Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000765.1 Hibiscus syriacus cultivar Beakdansim tig00001487_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: 86265
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2231 original size:15 final size:15
Alignment explanation
Indices: 2211--2240 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2201 TGTATATTTC
2211 TTTATTAATGGTAAA
1 TTTATTAATGGTAAA
2226 TTTATTAATGGTAAA
1 TTTATTAATGGTAAA
2241 AGTCATCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
TTTATTAATGGTAAA
Found at i:6367 original size:16 final size:16
Alignment explanation
Indices: 6346--6379 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6336 TTGAAAAATC
6346 AATCCATGTTTACATA
1 AATCCATGTTTACATA
6362 AATCCATGTTTACATA
1 AATCCATGTTTACATA
6378 AA
1 AA
6380 CAAAGATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (16 bp):
AATCCATGTTTACATA
Found at i:8897 original size:84 final size:85
Alignment explanation
Indices: 8803--8979 Score: 293
Period size: 84 Copynumber: 2.1 Consensus size: 85
8793 GACGCGCAAC
* * *
8803 TGTGCGTCATAAATTTATGACGCGCATTTATGACTTACATTGCGCGTCATTG-AGGCCCCGTCAT
1 TGTGTGTCATAAATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCAT
*
8867 AAATGAAGATGACACACATT
66 AAATGAAAATGACACACATT
*
8887 TGTGTGTCATAAATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCAT
1 TGTGTGTCATAAATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCAT
8952 AAATGAAAATGACACACATT
66 AAATGAAAATGACACACATT
*
8972 CGTGTGTC
1 TGTGTGTC
8980 GTGATTGTAT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
84 49 0.57
85 37 0.43
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (85 bp):
TGTGTGTCATAAATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCAT
AAATGAAAATGACACACATT
Found at i:22874 original size:32 final size:32
Alignment explanation
Indices: 22834--22918 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
22824 TAAAGTGACC
22834 CTTAGGTAGGCTCTTAGGCCCCAAGGTACTCT
1 CTTAGGTAGGCTCTTAGGCCCCAAGGTACTCT
* * *
22866 CTTGGGTAGGCTCTAAGGCCTCAAGGTACTCT
1 CTTAGGTAGGCTCTTAGGCCCCAAGGTACTCT
* *
22898 CTTAGGTTGGCTCTTATGCCC
1 CTTAGGTAGGCTCTTAGGCCC
22919 AATGAGCCTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.31
Consensus pattern (32 bp):
CTTAGGTAGGCTCTTAGGCCCCAAGGTACTCT
Found at i:35673 original size:138 final size:138
Alignment explanation
Indices: 35353--36085 Score: 842
Period size: 138 Copynumber: 5.3 Consensus size: 138
35343 TCCATTATTC
* * *
35353 ATGTTATCATTGCCCCTATTATGTCACTTATGTCCCCCGAGGGCACTATTCATGAATG-CCCTAT
1 ATGTTATCATTG-CCCTATTATGTCACTCATGTCCCCCGGGGGCACTATTCATGAATGTACCTAT
**** * * *
35417 TATGTTTGAGGGGACACATCAAAGTAGTGAAAACGCG-TTTCCGGGGGGGCGTCGTCTTTCATTA
65 TATGTTTGAGGGGACTTGGCAAAGTGGTG-AAA-GCGATTTCC--GGGGGCG-CGCCTTCCATTA
*
35481 TTTTGTCAGAGAAC
125 TTTTGTCAGAGAAT
*
35495 ATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGGCACTATTCATGAATG-CCCTATT
1 ATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGGCACTATTCATGAATGTACCTATT
* * *
35559 ATTTTTTAGGGGACTTGGCAAAGTGGTAAAAGCGTATTTCCGGGGGCGCGCCTTCCATTATTTTG
