Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004320.1 Hibiscus syriacus cultivar Beakdansim tig00009471_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: 75823
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:281 original size:23 final size:23
Alignment explanation
Indices: 255--307 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
245 CTCATATAAA
*
255 TGCACTGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
278 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
301 TGCACCG
1 TGCACCG
308 TATGCCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:308 original size:23 final size:23
Alignment explanation
Indices: 263--314 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
253 AATGCACTGA
263 AGTGCCACATAGAATTGCACCGT
1 AGTGCCACATAGAATTGCACCGT
*
286 AGTGCCACGTAGAATTGCACCGT
1 AGTGCCACATAGAATTGCACCGT
309 A-TGCCA
1 AGTGCCA
315 TATAATATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (23 bp):
AGTGCCACATAGAATTGCACCGT
Found at i:1610 original size:19 final size:19
Alignment explanation
Indices: 1586--1629 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1576 TCTTTTATAT
1586 TCATATAATTTATATCATA
1 TCATATAATTTATATCATA
**
1605 TCATATGGTTTATATCATA
1 TCATATAATTTATATCATA
*
1624 ACATAT
1 TCATAT
1630 CACTATTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (19 bp):
TCATATAATTTATATCATA
Found at i:2080 original size:21 final size:21
Alignment explanation
Indices: 2050--2094 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2040 ATTCTGTCGT
* *
2050 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2071 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2092 TTG
1 TTG
2095 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3063 original size:15 final size:15
Alignment explanation
Indices: 3039--3076 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3029 TATATATAGT
3039 ATTA-TTTTCTATTC
1 ATTATTTTTCTATTC
*
3053 ATTATTTTTCTATTT
1 ATTATTTTTCTATTC
*
3068 TTTATTTTT
1 ATTATTTTT
3077 ATTTATACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTATTTTTCTATTC
Found at i:3080 original size:21 final size:21
Alignment explanation
Indices: 3054--3114 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
3044 TTTCTATTCA
3054 TTATTTTTCTATTTTTTATTT
1 TTATTTTTCTATTTTTTATTT
* * *
3075 TTATTTATACTATTATAT-TTT
1 TTATTT-TTCTATTTTTTATTT
* *
3096 TTAATTAT-TATTTTTTATT
1 TTATTTTTCTATTTTTTATT
3115 ATGTATGTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
19 6 0.20
20 2 0.07
21 14 0.47
22 8 0.27
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATTTTTCTATTTTTTATTT
Found at i:3181 original size:2 final size:2
Alignment explanation
Indices: 3176--3216 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3166 TTATGTACGT
3176 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
3217 TATTTATTTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3624 original size:22 final size:21
Alignment explanation
Indices: 3598--3648 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
3588 TTTTGTTTTA
3598 TTTTTATTCATTCTAT-TATT
1 TTTTTATTCATTCTATCTATT
*
3618 TCGTTTTATTTATTCTATCTATT
1 T--TTTTATTCATTCTATCTATT
3641 TTTTTATT
1 TTTTTATT
3649 TTTTTATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.04
21 7 0.26
22 14 0.52
23 5 0.19
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTATTCATTCTATCTATT
Found at i:3660 original size:25 final size:25
Alignment explanation
Indices: 3598--3673 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 25
3588 TTTTGTTTTA
* **
3598 TTTTTATTC-ATTCTATTATTTCGTT
1 TTTTTATTCTA-TCTATTTTTTTATT
3623 TTATTTATTCTATCTATTTTTTTATT
1 TT-TTTATTCTATCTATTTTTTTATT
3649 TTTTTATTCTATCTA-TTTTTTATT
1 TTTTTATTCTATCTATTTTTTTATT
3673 T
1 T
3674 AATTTTATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
