Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000202.1 Hibiscus syriacus cultivar Beakdansim tig00000361_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: 90952
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3711 original size:23 final size:23
Alignment explanation
Indices: 3685--3728 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3675 AACAACACTA
*
3685 TAACAATTGTTATATTTCAACTG
1 TAACAATCGTTATATTTCAACTG
*
3708 TAACAATCGTTCTATTTCAAC
1 TAACAATCGTTATATTTCAAC
3729 AAATAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (23 bp):
TAACAATCGTTATATTTCAACTG
Found at i:4074 original size:31 final size:31
Alignment explanation
Indices: 4048--4122 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
4038 ATTTATACAC
* *
4048 TTTTGGTCACTTATGTTATTGTTTTATTAAG
1 TTTTGGTCACTTACGTTATCGTTTTATTAAG
*
4079 TTTTGGTTACTTACGTTATCGTTTTATTAAG
1 TTTTGGTCACTTACGTTATCGTTTTATTAAG
4110 TTTTGGTCACTTA
1 TTTTGGTCACTTA
4123 GGCATTGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.19, C:0.09, G:0.16, T:0.56
Consensus pattern (31 bp):
TTTTGGTCACTTACGTTATCGTTTTATTAAG
Found at i:4670 original size:29 final size:29
Alignment explanation
Indices: 4601--4668 Score: 129
Period size: 28 Copynumber: 2.4 Consensus size: 29
4591 TTGGAAAGGT
4601 TCAAATTCAAACCGGAAAAAAAATTAAAG
1 TCAAATTCAAACCGGAAAAAAAATTAAAG
4630 TCAAATTCAAACCGG-AAAAAAATTAAAG
1 TCAAATTCAAACCGGAAAAAAAATTAAAG
4658 TCAAATTCAAA
1 TCAAATTCAAA
4669 ACAAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
28 24 0.62
29 15 0.38
ACGTcount: A:0.57, C:0.15, G:0.09, T:0.19
Consensus pattern (29 bp):
TCAAATTCAAACCGGAAAAAAAATTAAAG
Found at i:4676 original size:28 final size:28
Alignment explanation
Indices: 4601--4680 Score: 124
Period size: 28 Copynumber: 2.8 Consensus size: 28
4591 TTGGAAAGGT
4601 TCAAATTCAAACCGGAAAAAAAATTAAAG
1 TCAAATTCAAACC-GAAAAAAAATTAAAG
*
4630 TCAAATTCAAACCGGAAAAAAATTAAAG
1 TCAAATTCAAACCGAAAAAAAATTAAAG
* *
4658 TCAAATTCAAAACAAAAAAAAAT
1 TCAAATTCAAACCGAAAAAAAAT
4681 GAAATACCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 34 0.72
29 13 0.28
ACGTcount: A:0.61, C:0.14, G:0.07, T:0.17
Consensus pattern (28 bp):
TCAAATTCAAACCGAAAAAAAATTAAAG
Found at i:8768 original size:13 final size:13
Alignment explanation
Indices: 8750--8793 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
8740 TGATAAATAA
*
8750 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
8763 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
8776 AAACAACTACAAT
1 AAAAAACTACAAT
8789 AAAAA
1 AAAAA
8794 GTATTAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:11055 original size:9 final size:9
Alignment explanation
Indices: 11041--11074 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
11031 TAAGTAAAAT
11041 ATTAAATAA
1 ATTAAATAA
11050 ATTAAA-AA
1 ATTAAATAA
*
11058 CTTAAATAA
1 ATTAAATAA
11067 ATTAAATA
1 ATTAAATA
11075 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
ATTAAATAA
Found at i:12194 original size:20 final size:20
Alignment explanation
Indices: 12158--12195 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12148 TTATTCATAA
*
12158 TATTATAATTTAAAATTTCT
1 TATTATAATTAAAAATTTCT
12178 TATTAT-ATTAAATAATTT
1 TATTATAATTAAA-AATTT
12196 AACGTCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTATAATTAAAAATTTCT
Found at i:13167 original size:22 final size:22
Alignment explanation
Indices: 13139--13185 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
13129 TGATTTGCGA
13139 TTTGTCGGTGGTCATTCAGTAG
1 TTTGTCGGTGGTCATTCAGTAG
13161 TTTGTCGGTGGTCATTCAGTAG