66 ATGTTTGAGGGGACTTGGCAAAGTGGTGAAAGCG-ATTTCCGGGGGCGCGCCTTCCATTATTTTG
35624 TCAGAGAAT
130 TCAGAGAAT
35633 ATGTTATCATTGCCCTATTATGTCACTCATGTCCCCC-GGGGCACTATTCATGTAA-GTACCTAT
1 ATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGGCACTATTCATG-AATGTACCTAT
* * *
35696 TATGTTTGAGGGGACTTGGCAAAGTGGTGAAAGCGCATTTCTGGGGACGCGCCTTTCATTATTTT
65 TATGTTTGAGGGGACTTGGCAAAGTGGTGAAAGCG-ATTTCCGGGGGCGCGCCTTCCATTATTTT
35761 GTCAGAGAAT
129 GTCAGAGAAT
* * ** * ** *
35771 ATGTTATCATTGCCCTATTATGTAAC-CCTAAACCCTCATGGGCACTATTCATGTCA-GTACCTA
1 ATGTTATCATTGCCCTATTATGTCACTCAT-GTCCCCCGGGGGCACTATTCATG-AATGTACCTA
**
35834 TTATGTTTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCTCGGGGG-GCGCCTTCCATTATTT
64 TTATGTTTGAGGGGACTTGGCAAAGTGGTGAAAGCGATTTC-CGGGGGCGCGCCTTCCATTATTT
*
35898 TGTTAGAGAAT
128 TGTCAGAGAAT
* * * ** *
35909 ATGTTATCATTACCCTATTATGTAAC-CCTAAACCCCCGAGGAGCACTATTCAT--ATCAGTACC
1 ATGTTATCATTGCCCTATTATGTCACTCAT-GTCCCCCG-GGGGCACTATTCATGAAT--GTACC
* * **
35971 TATTATGTTTGAGGGAACTTGGCAAAGTGGTGAAAGCGCATTTCCGGGGG-GCGCCTTCGATTGG
62 TATTATGTTTGAGGGGACTTGGCAAAGTGGTGAAAGCG-ATTTCCGGGGGCGCGCCTTCCATTAT
*
36035 TATGTCAGAGAAT
126 TTTGTCAGAGAAT
* * *
36048 ATGTTATCATTGCCATATTATGTGAGTCATGTCCCCCG
1 ATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCG
36086 AAGACGCAAC
Statistics
Matches: 524, Mismatches: 54, Indels: 29
0.86 0.09 0.05
Matches are distributed among these distances:
136 1 0.00
137 18 0.03
138 227 0.43
139 183 0.35
140 8 0.02
141 75 0.14
142 12 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (138 bp):
ATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCGGGGGCACTATTCATGAATGTACCTATT
ATGTTTGAGGGGACTTGGCAAAGTGGTGAAAGCGATTTCCGGGGGCGCGCCTTCCATTATTTTGT
CAGAGAAT
Found at i:37106 original size:21 final size:21
Alignment explanation
Indices: 37055--37106 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
37045 GGTGTCATAA
* *
37055 AACCCTGCGGGCTAGGCATGT
1 AACCCTGAGGGCTAGGAATGT
37076 AA-CCTGGAGGGCTAGGAATGT
1 AACCCT-GAGGGCTAGGAATGT
37097 AACCCTGAGG
1 AACCCTGAGG
37107 ATATGGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 3 0.11
ACGTcount: A:0.25, C:0.23, G:0.35, T:0.17
Consensus pattern (21 bp):
AACCCTGAGGGCTAGGAATGT
Found at i:37130 original size:42 final size:42
Alignment explanation
Indices: 37098--37184 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
37088 TAGGAATGTA
* *
37098 ACCC-TGAGGATATGGCATATGAATTGGTGGGCTTGACATAT
1 ACCCTTGAGGAGATGGCATATGAATTGGTGGGCTGGACATAT
* * * * *
37139 ACCCTTGAGGAGATGTCATATGAATTGGAGGGTTGGGCATGT
1 ACCCTTGAGGAGATGGCATATGAATTGGTGGGCTGGACATAT
37181 ACCC
1 ACCC
37185 CTATGGCATC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 4 0.11
42 34 0.89
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (42 bp):
ACCCTTGAGGAGATGGCATATGAATTGGTGGGCTGGACATAT
Found at i:37765 original size:23 final size:22
Alignment explanation
Indices: 37725--37769 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
37715 ACTGAAACTG
37725 AAATATAAATATGCAATTCATAT
1 AAATATAAATATGCAATT-ATAT
*
37748 AAATAT-AATATTCTAATTATAT
1 AAATATAAATATGC-AATTATAT
