Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006361.1 Hibiscus syriacus cultivar Beakdansim tig00015251_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: 52156
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:352 original size:18 final size:18
Alignment explanation
Indices: 311--352 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
301 GTTAATCCAT
*
311 AAAAGATAAATTGAATTTC
1 AAAA-ATAAATTGAATCTC
*
330 GAAAATAAATTGAATCTC
1 AAAAATAAATTGAATCTC
348 AAAAA
1 AAAAA
353 ATTGAACTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (18 bp):
AAAAATAAATTGAATCTC
Found at i:704 original size:10 final size:10
Alignment explanation
Indices: 689--763 Score: 91
Period size: 10 Copynumber: 7.5 Consensus size: 10
679 TCTTGATCCC
689 TTTTTCTTCT
1 TTTTTCTTCT
699 TTTTTCTTCT
1 TTTTTCTTCT
709 TTTTTCTT-T
1 TTTTTCTTCT
*
718 TCTTTCTTCTT
1 TTTTTCTTC-T
729 TTTTTCTT-T
1 TTTTTCTTCT
*
738 TCTTTCTTCTT
1 TTTTTCTTC-T
*
749 TTTTTGTTCT
1 TTTTTCTTCT
759 TTTTT
1 TTTTT
764 TTTCAAGCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
9 16 0.29
10 24 0.43
11 16 0.29
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.81
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:714 original size:20 final size:20
Alignment explanation
Indices: 689--753 Score: 105
Period size: 20 Copynumber: 3.2 Consensus size: 20
679 TCTTGATCCC
*
689 TTTTTCTTCTTTTTTCTTC-T
1 TTTTTCTT-TTCTTTCTTCTT
709 TTTTTCTTTTCTTTCTTCTT
1 TTTTTCTTTTCTTTCTTCTT
729 TTTTTCTTTTCTTTCTTCTT
1 TTTTTCTTTTCTTTCTTCTT
749 TTTTT
1 TTTTT
754 GTTCTTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
19 9 0.21
20 34 0.79
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTCTTTCTTCTT
Found at i:720 original size:12 final size:12
Alignment explanation
Indices: 695--763 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
685 TCCCTTTTTC
695 TTCTTTTTTC--
1 TTCTTTTTTCTT
705 TTCTTTTTTCTT
1 TTCTTTTTTCTT
*
717 TTCTTTCTTCTT
1 TTCTTTTTTCTT
*
729 TTTTTCTTTTCTTT
1 TTCTT-TTTTC-TT
*
743 CTTCTTTTTT-TG
1 -TTCTTTTTTCTT
755 TTCTTTTTT
1 TTCTTTTTT
764 TTTCAAGCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
10 10 0.20
11 9 0.18
12 16 0.33
13 4 0.08
14 6 0.12
15 4 0.08
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.81
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:741 original size:32 final size:29
Alignment explanation
Indices: 689--764 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 29
679 TCTTGATCCC
*
689 TTTTTCTTC-TTTTTTCTTCTTTTTTCTT
1 TTTTTCTTCTTTTTTTCTTCTTTCTTCTT
717 TTCTTTCTTCTTTTTTTCTTTTCTTTCTTCTT
1 TT-TTTCTTCTTTTTTTC--TTCTTTCTTCTT
*
749 TTTTTGTTCTTTTTTT
1 TTTTTCTTCTTTTTTT
765 TTCAAGCATA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 2 0.05
29 7 0.17
30 7 0.17
31 13 0.31
32 13 0.31
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (29 bp):
TTTTTCTTCTTTTTTTCTTCTTTCTTCTT
Found at i:5238 original size:16 final size:18
Alignment explanation
Indices: 5217--5254 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
5207 AACTTCTTTT
5217 AAAAATAA-TTTTAAGA-
1 AAAAATAATTTTTAAGAC
5233 AAAAATAATTTTTAAGAC
1 AAAAATAATTTTTAAGAC
5251 AAAA
1 AAAA
5255 GCTGGTCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 8 0.40
18 4 0.20
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAAATAATTTTTAAGAC
Found at i:8651 original size:91 final size:92
Alignment explanation
Indices: 8481--8654 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 92
8471 TGATAGGTCA
* *
