Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000552.1 Hibiscus syriacus cultivar Beakdansim tig00001078_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: 67008
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:996 original size:22 final size:23
Alignment explanation
Indices: 971--1013 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
961 AAATTAAATG
971 AATAAAAATAAT-AAATAATAAA
1 AATAAAAATAATAAAATAATAAA
*
993 AATAACAATAATAAAATAATA
1 AATAAAAATAATAAAATAATA
1014 TTATTCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (23 bp):
AATAAAAATAATAAAATAATAAA
Found at i:1109 original size:35 final size:35
Alignment explanation
Indices: 1051--1241 Score: 189
Period size: 34 Copynumber: 5.4 Consensus size: 35
1041 TTTATTTTCC
* *
1051 CAAAATATTTT-TAAAACCATATATTATATGTTTT
1 CAAAATATTTTCAAAAACTATATATTATATGTTTT
* *
1085 CAAAATGTTTTCAAAAACTATATATTATATATATTTTTT
1 CAAAATATTTTCAAAAAC--TATA-TAT-TATATGTTTT
*
1124 CAAAATATTTTCAAAAACTATA-ATAATATGTTTT
1 CAAAATATTTTCAAAAACTATATATTATATGTTTT
* * *
1158 TAAAATATTTTCAAAAACTATATATTATATATATT
1 CAAAATATTTTCAAAAACTATATATTATATGTTTT
1193 CAAAAATAATTTTC-AAAAC-A-ATA-TATAT-TTTT
1 C-AAAAT-ATTTTCAAAAACTATATATTATATGTTTT
1225 CAAAAATCATTTTCAAA
1 C-AAAAT-ATTTTCAAA
1242 CCATAATATA
Statistics
Matches: 134, Mismatches: 14, Indels: 19
0.80 0.08 0.11
Matches are distributed among these distances:
32 16 0.12
33 7 0.05
34 42 0.31
35 17 0.13
36 10 0.07
37 13 0.10
38 3 0.02
39 26 0.19
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (35 bp):
CAAAATATTTTCAAAAACTATATATTATATGTTTT
Found at i:1128 original size:73 final size:73
Alignment explanation
Indices: 1030--1241 Score: 242
Period size: 73 Copynumber: 3.0 Consensus size: 73
1020 AATAAATATA
* * * * *
1030 TATATATTATATTTATTTTCCCAAAATATTTT-TAAAACCATATATTATATGTTTTCAAAATGTT
1 TATATATTATATATATTTTCCCAAAATATTTTCAAAAACTATA-ATAATATGTTTTCAAAATATT
1094 TTCAAAAAC
65 TTCAAAAAC
** *
1103 TATATATTATATATATTTTTTCAAAATATTTTCAAAAACTATAATAATATGTTTTTAAAATATTT
1 TATATATTATATATATTTTCCCAAAATATTTTCAAAAACTATAATAATATGTTTTCAAAATATTT
1168 TCAAAAAC
66 TCAAAAAC
* *
1176 TATATATTATATATA--TT-CAAAAATAATTTTC-AAAACAAT-AT-ATAT-TTTTCAAAAATCA
1 TATATATTATATATATTTTCCCAAAAT-ATTTTCAAAAACTATAATAATATGTTTTC-AAAAT-A
1234 TTTTCAAA
63 TTTTCAAA
1242 CCATAATATA
Statistics
Matches: 123, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
67 4 0.03
68 9 0.07
69 11 0.09
70 12 0.10
71 8 0.07
73 71 0.58
74 8 0.07
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.45
Consensus pattern (73 bp):
TATATATTATATATATTTTCCCAAAATATTTTCAAAAACTATAATAATATGTTTTCAAAATATTT
TCAAAAAC
Found at i:1287 original size:36 final size:33
Alignment explanation
Indices: 1111--1297 Score: 120
Period size: 34 Copynumber: 5.5 Consensus size: 33
1101 ACTATATATT
*
1111 ATATATATTTTTTC-AAAAT-ATTTTCAAAAACT-
1 ATATATA-TTTTTCAAAAATAATTTTC-CAAACTA
* *
1143 ATAATAATATGTTTT-TAAAAT-ATTTTCAAAAACTA
1 AT-AT-ATAT-TTTTCAAAAATAATTTTC-CAAACTA
* *
1178 TATATTATATATATTCAAAAATAATTTTCAAAAC-A
1 -ATA-TATAT-TTTTCAAAAATAATTTTCCAAACTA
*
1213 ATATATATTTTTCAAAAATCATTTT-CAAACCATA
1 ATATATATTTTTCAAAAATAATTTTCCAAA-C-TA
* *
1247 ATATATGTATTTTCAAAAATAATTTTCCAAACTG
1 ATATATAT-TTTTCAAAAATAATTTTCCAAACTA
* *
1281 TTATATA-CTTTCAAAAA
1 ATATATATTTTTCAAAAA
1298 CGAAAAAGAA
Statistics
