Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005332.1 Hibiscus syriacus cultivar Beakdansim tig00012076_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: 63962
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:1769 original size:11 final size:11
Alignment explanation
Indices: 1753--1779 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1743 TGAAGATTAT
1753 TTAAGATAACC
1 TTAAGATAACC
1764 TTAAGATAACC
1 TTAAGATAACC
1775 TTAAG
1 TTAAG
1780 GTGATATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (11 bp):
TTAAGATAACC
Found at i:3614 original size:19 final size:17
Alignment explanation
Indices: 3592--3629 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 17
3582 ATATGGGAAA
3592 ATACTATAAATATATATAT
1 ATACTAT-AATATAT-TAT
3611 ATACTATAATATATTAT
1 ATACTATAATATATTAT
3628 AT
1 AT
3630 GAAACATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 7 0.37
19 7 0.37
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
ATACTATAATATATTAT
Found at i:3885 original size:23 final size:23
Alignment explanation
Indices: 3855--3905 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
3845 AGTCAAGGGT
*
3855 TCTATGTGGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGAGACAAA
*
3878 TCTATGTGGTCCTTCGAGACAAT
1 TCTATGTGGTCCTTCGAGACAAA
3901 TCTAT
1 TCTAT
3906 ATGGCACTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGAGACAAA
Found at i:6014 original size:25 final size:25
Alignment explanation
Indices: 5986--6035 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5976 TAAGATTTTA
*
5986 TATTAA-ATAATAAATTTTTAAAATT
1 TATTAAGA-AATAAATTTATAAAATT
*
6011 TATTAAGAGATAAATTTATAAAATT
1 TATTAAGAAATAAATTTATAAAATT
6036 ATAGTGAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
TATTAAGAAATAAATTTATAAAATT
Found at i:6555 original size:9 final size:9
Alignment explanation
Indices: 6541--6845 Score: 64
Period size: 9 Copynumber: 30.8 Consensus size: 9
6531 GTATATATAT
6541 TTTTTTTTA
1 TTTTTTTTA
6550 TTTTTTATT-
1 TTTTTT-TTA
*
6559 TTTTTTTCTC
1 TTTTTTT-TA
6569 TTTATCTATTTA
1 TTT-T-T-TTTA
*
6581 TCTTATTTTA
1 T-TTTTTTTA
6591 TTTTTTTTA
1 TTTTTTTTA
*
6600 TCTTTATTTCA
1 T-TTT-TTTTA
6611 TTTGTTTTTTA
1 -TT-TTTTTTA
6622 TATATTTTTTA
1 T-T-TTTTTTA
*
6633 TTTTTATTTTC
1 -TTTT-TTTTA
6644 TTCTTGTTGTTA
1 TT-TT-TT-TTA
*
6656 -TTTATTTA
1 TTTTTTTTA
6664 TTTATTTATTA
1 TTT-TTT-TTA
* * *
6675 TATATATTA
1 TTTTTTTTA
**
6684 TTTTTACTA
1 TTTTTTTTA
6693 TTTTTCTTTA
1 TTTTT-TTTA
**
6703 --TTTGGTA
1 TTTTTTTTA
6710 -TTTTTTTA
1 TTTTTTTTA
6718 TTTATTTTTA
1 TTT-TTTTTA
6728 TTCCATTTTCTT-
1 TT---TTTT-TTA
6740 TTTTTTTTA
1 TTTTTTTTA
*
6749 TCTTTACTTTA
1 T-TTT-TTTTA
*
6760 TCTTTTTTATT
1 T-TTTTTT-TA
6771 TTTTTATTTA
1 TTTTT-TTTA
6781 TCTTTTTTTA
1 T-TTTTTTTA
* *
6791 CTTTCTTTA
1 TTTTTTTTA
* * *
6800 TCTTATCTTC
1 T-TTTTTTTA
* *
6810 TTTATTTCA
1 TTTTTTTTA
6819 TTTGTTTTTTA
1 -TT-TTTTTTA
*
6830 TTTTCTTTA
1 TTTTTTTTA
6839 TTTTTTT
1 TTTTTTT
6846 AAAAATAAAC
Statistics
Matches: 219, Mismatches: 41, Indels: 72
0.66 0.12 0.22
Matches are distributed among these distances:
7 2 0.01
8 14 0.06
9 69 0.32
10 57 0.26
11 56 0.26
12 14 0.06
13 7 0.03
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:6573 original size:43 final size:44
Alignment explanation
Indices: 6526--6642 Score: 103
Period size: 43 Copynumber: 2.6 Consensus size: 44
6516 AGACACATTT
* * *
