Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000326.1 Hibiscus syriacus cultivar Beakdansim tig00000608_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: 136251
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:793 original size:21 final size:21
Alignment explanation
Indices: 748--793 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
738 CGCGATTATC
*
748 ACATGTTCGCTTTCTTTTTAA
1 ACATGTTCACTTTCTTTTTAA
*
769 ACAT-TTCACTTTTTTTTTAA
1 ACATGTTCACTTTCTTTTTAA
789 TACAT
1 -ACAT
794 CATACGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.24, C:0.17, G:0.04, T:0.54
Consensus pattern (21 bp):
ACATGTTCACTTTCTTTTTAA
Found at i:3382 original size:22 final size:22
Alignment explanation
Indices: 3356--3402 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
3346 ACTTTATAAG
*
3356 TTTTTATAAATGATAATTA-ATT
1 TTTTTATAAAGGAT-ATTATATT
3378 TTTTTATAAAGGATATTATATT
1 TTTTTATAAAGGATATTATATT
3400 TTT
1 TTT
3403 ATATGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTTATAAAGGATATTATATT
Found at i:5955 original size:22 final size:23
Alignment explanation
Indices: 5908--5955 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
5898 CATTTAGATT
*
5908 TTTAACTAATTTATAATTATACG
1 TTTAACTAATTTATAATTATAAG
*
5931 TTTAA-TACTTTATAATT-TAAAG
1 TTTAACTAATTTATAATTAT-AAG
5953 TTT
1 TTT
5956 TATAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 1 0.05
22 16 0.73
23 5 0.23
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAACTAATTTATAATTATAAG
Found at i:14319 original size:13 final size:13
Alignment explanation
Indices: 14295--14329 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
14285 AAAAAATCAA
14295 ATTAAATATTAAAT
1 ATTAAAT-TTAAAT
14309 ATTAAATTTAAAT
1 ATTAAATTTAAAT
14322 ATTAAATT
1 ATTAAATT
14330 GAGAACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTAAATTTAAAT
Found at i:14319 original size:20 final size:19
Alignment explanation
Indices: 14255--14328 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
14245 TTGACCACTA
*
14255 AAATTTAAT-TTAAATATT
1 AAATTAAATATTAAATATT
* * * *
14273 TAATTAAAAATTAAAAAATC
1 AAATTAAATATT-AAATATT
14293 AAATTAAATATTAAATATT
1 AAATTAAATATTAAATATT
14312 AAATTTAAATATTAAAT
1 AAA-TTAAATATTAAAT
14329 TGAGAACAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 6 0.14
19 10 0.23
20 28 0.64
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTAAATATTAAATATT
Found at i:14328 original size:7 final size:7
Alignment explanation
Indices: 14295--14328 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
14285 AAAAAATCAA
14295 ATTAAAT
1 ATTAAAT
14302 ATTAAAT
1 ATTAAAT
14309 ATTAAAT
1 ATTAAAT
14316 -TTAAAT
1 ATTAAAT
14322 ATTAAAT
1 ATTAAAT
14329 TGAGAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTAAAT
Found at i:21699 original size:27 final size:27
Alignment explanation
Indices: 21669--21726 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
21659 TATTTATTAT
*
21669 ATCTTATTAAATTAAGAAATCATGTAC
1 ATCTTATTAAATTAAAAAATCATGTAC
21696 ATCTTATTAAATTAAAAAATCATGTAC
1 ATCTTATTAAATTAAAAAATCATGTAC
21723 ATCT
1 ATCT
21727 GTATGTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (27 bp):
ATCTTATTAAATTAAAAAATCATGTAC
Found at i:21863 original size:31 final size:31
Alignment explanation
Indices: 21825--21883 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
21815 GCAGACAAGT
*
21825 TAAAATAATCCTTCTGCAACGAGAAAAAAAA
1 TAAAATAATCCTTCTCCAACGAGAAAAAAAA
21856 TAAAATAATCCTTCTCCAACGAGAAAAA
1 TAAAATAATCCTTCTCCAACGAGAAAAA
21884 GAAGAGATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.20
Consensus pattern (31 bp):
TAAAATAATCCTTCTCCAACGAGAAAAAAAA
Found at i:27554 original size:21 final size:20
Alignment explanation
Indices: 27468--27625 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
27458 AAATGACCAA
**
27468 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
27487 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
27507 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
27527 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
27548 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
27569 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
27589 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
27610 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
27626 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:27654 original size:20 final size:20
Alignment explanation
Indices: 27593--27781 Score: 161
Period size: 20 Copynumber: 9.4 Consensus size: 20
27583 GATTTTCCAG
* ** *
27593 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