1 TTTGTCGGTGGTCATTCAGTAG
13183 TTT
1 TTT
13186 CATCTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.30, T:0.45
Consensus pattern (22 bp):
TTTGTCGGTGGTCATTCAGTAG
Found at i:19556 original size:15 final size:14
Alignment explanation
Indices: 19544--19572 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19534 AAAAATATTC
19544 AAAAATTAAATATA
1 AAAAATTAAATATA
19558 AAAAATTAAAT-TA
1 AAAAATTAAATATA
19571 AA
1 AA
19573 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATTAAATATA
Found at i:19573 original size:24 final size:26
Alignment explanation
Indices: 19519--19574 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 26
19509 TTACAATATT
*
19519 TTAAACTTAAAATATAAAAATATTCAA
1 TTAAA-TTAAAATATAAAAATATTAAA
19546 --AAATT-AAATATAAAAA-ATTAAA
1 TTAAATTAAAATATAAAAATATTAAA
19568 TTAAATT
1 TTAAATT
19575 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 5 0.19
23 11 0.42
24 7 0.27
25 3 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (26 bp):
TTAAATTAAAATATAAAAATATTAAA
Found at i:20168 original size:2 final size:2
Alignment explanation
Indices: 20161--20188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20151 AAATTCGAGG
20161 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
20189 AAATTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20225 original size:15 final size:14
Alignment explanation
Indices: 20202--20265 Score: 53
Period size: 15 Copynumber: 4.5 Consensus size: 14
20192 TTTTTTACTA
20202 ATTTA-ATTTTTAT
1 ATTTATATTTTTAT
*
20215 TTTTGATATTTTTAT
1 ATTT-ATATTTTTAT
20230 ATTTAT-TTTTTAAT
1 ATTTATATTTTT-AT
*
20244 ATTGT-TATATTTTAA
1 ATT-TATAT-TTTTAT
20259 ATTTATA
1 ATTTATA
20266 ATATTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
13 8 0.20
14 10 0.24
15 19 0.46
16 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
ATTTATATTTTTAT
Found at i:20240 original size:22 final size:21
Alignment explanation
Indices: 20210--20255 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
20200 TAATTTAATT
* *
20210 TTTATTTTTGATATTTTTATA
1 TTTATTTTTAATATTGTTATA
20231 TTTATTTTTTAATATTGTTATA
1 TTTA-TTTTTAATATTGTTATA
20253 TTT
1 TTT
20256 TAAATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTATTTTTAATATTGTTATA
Found at i:21555 original size:40 final size:40
Alignment explanation
Indices: 21500--21611 Score: 179
Period size: 40 Copynumber: 2.8 Consensus size: 40
21490 AAGCGTTGCA
** *
21500 CCAGAATATTGAATAACATGCATCATACATATAAATTAAG
1 CCAGAATATCAAATAACATGCATCATGCATATAAATTAAG
* *
21540 CCAGAATATCAAATAATATGCATCATGCATGTAAATTAAG
1 CCAGAATATCAAATAACATGCATCATGCATATAAATTAAG
21580 CCAGAATATCAAATAACATGCATCATGCATAT
1 CCAGAATATCAAATAACATGCATCATGCATAT
21612 GAACTTGTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.27
Consensus pattern (40 bp):
CCAGAATATCAAATAACATGCATCATGCATATAAATTAAG
Found at i:33089 original size:31 final size:32
Alignment explanation
Indices: 33054--33137 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 32
33044 CTTGACTATG
*
33054 GGACATTACTTTTTCGAGTCCCTC-GAATAT-A
1 GGACATTACTTTTT-GAGTCCCCCTGAATATAA
*
33085 GGACATTACTTTGTTGAGTCCCCCTGACTATAA
1 GGACATTACTTT-TTGAGTCCCCCTGAATATAA
33118 GG-CATTACTTTTTTGAGTCC
1 GGACATTAC-TTTTTGAGTCC
33138 TCAACTACTA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
31 20 0.43
32 21 0.45
33 6 0.13
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.37
Consensus pattern (32 bp):
GGACATTACTTTTTGAGTCCCCCTGAATATAA
Found at i:34028 original size:26 final size:26
Alignment explanation
Indices: 33972--34028 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
