Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004440.1 Hibiscus syriacus cultivar Beakdansim tig00009740_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: 59226
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1935 original size:20 final size:21
Alignment explanation
Indices: 1910--1950 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1900 AAGATTTATA
1910 ATAAGG-ATAATTAATATAAT
1 ATAAGGTATAATTAATATAAT
1930 ATAAGGTTATAATTAATATAA
1 ATAAGG-TATAATTAATATAA
1951 AAAATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (21 bp):
ATAAGGTATAATTAATATAAT
Found at i:1966 original size:24 final size:23
Alignment explanation
Indices: 1917--1983 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
1907 ATAATAAGGA
* * **
1917 TAATTAATATAATATAAGGTTA-
1 TAATTAATATAAAAAAAATTTAT
1939 TAATTAATATAAAAAATAATTTAT
1 TAATTAATATAAAAAA-AATTTAT
*
1963 TAATTAATATAATAAAAATTT
1 TAATTAATATAAAAAAAATTT
1984 GTTTAACTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
22 14 0.37
23 9 0.24
24 15 0.39
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
TAATTAATATAAAAAAAATTTAT
Found at i:1989 original size:24 final size:24
Alignment explanation
Indices: 1939--1983 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1929 TATAAGGTTA
1939 TAATTAATATAAAAAATAATTTAT
1 TAATTAATATAAAAAATAATTTAT
*
1963 TAATTAATATAATAAA-AATTT
1 TAATTAATATAAAAAATAATTT
1984 GTTTAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATTAATATAAAAAATAATTTAT
Found at i:6149 original size:5 final size:5
Alignment explanation
Indices: 6127--6165 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
6117 GCAAAGTCTA
* *
6127 ATGAT ATGAAA ATGAT ATAAT ATGAT ATGAT ATGAT ATG
1 ATGAT ATG-AT ATGAT ATGAT ATGAT ATGAT ATGAT ATG
6166 CATGTTCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (5 bp):
ATGAT
Found at i:8639 original size:14 final size:14
Alignment explanation
Indices: 8620--8646 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8610 ATTACTCCCT
8620 CTTACTTTAATATC
1 CTTACTTTAATATC
8634 CTTACTTTAATAT
1 CTTACTTTAATAT
8647 TTCTCCCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.52
Consensus pattern (14 bp):
CTTACTTTAATATC
Found at i:10050 original size:24 final size:24
Alignment explanation
Indices: 10006--10055 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
9996 ATAAAGAACC
*
10006 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
10030 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
10054 AA
1 AA
10056 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:18853 original size:24 final size:24
Alignment explanation
Indices: 18809--18858 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
18799 ATAAAGAACC
*
18809 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
18833 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
18857 AA
1 AA
18859 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:19081 original size:24 final size:25
Alignment explanation
Indices: 19033--19081 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
19023 CCACGAACCA
* *
19033 CCTAGCTCGCTAGCTCCTTTCAGCT
1 CCTAGCTCGCCAGCTCCTTGCAGCT
*
19058 CCTAGCTCGCCA-CTCCTTGGAGCT
1 CCTAGCTCGCCAGCTCCTTGCAGCT
19082 TTATCAATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.12, C:0.41, G:0.18, T:0.29
Consensus pattern (25 bp):
CCTAGCTCGCCAGCTCCTTGCAGCT
Found at i:20850 original size:27 final size:27
Alignment explanation
Indices: 20800--20852 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
20790 TGGGAATTGT
* **
20800 TTTTTTGAAAAACAATAGTTTATATAA
1 TTTTATGAAAAACAATAGGATATATAA
*
20827 TTTTATGAAACACAATAGGATATATA
1 TTTTATGAAAAACAATAGGATATATA
20853 TATATATGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (27 bp):
TTTTATGAAAAACAATAGGATATATAA
Found at i:20913 original size:3 final size:3
Alignment explanation
Indices: 20905--20976 Score: 99
Period size: 3 Copynumber: 24.0 Consensus size: 3
20895 ATTAATTTAT
* * * * *
20905 TTA TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TAA TTA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20953 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
20977 AATACATTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:20996 original size:9 final size:9
Alignment explanation
Indices: 20933--20998 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 9
20923 TAATTATTAT
*
20933 TATTATAAT
1 TATTATAAA
20942 TATTATAAA
1 TATTATAAA
* *
20951 TATTATTAT
1 TATTATAAA
* *
20960 TATTATTAT
1 TATTATAAA
20969 TATTATTAAA
1 TATTA-TAAA
*
20979 TA-CATTAAA
1 TATTA-TAAA
20988 TATTATAAA
1 TATTATAAA
20997 TA
1 TA
20999 ATAATAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
9 43 0.90
10 5 0.10
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (9 bp):
TATTATAAA
Found at i:33717 original size:7 final size:7
Alignment explanation
Indices: 33705--33763 Score: 75
Period size: 7 Copynumber: 8.0 Consensus size: 7
33695 ATGCTTGAAG
33705 GAAAAAA
1 GAAAAAA
33712 GAAAAAA
1 GAAAAAA
33719 GAAAAAA
1 GAAAAAA
33726 -AAAGAGAA
1 GAAA-A-AA
33734 GGAAAAAA
