Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000869.1 Hibiscus syriacus cultivar Beakdansim tig00001680_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: 108642
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:634 original size:3 final size:3
Alignment explanation
Indices: 628--682 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
618 ATTTTAAAAT
* *
628 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
674 TTA ATA TTA
1 TTA TTA TTA
683 CAAAACCCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2188 original size:138 final size:136
Alignment explanation
Indices: 2038--2341 Score: 316
Period size: 138 Copynumber: 2.2 Consensus size: 136
2028 TTGTTTATTC
* * *
2038 AATAAAAATCTTATTTATAAATTTAATTTTATAAAT-TACTTTTAAGAAAATAAACATATTTTGA
1 AATAAACATCTTATTTATAAATTTAATTATATAAATCTACTTTTAAG---AT-AA-ATATTTTAA
* * *
2102 TATGTATTTATTATTTAATATCTAA-GAAAGAGCTG-TTAAAATACCTAGAAG-TCATTTTCTGA
61 TATGTATTTATTATTTAATATCAAAGGAAAGAACTGCTTAAAACACCTAGAAGCT-ATTTTCTGA
2164 TA-TTCTTAAATA
125 TATTTC-TAAATA
** * * * *
2176 AATAAATGTCTTACTTTTATAAATTGT-A-TATATTAATCTATTTTTTAGATAAATGTTTTAATA
1 AATAAACATCTTA--TTTATAAATT-TAATTATATAAATCTACTTTTAAGATAAATATTTTAATA
* *
2239 TTTATTTATTTTTTAATATCAAAGGAAAGAACTGTCTTAAAACACCTAGAAGCTATTTTCTGATA
63 TGTATTTATTATTTAATATCAAAGGAAAGAACTG-CTTAAAACACCTAGAAGCTATTTTCTGATA
2304 TTTCTAAATA
127 TTTCTAAATA
*
2314 AATAAACATCTTATTTATATAAATTAAT
1 AATAAACATCTTATTTATA-AATTTAAT
2342 AATTTACTTA
Statistics
Matches: 138, Mismatches: 16, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
135 29 0.21
136 18 0.13
137 6 0.04
138 54 0.39
139 11 0.08
140 19 0.14
141 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (136 bp):
AATAAACATCTTATTTATAAATTTAATTATATAAATCTACTTTTAAGATAAATATTTTAATATGT
ATTTATTATTTAATATCAAAGGAAAGAACTGCTTAAAACACCTAGAAGCTATTTTCTGATATTTC
TAAATA
Found at i:7427 original size:18 final size:20
Alignment explanation
Indices: 7390--7427 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
7380 CACGGAATGT
*
7390 AAGATTATCAATACGAATAA
1 AAGATTATCAAGACGAATAA
7410 AAGATTATC-AGA-GAATAA
1 AAGATTATCAAGACGAATAA
7428 GATTACTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.24
Consensus pattern (20 bp):
AAGATTATCAAGACGAATAA
Found at i:13151 original size:21 final size:21
Alignment explanation
Indices: 13122--13166 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13112 ATTTATCGTG
* * *
13122 ATTGTGACCGTCGCGGGCGCT
1 ATTGAGACCATCGCGAGCGCT
*
13143 ATTGAGACCATCGCGATCGCT
1 ATTGAGACCATCGCGAGCGCT
13164 ATT
1 ATT
13167 ACGGTCTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (21 bp):
ATTGAGACCATCGCGAGCGCT
Found at i:14429 original size:18 final size:20
Alignment explanation
Indices: 14397--14437 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
14387 GCCTTTTAAC
14397 ATTTTTAATGATATT-ATCG
1 ATTTTTAATGATATTGATCG
*
14416 ATTTTTAAT-TTATTGATCG
1 ATTTTTAATGATATTGATCG
