Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005383.1 Hibiscus syriacus cultivar Beakdansim tig00012322_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: 64311
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2211 original size:19 final size:20
Alignment explanation
Indices: 2169--2212 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
2159 ATAACGCCCA
*
2169 AAATTGTACTTATTAATTAT
1 AAATTGTACTTATTAATTAG
2189 AAATTGT-CTCTATT-ATTAG
1 AAATTGTACT-TATTAATTAG
2208 AAATT
1 AAATT
2213 TAAAATTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (20 bp):
AAATTGTACTTATTAATTAG
Found at i:4085 original size:15 final size:15
Alignment explanation
Indices: 4065--4131 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
4055 TTTTTGGGCC
4065 TGTAATAATAATATT
1 TGTAATAATAATATT
* *
4080 TGTAATTAT-TTATT
1 TGTAATAATAATATT
*
4094 ATTTAATAATAATA--
1 -TGTAATAATAATATT
4108 T-TAATAATAATATT
1 TGTAATAATAATATT
**
4122 AATAATAATA
1 TGTAATAATA
4132 TAATAAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
12 11 0.27
13 1 0.02
14 4 0.10
15 23 0.56
16 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TGTAATAATAATATT
Found at i:4103 original size:3 final size:3
Alignment explanation
Indices: 4097--4153 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
4087 ATTTATTATT
* *
4097 TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA TAA T-A TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
4142 TTA TAA TAA TAA
1 TAA TAA TAA TAA
4154 ATCAAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:4113 original size:12 final size:12
Alignment explanation
Indices: 4096--4153 Score: 84
Period size: 12 Copynumber: 4.8 Consensus size: 12
4086 TATTTATTAT
4096 TTAATAATAATA
1 TTAATAATAATA
4108 TTAATAATAATA
1 TTAATAATAATA
4120 TTAATAATAATA
1 TTAATAATAATA
4132 -TAATAAATAAT-
1 TTAAT-AATAATA
4143 TATAATAATAA
1 T-TAATAATAA
4154 ATCAAAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.09
12 35 0.81
13 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TTAATAATAATA
Found at i:4163 original size:24 final size:24
Alignment explanation
Indices: 4096--4165 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
4086 TATTTATTAT
* *
4096 TTAATAATAATATTAATAATAATA
1 TTAATAATAATATAAAAAATAATA
*
4120 TTAATAATAATATAATAAATAAT-
1 TTAATAATAATATAAAAAATAATA
4143 TATAATAATAA-ATCAAAAAATAA
1 T-TAATAATAATAT-AAAAAATAA
4166 AAACAAATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.08
24 37 0.93
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (24 bp):
TTAATAATAATATAAAAAATAATA
Found at i:5030 original size:228 final size:229
Alignment explanation
Indices: 4548--5202 Score: 934
Period size: 228 Copynumber: 2.9 Consensus size: 229
4538 GTTGAACAAG
* * *
4548 TTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACAC-TTCTAGAAATGTTGATACTGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGATCTCTTTCGA-AAATGTTGAT-CTG--
* **
4611 CTATCTCCTTCTGTGATAGAATCA-AAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
62 -TAT-TCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
* *
4675 TTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAA-GTTGATCC-ATCGAGTGAT
125 TT-CTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCAAT-GAGTGAT
