Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001044.1 Hibiscus syriacus cultivar Beakdansim tig00002072_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: 43848
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2748 original size:10 final size:9
Alignment explanation
Indices: 2732--2794 Score: 76
Period size: 10 Copynumber: 6.9 Consensus size: 9
2722 TATGCTTGAA
2732 GAAAAAAAT
1 GAAAAAAAT
2741 GTAAAAAAAT
1 G-AAAAAAAT
2751 GAAGAAAAAT
1 GAA-AAAAAT
2761 G-AAAAAAT
1 GAAAAAAAT
2769 G-AAAAAAT
1 GAAAAAAAT
*
2777 GAAAAAAAAA
1 G-AAAAAAAT
2787 GAAAAAAA
1 GAAAAAAA
2795 AAGAAGGGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
8 15 0.31
9 11 0.22
10 23 0.47
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:2766 original size:8 final size:8
Alignment explanation
Indices: 2734--2783 Score: 64
Period size: 8 Copynumber: 5.8 Consensus size: 8
2724 TGCTTGAAGA
2734 AAAAAATG
1 AAAAAATG
2742 TAAAAAAATG
1 --AAAAAATG
2752 AAGAAAAATG
1 -A-AAAAATG
2762 AAAAAATG
1 AAAAAATG
2770 AAAAAATG
1 AAAAAATG
2778 AAAAAA
1 AAAAAA
2784 AAAGAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
8 21 0.54
9 3 0.08
10 15 0.38
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:2767 original size:18 final size:18
Alignment explanation
Indices: 2744--2792 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 18
2734 AAAAAATGTA
2744 AAAAAATGAAGAAAAATG
1 AAAAAATGAAGAAAAATG
2762 AAAAAATG-A-AAAAATG
1 AAAAAATGAAGAAAAATG
*
2778 AAAAAA-AAAGAAAAA
1 AAAAAATGAAGAAAAA
2793 AAAAGAAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 14 0.50
17 6 0.21
18 8 0.29
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (18 bp):
AAAAAATGAAGAAAAATG
Found at i:2773 original size:26 final size:27
Alignment explanation
Indices: 2734--2793 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 27
2724 TGCTTGAAGA
* *
2734 AAAAAATGTAAAAAAATGAAGAAAAATG
1 AAAAAATG-AAAAAAATGAAAAAAAAAG
2762 AAAAAATG-AAAAAATGAAAAAAAAAG
1 AAAAAATGAAAAAAATGAAAAAAAAAG
2788 AAAAAA
1 AAAAAA
2794 AAAGAAGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 22 0.73
28 8 0.27
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (27 bp):
AAAAAATGAAAAAAATGAAAAAAAAAG
Found at i:2795 original size:10 final size:10
Alignment explanation
Indices: 2770--2799 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2760 TGAAAAAATG
*
2770 AAAAAATGAA
1 AAAAAAAGAA
2780 AAAAAAAGAA
1 AAAAAAAGAA
2790 AAAAAAAGAA
1 AAAAAAAGAA
2800 GGGGTCAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:4690 original size:113 final size:113
Alignment explanation
Indices: 4360--4717 Score: 682
Period size: 113 Copynumber: 3.2 Consensus size: 113
4350 TTTTAGTTAG
4360 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
4425 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
*
4473 AGTTCATAATGAGAAGAACTCATCTGAAGAATG-AGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
*
4537 AACCTTTTTCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
4585 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
*
4650 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGTTTTTCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
4698 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
4718 TGTTCAACCT
Statistics
Matches: 239, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
112 110 0.46
113 129 0.54
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
Found at i:4744 original size:73 final size:73
Alignment explanation
Indices: 4624--4790 Score: 280
Period size: 73 Copynumber: 2.3 Consensus size: 73
4614 AAGGAAGAAG
* **
4624 AAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGTTTT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTT
4689 TCCAGAGA
66 TCCAGAGA
* *
4697 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTT
*
4762 TCTAGAGA
66 TCCAGAGA
4770 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
4791 CATCTGAAGG
