Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002410.1 Hibiscus syriacus cultivar Beakdansim tig00004929_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: 198433
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:107129 original size:171 final size:172
Alignment explanation
Indices: 106834--107181 Score: 563
Period size: 171 Copynumber: 2.0 Consensus size: 172
106824 GTTGAACTTT
* *
106834 ATTGATGGGATTGGGTTAGCTTGCAATGGCGAAAAAATCATCGTTTTCATGACCAACCTTGTCGA
1 ATTGACGGGATTGGGTCAGCTTGCAATGGCGAAAAAATCATCGTTTTCATGACCAACCTTGTCGA
* *
106899 GAAGCTTGATCTGGCATTGATCTGGAGAGAAAAAATGGATAAACACATAGAGATGTCGTATTGTA
66 GAAGCTTAATCCGGCATTGATCTGGAGAGAAAAAATGGATAAACACATAGAGATGTCGTATTGTA
*
106964 GGTTTGAAGCATTCAAGGTGTTGGTGAATAACT-ACCTGGAC
131 GGTTTGAAGCATTCAAGGTGTTGGCGAATAACTAACCTGGAC
* *
107005 ATTGACGGGATTGGGTCAGCTTGCAATGGCGAAAGAATCATCGTTTTCATGACCAATCTTGTCGA
1 ATTGACGGGATTGGGTCAGCTTGCAATGGCGAAAAAATCATCGTTTTCATGACCAACCTTGTCGA
* * * ** *
107070 TAATCTTAATCCGGCTTTGATCTGGAGAGGGAAAATGGATAAACACATAGAGGTGTCGTATTGTA
66 GAAGCTTAATCCGGCATTGATCTGGAGAGAAAAAATGGATAAACACATAGAGATGTCGTATTGTA
*
107135 GGTTTGAAGCATTCAAGGTGTTGGCGAATAACTAACTTGGAC
131 GGTTTGAAGCATTCAAGGTGTTGGCGAATAACTAACCTGGAC
107177 ATTGA
1 ATTGA
107182 TTATCATCCG
Statistics
Matches: 162, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
171 150 0.93
172 12 0.07
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (172 bp):
ATTGACGGGATTGGGTCAGCTTGCAATGGCGAAAAAATCATCGTTTTCATGACCAACCTTGTCGA
GAAGCTTAATCCGGCATTGATCTGGAGAGAAAAAATGGATAAACACATAGAGATGTCGTATTGTA
GGTTTGAAGCATTCAAGGTGTTGGCGAATAACTAACCTGGAC
Found at i:107723 original size:17 final size:17
Alignment explanation
Indices: 107701--107734 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
107691 TACTTACCCA
107701 AATATTAGGGACCATTT
1 AATATTAGGGACCATTT
*
107718 AATATTAGTGACCATTT
1 AATATTAGGGACCATTT
107735 GCGTAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (17 bp):
AATATTAGGGACCATTT
Found at i:108360 original size:21 final size:22
Alignment explanation
Indices: 108331--108371 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
108321 TTCACAGTGA
108331 TGACATGACAACTTA-CTGTGC
1 TGACATGACAACTTATCTGTGC
* *
108352 TGACGTGACAATTTATCTGT
1 TGACATGACAACTTATCTGT
108372 CATATTTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (22 bp):
TGACATGACAACTTATCTGTGC
Found at i:117244 original size:18 final size:18
Alignment explanation
Indices: 117221--117263 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
117211 ACTCCAAATT
*
117221 TTTCTTTCCCTCTTATTA
1 TTTCTTTCCATCTTATTA
117239 TTTCTTTCCATCTTATTA
1 TTTCTTTCCATCTTATTA
117257 TTTCTTT
1 TTTCTTT
117264 TCACGTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCTTTCCATCTTATTA
Found at i:125356 original size:13 final size:14
Alignment explanation
Indices: 125340--125378 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
125330 CAATAAATAC
125340 AATAAGAAA-ATTA
1 AATAAGAAACATTA
125353 AAT-AGAAACATTA
1 AATAAGAAACATTA
125366 AATAA-AAACATTA
1 AATAAGAAACATTA
125379 CAAACTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 18 0.75
14 1 0.04
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (14 bp):
AATAAGAAACATTA
Found at i:125944 original size:21 final size:21
Alignment explanation
Indices: 125918--125977 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
125908 ACCCTAAGAT
125918 AGTGGCATCTGAACTGGCTGC
1 AGTGGCATCTGAACTGGCTGC
* *
125939 AGTGGCGTCTGAACTGACTGC
1 AGTGGCATCTGAACTGGCTGC
* *
125960 GGTGCCATCTGAACTGGC
1 AGTGGCATCTGAACTGGC
125978 GGTGTACCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.23
Consensus pattern (21 bp):
AGTGGCATCTGAACTGGCTGC
Found at i:127005 original size:2 final size:2
Alignment explanation
Indices: 126998--127027 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
126988 ACTAAAACAA
126998 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