*
4738 GAATTCTAGCAAAGGTTTGAACAAATTCTTCTCATTATGAAT
188 GAATTCAAGCAAAGGTTTGAACAAATTCTTCTCATTATGAAT
*
4780 TTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGATCTCTTTCGAAAATGTTGATCTGT-TT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGATCTCTTTCGAAAATGTTGATCTGTATT
4844 CCTTCTGTGATAGAGTCATGCAAAAGG-TGAACAAGTTCTTCTCATTATGAA-TTCTTCTTACTC
66 CCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTC
4907 TTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCAATGAGTGATGAATTCA
130 TTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCAATGAGTGATGAATTCA
4972 AGCAAAAGGTTTGAACAAATTCTTCTCATTATGAAT
195 AGC-AAAGGTTTGAACAAATTCTTCTCATTATGAAT
* * * * * *
5008 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAT-TGTTTTGGAAATGTTGATATATCT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG-ATCTCTTTCGAAAATGTTGATCTGTAT
*
5072 T-CTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCAT
65 TCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-T
* * * * *
5136 ATTCAGATAATTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCATTGAGTAATGGATTC
129 CTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCAATGAGTGATGAATTC
5201 AA
194 AA
5203 TCTTTGCTAA
Statistics
Matches: 390, Mismatches: 22, Indels: 24
0.89 0.05 0.06
Matches are distributed among these distances:
226 48 0.12
227 66 0.17
228 120 0.31
229 30 0.08
230 71 0.18
232 9 0.02
233 42 0.11
234 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (229 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGATCTCTTTCGAAAATGTTGATCTGTATT
CCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCT
TCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCAATGAGTGATGAATTCAA
GCAAAGGTTTGAACAAATTCTTCTCATTATGAAT
Found at i:6956 original size:9 final size:9
Alignment explanation
Indices: 6947--6977 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
6937 TTTGATATTA
6947 TTATTATTAT
1 TTATT-TTAT
6957 TTATTTTAT
1 TTATTTTAT
6966 TTATTTTAT
1 TTATTTTAT
6975 TTA
1 TTA
6978 ATGAATGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTAT
Found at i:9732 original size:14 final size:14
Alignment explanation
Indices: 9713--9739 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9703 TGCAAAAAGT
9713 AAAAAAAAAGAAAA
1 AAAAAAAAAGAAAA
9727 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
9740 TGAATTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAA
Found at i:11211 original size:2 final size:2
Alignment explanation
Indices: 11200--11247 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
11190 AAATAAATAA
11200 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11241 AT AT AT A
1 AT AT AT A
11248 ATAATAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11409 original size:28 final size:29
Alignment explanation
Indices: 11359--11414 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
11349 ATAAATGAAA
*
11359 ATATTAAAATTAGTAACTAAA-TTATAAC
1 ATATTAAAATTAATAACTAAATTTATAAC
*
11387 ATATTAAAATTAAATACCT-AATTTATAA
1 ATATTAAAATT-AATAACTAAATTTATAA
11415 TTAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (29 bp):
ATATTAAAATTAATAACTAAATTTATAAC
Found at i:11813 original size:43 final size:43
