Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006000.1 Hibiscus syriacus cultivar Beakdansim tig00014146_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: 34830
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:574 original size:14 final size:14
Alignment explanation
Indices: 557--600 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
547 ATAAATAAAT
557 ATAATTTATTTTTA
1 ATAATTTATTTTTA
*
571 ATAAATTA-TTTTA
1 ATAATTTATTTTTA
584 AT-ATTTATTTTTCA
1 ATAATTTATTTTT-A
598 ATA
1 ATA
601 TCGAAGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.16
13 11 0.44
14 10 0.40
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (14 bp):
ATAATTTATTTTTA
Found at i:11885 original size:1 final size:1
Alignment explanation
Indices: 11874--11932 Score: 73
Period size: 1 Copynumber: 59.0 Consensus size: 1
11864 ATGCTTAAAG
* * * * *
11874 AAAAAATAAAAAAGAAAAAAAAAAAAAAAGAAAAAAAAAAAAAGAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11933 GGGGGGGTCA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.92, C:0.00, G:0.07, T:0.02
Consensus pattern (1 bp):
A
Found at i:11889 original size:14 final size:13
Alignment explanation
Indices: 11870--11932 Score: 85
Period size: 13 Copynumber: 4.8 Consensus size: 13
11860 TATTATGCTT
11870 AAAGAAAAAATAAA
1 AAAGAAAAAA-AAA
11884 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
11897 AAA-AAAGAAAAAA
1 AAAGAAA-AAAAAA
11910 AAA-AAAAGAAAAA
1 AAAGAAAA-AAAAA
11923 AAAGAAAAAA
1 AAAGAAAAAA
11933 GGGGGGGTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.09
13 28 0.61
14 14 0.30
ACGTcount: A:0.90, C:0.00, G:0.08, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:11895 original size:16 final size:15
Alignment explanation
Indices: 11870--11933 Score: 87
Period size: 15 Copynumber: 4.3 Consensus size: 15
11860 TATTATGCTT
*
11870 AAAG-AAAAAATAAA
1 AAAGAAAAAAAAAAA
11884 AAAGAAAAAAAAAAA
1 AAAGAAAAAAAAAAA
11899 AAA-AGAAAAAAAAAA
1 AAAGA-AAAAAAAAAA
11914 AAAGAAAAAAAAGAAA
1 AAAGAAAAAAAA-AAA
11930 AAAG
1 AAAG
11934 GGGGGGTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
14 5 0.11
15 32 0.71
16 8 0.18
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAAAAAAA
Found at i:11902 original size:23 final size:24
Alignment explanation
Indices: 11874--11933 Score: 97
Period size: 23 Copynumber: 2.6 Consensus size: 24
11864 ATGCTTAAAG
*
11874 AAAAAATAAAAAAGAAAAAAA-AA
1 AAAAAAGAAAAAAGAAAAAAAGAA
11897 AAAAAAGAAAAAA-AAAAAAAGAA
1 AAAAAAGAAAAAAGAAAAAAAGAA
11920 AAAAAAGAAAAAAG
1 AAAAAAGAAAAAAG
11934 GGGGGGTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 7 0.21
23 27 0.79
ACGTcount: A:0.90, C:0.00, G:0.08, T:0.02
Consensus pattern (24 bp):
AAAAAAGAAAAAAGAAAAAAAGAA
Found at i:11905 original size:30 final size:30
Alignment explanation
Indices: 11870--11933 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
11860 TATTATGCTT
*
11870 AAAGAAAAAATAAAAAAGAAAAAAAAAAAA
1 AAAGAAAAAAAAAAAAAGAAAAAAAAAAAA
*
11900 AAAGAAAAAAAAAAAAAGAAAAAAAAGAAA
1 AAAGAAAAAAAAAAAAAGAAAAAAAAAAAA
11930 AAAG
1 AAAG
11934 GGGGGGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.02
Consensus pattern (30 bp):
AAAGAAAAAAAAAAAAAGAAAAAAAAAAAA
Found at i:13214 original size:83 final size:83
Alignment explanation
Indices: 13075--13550 Score: 835
Period size: 83 Copynumber: 5.7 Consensus size: 83
13065 ACTGGAACAA
13075 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
*
13140 AATTATTGAATTTGAAAG
66 AGTTATTGAATTTGAAAG
* *
13158 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGGCATAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
13223 AGTTATTGAATTTGAAAG
66 AGTTATTGAATTTGAAAG
13241 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
*
13306 ATTTATTGAATTTGAAAG
66 AGTTATTGAATTTGAAAG
13324 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
13389 AGTTATTGAATTTGAAAG
66 AGTTATTGAATTTGAAAG
* * *
13407 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACT
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
13472 AGTTATTGAATTTAGAAAG
66 AGTTATTGAATTT-GAAAG
* * *
13491 ATGAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 ATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
13551 TATGAACCCC
Statistics
Matches: 377, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
83 317 0.84
84 12 0.03
85 2 0.01
86 46 0.12
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
AGTTATTGAATTTGAAAG
Found at i:13699 original size:114 final size:114
Alignment explanation
Indices: 13494--13703 Score: 321
Period size: 114 Copynumber: 1.8 Consensus size: 114
13484 TAGAAAGATG
* ** *
13494 AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACC
1 AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCAGTAGGAACC
* *
13559 CCAAAACTAATCATTAGATTTAAAAGATGAATTTGCTCATAGTAGAAAT
66 CCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCATAGTAGAAAT
13608 AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCAGTAGGAACC
1 AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCAGTAGGAACC
* * * * *
