Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002055.1 Hibiscus syriacus cultivar Beakdansim tig00004188_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: 63309
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1604 original size:23 final size:23
Alignment explanation
Indices: 1564--1609 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1554 ATTGTAATTA
*
1564 TTTTATATATTTTAATTAAATAT
1 TTTTATAGATTTTAATTAAATAT
*
1587 TTTTATAAGATTTT-ATTATATAT
1 TTTTAT-AGATTTTAATTAAATAT
1610 CTCTCATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTATAGATTTTAATTAAATAT
Found at i:2134 original size:26 final size:26
Alignment explanation
Indices: 2098--2150 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2088 CGTCTACTCC
* *
2098 TATTTGCTATCTGTATTTATTTCTTT
1 TATTTGCTATCTATATTTATTTATTT
2124 TATTTGCTATCTATATTTATTTATTT
1 TATTTGCTATCTATATTTATTTATTT
2150 T
1 T
2151 TATCATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.09, G:0.06, T:0.66
Consensus pattern (26 bp):
TATTTGCTATCTATATTTATTTATTT
Found at i:2798 original size:22 final size:22
Alignment explanation
Indices: 2768--2845 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
2758 GCTCTGAATG
*
2768 GAACTATTCAGCGTTGAATGCT
1 GAACCATTCAGCGTTGAATGCT
2790 GAACCATTCAGCGTTGAATGCT
1 GAACCATTCAGCGTTGAATGCT
* * *
2812 GAACTATTCAACGTTGAATGTT
1 GAACCATTCAGCGTTGAATGCT
*
2834 GAACCGTTCAGC
1 GAACCATTCAGC
2846 ATTCAGACTG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (22 bp):
GAACCATTCAGCGTTGAATGCT
Found at i:24079 original size:20 final size:18
Alignment explanation
Indices: 24040--24079 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
24030 ATTAATTCAA
24040 TTATTTTTTATAATTAAT
1 TTATTTTTTATAATTAAT
24058 TTATTTTTTA-AA-TAAT
1 TTATTTTTTATAATTAAT
*
24074 ATATTT
1 TTATTT
24080 GACCAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
18 10 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTTTTATAATTAAT
Found at i:24462 original size:16 final size:16
Alignment explanation
Indices: 24441--24497 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
24431 ATATTTACTT
24441 TTATTTTTTAATTATA
1 TTATTTTTTAATTATA
*
24457 TTA-TTTTTAATTTTAA
1 TTATTTTTTAATTAT-A
* *
24473 TT-TTATTTAATCATA
1 TTATTTTTTAATTATA
24488 TTATTTTTTA
1 TTATTTTTTA
24498 TGTTTGGATC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 13 0.39
16 20 0.61
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTTTAATTATA
Found at i:24465 original size:15 final size:15
Alignment explanation
Indices: 24445--24495 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
24435 TTACTTTTAT
24445 TTTTTAATTATATTA
1 TTTTTAATTATATTA
*
24460 TTTTTAATTTTAATT-
1 TTTTTAATTAT-ATTA
*
24475 TTATTTAATCATATTA
1 TT-TTTAATTATATTA
24491 TTTTT
1 TTTTT
24496 TATGTTTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTAATTATATTA
Found at i:25847 original size:22 final size:22
Alignment explanation
Indices: 25822--25896 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
25812 AGCAAGTAGT
*
25822 GTTTTAGAACAGTGATGGTGTC
1 GTTTAAGAACAGTGATGGTGTC
* * ** **
25844 GTTTAAGAAAAAGGGAAAGCAT-
1 GTTTAAG-AACAGTGATGGTGTC
*
25866 GTTTTAGAACAGTGATGGTGTC
1 GTTTAAGAACAGTGATGGTGTC
25888 GTTTAAGAA
1 GTTTAAGAA
25897 AAAGGGAAAG
Statistics
Matches: 36, Mismatches: 15, Indels: 4
0.65 0.27 0.07
Matches are distributed among these distances:
21 8 0.22
22 20 0.56
23 8 0.22
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (22 bp):
GTTTAAGAACAGTGATGGTGTC
Found at i:25848 original size:21 final size:21
Alignment explanation
Indices: 25824--25892 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
25814 CAAGTAGTGT
