Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003739.1 Hibiscus syriacus cultivar Beakdansim tig00007998_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: 70406
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:6808 original size:144 final size:146
Alignment explanation
Indices: 6628--6930 Score: 517
Period size: 144 Copynumber: 2.1 Consensus size: 146
6618 AGAGGGTCTA
*
6628 CGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTC-TGGAAAGACACATACTTG
1 CGGTCCTTCGGGA-ATATATATATTC-TTGGAACATGTGTGAAGTCTTGGAAAGACACATACTTG
6692 ATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCC-TATGGACATCATTATATGG
64 ATCCCTAGTATATGTATATG-TTCTTAAGG-ATTCTATGTGGTCCTTATGGACATCATTATATGG
6756 CACTACGGTGCAATTCTACG
127 CACTACGGTGCAATTCTACG
6776 CGGTCCTTCGGG-ATATATATATTC-TGGAACATGTGTGAAGTCTTGGAAAGACACATACTTGAT
1 CGGTCCTTCGGGAATATATATATTCTTGGAACATGTGTGAAGTCTTGGAAAGACACATACTTGAT
6839 CCCTAGTATATGTATATGTTCTTAAGGATTCTATGTGGTCCTTATGGACATCATTATATGGCACT
66 CCCTAGTATATGTATATGTTCTTAAGGATTCTATGTGGTCCTTATGGACATCATTATATGGCACT
6904 ACGGTGCAATTCTACG
131 ACGGTGCAATTCTACG
6920 CGG-CACTTCGG
1 CGGTC-CTTCGG
6931 TGCATTTATA
Statistics
Matches: 151, Mismatches: 1, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
143 15 0.10
144 75 0.50
145 38 0.25
146 11 0.07
148 12 0.08
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (146 bp):
CGGTCCTTCGGGAATATATATATTCTTGGAACATGTGTGAAGTCTTGGAAAGACACATACTTGAT
CCCTAGTATATGTATATGTTCTTAAGGATTCTATGTGGTCCTTATGGACATCATTATATGGCACT
ACGGTGCAATTCTACG
Found at i:6942 original size:23 final size:23
Alignment explanation
Indices: 6898--6942 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6888 ATCATTATAT
*
6898 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
6921 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
6943 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:12248 original size:23 final size:23
Alignment explanation
Indices: 12222--12268 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
12212 CTATAATGGT
12222 CTTATGACATACACGAGTGAATG
1 CTTATGACATACACGAGTGAATG
12245 CTTATGACATACACGAGTGAATG
1 CTTATGACATACACGAGTGAATG
12268 C
1 C
12269 GAGACTACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (23 bp):
CTTATGACATACACGAGTGAATG
Found at i:16942 original size:22 final size:23
Alignment explanation
Indices: 16917--16969 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
16907 TAAATCCTTG
16917 TTTTTTATTGAATAAAAAT-AAT
1 TTTTTTATTGAATAAAAATAAAT
16939 TTTTTT-TTGAATAAAAATAAAT
1 TTTTTTATTGAATAAAAATAAAT
16961 TTTTTTATT
1 TTTTTTATT
16970 ATTTCAGATC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.41
22 15 0.52
23 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTTTATTGAATAAAAATAAAT
Found at i:16966 original size:21 final size:21
Alignment explanation
Indices: 16917--16966 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
16907 TAAATCCTTG
*
16917 TTTTTTATTGAATAAAAATAAT
1 TTTTTT-TTGAATAAAAATAAA
16939 TTTTTTTTGAATAAAAATAAA
1 TTTTTTTTGAATAAAAATAAA
16960 TTTTTTT
1 TTTTTTT
16967 ATTATTTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTTTTTGAATAAAAATAAA
Found at i:19666 original size:8 final size:8
Alignment explanation
Indices: 19653--19679 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
19643 TATTATAGAC
19653 TTTAAATT
1 TTTAAATT
19661 TTTAAATT
1 TTTAAATT
19669 TTTAAATT
1 TTTAAATT
19677 TTT
1 TTT
19680 CTATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAAATT
Found at i:21039 original size:24 final size:24
Alignment explanation
Indices: 21009--21069 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
20999 ATTGAATTAT
21009 AAATATTTGATTGAAAATTTATAA
1 AAATATTTGATTGAAAATTTATAA
*
21033 AAATATTTGAATGAAAATTTATAA
1 AAATATTTGATTGAAAATTTATAA
21057 AAATATTTTGATT
1 AAATA-TTTGATT
21070 ATTACACTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 28 0.82
25 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (24 bp):
AAATATTTGATTGAAAATTTATAA
Found at i:23224 original size:2 final size:2
Alignment explanation
Indices: 23217--23254 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
23207 ACTGGAAATG
23217 AT AT AT AT AT 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
23255 GATTGAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38095 original size:2 final size:2
Alignment explanation
Indices: 38088--38128 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
38078 AACACCAAAA
38088 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
38129 ATATCAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39125 original size:25 final size:25
Alignment explanation
Indices: 39090--39154 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
39080 GATTATAAAT
*
39090 TATAAATATATTT-AAATTAATATTA
