Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009244.1 Hibiscus syriacus cultivar Beakdansim tig00112879_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: 51011
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1029 original size:30 final size:29
Alignment explanation
Indices: 965--1029 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
955 TTCGAATGAA
* *
965 GATTATTTTGTAAATGCTTAAAAATATAAT
1 GATTATTTTGTAAAT-CTTAAAAAAATAAC
*
995 GATTATTTTGTAATAT-TTGAAAAAAATACC
1 GATTATTTTGTAA-ATCTT-AAAAAAATAAC
1025 GATTA
1 GATTA
1030 AAATAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 2 0.07
30 26 0.87
31 2 0.07
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.42
Consensus pattern (29 bp):
GATTATTTTGTAAATCTTAAAAAAATAAC
Found at i:8319 original size:22 final size:21
Alignment explanation
Indices: 8288--8370 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 21
8278 GTCTAAACTG
8288 TGTTTAATTATATGAAGTGAT
1 TGTTTAATTATATGAAGTGAT
* ** *
8309 TGGTTTTATTAGCTGAA-TGAA
1 T-GTTTAATTATATGAAGTGAT
* *
8330 TG-ATAATTATATGAACTG--
1 TGTTTAATTATATGAAGTGAT
8348 TGTTTAATTATATGAAGTGAT
1 TGTTTAATTATATGAAGTGAT
8369 TG
1 TG
8371 GTTTTATGAA
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
18 2 0.04
19 23 0.49
20 3 0.06
21 7 0.15
22 12 0.26
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (21 bp):
TGTTTAATTATATGAAGTGAT
Found at i:12881 original size:42 final size:42
Alignment explanation
Indices: 12833--12952 Score: 195
Period size: 42 Copynumber: 2.9 Consensus size: 42
12823 ACTTCGACTA
*
12833 TCGCGTTGCGATTTATTCCAAATTTGTTGCGATAGTCCAAGT
1 TCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT
* * *
12875 TTGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCTAAGT
1 TCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT
*
12917 TCGCGTTGCGATTTATTCCAAATTCGTTGTGATAGT
1 TCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGT
12953 TCAAAATCGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (42 bp):
TCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT
Found at i:12944 original size:21 final size:21
Alignment explanation
Indices: 12836--12945 Score: 93
Period size: 21 Copynumber: 5.2 Consensus size: 21
12826 TCGACTATCG
12836 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* * *
12857 TGTTGCGA--TAGTCCAAGTTT
1 CGTTGCGATTTATTCCAA-ATT
*
12877 GCGTTGCGATTTATTACAAATT
1 -CGTTGCGATTTATTCCAAATT
* * *
12899 CGTTGCGA--TAGTCTAAGTT
1 CGTTGCGATTTATTCCAAATT
12918 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
12941 CGTTG
1 CGTTG
12946 TGATAGTTCA
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
19 14 0.21
20 2 0.03
21 35 0.52
22 2 0.03
23 14 0.21
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:13851 original size:21 final size:21
Alignment explanation
Indices: 13827--14085 Score: 223
Period size: 21 Copynumber: 12.4 Consensus size: 21
13817 TTTGGAATAA
*
13827 ATCGCAACGCGGACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
13848 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
13867 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* *
13890 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
13909 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * *
13932 ATCGTAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
* *
13951 AAATCACAACGTGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
13974 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
13995 ATCGCAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* *
14014 ATCGCAACGCGAATTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * *
14035 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
*
14054 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTCGACT
14077 ATCGCAACG
1 ATCGCAACG
14086 AATTTGGAAA
Statistics
Matches: 196, Mismatches: 24, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
19 58 0.30
21 99 0.51
23 39 0.20
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:13864 original size:42 final size:42
