Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000385.1 Hibiscus syriacus cultivar Beakdansim tig00000708_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: 47630
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:11715 original size:24 final size:26
Alignment explanation
Indices: 11660--11712 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
11650 GAACAATTTA
* *
11660 ATTAATGGTGTGTATCGATGTGTCAC
1 ATTAATGGTGTGTATCAATGTGACAC
*
11686 ATTAATGGTGTGTTTCAATGT-ACAC
1 ATTAATGGTGTGTATCAATGTGACAC
11711 AT
1 AT
11713 AATTTTCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTAATGGTGTGTATCAATGTGACAC
Found at i:12889 original size:31 final size:31
Alignment explanation
Indices: 12853--12913 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
12843 AACTTAAAAG
* *
12853 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
12884 AGTTTTACAATACTGAAATTTAAATAATTT
1 AGTTTTACAATACTGAAATTTAAATAATTT
12914 ATACAACTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:12987 original size:22 final size:22
Alignment explanation
Indices: 12938--12986 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12928 ATAAATTATT
* **
12938 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
12960 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
12983 TAAA
1 TAAA
12987 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:12990 original size:54 final size:54
Alignment explanation
Indices: 12926--13478 Score: 430
Period size: 54 Copynumber: 10.4 Consensus size: 54
12916 ACAACTACAA
*
12926 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
12980 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * *
13034 AAATAAATTATTTAAAATAAATCAATCCATA-CTAATAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTA-AAATAAATCAATCCATAC
* * *** * * *
13088 TAATAAATTATTTAAAATAAATAAATCTATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
* * ** * *
13141 -CAT--A-T-TTTAAAACAAATCAATCCATACTAATAAATCATTTAAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATAC
* ** * ** * **
13195 -CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATAC
** ** * ** * **
13245 -AATCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C
1 TAATAAATTA-TTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATAC
** ** ** *
13299 -AATTCA-TA-CAACTATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
13350 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
13404 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
13458 TAAT-AATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
13479 TATTTAAAAT
Statistics
Matches: 433, Mismatches: 48, Indels: 37
0.84 0.09 0.07
Matches are distributed among these distances:
48 23 0.05
49 3 0.01
50 18 0.04
51 9 0.02
52 25 0.06
53 22 0.05
54 329 0.76
55 3 0.01
56 1 0.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:12996 original size:32 final size:32
Alignment explanation
Indices: 12958--13478 Score: 307
Period size: 32 Copynumber: 18.4 Consensus size: 32
12948 CAATCTATAT
12958 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
12990 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
13012 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
13044 TTTAAAATAAATCAATCCATAC---T--A--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
13069 --T-AAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * *
13098 TTTAAAATAAATAAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
13128 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
13146 TTTAAAACAAATCAATCCATACTAATAAATCA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
13178 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
13200 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
13232 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
13254 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
13286 TTTAAAATAAATCAATTCATACAACTATAAATCAATCCATA
1 TTTAAAATAAATCAATCCAT---AC--T-AATAAAT---TA
*
13327 TTTTAAAATAAATCAATTCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
13360 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
13382 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
13414 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
13436 TTTAAAATAAATCAATCCATACTAAT-AATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
