Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002139.1 Hibiscus syriacus cultivar Beakdansim tig00004373_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: 79600
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3337 original size:13 final size:13
Alignment explanation
Indices: 3321--3346 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3311 TAAATGAATT
3321 TAATTTTTTAAAG
1 TAATTTTTTAAAG
3334 TAATTTTTTAAAG
1 TAATTTTTTAAAG
3347 AGTTTGCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TAATTTTTTAAAG
Found at i:5365 original size:18 final size:18
Alignment explanation
Indices: 5325--5367 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5315 CTACAAAGAG
*
5325 TAATAAAAAAAACTAATA
1 TAATAAAAAAAACTAAAA
*
5343 CAATAAAATAAAA-TAAAA
1 TAATAAAA-AAAACTAAAA
5361 TAATAAA
1 TAATAAA
5368 CTATTAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (18 bp):
TAATAAAAAAAACTAAAA
Found at i:6598 original size:24 final size:25
Alignment explanation
Indices: 6566--6635 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
6556 ACCTCACCCA
*
6566 ATATATGTTTAATAATTAATATAAT
1 ATATTTGTTTAATAATTAATATAAT
*
6591 A-ATTTGTTTAATAATATAA-ATTAT
1 ATATTTGTTTAATAAT-TAATATAAT
*
6615 ATATTT-TTTAAAAAGTTAATA
1 ATATTTGTTTAATAA-TTAATA
6636 ATTTAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 28 0.74
25 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
ATATTTGTTTAATAATTAATATAAT
Found at i:9601 original size:25 final size:25
Alignment explanation
Indices: 9567--9616 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
9557 TATAACTAAA
9567 AAAAGTTATTAT-TTTATAATAATTT
1 AAAAGTTATTATGTTTATAA-AATTT
* *
9592 AAAATTTATTTTGTTTATAAAATTT
1 AAAAGTTATTATGTTTATAAAATTT
9617 TAATAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
AAAAGTTATTATGTTTATAAAATTT
Found at i:11410 original size:12 final size:13
Alignment explanation
Indices: 11387--11415 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
11377 GTTATTGATA
11387 ATTTTAAATTATT
1 ATTTTAAATTATT
11400 ATTTT-AATTATT
1 ATTTTAAATTATT
11412 ATTT
1 ATTT
11416 AATAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTTTAAATTATT
Found at i:11485 original size:67 final size:68
Alignment explanation
Indices: 11348--11488 Score: 212
Period size: 67 Copynumber: 2.1 Consensus size: 68
11338 AGATCAAATA
* * * *
11348 AATAATACATTTTCTTAATATGCCAAGTGGTTATTGATAATTTTAAATTATTATTTTAATTATTA
1 AATAATACATCTTCTTAATATGCAAAGTGGTTATGGATAATTTTAAATTATTATATTAATTATTA
11413 TTT
66 TTT
* * *
11416 AATAATACATCTTCTTAATATGTAAAGTGG-TGTGGATAATTTTTAATTATTATATTAATTATTA
1 AATAATACATCTTCTTAATATGCAAAGTGGTTATGGATAATTTTAAATTATTATATTAATTATTA
11480 TTT
66 TTT
11483 AATAAT
1 AATAAT
11489 CTAAAAATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
67 39 0.59
68 27 0.41
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.50
Consensus pattern (68 bp):
AATAATACATCTTCTTAATATGCAAAGTGGTTATGGATAATTTTAAATTATTATATTAATTATTA
TTT
Found at i:12495 original size:10 final size:10
Alignment explanation
Indices: 12482--12523 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
12472 GGCCATCCGA
12482 CCGAGGCCAT
1 CCGAGGCCAT
*
12492 CCGAAAG-CAT
1 CCG-AGGCCAT
*
12502 TCGAGGCCAT
1 CCGAGGCCAT
12512 CCGAGGCCAT
1 CCGAGGCCAT
12522 CC
1 CC
12524 AAACGAGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.08
10 22 0.85
11 2 0.08
ACGTcount: A:0.24, C:0.38, G:0.26, T:0.12
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:12539 original size:23 final size:23