25824 TTTAGAACAGTGATGGTGTCG
1 TTTAGAACAGTGATGGTGTCG
* * * *
25845 TTTAAGAAAAAGGGAAAGCATGT--
1 TTT-AG-AACAGTG-ATG-GTGTCG
25868 TTTAGAACAGTGATGGTGTCG
1 TTTAGAACAGTGATGGTGTCG
25889 TTTA
1 TTTA
25893 AGAAAAAGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 12 0.35
22 4 0.12
23 8 0.24
24 2 0.06
25 3 0.09
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (21 bp):
TTTAGAACAGTGATGGTGTCG
Found at i:25870 original size:44 final size:44
Alignment explanation
Indices: 25821--25908 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
25811 AAGCAAGTAG
25821 TGTTTTAGAACAGTGATGGTGTCGTTTAAGAAAAAGGGAAAGCA
1 TGTTTTAGAACAGTGATGGTGTCGTTTAAGAAAAAGGGAAAGCA
25865 TGTTTTAGAACAGTGATGGTGTCGTTTAAGAAAAAGGGAAAGCA
1 TGTTTTAGAACAGTGATGGTGTCGTTTAAGAAAAAGGGAAAGCA
25909 AAACACAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.07, G:0.30, T:0.27
Consensus pattern (44 bp):
TGTTTTAGAACAGTGATGGTGTCGTTTAAGAAAAAGGGAAAGCA
Found at i:38828 original size:84 final size:86
Alignment explanation
Indices: 38667--38875 Score: 212
Period size: 84 Copynumber: 2.4 Consensus size: 86
38657 TGGAGGTCCT
* * * * *
38667 TAATTTTTTTCAATCCCATTTTTTTACATTTATTATTGATATCCTAATTTTTTTCAATCCCACCT
1 TAATCTTTTTCAATCTCA-CTTTTTACATTTATAATTGAGATCCTAATTTTTTTCAATCCCACCT
*
38732 TGTACCTTTATAA-TTAAACTCC
65 TGTACCTATATAATTTAAAC-CC
* * **
38754 T-A-CTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGTCCCTAA-TTTTTTCAATCCCATTT
1 TAATCTTTTTCAATCTCACTTTTTACATTTATAATTGAGAT-CCTAATTTTTTTCAATCCCACCT
* **
38816 TTTA-CTCATATAATTTAGGCCC
65 TGTACCT-ATATAATTTAAACCC
* *
38838 TAATTTTTTTCAATCTCACTTTTTACATTTAAAATTGA
1 TAATCTTTTTCAATCTCACTTTTTACATTTATAATTGA
38876 TGCCCATATT
Statistics
Matches: 101, Mismatches: 16, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
83 2 0.02
84 44 0.44
85 22 0.22
86 32 0.32
87 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.50
Consensus pattern (86 bp):
TAATCTTTTTCAATCTCACTTTTTACATTTATAATTGAGATCCTAATTTTTTTCAATCCCACCTT
GTACCTATATAATTTAAACCC
Found at i:38839 original size:42 final size:44
Alignment explanation
Indices: 38599--38948 Score: 235
Period size: 43 Copynumber: 8.2 Consensus size: 44
38589 TAATTTTAAT
* * *
38599 TTTTTATCTTTATAATTGAGGTCCCTAATTTTTGT-AATC-CTAC
1 TTTTTACCTATATAATTGAGGTCCCTAATTTTTTTCAATCTC-AC
* * * * * * *
38642 TTTTGATCTTTATAATGGAGGTCCTTAATTTTTTTCAATCCCATT
1 TTTTTACCTATATAATTGAGGTCCCTAATTTTTTTCAATCTCA-C
* * * ** *
38687 TTTTTACATTTATTATTGATAT-CCTAATTTTTTTCAATCCCAC
1 TTTTTACCTATATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
* * * * ** *
38730 CTTGTACCTTTATAATTAAACT-CCT-A-CTTTTTCAATCTCAC
1 TTTTTACCTATATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
* * *
38771 TTTTTACCTTTATAATTGAGGTCCCTAA-TTTTTTCAATCCCAT
1 TTTTTACCTATATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
*
38814 TTTTTA-CTCATATAATTTAGG-CCCTAATTTTTTTCAATCTCAC
1 TTTTTACCT-ATATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
* * * * * *
38857 TTTTTACATTTAAAATTGATG-CCC--ATATTTTTCTAATATCAC
1 TTTTTACCTATATAATTGAGGTCCCTAATTTTTTTC-AATCTCAC
*
38899 TTTTTACCTTTATAATT-AGGGTCCCTAA-TTTTTTCAATCAT-AC
1 TTTTTACCTATATAATTGA-GGTCCCTAATTTTTTTCAATC-TCAC
38942 TTTTTAC
1 TTTTTAC
38949 TTTTATAGTT
Statistics
Matches: 246, Mismatches: 47, Indels: 28
0.77 0.15 0.09
Matches are distributed among these distances:
41 39 0.16
42 35 0.14
43 123 0.50
44 32 0.13
45 17 0.07
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (44 bp):
TTTTTACCTATATAATTGAGGTCCCTAATTTTTTTCAATCTCAC
Found at i:38846 original size:85 final size:86
Alignment explanation
Indices: 38599--38955 Score: 308
Period size: 85 Copynumber: 4.2 Consensus size: 86
