Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005111.1 Hibiscus syriacus cultivar Beakdansim tig00011487_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: 61242
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:11895 original size:56 final size:55
Alignment explanation
Indices: 11809--11915 Score: 196
Period size: 56 Copynumber: 1.9 Consensus size: 55
11799 GCGGATTACA
11809 TATATATTTGATATCATACTATATTAATAATTAACTTTATTTTATAATAATTTATG
1 TATATATTTGATATCATACTATATTAATAATTAACTTTA-TTTATAATAATTTATG
*
11865 TATATATTTGATATCATACTGTATTAATAATTAACTTTATTTATAATAATT
1 TATATATTTGATATCATACTATATTAATAATTAACTTTATTTATAATAATT
11916 ATAAATAAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 12 0.24
56 38 0.76
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (55 bp):
TATATATTTGATATCATACTATATTAATAATTAACTTTATTTATAATAATTTATG
Found at i:12268 original size:28 final size:31
Alignment explanation
Indices: 12237--12308 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 31
12227 AAATTAAATT
* *
12237 AAAATATATATTTTT-TTATTAT-TTA-TTA
1 AAAATATATATTTTTATTATTATCTAACATA
*
12265 AAAATATA-ATTTTTATTCTTATCTAACATA
1 AAAATATATATTTTTATTATTATCTAACATA
12295 AAAATATATATTTT
1 AAAATATATATTTT
12309 ATCTCATCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.16
28 14 0.38
29 2 0.05
30 10 0.27
31 5 0.14
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (31 bp):
AAAATATATATTTTTATTATTATCTAACATA
Found at i:12286 original size:24 final size:27
Alignment explanation
Indices: 12234--12286 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
12224 ATCAAATTAA
* *
12234 ATTAAAATATATATTTTTTTATTATTT
1 ATTAAAATATATATATTTTTATTACTT
12261 ATTAAAA-ATATA-ATTTTTATT-CTT
1 ATTAAAATATATATATTTTTATTACTT
12285 AT
1 AT
12287 CTAACATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.17
25 8 0.33
26 5 0.21
27 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTAAAATATATATATTTTTATTACTT
Found at i:12309 original size:30 final size:28
Alignment explanation
Indices: 12212--12310 Score: 92
Period size: 30 Copynumber: 3.4 Consensus size: 28
12202 AACTTTTTAA
* *
12212 ATATATTTTATTATCAAATTAAATTAAAAT
1 ATATATTTTATTAT--TATTAAATAAAAAT
* * *
12242 ATATATTTTTTTATTATTTATTAAAAAT
1 ATATATTTTATTATTATTAAATAAAAAT
*
12270 ATA-ATTTTTATTCTTATCTAACATAAAAAT
1 ATATA-TTTTATTATTAT-TAA-ATAAAAAT
12300 ATATATTTTAT
1 ATATATTTTAT
12311 CTCATCCTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
27 1 0.02
28 23 0.41
29 2 0.04
30 29 0.52
31 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (28 bp):
ATATATTTTATTATTATTAAATAAAAAT
Found at i:12436 original size:121 final size:121
Alignment explanation
Indices: 12298--12774 Score: 633
Period size: 121 Copynumber: 4.0 Consensus size: 121
12288 TAACATAAAA
* * *
12298 ATATATATTTTATCTCATCCTAATTTTTAAAATTTAATAAAATTGATATAATTATACATTTGTCA
1 ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGTCA
* * **
12363 CTTATACTTTTATATTTTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATATAT
66 CTTATACTTATATATTCTATCAATTTAGTAGTAATTTTAAAAAATTAAAAATATAT
12419 ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTC
1 ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTT-GTC
* * ** *
12484 ACTTTTTCTTATATATTCTATCAATTTAGTCCTAATTTTAATAAATT-AAAAT-TACT
65 ACTTATACTTATATATTCTATCAATTTAGTAGTAATTTTAAAAAATTAAAAATATA-T
* *
12540 TTATAT-TTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTC
1 ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACAT-TTGTC
* * * * *
12604 ACTTACACTTTTATATTCTATCAATTTAGTTGTAATTTTAAAAAATTATAATTA-AT
65 ACTTATACTTATATATTCTATCAATTTAGTAGTAATTTTAAAAAATTAAAAATATAT
* * * *
12660 TTATATATTTTATCTCGTCTTAACTTTGAAAACTTAATAAAATTGATATAATTACACATTTGATC
1 ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTG-TC
* * *
12725 ACTTTTACTTATATA-TATATCAATTTAGTCA-TAATTTTAATAAATTAAAA
65 ACTTATACTTATATATTCTATCAATTTAGT-AGTAATTTTAAAAAATTAAAA
12775 TTAATTTAAT
Statistics
