Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003562.1 Hibiscus syriacus cultivar Beakdansim tig00007520_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: 104616
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1402 original size:21 final size:23
Alignment explanation
Indices: 1376--1428 Score: 92
Period size: 21 Copynumber: 2.4 Consensus size: 23
1366 GTCAACAATA
1376 AAAGTCAACATCGGTC-ATGATC
1 AAAGTCAACATCGGTCAATGATC
1398 -AAGTCAACATCGGTCAATGATC
1 AAAGTCAACATCGGTCAATGATC
1420 AAAGTCAAC
1 AAAGTCAAC
1429 TTTAGTCAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.52
22 6 0.21
23 8 0.28
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (23 bp):
AAAGTCAACATCGGTCAATGATC
Found at i:1436 original size:23 final size:23
Alignment explanation
Indices: 1376--1444 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
1366 GTCAACAATA
*
1376 AAAGTCAACATCGGTC-ATGATC
1 AAAGTCAACATCAGTCAATGATC
*
1398 -AAGTCAACATCGGTCAATGATC
1 AAAGTCAACATCAGTCAATGATC
* * *
1420 AAAGTCAACTTTAGTCAACGATC
1 AAAGTCAACATCAGTCAATGATC
1443 AA
1 AA
1445 CAATAATCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
21 15 0.37
22 6 0.15
23 20 0.49
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (23 bp):
AAAGTCAACATCAGTCAATGATC
Found at i:4950 original size:55 final size:55
Alignment explanation
Indices: 4903--5267 Score: 404
Period size: 55 Copynumber: 6.7 Consensus size: 55
4893 TTCAAATGAT
* * * * *
4903 AAGTCTGCTCCCTATTCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAATAAAC
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAAC
** * * * *
4958 GGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCAAACAATCTTCATA-AAAT
1 AAGTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAAC
**
5013 GGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
* * *
5068 GAGTCCACTCTCTATTCCTTAAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
* * *
5123 AGGTTCGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
** *
5178 GGGTCCGCTCTCTATTCCTTCAGAGAGTATA-AGACTCG----ATCTTCAATAAAC
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAAC
** * *
5229 GTGTCCGCTCACTATTCCTTCAGAGAGTATAGGACTCGA
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGA
5268 TATTCAACAA
Statistics
Matches: 276, Mismatches: 26, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
51 46 0.17
54 5 0.02
55 220 0.80
56 5 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (55 bp):
AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
Found at i:5096 original size:110 final size:109
Alignment explanation
Indices: 4909--5302 Score: 461
Period size: 110 Copynumber: 3.7 Consensus size: 109
4899 TGATAAGTCT
* * * * *
4909 GCTCCCTATTCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAATAAACGGGTCCGCTCCCTA-
1 GCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTAT
* *
4972 TCCGTTCAGGGAGTATAGAACTCAAACAATCTTCATA-AAATGGGTCC
65 TCC-TTCAGAGAGTATAGAACTC-AACAATCTTCA-ACAAACGGGTCC
* *
5019 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGAGTCCACTCTCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATT
* * *
5084 CCTTAAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTTC
66 CCTTCAGAGAGTATAGAACTC-AACAATCTTCAACAAACGGGTCC
*
5129 GCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATT
* * *
5194 CCTTCAGAGAGTATA-AGACT---CGATCTTCAATAAACGTGTCC
66 CCTTCAGAGAGTATAGA-ACTCAACAATCTTCAACAAACGGGTCC
* * * *
5235 GCTCACTATTCCTTCAGAGAGTATAGGACTCG----ATATTCAACAAACGTGTCCGCTC-CTTAT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTC-TAT
