Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008101.1 Hibiscus syriacus cultivar Beakdansim tig00110631_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: 79784
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:725 original size:34 final size:33
Alignment explanation
Indices: 647--896 Score: 185
Period size: 35 Copynumber: 7.3 Consensus size: 33
637 TTTTAAAAAG
* *
647 AAAACATTTTGAAAA-TATGGGTAATATATTTTTTT
1 AAAACATTTTGAAAACTAT--ATAATATA-GTTTTT
*
682 AAAATATTTTGAAAACTATATACATATAGTTTTT
1 AAAACATTTTGAAAACTATATA-ATATAGTTTTT
716 AAAACATTTTAGAAAA-TATATAAACATATAG-TTTT
1 AAAACATTTT-GAAAACTATAT--A-ATATAGTTTTT
*
751 AAAATCATTTT-AAAACCTTATATAATATAGTTTTA
1 AAAA-CATTTTGAAAA-C-TATATAATATAGTTTTT
* *
786 AAAACATTTTTGAATAAATTATATAGTATATAGTTTTA
1 AAAACA-TTTTG-A-AAACTATATA--ATATAGTTTTT
* *
824 AAAATATTTTTTAAAACT-TAT-ATAATA-TTTTT
1 AAAACA-TTTTGAAAACTATATAAT-ATAGTTTTT
*
856 AAAACATTTTGAAAACTATAT-A-ATAGTTTTG
1 AAAACATTTTGAAAACTATATAATATAGTTTTT
*
887 AAAACTTTTT
1 AAAACATTTT
897 AAATATAATA
Statistics
Matches: 182, Mismatches: 14, Indels: 42
0.76 0.06 0.18
Matches are distributed among these distances:
30 3 0.02
31 23 0.13
32 15 0.08
33 3 0.02
34 33 0.18
35 47 0.26
36 27 0.15
37 7 0.04
38 24 0.13
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (33 bp):
AAAACATTTTGAAAACTATATAATATAGTTTTT
Found at i:790 original size:70 final size:66
Alignment explanation
Indices: 647--878 Score: 222
Period size: 69 Copynumber: 3.3 Consensus size: 66
637 TTTTAAAAAG
* * **
647 AAAACATTTTGAAAATATGGGT-AATATATTTTTTTAAAATATTTTGAAAAC-TATATACATATA
1 AAAACATTTTGAAAATAT--ATAAACATATAGTTTTAAAATATTTT-AAAACTTATATA-ATATA
710 GTTTTT
62 G-TTTT
716 AAAACATTTTAGAAAATATATAAACATATAGTTTTAAAATCATTTTAAAACCTTATATAATATAG
1 AAAACATTTT-GAAAATATATAAACATATAGTTTTAAAAT-ATTTTAAAA-CTTATATAATATAG
781 TTTT
63 TTTT
**
785 AAAAACATTTTTGAATAA-ATTATATAGTATATAGTTTTAAAAATATTTTTTAAAACTTATATAA
1 -AAAACA-TTTTGAA-AATA-TATA-AACATATAGTTTT-AAAATA--TTTTAAAACTTATATAA
849 TAT--TTTT
58 TATAGTTTT
856 AAAACATTTTGAAAACTATATAA
1 AAAACATTTTGAAAA-TATATAA
879 TAGTTTTGAA
Statistics
Matches: 142, Mismatches: 6, Indels: 31
0.79 0.03 0.17
Matches are distributed among these distances:
68 4 0.03
69 44 0.31
70 37 0.26
71 20 0.14
72 12 0.08
73 17 0.12
74 8 0.06
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (66 bp):
AAAACATTTTGAAAATATATAAACATATAGTTTTAAAATATTTTAAAACTTATATAATATAGTTT
T
Found at i:1201 original size:19 final size:18
Alignment explanation
Indices: 1150--1201 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
1140 TGACCCAATC
1150 CAACGGCCAGAAAGCAAGT
1 CAACGGCCAG-AAGCAAGT
** *
1169 CAACATCC-GAAGCAATTT
1 CAACGGCCAGAAGCAA-GT
1187 CAACGGCCAGAAGCA
1 CAACGGCCAGAAGCA
1202 TCAGTCGTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 12 0.46
