Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007444.1 Hibiscus syriacus cultivar Beakdansim tig00020342_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: 49084
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4839 original size:12 final size:12
Alignment explanation
Indices: 4822--4856 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
4812 ATAAATATAA
4822 ATGACGTTGGAC
1 ATGACGTTGGAC
*
4834 ATGACGTTGAAC
1 ATGACGTTGGAC
4846 ATGACGTTGGA
1 ATGACGTTGGA
4857 GAACCATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (12 bp):
ATGACGTTGGAC
Found at i:10817 original size:20 final size:20
Alignment explanation
Indices: 10794--10885 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
10784 ATACAAACGT
*
10794 AAAGATGCGAATGCAAATGC
1 AAAGATGTGAATGCAAATGC
*
10814 AAAGATGTGAATGTAAAATG-
1 AAAGATGTGAATG-CAAATGC
* * * *
10834 AAA-ATGTAAATACAAACGT
1 AAAGATGTGAATGCAAATGC
* *
10853 AAATATGCGAATGCAAATGC
1 AAAGATGTGAATGCAAATGC
10873 AAAGATGTGAATG
1 AAAGATGTGAATG
10886 TAAAATGAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
18 4 0.07
19 10 0.18
20 37 0.66
21 5 0.09
ACGTcount: A:0.49, C:0.09, G:0.22, T:0.21
Consensus pattern (20 bp):
AAAGATGTGAATGCAAATGC
Found at i:10834 original size:59 final size:59
Alignment explanation
Indices: 10769--10894 Score: 234
Period size: 59 Copynumber: 2.1 Consensus size: 59
10759 GCAAATGCAA
10769 AAAATGAAAATATAAATACAAACGTAAAGATGCGAATGCAAATGCAAAGATGTGAATGT
1 AAAATGAAAATATAAATACAAACGTAAAGATGCGAATGCAAATGCAAAGATGTGAATGT
* *
10828 AAAATGAAAATGTAAATACAAACGTAAATATGCGAATGCAAATGCAAAGATGTGAATGT
1 AAAATGAAAATATAAATACAAACGTAAAGATGCGAATGCAAATGCAAAGATGTGAATGT
10887 AAAATGAA
1 AAAATGAA
10895 TATAAAAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.21
Consensus pattern (59 bp):
AAAATGAAAATATAAATACAAACGTAAAGATGCGAATGCAAATGCAAAGATGTGAATGT
Found at i:10929 original size:14 final size:16
Alignment explanation
Indices: 10899--10931 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
10889 AATGAATATA
10899 AAAAATGCAGAAATGC
1 AAAAATGCAGAAATGC
10915 AAAAATG-AG-AATGC
1 AAAAATGCAGAAATGC
10929 AAA
1 AAA
10932 TGCATGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.61, C:0.09, G:0.18, T:0.12
Consensus pattern (16 bp):
AAAAATGCAGAAATGC
Found at i:10934 original size:20 final size:20
Alignment explanation
Indices: 10802--10935 Score: 55
Period size: 20 Copynumber: 6.7 Consensus size: 20
10792 GTAAAGATGC
* *
10802 GAATGCAAATGCAAAGATGT
1 GAATGCAAATGCAAAAATGA
*
10822 GAATGTAAAATG--AAAATGTA
1 GAATG-CAAATGCAAAAATG-A
* * * * *
10842 -AATACAAACGTAAATATGC
1 GAATGCAAATGCAAAAATGA
* *
10861 GAATGCAAATGCAAAGATGT
1 GAATGCAAATGCAAAAATGA
*
10881 GAATGTAAAATG-AATATAA--A
1 GAATG-CAAATGCAA-A-AATGA
*
10901 AAATGCAGAAATGCAAAAATGA
1 GAATGC--AAATGCAAAAATGA
10923 GAATGCAAATGCA
1 GAATGCAAATGCA
10936 TGTATGCACA
Statistics
Matches: 82, Mismatches: 19, Indels: 26
0.65 0.15 0.20
Matches are distributed among these distances:
18 4 0.05
19 8 0.10
20 44 0.54
21 17 0.21
22 9 0.11
ACGTcount: A:0.52, C:0.08, G:0.19, T:0.20
Consensus pattern (20 bp):
GAATGCAAATGCAAAAATGA
Found at i:11749 original size:45 final size:45
Alignment explanation
Indices: 11699--11793 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
11689 AAAAGCATAA
* * * *
11699 AAAGAAATAAATAATGTACAACACACAAATATAATCTTTAAATCT
1 AAAGAAACAAATAATGTACAACAAAAAAATATAATCTTTAAATAT
* * *
11744 AAAGAAACAAATAATGTACAACAAAAAAATTTATTCTTTCAATAT
