Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003692.1 Hibiscus syriacus cultivar Beakdansim tig00007889_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: 72877
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1038 original size:59 final size:59
Alignment explanation
Indices: 919--1049 Score: 151
Period size: 59 Copynumber: 2.2 Consensus size: 59
909 AAAAATAGCG
* *
919 TAAAG-TACACAAGTGATCCCCTAACTATAGGGCGTTGCTTTATTGATTCTCTCTATTAT
1 TAAAGTTACA-AAGTGATCCCCTAACTATAGGGCGCTGCTTTATTGATTCTCTCTACTAT
* * * *
978 TAAAGTTACAAAGTGATCCCCTAACTATATGGTGCTGCTTTGTTGAGTT-T-TTTGACTAT
1 TAAAGTTACAAAGTGATCCCCTAACTATAGGGCGCTGCTTTATTGA-TTCTCTCT-ACTAT
1037 TAAAAGTTACAAA
1 T-AAAGTTACAAA
1050 ATGGTCACCT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 2 0.03
59 43 0.69
60 17 0.27
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (59 bp):
TAAAGTTACAAAGTGATCCCCTAACTATAGGGCGCTGCTTTATTGATTCTCTCTACTAT
Found at i:1477 original size:2 final size:2
Alignment explanation
Indices: 1466--1494 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1456 TATTTCCTCG
1466 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1495 AACATCTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1864 original size:23 final size:23
Alignment explanation
Indices: 1834--1890 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
1824 GTTAAAATTC
*
1834 TTTTAAAAATATATTA-ATTTTAT
1 TTTTAAAAA-ATATTATATTTAAT
1857 TTTTAAAAAATATTATATTTAAT
1 TTTTAAAAAATATTATATTTAAT
*
1880 TTATAAAAAAT
1 TTTTAAAAAAT
1891 TATTTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 6 0.19
23 25 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTAAAAAATATTATATTTAAT
Found at i:1888 original size:24 final size:22
Alignment explanation
Indices: 1834--1894 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1824 GTTAAAATTC
* *
1834 TTTTAAAAATATATTAATTTTA
1 TTTTAAAAAAATATTAATTTAA
*
1856 TTTTTAAAAAATATTATATTTAA
1 TTTTAAAAAAATATTA-ATTTAA
*
1879 TTTATAAAAAATTATT
1 TTT-TAAAAAAATATT
1895 TTTTCAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 14 0.44
23 8 0.25
24 10 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAAAAAATATTAATTTAA
Found at i:3252 original size:20 final size:20
Alignment explanation
Indices: 3229--3266 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3219 TAATATATTT
3229 TTAAA-AAAATATTGACACCC
1 TTAAATAAAA-ATTGACACCC
*
3249 TTAAATATAAATTGACAC
1 TTAAATAAAAATTGACAC
3267 TCATTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (20 bp):
TTAAATAAAAATTGACACCC
Found at i:7616 original size:27 final size:28
Alignment explanation
Indices: 7586--7643 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
7576 AAAGTTATAT
* * *
7586 TTTTA-GTTAAAATATGTACCTAAAGTA
1 TTTTATGTCAAAATAGGTACCTAAACTA
7613 TTTTATGTCAAAATAGGTACCTAAACTA
1 TTTTATGTCAAAATAGGTACCTAAACTA
7641 TTT
1 TTT
7644 AAACTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (28 bp):
TTTTATGTCAAAATAGGTACCTAAACTA
Found at i:7760 original size:30 final size:29
Alignment explanation
Indices: 7726--7823 Score: 119
Period size: 28 Copynumber: 3.4 Consensus size: 29
7716 AAAAATTTGA
* *
7726 ATACTTTATGTAACTATTTTGATTAAAAAT
1 ATACTTTAGGTAACTATTTTGA-CAAAAAT
*
7756 ATACTTTAGGTACCTATTTTGACAAAAAT
1 ATACTTTAGGTAACTATTTTGACAAAAAT
* * *
7785 A-ACTTTAGGTAATTATTTTCACCAAAA-
1 ATACTTTAGGTAACTATTTTGACAAAAAT
7812 ATACTTTAGGTA
1 ATACTTTAGGTA
