Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009476.1 Hibiscus syriacus cultivar Beakdansim tig00114243_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: 25500
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.23
Found at i:7940 original size:33 final size:32
Alignment explanation
Indices: 7903--7991 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
7893 GCGTGAGCCC
*
7903 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
7936 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
7968 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
7992 CATTGGTGAG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 23 0.49
33 24 0.51
ACGTcount: A:0.20, C:0.37, G:0.28, T:0.15
Consensus pattern (32 bp):
CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
Found at i:8079 original size:32 final size:32
Alignment explanation
Indices: 8038--8170 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
8028 GTGCGTGAGG
* *
8038 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
8070 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
8102 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
8134 CTCGGTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
8166 CTCGG
1 CTCGG
8171 CAACCCCAGG
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 83 0.87
33 12 0.13
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.14
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:8294 original size:31 final size:31
Alignment explanation
Indices: 8253--8350 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
8243 CAACCCCCGA
8253 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
* * * ****
8284 CGGGGGCCTCGGTC-ACCATC-GGCAACCCCCG
1 CGGGTGCCTCGG-CAACC-CCAGGCCACGGGTG
8315 ACGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 -CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
8347 CGGG
1 CGGG
8351 AGTGCCGCAC
Statistics
Matches: 48, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
31 26 0.54
32 22 0.46
ACGTcount: A:0.13, C:0.40, G:0.38, T:0.09
Consensus pattern (31 bp):
CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
Found at i:8315 original size:63 final size:63
Alignment explanation
Indices: 8216--8350 Score: 261
Period size: 63 Copynumber: 2.1 Consensus size: 63
8206 GCCGAGAGTT
*
8216 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
8279 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
8342 GGGTGCGGG
1 GGGTGCGGG
8351 AGTGCCGCAC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.13, C:0.39, G:0.37, T:0.10
Consensus pattern (63 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:8327 original size:157 final size:158
Alignment explanation
Indices: 8134--8422 Score: 451
Period size: 157 Copynumber: 1.8 Consensus size: 158
8124 AGACGGGTGT
* *
8134 CTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCAC-GGTGCGGGAGTTC
1 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * *
8198 CGGACAGAGCCGAGAGTTGGGTGCG-G-GGTCCTCGGTCACCATCGGCAACCCCCGACGGGT-GC
66 CGCACAGAACCGAGAGTT-GGTGCGTGAGG--CTCGGTCACCATCGGCAACCCCAGACGGGTGGC
8260 CTCGGCAACCCCAGGCCACGGGTGCGGGGGC
128 CTCGGCAACCCCAGGCCACGGGTGCGGGGGC
8291 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * *
8356 CGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTC
66 CGCACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTC
8421 GG
131 GG
8423 TCACCATTGG
Statistics
Matches: 120, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
157 83 0.69
158 35 0.29
159 2 0.02
ACGTcount: A:0.16, C:0.36, G:0.36, T:0.12
Consensus pattern (158 bp):
CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
CGCACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTC
GGCAACCCCAGGCCACGGGTGCGGGGGC
Found at i:8423 original size:190 final size:191
Alignment explanation
Indices: 8227--8593 Score: 512
Period size: 191 Copynumber: 1.9 Consensus size: 191
8217 GGTGCGGGGT
* * * ** *
8227 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG-CAACC-CCAGGC-CA-CGGGTGCGGG
1 CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTC-ACCACC-GGCAAACCCAG-ACGGG
8288 GGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAG
63 GGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC-GGTGCGGGAG
*
8353 TGCCGCACAGAACCGAGCGTT-GGTGCGTGAGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTG
127 TGCCGCACAGAACCGAGAGTTGGGTGCG-GAGGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
8416 G
191 G
* * * * * *
8417 CCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCACCGGCAAACCCAGACGGGGGC
8482 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGTGCGGGAGTGCC
66 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGTGCGGGAGTGCC
* *
8547 GCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCACCATCGGCAA
131 GCACAGAACCGAGAGTTGGGTGCGGAGGCCTCGGTCACCATCGGCAA
8594 CACCCGACGG
Statistics
Matches: 156, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
190 71 0.46
191 83 0.53
192 2 0.01
ACGTcount: A:0.17, C:0.36, G:0.34, T:0.13
Consensus pattern (191 bp):
CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCACCGGCAAACCCAGACGGGGGC
CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGTGCGGGAGTGCC
GCACAGAACCGAGAGTTGGGTGCGGAGGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGG
Found at i:8459 original size:32 final size:32
Alignment explanation
Indices: 8385--8518 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
8375 GTGCGTGAGG
* *
8385 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
8418 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
8450 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
8482 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
8514 CTCGG
1 CTCGG
8519 CAACCCCAGG
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
32 65 0.71
33 26 0.29
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:8613 original size:348 final size:347
Alignment explanation
Indices: 7977--8635 Score: 1192
Period size: 348 Copynumber: 1.9 Consensus size: 347
7967 TCGGTCACCA
**
7977 TCGGCAACCCCAGGCCATTGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
8042 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
66 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
*
8107 TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGC
131 TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGC
* * *
8172 AACCCCAGGCCACGGTGCGGGAGTTCCGGACAGAGCCGAGAGTTGGGTGCGGGGTCCTCGGTCAC
196 AACCCCAGGCCACGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCAC
*
8237 CATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCA
261 CATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCA
8302 TCGGCAACCCCCGACGGGTGCC
326 TCGGCAACCCCCGACGGGTGCC
*
8324 TCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
* *
8389 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCG
66 GTCACCATCGGCAA-CCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCG
8454 GTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
130 GTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
8519 CAACCCCAGGCCACGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCA
195 CAACCCCAGGCCACGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCA
* **
8584 CCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTGGTGCGGG
260 CCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
8636 AGTGCCGCAC
Statistics
Matches: 298, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
347 76 0.26
348 222 0.74
ACGTcount: A:0.17, C:0.35, G:0.35, T:0.13
Consensus pattern (347 bp):
TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGC
AACCCCAGGCCACGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCAC
CATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCA
TCGGCAACCCCCGACGGGTGCC
Found at i:16891 original size:32 final size:32
Alignment explanation
Indices: 16852--16939 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
16842 GCGTGAGCCC
*
16852 CGGTCACCATCGGCAATCCCAGGC-GGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
16884 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
16916 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
16940 CATTGGTGAG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
32 43 0.93
33 3 0.07
ACGTcount: A:0.20, C:0.38, G:0.27, T:0.15
Consensus pattern (32 bp):
CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
Found at i:17027 original size:32 final size:32
Alignment explanation
Indices: 16986--17118 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
16976 GTGCGTGAGG
* *
16986 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
17018 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
17050 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
17082 CTCGGTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
17114 CTCGG
1 CTCGG
17119 CAACCCCAGG
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 83 0.87
33 12 0.13
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.14
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:17243 original size:31 final size:31
Alignment explanation
Indices: 17202--17299 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
17192 CAACCCCCGA
17202 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
* * * ****