6526 TTTATGTATATATATTTTTTTTTATTTTTTATTTTTTTTTC-TC
1 TTTATCTATATATATTTTTTTTTATTTTTTATCTTTATTTCATC
* * * *
6569 TTTATCTATTTATCTTATTTTATT-TTTTTTATCTTTATTTCATT
1 TTTATCTATATATATT-TTTTTTTATTTTTTATCTTTATTTCATC
* * *
6613 TGTTTTTTATATATTTTTTATTTTTATTTT
1 T-TTATCTATATATATTTT-TTTTTATTTT
6643 CTTCTTGTTG
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
43 28 0.49
44 10 0.18
45 15 0.26
46 4 0.07
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (44 bp):
TTTATCTATATATATTTTTTTTTATTTTTTATCTTTATTTCATC
Found at i:6630 original size:33 final size:32
Alignment explanation
Indices: 6546--6846 Score: 108
Period size: 33 Copynumber: 9.1 Consensus size: 32
6536 TATATTTTTT
* *
6546 TTTATTTTTTAT-TTTTTTTTCTCTTTATCTA
1 TTTATTTTTTATATTTTTTTTATCTTTATTTA
6577 TTTATCTTATTT-TATTTTTTTTATCTTTATTTCA
1 TTTAT-TT-TTTATATTTTTTTTATCTTTATTT-A
* * *
6611 TTTGTTTTTTATATATTTTTTATTTTTATTT-
1 TTTATTTTTTATATTTTTTTTATCTTTATTTA
* * *
6642 TCTTCTTGTTGTTAT-TTATTTATTTATTTATTATATA
1 T-TTATT-TT-TTATATT-TTT-TTTATCT-TTATTTA
*
6679 TATTA-TTTTTACTATTTTTCTTTAT-TTGGTATTTT
1 T-TTATTTTTTA-TATTTTT-TTTATCTT--TATTTA
* *** *
6714 TTTATTTATTTTTATTCCATTT-TCTTT-TTTT
1 TTTATTT-TTTATATTTTTTTTATCTTTATTTA
*
6745 TTTATCTTTACTT-TATCTTTTTTAT-TTT-TTTA
1 TTTAT-TTT--TTATATTTTTTTTATCTTTATTTA
* * * *
6777 TTTATCTTTTTTTACTTTCTTTATC-TTATCTTC
1 TTTAT-TTTTTATATTTTTTTTATCTTTAT-TTA
* *
6810 TTTATTTCATTTGT-TTTTTATTT-TCTTTATTTT
1 TTTATTT--TTTATATTTTT-TTTATCTTTATTTA
6843 TTTA
1 TTTA
6847 AAAATAAACA
Statistics
Matches: 209, Mismatches: 30, Indels: 60
0.70 0.10 0.20
Matches are distributed among these distances:
30 2 0.01
31 27 0.13
32 37 0.18
33 65 0.31
34 35 0.17
35 29 0.14
36 11 0.05
37 3 0.01
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (32 bp):
TTTATTTTTTATATTTTTTTTATCTTTATTTA
Found at i:6705 original size:77 final size:76
Alignment explanation
Indices: 6538--6716 Score: 170
Period size: 77 Copynumber: 2.3 Consensus size: 76
6528 TATGTATATA
* * * *
6538 TATTTTTTTTTATTTTTTATTTTTTTTTCTCTTTATCTATTTATCTTATTTTATTTTTTTTATCT
1 TATTTTTATTTATTTTTTATTTTTTTTTCTCTTTATCTATTTATCTTATTTTATTTATTATATAT
**
6603 TTATTTCATTTG
66 TTATTT-ATTAC
* *
6615 T-TTTTTATATATTTTTTATTTTTATTTTCTTCTTGT-TGTTATTTAT-TTA-TTTATTTATTAT
1 TATTTTTATTTATTTTTTATTTTT-TTTTC-TCTT-TAT-CTATTTATCTTATTTTATTTATTAT
6676 ATATATTATTT-TTAC
62 ATAT-TTATTTATTAC
* **
6691 TATTTTTCTTTATTTGGTATTTTTTT
1 TATTTTTATTTATTTTTTATTTTTTT
6717 ATTTATTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
76 25 0.30
77 37 0.44
78 14 0.17
79 8 0.10
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (76 bp):
TATTTTTATTTATTTTTTATTTTTTTTTCTCTTTATCTATTTATCTTATTTTATTTATTATATAT
TTATTTATTAC
Found at i:6760 original size:32 final size:32
Alignment explanation
Indices: 6708--6785 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 32
6698 CTTTATTTGG
*
6708 TATTTTTTTATTTAT-TTT--TAT-TCCATTT
1 TATTTTTTTATTTATCTTTACTTTATCCATTT
* **
6736 TCTTTTTTT-TTTATCTTTACTTTATCTTTTT
1 TATTTTTTTATTTATCTTTACTTTATCCATTT
6767 TATTTTTTTATTTATCTTT
1 TATTTTTTTATTTATCTTT
6786 TTTTACTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 5 0.12
28 11 0.28
30 2 0.05
31 13 0.32
32 9 0.22
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (32 bp):
TATTTTTTTATTTATCTTTACTTTATCCATTT
Found at i:6785 original size:27 final size:31
Alignment explanation
