Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009472.1 Hibiscus syriacus cultivar Beakdansim tig00114146_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: 19768
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.22
Found at i:1011 original size:92 final size:92
Alignment explanation
Indices: 854--1033 Score: 281
Period size: 92 Copynumber: 2.0 Consensus size: 92
844 TGTGCGGCTG
* *
854 CCGCACCCAGCGCTCGTTCTGTGCGGCACTCCCGCACCAATGGACTGGGTTGCCGAGGCACCCGT
1 CCGCACCCAACGCTCGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGTTGCCGAGGCACCCGT
*
919 CGGTGTTGCCGATGGTGACCGAGGCCC
66 CGGGGTTGCCGATGGTGACCGAGGCCC
* ** *
946 CCGCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGT-GCCTGGGTTGCCGAGGCACCCG
1 CCGCACCCAACGCTC-GCTCTGTGCGGCACTCCCGCACCAATGGACTGGGTTGCCGAGGCACCCG
1010 TCGGGGTTGCCGATGGTGACCGAG
65 TCGGGGTTGCCGATGGTGACCGAG
1034 ACACCCGTCT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 57 0.71
93 23 0.29
ACGTcount: A:0.12, C:0.38, G:0.33, T:0.17
Consensus pattern (92 bp):
CCGCACCCAACGCTCGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGTTGCCGAGGCACCCGT
CGGGGTTGCCGATGGTGACCGAGGCCC
Found at i:1057 original size:32 final size:32
Alignment explanation
Indices: 998--1130 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
988 GCCTGGGTTG
* *
998 CCGAGGCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1029 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
1061 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
1093 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
1126 CCGAG
1 CCGAG
1131 CCTCACGCAC
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
31 13 0.14
32 51 0.56
33 27 0.30
ACGTcount: A:0.16, C:0.31, G:0.35, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:1118 original size:65 final size:63
Alignment explanation
Indices: 998--1130 Score: 185
Period size: 65 Copynumber: 2.1 Consensus size: 63
988 GCCTGGGTTG
* * * * *
998 CCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGACACCCGCCTGGGATTGCCGATGGTGA
* *
1061 CCGAGACACCCGTCTGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGAGACACCCGTC-GGCGTTGCCAATGGTGACCGA-GACACCCGCCTGGGATTGCCGATGGTGA
1126 CCGAG
1 CCGAG
1131 CCTCACGCAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 13 0.21
64 18 0.30
65 30 0.49
ACGTcount: A:0.16, C:0.31, G:0.35, T:0.18
Consensus pattern (63 bp):
CCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGACACCCGCCTGGGATTGCCGATGGTGA
Found at i:1222 original size:30 final size:30
Alignment explanation
Indices: 1188--1287 Score: 75
Period size: 30 Copynumber: 3.4 Consensus size: 30
1178 CCTGGGGTTG
1188 CCGAGGCACCCGTCGGGGGGCCGATGGTGA
1 CCGAGGCACCCGTCGGGGGGCCGATGGTGA
* * ** *
1218 CCGAGGCCCCCGCACCCGTGGCC--TGGGTTG-
1 CCGAGGCACCCG-TCGGGGGGCCGAT-GG-TGA
*
1248 CCGAGGCACCCGTCGGGGTTGCCGAT-GTGA
1 CCGAGGCACCCGTCGGGG-GGCCGATGGTGA
1278 CCGAGG-ACCC
1 CCGAGGCACCC
1288 CGCACCCAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 15
0.67 0.14 0.19
Matches are distributed among these distances:
29 9 0.17
30 34 0.65
31 8 0.15
32 1 0.02
ACGTcount: A:0.12, C:0.36, G:0.40, T:0.12
Consensus pattern (30 bp):
CCGAGGCACCCGTCGGGGGGCCGATGGTGA
Found at i:1260 original size:60 final size:61
Alignment explanation
Indices: 1165--1294 Score: 219
Period size: 60 Copynumber: 2.1 Consensus size: 61
1155 GTGCGGCACT
*
1165 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGG-GGCCGATGGTGACCGAGGCC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTGGCCGAT-GTGACCGAGGAC
*
1226 CCCGCACCCGTGGCCT-GGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGTGACCGAGGAC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTGGCCGATGTGACCGAGGAC
1286 CCCGCACCC
1 CCCGCACCC
1295 AACTCTCGGC
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
60 44 0.67
61 22 0.33
ACGTcount: A:0.11, C:0.38, G:0.38, T:0.12
Consensus pattern (61 bp):
CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTGGCCGATGTGACCGAGGAC
Found at i:1400 original size:32 final size:32
Alignment explanation
Indices: 1341--1472 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
1331 CCTGGGGTTG
* *
1341 CCGAGCCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1372 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1404 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
1436 CCGAGGCCACCCGCCTGGG-TTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
1468 CCGAG
1 CCGAG
1473 CCTCACGCAC
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
31 14 0.15
32 69 0.73
33 12 0.13
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:1447 original size:153 final size:153
Alignment explanation
Indices: 1029--1447 Score: 458
Period size: 153 Copynumber: 2.7 Consensus size: 153
1019 CCGATGGTGA
* *
1029 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGTGAC
1 CCGAGACACCCGTC-GGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCC-ATGGTGAC
* * * * * *
1094 CGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTGC
64 CGA-GACACCCGTCTGGGATTGCCGATGGTGACCGAGGCGCA--C-CCAACGCTCGGCTCTGTCC
*
1159 GGCACTCCCGCACCCGTGGCCTGGGGTTG
125 GGAACTCCCGCACCCGTGGCCTGGGGTTG
* * * * *** *
1188 CCGAGGCACCCGTCGGGG-GGCCGATGGTGACCGAGGCCCCCG-CACCCG-TGGCC-TGGGTTG-
1 CCGAGACACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTC-TGGGTTTGCCAT-GG-TGA
* * *
1248 CCGAGGCACCCGTC-GGGGTTGCCGAT-GTGACCGAGGACCCCGCACCCAACTCTCGGCTCTGTC
63 CCGAGACACCCGTCTGGGATTGCCGATGGTGACCGAGG----CGCACCCAACGCTCGGCTCTGTC
1311 CGGAACTCCCGCACCCGTGGCCTGGGGTTG
124 CGGAACTCCCGCACCCGTGGCCTGGGGTTG
*
1341 CCGAGCCACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACC
1 CCGAGACACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCC-ATGGTGACC
*
1406 GAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGC-CACCC
65 GAGACACCCGTCTGGGATTGCCGATGGTGACCGAGGCGCACCC
1448 GCCTGGGTTG
Statistics
Matches: 216, Mismatches: 29, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
152 9 0.04
153 77 0.36
154 33 0.15
155 13 0.06
156 25 0.12
157 33 0.15
158 13 0.06
159 13 0.06
ACGTcount: A:0.14, C:0.35, G:0.34, T:0.17
Consensus pattern (153 bp):
CCGAGACACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCATGGTGACCG
AGACACCCGTCTGGGATTGCCGATGGTGACCGAGGCGCACCCAACGCTCGGCTCTGTCCGGAACT
CCCGCACCCGTGGCCTGGGGTTG
Found at i:1587 original size:343 final size:337
Alignment explanation
Indices: 898--1530 Score: 1078
Period size: 343 Copynumber: 1.9 Consensus size: 337
888 CACCAATGGA
* *
898 CTGGGTTGCCGAGGCACCCGTCGGTGTTGCCGATGGTGACCGAGGCCCCCGCACCCAACTCTCGG
1 CTGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTCGG
* * *
963 CTCTGTGCGGCACTCCCGCACCCGTGCCTGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTG
66 CTCTGTCCGGAACTCCCGCACCCGTGCCTGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTG
1028 ACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGTGA
131 ACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1093 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTG
196 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTG
* *
1158 CGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGGCCGATGGTGACCGAG
261 CGGCACTCCCGCACCCATGGCCTGGGGTTGCCGAGACACCCGTCGGGGGGCCGATGGTGACCGAG
1223 GCCCCCGCACCCGTGGC
326 G---CCGCACCC--GGC
1240 CTGGGTTGCCGAGGCACCCGTCGGGGTTGCCGAT-GTGACCGAGGACCCCGCACCCAACTCTCGG
1 CTGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTCGG
1304 CTCTGTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGG
66 CTCTGTCCGGAACTCCCGCACCCGT-GCCT-GGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGG
* *
1369 TGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
129 TGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGT
1434 GACCGAGGCCACCCGCCTGGG-TTGCCGATGGTGACCGAGCCTCACGCACCAACGCTC-GTTCTG
194 GACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTG
*
1497 TGCGGCACTCCCTCA-CCATGGCCT-GGGTTGCCGA
259 TGCGGCACTCCCGCACCCATGGCCTGGGGTTGCCGA