37770 CTAGCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATAAATATGCAATTATAT
Found at i:38959 original size:30 final size:30
Alignment explanation
Indices: 38913--38988 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
38903 TAAGTAATAA
* *
38913 ATTTAAATAAATAATAATTATATAAAT-ATT
1 ATTTTAATAAAAAATAA-TATATAAATAATT
* *
38943 ATTTTAATAAAAAATAATATTTATATAATT
1 ATTTTAATAAAAAATAATATATAAATAATT
* *
38973 ATATTAATATAAAATA
1 ATTTTAATAAAAAATA
38989 TAACAACTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 7 0.18
30 32 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATTTTAATAAAAAATAATATATAAATAATT
Found at i:47325 original size:16 final size:16
Alignment explanation
Indices: 47304--47353 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
47294 ATAAGAAGAA
47304 TTTAAACTTATAAAAT
1 TTTAAACTTATAAAAT
**
47320 TTTAAAGGGT-T-AAAT
1 TTTAAA-CTTATAAAAT
47335 TTT-AACTTATAAAAT
1 TTTAAACTTATAAAAT
47350 TTTA
1 TTTA
47354 GAGGAATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 1 0.04
14 3 0.12
15 14 0.54
16 7 0.27
17 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (16 bp):
TTTAAACTTATAAAAT
Found at i:48589 original size:35 final size:35
Alignment explanation
Indices: 48546--48665 Score: 208
Period size: 35 Copynumber: 3.5 Consensus size: 35
48536 AATATCAACC
*
48546 TTGA-TCAAA-TTCAACTTTACTCGAATTCAATGAT
1 TTGAGTCAAAGTT-AACTTTACTCAAATTCAATGAT
48580 TTGAGTCAAAGTTAACTTTACTCAAATTCAATGAT
1 TTGAGTCAAAGTTAACTTTACTCAAATTCAATGAT
48615 TTGAGTCAAAGTTAACTTTACTCAAATTCAATGAT
1 TTGAGTCAAAGTTAACTTTACTCAAATTCAATGAT
48650 TTGAGTCAAAGTTAAC
1 TTGAGTCAAAGTTAAC
48666 GAGTCTGACT
Statistics
Matches: 83, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
34 4 0.05
35 77 0.93
36 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (35 bp):
TTGAGTCAAAGTTAACTTTACTCAAATTCAATGAT
Found at i:53466 original size:3 final size:3
Alignment explanation
Indices: 53451--53495 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
53441 AGTTAAAAAA
* *
53451 TAT TAT TA- AAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
53496 AGTGTGTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:54727 original size:49 final size:47
Alignment explanation
Indices: 54629--54930 Score: 175
Period size: 49 Copynumber: 6.1 Consensus size: 47
54619 GTACATTTAC
* *
54629 CTTGGAAATTGATTCTTTGTTCATATATATATATTTATTTAATGTGT
1 CTTGGAAACTGATTCTTTGTTCATATATATATATTTATTTAACGTGT
*
54676 CTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAACGTGT
1 CTTGGAAACTGATTCTTTGTTCATAT--ATATATATTTATTTAACGTGT
* ** * * * * * * * *
54725 CTTAGGAAGAAT-AACCATTGTTTATTTGTTTAACATATAGCTT-A-GTTGGAT
1 CTT-GGAA-ACTGATTCTTTGTTCATATATAT-ATATTTA-TTTAACG-T-G-T
* * * * * *
54776 ATTTGTTAAAC-GTATATATAT-AT-ATATATATATATTTATTTAATGTGT
1 -CTTG-GAAACTG-AT-TCTTTGTTCATATATATATATTTATTTAACGTGT
* * *
54824 CTTGGAAACTGATTTTTTTGTTCATATATATATATATTTGTTTAACATGT
1 CTTGGAAACTGA-TTCTTTGTTC--ATATATATATATTTATTTAACGTGT
*
54874 CTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAACGTGT
1 CTTGGAAACTGATTCTTTGTTCATAT--ATATATATTTATTTAACGTGT
54923 CTTAGGAA
1 CTT-GGAA
54931 GAATAACCAT
