Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006430.1 Hibiscus syriacus cultivar Beakdansim tig00015524_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: 96563
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:410 original size:131 final size:130
Alignment explanation
Indices: 193--533 Score: 468
Period size: 131 Copynumber: 2.6 Consensus size: 130
183 TGGTTTTTAT
*
193 GATGAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGATG
1 GATGAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATG
* ** * **
258 ACATTTATTCTCGATTTGAAATAATTGGATATTATCGTTTTCTCTC-AGATTAATATTTAATTGT
66 TCATTTATTCTCGATCGGAAATAATTGGATATTATCG-TTCCTCTCGA-ATTAATATCGAATTGT
322 AG
129 AG
* * * *
324 GATGAAATAATAATATCTCTTCATTTCGTTTGGAGTAATAAATGACTACTTTAAGGCATGAGATG
1 GATGAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATG
*
389 TCATTTATTCTCGATCGGAAATAATTGGATATTATCGTTCCTCTCGAATTAATATCGAATTTTAG
66 TCATTTATTCTCGATCGGAAATAATTGGATATTATCGTTCCTCTCGAATTAATATCGAATTGTAG
* * * * * * *
454 AAGGAAATAGTAATATTTCTTTATTTTGATTGGAGTAAGAAATGACTGCTTTAAGGCATGAGAGG
1 GATGAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATG
* *
519 TCGTTTCTTCTCGAT
66 TCATTTATTCTCGAT
534 AAAAGATAAT
Statistics
Matches: 185, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
130 90 0.49
131 95 0.51
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (130 bp):
GATGAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATG
TCATTTATTCTCGATCGGAAATAATTGGATATTATCGTTCCTCTCGAATTAATATCGAATTGTAG
Found at i:551 original size:130 final size:130
Alignment explanation
Indices: 196--544 Score: 450
Period size: 130 Copynumber: 2.7 Consensus size: 130
186 TTTTTATGAT
* *
196 GAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGATGACA
1 GAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATGTCA
* * ** *
261 TTTATTCTCGATTTGAAATAATTGGATATTATCGTTTTCTCTCAGATTAATATTTAATTGTAGGA
66 TTTATTCTCGA-TAGAAATAATTGGATATTATCGTTTCCTCTCAGATTAATATCGAATTGTAGAA
*
326 T
130 G
* * * *
327 GAAATAATAATATCTCTTCATTTCGTTTGGAGTAATAAATGACTACTTTAAGGCATGAGATGTCA
1 GAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATGTCA
* *
392 TTTATTCTCGATCGGAAATAATTGGATATTATCG-TTCCTCTC-GAATTAATATCGAATTTTAGA
66 TTTATTCTCGAT-AGAAATAATTGGATATTATCGTTTCCTCTCAG-ATTAATATCGAATTGTAGA
455 AG
129 AG
* * * * * *
457 GAAATAGTAATATTTCTTTATTTTGATTGGAGTAAGAAATGACTGCTTTAAGGCATGAGAGGTCG
1 GAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATGTCA
* *
522 TTTCTTCTCGATAAAAGATAATT
66 TTTATTCTCGATAGAA-ATAATT
545 AAATATTTTC
Statistics
Matches: 190, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
129 3 0.02
130 97 0.51
131 90 0.47
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (130 bp):
GAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATGTCA
TTTATTCTCGATAGAAATAATTGGATATTATCGTTTCCTCTCAGATTAATATCGAATTGTAGAAG
Found at i:2095 original size:17 final size:17
Alignment explanation
Indices: 2075--2108 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2065 TATTTGATTC
2075 ATAAT-TATATTAAATAA
1 ATAATATAT-TTAAATAA
2092 ATAATATATTTAAATAA
1 ATAATATATTTAAATAA
2109 TTTGTTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATATATTTAAATAA
Found at i:4886 original size:20 final size:22
Alignment explanation
Indices: 4851--4892 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4841 TGTATCTACT
4851 AATTATGATAAATTAA-AAATA
1 AATTATGATAAATTAATAAATA
