Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006239.1 Hibiscus syriacus cultivar Beakdansim tig00014867_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: 85424
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:409 original size:18 final size:17
Alignment explanation
Indices: 355--418 Score: 101
Period size: 17 Copynumber: 3.7 Consensus size: 17
345 ATATGGAATT
355 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
*
372 GATTCTAATTCCTGACA
1 GATTCCAATTCCTGACA
*
389 GATTCCAATTCCTTCACA
1 GATTCCAATTCC-TGACA
407 GATTCCAATTCC
1 GATTCCAATTCC
419 CTCAAAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
17 27 0.63
18 16 0.37
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:1066 original size:9 final size:9
Alignment explanation
Indices: 1046--1095 Score: 57
Period size: 9 Copynumber: 5.2 Consensus size: 9
1036 TATATAACTA
1046 ATATAAAA-
1 ATATAAAAT
1054 ATATAAAAT
1 ATATAAAAT
1063 ATATATATAATT
1 ATATA-A-AA-T
1075 AATATAAAAT
1 -ATATAAAAT
1085 ATATAAAAT
1 ATATAAAAT
1094 AT
1 AT
1096 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 8 0.22
9 16 0.43
10 2 0.05
11 4 0.11
12 2 0.05
13 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATATAAAAT
Found at i:1071 original size:30 final size:32
Alignment explanation
Indices: 1028--1103 Score: 120
Period size: 30 Copynumber: 2.4 Consensus size: 32
1018 CCCGAACCCG
*
1028 AAATATTTTATATAACTAATATAAAA-ATATA
1 AAATATTATATATAACTAATATAAAATATATA
*
1059 AAATA-TATATATAATTAATATAAAATATATA
1 AAATATTATATATAACTAATATAAAATATATA
1090 AAATATTATATATA
1 AAATATTATATATA
1104 TAATCGGGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 18 0.44
31 15 0.37
32 8 0.20
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATATTATATATAACTAATATAAAATATATA
Found at i:6804 original size:23 final size:24
Alignment explanation
Indices: 6751--6797 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6741 AATGAATGTA
* *
6751 CTACAAGAGCATAGAAAACACATG
1 CTACAAGAGAAGAGAAAACACATG
6775 CTACAAGAGAAGAGAAAA-ACATG
1 CTACAAGAGAAGAGAAAACACATG
6798 TCACAAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.53, C:0.17, G:0.19, T:0.11
Consensus pattern (24 bp):
CTACAAGAGAAGAGAAAACACATG
Found at i:8127 original size:20 final size:20
Alignment explanation
Indices: 8102--8145 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
8092 TCCCTTTTTA
*
8102 TCTTGTTCGGATT-ACGATTT
1 TCTTGTCCGGATTGA-GATTT
*
8122 TCTTGTCCGGGTTGAGATTT
1 TCTTGTCCGGATTGAGATTT
8142 TCTT
1 TCTT
8146 TCGTTTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TCTTGTCCGGATTGAGATTT
Found at i:9473 original size:15 final size:15
Alignment explanation
Indices: 9453--9487 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
9443 CAAAGACAAT
9453 AAATCCGATG-GCAAG
1 AAATCCGATGCG-AAG
9468 AAATCCGATGCGAAG
1 AAATCCGATGCGAAG
9483 AAATC
1 AAATC
9488 TGATAAGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (15 bp):
AAATCCGATGCGAAG
Found at i:12977 original size:122 final size:122
Alignment explanation
Indices: 12758--13020 Score: 323
Period size: 122 Copynumber: 2.1 Consensus size: 122
12748 CGCTCCTCTC
* * * * * *
