Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006716.1 Hibiscus syriacus cultivar Beakdansim tig00016794_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: 83707
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:4113 original size:2 final size:2
Alignment explanation
Indices: 4106--4141 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4096 GGCTTGGATT
4106 GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4142 GACATGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4126 original size:17 final size:17
Alignment explanation
Indices: 4106--4139 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4096 GGCTTGGATT
4106 GAGAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAGAG
4123 GAGAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAGAG
4140 AGGACATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (17 bp):
GAGAGAGAGAGAGAGAG
Found at i:4128 original size:19 final size:19
Alignment explanation
Indices: 4106--4143 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4096 GGCTTGGATT
4106 GAGAGAGAGAGAGAGAGGA
1 GAGAGAGAGAGAGAGAGGA
4125 GAGAGAGAGAGAGAGAGGA
1 GAGAGAGAGAGAGAGAGGA
4144 CATGAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (19 bp):
GAGAGAGAGAGAGAGAGGA
Found at i:11175 original size:30 final size:29
Alignment explanation
Indices: 11141--11233 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 29
11131 GTGAGCCACC
11141 TTTCAAATGTTAGAAAATAATTATTGAACT
1 TTTCAAATGTTA-AAAATAATTATTGAACT
* * * *
11171 TTTCAAATGATTAAAAATAGTCACTGAAAT
1 TTTCAAATG-TTAAAAATAATTATTGAACT
*
11201 TTATTAAATAGTTATAAAATAATCT-TTGAACT
1 TT-TCAAAT-GTTA-AAAATAAT-TATTGAACT
11233 T
1 T
11234 ATTAAACTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
30 24 0.49
31 11 0.22
32 14 0.29
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (29 bp):
TTTCAAATGTTAAAAATAATTATTGAACT
Found at i:11747 original size:2 final size:2
Alignment explanation
Indices: 11742--11772 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11732 TCGTATCAAT
11742 TA TA 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 TA TA T
11773 TATCTGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12747 original size:15 final size:16
Alignment explanation
Indices: 12727--12759 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
12717 TATGTTCATA
12727 TAAAAT-AATATATTT
1 TAAAATCAATATATTT
12742 TAAAATCGAATATATTT
1 TAAAATC-AATATATTT
12759 T
1 T
12760 TGTATGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
TAAAATCAATATATTT
Found at i:15408 original size:20 final size:20
Alignment explanation
Indices: 15366--15408 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
15356 AGTTAATCTG
*
15366 ATATATTTAATTTAATTAAA
1 ATATATTTAATTTAAATAAA
*
15386 ATATA-TTATTTTAAATAATA
1 ATATATTTAATTTAAATAA-A
15406 ATA
1 ATA
15409 AGTAGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATATTTAATTTAAATAAA
Found at i:17079 original size:2 final size:2
Alignment explanation
Indices: 17074--17104 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
17064 ATTAAAAGTA
17074 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
17105 CATCGTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18620 original size:19 final size:18
Alignment explanation
Indices: 18596--18632 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
18586 ATAAATTATT
*
18596 ATTATTTTATTTATTTTAA
1 ATTATTTT-TATATTTTAA
18615 ATTATTTTTATATTTTAA
1 ATTATTTTTATATTTTAA
18633 TAATGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTATTTTTATATTTTAA
Found at i:22647 original size:27 final size:27
Alignment explanation
Indices: 22617--22760 Score: 234
Period size: 27 Copynumber: 5.3 Consensus size: 27
22607 AAAACAATGT
*
22617 TGAATGATTCAGCATAAAAGTACATTC
1 TGAATGATTCAACATAAAAGTACATTC
*
22644 TGAATGATTCAGCATAAAAGTACATTC
1 TGAATGATTCAACATAAAAGTACATTC
22671 TGAATGATTCAACATAAAAGTACATTC
1 TGAATGATTCAACATAAAAGTACATTC
* *
22698 TGAATGATTCAACATAAAAATACATTA
1 TGAATGATTCAACATAAAAGTACATTC
* *
22725 TGAATGATTCAACATAGAAGTACATTT
1 TGAATGATTCAACATAAAAGTACATTC
22752 TGAATGATT
1 TGAATGATT
22761 AAGACCCATT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 111 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (27 bp):