Alignment explanation
Indices: 11760--11971 Score: 212
Period size: 43 Copynumber: 4.9 Consensus size: 43
11750 TTTTTTTGTT
* * * *
11760 AAAAATGCCGCTATAGGTATTGATATTTAGCGGCGTTTGTCAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
* * *
11803 AAAAACGCCGCAATAGGTGTTGATATTTATCGGTGTTTTTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
** *
11846 AAAAACATCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
* * * **
11889 ACAAACGCTGCAATAGGT-TATGATGTTTAGCGGCGTTTTTCTCC
1 AAAAACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTTTC-AG
* * * * *
11933 AAAAA-GCCACAGTAGGTGTTGATGTTTTGCTGCGTTTTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT
11972 GCTAAAATGC
Statistics
Matches: 139, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
42 1 0.01
43 133 0.96
44 5 0.04
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAG
Found at i:12431 original size:21 final size:21
Alignment explanation
Indices: 12384--12455 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
12374 GCTGATATGT
12384 TGCTTCTCTCTGTGCTACCGC
1 TGCTTCTCTCTGTGCTACCGC
* * **
12405 TACTTCTCTTTGTGCTGTCGC
1 TGCTTCTCTCTGTGCTACCGC
* * * *
12426 TGCTTCTTTCTCTGCTTCTGC
1 TGCTTCTCTCTGTGCTACCGC
*
12447 TGCTGCTCT
1 TGCTTCTCT
12456 GGCTGCGTCT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.03, C:0.33, G:0.18, T:0.46
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTACCGC
Found at i:21561 original size:42 final size:42
Alignment explanation
Indices: 21469--21561 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
21459 ATAATATTTC
*
21469 GCGGCGTTTGTAAACCAAACGCCACCACATGCCAACTCTACT
1 GCGGCGTTTGTAAACCAAACACCACCACATGCCAACTCTACT
* * * * * *
21511 GTGACGTTTGTAAACCAAACACCACTATATTCCAACTCTATT
1 GCGGCGTTTGTAAACCAAACACCACCACATGCCAACTCTACT
21553 GCGGCGTTT
1 GCGGCGTTT
21562 ACTAAAAACG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (42 bp):
GCGGCGTTTGTAAACCAAACACCACCACATGCCAACTCTACT
Found at i:23221 original size:41 final size:40
Alignment explanation
Indices: 23073--23223 Score: 160
Period size: 41 Copynumber: 3.7 Consensus size: 40
23063 ATTTATACAA
* * * **
23073 AAAAATGCCACAATTGATT-GCACTATTGTGGCGTTTGTT
1 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTT
* * *
23112 AAAACAACGCCACTATTAATTAAAACTATTACGGCGTTTTTTT
1 -AAA-AACGCCACTATTGATTAACACTATTACGGCG-TTTGTT
23155 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTCT
1 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGT-T
* * *
23196 AAAAATGCCACTATTTATTATCACTATT
1 AAAAACGCCACTATTGATTAACACTATT
23224 GCGACATTTT
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
40 7 0.08
41 68 0.73
42 13 0.14
43 5 0.05
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (40 bp):
AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTT
Found at i:23284 original size:42 final size:40
Alignment explanation
Indices: 23137--23398 Score: 144
Period size: 42 Copynumber: 6.3 Consensus size: 40
23127 TTAATTAAAA
** * *
23137 CTATTACGGCGTTTTTTTAAAAACGCCACTAT-TGATTAACA
1 CTATTACGGCGTTTTGGTATAAACGCCACTATATG-TTAA-T
* * * * *
23178 CTATTACGGCG-TTTGTCTAAAAATGCCACTATTTATT-AT
1 CTATTACGGCGTTTTG-GTATAAACGCCACTATATGTTAAT
* * * *
23217 CACTATTGCGACATTTTAGGAATAAACGCCACTATATGTGTAAT
