Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007232.1 Hibiscus syriacus cultivar Beakdansim tig00019143_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: 112919
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13789 original size:2 final size:2
Alignment explanation
Indices: 13782--13822 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
13772 ACTTATCCAA
*
13782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13823 ATTATTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:13932 original size:2 final size:2
Alignment explanation
Indices: 13921--13963 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
13911 AAATATTTAT
13921 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
13962 TA
1 TA
13964 ATAATTGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14872 original size:59 final size:59
Alignment explanation
Indices: 14799--14912 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
14789 ATAAATAACT
14799 TTAATAGTATATTTC-ATTGGACAATGTTAACCAAGTTTGATATAAATCCAAAAAACTCG
1 TTAATAGTATATTTCGA-TGGACAATGTTAACCAAGTTTGATATAAATCCAAAAAACTCG
* * * *
14858 TTAATTGTATATTTCGATGTACAATGTTAATCAAGTTTGATATAAATTCAAAAAA
1 TTAATAGTATATTTCGATGGACAATGTTAACCAAGTTTGATATAAATCCAAAAAA
14913 TGAAAAGGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 49 0.98
60 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (59 bp):
TTAATAGTATATTTCGATGGACAATGTTAACCAAGTTTGATATAAATCCAAAAAACTCG
Found at i:16328 original size:23 final size:23
Alignment explanation
Indices: 16263--16329 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
16253 TGGCTATAAG
* *
16263 TTAATTTTTCACTTTATTTTTAAC
1 TTAATTTTTTA-TATATTTTTAAC
* * *
16287 -TAACTTTTTA-ATATATTTATC
1 TTAATTTTTTATATATTTTTAAC
*
16308 TTAATTTTTTATCTATTTTTAA
1 TTAATTTTTTATATATTTTTAA
16330 TTGTTTTTTA
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
21 8 0.25
22 9 0.28
23 15 0.47
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (23 bp):
TTAATTTTTTATATATTTTTAAC
Found at i:16331 original size:18 final size:17
Alignment explanation
Indices: 16308--16354 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
16298 TATATTTATC
16308 TTAATTTTTTATCTATTT
1 TTAATTTTTTAT-TATTT
16326 TTAATTGTTTT-TTATTT
1 TTAATT-TTTTATTATTT
*
16343 TTCAATATTTTA
1 TT-AATTTTTTA
16355 GATGGTACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 11 0.44
18 10 0.40
19 4 0.16
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (17 bp):
TTAATTTTTTATTATTT
Found at i:19008 original size:25 final size:24
Alignment explanation
Indices: 18978--19025 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
18968 CATTTAAAAA
*
18978 AAATATTTAATAATATATTAATTAT
1 AAATATTTAATAAAAT-TTAATTAT
*
19003 AAATATTTTATAAAATTTAATTA
1 AAATATTTAATAAAATTTAATTA
19026 ATATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAATATTTAATAAAATTTAATTAT
Found at i:19902 original size:32 final size:34
Alignment explanation
Indices: 19852--19934 Score: 109
Period size: 34 Copynumber: 2.4 Consensus size: 34
19842 TAGCTAATGA
*
19852 TATAAATATCTCTTTACA-TT-TTAGACATAAAAT
1 TATAAATAT-TTTTTACATTTATTAGACATAAAAT
19885 TCA-AAATATTTTTTACATTTATTAGACATAAAAT
1 T-ATAAATATTTTTTACATTTATTAGACATAAAAT
19919 TATAAATATTTATTTA
1 TATAAATATTT-TTTA
19935 TTAATTAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
32 7 0.16
33 10 0.23
34 23 0.52
35 4 0.09
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.46
Consensus pattern (34 bp):
TATAAATATTTTTTACATTTATTAGACATAAAAT
Found at i:20406 original size:2 final size:2
Alignment explanation
Indices: 20399--20428 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20389 GATATACAAG
20399 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20429 CTCTGCATTT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34806 original size:7 final size:8
