Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007239.1 Hibiscus syriacus cultivar Beakdansim tig00019176_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: 61456
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3776 original size:42 final size:42
Alignment explanation
Indices: 3729--3810 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
3719 AAGGGGCATA
* *
3729 CTATTGCGATGTTTAT-TACAAAAATGCCACTAAATTACAACT
1 CTATTGCGATGTTTATGT-CAAAAACGCCACTAAAGTACAACT
*
3771 CTATTGCGGTGTTTATGTCAAAAACGCCACTAAAGTACAA
1 CTATTGCGATGTTTATGTCAAAAACGCCACTAAAGTACAA
3811 TTTTTTAGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (42 bp):
CTATTGCGATGTTTATGTCAAAAACGCCACTAAAGTACAACT
Found at i:5308 original size:41 final size:41
Alignment explanation
Indices: 5220--5330 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 41
5210 GCGTTTATAC
* * *
5220 AAAAAAACACCACTATTGATTACACTATTGTGGCGTTTGTT
1 AAAAAAACACCACTATTGATTAAACTATTGCGGCATTTGTT
* *
5261 AAAAAAATACCATTATTGATTAAAACTATTGCGGCATTT-TT
1 AAAAAAACACCACTATTGATT-AAACTATTGCGGCATTTGTT
** * *
5302 CTAAAAACGCCACTATTAATTAACACTAT
1 AAAAAAACACCACTATTGATTAA-ACTAT
5331 GTGGTGTTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
40 2 0.04
41 41 0.72
42 14 0.25
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (41 bp):
AAAAAAACACCACTATTGATTAAACTATTGCGGCATTTGTT
Found at i:5432 original size:42 final size:39
Alignment explanation
Indices: 5367--5546 Score: 143
Period size: 42 Copynumber: 4.4 Consensus size: 39
5357 TTTATTATCA
* * *
5367 CTATTACAGTGTTTTAGGAATAAACGCCACTATATGTGTAAT
1 CTATTACGGCGTTTT-GGTATAAACGCCACTATAT-T-TAAT
* *
5409 CTATTACGGTGTTTGTGGTATAAAC-ACAGCTA-ATTTACCGAT
1 CTATTACGGCGTTT-TGGTATAAACGCCA-CTATATTTA---AT
5451 CTATTACGGCGTTTTGGCTA-AAACGCCACTATATATTAAT
1 CTATTACGGCGTTTTGG-TATAAACGCCACTATAT-TTAAT
*
5491 CTATTGCGGCGTTTTTGGTATAAACGCCACTA-ATTTACCATT
1 CTATTACGGCG-TTTTGGTATAAACGCCACTATATTTA--A-T
*
5533 CTATTGCGGCGTTT
1 CTATTACGGCGTTT
5547 GTTAAAAACA
Statistics
Matches: 118, Mismatches: 6, Indels: 29
0.77 0.04 0.19
Matches are distributed among these distances:
39 5 0.04
40 17 0.14
41 35 0.30
42 57 0.48
43 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (39 bp):
CTATTACGGCGTTTTGGTATAAACGCCACTATATTTAAT
Found at i:5510 original size:82 final size:83
Alignment explanation
Indices: 5388--5546 Score: 225
Period size: 82 Copynumber: 1.9 Consensus size: 83
5378 TTTTAGGAAT
* *
5388 AAACGCCACTATATGTGTAATCTATTACGGTGTTTGTGGTATAAAC-ACAGCTAATTTACCGA-T
1 AAACGCCACTATATATGTAATCTATTACGGCGTTTGTGGTATAAACGACA-CTAATTTACC-ATT
5451 CTATTACGGCGTTTTGGCTA
64 CTATTACGGCGTTTTGGCTA
* * *
5471 AAACGCCACTATATAT-TAATCTATTGCGGCGTTTTTGGTATAAACGCCACTAATTTACCATTCT
1 AAACGCCACTATATATGTAATCTATTACGGCGTTTGTGGTATAAACGACACTAATTTACCATTCT
*
5535 ATTGCGGCGTTT
66 ATTACGGCGTTT
5547 GTTAAAAACA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
81 1 0.01
82 50 0.74
83 17 0.25
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (83 bp):
AAACGCCACTATATATGTAATCTATTACGGCGTTTGTGGTATAAACGACACTAATTTACCATTCT