1 AAAGAAACAAATAATGTACAACAAAAAAATATAATCTTTAAATAT
11789 AAAGA
1 AAAGA
11794 GATATAATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.26
Consensus pattern (45 bp):
AAAGAAACAAATAATGTACAACAAAAAAATATAATCTTTAAATAT
Found at i:12808 original size:19 final size:20
Alignment explanation
Indices: 12760--12808 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
12750 TTAATAATGG
12760 TATTA-TTTTATGTCATTAT
1 TATTATTTTTATGTCATTAT
12779 TATTAGTTTTTCTAT-TCATTA-
1 TATTA--TTTT-TATGTCATTAT
12800 TATTATTTT
1 TATTATTTT
12809 ATTTTAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 9 0.35
21 5 0.19
22 9 0.35
23 3 0.12
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (20 bp):
TATTATTTTTATGTCATTAT
Found at i:13448 original size:19 final size:19
Alignment explanation
Indices: 13405--13441 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13395 CGATCAGTTA
13405 CTATTCACGCCACCGGTCT
1 CTATTCACGCCACCGGTCT
*
13424 CTATTCACGCTACCGGTC
1 CTATTCACGCCACCGGTC
13442 ATTATTCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.41, G:0.16, T:0.27
Consensus pattern (19 bp):
CTATTCACGCCACCGGTCT
Found at i:25088 original size:60 final size:59
Alignment explanation
Indices: 24965--25110 Score: 159
Period size: 60 Copynumber: 2.5 Consensus size: 59
24955 ATTTAGTTTG
* * **
24965 GGATGAAATTGGAATGTTAAAAAGTTTGGGACCAATTTTGAATAAAGGTCATAGTTTGG
1 GGATGAAATTGAAATGTTAAAAAGTTTGGGACCAATTTAGAATAAAGGTCATAGTTTAA
* * * *
25024 GGATGAAATTGAAATGTTCAAAATTTTGAGGACTAATTTAGAATGATA-GTCATAGTTTAA
1 GGATGAAATTGAAATGTTAAAAAGTTTG-GGACCAATTTAGAAT-AAAGGTCATAGTTTAA
* * * *
25084 GGATGAAGTTCAAATATTTAAAAGTTT
1 GGATGAAATTGAAATGTTAAAAAGTTT
25111 AGAAATCAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 25 0.35
60 45 0.62
61 2 0.03
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (59 bp):
GGATGAAATTGAAATGTTAAAAAGTTTGGGACCAATTTAGAATAAAGGTCATAGTTTAA
Found at i:25631 original size:29 final size:29
Alignment explanation
Indices: 25589--25647 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
25579 ATTTTCACCT
25589 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
25618 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
25647 A
1 A
25648 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:29534 original size:22 final size:22
Alignment explanation
Indices: 29508--29582 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
29498 ATATGCCTGA
* *
29508 GGGTATCGGTACCATTGCATAG
1 GGGTATCGATACCATTGCATGG
29530 GGGTATCGATACC--T--ATGG
1 GGGTATCGATACCATTGCATGG
*
29548 GGGTATCGGTACCATTGCATGG
1 GGGTATCGATACCATTGCATGG
*
29570 GGGTGTCGATACC
1 GGGTATCGATACC
29583 TATGGAGGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 15 0.34
20 2 0.05
22 27 0.61
ACGTcount: A:0.20, C:0.19, G:0.35, T:0.27
Consensus pattern (22 bp):
GGGTATCGATACCATTGCATGG
Found at i:29552 original size:18 final size:18
Alignment explanation
Indices: 29529--29600 Score: 72
Period size: 18 Copynumber: 3.8 Consensus size: 18
29519 CCATTGCATA
29529 GGGGTATCGATACCTATG
1 GGGGTATCGATACCTATG
*
29547 GGGGTATCGGTACCATTGCATG
1 GGGGTATCGATACC--T--ATG
*
29569 GGGGTGTCGATACCTATG
1 GGGGTATCGATACCTATG
* *
29587 GAGGTATCGGTACC
1 GGGGTATCGATACC
29601 ATCCGAGCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 27 0.61
20 2 0.05
22 15 0.34
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.26
Consensus pattern (18 bp):
GGGGTATCGATACCTATG
Found at i:29563 original size:40 final size:40