14435 ATT
1 ATT
14438 AATCAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (20 bp):
ATTTTTAATGATATTGATCG
Found at i:21900 original size:201 final size:199
Alignment explanation
Indices: 21550--21919 Score: 505
Period size: 201 Copynumber: 1.8 Consensus size: 199
21540 GTAGTTGTCA
** * * *
21550 GATGATCATTGGTTTGGTATGCTACTGATTCTTTGTTATTATTTGCGATCGTTTAGTTGTCATTA
1 GATGATCATTGGTTTGGTATGCTACTGAAACTTTGTTATTATTTGCGATCATTTAATCGTCATTA
* * * *
21615 TCCGTAATAAACTGTCGTACGAGAAGGTCTCGATTCTAACCCAGAAAAGCACACCATACGGTGAA
66 TCCGTAATAAACTCTCGTACGAGAAGGCCTCGACTCGAACCCAGAAAAGCACACCATACGGTGAA
* *
21680 GAATTGTTGCAACGTTGGTGGACATCTAATGAGGACAATCCCTGCAGCTACAGATAAAAATTGGT
131 GAATTCTTACAACGTTGGTGGACATCTAATGAGGACAATCCCTGCAGCTACAGATAAAAATTGGT
21745 GTTT
196 GTTT
*
21749 GATGATCATTGGTTT-GTATGCT-CATGTAAAACTTTGTTATTATTTTGCGGTCATTTAATCGTC
1 GATGATCATTGGTTTGGTATGCTAC-TG--AAACTTTGTTATTA-TTTGCGATCATTTAATCGTC
* ** *
21812 GTTATCCGTAATAAACTCTCGTACGAGAAGGCCTCGACTCGAACCTGGAAAGGCACACCATA-GG
62 ATTATCCGTAATAAACTCTCGTACGAGAAGGCCTCGACTCGAACCCAGAAAAGCACACCATACGG
*
21876 ATGAAG-ATTCCTTACAATGTTGGTGGACATCTAATGAGGACAAT
127 -TGAAGAATT-CTTACAACGTTGGTGGACATCTAATGAGGACAAT
21920 AATTGCAGCT
Statistics
Matches: 148, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
197 1 0.01
198 9 0.06
199 15 0.10
200 17 0.11
201 106 0.72
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (199 bp):
GATGATCATTGGTTTGGTATGCTACTGAAACTTTGTTATTATTTGCGATCATTTAATCGTCATTA
TCCGTAATAAACTCTCGTACGAGAAGGCCTCGACTCGAACCCAGAAAAGCACACCATACGGTGAA
GAATTCTTACAACGTTGGTGGACATCTAATGAGGACAATCCCTGCAGCTACAGATAAAAATTGGT
GTTT
Found at i:44858 original size:14 final size:15
Alignment explanation
Indices: 44835--44882 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
44825 ACGTTTAGTA
*
44835 TTTAAATTATTT-AT
1 TTTAATTTATTTAAT
44849 TTTAATTTATTTTAATT
1 TTTAATTTA-TTTAA-T
44866 TTTAATTT-TTTAAT
1 TTTAATTTATTTAAT
44880 TTT
1 TTT
44883 TTAAAAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 12 0.40
15 8 0.27
16 1 0.03
17 9 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTAATTTATTTAAT
Found at i:44876 original size:15 final size:17
Alignment explanation
Indices: 44848--44883 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
44838 AAATTATTTA
44848 TTTTAATTTATTTTAAT
1 TTTTAATTTATTTTAAT
44865 TTTTAA-TT-TTTTAAT
1 TTTTAATTTATTTTAAT
44880 TTTT
1 TTTT
44884 TAAAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 2 0.11
17 6 0.32
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTAATTTATTTTAAT
Found at i:44877 original size:8 final size:8
Alignment explanation
Indices: 44848--44886 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
44838 AAATTATTTA
44848 TTTTAATTT
1 TTTTAA-TT
44857 ATTTTAA-T
1 -TTTTAATT
44865 TTTTAATT
1 TTTTAATT
44873 TTTTAATT
1 TTTTAATT
44881 TTTTAA
1 TTTTAA
44887 AAAGTATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.21
8 16 0.57
