Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003952.1 Hibiscus syriacus cultivar Beakdansim tig00008540_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: 109177
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3686 original size:20 final size:20
Alignment explanation
Indices: 3661--3772 Score: 206
Period size: 20 Copynumber: 5.6 Consensus size: 20
3651 TTTGGGTTTA
* *
3661 AGTATCAATACTAGAAGAAC
1 AGTATCGATACTGGAAGAAC
3681 AGTATCGATACTGGAAGAAC
1 AGTATCGATACTGGAAGAAC
3701 AGTATCGATACTGGAAGAAC
1 AGTATCGATACTGGAAGAAC
3721 AGTATCGATACTGGAAGAAC
1 AGTATCGATACTGGAAGAAC
3741 AGTATCGATACTGGAAGAAC
1 AGTATCGATACTGGAAGAAC
3761 AGTATCGATACT
1 AGTATCGATACT
3773 ATAAGGTAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.21
Consensus pattern (20 bp):
AGTATCGATACTGGAAGAAC
Found at i:4191 original size:2 final size:2
Alignment explanation
Indices: 4184--4215 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4174 TTCATATTAC
4184 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4216 TGTTTTATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4482 original size:44 final size:45
Alignment explanation
Indices: 4415--4500 Score: 147
Period size: 44 Copynumber: 1.9 Consensus size: 45
4405 AATATAAGCA
4415 TAGTTTTGATTAAGTTACTACGTGAACATGCACTATTTAATAGCC
1 TAGTTTTGATTAAGTTACTACGTGAACATGCACTATTTAATAGCC
* *
4460 TAGTTTTGATT-TGTTACTACGTGAACATGCACTGTTTAATA
1 TAGTTTTGATTAAGTTACTACGTGAACATGCACTATTTAATA
4501 CTATATGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 28 0.72
45 11 0.28
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (45 bp):
TAGTTTTGATTAAGTTACTACGTGAACATGCACTATTTAATAGCC
Found at i:9811 original size:21 final size:21
Alignment explanation
Indices: 9760--9818 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
9750 TCCGAGCTTT
*
9760 TTTATTTTTATTTTTCA-TTATT
1 TTTA-TTTTATTTTT-AGTTATA
9782 TTTATTTTATTTTTAGTTAATA
1 TTTATTTTATTTTTAGTT-ATA
*
9804 TTTA-TTTATTATTAG
1 TTTATTTTATTTTTAG
9819 AAAATAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 1 0.03
21 22 0.67
22 10 0.30
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (21 bp):
TTTATTTTATTTTTAGTTATA
Found at i:9824 original size:21 final size:22
Alignment explanation
Indices: 9782--9824 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
9772 TTTCATTATT
* **
9782 TTTATTTTATTTTTAGTTAATA
1 TTTATTTTATTATTAGAAAATA
9804 TTTA-TTTATTATTAGAAAATA
1 TTTATTTTATTATTAGAAAATA
9825 AATCATCATC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTATTTTATTATTAGAAAATA
Found at i:13876 original size:12 final size:12
Alignment explanation
Indices: 13859--13913 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
13849 ACTATATGGT
13859 ATGAACAGTACC
1 ATGAACAGTACC
13871 ATGAACAGTA--
1 ATGAACAGTACC
*
13881 ATGAACAATACC
1 ATGAACAGTACC
* * *
13893 GTGAACAGTGCA
1 ATGAACAGTACC
13905 ATGAACAGT
1 ATGAACAGT
13914 GAAAATTTCG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 9 0.26
12 26 0.74
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:13887 original size:22 final size:23
Alignment explanation
Indices: 13859--13913 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
13849 ACTATATGGT
13859 ATGAACAGTACCATGAACAGT-A
1 ATGAACAGTACCATGAACAGTCA
* *
13881 ATGAACAATACCGTGAACAGTGCA
1 ATGAACAGTACCATGAACAGT-CA
13905 ATGAACAGT
1 ATGAACAGT
13914 GAAAATTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 19 0.68
24 9 0.32
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (23 bp):
ATGAACAGTACCATGAACAGTCA
Found at i:14890 original size:32 final size:32
Alignment explanation
Indices: 14806--14892 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
14796 GTTCCTTAGA
* *
14806 ACATAGGT-A-TATTGTCCATATGTCTCAAAAT
1 ACATAGGTAATTA-TGTCCATATGTCCCAAAAG
* * * *
14837 ACATAGGTAATTCTATTCATATGTCCCGAAAG
1 ACATAGGTAATTATGTCCATATGTCCCAAAAG
14869 ACATAGGTAATTATGTCCATATGT
1 ACATAGGTAATTATGTCCATATGT