38589 TAATTTTAAT
* * * *
38599 TTTTTATC-TTTATAATTGAGGTCCCTAATTTTTGT-AATCCTACTTTTGATCTTTATAATGGAG
1 TTTTTA-CATTTATAATTGAGGTCCCTAATTTTT-TCAATCCCACTTTTTACCTTTATAAT-TAG
* * *
38662 GTCCTTAATTTTTTTCAATCCCATT
63 GTCCCTAATTTTTTTCAATCTCA-C
* ** * * **
38687 TTTTTACATTTATTATTGATAT-CCTAATTTTTTTCAATCCCACCTTGTACCTTTATAATTA-AA
1 TTTTTACATTTATAATTGAGGTCCCTAA-TTTTTTCAATCCCACTTTTTACCTTTATAATTAGGT
*
38750 CTCCT-A-CTTTTTCAATCTCAC
65 C-CCTAATTTTTTTCAATCTCAC
* * *
38771 TTTTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCCCATTTTTTA-CTCATATAATTTAGG
1 TTTTTACATTTATAATTGAGGTCCCTAATTTTTTCAATCCCACTTTTTACCT-TTATAA-TTAGG
38835 -CCCTAATTTTTTTCAATCTCAC
64 TCCCTAATTTTTTTCAATCTCAC
* * **
38857 TTTTTACATTTAAAATTGATG-CCC--ATATTTTTCTAATATCACTTTTTACCTTTATAATTAGG
1 TTTTTACATTTATAATTGAGGTCCCTAAT-TTTTTC-AATCCCACTTTTTACCTTTATAATTA-G
38919 GTCCCTAA-TTTTTTCAATCAT-AC
63 GTCCCTAATTTTTTTCAATC-TCAC
*
38942 TTTTTACTTTTATA
1 TTTTTACATTTATA
38956 GTTTAAGCTC
Statistics
Matches: 219, Mismatches: 34, Indels: 35
0.76 0.12 0.12
Matches are distributed among these distances:
83 4 0.02
84 53 0.24
85 68 0.31
86 43 0.20
87 10 0.05
88 41 0.19
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (86 bp):
TTTTTACATTTATAATTGAGGTCCCTAATTTTTTCAATCCCACTTTTTACCTTTATAATTAGGTC
CCTAATTTTTTTCAATCTCAC
Found at i:38904 original size:128 final size:128
Alignment explanation
Indices: 38640--38937 Score: 345
Period size: 128 Copynumber: 2.3 Consensus size: 128
38630 TTGTAATCCT
* * * * * *
38640 ACTTTTGATCTTTATAATGGAGGTCCTTAATTTTTTTCAATCCCATTTTTTTACATTTATTATTG
1 ACTTTTTACCTTTATAATTGAGGTCCCTAA-TTTTTTCAATCCCATTTTTTTACATATATAATTG
* * * * *
38705 ATATCCTAATTTTTTTCAATCCCACCTTGTACCTTTATAATTAAACTCCTACTTTTTCAATCTC
65 AGACCCTAATTTTTTTCAATCCCACCTTGTACATTTAAAATTAAACTCCTACTTTTTCAATATC
*
38769 ACTTTTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCCCA-TTTTTTAC-TCATATAATTT
1 ACTTTTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCCCATTTTTTTACAT-ATATAATTG
* * * * **
38832 AGGCCCTAATTTTTTTCAATCTCACTTTTTACATTTAAAATTGATGC-CCATA-TTTTTCTAATA
65 AGACCCTAATTTTTTTCAATCCCACCTTGTACATTTAAAATT-AAACTCC-TACTTTTTC-AATA
38895 TC
127 TC
38897 ACTTTTTACCTTTATAATT-AGGGTCCCTAATTTTTTCAATC
1 ACTTTTTACCTTTATAATTGA-GGTCCCTAATTTTTTCAATC
38938 ATACTTTTTA
Statistics
Matches: 146, Mismatches: 18, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
126 1 0.01
127 57 0.39
128 62 0.42
129 26 0.18
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (128 bp):
ACTTTTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCCCATTTTTTTACATATATAATTGA
GACCCTAATTTTTTTCAATCCCACCTTGTACATTTAAAATTAAACTCCTACTTTTTCAATATC
Found at i:38946 original size:128 final size:128
Alignment explanation
Indices: 38708--38972 Score: 331
Period size: 128 Copynumber: 2.1 Consensus size: 128
38698 ATTATTGATA
* * *
38708 TCCTAATTTTTTTCAATCCCACCTTGTACCTTTATAATTAAACTCCTACTTTTTCAATCTCACTT
1 TCCTAATTTTTTTCAATCCCACCTTGTACATTTAAAATTAAACTCCTACTTTTTCAATATCACTT
* * *
38773 TTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCCCATTTTTTACTCATATAATTTAGGC
66 TTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCACACTTTTTACTCATATAATTTAAGC
* * * **
38836 -CCTAATTTTTTTCAATCTCACTTTTTACATTTAAAATTGATGC-CCATA-TTTTTCTAATATCA
1 TCCTAATTTTTTTCAATCCCACCTTGTACATTTAAAATT-AAACTCC-TACTTTTTC-AATATCA
* ** *
38898 CTTTTTACCTTTATAATT-AGGGTCCCTAATTTTTTCAATCATACTTTTTACTTTTATAGTTTAA
63 CTTTTTACCTTTATAATTGA-GGTCCCTAATTTTTTCAATCACACTTTTTACTCATATAATTTAA
38962 GC
127 GC
38964 TCCTAATTT
1 TCCTAATTT
38973 AATCATTTTA
Statistics
Matches: 117, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
127 42 0.36
128 67 0.57
129 8 0.07
