Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007505.1 Hibiscus syriacus cultivar Beakdansim tig00020814_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: 63522
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3996 original size:63 final size:63
Alignment explanation
Indices: 3924--4042 Score: 220
Period size: 63 Copynumber: 1.9 Consensus size: 63
3914 GTTTCAGGGG
* *
3924 AAAAAGGTATTAGGAGTCTGTCAGACAGCTGCGCGACCATCCCGGGAAGACGAGGCAGGGAAA
1 AAAAAGGTATTAGGAGTCTGTCAGACAGCTGCACGACCATCCAGGGAAGACGAGGCAGGGAAA
3987 AAAAAGGTATTAGGAGTCTGTCAGACAGCTGCACGACCATCCAGGGAAGACGAGGC
1 AAAAAGGTATTAGGAGTCTGTCAGACAGCTGCACGACCATCCAGGGAAGACGAGGC
4043 TAACCGAGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.34, C:0.21, G:0.32, T:0.13
Consensus pattern (63 bp):
AAAAAGGTATTAGGAGTCTGTCAGACAGCTGCACGACCATCCAGGGAAGACGAGGCAGGGAAA
Found at i:9085 original size:182 final size:184
Alignment explanation
Indices: 8763--9148 Score: 600
Period size: 182 Copynumber: 2.1 Consensus size: 184
8753 TTTTCTAATT
* * * *
8763 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
*
8827 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTGATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTGATT
* * * *
8892 GGATTTTAAATTATTAATTGGGCTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 AGATCTTAAATTATTAATTGGGCTTTAAATGATTTGAG-TTGAGCCCATATGTTA
*
8946 TATATAATATATTTAATATTTTTTAATT-AAAAACAGTTTACAAATAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
* * *
9010 TATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAATTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTGATT
* *
9074 AGATCTTAAATTATTAATTGGGTTTTAAATGATTTGAGTTGAGCTCATATGTTA
131 AGATCTTAAATTATTAATTGGGCTTTAAATGATTTGAGTTGAGCCCATATGTTA
9128 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
9149 AAAATTTAAT
Statistics
Matches: 186, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
181 2 0.01
182 107 0.58
183 59 0.32
184 18 0.10
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTGATT
AGATCTTAAATTATTAATTGGGCTTTAAATGATTTGAGTTGAGCCCATATGTTA
Found at i:10346 original size:10 final size:11
Alignment explanation
Indices: 10328--10389 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 11
10318 ATATTTAAAA
10328 TTTATTTTTAT
1 TTTATTTTTAT
10339 TTTA-TTTTAT
1 TTTATTTTTAT
*
10349 TTTAGTATTTAAAGT
1 TTTA-T-TTT-TA-T
10364 TTTAGTTTTTAT
1 TTTA-TTTTTAT
10376 TTTATTATTTAT
1 TTTATT-TTTAT
10388 TT
1 TT
10390 AAGATTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
10 10 0.23
11 6 0.14
12 12 0.28
13 4 0.09
14 4 0.09
15 7 0.16
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:10408 original size:37 final size:37
Alignment explanation
Indices: 10319--10408 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 37
10309 TTTAAAATTA
* *
10319 TATTTAAAATTT-A-TTTTTATTTTATTTTATTTTAG
1 TATTTAAAGTTTGAGTTTTTATTTTATTTTATTTAAG
*
10354 TATTTAAAGTTTTAGTTTTTATTTTATTATTTATTTAAG
1 TATTTAAAGTTTGAGTTTTTATTTTA-T-TTTATTTAAG
*
10393 -ATTTAATG-TTGAGTTT
1 TATTTAAAGTTTGAGTTT
10409 AAAAAATTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
35 11 0.23
36 1 0.02
37 18 0.38
38 8 0.17
39 9 0.19
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (37 bp):
TATTTAAAGTTTGAGTTTTTATTTTATTTTATTTAAG
Found at i:11393 original size:33 final size:33
Alignment explanation
Indices: 11346--11412 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
11336 TTTGACCTTG
*
11346 GTATGTAACCATTGTTAAAGATATACACGAGAC
1 GTATATAACCATTGTTAAAGATATACACGAGAC
11379 GTATATAACCATTGTTAAAGATATACACGAGAC
1 GTATATAACCATTGTTAAAGATATACACGAGAC
11412 G
1 G
11413 GATGAAATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (33 bp):
GTATATAACCATTGTTAAAGATATACACGAGAC
Found at i:11574 original size:31 final size:30
Alignment explanation
Indices: 11501--11591 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 30
11491 ACTTTAAATA
11501 TTTTTATCAAAATAAGTA-CTTAAAGTA-TT
1 TTTTTATCAAAATAAGTATC-TAAAGTATTT
* *
11530 TTTTTGTCAAAATAAATATCT-AAGTTATTT
1 TTTTTATCAAAATAAGTATCTAAAG-TATTT
*
11560 TCTTTTATCAAAATAGGTATCTAAAGTATTT
1 T-TTTTATCAAAATAAGTATCTAAAGTATTT
11591 T
1 T
11592 ATGTCAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.06
29 19 0.37
30 4 0.08
31 23 0.44
32 3 0.06
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (30 bp):
TTTTTATCAAAATAAGTATCTAAAGTATTT
Found at i:11608 original size:28 final size:29
Alignment explanation
Indices: 11521--11617 Score: 108
Period size: 28 Copynumber: 3.3 Consensus size: 29
11511 AATAAGTACT
*
11521 TAAAGTATTTTTTTGTCAAAATAAATATC
1 TAAAGTATTTTTTTGTCAAAATAGATATC
* *
11550 T-AAGTTATTTTCTTTTATCAAAATAGGTATC
1 TAAAG-TA-TTT-TTTTGTCAAAATAGATATC
*
11581 TAAAGTA-TTTTATGTCAAAATAGATATC
1 TAAAGTATTTTTTTGTCAAAATAGATATC
*
11609 TAAACTATT
1 TAAAGTATT
11618 CAAAAATTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
28 25 0.45
29 6 0.11
30 3 0.05
31 19 0.34
32 3 0.05
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (29 bp):
TAAAGTATTTTTTTGTCAAAATAGATATC
Found at i:17237 original size:18 final size:18
Alignment explanation
Indices: 17184--17238 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
17174 AATTCTATAA
* *
17184 AATAAAAAAATAAAATATT
1 AATAAAAATATTAAA-ATT
*
17203 AATAAAAATATTTAAATT
1 AATAAAAATATTAAAATT
17221 ATATAAAAAT-TTAAAATT
1 A-ATAAAAATATTAAAATT
17239 TTCAAAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 11 0.35
19 20 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAAAATATTAAAATT
Found at i:24670 original size:23 final size:23
Alignment explanation
Indices: 24644--24691 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
24634 ATAAAGTACA
*
24644 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
24667 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
24690 AT
1 AT
24692 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:25441 original size:18 final size:18
Alignment explanation
Indices: 25418--25454 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25408 CGAAATATAT
25418 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