13467 TTTAAAATAAAT
1 TTTAAAATAAAT
13479 TATTTAAAAT
Statistics
Matches: 391, Mismatches: 13, Indels: 171
0.68 0.02 0.30
Matches are distributed among these distances:
20 1 0.00
22 111 0.28
23 10 0.03
24 7 0.02
25 3 0.01
26 28 0.07
27 2 0.01
28 16 0.04
29 3 0.01
30 6 0.02
31 24 0.06
32 138 0.35
33 2 0.01
35 2 0.01
36 6 0.02
37 2 0.01
38 6 0.02
39 2 0.01
41 2 0.01
42 20 0.05
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:13075 original size:22 final size:22
Alignment explanation
Indices: 13048--13095 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
13038 AAATTATTTA
13048 AAATAAATCAATCCATACTAAT
1 AAATAAATCAATCCATACTAAT
13070 AAATAAATCAATCCATACTAAT
1 AAATAAATCAATCCATACTAAT
13092 AAAT
1 AAAT
13096 TATTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACTAAT
Found at i:13204 original size:22 final size:22
Alignment explanation
Indices: 13178--13220 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
13168 TAATAAATCA
13178 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
13200 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
13221 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:13229 original size:22 final size:22
Alignment explanation
Indices: 13180--13228 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
13170 ATAAATCATT
**
13180 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
13202 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
13225 TAAA
1 TAAA
13229 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:13258 original size:22 final size:22
Alignment explanation
Indices: 13232--13274 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
13222 TAATAAATTA
13232 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
13254 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
13275 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:13283 original size:22 final size:22
Alignment explanation
Indices: 13234--13356 Score: 77
Period size: 22 Copynumber: 5.2 Consensus size: 22
13224 ATAAATTATT
**
13234 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
13256 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
* * *
13279 TAAATTATTTAAAATAAATCAAT-TCA
1 TAAA--A--T-AAATCAATCCATATAA
**
13305 TACAACTATAAATCAATCCATATTT
1 TA-AA--ATAAATCAATCCATATAA
*
13330 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
13353 TAAA
1 TAAA
13357 TTATTTAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
22 33 0.42
23 10 0.13
24 12 0.15
25 5 0.06
26 4 0.05
27 5 0.06
28 10 0.13
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:13332 original size:74 final size:74
Alignment explanation
Indices: 13238--13380 Score: 268
Period size: 74 Copynumber: 1.9 Consensus size: 74
13228 ATTATTTAAA
*
13238 ATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATT
1 ATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
13303 CATACAACT
66 CATACAACT
*
13312 ATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATC
1 ATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
13377 CATA
66 CATA
13381 TTTTAAAATA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (74 bp):
ATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
CATACAACT
Found at i:13352 original size:128 final size:128
Alignment explanation
Indices: 13181--13512 Score: 495
Period size: 128 Copynumber: 2.6 Consensus size: 128
13171 TAAATCATTT
*
13181 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 AAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCA
*
13246 ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATA-C
66 ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATC
*
13308 AACTATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATC
1 AA-AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATC
13373 AATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTT
65 AATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA--T
*
13438 T
128 C
* * *
13439 AAAATAAATCAATCCATA--CT--AAT-AAT-TATT--TA-AAATAAATTATTTAAAATAAATCA
1 AAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCA
*
13495 ATCCATATTTTATAATAA
66 ATCCATATTTTAAAATAA
13513 TTTATTTTAA
Statistics
Matches: 192, Mismatches: 9, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
121 40 0.21
