Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000884.1 Hibiscus syriacus cultivar Beakdansim tig00001720_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: 117037
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:6334 original size:12 final size:12
Alignment explanation
Indices: 6291--6334 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
6281 TATTGATTTC
6291 TTTCATTTTGCA
1 TTTCATTTTGCA
*
6303 TTTCA-CTTGCA
1 TTTCATTTTGCA
* *
6314 TTTCTTTTTGTA
1 TTTCATTTTGCA
6326 TTTCATTTT
1 TTTCATTTT
6335 TGTTGTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.14, C:0.16, G:0.07, T:0.64
Consensus pattern (12 bp):
TTTCATTTTGCA
Found at i:8465 original size:19 final size:20
Alignment explanation
Indices: 8424--8474 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
8414 GAAACCCCTT
*
8424 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
8444 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
8463 TGAAGATACATG
1 TGAAAATACATG
8475 CTCTTGGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:11791 original size:8 final size:8
Alignment explanation
Indices: 11780--11804 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11770 TCTATTTCTT
11780 TTCTTTTC
1 TTCTTTTC
11788 TTCTTTTC
1 TTCTTTTC
11796 TTCTTTTC
1 TTCTTTTC
11804 T
1 T
11805 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:13533 original size:30 final size:31
Alignment explanation
Indices: 13494--13553 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
13484 ACATGCTGCC
**
13494 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
13525 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
13554 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:15671 original size:597 final size:605
Alignment explanation
Indices: 14525--15730 Score: 1982
Period size: 597 Copynumber: 2.0 Consensus size: 605
14515 TATATTCAGC
* *
14525 TCCAAATAGTCCAACTAGCTGAGTTTAGCTAGCCTTAAGCTCCTCCAGCTGAATCGATCTTTCTT
1 TCCAAATAGTCCAACTAGCTGAGTTTAGCTAGCCTTAAGCTCCTCCAGCTGAATCAATCTTTCCT
*
14590 TATTGCCCCATGAGTTGCCTTGCACTTTGTGAGCTTTTTGTGAGCTACATATGACGTCCAAATCA
66 TAGTGCCCCATGA--TGCCTTGCACTTTGTGAGC-TTTTGTGAGCTACATATGACGTCCAAATCA
* * * *
14655 TCCTTTAAGCTATCTCAACGTGCATCACACTCCAATGTACCTACATGTGCAAGGAAACAAGGTAA
128 TCCATCAAGATATCTCAACGTGCAACACACTCCAATGTACCTACATGTGCAAGGAAACAAGGTAA
* * * *
14720 GTCCATGATATTGAGCTGATATGAGCTAAATATCTTGCTGTCATGTATTATTATGGTAATGTGAG
193 GTCCATGATATTGAGCTGATATGAGCTAAATACCTTGCTGCCATGTATGATTAGGGTAATGTGAG
* *
14785 CTATTATTGAATGCCATGAGCTAATTATATCATCTCATAATATGTGTAAGATTATGCAAGAAGCT
258 CTATTATTGAAAGCCATGAGCTAAATATATCATCTCATAATATGTGTAAGATTATGCAAGAAGCT
*
14850 TAAAAGCTAATATGAATGCATATGAACTAAGTAAATGAATTATACATATGATGCCTTGATATATA
323 TAAAAGCTAATATGAATGCATATGAACTAAGTAAATGAATTATAAATATGATGCCTTGATATATA
*
14915 TATGATAATCATGCTTAAAATGATTATAAGACTATCCTAACATGCTTAAATATCGACGTGCATGT
388 TATGATAATCATGCTTAAAATGATTATAAGACTATCATAACATGCTTAAATATCGACGTGCATGT
*
14980 TGTGTTCATACTAAGTTATTCTTTAACTTCATAACAAGTATTCTTATCATGAAATGTATTATATA
453 TGTGTTCATACTAAGTTATTCTTTAACTACATAACAAGTATTCTTATCATGAAATGTATTATATA
* * *
15045 AGCATATAGTATATAAACAATACAAATTAGATTCAGA-ATAAAGGTTTTCAAGAGTACTCCCTTT
518 AGCATATAGTATATAAACAATACAAATTAGATTCA-ATATAAAGATGTTCAAAAGTACTCCCTTT
* * *
15109 GTAGGTGAAAATGTGTTTGTATCA
582 GTAGGTGAAAACGTGCTTGCATCA
* *
15133 TCCAAATAGTCCAACTAGTTGAGTTTAGCTAGCCTTAAGCTCCTTCAGCTGAATCAATCTTTCCT
1 TCCAAATAGTCCAACTAGCTGAGTTTAGCTAGCCTTAAGCTCCTCCAGCTGAATCAATCTTTCCT
* *
