Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007520.1 Hibiscus syriacus cultivar Beakdansim tig00020958_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: 66630
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:4386 original size:134 final size:134
Alignment explanation
Indices: 4231--5053 Score: 963
Period size: 134 Copynumber: 6.1 Consensus size: 134
4221 CTAAAAGGAT
* * *
4231 AGTGGAATGAGTCAACATCCCCAGATCTGATTTTACCTCAAGAAAAAGTGGAACATATCCCTCTC
1 AGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAAAAGTGGAACAAATCCCTCTC
* * * * * * * *
4296 TTTCATGATTTGATATTCCCTTACTAATACTGGAACAAGTCTACCTCGATTCAATCTTCTCTGCG
66 TTTCAAGATTTGATATTCCCTTAGTAACAGTGGAACAAGTCTGCCTCAATTCAATCTTCCCTGAG
4361 TAAC
131 TAAC
4365 AGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAGAAA-TGGAACAAATCCCTCT
1 AGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAA-AAAGTGGAACAAATCCCTCT
* * * * *
4429 CTTTCAAGTTTTGATATTTCCTTAGTAATAGTGGAACAAGTCTGCCTCAATTTAATCTTCCATGA
65 CTTTCAAGATTTGATATTCCCTTAGTAACAGTGGAACAAGTCTGCCTCAATTCAATCTTCCCTGA
* *
4494 GTGAT
130 GTAAC
* * * * * * * * * **
4499 AGTAGAATGAATCCATATCCCCAAATCTGATTTTCCCCCAAGAAGAAGCGAAACAGATCATTCTC
1 AGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAAAAGTGGAACAAATCCCTCTC
** *
4564 TTTCAAGATTTGATATT-CCTTGAGTAACAGTGGATTAAGTCTTCCTCAATTCAATCTTCCCTGA
66 TTTCAAGATTTGATATTCCCTT-AGTAACAGTGGAACAAGTCTGCCTCAATTCAATCTTCCCTGA
*
4628 GTGAC
130 GTAAC
* * * * *** * *
4633 AGTGGAATTAATCAACATCCCCATATATGATTTTCCCTTAAGAAAAAGCATAACAAATCCATCTT
1 AGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAAAAGTGGAACAAATCCCTCTC
4698 TTTCAAGATTTGATATTCCCTTAGTAACAGTGGAACAAGTCTGCCTCAATTCAATCTTCCCTGAG
66 TTTCAAGATTTGATATTCCCTTAGTAACAGTGGAACAAGTCTGCCTCAATTCAATCTTCCCTGAG
*
4763 CAAC
131 TAAC
* * * * * * *
4767 AATGGAAGGAATCAATAGTCCCCATATCTGATTTTTCCCTCAAGAAGAAGTGGAACAGATCTCTC
1 AGTGGAATGAATCAACA-TCCCCAGATCTGA-TTTTCCCTCAAGAAAAAGTGGAACAAATCCCTC
* * * * * *
4832 TCTTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC-GAACACGATTCAAACTTCCT
64 TC-TTTCAAGATTTGATATTCCCTTAGTAACAGTGGAACAAGTCTG-CCTCAATTCAATCTTCCC
4896 TGAGTGAA-
127 TGAGT-AAC
* * *
4904 AGTGGAATGAATCAACATCCCTAGATCTGATTTTCCCTCAAGAAGAAGTGGAACAAATCCTTCTC
1 AGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAAAAGTGGAACAAATCCCTCTC
* * **
4969 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAAAAGTCTGCCTTGATTCAATCTTCCCTGAA
66 TTTCAAGATTTGATATTCCCTTAGTAACAGTGGAACAAGTCTGCCTCAATTCAATCTTCCCTG-A
5034 G-AAC
130 GTAAC
*
5038 AGTAGAATGAATCAAC
1 AGTGGAATGAATCAAC
5054 TTTTCTCGAT
Statistics
Matches: 586, Mismatches: 91, Indels: 24
0.84 0.13 0.03
Matches are distributed among these distances:
133 8 0.01
134 413 0.70
135 54 0.09
136 38 0.06
137 71 0.12
138 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (134 bp):
AGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAAGAAAAAGTGGAACAAATCCCTCTC
TTTCAAGATTTGATATTCCCTTAGTAACAGTGGAACAAGTCTGCCTCAATTCAATCTTCCCTGAG
TAAC
Found at i:5240 original size:3 final size:3
Alignment explanation
Indices: 5232--5263 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5222 TTAATATTCG
5232 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5264 CTTTAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:7537 original size:131 final size:131
