Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008611.1 Hibiscus syriacus cultivar Beakdansim tig00111567_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: 95598
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:421 original size:226 final size:221
Alignment explanation
Indices: 1--436 Score: 723
Period size: 222 Copynumber: 2.0 Consensus size: 221
* *
1 TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTTAATA
1 TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATCATTAGTTAATA
**
66 TTGTTAAATTTAAAATCTAAAAATATTTTATAAAATATCAAACAATCAAATAATTTTTTGGTAAA
66 TTGTTAAATTTAAAATCTAAAAATATTTTATAAAATATCAAACAATCAAATAAAATTTTGGTAAA
131 TGAAATTATTAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAACATAAAT
131 TGAAATTATTAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAACATAAAT
196 TACATAACTTTCAAAAAGTATATATCA
196 TACATAACTTT-AAAAAGTATATATCA
*
223 TTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTAT-ATTGGTTAAT
1 TTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATCATTAGTTAAT
*
287 ATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTG
65 ATTGTTAAATTTAAAATCTAAA-AATATTTTATAAAATATC-AAACAATCAAATAAAATTTTG-G
* *
352 TAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AATAAATTGAAAC
127 TAAATGAAATTATT-AATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG-AAC
416 ATAAATTACATAACTTTAAAA
190 ATAAATTACATAACTTTAAAA
437 GCAGTTTAAA
Statistics
Matches: 200, Mismatches: 8, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
222 61 0.31
223 38 0.19
224 19 0.09
225 26 0.13
226 56 0.28
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (221 bp):
TTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATCATTAGTTAATA
TTGTTAAATTTAAAATCTAAAAATATTTTATAAAATATCAAACAATCAAATAAAATTTTGGTAAA
TGAAATTATTAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAACATAAAT
TACATAACTTTAAAAAGTATATATCA
Found at i:523 original size:20 final size:19
Alignment explanation
Indices: 500--545 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
490 CGATATACCA
500 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
520 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
540 GGTAAA
1 GGTAAA
546 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:689 original size:20 final size:19
Alignment explanation
Indices: 666--712 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
656 CGATATAACA
666 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
686 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
706 GGTAAAA
1 GGTAAAA
713 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:714 original size:17 final size:19
Alignment explanation
Indices: 675--717 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
665 AGGTAAAAAT
675 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
695 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
712 ATGATA
1 ATGATA
718 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:2975 original size:21 final size:21
Alignment explanation
Indices: 2928--2992 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2918 AAGACAATCA
* *
2928 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
2950 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
2970 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
2991 AG
1 AG
2993 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:3068 original size:33 final size:33
Alignment explanation
Indices: 3026--3091 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3016 AAATAGATGG
*
3026 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
3059 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
3092 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:4923 original size:18 final size:19
Alignment explanation
Indices: 4879--4926 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
4869 AATGTAGGGT
4879 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
4898 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
4917 T-ATTTTGTAT
1 TAATTTTGTAT
4927 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:6821 original size:6 final size:6
Alignment explanation
Indices: 6797--6876 Score: 61
