Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003784.1 Hibiscus syriacus cultivar Beakdansim tig00008101_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: 76052
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:18861 original size:31 final size:31
Alignment explanation
Indices: 18825--18884 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
18815 AACTTAAAAG
* *
18825 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
18856 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
18885 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:19398 original size:20 final size:20
Alignment explanation
Indices: 19350--19411 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
19340 AACTTAAATC
*
19350 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
19370 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
19388 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
19407 AAAAT
1 AAAAT
19412 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:19495 original size:62 final size:63
Alignment explanation
Indices: 19406--19567 Score: 226
Period size: 67 Copynumber: 2.6 Consensus size: 63
19396 TTATATGATA
19406 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
19469 TAAAATTAATATCTATAATATAATATTAAAAAATTATTAATATTTAATTTATTTAAAAAATTGAT
1 TAAAATTAATATCTATAATATAATATT--AAAA--ATTAATATTTAATTTATTTAAAAAATTAAT
19534 AT
62 AT
*
19536 TAAAATTAAAATC-A-AATATAATA-T-AAAATTAA
1 TAAAATTAATATCTATAATATAATATTAAAAATTAA
19568 ATATAAAACC
Statistics
Matches: 92, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
59 5 0.05
61 3 0.03
62 20 0.22
63 7 0.08
64 5 0.05
65 9 0.10
66 20 0.22
67 23 0.25
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.42
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:19511 original size:31 final size:27
Alignment explanation
Indices: 19473--19530 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 27
19463 TAATATTAAA
19473 ATTAATATCTATAATATAATATTAAAAAATT
1 ATTAATAT-T-TAAT-TAAT-TTAAAAAATT
*
19504 ATTAATATTTAATTTATTTAAAAAATT
1 ATTAATATTTAATTAATTTAAAAAATT
19531 GATATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 3 0.12
29 4 0.15
30 1 0.04
31 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTAATATTTAATTAATTTAAAAAATT
Found at i:19539 original size:67 final size:64
Alignment explanation
Indices: 19401--19563 Score: 230
Period size: 62 Copynumber: 2.6 Consensus size: 64
19391 ATAATTTATA
19401 TGATA-TAAAATTAAATATCTATAATATAATATT--AAAAATTAATATTTAATTTATTTAAAAAT
1 TGATATTAAAATT-AATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTTAAAAAT
*
19463 TAATATTAAAATTAATATCTATAATATAATATTAAAAAATTATTAATATTTAATTTATTTAAAAA
1 TGATATTAAAATTAATATCTATAATATAATATTAAAAAA--ATTAATATTTAATTTATTT-AAAA
19528 AT
63 AT
*
19530 TGATATTAAAATTAAAATC-A-AATATAATA-TAAAA
1 TGATATTAAAATTAATATCTATAATATAATATTAAAA
19564 TTAAATATAA
Statistics
Matches: 92, Mismatches: 3, Indels: 10
0.88 0.03 0.10
Matches are distributed among these distances:
62 24 0.26
63 7 0.08
64 9 0.10
65 9 0.10
66 20 0.22
67 23 0.25
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (64 bp):
TGATATTAAAATTAATATCTATAATATAATATTAAAAAAATTAATATTTAATTTATTTAAAAAT
Found at i:29521 original size:113 final size:112
Alignment explanation
Indices: 28853--29514 Score: 960
Period size: 112 Copynumber: 5.9 Consensus size: 112
28843 AGAGTCATGC
28853 AAAGGTTGAACAAGTTCTTCTCATTATGAAC-TCTTC-TCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * * *
28915 ATGAACTCGAACTGGCAATGCTGATCCATCGAATGACGAATTCAAGCA
66 ATGAACTC-TTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAGCA
* * *
28963 AAATGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCAT-AT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC-TCAT
*
29027 TATGAACTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
65 TATGAACTCTTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAGCA
* *
29075 AAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
29140 ATGAACTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTCTTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAGCA
* *
29187 AAAGGTTGAACAAGTTCTTCTCATTATGAAGTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* **
29252 ATGAACTCTTCTGGAAAAGCTGATCCATC-AGATGATGGATTTGAGCA
66 ATGAACTCTTCTGGAAAAGCTGATCCATCGA-ATGATGAATTCAAGCA
* * *