Matches: 314, Mismatches: 34, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
120 136 0.43
121 137 0.44
122 41 0.13
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.47
Consensus pattern (121 bp):
ATATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGTCA
CTTATACTTATATATTCTATCAATTTAGTAGTAATTTTAAAAAATTAAAAATATAT
Found at i:12586 original size:120 final size:121
Alignment explanation
Indices: 12299--12782 Score: 686
Period size: 120 Copynumber: 4.0 Consensus size: 121
12289 AACATAAAAA
* * *
12299 TATATATTTTATCTCATCCTAATTTTTAAAATTTAATAAAATTGATATAATTATACATTT-GTCA
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCA
* * *** * *
12363 CTTATACTTTTATATTTTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATATATA
66 CTTATACTTATATATTCTATCAATTTAGTCGTAATTTTAAAAAATTAAAATTA-ATT
12420 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCA
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCA
* * * * *
12485 CTTTTTCTTATATATTCTATCAATTTAGTCCTAATTTTAATAAATTAAAATTACTT
66 CTTATACTTATATATTCTATCAATTTAGTCGTAATTTTAAAAAATTAAAATTAATT
*
12541 TATAT-TTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTCA
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCA
* * * *
12605 CTTACACTTTTATATTCTATCAATTTAGTTGTAATTTTAAAAAATTATAATTAATT
66 CTTATACTTATATATTCTATCAATTTAGTCGTAATTTTAAAAAATTAAAATTAATT
* * * *
12661 TATATATTTTATCTCGTCTTAACTTTGAAAACTTAATAAAATTGATATAATTACACATTTGATCA
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCA
* * * *
12726 CTTTTACTTATATA-TATATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
66 CTTATACTTATATATTCTATCAATTTAGTCGTAATTTTAAAAAATTAAAATTAATT
12781 TA
1 TA
12783 ATCTTTGAAT
Statistics
Matches: 323, Mismatches: 38, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
120 148 0.46
121 128 0.40
122 47 0.15
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (121 bp):
TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCA
CTTATACTTATATATTCTATCAATTTAGTCGTAATTTTAAAAAATTAAAATTAATT
Found at i:12592 original size:241 final size:241
Alignment explanation
Indices: 12299--12782 Score: 756
Period size: 241 Copynumber: 2.0 Consensus size: 241
12289 AACATAAAAA
* * *
12299 TATATATTTTATCTCATCCTAATTTTTAAAATTTAATAAAATTGATATAATTATACAT-TTGTCA
1 TATATATTTTATCTCATCCTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTCA
* *
12363 CTTATACTTTTATATTTTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATATATATATATATT
66 CTTACACTTTTATATTCTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATA-ATATATATATT
* * * *
12428 TTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCACTTTTTCT
130 TTATCTCATCTTAACTTTGAAAACTTAATAAAATTGATATAATTACACATTTGATCACTTTTACT
* * *
12493 TATATATTCTATCAATTTAGTCCTAATTTTAATAAATTAAAATTACTT
195 TATATA-TATATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
*
12541 TATAT-TTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTCA
1 TATATATTTTATCTCATCCTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTCA
*** * * *
12605 CTTACACTTTTATATTCTATCAATTTAGTTGTAATTTTAAAAAATTATAATTAATTTATATATTT
66 CTTACACTTTTATATTCTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATAATATATATATTT
*
12670 TATCTCGTCTTAACTTTGAAAACTTAATAAAATTGATATAATTACACATTTGATCACTTTTACTT
131 TATCTCATCTTAACTTTGAAAACTTAATAAAATTGATATAATTACACATTTGATCACTTTTACTT
12735 ATATATATATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
196 ATATATATATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
12781 TA
1 TA
12783 ATCTTTGAAT
Statistics
Matches: 221, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
240 40 0.18
241 125 0.57
242 56 0.25
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (241 bp):
TATATATTTTATCTCATCCTAACTTTTAAAATTTAATAAAATTGATATAATTACACATATGGTCA
CTTACACTTTTATATTCTATCAATTTAAAAGTAATTTTAAAAAATTAAAAATAATATATATATTT
TATCTCATCTTAACTTTGAAAACTTAATAAAATTGATATAATTACACATTTGATCACTTTTACTT
ATATATATATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
