Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003374.1 Hibiscus syriacus cultivar Beakdansim tig00007091_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: 66021
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2584 original size:185 final size:182
Alignment explanation
Indices: 2231--2584 Score: 439
Period size: 185 Copynumber: 1.9 Consensus size: 182
2221 CTGTAAAGTC
* * *
2231 TAAAGAATTTAAGGACATGTAGAGTAATTTACTATTTTAACGGACATGTTCGTGAACACTAACTA
1 TAAAGAACTTAAGGACATGTAGAGTAATTTACTATTTTAACGGACATGCTCGCGAACACTAACTA
* *** * * * *
2296 ACGTGGTGAATCTAAACAAACATGTTGACGATCATTAAATGTATGTTTGCGAACGCTAAACGAAC
66 ACATGCACAATCTAAACAAACATGTTGACGACCATTAAATGTATGTTCGAGAACACTAAACGAAC
*
2361 TAAATATGTTCATAACGGTAAACAAACCAAACACAAACACCTTAAAAAAATAATA
131 TAAATATGTTCATAACAGT--A-AAACCAAACACAAACACCTTAAAAAAATAATA
*
2416 TAAAGAACTTAAGGACATGTAGAGTAATTTTACTATTTTGACAGG-CATGCTCGCGAA-ATCTAA
1 TAAAGAACTTAAGGACATGTAGAGTAA-TTTACTATTTTAAC-GGACATGCTCGCGAACA-CTAA
* *
2479 CTATTCATTCACAATGCTAAACAAACATGTTGACGACCATTAAATGCATATGTTCGAGAACACTA
63 CTA-ACATGCACAAT-CTAAACAAACATGTTGACGACCATTAAATG--TATGTTCGAGAACACTA
2544 AACGAACTAAATATGTTCATAAACAGT-AAA-CAAA-ACAAACA
124 AACGAACTAAATATGTTCAT-AACAGTAAAACCAAACACAAACA
2585 AATGAACACA
Statistics
Matches: 146, Mismatches: 15, Indels: 16
0.82 0.08 0.09
Matches are distributed among these distances:
185 34 0.23
186 34 0.23
187 10 0.07
188 29 0.20
190 34 0.23
191 5 0.03
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (182 bp):
TAAAGAACTTAAGGACATGTAGAGTAATTTACTATTTTAACGGACATGCTCGCGAACACTAACTA
ACATGCACAATCTAAACAAACATGTTGACGACCATTAAATGTATGTTCGAGAACACTAAACGAAC
TAAATATGTTCATAACAGTAAAACCAAACACAAACACCTTAAAAAAATAATA
Found at i:4080 original size:9 final size:9
Alignment explanation
Indices: 4066--4100 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4056 GAGGAAGGAG
*
4066 AAGAAAATA
1 AAGAAAAAA
4075 AAGAAAGAAA
1 AAGAAA-AAA
4085 AAGAAAAAA
1 AAGAAAAAA
4094 AAGAAAA
1 AAGAAAA
4101 GAAATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:4090 original size:19 final size:20
Alignment explanation
Indices: 4066--4104 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4056 GAGGAAGGAG
*
4066 AAGAAAATAAAG-AAAGAAA
1 AAGAAAAAAAAGAAAAGAAA
4085 AAGAAAAAAAAGAAAAGAAA
1 AAGAAAAAAAAGAAAAGAAA
4105 TATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (20 bp):
AAGAAAAAAAAGAAAAGAAA
Found at i:7439 original size:36 final size:36
Alignment explanation
Indices: 7392--7463 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
7382 TATAAGAAAA
7392 GGTTAACTTCAAGCTTTAGCTTTGGGTTTGAAGATG
1 GGTTAACTTCAAGCTTTAGCTTTGGGTTTGAAGATG
7428 GGTTAACTTCAAGCTTTAGCTTTGGGTTTGAAGATG
1 GGTTAACTTCAAGCTTTAGCTTTGGGTTTGAAGATG
7464 TTTTAGGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (36 bp):
GGTTAACTTCAAGCTTTAGCTTTGGGTTTGAAGATG
Found at i:17152 original size:2 final size:2
Alignment explanation
Indices: 17145--17174 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17135 TTTAAAAATG
17145 AT AT AT AT AT 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
17175 TGGTATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17646 original size:5 final size:5
Alignment explanation
Indices: 17636--17665 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