ATTACGGCGTTTTGGCTA
Found at i:10966 original size:86 final size:81
Alignment explanation
Indices: 10811--11213 Score: 288
Period size: 90 Copynumber: 4.8 Consensus size: 81
10801 ATGCCATTAG
* * * * *
10811 AGTACAAATATTTTACGGCGTTTGTTAAAAACGTCACTATATATTATACCTATTACGGTGTTTAT
1 AGTATAAATATTTTGCGGCGTTTGTTAAAAACGCCACTATATATTAAACCTATTACGGCGTTTAT
10876 ACAAAAAAGCCGCTAA
66 ACAAAAAAGCCGCTAA
*
10892 AGTATAAATATTTTTGCGGCGTTTGTTGAAATAACGCCACTATATATATCAAACCTATTGCGGCG
1 AGTATAAATA-TTTTGCGGCGTTTGTT-AAA-AACGCCACTATATAT-T-AAACCTATTACGGCG
* *
10957 TTTGA-ACAAAAATGTCGCTAA
61 TTT-ATACAAAAAAGCCGCTAA
* * * * * *
10978 AGTATAAATATTTTGCGGCGTTTTTTATCCAAACGCCACTATAGATTACACCTATTGCGGCATTT
1 AGTATAAATATTTTGCGGCGTTTGTTA--AAAACGCCACTATATATTAAACCTATTACGGC--GT
* * **
11043 TTATAAAAACTAAAAATGCCACTTT
62 TTAT----AC-AAAAAAGCCGCTAA
* * * * * *
11068 TGTATAAATATTTTGTGGCGTTTGGTATTAAAATGCCACTATAGATTACACCTATTACGGCGTTT
1 AGTATAAATATTTTGCGGCGTTT-GT-TAAAAACGCCACTATATATTAAACCTATTACGGCGTTT
* * * *
11133 GTATAAAAATGCAGCTAA
64 ATACAAAAAAGCCGCTAA
* * * * *** * * *
11151 AGTACAAATATTTTTGCGACATTTG-AAAAAACAAAACTATATAGTAAACCTATTGCGACGTTT
1 AGTATAAATA-TTTTGCGGCGTTTGTTAAAAACGCCACTATATATTAAACCTATTACGGCGTTT
11214 TTTATTTAAA
Statistics
Matches: 256, Mismatches: 47, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
81 36 0.14
82 15 0.06
83 35 0.14
84 28 0.11
85 33 0.13
86 40 0.16
87 1 0.00
88 4 0.02
89 2 0.01
90 60 0.23
91 1 0.00
92 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (81 bp):
AGTATAAATATTTTGCGGCGTTTGTTAAAAACGCCACTATATATTAAACCTATTACGGCGTTTAT
ACAAAAAAGCCGCTAA
Found at i:11519 original size:73 final size:73
Alignment explanation
Indices: 11400--11549 Score: 275
Period size: 73 Copynumber: 2.1 Consensus size: 73
11390 AAAAGTGATG
*
11400 CATAAAATTAATACTTAACAACAGAATACATTAAAATTTAGAAACATTAAAGTTATGCATAAATA
1 CATAAAATTAATACTTAACAACAGAATACATTAAAATTTAGAAACATTAAAGTTATGCATAAAAA
11465 GTCTTCAC
66 GTCTTCAC
11473 CATAAAATTAATACTTAACAACA-AATTACATTAAAATTTAGAAACATTAAAGTTATGCATAAAA
1 CATAAAATTAATACTTAACAACAGAA-TACATTAAAATTTAGAAACATTAAAGTTATGCATAAAA
11537 AGTCTTCAC
65 AGTCTTCAC
11546 CATA
1 CATA
11550 TTGTTCACTT
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
72 2 0.03
73 73 0.97
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (73 bp):
CATAAAATTAATACTTAACAACAGAATACATTAAAATTTAGAAACATTAAAGTTATGCATAAAAA
GTCTTCAC
Found at i:12345 original size:22 final size:22
Alignment explanation
Indices: 12303--12352 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12293 TCACGTTTTA
12303 AAAAGCTATTATTATCATATTC
1 AAAAGCTATTATTATCATATTC
* *
12325 GAAAGCTATTATTTTTC-TATTC
1 AAAAGCTATTA-TTATCATATTC
12347 AAAAGC
1 AAAAGC
12353 AGAAAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (22 bp):
AAAAGCTATTATTATCATATTC
Found at i:12995 original size:82 final size:81
Alignment explanation
Indices: 12903--13086 Score: 210
Period size: 83 Copynumber: 2.2 Consensus size: 81
12893 TCTATAACAT
* * * *
12903 CGTTTGTTGAACAAACGCCACTATAAACAACCCTGTTGT-GGTGTTTTTA-TACAAACGCCGTTA