1531 TGGTGACCGA
Statistics
Matches: 280, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
339 10 0.04
340 8 0.03
341 72 0.26
342 73 0.26
343 117 0.42
ACGTcount: A:0.13, C:0.36, G:0.34, T:0.18
Consensus pattern (337 bp):
CTGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTCGG
CTCTGTCCGGAACTCCCGCACCCGTGCCTGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTG
ACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGTGA
CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTG
CGGCACTCCCGCACCCATGGCCTGGGGTTGCCGAGACACCCGTCGGGGGGCCGATGGTGACCGAG
GCCGCACCCGGC
Found at i:1593 original size:33 final size:31
Alignment explanation
Indices: 1517--1604 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 31
1507 CCTCACCATG
1517 GCCTGGGTTGCCGATGGTGACCGAGACACCC
1 GCCTGGGTTGCCGATGGTGACCGAGACACCC
** * *
1548 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGG-GTTGCCGATGGTGACCGA-GACACCC
1581 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGG-TTGCCGATGGTGACCG
1605 GGCTCACGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 4 0.09
32 17 0.36
33 26 0.55
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.20
Consensus pattern (31 bp):
GCCTGGGTTGCCGATGGTGACCGAGACACCC
Found at i:9933 original size:95 final size:95
Alignment explanation
Indices: 9753--9933 Score: 301
Period size: 95 Copynumber: 1.9 Consensus size: 95
9743 GCCGCACCCG
*
9753 CTCGGTTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGGTGTTGC
1 CTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGGTGTTGC
*
9818 CGATGGTGACCGAGGCCCCCGCACCCAACT
66 CGATGGTGACCGAGACCCCCGCACCCAACT
** *
9848 CTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGG-GTTGC
1 CTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGGTGTTGC
9912 CGATGGTGACCGAGACACCCCG
66 CGATGGTGACCGAGAC-CCCCG
9934 TCTGGGTTTG
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 20 0.25
95 60 0.75
ACGTcount: A:0.12, C:0.36, G:0.34, T:0.17
Consensus pattern (95 bp):
CTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGGTGTTGC
CGATGGTGACCGAGACCCCCGCACCCAACT
Found at i:9950 original size:33 final size:32
Alignment explanation
Indices: 9890--10021 Score: 176
Period size: 33 Copynumber: 4.1 Consensus size: 32
9880 CCTGGGGTTG
* *
9890 CCGAGGCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
9921 CCGAGACACCCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACA-CCCGTCTGGGTTTGCCGATGGTGA
* *
9954 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
9986 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
10019 CCG
1 CCG
10022 CTCACGCACC
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 7 0.08
32 32 0.36
33 50 0.56
ACGTcount: A:0.15, C:0.32, G:0.35, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:10004 original size:65 final size:64
Alignment explanation
Indices: 9890--10021 Score: 176
Period size: 65 Copynumber: 2.0 Consensus size: 64
9880 CCTGGGGTTG
* * * * *
9890 CCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGACACCCCGCCTGGGATTGCCGATGGTGA
* *
9954 CCGAGACACCCGTCTGGCTTTGCCAATGGTGACCGAGGC-CACCCGCCTGGGATTGCCGATGGTG
1 CCGAGACACCCGTC-GGCGTTGCCAATGGTGACCGAGACAC-CCCGCCTGGGATTGCCGATGGTG
10018 A
64 A
10019 CCG
1 CCG
10022 CTCACGCACC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 14 0.24
65 45 0.76
ACGTcount: A:0.15, C:0.32, G:0.35, T:0.18
Consensus pattern (64 bp):
CCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGACACCCCGCCTGGGATTGCCGATGGTGA
Found at i:10112 original size:32 final size:32
Alignment explanation
Indices: 10076--10179 Score: 101
Period size: 31 Copynumber: 3.3 Consensus size: 32
10066 GCCTGGGTTG
10076 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
* **** *
10108 CCGAGGCCCCCG-CACCCGTGGCC--TGGGTTG-
1 CCGAGGCACCCGTCGGGGGTTGCCGAT-GG-TGA
10138 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
10170 CCGAGG-ACCC
1 CCGAGGCACCC
10180 CGCACCCAAC
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