17626 CCTCCAATTG
17636 CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC
1 CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC
17666 TCCTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CCCTC
Found at i:17754 original size:26 final size:26
Alignment explanation
Indices: 17725--17775 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
17715 TCTTCCTATC
* *
17725 TTCCACTTTCCAGTATTTTAAGGTTG
1 TTCCACTTTCCAGTATATGAAGGTTG
17751 TTCCACTTTCCAGTATATGAAGGTT
1 TTCCACTTTCCAGTATATGAAGGTT
17776 CGTTGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.43
Consensus pattern (26 bp):
TTCCACTTTCCAGTATATGAAGGTTG
Found at i:21022 original size:32 final size:32
Alignment explanation
Indices: 20956--21032 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
20946 CATTATAAAA
* *
20956 AAAGTTGTATGTCTATGATTTTATTCACTGTTT
1 AAAG-TGTATGTCTATGACTTTATTCACTATTT
* **
20989 AATGTGTATGTCTATGACTTTATTTTCTATTT
1 AAAGTGTATGTCTATGACTTTATTCACTATTT
*
21021 AAAGTGTTTGTC
1 AAAGTGTATGTC
21033 CATGTTTTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 34 0.92
33 3 0.08
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.52
Consensus pattern (32 bp):
AAAGTGTATGTCTATGACTTTATTCACTATTT
Found at i:22291 original size:122 final size:121
Alignment explanation
Indices: 22068--22391 Score: 382
Period size: 122 Copynumber: 2.7 Consensus size: 121
22058 CCATCATATA
* * *
22068 AAAAACAAAA-TTCAATTAATTGACTGAGAAATGCAGAAAAATCAGATAAACTTAATGAAAGGCT
1 AAAAATAAAACTTCAATTAATTGACTGAGAAATACAGAAAAATCAGAAAAACTTAATGAAAGGCT
* * * * *
22132 CGTTGCAAGGGACACACTTTCCCTTTTTTTTGTAGAGAATCTATGCCATGTCAT-G
66 CGTTGCAGGGGACACACTTTCCCCTTTCTTTGCAGAGAATCTATACCATGTCATAG
** * * * * *
22187 TAAAAAATAAATTTTTAATTAATTGACTGAGAAATACAGAAAACTCATACAAACTTAATGACAGG
1 --AAAAATAAAACTTCAATTAATTGACTGAGAAATACAGAAAAATCAGAAAAACTTAATGAAAGG
* ** * *
22252 CTCGTTGCAGGGGGCGTACTTTCCCCTTTCTTTGCAGAGAATCTCTACCATTTCATAG
64 CTCGTTGCAGGGGACACACTTTCCCCTTTCTTTGCAGAGAATCTATACCATGTCATAG
* * * *
22310 AAAAATAAAACTTCAATTAATTGATTGAGAAATACAAAAAAATAAGAAAAACTTAATGAAATGCT
1 AAAAATAAAACTTCAATTAATTGACTGAGAAATACAGAAAAATCAGAAAAACTTAATGAAAGGCT
* *
22375 CATTGCAGGAGACACAC
66 CGTTGCAGGGGACACAC
22392 ATCCCTTTTT
Statistics
Matches: 167, Mismatches: 34, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
121 74 0.44
122 92 0.55
123 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (121 bp):
AAAAATAAAACTTCAATTAATTGACTGAGAAATACAGAAAAATCAGAAAAACTTAATGAAAGGCT
CGTTGCAGGGGACACACTTTCCCCTTTCTTTGCAGAGAATCTATACCATGTCATAG
Found at i:22907 original size:122 final size:123
Alignment explanation
Indices: 22646--23076 Score: 412
Period size: 122 Copynumber: 3.5 Consensus size: 123
22636 TAAAATTGCC
* * * *
22646 CAATTAATTGATT-AGGAAATGCT-GAAAAATCAGATAAACTTAATGAAAGGCTCGTTGAAGGGG
1 CAATTAATTGATTGA-GAAATG-TAGGAAAATCAGACAAACTTAATGAAAGGCTCATTGCAGGGG
* * *
22709 ACACGCTTTCCTTTTTTTTCTTGCAGCGAATCTCTGCCATGTCATGTAAAAATCAAACCT
64 ACACGCTTTCCTATTTTTTCTTACAGAGAATCTCTGCCATGTCATGTAAAAATCAAACCT
* * *
22769 AAATTAATTGACTGAGAAATGTAGGAAAATCAGACAAACTTAATGAAATGCTCATTGCAGGGGAC
1 CAATTAATTGATTGAGAAATGTAGGAAAATCAGACAAACTTAATGAAAGGCTCATTGCAGGGGAC
* * * *
22834 GCG-TTTCCCTATTTTTT-TTACAGAGAATCTTTGCCATGTCATTTAAAAATCAAACTT
