Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007348.1 Hibiscus syriacus cultivar Beakdansim tig00019690_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: 75440
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:5768 original size:2 final size:2
Alignment explanation
Indices: 5761--5799 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5751 TGTTTAAAGC
5761 AT AT AT AT AT -T AT 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
5800 GAATGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:14801 original size:143 final size:144
Alignment explanation
Indices: 14645--14932 Score: 524
Period size: 144 Copynumber: 2.0 Consensus size: 144
14635 ATATATTTTT
* *
14645 AACAAAAACAATTCGTATATAAAATTATTATTAATGAATTATCTTAAAATA-TTTTTATATATTT
1 AACAAAAAAAATTCGTATATAAAATTATTATTAATGAATTATCTAAAAATATTTTTTATATATTT
14709 ATTATAGCTTTAATATCATATAACAAGATATTGGGATACTAAATTAACAAACTGTCAATTTAATT
66 ATTATAGCTTTAATATCATATAACAAGATATTGGGATACTAAATTAACAAACTGTCAATTTAATT
*
14774 TTTTTTAAATTCAC
131 TTTTTAAAATTCAC
*
14788 AACAAAAAAAATTCGTATATAAAATTATTATTAATGAATTATGTAAAAATATTTTTTATATATTT
1 AACAAAAAAAATTCGTATATAAAATTATTATTAATGAATTATCTAAAAATATTTTTTATATATTT
*
14853 ATTATAGTTTTAATATCATATAACAAGATATTGGGATACTAAATTAACAAACTGTCAATTTAATT
66 ATTATAGCTTTAATATCATATAACAAGATATTGGGATACTAAATTAACAAACTGTCAATTTAATT
14918 TTTTTAAAATTCAC
131 TTTTTAAAATTCAC
14932 A
1 A
14933 TATCACTCCT
Statistics
Matches: 139, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
143 48 0.35
144 91 0.65
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (144 bp):
AACAAAAAAAATTCGTATATAAAATTATTATTAATGAATTATCTAAAAATATTTTTTATATATTT
ATTATAGCTTTAATATCATATAACAAGATATTGGGATACTAAATTAACAAACTGTCAATTTAATT
TTTTTAAAATTCAC
Found at i:15170 original size:21 final size:22
Alignment explanation
Indices: 15122--15177 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
15112 TTGTGACATG
*
15122 TTCTCTGTTTTTATGACACATTT
1 TTCTCTGTCTTTATGA-ACATTT
* *
15145 ATCTCTGTCTTTATG-ATATTT
1 TTCTCTGTCTTTATGAACATTT
*
15166 TTCTCTGACTTT
1 TTCTCTGTCTTT
15178 TGGTAGCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 15 0.54
23 13 0.46
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.57
Consensus pattern (22 bp):
TTCTCTGTCTTTATGAACATTT
Found at i:18317 original size:80 final size:81
Alignment explanation
Indices: 18165--18327 Score: 283
Period size: 80 Copynumber: 2.0 Consensus size: 81
18155 AATAAAGCCT
* * *
18165 CTCTAAGAAGGTGAACTTATTGACAATGCAACTAGTCTCATTTTAGGTAAAATACCCTGATTATG
1 CTCTAAGAAGGTGAACTTATTGACAATGCAACTAGGCTCATTATAGGTAAAATACACTGATTATG
18230 TGCCGATTACAAGTAG
66 TGCCGATTACAAGTAG
*
18246 CTCTAAGAAGGTGAACTTATTGACAATGCAA-TAGGCTCATTATAGGTAAAGTACACTGATTATG
1 CTCTAAGAAGGTGAACTTATTGACAATGCAACTAGGCTCATTATAGGTAAAATACACTGATTATG
18310 TGCCGATTACAAGTAG
66 TGCCGATTACAAGTAG
18326 CT
1 CT
18328 TCCTCAATCT
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
80 47 0.60
81 31 0.40
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (81 bp):
CTCTAAGAAGGTGAACTTATTGACAATGCAACTAGGCTCATTATAGGTAAAATACACTGATTATG
TGCCGATTACAAGTAG
Found at i:20283 original size:14 final size:14
Alignment explanation
Indices: 20264--20330 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
20254 TTATATTACA
20264 TTTAAAAATATATT
1 TTTAAAAATATATT
20278 TTTAAAAATTTATAATT
1 TTTAAAAA--TAT-ATT
* * *
20295 ATCAATAATATATT
1 TTTAAAAATATATT
* * *
20309 TTTAATAATGTAAT
1 TTTAAAAATATATT
20323 TTTAAAAA
1 TTTAAAAA
20331 AATCTAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
14 28 0.67
15 3 0.07
16 3 0.07
17 8 0.19
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (14 bp):
TTTAAAAATATATT
Found at i:23984 original size:52 final size:52
Alignment explanation
Indices: 23922--24025 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
23912 TCTGTCATTC
23922 AAAATTCTGCTCAATGCATTACTGTTAGAGGATCTCACAAAGGTATTCCAAT
1 AAAATTCTGCTCAATGCATTACTGTTAGAGGATCTCACAAAGGTATTCCAAT
23974 AAAATTCTGCTCAATGCATTACTGTTAGAGGATCTCACAAAGGTATTCCAAT
1 AAAATTCTGCTCAATGCATTACTGTTAGAGGATCTCACAAAGGTATTCCAAT
24026 GTTTATTTCG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (52 bp):
AAAATTCTGCTCAATGCATTACTGTTAGAGGATCTCACAAAGGTATTCCAAT
Found at i:24249 original size:16 final size:16
Alignment explanation
Indices: 24225--24267 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
24215 CAGACTGCTA
*
24225 AAATGAACTGAAATAT
1 AAATAAACTGAAATAT
24241 AAATAAACTGAAATAT
1 AAATAAACTGAAATAT
24257 AAATAAACTGA
1 AAATAAACTGA