5295 TCCTTCAG
65 TCCTTCAG
5303 TGTATGGAAC
Statistics
Matches: 252, Mismatches: 27, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
101 1 0.00
102 32 0.13
106 45 0.18
109 2 0.01
110 168 0.67
111 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (109 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTCAACAATCTTCAACAAACGGGTCC
Found at i:5167 original size:165 final size:161
Alignment explanation
Indices: 4914--5267 Score: 471
Period size: 165 Copynumber: 2.2 Consensus size: 161
4904 AGTCTGCTCC
* * * *
4914 CTATTCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAATAAACGGGTCCGCTCCCTATCCGTT
1 CTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTATCCGTT
* *
4978 CAGGGAGTATAGAACTCAAACAATCTTCATA-AAATGGGTCCGCTCTCTATTCCTTCAGAGAGTA
65 CAGAGAGTATAGAACTCAAACAATCTTCA-ACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTA
*
5042 T-AGAACTCGAACAATCTTCAACAAACGAGTCCACTCT
129 TAAG-ACTCG----ATCTTCAACAAACGAGTCCACTCA
* * * * *
5079 CTATTCCTTAAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTTCGCTCTCTATTCTTTC
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTATCCGTTC
*
5144 AGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
66 AGAGAGTATAGAACTCAAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
* * *
5209 AGACTCGATCTTCAATAAACGTGTCCGCTCA
131 AGACTCGATCTTCAACAAACGAGTCCACTCA
*
5240 CTATTCCTTCAGAGAGTATAGGACTCGA
1 CTATTCCTTCAGAGAGTATAGAACTCGA
5268 TATTCAACAA
Statistics
Matches: 168, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
161 46 0.27
164 1 0.01
165 118 0.70
166 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (161 bp):
CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTATCCGTTC
AGAGAGTATAGAACTCAAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
AGACTCGATCTTCAACAAACGAGTCCACTCA
Found at i:5367 original size:54 final size:54
Alignment explanation
Indices: 5304--5760 Score: 770
Period size: 54 Copynumber: 8.5 Consensus size: 54
5294 TTCCTTCAGT
* * *
5304 GTATGGAACTCAAACATCTTCTTCTTATGGGTTCGCTCCCTCTTTATCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
* *
5358 GTATGGAACTCGAACATCTTCTTCTTACGGATTTGCTCCCTCTTTCTCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
*
5412 GTATGGAACTCGAGCATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
* * *
5466 GTATGGAACTCAAACATATTCTTCTTACAGGTTCGCTCCCTCTTTCTCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
*
5520 GTATGGAACTCGAATATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
*
5574 GTATGGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
* *
5628 GTATGGAACTCGAACATCTTCTTCTTATGGGTTCGCTCCCTCTTTCTCTAGAGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
* * *
5682 GTATGAAACTCGAACATCTTCTTCTTACGGGTTCGCTCCTTCTTTCTTTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
5736 GTATGGAACTCGAACATCTTCTTCT
1 GTATGGAACTCGAACATCTTCTTCT
5761 GCTTTACTAC
Statistics
Matches: 376, Mismatches: 27, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 376 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37
Consensus pattern (54 bp):
GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
Found at i:6188 original size:37 final size:37
Alignment explanation
Indices: 6137--6260 Score: 144
Period size: 37 Copynumber: 3.4 Consensus size: 37
6127 TTGCTCCAAC
* * * *
6137 ACTCTTCCGAGAAGGCTTAAAAAGGATATT-ATTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGAT-TTGCTTCACT
*