122 2 0.01
124 3 0.02
125 3 0.02
126 3 0.02
127 2 0.01
128 122 0.64
130 15 0.08
131 2 0.01
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (128 bp):
AAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCA
ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATC
Found at i:13386 original size:22 final size:22
Alignment explanation
Indices: 13360--13402 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
13350 TAATAAATTA
13360 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
13382 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
13403 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:13411 original size:22 final size:22
Alignment explanation
Indices: 13362--13410 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
13352 ATAAATTATT
**
13362 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
13384 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
13407 TAAA
1 TAAA
13411 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:13440 original size:22 final size:22
Alignment explanation
Indices: 13414--13456 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
13404 TAATAAATTA
13414 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
13436 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
13457 CTAATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:13498 original size:45 final size:47
Alignment explanation
Indices: 13325--13589 Score: 252
Period size: 54 Copynumber: 5.3 Consensus size: 47
13315 AATCAATCCA
*
13325 TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT--A--AAT
13376 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 ---TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT--A--AAT
13430 CCATATTTTAAAATAAATCAATCCATACTAAT-AATTATTTAAAATAAAT
1 ---TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
* *
13479 TA-TTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAATCCATA----CTAATAAATTA-TTTAAAATAAAT
* * **
13530 TATTTTATAATAAAT-TAT-TTTA-TAATAAATTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTAAAATAAAT
13575 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
13590 AAGCTTATTA
Statistics
Matches: 195, Mismatches: 9, Indels: 23
0.86 0.04 0.10
Matches are distributed among these distances:
45 57 0.29
46 2 0.01
49 7 0.04
50 6 0.03
51 17 0.09
52 11 0.06
53 13 0.07
54 82 0.42
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (47 bp):
TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
Found at i:13516 original size:32 final size:33
Alignment explanation
Indices: 13382--13516 Score: 95
Period size: 32 Copynumber: 4.1 Consensus size: 33
13372 CAATCCATAT
* *
13382 TTTAAAATAAATCAATCCATA-CTAATAAATTA
1 TTTAAAATAAATCAATCCATATTTAATAAATAA
*
13414 TTTAAAATAAATCAATCCATATTTTA-AAATAA
1 TTTAAAATAAATCAATCCATATTTAATAAATAA
* * * *
13446 ATCAATCCATACTAAT-AAT---TATTTAAAATAAATTA
1 TTTAA--AATA--AATCAATCCATATTT--AATAAATAA
*
13481 TTTAAAATAAATCAATCCATATTTTAT-AATAA
1 TTTAAAATAAATCAATCCATATTTAATAAATAA
13513 TTTA
1 TTTA
13517 TTTTAAAATA
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
31 3 0.04
32 45 0.58
33 7 0.09
34 4 0.05
35 16 0.21
36 3 0.04
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (33 bp):
TTTAAAATAAATCAATCCATATTTAATAAATAA
Found at i:13520 original size:15 final size:15
Alignment explanation
Indices: 13500--13589 Score: 144
Period size: 15 Copynumber: 6.0 Consensus size: 15
13490 AATCAATCCA
* *
13500 TATTTTATAATAATT
1 TATTTTAAAATAAAT
13515 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
13530 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
*
13545 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
13560 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
13575 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
13590 AAGCTTATTA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:13557 original size:67 final size:67
Alignment explanation
Indices: 13404--13559 Score: 192
Period size: 67 Copynumber: 2.3 Consensus size: 67
13394 CAATCCATAC
*
13404 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAATTATT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAATTATT
13469 TA
66 TA
* * ** **
13471 AAATAAATTATTTAAAATAAATCAATCCATATTTTATAAT-AATTTAT-TTTA-AAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAAT-AATTA-