1 CGTTTGTTGAA-AAACGCCACTATAAACAAACCTATT-TCGG-CTTTTTACTACAAACGCCGCTA
*
12966 AATTACTACTCTATTGCGG
63 AATTACCACTCTATTGCGG
* * ** *
12985 CGTTTATTGAAAAAACGCCACTGTAAACAAATTTATTTCGGCTTTTTAGCTATAAACGCCGCTAA
1 CGTTTGTTG-AAAAACGCCACTATAAACAAACCTATTTCGGCTTTTTA-CTACAAACGCCGCTAA
13050 ATTACCACTCTATTGCGG
64 ATTACCACTCTATTGCGG
13068 CGTTTGTTGGAAAAACGCC
1 CGTTTGTT-GAAAAACGCC
13087 GCTAAAGTAT
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
81 7 0.08
82 30 0.35
83 48 0.56
84 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (81 bp):
CGTTTGTTGAAAAACGCCACTATAAACAAACCTATTTCGGCTTTTTACTACAAACGCCGCTAAAT
TACCACTCTATTGCGG
Found at i:13169 original size:41 final size:38
Alignment explanation
Indices: 13078--13170 Score: 89
Period size: 41 Copynumber: 2.3 Consensus size: 38
13068 CGTTTGTTGG
*
13078 AAAAACGCCGCTAAAGTATAATTTTGTGGCGTTTGGAT
1 AAAAACGCCGCTAAAGTATAATTTTGTGGCGTTTGCAT
* * * *
13116 AGTAAAA-ACCGCTACATGTTTAAATTTTGTGGCGTTTAGCCT
1 A--AAAACGCCGCTA-AAGTAT-AATTTTGTGGCGTTT-GCAT
13158 AAAAACGCCGCTA
1 AAAAACGCCGCTA
13171 TAGAACACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
38 1 0.02
39 6 0.14
40 12 0.28
41 21 0.49
42 3 0.07
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (38 bp):
AAAAACGCCGCTAAAGTATAATTTTGTGGCGTTTGCAT
Found at i:17652 original size:16 final size:17
Alignment explanation
Indices: 17627--17669 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
17617 ATCCTTTTAG
17627 TATT-TATATTTA-AAA
1 TATTATATATTTATAAA
17642 TATTATATATTTATAAA
1 TATTATATATTTATAAA
17659 T-TTCATATATT
1 TATT-ATATATT
17670 GTGTACTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.16
16 10 0.40
17 11 0.44
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTATATATTTATAAA
Found at i:24481 original size:35 final size:36
Alignment explanation
Indices: 24396--24482 Score: 106
Period size: 35 Copynumber: 2.4 Consensus size: 36
24386 TACCAAAATT
* *
24396 TTACCAAACTTTG-AAAAACATTTTTCAAAGAAACAT
1 TTACCAAACTTTGAAAAAACATTTTCCAAAG-AACAG
* *
24432 TTACCAAACTTTGAAAAAACATTTTCCAAAG-TCGG
1 TTACCAAACTTTGAAAAAACATTTTCCAAAGAACAG
*
24467 TTGCCAAACTTTGAAA
1 TTACCAAACTTTGAAA
24483 CTTTTAACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 16 0.36
36 13 0.29
37 16 0.36
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (36 bp):
TTACCAAACTTTGAAAAAACATTTTCCAAAGAACAG
Found at i:32866 original size:28 final size:28
Alignment explanation
Indices: 32832--32898 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
32822 AAAAAATGTT
* *
32832 TTAAATATATGTATTAATTTGAGTTTAG
1 TTAAATATATGTATAAAATTGAGTTTAG
*
32860 TTAAATATGTGTATAAAATTGAGTTTAG
1 TTAAATATATGTATAAAATTGAGTTTAG
32888 TTAAATATATG
1 TTAAATATATG
32899 GTTATTGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (28 bp):
TTAAATATATGTATAAAATTGAGTTTAG
Found at i:36042 original size:147 final size:147
Alignment explanation
Indices: 35665--36398 Score: 1035
Period size: 148 Copynumber: 5.0 Consensus size: 147
35655 AAGTCAAATG
* * * * *
35665 AATAATGCACCATGCCTGAAAATGTCAAAACGAGCCATTAATACTCTTCAGAATGGACCATTAAC
