Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002572.1 Hibiscus syriacus cultivar Beakdansim tig00005215_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: 126268
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6296 original size:14 final size:14
Alignment explanation
Indices: 6268--6304 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
6258 GTATTCAGAA
6268 TTATAA-TAAAAGT
1 TTATAACTAAAAGT
*
6281 TTATAACTATAAGT
1 TTATAACTAAAAGT
6295 TTA-AACTAAA
1 TTATAACTAAA
6305 CATATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (14 bp):
TTATAACTAAAAGT
Found at i:17169 original size:35 final size:35
Alignment explanation
Indices: 17037--17148 Score: 179
Period size: 35 Copynumber: 3.2 Consensus size: 35
17027 GTTGGTAGAA
* * *
17037 TAAGTTGAGAGGGGCATGGGACTCGAACCCAACGG
1 TAAGTAGAGAGGGGTATGGGACCCGAACCCAACGG
* *
17072 TAAGTAGAGAGGGGTATAGGACCCGAATCCAACGG
1 TAAGTAGAGAGGGGTATGGGACCCGAACCCAACGG
17107 TAAGTAGAGAGGGGTATGGGACCCGAACCCAACGG
1 TAAGTAGAGAGGGGTATGGGACCCGAACCCAACGG
17142 TAAGTAG
1 TAAGTAG
17149 GGATGAATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (35 bp):
TAAGTAGAGAGGGGTATGGGACCCGAACCCAACGG
Found at i:24281 original size:15 final size:15
Alignment explanation
Indices: 24257--24299 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
24247 ACATCACTAA
*
24257 ATTAATTTATAAAGT
1 ATTAAATTATAAAGT
24272 ATTAAATTATAAAGT
1 ATTAAATTATAAAGT
24287 ATTAAATATATAA
1 ATTAAAT-TATAA
24300 TTATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAGT
Found at i:26289 original size:9 final size:9
Alignment explanation
Indices: 26275--26309 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
26265 ATAGTCTTTT
26275 AAATTAAAA
1 AAATTAAAA
26284 AAATTAAAA
1 AAATTAAAA
*
26293 AAAGTAAAA
1 AAATTAAAA
*
26302 AATTTAAA
1 AAATTAAA
26310 GATGAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (9 bp):
AAATTAAAA
Found at i:26573 original size:13 final size:13
Alignment explanation
Indices: 26555--26579 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26545 ACTCATATTA
26555 ATATATATAATAT
1 ATATATATAATAT
26568 ATATATATAATA
1 ATATATATAATA
26580 AACCAATAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATATAATAT
Found at i:28733 original size:24 final size:25
Alignment explanation
Indices: 28697--28743 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
28687 TGTGTAATTA
* **
28697 AAAAAATTAAATATTTAATTACAAC
1 AAAAAACTAAATATCAAATTACAAC
28722 AAAAAACT-AATATCAAATTACA
1 AAAAAACTAAATATCAAATTACA
28744 CCATTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAAAACTAAATATCAAATTACAAC
Found at i:29147 original size:31 final size:31
Alignment explanation
Indices: 29109--29167 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
29099 TGTTCTTAAT
29109 ATTATCGATCCATTCGATTTTAATCCCTAAC
1 ATTATCGATCCATTCGATTTTAATCCCTAAC
* * *
29140 ATTATCGATCCGTTTGATTTTAGTCCCT
1 ATTATCGATCCATTCGATTTTAATCCCT
29168 CAGCTGTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (31 bp):
ATTATCGATCCATTCGATTTTAATCCCTAAC
Found at i:30014 original size:23 final size:23
Alignment explanation
Indices: 29932--30017 Score: 62
Period size: 23 Copynumber: 3.9 Consensus size: 23
29922 AGGTTTTATA
* *
29932 TTTAATTTTATATTATATT-TGAT
1 TTTAATATTATATTATATTAT-TT
29955 TTTAAT-TT-TA--ATATTATTT
1 TTTAATATTATATTATATTATTT
29974 TTTAA-A-TA-AGTTAAATATTATTT
1 TTTAATATTATA-TT--ATATTATTT
29997 TTTAATATTATATTATATTAT
1 TTTAATATTATATTATATTAT
30018 ATATATTAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 22
0.69 0.01 0.30
Matches are distributed among these distances:
18 2 0.04
19 11 0.22
20 1 0.02
21 2 0.04
22 2 0.04
23 27 0.53
24 1 0.02
25 4 0.08
26 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTAATATTATATTATATTATTT
Found at i:30048 original size:14 final size:12
Alignment explanation
Indices: 29933--30065 Score: 70
Period size: 12 Copynumber: 11.7 Consensus size: 12
29923 GGTTTTATAT
29933 TTAATTTT-ATA
1 TTAATTTTAATA
* *
29944 TT-ATATTTGATT
1 TTAAT-TTTAATA