127028 TATCAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128183 original size:26 final size:26
Alignment explanation
Indices: 128144--128202 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
128134 ACCACTGGAA
*
128144 AAAATAATAAAAAACAATTAGTAAAT
1 AAAATAATAAAAAACAATAAGTAAAT
* * *
128170 AAAATATTATAAAATAATAAGTAAAT
1 AAAATAATAAAAAACAATAAGTAAAT
*
128196 ATAATAA
1 AAAATAA
128203 AATAAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (26 bp):
AAAATAATAAAAAACAATAAGTAAAT
Found at i:128207 original size:26 final size:26
Alignment explanation
Indices: 128144--128209 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
128134 ACCACTGGAA
*
128144 AAAATAATAA-AAAACAATTAGTAAAT
1 AAAATAA-AATAAAACAATAAGTAAAT
** *
128170 AAAATATTATAAAATAATAAGTAAAT
1 AAAATAAAATAAAACAATAAGTAAAT
*
128196 ATAATAAAATAAAA
1 AAAATAAAATAAAA
128210 ATATTTTTAC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
25 1 0.03
26 31 0.97
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.26
Consensus pattern (26 bp):
AAAATAAAATAAAACAATAAGTAAAT
Found at i:128227 original size:30 final size:30
Alignment explanation
Indices: 128191--128251 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
128181 AAATAATAAG
*
128191 TAAATATAATAAAATAAAAATATTTTTACC
1 TAAATATAATAAAATAAAAATATTTGTACC
128221 TAAATATAATAAAATAAAAATATTTGTACC
1 TAAATATAATAAAATAAAAATATTTGTACC
128251 T
1 T
128252 CCTAAAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (30 bp):
TAAATATAATAAAATAAAAATATTTGTACC
Found at i:133206 original size:36 final size:36
Alignment explanation
Indices: 133146--133215 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
133136 TAAGCTTGGT
** * *
133146 TCCATCAAGAGCGCATGAGTTGTGCGAAGAAGAACG
1 TCCATCAAGAGCGCACAAGCTGTGCCAAGAAGAACG
*
133182 TCCATCAAGAGTGCACAAGCTGTGCCAAGAAGAA
1 TCCATCAAGAGCGCACAAGCTGTGCCAAGAAGAA
133216 GGAGAATAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.36, C:0.21, G:0.27, T:0.16
Consensus pattern (36 bp):
TCCATCAAGAGCGCACAAGCTGTGCCAAGAAGAACG
Found at i:133711 original size:18 final size:18
Alignment explanation
Indices: 133688--133725 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
133678 AAGTGTGATA
**
133688 TTCGGGTCGGGTTTAGGG
1 TTCGGGTCAAGTTTAGGG
133706 TTCGGGTCAAGTTTAGGG
1 TTCGGGTCAAGTTTAGGG
133724 TT
1 TT
133726 TTTTTAAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.42, T:0.37
Consensus pattern (18 bp):
TTCGGGTCAAGTTTAGGG
Found at i:140853 original size:8 final size:8
Alignment explanation
Indices: 140840--140880 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
140830 CTCATTTTCA
140840 GAGAATTT
1 GAGAATTT
140848 GAGAATTT
1 GAGAATTT
*
140856 -AGAGTTT
1 GAGAATTT
*
140863 GGGAATTT
1 GAGAATTT
140871 GAGAATTT
1 GAGAATTT
140879 GA
1 GA
140881 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:141304 original size:128 final size:128
Alignment explanation
Indices: 140963--142076 Score: 1959
Period size: 128 Copynumber: 8.7 Consensus size: 128
140953 TATTCACATT
*
140963 AAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
141028 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGAACTTG
66 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
* * *
141091 AAGGTGCGTTCCCGGGGG-GCGTCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
141155 ATGTCACTCATGTCCCTCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
66 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
*
141218 AAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
141283 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAAGGGACTTG
66 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
*
141346 AAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
* * *
141411 ATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAAGGGACTTA
66 ATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACTTG
141474 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
141539 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
