Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004488.1 Hibiscus syriacus cultivar Beakdansim tig00009887_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: 57734
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1034 original size:59 final size:59
Alignment explanation
Indices: 585--1184 Score: 803
Period size: 59 Copynumber: 10.3 Consensus size: 59
575 TAAATTTAAT
* * * * * *
585 TGGAATTTCATACAAACAATATGATTTCCTTATCATTTTAGCACACAGAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
644 TGGAAAATTCATACACTTAGTATGATTTTCTTACTC-TTTTAGCACACAAAGTGCCCTATC
1 TGG-AAATTCATACACATAGTATGATTTCCTTAC-CATTTTAGCACACAAAGTGCCCTATC
*
704 TGGAAATTCATAC-CCT--T-TGTATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATG-ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
760 TGGAAATTCATACACCATAGTATGATTTCCTTACCATTTTAGCACA-AAAGTGCCCTATC
1 TGGAAATTCATACA-CATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * * * *
819 TGGAAA-TCAT--ACATAGTATG-TTTCCTCACCGTTTTAGCTCATAAAGTGCTCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
874 TGGAAATTCATAAACATAGTATGA-TTCCTTACCATTTTAGCACACAAAGTG-CCTATA
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
931 TGGAAATTCATTCACATAGTATGA-TTCCTTACCATTTTAACACACAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
989 AGGAAATTCATACACATGGTATAATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* **
1048 AGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTATCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
1107 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAACACACAAAGTTCCTTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
1166 TAGAAATTCACTATACATA
1 TGGAAATTCA-TACACATA
1185 CATCAATAAA
Statistics
Matches: 483, Mismatches: 41, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
54 18 0.04
55 30 0.06
56 52 0.11
57 52 0.11
58 66 0.14
59 183 0.38
60 79 0.16
61 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.34
Consensus pattern (59 bp):
TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:1153 original size:31 final size:31
Alignment explanation
Indices: 1059--1153 Score: 72
Period size: 31 Copynumber: 3.2 Consensus size: 31
1049 GGAAATTCAT
*
1059 ACACATAGTATGATTTCCTTACCATTTTAGC
1 ACACATAGTATGATTTCCTTACCATTTTAAC
* ** * * * * *
1090 ACACAAAGTATCCTAT-CTGGA--A-ATTCAT
1 ACACATAGTATGATTTCCT-TACCATTTTAAC
1118 ACACATAGTATGATTTCCTTACCATTTTAAC
1 ACACATAGTATGATTTCCTTACCATTTTAAC
1149 ACACA
1 ACACA
1154 AAGTTCCTTA
Statistics
Matches: 42, Mismatches: 17, Indels: 10
0.61 0.25 0.14
Matches are distributed among these distances:
28 15 0.36
29 3 0.07
30 3 0.07
31 21 0.50
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (31 bp):
ACACATAGTATGATTTCCTTACCATTTTAAC
Found at i:3059 original size:21 final size:23
Alignment explanation
Indices: 3033--3076 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
3023 CATTCAAAAG
3033 GTATCGATACC-T-AGGAAGGTA
1 GTATCGATACCATAAGGAAGGTA
3054 GTATCGATACCATAAGGAAGGTA
1 GTATCGATACCATAAGGAAGGTA
3077 TTAATACCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.52
22 1 0.05
23 9 0.43
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (23 bp):
