Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000850.1 Hibiscus syriacus cultivar Beakdansim tig00001639_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: 46817
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4401 original size:19 final size:21
Alignment explanation
Indices: 4372--4412 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
4362 TAGGGAGAGG
*
4372 ATTGAAAAG-TTAAGACCTTT
1 ATTGAAAAGTTTAAGACATTT
4392 ATTG-AAAGTTTAAGACATTT
1 ATTGAAAAGTTTAAGACATTT
4412 A
1 A
4413 AATGAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (21 bp):
ATTGAAAAGTTTAAGACATTT
Found at i:6897 original size:21 final size:21
Alignment explanation
Indices: 6871--6910 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6861 ATTATTTTTC
6871 ATTTTTAAGCTTACATGATTG
1 ATTTTTAAGCTTACATGATTG
6892 ATTTTTAAGCTTACATGAT
1 ATTTTTAAGCTTACATGAT
6911 AATATTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (21 bp):
ATTTTTAAGCTTACATGATTG
Found at i:7062 original size:32 final size:32
Alignment explanation
Indices: 7021--7085 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
7011 TGTTGGAGAT
*
7021 TAATTCTAAGGCTTGTGTGATGATTAAAATTA
1 TAATTCTAAGGCTTGTGTGACGATTAAAATTA
* *
7053 TAATTCTAAGGTTTGTTTGACGATTAAAATTA
1 TAATTCTAAGGCTTGTGTGACGATTAAAATTA
7085 T
1 T
7086 GTGTAAAGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (32 bp):
TAATTCTAAGGCTTGTGTGACGATTAAAATTA
Found at i:10864 original size:25 final size:26
Alignment explanation
Indices: 10808--10863 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
10798 AGAAAGATAT
*
10808 AATAAAAT--AAAATAAATAATAATA
1 AATAAAATGGAAAATAAATAATAAAA
10832 AATAAAATGGAAAA-AAATAATAAAA
1 AATAAAATGGAAAATAAATAATAAAA
10857 CAATAAA
1 -AATAAA
10864 TAATAGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 8 0.29
25 10 0.36
26 10 0.36
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (26 bp):
AATAAAATGGAAAATAAATAATAAAA
Found at i:10947 original size:18 final size:18
Alignment explanation
Indices: 10905--10966 Score: 97
Period size: 18 Copynumber: 3.4 Consensus size: 18
10895 GTTGTTTTTA
* *
10905 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAATAATT
10923 AAAATAAAAGAAAATAATT
1 -AAATAAAAGAAAATAATT
10942 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
10960 AAATAAA
1 AAATAAA
10967 TGATTTAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
18 25 0.61
19 16 0.39
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:11681 original size:12 final size:12
Alignment explanation
Indices: 11666--11693 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
11656 GATAAAATAC
11666 AATAATATCCTA
1 AATAATATCCTA
11678 AATAATATCCTA
1 AATAATATCCTA
11690 AATA
1 AATA
11694 CTAATTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAATATCCTA
Found at i:11725 original size:85 final size:84
Alignment explanation
Indices: 11592--11748 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 84
11582 ATAATTCATA
* * **
11592 AAATAATATCTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAATTAAAG
1 AAATAATATCCTAAATACTAATTAAAACACTTAAAACTATTTAAACT-AAATACCTAAAACAAAG
11657 ATAAAATACAATAATATCCT
65 ATAAAATACAATAATATCCT
* * * *
11677 AAATAATATCCTAAATACTAATTGAAATA-TTAACATCTATTTAAACTAAATATCTAAAACAAAG
1 AAATAATATCCTAAATACTAATTAAAACACTTAA-AACTATTTAAACTAAATACCTAAAACAAAG
11741 ATAAAATA
65 ATAAAATA
11749 TAATGTTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
84 26 0.41
85 37 0.59
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.31
Consensus pattern (84 bp):
AAATAATATCCTAAATACTAATTAAAACACTTAAAACTATTTAAACTAAATACCTAAAACAAAGA
TAAAATACAATAATATCCT
Found at i:13515 original size:11 final size:11
Alignment explanation
Indices: 13486--13528 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
13476 AAGTTTTCTA
*
13486 AAAAT-AAACC
1 AAAATAAAACG
*
13496 AAAATTAAAATG
1 AAAA-TAAAACG
13508 AAAATAAAACG
1 AAAATAAAACG
13519 AAAATAAAAC
1 AAAATAAAAC
13529 TAACTGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 4 0.14
11 17 0.61
12 7 0.25
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAATAAAACG
Found at i:19176 original size:19 final size:19
Alignment explanation
Indices: 19134--19180 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
19124 AAAGTTATTT
*
19134 TTAAAATAAAAGATAAGAA
1 TTAAAATAAAAGAAAAGAA
* *
19153 CTAAAATAAAAGAAAATAA
1 TTAAAATAAAAGAAAAGAA
19172 TT-AAATAAA
1 TTAAAATAAA
19181 TAATTTAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (19 bp):
TTAAAATAAAAGAAAAGAA
Found at i:19710 original size:18 final size:19
Alignment explanation
Indices: 19675--19711 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
19665 CACGAAATGT
19675 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
19695 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
19712 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:19930 original size:36 final size:36
Alignment explanation
Indices: 19859--19931 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
19849 GTTGGAAAAT
*
19859 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
*
19895 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATT-AAAATCATAAA
19931 A
1 A
19932 AGATTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 24 0.73
37 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:20445 original size:85 final size:88
Alignment explanation
Indices: 20313--20502 Score: 255
Period size: 85 Copynumber: 2.2 Consensus size: 88
20303 AGATAATTCC
*
20313 TAAAATAATATCTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAA
1 TAAAATAATATCTTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAACAA
20378 AGATAAAA-T-AAA-ATAATATT
66 AGATAAAATTAAAATATAATATT
* * * * *
20398 TAAAATAATATCCTAAATCTTAATTGAAATAC-TAACATA-TATCTAAACTAAAATATCTAAAAC
1 TAAAATAATATCTTAAATCCTAATTAAAACACTTAA-A-ACTATCTAAACTAAAATACCTAAAAC
*
20461 AAAGATAAAATTAAAATATAATGTT
64 AAAGATAAAATTAAAATATAATATT
*
20486 TAAAATATTATCTTAAA
1 TAAAATAATATCTTAAA
20503 CCTTGAGTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
84 3 0.03
85 61 0.67
86 2 0.02
87 3 0.03
88 22 0.24
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.32
Consensus pattern (88 bp):
TAAAATAATATCTTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAACAA
AGATAAAATTAAAATATAATATT
Found at i:21929 original size:16 final size:16
Alignment explanation
Indices: 21903--21939 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
21893 CGAAATACAA
21903 AATAT-AATAATCCAT
1 AATATAAATAATCCAT
21918 AATATAAATAATCCAT
1 AATATAAATAATCCAT
*
21934 TATATA
1 AATATA
21940 TATGTATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATAAATAATCCAT
Found at i:23634 original size:22 final size:21
Alignment explanation
Indices: 23605--23646 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
23595 TGATCAAATG
23605 ATATTATTTTAGT-ATTTTTAT
1 ATATTATTTT-GTGATTTTTAT
23626 ATATATATTTTGTGATTTTTA
1 ATAT-TATTTTGTGATTTTTA
23647 GGTAGAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATATTATTTTGTGATTTTTAT
Found at i:24651 original size:14 final size:14
Alignment explanation
Indices: 24632--24664 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
24622 TGATTTGGTT
24632 GAAAAGTGTAAAGG
1 GAAAAGTGTAAAGG
24646 GAAAAGTGTAAAGG
1 GAAAAGTGTAAAGG
24660 GAAAA
1 GAAAA
24665 TTGTTCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (14 bp):
GAAAAGTGTAAAGG
Found at i:34606 original size:132 final size:132
Alignment explanation
Indices: 34369--34730 Score: 334
Period size: 133 Copynumber: 2.7 Consensus size: 132
34359 ATTCACTTCG
* * * *
34369 CTGCTCTTCAGGGAATATTGAATCGAACTTGATTTGTTTCATTGCTCTTCAGGAAGATCAAATCT
1 CTGCTCTTCAGGGAATATTGAATCGAACTCGATTTGCTTCATTGCTCTTCAGGAAGACCAAATAT
** * * ** *
34434 AAAAGAAGTCGAGTCTGCTCCACTACTCTTTAGGGAAGATCAGACTCATAAATTATGATCCTCTG
66 AAAAGAAGAAGAATCCGCTCCACTACTCTTTACAGAAGATCAAACTCATAAATTATGATCCTCTG
34499 CA
131 CA
* *
34501 CTGCTCTTTAGGGAATATTGAATTGGAA-TCGATTTGCTTCACTTG-TCTTCAGGAAGACCAAAT
1 CTGCTCTTCAGGGAATATTGAA-TCGAACTCGATTTGCTTCA-TTGCTCTTCAGGAAGACCAAAT
* * * * *
34564 ATGAAAGAAGAATAATCCGCTCCACTACTCTTTAACAG-AGATCAAACTCAAAAAATTTTGTTCC
64 ATAAAAGAAGAAGAATCCGCTCCACTACTCTTT-ACAGAAGATCAAACTC-ATAAATTATGATCC
* * *
34628 ACTTCG
127 TCTGCA
* * * * * * * * * * *
34634 TTGCTCTTCAGGGAAGATTAAATCAAACTTGATTTACTTTATTTCTATTCAGGAATACCAAATCT
1 CTGCTCTTCAGGGAATATTGAATCGAACTCGATTTGCTTCATTGCTCTTCAGGAAGACCAAATAT
* * * **
34699 GAAAGAAGGAGGATTTGCTCCACTACTCTTTA
66 AAAAGAAGAAGAATCCGCTCCACTACTCTTTA
34731 GGGGAAAACA
Statistics
Matches: 185, Mismatches: 39, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
132 91 0.49
133 94 0.51
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (132 bp):
CTGCTCTTCAGGGAATATTGAATCGAACTCGATTTGCTTCATTGCTCTTCAGGAAGACCAAATAT
AAAAGAAGAAGAATCCGCTCCACTACTCTTTACAGAAGATCAAACTCATAAATTATGATCCTCTG
CA
Found at i:34828 original size:131 final size:132
Alignment explanation
Indices: 34351--34921 Score: 372
Period size: 132 Copynumber: 4.3 Consensus size: 132
34341 TTAGGTCTGG
* * * * *
34351 AAAA-TTTGATTCACTTCGCTGCTCTTCAGGGAATATTGAATC-GAACTTGATTTGTTTCA-TTG
1 AAAATTTTGATCCACTTCGTTGCTCTTAAGGGAAGATTGAATCGGAA-TCGATTTGTTTCACTT-
* * ** * * ** *
34413 CTCTTCAGGAAGATCAAATCTAAAAGAAGTCGAGTCTGCTCCACTACTCTTT-AGGGAAGATCAG