*
4872 AATTAT-ATCAATTAATAAATA
1 AATTATGATAAATTAATAAATA
4893 CTCTACTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AATTATGATAAATTAATAAATA
Found at i:5101 original size:4 final size:4
Alignment explanation
Indices: 5092--5116 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5082 AATTTTAGAG
5092 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
5117 ATTATGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:8214 original size:20 final size:18
Alignment explanation
Indices: 8175--8215 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
8165 TAATTATGAT
*
8175 TTTATGATTTTTTTTGCC
1 TTTATGATTTTTTTTACC
8193 TTTATGATATTTTTTCTACC
1 TTTATGAT-TTTTTT-TACC
8213 TTT
1 TTT
8216 TGACACGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.15, C:0.12, G:0.07, T:0.66
Consensus pattern (18 bp):
TTTATGATTTTTTTTACC
Found at i:8571 original size:12 final size:13
Alignment explanation
Indices: 8554--8582 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
8544 CATATTTATC
8554 TTTTGTTTA-AGA
1 TTTTGTTTATAGA
8566 TTTTGTTTATAGA
1 TTTTGTTTATAGA
8579 TTTT
1 TTTT
8583 TTATCTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (13 bp):
TTTTGTTTATAGA
Found at i:9312 original size:60 final size:60
Alignment explanation
Indices: 9197--9312 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
9187 TAATTATTTT
* * * * * *
9197 TATTCTAAATTAATTCCTAAACTTTTAAATATTGTAATTTCATCCTTAGACTATTACTAG
1 TATTCTAAATTAAGTCCTAAACTTTTAAATACTGTAAGTTCATCCCTAAAATATTACTAG
*
9257 TATTCTAAATT-AGTCCTCAAATTTTTAAATACT-TAAGTTCTATCCCTAAAATATTA
1 TATTCTAAATTAAGTCCT-AAACTTTTAAATACTGTAAGTTC-ATCCCTAAAATATTA
9313 TCTTCATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 11 0.23
60 36 0.77
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (60 bp):
TATTCTAAATTAAGTCCTAAACTTTTAAATACTGTAAGTTCATCCCTAAAATATTACTAG
Found at i:17103 original size:32 final size:33
Alignment explanation
Indices: 17064--17130 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
17054 AAAGATGGAC
*
17064 TTCGTTGCAAA-TTCTTCTTTCTTTGGGCTCCG
1 TTCGTTGCAAATTTCTGCTTTCTTTGGGCTCCG
17096 TTCGTTGCAAATTTCTGCTTTCTTTGGGCTCCG
1 TTCGTTGCAAATTTCTGCTTTCTTTGGGCTCCG
17129 TT
1 TT
17131 TTCATTTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 11 0.33
33 22 0.67
ACGTcount: A:0.09, C:0.24, G:0.19, T:0.48
Consensus pattern (33 bp):
TTCGTTGCAAATTTCTGCTTTCTTTGGGCTCCG
Found at i:17340 original size:23 final size:23
Alignment explanation
Indices: 17314--17363 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
17304 ATCAAGTACA
17314 ATAACATAATAGGTAGAGCTTAT
1 ATAACATAATAGGTAGAGCTTAT
** * *
17337 ATAATGTAATAGGTAGCGGTTAT
1 ATAACATAATAGGTAGAGCTTAT
17360 ATAA
1 ATAA
17364 TAAAATAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGAGCTTAT
Found at i:17364 original size:23 final size:23
Alignment explanation
Indices: 17320--17364 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17310 TACAATAACA
17320 TAATAGGTAGAGCTTATATAATG
1 TAATAGGTAGAGCTTATATAATG
* *
17343 TAATAGGTAGCGGTTATATAAT
1 TAATAGGTAGAGCTTATATAAT
17365 AAAATAAACA
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:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (23 bp):
TAATAGGTAGAGCTTATATAATG
Found at i:17370 original size:23 final size:23
Alignment explanation
Indices: 17321--17370 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
17311 ACAATAACAT
