Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005150.1 Hibiscus syriacus cultivar Beakdansim tig00011605_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: 126880
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
File 2 of 2
Found at i:94635 original size:22 final size:22
Alignment explanation
Indices: 94607--94657 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 22
94597 TTTTTGCTTT
94607 TTATATAAAATGATAATATAGTTA
1 TTATATAAAATGATAA-AT-GTTA
*
94631 TTATATAAAATGATAAATTTTA
1 TTATATAAAATGATAAATGTTA
94653 TTATA
1 TTATA
94658 AATGCAGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 8 0.31
23 2 0.08
24 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (22 bp):
TTATATAAAATGATAAATGTTA
Found at i:95134 original size:33 final size:33
Alignment explanation
Indices: 95092--95158 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
95082 AAATAGATGG
95092 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
* *
95125 AGTGGTGAAAGAAGTTGAGGTGTTGAGTGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
95158 A
1 A
95159 CTAAAGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.45, T:0.25
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
Found at i:96957 original size:19 final size:19
Alignment explanation
Indices: 96911--96959 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
96901 AATCTAGGGT
*
96911 TAATTTTGAATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
96930 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
96949 TAATTTTGTAT
1 TAATTTTGTAT
96960 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:98011 original size:201 final size:201
Alignment explanation
Indices: 97408--98754 Score: 2029
Period size: 201 Copynumber: 6.8 Consensus size: 201
97398 GTAAACAGAT
* * *
97408 GTGTCGATACATTTATAAAACGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATA
1 GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
97473 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTTTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
*
97538 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTGGGTGCACG
131 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
97603 CATAAA
196 CATAAA
* * * *
97609 GTGTCGATACATTTATAAAAAGTATAGATCCCAAAAACATTGAAACTCATAATTATAATGTAATA
1 GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
97674 GGTAATTTTTCAATGTAACCGGTATAAATATATC-GTTTTAAGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* *
97738 ATCGACACTTTTTATGTTTGTGTCGATACTTTTTTTCCAGAATGAATGCCCAAACTAGGTGCACG
131 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
97803 CATAAA
196 CATAAA
* *
97809 GTGGCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
** *
97874 GGTAATTTTTCAATGTAACTAGTATAAATATACCGGTTTTATGAGAGAATATGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* *
97939 ATCAACACTTTTTAAGTTTGTGTCGATACTTTTTGTCTAGAATGAATGCCCAAACTAGGTGCACG
131 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
98004 CATAAA
196 CATAAA
* * * * * *
98010 GTGTCAATATATTTATAAAAACTATCGATCTCAAAAATATCGAAACTCATAATTATAAAGTAATA
1 GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
98075 CGTAATTTTTCAATGTAACCGGTATAAATATATCGGTTTTATGAGAGAATAGGTATACATAATGC
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* *
98140 ATCGACACTTTTTAAGTTTGTATCGATACTTTTTGTCCAGAATGAATGCCCGAACTAGGTGCACG
131 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
*
98205 CAAAAA
196 CATAAA
*
98211 GTGTCGATATATTTATAAAAA--A---AT---------ATCGAAACCCATAATTATAATGTTATA
1 GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