24268 TTTTTTAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.23
Consensus pattern (16 bp):
AAATAAACTGAAATAT
Found at i:24384 original size:22 final size:22
Alignment explanation
Indices: 24359--24405 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
24349 CAACTACAAT
24359 AATAAAT-TATTTAAAATAAATC
1 AATAAATAT-TTTAAAATAAATC
*
24381 AATACATATTTTAAAATAAATC
1 AATAAATATTTTAAAATAAATC
24403 AAT
1 AAT
24406 TAAAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAATATTTTAAAATAAATC
Found at i:24399 original size:36 final size:32
Alignment explanation
Indices: 24358--24457 Score: 110
Period size: 32 Copynumber: 3.0 Consensus size: 32
24348 ACAACTACAA
*
24358 TAATAAATTATTTAAAATAAATCAATACATATTT
1 TAATAAATTATTTAAAATAAATCAATACATA--C
* * *
24392 TAAAATAAATCAATTAAAATAAATCAATCCATAC
1 T--AATAAATTATTTAAAATAAATCAATACATAC
* *
24426 TAATAAATTATTTAAAATAAACCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATACATAC
24458 CACTACAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
32 27 0.48
34 2 0.04
36 27 0.48
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (32 bp):
TAATAAATTATTTAAAATAAATCAATACATAC
Found at i:24408 original size:14 final size:14
Alignment explanation
Indices: 24391--24419 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
24381 AATACATATT
24391 TTAAAATAAATCAA
1 TTAAAATAAATCAA
24405 TTAAAATAAATCAA
1 TTAAAATAAATCAA
24419 T
1 T
24420 CCATACTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAATAAATCAA
Found at i:24617 original size:80 final size:80
Alignment explanation
Indices: 24405--24609 Score: 374
Period size: 80 Copynumber: 2.6 Consensus size: 80
24395 AATAAATCAA
* **
24405 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAACCAATTCATACCACTACAATAAT
1 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATATAACTACAATAAT
24470 AAATCAATCTATATT
66 AAATCAATCTATATT
24485 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATATAACTACAATAAT
1 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATATAACTACAATAAT
24550 AAATCAATCTATATT
66 AAATCAATCTATATT
*
24565 TTAAAATAAATCAATCCATACTAATAAATTATTTGAAATAAATCA
1 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
24610 GTCCATATTT
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 121 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (80 bp):
TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATATAACTACAATAAT
AAATCAATCTATATT
Found at i:24618 original size:134 final size:134
Alignment explanation
Indices: 24467--24795 Score: 579
Period size: 134 Copynumber: 2.5 Consensus size: 134
24457 CCACTACAAT
* *
24467 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
* *
24532 -TCATATAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTA
66 CT-ATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
*
24596 TTTGA
130 TTTAA
*
24601 AATAAATCAGTCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
24666 CTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
66 CTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
24731 TTAA
131 TTAA
*
24735 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAATTTATTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
24796 TATTTTAAAA
Statistics
Matches: 186, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
134 185 0.99
135 1 0.01
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.36
Consensus pattern (134 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
CTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAA
Found at i:24629 original size:54 final size:54
Alignment explanation
Indices: 24547--24666 Score: 204
Period size: 54 Copynumber: 2.2 Consensus size: 54
24537 TAACTACAAT
* *
24547 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTGA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
24601 AATAAATCAGTCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
24655 AATAAATCAATC
1 AATAAATCAATC
24667 TATACAACTA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:24727 original size:22 final size:22
Alignment explanation
Indices: 24652--24726 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
24642 ATAAATTATT
* *
24652 TAAAATAAATCAATCTATACAA
1 TAAAATAAATCAATCCATATAA
**
24674 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
24700 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
24723 TAAA
1 TAAA
24727 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:24745 original size:54 final size:54
Alignment explanation