1 TATAAAAATATTTCAAATTAA-ATTA
*
39115 TATAAAAATATTTCAATTTAAATTA
1 TATAAAAATATTTCAAATTAAATTA
39140 TA-AAGAAATATTTCA
1 TATAA-AAATATTTCA
39155 TGATGATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 2 0.06
25 28 0.78
26 6 0.17
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (25 bp):
TATAAAAATATTTCAAATTAAATTA
Found at i:39786 original size:20 final size:20
Alignment explanation
Indices: 39761--39853 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
39751 TTTTCCCAAT
39761 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
39781 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
39801 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
39822 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
39843 TCGCAATGCGA
1 TCGCAATGCGA
39854 TAATAAAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:39803 original size:41 final size:41
Alignment explanation
Indices: 39758--39871 Score: 185
Period size: 41 Copynumber: 2.8 Consensus size: 41
39748 CGATTTTCCC
39758 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
39799 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
* *
39840 AAATCGCAATGCGATAATAA-AAAATCGCAACG
1 AATTCGCAATGCG--AATAAGTAAATCGCAACG
39872 AGATACTTAC
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 53 0.77
42 11 0.16
43 5 0.07
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:39807 original size:21 final size:20
Alignment explanation
Indices: 39761--39853 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
39751 TTTTCCCAAT
*
39761 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
39781 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
39801 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
39822 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
39843 TCGCAATGCGA
1 TCGCAATGCGA
39854 TAATAAAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:39889 original size:20 final size:20
Alignment explanation
Indices: 39864--39916 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
39854 TAATAAAAAA
* *
39864 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
39884 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
39904 TCGCAACGCGATA
1 TCGCAACGCGATA
39917 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:40132 original size:22 final size:22
Alignment explanation
Indices: 40104--40147 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40094 CACTCTCTCA
40104 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
40126 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
40148 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:40420 original size:20 final size:20
Alignment explanation
Indices: 40391--40434 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
40381 GCGATTTTAG
40391 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
40411 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
40431 TTTC
1 TTTC
40435 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:41774 original size:18 final size:18
Alignment explanation
Indices: 41753--41797 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
41743 TCCACTTCGG
*
41753 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
41771 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
41789 GAGCCATCA
1 GAGCCATCA
41798 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:42295 original size:20 final size:20
Alignment explanation
Indices: 42270--42315 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
42260 TAGTTTACTT
*
42270 TCGCAACACGAAAATGATTA
1 TCGCAACACGAAAATGACTA
* * *
42290 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
42310 TCGCAA
1 TCGCAA
42316 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:42331 original size:19 final size:18
Alignment explanation
Indices: 42309--42366 Score: 63
Period size: 14 Copynumber: 3.4 Consensus size: 18
42299 GGAAATGGCT
42309 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
42328 ATCGCAA-CG-AA--AAA
1 ATCGCAAGCGAAATGAAA
42342 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
42360 ATCGCAA
1 ATCGCAA
42367 CGACAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
14 10 0.29
16 4 0.12
17 4 0.12
18 9 0.26
19 7 0.21
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:42356 original size:13 final size:14
Alignment explanation
Indices: 42325--42375 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
42315 ATGCGAAATG
42325 AAAATCGCAACGAA
1 AAAATCGCAACGAA
42339 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAA
*
42355 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAA
42371 AAAAT
1 AAAAT
42376 TAGTATATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 14 0.44
16 9 0.28
18 9 0.28
