Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007350.1 Hibiscus syriacus cultivar Beakdansim tig00019693_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: 96596
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:605 original size:35 final size:34
Alignment explanation
Indices: 566--678 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
556 AAAACAATCC
*
566 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
601 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
636 TCAATTACATTCTAAAGCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTCCAAAATAAT
671 TCAATTTC
1 TCAATTTC
679 TGTCTTTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:1948 original size:29 final size:29
Alignment explanation
Indices: 1916--1971 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
1906 AGCCCGAAGG
1916 ACTATCCAGAGG-CATAAAGATCCTCGGTA
1 ACTATCCAGAGGTCA-AAAGATCCTCGGTA
1945 ACTATCCAGAGGTCAAAAGATCCTCGG
1 ACTATCCAGAGGTCAAAAGATCCTCGG
1972 CAACGTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (29 bp):
ACTATCCAGAGGTCAAAAGATCCTCGGTA
Found at i:2089 original size:32 final size:32
Alignment explanation
Indices: 1976--2097 Score: 105
Period size: 32 Copynumber: 4.0 Consensus size: 32
1966 CCTCGGCAAC
* ** * *
1976 GTCCATAGGTTCCGAAGAACCTTGGTAA-ACT
1 GTCCATATGTTCCTTAGAACATAGGTAATACT
2007 GTCC--ATGTTCCTTAGAACATA-GT-ATACT
1 GTCCATATGTTCCTTAGAACATAGGTAATACT
*** *
2035 GTCCATATGTCTCGAAAG-ACATAGGTAATTCT
1 GTCCATATGT-TCCTTAGAACATAGGTAATACT
2067 GTCCATATGTTCCTTAGAACATAGGT-ATACT
1 GTCCATATGTTCCTTAGAACATAGGTAATACT
2098 CTCGACTCTT
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
27 1 0.01
28 9 0.13
29 12 0.17
30 9 0.13
31 18 0.25
32 22 0.31
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (32 bp):
GTCCATATGTTCCTTAGAACATAGGTAATACT
Found at i:3378 original size:64 final size:62
Alignment explanation
Indices: 3236--3450 Score: 210
Period size: 64 Copynumber: 3.5 Consensus size: 62
3226 TAATGAAGGT
* * * * *
3236 ATGCATCGATGCACTAC---TGCATCGGTGCA-TAAAATACATTCGATG-TTGTTTTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTTTATTTTAATGGG
* *
3294 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTT-ATT-TTAATGGG
* **
3358 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATG--TTTATTTTAATGGG
**
3421 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
3451 ACACCTTCAA
Statistics
Matches: 132, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
57 1 0.01
58 14 0.11
61 23 0.17
62 3 0.02
63 4 0.03
64 81 0.61
65 3 0.02
66 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTATTTTAATGGG
Found at i:4779 original size:35 final size:33
Alignment explanation
Indices: 4732--4841 Score: 148
Period size: 35 Copynumber: 3.2 Consensus size: 33
4722 TTCCTCCTTA
* *
4732 AATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AATTGAATTATTTTGGAATTTGGG-TTTAGAATG
4766 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 -AATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
4801 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 -AATTGAATTATTTTGGAATTT-GGGTTTAGAATG
4836 AATTGA
1 AATTGA
4842 GAATTGTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
34 6 0.09
35 60 0.87
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.43
Consensus pattern (33 bp):
AATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:11414 original size:18 final size:18
Alignment explanation
Indices: 11387--11426 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
11377 AACCTTGTGA
*
11387 ATATATGTGGAATAAAAT
1 ATATAAGTGGAATAAAAT
11405 ATATAAGTGGAATAAAAT
1 ATATAAGTGGAATAAAAT
11423 ATAT
1 ATAT
11427 TTATAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (18 bp):
ATATAAGTGGAATAAAAT
Found at i:11494 original size:2 final size:2
Alignment explanation
Indices: 11489--11514 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11479 TGTGTGTGTG
11489 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