GTATCGATACCATAAGGAAGGTA
Found at i:12804 original size:45 final size:45
Alignment explanation
Indices: 12753--12846 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
12743 CATGGTGCTG
*
12753 GTGGTGCAAAAGGTATTGGAGGAGGCTGGAAAGGGTTTGGAAATA
1 GTGGTGCAAAAGGTACTGGAGGAGGCTGGAAAGGGTTTGGAAATA
*** * * *
12798 GTGGTGCTGGAGGTGCTGGAGGAGGCTGGAAGGGGTTTGGAATTA
1 GTGGTGCAAAAGGTACTGGAGGAGGCTGGAAAGGGTTTGGAAATA
12843 GTGG
1 GTGG
12847 AGCTGGAGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.23, C:0.05, G:0.48, T:0.23
Consensus pattern (45 bp):
GTGGTGCAAAAGGTACTGGAGGAGGCTGGAAAGGGTTTGGAAATA
Found at i:12852 original size:36 final size:36
Alignment explanation
Indices: 12812--12933 Score: 102
Period size: 36 Copynumber: 3.1 Consensus size: 36
12802 TGCTGGAGGT
*
12812 GCTGGAGGAGGCTGGAAGGGGTTTGGAATTAGTGGA
1 GCTGGAGGAGGCTGAAAGGGGTTTGGAATTAGTGGA
* * * *
12848 GCTGGAGGTGTCTGAGGAGGCTGAAATGGATTTGGAATAAGAGGA
1 GC------TG---GAGGAGGCTGAAAGGGGTTTGGAATTAGTGGA
12893 GCT-GATGGAGGCTGAAAGGGGTTTGGAATTAGTGGA
1 GCTGGA-GGAGGCTGAAAGGGGTTTGGAATTAGTGGA
12929 GCTGG
1 GCTGG
12934 TGGAAGTTGA
Statistics
Matches: 66, Mismatches: 9, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
35 2 0.03
36 31 0.47
37 1 0.02
39 1 0.02
42 2 0.03
45 29 0.44
ACGTcount: A:0.25, C:0.07, G:0.46, T:0.23
Consensus pattern (36 bp):
GCTGGAGGAGGCTGAAAGGGGTTTGGAATTAGTGGA
Found at i:12852 original size:45 final size:44
Alignment explanation
Indices: 12771--12933 Score: 173
Period size: 45 Copynumber: 3.8 Consensus size: 44
12761 AAAGGTATTG
* *
12771 GAGGAGGCTGGAAA-GGGTTTGGAAATAGTGGTGCTGGAGGTGCT
1 GAGGAGGCT-GAAAGGGGTTTGGAATTAGTGGAGCTGGAGGTGCT
*
12815 GGAGGAGGCTGGAAGGGGTTTGGAATTAGTGGAGCTGGAGGTGTCT
1 -GAGGAGGCTGAAAGGGGTTTGGAATTAGTGGAGCTGGAGGTG-CT
* * * *
12861 GAGGAGGCTGAAATGGATTTGGAATAAGAGGAGCT-GA-----T
1 GAGGAGGCTGAAAGGGGTTTGGAATTAGTGGAGCTGGAGGTGCT
12899 --GGAGGCTGAAAGGGGTTTGGAATTAGTGGAGCTGG
1 GAGGAGGCTGAAAGGGGTTTGGAATTAGTGGAGCTGG
12934 TGGAAGTTGA
Statistics
Matches: 103, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
36 29 0.28
37 1 0.01
38 1 0.01
44 5 0.05
45 65 0.63
46 2 0.02
ACGTcount: A:0.25, C:0.06, G:0.47, T:0.23
Consensus pattern (44 bp):
GAGGAGGCTGAAAGGGGTTTGGAATTAGTGGAGCTGGAGGTGCT
Found at i:12945 original size:36 final size:36
Alignment explanation
Indices: 12859--12959 Score: 105
Period size: 36 Copynumber: 2.8 Consensus size: 36
12849 CTGGAGGTGT
* * *
12859 CTGA-GGAGGCTGAAATGGATTTGGAATAAGAGGAG
1 CTGATGGAAGCTGAAAAGGATTTGGAATTAGAGGAG
* * * *
12894 CTGATGGAGGCTGAAAGGGGTTTGGAATTAGTGGAG
1 CTGATGGAAGCTGAAAAGGATTTGGAATTAGAGGAG
* * *
12930 CTGGTGGAAGTTGAAAAAGATTTGGAATTA
1 CTGATGGAAGCTGAAAAGGATTTGGAATTA
12960 ACGGAGCGGG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 4 0.07
36 51 0.93
ACGTcount: A:0.32, C:0.05, G:0.39, T:0.25
Consensus pattern (36 bp):
CTGATGGAAGCTGAAAAGGATTTGGAATTAGAGGAG
Found at i:12987 original size:3 final size:3
Alignment explanation
Indices: 12979--13022 Score: 70
Period size: 3 Copynumber: 14.0 Consensus size: 3
12969 GTCGAAAAAA
12979 TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT T-AT TAT