Alignment explanation
Indices: 7280--7644 Score: 350
Period size: 131 Copynumber: 2.8 Consensus size: 131
7270 TCGATATTGA
* * *
7280 GAATAATAATATCTTTTCATTTCGATCGGAGTC-ATAAATGATTGCTTTAAGGCTTGATAGGTCA
1 GAATAATAATATCTCTTCATTTCGATTGGAG-CAATAAATGATTGCTTTAAGGCTCGATAGGTCA
* * * * *
7344 TTTATTATCGATTGAAAATAATTTGATATTGTTGTTTTCTCTCGAATTAATACCGATATTTAAGA
65 TTTATTATCGATTGAAAATAATTAGATATTATCGTTTTCTCTCGAATCAATACCAATATTTAAGA
*
7409 TG
130 CG
* *
7411 GAATAATGATATCTCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGG-TACGAGT-GGTC
1 GAATAATAATATCTCTTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGCT-CGA-TAGGTC
* * * *
7474 ATTTATTCTCGATTGAAAATCAA-TAGATATTATCGTTTT-TACTTGAATCGATATTCAAT-TTT
64 ATTTATTATCGATTGAAAAT-AATTAGATATTATCGTTTTCT-CTCGAATCAATA-CCAATATTT
7536 AAGACG
126 AAGACG
* * * * * * * * * * *
7542 AAATAGTAATATCTCTTTATTTCAATTAGG-GAAATAAATGATTGTTTTAATGCACAAAAGGTTA
1 GAATAATAATATCTCTTCATTTCGATT-GGAGCAATAAATGATTGCTTTAAGGCTCGATAGGTCA
* *
7606 TTTATTATCGATT-AGAAATAATTAGATGTTATCATTTTC
65 TTTATTATCGATTGA-AAATAATTAGATATTATCGTTTTC
7645 AGTCTTAAAA
Statistics
Matches: 191, Mismatches: 31, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
130 6 0.03
131 177 0.93
132 8 0.04
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (131 bp):
GAATAATAATATCTCTTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGCTCGATAGGTCAT
TTATTATCGATTGAAAATAATTAGATATTATCGTTTTCTCTCGAATCAATACCAATATTTAAGAC
G
Found at i:10806 original size:12 final size:11
Alignment explanation
Indices: 10784--10817 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
10774 ATTTTAGAGA
10784 TTTTTTCTTTT
1 TTTTTTCTTTT
*
10795 CTTTTTCTTTT
1 TTTTTTCTTTT
10806 TTTTCTTCTTTT
1 TTTT-TTCTTTT
10818 AACAACGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:18030 original size:30 final size:30
Alignment explanation
Indices: 17982--18042 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
17972 ATATGTATAC
*
17982 TATATGTATTTTTAAAAAAATTATATAATA
1 TATATGTATTTTTAAAAAAACTATATAATA
*
18012 TATAT-TATATTTTCAAAAAACTATATAATA
1 TATATGTAT-TTTTAAAAAAACTATATAATA
18042 T
1 T
18043 TTTTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (30 bp):
TATATGTATTTTTAAAAAAACTATATAATA
Found at i:18044 original size:52 final size:53
Alignment explanation
Indices: 17980--18098 Score: 134
Period size: 52 Copynumber: 2.2 Consensus size: 53
17970 TAATATGTAT
* *
17980 ACTATATGTATTTTTAAAAAAATTATATAATATA-TAT-TATATTTTCAAAAA
1 ACTATATATATTTTTAAAAAAACTATATAATATATTATATATATTTTCAAAAA
** * *
18031 ACTATATAATATTTTTTCAAAAACTATATTATATATTCTATATATTTTCAAACAAA
1 ACTATAT-ATATTTTTAAAAAAACTATATAATATATTATATATATTTTC-AA-AAA
*
18087 ATTATATATATT
1 ACTATATATATT
18099 ATATATTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
51 7 0.12
52 22 0.39
53 2 0.04
54 9 0.16
55 7 0.12
56 9 0.16
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (53 bp):
ACTATATATATTTTTAAAAAAACTATATAATATATTATATATATTTTCAAAAA
Found at i:18052 original size:22 final size:23
Alignment explanation
Indices: 18010--18067 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
18000 AATTATATAA
*
18010 TATATATTATATTTTCAAAAAAC
1 TATATAATATATTTTCAAAAAAC
*
18033 TATATAATATTTTTTC-AAAAAC
1 TATATAATATATTTTCAAAAAAC
*
