Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001663.1 Hibiscus syriacus cultivar Beakdansim tig00003327_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: 45250
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:8256 original size:181 final size:182
Alignment explanation
Indices: 7908--8382 Score: 641
Period size: 182 Copynumber: 2.6 Consensus size: 182
7898 GATCCAAATT
* * * **
7908 AAAAATGTATCGATCCACAAATGATATAACAGGTTAAACA-ATGACAAAACCGGTATTGAAATGA
1 AAAAATGTATCGATCAAC-AATGATATAACAGG-TAAAAATATGATAAAACCGGTATCAAAATGA
* * * * *
7972 TAAAACCGGTAAAGCGTTACCGAATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACATT
64 TAAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACATT
* * *
8037 TCGTTAATTTAAAAGAGAAGTAGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
129 TCGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * ** * *
8091 AAAAATATATCGATCAACAACGATATAACAGGTAAAAATATGATAAAATTGATATCAAAATGATG
1 AAAAATGTATCGATCAACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
8156 AAACCGGTAAAACGCTATCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACA-TTT
* *
8220 -GTGAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAGTGTCGATATTTTAA
130 CGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
*
8272 AAAAATGTATCGATCAAACAATGATATAATAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
* *
8337 AAAATCGGTAAAATGATACCGGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
8383 CGTAAGTACG
Statistics
Matches: 253, Mismatches: 36, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
181 81 0.32
182 156 0.62
183 16 0.06
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (182 bp):
AAAAATGTATCGATCAACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACATTTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:8326 original size:20 final size:19
Alignment explanation
Indices: 8303--8349 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
8293 TGATATAATA
8303 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
8323 GGTATCAAAATGATAAAATC
1 GGTA-AAAAATGATAAAACC
8343 GGTAAAA
1 GGTAAAA
8350 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:10509 original size:15 final size:15
Alignment explanation
Indices: 10489--10521 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10479 TGGTTGTATT
*
10489 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
10504 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
10519 GGG
1 GGG
10522 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.64, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:10631 original size:21 final size:21
Alignment explanation
Indices: 10605--10645 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10595 AAGACAATCA
10605 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
* *
10626 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGAGAAACTTGA
10646 GAGGCATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:10940 original size:15 final size:15
Alignment explanation
Indices: 10920--10974 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
10910 AGAGGGAGGA
10920 GGAAGAAGAAGAGAT
1 GGAAGAAGAAGAGAT
*
10935 GGAAGAA-AAGAGGGAGGA
1 GGAAGAAGAAGA--GA--T
10953 GGAAGAAGAAGAGAT
1 GGAAGAAGAAGAGAT
10968 GGAAGAA
1 GGAAGAA
10975 ATGAGGAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 4 0.12
15 14 0.42
16 2 0.06
17 2 0.06
18 7 0.21
19 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.04
Consensus pattern (15 bp):
GGAAGAAGAAGAGAT
Found at i:10946 original size:33 final size:33
Alignment explanation
Indices: 10904--10990 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
10894 AAATATGAAA
10904 AAGAAAAGAGGGAGGAGGAAGAAGAAGAGATGG
1 AAGAAAAGAGGGAGGAGGAAGAAGAAGAGATGG
10937 AAGAAAAGAGGGAGGAGGAAGAAGAAGAGATGG
1 AAGAAAAGAGGGAGGAGGAAGAAGAAGAGATGG
*
10970 AAGAAATGA-GGAGGAAGGAAG
1 AAGAAAAGAGGGAGG-AGGAAG
10991 TCGATGTCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 5 0.10
33 47 0.90
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (33 bp):
AAGAAAAGAGGGAGGAGGAAGAAGAAGAGATGG
Found at i:12559 original size:19 final size:20
Alignment explanation
Indices: 12535--12583 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
12525 AATGTAGGGT
12535 TAATTTTGTATTA-GATTTA
1 TAATTTTGTATTACGATTTA
12554 TAATTTTGTA-TACGATTTA
1 TAATTTTGTATTACGATTTA
12573 TAATTTTGTAT
1 TAATTTTGTAT
12584 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (20 bp):
TAATTTTGTATTACGATTTA
Found at i:13166 original size:200 final size:200
Alignment explanation
Indices: 12818--13399 Score: 1014
Period size: 200 Copynumber: 2.9 Consensus size: 200
12808 AATTTACAAT
*
12818 ATGGCAAACAGGGTGCAGCCATAAAGTGTCGATCCATATATAAAATGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAATGTGTCGATCCCAGAAACAT
*
12883 TGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
* * *
12948 ATGAGAGAATATGTGTAATATATGTATTGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAT
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
*
13013 AATGA
196 AATAA
*
