Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001296.1 Hibiscus syriacus cultivar Beakdansim tig00002535_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: 79180
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2857 original size:14 final size:14
Alignment explanation
Indices: 2819--2857 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2809 ATTTTAAATA
*
2819 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
2833 TTTTACATTTGCAT
1 ATTTACATTTGCAT
2847 ATTTACATTTG
1 ATTTACATTTG
2858 GAATCTTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:10457 original size:22 final size:21
Alignment explanation
Indices: 10403--10457 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
10393 ATTTACACTC
10403 TTCAAAGATGATAGATTCTCT
1 TTCAAAGATGATAGATTCTCT
* *
10424 CTCTAAAGATGATATATTCTCTT
1 TTC-AAAGATGATAGATTCTC-T
*
10447 TTCAAATATGA
1 TTCAAAGATGA
10458 AAGCTTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.07
22 23 0.82
23 3 0.11
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (21 bp):
TTCAAAGATGATAGATTCTCT
Found at i:11062 original size:113 final size:113
Alignment explanation
Indices: 10826--11598 Score: 1024
Period size: 113 Copynumber: 6.8 Consensus size: 113
10816 CCATTACTCA
* * *
10826 ATGGATCAAC-ATTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAG
1 ATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * **
10889 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTT-AATTCATCACCCG
65 TTCATAATGAGAAGAATTTGTTAAACCTTTTG-TTTGAATTCATCATTCG
* * * *
10938 ATGGATTAGCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * ** * *
11003 TCATAATGAGAAGAACTTGTTTAACCTTTTGCTCAAATCCATGACTT-G
66 TCATAATGAGAAGAATTTGTTAAACCTTTTGTTTGAATTCATCA-TTCG
* * * * * * *
11051 ATAGATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCTGAAGAAGGAAGAAGAAA
1 ATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * * * *
11115 TTCATAATGAGAAGATTTTGTTCAACTTTTTGTTTGAATTCATCACTCA
65 TTCATAATGAGAAGAATTTGTTAAACCTTTTGTTTGAATTCATCATTCG
*
11164 ATGGATTAACTTTTCCAGATG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAG
1 ATGGATCAACTTTTCCAGA-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
11227 TTCATAATAAGAACAATTTGTTCAAACCTTTTGTTTGAATTCATCATTCG
65 TTCATAATGAGAAGAATTTGTT-AAACCTTTTGTTTGAATTCATCATTCG
*
11277 ATGGATCAACTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
11341 TCATAATGAGAAGAATTTGTTCAAACTTTTTGTTTGAATTCATCATTCG
66 TCATAATGAGAAGAATTTGTT-AAACCTTTTGTTTGAATTCATCATTCG
* * *
11390 ATGAATCAACTTTTCCATAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* *
11454 TTATAATCAGAAGAATTTGTTCAAACCTTTTGTTTGAATTCATCATTCG
66 TCATAATGAGAAGAATTTGTT-AAACCTTTTGTTTGAATTCATCATTCG
11503 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* **
11568 TCATAATGAGAAGAGTTTGTTCGACCTTTTG
66 TCATAATGAGAAGAATTTGTTAAACCTTTTG
11599 CATGACTCTA
Statistics
Matches: 589, Mismatches: 61, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
112 38 0.06
113 522 0.89
114 28 0.05
115 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAATTTGTTAAACCTTTTGTTTGAATTCATCATTCG
Found at i:11955 original size:3 final size:3
Alignment explanation
Indices: 11937--12010 Score: 98
Period size: 3 Copynumber: 25.3 Consensus size: 3
11927 TATCCATTTT
* *
11937 TTA TTG TTA ATA TTA TTA TT- TTA TTA TTA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
**
11983 TTA TTA TTA TTA AAA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12011 AAATAAGCCA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 4 0.07
3 57 0.93
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:11960 original size:20 final size:19
Alignment explanation
Indices: 11935--11993 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
11925 TTTATCCATT
*
11935 TTTTATTGTTAATATTATTA
1 TTTTATT-TTATTATTATTA
11955 TTTTA--TTATTATTATTA
1 TTTTATTTTATTATTATTA
11972 TTTTATTATTATTATTATTA
1 TTTTATT-TTATTATTATTA
11992 TT
1 TT
11994 AAAATTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
17 16 0.46
20 19 0.54
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTATTTTATTATTATTA
Found at i:11969 original size:17 final size:17
Alignment explanation