29299 AAAGGTCGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * **
29364 ATGAACTTTTTATGGAAAAGCTGATCCATC-AGATGATGGATTTGAGCA
66 ATGAAC-TCTTCTGGAAAAGCTGATCCATCGA-ATGATGAATTCAAGCA
* *
29412 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
29477 ATGAACTTTTTCTGGAAAAGCTGATCCATC-ATATGATG
66 ATGAAC-TCTTCTGGAAAAGCTGATCCATCGA-ATGATG
29515 GATTTGAATC
Statistics
Matches: 522, Mismatches: 23, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
110 29 0.06
111 7 0.01
112 318 0.61
113 167 0.32
114 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (112 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAGCA
Found at i:32759 original size:114 final size:113
Alignment explanation
Indices: 32560--32783 Score: 376
Period size: 114 Copynumber: 2.0 Consensus size: 113
32550 ACGATCATGC
* * *
32560 AATTCATCCTTTAATTCCAATGATGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAG
1 AATTCATCCTTTAAATCCAATGATGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
32625 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
* * *
32673 AATTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATACCTCAAA
1 AATTCATCCTTTAAATCCAATGA-TGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
*
32738 GAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
65 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
32784 TCACCTGGAA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
113 21 0.20
114 82 0.80
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (113 bp):
AATTCATCCTTTAAATCCAATGATGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
Found at i:38371 original size:14 final size:15
Alignment explanation
Indices: 38337--38375 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
38327 CATAAAAATA
*
38337 CAAATGCAAAGATGC
1 CAAATGTAAAGATGC
*
38352 CAAATGTAAATATG-
1 CAAATGTAAAGATGC
38366 CAAATGTAAA
1 CAAATGTAAA
38376 CATGTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (15 bp):
CAAATGTAAAGATGC
Found at i:38384 original size:14 final size:14
Alignment explanation
Indices: 38337--38384 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
38327 CATAAAAATA
* *
38337 CAAATGCAAAGATG
1 CAAATGTAAACATG
*
38351 CCAAATGTAAATATG
1 -CAAATGTAAACATG
38366 CAAATGTAAACATG
1 CAAATGTAAACATG
*
38380 TAAAT
1 CAAAT
38385 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (14 bp):
CAAATGTAAACATG
Found at i:40453 original size:8 final size:7
Alignment explanation
Indices: 40432--40461 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
40422 TGTCTCTATT
40432 ATTAAAA
1 ATTAAAA
40439 ATTAAAA
1 ATTAAAA
40446 ATTAAAA
1 ATTAAAA
*
40453 ATTCAAA
1 ATTAAAA
40460 AT
1 AT
40462 ATATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (7 bp):
ATTAAAA
Found at i:42785 original size:28 final size:29
Alignment explanation
Indices: 42744--42819 Score: 136
Period size: 28 Copynumber: 2.7 Consensus size: 29
42734 CTTCCCAGCA
42744 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
*
42773 TAGGTTG-CATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
42801 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
42820 CCTGCTCCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 27 0.61
29 17 0.39
ACGTcount: A:0.14, C:0.33, G:0.26, T:0.26
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:42900 original size:14 final size:14
Alignment explanation
Indices: 42881--42912 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
42871 TCGAATGGCA
42881 TCGGTCGGATGCCC
1 TCGGTCGGATGCCC
*
42895 TCGGTCGGATGCCT
1 TCGGTCGGATGCCC
42909 TCGG
1 TCGG
42913 ATGCCCAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.31, G:0.38, T:0.25
Consensus pattern (14 bp):
TCGGTCGGATGCCC
Found at i:49980 original size:25 final size:26
Alignment explanation
Indices: 49924--49982 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
49914 TTTGGTTGGA
*
49924 TGGAATCCTTTGGAGTTGGGGGGAAT
1 TGGAATCCTTTGGAATTGGGGGGAAT
*
49950 TTGAATCCTTTGGAATT-GGGGGAAT
1 TGGAATCCTTTGGAATTGGGGGGAAT
49975 TGGAATCC
1 TGGAATCC
49983 AATTCTACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 15 0.50
26 15 0.50
ACGTcount: A:0.22, C:0.10, G:0.36, T:0.32
Consensus pattern (26 bp):
TGGAATCCTTTGGAATTGGGGGGAAT
Found at i:50480 original size:37 final size:37
Alignment explanation
Indices: 50435--50560 Score: 170