13023 CTTACATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:13005 original size:19 final size:19
Alignment explanation
Indices: 12980--13022 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
12970 TCGAAAAAAT
12980 ATTATTATTATTATTATTA
1 ATTATTATTATTATTATTA
*
12999 TTTATTATTATTATTATTA
1 ATTATTATTATTATTATTA
13018 ATTAT
1 ATTAT
13023 CTTACATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:14402 original size:9 final size:9
Alignment explanation
Indices: 14384--14412 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
14374 GTAAAATATG
14384 TTTA-TTTA
1 TTTATTTTA
14392 TTTATTTTA
1 TTTATTTTA
14401 TTTATTTTA
1 TTTATTTTA
14410 TTT
1 TTT
14413 TAATGCCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTTA
Found at i:20437 original size:12 final size:12
Alignment explanation
Indices: 20394--20439 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
20384 ATCGAGAAAA
20394 ACATATATACAT
1 ACATATATACAT
*
20406 ACATACATACAT
1 ACATATATACAT
*
20418 ACAGATATACACAT
1 AC--ATATATACAT
20432 ACATATAT
1 ACATATAT
20440 GATACATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 18 0.64
14 10 0.36
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (12 bp):
ACATATATACAT
Found at i:20836 original size:36 final size:38
Alignment explanation
Indices: 20740--20865 Score: 107
Period size: 36 Copynumber: 3.3 Consensus size: 38
20730 GTTTTTCTCG
* *
20740 AAACAAAATGTCGTCTCA-TTAGAGACAGTTTCTTTTGAA
1 AAAC-AAATTTCGTCTCACTT-GAGACAATTTCTTTTGAA
** *
20779 AAACAAATTTTTTCT-AGCTTGAGACAATTTC-TTT-CA
1 AAACAAATTTCGTCTCA-CTTGAGACAATTTCTTTTGAA
* * *
20815 AAACAAATTTCGTCTCACTTGAGACATTTTTCCTTTGAG
1 AAACAAATTTCGTCTCACTTGAGACA-ATTTCTTTTGAA
*
20854 ATACAAATTTCG
1 AAACAAATTTCG
20866 AATTTGTTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
36 23 0.33
37 9 0.13
38 21 0.30
39 17 0.24
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.37
Consensus pattern (38 bp):
AAACAAATTTCGTCTCACTTGAGACAATTTCTTTTGAA
Found at i:20979 original size:138 final size:136
Alignment explanation
Indices: 20777--21038 Score: 368
Period size: 138 Copynumber: 1.9 Consensus size: 136
20767 GTTTCTTTTG
* *
20777 AAAAACAAATTTTTTCTAGCTTGAGACAATTTCTTTCAAAACAAATTTCGTCTCACTTGAGACAT
1 AAAAACAAATTTTGTCTAGCTTGAGACAATTTCTCTCAAAACAAATTTCGTCTCACTTGAGACAT
* * * *
20842 TTTTCCTT-TGAGATACAAATTTCGAATTTGTT-TCACATT-AAACAAAGTTTATCTCACTTGAT
66 TTTT--TTATGAGATACAAATTT-AAATTTATTGT-AC-TTGAAACAAAATTAATCTCACTTGAT
20904 ATCGTTTTCTC
126 ATCGTTTTCTC
* * * *
20915 AAAAACACATTTTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATTTCGTTTCGCTTGAGACAT
1 AAAAACAAATTTTGTCTAGCTTGAGACAATTTCTCTCAAAACAAATTTCGTCTCACTTGAGACAT
20980 TTTTTTATGAGATACAAATTTAAATTTATTGTACTTGAAACAAAATTAATCTCACTTGA
66 TTTTTTATGAGATACAAATTTAAATTTATTGTACTTGAAACAAAATTAATCTCACTTGA
21039 GATTTTCAAA
Statistics
Matches: 111, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
135 2 0.02
136 31 0.28
137 15 0.14
138 63 0.57
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (136 bp):
AAAAACAAATTTTGTCTAGCTTGAGACAATTTCTCTCAAAACAAATTTCGTCTCACTTGAGACAT
TTTTTTATGAGATACAAATTTAAATTTATTGTACTTGAAACAAAATTAATCTCACTTGATATCGT
TTTCTC
