Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004236.1 Hibiscus syriacus cultivar Beakdansim tig00009281_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: 47518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1626 original size:175 final size:176
Alignment explanation
Indices: 1237--1647 Score: 436
Period size: 177 Copynumber: 2.4 Consensus size: 176
1227 TTCGATATTT
* * * * *
1237 AGAATTTTGAAA-CGTTTACTTTAAA-TAATATGTAAATTT---ATGTAAACAGTAACAATCTAT
1 AGAA-TTTGAAACCGATTACTTTAAAGT-ATAGGTAAATTTACAATGTAAACGGTAAAAATCTAA
* * * *
1297 TGGTTTAATGATAATAGGCGTAAACTAACGTATTGATATTATTATTCCAATATGCTTATCAAACA
64 TGGTTTAATGATAATAGGCGTAAAATAAAGTATCGATACTATTATTCCAATATGC-TATCAAACA
* **
1362 ATTTTGAACGCACAAAGTATCGATACATTCATAACACGTATCGATACTT
128 ATTTTGAACGCAAAAAGTATCGATACATTCATAACACGTATCGATACGC
* * *
1411 ATAATTTGAAACCTATTTCTTTAAAGTATAGGTAAATTTACAATGTAAACGGTAAAAATCTACAT
1 AGAATTTGAAACCGATTACTTTAAAGTATAGGTAAATTTACAATGTAAACGGTAAAAATCTA-AT
* *
1476 -GTTTAATGATAATAGGCGTAAAATAAAGTATCGATACT-TTATTTCAGTATG-TACCTCAAACA
65 GGTTTAATGATAATAGGCGTAAAATAAAGTATCGATACTATTATTCCAATATGCTA--TCAAACA
* *
1538 ATTTT-CACGCAAAAAGTATCGATATAGATGT-ATAA-A-GTATCGATACGC
128 ATTTTGAACGCAAAAAGTATCG--ATACAT-TCATAACACGTATCGATACGC
* *
1586 AGAATTTCGAAACGGATTACTTTAAAGTTATA-G-AAATTTACAATGTAAACGGTAAAAGTCTA
1 AGAATTT-GAAACCGATTACTTTAAAG-TATAGGTAAATTTACAATGTAAACGGTAAAAATCTA
1648 TCGCTGATTG
Statistics
Matches: 200, Mismatches: 24, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
173 7 0.04
174 26 0.13
175 59 0.29
176 41 0.20
177 65 0.32
178 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (176 bp):
AGAATTTGAAACCGATTACTTTAAAGTATAGGTAAATTTACAATGTAAACGGTAAAAATCTAATG
GTTTAATGATAATAGGCGTAAAATAAAGTATCGATACTATTATTCCAATATGCTATCAAACAATT
TTGAACGCAAAAAGTATCGATACATTCATAACACGTATCGATACGC
Found at i:1900 original size:38 final size:40
Alignment explanation
Indices: 1835--1923 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 40
1825 ACAGGTAACG
* *
1835 AATTTGACAAAACCGATTGGAAATTGA-TAAAACGGTTAA
1 AATTTGACAAAACCAATTGGAAATTGATTAAAACAGTTAA
*
1874 AA-TTGACAAAATCAATT-GAAATTTGATTAAAACAGTTAA
1 AATTTGACAAAACCAATTGGAAA-TTGATTAAAACAGTTAA
1913 AATTTGACAAA
1 AATTTGACAAA
1924 GTATCGATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
37 4 0.09
38 17 0.39
39 15 0.34
40 8 0.18
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.28
Consensus pattern (40 bp):
AATTTGACAAAACCAATTGGAAATTGATTAAAACAGTTAA
Found at i:1915 original size:20 final size:19
Alignment explanation
Indices: 1858--1919 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
1848 CGATTGGAAA
*
1858 TTGATAAAACGGTTAAAA-
1 TTGATAAAACAGTTAAAAT
* * *
1876 TTGACAAAATCAATTGAAAT
1 TTGATAAAA-CAGTTAAAAT
1896 TTGATTAAAACAGTTAAAAT
1 TTGA-TAAAACAGTTAAAAT
1916 TTGA
1 TTGA
1920 CAAAGTATCG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 16 0.47
21 4 0.12
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (19 bp):
TTGATAAAACAGTTAAAAT
Found at i:4087 original size:15 final size:15
Alignment explanation
Indices: 4067--4096 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4057 GTAATAGGTT
*
4067 TCGAAATTCCAAGTA
1 TCGAAACTCCAAGTA
4082 TCGAAACTCCAAGTA
1 TCGAAACTCCAAGTA
4097 GCGGTATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
TCGAAACTCCAAGTA
Found at i:6066 original size:15 final size:15