Found at i:14149 original size:10 final size:10
Alignment explanation
Indices: 14100--14149 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
14090 ATAAATAAAG
14100 AAATA-AATAT
1 AAATAGAAT-T
14110 AAAT-GAATT
1 AAATAGAATT
*
14119 AAATCGAATT
1 AAATAGAATT
*
14129 AAATAAAATT
1 AAATAGAATT
*
14139 AAATAGTATT
1 AAATAGAATT
14149 A
1 A
14150 TTATTATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 5 0.15
10 29 0.85
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (10 bp):
AAATAGAATT
Found at i:15152 original size:21 final size:18
Alignment explanation
Indices: 15128--15177 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 18
15118 TCTACCATTT
15128 AATAATAATAATTTATTCTCA
1 AATAATAATAATTTA-T-T-A
*
15149 AATAATAATATTTTATTA
1 AATAATAATAATTTATTA
15167 AATAATAATAA
1 AATAATAATAA
15178 CACCATCGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 11 0.41
19 1 0.04
20 1 0.04
21 14 0.52
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAATAATAATTTATTA
Found at i:15154 original size:18 final size:18
Alignment explanation
Indices: 15131--15176 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
15121 ACCATTTAAT
*
15131 AATAATAAT-TTATTCTCA
1 AATAATAATATT-TTATCA
*
15149 AATAATAATATTTTATTA
1 AATAATAATATTTTATCA
15167 AATAATAATA
1 AATAATAATA
15177 ACACCATCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAATAATATTTTATCA
Found at i:19950 original size:22 final size:23
Alignment explanation
Indices: 19905--19965 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
19895 GATTCCCCTG
*
19905 GGGGGAATCGGTTCCTCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
19928 GGGGGAATCGGTTCCCCTT-AAA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
19950 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
19966 TCTGCCTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.25
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:21965 original size:29 final size:30
Alignment explanation
Indices: 21932--21992 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
21922 AAATTTTGTC
**
21932 TAGTGACTAAAATATAAGTTTTG-AAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
* *
21961 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
21991 TA
1 TA
21993 AGGACCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (30 bp):
TAGTGACTAAAATATAAACTTTGAAAAGTT
Found at i:24060 original size:23 final size:22
Alignment explanation
Indices: 24017--24060 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
24007 GTGATGGGAA
*
24017 ATTTAATTGTATGTCTATTGAG
1 ATTTAATTGTATGTATATTGAG
24039 ATTTATATTGTAT-TATACTTGA
1 ATTTA-ATTGTATGTATA-TTGA
24061 TTTTTGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.52
Consensus pattern (22 bp):
ATTTAATTGTATGTATATTGAG
Found at i:24300 original size:49 final size:49
Alignment explanation
Indices: 24220--24381 Score: 270
Period size: 49 Copynumber: 3.3 Consensus size: 49
24210 AGGTGGAGCT
*
24220 TTTAGCACGTCTGACATCTTTGTGACTGTGGTGCTACGATTGATGATGA
1 TTTAGCACGTCTGACATCTTTGTGACGGTGGTGCTACGATTGATGATGA
* *
24269 TTTAGCACGTCTGACATCTTTGTAACGGTGGTGCTATGATTGATGATGA
1 TTTAGCACGTCTGACATCTTTGTGACGGTGGTGCTACGATTGATGATGA
* * *
24318 TTTAGCACGTCTGACGTCTTTGTGACGATGGTGCTACGGTTGATGATGA
1 TTTAGCACGTCTGACATCTTTGTGACGGTGGTGCTACGATTGATGATGA
24367 TTTAGCACGTCTGAC
1 TTTAGCACGTCTGAC
24382 GTTACAGATG
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 105 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (49 bp):
TTTAGCACGTCTGACATCTTTGTGACGGTGGTGCTACGATTGATGATGA
Found at i:26822 original size:23 final size:23
Alignment explanation
Indices: 26796--26840 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
26786 CACCACAGCT
*
26796 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
26819 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
26841 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:28683 original size:21 final size:21
