Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003250.1 Hibiscus syriacus cultivar Beakdansim tig00006833_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: 86110
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:99 original size:22 final size:22
Alignment explanation
Indices: 74--117 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
64 TAGATAATCT
74 CAATGCGAATATGTAAATCGCA
1 CAATGCGAATATGTAAATCGCA
*
96 CAATGTGAATATGTAAATCGCA
1 CAATGCGAATATGTAAATCGCA
118 ACACGATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (22 bp):
CAATGCGAATATGTAAATCGCA
Found at i:158 original size:20 final size:20
Alignment explanation
Indices: 133--259 Score: 166
Period size: 20 Copynumber: 6.3 Consensus size: 20
123 ATAACACGTG
133 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
153 ATCGCAACGCTATTCGGACT
1 ATCGCAACGCGATTCTGACT
173 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
193 ATCGCAATGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
*
213 GATCGCAACGTGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
234 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
254 AACGCA
1 ATCGCA
260 TCATTGAATT
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 74 0.81
21 13 0.14
22 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:3357 original size:17 final size:17
Alignment explanation
Indices: 3335--3368 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3325 AGCAAAAGGC
*
3335 AATCAAAATCGCAATCA
1 AATCAAAATCCCAATCA
3352 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
3369 CAAACGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.18
Consensus pattern (17 bp):
AATCAAAATCCCAATCA
Found at i:3568 original size:20 final size:20
Alignment explanation
Indices: 3543--3790 Score: 162
Period size: 20 Copynumber: 13.4 Consensus size: 20
3533 CACATTCATT
3543 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
3563 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
3583 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
3600 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
3617 TGACTATCGCAACTCGAATT
1 TGACTATCGCAACGCGAATA
3637 TGACTATCGCAACG-G---A
1 TGACTATCGCAACGCGAATA
* *
3653 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
3670 TGACTATCGCAATGCGAATT
1 TGACTATCGCAACGCGAATA
*
3690 TGACTATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
3707 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
* *
3723 TGACTATCGCAACACGAATT
1 TGACTATCGCAACGCGAATA
* *
3743 TGATTATCGCAACG-GGATA
1 TGACTATCGCAACGCGAATA
*
3762 TTGACTATCGCAACG-GAAATT
1 -TGACTATCGCAACGCG-AATA
3783 TGACTATC
1 TGACTATC
3791 ACAAGAAAAA
Statistics
Matches: 179, Mismatches: 27, Indels: 44
0.72 0.11 0.18
Matches are distributed among these distances:
13 8 0.04
14 16 0.09
15 2 0.01
16 7 0.04
17 9 0.05
18 4 0.02
19 17 0.09
20 114 0.64
21 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:3677 original size:53 final size:53
Alignment explanation
Indices: 3548--3757 Score: 309
Period size: 53 Copynumber: 3.9 Consensus size: 53
3538 TCATTTGACT
* *
3548 ATCGCAACGCGAATATGACTATCGCAACGT-GAATTTGAATATCGCAACGGGATA
1 ATCGCAACGCGAAAATGACTATCGCAAC-TCGAATTTGACTATCGCAAC-GGATA
*
3602 ATCGCAATGCGAAAATGACTATCGCAACTCGAATTTGACTATCGCAACGGATA
1 ATCGCAACGCGAAAATGACTATCGCAACTCGAATTTGACTATCGCAACGGATA
*
3655 ATCGCAATGCGAAAATGACTATCGCAA-TGCGAATTTGACTATCGCAACGAGATA
1 ATCGCAACGCGAAAATGACTATCGCAACT-CGAATTTGACTATCGCAACG-GATA
* *
3709 ATCGCAACGCG-AAATGACTATCGCAACACGAATTTGATTATCGCAACGG
1 ATCGCAACGCGAAAATGACTATCGCAACTCGAATTTGACTATCGCAACGG
3758 GATATTGACT
Statistics
Matches: 146, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
52 2 0.01
53 87 0.60
54 57 0.39
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (53 bp):
ATCGCAACGCGAAAATGACTATCGCAACTCGAATTTGACTATCGCAACGGATA
Found at i:3761 original size:107 final size:107
Alignment explanation
Indices: 3548--3757 Score: 332
Period size: 107 Copynumber: 2.0 Consensus size: 107
3538 TCATTTGACT
* * * *
3548 ATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGCAACGGGATAATCGCAATGCG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGAATATCGCAACGAGATAATCGCAACGCG