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 88 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (73 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTT
TCCAGAGA
Found at i:4746 original size:186 final size:186
Alignment explanation
Indices: 4511--4845 Score: 580
Period size: 186 Copynumber: 1.8 Consensus size: 186
4501 GAATGAGAAG
* * *
4511 AAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTTCTCAAATCCATCACTTGATGGATCAGCTTT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTT
4576 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
66 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
4641 AGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGTTTTTCCAGAGA
131 AGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGTTTTTCCAGAGA
* *
4697 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTT
* * *
4762 TCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGGAAGAGGAAGTTCATAATGAGAAG
66 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
* *
4827 AGTTTGTTCGACCTTTTGC
131 AGCTTGTTCAACCTTTTGC
4846 ATGACACTAT
Statistics
Matches: 139, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
186 139 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (186 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTT
TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
AGCTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGTTTTTCCAGAGA
Found at i:5187 original size:3 final size:3
Alignment explanation
Indices: 5181--5246 Score: 66
Period size: 3 Copynumber: 22.7 Consensus size: 3
5171 TTCATTTGAA
* * *
5181 TAT TAT T-T ATAT TAT TAT TAT AAT TAT AAT TA- TAA TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5225 TAT AAT TAT T-T TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
5247 CAAGCCTAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
2 5 0.10
3 46 0.88
4 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5239 original size:20 final size:20
Alignment explanation
Indices: 5190--5246 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
5180 ATATTATTTA
*
5190 TATTATTATTATAATTATAAT
1 TATT-TTATTATTATTATAAT
**
5211 TATAATATTATTATTATAAT
1 TATTTTATTATTATTATAAT
5231 TATTTTATTATTATTA
1 TATTTTATTATTATTA
5247 CAAGCCTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTATTATTATTATAAT
Found at i:6603 original size:3 final size:3
Alignment explanation
Indices: 6595--6624 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
6585 TTTACTTTTA
*
6595 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6625 TAGCCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:6825 original size:115 final size:114
Alignment explanation
Indices: 6706--6928 Score: 279
Period size: 116 Copynumber: 1.9 Consensus size: 114
6696 GTTTTAATAT
* ** * * *
6706 TTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCCATTTTCTGATA
1 TTATTTATTTTTCAATATCAAAGAAAAGAACAGTCTTAAAACAACTAGAAGTCC-TTTTATGATA
* *
6769 TTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTATTTTAA
65 TTTCTAAATAAATAAATATCTTA-TTTATAAA-TATATATAAATTATTTTAA
* * ** *
6821 TTATTTATTTTTTAATATCAAAGAAAAGAACTGTCTTAAGGCACCTAGAAGTCCTTTTATGATAT
1 TTATTTATTTTTCAATATCAAAGAAAAGAACAGTCTTAAAACAACTAGAAGTCCTTTTATGATAT
*
6886 TTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTA
66 TTCTAAATAAATAAATATCTTATTTATAAATATATATAAATTA
6929 ATATATATTT
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
114 12 0.13
115 25 0.27
116 33 0.36
117 22 0.24
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (114 bp):
TTATTTATTTTTCAATATCAAAGAAAAGAACAGTCTTAAAACAACTAGAAGTCCTTTTATGATAT
TTCTAAATAAATAAATATCTTATTTATAAATATATATAAATTATTTTAA
Found at i:6937 original size:33 final size:32
Alignment explanation
Indices: 6889--6951 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
6879 ATGATATTTC
6889 TAAATAAATAAATATTTTATTTATAAATATATA
1 TAAATAAATAAATATTTT-TTTATAAATATATA
* * *
6922 TAAATTAATATATATTTTTTTATAATTATA