Statistics
Matches: 190, Mismatches: 40, Indels: 47
0.69 0.14 0.17
Matches are distributed among these distances:
46 8 0.04
47 35 0.18
48 4 0.02
49 63 0.33
50 62 0.33
51 11 0.06
52 6 0.03
53 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.48
Consensus pattern (47 bp):
CTTGGAAACTGATTCTTTGTTCATATATATATATTTATTTAACGTGT
Found at i:54818 original size:99 final size:99
Alignment explanation
Indices: 54698--54996 Score: 301
Period size: 99 Copynumber: 3.0 Consensus size: 99
54688 TTCTTTGTTC
54698 ATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAACATAT
1 ATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAACATAT
54763 AGCTTAGTTGGATATTTGTTAAACGTATATATAT
66 AGCTTAGTTGGATATTTGTTAAACGTATATATAT
* * * * * *
54797 ATATATATATATATTTATTTAATGTGTCTT-GGAA-ACT---GA-T-TTT-TTTGTTCATATATA
1 ATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTT--TA-ACA
** * ** * * * * * *
54854 TATATATTTGTTTAACATGTCTTGGAAAC-TGATTCTTTGTT
63 TATAGCTTAGTTGGATATTTGTT--AAACGT-A-TATAT-AT
54895 CATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAACATA
1 -ATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAACATA
54960 TAGCTTAGTTGGATATTTGTTAAACGTATATATAT
65 TAGCTTAGTTGGATATTTGTTAAACGTATATATAT
54995 AT
1 AT
54997 TTTTATTTAA
Statistics
Matches: 148, Mismatches: 34, Indels: 36
0.68 0.16 0.17
Matches are distributed among these distances:
91 6 0.04
92 3 0.02
93 3 0.02
94 18 0.12
95 1 0.01
96 5 0.03
97 5 0.03
98 5 0.03
99 56 0.38
100 5 0.03
101 5 0.03
102 5 0.03
103 1 0.01
104 18 0.12
105 3 0.02
106 3 0.02
107 6 0.04
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (99 bp):
ATATACATATATATTTGTTTAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAACATAT
AGCTTAGTTGGATATTTGTTAAACGTATATATAT
Found at i:54855 original size:50 final size:49
Alignment explanation
Indices: 54797--54930 Score: 205
Period size: 50 Copynumber: 2.7 Consensus size: 49
54787 GTATATATAT
* * *
54797 ATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTC
1 ATATATATATATATTTGTTTAACGTGTCTTGGAAACTGA-TTCTTTGTTC
*
54847 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ATATATATATATATTTGTTTAACGTGTCTTGGAAACTGATTCTTTGTTC
*
54896 ATATACATATATATTTGTTTAACGTGTCTTAGGAA
1 ATATATATATATATTTGTTTAACGTGTCTT-GGAA
54931 GAATAACCAT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 37 0.48
50 40 0.52
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (49 bp):
ATATATATATATATTTGTTTAACGTGTCTTGGAAACTGATTCTTTGTTC
Found at i:55095 original size:57 final size:57
Alignment explanation
Indices: 54986--55163 Score: 292
Period size: 53 Copynumber: 3.2 Consensus size: 57
54976 TTGTTAAACG
* *
54986 TATATATATATTTTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC--ATATATA
1 TATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTTTCATATATATA
55041 TATATATATATA--TATTTAATGTGTCTTGGAAACTGATTTTTTTTTCATATATATA
1 TATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTTTCATATATATA
55096 TATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTTGTTCATATATATA
1 TATATATATATATTTATTTAATGTGTCTTGGAAACTGA-TTTTTTT-TTCATATATATA