*
3613 AAAATGACTATCGCAACTCGAATTTGACTATCGCAACGGATA
66 AAAATGACTATCGCAACACGAATTTGACTATCGCAACGGATA
* * *
3655 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAGATAATCGCAACGCG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGAATATCGCAACGAGATAATCGCAACGCG
*
3720 -AAATGACTATCGCAACACGAATTTGATTATCGCAACGG
66 AAAATGACTATCGCAACACGAATTTGACTATCGCAACGG
3758 GATATTGACT
Statistics
Matches: 94, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
106 36 0.38
107 58 0.62
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (107 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGAATATCGCAACGAGATAATCGCAACGCG
AAAATGACTATCGCAACACGAATTTGACTATCGCAACGGATA
Found at i:3968 original size:36 final size:34
Alignment explanation
Indices: 3928--4007 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 34
3918 TCAACTTTTA
*
3928 ATCAATTAAACAAGCACAAATAATAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
3964 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
3994 ATCAATTAAACAAA
1 ATCAATTAAACAAA
4008 TCAACTCTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
30 27 0.69
32 2 0.05
34 3 0.08
36 7 0.18
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.28
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:3978 original size:30 final size:30
Alignment explanation
Indices: 3943--4008 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
3933 TTAAACAAGC
*
3943 ACAAATAATAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
3973 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
4003 ACAAAT
1 ACAAAT
4009 CAACTCTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:5984 original size:20 final size:20
Alignment explanation
Indices: 5959--5998 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5949 GAATAGTTTT
5959 TGAAACTTAAAATCGCAACA
1 TGAAACTTAAAATCGCAACA
*
5979 TGAAACTTAAAATCGTAACA
1 TGAAACTTAAAATCGCAACA
5999 CAAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (20 bp):
TGAAACTTAAAATCGCAACA
Found at i:6114 original size:34 final size:34
Alignment explanation
Indices: 6053--6190 Score: 132
Period size: 34 Copynumber: 3.9 Consensus size: 34
6043 ACTAAATTCA
**
6053 CGTTGCGATAGTCGATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTC-AAATTCGCATTGCGATTATCC
* **
6088 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTATG
1 CGTTGCGATAGTCAAATTCGCATTGCGAT--T-A--T-CC
***
6128 CGTTGCGATAGTCGTTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGCATTGCGATTATCC
*
6162 CGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCATTGCGAT
6191 AATCATTTTC
Statistics
Matches: 82, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
34 38 0.46
35 14 0.17
36 1 0.01
37 2 0.02
38 1 0.01
39 1 0.01
40 25 0.30
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCATTGCGATTATCC
Found at i:6201 original size:20 final size:20
Alignment explanation
Indices: 6053--6209 Score: 106
Period size: 20 Copynumber: 8.4 Consensus size: 20
6043 ACTAAATTCA
6053 CGTTGCGATAGTCGATTTTCG
1 CGTTGCGATAGTC-ATTTTCG
* *
6074 CATTGCGAT--T-A---TCC
1 CGTTGCGATAGTCATTTTCG
**
6088 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
6108 CGTTGCGATAGTCATTTAT-G
1 CGTTGCGATAGTCATTT-TCG
*
6128 CGTTGCGATAGTCGTTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
6148 CATTGCGAT--T-A---TCC
1 CGTTGCGATAGTCATTTTCG
**
6162 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
6182 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
6202 TGTTGCGA
1 CGTTGCGA
6210 CTATTTTCTT
Statistics
Matches: 106, Mismatches: 16, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
14 20 0.19
16 2 0.02
17 3 0.03
18 1 0.01
19 2 0.02
20 69 0.65
21 9 0.08
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:6209 original size:74 final size:75
Alignment explanation
Indices: 6053--6198 Score: 276
Period size: 74 Copynumber: 2.0 Consensus size: 75
6043 ACTAAATTCA
6053 CGTTGCGATAGTCGATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATA
1 CGTTGCGATAGTCGATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATA
*
6118 GTCATTTATG
66 ATCATTTATG
6128 CGTTGCGATAGTCG-TTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATA
1 CGTTGCGATAGTCGATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATA
6192 ATCATTT
66 ATCATTT
6199 TCGTGTTGCG
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 56 0.80
75 14 0.20
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (75 bp):
CGTTGCGATAGTCGATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATA
ATCATTTATG
Found at i:8131 original size:20 final size:20
Alignment explanation
Indices: 8106--8161 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
8096 TCTAAAACTT
8106 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
8126 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
8146 ATTATCGCAACGCGAA
1 AAAATCGCAACACGAA
8162 TTTGACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:8171 original size:20 final size:20
Alignment explanation
Indices: 8129--8184 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
8119 GAAAATGAAA
* ** *
8129 ATCGCAACACGAAAATGATT
1 ATCGCAACGCGAATTTGACT
8149 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
8169 ATCGCAACGCGAATTT
1 ATCGCAACGCGAATTT
8185 TGTCGTTGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:8737 original size:20 final size:20
Alignment explanation
Indices: 8708--8801 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
8698 ATTTTATATT
*
8708 ATCGCGTTGCGATAGTAAGA
1 ATCGCGTTGCGATAGTCAGA
* **
8728 ATCCCGTTGCGATCACGT-ATT
1 ATCGCGTTGCGAT-A-GTCAGA
*
8749 ATCGCGTTGCGATAGTCCGA
1 ATCGCGTTGCGATAGTCAGA
*
8769 ATCACGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
8789 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
8802 CACGTGTTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.70
21 14 0.23
22 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:8750 original size:41 final size:41
Alignment explanation
Indices: 8704--8781 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
8694 TGCGATTTTA
*
8704 TATTATCGCGTTGCGATAGTAAGAATCCCGTTGCGATCACG
1 TATTATCGCGTTGCGATAGTAAGAATCACGTTGCGATCACG
**
8745 TATTATCGCGTTGCGATAGTCCGAATCACGTTGCGAT
1 TATTATCGCGTTGCGATAGTAAGAATCACGTTGCGAT
8782 AGTCAGAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (41 bp):
TATTATCGCGTTGCGATAGTAAGAATCACGTTGCGATCACG
Found at i:8840 original size:61 final size:60
Alignment explanation
Indices: 8687--8842 Score: 177
Period size: 61 Copynumber: 2.5 Consensus size: 60
8677 CGCTTTGAAA
* *
8687 ATCGCATTGCGATTTTATATTATCGCGTTGCGATAGTAAGAATCCCGTTGCGATCACGTATT
1 ATCGCGTTGCGATTTCATA-T-TCGCGTTGCGATAGTAAGAATCCCGTTGCGATCACGTATT
* ** * * * * *
8749 ATCGCGTTGCGATAGTCCGAATCACGTTGCGATAGTCAGAATCGCGTTGCGATCACGTGTT
1 ATCGCGTTGCGAT-TTCATATTCGCGTTGCGATAGTAAGAATCCCGTTGCGATCACGTATT
*
8810 ATCGCGTTGCGATTTACATATTCGCATTGCGAT
1 ATCGCGTTGCGATTT-CATATTCGCGTTGCGAT
8843 TATCTAAAAT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
60 1 0.01
61 61 0.80
62 12 0.16
63 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (60 bp):
ATCGCGTTGCGATTTCATATTCGCGTTGCGATAGTAAGAATCCCGTTGCGATCACGTATT
Found at i:8892 original size:20 final size:19
Alignment explanation
Indices: 8831--8896 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 19
8821 ATTTACATAT
*
8831 TCGCATTGCGATTATCTAAAA
1 TCGCAATGCGATT-T-TAAAA
*
8852 TCGCAACGCGGATTTTGAAAA
1 TCGCAATGC-GATTTT-AAAA
8873 TCGCAATGCGATTGTTAAAA
1 TCGCAATGCGATT-TTAAAA
8893 TCGC
1 TCGC
8897 GTTGCGAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 13 0.33
21 22 0.56
22 4 0.10
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (19 bp):
TCGCAATGCGATTTTAAAA
Found at i:9545 original size:2 final size:2
Alignment explanation
Indices: 9534--9563 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9524 TTTCATTGTC
9534 TA TA -A 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 TA TA TA T
9564 GGTTGAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12795 original size:75 final size:75
Alignment explanation
Indices: 12672--12820 Score: 298
Period size: 75 Copynumber: 2.0 Consensus size: 75
12662 CTACTTTTTC
