Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001458.1 Hibiscus syriacus cultivar Beakdansim tig00002813_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: 210874
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:150281 original size:31 final size:31
Alignment explanation
Indices: 150246--150310 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
150236 TAACTATATC
* * *
150246 TTAATTAAATGAAAATGAAAGTAATCAAATA
1 TTAATTAAATAAAAACGAAAGTAACCAAATA
*
150277 TTAATTAAATAAAAACGAAAGTGACCAAATA
1 TTAATTAAATAAAAACGAAAGTAACCAAATA
150308 TTA
1 TTA
150311 TATTTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (31 bp):
TTAATTAAATAAAAACGAAAGTAACCAAATA
Found at i:151390 original size:31 final size:31
Alignment explanation
Indices: 151327--151391 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
151317 TGGCTACATC
*
151327 TTAATTAAATAAAAATGAAAGTAACCACATA
1 TTAATTAAATAAAAATGAAAGTAACCAAATA
* * **
151358 TTAATTAAATAGAAATTAAAGTGGCCAAATA
1 TTAATTAAATAAAAATGAAAGTAACCAAATA
151389 TTA
1 TTA
151392 TATTTTTACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (31 bp):
TTAATTAAATAAAAATGAAAGTAACCAAATA
Found at i:153116 original size:40 final size:40
Alignment explanation
Indices: 153037--153135 Score: 135
Period size: 40 Copynumber: 2.4 Consensus size: 40
153027 GTAGCGTTAG
* *
153037 GTTATGATATTTAGCAGCGTTTTTTCATAAACGTCGCAACAT
1 GTTATGATATTTAGC-G-GGTTTTTAATAAACGTCGCAACAT
*
153079 GTTATGATATTTAGCGGGTTTTTAATAAACGTTGCAACAT
1 GTTATGATATTTAGCGGGTTTTTAATAAACGTCGCAACAT
* *
153119 GTTATTACATTTAGCGG
1 GTTATGATATTTAGCGG
153136 CCTTTTTTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 36 0.69
41 1 0.02
42 15 0.29
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.39
Consensus pattern (40 bp):
GTTATGATATTTAGCGGGTTTTTAATAAACGTCGCAACAT
Found at i:153160 original size:45 final size:46
Alignment explanation
Indices: 153111--153223 Score: 122
Period size: 48 Copynumber: 2.4 Consensus size: 46
153101 TAATAAACGT
153111 TGCAACATGTTATTACATTTAGCG-G-CCTTTTTTTGGTATAAATGC
1 TGCAACATGTTATTACATTTAGCGAGTCCTTTTTTT-GTATAAATGC
* * * * *
153156 TGCAATATGTTATGATATTTAGTGATGTTTCTTTTTTTGTATAAATGC
1 TGCAACATGTTATTACATTTAGCGA-G-TCCTTTTTTTGTATAAATGC
* *
153204 CGCAACAAGTTATTACATTT
1 TGCAACATGTTATTACATTT
153224 TATGATATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
45 20 0.37
47 1 0.02
48 25 0.46
49 8 0.15
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (46 bp):
TGCAACATGTTATTACATTTAGCGAGTCCTTTTTTTGTATAAATGC
Found at i:153553 original size:26 final size:27
Alignment explanation
Indices: 153493--153555 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
153483 TCAAGCAATG
153493 TAGTTCAACATTAAGTGAAATGTAATA
1 TAGTTCAACATTAAGTGAAATGTAATA
*
153520 TAGTTCAATATTAAGTGAAATGT-ATA
1 TAGTTCAACATTAAGTGAAATGTAATA
153546 TAGTTCAACA
1 TAGTTCAACA
153556 AGTATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (27 bp):
TAGTTCAACATTAAGTGAAATGTAATA
Found at i:157023 original size:24 final size:24
Alignment explanation
Indices: 156932--157025 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
156922 TTCAATTTGA
* * *
156932 ATTCTGTTATGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACCTGG
* **
156956 ATTCTGATTTGATAC-TGATATGG
1 ATTCTGATCTGATACTTGACCTGG
*
156979 ATTCTAATCTGATA-TATGACCTGG
1 ATTCTGATCTGATACT-TGACCTGG
157003 ATTCTGATCTGATACTTGACCTG