25436 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
25454 A
1 A
25455 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:25684 original size:23 final size:23
Alignment explanation
Indices: 25658--25722 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
25648 ATGCGAGATA
25658 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
25681 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
25704 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
25723 GTTACCTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:26103 original size:21 final size:20
Alignment explanation
Indices: 26073--26126 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
26063 GATAGACACT
*
26073 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
26094 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
26117 TTACATTATA
1 TTACATTATA
26127 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:26114 original size:23 final size:23
Alignment explanation
Indices: 26088--26150 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
26078 ATATAACCAT
26088 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
26111 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
26134 TACCTATTACATCATAT
1 TACCTATTACATTATAT
26151 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:29673 original size:367 final size:365
Alignment explanation
Indices: 28701--29732 Score: 1898
Period size: 367 Copynumber: 2.8 Consensus size: 365
28691 TTTTAAATTG
* *
28701 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
* *
28766 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG--AC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
28829 GCTCG-G-AAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATA
131 GAT-GTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATA
28892 AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGT
195 AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGT
*
28957 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGACGCTCGGAAAATG
260 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGACGATCGGAAAATG
29022 TCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
325 TCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
29063 TATGGACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
29127 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
29192 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
29257 AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTA
196 AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTA
*
29322 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGAT-GTGTAAA
261 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG--ACGATCG-G-AAA
29386 ATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
322 ATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
29430 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
29495 TAAGACCGGTATATTTATATCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
29560 GATGTGTAAAATGTCGACAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
29624 AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTA
196 AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTA
29689 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
261 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
29733 ATGTTGAAAG
Statistics
Matches: 653, Mismatches: 8, Indels: 13
0.97 0.01 0.02
Matches are distributed among these distances:
361 94 0.14
362 29 0.04
363 4 0.01
364 173 0.26
365 1 0.00
366 4 0.01
367 228 0.35
368 120 0.18
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (365 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAA
AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTA
TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGACGATCGGAAAATGT
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:29704 original size:183 final size:184
Alignment explanation
Indices: 28701--29732 Score: 1904
Period size: 184 Copynumber: 5.7 Consensus size: 184
28691 TTTTAAATTG
* *
28701 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
* *
28766 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG--AC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
28829 GCTCG-G-AAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GAT-GTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
28882 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
28947 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG--AC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
29010 GCTCG-G-AAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GAT-GTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
29063 TATGGACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
29127 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
29192 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
29246 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
29311 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
29376 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
29430 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
29495 TAAGACCGGTATATTTATATCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
29560 GATGTGTAAAATGTCGACAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
29613 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
29678 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
29733 ATGTTGAAAG
Statistics
Matches: 839, Mismatches: 7, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
180 97 0.12
181 207 0.25
182 4 0.00
183 227 0.27
184 304 0.36
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:32105 original size:199 final size:200
Alignment explanation
Indices: 31677--33092 Score: 2533
Period size: 199 Copynumber: 7.1 Consensus size: 200
31667 TTTAAATTAG
* *
31677 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
31742 ATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
31806 CGACAC--TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
31868 AAAAA
196 AAAAA
*
31873 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