1 -GAAAAAA
33742 GAAAAAA
1 GAAAAAA
33749 GAAAAAA
1 GAAAAAA
33756 GAAGAAAA
1 GAA-AAAA
33764 AGGGGGGACA
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
6 3 0.06
7 32 0.68
8 8 0.17
9 1 0.02
10 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:33736 original size:30 final size:30
Alignment explanation
Indices: 33701--33760 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
33691 TATTATGCTT
33701 GAAGGAAAAAAGAAAAAAGAAAAAAAAAGA
1 GAAGGAAAAAAGAAAAAAGAAAAAAAAAGA
*
33731 GAAGGAAAAAAGAAAAAAGAAAAAAGAAGA
1 GAAGGAAAAAAGAAAAAAGAAAAAAAAAGA
33761 AAAAGGGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (30 bp):
GAAGGAAAAAAGAAAAAAGAAAAAAAAAGA
Found at i:34968 original size:83 final size:82
Alignment explanation
Indices: 34812--35107 Score: 448
Period size: 83 Copynumber: 3.5 Consensus size: 82
34802 AAATGCCAGG
* *
34812 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCAGGTTTGGTAAAACCAATCATT
1 TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
*
34877 GAAGTTGGAAAATGAATA
66 CAA-TTGGAAAATGAATA
* *
34895 TGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGGTCTGGTTTGGTAAAACCAATCATT
1 TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
* *
34960 TAATTTGGAAAGATGAATG
66 CAA-TTGGAAA-ATGAATA
* * *
34979 TGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCAT
1 TG-CTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCAT
35044 TGCAATTGGAAAATGAATA
65 T-CAATTGGAAAATGAATA
*
35063 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
35108 ATTCGGTAGG
Statistics
Matches: 194, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
83 111 0.57
84 16 0.08
85 65 0.34
86 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (82 bp):
TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATT
CAATTGGAAAATGAATA
Found at i:36035 original size:113 final size:112
Alignment explanation
Indices: 35832--36614 Score: 1141
Period size: 113 Copynumber: 7.0 Consensus size: 112
35822 GCAAAGCTTT
* * * **** *
35832 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCACCTGAAG
1 AAATTCATCA-TTGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
35897 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
35945 AAATTCATCATATGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCAT-TGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
36010 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * ****
36058 AAA-TCTATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTC-ATCA-TTGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
36122 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
64 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
36171 AAATTCATCATATGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAATAACTCATCTGAAG
1 AAATTCATCAT-TGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
36236 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
36284 AAATTCATCATATGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCAT-TGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
36349 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
36397 AAA-TCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTC-ATCA-TTGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
* * **
36461 G-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTCACTC
64 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
** **** *
36509 AAA-TCTATCACTTGATGGATTAAAATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAA
1 AAATTC-ATCA-TTGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
* ** *
36573 GAA-GA-G--GAAGTTCATAATAAGAAGAGCTTATTCAACCTTTTG
64 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
36615 ACTATGTCAC
Statistics
Matches: 620, Mismatches: 42, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
109 29 0.05
111 1 0.00
112 108 0.17
113 478 0.77
114 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (112 bp):
AAATTCATCATTGATGGATTAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:36841 original size:3 final size:3
Alignment explanation
Indices: 36833--36897 Score: 57
Period size: 3 Copynumber: 23.0 Consensus size: 3
36823 CCATATTAAT
* * * * *
36833 TTA TTA TTA TTA -TA TAA TTA TAA TTA -TA TTA -TA ATA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36878 TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
36898 ATACATTAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
2 8 0.16
3 41 0.84
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:36853 original size:17 final size:17
Alignment explanation
Indices: 36833--36897 Score: 62
Period size: 17 Copynumber: 3.7 Consensus size: 17
36823 CCATATTAAT
36833 TTATTATTATTATATAA
1 TTATTATTATTATATAA
*
36850 TTATAATTA-TATTATAA
1 TTATTATTATTA-TATAA
*
36867 -TATTATAAATATTATATTA
1 TTATTAT---TATTATATAA
36886 TTATTATTATTA
1 TTATTATTATTA
36898 ATACATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
16 7 0.18
17 18 0.46
19 6 0.15
20 8 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTATTATTATATAA
Found at i:37042 original size:19 final size:19
Alignment explanation
