Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002551.1 Hibiscus syriacus cultivar Beakdansim tig00005178_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: 84137
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4168 original size:34 final size:34
Alignment explanation
Indices: 4130--4232 Score: 129
Period size: 34 Copynumber: 3.1 Consensus size: 34
4120 ATTTGTGAAA
* *
4130 ATATATTATGGTTTTGAAAAT-ATGTTTTAAAAAC
1 ATATATTATAGTTTTAAAAATAAT-TTTTAAAAAC
*
4164 ATATATTATAGTTTTAAAAATAATTTTTGAAAAC
1 ATATATTATAGTTTTAAAAATAATTTTTAAAAAC
* **
4198 ATAT-TTATAATTTTAAAAATAATTTTCGAAAAC
1 ATATATTATAGTTTTAAAAATAATTTTTAAAAAC
4231 AT
1 AT
4233 GTATATATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
33 29 0.46
34 32 0.51
35 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (34 bp):
ATATATTATAGTTTTAAAAATAATTTTTAAAAAC
Found at i:4212 original size:33 final size:33
Alignment explanation
Indices: 4104--4232 Score: 136
Period size: 33 Copynumber: 3.9 Consensus size: 33
4094 TCATATAATA
* * * *
4104 TATAATTTTAAAATTGATTTGTGAAAATATA-T
1 TATAATTTTAAAAATAATTTTTGAAAACATATT
** * *
4136 TATGGTTTTGAAAAT-ATGTTTTAAAAACATATAT
1 TATAATTTTAAAAATAAT-TTTTGAAAACATAT-T
*
4170 TATAGTTTTAAAAATAATTTTTGAAAACATATT
1 TATAATTTTAAAAATAATTTTTGAAAACATATT
*
4203 TATAATTTTAAAAATAATTTTCGAAAACAT
1 TATAATTTTAAAAATAATTTTTGAAAACAT
4233 GTATATATTA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
31 2 0.02
32 21 0.26
33 29 0.36
34 27 0.33
35 2 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (33 bp):
TATAATTTTAAAAATAATTTTTGAAAACATATT
Found at i:4293 original size:36 final size:35
Alignment explanation
Indices: 4159--4315 Score: 117
Period size: 36 Copynumber: 4.4 Consensus size: 35
4149 ATATGTTTTA
* **
4159 AAAACATATAT-TATAGTTTT-AAAAATAATTTTTG
1 AAAACGTATATATATAGTTTTGAAAAA-AAAATTTG
* * * *
4193 AAAAC--ATATTTATAATTTT-AAAAATAATTTTCG
1 AAAACGTATATATATAGTTTTGAAAAAAAAATTT-G
4226 AAAACATGTATATATTATATAGTTTTGAAAAAAAAATTTG
1 AAAAC--G--TATA-TATATAGTTTTGAAAAAAAAATTTG
* * *
4266 AAAACGTATATATATAGTTTTTTAAAAAATATTTTG
1 AAAACGTATATATATAG-TTTTGAAAAAAAAATTTG
4302 AAAACGTATATATA
1 AAAACGTATATATA
4316 ATATATATAT
Statistics
Matches: 102, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
32 9 0.09
33 19 0.19
34 5 0.05
35 7 0.07
36 33 0.32
38 1 0.01
39 3 0.03
40 15 0.15
41 10 0.10
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (35 bp):
AAAACGTATATATATAGTTTTGAAAAAAAAATTTG
Found at i:4371 original size:36 final size:36
Alignment explanation
Indices: 4233--4397 Score: 143
Period size: 36 Copynumber: 4.3 Consensus size: 36
4223 TCGAAAACAT
* * * *
4233 GTATATATTATATAGTTTTGAAAAAAAAATTTGAAAAC
1 GTATATA-TATA-ATTTTTTAAAAAATATTTTGAAAAC
*
4271 GTATATATATAGTTTTTTAAAAAATATTTTGAAAAC
1 GTATATATATAATTTTTTAAAAAATATTTTGAAAAC
* *
4307 GTATATATAATATATATATATTTTAAAAATACTTTTGAAAAT
1 GTATATAT-ATA-AT-T-T-TTTAAAAAATA-TTTTGAAAAC
*
4349 GTATA-ATATAATTTTTAAAAAAAATATTTTTGAAAAC