29956 TTAATTTTAATA
1 TTAATTTTAATA
*
29968 TTATTTTTTAA-A
1 TTA-ATTTTAATA
* *
29980 -TAAGTTAAATA
1 TTAATTTTAATA
*
29991 TTATTTTTTAATA
1 TTA-ATTTTAATA
*
30004 TT-ATATT-ATA
1 TTAATTTTAATA
*
30014 TT-A-TAT-ATA
1 TTAATTTTAATA
30023 TTAATTTTAATA
1 TTAATTTTAATA
30035 TTAATTTTAA-A
1 TTAATTTTAATA
* * *
30046 ATAAATTAAATA
1 TTAATTTTAATA
30058 TTAATTTT
1 TTAATTTT
30066 TTTAATATTA
Statistics
Matches: 90, Mismatches: 21, Indels: 21
0.68 0.16 0.16
Matches are distributed among these distances:
9 6 0.07
10 13 0.14
11 21 0.23
12 34 0.38
13 16 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:30048 original size:67 final size:67
Alignment explanation
Indices: 29932--30082 Score: 218
Period size: 67 Copynumber: 2.3 Consensus size: 67
29922 AGGTTTTATA
* * * *
29932 TTTAATTTTATATTATATTTGATTTTAATTTTAATATTATTTTTTAAATAAGTTAAATATT-A-T
1 TTTAATATTATATTATATTTGATTTTAATTTTAATATTAATTTTAAAATAAATTAAATATTAATT
29995 TT
66 TT
29997 TTTAATATTATATTATATTAT-ATATATTAATTTTAATATTAATTTTAAAATAAATTAAATATTA
1 TTTAATATTATATTATATT-TGAT-T-TTAATTTTAATATTAATTTTAAAATAAATTAAATATTA
30061 ATTTT
63 ATTTT
30066 TTTAATATTATATTATA
1 TTTAATATTATATTATA
30083 GATATTTAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
65 20 0.26
66 2 0.03
67 34 0.44
68 1 0.01
69 20 0.26
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (67 bp):
TTTAATATTATATTATATTTGATTTTAATTTTAATATTAATTTTAAAATAAATTAAATATTAATT
TT
Found at i:30123 original size:26 final size:24
Alignment explanation
Indices: 30055--30123 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 24
30045 AATAAATTAA
* *
30055 ATATTAATTTTTTTAATATTATAT
1 ATATAAATTATTTTAATATTATAT
* *
30079 -TATAGA-TA-TTTAATTTTATAT
1 ATATAAATTATTTTAATATTATAT
30100 CATATAAATTATTTTATATATTAT
1 -ATATAAATTATTTTA-ATATTAT
30124 TAAAATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
21 12 0.35
22 1 0.03
23 9 0.26
24 2 0.06
25 4 0.12
26 6 0.18
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (24 bp):
ATATAAATTATTTTAATATTATAT
Found at i:30151 original size:20 final size:19
Alignment explanation
Indices: 30091--30152 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
30081 TAGATATTTA
*
30091 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
30110 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
30128 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
30148 ATTTT
1 ATTTT
30153 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:30670 original size:31 final size:31
Alignment explanation
Indices: 30617--30677 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
30607 GTAGTTGTAT
* * *
30617 AAATTATTTAAATTTTAATATTGTAAAACTA
1 AAATTATTTAAATCTCAATATTGCAAAACTA
*
30648 AAATTATTTAAATCTCAGTATTGCAAAACT
1 AAATTATTTAAATCTCAATATTGCAAAACT
30678 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (31 bp):
AAATTATTTAAATCTCAATATTGCAAAACTA
Found at i:31388 original size:2 final size:2
Alignment explanation
Indices: 31383--31417 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31373 GACGAAAATA
31383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31418 CAACGAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61842 original size:18 final size:19
Alignment explanation
Indices: 61815--61853 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
61805 TGATCTTAGT
61815 AATATAATA-TAATTTATA
1 AATATAATATTAATTTATA
*
61833 AATATTATATTAATTTATA
1 AATATAATATTAATTTATA
61852 AA
1 AA
61854 CAACTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATAATATTAATTTATA
Found at i:65799 original size:2 final size:2
Alignment explanation
Indices: 65792--65816 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65782 ATGCAGATGA
65792 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
65817 GTTTTGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67196 original size:60 final size:60
Alignment explanation
Indices: 67095--67207 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
67085 ATAGTTGGGT
* * * *
67095 GACCATTTTGTAACTTTTAATAGTTGAATGACTCAACAAAGTAATATCCTATAGTCAATG
