Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002178.1 Hibiscus syriacus cultivar Beakdansim tig00004437_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: 56358
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:3105 original size:10 final size:10
Alignment explanation
Indices: 3077--3106 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
3067 GTTTATTTTT
3077 CTTTATATTA
1 CTTTATATTA
3087 CTGTTATATTA
1 CT-TTATATTA
3098 CTTTATATT
1 CTTTATATT
3107 CGGTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.27, C:0.10, G:0.03, T:0.60
Consensus pattern (10 bp):
CTTTATATTA
Found at i:5706 original size:18 final size:18
Alignment explanation
Indices: 5680--5718 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5670 CCATTTCTTG
*
5680 AGTACAAGGAATAGCTTA
1 AGTACAAGGAATAACTTA
*
5698 AGTATAAGGAATAACTTA
1 AGTACAAGGAATAACTTA
5716 AGT
1 AGT
5719 TTGGGGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.26
Consensus pattern (18 bp):
AGTACAAGGAATAACTTA
Found at i:10716 original size:5 final size:5
Alignment explanation
Indices: 10706--11278 Score: 1054
Period size: 5 Copynumber: 115.8 Consensus size: 5
10696 TAATATTTAT
10706 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
10756 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
10806 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC --ATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
10854 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
10904 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
10954 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
11004 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
11054 ATAT- ATATC --ATC ATATC ATATC --ATC ATATC AT-TC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
11098 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
11148 ATATC ATATC ATATC ATATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC --ATATC ATATC ATATC ATATC ATATC ATATC ATATC
11200 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
* *
11250 ATATC ATATC ATATC ATATT ATATT ATAT
1 ATATC ATATC ATATC ATATC ATATC ATAT
11279 ATACTATAGT
Statistics
Matches: 557, Mismatches: 1, Indels: 20
0.96 0.00 0.03
Matches are distributed among these distances:
3 9 0.02
4 8 0.01
5 535 0.96
7 5 0.01
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATC
Found at i:11286 original size:5 final size:4
Alignment explanation
Indices: 10694--11402 Score: 149
Period size: 5 Copynumber: 152.5 Consensus size: 4
10684 TATATTGTTT
*
10694 TATA -ATA TTTA TATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TATA TATA TATA TATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA
10744 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA
10794 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA
10844 TCATA TCATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 T-ATA T-AT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A
10895 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A
10945 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A
10995 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A
11045 TATCA TATCA TATA TATCA TCATA TCATA TCATCA TATCA T-TCA TATCA
1 TAT-A TAT-A TATA TAT-A T-ATA T-ATA T-AT-A TAT-A TAT-A TAT-A
11094 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A TAT-A
11144 TATCA TATCA TATCA TATCA TATA TCATA TCATA TCATA TCATA TCATA
1 TAT-A TAT-A TAT-A TAT-A TATA T-ATA T-ATA T-ATA T-ATA T-ATA
11193 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA T-ATA
11243 TCATA TCATA TCATA TCATA TCATA T-TA TAT- TATA TATA CTATA GTAT-
1 T-ATA T-ATA T-ATA T-ATA T-ATA TATA TATA TATA TATA -TATA -TATA
* * * *
11291 TATG T-TA T-TA TATA T-TA TGTA T-TA GATA T-TG TATA GTATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA -TATA TATA
* * *