12758 CCTGAAAGATGTTGAATTTGGTGACGTTCTCACTTTTTTCCCTGAAATATGTTGAGTCATGGGAC
1 CCTGAAGGATGTTGAATCTGGTGACGATCTCACTTATTTCCCTGAAAGATGTTGAGTCATAGGAC
** *
12823 GATCTTACGCCTTTCCCTGAAGGATGCTAAGTCGTATTTCAAGCAATCCACTCATTT
66 GATCTTACGCCTTTCCCTGAAGGACACTAAGTCGTACTTCAAGCAATCCACTCATTT
* *
12880 CTCTGAAGGATGTTGAATCTGGTGACGATCTCAC-TATTTCCCTGAAAGATGTTGAGTCGTATGA
1 C-CTGAAGGATGTTGAATCTGGTGACGATCTCACTTATTTCCCTGAAAGATGTTGAGTCATAGGA
* * ** *
12944 CGATCTTA-GTCCTTTCCCTGAAGGACATTAAGTCGTACTTCGAGTGATCCACTCCTTT
65 CGATCTTACG-CCTTTCCCTGAAGGACACTAAGTCGTACTTCAAGCAATCCACTCATTT
**
13002 CCCCAAGGGATGTTGAATC
1 CCTGAA-GGATGTTGAATC
13021 GTGATTCAGG
Statistics
Matches: 120, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
121 4 0.03
122 87 0.73
123 29 0.24
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (122 bp):
CCTGAAGGATGTTGAATCTGGTGACGATCTCACTTATTTCCCTGAAAGATGTTGAGTCATAGGAC
GATCTTACGCCTTTCCCTGAAGGACACTAAGTCGTACTTCAAGCAATCCACTCATTT
Found at i:13127 original size:288 final size:288
Alignment explanation
Indices: 12611--13146 Score: 716
Period size: 288 Copynumber: 1.9 Consensus size: 288
12601 TATTTTTGCT
*
12611 TGGTGACGATCTCACTCTTTTCCCTGAAAGATATTGAGTAGTAGGACAATCTTACTCCTTTCCCT
1 TGGTGACGATCTCACTCATTTCCCTGAAAGATATTGAGTAGTAGGACAATCTTACTCCTTTCCCT
* * * *
12676 AAAGGACTCTTAATCTTATTTGACTGATCCACTCATTTCCCTAAAGGATGTTGAATCATGATTCA
66 AAAGGACTATTAATCGTATTCGACTGATCCACTCATTTCCCCAAAGGATGTTGAATCATGATTCA
* * * **** * * *
12741 GGTGATCCGCTCCTCTCCCTGAAAGATGTTGAATTTGGTGACGTTCTCACTTTTTTCCCTGAAAT
131 GGTGATCCGCTCCTCTCACTGAAAGATGCTGAATCTGGTGACAAAATCACTCTTTTCCCTAAAAG
* * * *
12806 ATGTTGAGTCATGGGACGATCTTACGCCTTTCCCTGAAGGATGCTAAGTCGTATTTCAAGCAATC
196 ATGTTGAGTCATAGGACAATCTTACGCCTTTCCCTGAAGGATACTAAATCGTATTTCAAGCAATC
12871 CACTCATTTCTCTGAAGGATGTTGAATC
261 CACTCATTTCTCTGAAGGATGTTGAATC
* * * * *
12899 TGGTGACGATCTCACT-ATTTCCCTGAAAGATGTTGAGTCGTATGACGATCTTAGTCCTTTCCCT
1 TGGTGACGATCTCACTCATTTCCCTGAAAGATATTGAGTAGTAGGACAATCTTACTCCTTTCCCT
* * * * *
12963 GAAGGAC-ATTAAGTCGTACTTCGAGTGATCCACTCCTTTCCCCAAGGGATGTTGAATCGTGATT
66 AAAGGACTATTAA-TCGTA-TTCGACTGATCCACTCATTTCCCCAAAGGATGTTGAATCATGATT
* * *
13027 CAGGTGATTCGCTCCTTTCACTGAAGGATGCTGAATCTGGTGACAAAATCACTCTTTTCCCTAAA
129 CAGGTGATCCGCTCCTCTCACTGAAAGATGCTGAATCTGGTGACAAAATCACTCTTTTCCCTAAA
** **
13092 AGATGTTGAGTTGTAGGACAATCTTACTTCTTTCCCTGAAGGATACTAAATCGTA
194 AGATGTTGAGTCATAGGACAATCTTACGCCTTTCCCTGAAGGATACTAAATCGTA
13147 ATTCGGGTAA
Statistics
Matches: 210, Mismatches: 36, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
286 4 0.02
287 52 0.25
288 154 0.73
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (288 bp):
TGGTGACGATCTCACTCATTTCCCTGAAAGATATTGAGTAGTAGGACAATCTTACTCCTTTCCCT
AAAGGACTATTAATCGTATTCGACTGATCCACTCATTTCCCCAAAGGATGTTGAATCATGATTCA
GGTGATCCGCTCCTCTCACTGAAAGATGCTGAATCTGGTGACAAAATCACTCTTTTCCCTAAAAG
ATGTTGAGTCATAGGACAATCTTACGCCTTTCCCTGAAGGATACTAAATCGTATTTCAAGCAATC
CACTCATTTCTCTGAAGGATGTTGAATC
Found at i:13319 original size:37 final size:36
Alignment explanation
Indices: 13208--13355 Score: 156
Period size: 36 Copynumber: 4.1 Consensus size: 36
13198 TAGGGAAACA
* * * *
13208 ATCCTAAGAAGGATTCTAATATATTTCTAGAAAATG