Matches: 129, Mismatches: 12, Indels: 28
0.76 0.07 0.17
Matches are distributed among these distances:
31 3 0.02
32 27 0.21
33 8 0.06
34 42 0.33
35 26 0.20
36 17 0.13
37 6 0.05
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (33 bp):
ATATATATTTTTCAAAAATAATTTTCCAAACTA
Found at i:2076 original size:15 final size:16
Alignment explanation
Indices: 2050--2083 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2040 TTTAATGAGG
2050 AAAAATACAAAAAAAT
1 AAAAATACAAAAAAAT
*
2066 AAAAATA-AAAAAGAT
1 AAAAATACAAAAAAAT
2081 AAA
1 AAA
2084 TCTTGTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAATACAAAAAAAT
Found at i:5647 original size:17 final size:17
Alignment explanation
Indices: 5625--5658 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5615 TAAAATAAAA
*
5625 TTTAGATCGATCACTGT
1 TTTAGATCCATCACTGT
5642 TTTAGATCCATCACTGT
1 TTTAGATCCATCACTGT
5659 CTTAACTTGG
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:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (17 bp):
TTTAGATCCATCACTGT
Found at i:6386 original size:23 final size:23
Alignment explanation
Indices: 6334--6386 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
6324 ACTCAGATTG
* *
6334 TTAAATTAATAATTTTATGTATG
1 TTAAATTAATAATTTTATATATA
*
6357 TTAAATTAATATTTTTATATATA
1 TTAAATTAATAATTTTATATATA
*
6380 TTTAATT
1 TTAAATT
6387 GATGATGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TTAAATTAATAATTTTATATATA
Found at i:8643 original size:55 final size:55
Alignment explanation
Indices: 8559--8669 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
8549 AGCACTATAG
8559 GAATATGGTGACAGCATATGTTTTATGCTTGACCTTTGAGAGACCATGCAATTAA
1 GAATATGGTGACAGCATATGTTTTATGCTTGACCTTTGAGAGACCATGCAATTAA
*
8614 GAATATGGTGACAGCATATGTTTTATGCTTGACCTTTGAGAGACCATGCAGTTAA
1 GAATATGGTGACAGCATATGTTTTATGCTTGACCTTTGAGAGACCATGCAATTAA
8669 G
1 G
8670 GAACCTTGAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (55 bp):
GAATATGGTGACAGCATATGTTTTATGCTTGACCTTTGAGAGACCATGCAATTAA
Found at i:10832 original size:29 final size:28
Alignment explanation
Indices: 10789--10869 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
10779 GATTTTGTGA
* *
10789 TAAAAATTTGGGAAGGTTTACTTAAAACTT
1 TAAAAATTT--GAAGATTTAATTAAAACTT
*
10819 TAAAATATTTGAAGATTTAATTAAAATTT
1 TAAAA-ATTTGAAGATTTAATTAAAACTT
*
10848 TAAAAATTTGATGAGTTTAATT
1 TAAAAATTTGAAGA-TTTAATT
10870 TACTTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 8 0.18
29 28 0.62
30 5 0.11
31 4 0.09
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.42
Consensus pattern (28 bp):
TAAAAATTTGAAGATTTAATTAAAACTT
Found at i:11070 original size:34 final size:34
Alignment explanation
Indices: 11032--11099 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
11022 TTTTGAAAAA
11032 TTTAAAGGTCTAAAGCATAATCTTTT-AAATTTTG
1 TTTAAAGGTCTAAAGCATAAT-TTTTAAAATTTTG
* *
11066 TTTAAGGGTCTAAATCATAATTTTTAAAATTTTG
1 TTTAAAGGTCTAAAGCATAATTTTTAAAATTTTG
11100 AGGGGCACGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (34 bp):
TTTAAAGGTCTAAAGCATAATTTTTAAAATTTTG
Found at i:11226 original size:20 final size:19
Alignment explanation
Indices: 11185--11222 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
11175 TAAATTATAA
*
11185 ATAAATATAAAGCTTAAAT
1 ATAAATATAAAGATTAAAT
11204 ATAAA-ATAAGAGATTAAAT