Alignment explanation
Indices: 28659--28703 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28649 TTTTGTTCGT
* *
28659 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
28680 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
28701 TTG
1 TTG
28704 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:32008 original size:23 final size:23
Alignment explanation
Indices: 31982--32026 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
31972 CACCACAGCT
* *
31982 CGTATAAATGCATCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
32005 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
32027 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:35033 original size:23 final size:23
Alignment explanation
Indices: 35007--35051 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
34997 CACCACAGCC
*
35007 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
35030 CGTAGAATTGTACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
35052 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:36898 original size:21 final size:21
Alignment explanation
Indices: 36874--36918 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
36864 TTTTGTTCGT
* *
36874 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
36895 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
36916 TTG
1 TTG
36919 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:40143 original size:21 final size:21
Alignment explanation
Indices: 40119--40161 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40109 AAGATAGCTT
40119 CAGATAGACAGAAATCTTATG
1 CAGATAGACAGAAATCTTATG
40140 CAGATAGACAGAAATCTTATG
1 CAGATAGACAGAAATCTTATG
40161 C
1 C
40162 TGATTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (21 bp):
CAGATAGACAGAAATCTTATG
Found at i:40728 original size:29 final size:30
Alignment explanation
Indices: 40686--40746 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
40676 AAATTTTGTC
**
40686 TAGTGACTAAAGTATAAGTTTTG-AAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
*
40715 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
40745 TA
1 TA
40747 AGGACCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (30 bp):
TAGTGACTAAAGTATAAACTTTGAAAAGTT
Found at i:42795 original size:23 final size:22
Alignment explanation
Indices: 42752--42795 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
42742 GTGATGGGAA
*
42752 ATTTAATTGTATGTCTATTGAG
1 ATTTAATTGTATGTATATTGAG
42774 ATTTATATTGTAT-TATACTTGA
1 ATTTA-ATTGTATGTATA-TTGA
42796 TTTTTGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.52
Consensus pattern (22 bp):
ATTTAATTGTATGTATATTGAG
Found at i:42846 original size:53 final size:53
Alignment explanation
Indices: 42782--42888 Score: 137
Period size: 53 Copynumber: 2.0 Consensus size: 53
42772 AGATTTATAT
* * * *
42782 TGTATTATACTTGATTTTTGTTAATGTTT-AAAAAGATTTTGAT-GAGTGAATGA
1 TGTATGATACTTGA-TTTTGATAATATTTGAAAAAGATTCTGATAG-GTGAATGA
*
42835 TGTATGATACTTGATTTTGATGATATTTGAAAAAGATTCTGATAGGTGAATGA
1 TGTATGATACTTGATTTTGATAATATTTGAAAAAGATTCTGATAGGTGAATGA
42888 T
1 T
42889 AAATGATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 11 0.23
53 35 0.74
54 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.44
Consensus pattern (53 bp):
TGTATGATACTTGATTTTGATAATATTTGAAAAAGATTCTGATAGGTGAATGA
Found at i:43024 original size:49 final size:49
Alignment explanation
Indices: 42952--43111 Score: 275
Period size: 49 Copynumber: 3.3 Consensus size: 49
42942 AGGTGGAGCT
*
42952 TTTAGCACGTCTGACATCTTTGTGACTGTGGTGCTACGATTGATGATGA
1 TTTAGCACGTCTGACATCTTTGTGACAGTGGTGCTACGATTGATGATGA
* *
43001 TTTAGCACGTCTGACGTCTTTGTGACAGTGGTGCTATGATTGATGATGA
1 TTTAGCACGTCTGACATCTTTGTGACAGTGGTGCTACGATTGATGATGA
* *
43050 TTTAGCACGTCTGACATCTTTGTGACGGTGGTGCTGCGATTGATGATGA
1 TTTAGCACGTCTGACATCTTTGTGACAGTGGTGCTACGATTGATGATGA
43099 TTTAGCACGTCTG
1 TTTAGCACGTCTG
43112 GCGTTACAGA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 104 1.00