29 1 0.02
30 13 0.24
31 20 0.37
32 19 0.35
33 1 0.02
ACGTcount: A:0.12, C:0.35, G:0.40, T:0.13
Consensus pattern (32 bp):
CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
Found at i:10126 original size:62 final size:62
Alignment explanation
Indices: 10058--10186 Score: 249
Period size: 62 Copynumber: 2.1 Consensus size: 62
10048 CGGCACTCCC
*
10058 CACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGCCCCCG
1 CACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGACCCCG
10120 CACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGACCCCG
1 CACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGACCCCG
10182 CACCC
1 CACCC
10187 AACTCTCGGC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.11, C:0.36, G:0.39, T:0.14
Consensus pattern (62 bp):
CACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGACCCCG
Found at i:10268 original size:26 final size:27
Alignment explanation
Indices: 10232--10358 Score: 85
Period size: 32 Copynumber: 4.2 Consensus size: 27
10222 GCCTGGGTTG
*
10232 CCGAGCCACCCGG-TTGCCGATGGTGA
1 CCGAGACACCCGGTTTGCCGATGGTGA
10258 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACA-CC--C--GGTTTGCCGATGGTGA
10290 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACA-CC--C--GGTTTGCCGATGGTGA
* *
10322 CCGAGGCCACCCGCCTGGGTTGCCGATGGTGA
1 CCGA-G--ACAC-CC-GGTTTGCCGATGGTGA
10354 CCGAG
1 CCGAG
10359 CCTCACCACC
Statistics
Matches: 87, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
26 7 0.08
27 2 0.02
29 1 0.01
31 3 0.03
32 68 0.78
33 2 0.02
34 1 0.01
35 3 0.03
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.18
Consensus pattern (27 bp):
CCGAGACACCCGGTTTGCCGATGGTGA
Found at i:10286 original size:32 final size:32
Alignment explanation
Indices: 10245--10358 Score: 194
Period size: 32 Copynumber: 3.6 Consensus size: 32
10235 AGCCACCCGG
10245 TTGCCGATGGTGACCGAGACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGACACCCGTCTGGGT
10277 TTGCCGATGGTGACCGAGACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGACACCCGTCTGGGT
* *
10309 TTGCCGATGGTGACCGAGGCCACCCGCCTGGG-
1 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
10341 TTGCCGATGGTGACCGAG
1 TTGCCGATGGTGACCGAG
10359 CCTCACCACC
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
31 1 0.01
32 66 0.84
33 12 0.15
ACGTcount: A:0.15, C:0.29, G:0.36, T:0.20
Consensus pattern (32 bp):
TTGCCGATGGTGACCGAGACACCCGTCTGGGT
Found at i:10451 original size:32 final size:33
Alignment explanation
Indices: 10406--10490 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
10396 CACCAATGCC
*
10406 TGGG-TTGCCGATGGTGACCGA-GACACCCGTA
1 TGGGATTGCCGATGGTGACCGAGGACACCCGCA
** * *
10437 TGGTTTTGCCGATGGTGACCGAGGCCACCCGCC
1 TGGGATTGCCGATGGTGACCGAGGACACCCGCA
10470 TGGGATTGCCGATGGTGACCG
1 TGGGATTGCCGATGGTGACCG
10491 GGCTCACGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 3 0.07
32 17 0.37
33 26 0.57
ACGTcount: A:0.15, C:0.27, G:0.36, T:0.21
Consensus pattern (33 bp):
TGGGATTGCCGATGGTGACCGAGGACACCCGCA
Found at i:18751 original size:94 final size:94
Alignment explanation
Indices: 18598--18982 Score: 368
Period size: 94 Copynumber: 4.1 Consensus size: 94
18588 TGCGAGGCTG
* ** *
18598 CCGCACCCAGCGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
*
18663 GTCGGTGTTGCCGATGGTGACCGAGGCCC
66 GTCGGGGTTGCCGATGGTGACCGAGGCCC
* *
18692 CCGCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
* *
18757 GTCGGGGTTGCCGATGGTGACCGAGACAC
66 GTCGGGGTTGCCGATGGTGACCGAGGCCC
******* * ** ** * *** * * ***
18786 CCGTCTGGGTTTGC-CGATGGTGACCGAG-ACACCCGTCTGGCTTTGCCAATGG-TGACCGAGGC
1 CCG-CACCCAACGCTCGGTTCTGTGCG-GCACTCCCG-CACCCGTGGCCTGGGGTTG-CCGAGG-
* *
18848 CACCCGCCTGGGATTGCCGATGGTGACCGA-GCCTC
61 CACCCGTC-GGGGTTGCCGATGGTGACCGAGGCC-C
*
18883 ACGCA-CCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCT-GGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
18946 GTCGGGGTTGCCGATGGTGACCGAGGCCC
