Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003820.1 Hibiscus syriacus cultivar Beakdansim tig00008194_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: 59168
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3669 original size:20 final size:20
Alignment explanation
Indices: 3640--3685 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3630 TTTCAAAGTG
*
3640 ATGCACCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
* *
3660 ATGCATCGATGCACCGATGC
1 ATGCATCGATGCACCAATCC
3680 ATGCAT
1 ATGCAT
3686 GCACCATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:3856 original size:64 final size:66
Alignment explanation
Indices: 3704--3863 Score: 188
Period size: 65 Copynumber: 2.5 Consensus size: 66
3694 AAATAAATTG
* *
3704 AACATCGAATGCATTTCATGCATCGATGCA-CATACTAAGTATCGAGCCACTCAGAGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCAAGCATCGAGCCACTCAGAGTTTTATGA
3768 A
66 A
* * * * *
3769 AACATCGAATGCATTTAATGCATCGATGCACCA-GCCATGCATCGATG-TACTCTG-GCTATTT-
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCAAGCATCGA-GCCACTCAGAG-T-TTTA
3830 TG-A
63 TGAA
3833 AACATCGAATGCATTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
3864 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
64 32 0.39
65 45 0.54
66 6 0.07
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCAAGCATCGAGCCACTCAGAGTTTTATGA
A
Found at i:10647 original size:23 final size:22
Alignment explanation
Indices: 10579--10657 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
10569 CTTAACAGTG
*
10579 CATCGATGCATCCCTTTGAATGTG
1 CATCGATGCA-CCC-TTGAATGTA
* * *
10603 CATCGATACA-CCATGAAGGTA
1 CATCGATGCACCCTTGAATGTA
10624 CATCGATGCACGCCTTGAATGTA
1 CATCGATGCAC-CCTTGAATGTA
10647 CATCGATGCAC
1 CATCGATGCAC
10658 AAGGCCATGC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 20 0.43
24 9 0.20
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (22 bp):
CATCGATGCACCCTTGAATGTA
Found at i:13424 original size:64 final size:63
Alignment explanation
Indices: 13300--13506 Score: 208
Period size: 64 Copynumber: 3.2 Consensus size: 63
13290 TTTCAAAGTG
* * * **
13300 ATGCACCGATGCACCAATCTATGCATCGATGCACT-ATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATT
13363 TC
62 TC
* *
13365 ATGCACCGATGCACATACTATGCATCGATGCACTCAGTG-T-TTTATGAAAACATCG-ATGCATT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATT
*
13427 TG
62 TC
* *
13429 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
13493 ATGCATCGATGCAC
1 ATGCATCGATGCAC
13507 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 8, Indels: 22
0.81 0.05 0.14
Matches are distributed among these distances:
62 1 0.01
63 13 0.10
64 82 0.66
65 28 0.23
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
Found at i:25041 original size:31 final size:31
Alignment explanation
Indices: 25003--25107 Score: 160
Period size: 31 Copynumber: 3.4 Consensus size: 31
24993 AATAGTCAAT
25003 TCTGATTTTTTTTATTG-TTTATATAACTGAA
1 TCTGA-TTTTTTTATTGCTTTATATAACTGAA
*
25034 TCTGA-TTTTTTATTGTTTTATATAACTGAA
1 TCTGATTTTTTTATTGCTTTATATAACTGAA
*
25064 TCTGATTTTTTTATTGCTTTATATCAAATGAA
1 TCTGATTTTTTTATTGCTTTATAT-AACTGAA
25096 TCTGATTTTTTT
1 TCTGATTTTTTT
25108 TCTTGCTTGC
Statistics
Matches: 69, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
29 10 0.14
30 19 0.28
31 22 0.32
32 18 0.26
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.58
Consensus pattern (31 bp):
TCTGATTTTTTTATTGCTTTATATAACTGAA
Found at i:27453 original size:14 final size:14
Alignment explanation
Indices: 27434--27462 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27424 TTACTATTTG