TGAATGATTCAACATAAAAGTACATTC
Found at i:29989 original size:15 final size:16
Alignment explanation
Indices: 29944--29983 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
29934 TTTTTAATAT
29944 TTTTAAAAAATATAAA
1 TTTTAAAAAATATAAA
29960 TTTTAAAAAATATAAA
1 TTTTAAAAAATATAAA
29976 TTTTAAAA
1 TTTTAAAA
29984 TTATAAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTTAAAAAATATAAA
Found at i:32760 original size:14 final size:15
Alignment explanation
Indices: 32743--32783 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
32733 ACTGCTTACA
32743 ACATAACACTTAA-T
1 ACATAACACTTAATT
32757 ACATAACAC-TAATT
1 ACATAACACTTAATT
32771 ACATAACACTTAA
1 ACATAACACTTAA
32784 ACCAAAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.12
14 19 0.76
15 3 0.12
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (15 bp):
ACATAACACTTAATT
Found at i:37494 original size:313 final size:311
Alignment explanation
Indices: 36922--37545 Score: 1122
Period size: 313 Copynumber: 2.0 Consensus size: 311
36912 ACTCCTCAAC
* * *
36922 CTCCTCGATAGGCACTTAGAGAGGATCTTATATAATCCACCAACTAAGCTAATAGGCTTATAGTC
1 CTCCTCGATAGGCACTTAGAGAGGATCTTATATAATCCAACAACTAAGCTAAAAGGCCTATAGTC
*
36987 ATCAAGATCACCACTGTTAGAGACCTTAGGAATAAGAGTAATAAAGGTATGATTGATGCCATGAT
66 ATCAAGATCACCACTGTTAGAGACCTTAGGAATAAGAGTAATAAAGGTATGATTAATGCCATGAT
* *
37052 CCCAATCTTTCCCCAAATAGACGTTATGGAAGAACTTTATAATCTCTCCTTTAAGTACATGCCAA
131 CCCAATCTTTCCCCAAATAGAAGTTATGGAAGAACTTTATAATCTCTCCTTCAAGTACATGCCAA
*
37117 TATCTTTTGAAAAAACCCAAATTAAAACCATCTGGCACGGAGCTTTATTGCTATTGCAAGACTTT
196 TATCTTTTGAAAAAACCCAAATTAAAACCATCTGGCACAGAGCTTTATTGCTATTGCAAGACTTT
37182 AAAGTATCCCATATTTCCTCCTCTGTGAATTCTTTCTCCAAACTCAAACTCTG
261 AAAGTATCCCATATTTCCTCCTC--TGAATTCTTTCTCCAAACTCAAACTCTG
37235 CTCCTCGATAGGCACTTAGAGAGGATCTTATATAATCCAACAACTAAGCTAAAAGGCCTATAGTC
1 CTCCTCGATAGGCACTTAGAGAGGATCTTATATAATCCAACAACTAAGCTAAAAGGCCTATAGTC
37300 ATCAAGATCACCACTGTTAGAGACCTTAGGAATAAGAGTAATAAAGGTATGATTAATGCCATGAT
66 ATCAAGATCACCACTGTTAGAGACCTTAGGAATAAGAGTAATAAAGGTATGATTAATGCCATGAT
37365 CCCAATCTTTCCCCAAATAGAAGTTATGGAAGAACTTTATAATCTCTCCTTCAAGTACATGCCAA
131 CCCAATCTTTCCCCAAATAGAAGTTATGGAAGAACTTTATAATCTCTCCTTCAAGTACATGCCAA
* * * * *
37430 TATCTTTTGAAAAATCCCAAATTAAAACCATCTGGCCCATAGCTTTATTGCTATTTCCAGACTTT
196 TATCTTTTGAAAAAACCCAAATTAAAACCATCTGGCACAGAGCTTTATTGCTATTGCAAGACTTT
37495 AAAGTATCCCATATTTCCTCCTCTGAATTCTTTCTCCAAACTCAAACTCTG
261 AAAGTATCCCATATTTCCTCCTCTGAATTCTTTCTCCAAACTCAAACTCTG
37546 TTGAACTGAA
Statistics
Matches: 299, Mismatches: 12, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
311 28 0.09
313 271 0.91
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (311 bp):
CTCCTCGATAGGCACTTAGAGAGGATCTTATATAATCCAACAACTAAGCTAAAAGGCCTATAGTC
ATCAAGATCACCACTGTTAGAGACCTTAGGAATAAGAGTAATAAAGGTATGATTAATGCCATGAT
CCCAATCTTTCCCCAAATAGAAGTTATGGAAGAACTTTATAATCTCTCCTTCAAGTACATGCCAA
TATCTTTTGAAAAAACCCAAATTAAAACCATCTGGCACAGAGCTTTATTGCTATTGCAAGACTTT
AAAGTATCCCATATTTCCTCCTCTGAATTCTTTCTCCAAACTCAAACTCTG
Found at i:44102 original size:20 final size:23
Alignment explanation
Indices: 44063--44103 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
44053 AGACCCGACC
44063 CGTTGACTCGACTCGTTGACCGG
1 CGTTGACTCGACTCGTTGACCGG
44086 CGTTGAC-C-ACT-GTTGACC
1 CGTTGACTCGACTCGTTGACC
44104 AAAACTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 1 0.06
23 7 0.39
ACGTcount: A:0.15, C:0.32, G:0.27, T:0.27
Consensus pattern (23 bp):
CGTTGACTCGACTCGTTGACCGG
Found at i:46691 original size:24 final size:24
Alignment explanation
Indices: 46573--46684 Score: 138
Period size: 24 Copynumber: 4.7 Consensus size: 24
46563 ATTTGAATTT
46573 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
46597 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
* *
46621 TGATCTAATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
46645 CGATCTGTTACTTGACCT-GATTTC
1 TGATCTGATACTTGACATGGA-TTC
*
46669 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
46685 CTGATTTATG
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
23 3 0.04
24 72 0.95
25 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:51430 original size:24 final size:24
Alignment explanation
Indices: 51308--51423 Score: 128
Period size: 24 Copynumber: 4.8 Consensus size: 24
