Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003221.1 Hibiscus syriacus cultivar Beakdansim tig00006785_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: 103974
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4479 original size:65 final size:62
Alignment explanation
Indices: 4360--4569 Score: 201
Period size: 65 Copynumber: 3.3 Consensus size: 62
4350 TTTGTCAGAG
* * ** **
4360 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGCAT
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACC-TG-GCTATTTTGAAACATCGAATGCAT
4424 T
62 T
*
4425 TCATGCATCGATGCACATACCATGCACCGATGCA-CTGAG-TATTTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACCTG-GCTA-TTT-TG-AAACATCGAATGCA
4488 TT
61 TT
* * *
4490 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCAC-CTGGCTATTTTGAAACATCGAATGCATT
*
4554 TGATGCATGGATGCAC
1 TGATGCATCGATGCAC
4570 TCTTAGTGCA
Statistics
Matches: 125, Mismatches: 11, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
61 2 0.02
62 4 0.03
63 4 0.03
64 45 0.36
65 59 0.47
66 6 0.05
67 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (62 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACCTGGCTATTTTGAAACATCGAATGCATT
Found at i:4569 original size:17 final size:19
Alignment explanation
Indices: 4541--4589 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
4531 TATTTTGAAA
4541 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
* *
4559 CATGGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
4578 CATCGATGCACT
1 CATCGATGCACT
4590 AAGGGTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
19 13 0.50
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:9796 original size:15 final size:15
Alignment explanation
Indices: 9775--9812 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
9765 ATTATTTTAT
*
9775 TACTTATTCGATGTA
1 TACTTATTCGACGTA
*
9790 TATTTATTCGACGTA
1 TACTTATTCGACGTA
9805 TACTTATT
1 TACTTATT
9813 ATTTCTCGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (15 bp):
TACTTATTCGACGTA
Found at i:16247 original size:22 final size:22
Alignment explanation
Indices: 16222--16272 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
16212 GTTGACCACT
* *
16222 GTTGACCAGAAATTTGATCGGC
1 GTTGACCAGAAATTTGACCGGA
** *
16244 GTTGATTAGAACTTTGACCGGA
1 GTTGACCAGAAATTTGACCGGA
16266 GTTGACC
1 GTTGACC
16273 GGCCATTGAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (22 bp):
GTTGACCAGAAATTTGACCGGA
Found at i:18628 original size:25 final size:24
Alignment explanation
Indices: 18606--18657 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 24
18596 CGAAAAATAT
18606 GAATTGTACATGATTTATGAAATCATG
1 GAATT-TAC-TGATTTAT-AAATCATG
* *
18633 GAATTTACTGGTTTATAAATTATG
1 GAATTTACTGATTTATAAATCATG
18657 G
1 G
18658 TTACCTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.35
25 7 0.30
26 3 0.13
27 5 0.22
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (24 bp):
GAATTTACTGATTTATAAATCATG
Found at i:21707 original size:17 final size:17
Alignment explanation
Indices: 21665--21715 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
21655 TTAAAGATTT
*
21665 AATAATTTTT-ATTTTA
1 AATATTTTTTAATTTTA
** *
21681 TTTATGTTTTAATTTTA
1 AATATTTTTTAATTTTA
*
21698 AATATTTTTTACTTTTA
1 AATATTTTTTAATTTTA
21715 A
1 A
21716 TGTCTTGGGT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
AATATTTTTTAATTTTA
Found at i:21872 original size:591 final size:593
Alignment explanation
Indices: 20716--21898 Score: 2156
Period size: 591 Copynumber: 2.0 Consensus size: 593
20706 TAAAGCTTGA
* *
20716 AAGAAAGAAAAAAAAGGAAAAGGACCAGATTCACAGCCAGACATTTACCGGCTATGTTATTTTTC
1 AAGAAAGAAAAAAAAGGAAAAGGACCAGATTCACAGCCAGACACTTACCAGCTATGTTATTTTTC
*
20781 AACCCTTTAAGAAAGTGAAGAAGGAGTTTGATCTTCTCTGTCTCTGCCTCTGGCGTCTCCTTTGG
66 AACCCTTTAAGAAAGTGAAGAAGGAGTTTGATCTTCTCCGTCTCTGCCTCTGGCGTCTCCTTTGG
* * * *
20846 TGGCAGAACCGGACCTATACCTATTTTTTGGACAAGAAAGAGAGGAAAATATGAGACTCGATTTT
131 TGGAAGAACCAGACCTATACCTATTTTTTGGACAAGAAAGAGAGGAAAATATGAGACCCGATGTT
20911 CCAATTGATGATTTTTCAACAAAGAAAGACCAGGGAAGCTTTCAACAATACAACTACAAGAAAAG
196 CCAATTGATGATTTTTCAACAAAGAAAGACCAGGGAAGCTTTCAACAATACAACTACAAGAAAAG
* * *
20976 AAAAGAAGTTTTTTTTTTTATGAAAAACACAGACATAAAACAAACATGGGAGTCCAAATTTTTCT
261 AAAAGAAGATTTTTTTATTATGAAAAACACAAACATAAAACAAACATGGGAGTCCAAATTTTTCT
21041 GATTTTGATGAAAAGAAGAGGCTTAAAGATTTAATAATTTTTATTTTATTTATGTTTTAGATTTT
326 GATTTTGATGAAAAGAAGAGGCTTAAAGATTTAATAATTTTTATTTTATTTATGTTTTAGATTTT
21106 AAATATTTTTTACTTTTAATGTCTTAGGTTTGAACCAAAAGAAACCCCAATAAATTAATAAGATT