31938 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
32003 CGACACTTTTTTATATATGGATCGACACTTTAT-GGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
32067 AAAAA
196 AAAAA
32072 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
32137 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
32201 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
32266 AAAAA
196 AAAAA
*
32271 TATCGACAAAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
32336 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
32400 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
32465 AAAAA
196 AAAAA
32470 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
32535 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
32600 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTTAATTCATTCTGGAAA
131 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
32664 AAAAAA
195 AAAAAA
32670 TATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* * *
32732 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTTGGGTTCGATGATTTGGGGA
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATAC-TTTTGGGTTCGATGATTTTGGGA
* *
32797 TCGACAC--TTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAA
130 TCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAA
32860 AAAAAA
195 AAAAAA
32866 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
32930 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
32994 CGACAC-TTTTT-TATATGGATCGACACTTTGGGTGCGTGCACCTTGTTTTTAATTCATTCTGGA
131 CGACACTTTTTTATATATGGATCGACACTTT--ATGGGTGCACCTTGTTTTTAATTCATTCTGGA
33057 AAAAAAA
194 AAAAAAA
* *
33064 TTTCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
33093 TGACCCTTAA
Statistics
Matches: 1187, Mismatches: 19, Indels: 26
0.96 0.02 0.02
Matches are distributed among these distances:
196 173 0.15
197 156 0.13
198 236 0.20
199 528 0.44
200 94 0.08
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
AAAAA
Found at i:33198 original size:19 final size:19
Alignment explanation
Indices: 33171--33215 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
33161 TATTCACATA
*
33171 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
33190 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
33209 AAAATTA
1 AAAATTA
33216 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:35037 original size:32 final size:32
Alignment explanation
Indices: 35001--35064 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
34991 CATCTTAATA
*
35001 TCACCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCTCAACACCGAAACTTCTTTCACCACT
***
35033 TCACCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCTCAACACCGAAACTTCTTTCACCACT
35065 CCATCTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.44, G:0.02, T:0.30
Consensus pattern (32 bp):
TCACCCTCAACACCGAAACTTCTTTCACCACT
Found at i:37216 original size:23 final size:23
Alignment explanation
Indices: 37190--37236 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
37180 TATTTTCAGA
*
37190 GGATAT-TTAGCTTATATTTCATC
1 GGATATGTTA-CTTATATTTAATC
*
37213 GGATATGTTATTTATATTTAATC
1 GGATATGTTACTTATATTTAATC
37236 G
1 G
37237 ATACAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (23 bp):
GGATATGTTACTTATATTTAATC
Found at i:37567 original size:20 final size:20
Alignment explanation
Indices: 37541--37586 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
37531 CACTTTTAAA
37541 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
37560 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
37581 TTTACC
1 TTTACC
37587 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:39289 original size:29 final size:28
Alignment explanation
Indices: 39245--39302 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
39235 TTAGGCGTTG
*
39245 TATCATTTATACCATTAAACTTTCAATTT
1 TATCAATTATACCATTAAACTTT-AATTT
* *
39274 TATCAATTATAGCATTGAACTTTAATTT
1 TATCAATTATACCATTAAACTTTAATTT
39302 T
1 T
39303 CATTTCAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.48
Consensus pattern (28 bp):
TATCAATTATACCATTAAACTTTAATTT
Found at i:43663 original size:2 final size:2
Alignment explanation
Indices: 43656--43698 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
43646 CTTTTTACAT
*
43656 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43698 T
1 T
43699 GATGTACACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:43911 original size:2 final size:2
Alignment explanation
Indices: 43904--43931 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43894 AGTGAATCGC
43904 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
43932 CTTAATTTTA
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
Found at i:46595 original size:22 final size:21
Alignment explanation
Indices: 46542--46595 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
46532 CCGATATATC
* * *
46542 AAATATTATATTTATTATATA
1 AAATAATATATCTATTACATA
46563 AAATCAATATATCTATTACATTA
1 AAAT-AATATATCTATTACA-TA
*
46586 AAATAGTATA
1 AAATAATATA
46596 CTTATATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 17 0.63
23 6 0.22
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATAATATATCTATTACATA
Found at i:47000 original size:14 final size:14
Alignment explanation
Indices: 46957--47012 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
46947 ATCTGATTAT
46957 TATTTTATA-AATAA
1 TATTTTATATAA-AA
*
46971 -ATTTTGT-TAAATA
1 TATTTTATATAAA-A
46984 TATTTTATATAAAA
1 TATTTTATATAAAA
*
46998 TATTTTATTTAAAA
1 TATTTTATATAAAA
47012 T
1 T
47013 TATTAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 1 0.03
13 9 0.26
14 21 0.60
15 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
TATTTTATATAAAA
Found at i:55164 original size:16 final size:16
Alignment explanation
Indices: 55143--55175 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55133 TGAAATAGTG
55143 GGAGCTATCCGTAATA
1 GGAGCTATCCGTAATA
55159 GGAGCTATCCGTAATA
1 GGAGCTATCCGTAATA
55175 G
1 G
55176 AAGATATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (16 bp):
GGAGCTATCCGTAATA
Done.