Indices: 24681--24795 Score: 212
Period size: 54 Copynumber: 2.1 Consensus size: 54
24671 CAACTACAAT
24681 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
24735 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAATTTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
24789 AATAAAT
1 AATAAAT
24796 TATTTTAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:24756 original size:22 final size:22
Alignment explanation
Indices: 24730--24772 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
24720 TAATAAATTA
24730 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
24752 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
24773 CTAATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:24802 original size:15 final size:15
Alignment explanation
Indices: 24775--24891 Score: 103
Period size: 15 Copynumber: 7.5 Consensus size: 15
24765 AATTCATACT
*
24775 AATAATTTA-TTTAA
1 AATAAATTATTTTAA
24789 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
24804 AATAAATTAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
24826 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
24841 AATAATTTATTTT-A
1 AATAAATTATTTTAA
*
24855 AATAATTTATTTTAA
1 AATAAATTATTTTAA
24870 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
24885 AAGAAAT
1 AATAAAT
24892 AACCTTATTA
Statistics
Matches: 88, Mismatches: 6, Indels: 17
0.79 0.05 0.15
Matches are distributed among these distances:
14 22 0.25
15 49 0.56
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:24808 original size:29 final size:30
Alignment explanation
Indices: 24775--24891 Score: 112
Period size: 29 Copynumber: 3.7 Consensus size: 30
24765 AATTCATACT
24775 AATAATTTA-TTTAAAATAAATTATTTTAA
1 AATAATTTATTTTAAAATAAATTATTTTAA
* *
24804 AATAAATTAATCCATATTTTATAATAATTTATTTTAA
1 AAT-AA-T--T---TATTTTAAAATAAATTATTTTAA
*
24841 AATAATTTATTTT-AAATAATTTATTTTAA
1 AATAATTTATTTTAAAATAAATTATTTTAA
* *
24870 AATAAATTATTTTAAAAGAAAT
1 AATAATTTATTTTAAAATAAAT
24892 AACCTTATTA
Statistics
Matches: 73, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
29 30 0.41
30 14 0.19
31 1 0.01
33 2 0.03
35 1 0.01
36 4 0.05
37 21 0.29
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (30 bp):
AATAATTTATTTTAAAATAAATTATTTTAA
Found at i:32341 original size:15 final size:15
Alignment explanation
Indices: 32323--32370 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
32313 ATTTTTTCAA
32323 TTTAATTACTTAATT
1 TTTAATTACTTAATT
*
32338 TTTAAATTAC-TATTAT
1 TTT-AATTACTTAAT-T
32354 TTTAATTACTATAATT
1 TTTAATTACT-TAATT
32370 T
1 T
32371 ATTTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 12 0.44
16 12 0.44
17 3 0.11
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATTACTTAATT
Found at i:32384 original size:30 final size:29
Alignment explanation
Indices: 32323--32385 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
32313 ATTTTTTCAA
32323 TTTAATTACTTAATTTTTAAATTACTATTAT
1 TTTAATTACTTAATTTTT--ATTACTATTAT
*
32354 TTTAATTACTATAATTTATT-TTATTATTAT
1 TTTAATTACT-TAATTT-TTATTACTATTAT
32384 TT
1 TT
32386 ATGTATGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 11 0.38
31 10 0.34
32 6 0.21
33 2 0.07
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTAATTACTTAATTTTTATTACTATTAT
Found at i:34352 original size:20 final size:20
Alignment explanation
Indices: 34324--34377 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
34314 TAATCACCTT
*
34324 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
* *
34344 AGGAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
34364 AGAAAATCGCAACG
1 AGAAAATCGCAACG
34378 CGAGCTTCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.50, C:0.19, G:0.20, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:34437 original size:20 final size:20
Alignment explanation
Indices: 34412--34499 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
34402 TTTAGAAGAA
* *
34412 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGACTGAGAG
34432 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAG
34452 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAG
* * *
34472 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGACTGAGAG
34492 AATCGCAA
1 AATCGCAA
34500 CGTTGAAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (20 bp):
AATCGCAATGCGACTGAGAG
Found at i:34620 original size:6 final size:6
Alignment explanation
Indices: 34609--34754 Score: 285
Period size: 6 Copynumber: 24.5 Consensus size: 6