55155 TATATATAT
1 TATATATAT
55164 TTGTTTAACA
Statistics
Matches: 115, Mismatches: 2, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
53 33 0.29
55 30 0.26
57 24 0.21
58 7 0.06
59 21 0.18
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (57 bp):
TATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTTTCATATATATA
Found at i:55301 original size:2 final size:2
Alignment explanation
Indices: 55225--55283 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
55215 GCTTAGCTGG
55225 AT AT AT AT AT 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
55267 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
55284 AATTATTAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55408 original size:24 final size:24
Alignment explanation
Indices: 55379--55425 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
55369 TTTATATTCT
55379 TTATCATTTATTTAATAAGTATAG
1 TTATCATTTATTTAATAAGTATAG
55403 TTATCATTTATTTAATAAGTATA
1 TTATCATTTATTTAATAAGTATA
55426 ATGTTCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (24 bp):
TTATCATTTATTTAATAAGTATAG
Found at i:67188 original size:14 final size:14
Alignment explanation
Indices: 67167--67237 Score: 78
Period size: 14 Copynumber: 5.2 Consensus size: 14
67157 AAAAAGGAAC
*
67167 AAAT-AAAAGATGA
1 AAATGAAAAAATGA
67180 AAATGAAAAAATGA
1 AAATGAAAAAATGA
67194 AAA-GAAAAAAATGA
1 AAATG-AAAAAATGA
*
67208 AAATGAAAAAA-AA
1 AAATGAAAAAATGA
67221 GAAATGAAAAAAT-A
1 -AAATGAAAAAATGA
67235 AAA
1 AAA
67238 AGAGAAAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 9 0.18
14 41 0.80
15 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (14 bp):
AAATGAAAAAATGA
Found at i:67189 original size:28 final size:28
Alignment explanation
Indices: 67156--67249 Score: 86
Period size: 28 Copynumber: 3.3 Consensus size: 28
67146 GCTTGAAGAA
*
67156 AAAAAAGGAACAA-ATAAAAGATGAAAATG
1 AAAAAAGGAA-AAGA-AAAAAATGAAAATG
*
67185 AAAAAATGAAAAGAAAAAAATGAAAATG
1 AAAAAAGGAAAAGAAAAAAATGAAAATG
* * *
67213 AAAAAAAAGAAATG-AAAAAAT-AAAAAG
1 -AAAAAAGGAAAAGAAAAAAATGAAAATG
67240 AGAAAAAGGA
1 A-AAAAAGGA
67250 GGGTTTGAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.02
27 12 0.21
28 22 0.39
29 21 0.38
ACGTcount: A:0.74, C:0.01, G:0.16, T:0.09
Consensus pattern (28 bp):
AAAAAAGGAAAAGAAAAAAATGAAAATG
Found at i:67210 original size:20 final size:20
Alignment explanation
Indices: 67187--67230 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
67177 TGAAAATGAA
67187 AAAATGAAAAGAAAA-AAATG
1 AAAATGAAAA-AAAAGAAATG
67207 AAAATGAAAAAAAAGAAATG
1 AAAATGAAAAAAAAGAAATG
67227 AAAA
1 AAAA
67231 AATAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
AAAATGAAAAAAAAGAAATG
Found at i:67216 original size:34 final size:35
Alignment explanation
Indices: 67158--67238 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 35
67148 TTGAAGAAAA
* * *
67158 AAAAGGAACAAATAAAAGATGAAAATGAAA-AAATG
1 AAAAGAAAAAAATAAAAGATGAAAA-AAAAGAAATG
*
67193 AAAAGAAAAAAATGAAA-ATGAAAAAAAAGAAATG
1 AAAAGAAAAAAATAAAAGATGAAAAAAAAGAAATG
67227 AAAA-AATAAAAA
1 AAAAGAA-AAAAA
67239 GAGAAAAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 5 0.12