1 GACCATTTTATAACTTTTAATAGTCGAATAACTCAACAAAGTAACATCCTATAGTCAATG
* * * *
67155 GACCATTTTATAATTTTTAATAGTCCG-ATAACTCGATAAAGTAACATCTTATA
1 GACCATTTTATAACTTTTAATAGT-CGAATAACTCAACAAAGTAACATCCTATA
67208 ATTAGAGATC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 43 0.98
61 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (60 bp):
GACCATTTTATAACTTTTAATAGTCGAATAACTCAACAAAGTAACATCCTATAGTCAATG
Found at i:69845 original size:18 final size:19
Alignment explanation
Indices: 69806--69849 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
69796 CTTTTATTGT
*
69806 TTATTAAAAAAGTAATAGA
1 TTATTAAAAAAGCAATAGA
69825 TTATTAAAATAA-CAATA-A
1 TTATTAAAA-AAGCAATAGA
69843 TTATTAA
1 TTATTAA
69850 TCAGTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 13 0.57
20 2 0.09
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
TTATTAAAAAAGCAATAGA
Found at i:75429 original size:31 final size:31
Alignment explanation
Indices: 75388--75476 Score: 134
Period size: 26 Copynumber: 3.0 Consensus size: 31
75378 ATTTTTTTCT
*
75388 TTACTGTCAGAGCGACAAGTGTTTTATTTTG
1 TTACTCTCAGAGCGACAAGTGTTTTATTTTG
75419 TTACTCTCAGAGCGACAAGTG----A-TTTG
1 TTACTCTCAGAGCGACAAGTGTTTTATTTTG
75445 TTACTCTCAGAGCGACAAGTGTTTTATTTTG
1 TTACTCTCAGAGCGACAAGTGTTTTATTTTG
75476 T
1 T
75477 GTTTCTAGGA
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
26 25 0.48
27 1 0.02
30 1 0.02
31 25 0.48
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (31 bp):
TTACTCTCAGAGCGACAAGTGTTTTATTTTG
Found at i:80478 original size:108 final size:108
Alignment explanation
Indices: 80301--80517 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
80291 ATATAATATC
80301 ATTAAATTTTAATAGGAATATCTTTTCAAGAAATTATATCTAAATTCTCCATTTAATAGGCACAC
1 ATTAAATTTTAATAGGAATATCTTTTCAAGAAATTATATCTAAATTCTCCATTTAATAGGCACAC
80366 GTGTTTAGAGTTTGATCCATTTATTTTAGGTAAATACCACATT
66 GTGTTTAGAGTTTGATCCATTTATTTTAGGTAAATACCACATT
80409 ATTAAATTTTAATAGGAATATCTTTTCAAGAAATTATATCTAAATTCTCCATTTAATAGGCACAC
1 ATTAAATTTTAATAGGAATATCTTTTCAAGAAATTATATCTAAATTCTCCATTTAATAGGCACAC
80474 GTGTTTAGAGTTTGATCCATTTATTTTAGGTAAATACCACATT
66 GTGTTTAGAGTTTGATCCATTTATTTTAGGTAAATACCACATT
80517 A
1 A
80518 GGTCTAAGTT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (108 bp):
ATTAAATTTTAATAGGAATATCTTTTCAAGAAATTATATCTAAATTCTCCATTTAATAGGCACAC
GTGTTTAGAGTTTGATCCATTTATTTTAGGTAAATACCACATT
Found at i:82274 original size:29 final size:30
Alignment explanation
Indices: 82220--82290 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
82210 CTCTTTTAGG
* *
82220 TATTCTTATATTCTATCAACTAAATA-T-T
1 TATTCTTATATTTTATCAACCAAATACTAT
*
82248 TATATCTTATATTTTATCAACCGAATACTAT
1 TAT-TCTTATATTTTATCAACCAAATACTAT
82279 TATT-TTATATTT
1 TATTCTTATATTT
82291 CAATTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.08
29 28 0.76
30 2 0.05
31 4 0.11
ACGTcount: A:0.34, C:0.13, G:0.01, T:0.52
Consensus pattern (30 bp):
TATTCTTATATTTTATCAACCAAATACTAT
Found at i:83569 original size:19 final size:19
Alignment explanation
Indices: 83535--83583 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
83525 AAAACGTTTT
*
83535 TATGAACAATAATAT-ATGG
1 TATGAACAGTAATATAAT-G
* *
83554 TTTGAACAGTATTATAATG
1 TATGAACAGTAATATAATG
83573 TATGAACAGTA
1 TATGAACAGTA
83584 CTATGAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (19 bp):
TATGAACAGTAATATAATG
Found at i:84228 original size:23 final size:23
Alignment explanation
Indices: 84202--84246 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
84192 CACCACAGCT
*
84202 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
84225 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
84247 ATATAATAAT
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:84908 original size:19 final size:20
Alignment explanation
Indices: 84871--84908 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
84861 TTTTTATATA
*
84871 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
84891 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
