Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000822.1 Hibiscus syriacus cultivar Beakdansim tig00001590_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: 57122
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Found at i:3926 original size:39 final size:39
Alignment explanation
Indices: 3843--3919 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
3833 TATGGTAAAG
** * * *
3843 ACTTACCCTGTGCACAAAGTAGAGGAGCCTGCGGTAAGA
1 ACTTACCCTGAACACAAAGTAAAAGAGCCTGCGATAAGA
3882 ACTTACCCTGAACACAAAGTAAAAGAGCCTGCGATAAG
1 ACTTACCCTGAACACAAAGTAAAAGAGCCTGCGATAAG
3920 GTCTTACAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.17
Consensus pattern (39 bp):
ACTTACCCTGAACACAAAGTAAAAGAGCCTGCGATAAGA
Found at i:8004 original size:57 final size:57
Alignment explanation
Indices: 7919--8028 Score: 184
Period size: 57 Copynumber: 1.9 Consensus size: 57
7909 ATCAAATCAT
*
7919 TCAAATGTTGAGTGCTATAACTGCGGCAAGCATGGGCACTATGCAAAAGAGTGCAAA
1 TCAAATGTCGAGTGCTATAACTGCGGCAAGCATGGGCACTATGCAAAAGAGTGCAAA
* * *
7976 TCAAATGTCGAGTGCTATAATTGTGGCAAGCATGGGCACTATGCAAAGGAGTG
1 TCAAATGTCGAGTGCTATAACTGCGGCAAGCATGGGCACTATGCAAAAGAGTG
8029 TTATTCCGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (57 bp):
TCAAATGTCGAGTGCTATAACTGCGGCAAGCATGGGCACTATGCAAAAGAGTGCAAA
Found at i:20571 original size:56 final size:56
Alignment explanation
Indices: 20485--20596 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
20475 ACAATCCTAC
20485 GGATTTATGTGCCTCATCAAAAACTTCCCTAAACCTATTTGGAGGAAAAAAAGTAT
1 GGATTTATGTGCCTCATCAAAAACTTCCCTAAACCTATTTGGAGGAAAAAAAGTAT
20541 GGATTTATGTGCCTCATCAAAAACTTCCCTAAACCTATTTGGAGGAAAAAAAGTAT
1 GGATTTATGTGCCTCATCAAAAACTTCCCTAAACCTATTTGGAGGAAAAAAAGTAT
20597 AACACAACTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (56 bp):
GGATTTATGTGCCTCATCAAAAACTTCCCTAAACCTATTTGGAGGAAAAAAAGTAT
Found at i:30240 original size:6 final size:6
Alignment explanation
Indices: 30229--30352 Score: 194
Period size: 6 Copynumber: 20.3 Consensus size: 6
30219 GTCCACATGA
* * * *
30229 ATACAT ATACATAT ATATAT ATACGT ATACAT ATACGT ATACGT ATACAT
1 ATACAT ATAC--AT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30279 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30327 ATACAT ATACAT ATACAT ATACAT AT
1 ATACAT ATACAT ATACAT ATACAT AT
30353 TATTAGCATA
Statistics
Matches: 110, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
6 105 0.95
8 5 0.05
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (6 bp):
ATACAT
Found at i:33879 original size:6 final size:6
Alignment explanation
Indices: 33868--35717 Score: 3465
Period size: 6 Copynumber: 310.7 Consensus size: 6
33858 GCATTCTATC
33868 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
33916 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
33964 ACATAT ACATAT ACATATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT AC--ATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34014 ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34060 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34106 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34154 ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34200 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34248 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34296 ACATAT AC--AT ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
*