**
17321 AATAGGTAGAGCTTATATAATGT
1 AATAGGTAGAGCTTATATAATAA
* *
17344 AATAGGTAGCGGTTATATAATAA
1 AATAGGTAGAGCTTATATAATAA
17367 AATA
1 AATA
17371 AACATTTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (23 bp):
AATAGGTAGAGCTTATATAATAA
Found at i:18008 original size:198 final size:197
Alignment explanation
Indices: 17429--18087 Score: 845
Period size: 198 Copynumber: 3.3 Consensus size: 197
17419 CTTATATTAC
* * *
17429 CTATTTTCTAACT-AAACCGGTATATTTATACGGTAACATTGCAAATTTACCTATTACATTATAA
1 CTATTTTCTCA-TAAAACCGGTATATTTATACGGTTACATTGTAAATTTACCTATTACATTATAA
* *
17493 TTATCGGTTTCGATG-TTTTGGGATCGATACAATTT--TAAATGTATCGACACTTTATGTGTGCA
65 TTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCA
* * *
17555 CCTCG-TTGGACATTCTTTCTGGAAAAAAAAATATCGACACAAACTTAAAAAGTGTCGATACATT
129 CCTCGTTTGGACATTCATTCTGG--ACAAAAGTATCGACACAAA-TTAAAAAGTGTCGATACATT
* *
17619 GTGTAGA
191 ATGTTGA
* * * * *
17626 CTTATTTTCTCATAAAACCGATATATTTCTATCGGGTGCATTGTAAATTTACCTATTACATTGTA
1 C-TATTTTCTCATAAAACCGGTATATTTATA-CGGTTACATTGTAAATTTACCTATTACATTATA
* *
17691 ATTATCGGTTTCGATGTTTTTAGGATCGATACTTTTAATAACTGTATCGACACTTTATGCGTGCA
64 ATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCA
* * *
17756 CAC-CGTTT-GACACTCATTATGGACAAATTGTATCGACACAAATTTAAAAAGTGTCGATACATT
129 C-CTCGTTTGGACATTCATTCTGGACAAA-AGTATCGACACAAA-TTAAAAAGTGTCGATACATT
17819 ATGTTGA
191 ATGTTGA
* * *
17826 C-ATTCTCTCATAAAACCGGTATATTTATACTGATTACATTATAAATTTA-CTATTACATTATAA
1 CTATTTTCTCATAAAACCGGTATATTTATAC-GGTTACATTGTAAATTTACCTATTACATTATAA
*
17889 TTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGATACTTTATGCGTGCAC
65 TTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCAC
* * *
17954 CTCGTTTGGGCATTCATTCTGGACAATAAGTATCGACACAAATTCCACAAGTGTCGATACATTAT
130 CTCGTTTGGACATTCATTCTGGACAA-AAGTATCGACACAAATT-AAAAAGTGTCGATACATTAT
18019 GTTGA
193 GTTGA
* * *
18024 CCTATTTTCTAAT-TAACCGGTATATTTATACGGTTACATTGTTAATTTA-CTATTACATTATAA
1 -CTATTTTCTCATAAAACCGGTATATTTATACGGTTACATTGTAAATTTACCTATTACATTATAA
18087 T
65 T
18088 CGATTTTTGG
Statistics
Matches: 402, Mismatches: 44, Indels: 31
0.84 0.09 0.06
Matches are distributed among these distances:
196 1 0.00
197 85 0.21
198 144 0.36
199 70 0.17
200 60 0.15
201 39 0.10
202 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (197 bp):
CTATTTTCTCATAAAACCGGTATATTTATACGGTTACATTGTAAATTTACCTATTACATTATAAT
TATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACC
TCGTTTGGACATTCATTCTGGACAAAAGTATCGACACAAATTAAAAAGTGTCGATACATTATGTT
GA
Found at i:23076 original size:17 final size:17
Alignment explanation
Indices: 23046--23079 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
23036 TCATGAAAAC
23046 AACATAATTAAATCAAA
1 AACATAATTAAATCAAA
23063 AACATCAATT-AATCAAA
1 AACAT-AATTAAATCAAA
23080 TATTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
AACATAATTAAATCAAA
Found at i:23603 original size:44 final size:44
Alignment explanation
Indices: 23500--23606 Score: 151
Period size: 44 Copynumber: 2.4 Consensus size: 44
23490 CGGTACATTG
* * * **
23500 CATAGTGTATTGATACACATTCAAGGAATGCATCGGTGCACCTT
1 CATAGTGTATTGATGCATATTCAAGAAATGCATCGGCACACCTT
*
23544 CATAGTGTATTGATGCATATTCAAGAAATGCATCGGCACACTTT
1 CATAGTGTATTGATGCATATTCAAGAAATGCATCGGCACACCTT
*
23588 CATAGTGTATCGATGCATA
1 CATAGTGTATTGATGCATA
23607 GTGCACAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (44 bp):
CATAGTGTATTGATGCATATTCAAGAAATGCATCGGCACACCTT