Indices: 37018--37063 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
37008 CCCGTGTGCC
** *
37018 GCCGCCTCAATGGTTTCCA
1 GCCGCCTCAACAGCTTCCA
37037 GCCGCCTCAACAGCTTCCA
1 GCCGCCTCAACAGCTTCCA
37056 GCCGCCTC
1 GCCGCCTC
37064 TGCTGCCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.15, C:0.46, G:0.20, T:0.20
Consensus pattern (19 bp):
GCCGCCTCAACAGCTTCCA
Found at i:39239 original size:20 final size:20
Alignment explanation
Indices: 39210--39247 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39200 CCTAAAACCG
* *
39210 TCGAGTAGTATCGGTACTCC
1 TCGAGGAGTATCGATACTCC
39230 TCGAGGAGTATCGATACT
1 TCGAGGAGTATCGATACT
39248 TCAAGGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (20 bp):
TCGAGGAGTATCGATACTCC
Found at i:39396 original size:42 final size:40
Alignment explanation
Indices: 39350--39437 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 40
39340 AACATTATTG
* *
39350 ATACTATATGAGTAGTATCGATACCAAGCAAGAGTAGTATCA
1 ATACTACATGAGTAGTATCAATA-CAAG-AAGAGTAGTATCA
* * *
39392 ATACTACATGAGTAGTATCAATACTAGATGAGTAGTATCG
1 ATACTACATGAGTAGTATCAATACAAGAAGAGTAGTATCA
39432 ATACTA
1 ATACTA
39438 AGTGCATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 17 0.41
41 3 0.07
42 21 0.51
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (40 bp):
ATACTACATGAGTAGTATCAATACAAGAAGAGTAGTATCA
Found at i:39406 original size:20 final size:20
Alignment explanation
Indices: 39350--39437 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
39340 AACATTATTG
* *
39350 ATACTATATGAGTAGTATCG
1 ATACTACATGAGTAGTATCA
* *
39370 ATACCAAGCAAGAGTAGTATCA
1 ATA-CTA-CATGAGTAGTATCA
39392 ATACTACATGAGTAGTATCA
1 ATACTACATGAGTAGTATCA
* *
39412 ATACTAGATGAGTAGTATCG
1 ATACTACATGAGTAGTATCA
39432 ATACTA
1 ATACTA
39438 AGTGCATAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 40 0.69
21 4 0.07
22 14 0.24
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (20 bp):
ATACTACATGAGTAGTATCA
Found at i:48121 original size:10 final size:10
Alignment explanation
Indices: 48106--48164 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
48096 CATTTAATAA
*
48106 ATAAACGATC
1 ATAAACGAAC
48116 ATAAACGAAC
1 ATAAACGAAC
* *
48126 ATGAAC-ATAA
1 ATAAACGA-AC
48136 ATGAACACGAAC
1 AT-AA-ACGAAC
48148 ATAAACGAAC
1 ATAAACGAAC
48158 ATAAACG
1 ATAAACG
48165 TTGGAGACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
9 1 0.03
10 30 0.75
11 3 0.08
12 5 0.12
13 1 0.03
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.14
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:48136 original size:16 final size:16
Alignment explanation
Indices: 48115--48159 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
48105 AATAAACGAT
48115 CATAAACGAACATGAA
1 CATAAACGAACATGAA
* *
48131 CATAAATGAACACGAA
1 CATAAACGAACATGAA
48147 CATAAACGAACAT
1 CATAAACGAACAT
48160 AAACGTTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (16 bp):
CATAAACGAACATGAA
Found at i:49218 original size:14 final size:14
Alignment explanation
Indices: 49199--49230 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
49189 AATGAACATA
49199 AACGAACATAACCG
1 AACGAACATAACCG
49213 AACGAACATAACCG
1 AACGAACATAACCG
49227 AACG
1 AACG
49231 TTCACGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:51208 original size:13 final size:13
Alignment explanation
Indices: 51192--51238 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
51182 TTTTGAATGA
51192 TTATAATTAAGAT
1 TTATAATTAAGAT
*
51205 TTATAATATCAGGA-
1 TTATAAT-T-AAGAT
51219 TTATAATTAAGAT
1 TTATAATTAAGAT
51232 TTATAAT
1 TTATAAT
51239 ACCAGGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 3 0.10
13 15 0.52
14 8 0.28
15 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (13 bp):
TTATAATTAAGAT
Found at i:51224 original size:14 final size:14
Alignment explanation
Indices: 51205--51252 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
51195 TAATTAAGAT
51205 TTATAATATCAGGA
1 TTATAATATCAGGA
*
51219 TTATAAT-T-AAGA
1 TTATAATATCAGGA
*
51231 TTTATAATACCAGGA
1 -TTATAATATCAGGA
51246 TTATAAT
1 TTATAAT
51253 TAATATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
14 14 0.50
15 3 0.11
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (14 bp):
TTATAATATCAGGA
Found at i:51266 original size:27 final size:27
Alignment explanation
Indices: 51190--51255 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
51180 ATTTTTGAAT
*
51190 GATTATAATTAAGATTTATAATATCAG
1 GATTATAATTAAGATTTATAATACCAG
51217 GATTATAATTAAGATTTATAATACCAG
1 GATTATAATTAAGATTTATAATACCAG
51244 GATTATAATTAA
1 GATTATAATTAA
51256 TATAAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (27 bp):
GATTATAATTAAGATTTATAATACCAG
Found at i:51501 original size:16 final size:16
Alignment explanation
Indices: 51482--51523 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
51472 TAATATTAGA
*
51482 TCAGGTTAATATCAAG
1 TCAGGTTAATAACAAG
*
51498 TCAGGTTGATAACAAG
1 TCAGGTTAATAACAAG
51514 TCAGG-TAATA
1 TCAGGTTAATA
51524 CCAGTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (16 bp):
TCAGGTTAATAACAAG
Done.