Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005183.1 Hibiscus syriacus cultivar Beakdansim tig00011705_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: 70088
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:15295 original size:16 final size:14
Alignment explanation
Indices: 15274--15317 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
15264 CTTTAGCAGT
15274 TGTAGAAAACAAAC
1 TGTAGAAAACAAAC
* *
15288 TGTGTAGAAAATAGAC
1 --TGTAGAAAACAAAC
15304 TGTAGAAAACAAAC
1 TGTAGAAAACAAAC
15318 AAGTCTGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
16 12 0.50
ACGTcount: A:0.52, C:0.11, G:0.18, T:0.18
Consensus pattern (14 bp):
TGTAGAAAACAAAC
Found at i:17616 original size:51 final size:51
Alignment explanation
Indices: 17540--17640 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
17530 TAAGGAAATG
* *
17540 ATAGGCTGTAAAGAAATATCGGTTTGAACAAGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAAGCTAAAATTCCTTGTAACTA
*
17591 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTAAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAAGCTAAAATTCCTTGTAACT
17641 CTCCCCCTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAAGCTAAAATTCCTTGTAACTA
Found at i:19735 original size:13 final size:13
Alignment explanation
Indices: 19694--19724 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19684 CGACCCGTTT
*
19694 ACCCGTTTACCCG
1 ACCCGTTGACCCG
19707 ACCCGTTGACCCG
1 ACCCGTTGACCCG
19720 ACCCG
1 ACCCG
19725 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:19805 original size:29 final size:29
Alignment explanation
Indices: 19743--19818 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
19733 ACCGTTGACC
** *
19743 GGTGCTATTCTGGGAATTAATTCAGTTTT
1 GGTGCTATTCTGGGAATTAATTCAGAATG
*
19772 AGTGCTATTCTGGGAATTAATTC-GAAATG
1 GGTGCTATTCTGGGAATTAATTCAG-AATG
* *
19801 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
19819 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 1 0.03
29 38 0.97
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCAGAATG
Found at i:21532 original size:29 final size:29
Alignment explanation
Indices: 21471--21546 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
21461 ACCGTTGACC
* ** *
21471 GGTGCTATTCTTGGAATTAATTCAGTTTT
1 GGTGCTATTCTGGGAATTAATTCAGAATG
21500 GGTGCTATTCTGGGAATTAATTC-GAAATG
1 GGTGCTATTCTGGGAATTAATTCAG-AATG
* *
21529 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
21547 TTTTAAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCAGAATG
Found at i:27888 original size:3 final size:3
Alignment explanation
Indices: 27880--27935 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
27870 TCATCAACAC
*
27880 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT GCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
27928 TAT TCT TC
1 TCT TCT TC
27936 CACTCATTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:28502 original size:2 final size:2
Alignment explanation
Indices: 28489--28523 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28479 GAAAATAATA
*
28489 AT AT AT AC 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 AT AT A
28524 GAAACATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:29560 original size:19 final size:18
Alignment explanation
Indices: 29536--29593 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
29526 TGACGACTGA
29536 TGCTTCTGGCCGTTGAAAT
1 TGCTTCTGGCCGTTG-AAT
** *
29555 TGCTTCTGGATGTTGACT
1 TGCTTCTGGCCGTTGAAT
*
29573 TGCTTTCTGGCCGTTGGAT
1 TGC-TTCTGGCCGTTGAAT
29592 TG
1 TG