Indices: 6708--6785 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 31
6698 CTTTATTTGG
*
6708 TATTTTTTTATTTATTTTTATTCCATTTTCT
1 TATTTTTTTATTTATCTTTATTCCATTTTCT
*
6739 TTTTTTTTTATCTT-TACTTTA-T-C-TTTT-T
1 TATTTTTTTAT-TTAT-CTTTATTCCATTTTCT
6767 TATTTTTTTATTTATCTTT
1 TATTTTTTTATTTATCTTT
6786 TTTTACTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
27 6 0.15
28 12 0.29
29 4 0.10
30 1 0.02
31 12 0.29
32 6 0.15
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (31 bp):
TATTTTTTTATTTATCTTTATTCCATTTTCT
Found at i:7253 original size:21 final size:21
Alignment explanation
Indices: 7224--7276 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
7214 ATTCTGACTA
7224 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
7245 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
7266 TCGCAATGCGA
1 TCGCATTGCGA
7277 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:7291 original size:20 final size:20
Alignment explanation
Indices: 7266--7378 Score: 208
Period size: 20 Copynumber: 5.7 Consensus size: 20
7256 TTTTCCTAAT
7266 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
7286 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
7306 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
7326 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
7346 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
7366 TCACAACGCGAAT
1 TCGCAATGCGAAT
7379 CTGACTATCG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 91 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:7392 original size:20 final size:20
Alignment explanation
Indices: 7369--7411 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
7359 ACGTAAATCA
*
7369 CAACGCGAATCTGACTATCG
1 CAACGAGAATCTGACTATCG
*
7389 CAACGAGATTCTGACTATCG
1 CAACGAGAATCTGACTATCG
7409 CAA
1 CAA
7412 TACTGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (20 bp):
CAACGAGAATCTGACTATCG
Found at i:8097 original size:19 final size:19
Alignment explanation
Indices: 8073--8116 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
8063 CACAATTTCA
8073 TCACCAAACAAATATTGTT
1 TCACCAAACAAATATTGTT
*
8092 TCACCAAGCAAATATTGTT
1 TCACCAAACAAATATTGTT
8111 TCACCA
1 TCACCA
8117 CATTTCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.30
Consensus pattern (19 bp):
TCACCAAACAAATATTGTT
Found at i:10769 original size:20 final size:19
Alignment explanation
Indices: 10744--10832 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 19
10734 CAACGCGGAA
10744 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAAT-TGACT
10764 ATCGCAACGCGGAATTGACT
1 ATCGCAACGC-GAATTGACT
10784 ATCGCAATACG-GAATTGACT
1 ATCGC-A-ACGCGAATTGACT
*
10804 ATCGCAACGCGTAAATGACT
1 ATCGCAACGCG-AATTGACT
10824 ATCGCAACG
1 ATCGCAACG
10833 AGAGAATCGC
Statistics
Matches: 63, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
18 3 0.05
19 2 0.03
20 50 0.79
21 5 0.08
22 3 0.05
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (19 bp):
ATCGCAACGCGAATTGACT
Found at i:10803 original size:40 final size:41
Alignment explanation
Indices: 10754--10830 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
10744 ATCGCAACGC
*
10754 GAATATGACTATCGCAACGCGGAATTGACTATCGCAATACG
1 GAATATGACTATCGCAACGCGGAAATGACTATCGCAATACG
*
10795 GAAT-TGACTATCGCAACGCGTAAATGACTATCGCAA
1 GAATATGACTATCGCAACGCGGAAATGACTATCGCAA
10831 CGAGAGAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 30 0.88
