Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007102.1 Hibiscus syriacus cultivar Beakdansim tig00018556_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: 149001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6911 original size:24 final size:25
Alignment explanation
Indices: 6884--6931 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
6874 CCATGAGAAT
* *
6884 TGTGTCACAAGAGCAGA-AAAAATG
1 TGTGCCACAAGAACAGAGAAAAATG
6908 TGTGCCACAAGAACAGAGAAAAAT
1 TGTGCCACAAGAACAGAGAAAAAT
6932 CATATCACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.15
Consensus pattern (25 bp):
TGTGCCACAAGAACAGAGAAAAATG
Found at i:8193 original size:3 final size:3
Alignment explanation
Indices: 8185--8212 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8175 CCAAAGGACA
8185 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
8213 CATAACCCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:9815 original size:17 final size:20
Alignment explanation
Indices: 9762--9813 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
9752 AATAAATCAA
*
9762 AATTAAATATTGTTTTA-AAT
1 AATTATATATT-TTTTATAAT
9782 AATTATATATTTTTTATAAT
1 AATTATATATTTTTTATAAT
9802 AA-TA-ATATTTTT
1 AATTATATATTTTT
9814 ATCTCATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 8 0.27
19 7 0.23
20 15 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AATTATATATTTTTTATAAT
Found at i:12734 original size:13 final size:13
Alignment explanation
Indices: 12716--12740 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12706 GAGTTTGAGC
12716 TTAATATATATAT
1 TTAATATATATAT
12729 TTAATATATATA
1 TTAATATATATA
12741 ATATATTACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAATATATATAT
Found at i:23761 original size:37 final size:37
Alignment explanation
Indices: 23706--23793 Score: 167
Period size: 37 Copynumber: 2.4 Consensus size: 37
23696 GCGAAAACGA
*
23706 AATTCGCGTTGCGATAGTCGTGTTTACCTATATCGGT
1 AATTAGCGTTGCGATAGTCGTGTTTACCTATATCGGT
23743 AATTAGCGTTGCGATAGTCGTGTTTACCTATATCGGT
1 AATTAGCGTTGCGATAGTCGTGTTTACCTATATCGGT
23780 AATTAGCGTTGCGA
1 AATTAGCGTTGCGA
23794 AATTCGCGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (37 bp):
AATTAGCGTTGCGATAGTCGTGTTTACCTATATCGGT
Found at i:26802 original size:2 final size:2
Alignment explanation
Indices: 26795--26822 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26785 CACCGCATGG
26795 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
26823 TAGTTAACCA
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):
AT
Found at i:27133 original size:2 final size:2
Alignment explanation
Indices: 27126--27161 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
27116 CCTGGAAACA
27126 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
27162 GTCTTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31960 original size:31 final size:31
Alignment explanation
Indices: 31900--32087 Score: 195
Period size: 31 Copynumber: 6.0 Consensus size: 31
31890 GATCCTCGGT
* * *
31900 AACTGTCTATAGGTTCCG-ATGAACCTAGGTA
1 AACTGTCCATATGTTCCGTA-GAACATAGGTA
*
31931 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
31962 TACTGTCCATATG-TCTCG-AAAGACATAGGTA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTA
*
31993 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGTAGAACATAGGTA
* * *
32025 TACTGTCCATATG-TCTCGAAAAACATAGGTA
1 AACTGTCCATATGTTC-CGTAGAACATAGGTA
*
32056 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGTAGAACATAGGTA
32088 TACCCTCGAC
Statistics
Matches: 130, Mismatches: 18, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
30 6 0.05
31 71 0.55
32 47 0.36
33 6 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:32008 original size:63 final size:63
Alignment explanation
Indices: 31925--32090 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
31915 CCGATGAACC
* * *
31925 TAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACA
31987 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACA
32050 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
32091 CCTCGACTCT
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.07
63 93 0.93
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAAACA
Found at i:36589 original size:32 final size:31
Alignment explanation
Indices: 36538--36655 Score: 157
Period size: 32 Copynumber: 3.7 Consensus size: 31
36528 ATTCCTTAGA
36538 ACATAGGTATACTGTCCATATGTCTCGAAAG
1 ACATAGGTATACTGTCCATATGTCTCGAAAG
* * *
36569 ACATAGGTAATTCTGTCCATATGT-TCCATAG
1 ACATAGGT-ATACTGTCCATATGTCTCGAAAG
*
36600 AACATAGGTATACTGTCCATATGTCTCGAAAA
1 -ACATAGGTATACTGTCCATATGTCTCGAAAG
*
36632 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGT-ATACTGTCCATATGT
36656 TCCGTAGAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
31 35 0.47
32 40 0.53
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (31 bp):
ACATAGGTATACTGTCCATATGTCTCGAAAG
Found at i:36601 original size:63 final size:63
Alignment explanation
Indices: 36510--36675 Score: 280
Period size: 63 Copynumber: 2.7 Consensus size: 63
36500 CCGATGAACC
* * * *
36510 TAGGTAA-ACTGTCCATATATTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAAACA
36572 TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAAACA
1 TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAAACA
*
36635 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
1 TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATAC
36676 CCTCGACTCT
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
62 7 0.07
63 91 0.93
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAAACA
Found at i:36667 original size:32 final size:32
Alignment explanation
Indices: 36486--36672 Score: 190
Period size: 31 Copynumber: 5.9 Consensus size: 32
36476 ATCCTCGGTA
* * *
36486 ACTGTCTATAGGTTCCG-ATGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTA-GAACATAGGTAAT
* *
36517 ACTGTCCATATATTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
36548 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
* *
36580 TCTGTCCATATGTTCCATAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
36611 ACTGTCCATATG-TCTCGAAAAACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGAACATAGGTAAT
*
36643 TCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTTCCGTAGAACATAGGTA
36673 TACCCTCGAC
Statistics
Matches: 128, Mismatches: 18, Indels: 19
0.78 0.11 0.12
Matches are distributed among these distances:
30 7 0.05
31 66 0.52
32 49 0.38
33 6 0.05
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:40917 original size:30 final size:29
Alignment explanation
Indices: 40882--40940 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
40872 TAAATACCTC
*
40882 ATTCATACATA-AATTATATTAAATTCTCGA
1 ATTCATACATATAATT-TA-AAAATTCTCGA
40912 ATTCATACATATAATTTAAAAATTCTCGA
1 ATTCATACATATAATTTAAAAATTCTCGA
40941 TTTTATAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.37
30 13 0.48
31 4 0.15
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (29 bp):
ATTCATACATATAATTTAAAAATTCTCGA
Found at i:42237 original size:3 final size:3
Alignment explanation
Indices: 42229--42289 Score: 68
Period size: 3 Copynumber: 19.0 Consensus size: 3
42219 TTGCAGCCAA
* *
42229 GAT GAT GAT AAGT GAT GAT GAT AAGT GAT GAT GAT GAGT GAT GAT GAT
1 GAT GAT GAT GA-T GAT GAT GAT GA-T GAT GAT GAT GA-T GAT GAT GAT
42277 GAGT GAT GAT GAT
1 GA-T GAT GAT GAT
42290 AAAGAACATA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
3 40 0.80
4 10 0.20
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:42247 original size:13 final size:13
Alignment explanation
Indices: 42229--42291 Score: 108
Period size: 13 Copynumber: 4.8 Consensus size: 13
42219 TTGCAGCCAA
42229 GATGATGATAAGT
1 GATGATGATAAGT
42242 GATGATGATAAGT
1 GATGATGATAAGT
*
42255 GATGATGATGAGT
1 GATGATGATAAGT
*
42268 GATGATGATGAGT
1 GATGATGATAAGT
42281 GATGATGATAA
1 GATGATGATAA
42292 AGAACATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (13 bp):
GATGATGATAAGT
