Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003238.1 Hibiscus syriacus cultivar Beakdansim tig00006810_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: 120169
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2708 original size:42 final size:41
Alignment explanation
Indices: 2646--2734 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 41
2636 AATTGGTAAG
* * * *
2646 TCCTTCAGTCTATCATTAAGTCTTTCGAGTATGATGATTAAA
1 TCCTTCAGTCTATCATTAAGTATTTCGAGCAAGAAGA-TAAA
2688 TCCTTCAGGTC-ATC-TGTAAGTATTTCGAGCAAGAAGATAAA
1 TCCTTCA-GTCTATCAT-TAAGTATTTCGAGCAAGAAGATAAA
2729 TCCTTC
1 TCCTTC
2735 GGGCCATCCG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 11 0.27
42 27 0.66
43 3 0.07
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (41 bp):
TCCTTCAGTCTATCATTAAGTATTTCGAGCAAGAAGATAAA
Found at i:10383 original size:26 final size:26
Alignment explanation
Indices: 10344--10397 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
10334 CTAAAGTGCA
*
10344 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGAACGACCTTATGTGTAT
10370 TATGGTGGGAACGACCTTATGTGTAT
1 TATGGTGGGAACGACCTTATGTGTAT
10396 TA
1 TA
10398 GCACTTCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (26 bp):
TATGGTGGGAACGACCTTATGTGTAT
Found at i:11063 original size:21 final size:20
Alignment explanation
Indices: 11015--11063 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
11005 ATATTTATCT
*
11015 CAAGGCTTTGGTATGGATAA
1 CAAGCCTTTGGTATGGATAA
* * *
11035 GAAACCTTTCGGTATGGATAC
1 CAAGCCTTT-GGTATGGATAA
11056 CAAGCCTT
1 CAAGCCTT
11064 CGTTACAGAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (20 bp):
CAAGCCTTTGGTATGGATAA
Found at i:16377 original size:28 final size:27
Alignment explanation
Indices: 16342--16394 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
16332 AGTTTCTTAC
*
16342 CCACTAAGGATATTTTGGTAATTTATA
1 CCACTAAGGATATTCTGGTAATTTATA
* *
16369 CCACTTAAGGGTATTCTGGTTATTTA
1 CCAC-TAAGGATATTCTGGTAATTTA
16395 CCAATCTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (27 bp):
CCACTAAGGATATTCTGGTAATTTATA
Found at i:16669 original size:70 final size:69
Alignment explanation
Indices: 16591--16741 Score: 232
Period size: 70 Copynumber: 2.2 Consensus size: 69
16581 TGTTGTTACG
* *
16591 TAGAAAACCTTTTGTTTACTCAAAATATGAATAGTATCGACACTACATGAA-CAATATCGATACT
1 TAGAAAACCCTTT-TTTACTCAAAATATAAATAGTATCGACACTACAT-AAGCAATATCGATACT
16655 ACAACC
64 ACAACC
* *
16661 TAGAAAACCCCTTTTTTACTCAAAATATAAATAGTATCGATACTACATAAGTAATATCGATACTA
1 TAGAAAA-CCCTTTTTTACTCAAAATATAAATAGTATCGACACTACATAAGCAATATCGATACTA
16726 CAACC
65 CAACC
16731 TAGAAAACCCT
1 TAGAAAACCCT
16742 AAACTGGGCT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
69 6 0.08
70 64 0.85
71 5 0.07
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (69 bp):
TAGAAAACCCTTTTTTACTCAAAATATAAATAGTATCGACACTACATAAGCAATATCGATACTAC
AACC
Found at i:29734 original size:45 final size:45
Alignment explanation
Indices: 29643--29805 Score: 267
Period size: 45 Copynumber: 3.6 Consensus size: 45
29633 TATTTATCCT
*
29643 ATAAGCTCATAAGATTATTTTACCAATATATACTTACCATTTGTTCC
1 ATAAGCTCATAAGCTTATTTTACC-A-ATATACTTACCATTTGTTCC