Found at i:37179 original size:21 final size:20
Alignment explanation
Indices: 37153--37196 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
37143 CATAGGTTAA
*
37153 AATATAAAAATTAATGAATCT
1 AATATAAAAATTAAT-AATAT
*
37174 AATATAAAGATTAATAATAT
1 AATATAAAAATTAATAATAT
37194 AAT
1 AAT
37197 TAATCCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (20 bp):
AATATAAAAATTAATAATAT
Found at i:38458 original size:19 final size:22
Alignment explanation
Indices: 38435--38486 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
38425 AACCTAATTT
38435 AGGTATCGATA-CC-TAGG-AA
1 AGGTATCGATACCCTTAGGTAA
* *
38454 GGGTATCGGTACCCTTAGGTAA
1 AGGTATCGATACCCTTAGGTAA
38476 AGGTATCGATA
1 AGGTATCGATA
38487 TTGTACCTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 9 0.35
20 2 0.08
21 4 0.15
22 11 0.42
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (22 bp):
AGGTATCGATACCCTTAGGTAA
Found at i:39547 original size:30 final size:30
Alignment explanation
Indices: 39477--39565 Score: 99
Period size: 32 Copynumber: 2.9 Consensus size: 30
39467 AAGAGTCGAG
* * *
39477 GGTTACCTATGTCTTTTGGGATATATGGACA
1 GGTTACCTATGTC-TTCGGGACATATGAACA
39508 GGATTACCTATGTCATTCGGGACATATGAACA
1 GG-TTACCTATGTC-TTCGGGACATATGAACA
*
39540 -GTTACCTATGTTCTTCGGAACATATG
1 GGTTACCTATG-TCTTCGGGACATATG
39566 GATAGGTCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
30 21 0.41
31 5 0.10
32 25 0.49
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (30 bp):
GGTTACCTATGTCTTCGGGACATATGAACA
Found at i:44876 original size:23 final size:23
Alignment explanation
Indices: 44856--44901 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
44846 ATATTTATAG
44856 AAATTATTTATTATATGTTATGC
1 AAATTATTTATTATATGTTATGC
44879 AAATTATTTATTATATGTTATGC
1 AAATTATTTATTATATGTTATGC
44902 CTCACCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (23 bp):
AAATTATTTATTATATGTTATGC
Found at i:44992 original size:17 final size:17
Alignment explanation
Indices: 44970--45003 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
44960 AGGATCAACC
44970 TTAGGATTGGCGGAGCA
1 TTAGGATTGGCGGAGCA
44987 TTAGGATTGGCGGAGCA
1 TTAGGATTGGCGGAGCA
45004 GCATATCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.41, T:0.24
Consensus pattern (17 bp):
TTAGGATTGGCGGAGCA
Found at i:47265 original size:6 final size:6
Alignment explanation
Indices: 47255--47295 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
47245 GCGATAATGA
* *
47255 TCCCTA TCCCTG TCCCTG TCCCTG TCCCTG TCCCTA TCCCT
1 TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TCCCTG TCCCT
47296 CTCACGGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.05, C:0.51, G:0.10, T:0.34
Consensus pattern (6 bp):
TCCCTG
Found at i:49659 original size:23 final size:21
Alignment explanation
Indices: 49628--49669 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
49618 AAATGATTAA
49628 TATTATAAAAATATAAATATTCT
1 TATTAT-AAAATA-AAATATTCT
*
49651 TATTCTAAAATAAAATATT
1 TATTATAAAATAAAATATT
49670 AATACCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
TATTATAAAATAAAATATTCT
Found at i:62342 original size:33 final size:34
Alignment explanation
Indices: 62294--62358 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
62284 TGGGGATTCT
*
62294 ATTATTAAAGATTATAAAATAAT-TTTTTATTTA
1 ATTATTAAAGATTATAAAATAATCATTTTATTTA
62327 ATTATTAAA-AGTTATAAAATAATCATTTTATT