10 6 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTAATT
Found at i:54018 original size:14 final size:14
Alignment explanation
Indices: 54001--54046 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
53991 AAACAAACAC
* *
54001 AAACGAACAGACAT
1 AAACGAACACAAAT
54015 AAACGAACACAAAT
1 AAACGAACACAAAT
*
54029 AAACGAACATAAAT
1 AAACGAACACAAAT
54043 AAAC
1 AAAC
54047 ATAAACGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.63, C:0.20, G:0.09, T:0.09
Consensus pattern (14 bp):
AAACGAACACAAAT
Found at i:54038 original size:24 final size:24
Alignment explanation
Indices: 53989--54052 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
53979 CGTATAAATG
*
53989 ATAAACAAACACAAACGAACAGAC
1 ATAAACAAACACAAACAAACAGAC
* *
54013 ATAAACGAACACAAATAAAC-GAAC
1 ATAAACAAACACAAACAAACAG-AC
* *
54037 ATAAATAAACATAAAC
1 ATAAACAAACACAAAC
54053 GAATAAACAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 1 0.03
24 31 0.97
ACGTcount: A:0.64, C:0.20, G:0.06, T:0.09
Consensus pattern (24 bp):
ATAAACAAACACAAACAAACAGAC
Found at i:58017 original size:12 final size:12
Alignment explanation
Indices: 58000--58039 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
57990 TTAACCTCAG
58000 CAACCATGTCCT
1 CAACCATGTCCT
58012 CAACCATGTCCT
1 CAACCATGTCCT
58024 CAACCA-GTTCCT
1 CAACCATG-TCCT
58036 CAAC
1 CAAC
58040 TTGAGGATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 1 0.04
12 26 0.96
ACGTcount: A:0.28, C:0.42, G:0.07, T:0.23
Consensus pattern (12 bp):
CAACCATGTCCT
Found at i:59368 original size:40 final size:41
Alignment explanation
Indices: 59323--59402 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 41
59313 AATGAGCCAT
*
59323 TTGTTCGTATTCGTTCATTTAAT-TAAACGAACATAAAAAC
1 TTGTTCATATTCGTTCATTTAATATAAACGAACATAAAAAC
* *
59363 TTGTTCATATTTGTTCGTTTAATAAATAAACGAACATAAA
1 TTGTTCATATTCGTTCATTTAAT--ATAAACGAACATAAA
59403 CAAACTTCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 20 0.59
43 14 0.41
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (41 bp):
TTGTTCATATTCGTTCATTTAATATAAACGAACATAAAAAC
Found at i:59779 original size:17 final size:17
Alignment explanation
Indices: 59731--59784 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
59721 ATATATATAA
*
59731 TAAAATTAAATATTTT-T
1 TAAAATTTAAT-TTTTAT
*
59748 TATAGATTT-ATTTTTAT
1 TA-AAATTTAATTTTTAT
59765 TAAAATTTAATTTTTAT
1 TAAAATTTAATTTTTAT
59782 TAA
1 TAA
59785 CATCAAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.29
17 18 0.58
18 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAAAATTTAATTTTTAT
Found at i:65586 original size:15 final size:16
Alignment explanation
Indices: 65563--65597 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
65553 AACTTTTATT
65563 ATTAATTTGTAAT-AA
1 ATTAATTTGTAATGAA
*
65578 ATTAGTTTGTAATGAA
1 ATTAATTTGTAATGAA
65594 ATTA
1 ATTA
65598 TTTTAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (16 bp):