Indices: 11947--12008 Score: 97
Period size: 17 Copynumber: 3.6 Consensus size: 17
11937 TTATTGTTAA
11947 TATTATTATTTTATTAT
1 TATTATTATTTTATTAT
11964 TATTATTATTTTATTAT
1 TATTATTATTTTATTAT
**
11981 TATTATTATTATTAAAAT
1 TATTATTATT-TTATTAT
11999 TATTATTATT
1 TATTATTATT
12009 ATAAATAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
17 27 0.64
18 15 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTATTTTATTAT
Found at i:15223 original size:43 final size:43
Alignment explanation
Indices: 15171--15394 Score: 263
Period size: 43 Copynumber: 5.2 Consensus size: 43
15161 TTTGAGAAAA
*
15171 AAACACCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAAC
*
15214 AAACGCCGCAAAAGGTAGAGATCTATAGCGACGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAAC
* ** * * * *
15257 AAACGTCGTGAAAGATTGATATCTATAGCGGA-ATTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGC-GACGTTTTTGGAAC
* * * * *
15300 AAACGCTGTAAAAGATCGATATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAAC
* *
15343 AAACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGA-AC
*
15386 AAATGCCGC
1 AAACGCCGC
15395 TAATTACATT
Statistics
Matches: 157, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
42 22 0.14
43 133 0.85
44 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGACGTTTTTGGAAC
Found at i:21302 original size:25 final size:24
Alignment explanation
Indices: 21258--21317 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
21248 ATATACAATA
*
21258 AATAATATTATTTATTAATAAAAT
1 AATAATACTATTTATTAATAAAAT
21282 AATAATACTATTT-TTAA-AATAAT
1 AATAATACTATTTATTAATAA-AAT
21305 -ATAATA--ATTTATT
1 AATAATACTATTTATT
21318 TAACAATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 8 0.24
23 7 0.21
24 12 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AATAATACTATTTATTAATAAAAT
Found at i:21415 original size:32 final size:32
Alignment explanation
Indices: 21363--21423 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
21353 TATATCTACA
21363 ATTTTATAAATAAAAATATTA-AAATTATCAT
1 ATTTTATAAATAAAAATATTATAAATTATCAT
* *
21394 ATTTTATTAAATTAAATTATTATAAATTAT
1 ATTTTA-TAAATAAAAATATTATAAATTAT
21424 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 6 0.23
32 13 0.50
33 7 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
ATTTTATAAATAAAAATATTATAAATTATCAT
Found at i:21484 original size:18 final size:19
Alignment explanation
Indices: 21454--21489 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
21444 CTATTTATAT
21454 TAATTACTTATTAAAATAA
1 TAATTACTTATTAAAATAA
21473 TAATTA-TTATTAAAATA
1 TAATTACTTATTAAAATA
21490 TTAAAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATTACTTATTAAAATAA
Found at i:24657 original size:41 final size:41
Alignment explanation
Indices: 24634--24727 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
24624 ATATTTGTAT
* * *
24634 TTTAGTGGCGTTTGTATGAAAACGCCGCTATAGACTTCTAC
1 TTTAGTGGCATTCGTATGAAAACGCCGCTAAAGACTTCTAC
*
24675 TTTAGTGGCATTCGTATGAAAACGCCGCTATAGAC-TCATAC
1 TTTAGTGGCATTCGTATGAAAACGCCGCTAAAGACTTC-TAC
*
24716 TTTAGTGACATT
1 TTTAGTGGCATT
24728 TTTGTTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
40 2 0.04
41 47 0.96
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (41 bp):
TTTAGTGGCATTCGTATGAAAACGCCGCTAAAGACTTCTAC
Found at i:27628 original size:86 final size:86
Alignment explanation
Indices: 27493--27719 Score: 280
Period size: 86 Copynumber: 2.6 Consensus size: 86
27483 TCTTAATCTA
* * * * * *
27493 AAAACCTACTGCGACGTTTGTGGGAGAAACGCCGCTAAACATCATCACCTATTGCGGCGTTTGTT
1 AAAACCTACTGCGGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTA
27558 GAAAAAACGCCGC-AAAATATC
66 GAAAAAACGCCGCTAAAA-ATC
* * *
27579 AACACCTACTGTGGCGTTTGTATGGA-AAACGCCGCTAAATATCAACACCTACTGCGGCGTTTGT
1 AAAACCTACTGCGGCGTTTGT-TGGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT
**
27643 AGGGAAAACGCCGCTAAAAATC
65 AGAAAAAACGCCGCTAAAAATC
* * *
27665 AAAAACTATTGCGGCGTTT-TTGTGACAAACGCCGCTAAATAACAACACCTATTGC
1 AAAACCTACTGCGGCGTTTGTTG-GACAAACGCCGCTAAATATCAACACCTATTGC
27720 TGTGTTTTTT
Statistics
Matches: 121, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
84 2 0.02
85 3 0.02
86 109 0.90
87 7 0.06
