Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007622.1 Hibiscus syriacus cultivar Beakdansim tig00023068_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: 55702
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:2082 original size:20 final size:21
Alignment explanation
Indices: 2046--2085 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2036 GTCATCGAGT
*
2046 CAACTCGATCTGAGTCAACCC
1 CAACTCGATCAGAGTCAACCC
2067 CAACTCG-TCAGAGTCAACC
1 CAACTCGATCAGAGTCAACC
2086 TATCTTAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.30, C:0.38, G:0.15, T:0.17
Consensus pattern (21 bp):
CAACTCGATCAGAGTCAACCC
Found at i:2095 original size:14 final size:14
Alignment explanation
Indices: 2078--2123 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
2068 AACTCGTCAG
*
2078 AGTCAACCTATCTT
1 AGTCAACCTATCTA
2092 AGTCAA-CTCATCTA
1 AGTCAACCT-ATCTA
*
2106 AGTCAACCTATCTG
1 AGTCAACCTATCTA
2120 AGTC
1 AGTC
2124 TACCCGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.30
Consensus pattern (14 bp):
AGTCAACCTATCTA
Found at i:2142 original size:14 final size:14
Alignment explanation
Indices: 2125--2168 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
2115 ATCTGAGTCT
*
2125 ACCCGTTGACTTTG
1 ACCCATTGACTTTG
2139 ACCCATTGACTTTG
1 ACCCATTGACTTTG
*
2153 ACTCATTGAC-TTG
1 ACCCATTGACTTTG
2166 ACC
1 ACC
2169 GTAAACCGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (14 bp):
ACCCATTGACTTTG
Found at i:4184 original size:67 final size:66
Alignment explanation
Indices: 4096--4221 Score: 189
Period size: 67 Copynumber: 1.9 Consensus size: 66
4086 AGAGTCTGGT
* * * * **
4096 AGGTTCAGTCGTGTTGGTAATTCCTTGTATAGGTTTAGCATCGACTGGTAATTCCTTATCTTTGG
1 AGGTTCAGTCGTGTTGGTAATTCCTTGAATAGGTTCAACACCGACTAATAATTCCTTATCTTTGG
4161 C
66 C
4162 AGGTTCAGTCGCTGTTGGTAATTCCTTGAATAGGTTCAACACCGACTAATAATTCCTTAT
1 AGGTTCAGTCG-TGTTGGTAATTCCTTGAATAGGTTCAACACCGACTAATAATTCCTTAT
4222 GGATCTAAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
66 11 0.21
67 42 0.79
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (66 bp):
AGGTTCAGTCGTGTTGGTAATTCCTTGAATAGGTTCAACACCGACTAATAATTCCTTATCTTTGG
C
Found at i:12823 original size:7 final size:7
Alignment explanation
Indices: 12811--12838 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
12801 TTCGCTTCTA
12811 TTCGATT
1 TTCGATT
12818 TTCGATT
1 TTCGATT
12825 TTCGATT
1 TTCGATT
12832 TTCGATT
1 TTCGATT
12839 GACCGAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (7 bp):
TTCGATT
Found at i:13872 original size:25 final size:25
Alignment explanation
Indices: 13838--13892 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
13828 CTATTAGCTT
*
13838 TCCAATGGTACTTAGAATGCGTCAA
1 TCCAACGGTACTTAGAATGCGTCAA
13863 TCCAACGGTACTTAGAATGCGTCAA
1 TCCAACGGTACTTAGAATGCGTCAA
13888 TCCAA
1 TCCAA
13893 TTCAGGAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (25 bp):
TCCAACGGTACTTAGAATGCGTCAA
Found at i:14428 original size:23 final size:24
Alignment explanation
Indices: 14401--14447 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
14391 ACTATCTCTC
14401 AATCACCATCATCAT-CATCATCA
1 AATCACCATCATCATCCATCATCA
*
14424 AATCACCATTATCATCCATCATCA
1 AATCACCATCATCATCCATCATCA
14448 CCACTACCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (24 bp):
AATCACCATCATCATCCATCATCA
Found at i:14466 original size:17 final size:17
Alignment explanation
Indices: 14444--14477 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
14434 ATCATCCATC
*
14444 ATCACCACTACCTTAAT
1 ATCACCACTACCCTAAT
14461 ATCACCACTACCCTAAT
1 ATCACCACTACCCTAAT
14478 TTTGGCTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.26
Consensus pattern (17 bp):
ATCACCACTACCCTAAT
Found at i:14580 original size:21 final size:19
Alignment explanation
Indices: 14554--14596 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
14544 ATCTATTGTT
*
14554 TTAATCTTCATTTTCTTAATC
1 TTAATCTT-ATATTCTT-ATC
14575 TTAATCTTATATTCTTATC
1 TTAATCTTATATTCTTATC
14594 TTA
1 TTA
14597 GTTTTCTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
21 8 0.38
