Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002710.1 Hibiscus syriacus cultivar Beakdansim tig00005593_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: 84651
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:17536 original size:2 final size:2
Alignment explanation
Indices: 17529--17560 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17519 ATTTTTATTA
17529 AT AT 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 AT AT
17561 TCATATGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19568 original size:30 final size:30
Alignment explanation
Indices: 19534--19593 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
19524 CCTATGTTCC
*
19534 AAATAATTTCTTTTCTTGTATCCTCCCAGA
1 AAATAATTTATTTTCTTGTATCCTCCCAGA
19564 AAATAATTTATTTTCTTGTATCCTCCCAGA
1 AAATAATTTATTTTCTTGTATCCTCCCAGA
19594 CTCTCGTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (30 bp):
AAATAATTTATTTTCTTGTATCCTCCCAGA
Found at i:24109 original size:137 final size:137
Alignment explanation
Indices: 23863--24640 Score: 943
Period size: 137 Copynumber: 5.6 Consensus size: 137
23853 ACATGAAGGT
* * * * * *
23863 GCGTTCCCGAAGGCGTGCCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATATC
1 GCGTTCCCGAGGGCGCGCCTTCGATTATTATGTCAGAGAATATGTTATCATTGCCCTATTATGTC
*
23928 ACTCATGTCCCCAGGGAACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAGTGG
66 ACTCATGTCCCCCGGGAACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAGTGG
23993 TGAAAGC
131 TGAAAGC
* * * * * *
24000 GCGTTTCCGAGGGCGTGCCTTCTATTATTTTGTCAGAGAATAT-ATATCATTGCCATATTATGTC
1 GCGTTCCCGAGGGCGCGCCTTCGATTATTATGTCAGAGAATATGTTATCATTGCCCTATTATGTC
24064 ACTCATGTCCCCCGGTGAACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAGTG
66 ACTCATGTCCCCCGG-GAACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAGTG
*
24129 GTGAAAGT
130 GTGAAAGC
* * *
24137 GCGTTTCCGAGGGCGCGCCTTCGATTGTTATGTCAGAGAATATGTTATCATTGCTCTATTATGTC
1 GCGTTCCCGAGGGCGCGCCTTCGATTATTATGTCAGAGAATATGTTATCATTGCCCTATTATGTC
** *
24202 ACTCATGTCCCCTAAGGAACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGACAAAGTG
66 ACTCATGTCCCC-CGGGAACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAGTG
24267 GTGAAAGC
130 GTGAAAGC
* ** * * * * *
24275 GCGTTCCCGGGGGTACGCCTTC-ACGTGAATAGGTCAGAGACTATGTTATCATTGCCCCATTATG
1 GCGTTCCCGAGGGCGCGCCTTCGA--TTATTATGTCAGAGAATATGTTATCATTGCCCTATTATG
* * * **
24339 TCACTCATGTCCCTCGAAGAACTATTCATGTCAGTATCTATTATGTTTGAGGACACTTGGCAAAG
64 TCACTCATGTCCCCCG-GGAACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAG
24404 TGGTGAAAGC
128 TGGTGAAAGC
* * * * * * *
24414 GCGTTCCCGGGGGCGCACCTTCACGTGAATCACGTGAATAGGTCATAGAATATGATATTATTGCC
1 GCGTTCCCGAGGGCGCGCCTT--C--G-AT----T-ATTATGTCAGAGAATATGTTATCATTGCC
* * *
24479 CTATTATATCACTCATGTCCCCCAGCGAACTATTCATGTCAGTACCTATTAT-TTTTAGGGGACT
56 CTATTATGTCACTCATGTCCCCC-GGGAACTATTCATGTCAGTACCTATTATGTTTGAGGGGACT
*
24543 TGGCAAAGTGGTGAAACC
120 TGGCAAAGTGGTGAAAGC
* * * *
24561 GCGTT-TCAAGGGGCGCGCCTTCGATTGTTATGTCAGAGAATATGTTATCATTGGCCTATTATGT
1 GCGTTCCCGA-GGGCGCGCCTTCGATTATTATGTCAGAGAATATGTTATCATTGCCCTATTATGT
24625 CACTCATGTCCCCCGG
65 CACTCATGTCCCCCGG
24641 AGACACAGAG
Statistics
Matches: 553, Mismatches: 69, Indels: 39
0.84 0.10 0.06
Matches are distributed among these distances:
136 33 0.06
137 179 0.32
138 104 0.19
139 117 0.21
141 1 0.00
142 2 0.00
143 2 0.00
145 2 0.00
146 1 0.00
147 41 0.07
148 70 0.13
149 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (137 bp):
GCGTTCCCGAGGGCGCGCCTTCGATTATTATGTCAGAGAATATGTTATCATTGCCCTATTATGTC
ACTCATGTCCCCCGGGAACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAGTGG
TGAAAGC
Found at i:24622 original size:148 final size:147
Alignment explanation
Indices: 24295--24582 Score: 364
Period size: 148 Copynumber: 2.0 Consensus size: 147
24285 GGGTACGCCT
* * * * * * *