ACGTcount: A:0.53, C:0.22, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:42367 original size:32 final size:33
Alignment explanation
Indices: 42309--42375 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
42299 GGAAATGGCT
*
42309 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
*
42342 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
42374 AT
1 AT
42376 TAGTATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
Found at i:44230 original size:14 final size:14
Alignment explanation
Indices: 44211--44264 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
44201 GCGAAATGAA
44211 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
44225 AATCGCAATGCGAAATG
1 AATCGCAA--CGAGA-G
*
44242 AAATCGCAACGAGGG
1 -AATCGCAACGAGAG
44257 AATCGCAA
1 AATCGCAA
44265 TGCGAAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 16 0.48
15 1 0.03
16 7 0.21
17 1 0.03
18 8 0.24
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:44251 original size:32 final size:33
Alignment explanation
Indices: 44193--44285 Score: 170
Period size: 32 Copynumber: 2.8 Consensus size: 33
44183 GGAAATTACT
44193 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
44226 ATCGCAATGCGAAATG-AAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
44258 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
44286 CGAATTTAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.53
33 27 0.47
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:44307 original size:19 final size:20
Alignment explanation
Indices: 44285--44327 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
44275 AAATCGCAAC
44285 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
44304 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
44324 GCGA
1 GCGA
44328 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:44312 original size:14 final size:14
Alignment explanation
Indices: 44313--44346 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44303 TGCGATTTTC
44313 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
44327 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
44341 ATTTTC
1 ATTTTC
44347 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:44487 original size:14 final size:14
Alignment explanation
Indices: 44468--44504 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
44458 CATCAATTAA
44468 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
44482 ACAAATCACCTTTT
1 ACAAATCAACTTTT
44496 ACAAATCAA
1 ACAAATCAA
44505 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:45920 original size:21 final size:21
Alignment explanation
Indices: 45854--45920 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
45844 GTGAATCGGG
*
45854 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
45874 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
45896 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
45917 CTCT
1 CTCT
45921 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:45939 original size:42 final size:41
Alignment explanation
Indices: 45854--45976 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
45844 GTGAATCGGG
* * * * *
45854 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
45896 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
45938 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
45977 CGAGTCGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:48034 original size:14 final size:14
Alignment explanation
Indices: 48015--48070 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
48005 GGAAATGACT
48015 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
48029 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
48046 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
48062 ATCGCAACG
1 ATCGCAACG
48071 CGAAATGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:48048 original size:33 final size:33
Alignment explanation
Indices: 47991--48121 Score: 208
Period size: 33 Copynumber: 3.9 Consensus size: 33
47981 ACGAGATAAT
47991 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
48025 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* *
48058 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
48091 GACAATCGCAACGCGAAATGAAAATCGCAAC
1 GAGAATCGCAACGCGAAATGACTATCGCAAC
48122 CGCGAAATTA
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
33 77 0.85
34 14 0.15
ACGTcount: A:0.40, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:48053 original size:19 final size:19
Alignment explanation
Indices: 47966--48183 Score: 178
Period size: 19 Copynumber: 12.1 Consensus size: 19
47956 TCTTTTGGTT
*
47966 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
47985 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
48005 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
