Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005934.1 Hibiscus syriacus cultivar Beakdansim tig00013931_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: 89648
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:69 original size:39 final size:39
Alignment explanation
Indices: 15--100 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
5 ACCCGAATGT
15 CCTCTATTTTTCTCTATTTGTATTTTATGTTTGCTTCCC
1 CCTCTATTTTTCTCTATTTGTATTTTATGTTTGCTTCCC
54 CCTCTATTTTTCTCTATTTGTATTTTATGTTTGCTTCCC
1 CCTCTATTTTTCTCTATTTGTATTTTATGTTTGCTTCCC
*
93 CCTGTATT
1 CCTCTATT
101 CTGGTGAGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.10, C:0.23, G:0.08, T:0.58
Consensus pattern (39 bp):
CCTCTATTTTTCTCTATTTGTATTTTATGTTTGCTTCCC
Found at i:2183 original size:41 final size:41
Alignment explanation
Indices: 2126--2208 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
2116 TCAAGTTTTA
*
2126 AGAGCATGTAACTTGTTGGCTACAGTTTCAAATAGCAAAGC
1 AGAGCATGTAACTTGTTGGCCACAGTTTCAAATAGCAAAGC
2167 AGAGCATGTAACTTGTTGGCCACAGTTTCAAATAGCAAAGC
1 AGAGCATGTAACTTGTTGGCCACAGTTTCAAATAGCAAAGC
2208 A
1 A
2209 TTTATCAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (41 bp):
AGAGCATGTAACTTGTTGGCCACAGTTTCAAATAGCAAAGC
Found at i:6471 original size:22 final size:25
Alignment explanation
Indices: 6413--6465 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
6403 TCTTAATTTA
6413 TTATGAGAAAAAAATAATCTCTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
*
6438 TTATGAGAAAAAAATAATCTTTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
6463 TTA
1 TTA
6466 GAAAAACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.32
Consensus pattern (25 bp):
TTATGAGAAAAAAATAATCTCTAAC
Found at i:15682 original size:16 final size:16
Alignment explanation
Indices: 15663--15696 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15653 CAATATACGA
15663 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
15679 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
15695 AT
1 AT
15697 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:15770 original size:16 final size:18
Alignment explanation
Indices: 15738--15771 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
15728 TATTAATGTA
15738 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
15756 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
15772 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:16443 original size:130 final size:130
Alignment explanation
Indices: 16239--16486 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
16229 AATTTTCTTC
* *
16239 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
16304 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
16369 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
16434 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
16487 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:16934 original size:35 final size:35
Alignment explanation
Indices: 16884--16959 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
16874 AATTGAATTT
* *
16884 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
16919 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
16954 AATTGA
1 AATTGA
16960 GGACTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:36957 original size:29 final size:29
Alignment explanation
Indices: 36916--37025 Score: 107
Period size: 29 Copynumber: 3.8 Consensus size: 29
36906 GATGAGTAAT
36916 ATTAAAAAA-ATATTTTATTTTTATTTTA
1 ATTAAAAAATATATTTTATTTTTATTTTA
* * *
36944 ATTAAAAAATATATTTTAATATTATCTTAA
1 ATTAAAAAATATATTTTATTTTTAT-TTTA
* * *
36974 ATT-AAAAATATAATTTATTCTTATCTTA