66 ACGCTTT-CCTATTTTTTCTTACAGAGAATCTCTGCCATGTCATGTAAAAATCAAACCT
* * * * *
22891 CAATTAATTGGTTGAGAAATGAAAGAAAACCAGACAAACTTAATGAAAGGCTCATTACAGGGGAC
1 CAATTAATTGATTGAGAAATGTAGGAAAATCAGACAAACTTAATGAAAGGCTCATTGCAGGGGAC
* * *** * *
22956 ACACTTTCC-ATTTTTTC---CAGAAAATCTCTATAATTTCAT-TAAAAAAAATCAAAACTT
66 ACGCTTTCCTATTTTTTCTTACAGAGAATCTCTGCCATGTCATGT---AAAAATC-AAACCT
* * * ** ** * * *
23013 CAATTGATTGACTAAGAAATACATAAAAAACAAACAAACTTAATGAAAGGCTCGTTGCAGGGGA
1 CAATTAATTGATTGAGAAATGTAGGAAAATCAGACAAACTTAATGAAAGGCTCATTGCAGGGGA
23077 TGCGGTTTCC
Statistics
Matches: 257, Mismatches: 42, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
118 1 0.00
119 16 0.06
121 14 0.05
122 157 0.61
123 68 0.26
124 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (123 bp):
CAATTAATTGATTGAGAAATGTAGGAAAATCAGACAAACTTAATGAAAGGCTCATTGCAGGGGAC
ACGCTTTCCTATTTTTTCTTACAGAGAATCTCTGCCATGTCATGTAAAAATCAAACCT
Found at i:26273 original size:2 final size:2
Alignment explanation
Indices: 26266--26292 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26256 GTCCATTTCT
26266 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 T
26293 TCAATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28171 original size:18 final size:18
Alignment explanation
Indices: 28148--28184 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28138 AGACGGCCAC
* *
28148 TATTAATTTATTTTTATT
1 TATTAAATTATTGTTATT
28166 TATTAAATTATTGTTATT
1 TATTAAATTATTGTTATT
28184 T
1 T
28185 TCTCAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTAAATTATTGTTATT
Found at i:30238 original size:2 final size:2
Alignment explanation
Indices: 30233--30264 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30223 ACACACACAC
30233 AT AT AT AT AT AT 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
30265 TCCGATTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30793 original size:28 final size:28
Alignment explanation
Indices: 30713--30787 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
30703 AAGTGAAGAC
* * *
30713 ATTAAATTTTTAGAAAATAAAAGT--CGG
1 ATTAAATTCTTA-AAAATAAAAATAGGGG
**
30740 ATTAAATTCTTGGAAATAAAAATAGGGG
1 ATTAAATTCTTAAAAATAAAAATAGGGG
*
30768 ATTGAATTCTTAAAAATAAA
1 ATTAAATTCTTAAAAATAAA
30788 GGTAGGACTA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 9 0.24
27 10 0.26
28 19 0.50
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (28 bp):
ATTAAATTCTTAAAAATAAAAATAGGGG
Found at i:32825 original size:52 final size:52
Alignment explanation
Indices: 32763--32869 Score: 169
Period size: 52 Copynumber: 2.1 Consensus size: 52
32753 AACTCATCCA
* * *
32763 ACTCGAACCCAAGATGGCCCTCAGCTAAAACTACTCTCAATCCAACCAAATG
1 ACTCGAACCCAAAATGACCCTAAGCTAAAACTACTCTCAATCCAACCAAATG
* *
32815 ACTCGAACCCAAAATGACCCTAAGCTAAAACTACTCTTAATCCCACCAAATG
1 ACTCGAACCCAAAATGACCCTAAGCTAAAACTACTCTCAATCCAACCAAATG
32867 ACT
1 ACT
32870 TAAAAACCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.38, C:0.34, G:0.09, T:0.19
Consensus pattern (52 bp):
ACTCGAACCCAAAATGACCCTAAGCTAAAACTACTCTCAATCCAACCAAATG
Found at i:38312 original size:18 final size:20
Alignment explanation
Indices: 38283--38319 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
38273 CAAAACACAA
38283 AAAAGAAAGGGGA-AAAAAC