14893 TCCGTAGAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 8 0.18
32 36 0.80
33 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
ACATAGGTAATTATGTCCATATGTCCCAAAAG
Found at i:15352 original size:32 final size:29
Alignment explanation
Indices: 15311--15398 Score: 86
Period size: 32 Copynumber: 2.9 Consensus size: 29
15301 TCATATATAT
15311 ATATGGTTCACTTTCACATATCACATTTAATC
1 ATAT-GTTCACTTTCACATATCACATTT--TC
* ** * *
15343 ATGTAGTTCACTCACACGTAACACATTTTC
1 ATAT-GTTCACTTTCACATATCACATTTTC
15373 ATATGATTCACTTTCACATATCACAT
1 ATATG-TTCACTTTCACATATCACAT
15399 ATTCCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
29 1 0.02
30 21 0.48
32 22 0.50
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (29 bp):
ATATGTTCACTTTCACATATCACATTTTC
Found at i:15398 original size:30 final size:30
Alignment explanation
Indices: 15311--15398 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
15301 TCATATATAT
*
15311 ATATGGTTCACTTTCACATATCACA-TTTA
1 ATATGATTCACTTTCACATATCACATTTTA
** * * *
15340 ATCATGTAGTTCACTCACACGTAACACATTTTC
1 AT-ATG-A-TTCACTTTCACATATCACATTTTA
15373 ATATGATTCACTTTCACATATCACAT
1 ATATGATTCACTTTCACATATCACAT
15399 ATTCCTTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
29 2 0.04
30 19 0.42
31 1 0.02
32 18 0.40
33 5 0.11
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
ATATGATTCACTTTCACATATCACATTTTA
Found at i:19224 original size:115 final size:116
Alignment explanation
Indices: 19036--19261 Score: 384
Period size: 115 Copynumber: 2.0 Consensus size: 116
19026 GTGTGGCTAC
*
19036 TAAGTCATTATGATGATGAATATGACATGTTCATATTACATGTTAGTAGATAAGTTAATTGTAAT
1 TAAGTCATTATGATGATGAATATGACATGCTCATATTACATGTTAGTAGATAAGTTAATTGTAAT
*
19101 AATATCTCTCT-TATATTATTTTTCAGTTAGAT-CTATGTGTGTGTGGTTGT
66 AATATCTCTCTATATATTATTTTTCAATTAGATCCT-TGTGTGTGTGGTTGT
* *
19151 TAAGTCATTATGATGATGAATATGGCATGCTCATATTACATGTTAGTAGATAAGTTAATTTTAAT
1 TAAGTCATTATGATGATGAATATGACATGCTCATATTACATGTTAGTAGATAAGTTAATTGTAAT
*
19216 AATCTCTCTCTATATATTATTTTTCAATTAGATCCTTGTGTGTGTG
66 AATATCTCTCTATATATTATTTTTCAATTAGATCCTTGTGTGTGTG
19262 TCAGGTCGAG
Statistics
Matches: 104, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
115 72 0.69
116 30 0.29
117 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (116 bp):
TAAGTCATTATGATGATGAATATGACATGCTCATATTACATGTTAGTAGATAAGTTAATTGTAAT
AATATCTCTCTATATATTATTTTTCAATTAGATCCTTGTGTGTGTGGTTGT
Found at i:19404 original size:84 final size:84
Alignment explanation
Indices: 19261--19415 Score: 265
Period size: 84 Copynumber: 1.8 Consensus size: 84
19251 TTGTGTGTGT
* *
19261 GTCAGGTCGAGTTTTATCTGAAAATACAGGTCAAATTTCAAATCGGGTGAAGTCACTTTAAACCC
1 GTCAGGTCGAGTTTTATCTAAAAATACAGGTCAAATTTCAAATCGAGTGAAGTCACTTTAAACCC
19326 AGGTTGGGTTGCGTTTCAG
66 AGGTTGGGTTGCGTTTCAG
* * *
19345 GTCAGGTCGAGTTTTATCTAAAAATACGGGTCAAATTTCAGATCGAGTGAAGTCGCTTTAAACCC
1 GTCAGGTCGAGTTTTATCTAAAAATACAGGTCAAATTTCAAATCGAGTGAAGTCACTTTAAACCC
19410 AGGTTG
66 AGGTTG
19416 AATCGAATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (84 bp):
GTCAGGTCGAGTTTTATCTAAAAATACAGGTCAAATTTCAAATCGAGTGAAGTCACTTTAAACCC
AGGTTGGGTTGCGTTTCAG
Found at i:20129 original size:2 final size:2
Alignment explanation
Indices: 20122--20152 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20112 TTTTCTCTAA
20122 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 A
20153 ATTATAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22912 original size:60 final size:59
Alignment explanation
Indices: 22842--23038 Score: 223
Period size: 60 Copynumber: 3.3 Consensus size: 59
22832 TAAATGTTTT
* ** *
22842 AATTTCATCCCTAAATTATTACTATCATTCTAACTTAGTCCCCAAACTTTTGAACATTTC
1 AATTTCATCCC-AAACTAAAACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTTC
* * * * * *
22902 AATTTAATCCCAAACCAAAAATATCATTCTAAATTAGTCCCTAAAGTTTTGAACATTTT
1 AATTTCATCCCAAACTAAAACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTTC
* * * * * *
22961 AATTTCATCCCCGAACTACAACTTTCATTCTAAGTTAATCCCCAAACTTTTTGAACATTCC