41 4 0.12
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (41 bp):
GAATATGACTATCGCAACGCGGAAATGACTATCGCAATACG
Found at i:11042 original size:14 final size:14
Alignment explanation
Indices: 11023--11059 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11013 CATCAATTAA
11023 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
11037 ACAAATCATCTTTT
1 ACAAATCAACATTT
11051 ACAAATCAA
1 ACAAATCAA
11060 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:12547 original size:40 final size:39
Alignment explanation
Indices: 12442--12547 Score: 97
Period size: 40 Copynumber: 2.6 Consensus size: 39
12432 TCTAGAATGT
* * *
12442 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGG-CCTCTTGAACGATG--AGGGGCCTCTTGAACGA
* **
12484 TGGGAGGGGACTCTTGAGGGATGAGGGGCCTCTTGAACGA
1 TGGGA-GGGCCTCTTGAACGATGAGGGGCCTCTTGAACGA
12524 TAAGGGA-GGCCTCTTGAACGATGA
1 T--GGGAGGGCCTCTTGAACGATGA
12548 CAGGTGAGTC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
40 30 0.58
42 19 0.37
43 3 0.06
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.21
Consensus pattern (39 bp):
TGGGAGGGCCTCTTGAACGATGAGGGGCCTCTTGAACGA
Found at i:13035 original size:20 final size:20
Alignment explanation
Indices: 13010--13198 Score: 201
Period size: 20 Copynumber: 9.7 Consensus size: 20
13000 TGCAGAAGAA
13010 GACTATCGCAACGCGAAAAT
1 GACTATCGCAACGCGAAAAT
13030 GACTATCGCAACGCGAAAAT
1 GACTATCGCAACGCGAAAAT
* * **
13050 AACTATCGCAATGCGAATTT
1 GACTATCGCAACGCGAAAAT
* **
13070 GACTATCGCAATGCGAATTT
1 GACTATCGCAACGCGAAAAT
*
13090 GACTATCGCAA--CG-AGA-
1 GACTATCGCAACGCGAAAAT
13106 GA--ATCGCAATGCGCGAAAAT
1 GACTATCGCAA--CGCGAAAAT
13126 GACTATCGCAACGCGAAAAT
1 GACTATCGCAACGCGAAAAT
*
13146 GACTATCGCAATGCGAAAAT
1 GACTATCGCAACGCGAAAAT
* * **
13166 GACTATCGCAATGTGAATTT
1 GACTATCGCAACGCGAAAAT
13186 GACTATCGCAACG
1 GACTATCGCAACG
13199 AGAGAATCGC
Statistics
Matches: 148, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
14 7 0.05
16 2 0.01
17 1 0.01
18 4 0.03
19 2 0.01
20 125 0.84
22 7 0.05
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (20 bp):
GACTATCGCAACGCGAAAAT
Found at i:13131 original size:76 final size:74
Alignment explanation
Indices: 13034--13176 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 74
13024 GAAAATGACT
* ** **
13034 ATCGCAACGCGAAAATAACTATCGCAATGCGAATTTGACTATCGCAATGCGAATTTGACTATCGC
1 ATCGCAACGCGAAAATAACTATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACTATCGC
13099 AACGAGAGA
66 AACGAGAGA
*
13108 ATCGCAATGCGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACTATC
1 ATCGCAA--CGCGAAAATAACTATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACTATC
13173 GCAA
64 GCAA
13177 TGTGAATTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 7 0.11
76 54 0.89
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (74 bp):
ATCGCAACGCGAAAATAACTATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACTATCGC
AACGAGAGA
Found at i:13185 original size:96 final size:96
Alignment explanation
Indices: 13014--13214 Score: 352
Period size: 96 Copynumber: 2.1 Consensus size: 96
13004 GAAGAAGACT
**
13014 ATCGCAA--CGCGAAAATGACTATCGCAACGCGAAAATAACTATCGCAATGCGAATTTGACTATC
1 ATCGCAATGCGCGAAAATGACTATCGCAACGCGAAAATAACTATCGCAATGCGAAAATGACTATC
13077 GCAATGCGAATTTGACTATCGCAACGAGAGA
66 GCAATGCGAATTTGACTATCGCAACGAGAGA