27434 TTTTATTGTGTTGT
1 TTTTATTGTGTTGT
27448 TTTTATTGTGTTGT
1 TTTTATTGTGTTGT
27462 T
1 T
27463 AAGACTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.21, T:0.72
Consensus pattern (14 bp):
TTTTATTGTGTTGT
Found at i:29212 original size:19 final size:19
Alignment explanation
Indices: 29188--29227 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
29178 GTTAAAAATG
*
29188 ATTTGATTTTGAAAGCAAA
1 ATTTGATTTTGAAAACAAA
29207 ATTTGATTTTGAAAACAAA
1 ATTTGATTTTGAAAACAAA
29226 AT
1 AT
29228 GAAATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (19 bp):
ATTTGATTTTGAAAACAAA
Found at i:29234 original size:19 final size:19
Alignment explanation
Indices: 29193--29240 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
29183 AAATGATTTG
* ***
29193 ATTTTGAAAGCAAAATTTG
1 ATTTTGAAAACAAAATGAA
29212 ATTTTGAAAACAAAATGAA
1 ATTTTGAAAACAAAATGAA
29231 ATTTTGAAAA
1 ATTTTGAAAA
29241 ATGATTTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.33
Consensus pattern (19 bp):
ATTTTGAAAACAAAATGAA
Found at i:31583 original size:22 final size:23
Alignment explanation
Indices: 31545--31589 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31535 ATAAGCGCAA
*
31545 AAAAATATGTCATAAAAATAGAG
1 AAAAACATGTCATAAAAATAGAG
*
31568 AAAAACATGTCA-AAAAGTAGAG
1 AAAAACATGTCATAAAAATAGAG
31590 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.60, C:0.07, G:0.16, T:0.18
Consensus pattern (23 bp):
AAAAACATGTCATAAAAATAGAG
Found at i:32741 original size:15 final size:15
Alignment explanation
Indices: 32721--32777 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
32711 AACCGGGTAT
32721 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
32736 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
*
32753 CGGATACCCGATTAC
1 CGGGTACCCGATTAC
32768 CGGGTACCCG
1 CGGGTACCCG
32778 TAACATCCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:32766 original size:32 final size:32
Alignment explanation
Indices: 32725--32787 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
32715 GGGTATCGGG
32725 TACCCGATTACCGGGTACCCGCAAAATCCGGA
1 TACCCGATTACCGGGTACCCGCAAAATCCGGA
* *
32757 TACCCGATTACCGGGTACCCGTAACATCCGG
1 TACCCGATTACCGGGTACCCGCAAAATCCGG
32788 GTCGGAACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.35, G:0.22, T:0.17
Consensus pattern (32 bp):
TACCCGATTACCGGGTACCCGCAAAATCCGGA
Found at i:32789 original size:17 final size:16
Alignment explanation
Indices: 32721--32789 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
32711 AACCGGGTAT
**
32721 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
32736 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
* **
32753 CGGATACCCGATTA-C
1 CGGGTACCCGAAAATC
*
32768 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
32785 CGGGT
1 CGGGT
32790 CGGAACACGG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:33145 original size:32 final size:32
Alignment explanation
Indices: 33102--33165 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
33092 AAACATATTA
* *
33102 ATATATAAATTATAACTTATATATATATATAT
1 ATATATAAATTATAAATTATAAATATATATAT
* *
33134 ATATATGAATTATAAATTATAAATATTTATAT
1 ATATATAAATTATAAATTATAAATATATATAT
33166 TTTGTTAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (32 bp):
ATATATAAATTATAAATTATAAATATATATAT
Found at i:34977 original size:18 final size:17
Alignment explanation
Indices: 34954--35013 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
34944 GTGGATAAAT
34954 TAGTTATATTTAATTTGA
1 TAGTTATATTTAATTT-A
*
34972 TAGTTATA--TAA-AT-
1 TAGTTATATTTAATTTA
*
34985 TAGTTAAATTTAATTTAA