1 TAAATAAATAAATATTTTTTTATAAATATA
6952 ATTTTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TAAATAAATAAATATTTTTTTATAAATATATA
Found at i:10448 original size:110 final size:110
Alignment explanation
Indices: 10303--10501 Score: 310
Period size: 110 Copynumber: 1.8 Consensus size: 110
10293 AACCAGGAAA
* * * *
10303 TTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATA
1 TTGTTTGTTGACAATCAGCCACCCCTTCGCTGTGAAGTTGAGCTTCTGCTGTCTCGAGTCCAATA
*
10368 TTCTTCGCTGTGAAGTTGAAATTGACTCAGAATGAAACTAAAAAG
66 TCCTTCGCTGTGAAGTTGAAATTGACTCAGAATGAAACTAAAAAG
* *
10413 TTGTTTGTTGACAATCAGCCACCCCTTCG-TCGTGAAGTTGAGCTTCTGTTGTCTTGAGTCCAAT
1 TTGTTTGTTGACAATCAGCCACCCCTTCGCT-GTGAAGTTGAGCTTCTGCTGTCTCGAGTCCAAT
*
10477 ATCCTTCGTTGTGAAGTTGAAATTG
65 ATCCTTCGCTGTGAAGTTGAAATTG
10502 GCTTTGAAAT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
109 1 0.01
110 79 0.99
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (110 bp):
TTGTTTGTTGACAATCAGCCACCCCTTCGCTGTGAAGTTGAGCTTCTGCTGTCTCGAGTCCAATA
TCCTTCGCTGTGAAGTTGAAATTGACTCAGAATGAAACTAAAAAG
Found at i:11652 original size:19 final size:19
Alignment explanation
Indices: 11628--11670 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
11618 ACCCACCTTA
11628 TTTTTCTTCTCTT-TTTCTT
1 TTTTTCTTCTCTTCTTT-TT
*
11647 TTTTTCTTCTGTTCTTTTT
1 TTTTTCTTCTCTTCTTTTT
11666 TTTTT
1 TTTTT
11671 TTCAATTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTTCTTCTCTTCTTTTT
Found at i:22191 original size:23 final size:23
Alignment explanation
Indices: 22150--22193 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
22140 TAAGGAAGGT
*
22150 GAAAAAATAAATGCAATAAAGTA
1 GAAAAAATAAATACAATAAAGTA
22173 GAAAAAATAAA-ACAGATAAAG
1 GAAAAAATAAATACA-ATAAAG
22194 AAAATGTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.68, C:0.05, G:0.14, T:0.14
Consensus pattern (23 bp):
GAAAAAATAAATACAATAAAGTA
Found at i:22423 original size:3 final size:3
Alignment explanation
Indices: 22364--22407 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
22354 TATATAGCAT
* *
22364 ATA ATA ATA GTA ATA A-A AAA AT- ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
22408 AGGCAAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:23462 original size:30 final size:30
Alignment explanation
Indices: 23428--23494 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
23418 AGTGAACCGA
*
23428 CGGTTCAAACCGATTTTGCCGATTTTCAAC
1 CGGTTCAAACCGATTTTACCGATTTTCAAC
** * *
23458 CGGTTCACCCCGGTTTTACCGGTTTTCAAC
1 CGGTTCAAACCGATTTTACCGATTTTCAAC
*
23488 CAGTTCA
1 CGGTTCA
23495 TTGTCAGCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (30 bp):
CGGTTCAAACCGATTTTACCGATTTTCAAC
Found at i:24891 original size:17 final size:17
Alignment explanation
Indices: 24869--24909 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
24859 GAATTACATA
24869 ATATAGTTTATAATACT
1 ATATAGTTTATAATACT
24886 ATATAGTTTATAATACT
1 ATATAGTTTATAATACT
24903 ATATAGT
1 ATATAGT
24910 ATAACATCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (17 bp):
ATATAGTTTATAATACT
Found at i:29345 original size:2 final size:2
Alignment explanation
Indices: 29338--29388 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
29328 TACTTATACT
29338 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
29380 TA TA TA TA T
1 TA TA TA TA T
29389 GAGTGAGTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34245 original size:18 final size:18
Alignment explanation
Indices: 34222--34256 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34212 TTCCATCCGG
*
34222 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
34240 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
34257 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:39067 original size:10 final size:10
Alignment explanation
Indices: 39038--39106 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
39028 GCTGCTGGAA
39038 AACCGGTTTG
1 AACCGGTTTG
*
39048 -ACCAGTTTTG
1 AACC-GGTTTG