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (86 bp):
AAAACCTACTGCGGCGTTTGTTGGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTA
GAAAAAACGCCGCTAAAAATC
Found at i:27719 original size:43 final size:42
Alignment explanation
Indices: 27496--27715 Score: 253
Period size: 43 Copynumber: 5.1 Consensus size: 42
27486 TAATCTAAAA
* * * *
27496 ACCTACTGCGACGTTTGTGGGAGAAACGCCGCTAAACATCATC
1 ACCTACTGCGGCGTTTGTTGGA-AAACGCCGCTAAATATCAAC
* * *
27539 ACCTATTGCGGCGTTTGTTGAAAAAACGCCGCAAAATATCAAC
1 ACCTACTGCGGCGTTTGTTG-GAAAACGCCGCTAAATATCAAC
*
27582 ACCTACTGTGGCGTTTGTATGGAAAACGCCGCTAAATATCAAC
1 ACCTACTGCGGCGTTTGT-TGGAAAACGCCGCTAAATATCAAC
* * *
27625 ACCTACTGCGGCGTTTGTAGGGAAAACGCCGCTAAAAATCAAA
1 ACCTACTGCGGCGTTTGT-TGGAAAACGCCGCTAAATATCAAC
* * *
27668 AACTATTGCGGCGTTT-TTGTGACAAACGCCGCTAAATAACAAC
1 ACCTACTGCGGCGTTTGTTG-GA-AAACGCCGCTAAATATCAAC
27711 ACCTA
1 ACCTA
27716 TTGCTGTGTT
Statistics
Matches: 151, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 3 0.02
43 144 0.95
44 3 0.02
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (42 bp):
ACCTACTGCGGCGTTTGTTGGAAAACGCCGCTAAATATCAAC
Found at i:29013 original size:19 final size:19
Alignment explanation
Indices: 28976--29076 Score: 121
Period size: 20 Copynumber: 5.1 Consensus size: 19
28966 AACAAAGAAG
28976 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
*
28997 TCAAATTCGTAACTGAATT
1 TCAAATTCGCAACTGAATT
*
29016 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
*
29036 TCAAATTCGCAACTTGATTT
1 TCAAATTCGCAAC-TGAATT
*
29056 TCGAATTCGCAACATGAATT
1 TCAAATTCGCAAC-TGAATT
29076 T
1 T
29077 AATTTCGAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
19 21 0.29
20 41 0.57
21 10 0.14
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:29022 original size:40 final size:41
Alignment explanation
Indices: 28976--29076 Score: 136
Period size: 40 Copynumber: 2.5 Consensus size: 41
28966 AACAAAGAAG
*
28976 TCAAATTCGCAACACTGAATTTCAAATTCGTAAC-TGAATT
1 TCAAATTCGCAACACTGAATTTCAAATTCGCAACTTGAATT
* * *
29016 TCAAATTCGCAACTC-GATTTTCAAATTCGCAACTTGATTT
1 TCAAATTCGCAACACTGAATTTCAAATTCGCAACTTGAATT
*
29056 TCGAATTCGCAACA-TGAATTT
1 TCAAATTCGCAACACTGAATTT
29077 AATTTCGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 16 0.31
40 36 0.69
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (41 bp):
TCAAATTCGCAACACTGAATTTCAAATTCGCAACTTGAATT
Found at i:30076 original size:25 final size:24
Alignment explanation
Indices: 30023--30077 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
30013 GTATTCAAAA
*
30023 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAAAACCCGGAC
* *
30047 TTTGATCTTGGTCAAAATCTCGGAT
1 TTTGATCTTGGTCAAAA-CCCGGAC
30072 TTTGAT
1 TTTGAT
30078 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (24 bp):
TTTGATCTTGGTCAAAACCCGGAC
Found at i:32983 original size:64 final size:65
Alignment explanation
Indices: 32847--33005 Score: 284
Period size: 64 Copynumber: 2.4 Consensus size: 65
32837 TTGAATAAAC
32847 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
* *
32912 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
32976 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
33006 ATTCAATTAA
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
64 53 0.58
65 38 0.42
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.30
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:34325 original size:21 final size:20
Alignment explanation
Indices: 34299--34412 Score: 93
Period size: 21 Copynumber: 5.5 Consensus size: 20
34289 GTGAATCGGG
*
34299 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGG-C
* **
34320 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGA-GGGC
34341 CTCTTGAACGGTGGGATGGGC
1 CTCTTGAACGGTGGGA-GGGC
* **
34362 CTCTTGAACGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGC
* * *
34383 CTCTTGAACGATAGGAGATGC
1 CTCTTGAACGGTGGGAG-GGC
34404 CTCTTGAAC
1 CTCTTGAAC
34413 AATGACAGGT
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 1 0.01
21 71 0.95
22 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGC
Found at i:34365 original size:42 final size:42
Alignment explanation
Indices: 34299--34421 Score: 162