*
13108 ATCGCAATGCGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACTATC
1 ATCGCAATGCGCGAAAATGACTATCGCAACGCGAAAATAACTATCGCAATGCGAAAATGACTATC
*
13173 GCAATGTGAATTTGACTATCGCAACGAGAGA
66 GCAATGCGAATTTGACTATCGCAACGAGAGA
13204 ATCGCAATGCG
1 ATCGCAATGCG
13215 ATTTTCATTT
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 7 0.07
96 94 0.93
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (96 bp):
ATCGCAATGCGCGAAAATGACTATCGCAACGCGAAAATAACTATCGCAATGCGAAAATGACTATC
GCAATGCGAATTTGACTATCGCAACGAGAGA
Found at i:13286 original size:20 final size:20
Alignment explanation
Indices: 13241--13286 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
13231 GCGATTCTTT
13241 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
13261 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
13281 CGTTGC
1 CGTTGC
13287 AATTTTGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:13319 original size:87 final size:87
Alignment explanation
Indices: 13211--13373 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 87
13201 AGAATCGCAA
* *
13211 TGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCAT
*
13276 TTTCGCGTTGCAATTTTGTTGT
66 TTTCGCATTGCAATTTTGTTGT
* ** *
13298 TGCGATTTTCATTTCGTATTGCGATTCTCTCATTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCAT
13363 TTTCGCATTGC
66 TTTCGCATTGC
13374 GATAGTAAAC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.44
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCAT
TTTCGCATTGCAATTTTGTTGT
Found at i:13343 original size:33 final size:33
Alignment explanation
Indices: 13261--13353 Score: 78
Period size: 33 Copynumber: 2.8 Consensus size: 33
13251 GTCAAATTCG
* * *
13261 CATTGCGATAGTCATTTTCGCGTTGCAATTTTGT
1 CATTGCGATAGTCA-TTTCGCATTGCAATTCTCT
** ** * *
13295 TGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CATTGCGATAGTCATTTCGCATTGCAATTCTCT
*
13328 CATTGCGATAGTCATTTTCGCGTTGC
1 CATTGCGATAGTCA-TTTCGCATTGC
13354 GATAGTCATT
Statistics
Matches: 43, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
33 24 0.56
34 19 0.44
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.45
Consensus pattern (33 bp):
CATTGCGATAGTCATTTCGCATTGCAATTCTCT
Found at i:13355 original size:20 final size:20
Alignment explanation
Indices: 13328--13379 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
13318 GCGATTCTCT
13328 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
13348 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
13368 CATTGCGATAGT
1 CATTGCGATAGT
13380 AAACTATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:15273 original size:20 final size:20
Alignment explanation
Indices: 15250--15319 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
15240 TCTGAAACTT
15250 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
15270 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
15290 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
15309 AAAATCACAAC
1 AAAATCGCAAC
15320 GACAGAATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 13 0.30
20 31 0.70
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:15891 original size:20 final size:20
Alignment explanation
Indices: 15868--15920 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
15858 CGATAGTCAG
*
15868 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
15888 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