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.36
Consensus pattern (49 bp):
TTTAGCACGTCTGACATCTTTGTGACAGTGGTGCTACGATTGATGATGA
Found at i:47647 original size:18 final size:17
Alignment explanation
Indices: 47605--47644 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
47595 TAAAATGAAT
47605 ATTGAATGAAAAATAGG
1 ATTGAATGAAAAATAGG
47622 ATTGAATGAAAAATAGG
1 ATTGAATGAAAAATAGG
*
47639 CTTGAA
1 ATTGAA
47645 ATGCTCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.23, T:0.25
Consensus pattern (17 bp):
ATTGAATGAAAAATAGG
Found at i:48876 original size:24 final size:24
Alignment explanation
Indices: 48848--48931 Score: 168
Period size: 24 Copynumber: 3.5 Consensus size: 24
48838 CATTATACCA
48848 TGCATCGATGCATCCCTTAACATG
1 TGCATCGATGCATCCCTTAACATG
48872 TGCATCGATGCATCCCTTAACATG
1 TGCATCGATGCATCCCTTAACATG
48896 TGCATCGATGCATCCCTTAACATG
1 TGCATCGATGCATCCCTTAACATG
48920 TGCATCGATGCA
1 TGCATCGATGCA
48932 CTACTCATGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTAACATG
Found at i:50058 original size:25 final size:24
Alignment explanation
Indices: 50006--50102 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 24
49996 TCATCTCTTA
*
50006 TTCTTCTTCTTTTTTCCTTC-TTC
1 TTCTTCTTCTTTTTTTCTTCTTTC
50029 TTTCTTCTTCTTTTATTTCTTCTTTC
1 -TTCTTCTTCTTTT-TTTCTTCTTTC
* *
50055 TTCTTTTTCCTTTCTTTCTTCCTTCTC
1 TTCTTCTT-CTTTTTTTCTT-CTT-TC
* *
50082 CTCTTTTTC-TTTTTTCTTCTT
1 TTCTTCTTCTTTTTTTCTTCTT
50103 GGTGCCCCTC
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
24 16 0.25
25 27 0.43
26 11 0.17
27 9 0.14
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (24 bp):
TTCTTCTTCTTTTTTTCTTCTTTC
Found at i:50069 original size:18 final size:17
Alignment explanation
Indices: 50022--50102 Score: 66
Period size: 16 Copynumber: 4.9 Consensus size: 17
50012 TTCTTTTTTC
50022 CTTCTTCTTT-CTTC-TT
1 CTTCTT-TTTCCTTCTTT
50038 CTT-TTATTT-CTTCTTT
1 CTTCTT-TTTCCTTCTTT
50054 CTTCTTTTTCCTTTCTTT
1 CTTCTTTTTCC-TTCTTT
* *
50072 CTTCCTTCTCC-TCTTT
1 CTTCTTTTTCCTTCTTT
*
50088 -TTCTTTTTTCTTCTT
1 CTTCTTTTTCCTTCTT
50103 GGTGCCCCTC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
15 16 0.30
16 20 0.37
17 3 0.06
18 15 0.28
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (17 bp):
CTTCTTTTTCCTTCTTT
Found at i:50070 original size:43 final size:42
Alignment explanation
Indices: 50009--50102 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 42
49999 TCTCTTATTC
* * *
50009 TTCTTCTTTTTTCCTTC-TTCTTTCTTCTTCTTTTATTTCTTCT
1 TTCTTC-TTTTTCCTTCTTTCTTCCTTCTCCTCTT-TTTCTTCT
*
50052 TTCTTCTTTTTCCTTTCTTTCTTCCTTCTCCTCTTTTTCTTTT
1 TTCTTCTTTTTCC-TTCTTTCTTCCTTCTCCTCTTTTTCTTCT
50095 TTCTTCTT
1 TTCTTCTT
50103 GGTGCCCCTC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
42 7 0.16
43 24 0.53
44 14 0.31
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (42 bp):
TTCTTCTTTTTCCTTCTTTCTTCCTTCTCCTCTTTTTCTTCT
Found at i:55909 original size:48 final size:48
Alignment explanation
Indices: 55806--55910 Score: 147
Period size: 48 Copynumber: 2.2 Consensus size: 48
55796 CAGAAATAAT
* * *
55806 TAAACTGCTAAGGGCAGGCTGATTCTAGGACCCTGATAGTCGTCGGAA
1 TAAACTGCGAAGGGCAGGCTGATTCTAAGACCCTGATAGTCGTCGAAA
** * *
55854 TTCACTGCGACGGGCAGGCTGATTCTAAGATCCTGATAGTCGTCGAAA
1 TAAACTGCGAAGGGCAGGCTGATTCTAAGACCCTGATAGTCGTCGAAA
55902 TAAACTGCG
1 TAAACTGCG
55911 GGTAAAGGGC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (48 bp):
TAAACTGCGAAGGGCAGGCTGATTCTAAGACCCTGATAGTCGTCGAAA
Found at i:56973 original size:22 final size:22
Alignment explanation
Indices: 56945--56990 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
56935 GATCACAAAC
56945 AATATGTGGGGCTGAAGCCAGG
1 AATATGTGGGGCTGAAGCCAGG
*
56967 AATATGTGGGGCTTAAGCCAGG
1 AATATGTGGGGCTGAAGCCAGG
56989 AA
1 AA
56991 AGGGAAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.37, T:0.20
Consensus pattern (22 bp):
AATATGTGGGGCTGAAGCCAGG
Done.