13018 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAATGTGTCGATCCTAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAATGTGTCGATCCCAGAAACAT
*
13083 CGAAACTCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
*
13148 ATGAGAGAATAGGTGTAATATATGTATCGACGCTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
13213 AATAA
196 AATAA
* *
13218 ATGGCAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAATGTGTCGATCCCAGAAACAT
13283 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACC-G-----GTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
*
13342 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATATTATT
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
13400 TTTAAATATC
Statistics
Matches: 367, Mismatches: 15, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
194 69 0.19
199 1 0.00
200 297 0.81
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAATGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATAA
Found at i:15577 original size:183 final size:184
Alignment explanation
Indices: 15250--15597 Score: 556
Period size: 183 Copynumber: 1.9 Consensus size: 184
15240 ATATCAGCAT
* ** * ** *
15250 AAAGTGTCGATGCCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAATGCATAATTATAATGTA
1 AAAGTGTCGATACCTTTGAAAAAAGTGTCGATTGAAAAAACATCGAAACCCACAATTATAATGTA
* * * *
15315 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTTTGAGAGAATAGGTATACAACC
66 ATAGGTAATTTTGTAATATAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTATACAACC
15380 TATATCGACACTTTTTAATATTGTGTCGC-TACTTTATGTCCATAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTC-CATACTTTATGTCCATAATGGATGAAA
15434 AAAGTGTCGATACC-TTGAAAAAAGTGTCGATTGAAAAAACATCGAAACCCACAATTATAATGTA
1 AAAGTGTCGATACCTTTGAAAAAAGTGTCGATTGAAAAAACATCGAAACCCACAATTATAATGTA
* *
15498 ATAGGTAATTTTTTAATATAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTATACAACC
15563 TATATCGACACTTTTTAATATTGTGTCCATACTTT
131 TATATCGACACTTTTTAATATTGTGTCCATACTTT
15598 TAAGTAACGC
Statistics
Matches: 150, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
182 1 0.01
183 136 0.91
184 13 0.09
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (184 bp):
AAAGTGTCGATACCTTTGAAAAAAGTGTCGATTGAAAAAACATCGAAACCCACAATTATAATGTA
ATAGGTAATTTTGTAATATAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTATACAACC
TATATCGACACTTTTTAATATTGTGTCCATACTTTATGTCCATAATGGATGAAA
Found at i:18778 original size:180 final size:181
Alignment explanation
Indices: 18297--18800 Score: 906
Period size: 181 Copynumber: 2.8 Consensus size: 181
18287 TTTTACCTTT
*
18297 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
18362 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
18427 CGGTTATGTTGAAAGTGTCGATAATTTATTATATGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA-ACTTTTGGAA
* *
18479 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCAATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
18543 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
18608 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG-ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGAACTTTTGGAA
*
18658 -TTAATAAGAGAAGAAGTTATAGCGTCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
18722 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
*
18787 CCGGTTATGATGAA
130 CCGGTTATGTTGAA
18801 TTTAAAAGAG
Statistics
Matches: 311, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
178 4 0.01
179 18 0.06
180 125 0.40
181 151 0.49
182 13 0.04
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (181 bp):
TTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGAACTTTTGGAA
Found at i:18913 original size:143 final size:144
Alignment explanation
Indices: 18658--18931 Score: 487
Period size: 143 Copynumber: 1.9 Consensus size: 144
18648 ACTTTTGGAA
* *
18658 TTAATAAGAGAAGAAGTTATAGCGTCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
18723 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
18788 CGGTTATGATGAAT
131 CGGTTATGATGAAT
* *
18802 TTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTTGATATTTTATAAAAATGTATCGATCCAT
1 TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
18866 AACAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
18931 C
131 C
18932 AGATATGTTG
Statistics
Matches: 124, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
143 120 0.97
144 4 0.03
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.24
Consensus pattern (144 bp):
TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGATGAAT
Found at i:19105 original size:182 final size:182
Alignment explanation
Indices: 18798--20004 Score: 2091
Period size: 182 Copynumber: 6.6 Consensus size: 182
18788 CGGTTATGAT
* *
18798 GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTTGATATTTTATAAAAATGTATCGATC
1 GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATC
* *
18863 CATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAACAGGTAAAGCGC
66 CATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGC
* *
18928 TACCAGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