18055 TATATTATATATT
1 TATATAATATATT
18068 CTATATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATAATATATTTTCAAAAAAC
Found at i:18081 original size:31 final size:31
Alignment explanation
Indices: 18033--18131 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 31
18023 TTCAAAAAAC
* *
18033 TATATAATATTTTTTCAAAAACTATATTATA
1 TATATTATATATTTTCAAAAACTATATTATA
18064 TAT-TCTATATATTTTCAAACAA--A-ATTATA
1 TATAT-TATATATTTTCAAA-AACTATATTATA
18093 TATATTATATATTTT-ATAAAACTATA-TATA
1 TATATTATATATTTTCA-AAAACTATATTATA
*
18123 TATAATATA
1 TATATTATA
18132 AATACTGCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
28 3 0.05
29 21 0.36
30 16 0.28
31 16 0.28
32 2 0.03
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.47
Consensus pattern (31 bp):
TATATTATATATTTTCAAAAACTATATTATA
Found at i:18131 original size:21 final size:22
Alignment explanation
Indices: 18093--18133 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18083 CAAAATTATA
**
18093 TATATTATATATTTTATAAAAC
1 TATATTATATATAATATAAAAC
18115 TATA-TATATATAATATAAA
1 TATATTATATATAATATAAA
18134 TACTGCAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TATATTATATATAATATAAAAC
Found at i:25755 original size:15 final size:16
Alignment explanation
Indices: 25729--25768 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
25719 GACAATCCAT
*
25729 TTTTAA-TTTCATTTA
1 TTTTAATTTTCATTAA
25744 -TTTAATTTTCATTAA
1 TTTTAATTTTCATTAA
25759 TTTTAATTTT
1 TTTTAATTTT
25769 TATTCTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 8 0.36
16 9 0.41
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATTTTCATTAA
Found at i:28843 original size:28 final size:28
Alignment explanation
Indices: 28830--28901 Score: 144
Period size: 28 Copynumber: 2.6 Consensus size: 28
28820 GAAATTATCT
28830 TTGTTGCTTATGTTTATTTTACTTATTC
1 TTGTTGCTTATGTTTATTTTACTTATTC
28858 TTGTTGCTTATGTTTATTTTACTTATTC
1 TTGTTGCTTATGTTTATTTTACTTATTC
28886 TTGTTGCTTATGTTTA
1 TTGTTGCTTATGTTTA
28902 CTTTGCTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.14, C:0.10, G:0.12, T:0.64
Consensus pattern (28 bp):
TTGTTGCTTATGTTTATTTTACTTATTC
Found at i:29038 original size:41 final size:41
Alignment explanation
Indices: 28981--29063 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
28971 CTTATTCCCC
28981 ACCTTTTCCTAAGCCCCATTACACCCCTTTTTCAAGACCCA
1 ACCTTTTCCTAAGCCCCATTACACCCCTTTTTCAAGACCCA
29022 ACCTTTTCCTAAGCCCCATTACACCCCTTTTTCAAGACCCA
1 ACCTTTTCCTAAGCCCCATTACACCCCTTTTTCAAGACCCA
29063 A
1 A
29064 TGATTATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.25, C:0.41, G:0.05, T:0.29
Consensus pattern (41 bp):
ACCTTTTCCTAAGCCCCATTACACCCCTTTTTCAAGACCCA
Found at i:36633 original size:17 final size:17
Alignment explanation
Indices: 36602--36634 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
36592 AAATATTATT
36602 TTATTATTTATTTTAAG
1 TTATTATTTATTTTAAG
36619 TTATT-TTTATATTTAA
1 TTATTATTTAT-TTTAA
36635 TAATACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTTAAG
Found at i:38675 original size:6 final size:6
Alignment explanation
Indices: 38665--38699 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
38655 AACAAAGAAA
* *
38665 AAGAGG GAGAGG GAGAGG AAGAGG AAGAGG AAGAG
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAG
38700 AATGGGGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:45434 original size:43 final size:42
Alignment explanation
Indices: 45314--45442 Score: 125
Period size: 43 Copynumber: 3.0 Consensus size: 42
45304 CGGCGTTTCA
* * * *
45314 TGTACAAACGTCGCTAAATGACCTAACCTATTACGATATTTTT
1 TGTACAAACGCCGCTAAATGATCTAA-CTATTGCGGTATTTTT
* * *
45357 TGTAAAAATGCCGTTAAATGATCTAACATATTGCGGTATTTTAT
1 TGTACAAACGCCGCTAAATGATCTAAC-TATTGCGGTATTTT-T
* * *
45401 T-TACAAACGCCGCTAAATGATCTAGTCTGTTGCGGCATTTTT
1 TGTACAAACGCCGCTAAATGATCTA-ACTATTGCGGTATTTTT
45443 GTTTACAGAC
Statistics
Matches: 70, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
42 2 0.03
43 65 0.93
44 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (42 bp):
TGTACAAACGCCGCTAAATGATCTAACTATTGCGGTATTTTT
Found at i:47924 original size:31 final size:31
Alignment explanation
Indices: 47881--47948 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
47871 ACACTTTTTA
*
47881 TCACTTACGTTATCGTTTTATTAAGTTTTGG
1 TCACTTACGTTATCGTTTTATCAAGTTTTGG
*
47912 TCACTTATGTTATCGTTTTATCAAGTTTTGG
1 TCACTTACGTTATCGTTTTATCAAGTTTTGG
47943 TCACTT
1 TCACTT
47949 GGAAATGAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (31 bp):
TCACTTACGTTATCGTTTTATCAAGTTTTGG
Found at i:48119 original size:2 final size:2
Alignment explanation
Indices: 48112--48146 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48102 GGTTTTTGAA
48112 AT AT 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 AT AT A
48147 GTTTTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48170 original size:25 final size:25
Alignment explanation
Indices: 48136--48207 Score: 101
Period size: 25 Copynumber: 2.8 Consensus size: 25
48126 ATATATATAT
48136 ATATATATATAGTTTTTAAAAACTC
1 ATATATATATAGTTTTTAAAAACTC
*
48161 ATATATATATAG-TTTTAGAAAACTT
1 ATATATATATAGTTTTTA-AAAACTC
*
48186 ATATAATATATAGTTTTGAAAA
1 ATAT-ATATATAGTTTTTAAAA
48208 TATTTTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
24 5 0.12
25 22 0.52
26 11 0.26
27 4 0.10
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (25 bp):
ATATATATATAGTTTTTAAAAACTC
Found at i:48226 original size:37 final size:37
Alignment explanation
Indices: 48173--48621 Score: 412
Period size: 37 Copynumber: 12.6 Consensus size: 37
48163 ATATATATAG
* * *
48173 TTTTAGAAAACTTATATAATATATAGTTTTGAAAATA
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAACA
*
48210 TTTTTAAAAACATATATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAACATATATAATATATAG-TTTTGAAAACA
*
48248 -TTTTGAAAACTTATATAATATATA-----G------
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAACA
*
48273 TTTTTGAAAACATATATAATGTATAGTTTTGAAAACA
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAACA
* *
48310 TATTTGAAAACTTATATAATATATAGTTTTGAAAACA
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAACA
* *
48347 TTTTTGAAATCTTATATAATATATA-----G------
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAACA
*
48373 -TTTTGAAAACATATATAATGTATAGTTTTGAAAACA
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAACA
* *
48409 TATTTGAAAACTTATATAATATATAGTTTTGAAAACA
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAACA
**
48446 TTTTTGAAAAC--ATATAATATATAGTTTTGAAATTA
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAACA
48481 TTTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAAC--ATATATAATATATAG-TTTTGAAAACA
***
48521 -TTTTGAAAACATATATATAATATATAGTTTTTGAAATTT
1 TTTTTGAAAAC--ATATATAATATATAG-TTTTGAAAACA
* * * *
48560 TTTTTGAATATATATATATTATATAGTTTTGAAAATAA
1 TTTTTGAAAACATATATAATATATAGTTTTGAAAA-CA
* * *
48598 TTTTTGAAAATACATATATTATAT
1 TTTTTGAAAACATATATAATATAT
48622 TTGAAAGCAA
Statistics
Matches: 345, Mismatches: 35, Indels: 63
0.78 0.08 0.14
Matches are distributed among these distances:
25 21 0.06
26 22 0.06
30 1 0.00
31 2 0.01
32 1 0.00
35 33 0.10
37 153 0.44
38 46 0.13
39 49 0.14
40 17 0.05
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
TTTTTGAAAACATATATAATATATAGTTTTGAAAACA
Found at i:48277 original size:26 final size:25
Alignment explanation
Indices: 48248--48411 Score: 120
Period size: 25 Copynumber: 6.6 Consensus size: 25
48238 TTTGAAAACA
*
48248 TTTTGAAAACTTATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
*
48273 TTTTTGAAAACATATATAATGTATAG
1 -TTTTGAAAACATATATAATATATAG
* * *
48299 TTTTGAAAACATATTTGA-A-A-AC
1 TTTTGAAAACATATATAATATATAG
* * * ** * * *
48321 TTAT-ATAATATATAGTTTTGAAAACAT
1 TTTTGAAAACATATA-TAAT--ATATAG
* *
48348 TTTTGAAATCTTATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
*
48373 TTTTGAAAACATATATAATGTATAG
1 TTTTGAAAACATATATAATATATAG
48398 TTTTGAAAACATAT
1 TTTTGAAAACATAT
48412 TTGAAAACTT
Statistics
Matches: 105, Mismatches: 26, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
21 7 0.07
22 5 0.05
23 1 0.01
25 56 0.53
26 24 0.23
27 6 0.06
28 6 0.06
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (25 bp):
TTTTGAAAACATATATAATATATAG
Found at i:48445 original size:62 final size:62
Alignment explanation
Indices: 48312--48521 Score: 240
Period size: 62 Copynumber: 3.2 Consensus size: 62
48302 TGAAAACATA
* * *
48312 TTTGAAAACTTATATAATATATAGTTTTGAAAACATTTTTGAAATCTTATATAATATATAGT
1 TTTGAAAACATATATAATATATAGTTTTGAAAACATATTTGAAAACTTATATAATATATAGT
*
48374 TTTGAAAACATATATAATGTATAGTTTTGAAAACATATTTGAAAACTTATATAATATATAGT
1 TTTGAAAACATATATAATATATAGTTTTGAAAACATATTTGAAAACTTATATAATATATAGT
** *
48436 TTTGAAAACATTTTTGAAAACATATAATATATAGTTTTGAAATTATTTTTGAAAACATATATATA
1 TTTGAAAACA----T------ATATAATATATAGTTTTGAAAACATATTTGAAAAC-T-TATATA
48501 ATATATAGTT
54 ATATATAG-T
48511 TTTGAAAACAT
1 TTTGAAAACAT
48522 TTTGAAAACA
Statistics
Matches: 127, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
62 68 0.54
66 1 0.01
71 1 0.01
72 31 0.24
73 1 0.01
74 14 0.11
75 11 0.09
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.43
Consensus pattern (62 bp):
TTTGAAAACATATATAATATATAGTTTTGAAAACATATTTGAAAACTTATATAATATATAGT
Found at i:48534 original size:28 final size:28
Alignment explanation
Indices: 48481--48535 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
48471 TTTGAAATTA
* *
48481 TTTTTGAAAACATATATATAATATATAG
1 TTTTTGAAAACATATATAAAACATATAG
*
48509 TTTTTGAAAACAT-TTTGAAAACATATA
1 TTTTTGAAAACATATAT-AAAACATATA
48536 TATAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (28 bp):
TTTTTGAAAACATATATAAAACATATAG
Found at i:49189 original size:22 final size:22
Alignment explanation
Indices: 49148--49189 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
49138 GCACAACAAA
* *
49148 AACATCAAAATATCAGCAAAAC