15908 ATTCGCATTGCGA
1 ATTCGCATTGCGA
15921 ATTAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:15941 original size:21 final size:21
Alignment explanation
Indices: 15917--15962 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
15907 TATTCGCATT
15917 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
15938 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
15959 GCGA
1 GCGA
15963 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:27172 original size:12 final size:12
Alignment explanation
Indices: 27155--27180 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27145 TTAAATATAA
27155 AAATAATAAAAT
1 AAATAATAAAAT
27167 AAATAATAAAAT
1 AAATAATAAAAT
27179 AA
1 AA
27181 TATTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:29470 original size:2 final size:2
Alignment explanation
Indices: 29463--29493 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29453 GGATGCGCTG
29463 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
29494 CATGGTTATA
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:30246 original size:20 final size:20
Alignment explanation
Indices: 30221--30266 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
30211 GAAATTTCTG
30221 GAACCGATTTGACCTAACCC
1 GAACCGATTTGACCTAACCC
*
30241 GAACCGATTTGACCTGACCC
1 GAACCGATTTGACCTAACCC
30261 GAACCG
1 GAACCG
30267 GTGACAGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (20 bp):
GAACCGATTTGACCTAACCC
Found at i:41463 original size:16 final size:16
Alignment explanation
Indices: 41444--41476 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41434 AAATAAAAAC
41444 ATAAATAATAATAATA
1 ATAAATAATAATAATA
*
41460 ATAAATATTAATAATA
1 ATAAATAATAATAATA
41476 A
1 A
41477 CAACCTAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAATAATAATAATA
Found at i:42028 original size:196 final size:196
Alignment explanation
Indices: 41694--42083 Score: 529
Period size: 196 Copynumber: 2.0 Consensus size: 196
41684 AGTTTACTAG
* * **
41694 GTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTTGAAACTACTAAATGA
1 GTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATTTCATTTTCAGAAACTACTAAATGA
* * ** *
41759 GAAACATTGAAAATTGATTTTCTCATTTTTCACAAACATGTGAAAACATCCTGCCCGAAGGTCTT
66 GAAACATTGAAAATTCACTTTCTCATTTTTCACAAACACATGAAAACATCCTACCCGAAGGTCTT
* *
41824 ATGGATGGCCCGAAGGACTTATCATCTTGCT-AGAAAGACTGACAGATGAC-CAGAAGGATTTAA
131 ATGGATGGCCCGAAGGACTTATCATATTGCTCA-AAAGACTGACAGATGACTC-GAAGGACTTAA
41887 TAA
194 TAA
* *
41890 GTAAGAAACTTTGGAAATCATTTTCTTACTCTTCAAAAATTTCATTTTCAGAAAAC-ATTAAATG
1 GTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATTTCATTTTCAG-AAACTACTAAATG
* * * *
41954 AGAAACTTTGGAAA-TCACTTTCTCATTTTTTGA-AAATCACATGAAAACATCCTACCTGAAGGT
65 AGAAACATTGAAAATTCACTTTCTCA-TTTTTCACAAA-CACATGAAAACATCCTACCCGAAGGT
* *
42017 CTTATGGATGGCCCGAATGACTTATCATATTGCTCAAAAGACTGATAGATGACTCGAAGGACTTA
128 CTTATGGATGGCCCGAAGGACTTATCATATTGCTCAAAAGACTGACAGATGACTCGAAGGACTTA
42082 AT
193 AT
42084 CTTGCTTAAA
Statistics
Matches: 170, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
195 12 0.07
196 152 0.89
197 6 0.04
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (196 bp):
GTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATTTCATTTTCAGAAACTACTAAATGA
GAAACATTGAAAATTCACTTTCTCATTTTTCACAAACACATGAAAACATCCTACCCGAAGGTCTT
