Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006416.1 Hibiscus syriacus cultivar Beakdansim tig00015481_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: 91721
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2965 original size:31 final size:31
Alignment explanation
Indices: 2924--2991 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
2914 TTATAATACA
2924 ATCCCCCAACATTTAGCCCATTTGCAATATG
1 ATCCCCCAACATTTAGCCCATTTGCAATATG
* *
2955 ATCCCTCAACATTTAGTCCATTTGCAATATG
1 ATCCCCCAACATTTAGCCCATTTGCAATATG
*
2986 GTCCCC
1 ATCCCC
2992 TACGTAACTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.31
Consensus pattern (31 bp):
ATCCCCCAACATTTAGCCCATTTGCAATATG
Found at i:18388 original size:26 final size:26
Alignment explanation
Indices: 18359--18411 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
18349 TAAGTTGTTC
18359 GTTTTTTTTGTCTTTATTAATCTACG
1 GTTTTTTTTGTCTTTATTAATCTACG
*
18385 GTTTTTTTTGTTTTTATTAATCTACG
1 GTTTTTTTTGTCTTTATTAATCTACG
18411 G
1 G
18412 CGGCACTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.09, G:0.13, T:0.62
Consensus pattern (26 bp):
GTTTTTTTTGTCTTTATTAATCTACG
Found at i:19688 original size:2 final size:2
Alignment explanation
Indices: 19681--19734 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
19671 AAAAATGTGC
19681 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
19723 AT AT AT AT AT AT
1 AT AT AT AT AT AT
19735 CGCTTTCCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20660 original size:60 final size:60
Alignment explanation
Indices: 20524--20660 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
20514 ATAGTCAGAT
*
20524 GACCATTTTGTAACTTTTAATAGTTGGAGGACTTAACAAAGCAACATCCTATAGTTGAGG
1 GACCATTTTGTAACTTTTAATAGTTGGAGGACTCAACAAAGCAACATCCTATAGTTGAGG
* * * * **
20584 GATCAATTTT-TAACTTTTGATATTTAGGA-GACTCAACAAAGTATTATCCTATAGTTGAGG
1 GA-CCATTTTGTAACTTTTAATAGTT-GGAGGACTCAACAAAGCAACATCCTATAGTTGAGG
20644 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
20661 ACCCATAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
59 5 0.08
60 50 0.77
61 10 0.15
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTTGGAGGACTCAACAAAGCAACATCCTATAGTTGAGG
Found at i:22008 original size:22 final size:22
Alignment explanation
Indices: 21968--22009 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21958 TGTTTTGATA
* * *
21968 AAAAAAATAGTTTAGAGACTCT
1 AAAAAAATAATTGAAAGACTCT
21990 AAAAAAATAATTGAAAGACT
1 AAAAAAATAATTGAAAGACT
22010 TATTTTACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.12, T:0.24
Consensus pattern (22 bp):
AAAAAAATAATTGAAAGACTCT
Found at i:25496 original size:37 final size:37
Alignment explanation
Indices: 25420--25496 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
25410 TTTTTATATT
*
25420 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
25457 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
25494 TTT
1 TTT
25497 GTAACATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:30992 original size:43 final size:43
Alignment explanation
Indices: 30945--31240 Score: 246
Period size: 42 Copynumber: 6.9 Consensus size: 43
30935 ATTATGAGTT
* *
30945 TCAATTATAAATGTAAAAAGTGGGATTGAAAAAATTAGGGACC