1 ATTAAAAAATATATTTTATTTTTATTTTA
**
37002 ACTTAAATATTTATATTTTATTTT
1 A-TTAAA-AAATATATTTTATTTT
37026 GATAATATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
28 12 0.18
29 33 0.51
30 8 0.12
31 12 0.18
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTAAAAAATATATTTTATTTTTATTTTA
Found at i:37070 original size:22 final size:22
Alignment explanation
Indices: 37045--37086 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37035 TTAAATTTTA
*
37045 AGTTAATTAAATTGAGTTATCT
1 AGTTAATTAAATTAAGTTATCT
**
37067 AGTTTTTTAAATTAAGTTAT
1 AGTTAATTAAATTAAGTTAT
37087 TTGAGTTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (22 bp):
AGTTAATTAAATTAAGTTATCT
Found at i:37993 original size:31 final size:31
Alignment explanation
Indices: 37958--38025 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
37948 GGATGGTCAC
37958 ATCTTAATTAAATAAAAACGAAAGTGACAAT
1 ATCTTAATTAAATAAAAACGAAAGTGACAAT
* *
37989 ATCTTAATTAAATAAAAACGTAAGTGACCAT
1 ATCTTAATTAAATAAAAACGAAAGTGACAAT
38020 ATCTTA
1 ATCTTA
38026 TGTATTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACGAAAGTGACAAT
Found at i:42248 original size:34 final size:34
Alignment explanation
Indices: 42205--42272 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
42195 ACGTTCTGCA
42205 ACTCCATTCTGTTGAGGAGTACGAACACAAGAAC
1 ACTCCATTCTGTTGAGGAGTACGAACACAAGAAC
42239 ACTCCATTCTGTTGAGGAGTACGAACACAAGAAC
1 ACTCCATTCTGTTGAGGAGTACGAACACAAGAAC
42273 TTTGATGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (34 bp):
ACTCCATTCTGTTGAGGAGTACGAACACAAGAAC
Found at i:46634 original size:37 final size:36
Alignment explanation
Indices: 46566--46637 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
46556 AAAAGAACGA
* *
46566 AATAAAGAAAGTAATATAAAATAAAGAAAATAAATG
1 AATAAAAAAAGTAAGATAAAATAAAGAAAATAAATG
*
46602 AATAAAAAAAGTAAAGATAAAAATAAA-TAAATAAAT
1 AATAAAAAAAGT-AAGAT-AAAATAAAGAAAATAAAT
46638 AAAATGAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 11 0.35
37 12 0.39
38 8 0.26
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (36 bp):
AATAAAAAAAGTAAGATAAAATAAAGAAAATAAATG
Found at i:46881 original size:2 final size:2
Alignment explanation
Indices: 46870--46933 Score: 75
Period size: 2 Copynumber: 34.0 Consensus size: 2
46860 TTAATGTGGG
46870 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A TA GTA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
46909 TA -A AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
46934 ACAACAACAA
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
1 5 0.09
2 48 0.87
3 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:46947 original size:29 final size:31
Alignment explanation
Indices: 46882--46944 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
46872 TAATATATAT
** *
46882 ATATATATATATATATAATAATAGTAATAAA
1 ATATATATATATATATAATAATAACAACAAA
*
46913 ATATATATATATATATATATAACAACAACAAA
1 ATATATATATATATATA-ATAATAACAACAAA
46945 TATCAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (31 bp):
ATATATATATATATATAATAATAACAACAAA
Found at i:49206 original size:106 final size:106
Alignment explanation
Indices: 49016--49226 Score: 316
Period size: 106 Copynumber: 2.0 Consensus size: 106
49006 GTATTGTTTC
* * * *
49016 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAATTTGTTTGTTGACAA
1 GAGTCCAATATCCTCCGCCATGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
* *
49081 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGTCGTCCATTCATTGTGAAGTTGAACTTGTGTTGTCTT
* * *
49122 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTCCGCCATGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