391 AAATATTTTTTACTTTTAATGTCTTAGGTTTGAACCAAAAGAAACCCCAATAAATTAATAAGATT
21171 TGGGTTACAATGTTATGAGTTTTTTGTTGGGTTTGTTTTAGTTTTAAAGTTTAATATGTTGTTTT
456 TGGGTTACAATGTTATGAGTTTTTTGTTGGGTTTGTTTTAGTTTTAAAGTTTAATATGTTGTTTT
21236 TGGTGAGTGAATAATAATAGATAATTTTATGGGTTAATGTTTTAAATGGTTATGATTTATTTTAG
521 TGGTGAGTGAATAATAATAGATAATTTTATGGGTTAATGTTTTAAATGGTTATGATTTATTTTAG
21301 GAGATTGG
586 GAGATTGG
*
21309 AAGAAAGAAAAAAGAAGGAAAAGGACCAGATTCACAGCCAGACACTTACCAGCTGTGTTATTTTT
1 AAGAAAGAAAAAA-AAGGAAAAGGACCAGATTCACAGCCAGACACTTACCAGCTATGTTATTTTT
21374 CAACCCTTTAAGAAAGTGAAGAAGGAGTTTGATCTTCTCCGTCTCTGCCTCTGGCGTCTCCTTTG
65 CAACCCTTTAAGAAAGTGAAGAAGGAGTTTGATCTTCTCCGTCTCTGCCTCTGGCGTCTCCTTTG
* * * *
21439 GTGGAAGAACCAGCCCTATACCTGTTTTTTGGATAAGAAAGCGAGGAAAATATGAGACCCGATGT
130 GTGGAAGAACCAGACCTATACCTATTTTTTGGACAAGAAAGAGAGGAAAATATGAGACCCGATGT
21504 TCCAATTGATGATTTTTCAACAAAGAAAGA-CAGGGAAGCTTTCAACAATACAACTACAAGAAAA
195 TCCAATTGATGATTTTTCAACAAAGAAAGACCAGGGAAGCTTTCAACAATACAACTACAAGAAAA
* *
21568 GAAATGAA-ATTTTTTTATTATGAAAAACACAAACATAAAACAAACATGGGAGTCTAAATTTTTC
260 GAAAAGAAGATTTTTTTATTATGAAAAACACAAACATAAAACAAACATGGGAGTCCAAATTTTTC
21632 TGATTTTGATGAAAAGAAGAGGCTTAAAGATTTAATAATTTTTATTTTATTTATGTTTTA-ATTT
325 TGATTTTGATGAAAAGAAGAGGCTTAAAGATTTAATAATTTTTATTTTATTTATGTTTTAGATTT
*
21696 TAAATATTTTTTACTTTTAATGTCTTGGGTTTGAACCAAAAGAAACCCCAATAAATTAATAAGAT
390 TAAATATTTTTTACTTTTAATGTCTTAGGTTTGAACCAAAAGAAACCCCAATAAATTAATAAGAT
*
21761 TTGTGTTACAATGTTATGAGTTTTTTGTTGGGTTTGTTTTAGTTTTAAAGTTTAATATGTTGTTT
455 TTGGGTTACAATGTTATGAGTTTTTTGTTGGGTTTGTTTTAGTTTTAAAGTTTAATATGTTGTTT
*
21826 TTGGTGAGTGAATAATAATAGATAATTTTATGGGTTAATTTTTTAAATGGTTATGATTTATTTTA
520 TTGGTGAGTGAATAATAATAGATAATTTTATGGGTTAATGTTTTAAATGGTTATGATTTATTTTA
21891 GGAGATTG
585 GGAGATTG
21899 AATGTTGAAT
Statistics
Matches: 569, Mismatches: 20, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
591 204 0.36
592 112 0.20
593 54 0.09
594 199 0.35
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (593 bp):
AAGAAAGAAAAAAAAGGAAAAGGACCAGATTCACAGCCAGACACTTACCAGCTATGTTATTTTTC
AACCCTTTAAGAAAGTGAAGAAGGAGTTTGATCTTCTCCGTCTCTGCCTCTGGCGTCTCCTTTGG
TGGAAGAACCAGACCTATACCTATTTTTTGGACAAGAAAGAGAGGAAAATATGAGACCCGATGTT
CCAATTGATGATTTTTCAACAAAGAAAGACCAGGGAAGCTTTCAACAATACAACTACAAGAAAAG
AAAAGAAGATTTTTTTATTATGAAAAACACAAACATAAAACAAACATGGGAGTCCAAATTTTTCT
GATTTTGATGAAAAGAAGAGGCTTAAAGATTTAATAATTTTTATTTTATTTATGTTTTAGATTTT
AAATATTTTTTACTTTTAATGTCTTAGGTTTGAACCAAAAGAAACCCCAATAAATTAATAAGATT
TGGGTTACAATGTTATGAGTTTTTTGTTGGGTTTGTTTTAGTTTTAAAGTTTAATATGTTGTTTT
TGGTGAGTGAATAATAATAGATAATTTTATGGGTTAATGTTTTAAATGGTTATGATTTATTTTAG
GAGATTGG
Found at i:23265 original size:15 final size:16
Alignment explanation
Indices: 23245--23277 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23235 AAAGTAATGA
23245 TACTCAT-GTTAGTAT
1 TACTCATCGTTAGTAT
*
23260 TACTCATCGTTATTAT
1 TACTCATCGTTAGTAT
23276 TA
1 TA
23278 GTAATTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.48
Consensus pattern (16 bp):
TACTCATCGTTAGTAT
Found at i:24434 original size:14 final size:14
Alignment explanation
Indices: 24401--24463 Score: 67
Period size: 14 Copynumber: 4.6 Consensus size: 14
24391 ATTATAAAGA
*
24401 AAAAAATAAAATAA
1 AAAAAATAAAATAT
24415 AAAAAATAAAATAT
1 AAAAAATAAAATAT
**
24429 CTAAAATATAAATAT
1 AAAAAATA-AAATAT
*
24444 -AAAAATATAAT-T
1 AAAAAATAAAATAT
24456 AAAAAATA
1 AAAAAATA
24464 GGAGCCTATG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
12 1 0.02
13 10 0.24
14 25 0.60
15 6 0.14
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAAATAAAATAT
Found at i:24777 original size:29 final size:29
Alignment explanation
Indices: 24740--24801 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
24730 GCATCATCGA
24740 GAACAACATTCTATAAGATAAGCCTCATC
1 GAACAACATTCTATAAGATAAGCCTCATC
24769 GAACAACATTCTATAAGATAAGCCTCATC
1 GAACAACATTCTATAAGATAAGCCTCATC
24798 GAAC
1 GAAC
24802 GATCGACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.23
Consensus pattern (29 bp):
GAACAACATTCTATAAGATAAGCCTCATC
Found at i:24970 original size:3 final size:3
Alignment explanation
Indices: 24962--25012 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
24952 TTTACCCGGG
* * *
24962 TTA TTA TTA ATA TTTA ATA TTA TTA TTA TTA TTA TTAA TT- TTT TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
25008 TTA TT
1 TTA TT
25013 TTTTACAGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28708 original size:12 final size:11
Alignment explanation