1 AATTTCAT-CCCAAACTAAAACTATCATTCTAAATTAGTCCCCAAAC-TTTTGAACATTTC
23022 AATTTCATCCCAAACTA
1 AATTTCATCCCAAACTA
23039 TACTTATATG
Statistics
Matches: 112, Mismatches: 23, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
59 46 0.41
60 47 0.42
61 19 0.17
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (59 bp):
AATTTCATCCCAAACTAAAACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTTC
Found at i:22939 original size:59 final size:59
Alignment explanation
Indices: 22864--23036 Score: 211
Period size: 59 Copynumber: 2.9 Consensus size: 59
22854 AAATTATTAC
* *
22864 TATCATTCTAACTTAGTCCCCAAACTTTTGAACATTTCAATTTAATCCCAAACCAAAAA
1 TATCATTCTAAATTAGTCCCCAAACTTTTGAACATTTCAATTTCATCCCAAACCAAAAA
* * * * * * *
22923 TATCATTCTAAATTAGTCCCTAAAGTTTTGAACATTTTAATTTCATCCCCGAACTACAAC
1 TATCATTCTAAATTAGTCCCCAAACTTTTGAACATTTCAATTTCAT-CCCAAACCAAAAA
* * * *
22983 TTTCATTCTAAGTTAATCCCCAAACTTTTTGAACATTCCAATTTCATCCCAAAC
1 TATCATTCTAAATTAGTCCCCAAAC-TTTTGAACATTTCAATTTCATCCCAAAC
23037 TATACTTATA
Statistics
Matches: 95, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
59 41 0.43
60 35 0.37
61 19 0.20
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (59 bp):
TATCATTCTAAATTAGTCCCCAAACTTTTGAACATTTCAATTTCATCCCAAACCAAAAA
Found at i:27746 original size:19 final size:18
Alignment explanation
Indices: 27704--27746 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
27694 TGTAAAACTG
*
27704 ATTAAATTTTAATTTAAC
1 ATTAAATTTTAATTGAAC
*
27722 ACTTAAATTTTAGATTGAAT
1 A-TTAAATTTTA-ATTGAAC
27742 ATTAA
1 ATTAA
27747 TTTGATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 14 0.67
20 6 0.29
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (18 bp):
ATTAAATTTTAATTGAAC
Found at i:28471 original size:2 final size:2
Alignment explanation
Indices: 28464--28489 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28454 CAGTTTATTC
28464 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
28490 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28494 original size:2 final size:2
Alignment explanation
Indices: 28489--28525 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28479 TCTCTCTCTC
28489 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 T
28526 TCAACTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32388 original size:20 final size:20
Alignment explanation
Indices: 32357--32415 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
32347 CTAGCCGTTG
32357 AGCCTGATGGTATCGATACTA
1 AGCCT-ATGGTATCGATACTA
* *
32378 AGTCTATGGTATCGATATTA
1 AGCCTATGGTATCGATACTA
*
32398 AGCCTATGGTATTGATAC
1 AGCCTATGGTATCGATAC
32416 AACTATGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 29 0.88
21 4 0.12
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (20 bp):
AGCCTATGGTATCGATACTA
Found at i:38182 original size:6 final size:6
Alignment explanation
Indices: 38171--38199 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
38161 CAATAACACC
38171 TCCTCT TCCTCT TCCTCT TCCTCT TCCTC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTC
38200 CGCCTCCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TCCTCT
Found at i:38205 original size:18 final size:18
Alignment explanation
Indices: 38169--38215 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
38159 AGCAATAACA
**
38169 CCTCCTCTTCCTCTTCCT
1 CCTCCTCTTCCTCCGCCT
*
38187 CTTCCTCTTCCTCCGCCT
1 CCTCCTCTTCCTCCGCCT
*
38205 CCACCTCTTCC
1 CCTCCTCTTCC
38216 CCCAGTTCCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.02, C:0.57, G:0.02, T:0.38
Consensus pattern (18 bp):
CCTCCTCTTCCTCCGCCT
Found at i:46616 original size:32 final size:32
Alignment explanation
Indices: 46512--46636 Score: 139
Period size: 31 Copynumber: 4.0 Consensus size: 32
46502 AACCTTGGCA
* * *
46512 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTCCCAAAGAACATAGGTAAT
* **
46543 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTCCCAAAGAACATAGGTAAT
46574 ACTGTCCATATGTCCCAAA-AGACATAGGTAAT
1 ACTGTCCATATGTCCCAAAGA-ACATAGGTAAT
* * *
46606 TCTGTCCATATGTTCCATAGAACATAGGTAA
1 ACTGTCCATATGTCCCAAAGAACATAGGTAA
46637 ACCCTCGACT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
30 2 0.03
31 48 0.61
32 28 0.35
33 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (32 bp):
ACTGTCCATATGTCCCAAAGAACATAGGTAAT
Found at i:46629 original size:63 final size:62
Alignment explanation
Indices: 46512--46635 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
46502 AACCTTGGCA
* * *
46512 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCATAGAACATAGGTAT
* *
46574 ACTGTCCATATGTCCCAAA-AGACATAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTA
1 ACTGTCCATAGGTCCCAAAGA-ACATAGGTAA-ACTGTCCATATGTTCCATAGAACATAGGTA
46636 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 1 0.02
62 26 0.47
63 28 0.51
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCATAGAACATAGGTAT
Found at i:47094 original size:2 final size:2
Alignment explanation
Indices: 47087--47117 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47077 ATATGCAATA
47087 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 A
47118 CACATACACT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47696 original size:19 final size:19
Alignment explanation
Indices: 47643--47696 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
47633 TCTTAATGGG
*
47643 GTGTATCGATGCACTACCT
1 GTGTATCGATGCACTCCCT
* *
47662 GTGCAACGATGCACTCCCT
1 GTGTATCGATGCACTCCCT
47681 GTGTATCGATGCACTC
1 GTGTATCGATGCACTC
47697 ATTGCATTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (19 bp):
GTGTATCGATGCACTCCCT
Found at i:50482 original size:14 final size:16
Alignment explanation
Indices: 50452--50486 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
50442 TCAAAAATTC
50452 AATAAATAAATTTAAA
1 AATAAATAAATTTAAA
50468 AATAAA-AAA-TTAAA
1 AATAAATAAATTTAAA
50482 AATAA
1 AATAA
50487 TACTCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 3 0.16
16 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATAAATTTAAA
Found at i:53545 original size:34 final size:35
Alignment explanation
Indices: 53483--53551 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 35
53473 CTTCATTTAC
*
53483 ATCTCGATCAATATTGGTCCTAGATGCTCTTAATT
1 ATCTCGATCAATATTGATCCTAGATGCTCTTAATT
*
53518 ATCTCGATCAATA-TGATCCTAGGTGCTCTTAATT
1 ATCTCGATCAATATTGATCCTAGATGCTCTTAATT
53552 TGTATCGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 19 0.59
35 13 0.41
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (35 bp):
ATCTCGATCAATATTGATCCTAGATGCTCTTAATT
Found at i:57342 original size:20 final size:20
Alignment explanation
Indices: 57317--57354 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
57307 ATCTTACATA
57317 GGGGTATCGGTACCCTCTTG
1 GGGGTATCGGTACCCTCTTG
57337 GGGGTATCGGTACCCTCT
1 GGGGTATCGGTACCCTCT
57355 AGGCAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.26, G:0.34, T:0.29
Consensus pattern (20 bp):
GGGGTATCGGTACCCTCTTG
Found at i:57688 original size:13 final size:14
Alignment explanation
Indices: 57670--57714 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
57660 GATTTTCTAA
*
57670 TTGAAAATC-ATTT
1 TTGAAAATCAAGTT
57683 TTG-AAATCAAGTT
1 TTGAAAATCAAGTT
*
57696 TTG-AAATTAAGTT
1 TTGAAAATCAAGTT
57709 TTGAAA
1 TTGAAA
57715 TTACCCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 5 0.18
13 21 0.75
14 2 0.07
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (14 bp):
TTGAAAATCAAGTT
Found at i:57715 original size:13 final size:13
Alignment explanation
Indices: 57681--57717 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
57671 TGAAAATCAT
*
57681 TTTTGAAATCAAG
1 TTTTGAAATTAAG
57694 TTTTGAAATTAAG
1 TTTTGAAATTAAG
57707 TTTTGAAATTA
1 TTTTGAAATTA
57718 CCCTTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.46
Consensus pattern (13 bp):
TTTTGAAATTAAG
Found at i:59300 original size:31 final size:30