Alignment explanation
Indices: 34785--34810 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
34775 AAGAATTTAT
34785 TTAAAAAA
1 TTAAAAAA
34793 TTAAAAAA
1 TTAAAAAA
34801 TTAAAAAA
1 TTAAAAAA
34809 TT
1 TT
34811 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
TTAAAAAA
Found at i:35223 original size:20 final size:20
Alignment explanation
Indices: 35193--35230 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
35183 TATAACTTCG
35193 GTAAAAAATT-AACTTTTTT
1 GTAAAAAATTAAACTTTTTT
35212 GTAAATAAATTAAACTTTT
1 GTAAA-AAATTAAACTTTT
35231 ATTTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
GTAAAAAATTAAACTTTTTT
Found at i:35267 original size:24 final size:23
Alignment explanation
Indices: 35195--35270 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 23
35185 TAACTTCGGT
*
35195 AAAAAATT-AAC-TTT-TTTGTA
1 AAAAAATTAAACTTTTATTTATA
* *
35215 AATAAATTAAACTTTTATTTTTA
1 AAAAAATTAAACTTTTATTTATA
* *
35238 TTAAAAATTAATATTTTTATTTATA
1 -AAAAAATTAA-ACTTTTATTTATA
35263 AAAAAATT
1 AAAAAATT
35271 TAAATATATA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 7 0.16
21 3 0.07
22 3 0.07
23 5 0.11
24 15 0.34
25 11 0.25
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (23 bp):
AAAAAATTAAACTTTTATTTATA
Found at i:35268 original size:25 final size:24
Alignment explanation
Indices: 35195--35274 Score: 60
Period size: 25 Copynumber: 3.5 Consensus size: 24
35185 TAACTTCGGT
*
35195 AAAAAATT-AAC-TTT-TTTGT-A
1 AAAAAATTAAACTTTTATTTATAA
* * *
35215 AATAAATTAAACTTTTATTTTTAT
1 AAAAAATTAAACTTTTATTTATAA
* *
35239 TAAAAATTAATATTTTTATTTATAA
1 AAAAAATTAA-ACTTTTATTTATAA
*
35264 AAAAATTTAAA
1 AAAAAATTAAA
35275 TATATAACGG
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 7 0.16
21 3 0.07
22 3 0.07
23 4 0.09
24 9 0.20
25 19 0.42
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (24 bp):
AAAAAATTAAACTTTTATTTATAA
Found at i:35459 original size:39 final size:40
Alignment explanation
Indices: 35402--35479 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 40
35392 TACCACTTAC
*
35402 CTTTACACGTGGAAATGCTGTTTTCTTTT-CAAACCGAGG
1 CTTTACACGTGGAAATGCTATTTTCTTTTCCAAACCGAGG
*
35441 CTTTACACGTGGACATGCTATTTTCTTTTCCAAACCGAG
1 CTTTACACGTGGAAATGCTATTTTCTTTTCCAAACCGAG
35480 TCTGCCGTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 27 0.75
40 9 0.25
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (40 bp):
CTTTACACGTGGAAATGCTATTTTCTTTTCCAAACCGAGG
Found at i:35763 original size:21 final size:21
Alignment explanation
Indices: 35737--35778 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
35727 ATAAAAAAAA
*
35737 TATTTAAAATATTATTATTTT
1 TATTTAAAATATTAATATTTT
35758 TATTTAAAATATTAATATTTT
1 TATTTAAAATATTAATATTTT
35779 CTGTAACTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTAAAATATTAATATTTT
Found at i:36377 original size:17 final size:17
Alignment explanation
Indices: 36355--36389 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
36345 TAAAGATAAC
36355 TCTAAACCGTTTTCTAT
1 TCTAAACCGTTTTCTAT
36372 TCTAAACCGTTTTCTAT
1 TCTAAACCGTTTTCTAT
36389 T
1 T
36390 GAATGCCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (17 bp):
TCTAAACCGTTTTCTAT
Found at i:40379 original size:44 final size:45
Alignment explanation
Indices: 40257--40408 Score: 227
Period size: 44 Copynumber: 3.4 Consensus size: 45
40247 ATAAAATCTT
* *
40257 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGATTATTTTACCAATATAC
* *
40302 TTACCATTTAATACCATAAGCTCGTAAGTTTATTTTACCAATATAC
1 TTACCATTT-ATTCCATAAGCTCGTAAGATTATTTTACCAATATAC
*
40348 TTACCA-TTATTCCATAAGCTCGTAAGATTATTTTACCAATACAC
1 TTACCATTTATTCCATAAGCTCGTAAGATTATTTTACCAATATAC
*
40392 TTTCCA-TTATTCCATAA
1 TTACCATTTATTCCATAA
40409 CCATATACCA
Statistics