Indices: 28679--28708 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28669 TTGTATTAAC
28679 TTGTTTTTATG
1 TTGTTTTTATG
28690 TTGTTTTTATG
1 TTGTTTTTATG
*
28701 TTGCTTTT
1 TTGTTTTT
28709 CTTTCTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.03, G:0.17, T:0.73
Consensus pattern (11 bp):
TTGTTTTTATG
Found at i:31825 original size:38 final size:37
Alignment explanation
Indices: 31751--31826 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 37
31741 GTTGAAAAAT
* *
31751 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
31788 ATTTATATAATTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-A-TTTTCTTTAAAAAATTGAAAATCATAAA
31826 A
1 A
31827 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.24
38 7 0.21
39 18 0.55
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:35108 original size:17 final size:16
Alignment explanation
Indices: 35065--35128 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
35055 TGGATCTGTT
* *
35065 TTCTTTATTCTTTCT-
1 TTCTTTCTTCTTTTTC
35080 TTCATTTC-TCTTTTTC
1 TTC-TTTCTTCTTTTTC
* *
35096 TATTTTTCTTCTTTCTC
1 T-TCTTTCTTCTTTTTC
35113 TTCTTTCTTTCTTTTT
1 TTCTTTC-TTCTTTTT
35129 GTGTGCTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
15 9 0.24
16 13 0.34
17 16 0.42
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (16 bp):
TTCTTTCTTCTTTTTC
Found at i:35114 original size:9 final size:8
Alignment explanation
Indices: 35072--35126 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
35062 GTTTTCTTTA
35072 TTCTTTCT
1 TTCTTTCT
35080 TTCATTTCT
1 TTC-TTTCT
35089 CTT-TTTCT
1 -TTCTTTCT
35097 ATT-TTTC-
1 -TTCTTTCT
35104 TTCTTTCT
1 TTCTTTCT
35112 CTTCTTTCT
1 -TTCTTTCT
35121 TTCTTT
1 TTCTTT
35127 TTGTGTGCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
6 2 0.05
7 4 0.10
8 20 0.49
9 13 0.32
10 2 0.05
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.73
Consensus pattern (8 bp):
TTCTTTCT
Found at i:35116 original size:28 final size:27
Alignment explanation
Indices: 35063--35128 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
35053 GTTGGATCTG
*
35063 TTTTCTTTATTCTTTCTTTCATTTCTCT
1 TTTTCTTTTTTCTTTCTTTCATTTCT-T
35091 TTTTCTATTTTTC-TTCTTTC-TCTTCTT
1 TTTTCT-TTTTTCTTTCTTTCAT-TTCTT
35118 TCTTTCTTTTT
1 T-TTTCTTTTT
35129 GTGTGCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 7 0.21
28 22 0.65
29 5 0.15
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTTCTTTTTTCTTTCTTTCATTTCTT
Found at i:35455 original size:2 final size:2
Alignment explanation
Indices: 35448--35489 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
35438 GAAACAAGGG
*
35448 AT AT AT AT GT 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
35490 GAAAGGATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50235 original size:10 final size:10
Alignment explanation
Indices: 50222--50246 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
50212 AAATAATAAA
50222 AAATAAGCAT
1 AAATAAGCAT
50232 AAATAAGCAT
1 AAATAAGCAT
50242 AAATA
1 AAATA
50247 TAAGGACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (10 bp):
AAATAAGCAT
Found at i:50335 original size:32 final size:29
Alignment explanation
Indices: 50294--50353 Score: 75
Period size: 32 Copynumber: 2.0 Consensus size: 29
50284 AAAAAGAACA
*
50294 AATTGAAAATGCAGTAGGGACTAAATTAAAAT
1 AATTCAAAATGCA--AGGGA-TAAATTAAAAT
*
50326 AATTCAAAATGTAAGGGATAAATTAAAA
1 AATTCAAAATGCAAGGGATAAATTAAAA
50354 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 10 0.38
30 5 0.19
32 11 0.42
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.25
Consensus pattern (29 bp):
AATTCAAAATGCAAGGGATAAATTAAAAT
Found at i:50365 original size:30 final size:30
Alignment explanation
Indices: 50309--50365 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
50299 AAAATGCAGT
* **
50309 AGGGACTAAATTAAAATAATTCAAAATGTA
1 AGGGACTAAATTAAAAAAATAAAAAATGTA
50339 AGGGA-TAAATTAAAAAAAATAAAAAAT
1 AGGGACTAAATT-AAAAAAATAAAAAAT
50366 AGATTTAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 6 0.26
30 17 0.74
ACGTcount: A:0.61, C:0.04, G:0.12, T:0.23
Consensus pattern (30 bp):
AGGGACTAAATTAAAAAAATAAAAAATGTA
Found at i:53789 original size:12 final size:12
Alignment explanation
Indices: 53760--53866 Score: 85
Period size: 12 Copynumber: 8.9 Consensus size: 12
53750 GAATGTTTTA
*
53760 TCTGATTTCTGAT
1 TCTGAATTCTG-T
53773 T-TGAATTCTGT
1 TCTGAATTCTGT
* * *
53784 TATGAATTATGA
1 TCTGAATTCTGT
53796 TCTGAATTCTGT
1 TCTGAATTCTGT
*
53808 TCTGATTTCTGAT
1 TCTGAATTCTG-T
*
53821 T-TGGATTCTGT
1 TCTGAATTCTGT
*
53832 TATGATATT-TGT
1 TCTGA-ATTCTGT