1 GTATATATATAATTTTT-TAAAAAATA-TTTTGAAAAC
*
4386 ATAATATATATA
1 GT-ATATATATA
4398 TATATATATT
Statistics
Matches: 105, Mismatches: 13, Indels: 17
0.78 0.10 0.13
Matches are distributed among these distances:
36 30 0.29
37 25 0.24
38 12 0.11
39 8 0.08
40 4 0.04
41 12 0.11
42 14 0.13
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (36 bp):
GTATATATATAATTTTTTAAAAAATATTTTGAAAAC
Found at i:4414 original size:79 final size:78
Alignment explanation
Indices: 4164--4415 Score: 252
Period size: 78 Copynumber: 3.3 Consensus size: 78
4154 TTTTAAAAAC
* * * *
4164 ATATAT-TATAGTTTTAAAAATAATTTTTGAAAAC--ATATTTATAA-TTTTAAAAATA-ATTTT
1 ATATATATATA-TTTGAAAAATAA-ATTTGAAAACGTATATATATAATTTTTAAAAAAATATTTT
* *
4224 CGAAAACATGTATAT
64 TGAAAACATATATAT
* * *
4239 AT-TATATAGT-TTTGAAAAAAAAATTTGAAAACGTATATATATAGTTTTTTAAAAAATA-TTTT
1 ATATATATA-TATTTGAAAAATAAATTTGAAAACGTATATATATAATTTTTAAAAAAATATTTTT
*
4301 GAAAACGTATATAT
65 GAAAACATATATAT
* ** *
4315 AATATATATATATTTTAAAAATACTTTTGAAAATGTATA-ATATAATTTTTAAAAAAAATATTTT
1 -ATATATATATATTTGAAAAATAAATTTGAAAACGTATATATATAATTTTT-AAAAAAATATTTT
4379 TGAAAACATAATATAT
64 TGAAAACAT-ATATAT
*
4395 ATATATATATATTAGAAAAAT
1 ATATATATATATTTGAAAAAT
4416 GATTTTTTAT
Statistics
Matches: 145, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
73 9 0.06
74 13 0.09
75 12 0.08
76 25 0.17
77 14 0.10
78 36 0.25
79 30 0.21
80 6 0.04
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (78 bp):
ATATATATATATTTGAAAAATAAATTTGAAAACGTATATATATAATTTTTAAAAAAATATTTTTG
AAAACATATATAT
Found at i:6546 original size:15 final size:17
Alignment explanation
Indices: 6522--6553 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6512 ATAAATATCG
6522 TTAAATTTTATA-TTTT
1 TTAAATTTTATAGTTTT
6538 TTAAA-TTTATAGTTTT
1 TTAAATTTTATAGTTTT
6554 AGATTTAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TTAAATTTTATAGTTTT
Found at i:10048 original size:39 final size:40
Alignment explanation
Indices: 9949--10050 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 40
9939 GTATGTTTTT
* * *
9949 CTGAAAACTGTTTGA-GCGAGAATACGGAAATGCATTCTG
1 CTGAAAACTGCTCGATGCGAGAATACGGAAATGCATCCTG
* * * * *
9988 CTTAAAACTGCTGGAT-TGAGAATATGGAGATGCATCCTG
1 CTGAAAACTGCTCGATGCGAGAATACGGAAATGCATCCTG
*
10027 CTGGAAACTGCTCG-TGCGAGAATA
1 CTGAAAACTGCTCGATGCGAGAATA
10051 AGACTTCTGG
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
38 1 0.02
39 49 0.98
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (40 bp):
CTGAAAACTGCTCGATGCGAGAATACGGAAATGCATCCTG
Found at i:15300 original size:2 final size:2
Alignment explanation
Indices: 15293--15339 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
15283 TCAATCTATT
15293 TA TA TA TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
15335 TA TA T
1 TA TA T
15340 CCACTAGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17060 original size:2 final size:2
Alignment explanation
Indices: 17055--17109 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