1 ATCCTAAGAAGGACTCAAACAAATTTCTAGAAAATG
* ** *
13244 ATCCTAAGAAGGAATTTAACAAA-TTCTAGAAAAACG
1 ATCCTAAGAAGGACTCAAACAAATTTCTAG-AAAATG
* *
13280 ATCCTAAGAATGACTCAAACAAATTTCTAGATAATCG
1 ATCCTAAGAAGGACTCAAACAAATTTCTAGAAAAT-G
*
13317 ATCCTACGAAGGACTCAAA-AGAATTTCTAGAAAATG
1 ATCCTAAGAAGGACTCAAACA-AATTTCTAGAAAATG
13353 ATC
1 ATC
13356 GACCTCACTA
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
35 6 0.06
36 51 0.54
37 37 0.39
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.26
Consensus pattern (36 bp):
ATCCTAAGAAGGACTCAAACAAATTTCTAGAAAATG
Found at i:13450 original size:44 final size:45
Alignment explanation
Indices: 13362--13533 Score: 222
Period size: 44 Copynumber: 3.9 Consensus size: 45
13352 GATCGACCTC
* *
13362 ACTAAAAGATTGACTCCTCTGCACGAGAAAGTCAAGAATAACATT
1 ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATAACATT
*
13407 ACTAAAAGGTTGACTCCTCTTCATG-GAAAGTCAAGAATAACATT
1 ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATAACATT
* * * * * *
13451 ACTAAAAGGATGACTCCTCTTCGCGAGAAAGCCAATAATGACATC
1 ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATAACATT
* * *
13496 A-TTAAAGGTTGACTCTTCTTCACGAGAAAGTCAGGAAT
1 ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAAT
13534 GTTTCTAGGA
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
44 71 0.65
45 38 0.35
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (45 bp):
ACTAAAAGGTTGACTCCTCTTCACGAGAAAGTCAAGAATAACATT
Found at i:13525 original size:89 final size:89
Alignment explanation
Indices: 13362--13533 Score: 222
Period size: 89 Copynumber: 1.9 Consensus size: 89
13352 GATCGACCTC
* *
13362 ACTAAAAGATTGACTCCTCTGCACGAGAAAGTCAAGAATAACATTACTAAAAGGTTGACTCCTCT
1 ACTAAAAGATTGACTCCTCTGCACGAGAAAGCCAAGAATAACATCACTAAAAGGTTGACTCCTCT
*
13427 TCATGGAAAGTCAAGAATAACATT
66 TCACGGAAAGTCAAGAATAACATT
* * * * * *
13451 ACTAAAAGGA-TGACTCCTCTTCGCGAGAAAGCCAATAATGACATCA-TTAAAGGTTGACTCTTC
1 ACTAAAA-GATTGACTCCTCTGCACGAGAAAGCCAAGAATAACATCACTAAAAGGTTGACTCCTC
*
13514 TTCACGAGAAAGTCAGGAAT
65 TTCACG-GAAAGTCAAGAAT
13534 GTTTCTAGGA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
88 20 0.28
89 49 0.69
90 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (89 bp):
ACTAAAAGATTGACTCCTCTGCACGAGAAAGCCAAGAATAACATCACTAAAAGGTTGACTCCTCT
TCACGGAAAGTCAAGAATAACATT
Found at i:14992 original size:13 final size:13
Alignment explanation
Indices: 14976--15002 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14966 CCTTTTTCGA
14976 TCTAATTTTTTCT
1 TCTAATTTTTTCT
14989 TCTAATTTTTTCT
1 TCTAATTTTTTCT
15002 T
1 T
15003 TCAACTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TCTAATTTTTTCT
Found at i:15557 original size:18 final size:18
Alignment explanation
Indices: 15534--15582 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
15524 CTACAAAATG
*
15534 TAATATAATAGTAATAAA
1 TAATATAATAATAATAAA
*
15552 TAATATAATAATAATAGA
1 TAATATAATAATAATAAA
*
15570 TGATATAATAATA
1 TAATATAATAATA
15583 CAATTAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
TAATATAATAATAATAAA
Found at i:16613 original size:18 final size:18
Alignment explanation
Indices: 16590--16624 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
