Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005401.1 Hibiscus syriacus cultivar Beakdansim tig00012385_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: 109280
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:7781 original size:7 final size:7
Alignment explanation
Indices: 7765--7823 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
7755 ATTATATATA
*
7765 TATATAT
1 TATATTT
7772 TATATTT
1 TATATTT
7779 TATATTTT
1 TATA-TTT
7787 TATATTAAT
1 TATATT--T
*
7796 TATATAT
1 TATATTT
*
7803 AATATTT
1 TATATTT
7810 TATATTTT
1 TATA-TTT
7818 TATATT
1 TATATT
7824 AATTATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
7 23 0.53
8 14 0.33
9 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TATATTT
Found at i:7801 original size:33 final size:31
Alignment explanation
Indices: 7765--7835 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
7755 ATTATATATA
*
7765 TATATATTATATTTTATATTTTTATATTAAT
1 TATATATAATATTTTATATTTTTATATTAAT
7796 TATATATAATATTTTATATTTTTATATTAAT
1 TATATATAATATTTTATATTTTTATATTAAT
7827 TATATATAA
1 TATATATAA
7836 AATATTTTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TATATATAATATTTTATATTTTTATATTAAT
Found at i:7840 original size:33 final size:32
Alignment explanation
Indices: 7763--7843 Score: 128
Period size: 31 Copynumber: 2.5 Consensus size: 32
7753 CGATTATATA
*
7763 TATATATATTATATTTTATATTTTTATATTAAT
1 TATATATA-AATATTTTATATTTTTATATTAAT
7796 TATATAT-AATATTTTATATTTTTATATTAAT
1 TATATATAAATATTTTATATTTTTATATTAAT
7827 TATATATAAAATATTTT
1 TATATAT-AAATATTTT
7844 CGAGTTCAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
31 30 0.67
33 15 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TATATATAAATATTTTATATTTTTATATTAAT
Found at i:20656 original size:14 final size:14
Alignment explanation
Indices: 20637--20667 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
20627 GTCTCCATAA
20637 CAACATTAGTAAAG
1 CAACATTAGTAAAG
20651 CAACATTAGTAAAG
1 CAACATTAGTAAAG
20665 CAA
1 CAA
20668 GCAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.19
Consensus pattern (14 bp):
CAACATTAGTAAAG
Found at i:23706 original size:29 final size:29
Alignment explanation
Indices: 23673--23757 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
23663 AGCAGGGGAT
* * **
23673 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* * *
23702 GTCGCCGGGCGTGCATGGCAACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
23731 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
23758 GCCACTGTTG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.14, C:0.29, G:0.39, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:27186 original size:26 final size:26
Alignment explanation
Indices: 27156--27226 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 26
27146 AAAGTCCAAC
27156 AAATTTAACAAAATAAAGTAAATATT
1 AAATTTAACAAAATAAAGTAAATATT
*
27182 AAA-TTAA-ATAAT-AA--AAA-ATT
1 AAATTTAACAAAATAAAGTAAATATT
27202 ACAATTTAACAAAATAAAGTAAATA
1 A-AATTTAACAAAATAAAGTAAATA
27227 CAAATATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
20 4 0.11
21 5 0.14
22 4 0.11
23 6 0.17
24 6 0.17
25 4 0.11
26 6 0.17
27 1 0.03
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (26 bp):
AAATTTAACAAAATAAAGTAAATATT
Found at i:32104 original size:12 final size:12
Alignment explanation
Indices: 32087--32116 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
32077 AAATTTTGGA
32087 TTTTTTGGCTTT
1 TTTTTTGGCTTT
*
32099 TTTTTTTGCTTT
1 TTTTTTGGCTTT
32111 TTTTTT
1 TTTTTT
32117 TTGTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (12 bp):
TTTTTTGGCTTT
Found at i:32117 original size:12 final size:12
Alignment explanation
Indices: 32087--32126 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