1 TAGTTATATTTAATTT-A
35003 TAGTTATATTT
1 TAGTTATATTT
35014 TTTTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
13 7 0.21
15 4 0.12
16 4 0.12
18 18 0.55
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.53
Consensus pattern (17 bp):
TAGTTATATTTAATTTA
Found at i:34983 original size:31 final size:31
Alignment explanation
Indices: 34948--35011 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
34938 AATGAAGTGG
* *
34948 ATAAATTAGTTATATTTAATTTGATAGTTAT
1 ATAAATTAGTTAAATTTAATTTAATAGTTAT
34979 ATAAATTAGTTAAATTTAATTTAATAGTTAT
1 ATAAATTAGTTAAATTTAATTTAATAGTTAT
35010 AT
1 AT
35012 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (31 bp):
ATAAATTAGTTAAATTTAATTTAATAGTTAT
Found at i:39799 original size:20 final size:20
Alignment explanation
Indices: 39769--39814 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
39759 TTAAAAATCT
39769 GTTTCACCCCCT-AGAATTTTA
1 GTTT-ACCCCCTGA-AATTTTA
39790 GTTTACCCCCTGAAATTTTA
1 GTTTACCCCCTGAAATTTTA
39810 GTTTA
1 GTTTA
39815 TCCCTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (20 bp):
GTTTACCCCCTGAAATTTTA
Found at i:40573 original size:18 final size:18
Alignment explanation
Indices: 40541--40598 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
40531 GTTCAGTATT
*
40541 TGTCCCGATGGACCACTA
1 TGTCCCGAAGGACCACTA
*
40559 TGTCCCGAAGTACCACTGAA
1 TGTCCCGAAGGACCACT--A
*
40579 TACGTCCCGAATGACCACTA
1 T--GTCCCGAAGGACCACTA
40599 AATACGTCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 15 0.47
20 3 0.09
22 14 0.44
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:40588 original size:22 final size:22
Alignment explanation
Indices: 40560--40642 Score: 132
Period size: 22 Copynumber: 3.8 Consensus size: 22
40550 GGACCACTAT
*
40560 GTCCCGAA-GTACCACTGAATAC
1 GTCCCGAATG-ACCACTAAATAC
40582 GTCCCGAATGACCACTAAATAC
1 GTCCCGAATGACCACTAAATAC
40604 GTCCCGAATGACCACTAAATAC
1 GTCCCGAATGACCACTAAATAC
*
40626 ATCCCGAATGACCACTA
1 GTCCCGAATGACCACTA
40643 TACCCTCGAC
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
22 57 0.98
23 1 0.02
ACGTcount: A:0.35, C:0.33, G:0.14, T:0.18
Consensus pattern (22 bp):
GTCCCGAATGACCACTAAATAC
Found at i:41246 original size:63 final size:64
Alignment explanation
Indices: 41137--41294 Score: 171
Period size: 63 Copynumber: 2.5 Consensus size: 64
41127 ATTCCTTAAC
* * *
41137 GGGTGCATCGATGCACT-ACTTATGCATCGGTGCATAAATCATATTCGATGTTTGTATTTAAT-G
1 GGGTGCATCGATGCACTCA-TTATGCATCGATGCATAAATCACATTCGATGTTTGTATTTAATCA
** * * *
41200 GGGTGCATCGATGCACTCATTATGCATCGATGCACT-AATGGCATTCGATGTTTTTGTTTTATCA
1 GGGTGCATCGATGCACTCATTATGCATCGATGCA-TAAATCACATTCGATGTTTGTATTTAATCA
* *
41264 GAGTGCATCGATGCACTTCA-TGTGCATCGAT
1 GGGTGCATCGATGCAC-TCATTATGCATCGAT
41295 ACACCTTGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 51 0.63
64 27 0.33
65 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (64 bp):
GGGTGCATCGATGCACTCATTATGCATCGATGCATAAATCACATTCGATGTTTGTATTTAATCA
Found at i:46105 original size:27 final size:27
Alignment explanation
Indices: 46053--46106 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
46043 TTAATAGAAA
*
46053 TAAAATGATTAAATATAATCTTAAAAT
1 TAAAATGATTAAATATAATCTAAAAAT
* *
46080 TAAAATTATTAAATTTAAT-TCAAAAAT
1 TAAAATGATTAAATATAATCT-AAAAAT
46107 CAACAAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAAATGATTAAATATAATCTAAAAAT
Found at i:49649 original size:39 final size:39
Alignment explanation
Indices: 49604--49696 Score: 186
Period size: 39 Copynumber: 2.4 Consensus size: 39
49594 ACGATCACTT
49604 ATGTGCTGTTCATATATTTATTGGTTTAGACAAATACTA