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGACC
* *
30988 TCAATTATAAAGGTAAAAAGTGGGATTG-AAAAATTAGAGG-TC
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAG-GGACC
* *
31030 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATAAGGGGCC
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGACC
* * * * ***
31073 TCAATTTTAATGATAAAATA-TGATATTGAAAAAATTTAGGGTGT
1 TCAATTATAAAGGTAAAA-AGTGAGATTGAAAAAA-TTAGGGACC
* * * * **
31117 TCAATTATAAAGGTGAAAAGTGATATTGAAAAAAATA-TGAGT
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGACC
* * * * * **
31159 TAAATTATAAAGATAAAACGTGGGATT-ACAAAAATTA-GAATA
1 TCAATTATAAAGGTAAAAAGTGAGATTGA-AAAAATTAGGGACC
*
31201 TCAATTATAAAAGTAAAAAGT-ATGATTGAAAAAAATTAGG
1 TCAATTATAAAGGTAAAAAGTGA-GATTG-AAAAAATTAGG
31241 ACCCTGAGCA
Statistics
Matches: 206, Mismatches: 36, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.00
42 92 0.45
43 77 0.37
44 36 0.17
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (43 bp):
TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGACC
Found at i:31033 original size:42 final size:43
Alignment explanation
Indices: 30926--31239 Score: 270
Period size: 43 Copynumber: 7.3 Consensus size: 43
30916 ATTTTACGGT
* * *
30926 ATTGAAAAAATTATGA-GTTTCAATTATAAATGTAAAAAGTGGG
1 ATTGAAAAAATTA-GAGGTCTCAATTATAAAGGTAAAAAGTGAG
* *
30969 ATTGAAAAAATTAG-GGACCTCAATTATAAAGGTAAAAAGTGGG
1 ATTGAAAAAATTAGAGG-TCTCAATTATAAAGGTAAAAAGTGAG
31012 ATTG-AAAAATTAGAGGTCTCAATTATAAAGGTAAAAAGTGAG
1 ATTGAAAAAATTAGAGGTCTCAATTATAAAGGTAAAAAGTGAG
* * * * * * *
31054 ATTGAAAAAATAAGGGGCCTCAATTTTAATGATAAAATA-TGAT
1 ATTGAAAAAATTAGAGGTCTCAATTATAAAGGTAAAA-AGTGAG
* * *
31097 ATTGAAAAAATTTAG-GGTGTTCAATTATAAAGGTGAAAAGTGAT
1 ATTGAAAAAA-TTAGAGGT-CTCAATTATAAAGGTAAAAAGTGAG
* * * * *
31141 ATTGAAAAAAATATGA-GT-TAAATTATAAAGATAAAACGTGGG
1 ATTGAAAAAATTA-GAGGTCTCAATTATAAAGGTAAAAAGTGAG
* * *
31183 ATT-ACAAAAATTAGA-ATATCAATTATAAAAGTAAAAAGT-ATG
1 ATTGA-AAAAATTAGAGGTCTCAATTATAAAGGTAAAAAGTGA-G
31225 ATTGAAAAAAATTAG
1 ATTG-AAAAAATTAG
31240 GACCCTGAGC
Statistics
Matches: 223, Mismatches: 33, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
41 4 0.02
42 88 0.39
43 95 0.43
44 36 0.16
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.28
Consensus pattern (43 bp):
ATTGAAAAAATTAGAGGTCTCAATTATAAAGGTAAAAAGTGAG
Found at i:31037 original size:85 final size:85
Alignment explanation
Indices: 30926--31240 Score: 325
Period size: 85 Copynumber: 3.7 Consensus size: 85
30916 ATTTTACGGT
* *
30926 ATTGAAAAAATTATGAGTTTCAATTATAAATGTAAAAAGTGGGATTGAAAAAATTAGGGACCTCA
1 ATTGAAAAAATTA-GAGTTTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGACCTCA
*
30991 ATTATAAAGGTAAAAAGTGGG
65 ATTATAAAGATAAAAAGTGGG
* * *
31012 ATTG-AAAAATTAGAGGTCTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATAAGGGGCCTCA
1 ATTGAAAAAATTAGA-GTTTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGACCTCA
* * **
31076 ATTTTAATGATAAAATA-TGAT
65 ATTATAAAGATAAAA-AGTGGG
* * * * * ** *
31097 ATTGAAAAAATTTAGGGTGTTCAATTATAAAGGTGAAAAGTGATATTGAAAAAAATA-TGAGTTA
1 ATTGAAAAAA-TTAGAGT-TTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGACCTC
*
31161 AATTATAAAGATAAAACGTGGG
64 AATTATAAAGATAAAAAGTGGG
* * *
31183 ATT-ACAAAAATTAGAATATCAATTATAAAAGTAAAAAGT-ATGATTGAAAAAAATTAGG
