Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004962.1 Hibiscus syriacus cultivar Beakdansim tig00011153_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: 72127
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:4803 original size:33 final size:35
Alignment explanation
Indices: 4757--4860 Score: 126
Period size: 34 Copynumber: 3.1 Consensus size: 35
4747 TATTAATTAA
*
4757 CCTG-AATTACATAAGATACAAAATGCACTC-AAC
1 CCTGAAATTACATAAGATACAAAATACACTCTAAC
* *
4790 CCT-AAATTACATAAGATACACATTACACTCTAAC
1 CCTGAAATTACATAAGATACAAAATACACTCTAAC
* * *
4824 CCTGAAA-TACATAAGATACGAATTACACTATAAC
1 CCTGAAATTACATAAGATACAAAATACACTCTAAC
4858 CCT
1 CCT
4861 CCTTGATTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
33 26 0.42
34 33 0.53
35 3 0.05
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.24
Consensus pattern (35 bp):
CCTGAAATTACATAAGATACAAAATACACTCTAAC
Found at i:11916 original size:21 final size:22
Alignment explanation
Indices: 11876--11917 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
11866 TATATAGTTC
* *
11876 AGAGAATAAACAATCTTTAAAG
1 AGAGAATAAAAAATCCTTAAAG
11898 AGAGAA-AAAAAATCCTTAAA
1 AGAGAATAAAAAATCCTTAAA
11918 ATAATAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (22 bp):
AGAGAATAAAAAATCCTTAAAG
Found at i:29625 original size:12 final size:12
Alignment explanation
Indices: 29608--29639 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
29598 TCAAAGGGGC
29608 GAAGTAGAAGTT
1 GAAGTAGAAGTT
29620 GAAGTAGAAGTT
1 GAAGTAGAAGTT
29632 GAAGTAGA
1 GAAGTAGA
29640 TGGATGGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (12 bp):
GAAGTAGAAGTT
Found at i:30549 original size:20 final size:20
Alignment explanation
Indices: 30526--30612 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
30516 GTTTCCAAAT
*
30526 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
30546 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
** *
30566 TCGCAATACGAATCTGTAAA
1 TCGCAACGCGAATTTGTAAA
*
30586 TCGCAACGCGAATTTGTAAT
1 TCGCAACGCGAATTTGTAAA
30606 TCGCAAC
1 TCGCAAC
30613 ACATAAGTCA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:30630 original size:40 final size:39
Alignment explanation
Indices: 30526--30631 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 39
30516 GTTTCCAAAT
* *
30526 TCGCAACGCGAATATGTAAATCGCAACGCGAATTTGTAAA
1 TCGCAACAC-AATAAGTAAATCGCAACGCGAATTTGTAAA
* ** *
30566 TCGCAATACGAATCTGTAAATCGCAACGCGAATTTGTAAT
1 TCGCAACAC-AATAAGTAAATCGCAACGCGAATTTGTAAA
30606 TCGCAACAC-ATAAGTCAAATTCGCAA
1 TCGCAACACAATAAGT-AAA-TCGCAA
30632 AGCGCGTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 4 0.07
39 3 0.05
40 50 0.88
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.24
Consensus pattern (39 bp):
TCGCAACACAATAAGTAAATCGCAACGCGAATTTGTAAA
Found at i:30814 original size:22 final size:22
Alignment explanation
Indices: 30789--30830 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
30779 CGGCGACATC
30789 CGTCCCCATCTCCGACGAAACT
1 CGTCCCCATCTCCGACGAAACT
* *
30811 CGTCCCTATCTCCGGCGAAA
1 CGTCCCCATCTCCGACGAAA
30831 TCCATCTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.43, G:0.17, T:0.19
Consensus pattern (22 bp):
CGTCCCCATCTCCGACGAAACT
Found at i:31198 original size:20 final size:20
Alignment explanation
Indices: 31173--31213 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
31163 AAACTTAAAT
31173 TCGCAACACAAAAATGAAAA
1 TCGCAACACAAAAATGAAAA
* *
31193 TCGCAACGCGAAAATGAAAA
1 TCGCAACACAAAAATGAAAA
31213 T
1 T
31214 AGCGTTGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.20, G:0.15, T:0.12
Consensus pattern (20 bp):
TCGCAACACAAAAATGAAAA
Found at i:33309 original size:21 final size:21
Alignment explanation
Indices: 33279--33375 Score: 99
Period size: 21 Copynumber: 4.6 Consensus size: 21
33269 GGTTCACCTG
*
33279 TCATCGTTCAAGAGGCCTCTC
1 TCATCATTCAAGAGGCCTCTC
* *
33300 -CTATCATTCAAGAGGCCCCTG
1 TC-ATCATTCAAGAGGCCTCTC
*
33321 TCATCCTTCAAGAGGCC-CTTC
1 TCATCATTCAAGAGGCCTC-TC
* * *
33342 CCACCATTCAAGAGGCCTCTG
1 TCATCATTCAAGAGGCCTCTC
33363 TCATCATTCAAGA
1 TCATCATTCAAGA
33376 AGTCCCTCCC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.03
21 57 0.93
22 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCTCTC
Found at i:33322 original size:42 final size:42
Alignment explanation
Indices: 33275--33388 Score: 142
Period size: 42 Copynumber: 2.7 Consensus size: 42
33265 GCCTGGTTCA
* * *
33275 CCTGTCATCGTTCAAGAGG-CCTCTCCTATCATTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCCCT-TCCCACCATTCAAGAGGCC
*
33317 CCTGTCATCCTTCAAGAGGCCCTTCCCACCATTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCCCTTCCCACCATTCAAGAGGCC
* *
33359 TCTGTCATCATTCAAGAAGTCCC-TCCCACC
1 CCTGTCATCATTCAAG-AGGCCCTTCCCACC
33389 GTTCGAAAGC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
42 56 0.88
43 8 0.12
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.25
Consensus pattern (42 bp):