ACGTcount: A:0.40, C:0.29, G:0.21, T:0.10
Consensus pattern (18 bp):
CAACGGCCAGAAGCAAGT
Found at i:2549 original size:17 final size:18
Alignment explanation
Indices: 2501--2543 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2491 TACTTTTTCC
* *
2501 TTTGTTT-TTATTCTGTT
1 TTTGTTTATTATTTTCTT
2518 TTTGTTTATTATTTTCTT
1 TTTGTTTATTATTTTCTT
2536 TTT-TTTAT
1 TTTGTTTAT
2544 GTTTTTGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.09, C:0.05, G:0.07, T:0.79
Consensus pattern (18 bp):
TTTGTTTATTATTTTCTT
Found at i:2579 original size:32 final size:30
Alignment explanation
Indices: 2505--2579 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
2495 TTTTCCTTTG
*
2505 TTTTTATTCTGTTTTTGTTTATTATTTTCT
1 TTTTTATTATGTTTTTGTTTATTATTTTCT
2535 TTTTT-TTATGTTTTTGTTGT-TTATTTTCAT
1 TTTTTATTATGTTTTTGTT-TATTATTTTC-T
2565 TCTATTTATT-TGTTT
1 T-T-TTTATTATGTTT
2580 ATTACTCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 20 0.51
30 8 0.21
31 1 0.03
32 8 0.21
33 2 0.05
ACGTcount: A:0.11, C:0.05, G:0.08, T:0.76
Consensus pattern (30 bp):
TTTTTATTATGTTTTTGTTTATTATTTTCT
Found at i:11903 original size:17 final size:17
Alignment explanation
Indices: 11881--11918 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
11871 CATATTTCTA
11881 TTTAATAAAAATAATAT
1 TTTAATAAAAATAATAT
* *
11898 TTTAATAAATATATTAT
1 TTTAATAAAAATAATAT
11915 TTTA
1 TTTA
11919 GATCGGGTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAATAAAAATAATAT
Found at i:14370 original size:31 final size:31
Alignment explanation
Indices: 14325--14400 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
14315 GTATTCTCTT
* * *
14325 AATGCAAACATGACATATTGTGCATTGTCTG
1 AATGCAAACATGACATACTATGCATTATCTG
* * *
14356 AATGCGAACCTGACATACTATGCATTATCTT
1 AATGCAAACATGACATACTATGCATTATCTG
*
14387 AATGCAAGCATGAC
1 AATGCAAACATGAC
14401 TAGTATATGC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (31 bp):
AATGCAAACATGACATACTATGCATTATCTG
Found at i:27352 original size:100 final size:100
Alignment explanation
Indices: 27159--27352 Score: 219
Period size: 100 Copynumber: 1.9 Consensus size: 100
27149 TGCAGACAAC
* * * * * *
27159 CCCTACTGTCCTGTCTCTGGCATAATTTAGAAACACCTTGATCTAATTTAGTCAGCATTTCTGGA
1 CCCTACTGTCCTGTCTATGGCACAATTAAGAAACACATTGATCTAATTTAGCCAGCATTTCTAGA
* *
27224 TTGTCTTTTTTTTTTTTTCTCAAAGGTCTATTTGT
66 TTGTCTTTTTCTGTTTTTCTCAAAGGTCTATTTGT
* * * * * * * *
27259 CCCTACTGTCCTTTCTATGGCACAGTTAAGCAACATATTGATTTAATTTTGCCAGCCTTTGTAGA
1 CCCTACTGTCCTGTCTATGGCACAATTAAGAAACACATTGATCTAATTTAGCCAGCATTTCTAGA
*
27324 TTGTCTTTGTTCTGTTTTT-TCAAGGGTCT
66 TTGTCTTT-TTCTGTTTTTCTCAAAGGTCT
27353 GTTTCATTCA
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
100 68 0.89
101 8 0.11
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (100 bp):
CCCTACTGTCCTGTCTATGGCACAATTAAGAAACACATTGATCTAATTTAGCCAGCATTTCTAGA