64 CTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCCGCTCCACTACTCTTTAACAG-AGA-CAA
34477 ACTC-A
127 ACTCAA
* * * * ** * * * * *
34482 TAAATTATGATCCTCTGCACTGCTCTTTAGGGAATATTGAATTGGAATCGATTTGCTTCACTTGT
1 AAAATTTTGATCCACTTCGTTGCTCTTAAGGGAAGATTGAATCGGAATCGATTTGTTTCACTTCT
* *
34547 CTTCAGGAAGACCAAATATGAAAGAAGAATAATCCGCTCCACTACTCTTTAACAGAGATCAAACT
66 CTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCCGCTCCACTACTCTTTAACAGAGA-CAAACT
34612 CAA
130 CAA
* * * * * * *
34615 AAAATTTTGTTCCACTTCGTTGCTCTTCAGGGAAGATTAAATC-AAACTTGATTTACTTT-ATTT
1 AAAATTTTGATCCACTTCGTTGCTCTTAAGGGAAGATTGAATCGGAA-TCGATTT-GTTTCACTT
* * * * ** * *
34678 CTATTCAGGAATACCAAATCTGAAAGAAGGAGGATTTGCTCCACTACTCTTT-A-GGGGA-AAAC
64 CTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCCGCTCCACTACTCTTTAACAGAGACAAAC
*
34740 ATACAC
129 -T-CAA
** * * *
34746 GTAATTTTGATCCACTTTGTTGTTTTTAAGGGAAGATTGAATCGGAATCGATTTGTTTCACTTCT
1 AAAATTTTGATCCACTTCGTTGCTCTTAAGGGAAGATTGAATCGGAATCGATTTGTTTCACTTCT
* * ** * ** * * ** **
34811 CTTTAGGAAGACAAAATCTTTAAGAA-AAAAATATGCTCTACTACTTTTTTAGGAGAGATCAGGC
66 CTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCCGCTCCACTAC-TCTTTAACAGAGA-CAAAC
*
34875 TCGAG
129 TC-AA
* * *
34880 AAAATTTTGATCCACTTCGCTACTCTTCAGGGAAGATTGAAT
1 AAAATTTTGATCCACTTCGTTGCTCTTAAGGGAAGATTGAAT
34922 ATGAAATAAA
Statistics
Matches: 335, Mismatches: 88, Indels: 31
0.74 0.19 0.07
Matches are distributed among these distances:
129 4 0.01
130 17 0.05
131 78 0.23
132 100 0.30
133 96 0.29
134 38 0.11
135 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (132 bp):
AAAATTTTGATCCACTTCGTTGCTCTTAAGGGAAGATTGAATCGGAATCGATTTGTTTCACTTCT
CTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCCGCTCCACTACTCTTTAACAGAGACAAACTC
AA
Found at i:34886 original size:265 final size:264
Alignment explanation
Indices: 34350--34917 Score: 612
Period size: 265 Copynumber: 2.1 Consensus size: 264
34340 ATTAGGTCTG
* * * *
34350 GAAAA-TTTGATT-CACTTCGCTGCTCTTCAGGGAATATTGAATCGAACTTGATTTGTTTCATTG
1 GAAAATTTTG-TTCCACTTCGCTGCTCTTCAGGGAAGATTAAATCAAACTTGATTTCTTTCATTG
* * *
34413 CTCTTCAGGAAGATCAAATCTAAAAGAAGTCGAGTCTGCTCCACTACTCTTTAGGGAAGATCAGA
65 CTATTCAGGAAGACCAAATCTAAAAGAAG-CGAGTCTGCTCCACTACTCTTTAGGGAAGAACAGA
* * * *
34478 CTCATAAATTATGATCCTCTGCACTGCTCTTTAGGGAATATTGAATTGGAATCGATTTGCTTCAC
129 CACATAAATTATGATCCACTGCACTGCTCTTTAGGGAAGATTGAATCGGAATCGATTTGCTTCAC
* * * *
34543 TTGTCTTCAGGAAGACCAAATATGAAAGAAGAATAATCCGCTCCACTACTCTTTAACAGAGATCA
194 TTCTCTTCAGGAAGACAAAATATGAAAGAAGAAAAATACGCTCCACTACTCTTTAACAGAGATCA
34608 AACTCA
259 AACTCA
* * *
34614 AAAAATTTTGTTCCACTTCGTTGCTCTTCAGGGAAGATTAAATCAAACTTGATTTACTTT-ATTT
1 GAAAATTTTGTTCCACTTCGCTGCTCTTCAGGGAAGATTAAATCAAACTTGATTT-CTTTCATTG
* * *
34678 CTATTCAGGAATACCAAATCTGAAAGAAG-GAGGATTTGCTCCACTACTCTTTAGGGGAA-AACA
65 CTATTCAGGAAGACCAAATCTAAAAGAAGCGA-G-TCTGCTCCACTACTCTTTA-GGGAAGAACA
* * * **** * *
34741 TACACGT-AATTTTGATCCACTTTGTTG-TTTTTAAGGGAAGATTGAATCGGAATCGATTTGTTT
127 GACACATAAATTATGATCCACTGCACTGCTCTTT-AGGGAAGATTGAATCGGAATCGATTTGCTT
* * ** * * * **