33962 TTAATATTAA
**
33972 TTCTTATTTTTTGGTGATTATTAGTT
1 TTCTTATTTTTTAATGATTATTAGTT
* *
33998 CTCTTATTTTTTAAT-ATTATATATTT
1 TTCTTATTTTTTAATGATTAT-TAGTT
34024 TTCTT
1 TTCTT
34029 TTAATTTCTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (26 bp):
TTCTTATTTTTTAATGATTATTAGTT
Found at i:34593 original size:17 final size:17
Alignment explanation
Indices: 34568--34601 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34558 TTATTATTAC
34568 ATTAAATTATAAAATAA
1 ATTAAATTATAAAATAA
* *
34585 ATTATATTATAATATAA
1 ATTAAATTATAAAATAA
34602 GTATATGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAATTATAAAATAA
Found at i:35523 original size:25 final size:25
Alignment explanation
Indices: 35490--35543 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
35480 CAAATCTGTG
35490 GGGAGGCTATTCCGACGTATGTTAT
1 GGGAGGCTATTCCGACGTATGTTAT
35515 GGGAGGCTATTCCGACGTATGTTAT
1 GGGAGGCTATTCCGACGTATGTTAT
35540 GGGA
1 GGGA
35544 TGCTTTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.15, G:0.35, T:0.30
Consensus pattern (25 bp):
GGGAGGCTATTCCGACGTATGTTAT
Found at i:37419 original size:201 final size:201
Alignment explanation
Indices: 37074--37478 Score: 650
Period size: 201 Copynumber: 2.0 Consensus size: 201
37064 AAAAAAGGTA
* ** * * *
37074 TAAGTAAAAGTAGTAAAGCATGTAGTAGATGATGTAGGTGTGTAAGAAATTACTAAAGTAAATAG
1 TAAGTAAAAGTAGTAAAACAAATAGTAGATGATGTAGGTGCGTAAGAAAGTACTAAAGCAAATAG
* * *
37139 TAGAGAATTTTTTTTGAAGTGTTAAAATAATTGGAAAAAATGAATTTAAAAATCAAAATATTAAA
66 TAGAGAATTTGTTTGGAAGTGTTAAAATAATTGAAAAAAATGAATTTAAAAATCAAAATATTAAA
* * *
37204 AATAATTCACAATCAAAGTAAGAAGTAAAGAAGGCAACGGGAGGAAGCATAAAAACTCTAGTTTC
131 AATAAATCACAATCAAAGTAAAAAGTAAAGAAGGCAACGGGAGGAAGCAGAAAAACTCTAGTTTC
37269 AAAGTG
196 AAAGTG
*
37275 TAAGTAAATGTAGTAAAACAAATAGTAGATGATGTAGGTGCGTAAGAAAGTACTAAAGCAAATAG
1 TAAGTAAAAGTAGTAAAACAAATAGTAGATGATGTAGGTGCGTAAGAAAGTACTAAAGCAAATAG
37340 TAGAGAATTTGTTTGGAAGTGTTAAAAATAATTGAAAAAAATGAATTTAAAAATCAAAATATTAA
66 TAGAGAATTTGTTTGGAAGTGTT-AAAATAATTGAAAAAAATGAATTTAAAAATCAAAATATTAA
* * *
37405 AAA-AAATCACAATCAAAGTAAAAAGTAAAGAAGGCAACGGGAGGAAGTAGAGAAACTTTAGTTT
130 AAATAAATCACAATCAAAGTAAAAAGTAAAGAAGGCAACGGGAGGAAGCAGAAAAACTCTAGTTT
37469 CAAAGTG
195 CAAAGTG
37476 TAA
1 TAA
37479 ACCTTTCATC
Statistics
Matches: 187, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
201 144 0.77
202 43 0.23
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (201 bp):
TAAGTAAAAGTAGTAAAACAAATAGTAGATGATGTAGGTGCGTAAGAAAGTACTAAAGCAAATAG
TAGAGAATTTGTTTGGAAGTGTTAAAATAATTGAAAAAAATGAATTTAAAAATCAAAATATTAAA
AATAAATCACAATCAAAGTAAAAAGTAAAGAAGGCAACGGGAGGAAGCAGAAAAACTCTAGTTTC
AAAGTG
Found at i:39228 original size:23 final size:23
Alignment explanation
Indices: 39194--39258 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
39184 CACCACAGCT
*
39194 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
39217 CGTAGAATTGCATCTAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
39240 CGTAGAAATGCACCGAAGT
1 CGTAGAAATGCACCGAAGT
39259 TCCATATAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:40691 original size:20 final size:22
Alignment explanation
Indices: 40666--40723 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
40656 TTCCCCTTGA
40666 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
40686 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
40709 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
40724 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:40798 original size:64 final size:62
Alignment explanation