1 AATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCTTCAGAACGGACCATTAAT
*
35730 AATGCAGGGTGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTT
66 AATGCAGGATGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTT
*
35795 CAGTGAAATGTCATCTTT
131 CAGTGAAATGTCATC-TC
*
35813 AATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCTTCAGAACGGGCCATTAAT
1 AATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCTTCAGAACGGACCATTAAT
* * * *
35878 AATGCAGGATGCTAGAAAATGCCAGCAAATTTTCAGTGCCTCATCAATCATCTTCAGCAACTTTT
66 AATGCAGGATGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTT
* *
35943 CAGTTAAATGTTATCTC
131 CAGTGAAATGTCATCTC
** * ** * * *
35960 AATAATGCACCATGCTTGAAAATGTCAAAATGGGCCATTAATACTCTTTAGAAATGTCCAATAAC
1 AATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCTTCAGAACGGACCATTAAT
* * * *
36025 AATGCAGGGTACCAGAAAATGCCAACAACTTTTCAATGCCCCATCAATCATCTTCATCAACTTTT
66 AATGCAGGATGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTT
*
36090 CAATGAAATGTCATCTC
131 CAGTGAAATGTCATCTC
36107 TAATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCTTCAGAACGGACCATTAA
1 -AATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCTTCAGAACGGACCATTAA
* * * *
36172 TAATGCAAGATGCCAGAAAATGCCAGCAACTTTTCAGTGCCTCATCAATCATCTTCAGTAACTTT
65 TAATGCAGGATGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTT
* *
36237 TTAGTGAAATGTTATCTC
130 TCAGTGAAATGTCATCTC
* * * * * *
36255 AATAATGTACCATGCTCGAAAATGTCAAAACGAGCCATTAATACTCTTTAGAACGGGCCATTAAT
1 AATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCTTCAGAACGGACCATTAAT
* * *
36320 AATGCAGGATGCCAGAAAAT----ACAACTTTTTAGTGCCCCGTCAATCATCTTCAGCAACGTTT
66 AATGCAGGATGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTT
*
36381 CAGTGAAATGTCAACTC
131 CAGTGAAATGTCATCTC
36398 A
1 A
36399 TCTCTGAAAA
Statistics
Matches: 517, Mismatches: 68, Indels: 7
0.87 0.11 0.01
Matches are distributed among these distances:
143 50 0.10
147 207 0.40
148 260 0.50
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (147 bp):
AATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCTTCAGAACGGACCATTAAT
AATGCAGGATGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTT
CAGTGAAATGTCATCTC
Found at i:36195 original size:295 final size:295
Alignment explanation
Indices: 35665--36393 Score: 1162
Period size: 295 Copynumber: 2.5 Consensus size: 295
35655 AAGTCAAATG
* *
35665 AATAATGCACCATGCCTGAAAATGTCAAAACGAGCCATTAATACTCTTCAG-AATGGACCATTAA
1 AATAATGCACCATGCTTGAAAATGTCAAAACGAGCCATTAATACTCTTTAGAAAT-GACCATTAA
35729 CAATGCAGGGTGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTT
65 CAATGCAGGGTGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTT
*
35794 TCAGTGAAATGTCATCTTTAATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTC
130 TCAGTGAAATGTCATCTCTAATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTC
* * *
35859 TTCAGAACGGGCCATTAATAATGCAGGATGCTAGAAAATGCCAGCAAATTTTCAGTGCCTCATCA
195 TTCAGAACGGACCATTAATAATGCAAGATGCCAGAAAATGCCAGCAAATTTTCAGTGCCTCATCA