24 10 0.22
25 15 0.33
26 20 0.43
27 1 0.02
ACGTcount: A:0.17, C:0.09, G:0.01, T:0.72
Consensus pattern (25 bp):
TTTTTATTCTATCTATTTTTTTATT
Found at i:3679 original size:29 final size:26
Alignment explanation
Indices: 3621--3678 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
3611 TATTATTTCG
3621 TTTTATTTATTCTATCTATTTTTTTA
1 TTTTATTTATTCTATCTATTTTTTTA
3647 TTTT-TTTATTCTATCTA-TTTTTTA
1 TTTTATTTATTCTATCTATTTTTTTA
*
3671 TTTAATTT
1 TTTTATTT
3679 TATGTCTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 10 0.33
25 16 0.53
26 4 0.13
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTTATTTATTCTATCTATTTTTTTA
Found at i:10973 original size:21 final size:20
Alignment explanation
Indices: 10939--11032 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 20
10929 AATATAAAAT
*
10939 TGTCCCTAAGGACCTCATATA
1 TGTCCC-AAAGACCTCATATA
10960 TGTCCCAAATGACCAT-ATATA
1 TGTCCCAAA-GACC-TCATATA
* * * *
10981 TATCTCGAAAGACCACATATG
1 TGTC-CCAAAGACCTCATATA
**
11002 TGTCCCAAAGAACGACATATA
1 TGTCCCAAAG-ACCTCATATA
*
11023 TGTTCCAAAG
1 TGTCCCAAAG
11033 GATTACATAC
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
20 7 0.12
21 46 0.79
22 5 0.09
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (20 bp):
TGTCCCAAAGACCTCATATA
Found at i:11040 original size:21 final size:21
Alignment explanation
Indices: 11002--11062 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
10992 ACCACATATG
* * *
11002 TGTCCCAAAGAACGACATATA
1 TGTCCCAAAGGACTACATACA
* *
11023 TGTTCCAAAGGATTACATACA
1 TGTCCCAAAGGACTACATACA
*
11044 TGTCCCGAAGGACTACATA
1 TGTCCCAAAGGACTACATA
11063 GAACCCTCGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (21 bp):
TGTCCCAAAGGACTACATACA
Found at i:17375 original size:21 final size:22
Alignment explanation
Indices: 17342--17385 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
17332 AGTTGATCCA
17342 TACCGTGTATGATATTTTGTAT
1 TACCGTGTATGATATTTTGTAT
* * *
17364 TACCTTGT-TGATTTTTTTTAT
1 TACCGTGTATGATATTTTGTAT
17385 T
1 T
17386 TCTACGATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.18, C:0.09, G:0.14, T:0.59
Consensus pattern (22 bp):
TACCGTGTATGATATTTTGTAT
Found at i:23916 original size:29 final size:30
Alignment explanation
Indices: 23884--23940 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
23874 GTTTAGAGCT
*
23884 CTAATTATAAATA-TAAAAAATTGGGAGAC
1 CTAATTATAAATACAAAAAAATTGGGAGAC
23913 CTAATTATAAATACAAAAAAATTGGGAG
1 CTAATTATAAATACAAAAAAATTGGGAG
23941 CACTGAGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (30 bp):
CTAATTATAAATACAAAAAAATTGGGAGAC
Found at i:26665 original size:14 final size:14
Alignment explanation
Indices: 26595--26691 Score: 85
Period size: 15 Copynumber: 7.0 Consensus size: 14
26585 AAGAATGGTT
26595 ATTTATTA-AAATA
1 ATTTATTATAAATA
* *
26608 ATTTA--ATAAGGTT
1 ATTTATTATAA-ATA
*
26621 ATTTATTTTAAAATA
1 ATTTATTAT-AAATA
*
26636 ATTTATTTTAAAATA
1 ATTTATTAT-AAATA
26651 ATTTATTATAAATA
1 ATTTATTATAAATA
*
26665 ATTTATT-TTAATA
1 ATTTATTATAAATA
*
26678 AATTATTATAAATA
1 ATTTATTATAAATA
26692 TGGATTGATT
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
11 1 0.01
12 2 0.03
13 22 0.32
14 17 0.25
15 25 0.36
16 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
ATTTATTATAAATA
Found at i:26706 original size:63 final size:67
Alignment explanation
Indices: 26636--26789 Score: 210
Period size: 63 Copynumber: 2.3 Consensus size: 67
26626 TTTTAAAATA
26636 ATTTATTTTAAAATAATTTATTATAAATAATTTATT-T-TA-A-TAAATTATTAT-AAATATGGA
1 ATTTATTTT-AAATAATTTATTATAAATAATTTATTATATAGATTAAATTATTATAAAATATGGA
26696 TTG
65 TTG
* * * *
26699 ATTTATTTTTAAATAATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGG
1 ATTTA-TTTTAAATAATTTATTATAAATAATTTATTA-TATAGATTAAATTATTATAAAATATGG
26764 ATTG
64 ATTG