34 21 0.52
35 14 0.35
ACGTcount: A:0.75, C:0.01, G:0.14, T:0.10
Consensus pattern (35 bp):
AAAAGAAAAAAATAAAAGATGAAAAAAAAGAAATG
Found at i:67237 original size:20 final size:20
Alignment explanation
Indices: 67180--67244 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
67170 TAAAAGATGA
*
67180 AAATGAAAAAATGAAAAGAAAA
1 AAATGAAAAAAT-AAAA-AAAG
*
67202 AAATGAAAATGA-AAAAAAAG
1 AAATGAAAA-AATAAAAAAAG
*
67222 AAATGAAAAAATAAAAAGAG
1 AAATGAAAAAATAAAAAAAG
67242 AAA
1 AAA
67245 AAGGAGGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 22 0.59
21 4 0.11
22 9 0.24
23 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
AAATGAAAAAATAAAAAAAG
Found at i:67244 original size:15 final size:15
Alignment explanation
Indices: 67184--67246 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 15
67174 AGATGAAAAT
*
67184 GAAAAAATGAAAAGA
1 GAAAAAATAAAAAGA
*
67199 -AAAAAATGAAAATGA
1 GAAAAAAT-AAAAAGA
* *
67214 -AAAAAA-AGAAA-T
1 GAAAAAATAAAAAGA
67226 GAAAAAATAAAAAGA
1 GAAAAAATAAAAAGA
67241 GAAAAA
1 GAAAAA
67247 GGAGGGTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
13 9 0.24
14 11 0.30
15 17 0.46
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (15 bp):
GAAAAAATAAAAAGA
Found at i:67245 original size:14 final size:13
Alignment explanation
Indices: 67179--67246 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 13
67169 ATAAAAGATG
*
67179 AAAATGAAAAAAT
1 AAAAAGAAAAAAT
*
67192 GAAAAGAAAAAAAT
1 AAAAAG-AAAAAAT
*
67206 GAAAATGAAAAAA-
1 -AAAAAGAAAAAAT
67219 AAGAAATGAAAAAAT
1 AA-AAA-GAAAAAAT
67234 AAAAAGAGAAAAA
1 AAAAAGA-AAAAA
67247 GGAGGGTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
12 2 0.05
13 8 0.18
14 28 0.64
15 6 0.14
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAAAAT
Found at i:68735 original size:104 final size:103
Alignment explanation
Indices: 68468--68749 Score: 316
Period size: 104 Copynumber: 2.7 Consensus size: 103
68458 CTCGCTTGAG
*
68468 GGATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCA-TCATAAAGGAGAAAGTTCATA
1 GGATCAACATTTCCAA--AAGAGTTCATAATGAGAAGAACTCATTC--AAAGGAGAAAGTTCATA
* * * *
68532 ATGAGAAGAACTTGTTCCTTTCAAATTCACCACAGATGGAGGT
62 ATGAGAA-AACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
* * ** * *
68575 GAACCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
1 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATTC-AAAGGAGAAAGTTCATAATG
* * **
68640 AGAAAACATGTT-CTTTCTAAGTCCACCGCAAAAGGATTT
65 AGAAAACATGTTCCTTTC-AAATCCACCACAAAAGGAGGT
* * *
68679 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATTCACGAGAAAAAAGTTCATAATG
1 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATTCA-AAGGAGAAAGTTCATAATG
68744 AGAAAA
65 AGAAAA
68750 ACTTGTTCAA
Statistics
Matches: 148, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
103 6 0.04
104 81 0.55
105 49 0.33
106 1 0.01
107 11 0.07
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (103 bp):
GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATTCAAAGGAGAAAGTTCATAATGA
GAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
