Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008370.1 Hibiscus syriacus cultivar Beakdansim tig00111125_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: 48683
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4035 original size:18 final size:19
Alignment explanation
Indices: 4007--4045 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3997 CTCTTAATTT
4007 TTTACTTTAATTGCTTTTA
1 TTTACTTTAATTGCTTTTA
*
4026 TTTA-TTTAATTGTTTTTA
1 TTTACTTTAATTGCTTTTA
4044 TT
1 TT
4046 ACTACTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTACTTTAATTGCTTTTA
Found at i:10484 original size:31 final size:30
Alignment explanation
Indices: 10409--10491 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 30
10399 CTCTCCATCG
*
10409 AAAAAAAATGTT-GAAAGAAAGAAAGAAGA
1 AAAAAAAATGTTCGAAAGAAAGAAAAAAGA
*
10438 AAAAAATAACAGTTCGAAA-AAAGAAAAAAGA
1 AAAAAA-AA-TGTTCGAAAGAAAGAAAAAAGA
10469 AAAAAAAAGTTGTTCGAAAGAAA
1 AAAAAAAA--TGTTCGAAAGAAA
10492 AAGAGAGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 6 0.13
30 4 0.09
31 28 0.62
32 7 0.16
ACGTcount: A:0.67, C:0.04, G:0.17, T:0.12
Consensus pattern (30 bp):
AAAAAAAATGTTCGAAAGAAAGAAAAAAGA
Found at i:10501 original size:31 final size:29
Alignment explanation
Indices: 10409--10507 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 29
10399 CTCTCCATCG
10409 AAAAAAAATGTT-GAAAGAAAGAAAGAAGA
1 AAAAAAAATGTTCGAAAGAAAGAAAG-AGA
* *
10438 AAAAAATAACAGTTCGAAA-AAAGAAAAAAGA
1 AAAAAA-AA-TGTTCGAAAGAAAG-AAAGAGA
10469 AAAAAAAAGTTGTTCGAAAGAAA-AAGAGAGA
1 AAAAAAAA--TGTTCGAAAGAAAGAA-AGAGA
*
10500 AAAGAAAA
1 AAAAAAAA
10508 GACATGAAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
29 6 0.11
30 6 0.11
31 35 0.61
32 10 0.18
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.10
Consensus pattern (29 bp):
AAAAAAAATGTTCGAAAGAAAGAAAGAGA
Found at i:12767 original size:9 final size:9
Alignment explanation
Indices: 12753--12778 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12743 AAAATACAAG
12753 GGAAAATAT
1 GGAAAATAT
12762 GGAAAATAT
1 GGAAAATAT
12771 GGAAAATA
1 GGAAAATA
12779 ATAAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (9 bp):
GGAAAATAT
Found at i:14336 original size:18 final size:18
Alignment explanation
Indices: 14315--14351 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
14305 TTACTTTCAA
14315 TGAACCAATAACCTGCAC
1 TGAACCAATAACCTGCAC
14333 TGAACCAATAACCTGCAC
1 TGAACCAATAACCTGCAC
14351 T
1 T
14352 TTTCAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.19
Consensus pattern (18 bp):
TGAACCAATAACCTGCAC
Found at i:16134 original size:36 final size:36
Alignment explanation
Indices: 16092--16168 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
16082 AATGAATTAA
*
16092 AAAATTTATTTTATGCTAAAAGACCTTGTTACCATT
1 AAAATTTATTTTATGCTAAAAGAACTTGTTACCATT
* *
16128 AAAATTTATTTTATGCTAAAAGAATTTTTTACCATT
1 AAAATTTATTTTATGCTAAAAGAACTTGTTACCATT
16164 AAAAT
1 AAAAT
16169 ATCATGATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.43
Consensus pattern (36 bp):
AAAATTTATTTTATGCTAAAAGAACTTGTTACCATT
Found at i:18167 original size:28 final size:28
Alignment explanation
Indices: 18127--18183 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
18117 ATGCACCGCC
18127 AATGACAAGACCACATTTACTGTTGACG
1 AATGACAAGACCACATTTACTGTTGACG
18155 AATGACAAGACCACATTTACTGTTGACG
1 AATGACAAGACCACATTTACTGTTGACG
18183 A
1 A
18184 CTTCACAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (28 bp):
AATGACAAGACCACATTTACTGTTGACG
Found at i:19010 original size:16 final size:16
Alignment explanation
Indices: 18986--19026 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
18976 TACATAGCTA
*
18986 GCACCAGCTACAACTG
1 GCACTAGCTACAACTG
*
19002 GCACTAGCTATAACTG
1 GCACTAGCTACAACTG
*
19018 GAACTAGCT
1 GCACTAGCT
19027 GATAACAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (16 bp):
GCACTAGCTACAACTG
Found at i:19536 original size:6 final size:6
Alignment explanation
Indices: 19525--19558 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
19515 GCTTCTCCAA
*
19525 TCTTTC TCTTTC TCTTTC TCTTTCC TCTTCC TCT
1 TCTTTC TCTTTC TCTTTC TCTTT-C TCTTTC TCT
19559 ATCAAAGCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (6 bp):
TCTTTC
Found at i:26072 original size:30 final size:30
Alignment explanation
Indices: 26036--26116 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
26026 TGGATTTTCG
*
26036 AAAAAATGACCGAAAATATTATTAGACGCT
1 AAAAAATGACCGAAAATATTACTAGACGCT
*
26066 AAAAAATGACCGAAAATATTACTAGGCGCT
1 AAAAAATGACCGAAAATATTACTAGACGCT
26096 AAAAAATGACCGAAAATATTA
1 AAAAAATGACCGAAAATATTA
26117 AAAAATGATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.21
Consensus pattern (30 bp):
AAAAAATGACCGAAAATATTACTAGACGCT
Found at i:27788 original size:21 final size:20
Alignment explanation
Indices: 27702--27859 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
27692 AAATGACCAA
**
27702 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
27721 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
27741 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
27761 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
27782 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
27803 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
27823 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
27844 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
27860 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:27850 original size:20 final size:20