53844 TCTGAATTCTGT
1 TCTGAATTCTGT
* *
53856 TTTGATTTCTG
1 TCTGAATTCTG
53867 ATATCTCCGT
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
11 7 0.09
12 63 0.83
13 6 0.08
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.53
Consensus pattern (12 bp):
TCTGAATTCTGT
Found at i:53801 original size:24 final size:23
Alignment explanation
Indices: 53769--53856 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 23
53759 ATCTGATTTC
*
53769 TGATTTGAATTCTGTTATGAATT
1 TGATCTGAATTCTGTTATGAATT
* *
53792 ATGATCTGAATTCTGTTCTGATTT
1 -TGATCTGAATTCTGTTATGAATT
* *
53816 CTGATTTGGATTCTGTTATGATATT
1 -TGATCTGAATTCTGTTATGA-ATT
*
53841 TGTTCTGAATTCTGTT
1 TGATCTGAATTCTGTT
53857 TTGATTTCTG
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 50 0.96
25 2 0.04
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.52
Consensus pattern (23 bp):
TGATCTGAATTCTGTTATGAATT
Found at i:53812 original size:48 final size:48
Alignment explanation
Indices: 53760--53868 Score: 175
Period size: 48 Copynumber: 2.3 Consensus size: 48
53750 GAATGTTTTA
53760 TCTGATTTCTGATTTGAATTCTGTTATGA-ATTATGATCTGAATTCTGT
1 TCTGATTTCTGATTTGAATTCTGTTATGATATT-TGATCTGAATTCTGT
* *
53808 TCTGATTTCTGATTTGGATTCTGTTATGATATTTGTTCTGAATTCTGT
1 TCTGATTTCTGATTTGAATTCTGTTATGATATTTGATCTGAATTCTGT
*
53856 TTTGATTTCTGAT
1 TCTGATTTCTGAT
53869 ATCTCCGTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 54 0.95
49 3 0.05
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.53
Consensus pattern (48 bp):
TCTGATTTCTGATTTGAATTCTGTTATGATATTTGATCTGAATTCTGT
Found at i:58317 original size:21 final size:22
Alignment explanation
Indices: 58285--58342 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
58275 AATTTAATTT
*
58285 TAAAAAA-TTAAAATATCA-AA
1 TAAAAAACATAAAATATCATAA
58305 TAAAAAACATAAAA-A-CATAA
1 TAAAAAACATAAAATATCATAA
*
58325 AAAATAAACATAAAATAT
1 TAAA-AAACATAAAATAT
58343 GAGGGTCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 2 0.06
20 13 0.42
21 15 0.48
22 1 0.03
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAAAAACATAAAATATCATAA
Found at i:60854 original size:22 final size:23
Alignment explanation
Indices: 60828--60882 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
60818 ATAGGGCAGA
*
60828 GGGAATCGATAC-CCCCTTGAAG
1 GGGAACCGATACTCCCCTTGAAG
* * *
60850 GGGAACCGATTCTCCCTTTGAAT
1 GGGAACCGATACTCCCCTTGAAG
60873 GGGAACCGAT
1 GGGAACCGAT
60883 TCCTTTCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.22
Consensus pattern (23 bp):
GGGAACCGATACTCCCCTTGAAG
Found at i:60893 original size:23 final size:22
Alignment explanation
Indices: 60842--60924 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 22
60832 ATCGATACCC
*
60842 CCTTGAAGGGGAACCGATT-CTC
1 CCTTGAA-GGGAACCGATTCCTT
60864 CCTTTGAATGGGAACCGATTCCTT
1 CC-TTGAA-GGGAACCGATTCCTT
*
60888 TCTTG-AGGGAACCGATTCCTT
1 CCTTGAAGGGAACCGATTCCTT
*
60909 CCTTG-AGGGAATCGAT
1 CCTTGAAGGGAACCGAT
60925 ACCCCCCACA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
21 29 0.54
22 3 0.06
23 19 0.35
24 3 0.06
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (22 bp):
CCTTGAAGGGAACCGATTCCTT
Found at i:67825 original size:23 final size:22
Alignment explanation
Indices: 67783--67847 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 22
67773 AATTTAATTT
* * *
67783 AAAAAATTAAAATATCAAATAA
1 AAAAAAATAAAACATAAAATAA
* *
67805 AAAAGCAGTAAAACATAAAATAA
1 AAAA-AAATAAAACATAAAATAA
67828 AAAAAAAT-AAACATAAAATA
1 AAAAAAATAAAACATAAAATA
67848 TGAGGACCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 12 0.33
22 6 0.17
23 18 0.50
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (22 bp):
AAAAAAATAAAACATAAAATAA
Found at i:69113 original size:3 final size:3
Alignment explanation
Indices: 69107--69163 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
69097 GTAACTTGTA
69107 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
69155 AAT AAT AAT
1 AAT AAT AAT
69164 TATTATTATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:69359 original size:15 final size:16
Alignment explanation
Indices: 69318--69369 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
69308 AAATAATTCA
* *
69318 TATTATATAAATTTAAA
1 TATTTTATAAA-TTAAT
69335 TATATTTATAAATT-AT
1 TAT-TTTATAAATTAAT
*
69351 TATTTTATATATTAAT
1 TATTTTATAAATTAAT
69367 TAT
1 TAT
69370 ATATAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 9 0.30
16 9 0.30
17 5 0.17
18 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTATAAATTAAT
Found at i:69563 original size:6 final size:6