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAATCTTATATTCTTATC
Found at i:14940 original size:9 final size:9
Alignment explanation
Indices: 14934--14968 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
14924 ATAAAAAATG
14934 GAAAAAAGA
1 GAAAAAAGA
14943 GAAAAAAGA
1 GAAAAAAGA
14952 GAAAAAAGA
1 GAAAAAAGA
*
14961 GCAAAAAG
1 GAAAAAAG
14969 TAAAAAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (9 bp):
GAAAAAAGA
Found at i:14949 original size:18 final size:17
Alignment explanation
Indices: 14926--14976 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
14916 TACTTTTCAT
14926 AAAAAATGGAAAAAAGAG
1 AAAAAA-GGAAAAAAGAG
14944 AAAAAAGAGAAAAAAGAG
1 AAAAAAG-GAAAAAAGAG
* *
14962 CAAAAAGTAAAAAAG
1 AAAAAAGGAAAAAAG
14977 TAAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 8 0.27
18 22 0.73
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (17 bp):
AAAAAAGGAAAAAAGAG
Found at i:18943 original size:16 final size:18
Alignment explanation
Indices: 18912--18949 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
18902 AAATAATAAT
*
18912 AAAAGCATTTTAAAG-TG
1 AAAAGCATTGTAAAGTTG
18929 AAAAG-ATTGTAAAGTTG
1 AAAAGCATTGTAAAGTTG
18946 AAAA
1 AAAA
18950 TCAATACGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (18 bp):
AAAAGCATTGTAAAGTTG
Found at i:21223 original size:16 final size:16
Alignment explanation
Indices: 21202--21244 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
21192 CGCAAATACA
*
21202 ATCAACACATACTAGC
1 ATCAACACATACTACC
21218 ATCAACACATACTACC
1 ATCAACACATACTACC
*
21234 ATCAAAACATA
1 ATCAACACATA
21245 GAGATAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.19
Consensus pattern (16 bp):
ATCAACACATACTACC
Found at i:25065 original size:46 final size:46
Alignment explanation
Indices: 25014--25177 Score: 267
Period size: 46 Copynumber: 3.6 Consensus size: 46
25004 AAAATGAATC
* *
25014 CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGGT-T
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
*
25059 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGT
1 -CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
*
25106 CATAAATGAAATGCCTGAAAGGATGCATTAAGGCATGAAAGGATGT
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
*
25152 CATAAATGAAATGTATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGC
25178 CATAAATGAA
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
46 109 0.99
47 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.23
Consensus pattern (46 bp):
CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
Found at i:25077 original size:26 final size:25
Alignment explanation
Indices: 25014--25243 Score: 131
Period size: 26 Copynumber: 9.8 Consensus size: 25
25004 AAAATGAATC
* *
25014 CATAAATGAAATGCATGAAATGATG
1 CATAAATGAAATGCATGAAAGGATT
* *
25039 CAT---T--AAGGCATGAAAGGGTT
1 CATAAATGAAATGCATGAAAGGATT
*
25059 CCATAAATGAAATGCATGAAAGGATG
1 -CATAAATGAAATGCATGAAAGGATT
* *
25085 CAT---T--AAGGCATGAAAAGATGT
1 CATAAATGAAATGCATGAAAGGAT-T
* *
25106 CATAAATGAAATGCCTGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATT
*
25131 CAT---T--AAGGCATGAAAGGATGT
1 CATAAATGAAATGCATGAAAGGAT-T
* *
25152 CATAAATGAAATGTATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGAT-T
*
25178 CATAAATGAAATGCATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATT
* * *
25203 CAT---T--AAGGCATAAAAGGATGC
1 CATAAATGAAATGCATGAAAGGAT-T
25224 CATAAATGAAATGCATGAAA
1 CATAAATGAAATGCATGAAA
25244 TGATGCATTA
Statistics
Matches: 154, Mismatches: 27, Indels: 47
0.68 0.12 0.21
Matches are distributed among these distances:
20 51 0.33
21 12 0.08
22 4 0.03
24 4 0.03
25 12 0.08
26 71 0.46
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (25 bp):
CATAAATGAAATGCATGAAAGGATT
Found at i:25171 original size:72 final size:72
Alignment explanation
Indices: 25092--25249 Score: 253
Period size: 72 Copynumber: 2.2 Consensus size: 72
25082 ATGCATTAAG
* * * *
25092 GCATGAAAAGATGTCATAAATGAAATGCCTGAAAGGATGCATTAAGGCATGAAAGGATGTCATAA
1 GCATGAAAAGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATAA
25157 ATGAAAT