1 AACAACAAAATAACAGCAAAAC
*
49170 AACAACAAAATAACATCAAA
1 AACAACAAAATAACAGCAAA
49190 CAAACCCGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.21, G:0.02, T:0.12
Consensus pattern (22 bp):
AACAACAAAATAACAGCAAAAC
Found at i:50072 original size:5 final size:5
Alignment explanation
Indices: 50064--50089 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
50054 TACATTTTAT
50064 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
50090 CTTTTAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:51406 original size:33 final size:33
Alignment explanation
Indices: 51364--51428 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
51354 TTCCTGAGTA
*
51364 ATGATGTTGCCAAATGAGTTGATCACCTTCATT
1 ATGATGTTGCCAAATGAATTGATCACCTTCATT
* *
51397 ATGATGTTGCCAGATGAATTGATCGCCTTCAT
1 ATGATGTTGCCAAATGAATTGATCACCTTCAT
51429 GGGGGGTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (33 bp):
ATGATGTTGCCAAATGAATTGATCACCTTCATT
Found at i:52799 original size:17 final size:18
Alignment explanation
Indices: 52726--52800 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
52716 TCTACGTCTA
* **
52726 ATAACTGTAAAACATCAA
1 ATAACTGTAAATCATCTG
*
52744 ATAACTGT-AATCATTTG
1 ATAACTGTAAATCATCTG
* *
52761 ATAACTGAAAATCATTTG
1 ATAACTGTAAATCATCTG
52779 ATAACTGTAAAT-ATCTG
1 ATAACTGTAAATCATCTG
52796 ATAAC
1 ATAAC
52801 GGTGAAATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
17 21 0.43
18 28 0.57
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (18 bp):
ATAACTGTAAATCATCTG
Found at i:58628 original size:37 final size:37
Alignment explanation
Indices: 58586--58661 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
58576 CATATCAGAT
*
58586 CAGTAATATCTACATCCTAGTGGCATGTACATATTTC
1 CAGTAATATCGACATCCTAGTGGCATGTACATATTTC
58623 CAGTAATATCGACATCCTAGTGGCATGTACATATTTC
1 CAGTAATATCGACATCCTAGTGGCATGTACATATTTC
58660 CA
1 CA
58662 ACATAAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (37 bp):
CAGTAATATCGACATCCTAGTGGCATGTACATATTTC
Found at i:58764 original size:20 final size:20
Alignment explanation
Indices: 58726--58766 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
58716 CCAATAAATG
*
58726 TAACACTCATAACATGTATA
1 TAACACTCATAACACGTATA
* *
58746 TAACACTCGTAACCCGTATA
1 TAACACTCATAACACGTATA
58766 T
1 T
58767 GTAACGCCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.29
Consensus pattern (20 bp):
TAACACTCATAACACGTATA
Found at i:59919 original size:18 final size:18
Alignment explanation
Indices: 59886--59924 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
59876 TTAATCTACG
*
59886 TCTGATAACTATAAATTA
1 TCTGATAACTATAAATCA
59904 TCTGATAACTGA-AAATCA
1 TCTGATAACT-ATAAATCA
59922 TCT
1 TCT
59925 AATATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (18 bp):
TCTGATAACTATAAATCA
Found at i:60844 original size:35 final size:35
Alignment explanation
Indices: 60795--60871 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
60785 CAACATTGGC
* * *
60795 TCATCGCAATACTTAAGTATTTGAAAACTTGTAATT
1 TCATC-CAACACTTAAATATTTGAAAACTTGTAACT
60831 TCATCCAACACTTAAATATTTGAAAACTTGTAACT
1 TCATCCAACACTTAAATATTTGAAAACTTGTAACT
60866 TCATCC
1 TCATCC
60872 TTCATTTTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (35 bp):
TCATCCAACACTTAAATATTTGAAAACTTGTAACT
Done.