11515 GGTATTATCT
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):
TA
Found at i:15399 original size:31 final size:31
Alignment explanation
Indices: 15362--15453 Score: 121
Period size: 31 Copynumber: 3.0 Consensus size: 31
15352 TAATCACATC
*
15362 TTAATTAAATAAAAACGAAGATGACCATATA
1 TTAATTAAGTAAAAACGAAGATGACCATATA
* *
15393 TTAATTAAGTAAAAAGGAAGGTGACCATATA
1 TTAATTAAGTAAAAACGAAGATGACCATATA
** * *
15424 TTAATTTGGTAAAAATGAAAATGACCATAT
1 TTAATTAAGTAAAAACGAAGATGACCATAT
15454 CTTATGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (31 bp):
TTAATTAAGTAAAAACGAAGATGACCATATA
Found at i:20737 original size:12 final size:12
Alignment explanation
Indices: 20720--20750 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20710 TAGGGTTTAG
20720 GGTTTTAAATTA
1 GGTTTTAAATTA
*
20732 GGTTTTAAGTTA
1 GGTTTTAAATTA
20744 GGTTTTA
1 GGTTTTA
20751 GGGTTCAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (12 bp):
GGTTTTAAATTA
Found at i:27748 original size:17 final size:19
Alignment explanation
Indices: 27726--27760 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27716 AACATTAAAC
27726 TTTAAAA-A-TTAATATTA
1 TTTAAAACATTTAATATTA
27743 TTTAAAACATTTAATATT
1 TTTAAAACATTTAATATT
27761 TCATCTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAACATTTAATATTA
Found at i:29379 original size:17 final size:16
Alignment explanation
Indices: 29359--29392 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
29349 TACCTTTACA
29359 TTTTATTTAATTTGTTT
1 TTTTATTTAATTT-TTT
*
29376 TTTTATTTTATTTTTT
1 TTTTATTTAATTTTTT
29392 T
1 T
29393 AATAAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTATTTAATTTTTT
Found at i:30711 original size:2 final size:2
Alignment explanation
Indices: 30704--30747 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
30694 CATCAAAGTA
30704 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
30746 AT
1 AT
30748 GTAATAATCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31296 original size:3 final size:3
Alignment explanation
Indices: 31275--31335 Score: 95
Period size: 3 Copynumber: 20.0 Consensus size: 3
31265 ACACTCAAAA
* *
31275 TAT TAT CAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
31321 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
31336 ATTCTTTTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:31768 original size:18 final size:19
Alignment explanation
Indices: 31745--31798 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
31735 TAATTATTTA
*
31745 ATTACT-TATTAAAATAAT
1 ATTACTATAATAAAATAAT
31763 ATTACTAATAATAAAATAAT
1 ATTACT-ATAATAAAATAAT
* * *
31783 AATAGTAAAATAAAAT
1 ATTACTATAATAAAAT
31799 TATTATACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.20
19 9 0.30
20 15 0.50
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTACTATAATAAAATAAT
Found at i:31779 original size:20 final size:19
Alignment explanation
Indices: 31754--31808 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
31744 AATTACTTAT
*
31754 TAAAATAATATTACTAATAA
1 TAAAATAATAATACTAA-AA
*
31774 TAAAATAATAATAGTAAAA
1 TAAAATAATAATACTAAAA
* *
31793 TAAAATTATTATACTA
1 TAAAATAATAATACTA
31809 TATTTTAAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
TAAAATAATAATACTAAAA
Found at i:34375 original size:38 final size:38
Alignment explanation
Indices: 34324--34405 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
34314 TAGAACCATT
*
34324 AGAAAGGGCTGTTTTGGAACCATTACCTCCGAAAGATG
1 AGAAAGAGCTGTTTTGGAACCATTACCTCCGAAAGATG
34362 AGAAAGAGCTGTTTTGGAACCATTACCTCCGAAAGATG
1 AGAAAGAGCTGTTTTGGAACCATTACCTCCGAAAGATG
34400 AGAAAG
1 AGAAAG
34406 GTCCTCTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (38 bp):
AGAAAGAGCTGTTTTGGAACCATTACCTCCGAAAGATG
Found at i:41152 original size:2 final size:2
Alignment explanation
Indices: 41145--41179 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41135 ATCCTAACCC