34340 ACATAT GCATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34388 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34436 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34484 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34532 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34580 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34628 ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34674 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34722 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34770 ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34816 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34864 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34912 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
34960 ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35006 ACATAT ACATAT AC--AT ACATAT AC--AT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35050 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35098 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35146 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35194 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35242 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT AC--ATAT
35292 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT AC--ATAT
35342 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35390 ACATAT ACATAT ACATAT ACATATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT AC--ATAT ACATAT ACATAT ACATAT ACATAT
35440 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35488 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35536 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35582 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35630 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35678 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACAT
35718 TCTAATTTTA
Statistics
Matches: 1812, Mismatches: 2, Indels: 60
0.97 0.00 0.03
Matches are distributed among these distances:
4 44 0.02
6 1744 0.96
8 24 0.01
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:38238 original size:3 final size:3
Alignment explanation
Indices: 38230--38314 Score: 127
Period size: 3 Copynumber: 28.7 Consensus size: 3
38220 TCCGGGTTTA
38230 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
38277 TAT TAT TAC TAA TAC TAT TAT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
38315 CATTTGCAGG
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:44480 original size:30 final size:29
Alignment explanation
Indices: 44440--44558 Score: 118
Period size: 30 Copynumber: 4.1 Consensus size: 29
44430 ACTCATCTAT
*
44440 AAAAAAAGAAAGAAAAGAGAGAAAAAAAG
1 AAAAGAAGAAAGAAAAGAGAGAAAAAAAG
* * *
44469 AAAAGAGAGAAAAAAAAGAAAGAAAAGAA-
1 AAAAGA-AGAAAGAAAAGAGAGAAAAAAAG
* *
44498 AAAAGAAAAAAGAAAAAAGA-AAAAAAAG
1 AAAAGAAGAAAGAAAAGAGAGAAAAAAAG
* *
44526 AAAAGAAAAGAAA-AAAAGATATAAAAAAAG
1 AAAAG--AAGAAAGAAAAGAGAGAAAAAAAG
44556 AAA
1 AAA
44559 TTGAATCAAG
Statistics
Matches: 73, Mismatches: 12, Indels: 9
0.78 0.13 0.10
Matches are distributed among these distances:
27 6 0.08
28 15 0.21
29 17 0.23
30 35 0.48
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (29 bp):
AAAAGAAGAAAGAAAAGAGAGAAAAAAAG
Found at i:44485 original size:39 final size:38
Alignment explanation
Indices: 44440--44540 Score: 141
Period size: 39 Copynumber: 2.6 Consensus size: 38
44430 ACTCATCTAT
* *
44440 AAAAAAAGAAAGAAAAGAGAGA-AAAAAAGAAAAGAGAGA
1 AAAAAAAGAAAGAAAAGAAAAAGAAAAAAGAAAA-A-AGA
44479 AAAAAAAGAAAGAAAAGAAAAAAGAAAAAAGAAAAAAGA
1 AAAAAAAGAAAGAAAAG-AAAAAGAAAAAAGAAAAAAGA
44518 AAAAAAAGAAAAGAAAAGAAAAA
1 AAAAAAAG-AAAGAAAAGAAAAA
44541 AAGATATAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
39 33 0.58
40 13 0.23
