Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007089.1 Hibiscus syriacus cultivar Beakdansim tig00018510_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: 64955
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1626 original size:55 final size:55
Alignment explanation
Indices: 1539--1642 Score: 192
Period size: 55 Copynumber: 1.9 Consensus size: 55
1529 TGCAGCGCTC
1539 TTATGCAGGCATGTATCAATTAGGGAGAGTTTCTATGGCATGTGAAATTTGGAGA
1 TTATGCAGGCATGTATCAATTAGGGAGAGTTTCTATGGCATGTGAAATTTGGAGA
1594 TTATGCAAGGCATGTATCAATTA-GGAGAGTTTCTATGGCATGTGAAATT
1 TTATGC-AGGCATGTATCAATTAGGGAGAGTTTCTATGGCATGTGAAATT
1643 ATGGCTGACC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 32 0.67
56 16 0.33
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.34
Consensus pattern (55 bp):
TTATGCAGGCATGTATCAATTAGGGAGAGTTTCTATGGCATGTGAAATTTGGAGA
Found at i:1633 original size:28 final size:28
Alignment explanation
Indices: 1546--1636 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 28
1536 CTCTTATGCA
1546 GGCATGTATCAATTAGGGAGAGTTTCTAT
1 GGCATGTATCAATTA-GGAGAGTTTCTAT
* *
1575 GGCATGTGA--AATTTGGAGA-TTATGC-AA
1 GGCATGT-ATCAATTAGGAGAGTT-T-CTAT
1602 GGCATGTATCAATTAGGAGAGTTTCTAT
1 GGCATGTATCAATTAGGAGAGTTTCTAT
1630 GGCATGT
1 GGCATGT
1637 GAAATTATGG
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
26 3 0.06
27 15 0.29
28 23 0.45
29 9 0.18
30 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (28 bp):
GGCATGTATCAATTAGGAGAGTTTCTAT
Found at i:11092 original size:79 final size:79
Alignment explanation
Indices: 10961--11120 Score: 295
Period size: 79 Copynumber: 2.0 Consensus size: 79
10951 TGTTCTCCCT
10961 TAATCGAAGGATGCCATAATATAGTTTATTCTAAGACTTATGGTAGAAAATACAACATACATCTC
1 TAATCGAAGGATGCCATAATATAGTTTATTCTAAGACTTATGGTAGAAAATACAACATACATCTC
11026 TCAATTTAGTTCAA
66 TCAATTTAGTTCAA
*
11040 TAATCGAAGGATGCCATAATATAGTTTGA-TCTATGACTTATGGTAGAAAATACAACATACATCT
1 TAATCGAAGGATGCCATAATATAGTTT-ATTCTAAGACTTATGGTAGAAAATACAACATACATCT
11104 CTCAATTTAGTTCAA
65 CTCAATTTAGTTCAA
11119 TA
1 TA
11121 GCAGAGGTGT
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
79 78 0.99
80 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (79 bp):
TAATCGAAGGATGCCATAATATAGTTTATTCTAAGACTTATGGTAGAAAATACAACATACATCTC
TCAATTTAGTTCAA
Found at i:15826 original size:20 final size:20
Alignment explanation
Indices: 15801--15848 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
15791 TGTTTGATTT
* *
15801 TCAAGTTTAATTTGAGTCCA
1 TCAAGTCTAATTTAAGTCCA
*
15821 TCAAGTCTGATTTAAGTCCA
1 TCAAGTCTAATTTAAGTCCA
15841 TCAAGTCT
1 TCAAGTCT
15849 TTATGATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (20 bp):
TCAAGTCTAATTTAAGTCCA
Found at i:17392 original size:18 final size:18
Alignment explanation
Indices: 17369--17404 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17359 AATAAAACAT
17369 ATAAATATTAATATAAAA
1 ATAAATATTAATATAAAA
* *
17387 ATAAATTTTATTATAAAA
1 ATAAATATTAATATAAAA
17405 CATAGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAATATTAATATAAAA
Found at i:29943 original size:34 final size:34
Alignment explanation
Indices: 29905--29979 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
29895 CAATTTTGAT
29905 ATTGGTACCAAGAGTGGGTAACGATACTGAAAGG
1 ATTGGTACCAAGAGTGGGTAACGATACTGAAAGG
29939 ATTGGTACCAAGAGTGGGTAACGATACTGAAAGG
1 ATTGGTACCAAGAGTGGGTAACGATACTGAAAGG
*
29973 GTTGGTA
1 ATTGGTA
29980 TCAATACCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.23
Consensus pattern (34 bp):
ATTGGTACCAAGAGTGGGTAACGATACTGAAAGG
Found at i:31029 original size:59 final size:59
Alignment explanation
Indices: 30966--31323 Score: 261
Period size: 59 Copynumber: 6.1 Consensus size: 59
30956 TAGCACTATC
* * * *
30966 AGTGCTCTATCTGGAAAAT-CATACACTTAGTATGCTTCCCTTTTCATTTTAGCACACAA
1 AGTGCCCTATCTGG-AAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
** * * ** *
31025 AGTGCCCTAT-TCAAAAATCCACACAATTAGTATGATTTTGTTATCATTTTAGCACATAA
1 AGTGCCCTATCT-GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
* ** * **
31084 TA-TGCCCTATATGGAAATCCATA-TTTTCAATATGATTTCCTTATCA-TTTAGCAC-CTTT
1 -AGTGCCCTATCTGGAAATCCATACACTT-AGTATGATTTCCTTATCATTTTAGCACAC-AA
** * * * *
31142 AGTGCTTTATCTGGAAA-CCTATACACTCAGTATGATTCCCTTACCATTTTAGCACATAA
1 AGTGCCCTATCTGGAAATCC-ATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
* * * * **
31201 TA-TGCCCTATCTGAAAATCCATA-ATTTCAATATGATTTCATTATCA-TTTAGCACACTC
1 -AGTGCCCTATCTGGAAATCCATACACTT-AGTATGATTTCCTTATCATTTTAGCACACAA
* * *
31259 AGTGCTCC-ATATGGAAATCCATACACTCAGTATGATTTACTTATCATTTTAGCACACAA
1 AGTGC-CCTATCTGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
*
31318 AATGCC
1 AGTGCC
31324 ATTCGGTAAT
Statistics
Matches: 225, Mismatches: 56, Indels: 37