32077 AAATTTTGGA
*
32087 TTTTTTGGCTTT
1 TTTTTTTGCTTT
32099 TTTTTTTGCTTTT
1 TTTTTTTGC-TTT
32112 TTTTTTTG-TTT
1 TTTTTTTGCTTT
32123 TTTT
1 TTTT
32127 GGAAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.27
12 8 0.31
13 11 0.42
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (12 bp):
TTTTTTTGCTTT
Found at i:35239 original size:17 final size:18
Alignment explanation
Indices: 35196--35236 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
35186 AATTTATATT
35196 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
35213 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
35231 ATTAAA
1 AGTAAA
35237 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:35566 original size:30 final size:29
Alignment explanation
Indices: 35504--35566 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
35494 TACTGCTACG
** *
35504 GGTGTTAGATCGGGAAATATAATTTGACC
1 GGTGTTAGATCGGGAAATATAAGATCACC
* *
35533 GGTGTTAGATCGGTAAATATACCGATCACC
1 GGTGTTAGATCGGGAAATATA-AGATCACC
35563 GGTG
1 GGTG
35567 ATATTTCGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAAGATCACC
Found at i:36381 original size:15 final size:16
Alignment explanation
Indices: 36327--36383 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
36317 TTCAAAGCCA
*
36327 AATCATTCAGAGCATTTA
1 AATCATTCA-A-CATTTG
36345 AATCATTCAACATTTG
1 AATCATTCAACATTTG
* *
36361 AATCATTCACCGTTT-
1 AATCATTCAACATTTG
36376 AATCATTC
1 AATCATTC
36384 TGAAGTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.22
16 18 0.50
17 1 0.03
18 9 0.25
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (16 bp):
AATCATTCAACATTTG
Found at i:41760 original size:27 final size:25
Alignment explanation
Indices: 41730--41782 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
41720 ATATTTTATT
*
41730 ATATTTATT-TTTAATATAAAATTTAAA
1 ATATTT-TTATTTAA-A-AAAATTAAAA
41757 ATATTTTTATTTAAAAAAATTAAAA
1 ATATTTTTATTTAAAAAAATTAAAA
41782 A
1 A
41783 GCCCTTGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATTTTTATTTAAAAAAATTAAAA
Found at i:52035 original size:23 final size:23
Alignment explanation
Indices: 52009--52099 Score: 119
Period size: 23 Copynumber: 4.0 Consensus size: 23
51999 ATTATTATAT
*
52009 GGCACTACAGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* * * *
52032 GGCACTTCGGTGTAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
52055 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* *
52078 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
52100 AGCTGTGGTG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:53447 original size:28 final size:28
Alignment explanation
Indices: 53407--53467 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
53397 AAGTAAGATT
*
53407 GTGGATATGATAAAGGTTTGTATTTCAG
1 GTGGATATGATAAAGGTTTGTATTCCAG
53435 GTGGATATGATAAAGGTTTGTATTCCAG
1 GTGGATATGATAAAGGTTTGTATTCCAG
*
53463 ATGGA
1 GTGGA
53468 AAGAGTTAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.36
Consensus pattern (28 bp):
GTGGATATGATAAAGGTTTGTATTCCAG
Found at i:56979 original size:23 final size:23
Alignment explanation
Indices: 56952--57030 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
56942 TATGGTACTA
*
56952 CGGTGCATTTCTACGCGTCACTT
1 CGGTGCATTTCTACGCGACACTT
* * * * *
56975 TGGTGCAATTCTACGTGGCACTA
1 CGGTGCATTTCTACGCGACACTT
*
56998 CGGTGCATTTCTATGCGACACTT
1 CGGTGCATTTCTACGCGACACTT
*
57021 CGATGCATTT
1 CGGTGCATTT
57031 ATACAAGCTG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (23 bp):
CGGTGCATTTCTACGCGACACTT
Found at i:58038 original size:25 final size:25
Alignment explanation
Indices: 57990--58038 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
57980 ACCACCACAG
*
57990 CTGCCCTTGACGCAAAATATGAAAA
1 CTGCCCTTGACGCAAAAGATGAAAA
*