66 ATGAAAT
* *
25164 GTATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATAA
1 GCATGAAAAGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATAA
25229 ATGAAAT
66 ATGAAAT
*
25236 GCATGAAATGATGC
1 GCATGAAAAGATGC
25250 ATTAAGGCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 78 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (72 bp):
GCATGAAAAGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATAA
ATGAAAT
Found at i:25191 original size:118 final size:118
Alignment explanation
Indices: 25048--25281 Score: 398
Period size: 118 Copynumber: 2.0 Consensus size: 118
25038 GCATTAAGGC
* * *
25048 ATGAAAGGGTTCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAA-GATGTCATAAA
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCAT-AAAAGGATGCCATAAA
* *
25112 TGAAATGCCTGAAAGGATGCATTAAGGCATGAAAGGATGTCATAAATGAAATGT
65 TGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGT
25166 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATAAAT
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATAAAT
*
25231 GAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
66 GAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAAT
25282 TAACGAATAA
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
117 4 0.04
118 105 0.96
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (118 bp):
ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCATAAAT
GAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGT
Found at i:25219 original size:46 final size:46
Alignment explanation
Indices: 25169--25281 Score: 208
Period size: 46 Copynumber: 2.5 Consensus size: 46
25159 GAAATGTATG
25169 AAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATA
1 AAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATA
* *
25215 AAAGGATGCCATAAATGAAATGCATGAAATGATGCATTAAGGCATG
1 AAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATA
25261 AAAGGATGCCATAAATGAAAT
1 AAAGGATGCCATAAATGAAAT
25282 TAACGAATAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (46 bp):
AAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATA
Found at i:25926 original size:81 final size:81
Alignment explanation
Indices: 25664--25918 Score: 429
Period size: 81 Copynumber: 3.1 Consensus size: 81
25654 TATTCTAAAA
* * *
25664 TAAAAGATTAAAAGCCTAATTGTGCCTTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAATG
1 TAAAAGACTAAAAGCCTAACTGTGCCTTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
25729 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
25745 TAAAAGACTAAAAGCCTAACTGTGCCTTTGGCAGAAAGATGTCAATCATGCTAGTTAGATGAAAG
1 TAAAAGACTAAAAGCCTAACTGTGCCTTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
25810 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
25826 TAAAAGACTAAAAGCCTAACTGTACCTTTGGTAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
1 TAAAAGACTAAAAGCCTAACTGTGCCTTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
* *
25891 GCTAAATACCTTTGGG
66 GTTAAATACCTTTGAG
25907 TAAAAGACTAAA
1 TAAAAGACTAAA
25919 TGTCTAACGG
Statistics
Matches: 163, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 163 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (81 bp):
TAAAAGACTAAAAGCCTAACTGTGCCTTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:25968 original size:81 final size:79
Alignment explanation
Indices: 25664--25969 Score: 335
Period size: 81 Copynumber: 3.8 Consensus size: 79
25654 TATTCTAAAA
* * ** * * *
25664 TAAAAGATTAAAAGCCTAATTGTGCCTTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAATG
1 TAAAAGACTAAAAGCCTAA-CGTGTATTTGGAAGAAAGATGTCAATCAT-CCAGTTAGATGAAAG
25729 GTTAAATACCTTTGAG
64 GTTAAATACCTTTGAG
** * *
25745 TAAAAGACTAAAAGCCTAACTGTGCCTTTGGCAGAAAGATGTCAATCATGCTAGTTAGATGAAAG
1 TAAAAGACTAAAAGCCTAAC-GTGTATTTGGAAGAAAGATGTCAATCAT-CCAGTTAGATGAAAG
25810 GTTAAATACCTTTGAG
64 GTTAAATACCTTTGAG
* *
25826 TAAAAGACTAAAAGCCTAAC-TGTACCTTTGGTAGAAAGGTGTCAATCATGCCAGTTAGATGAAA
1 TAAAAGACTAAAAGCCTAACGTGTA--TTTGGAAGAAAGATGTCAATCAT-CCAGTTAGATGAAA
* *
25890 GGCTAAATACCTTTGGG
63 GGTTAAATACCTTTGAG
* * * * * *