Found at i:21231 original size:27 final size:26
Alignment explanation
Indices: 21203--21283 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 26
21193 TTTATCTCTC
21203 TTGAGATAGTTTCTCTTGAAACAAATCT
1 TTGAG-TAGTTTCTCTTGAAA-AAATCT
* * *
21231 TTGAGTCTGTTCCTTTTGAAAAAATCT
1 TTGAGT-AGTTTCTCTTGAAAAAATCT
21258 TTGAGTATGTTTCTCTT-AACAAAATC
1 TTGAGTA-GTTTCTCTTGAA-AAAATC
21284 ATCTGTGAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
26 2 0.05
27 26 0.59
28 16 0.36
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.42
Consensus pattern (26 bp):
TTGAGTAGTTTCTCTTGAAAAAATCT
Found at i:21552 original size:35 final size:35
Alignment explanation
Indices: 21466--21562 Score: 108
Period size: 35 Copynumber: 2.7 Consensus size: 35
21456 TTTGAGAAAA
* ** *
21466 ATCTTTGAGTTTGTTT-CTTTGGAAACAAAATTTACC
1 ATCTTTGAG-TTGTTTCCCTT-GAAACAAAATCAAAC
21502 ATCTTTGAGTATGTTTCCCTTGAAACAAAA-CAAAC
1 ATCTTTGAGT-TGTTTCCCTTGAAACAAAATCAAAC
21537 ATCTTTGAGATTGTTTCCCTTGAAAC
1 ATCTTTGAG-TTGTTTCCCTTGAAAC
21563 GAATTTTGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
35 27 0.50
36 24 0.44
37 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (35 bp):
ATCTTTGAGTTGTTTCCCTTGAAACAAAATCAAAC
Found at i:21648 original size:67 final size:67
Alignment explanation
Indices: 21550--21724 Score: 289
Period size: 67 Copynumber: 2.6 Consensus size: 67
21540 TTTGAGATTG
* * *
21550 TTTCCCTT-GAAACGAATTTTGTCTCAATTGAGACAGTTTCCCATGAAACACCGATATTTTAGAA
1 TTTCCCTTAAAAACGAATTTTGTCTCAATTGAGACAGTTTCCCATGAAACACCAATATTTGAGAA
21614 CA
66 CA
*
21616 TTTCCCTTAAAAATGAATTTTGTCTCAATTGAGACAGTTTCCCATGAAACACCAATATTTGAGAA
1 TTTCCCTTAAAAACGAATTTTGTCTCAATTGAGACAGTTTCCCATGAAACACCAATATTTGAGAA
21681 CA
66 CA
* *
21683 TTTCCCTTAAAAACAAATTTTGTCTCACTTGAGACAGTTTCC
1 TTTCCCTTAAAAACGAATTTTGTCTCAATTGAGACAGTTTCC
21725 TTTAAACGTC
Statistics
Matches: 101, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 8 0.08
67 93 0.92
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (67 bp):
TTTCCCTTAAAAACGAATTTTGTCTCAATTGAGACAGTTTCCCATGAAACACCAATATTTGAGAA
CA
Found at i:21833 original size:28 final size:28
Alignment explanation
Indices: 21787--21883 Score: 106
Period size: 28 Copynumber: 3.4 Consensus size: 28
21777 GAGACAGTTG
*
21787 CTTTTGAAACACATTATCTTTGAGTTTATTT
1 CTTTTGAAACA-A--ATCTTTGAGTCTATTT
*
21818 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTATTT
**
21846 CTTTTGAAACAAATCTTTGAGTCGGTTT
1 CTTTTGAAACAAATCTTTGAGTCTATTT
*
21874 CTCTTGAAAC
1 CTTTTGAAAC
21884 CATTATCCCT
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
28 47 0.78
29 2 0.03
30 3 0.05
31 8 0.13
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTATTT
Found at i:22124 original size:39 final size:38
Alignment explanation
Indices: 22060--22133 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
22050 CACGTAGAAA
* *
22060 CCGTGTCATCCCCGACCAGACCTCCTCACCACGTATGG
1 CCGTATCATCCCCGACAAGACCTCCTCACCACGTATGG
* *
22098 CCGTATCATCCCCTGACAAGATCTCCTCATCACGTA
1 CCGTATCATCCCC-GACAAGACCTCCTCACCACGTA
22134 GGAGTCGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 12 0.39
39 19 0.61
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.22