Alignment explanation
Indices: 29508--29602 Score: 163
Period size: 40 Copynumber: 2.4 Consensus size: 40
29498 ATATGCCTGA
29508 GGGTATCGGTACCATTGCATAGGGGTATCGATACCTATGG
1 GGGTATCGGTACCATTGCATAGGGGTATCGATACCTATGG
* *
29548 GGGTATCGGTACCATTGCATGGGGGTGTCGATACCTATGG
1 GGGTATCGGTACCATTGCATAGGGGTATCGATACCTATGG
*
29588 AGGTATCGGTACCAT
1 GGGTATCGGTACCAT
29603 CCGAGCATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (40 bp):
GGGTATCGGTACCATTGCATAGGGGTATCGATACCTATGG
Found at i:32231 original size:21 final size:21
Alignment explanation
Indices: 32140--32285 Score: 153
Period size: 21 Copynumber: 6.9 Consensus size: 21
32130 TAAACCTGAC
32140 AGGGGGTATCGATACC-A-TA
1 AGGGGGTATCGATACCTATTA
32159 AGGGGGTATCGATACC-A-TA
1 AGGGGGTATCGATACCTATTA
32178 AGGGGGGTATCGATA-CTCATTCAA
1 A-GGGGGTATCGATACCT-ATT--A
*
32202 AGAGGGTATCGATACCTATTCA
1 AGGGGGTATCGATACCTATT-A
32224 A-GGGGTATCGATACCTATTCA
1 AGGGGGTATCGATACCTATT-A
*
32245 AGGGGGTATCGATACCTGTATA
1 AGGGGGTATCGATACCTAT-TA
32267 A-GGGGTATCGATACTCTAT
1 AGGGGGTATCGATAC-CTAT
32286 GCACAAAAAT
Statistics
Matches: 112, Mismatches: 5, Indels: 17
0.84 0.04 0.13
Matches are distributed among these distances:
19 21 0.19
20 13 0.12
21 34 0.30
22 24 0.21
23 16 0.14
24 4 0.04
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (21 bp):
AGGGGGTATCGATACCTATTA
Found at i:32252 original size:43 final size:42
Alignment explanation
Indices: 32142--32285 Score: 165
Period size: 43 Copynumber: 3.4 Consensus size: 42
32132 AACCTGACAG
32142 GGGGTATCGATACC-A-T-AAGGGGGTATCGATACC-A-TAA
1 GGGGTATCGATACCTATTCAAGGGGGTATCGATACCTATTAA
*
32179 GGGGGGTATCGATA-CTCATTCAAAGAGGGTATCGATACCTATTCAA
1 --GGGGTATCGATACCT-ATTC-AAGGGGGTATCGATACCTATT-AA
*
32225 GGGGTATCGATACCTATTCAAGGGGGTATCGATACCTGTATAA
1 GGGGTATCGATACCTATTCAAGGGGGTATCGATACCTAT-TAA
32268 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
32286 GCACAAAAAT
Statistics
Matches: 91, Mismatches: 3, Indels: 17
0.82 0.03 0.15
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 1 0.01
41 1 0.01
43 49 0.54
44 22 0.24
45 3 0.03
46 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (42 bp):
GGGGTATCGATACCTATTCAAGGGGGTATCGATACCTATTAA
Found at i:32273 original size:64 final size:63
Alignment explanation
Indices: 32142--32285 Score: 167
Period size: 64 Copynumber: 2.3 Consensus size: 63
32132 AACCTGACAG
32142 GGGGTATCGATACC-A-TAAGGGGGTATCGATACCATAAGGGGGGTATCGATACTCATTCAAA
1 GGGGTATCGATACCTATTAAGGGGGTATCGATACCATAAGGGGGGTATCGATACTCATTCAAA
32203 GAGGGTATCGATACCTATTCAA-GGGGTATCGATACCTATTCAA-GGGGGTATCGATAC-C-TGT
1 G-GGGTATCGATACCTATT-AAGGGGGTATCGATACC-A-T-AAGGGGGGTATCGATACTCAT-T
32264 -ATAA
60 CA-AA
32268 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
32286 GCACAAAAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 16
0.82 0.00 0.18
Matches are distributed among these distances:
61 1 0.01
62 13 0.18
63 1 0.01
64 29 0.40
65 12 0.16
66 15 0.21
67 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (63 bp):
GGGGTATCGATACCTATTAAGGGGGTATCGATACCATAAGGGGGGTATCGATACTCATTCAAA
Found at i:32849 original size:3 final size:3
Alignment explanation
Indices: 32843--32918 Score: 102
Period size: 3 Copynumber: 25.7 Consensus size: 3
32833 ATTTTTAATA
* *
32843 ATT ATT ATT -TT ACT ATT ATT ATT ATTT ATT GTT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
*
32887 ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