26768 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
26790 GTATGGATTG
Statistics
Matches: 79, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
63 30 0.38
64 4 0.05
65 1 0.01
66 2 0.03
67 1 0.01
68 24 0.30
69 17 0.22
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (67 bp):
ATTTATTTTAAATAATTTATTATAAATAATTTATTATATAGATTAAATTATTATAAAATATGGAT
TG
Found at i:26712 original size:22 final size:22
Alignment explanation
Indices: 26686--26781 Score: 70
Period size: 22 Copynumber: 4.3 Consensus size: 22
26676 TAAATTATTA
26686 TAAATATGGATTGATTTATTTT
1 TAAATATGGATTGATTTATTTT
** * * *
26708 TAAATAATTTATTTTAAATAATTTAT
1 TAAAT-ATGGA--TTGATTTATTT-T
* *
26734 T-AGTATAGATTGATTTATTTT
1 TAAATATGGATTGATTTATTTT
*
26755 AAAATATGGATTGATTTA-TTT
1 TAAATATGGATTGATTTATTTT
26776 TAAATA
1 TAAATA
26782 ATTTATTAGT
Statistics
Matches: 54, Mismatches: 15, Indels: 11
0.68 0.19 0.14
Matches are distributed among these distances:
21 9 0.17
22 27 0.50
23 3 0.06
24 3 0.06
25 10 0.19
26 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TAAATATGGATTGATTTATTTT
Found at i:26724 original size:14 final size:14
Alignment explanation
Indices: 26699--26734 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
26689 ATATGGATTG
26699 ATTTATTTTTAAATA
1 ATTTA-TTTTAAATA
26714 ATTTATTTTAAATA
1 ATTTATTTTAAATA
26728 ATTTATT
1 ATTTATT
26735 AGTATAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:26755 original size:32 final size:31
Alignment explanation
Indices: 26714--26919 Score: 169
Period size: 32 Copynumber: 7.4 Consensus size: 31
26704 TTTTTAAATA
26714 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
26746 ATTTATTTT-AA-AA--TA-T-G---GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
26768 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
26800 ATTTATTTT-AA-AA--TA-T-G---GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
*
26822 ATTTATTTTAAATAATTTATTAGTATGGATTA
1 ATTTATTTTAAATAATTTATTAGTAT-GATTG
26854 ATTTATTTT-AA-AA--TA-T-G---GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTG
*
26876 ATTTATTTTACATAATTTATTAGTATGTATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTG
26908 ATTTATTTTAAA
1 ATTTATTTTAAA
26920 ATATGGATTG
Statistics
Matches: 140, Mismatches: 4, Indels: 60
0.69 0.02 0.29
Matches are distributed among these distances:
22 41 0.29
23 5 0.04
24 6 0.04
26 9 0.06
27 6 0.04
28 9 0.06
30 6 0.04
31 7 0.05
32 51 0.36
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTAGTATGATTG
Found at i:26778 original size:54 final size:54
Alignment explanation
Indices: 26714--26936 Score: 410
Period size: 54 Copynumber: 4.1 Consensus size: 54
26704 TTTTTAAATA
*
26714 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
26768 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
26822 ATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
26876 ATTTATTTTACATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
26930 ATTTATT
1 ATTTATT
26937 ATTGTAGTTG
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 164 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:26816 original size:22 final size:22
Alignment explanation
Indices: 26791--26833 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
26781 AATTTATTAG
26791 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
26813 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
26834 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:26915 original size:22 final size:22
Alignment explanation
Indices: 26890--26962 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
26880 ATTTTACATA
26890 ATTTATTAGTATGTATTGATTT
1 ATTTATTAGTATGTATTGATTT
* * *
26912 ATTT-TAAAATATGGATTGATTT
1 ATTTAT-TAGTATGTATTGATTT
* *
26934 A-TTATT-GTAGTTGTATGGATTG
1 ATTTATTAGTA--TGTATTGATTT
26956 ATTTATT
1 ATTTATT