Found at i:42755 original size:60 final size:60
Alignment explanation
Indices: 42629--42771 Score: 187
Period size: 60 Copynumber: 2.4 Consensus size: 60
42619 GTATTATATG
** * * * **
42629 TCCTCAAACTATGACTTTTATTATAAATTAGTCCATAAACTTTTAAACATTATGAATTTA
1 TCCTCAAACTATGACCCTCATTCTAAATTAGTCCATAAACTTTTAAACATTATAAATGCA
* * *
42689 TACTCAAACTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTGTAAATGCA
1 TCCTCAAACTATGACCCTCATTCTAAATTAGTCCATAAACTTTTAAACATTATAAATGCA
*
42749 TCCTCAAATTATGACCCTCATTC
1 TCCTCAAACTATGACCCTCATTC
42772 CCTGCAAACT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.38
Consensus pattern (60 bp):
TCCTCAAACTATGACCCTCATTCTAAATTAGTCCATAAACTTTTAAACATTATAAATGCA
Found at i:42926 original size:60 final size:60
Alignment explanation
Indices: 42838--43005 Score: 180
Period size: 60 Copynumber: 2.8 Consensus size: 60
42828 GAAGTTATTG
*
42838 GAATGTTCAAAAGTTTGAGGGCTAATTTAGAATGA-GAGTCATAGTTTAGGGATAAAATTA
1 GAATGTTCAAAAGTTTGAGGACTAATTTAGAATGAGGA-TCATAGTTTAGGGATAAAATTA
* * * * *
42898 GAATGTTCAAAAGTTTG-GATACTTATTTAGAATGAGGATCATGGTTTAGGGGTGAAATTA
1 GAATGTTCAAAAGTTTGAG-GACTAATTTAGAATGAGGATCATAGTTTAGGGATAAAATTA
* * * * * *
42958 GAATGTTTAAAAG-TTGAAGGGCTAATTTAAAATTAGGGTCATAATTTA
1 GAATGTTCAAAAGTTTG-AGGACTAATTTAGAATGAGGATCATAGTTTA
43006 AGGTTGTACA
Statistics
Matches: 89, Mismatches: 15, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
59 4 0.04
60 82 0.92
61 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (60 bp):
GAATGTTCAAAAGTTTGAGGACTAATTTAGAATGAGGATCATAGTTTAGGGATAAAATTA
Found at i:44195 original size:2 final size:2
Alignment explanation
Indices: 44190--44216 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44180 TAAGAGAGTG
44190 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
44217 ATTTGTTTTT
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:55199 original size:20 final size:20
Alignment explanation
Indices: 55174--55217 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
55164 CCATTATTGT
55174 CACAATTGCAATAAACACAA
1 CACAATTGCAATAAACACAA
*
55194 CACAATTGCAATAAACATAA
1 CACAATTGCAATAAACACAA
55214 CACA
1 CACA
55218 GCCGAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.25, G:0.05, T:0.16
Consensus pattern (20 bp):
CACAATTGCAATAAACACAA
Found at i:55526 original size:12 final size:12
Alignment explanation
Indices: 55511--55550 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
55501 CTTAAACCCT
*
55511 TTCTTCCCTTCC
1 TTCTTCGCTTCC
55523 TTCTTCGCTTCC
1 TTCTTCGCTTCC
*
55535 TTTTTCGCTTCC
1 TTCTTCGCTTCC
55547 TTCT
1 TTCT
55551 CCACCCCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.05, T:0.55
Consensus pattern (12 bp):
TTCTTCGCTTCC
Found at i:58281 original size:26 final size:25
Alignment explanation
Indices: 58217--58281 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
58207 TGTTCTACTT
58217 TCATGTGTTGGGTAT-TTTCTGTCC
1 TCATGTGTTGGGTATGTTTCTGTCC
*
58241 T-AT-T-TTGGGAATGTTTGCT-TCC
1 TCATGTGTTGGGTATGTTT-CTGTCC
58263 TCCATGTGTTGGGTATGTT
1 T-CATGTGTTGGGTATGTT
58282 GATCAATGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
21 7 0.21
22 8 0.24
23 4 0.12
24 3 0.09
25 1 0.03
26 10 0.30
ACGTcount: A:0.11, C:0.14, G:0.26, T:0.49
Consensus pattern (25 bp):
TCATGTGTTGGGTATGTTTCTGTCC
Found at i:64531 original size:3 final size:3
Alignment explanation
Indices: 64523--64572 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
64513 TTTTTCTTAA
** *
64523 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AAT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
64569 ATT A
1 ATT A
64573 ATTACAAGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:65822 original size:16 final size:16
Alignment explanation
Indices: 65801--65842 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
65791 TTACTTTTAA
65801 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
65817 ATTTATTTATAATATT
1 ATTTATTTATAATATT
65833 AATTT-TTTAT
1 -ATTTATTTAT