13533 TTTA
64 TTTA
*
13537 TAATAAATTATTTTATAATAAAT
1 TAATAAATTA-TTTAAAATAAAT
13560 TATTTTAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
64 3 0.04
65 7 0.09
66 18 0.23
67 49 0.64
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (67 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAATTATT
TA
Found at i:17913 original size:11 final size:12
Alignment explanation
Indices: 17897--17936 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
17887 ATGATAATGC
17897 ATGTATAC-ATA
1 ATGTATACTATA
17908 ATGTATACTATA
1 ATGTATACTATA
*
17920 CT-TATACTATA
1 ATGTATACTATA
17931 A-GTATA
1 ATGTATA
17937 TGTATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 21 0.84
12 4 0.16
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40
Consensus pattern (12 bp):
ATGTATACTATA
Found at i:18088 original size:18 final size:18
Alignment explanation
Indices: 18065--18123 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
18055 TACTTCTAAG
*
18065 TATATAATA-TATTAATTA
1 TATATAA-AGTATAAATTA
18083 TATATAAAGTATAAATTA
1 TATATAAAGTATAAATTA
*
18101 TA-AGTATAAGTATAAAGTA
1 TATA-TA-AAGTATAAATTA
18120 TATA
1 TATA
18124 CTTGTGGGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 2 0.06
18 19 0.54
19 13 0.37
20 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.41
Consensus pattern (18 bp):
TATATAAAGTATAAATTA
Found at i:18095 original size:7 final size:7
Alignment explanation
Indices: 18085--18121 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
18075 ATTAATTATA
18085 TATAAAG
1 TATAAAG
*
18092 TATAAAT
1 TATAAAG
18099 TAT-AAG
1 TATAAAG
18105 TAT-AAG
1 TATAAAG
18111 TATAAAG
1 TATAAAG
18118 TATA
1 TATA
18122 TACTTGTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 11 0.41
7 16 0.59
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (7 bp):
TATAAAG
Found at i:18118 original size:13 final size:13
Alignment explanation
Indices: 18084--18121 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
18074 TATTAATTAT
18084 ATATAAAGTATAA
1 ATATAAAGTATAA
18097 AT-TATAAGTATAA
1 ATATA-AAGTATAA
*
18110 GTATAAAGTATA
1 ATATAAAGTATA
18122 TACTTGTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 2 0.09
13 18 0.82
14 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (13 bp):
ATATAAAGTATAA
Found at i:18410 original size:108 final size:104
Alignment explanation
Indices: 18282--18525 Score: 323
Period size: 108 Copynumber: 2.3 Consensus size: 104
18272 AATTATAATA
* *
18282 TATATA-TATATATAATTATATGATAATATAATA-TGTGTGATGAATGTTATGATAATACGATGC
1 TATATACT-TATATAA-TATAT-ATAATATAATATTGTATGATGAATGTTATGATAATACAATGC
18345 ATGTATATATCATAATGTACATTATACTTATGCATACATCATAAG
63 ATG--TATAT-ATAATGTACATTATACTTATGCATACATCATAAG
*
18390 TATATACTTATATAAGTATATATATATATATATATTTGTATGATGAATGTTATGATAATATAATG
1 TATATACTTATATAA-TATATATA-ATATA-ATA-TTGTATGATGAATGTTATGATAATACAATG
* * *
18455 CATGTATATATAATGTCCATTATACTTATGCATTCATTATAAG
62 CATGTATATATAATGTACATTATACTTATGCATACATCATAAG
18498 TATATACTTATATAA-ATATATAATATAA
1 TATATACTTATATAATATATATAATATAA
18526 GTATACATTA
Statistics
Matches: 124, Mismatches: 7, Indels: 14
0.86 0.05 0.10
Matches are distributed among these distances:
104 1 0.01
105 5 0.04
106 7 0.06
107 3 0.02
108 69 0.56
109 9 0.07
111 30 0.24
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (104 bp):
TATATACTTATATAATATATATAATATAATATTGTATGATGAATGTTATGATAATACAATGCATG
TATATATAATGTACATTATACTTATGCATACATCATAAG
Found at i:19880 original size:39 final size:39
Alignment explanation
Indices: 19822--19915 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
19812 TATATGACTT
* *
19822 GTAAGACCTTACCGCAGGCTCCTCTGCTTTGTGCTCAAG
1 GTAAGTCCTTACCGCAGGCTCCTCTGCTTTGTCCTCAAG
* * *
19861 GTAAGTCCTTACTGTAGGCTCCTCTGCTTTGTCCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCTGCTTTGTCCTCAAG
*
19900 GTAAATCCTTACCGCA
1 GTAAGTCCTTACCGCA
19916 AGTCCTTCTG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.31
Consensus pattern (39 bp):
GTAAGTCCTTACCGCAGGCTCCTCTGCTTTGTCCTCAAG
Found at i:21043 original size:7 final size:7
Alignment explanation
Indices: 21031--21056 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21021 GAGATGGACT
21031 TGAGACC
1 TGAGACC
21038 TGAGACC
1 TGAGACC
21045 TGAGACC
1 TGAGACC