66 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
* *
141602 AAGGCGCGTTCCCGGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTACCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
* *
141667 ATGTCACTCATGTCCCTCGGGAACACTATTCATATCAGAACCTATTATTTCTCAGGGGACTTG
66 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
* *
141730 AAAGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
141795 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
66 ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
* * *
141858 AAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTT-ACAGAGAATATGTTATCATTGTCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
* *
141922 ATATCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACTTG
66 ATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACTTG
*
141985 AAGGCACGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
142049 ATGTCACTCATGTCCCTCGGGGACACTA
66 ATGTCACTCATGTCCCTCGGGGACACTA
142077 GATGGATTGT
Statistics
Matches: 942, Mismatches: 39, Indels: 11
0.95 0.04 0.01
Matches are distributed among these distances:
126 17 0.02
127 276 0.29
128 648 0.69
129 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (128 bp):
AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
ATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
Found at i:142226 original size:23 final size:22
Alignment explanation
Indices: 142190--142232 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
142180 AAATTAGATA
*
142190 AAATGTTATGGATAAATTGAAT
1 AAATGTTAAGGATAAATTGAAT
*
142212 AAATGTTAAGTGATAAGTTGA
1 AAATGTTAAG-GATAAATTGA
142233 TTGTGACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (22 bp):
AAATGTTAAGGATAAATTGAAT
Found at i:142480 original size:34 final size:34
Alignment explanation
Indices: 142441--142513 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
142431 TAAGTTGAAA
*
142441 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATGTTAAATTTCGAATAATATAATTTATAT
* * *
142475 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATGTTAAATTTCGAATAATATAATTTATAT
142509 TTTAA
1 TTTAA
142514 ATTTTTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATAATATAATTTATAT
Found at i:142503 original size:28 final size:27
Alignment explanation
Indices: 142472--142542 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 27
142462 CTATAATTTA
142472 TATTTTAATTTTAAATTTCGAATAATAT
1 TATTTT-ATTTTAAATTTCGAATAATAT
**
142500 TATTTTTATTTTAAATTTTTAATAATAT
1 TA-TTTTATTTTAAATTTCGAATAATAT
*
142528 AATTTGTATTTTAAA
1 TATTT-TATTTTAAA
142543 AACATTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 3 0.08
28 31 0.82
29 4 0.11
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (27 bp):
TATTTTATTTTAAATTTCGAATAATAT
Found at i:143120 original size:21 final size:21
Alignment explanation
Indices: 143061--143121 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
143051 ATAAAACCCT
*
143061 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
** *
143082 GCGGGCTAGGAACATAACCTT
1 GCGGGCTAGGAATGTAACCTG
* *
143103 GTGGGCTCGGAATGTAACC
1 GCGGGCTAGGAATGTAACC
143122 CTGCGGAGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.20
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:144659 original size:10 final size:10
Alignment explanation
Indices: 144630--144717 Score: 85
Period size: 10 Copynumber: 9.1 Consensus size: 10
144620 GCTGCTGGAA
144630 AACCGGTTTG
1 AACCGGTTTG
*
144640 -ACCAGTTTTG
1 AACC-GGTTTG
144650 AACCGGTTTG
1 AACCGGTTTG
*
144660 -ACCGGTTCG
1 AACCGGTTTG
144669 AACCGGTTTG
1 AACCGGTTTG
*
144679 -ACCGGTCTG
1 AACCGGTTTG
144688 AACCGGTTTG
1 AACCGGTTTG
* *
144698 -ACCAGTCTG
1 AACCGGTTTG
*
144707 AACCGGGTTG
1 AACCGGTTTG
144717 A
1 A
144718 CCCGACCCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 26 0.42
10 33 0.53
11 3 0.05
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:144673 original size:19 final size:19
Alignment explanation
