Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008440.1 Hibiscus syriacus cultivar Beakdansim tig00111239_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: 518054
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:465943 original size:6 final size:6
Alignment explanation
Indices: 465934--465959 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
465924 TTTGTTTTTT
465934 TTGAAA TTGAAA TTGAAA TTGAAA TT
1 TTGAAA TTGAAA TTGAAA TTGAAA TT
465960 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (6 bp):
TTGAAA
Found at i:466012 original size:15 final size:16
Alignment explanation
Indices: 465980--466021 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
465970 CAATTATTTA
*
465980 ATATTATTTTAATTAAT
1 ATATTATTTCAA-TAAT
465997 ATATTATTTCAA-AAT
1 ATATTATTTCAATAAT
466012 ATAATTATTT
1 AT-ATTATTT
466022 ATAAAATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 7 0.30
17 11 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTATTTCAATAAT
Found at i:471108 original size:12 final size:12
Alignment explanation
Indices: 471091--471115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
471081 GATCATAAGA
471091 GATAAAATATAT
1 GATAAAATATAT
471103 GATAAAATATAT
1 GATAAAATATAT
471115 G
1 G
471116 TGAAAGTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (12 bp):
GATAAAATATAT
Found at i:477695 original size:42 final size:42
Alignment explanation
Indices: 477636--477728 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
477626 AGTTGTTAGA
*
477636 GCTTCAGAACTCTCTGGTTCTTGTTCATCATATGCTGGTTTT
1 GCTTCAGAACTCTCTGGTTCTTGTTCATCATATGCTGGTTCT
* *
477678 GCTTCAGAGCTCTCTGGTTCTTGTTCATCATGTGCTGGTTCT
1 GCTTCAGAACTCTCTGGTTCTTGTTCATCATATGCTGGTTCT
477720 GCTTCAGAA
1 GCTTCAGAA
477729 TAATCTCCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (42 bp):
GCTTCAGAACTCTCTGGTTCTTGTTCATCATATGCTGGTTCT
Found at i:477725 original size:21 final size:21
Alignment explanation
Indices: 477649--477719 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
477639 TCAGAACTCT
*
477649 CTGGTTCTTGTTCATCATATG
1 CTGGTTCTTGTTCATCATGTG
* *
477670 CTGGTT-TTGCTTCA-GA-GCTCT
1 CTGGTTCTTG-TTCATCATG-T-G
477691 CTGGTTCTTGTTCATCATGTG
1 CTGGTTCTTGTTCATCATGTG
477712 CTGGTTCT
1 CTGGTTCT
477720 GCTTCAGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
20 5 0.13
21 28 0.72
22 5 0.13
23 1 0.03
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (21 bp):
CTGGTTCTTGTTCATCATGTG
Found at i:480713 original size:73 final size:72
Alignment explanation
Indices: 480595--480741 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 72
480585 AATCCCTCTT
480595 CTCCATTTTGGTTTATTTCTCATTTGGTTTAGTAATAAATATAGCAATCACAAATGCTTCCTTCA
1 CTCCATTTTGGTTTATTTCTCATTTGGTTTAGTAATAAATATAGCAATCACAAATGCTTCCTTCA
480660 TTCCTTC
66 TTCCTTC
480667 CTCCATTTTTGGTTTATTTCTCATTTGGTTTAGTAATAAATATAGCAATCACAAATGCTTCCTTC
1 CTCCA-TTTTGGTTTATTTCTCATTTGGTTTAGTAATAAATATAGCAATCACAAATGCTTCCTTC
480732 ATTCCTTC
65 ATTCCTTC
480740 CT
1 CT
480742 TCTAGACAGT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 5 0.07
73 69 0.93
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (72 bp):
CTCCATTTTGGTTTATTTCTCATTTGGTTTAGTAATAAATATAGCAATCACAAATGCTTCCTTCA
TTCCTTC
Found at i:486295 original size:24 final size:23
Alignment explanation
Indices: 486245--486296 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
486235 TTTTCACTCT
*
486245 TAAAATTTTATACGTTATTCTCC
1 TAAAATTTTATACGTTATTCACC
*
486268 TAAAATTTTATTA-GTTAATTCACG
1 TAAAATTTTA-TACGTT-ATTCACC
486292 TAAAA
1 TAAAA
486297 CCACCCAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (23 bp):
TAAAATTTTATACGTTATTCACC
