Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000425.1 Hibiscus syriacus cultivar Beakdansim tig00000776_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: 85765
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1343 original size:29 final size:29
Alignment explanation
Indices: 1310--1367 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1300 AGAACAAGAG
1310 AACCGAGTAAATGAACCTATAAATGAGTC
1 AACCGAGTAAATGAACCTATAAATGAGTC
1339 AACCGAGTAAATGAACCTATAAATGAGTC
1 AACCGAGTAAATGAACCTATAAATGAGTC
1368 GATAAATGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (29 bp):
AACCGAGTAAATGAACCTATAAATGAGTC
Found at i:3851 original size:143 final size:145
Alignment explanation
Indices: 3681--3968 Score: 494
Period size: 143 Copynumber: 2.0 Consensus size: 145
3671 TTATGTGAAA
*
3681 TATGGACAATACACACATACTTACAAAATGTAACTACTCGAATTTTATTAGGTACAGTGATACCC
1 TATGGACAATACACACATACTTACAAAATGTAACTACTCGAATTTTATTAGGTACACTGATACCC
3746 TTAAATTTTGACAAAATTTTTATATGATACATGTA-TTCCAAAAT-TTCAA-TTCTCTTTATACT
66 TTAAATTTTG--AAAATTTTTATATGATACATGTATTTCCAAAATATTCAATTTCTCTTTATACT
3808 TTCTTTTGGCATTCTTT
129 TTCTTTTGGCATTCTTT
* *
3825 TATGGAC-ATACACACATACTTGCAAAATGTAACTACTCGAATTTTATTAGGTACACTGATGCCC
1 TATGGACAATACACACATACTTACAAAATGTAACTACTCGAATTTTATTAGGTACACTGATACCC
*
3889 TTAAATTTTGAAAATTTTTATATGATATATGTATTTCCAAAATATTCAATTTCTCTTTATACTTT
66 TTAAATTTTGAAAATTTTTATATGATACATGTATTTCCAAAATATTCAATTTCTCTTTATACTTT
3954 CTTTTGGCATTCTTT
131 CTTTTGGCATTCTTT
3969 ATGATTAGTG
Statistics
Matches: 137, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
141 22 0.16
142 9 0.07
143 69 0.50
144 37 0.27
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.42
Consensus pattern (145 bp):
TATGGACAATACACACATACTTACAAAATGTAACTACTCGAATTTTATTAGGTACACTGATACCC
TTAAATTTTGAAAATTTTTATATGATACATGTATTTCCAAAATATTCAATTTCTCTTTATACTTT
CTTTTGGCATTCTTT
Found at i:5960 original size:16 final size:16
Alignment explanation
Indices: 5921--5965 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
5911 TTTTAAATAT
5921 ATATTTATAAA-ATTTA
1 ATATTTA-AAATATTTA
5937 ATTATTTAAAATATTTA
1 A-TATTTAAAATATTTA
5954 ATATTTAAAATA
1 ATATTTAAAATA
5966 ATCATAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTTAAAATATTTA
Found at i:13341 original size:2 final size:2
Alignment explanation
Indices: 13336--13364 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13326 TTTTTTGTTC
13336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13365 AGAGAAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18269 original size:17 final size:18
Alignment explanation
Indices: 18246--18287 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
18236 GTTGTTTTTA
*
18246 AAATAAAAGACAAGAATT
1 AAATAAAAGAAAAGAATT
*
18264 -AATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
18281 AAATAAA
1 AAATAAA
18288 TAATTTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:21070 original size:20 final size:19
Alignment explanation
Indices: 21024--21074 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
21014 ACCGATTCAA
21024 GTGGTATCGATACCAAGAG
1 GTGGTATCGATACCAAGAG
* * *
21043 GGGAGTATCGATACTATGAG
1 GTG-GTATCGATACCAAGAG
21063 GATGGTATCGAT
1 G-TGGTATCGAT
21075 GCCATGGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 23 0.88
21 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.25
Consensus pattern (19 bp):
GTGGTATCGATACCAAGAG
Found at i:21444 original size:15 final size:15
Alignment explanation
Indices: 21424--21452 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21414 TGCATTTAAT
21424 TGTGTAACTATATGG
1 TGTGTAACTATATGG
21439 TGTGTAACTATATG
1 TGTGTAACTATATG