*
35924 ATCATCTTCAGCAACTTTTCAGTTAAATGTTATCTC
260 ATCATCTTCAGCAACTTTTCAGTGAAATGTTATCTC
* * * *
35960 AATAATGCACCATGCTTGAAAATGTCAAAATGGGCCATTAATACTCTTTAGAAATGTCCAATAAC
1 AATAATGCACCATGCTTGAAAATGTCAAAACGAGCCATTAATACTCTTTAGAAATGACCATTAAC
* * *
36025 AATGCAGGGTACCAGAAAATGCCAACAACTTTTCAATGCCCCATCAATCATCTTCATCAACTTTT
66 AATGCAGGGTGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTT
*
36090 CAATGAAATGTCATCTCTAATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCT
131 CAGTGAAATGTCATCTCTAATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCT
*
36155 TCAGAACGGACCATTAATAATGCAAGATGCCAGAAAATGCCAGCAACTTTTCAGTGCCTCATCAA
196 TCAGAACGGACCATTAATAATGCAAGATGCCAGAAAATGCCAGCAAATTTTCAGTGCCTCATCAA
* *
36220 TCATCTTCAGTAACTTTTTAGTGAAATGTTATCTC
261 TCATCTTCAGCAACTTTTCAGTGAAATGTTATCTC
* * ** * *
36255 AATAATGTACCATGCTCGAAAATGTCAAAACGAGCCATTAATACTCTTTAGAACGGGCCATTAAT
1 AATAATGCACCATGCTTGAAAATGTCAAAACGAGCCATTAATACTCTTTAGAAATGACCATTAAC
* * * *
36320 AATGCAGGATGCCAGAAAAT----ACAACTTTTTAGTGCCCCGTCAATCATCTTCAGCAACGTTT
66 AATGCAGGGTGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTT
36381 CAGTGAAATGTCA
131 CAGTGAAATGTCA
36394 ACTCATCTCT
Statistics
Matches: 398, Mismatches: 35, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
291 48 0.12
295 347 0.87
296 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (295 bp):
AATAATGCACCATGCTTGAAAATGTCAAAACGAGCCATTAATACTCTTTAGAAATGACCATTAAC
AATGCAGGGTGCCAGAAAATGCCAACAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTT
CAGTGAAATGTCATCTCTAATAATGCACCATGCCCGAAAATGTCAAAATGGGCCATTAATACTCT
TCAGAACGGACCATTAATAATGCAAGATGCCAGAAAATGCCAGCAAATTTTCAGTGCCTCATCAA
TCATCTTCAGCAACTTTTCAGTGAAATGTTATCTC
Found at i:42129 original size:31 final size:31
Alignment explanation
Indices: 42066--42187 Score: 158
Period size: 31 Copynumber: 4.0 Consensus size: 31
42056 AAGAGTCAAG
*
42066 GATTACCTATGTTCTTCGGGAC--ATGGACT
1 GATTACCTATGTTCTTAGGGACATATGGACT
* *
42095 GATTACCTATGTTCTTAAGGACATATGGAAT
1 GATTACCTATGTTCTTAGGGACATATGGACT
* *
42126 GATTACCTATGTTCTTTGGGACATATAGACT
1 GATTACCTATGTTCTTAGGGACATATGGACT
* * *
42157 GATTACCTAGGTTCTTATGGACCTATGGACT
1 GATTACCTATGTTCTTAGGGACATATGGACT
42188 TGTCCTTCGG
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
29 20 0.25
31 59 0.75
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (31 bp):
GATTACCTATGTTCTTAGGGACATATGGACT
Found at i:42184 original size:62 final size:60
Alignment explanation
Indices: 42066--42185 Score: 177
Period size: 62 Copynumber: 2.0 Consensus size: 60
42056 AAGAGTCAAG
* *
42066 GATTACCTATGTTCTTCGGGACATGGACTGATTACCTATGTTCTTAAGGACATATGGAAT
1 GATTACCTATGTTCTTCGGGACATAGACTGATTACCTAGGTTCTTAAGGACATATGGAAT
* * *
42126 GATTACCTATGTTCTTTGGGACATATAGACTGATTACCTAGGTTCTTATGGACCTATGGA
1 GATTACCTATGTTCTTCGGGAC--ATAGACTGATTACCTAGGTTCTTAAGGACATATGGA
42186 CTTGTCCTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 21 0.40
62 32 0.60
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (60 bp):
GATTACCTATGTTCTTCGGGACATAGACTGATTACCTAGGTTCTTAAGGACATATGGAAT