Indices: 144630--144719 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
144620 GCTGCTGGAA
* *
144630 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
144650 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
144669 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
144688 AACCGGTTTGACCAGTCTG
1 AACCGGTTTGACCGGTCTG
*
144707 AACCGGGTTGACC
1 AACCGGTTTGACC
144720 CGACCCGACT
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.02
19 50 0.77
20 14 0.22
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:144735 original size:17 final size:17
Alignment explanation
Indices: 144713--144770 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
144703 TCTGAACCGG
*
144713 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
144730 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
144747 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
144764 GTTGACC
1 GTTGACC
144771 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:144777 original size:6 final size:7
Alignment explanation
Indices: 144760--144789 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
144750 GACCCGACCC
144760 GACCGTT
1 GACCGTT
144767 GACCG-T
1 GACCGTT
144773 GACCGTT
1 GACCGTT
144780 GACCGTT
1 GACCGTT
144787 GAC
1 GAC
144790 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:144778 original size:13 final size:13
Alignment explanation
Indices: 144760--144785 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
144750 GACCCGACCC
144760 GACCGTTGACCGT
1 GACCGTTGACCGT
144773 GACCGTTGACCGT
1 GACCGTTGACCGT
144786 TGACTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:145727 original size:63 final size:63
Alignment explanation
Indices: 145659--145782 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
145649 CTAATGTGAC
* * *
145659 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
145721 T
63 T
* *
145722 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
145783 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:145742 original size:32 final size:32
Alignment explanation
Indices: 145659--145782 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
145649 CTAATGTGAC
* * *
145659 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
145689 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
145722 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
145753 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
145783 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:152021 original size:10 final size:10
Alignment explanation
Indices: 151992--152060 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
151982 GCTGCTGGAA
151992 AACCGGTTTG
1 AACCGGTTTG
*
152002 -ACCAGTTTTG
1 AACC-GGTTTG
152012 AACCGGTTTG
1 AACCGGTTTG
**
152022 -ACCGGTCCG
1 AACCGGTTTG
152031 AACCGGTTTG
1 AACCGGTTTG
*
152041 -ACCGGTCTG
1 AACCGGTTTG
*
152050 AACCGGGTTG
1 AACCGGTTTG
152060 A
1 A
152061 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 18 0.39
10 25 0.54
11 3 0.07
ACGTcount: A:0.19, C:0.25, G:0.30, T:0.26
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:152035 original size:19 final size:19
Alignment explanation
Indices: 151992--152062 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
151982 GCTGCTGGAA
* *
151992 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
*
152012 AACCGGTTTGACCGGTCCG
1 AACCGGTTTGACCGGTCTG
152031 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
152050 AACCGGGTTGACC
1 AACCGGTTTGACC
152063 CGACCCGACT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 33 0.72
20 13 0.28
ACGTcount: A:0.18, C:0.27, G:0.30, T:0.25
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:152078 original size:17 final size:17
Alignment explanation
Indices: 152056--152113 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
152046 TCTGAACCGG
*
152056 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
*
152073 GTTGACTCGACCCGACC
1 GTTGACCCGACCCGACC