0.71 0.18 0.12
Matches are distributed among these distances:
57 4 0.02
58 88 0.39
59 128 0.57
60 5 0.02
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (59 bp):
AGTGCCCTATCTGGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
Found at i:31174 original size:117 final size:117
Alignment explanation
Indices: 31039--31323 Score: 376
Period size: 117 Copynumber: 2.4 Consensus size: 117
31029 CCCTATTCAA
* * * ** *
31039 AAATCCACACAATTAGTATGATTTTGTTATCATTTTAGCACATAATATGCCCTATATGGAAATCC
1 AAATCCATACACTCAGTATGATTTACTTATCATTTTAGCACATAATATGCCCTATATGAAAATCC
* * * ** *
31104 ATATTTTCAATATGATTTCCTTATCATTTAGCAC-CTTTAGTGCTTTATCTGG
66 ATAATTTCAATATGATTTCATTATCATTTAGCACAC-TCAGTGCTCCATATGG
** * *
31156 AAA-CCTATACACTCAGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGAAAATC
1 AAATCC-ATACACTCAGTATGATTTACTTATCATTTTAGCACATAATATGCCCTATATGAAAATC
31220 CATAATTTCAATATGATTTCATTATCATTTAGCACACTCAGTGCTCCATATGG
65 CATAATTTCAATATGATTTCATTATCATTTAGCACACTCAGTGCTCCATATGG
* *
31273 AAATCCATACACTCAGTATGATTTACTTATCATTTTAGCACACAAAATGCC
1 AAATCCATACACTCAGTATGATTTACTTATCATTTTAGCACATAATATGCC
31324 ATTCGGTAAT
Statistics
Matches: 145, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
116 2 0.01
117 140 0.97
118 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.36
Consensus pattern (117 bp):
AAATCCATACACTCAGTATGATTTACTTATCATTTTAGCACATAATATGCCCTATATGAAAATCC
ATAATTTCAATATGATTTCATTATCATTTAGCACACTCAGTGCTCCATATGG
Found at i:31249 original size:176 final size:176
Alignment explanation
Indices: 30966--31313 Score: 404
Period size: 176 Copynumber: 2.0 Consensus size: 176
30956 TAGCACTATC
* * **
30966 AGTGCTCTATCTGGAAAATCATACACTTAGTATGCTTCCCTTTTCATTTTAGCACACAAAGTGCC
1 AGTGCTCTATCTGGAAAATCATACACTCAGTATGATTCCCTTACCATTTTAGCACACAAAGTGCC
* **
31031 CTATTCAAAAATCCACACAATTAGTATGATTTTGTTATCATTTTAGCACA-TAATATGC-CCTAT
66 CTATTCAAAAATCCACACAATTAATATGATTTCATTATCA-TTTAGCACACTAA-ATGCTCC-AT
*** *
31094 ATGGAAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGCACCTTT
128 ATGGAAATCCATACACTCAATATGATTTACTTATCATTTTAGCACCTTT
* * *
31142 AGTGCTTTATCTGG-AAACCTATACACTCAGTATGATTCCCTTACCATTTTAGCACATAATA-TG
1 AGTGCTCTATCTGGAAAATC-ATACACTCAGTATGATTCCCTTACCATTTTAGCACACAA-AGTG
* * * * *
31205 CCCTA-TCTGAAAATCCATA-ATTTCAATATGATTTCATTATCATTTAGCACACTCAGTGCTCCA
64 CCCTATTC-AAAAATCCACACAATT-AATATGATTTCATTATCATTTAGCACACTAAATGCTCCA
*
31268 TATGGAAATCCATACACTCAGTATGATTTACTTATCATTTTAGCAC
127 TATGGAAATCCATACACTCAATATGATTTACTTATCATTTTAGCAC
31314 ACAAAATGCC
Statistics
Matches: 145, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
175 54 0.37
176 90 0.62
177 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (176 bp):
AGTGCTCTATCTGGAAAATCATACACTCAGTATGATTCCCTTACCATTTTAGCACACAAAGTGCC
CTATTCAAAAATCCACACAATTAATATGATTTCATTATCATTTAGCACACTAAATGCTCCATATG
GAAATCCATACACTCAATATGATTTACTTATCATTTTAGCACCTTT
Found at i:34577 original size:25 final size:23
Alignment explanation
Indices: 34529--34579 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
34519 GCCTACAAAA
34529 AATAATAA-AAATTAAATTAAAT
1 AATAATAATAAATTAAATTAAAT
34551 AATAATAATAAA-TAAA-T-AAT
1 AATAATAATAAATTAAATTAAAT
34571 AAT-ATAATA
1 AATAATAATA
34580 TAATATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 1 0.04
22 12 0.43
23 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AATAATAATAAATTAAATTAAAT
Found at i:34582 original size:17 final size:17
Alignment explanation
Indices: 34528--34574 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
34518 GGCCTACAAA
*
34528 AAATAATAAAAATTAAATT
1 AAATAATAATAA-TAAA-T
34547 AAATAATAATAATAAAT
1 AAATAATAATAATAAAT
34564 AAATAATAATA
1 AAATAATAATA
34575 TAATATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 12 0.44
18 4 0.15
19 11 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAATAATAATAAAT
Found at i:35000 original size:81 final size:80
Alignment explanation
Indices: 34835--35082 Score: 289
Period size: 84 Copynumber: 3.0 Consensus size: 80
34825 GTTTTATTGG
* * * * * *
34835 TTGGCATATAGCCCTTCTCGACTTAAGTTATGCTTTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCATATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTCG-AGCTGAGCGTAG
*
34900 TCGAACTCGAGGGTCT
65 TCGAACTCGAAGGTCT
* * * *
34916 TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
1 TTGGCATATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTCGAGCTGAGCGTAGT
*
34981 CGAACTCAAAGGTCTT
66 CGAACTCGAAGGTC-T
* * ** *
34997 TTGGTGACATATAACCCTTCTAGCCTTGTGCTATGCTGTAATTGATGTGCCTTCGAGCTGAGCGT
1 TT-G-G-CATATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTCGAGCTGAGCGT
*
35062 AGTCGAACTCGAAGGTAT
63 AGTCGAACTCGAAGGTCT
35080 TTG
1 TTG
35083 TTGATAAATA
Statistics