1 ATAAATATAA-AGATTAAAT
11223 TATATCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (19 bp):
ATAAATATAAAGATTAAAT
Found at i:14165 original size:47 final size:47
Alignment explanation
Indices: 14104--14204 Score: 202
Period size: 47 Copynumber: 2.1 Consensus size: 47
14094 TATCTGATCC
14104 GATCCGAGTAACACATACTCGAATATCATATAATTGAATTCTGATTT
1 GATCCGAGTAACACATACTCGAATATCATATAATTGAATTCTGATTT
14151 GATCCGAGTAACACATACTCGAATATCATATAATTGAATTCTGATTT
1 GATCCGAGTAACACATACTCGAATATCATATAATTGAATTCTGATTT
14198 GATCCGA
1 GATCCGA
14205 ATGACAATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.33
Consensus pattern (47 bp):
GATCCGAGTAACACATACTCGAATATCATATAATTGAATTCTGATTT
Found at i:14242 original size:16 final size:16
Alignment explanation
Indices: 14221--14265 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
14211 ATATTCAATA
14221 ACAAATATTCTGAAGC
1 ACAAATATTCTGAAGC
*
14237 ACAAATATTCTAAAGC
1 ACAAATATTCTGAAGC
14253 ACAAATATTCTGA
1 ACAAATATTCTGA
14266 TTCTGATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.27
Consensus pattern (16 bp):
ACAAATATTCTGAAGC
Found at i:15019 original size:47 final size:47
Alignment explanation
Indices: 14911--15011 Score: 193
Period size: 47 Copynumber: 2.1 Consensus size: 47
14901 ATATTGTCAT
*
14911 TCGGATCAAATAAGAATTCAATTATATGATATTCGAGTATGTGTTAC
1 TCGGATCAAATCAGAATTCAATTATATGATATTCGAGTATGTGTTAC
14958 TCGGATCAAATCAGAATTCAATTATATGATATTCGAGTATGTGTTAC
1 TCGGATCAAATCAGAATTCAATTATATGATATTCGAGTATGTGTTAC
15005 TCGGATC
1 TCGGATC
15012 GGATCAGATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (47 bp):
TCGGATCAAATCAGAATTCAATTATATGATATTCGAGTATGTGTTAC
Found at i:15817 original size:44 final size:44
Alignment explanation
Indices: 15767--15900 Score: 205
Period size: 44 Copynumber: 3.0 Consensus size: 44
15757 TGTTACCGAA
* *
15767 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATACATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
15811 ATAAATGAAAATACATGACGGTGCATTATTGGCAGAAATGTGCC
1 ATAAATGAAAATACATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
15855 ATAAATGAAAATACATAAAGGTGTATTATTGGCAGAAAAGGTGCC
1 ATAAATGAAAATACATAACGGTGCATTATTGGCAG-AAAGGTGCC
15900 A
1 A
15901 CTCGTGGTAT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 72 0.89
45 9 0.11
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (44 bp):
ATAAATGAAAATACATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:18909 original size:31 final size:31
Alignment explanation
Indices: 18871--18967 Score: 185
Period size: 31 Copynumber: 3.1 Consensus size: 31
18861 TGTATGCCAA
18871 ATTGTCCAAGTGTGAATTTTGGTTAGCTGAG
1 ATTGTCCAAGTGTGAATTTTGGTTAGCTGAG
18902 ATTGTCCAAGTGTGAATTTTGGTTAGCTGAG
1 ATTGTCCAAGTGTGAATTTTGGTTAGCTGAG
*
18933 ATTGTCCAAGTGTGAATTTTGGTTAGCTGAT
1 ATTGTCCAAGTGTGAATTTTGGTTAGCTGAG
18964 ATTG
1 ATTG
18968 CTTTCCTTGG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.40
Consensus pattern (31 bp):
ATTGTCCAAGTGTGAATTTTGGTTAGCTGAG
Found at i:24750 original size:157 final size:156
Alignment explanation
Indices: 24479--24988 Score: 593
Period size: 157 Copynumber: 3.3 Consensus size: 156
24469 GAACATGTGT
* * * * *
24479 TTCAAATTTAGTAAAATC-ATAATTAAAAT-AAGGATGAAATA-AAGAAATAAGGAAATTATAAA
1 TTCAAATTTGGTAAAAACGA-ACTTAAAATAAAGGATG-AATAGAAGAAAAAAAGAAATTATAAA