Indices: 40714--40871 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 62
40704 TTAACATGTG
* *
40714 CATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAGGGGATA
1 CATCGATGCACT-CCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGGG-TA
* * * * * * * *
40778 CATCGATGCACTCCTTATGCATCTATGCACCACTTGCATTCGATGTTTCCATTTTAATGTGTG
1 CATCGATGCACTCC-TATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGGGTA
*
40841 CATCGATGCACTTCCTGTGCATCGATACACA
1 CATCGATGCAC-TCCTATGCATCGATACACA
40872 CTGAACAATT
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
63 26 0.33
64 52 0.67
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (62 bp):
CATCGATGCACTCCTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAGGGGTA
Found at i:43727 original size:21 final size:21
Alignment explanation
Indices: 43698--43739 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43688 ATCGACGTCA
*
43698 AGTGGTGGTGATGATGATGAT
1 AGTGATGGTGATGATGATGAT
* *
43719 AGTGATGGTGGTGGTGATGAT
1 AGTGATGGTGATGATGATGAT
43740 GATCATGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.33
Consensus pattern (21 bp):
AGTGATGGTGATGATGATGAT
Found at i:43751 original size:24 final size:24
Alignment explanation
Indices: 43699--43752 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
43689 TCGACGTCAA
43699 GTGGTGGTGATGATGATGATAGTG
1 GTGGTGGTGATGATGATGATAGTG
* *
43723 ATGGTGGTGGTGATGATGATCA-TG
1 GTGGTGGTGATGATGATGAT-AGTG
43747 GTGGTG
1 GTGGTG
43753 ATAATGAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.19, C:0.02, G:0.46, T:0.33
Consensus pattern (24 bp):
GTGGTGGTGATGATGATGATAGTG
Found at i:56721 original size:144 final size:144
Alignment explanation
Indices: 56547--56839 Score: 559
Period size: 144 Copynumber: 2.0 Consensus size: 144
56537 AATATTAATC
56547 TATACAAAAAGAAAAACAAGTAATTTAGGAGAGTAAAGATTATATTAGCATAATTTTTAAAATTT
1 TATACAAAAAGAAAAACAAGTAATTTAGGAGAGTAAAGATTATATTAGCATAATTTTTAAAATTT
56612 AAGATTTAAATTTATTGAATTGTTTTGAAAAAGAACCAATTTGATAAAATGTGTAACTTTTGGAA
66 AAGATTTAAATTTATTGAATTGTTTTGAAAAAGAACCAATTTGATAAAATGTGTAACTTTTGGAA
* *
56677 ACTGAATTTATTAT
131 ACTAAATTTACTAT
56691 TATACAAAAAGAAAAACAAGTAATTTAGGAGAGTAAAGATTATATTAGCATAATTTTTAAAATTT
1 TATACAAAAAGAAAAACAAGTAATTTAGGAGAGTAAAGATTATATTAGCATAATTTTTAAAATTT
*
56756 AAGATTTAAATTTATTGAATTGTTTTGAAATAGAACCAATTTGATAAAATGTGTAACTTTTGGAA
66 AAGATTTAAATTTATTGAATTGTTTTGAAAAAGAACCAATTTGATAAAATGTGTAACTTTTGGAA
56821 ACTAAATTTACTAT
131 ACTAAATTTACTAT
56835 TATAC
1 TATAC
56840 TAGGCCAAGT
Statistics
Matches: 146, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
144 146 1.00
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (144 bp):
TATACAAAAAGAAAAACAAGTAATTTAGGAGAGTAAAGATTATATTAGCATAATTTTTAAAATTT
AAGATTTAAATTTATTGAATTGTTTTGAAAAAGAACCAATTTGATAAAATGTGTAACTTTTGGAA
ACTAAATTTACTAT
Found at i:62270 original size:23 final size:22
Alignment explanation
Indices: 62244--62301 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
62234 ATGTATTATG
62244 ATGAATATATGTAACTATTCATC
1 ATGAATATATGT-ACTATTCATC
*
62267 ATGAATGAATAT-TACTATTCATG
1 ATGAAT--ATATGTACTATTCATC
*
62290 ATGAATAAATGT
1 ATGAATATATGT
62302 GACCATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 3 0.10
22 1 0.03
23 21 0.70
24 1 0.03
25 4 0.13
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (22 bp):
ATGAATATATGTACTATTCATC
Found at i:76856 original size:24 final size:24
Alignment explanation
Indices: 76829--76906 Score: 147
Period size: 24 Copynumber: 3.2 Consensus size: 24
76819 TTATTTTTAT
76829 GGTGTTGTTTAGATTTGAACATAA