1 ATTATTAAAGA-TTATAAAATAATCATTTTATT
62359 ATTCATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 1 0.03
33 21 0.72
34 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (34 bp):
ATTATTAAAGATTATAAAATAATCATTTTATTTA
Found at i:62956 original size:77 final size:78
Alignment explanation
Indices: 62869--63013 Score: 202
Period size: 78 Copynumber: 1.9 Consensus size: 78
62859 CAATTATTAT
* * *
62869 ATTAATTTAAATATTTATTATAGTTGTTGTTT-AAAGAAAAATCATAAAGCATGGTAAAATAAAA
1 ATTAAATTAAATATTTATTATAATTGTTGTTTCAAAGAAAAATCATAAAGAATGGTAAAATAAAA
62933 TAAGTTTTTTGAA
66 TAAGTTTTTTGAA
* * ** * *
62946 ATTAAATTAAATTTTTATTATAATTGTTTTTTCTTAGAAAACTCATAGAGAATGGTAAAATAAAA
1 ATTAAATTAAATATTTATTATAATTGTTGTTTCAAAGAAAAATCATAAAGAATGGTAAAATAAAA
63011 TAA
66 TAA
63014 TATTATTGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
77 28 0.48
78 30 0.52
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (78 bp):
ATTAAATTAAATATTTATTATAATTGTTGTTTCAAAGAAAAATCATAAAGAATGGTAAAATAAAA
TAAGTTTTTTGAA
Found at i:63023 original size:78 final size:78
Alignment explanation
Indices: 62861--63023 Score: 197
Period size: 78 Copynumber: 2.1 Consensus size: 78
62851 TGATCCTCCA
* * * *
62861 ATTATT-ATATTAATTTAAATATTTATTATAGTTGTTGTTTAAAGAAAAATCATAAAGCATGGTA
1 ATTATTGAAATTAAATTAAATATTTATTATAATTGTTGTTTAAAGAAAAATCATAAAGAATGGTA
62925 AAATAAAATAAGT
66 AAATAAAATAAGT
* * * ** * *
62938 -TTTTTGAAATTAAATTAAATTTTTATTATAATTGTTTTTTCTTAGAAAACTCATAGAGAATGGT
1 ATTATTGAAATTAAATTAAATATTTATTATAATTGTTGTTT-AAAGAAAAATCATAAAGAATGGT
63002 AAAATAAAATAA-T
65 AAAATAAAATAAGT
63015 ATTATTGAA
1 ATTATTGAA
63024 TTATATTGAG
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
76 4 0.06
77 30 0.42
78 37 0.52
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (78 bp):
ATTATTGAAATTAAATTAAATATTTATTATAATTGTTGTTTAAAGAAAAATCATAAAGAATGGTA
AAATAAAATAAGT
Found at i:66422 original size:31 final size:31
Alignment explanation
Indices: 66384--66452 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
66374 CGTTAGAGAC
*
66384 CATATTGCAAATAGACTAAATGTTGAGGG-AT
1 CATATTGCAAATAGACTAAATATTG-GGGAAT
*
66415 CATATTGCAAATGGACTAAATATTGGGGAAT
1 CATATTGCAAATAGACTAAATATTGGGGAAT
*
66446 TATATTG
1 CATATTG
66453 TAATTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.32
Consensus pattern (31 bp):
CATATTGCAAATAGACTAAATATTGGGGAAT
Found at i:67531 original size:31 final size:31
Alignment explanation
Indices: 67481--67556 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
67471 TTAAAACTTG
* * *
67481 CAATATAATCCCCCCAACATTTAGTCTATTTA
1 CAATATGAT-CCCTCAACATTTAGTCCATTTA
* *
67513 CAATATGGTCCCTCAACATTTAGTCCATTTG
1 CAATATGATCCCTCAACATTTAGTCCATTTA
*
67544 TAATATGATCCCT
1 CAATATGATCCCT
67557 GACGTAACTG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 30 0.81
32 7 0.19
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (31 bp):
CAATATGATCCCTCAACATTTAGTCCATTTA
Found at i:67839 original size:2 final size:2
Alignment explanation
Indices: 67832--67936 Score: 50
Period size: 2 Copynumber: 55.0 Consensus size: 2
67822 TATGTATAAG
67832 TA TA TA TA TA TA TA TA TA CT- TA TA -A GTA T- TA GT- TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA
* * * *
67871 TA T- TA TA TA TT TA TA TA -A GTA TA TA CT- TA TA -A TG TA TG CA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
*
67911 TA -A CA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67937 AAAAAGTATA