58015 CTGCCCTTGACTGCAACAGA-GAAA
1 CTGCCCTTGAC-GCAAAAGATGAAA
58039 GAGATGTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (25 bp):
CTGCCCTTGACGCAAAAGATGAAAA
Found at i:68533 original size:32 final size:32
Alignment explanation
Indices: 68497--68560 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
68487 CCCTCATTGC
68497 TTTTCTACCCACTTCAAAGATATTTTTGCAGT
1 TTTTCTACCCACTTCAAAGATATTTTTGCAGT
*
68529 TTTTCTACCTACTTCAAAGATATTTTTGCAGT
1 TTTTCTACCCACTTCAAAGATATTTTTGCAGT
68561 CCAACCACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.45
Consensus pattern (32 bp):
TTTTCTACCCACTTCAAAGATATTTTTGCAGT
Found at i:68582 original size:5 final size:5
Alignment explanation
Indices: 68572--68769 Score: 328
Period size: 5 Copynumber: 38.8 Consensus size: 5
68562 CAACCACATA
68572 TATAT TATAT TATAT TATAT TATAT TATAT TATATT ATATAT TATAT TATATT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA-T -TATAT TATAT TATA-T
68625 ATATAT TATAT TATATT ATATAT TATAT TATA- T-TAT TATAT TATAT
1 -TATAT TATAT TATA-T -TATAT TATAT TATAT TATAT TATAT TATAT
68671 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
68721 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
68770 AGTTTATTTC
Statistics
Matches: 185, Mismatches: 0, Indels: 16
0.92 0.00 0.08
Matches are distributed among these distances:
3 2 0.01
4 2 0.01
5 163 0.88
6 6 0.03
7 12 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:68819 original size:55 final size:55
Alignment explanation
Indices: 68755--68875 Score: 199
Period size: 55 Copynumber: 2.2 Consensus size: 55
68745 TTATATTATA
* * *
68755 TTATATTATATTATAAGTTTATTTCATATTTGTGCCCCA-CCTCTTCAATTTGCTT
1 TTATTTTATATTATAAGTTTATTTAATATTTATGCCCCACCCT-TTCAATTTGCTT
68810 TTATTTTATATTATAAGTTTATTTAATATTTATGCCCCACCCTTTCAATTTGCTT
1 TTATTTTATATTATAAGTTTATTTAATATTTATGCCCCACCCTTTCAATTTGCTT
68865 TTATTTTATAT
1 TTATTTTATAT
68876 ATCCTTCTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
55 59 0.95
56 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.54
Consensus pattern (55 bp):
TTATTTTATATTATAAGTTTATTTAATATTTATGCCCCACCCTTTCAATTTGCTT
Found at i:82440 original size:2 final size:2
Alignment explanation
Indices: 82427--82467 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
82417 TGCACCTTTC
* *
82427 AT AT AT -T A- AT AT AT AT AT AT AT TT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82467 A
1 A
82468 ATCCACGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:82889 original size:31 final size:31
Alignment explanation
Indices: 82835--82962 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
82825 GAACCTCGGC
* * *
82835 AACTGTCCATA-GGTCTCAAAGAACCTAGGTA
1 AACTGTCCATATGTTC-CATAGAACATAGGTA
* *
82866 AACTGTTCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * *
82897 TACTGTCCATATGTCTCGAAAGAA-ATAGGTAA
1 AACTGTCCATATGT-TCCATAGAACATAGGT-A
*
82929 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
82960 AAC
1 AAC
82963 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
31 50 0.63
32 29 0.37
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:82945 original size:63 final size:62
Alignment explanation
Indices: 82836--82959 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 62
82826 AACCTCGGCA
* * *
82836 ACTGTCCATAGGTCTCAAAGAACCTAGGTAAACTGTTCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCTCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
*
82898 ACTGTCCATATGTCTCGAAAGAA-ATAGGTAAAACTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTCTC-AAAGAACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAGGTA
82960 AACCCTCGAC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 20 0.36
63 36 0.64
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (62 bp):
ACTGTCCATAGGTCTCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:83679 original size:21 final size:21
Alignment explanation
Indices: 83647--83689 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
83637 TGTTTGTTTA
83647 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
83668 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
83689 A
1 A
83690 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:91903 original size:7 final size:8
Alignment explanation
Indices: 91886--91917 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
91876 ACCCTCTTTC
91886 AAAAAGAA
1 AAAAAGAA
91894 AAAAAGAA
1 AAAAAGAA
91902 AAAAAGAA
1 AAAAAGAA
91910 AAAAAGAA
1 AAAAAGAA
91918 GAAGAGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:95726 original size:14 final size:13
Alignment explanation
Indices: 95688--95737 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
95678 TACTTACTCC
*
95688 TATTAATAATGTT
1 TATTAAAAATGTT
95701 T-TTAAAAA-GTT
1 TATTAAAAATGTT
95712 TAATTAAAAATGTT
1 T-ATTAAAAATGTT
*
95726 T-TTTAAAATGTT
1 TATTAAAAATGTT
95738 GCGAACAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 4 0.12
12 16 0.50
13 8 0.25
14 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (13 bp):
TATTAAAAATGTT
Found at i:95884 original size:14 final size:15
Alignment explanation
Indices: 95846--95891 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
95836 TAAATTAATT
*
95846 TAAATTATATTAATGA
1 TAAATTATA-TAATAA
95862 TATAATTATATAA-AA
1 TA-AATTATATAATAA
95877 TAAATTATAT-ATAA
1 TAAATTATATAATAA
95891 T
1 T
95892 TATACCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 1 0.04
14 11 0.41
15 3 0.11
16 5 0.19
17 7 0.26
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
TAAATTATATAATAA
Found at i:95947 original size:10 final size:10
Alignment explanation
Indices: 95932--95971 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
95922 AGAAGAAATA
95932 AATTATATAT
1 AATTATATAT
95942 AATTATAT-T
1 AATTATATAT
*
95951 AA-TGT-TAT
1 AATTATATAT
95959 AATTATATAT
1 AATTATATAT
95969 AAT
1 AAT
95972 ATTGAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
7 1 0.04
8 5 0.20
9 5 0.20
10 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (10 bp):
AATTATATAT
Found at i:100748 original size:2 final size:2
Alignment explanation
Indices: 100705--100732 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
100695 TCTCTCTCTC
100705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
100733 GACGTAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107322 original size:22 final size:22
Alignment explanation
Indices: 107294--107346 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
107284 GAAAACCCCC
107294 AACTCATAACCCACTCCTAGGT
1 AACTCATAACCCACTCCTAGGT
107316 AACTCATAACCCACTCCTAGGT
1 AACTCATAACCCACTCCTAGGT
107338 AAC-CATAAC
1 AACTCATAAC
107347 TTGATTACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.36, C:0.36, G:0.08, T:0.21
Consensus pattern (22 bp):
AACTCATAACCCACTCCTAGGT
Found at i:109014 original size:59 final size:58
Alignment explanation
Indices: 108937--109066 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 58
108927 TATTATATTT
* * * *
108937 ATTAAAACAAAT-TCTTAAATTATTA-TTTG-TAACCCTTTAAATATTTAGATTATTCTTTA
1 ATTAAAATAAATATCTTAAATTATAATTTTGTTAA---TTTAAATATTTAAAATA-TCTTTA
* *
108996 ATTAAAATAAATAT-TTAAATTATAATTTTGTTTATTTAAATATTTAAAATATCTTTT
1 ATTAAAATAAATATCTTAAATTATAATTTTGTTAATTTAAATATTTAAAATATCTTTA
109053 ATTAAAATAAATAT
1 ATTAAAATAAATAT
109067 ATAATTTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
57 19 0.31
58 15 0.24
59 21 0.34
60 5 0.08
61 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.48
Consensus pattern (58 bp):
ATTAAAATAAATATCTTAAATTATAATTTTGTTAATTTAAATATTTAAAATATCTTTA
Done.