29690 ATAAGCT-AGTAAGCTTATTTTACCAATATACTTACCATTTGTTCC
1 ATAAGCTCA-TAAGCTTATTTTACCAATATACTTACCATTTGTTCC
*
29735 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTGTTCC
1 ATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTGTTCC
29780 ATAAGCTCATAAGCTTATTTT-CCAAT
1 ATAAGCTCATAAGCTTATTTTACCAAT
29806 TTATCATTTA
Statistics
Matches: 111, Mismatches: 3, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
44 5 0.05
45 83 0.75
46 2 0.02
47 21 0.19
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (45 bp):
ATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTGTTCC
Found at i:43155 original size:36 final size:35
Alignment explanation
Indices: 43115--43184 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
43105 ATAACTTGTT
43115 CCTAAATAAAATAA-TAATAA-AATAATCAACCAAAAA
1 CCTAAATAAAA-AAGTAATAATAA-AAT-AACCAAAAA
43151 CCTAAATAAAAAAGTAATAATAAAATAACCAAAA
1 CCTAAATAAAAAAGTAATAATAAAATAACCAAAA
43185 TAAAAATCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
35 10 0.31
36 20 0.62
37 2 0.06
ACGTcount: A:0.67, C:0.13, G:0.01, T:0.19
Consensus pattern (35 bp):
CCTAAATAAAAAAGTAATAATAAAATAACCAAAAA
Found at i:53362 original size:20 final size:20
Alignment explanation
Indices: 53337--53385 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
53327 AATTAATGAG
53337 TTTCAAAACTTT-G-TTCGAGT
1 TTTCAAAACTTTAGATT-GA-T
53357 TTTC-AAACTTTAGATTGAT
1 TTTCAAAACTTTAGATTGAT
53376 TTTCAAAACT
1 TTTCAAAACT
53386 ATATGTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 12 0.46
20 12 0.46
21 2 0.08
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTCAAAACTTTAGATTGAT
Found at i:53475 original size:50 final size:50
Alignment explanation
Indices: 53419--53524 Score: 203
Period size: 50 Copynumber: 2.1 Consensus size: 50
53409 TTGCAAGTTT
53419 TGATATTTTGAAACAATTCTAACTTTGAGAAATATTATAAATTATATGAA
1 TGATATTTTGAAACAATTCTAACTTTGAGAAATATTATAAATTATATGAA
*
53469 TTATATTTTGAAACAATTCTAACTTTGAGAAATATTATAAATTATATGAA
1 TGATATTTTGAAACAATTCTAACTTTGAGAAATATTATAAATTATATGAA
53519 TGATAT
1 TGATAT
53525 AATTTTTACT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (50 bp):
TGATATTTTGAAACAATTCTAACTTTGAGAAATATTATAAATTATATGAA
Found at i:62389 original size:21 final size:21
Alignment explanation
Indices: 62356--62478 Score: 122
Period size: 21 Copynumber: 5.7 Consensus size: 21
62346 TTTTCGTAAG
*
62356 AGTAATTTGTGTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
* *
62377 AGTACTTTATGTATTATGGCAAG-
1 AGTACTTTGTGTACT-TGG--AGT
*
62400 AGTACTTTGTGTACTTGGCGT
1 AGTACTTTGTGTACTTGGAGT
* *
62421 AGTACTTTGTGTATTATGGCAAT
1 AGTACTTTGTGTACT-TGG-AGT
* *
62444 AGTACTTTATGTACTTGTAGT
1 AGTACTTTGTGTACTTGGAGT
62465 AGTACTTTGTGTAC
1 AGTACTTTGTGTAC
62479 AATGGCACTT
Statistics
Matches: 82, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.01
21 41 0.50
22 11 0.13
23 27 0.33
24 2 0.02
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.43
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:62403 original size:23 final size:23
Alignment explanation
Indices: 62377--62456 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
62367 TACTTGGAGT
62377 AGTACTTTATGTATTATGGCAAG
1 AGTACTTTATGTATTATGGCAAG