Matches: 140, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
80 23 0.16
81 47 0.34
82 2 0.01
83 4 0.03
84 64 0.46
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (80 bp):
TTGGCATATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTCGAGCTGAGCGTAGT
CGAACTCGAAGGTCT
Found at i:35448 original size:106 final size:106
Alignment explanation
Indices: 35263--36677 Score: 2483
Period size: 106 Copynumber: 13.4 Consensus size: 106
35253 GCATTGTTCC
* ** * * * * * *
35263 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTATTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
35328 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
35369 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
*
35434 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
35475 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
35540 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
35581 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
*
35646 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
35687 GAGTCCAATATCTTTCGCTGTGAAGCTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
35751 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
35792 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
*
35857 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
35898 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
*
35963 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
36004 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
36069 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
36110 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
*
36175 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
36216 GAGTCCAATATCTTTCGCTGTGAAGCTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
36280 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
36321 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
*
36386 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
36427 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
*
36492 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
36533 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
36598 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
36639 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
36678 AAAGGCTGTA
Statistics
Matches: 1259, Mismatches: 48, Indels: 4
0.96 0.04 0.00
Matches are distributed among these distances:
105 198 0.16
106 1061 0.84
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:36116 original size:423 final size:423
Alignment explanation
Indices: 35263--36677 Score: 2490
Period size: 423 Copynumber: 3.3 Consensus size: 423
35253 GCATTGTTCC
* * * * * * * *
35263 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTATTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
35328 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
35393 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAG-AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
35458 TGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG
195 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
* * *
35523 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
260 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCA
*
35588 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
325 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGG
*
35653 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
390 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
35687 GAGTCCAATATCTTTCGCTGTGAAGCTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
35751 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
35816 GTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
35881 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
195 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
35946 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCA
260 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCA
*
36011 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTTGTTTATTGACAACCAGCGG
325 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGG
36076 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
390 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
36110 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
* * *
36175 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCTTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
36240 GCTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 GTTGAAATTGGCTCTGAAATTGAGAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
36305 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
196 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