17045 TCTCCATCCC
17055 TA TA TA TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
17097 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
17110 TAAAATAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23509 original size:13 final size:13
Alignment explanation
Indices: 23491--23516 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23481 AGGACATGTT
23491 ATCCGTTTTAGTG
1 ATCCGTTTTAGTG
23504 ATCCGTTTTAGTG
1 ATCCGTTTTAGTG
23517 GTAAAAAAGA
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:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
ATCCGTTTTAGTG
Found at i:32585 original size:9 final size:9
Alignment explanation
Indices: 32563--32603 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
32553 CGGTCATACT
32563 ACCGGTTC-
1 ACCGGTTCA
32571 ACCGGTTCA
1 ACCGGTTCA
32580 ACCGG-TCGA
1 ACCGGTTC-A
*
32589 ACCGGTTCG
1 ACCGGTTCA
32598 ACCGGT
1 ACCGGT
32604 CGGAAGAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 10 0.34
9 17 0.59
10 2 0.07
ACGTcount: A:0.17, C:0.34, G:0.29, T:0.20
Consensus pattern (9 bp):
ACCGGTTCA
Found at i:32594 original size:18 final size:18
Alignment explanation
Indices: 32571--32605 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32561 CTACCGGTTC
32571 ACCGGTTCAACCGGTCGA
1 ACCGGTTCAACCGGTCGA
*
32589 ACCGGTTCGACCGGTCG
1 ACCGGTTCAACCGGTCG
32606 GAAGAATCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (18 bp):
ACCGGTTCAACCGGTCGA
Found at i:40344 original size:16 final size:16
Alignment explanation
Indices: 40303--40369 Score: 73
Period size: 16 Copynumber: 4.1 Consensus size: 16
40293 TTGGAATGTT
*
40303 TATGAGGGAATTGGAA
1 TATGAAGGAATTGGAA
*
40319 TCTGTGAAGGAATTGGAA
1 --TATGAAGGAATTGGAA
*
40337 TATGAAGGAATTGGAT
1 TATGAAGGAATTGGAA
40353 TATGTAA-GAATTGGAA
1 TATG-AAGGAATTGGAA
40369 T
1 T
40370 CCAATTCCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
16 27 0.63
17 2 0.05
18 14 0.33
ACGTcount: A:0.37, C:0.01, G:0.31, T:0.30
Consensus pattern (16 bp):
TATGAAGGAATTGGAA
Found at i:40347 original size:34 final size:32
Alignment explanation
Indices: 40303--40369 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 32
40293 TTGGAATGTT
* *
40303 TATGAGGGAATTGGAATCTGTGAAGGAATTGGAA
1 TATGAAGGAATTGGAATATGT-AA-GAATTGGAA
*
40337 TATGAAGGAATTGGATTATGTAAGAATTGGAA
1 TATGAAGGAATTGGAATATGTAAGAATTGGAA
40369 T
1 T
40370 CCAATTCCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 10 0.33
33 2 0.07
34 18 0.60
ACGTcount: A:0.37, C:0.01, G:0.31, T:0.30
Consensus pattern (32 bp):
TATGAAGGAATTGGAATATGTAAGAATTGGAA
Found at i:41171 original size:43 final size:42
Alignment explanation
Indices: 41121--41203 Score: 157
Period size: 43 Copynumber: 2.0 Consensus size: 42
41111 GAACCCAATC
41121 CGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACT
1 CGACCCGACCCGAATATCACACTT-AAAAAACCCGACCCGACT
41164 CGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGA
1 CGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGA
41204 ACAAAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 16 0.40
43 24 0.60
ACGTcount: A:0.37, C:0.40, G:0.12, T:0.11
Consensus pattern (42 bp):
CGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGACT
Found at i:41199 original size:259 final size:258
Alignment explanation
Indices: 40892--41432 Score: 750
Period size: 269 Copynumber: 2.1 Consensus size: 258
40882 TTCACCCTAA
*
40892 ACCCGACCCGACTCGACCCGAATACCACACTTTAAAAACCCGACCCGACCCGAACAAAATAAAGT
1 ACCCGACCCGACCCGACCCGAATACCACACTTTAAAAA--C-ACCCGACCCGAACAAAATAAAGT
40957 TTCATCCGAACCGACCCGAATATATGAATTAGAAA-T-CCGACCCGACCCGAAATAATAAAAAAT
63 TTCATCCGAACCGACCCGAATATATGAATTAGAAATTCCCGACCCGACCCGAAATAATAAAAAAT
* *
41020 TATTTTTATTTAATAAAAACAGTGAATTAATCCGACACAACCCGAATTATATATATTTTCGGTTC
128 TATTTTTATTTAATAAAAACAGTGAATTAATCCGACACAACACGAATTATATATATTTTCGGGTC
*
41085 GGTCCGA-TTTTTTTCACCCTAAACCCGAACCCAATCCGACCCGACCCGAATATCACACTTAAAA
193 GGTCC-ATTTTTTTTCACCCCAAACCCGAA-CC--T--GACCCGACCCGAATATCACACTTAAAA
41149 AAACCCG
252 AAACCCG
* *
41156 ACCCGACTCGACCCGACCCGAATATCACAC-TTAAAAA-ACCCGACCCGAACAAAATAAAGTTTC
1 ACCCGACCCGACCCGACCCGAATACCACACTTTAAAAACACCCGACCCGAACAAAATAAAGTTTC
* *
41219 ATCCGACCCGACCCGAATATATGAATTAGAAATTCAACCCGACCCGACCCGACCCGAAATATTAA
66 ATCCGAACCGACCCGAATATATGAATTAGAAATT--------CCCGACCCGACCCGAAATAATAA
* * * *
41284 AAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACATGAATTATATATATTTTC
123 AAAATTATTTTTATTTAATAAAAACAGTGAATTAATCCGACACAACACGAATTATATATATTTTC
* **
41349 GGGTCGGTCCATTTTTTTTCACCCCAAACCCGAACCTGACCCTACTTGAATATCACACTTAAAAA
188 GGGTCGGTCCATTTTTTTTCACCCCAAACCCGAACCTGACCCGACCCGAATATCACACTTAAAAA
41414 AACCCG
253 AACCCG
*
41420 ATCCGACCCGACC
1 ACCCGACCCGACC
41433 AAAATAAAAT
Statistics
Matches: 249, Mismatches: 17, Indels: 22
0.86 0.06 0.08
Matches are distributed among these distances:
259 57 0.23
260 1 0.00
263 7 0.03
264 69 0.28
266 1 0.00
268 3 0.01
269 111 0.45
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (258 bp):
ACCCGACCCGACCCGACCCGAATACCACACTTTAAAAACACCCGACCCGAACAAAATAAAGTTTC
ATCCGAACCGACCCGAATATATGAATTAGAAATTCCCGACCCGACCCGAAATAATAAAAAATTAT
TTTTATTTAATAAAAACAGTGAATTAATCCGACACAACACGAATTATATATATTTTCGGGTCGGT
CCATTTTTTTTCACCCCAAACCCGAACCTGACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:43317 original size:19 final size:20
Alignment explanation
Indices: 43293--43331 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
43283 AGTTTATGCA
43293 TTTTAAAAATTT-ATTATTT
1 TTTTAAAAATTTCATTATTT
*
43312 TTTTAAAATTTTCATTATTT
1 TTTTAAAAATTTCATTATTT
43332 CCCTTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAAAATTTCATTATTT
Found at i:50847 original size:24 final size:24
Alignment explanation
Indices: 50820--50874 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
50810 GTTGGTGAAC
50820 TTATGTTCGTTTATGT-TCATTTAT
1 TTATGTTCGTTTATGTGT-ATTTAT
*
50844 TTATGTTCGTTTATGTGTGTTTAT
1 TTATGTTCGTTTATGTGTATTTAT
50868 TTATGTT
1 TTATGTT