Period size: 6 Copynumber: 13.3 Consensus size: 6
6787 AGCGGTCGCA
* * * * * **
6797 GAAGAT GAAGCT GACGAT GAAGAT GATGAT GACGAT GAAGCT GGCGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * *
6845 GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
6877 TGATCCAAAC
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:6826 original size:3 final size:3
Alignment explanation
Indices: 6812--6880 Score: 57
Period size: 3 Copynumber: 23.0 Consensus size: 3
6802 TGAAGCTGAC
* * * * ** * *
6812 GAT GAA GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
6860 GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT
6881 CCAAACAAGT
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:6836 original size:30 final size:30
Alignment explanation
Indices: 6800--6864 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
6790 GGTCGCAGAA
*
6800 GATGAAGCTGACGATGAAGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGACGAC
* *
6830 GATGAAGCTGGCGATGAAGATGATGACGAT
1 GATGAAGCTGACGATGAAGATGATGACGAC
6860 GATGA
1 GATGA
6865 TGATGAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.20
Consensus pattern (30 bp):
GATGAAGCTGACGATGAAGATGATGACGAC
Found at i:6877 original size:12 final size:12
Alignment explanation
Indices: 6797--6880 Score: 69
Period size: 12 Copynumber: 7.0 Consensus size: 12
6787 AGCGGTCGCA
* *
6797 GAAGATGAAGCT
1 GAAGATGATGAT
* *
6809 GACGATGAAGAT
1 GAAGATGATGAT
* *
6821 GATGATGACGAT
1 GAAGATGATGAT
* **
6833 GAAGCTGGCGAT
1 GAAGATGATGAT
*
6845 GAAGATGATGAC
1 GAAGATGATGAT
*
6857 GATGATGATGAT
1 GAAGATGATGAT
6869 GAAGATGATGAT
1 GAAGATGATGAT
6881 CCAAACAAGT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 58 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (12 bp):
GAAGATGATGAT
Found at i:6878 original size:18 final size:18
Alignment explanation
Indices: 6797--6880 Score: 87
Period size: 18 Copynumber: 4.7 Consensus size: 18
6787 AGCGGTCGCA
* *
6797 GAAGATGAAGCTGACGAT
1 GAAGATGATGATGACGAT
6815 GAAGATGATGATGACGAT
1 GAAGATGATGATGACGAT
* ** *
6833 GAAGCTGGCGATGAAGAT
1 GAAGATGATGATGACGAT
* * *
6851 GATGACGATGATGATGAT
1 GAAGATGATGATGACGAT
6869 GAAGATGATGAT
1 GAAGATGATGAT
6881 CCAAACAAGT
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGATGATGACGAT
Found at i:8654 original size:183 final size:183
Alignment explanation
Indices: 8346--8959 Score: 1029
Period size: 183 Copynumber: 3.4 Consensus size: 183
8336 CTTTCAACAT
** * * * * *
8346 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTGTATGAGCGAATA
8411 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
8476 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
8529 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTGTATGAGCGAATA
8594 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
8659 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
8712 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AA-ATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTGTATGAGCGAATA
*
8775 GGTCTACAACCTATATCGACACTTTTTAATATTGTGCCGGTACTTTATGT-C---------G-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
8829 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* *
8882 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTGTATGAGCGAATA
*
8947 TGTCTACAACCTA
66 GGTCTACAACCTA
8960 AAATGTGTCG
Statistics
Matches: 416, Mismatches: 13, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
170 94 0.23
171 3 0.01
172 32 0.08
180 1 0.00
181 71 0.17
182 2 0.00
183 213 0.51
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTGTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:11483 original size:23 final size:23
Alignment explanation
Indices: 11435--11485 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
11425 TAACTACAAG
*
11435 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTATCGGT
11458 TATATAATGTAATAGGTAGT-GGT
1 TATATAATGTAATAGGTA-TCGGT
11481 TATAT
1 TATAT
11486 TGTAAAGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (23 bp):
TATATAATGTAATAGGTATCGGT
Found at i:11928 original size:18 final size:18
Alignment explanation
Indices: 11907--11943 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11897 GTAATTGGAG