16580 ACTTAAAATT
16590 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
16608 TGTCCCGAATGACCACT
1 TGTCCCGAATGACCACT
16625 CCTTAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:16890 original size:15 final size:17
Alignment explanation
Indices: 16849--16901 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 17
16839 AGCTTATTTT
*
16849 CATATAATTCACTTTCA
1 CATATGATTCACTTTCA
16866 CAT-TGA-TCAC-TTC-
1 CATATGATTCACTTTCA
*
16879 CATATGATTCACATGTCA
1 CATATGATTCAC-TTTCA
16897 CATAT
1 CATAT
16902 CTCATGGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 3 0.10
14 6 0.21
15 8 0.28
16 2 0.07
17 5 0.17
18 5 0.17
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (17 bp):
CATATGATTCACTTTCA
Found at i:19067 original size:2 final size:2
Alignment explanation
Indices: 19056--19116 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
19046 GTAAATTTTC
*
19056 AT AT -T AT AT AT AT AT AT AT TT 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
19097 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
19117 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:24692 original size:16 final size:16
Alignment explanation
Indices: 24671--24792 Score: 178
Period size: 16 Copynumber: 7.8 Consensus size: 16
24661 TTTCTCTAGC
24671 AGGTTAAAGAAGTCTG
1 AGGTTAAAGAAGTCTG
24687 AGGTTAAAGAAGTCTG
1 AGGTTAAAGAAGTCTG
*
24703 AGGTTAAAGAAGTCCG
1 AGGTTAAAGAAGTCTG
24719 AGGTTAAAGAAGTCTG
1 AGGTTAAAGAAGTCTG
24735 AGGTTAAAGAAGTCTG
1 AGGTTAAAGAAGTCTG
* *
24751 AGGTTAAAGATGCCT-
1 AGGTTAAAGAAGTCTG
* *
24766 --TTTACAGAAGTCTG
1 AGGTTAAAGAAGTCTG
24780 AGGTTAAAGAAGT
1 AGGTTAAAGAAGT
24793 TTTTGTTCAG
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
13 9 0.10
16 84 0.90
ACGTcount: A:0.37, C:0.08, G:0.30, T:0.25
Consensus pattern (16 bp):
AGGTTAAAGAAGTCTG
Found at i:28855 original size:14 final size:15
Alignment explanation
Indices: 28836--28864 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28826 AATTTGATGA
28836 TTTTAAAAT-TTATT
1 TTTTAAAATATTATT
28850 TTTTAAAATATTATT
1 TTTTAAAATATTATT
28865 ATAATTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAAATATTATT
Found at i:30283 original size:11 final size:11
Alignment explanation
Indices: 30267--30294 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
30257 TCTTTGGGTG
30267 TTAAGGAAAGC
1 TTAAGGAAAGC
30278 TTAAGGAAAGC
1 TTAAGGAAAGC
30289 TTAAGG
1 TTAAGG
30295 TGGATTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.07, G:0.29, T:0.21
Consensus pattern (11 bp):
TTAAGGAAAGC
Found at i:31390 original size:45 final size:44
Alignment explanation
Indices: 31319--31421 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 44
31309 TATATTTCAT
*
31319 GCTATGTGATATGACTTACGTGATTATATGAAAATGCGATATAA
1 GCTATGTGATATGACTTACGTAATTATATGAAAATGCGATATAA
* * *
31363 GTTATGTGATATTGAAC-TACGTAATTATATGATAATGTGATATAA
1 GCTATGTGATA-TG-ACTTACGTAATTATATGAAAATGCGATATAA
*
31408 GCTATGTGACATGA
1 GCTATGTGATATGA
31422 TCTATGTGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 12 0.24
45 36 0.71
46 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (44 bp):