Alignment explanation
Indices: 13802--14022 Score: 315
Period size: 42 Copynumber: 5.3 Consensus size: 42
13792 TGCGATTTTG
* * *
13802 GACTATCGCAATGAATTTGGAATAAATCGCAACGCGGACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
13844 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
13886 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
13928 GACTATCGTAACGAACTTGGAATAAATCACAACGTGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
13970 GACTATCGCAACGCGAACTTCGACT--ATCGCAA--CGAACTTG
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
14010 GACTATCGCAACG
1 GACTATCGCAACG
14023 CGAATTTGGA
Statistics
Matches: 165, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
38 2 0.01
40 17 0.10
42 136 0.82
44 10 0.06
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:14101 original size:19 final size:19
Alignment explanation
Indices: 13798--14093 Score: 160
Period size: 21 Copynumber: 14.3 Consensus size: 19
13788 TCGTTGCGAT
*
13798 TTTGGACTATCGCAATGAA
1 TTTGGACTATCGCAACGAA
* *
13817 TTTGGAATAAATCGCAACGCGGA
1 TTTGGACT--ATCGCAA--CGAA
* *
13840 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
* *
13859 CTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
* *
13882 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
* *
13901 CTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
* * *
13924 CTTCGACTATCGTAACGAA
1 TTTGGACTATCGCAACGAA
* * *
13943 CTTGGAATAAATCACAACGTGAA
1 TTTGGACT--ATCGCAAC--GAA
* *
13966 CTTCGACTATCGCAACGCGAA
1 TTTGGACTATCGCAA--CGAA
* *
13987 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
14006 CTTGGACTATCGCAACGCGAA
1 TTTGGACTATCGCAA--CGAA
14027 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
14046 TTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
*
14069 CTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
14088 TTTGGA
1 TTTGGA
14094 AAATCGCATT
Statistics
Matches: 224, Mismatches: 29, Indels: 48
0.74 0.10 0.16
Matches are distributed among these distances:
19 74 0.33
21 103 0.46
23 47 0.21
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:14126 original size:21 final size:21
Alignment explanation
Indices: 14097--14149 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
14087 ATTTGGAAAA
*
14097 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* *
14118 TCGCGTTGCGATAGTTGATGT
1 TCGCGTTGCGATAGTCGAAGT
14139 TCGCGTTGCGA
1 TCGCGTTGCGA
14150 AGCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:16482 original size:64 final size:63
Alignment explanation
Indices: 16382--16511 Score: 190
Period size: 64 Copynumber: 2.0 Consensus size: 63
16372 AAAAAACTTT
* * *
16382 GAAAAAAATATTTTTAGGTGGATTTTTTTATATTTAATATTATATCTAGAATTATCTATAGAA
1 GAAAAAAATATTTTTAGATGGATTTTTTAATATTTAATATTATATCCAGAATTATCTATAGAA
* *
16445 GAAAAAAATATTTATTAGAT-GATATTTTTAATATTTAATATTATGTCCATAATTATCTATAGAA
1 GAAAAAAATATTT-TTAGATGGAT-TTTTTAATATTTAATATTATATCCAGAATTATCTATAGAA
16509 GAA
1 GAA
16512 TCTAGTTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
63 16 0.27
64 44 0.73
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (63 bp):
GAAAAAAATATTTTTAGATGGATTTTTTAATATTTAATATTATATCCAGAATTATCTATAGAA
Found at i:19777 original size:13 final size:13
Alignment explanation
Indices: 19759--19783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19749 TCGTTGATGG
19759 TCCTGATAGTCCC
1 TCCTGATAGTCCC
19772 TCCTGATAGTCC
1 TCCTGATAGTCC
19784 TTGGTCGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (13 bp):
TCCTGATAGTCCC
Found at i:23234 original size:23 final size:23
Alignment explanation
Indices: 23195--23403 Score: 168
Period size: 23 Copynumber: 8.7 Consensus size: 23
23185 CAATAAACAT
*
23195 TTTCTTCTTCTTCCATAAACTCA
1 TTTCTTTTTCTTCCATAAACTCA
* * *
23218 TTACTTTTTCTTTCATAAACCCA
1 TTTCTTTTTCTTCCATAAACTCA
*
23241 TTTCTTCTTCTTCCATAAACTCA
1 TTTCTTTTTCTTCCATAAACTCA
*
23264 TTTCTTCTTCTTGTTCTTCCATAAACAT-G
1 --T-TTC-T-TT-TTCTTCCATAAAC-TCA
*
23293 TTTCTTCTTCTTCCATAAACTCA