32919 AACAAACAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.06
3 57 0.89
4 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:36665 original size:6 final size:7
Alignment explanation
Indices: 36624--36664 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
36614 TTTTCATACA
36624 TGCA-TT
1 TGCATTT
36630 TGCATTT
1 TGCATTT
*
36637 TACATCTT
1 TGCAT-TT
36645 TGCATTT
1 TGCATTT
36652 T-CATTT
1 TGCATTT
36658 TGCATTT
1 TGCATTT
36665 GTTGTTTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
6 10 0.33
7 14 0.47
8 6 0.20
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:39865 original size:20 final size:20
Alignment explanation
Indices: 39840--39877 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39830 TTCATCGAAA
39840 AAAAGAAAA-AGAGAAAAAAG
1 AAAAGAAAAGA-AGAAAAAAG
39860 AAAAGAAAAGAAGAAAAA
1 AAAAGAAAAGAAGAAAAA
39878 TTTTGAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAGAAGAAAAAAG
Found at i:39873 original size:13 final size:13
Alignment explanation
Indices: 39840--39876 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
39830 TTCATCGAAA
39840 AAAAGAA-AAAGAG
1 AAAAGAAGAAA-AG
39853 AAAA-AAGAAAAG
1 AAAAGAAGAAAAG
39865 AAAAGAAGAAAA
1 AAAAGAAGAAAA
39877 ATTTTGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAG
Found at i:43383 original size:74 final size:76
Alignment explanation
Indices: 43147--43367 Score: 265
Period size: 74 Copynumber: 3.0 Consensus size: 76
43137 AATGAATATT
* * ** * *
43147 TGGGGCATGTTGAAAGCCCATTTCAATTAGAAGT-TGGAATATT-AATGCATTTTGAACGTTTCT
1 TGGGGCATGCTGAAAGCCCATTTCAATCAGAA-TCAAGAATATTGACTGCATTTTGAACGTTTGT
43210 ATCAGCAAATAC
65 ATCAGCAAATAC
* *
43222 TGGGGCAGGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACT-CATTTT-AACATTTGTA
1 TGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACTGCATTTTGAACGTTTGTA
43285 TCAGCAAATAC
66 TCAGCAAATAC
* * * * * *
43296 TGGGGCATACTGAAAGCCC-TTTTAATCAGAATCACGAATGTTG-GTGCATTTTGAACGTCTGTA
1 TGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACTGCATTTTGAACGTTTGTA
43359 TCAGCAAAT
66 TCAGCAAAT
43368 GTTAGGACAT
Statistics
Matches: 126, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
72 1 0.01
73 27 0.21
74 54 0.43
75 42 0.33
76 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (76 bp):
TGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACTGCATTTTGAACGTTTGTA
TCAGCAAATAC
Found at i:44650 original size:22 final size:22
Alignment explanation
Indices: 44622--44769 Score: 150
Period size: 22 Copynumber: 7.1 Consensus size: 22
44612 TATCTACATC
*
44622 TTCTCTCTTCAAAGATGATAAA
1 TTCTCTCTTCAAAGATGATAGA
44644 TTCTCTCTTC-AA-AT-AT-GA
1 TTCTCTCTTCAAAGATGATAGA
* *
44662 TTTTCTTTTCAAAGATGATAGA
1 TTCTCTCTTCAAAGATGATAGA
*
44684 -T-TCTCTTCAAATATGATAGA
1 TTCTCTCTTCAAAGATGATAGA
*
44704 TACTCTCTTCAAAGATGAT--A
1 TTCTCTCTTCAAAGATGATAGA
* *
44724 TTTTCTCTTCAAAGATTATAGA
1 TTCTCTCTTCAAAGATGATAGA
* * *
44746 TTCTCTTTTCAAAGAAGAAAGA
1 TTCTCTCTTCAAAGATGATAGA
44768 TT
1 TT
44770 TATTGGATTT
Statistics
Matches: 103, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
18 9 0.09
19 4 0.04
20 38 0.37
21 5 0.05
22 47 0.46
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
TTCTCTCTTCAAAGATGATAGA
Found at i:44674 original size:18 final size:19
Alignment explanation
Indices: 44625--44752 Score: 96
Period size: 20 Copynumber: 6.3 Consensus size: 19
44615 CTACATCTTC
*
44625 TCTCTTCAAAGATGATAAATT
1 TCTCTTCAAATATGAT-AA-T
