Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009561.1 Hibiscus syriacus cultivar Beakdansim tig00116599_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: 25541
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Found at i:2070 original size:95 final size:94
Alignment explanation
Indices: 1915--2300 Score: 356
Period size: 95 Copynumber: 4.1 Consensus size: 94
1905 TGCGAGGCTG
* * ** *
1915 CCGCACCCAGCGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
1980 GTCGGGTGTTGCCGATGGTGACCGAGGCCC
66 GTCGGG-GTTGCCGATGGTGACCGAGGCCC
*
2010 CCGCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
* *
2075 GTCGGGGTTGCCGATGGTGACCGAGACAC
66 GTCGGGGTTGCCGATGGTGACCGAGGCCC
* *** * * * ** * *** * * ***
2104 CCG---TCTGGGTTTGCCGATGTGACCGAG-ACACCCGTCTGGCTTTGCCAATGG-TGACCGAGG
1 CCGCACCCAACGCTCGGCTCTGTG--CG-GCACTCCCG-CACCCGTGGCCTGGGGTTG-CCGAGG
* *
2164 CCACCCGCCTGGGATTGCCGATGGTGACCGA-GCCTC
61 -CACCCGTC-GGGGTTGCCGATGGTGACCGAGGCC-C
* *
2200 ACGCA-CCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
2264 -TCGGGGGTTGCCGATGGTGACCGAGGCCC
66 GTC-GGGGTTGCCGATGGTGACCGAGGCCC
2293 CCGCACCC
1 CCGCACCC
2301 GTGGCCTGGG
Statistics
Matches: 222, Mismatches: 55, Indels: 29
0.73 0.18 0.09
Matches are distributed among these distances:
91 8 0.04
93 36 0.16
94 49 0.22
95 88 0.40
96 33 0.15
98 8 0.04
ACGTcount: A:0.13, C:0.37, G:0.33, T:0.17
Consensus pattern (94 bp):
CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
GTCGGGGTTGCCGATGGTGACCGAGGCCC
Found at i:2099 original size:31 final size:32
Alignment explanation
Indices: 2064--2195 Score: 178
Period size: 31 Copynumber: 4.2 Consensus size: 32
2054 CCTGGGGTTG
* *
2064 CCGAGGCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
2095 CCGAGACACCCGTCTGGGTTTGCCGAT-GTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
2126 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
2158 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
2191 CCGAG
1 CCGAG
2196 CCTCACGCAC
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
31 42 0.47
32 20 0.22
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:2288 original size:31 final size:31
Alignment explanation
Indices: 2253--2357 Score: 81
Period size: 31 Copynumber: 3.4 Consensus size: 31
2243 CCTGGGGTTG
2253 CCGAGGCACCCTCGGGGGTTGCCGATGGTGA
1 CCGAGGCACCCTCGGGGGTTGCCGATGGTGA
* * **** * *
2284 CCGAGGCCCCCGCACCCGTGGCCTG-GGGTTG-
1 CCGAGGCACCCTCGGGGGTTGCC-GATGG-TGA
2315 CCGAGGCACCCGTCGGGGGTTTGCCGATGGTGA
1 CCGAGGCACCC-TCGGGGG-TTGCCGATGGTGA
2348 CCGAGG-ACCC
1 CCGAGGCACCC
2358 CGCACCCAAC
Statistics
Matches: 52, Mismatches: 16, Indels: 11
0.66 0.20 0.14
Matches are distributed among these distances:
31 28 0.54
32 12 0.23
33 12 0.23
ACGTcount: A:0.11, C:0.34, G:0.40, T:0.14
Consensus pattern (31 bp):
CCGAGGCACCCTCGGGGGTTGCCGATGGTGA
Found at i:2306 original size:62 final size:64
Alignment explanation
Indices: 2230--2364 Score: 247
Period size: 62 Copynumber: 2.1 Consensus size: 64
2220 GTGCGGCACT
*
2230 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC-TCGGGGG-TTGCCGATGGTGACCGAGGCC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTTGCCGATGGTGACCGAGGAC
2292 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTTGCCGATGGTGACCGAGGAC
2356 CCCGCACCC
1 CCCGCACCC
2365 AACTCTCGGC
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
62 34 0.49
63 7 0.10
64 29 0.41
ACGTcount: A:0.10, C:0.37, G:0.39, T:0.14
Consensus pattern (64 bp):
CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTTGCCGATGGTGACCGAGGAC
Found at i:2327 original size:189 final size:191
Alignment explanation
Indices: 1988--2353 Score: 503
Period size: 189 Copynumber: 1.9 Consensus size: 191
1978 CCGTCGGGTG
* *
1988 TTGCCGATGGTGACCGAGGCCCCCGCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGTG
1 TTGCCGATGGTGACCGAGGCCCACGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCCGTG
* * **
2053 GCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGC
66 GCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGCCCGGGCCTGC
*
2118 CGATGTGACCGAGACACCCGTC-TGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGA
131 CGATGTGACCGAGACACCCGTCGGGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGA
*
2178 TTGCCGATGGTGACCGA-GCCTCACGCA-CCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGT
1 TTGCCGATGGTGACCGAGGCC-CACGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCCGT
* *
2241 GGCCTGGGGTTGCCGAGGCACCC-TCGGGGGTTGCCGATGGTGACCGAGGCCCCCGCACCCGTGG
65 GGCCTGGGGTTGCCGAGGCACCCGTC-GGGGTTGCCGATGGTGACCGAGACACCCG--CCCG-GG
* * * * *
2305 CCTG-GGGT-TG-CCGAGGCACCCGTCGGGGGTTTGCCGATGGTGACCGAGG
126 CCTGCCGATGTGACCGAGACACCCGTCGGGGCTTTGCCAATGGTGACCGAGG
2354 ACCCCGCACC
Statistics
Matches: 155, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
188 2 0.01
189 100 0.65
190 45 0.29
191 4 0.03
192 4 0.03
ACGTcount: A:0.13, C:0.35, G:0.35, T:0.17
Consensus pattern (191 bp):
TTGCCGATGGTGACCGAGGCCCACGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCCGTG
GCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGCCCGGGCCTGC
CGATGTGACCGAGACACCCGTCGGGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:2453 original size:32 final size:32
Alignment explanation
Indices: 2411--2543 Score: 196
Period size: 32 Copynumber: 4.2 Consensus size: 32
2401 CCTGGGGTTG
* *
2411 CCGAGCCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGGTTGCCGATGGTGA
*
2443 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGGTTGCCGATGGTGA
*
2475 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGGTTGCCGATGGTGA
* *
2507 CCGAGGCCACCCGCCT-GGGTTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGGTTGCCGATGGTGA
2539 CCGAG
1 CCGAG
2544 CCTCACGCAC
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
31 1 0.01
32 84 0.89
33 9 0.10
ACGTcount: A:0.14, C:0.31, G:0.37, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGGTTGCCGATGGTGA
Found at i:2530 original size:64 final size:64
Alignment explanation
Indices: 2411--2676 Score: 204
Period size: 64 Copynumber: 4.0 Consensus size: 64
2401 CCTGGGGTTG
* * * * * *
2411 CCGAGCCACCCGTCGGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGCCACCCGCCTGGGATTGCCGATGGTGA
2475 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTGGG-TTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGA-GCCACCCGCCTGGGATTGCCGATGGTGA
* * * * * *** *
2539 CCGAGCCTCACGCACCAACG-CT-CGTTCTGTGCGCA--CT-CCCTCA-CCAATGGCCTGGGGTT
1 CCGAG----A--CACC--CGTCTGGGTT-TG-CCG-ATGGTGACC-GAGCCACCCGCCTGGGATT
2598 GCCGATGGTGA
54 GCCGATGGTGA
* *
2609 CCGAGACACCCGTATGGTTTTGCCGATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGA-GCCACCCGCCTGGGATTGCCGATGGTGA
2674 CCG
1 CCG
2677 GGCTCACGCA
Statistics
Matches: 157, Mismatches: 24, Indels: 41
0.71 0.11 0.18
Matches are distributed among these distances:
61 1 0.01
62 4 0.03
63 5 0.03
64 59 0.38
65 38 0.24
66 1 0.01
68 1 0.01
69 10 0.06
70 27 0.17
71 6 0.04
72 4 0.03
73 1 0.01
ACGTcount: A:0.15, C:0.32, G:0.33, T:0.19
Consensus pattern (64 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGCCACCCGCCTGGGATTGCCGATGGTGA
Found at i:2665 original size:33 final size:32
Alignment explanation
Indices: 2588--2676 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
2578 CTCACCAATG
*
2588 GCCTGGGGTTGCCGATGGTGACCGAGACACCC
1 GCCTGGGATTGCCGATGGTGACCGAGACACCC
** ** *
2620 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGGGATTGCCGATGGTGACCGA-GACACCC
2653 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGGATTGCCGATGGTGACCG
2677 GGCTCACGCA
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
Found at i:6764 original size:39 final size:38
Alignment explanation
Indices: 6706--6781 Score: 143
Period size: 39 Copynumber: 2.0 Consensus size: 38
6696 CGAGCCGAGA
6706 TATCCGTTGCCGAGAGTCGTTTTTGTGTTTTCACGACG
1 TATCCGTTGCCGAGAGTCGTTTTTGTGTTTTCACGACG
6744 TATCTCGTTGCCGAGAGTCGTTTTTGTGTTTTCACGAC
1 TATC-CGTTGCCGAGAGTCGTTTTTGTGTTTTCACGAC
6782 AAAGCAGGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 4 0.11
39 33 0.89
ACGTcount: A:0.13, C:0.21, G:0.25, T:0.41