Statistics
Matches: 79, Mismatches: 9, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
1 10 0.13
2 64 0.81
3 5 0.06
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:67840 original size:16 final size:16
Alignment explanation
Indices: 67800--67845 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
67790 TGTGTAATTA
*
67800 TATATATAGGTATAAG
1 TATATATATGTATAAG
* *
67816 TGTACATATGTATAAG
1 TATATATATGTATAAG
*
67832 TATATATATATATA
1 TATATATATGTATA
67846 TATACTTATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.41
Consensus pattern (16 bp):
TATATATATGTATAAG
Found at i:67988 original size:23 final size:24
Alignment explanation
Indices: 67953--68009 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
67943 TATAGTGTAC
*
67953 ATTATATATACATGCATTAT-CAT
1 ATTATATATACATGCATCATACAT
*
67976 ATTATCATA-ACATTCATCATACAT
1 ATTAT-ATATACATGCATCATACAT
68000 ATTATATATA
1 ATTATATATA
68010 TATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (24 bp):
ATTATATATACATGCATCATACAT
Found at i:76723 original size:30 final size:31
Alignment explanation
Indices: 76643--76730 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 31
76633 GTTTCACCTC
*
76643 TAAACTTTAGATGAAATAT-TAATTTAACTCT
1 TAAACTTTAGATAAAATATCT-ATTTAACTCT
* * *
76674 TAAACTTTAAATAAAATATCTATTTGACTTT
1 TAAACTTTAGATAAAATATCTATTTAACTCT
* *
76705 TGAACTTTAGAT-AAATATCAATTTAA
1 TAAACTTTAGATAAAATATCTATTTAA
76731 TCCCAAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 12 0.25
31 35 0.73
32 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (31 bp):
TAAACTTTAGATAAAATATCTATTTAACTCT
Found at i:77320 original size:31 final size:31
Alignment explanation
Indices: 77257--77322 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
77247 TTTATAGATT
*
77257 AAATTGAAATTTTATCTAAAGTATAAGGGTC
1 AAATTGAAATTTTATCTAAAGTATAAAGGTC
* * * *
77288 AAATTGATATTTTATTTAAAGTTTAAATGTC
1 AAATTGAAATTTTATCTAAAGTATAAAGGTC
77319 AAAT
1 AAAT
77323 CACTATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (31 bp):
AAATTGAAATTTTATCTAAAGTATAAAGGTC
Found at i:78603 original size:27 final size:27
Alignment explanation
Indices: 78565--78618 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
78555 TCGGACAAAG
78565 GATGTTAAAAAGCCAACATTTAATCTT
1 GATGTTAAAAAGCCAACATTTAATCTT
78592 GATGTTAAAAAGCCAACATTTAATCTT
1 GATGTTAAAAAGCCAACATTTAATCTT
78619 TCTAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (27 bp):
GATGTTAAAAAGCCAACATTTAATCTT
Found at i:79602 original size:29 final size:29
Alignment explanation
Indices: 79548--79603 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
79538 ATTAATAATA
** *
79548 AAAATATTAAAGTTAAGTGATTGAATTAT
1 AAAATATTAAAGTTAAAAGATAGAATTAT
79577 AAAATATTTAAA-TTAAAAGATAGAATT
1 AAAATA-TTAAAGTTAAAAGATAGAATT
79604 CGAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.36
Consensus pattern (29 bp):
AAAATATTAAAGTTAAAAGATAGAATTAT
Found at i:80387 original size:21 final size:21
Alignment explanation
Indices: 80362--80404 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
80352 TCGTAATGAT
*
80362 GAATCCTAT-TGGTGAGTCACC
1 GAAT-CTATATGGTGACTCACC
80383 GAATCTATGATGGTGACTCACC
1 GAATCTAT-ATGGTGACTCACC
80405 ATAGGGCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 11 0.58
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
GAATCTATATGGTGACTCACC
Found at i:80786 original size:19 final size:19