11335 T-TA TATA T-TA CTAT- TGTA -AT- TATA GCATA TATT TATA TATA T-TA
1 TATA TATA TATA -TATA TATA TATA TATA -TATA TATA TATA TATA TATA
* *
11379 TATA TATG T-TA TATT TATA T-TA TA
1 TATA TATA TATA TATA TATA TATA TA
11403 GTTATATTAT
Statistics
Matches: 660, Mismatches: 18, Indels: 54
0.90 0.02 0.07
Matches are distributed among these distances:
3 42 0.06
4 61 0.09
5 551 0.83
6 6 0.01
ACGTcount: A:0.40, C:0.16, G:0.01, T:0.43
Consensus pattern (4 bp):
TATA
Found at i:11333 original size:14 final size:14
Alignment explanation
Indices: 11269--11358 Score: 55
Period size: 14 Copynumber: 6.6 Consensus size: 14
11259 CATATCATAT
**
11269 TATATTATATATAC
1 TATATTATATATTG
*
11283 TATAGTAT-TA-TG
1 TATATTATATATTG
*
11295 T-TATTATATATTA
1 TATATTATATATTG
* *
11308 TGTATTAGATATTG
1 TATATTATATATTG
*
11322 TATAGTATATATATTA
1 TATA-T-TATATATTG
*
11338 TATATTA-CTATTG
1 TATATTATATATTG
11351 TA-ATTATA
1 TATATTATA
11359 GCATATATTT
Statistics
Matches: 57, Mismatches: 13, Indels: 13
0.69 0.16 0.16
Matches are distributed among these distances:
11 5 0.09
12 7 0.12
13 10 0.18
14 22 0.39
15 2 0.04
16 11 0.19
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (14 bp):
TATATTATATATTG
Found at i:11378 original size:22 final size:23
Alignment explanation
Indices: 11353--11412 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
11343 TACTATTGTA
11353 ATTATAGCATATATT-TATATAT
1 ATTATAGCATATATTATATATAT
* * *
11375 ATTATA-TATATGTTATATTTAT
1 ATTATAGCATATATTATATATAT
*
11397 ATTATAG-TTATATTAT
1 ATTATAGCATATATTAT
11413 TACGTTATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
ATTATAGCATATATTATATATAT
Found at i:11444 original size:11 final size:11
Alignment explanation
Indices: 11331--11456 Score: 56
Period size: 11 Copynumber: 11.7 Consensus size: 11
11321 GTATAGTATA
11331 TATATTATATAT
1 TATATTATA-AT
*
11343 TACTATTGTAAT
1 TA-TATTATAAT
**
11355 TATAGCAT-A-
1 TATATTATAAT
11364 TAT-TTAT-A-
1 TATATTATAAT
11372 TATATTAT-AT
1 TATATTATAAT
* *
11382 ATATGTTATATT
1 -TATATTATAAT
*
11394 TATATTATAGT
1 TATATTATAAT
*
11405 TATATTATTACGT
1 TATATTA-TA-AT
11418 TATA-TATATAT
1 TATATTATA-AT
11429 T-TATTATAAT
1 TATATTATAAT
11439 TATATT-TACAT
1 TATATTATA-AT
11450 TAT-TTAT
1 TATATTAT
11457 TTATTTGTTA
Statistics
Matches: 91, Mismatches: 12, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
8 6 0.07
9 8 0.09
10 10 0.11
11 44 0.48
12 11 0.12
13 12 0.13
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (11 bp):
TATATTATAAT
Found at i:11451 original size:17 final size:17
Alignment explanation
Indices: 11387--11452 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
11377 TATATATATG
* *
11387 TTATATTTATATTATAG
1 TTATATTTACATTATAA
*
11404 TTATATTATTACGTTAT-A
1 TTATA-T-TTACATTATAA
11422 TATATATTT--ATTATAA
1 T-TATATTTACATTATAA
11438 TTATATTTACATTAT
1 TTATATTTACATTAT
11453 TTATTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
15 11 0.28
16 2 0.05
17 12 0.31
18 3 0.08
19 11 0.28
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATATTTACATTATAA
Found at i:14739 original size:32 final size:32
Alignment explanation
Indices: 14703--14772 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
14693 CCATAATTTC
* *
14703 TTTTATTATA-TCATATTATATACTATATATTA
1 TTTTATAATATTCATATAATAT-CTATATATTA
*
14735 TTTTATAATATTTATATAATATCTATATATTA
1 TTTTATAATATTCATATAATATCTATATATTA
*
14767 TATTAT
1 TTTTAT
14773 GTTGTGTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 24 0.73
33 9 0.27
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (32 bp):
TTTTATAATATTCATATAATATCTATATATTA
Found at i:14764 original size:13 final size:11
Alignment explanation
Indices: 14726--14763 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
14716 TATTATATAC
*
14726 TATATATTATT
1 TATATAATATT
14737 T-TATAATATT
1 TATATAATATT
*
14747 TATATAATATC
1 TATATAATATT
14758 TATATA