Alignment explanation
Indices: 12513--12563 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
12503 CGAGGCCATC
*
12513 CGAGGCCATCCAAACGAGCTATG
1 CGAGGCCAACCAAACGAGCTATG
* * *
12536 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGCCAACCAAACGAGCTATG
12559 CGAGG
1 CGAGG
12564 GAATCCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.35, T:0.10
Consensus pattern (23 bp):
CGAGGCCAACCAAACGAGCTATG
Found at i:12564 original size:23 final size:23
Alignment explanation
Indices: 12527--12572 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12517 GCCATCCAAA
12527 CGAGCTATGCGAGGGCAA-CCGAG
1 CGAGCTATGCGAGGG-AATCCGAG
12550 CGAGCTATGCGAGGGAATCCGAG
1 CGAGCTATGCGAGGGAATCCGAG
12573 GGCAACCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.26, C:0.24, G:0.39, T:0.11
Consensus pattern (23 bp):
CGAGCTATGCGAGGGAATCCGAG
Found at i:12691 original size:23 final size:23
Alignment explanation
Indices: 12633--12692 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
12623 CTCGGTTGCC
*
12633 CTCGGATTCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
12656 CTCGGTTGCCCTCGCATAGCTTG
1 CTCGGATGCCCTCGCATAGCTCG
* *
12679 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
12693 GTCGGATGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.28
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:12699 original size:14 final size:14
Alignment explanation
Indices: 12680--12707 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12670 CATAGCTTGT
12680 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
12694 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
12708 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:13736 original size:12 final size:12
Alignment explanation
Indices: 13721--13775 Score: 83
Period size: 12 Copynumber: 4.6 Consensus size: 12
13711 GTTATTTAAA
13721 CGGGTATTGGGC
1 CGGGTATTGGGC
*
13733 CGGGTATTGGGT
1 CGGGTATTGGGC
13745 CGGGTATTGGGC
1 CGGGTATTGGGC
* *
13757 CGGGAATCGGGC
1 CGGGTATTGGGC
13769 CGGGTAT
1 CGGGTAT
13776 ATATATATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.11, C:0.16, G:0.49, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:13858 original size:13 final size:12
Alignment explanation
Indices: 13827--13863 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
13817 TTTTAATATT
*
13827 TATCGGGTCGGG
1 TATCGGGGCGGG
13839 TATCGGGGCGGG
1 TATCGGGGCGGG
13851 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
13864 GATTATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:15771 original size:60 final size:60
Alignment explanation
Indices: 15625--15756 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 60
15615 AACATAATAA
* *
15625 ATAGTCGAGTGATCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCAACACTAT
1 ATAGTCGGGTGATCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCAACACTAT
* * * * * * *
15685 GTAGTCGGATGATCATTTTATAACTTTTAATAGTCAATGGACTTAATAAAGTAATA-TCAT
1 ATAGTCGGGTGATCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCAACACT-AT
15745 ATAGTCGGGTGA
1 ATAGTCGGGTGA
15757 CTATTTGTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.02
60 59 0.98
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (60 bp):
ATAGTCGGGTGATCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCAACACTAT
Found at i:30915 original size:21 final size:21
Alignment explanation
Indices: 30891--30930 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30881 CCAGAAATGT
*