Found at i:42794 original size:20 final size:20
Alignment explanation
Indices: 42769--42843 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
42759 GTTTTTGTGC
42769 ATCGATACTGTTCATACAGT
1 ATCGATACTGTTCATACAGT
*
42789 ATCGATACTATTTCCAT--AGT
1 ATCGATACT-GTT-CATACAGT
**
42809 ATCGGCACTGTTCATACAGT
1 ATCGATACTGTTCATACAGT
* *
42829 ATAG-TACTATTCATA
1 ATCGATACTGTTCATA
42844 AAAATATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.07
19 11 0.25
20 25 0.57
21 2 0.05
22 3 0.07
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (20 bp):
ATCGATACTGTTCATACAGT
Found at i:46776 original size:31 final size:31
Alignment explanation
Indices: 46713--46835 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
46703 AAGAGTCGAG
46713 GATTACCTATGTTCTTCAGGACATA--GACT
1 GATTACCTATGTTCTTCAGGACATATGGACT
*
46742 GATTACCTATGTTCTTCGGGACATATGGACT
1 GATTACCTATGTTCTTCAGGACATATGGACT
46773 GATTACCTATGTTCTTCAGGACATATGGACT
1 GATTACCTATGTTCTTCAGGACATATGGACT
* *
46804 GATTACCTAGGTTCTT-ATGGACCTATGGACT
1 GATTACCTATGTTCTTCA-GGACATATGGACT
46835 G
1 G
46836 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
29 24 0.28
30 1 0.01
31 62 0.71
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (31 bp):
GATTACCTATGTTCTTCAGGACATATGGACT
Found at i:49217 original size:32 final size:34
Alignment explanation
Indices: 49170--49266 Score: 90
Period size: 35 Copynumber: 2.8 Consensus size: 34
49160 TAAAATAGTC
*
49170 ATTATATTTTATATT-AAT-ATAATTATATAAAT
1 ATTATTTTTTATATTAAATAATAATTATATAAAT
* * *
49202 ATTATTTTTTTTATTAAAATAATATTTATATAATT
1 ATTATTTTTTATATT-AAATAATAATTATATAAAT
* * *
49237 ATTATTTATTTAAATTTATTAATTAATTAT
1 ATTATTT-TTTATATTAAATAA-TAATTAT
49267 TTTTTGTGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
32 13 0.25
34 3 0.06
35 23 0.45
36 12 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
ATTATTTTTTATATTAAATAATAATTATATAAAT
Found at i:51076 original size:21 final size:21
Alignment explanation
Indices: 51050--51120 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
51040 TGTCATCTCT
51050 GCAGGGTTACATTCCTAGCCC
1 GCAGGGTTACATTCCTAGCCC
*
51071 GCAGGGTTACATTCCTAGTCC
1 GCAGGGTTACATTCCTAGCCC
* *
51092 GCCA-GGTTACATGCCTAGCTC
1 G-CAGGGTTACATTCCTAGCCC
51113 GCAGGGTT
1 GCAGGGTT
51121 TTATACCATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (21 bp):
GCAGGGTTACATTCCTAGCCC
Found at i:51676 original size:34 final size:34
Alignment explanation
Indices: 51633--51739 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
51623 ATAAATATTT
51633 TTAAAATACAAATTATAGTATTTGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTTGAAATTTAAAA
* * *
51667 TTAAAATACAAATAATATTATTTGAAATTTAAAT
1 TTAAAATACAAATTATAGTATTTGAAATTTAAAA
* ** *
51701 TTAAAATATAAATTATAGTATTCAAAATTTAACA
1 TTAAAATACAAATTATAGTATTTGAAATTTAAAA
51735 TTAAA
1 TTAAA
51740 TTCAACTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTTGAAATTTAAAA
Found at i:52425 original size:125 final size:127
Alignment explanation
Indices: 52142--52665 Score: 860