152090 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
152107 GTTGACC
1 GTTGACC
152114 GTGACCGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:152120 original size:6 final size:7
Alignment explanation
Indices: 152103--152145 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
152093 GACCCGACCC
152103 GACCGTT
1 GACCGTT
152110 GACCG-T
1 GACCGTT
152116 GACCGTT
1 GACCGTT
152123 GACCG-T
1 GACCGTT
*
152129 GACCATT
1 GACCGTT
152136 GACCGTT
1 GACCGTT
152143 GAC
1 GAC
152146 TTTCTTTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:152121 original size:13 final size:13
Alignment explanation
Indices: 152103--152141 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
152093 GACCCGACCC
152103 GACCGTTGACCGT
1 GACCGTTGACCGT
152116 GACCGTTGACCGT
1 GACCGTTGACCGT
*
152129 GACCATTGACCGT
1 GACCGTTGACCGT
152142 TGACTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:152128 original size:20 final size:20
Alignment explanation
Indices: 152103--152145 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
152093 GACCCGACCC
*
152103 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCATGACCGTT
152123 GACCG-TGACCATTGACCGTT
1 GACCGTTGACCA-TGACCGTT
152143 GAC
1 GAC
152146 TTTCTTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCATGACCGTT
Found at i:153082 original size:63 final size:63
Alignment explanation
Indices: 153014--153137 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
153004 CTAATGTGAC
* * *
153014 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
153076 T
63 T
* *
153077 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
153138 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:153097 original size:32 final size:32
Alignment explanation
Indices: 153014--153137 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
153004 CTAATGTGAC
* * *
153014 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
153044 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
153077 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
153108 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
153138 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:154736 original size:34 final size:31
Alignment explanation
Indices: 154692--154780 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
154682 TTAATAATTC
*
154692 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
154726 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
154757 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
154781 AAATACTAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 6 0.13
32 16 0.35
33 2 0.04
34 22 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:154757 original size:31 final size:33
Alignment explanation
Indices: 154692--154771 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
154682 TTAATAATTC
* *
154692 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
154726 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
154757 TATAAAATATAATAA
1 TA-AAAAAATAATAA
154772 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:159019 original size:12 final size:12
Alignment explanation
Indices: 159002--159026 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
158992 TATTAATTTT
159002 AAAAAATATTAA
1 AAAAAATATTAA
159014 AAAAAATATTAA
1 AAAAAATATTAA
159026 A
1 A
159027 TTCTATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAATATTAA
Found at i:160115 original size:2 final size:2
Alignment explanation
Indices: 160108--160132 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
160098 ATTAGTTGTG
160108 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
160133 GGATATTTTT
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:160855 original size:41 final size:42
Alignment explanation
Indices: 160796--160889 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 42
160786 TCTGAAATCT
*
160796 CGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATGTTTT-C
1 CGTGTTTGTTTCAAGTAATTCGTTTTCCGGAAAATGTTTTAC