41 11 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (38 bp):
AAAAAAAGAAAGAAAAGAAAAAGAAAAAAGAAAAAAGA
Found at i:44498 original size:35 final size:34
Alignment explanation
Indices: 44441--44558 Score: 116
Period size: 35 Copynumber: 3.4 Consensus size: 34
44431 CTCATCTATA
*
44441 AAAAAAGAAAGAAA-AGAGAGAAAAAAAGAAAAGAG
1 AAAAAA-AAAGAAAGA-AAAGAAAAAAAGAAAAGAG
*
44476 AGAAAAAAAAGAAAGAAAAG-AAAAAAGAAAAAAG
1 A-AAAAAAAAGAAAGAAAAGAAAAAAAGAAAAGAG
* *
44510 AAAAAAGAAAAAAAAGAAAAGAAAAGAAA-AAAAGAT
1 -AAAAA-AAAAGAAAGAAAAGAAAA-AAAGAAAAGAG
*
44546 ATAAAAAAAGAAA
1 AAAAAAAAAGAAA
44559 TTGAATCAAG
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
34 24 0.34
35 29 0.41
36 14 0.20
37 3 0.04
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (34 bp):
AAAAAAAAAGAAAGAAAAGAAAAAAAGAAAAGAG
Found at i:44553 original size:39 final size:37
Alignment explanation
Indices: 44440--44558 Score: 132
Period size: 39 Copynumber: 3.1 Consensus size: 37
44430 ACTCATCTAT
* *
44440 AAAAAAAGAAAGAAAAGAGAGAAAAA-AAGAAAAGAGAGA
1 AAAAAAAGAAAGAAAAGA-A-AAAAAGAA-AAAAAAAAGA
*
44479 AAAAAAAGAAAGAAAAGAAAAAAGAAAAAAGAAAAAAGA
1 AAAAAAAGAAAGAAAAGAAAAAA-AGAAAA-AAAAAAGA
*
44518 AAAAAAAGAAAAGAAAAGAAAAAAAGATATAAAAAAAGA
1 AAAAAAAG-AAAGAAAAGAAAAAAAGA-AAAAAAAAAGA
44557 AA
1 AA
44559 TTGAATCAAG
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
37 4 0.06
38 4 0.06
39 46 0.65
40 17 0.24
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (37 bp):
AAAAAAAGAAAGAAAAGAAAAAAAGAAAAAAAAAAGA
Found at i:46123 original size:52 final size:53
Alignment explanation
Indices: 46064--46198 Score: 177
Period size: 52 Copynumber: 2.6 Consensus size: 53
46054 TATCCATGTA
* *
46064 GGTATCTTGAAGGCTCACATCATCATGAAAAAA-ATAGAAGTAATCCATATGG
1 GGTATCTTGAAGGCTCACATCAGCATGAAAAAATACAGAAGTAATCCATATGG
* * * *
46116 GGTATCTTGAGGGTTCACATCAGCAT-AAAAAATACATAAGTAATCCATGTGG
1 GGTATCTTGAAGGCTCACATCAGCATGAAAAAATACAGAAGTAATCCATATGG
*
46168 GGCATCTTGAAGGCTCAC-TCCAGCATGAAAA
1 GGTATCTTGAAGGCTCACAT-CAGCATGAAAA
46199 TGTTGGAATA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
51 7 0.10
52 60 0.85
53 4 0.06
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (53 bp):
GGTATCTTGAAGGCTCACATCAGCATGAAAAAATACAGAAGTAATCCATATGG
Found at i:48372 original size:32 final size:33
Alignment explanation
Indices: 48295--48380 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
48285 AAAAGATTGG
* * *
48295 ATTTCAACTTCACAACGAAGGATATCCAACTCAA
1 ATTTCAACTTCACGACGAAGGA-AGCCAACCCAA
*
48329 AGTTCAACTTCACGACGAAGG-AGCC-ACCCACA
1 ATTTCAACTTCACGACGAAGGAAGCCAACCCA-A
*
48361 ATTTCAACTTCACGAAGAAG
1 ATTTCAACTTCACGACGAAG
48381 ACTATTGTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 4 0.09
32 22 0.49
34 19 0.42
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (33 bp):
ATTTCAACTTCACGACGAAGGAAGCCAACCCAA
Found at i:48496 original size:46 final size:44
Alignment explanation
Indices: 48423--48905 Score: 225
Period size: 46 Copynumber: 11.1 Consensus size: 44
48413 TAACAATTTG
* *
48423 TCACTCTAGATAA-CTAATCGTCCTCATCACGTAGGAACCGTGTTA
1 TCAC-CTAGATAACCTGA-CGTCCTCATCACGTAGGAACCGTGTCA
48468 TCACCTATAGATAACCTGACGTCCTCATCACGTAGGAACCGTGTCA
1 TCACC--TAGATAACCTGACGTCCTCATCACGTAGGAACCGTGTCA
* * * * * *
48514 TCA-CT---CAACCTGGCCTCTTCATCACGTAGGAGCTGTGTCA
1 TCACCTAGATAACCTGACGTCCTCATCACGTAGGAACCGTGTCA
* * * * *
48554 -AACCCAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCACCTAGATAACCTGACGTCCTCATCACGTAGGAACCGTGTCA
* * * * *
48597 TCACCTATAGATGACTTGATGTCCTCATCATGTAGGAACCTTGTCA
1 TCACC--TAGATAACCTGACGTCCTCATCACGTAGGAACCGTGTCA
* * * *