Alignment explanation
Indices: 69549--69591 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
69539 ATTAAATTAA
69549 AATTCTT AATTTT AA-TTT -ATTTT AATTTT ATATTTT AATTTT A
1 AATT-TT AATTTT AATTTT AATTTT AATTTT A-ATTTT AATTTT A
69592 TATGATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
4 1 0.03
5 6 0.18
6 16 0.48
7 10 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:69565 original size:13 final size:12
Alignment explanation
Indices: 69549--69591 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
69539 ATTAAATTAA
69549 AATTCTTAATTTT
1 AATT-TTAATTTT
69562 AA-TTT-ATTTT
1 AATTTTAATTTT
69572 AATTTTATATTTT
1 AATTTTA-ATTTT
69585 AATTTTA
1 AATTTTA
69592 TATGATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.26
11 5 0.19
12 1 0.04
13 14 0.52
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
AATTTTAATTTT
Found at i:69592 original size:13 final size:13
Alignment explanation
Indices: 69566--69594 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
69556 AATTTTAATT
69566 TATTTTAATTTTA
1 TATTTTAATTTTA
69579 TATTTTAATTTTA
1 TATTTTAATTTTA
69592 TAT
1 TAT
69595 GATAAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTTAATTTTA
Found at i:72995 original size:3 final size:3
Alignment explanation
Indices: 72987--73017 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
72977 GTTAATTTTC
72987 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
73018 TTATTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:73022 original size:3 final size:3
Alignment explanation
Indices: 73016--73046 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
73006 ATAATAATAA
73016 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
73047 TTCACTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:77154 original size:2 final size:2
Alignment explanation
Indices: 77147--77177 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
77137 ATTATATTGA
77147 AT 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 AT A
77178 GTGAACTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:81249 original size:12 final size:12
Alignment explanation
Indices: 81232--81265 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
81222 CTTGATGCAT
81232 GGATGCATCGTA
1 GGATGCATCGTA
81244 GGATGCATCGTA
1 GGATGCATCGTA
81256 GGATGCATCG
1 GGATGCATCG
81266 ATGCATGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (12 bp):
GGATGCATCGTA
Found at i:81281 original size:21 final size:20
Alignment explanation
Indices: 81257--81331 Score: 132
Period size: 20 Copynumber: 3.7 Consensus size: 20
81247 TGCATCGTAG
*
81257 GATGCATCGATGCATGGCAA
1 GATGCATCGATGCATAGCAA
81277 GGATGCATCGATGCATAGCAA
1 -GATGCATCGATGCATAGCAA
81298 GATGCATCGATGCATAGCAA
1 GATGCATCGATGCATAGCAA
81318 GATGCATCGATGCA
1 GATGCATCGATGCA
81332 CTAATTGCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 34 0.64
21 19 0.36
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (20 bp):
GATGCATCGATGCATAGCAA
Found at i:81303 original size:12 final size:12
Alignment explanation
Indices: 81286--81324 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
81276 AGGATGCATC
81286 GATGCATAGCAA
1 GATGCATAGCAA
81298 GATGCAT--C--
1 GATGCATAGCAA
81306 GATGCATAGCAA
1 GATGCATAGCAA
81318 GATGCAT
1 GATGCAT
81325 CGATGCACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
10 2 0.09
12 14 0.61
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (12 bp):
GATGCATAGCAA
Found at i:81361 original size:8 final size:8
Alignment explanation
Indices: 81350--81457 Score: 53
Period size: 8 Copynumber: 15.0 Consensus size: 8
81340 ATTCGATGTT
81350 TGGATGCA
1 TGGATGCA
81358 TGGATGCA
1 TGGATGCA
*
81366 T---TACA
1 TGGATGCA
81371 T-GATGCA
1 TGGATGCA
*
81378 TCGATGCA
1 TGGATGCA
*
81386 T-TAGTGCA
1 TGGA-TGCA
81394 --GATGCA
1 TGGATGCA
81400 TGGATGCA
1 TGGATGCA
81408 T---TGCA
1 TGGATGCA
* *
81413 AGGATTCA
1 TGGATGCA
81421 TGGATGCA
1 TGGATGCA
*
81429 ---CTGCA
1 TGGATGCA
*
81434 CGGATGCA
1 TGGATGCA
81442 TGGATGCA
1 TGGATGCA
81450 TGGATGCA
1 TGGATGCA
81458 CTTTGACACC
Statistics
Matches: 77, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
5 12 0.16
6 4 0.05
7 6 0.08
8 55 0.71
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.26
Consensus pattern (8 bp):
TGGATGCA
Found at i:81424 original size:21 final size:21
Alignment explanation
Indices: 81351--81450 Score: 98
Period size: 21 Copynumber: 4.8 Consensus size: 21
81341 TTCGATGTTT
*
81351 GGATGCATGGATGCATTAC-A
1 GGATGCATGGATGCATTGCAA
* *