29594 GGTCAGATCC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.41
Consensus pattern (18 bp):
TGCTTCTGGCCGTTGAAT
Found at i:29781 original size:15 final size:14
Alignment explanation
Indices: 29749--29777 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29739 AAAAAAAAAC
29749 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
29763 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
29777 A
1 A
29778 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:29854 original size:32 final size:32
Alignment explanation
Indices: 29817--29987 Score: 111
Period size: 31 Copynumber: 5.2 Consensus size: 32
29807 ATATAATACA
*
29817 TATATTTCAAAAATATTTTTTAAACTATATAT
1 TATATTTCAAAAATATTTTTAAAACTATATAT
*
29849 TATATTT-AAAAA-AGTTTTCAAAACTATAT-T
1 TATATTTCAAAAATA-TTTTTAAAACTATATAT
* *
29879 ATATAGTTTTC-AAAAT-GTTTTAAAAATATTATAT
1 -TATA--TTTCAAAAATATTTTTAAAACTA-TATAT
* * **
29913 AAGT-TTTAAAAAACGTTTTTAAAACTATATATT
1 TA-TATTTCAAAAATATTTTTAAAACTATATA-T
*
29946 ATATAATTTATTCAAAAATGTTTTTAAAACTATATAT
1 -TAT-A--T-TTCAAAAATATTTTTAAAACTATATAT
29983 TATAT
1 TATAT
29988 AAGTTTTTAA
Statistics
Matches: 108, Mismatches: 13, Indels: 35
0.69 0.08 0.22
Matches are distributed among these distances:
30 2 0.02
31 25 0.23
32 24 0.22
33 24 0.22
34 3 0.03
35 1 0.01
36 3 0.03
37 2 0.02
38 24 0.22
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATTTCAAAAATATTTTTAAAACTATATAT
Found at i:29882 original size:36 final size:33
Alignment explanation
Indices: 29816--30072 Score: 165
Period size: 38 Copynumber: 7.4 Consensus size: 33
29806 TATATAATAC
* * *
29816 ATATATTTCAAAAATATTTTTTAAACTATA-TAT
1 ATATATTTTAAAAAT-GTTTTAAAACTATATTAT
*
29849 -TATA-TTTAAAAAAGTTTTCAAAACTATATTAT
1 ATATATTTTAAAAATGTTTT-AAAACTATATTAT
* *
29881 ATA-GTTTTCAAAATGTTTTAAAA--ATATTAT
1 ATATATTTTAAAAATGTTTTAAAACTATATTAT
*
29911 ATA-AGTTTTAAAAAACGTTTTTAAAACTATA-TATT
1 ATATA-TTTT-AAAAATG-TTTTAAAACTATATTA-T
29946 ATATAATTTATTCAAAAATGTTTTTAAAACTATA-TATT
1 ATAT-A-TT-TT-AAAAATG-TTTTAAAACTATATTA-T
*
29984 ATATAAGTTTTTAAAATGATTTTAAAACTATATGTTAT
1 ATAT-A-TTTTAAAAATG-TTTTAAAACTATA--TTAT
*
30022 ATATATTTTCTAAAATGTTTTAAAAACTATATGT-T
1 ATATATTTT-AAAAATGTTTT-AAAACTATAT-TAT
30057 ATATAGTTTTCAAAAA
1 ATATA-TTTT-AAAAA
30073 AACTATATAT
Statistics
Matches: 187, Mismatches: 17, Indels: 37
0.78 0.07 0.15
Matches are distributed among these distances:
30 14 0.07
31 19 0.10
32 16 0.09
33 22 0.12
34 2 0.01
35 14 0.07
36 37 0.20
37 22 0.12
38 39 0.21
39 2 0.01
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (33 bp):
ATATATTTTAAAAATGTTTTAAAACTATATTAT
Found at i:29948 original size:37 final size:37
Alignment explanation
Indices: 29825--30073 Score: 219
Period size: 37 Copynumber: 7.1 Consensus size: 37
29815 CATATATTTC
* *
29825 AAAAATATTTTTTAAACTATATA-T-TAT-A--TTTA
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTA
*
29857 AAAAA-GTTTTCAAAAC--TATATTATAT-AGTTTT-
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTA
*
29889 CAAAATG-TTTT-AAA--A-ATATTATATAAGTTTTA
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTA
* * *
29921 AAAAACGTTTTTAAAACTATATATTATATAATTTATTC
1 AAAAATGTTTTTAAAACTATATATTATATAAGTT-TTA
29959 AAAAATGTTTTTAAAACTATATATTATATAAGTTTT-
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTA
* * * *
29995 TAAAATGATTTTAAAACTATATGTTATATATA-TTTTC
1 AAAAATGTTTTTAAAACTATATATTATATA-AGTTTTA
* * *
30032 TAAAATGTTTTAAAAACTATATGTTATAT-AGTTTTCA
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTT-A
30069 AAAAA
1 AAAAA
30074 ACTATATATT
Statistics