8481 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGACGAGTTCTTCTCATTATGAGCTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTCGGACGAGTTCTTCTCATTATGAACTC
8546 TCCATTAAAAATGTTGATGTGAAGTTG
66 TCCATTAAAAATGTTGATGTGAAGTTG
* * *
8573 AACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTT-GGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTCGGACGAGTTCTTCTCATTATGAACTC
* **
8637 TCTATTGGAAATGTTGAT
66 TCCATTAAAAATGTTGAT
8655 CCATCTCTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 39 0.53
92 35 0.47
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (92 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTCGGACGAGTTCTTCTCATTATGAACTC
TCCATTAAAAATGTTGATGTGAAGTTG
Found at i:8892 original size:332 final size:330
Alignment explanation
Indices: 8235--8893 Score: 1018
Period size: 332 Copynumber: 2.0 Consensus size: 330
8225 CCTTCGTCGT
*
8235 TGAATTGAACAAGTTCTTCTCATCATGAACTTCTTCTCTCTTGTGGATGAGTTCTTCTCATTATG
1 TGAATTGAACAAGTTCTTCTCATCATGAACTTCTTCTCTCTCGTGGATGAGTTCTTCTCATTATG
*
8300 AACTCTTCACTGAAAATGTTGAGTCACCTATTTCTGTGGTGGACTTGAAAGGAACAAGTTCTTCT
66 AACTCTTCACTGAAAATGTTGAGTCACCTATTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCT
* * *
8365 CATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTTTGGAAATGTCAATCC
131 CATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCA
* * * *
8430 CTCTAACGAGGTGTTACTGATTCGAAATGTCGTGAATCGAGTGATAGGTCAAACAAGCTCTTCTC
196 CTCTAACGAGGTATCACTGATTCGAAATGACGTGAATCGAGTGATAGGTCAAACAAGATCTTCTC
* * * *
8495 ATTATGAACTTCTTCTCCCTCTTTCGGACGAGTTCTTCTCATTATGAGCTCTCCATTAAAAATGT
261 ATTATGAACTTCTTCTCCCTCTGTCGGACAAGTTCTTCTCATTATGAACTATCCATTAAAAATGT
8560 TGATG
326 TGATG
*
8565 TGAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTA
1 TGAA-TTGAACAAGTTCTTCTCATCATGAACTTCTTCTCTCTCG-TGGATGAGTTCTTCTCATTA
* * * *
8630 TGAACTC-TCTATTGGAAATGTTGA-TCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTC
64 TGAACTCTTC-ACTGAAAATGTTGAGT-CACCTATTTCTGTGATGGACTTGAAAGGAACAAGTTC
*
8693 TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCA
127 TTCTCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCA
**
8758 ATCACTC-AAGCGAGGTATCACTGATTCGAAATGACGTGAATCGAGTGATAGGTTGAACAAGATC
192 ATCACTCTAA-CGAGGTATCACTGATTCGAAATGACGTGAATCGAGTGATAGGTCAAACAAGATC
* * * **
8822 TTCTCATTATGAACTTTTTCTTCCTCTGTCGGATAAGTTCTTCTCATTATGAACTATCCATTGGA
256 TTCTCATTATGAACTTCTTCTCCCTCTGTCGGACAAGTTCTTCTCATTATGAACTATCCATTAAA
8887 AATGTTG
321 AATGTTG
8894 GTTCACCTCC
Statistics
Matches: 298, Mismatches: 26, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
330 4 0.01
331 42 0.14
332 252 0.85
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (330 bp):
TGAATTGAACAAGTTCTTCTCATCATGAACTTCTTCTCTCTCGTGGATGAGTTCTTCTCATTATG
AACTCTTCACTGAAAATGTTGAGTCACCTATTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCT
CATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTCAATCA
CTCTAACGAGGTATCACTGATTCGAAATGACGTGAATCGAGTGATAGGTCAAACAAGATCTTCTC
ATTATGAACTTCTTCTCCCTCTGTCGGACAAGTTCTTCTCATTATGAACTATCCATTAAAAATGT
TGATG
Found at i:9778 original size:8 final size:8
Alignment explanation
Indices: 9767--9827 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
9757 CCTTTTTCTC
9767 TTTTCATT
1 TTTTCATT
9775 TTTTCATT
1 TTTTCATT
**
9783 TCTTTTTTT
1 T-TTTCATT
*
9792 TTTTCATC
1 TTTTCATT
9800 TTTTCATCT
1 TTTTCAT-T
9809 TTTT-ATT
1 TTTTCATT
* *
9816 TGTTCCTT
1 TTTTCATT
9824 TTTT
1 TTTT
9828 TCTTCAAGCA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 4 0.10
8 27 0.66