131 TACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
* *
18980 GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTAGATACTTTATAAAAATATATCGATC
1 GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATC
19045 CATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGC
66 CATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGC
* *
19110 TACCGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTA
131 TACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
* * *
19162 GAATTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTTGATACGTTATAAAAATGTATCTATC
1 GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATC
* **
19226 CATAACAATATAACATGTAAAAATATGACAAAACCGGTCTAGAAATGACAAAACATATAAAGCGC
66 CATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGC
19291 TACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTG
131 TACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
*
19341 GAA-TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGAT
1 GAATTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGAT
19405 CCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCG
65 CCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCG
19470 CTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
130 CTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
19523 GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATC
1 GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATC
* * * *
19588 CATAACAATATAACAGGTAATAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAAGTGC
66 CATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGC
19653 TACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
131 TACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
19705 GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATC
1 GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATC
* * *
19770 CATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAATAGGTAAAGTGC
66 CATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGC
*
19835 TACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
131 TACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
19887 GAA-TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGAT
1 GAATTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGAT
* * * **
19951 CCATAATAATATAACATGGAAAAATATGATAAAACCGGTCTATAAATGACAAAA
65 CCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
20005 TGTGAACGCA
Statistics
Matches: 979, Mismatches: 40, Indels: 12
0.95 0.04 0.01
Matches are distributed among these distances:
178 4 0.00
179 17 0.02
180 149 0.15
181 152 0.16
182 653 0.67
183 4 0.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATC
CATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGC
TACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTG
Found at i:21509 original size:11 final size:11
Alignment explanation
Indices: 21482--21511 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
21472 AAAACTAATT
21482 AAAATGAAAAAA
1 AAAAT-AAAAAA
21494 AAAATAAAAAA
1 AAAATAAAAAA
21505 AAAATAA
1 AAAATAA
21512 TGTTGGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:25020 original size:188 final size:188
Alignment explanation
Indices: 24703--25078 Score: 743
Period size: 188 Copynumber: 2.0 Consensus size: 188
24693 TCCTCAAAAA
24703 TGACATCTGTTGCCTAATGGTTTATGCCTTATGTTAGTCCTTCCTTGAGCTTAGTAATTGAGACT
1 TGACATCTGTTGCCTAATGGTTTATGCCTTATGTTAGTCCTTCCTTGAGCTTAGTAATTGAGACT
24768 GATGCTTCAGTATTTATACTATTTTAACAATAACATATGATTCTTGCAAATATCTTACATGACAT
66 GATGCTTCAGTATTTATACTATTTTAACAATAACATATGATTCTTGCAAATATCTTACATGACAT
24833 ATTAAACTAGTGGGCATCTAAGGGTTTCTGCATGTGTACTCTTTTAAAATATTTGTTG
131 ATTAAACTAGTGGGCATCTAAGGGTTTCTGCATGTGTACTCTTTTAAAATATTTGTTG
*
24891 TGACATCTGTTGCCTGATGGTTTATGCCTTATGTTAGTCCTTCCTTGAGCTTAGTAATTGAGACT
1 TGACATCTGTTGCCTAATGGTTTATGCCTTATGTTAGTCCTTCCTTGAGCTTAGTAATTGAGACT
24956 GATGCTTCAGTATTTATACTATTTTAACAATAACATATGATTCTTGCAAATATCTTACATGACAT
66 GATGCTTCAGTATTTATACTATTTTAACAATAACATATGATTCTTGCAAATATCTTACATGACAT
25021 ATTAAACTAGTGGGCATCTAAGGGTTTCTGCATGTGTACTCTTTTAAAATATTTGTTG
131 ATTAAACTAGTGGGCATCTAAGGGTTTCTGCATGTGTACTCTTTTAAAATATTTGTTG
25079 GCGATTGCTT
Statistics
Matches: 187, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
188 187 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (188 bp):
TGACATCTGTTGCCTAATGGTTTATGCCTTATGTTAGTCCTTCCTTGAGCTTAGTAATTGAGACT
GATGCTTCAGTATTTATACTATTTTAACAATAACATATGATTCTTGCAAATATCTTACATGACAT
ATTAAACTAGTGGGCATCTAAGGGTTTCTGCATGTGTACTCTTTTAAAATATTTGTTG
Found at i:38594 original size:29 final size:30
Alignment explanation
Indices: 38535--38595 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
38525 ATTTAACAGC
38535 TCAGTGGTATAATTGAAACAAAAATCAAAGT
1 TCAGTGGTATAATTG-AACAAAAATCAAAGT
* * *
38566 TCAGTGTTATAATTG-ACAAAATTGAAAGT
1 TCAGTGGTATAATTGAACAAAAATCAAAGT
38595 T
1 T
38596 TATTGGTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 13 0.48
31 14 0.52
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.31
Consensus pattern (30 bp):
TCAGTGGTATAATTGAACAAAAATCAAAGT
Done.