1 --CTATTACGGCGTTTT-GGTATAAACGCCACTATATGT-TAAT
* *
23261 CTATTACGGTGTTTGTGGTATAAACACCACTA-AT-TTACCGAT
1 CTATTACGGCGTTT-TGGTATAAACGCCACTATATGTTA---AT
* *
23303 CTATTGCGGCATTTTGGCTA-AAACGCCACTATATGTTAAT
1 CTATTACGGCGTTTTGG-TATAAACGCCACTATATGTTAAT
* * *
23343 CTATTACGGCGTTTATTGTATAAACACTACTA-AT-TTACCACT
1 CTATTACGGCGTTT-TGGTATAAACGCCACTATATGTTA--A-T
23385 CTATTACGGCGTTT
1 CTATTACGGCGTTT
23399 GTTAAAAAAC
Statistics
Matches: 172, Mismatches: 29, Indels: 39
0.72 0.12 0.16
Matches are distributed among these distances:
39 5 0.03
40 23 0.13
41 62 0.36
42 74 0.43
43 6 0.03
44 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (40 bp):
CTATTACGGCGTTTTGGTATAAACGCCACTATATGTTAAT
Found at i:23366 original size:82 final size:83
Alignment explanation
Indices: 23240--23394 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 83
23230 TTTTAGGAAT
* *
23240 AAACGCCACTATATGTGTAATCTATTACGGTGTTTGTGGTATAAACACCACTAATTTACCGA-TC
1 AAACGCCACTATATGTGTAATCTATTACGGCGTTTATGGTATAAACACCACTAATTTACC-ACTC
*
23304 TATTGCGGCATTTTGGCTA
65 TATTACGGCATTTTGGCTA
* *
23323 AAACGCCACTATATGT-TAATCTATTACGGCGTTTATTGTATAAACACTACTAATTTACCACTCT
1 AAACGCCACTATATGTGTAATCTATTACGGCGTTTATGGTATAAACACCACTAATTTACCACTCT
23387 ATTACGGC
66 ATTACGGC
23395 GTTTGTTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 1 0.02
82 49 0.74
83 16 0.24
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (83 bp):
AAACGCCACTATATGTGTAATCTATTACGGCGTTTATGGTATAAACACCACTAATTTACCACTCT
ATTACGGCATTTTGGCTA
Found at i:24699 original size:3 final size:3
Alignment explanation
Indices: 24693--24745 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
24683 ATTTATTATT
* * *
24693 TAA TAA TAA CAA TAA TAA TAA TAT TAA TAA TAA TAA -AA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24740 TAA TAA
1 TAA TAA
24746 ATCAGAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28270 original size:18 final size:18
Alignment explanation
Indices: 28242--28278 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28232 AAAAAAACTA
28242 TTTTGATTTTAATTGTTGT
1 TTTTGATTTTAATT-TTGT
28261 TTTTGA-TTTAATTTTGT
1 TTTTGATTTTAATTTTGT
28278 T
1 T
28279 GCTTTCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (18 bp):
TTTTGATTTTAATTTTGT
Found at i:29776 original size:16 final size:16
Alignment explanation
Indices: 29755--29810 Score: 76
Period size: 16 Copynumber: 3.3 Consensus size: 16
29745 ATTTTGGATG
29755 TTTGTGAATGTTTGAA
1 TTTGTGAATGTTTGAA
*
29771 TTTGTGGATGTTTGAA
1 TTTGTGAATGTTTGAA
29787 TTTGTTTTGAATGTTTGAA
1 TTTG---TGAATGTTTGAA
29806 TTTGT
1 TTTGT
29811 TTTGGATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 20 0.57
19 15 0.43
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (16 bp):
TTTGTGAATGTTTGAA
Found at i:29798 original size:35 final size:37
Alignment explanation
Indices: 29753--29824 Score: 112
Period size: 35 Copynumber: 1.9 Consensus size: 37
29743 ACATTTTGGA
29753 TGTTTGTGAATGTTTGAATTTG-TGGATGTTTGAATT
1 TGTTTGTGAATGTTTGAATTTGTTGGATGTTTGAATT
29789 TGTTT-TGAATGTTTGAATTTGTTTTGGATGTTTGAA
1 TGTTTGTGAATGTTTGAATTTG--TTGGATGTTTGAA
29825 CTTAAATGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 16 0.48
36 5 0.15
38 12 0.36