98262 GGTAATTTTTCAATGAAACCGGTATAAATATACAGGTTTTATGAGAGAATATGTCTCCATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* *
98327 ATCGACATTTTTTAAGTTTGTGTCGATACTTTTTGTCTAGAATGAATG------CTAGGTGCACG
131 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
98386 CATAAA
196 CATAAA
98392 GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
98457 GGTAATTTTTCAATGTAACCGGTATATATATACCGGTTTTATGAGAGAATAGGTCTACATATTGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * *
98522 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTTCAGAATGAATGCCCAAACTAGGTGCATG
131 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
98587 CATAAA
196 CATAAA
* *
98593 GTGTCGATA-ATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTAAAATGTAATA
1 GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
98657 GGTAAATTTCCAATGTAA-CGGTATAAATATACCAGTTTTAAGAGAAAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * *
98721 ATCGAAAATTTTTAAATTTGTGTCGATACTTTTT
131 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTT
98755 TAAATTTCAC
Statistics
Matches: 1041, Mismatches: 84, Indels: 44
0.89 0.07 0.04
Matches are distributed among these distances:
181 37 0.04
183 1 0.00
186 2 0.00
187 126 0.12
195 129 0.12
196 2 0.00
199 74 0.07
200 254 0.24
201 416 0.40
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (201 bp):
GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
CATAAA
Found at i:98499 original size:195 final size:195
Alignment explanation
Indices: 98229--98754 Score: 788
Period size: 195 Copynumber: 2.7 Consensus size: 195
98219 ATATTTATAA
* * *
98229 AAAAATATCGAAACCCATAATTATAATGTTATAGGTAATTTTTCAATGAAACCGGTATAAATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
* * * * *
98294 CAGGTTTTATGAGAGAATATGTCTCCATAATGTATCGACATTTTTTAAGTTTGTGTCGATACTTT
66 CCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACAATTTTTAAATTTGTGTCGATACTTT
98359 TTG-TCTAGAATGAATG-CTAGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTATCGATC
131 TTGTTC-AGAATGAATGACTAGGTGCACGCATAAAGTGTCGATA-ATTTATAAAAAGTATCGATC
98422 CC
194 CC
*
98424 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATATATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
* *
98489 CCGGTTTTATGAGAGAATAGGTCTACATATTGTATCGACACTTTTTAAATTTGTGTCGATACTTT
66 CCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACAATTTTTAAATTTGTGTCGATACTTT
*
98554 TTGTTCAGAATGAATGCCCAAACTAGGTGCATGCATAAAGTGTCGATAATTTATAAAAAGTATCG
131 TTGTTCAGAATGAATG-----ACTAGGTGCACGCATAAAGTGTCGATAATTTATAAAAAGTATCG
98619 ATCCC
191 ATCCC
* * * *
98624 AAAAACATCGAAACCGATAATTAAAATGTAATAGGTAAATTTCCAATGTAA-CGGTATAAATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
* * * *
98688 CCAGTTTTAAGAGAAAATAGGTCTACATAATGTATCGAAAATTTTTAAATTTGTGTCGATACTTT
66 CCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACAATTTTTAAATTTGTGTCGATACTTT
98753 TT
131 TT
98755 TAAATTTCAC
Statistics
Matches: 302, Mismatches: 22, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
195 133 0.44
196 2 0.01
199 73 0.24
200 69 0.23
201 25 0.08
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (195 bp):
AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
CCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACAATTTTTAAATTTGTGTCGATACTTT
TTGTTCAGAATGAATGACTAGGTGCACGCATAAAGTGTCGATAATTTATAAAAAGTATCGATCCC
Found at i:103263 original size:199 final size:198
Alignment explanation
Indices: 102921--104300 Score: 1781
Period size: 198 Copynumber: 7.0 Consensus size: 198
102911 TTCAGTAATC
* * * *
102921 TCCAGAATGAATGCCCAACCGAGGTGCATGAATAAAGTGTTGATGCATTTATTAAAAGTATCGAT
1 TCCAGAATGAATG-CCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGAT
* * * *