13673 CCAGAACCGATCGTTGGAATTGAAAGATGAA
66 CCAAAACCAATCATTAGAATTAAAAGATGAA
13704 CTGCATGATC
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 85 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCAGTAGGAACC
CCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCATAGTAGAAAT
Found at i:14577 original size:113 final size:113
Alignment explanation
Indices: 14380--15266 Score: 1398
Period size: 113 Copynumber: 7.8 Consensus size: 113
14370 TAGCAAAGAT
*
14380 TTAAATCCATCACTTGATGGATTAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * * *
14445 AGGAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTATGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
14493 TTAAATCCATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
14558 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
14606 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
14671 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * ****
14719 TTAAATCCATTACTTGATGGATTAGATTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* **
14784 AGAAGGAAGAAGAAGTTCATAATTAGAAGAATTTGTTCAAAATTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * ****
14832 TTAAATCCATTACTTGATGGATTAGATTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
**
14897 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAAATTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* ****
14945 TTAAATCCATTACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
15010 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAACTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
****
15058 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TTAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
15123 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
15171 TCAAATCTATCACTTGATGGATCCA-CTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TTAAATCCATCACTTGATGGAT-TAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
*
15235 AAGAAGGATGAAGAAGTTCATAATGAGAAGAA
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
15267 CTCATCAAGA
Statistics
Matches: 742, Mismatches: 31, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
113 741 1.00
114 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (113 bp):
TTAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:15523 original size:3 final size:3
Alignment explanation
Indices: 15517--15616 Score: 103
Period size: 3 Copynumber: 32.7 Consensus size: 3
15507 TTCATTTAAA
*
15517 TAT TAT T-T ATAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
15562 AAT TAT AAT TAC TAA TAT TAT TATT TAT TAT TAA TAT TAT TAT TAAA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT
15609 TAT TAT TA
1 TAT TAT TA
15617 CAAGCCCAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
2 1 0.01
3 73 0.91
4 6 0.08
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:16026 original size:18 final size:19
Alignment explanation
Indices: 16005--16042 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
15995 AGAAAAGAAG
16005 AGAGACAGA-GAATACAAC
1 AGAGACAGAGGAATACAAC
* *
16023 AGAGACGGAGGAATCCAAC
1 AGAGACAGAGGAATACAAC
16042 A
1 A
16043 AAAAAAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.18, G:0.26, T:0.05
Consensus pattern (19 bp):
AGAGACAGAGGAATACAAC
Found at i:20787 original size:2 final size:2
Alignment explanation
Indices: 20780--20846 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
20770 CAACCATGTA
20780 AT AT AT AT AT AT 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 AT AT AT AT AT AT
20822 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 A
20847 CTTTTCACAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26368 original size:19 final size:19
Alignment explanation
Indices: 26344--26403 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
26334 GCGTCACATT
26344 TATATTTTTTAAAAATATA
1 TATATTTTTTAAAAATATA
26363 TATA--TTTT-AAAATA-A
1 TATATTTTTTAAAAATATA
* *
26378 TATTTTATGTTTAAATATATA
1 TATATT-T-TTTAAAAATATA
26399 TATAT
1 TATAT
26404 ATATATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
15 4 0.12
16 6 0.19
17 4 0.12
18 1 0.03
19 7 0.22
20 5 0.16
21 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TATATTTTTTAAAAATATA
Found at i:26399 original size:2 final size:2
Alignment explanation
Indices: 26392--26420 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26382 TTATGTTTAA
26392 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
26421 ACACGTGTCA
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:26650 original size:14 final size:15
Alignment explanation
Indices: 26624--26652 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
26614 TTTGGTTTTT
26624 TAAATTAAAATAATA
1 TAAATTAAAATAATA
26639 TAAATT-AAATAATA
1 TAAATTAAAATAATA
26653 GAATATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATTAAAATAATA
Found at i:27872 original size:2 final size:2
Alignment explanation
Indices: 27861--27931 Score: 98
Period size: 2 Copynumber: 38.0 Consensus size: 2
27851 AGAAATCAAT