15198 TAGTGCTCCATGA-G-C-TGC-C-TTGT-A-C-TTTGTGAGCTGCATATGACGTCCAAATCATCC
66 TAGTGCCCCATGATGCCTTGCACTTTGTGAGCTTTTGTGAGCTACATATGACGTCCAAATCATCC
*
15255 ATCAAGATATCTCAACGTGCAACACACTCCAATGTACCTATATGTGCAAGGAAACAAGGTAAGTC
131 ATCAAGATATCTCAACGTGCAACACACTCCAATGTACCTACATGTGCAAGGAAACAAGGTAAGTC
* *
15320 CATGATATTGAGTTGTTATGAGCTAAATACCTTGCTGCCATGTATGATTAGGGTAATGTGAGCTA
196 CATGATATTGAGCTGATATGAGCTAAATACCTTGCTGCCATGTATGATTAGGGTAATGTGAGCTA
*
15385 TGT-TTGAAAGCCATGAGCTAAATATATCATCTCATAATATGTGTAAGATTATGCATGAAGCTTA
261 T-TATTGAAAGCCATGAGCTAAATATATCATCTCATAATATGTGTAAGATTATGCAAGAAGCTTA
* * *
15449 AGAGCTAATATGAATGCATATGAACTAAGTAAATGAATTATAAATATGCTGCCTTGATGTATATA
325 AAAGCTAATATGAATGCATATGAACTAAGTAAATGAATTATAAATATGATGCCTTGATATATATA
*
15514 TGATAATCATGCTTAAAATGATTATAAGACTATCATAACATGCTTAAATATCGATGTGCATGTTG
390 TGATAATCATGCTTAAAATGATTATAAGACTATCATAACATGCTTAAATATCGACGTGCATGTTG
15579 TGTTCATACTAAGTTATTCTTTAACTACATAACAAGTATTCTTATCATGAAATGTATTATATAAG
455 TGTTCATACTAAGTTATTCTTTAACTACATAACAAGTATTCTTATCATGAAATGTATTATATAAG
*
15644 CATATAGTATATAAACAATATAAATTAGATTCAATATAAAGATGTTCAAAAGTACTCCCTTTGTA
520 CATATAGTATATAAACAATACAAATTAGATTCAATATAAAGATGTTCAAAAGTACTCCCTTTGTA
15709 GGTGAAAACGTGCTTGCATCA
585 GGTGAAAACGTGCTTGCATCA
15730 T
1 T
15731 TAGATGTAGC
Statistics
Matches: 561, Mismatches: 35, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
596 1 0.00
597 475 0.85
598 1 0.00
599 1 0.00
600 1 0.00
601 4 0.01
602 1 0.00
603 3 0.01
604 1 0.00
605 1 0.00
608 72 0.13
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (605 bp):
TCCAAATAGTCCAACTAGCTGAGTTTAGCTAGCCTTAAGCTCCTCCAGCTGAATCAATCTTTCCT
TAGTGCCCCATGATGCCTTGCACTTTGTGAGCTTTTGTGAGCTACATATGACGTCCAAATCATCC
ATCAAGATATCTCAACGTGCAACACACTCCAATGTACCTACATGTGCAAGGAAACAAGGTAAGTC
CATGATATTGAGCTGATATGAGCTAAATACCTTGCTGCCATGTATGATTAGGGTAATGTGAGCTA
TTATTGAAAGCCATGAGCTAAATATATCATCTCATAATATGTGTAAGATTATGCAAGAAGCTTAA
AAGCTAATATGAATGCATATGAACTAAGTAAATGAATTATAAATATGATGCCTTGATATATATAT
GATAATCATGCTTAAAATGATTATAAGACTATCATAACATGCTTAAATATCGACGTGCATGTTGT
GTTCATACTAAGTTATTCTTTAACTACATAACAAGTATTCTTATCATGAAATGTATTATATAAGC
ATATAGTATATAAACAATACAAATTAGATTCAATATAAAGATGTTCAAAAGTACTCCCTTTGTAG
GTGAAAACGTGCTTGCATCA
Found at i:18623 original size:36 final size:36
Alignment explanation
Indices: 18583--18655 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
18573 TCAGACTATT
18583 TTGATTAATATAAGTGAGATTATTCTATTCCTTAAG
1 TTGATTAATATAAGTGAGATTATTCTATTCCTTAAG
* *
18619 TTGATTAATATAAGTGAGATTATTCTCTTTCTTAAG
1 TTGATTAATATAAGTGAGATTATTCTATTCCTTAAG
18655 T
1 T
18656 CCCAATGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (36 bp):
TTGATTAATATAAGTGAGATTATTCTATTCCTTAAG
Found at i:19195 original size:23 final size:25
Alignment explanation
Indices: 19160--19214 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
19150 AAATCCAGCA
19160 AAGAAAATCAAAGCACTC-AAAA-G
1 AAGAAAATCAAAGCACTCAAAAATG
* * *
19183 AAGAAATTGAAAGCATTCAAAAATG
1 AAGAAAATCAAAGCACTCAAAAATG
19208 AAGAAAA
1 AAGAAAA
19215 AGAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 15 0.58
24 4 0.15
25 7 0.27
ACGTcount: A:0.62, C:0.11, G:0.15, T:0.13
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAAATG
Found at i:32637 original size:16 final size:16
Alignment explanation
Indices: 32616--32653 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
32606 AACAGTCCAC
32616 CTATTCTCACCCATAG
1 CTATTCTCACCCATAG
32632 CTATTCTCACCCATAG
1 CTATTCTCACCCATAG
*
32648 CCATTC
1 CTATTC