81371 TGATGCATCGATGCATTAGTGC-A
1 GGATGCATGGATGCA-T--TGCAA
81394 -GATGCATGGATGCATTGCAA
1 GGATGCATGGATGCATTGCAA
* * *
81414 GGATTCATGGATGCACTGCAC
1 GGATGCATGGATGCATTGCAA
81435 GGATGCATGGATGCAT
1 GGATGCATGGATGCAT
81451 GGATGCACTT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.05
20 14 0.21
21 33 0.50
22 13 0.20
23 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (21 bp):
GGATGCATGGATGCATTGCAA
Found at i:81598 original size:30 final size:30
Alignment explanation
Indices: 81541--81598 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
81531 AACTTTGAAT
81541 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
81571 AAATTCAATTCAAGTCCAAAAACATTTT
1 AAATTCAATTCAAATCCAAAAACATTTT
81599 TCCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:83406 original size:14 final size:15
Alignment explanation
Indices: 83387--83415 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
83377 ATGCCTACCT
83387 CTTTCTT-ATCTTCC
1 CTTTCTTCATCTTCC
83401 CTTTCTTCATCTTCC
1 CTTTCTTCATCTTCC
83416 TTTACCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.07, C:0.38, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTTCTTCATCTTCC
Found at i:84840 original size:20 final size:20
Alignment explanation
Indices: 84815--84909 Score: 104
Period size: 20 Copynumber: 4.7 Consensus size: 20
84805 TTGCAGCCTT
* * *
84815 GATGCATGGATGCATCGTAG
1 GATGCATCGATGCATAGAAG
*
84835 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATAG-AAG
84856 GATGCATCGATGCATAGCAA-
1 GATGCATCGATGCATAG-AAG
84876 GATGCATCGATGCATAGCAA-
1 GATGCATCGATGCATAG-AAG
*
84896 GATGTATCGATGCA
1 GATGCATCGATGCA
84910 CTAATTGCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
20 48 0.70
21 21 0.30
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (20 bp):
GATGCATCGATGCATAGAAG
Found at i:84860 original size:41 final size:40
Alignment explanation
Indices: 84815--84909 Score: 127
Period size: 41 Copynumber: 2.4 Consensus size: 40
84805 TTGCAGCCTT
* * * * *
84815 GATGCATGGATGCATCGTAGGATGCATCGATGCATGGCAA
1 GATGCATCGATGCATAGCAAGATGCATCGATGCATAGCAA
84855 GGATGCATCGATGCATAGCAAGATGCATCGATGCATAGCAA
1 -GATGCATCGATGCATAGCAAGATGCATCGATGCATAGCAA
*
84896 GATGTATCGATGCA
1 GATGCATCGATGCA
84910 CTAATTGCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (40 bp):
GATGCATCGATGCATAGCAAGATGCATCGATGCATAGCAA
Found at i:84939 original size:8 final size:8
Alignment explanation
Indices: 84928--85035 Score: 53
Period size: 8 Copynumber: 15.0 Consensus size: 8
84918 ATTCGATGTT
84928 TGGATGCA
1 TGGATGCA
84936 TGGATGCA
1 TGGATGCA
*
84944 T---TACA
1 TGGATGCA
84949 T-GATGCA
1 TGGATGCA
*
84956 TCGATGCA
1 TGGATGCA
*
84964 T-TAGTGCA
1 TGGA-TGCA
84972 --GATGCA
1 TGGATGCA
84978 TGGATGCA
1 TGGATGCA
84986 T---TGCA
1 TGGATGCA
* *
84991 AGGATTCA
1 TGGATGCA
84999 TGGATGCA
1 TGGATGCA
*
85007 ---CTGCA
1 TGGATGCA
*
85012 CGGATGCA
1 TGGATGCA
85020 TGGATGCA
1 TGGATGCA
85028 TGGATGCA
1 TGGATGCA
85036 CTTTGACACC
Statistics
Matches: 77, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
5 12 0.16
6 4 0.05
7 6 0.08
8 55 0.71
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.26
Consensus pattern (8 bp):
TGGATGCA
Found at i:85002 original size:21 final size:21
Alignment explanation
Indices: 84929--85028 Score: 98
Period size: 21 Copynumber: 4.8 Consensus size: 21
84919 TTCGATGTTT
*
84929 GGATGCATGGATGCATTAC-A
1 GGATGCATGGATGCATTGCAA
* *
84949 TGATGCATCGATGCATTAGTGC-A
1 GGATGCATGGATGCA-T--TGCAA
84972 -GATGCATGGATGCATTGCAA
1 GGATGCATGGATGCATTGCAA
* * *
84992 GGATTCATGGATGCACTGCAC
1 GGATGCATGGATGCATTGCAA
85013 GGATGCATGGATGCAT
1 GGATGCATGGATGCAT
85029 GGATGCACTT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.05
20 14 0.21
21 33 0.50
22 13 0.20
23 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (21 bp):
GGATGCATGGATGCATTGCAA
Found at i:85176 original size:30 final size:30
Alignment explanation
Indices: 85119--85178 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
85109 AACTTTGAAT
85119 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
85149 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
85179 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:86985 original size:14 final size:15
Alignment explanation
Indices: 86966--86994 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
86956 ATGCCTACCT
86966 CTTTCTT-ATCTTCC
1 CTTTCTTCATCTTCC
86980 CTTTCTTCATCTTCC
1 CTTTCTTCATCTTCC
86995 TTTACCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.07, C:0.38, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTTCTTCATCTTCC
Found at i:88426 original size:12 final size:12
Alignment explanation
Indices: 88409--88442 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
88399 CTTGATGCAT
88409 GGATGCATCGTA
1 GGATGCATCGTA
88421 GGATGCATCGTA
1 GGATGCATCGTA
* *
88433 AGATGTATCG
1 GGATGCATCG
88443 ATGCATGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.26
Consensus pattern (12 bp):
GGATGCATCGTA
Found at i:88445 original size:20 final size:20
Alignment explanation
Indices: 88422--88508 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
88412 TGCATCGTAG
* * *
88422 GATGCATCGTAAGATGTATC
1 GATGCATAGCAAGATGCATC
*
88442 GATGCATGGCAAGGATGCATC
1 GATGCATAGCAA-GATGCATC
88463 GATGCATAGCAAGATGCATC
1 GATGCATAGCAAGATGCATC
88483 GATGCATAGCAAGATGCATC
1 GATGCATAGCAAGATGCATC
88503 GATGCA
1 GATGCA
88509 CTAATTGCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 44 0.71
21 18 0.29
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (20 bp):
GATGCATAGCAAGATGCATC
Found at i:88477 original size:41 final size:40
Alignment explanation
Indices: 88422--88508 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 40
88412 TGCATCGTAG
* * * *
88422 GATGCATCGTAAGATGTATCGATGCATGGCAAGGATGCATC
1 GATGCATAGCAAGATGCATCGATGCATAGCAA-GATGCATC
88463 GATGCATAGCAAGATGCATCGATGCATAGCAAGATGCATC
1 GATGCATAGCAAGATGCATCGATGCATAGCAAGATGCATC
88503 GATGCA
1 GATGCA
88509 CTAATTGCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 14 0.33
41 28 0.67
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (40 bp):
GATGCATAGCAAGATGCATCGATGCATAGCAAGATGCATC
Found at i:88480 original size:12 final size:12
Alignment explanation
Indices: 88463--88501 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
88453 AGGATGCATC
88463 GATGCATAGCAA
1 GATGCATAGCAA
88475 GATGCAT--C--
1 GATGCATAGCAA
88483 GATGCATAGCAA
1 GATGCATAGCAA
88495 GATGCAT
1 GATGCAT
88502 CGATGCACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
10 2 0.09
12 14 0.61
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (12 bp):
GATGCATAGCAA
Found at i:88538 original size:8 final size:8
Alignment explanation
Indices: 88527--88634 Score: 53
Period size: 8 Copynumber: 15.0 Consensus size: 8
88517 ATTCGATGTT
88527 TGGATGCA
1 TGGATGCA
88535 TGGATGCA
1 TGGATGCA
*
88543 T---TACA
1 TGGATGCA
88548 T-GATGCA
1 TGGATGCA
*
88555 TCGATGCA
1 TGGATGCA
*
88563 T-TAGTGCA
1 TGGA-TGCA
88571 --GATGCA
1 TGGATGCA
88577 TGGATGCA
1 TGGATGCA
88585 T---TGCA
1 TGGATGCA
* *
88590 AGGATTCA
1 TGGATGCA
88598 TGGATGCA
1 TGGATGCA
*
88606 ---CTGCA
1 TGGATGCA
*
88611 CGGATGCA
1 TGGATGCA
88619 TGGATGCA
1 TGGATGCA
88627 TGGATGCA
1 TGGATGCA
88635 CTTTGACACC
Statistics
Matches: 77, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
5 12 0.16
6 4 0.05
7 6 0.08
8 55 0.71
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.26
Consensus pattern (8 bp):
TGGATGCA
Found at i:88601 original size:21 final size:21
Alignment explanation
Indices: 88528--88627 Score: 98
Period size: 21 Copynumber: 4.8 Consensus size: 21
88518 TTCGATGTTT
*
88528 GGATGCATGGATGCATTAC-A
1 GGATGCATGGATGCATTGCAA
* *
88548 TGATGCATCGATGCATTAGTGC-A
1 GGATGCATGGATGCA-T--TGCAA
88571 -GATGCATGGATGCATTGCAA
1 GGATGCATGGATGCATTGCAA
* * *
88591 GGATTCATGGATGCACTGCAC
1 GGATGCATGGATGCATTGCAA
88612 GGATGCATGGATGCAT
1 GGATGCATGGATGCAT
88628 GGATGCACTT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.05
20 14 0.21
21 33 0.50
22 13 0.20
23 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (21 bp):
GGATGCATGGATGCATTGCAA
Found at i:88775 original size:30 final size:30
Alignment explanation
Indices: 88718--88777 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
88708 AACTTTGAAT
88718 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
88748 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
88778 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:92023 original size:20 final size:20
Alignment explanation
Indices: 91998--92072 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
91988 TTGTAGCCTT
* *
91998 GATGCATGGATGCATCGCAG
1 GATGCATCGATGCATAGCAG
*
92018 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATAGC-AG
*
92039 GATGCATCGATGCATAGCAA
1 GATGCATCGATGCATAGCAG
92059 GATGCATCGATGCA
1 GATGCATCGATGCA
92073 CTAATTGTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 31 0.62
21 19 0.38
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (20 bp):
GATGCATCGATGCATAGCAG
Found at i:92161 original size:8 final size:8
Alignment explanation