65843 TACATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:66686 original size:16 final size:15
Alignment explanation
Indices: 66665--66699 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
66655 TCTTTCAAAT
66665 TTTTTATTACTTATTA
1 TTTTTA-TACTTATTA
*
66681 TTTTTATACTTTTTA
1 TTTTTATACTTATTA
66696 TTTT
1 TTTT
66700 ATTTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATACTTATTA
Found at i:71977 original size:7 final size:7
Alignment explanation
Indices: 71958--72058 Score: 89
Period size: 7 Copynumber: 13.3 Consensus size: 7
71948 ATACTCATCT
71958 AAGAAAGA
1 AAGAAA-A
71966 AAGAAAA
1 AAGAAAA
71973 AAGAAAA
1 AAGAAAA
71980 ACCAGCAAAAA
1 A--AG--AAAA
71991 AAGAAAA
1 AAGAAAA
71998 AAGAAGAAA
1 AAG-A-AAA
72007 AAGATGAAA
1 AAGA--AAA
72016 AAGGAAAA
1 AA-GAAAA
72024 AAGAAAA
1 AAGAAAA
*
72031 AA-AGAA
1 AAGAAAA
72037 AA-AAAA
1 AAGAAAA
72043 AAGAAAA
1 AAGAAAA
72050 AAGAAAA
1 AAGAAAA
72057 AA
1 AA
72059 AGGAAAAAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 19
0.80 0.02 0.18
Matches are distributed among these distances:
6 10 0.12
7 36 0.44
8 13 0.16
9 16 0.20
10 2 0.02
11 5 0.06
ACGTcount: A:0.80, C:0.03, G:0.16, T:0.01
Consensus pattern (7 bp):
AAGAAAA
Found at i:72068 original size:26 final size:25
Alignment explanation
Indices: 71965--72070 Score: 124
Period size: 26 Copynumber: 4.2 Consensus size: 25
71955 TCTAAGAAAG
* *
71965 AAAGAAAAAAGAAAAACCAG-CAAAA
1 AAAGAAAAAAGAAAAA-AAGAAAAAA
**
71990 AAAGAAAAAAGAAGAAAAAGATGAAA
1 AAAGAAAAAAGAA-AAAAAGAAAAAA
*
72016 AAGGAAAAAAGAAAAAAAGAAAAAAA
1 AAAGAAAAAAGAAAAAAAG-AAAAAA
*
72042 AAAGAAAAAAGAAAAAAAGGAAAAA
1 AAAGAAAAAAGAAAAAAAGAAAAAA
72067 AAAG
1 AAAG
72071 GAGAAATTGA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
25 30 0.43
26 40 0.57
ACGTcount: A:0.80, C:0.03, G:0.16, T:0.01
Consensus pattern (25 bp):
AAAGAAAAAAGAAAAAAAGAAAAAA
Found at i:72072 original size:10 final size:9
Alignment explanation
Indices: 71969--72070 Score: 88
Period size: 9 Copynumber: 11.8 Consensus size: 9
71959 AGAAAGAAAG
71969 AAAAAAGAA
1 AAAAAAGAA
** *
71978 AAACCAGCA
1 AAAAAAGAA
71987 AAAAAAG--
1 AAAAAAGAA
71994 AAAAAAGAA
1 AAAAAAGAA
* *
72003 GAAAAAGAT
1 AAAAAAGAA
* *
72012 GAAAAAG-G
1 AAAAAAGAA
72020 AAAAAAG-A
1 AAAAAAGAA
72028 AAAAAAGAA
1 AAAAAAGAA
72037 AAAAAA-AA
1 AAAAAAGAA
72045 GAAAAAAGAA
1 -AAAAAAGAA
*
72055 AAAAAGGAA
1 AAAAAAGAA
72064 AAAAAAG
1 AAAAAAG
72071 GAGAAATTGA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
7 7 0.09
8 15 0.20
9 52 0.68
10 2 0.03
ACGTcount: A:0.80, C:0.03, G:0.16, T:0.01
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:74418 original size:114 final size:114
Alignment explanation
Indices: 74217--74440 Score: 367
Period size: 114 Copynumber: 2.0 Consensus size: 114
74207 GTGCCACGTT
* *
74217 CTCATTGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
** * *
74282 GTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTG
66 GTTCAGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
*
74331 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
* *
74396 GTTCAGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GTTCAGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
74441 CTGCATGATC
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
GTTCAGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
Found at i:76570 original size:40 final size:41
Alignment explanation
Indices: 76515--76604 Score: 146
Period size: 40 Copynumber: 2.2 Consensus size: 41
76505 TGAGCAGAAG
* *
76515 CCACAGAAAATGATGAATGTGTTGTCAAGTGTTTTACATC-
1 CCACAGAAAAGGATGAACGTGTTGTCAAGTGTTTTACATCT
76555 CCACAGAAAAGGATGAACGTGTTGTCAAGTGTTTTACATCT
1 CCACAGAAAAGGATGAACGTGTTGTCAAGTGTTTTACATCT
*
76596 CGACAGAAA
1 CCACAGAAA
76605 CCACATGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 38 0.83
41 8 0.17
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (41 bp):
CCACAGAAAAGGATGAACGTGTTGTCAAGTGTTTTACATCT
Found at i:76821 original size:12 final size:12
Alignment explanation