26963 TTAAATAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 28 0.74
23 5 0.13
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (22 bp):
ATTTATTAGTATGTATTGATTT
Found at i:26977 original size:134 final size:134
Alignment explanation
Indices: 26813--27172 Score: 578
Period size: 134 Copynumber: 2.7 Consensus size: 134
26803 TATTTTAAAA
* *
26813 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAAT
*
26878 TTATTTTACATAATTTATTAGTAT-GTATTGATTTATTTTAAAATATGGATTGATTTATTATTGT
66 TTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTTAAAATATGGATTGATTTATTATTGT
26942 AGTTG
130 AGTTG
* * *
26947 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGTATCAAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAAT
*
27012 TTATTTTAAATAATTTATCAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
66 TTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
27077 GTTG
131 GTTG
* ****
27081 TATGGATTGATTTATTTTAAATAATTTAGTAGTATGGATTGATTTAAGCAAAAAATATGGATTAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTT-ATTTTAAAATATGGATTAA
*
27146 TTTATTTTAAATAATTTATTATTATAG
65 TTTATTTTAAATAATTTATTAGTATAG
27173 TTGTATGGAT
Statistics
Matches: 207, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
134 168 0.81
135 39 0.19
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.51
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAAT
TTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
GTTG
Found at i:26992 original size:32 final size:32
Alignment explanation
Indices: 26946--27053 Score: 119
Period size: 32 Copynumber: 3.7 Consensus size: 32
26936 TATTGTAGTT
*
26946 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATAGATTGATTTATTTTAAATAATTTATTA
26978 GTATAGATTGATTTATTTT-AA-AA--TA-T-
1 GTATAGATTGATTTATTTTAAATAATTTATTA
* *
27004 GTAT-CA---ATTTATTTTAAATAATTTATCA
1 GTATAGATTGATTTATTTTAAATAATTTATTA
27032 GTATAGATTGATTTATTTTAAA
1 GTATAGATTGATTTATTTTAAA
27054 ATATGGATTG
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
22 9 0.15
23 2 0.03
24 2 0.03
25 1 0.02
26 6 0.10
27 1 0.02
28 6 0.10
29 1 0.02
30 2 0.03
31 2 0.03
32 30 0.48
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (32 bp):
GTATAGATTGATTTATTTTAAATAATTTATTA
Found at i:27014 original size:80 final size:80
Alignment explanation
Indices: 26714--27016 Score: 248
Period size: 80 Copynumber: 3.8 Consensus size: 80
26704 TTTTTAAATA
**
26714 ATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTTAAAATATGGATTGATTTATTTTA
1 ATTTATTTTAAATAATTTATTAGTAT-GTATTGATTTATTTTAAAATATGGATCAATTTA--TT-
*
26778 AATAATTTA-TTAGTATGGATTG
62 -AT--TGTAGTT-GTATGGATTG
** * * ** * * * *
26800 ATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTAATTTA-T-
1 ATTTATTTTAAATA-ATTTATTAGTATGTA-TTGATTTATTTTA-AAATATGGATCAATTTATTA
***
26860 TT-TA-AAATATGGATTG
63 TTGTAGTTGTATGGATTG
* **
26876 ATTTATTTTACATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATCAATTTATTATTG
26941 TAGTTGTATGGATTG
66 TAGTTGTATGGATTG
*
26956 ATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTTAAAATATGTATCAATTTATT
1 ATTTATTTTAAATAATTTATTAGTAT-GTATTGATTTATTTTAAAATATGGATCAATTTATT
27017 TTAAATAATT
Statistics
Matches: 174, Mismatches: 31, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
76 39 0.22
77 14 0.08
78 7 0.04
79 2 0.01
80 65 0.37
81 1 0.01
83 1 0.01
84 3 0.02
85 11 0.06
86 31 0.18
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.53
Consensus pattern (80 bp):
ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATCAATTTATTATTG
TAGTTGTATGGATTG
Found at i:27068 original size:54 final size:54
Alignment explanation
Indices: 26947--27070 Score: 212
Period size: 54 Copynumber: 2.3 Consensus size: 54
26937 ATTGTAGTTG
*
26947 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATCAGTATAGATTGATTTATTTTAAAA
* **