* *
62400 AGTACTTTGTGTACT-TGGC--G
1 AGTACTTTATGTATTATGGCAAG
* *
62420 TAGTACTTTGTGTATTATGGCAAT
1 -AGTACTTTATGTATTATGGCAAG
62444 AGTACTTTATGTA
1 AGTACTTTATGTA
62457 CTTGTAGTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.02
21 14 0.29
22 8 0.17
23 25 0.52
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (23 bp):
AGTACTTTATGTATTATGGCAAG
Found at i:62485 original size:44 final size:44
Alignment explanation
Indices: 62353--62477 Score: 196
Period size: 44 Copynumber: 2.8 Consensus size: 44
62343 GGATTTTCGT
* *
62353 AAGAGTAATTTGTGTACTTGGAGTAGTACTTTATGTATTATGGC
1 AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTATTATGGC
*
62397 AAGAGTACTTTGTGTACTTGGCGTAGTACTTTGTGTATTATGGC
1 AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTATTATGGC
* * *
62441 AATAGTACTTTATGTACTTGTAGTAGTACTTTGTGTA
1 AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTA
62478 CAATGGCACT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (44 bp):
AAGAGTACTTTGTGTACTTGGAGTAGTACTTTGTGTATTATGGC
Found at i:64364 original size:17 final size:16
Alignment explanation
Indices: 64308--64387 Score: 51
Period size: 17 Copynumber: 5.0 Consensus size: 16
64298 GATAAGAGCA
* *
64308 AATAAACTAAAAACAT
1 AATAAAATAAAAAAAT
*
64324 AATGAAAATAAATAAAT
1 AAT-AAAATAAAAAAAT
*
64341 AGT---ATAAATAAAAT
1 AATAAAATAAA-AAAAT
64355 AATAAAAT-AAAAAAT
1 AATAAAATAAAAAAAT
*
64370 ATATAAAAATATAAAAAT
1 A-AT-AAAATAAAAAAAT
64388 GTATGTATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
13 5 0.10
14 6 0.12
15 6 0.12
16 7 0.14
17 19 0.39
18 6 0.12
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
AATAAAATAAAAAAAT
Found at i:64366 original size:13 final size:14
Alignment explanation
Indices: 64331--64372 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
64321 CATAATGAAA
*
64331 ATAAAT-AAATAGT
1 ATAAATAAAATAAT
64344 ATAAATAAAATAAT
1 ATAAATAAAATAAT
64358 A-AAATAAAA-AAT
1 ATAAATAAAATAAT
64370 ATA
1 ATA
64373 TAAAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 4 0.15
13 15 0.58
14 7 0.27
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (14 bp):
ATAAATAAAATAAT
Found at i:64594 original size:2 final size:2
Alignment explanation
Indices: 64584--64615 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
64574 AAAAATAACA
64584 AT AT A- 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 AT AT AT A
64616 ATAGGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:64691 original size:10 final size:10
Alignment explanation
Indices: 64657--64706 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
64647 AAATGAAAAA
64657 AAAATATAAT
1 AAAATATAAT
*
64667 AAATAAATAAAT
1 AAA-ATAT-AAT
64679 AAAATATAAT
1 AAAATATAAT
64689 AAAATATAAT
1 AAAATATAAT
*
64699 AATATATA
1 AAAATATA
64707 TATATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 23 0.66
11 6 0.17
12 6 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAATATAAT
Found at i:65160 original size:37 final size:37
Alignment explanation
Indices: 65119--65211 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
65109 ATGCTTGTGG
* * *
65119 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