Period size: 42 Copynumber: 2.9 Consensus size: 42
34289 GTGAATCGGG
*
34299 CTCTTGAATGGTGGGA-GGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGATGGG-CCTCTTGAACGATGACAGGGGC
*
34341 CTCTTGAACGGTGGGATGGGCCTCTTGAACGATGATAGGGGC
1 CTCTTGAACGGTGGGATGGGCCTCTTGAACGATGACAGGGGC
* *
34383 CTCTTGAACGATAGGAGAT--GCCTCTTGAACAATGACAGG
1 CTCTTGAACGGT-GG-GATGGGCCTCTTGAACGATGACAGG
34422 TGCATCGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
42 65 0.89
43 5 0.07
44 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGATGGGCCTCTTGAACGATGACAGGGGC
Found at i:34840 original size:63 final size:64
Alignment explanation
Indices: 34730--34869 Score: 151
Period size: 63 Copynumber: 2.2 Consensus size: 64
34720 GTAAAGTAGA
* * * * *
34730 TACCTCACCACGTAGCGCACCATTGTCATCGCGAAAAATATCCACCTCACCATGTAAAG-ACCG
1 TACCTCATCACGTAGCGCACCATTATCATCACGAAAAATATCCACCTCACCACGCAAAGCACCG
* * * * **
34793 TACCTCATCACGTAGTGCACCATTATCTTCACGTAAAGTA-CCGACCTCATGACGCAAAGCACCG
1 TACCTCATCACGTAGCGCACCATTATCATCACGAAAAATATCC-ACCTCACCACGCAAAGCACCG
34857 -ACCTCATCACGTA
1 TACCTCATCACGTA
34870 ACTCTCCTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
62 2 0.03
63 58 0.91
64 4 0.06
ACGTcount: A:0.31, C:0.34, G:0.14, T:0.21
Consensus pattern (64 bp):
TACCTCATCACGTAGCGCACCATTATCATCACGAAAAATATCCACCTCACCACGCAAAGCACCG
Found at i:36472 original size:20 final size:20
Alignment explanation
Indices: 36449--36601 Score: 227
Period size: 20 Copynumber: 7.7 Consensus size: 20
36439 AAACTTAAAT
*
36449 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
36469 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
36489 TCGCATCGCGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
36509 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
36529 TCGCAACGC-AAACATGAAAA
1 TCGCAACGCGAAA-ATGAAAA
*
36549 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
36569 TTGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
36589 TCGCAACGCGAAA
1 TCGCAACGCGAAA
36602 CTAAATTCAC
Statistics
Matches: 122, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 2 0.02
20 117 0.96
21 3 0.02
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:36663 original size:20 final size:20
Alignment explanation
Indices: 36620--36663 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
36610 ACGTTGCGAT
* * * *
36620 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCAAATTTAAG
36640 TTTCGTGTTGCAAATTTAAG
1 TTTCGTGTTGCAAATTTAAG
36660 TTTC
1 TTTC
36664 AAAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCAAATTTAAG
Found at i:37014 original size:22 final size:22
Alignment explanation
Indices: 36984--37041 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
36974 GATGGAGATA
36984 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
37006 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
37028 GACGGATGTCGTCG
1 GACGGATTTCGTCG
37042 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.14, G:0.45, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:37186 original size:20 final size:20
Alignment explanation
Indices: 37161--37220 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
37151 ATGCGCTTTT
37161 ACTTATGTGTTGCGAATTTG
1 ACTTATGTGTTGCGAATTTG
37181 ACTTATGTGTTGCGAATTTG
1 ACTTATGTGTTGCGAATTTG
*
37201 ACTTCTGTGTTGCGAATTTG
1 ACTTATGTGTTGCGAATTTG
37221 GAAAATCGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.45
Consensus pattern (20 bp):
ACTTATGTGTTGCGAATTTG
Found at i:41085 original size:51 final size:51
Alignment explanation
Indices: 41030--41132 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
41020 TCACGATACA
*
41030 TGTTTCATTTGTATACTTCGTATTTTTTTAGTAAATTTGGAGGTCACATAT
1 TGTTTCATTTGTATACTTCGTATTTTTTTAGTAAATTTGGAGGACACATAT
41081 TGTTTCATTTGTATACTTCGTATTTTTTTAGTAAATTTGGAGGACACATAT
1 TGTTTCATTTGTATACTTCGTATTTTTTTAGTAAATTTGGAGGACACATAT
41132 T
1 T
41133 ATTACATCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (51 bp):
TGTTTCATTTGTATACTTCGTATTTTTTTAGTAAATTTGGAGGACACATAT
Found at i:42376 original size:15 final size:14
Alignment explanation
Indices: 42336--42378 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