Indices: 76804--76830 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
76794 AGAAACTAGT
76804 GGTACCAACTAA
1 GGTACCAACTAA
76816 GGTACCAACTAA
1 GGTACCAACTAA
76828 GGT
1 GGT
76831 TGAACTACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (12 bp):
GGTACCAACTAA
Found at i:77057 original size:22 final size:22
Alignment explanation
Indices: 77025--77079 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
77015 ATCTACACTC
*
77025 TTCAAGGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
77047 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
77069 TTCAAAGATGA
1 TTCAAAGATGA
77080 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:77905 original size:165 final size:167
Alignment explanation
Indices: 77602--77917 Score: 487
Period size: 165 Copynumber: 1.9 Consensus size: 167
77592 CATTATCTTC
* *
77602 AGATTGGGTCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACGATTTTCAT
1 AGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACGATTTCCAT
** *
77667 AGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTTCTTAGTTT
66 AGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTTCATAGTTT
* *
77732 TTTTACTTAGTAAATTATTTCTAACAACCTTATTTTG
131 TCTTACTTAGTAAACTATTTCTAACAACCTTATTTTG
* ** *
77769 AGATTGGGGCATGTTAGCCAATCAACATGTTATTT-TGAAAA-ATAATGAGAAAACGATTTCCAT
1 AGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACGATTTCCAT
77832 AGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAACT-ATTTTCATAG-
66 AGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAA-TGATTTTCATAGT
77895 TTTCTTACTTAGTAAACTATTTC
129 TTTCTTACTTAGTAAACTATTTC
77918 CCACATTTGT
Statistics
Matches: 136, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
165 61 0.45
166 41 0.30
167 34 0.25
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (167 bp):
AGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACGATTTCCAT
AGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTTCATAGTTT
TCTTACTTAGTAAACTATTTCTAACAACCTTATTTTG
Found at i:78051 original size:76 final size:76
Alignment explanation
Indices: 77925--78357 Score: 839
Period size: 76 Copynumber: 5.7 Consensus size: 76
77915 TTCCCACATT
77925 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
77990 TTAGGGTCATC
66 TTAGGGTCATC
78001 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
78066 TTAGGGTCATC
66 TTAGGGTCATC
78077 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
78142 TTAGGGTCATC
66 TTAGGGTCATC
78153 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
78218 TTAGGGTCATC
66 TTAGGGTCATC
* *
78229 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGCAGCTTTTTGATGTTTTCAAAACC
1 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
78294 TTAGGGTCATC
66 TTAGGGTCATC
*
78305 TGTAAGTCCTGCAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGAT
1 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
78358 ATTGTTATTT
Statistics
Matches: 353, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 353 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (76 bp):
TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
TTAGGGTCATC
Found at i:78751 original size:3 final size:3
Alignment explanation
Indices: 78745--78795 Score: 66
Period size: 3 Copynumber: 16.3 Consensus size: 3
78735 TTTTTTTAAA
**
78745 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT A-TT ATT
78792 ATT A
1 ATT A
78796 ATTACAAGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:78757 original size:12 final size:12
Alignment explanation
Indices: 78740--78766 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
78730 TTTCATTTTT
78740 TTAAAATTATTA
1 TTAAAATTATTA
78752 TTAAAATTATTA
1 TTAAAATTATTA
78764 TTA
1 TTA
78767 TTATTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAAATTATTA
Found at i:78779 original size:13 final size:13
Alignment explanation
Indices: 78757--78795 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
78747 TATTATTAAA
78757 ATTA-TTATTATT