* *
24541 AAATTAAGGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAGATAT
64 AAATTAAGGGACTAAATTGAAAAATAGAAAATTTGTTA-CAAAAAGAGGAATTGAAAGTACATAT
* *
24606 GTATTCTACGATGGTTTAGGAGTATTTGA
128 GTATTCTACGATGGTTTAGGAGCATATGA
* **
24635 TTCAAATTTGGTAAAAACGAAATTAAAATAAAGGAAT-AATAGAAGAAAAAAATTAATTATAAAA
1 TTCAAATTTGGTAAAAACGAACTTAAAATAAAGG-ATGAATAGAAGAAAAAAAGAAATTATAAAA
* * *
24699 AATTGAGGGACTAAATTAAAAAATAGAAAATTT-TTACCAAAAAGGAGGAATTGAAAGTACACAT
65 AATTAAGGGACTAAATTGAAAAATAGAAAATTTGTTA-CAAAAA-GAGGAATTGAAAGTACATAT
* *
24763 GTATTCTACAATGGTTTAGGAGCATATGT
128 GTATTCTACGATGGTTTAGGAGCATATGA
* * * * * *
24792 TTTAAATATGGTAAAAAAC-ATACTTAAAATAAATGATGAATTGAAGAAATAAGGAAATTAT-AA
1 TTCAAATTTGGT-AAAAACGA-ACTTAAAATAAAGGATGAATAGAAGAAAAAAAGAAATTATAAA
* * *
24855 AAATTAAGAGACTAAATTGAAAAATAGAAAATTTGTTATAAAAAAGAGGAATAGAAAGTACATAT
64 AAATTAAGGGACTAAATTGAAAAATAGAAAATTTGTTA-CAAAAAGAGGAATTGAAAGTACATAT
* * * *
24920 TTATTTTAAGATGGTTTAGGAGCATATGG
128 GTATTCTACGATGGTTTAGGAGCATATGA
* * *
24949 TTCAAATTTGGTAAAAATGTACTTAAAATAAAAGATGAAT
1 TTCAAATTTGGTAAAAACGAACTTAAAATAAAGGATGAAT
24989 TAAATGAATA
Statistics
Matches: 302, Mismatches: 42, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
156 62 0.21
157 194 0.64
158 46 0.15
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.29
Consensus pattern (156 bp):
TTCAAATTTGGTAAAAACGAACTTAAAATAAAGGATGAATAGAAGAAAAAAAGAAATTATAAAAA
ATTAAGGGACTAAATTGAAAAATAGAAAATTTGTTACAAAAAGAGGAATTGAAAGTACATATGTA
TTCTACGATGGTTTAGGAGCATATGA
Found at i:37892 original size:19 final size:19
Alignment explanation
Indices: 37867--37963 Score: 135
Period size: 19 Copynumber: 5.1 Consensus size: 19
37857 ACCGGTTTTC
*
37867 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
37887 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
37906 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
37925 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
37944 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
37963 A
1 A
37964 CCCGACCCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
18 2 0.03
19 60 0.85
20 9 0.13
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:37900 original size:29 final size:29
Alignment explanation
Indices: 37848--37965 Score: 127
Period size: 29 Copynumber: 4.1 Consensus size: 29
37838 GCTGCTGGAA
* *
37848 ACCGATTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
37878 ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* *
37906 AACCGGTTTGACCGGTCTGAACCGGTT-TG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCTG
* *
37935 ACCGGTCTGAACCGGTTT-GACCGG-TCTG
1 ACCGGTTTG-ACCGGTTTCAACCGGTTCTG
37963 ACC
1 ACC
37966 CGACCCGACC
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.01
28 19 0.25
29 45 0.58
30 12 0.16
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.28
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:37921 original size:38 final size:37
Alignment explanation
Indices: 37848--37965 Score: 139
Period size: 38 Copynumber: 3.1 Consensus size: 37
37838 GCTGCTGGAA
* * * *
37848 ACCGATTTAACCGGTTTTCAACCGGTTCTGACCGGTTTG
1 ACCGGTTTAACCGG-TCTGAACCGGTT-TGACCGGTCTG
37887 ACCGGTTTCAACCGGT-TCGAACCGGTTTGACCGGTCTG
1 ACCGGTTT-AACCGGTCT-GAACCGGTTTGACCGGTCTG
*
37925 AACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTCTG
1 -ACCGGTTTAACCGGTCTGAACCGGTTTGACCGGTCTG
37963 ACC
1 ACC
37966 CGACCCGACC
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
37 3 0.04
38 37 0.52
39 25 0.35
40 6 0.08
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.28
Consensus pattern (37 bp):
ACCGGTTTAACCGGTCTGAACCGGTTTGACCGGTCTG
Found at i:37976 original size:38 final size:38
Alignment explanation
Indices: 37897--37976 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
37887 ACCGGTTTCA
****
37897 ACCGGTTCGAACCGGTTTGACCGGTCTGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTGACCGGTCTGAACCGACCCG
*
37935 ACCGG-TCTGAACCGGTTTGACCGGTCTGACCCGACCCG
1 ACCGGTTC-GAACCGGTTTGACCGGTCTGAACCGACCCG
37973 ACCG
1 ACCG
37977 TTGACCCGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.16, C:0.33, G:0.30, T:0.21
Consensus pattern (38 bp):
ACCGGTTCGAACCGGTTTGACCGGTCTGAACCGACCCG
Found at i:37988 original size:22 final size:22
Alignment explanation
Indices: 37962--38004 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
37952 TGACCGGTCT
37962 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
37984 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
38005 ATTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:38009 original size:7 final size:7
Alignment explanation
Indices: 37994--38031 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
37984 GACCCGACCC
37994 GACCGTT
1 GACCGTT
*
38001 GACCATT
1 GACCGTT
38008 GACCGTT
1 GACCGTT
38015 GACCGTT
1 GACCGTT
38022 GACCGTT
1 GACCGTT
38029 GAC
1 GAC
38032 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:45179 original size:19 final size:19
Alignment explanation
Indices: 45155--45212 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
45145 GGCTGCTGGA
*
45155 AACCGGTTTAACCAGT-TCG
1 AACCGGTTTAACCGGTCT-G
*
45174 AACCGGTTTGACCGGTCTG
1 AACCGGTTTAACCGGTCTG
*
45193 AACCGGTTTGACCGGTCTG
1 AACCGGTTTAACCGGTCTG
45212 A
1 A
45213 CCCGACCCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 35 0.97
20 1 0.03
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (19 bp):
AACCGGTTTAACCGGTCTG
Found at i:45189 original size:9 final size:9
Alignment explanation
Indices: 45156--45214 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
45146 GCTGCTGGAA
*
45156 ACCGGTTTA
1 ACCGGTTTG
* *
45165 ACCAGTTCG
1 ACCGGTTTG
45174 AACCGGTTTG
1 -ACCGGTTTG
*
45184 ACCGGTCTG
1 ACCGGTTTG
45193 AACCGGTTTG
1 -ACCGGTTTG
*
45203 ACCGGTCTG
1 ACCGGTTTG
45212 ACC
1 ACC
45215 CGACCCGACC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
9 25 0.62
10 15 0.38
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:45221 original size:5 final size:5
Alignment explanation
Indices: 45211--45268 Score: 71
Period size: 5 Copynumber: 10.8 Consensus size: 5
45201 TGACCGGTCT
*
45211 GACCC GACCC GACCGTC GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
45260 GACCC GACC
1 GACCC GACC
45269 GTTGACCGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
5 38 0.81
7 9 0.19
ACGTcount: A:0.19, C:0.53, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:45237 original size:22 final size:22
Alignment explanation
Indices: 45211--45275 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
45201 TGACCGGTCT
*
45211 GACCCGACCCGACCGTCGACCC
1 GACCCGACCCGACCGTTGACCC