Period size: 127 Copynumber: 4.2 Consensus size: 127
52132 ATCTATAGTT
* * * * * *
52142 CCCCGGGAACGCG-CTTTAAAGTCCCCTAAGAAATAGTAGGTATTGACATAAATAGTTCTCAGGG
1 CCCCGGGAACGCGCCTTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCAGGG
* *
52206 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAATGTGCGC
66 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
52268 CCCCGGGAACGCGCCTTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCC-GAG
1 CCCCGGGAACGCGCCTTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCAG-G
*
52332 GGACATAAGTGACATAATAGAGCAATGAT-A-ATATTCTCTGACAAAATAATGGAAGGCGCGC
65 GGACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
** *
52393 CCCCGGGAACGCGCCTTCATGGTCCCCTAAGGAATAATAGGTATTGACATTAATAGTTCCCAGGG
1 CCCCGGGAACGCGCCTTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCAGGG
*
52458 GACATAAGTGACATAATAGGGCAATGTTAACATATTCTCTGACAAAATAATGGAAGGCGCGC
66 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
* *
52520 CCCCGGGAATGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCC-GGG
1 CCCCGGGAACGCGCCTTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCAGGG
52584 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
66 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
*
52646 CCCCGGGAACGCGCATTCAC
1 CCCCGGGAACGCGCCTTCAC
52666 GTGAATAGTA
Statistics
Matches: 373, Mismatches: 20, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
125 115 0.31
126 99 0.27
127 159 0.43
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (127 bp):
CCCCGGGAACGCGCCTTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCAGGG
GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
Found at i:52471 original size:252 final size:253
Alignment explanation
Indices: 52142--52664 Score: 890
Period size: 252 Copynumber: 2.1 Consensus size: 253
52132 ATCTATAGTT
* * *
52142 CCCCGGGAACGCG-CTTTAAAGTCCCCTAAGAAATAGTAGGTATTGACATAAATAGTTCTCAGGG
1 CCCCGGGAACGCGCCTTCAAAGTCCCCTAAGAAATAATAGGTATTGACATAAATAGTTCCCAGGG
* *
52206 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAATGTGCGCCCC
66 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCC
52271 CGGGAACGCGCCTTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGAGGGAC
131 CGGGAACGCGCCTTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCG-GGGAC
52336 ATAAGTGACATAATAGAGCAATGAT-A-ATATTCTCTGACAAAATAATGGAAGGCGCGC
195 ATAAGTGACATAATAGAGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
** * *
52393 CCCCGGGAACGCGCCTTCATGGTCCCCTAAGGAATAATAGGTATTGACATTAATAGTTCCCAGGG
1 CCCCGGGAACGCGCCTTCAAAGTCCCCTAAGAAATAATAGGTATTGACATAAATAGTTCCCAGGG
*
52458 GACATAAGTGACATAATAGGGCAATGTTAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCC
66 GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCC
* *
52523 CGGGAATGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGACA
131 CGGGAACGCGCCTTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGACA
*
52588 TAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
196 TAAGTGACATAATAGAGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
*