27613 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
27633 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
27653 AACCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
27673 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
27693 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* *
27713 AATCGCAACG-ATAATCTGTA
1 AATCGCAACGCGT-ATCCGTA
*
27733 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
27753 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
27773 AATCACAAC
1 AATCGCAAC
27782 ACTGAAATTT
Statistics
Matches: 145, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 141 0.97
21 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:28513 original size:24 final size:24
Alignment explanation
Indices: 28474--28520 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28464 AAATTTGGTC
28474 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
28498 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
28521 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:28712 original size:12 final size:12
Alignment explanation
Indices: 28695--28719 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28685 ATATAATCCT
28695 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28707 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28719 G
1 G
28720 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:30035 original size:25 final size:25
Alignment explanation
Indices: 30001--30055 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
29991 TTAACATTCG
30001 TTTTACTAGTTTATCGTTTTCTTCA
1 TTTTACTAGTTTATCGTTTTCTTCA
30026 TTTTACTAGTTTATCGTTTTCTTCA
1 TTTTACTAGTTTATCGTTTTCTTCA
30051 TTTTA
1 TTTTA
30056 TATGACTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.16, C:0.15, G:0.07, T:0.62
Consensus pattern (25 bp):
TTTTACTAGTTTATCGTTTTCTTCA
Found at i:38048 original size:31 final size:33
Alignment explanation
Indices: 37978--38053 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
37968 CTAAACCCGA
* *
37978 ACCCGACCCGAATATCACACTTAAAAAAACCTG
1 ACCCGACCCAAATACCACACTTAAAAAAACCTG
*
38011 ACCCGACCCAAATACCACACTTAAAAAAATC-G
1 ACCCGACCCAAATACCACACTTAAAAAAACCTG
38043 A-CCGACCCAAA
1 ACCCGACCCAAA
38054 CCCGAACCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 10 0.25
32 2 0.05
33 28 0.70
ACGTcount: A:0.45, C:0.36, G:0.08, T:0.12
Consensus pattern (33 bp):
ACCCGACCCAAATACCACACTTAAAAAAACCTG
Found at i:38155 original size:28 final size:28
Alignment explanation
Indices: 38124--38181 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
38114 GACCCAACTC
* * *
38124 GAATATCACACTTAAAGAAACCCGACCT
1 GAATATCAAACTTAAAAAAACCAGACCT
*
38152 GAATATCAAACTTAAAAAAATCAGACCT
1 GAATATCAAACTTAAAAAAACCAGACCT
38180 GA
1 GA
38182 CCCCGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.48, C:0.22, G:0.10, T:0.19
Consensus pattern (28 bp):
GAATATCAAACTTAAAAAAACCAGACCT
Found at i:40343 original size:23 final size:23
Alignment explanation
Indices: 40317--40364 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
40307 ATAAAGTACA
*
40317 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
40340 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
40363 AT
1 AT
40365 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:40782 original size:23 final size:23
Alignment explanation
Indices: 40756--40818 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
40746 ATATAACCAC
40756 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* ** *
40779 TACCTATTATATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
40802 TACCTATTACATCATAT
1 TACCTATTACATTATAT
40819 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:43970 original size:20 final size:21
Alignment explanation
Indices: 43941--43981 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
43931 TTCCACAGTG
43941 AAAAAAGTATCGACAC-TTTT
1 AAAAAAGTATCGACACATTTT
*
43961 AAAAAGGTATCGACACATTTT
1 AAAAAAGTATCGACACATTTT
43982 TATACCGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAAAAGTATCGACACATTTT
Found at i:44469 original size:183 final size:183
Alignment explanation
Indices: 43977--44670 Score: 1232
Period size: 183 Copynumber: 3.8 Consensus size: 183
43967 GTATCGACAC
43977 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
44042 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
44107 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
44160 A-TTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
44224 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