45233 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
45255 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
45276 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.18, C:0.51, G:0.23, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:45277 original size:7 final size:7
Alignment explanation
Indices: 45265--45302 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
45255 GACCCGACCC
45265 GACCGTT
1 GACCGTT
45272 GACCGTT
1 GACCGTT
45279 GACCGTT
1 GACCGTT
45286 GACCGTT
1 GACCGTT
45293 GACCGTT
1 GACCGTT
45300 GAC
1 GAC
45303 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:50355 original size:59 final size:59
Alignment explanation
Indices: 50290--50429 Score: 151
Period size: 60 Copynumber: 2.4 Consensus size: 59
50280 GATTTTCAAT
*
50290 AAATAAATTTAACGATTTATTT-CTTTAT-TACAAAATAGAATCATACTTGA-TTCTCAAGA
1 AAATAAATTTAACGATTTATTTCCTTT-TCT-CAAAATAGAATCATACTTAATTTCT-AAGA
** * * *
50349 AAATAAATTTAATAATTTATTTTCCTTTTCTTAAAGTATAATCATACTTAATTTCTAAGA
1 AAATAAATTTAACGATTTA-TTTCCTTTTCTCAAAATAGAATCATACTTAATTTCTAAGA
**
50409 AAATAAATCCAACGATTTATT
1 AAATAAATTTAACGATTTATT
50430 GTATTGAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
59 19 0.28
60 39 0.58
61 9 0.13
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.41
Consensus pattern (59 bp):
AAATAAATTTAACGATTTATTTCCTTTTCTCAAAATAGAATCATACTTAATTTCTAAGA
Found at i:52316 original size:45 final size:45
Alignment explanation
Indices: 52246--52449 Score: 196
Period size: 45 Copynumber: 4.5 Consensus size: 45
52236 CAAGGCTTTT
* * *
52246 GATTATTGAGTTGTC-AAAATCAAAATAAAAAGATTAGTTCGTTTC
1 GATTATTGGGTTG-CGAAAATTAAAATCAAAAGATTAGTTCGTTTC
* * * *
52291 AATTATTGGGTTGCGAAAATTAAAATCAAATGATCAGTTCGTTTT
1 GATTATTGGGTTGCGAAAATTAAAATCAAAAGATTAGTTCGTTTC
* * *
52336 GATTATTGGATTGCGGAAATTATAATCAAAAGATTAGTTTC-TTTC
1 GATTATTGGGTTGCGAAAATTAAAATCAAAAGATTAG-TTCGTTTC
* * * * * * * *
52381 TATTATTGGATTGTGAAAATTAAAATCAAATGATGAATTCCTTTT
1 GATTATTGGGTTGCGAAAATTAAAATCAAAAGATTAGTTCGTTTC
* *
52426 GATTATTGAGTTGCTAAAATTAAA
1 GATTATTGGGTTGCGAAAATTAAA
52450 GGATTAATTC
Statistics
Matches: 129, Mismatches: 27, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
44 4 0.03
45 122 0.95
46 3 0.02
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (45 bp):
GATTATTGGGTTGCGAAAATTAAAATCAAAAGATTAGTTCGTTTC
Found at i:52446 original size:90 final size:90
Alignment explanation
Indices: 52241--52449 Score: 271
Period size: 90 Copynumber: 2.3 Consensus size: 90
52231 TAATCCAAGG
* *
52241 CTTTTGATTATTGAGTTG-TCAAAATCAAAATAAAAAGATTAGTTCGTTTCAATTATTGGGTTGC
1 CTTTTGATTATTGAGTTGCT-AAAATTAAAATAAAAAGATTAGTTCGTTTCAATTATTGGATTGC
*
52305 GAAAATTAAAATCAAATGATCAGTTC
65 GAAAATTAAAATCAAATGATCAATTC
* ** * * *
52331 GTTTTGATTATTG-GATTGCGGAAATTATAATCAAAAGATTAGTTTC-TTTCTATTATTGGATTG
1 CTTTTGATTATTGAG-TTGCTAAAATTAAAATAAAAAGATTAG-TTCGTTTCAATTATTGGATTG
* *
52394 TGAAAATTAAAATCAAATGATGAATTC
64 CGAAAATTAAAATCAAATGATCAATTC
52421 CTTTTGATTATTGAGTTGCTAAAATTAAA
1 CTTTTGATTATTGAGTTGCTAAAATTAAA
52450 GGATTAATTC
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
89 1 0.01
90 95 0.95
91 4 0.04
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (90 bp):
CTTTTGATTATTGAGTTGCTAAAATTAAAATAAAAAGATTAGTTCGTTTCAATTATTGGATTGCG
AAAATTAAAATCAAATGATCAATTC
Found at i:52717 original size:54 final size:54