52646 CCCCGGGAACGCGCATTCA
1 CCCCGGGAACGCGCCTTCA
52665 CGTGAATAGT
Statistics
Matches: 255, Mismatches: 14, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
251 42 0.16
252 164 0.64
253 49 0.19
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (253 bp):
CCCCGGGAACGCGCCTTCAAAGTCCCCTAAGAAATAATAGGTATTGACATAAATAGTTCCCAGGG
GACATAAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCC
CGGGAACGCGCCTTCACAGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGACA
TAAGTGACATAATAGAGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGC
Found at i:58262 original size:112 final size:112
Alignment explanation
Indices: 57932--58281 Score: 540
Period size: 112 Copynumber: 3.1 Consensus size: 112
57922 TTGTCGGTTT
* * *
57932 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
* *
57997 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
* *
58044 GTGCCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
*
58108 GGTCTATAAATGACAAAACAGGTAAAGCGTTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
* * *
58155 GTGTTGATACTTTATAAAAATGCATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
** * * **
58220 GGTCTCGAAATGACAAAACCGGTAAAGAGCTACTAGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
58267 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
58282 TATAAGTATC
Statistics
Matches: 216, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
111 103 0.48
112 113 0.52
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
Found at i:59064 original size:23 final size:23
Alignment explanation
Indices: 59035--59082 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
59025 AAATAAGTCA
* *
59035 ATATAAGTGATACCTATTACATT
1 ATATAAGCGATACCTAATACATT
* *
59058 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGATACCTAATACATT
59081 AT
1 AT
59083 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGATACCTAATACATT
Found at i:60838 original size:6 final size:6
Alignment explanation
Indices: 60789--60820 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
60779 TTAATAAAGA
60789 AATATT AATATT AATATT AATA-T AATATT AAT
1 AATATT AATATT AATATT AATATT AATATT AAT
60821 TAAAATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AATATT
Found at i:61039 original size:84 final size:82
Alignment explanation
Indices: 60897--61059 Score: 236
Period size: 84 Copynumber: 2.0 Consensus size: 82
60887 CCCTTTTTGC
* *
60897 ACATTCTTGTGTTAACAAGGATAAGACAGAAGAAAAAGACAACCAATTTTTGTCCGATAAATGAA
1 ACATTCTTGTGTTAACAAAGATAAGACAGAAGAAAAAGACAAACAATTTTTGTCCGATAAATGAA
60962 ACATGTGACATAAACAA
66 ACATGTGACATAAACAA
* * * * * *
60979 ACATTTTTGTGTTAATAAAGATATGACAAAGACGAAAAAGACAAACAGTTTTTGTTCGATAAATG
1 ACATTCTTGTGTTAACAAAGATAAGAC--AGAAGAAAAAGACAAACAATTTTTGTCCGATAAATG
61044 AAACATGTGACATAAA
64 AAACATGTGACATAAA
61060 TAAAAATATA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 23 0.32
84 48 0.68
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (82 bp):
ACATTCTTGTGTTAACAAAGATAAGACAGAAGAAAAAGACAAACAATTTTTGTCCGATAAATGAA
ACATGTGACATAAACAA
Done.