36370 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAA
261 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAA
* *
36435 TATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGT
326 TATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGT
*
36500 CCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
391 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
36533 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
36598 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
36663 GTTGAAATTGGCTCT
131 GTTGAAATTGGCTCT
36678 AAAGGCTGTA
Statistics
Matches: 947, Mismatches: 42, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
422 2 0.00
423 802 0.85
424 143 0.15
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (423 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAA
TATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGT
CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:36261 original size:529 final size:529
Alignment explanation
Indices: 35263--36677 Score: 2659
Period size: 529 Copynumber: 2.7 Consensus size: 529
35253 GCATTGTTCC
* ** * * * * * *
35263 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTATTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAA
*
35328 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* *
35393 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* * *
35458 TGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG
196 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
* *
35523 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
261 AATTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
35588 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
326 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
35653 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCTTTCGCTGTGAAGCTGAAA
391 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCTTTCGCTGTGAAGCTGAAA
35718 TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
456 TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
35783 CGTTGTCTG
521 CGTTGTCTG
35792 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAA
35857 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
35922 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
35987 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
196 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
36052 AATTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
261 AATTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
36117 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
326 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
36182 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCTTTCGCTGTGAAGCTGAAA
391 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCTTTCGCTGTGAAGCTGAAA
36247 TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
456 TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
36312 CGTTGTCTG
521 CGTTGTCTG
*
36321 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAA
*
36386 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCATTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
36451 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
36516 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
196 TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
36581 AATTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
261 AATTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
36646 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
326 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
36678 AAAGGCTGTA
Statistics
Matches: 867, Mismatches: 19, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
529 867 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (529 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
AATTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCTTTCGCTGTGAAGCTGAAA
TTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTG
Found at i:41874 original size:17 final size:18
Alignment explanation
Indices: 41847--41880 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
41837 ATAAAAAAAT
41847 TAAATTAAATAATAATAA
1 TAAATTAAATAATAATAA
41865 TAAA-TAAATAATAATA
1 TAAATTAAATAATAATA
41881 TAATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAATTAAATAATAATAA
Found at i:42059 original size:22 final size:22
Alignment explanation
Indices: 42034--42086 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
42024 AGTGCAAATA
* *
42034 CACTTTCGTATTAGTGT-TGAGG
1 CACTTTCGTACTAGT-TCTAAGG
*
42056 CACTTTAGTACTAGTTCTAAGG
1 CACTTTCGTACTAGTTCTAAGG
42078 CACTTTCGT
1 CACTTTCGT
42087 TAATCGATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (22 bp):
CACTTTCGTACTAGTTCTAAGG
Done.