25907 TAAAAGACTAAATGTCTAACGGTGTATTTGGAAGAAATATGCCAATAATCCAAGTTGGATGAA
1 TAAAAGACTAAAAGCCTAAC-GTGTATTTGGAAGAAAGATGTCAATCATCC-AGTTAGATGAA
25970 GGATTAATTG
Statistics
Matches: 199, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
79 2 0.01
80 2 0.01
81 191 0.96
83 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (79 bp):
TAAAAGACTAAAAGCCTAACGTGTATTTGGAAGAAAGATGTCAATCATCCAGTTAGATGAAAGGT
TAAATACCTTTGAG
Found at i:28124 original size:2 final size:2
Alignment explanation
Indices: 28117--28145 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28107 AAATAATGTC
28117 AT AT 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 A
28146 GCTTTTCTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30128 original size:42 final size:41
Alignment explanation
Indices: 30042--30134 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
30032 TGTCAAAATG
* * * * *
30042 GTATCGATACTGAAATAGAGTATCGGTACCGTAGTACAGTA
1 GTATCGATACTGAAAAAGAGTATCAGTACCATAATACAGAA
*
30083 GTATCGATACTGAGAGAAAG-GTATCAGTACCATAATATAGAA
1 GTATCGATACTGA-A-AAAGAGTATCAGTACCATAATACAGAA
30125 GTATCGATAC
1 GTATCGATAC
30135 CATGGTAGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 13 0.30
42 28 0.64
43 3 0.07
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (41 bp):
GTATCGATACTGAAAAAGAGTATCAGTACCATAATACAGAA
Found at i:30633 original size:45 final size:46
Alignment explanation
Indices: 30567--30729 Score: 220
Period size: 46 Copynumber: 3.6 Consensus size: 46
30557 TAAAATGAAT
* *
30567 CATAAATGAAATTCATGAAAGGATGCATTAAGGCATGAAA-GATAC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * * *
30612 CATAAATAAAATGCATTAAAGGATGCATAAAGTCATTAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
30658 CATAAATGAAATGAATTAAAGGATGCATTAAGGCACGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
30704 CATAAATGAAATGGATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGC
30730 CATAAATGAA
Statistics
Matches: 102, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
45 34 0.33
46 68 0.67
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.21
Consensus pattern (46 bp):
CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:30639 original size:12 final size:12
Alignment explanation
Indices: 30622--30688 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
30612 CATAAATAAA
30622 ATGCATTAAAGG
1 ATGCATTAAAGG
30634 ATGCA-TAAA-G
1 ATGCATTAAAGG
30644 -T-CATTAAAGG
1 ATGCATTAAAGG
*
30654 ATGCCA-TAAATGAA
1 ATG-CATTAAA-G-G
*
30668 ATGAATTAAAGG
1 ATGCATTAAAGG
30680 ATGCATTAA
1 ATGCATTAA
30689 GGCACGAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
8 2 0.05
9 5 0.12
10 2 0.05
11 5 0.12
12 17 0.40
13 5 0.12
14 7 0.16
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.25
Consensus pattern (12 bp):
ATGCATTAAAGG
Found at i:30650 original size:20 final size:21
Alignment explanation
Indices: 30625--30663 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
30615 AAATAAAATG
30625 CATTAAAGGATG-CATAAAGT
1 CATTAAAGGATGCCATAAAGT
30645 CATTAAAGGATGCCATAAA
1 CATTAAAGGATGCCATAAA
30664 TGAAATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (21 bp):
CATTAAAGGATGCCATAAAGT
Found at i:30679 original size:91 final size:93
Alignment explanation
Indices: 30567--30735 Score: 252
Period size: 91 Copynumber: 1.8 Consensus size: 93
30557 TAAAATGAAT
** * *
30567 CATAAATGAAATTCATGAAAGGATGCATTAAGGCATGAAA-GATACCATAAATAAAATGCATTAA
1 CATAAATGAAATGAATGAAAGGATGCATTAAGGCACGAAAGGATACCATAAATAAAATGCATGAA
30631 AGGATG-CATAAAGTCATTAAAGGATGC
66 AGGATGCCATAAAGTCATTAAAGGATGC
* * * *
30658 CATAAATGAAATGAATTAAAGGATGCATTAAGGCACGAAAGGATGCCATAAATGAAATGGATGAA
1 CATAAATGAAATGAATGAAAGGATGCATTAAGGCACGAAAGGATACCATAAATAAAATGCATGAA
30723 AGGATGCCATAAA
66 AGGATGCCATAAA
30736 TGAAATGCAT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
91 36 0.53
92 26 0.38
93 6 0.09
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (93 bp):
CATAAATGAAATGAATGAAAGGATGCATTAAGGCACGAAAGGATACCATAAATAAAATGCATGAA
AGGATGCCATAAAGTCATTAAAGGATGC
Found at i:30682 original size:26 final size:26
Alignment explanation