6174 ACTCTTCGGTGAAGGCTTAAGATGG-TTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
* * *
6210 ACTCTTTGGTGAAGGCTCAAAATGGATTTGCTTCATT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
*
6247 ACTCTTTGGTGAAG
1 ACTCTTCGGTGAAG
6261 ACTTGACTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
35 2 0.03
36 29 0.38
37 45 0.59
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
Found at i:6215 original size:36 final size:37
Alignment explanation
Indices: 6168--6260 Score: 143
Period size: 36 Copynumber: 2.5 Consensus size: 37
6158 AAGGATATTA
* * *
6168 TTCACTACTCTTCGGTGAAGGCTTAAGATGG-TTTGC
1 TTCACTACTCTTTGGTGAAGGCTCAAAATGGATTTGC
6204 TTCACTACTCTTTGGTGAAGGCTCAAAATGGATTTGC
1 TTCACTACTCTTTGGTGAAGGCTCAAAATGGATTTGC
*
6241 TTCATTACTCTTTGGTGAAG
1 TTCACTACTCTTTGGTGAAG
6261 ACTTGACTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 28 0.54
37 24 0.46
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (37 bp):
TTCACTACTCTTTGGTGAAGGCTCAAAATGGATTTGC
Found at i:10971 original size:70 final size:70
Alignment explanation
Indices: 10858--10999 Score: 239
Period size: 70 Copynumber: 2.0 Consensus size: 70
10848 CCCTAATAGG
* *
10858 TTCTTGATAAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTTT
1 TTCTTGATAAGTTACTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCT
10923 TCATA
66 TCATA
* * *
10928 TTCTTGATCATTTACTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTCT
1 TTCTTGATAAGTTACTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCT
10993 TCATA
66 TCATA
10998 TT
1 TT
11000 TTCTTGTGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (70 bp):
TTCTTGATAAGTTACTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCT
TCATA
Found at i:15266 original size:20 final size:20
Alignment explanation
Indices: 15241--15278 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
15231 TTTGGTTCAC
15241 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
15261 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
15279 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:17282 original size:60 final size:59
Alignment explanation
Indices: 17171--17283 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
17161 ATAGTTTAAG
* * * *
17171 GATGAAATTAAAATGTTCTAAAATTAAAAATTAATTTGAAATGAAACTCATAATTTAGA
1 GATGAAATTAAAATATTCAAAAATTAAAAATTAATTTAAAATGAAAATCATAATTTAGA
* *
17230 GATGAAATTATAATATTCAAAAGATTAAAGATTAATTTAAAAT-AAAGATCATAA
1 GATGAAATTAAAATATTCAAAA-ATTAAAAATTAATTTAAAATGAAA-ATCATAA
17284 GATTCAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 22 0.48
60 24 0.52
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (59 bp):
GATGAAATTAAAATATTCAAAAATTAAAAATTAATTTAAAATGAAAATCATAATTTAGA
Found at i:18013 original size:2 final size:2
Alignment explanation
Indices: 18006--18045 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
17996 TAGGTGTTTA
18006 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
18046 TACTATCTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23375 original size:74 final size:73
Alignment explanation
Indices: 23254--23403 Score: 264
Period size: 74 Copynumber: 2.0 Consensus size: 73
23244 AGAGTAATTA
*
23254 TCTGTTAAACTCATATGTATTATGTAAGATTGGTTACATATTTATATACAAGCTATAACCTTAAC
1 TCTGTCAAACTCATATGTATTATGTAAGATTGGTTACATATTTATATACAAGCTATAACCTTAAC
23319 TTAGAAAAC
66 TTAG-AAAC
* *
23328 TCTGTCAAACTCATATGTATTTTGTAAGATTTGTTACATATTTATATACAAGCTATAACCTTAAC
1 TCTGTCAAACTCATATGTATTATGTAAGATTGGTTACATATTTATATACAAGCTATAACCTTAAC
23393 TTAGAAAC