1 ATTGA-AAAAATTAGAGTTTCAATTATAAAGGTAAAAAGTGA-GATTG-AAAAAATTAGG
31241 ACCCTGAGCA
Statistics
Matches: 185, Mismatches: 34, Indels: 20
0.77 0.14 0.08
Matches are distributed among these distances:
83 1 0.01
84 25 0.14
85 84 0.45
86 38 0.21
87 37 0.20
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (85 bp):
ATTGAAAAAATTAGAGTTTCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGACCTCAA
TTATAAAGATAAAAAGTGGG
Found at i:32421 original size:21 final size:21
Alignment explanation
Indices: 32392--32432 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32382 TTGTTATAAT
32392 TTAACTTTGAT-TCTTAAAAG
1 TTAACTTTGATATCTTAAAAG
*
32412 TTAACCTTTGATATTTTAAAA
1 TTAA-CTTTGATATCTTAAAA
32433 ATACATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (21 bp):
TTAACTTTGATATCTTAAAAG
Found at i:35131 original size:25 final size:25
Alignment explanation
Indices: 35082--35132 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
35072 ACAATCGACT
*
35082 TTGTTTCCAATCACTTGAACCAATC
1 TTGTTTCCAATCACTTGAAACAATC
* * *
35107 TTGTTTTCAATCATTTGAAATAATC
1 TTGTTTCCAATCACTTGAAACAATC
35132 T
1 T
35133 CTCCCTACAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (25 bp):
TTGTTTCCAATCACTTGAAACAATC
Found at i:47987 original size:49 final size:50
Alignment explanation
Indices: 47933--48033 Score: 195
Period size: 49 Copynumber: 2.0 Consensus size: 50
47923 GTTAAAACTC
47933 ACCCCAATGTAACATGTTTAGTTGTAACCAAAACTATTACAAATTAT-TA
1 ACCCCAATGTAACATGTTTAGTTGTAACCAAAACTATTACAAATTATATA
47982 ACCCCAATGTAACATGTTTAGTTGTAACCAAAACTATTACAAATTATATA
1 ACCCCAATGTAACATGTTTAGTTGTAACCAAAACTATTACAAATTATATA
48032 AC
1 AC
48034 TTTTTAAGGC
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 47 0.92
50 4 0.08
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.32
Consensus pattern (50 bp):
ACCCCAATGTAACATGTTTAGTTGTAACCAAAACTATTACAAATTATATA
Found at i:48009 original size:26 final size:26
Alignment explanation
Indices: 47933--48010 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
47923 GTTAAAACTC
47933 ACCCCAATGTAACATGTTTAGTTGTA
1 ACCCCAATGTAACATGTTTAGTTGTA
** * * **
47959 ACCAAAACTATTACA-AATTA--T-TA
1 ACCCCAA-TGTAACATGTTTAGTTGTA
47982 ACCCCAATGTAACATGTTTAGTTGTA
1 ACCCCAATGTAACATGTTTAGTTGTA
48008 ACC
1 ACC
48011 AAAACTATTA
Statistics
Matches: 35, Mismatches: 12, Indels: 10
0.61 0.21 0.18
Matches are distributed among these distances:
22 5 0.14
23 10 0.29
24 1 0.03
25 1 0.03
26 13 0.37
27 5 0.14
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (26 bp):
ACCCCAATGTAACATGTTTAGTTGTA
Found at i:58167 original size:55 final size:54
Alignment explanation
Indices: 58083--58194 Score: 215
Period size: 55 Copynumber: 2.1 Consensus size: 54
58073 TGACCTTATC
58083 TACTTCCATGGCTTGAAGAATAATAATTCACTATAAACGTAAAGAATATGAAGAA
1 TACTTCCATGGCTTGAAGAATAATAATTCACTAT-AACGTAAAGAATATGAAGAA
58138 TACTTCCATGGCTTGAAGAATAATAATTCACTATAACGTAAAGAATATGAAGAA
1 TACTTCCATGGCTTGAAGAATAATAATTCACTATAACGTAAAGAATATGAAGAA
58192 TAC
1 TAC
58195 AAATACATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 23 0.40
55 34 0.60
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (54 bp):
TACTTCCATGGCTTGAAGAATAATAATTCACTATAACGTAAAGAATATGAAGAA
Found at i:58504 original size:14 final size:14