24295 TCACGTGAATAGGTCAGAGACTATGTTATCATTGCCCCATTATGTCACTCATGTCCCTCGAAGAA
1 TCACGAGAATAGGT-ATAGAATATGATATTATTGCCCCATTATATCACTCATGTCCCCCGAAGAA
* * **
24360 CTATTCATGTCAGTATCTATTATGTTTGAGGACACTTGGCAAAGTGGTGAAAGCGCGTTCCCGGG
65 CTATTCATGTCAGTACCTATTATGTTTGAGGACACTTGGCAAAGTGGTGAAACCGCGTTCCAAGG
24425 GGCGCACCTTCACGTGAA
130 GGCGCACCTTCACGTGAA
* * *
24443 TCACGTGAATAGGTCATAGAATATGATATTATTGCCCTATTATATCACTCATGTCCCCC-AGCGA
1 TCACGAGAATAGGT-ATAGAATATGATATTATTGCCCCATTATATCACTCATGTCCCCCGA-AGA
* ** *
24507 ACTATTCATGTCAGTACCTATTAT-TTTTAGGGGACTTGGCAAAGTGGTGAAACCGCGTTTCAAG
64 ACTATTCATGTCAGTACCTATTATGTTTGAGGACACTTGGCAAAGTGGTGAAACCGCGTTCCAAG
*
24571 GGGCGCGCCTTC
129 GGGCGCACCTTC
24583 GATTGTTATG
Statistics
Matches: 122, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
147 45 0.37
148 77 0.63
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (147 bp):
TCACGAGAATAGGTATAGAATATGATATTATTGCCCCATTATATCACTCATGTCCCCCGAAGAAC
TATTCATGTCAGTACCTATTATGTTTGAGGACACTTGGCAAAGTGGTGAAACCGCGTTCCAAGGG
GCGCACCTTCACGTGAA
Found at i:24756 original size:29 final size:29
Alignment explanation
Indices: 24720--24778 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
24710 AAGTTAAGGA
24720 TAAAATCATACATATGAATAAATTTAAGT
1 TAAAATCATACATATGAATAAATTTAAGT
*
24749 TAAAATCATACATATGGATAAATTTAAGT
1 TAAAATCATACATATGAATAAATTTAAGT
24778 T
1 T
24779 TGTAACTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (29 bp):
TAAAATCATACATATGAATAAATTTAAGT
Found at i:27281 original size:60 final size:61
Alignment explanation
Indices: 27184--27314 Score: 194
Period size: 60 Copynumber: 2.2 Consensus size: 61
27174 TTAATGGAAG
* * * * *
27184 GCGCGTCCTCGGGGATGCGCCTTACCCCCGTGTCATCCGACTCAGC-AAAACCC-CGTGAAA
1 GCGCGTCCCCGGGGATGCGCCTTACCCACGTGGCATCCAACTCAGCAAAAACCCAGGT-AAA
27244 GCGCGTCCCCGGGGATGCGCCTTACCCACGTGGCATCCAACTCAGCAAAAACCCAGGTAAA
1 GCGCGTCCCCGGGGATGCGCCTTACCCACGTGGCATCCAACTCAGCAAAAACCCAGGTAAA
27305 GCGCGTCCCC
1 GCGCGTCCCC
27315 AAGGATGCAC
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 42 0.66
61 20 0.31
62 2 0.03
ACGTcount: A:0.21, C:0.39, G:0.25, T:0.15
Consensus pattern (61 bp):
GCGCGTCCCCGGGGATGCGCCTTACCCACGTGGCATCCAACTCAGCAAAAACCCAGGTAAA
Found at i:33497 original size:20 final size:20
Alignment explanation
Indices: 33472--33514 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
33462 TCTAAGAGCC
33472 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* * *
33492 CATTTATGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
33512 CAT
1 CAT
33515 GTGTGGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:35074 original size:20 final size:22
Alignment explanation
Indices: 35049--35089 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35039 ATACTACCAT
35049 CATTTCA-TTT-CCACAACATA
1 CATTTCATTTTGCCACAACATA
35069 CATTTCATTTTGCCACAACAT
1 CATTTCATTTTGCCACAACAT
35090 TATCATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 9 0.47
ACGTcount: A:0.32, C:0.29, G:0.02, T:0.37
Consensus pattern (22 bp):
CATTTCATTTTGCCACAACATA
Found at i:40061 original size:44 final size:48
Alignment explanation
Indices: 39995--40091 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 48
39985 TTATTTTCGT
39995 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* *
40042 TTTTT-GAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
40087 TTTTT
1 TTTTT
40092 ATGGATAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
44 28 0.60
45 10 0.21
46 4 0.09
47 5 0.11
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:49760 original size:9 final size:8
Alignment explanation
Indices: 49746--49873 Score: 53
Period size: 8 Copynumber: 14.4 Consensus size: 8
49736 TTGCTTAAAG
49746 AAGAAATAA
1 AAGAAA-AA
49755 AAGAAAAA
1 AAGAAAAA
*
49763 AGGAGAAAA
1 AAGA-AAAA
49772 AAGAAAAA
1 AAGAAAAA
49780 TGATGATGGAAAAA