1 ATTATTTATTATT
78769 ATTATTTATTATT
1 ATTATTTATTATT
78782 ATTATTTATTATT
1 ATTATTTATTATT
78795 A
1 A
78796 ATTACAAGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTATTTATTATT
Found at i:78779 original size:16 final size:15
Alignment explanation
Indices: 78745--78795 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
78735 TTTTTTTAAA
**
78745 ATTATTATTAAAATT
1 ATTATTATTATTATT
78760 ATTATTATTATTATTT
1 ATTATTATTATTA-TT
78776 ATTATTATTATTTATT
1 ATTATTATTA-TTATT
78792 ATTA
1 ATTA
78796 ATTACAAGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 11 0.34
16 18 0.56
17 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTATTATT
Found at i:80044 original size:16 final size:16
Alignment explanation
Indices: 80023--80055 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
80013 TTACTTTTAA
80023 ATTTATTT-TAAATATT
1 ATTTATTTAT-AATATT
80039 ATTTATTTATAATATT
1 ATTTATTTATAATATT
80055 A
1 A
80056 ATTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTATAATATT
Found at i:80083 original size:17 final size:17
Alignment explanation
Indices: 80061--80094 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
80051 TATTAATTTG
80061 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
80078 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
80095 GTCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:80115 original size:2 final size:2
Alignment explanation
Indices: 80108--80175 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
80098 ACATAAATAA
* *
80108 AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT TT 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
80150 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
80176 TTTTTAAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88048 original size:159 final size:159
Alignment explanation
Indices: 87759--88069 Score: 360
Period size: 159 Copynumber: 2.0 Consensus size: 159
87749 GCTTCTAACA
* * * *
87759 GTCTTCACAAATATAAAGTTGTGACGGAAGTCCCAATGAGCTATGAGAGTATCTCCAGTTTTCAT
1 GTCTTCACAAATATAAAGTCGTGACAGAAGTCCCAATGAACTATGAGAGTACCTCCAGTTTTCAT
* * * *
87824 TTTGGCTACACAGAGAAATGTAATCTAAGAAATTAATATCCAGAAATATCGCATTGATCGGAAAG
66 TTTGGCGACACAGAGAAATATAAACTAAGAAATTAATATCCAGAAATATCGCATTGATCAGAAAG
* *
87889 GGGTAGAGCACGGGGACAAGTGCGAATCT
131 GGCTAGAGCACAGGGACAAGTGCGAATCT
** * * **
87918 GTCTTCACAAATATAAAGTCGT-ACTAGATTTCCCAATGAACTATGGGATTACCTCTGGTTTTCA
1 GTCTTCACAAATATAAAGTCGTGAC-AGAAGTCCCAATGAACTATGAGAGTACCTCCAGTTTTCA
* * * *
87982 TTTTGGCGACTC-GAAGAAATATAAACTAAGAAATTCATATCCAGAATTATTGCAATT-A-CTAG
65 TTTTGGCGACACAG-AGAAATATAAACTAAGAAATTAATATCCAGAAATATCGC-ATTGATC-AG
* *
88044 AAAGGGCTAGAGGACAGGGACGAGTG
127 AAAGGGCTAGAGCACAGGGACAAGTG
88070 GGAGCGGTTT
Statistics
Matches: 126, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
158 4 0.03
159 119 0.94
160 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (159 bp):
GTCTTCACAAATATAAAGTCGTGACAGAAGTCCCAATGAACTATGAGAGTACCTCCAGTTTTCAT
TTTGGCGACACAGAGAAATATAAACTAAGAAATTAATATCCAGAAATATCGCATTGATCAGAAAG
GGCTAGAGCACAGGGACAAGTGCGAATCT
Found at i:89926 original size:31 final size:31
Alignment explanation
Indices: 89882--89943 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
89872 TGGGATAAAA
*
89882 GAAAATGACTTTACTACATAGAATTTAGACT
1 GAAAATGACTTTACTACATAGAATCTAGACT
89913 GAAAATG-CATTTACTACATAGAATCTAGACT
1 GAAAATGAC-TTTACTACATAGAATCTAGACT
89944 AAGTTTCCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (31 bp):
GAAAATGACTTTACTACATAGAATCTAGACT
Found at i:103806 original size:15 final size:15
Alignment explanation
Indices: 103783--103819 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
103773 TCATATATTT
*
103783 ATTATCCCATAAGTA
1 ATTACCCCATAAGTA
103798 ATTACCCCATAAGTA
1 ATTACCCCATAAGTA
103813 ATTACCC
1 ATTACCC
103820 AACGCTACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (15 bp):
ATTACCCCATAAGTA
Found at i:107828 original size:20 final size:20
Alignment explanation