*
160837 CGTGTTTGTTTCAAGTAATTCGTTTTCCGTAAAATGTTTTAC
1 CGTGTTTGTTTCAAGTAATTCGTTTTCCGGAAAATGTTTTAC
*
160879 AGTGTTTGTTT
1 CGTGTTTGTTT
160890 GGAGGAAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 38 0.78
42 11 0.22
ACGTcount: A:0.18, C:0.13, G:0.19, T:0.50
Consensus pattern (42 bp):
CGTGTTTGTTTCAAGTAATTCGTTTTCCGGAAAATGTTTTAC
Found at i:161145 original size:22 final size:22
Alignment explanation
Indices: 161120--161186 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
161110 ATATATTTAT
*
161120 TAATATTTATAATAATATAATA
1 TAATATTTATAATATTATAATA
*
161142 TAATATTTTTAATATTATAATA
1 TAATATTTATAATATTATAATA
* * *
161164 AAATAATTAATTATATTATAATA
1 TAAT-ATTTATAATATTATAATA
161187 ATATAAGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
22 23 0.61
23 15 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATATTTATAATATTATAATA
Found at i:161161 original size:27 final size:27
Alignment explanation
Indices: 161131--161292 Score: 81
Period size: 27 Copynumber: 5.9 Consensus size: 27
161121 AATATTTATA
161131 ATAATATAATATAATATTTTTAATATT
1 ATAATATAATATAATATTTTTAATATT
* * *
161158 ATAATAAAATAATTAATTATATTATAATAAT
1 ATAATATAAT-A-TAA-TAT-TTTTAATATT
* * * *
161189 ATAAGATATTATTAT-TTTTTAATA-A
1 ATAATATAATATAATATTTTTAATATT
*
161214 AT-ATAT-A-ATAATTTTTTTATATATT
1 ATAATATAATATAATATTTTTA-ATATT
*
161239 -TAATAATGA-ATAAT-TTATTTATATATT
1 ATAAT-ATAATATAATATT-TTTA-ATATT
161266 -TAATATTAATATAATAATATTTTAATA
1 ATAATA-TAATATAAT-AT-TTTTAATA
161293 AATATATTTA
Statistics
Matches: 105, Mismatches: 14, Indels: 30
0.70 0.09 0.20
Matches are distributed among these distances:
22 4 0.04
23 6 0.06
24 7 0.07
25 4 0.04
26 12 0.11
27 32 0.30
28 7 0.07
29 8 0.08
30 9 0.09
31 16 0.15
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
ATAATATAATATAATATTTTTAATATT
Found at i:161199 original size:23 final size:23
Alignment explanation
Indices: 161153--161226 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
161143 AATATTTTTA
*
161153 ATATTATAATAAAATAATTAATT
1 ATATTATAATAAAATAAATAATT
*
161176 ATATTATAATAATATAAGATATTATT
1 ATATTATAATAAAATAA-ATA--ATT
* *
161202 ATTTTTTAATAAATATATAATAATT
1 ATATTATAATAAA-ATA-AATAATT
161227 TTTTTATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
23 16 0.39
24 2 0.05
25 3 0.07
26 13 0.32
27 6 0.15
28 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (23 bp):
ATATTATAATAAAATAAATAATT
Found at i:161231 original size:80 final size:80
Alignment explanation
Indices: 161120--161308 Score: 201
Period size: 80 Copynumber: 2.4 Consensus size: 80
161110 ATATATTTAT
161120 TAATATTTATAAT-AATATA-ATATAATATTTTTA-ATATTATAATAA-AATAATTAA-TTATAT
1 TAATATTT-TAATAAATATATATATAATATTTTTATATATT-TAATAAGAATAATTAATTTATA-
*
161180 TATAATAATATAAGATATTA
63 TAT-ATAATATAA-ATATAA
* * * *
161200 TTATTTTTTAATAAATATATA-ATAATTTTTTTATATATTTAATAATGAATAATTTATTTATATA
1 TAATATTTTAATAAATATATATATAATATTTTTATATATTTAATAA-GAATAATTAATTTATATA
* *
161264 TTTAATATTAATATAA
65 TATAATATAAATATAA
* *
161280 TAATATTTTAATAAATATATTTAAAATAT
1 TAATATTTTAATAAATATATATATAATAT
161309 ACTAATTAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 13
0.78 0.10 0.11
Matches are distributed among these distances:
79 4 0.04
80 52 0.58
81 18 0.20
82 11 0.12
83 5 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (80 bp):
TAATATTTTAATAAATATATATATAATATTTTTATATATTTAATAAGAATAATTAATTTATATAT
ATAATATAAATATAA
Found at i:161298 original size:35 final size:34
Alignment explanation
Indices: 161259--161332 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 34
161249 TAATTTATTT
*
161259 ATATATTTAATATTAATA-TAA-TAATATTTTAATAA
1 ATATATTTAA-AAT-ATACTAATTAATATTTTAA-AA
*
161294 ATATATTTAAAATATACTAATTAATATTTTTAAA
1 ATATATTTAAAATATACTAATTAATATTTTAAAA
161328 ATATA
1 ATATA
161333 ATATGACACT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 3 0.09
34 12 0.34
35 20 0.57
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (34 bp):