66 GTCGGGGTTGCCGATGGTGACCGAGGCCC
18975 CCGCACCC
1 CCGCACCC
18983 GTGGCCTGGG
Statistics
Matches: 220, Mismatches: 59, Indels: 25
0.72 0.19 0.08
Matches are distributed among these distances:
92 25 0.11
93 12 0.05
94 110 0.50
95 28 0.13
96 22 0.10
97 23 0.10
ACGTcount: A:0.13, C:0.37, G:0.33, T:0.17
Consensus pattern (94 bp):
CCGCACCCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
GTCGGGGTTGCCGATGGTGACCGAGGCCC
Found at i:18805 original size:32 final size:32
Alignment explanation
Indices: 18746--18878 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
18736 CCTGGGGTTG
* *
18746 CCGAGGCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
18777 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
18809 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
18841 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
18874 CCGAG
1 CCGAG
18879 CCTCACGCAC
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
31 13 0.14
32 51 0.56
33 27 0.30
ACGTcount: A:0.16, C:0.31, G:0.35, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:18866 original size:65 final size:63
Alignment explanation
Indices: 18746--18878 Score: 185
Period size: 65 Copynumber: 2.1 Consensus size: 63
18736 CCTGGGGTTG
* * * * *
18746 CCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGACACCCGCCTGGGATTGCCGATGGTGA
* *
18809 CCGAGACACCCGTCTGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGAGACACCCGTC-GGCGTTGCCAATGGTGACCGA-GACACCCGCCTGGGATTGCCGATGGTGA
18874 CCGAG
1 CCGAG
18879 CCTCACGCAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 13 0.21
64 18 0.30
65 30 0.49
ACGTcount: A:0.16, C:0.31, G:0.35, T:0.18
Consensus pattern (63 bp):
CCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGACACCCGCCTGGGATTGCCGATGGTGA
Found at i:18970 original size:31 final size:31
Alignment explanation
Indices: 18935--19037 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
18925 GCCTGGGTTG
18935 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
* *** * *
18966 CCGAGGCCCCCG-CACCCGTGGCCTG-GGGTTG-
1 CCGAGGCACCCGTC-GGGGTTGCC-GATGG-TGA
18997 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
19028 CCGAGG-ACCC
1 CCGAGGCACCC
19038 CGCACCCAAC
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
30 8 0.15
31 42 0.78
32 4 0.07
ACGTcount: A:0.12, C:0.35, G:0.40, T:0.14
Consensus pattern (31 bp):
CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
Found at i:18988 original size:61 final size:62
Alignment explanation
Indices: 18913--19044 Score: 248
Period size: 62 Copynumber: 2.1 Consensus size: 62
18903 GTGCGGCACT
*
18913 CCCGCACCCGTGGCCT-GGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGCC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
18974 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
19036 CCCGCACCC
1 CCCGCACCC
19045 AACTCTCGGC
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
61 16 0.23
62 53 0.77
ACGTcount: A:0.11, C:0.38, G:0.38, T:0.14
Consensus pattern (62 bp):
CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
Found at i:19069 original size:155 final size:156
Alignment explanation
Indices: 18841--19125 Score: 452
Period size: 155 Copynumber: 1.8 Consensus size: 156
18831 CCAATGGTGA
* *
18841 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTG
1 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGCTCTGTC
* *
18906 CGGCACTCCCGCACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAG
66 CGGAACTCCCGCACCCGTGGCCTGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTGACCGAG
18971 GCCCCCGCACCCGTGGCCTGGGGTTG
131 GCCCCCGCACCCGTGGCCTGGGGTTG
* * *
18997 CCGAGG-CACCCGTC-GGGGTTGCCGATGGTGACCGAGGACC-C-CGCACCCAACTCTCGGCTCT
1 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGA-G-CCTCACGCA-CCAACGCTCGGCTCT
19058 GTCCGGAACTCCCGCACCCGTGGCCTGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTGACC
63 GTCCGGAACTCCCGCACCCGTGGCCTGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTGACC
19123 GAG
128 GAG
19126 ACACCCGTCT
Statistics
Matches: 119, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
154 24 0.20
155 87 0.73
156 8 0.07
ACGTcount: A:0.12, C:0.37, G:0.35, T:0.16
Consensus pattern (156 bp):
CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGCTCTGTC
CGGAACTCCCGCACCCGTGGCCTGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTGACCGAG
GCCCCCGCACCCGTGGCCTGGGGTTG
Found at i:19149 original size:32 final size:32
Alignment explanation
Indices: 19090--19221 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
19080 GCCTGGGTTG
* *
19090 CCGAGCCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
19121 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
19153 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
19185 CCGAGGCCACCCGCCTGGG-TTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
19217 CCGAG
1 CCGAG
19222 CCTCACGCAC
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
31 14 0.15
32 69 0.73
33 12 0.13
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:19279 original size:344 final size:345
Alignment explanation
Indices: 18629--19282 Score: 1168
Period size: 344 Copynumber: 1.9 Consensus size: 345
18619 GTGCGGCACT
* *
18629 CCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGTGTTGCCGATGGTGACCGAGGCCCCC
1 CCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCC
* * *
18694 GCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGT
66 GCACCCAACTCTCGGCTCTGTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGT
18759 CGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCT
131 CGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCT
18824 GGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCAC
196 GGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCAC
**
18889 CAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGGT
261 CAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGCCTGGGTTGCCGAGGCACCCGTCGGGGT
18954 TGCCGATGGTGACCGAGGCC
326 TGCCGATGGTGACCGAGGCC
** *
18974 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCC
1 CCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCC
19039 GCACCCAACTCTCGGCTCTGTCCGGAACTCCCGCACCCGTGGCCT-GGGTTGCCGAGCCACCCGT
66 GCACCCAACTCTCGGCTCTGTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGT
19103 CGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCT
131 CGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCT
* *
19168 GGGTTTGCCGATGGTGACCGAGGCCACCCGCCTGGG-TTGCCGATGGTGACCGAGCCTCACGCAC
196 GGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCAC
*
19232 CAACGCTCGGTTCTGTGCGGCACTCCCTCACCAATGGCCTGGGGTTGCCGA
261 CAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGCCT-GGGTTGCCGA
19283 TGGTGACCGA
Statistics
Matches: 295, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
343 65 0.22
344 127 0.43
345 103 0.35
ACGTcount: A:0.13, C:0.35, G:0.34, T:0.18
Consensus pattern (345 bp):
CCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCC
GCACCCAACTCTCGGCTCTGTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGT
CGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCT
GGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCAC
CAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGCCTGGGTTGCCGAGGCACCCGTCGGGGT
TGCCGATGGTGACCGAGGCC
Found at i:19345 original size:33 final size:32
Alignment explanation
Indices: 19268--19356 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
19258 CTCACCAATG
*
19268 GCCTGGGGTTGCCGATGGTGACCGAGACACCC
1 GCCTGGGATTGCCGATGGTGACCGAGACACCC
** ** *
19300 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGGGATTGCCGATGGTGACCGA-GACACCC
19333 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGGATTGCCGATGGTGACCG
19357 GGGCTCACGC
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 21 0.45
33 26 0.55
ACGTcount: A:0.15, C:0.28, G:0.37, T:0.20
Consensus pattern (32 bp):
GCCTGGGATTGCCGATGGTGACCGAGACACCC
Done.