44289 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
*
44342 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
*
44407 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
*
44472 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
* *
44525 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTTTTTT
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATG---TGT
* * * * **
44590 CAA--TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTTCATTCTGGACATAAAGTACAAA
63 AAATGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGA
*
44653 CACAATATTAAAAAGTGT
128 CACAATATTAGAAAGTGT
44671 GAAAACTTTG
Statistics
Matches: 495, Mismatches: 12, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
182 182 0.37
183 236 0.48
184 73 0.15
186 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
Found at i:45876 original size:3 final size:3
Alignment explanation
Indices: 45868--45942 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
45858 ACTTGTTTGG
* * * **
45868 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
45916 AGC TTC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
45943 GTCAGCTTCA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:47750 original size:198 final size:198
Alignment explanation
Indices: 47412--48579 Score: 2257
Period size: 198 Copynumber: 5.9 Consensus size: 198
47402 TATTTAAATT
47412 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
47477 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
47542 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
47607 AAA
196 AAA
47610 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
47675 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
47740 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTATGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
47805 AAA
196 AAA
*
47808 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTTATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
*
47873 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTCTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
47938 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCATCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
48003 AAA
196 AAA
48006 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
48071 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
48136 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
48201 AAA
196 AAA
48204 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
48269 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
48333 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTAGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
48398 AAA
196 AAA
48401 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
48466 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
48531 ATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 ATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
48580 GGCCATATTG
Statistics
Matches: 957, Mismatches: 11, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
197 196 0.20
198 722 0.75
199 39 0.04
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (198 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
AAA
Found at i:48744 original size:19 final size:19
Alignment explanation
Indices: 48698--48746 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
48688 TTATATTCAC
*
48698 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
48717 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
48736 ATACAAAATTA
1 ATACAAAATTA
48747 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:50569 original size:33 final size:33
Alignment explanation
Indices: 50532--50597 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
50522 CATCTTAATA
*
50532 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
50565 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
50598 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:50671 original size:21 final size:21
Alignment explanation
Indices: 50631--50695 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
50621 CCCCTTATTC
* *
50631 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
50652 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
50673 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
50694 CT
1 CT
50696 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:52935 original size:17 final size:18
Alignment explanation
Indices: 52913--52955 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
52903 ATATATCCGG
52913 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