1 AAAAGAAAGGGGACAAAAAC
38302 AAAAG-AAGGGGACAAAAA
1 AAAAGAAAGGGGACAAAAA
38320 GGGTAACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.68, C:0.05, G:0.27, T:0.00
Consensus pattern (20 bp):
AAAAGAAAGGGGACAAAAAC
Found at i:46042 original size:21 final size:21
Alignment explanation
Indices: 46012--46087 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
46002 GATTTACATA
*
46012 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* * *
46033 TTCGCGTTGCGATTTATTCCACG
1 TTCGCGTTGCGA--TAGTCGAAG
46056 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
46075 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
46088 TTATTCTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 8 0.18
21 28 0.64
23 8 0.18
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:46069 original size:42 final size:42
Alignment explanation
Indices: 46018--46112 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
46008 CATATTCGCA
**
46018 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCACGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
46060 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
46102 TTGCGATAGTC
1 TTGCGATAGTC
46113 CAAAATCGCA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:46734 original size:16 final size:16
Alignment explanation
Indices: 46713--46748 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
46703 TCGTCTCGTC
46713 TCGTCTCGGGTCGTGG
1 TCGTCTCGGGTCGTGG
*
46729 TCGTCTTGGGTCGTGG
1 TCGTCTCGGGTCGTGG
46745 TCGT
1 TCGT
46749 GGTAATACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.42, T:0.36
Consensus pattern (16 bp):
TCGTCTCGGGTCGTGG
Found at i:46872 original size:21 final size:21
Alignment explanation
Indices: 46848--47051 Score: 99
Period size: 21 Copynumber: 9.8 Consensus size: 21
46838 AACTTGGACT
* *
46848 ATCGCAACGAATTTTGAATAA
1 ATCGCAACGAACTTCGAATAA
*
46869 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTCGAATAA
* *
46890 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTCGAATAA
* *
46911 ATCACAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTCGAATAA
* *
46932 ATCGCAACGAA-TTTGGA-AA
1 ATCGCAACGAACTTCGAATAA
*
46951 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTCGAATAA
* *
46972 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTCGAATAA
*
46993 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTCGAATAA
* *
47014 ATCGCAACGAA-TTTGGA-AA
1 ATCGCAACGAACTTCGAATAA
47033 ATCGCAACGCGAACTTCGA
1 ATCGCAA--CGAACTTCGA
47052 CTATAGCAAC
Statistics
Matches: 134, Mismatches: 28, Indels: 41
0.66 0.14 0.20
Matches are distributed among these distances:
18 6 0.04
19 40 0.30
21 55 0.41
22 6 0.04
23 27 0.20
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTCGAATAA
Found at i:46964 original size:40 final size:41
Alignment explanation
Indices: 46831--47100 Score: 447
Period size: 42 Copynumber: 6.6 Consensus size: 41
46821 TACCACCAGT
* *
46831 CAACGCGAACTTGGACTATCGCAACGAATTTTGAATAAATCG
1 CAACGCGAACTTCGACTATCGCAACGAA-TTTGGATAAATCG
*
46873 CAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCA
1 CAACGCGAACTTCGACTATCGCAACGAATTTGG-ATAAATCG
46915 CAACGCGAACTTCGACTATCGCAACGAATTTGGA-AAATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGATAAATCG
46955 CAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGG-ATAAATCG
46997 CAACGCGAACTTCGACTATCGCAACGAATTTGGA-AAATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGATAAATCG
*
47037 CAACGCGAACTTCGACTATAGCAACGAATTTGGA-AAATCG
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGATAAATCG
*
47077 CAACGCGAACTTGGACTATCGCAA
1 CAACGCGAACTTCGACTATCGCAA
47101 TGCGAATATG
Statistics
Matches: 218, Mismatches: 7, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
40 105 0.48
41 7 0.03
42 106 0.49
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (41 bp):
CAACGCGAACTTCGACTATCGCAACGAATTTGGATAAATCG
Found at i:47107 original size:82 final size:82
Alignment explanation
Indices: 46831--47100 Score: 463
Period size: 82 Copynumber: 3.3 Consensus size: 82
46821 TACCACCAGT
* *
46831 CAACGCGAACTTGGACTATCGCAACGAATTTTGAATAAATCGCAACGCGAACTTCGACTATCGCA
1 CAACGCGAACTTCGACTATCGCAACGAA-TTTGGA-AAATCGCAACGCGAACTTCGACTATCGCA
*
46896 ACGAATTTGGAATAAATCA
64 ACGAATTTGGAATAAATCG
46915 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAC
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAC
46980 GAATTTGGAATAAATCG
66 GAATTTGGAATAAATCG
*
46997 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATAGCAAC
1 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAC
47062 GAATTTGG-A-AAATCG
66 GAATTTGGAATAAATCG
*
47077 CAACGCGAACTTGGACTATCGCAA
1 CAACGCGAACTTCGACTATCGCAA
47101 TGCGAATATG
Statistics
Matches: 181, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
80 29 0.16
81 1 0.01
82 119 0.66
83 5 0.03
84 27 0.15
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (82 bp):
CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAC
GAATTTGGAATAAATCG
Found at i:47140 original size:21 final size:21
Alignment explanation
Indices: 47115--47165 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
47105 AATATGTAAA
47115 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
47136 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
47157 TCGCGTTGC
1 TCGCATTGC
47166 AAATCTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:47398 original size:19 final size:20
Alignment explanation
Indices: 47360--47402 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
47350 TTAGTAAAAA
*
47360 TTATTTAAAATATTATTATTT
1 TTATCTAAAATA-TATTATTT
47381 TTATCTAAAATA-ATTATTT
1 TTATCTAAAATATATTATTT
47400 TTA
1 TTA
47403 ATATTTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATCTAAAATATATTATTT
Found at i:61408 original size:17 final size:16
Alignment explanation
Indices: 61386--61419 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61376 TTCCCAAAAC
61386 TTAAAAAGAAAAAAGAA
1 TTAAAAA-AAAAAAGAA
*
61403 TTAAAAACAAAAAGAA
1 TTAAAAAAAAAAAGAA
61419 T
1 T
61420 GTTCAGTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.15
Consensus pattern (16 bp):
TTAAAAAAAAAAAGAA
Found at i:65379 original size:20 final size:20
Alignment explanation
Indices: 65350--65390 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
65340 TCAAAATCAG
*
65350 CAAAATTTCATTCACAATAC
1 CAAAACTTCATTCACAATAC
65370 CAAAACTTCATTCACAATAC
1 CAAAACTTCATTCACAATAC
65390 C
1 C
65391 TCAAAGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (20 bp):
CAAAACTTCATTCACAATAC
Done.