Period size: 37 Copynumber: 3.5 Consensus size: 37
50425 TTTATTTTGT
*
50435 TCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTTGGG
1 TCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTCGGG
* *
50472 TCGAGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTCGGG
* *
50509 TTGGGTCGGG-T---TTTTTTAAGTGTGATATTCGAG
1 TCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTCGGG
50542 TCGGGTCGGGTTCGGGTTT
1 TCGGGTCGGGTT-GGGTTT
50561 AGGGTAAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
33 30 0.39
34 1 0.01
37 42 0.55
38 3 0.04
ACGTcount: A:0.11, C:0.09, G:0.39, T:0.41
Consensus pattern (37 bp):
TCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTCGGG
Found at i:50529 original size:33 final size:32
Alignment explanation
Indices: 50434--50553 Score: 150
Period size: 33 Copynumber: 3.6 Consensus size: 32
50424 CTTTATTTTG
*
50434 TTCGGGTCGGGTTGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
*
50466 TTTGGGTCGAGTCGGGTCGGGTTTTTTAAGTGTGATA
1 --T---TCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
*
50503 TTCGGGTTGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGG-TTTTTTAAGTGTGATA
*
50536 TTCGAGTCGGGTCGGGTT
1 TTCGGGTCGGGTCGGGTT
50554 CGGGTTTAGG
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
32 15 0.20
33 30 0.39
34 1 0.01
35 1 0.01
37 29 0.38
ACGTcount: A:0.12, C:0.08, G:0.38, T:0.42
Consensus pattern (32 bp):
TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
Found at i:51151 original size:17 final size:18
Alignment explanation
Indices: 51129--51167 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
51119 TATGAAATTG
*
51129 GATTCTAATT-CTTGACA
1 GATTCTAATTCCTTCACA
51146 GATTCTAATTCCTTCACA
1 GATTCTAATTCCTTCACA
51164 GATT
1 GATT
51168 TCAATTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (18 bp):
GATTCTAATTCCTTCACA
Found at i:51384 original size:92 final size:91
Alignment explanation
Indices: 51228--51399 Score: 326
Period size: 92 Copynumber: 1.9 Consensus size: 91
51218 CTCCTCGCGC
*
51228 ACCCTCATAACGTGAGAAACAAAGAATGCGTAGTTCACACGCGTCCCCTGATGCGACTGCTTATA
1 ACCCTCATAACGTGAGAAACAAAGAATGCGTAGCTCACACGCGTCCCCTGATGCGACTGCTTATA
51293 TGATATAACACCTGGAATAAGCCGGT
66 TGATATAACACCTGGAATAAGCCGGT
51319 ACCCTCATAACGTGAGAAACAAAAGAATGCGTAGCTCACACGCGTCCCCTGATGCGACTGCTTAT
1 ACCCTCATAACGTGAGAAAC-AAAGAATGCGTAGCTCACACGCGTCCCCTGATGCGACTGCTTAT
51384 ATGATATAACACCTGG
65 ATGATATAACACCTGG
51400 TATGTCCAAA
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
91 20 0.25
92 59 0.75
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (91 bp):
ACCCTCATAACGTGAGAAACAAAGAATGCGTAGCTCACACGCGTCCCCTGATGCGACTGCTTATA
TGATATAACACCTGGAATAAGCCGGT
Found at i:59320 original size:42 final size:42
Alignment explanation
Indices: 59273--59354 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
59263 AAATAGACTT
* *
59273 ATTGTGCGCAT-TACTATCGAGAGCAGCACAACCCTCCAACAC
1 ATTGTGCGCATGAACT-TCGAGAGCAGCACAACACTCCAACAC
* * *
59315 ATTGTGTGCATGAACTTCGATAGCAGCAGAACACTCCAAC
1 ATTGTGCGCATGAACTTCGAGAGCAGCACAACACTCCAAC
59355 TCGGGAACCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (42 bp):
ATTGTGCGCATGAACTTCGAGAGCAGCACAACACTCCAACAC
Found at i:59724 original size:10 final size:10
Alignment explanation
Indices: 59709--59742 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
59699 TTTGAATTTA
59709 AAAAAATCAG
1 AAAAAATCAG
*
59719 AAAAAAT-AC
1 AAAAAATCAG
59728 AAAAAATCAG
1 AAAAAATCAG
59738 AAAAA
1 AAAAA
59743 TTACAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (10 bp):
AAAAAATCAG
Found at i:59733 original size:19 final size:19
Alignment explanation
Indices: 59709--59752 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
59699 TTTGAATTTA
59709 AAAAAATCAGAAAAAATAC
1 AAAAAATCAGAAAAAATAC
*
59728 AAAAAATCAGAAAAATTAC
1 AAAAAATCAGAAAAAATAC
59747 AAAAAA
1 AAAAAA
59753 AATTAGTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.75, C:0.09, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAAAATCAGAAAAAATAC
Found at i:59913 original size:104 final size:104
Alignment explanation
Indices: 59719--59932 Score: 342
Period size: 104 Copynumber: 2.1 Consensus size: 104
59709 AAAAAATCAG
*
59719 AAAAAATACAAAAAATCAGAAAAATTACAAAAAAAATTAGTATGTTTATTTATCTAATTTCAATG
1 AAAAAATACAAAAAATCAGAAAAATTACAAAAAAAATTAGTATGTTTATATATCTAATTTCAATG