Found at i:486518 original size:17 final size:17
Alignment explanation
Indices: 486496--486533 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
486486 AGCGTCTTAC
*
486496 TAAAGACGTCAGATAAT
1 TAAAGACGCCAGATAAT
*
486513 TAAAGACGCCATATAAT
1 TAAAGACGCCAGATAAT
486530 TAAA
1 TAAA
486534 ATCAACTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (17 bp):
TAAAGACGCCAGATAAT
Found at i:492076 original size:20 final size:20
Alignment explanation
Indices: 492034--492078 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
492024 ATGTAGTTGG
* * *
492034 TGCATTCATACATGCATGTA
1 TGCATGCATACATACATGCA
*
492054 TGCATGCATACATACTTGCA
1 TGCATGCATACATACATGCA
492074 TGCAT
1 TGCAT
492079 ACTTTAATAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (20 bp):
TGCATGCATACATACATGCA
Found at i:492507 original size:43 final size:43
Alignment explanation
Indices: 492446--492544 Score: 180
Period size: 43 Copynumber: 2.3 Consensus size: 43
492436 AGAGCAGCTC
492446 GAGTTTGACTCGATCAACGTTCGACTCGAGCTAATTTGAATTT
1 GAGTTTGACTCGATCAACGTTCGACTCGAGCTAATTTGAATTT
* *
492489 GAGTTTGACTCGATCAACGTTCGACTCGAGGTGATTTGAATTT
1 GAGTTTGACTCGATCAACGTTCGACTCGAGCTAATTTGAATTT
492532 GAGTTTGACTCGA
1 GAGTTTGACTCGA
492545 GACCTTAACG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (43 bp):
GAGTTTGACTCGATCAACGTTCGACTCGAGCTAATTTGAATTT
Found at i:501861 original size:13 final size:13
Alignment explanation
Indices: 501843--501962 Score: 52
Period size: 13 Copynumber: 8.8 Consensus size: 13
501833 GAAAAAAATT
501843 TAATATATATATA
1 TAATATATATATA
501856 TAATATAAGTTTATATA
1 TAATAT-A---TATATA
501873 TAA-ACTATATATA
1 TAATA-TATATATA
*
501886 TAA-ACTATATTTA
1 TAATA-TATATATA
* *
501899 TATTATAAACTATA
1 TAATATATA-TATA
501913 TAAT-TAT-TATA
1 TAATATATATATA
*
501924 -AGTTATATATATA
1 TA-ATATATATATA
* * *
501937 TATTATGTTTATA
1 TAATATATATATA
501950 TGAACTATATATA
1 T-AA-TATATATA
501963 ACCTATATAT
Statistics
Matches: 82, Mismatches: 12, Indels: 24
0.69 0.10 0.20
Matches are distributed among these distances:
10 1 0.01
11 5 0.06
12 3 0.04
13 45 0.55
14 10 0.12
15 6 0.07
16 2 0.02
17 10 0.12
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (13 bp):
TAATATATATATA
Found at i:501884 original size:30 final size:30
Alignment explanation
Indices: 501848--501936 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 30
501838 AAATTTAATA
501848 TATATATATAATATAAGTTTATATATAAAC
1 TATATATATAATATAAGTTTATATATAAAC
501878 TATATATATAA-ACTATA-TTTATATTATAAAC
1 TATATATATAATA-TA-AGTTTATA-TATAAAC
*
501909 TATATA-ATTATTATAAGTTATATATATA
1 TATATATA-TAATATAAGTT-TATATATA
501937 TATTATGTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
29 1 0.02
30 21 0.41
31 24 0.47
32 5 0.10
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (30 bp):
TATATATATAATATAAGTTTATATATAAAC
Found at i:501914 original size:20 final size:20
Alignment explanation
Indices: 501878--501942 Score: 77
Period size: 18 Copynumber: 3.5 Consensus size: 20
501868 ATATATAAAC
501878 TATATA-TATAAACTATAT-
1 TATATATTATAAACTATATA
501896 T-TATATTATAAACTATATA
1 TATATATTATAAACTATATA
**
501915 -AT-TATTATAAGTTATATA
1 TATATATTATAAACTATATA
501933 TATATATTAT
1 TATATATTAT
501943 GTTTATATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.10
18 27 0.68
19 3 0.08
20 6 0.15
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (20 bp):
TATATATTATAAACTATATA
Found at i:502184 original size:19 final size:19
Alignment explanation
Indices: 502149--502232 Score: 84
Period size: 20 Copynumber: 4.5 Consensus size: 19
502139 TTGAGAAATT
*
502149 TTGAGAATATAGA--GAAA
1 TTGAGAATTTAGAGGGAAA
502166 TTGAGAATTTAGAGGGAAA