Alignment explanation
Indices: 59265--59372 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 30
59255 TAGGTCCCGA
*
59265 AGAACCTAGATAAACTGTCCATATGTTCCTT
1 AGAACATAGATAAA-TGTCCATATGTTCCTT
* *
59296 AGAACATAGGTATAATGTCCATATG-TCCTG
1 AGAACATAGATA-AATGTCCATATGTTCCTT
* * *
59326 AAAGACATAAATAATTATGTCCATATGTTCCGT
1 AGA-ACATAGATAA--ATGTCCATATGTTCCTT
*
59359 AGAACATAGGTAAA
1 AGAACATAGATAAA
59373 CCCTCGACTC
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
30 8 0.13
31 27 0.44
32 21 0.34
33 5 0.08
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (30 bp):
AGAACATAGATAAATGTCCATATGTTCCTT
Found at i:59366 original size:32 final size:30
Alignment explanation
Indices: 59280--59366 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 30
59270 CTAGATAAAC
**
59280 TGTCCATATGTTCCTTAGAACATAGGTATAA
1 TGTCCATATGTTCC-TAGAACATAAATATAA
* *
59311 TGTCCATATG-TCCTGAAAGACATAAATAATTA
1 TGTCCATATGTTCCT-AGA-ACATAAAT-ATAA
59343 TGTCCATATGTTCCGTAGAACATA
1 TGTCCATATGTTCC-TAGAACATA
59367 GGTAAACCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
29 1 0.02
30 5 0.11
31 16 0.35
32 18 0.39
33 5 0.11
34 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (30 bp):
TGTCCATATGTTCCTAGAACATAAATATAA
Found at i:59763 original size:15 final size:15
Alignment explanation
Indices: 59745--59774 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59735 ATCACATAAA
*
59745 CCCATATCTTCTTAT
1 CCCATAACTTCTTAT
59760 CCCATAACTTCTTAT
1 CCCATAACTTCTTAT
59775 TATATCATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.43
Consensus pattern (15 bp):
CCCATAACTTCTTAT
Found at i:75357 original size:25 final size:25
Alignment explanation
Indices: 75324--75373 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
75314 CATGTAAATA
75324 AAACTGGGAGTTGTACTTTCAAGGT
1 AAACTGGGAGTTGTACTTTCAAGGT
75349 AAACTGGGAGTTGTACTTTCAAGGT
1 AAACTGGGAGTTGTACTTTCAAGGT
75374 TCTTGCATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (25 bp):
AAACTGGGAGTTGTACTTTCAAGGT
Found at i:80126 original size:26 final size:26
Alignment explanation
Indices: 80090--80141 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
80080 TATCCATTTC
*
80090 AGCAGAACCAGACATGAAATTAAGTG
1 AGCAAAACCAGACATGAAATTAAGTG
80116 AGCAAAACCAGACATGAAATTAAGTG
1 AGCAAAACCAGACATGAAATTAAGTG
80142 TAAATTCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.15
Consensus pattern (26 bp):
AGCAAAACCAGACATGAAATTAAGTG
Found at i:83535 original size:33 final size:33
Alignment explanation
Indices: 83498--83597 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
83488 AATTTGGCAA
83498 GTTGGAAAATTCATCTTGGTTGGTGGCCAACTT
1 GTTGGAAAATTCATCTTGGTTGGTGGCCAACTT
83531 GTTGGAAAATTCATCTTGGTTGGTGGCCAACTT
1 GTTGGAAAATTCATCTTGGTTGGTGGCCAACTT
* * *
83564 ATTGGAAAATTAATCTTTGGTAGGTGGCCAACTT
1 GTTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
83598 TGCACATGAG
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
33 46 0.73
34 17 0.27
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (33 bp):
GTTGGAAAATTCATCTTGGTTGGTGGCCAACTT
Found at i:86377 original size:11 final size:11
Alignment explanation
Indices: 86361--86409 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
86351 AACATAATTG
86361 AAATAATTTAT
1 AAATAATTTAT
86372 AAATAATTTAT
1 AAATAATTTAT
86383 -AA-AATTTAT
1 AAATAATTTAT
86392 AAATAGGA-TTAT
1 AAATA--ATTTAT
86404 AAATAA
1 AAATAA
86410 ATATTACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 7 0.21
10 5 0.15
11 12 0.35
12 9 0.26
13 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
AAATAATTTAT
Found at i:86379 original size:20 final size:20
Alignment explanation
Indices: 86354--86396 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
86344 ATTTAAAAAC
86354 ATAATTGA-AATAATTTATAA
1 ATAATTGATAA-AATTTATAA
*
86374 ATAATTTATAAAATTTATAA
1 ATAATTGATAAAATTTATAA
86394 ATA
1 ATA
86397 GGATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAATTGATAAAATTTATAA
Found at i:86508 original size:2 final size:2
Alignment explanation
Indices: 86501--86527 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
86491 ACTAAAATCA
86501 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 A
86528 ATAATAATAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:87494 original size:20 final size:20
Alignment explanation
Indices: 87465--87502 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
87455 GTAAAGGGTG
* *
87465 GCTATTTGGTGAGTCACCGA
1 GCTATGTGGTGACTCACCGA
87485 GCTATGTGGTGACTCACC
1 GCTATGTGGTGACTCACC
87503 CTAATAGCTG
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:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (20 bp):
GCTATGTGGTGACTCACCGA
Found at i:87812 original size:3 final size:3
Alignment explanation
Indices: 87804--87852 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
87794 AATTATTTAG
*
87804 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
87852 T
1 T
87853 CAAATGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:92318 original size:23 final size:23
Alignment explanation
Indices: 92288--92340 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
92278 TAGTAATGCG
* *
92288 GATTGGACCTTCTGGAAGACGCT
1 GATTGGACCTTCAGGAAGACGCC
92311 GATTGGACCTTCAGGAAGACGCC
1 GATTGGACCTTCAGGAAGACGCC
92334 GATTGGA
1 GATTGGA
92341 TCTTTTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.23
Consensus pattern (23 bp):
GATTGGACCTTCAGGAAGACGCC
Found at i:92351 original size:23 final size:22
Alignment explanation
Indices: 92288--92351 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
92278 TAGTAATGCG
* * *
92288 GATTGGACCTTCTGGAAGACGCT
1 GATTGGA-CTTTTAGAAGACGCC
* *
92311 GATTGGACCTTCAGGAAGACGCC
1 GATTGGACTTTTA-GAAGACGCC
92334 GATTGGATCTTTTAGAAG
1 GATTGGA-CTTTTAGAAG
92352 CTGCTAGATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
22 2 0.06
23 26 0.81
24 4 0.12
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (22 bp):
GATTGGACTTTTAGAAGACGCC
Found at i:93875 original size:24 final size:24
Alignment explanation
Indices: 93843--93888 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
93833 GGAAATTGAC
93843 TATATTACTATAATATTAAAAAAG
1 TATATTACTATAATATTAAAAAAG
93867 TATATTACTATAATATTAAAAA
1 TATATTACTATAATATTAAAAA
93889 GTTAAGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (24 bp):
TATATTACTATAATATTAAAAAAG
Found at i:94052 original size:20 final size:20
Alignment explanation
Indices: 94029--94077 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
94019 AATATAATTG
94029 AAAATATTACTATAATATTA
1 AAAATATTACTATAATATTA
* *
94049 AAAAGTA-TATTATATTATTA
1 AAAA-TATTACTATAATATTA
*
94069 GAAATATTA
1 AAAATATTA
94078 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (20 bp):
AAAATATTACTATAATATTA
Found at i:101007 original size:18 final size:19
Alignment explanation
Indices: 100967--101010 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
100957 TTTGGTTCAC
* *
100967 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTACCAG-G
100987 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
101005 GGAATA
1 GGAATA
101011 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:101149 original size:18 final size:18
Alignment explanation
Indices: 101126--101173 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
101116 AAATTGTCCT
* *
101126 TATTATATATTTGTATAA
1 TATTATATATTTGGAAAA
*
101144 TATTATA-AGTTGGAAAA
1 TATTATATATTTGGAAAA
101161 TATTTATATATTT
1 TA-TTATATATTT
101174 TCTTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (18 bp):
TATTATATATTTGGAAAA
Found at i:101234 original size:36 final size:37
Alignment explanation
Indices: 101162--101235 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
101152 GTTGGAAAAT
* *
101162 ATTTATATATTTTCTTTTAAAAAATTAAATTCATAAA
1 ATTTATATAATTTCTTTTAAAAAATTAAAATCATAAA
*
101199 ATTTATATAATTT-TTTTACAAAATTAAAAAT-ATAAA
1 ATTTATATAATTTCTTTTAAAAAATT-AAAATCATAAA