GCTATGTGATATGACTTACGTAATTATATGAAAATGCGATATAA
Found at i:31416 original size:14 final size:14
Alignment explanation
Indices: 31397--31460 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
31387 TTATATGATA
31397 ATGTGATATAAGCT
1 ATGTGATATAAGCT
* * *
31411 ATGTGACATGATCT
1 ATGTGATATAAGCT
**
31425 ATGTGATTATTTGTCT
1 ATGTGA-TATAAG-CT
31441 ATGTGATATAAGCT
1 ATGTGATATAAGCT
31455 ATGTGA
1 ATGTGA
31461 AATGGTATAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
14 25 0.64
15 6 0.15
16 8 0.21
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.41
Consensus pattern (14 bp):
ATGTGATATAAGCT
Found at i:42913 original size:11 final size:11
Alignment explanation
Indices: 42899--42924 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42889 ATATATATAA
42899 TATATATTATT
1 TATATATTATT
42910 TATATATTATT
1 TATATATTATT
42921 TATA
1 TATA
42925 AATTTCGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATATTATT
Found at i:47778 original size:3 final size:3
Alignment explanation
Indices: 47770--47817 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
47760 ATGTAATTGT
*
47770 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA TATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
47815 ATA
1 ATA
47818 TTTGTGTAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:60453 original size:2 final size:2
Alignment explanation
Indices: 60448--60475 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60438 AAACAAAACT
60448 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
60476 CTTTTGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61992 original size:3 final size:3
Alignment explanation
Indices: 61984--62013 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
61974 TGATTTTCAA
*
61984 ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
62014 TGTGTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:62764 original size:44 final size:45
Alignment explanation
Indices: 62710--62795 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 45
62700 TATTTTAATA
* *
62710 ATATATAATAA-ATTGTTAATAAAATTTATATTATTTATTAATTTC
1 ATATATAATAATATTATTAA-AAAATTAATATTATTTATTAATTTC
** *
62755 ATATA-AATAATATTATTAAATTATTAATATTTTTTATTAAT
1 ATATATAATAATATTATTAAAAAATTAATATTATTTATTAAT
62796 CGGGAGTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 23 0.66
45 12 0.34
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (45 bp):
ATATATAATAATATTATTAAAAAATTAATATTATTTATTAATTTC
Found at i:62962 original size:21 final size:21
Alignment explanation
Indices: 62936--62977 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
62926 TAATTCTAAT
62936 ATTTTA-AATATAATAATATTA
1 ATTTTATAATA-AATAATATTA
*
62957 ATTTTATGATAAATAATATTA
1 ATTTTATAATAAATAATATTA
62978 TTTATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTTTATAATAAATAATATTA
Found at i:64152 original size:60 final size:60
Alignment explanation
Indices: 64037--64153 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
64027 GATCATTTTG
* * * *
64037 TAACTTTTAATAGTCGAGTGACTCAACAAAGCAACACTCTATAGTCGGAGAACCATTATA
1 TAACTTTTAATAGTCAAGAGACTCAACAAAGCAACACCCTATAGCCGGAGAACCATTATA
* * * * *