1 ATGTGCTGTTCATATATTTATTGGTTTAGACAAATACTA
49643 ATGTGCTGTTCATATATTTATTGGTTTAGACAAATACTA
1 ATGTGCTGTTCATATATTTATTGGTTTAGACAAATACTA
49682 ATGTGCTGTTCATAT
1 ATGTGCTGTTCATAT
49697 GTGACAAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (39 bp):
ATGTGCTGTTCATATATTTATTGGTTTAGACAAATACTA
Found at i:49921 original size:36 final size:36
Alignment explanation
Indices: 49849--49987 Score: 124
Period size: 36 Copynumber: 3.9 Consensus size: 36
49839 TCAAGACACA
* * **
49849 TATAATTCTATAATTTTAATTATACTTAATGCTAAT
1 TATAATTCTATAATTATAATTATATTTAATTATAAT
* * * *
49885 TACAATTCTATAATTCTAATTACATTTAATTTTAATT
1 TATAATTCTATAATTATAATTATATTTAATTATAA-T
*
49922 TTTAA-T-TATAATTATAA-TATATTTAATTATAAT
1 TATAATTCTATAATTATAATTATATTTAATTATAAT
* *
49955 TATAATTCTACTTAATTAAAATTA-AATTAATTA
1 TATAATTCTA--TAATTATAATTATATTTAATTA
49988 AAGTCCTATT
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
33 5 0.06
34 14 0.17
35 12 0.14
36 30 0.36
37 20 0.24
38 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.50
Consensus pattern (36 bp):
TATAATTCTATAATTATAATTATATTTAATTATAAT
Found at i:49948 original size:21 final size:22
Alignment explanation
Indices: 49922--49983 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
49912 AATTTTAATT
49922 TTTAATTATAATTATAA-TATA
1 TTTAATTATAATTATAATTATA
*
49943 TTTAATTATAATTATAATTCTA
1 TTTAATTATAATTATAATTATA
* *
49965 CTTAATTAAAATTA-AATTA
1 TTTAATTATAATTATAATTA
49984 ATTAAAGTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATTATAATTATAATTATA
Found at i:49954 original size:6 final size:6
Alignment explanation
Indices: 49893--49961 Score: 58
Period size: 6 Copynumber: 12.2 Consensus size: 6
49883 ATTACAATTC
* * * *
49893 TATAAT TCTAAT TA-CAT T-TAAT TTTAATT TTTAAT TATAAT TATAA-
1 TATAAT TATAAT TATAAT TATAAT TATAA-T TATAAT TATAAT TATAAT
49939 TAT-AT T-TAAT TATAAT TATAAT T
1 TATAAT TATAAT TATAAT TATAAT T
49962 CTACTTAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
4 2 0.04
5 13 0.25
6 31 0.60
7 6 0.12
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (6 bp):
TATAAT
Found at i:50464 original size:2 final size:2
Alignment explanation
Indices: 50457--50481 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50447 TATTTCAGAT
50457 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
50482 TGCATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50745 original size:3 final size:3
Alignment explanation
Indices: 50737--50770 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
50727 TGACATAATA
*
50737 TAT TAT TATT TAT TAT TAT TAT TAT AAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
50771 AAAAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:51382 original size:2 final size:2
Alignment explanation
Indices: 51375--51409 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
51365 ATATACCAGA
51375 AT AT 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 AT AT A
51410 CAATAAAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52286 original size:21 final size:22
Alignment explanation
Indices: 52245--52287 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
52235 AAGATAGAAG
*
52245 TTGGGGCAAGGGAAACTAAATT
1 TTGGGGCAAGGAAAACTAAATT
52267 TTGGGGCAAGGAAAAC-AAATT
1 TTGGGGCAAGGAAAACTAAATT
52288 GTCTCAGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (22 bp):
TTGGGGCAAGGAAAACTAAATT
Found at i:52417 original size:14 final size:15
Alignment explanation
Indices: 52398--52429 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
52388 ATCGAGAAAT
52398 CATACATACAT-ACA
1 CATACATACATGACA
52412 CATACATACATGACA
1 CATACATACATGACA