65156 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
65193 ATCCTATTTTTAGGGGTTT
1 ATCCTATTTTTAGGAGTTT
65212 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:66166 original size:106 final size:106
Alignment explanation
Indices: 65972--66530 Score: 655
Period size: 106 Copynumber: 5.3 Consensus size: 106
65962 AGCATTGTTC
* ** * * * *
65972 CGAGTCCAATATCCTCCATTATGAAGTTGAAATTTGCTCTGGAACTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* *
66037 ACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
66078 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* *
66143 ACCAGCCGTCCCTTTGTTATGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
66184 CGAGTCCAATATCCTTCGTTTTGAAGTTAAAATTGCCTCTGAAAATGGGAAGTTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* * *
66249 ACCAGCCGTCCCTTCATTTGTGAAGTTG-ATTTGTGATGTCT
66 ACCAGCCGTCCCTTC-GTTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
66290 CGAGTCTAATATCATTCACTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
* * * *
66349 ATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
66390 TGGGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGATA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
** * * *
66455 GTCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
66496 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
66531 ACTGAATGAA
Statistics
Matches: 381, Mismatches: 64, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
99 10 0.03
100 66 0.17
101 3 0.01
102 4 0.01
104 4 0.01
105 3 0.01
106 281 0.74
107 10 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:66441 original size:206 final size:206
Alignment explanation
Indices: 65972--66544 Score: 688
Period size: 206 Copynumber: 2.8 Consensus size: 206
65962 AGCATTGTTC
* * * * *
65972 CGAGTCCAATATCC-TC-CATTATGAAGTTGAAATTTGCTCTGGAACTGGGAAATTATTTGTTGA
1 CGAGTCCAATATCCTTCGC-TGA-GAAGTTGAAATTGGCTCTGAAAATGGGAAGTTATTTGTTGA
* * * *
66035 CAACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAATATCCTTCGCTGT
64 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGATGTCTCGAGTCTAATATCCTTCGCTGT
* * * * * *
66100 GAAGTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAACCAGCCGTCCCTTTGTTATGA
129 GAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTATTGACAACCAGCCGCCCCTTCGTCATGA
66165 AGTTGAACTTGTGTTGTCT
188 AGTTGAACTTGTGTTGTCT
* ** * *
66184 CGAGTCCAATATCCTTCGTTTTGAAGTTAAAATTGCCTCTGAAAATGGGAAGTTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAAATGGGAAGTTATTTGTTGACA
* * * *
66249 ACCAGCCGTCCCTTCATTTGTGAAGTTG-ATTTGTGATGTCTCGAGTCTAATATCATTCACTGTG
66 ACCAGCCGTCCCTTC-GTTGTGAAGTTGAACTTGTGATGTCTCGAGTCTAATATCCTTCGCTGTG
* * *
66313 AAGTTGAAATTGACTCTGAATGAAATTTTATTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAG
130 AAGTTGAAATTGACTCTGAATGAAATTTTATTGACAACCAGCCGCCCCTTCGTCATGAAGTTGAA
66378 CTTGTGTTGTCT
195 CTTGTGTTGTCT
* * * * *
66390 TGGGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGATA
1 CGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAAATGGGAAGTTATTTGTTGACA
** * * * *
66455 GTCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCTAATATCCTTCGTTGTGA
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGATGTCTCGAGTCTAATATCCTTCGCTGTGA