1 --A--A--GAAAAA
49794 ACGAGAAAAAA
1 A--AGA-AAAA
49805 AAGAAAAA
1 AAGAAAAA
49813 AA-AAAGAA
1 AAGAAA-AA
*
49821 GAGAAAAA
1 AAGAAAAA
* *
49829 ATGGAAAA
1 AAGAAAAA
*
49837 AA-ATAAA
1 AAGAAAAA
49844 AAGAGAAAA
1 AAGA-AAAA
*
49853 ATGAAAAA
1 AAGAAAAA
49861 AGAGAAATAA
1 A-AGAAA-AA
49871 AAG
1 AAG
49874 GAGGGTTCAA
Statistics
Matches: 92, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
7 8 0.09
8 32 0.35
9 31 0.34
10 6 0.07
11 5 0.05
12 4 0.04
14 6 0.07
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (8 bp):
AAGAAAAA
Found at i:49769 original size:19 final size:17
Alignment explanation
Indices: 49742--49867 Score: 62
Period size: 17 Copynumber: 7.0 Consensus size: 17
49732 TATTTTGCTT
49742 AAAGAAGAAATAAAAGAAA
1 AAAGAAG-AA-AAAAGAAA
*
49761 AAAGGAGAAAAAAGAAA
1 AAAGAAGAAAAAAGAAA
*
49778 AATGATGATGGAAAAAACGAGAA
1 AA--A-GA-AGAAAAAA-GA-AA
*
49801 AAAAAAGAAAAAA-AAA
1 AAAGAAGAAAAAAGAAA
*
49817 AGAAG-AGAAAAAATGGAA
1 A-AAGAAGAAAAAA-GAAA
*
49835 AAA-AATAAAAAGAGAAA
1 AAAGAAGAAAAA-AGAAA
* *
49852 AATGAA-AAAAGAGAAA
1 AAAGAAGAAAAAAGAAA
49868 TAAAAGGAGG
Statistics
Matches: 84, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
16 16 0.19
17 30 0.36
18 8 0.10
19 14 0.17
20 2 0.02
21 8 0.10
22 2 0.02
23 4 0.05
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.06
Consensus pattern (17 bp):
AAAGAAGAAAAAAGAAA
Found at i:49805 original size:11 final size:11
Alignment explanation
Indices: 49789--49839 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
49779 ATGATGATGG
*
49789 AAAAAACGAGA
1 AAAAAAAGAGA
*
49800 AAAAAAAGAAA
1 AAAAAAAGAGA
49811 AAAAAAAGAAGA
1 AAAAAAAG-AGA
*
49823 GAAAAAATG-GA
1 -AAAAAAAGAGA
49834 AAAAAA
1 AAAAAA
49840 TAAAAAGAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 6 0.18
11 19 0.56
12 2 0.06
13 7 0.21
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:49815 original size:23 final size:22
Alignment explanation
Indices: 49789--49861 Score: 65
Period size: 24 Copynumber: 3.1 Consensus size: 22
49779 ATGATGATGG
*
49789 AAAAAACGAGAAAAAAAAGAAA
1 AAAAAAAGAGAAAAAAAAGAAA
*
49811 AAAAAAAGAAGAGAAAAAATGGAAA
1 AAAAAAAG-AGA-AAAAAA-AGAAA
* * *
49836 AAAATAAAAAGAGAAAAATGAAA
1 AAAA-AAAGAGAAAAAAAAGAAA
49859 AAA
1 AAA
49862 GAGAAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
22 7 0.17
23 10 0.24
24 11 0.26
25 11 0.26
26 3 0.07
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.04
Consensus pattern (22 bp):
AAAAAAAGAGAAAAAAAAGAAA
Found at i:49817 original size:25 final size:24
Alignment explanation
Indices: 49789--49853 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
49779 ATGATGATGG
*
49789 AAAAAACGAGAAAAAAAAGAAAAA
1 AAAAAAAGAGAAAAAAAAGAAAAA
**
49813 AAAAAGAAGAGAAAAAATGGAAAAA
1 AAAAA-AAGAGAAAAAAAAGAAAAA
49838 AATAAAAAGAGAAAAA
1 AA-AAAAAGAGAAAAA
49854 TGAAAAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.14
25 28 0.78
26 3 0.08
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (24 bp):
AAAAAAAGAGAAAAAAAAGAAAAA
Found at i:49861 original size:25 final size:25
Alignment explanation
Indices: 49789--49861 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
49779 ATGATGATGG
*
49789 AAAAAACGAGAAAAA--AAAGAAAAA
1 AAAAAAAGAGAAAAATGAAA-AAAAA
*
49813 AAAAAGAAGAGAAAAAATG-GAAAAAA
1 AAAAA-AAGAG-AAAAATGAAAAAAAA
*
49839 ATAAAAAGAGAAAAATGAAAAAA
1 AAAAAAAGAGAAAAATGAAAAAA
49862 GAGAAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 12 0.30
25 13 0.32
26 14 0.35
27 1 0.03
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.04
Consensus pattern (25 bp):
AAAAAAAGAGAAAAATGAAAAAAAA
Found at i:49868 original size:14 final size:14
Alignment explanation
Indices: 49800--49872 Score: 53
Period size: 14 Copynumber: 5.3 Consensus size: 14
49790 AAAAACGAGA
*
49800 AAAAAAAGAAAAA-
1 AAAAAGAGAAAAAT
*
49813 AAAAAGAAGAGAAA-
1 AAAAAG-AGAAAAAT