51298 TTCGATTTGA
* *
51308 ATTCTGATCTGATACTTGACATAG
1 ATTCTGATATGATACTTGACATGG
51332 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
*
51356 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* * * * *
51380 ATTATGATCTGTTATTTGACCT-G
1 ATTCTGATATGATACTTGACATGG
51403 ATTTCTGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
51424 CTGATTTATG
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
23 3 0.04
24 73 0.95
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:51433 original size:48 final size:48
Alignment explanation
Indices: 51308--51423 Score: 144
Period size: 48 Copynumber: 2.4 Consensus size: 48
51298 TTCGATTTGA
* *
51308 ATTCTGATCTGATACTTGACATAGATTCTGATATGATATCTGACATGG
1 ATTCTGATATGATACTTGACATAGATTATGATATGATATCTGACATGG
* * * * * *
51356 ATTCTGATATGATACTTGACTTGGATTATGATCTGTTATTTGACCT-G
1 ATTCTGATATGATACTTGACATAGATTATGATATGATATCTGACATGG
51403 ATTTCTGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
51424 CTGATTTATG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
47 2 0.03
48 57 0.97
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (48 bp):
ATTCTGATATGATACTTGACATAGATTATGATATGATATCTGACATGG
Found at i:51446 original size:24 final size:24
Alignment explanation
Indices: 51336--51433 Score: 83
Period size: 24 Copynumber: 4.1 Consensus size: 24
51326 ACATAGATTC
* * *
51336 TGATATGATATCTGACATGGA-TTC
1 TGATATGATATTTGACCT-GATTTA
* *
51360 TGATATGATACTTGACTTGGA-TTA
1 TGATATGATATTTGACCT-GATTTA
* * *
51384 TGATCTGTTATTTGACCTGATTTC
1 TGATATGATATTTGACCTGATTTA
*
51408 TGATATGATACTTGACCTGATTTA
1 TGATATGATATTTGACCTGATTTA
51432 TG
1 TG
51434 TTTTGATTTT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 2 0.03
24 58 0.97
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATATTTGACCTGATTTA
Found at i:53001 original size:2 final size:2
Alignment explanation
Indices: 52994--53020 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52984 TTTCTACTTT
52994 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
53021 CCTCAAACAG
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:54721 original size:2 final size:2
Alignment explanation
Indices: 54714--54771 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
54704 GGTTAGTGTT
54714 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
*
54756 TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA
54772 GATAGATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:55072 original size:2 final size:2
Alignment explanation
Indices: 55065--55096 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
55055 CATCAGTCAT
55065 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
55097 ATGCAATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56489 original size:28 final size:28
Alignment explanation
Indices: 56457--56513 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
56447 CAATAATGTA
56457 TATATTGATGCTATAATTAATGCCACCC
1 TATATTGATGCTATAATTAATGCCACCC
56485 TATATTGATGCTATAATTAATGCCACCC
1 TATATTGATGCTATAATTAATGCCACCC
56513 T
1 T
56514 CAAAATTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (28 bp):
TATATTGATGCTATAATTAATGCCACCC
Found at i:56787 original size:18 final size:18
Alignment explanation
Indices: 56739--56787 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
56729 TATAAACTAT
56739 TATTTAAA-ATATATTTA
1 TATTTAAATATATATTTA
*
56756 TA-TAAATATATATATTTA
1 TATTTAA-ATATATATTTA
*
56774 TATTTAAATGTATA
1 TATTTAAATATATA
56788 AATAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 17 0.65
19 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TATTTAAATATATATTTA
Found at i:56799 original size:32 final size:32
Alignment explanation
Indices: 56757--56818 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
56747 ATATATTTAT
*
56757 ATAAATATATATATT-TATATTTAAATGTATAA
1 ATAAAAATATAT-TTATATATTTAAATGTATAA
56789 ATAAAAATATATTTATATATTTAAATGTAT
1 ATAAAAATATATTTATATATTTAAATGTAT
56819 GAATCATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 2 0.07
32 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
ATAAAAATATATTTATATATTTAAATGTATAA
Found at i:56836 original size:32 final size:31
Alignment explanation
Indices: 56757--56836 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 31