ATGGATGGCCCGAAGGACTTATCATATTGCTCAAAAGACTGACAGATGACTCGAAGGACTTAATA
A
Found at i:42095 original size:39 final size:39
Alignment explanation
Indices: 42046--42121 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
42036 ACTTATCATA
*
42046 TTGCTCAAAAGACTGATAGATGACTCGAAGGACTTAATC
1 TTGCTCAAAAGACCGATAGATGACTCGAAGGACTTAATC
* * *
42085 TTGCTTAAAAGACCGGTAGATGACTCGAAGGATTTAA
1 TTGCTCAAAAGACCGATAGATGACTCGAAGGACTTAA
42122 AAGGTAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (39 bp):
TTGCTCAAAAGACCGATAGATGACTCGAAGGACTTAATC
Found at i:45457 original size:68 final size:68
Alignment explanation
Indices: 45286--45586 Score: 426
Period size: 68 Copynumber: 4.4 Consensus size: 68
45276 AAAAGATTAA
**
45286 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGATTAAGTGCC-
1 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
45350 TTG
66 TTG
*
45353 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATTCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
45418 TTG
66 TTG
* * * *
45421 AGGCCTAACTGTGAATTTGATAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGCTAAATACCT
1 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
45486 TTG
66 TTG
* * * * * * *
45489 ATGCTTAACTGTGCATATGACAGAAAGGTGT-ACATTATTCCAGTTAGATGAAAAGCTAAGTGTC
1 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCA-ATTATGCCAGTTAGATGAAAGGCTAAGTGCC
*
45553 TTTC
65 TTTG
* *
45557 AGGCCTAGCTGTGCATTTGAGAGAAAGGTG
1 AGGCCTAACTGTGCATTTGATAGAAAGGTG
45587 CAGTTAGATG
Statistics
Matches: 207, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
67 62 0.30
68 145 0.70
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:45724 original size:81 final size:81
Alignment explanation
Indices: 45589--45947 Score: 470
Period size: 81 Copynumber: 4.4 Consensus size: 81
45579 GAAAGGTGCA
* * * * *
45589 GTTAGATGAACGGTTAAGTATCGTTGAGTAAAAGAATAATATCCTAGCTATGCATTTGACAAAAA
1 GTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGACAGAAA
45654 GGTGTCAATTATGCCT
66 GGTGTCAATTATGCCT
* *
45670 GTTAGATGAATGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGATAGAAA
1 GTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGACAGAAA
*
45735 GGTGTCAATTATGCCA
66 GGTGTCAATTATGCCT
* * * *
45751 GTTAGATGAACAGATAAGTACCATTGAGTAAAAGAATAATAGCCTAATTGTGCATTTGACAGAAA
1 GTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGACAGAAA
* *
45816 TGTGTCAATTATG-TT
66 GGTGTCAATTATGCCT
* * * *
45831 ATTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGATGTGTATTTGATAGAA
1 -GTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGACAGAA
*
45896 AGGTGTCAATTATG-TT
65 AGGTGTCAATTATGCCT
* ** * *
45912 AGTTAGAGGAACGGTTAAACACGGTTGAGCAAAAGA
1 -GTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGA
45948 TGAACGGTTA
Statistics
Matches: 245, Mismatches: 32, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
81 245 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (81 bp):
GTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAATAATAGCCTAGTTGTGCATTTGACAGAAA
GGTGTCAATTATGCCT
Found at i:61204 original size:9 final size:9
Alignment explanation
Indices: 61172--61196 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
61162 CTCCTTTATT
61172 TTTTATTTG
1 TTTTATTTG
61181 TTTTATTTG
1 TTTTATTTG
61190 TTTTATT
1 TTTTATT
61197 ATTTTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (9 bp):
TTTTATTTG
Done.