52930 TATCATTTTGTTACCGGTTT
1 TATCA--TTGTTACCGGTTT
52950 TATCAT
1 TATCAT
52956 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:52945 original size:20 final size:20
Alignment explanation
Indices: 52918--52964 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
52908 TCCGGTATCA
52918 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
52937 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
52958 TTTTACC
1 TTTTACC
52965 TGTTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:53108 original size:20 final size:20
Alignment explanation
Indices: 53082--53127 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
53072 CACTTTTAAA
53082 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
53101 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
53122 TTTACC
1 TTTACC
53128 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:53594 original size:228 final size:227
Alignment explanation
Indices: 53192--53639 Score: 783
Period size: 228 Copynumber: 2.0 Consensus size: 227
53182 TTAAAACTGC
53192 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
53257 TTAATTTAATAATTTAATTTACACAAAATTATATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAATATATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
53322 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
* *
53387 GTATGGACAGTTTTATAAAAATGATATATACTT
195 GTATGGACACTTTTATAAAAAGGATATATACTT
53420 TTTTGAAAGTTATGTAATTTATGTTTCAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
53484 ATTAATTTAATAATTTCATTTACACAAAAA-ATTATTTGATTGTTTTGATATTTTATAAAATATT
65 ATTAATTTAATAATTTAATTTACACAAAAATA-TATTTGATTGTTTTGATATTTTATAAAATATT
* *
53548 ATTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATA
129 ATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATA
53613 AGTATGGACACTTTTATAAAAAGGATA
194 AGTATGGACACTTTTATAAAAAGGATA
53640 GATAATTTAC
Statistics
Matches: 210, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
227 37 0.18
228 146 0.70
229 27 0.13
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (227 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAATATATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTT
Found at i:64938 original size:45 final size:45
Alignment explanation
Indices: 64861--64992 Score: 214
Period size: 45 Copynumber: 3.0 Consensus size: 45
64851 AGGATGATTT
* *
64861 CCCATGGTAACAAAGC-GTTTGTATTTTTCATCGGCATCAGACTA
1 CCCATGGGAACAAAGCGGTCTGTATTTTTCATCGGCATCAGACTA
* *
64905 CCCATGGGAGCAAAGCGGTCTGTATTTTTCATCGGCATCAGACTT
1 CCCATGGGAACAAAGCGGTCTGTATTTTTCATCGGCATCAGACTA
64950 CCCATGGGAACAAAGCGGTC-GTATTTTTCATCGGCATCAGACT
1 CCCATGGGAACAAAGCGGTCTGTATTTTTCATCGGCATCAGACT
64993 GCTCAGATGA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 37 0.45
45 45 0.55
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (45 bp):
CCCATGGGAACAAAGCGGTCTGTATTTTTCATCGGCATCAGACTA
Found at i:69280 original size:3 final size:3
Alignment explanation
Indices: 69272--69342 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
69262 AAAATAAACA
69272 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
69320 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
69343 AAGACAAGAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:77626 original size:2 final size:2
Alignment explanation
Indices: 77619--77644 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
77609 GGTATCTGCA
77619 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
77645 TTGAAGTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78469 original size:2 final size:2
Alignment explanation
Indices: 78464--78519 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
78454 GAAAAAAATA
78464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78506 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
78520 TCCAAAGCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85110 original size:36 final size:35
Alignment explanation
Indices: 85011--85151 Score: 210
Period size: 36 Copynumber: 4.0 Consensus size: 35
85001 TTCGTTCTAG
* *
85011 TTGAATCGGAAGTGCGATGCTTCTTTCCGTTCGAC
1 TTGAATCGGAAGTGCGATGCTTCCTTCCGTTCGAT
* *
85046 TTGAACCGGAAGTGCGATGCTTCTTTCCGTTCGAT
1 TTGAATCGGAAGTGCGATGCTTCCTTCCGTTCGAT
*
85081 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCGAT
1 TTGAATCGGAAGTG-CGATGCTTCCTTCCGTTCGAT
*
85117 TTAAATCGGAAGTGCCGATGCTTCCTTCCGTTCGA
1 TTGAATCGGAAGTG-CGATGCTTCCTTCCGTTCGA
85152 CTAGAAACGC
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
35 45 0.46
36 52 0.54
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (35 bp):
TTGAATCGGAAGTGCGATGCTTCCTTCCGTTCGAT