41145 TA TA 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 TA TA T
41180 GGTGACATGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43544 original size:2 final size:2
Alignment explanation
Indices: 43539--43579 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
43529 CACGCACGTG
43539 TA TA TA TA TA 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 TA TA TA TA TA T
43580 TTCTAATTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43962 original size:31 final size:31
Alignment explanation
Indices: 43922--43987 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
43912 ACATATAGTC
*
43922 ATTAAATTTATCGAATTGTTATAAAATGATA
1 ATTAAATTTATCAAATTGTTATAAAATGATA
* *
43953 ATTAGATTTATCAAATTGTTATAAAATGATC
1 ATTAAATTTATCAAATTGTTATAAAATGATA
43984 ATTA
1 ATTA
43988 TACTCCTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (31 bp):
ATTAAATTTATCAAATTGTTATAAAATGATA
Found at i:44710 original size:2 final size:2
Alignment explanation
Indices: 44703--44735 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44693 TTAAAGGAAA
44703 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
44736 AAAGAAGTTT
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:47841 original size:14 final size:14
Alignment explanation
Indices: 47822--47849 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47812 TCGATTATAT
47822 GTTCATTTATGTTC
1 GTTCATTTATGTTC
47836 GTTCATTTATGTTC
1 GTTCATTTATGTTC
47850 ATTTATGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:58424 original size:39 final size:39
Alignment explanation
Indices: 58360--58434 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
58350 ATATTTTTTC
*
58360 TGTTTGATTAATTCTTTTGACAATAATTTTTGGAATTTG
1 TGTTTGATTAATTCTTTTGAAAATAATTTTTGGAATTTG
* *
58399 TGTTTGGTTAATT-TTTGTGAAAATAATTTTTTGAAT
1 TGTTTGATTAATTCTTT-TGAAAATAATTTTTGGAAT
58435 CTGTTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 3 0.09
39 29 0.91
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.55
Consensus pattern (39 bp):
TGTTTGATTAATTCTTTTGAAAATAATTTTTGGAATTTG
Found at i:64144 original size:28 final size:28
Alignment explanation
Indices: 64112--64174 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
64102 AACCGGTATA
*
64112 GATTGAACCGGACTAGACAACAATTTCC
1 GATTGAACCGGACTAGACAACAATTCCC
*
64140 GATTGAACCGGACTAGACAACGATTCCC
1 GATTGAACCGGACTAGACAACAATTCCC
*
64168 GGTTGAA
1 GATTGAA
64175 TCGGTCGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (28 bp):
GATTGAACCGGACTAGACAACAATTCCC
Found at i:64609 original size:52 final size:52
Alignment explanation
Indices: 64531--64638 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
64521 GATAAACGAC
64531 GATGGCTTGAGTAATCGTCGCCGGTGAGAAGAGTACTTGATAGGATGATTTG
1 GATGGCTTGAGTAATCGTCGCCGGTGAGAAGAGTACTTGATAGGATGATTTG
64583 GATGGCTTGAGTAATCGTCGCCGGTGAGAAGAGTACTTGATAGGATGATTTG
1 GATGGCTTGAGTAATCGTCGCCGGTGAGAAGAGTACTTGATAGGATGATTTG
64635 GATG
1 GATG
64639 TAAAGAGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.25, C:0.11, G:0.35, T:0.29
Consensus pattern (52 bp):
GATGGCTTGAGTAATCGTCGCCGGTGAGAAGAGTACTTGATAGGATGATTTG
Found at i:67246 original size:143 final size:143
Alignment explanation
Indices: 67052--67730 Score: 1112
Period size: 143 Copynumber: 4.7 Consensus size: 143
67042 AGTTGATTTT
**
67052 TTTTACTTCTTTCGATGATGTTGTCGGGAATCATATATTGTTACCACTCATCTTGAGGTATATTG
1 TTTT-CTTCTTTCGATGATGTTGTCGGGAATCATATATCCTTACCACTCATCTTGAGGTATATTG
*
67117 CATTTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATGGTATTGAAG
65 CATTTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATAGTATTGAAG
67182 TTGATTTTTTGTAC
130 TTGATTTTTTGTAC
*
67196 TTTTCTTCTTTCTATGATGTTGTCGGGAATCATATATCCTTACCACTCATCTTGAGGTATATTGC
1 TTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATCCTTACCACTCATCTTGAGGTATATTGC
*
67261 ATTTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATGGTATTGAAGT
66 ATTTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATAGTATTGAAGT
67326 TGATTTTTTGTAC
131 TGATTTTTTGTAC
67339 TTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATCCTTACCACTCATCTTGAGGTATATTGC
1 TTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATCCTTACCACTCATCTTGAGGTATATTGC
* *
67404 ATTTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGGAGT
66 ATTTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATAGTATTGAAGT
*
67469 TGATTTTTTTTTAC
131 TGA-TTTTTTGTAC
* *
67483 TTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATTGTTACCAGTGCCACTCATCTTGAGGTA
1 TTTTCTTCTTTCGATGATGTTGTCGGGAATCATATA----T-CC-TTACCACTCATCTTGAGGTA
* *
67548 TATTGCATTTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCT
60 TATTGCATTTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATAGTAT
67613 TGAAGTTGA-TTTTT-TAC
125 TGAAGTTGATTTTTTGTAC
*
67630 TTTTCTTCTTTCGATGATGTTG-CTGGGAATCATATATCGTTACCACTCATCTTGAGGTATATTG
1 TTTTCTTCTTTCGATGATGTTGTC-GGGAATCATATATCCTTACCACTCATCTTGAGGTATATTG
** *
67694 TGTTTTGTTGATTGATTATGTTTCGAATCCCACTTGA
65 CATTTTGTTGATTGATTATGTTTTGAATCCCACTTGA
67731 GGAATATTGT
Statistics
Matches: 510, Mismatches: 17, Indels: 19
0.93 0.03 0.03
Matches are distributed among these distances:
141 58 0.11
142 1 0.00
143 266 0.52
144 49 0.10
146 1 0.00
147 37 0.07
148 6 0.01
149 2 0.00
150 90 0.18
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.46
Consensus pattern (143 bp):
TTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATCCTTACCACTCATCTTGAGGTATATTGC
ATTTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATAGTATTGAAGT
TGATTTTTTGTAC
Found at i:67600 original size:150 final size:145
Alignment explanation
Indices: 66974--67730 Score: 1034
Period size: 143 Copynumber: 5.2 Consensus size: 145
66964 GCATTTGCCA
* *
66974 TTTGCTTGATTGATCATGTTTCGAACCCCACTTGAATGCACATATTTGAAATTTTGAATATAGTC
1 TTTG-TTGATTGATTATGTTTCGAATCCCACTTGAATGCAC--A--T---A-TTTGAATATAGTC
*
67039 TT-CAGTTGATTTTTTTTA-----CTTCTTTCGATGATGTTGTCGGGAATCATATATTGTT--A-
57 TTGAAGTTGATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATA-TGTTCCAT
67095 CCACTCATCTTGAGGTATATTGCAT
121 CCACTCATCTTGAGGTATATTGCAT
* * *
67120 TTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATGGTATTGAAGTTG
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
* * *
67185 ATTTTTTGTACTTTTCTTCTTTCTATGATGTTGTCGGGAATCATATA---TCCTTACCACTCATC
66 ATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATGTTCCAT-CCACTCATC
67247 TTGAGGTATATTGCAT
130 TTGAGGTATATTGCAT
* * *
67263 TTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATGGTATTGAAGTTG
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
* *
67328 ATTTTTTGTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATA---TCCTTACCACTCATC
66 ATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATGTTCCAT-CCACTCATC
67390 TTGAGGTATATTGCAT
130 TTGAGGTATATTGCAT
* *
67406 TTTGTTGATTGATTATGTTTTGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGGAGTTG
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
67471 ATTTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATTGTTACCAGTGCCACT
66 A-TTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATA-TGTT-CCA-T-CCACT
67536 CATCTTGAGGTATATTGCAT
126 CATCTTGAGGTATATTGCAT
67556 TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
67621 A--TTTTTTACTTTTCTTCTTTCGATGATGTTG-CTGGGAATCATATATCGTT--A-CCACTCAT
66 ATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTC-GGGAATCATATAT-GTTCCATCCACTCAT
**
67680 CTTGAGGTATATTGTGT
129 CTTGAGGTATATTGCAT
67697 TTTGTTGATTGATTATGTTTCGAATCCCACTTGA
1 TTTGTTGATTGATTATGTTTCGAATCCCACTTGA
67731 GGAATATTGT
Statistics
Matches: 572, Mismatches: 20, Indels: 43
0.90 0.03 0.07
Matches are distributed among these distances:
137 13 0.02
138 15 0.03
139 1 0.00
141 58 0.10
143 262 0.46
144 46 0.08
145 33 0.06
146 6 0.01
147 45 0.08
148 1 0.00
149 2 0.00
150 90 0.16
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.45
Consensus pattern (145 bp):