17233 CGGGGGCCTCGGTC-ACCATC-GGCAACCCCCG
1 CGGGTGCCTCGG-CAACC-CCAGGCCACGGGTG
17264 ACGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 -CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
17296 CGGG
1 CGGG
17300 AGTGCCGCAC
Statistics
Matches: 48, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
31 26 0.54
32 22 0.46
ACGTcount: A:0.13, C:0.40, G:0.38, T:0.09
Consensus pattern (31 bp):
CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
Found at i:17264 original size:63 final size:63
Alignment explanation
Indices: 17165--17299 Score: 261
Period size: 63 Copynumber: 2.1 Consensus size: 63
17155 GCCGAGAGTT
*
17165 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
17228 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
17291 GGGTGCGGG
1 GGGTGCGGG
17300 AGTGCCGCAC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.13, C:0.39, G:0.37, T:0.10
Consensus pattern (63 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:17275 original size:95 final size:94
Alignment explanation
Indices: 17050--17276 Score: 244
Period size: 95 Copynumber: 2.4 Consensus size: 94
17040 AGACGGGTGT
* *
17050 CTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCC
17115 TCGGCAACCCCAGGCCACGGGTGCGGGAG
66 TCGGCAACCCCAGGCCACGGGTGCGGGAG
* * * * * ***** *
17144 TTCCGGACA-GAGCCG-AGAGTTGGGTGCGGG-GTCCTCGGTCACCATCGGCAACCCCCGACGGG
1 CT-CGGTCACCATCGGCA-AACCCAG-ACGGGTG-CCTCGGTCACCATCGGCAACCCCCGACGGG
*
17206 TGCCTCGGCAACCCCAGGCCACGGGTGCGGGGG
62 TGCCTCGGCAACCCCAGGCCACGGGTGCGGGAG
* *
17239 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
1 -CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGG
17277 CAACCCCAGG
Statistics
Matches: 100, Mismatches: 25, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
93 1 0.01
94 7 0.07
95 84 0.84
96 7 0.07
97 1 0.01
ACGTcount: A:0.16, C:0.37, G:0.35, T:0.12
Consensus pattern (94 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCC
TCGGCAACCCCAGGCCACGGGTGCGGGAG
Found at i:17276 original size:158 final size:158
Alignment explanation
Indices: 17082--17371 Score: 460
Period size: 158 Copynumber: 1.8 Consensus size: 158
17072 AGACGGGTGT
* *
17082 CTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTTC
1 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * *
17147 CGGACAGAGCCGAGAGTTGGGTGCG-G-GGTCCTCGGTCACCATCGGCAACCCCCGACGGGT-GC
66 CGCACAGAACCGAGAGTT-GGTGCGTGAGG--CTCGGTCACCATCGGCAACCCCAGACGGGTGGC
17209 CTCGGCAACCCCAGGCCACGGGTGCGGGGGC
128 CTCGGCAACCCCAGGCCACGGGTGCGGGGGC
17240 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * *
17305 CGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTC
66 CGCACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTC
17370 GG
131 GG
17372 TCACCATTGG
Statistics
Matches: 121, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
157 33 0.27
158 86 0.71
159 2 0.02
ACGTcount: A:0.16, C:0.36, G:0.37, T:0.12
Consensus pattern (158 bp):
CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
CGCACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTC
GGCAACCCCAGGCCACGGGTGCGGGGGC
Found at i:17408 original size:32 final size:32
Alignment explanation
Indices: 17334--17467 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
17324 GTGCGTGAGG
* *
17334 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
17367 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
17399 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
17431 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
17463 CTCGG
1 CTCGG
17468 CAACCCCAGG
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
32 65 0.71
33 26 0.29
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:17505 original size:349 final size:348
Alignment explanation
Indices: 16925--17585 Score: 1196
Period size: 349 Copynumber: 1.9 Consensus size: 348
16915 TCGGTCACCA
**
16925 TCGGCAACCCCAGGCCATTGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
16990 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
66 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
*
17055 TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGC
131 TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGC
* * *
17120 AACCCCAGGCCACGGGTGCGGGAGTTCCGGACAGAGCCGAGAGTTGGGTGCGGGGTCCTCGGTCA
196 AACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCA
*
17185 CCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACC
261 CCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACC
17250 ATCGGCAACCCCCGACGGGTGCC
326 ATCGGCAACCCCCGACGGGTGCC
*
17273 TCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
* *