1 TTGAGAATTTAGAGGGAAA
*
502185 TTGGAAAATTTAGAGGG-AA
1 TT-GAGAATTTAGAGGGAAA
* * *
502204 TAGAAAATTTTGGAGGGAAA
1 TTGAGAA-TTTAGAGGGAAA
502224 TTGAGAATT
1 TTGAGAATT
502233 GAGATTTTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
17 12 0.21
18 5 0.09
19 19 0.34
20 20 0.36
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (19 bp):
TTGAGAATTTAGAGGGAAA
Found at i:502196 original size:20 final size:20
Alignment explanation
Indices: 502162--502226 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
502152 AGAATATAGA
*
502162 GAAATT-GAGAATTTAGAGG
1 GAAATTGGAAAATTTAGAGG
502181 GAAATTGGAAAATTTAGAGG
1 GAAATTGGAAAATTTAGAGG
* *
502201 G-AA-TAGAAAATTTTGGAGG
1 GAAATTGGAAAA-TTTAGAGG
502220 GAAATTG
1 GAAATTG
502227 AGAATTGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
18 6 0.16
19 16 0.42
20 15 0.39
21 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.26
Consensus pattern (20 bp):
GAAATTGGAAAATTTAGAGG
Found at i:502207 original size:46 final size:45
Alignment explanation
Indices: 502124--502212 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 45
502114 TTTTATTTGG
*
502124 GAATTTAGAGGGAAATTGAGAAATTTTGAGAATATAGAGAAATTGA
1 GAATTTAGAGGGAAATTGAGAAATTTAGAGAATATAGA-AAATTGA
*
502170 GAATTTAGAGGGAAATTG-GAAAATTTAGAGGGA-ATAGAAAATT
1 GAATTTAGAGGGAAATTGAG-AAATTTAGA-GAATATAGAAAATT
502213 TTGGAGGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 6 0.15
46 31 0.79
47 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (45 bp):
GAATTTAGAGGGAAATTGAGAAATTTAGAGAATATAGAAAATTGA
Found at i:502401 original size:10 final size:11
Alignment explanation
Indices: 502377--502455 Score: 64
Period size: 10 Copynumber: 7.6 Consensus size: 11
502367 ATATAAACTT
502377 TATATAGTATA
1 TATATAGTATA
*
502388 TATAT-GTATG
1 TATATAGTATA
*
502398 TATA-ATTA-A
1 TATATAGTATA
502407 TATA-AGTA-A
1 TATATAGTATA
*
502416 TCTATAGATTATA
1 TATATAG--TATA
502429 TATATA-TATA
1 TATATAGTATA
502439 TATATA-TATA
1 TATATAGTATA
502449 TATATAG
1 TATATAG
502456 AAACACTATG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
9 11 0.20
10 32 0.57
11 5 0.09
12 2 0.04
13 6 0.11
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.46
Consensus pattern (11 bp):
TATATAGTATA
Found at i:502432 original size:2 final size:2
Alignment explanation
Indices: 502425--502454 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
502415 ATCTATAGAT
502425 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
502455 GAAACACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:502631 original size:24 final size:24
Alignment explanation
Indices: 502583--502631 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
502573 CTTATAGTAC
* *
502583 ATGTATGTATAAACCATATATAGT
1 ATGTATATATAAACCATATAAAGT
*
502607 ATGTATATATAAACTATATAAAGT
1 ATGTATATATAAACCATATAAAGT
502631 A
1 A
502632 AATTACTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (24 bp):
ATGTATATATAAACCATATAAAGT
Found at i:502753 original size:14 final size:15
Alignment explanation
Indices: 502736--502768 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
502726 CCCTAAATCC
502736 TAAACT-TTAAACCA
1 TAAACTGTTAAACCA
502750 TAAA-TGTTAAACCA
1 TAAACTGTTAAACCA
502764 TAAAC
1 TAAAC
502769 CCTAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.06
14 16 0.94
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.27
Consensus pattern (15 bp):
TAAACTGTTAAACCA
Found at i:503131 original size:20 final size:19
Alignment explanation
Indices: 503099--503157 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 19
503089 ATTTCATATA
*
503099 ATAT-GTATGTATAAACCAT
1 ATATAGTATATATAAACC-T
*
503118 GTATAGTATATATAAA-CT