TTTGTTGATTGATTATGTTTCGAATCCCACTTGAATGCACATATTTGAATATAGTCTTGAAGTTG
ATTTTTTTTACTTTTCTTCTTTCGATGATGTTGTCGGGAATCATATATGTTCCATCCACTCATCT
TGAGGTATATTGCAT
Found at i:69883 original size:60 final size:60
Alignment explanation
Indices: 69746--69883 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
69736 TAAAGTACTC
* *
69746 AAATGGTCCCCCGACTATAGGATAATGTTTTATTGAATCTCTTGACTATTAAAAGTTACA
1 AAATGGTCCCTCGACTATAGGATAATGCTTTATTGAATCTCTTGACTATTAAAAGTTACA
* * * * * * *
69806 AAATGATCCCTCAACTATAGGA-AGTTGCTTTGTTGAGTC-CTTCGACTATTAAAATTTATA
1 AAATGGTCCCTCGACTATAGGATA-ATGCTTTATTGAATCTCTT-GACTATTAAAAGTTACA
*
69866 AAATGGTCACTCGACTAT
1 AAATGGTCCCTCGACTAT
69884 TAGTTATATT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 4 0.06
60 60 0.94
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (60 bp):
AAATGGTCCCTCGACTATAGGATAATGCTTTATTGAATCTCTTGACTATTAAAAGTTACA
Found at i:74165 original size:3 final size:3
Alignment explanation
Indices: 74157--74190 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
74147 AACTTAAATA
74157 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
74191 CAATTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:91208 original size:17 final size:16
Alignment explanation
Indices: 91172--91205 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
91162 TTTATAGATG
91172 AAGAAAAATAAAATAA
1 AAGAAAAATAAAATAA
91188 AAGAAAAA-AATAATAA
1 AAGAAAAATAA-AATAA
91204 AA
1 AA
91206 AGATTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAGAAAAATAAAATAA
Found at i:91214 original size:21 final size:21
Alignment explanation
Indices: 91190--91229 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
91180 TAAAATAAAA
91190 GAAAA-AAATAATAAAAAGATT
1 GAAAAGAAAT-ATAAAAAGATT
*
91211 GAAAAGAAATTTAAAAAGA
1 GAAAAGAAATATAAAAAGA
91230 AAGTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (21 bp):
GAAAAGAAATATAAAAAGATT
Found at i:92135 original size:6 final size:6
Alignment explanation
Indices: 92124--92152 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
92114 CGTATTACCA
92124 CGACCC CGACCC CGACCC CGA-CC CGACCC
1 CGACCC CGACCC CGACCC CGACCC CGACCC
92153 GACACGACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.66, G:0.17, T:0.00
Consensus pattern (6 bp):
CGACCC
Found at i:92870 original size:41 final size:41
Alignment explanation
Indices: 92747--92924 Score: 232
Period size: 41 Copynumber: 4.3 Consensus size: 41
92737 CTTTTTTTTA
* *
92747 ACTATCGCAACGAATTTGGAAAATCTCAACGATAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
* * * * ** *
92788 ACTTTCGCAACAACAACTGTAGACTATCGCAACAACAACTGTAG
1 ACTATCGCAAC--GAA-TTTGGAAAATCGCAACGACAACTGTAG
92832 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
*
92873 ACTATCGCAACGAATTTGGAAAATCGCAACGAC-ATTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
92913 ACTATCGCAACG
1 ACTATCGCAACG
92925 CGAAATGCAA
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
40 18 0.15
41 65 0.56
42 2 0.02
43 2 0.02
44 30 0.26
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
Found at i:92884 original size:22 final size:22
Alignment explanation
Indices: 92773--92924 Score: 138
Period size: 22 Copynumber: 7.2 Consensus size: 22
92763 TGGAAAATCT
* *
92773 CAACGATAACTGTAGACTTTCG
1 CAACGACAACTGTAGACTATCG
*
92795 CAACAACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
*
92817 CAACAACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
* * **
92839 CAACG--AA-TTTGGAAAATCG
1 CAACGACAACTGTAGACTATCG
92858 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
* * **
92880 CAACG--AA-TTTGGAAAATCG
1 CAACGACAACTGTAGACTATCG
*
92899 CAACGAC-ATTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
92920 CAACG
1 CAACG
92925 CGAAATGCAA
Statistics
Matches: 104, Mismatches: 20, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
19 26 0.25
20 5 0.05
21 15 0.14
22 58 0.56
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (22 bp):
CAACGACAACTGTAGACTATCG
Done.