Indices: 30567--31075 Score: 285
Period size: 26 Copynumber: 21.9 Consensus size: 26
30557 TAAAATGAAT
*
30567 CATAAATGAAATTCATGAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGC
* *
30592 CAT---T--AAGGCATGAAA-GATAC
1 CATAAATGAAATGCATGAAAGGATGC
* *
30612 CATAAATAAAATGCATTAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGC
*
30637 CATAAA-G---T-CATTAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGC
* *
30658 CATAAATGAAATGAATTAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGC
* *
30683 CAT---T--AAGGCACGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGC
*
30704 CATAAATGAAATGGATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGC
30730 CATAAATGAAATGCATGAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGC
* *
30755 CAT---T--AAGGCATGAAAAGATGC
1 CATAAATGAAATGCATGAAAGGATGC
* *
30776 CATAAATGAAATTCTTGAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGC
* *
30801 CAT---T--AAGGCATGAAAGGATTC
1 CATAAATGAAATGCATGAAAGGATGC
* *
30822 CATAAACGAAATGCATTAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGC
* *
30847 CAT---T--AAGGCATGAAAGGATGT
1 CATAAATGAAATGCATGAAAGGATGC
*
30868 CATAAATAAAATGCATGAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGC
* * * *
30893 CAT---T--AAGGAATGAAATGATAC
1 CATAAATGAAATGCATGAAAGGATGC
30914 CATAAATGAAATGCATGAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGC
*
30939 CAT---T--AAGGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGC
*
30960 CATAAATAAAATGCATGAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGC
* * * *
30985 CAT---T--AAGGAATGAAATGATAC
1 CATAAATGAAATGCATGAAAGGATGC
31006 CATAAATGAAATGCATGAAAGGATG-
1 CATAAATGAAATGCATGAAAGGATGC
* *
31031 CAT---T--AAGGCATGAAAGGATAC
1 CATAAATGAAATGCATGAAAGGATGC
31052 CATAAATGAAATGCATGAAAGGAT
1 CATAAATGAAATGCATGAAAGGAT
31076 ATATTAAGGT
Statistics
Matches: 368, Mismatches: 55, Indels: 121
0.68 0.10 0.22
Matches are distributed among these distances:
19 3 0.01
20 129 0.35
21 31 0.08
22 9 0.02
23 1 0.00
24 7 0.02
25 43 0.12
26 145 0.39
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.21
Consensus pattern (26 bp):
CATAAATGAAATGCATGAAAGGATGC
Found at i:30731 original size:72 final size:72
Alignment explanation
Indices: 30649--30801 Score: 243
Period size: 72 Copynumber: 2.1 Consensus size: 72
30639 TAAAGTCATT
* *
30649 AAAGGATGCCATAAATGAAATGAATTAAAGGATGCATTAAGGCACGAAAGGATGCCATAAATGAA
1 AAAGGATGCCATAAATGAAATGAATGAAAGGATGCATTAAGGCACGAAAAGATGCCATAAATGAA
*
30714 ATGGATG
66 ATGCATG
* *
30721 AAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATGAA
1 AAAGGATGCCATAAATGAAATGAATGAAAGGATGCATTAAGGCACGAAAAGATGCCATAAATGAA
* *
30786 ATTCTTG
66 ATGCATG
30793 AAAGGATGC
1 AAAGGATGC
30802 ATTAAGGCAT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.20
Consensus pattern (72 bp):
AAAGGATGCCATAAATGAAATGAATGAAAGGATGCATTAAGGCACGAAAAGATGCCATAAATGAA
ATGCATG
Found at i:30768 original size:46 final size:46
Alignment explanation
Indices: 30718--31155 Score: 642
Period size: 46 Copynumber: 9.5 Consensus size: 46
30708 AATGAAATGG
30718 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
* * *
30764 ATGAAAAGATGCCATAAATGAAATTCTTGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
* * *
30810 ATGAAAGGATTCCATAAACGAAATGCATTAAAGGATGCATTAAGGC
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
* * *
30856 ATGAAAGGATGTCATAAATAAAATGCATGAAAGGATGCATTAAGGA
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
* *
30902 ATGAAATGATACCATAAATGAAATGCATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
* *
30948 ATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGA
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
* *
30994 ATGAAATGATACCATAAATGAAATGCATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
* ** *
31040 ATGAAAGGATACCATAAATGAAATGCATGAAAGGATATATTAAGGT
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
* * * *
31086 ATGAAGGGATGCCATAAATGAAATACATGAAATGATGTATTAAGGC
1 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
* * *
31132 AAGAAAGGATGTCATAACTGAAAT
1 ATGAAAGGATGCCATAAATGAAAT