21052 TGAGA
1 TGAGA
21057 AAAAGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (7 bp):
TGAGACC
Found at i:23638 original size:39 final size:39
Alignment explanation
Indices: 23556--23644 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
23546 CTATGACTTG
* * * *
23556 TAAGACCTTACCGCAGGTTCCTCTGCTTTGGGCTCGGGA
1 TAAGTCCTTACCGCAGGCTCCTCTACTTTGGACTCGGGA
* *
23595 TAAGTCTTTACCGCAGGCTCCTCTACTTTGTACTCAGGG-
1 TAAGTCCTTACCGCAGGCTCCTCTACTTTGGACTC-GGGA
23634 TAAGTCCTTAC
1 TAAGTCCTTAC
23645 TGAAGTTCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 39 0.93
40 3 0.07
ACGTcount: A:0.18, C:0.28, G:0.22, T:0.31
Consensus pattern (39 bp):
TAAGTCCTTACCGCAGGCTCCTCTACTTTGGACTCGGGA
Found at i:24222 original size:2 final size:2
Alignment explanation
Indices: 24215--24298 Score: 136
Period size: 2 Copynumber: 42.5 Consensus size: 2
24205 GTCTAGGGGT
24215 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
*
24257 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA CA TA CT- 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
24298 T
1 T
24299 GTACTCATAA
Statistics
Matches: 77, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 2 0.03
2 74 0.96
3 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25427 original size:2 final size:2
Alignment explanation
Indices: 25420--25478 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
25410 AATTGAAACA
25420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
25461 AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT A
25479 ATGGATGCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25831 original size:2 final size:2
Alignment explanation
Indices: 25824--25923 Score: 184
Period size: 2 Copynumber: 50.0 Consensus size: 2
25814 TCAGTGAAGA
25824 AT AT AT AT GA- 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
25866 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
25908 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
25924 GGATTGGTCT
Statistics
Matches: 96, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.01
2 94 0.98
3 1 0.01
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33375 original size:23 final size:22
Alignment explanation
Indices: 33323--33375 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
33313 CCTTTTTATA
*
33323 TTTTCAATTTTATAATAAAAAT
1 TTTTAAATTTTATAATAAAAAT
* **
33345 TATATAAATTTTATGAATTTAAAT
1 T-TTTAAATTTTAT-AATAAAAAT
33369 TTTTAAA
1 TTTTAAA
33376 GAAAATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 1 0.04
23 15 0.62
24 8 0.33
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTAAATTTTATAATAAAAAT
Found at i:33580 original size:20 final size:20
Alignment explanation
Indices: 33544--33581 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33534 TAATCCTATT
**
33544 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
33564 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
33582 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:38360 original size:2 final size:2
Alignment explanation
Indices: 38353--38383 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38343 GGGATAGGGG
38353 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
38384 GTTTTAAAAG
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:42700 original size:24 final size:25
Alignment explanation
Indices: 42673--42728 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
42663 AAATATTTTA
* *
42673 TCTGATTTC-CGACTTGAATTATGT
1 TCTGATTACACGACCTGAATTATGT
*
42697 TCTGA-TACATGACCTGAATTATGT
1 TCTGATTACACGACCTGAATTATGT
42721 TCTGATTA
1 TCTGATTA
42729 TGATCTGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 23 0.85
25 2 0.07
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (25 bp):
TCTGATTACACGACCTGAATTATGT
Found at i:44447 original size:31 final size:29
Alignment explanation
Indices: 44390--44449 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
44380 AATTCAGATA
* *
44390 AAAAATATATGATTTGGATTTGATCAAAT
1 AAAAATATATAATTTGGAATTGATCAAAT
*
44419 AAAAATATATAATCTTTGAATTGAATCAAAT
1 AAAAATATATAAT-TTGGAATTG-ATCAAAT
44450 TTATCGAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 12 0.46
30 7 0.27
31 7 0.27
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (29 bp):
AAAAATATATAATTTGGAATTGATCAAAT
Done.