102986 CCCAAAAACATCGAATA-AGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGAATATA
64 CCCAAAAACATCGAA-ACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAA
* * ** * * *
103050 TGTATCAATTAATTAGAAAATATGTCTACGTAATATATCGACACTTTTTAAA-TTGTGTCGATAC
128 TATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATAC
103114 TTTTTG
193 TTTTTG
103120 TCCAGAATGAATGACCAACCGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGAT
1 TCCAGAATGAATG-CCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGAT
*
103185 CCCAAAAACATCGAATA-AGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAA
64 CCCAAAAACATCGAA-ACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAA
103249 TATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATAC
128 TATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATAC
*
103314 GTTTTG
193 TTTTTG
* * * * *
103320 ACCAGAATGAATGCCCAACGATGTGCACAAATAAAGTATCGATACATTTATAAAACGTATCGATC
1 TCCAGAATGAATG-CCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATC
* * *
103385 CCAAAAACATCGAAACCGATAAATATAATGTAATAGGTAAATTTTCAATATAACCGGTAGAAATA
65 CCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATA
* * * * * *
103450 TACCGGATAATTAGAGAATAGGTCTACATCATGTATCGACACTTGTGAAATTTGTGTCGATATTT
130 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTT
103515 TTTG
195 TTTG
* * **
103519 TCCAGAATGAATGCCTAA-AAGAGTGCAC-ACATAAAGTGTCGATACATTGA-AAATGGTATCGA
1 TCCAGAATGAATGCC-AACGAG-GTGCACGA-ATAAAGTGTCGATACATTTATAAAAAGTATCGA
* *
103581 TCCCAAAAACATCGAAACCGAAAATTATAATGTAATAGGTAACTTTACAATGTAACCGGTAGAAA
63 TCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAA
*
103646 TATACCGGTTAATTAGAAAATATGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATAC
128 TATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATAC
*
103711 GTTTTG
193 TTTTTG
* * * * * * ** *
103717 ACCAGAAAGAATGCCCAACGGGGTGTACGAATAAAGTATCAATACATTTA-AAATTGTATTGATC
1 TCCAGAATGAATG-CCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATC
* *
103781 TCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAACTTTACAATGTAACCGGTAGAAATA
65 CCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATA
* * * **
103846 TACCGGTTAATTAGAAAATAGGTCTACATCATTTATCGACACTTGTGGAATTTGTGTCGATACTT
130 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTT
103911 TTTG
195 TTTG
* * * * **
103915 TCTAGAATGAATGCCTAA-AAGAGTGCACGCATAAAGTGTTGATACATTTA-AAATTGTATCGAT
1 TCCAGAATGAATGCC-AACGAG-GTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGAT
* *
103978 CCCAAAAACATCGAAACTGATAATTATAATGTAATAGGTAACTTTACAATGTAACCGGTAGAAAT
64 CCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAAT
* * * * *
104043 ATACTGGTTAATTAGAAAATAAGTCTACATAATGTAT--AGACTTTTTAAATTTGCGTCGATACG
129 ATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACT
104106 TTTTG
194 TTTTG
* ** * * *
104111 ACCAGAAAAAATGCCTAACGGGGTGTACGAATAAAGTGTCAATACATTTATAAAAAGTATCGAT-
1 TCCAGAATGAATGCC-AACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATC
* * * *
104175 CCATAAACATCGAAACCGATAAATATAATATAATAGGTAAATTTTCAATGTAACCGGTAGAAATA
65 CCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATA
* *
104240 TACCGGTTAA-T------TAGGTCTACATAATGTATCGACACTATTTAAAGTTGTGTCGATACTT
130 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTT
104298 TTT
195 TTT
104301 TAAATTACCC
Statistics
Matches: 1047, Mismatches: 120, Indels: 36
0.87 0.10 0.03
Matches are distributed among these distances:
189 17 0.02
191 25 0.02
195 1 0.00
196 131 0.13
197 15 0.01
198 453 0.43
199 372 0.36
200 33 0.03
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (198 bp):
TCCAGAATGAATGCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
CAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATAT
ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTT
TTG
Found at i:105897 original size:19 final size:19
Alignment explanation
Indices: 105873--105936 Score: 119
Period size: 19 Copynumber: 3.4 Consensus size: 19
105863 TTGTAGGGGA
105873 AATTTTGTATACGATTCAT
1 AATTTTGTATACGATTCAT
105892 AATTTTGTATACGATTCAT
1 AATTTTGTATACGATTCAT
*
105911 AATTTTGTATACGATTTAT
1 AATTTTGTATACGATTCAT
105930 AATTTTG
1 AATTTTG
105937 AATGTGAATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (19 bp):
AATTTTGTATACGATTCAT
Found at i:106966 original size:15 final size:15
Alignment explanation
Indices: 106946--106981 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
106936 GTGTTTTAGT
106946 GCATTCGCGAGTGAA
1 GCATTCGCGAGTGAA
106961 GCATTCGCGAGTGAA
1 GCATTCGCGAGTGAA
106976 GCATTC
1 GCATTC
106982 ATAGACTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (15 bp):
GCATTCGCGAGTGAA
Found at i:109058 original size:200 final size:199
Alignment explanation
Indices: 108686--109207 Score: 692
Period size: 200 Copynumber: 2.6 Consensus size: 199
108676 AAAAATATGT
* *
108686 TCGATACATTT-TCTAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATAGG
1 TCGATACATTTAT-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGG
* * * * *
108750 TAAATTAACAATGTAACCGATATAAATATACCGGTTAATTACAAAACAGGTAAACATAATGTATC
65 TAAATTTACAATGTAACCGATATAAATATACCGGTTTATTAGAAAATAGGTCAACATAATGTATC
* * *
108815 GACACTTGTGGAATTTGTGTCGATACTTATTGTCAAGAATGAATGCCCAAACGAGGTGCACGCAT
130 AACACTTGTGAAATATGTGTCGATACTTATTGTCAAGAATGAATGCCC-AACGAGGTGCACGCAT
108880 AAAGTG
194 AAAGTG
* *
108886 TCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATAATGATGTAATAGGT
1 TCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
* * *
108951 AAATTTACAATGTAACCGATATAAATATACTGGTTTTATGAGAGAATAGGTCAACATAATGTATC
66 AAATTTACAATGTAACCGATATAAATATACCGG-TTTATTAGAAAATAGGTCAACATAATGTATC
* * * * * * * *
109016 AACACTTTTTAAATATGTGTCGATA-TTTTTTTCCATAATGAATGCCCAACTAGGTGCACGTATA
130 AACACTTGTGAAATATGTGTCGATACTTATTGTCAAGAATGAATGCCCAACGAGGTGCACGCATA
109080 AAGTG
195 AAGTG
* * *
109085 TCGATACATTTA--AAATTGTATTGATCCCAAAAACATCGAAAACGATAATTATAATGTAATAGG
1 TCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGG
* * * * *
109148 TAAATTTGCAATGTCACCGGTATAAATAAACCGGTTTAGTTAGAAAATAGGTCAATATAA
65 TAAATTTACAATGTAACCGATATAAATATACCGGTTTA-TTAGAAAATAGGTCAACATAA
109208 GCGCTACCTA
Statistics
Matches: 282, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
197 7 0.02
198 89 0.32
199 32 0.11
200 108 0.38
201 46 0.16
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (199 bp):
TCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
AAATTTACAATGTAACCGATATAAATATACCGGTTTATTAGAAAATAGGTCAACATAATGTATCA
ACACTTGTGAAATATGTGTCGATACTTATTGTCAAGAATGAATGCCCAACGAGGTGCACGCATAA
AGTG
Found at i:109304 original size:87 final size:87
Alignment explanation
Indices: 109202--109364 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
109192 AAATAGGTCA
* * * *
109202 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCACTACCTATTACATTATATAAGCGATACCTAATATGTTATTGAACTAGATAATATTT
109267 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
*
109289 ATATAAGCACTACCTATTACATTATATAAGCGATACCTAATATGTTATTGAACTAGATGATATTT
1 ATATAAGCACTACCTATTACATTATATAAGCGATACCTAATATGTTATTGAACTAGATAATATTT
*
109354 TCGGTTAAATG
66 CCGGTTAAATG
109365 ATATAACATA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (87 bp):
ATATAAGCACTACCTATTACATTATATAAGCGATACCTAATATGTTATTGAACTAGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:109336 original size:23 final size:23