Matches: 100, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
44 49 0.49
45 11 0.11
46 40 0.40
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGATTATTTTACCAATATAC
Found at i:40615 original size:59 final size:59
Alignment explanation
Indices: 40500--40617 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 59
40490 CCTGAGTATA
* * ** *
40500 ACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAATCTCGAATATG
1 ACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAATCTAGAATATG
* * ** *
40559 ACACATAAGGTTGTGCCCACCATATACACTAGGTATCCTTTAGTGTATTCTAGAATATG
1 ACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAATCTAGAATATG
40618 CAGCCAACTG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (59 bp):
ACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAATCTAGAATATG
Found at i:40801 original size:21 final size:22
Alignment explanation
Indices: 40762--40802 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40752 TCGAAATAAC
40762 ATTCATGATAAAAATCATATAT
1 ATTCATGATAAAAATCATATAT
*
40784 ATTCATGAT-AACATCATAT
1 ATTCATGATAAAAATCATAT
40803 GTAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (22 bp):
ATTCATGATAAAAATCATATAT
Found at i:48805 original size:19 final size:19
Alignment explanation
Indices: 48781--48841 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 19
48771 TTTTTGTGCA
*
48781 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
48800 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCC-CT
48821 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGA-TCCCCCC
48842 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.29
20 6 0.17
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:54638 original size:12 final size:12
Alignment explanation
Indices: 54601--54640 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
54591 TCAGACAGCG
54601 GCAACCGACTCA
1 GCAACCGACTCA
* *
54613 GCACCCATACTCA
1 GCAACC-GACTCA
54626 GCAACCGACTCA
1 GCAACCGACTCA
54638 GCA
1 GCA
54641 CTGATCATGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.33, C:0.42, G:0.15, T:0.10
Consensus pattern (12 bp):
GCAACCGACTCA
Found at i:57519 original size:12 final size:10
Alignment explanation
Indices: 57492--57540 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
57482 AACATAAATG
57492 AACGAACATA
1 AACGAACATA
57502 AACGAACATA
1 AACGAACATA
57512 TAATCGAACATA
1 -AA-CGAACATA
*
57524 AACGAACGTA
1 AACGAACATA
*
57534 AATGAAC
1 AACGAAC
57541 GAACGAGCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 23 0.66
11 4 0.11
12 8 0.23
ACGTcount: A:0.55, C:0.18, G:0.12, T:0.14
Consensus pattern (10 bp):
AACGAACATA
Found at i:68147 original size:2 final size:2
Alignment explanation
Indices: 68140--68217 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
68130 CCTTCCTTAA
68140 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
68182 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
68218 CCGTTTTAAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68496 original size:18 final size:17
Alignment explanation
Indices: 68459--68498 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
68449 TAATATTGTT
* *
68459 AATAATTTATTTTTTTA
1 AATAATATATTTTTTGA
68476 AATAATATATTTTTATGA
1 AATAATATATTTTT-TGA
68494 AATAA
1 AATAA
68499 ATGAAACGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATAATATATTTTTTGA
Found at i:68684 original size:70 final size:70
Alignment explanation
Indices: 68602--68743 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
68592 GTTTTCTCTG
68602 AACTCCATATTTATAAGCATAAAGAGTATATATAATATAGAACTCTAACTCTAATCTATATTAAA
1 AACTCCATATTTATAAGCATAAAGAGTATATATAATATAGAACTCTAACTCTAATCTATATTAAA
68667 GTCCT
66 GTCCT
68672 AACTCCATATTTATAAGCATAAAGAGTATATATAATATAGAACTCTAACTCTAATCTATATTAAA
1 AACTCCATATTTATAAGCATAAAGAGTATATATAATATAGAACTCTAACTCTAATCTATATTAAA