66520 AGTTGAAATTGA--CTGAATGAAATTT
131 AGTTGAAATTGACTCTGAATGAAATTT
66545 GAAAAAGTTA
Statistics
Matches: 312, Mismatches: 45, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
204 13 0.04
205 10 0.03
206 155 0.50
207 1 0.00
208 4 0.01
210 1 0.00
211 2 0.01
212 111 0.36
213 15 0.05
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (206 bp):
CGAGTCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAAATGGGAAGTTATTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGATGTCTCGAGTCTAATATCCTTCGCTGTGA
AGTTGAAATTGACTCTGAATGAAATTTTATTGACAACCAGCCGCCCCTTCGTCATGAAGTTGAAC
TTGTGTTGTCT
Found at i:66963 original size:37 final size:37
Alignment explanation
Indices: 66890--66969 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
66880 ATGAGAAACG
* * **
66890 GTCTCAAGGGAGACAAAATTTTGTTTTAAAAAAAATT
1 GTCTCAAGAGAGACAAAATTTAGTTCCAAAAAAAATT
* *
66927 GTCTCAAGAGAGACAAAATTTAGTTCCATAAGAAATT
1 GTCTCAAGAGAGACAAAATTTAGTTCCAAAAAAAATT
66964 GTCTCA
1 GTCTCA
66970 CGGGGAGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (37 bp):
GTCTCAAGAGAGACAAAATTTAGTTCCAAAAAAAATT
Found at i:67878 original size:24 final size:24
Alignment explanation
Indices: 67851--67911 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
67841 ATATCAAAAA
67851 AAGAGTTTTGAAAGATGTTTAATC
1 AAGAGTTTTGAAAGATGTTTAATC
*
67875 AAGAGTTTTGAAAGATGTTTAATT
1 AAGAGTTTTGAAAGATGTTTAATC
*
67899 AAAAGTTTTGAAA
1 AAGAGTTTTGAAA
67912 ATATTGTCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.38
Consensus pattern (24 bp):
AAGAGTTTTGAAAGATGTTTAATC
Found at i:73481 original size:22 final size:22
Alignment explanation
Indices: 73462--73505 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
73452 AAACATAATG
*
73462 AAAATAAATAAATAGTATAAAT
1 AAAATAAAAAAATAGTATAAAT
*
73484 AAAATAAAAAAATA-TAAAAAT
1 AAAATAAAAAAATAGTATAAAT
73505 A
1 A
73506 TAAAAATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAATAAAAAAATAGTATAAAT
Found at i:73755 original size:21 final size:21
Alignment explanation
Indices: 73714--73762 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
73704 TAGATAAAAA
* *
73714 ATAATAATATAATATATATAT
1 ATAATAATAGAAAATATATAT
73735 ATAATAATAGGAAAATAATATAAT
1 ATAATAATA-GAAAAT-ATAT-AT
73759 ATAA
1 ATAA
73763 CGCAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
23 4 0.17
24 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAATAATAGAAAATATATAT
Found at i:74275 original size:37 final size:37
Alignment explanation
Indices: 74234--74326 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
74224 ATGCTTGTGG
** * *
74234 ATCCTATCGTTAGGAGTTTAAATAATAGTATAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
74271 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
74308 ATCCTATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
74327 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:74950 original size:18 final size:19
Alignment explanation
Indices: 74917--74957 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
74907 CTAATGTAAT
*
74917 TATTATTTACAATATGCCAC
1 TATTATTTA-AATATGCAAC
74937 TATTATTT-AATATGCAAC
1 TATTATTTAAATATGCAAC
74955 TAT