39058 AACCGGTTTG
1 AACCGGTTTG
*
39068 -ACCGGTTCG
1 AACCGGTTTG
39077 AACCGGTTTG
1 AACCGGTTTG
*
39087 -ACCGGTCTG
1 AACCGGTTTG
*
39096 AACCGGGTTG
1 AACCGGTTTG
39106 A
1 A
39107 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:39081 original size:19 final size:19
Alignment explanation
Indices: 39038--39108 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
39028 GCTGCTGGAA
* *
39038 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
39058 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
39077 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
39096 AACCGGGTTGACC
1 AACCGGTTTGACC
39109 CGACCCGACT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 2 0.04
19 32 0.68
20 13 0.28
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:39124 original size:17 final size:17
Alignment explanation
Indices: 39102--39176 Score: 132
Period size: 17 Copynumber: 4.4 Consensus size: 17
39092 TCTGAACCGG
*
39102 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
*
39119 GTTGACCCAACCCGACC
1 GTTGACCCGACCCGACC
39136 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
39153 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
39170 GTTGACC
1 GTTGACC
39177 GTGACCGTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.19, C:0.44, G:0.23, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:39183 original size:6 final size:7
Alignment explanation
Indices: 39166--39195 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
39156 GACCCGACCC
39166 GACCGTT
1 GACCGTT
39173 GACCG-T
1 GACCGTT
39179 GACCGTT
1 GACCGTT
39186 GACCGTT
1 GACCGTT
39193 GAC
1 GAC
39196 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:39184 original size:13 final size:13
Alignment explanation
Indices: 39166--39191 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39156 GACCCGACCC
39166 GACCGTTGACCGT
1 GACCGTTGACCGT
39179 GACCGTTGACCGT
1 GACCGTTGACCGT
39192 TGACTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:40683 original size:18 final size:18
Alignment explanation
Indices: 40660--40694 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40650 TTCCATCCGG
*
40660 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
40678 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
40695 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:42007 original size:13 final size:13
Alignment explanation
Indices: 41989--42013 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41979 ACGGTCAACG
41989 GTCAACGGGTCGA
1 GTCAACGGGTCGA
42002 GTCAACGGGTCG
1 GTCAACGGGTCG
42014 GGTCGGGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:42017 original size:18 final size:18
Alignment explanation
Indices: 41994--42034 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
41984 CAACGGTCAA
41994 CGGGTCGAGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
*
42012 CGGGTCGGGTCAACGGGT
1 CGGGTCGAGTCAACGGGT
42030 CGGGT
1 CGGGT
42035 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGAGTCAACGGGT
Found at i:42025 original size:31 final size:31
Alignment explanation
Indices: 41988--42052 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
41978 GACGGTCAAC
*
41988 GGTCAACGGGTCGAGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGAGTAAACGGGTCGGGTCG
*
42019 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGAGTAAACGGGTCGGGTCG
42050 GGT
1 GGT
42053 TGTGACCGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.15, C:0.20, G:0.48, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGAGTAAACGGGTCGGGTCG
Found at i:42028 original size:13 final size:13
Alignment explanation
Indices: 42012--42048 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
42002 GTCAACGGGT
42012 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
42025 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
42038 CGGGTCGGGTC
1 CGGGTCGGGTC
42049 GGGTTGTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Done.