1 TTTCTTTTTCTTCCATAAACTCA
* * *
23316 TTTATTTTTCTTTCATAAACTCGTT
1 TTTCTTTTTCTTCCATAAACTC--A
* *
23341 TCTTCTTTTTCTTCCACAAACTCC
1 T-TTCTTTTTCTTCCATAAACTCA
* * **
23365 TTTCTTCTTCTTCCACAAACTTG
1 TTTCTTTTTCTTCCATAAACTCA
*
23388 TTTCTTCTTCTTCCAT
1 TTTCTTTTTCTTCCAT
23404 TCGTCTGAGA
Statistics
Matches: 151, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
22 1 0.01
23 104 0.69
24 2 0.01
25 3 0.02
26 24 0.16
27 2 0.01
28 1 0.01
29 13 0.09
30 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTCTTTTTCTTCCATAAACTCA
Found at i:23251 original size:46 final size:47
Alignment explanation
Indices: 23195--23403 Score: 219
Period size: 46 Copynumber: 4.3 Consensus size: 47
23185 CAATAAACAT
* * *
23195 TTTCTTCTTCTTCCATAAACTCA-TTACTTTTTCTTTCATAAACCCA
1 TTTCTTCTTCTTCCATAAACTCATTTACTTTTTCTTCCATAAACTCG
*
23241 TTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTGTTCTTCCATAAACAT-G
1 TTTCTTCTTCTTCCATAAACTCA-TT-TAC-T-TT-TTCTTCCATAAAC-TCG
*
23293 TTTCTTCTTCTTCCATAAACTCATTTA-TTTTTCTTTCATAAACTCG
1 TTTCTTCTTCTTCCATAAACTCATTTACTTTTTCTTCCATAAACTCG
* * * * *
23339 TTTCTTCTTTTTCTTCCACAAACTCCTTT-CTTCTTCTTCCACAAACTTG
1 TTTCTTC---TTCTTCCATAAACTCATTTACTTTTTCTTCCATAAACTCG
23388 TTTCTTCTTCTTCCAT
1 TTTCTTCTTCTTCCAT
23404 TCGTCTGAGA
Statistics
Matches: 138, Mismatches: 13, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
45 1 0.01
46 51 0.37
47 2 0.01
48 2 0.01
49 41 0.30
50 2 0.01
51 4 0.03
52 35 0.25
ACGTcount: A:0.19, C:0.28, G:0.02, T:0.51
Consensus pattern (47 bp):
TTTCTTCTTCTTCCATAAACTCATTTACTTTTTCTTCCATAAACTCG
Found at i:23281 original size:29 final size:28
Alignment explanation
Indices: 23242--23376 Score: 114
Period size: 26 Copynumber: 5.2 Consensus size: 28
23232 ATAAACCCAT
23242 TTCTTCTTCTTCCATAAACTCATTTCTTC
1 TTCTT-TTCTTCCATAAACTCATTTCTTC
*
23271 TTCTTGTTCTTCCATAAA--CATGT-TTC
1 TTCTT-TTCTTCCATAAACTCATTTCTTC
23297 TTC--TTCTTCCATAAACTCA--T-TT-
1 TTCTTTTCTTCCATAAACTCATTTCTTC
* * *
23319 AT-TTTTCTTTCATAAACTCGTTTCTTC
1 TTCTTTTCTTCCATAAACTCATTTCTTC
* *
23346 -T-TTTTCTTCCACAAACTCCTTTCTTC
1 TTCTTTTCTTCCATAAACTCATTTCTTC
23372 TTCTT
1 TTCTT
23377 CCACAAACTT
Statistics
Matches: 88, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
22 1 0.01
23 29 0.33
25 3 0.03
26 31 0.35
27 5 0.06
28 2 0.02
29 17 0.19
ACGTcount: A:0.18, C:0.27, G:0.02, T:0.53
Consensus pattern (28 bp):
TTCTTTTCTTCCATAAACTCATTTCTTC
Found at i:23283 original size:75 final size:74
Alignment explanation
Indices: 23196--23403 Score: 242
Period size: 75 Copynumber: 2.8 Consensus size: 74
23186 AATAAACATT
* * * *
23196 TTCTTCTTCTTCCATAAACTCATTACTTTTTCTTTCATAAACCCATTTCTTCTTCTTCCATAAAC
1 TTCTT-TTCTTCCATAAACTCATTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTCCATAAAC
23261 TCATTTCTTC
65 TCATTTCTTC
* * * *
23271 TTCTTGTTCTTCCATAAACAT-GTTTCTTCTTCTTCCATAAACTCATTTATTTTTCTTTCATAAA
1 TTCTT-TTCTTCCATAAAC-TCATTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTCCATAAA
*
23335 CTCGTTTCTTC
64 CTCATTTCTTC
* * * **
23346 -T-TTTTCTTCCACAAACTCCTTTCTTCTTCTTCCACAAACTTGTTTCTTCTTCTTCCAT
1 TTCTTTTCTTCCATAAACTCATTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTCCAT
23404 TCGTCTGAGA
Statistics
Matches: 113, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
71 1 0.01
72 45 0.40
73 2 0.02
74 1 0.01
75 63 0.56
76 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.02, T:0.50
Consensus pattern (74 bp):
TTCTTTTCTTCCATAAACTCATTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTCCATAAACT
CATTTCTTC
Found at i:23396 original size:98 final size:95
Alignment explanation
Indices: 23177--23403 Score: 284
Period size: 98 Copynumber: 2.4 Consensus size: 95
23167 TTTTGAACCA
* *
23177 TTCTTCTTCAATAAACAT-TTTCTTCTTCTTCCATAAACTCATTACTTTTTCTTTCATAAACCCA
1 TTCTTCTTCCACAAACATGTTTCTTCTTCTTCCATAAACTCATTACTTTTTCTTTCATAAACCCA
*
23241 TTTCTTCTTCTTCCATAAACTCATTTCTTCTTC
66 TTTCTTCTTCTTCCACAAACTC---TCTTCTTC
* * *
23274 TTGTTCTTCCATAAACATGTTTCTTCTTCTTCCATAAACTCATTTA-TTTTTCTTTCATAAACTC