Alignment explanation
Indices: 58472--58516 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
58462 TTTCATTTTT
58472 AAATATTTTT-AT-
1 AAATATTTTTCATA
*
58484 TAATATTTTTCATA
1 AAATATTTTTCATA
58498 AAATATTTTTTCA-A
1 AAATA-TTTTTCATA
58512 AAATA
1 AAATA
58517 GAAATGATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 9 0.32
13 2 0.07
14 10 0.36
15 7 0.25
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (14 bp):
AAATATTTTTCATA
Found at i:64319 original size:23 final size:21
Alignment explanation
Indices: 64281--64373 Score: 98
Period size: 23 Copynumber: 4.2 Consensus size: 21
64271 TATTAAAATA
*
64281 TTTAA-AATATATTATTAATAT
1 TTTAATAATATAATATT-ATAT
64302 TTCTAATAATATAATATTATAT
1 TT-TAATAATATAATATTATAT
*
64324 TTTAATATTATAATCAATTATAT
1 TTTAATAATATAAT--ATTATAT
*
64347 TATAATAATATAAGATATTATAT
1 TTTAATAATAT-A-ATATTATAT
64370 TTTA
1 TTTA
64374 TTTTAATAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
21 13 0.21
22 9 0.15
23 36 0.59
24 1 0.02
25 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (21 bp):
TTTAATAATATAATATTATAT
Found at i:64452 original size:17 final size:17
Alignment explanation
Indices: 64430--64486 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
64420 ATTTCATAGA
64430 AATAATATTAAATTATT
1 AATAATATTAAATTATT
*
64447 AATAATGAATAATATTATT
1 AATAAT-ATTAA-ATTATT
*
64466 -AT-ATATTTAA-TATT
1 AATAATATTAAATTATT
64480 AATAATA
1 AATAATA
64487 ATCTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 4 0.12
15 3 0.09
16 6 0.18
17 8 0.24
18 6 0.18
19 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AATAATATTAAATTATT
Found at i:64493 original size:17 final size:16
Alignment explanation
Indices: 64294--64494 Score: 55
Period size: 17 Copynumber: 12.4 Consensus size: 16
64284 AAAATATATT
**
64294 ATTAATATTTCTAATA
1 ATTAATATTAATAATA
64310 ATATAATATT-AT-AT-
1 AT-TAATATTAATAATA
*
64324 TTTAATATT-ATAATCA
1 ATTAATATTAATAAT-A
64340 ATT-ATATT-ATAATA
1 ATTAATATTAATAATA
* *
64354 ATATAAGA-T-ATTATA
1 AT-TAATATTAATAATA
* * *
64369 TTTTATTTTAATAATATA
1 ATTAATATTAAT-A-ATA
*
64387 ATAAATTATTAATAA-A
1 ATTAA-TATTAATAATA
* * *
64403 ATTTATATTATTTATTA
1 ATTAATATTA-ATAATA
* **
64420 ATTTCATAGAAATAAT-
1 A-TTAATATTAATAATA
64436 ATTAAATTATTAATAATGA
1 ATT-AA-TATTAATAAT-A
*
64455 A-TAATATTATTATATA
1 ATTAATATTAATA-ATA
*
64471 TTTAATATTAATAATA
1 ATTAATATTAATAATA
64487 ATCTAATA
1 AT-TAATA
64495 ATATTTTAAT
Statistics
Matches: 134, Mismatches: 30, Indels: 41
0.65 0.15 0.20
Matches are distributed among these distances:
13 9 0.07
14 8 0.06
15 28 0.21
16 29 0.22
17 40 0.30
18 13 0.10
19 7 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (16 bp):
ATTAATATTAATAATA
Found at i:64705 original size:22 final size:23
Alignment explanation
Indices: 64674--64721 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
64664 ACAAATTATT
64674 TTAATATTTTAAAA-ATAATAATA
1 TTAATATTTTAAAATA-AATAATA
*
64697 TTAAT-TTTTATAATAAATAATA
1 TTAATATTTTAAAATAAATAATA
64719 TTA
1 TTA
64722 TTTCTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAATATTTTAAAATAAATAATA
Found at i:68745 original size:29 final size:29
Alignment explanation
Indices: 68690--68745 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