1 TATATA
14764 TTATATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATAATATT
Found at i:14780 original size:5 final size:5
Alignment explanation
Indices: 14772--14813 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
14762 TATTATATTA
* *
14772 TGTTG TGTTG TGTTA TG-TG TGTTG TCTTG TGTTG TGTTG TGT
1 TGTTG TGTTG TGTTG TGTTG TGTTG TGTTG TGTTG TGTTG TGT
14814 ATCATATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 3 0.09
5 29 0.91
ACGTcount: A:0.02, C:0.02, G:0.36, T:0.60
Consensus pattern (5 bp):
TGTTG
Found at i:14892 original size:17 final size:17
Alignment explanation
Indices: 14872--14906 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
14862 TTTATATAGA
14872 TTATA-TATATGTTATAT
1 TTATACTAT-TGTTATAT
14889 TTATACTATTGTTATAT
1 TTATACTATTGTTATAT
14906 T
1 T
14907 ATTACATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (17 bp):
TTATACTATTGTTATAT
Found at i:14932 original size:17 final size:17
Alignment explanation
Indices: 14817--14965 Score: 56
Period size: 15 Copynumber: 9.1 Consensus size: 17
14807 GTTGTGTATC
14817 ATATAGTATATA-TT-TT
1 ATATA-TATATATTTATT
14833 ATATAT-TACTATTATAATT
1 ATATATATA-TATT-T-ATT
*
14852 ATA-GTATATATTTA-T
1 ATATATATATATTTATT
* *
14867 ATAGAT-TATATATATGT
1 ATATATATATATTTAT-T
* *
14884 -TATATTTATA-CTATT
1 ATATATATATATTTATT
* *
14899 GT-TATAT-TATTACATT
1 ATATATATATATT-TATT
14915 ATATATATATATTTATT
1 ATATATATATATTTATT
14932 ATA-AT-TATATTTACATT
1 ATATATATATATTT--ATT
*
14949 AT-T-TATTTATTTATT
1 ATATATATATATTTATT
14964 AT
1 AT
14966 TTCAGATCCA
Statistics
Matches: 103, Mismatches: 11, Indels: 39
0.67 0.07 0.25
Matches are distributed among these distances:
14 4 0.04
15 31 0.30
16 23 0.22
17 29 0.28
18 9 0.09
19 7 0.07
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
ATATATATATATTTATT
Found at i:14942 original size:11 final size:11
Alignment explanation
Indices: 14831--14954 Score: 50
Period size: 11 Copynumber: 11.4 Consensus size: 11
14821 AGTATATATT
14831 TTATATATTACTA
1 TTATA-ATTA-TA
14844 TTATAATTATA
1 TTATAATTATA
*
14855 GTAT-A-TAT-
1 TTATAATTATA
*
14863 TTAT-A-TAGA
1 TTATAATTATA
*
14872 TTAT-ATATATG
1 TTATAAT-TATA
*
14883 TTATATTTATA
1 TTATAATTATA
* **
14894 CTATTGTTATA
1 TTATAATTATA
14905 TTATTACATTATA
1 TTA-TA-ATTATA
14918 TATATATATT-TA
1 T-TATA-ATTATA
14930 TTATAATTATA
1 TTATAATTATA
14941 TT-TACATTAT-
1 TTATA-ATTATA
14951 TTAT
1 TTAT
14955 TTATTTATTA
Statistics
Matches: 87, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
8 6 0.07
9 8 0.09
10 8 0.09
11 38 0.44
12 9 0.10
13 16 0.18
14 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (11 bp):
TTATAATTATA
Found at i:15426 original size:19 final size:19
Alignment explanation
Indices: 15402--15442 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
15392 CAACAAGCAT
*
15402 AAAAAAACAGTCGAAATAG
1 AAAAAAACAGCCGAAATAG
*
15421 AAAAAAACAGCCGAAATTG
1 AAAAAAACAGCCGAAATAG
15440 AAA
1 AAA
15443 GCAAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.63, C:0.12, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAAAAACAGCCGAAATAG
Found at i:36836 original size:3 final size:3
Alignment explanation
Indices: 36828--36873 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
36818 TTTTCTGGTC
36828 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
36874 CGAAATGTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38907 original size:21 final size:21
Alignment explanation
Indices: 38883--38927 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
38873 AGCAATACTA
* *
38883 TTCAGAATTTTACTTTCTTAT
1 TTCAGAATTTCACTTCCTTAT
38904 TTCAGAATTTCACTTCCTTAT
1 TTCAGAATTTCACTTCCTTAT
38925 TTC
1 TTC
38928 GGGTATATGA
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:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTCAGAATTTCACTTCCTTAT
Found at i:41914 original size:17 final size:17