Found at i:85127 original size:71 final size:71
Alignment explanation
Indices: 85011--85151 Score: 212
Period size: 71 Copynumber: 2.0 Consensus size: 71
85001 TTCGTTCTAG
* * * *
85011 TTGAATCGGAAGTGCGATGCTTCTTTCCGTTCGACTTGAACCGGAAGTG-CGATGCTTCTTTCCG
1 TTGAATCGAAAGTGCGATGCTTCCTTCCGTTCGACTTAAACCGGAAGTGCCGATGCTTCCTTCCG
85075 TTCGAT
66 TTCGAT
* *
85081 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCGATTTAAATCGGAAGTGCCGATGCTTCCTTCC
1 TTGAATCGAAAGTG-CGATGCTTCCTTCCGTTCGACTTAAACCGGAAGTGCCGATGCTTCCTTCC
85146 GTTCGA
65 GTTCGA
85152 CTAGAAACGC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 13 0.21
71 31 0.49
72 19 0.30
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (71 bp):
TTGAATCGAAAGTGCGATGCTTCCTTCCGTTCGACTTAAACCGGAAGTGCCGATGCTTCCTTCCG
TTCGAT
Found at i:86392 original size:20 final size:20
Alignment explanation
Indices: 86367--86415 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
86357 ATACATTGTA
*
86367 TATTCTAGAATACAATCGTG
1 TATTCTAGAATACAATAGTG
86387 TATTCTAGAATACAATAGTG
1 TATTCTAGAATACAATAGTG
86407 TATTCTAGA
1 TATTCTAGA
86416 TACTCTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (20 bp):
TATTCTAGAATACAATAGTG
Found at i:94605 original size:16 final size:18
Alignment explanation
Indices: 94563--94608 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
94553 TTCACGAAAT
94563 GTAAGATTACCAGTGGGAA
1 GTAAGATTACCAG-GGGAA
94582 TGTAAGATTACCA-GGGAA
1 -GTAAGATTACCAGGGGAA
94600 -TAAGATTAC
1 GTAAGATTAC
94609 TGGAATGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.35
18 5 0.19
20 12 0.46
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (18 bp):
GTAAGATTACCAGGGGAA
Found at i:94825 original size:37 final size:38
Alignment explanation
Indices: 94745--94825 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
94735 AACAAGTTAG
* *
94745 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
94784 -AAAATTTATATAATTTT-TTTACAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAATTGAAAATCAT
94820 AAAAAT
1 AAAAAT
94826 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 2 0.05
37 27 0.73
38 8 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:95161 original size:95 final size:95
Alignment explanation
Indices: 95054--95251 Score: 351
Period size: 95 Copynumber: 2.1 Consensus size: 95
95044 GAGGTAATGA
* *
95054 CATTCCCAGTAATATACTCAAAAAAATCCACTATTGGTAATCTTACATTACCGAGAATGAGATTC
1 CATTCCCAGTAATATACCCAAAAAAATCCACTATTGGTAATCTTACATTACCGAGAATGAGATTA
95119 CCAGCTAACCAAACGGGGGAATGTAGATTC
66 CCAGCTAACCAAACGGGGGAATGTAGATTC
* * *
95149 CATTCCCGGTAATATACCCAAAAAAATCCACTATTGGTAATCTTATATTACCGGGAATGAGATTA
1 CATTCCCAGTAATATACCCAAAAAAATCCACTATTGGTAATCTTACATTACCGAGAATGAGATTA
95214 CCAGCTAACCAAACGGGGGAATGTAGATTC
66 CCAGCTAACCAAACGGGGGAATGTAGATTC
95244 CATTCCCA
1 CATTCCCA
95252 TGGGAATCCC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (95 bp):
CATTCCCAGTAATATACCCAAAAAAATCCACTATTGGTAATCTTACATTACCGAGAATGAGATTA
CCAGCTAACCAAACGGGGGAATGTAGATTC
Found at i:98547 original size:2 final size:2
Alignment explanation
Indices: 98540--98566 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
98530 TGGTTAGTTT
98540 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
98567 GTCAACATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:100642 original size:5 final size:5
Alignment explanation
Indices: 100632--100675 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
100622 GCCTGCAAAA
100632 ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
100676 AATTATTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 33 0.89
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:100658 original size:18 final size:18
Alignment explanation
Indices: 100637--100676 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
100627 CAAAAATAAT
100637 ATAATATAATATAATATA
1 ATAATATAATATAATATA
100655 ATAATATAATATAATATA
1 ATAATATAATATAATATA
100673 ATAA
1 ATAA
100677 ATTATTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATATAATATAATATA
Found at i:100676 original size:13 final size:13
Alignment explanation
Indices: 100632--100670 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 13
100622 GCCTGCAAAA
100632 ATAATATAATATAAT
1 ATAATAT-A-ATAAT
100647 ATAATATAATAAT
1 ATAATATAATAAT
100660 ATAATATAATA
1 ATAATATAATA
100671 TAATAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 16 0.67
14 1 0.04
15 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:105421 original size:2 final size:2
Alignment explanation
Indices: 105414--105489 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