1 ATTCTGATCTGATACTTGACCTG
157026 TATTATGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
23 18 0.31
24 39 0.67
25 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:157230 original size:14 final size:15
Alignment explanation
Indices: 157211--157239 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
157201 AGTGTTTATA
157211 TTTTAAAAA-ATATG
1 TTTTAAAAAGATATG
157225 TTTTAAAAAGATATG
1 TTTTAAAAAGATATG
157240 AAAAGTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
TTTTAAAAAGATATG
Found at i:165026 original size:40 final size:42
Alignment explanation
Indices: 164949--165050 Score: 97
Period size: 40 Copynumber: 2.5 Consensus size: 42
164939 ATGGTTGACC
* * ** *
164949 CAAGGTGATGCTAATCCTACTCCTTATGTAATCGACGA-C-A
1 CAAGGTGATGCTGATCCAACTCCCAATATAATCGACGAGCGA
* *
164989 CAAGGTGATGCTGATCCAACTCCCAATATGATGGACGAGCGA
1 CAAGGTGATGCTGATCCAACTCCCAATATAATCGACGAGCGA
*
165031 -AA--TGATGATGATCCAACTCC
1 CAAGGTGATGCTGATCCAACTCC
165051 TTATGTGACG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 17 0.33
40 31 0.60
41 3 0.06
42 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (42 bp):
CAAGGTGATGCTGATCCAACTCCCAATATAATCGACGAGCGA
Found at i:166214 original size:37 final size:37
Alignment explanation
Indices: 166171--166243 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
166161 TCTTAATAAG
**
166171 GACTCAAATGACATCCCAGAAAAATGATCCTAAGAAT
1 GACTCAAAAAACATCCCAGAAAAATGATCCTAAGAAT
* * * *
166208 GACTCAAAAAATATTCTATAAAAATGATCCTAAGAA
1 GACTCAAAAAACATCCCAGAAAAATGATCCTAAGAA
166244 GGACAAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.22
Consensus pattern (37 bp):
GACTCAAAAAACATCCCAGAAAAATGATCCTAAGAAT
Found at i:167239 original size:54 final size:53
Alignment explanation
Indices: 167168--167641 Score: 245
Period size: 55 Copynumber: 8.7 Consensus size: 53
167158 ATGAAGAAAC
* * *
167168 CCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAGCCATCAACAAAA
1 CCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGACATCAA-AAAA
* * * * *
167222 CCCTAAAAATCATGCTTAGCTTCTTTTAAAATCCTTTTAAAGACATCAAAAAAA
1 CCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGACATC-AAAAAA
* * * * * *
167276 CCACTAAAAATTAGGATTAGCTTCGTTCAGAA-TCTATTTGAATACATCAAGAAAC
1 CC-CTAAAAATCAGGCTTAGCTTCTTTCAAAATTC-ATTTGAAGACATCAA-AAAA
* * * * * * *
167331 CCCTAAAAA-CTAGGCTTAACATATTTCAAAATCCATTTGAATATATCAAGAAA
1 CCCTAAAAATC-AGGCTTAGCTTCTTTCAAAATTCATTTGAAGACATCAAAAAA
* * * * * * * *
167384 CTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTT-ATAAATAATCCAGAAA
1 C-CCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGA-AGA-CATCAAAAAA
* ** * * * * * * *
167439 -CTTATGAAAATCAAACCTAGTTTCTTTGAAAACTCATTTAAAAATCATCAAGAAA
1 CCCTA--AAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA-CATCAAAAAA
* * * * * *
167494 CTTCTAAAAATCAGTCTTAGTTTCTTTGAAAATTCATTTGAAAACATCAAGAAAC
1 C-CCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGACATCAA-AAAA
* * * * * * * *
167549 CCCTGAAAATCAGGCTTTGCTTATTTGAAAACTCATTTAAAAATCATCAAGAAA
1 CCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA-CATCAAAAAA
** * * * *
167603 CTTTTGAAAACCAGGCTTAGTTTCTTTGAAAATTCATTT
1 C-CCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTT
167642 AAAAATCATC
Statistics
Matches: 329, Mismatches: 73, Indels: 35
0.75 0.17 0.08
Matches are distributed among these distances:
53 6 0.02