Consensus pattern (38 bp):
TATCCGTTGCCGAGAGTCGTTTTTGTGTTTTCACGACG
Found at i:10975 original size:94 final size:95
Alignment explanation
Indices: 10822--11006 Score: 300
Period size: 94 Copynumber: 2.0 Consensus size: 95
10812 TGCGAGGCTG
* *
10822 CCGCACCCAGCGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
*
10887 GTC-GGTGTTGCCGATGGTGACCGAGGCCC
66 GTCGGGGGTTGCCGATGGTGACCGAGGCCC
* ** *
10916 CCGCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
10981 GTCGGGGGTTGCCGATGGTGACCGAG
66 GTCGGGGGTTGCCGATGGTGACCGAG
11007 ACACCCGTCT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 62 0.75
95 21 0.25
ACGTcount: A:0.12, C:0.37, G:0.35, T:0.17
Consensus pattern (95 bp):
CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
GTCGGGGGTTGCCGATGGTGACCGAGGCCC
Found at i:11006 original size:32 final size:32
Alignment explanation
Indices: 10970--11103 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
10960 CCTGGGGTTG
* * *
10970 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
11002 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
11034 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
11066 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
11099 CCGAG
1 CCGAG
11104 CCTCACGCAC
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 64 0.70
33 27 0.30
ACGTcount: A:0.16, C:0.31, G:0.36, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:11220 original size:57 final size:57
Alignment explanation
Indices: 11137--11263 Score: 177
Period size: 57 Copynumber: 2.2 Consensus size: 57
11127 GTGCGGCACT
*
11137 CCCGCACCCGTGCCTGGGTTGCCGAGGCACCCGTC-GGGTTGCC-GTGACCGAGGCC
1 CCCGCACCCGTGCCTGGGTTGCCGAGGCACCCGTCGGGGTTGCCGGTGACCGAGGAC
11192 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGT-GCCT-GGGTTGCCGAGGCACCCGTC-GGGGTTGCC---GGTGACCGAGGAC
11255 CCCGCACCC
1 CCCGCACCC
11264 AACTCTCGGC
Statistics
Matches: 63, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
55 11 0.17
56 4 0.06
57 20 0.32
59 8 0.13
63 20 0.32
ACGTcount: A:0.10, C:0.39, G:0.37, T:0.13
Consensus pattern (57 bp):
CCCGCACCCGTGCCTGGGTTGCCGAGGCACCCGTCGGGGTTGCCGGTGACCGAGGAC
Found at i:11369 original size:32 final size:32
Alignment explanation
Indices: 11310--11441 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
11300 CCTGGGGTTG
* *
11310 CCGAGCCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
11341 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
11373 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
11405 CCGAGGCCACCCGCCTGGG-TTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
11437 CCGAG
1 CCGAG
11442 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:11493 original size:339 final size:340
Alignment explanation
Indices: 10853--11501 Score: 1126
Period size: 339 Copynumber: 1.9 Consensus size: 340
10843 GTGCGGCACT
* *
10853 CCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGTGTTGCCGATGGTGACCGAGGCCCCC
1 CCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCC
* * *
10918 GCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGT
66 GCACCCAACTCTCGGCTCTGTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGT
10983 CGGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTC
131 CGGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTC
11048 TGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCA
196 TGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCA
**
11113 CCAACGCTCGTTCTGTGCGGCACTCCCGCACCCGTGCCT-GGGTTGCCGAGGCACCCGTCGGGTT
261 CCAACGCTCGTTCTGTGCGGCACTCCCGCACCAATGCCTGGGGTTGCCGAGGCACCCGTCGGGTT
11177 GCCGTGACCGAGGCC
326 GCCGTGACCGAGGCC
** *
11192 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGACCC
1 CCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTC-GGGGTTGCCGATGGTGACCGAGGACCC
11257 CGCACCCAACTCTCGGCTCTGTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCG
65 CGCACCCAACTCTCGGCTCTGTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCG
11322 TC-GGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGT
130 TCGGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGT
* *
11386 CTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTGGG-TTGCCGATGGTGACCGAGCCTCACGC
195 CTGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGC
*
11450 ACCAACGCTCGGTTCTGTGC-GCACTCCCTCACCAATGGCCTGGGGTTGCCGA
260 ACCAACGCTC-GTTCTGTGCGGCACTCCCGCACCAAT-GCCTGGGGTTGCCGA
11502 TGGTGACCGA
Statistics
Matches: 293, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
338 49 0.17
339 145 0.49
340 99 0.34
ACGTcount: A:0.13, C:0.36, G:0.34, T:0.18
Consensus pattern (340 bp):
CCCGCACCAATGGACTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCC
GCACCCAACTCTCGGCTCTGTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGT
CGGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTC
TGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCA
CCAACGCTCGTTCTGTGCGGCACTCCCGCACCAATGCCTGGGGTTGCCGAGGCACCCGTCGGGTT
GCCGTGACCGAGGCC
Found at i:11564 original size:33 final size:32
Alignment explanation
Indices: 11487--11575 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
11477 CTCACCAATG
*
11487 GCCTGGGGTTGCCGATGGTGACCGAGACACCC
1 GCCTGGGATTGCCGATGGTGACCGAGACACCC
** ** *
11519 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGGGATTGCCGATGGTGACCGA-GACACCC
11552 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGGATTGCCGATGGTGACCG
11576 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
Found at i:19926 original size:32 final size:32
Alignment explanation
Indices: 19890--20022 Score: 178
Period size: 32 Copynumber: 4.2 Consensus size: 32
19880 GCCTGGGTTG
* * *
19890 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
19922 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
19954 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
19986 CCGAGGCCACCC-CCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
20018 CCGAG
1 CCGAG
20023 CCTCACGCAC
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
31 1 0.01
32 83 0.92
33 6 0.07
ACGTcount: A:0.16, C:0.31, G:0.35, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:20114 original size:31 final size:31
Alignment explanation
Indices: 20079--20181 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
20069 GCCTGGGTTG
20079 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
* *** * *
20110 CCGAGGCCCCCG-CACCCGTGGCCTG-GGGTTG-
1 CCGAGGCACCCGTC-GGGGTTGCC-GATGG-TGA
20141 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
20172 CCGAGG-ACCC
1 CCGAGGCACCC
20182 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:20132 original size:61 final size:62
Alignment explanation
Indices: 20057--20188 Score: 248
Period size: 62 Copynumber: 2.1 Consensus size: 62
20047 GTGCGGCACT
*
20057 CCCGCACCCGTGGCCT-GGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGCC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
20118 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
20180 CCCGCACCC
1 CCCGCACCC
20189 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:20293 original size:32 final size:32
Alignment explanation
Indices: 20234--20365 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
20224 GCCTGGGTTG
* *
20234 CCGAGCCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
20265 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
20297 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
20329 CCGAGGCCACCCGCCTGGG-TTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
20361 CCGAG
1 CCGAG
20366 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:20489 original size:33 final size:32
Alignment explanation
Indices: 20412--20500 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
20402 CTCACCAATG
*
20412 GCCTGGGGTTGCCGATGGTGACCGAGACACCC
1 GCCTGGGATTGCCGATGGTGACCGAGACACCC
** ** *
20444 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGGGATTGCCGATGGTGACCGA-GACACCC
20477 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGGATTGCCGATGGTGACCG
20501 GGCTCACGCA
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.