Alignment explanation
Indices: 41870--41915 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
41860 TTTTTAAAGA
*
41870 AATATATAAATATTTTAC
1 AATATAT-AATATTATAC
* *
41888 AATTTGTAATATTATAC
1 AATATATAATATTATAC
41905 AATATATAATA
1 AATATATAATA
41916 AGGACAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATATAATATTATAC
Found at i:43373 original size:44 final size:44
Alignment explanation
Indices: 43222--43644 Score: 622
Period size: 44 Copynumber: 9.7 Consensus size: 44
43212 CCATTTAATC
* *
43222 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTAAATCT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA-T-AATTT
** * * * *
43268 C-TAAGCTAATAAGTTTATTTTACCAATATACTTACCATTA-TC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
43310 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
43354 CATAAGCTCGTAAGATTATTTTACCAATATACTTACTATAGTTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
43398 CATAAGCTCGTAGGCTTATTTTACCAATATACTTATTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
43442 CATAAGCTCATAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* * *
43486 CATAAGCTCGTAAACTTATTTTACAAATACACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
43530 CATAAGCTCGTAAGCTTATTTTA-C--TATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
43571 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACTATAATCTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAAT-TT
43616 CATAAGCTCGTAAGCTTATTTTACCAATA
1 CATAAGCTCGTAAGCTTATTTTACCAATA
43645 ATACCAATTG
Statistics
Matches: 341, Mismatches: 30, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
41 39 0.11
42 2 0.01
43 35 0.10
44 202 0.59
45 62 0.18
46 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (44 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
Found at i:43724 original size:17 final size:16
Alignment explanation
Indices: 43704--43736 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
43694 AAAATTTATT
43704 ATTAATCTTTCTACAAC
1 ATTAATCTTTC-ACAAC
43721 ATTAATCTTTCACAAC
1 ATTAATCTTTCACAAC
43737 TTTTCGTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAATCTTTCACAAC
Found at i:47335 original size:21 final size:21
Alignment explanation
Indices: 47311--47351 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47301 AATGTGTATC
*
47311 GATGCACTTCTACAGTACATA
1 GATGCACTGCTACAGTACATA
*
47332 GATGCACTGCTATAGTACAT
1 GATGCACTGCTACAGTACAT
47352 TTCGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (21 bp):
GATGCACTGCTACAGTACATA
Found at i:47824 original size:44 final size:44
Alignment explanation
Indices: 47704--48004 Score: 410
Period size: 44 Copynumber: 6.8 Consensus size: 44
47694 ACATACCATT
*
47704 TAATC-CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAA
1 TAATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTA-CTA
* *
47748 TAAATCTC-TAAGCTCGTAAGTTTATTTTACCAATATACTTACCA
1 T-AATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
* *
47792 -ACATCCCATAAGATCGTAAGCTTATTTTACCAATATACTTACTA
1 TA-ATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
* * * *
47836 TAATTTCATAAGCTCGTAAGCTTATTTTTCAAATACACTTACTA
1 TAATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
*
47880 TAATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
1 TAATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
* * * *
47924 TAATTTCATAAACACGTAAGCTTATTTTACCAATAAACTTACTA
1 TAATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
*
47968 TAATCTCCATAAGCTCGTAATCTTATTTTACCAATAT
1 TAATCT-CATAAGCTCGTAAGCTTATTTTACCAATAT
48005 TACCAATTGT
Statistics
Matches: 228, Mismatches: 23, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.00
43 4 0.02
44 159 0.70
45 63 0.28
46 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (44 bp):
TAATCTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA
Done.