30891 TAGAAACATTAATGTTTTATG
1 TAGAAACAATAATGTTTTATG
*
30912 TAGAAATAATAATGTTTTA
1 TAGAAACAATAATGTTTTA
30931 AGTAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (21 bp):
TAGAAACAATAATGTTTTATG
Found at i:31582 original size:30 final size:30
Alignment explanation
Indices: 31546--31609 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
31536 TCGTTTAAAA
31546 TTTAAACGAAATGACCGATGTGGAATTACT
1 TTTAAACGAAATGACCGATGTGGAATTACT
31576 TTTAAACGAAATGACCGATGTGGAATTACT
1 TTTAAACGAAATGACCGATGTGGAATTACT
31606 TTTA
1 TTTA
31610 TGTTTTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (30 bp):
TTTAAACGAAATGACCGATGTGGAATTACT
Found at i:32988 original size:25 final size:25
Alignment explanation
Indices: 32951--33028 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
32941 TATTTTTATA
*
32951 TAATTTTCTATATATACTCATTAA-AT
1 TAATTTT-AATATATA-TCATTAATAT
* *
32977 TATTTTTAATATA-ATTATTAATTAT
1 TAATTTTAATATATATCATTAA-TAT
33002 TAATTTTAATATATAT-A-T-ATAT
1 TAATTTTAATATATATCATTAATAT
33024 TAATT
1 TAATT
33029 AGGTTAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 8 0.18
23 7 0.16
24 2 0.04
25 20 0.44
26 8 0.18
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
TAATTTTAATATATATCATTAATAT
Found at i:33133 original size:19 final size:19
Alignment explanation
Indices: 33105--33172 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
33095 GTTTCGATAA
* * *
33105 AAATTAATTTTTAATTTTT
1 AAATTTATTTTTAAATATT
*
33124 AAATTTATTTTAAAATATT
1 AAATTTATTTTTAAATATT
33143 AAATTTATTTTAATAAATATT
1 AAATTTATTTT--TAAATATT
33164 AAATTTATT
1 AAATTTATT
33173 ATTATTTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 26 0.62
21 16 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTTATTTTTAAATATT
Found at i:33169 original size:55 final size:54
Alignment explanation
Indices: 33101--33210 Score: 125
Period size: 55 Copynumber: 2.0 Consensus size: 54
33091 TCAAGTTTCG
*
33101 ATAAAAATTAATTT-TTAAT-TTTTAAATTTATTTTAAAATATTAAATTTATTTTA
1 ATAAAAATTAATTTATTAATATTTTAAA--TATTATAAAATATTAAATTTATTTTA
* * ** *
33155 ATAAATATTAAATTTATTATTATTTTAAATATTATAGTATATTAATTTTATTTTA
1 ATAAAAATT-AATTTATTAATATTTTAAATATTATAAAATATTAAATTTATTTTA
33210 A
1 A
33211 ATTTATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
54 8 0.17
55 28 0.60
56 4 0.09
57 7 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (54 bp):
ATAAAAATTAATTTATTAATATTTTAAATATTATAAAATATTAAATTTATTTTA
Found at i:33174 original size:24 final size:20
Alignment explanation
Indices: 33122--33177 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 20
33112 TTTTTAATTT
33122 TTAAATTTATTTTA-AAATA
1 TTAAATTTATTTTATAAATA
33141 TTAAATTTATTTTAATAAATA
1 TTAAATTTATTTT-ATAAATA
33162 TTAAATTTATTATTAT
1 TTAAATTTATT-TTAT
33178 TTTAAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.38
20 1 0.03
21 18 0.53
22 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAATTTATTTTATAAATA
Found at i:33183 original size:24 final size:23
Alignment explanation
Indices: 33127--33212 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 23
33117 AATTTTTAAA
33127 TTTATTTTAAAATATTAAATTTAT
1 TTTATTTT-AAATATTAAATTTAT
*
33151 TTTA--ATAAATATTAAATTTAT
1 TTTATTTTAAATATTAAATTTAT
33172 TATTATTTTAAATATTATAGTATATTAAT
1 T-TTATTTTAAATATTA-A--AT-TT-AT
33201 TTTATTTTAAAT
1 TTTATTTTAAAT
33213 TTATTTTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
21 16 0.31
22 4 0.08
24 13 0.25
25 1 0.02
27 2 0.04
28 13 0.25
29 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (23 bp):