12672 TAGTTTAAGCCTTTAAAATACGACAATCATATATATCTAAACTTATTAGTTTATAAATAGTTATA
1 TAGTTTAAGCCTTTAAAATACGACAATCATATATATCTAAACTTATTAGTTTATAAATAGTTATA
12737 ACAATCTTAT
66 ACAATCTTAT
12747 TAGTTTAAGCCTTTAAAATACGACAATCATATATATCTAAACTTATTAGTTTATAAATAGTTATA
1 TAGTTTAAGCCTTTAAAATACGACAATCATATATATCTAAACTTATTAGTTTATAAATAGTTATA
12812 ACAATCTTA
66 ACAATCTTA
12821 CTATTGACGA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (75 bp):
TAGTTTAAGCCTTTAAAATACGACAATCATATATATCTAAACTTATTAGTTTATAAATAGTTATA
ACAATCTTAT
Found at i:15776 original size:49 final size:50
Alignment explanation
Indices: 15719--15816 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
15709 TCCAAGTTTA
* *
15719 GGACCAAGTT-GGAAATGCTGTCAAGTTCCAGGGCTAATGTGAAGCAAAG
1 GGACCAAGTTAGGAAAAGCTGTCAAGTTCCAGGACTAATGTGAAGCAAAG
* * *
15768 GGACCAAGTTAGGAAAAGTTGTCAATTTCCAGGACTAATGTGTAGCAAA
1 GGACCAAGTTAGGAAAAGCTGTCAAGTTCCAGGACTAATGTGAAGCAAA
15817 AAAAGTTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 10 0.23
50 33 0.77
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (50 bp):
GGACCAAGTTAGGAAAAGCTGTCAAGTTCCAGGACTAATGTGAAGCAAAG
Found at i:23331 original size:30 final size:33
Alignment explanation
Indices: 23297--23361 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
23287 GATGGTAAAA
* *
23297 AAATT-AA-CAAAAAATT-ATAATTAGAATATT
1 AAATTAAATCAAAAAATTAATAATAAGAAAATT
*
23327 AAATTAAATTAAAAAATTAATAATAAGAAAATT
1 AAATTAAATCAAAAAATTAATAATAAGAAAATT
23360 AA
1 AA
23362 TAAATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 5 0.17
31 2 0.07
32 8 0.28
33 14 0.48
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (33 bp):
AAATTAAATCAAAAAATTAATAATAAGAAAATT
Found at i:23345 original size:18 final size:19
Alignment explanation
Indices: 23308--23346 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
23298 AATTAACAAA
* *
23308 AAATTATAATTAGAATATT
1 AAATTATAATTAAAAAATT
23327 AAATTA-AATTAAAAAATT
1 AAATTATAATTAAAAAATT
23345 AA
1 AA
23347 TAATAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AAATTATAATTAAAAAATT
Found at i:23359 original size:15 final size:14
Alignment explanation
Indices: 23327--23364 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
23317 TTAGAATATT
*
23327 AAATTAA-ATTAAA
1 AAATTAATAATAAA
23340 AAATTAATAATAAGA
1 AAATTAATAATAA-A
23355 AAATTAATAA
1 AAATTAATAA
23365 ATAATTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.32
14 4 0.18
15 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AAATTAATAATAAA
Found at i:29601 original size:18 final size:19
Alignment explanation
Indices: 29578--29615 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
29568 ATGAGTTTAA
29578 TATTTTTATT-ATTTAAAT
1 TATTTTTATTGATTTAAAT
*
29596 TATTTTTTTTGATTTAAAT
1 TATTTTTATTGATTTAAAT
29615 T
1 T
29616 TTCTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TATTTTTATTGATTTAAAT
Found at i:29644 original size:28 final size:31
Alignment explanation
Indices: 29613--29670 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
29603 TTTGATTTAA
29613 ATTTTCTAA-ATAATTT-TA-ATT-TTATTTT
1 ATTTT-TAATATAATTTATATATTCTTATTTT
29641 ATTTTTAATATAATTTATATATTCTTATTT
1 ATTTTTAATATAATTTATATATTCTTATTT
29671 AAAAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 3 0.12
28 12 0.46
29 2 0.08
30 3 0.12
31 6 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (31 bp):
ATTTTTAATATAATTTATATATTCTTATTTT
Found at i:39841 original size:31 final size:31
Alignment explanation
Indices: 39799--39868 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
39789 CTCTGTAGGG
*
39799 TCAGTTGCTTGAATCTCGTAATGGATGCCAT
1 TCAGTTCCTTGAATCTCGTAATGGATGCCAT
39830 TCAGTTCCTTGAATCTCGTAATGGATGCCAT
1 TCAGTTCCTTGAATCTCGTAATGGATGCCAT
39861 TCAGTTCC
1 TCAGTTCC
39869 CTTCTAAGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (31 bp):
TCAGTTCCTTGAATCTCGTAATGGATGCCAT
Found at i:41418 original size:2 final size:2
Alignment explanation
Indices: 41411--41446 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41401 ATAAAGCTAC
41411 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