1 TAT
74958 ATGATATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (19 bp):
TATTATTTAAATATGCAAC
Found at i:76724 original size:18 final size:19
Alignment explanation
Indices: 76678--76725 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
76668 TAATATACTA
*
76678 ATGAAATTATTATTTACAAT
1 ATGAAACTATTATTTA-AAT
**
76698 ATGCCACTATTATTT-AAT
1 ATGAAACTATTATTTAAAT
76716 ATGAAACTAT
1 ATGAAACTAT
76726 ATGATATGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 11 0.48
20 12 0.52
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (19 bp):
ATGAAACTATTATTTAAAT
Found at i:78890 original size:13 final size:12
Alignment explanation
Indices: 78867--78911 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
78857 TTCCATTTTC
*
78867 TTTTATTTTTAT
1 TTTTTTTTTTAT
78879 TTTCTTTTTTTAT
1 TTT-TTTTTTTAT
* *
78892 TTTTTCTCTTAT
1 TTTTTTTTTTAT
78904 TTTTTTTT
1 TTTTTTTT
78912 CGTTTCTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:78928 original size:21 final size:21
Alignment explanation
Indices: 78879--78928 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
78869 TTATTTTTAT
**
78879 TTTCTTTTTTTATTTTTTCTC
1 TTTCTTTTTTTATCGTTTCTC
78900 TTAT-TTTTTTT-TCGTTTCTTC
1 TT-TCTTTTTTTATCGTTTC-TC
78921 TTTCTTTT
1 TTTCTTTT
78929 CTTCTTCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 6 0.25
21 17 0.71
22 1 0.04
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTCTTTTTTTATCGTTTCTC
Found at i:84309 original size:344 final size:345
Alignment explanation
Indices: 83358--84397 Score: 2073
Period size: 345 Copynumber: 3.0 Consensus size: 345
83348 CATTACAATG
83358 GGTGGTGATATTCAAGGGCTTTACAAAACTCCTGTCCCTTCTAGGATCACGTCATCGGTGAAGCT
1 GGTGGTGATATTCAAGGGCTTTACAAAACTCCTGTCCCTTCTAGGATCACGTCATCGGTGAAGCT
83423 AATATAATTATCTGTAGATATATGCTTCACTATTCGGTCTAGCTTATTCACATATATGTCTTCCA
66 AATATAATTATCTGTAGATATATGCTTCACTATTCGGTCTAGCTTATTCACATATATGTCTTCCA
83488 GTATGAAAGTTTGATTCATCATCTTTAATAAAGTATTTCAGTGCACCTCATAGTTCATAAACATA
131 GTATGAAAGTTTGATTCATCATCTTTAATAAAGTATTTCAGTGCACCTCATAGTTCATAAACATA
83553 TCTAATATCAAGATTCATTCTTGCTACCTATGCAGTTGCTTCACCACACTATATTCATTATGTTC
196 TCTAATATCAAGATTCATTCTTGCTACCTATGCAGTTGCTTCACCACACTATATTCATTATGTTC
83618 CAGAAATTTCAAGAACTTTTGGGATTGAGCTTCAGTAATAGGCTCATTAACTCTTAGTGGGGGCT
261 CAGAAATTTCAAGAACTTTTGGGATTGAGCTTCAGTAATAGGCTCATTAACTCTTAGTGGGGGCT
83683 CATTCTCAAATATCATTTGA
326 CATTCTCAAATATCATTTGA
83703 GGTGGTGATATTCAAGGGCTTTACAAAACTCCTGTCCCTTCTAGGATCACGTCATCGGTGAAGCT
1 GGTGGTGATATTCAAGGGCTTTACAAAACTCCTGTCCCTTCTAGGATCACGTCATCGGTGAAGCT
83768 AATATAATTATCTGTAGATATATGCTTCACTATTCGGTCTAGCTTATTCACATATATGTCTTCCA
66 AATATAATTATCTGTAGATATATGCTTCACTATTCGGTCTAGCTTATTCACATATATGTCTTCCA
83833 GTATGAAAGTTTGATTCATCATCTTTAATAAAGTATTTCAGTGCACCTCATAGTTCATAAACATA
131 GTATGAAAGTTTGATTCATCATCTTTAATAAAGTATTTCAGTGCACCTCATAGTTCATAAACATA
83898 TCTAATATCAAGATTCATTCTTGCTACCTATGCAGTTGCTTCACCACACTATATTCATTATGTTC
196 TCTAATATCAAGATTCATTCTTGCTACCTATGCAGTTGCTTCACCACACTATATTCATTATGTTC
83963 CAGAAATTTCAAGAACTTTTGGGATTGAGCTTCAGTAATAGGCTCATTAACTCTTAGTGGGGG-T
261 CAGAAATTTCAAGAACTTTTGGGATTGAGCTTCAGTAATAGGCTCATTAACTCTTAGTGGGGGCT
84027 CATTCTCAAATATCATTTGA
326 CATTCTCAAATATCATTTGA