1 GGTGTTGTTTAGATTTGAACATAA
*
76853 GGTGTTGTTTAGATTTAAACATAA
1 GGTGTTGTTTAGATTTGAACATAA
76877 GGTGTTGTTTAGATTTGAACATAA
1 GGTGTTGTTTAGATTTGAACATAA
76901 GGTGTT
1 GGTGTT
76907 TGATGAAATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.42
Consensus pattern (24 bp):
GGTGTTGTTTAGATTTGAACATAA
Found at i:80725 original size:20 final size:21
Alignment explanation
Indices: 80700--80739 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
80690 AAATTCACAT
80700 TCTAACATCAATTT-CAGCAC
1 TCTAACATCAATTTCCAGCAC
*
80720 TCTAACATTAATTTCCAGCA
1 TCTAACATCAATTTCCAGCA
80740 TAATACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (21 bp):
TCTAACATCAATTTCCAGCAC
Found at i:81685 original size:83 final size:83
Alignment explanation
Indices: 81592--81759 Score: 336
Period size: 83 Copynumber: 2.0 Consensus size: 83
81582 TTTTTCAAAA
81592 ATTTCAATCTTGCCATTTTAATCCAATGGTCCAAATTGAACATGGAAATAAATTCTCAAATGCAA
1 ATTTCAATCTTGCCATTTTAATCCAATGGTCCAAATTGAACATGGAAATAAATTCTCAAATGCAA
81657 TGATCCATATTATTTTCC
66 TGATCCATATTATTTTCC
81675 ATTTCAATCTTGCCATTTTAATCCAATGGTCCAAATTGAACATGGAAATAAATTCTCAAATGCAA
1 ATTTCAATCTTGCCATTTTAATCCAATGGTCCAAATTGAACATGGAAATAAATTCTCAAATGCAA
81740 TGATCCATATTATTTTCC
66 TGATCCATATTATTTTCC
81758 AT
1 AT
81760 CATTTTAAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (83 bp):
ATTTCAATCTTGCCATTTTAATCCAATGGTCCAAATTGAACATGGAAATAAATTCTCAAATGCAA
TGATCCATATTATTTTCC
Found at i:81829 original size:25 final size:25
Alignment explanation
Indices: 81801--81848 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
81791 GCTTAATTTA
81801 ATACCATTCCAATTTTCTCAAATAT
1 ATACCATTCCAATTTTCTCAAATAT
81826 ATACCATTCCAATTTTCTCAAAT
1 ATACCATTCCAATTTTCTCAAAT
81849 TTTTATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (25 bp):
ATACCATTCCAATTTTCTCAAATAT
Found at i:82026 original size:30 final size:29
Alignment explanation
Indices: 81990--82054 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
81980 CAAAATACAT
81990 AACTTTTAAAAACTACACTTTTGGTCCCTA
1 AACTTTTAAAAACTACACTTTTGGT-CCTA
* * * *
82020 AACTTTTGAGAATTACCCTTTTGGTCCTA
1 AACTTTTAAAAACTACACTTTTGGTCCTA
82049 AACTTT
1 AACTTT
82055 ATACTTTGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (29 bp):
AACTTTTAAAAACTACACTTTTGGTCCTA
Found at i:83297 original size:51 final size:49
Alignment explanation
Indices: 83213--83313 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 49
83203 CATGACAACA
*
83213 CAAGCTTATATGAGACAGGGTAGTGAGTTCACTCAACTTCTTCATAAGG
1 CAAGCTTATATGAGACAGGGTAGTGAGTTCACTCAACTTCTTCACAAGG
*
83262 CAAGCTTATATGAGACAAAGGGTTGTGAGTTCACTCAACTTCTTCACAAGG
1 CAAGCTTATATGAGAC--AGGGTAGTGAGTTCACTCAACTTCTTCACAAGG
83313 C
1 C
83314 CTTTCTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 16 0.33
51 32 0.67
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (49 bp):
CAAGCTTATATGAGACAGGGTAGTGAGTTCACTCAACTTCTTCACAAGG
Found at i:83400 original size:22 final size:22
Alignment explanation
Indices: 83374--83424 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
83364 CGAGAGACGA
*
83374 TTTTGGAAGACCAAGATATAAT
1 TTTTGGAAGACCAAGACATAAT
83396 TTTTGGAAGACCAAGACATAAT
1 TTTTGGAAGACCAAGACATAAT
83418 TTTTGGA
1 TTTTGGA
83425 TTTGGTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGACCAAGACATAAT
Found at i:88697 original size:2 final size:2
Alignment explanation
Indices: 88690--88722 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
88680 TTTACATCCT
88690 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 T
88723 TAATGACCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.