27001 TATGTATCAATTTATTTTAAATAATTTATCAGTATAGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATCAGTATAGATTGATTTATTTTAAAA
27055 TATGGATTGATTTATT
1 TATGGATTGATTTATT
27071 ATTGTAGTTG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATCAGTATAGATTGATTTATTTTAAAA
Found at i:30459 original size:13 final size:14
Alignment explanation
Indices: 30429--30461 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
30419 GGATTTAGAA
*
30429 ATTTAGATTTTGGG
1 ATTTAGAGTTTGGG
30443 ATTTAGAGTTT-GG
1 ATTTAGAGTTTGGG
30456 ATTTAG
1 ATTTAG
30462 GAATCTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (14 bp):
ATTTAGAGTTTGGG
Found at i:30680 original size:32 final size:32
Alignment explanation
Indices: 30610--30691 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 32
30600 GCTTTGAGAT
* *
30610 TAAAATTTTTGAAGTTTTTTTAAAGATTTTAG
1 TAAAAATTTTGAAGTTTTTTTAAAGATTTTAA
* *
30642 T-GAAATTTTGATA-TTTTTTTTAAGATTTTAA
1 TAAAAATTTTGA-AGTTTTTTTAAAGATTTTAA
30673 TAAAAA-TTT-AAGTTTTTTT
1 TAAAAATTTTGAAGTTTTTTT
30692 TTATAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
29 1 0.02
30 8 0.19
31 28 0.67
32 5 0.12
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (32 bp):
TAAAAATTTTGAAGTTTTTTTAAAGATTTTAA
Found at i:31187 original size:18 final size:19
Alignment explanation
Indices: 31152--31188 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
31142 CACGGAATGT
31152 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
31172 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
31189 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:55706 original size:18 final size:18
Alignment explanation
Indices: 55679--55714 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55669 GGTTTTGCTC
55679 GCCCCATCCCCGAACCTG
1 GCCCCATCCCCGAACCTG
*
55697 GCCCCGTCCCCGAACCTG
1 GCCCCATCCCCGAACCTG
55715 AAATAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.56, G:0.19, T:0.11
Consensus pattern (18 bp):
GCCCCATCCCCGAACCTG
Found at i:55890 original size:31 final size:31
Alignment explanation
Indices: 55843--55920 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
55833 CGAAAATATT
*
55843 TTATATATAATTAATATAAAAAATATAAAATA
1 TTATATAT-ATTAATATAAAAAATAAAAAATA
55875 TTATATATATTAATATAAAAAATAAAAAATA
1 TTATATATATTAATATAAAAAATAAAAAATA
55906 TTATATATATATAAT
1 TTATATATAT-TAAT
55921 CGGGGCAGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 32 0.73
32 12 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
TTATATATATTAATATAAAAAATAAAAAATA
Found at i:55999 original size:25 final size:25
Alignment explanation
Indices: 55969--56029 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
55959 TATCCCTAAT
*
55969 ACCCGACCCGACCCGATATCATTCA
1 ACCCGACCCGACCCGATAACATTCA
*
55994 ACCCGACCCGACCTGATAACATTCA
1 ACCCGACCCGACCCGATAACATTCA
56019 ACCCGACCCGA
1 ACCCGACCCGA
56030 ACTTGACCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.30, C:0.44, G:0.13, T:0.13
Consensus pattern (25 bp):
ACCCGACCCGACCCGATAACATTCA
Found at i:68409 original size:27 final size:27
Alignment explanation
Indices: 68362--68413 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
68352 CAATTTAATG
*
68362 TCATGCAACTAATAAACTCATGCAAAT
1 TCATGCAACTAATAAAATCATGCAAAT
*
68389 TCATGC-ACTAGTAAAAATCATGCAA
1 TCATGCAACTAAT-AAAATCATGCAA
68414 TGAATGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (27 bp):
TCATGCAACTAATAAAATCATGCAAAT
Found at i:69919 original size:14 final size:14
Alignment explanation
Indices: 69900--69928 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
69890 TCTTTACTTT
69900 CATTGGTTCTAATG
1 CATTGGTTCTAATG
69914 CATTGGTTCTAATG
1 CATTGGTTCTAATG
69928 C
1 C
69929 TTCTTATTAG
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:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (14 bp):
CATTGGTTCTAATG
Done.