84047 GGTGGTGATATTCAAGGGCTTTACAAAACTCCTGTCCCTTCTAGGATCACGTCATCGGTGAAGCT
1 GGTGGTGATATTCAAGGGCTTTACAAAACTCCTGTCCCTTCTAGGATCACGTCATCGGTGAAGCT
84112 AATATAATTATCTGTAGATATATGCTTCACTATTCGGTCTAGCTTATTCACATATATGTCTTCCA
66 AATATAATTATCTGTAGATATATGCTTCACTATTCGGTCTAGCTTATTCACATATATGTCTTCCA
84177 GTATGAAAGTTTGATTCATCATCTTTAATAAAGTATTTCAGTGCACCTCATAGTTCATAAACATA
131 GTATGAAAGTTTGATTCATCATCTTTAATAAAGTATTTCAGTGCACCTCATAGTTCATAAACATA
84242 TCTAATATCAAGATTCATTCTTGCTACCTATGCAGTTGCTTCACCACACTATATTCATTATGTTC
196 TCTAATATCAAGATTCATTCTTGCTACCTATGCAGTTGCTTCACCACACTATATTCATTATGTTC
84307 CAGAAATTTCAAGAACTTTTGGGATTGAGCTTCAGTAATAGGCTCATTAACTCTTAGTGGGGGCT
261 CAGAAATTTCAAGAACTTTTGGGATTGAGCTTCAGTAATAGGCTCATTAACTCTTAGTGGGGGCT
84372 CATTCTCAAATATCATTTGA
326 CATTCTCAAATATCATTTGA
84392 GGTGGT
1 GGTGGT
84398 TGTACTTTTT
Statistics
Matches: 694, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
344 344 0.50
345 350 0.50
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (345 bp):
GGTGGTGATATTCAAGGGCTTTACAAAACTCCTGTCCCTTCTAGGATCACGTCATCGGTGAAGCT
AATATAATTATCTGTAGATATATGCTTCACTATTCGGTCTAGCTTATTCACATATATGTCTTCCA
GTATGAAAGTTTGATTCATCATCTTTAATAAAGTATTTCAGTGCACCTCATAGTTCATAAACATA
TCTAATATCAAGATTCATTCTTGCTACCTATGCAGTTGCTTCACCACACTATATTCATTATGTTC
CAGAAATTTCAAGAACTTTTGGGATTGAGCTTCAGTAATAGGCTCATTAACTCTTAGTGGGGGCT
CATTCTCAAATATCATTTGA
Found at i:91327 original size:67 final size:66
Alignment explanation
Indices: 91248--91387 Score: 244
Period size: 67 Copynumber: 2.1 Consensus size: 66
91238 TGAACTTGTA
91248 TAAAACCTTTAGCGACTAATCGCCCCTTGTATGTTTGTACATTACCATCAATGTCGATTTTCTTC
1 TAAAACCTTTAGCGACTAATCGCCCCTTGTATGTTTGTACATTACCATCAATGTCGATTTTCTTC
91313 T
66 T
* * *
91314 TGAAAACCTTTAGCGACTAATTGCCCCTTGTATGTTTGTACATTACCATCCATGTCGGTTTTCTT
1 T-AAAACCTTTAGCGACTAATCGCCCCTTGTATGTTTGTACATTACCATCAATGTCGATTTTCTT
91379 CT
65 CT
91381 TAAAACC
1 TAAAACC
91388 CCATTTACAC
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 7 0.10
67 63 0.90
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (66 bp):
TAAAACCTTTAGCGACTAATCGCCCCTTGTATGTTTGTACATTACCATCAATGTCGATTTTCTTC
T
Found at i:98724 original size:18 final size:19
Alignment explanation
Indices: 98684--98731 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
98674 TAATATACTA
*
98684 ATGCAATTATTATTTACAAT
1 ATGCAACTATTATTTA-AAT
*
98704 ATGCCACTATTATTT-AAT
1 ATGCAACTATTATTTAAAT
98722 ATGCAACTAT
1 ATGCAACTAT
98732 ATGATATGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.48
20 13 0.52
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (19 bp):
ATGCAACTATTATTTAAAT
Found at i:98915 original size:244 final size:243
Alignment explanation
Indices: 98396--99122 Score: 1157
Period size: 244 Copynumber: 2.9 Consensus size: 243
98386 TACTAACAAT
*
98396 TATATGAACTATGTAATATACTAATGCAATTATTATTTACAAAATGCCACTATTATTTAATATGC
1 TATATGAACTATGTAATATACTAATGCAATTATTATTTACAATATGCCACTATTATTTAATATGC
*
98461 TACTATATGATATGCAATATAACATATTTAATATGTACTATGTAATATGTAATATGCCATTATCA
66 AACTATATGATATGCAATATAACATATTTAATATGTAC----T-ATA--TAATATGCCATTATCA
98526 CATGCAATTATACTATATGATATATGAAACATTATATATTAAACAAAATGATATATGATATATGG