52427 CAT
1 CAT
52430 GAAATTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.22
Consensus pattern (15 bp):
CATACATACATGACA
Found at i:53277 original size:96 final size:94
Alignment explanation
Indices: 53101--53277 Score: 223
Period size: 96 Copynumber: 1.9 Consensus size: 94
53091 ATTTATAGTC
* * *
53101 TTTGAGTCTGTTTCTCTTGAAACACCCACCTTTGAGATCGTTTCTATTGAAACAATTTTGTCTCC
1 TTTGAGTCTGTTTCTCTTGAAACACCCACCTTTGAGATCATTTCCATTGAAACAATTTTATCTCC
* *
53166 CTTGAGGCAATTTCTCGGGAAACACAATA
66 CTTAAGACAATTTCTCGGGAAACACAATA
* * *
53195 TTTGAGTCTGTTT-TACTTGAAACAAAGCCATCTTTGAG-TCATTTCCCTTGAAACGAATTTTAT
1 TTTGAGTCTGTTTCT-CTTGAAAC--ACCCACCTTTGAGATCATTTCCATTGAAAC-AATTTTAT
*
53258 CTCTCTTAAGACAATTTCTC
62 CTCCCTTAAGACAATTTCTC
53278 TTAAAACAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
93 1 0.01
94 21 0.30
95 13 0.19
96 35 0.50
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (94 bp):
TTTGAGTCTGTTTCTCTTGAAACACCCACCTTTGAGATCATTTCCATTGAAACAATTTTATCTCC
CTTAAGACAATTTCTCGGGAAACACAATA
Found at i:53541 original size:36 final size:36
Alignment explanation
Indices: 53476--53579 Score: 90
Period size: 36 Copynumber: 2.9 Consensus size: 36
53466 TCTGAGAAAA
** * *
53476 ATCTTTGAGTCTGTTT-ATTTGGAATCAAAATTTTCC
1 ATCTTTGAGTCTGTTTCCCTT-GAAACAAAATTTTAC
***
53512 ATCTTTGAGTCTGTTTCCCTTGAAACAAAA-CAAAC
1 ATCTTTGAGTCTGTTTCCCTTGAAACAAAATTTTAC
*
53547 ATCTTTGAGAAC-GTTTCCCTTGAAAC-AAATTTT
1 ATCTTTGAG-TCTGTTTCCCTTGAAACAAAATTTT
53580 GTCTCATTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
34 3 0.06
35 24 0.44
36 25 0.46
37 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (36 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACAAAATTTTAC
Found at i:53775 original size:28 final size:28
Alignment explanation
Indices: 53729--53825 Score: 117
Period size: 28 Copynumber: 3.4 Consensus size: 28
53719 AAGACAGTTG
*
53729 CTTTTGAAACACATCATCTTTGAGTTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTCTGTTT
53760 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
53788 CTTTTGAAACAAATCTTTGAGTC-GATTT
1 CTTTTGAAACAAATCTTTGAGTCTG-TTT
*
53816 CTCTTGAAAC
1 CTTTTGAAAC
53826 CATAATTCCT
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
27 1 0.02
28 47 0.77
29 2 0.03
30 3 0.05
31 8 0.13
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.44
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:54142 original size:134 final size:129
Alignment explanation
Indices: 53850--54180 Score: 351
Period size: 134 Copynumber: 2.5 Consensus size: 129
53840 TGGTCTGCCA
* * * * * *
53850 TCCTCATCATGTAGGAACCGTGTCATCCCCCGATCAGACCTCCTCATCACGTAGGAGTCGTGTCA
1 TCCTCATCACGTACGAACCGTGTCAT-CCACGACCAGACCTCCTAATCACGTAGGAGCCGTGTCA
* * * *
53915 CCTCAGAAAACCAGCCATCCTCATCACGTAGGAATCATGTTATCATTCTTAAAGATGGCATGTCG
65 CCCCAGAAAACCAGCCATCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCATGACG
* * *
53980 TCCTCATCACATACGAACCGTGTCATCCATCGACCAGACCTCCTTATCATGTAGGAGCCGTGTCA
1 TCCTCATCACGTACGAACCGTGTCATCCA-CGACCAGACCTCCTAATCACGTAGGAGCCGTGTCA
* ** * * *
54045 CCCCTAGATAACCAGCTGTCTTCATCGCGTAGGAACCGTGTTATCATCCTTCCTAAAGATGGCCA
65 CCCC-AGAAAACCAGCCATCCTCATCACGTAGGAACCATGTTATCA---TTCCTAAAGATGG-CA
54110 -GAAC-
125 TG-ACG
* * * * *
54114 TCTTCATCACGTATGAGCCGTGTCATCCACTGACCATATCTCCTAATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTACGAACCGTGTCATCCAC-GACCAGACCTCCTAATCACGTAGGAGCCGTGTCA
54179 CC
65 CC
54181 TTTAGACGAC
Statistics
Matches: 167, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
129 2 0.01
130 57 0.34
131 34 0.20
133 1 0.01
134 70 0.42
135 3 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (129 bp):