** *
49827 AAATGGAAAAAAAT
1 AAAAAGAGAAAAAT
49841 AAAAAGAGAAAAAT
1 AAAAAGAGAAAAAT
*
49855 GAAAAA-AGAGAAAT
1 -AAAAAGAGAAAAAT
49869 AAAA
1 AAAA
49873 GGAGGGTTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
13 14 0.30
14 28 0.60
15 5 0.11
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (14 bp):
AAAAAGAGAAAAAT
Found at i:51065 original size:51 final size:51
Alignment explanation
Indices: 50998--51613 Score: 1124
Period size: 51 Copynumber: 12.0 Consensus size: 51
50988 TGAAGCAAAT
50998 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
*
51049 AAATTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
51100 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
51151 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
51202 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
51253 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
51304 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
51355 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
51406 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
* *
51457 AAGTTTGTTGAAGATTGAGTCCTATACTCTCTGAGTGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
51508 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
** * * *
51559 AAGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 AAGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
51614 CCGTTTTATT
Statistics
Matches: 550, Mismatches: 11, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
51 516 0.94
54 2 0.00
55 32 0.06
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (51 bp):
AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
Found at i:51648 original size:56 final size:56
Alignment explanation
Indices: 51014--51720 Score: 354
Period size: 51 Copynumber: 13.6 Consensus size: 56
51004 GTTGAAGATT
* * * ** **
51014 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA-AATTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * * **
51065 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * * **
51116 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * * **
51167 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * * **
51218 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * * **
51269 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * * **
51320 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * * **
51371 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * * *
51422 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTTGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * **
51473 GAGTCCTATACTCTCTG-AGTGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAG-GAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * * *
51524 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
*
51579 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
* * * * **
51635 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTA-TGAAGATTGCTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
*
51690 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC
51721 AGGCTCGTCA
Statistics
Matches: 621, Mismatches: 24, Indels: 18
0.94 0.04 0.03
Matches are distributed among these distances:
50 1 0.00
51 495 0.80
52 1 0.00
54 3 0.00
55 68 0.11
56 52 0.08
57 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (56 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTGAAGATTATTC
Found at i:51750 original size:55 final size:54
Alignment explanation
Indices: 51525--51750 Score: 183
Period size: 55 Copynumber: 4.1 Consensus size: 54
51515 TTGAAGATTG
* * * * * *
51525 AGTCCTATACTCTCTGAATGAATAGGGAGC-GGACAAGTTTATTGAAGATTTTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGG-CACGTTT-TTGAAGATTATTCA
*
51580 AGT-TCTATACTCTCTGAAGGAATAGAGAGC-GGACCCGTTTTATTGAAGATTATTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCAGG-CACG-TTT-TTGAAGATTATTCA