ATTAATTTGTAATGAA
Found at i:65864 original size:127 final size:127
Alignment explanation
Indices: 65631--65861 Score: 331
Period size: 127 Copynumber: 1.8 Consensus size: 127
65621 TCATCATGTT
* * *
65631 GACATGATGAGTCCCGTTATTTTTAATTATTTTAAATTAAAAATAATTGCTTAATTTTTAAAATA
1 GACATGATGAGTCCCGCTATTTTTAATTATTTTAAATTAAAAATAATTGCTTAATTTTAAAAAAA
* *
65696 TATATTTTATATAGAATCATCACATCAATGTGACAATTTCTTCCAATGAAAGTCTTCACGTC
66 AATATTTTATATAGAATCATCACATCAACGTGACAATTTCTTCCAATGAAAGTCTTCACGTC
* *
65758 GACATGATGAGTCCCGCTATTTTTTAATTATTTTAAATTTTAAAA-AATTG-TTTATTTTAAAAA
1 GACATGATGAGTCCCGCTA-TTTTTAATTATTTTAAA-TTAAAAATAATTGCTTAATTTTAAAAA
* * *
65821 AAAATATTTTATATGGAATTATCACATCGACGTGACGAATT
64 AAAATATTTTATATAGAATCATCACATCAACGTGAC-AATT
65862 CTTAAAAATA
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
127 59 0.65
128 26 0.29
129 6 0.07
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (127 bp):
GACATGATGAGTCCCGCTATTTTTAATTATTTTAAATTAAAAATAATTGCTTAATTTTAAAAAAA
AATATTTTATATAGAATCATCACATCAACGTGACAATTTCTTCCAATGAAAGTCTTCACGTC
Found at i:67232 original size:23 final size:22
Alignment explanation
Indices: 67195--67237 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
67185 GTTTTTCTTT
67195 GTAAAGATAGAGAGAAATGGAAA
1 GTAAAGATAGAGAG-AATGGAAA
67218 GTAAAGA-AGACGAGAATGGA
1 GTAAAGATAGA-GAGAATGGA
67238 GGACAACACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.53, C:0.02, G:0.33, T:0.12
Consensus pattern (22 bp):
GTAAAGATAGAGAGAATGGAAA
Found at i:80885 original size:30 final size:28
Alignment explanation
Indices: 80849--81052 Score: 121
Period size: 29 Copynumber: 7.0 Consensus size: 28
80839 TAAATTCATA
*
80849 TCTTAACATTAAAAATATGTTTTATTTTT
1 TCTTAAC-TTAAAAATATATTTTATTTTT
* * *
80878 GTCTTAACTCATTAAATACATTTT-TTTTT
1 -TCTTAACTTA-AAAATATATTTTATTTTT
* *
80907 ATTTTAACTTAAAAATATATTTTAGTCTTAT
1 -TCTTAACTTAAAAATATATTTTA-T-TTTT
*
80938 TC-TAACTTAAAAATATATTTTAATCTTAT
1 TCTTAACTTAAAAATATATTTT-AT-TTTT
*
80967 T-TTATTCTTAAAAATATATTTTAATTTTAT
1 TCTTA-ACTTAAAAATATATTTT-ATTTT-T
* * * *
80997 T-TTAGCTCAAAAA-GTATTTTGTTTTT
1 TCTTAACTTAAAAATATATTTTATTTTT
* * *
81023 ATCTTAACTTATGAGATATATTTTACTTTT
1 -TCTTAACTTA-AAAATATATTTTATTTTT
81053 ATTTTAATTT
Statistics
Matches: 138, Mismatches: 24, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.01
27 5 0.04
28 22 0.16
29 54 0.39
30 53 0.38
31 3 0.02
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (28 bp):
TCTTAACTTAAAAATATATTTTATTTTT
Found at i:80937 original size:29 final size:29
Alignment explanation
Indices: 80851--81064 Score: 171
Period size: 30 Copynumber: 7.3 Consensus size: 29
80841 AATTCATATC
* * * *
80851 TTAACATTAAAAATATGTTTTATTTTTGTC
1 TTAAC-TTAAAAATATATTTTAATTTTATT
* * * *
80881 TTAACTCATTAAATACATTTT-TTTTTATT
1 TTAACTTA-AAAATATATTTTAATTTTATT
* *
80910 TTAACTTAAAAATATATTTTAGTCTTATT
1 TTAACTTAAAAATATATTTTAATTTTATT
* *
80939 CTAACTTAAAAATATATTTTAATCTTATT