Consensus pattern (38 bp):
CCGTATCATCCCCGACAAGACCTCCTCACCACGTATGG
Found at i:22492 original size:10 final size:10
Alignment explanation
Indices: 22477--22512 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
22467 TCAAAAAAAA
22477 TATTATTTAT
1 TATTATTTAT
22487 TATTATTTAT
1 TATTATTTAT
22497 TATTA-TTAT
1 TATTATTTAT
22506 TAATTAT
1 T-ATTAT
22513 CTTACATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTATTTAT
Found at i:22499 original size:13 final size:13
Alignment explanation
Indices: 22477--22512 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
22467 TCAAAAAAAA
*
22477 TATTATTTATTAT
1 TATTAATTATTAT
*
22490 TATTTATTATTAT
1 TATTAATTATTAT
22503 TATTAATTAT
1 TATTAATTAT
22513 CTTACATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTAATTATTAT
Found at i:23890 original size:13 final size:13
Alignment explanation
Indices: 23872--23900 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
23862 GTAAAATATG
23872 TTTATTTATTTTA
1 TTTATTTATTTTA
23885 TTTATTTATTTTA
1 TTTATTTATTTTA
23898 TTT
1 TTT
23901 TAATGCCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:25118 original size:36 final size:36
Alignment explanation
Indices: 25063--25157 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
25053 AGGTGCAGGA
* *
25063 GGAGGCTGAAATGGATTTGGAGTAAGAGGAGCTGGT
1 GGAGGCTGAAAGGGATTTGGAATAAGAGGAGCTGGT
* ** *
25099 GGAGGCTGAAAGGGGTTTGGAATTGGTGGAGCTGGT
1 GGAGGCTGAAAGGGATTTGGAATAAGAGGAGCTGGT
* * **
25135 GGATGTTGAAAAAGATTTGGAAT
1 GGAGGCTGAAAGGGATTTGGAAT
25158 TAACGGAGCG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.27, C:0.04, G:0.43, T:0.25
Consensus pattern (36 bp):
GGAGGCTGAAAGGGATTTGGAATAAGAGGAGCTGGT
Found at i:29568 original size:19 final size:20
Alignment explanation
Indices: 29530--29568 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
29520 TATGATTGAT
29530 AAAATTAAAAGATGGATAATC
1 AAAATTAAAAGA-GGATAATC
29551 AAAATTAAAAGA-GATAAT
1 AAAATTAAAAGAGGATAAT
29569 AATTAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
21 12 0.67
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.23
Consensus pattern (20 bp):
AAAATTAAAAGAGGATAATC
Found at i:40553 original size:12 final size:12
Alignment explanation
Indices: 40536--40565 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
40526 ATATTAATAT
40536 TTTAAAAGTTGA
1 TTTAAAAGTTGA
40548 TTTAAAAGTTGA
1 TTTAAAAGTTGA
40560 TTTAAA
1 TTTAAA
40566 TACAAAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (12 bp):
TTTAAAAGTTGA
Found at i:44947 original size:29 final size:27
Alignment explanation
Indices: 44886--44989 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 27
44876 TTTGACGTTC
44886 ATTGTAATTTATAAAAAAAGTTTGTCTTAT
1 ATTGTAATTTAT--AAAAAGTTTGTCTT-T
*
44916 ATTGTAATTTATAAAAGGTTCTGTCATTT
1 ATTGTAATTTATAAAAAGTT-TGTC-TTT
* *
44945 ATTATAATTTATAAAAAGTTTTATCCTTT
1 ATTGTAATTTATAAAAAG-TTTGT-CTTT
* *
44974 AATGCAATTTATAAAA
1 ATTGTAATTTATAAAA
44990 GATTTATTCC
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
28 7 0.11
29 39 0.62
30 17 0.27
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (27 bp):
ATTGTAATTTATAAAAAGTTTGTCTTT
Done.