34599 GACACGTATT
34609 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
34657 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
34705 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
34752 ACC
1 ACC
34755 CGAGACGAGA
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.04
6 135 0.96
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:35461 original size:6 final size:6
Alignment explanation
Indices: 35445--35476 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
35435 TCTCGTCTCG
35445 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
35477 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:35570 original size:20 final size:20
Alignment explanation
Indices: 35545--35588 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
35535 TTTTTACCTA
*
35545 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
35565 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
35585 TTCT
1 TTCT
35589 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:35598 original size:20 final size:20
Alignment explanation
Indices: 35575--35872 Score: 125
Period size: 20 Copynumber: 14.6 Consensus size: 20
35565 TTCTTTTTAA
35575 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
35595 CGTTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
*** * * *
35615 CAACGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * * *
35635 CATTGCGATTCTCTCAGTCA
1 CGTTGCGATTTTCTAAATCG
* * * * *
35655 CATTGCTATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
35675 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
35698 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
35718 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
35738 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
35761 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
35782 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
35800 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
35822 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
35842 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
35861 CGTTGCGATTTT
1 CGTTGCGATTTT
35873 ATTGGTCATT
Statistics
Matches: 219, Mismatches: 48, Indels: 23
0.76 0.17 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 152 0.69
21 14 0.06
22 6 0.03
23 28 0.13
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:35666 original size:40 final size:40
Alignment explanation
Indices: 35577--35747 Score: 171
Period size: 40 Copynumber: 4.2 Consensus size: 40
35567 CTTTTTAACG
* * * * * *
35577 TTGCGATTTTCTAAATCGCGTTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAATCGCA
** * *
35617 ACGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCACA
1 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAATCGCA
* * *
35657 TTGCTATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAGTCGCATTGCGA--TTC-TCTCAATCGCA
* * *
35700 TTGCGACTCTCTCAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAATCGCA
35740 TTGCGATT
1 TTGCGATT
35748 TTCTTCTAAA
Statistics
Matches: 104, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
40 68 0.65
41 3 0.03
42 3 0.03
43 30 0.29
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAATCGCA
Found at i:35722 original size:63 final size:63
Alignment explanation
Indices: 35597--35768 Score: 215
Period size: 63 Copynumber: 2.8 Consensus size: 63
35587 CTAAATCGCG
* ** * * * * *
35597 TTGCGATTCTATAAATCGCAACGCGA--TTC-TCTCAGTCGCATTGCGATTCTCTCAGTCACA
1 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCACA
* * * *
35657 TTGCTATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCACA
35720 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
35769 ACTTGGAAGC
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
60 20 0.21
62 3 0.03
63 71 0.76
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (63 bp):
TTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCACA
Found at i:35862 original size:19 final size:20
Alignment explanation
Indices: 35822--35872 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
35812 TTCTTTTTAA
*
35822 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
35842 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
35861 CGTTGCGATTTT
1 CGTTGCGATTTT
35873 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:36483 original size:18 final size:19
Alignment explanation
Indices: 36460--36495 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
36450 AAAATAGGTT
36460 TATAATATAT-ATAATTTA