1 TTCTTCTTCCACAAACATGTTTCTTCTTCTTCCATAAACTCA-TTACTTTTTCTTTCATAAACCC
*
23338 GTTTCTTCTTTTTCTTCCACAAACTC-C-T-TTC
65 ATTTCTTC---TTCTTCCACAAACTCTCTTCTTC
*
23369 TTCTTCTTCCACAAACTTGTTTCTTCTTCTTCCAT
1 TTCTTCTTCCACAAACATGTTTCTTCTTCTTCCAT
23404 TCGTCTGAGA
Statistics
Matches: 117, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
95 35 0.30
96 1 0.01
97 17 0.15
98 47 0.40
99 3 0.03
101 14 0.12
ACGTcount: A:0.20, C:0.28, G:0.02, T:0.50
Consensus pattern (95 bp):
TTCTTCTTCCACAAACATGTTTCTTCTTCTTCCATAAACTCATTACTTTTTCTTTCATAAACCCA
TTTCTTCTTCTTCCACAAACTCTCTTCTTC
Found at i:27349 original size:20 final size:20
Alignment explanation
Indices: 27306--27343 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
27296 AATTTTTTTT
*
27306 AGATTTATTAAATTTTATGA
1 AGATTTATTAAATTTCATGA
27326 AGATTTA-TAAATTTCATG
1 AGATTTATTAAATTTCATG
27344 TGAGATAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (20 bp):
AGATTTATTAAATTTCATGA
Found at i:28955 original size:31 final size:30
Alignment explanation
Indices: 28920--28993 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
28910 GGGGCCGTGG
*
28920 GGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
28951 GGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGCCTACCTAAGAAACATCTCAGGGCCGCA
28981 GAGCCTACCTAAG
1 G-GCCTACCTAAG
28994 TGTCACATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.27, C:0.32, G:0.26, T:0.15
Consensus pattern (30 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:28988 original size:62 final size:63
Alignment explanation
Indices: 28872--28993 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 63
28862 ACCTAAGGGA
* * ** *
28872 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
*
28935 ACATCTTAGGGCC-GCAG-GCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
28994 TGTCACATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
61 1 0.02
62 35 0.69
63 15 0.29
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:30505 original size:18 final size:18
Alignment explanation
Indices: 30482--30516 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30472 TTCCATCCGG
*
30482 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
30500 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
30517 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:31826 original size:8 final size:8
Alignment explanation
Indices: 31796--31852 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
31786 GGTCAACAAT
31796 GGTCAACG
1 GGTCAACG
31804 CCGGTCAAC-
1 --GGTCAACG
31813 GGTCAACG
1 GGTCAACG
31821 GGTCAAC-
1 GGTCAACG
*
31828 GGTCAATG
1 GGTCAACG
31836 GGT---CG
1 GGTCAACG
31841 GGTCAACG
1 GGTCAACG
31849 GGTC
1 GGTC
31853 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
5 4 0.10
7 13 0.32
8 16 0.40
10 7 0.17
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:31826 original size:15 final size:15
Alignment explanation
Indices: 31796--31852 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
31786 GGTCAACAAT
31796 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
31813 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
* *
31828 GGTCAATGGGTC--G
1 GGTCAACGGGTCAAC
31841 GGTCAACGGGTC
1 GGTCAACGGGTC
31853 GGGTCGGGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 11 0.30
15 18 0.49
17 8 0.22
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:31846 original size:13 final size:13
Alignment explanation
Indices: 31813--31857 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
31803 GCCGGTCAAC
*
31813 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
*
31828 GGTCAATGGGTCG
1 GGTCAACGGGTCG
31841 GGTCAACGGGTCG
1 GGTCAACGGGTCG
31854 GGTC
1 GGTC
31858 GGGTCAACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 16 0.59
15 11 0.41
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:31892 original size:13 final size:13
Alignment explanation
Indices: 31852--31900 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
31842 GTCAACGGGT
*