* *
59784 TATTTTTATCTATCTTGCAAATTAATCT-ATTTGAATTTT
66 TATTTTTATCTATATTACAAATTAATCTAATTT-AATTTT
59823 AAAAAATCACAAAAAATCAGAAAAATTACAAAAAAAA-TAGTATGTTTATATATCTAATTTCAAT
1 AAAAAAT-ACAAAAAATCAGAAAAATTACAAAAAAAATTAGTATGTTTATATATCTAATTTCAAT
* * *
59887 GTATTTTTATTTATATTATAATTTAATCTAATTTAATTTT
65 GTATTTTTATCTATATTACAAATTAATCTAATTTAATTTT
59927 AAAAAA
1 AAAAAA
59933 AAGGAAATGT
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
104 69 0.68
105 33 0.32
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (104 bp):
AAAAAATACAAAAAATCAGAAAAATTACAAAAAAAATTAGTATGTTTATATATCTAATTTCAATG
TATTTTTATCTATATTACAAATTAATCTAATTTAATTTT
Found at i:63789 original size:14 final size:14
Alignment explanation
Indices: 63770--63796 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
63760 AGAGTACTAG
63770 TAAAAAAATATAAT
1 TAAAAAAATATAAT
63784 TAAAAAAATATAA
1 TAAAAAAATATAA
63797 AAAAATAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAAAAATATAAT
Found at i:63949 original size:20 final size:20
Alignment explanation
Indices: 63926--63977 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
63916 CTCAGTTTCC
* *
63926 AAAATCGCAGCGTAAATAGT
1 AAAATCGCAACGCAAATAGT
* *
63946 AAAATCGTAACGCGAATAGT
1 AAAATCGCAACGCAAATAGT
*
63966 AAAATCGTAACG
1 AAAATCGCAACG
63978 TGATCGCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCAAATAGT
Found at i:64423 original size:40 final size:39
Alignment explanation
Indices: 64379--64467 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 39
64369 ACTATTCACA
* *
64379 TTGCGATTTTACTATTCACGTTACGAATTTGACTTTTGTG
1 TTGCGATTTGACT-TTCACGTTACGAATTTGACTTCTGTG
*** *
64419 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTG
1 TTGCG-ATTTGACTTTCACGTTACGAATTTGACTTCTGTG
64459 TTGCGATTT
1 TTGCGATTT
64468 ACAAATTCGA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 4 0.10
40 31 0.74
41 7 0.17
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.48
Consensus pattern (39 bp):
TTGCGATTTGACTTTCACGTTACGAATTTGACTTCTGTG
Found at i:64427 original size:20 final size:20
Alignment explanation
Indices: 64402--64464 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
64392 ATTCACGTTA
64402 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
64422 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTTTGTGTTG
*
64442 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTTTGTGTTG
64462 CGA
1 CGA
64465 TTTACAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.16, C:0.13, G:0.25, T:0.46
Consensus pattern (20 bp):
CGAATTTGACTTTTGTGTTG
Found at i:64502 original size:20 final size:20
Alignment explanation
Indices: 64458--64504 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
64448 TGACTTCTGT
64458 GTTGCGATTTACAAATTCGA
1 GTTGCGATTTACAAATTCGA
* *
64478 ATTGCGATTTACAGATTC-A
1 GTTGCGATTTACAAATTCGA
64497 CGTTGCGA
1 -GTTGCGA
64505 ATTTGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGA
Found at i:67383 original size:36 final size:37
Alignment explanation
Indices: 67336--67410 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
67326 AAGCACGAAT
67336 CATTTTCGCCCA-ATTGGAACACGAATCACATTCAGC
1 CATTTTCGCCCACATTGGAACACGAATCACATTCAGC
67372 CATTTTCGCCCACATTGGAACACGAATCACATTCAGC
1 CATTTTCGCCCACATTGGAACACGAATCACATTCAGC
67409 CA
1 CA
67411 CGTGCACTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 12 0.32
37 26 0.68
ACGTcount: A:0.31, C:0.32, G:0.13, T:0.24
Consensus pattern (37 bp):
CATTTTCGCCCACATTGGAACACGAATCACATTCAGC
Found at i:70338 original size:22 final size:22
Alignment explanation
Indices: 70305--70355 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
70295 ATAAATGCAC
*
70305 AAGTGCCACGTAGAATTGCACCG
1 AAGTG-CACGTAGAATTGAACCG
70328 AAGTGCACGTAGAATTGAACCG
1 AAGTGCACGTAGAATTGAACCG
70350 AAGTGC
1 AAGTGC
70356 CATATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (22 bp):
AAGTGCACGTAGAATTGAACCG
Found at i:74708 original size:22 final size:23
Alignment explanation
Indices: 74662--74717 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
74652 CTCGTATAAA
* *
74662 TGCACCTAAGTGCCACGTAGAAT
1 TGCACCGAAGTACCACGTAGAAT
*
74685 TGCACCGAAGTACCGCG-AGAAT
1 TGCACCGAAGTACCACGTAGAAT
74707 TGCACCGAAGT
1 TGCACCGAAGT
74718 GCCATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTACCACGTAGAAT
Done.