Alignment explanation
Indices: 27826--28075 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
27816 CGATTTTCCA
** *
27826 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
27846 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
27866 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
27886 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
27906 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
27926 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
27946 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
27966 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
27986 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
28006 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
28026 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
28046 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
28066 AAATCACAAC
1 AAATCGCAAC
28076 ACTGAAATTT
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:28796 original size:24 final size:24
Alignment explanation
Indices: 28757--28803 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28747 AAATTTGGTC
28757 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
28781 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
28804 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:28995 original size:12 final size:12
Alignment explanation
Indices: 28978--29002 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28968 ATATAATCCT
28978 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28990 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29002 G
1 G
29003 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:31374 original size:19 final size:19
Alignment explanation
Indices: 31334--31431 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
31324 GATTCTCTCG
31334 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
31354 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
31373 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
31387 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31406 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31425 TTGCGAT
1 TTGCGAT
31432 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:31428 original size:52 final size:53
Alignment explanation
Indices: 31315--31431 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
31305 GAAATGAAAA
31315 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
31368 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
31420 TCGCATTGCGAT
1 TCGCATTGCGAT
31432 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:31542 original size:33 final size:33
Alignment explanation
Indices: 31490--31581 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
31480 CCATTACATT
*
31490 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAAAGAA
31524 TCGCAATGCGAAATGAAAATCGCAACGAAAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAAAGAA
31557 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
31582 TGCGAAATGA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
33 48 0.84
34 9 0.16
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAAAGAA
Found at i:31581 original size:52 final size:52
Alignment explanation
Indices: 31522--31638 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
31512 GCAACGAGAG
31522 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
* * *
31574 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
*
31626 AATCGCATTGCGA
1 AATCGCAATGCGA
31639 TTCTCCCATT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:31687 original size:19 final size:19
Alignment explanation
Indices: 31645--31744 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
31635 GCGATTCTCC
31645 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
31665 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
31684 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
31700 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
31717 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
31736 CATTGCGAT
1 CATTGCGAT
31745 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:31741 original size:52 final size:53
Alignment explanation
Indices: 31628--31744 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
31618 GAAATTAAAA
31628 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
31681 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
31733 TCGCATTGCGAT
1 TCGCATTGCGAT
31745 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:31870 original size:14 final size:14
Alignment explanation
Indices: 31851--31887 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
31841 CATCAATTAC
31851 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
31865 ACAAATCATCTTTT
1 ACAAATCAACTTTT
31879 ACAAATCAA
1 ACAAATCAA
31888 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:33881 original size:14 final size:14
Alignment explanation
Indices: 33862--33918 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
33852 GCGAAATGAA
*
33862 AATCGCAACGACAG
1 AATCGCAACGAAAG
33876 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
33893 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
33909 AATCGCAACG
1 AATCGCAACG
33919 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:33889 original size:33 final size:33
Alignment explanation
Indices: 33843--33935 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
33833 GCGAAACCAA
*