31852 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
* * *
31865 CTGGTTGGATAAA
1 CGGGTCGGGTAAA
31878 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
31891 CGGGTCGGGT
1 CGGGTCGGGT
31901 CGGGTCGGGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:33971 original size:31 final size:30
Alignment explanation
Indices: 33936--34009 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
33926 GGGGCCGTGG
*
33936 GGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
33967 GGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGCCTACCTAAGAAACATCTCAGGGCCGCA
33997 GAGCCTACCTAAG
1 G-GCCTACCTAAG
34010 TGTCACATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.27, C:0.32, G:0.26, T:0.15
Consensus pattern (30 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:34004 original size:62 final size:63
Alignment explanation
Indices: 33888--34009 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 63
33878 ACCTAAGGGA
* * ** *
33888 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
*
33951 ACATCTTAGGGCC-GCAG-GCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
34010 TGTCACATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
61 1 0.02
62 35 0.69
63 15 0.29
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:35520 original size:18 final size:18
Alignment explanation
Indices: 35497--35531 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35487 TTCCATCCGG
*
35497 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
35515 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
35532 GTCCTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:36839 original size:8 final size:8
Alignment explanation
Indices: 36809--36865 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
36799 GGTCAACAAT
36809 GGTCAACG
1 GGTCAACG
36817 CCGGTCAAC-
1 --GGTCAACG
36826 GGTCAACG
1 GGTCAACG
36834 GGTCAAC-
1 GGTCAACG
*
36841 GGTCAATG
1 GGTCAACG
36849 GGT---CG
1 GGTCAACG
36854 GGTCAACG
1 GGTCAACG
36862 GGTC
1 GGTC
36866 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
5 4 0.10
7 13 0.32
8 16 0.40
10 7 0.17
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:36839 original size:15 final size:15
Alignment explanation
Indices: 36809--36865 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
36799 GGTCAACAAT
36809 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
36826 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
* *
36841 GGTCAATGGGTC--G
1 GGTCAACGGGTCAAC
36854 GGTCAACGGGTC
1 GGTCAACGGGTC
36866 GGGTCGGGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 11 0.30
15 18 0.49
17 8 0.22
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:36859 original size:13 final size:13
Alignment explanation
Indices: 36826--36870 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
36816 GCCGGTCAAC
*
36826 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
*
36841 GGTCAATGGGTCG
1 GGTCAACGGGTCG
36854 GGTCAACGGGTCG
1 GGTCAACGGGTCG
36867 GGTC
1 GGTC
36871 GGGTCGGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 16 0.59
15 11 0.41
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:40996 original size:23 final size:24
Alignment explanation
Indices: 40961--41007 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
40951 ACGATCAGAC
*
40961 TGGTCAACGGTCAATGAGTTAACT
1 TGGTCAACAGTCAATGAGTTAACT
40985 TGGTCAA-AGTCAATGAGTTAACT
1 TGGTCAACAGTCAATGAGTTAACT
41008 CAGTGACTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (24 bp):
TGGTCAACAGTCAATGAGTTAACT
Found at i:43881 original size:15 final size:14
Alignment explanation
Indices: 43842--43885 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 14
43832 TTAACTTTTT
43842 CGGTCAAAGT-TAA
1 CGGTCAAAGTCTAA
43855 CGGTCAATAGTCTAA
1 CGGTCAA-AGTCTAA
43870 CCGGTCAAAGTC-AA
1 -CGGTCAAAGTCTAA
43884 CG
1 CG
43886 ATCAGACCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.32
14 5 0.18
15 7 0.25
16 7 0.25
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (14 bp):
CGGTCAAAGTCTAA
Done.