101235 A
1 A
101236 AAGGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 17 0.52
37 16 0.48
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (37 bp):
ATTTATATAATTTCTTTTAAAAAATTAAAATCATAAA
Found at i:102487 original size:129 final size:129
Alignment explanation
Indices: 102061--102510 Score: 679
Period size: 130 Copynumber: 3.5 Consensus size: 129
102051 ATATTATCGC
102061 GTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATAC-TT
1 GTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTTT
* * ** *
102125 ATATGACAATATCGATACTTGTACATTTACGCCTATTTTCATTATACTAGTAGAAATGTTTACCG
66 ATATG--AGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAGAAACGTTTACCG
102190 T
129 T
*
102191 GTACATTGTTAATTTACCTATTACTTTAAAGTAATAGATTTCGAAATTATAAGTATCGATACTTT
1 GTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATAC-TT
* * * * *
102256 ATATATGAGTATCGACACTTGGACATTTACGCATATTTTCATTCTATCGGTAAAAAC-TTTACCG
65 -TATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAGAAACGTTTACCG
102320 T
129 T
* * ** *
102321 GTACATTGCTAATTTACATATTACTTTAAAGTAATAGGTTTTAAAATTATAAGTATAGATACTTT
1 GTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTTT
* *
102386 GTATGAGTATCGATACTTGGACATTTACGCCTATATTCATTATACCGGTAGAAACGTTTACCGT
66 ATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAGAAACGTTTACCGT
*
102450 GTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTTGAAATTATAAGTATCGATA
1 GTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATA
102511 TAGTTTGTGT
Statistics
Matches: 288, Mismatches: 28, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
128 49 0.17
129 67 0.23
130 125 0.43
131 40 0.14
132 1 0.00
133 6 0.02
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (129 bp):
GTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTTT
ATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAGAAACGTTTACCGT
Found at i:103387 original size:199 final size:199
Alignment explanation
Indices: 103047--103748 Score: 1040
Period size: 199 Copynumber: 3.5 Consensus size: 199
103037 TATTATTTTA
* *
103047 AAGTATCGATACTTTATATATGTCTATCGATACATTTTGAGTGCACATTGTTTGAGAAGCATACT
1 AAGTATCGATACTTTATATATGTGTATCGATACATTTTGAGTGCAAATTGTTTGAGAAGCATACT
* *
103112 GGAATAAAAGTATCCATACCTATATAAAAGTATCGATACTTGATATTTACGCCTATTATCATTGT
66 GGAATAAAAGTATCCATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTAT
* * * * *
103177 A-TCAGTAGACTTTTACTGTTTACATTGTTAATTTACCTATTACTTTAAAATAATATGTTTCAAA
131 ACT-GGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTCCAAA
*
103241 ATTTC
195 ATTCC
* *
103246 AAGTATCGATACTTTATATATGTGTATCGATACATTTTGCGTGCAAATTATTTGAGAAGCATACT
1 AAGTATCGATACTTTATATATGTGTATCGATACATTTTGAGTGCAAATTGTTTGAGAAGCATACT
*
103311 GGAATAAAAGTATCGATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTAT
66 GGAATAAAAGTATCCATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTAT
* *
103376 ACTGGTAGACTTTTACCATTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTCCGAAA
131 ACTGGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTCCAAAA
103441 TTCC
196 TTCC
* * * *
103445 AAGTATCGATACGTTATACA--TGTATCAATACATTTTGAGTGCAAATTGTTTGAGAAGCATATT
1 AAGTATCGATACTTTATATATGTGTATCGATACATTTTGAGTGCAAATTGTTTGAGAAGCATACT
* *
103508 GGAATAAAAGTATCCATACCTATATAAAGAGTATCAATACTTGGTATTTATGCCTATTATCATTA
66 GGAATAAAAGTATCCATACCTATATAAA-AGTATCGATACTTGGTATTTACGCCTATTATCATTA
* *
103573 TACCGGTAGACTTTTACCGTTTGCATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTCCAAA
130 TACTGGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTCCAAA
103638 ATTCC
195 ATTCC
**
103643 AAGTATCGATAC-TT-TATATGTGTATCGATACATTTTGCA-TGCAAATTGTTTGAGAATAATAC
1 AAGTATCGATACTTTATATATGTGTATCGATACATTTTG-AGTGCAAATTGTTTGAGAAGCATAC
* * *** *
103705 T-GAATGAAAGTATCCACACCGGCATAAGAAGTATCAATACTTGG
65 TGGAATAAAAGTATCCATACCTATATAA-AAGTATCGATACTTGG
103749 ACATTTTCAT
Statistics
Matches: 459, Mismatches: 38, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