Alignment explanation
Indices: 6046--6075 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6036 GTAATAGGTT
*
6046 TCGAAATTCCAAGTA
1 TCGAAACTCCAAGTA
6061 TCGAAACTCCAAGTA
1 TCGAAACTCCAAGTA
6076 GCGGTATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
TCGAAACTCCAAGTA
Found at i:8042 original size:15 final size:15
Alignment explanation
Indices: 8022--8051 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8012 AGTAATGGTT
*
8022 TCGAAATTCCAAGTA
1 TCGAAACTCCAAGTA
8037 TCGAAACTCCAAGTA
1 TCGAAACTCCAAGTA
8052 GCGGTATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
TCGAAACTCCAAGTA
Found at i:10019 original size:15 final size:15
Alignment explanation
Indices: 9999--10028 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9989 GTAATAGGTT
*
9999 TCGAAATTCCAAGTA
1 TCGAAACTCCAAGTA
10014 TCGAAACTCCAAGTA
1 TCGAAACTCCAAGTA
10029 GCGGTATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
TCGAAACTCCAAGTA
Found at i:11936 original size:15 final size:15
Alignment explanation
Indices: 11916--11945 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11906 GTAATAGGTT
*
11916 TCGAAATTCCAAGTA
1 TCGAAACTCCAAGTA
11931 TCGAAACTCCAAGTA
1 TCGAAACTCCAAGTA
11946 GCGGTATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
TCGAAACTCCAAGTA
Found at i:15890 original size:15 final size:15
Alignment explanation
Indices: 15870--15899 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15860 GTAATAGGTT
*
15870 TCGAAATTCCAAGTA
1 TCGAAACTCCAAGTA
15885 TCGAAACTCCAAGTA
1 TCGAAACTCCAAGTA
15900 GCGGTATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
TCGAAACTCCAAGTA
Found at i:16559 original size:130 final size:129
Alignment explanation
Indices: 16331--16567 Score: 286
Period size: 130 Copynumber: 1.8 Consensus size: 129
16321 CGATACGTGG
* * * *
16331 AATTTTGAAATCTATTACTTTATAGTAATAGGTAAATTAACAATGTACACAGTAAACTTTTCTAC
1 AATTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACAGTAAACTGTTCAAC
** * *
16396 CGGTATAATCAAAATAGGAGTAAATGTTCAAGTATTGATACTGTCATATAAGTATCGATTCTTAT
66 CGGTATAATC-AAATAGGAGTAAATCATAAAGTATCGATACTGTCATATAAGTATCGATTCTTAT
* *
16461 AATTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGGTAATA-TGTTGAA
1 AATTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACAGTAA-ACTGTTCAA
16525 CCTTGGTACCTAA-C-AATAGGCA-TAAA-CATAAAGTATCGATACT
65 CC--GGTA--TAATCAAATAGG-AGTAAATCATAAAGTATCGATACT
16568 CTTTGTATAG
Statistics
Matches: 91, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
130 71 0.78
131 11 0.12
132 5 0.05
133 1 0.01
134 3 0.03
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (129 bp):
AATTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACAGTAAACTGTTCAAC
CGGTATAATCAAATAGGAGTAAATCATAAAGTATCGATACTGTCATATAAGTATCGATTCTTAT
Found at i:16793 original size:199 final size:200
Alignment explanation
Indices: 16539--16990 Score: 663
Period size: 200 Copynumber: 2.3 Consensus size: 200
16529 GGTACCTAAC
*
16539 AATAGGCATAAACATAAAGTATCGATACTCTTTGTATAGGTATCGATACTTTTAGTCCAATATGT
1 AATAGGCATAAACATAAAGTATCGATACTCTTTGTATAGGTATCGATACTTTTAGTCCAATATGC
** * * *
16604 TTCTC-AACAATTTATACGCAAAAAGTATCGATACATGTATAACAAGTATCGATACTTATAATTT
66 TTCTCAAACAACATACACACAAAAAGTATCGATACATGTATAACAAGTATCAATACTTATAATTT
* * * * * *
16668 CGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAATGATAAAAATCTATCGGTTTA
131 CGAAACCGATTACATTAAAGTAATAGGTAAATATACAATATAAATGATAAAAATCTACCAGTTTA
16733 ATGAT
196 ATGAT
* * **
16738 AATAGGCGTAAACATAAAATATCGATACTCTTTGTATATATATCGATACTTTTAGTCCAATATGC
1 AATAGGCATAAACATAAAGTATCGATACTCTTTGTATAGGTATCGATACTTTTAGTCCAATATGC
* * *
16803 TTCTCAAATAACATGCACACAAAAAGTATCGATACATGTATCACAAGTATCAATACTTATAATTT
66 TTCTCAAACAACATACACACAAAAAGTATCGATACATGTATAACAAGTATCAATACTTATAATTT
* * *
16868 TGAAACCTATTACATTAAAGTAATAGGTAAATATACAATATAAATGGTAAAAATCTACCAGTTTA
131 CGAAACCGATTACATTAAAGTAATAGGTAAATATACAATATAAATGATAAAAATCTACCAGTTTA
16933 ATGAT
196 ATGAT
* * * *
16938 AATAGGCTTGAACATAAAGTTTCGATACTTTTTGTATAGGTATCGATACTTTT
1 AATAGGCATAAACATAAAGTATCGATACTCTTTGTATAGGTATCGATACTTTT
16991 GATCTAAACA
Statistics
Matches: 223, Mismatches: 29, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
199 65 0.29
200 158 0.71
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (200 bp):
AATAGGCATAAACATAAAGTATCGATACTCTTTGTATAGGTATCGATACTTTTAGTCCAATATGC
TTCTCAAACAACATACACACAAAAAGTATCGATACATGTATAACAAGTATCAATACTTATAATTT
CGAAACCGATTACATTAAAGTAATAGGTAAATATACAATATAAATGATAAAAATCTACCAGTTTA
ATGAT
Found at i:17600 original size:226 final size:224
Alignment explanation
Indices: 17173--17859 Score: 878
Period size: 226 Copynumber: 3.0 Consensus size: 224
17163 TAACAAATCA
* * * * * * *
17173 AGTAATTAACCTATTTTATTATCTTCAAATTTCTAAGGCTCCATCATCTTTAAACTTTTGAAACA
1 AGTAATTAACATATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAGC-TTAAACTTTGGTAACA
*
17238 TTTTAGGCGCTACCTAATATGTTGATAATAATGATAACAAATTAAGTAATTAACCTATTTTGTT-
65 TTTTAGGCGCTACCTAATATGTTGATAATAATAATAACAAATTAAGTAATTAACCTATTTTGTTA
* *
17302 GCGTC-AGATTTCTAAGGTCCCATCAGCTTTAAACATA-CGCTACCTATTATATTAAATAAGCGA
130 TCGTCGA-ATTTCTAAGG-CCCATCAGCTTTAAA-A-AGCGCTACCTATTATGTTAAATAAGCGA
17365 TACTTGTTATGTTATTATGGTTGATAATGTTTCC
191 TACTTGTTATGTTATTATGGTTGATAATGTTTCC
* *
17399 AGTAATTAACATATTTTGTTATCGT-AGGGTTTCTAAGGCTCCATCAGCATAAACTTTGGTAACA
1 AGTAATTAACATATTTTGTTATCGTCA-GATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACA
* * *
17463 TTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACATATTTTGTTA
65 TTTTAGGCGCTACCTAATATGTTGATAATAATAATAACAAATTAAGTAATTAACCTATTTTGTTA
* * ** *
17528 TAGTCGAATTTCCAAGGCCTCATCAGCTTTAAATAAGCGCTACCTATTATGTTAAATAAATGTTA
130 TCGTCGAATTTCTAAGGCC-CATCAGCTTTAAA-AAGCGCTACCTATTATGTTAAATAAGCGATA
* *
17593 GTTGTTATGTTATTATGGTTGATAATATTTCC
193 CTTGTTATGTTATTATGGTTGATAATGTTTCC
* * * *
17625 AATAATTAACATATTTTGTTATTGTCAGATTTCTAAGACTCCATCAGCTTAAACTTTGGTAATAT
1 AGTAATTAACATATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * * * *
17690 TTTAGGCACTACCTAATATATTGATAATATTAATAACAAATCAAGTAATTAACCTATTTTATTAT
66 TTTAGGCGCTACCTAATATGTTGATAATAATAATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * * * *
17755 CGTCGGATTTCTAAGTCCCCATCAACTTTAAAAATGCGCTACCTATTACGATACATAAGCGCTAC
131 CGTCGAATTTCTAAG-GCCCATCAGCTTTAAAAA-GCGCTACCTATTATGTTAAATAAGCGATAC
****
17820 AAAATATGTTATTATGGTTGATAATGTTTCC
194 TTGTTATGTTATTATGGTTGATAATGTTTCC
17851 AGTAATTAA
1 AGTAATTAA
17860 TCGGTTATGT
Statistics
Matches: 399, Mismatches: 54, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
225 79 0.20
226 316 0.79
227 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (224 bp):
AGTAATTAACATATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