Matches: 181, Mismatches: 18, Indels: 31
0.79 0.08 0.13
Matches are distributed among these distances:
29 4 0.02
30 10 0.06
31 21 0.12
32 17 0.09
33 8 0.04
34 3 0.02
35 1 0.01
36 36 0.20
37 47 0.26
38 34 0.19
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (37 bp):
AAAAATGTTTTTAAAACTATATATTATATAAGTTTTA
Found at i:31108 original size:163 final size:163
Alignment explanation
Indices: 30701--31379 Score: 1135
Period size: 163 Copynumber: 4.1 Consensus size: 163
30691 AGTTTTATTG
* * * * * * * * * *
30701 ACAGATAGCCCTTCTTGCGTTGAGTTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAAT
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGTGTAAT
**
30765 CGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
64 CGAACTCGGGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
*
30830 GGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTC
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTC--TTGGTC
30867 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
30932 AACTCGGGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
30997 AGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTC
31030 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*
31095 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
31160 AGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTC
31193 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*
31258 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
*
31323 AGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTG
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTC
* * * *
31356 GCAGGTAGCCCTTCTGGCCTTGAG
1 ACAGATAACCCTTCTAGCCTTGAG
31380 CTAAGCTGCA
Statistics
Matches: 493, Mismatches: 19, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
163 350 0.71
164 6 0.01
165 106 0.22
166 31 0.06
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (163 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
AACTCGGGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTC
Found at i:37608 original size:19 final size:18
Alignment explanation
Indices: 37584--37641 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
37574 TGACGACTGA
37584 TGCTTCTGGCCGTTGAAAT
1 TGCTTCTGGCCGTTG-AAT
** *
37603 TGCTTCTGGATGTTGACT
1 TGCTTCTGGCCGTTGAAT
*
37621 TGCTTTCTGGCCGTTGGAT
1 TGC-TTCTGGCCGTTGAAT
37640 TG
1 TG
37642 GGTCAGATCC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.41
Consensus pattern (18 bp):
TGCTTCTGGCCGTTGAAT
Found at i:37829 original size:15 final size:14
Alignment explanation
Indices: 37797--37825 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
37787 AAAAAAAAAC
37797 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
37811 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
37825 A
1 A
37826 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:37902 original size:32 final size:32
Alignment explanation
Indices: 37865--38035 Score: 143
Period size: 32 Copynumber: 5.2 Consensus size: 32
37855 ATATAATACA
* *
37865 TATATTTAAAAAATATTTTTTAAACTATATAT
1 TATATTTAAAAAATGTTTTTAAAACTATATAT
* *
37897 TATATTTTAAAAA-GTTTTCAAAACTATAT-T
1 TATATTTAAAAAATGTTTTTAAAACTATATAT
** *
37927 ATATAGTTTTCAAAATG-TTTTAAAAATATTATAT
1 -TATA-TTTAAAAAATGTTTTTAAAACTA-TATAT
* *
37961 AAGT-TTTAAAAAACGTTTTTAAAACTATATATT
1 TA-TATTTAAAAAATGTTTTTAAAACTATATA-T
37994 ATATAATTTATTCAAAAATGTTTTTAAAACTATATAT
1 -TAT-ATTTA---AAAAATGTTTTTAAAACTATATAT
38031 TATAT
1 TATAT
38036 AAGTTTTTAA
Statistics
Matches: 111, Mismatches: 14, Indels: 25
0.74 0.09 0.17
Matches are distributed among these distances:
30 1 0.01
31 17 0.15
32 41 0.37
33 17 0.15
34 3 0.03
35 6 0.05
36 3 0.03
37 1 0.01
38 22 0.20
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (32 bp):
TATATTTAAAAAATGTTTTTAAAACTATATAT
Found at i:37930 original size:36 final size:33
Alignment explanation
Indices: 37881--38120 Score: 158
Period size: 38 Copynumber: 7.0 Consensus size: 33
37871 TAAAAAATAT
*
37881 TTTTTAAACTATA-TAT-TATA-TTTTAAAAAG
1 TTTTAAAACTATATTATATATATTTTTAAAAAG
* * *
37911 TTTTCAAAACTATATTATATA-GTTTTCAAAATG
1 TTTT-AAAACTATATTATATATATTTTTAAAAAG
*
37944 TTTTAAAA--ATATTATATA-AGTTTTAAAAAACG
1 TTTTAAAACTATATTATATATA-TTTTTAAAAA-G
37976 TTTTTAAAACTATA-TATTATATAATTTATTCAAAAATG
1 -TTTTAAAACTATATTA-TATAT-ATTT-TT-AAAAA-G
*
38014 TTTTTAAAACTATA-TATTATATAAGTTTTTAAAATG
1 -TTTTAAAACTATATTA-TATAT-A-TTTTTAAAAAG
*
38050 ATTTTAAAACTATATGTTATATATATTTTCTAAAATG
1 -TTTTAAAACTATA--TTATATATATTTT-TAAAAAG
*
38087 TTTTAAAAACTATATGT-TATATAGTTTTCAAAAA
1 TTTT-AAAACTATAT-TATATATA-TTTTTAAAAA
38121 AACTATATAT
Statistics
Matches: 175, Mismatches: 13, Indels: 39
0.77 0.06 0.17
Matches are distributed among these distances:
30 14 0.08
31 16 0.09
32 8 0.05
33 22 0.13
34 2 0.01
35 18 0.10
36 30 0.17
37 23 0.13
38 37 0.21
39 5 0.03
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (33 bp):
TTTTAAAACTATATTATATATATTTTTAAAAAG
Found at i:37980 original size:96 final size:106
Alignment explanation
Indices: 37869--38058 Score: 256
Period size: 96 Copynumber: 1.9 Consensus size: 106
37859 AATACATATA
* *
37869 TTTAAAAAATATTTTTTAAACTATATA-T-TAT-A-TT-TT-AAAAA-GTTTTCAAAAC-TATAT
1 TTTAAAAAACATTTTTAAAACTATATATTATATAATTTATTCAAAAATGTTTTCAAAACATATAT
37926 TATAT-AGTTTTCAAAATG-TTTTAAAAATATTATATAAGT
66 TATATAAGTTTTCAAAATGATTTTAAAAATATTATATAAGT
* *
37965 TTTAAAAAACGTTTTTAAAACTATATATTATATAATTTATTCAAAAATGTTTTTAAAACTATATA
1 TTTAAAAAACATTTTTAAAACTATATATTATATAATTTATTCAAAAATGTTTTCAAAAC-ATATA
*
38030 TTATATAAGTTTTTAAAATGATTTTAAAA
65 TTATATAAGTTTTCAAAATGATTTTAAAA
38059 CTATATGTTA
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
96 24 0.31
97 1 0.01
98 3 0.04
99 1 0.01
100 2 0.03
101 2 0.03
102 5 0.06
103 10 0.13
105 10 0.13
106 12 0.15
107 8 0.10
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (106 bp):
TTTAAAAAACATTTTTAAAACTATATATTATATAATTTATTCAAAAATGTTTTCAAAACATATAT
TATATAAGTTTTCAAAATGATTTTAAAAATATTATATAAGT
Found at i:37996 original size:37 final size:36
Alignment explanation
Indices: 37873--38120 Score: 229
Period size: 37 Copynumber: 7.1 Consensus size: 36
37863 CATATATTTA
* *
37873 AAAAATATTTTTTAAACTATATA-T-TAT-A-TTTT
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTT
*
37905 AAAAA-GTTTTCAAAAC--TATATTATAT-AGTTTT
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTT
*
37937 CAAAATG-TTTT-AAA--A-ATATTATATAAGTTTT
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTT
* *
37968 AAAAAACGTTTTTAAAACTATATATTATATAATTTATT
1 -AAAAATGTTTTTAAAACTATATATTATATAAGTT-TT
38006 CAAAAATGTTTTTAAAACTATATATTATATAAGTTTT
1 -AAAAATGTTTTTAAAACTATATATTATATAAGTTTT
* * *
38043 TAAAATGATTTTAAAACTATATGTTATATATA-TTTT
1 AAAAATGTTTTTAAAACTATATATTATATA-AGTTTT
* * *
38079 CTAAAATGTTTTAAAAACTATATGTTATAT-AGTTTT
1 -AAAAATGTTTTTAAAACTATATATTATATAAGTTTT
38115 CAAAAA
1 -AAAAA
38121 AACTATATAT
Statistics
Matches: 183, Mismatches: 17, Indels: 28
0.80 0.07 0.12
Matches are distributed among these distances:
29 4 0.02
30 10 0.05
31 21 0.11
32 21 0.11
33 5 0.03
34 3 0.02
35 1 0.01
36 41 0.22
37 43 0.23
38 34 0.19
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (36 bp):