*
49187 TCAG-CTGTCCATTCATTGTGAAGTTGAACTTGTGTTGTCT
66 CCAGTC-GTCCATTCATTGTGAAGTTGAACTTGTGTTGTCT
49227 CGGGTGGCGC
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
105 1 0.01
106 93 0.99
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (106 bp):
GAGTCCAATATCCTCCGCCATGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
CCAGTCGTCCATTCATTGTGAAGTTGAACTTGTGTTGTCTT
Found at i:50362 original size:8 final size:8
Alignment explanation
Indices: 50351--50398 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
50341 GTTTTTTTCC
50351 TTTTTATT
1 TTTTTATT
*
50359 TTTTTCTTT
1 TTTTT-ATT
*
50368 TTTTGTGTTT
1 TTTT-T-ATT
50378 TTTTTATT
1 TTTTTATT
50386 TTTTTATT
1 TTTTTATT
50394 TTTTT
1 TTTTT
50399 CTTTCGACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 20 0.57
9 7 0.20
10 8 0.23
ACGTcount: A:0.06, C:0.02, G:0.04, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:59821 original size:14 final size:14
Alignment explanation
Indices: 59808--59849 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
59798 AGTAAAATAA
59808 AAATAAAT--AAAT
1 AAATAAATAAAAAT
59820 AAATAAATAAAAAT
1 AAATAAATAAAAAT
**
59834 AACGAAATAAAAAT
1 AAATAAATAAAAAT
59848 AA
1 AA
59850 GAAGATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 8 0.31
14 18 0.69
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:59827 original size:22 final size:22
Alignment explanation
Indices: 59802--59844 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
59792 CAAGTCAGTA
*
59802 AAATAAAAATAAATAAATAAAT
1 AAATAAAAATAAAGAAATAAAT
*
59824 AAATAAAAATAACGAAATAAA
1 AAATAAAAATAAAGAAATAAA
59845 AATAAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATAAAAATAAAGAAATAAAT
Found at i:61105 original size:2 final size:2
Alignment explanation
Indices: 61094--61145 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
61084 TTAATGTGGG
*
61094 TA TA -A TA TA TA TA TA TA TA -A TA -A TA GTA -A TA -A AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
61132 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
61146 ACAACAAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
1 5 0.12
2 36 0.84
3 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (2 bp):
TA
Found at i:62398 original size:2 final size:2
Alignment explanation
Indices: 62377--62449 Score: 100
Period size: 2 Copynumber: 38.5 Consensus size: 2
62367 ATAATAAATC
*
62377 AT AT GT AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
62417 AT AT AT AT AT AT AT A- AA AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62450 AATGATGACA
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
1 4 0.06
2 60 0.94
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64457 original size:56 final size:55
Alignment explanation
Indices: 64322--64503 Score: 147
Period size: 56 Copynumber: 3.3 Consensus size: 55
64312 GGGGTTCGGA
* * * * * ** ** *
64322 AATCGATTATATCTATCCGTTGTTGTCATTAATAAGCAT-AAAAATAGGGGGCCAA
1 AATCGAATATATCTATCAGATGTTGCCATTAAGAA-CATAAAAAATAAAGCCCCAG
* * * *
64377 AATC-AAGTATATTTATTAGTTGTTGCCATTAAGAA-ATATAAAAATAAAAGTCCC-G
1 AATCGAA-TATATCTATCAGATGTTGCCATTAAGAACATA-AAAAAT-AAAGCCCCAG
*
64432 AAATCGAATATATCTATCAGATGTTGCCATTAAGAAGCATAAAAAATAGAGCCCCAG
1 -AATCGAATATATCTATCAGATGTTGCCATTAAGAA-CATAAAAAATAAAGCCCCAG
64489 AATCGAATATATCTA
1 AATCGAATATATCTA
64504 GAAAATAAGG
Statistics
Matches: 102, Mismatches: 16, Indels: 17
0.76 0.12 0.13
Matches are distributed among these distances:
53 2 0.02
54 1 0.01
55 33 0.32
56 54 0.53
57 9 0.09
58 3 0.03
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (55 bp):