TTTAGGCGCTACCTAATATGTTGATAATAATAATAACAAATTAAGTAATTAACCTATTTTGTTAT
CGTCGAATTTCTAAGGCCCATCAGCTTTAAAAAGCGCTACCTATTATGTTAAATAAGCGATACTT
GTTATGTTATTATGGTTGATAATGTTTCC
Found at i:21820 original size:226 final size:226
Alignment explanation
Indices: 21422--21879 Score: 819
Period size: 226 Copynumber: 2.0 Consensus size: 226
21412 TAAAATTTTC
21422 TAATTTATATAAAAATTAAATATTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATAT
1 TAATTTATATAAAAATTAAATATTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATAT
21487 ATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAG
66 ATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAG
21552 TTATTGAATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTAAACTCATATGTTATATATA
131 TTATTGAATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTAAACTCATATGTTATATATA
* *
21617 ATATATTTAATATTTAAAATTTAATTTCGGT
196 ATATATTTAAAATTTAAAATTAAATTTCGGT
21648 TAATTTATATAAAAATTAAATATTTTTTAATTC-AAAAAACAGTTTACAATTAATTTAAATAATA
1 TAATTTATATAAAAATTAAATA-TTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATA
21712 TATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAA
65 TATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAA
* * * * **
21777 GTTATTGGATCTTAAATTATTAATTGTGTTTTAAATGGTTTGGGCTGAGGTCATATGTTATATAT
130 GTTATTGAATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTAAACTCATATGTTATATAT
*
21842 AATATATTTAAAATTTAAAATTAAATTTCGTT
195 AATATATTTAAAATTTAAAATTAAATTTCGGT
21874 TAATTT
1 TAATTT
21880 GGTTAATTAA
Statistics
Matches: 222, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
226 212 0.95
227 10 0.05
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (226 bp):
TAATTTATATAAAAATTAAATATTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATAT
ATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAG
TTATTGAATCTTAAATTATTAATTGAGTTTTAAATAGTTTGGGCTAAACTCATATGTTATATATA
ATATATTTAAAATTTAAAATTAAATTTCGGT
Found at i:25662 original size:35 final size:35
Alignment explanation
Indices: 25622--25715 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 35
25612 TGCCATCTCA
* * * *
25622 TAATGCTCTATTTCAGCAACTTTTCAATGGTCAAT
1 TAATGCACAATTTAAGCAACTTTTCAATGGCCAAT
* * *
25657 TAATGCACCATTTTAA-TAACTTTTCAGTGGCCAAT
1 TAATGCA-CAATTTAAGCAACTTTTCAATGGCCAAT
*
25692 TAATGCACAATATAAGCAACTTTT
1 TAATGCACAATTTAAGCAACTTTT
25716 TAGAAAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
34 6 0.13
35 36 0.77
36 5 0.11
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (35 bp):
TAATGCACAATTTAAGCAACTTTTCAATGGCCAAT
Found at i:26087 original size:138 final size:141
Alignment explanation
Indices: 25939--26193 Score: 340
Period size: 142 Copynumber: 1.8 Consensus size: 141
25929 GGTCATTTAG
** *
25939 TCATCTTCAACAACTTTTCAGTGATATAT-AC-ATTTCAG-AAAACTTTTAACTGGTGCATTATC
1 TCATCTTCAACAAAATTTCAGTGATATATAACTATTTCAGAAAAAATTTT-ACTGGTGCATTATC
* *
26001 ACTTCATAT-AAGAAAACA-TGTATTTCTCATAAGCCAAATAATACACCATGGCAAAAACTTTTC
65 AATTCATATGAA-AAAAAAGTGTATTTCTCATAAGCCAAATAATACACCATGGCAAAAACTTTTC
26064 AATACACAATTAA
129 AATACACAATTAA
* *
26077 TCATCTTCAACAAAATTTCAGTGATATATCAACTTATTTTAGAAAAAATTTTAGTGGTGCATTAT
1 TCATCTTCAACAAAATTTCAGTGATATAT-AAC-TATTTCAGAAAAAATTTTACTGGTGCATTAT
* * *
26142 TAATTCATATGAAAAAAAATGTGTATTTCTCATAAGCTAAATAATGCACCAT