68737 GTCCT
66 GTCCT
68742 AA
1 AA
68744 TAATAAAGTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (70 bp):
AACTCCATATTTATAAGCATAAAGAGTATATATAATATAGAACTCTAACTCTAATCTATATTAAA
GTCCT
Found at i:83711 original size:10 final size:10
Alignment explanation
Indices: 83698--83768 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
83688 ACACGCTGGG
83698 CATCCGAGAC
1 CATCCGAGAC
83708 CATCCGATCGAGGC
1 CATCCGA--GA--C
* * *
83722 CATCTGAAAG
1 CATCCGAGAC
*
83732 CATCCGAGGC
1 CATCCGAGAC
*
83742 CATCCGAGAG
1 CATCCGAGAC
*
83752 CATCCGAGGC
1 CATCCGAGAC
83762 CATCCGA
1 CATCCGA
83769 ACGAGCTATG
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
10 36 0.78
12 3 0.07
14 7 0.15
ACGTcount: A:0.27, C:0.35, G:0.25, T:0.13
Consensus pattern (10 bp):
CATCCGAGAC
Found at i:83741 original size:20 final size:20
Alignment explanation
Indices: 83716--83769 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
83706 ACCATCCGAT
*
83716 CGAGGCCATCTGAAAGCATC
1 CGAGGCCATCCGAAAGCATC
*
83736 CGAGGCCATCCGAGAGCATC
1 CGAGGCCATCCGAAAGCATC
83756 CGAGGCCATCCGAA
1 CGAGGCCATCCGAA
83770 CGAGCTATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.28, T:0.11
Consensus pattern (20 bp):
CGAGGCCATCCGAAAGCATC
Found at i:83917 original size:14 final size:14
Alignment explanation
Indices: 83895--83999 Score: 110
Period size: 14 Copynumber: 7.4 Consensus size: 14
83885 CTTCGCATAG
*
83895 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
83909 CTCGGTCGGATGG-
1 CTCGGTCGGATGGC
83922 C-C--TCGGATGGC
1 CTCGGTCGGATGGC
83933 CTCGGATGCTTTCGGATGGC
1 CTC-G--G---TCGGATGGC
83953 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
83967 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
*
83981 CTCGGTCGGATGAC
1 CTCGGTCGGATGGC
83995 CTCGG
1 CTCGG
84000 ATGCCCAACG
Statistics
Matches: 79, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
10 8 0.10
11 1 0.01
12 2 0.03
13 1 0.01
14 53 0.67
17 1 0.01
19 1 0.01
20 12 0.15
ACGTcount: A:0.09, C:0.29, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:83927 original size:24 final size:25
Alignment explanation
Indices: 83900--84002 Score: 112
Period size: 24 Copynumber: 4.3 Consensus size: 25
83890 CATAGCTCGT
83900 TCGGATGGCCTCGGTCGGATGGC-C
1 TCGGATGGCCTCGGTCGGATGGCTC
*
83924 TCGGATGG-C-C--TCGGAT-GCTT
1 TCGGATGGCCTCGGTCGGATGGCTC
83944 TCGGATGGCCTCGGTCGGATGGCCTC
1 TCGGATGGCCTCGGTCGGATGG-CTC
*
83970 GGTCGGATGGCCTCGGTCGGATGAC-C
1 --TCGGATGGCCTCGGTCGGATGGCTC
83996 TCGGATG
1 TCGGATG
84003 CCCAACGTGT
Statistics
Matches: 67, Mismatches: 3, Indels: 18
0.76 0.03 0.20
Matches are distributed among these distances:
19 2 0.03
20 14 0.21
21 1 0.01
22 2 0.03
23 1 0.01
24 21 0.31
25 1 0.01
26 3 0.04
27 1 0.01
28 21 0.31
ACGTcount: A:0.10, C:0.27, G:0.40, T:0.23
Consensus pattern (25 bp):
TCGGATGGCCTCGGTCGGATGGCTC
Found at i:83985 original size:10 final size:10
Alignment explanation
Indices: 83914--83957 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
83904 ATGGCCTCGG
83914 TCGGATGGCC
1 TCGGATGGCC
83924 TCGGATGGCC
1 TCGGATGGCC
*
83934 TCGGAT-GCTT
1 TCGGATGGC-C
83944 TCGGATGGCC
1 TCGGATGGCC
83954 TCGG
1 TCGG
83958 TCGGATGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.07
10 26 0.87
11 2 0.07
ACGTcount: A:0.09, C:0.27, G:0.39, T:0.25
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:103974 original size:19 final size:19
Alignment explanation
Indices: 103950--103998 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
103940 AAAAATGTTT
*
103950 TATGAATAGTATTATACTA
1 TATGAATAGTAATATACTA
* *
103969 TATGAATAGTAATGTACTG
1 TATGAATAGTAATATACTA
103988 TATGAATAGTA
1 TATGAATAGTA
103999 CAAATATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (19 bp):
TATGAATAGTAATATACTA
Done.