41447 CACTTGATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41474 original size:18 final size:18
Alignment explanation
Indices: 41451--41508 Score: 116
Period size: 18 Copynumber: 3.2 Consensus size: 18
41441 TATATACACT
41451 TGATTAAAACTAATATTG
1 TGATTAAAACTAATATTG
41469 TGATTAAAACTAATATTG
1 TGATTAAAACTAATATTG
41487 TGATTAAAACTAATATTG
1 TGATTAAAACTAATATTG
41505 TGAT
1 TGAT
41509 ATATCTACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (18 bp):
TGATTAAAACTAATATTG
Found at i:44397 original size:16 final size:15
Alignment explanation
Indices: 44371--44406 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
44361 CGAAATACAA
44371 AATATAATAATTCAT
1 AATATAATAATTCAT
44386 AATATAAATAATTCAT
1 AATAT-AATAATTCAT
*
44402 TATAT
1 AATAT
44407 TTTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAATAATTCAT
Found at i:56706 original size:19 final size:19
Alignment explanation
Indices: 56674--56710 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56664 TCATTTCTTT
* *
56674 CCCTTGAATTTTATTTTAC
1 CCCTTCAATATTATTTTAC
56693 CCCTTCAATATTATTTTA
1 CCCTTCAATATTATTTTA
56711 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.22, G:0.03, T:0.51
Consensus pattern (19 bp):
CCCTTCAATATTATTTTAC
Found at i:56800 original size:5 final size:6
Alignment explanation
Indices: 56763--56800 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
56753 GTCACCCTTC
*
56763 TCAATT TTAATT TCAATT TCAATT TCAATT TC-ATT TCA
1 TCAATT TCAATT TCAATT TCAATT TCAATT TCAATT TCA
56801 CAAATTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (6 bp):
TCAATT
Found at i:63886 original size:25 final size:23
Alignment explanation
Indices: 63850--63895 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
63840 CACTTGAAAG
63850 TTTTAAATTATTATATATTATATA
1 TTTTAAATTATTATAT-TTATATA
* *
63874 TTTTTAATATATTTTATTTATA
1 TTTTAAAT-TATTATATTTATA
63896 ATCTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTAAATTATTATATTTATATA
Found at i:63891 original size:16 final size:16
Alignment explanation
Indices: 63857--63904 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
63847 AAGTTTTAAA
*
63857 TTATTATATATTATATAT
1 TTATAATATATT-T-TAT
*
63875 TTTTAATATATTTTAT
1 TTATAATATATTTTAT
*
63891 TTATAATCTATTTT
1 TTATAATATATTTT
63905 TATATTTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 15 0.58
17 1 0.04
18 10 0.38
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATAATATATTTTAT
Found at i:69812 original size:23 final size:23
Alignment explanation
Indices: 69786--69832 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
69776 AAAAAAATTC
*
69786 AAATCAAGTCGATTCAATTTTCT
1 AAATCAAGTCAATTCAATTTTCT
69809 AAATCAAGTCAATTCAATTTTCT
1 AAATCAAGTCAATTCAATTTTCT
69832 A
1 A
69833 CTTAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
AAATCAAGTCAATTCAATTTTCT
Found at i:74475 original size:4 final size:4
Alignment explanation
Indices: 74466--74490 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
74456 ACGTACCTTT
74466 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
74491 CTTAGCTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:74910 original size:20 final size:20
Alignment explanation
Indices: 74885--74924 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
74875 TTTAAGTTAG
74885 GTCAATATCAAATCAATTAA
1 GTCAATATCAAATCAATTAA
74905 GTCAATATCAAATCAATTAA
1 GTCAATATCAAATCAATTAA
74925 TATTGAATCA
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:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (20 bp):
GTCAATATCAAATCAATTAA
Found at i:77028 original size:2 final size:2
Alignment explanation
Indices: 77021--77047 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
77011 CATGACATGA
77021 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 A
77048 ATTAACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84714 original size:2 final size:2
Alignment explanation
Indices: 84707--84734 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
84697 AATAATGTGA
84707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84735 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.