42326 ATATTTTTTT
*
42336 TTTTAAATAAAATA
1 TTTTAAATAATATA
42350 TTATTAAA-AATATA
1 TT-TTAAATAATATA
42364 TTTTAAAATAATATA
1 TTTT-AAATAATATA
42379 GATGTGACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.08
14 12 0.48
15 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTTAAATAATATA
Found at i:42799 original size:2 final size:2
Alignment explanation
Indices: 42792--42879 Score: 75
Period size: 2 Copynumber: 48.0 Consensus size: 2
42782 CTGCCCCGAT
* *
42792 TA TA TA TA TA TA TA -A AA AA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
42832 TA TA TA TA TA TA AA TA -A TA T- TT TA TA TA T- TT TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42870 -A T- TA TA TA TA
1 TA TA TA TA TA TA
42880 ATACAAACAA
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
1 8 0.11
2 65 0.89
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42843 original size:38 final size:37
Alignment explanation
Indices: 42792--42880 Score: 119
Period size: 38 Copynumber: 2.4 Consensus size: 37
42782 CTGCCCCGAT
42792 TATATATATATATAAAAAATATTATATATATATATATA
1 TATATATATATATAAAAAATATTATATATAT-TATATA
* * *
42830 TATATATATATATAAATAATATTTTATATATTTTATA
1 TATATATATATATAAAAAATATTATATATATTATATA
42867 T-TA-ATTATATATAA
1 TATATA-TATATATAA
42881 TACAAACAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
35 1 0.02
36 11 0.23
37 6 0.13
38 29 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TATATATATATATAAAAAATATTATATATATTATATA
Found at i:48804 original size:15 final size:15
Alignment explanation
Indices: 48786--48863 Score: 52
Period size: 15 Copynumber: 5.2 Consensus size: 15
48776 AACGAAATAA
*
48786 AAAATAAAATTACAT
1 AAAATAAAATAACAT
* * * *
48801 AAAATAGAAGACCAG
1 AAAATAAAATAACAT
48816 AAAATAAAATAACAT
1 AAAATAAAATAACAT
* *
48831 AAATTACAAT-AC-T
1 AAAATAAAATAACAT
*
48844 AGAAATTAAAATAATAT
1 A-AAA-TAAAATAACAT
48861 AAA
1 AAA
48864 GTCTAATACC
Statistics
Matches: 45, Mismatches: 14, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
13 2 0.04
14 4 0.09
15 34 0.76
16 3 0.07
17 2 0.04
ACGTcount: A:0.65, C:0.08, G:0.05, T:0.22
Consensus pattern (15 bp):
AAAATAAAATAACAT
Found at i:48848 original size:30 final size:30
Alignment explanation
Indices: 48786--48863 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
48776 AACGAAATAA
* *
48786 AAAATAAAATTACATAAAATAGAAGACCAG
1 AAAATAAAATAACATAAAATACAAGACCAG
* * *
48816 AAAATAAAATAACATAAATTACAATACTAG
1 AAAATAAAATAACATAAAATACAAGACCAG
* *
48846 AAATTAAAATAATATAAA
1 AAAATAAAATAACATAAA
48864 GTCTAATACC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.65, C:0.08, G:0.05, T:0.22
Consensus pattern (30 bp):
AAAATAAAATAACATAAAATACAAGACCAG
Found at i:53094 original size:22 final size:22
Alignment explanation
Indices: 53062--53105 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53052 TAACACATAA
53062 TAAGAGAATAATAATATACCAT
1 TAAGAGAATAATAATATACCAT
*
53084 TAAGAGCATAATAATATACCAT
1 TAAGAGAATAATAATATACCAT
53106 GAACCCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.27
Consensus pattern (22 bp):
TAAGAGAATAATAATATACCAT
Found at i:53824 original size:18 final size:19
Alignment explanation
Indices: 53791--53826 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
53781 ATAATATAAA
*
53791 AACTAAATATATAATATTC
1 AACTAAATACATAATATTC
53810 AACTAAA-ACATAATATT
1 AACTAAATACATAATATT
53827 AAATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (19 bp):
AACTAAATACATAATATTC
Found at i:58459 original size:2 final size:2
Alignment explanation
Indices: 58438--58478 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
58428 TGTTCTTCAA
* * *
58438 AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58479 GTAATGTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:62021 original size:29 final size:29
Alignment explanation
Indices: 61959--62023 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
61949 TAAGCTATAC
*
61959 ATTTAGTGCCTAAAATATTAGTCTTTTTA
1 ATTTAGTACCTAAAATATTAGTCTTTTTA
* *
61988 TTTTAGTACCT-AAATATTA-TTTTTTTCAA
1 ATTTAGTACCTAAAATATTAGTCTTTTT--A
62017 ATTTAGT
1 ATTTAGT
62024 CTAAGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 6 0.20
28 8 0.27
29 16 0.53