Indices: 92150--92198 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
92140 ATGGATGCAT
*
92150 TGCAGGGA
1 TGCATGGA
92158 TGCATGGA
1 TGCATGGA
*
92166 TGCA---C
1 TGCATGGA
*
92171 TGCACGGA
1 TGCATGGA
92179 TGCATGGA
1 TGCATGGA
92187 TGCATGGA
1 TGCATGGA
92195 TGCA
1 TGCA
92199 CTTTGACACC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 4 0.12
8 30 0.88
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.20
Consensus pattern (8 bp):
TGCATGGA
Found at i:92164 original size:21 final size:21
Alignment explanation
Indices: 92092--92191 Score: 89
Period size: 21 Copynumber: 4.8 Consensus size: 21
92082 TTCGATGTTT
*
92092 GGATGCATGGATGCATTACA-
1 GGATGCATGGATGCATTGCAG
* * *
92112 TGATACATCGATGCATT--AG
1 GGATGCATGGATGCATTGCAG
*
92131 TGCAGATGTATGGATGCATTGCAG
1 -G--GATGCATGGATGCATTGCAG
* *
92155 GGATGCATGGATGCACTGCAC
1 GGATGCATGGATGCATTGCAG
92176 GGATGCATGGATGCAT
1 GGATGCATGGATGCAT
92192 GGATGCACTT
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.02
20 14 0.22
21 32 0.51
22 13 0.21
23 1 0.02
24 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (21 bp):
GGATGCATGGATGCATTGCAG
Found at i:92369 original size:30 final size:30
Alignment explanation
Indices: 92282--92369 Score: 167
Period size: 30 Copynumber: 2.9 Consensus size: 30
92272 AACTTTGAAT
*
92282 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAGTCCAAAAACATTTTGC
92312 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAGTCCAAAAACATTTTGC
92342 AAATTCAATTCAAGTCCAAAAACATTTT
1 AAATTCAATTCAAGTCCAAAAACATTTT
92370 CCCTTAAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATTCAATTCAAGTCCAAAAACATTTTGC
Found at i:95984 original size:23 final size:22
Alignment explanation
Indices: 95944--96022 Score: 76
Period size: 23 Copynumber: 3.7 Consensus size: 22
95934 AGGATAGAGT
* *
95944 GAATGGATACCCCCTTGAAGGG
1 GAATCGATTCCCCCTTGAAGGG
95966 GAATCGATTCCCCCTTTGAAGGG
1 GAATCGATTCCCCC-TTGAAGGG
*
95989 GAA-CTGATTCCCCC---CAGGG
1 GAATC-GATTCCCCCTTGAAGGG
*
96008 GAATCGATACCCCCT
1 GAATCGATTCCCCCT
96023 GAGGGTTCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
19 15 0.31
20 1 0.02
22 13 0.27
23 20 0.41
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.20
Consensus pattern (22 bp):
GAATCGATTCCCCCTTGAAGGG
Found at i:99956 original size:37 final size:37
Alignment explanation
Indices: 99879--99962 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
99869 ATTAATCTTT
** *
99879 TTGTGTC-AAAAATTTAGTCACAAAAAGAATAAGTAT
1 TTGTGTCAAAAAAAGTAGTCACAAAAAGAATAAGTAA
** *
99915 TTGTGTCAAAAAAAGTAGTCACAAAAATCATATGTAA
1 TTGTGTCAAAAAAAGTAGTCACAAAAAGAATAAGTAA
*
99952 TTGTGACAAAA
1 TTGTGTCAAAA
99963 TTCAATAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 7 0.17
37 33 0.82
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (37 bp):
TTGTGTCAAAAAAAGTAGTCACAAAAAGAATAAGTAA
Found at i:102330 original size:16 final size:17
Alignment explanation
Indices: 102309--102340 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
102299 AAAGGGGGTT
102309 AAATTTAAAAA-AAAAA
1 AAATTTAAAAAGAAAAA
102325 AAATTTAAAAAGAAAA
1 AAATTTAAAAAGAAAA
102341 TTCAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (17 bp):
AAATTTAAAAAGAAAAA
Found at i:102539 original size:13 final size:13
Alignment explanation
Indices: 102523--102562 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
102513 CAAATGACAG
102523 AAATAAATAAAAT
1 AAATAAATAAAAT
102536 AAATAAATAAAAAT
1 AAATAAAT-AAAAT
*
102550 AAATAGATAAAAT
1 AAATAAATAAAAT
102563 TAAAGGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:102550 original size:14 final size:14
Alignment explanation
Indices: 102523--102566 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
102513 CAAATGACAG
102523 AAATAAAT-AAAAT
1 AAATAAATAAAAAT
102536 AAATAAATAAAAAT
1 AAATAAATAAAAAT
* *
102550 AAATAGATAAAATT
1 AAATAAATAAAAAT
102564 AAA
1 AAA
102567 GGATCAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 8 0.29
14 20 0.71
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:103830 original size:5 final size:5
Alignment explanation
Indices: 103820--103877 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
103810 ATAAATAAGT
* *
103820 AAATA AAATAA AAATA AAA-A CAAAAA ACAAAA AAATA AAATA AAATA
1 AAATA AAAT-A AAATA AAATA -AAATA A-AATA AAATA AAATA AAATA
103867 AAATA ATAATA
1 AAATA A-AATA
103878 TGTATATACT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
4 1 0.02
5 31 0.66
6 15 0.32
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (5 bp):
AAATA
Done.