TTGTCTTTTTCTGTTTTTCTCAAAGGTCTATTTGT
Found at i:28292 original size:70 final size:64
Alignment explanation
Indices: 28204--28339 Score: 182
Period size: 64 Copynumber: 2.0 Consensus size: 64
28194 GCTAATAATA
*
28204 TGCCTTTCCTAAGTTTAGCATATCTAGATTTTGTCAAATATTAGATATTTTCTTTTAGTATTGGC
1 TGCCTTTCCTAAGTTTAGCATATCTAGA--TT-T---ATATTAGATATGTTCTTTTAGTATTGGC
28269 AGATC
60 AGATC
* * *
28274 TGCCTTTCTTAAGTTTAGCTTATGTAGATTTATATTAGATATGTTCTTTTAGTATTGGCAGATC
1 TGCCTTTCCTAAGTTTAGCATATCTAGATTTATATTAGATATGTTCTTTTAGTATTGGCAGATC
28338 TG
1 TG
28340 TCTTCTATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
64 34 0.55
67 1 0.02
68 2 0.03
70 25 0.40
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.47
Consensus pattern (64 bp):
TGCCTTTCCTAAGTTTAGCATATCTAGATTTATATTAGATATGTTCTTTTAGTATTGGCAGATC
Found at i:35341 original size:60 final size:60
Alignment explanation
Indices: 35259--35383 Score: 189
Period size: 60 Copynumber: 2.1 Consensus size: 60
35249 TCCCTAAACG
* * *
35259 TTTAGGGCGCTCGCATTATGGTCATCC-AGCTTTTAAAACATGCAATACAGTCTCTGAACT
1 TTTAGGACGCTCGCATTATGGTCA-CCAAACTTTTAAAACATGCAATACAGTCACTGAACT
* *
35319 TTTAGGACGCTTGCATTTTGGTCACCAAACTTTTAAAACATGCAATACAGTCACTGAACT
1 TTTAGGACGCTCGCATTATGGTCACCAAACTTTTAAAACATGCAATACAGTCACTGAACT
35379 TTTAG
1 TTTAG
35384 TTCATTTTCA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 2 0.03
60 57 0.97
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (60 bp):
TTTAGGACGCTCGCATTATGGTCACCAAACTTTTAAAACATGCAATACAGTCACTGAACT
Found at i:36361 original size:56 final size:56
Alignment explanation
Indices: 36289--36436 Score: 181
Period size: 56 Copynumber: 2.6 Consensus size: 56
36279 AAAAAAAAAG
* *
36289 TATATTTATCAATTATTGTCATTAATAAGCATAAAAATAGAGG-CCCTGAAATCGAA
1 TATATTTATCAGTTATTGTCATTAAAAAGCATAAAAATAGAGGTCCC-GAAATCGAA
* * * * *
36345 TATATCTATCAGTTATTGTTATTAAGAAGCATAAAAATAGGGGTCCCGAAATCGAG
1 TATATTTATCAGTTATTGTCATTAAAAAGCATAAAAATAGAGGTCCCGAAATCGAA
* * * *
36401 TATATTTATCGGTTGTTGCCATTAAAAATCATAAAA
1 TATATTTATCAGTTATTGTCATTAAAAAGCATAAAA
36437 TAGGTATCCC
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
56 75 0.96
57 3 0.04
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (56 bp):
TATATTTATCAGTTATTGTCATTAAAAAGCATAAAAATAGAGGTCCCGAAATCGAA
Found at i:36460 original size:55 final size:56
Alignment explanation
Indices: 36289--36463 Score: 158
Period size: 56 Copynumber: 3.1 Consensus size: 56
36279 AAAAAAAAAG
* * * * *
36289 TATATTTATCAATTATTGTCATTAATAAGCATAAAAATAGAGG--CCCTGAAATCGAA
1 TATATCTATCAGTTATTGCCATTAAAAAGCATAAAAATAG-GGATCCC-AAAATCGAA
** * * * *
36345 TATATCTATCAGTTATTGTTATTAAGAAGCATAAAAATAGGGGTCCCGAAATCGAG
1 TATATCTATCAGTTATTGCCATTAAAAAGCATAAAAATAGGGATCCCAAAATCGAA
* * * * * *
36401 TATATTTATCGGTTGTTGCCATTAAAAATCAT-AAAATAGGTATCCCAAAATCAAA