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (29 bp):
ATTTAGTACCTAAAATATTAGTCTTTTTA
Found at i:62094 original size:3 final size:3
Alignment explanation
Indices: 62086--62114 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
62076 CATGCCAATG
62086 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
62115 TTTCACATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:64369 original size:165 final size:165
Alignment explanation
Indices: 64091--64870 Score: 1168
Period size: 165 Copynumber: 4.7 Consensus size: 165
64081 AAAACATATT
*
64091 TTTATTCAAAAACCATAGTAATCCCTCCAACTGAACACACCAGAATGTGTAGGTTCCCCAGAACC
1 TTTA-TCAAAAACCATAGTAATCCCTCCAACCGAACACACCAGAATGTGTAGGTTCCCCAGAACC
* * * * * * *
64156 ATACACCCACCAGTACACCAAGTAAAGCCTTGAGCATAAAGTAGAGGAGTCTGCAGTAACTGTAA
65 ATACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAGCAGAGGAGCCTGCAGTAACGGTAA
64221 AGGTAACTTCCTCCAACAACACCCTCCCATAAAACA
130 AGGTAACTTCCTCCAACAACACCCTCCCATAAAACA
*
64257 TTTATCAAAAACCATAGTAATCCCTCCAACCGAACATACCAGAATGTGTAGGTTCCCCAGAACCA
1 TTTATCAAAAACCATAGTAATCCCTCCAACCGAACACACCAGAATGTGTAGGTTCCCCAGAACCA
* *
64322 TACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAGCAGAGGAGCCTACAGTAACGGTAAC
66 TACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAGCAGAGGAGCCTGCAGTAACGGTAAA
* * * *
64387 GGTAGCTTTCTCTAACTACACCCTCCCATAAAACA
131 GGTAACTTCCTCCAACAACACCCTCCCATAAAACA
* * * **
64422 TTTATAAAAAATCATAGTAGTCTATCCAACCGAACACACCAGAATGTGTCA-GTTCCCCAGAACC
1 TTTATCAAAAACCATAGTAATCCCTCCAACCGAACACACCAGAATGTGT-AGGTTCCCCAGAACC
* * * * * *
64486 ATACACCCACCAGCACACCAAGTAAAGCCTTGAGCATAAAGTAGAGGTGCCTGCAGTAACTGTAA
65 ATACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAGCAGAGGAGCCTGCAGTAACGGTAA
64551 AGGTAACTTCCTCCAACAACACCCTCCCATAAAACA
130 AGGTAACTTCCTCCAACAACACCCTCCCATAAAACA
64587 TTTATCAAAAACCATAGTAATCCCTCCAACCGAACACACCAGAATGTGTAGGTTCCCCAGAACCA
1 TTTATCAAAAACCATAGTAATCCCTCCAACCGAACACACCAGAATGTGTAGGTTCCCCAGAACCA
* *
64652 TACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAGCAGAGGAGCCTACAGTAACGGTAAC
66 TACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAGCAGAGGAGCCTGCAGTAACGGTAAA
* * *
64717 GGTAACTTTCTCCAACTACACCCTCCCATAAAAAA
131 GGTAACTTCCTCCAACAACACCCTCCCATAAAACA
* * * * * * *
64752 TTTATAAAAAATCATAGTAGTCCATCCAACTGAACACACCAGAATGTGTCGGTTCCTCAGAACCA
1 TTTATCAAAAACCATAGTAATCCCTCCAACCGAACACACCAGAATGTGTAGGTTCCCCAGAACCA
*
64817 TACACCCACCAGCACACCAAGTAAGGCCCCTGAGCAC-AAGCCGAGGAGCCTGCA
66 TACACCCACCAGCACACCAAGTAAGG-CCCTGAGCACAAAGCAGAGGAGCCTGCA
64871 TATATACTTC
Statistics
Matches: 553, Mismatches: 58, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
164 1 0.00
165 537 0.97
166 15 0.03
ACGTcount: A:0.37, C:0.31, G:0.15, T:0.18
Consensus pattern (165 bp):
TTTATCAAAAACCATAGTAATCCCTCCAACCGAACACACCAGAATGTGTAGGTTCCCCAGAACCA
TACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAGCAGAGGAGCCTGCAGTAACGGTAAA
GGTAACTTCCTCCAACAACACCCTCCCATAAAACA
Found at i:64870 original size:330 final size:330
Alignment explanation
Indices: 64098--64840 Score: 1351
Period size: 330 Copynumber: 2.3 Consensus size: 330
64088 ATTTTTATTC
* * * *
64098 AAAAACCATAGTAATCCCTCCAACTGAACACACCAGAATGTGTAGGTTCCCCAGAACCATACACC
1 AAAAATCATAGTAGTCCATCCAACTGAACACACCAGAATGTGTCGGTTCCCCAGAACCATACACC
* *
64163 CACCAGTACACCAAGTAAAGCCTTGAGCATAAAGTAGAGGAGTCTGCAGTAACTGTAAAGGTAAC
66 CACCAGCACACCAAGTAAAGCCTTGAGCATAAAGTAGAGGAGCCTGCAGTAACTGTAAAGGTAAC
64228 TTCCTCCAACAACACCCTCCCATAAAACATTTATCAAAAACCATAGTAATCCCTCCAACCGAACA
131 TTCCTCCAACAACACCCTCCCATAAAACATTTATCAAAAACCATAGTAATCCCTCCAACCGAACA
*
64293 TACCAGAATGTGTAGGTTCCCCAGAACCATACACCCACCAGCACACCAAGTAAGGCCCTGAGCAC
196 CACCAGAATGTGTAGGTTCCCCAGAACCATACACCCACCAGCACACCAAGTAAGGCCCTGAGCAC
* * *
64358 AAAGCAGAGGAGCCTACAGTAACGGTAACGGTAGCTTTCTCTAACTACACCCTCCCATAAAACAT
261 AAAGCAGAGGAGCCTACAGTAACGGTAACGGTAACTTTCTCCAACTACACCCTCCCATAAAAAAT
64423 TTATA
326 TTATA
* * *
64428 AAAAATCATAGTAGTCTATCCAACCGAACACACCAGAATGTGTCAGTTCCCCAGAACCATACACC
1 AAAAATCATAGTAGTCCATCCAACTGAACACACCAGAATGTGTCGGTTCCCCAGAACCATACACC
*
64493 CACCAGCACACCAAGTAAAGCCTTGAGCATAAAGTAGAGGTGCCTGCAGTAACTGTAAAGGTAAC