56747 ATATATTTAT
56757 ATAAATATATATATT-TATATTTAAATGTATAA
1 ATAAATATAT-T-TTATATATTTAAATGTATAA
* *
56789 ATAAAAATATATTTATATATTTAAATGTATGA
1 ATAAATATAT-TTTATATATTTAAATGTATAA
**
56821 ATCATTTATATTTTAT
1 AT-AAATATATTTTAT
56837 GTACATTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 2 0.05
32 34 0.83
33 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (31 bp):
ATAAATATATTTTATATATTTAAATGTATAA
Found at i:56986 original size:15 final size:15
Alignment explanation
Indices: 56966--57001 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
56956 AATATAAATC
56966 TTAAATTTAATTTTA
1 TTAAATTTAATTTTA
56981 TTAAATTTAATTTTA
1 TTAAATTTAATTTTA
*
56996 TGAAAT
1 TTAAAT
57002 CTATCCCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TTAAATTTAATTTTA
Found at i:56986 original size:28 final size:28
Alignment explanation
Indices: 56898--56980 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
56888 TTAAGATTAT
*
56898 ATATATAATCATTAAATTATAAATGTT-AAAA
1 ATATA-AAT-ATTAAATT-T-AATTTTAAAAA
*
56929 ATATAAATATTAAATTTAGTTTTAAAAA
1 ATATAAATATTAAATTTAATTTTAAAAA
*
56957 ATATAAATCTTAAATTTAATTTTA
1 ATATAAATATTAAATTTAATTTTA
56981 TTAAATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.09
28 27 0.57
29 8 0.17
30 3 0.06
31 5 0.11
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
ATATAAATATTAAATTTAATTTTAAAAA
Found at i:60697 original size:13 final size:13
Alignment explanation
Indices: 60679--60704 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60669 TTTGAACCAA
60679 ATATTATAAAAAT
1 ATATTATAAAAAT
60692 ATATTATAAAAAT
1 ATATTATAAAAAT
60705 GATCATTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATTATAAAAAT
Found at i:61152 original size:2 final size:2
Alignment explanation
Indices: 61141--61190 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
61131 AAACTTTTTG
61141 TA TA -A 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
61182 TA TA TA TA T
1 TA TA TA TA T
61191 CAATTATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67738 original size:9 final size:9
Alignment explanation
Indices: 67724--67748 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
67714 TATATATTTT
67724 TTAAAATTA
1 TTAAAATTA
67733 TTAAAATTA
1 TTAAAATTA
67742 TTAAAAT
1 TTAAAAT
67749 GATCATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAAAATTA
Found at i:68550 original size:2 final size:2
Alignment explanation
Indices: 68543--68575 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
68533 TCCGACACAA
68543 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 A
68576 CTCATTTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73035 original size:37 final size:37
Alignment explanation
Indices: 72985--73058 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
72975 AACTCAATCC
*
72985 GATTCAATCGAATCTAAACTCAAACTCAAATTGCCAA
1 GATTCAATCGAATCTAAACTCAAACTCAAAATGCCAA
* *
73022 GATTCAATTGAATCTAATCTCAAACTCAAAATGCCAA
1 GATTCAATCGAATCTAAACTCAAACTCAAAATGCCAA
73059 CAATCTAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (37 bp):
GATTCAATCGAATCTAAACTCAAACTCAAAATGCCAA
Found at i:75509 original size:129 final size:129
Alignment explanation
Indices: 75279--75533 Score: 474
Period size: 129 Copynumber: 2.0 Consensus size: 129
75269 GAAAAGGTGC
* *
75279 AAATAGTTATTTTCATAAAGTAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGTGAG
1 AAATAGTTATTTTCATAAAGCAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGAGAG
75344 TTTTCTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGTAGA
66 TTTTCTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGTAGA
75408 AAATAGTTATTTTCATAAAGCAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGAGAG
1 AAATAGTTATTTTCATAAAGCAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGAGAG
* *
75473 TTTTCTTGATGTTCAAAGTGATGAACTCACTGATATTGAACTAACTAGCAACTCAATCAGT
66 TTTTCTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGT
75534 GCCACTGCTC
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 122 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (129 bp):
AAATAGTTATTTTCATAAAGCAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGAGAG
TTTTCTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGTAGA
Done.