27861 TA TA -A TA TA TA TA TA TA 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 TA TA TA TA TA TA
*
27902 GA TA TA TA TA TA -A TA TA TA -A TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27932 ATTATAGTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
1 5 0.08
2 57 0.92
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:28327 original size:27 final size:27
Alignment explanation
Indices: 28281--28340 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
28271 ACTAATAAAT
28281 AAATA-TAAAACTAAATTTAATT-TAA
1 AAATATTAAAACTAAATTTAATTATAA
28306 AAATATTAAAATCTTAAA-TTAATTATAA
1 AAATATTAAAA-C-TAAATTTAATTATAA
28334 ATAATAT
1 A-AATAT
28341 ATTATATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 5 0.17
26 5 0.17
27 7 0.23
28 8 0.27
29 5 0.17
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATATTAAAACTAAATTTAATTATAA
Found at i:28420 original size:13 final size:13
Alignment explanation
Indices: 28402--28427 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28392 AACCAGTTGT
28402 TCTAGTGGGATGA
1 TCTAGTGGGATGA
28415 TCTAGTGGGATGA
1 TCTAGTGGGATGA
28428 GGCACTAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.38, T:0.31
Consensus pattern (13 bp):
TCTAGTGGGATGA
Found at i:29669 original size:16 final size:15
Alignment explanation
Indices: 29632--29671 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
29622 TTATTATTGA
*
29632 ACTGATTTGATATTT
1 ACTGACTTGATATTT
29647 ACTTGACTTGATATTT
1 AC-TGACTTGATATTT
29663 ATCTGACTT
1 A-CTGACTT
29672 ATAAGTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 19 0.86
17 1 0.05
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (15 bp):
ACTGACTTGATATTT
Found at i:29847 original size:18 final size:18
Alignment explanation
Indices: 29826--29864 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29816 ATTTTAATCT
29826 TTATAAT-ATAAAACTTAA
1 TTATAATCATAAAA-TTAA
*
29844 TTATAATCATTAAATTAA
1 TTATAATCATAAAATTAA
29862 TTA
1 TTA
29865 AATTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATAATCATAAAATTAA
Found at i:29984 original size:16 final size:15
Alignment explanation
Indices: 29959--29988 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29949 GTAATCATTG
29959 ATAAATAATTTAAAT
1 ATAAATAATTTAAAT
29974 ATAATATAATTTAAA
1 ATAA-ATAATTTAAA
29989 ATTTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATAATTTAAAT
Found at i:29988 original size:25 final size:24
Alignment explanation
Indices: 29960--30006 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
29950 TAATCATTGA
29960 TAAATAATTT-AAATATAATATAATT
1 TAAA-AATTTAAAATAT-ATATAATT
*
29985 TAAAATTTTAAAATATATATAA
1 TAAAAATTTAAAATATATATAA
30007 AAGATGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAAATTTAAAATATATATAATT
Found at i:30238 original size:39 final size:39
Alignment explanation
Indices: 30195--30269 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
30185 TTTAATACAC
* * *
30195 TAAAAGTCCAATACATTTCATTTAGCATCCATTTACATA
1 TAAAAGCCCAATACAATTCATATAGCATCCATTTACATA
30234 TAAAAGCCCAATACAATTCATATAGCATCCATTTAC
1 TAAAAGCCCAATACAATTCATATAGCATCCATTTAC
30270 TTGTAGCCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (39 bp):
TAAAAGCCCAATACAATTCATATAGCATCCATTTACATA
Found at i:30495 original size:2 final size:2
Alignment explanation
Indices: 30490--30521 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30480 ATAAATTATG
30490 AT 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 AT
30522 GCATTTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30602 original size:32 final size:33
Alignment explanation
Indices: 30528--30604 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 33
30518 ATATGCATTT
* *
30528 ATGTACATACATGCATCATAAATAATCGTATAT
1 ATGTACATACATGCATCATAAATAATCATATAC
* * *
30561 ATGTACATACATGCAT-ATATATACTTATATAC
1 ATGTACATACATGCATCATAAATAATCATATAC
30593 ATGTACATACAT
1 ATGTACATACAT
30605 CATTAATCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 23 0.59
33 16 0.41
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (33 bp):
ATGTACATACATGCATCATAAATAATCATATAC
Found at i:30622 original size:32 final size:32
Alignment explanation
Indices: 30528--30624 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 32
30518 ATATGCATTT
* * *
30528 ATGTACATACATGCATCATAAATA-ATCGTATAT
1 ATGTACATACATGCAT-ATATATACAT-ATATAC
*
30561 ATGTACATACATGCATATATATACTTATATAC
1 ATGTACATACATGCATATATATACATATATAC
30593 ATGTACATACAT-CAT-TAATCATACATATATAC
1 ATGTACATACATGCATAT-AT-ATACATATATAC
30625 TTAATTACTT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 5 0.09
32 33 0.59
33 17 0.30
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (32 bp):
ATGTACATACATGCATATATATACATATATAC
Found at i:30943 original size:15 final size:15
Alignment explanation
Indices: 30923--30954 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30913 TTTGATAGTC
30923 TAGGTAATTAAAGTA
1 TAGGTAATTAAAGTA
*
30938 TAGGTAATTAAATTA
1 TAGGTAATTAAAGTA
30953 TA
1 TA
30955 TAAATGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (15 bp):
TAGGTAATTAAAGTA
Done.