66 TTAGAAAC
23401 TCT
1 TCT
23404 TAAGTTAGGA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 7 0.10
74 66 0.90
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (73 bp):
TCTGTCAAACTCATATGTATTATGTAAGATTGGTTACATATTTATATACAAGCTATAACCTTAAC
TTAGAAAC
Found at i:33136 original size:95 final size:96
Alignment explanation
Indices: 33014--33204 Score: 323
Period size: 95 Copynumber: 2.0 Consensus size: 96
33004 CCACAAACAC
*
33014 CCCCCTCCCCCCCACACACACAAAGTTGGAATCTGTCTGCACTGTATTTCTGCTGCTATCATTTG
1 CCCCCACCCCCCCACACACACAAAGTTGGAATCTGTCTGCACTGTATTTCTGCTGCTATCATTTG
33079 TAGATTTGCTATCACTCTTGTTGAATCATAT
66 TAGATTTGCTATCACTCTTGTTGAATCATAT
* * *
33110 CCCCCACCCCCTCC-CA-ACACACAGTTGGCATCTGTCTGCACTGTATTTCTGCTGTTATCATTT
1 CCCCCACCCCC-CCACACACACAAAGTTGGAATCTGTCTGCACTGTATTTCTGCTGCTATCATTT
33173 GTAGATTTGCTATCACTCTTGTTGAATCATAT
65 GTAGATTTGCTATCACTCTTGTTGAATCATAT
33205 TCTTTTCAGG
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
95 76 0.84
96 12 0.13
97 2 0.02
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (96 bp):
CCCCCACCCCCCCACACACACAAAGTTGGAATCTGTCTGCACTGTATTTCTGCTGCTATCATTTG
TAGATTTGCTATCACTCTTGTTGAATCATAT
Found at i:39522 original size:13 final size:13
Alignment explanation
Indices: 39504--39555 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
39494 ATTTTAAGAT
39504 TTTTGAAATCAAG
1 TTTTGAAATCAAG
* *
39517 TTTTGAAATTAGAAAAA
1 TTTTGAAA-T---CAAG
39534 TTTTGAAATCAAG
1 TTTTGAAATCAAG
39547 TTTTGAAAT
1 TTTTGAAAT
39556 TAAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 19 0.61
14 1 0.03
16 1 0.03
17 10 0.32
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (13 bp):
TTTTGAAATCAAG
Found at i:39539 original size:30 final size:30
Alignment explanation
Indices: 39504--39563 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
39494 ATTTTAAGAT
*
39504 TTTTGAAATCAAGTTTTGAAATTAGAAAAA
1 TTTTGAAATCAAGTTTTGAAATTAAAAAAA
39534 TTTTGAAATCAAGTTTTGAAATTAAAAAAA
1 TTTTGAAATCAAGTTTTGAAATTAAAAAAA
39564 AATGAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.37
Consensus pattern (30 bp):
TTTTGAAATCAAGTTTTGAAATTAAAAAAA
Found at i:39571 original size:29 final size:30
Alignment explanation
Indices: 39507--39571 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
39497 TTAAGATTTT
***
39507 TGAAATCAAGTTTTGAAATTAGAAAAATTT
1 TGAAATCAAGTTTTGAAATTAGAAAAAAAA
39537 TGAAATCAAGTTTTGAAATTA-AAAAAAAA
1 TGAAATCAAGTTTTGAAATTAGAAAAAAAA
39566 TGAAAT
1 TGAAAT
39572 TAGAAATTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.32
Consensus pattern (30 bp):
TGAAATCAAGTTTTGAAATTAGAAAAAAAA
Found at i:41867 original size:21 final size:20
Alignment explanation
Indices: 41837--41917 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 20
41827 GAACCCCCAT
*
41837 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCT-TG
* *
41858 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTT---G
*
41881 GGGGGAATCGGTTCCCTCATTG
1 GGGGGAATCGATTCCC-C-TTG
41903 GGGGG-ATCGATTCCC
1 GGGGGAATCGATTCCC
41918 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.02
21 25 0.50
22 5 0.10
23 16 0.32
24 1 0.02
25 2 0.04
ACGTcount: A:0.15, C:0.25, G:0.36, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTTG
Found at i:52313 original size:64 final size:63
Alignment explanation
Indices: 52192--52332 Score: 153
Period size: 64 Copynumber: 2.2 Consensus size: 63
52182 CATATTCAAT
* *
52192 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAATGCAATTAGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTAAAAGAAGAAACATCGAAGGCAATTAGTGCATCGATGCAT-AGGTA