Found at i:68901 original size:3 final size:3
Alignment explanation
Indices: 68895--68952 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
68885 ATTATTAAAA
68895 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
68943 TA- TAT TAT TA
1 TAT TAT TAT TA
68953 AGTGTGTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:70157 original size:46 final size:47
Alignment explanation
Indices: 70091--70191 Score: 136
Period size: 48 Copynumber: 2.1 Consensus size: 47
70081 GTACATTTAC
* *
70091 CTTGG-AATTGATTCTTTGTTCATAT-ATATATATTAT-TTAATGTGT
1 CTTGGAAACTGATTCTTTGTTCATATAATATATATT-TGTTAACGTGT
70136 CTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTAACGTGT
1 CTTGGAAACTGATTCTTTGTTCATATA-ATATATATTTGTTAACGTGT
70184 CTTAGGAA
1 CTT-GGAA
70192 GAATAACCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
45 5 0.10
46 19 0.39
47 1 0.02
48 20 0.41
49 4 0.08
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.48
Consensus pattern (47 bp):
CTTGGAAACTGATTCTTTGTTCATATAATATATATTTGTTAACGTGT
Found at i:70305 original size:51 final size:48
Alignment explanation
Indices: 70250--70383 Score: 182
Period size: 51 Copynumber: 2.8 Consensus size: 48
70240 AAACGTATAT
* *
70250 ATATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATATTTGTTTAACGTGTCTTGGAAACTGA---TTTGTTC
*
70301 ATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTGTTC
1 ATATATATATATATATTTGTTTAACGTGTCTTGGAAACTGATTTGTTC
*
70349 --ATATACATATATATTTGTTTAACGTGTCTTAGGAA
1 ATATATATATATATATTTGTTTAACGTGTCTT-GGAA
70384 GAATAACCAT
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
46 28 0.36
47 4 0.05
48 7 0.09
51 38 0.49
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (48 bp):
ATATATATATATATATTTGTTTAACGTGTCTTGGAAACTGATTTGTTC
Found at i:70491 original size:2 final size:2
Alignment explanation
Indices: 70486--70513 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
70476 TTTTTTGTTC
70486 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
70514 TAATGTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70509 original size:58 final size:59
Alignment explanation
Indices: 70439--70557 Score: 204
Period size: 58 Copynumber: 2.0 Consensus size: 59
70429 TTGTTAAACG
* *
70439 TATATATATATATTTATTAATGTGTCTTGGAAACTGA-TTTTTTGTTCATATATATATA
1 TATATATATATATATATTAATGTGTCTTGGAAACTGATTTTTTTGTTAATATATATATA
70497 TATATATATATATATATTAATGTGTCTTGGAAACTGATTTTTTTTGTTAATATATATATA
1 TATATATATATATATATTAATGTGTCTTGGAAACTGA-TTTTTTTGTTAATATATATATA
70557 T
1 T
70558 TTGTTTAACA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
58 36 0.63
60 21 0.37
ACGTcount: A:0.34, C:0.04, G:0.10, T:0.52
Consensus pattern (59 bp):
TATATATATATATATATTAATGTGTCTTGGAAACTGATTTTTTTGTTAATATATATATA
Found at i:70604 original size:195 final size:193
Alignment explanation
Indices: 70112--70623 Score: 692
Period size: 195 Copynumber: 2.6 Consensus size: 193
70102 TTCTTTGTTC
*
70112 ATATATATATATTAT-TTAATGTGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTTG-
1 ATATATATATATTATATTAATGTGTCTTGGAAACTGATTTTTTGTT-A-ATACATATATATTTGT