31156 TAACGAATAA
Statistics
Matches: 350, Mismatches: 42, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 350 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGC
Found at i:30842 original size:164 final size:163
Alignment explanation
Indices: 30567--30893 Score: 503
Period size: 164 Copynumber: 2.0 Consensus size: 163
30557 TAAAATGAAT
*
30567 CATAAATGAAATTCATGAAAGGATGCATTAAGGCATGAAAGATACCATAAATAAAATGCATTAAA
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGATACCATAAATAAAATGCATTAAA
* * *
30632 GGATGCATAAAGTCATTAAAGGATGCCATAAATGAAATGAATTAAAGGATGCATTAAGGCACGAA
66 GGATGCATAAAGGCATGAAAGGATGCCATAAACGAAATGAATTAAAGGATGCATTAAGGCACGAA
* *
30697 AGGATGCCATAAATGAAATGGATGAAAGGATGC
131 AGGATGCCATAAATAAAATGCATGAAAGGATGC
* * *
30730 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATGAAATTC-TTGA
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATG-AAAGATACCATAAATAAAATGCATT-A
* * * *
30794 AAGGATGCATTAAGGCATGAAAGGATTCCATAAACGAAATGCATTAAAGGATGCATTAAGGCATG
64 AAGGATGCATAAAGGCATGAAAGGATGCCATAAACGAAATGAATTAAAGGATGCATTAAGGCACG
*
30859 AAAGGATGTCATAAATAAAATGCATGAAAGGATGC
129 AAAGGATGCCATAAATAAAATGCATGAAAGGATGC
30894 ATTAAGGAAT
Statistics
Matches: 148, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
163 38 0.26
164 110 0.74
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (163 bp):
CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGATACCATAAATAAAATGCATTAAA
GGATGCATAAAGGCATGAAAGGATGCCATAAACGAAATGAATTAAAGGATGCATTAAGGCACGAA
AGGATGCCATAAATAAAATGCATGAAAGGATGC
Found at i:31668 original size:81 final size:81
Alignment explanation
Indices: 31487--31660 Score: 258
Period size: 81 Copynumber: 2.1 Consensus size: 81
31477 TGTTCTAAAC
* * *
31487 TAAAAGATTAAAAGCCTAATTGTGCCTTTGGCAGAAAGGTCTCAATCATGCCAATTAGATGAAAT
1 TAAAAGACTAAAAGCCTAACTGTGCCTTTGGCAGAAAGGTCTCAATCATGCCAATTAGATGAAAG
*
31552 GTTAAATACCTTCGAG
66 GTTAAATAACTTCGAG
* * * *
31568 TAAAACACTAAAAGCCTAACTGTGCCTTTGGCAGAAAGGTGTCAATCTTGCCAGTTAGATGAAAG
1 TAAAAGACTAAAAGCCTAACTGTGCCTTTGGCAGAAAGGTCTCAATCATGCCAATTAGATGAAAG
* *
31633 GTTAAATAACTTTGGG
66 GTTAAATAACTTCGAG
31649 TAAAAGACTAAA
1 TAAAAGACTAAA
31661 TGTCTAACAA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (81 bp):
TAAAAGACTAAAAGCCTAACTGTGCCTTTGGCAGAAAGGTCTCAATCATGCCAATTAGATGAAAG
GTTAAATAACTTCGAG
Found at i:31679 original size:81 final size:81
Alignment explanation
Indices: 31495--31686 Score: 213
Period size: 81 Copynumber: 2.4 Consensus size: 81
31485 ACTAAAAGAT
*** * *
31495 TAAAAGCCTAATTGTGCCTTTGGCAGAAAGGTCTCAATCATGCCAATTAGATGAAATGTTAAATA
1 TAAAAGCCTAACAATGCATTTGGCAGAAAGGTCTCAATCATGCCAATTAGATGAAAGGTTAAATA
*
31560 CCTTCGAGTAAAACAC
66 ACTTCGAGTAAAACAC
** * * * *
31576 TAAAAGCCTAACTGTGCCTTTGGCAGAAAGGTGTCAATCTTGCCAGTTAGATGAAAGGTTAAATA
1 TAAAAGCCTAACAATGCATTTGGCAGAAAGGTCTCAATCATGCCAATTAGATGAAAGGTTAAATA
* * *
31641 ACTTTGGGTAAAAGAC
66 ACTTCGAGTAAAACAC
* * * *
31657 TAAATGTCTAACAATGTATTTGGCATAAAG
1 TAAAAGCCTAACAATGCATTTGGCAGAAAG
31687 ATGCCAATAA
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 95 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (81 bp):
TAAAAGCCTAACAATGCATTTGGCAGAAAGGTCTCAATCATGCCAATTAGATGAAAGGTTAAATA
ACTTCGAGTAAAACAC
Found at i:31815 original size:2 final size:2
Alignment explanation
Indices: 31808--31842 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31798 TGATAAATGA
31808 AT AT AT AT AT 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 A
31843 ACAGTGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37843 original size:59 final size:59
Alignment explanation
Indices: 37760--37876 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 59
37750 TTGAAAAATG
* * **
37760 GATCAATCCTTTTTGCAAAGGGATCGATCATTTTTCTGGAAAATGCAAGGGATCGACCA
1 GATCAATCCTTTTTACAAACGGATCGATCATTTTTCTGGAAAATAAAAGGGATCGACCA
*
37819 GATCGATCCTTTTTACAAACGGATCGATCATTTTTCTGGAAAATAAAAGGGATCGACC
1 GATCAATCCTTTTTACAAACGGATCGATCATTTTTCTGGAAAATAAAAGGGATCGACC
37877 CTTTGCACAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (59 bp):
GATCAATCCTTTTTACAAACGGATCGATCATTTTTCTGGAAAATAAAAGGGATCGACCA