CCTGTCATCATTCAAGAGGCCCTTCCCACCATTCAAGAGGCC
Found at i:33787 original size:2 final size:2
Alignment explanation
Indices: 33780--33811 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
33770 AAATTCACTA
33780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33812 AAACAGCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34774 original size:14 final size:14
Alignment explanation
Indices: 34755--34788 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
34745 AAATTTATGT
34755 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
34769 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
34783 ATTTGT
1 ATTTGT
34789 TTAATTGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:34849 original size:14 final size:14
Alignment explanation
Indices: 34830--34864 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
34820 GCTTGTTTAA
34830 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
34844 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
34858 TTGATTT
1 TTGATTT
34865 TTTAATTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:34907 original size:77 final size:78
Alignment explanation
Indices: 34755--34929 Score: 298
Period size: 77 Copynumber: 2.3 Consensus size: 78
34745 AAATTTATGT
34755 ATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT
1 ATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT
34820 GCTTGTTTAATTG
66 GCTTGTTTAATTG
* * ***
34833 ATTTGTAAAAGTTGATTTGTAAAAGTTGATTT-TTTAATTGATGTGTAAATAATTCTTATTTTTT
1 ATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT
34897 GCTTGTTTAATTG
66 GCTTGTTTAATTG
34910 ATTTGTAAAAGTTGATTTGT
1 ATTTGTAAAAGTTGATTTGT
34930 TGTTTTAAAT
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 60 0.65
78 32 0.35
ACGTcount: A:0.30, C:0.02, G:0.18, T:0.50
Consensus pattern (78 bp):
ATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT
GCTTGTTTAATTG
Found at i:34917 original size:37 final size:37
Alignment explanation
Indices: 34811--34918 Score: 101
Period size: 37 Copynumber: 2.8 Consensus size: 37
34801 GAAATAAGAA
*
34811 TTATTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATT
1 TTATTTTTTGCTTGTTTAATTGATTTGT-AAAG-TAATT
**** * * *
34850 TGTAAAAGTTGATTTTTTAATTGATGTGTAAA-TAATT
1 T-TATTTTTTGCTTGTTTAATTGATTTGTAAAGTAATT
34887 CTTATTTTTTGCTTGTTTAATTGATTTGTAAA
1 -TTATTTTTTGCTTGTTTAATTGATTTGTAAA
34919 AGTTGATTTG
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
37 27 0.52
38 1 0.02
39 4 0.08
40 20 0.38
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.56
Consensus pattern (37 bp):
TTATTTTTTGCTTGTTTAATTGATTTGTAAAGTAATT
Found at i:35301 original size:18 final size:18
Alignment explanation
Indices: 35278--35313 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35268 AAGCCGGTTG
*
35278 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
35296 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
35314 CCTTTTGCTT
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:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:39573 original size:31 final size:31
Alignment explanation
Indices: 39535--39657 Score: 176
Period size: 31 Copynumber: 4.0 Consensus size: 31
39525 CCCGAAGGAC
* * *
39535 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
39566 CAGTCCATATGTTCCGAAGAACGTAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
39597 CAGTCCATATGTCCCGAAGAACATGGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
39628 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
39658 CCCTCGACCC
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:40664 original size:21 final size:21
Alignment explanation
Indices: 40639--40684 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
40629 TTCTGGTTCG
* * *
40639 CTTGAGGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
40660 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
40681 CTTG
1 CTTG
40685 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:43589 original size:16 final size:18
Alignment explanation
Indices: 43556--43589 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
43546 TATAATATTT
43556 CATATAACATAAAGCATA
1 CATATAACATAAAGCATA
43574 CATA-AACATAAA-CATA
1 CATATAACATAAAGCATA
43590 TACCATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.59, C:0.18, G:0.03, T:0.21
Consensus pattern (18 bp):
CATATAACATAAAGCATA
Found at i:43863 original size:31 final size:31
Alignment explanation
Indices: 43825--43916 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
43815 CCCGAAGGAC
* ** * *
43825 CAGTCCATAGATTCTGAAGAACCTAGGTAAT
1 CAGTCCATAGATCCCAAAGAACATAGGTAAA
*
43856 CAGTCCATATATCCCAAAGAACATAGGTAAA
1 CAGTCCATAGATCCCAAAGAACATAGGTAAA
*
43887 CAGTCCATATG-TCCCGAAGAACATAGGTAA
1 CAGTCCATA-GATCCCAAAGAACATAGGTAA
43917 CCCTCGACCC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (31 bp):
CAGTCCATAGATCCCAAAGAACATAGGTAAA
Found at i:45803 original size:36 final size:36