84909 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:84959 original size:21 final size:21
Alignment explanation
Indices: 84935--84976 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
84925 TTCATATTCG
* *
84935 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
84956 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
84977 CAGCCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:91041 original size:23 final size:23
Alignment explanation
Indices: 91015--91059 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
91005 CACCACAGCT
*
91015 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
91038 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
91060 ATATAATAAT
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:91722 original size:19 final size:20
Alignment explanation
Indices: 91685--91722 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
91675 TTTTTTTATA
*
91685 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
91705 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
91723 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:91773 original size:21 final size:21
Alignment explanation
Indices: 91749--91790 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
91739 TTCATATTCG
* *
91749 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
91770 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
91791 CAGCCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:93411 original size:32 final size:32
Alignment explanation
Indices: 93365--93488 Score: 196
Period size: 32 Copynumber: 3.9 Consensus size: 32
93355 TATAGGTAAC
93365 TGTCCATATGTCCCGAAAGACATAGGTAAT-T
1 TGTCCATATGTCCCGAAAGACATAGGTAATAT
* *
93396 CTGTCTATATATCCCGAAAGACATAGGTAATAT
1 -TGTCCATATGTCCCGAAAGACATAGGTAATAT
*
93429 TGTCCATATGTCCCGAAAGACATAAGTAATAT
1 TGTCCATATGTCCCGAAAGACATAGGTAATAT
*
93461 TGCCCATATGTCCCGAAAGACATAGGTA
1 TGTCCATATGTCCCGAAAGACATAGGTA
93489 CTCCCTCGAC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 83 0.99
33 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAAGACATAGGTAATAT
Found at i:94280 original size:31 final size:30
Alignment explanation
Indices: 94212--94280 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
94202 TACTCTAATT
* * *
94212 TTTCCTTTCTTGAACTAAAGAAAGTGTTAC
1 TTTCATTTCTTGAACTAAAGAAAGTCTTAA
*
94242 TTTCATTTCTTGGACTAAACGAAAAG-CTTAA
1 TTTCATTTCTTGAACTAAA-G-AAAGTCTTAA
94273 TTTCATTT
1 TTTCATTT
94281 TCTCTTATGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 17 0.52
31 12 0.36
32 4 0.12
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (30 bp):
TTTCATTTCTTGAACTAAAGAAAGTCTTAA
Found at i:106859 original size:15 final size:16
Alignment explanation
Indices: 106839--106868 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
106829 ATTCACATAA
106839 ATAATTTAAA-ATTTC
1 ATAATTTAAAGATTTC
106854 ATAATTTAAAGATTT
1 ATAATTTAAAGATTT
106869 TTATATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAATTTAAAGATTTC
Found at i:114192 original size:18 final size:19
Alignment explanation
Indices: 114171--114224 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 19
114161 TAAAATATTT
*
114171 TAAATGCTTT-TTATATAA
1 TAAATGCTTTATTATAAAA
*
114189 TAAA-GTTTTATTATAAAA
1 TAAATGCTTTATTATAAAA
*
114207 TAAAT--TTTATTACAAAA
1 TAAATGCTTTATTATAAAA
114224 T
1 T
114225 GAATATTGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (19 bp):
TAAATGCTTTATTATAAAA
Found at i:114216 original size:17 final size:18
Alignment explanation
Indices: 114181--114224 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
114171 TAAATGCTTT
*
114181 TTATATAATAAAGTTTTA
1 TTATAAAATAAAGTTTTA
114199 TTATAAAATAAA-TTTTA
1 TTATAAAATAAAGTTTTA
*
114216 TTACAAAAT
1 TTATAAAAT
114225 GAATATTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TTATAAAATAAAGTTTTA
Found at i:116045 original size:18 final size:18
Alignment explanation
Indices: 116025--116083 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