7824 TTTAAATGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
27 1 0.02
28 32 0.53
29 7 0.12
30 20 0.33
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (29 bp):
ATACTTTAGGTAACTATTTTGACAAAAAT
Found at i:12249 original size:16 final size:16
Alignment explanation
Indices: 12213--12253 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
12203 GTCAAACAAG
12213 CTAGTT-TTATGTATT
1 CTAGTTGTTATGTATT
12228 CATAGTTGTTACTGT-TT
1 C-TAGTTGTTA-TGTATT
12245 CTAGTTGTT
1 CTAGTTGTT
12254 CTAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 13 0.57
17 6 0.26
18 3 0.13
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.56
Consensus pattern (16 bp):
CTAGTTGTTATGTATT
Found at i:12401 original size:20 final size:20
Alignment explanation
Indices: 12376--12414 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12366 TGGTACCGAT
12376 ACTGA-CCCTTCAGTATCGAA
1 ACTGACCCCTT-AGTATCGAA
12396 ACTGACCCCTTAGTATCGA
1 ACTGACCCCTTAGTATCGA
12415 TGCTCACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
ACTGACCCCTTAGTATCGAA
Found at i:13445 original size:20 final size:23
Alignment explanation
Indices: 13404--13446 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
13394 TAGTTTAGCT
13404 TGAAGGAAGAATGGAGAAAAATG
1 TGAAGGAAGAATGGAGAAAAATG
13427 TGAAGGAA-AAT-GA-AAAAATG
1 TGAAGGAAGAATGGAGAAAAATG
13447 GAGTTCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 2 0.10
22 3 0.15
23 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.14
Consensus pattern (23 bp):
TGAAGGAAGAATGGAGAAAAATG
Found at i:13884 original size:23 final size:23
Alignment explanation
Indices: 13857--13900 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
13847 TATTATATGA
13857 CACAAAATAGTACATGGTGCATG
1 CACAAAATAGTACATGGTGCATG
*
13880 CACAATATAGTACATGGTGCA
1 CACAAAATAGTACATGGTGCA
13901 ATGTATTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (23 bp):
CACAAAATAGTACATGGTGCATG
Found at i:14013 original size:27 final size:27
Alignment explanation
Indices: 13954--14013 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 27
13944 ACATGTATAT
*
13954 TGTATATGGCACTATATGTGCAAATCG
1 TGTATATGGCACTAAATGTGCAAATCG
13981 -GTTATATGGCA-TAAAATGTGCAACAT-G
1 TG-TATATGGCACT-AAATGTGCAA-ATCG
14008 TGTATA
1 TGTATA
14014 CTAATATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
26 2 0.07
27 23 0.82
28 3 0.11
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (27 bp):
TGTATATGGCACTAAATGTGCAAATCG
Found at i:15711 original size:20 final size:20
Alignment explanation
Indices: 15645--15725 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
15635 TTTTAAATTA
*
15645 TTTAAAATTAAATAGATA-A-
1 TTTAAAAATAAATA-ATATAT
15664 TTTAAAAAT-AAT-AT-TAT
1 TTTAAAAATAAATAATATAT
15681 TTTAAATAAATAAATAATATAT
1 TTT-AA-AAATAAATAATATAT
15703 TTTAAAAATCAAATAA-ATAT
1 TTTAAAAAT-AAATAATATAT
15723 TTT
1 TTT
15726 TGTAATATTA
Statistics
Matches: 53, Mismatches: 1, Indels: 15
0.77 0.01 0.22
Matches are distributed among these distances:
16 3 0.06
17 3 0.06
18 5 0.09
19 12 0.23
20 14 0.26
21 10 0.19
22 6 0.11
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (20 bp):
TTTAAAAATAAATAATATAT
Found at i:15749 original size:23 final size:23
Alignment explanation
Indices: 15714--15782 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
15704 TTAAAAATCA
15714 AATA-AATATTTTTGTAATATTAT
1 AATATAATA-TTTTGTAATATTAT