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.54
Consensus pattern (37 bp):
TGTTTGTGAATGTTTGAATTTGTTGGATGTTTGAATT
Found at i:29802 original size:19 final size:19
Alignment explanation
Indices: 29753--29824 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 19
29743 ACATTTTGGA
29753 TGTTTGTGAATGTTTGAATT
1 TGTTT-TGAATGTTTGAATT
*
29773 TG---TGGATGTTTGAATT
1 TGTTTTGAATGTTTGAATT
29789 TGTTTTGAATGTTTGAATT
1 TGTTTTGAATGTTTGAATT
*
29808 TGTTTTGGATGTTTGAA
1 TGTTTTGAATGTTTGAA
29825 CTTAAATGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
16 15 0.33
19 29 0.63
20 2 0.04
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.54
Consensus pattern (19 bp):
TGTTTTGAATGTTTGAATT
Found at i:31408 original size:9 final size:10
Alignment explanation
Indices: 31389--31444 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
31379 ATATTTGTCT
*
31389 TATACATTTA
1 TATATATTTA
31399 TA-ATATTTA
1 TATATATTTA
*
31408 TATATATACTA
1 TATATAT-TTA
*
31419 TAT-TAATTA
1 TATATATTTA
*
31428 TATATATATA
1 TATATATTTA
31438 TATATAT
1 TATATAT
31445 ATTACTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 13 0.35
10 19 0.51
11 5 0.14
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (10 bp):
TATATATTTA
Found at i:31413 original size:2 final size:2
Alignment explanation
Indices: 31397--31446 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
31387 CTTATACATT
*
31397 TA TA -A TA TT TA TA TA TA TA CTA TA T- TA -A T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
31436 TA TA TA TA TA T
1 TA TA TA TA TA T
31447 TACTTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
1 4 0.10
2 35 0.85
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32601 original size:2 final size:2
Alignment explanation
Indices: 32594--32618 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32584 TATAAGTTAT
32594 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
32619 TACATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32709 original size:5 final size:5
Alignment explanation
Indices: 32699--32755 Score: 53
Period size: 5 Copynumber: 10.6 Consensus size: 5
32689 ATATATTATT
*
32699 TTTTA TTTTA TTTTA TTTTA TTTTTTA TTTTA TGTTTTA TTTT- TTTGTT
1 TTTTA TTTTA TTTTA TTTTA --TTTTA TTTTA --TTTTA TTTTA TTT-TA
32748 TTTTA TTT
1 TTTTA TTT
32756 AGTTCCATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
4 3 0.07
5 29 0.64
6 3 0.07
7 10 0.22
ACGTcount: A:0.14, C:0.00, G:0.04, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:32711 original size:12 final size:12
Alignment explanation
Indices: 32694--32755 Score: 78
Period size: 12 Copynumber: 5.5 Consensus size: 12
32684 TATGTATATA
32694 TTATTTTTTATT
1 TTATTTTTTATT
32706 TTA--TTTTATT
1 TTATTTTTTATT
32716 TTATTTTTTATT
1 TTATTTTTTATT
*
32728 TTATGTTTTATT
1 TTATTTTTTATT
*
32740 TT-TTTGTT-TT
1 TTATTTTTTATT
32750 TTATTT
1 TTATTT
32756 AGTTCCATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
10 14 0.32
11 7 0.16
12 23 0.52
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (12 bp):
TTATTTTTTATT
Found at i:32722 original size:22 final size:22
Alignment explanation
Indices: 32694--32755 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
32684 TATGTATATA
32694 TTATTTTTTATTTTATTTTATT