70175 TTAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAAC-ATAGCTTAGTTGGATATTTGT
64 TTAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAACTATAGCTTAGTTGGATATTTGT
70239 TAAACGTATATATATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATA
129 TAAACG-------ATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATA
70304 TATATAT
187 TATATAT
* * **
70311 ATATAT-T-TGTT-TA--ACA--TGTCTTGGAAACTGATTTGTTCAT-ATACATATATATTTGTT
1 ATATATATATATTATATTA-ATGTGTCTTGGAAACTGATTTTTTGTTAATACATATATATTTGTT
70368 TAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAACATATAGCTTAGTTGGATATTTGT
65 TAACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAAC-TATAGCTTAGTTGGATATTTGT
70433 TAAACG-TATATATATATATTTA-TTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATAT
129 TAAACGATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATAT
*
70496 ATATATATATATATATATTAATGTGTCTTGGAAACTGATTTTTTTTGTTAATATATATATATTTG
1 ATATATATATAT-TATATTAATGTGTCTTGGAAACTGA--TTTTTTGTTAATACATATATATTTG
* ** *
70561 TTTAACATGTCTTAGGAAGAATAGGCATAT-TTTATTTGTTTAACGTATAGCTTAGCTGGATAT
63 TTTAACGTGTCTTAGGAAGAATAACCAT-TGTTTATTTGTTTAAC-TATAGCTTAGTTGGATAT
70624 ATATATATAT
Statistics
Matches: 281, Mismatches: 15, Indels: 38
0.84 0.04 0.11
Matches are distributed among these distances:
185 47 0.17
186 17 0.06
187 2 0.01
188 1 0.00
189 2 0.01
190 1 0.00
191 16 0.06
192 58 0.21
194 53 0.19
195 71 0.25
196 3 0.01
197 3 0.01
198 1 0.00
199 6 0.02
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.47
Consensus pattern (193 bp):
ATATATATATATTATATTAATGTGTCTTGGAAACTGATTTTTTGTTAATACATATATATTTGTTT
AACGTGTCTTAGGAAGAATAACCATTGTTTATTTGTTTAACTATAGCTTAGTTGGATATTTGTTA
AACGATATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATAT
Found at i:79425 original size:30 final size:30
Alignment explanation
Indices: 79390--79495 Score: 162
Period size: 30 Copynumber: 3.5 Consensus size: 30
79380 AGGTTTGTAT
79390 TATATAATTAATATAAAAATATAAAATA-TA
1 TATATAATTAATATAAAAA-ATAAAATAGTA
79420 TATATAATTAATATAAAAAATAAAATAGTA
1 TATATAATTAATATAAAAAATAAAATAGTA
*
79450 TATATAATTAATAT-AAAAATAAAATATTA
1 TATATAATTAATATAAAAAATAAAATAGTA
79479 TATATAATATATATATA
1 TATATAAT-TA-ATATA
79496 TATATATATA
Statistics
Matches: 71, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
29 30 0.42
30 37 0.52
31 4 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (30 bp):
TATATAATTAATATAAAAAATAAAATAGTA
Found at i:79484 original size:2 final size:2
Alignment explanation
Indices: 79473--79505 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
79463 TAAAAATAAA
79473 AT AT -T AT AT AT A- 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
79506 ATCGGGACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80152 original size:21 final size:21
Alignment explanation
Indices: 80126--80173 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
80116 GAGAAATAAT
80126 GATACTACTAAATGGAGTATC
1 GATACTACTAAATGGAGTATC
80147 GATACTACTAAATGGAGTATC
1 GATACTACTAAATGGAGTATC
80168 GATACT
1 GATACT
80174 CTATGAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (21 bp):
GATACTACTAAATGGAGTATC
Done.