* *
15737 AATATAATATTTTAG-AATGTTTT
1 AATATAATATTTT-GTAATATTAT
* *
15760 AATATAA-ATTTTATAAAATTAT
1 AATATAATATTTTGTAATATTAT
15782 A
1 A
15783 TAAACTATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
22 11 0.30
23 21 0.57
24 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AATATAATATTTTGTAATATTAT
Found at i:16903 original size:30 final size:32
Alignment explanation
Indices: 16854--16934 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 32
16844 ATTTTGATAG
* * *
16854 ATTTAAGGACCATTATGTAATAGTTCAAT-AA
1 ATTTAATGATCATTTTGTAATAGTTCAATAAA
* **
16885 GTTT-ATGATCATTTTGTAATAGTTTGATAAA
1 ATTTAATGATCATTTTGTAATAGTTCAATAAA
16916 ATTTAATGATCA-TTTGTAA
1 ATTTAATGATCATTTTGTAA
16935 CGGTTGGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 19 0.46
31 15 0.37
32 7 0.17
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (32 bp):
ATTTAATGATCATTTTGTAATAGTTCAATAAA
Found at i:20999 original size:26 final size:25
Alignment explanation
Indices: 20970--21022 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
20960 TATAAATATC
20970 AAATATAATAA-ATAATTATTTATTAA
1 AAATA-AATAATATAATTATTT-TTAA
* *
20996 AAATAATTAATATTATTATTTTTAA
1 AAATAAATAATATAATTATTTTTAA
21021 AA
1 AA
21023 TATTGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AAATAAATAATATAATTATTTTTAA
Found at i:21007 original size:24 final size:24
Alignment explanation
Indices: 20974--21022 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
20964 AATATCAAAT
20974 ATAATAAATA-ATTATTTATTAAAA
1 ATAATAAATATATTATTT-TTAAAA
*
20998 ATAATTAATATTATTATTTTTAAAA
1 ATAATAAATA-TATTATTTTTAAAA
21023 TATTGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 6 0.27
26 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATAATAAATATATTATTTTTAAAA
Found at i:21054 original size:13 final size:14
Alignment explanation
Indices: 21030--21058 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21020 AAATATTGAA
21030 ATAATTTATTTAAT
1 ATAATTTATTTAAT
21044 ATAATTT-TTTAAT
1 ATAATTTATTTAAT
21057 AT
1 AT
21059 TATTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATAATTTATTTAAT
Found at i:21166 original size:33 final size:35
Alignment explanation
Indices: 21083--21171 Score: 105
Period size: 34 Copynumber: 2.6 Consensus size: 35
21073 CATTTTTAAA
* *
21083 ATTTTATAAATAAAAATATTA-AGACTATTATATT
1 ATTTAATAAATAAAAATATTATAGAATATTATATT
* *
21117 TTATTAA-AAATAAAAATTTTATA-AATATTA-ATT
1 AT-TTAATAAATAAAAATATTATAGAATATTATATT
21150 ATTTAATAAATAAAAATATTAT
1 ATTTAATAAATAAAAATATTAT
21172 CTTATTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
32 4 0.09
33 18 0.39
34 20 0.43
35 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (35 bp):
ATTTAATAAATAAAAATATTATAGAATATTATATT
Found at i:21183 original size:32 final size:31
Alignment explanation
Indices: 21083--21183 Score: 87
Period size: 33 Copynumber: 3.1 Consensus size: 31
21073 CATTTTTAAA
* *
21083 ATTTTATAAATAAAAATATTAAGACTATTATATT
1 ATTTAATAAATAAAAATATT-A-TCTATTA-ATT
* * *
21117 TTATTAA-AAATAAAAATTTTATAAATATTAATT
1 AT-TTAATAAATAAAAATATTAT--CTATTAATT
21150 ATTTAATAAATAAAAATATTATCTTATTAATT
1 ATTTAATAAATAAAAATATTATC-TATTAATT
21182 AT
1 AT
21184 ATTCTTTTAC
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
32 14 0.26
33 19 0.35
34 18 0.33
35 3 0.06
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (31 bp):
ATTTAATAAATAAAAATATTATCTATTAATT