* * * ** *
51636 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGCTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTTT-TGAAGATTATTCA
* * *
51691 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATTTGAAGATGT-TTCA
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCAGGCACGT-TTTTGAAGAT-TATTCA
51746 AGTCT
1 AGTCT
51751 CATTTATCCT
Statistics
Matches: 141, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
54 2 0.01
55 89 0.63
56 48 0.34
57 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (54 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTTTTGAAGATTATTCA
Found at i:65873 original size:19 final size:19
Alignment explanation
Indices: 65842--65898 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
65832 ACACATCAGC
*
65842 TAACAGCTCCATCATTCAA
1 TAACAGCTTCATCATTCAA
*
65861 TAATAGCTTCATCATTCAA
1 TAACAGCTTCATCATTCAA
*
65880 TAACAACTTCATCATTCAA
1 TAACAGCTTCATCATTCAA
65899 CATTCTCCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.32
Consensus pattern (19 bp):
TAACAGCTTCATCATTCAA
Found at i:69536 original size:18 final size:18
Alignment explanation
Indices: 69495--69539 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
69485 TCCACAATTG
* *
69495 AAGAACAAGGGTCAATCC
1 AAGAAGAAGAGTCAATCC
69513 AAGAAGAAGAGTCAATCC
1 AAGAAGAAGAGTCAATCC
69531 AAGAAGAAG
1 AAGAAGAAG
69540 CACAAGGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.16, G:0.24, T:0.09
Consensus pattern (18 bp):
AAGAAGAAGAGTCAATCC
Found at i:70318 original size:17 final size:17
Alignment explanation
Indices: 70296--70329 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
70286 TATAATCGGA
*
70296 GACAAGAGCTGGTTCAT
1 GACAAGAGCCGGTTCAT
70313 GACAAGAGCCGGTTCAT
1 GACAAGAGCCGGTTCAT
70330 AGAGCTTAAC
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:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (17 bp):
GACAAGAGCCGGTTCAT
Found at i:74156 original size:13 final size:13
Alignment explanation
Indices: 74138--74176 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
74128 ATAATATGAT
74138 TTTTCAAATATTG
1 TTTTCAAATATTG
*
74151 TTTTCAAA-ATAG
1 TTTTCAAATATTG
*
74163 TTTTCAAATTTTG
1 TTTTCAAATATTG
74176 T
1 T
74177 CCATTAGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTTCAAATATTG
Found at i:80133 original size:19 final size:19
Alignment explanation
Indices: 80109--80146 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
80099 ATACATCAGC
80109 TAACAGCTCCATCATTCAA
1 TAACAGCTCCATCATTCAA
*
80128 TAACAGCTTCATCATTCAA
1 TAACAGCTCCATCATTCAA
80147 CACTAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (19 bp):
TAACAGCTCCATCATTCAA
Found at i:81515 original size:15 final size:15
Alignment explanation
Indices: 81495--81533 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
81485 ATTTCAGAAT
*
81495 ATATTAATTAATAAA
1 ATATTAAATAATAAA
*
81510 ATATTAAATAATAAC
1 ATATTAAATAATAAA
*
81525 ATATAAAAT
1 ATATTAAAT
81534 GAAATAGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATTAAATAATAAA
Found at i:81692 original size:23 final size:24
Alignment explanation
Indices: 81666--81710 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
81656 AATAGAAATG
* *
81666 AATGTT-TTTTCATATATAATAAA
1 AATGTTATTTTAATAGATAATAAA
81689 AATGTTATTTTAATAGATAATA
1 AATGTTATTTTAATAGATAATA
81711 TATTAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (24 bp):
AATGTTATTTTAATAGATAATAAA
Found at i:82995 original size:19 final size:19
Alignment explanation
Indices: 82971--83007 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
82961 CCACACGTAA
82971 TGACTCATCAAAATCAAAT
1 TGACTCATCAAAATCAAAT
82990 TGACTCATCAAAATCAAA
1 TGACTCATCAAAATCAAA
83008 GTTATCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.24
Consensus pattern (19 bp):
TGACTCATCAAAATCAAAT
Done.