34804 CACTTCTCTTTAGGAAGACAAAATCTTTAAGAA-AAAAATATGCTCTACTACTTTTTTAGGAGAG
191 CACTTCTCTTCAGGAAGACAAAATATGAAAGAAGAAAAATACGCTCCACTAC-TCTTTAACAGAG
**
34868 ATCAGGCTCGA
255 ATCAAACTC-A
* *
34879 GAAAATTTTGATCCACTTCGCTACTCTTCAGGGAAGATT
1 GAAAATTTTGTTCCACTTCGCTGCTCTTCAGGGAAGATT
34918 GAATATGAAA
Statistics
Matches: 250, Mismatches: 45, Indels: 17
0.80 0.14 0.05
Matches are distributed among these distances:
263 20 0.08
264 91 0.36
265 131 0.52
266 8 0.03
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (264 bp):
GAAAATTTTGTTCCACTTCGCTGCTCTTCAGGGAAGATTAAATCAAACTTGATTTCTTTCATTGC
TATTCAGGAAGACCAAATCTAAAAGAAGCGAGTCTGCTCCACTACTCTTTAGGGAAGAACAGACA
CATAAATTATGATCCACTGCACTGCTCTTTAGGGAAGATTGAATCGGAATCGATTTGCTTCACTT
CTCTTCAGGAAGACAAAATATGAAAGAAGAAAAATACGCTCCACTACTCTTTAACAGAGATCAAA
CTCA
Found at i:36260 original size:10 final size:9
Alignment explanation
Indices: 36213--36316 Score: 52
Period size: 9 Copynumber: 10.9 Consensus size: 9
36203 TCTTGAACCC
36213 CTTTTTATTT
1 CTTTTT-TTT
* *
36223 ATTCTTTTTC
1 CTT-TTTTTT
*
36233 CTTATTTTT
1 CTTTTTTTT
36242 CTTTATTTTT
1 CTTT-TTTTT
36252 -TTATCTTTTAT
1 CTT-T-TTTT-T
36263 -TTTTTTTT
1 CTTTTTTTT
*
36271 CGTTTTTTT
1 CTTTTTTTT
*
36280 CATTTTTCTT
1 C-TTTTTTTT
36290 CTTTTTTTT
1 CTTTTTTTT
*
36299 -TCATTTTTT
1 CT-TTTTTTT
36308 CTTTATTTT
1 CTTT-TTTT
36317 GTGTAGGAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
8 2 0.03
9 35 0.49
10 29 0.40
11 6 0.08
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.79
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:36284 original size:20 final size:19
Alignment explanation
Indices: 36213--36316 Score: 67
Period size: 19 Copynumber: 5.4 Consensus size: 19
36203 TCTTGAACCC
*
36213 CTTTTTATTT-ATTCTTTTT
1 CTTTTTTTTTCATT-TTTTT
* *
36232 CCTTATTTTTC-TTTATTTT
1 CTTTTTTTTTCATTT-TTTT
*
36251 -TTTATCTTTT-ATTTTTTT
1 CTTT-TTTTTTCATTTTTTT
36269 -TTCGTTTTTTTCATTTTTCTT
1 CTT--TTTTTTTCATTTTT-TT
36290 CTTTTTTTTTCA-TTTTTT
1 CTTTTTTTTTCATTTTTTT
36308 CTTTATTTT
1 CTTT-TTTT
36317 GTGTAGGAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
18 15 0.22
19 33 0.49
20 16 0.24
21 2 0.03
22 2 0.03
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.79
Consensus pattern (19 bp):
CTTTTTTTTTCATTTTTTT
Found at i:39454 original size:2 final size:2
Alignment explanation
Indices: 39447--39486 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
39437 ACAAACGAGA
39447 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT -T 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
39487 GATACATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:46747 original size:20 final size:20
Alignment explanation
Indices: 46721--46777 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
46711 TTTCCCCTTG
46721 AAGTGCATCGATGCATTC-T
1 AAGTGCATCGATGCATTCTT
46740 ACAGTGCATCGATGCATTCTTT
1 A-AGTGCATCGATGCATTC-TT
46762 AATGTGCATCGATGCA
1 AA-GTGCATCGATGCA
46778 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.03
20 17 0.50
21 1 0.03
22 15 0.44
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (20 bp):
AAGTGCATCGATGCATTCTT
Done.