Found at i:21230 original size:14 final size:14
Alignment explanation
Indices: 21213--21242 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21203 TAAGAATATT
*
21213 ATTATAATATTCAA
1 ATTATAATATTAAA
21227 ATTATAATATTAAA
1 ATTATAATATTAAA
21241 AT
1 AT
21243 AAAATAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTATAATATTAAA
Found at i:21406 original size:23 final size:23
Alignment explanation
Indices: 21380--21424 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21370 AAAATACAAA
21380 TATAATATAATAAATTATTATAG
1 TATAATATAATAAATTATTATAG
* * *
21403 TATAATTTAGTATATTATTATA
1 TATAATATAATAAATTATTATA
21425 ATACTTAAAG
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:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TATAATATAATAAATTATTATAG
Found at i:25740 original size:32 final size:30
Alignment explanation
Indices: 25704--25779 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
25694 GTTTCAAATT
*
25704 TTAGTT-TATTTTGACCCTCCCAATTTCTATGG
1 TTAGTTATATTTTG-CCCT--CAATTTCTATGA
* *
25736 TTAGTTATACTTTGCCCTCATTTTCTATGA
1 TTAGTTATATTTTGCCCTCAATTTCTATGA
*
25766 TTAATTATATTTTG
1 TTAGTTATATTTTG
25780 TCTCCTTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 22 0.58
32 10 0.26
33 6 0.16
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (30 bp):
TTAGTTATATTTTGCCCTCAATTTCTATGA
Found at i:32807 original size:20 final size:21
Alignment explanation
Indices: 32782--32833 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
32772 AATATCATTT
* *
32782 GGTATCGATATCC-CCATATG
1 GGTATCGATATCCTCCACAAG
32802 GGTATCGATA-CCTCCACAAG
1 GGTATCGATATCCTCCACAAG
32822 GGTATCGATATC
1 GGTATCGATATC
32834 ACCCCTTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 25 0.89
21 1 0.04
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (21 bp):
GGTATCGATATCCTCCACAAG
Found at i:36405 original size:26 final size:26
Alignment explanation
Indices: 36369--36419 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
36359 ATTTTTTAAG
36369 AAAAAAACTTGCTCAAATAAACATTA
1 AAAAAAACTTGCTCAAATAAACATTA
36395 AAAAAAACTTGCTCAAATAAACATT
1 AAAAAAACTTGCTCAAATAAACATT
36420 CAAACCTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.57, C:0.16, G:0.04, T:0.24
Consensus pattern (26 bp):
AAAAAAACTTGCTCAAATAAACATTA
Found at i:44381 original size:2 final size:2
Alignment explanation
Indices: 44374--44403 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44364 TGTGAAAAGA
44374 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
44404 TTAAAGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48195 original size:70 final size:72
Alignment explanation
Indices: 48121--48273 Score: 197
Period size: 72 Copynumber: 2.2 Consensus size: 72
48111 ACAATATCAG
* *
48121 TTTAAAATTAAT-AGAATTAAACC-TTGAAC-CCAAATTTGTCTGGTTTAATTACTTTTTAAGAC
1 TTTAAAATTAATGA-AATTAAACCTTTCAACTCCAAATTTGTATGGTTTAATTACTTTTT-AGAC
48183 CTT-TGAAT
64 CTTATGAAT
* ** *
48191 TTTAAAATTAATGAAATTAAACCTTTCATCTCTTAATTTTTATGGTTTAATTACTTTTTAGACCT
1 TTTAAAATTAATGAAATTAAACCTTTCAACTCCAAATTTGTATGGTTTAATTACTTTTTAGACCT
*
48256 TATGTAT
66 TATGAAT
48263 TTTAAAATTAA
1 TTTAAAATTAA
48274 ACAATTTGCT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
70 21 0.29
71 12 0.17
72 39 0.54
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (72 bp):
TTTAAAATTAATGAAATTAAACCTTTCAACTCCAAATTTGTATGGTTTAATTACTTTTTAGACCT
TATGAAT