21453 TTATACTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (15 bp):
TGTGTAACTATATGG
Found at i:21782 original size:54 final size:54
Alignment explanation
Indices: 21508--21784 Score: 351
Period size: 54 Copynumber: 5.1 Consensus size: 54
21498 TTACCAAATA
* *
21508 GGCACTAAGTGTGCAAATCA-TAGAATTCATCATATGTTGATGAATAACCGTTTT
1 GGCACTAAGTGTGCAAATCACGA-AATTCATCATATGTTGATGAATAACCGTTTC
* *
21562 GGTACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACTGTTTC
1 GGCACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
*
21616 GGTACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * * *
21670 AGCACTAAGTGTGCAAAGT-ACGAAATTCATCATAGGTTAATGAATAATCGTTTC
1 GGCACTAAGTGTGCAAA-TCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* ** * * * * * * *
21724 GGCACTATGTGTATAAACCACGAAATTCGTAATATGTTTATGAATGACCGTATG
1 GGCACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
21778 GGCACTA
1 GGCACTA
21785 CGGGTGCATT
Statistics
Matches: 197, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
54 195 0.99
55 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (54 bp):
GGCACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:22594 original size:20 final size:21
Alignment explanation
Indices: 22571--22609 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
22561 TCATTCACAA
*
22571 AAAGGGATCGAT-CTTTTTGC
1 AAAGGGATCAATCCTTTTTGC
22591 AAAGGGATCAATCCTTTTT
1 AAAGGGATCAATCCTTTTT
22610 ATGGAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (21 bp):
AAAGGGATCAATCCTTTTTGC
Found at i:22646 original size:50 final size:49
Alignment explanation
Indices: 22572--22668 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 49
22562 CATTCACAAA
* *
22572 AAGGGATCGATCTTTTTGCAAAGGGATCAATCCTTTTTATGGAAAATGC
1 AAGGGATCGATCTTTTTGCAAAGGGATCAATCATTTTTATAGAAAATGC
* *
22621 AAGGGATCGATCCTTTTCT-CAAAGGGATCGATCATTTTTCTAGAAAAT
1 AAGGGATCGAT-CTTTT-TGCAAAGGGATCAATCATTTTTATAGAAAAT
22669 TGTATTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
49 11 0.26
50 30 0.71
51 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (49 bp):
AAGGGATCGATCTTTTTGCAAAGGGATCAATCATTTTTATAGAAAATGC
Found at i:30082 original size:16 final size:16
Alignment explanation
Indices: 30045--30090 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
30035 TATATAATCT
*
30045 AAAA-ATAAAAT-TTA
1 AAAATATAAAATATAA
*
30059 AAAGTATAAAATATAA
1 AAAATATAAAATATAA
*
30075 AAAATATAAATTATAA
1 AAAATATAAAATATAA
30091 TTATAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 3 0.12
15 7 0.27
16 16 0.62
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAATATAAAATATAA
Found at i:33302 original size:41 final size:40
Alignment explanation
Indices: 33222--33298 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
33212 TTAGTGTGCA
*
33222 AGTATCGATACTTCTTCATTGAGTATCAATATCATGGGTAG
1 AGTATCGATACTCCTTCATTGAGTATCAATA-CATGGGTAG
33263 AGTATCGATACTCCTT-ATATGAGTATCAATA-ATGGG
1 AGTATCGATACTCCTTCAT-TGAGTATCAATACATGGG
33299 GGTATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
39 5 0.15
40 2 0.06
41 27 0.79
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.35
Consensus pattern (40 bp):
AGTATCGATACTCCTTCATTGAGTATCAATACATGGGTAG
Found at i:35445 original size:14 final size:14
Alignment explanation
Indices: 35426--35454 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35416 TTAATTATTC
35426 ATTAATAAATTTAT
1 ATTAATAAATTTAT
35440 ATTAATAAATTTAT
1 ATTAATAAATTTAT
35454 A
1 A
35455 CTTTATAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTAATAAATTTAT
Found at i:35940 original size:15 final size:15
Alignment explanation