1 TTATTTTTTATTTTATTTTATT
32716 TTATTTTTTATTTTATGTTTTATT
1 TTATTTTTTATTTTA--TTTTATT
*
32740 TT-TTTGTT-TTTTATTT
1 TTATTTTTTATTTTATTT
32756 AGTTCCATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 3 0.08
22 20 0.54
23 5 0.14
24 9 0.24
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (22 bp):
TTATTTTTTATTTTATTTTATT
Found at i:32842 original size:26 final size:27
Alignment explanation
Indices: 32788--32858 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
32778 TCTTTGTTTT
*
32788 TTTTGTTTGTTTTGTTTTATTTTAACTTA
1 TTTTGTTT-TTTT-TTTAATTTTAACTTA
*
32817 TTTTGTTTTTTTTTTAATTTT-CCTTA
1 TTTTGTTTTTTTTTTAATTTTAACTTA
*
32843 TTTTATTATTTTTTTT
1 TTTTGTT-TTTTTTTT
32859 CTTTTTTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 16 0.42
28 4 0.11
29 8 0.21
ACGTcount: A:0.13, C:0.04, G:0.06, T:0.77
Consensus pattern (27 bp):
TTTTGTTTTTTTTTTAATTTTAACTTA
Found at i:43244 original size:13 final size:13
Alignment explanation
Indices: 43226--43255 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
43216 CATAAGTCGA
43226 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
43239 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
43252 AAAA
1 AAAA
43256 AGCATTTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:44298 original size:65 final size:68
Alignment explanation
Indices: 44194--44369 Score: 216
Period size: 65 Copynumber: 2.6 Consensus size: 68
44184 CGACACAATT
* * * *
44194 TACTCGAGATTGGATTTTAACTTCACAATGAAAGATATCCAACCCAAAGCCAATTTGGTG-A-AA
1 TACTCAAGATTGGATTTCAACTTCACAACGAAAGATATCCAACCCAAAGCCAATTTGATGAAGAA
*
44257 -CC
66 TAC
* *
44259 TACTCAAGATTGGATTTCAACTTCACGAA-GAAGGATATCCAACTCAAAGCCAATTTGATGAAGT
1 TACTCAAGATTGGATTTCAACTTCAC-AACGAAAGATATCCAACCCAAAGCCAATTTGATGAAG-
44323 AATAC
64 AATAC
* * *
44328 AACTCTAGATTGGATTTCAACTTTACAACGAAAGATATCCAA
1 TACTCAAGATTGGATTTCAACTTCACAACGAAAGATATCCAA
44370 TTCAAAGCTC
Statistics
Matches: 95, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
65 52 0.55
66 3 0.03
68 4 0.04
69 36 0.38
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (68 bp):
TACTCAAGATTGGATTTCAACTTCACAACGAAAGATATCCAACCCAAAGCCAATTTGATGAAGAA
TAC
Found at i:45413 original size:21 final size:21
Alignment explanation
Indices: 45387--45435 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
45377 ATTATTTTTA
45387 TTATTTATCT-TTTTTTACTGT
1 TTATTTATCTCTTTTTTA-TGT
* *
45408 TTATTTTATTTCTTTTTTATTT
1 TTA-TTTATCTCTTTTTTATGT
45430 TTATTT
1 TTATTT
45436 GTTTTCCTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 11 0.46
23 7 0.29
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (21 bp):
TTATTTATCTCTTTTTTATGT
Found at i:45428 original size:16 final size:17
Alignment explanation
Indices: 45407--45440 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
45397 TTTTTTACTG
45407 TTTA-TTTTATTTCTTT
1 TTTATTTTTATTTCTTT
*
45423 TTTATTTTTATTTGTTT
1 TTTATTTTTATTTCTTT
45440 T
1 T
45441 CCTAGTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTATTTTTATTTCTTT
Found at i:45518 original size:10 final size:9
Alignment explanation
Indices: 45498--45715 Score: 91
Period size: 10 Copynumber: 22.9 Consensus size: 9
45488 TATATGTATA
*
45498 TATTATTTT
1 TATTTTTTT