32654 ACTTGTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.39, G:0.05, T:0.32
Consensus pattern (16 bp):
CTATTCTCACCCATAG
Found at i:43214 original size:23 final size:23
Alignment explanation
Indices: 43162--43214 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
43152 TTTAATAATG
43162 AATATAAGTATATTATATGTTAT
1 AATATAAGTATATTATATGTTAT
* *
43185 AAGATAAGT-TA-TATATTTTAT
1 AATATAAGTATATTATATGTTAT
43206 GAAATATAA
1 --AATATAA
43215 AGCATATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 9 0.36
22 2 0.08
23 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.43
Consensus pattern (23 bp):
AATATAAGTATATTATATGTTAT
Found at i:55191 original size:35 final size:34
Alignment explanation
Indices: 55144--55221 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 34
55134 TAAGATACTA
* * *
55144 CCTATAATATCACCATCTTCCATCATCATTGCATG
1 CCTAT-ATATCACCAACTTCCATCACCATTGCACG
* *
55179 CCTATATCATCACCAACTTCTATCACCATTTCACG
1 CCTATAT-ATCACCAACTTCCATCACCATTGCACG
55214 CCTATATA
1 CCTATATA
55222 ACCACTAGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 3 0.08
35 34 0.92
ACGTcount: A:0.29, C:0.33, G:0.04, T:0.33
Consensus pattern (34 bp):
CCTATATATCACCAACTTCCATCACCATTGCACG
Found at i:60838 original size:35 final size:35
Alignment explanation
Indices: 60792--60877 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
60782 TAAGATACTA
* *
60792 CCTATAACATCACCATCTTCCATCACCATTGCACG
1 CCTATATCATCACCAACTTCCATCACCATTGCACG
* *
60827 CCTATATCATCACCAACTTCTATCACCATTTCACG
1 CCTATATCATCACCAACTTCCATCACCATTGCACG
* * *
60862 ACTATATAACCACCAA
1 CCTATATCATCACCAA
60878 TCCCTTACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.33, C:0.37, G:0.03, T:0.27
Consensus pattern (35 bp):
CCTATATCATCACCAACTTCCATCACCATTGCACG
Found at i:79572 original size:21 final size:20
Alignment explanation
Indices: 79527--79575 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
79517 TACCATATGT
*
79527 TAAAAGATAGATTATAAATA
1 TAAAAGATAGATCATAAATA
79547 T-AAAGAT-GATCATAATAATA
1 TAAAAGATAGATCAT-A-AATA
79567 TAAAAGATA
1 TAAAAGATA
79576 TAAAAGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 5 0.21
19 7 0.29
20 6 0.25
21 6 0.25
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (20 bp):
TAAAAGATAGATCATAAATA
Found at i:90231 original size:11 final size:10
Alignment explanation
Indices: 90215--90269 Score: 67
Period size: 10 Copynumber: 5.5 Consensus size: 10
90205 AAATTTTGGC
*
90215 TTTTTTGGTT
1 TTTTTTTGTT
*
90225 TTTTTTT-TG
1 TTTTTTTGTT
*
90234 TTTTTTTGCT
1 TTTTTTTGTT
90244 TTTTTTTGTCT
1 TTTTTTTGT-T
90255 TTTTTTTGTT
1 TTTTTTTGTT
90265 TTTTT
1 TTTTT
90270 GAAAAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
9 8 0.21
10 20 0.53
11 10 0.26
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:90232 original size:12 final size:11
Alignment explanation
Indices: 90215--90269 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
90205 AAATTTTGGC
*
90215 TTTTTTGGTTT
1 TTTTTTTGTTT
90226 TTTTTTTG---
1 TTTTTTTGTTT
*
90234 TTTTTTTG-CT
1 TTTTTTTGTTT
*
90244 TTTTTTTGTCT
1 TTTTTTTGTTT
90255 TTTTTTTGTTT
1 TTTTTTTGTTT
90266 TTTT
1 TTTT
90270 GAAAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 8 0.21
10 8 0.21
11 23 0.59
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:90238 original size:20 final size:20
Alignment explanation
Indices: 90215--90269 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
90205 AAATTTTGGC
* *
90215 TTTTTTGGTTTTTTTTTTGT
1 TTTTTTGGTTTTTTTTGTCT
*