TTTATTTTAAATATTAAATTTAT
Found at i:33199 original size:17 final size:17
Alignment explanation
Indices: 33159--33206 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
33149 ATTTTAATAA
*
33159 ATATTAAATTTATTATT
1 ATATTAAATTTATTAGT
*
33176 ATTTTAAATATTA-TAGT
1 ATATTAAAT-TTATTAGT
*
33193 ATATTAATTTTATT
1 ATATTAAATTTATT
33207 TTAAATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 19 0.76
18 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATATTAAATTTATTAGT
Found at i:33206 original size:28 final size:28
Alignment explanation
Indices: 33138--33216 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
33128 TTATTTTAAA
* * *
33138 ATATTAAATTTATTTT-AATA-AATATT
1 ATATTAATTTTATTTTAAATATTATAGT
* *
33164 AAATTTATTATTATTTTAAATATTATAGT
1 ATATTAATT-TTATTTTAAATATTATAGT
33193 ATATTAATTTTATTTTAAAT-TTAT
1 ATATTAATTTTATTTTAAATATTAT
33217 TTTTTATATA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
26 6 0.14
27 11 0.26
28 15 0.35
29 11 0.26
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
ATATTAATTTTATTTTAAATATTATAGT
Found at i:39637 original size:231 final size:231
Alignment explanation
Indices: 39231--39694 Score: 838
Period size: 231 Copynumber: 2.0 Consensus size: 231
39221 CCTCCGCATA
*
39231 CTTGGACTAACCATTTCCACAATAACCTCGCTGCACCAGCTCTCCGGCATTAGAAGTTTAATCAG
1 CTTGGACTAACCATTTCCACAATAACCTCGCTGCACAAGCTCTCCGGCATTAGAAGTTTAATCAG
*
39296 ATGCATACAGTATTTATTCATAAAAGAATGAGAAGGTCTGCATCAACTAGAATTATCACCAACTT
66 ATGCATACAGTATTTATTCATAAAAGAATGAGAAGGTCTGCATCAACTAGAATCATCACCAACTT
39361 TCGGTTACAGTAAACGACTGAGAAGACTTAGCATCAAAGACTGCAATGACTTAAATTGCTTGGTA
131 TCGGTTACAGTAAACGACTGAGAAGACTTAGCATCAAAGACTGCAATGACTTAAATTGCTTGGTA
*
39426 GTGGATGCCGAGGATGGAGAGAATTGGTTACCTAAT
196 GTGGATGCCGAGGATGGAGAGAACTGGTTACCTAAT
* *
39462 CTTGGACTAACCATTTCCACAATAACCTCGCTGCACAAGCTCTTCGGCATTAGAAGTTTAATTAG
1 CTTGGACTAACCATTTCCACAATAACCTCGCTGCACAAGCTCTCCGGCATTAGAAGTTTAATCAG
* * *
39527 ATGCATACAGTATTTATTCATAAAAGAATGTGAAGGTCTGCATCAATTAGAATCATCACTAACTT
66 ATGCATACAGTATTTATTCATAAAAGAATGAGAAGGTCTGCATCAACTAGAATCATCACCAACTT
* *
39592 TCGGTTACAGTAAACGACTGAGAAGACTTAGCATCAAATACTGCAATGACTTCAATTGCTTGGTA
131 TCGGTTACAGTAAACGACTGAGAAGACTTAGCATCAAAGACTGCAATGACTTAAATTGCTTGGTA
39657 GTGGATGCCGAGGATGGAGAGAACTGGTTACCTAAT
196 GTGGATGCCGAGGATGGAGAGAACTGGTTACCTAAT
39693 CT
1 CT
39695 GGAAGTTTTA
Statistics
Matches: 223, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
231 223 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (231 bp):
CTTGGACTAACCATTTCCACAATAACCTCGCTGCACAAGCTCTCCGGCATTAGAAGTTTAATCAG
ATGCATACAGTATTTATTCATAAAAGAATGAGAAGGTCTGCATCAACTAGAATCATCACCAACTT
TCGGTTACAGTAAACGACTGAGAAGACTTAGCATCAAAGACTGCAATGACTTAAATTGCTTGGTA
GTGGATGCCGAGGATGGAGAGAACTGGTTACCTAAT
Found at i:41318 original size:17 final size:16
Alignment explanation
Indices: 41298--41332 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
41288 AAACACGAAT
41298 AAAATAAAAATTATGAA
1 AAAATAAAAATTAT-AA
*
41315 AAAATAATAATTATAA
1 AAAATAAAAATTATAA
41331 AA
1 AA
41333 CTAGAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAATAAAAATTATAA
Found at i:42094 original size:15 final size:12
Alignment explanation
Indices: 42057--42083 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42047 TGTTTGTCTT
42057 TGTTAATATTTA
1 TGTTAATATTTA
42069 TGTTAATATTTA
1 TGTTAATATTTA
42081 TGT
1 TGT
42084 ATCAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (12 bp):
TGTTAATATTTA
Found at i:43652 original size:15 final size:14