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (128 bp):
TCCTAATTTTTTTCAATCCCACCTTGTACATTTAAAATTAAACTCCTACTTTTTCAATATCACTT
TTTACCTTTATAATTGAGGTCCCTAATTTTTTCAATCACACTTTTTACTCATATAATTTAAGC
Found at i:45464 original size:17 final size:18
Alignment explanation
Indices: 45434--45468 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
45424 AAAGTATAAC
45434 GTTAAAATTTTAATCCCA
1 GTTAAAATTTTAATCCCA
45452 GTTAAAA-TTTAATCCCA
1 GTTAAAATTTTAATCCCA
45469 ACATTTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (18 bp):
GTTAAAATTTTAATCCCA
Found at i:49335 original size:5 final size:5
Alignment explanation
Indices: 49327--49360 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
49317 TTCTTTTTTT
49327 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTC
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTC
49361 AAGGTTAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTCC
Found at i:49480 original size:2 final size:2
Alignment explanation
Indices: 49475--49505 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49465 CTCTTTAATC
49475 AT AT AT AT AT 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 A
49506 CTTGAATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49940 original size:12 final size:12
Alignment explanation
Indices: 49923--49949 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
49913 GCGTTATCAT
49923 ATATATACATAC
1 ATATATACATAC
49935 ATATATACATAC
1 ATATATACATAC
49947 ATA
1 ATA
49950 CATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATATACATAC
Found at i:49946 original size:16 final size:16
Alignment explanation
Indices: 49921--49957 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
49911 AAGCGTTATC
*
49921 ATATATATACATACAT
1 ATATACATACATACAT
49937 ATATACATACATACAT
1 ATATACATACATACAT
49953 ATATA
1 ATATA
49958 TATGTTCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATACATACATACAT
Found at i:50196 original size:31 final size:29
Alignment explanation
Indices: 50137--50194 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
50127 CTTGTATAAG
50137 CTTTAGGGCTTTATATATTACATATATAT
1 CTTTAGGGCTTTATATATTACATATATAT
50166 CTTTAGGGCTTTATATATTACATATATAT
1 CTTTAGGGCTTTATATATTACATATATAT
50195 ATTGCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (29 bp):
CTTTAGGGCTTTATATATTACATATATAT
Found at i:50205 original size:27 final size:29
Alignment explanation
Indices: 50139--50210 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
50129 TGTATAAGCT
* *
50139 TTAGGGCTTTATATATTACATATATATCT
1 TTAGCGCTTTATATATTACATATATATCA
*
50168 TTAGGGCTTTATATATTACATATATAT-A
1 TTAGCGCTTTATATATTACATATATATCA
**
50196 TT-GCTTTTTATATAT
1 TTAGCGCTTTATATAT
50211 GATATTTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 10 0.26
28 2 0.05
29 27 0.69
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (29 bp):
TTAGCGCTTTATATATTACATATATATCA
Found at i:53101 original size:30 final size:30
Alignment explanation
Indices: 53066--53138 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
53056 TTATTATATT
53066 CAAATAAGCCCTTCATCTTTACATCTTATC
1 CAAATAAGCCCTTCATCTTTACATCTTATC
53096 CAAATAAGCCCTTCATCTTTACATCTTATC
1 CAAATAAGCCCTTCATCTTTACATCTTATC
53126 CAAATAAGCCCTT
1 CAAATAAGCCCTT
53139 AACCTTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (30 bp):
CAAATAAGCCCTTCATCTTTACATCTTATC
Found at i:54416 original size:2 final size:2
Alignment explanation
Indices: 54411--54445 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
54401 TCATTCTATG
*
54411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54446 AGTCCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.