1 ATATAGTATATATAAACCT
503136 ATATA-TATATATAAA-CT
1 ATATAGTATATATAAACCT
503153 ATATA
1 ATATA
503158 AAGTAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 17 0.47
18 5 0.14
19 4 0.11
20 10 0.28
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (19 bp):
ATATAGTATATATAAACCT
Found at i:503138 original size:9 final size:9
Alignment explanation
Indices: 503126--503159 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
503116 ATGTATAGTA
503126 TATATAAAC
1 TATATAAAC
*
503135 TATATATA-
1 TATATAAAC
503143 TATATAAAC
1 TATATAAAC
503152 TATATAAA
1 TATATAAA
503160 GTAAATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (9 bp):
TATATAAAC
Found at i:503146 original size:17 final size:18
Alignment explanation
Indices: 503119--503157 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
503109 ATAAACCATG
503119 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
503137 TATA-TATATATAAACTA
1 TATAGTATATATAAACTA
503154 TATA
1 TATA
503158 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:503247 original size:7 final size:7
Alignment explanation
Indices: 503237--503288 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
503227 ATAGAATCCT
*
503237 TAAACTC
1 TAAACCC
503244 TAAACCC
1 TAAACCC
* *
503251 TAAATCA
1 TAAACCC
*
503258 TAAACCT
1 TAAACCC
**
503265 TAAACTT
1 TAAACCC
503272 TAAACCC
1 TAAACCC
503279 TAAACCC
1 TAAACCC
503286 TAA
1 TAA
503289 TATATGTATT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAACCC
Found at i:503310 original size:17 final size:16
Alignment explanation
Indices: 503288--503327 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
503278 CTAAACCCTA
503288 ATATATGTATTACATGC
1 ATATATGTA-TACATGC
*
503305 ATATATGTATATATGC
1 ATATATGTATACATGC
503321 ATA-ATGT
1 ATATATGT
503328 GTGTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 9 0.41
17 9 0.41
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (16 bp):
ATATATGTATACATGC
Found at i:503551 original size:23 final size:23
Alignment explanation
Indices: 503519--503572 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
503509 TATATTGATG
*
503519 TGTATG-ATATATGCATATATTA
1 TGTATGTATATATGCATATATGA
* *
503541 TGTATGTATATATGTATGTATGA
1 TGTATGTATATATGCATATATGA
*
503564 TGCATGTAT
1 TGTATGTAT
503573 TAAAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (23 bp):
TGTATGTATATATGCATATATGA
Found at i:504912 original size:32 final size:33
Alignment explanation
Indices: 504868--504934 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
504858 AAAGTATAAC
*
504868 ATATATAATATAAAGTA-ATAAAGTGTTGTTTA
1 ATATATAATATAAAGTATATAAAGTGTTGGTTA
504900 ATATA-AAGTATAAAGTATATAAAGTGTTGGTTA
1 ATATATAA-TATAAAGTATATAAAGTGTTGGTTA
504933 AT
1 AT
504935 TTATTCAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 2 0.06
32 14 0.44
33 16 0.50
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (33 bp):
ATATATAATATAAAGTATATAAAGTGTTGGTTA
Found at i:505038 original size:22 final size:22
Alignment explanation
Indices: 505013--505131 Score: 111
Period size: 22 Copynumber: 5.5 Consensus size: 22
505003 ATATATTATA
* *
505013 AAGTAATAAAGTGTT-TGAATAT
1 AAGTATTAAAGT-TTATAAATAT
505035 AAGTATTAAAGTTTATAAATAT
1 AAGTATTAAAGTTTATAAATAT
* *
505057 AAGTATTAAA-TATAAAATATAT
1 AAGTATTAAAGTTTATAA-ATAT
* *
505079 AAGTACTAAAGTATAT-AATAT
1 AAGTATTAAAGTTTATAAATAT
* *
505100 AAAGTATTAAACTATAT-AATAT
1 -AAGTATTAAAGTTTATAAATAT
505122 AAGTATTAAA
1 AAGTATTAAA
505132 TATAAAGTAT
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
21 21 0.25
22 60 0.71
23 4 0.05
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (22 bp):
AAGTATTAAAGTTTATAAATAT