90235 TTTTTTGCTTTTTTTTGTCT
1 TTTTTTGGTTTTTTTTGTCT
*
90255 TTTTTTTGTTTTTTT
1 TTTTTTGGTTTTTTT
90270 GAAAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (20 bp):
TTTTTTGGTTTTTTTTGTCT
Found at i:90247 original size:29 final size:29
Alignment explanation
Indices: 90215--90270 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
90205 AAATTTTGGC
*
90215 TTTTTTGGTTTTTTTTTTGTTTTTTTGCT
1 TTTTTTGGTCTTTTTTTTGTTTTTTTGCT
*
90244 TTTTTTTGTCTTTTTTTTGTTTTTTTG
1 TTTTTTGGTCTTTTTTTTGTTTTTTTG
90271 AAAAAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (29 bp):
TTTTTTGGTCTTTTTTTTGTTTTTTTGCT
Found at i:93640 original size:20 final size:19
Alignment explanation
Indices: 93598--93642 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
93588 CGAAGAGCAT
* * *
93598 GTATTTTCATTTATGTCAT
1 GTATTTTCATTAAAGTCAA
93617 GTATTTTCATTAAAAGTCAA
1 GTATTTTCATT-AAAGTCAA
93637 GTATTT
1 GTATTT
93643 CAAAGGGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (19 bp):
GTATTTTCATTAAAGTCAA
Found at i:99950 original size:17 final size:17
Alignment explanation
Indices: 99930--99982 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
99920 TTAATAAAGT
99930 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
99947 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
99964 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
99981 TA
1 TA
99983 ACTCTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:102856 original size:17 final size:17
Alignment explanation
Indices: 102836--102868 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
102826 TTAATAAATT
102836 TAGTTC-ATTAATTAAAA
1 TAGTTCAATT-ATTAAAA
102853 TAGTTCAATTATTAAA
1 TAGTTCAATTATTAAA
102869 CTAAATCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCAATTATTAAAA
Found at i:108116 original size:17 final size:17
Alignment explanation
Indices: 108053--108116 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
108043 TGTTAGTGAG
* * *
108053 ATTAATGCACTAGCTTA
1 ATTAATGAACTAACTTT
* *
108070 ATAAATGAACT-AGTTT
1 ATTAATGAACTAACTTT
108086 GATTAATGAACTAACTTT
1 -ATTAATGAACTAACTTT
108104 ATTAATGAACTAA
1 ATTAATGAACTAA
108117 ATGCATGAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 2 0.05
17 32 0.84
18 4 0.11
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (17 bp):
ATTAATGAACTAACTTT
Found at i:110051 original size:23 final size:23
Alignment explanation
Indices: 110025--110077 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
110015 AAAATCAGAA
* *
110025 AAGAAATTGAAGAACTCCAAAAG
1 AAGAAATTCAAGAACTCAAAAAG
* *
110048 AAGAAAATTCCAGCACTCAAAAAG
1 AAG-AAATTCAAGAACTCAAAAAG
110072 AAGAAA
1 AAGAAA
110078 AAGCAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.11
Consensus pattern (23 bp):
AAGAAATTCAAGAACTCAAAAAG
Found at i:110084 original size:16 final size:16
Alignment explanation
Indices: 110072--110103 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
110062 ACTCAAAAAG
110072 AAGAAAAAGCAAAGAA
1 AAGAAAAAGCAAAGAA
110088 AAGAAAAAG-AAAGAA
1 AAGAAAAAGCAAAGAA
110103 A
1 A
110104 GTTGAAGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGCAAAGAA
Found at i:110104 original size:19 final size:19
Alignment explanation
Indices: 110067--110104 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
110057 CCAGCACTCA
*
110067 AAAAGAAGAAAAAGCAAAG
1 AAAAGAAAAAAAAGCAAAG
110086 AAAAGAAAAAGAAAG-AAAG
1 AAAAGAAAAA-AAAGCAAAG
110105 TTGAAGCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAAAGCAAAG
Done.