Alignment explanation
Indices: 45751--45828 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
45741 TTACAAGTTC
* *
45751 TAGAATTAAGTGATAAAAGAAT-AAGCCATTGATATG
1 TAGATTTAAGTGATAAAAGAATCAA-CCATGGATATG
45787 TAGATTTAAGTGATAAAAGAATCAACCATGGATATG
1 TAGATTTAAGTGATAAAAGAATCAACCATGGATATG
45823 TAGATT
1 TAGATT
45829 ATAATTTATC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 37 0.95
37 2 0.05
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (36 bp):
TAGATTTAAGTGATAAAAGAATCAACCATGGATATG
Found at i:50467 original size:36 final size:36
Alignment explanation
Indices: 50427--50499 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
50417 AGTTCTCGAA
50427 TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
50463 TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
50499 T
1 T
50500 ATAATTTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
Found at i:50657 original size:17 final size:18
Alignment explanation
Indices: 50635--50668 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
50625 TGAAAATAAT
50635 TATTGATCTG-ATAAAAC
1 TATTGATCTGCATAAAAC
*
50652 TATTGATGTGCATAAAA
1 TATTGATCTGCATAAAA
50669 AAATGTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (18 bp):
TATTGATCTGCATAAAAC
Found at i:52319 original size:12 final size:12
Alignment explanation
Indices: 52304--52373 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
52294 GATAAATGAC
52304 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
52316 CTGATTTCTGAT
1 CTGAATTCTGTT
*
52328 CTGGATTCTGTT
1 CTGAATTCTGTT
*
52340 CTG-ATATCTTTT
1 CTGAAT-TCTGTT
52352 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
52364 TTGATTTCTG
1 CTGAATTCTG
52374 ATATCTCCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.17, T:0.53
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:52323 original size:48 final size:48
Alignment explanation
Indices: 52267--52375 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
52257 AAATATTTTA
52267 TCTGATTTCTGA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGTTCTGATAAATGACCTGAATTCTGT
* ** ***
52315 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTTTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
*
52363 TTTGATTTCTGAT
1 TCTGATTTCTGAT
52376 ATCTCCGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:52335 original size:24 final size:24
Alignment explanation
Indices: 52267--52375 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
52257 AAATATTTTA
52267 TCTGATTTCTGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
*** *
52291 TCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
52315 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* **
52339 TCTGATATCTTTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
52363 TTTGATTTCTGAT
1 TCTGATTTCTGAT
52376 ATCTCCGTTT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
24 67 0.99
25 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:52540 original size:2 final size:2
Alignment explanation
Indices: 52533--52591 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
52523 AGGATGTGAG
52533 TA TA TA 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
52575 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
52592 GTTTTAAAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53197 original size:24 final size:24
Alignment explanation
Indices: 53165--53211 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
53155 TTACATAAAA
53165 TCCGAGTATTGACCAAAATCAAAG
1 TCCGAGTATTGACCAAAATCAAAG
* *
53189 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAAATCAAA
53212 TTTTGAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTGACCAAAATCAAAG
Found at i:54191 original size:20 final size:20
Alignment explanation
Indices: 54168--54270 Score: 77
Period size: 19 Copynumber: 5.2 Consensus size: 20
54158 TACGAAATTA
*
54168 AAATTCGTGTTGCGAATTCG
1 AAATTCGAGTTGCGAATTCG
** *
54188 AAA-TCGAGTTGCGAAAACA
1 AAATTCGAGTTGCGAATTCG
* * *
54207 AAATTTGCGTTGCAAATTCAG
1 AAATTCGAGTTGCGAATTC-G
*
54228 AAATT-GAGTTGCGAATTTG
1 AAATTCGAGTTGCGAATTCG
*
54247 AAATTC-AGTATTGCGAATTTG
1 AAATTCGAG--TTGCGAATTCG
54268 AAA
1 AAA
54271 ACCGCAACAC
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
19 23 0.35
20 23 0.35
21 19 0.29
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
AAATTCGAGTTGCGAATTCG
Found at i:54210 original size:39 final size:40
Alignment explanation
Indices: 54167--54242 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 40
54157 GTACGAAATT
* *
54167 AAAATTCGTGTTGCGAATTC-GAAATCGAGTTGCGAAAAC
1 AAAATTCGCGTTGCAAATTCAGAAATCGAGTTGCGAAAAC
* *
54206 AAAATTTGCGTTGCAAATTCAGAAATTGAGTTGCGAA
1 AAAATTCGCGTTGCAAATTCAGAAATCGAGTTGCGAA
54243 TTTGAAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 17 0.53
40 15 0.47
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (40 bp):
AAAATTCGCGTTGCAAATTCAGAAATCGAGTTGCGAAAAC
Done.