45507 TATTCTTTTT
1 TATT-TTTTT
45517 TATTTTATTT
1 TATTTT-TTT
*
45527 TATTTTATT
1 TATTTTTTT
*
45536 T-TTTCTTT
1 TATTTTTTT
*
45544 TATATGTTTT
1 TAT-TTTTTT
*
45554 TGTTTTGTTT
1 TATTTT-TTT
*
45564 TGTTTTTGTT
1 TATTTTT-TT
*
45574 TTTGTTTTTT
1 TAT-TTTTTT
*
45584 TATTTAGTTT
1 TATTT-TTTT
*
45594 CATTATTTTT
1 TATT-TTTTT
*
45604 TCTTTTTTCT
1 TATTTTTT-T
*
45614 T-TTTTCTT
1 TATTTTTTT
*
45622 TCTTTTTATT
1 TATTTTT-TT
*
45632 TTTTATTTTT
1 TATT-TTTTT
45642 TATTATTTTT
1 TATT-TTTTT
*
45652 TATTTTTTG
1 TATTTTTTT
*
45661 TATTATTTT
1 TATTTTTTT
* *
45670 CACTTATTTTG
1 TA-TT-TTTTT
* *
45681 TATTATTTG
1 TATTTTTTT
*
45690 TATTTTGTAT
1 TATTTT-TTT
*
45700 TA-TTTTAT
1 TATTTTTTT
45708 TATTTTTT
1 TATTTTTT
45716 GTTCTATTTA
Statistics
Matches: 161, Mismatches: 31, Indels: 34
0.71 0.14 0.15
Matches are distributed among these distances:
8 13 0.08
9 56 0.35
10 80 0.50
11 12 0.07
ACGTcount: A:0.13, C:0.04, G:0.05, T:0.78
Consensus pattern (9 bp):
TATTTTTTT
Found at i:45524 original size:5 final size:5
Alignment explanation
Indices: 45504--45537 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
45494 TATATATTAT
45504 TTTTA TTCTT- TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTT
45538 TTCTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 2 0.07
5 23 0.85
6 2 0.07
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:45539 original size:7 final size:7
Alignment explanation
Indices: 45512--45732 Score: 67
Period size: 7 Copynumber: 29.6 Consensus size: 7
45502 ATTTTTATTC
45512 TTTTTTA
1 TTTTTTA
45519 TTTTATT-
1 TTTT-TTA
45526 TTATTTTA
1 TT-TTTTA
*
45534 TTTTTTC
1 TTTTTTA
*
45541 TTTTATA
1 TTTTTTA
*
45548 TGTTTTTG
1 T-TTTTTA
*
45556 TTTTGTTT
1 TTTT-TTA
*
45564 TGTTTTTG
1 T-TTTTTA
45572 TTTTTGT-
1 TTTTT-TA
45579 TTTTTTA
1 TTTTTTA
**
45586 TTTAGT-
1 TTTTTTA
**
45592 TTCATTA
1 TTTTTTA
*
45599 TTTTTTC
1 TTTTTTA
*
45606 TTTTTTCT
1 TTTTTT-A
*
45614 TTTTTCTT
1 TTTTT-TA
45622 TCTTTTTA
1 T-TTTTTA
45630 TTTTTTA
1 TTTTTTA
45637 TTTTTTA
1 TTTTTTA
45644 TTATTTT-
1 TT-TTTTA
45651 TTATTTT-
1 TT-TTTTA
*
45658 TTGTATTA
1 TT-TTTTA
45666 TTTTCACTTA
1 TTTT---TTA
*
45676 TTTTGTA
1 TTTTTTA
45683 TTATTTGTA
1 TT-TTT-TA
*
45692 TTTTGTA
1 TTTTTTA
45699 TTATTTTA
1 TT-TTTTA
45707 TTATTTT-
1 TT-TTTTA
*
45714 TTGTTCTA
1 TT-TTTTA
*
45722 TTTATTA
1 TTTTTTA
45729 TTTT
1 TTTT
45733 CATATTTATG
Statistics
Matches: 165, Mismatches: 28, Indels: 42
0.70 0.12 0.18
Matches are distributed among these distances:
6 5 0.03
7 91 0.55
8 50 0.30
9 12 0.07
10 7 0.04
ACGTcount: A:0.13, C:0.04, G:0.05, T:0.77
Consensus pattern (7 bp):
TTTTTTA
Found at i:45564 original size:11 final size:11
Alignment explanation
Indices: 45548--45581 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
45538 TTCTTTTATA
45548 TGTTTTTGTTT
1 TGTTTTTGTTT
45559 TG-TTTTGTTTT
1 TGTTTTTG-TTT
45570 TGTTTTTGTTT
1 TGTTTTTGTTT
45581 T
1 T
45582 TTTATTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.24
11 11 0.52
12 5 0.24
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (11 bp):
TGTTTTTGTTT
Found at i:45593 original size:13 final size:12
Alignment explanation
Indices: 45548--45582 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
45538 TTCTTTTATA