Indices: 35917--35963 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
35907 AATAAAATGC
* *
35917 TTAAGTAAAAATTGT
1 TTAACTAAAAATTAT
35932 TTAACTAAAAATTAT
1 TTAACTAAAAATTAT
* *
35947 TTAAATGAAAATTAT
1 TTAACTAAAAATTAT
35962 TT
1 TT
35964 TCAATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (15 bp):
TTAACTAAAAATTAT
Found at i:35969 original size:25 final size:25
Alignment explanation
Indices: 35941--36001 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
35931 TTTAACTAAA
*
35941 AATTATTT-AAATGAAAATTATTTTC
1 AATTATTTCAAA-AAAAATTATTTTC
*
35966 AATTTTTTCAAAAAAAATTATTTTC
1 AATTATTTCAAAAAAAATTATTTTC
35991 AA--ATTTCAAAA
1 AATTATTTCAAAA
36002 CAATTCTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 8 0.25
25 21 0.66
26 3 0.09
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (25 bp):
AATTATTTCAAAAAAAATTATTTTC
Found at i:37582 original size:27 final size:27
Alignment explanation
Indices: 37542--37623 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
37532 TCAGAATTCA
**
37542 TAAAA-AATAATATATATTATTTTAA-T
1 TAAAATAATAATATAT-TTATTAAAACT
37568 TAAAATAATAATATATTTATTAAAACT
1 TAAAATAATAATATATTTATTAAAACT
**
37595 TGTAATAATAATATATTTATTAAAACT
1 TAAAATAATAATATATTTATTAAAACT
37622 TA
1 TA
37624 TCACCTCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 12 0.24
27 37 0.76
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (27 bp):
TAAAATAATAATATATTTATTAAAACT
Found at i:38162 original size:10 final size:10
Alignment explanation
Indices: 38147--38197 Score: 93
Period size: 10 Copynumber: 5.1 Consensus size: 10
38137 ACACATGCAA
38147 AGCTTACATC
1 AGCTTACATC
38157 AGCTTACATC
1 AGCTTACATC
*
38167 AGCTTACATT
1 AGCTTACATC
38177 AGCTTACATC
1 AGCTTACATC
38187 AGCTTACATC
1 AGCTTACATC
38197 A
1 A
38198 TTCACTCAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 39 1.00
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.31
Consensus pattern (10 bp):
AGCTTACATC
Found at i:40642 original size:5 final size:5
Alignment explanation
Indices: 40628--40920 Score: 579
Period size: 5 Copynumber: 58.8 Consensus size: 5
40618 TTTATTTGAT
40628 AATA- AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
40677 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
40727 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
40777 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
40827 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
40877 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATA
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATA
40921 TGATTCAATT
Statistics
Matches: 288, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
4 4 0.01
5 284 0.99
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAC
Found at i:42753 original size:11 final size:11
Alignment explanation
Indices: 42737--42856 Score: 123
Period size: 11 Copynumber: 10.5 Consensus size: 11
42727 TAGCAGTCTT
42737 GAGCTTGAATC
1 GAGCTTGAATC
*
42748 GAGCTTGAATT
1 GAGCTTGAATC
**
42759 GAGCTCAAAATC
1 GAGCT-TGAATC
42771 GAGCTTGAATC
1 GAGCTTGAATC
42782 GAGCTTGAATC
1 GAGCTTGAATC
42793 GAGCTTGAATC
1 GAGCTTGAATC
*
42804 GAGCTTGAGTCTC
1 GAGCTTGA--ATC
*
42817 GAGCTTCAATC
1 GAGCTTGAATC
* *
42828 GAGCTCGAGTCTC
1 GAGCTTGA--ATC
*
42841 GAGCTTCAATC
1 GAGCTTGAATC
42852 GAGCT
1 GAGCT
42857 CTTGAAATTT
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
11 64 0.72
12 8 0.09
13 17 0.19
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (11 bp):
GAGCTTGAATC
Found at i:42760 original size:22 final size:22
Alignment explanation
Indices: 42737--42856 Score: 123
Period size: 24 Copynumber: 5.2 Consensus size: 22
42727 TAGCAGTCTT