11907 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
11925 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
11943 T
1 T
11944 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:11951 original size:24 final size:24
Alignment explanation
Indices: 11899--11945 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11889 TTTCATATGT
* *
11899 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
11923 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
11946 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:12732 original size:23 final size:23
Alignment explanation
Indices: 12701--12773 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
12691 ATAGGTAAAA
*
12701 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
12724 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
12747 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
12770 ATAT
1 ATAT
12774 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:14622 original size:2 final size:2
Alignment explanation
Indices: 14615--14675 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
14605 ACAACAAAAT
14615 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
14657 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
14676 TCCACCTAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16289 original size:33 final size:33
Alignment explanation
Indices: 16242--16354 Score: 111
Period size: 33 Copynumber: 3.4 Consensus size: 33
16232 CGAAGCCGAA
** *
16242 GCAAAGCCTGCAGAAGCTCAAGCTGAAGGAGAG
1 GCAAAGCCCACAGAAGCTCAAGCAGAAGGAGAG
* * * * *
16275 GCAAAGCCTACAGAAACTCCAGCAG-AGGCCGAA
1 GCAAAGCCCACAGAAGCTCAAGCAGAAGG-AGAG
* *
16308 GCAAAGCCCACGGAAGCTGAAGCAGAAGGAGAG
1 GCAAAGCCCACAGAAGCTCAAGCAGAAGGAGAG
*
16341 ACAAAGCCCACAGA
1 GCAAAGCCCACAGA
16355 GGCTGTTGCC
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
32 3 0.05
33 57 0.90
34 3 0.05
ACGTcount: A:0.40, C:0.26, G:0.29, T:0.05
Consensus pattern (33 bp):
GCAAAGCCCACAGAAGCTCAAGCAGAAGGAGAG
Found at i:17618 original size:87 final size:86
Alignment explanation
Indices: 17473--17632 Score: 205
Period size: 87 Copynumber: 1.8 Consensus size: 86
17463 GTACATGCAT
** * * * * * *
17473 AAGGATGAGCTTTTGCTCTTAATGGATTTATAGCTCAGATTTTGGGTGATCTTAGTGAGAATGAC
1 AAGGATGAGCTTTCACTCTTAATGAATTTATAACCCAGATTATGGGTGATCATAGTGAGAAGGAC
17538 TTGATGAATCCACCGACGTGA
66 TTGATGAATCCACCGACGTGA
* *
17559 AAGGATGAGCTTTACACTCTTAATGAATTTATAACCCAGGA-TATGGGTGGTCATAGTGAGACGG
1 AAGGATGAGCTTT-CACTCTTAATGAATTTATAACCCA-GATTATGGGTGATCATAGTGAGAAGG
17623 ACTTGATGAA
64 ACTTGATGAA
17633 CTCACTGACT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
86 13 0.21
87 47 0.76
88 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (86 bp):
AAGGATGAGCTTTCACTCTTAATGAATTTATAACCCAGATTATGGGTGATCATAGTGAGAAGGAC
TTGATGAATCCACCGACGTGA
Found at i:19318 original size:17 final size:17
Alignment explanation
Indices: 19296--19328 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19286 AAGTGTTTTT
*
19296 TTAAAATTATTAAAAAA
1 TTAAAATTATCAAAAAA
19313 TTAAAATTATCAAAAA
1 TTAAAATTATCAAAAA
19329 TGATTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATTATCAAAAAA
Found at i:31995 original size:54 final size:54
Alignment explanation
Indices: 31936--32043 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
31926 CGTTCACCCA
*
31936 CTAATCGATTATTACATTTTCTATTATCCCAAATACCTAAATACATAAATCCCT
1 CTAATCGATTATTACATTTTCTATCATCCCAAATACCTAAATACATAAATCCCT
* *
31990 CTAATCGATTATTACATTTTCTATCATCCCAAATTCCTAAATTCATAAATCCCT
1 CTAATCGATTATTACATTTTCTATCATCCCAAATACCTAAATACATAAATCCCT
32044 TCTCTTAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (54 bp):
CTAATCGATTATTACATTTTCTATCATCCCAAATACCTAAATACATAAATCCCT
Found at i:38171 original size:17 final size:18
Alignment explanation
Indices: 38151--38187 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
38141 TTAGATATTG
38151 TTTTA-AATAA-ATACATT
1 TTTTACAATAATA-ACATT
38168 TTTTACAATAATAACATT
1 TTTTACAATAATAACATT
38186 TT
1 TT
38188 CACCTCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 12 0.67
19 1 0.06
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTACAATAATAACATT
Found at i:40385 original size:13 final size:13
Alignment explanation
Indices: 40367--40391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40357 AATATTTTAA
40367 TAATTATAAGATT
1 TAATTATAAGATT
40380 TAATTATAAGAT
1 TAATTATAAGAT
40392 AAAATGACCT
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TAATTATAAGATT
Found at i:40655 original size:19 final size:18
Alignment explanation
Indices: 40631--40671 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
40621 TTTCGGTTTG
40631 AAAAAAACCGTTTTAAAGA
1 AAAAAAACCGTTTTAAA-A
40650 AAAAAAACCGTTTTAAAA
1 AAAAAAACCGTTTTAAAA
40668 AAAA
1 AAAA
40672 TCGGTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (18 bp):
AAAAAAACCGTTTTAAAA
Found at i:44416 original size:31 final size:30
Alignment explanation
Indices: 44350--44417 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
44340 ACCGAAATTT
44350 ATTCGGTTCGGTTAAGTTTTCAAAAAAAAA
1 ATTCGGTTCGGTTAAGTTTTCAAAAAAAAA
44380 A-TCGGTTCGGTTAA-TTGTT-AAAGAAAAAA
1 ATTCGGTTCGGTTAAGTT-TTCAAA-AAAAAA
44409 AGTTCGGTT
1 A-TTCGGTT
44418 TAATTCGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
28 5 0.15
29 22 0.65
30 1 0.03
31 6 0.18
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.34
Consensus pattern (30 bp):
ATTCGGTTCGGTTAAGTTTTCAAAAAAAAA
Found at i:46009 original size:38 final size:38
Alignment explanation
Indices: 45956--46034 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
45946 GAAATGAATA
*
45956 TTTACTACATTTTAAGATACTA-AAATTATCACAACAGT
1 TTTACTACATATTAAGATACTACAAA-TATCACAACAGT
* * *
45994 TTTACTAGATATTAAGATACTACAAATATCATAATAGT
1 TTTACTACATATTAAGATACTACAAATATCACAACAGT
46032 TTT
1 TTT
46035 TTTGGGGGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 33 0.92
39 3 0.08
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (38 bp):
TTTACTACATATTAAGATACTACAAATATCACAACAGT
Found at i:50567 original size:24 final size:24
Alignment explanation
Indices: 50535--50587 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
50525 TTAGACGTTT
*
50535 ATTTCAATTTTAACGATGAAATTG
1 ATTTGAATTTTAACGATGAAATTG
50559 ATTTGAATTTTAACGATGAAATTG
1 ATTTGAATTTTAACGATGAAATTG
50583 ATTTG
1 ATTTG
50588 TTTATTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (24 bp):
ATTTGAATTTTAACGATGAAATTG
Found at i:51553 original size:13 final size:13
Alignment explanation
Indices: 51537--51565 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
51527 TAATAGCATT
51537 TTTATTTTTAATA
1 TTTATTTTTAATA
51550 TTTATTTTTAATA
1 TTTATTTTTAATA
51563 TTT
1 TTT
51566 TAGTAATTTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTTAATA
Found at i:51995 original size:5 final size:5
Alignment explanation
Indices: 51985--52009 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
51975 ATCAGACAAA
51985 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
52010 GCAACCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:52101 original size:5 final size:5
Alignment explanation
Indices: 52088--52127 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
52078 ACACCCAATC
*
52088 ATCAA ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG
1 ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG
52128 TCTCTTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (5 bp):
ATCAG
Found at i:55731 original size:23 final size:23
Alignment explanation
Indices: 55705--55751 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
55695 GTGACCGATT
55705 GAGTGGTAATTCATTTGTCTGTG
1 GAGTGGTAATTCATTTGTCTGTG
55728 GAGTGGTAATTCATTTGTCTGTG
1 GAGTGGTAATTCATTTGTCTGTG
55751 G
1 G
55752 CAGATAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.09, G:0.32, T:0.43
Consensus pattern (23 bp):
GAGTGGTAATTCATTTGTCTGTG
Found at i:67692 original size:20 final size:20
Alignment explanation
Indices: 67667--67706 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
67657 GTTTTGTTTC
67667 TTGAAGAAAAAGAAACGACG
1 TTGAAGAAAAAGAAACGACG
67687 TTGAAGAAAAAGAAACGACG
1 TTGAAGAAAAAGAAACGACG
67707 GTTTTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.25, T:0.10
Consensus pattern (20 bp):
TTGAAGAAAAAGAAACGACG
Found at i:82415 original size:33 final size:32