1 TATATCTATCAGTTATTGCCATTAAAAAGCATAAAAATAGGGATCCCAAAATCGAA
36456 TATATCTA
1 TATATCTA
36464 GAAAAATAGG
Statistics
Matches: 99, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
55 27 0.27
56 69 0.70
57 3 0.03
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.33
Consensus pattern (56 bp):
TATATCTATCAGTTATTGCCATTAAAAAGCATAAAAATAGGGATCCCAAAATCGAA
Found at i:37279 original size:40 final size:40
Alignment explanation
Indices: 37224--37299 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
37214 AGGTAACATG
37224 CCCCCACGGTCCATCCCTGGAACTTATGCACATCCTGTTA
1 CCCCCACGGTCCATCCCTGGAACTTATGCACATCCTGTTA
37264 CCCCCACGGTCCATCCCTGGAACTTATGCACATCCT
1 CCCCCACGGTCCATCCCTGGAACTTATGCACATCCT
37300 TTCCTTCCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.20, C:0.42, G:0.14, T:0.24
Consensus pattern (40 bp):
CCCCCACGGTCCATCCCTGGAACTTATGCACATCCTGTTA
Found at i:52140 original size:53 final size:53
Alignment explanation
Indices: 52060--52168 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
52050 GGTAGTGATG
52060 CCCTCTGAAAACGCTATTATTTGACTGCAACACCCGCAATCACCGCAATAGCA
1 CCCTCTGAAAACGCTATTATTTGACTGCAACACCCGCAATCACCGCAATAGCA
52113 CCCTCTGAAAACGCTATTATTTGACTGCAACACCCGCAATCACCGCAATAGCA
1 CCCTCTGAAAACGCTATTATTTGACTGCAACACCCGCAATCACCGCAATAGCA
52166 CCC
1 CCC
52169 GCTATGCCCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.20
Consensus pattern (53 bp):
CCCTCTGAAAACGCTATTATTTGACTGCAACACCCGCAATCACCGCAATAGCA
Found at i:53487 original size:18 final size:18
Alignment explanation
Indices: 53466--53500 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53456 CTCTCTCTAT
53466 CCTTCTCCCTTTCCTTTG
1 CCTTCTCCCTTTCCTTTG
* *
53484 CCTTGTCTCTTTCCTTT
1 CCTTCTCCCTTTCCTTT
53501 TCTCTGTCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.40, G:0.06, T:0.54
Consensus pattern (18 bp):
CCTTCTCCCTTTCCTTTG
Found at i:55720 original size:19 final size:19
Alignment explanation
Indices: 55675--55714 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
55665 CCTTTTCATG
55675 ATTAAATTTGACTCCATCT
1 ATTAAATTTGACTCCATCT
*
55694 ATTAAATTTGATTCCATCT
1 ATTAAATTTGACTCCATCT
55713 AT
1 AT
55715 GTAATTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTAAATTTGACTCCATCT
Found at i:56118 original size:25 final size:25
Alignment explanation
Indices: 56084--56138 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
56074 GCCCCGAGGG
56084 AGCGCCTTAGGCCACCTAGGAGTAT
1 AGCGCCTTAGGCCACCTAGGAGTAT
56109 AGCGCCTTAGGCCACCTAGGAGTAT
1 AGCGCCTTAGGCCACCTAGGAGTAT
56134 AGCGC
1 AGCGC
56139 AGTTAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (25 bp):
AGCGCCTTAGGCCACCTAGGAGTAT
Found at i:58964 original size:9 final size:9
Alignment explanation
Indices: 58950--58983 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
58940 TAAGTAAAAT
58950 ATTAAATAA
1 ATTAAATAA