64 CAATTCATATGAAAAAAAA-GTGTATTTCTCATAAGCCAAATAATACACCAT
26194 TTCACCAACT
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
138 27 0.27
140 2 0.02
142 31 0.31
143 10 0.10
144 29 0.29
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (141 bp):
TCATCTTCAACAAAATTTCAGTGATATATAACTATTTCAGAAAAAATTTTACTGGTGCATTATCA
ATTCATATGAAAAAAAAGTGTATTTCTCATAAGCCAAATAATACACCATGGCAAAAACTTTTCAA
TACACAATTAA
Found at i:26221 original size:144 final size:138
Alignment explanation
Indices: 25884--26229 Score: 367
Period size: 138 Copynumber: 2.5 Consensus size: 138
25874 TTAATGCACC
* * *
25884 ATTTCTCATAGGCTAAATAATGCACCATGGT-AGAAACCTTTT-AGTGGTCATTTAGTCATCTTC
1 ATTTCTCATAAGCTAAATAATGCACCAT-GTCA-AAAACTTTTCAGTGGTCATTTAATCATCTTC
** * *
25947 AACAACTTTTCAGTGATATATACATTTCAGAAAACTTTTAACTGGTGCATTATCACTTCATATAA
64 AACAAAATTTCAGTGATATATACATTTCAGAAAAATTTTAACTGGTGCATTATCAATTCATATAA
*
26012 GAAAACATGT
129 GAAAAAATGT
* * * * *** *
26022 ATTTCTCATAAGCCAAATAATACACCATGGCAAAAACTTTTCAATACACAATTAATCATCTTCAA
1 ATTTCTCATAAGCTAAATAATGCACCATGTCAAAAACTTTTCAGTGGTCATTTAATCATCTTCAA
* * *
26087 CAAAATTTCAGTGATATATCAACTTATTTTAGAAAAAATTTT-AGTGGTGCATTATTAATTCATA
66 CAAAATTTCAGTGATATAT--AC--ATTTCAG-AAAAATTTTAACTGGTGCATTATCAATTCATA
26151 TGAA-AAAAAATGTGT
126 T-AAGAAAAAA--TGT
* ** *
26166 ATTTCTCATAAGCTAAATAATGCACCATTTCACCAACTTTTCAGTGGTCATTTAATAATCTTCA
1 ATTTCTCATAAGCTAAATAATGCACCATGTCAAAAACTTTTCAGTGGTCATTTAATCATCTTCA
26230 TCAACTATTA
Statistics
Matches: 167, Mismatches: 31, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
137 9 0.05
138 60 0.36
140 2 0.01
142 31 0.19
143 10 0.06
144 55 0.33
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.35
Consensus pattern (138 bp):
ATTTCTCATAAGCTAAATAATGCACCATGTCAAAAACTTTTCAGTGGTCATTTAATCATCTTCAA
CAAAATTTCAGTGATATATACATTTCAGAAAAATTTTAACTGGTGCATTATCAATTCATATAAGA
AAAAATGT
Found at i:27723 original size:13 final size:13
Alignment explanation
Indices: 27705--27731 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27695 AAGTACGTTG
27705 GGTCGTCGGCCTT
1 GGTCGTCGGCCTT
27718 GGTCGTCGGCCTT
1 GGTCGTCGGCCTT
27731 G
1 G
27732 ATCATTAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.30
Consensus pattern (13 bp):
GGTCGTCGGCCTT
Found at i:41963 original size:47 final size:49
Alignment explanation
Indices: 41761--41980 Score: 249
Period size: 49 Copynumber: 4.6 Consensus size: 49
41751 CAAAAGCATT
* * * ** *
41761 GTTATGAATTTAACTTGCATTAGT-GAACCTTTCT---AAAAACACACT
1 GTTATGCATTTAATTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACC
* *
41806 GTTATGCCTTT-ATCTTGCATTAGTGGCACATTTCTGCCAAAAATGCACC
1 GTTATGCATTTAAT-TTGCATTAGTGGCACCTTTCTGCCAAAAATGCACC
* * *
41855 GTTATGTATTTAAATTGCATTAGTGGCACCTTTATGCCAAAAATGCACC
1 GTTATGCATTTAATTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACC
* * *
41904 G-CATGCATTTAATTTACATTAGTGGCACCTTTCGGCC-AAAAT-CACC
1 GTTATGCATTTAATTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACC
41950 GTTATGCATTTAATTTGCATTAGTGGCACCT
1 GTTATGCATTTAATTTGCATTAGTGGCACCT
41981 ACAAAAAATG
Statistics
Matches: 147, Mismatches: 21, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
44 1 0.01
45 19 0.13
46 13 0.09
47 32 0.22
48 30 0.20
49 51 0.35
50 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (49 bp):
GTTATGCATTTAATTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACC
Done.