Alignment explanation
Indices: 109286--109330 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
109276 TGCCTATTTT
*
109286 ATTATATAAGCACTACCTATTAC
1 ATTATATAAGCACTACCTAATAC
109309 ATTATATAAGCGA-TACCTAATA
1 ATTATATAAGC-ACTACCTAATA
109331 TGTTATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCACTACCTAATAC
Found at i:111577 original size:25 final size:25
Alignment explanation
Indices: 111544--111627 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 25
111534 AATAATAATA
111544 ATAATTAAACTAAAATTTCAAAATT
1 ATAATTAAACTAAAATTTCAAAATT
* * *
111569 GTGATTAAATCGAAAAATATTCTCAAAATT
1 ATAATTAAA-C--TAAA-ATT-TCAAAATT
*
111599 ATAATTAAATTAAAATTTCAAAATT
1 ATAATTAAACTAAAATTTCAAAATT
111624 ATAA
1 ATAA
111628 ACTCTCGGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
25 19 0.40
26 4 0.09
27 3 0.06
28 3 0.06
29 3 0.06
30 15 0.32
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.36
Consensus pattern (25 bp):
ATAATTAAACTAAAATTTCAAAATT
Found at i:116164 original size:22 final size:22
Alignment explanation
Indices: 116129--116170 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
116119 GAAGAACGTA
*
116129 CAAAGCATGCACATACATAGTT
1 CAAAGAATGCACATACATAGTT
*
116151 CAAAGAATGTACATACATAG
1 CAAAGAATGCACATACATAG
116171 AAACTCGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAAGAATGCACATACATAGTT
Found at i:118528 original size:19 final size:19
Alignment explanation
Indices: 118504--118541 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
118494 AAATAACTAA
118504 TTTCTAATTAATGATGGAC
1 TTTCTAATTAATGATGGAC
118523 TTTCTAATTAATGATGGAC
1 TTTCTAATTAATGATGGAC
118542 AAATTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTCTAATTAATGATGGAC
Found at i:118658 original size:60 final size:59
Alignment explanation
Indices: 118594--118730 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 59
118584 TAAAGTACAT
* ** *
118594 AAATGGTCCTCTGACTATAAGGTATTATTTTATTAAGT-CTTTCGACTATTAAAAGTTATA
1 AAATGGTCATCTGACTATAAAATA-TATTTTATTAAGTCCCTT-GACTATTAAAAGTTATA
* * *
118654 AAATGGTCATTTGACTATAAAATATGTTTTGTTAAGTCCCTTGACTATTAAAAGTTATA
1 AAATGGTCATCTGACTATAAAATATATTTTATTAAGTCCCTTGACTATTAAAAGTTATA
** *
118713 ATGTCGTCATCTGACTAT
1 AAATGGTCATCTGACTAT
118731 TTATTATGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 42 0.65
60 23 0.35
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (59 bp):
AAATGGTCATCTGACTATAAAATATATTTTATTAAGTCCCTTGACTATTAAAAGTTATA
Found at i:121678 original size:38 final size:37
Alignment explanation
Indices: 121623--121694 Score: 135
Period size: 38 Copynumber: 1.9 Consensus size: 37
121613 TGACCAAGAC
121623 TACCCCAGATTTACCATATAAACCAAACTTTATGACT
1 TACCCCAGATTTACCATATAAACCAAACTTTATGACT
121660 TACCACCAGATTTACCATATAAACCAAACTTTATG
1 TACC-CCAGATTTACCATATAAACCAAACTTTATG
121695 CCTGCAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 4 0.12
38 30 0.88
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (37 bp):
TACCCCAGATTTACCATATAAACCAAACTTTATGACT
Found at i:121692 original size:19 final size:19
Alignment explanation
Indices: 121632--121692 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
121622 CTACCCCAGA
121632 TTTACCATATAAACCAAAC
1 TTTACCATATAAACCAAAC
** * *
121651 TTTATGACT-TACCACCAGA-
1 TTTACCA-TATA-AACCAAAC
121670 TTTACCATATAAACCAAAC
1 TTTACCATATAAACCAAAC
121689 TTTA
1 TTTA
121693 TGCCTGCAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
18 6 0.20
19 18 0.60
20 6 0.20
ACGTcount: A:0.41, C:0.25, G:0.03, T:0.31
Consensus pattern (19 bp):
TTTACCATATAAACCAAAC
Done.