9 10 0.24
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (8 bp):
TTTTCATT
Found at i:9826 original size:33 final size:32
Alignment explanation
Indices: 9759--9830 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
9749 CTAAAACCCC
**
9759 TTTTTCTCTTTTCATTTTTTCATTTCTTTTTT
1 TTTTTCTCTTTTCATTTTTTCATTTCTTCCTT
*
9791 TTTTTCATCTTTTCATCTTTTT-ATTTGTTCCTT
1 TTTTTC-TCTTTTCAT-TTTTTCATTTCTTCCTT
9824 TTTTTCT
1 TTTTTCT
9831 TCAAGCATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 7 0.20
33 23 0.66
34 5 0.14
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (32 bp):
TTTTTCTCTTTTCATTTTTTCATTTCTTCCTT
Found at i:20815 original size:16 final size:18
Alignment explanation
Indices: 20794--20831 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
20784 AACGTCTTTT
20794 AAAAATA-ATTTTAAGA-
1 AAAAATATATTTTAAGAC
*
20810 AAAAATATTTTTTAAGAC
1 AAAAATATATTTTAAGAC
20828 AAAA
1 AAAA
20832 GATGGTATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAAATATATTTTAAGAC
Found at i:21496 original size:13 final size:13
Alignment explanation
Indices: 21478--21538 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
21468 TGCGTCATAA
*
21478 ATTTATGACGTGC
1 ATTTATGACGCGC
* *
21491 ATTTATGACACGT
1 ATTTATGACGCGC
*
21504 ATTTATGACGCAC
1 ATTTATGACGCGC
*
21517 ATTTATGACGCGT
1 ATTTATGACGCGC
21530 ATTTATGAC
1 ATTTATGAC
21539 TCACATTGCG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:21519 original size:26 final size:26
Alignment explanation
Indices: 21478--21545 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
21468 TGCGTCATAA
**
21478 ATTTATGACGTGCATTTATGACACGT
1 ATTTATGACGCACATTTATGACACGT
*
21504 ATTTATGACGCACATTTATGACGCGT
1 ATTTATGACGCACATTTATGACACGT
*
21530 ATTTATGACTCACATT
1 ATTTATGACGCACATT
21546 GCGCGTCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (26 bp):
ATTTATGACGCACATTTATGACACGT
Found at i:21622 original size:85 final size:85
Alignment explanation
Indices: 21517--21674 Score: 244
Period size: 85 Copynumber: 1.9 Consensus size: 85
21507 TATGACGCAC
* * * *
21517 ATTTATGACGCGTATTTATGACTCACATTGCGCGTCATTGAAGCCCCTGTCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACTCACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
21582 CACACATTTTTGTGTCATAA
66 CACACATTTTTGTGTCATAA
* * * *
21602 ATTTATGACACGCATTTATGACTTACATTGTGTGTCATTGAAGCCCCCGTTATAAATGAAAATGA
1 ATTTATGACACGCATTTATGACTCACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
21667 CACACATT
66 CACACATT
21675 CGTGTGTCGT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 65 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACTCACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
CACACATTTTTGTGTCATAA
Found at i:32257 original size:182 final size:185
Alignment explanation
Indices: 32062--32447 Score: 584
Period size: 182 Copynumber: 2.1 Consensus size: 185
32052 TTAAATTTTT
* * *
32062 AATATTAAATATATTATATATAACATATGAGCTCAA-CCTAAACCGTTTAAAACTCAATTAATAA
1 AATATTAAATATATTATATATAACATATGAGCT-AAGCCCAAACCATTTAAAACCCAATTAATAA
* *
32126 TTTAAGATTCAATAACTTTTAAACCAAAATCAATATTAATTAATTAAAAAA-TTATATAAAATTT
65 TTTAAAATCCAATAACTTTTAAACCAAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
*
32190 TTATTTTATAATTATATATTATTTAAATTAATTGTAAAC-TGTTTTT-AATTAAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTGTTTTTGAATTAAAA
* *
32244 AATATTAAATATATTATATATAACGTATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAAT
1 AATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAAT
* * *
32309 TTAAAATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTTT
66 TTAAAATCCAATAACTTTTAAACCAAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTT
* *
32374 TATTTTATAATTATTTATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTTGTTTTTGAATTAAAA
* * *
32429 AACATTTAAT-TTTTATATA
1 AATATTAAATATATTATATA
32448 AATTAGAAAT
Statistics
Matches: 184, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
181 2 0.01
182 104 0.57
183 48 0.26
184 14 0.08
185 16 0.09
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (185 bp):
AATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAAT
TTAAAATCCAATAACTTTTAAACCAAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTTGTTTTTGAATTAAAA
Found at i:34605 original size:23 final size:23
Alignment explanation
Indices: 34573--34618 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
34563 ATGCCAACTT
*
34573 CTTTTTTTCTTC-TCATTCTTTTC
1 CTTTTCTTCTTCTTC-TTCTTTTC
34596 CTTTTCTTCTTCTTCTTCTTTTC
1 CTTTTCTTCTTCTTCTTCTTTTC
34619 TTTGAAGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (23 bp):
CTTTTCTTCTTCTTCTTCTTTTC
Found at i:39148 original size:90 final size:89
Alignment explanation
Indices: 39036--39208 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
39026 TAACCCCAAA
* *
39036 TATTTAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
39101 TAGGGTAACTTGGATATAAGAGGAT
65 TAGGGTAACTTGGATATAAGAGGAT
*
39126 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
*
39191 AGGGTAACTTGGCTATAA
66 AGGGTAACTTGGATATAA
39209 AAGGGTGTGT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 30 0.38
90 49 0.62
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAGAGGAT
Found at i:40379 original size:19 final size:20
Alignment explanation
Indices: 40340--40383 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
40330 ACAATTGAAT
40340 TTGCCACGACATTTCATCCAA
1 TTGCCACGACA-TTCATCCAA
40361 CTTGCCACGACA-T-ATCCAA
1 -TTGCCACGACATTCATCCAA
40380 TTGC
1 TTGC
40384 GACCACACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 1 0.05
22 11 0.50
ACGTcount: A:0.27, C:0.34, G:0.11, T:0.27
Consensus pattern (20 bp):
TTGCCACGACATTCATCCAA
Found at i:40738 original size:26 final size:29
Alignment explanation
Indices: 40685--40747 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 29
40675 CATAGCATTG
* *
40685 TTATTTTACTTGTTTATATTTCTTTTATA
1 TTATTTTACATGTTTATATTTCTCTTATA
*
40714 TTATTTTACAT-TTTAT-TTT-TCTTATC
1 TTATTTTACATGTTTATATTTCTCTTATA
*
40740 TTTTTTTA
1 TTATTTTA
40748 GTTTTCGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 12 0.40
27 3 0.10
28 5 0.17
29 10 0.33
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (29 bp):
TTATTTTACATGTTTATATTTCTCTTATA
Found at i:46651 original size:21 final size:19
Alignment explanation
Indices: 46622--46664 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
46612 GGGTACTGAC
* *
46622 ACTGACCCTTTAGTATCGAT
1 ACTGACCC-TGAGTATCAAT
46642 ACTGAACCCTGAGTATCAAT
1 ACTG-ACCCTGAGTATCAAT
46662 ACT
1 ACT
46665 TGCGTATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (19 bp):
ACTGACCCTGAGTATCAAT
Found at i:51690 original size:22 final size:23
Alignment explanation
Indices: 51652--51696 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
51642 ATAAAAATAT
*
51652 AATTTAAATATAGTTTT-ATTAA
1 AATTTAAATATAATTTTAATTAA
51674 AATTTAAACTA-AATTTTAATTAA
1 AATTTAAA-TATAATTTTAATTAA
51697 TGGTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTTAAATATAATTTTAATTAA
Done.