Alignment explanation
Indices: 52600--53132 Score: 272
Period size: 58 Copynumber: 9.4 Consensus size: 54
52590 TTTCATCGTT
* * *
52600 AGAATCTTGTACTGCTTCTAACTTTGTATGGAAAATAAATAATAGAATTTATTTCATTT-
1 AGAATCTTG-AATGATTCTAACTTTGTAAGGAAAATAAAT--T--AATTTATTTC-TTTG
* *
52659 AGAATCTTAAATGATTTTAACTTTGTAAGGAAAATAAATTAATTTATTTCTTTG
1 AGAATCTTGAATGATTCTAACTTTGTAAGGAAAATAAATTAATTTATTTCTTTG
* * *
52713 AGAATCTTAAATGATTCTAA-TATTATAAGAAAAATAAATT-A--TA-----TTG
1 AGAATCTTGAATGATTCTAACT-TTGTAAGGAAAATAAATTAATTTATTTCTTTG
* * * * ** *
52759 AGAATCGTGGATGATTATATCTTT-TAAAAAGAAATAAATTGTTAAATTTATTT-TGTCG
1 AGAATCTTGAATGATTCTAACTTTGTAAGGA-AAATAAA---TT-AATTTATTTCT-TTG
* * * *
52817 AGAATCTTGGATGATTCTAACTTTGGAAGGAAAAATAAATAGTTGAGTTTATTTCCTTG
1 AGAATCTTGAATGATTCTAACTTTGTAAGG-AAAAT-AA-A-TT-AATTTATTTCTTTG
* * *
52876 ATAATATTGAATGATTCTAACTTTGTAAGGAAAATAAATTATTTTTTAATTTATTTCCTTG
1 AGAATCTTGAATGATTCTAACTTTGTAAGGAAAAT-AA--A----TTAATTTATTTCTTTG
* *
52937 AGAATCTTGAATGATTCTAGCTTTGTAAGGAAAATAAATTAATTTTTAATTTATTTCCTTG
1 AGAATCTTGAATGATTCTAACTTTGTAAGGAAAAT--A--AA---TTAATTTATTTCTTTG
* * * *
52998 AGAATCTTGAATTATTCTAAATTTATAAGAAAAATAAATCGTTGAATTTATTT-TCTTG
1 AGAATCTTGAATGATTCTAACTTTGTAAGGAAAATAAA---TT-AATTTATTTCT-TTG
* *
53056 AGAATCTAGAATGATTCTATCTTT-TAAAAGG-AAATAAATTGTTAAATTTATTT-TCTTG
1 AGAATCTTGAATGATTCTAACTTTGT--AAGGAAAATAAA---TT-AATTTATTTCT-TTG
53114 AGAATCTT-AATTGATTCTA
1 AGAATCTTGAA-TGATTCTA
53133 TTTTTTAAAA
Statistics
Matches: 391, Mismatches: 50, Indels: 67
0.77 0.10 0.13
Matches are distributed among these distances:
45 5 0.01
46 27 0.07
47 1 0.00
49 2 0.01
51 3 0.01
53 7 0.02
54 45 0.12
56 1 0.00
57 8 0.02
58 129 0.33
59 59 0.15
60 3 0.01
61 95 0.24
62 5 0.01
64 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (54 bp):
AGAATCTTGAATGATTCTAACTTTGTAAGGAAAATAAATTAATTTATTTCTTTG
Found at i:52952 original size:61 final size:60
Alignment explanation
Indices: 52796--53132 Score: 334
Period size: 61 Copynumber: 5.7 Consensus size: 60
52786 AAAGAAATAA
* ** * * *
52796 ATTGTTAAATTTATTTTGTCGAGAATCTTGGATGATTCTAACTTTGGAAGGAAAAATAAAT
1 ATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAGG-AAAATAAAT
* * *
52857 A--GTTGAGTTTATTTCCTTGATAATATTGAATGATTCTAACTTTGTAAGGAAAATAAATT
1 ATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAGGAAAATAAA-T
* * *
52916 ATTTTTTAATTTATTTCCTTGAGAATCTTGAATGATTCTAGCTTTGTAAGGAAAATAAATT
1 ATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAGGAAAATAAA-T
* * * * *
52977 AATT-TTTAATTTATTTCCTTGAGAATCTTGAATTATTCTAAATTTATAAGAAAAAT-AA-
1 -ATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAGGAAAATAAAT
* * * *
53035 ATCGTTGAATTTATTTTCTTGAGAATCTAGAATGATTCTATCTTT-TAAAAGG-AAAT-AA-
1 ATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGT--AAGGAAAATAAAT
* *
53093 ATTGTTAAATTTATTTTCTTGAGAATCTT-AATTGATTCTA
1 ATTGTTGAATTTATTTCCTTGAGAATCTTGAA-TGATTCTA
53133 TTTTTTAAAA
Statistics
Matches: 237, Mismatches: 31, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
57 5 0.02
58 83 0.35
59 44 0.19
60 2 0.01
61 100 0.42
62 3 0.01
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (60 bp):
ATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAGGAAAATAAAT
Found at i:53073 original size:58 final size:58
Alignment explanation