54 156 0.47
55 164 0.50
56 1 0.00
57 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (53 bp):
CCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGACATCAAAAAA
Found at i:167296 original size:55 final size:54
Alignment explanation
Indices: 167168--167423 Score: 201
Period size: 54 Copynumber: 4.7 Consensus size: 54
167158 ATGAAGAAAC
* * * *
167168 CCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAGCCATCAACAAAA
1 CCCTAAAAATTAGGCTTAGCTTCTTTAAAAATCCATTTAAAGACATCAAAAAAA
* * * *
167222 CCCTAAAAATCATGCTTAGCTTCTTTTAAAATCCTTTTAAAGACATCAAAAAAA
1 CCCTAAAAATTAGGCTTAGCTTCTTTAAAAATCCATTTAAAGACATCAAAAAAA
* * * * * * * * *
167276 CCACTAAAAATTAGGATTAGCTTCGTTCAGAATCTATTTGAATACATCAAGAAAC
1 CC-CTAAAAATTAGGCTTAGCTTCTTTAAAAATCCATTTAAAGACATCAAAAAAA
* * * * * * * * *
167331 CCCTAAAAACTAGGCTTAACATATTTCAAAATCCATTTGAATATATC-AAGAAA
1 CCCTAAAAATTAGGCTTAGCTTCTTTAAAAATCCATTTAAAGACATCAAAAAAA
* * * *
167384 CTCCTGAAAATCAGACTTAGCTTCTTTGAAAA-CTCATTTA
1 C-CCTAAAAATTAGGCTTAGCTTCTTTAAAAATC-CATTTA
167424 TAAATAATCC
Statistics
Matches: 158, Mismatches: 41, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
53 5 0.03
54 111 0.70
55 42 0.27
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (54 bp):
CCCTAAAAATTAGGCTTAGCTTCTTTAAAAATCCATTTAAAGACATCAAAAAAA
Found at i:167362 original size:109 final size:109
Alignment explanation
Indices: 167164--167364 Score: 244
Period size: 109 Copynumber: 1.8 Consensus size: 109
167154 TATCATGAAG
* * * *
167164 AAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTGAAGCCATCAACAAAACCCTAAA
1 AAACCACTAAAAATTAGGATTAGCTTCGTTAAAAATTCATTTGAAGACATCAACAAAACCCTAAA
* * * * *
167229 AATCATGCTTAGCTTCTTTTAAAATCCTTTTAAAGACATCAAAA
66 AATCAGGCTTAACATATTTCAAAATCCTTTTAAAGACATCAAAA
* * * * *
167273 AAACCACTAAAAATTAGGATTAGCTTCGTTCAGAA-TCTATTTGAATACATCAAGAAACCCCTAA
1 AAACCACTAAAAATTAGGATTAGCTTCGTTAAAAATTC-ATTTGAAGACATCAACAAAACCCTAA
167337 AAA-CTAGGCTTAACATATTTCAAAATCC
65 AAATC-AGGCTTAACATATTTCAAAATCC
167365 ATTTGAATAT
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
108 3 0.04
109 73 0.96
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (109 bp):
AAACCACTAAAAATTAGGATTAGCTTCGTTAAAAATTCATTTGAAGACATCAACAAAACCCTAAA
AATCAGGCTTAACATATTTCAAAATCCTTTTAAAGACATCAAAA
Found at i:167447 original size:55 final size:55
Alignment explanation
Indices: 167375--167816 Score: 539
Period size: 55 Copynumber: 8.0 Consensus size: 55
167365 ATTTGAATAT
* * * *
167375 ATCAAGAAACTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTTATAAATA
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
* * * *
167430 ATCCAGAAACTTATGAAAATCAAACCTAGTTTCTTTGAAAACTCATTTAAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
* * * *
167485 ATCAAGAAACTTCTAAAAATCAGTCTTAGTTTCTTTGAAAATTCATTTGAAAA-C
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
** * * * *
167539 ATCAAGAAACCCCTGAAAATCAGGCTTTGCTTATTTGAAAACTCATTTAAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
* * * *
167594 ATCAAGAAACTTTTGAAAACCAGGCTTAGTTTCTTTGAAAATTCATTTAAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
* * * *
167649 ATCAAGAAATTTTTGAAAATCAGACTTAGTTTCTTTAAAAACTCGTTTAAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
* *
167704 ATCAAGAAACTTCTGAAAACCAGACTTAGTTTCTTTGAAAACTCATTTATAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
* * * * *