Alignment explanation
Indices: 43634--43691 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
43624 TTATAATATT
43634 TATGTTTTTTAATCA
1 TATGTTTTTTAAT-A
* *
43649 TATGTATCTTAATA
1 TATGTTTTTTAATA
*
43663 TATTTTTGTTTAATA
1 TATGTTT-TTTAATA
*
43678 TTTGTATTTTTAAT
1 TATGT-TTTTTAAT
43692 TTTAGTTGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
14 6 0.18
15 26 0.76
16 2 0.06
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (14 bp):
TATGTTTTTTAATA
Found at i:53308 original size:20 final size:19
Alignment explanation
Indices: 53283--53406 Score: 108
Period size: 20 Copynumber: 6.2 Consensus size: 19
53273 ATGTAAATCA
53283 CAACACAGAAGTCAAATTCG
1 CAACAC-GAAGTCAAATTCG
*
53303 CAACACAAAAGTCAAATTCG
1 CAACAC-GAAGTCAAATTCG
*
53323 CAACACGATAATCAAATTCG
1 CAACACGA-AGTCAAATTCG
**
53343 CAATTCGATAGTCAAATTCG
1 CAACACGA-AGTCAAATTCG
*
53363 CAACGCGAATTTGT-AAA-TCG
1 CAACACGAA---GTCAAATTCG
*
53383 TAACACAGAAGTCAAATTCG
1 CAACAC-GAAGTCAAATTCG
53403 CAAC
1 CAAC
53407 GAGAACTCCA
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.02
19 5 0.06
20 71 0.83
21 6 0.07
22 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (19 bp):
CAACACGAAGTCAAATTCG
Found at i:53462 original size:21 final size:20
Alignment explanation
Indices: 53420--53488 Score: 120
Period size: 20 Copynumber: 3.4 Consensus size: 20
53410 AACTCCAATT
53420 TCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
53440 TCGCAACGTGAATAGTAAAAA
1 TCGCAACGTGAATAGT-AAAA
*
53461 TCACAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
53481 TCGCAACG
1 TCGCAACG
53489 AATCTATATG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 27 0.59
21 19 0.41
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGTGAATAGTAAAA
Found at i:53874 original size:20 final size:20
Alignment explanation
Indices: 53844--53981 Score: 222
Period size: 20 Copynumber: 6.9 Consensus size: 20
53834 GATTTTCTAA
* *
53844 ATTCGCGTTGCGATCTTACT
1 ATTCACGTTGCGATTTTACT
*
53864 ATTTACGTTGCGATTTTACT
1 ATTCACGTTGCGATTTTACT
53884 ATTCACGTTGCGATTTTACT
1 ATTCACGTTGCGATTTTACT
*
53904 ATTTACGTTGCGATTTTACT
1 ATTCACGTTGCGATTTTACT
53924 ATTCACGTTGCGATTTTACT
1 ATTCACGTTGCGATTTTACT
*
53944 ATTCATGTTGCGATTTTACT
1 ATTCACGTTGCGATTTTACT
*
53964 ATTCACGCTGCGATTTTA
1 ATTCACGTTGCGATTTTA
53982 GAAATTGAGT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 109 1.00
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.46
Consensus pattern (20 bp):
ATTCACGTTGCGATTTTACT
Found at i:53994 original size:60 final size:60
Alignment explanation
Indices: 53868--53996 Score: 188
Period size: 60 Copynumber: 2.1 Consensus size: 60
53858 CTTACTATTT
* * **
53868 ACGTTGCGATTTTACTATTCACGTTGCGATTTTACTATTTACGTTGCGATTTTACTATTC
1 ACGTTGCGATTTTACTATTCACGTTGCGATTTTACTATTCACGCTGCGATTTTAAAATTC
* *
53928 ACGTTGCGATTTTACTATTCATGTTGCGATTTTACTATTCACGCTGCGATTTTAGAAATTG
1 ACGTTGCGATTTTACTATTCACGTTGCGATTTTACTATTCACGCTGCGATTTTA-AAATTC
53989 A-GTTGCGA
1 ACGTTGCGA
53997 AATTGGAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
60 58 0.94
61 4 0.06
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (60 bp):
ACGTTGCGATTTTACTATTCACGTTGCGATTTTACTATTCACGCTGCGATTTTAAAATTC
Found at i:60465 original size:12 final size:12
Alignment explanation
Indices: 60448--60472 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60438 ACGGCTAAAA
60448 TATTTGTTCTAT
1 TATTTGTTCTAT
60460 TATTTGTTCTAT
1 TATTTGTTCTAT
60472 T
1 T
60473 TTACTAGCAC
