTAGAGTTTAGGGTGTA----GTAATCAACATGT
*
51235 GGTTAATTAAATGAGCTTTTATTTTTCTTTTAG
1 GCTTAATTAAATGAGCTTTTATTTTTCTTTTAG
51268 TAATATACAA
Statistics
Matches: 176, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
162 5 0.03
163 115 0.65
164 9 0.05
165 3 0.02
169 39 0.22
170 5 0.03
ACGTcount: A:0.23, C:0.07, G:0.26, T:0.44
Consensus pattern (165 bp):
GCTTAATTAAATGAGCTTTTATTTTTCTTTTAGAACCCTATCACATAATTAGATTAAGGGTTTAG
GACTTAGGGCTTAGTGCTTATGGTTTGAGTTTGGGGTTTAGGTTTAGGTTTAGAGATTAGAGTTT
AGAGATTAGAGTTTAGGGTGTAGTAATCAACATGT
Found at i:59883 original size:2 final size:2
Alignment explanation
Indices: 59871--59918 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
59861 TGTTATATGA
59871 AT AT A- AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59911 AT AT AT AT
1 AT AT AT AT
59919 TAAAGATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60583 original size:23 final size:23
Alignment explanation
Indices: 60528--60583 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 23
60518 TGCCCTAAAA
60528 ATAAATCAAATTAATATAAACAAT
1 ATAAAT-AAATTAATATAAACAAT
60552 A-AAATAAATTAATATAAA-AAT
1 ATAAATAAATTAATATAAACAAT
60573 AGTAAATAAAT
1 A-TAAATAAAT
60584 AAAAGAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.13
22 13 0.43
23 12 0.40
24 1 0.03
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (23 bp):
ATAAATAAATTAATATAAACAAT
Found at i:60635 original size:15 final size:15
Alignment explanation
Indices: 60589--60637 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
60579 TAAATAAAAG
60589 AATTAAAAGAGAATTTA
1 AATTAAAA-AGAA-TTA
60606 AATTAAAAATG-ATTA
1 AATTAAAAA-GAATTA
*
60621 AATTGAAAAGAATTA
1 AATTAAAAAGAATTA
60636 AA
1 AA
60638 AATCAAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 1 0.03
15 17 0.59
16 2 0.07
17 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (15 bp):
AATTAAAAAGAATTA
Found at i:61516 original size:21 final size:23
Alignment explanation
Indices: 61470--61517 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
61460 ATCAAGTACA
*
61470 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
61493 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
61516 AT
1 AT
61518 TGACCTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:61758 original size:20 final size:20
Alignment explanation
Indices: 61744--61782 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61734 CCATTATATT
*
61744 TTTACCGGTTACATTGTAAA
1 TTTACCGGTTACATTATAAA
* *
61764 TTTACCTGTTACATAATAA
1 TTTACCGGTTACATTATAA
61783 TTATCGATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTACCGGTTACATTATAAA
Found at i:62369 original size:178 final size:180
Alignment explanation
Indices: 62069--62513 Score: 673
Period size: 178 Copynumber: 2.5 Consensus size: 180
62059 TTTTTACTAA
* * *
62069 CGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATATTGTTTTGGATCGATAC
1 CGGTTTTGTCATTTCGAGA-CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * *
62134 AATTTTATAAAATATCGACACTTTATTGGCGCTATAACTTATTTTCTTTTAAATTCCAAAAGTGT
65 -ATTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGT
*
62199 CGATAC-T-TAATAAAGTATCGACACTATCAACATA-TCGGTAACTCTTTAC
129 CGATACTTATAATAAAGTATCGACACTATCAACATATTCGGTAACGCTTTAC
*
62248 CGGTTTTGTCATTTCGAGACGGTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACA
1 CGGTTTTGTCATTTCGAGACGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
*
62313 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
66 -TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTC
**
62378 GATACTTATAATAAAGTATCGACACTATCAACATATTCGGTTGCGCTTTAC
130 GATACTTATAATAAAGTATCGACACTATCAACATATTCGGTAACGCTTTAC
* * ** * *
62429 CTGTTTTGTCAGTTATAGACTGGTTTTGTCATTTTTTTA-CTGTTTTATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGAC-GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
62493 ATTTTATAAAGTATCGACACT
65 ATTTTATAAAGTATCGACACT
62514 ATCAACATAT
Statistics
Matches: 243, Mismatches: 18, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
177 1 0.00
178 106 0.44
179 20 0.08
180 47 0.19
181 52 0.21
182 17 0.07
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (180 bp):
CGGTTTTGTCATTTCGAGACGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCG
ATACTTATAATAAAGTATCGACACTATCAACATATTCGGTAACGCTTTAC
Found at i:62953 original size:111 final size:112
Alignment explanation
Indices: 62388--62950 Score: 840
Period size: 111 Copynumber: 5.1 Consensus size: 112
62378 GATACTTATA
* * * * *
62388 ATAAAGTATCGACACTATCAACATAT-TCGGTTGCGCTTTACCTGTTTTGTCAGTTATAGACTGG
1 ATAAAGTATCGACACTTTCAATATATCT-GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
*
62452 TTTTGTCATTTTTTTA-CTGTTTTATTGTTATGGATCGATACA-TTTT
65 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
62498 ATAAAGTATCGACACTATCAACATATCTGGTAGCG--TTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
62561 TTTGTCA--TTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
62606 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
62671 TTTGTCATTTTTTTATCTGTTATATTGTTATGGATCGATACA-TTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
** *
62717 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACATGTTTT-TCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
62781 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
62828 ATAAAGTAGCGATACTTTCAATATATCTGGTAGCGCTTTACCTATTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * * *
62893 TTTATCA-TTTTTTACTTGTTATATTATTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
62939 ATAAAGTATCGA
1 ATAAAGTATCGA
62951 TACAAACCGA
Statistics
Matches: 420, Mismatches: 24, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
106 6 0.01
107 25 0.06
108 69 0.16
110 123 0.29
111 143 0.34
112 54 0.13
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Done.