Indices: 52756--53159 Score: 352
Period size: 58 Copynumber: 6.8 Consensus size: 58
52746 ATAAATTATA
* * * * * **
52756 TTGAGAATCGTGGATGATTATATCTTT-TAAAAAGAAATAAATTGTTAAATTTATTTTG
1 TTGAGAATCTTGAATGATTCTAACTTTGTAAGAA-AAATAAATTGTTAAATTTATTTCC
* * * * * *
52814 TCGAGAATCTTGGATGATTCTAACTTTGGAAGGAAAAATAAATAGTTGAGTTTATTTCC
1 TTGAGAATCTTGAATGATTCTAACTTTGTAA-GAAAAATAAATTGTTAAATTTATTTCC
* * * * *
52873 TTGATAATATTGAATGATTCTAACTTTGTAAGGAAAATAAATTATTTTTTAATTTATTTCC
1 TTGAGAATCTTGAATGATTCTAACTTTGTAAGAAAAAT-AA--ATTGTTAAATTTATTTCC
* * * *
52934 TTGAGAATCTTGAATGATTCTAGCTTTGTAAGGAAAATAAATTAATTTTTAATTTATTTCC
1 TTGAGAATCTTGAATGATTCTAACTTTGTAAGAAAAATAAA-T--TGTTAAATTTATTTCC
* * * * * *
52995 TTGAGAATCTTGAATTATTCTAAATTTATAAGAAAAATAAATCGTTGAATTTATTTTC
1 TTGAGAATCTTGAATGATTCTAACTTTGTAAGAAAAATAAATTGTTAAATTTATTTCC
* * *
53053 TTGAGAATCTAGAATGATTCTATCTTT-TAA-AAGGAAATAAATTGTTAAATTTATTTTC
1 TTGAGAATCTTGAATGATTCTAACTTTGTAAGAA--AAATAAATTGTTAAATTTATTTCC
* *
53111 TTGAGAATCTT-AATTGATTCT-ATTTTTTAA-AATGAAATAAATTGTTAAA
1 TTGAGAATCTTGAA-TGATTCTAACTTTGTAAGAA--AAATAAATTGTTAAA
53160 AGAAATTAAT
Statistics
Matches: 291, Mismatches: 43, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
56 2 0.01
57 8 0.03
58 125 0.43
59 50 0.17
60 5 0.02
61 101 0.35
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (58 bp):
TTGAGAATCTTGAATGATTCTAACTTTGTAAGAAAAATAAATTGTTAAATTTATTTCC
Found at i:53170 original size:17 final size:18
Alignment explanation
Indices: 53137--53176 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
53127 ATTCTATTTT
53137 TTAAAATGAAATAAATTG
1 TTAAAATGAAATAAATTG
*
53155 TTAAAA-GAAATTAATTG
1 TTAAAATGAAATAAATTG
53172 TTAAA
1 TTAAA
53177 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (18 bp):
TTAAAATGAAATAAATTG
Found at i:53560 original size:80 final size:80
Alignment explanation
Indices: 53425--53572 Score: 215
Period size: 80 Copynumber: 1.9 Consensus size: 80
53415 CAAATCATAA
* * * *
53425 AATTACACTCATTTTTATATTTGACCTTCTAATACAAATTAAACTCATAACTTAAAAGAGATAAA
1 AATTAAACTCATTTTCATATTTGACCTTCCAATAAAAATTAAACTCATAACTTAAAAGAGATAAA
53490 AAAAAATAAACATGG
66 AAAAAATAAACATGG
* * * * *
53505 AATTAAACTCGTTTTCATATTTGGCTTTCCAATAAAAATTAAACTCATAATTTAAAAGAGATTAA
1 AATTAAACTCATTTTCATATTTGACCTTCCAATAAAAATTAAACTCATAACTTAAAAGAGATAAA
53570 AAA
66 AAA
53573 TAAACATAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 59 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (80 bp):
AATTAAACTCATTTTCATATTTGACCTTCCAATAAAAATTAAACTCATAACTTAAAAGAGATAAA
AAAAAATAAACATGG
Found at i:53829 original size:21 final size:21
Alignment explanation
Indices: 53782--53822 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
53772 TTGCACACTT
53782 AATTTTAATCAGTTAGGATTA
1 AATTTTAATCAGTTAGGATTA
*
53803 AATTTTAATTAGTTAGGATT
1 AATTTTAATCAGTTAGGATT
53823 TTTTTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (21 bp):
AATTTTAATCAGTTAGGATTA
Found at i:63043 original size:6 final size:6
Alignment explanation
Indices: 63032--63075 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
63022 AGAGACACCA
*
63032 AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGAAG AA
1 AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AA
63076 AAACATTGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (6 bp):
AAGGAG
Done.