* * * * * *
52255 GTGCATTGATGCATCCCCTTAAAATGAA-AAA-ATCGAAGGTAATTTGTGTATCGTTGCATGGGT
1 GTGCATCGATGCA--CCCTTAAAA-GAAGAAACATCGAAGGCAATTAGTGCATCGATGCATAGGT
52318 A
63 A
52319 GTGCATCGATGCAC
1 GTGCATCGATGCAC
52333 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
62 1 0.02
63 14 0.22
64 36 0.55
65 11 0.17
66 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTAAAAGAAGAAACATCGAAGGCAATTAGTGCATCGATGCATAGGTA
Found at i:52347 original size:24 final size:24
Alignment explanation
Indices: 52320--52400 Score: 134
Period size: 24 Copynumber: 3.5 Consensus size: 24
52310 GCATGGGTAG
52320 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
52344 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
52368 TGCATCGATGCAC-TG-T--AGAA
1 TGCATCGATGCACATGTTAAAGAA
52388 TGCATCGATGCAC
1 TGCATCGATGCAC
52401 TTCAAGGGGA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
20 17 0.30
22 1 0.02
23 2 0.04
24 37 0.65
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAAGAA
Found at i:54486 original size:21 final size:21
Alignment explanation
Indices: 54462--54505 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
54452 GATACGTTAC
54462 TATGTTAATGTTTAATATCTA
1 TATGTTAATGTTTAATATCTA
54483 TATGTTAATGTTTAATATCTA
1 TATGTTAATGTTTAATATCTA
54504 TA
1 TA
54506 AATTAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (21 bp):
TATGTTAATGTTTAATATCTA
Found at i:54511 original size:21 final size:21
Alignment explanation
Indices: 54466--54512 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
54456 CGTTACTATG
**
54466 TTAATGTTTAATATCTATATG
1 TTAATGTTTAATATCTATAAA
54487 TTAATGTTTAATATCTATAAA
1 TTAATGTTTAATATCTATAAA
54508 TTAAT
1 TTAAT
54513 TAATTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (21 bp):
TTAATGTTTAATATCTATAAA
Found at i:67662 original size:4 final size:4
Alignment explanation
Indices: 67653--67728 Score: 55
Period size: 4 Copynumber: 19.0 Consensus size: 4
67643 ACGAGTGTGT
* * * * *
67653 GGTA GGTA GGTA GGCA GGTA GGTA GGTA -GTCA GGCA GGCA GGCA GGCA
1 GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGT-A GGTA GGTA GGTA GGTA
* * * *
67701 AGTA GGCA GGCA GGCA GGTA GGTA GGTA
1 GGTA GGTA GGTA GGTA GGTA GGTA GGTA
67729 AGTTTTCCCA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 2 0.03
4 59 0.95
5 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.47, T:0.14
Consensus pattern (4 bp):
GGTA
Found at i:67666 original size:8 final size:8
Alignment explanation
Indices: 67653--67728 Score: 80
Period size: 8 Copynumber: 9.5 Consensus size: 8
67643 ACGAGTGTGT
*
67653 GGTAGGTA
1 GGTAGGCA
67661 GGTAGGCA
1 GGTAGGCA
*
67669 GGTAGGTA
1 GGTAGGCA
*
67677 GGTAGTCA
1 GGTAGGCA
*
67685 GGCAGGCA
1 GGTAGGCA
*
67693 GGCAGGCA
1 GGTAGGCA
*
67701 AGTAGGCA
1 GGTAGGCA
*
67709 GGCAGGCA
1 GGTAGGCA
*
67717 GGTAGGTA
1 GGTAGGCA
67725 GGTA
1 GGTA
67729 AGTTTTCCCA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 56 1.00
ACGTcount: A:0.26, C:0.12, G:0.47, T:0.14
Consensus pattern (8 bp):
GGTAGGCA
Found at i:67674 original size:16 final size:16
Alignment explanation
Indices: 67653--67728 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 16
67643 ACGAGTGTGT
67653 GGTAGGTAGGTAGGCA
1 GGTAGGTAGGTAGGCA
*
67669 GGTAGGTAGGTAGTCA
1 GGTAGGTAGGTAGGCA
* * *
67685 GGCAGGCAGGCAGGCA
1 GGTAGGTAGGTAGGCA
* * *
67701 AGTAGGCAGGCAGGCA
1 GGTAGGTAGGTAGGCA
67717 GGTAGGTAGGTA
1 GGTAGGTAGGTA