48023 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
48039 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
48056 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
48072 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
48090 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
48105 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
48125 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
48144 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
48163 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
48182 GA
1 GA
48184 TTTTGGTTTC
Statistics
Matches: 162, Mismatches: 19, Indels: 36
0.75 0.09 0.17
Matches are distributed among these distances:
14 28 0.17
15 4 0.02
16 4 0.02
17 3 0.02
18 5 0.03
19 71 0.44
20 45 0.28
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:48137 original size:39 final size:38
Alignment explanation
Indices: 47966--48183 Score: 178
Period size: 33 Copynumber: 6.1 Consensus size: 38
47956 TCTTTTGGTT
* *
47966 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
48005 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** *
48039 GAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
48072 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
48105 GAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
*
48144 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
48182 GA
1 GA
48184 TTTTGGTTTC
Statistics
Matches: 159, Mismatches: 12, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
33 75 0.47
34 16 0.10
35 2 0.01
38 24 0.15
39 28 0.18
40 14 0.09
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:48212 original size:19 final size:19
Alignment explanation
Indices: 48179--48223 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
48169 AAAATCGCAA
*
48179 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
48198 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
48217 TGCGATT
1 TGCGATT
48224 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:48805 original size:20 final size:20
Alignment explanation
Indices: 48777--48828 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
48767 CGCTAAGTAA
* *
48777 ATCGCGTTGCGAAAGTCAGT
1 ATCGTGTTGCGAAAGTAAGT
48797 ATCGTGTTGCGAAAGTAAGT
1 ATCGTGTTGCGAAAGTAAGT
48817 ATC-TCGTTGCGA
1 ATCGT-GTTGCGA
48829 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCGTGTTGCGAAAGTAAGT
Found at i:48889 original size:41 final size:41
Alignment explanation
Indices: 48839--48932 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
48829 TTTTTTATTA
* * *
48839 TCGCATTGCGATAGT-CAGAATCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGAT-GTACAGAATCACATTGCGAATTTCCCAAT
* ** *
48880 TCGCGTTGCGATTTACTTATTCACATTGCGAATTTCCCAAT
1 TCGCGTTGCGATGTACAGAATCACATTGCGAATTTCCCAAT
48921 TCGCGTTGCGAT
1 TCGCGTTGCGAT
48933 TTACTTATTC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.02
41 44 0.98
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.35
Consensus pattern (41 bp):
TCGCGTTGCGATGTACAGAATCACATTGCGAATTTCCCAAT
Found at i:48908 original size:20 final size:20
Alignment explanation
Indices: 48859--48951 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
48849 ATAGTCAGAA
* **
48859 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
48880 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* * **
48900 TCACATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
48921 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
48941 TCGCATTGCGA
1 TCGCATTGCGA
48952 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:48933 original size:41 final size:41
Alignment explanation
Indices: 48862--48954 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
48852 GTCAGAATCG
*
48862 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
1 CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCA
*
48903 CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCA
48944 CATTGCGAATT
1 CATTGCGAATT
48955 GGGAAAATCG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (41 bp):
CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCA
Found at i:58065 original size:13 final size:13
Alignment explanation
Indices: 58047--58071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58037 GAGACCGAAG
58047 CCGTGATTGCAGA
1 CCGTGATTGCAGA
58060 CCGTGATTGCAG
1 CCGTGATTGCAG
58072 CATTATTGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (13 bp):
CCGTGATTGCAGA
Found at i:59077 original size:2 final size:2
Alignment explanation
Indices: 59072--59096 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59062 TTAATGTGTG
59072 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 T
59097 TTTATTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59293 original size:44 final size:43