1 TATAATATATAATAATTTA
*
36478 TATAATATTTAATAATTT
1 TATAATATATAATAATTT
36496 TGATTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATAATATATAATAATTTA
Found at i:41809 original size:16 final size:16
Alignment explanation
Indices: 41790--41822 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41780 TCCCATTATT
*
41790 TGTGTTTGATATTAAC
1 TGTGTCTGATATTAAC
41806 TGTGTCTGATATTAAC
1 TGTGTCTGATATTAAC
41822 T
1 T
41823 ATGCACATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (16 bp):
TGTGTCTGATATTAAC
Found at i:42483 original size:19 final size:19
Alignment explanation
Indices: 42461--42505 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
42451 GTTTAATTTA
42461 TTATTATAATTGTAA-ATAT
1 TTATTATAATT-TAAGATAT
42480 TTATTATAATTTAAGATAT
1 TTATTATAATTTAAGATAT
*
42499 TTTTTAT
1 TTATTAT
42506 TTTGAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TTATTATAATTTAAGATAT
Found at i:42504 original size:22 final size:22
Alignment explanation
Indices: 42456--42506 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 22
42446 TATGTGTTTA
*
42456 ATTTATTATTATAATTGTAAAT
1 ATTTTTTATTATAATTGTAAAT
42478 A---TTTATTATAATT-TAAGAT
1 ATTTTTTATTATAATTGTAA-AT
42497 ATTTTTTATT
1 ATTTTTTATT
42507 TTGAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
18 3 0.12
19 14 0.58
22 7 0.29
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (22 bp):
ATTTTTTATTATAATTGTAAAT
Found at i:42532 original size:2 final size:2
Alignment explanation
Indices: 42525--42558 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42515 AATTAATTGG
42525 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
42559 CAAGTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46571 original size:15 final size:15
Alignment explanation
Indices: 46551--46580 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
46541 CATCATTTCT
46551 AGAATTGTAGCAATC
1 AGAATTGTAGCAATC
46566 AGAATTGTAGCAATC
1 AGAATTGTAGCAATC
46581 CATTTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
AGAATTGTAGCAATC
Found at i:58943 original size:2 final size:2
Alignment explanation
Indices: 58936--58964 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58926 AAAATAAATG
58936 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58965 TCAATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59825 original size:18 final size:20
Alignment explanation
Indices: 59802--59844 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
59792 CTTGATTTCC
*
59802 ATTCAATTTCATT-CAT-AA
1 ATTCAACTTCATTACATCAA
*
59820 ATTCAACTTCTTTACATCAA
1 ATTCAACTTCATTACATCAA
59840 ATTCA
1 ATTCA
59845 TGTTCTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
19 3 0.14
20 7 0.33
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTCAACTTCATTACATCAA
Found at i:61881 original size:25 final size:25
Alignment explanation
Indices: 61853--61901 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
61843 TAATTAAATC
* *
61853 ATTAATAATTATGTTAAGAGATTGT
1 ATTAATAATCATATTAAGAGATTGT
*
61878 ATTAATAGTCATATTAAGAGATTG
1 ATTAATAATCATATTAAGAGATTG
61902 GATTTCGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (25 bp):
ATTAATAATCATATTAAGAGATTGT
Found at i:62024 original size:28 final size:26
Alignment explanation
Indices: 61989--62042 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
61979 ATATATGATT
*
61989 TAATTAATTAATTTAAATTAAGATTTAA
1 TAATTAA-TAATTTAAATCAA-ATTTAA
*
62017 TAATTAATAATTTTAATCAAATTTAA
1 TAATTAATAATTTAAATCAAATTTAA
62043 GTGAACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 11 0.46
28 7 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
TAATTAATAATTTAAATCAAATTTAA
Found at i:65097 original size:17 final size:17
Alignment explanation
Indices: 65064--65109 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
65054 TATTTAGTTC
65064 TTAATATTTATAT-ATTAT
1 TTAA-ATTTA-ATCATTAT
*
65082 TTCAATTTAATCATTAT
1 TTAAATTTAATCATTAT
65099 TTAAATTTAAT
1 TTAAATTTAAT
65110 TTAATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.08
17 20 0.80
18 3 0.12
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTAATCATTAT
Found at i:65113 original size:22 final size:23
Alignment explanation
Indices: 65080--65123 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
65070 TTTATATATT
*
65080 ATTTCAATTTAATCATTATTTAA
1 ATTTCAATTTAATAATTATTTAA
*
65103 ATTT-AATTTAATAATTTTTTA
1 ATTTCAATTTAATAATTATTTA
65124 TTTAATCGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTCAATTTAATAATTATTTAA
Done.