64097 TAACTTTTAATAGTTAAGAGACTTAATAAAGC-ACTACCCTATAGCCGGGGGACCATT
1 TAACTTTTAATAGTCAAGAGACTCAACAAAGCAAC-ACCCTATAGCCGGAGAACCATT
64154 TGTGTACTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (60 bp):
TAACTTTTAATAGTCAAGAGACTCAACAAAGCAACACCCTATAGCCGGAGAACCATTATA
Found at i:67273 original size:60 final size:60
Alignment explanation
Indices: 67173--67339 Score: 185
Period size: 60 Copynumber: 2.8 Consensus size: 60
67163 AATTAATTTG
* * ** **
67173 GGGATGTAATTTGAATATTCAAAAGTTTGGGGACTAATTTAGAAA-GATTGTCATAGTTTA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA-AAATGAGAGTCATAGTTTA
* * * *
67233 GGGATGAAATTAGAATGTTCAAAATTTTAAGGACTGATTTAAAATGAGAGTCGTAGTTTA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTA
* * * *
67293 GGG-TGAAATTAAAATATTTAAAAGTTTAGGGATTAATTTAAAATGAG
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAG
67340 GATAATAATT
Statistics
Matches: 89, Mismatches: 17, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
59 40 0.45
60 49 0.55
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.35
Consensus pattern (60 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTA
Found at i:67333 original size:59 final size:60
Alignment explanation
Indices: 67186--67339 Score: 186
Period size: 59 Copynumber: 2.6 Consensus size: 60
67176 ATGTAATTTG
* ** *
67186 AATATTCAAAAGTTTGGGGACTAATTTAGAAA-GATTGTCATAGTTTAGGGATGAAATTAG
1 AATATTCAAAAGTTTAGGGACTAATTTA-AAATGAGAGTCATAGTTTAGGGATGAAATTAA
* * * * *
67246 AATGTTCAAAATTTTAAGGACTGATTTAAAATGAGAGTCGTAGTTTAGGG-TGAAATTAA
1 AATATTCAAAAGTTTAGGGACTAATTTAAAATGAGAGTCATAGTTTAGGGATGAAATTAA
* *
67305 AATATTTAAAAGTTTAGGGATTAATTTAAAATGAG
1 AATATTCAAAAGTTTAGGGACTAATTTAAAATGAG
67340 GATAATAATT
Statistics
Matches: 78, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
59 40 0.51
60 38 0.49
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.34
Consensus pattern (60 bp):
AATATTCAAAAGTTTAGGGACTAATTTAAAATGAGAGTCATAGTTTAGGGATGAAATTAA
Found at i:72492 original size:24 final size:24
Alignment explanation
Indices: 72471--72532 Score: 124
Period size: 24 Copynumber: 2.6 Consensus size: 24
72461 ATATTCGTAT
72471 ACATATTCATTTATATTTTCGTCA
1 ACATATTCATTTATATTTTCGTCA
72495 ACATATTCATTTATATTTTCGTCA
1 ACATATTCATTTATATTTTCGTCA
72519 ACATATTCATTTAT
1 ACATATTCATTTAT
72533 CGTTAATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.03, T:0.50
Consensus pattern (24 bp):
ACATATTCATTTATATTTTCGTCA
Found at i:77973 original size:2 final size:2
Alignment explanation
Indices: 77966--78024 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
77956 CAAGTACGTA
77966 AT AT AT AT AT AT AT AT -T 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
78007 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
78025 GTTACTTTGC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:81891 original size:15 final size:15
Alignment explanation
Indices: 81867--81900 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
81857 TATCAGTGCA
*
81867 ACATAGTCTGCAAGT
1 ACATAATCTGCAAGT
81882 ACATAATCTGCAAGT
1 ACATAATCTGCAAGT
81897 ACAT
1 ACAT
81901 TTAGCTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (15 bp):
ACATAATCTGCAAGT
Done.