Alignment explanation
Indices: 82339--82416 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
82329 TTGAGTTCAT
* *
82339 ATCGATTATTTTTTAGCTCGAATCAATATCAG
1 ATCGATTATTTTTTAGCTAGAATCAATATCAA
*
82371 ATTGATTATTTTTTAGCTTAG-ATCAATATCAA
1 ATCGATTATTTTTTAGC-TAGAATCAATATCAA
*
82403 ATCGGTTGATTTTT
1 ATCGATT-ATTTTT
82417 GGGTCAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 31 0.79
33 8 0.21
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (32 bp):
ATCGATTATTTTTTAGCTAGAATCAATATCAA
Found at i:82710 original size:12 final size:12
Alignment explanation
Indices: 82693--82717 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
82683 AAGAAAAAAA
82693 TTTATTATAAAT
1 TTTATTATAAAT
82705 TTTATTATAAAT
1 TTTATTATAAAT
82717 T
1 T
82718 AAAATTTTAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATTATAAAT
Found at i:83048 original size:32 final size:32
Alignment explanation
Indices: 83002--83079 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
82992 CTAACATGAT
83002 TGAGGGACTAAAATTGAACGAGAGTTAACGAC
1 TGAGGGACTAAAATTGAACGAGAGTTAACGAC
*
83034 TGAGGGACTGAAATTGAACGAGAGTTAACGAC
1 TGAGGGACTAAAATTGAACGAGAGTTAACGAC
83066 TGAGGGACTAAAAT
1 TGAGGGACTAAAAT
83080 CTAATAGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.40, C:0.12, G:0.29, T:0.19
Consensus pattern (32 bp):
TGAGGGACTAAAATTGAACGAGAGTTAACGAC
Found at i:83106 original size:31 final size:30
Alignment explanation
Indices: 83068--83134 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
83058 TTAACGACTG
* *
83068 AGGGACTAAAATCTAATAGATTGATAACATT
1 AGGGACTAAAATC-AACAGATCGATAACATT
* * *
83099 AGGGACTAATATCGACAGATCGATAGCATT
1 AGGGACTAAAATCAACAGATCGATAACATT
83129 AGGGAC
1 AGGGAC
83135 CATTTTCCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.24
Consensus pattern (30 bp):
AGGGACTAAAATCAACAGATCGATAACATT
Found at i:83278 original size:21 final size:22
Alignment explanation
Indices: 83254--83294 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
83244 ATTATAAATA
83254 AAAAATAA-ATTTTTATATTGT
1 AAAAATAACATTTTTATATTGT
*
83275 AAAAATAACCTTTTTATATT
1 AAAAATAACATTTTTATATT
83295 AAATTTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAAATAACATTTTTATATTGT
Found at i:83805 original size:29 final size:28
Alignment explanation
Indices: 83767--83827 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
83757 TTAGACTTAG
* *
83767 ATATTTAATAAATTAAATTAGTTAAATA
1 ATATTTAATAAAATAAATAAGTTAAATA
* *
83795 ATATTTAAATAAAATAAATAATTTAAATT
1 ATATTT-AATAAAATAAATAAGTTAAATA
83824 ATAT
1 ATAT
83828 ATATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
ATATTTAATAAAATAAATAAGTTAAATA
Found at i:84156 original size:16 final size:16
Alignment explanation
Indices: 84045--84159 Score: 58
Period size: 16 Copynumber: 7.2 Consensus size: 16
84035 TTCAAATTGC
*
84045 TTTCGATTTGAGTTTCT
1 TTTCGATTTGAG-TTAT
*
84062 TTTAG-TTT-AGATTACT
1 TTTCGATTTGAG-TTA-T
* * *
84078 TTTTG-TTTGGGTTAC
1 TTTCGATTTGAGTTAT
* * *
84093 TTTCGATTAGGGTTGT
1 TTTCGATTTGAGTTAT
*
84109 TTTCGGTTTGAGTTAT
1 TTTCGATTTGAGTTAT
* * *
84125 ATTCAATTT-ATATTAT
1 TTTCGATTTGA-GTTAT
84141 TTTCGATTTGAGTTAT
1 TTTCGATTTGAGTTAT
84157 TTT
1 TTT
84160 TTATTCAAGA
Statistics
Matches: 72, Mismatches: 21, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
15 9 0.12
16 57 0.79
17 6 0.08
ACGTcount: A:0.17, C:0.07, G:0.18, T:0.57
Consensus pattern (16 bp):
TTTCGATTTGAGTTAT
Found at i:88367 original size:60 final size:60
Alignment explanation
Indices: 88282--88419 Score: 151
Period size: 60 Copynumber: 2.3 Consensus size: 60
88272 AGTATGACCC
* * *
88282 TCATTTTAAATTGGTCCTTAAACTTTTAAAT-GTTCCAATT-CTATCC-CTAAACTATGACTA-
1 TCATTCTAAATTAGTCCTTAAACTTTTAAATAGCT-CAATTAC-ATCCTC-AAACTATGA-TAT
*
88342 TCATTCTAAATTAGT-CTTCAAACTTTTGAATAGCTCAATTACATCCTCAAACTATGATAT
1 TCATTCTAAATTAGTCCTT-AAACTTTTAAATAGCTCAATTACATCCTCAAACTATGATAT
*
88402 TCATTCTAAATTGGTCCT
1 TCATTCTAAATTAGTCCT
88420 CTTTTTGAAC
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
59 5 0.07
60 56 0.84
61 6 0.09
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCTTAAACTTTTAAATAGCTCAATTACATCCTCAAACTATGATAT
Done.