58959 ATTAAAT-A
1 ATTAAATAA
*
58967 CTTAAATAA
1 ATTAAATAA
58976 ATTAAATA
1 ATTAAATA
58984 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:58982 original size:17 final size:17
Alignment explanation
Indices: 58946--58984 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
58936 TAATTAAGTA
58946 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
58962 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
58979 AAATAC
1 AAATAC
58985 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:59050 original size:10 final size:10
Alignment explanation
Indices: 59037--59065 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
59027 ATAAGAGTAT
59037 TTGAGAGAAG
1 TTGAGAGAAG
59047 TTGAGAGAAG
1 TTGAGAGAAG
59057 TTGAGAGAA
1 TTGAGAGAA
59066 TTTAGTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:59969 original size:38 final size:37
Alignment explanation
Indices: 59898--60094 Score: 147
Period size: 38 Copynumber: 5.2 Consensus size: 37
59888 ATTAATATAG
* * * *
59898 TATAGTTTTTGAAAATATTTTTTTTAAAA-ATATAATA
1 TATAATTTTTGAAAACA-ATTTTTGAAAATATATAATA
*
59935 TATAATTTTTAGAAAACGATTTTTG-AAA-ATAT-ATA
1 TATAATTTTT-GAAAACAATTTTTGAAAATATATAATA
* * *
59970 CAT-AGTTTTGAAAACAATTTTTTGAAAATAAGTATATTA
1 TATAATTTTTGAAAACAA-TTTTTGAAAAT-A-TATAATA
*
60009 TAT-AGTTTTGAAAACAATTTTTGAAAATATATATATTA
1 TATAATTTTTGAAAACAATTTTTGAAAATATATA-A-TA
* * *
60047 TTTAA-TTTCGAAAATAATTTTTGAAAAATATATATATCA
1 TATAATTTTTGAAAACAATTTTTG-AAAATATATA-AT-A
60086 TATAATTTT
1 TATAATTTT
60095 AAAAATGTTT
Statistics
Matches: 132, Mismatches: 15, Indels: 23
0.78 0.09 0.14
Matches are distributed among these distances:
33 7 0.05
34 11 0.08
35 8 0.06
36 11 0.08
37 16 0.12
38 40 0.30
39 36 0.27
40 3 0.02
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
TATAATTTTTGAAAACAATTTTTGAAAATATATAATA
Found at i:59975 original size:72 final size:72
Alignment explanation
Indices: 59899--60041 Score: 184
Period size: 72 Copynumber: 2.0 Consensus size: 72
59889 TTAATATAGT
* ** * *
59899 ATAGTTTTTGAAAA-TATTTTTTTTAAA-AA-TATAATATATAATTTTTAGAAAACGATTTTTGA
1 ATAG-TTTTGAAAACAATTTTTTGAAAATAAGTATAATATAT-AGTTTT-GAAAACAATTTTTGA
59961 AAATATATAC
63 AAATATATAC
*
59971 ATAGTTTTGAAAACAATTTTTTGAAAATAAGTATATTATATAGTTTTGAAAACAATTTTTGAAAA
1 ATAGTTTTGAAAACAATTTTTTGAAAATAAGTATAATATATAGTTTTGAAAACAATTTTTGAAAA
60036 TATATA
66 TATATA
60042 TATTATTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
71 9 0.15
72 37 0.60
73 7 0.11
74 9 0.15
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (72 bp):
ATAGTTTTGAAAACAATTTTTTGAAAATAAGTATAATATATAGTTTTGAAAACAATTTTTGAAAA
TATATAC
Found at i:60017 original size:39 final size:38
Alignment explanation
Indices: 59927--60126 Score: 171
Period size: 39 Copynumber: 5.3 Consensus size: 38
59917 TTTTTTAAAA
* *
59927 ATATAATATATAATTTTTAGAAAACGATTTTTG--AA-A-