AAAAATGTTTTTAAAACTATATATTATATAAGTTTT
Found at i:39371 original size:39 final size:39
Alignment explanation
Indices: 39296--39371 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
39286 TGGTGCTTGG
* *
39296 GATTTCTCGGTGTCTTTAGGGTTAATTTATTGCATGCTT
1 GATTTCTCGGCGTCTTTAGGGTTAATTTATTCCATGCTT
*
39335 GATTTCTCGGCGTCTTTGGGGTTAATATT-TTCCATGC
1 GATTTCTCGGCGTCTTTAGGGTTAAT-TTATTCCATGC
39372 ATATCGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (39 bp):
GATTTCTCGGCGTCTTTAGGGTTAATTTATTCCATGCTT
Found at i:40553 original size:13 final size:12
Alignment explanation
Indices: 40536--40565 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40526 TTTTCGTGTA
40536 ATTTTTAGTTGT
1 ATTTTTAGTTGT
40548 ATTTTTAGTT-T
1 ATTTTTAGTTGT
40559 ATTTTTA
1 ATTTTTA
40566 TATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (12 bp):
ATTTTTAGTTGT
Found at i:44702 original size:26 final size:25
Alignment explanation
Indices: 44625--44704 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 25
44615 TAATGAAACC
* *
44625 ATTAAATAATTTTAATATAAAATGTAAT
1 ATTAAATAAATATAATAT-AAA--TAAT
* *
44653 -TTAAATAAATAATATTATTAATAAT
1 ATTAAATAAAT-ATAATATAAATAAT
*
44678 ATTAAATAAATCTAATATAAGATAAT
1 ATTAAATAAATATAATATAA-ATAAT
44704 A
1 A
44705 ATAATAATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
25 10 0.24
26 16 0.38
27 11 0.26
28 5 0.12
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (25 bp):
ATTAAATAAATATAATATAAATAAT
Found at i:44882 original size:20 final size:20
Alignment explanation
Indices: 44853--44891 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44843 ATGATTTAAA
44853 TAAATCTAATAAAAATATTT
1 TAAATCTAATAAAAATATTT
* *
44873 TAAATTTAATATAAATATT
1 TAAATCTAATAAAAATATT
44892 ATTTGAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATCTAATAAAAATATTT
Found at i:45554 original size:51 final size:51
Alignment explanation
Indices: 45478--45581 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
45468 AATTGAAAGA
*
45478 TATGTTGTAAAAATAAAAAGACTAAATAGTTGAGTAGTCAGTGGTATGACT
1 TATGTGGTAAAAATAAAAAGACTAAATAGTTGAGTAGTCAGTGGTATGACT
*
45529 TATGTGGTAAAAATAAAAAGACTAAATAGTTGAGTAGTTAGTGGTATGACT
1 TATGTGGTAAAAATAAAAAGACTAAATAGTTGAGTAGTCAGTGGTATGACT
45580 TA
1 TA
45582 CCCTTCAACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (51 bp):
TATGTGGTAAAAATAAAAAGACTAAATAGTTGAGTAGTCAGTGGTATGACT
Found at i:55032 original size:17 final size:17
Alignment explanation
Indices: 55012--55045 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
55002 CTTTAACATT
55012 GCTTCTTCTTTGGCATG
1 GCTTCTTCTTTGGCATG
55029 GCTTCTTCTTTGGCATG
1 GCTTCTTCTTTGGCATG
55046 TTTGAGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.24, T:0.47
Consensus pattern (17 bp):
GCTTCTTCTTTGGCATG
Found at i:55812 original size:20 final size:20
Alignment explanation
Indices: 55787--55832 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
55777 TAAAACGGAC
55787 CAAAACTGATAATTT-AGATA
1 CAAAACTGATAATTTAAG-TA
55807 CAAAACTGATAATTTAAGTA
1 CAAAACTGATAATTTAAGTA
55827 CAAAAC
1 CAAAAC
55833 ACATTAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (20 bp):
CAAAACTGATAATTTAAGTA
Found at i:57187 original size:22 final size:22
Alignment explanation
Indices: 57162--57204 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
57152 CAGTACAAAC
57162 GCGTTCCAGTCGTTTCAAAATT
1 GCGTTCCAGTCGTTTCAAAATT
*
57184 GCGTTTCAGTCGTTTCAAAAT
1 GCGTTCCAGTCGTTTCAAAAT
57205 CGCGATTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (22 bp):
GCGTTCCAGTCGTTTCAAAATT
Done.