Found at i:505061 original size:44 final size:42
Alignment explanation
Indices: 504984--505188 Score: 156
Period size: 44 Copynumber: 4.8 Consensus size: 42
504974 TTTGGTACTT
* * *
504984 TATAT-ATA-AAGTA-TAAAATATATATTATAAAGTAATAAA
1 TATATAATATAAGTATTAAAGTATATAATATAAAGTATTAAA
* * *
505023 GTGTTTGAATATAAGTATTAAAGTTTATAA-ATATAAGTATTAAA
1 -TATAT-AATATAAGTATTAAAGTATATAATATA-AAGTATTAAA
* *
505067 TATAAAATATATAAGTACTAAAGTATATAATATAAAGTATTAAA
1 TAT-ATA-ATATAAGTATTAAAGTATATAATATAAAGTATTAAA
505111 CTATATAATATAAGTATTAAA-TATA-AAGTATTAAAGTATATAAA
1 -TATATAATATAAGTATTAAAGTATATAA-TA-TAAAGTAT-TAAA
* *
505155 TATA-AGTATTAATTA-TAAAGTATATTAATTATAA
1 TATATAATA-TAAGTATTAAAGTATA-TAA-TATAA
505189 TAATTAATAT
Statistics
Matches: 133, Mismatches: 16, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
40 3 0.02
41 2 0.02
42 16 0.12
43 45 0.34
44 57 0.43
45 10 0.08
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (42 bp):
TATATAATATAAGTATTAAAGTATATAATATAAAGTATTAAA
Found at i:505068 original size:65 final size:65
Alignment explanation
Indices: 504980--505158 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 65
504970 TTAATTTGGT
* * * * * *
504980 ACTTTATATATA-AAGTATAAAATATATATTATAAAGTAATAAAGTGTTTGAATAT-AAGTATTA
1 ACTTTATAAATATAAGTATTAAATATAAAATATAAAGTAATAAAGTATAT-AATATAAAGTATTA
505043 A
65 A
* *
505044 AGTTTATAAATATAAGTATTAAATATAAAATATATAAGTACTAAAGTATATAATATAAAGTATTA
1 ACTTTATAAATATAAGTATTAAATATAAAATATA-AAGTAATAAAGTATATAATATAAAGTATTA
505109 A
65 A
* *
505110 ACTATAT-AATATAAGTATTAAATATAAAGTATTAAAGTATATAAA-TATA
1 ACTTTATAAATATAAGTATTAAATATAAAATA-TAAAGTA-ATAAAGTATA
505159 AGTATTAATT
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
64 10 0.10
65 55 0.56
66 33 0.34
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (65 bp):
ACTTTATAAATATAAGTATTAAATATAAAATATAAAGTAATAAAGTATATAATATAAAGTATTAA
Found at i:505164 original size:36 final size:36
Alignment explanation
Indices: 505069--505177 Score: 141
Period size: 36 Copynumber: 3.0 Consensus size: 36
505059 GTATTAAATA
*
505069 TAAAATATATAAGTACTAAAGTA-TATAATATAAAGTAT
1 TAAAATATATAAATA-T-AAGTATTA-AATATAAAGTAT
*
505107 TAAACTATAT-AATATAAGTATTAAATATAAAGTAT
1 TAAAATATATAAATATAAGTATTAAATATAAAGTAT
* *
505142 TAAAGTATATAAATATAAGTATTAATTATAAAGTAT
1 TAAAATATATAAATATAAGTATTAAATATAAAGTAT
505178 ATTAATTATA
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
35 26 0.40
36 27 0.42
37 3 0.05
38 9 0.14
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (36 bp):
TAAAATATATAAATATAAGTATTAAATATAAAGTAT
Found at i:505195 original size:29 final size:30
Alignment explanation
Indices: 505142--505214 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
505132 TATAAAGTAT
*
505142 TAAAGTATA-TAAATATAAGTATTAAT-TA
1 TAAAGTATATTAATTATAAGTATTAATATA
505170 TAAAGTATATTAATTATAA-TAATTAATATA
1 TAAAGTATATTAATTATAAGT-ATTAATATA
*
505200 TAAA-TATATTTATTA
1 TAAAGTATATTAATTA
505215 ATTTAATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 10 0.25
29 24 0.60
30 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (30 bp):
TAAAGTATATTAATTATAAGTATTAATATA
Found at i:505426 original size:16 final size:16
Alignment explanation
Indices: 505386--505443 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
505376 TATCAGATCA
* *
505386 ATAACAAGTC-GGATC
1 ATAACAGGTCAGGTTC
505401 ATATACAGGTCAGGTTC
1 ATA-ACAGGTCAGGTTC
*
505418 ATAACAGGTCAGGTTG
1 ATAACAGGTCAGGTTC
*
505434 AAAACAGGTC
1 ATAACAGGTC
505444 GGGTAATACC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 3 0.08
16 27 0.73
17 7 0.19
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.22
Consensus pattern (16 bp):
ATAACAGGTCAGGTTC
Done.