167759 ATCAAGAAACTT-TCAATAATCGGACTTAGCTACTTTCAAAA-TCATTTGAAAACATC
1 ATCAAGAAACTTCTGAA-AATCAGACTTAGTTTCTTTGAAAACTCATTT-AAAA-ATC
167815 AT
1 AT
167817 ATTGTTTGGG
Statistics
Matches: 331, Mismatches: 52, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
54 54 0.16
55 272 0.82
56 5 0.02
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (55 bp):
ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATC
Found at i:167534 original size:164 final size:164
Alignment explanation
Indices: 167358--167770 Score: 574
Period size: 164 Copynumber: 2.5 Consensus size: 164
167348 AACATATTTC
* *
167358 AAAATCCATTTGAATATATCAAGAAACTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTT
1 AAAATTCATTTGAAAATATCAAGAAACTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTT
* * *
167423 ATAAATAATCCAGAAACTTATGAAAATCAAACCTAGTTTCTTTGAAAACTCATTTAAAAATCATC
66 ATAAATCATCAAGAAACTTATGAAAACCAAACCTAGTTTCTTTGAAAACTCATTTAAAAATCATC
* *
167488 AAGAAACTTCTAAAAATCAGTCTTAGTTTCTTTG
131 AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTA
* * * * *
167522 AAAATTCATTTGAAAACATCAAGAAACCCCTGAAAATCAGGCTTTGCTTATTTGAAAACTCATTT
1 AAAATTCATTTGAAAATATCAAGAAACTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTT
* * ** * *
167587 AAAAATCATCAAGAAACTTTTGAAAACCAGGCTTAGTTTCTTTGAAAATTCATTTAAAAATCATC
66 ATAAATCATCAAGAAACTTATGAAAACCAAACCTAGTTTCTTTGAAAACTCATTTAAAAATCATC
* * *
167652 AAGAAATTTTTGAAAATCAGACTTAGTTTCTTTA
131 AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTA
* * * * * *
167686 AAAACTCGTTTAAAAATCATCAAGAAACTTCTGAAAACCAGACTTAGTTTCTTTGAAAACTCATT
1 AAAATTCATTTGAAAAT-ATCAAGAAACTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATT
167751 TATAAATCATCAAGAAACTT
65 TATAAATCATCAAGAAACTT
167771 TCAATAATCG
Statistics
Matches: 215, Mismatches: 33, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
164 156 0.73
165 59 0.27
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (164 bp):
AAAATTCATTTGAAAATATCAAGAAACTCCTGAAAATCAGACTTAGCTTCTTTGAAAACTCATTT
ATAAATCATCAAGAAACTTATGAAAACCAAACCTAGTTTCTTTGAAAACTCATTTAAAAATCATC
AAGAAACTTCTAAAAATCAGACTTAGTTTCTTTA
Found at i:169199 original size:28 final size:29
Alignment explanation
Indices: 169117--169192 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
169107 TTAGGCTGAC
*
169117 TTGGGAAGGTAATGTGTTTCAGGTTAATT
1 TTGGGGAGGTAATGTGTTTCAGGTTAATT
*
169146 TTGAGGAGGTAATGTGTTTCAGGTTAA-T
1 TTGGGGAGGTAATGTGTTTCAGGTTAATT
*
169174 TTGGGGAGGTAATATGTTT
1 TTGGGGAGGTAATGTGTTT
169193 TGGGTTAGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 18 0.42
29 25 0.58
ACGTcount: A:0.24, C:0.03, G:0.33, T:0.41
Consensus pattern (29 bp):
TTGGGGAGGTAATGTGTTTCAGGTTAATT
Found at i:169488 original size:20 final size:20
Alignment explanation
Indices: 169441--169479 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
169431 GATGTCAACT
169441 AAAATTTTACGTCTTGAACC
1 AAAATTTTACGTCTTGAACC
169461 AAAATTTTACGTCTTGAAC
1 AAAATTTTACGTCTTGAAC
169480 ACTTATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAATTTTACGTCTTGAACC
Found at i:170558 original size:85 final size:85
Alignment explanation
Indices: 170415--170586 Score: 281
Period size: 85 Copynumber: 2.0 Consensus size: 85
170405 ATACAATCAC
* * *
170415 GACACACGAATGTGTGTCATTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTTATA
1 GACACACAAATGTGTATCATTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCATA
*
170480 AATGCGTGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
* * *
170500 GACACACAAATGTGTATCATTTTTATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATA
1 GACACACAAATGTGTATCATTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCATA
170565 AATGCGCGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
170585 GA
1 GA
170587 TGCACAGTTG
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (85 bp):
GACACACAAATGTGTATCATTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCGCGTCATAAATTTAT
Found at i:170971 original size:12 final size:12
Alignment explanation
Indices: 170947--170988 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
170937 CTTTTCTCTC
170947 TCTTTTA-TTCT
1 TCTTTTATTTCT
170958 TCTTTTATTTCT
1 TCTTTTATTTCT
*
170970 TCTCTTTCTTTCTT
1 TCT-TTTATTTC-T
170984 TCTTT
1 TCTTT
170989 CTTTCTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 7 0.26
12 7 0.26
13 9 0.33
14 4 0.15
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (12 bp):
TCTTTTATTTCT
Found at i:170981 original size:4 final size:4
Alignment explanation
Indices: 170965--170996 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
170955 TCTTCTTTTA
170965 TTTC TTCTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TT-TC TTTC TTTC TTTC TTTC TTTC TTT
170997 TTTTTCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:176005 original size:24 final size:24
Alignment explanation
Indices: 175966--176019 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
175956 TAAGAAGGGT
*
175966 TAGGGTTAGGTTAGAGTATTGGGC
1 TAGGGTTAGGTAAGAGTATTGGGC
*
175990 TAGGGTTTGGTAAGAGTATTGGGC
1 TAGGGTTAGGTAAGAGTATTGGGC
176014 TAGGGT
1 TAGGGT
176020 GTTTTTAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.04, G:0.43, T:0.33
Consensus pattern (24 bp):
TAGGGTTAGGTAAGAGTATTGGGC
Found at i:176113 original size:3 final size:3
Alignment explanation
Indices: 176105--176195 Score: 143
Period size: 3 Copynumber: 31.3 Consensus size: 3
176095 TTTGGGTTTG
* *
176105 TAA TAA TAA TAA TAA TAA CAA T-G TAA T-A TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
176150 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
176196 GGGTTGAAAA
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
2 5 0.06
3 76 0.94
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:176348 original size:41 final size:41
Alignment explanation
Indices: 176283--176429 Score: 177
Period size: 42 Copynumber: 3.5 Consensus size: 41
176273 TTGAAATAAC
* * *
176283 GGTGTTTGTTAAAAAAGCGCCACAAATTATGTATCATATTGA
1 GGTGTTCGTTAAAAAA-AGCCACAAACTATGTATCATATTGA
* * *
176325 GGCGTTCGTTAAAAAAAGTCACAAACTATGTATCATATTGT
1 GGTGTTCGTTAAAAAAAGCCACAAACTATGTATCATATTGA
* * * *
176366 GGTGTTTGTTAAAAAAAAGCCACAAACTATGCATCCTATTGC
1 GGTGTTCGTT-AAAAAAAGCCACAAACTATGTATCATATTGA
176408 GGTGTTCGTTAAAAAAATGCCA
1 GGTGTTCGTTAAAAAAA-GCCA
176430 TGTACTATGT
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 36 0.40
42 54 0.60
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (41 bp):
GGTGTTCGTTAAAAAAAGCCACAAACTATGTATCATATTGA
Found at i:176437 original size:42 final size:42
Alignment explanation
Indices: 176282--176447 Score: 172
Period size: 42 Copynumber: 4.0 Consensus size: 42
176272 ATTGAAATAA
* ** * *
176282 CGGTGTTTGTTAAAAAAGCGCCACAAATTATGTATCATATTG
1 CGGTGTTCGTTAAAAAAAAGCCACAAACTATGTATCCTATTG
* * * *