33843 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
33876 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
33909 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
33936 TGCGATTTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:33900 original size:19 final size:19
Alignment explanation
Indices: 33806--33940 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
33796 TAGTTTACTT
* *
33806 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
33826 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
33845 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
33864 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
33878 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
33897 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
33911 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
33930 TCGCAATGCGA
1 TCGCAACGCGA
33941 TTTGGTTTCG
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:33981 original size:33 final size:33
Alignment explanation
Indices: 33936--34026 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
33926 AAAATCGCAA
33936 TGCGA-TTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
33968 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
34001 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
34027 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 5 0.09
33 48 0.87
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:33989 original size:19 final size:19
Alignment explanation
Indices: 33936--34063 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
33926 AAAATCGCAA
33936 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
33954 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
33968 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
33987 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
34001 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
34020 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
34039 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
34059 TGCGA
1 TGCGA
34064 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 7 0.08
19 42 0.47
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:34272 original size:93 final size:93
Alignment explanation
Indices: 34107--34576 Score: 894
Period size: 93 Copynumber: 5.1 Consensus size: 93
34097 TTGAATGGAT
34107 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
34171 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
34199 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
34264 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
34292 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
34357 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
34385 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
34450 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
34478 AAA-TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAG-ATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
34540 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
34568 AAATTTACT
1 AAATTTACT
34577 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 3, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
90 36 0.10
91 53 0.14
92 46 0.12
93 237 0.64
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:36285 original size:14 final size:14
Alignment explanation
Indices: 36266--36322 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
36256 TTGAAATGAA
36266 AATCGCAACGAGAG
1 AATCGCAACGAGAG
36280 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
36297 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
36313 AATCGCAACG
1 AATCGCAACG
36323 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:36303 original size:33 final size:33
Alignment explanation
Indices: 36258--36341 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
36248 TCTTTTGGTT
36258 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
36291 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
36324 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
36342 CGAAATGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:36304 original size:19 final size:19
Alignment explanation
Indices: 36280--36363 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
36270 GCAACGAGAG
* *
36280 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
*
36299 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
36313 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
36332 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
36351 AATCGCAATGCGA
1 AATCGCAACGCGA
36364 TTTGGTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:36392 original size:14 final size:14
Alignment explanation
Indices: 36373--36421 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
36363 ATTTGGTTCG
36373 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
36387 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
36405 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
36419 CGT
1 CGT
36422 GCGCTTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 13 0.45
15 3 0.10
17 3 0.10
18 10 0.34
ACGTcount: A:0.08, C:0.27, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36480 original size:21 final size:21
Alignment explanation
Indices: 36416--36485 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 21
36406 GTTGCGATTC
*
36416 TCTCG-TGCGCTTTTC-TTTA
1 TCTCGTTGCGATTTTCATTTA
*** *
36435 TCTCGTTGCGACAGTCA--TC
1 TCTCGTTGCGATTTTCATTTA