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTTGTTCTAT
Found at i:62230 original size:12 final size:11
Alignment explanation
Indices: 62195--62248 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
62185 ATTGTGAATG
62195 TTTTATTT-TA
1 TTTTATTTATA
62205 TTTT-TTTA-A
1 TTTTATTTATA
62214 GTTTTAGTTTATA
1 -TTTTA-TTTATA
62227 TTTTAATTTATA
1 TTTT-ATTTATA
*
62239 TATTATTTAT
1 TTTTATTTAT
62249 TTAATTAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
9 4 0.11
10 8 0.22
11 6 0.16
12 17 0.46
13 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (11 bp):
TTTTATTTATA
Found at i:64798 original size:18 final size:18
Alignment explanation
Indices: 64775--64809 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
64765 CTAGGAGATT
64775 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
64793 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
64810 CTAGAGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:65811 original size:22 final size:22
Alignment explanation
Indices: 65737--65803 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
65727 TTATGGACAT
65737 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
65759 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
65781 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
65803 A
1 A
65804 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:68958 original size:22 final size:22
Alignment explanation
Indices: 68930--68976 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
68920 GATTTCTGGG
* *
68930 CAAGGGGGAATCGGTACCCATT
1 CAAGGGGGAACCGATACCCATT
*
68952 CAA-GGGGAACCGATACCCCTT
1 CAAGGGGGAACCGATACCCATT
68973 CAAG
1 CAAG
68977 CGAATATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (22 bp):
CAAGGGGGAACCGATACCCATT
Found at i:69584 original size:18 final size:18
Alignment explanation
Indices: 69561--69595 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
69551 CTAGGAGATT
69561 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
69579 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
69596 CTAGAGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:70552 original size:22 final size:22
Alignment explanation
Indices: 70524--70590 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
70514 TTATGGACAT
70524 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
70546 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
70568 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
70590 A
1 A
70591 TTATACGAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:78253 original size:22 final size:21
Alignment explanation
Indices: 78202--78253 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
78192 TCATTCTCCC
* *
78202 TATTTTACTCAAAATTATAAA
1 TATTTTAATAAAAATTATAAA
*
78223 T-TTAATAATAAAAATATATAAA
1 TATT-TTAATAAAAAT-TATAAA
78245 TATTTTAAT
1 TATTTTAAT
78254 TTAATAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.08
21 9 0.38
22 11 0.46
23 2 0.08
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTTTAATAAAAATTATAAA
Found at i:78681 original size:33 final size:33
Alignment explanation
Indices: 78644--78712 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
78634 TTACGTGAAG
78644 ACCGTCGGTTCACGGTTAAATCAGCTTATGAGT
1 ACCGTCGGTTCACGGTTAAATCAGCTTATGAGT
*
78677 ACCGTTGGTTCACGGTTAAATCAGCTTATGAGT
1 ACCGTCGGTTCACGGTTAAATCAGCTTATGAGT
78710 ACC
1 ACC
78713 ATGTCAGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (33 bp):
ACCGTCGGTTCACGGTTAAATCAGCTTATGAGT
Done.