17338 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCG
66 GTCACCATCGGCAA-CCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCG
17403 GTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
130 GTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
17468 CAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTC
195 CAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTC
* **
17533 ACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTGGTGCGGG
260 ACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
17586 AGTGCCGCAC
Statistics
Matches: 299, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
348 76 0.25
349 223 0.75
ACGTcount: A:0.17, C:0.34, G:0.35, T:0.13
Consensus pattern (348 bp):
TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGC
AACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCA
CCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACC
ATCGGCAACCCCCGACGGGTGCC
Found at i:17550 original size:95 final size:95
Alignment explanation
Indices: 17228--17616 Score: 369
Period size: 95 Copynumber: 4.1 Consensus size: 95
17218 CCCAGGCCAC
17228 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
17293 GTGCGGGAGTGCCGCACAGAACCGAGCG-T
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
* * * * * *** *
17322 TGGTGCGTGAGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTC-ACCATTGGCAA
1 GGGTGCG-GGGGCCTCGGTCACCATCGGCAACCCCCGACGGGT-GCCTCGG-CAACCCCAGGCCA
* *** * * * * * *
17385 AGCCAGACGGGTGT-CTCGGTCAC-CATCGGCA-AACC
63 CGGGTG-CGGGAGTGC-C-G-CACAGAACCG-AGAGCT
** * * *
17420 CAG-ACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
* *
17484 GTGCGGGAGTGCCGCACAGAGCCGAGAGTT
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
* * **
17514 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
17579 GTGCGGGAGTGCCGCACAGAACCGAGCGCT
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
17609 GGGTGCGG
1 GGGTGCGG
17617 CAGCCTCGCA
Statistics
Matches: 225, Mismatches: 55, Indels: 29
0.73 0.18 0.09
Matches are distributed among these distances:
93 4 0.02
94 39 0.17
95 117 0.52
96 27 0.12
97 33 0.15
98 5 0.02
ACGTcount: A:0.17, C:0.34, G:0.36, T:0.13
Consensus pattern (95 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
GTGCGGGAGTGCCGCACAGAACCGAGAGCT
Found at i:23390 original size:30 final size:31
Alignment explanation
Indices: 23296--23425 Score: 156
Period size: 32 Copynumber: 4.2 Consensus size: 31
23286 GTGCGTGAGG
* * *
23296 CTCGGTCACCATCGGCATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAACCCAGACGGGT-GT
* *
23328 CTC-GTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGC-AACCCAGACGGGTGT
23359 CTCGGTCACCATCGGCAACCCAGAC-GGTGT
1 CTCGGTCACCATCGGCAACCCAGACGGGTGT
* *
23389 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAA-CCCAGACGGGTGT
23421 CTCGG
1 CTCGG
23426 CAACCCCAGG
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
30 23 0.27
31 29 0.34
32 33 0.39
ACGTcount: A:0.17, C:0.37, G:0.30, T:0.16
Consensus pattern (31 bp):
CTCGGTCACCATCGGCAACCCAGACGGGTGT
Found at i:23425 original size:62 final size:63
Alignment explanation
Indices: 23296--23425 Score: 165
Period size: 62 Copynumber: 2.1 Consensus size: 63
23286 GTGCGTGAGG
* * * * *
23296 CTCGGTCACCATCGGCATCCCAGGCGGGTGGCCTCGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGTCACCATCGGCAAACCCAGACGGGTGC
* * *
23359 CTCGGTCACCATCGGCAACCCAGAC-GGT-GTCTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAACCCAGACGGGTGGCCTC-GTCACCATCGGCAAACCCAGACGGGTGC
23421 CTCGG
1 CTCGG
23426 CAACCCCAGG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
61 4 0.07
62 31 0.53
63 23 0.40
ACGTcount: A:0.17, C:0.37, G:0.30, T:0.16
Consensus pattern (63 bp):
CTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:23552 original size:87 final size:90
Alignment explanation
Indices: 23389--23564 Score: 236
Period size: 87 Copynumber: 2.0 Consensus size: 90
23379 CAGACGGTGT
*
23389 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGCGGGAGTGCCG
1 CTCGGTCACCATCGGCAACACCCGAC-GGTGCCTCGGCAACCCCAGGCCACGGGCGGGAGTGCCG
* *
23454 CACAGAGCCGAGAGTTGGGTGCGGGC
65 CACAGAACCGAGAGCTGGGTGCGGGC
* *
23480 CTCGGTCACCATCGGCAACACCCGAC-G-GCCTC-GCAACCCCAGTCCATTGGTGC-GG-GTGCC
1 CTCGGTCACCATCGGCAACACCCGACGGTGCCTCGGCAACCCCAGGCCA-CGG-GCGGGAGTGCC
*
23540 GCACAGAACCGAGCGCTGGGTGCGG
64 GCACAGAACCGAGAGCTGGGTGCGG
23565 CAGCCTCGCA
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
87 40 0.52
88 9 0.12
89 3 0.04
91 25 0.32
ACGTcount: A:0.17, C:0.37, G:0.35, T:0.11
Consensus pattern (90 bp):
CTCGGTCACCATCGGCAACACCCGACGGTGCCTCGGCAACCCCAGGCCACGGGCGGGAGTGCCGC
ACAGAACCGAGAGCTGGGTGCGGGC
Done.