36454 TCTCGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTA
36475 TCTCGTTGCGA
1 TCTCGTTGCGA
36486 CTCTTCTGCA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 20 0.53
20 6 0.16
21 12 0.32
ACGTcount: A:0.11, C:0.26, G:0.19, T:0.44
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTA
Found at i:37030 original size:20 final size:20
Alignment explanation
Indices: 37005--37193 Score: 185
Period size: 20 Copynumber: 9.7 Consensus size: 20
36995 GCTTAAATAT
37005 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
37025 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
37047 -TCG-TGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37065 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
37085 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
37105 CGCGTTGCGA-TTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37124 CACGTTGCGA-TTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
37143 CGCG-TGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
** *
37162 CGCGTTGCGATTT-CATATT
1 CGCGTTGCGATTTACGGATA
37181 CGCGTTGCGATTT
1 CGCGTTGCGATTT
37194 TGGAAAATCG
Statistics
Matches: 140, Mismatches: 21, Indels: 17
0.79 0.12 0.10
Matches are distributed among these distances:
18 7 0.05
19 60 0.43
20 63 0.45
21 8 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:37469 original size:14 final size:15
Alignment explanation
Indices: 37450--37488 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
37440 AGTTAATTCT
37450 TTTATATTTTAAT-A
1 TTTATATTTTAATCA
*
37464 TTTATATATTAATCA
1 TTTATATTTTAATCA
37479 TTTA-ATTTTA
1 TTTATATTTTA
37489 TGAGGTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATATTTTAATCA
Found at i:37875 original size:2 final size:2
Alignment explanation
Indices: 37870--37912 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
37860 CAAAAAAAAT
37870 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
37912 T
1 T
37913 GATTAAACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38543 original size:22 final size:22
Alignment explanation
Indices: 38518--38559 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
38508 TCGATATTGG
*
38518 CATACTAGGGTATGAATACTGT
1 CATACTAGGGTATCAATACTGT
* *
38540 CATATTGGGGTATCAATACT
1 CATACTAGGGTATCAATACT
38560 ACCCTTAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (22 bp):
CATACTAGGGTATCAATACTGT
Found at i:42127 original size:20 final size:20
Alignment explanation
Indices: 42074--42158 Score: 71
Period size: 25 Copynumber: 4.0 Consensus size: 20
42064 CAAATTCGTG
*
42074 TTCCATTTCGCGTTGCGATAG
1 TTCCATTTCGCGTTGCGAT-T
** **
42095 TTGAAAATCGCGTTGCGATT
1 TTCCATTTCGCGTTGCGATT
42115 TTCCATTTCGCGTTGCGATGCGATT
1 TTCCATTTCGCG-T----TGCGATT
42140 TTCCATTTCGCGTTGCGAT
1 TTCCATTTCGCGTTGCGAT
42159 AGTTGAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
20 14 0.28
21 16 0.32
24 1 0.02
25 19 0.38
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
TTCCATTTCGCGTTGCGATT
Found at i:42142 original size:25 final size:25
Alignment explanation
Indices: 42108--42158 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
42098 AAAATCGCGT
42108 TGCGATTTTCCATTTCGCGTTGCGA
1 TGCGATTTTCCATTTCGCGTTGCGA
42133 TGCGATTTTCCATTTCGCGTTGCGA
1 TGCGATTTTCCATTTCGCGTTGCGA
42158 T
1 T
42159 AGTTGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.41
Consensus pattern (25 bp):
TGCGATTTTCCATTTCGCGTTGCGA
Found at i:42310 original size:6 final size:6
Alignment explanation
Indices: 42299--42347 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
42289 GACACGTATT
42299 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
42345 ACC
1 ACC
42348 CGAGACGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.23
6 33 0.77
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:42918 original size:6 final size:6
Alignment explanation
Indices: 42903--42940 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
42893 GTCGGGCCCG
*
42903 GGTCG- GGTCGT TGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
42941 AATACGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GGTCGT
Found at i:46648 original size:79 final size:79
Alignment explanation
Indices: 46507--46743 Score: 318
Period size: 78 Copynumber: 3.0 Consensus size: 79
46497 TGGTTAGAAC
* * *
46507 TGCATGTATCCATGTGTCCAG-AGTTTTCATGTTCCACAGTGTGAGAGATTGATCATTTTATAAG
1 TGCATGTACCCATGTGTCAAGAAGTTTTCATGTT-C-CAGTGTGAAAGATTGATCATTTTATAAG
* *
46571 CTTAAGCGCCTTAGAG
64 CATAAGCACCTTAGAG
* * * *
46587 TGCATGTACCCATGTGACAAGAAGTTTTCGTGTTCCAGTGTGAAAGATCGCTCATTTTATAAGCA
1 TGCATGTACCCATGTGTCAAGAAGTTTTCATGTTCCAGTGTGAAAGATTGATCATTTTATAAGCA
46652 TAAGCACCTTAGAG
66 TAAGCACCTTAGAG
* *
46666 GGCA--TACCCATGTGTCGAGAAGTTTTTCATGTTCCAGTGTGAAAGATTGATCATTTTATAAGC
1 TGCATGTACCCATGTGTCAAGAAG-TTTTCATGTTCCAGTGTGAAAGATTGATCATTTTATAAGC
*
46729 ATAAGCTCCTTAGAG
65 ATAAGCACCTTAGAG
46744 CTTGCGTAAG
Statistics
Matches: 139, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
77 16 0.12
78 51 0.37
79 42 0.30
80 19 0.14
81 11 0.08
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (79 bp):
TGCATGTACCCATGTGTCAAGAAGTTTTCATGTTCCAGTGTGAAAGATTGATCATTTTATAAGCA
TAAGCACCTTAGAG
Found at i:47596 original size:2 final size:2
Alignment explanation
Indices: 47589--47613 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47579 GCAACCGATT
47589 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
47614 CTGGGCAAAA
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
Done.