124 CATGCAATTATACTATATGATATATGAAACATTATATATTAAACAAAATGATATATGATATATGG
98591 TTGTGAAATGCGCTTATTATATACTATATATATATACACTATATAATAGACCCACACATTTTTAT
189 TTGTGAAATGCGC-------ATAC------TATAT--ACTATATAATAGACCCACACATTTTTAT
98656 TGCTA
239 TGCTA
98661 TATATGAACTATGTAATATACTAATGCAATTATTATTTACAATATGCCACTATTATTTAATATGC
1 TATATGAACTATGTAATATACTAATGCAATTATTATTTACAATATGCCACTATTATTTAATATGC
98726 AACTATATGATATGCAATATAACATATTTAATATGTACTATATAATATGCCATTATCACATGCAA
66 AACTATATGATATGCAATATAACATATTTAATATGTACTATATAATATGCCATTATCACATGCAA
*
98791 TTATACTATATGTTATATGAAACATTATATATTAAACAAAATGATATATGATATATGGTTGTGAA
131 TTATACTATATGATATATGAAACATTATATATTAAACAAAATGATATATGATATATGGTTGTGAA
* * *
98856 ATGTGCATACTATATACTATATAATAGGCCCACACATTTTTTATTTCTA
196 ATGCGCATACTATATACTATATAATAGACCCACACA-TTTTTATTGCTA
*
98905 TATATGAACTATGTAATATACTAATGCAATTATTGTTTACAATATGCCACTATTATTTAATATGC
1 TATATGAACTATGTAATATACTAATGCAATTATTATTTACAATATGCCACTATTATTTAATATGC
*
98970 AACTAAATGATATGCAATATAACATATTTAATATGTACTATATAATATGCCATTATCACATGCAA
66 AACTATATGATATGCAATATAACATATTTAATATGTACTATATAATATGCCATTATCACATGCAA
99035 TTATACTATATGATATATGAAACATTATATATTAAACAAAATGATATATGATATATGGTTGTGAA
131 TTATACTATATGATATATGAAACATTATATATTAAACAAAATGATATATGATATATGGTTGTGAA
* *
99100 ATGCACATACTATATACAATATA
196 ATGCGCATACTATATACTATATA
99123 TATATACTAT
Statistics
Matches: 449, Mismatches: 12, Indels: 23
0.93 0.02 0.05
Matches are distributed among these distances:
243 20 0.04
244 223 0.50
245 5 0.01
251 4 0.01
258 92 0.20
260 3 0.01
261 1 0.00
265 101 0.22
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.39
Consensus pattern (243 bp):
TATATGAACTATGTAATATACTAATGCAATTATTATTTACAATATGCCACTATTATTTAATATGC
AACTATATGATATGCAATATAACATATTTAATATGTACTATATAATATGCCATTATCACATGCAA
TTATACTATATGATATATGAAACATTATATATTAAACAAAATGATATATGATATATGGTTGTGAA
ATGCGCATACTATATACTATATAATAGACCCACACATTTTTATTGCTA
Found at i:102365 original size:21 final size:21
Alignment explanation
Indices: 102339--102380 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
102329 ACAATCCTCA
102339 CACAACAAGCTACTATGGGAG
1 CACAACAAGCTACTATGGGAG
102360 CACAACAAGCTACTATGGGAG
1 CACAACAAGCTACTATGGGAG
102381 TGAATGGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (21 bp):
CACAACAAGCTACTATGGGAG
Found at i:103624 original size:20 final size:20
Alignment explanation
Indices: 103587--103625 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
103577 TTTCCACCAT
*
103587 ATGCAACTAAATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
* *
103607 ATGCATCTACATGATCCTA
1 ATGCAACTAAATGATCCTA
103626 TATGGGCTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:107680 original size:12 final size:12
Alignment explanation
Indices: 107665--107716 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
107655 CTTGAAAAAG
107665 ACAAGTAAAATA
1 ACAAGTAAAATA
107677 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
107690 TACAAAG-AAAATGA
1 -AC-AAGTAAAAT-A
*
107704 AGAAGTAAAATA
1 ACAAGTAAAATA
107716 A
1 A
107717 AAAATGCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 15 0.44
13 9 0.26
14 7 0.21
15 3 0.09
ACGTcount: A:0.65, C:0.08, G:0.12, T:0.15
Consensus pattern (12 bp):
ACAAGTAAAATA
Done.