196 3 0.01
197 104 0.23
198 150 0.33
199 201 0.44
200 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (199 bp):
AAGTATCGATACTTTATATATGTGTATCGATACATTTTGAGTGCAAATTGTTTGAGAAGCATACT
GGAATAAAAGTATCCATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTAT
ACTGGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTCCAAAA
TTCC
Found at i:103976 original size:146 final size:145
Alignment explanation
Indices: 103646--104009 Score: 450
Period size: 146 Copynumber: 2.5 Consensus size: 145
103636 AAATTCCAAG
* * *
103646 TATCGATACTTT-AT-ATGTGTATCGATACATTTTGCATGCAAATTGTTTG-AGAATAATACT-G
1 TATCAATACTTTAATAATGTGTATCGATACA-TTTGCGTGCAAATTGTTTGAAAAAT-ATACTGG
* *
103707 AATGAAAGTATCCACACCGGCATAAGAAGTATCAATACTTGGACATTTTCATACTTTACATACAT
64 AATAAAAGTATCCACACCGGCATAAAAAGTATCAATACTTGGACATTTTCATACTTTACATACAT
103772 TGTTTCAAAATTATAAA
129 TGTTTCAAAATTATAAA
* * * *
103789 TATCAATACTTTAATAATGTGTATCGATACATTTGGTGTGCACATTGTTCGAAAAATATATTGGA
1 TATCAATACTTTAATAATGTGTATCGATACATTT-GCGTGCAAATTGTTTGAAAAATATACTGGA
* * * * *
103854 ATAAAATTATCCATACC-GCATAAAAAGTATCGATACTTGGACATTTTGATACTTTGCATACATT
65 ATAAAAGTATCCACACCGGCATAAAAAGTATCAATACTTGGACATTTTCATACTTTACATACA-T
* **
103918 TTTTTTGAAATTATAAA
129 TGTTTCAAAATTATAAA
** * * *
103935 TATCTTTATTTTAATAATGTGTATCGATACATTTGACGTGCAAATTGTTTGACAAACATACTGGA
1 TATCAATACTTTAATAATGTGTATCGATACATTTG-CGTGCAAATTGTTTGAAAAATATACTGGA
104000 ATAAAAGTAT
65 ATAAAAGTAT
104010 TGATATCAGC
Statistics
Matches: 187, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
143 11 0.06
144 5 0.03
145 73 0.39
146 98 0.52
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (145 bp):
TATCAATACTTTAATAATGTGTATCGATACATTTGCGTGCAAATTGTTTGAAAAATATACTGGAA
TAAAAGTATCCACACCGGCATAAAAAGTATCAATACTTGGACATTTTCATACTTTACATACATTG
TTTCAAAATTATAAA
Found at i:104673 original size:178 final size:177
Alignment explanation
Indices: 104302--104678 Score: 558
Period size: 177 Copynumber: 2.1 Consensus size: 177
104292 TCAAATTGAA
* * * *
104302 ACCGGTTTTGTCAAATTTTAACTTATTATATCATCATATATCGATATATGTGTCTAAGGTATCGA
1 ACCGGTTTTGTCAAATTTAAACATATTATATCATCATATATCAATACATGTGTCTAAGGTATCGA
*
104367 TACTTTATAGGCGCTATTATTGCAATTCTTTTAAATTCCTAAAGTATCGATACTTTGCTACATAT
66 TACTTTATAGGCGCTATTATTGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGCTACATAT
** * *
104432 ACTTATAAAAGTATCGATACAATTTTCAACCATTCTAGTAGCTCTTT
131 ACTTATAAAAGTATCGATACAAACTTCAACAATTCCAGTAGCTCTTT
* ** *
104479 ACCGGTTTTGTCAAATTTAAACATGTTATATTGTCATGTATCAATACATGTGTCTAAGGTATCGA
1 ACCGGTTTTGTCAAATTTAAACATATTATATCATCATATATCAATACATGTGTCTAAGGTATCGA
* *
104544 TACTTTATA-GCTGTTATTATTGCAATTCTTTTAAATTCCTAAAAGTACCGATACTTTGGTACAT
66 TACTTTATAGGC-GCTATTATTGCAATTCTTTTAAATTCCT-AAAGTACCGATACTTTGCTACAT
* *
104608 ATACTTATAAATGTATCGATACAAACTTCAACAATTCCGGTAGCTCTTT
129 ATACTTATAAAAGTATCGATACAAACTTCAACAATTCCAGTAGCTCTTT
* *
104657 ACCGATTTTGTCAAATTGAAAC
1 ACCGGTTTTGTCAAATTTAAAC
104679 CGGTTTTGTC
Statistics
Matches: 179, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
176 2 0.01
177 93 0.52
178 84 0.47
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (177 bp):
ACCGGTTTTGTCAAATTTAAACATATTATATCATCATATATCAATACATGTGTCTAAGGTATCGA
TACTTTATAGGCGCTATTATTGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGCTACATAT
ACTTATAAAAGTATCGATACAAACTTCAACAATTCCAGTAGCTCTTT
Found at i:104884 original size:20 final size:20
Alignment explanation
Indices: 104859--104951 Score: 89
Period size: 20 Copynumber: 4.6 Consensus size: 20
104849 TCTTTACTGA
104859 TTTTGTCAAATTGAAACCGG
1 TTTTGTCAAATTGAAACCGG
* ** *
104879 TTTTGTCAATTTCCAATCGG
1 TTTTGTCAAATTGAAACCGG
** *
104899 TTTTGTCAAATTCGTTACCTG
1 TTTTGTCAAATT-GAAACCGG
*
104920 TTTTGTCAAATTGAAACCGAA
1 TTTTGTCAAATTGAAACCG-G
104941 TTTT-TCAAATT
1 TTTTGTCAAATT
104952 TCAACATGTT
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 38 0.67
21 19 0.33
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
TTTTGTCAAATTGAAACCGG
Done.