*
42737 GAGCTTGAATCGAGCTTGAATT
1 GAGCTTGAATCGAGCTTGAATC
**
42759 GAGCTCAAAATCGAGCTTGAATC
1 GAGCT-TGAATCGAGCTTGAATC
42782 GAGCTTGAATCGAGCTTGAATC
1 GAGCTTGAATCGAGCTTGAATC
* *
42804 GAGCTTGAGTCTCGAGCTTCAATC
1 GAGCTTGA--ATCGAGCTTGAATC
* * *
42828 GAGCTCGAGTCTCGAGCTTCAATC
1 GAGCTTGA--ATCGAGCTTGAATC
42852 GAGCT
1 GAGCT
42857 CTTGAAATTT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
22 28 0.32
23 19 0.22
24 40 0.46
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (22 bp):
GAGCTTGAATCGAGCTTGAATC
Found at i:42827 original size:24 final size:24
Alignment explanation
Indices: 42769--42856 Score: 126
Period size: 24 Copynumber: 3.8 Consensus size: 24
42759 GAGCTCAAAA
* *
42769 TCGAGCTTGAATCGAGCTTGA--A
1 TCGAGCTTCAATCGAGCTTGAGTC
*
42791 TCGAGCTTGAATCGAGCTTGAGTC
1 TCGAGCTTCAATCGAGCTTGAGTC
*
42815 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTTGAGTC
42839 TCGAGCTTCAATCGAGCT
1 TCGAGCTTCAATCGAGCT
42857 CTTGAAATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 21 0.34
24 40 0.66
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (24 bp):
TCGAGCTTCAATCGAGCTTGAGTC
Found at i:48652 original size:40 final size:39
Alignment explanation
Indices: 48582--48661 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
48572 CCCAAGAAAG
* *
48582 GAACCCCAAAAAATAAAAAAACCAGGACGAAGGAGAGAT
1 GAACCCCAAAAAATAAAAAAACCAGAACGAAGAAGAGAT
* *
48621 GAACCCCAAAAAA-ACGAAGAACCCAGAACGAAGAAGAGAT
1 GAACCCCAAAAAATA--AAAAAACCAGAACGAAGAAGAGAT
48661 G
1 G
48662 GGAAAAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 1 0.03
39 13 0.37
40 21 0.60
ACGTcount: A:0.55, C:0.20, G:0.21, T:0.04
Consensus pattern (39 bp):
GAACCCCAAAAAATAAAAAAACCAGAACGAAGAAGAGAT
Found at i:53389 original size:32 final size:33
Alignment explanation
Indices: 53348--53535 Score: 149
Period size: 32 Copynumber: 5.9 Consensus size: 33
53338 AGTCGACGGT
* * *
53348 TTACCTATGTTC-TACGGAACATATGGACAAAA
1 TTACCTATGTTCTTTCGGGACATATGGACAGAA
* *
53380 TTACCTATG-TCTTTCGGGACATATGTATAGAA
1 TTACCTATGTTCTTTCGGGACATATGGACAGAA
* * *
53412 TTACCTAT-TTCTTTTGGGGCATATGGATAGAA
1 TTACCTATGTTCTTTCGGGACATATGGACAGAA
* * *
53444 TTACCTACG-TCTTTCGGGGCATATGGACAGTA
1 TTACCTATGTTCTTTCGGGACATATGGACAGAA
** * * *
53476 -TACCTATGTTC-TAAGGAACATATGAACAG-T
1 TTACCTATGTTCTTTCGGGACATATGGACAGAA
* * *
53506 TTACCTAGGTTC-TTCGAGACCTATGGACAG
1 TTACCTATGTTCTTTCGGGACATATGGACAG
53536 TTGTCGAGGT
Statistics
Matches: 125, Mismatches: 26, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
31 44 0.35
32 81 0.65
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (33 bp):
TTACCTATGTTCTTTCGGGACATATGGACAGAA
Found at i:70890 original size:20 final size:20
Alignment explanation
Indices: 70865--70922 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
70855 TATTTAAGAA
70865 TAATTATAATAATATTTTT-T
1 TAATTA-AATAATATTTTTAT
70885 TAATTAAATAATTATTTTTAT
1 TAATTAAATAA-TATTTTTAT
*
70906 TGAATAAAAATAATATT
1 T-AAT-TAAATAATATT
70923 ATATTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.15
20 13 0.39
21 2 0.06
22 7 0.21
23 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATTAAATAATATTTTTAT
Found at i:70895 original size:22 final size:23
Alignment explanation
Indices: 70870--70922 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
70860 AAGAATAATT
70870 ATAATAATATTTTT-TT-AATTAA
1 ATAATAATATTTTTATTGAA-TAA
70892 ATAAT--TATTTTTATTGAATAA
1 ATAATAATATTTTTATTGAATAA
70913 A-AATAATATT
1 ATAATAATATT
70923 ATATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 10 0.37
21 6 0.22
22 11 0.41
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATAATAATATTTTTATTGAATAA
Done.