48643 TCA-CT---CAACCTGATC-TCCTCATCACGCAGGAGCCATGTCA
1 TCACCTAGATAACCTGA-CGTCCTCATCACGTAGGAACCGTGTCA
* * * * * *
48683 -AACCCAGAT-AGCTAACCGTCCTCATCACGTAGGAACCGTATTA
1 TCACCTAGATAACCTGA-CGTCCTCATCACGTAGGAACCGTGTCA
** * * *
48726 TCACCCTTAGAT-GGCTAGTCGTCCTCATCGCGTAGGTACCGTGTCA
1 TCA-CC-TAGATAACCT-GACGTCCTCATCACGTAGGAACCGTGTCA
* * ** *
48772 TCACC-CG---ACCTGATC-TCCTCATCAAGTAGGAGTCGTTTCA
1 TCACCTAGATAACCTGA-CGTCCTCATCACGTAGGAACCGTGTCA
* * * * * * *
48812 AC-CCCAGATAACC-AATCGTCCTCATCATGTAGGGACTGTGTTA
1 TCACCTAGATAACCTGA-CGTCCTCATCACGTAGGAACCGTGTCA
* ** * * *
48855 TCATCTATAGATGGCCTGCCGTCCTTATCACGTAGGAAACGTGTCA
1 TCA-C-CTAGATAACCTGACGTCCTCATCACGTAGGAACCGTGTCA
48901 TCACC
1 TCACC
48906 CGACTAGATT
Statistics
Matches: 318, Mismatches: 90, Indels: 61
0.68 0.19 0.13
Matches are distributed among these distances:
39 4 0.01
40 79 0.25
41 3 0.01
42 8 0.03
43 72 0.23
44 5 0.02
45 12 0.04
46 132 0.42
47 3 0.01
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (44 bp):
TCACCTAGATAACCTGACGTCCTCATCACGTAGGAACCGTGTCA
Found at i:48665 original size:129 final size:129
Alignment explanation
Indices: 48430--48904 Score: 587
Period size: 129 Copynumber: 3.7 Consensus size: 129
48420 TTGTCACTCT
* * *
48430 AGATAACTAATCGTCCTCATCACGTAGGAACCGTGTTATCACCTATAGATAACCTGACGTCCTCA
1 AGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGACCTGACGTCCTCA
** *
48495 TCACGTAGGAACCGTGTCATCACTCAACCTGGCCTCTTCATCACGTAGGAGCTGTGTCAAACCC
66 TCACGTAGGAACCGTGTCATCACTCAACCTGATCTCCTCATCACGTAGGAGCTGTGTCAAACCC
* * *
48559 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGACTTGATGTCCTCA
1 AGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGACCTGACGTCCTCA
* * * **
48624 TCATGTAGGAACCTTGTCATCACTCAACCTGATCTCCTCATCACGCAGGAGCCATGTCAAACCC
66 TCACGTAGGAACCGTGTCATCACTCAACCTGATCTCCTCATCACGTAGGAGCTGTGTCAAACCC
* * * * *
48688 AGATAGCTAACCGTCCTCATCACGTAGGAACCGTATTATCACCCT-TAGATG-GCTAGTCGTCCT
1 AGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCA-CCTATAGATGACCT-GACGTCCT
* * * * * * *
48751 CATCGCGTAGGTACCGTGTCATCACCCGACCTGATCTCCTCATCAAGTAGGAG-TCGTTTCAACC
64 CATCACGTAGGAACCGTGTCATCACTCAACCTGATCTCCTCATCACGTAGGAGCT-GTGTCAAAC
48815 CC
128 CC
* * * * * * * *
48817 AGATAACCAATCGTCCTCATCATGTAGGGACTGTGTTATCATCTATAGATGGCCTGCCGTCCTTA
1 AGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGACCTGACGTCCTCA
*
48882 TCACGTAGGAAACGTGTCATCAC
66 TCACGTAGGAACCGTGTCATCAC
48905 CCGACTAGAT
Statistics
Matches: 293, Mismatches: 48, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
128 3 0.01
129 285 0.97
130 5 0.02
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (129 bp):
AGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCACCTATAGATGACCTGACGTCCTCA
TCACGTAGGAACCGTGTCATCACTCAACCTGATCTCCTCATCACGTAGGAGCTGTGTCAAACCC
Found at i:49275 original size:3 final size:3
Alignment explanation
Indices: 49267--49349 Score: 130
Period size: 3 Copynumber: 27.7 Consensus size: 3
49257 TCTGGGTTTA
49267 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
49315 TAT TAC TAA TAA TAT TAT TAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
49350 CATTTGCAGG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:55198 original size:28 final size:28
Alignment explanation
Indices: 55167--55220 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
55157 ATAGAAACTT
**
55167 TTTTTGTTTTAACCGTTAACCGAACCAA
1 TTTTTGTTTTAACAATTAACCGAACCAA
* *
55195 TTTTTTTTTTAATAATTAACCGAACC
1 TTTTTGTTTTAACAATTAACCGAACC
55221 GAACAAAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (28 bp):
TTTTTGTTTTAACAATTAACCGAACCAA
Done.