TCCTCATCACGTACGAACCGTGTCATCCACGACCAGACCTCCTAATCACGTAGGAGCCGTGTCAC
CCCAGAAAACCAGCCATCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCATGACG
Found at i:54383 original size:3 final size:3
Alignment explanation
Indices: 54375--54411 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
54365 TATAAAAATA
54375 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
54412 ACATAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:55870 original size:30 final size:29
Alignment explanation
Indices: 55825--55929 Score: 79
Period size: 30 Copynumber: 3.5 Consensus size: 29
55815 TGTTAATACC
55825 ATTTTAGACCC-TTAAATTTTTGTTTTTACT
1 ATTTTAG-CCCTTTAAATTTTTGTTTTT-CT
* * *
55855 ATTTTAGCCCTTTAAAATTCTGTGTGTGTC-
1 ATTTTAGCCCTTT-AAATT-TTTGTTTTTCT
* * *
55885 ATTTTAGTCCTTTAAGTTTTAGTTTTTTCT
1 ATTTTAGCCCTTTAAATTTTTG-TTTTTCT
* *
55915 ATTTTGGTCCTTTAA
1 ATTTTAGCCCTTTAA
55930 GTTGCTATTC
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
28 2 0.03
29 11 0.18
30 35 0.58
31 6 0.10
32 6 0.10
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.55
Consensus pattern (29 bp):
ATTTTAGCCCTTTAAATTTTTGTTTTTCT
Found at i:55930 original size:30 final size:29
Alignment explanation
Indices: 55883--55965 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
55873 TCTGTGTGTG
* *
55883 TCATTTTAGTCCTTTAAGTTTTAGTT-TTT
1 TCATTTTGGTCCTTTAAGTTTTA-TTCTTC
*
55912 TCTATTTTGGTCCTTTAAGTTGCTATTCTTC
1 TC-ATTTTGGTCCTTTAAGTT-TTATTCTTC
55943 TCATTTTGGTCCTTGTAA-TTTTA
1 TCATTTTGGTCCTT-TAAGTTTTA
55966 AACATTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 4 0.09
30 33 0.72
31 9 0.20
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (29 bp):
TCATTTTGGTCCTTTAAGTTTTATTCTTC
Found at i:56070 original size:19 final size:19
Alignment explanation
Indices: 56029--56072 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
56019 TTTCAATCCG
**
56029 TATGTATATATTTGTATGT
1 TATGTATATATTTGTATCA
56048 TATGTAT-TCATTTGTATCA
1 TATGTATAT-ATTTGTATCA
56067 TATGTA
1 TATGTA
56073 ATTAAATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.55
Consensus pattern (19 bp):
TATGTATATATTTGTATCA
Found at i:57539 original size:60 final size:60
Alignment explanation
Indices: 57461--57586 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
57451 GAATATATGA
* *
57461 ATAGTTGAGTGACCATTTTATAACTTTT-AATACTCAACGA-ACTCAACAAAATAATGTCTT
1 ATAGTTGAGTGACCATTTTATAA-TTTTCAATAATC-ACGAGACTCAACAAAATAATGTCAT
* * **
57521 ATAGTTAGAG-GACTATTTTGTAATTTTCAATAATCGTGAGACTCAACAAAATAATGTCAT
1 ATAGTT-GAGTGACCATTTTATAATTTTCAATAATCACGAGACTCAACAAAATAATGTCAT
57581 ATAGTT
1 ATAGTT
57587 TAGGTATCAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
59 6 0.11
60 48 0.84
61 3 0.05
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (60 bp):
ATAGTTGAGTGACCATTTTATAATTTTCAATAATCACGAGACTCAACAAAATAATGTCAT
Found at i:58199 original size:43 final size:43
Alignment explanation
Indices: 58138--58272 Score: 195
Period size: 43 Copynumber: 3.2 Consensus size: 43
58128 TGTTTCAGGT
* *
58138 GAGCAACCACCAAAGATCATGTGTCGATCAACTACAACCCAGC
1 GAGCAACCACCCATGATCATGTGTCGATCAACTACAACCCAGC
58181 GAGCAACCACCCATGATCA---GTCGATCAACTACAACCCAGC
1 GAGCAACCACCCATGATCATGTGTCGATCAACTACAACCCAGC
** *
58221 GAGCAACCACCCATGATCATGTGTCGATCAACTATGACCCCGC
1 GAGCAACCACCCATGATCATGTGTCGATCAACTACAACCCAGC
*
58264 GAACAACCA
1 GAGCAACCA
58273 TAAGTGAACA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
40 40 0.48
43 43 0.52
ACGTcount: A:0.35, C:0.35, G:0.16, T:0.14
Consensus pattern (43 bp):
GAGCAACCACCCATGATCATGTGTCGATCAACTACAACCCAGC
Done.