45548 TGTTTTTG-TTT
1 TGTTTTTGTTTT
45559 TG-TTTTGTTTT
1 TGTTTTTGTTTT
45570 TGTTTTTGTTTT
1 TGTTTTTGTTTT
45582 T
1 T
45583 TTATTTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.23
11 7 0.32
12 10 0.45
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (12 bp):
TGTTTTTGTTTT
Found at i:53342 original size:27 final size:27
Alignment explanation
Indices: 53286--53361 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
53276 TGTTGGTTGA
* *
53286 TGAGACAGATCA-TGTTGAGGTTGTTAC
1 TGAGACAGA-CAGTGTTGAGGCTGGTAC
** * * *
53313 TGAGGTAGGCCGTGTTGAGGCTGGTGC
1 TGAGACAGACAGTGTTGAGGCTGGTAC
53340 TGAGACAGACAGTGTTGAGGCT
1 TGAGACAGACAGTGTTGAGGCT
53362 ACCTCAGTCT
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.21, C:0.13, G:0.38, T:0.28
Consensus pattern (27 bp):
TGAGACAGACAGTGTTGAGGCTGGTAC
Found at i:55105 original size:20 final size:20
Alignment explanation
Indices: 55063--55108 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
55053 TGCTTTCGTG
*
55063 AGTTTGCATATGTTGCTGTT
1 AGTTTGCATATGTTGCAGTT
*
55083 AGTTTGCGTATGTT-CAGTGT
1 AGTTTGCATATGTTGCAGT-T
55103 AGTTTG
1 AGTTTG
55109 GAGTGTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.15, C:0.09, G:0.28, T:0.48
Consensus pattern (20 bp):
AGTTTGCATATGTTGCAGTT
Found at i:56890 original size:64 final size:64
Alignment explanation
Indices: 56814--56957 Score: 218
Period size: 64 Copynumber: 2.3 Consensus size: 64
56804 CCTGAAGCCA
* *
56814 ACCTGCATCCGATATGAGAATGACCTGAACCCAAATTGAACCGATAATATGATAATTGAACTCG
1 ACCTGCATCCGATATGAGAATGACCTGAACCCAAATTAAACCGATAATATGATAATTGAACCCG
* ** *
56878 ACCTGCATCCGATCTGAGAATGACCTGAACCTGAATTAAACTGATAATATGATAATTGAACCCG
1 ACCTGCATCCGATATGAGAATGACCTGAACCCAAATTAAACCGATAATATGATAATTGAACCCG
*
56942 ACATGCATCCGA-ATGA
1 ACCTGCATCCGATATGA
56958 TATAAACCCA
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
63 3 0.04
64 69 0.96
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (64 bp):
ACCTGCATCCGATATGAGAATGACCTGAACCCAAATTAAACCGATAATATGATAATTGAACCCG
Found at i:56980 original size:64 final size:64
Alignment explanation
Indices: 56817--56980 Score: 170
Period size: 64 Copynumber: 2.6 Consensus size: 64
56807 GAAGCCAACC
* ** * * * * *
56817 TGCATCCGATATGAGAATGACCTGAACCCAAATTGAACCGATAATATGATAATTGAACTCGACC
1 TGCATCCGATATGAGAATAACCCAAACCCGAATTAAACTGATAATATGATAATTGAACCCGACA
* * ** *
56881 TGCATCCGATCTGAGAATGACCTGAACCTGAATTAAACTGATAATATGATAATTGAACCCGACA
1 TGCATCCGATATGAGAATAACCCAAACCCGAATTAAACTGATAATATGATAATTGAACCCGACA
*
56945 TGCATCCGA-ATGA-TATAAACCCAAACCCGAGATTAA
1 TGCATCCGATATGAGAAT-AACCCAAACCCGA-ATTAA
56981 CCTGGTAAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
62 2 0.02
63 12 0.14
64 71 0.84
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (64 bp):
TGCATCCGATATGAGAATAACCCAAACCCGAATTAAACTGATAATATGATAATTGAACCCGACA
Found at i:57022 original size:16 final size:16
Alignment explanation
Indices: 57001--57043 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
56991 AACTGATATT
57001 ACCTGACCTATTATCA
1 ACCTGACCTATTATCA
* * *
57017 ACCTGACATTTTATGA
1 ACCTGACCTATTATCA
57033 ACCTGACCTAT
1 ACCTGACCTAT
57044 AATTGACTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (16 bp):
ACCTGACCTATTATCA
Done.