*
44646 CTCTCTTCAAATATGAT-TT
1 -TCTCTTCAAATATGATAAT
* *
44665 TCTTTTCAAAGATGATAGAT
1 TCTCTTCAAATATGATA-AT
44685 TCTCTTCAAATATGATAGAT
1 TCTCTTCAAATATGATA-AT
* *
44705 ACTCTCTTCAAAGATGATATTT
1 --TCTCTTCAAATATGATA-AT
* *
44727 TCTCTTCAAAGATTATAGAT
1 TCTCTTCAAATATGATA-AT
44747 TCTCTT
1 TCTCTT
44753 TTCAAAGAAG
Statistics
Matches: 89, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
18 14 0.16
19 1 0.01
20 42 0.47
22 32 0.36
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.42
Consensus pattern (19 bp):
TCTCTTCAAATATGATAAT
Found at i:44730 original size:42 final size:41
Alignment explanation
Indices: 44623--44760 Score: 147
Period size: 42 Copynumber: 3.3 Consensus size: 41
44613 ATCTACATCT
*
44623 TCTCTCTTCAAAGATGATAAATTCTCTCTTCAAATATGAT---
1 TCTCTCTTCAAAGATGAT--ATTTTCTCTTCAAATATGATAGA
* * **
44663 TTTCTTTTCAAAGATGATAGATTCTCTTCAAATATGATAGA
1 TCTCTCTTCAAAGATGATATTTTCTCTTCAAATATGATAGA
* *
44704 TACTCTCTTCAAAGATGATATTTTCTCTTCAAAGATTATAGA
1 T-CTCTCTTCAAAGATGATATTTTCTCTTCAAATATGATAGA
*
44746 TTCTCTTTTCAAAGA
1 -TCTCTCTTCAAAGA
44761 AGAAAGATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
38 17 0.21
40 16 0.20
41 1 0.01
42 46 0.57
43 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (41 bp):
TCTCTCTTCAAAGATGATATTTTCTCTTCAAATATGATAGA
Found at i:45541 original size:219 final size:218
Alignment explanation
Indices: 45140--45562 Score: 561
Period size: 219 Copynumber: 1.9 Consensus size: 218
45130 CCATCACTCA
* * *
45140 GATGGATCAACATGCCAGGTAGAGTTCATAATGAGAAGAATTTATCTGAAGAGGAAGAAAAAGTT
1 GATGGATCAACATGCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAAAAGTT
***
45205 CATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGGATTGGCATTGCCAGGTA
66 CATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGGATCAACATTGCCAGGTA
* * *
45270 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG-AGAATTTGTT
131 AAGTTCATAAAGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTT
45334 CAACATTTTGCTTGAATTCACTT
196 CAACATTTTGCTTGAATTCACTT
* *
45357 GATGGATCAGCATTGCTAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAA
1 GATGGATCAACA-TGCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAA-AAA
* * * * *
45422 -TTCATAATGAGAAGAATTTGTTCAATCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTC
63 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACT---TGGATCAACATTGC
* * *
45486 CAGAG-AAAGTTCATAAAGAGAAGAACTTATCTGAAG-AGGAA-AA-AAGTTTATAATGAGAAGA
125 CAG-GTAAAGTTCATAAAGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGA
*
45547 ACTTGTTCAACCTTTT
189 ACTTGTTCAACATTTT
45563 CATGACTCTA
Statistics
Matches: 178, Mismatches: 20, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
217 11 0.06
218 35 0.20
219 64 0.36
220 22 0.12
221 5 0.03
222 40 0.22
223 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (218 bp):
GATGGATCAACATGCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAAAAGTT
CATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTTGGATCAACATTGCCAGGTA
AAGTTCATAAAGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTT
CAACATTTTGCTTGAATTCACTT
Found at i:45553 original size:110 final size:113
Alignment explanation
Indices: 45131--45696 Score: 555
Period size: 109 Copynumber: 5.1 Consensus size: 113
45121 GATTCGGGTC
* *
45131 CATCACTCAGATGGATCAACA-TGCCAGGTAGAGTTCATAATGAGAAGAATTTATCTGAAG-AGG
1 CATCACTC-GATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGG
*
45194 AAGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
65 AAGAAGAAA-TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*** * *
45243 CATCACT---TGGATTGGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
* *
45305 AGAAGAAATTCATAATGAG-AGAATTTGTTCAACATTTTGCTTGAA-T
66 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* * * *
45351 --TCACTTGATGGATCAGCATTGCTAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
* *
45414 AGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTTGAATT
66 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* * *
45462 CATCACTCGATGGATCAACTTTTCCAGAG-AAAGTTCATAAAGAGAAGAACTTATCTGAAG-AGG
1 CATCACTCGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGG
* * * *
45525 AA-AA-AAGTTTATAATGAGAAGAACTTGTTCAACCTTTT-CATG-ACT
65 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* * * * * *
45570 CTATCACAGAAGAAGATAGATTAGCATCAACATTTCCA-G-AAGTGTTCATAATGAGAACAACTC
1 C-ATCAC---------TCGA-T-GGATCAACATTGCCAGGTAA-AGTTCATAATGAGAAGAACTT
*
45633 ATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC--TTGCCTT-AATT
53 ATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTG-CTTGAATT
45691 CATCAC
1 CATCAC
45697 ATATGAACCA
Statistics
Matches: 385, Mismatches: 39, Indels: 52
0.81 0.08 0.11
Matches are distributed among these distances:
106 5 0.01
108 11 0.03
109 136 0.35
110 73 0.19
111 6 0.02
112 12 0.03
113 50 0.13
118 6 0.02
119 29 0.08
120 23 0.06
121 34 0.09
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
CATCACTCGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
Found at i:46047 original size:15 final size:15
Alignment explanation
Indices: 46029--46073 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
46019 TATCCATTTG
46029 TTTTTATTTTAATAT
1 TTTTTATTTTAATAT
*
46044 TTTTTATTTTATTA-
1 TTTTTATTTTAATAT
46058 TTTTTA--TTAATAT
1 TTTTTATTTTAATAT
46071 TTT
1 TTT
46074 ATAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 5 0.19
13 3 0.11
14 6 0.22
15 13 0.48
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATTTTAATAT
Found at i:46082 original size:3 final size:3
Alignment explanation
Indices: 46074--46103 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
46064 TTAATATTTT
46074 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46104 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46434 original size:20 final size:20
Alignment explanation
Indices: 46409--46458 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
46399 AATGCCTTAT
46409 GTGAGTCACCACATAGTTTG
1 GTGAGTCACCACATAGTTTG
46429 GTGAGTCACCACATAGTTTG
1 GTGAGTCACCACATAGTTTG
*
46449 GTGACTCACC
1 GTGAGTCACC
46459 GCAAAGAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (20 bp):
GTGAGTCACCACATAGTTTG
Found at i:47505 original size:19 final size:18
Alignment explanation
Indices: 47476--47514 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
47466 TTTTATATGT
47476 TTATTTTATTTTAT-TATA
1 TTATTTTA-TTTATCTATA
47494 TTATTCTTATTTATCTATA
1 TTATT-TTATTTATCTATA
47513 TT
1 TT
47515 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTTATTTATCTATA
Found at i:47532 original size:11 final size:11
Alignment explanation
Indices: 47516--47541 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47506 ATCTATATTT
47516 ATATATATATA
1 ATATATATATA
47527 ATATATATATA
1 ATATATATATA
47538 ATAT
1 ATAT
47542 TTATTTTCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATATATATA
Done.