116015 TTTTATTGAG
*
116025 AATAAAAGATTACCAGAG
1 AATAAAAGATTACCAGAA
116043 AATAAAAGATTACCAGAA
1 AATAAAAGATTACCAGAA
*
116061 AATAAAAGATTATCAGAA
1 AATAAAAGATTACCAGAA
116079 AATAA
1 AATAA
116084 GATTACTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.19
Consensus pattern (18 bp):
AATAAAAGATTACCAGAA
Found at i:118826 original size:36 final size:36
Alignment explanation
Indices: 118779--118892 Score: 147
Period size: 36 Copynumber: 3.1 Consensus size: 36
118769 TATTCATCAG
*
118779 CATGCCCGGATTCATACCCATGTTCATCTCCACTCC
1 CATGCCCGGATTCATACCCATGTTCATCCCCACTCC
* * *
118815 CATGCCTGGATTCATACCCATGTTCATCCCCATTTC
1 CATGCCCGGATTCATACCCATGTTCATCCCCACTCC
* *
118851 CATGCCCGGATTCATACTCATGTGGTTCATCCCCATTCC
1 CATGCCCGGATTCATACCCA--T-GTTCATCCCCACTCC
118890 CAT
1 CAT
118893 AGGCTGTTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 50 0.74
38 1 0.01
39 17 0.25
ACGTcount: A:0.19, C:0.38, G:0.12, T:0.31
Consensus pattern (36 bp):
CATGCCCGGATTCATACCCATGTTCATCCCCACTCC
Found at i:120119 original size:33 final size:33
Alignment explanation
Indices: 119704--120408 Score: 488
Period size: 33 Copynumber: 21.4 Consensus size: 33
119694 CTTGCTTGGA
* * *
119704 CAGGTTGGCAATGTGGGTTAGCATTTGGCTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * * *
119737 -TGAGTTGGCCGTTTGGGTTAGTATTTGGCTGTG
1 CAG-GTTGGCCATTTGGATTAGCATTTGGCTGTG
* * *
119770 CAGGTTGACCATTGGGATTAGCATTTGGCAGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* ** *
119803 CTGGTTCTCCATATT-GATTAGCATTTGGATGTG
1 CAGGTTGGCCAT-TTGGATTAGCATTTGGCTGTG
* ** **
119836 -TGAGTTGGCCATTCAGATTAGTGTTTGGCTGTG
1 CAG-GTTGGCCATTTGGATTAGCATTTGGCTGTG
* * *
119869 CAGGTAGGTCATATGGATTAGCATTTGGCTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * *
119902 CAGGTTGGCCATATGGATTAGCACTTGGTTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* ** *
119935 CAGGTTGGACATAGGGATTAGCATTTTGCTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * *
119968 CAGGCTGGCCATTTGGATTAGCATTTAGCTGCG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
** *
120001 TGGGTCT-GCCATTTGGATTAGCATTTGGCTGGG
1 CAGGT-TGGCCATTTGGATTAGCATTTGGCTGTG
* *
120034 CAGGTTGGCCATTTGGATTAGCAGTTGACTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * **
120067 CTGGTTGACCATAGGGATTAGCATTTGGCTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * ** *
120100 TC-GGATGGCCATTTAGATTAGTGTTTGGTTGTG
1 -CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* ** * * **
120133 CAGGTTGGACATAGGGACTAGCATTTGACTGCA
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * * *
120166 CGGGTTGACCGTTTGGATTAGCATTTGACTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * ** *
120199 CCGGTTGACCATAGGGATTAGCATTTTGCTGAATG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTG--TG
*
120234 --GGTTGGCCATTTGGATTAGCATTTGCCTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
** ** **
120265 CAGGTTGGCCATAGGGATTTTCATTTGGAAGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
** * * *
120298 TGGGTTGGCCATATGGATCAGCATTTGGCTGCG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * ** * ** * *
120331 TAGGTTGGCTATAAGGATTAACGCTTGACAGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * * * * **
120364 CAGATTGGCCATATGCATTAGGACTTGGCTGCC
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
120397 CAGGTTGGCCAT
1 CAGGTTGGCCAT
120409 ACATATTAGC
Statistics
Matches: 516, Mismatches: 142, Indels: 28
0.75 0.21 0.04
Matches are distributed among these distances:
31 2 0.00
32 6 0.01
33 501 0.97
34 5 0.01
35 2 0.00
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.34
Consensus pattern (33 bp):
CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
Found at i:124946 original size:12 final size:12
Alignment explanation
Indices: 124929--124953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
124919 GAAAAAAAGT
124929 AGACAACATTTG
1 AGACAACATTTG
124941 AGACAACATTTG
1 AGACAACATTTG
124953 A
1 A
124954 TAATTTTATT
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (12 bp):
AGACAACATTTG
Done.