Found at i:55032 original size:20 final size:20
Alignment explanation
Indices: 54995--55035 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54985 ACCTTTAAAC
* *
54995 ATTATAATATATATATATAT
1 ATTATAATATAAACATATAT
*
55015 ATTATAATGTAAACATATAT
1 ATTATAATATAAACATATAT
55035 A
1 A
55036 GACTAGACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTATAATATAAACATATAT
Found at i:62524 original size:12 final size:12
Alignment explanation
Indices: 62503--62545 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
62493 ACTATACGGT
*
62503 ATGAAAAGTACC
1 ATGAACAGTACC
62515 ATGAACAGTA--
1 ATGAACAGTACC
*
62525 ATAAACAGTACC
1 ATGAACAGTACC
62537 ATGAACAGT
1 ATGAACAGT
62546 GATACAGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.35
12 17 0.65
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:63374 original size:22 final size:22
Alignment explanation
Indices: 63349--63396 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
63339 TTACCCCAAT
* *
63349 GACCTATGTATTTGTCCTAAAG
1 GACCTATGTATATGTCCCAAAG
* *
63371 GACCTCTGTATATGTCCCGAAG
1 GACCTATGTATATGTCCCAAAG
63393 GACC
1 GACC
63397 GCGTAGAGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (22 bp):
GACCTATGTATATGTCCCAAAG
Found at i:63562 original size:28 final size:28
Alignment explanation
Indices: 63530--63583 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
63520 ACATATATCT
* * *
63530 CTTCTTTTCTGTCACGTATCACATGTTC
1 CTTCTCTTCTGTCACATACCACATGTTC
63558 CTTCTCTTCTGTCACATACCACATGT
1 CTTCTCTTCTGTCACATACCACATGT
63584 ATGTGTAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.09, T:0.43
Consensus pattern (28 bp):
CTTCTCTTCTGTCACATACCACATGTTC
Found at i:64725 original size:30 final size:31
Alignment explanation
Indices: 64682--64740 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
64672 CAACTATTTA
*
64682 TAACTTTTCCAAAAATTACAAATTGGTCCCC
1 TAACTTTTCCAAAAATTACAAAATGGTCCCC
64713 TAACTTTT-CAAAAATTACAAAATGGTCC
1 TAACTTTTCCAAAAATTACAAAATGGTCC
64741 TTAAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (31 bp):
TAACTTTTCCAAAAATTACAAAATGGTCCCC
Found at i:67272 original size:2 final size:2
Alignment explanation
Indices: 67265--67306 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
67255 GATAAGTATT
67265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67305 TA
1 TA
67307 AAATGTAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69073 original size:41 final size:41
Alignment explanation
Indices: 69010--69101 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 41
69000 ATAAAAATCA
* *
69010 ATTCATGTTTCTTTCTTATTCAGACACATTC-AGACTTTCAC
1 ATTCAT-TTTCTTTCCTATTCAGACACATTCAAAACTTTCAC
* *
69051 ATTTCATTTTCATTTCCT-TTCAGATACTTTCAAAACTTTCAC
1 A-TTCATTTTC-TTTCCTATTCAGACACATTCAAAACTTTCAC
69093 ATTCATTTT
1 ATTCATTTT
69102 TCATATCTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
41 24 0.55
42 20 0.45
ACGTcount: A:0.25, C:0.23, G:0.04, T:0.48
Consensus pattern (41 bp):
ATTCATTTTCTTTCCTATTCAGACACATTCAAAACTTTCAC
Found at i:71197 original size:22 final size:21
Alignment explanation
Indices: 71152--71198 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
71142 TGTCTTATAA
*
71152 TTATTTAAATGAATTTAAAAT
1 TTATTTAAATGAATTCAAAAT
* *
71173 TTATTTAATATGAATTCCAACT
1 TTATTTAA-ATGAATTCAAAAT
71195 TTAT
1 TTAT
71199 CCTTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (21 bp):
TTATTTAAATGAATTCAAAAT
Done.