Alignment explanation
Indices: 59206--59294 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 43
59196 TGTTAAGTGC
* * **
59206 TATACTTTTTTATTTTATTTACTTACACTGTTGTGTTAGGTGT
1 TATACTTTTTTATTTTATTCACTTACACCGTTGTAATAGGTGT
*
59249 TATACTTTTTTTATTTTATTCACTTACACCCG-TGTAATATGTGT
1 TATAC-TTTTTTATTTTATTCACTTACA-CCGTTGTAATAGGTGT
59293 TA
1 TA
59295 AGTGCTACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 5 0.13
44 32 0.82
45 2 0.05
ACGTcount: A:0.21, C:0.12, G:0.11, T:0.55
Consensus pattern (43 bp):
TATACTTTTTTATTTTATTCACTTACACCGTTGTAATAGGTGT
Found at i:59294 original size:51 final size:51
Alignment explanation
Indices: 59258--59462 Score: 251
Period size: 50 Copynumber: 4.1 Consensus size: 51
59248 TTATACTTTT
*
59258 TTTATTTTATTCACTTACACCCGTGTAA-TATGTGTTAAGTGCTACAATT-
1 TTTATTTTATTCACTTACACCCGTGTAAGTATGTGTTAAGTGCTACACTTG
* * * *
59307 TGTTGTTTTATTCACTTACACCAGTGAAAGTATGTATTAAGTGCTACACTTG
1 T-TTATTTTATTCACTTACACCCGTGTAAGTATGTGTTAAGTGCTACACTTG
*** *
59359 TTTATTTT-TTCACTTACATTGGTGTAAGTACGTGTTAAGTGCTACACTTG
1 TTTATTTTATTCACTTACACCCGTGTAAGTATGTGTTAAGTGCTACACTTG
* *
59409 TTTATTTTATTCACTTACA-CCGATGTAAATATGTGTTAATTGCTACA-TT-
1 TTTATTTTATTCACTTACACCCG-TGTAAGTATGTGTTAAGTGCTACACTTG
59458 TTTAT
1 TTTAT
59463 GTAGTATGAA
Statistics
Matches: 134, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
49 6 0.04
50 71 0.53
51 56 0.42
52 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (51 bp):
TTTATTTTATTCACTTACACCCGTGTAAGTATGTGTTAAGTGCTACACTTG
Found at i:59397 original size:101 final size:99
Alignment explanation
Indices: 59256--59462 Score: 260
Period size: 101 Copynumber: 2.1 Consensus size: 99
59246 TGTTATACTT
* * *
59256 TTTTTATTTTATTCACTTACACCCGTGTAATATGTGTTAAGTGCTACAATT-TGTTGTTTTATTC
1 TTTTTATTTTATTCACTTACACCCGTGTAATACGTGTTAAGTGCTACACTTGT-TTATTTTATTC
59320 ACTTACACC-A-GTGAAAGTATGTATTAAGTGCTACA
65 ACTTACACCGATGT-AAA-TATGTATTAAGTGCTACA
***
59355 CTTGTTTATTTT-TTCACTTACATTGGTGTAAGTACGTGTTAAGTGCTACACTTGTTTATTTTAT
1 -TT-TTTATTTTATTCACTTACACCCGTGTAA-TACGTGTTAAGTGCTACACTTGTTTATTTTAT
* *
59419 TCACTTACACCGATGTAAATATGTGTTAATTGCTACA
63 TCACTTACACCGATGTAAATATGTATTAAGTGCTACA
59456 TTTTTAT
1 TTTTTAT
59463 GTAGTATGAA
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
99 5 0.05
100 20 0.21
101 62 0.66
102 5 0.05
103 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (99 bp):
TTTTTATTTTATTCACTTACACCCGTGTAATACGTGTTAAGTGCTACACTTGTTTATTTTATTCA
CTTACACCGATGTAAATATGTATTAAGTGCTACA
Found at i:60360 original size:2 final size:2
Alignment explanation
Indices: 60353--60427 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
60343 TAATACTGAA
60353 AT AT AT AT AT AT AT 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 AT
60395 AT AT AT AT AT AT AT AT AT -T 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
60428 GCTATAATTT
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:65310 original size:23 final size:23
Alignment explanation
Indices: 65284--65328 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
65274 CACCACAGCT
*
65284 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
65307 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
65329 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:65570 original size:147 final size:147
Alignment explanation
Indices: 65296--65607 Score: 522
Period size: 147 Copynumber: 2.1 Consensus size: 147
65286 TATAATTGCA
*
65296 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
65360 TTCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTTC
65 TTCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTTC
*
65425 CACAGAATAT-ATATATC
130 CAAAGAATATAATATATC
*
65442 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATGTAATAATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
65507 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTTTCAAGACTTCACACATGTT
66 T-CTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCTCAAGACTTCACACATGTT
*
65571 CCAAAGAATATACATATGTC
129 CCAAAGAATATA-ATATATC
65591 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
65608 CCCTCGACTC
Statistics
Matches: 156, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
145 1 0.01
146 62 0.40
147 69 0.44
148 1 0.01
149 23 0.15
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (147 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTTCC
AAAGAATATAATATATC
Found at i:67124 original size:21 final size:21
Alignment explanation
Indices: 67094--67138 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
67084 TGTTGTTCGT
*
67094 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
67115 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
67136 TTG
1 TTG
67139 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.