ATATATTTAAAATATACTAATTAATATTTTAAAA
Found at i:161307 original size:23 final size:23
Alignment explanation
Indices: 161288--161332 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
161278 AATAATATTT
161288 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
161311 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
161333 ATATGACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:161452 original size:13 final size:13
Alignment explanation
Indices: 161414--161452 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
161404 TATTAATATT
*
161414 TTTATTAATAAAA
1 TTTAATAATAAAA
*
161427 TTATAAAAATAAAA
1 TT-TAATAATAAAA
161441 TTTAATAATAAA
1 TTTAATAATAAA
161453 TAAATCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAATAATAAAA
Found at i:165831 original size:22 final size:23
Alignment explanation
Indices: 165784--165834 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
165774 AGAAGACTTA
165784 TATTATCTAATTTTTTAATTAATT
1 TATTATCTAATTTTTTAATT-ATT
*
165808 TATT-TCTATTTTTTTATATT-TT
1 TATTATCTAATTTTTTA-ATTATT
165830 TATTA
1 TATTA
165835 GTATGGTACG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 6 0.25
23 11 0.46
24 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTATCTAATTTTTTAATTATT
Found at i:165962 original size:16 final size:16
Alignment explanation
Indices: 165943--165973 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
165933 TTCAAGTCTT
*
165943 ATAAATTTAAATATTA
1 ATAAAATTAAATATTA
165959 ATAAAATTAAATATT
1 ATAAAATTAAATATT
165974 TGTTTCTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTAAATATTA
Found at i:180943 original size:30 final size:29
Alignment explanation
Indices: 180865--180945 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
180855 ACTAATGACT
* * * *
180865 AAAATGTAATTTTTGAAAGTTTAGGGGCT
1 AAAATGTAAATTTTAAAAGTTTAGGGCCA
* *
180894 AAAGTATAAATTTGTAAAAGTTTAGGGACCA
1 AAAATGTAAATTT-TAAAAGTTTAGGG-CCA
*
180925 AAAATGTAAATTTAAAAAGTT
1 AAAATGTAAATTTTAAAAGTT
180946 ATGTATTTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 10 0.24
30 19 0.46
31 12 0.29
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (29 bp):
AAAATGTAAATTTTAAAAGTTTAGGGCCA
Found at i:188185 original size:12 final size:12
Alignment explanation
Indices: 188168--188207 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
188158 GAATTGAATG
188168 GAAATGAGCTAA
1 GAAATGAGCTAA
*
188180 GAAATGA---AT
1 GAAATGAGCTAA
188189 GAAATGAGCTAA
1 GAAATGAGCTAA
188201 GAAATGA
1 GAAATGA
188208 ATGAATGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
9 8 0.35
12 15 0.65
ACGTcount: A:0.53, C:0.05, G:0.25, T:0.17
Consensus pattern (12 bp):
GAAATGAGCTAA
Found at i:188194 original size:21 final size:21
Alignment explanation
Indices: 188162--188212 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
188152 TGAGCTGAAT
188162 TGAATGGAAATGAGCTAAGAAA
1 TGAAT-GAAATGAGCTAAGAAA
188184 TGAATGAAATGAGCTAAGAAA
1 TGAATGAAATGAGCTAAGAAA
188205 TGAATGAA
1 TGAATGAA
188213 TGAACATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.51, C:0.04, G:0.25, T:0.20
Consensus pattern (21 bp):
TGAATGAAATGAGCTAAGAAA
Found at i:191306 original size:15 final size:16
Alignment explanation
Indices: 191281--191316 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
191271 GCTTTGCTTT
*
191281 GTTAAATTAAAATAAA
1 GTTAAACTAAAATAAA
191297 -TTAAACTAAAATAAA
1 GTTAAACTAAAATAAA
191312 GTTAA
1 GTTAA
191317 TCTTCCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
GTTAAACTAAAATAAA
Found at i:196057 original size:33 final size:33
Alignment explanation
Indices: 196015--196078 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
196005 CAGTTTTATT
196015 AACATCATCAACCATTTTTACATTTACTTGTAA
1 AACATCATCAACCATTTTTACATTTACTTGTAA
196048 AACATCATCAACCATTTTTACATTTACTTGT
1 AACATCATCAACCATTTTTACATTTACTTGT
196079 TTACAAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (33 bp):
AACATCATCAACCATTTTTACATTTACTTGTAA
Done.