Alignment explanation
Indices: 80764--80815 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
80754 TATTTATTTG
80764 TAATAATAATATAATAAAA
1 TAATAATAATATAATAAAA
* *
80783 TAATAGTAATAT-ATATAA
1 TAATAATAATATAATAAAA
*
80801 TATATAATTATATAA
1 TA-ATAATAATATAA
80816 AAACAGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.26
19 19 0.70
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TAATAATAATATAATAAAA
Found at i:81005 original size:20 final size:20
Alignment explanation
Indices: 80958--81005 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
80948 TCATACCTGG
* * *
80958 AGGATTTATAGATGACCCGG
1 AGGATTTACAAATGACCCGA
* *
80978 AGGTTTTACAAATTACCCGA
1 AGGATTTACAAATGACCCGA
80998 AGGATTTA
1 AGGATTTA
81006 ATTTTCTAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (20 bp):
AGGATTTACAAATGACCCGA
Found at i:81128 original size:119 final size:119
Alignment explanation
Indices: 80942--81412 Score: 746
Period size: 119 Copynumber: 3.9 Consensus size: 119
80932 ATTAACAATA
* * * * *
80942 AAAACATCATA-CCTGGAGGATTTATAGATGACCCGGAGGTTTTACAAATTACCCGAAGGATTTA
1 AAAACATCATACCCT-GAGGTTTTACAGATGACCCAGAGGTTTTACAAATTACCCGGAGGTTTTA
*
81006 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTTATTTTCATGCG
65 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTCATGCG
* * *
81061 AAAACATCCTACCCTGAGGTTTTACAGATGACCTAGAGGTTTTACGAATTACCCGGAGGTTTTAA
1 AAAACATCATACCCTGAGGTTTTACAGATGACCCAGAGGTTTTACAAATTACCCGGAGGTTTTAA
81126 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTCATGCG
66 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTCATGCG
* * *
81180 AAAACATCATACCTTGAGGTTTTACAGATGATCCAGAGGTTTTACGAATTACCCGGAGGTTTTAA
1 AAAACATCATACCCTGAGGTTTTACAGATGACCCAGAGGTTTTACAAATTACCCGGAGGTTTTAA
* *
81245 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCA
66 TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTCATGCG
* * *
81299 AAAACATCCTACCCCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATTACCCTGAGGTTTTA
1 AAAACATCATA-CCCTGAGGTTTTACAGATGACCCAGAGGTTTTACAAATTACCCGGAGGTTTTA
**
81364 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGTTTTCTCATTTT
65 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTT
81413 TTGAAACAAC
Statistics
Matches: 328, Mismatches: 22, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
119 229 0.70
120 99 0.30
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (119 bp):
AAAACATCATACCCTGAGGTTTTACAGATGACCCAGAGGTTTTACAAATTACCCGGAGGTTTTAA
TTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTCATGCG
Found at i:81340 original size:20 final size:20
Alignment explanation
Indices: 81315--81363 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
81305 TCCTACCCCT
*
81315 GAGGTTTTACAGATGACCCG
1 GAGGTTTTACAAATGACCCG
* *
81335 GAGGTTTTACAAATTACCCT
1 GAGGTTTTACAAATGACCCG
81355 GAGGTTTTA
1 GAGGTTTTA
81364 ATTTTCTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (20 bp):
GAGGTTTTACAAATGACCCG
Found at i:84705 original size:22 final size:22
Alignment explanation
Indices: 84680--84739 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
84670 TGGGGGGGGA
84680 GGGAATCGGTTCCCTTCAAAGG
1 GGGAATCGGTTCCCTTCAAAGG
* *
84702 GGGAATCAGTTCCCCTTCAAGGG
1 GGGAATCGGTT-CCCTTCAAAGG
* *
84725 GGGTATCGATTCCCT
1 GGGAATCGGTTCCCT
84740 CTGCACTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (22 bp):
GGGAATCGGTTCCCTTCAAAGG
Done.