Found at i:38641 original size:134 final size:133
Alignment explanation
Indices: 38398--38842 Score: 475
Period size: 134 Copynumber: 3.3 Consensus size: 133
38388 AGCAAATCGA
* *
38398 ACTTGATTCAATCTTCCCTGAGTAACAATGGAATGAATCAACATCCCCATATATGATTTTCCCTC
1 ACTTGATTCAATCTTCCTTGAGTAACAATGGAATGAATCAACATCCCCATATATAATTTTCCCTC
* * * * *
38463 AAAAAGAAGGGGAACAAATCCCTCCCTTTCAAGATTTGATATTCCCTAAGTAACTGTGGAACAAG
66 AAAAAGAAGCGGAACATAT-CCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
*
38528 TTTG
130 TCTG
* **
38532 ACTTGATTCAATATTCCTTGAGTAACAATGGAATGAATCAACATCCCCATATCCAATTTTCCCTC
1 ACTTGATTCAATCTTCCTTGAGTAACAATGGAATGAATCAACATCCCCATATATAATTTTCCCTC
* ** * * * *
38597 AAGAAGAAGCATAACATATCCATATCTTTCAAGATTTGAGATTCCCTGAGTAACAGTGGAATAGG
66 AAAAAGAAGCGGAACATATCC-TCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
38662 TCTG
130 TCTG
* * ** ** * * * *
38666 CCTCGATTCAATCTTCCGTAAAG-AACAATAAAATAAATCAACGTCCCCAAATATTATTTTCCCT
1 ACTTGATTCAATCTTCC-TTGAGTAACAATGGAATGAATCAACATCCCCATATATAATTTTCCCT
* * *
38730 -AAAAAGAAGCGGAATATATCTCTCTCTTTCAAGATTTGATTTTCCCTGAGTATCAGTGGAACAA
65 CAAAAAGAAGCGGAACATATC-CTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
*
38794 GTC-C
129 GTCTG
** ** *
38798 ACCTCAATTCAATCTTCCCCGAAG-AACAGTGGAATGAATCAACAT
1 A-CTTGATTCAATCTTCCTTG-AGTAACAATGGAATGAATCAACAT
38843 TTATCGATAT
Statistics
Matches: 254, Mismatches: 52, Indels: 11
0.80 0.16 0.03
Matches are distributed among these distances:
133 90 0.35
134 161 0.63
135 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (133 bp):
ACTTGATTCAATCTTCCTTGAGTAACAATGGAATGAATCAACATCCCCATATATAATTTTCCCTC
AAAAAGAAGCGGAACATATCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTG
Found at i:39679 original size:20 final size:20
Alignment explanation
Indices: 39656--39705 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
39646 CTTGGGGCGT
*
39656 GTTTTTGGGGCTTTTATAGA
1 GTTTTTAGGGCTTTTATAGA
39676 GTTTTTAGGGCTTTTATAGA
1 GTTTTTAGGGCTTTTATAGA
39696 GTTTTTAGGG
1 GTTTTTAGGG
39706 AGTTTTAGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.04, G:0.30, T:0.50
Consensus pattern (20 bp):
GTTTTTAGGGCTTTTATAGA
Found at i:41290 original size:131 final size:132
Alignment explanation
Indices: 41057--41389 Score: 368
Period size: 131 Copynumber: 2.5 Consensus size: 132
41047 GCTATGAGTG
* * * * *
41057 ATAAATGACTATTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTTGATATTTTCC
1 ATAAATGATTGTTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCA
* * * * * *
41122 TTTTC-TCTCGAATTAATATTGGTTCTTAGGATAAAATAGTGATACCTCTTCATTTCAATTGGAG
66 TTTTCATCTCGAATCAATATTGATTCTTAAGACAAAATAATAATACCTCTTCATTTCAATTGGAG
41186 CA
131 CA
* *
41188 ATAAATGA-TGTCTTTAAGGTATGAGAGATCATTTATTCTCGATTGGAAATCATTAGATATTATC
1 ATAAATGATTGT-TTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
* * ** *
41252 ATTTTCAT-TCGAATCAATATTGAATT-TTAAGACGAAATAATAATATCTCTTTGTTTCTATTGG
65 ATTTTCATCTCGAATCAATATTG-ATTCTTAAGACAAAATAATAATACCTCTTCATTTCAATTGG
*
41315 AGTA
129 AGCA
* * * * * * * * *
41319 ATAAGTGATTGTTTTAATGCACGAAAGGTCATTTATTCTCGGTTGAAAATAATTAGATCTTATCG
1 ATAAATGATTGTTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCA
41384 TTTTCA
66 TTTTCA
41390 CTCTTAAAAT
Statistics
Matches: 169, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
130 2 0.01
131 161 0.95
132 6 0.04
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (132 bp):
ATAAATGATTGTTTTAAGGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCA
TTTTCATCTCGAATCAATATTGATTCTTAAGACAAAATAATAATACCTCTTCATTTCAATTGGAG
CA
Found at i:41778 original size:18 final size:18
Alignment explanation
Indices: 41742--41779 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41732 CAAGTTTGTT
*
41742 ATTTTAATTAAAATTAAA
1 ATTTTAATTAAAATGAAA
41760 ATTTT-ATTAAAATGGAAA
1 ATTTTAATTAAAAT-GAAA
41778 AT
1 AT
41780 ACGTTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
ATTTTAATTAAAATGAAA
Found at i:42592 original size:17 final size:17
Alignment explanation
Indices: 42570--42612 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