176324 AGGCGTTCGTT-AAAAAAAGTCACAAACTATGTATCATATTG
1 CGGTGTTCGTTAAAAAAAAGCCACAAACTATGTATCCTATTG
* * *
176365 TGGTGTTTGTTAAAAAAAAGCCACAAACTATGCATCCTATTG
1 CGGTGTTCGTTAAAAAAAAGCCACAAACTATGTATCCTATTG
* *** *
176407 CGGTGTTCGTTAAAAAAATGCCATGTACTATGTACCCTATT
1 CGGTGTTCGTTAAAAAAAAGCCACAAACTATGTATCCTATT
176448 ACCACATTTG
Statistics
Matches: 102, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
41 34 0.33
42 68 0.67
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (42 bp):
CGGTGTTCGTTAAAAAAAAGCCACAAACTATGTATCCTATTG
Found at i:176478 original size:41 final size:41
Alignment explanation
Indices: 176369--176525 Score: 127
Period size: 41 Copynumber: 3.8 Consensus size: 41
176359 ATATTGTGGT
* * * * ***
176369 GTTTGTTAAAAAAAAGCCACAAACTATGCATCCTATTGCGGT
1 GTTTGTT-AAAAAAAGCAACAAACTATGTACCCTATTACAAA
* * *** *
176411 GTTCGTTAAAAAAATGCCATGTACTATGTACCCTATTACCACA
1 GTTTGTTAAAAAAA-GCAACAAACTATGTACCCTATTA-CAAA
* * * *
176454 -TTTGTTTAAAAAAGCCAGAAACTATGTACCATATTACAAA
1 GTTTGTTAAAAAAAGCAACAAACTATGTACCCTATTACAAA
176494 GTTTGTTAAAAAAAGCAACAAACTATGTACCC
1 GTTTGTTAAAAAAAGCAACAAACTATGTACCC
176526 AATTGCGACG
Statistics
Matches: 91, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
40 3 0.03
41 53 0.58
42 34 0.37
43 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (41 bp):
GTTTGTTAAAAAAAGCAACAAACTATGTACCCTATTACAAA
Found at i:176544 original size:41 final size:41
Alignment explanation
Indices: 176433--176547 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 41
176423 AATGCCATGT
* * * * * *
176433 ACTATGTACCCTATTACCACATTTGTTTAAAAAAGCCAGAA
1 ACTATGTACCCAATTACAACGTTTGTTAAAAAAAGCAACAA
*
176474 ACTATGTA-CCATATTACAAAGTTTGTTAAAAAAAGCAACAA
1 ACTATGTACCCA-ATTACAACGTTTGTTAAAAAAAGCAACAA
* * *
176515 ACTATGTACCCAATTGCGACGTTTATTAAAAAA
1 ACTATGTACCCAATTACAACGTTTGTTAAAAAA
176548 CACCACAAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
40 2 0.03
41 56 0.92
42 3 0.05
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (41 bp):
ACTATGTACCCAATTACAACGTTTGTTAAAAAAAGCAACAA
Found at i:185850 original size:23 final size:23
Alignment explanation
Indices: 185806--185850 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
185796 AAAGAAAACT
**
185806 AATAAAATAACAAAATCTAAAAG
1 AATAAAATAACAAAATAAAAAAG
185829 AATAAAGATAA-AAAATAAAAAA
1 AATAAA-ATAACAAAATAAAAAA
185851 ATATAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (23 bp):
AATAAAATAACAAAATAAAAAAG
Found at i:187179 original size:32 final size:33
Alignment explanation
Indices: 187142--187203 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
187132 TTGTTGTGGT
*
187142 GGCTATGCAACTTGTT-TCGTGTCTGATGTCAG
1 GGCTATGCAACTTGTTGTCGTGACTGATGTCAG
* *
187174 GGCTATGCTACTTGTTGTTGTGACTGATGT
1 GGCTATGCAACTTGTTGTCGTGACTGATGT
187204 AGAGGCATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.15, C:0.16, G:0.29, T:0.40
Consensus pattern (33 bp):
GGCTATGCAACTTGTTGTCGTGACTGATGTCAG
Found at i:203637 original size:20 final size:20
Alignment explanation
Indices: 203612--203662 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
203602 ACTAAACTTT
203612 GTATCGATACCTC-CCTACGA
1 GTATCGATACCTCACCTAC-A
203632 GTATCGATACCTCACCTACA
1 GTATCGATACCTCACCTACA
*
203652 GTATAGATACC
1 GTATCGATACC
203663 GATTGCATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.25
Consensus pattern (20 bp):
GTATCGATACCTCACCTACA
Done.