67729 AGTTTTCCCA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.12, G:0.47, T:0.14
Consensus pattern (16 bp):
GGTAGGTAGGTAGGCA
Found at i:68697 original size:24 final size:24
Alignment explanation
Indices: 68669--68732 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
68659 CATCGATGCA
*
68669 TAAGGAGTGCATCGATGCACATGT
1 TAAGGAGTGCATCGATGCACATGG
*
68693 TAAGG-GATGCATTGAT--ACATGG
1 TAAGGAG-TGCATCGATGCACATGG
68715 T-AGGA-TGCATCGATGCAC
1 TAAGGAGTGCATCGATGCAC
68733 TTCAAGGGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
20 8 0.24
21 3 0.09
22 8 0.24
23 1 0.03
24 13 0.39
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (24 bp):
TAAGGAGTGCATCGATGCACATGG
Found at i:69770 original size:5 final size:5
Alignment explanation
Indices: 69762--69804 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
69752 GTGTGATAGC
69762 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATG
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATG
69805 TTCATGCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.40
Consensus pattern (5 bp):
ATGAT
Found at i:74507 original size:23 final size:23
Alignment explanation
Indices: 74481--74525 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
74471 CACCACAGCT
*
74481 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
74504 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
74526 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:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:75820 original size:18 final size:18
Alignment explanation
Indices: 75797--75831 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
75787 TCCCATCTAG
75797 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
75815 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
75832 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:76440 original size:21 final size:21
Alignment explanation
Indices: 76410--76454 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
76400 ATTCTGTCGT
* *
76410 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
76431 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
76452 TTG
1 TTG
76455 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:92876 original size:21 final size:21
Alignment explanation
Indices: 92847--92901 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
92837 TAAGACTATT
* *
92847 ATTGTTCTTATTCCCAAAGTG
1 ATTGATCTTACTCCCAAAGTG
92868 ATTGATCTTACTCCCAAAGTG
1 ATTGATCTTACTCCCAAAGTG
92889 ATTGATCTTACTC
1 ATTGATCTTACTC
92902 GTATAAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (21 bp):
ATTGATCTTACTCCCAAAGTG
Found at i:93894 original size:21 final size:21
Alignment explanation
Indices: 93870--93910 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
93860 AGTTATTGGT
93870 AGTCAGGTAATACTTATAAGC
1 AGTCAGGTAATACTTATAAGC
*
93891 AGTCAGGTAATACTTCTAAG
1 AGTCAGGTAATACTTATAAG
93911 TGTGGATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (21 bp):
AGTCAGGTAATACTTATAAGC
Found at i:97341 original size:33 final size:33
Alignment explanation
Indices: 97298--97361 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
97288 TAATCTCATA
*
97298 AAATCTATGAATCTCCAAGAACCTTAAAGCCAT
1 AAATCCATGAATCTCCAAGAACCTTAAAGCCAT
97331 AAATCCATGAATCTCCAAGAACCTTAAAGCC
1 AAATCCATGAATCTCCAAGAACCTTAAAGCC
97362 TATTAACACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.27, G:0.09, T:0.22
Consensus pattern (33 bp):
AAATCCATGAATCTCCAAGAACCTTAAAGCCAT
Done.