42560 AATAAGGTTT
42570 GAGGAATTGATTTTAAG
1 GAGGAATTGATTTTAAG
42587 GAGGAATTGATTTTAAG
1 GAGGAATTGATTTTAAG
42604 GAGGAATTG
1 GAGGAATTG
42613 GATTATAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (17 bp):
GAGGAATTGATTTTAAG
Found at i:45203 original size:21 final size:21
Alignment explanation
Indices: 45175--45221 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
45165 TTAATTCGAT
45175 TTAA-TCCCTAATTCTAGTAA
1 TTAAGTCCCTAATTCTAGTAA
45195 TTAAGTCCCTAATTCTAGTAA
1 TTAAGTCCCTAATTCTAGTAA
45216 TTAAGT
1 TTAAGT
45222 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (21 bp):
TTAAGTCCCTAATTCTAGTAA
Found at i:48674 original size:20 final size:21
Alignment explanation
Indices: 48638--48677 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
48628 GTCATCGAGT
*
48638 CAACTCGATCTGAGTCAACCC
1 CAACTCGATCAGAGTCAACCC
48659 CAACTCG-TCAGAGTCAACC
1 CAACTCGATCAGAGTCAACC
48678 TATCTTAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.30, C:0.38, G:0.15, T:0.17
Consensus pattern (21 bp):
CAACTCGATCAGAGTCAACCC
Found at i:48687 original size:14 final size:14
Alignment explanation
Indices: 48670--48719 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
48660 AACTCGTCAG
*
48670 AGTCAACCTATCTT
1 AGTCAACCTATCTA
48684 AGTCAA-CTCATCTA
1 AGTCAACCT-ATCTA
*
48698 AGTCAACCTATCTG
1 AGTCAACCTATCTA
48712 AGTCAACC
1 AGTCAACC
48720 CGTTGACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 2 0.06
14 28 0.88
15 2 0.06
ACGTcount: A:0.32, C:0.30, G:0.10, T:0.28
Consensus pattern (14 bp):
AGTCAACCTATCTA
Found at i:48734 original size:14 final size:14
Alignment explanation
Indices: 48717--48761 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
48707 ATCTGAGTCA
*
48717 ACCCGTTGACTTTG
1 ACCCATTGACTTTG
48731 ACCCATTGACTTTG
1 ACCCATTGACTTTG
*
48745 ACTCATTGACTTTG
1 ACCCATTGACTTTG
48759 ACC
1 ACC
48762 GTAAACCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.36
Consensus pattern (14 bp):
ACCCATTGACTTTG
Found at i:48794 original size:20 final size:21
Alignment explanation
Indices: 48753--48794 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
48743 TGACTCATTG
**
48753 ACTTTGACCGTAAACCGTTAA
1 ACTTTGACCGTAAAAAGTTAA
48774 ACTTTGACCG-AAAAAGTTAA
1 ACTTTGACCGTAAAAAGTTAA
48794 A
1 A
48795 TTTTTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (21 bp):
ACTTTGACCGTAAAAAGTTAA
Found at i:50706 original size:31 final size:31
Alignment explanation
Indices: 50671--50776 Score: 74
Period size: 31 Copynumber: 3.3 Consensus size: 31
50661 AAGAGTCTGG
50671 TAGGTTCAGTCGCTGTTGGTAATTCCTTGTA
1 TAGGTTCAGTCGCTGTTGGTAATTCCTTGTA
* * *
50702 TAGGTTTAGCATCGAC---TGGTAATTCCTTATCTT
1 TAGGTTCAG--TCG-CTGTTGGTAATTCC-T-TGTA
* *
50735 TGGCAGGTTCAGTCGTTGTTGGTAATTCCTTGAA
1 T---AGGTTCAGTCGCTGTTGGTAATTCCTTGTA
50769 TAGGTTCA
1 TAGGTTCA
50777 ACACCGACTA
Statistics
Matches: 56, Mismatches: 8, Indels: 22
0.65 0.09 0.26
Matches are distributed among these distances:
31 25 0.45
32 1 0.02
33 6 0.11
34 6 0.11
35 1 0.02
36 17 0.30
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.41
Consensus pattern (31 bp):
TAGGTTCAGTCGCTGTTGGTAATTCCTTGTA
Found at i:50785 original size:67 final size:67
Alignment explanation
Indices: 50672--50798 Score: 191
Period size: 67 Copynumber: 1.9 Consensus size: 67
50662 AGAGTCTGGT
* * * * **
50672 AGGTTCAGTCGCTGTTGGTAATTCCTTGTATAGGTTTAGCATCGACTGGTAATTCCTTATCTTTG
1 AGGTTCAGTCGCTGTTGGTAATTCCTTGAATAGGTTCAACACCGACTAATAATTCCTTATCTTTG
50737 GC
66 GC
*
50739 AGGTTCAGTCGTTGTTGGTAATTCCTTGAATAGGTTCAACACCGACTAATAATTCCTTAT
1 AGGTTCAGTCGCTGTTGGTAATTCCTTGAATAGGTTCAACACCGACTAATAATTCCTTAT
50799 GGATCTAAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (67 bp):
AGGTTCAGTCGCTGTTGGTAATTCCTTGAATAGGTTCAACACCGACTAATAATTCCTTATCTTTG
GC
Found at i:51902 original size:2 final size:2
Alignment explanation
Indices: 51895--51925 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51885 ACCTATCTGT
51895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51926 TAAGTATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.