66 CACCAGCACACCAAGTAAAGCCTTGAGCATAAAGTAGAGGAGCCTGCAGTAACTGTAAAGGTAAC
64558 TTCCTCCAACAACACCCTCCCATAAAACATTTATCAAAAACCATAGTAATCCCTCCAACCGAACA
131 TTCCTCCAACAACACCCTCCCATAAAACATTTATCAAAAACCATAGTAATCCCTCCAACCGAACA
64623 CACCAGAATGTGTAGGTTCCCCAGAACCATACACCCACCAGCACACCAAGTAAGGCCCTGAGCAC
196 CACCAGAATGTGTAGGTTCCCCAGAACCATACACCCACCAGCACACCAAGTAAGGCCCTGAGCAC
64688 AAAGCAGAGGAGCCTACAGTAACGGTAACGGTAACTTTCTCCAACTACACCCTCCCATAAAAAAT
261 AAAGCAGAGGAGCCTACAGTAACGGTAACGGTAACTTTCTCCAACTACACCCTCCCATAAAAAAT
64753 TTATA
326 TTATA
*
64758 AAAAATCATAGTAGTCCATCCAACTGAACACACCAGAATGTGTCGGTTCCTCAGAACCATACACC
1 AAAAATCATAGTAGTCCATCCAACTGAACACACCAGAATGTGTCGGTTCCCCAGAACCATACACC
64823 CACCAGCACACCAAGTAA
66 CACCAGCACACCAAGTAA
64841 GGCCCCTGAG
Statistics
Matches: 395, Mismatches: 18, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
330 395 1.00
ACGTcount: A:0.37, C:0.30, G:0.14, T:0.18
Consensus pattern (330 bp):
AAAAATCATAGTAGTCCATCCAACTGAACACACCAGAATGTGTCGGTTCCCCAGAACCATACACC
CACCAGCACACCAAGTAAAGCCTTGAGCATAAAGTAGAGGAGCCTGCAGTAACTGTAAAGGTAAC
TTCCTCCAACAACACCCTCCCATAAAACATTTATCAAAAACCATAGTAATCCCTCCAACCGAACA
CACCAGAATGTGTAGGTTCCCCAGAACCATACACCCACCAGCACACCAAGTAAGGCCCTGAGCAC
AAAGCAGAGGAGCCTACAGTAACGGTAACGGTAACTTTCTCCAACTACACCCTCCCATAAAAAAT
TTATA
Found at i:64956 original size:24 final size:24
Alignment explanation
Indices: 64928--64991 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
64918 AAATGGAGAT
64928 ATCAGAAATCAAAACATAATTTAAG
1 ATCAGAAATCAAAACATAA-TTAAG
** * **
64953 -TCAGCTATCATAACATAATTCCG
1 ATCAGAAATCAAAACATAATTAAG
64976 ATCAGAAATCAAAACA
1 ATCAGAAATCAAAACA
64992 GAATCCGGTC
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACATAATTAAG
Found at i:68528 original size:159 final size:162
Alignment explanation
Indices: 68151--68590 Score: 620
Period size: 159 Copynumber: 2.7 Consensus size: 162
68141 AAAACATATT
68151 TTTATTCAAAAACCATAGTAATCCCTCCAACCAAACACACCAGAATGTATAGGTTCCCCAGAACC
1 TTTA-TCAAAAACCATAGTAATCCCTCCAACCAAACACACCAGAATGTATAGGTTCCCCAGAACC
* * *
68216 ATACACCCACCAGCACACCAAGTAAGGCCTTGAGCACAAAGTAGAGGAGCCTGCAGTAACGGTAA
65 ATACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAGTAGAGGAGCATGCAATAACGG-AA
*
68281 TGGTAACTTCCTCCAGCAACACCCTCCCATAAAACA
129 --GTAACTTCCTCCAACAACACCCTCCCATAAAACA
* ** * *
68317 TTTTTCAAAAACCATAGTAATCCCTTTAACCAAACACACCAAAATGTATAGGTTCCCCAGAACTA
1 TTTATCAAAAACCATAGTAATCCCTCCAACCAAACACACCAGAATGTATAGGTTCCCCAGAACCA
* *
68382 TACACCCACCAGTACATCAAGTAAGGCCCTGAGCACAAAGTAGAGGAGCATGCAATAAC-G-A-T
66 TACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAGTAGAGGAGCATGCAATAACGGAAGT
* * *
68444 AACTTCTTCCAACAACACCCTTCCGTAAAACA
131 AACTTCCTCCAACAACACCCTCCCATAAAACA
** *
68476 TTTATCAAAAACCATAGTAATCCCTCCAACTGAACACACCAGAATGTGTAGGTTCCCCAGAACCA
1 TTTATCAAAAACCATAGTAATCCCTCCAACCAAACACACCAGAATGTATAGGTTCCCCAGAACCA
* * *
68541 TACACCCACCAGCATACCAAATAAGGGCCTGAGCAC-AAGCT-GAGGAGCAT
66 TACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAG-TAGAGGAGCAT
68591 ACATATATAC
Statistics
Matches: 246, Mismatches: 27, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
158 12 0.05
159 118 0.48
162 1 0.00
164 1 0.00
165 111 0.45
166 3 0.01
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.19
Consensus pattern (162 bp):
TTTATCAAAAACCATAGTAATCCCTCCAACCAAACACACCAGAATGTATAGGTTCCCCAGAACCA
TACACCCACCAGCACACCAAGTAAGGCCCTGAGCACAAAGTAGAGGAGCATGCAATAACGGAAGT
AACTTCCTCCAACAACACCCTCCCATAAAACA
Found at i:72362 original size:80 final size:81
Alignment explanation
Indices: 72228--72392 Score: 217
Period size: 80 Copynumber: 2.0 Consensus size: 81
72218 AAAAACTTAT
* * * *
72228 TCCACCTAACACCACTACCAAACCTGACATTGGAAACATACACCAAACCATTAACCTATTAGACT
1 TCCACCTAACACCACTACCAAACCAGACATTAGAAACATACACCAAACCATTAACCCATTAGACA
* *
72293 CTCCTAAAATACCAAA
66 ATCCTAAAACACCAAA
* * *
72309 TCCACCTAACACCACTACCACA-CAGACA-TAGAAAGCATACACCAAACTATTAACCCATTGGAC
1 TCCACCTAACACCACTACCAAACCAGACATTAGAAA-CATACACCAAACCATTAACCCATTAGAC
*
72372 AATCCTAAAACACTAAA
65 AATCCTAAAACACCAAA
72389 TCCA
1 TCCA
72393 TTTGTGTCAC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
79 5 0.07
80 47 0.64
81 21 0.29
ACGTcount: A:0.43, C:0.33, G:0.05, T:0.18
Consensus pattern (81 bp):