1 TTAACTTAAAAATATATTTTAATTTTATT
*
80968 TTATTCTTAAAAATATATTTTAATTTTATT
1 TTA-ACTTAAAAATATATTTTAATTTTATT
* * * ** *
80998 TTAGCTCAAAAA-GTATTTTGTTTTTATC
1 TTAACTTAAAAATATATTTTAATTTTATT
* * *
81026 TTAACTTATGAGATATATTTTACTTTTATT
1 TTAACTTA-AAAATATATTTTAATTTTATT
*
81056 TTAATTTAA
1 TTAACTTAA
81065 GATATCTTTT
Statistics
Matches: 147, Mismatches: 32, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
28 28 0.19
29 59 0.40
30 60 0.41
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTAATTTTATT
Found at i:81157 original size:29 final size:26
Alignment explanation
Indices: 81084--81164 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 26
81074 TTAAAAATCA
*
81084 ATATAA-AA-AATATATTTATAAGTT
1 ATATAAGAATAATATATTTTTAAGTT
*
81108 AATATAAGAATAATATTTTTTTAAAGTT
1 -ATATAAGAATAATATATTTTT-AAGTT
81136 ATATAAGAATAAGATATATTTTTAAGTT
1 ATATAAGAAT-A-ATATATTTTTAAGTT
81164 A
1 A
81165 AAATAAGAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
25 6 0.12
26 2 0.04
27 19 0.40
28 12 0.25
29 9 0.19
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.43
Consensus pattern (26 bp):
ATATAAGAATAATATATTTTTAAGTT
Found at i:81170 original size:29 final size:27
Alignment explanation
Indices: 81083--81248 Score: 114
Period size: 26 Copynumber: 6.2 Consensus size: 27
81073 TTTAAAAATC
*
81083 AATATAA-AA-AATATATTTATAAGTT
1 AATATAAGAATAATATATTTTTAAGTT
*
81108 AATATAAGAATAATATTTTTTTAAAGTT
1 AATATAAGAATAATATATTTTT-AAGTT
81136 -ATATAAGAATAAGATATATTTTTAAGTT
1 AATATAAGAAT-A-ATATATTTTTAAGTT
* * **
81164 AAAATAAGAGTAA-ACT-TTTTTAAAAT
1 AATATAAGAATAATA-TATTTTTAAGTT
* * * *
81190 AAAATAA-AAAAATATATTTAATAATTT
1 AATATAAGAATAATATATTT-TTAAGTT
* *
81217 AAGATAAAAATAAT-T-TTTTTAATGTT
1 AATATAAGAATAATATATTTTTAA-GTT
81243 AATATA
1 AATATA
81249 TAAATTTAAT
Statistics
Matches: 112, Mismatches: 17, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
25 14 0.12
26 32 0.29
27 32 0.29
28 17 0.15
29 17 0.15
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (27 bp):
AATATAAGAATAATATATTTTTAAGTT
Found at i:84897 original size:18 final size:18
Alignment explanation
Indices: 84853--84900 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
84843 TTTTTAAAGA
* *
84853 AAATATATAAATATTTTCC
1 AAATATAT-AATATTATAC
84872 AAAT-TATAATATTATAC
1 AAATATATAATATTATAC
84889 AAATATATAATA
1 AAATATATAATA
84901 CGTATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 12 0.46
18 10 0.38
19 4 0.15
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:94126 original size:15 final size:15
Alignment explanation
Indices: 94106--94143 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
94096 GTTCCAGTCC
94106 CAGAAGAAACAAAGA
1 CAGAAGAAACAAAGA
94121 CAGAAGAAACAAAGA
1 CAGAAGAAACAAAGA
94136 CAGAAGAA
1 CAGAAGAA
94144 CTCCAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.66, C:0.13, G:0.21, T:0.00
Consensus pattern (15 bp):
CAGAAGAAACAAAGA
Done.