50875 TAGCCAAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.15, C:0.05, G:0.16, T:0.64
Consensus pattern (24 bp):
TTATGTTCGTTTATGTGTATTTAT
Found at i:50848 original size:14 final size:14
Alignment explanation
Indices: 50829--50871 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
50819 CTTATGTTCG
50829 TTTATGTTCATTTA
1 TTTATGTTCATTTA
*
50843 TTTATGTTCGTTTA
1 TTTATGTTCATTTA
* * *
50857 TGTGTGTTTATTTA
1 TTTATGTTCATTTA
50871 T
1 T
50872 GTTTAGCCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.16, C:0.05, G:0.14, T:0.65
Consensus pattern (14 bp):
TTTATGTTCATTTA
Found at i:50958 original size:15 final size:15
Alignment explanation
Indices: 50938--50982 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
50928 TTGATACCCA
50938 TAAATATTTTAAAAT
1 TAAATATTTTAAAAT
50953 TAAATATTTTAAAAT
1 TAAATATTTTAAAAT
*
50968 TCAATTAATTTTAAA
1 T-AAAT-ATTTTAAA
50983 TACAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 16 0.59
16 3 0.11
17 8 0.30
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATATTTTAAAAT
Found at i:57681 original size:21 final size:20
Alignment explanation
Indices: 57657--57704 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
57647 AAACACATGT
*
57657 TTAATAGAATTTATATATTTA
1 TTAATAGAATTTA-ATAATTA
**
57678 TTAATTATTATTTAATAATTA
1 TTAA-TAGAATTTAATAATTA
57699 TTAATA
1 TTAATA
57705 CTAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 14 0.61
22 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAATAGAATTTAATAATTA
Found at i:57691 original size:14 final size:14
Alignment explanation
Indices: 57667--57701 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
57657 TTAATAGAAT
*
57667 TTATATATTTATTAA
1 TTAT-TATTTAATAA
57682 TTATTATTTAATAA
1 TTATTATTTAATAA
57696 TTATTA
1 TTATTA
57702 ATACTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTATTTAATAA
Found at i:59782 original size:2 final size:2
Alignment explanation
Indices: 59775--59825 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
59765 AAATTAAGAA
* * *
59775 AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
59815 AA AT AT AT AT A
1 AT AT AT AT AT A
59826 CCCGGCCCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:71043 original size:18 final size:17
Alignment explanation
Indices: 71017--71050 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
71007 TTTAATTTGT
*
71017 TATATAAATTTAAAAAA
1 TATATAAATTCAAAAAA
71034 TATATGAAATTCAAAAA
1 TATAT-AAATTCAAAAA
71051 CATTAATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
TATATAAATTCAAAAAA
Found at i:83283 original size:21 final size:21
Alignment explanation
Indices: 83250--83289 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
83240 CTTCCTATCC
*
83250 TCCTTTTTATTCTCCTTCTTT
1 TCCTTTTCATTCTCCTTCTTT
* *
83271 TCCTTTTCCTTCTCTTTCT
1 TCCTTTTCATTCTCCTTCT
83290 ATTCTTTGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.65
Consensus pattern (21 bp):
TCCTTTTCATTCTCCTTCTTT
Done.