68680 CACACACAAA
* *
68690 AACAGTTAAAATTAATTGTTTATTTTTTG
1 AACAGTTAAAATAAATTGTTAATTTTTTG
*
68719 AACAG-TAAAATAAATTGTTAATATTTT
1 AACAGTTAAAATAAATTGTTAATTTTTT
68746 ATATAGCACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (29 bp):
AACAGTTAAAATAAATTGTTAATTTTTTG
Found at i:70028 original size:18 final size:19
Alignment explanation
Indices: 69994--70048 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
69984 GTATTTAAGT
*
69994 TTTAATTGTTATTATTTCA
1 TTTATTTGTTATTATTTCA
*
70013 TTTATTTGTT-TTATTTTA
1 TTTATTTGTTATTATTTCA
*
70031 TTTATATGTATATT-TTTC
1 TTTATTTGT-TATTATTTC
70049 TTAATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 15 0.50
19 13 0.43
20 2 0.07
ACGTcount: A:0.22, C:0.04, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTATTTGTTATTATTTCA
Found at i:70375 original size:20 final size:20
Alignment explanation
Indices: 70350--70399 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
70340 AAACCTTTAT
70350 CTTTTTTTTAATCCGTATCC
1 CTTTTTTTTAATCCGTATCC
** **
70370 CTTTTTTAAAATTTGTATCC
1 CTTTTTTTTAATCCGTATCC
70390 CTTTTTTTTA
1 CTTTTTTTTA
70400 TTTTCGGTGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.04, T:0.60
Consensus pattern (20 bp):
CTTTTTTTTAATCCGTATCC
Found at i:78988 original size:19 final size:19
Alignment explanation
Indices: 78964--79011 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
78954 AAACCTTTAT
78964 CTTTTTTTAATCCGTATCC
1 CTTTTTTTAATCCGTATCC
* **
78983 CTTTTTTAAAATTTGTATCC
1 CTTTTTT-TAATCCGTATCC
79003 CTTTTTTTA
1 CTTTTTTTA
79012 TTTTCGGTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.19, C:0.19, G:0.04, T:0.58
Consensus pattern (19 bp):
CTTTTTTTAATCCGTATCC
Found at i:83870 original size:18 final size:18
Alignment explanation
Indices: 83847--83881 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
83837 TATTACATTC
* *
83847 AAAGTTTTTTAAGCAGTT
1 AAAGTTGTTTAAACAGTT
83865 AAAGTTGTTTAAACAGT
1 AAAGTTGTTTAAACAGT
83882 ATGAATCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (18 bp):
AAAGTTGTTTAAACAGTT
Found at i:86292 original size:13 final size:13
Alignment explanation
Indices: 86274--86299 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
86264 CAAAATAGAA
86274 GTCTTTTTATTTT
1 GTCTTTTTATTTT
86287 GTCTTTTTATTTT
1 GTCTTTTTATTTT
86300 AAAATAAAAC
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:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (13 bp):
GTCTTTTTATTTT
Found at i:88680 original size:23 final size:23
Alignment explanation
Indices: 88631--88680 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
88621 AACGACCGAA
*
88631 AAAGAAGACGAAAAACGTGTCAC
1 AAAGAAGACGAAAAACGTATCAC
* *
88654 AAAGACAGA-GAAAAATGTATCAT
1 AAAGA-AGACGAAAAACGTATCAC
88677 AAAG
1 AAAG
88681 GCATAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.56, C:0.12, G:0.20, T:0.12
Consensus pattern (23 bp):
AAAGAAGACGAAAAACGTATCAC
Found at i:88926 original size:2 final size:2
Alignment explanation
Indices: 88921--88971 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
88911 TAATAACATG
88921 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
88963 AT AT AT AT A
1 AT AT AT AT A
88972 CGAGTTAGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.