105404 CAGGTATGTG
105414 TA TA TA TA TA TA TA TA TA TA 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
105456 TA TA TA TA TA TA 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
105490 CAACAAGCAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109079 original size:15 final size:17
Alignment explanation
Indices: 109061--109096 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
109051 TATTTAAAAT
109061 TTAATTAAT-ATT-AAA
1 TTAATTAATGATTCAAA
109076 TTAATTAATGATTCAAA
1 TTAATTAATGATTCAAA
109093 TTAA
1 TTAA
109097 ACCAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 3 0.16
17 7 0.37
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTAATTAATGATTCAAA
Found at i:112186 original size:27 final size:27
Alignment explanation
Indices: 112156--112249 Score: 161
Period size: 27 Copynumber: 3.5 Consensus size: 27
112146 AACAGCGCTG
112156 AATGATTTAGCATCAAAGTATATTCTA
1 AATGATTTAGCATCAAAGTATATTCTA
*
112183 AATGATTTAGCATCAAAGTATATTATA
1 AATGATTTAGCATCAAAGTATATTCTA
*
112210 AATGATTTAGCATCAAAGTATATTCTG
1 AATGATTTAGCATCAAAGTATATTCTA
*
112237 AATGATTCAGCAT
1 AATGATTTAGCAT
112250 GTCACATTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (27 bp):
AATGATTTAGCATCAAAGTATATTCTA
Found at i:112441 original size:21 final size:20
Alignment explanation
Indices: 112405--112449 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
112395 CGATCATTAA
*
112405 TATTTAATTTAATTTAAATG
1 TATTAAATTTAATTTAAATG
112425 TATTAAATTTAAATTTAAATG
1 TATTAAATTT-AATTTAAATG
112446 TATT
1 TATT
112450 TTAATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
TATTAAATTTAATTTAAATG
Found at i:113474 original size:23 final size:20
Alignment explanation
Indices: 113435--113479 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
113425 AAATATAAAT
*
113435 TTAAAAAAAATTGAATTCCA
1 TTAAAAAAAATTGAATTACA
113455 TTAAAAAAAATATAGAAATTACA
1 TTAAAAAAAAT-T-G-AATTACA
113478 TT
1 TT
113480 TTAAATGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 1 0.05
22 1 0.05
23 8 0.38
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (20 bp):
TTAAAAAAAATTGAATTACA
Found at i:124905 original size:14 final size:14
Alignment explanation
Indices: 124861--124905 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
124851 GATTGTGCAA
124861 AATATAAATGAACG
1 AATATAAATGAACG
* *
124875 AACATAAATGAATG
1 AATATAAATGAACG
*
124889 AATATAAACGAACG
1 AATATAAATGAACG
124903 AAT
1 AAT
124906 TATTGAGCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.58, C:0.09, G:0.13, T:0.20
Consensus pattern (14 bp):
AATATAAATGAACG
Found at i:125169 original size:31 final size:30
Alignment explanation
Indices: 125134--125200 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
125124 AATTTGAAAA
* *
125134 TTTATAACAAAATTTAAAATATAATGTTCAT
1 TTTATAA-AAAATCTAAAATATAATGTTCAG
* *
125165 TTTAT-AAAAGTCTAAAATTTAATGTTCAG
1 TTTATAAAAAATCTAAAATATAATGTTCAG
125194 TTTATAA
1 TTTATAA
125201 TTTCTAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 24 0.77
30 2 0.06
31 5 0.16
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (30 bp):
TTTATAAAAAATCTAAAATATAATGTTCAG
Found at i:129618 original size:27 final size:27
Alignment explanation
Indices: 129581--129652 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
129571 GGTCGTTTCT
*
129581 TGCTGTTGCTGTTGTTGTAATTGCTGC
1 TGCTGCTGCTGTTGTTGTAATTGCTGC
*
129608 TGCTGCTGCTGTTGCTGTAATTGCTGC
1 TGCTGCTGCTGTTGTTGTAATTGCTGC
*
129635 TGCTGCAGCTGTTGTTGT
1 TGCTGCTGCTGTTGTTGT
129653 TGCCGTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.07, C:0.18, G:0.31, T:0.44
Consensus pattern (27 bp):
TGCTGCTGCTGTTGTTGTAATTGCTGC
Found at i:129689 original size:27 final size:27
Alignment explanation
Indices: 129659--129717 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
129649 TTGTTGCCGT
129659 TGTTGCAACTGCTGCTGCAATTGCAAC
1 TGTTGCAACTGCTGCTGCAATTGCAAC
*** * *
129686 TGTTGTTGCTGTTGCTGCAATTGCAAT
1 TGTTGCAACTGCTGCTGCAATTGCAAC
129713 TGTTG
1 TGTTG
129718 TTGCTGCTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (27 bp):
TGTTGCAACTGCTGCTGCAATTGCAAC
Found at i:129718 original size:27 final size:27
Alignment explanation
Indices: 129667--129730 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
129657 GTTGTTGCAA
129667 CTGCTGCTGCAATTGCAACTGTTGTTG
1 CTGCTGCTGCAATTGCAACTGTTGTTG
* *
129694 CTGTTGCTGCAATTGCAATTGTTGTTG
1 CTGCTGCTGCAATTGCAACTGTTGTTG
129721 CTGCTGCTGC
1 CTGCTGCTGC
129731 TGCTGGTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.27, T:0.39
Consensus pattern (27 bp):
CTGCTGCTGCAATTGCAACTGTTGTTG
Done.