1 ATATATTATATAA-TTTT-GAAAACAATTTTTGAAAATAT
* *
59963 ATATA-TACATAGTTTTGAAAACAATTTTTTGAAAATA-
1 ATATATTATATAATTTTGAAAACAA-TTTTTGAAAATAT
*
60000 AGTATATTATATAGTTTTGAAAACAATTTTTGAAAATAT
1 A-TATATTATATAATTTTGAAAACAATTTTTGAAAATAT
* * *
60039 ATATATTATTTAATTTCGAAAATAATTTTTGAAAAATAT
1 ATATATTATATAATTTTGAAAACAATTTTTG-AAAATAT
* * *** *
60078 ATATATCATATAATTTTAAAAATGTTTGTTTTAAAATAT
1 ATATATTATATAATTTTGAAAACAATT-TTTGAAAATAT
60117 -TATATTATAT
1 ATATATTATAT
60127 GCTTGCATAT
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
33 7 0.05
34 10 0.07
35 5 0.04
36 7 0.05
37 2 0.01
38 51 0.37
39 54 0.39
40 3 0.02
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (38 bp):
ATATATTATATAATTTTGAAAACAATTTTTGAAAATAT
Found at i:60184 original size:11 final size:11
Alignment explanation
Indices: 60161--60190 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
60151 TCTCATTACA
60161 TTATTTA-TAT
1 TTATTTATTAT
60171 TTATTTATTAT
1 TTATTTATTAT
60182 TTATTTATT
1 TTATTTATT
60191 TTATGTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:61722 original size:27 final size:27
Alignment explanation
Indices: 61678--61743 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
61668 TTTATATATG
*
61678 TTAACTTAAAAA-A-TTTA-TATTAAC
1 TTAATTTAAAAATATTTTATTATTAAC
*
61702 TT-A-TTAAATATATTTTATTATTAAC
1 TTAATTTAAAAATATTTTATTATTAAC
61727 TTAATTTAAAAATATTT
1 TTAATTTAAAAATATTT
61744 ATTTTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 6 0.17
23 2 0.06
24 6 0.17
25 9 0.26
26 1 0.03
27 11 0.31
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (27 bp):
TTAATTTAAAAATATTTTATTATTAAC
Found at i:61729 original size:25 final size:26
Alignment explanation
Indices: 61663--61743 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 26
61653 TTAAATTCAT
** *
61663 AATATTTTATA-TATGTTAACTTAAA
1 AATATTTTATATTAACTTAATTTAAA
61688 AA-A-TTTATATTAACTT-A-TTAAA
1 AATATTTTATATTAACTTAATTTAAA
*
61710 TATATTTTATTATTAACTTAATTTAAA
1 AATATTTTA-TATTAACTTAATTTAAA
61737 AATATTT
1 AATATTT
61744 ATTTTTATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
22 6 0.13
23 8 0.17
24 9 0.20
25 11 0.24
26 1 0.02
27 11 0.24
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (26 bp):
AATATTTTATATTAACTTAATTTAAA
Found at i:61940 original size:30 final size:31
Alignment explanation
Indices: 61874--61945 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
61864 CATATTTTTG
* * *
61874 ACCACATCTTAATTAAATAAAACCGAAAGTG
1 ACCATATCTTAATTAAATAAAACCAAAAGTA
*
61905 GCCATATCTTAATTAAATAAAA-CAAAAGTA
1 ACCATATCTTAATTAAATAAAACCAAAAGTA
61935 ACCATATCTTA
1 ACCATATCTTA
61946 TGTTTTTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 16 0.44
31 20 0.56
ACGTcount: A:0.49, C:0.18, G:0.07, T:0.26
Consensus pattern (31 bp):
ACCATATCTTAATTAAATAAAACCAAAAGTA
Done.