TCCACCTAACACCACTACCAAACCAGACATTAGAAACATACACCAAACCATTAACCCATTAGACA
ATCCTAAAACACCAAA
Found at i:75308 original size:19 final size:21
Alignment explanation
Indices: 75284--75354 Score: 85
Period size: 19 Copynumber: 3.5 Consensus size: 21
75274 TACAAAAATG
75284 GTATCGATACCATA-ATAG-A
1 GTATCGATACCATAGATAGTA
75303 GTATCGATACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
* **
75325 GTATCGATACCAT-GGTAGGG
1 GTATCGATACCATAGATAGTA
75345 GTATCGATAC
1 GTATCGATAC
75355 TATGGAGCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.30
20 13 0.28
21 5 0.11
22 14 0.30
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:75856 original size:54 final size:53
Alignment explanation
Indices: 75675--76168 Score: 590
Period size: 54 Copynumber: 9.3 Consensus size: 53
75665 TTACCAAACA
75675 GGCACTAAGTGTGCAATTCAC-AGAATTCATCATATGTTGATGAATAACTATTTC
1 GGCACTAAGTGTGCAATTCACGA-AATTCATCATATGTTGATGAATAAC-ATTTC
* * * * *
75729 GACACTAAGTGTGTAATTCATGAAA-T--TCATATGCTGATGAATAACCATTTT
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAA-CATTTC
75780 GGCAC----TGTGCAATTCACGAAATTCATCATATGTTGATGAATAACAGTTTC
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACA-TTTC
* * * *
75830 GACACTAAGTGTGCAATTCACGAAATTCATGAAATGTTGATGAATAACCATTTT
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAA-CATTTC
* *
75884 GGCATTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACTGTTTC
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAAC-ATTTC
* *
75938 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAA-CATTTC
* * *
75992 GACACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAATAACTATTTC
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAAC-ATTTC
** * *
76046 GGCACTAAGTGTTTAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTC
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAAC-ATTTC
* * * * * * *
76100 GGCACTAAGTGTGCAATCCACAAAATTCATAATATGTTTATGAATGACCATATG
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAAT-AACATTTC
*
76154 GGCACTACGTGTGCA
1 GGCACTAAGTGTGCA
76169 TTGCAAAGAA
Statistics
Matches: 383, Mismatches: 42, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
47 14 0.04
48 1 0.00
49 2 0.01
50 24 0.06
51 25 0.07
52 1 0.00
53 3 0.01
54 307 0.80
55 6 0.02
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (53 bp):
GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACATTTC
Found at i:76005 original size:162 final size:162
Alignment explanation
Indices: 75677--76144 Score: 673
Period size: 162 Copynumber: 2.9 Consensus size: 162
75667 ACCAAACAGG
*
75677 CACTAAGTGTGCAATTCAC-AGAATTCATCATATGTTGATGAATAACTATTTCGACACTAAGTGT
1 CACTAAGTGTGCAATTCACGA-AATTCATCATATGTTGATGAATAACTATTTCGGCACTAAGTGT
* * ** *
75741 GTAATTCATGAAA-T--TCATATGCTGATGAATAACCATTTTGGCAC----TGTGCAATTCACGA
65 GTAATTCACGAAATTCATCATATGTTGATGAATAACTGTTTCGGCACTAAGTGTGCAATTCACGA
75799 AATTCATCATATGTTGATGAATAACAGTTTCGA
130 AATTCATCATATGTTGATGAATAACAGTTTCGA
* * * * *
75832 CACTAAGTGTGCAATTCACGAAATTCATGAAATGTTGATGAATAACCATTTTGGCATTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACTATTTCGGCACTAAGTGTG
* *
75897 CAATTCACGAAATTCATCATATGTTGATGAATAACTGTTTCGGCACTAAGTGTGCAATTCACGGA
66 TAATTCACGAAATTCATCATATGTTGATGAATAACTGTTTCGGCACTAAGTGTGCAATTCACGAA
*
75962 ATTCATCATATGTTGATGAATAACCGTTTCGA
131 ATTCATCATATGTTGATGAATAACAGTTTCGA
* * *
75994 CACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAATAACTATTTCGGCACTAAGTGTT
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACTATTTCGGCACTAAGTGTG
* * *
76059 TAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTCGGCACTAAGTGTGCAATCCACAAA
66 TAATTCACGAAATTCATCATATGTTGATGAATAACTGTTTCGGCACTAAGTGTGCAATTCACGAA
* *
76124 ATTCATAATATGTTTATGAAT
131 ATTCATCATATGTTGATGAAT
76145 GACCATATGG
Statistics
Matches: 276, Mismatches: 29, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
155 67 0.24
156 2 0.01
158 26 0.09
162 181 0.66
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (162 bp):
CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACTATTTCGGCACTAAGTGTG
TAATTCACGAAATTCATCATATGTTGATGAATAACTGTTTCGGCACTAAGTGTGCAATTCACGAA
ATTCATCATATGTTGATGAATAACAGTTTCGA
Done.