AATCGAATATATCTATCAGATGTTGCCATTAAGAACATAAAAAATAAAGCCCCAG
Found at i:65068 original size:23 final size:23
Alignment explanation
Indices: 65042--65087 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
65032 ATTTTAAATT
*
65042 TATATACTTTTTAATAAAATTTA
1 TATATAATTTTTAATAAAATTTA
*
65065 TATATAATTTTTTATAAAATTTA
1 TATATAATTTTTAATAAAATTTA
65088 AAAGATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATAATTTTTAATAAAATTTA
Found at i:65095 original size:24 final size:23
Alignment explanation
Indices: 65049--65095 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
65039 ATTTATATAC
* *
65049 TTTTTAATAAAATTTATATATAA
1 TTTTTAATAAAATTTAAAGATAA
*
65072 TTTTTTATAAAATTTAAAAGATAA
1 TTTTTAATAAAATTT-AAAGATAA
65096 ATGGATAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTTAATAAAATTTAAAGATAA
Found at i:69404 original size:32 final size:31
Alignment explanation
Indices: 69330--69405 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
69320 CTAACGTGAC
* *
69330 TCTTAGGTAGGCTCTACGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATTAT
* * *
69361 T-TTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTT-AGGTAGGCCCTACGGCCCTAAGAT-TAT
69393 TCTTAGGTAGGCC
1 TCTTAGGTAGGCC
69406 TCGTGGCCCC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
30 2 0.06
31 21 0.58
32 11 0.31
33 2 0.06
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.30
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATTAT
Found at i:81224 original size:13 final size:12
Alignment explanation
Indices: 81202--81290 Score: 54
Period size: 13 Copynumber: 6.9 Consensus size: 12
81192 ACGTAAAAAT
81202 TAAATGAATATAA
1 TAAAT-AATATAA
81215 TAAATAAATATAA
1 TAAAT-AATATAA
81228 T-AATAATAATAA
1 TAAATAAT-ATAA
* *
81240 TTAGTAATATTAA
1 TAAATAATA-TAA
* *
81253 TTATTAAATATAA
1 TAAAT-AATATAA
* *
81266 TACATAATTAAAA
1 TAAATAA-TATAA
81279 TATAATAATATA
1 TA-AATAATATA
81291 GTAATTAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
11 3 0.05
12 11 0.18
13 39 0.64
14 8 0.13
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (12 bp):
TAAATAATATAA
Found at i:81232 original size:16 final size:16
Alignment explanation
Indices: 81211--81288 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 16
81201 TTAAATGAAT
81211 ATAATAAATAAATATA
1 ATAATAAATAAATATA
*
81227 ATAATAATAATAATTAGTA
1 ATAAT-A-AATAAATA-TA
*
81246 ATATTAATTATTAAATATA
1 ATAATAA--A-TAAATATA
*
81265 ATACATAATTAAAATATA
1 ATA-ATAAAT-AAATATA
81283 ATAATA
1 ATAATA
81289 TAGTAATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
16 5 0.10
17 6 0.12
18 18 0.37
19 12 0.24
20 8 0.16
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (16 bp):
ATAATAAATAAATATA
Found at i:81288 original size:21 final size:22
Alignment explanation
Indices: 81262--81302 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
81252 ATTATTAAAT
81262 ATAATACA-TAATTAAAATATA
1 ATAATACAGTAATTAAAATATA
*
81283 ATAATATAGTAATTAAAATA
1 ATAATACAGTAATTAAAATA
81303 GATATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
ATAATACAGTAATTAAAATATA
Found at i:84016 original size:20 final size:20
Alignment explanation
Indices: 83967--84036 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
83957 TATTGTTCAT
* * * *
83967 TACTGTTCACATAGTATTGG
1 TACTATTCATATAGTATCGA
83987 TACTATTCATATAGTATCGA
1 TACTATTCATATAGTATCGA
*
84007 TACTATTCATACAGTA-C-A
1 TACTATTCATATAGTATCGA
84025 GTACTATTCATA
1 -TACTATTCATA
84037 AAAACATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
18 1 0.02
19 12 0.27
20 31 0.70
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (20 bp):
TACTATTCATATAGTATCGA
Done.