Indices: 107803--107841 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
107793 TAAATTAAAT
* *
107803 ATTAGATAGGATCCGTTTTA
1 ATTAGATAGAATCAGTTTTA
107823 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
107842 TATTCTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:107880 original size:52 final size:52
Alignment explanation
Indices: 107802--107949 Score: 253
Period size: 53 Copynumber: 2.8 Consensus size: 52
107792 CTAAATTAAA
**
107802 TATTAGATAGGATCCGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
*
107854 TATTAGATATGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
107907 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
107950 ATGTTGCTAA
Statistics
Matches: 91, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
51 8 0.09
52 33 0.36
53 50 0.55
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:107888 original size:20 final size:21
Alignment explanation
Indices: 107855--107894 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
107845 TCTATTAGTT
107855 ATTAGATATGATCA-TTTTTA
1 ATTAGATATGATCAGTTTTTA
107875 ATTAGATA-GAATCAGTTTTT
1 ATTAGATATG-ATCAGTTTTT
107895 TATTCTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 12 0.67
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (21 bp):
ATTAGATATGATCAGTTTTTA
Found at i:107950 original size:19 final size:19
Alignment explanation
Indices: 107906--107950 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
107896 ATTCTATTAG
*
107906 TTATTAGATAGGATCATTT
1 TTATTAGATAGAATCATTT
107925 TTAATTAGATAGAATCATTT
1 TT-ATTAGATAGAATCATTT
107945 TTATTA
1 TTATTA
107951 TGTTGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (19 bp):
TTATTAGATAGAATCATTT
Found at i:112545 original size:20 final size:20
Alignment explanation
Indices: 112520--112610 Score: 63
Period size: 20 Copynumber: 5.0 Consensus size: 20
112510 TAAATTAAAT
* *
112520 ATTAGATAGGATCCGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
112540 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
112560 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
112572 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
112592 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
112611 TTATTCTATT
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.08
17 3 0.06
18 1 0.02
19 2 0.04
20 37 0.70
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:112597 original size:52 final size:52
Alignment explanation
Indices: 112519--112666 Score: 262
Period size: 53 Copynumber: 2.8 Consensus size: 52
112509 CTAAATTAAA
**
112519 TATTAGATAGGATCCGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
112571 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
112624 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
112667 ATGTTGCTAA
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 8 0.09
52 34 0.37
53 51 0.55
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:112650 original size:20 final size:20
Alignment explanation
Indices: 112625--112664 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
112615 TCTATTAGTT
*
112625 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
112645 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
112665 TTATGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:113066 original size:23 final size:23
Alignment explanation
Indices: 113040--113083 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
113030 TGAAGCTTAA
*
113040 TTGA-AAAAGAGAAATAAGAAATT
1 TTGATAAAAGA-AAAAAAGAAATT
*
113063 TTGATTAAAGAAAAAAAGAAA
1 TTGATAAAAGAAAAAAAGAAA
113084 AAGAGAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (23 bp):
TTGATAAAAGAAAAAAAGAAATT
Found at i:117046 original size:17 final size:17
Alignment explanation
Indices: 117012--117059 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
117002 TTTTATTTAT
*
117012 TTATTTAAAT-TAAAATA
1 TTATTTAAATAT-ATATA
117029 TTATTTAAATATATATA
1 TTATTTAAATATATATA
117046 TATATTTAAA-ATAT
1 T-TATTTAAATATAT
117060 GAATGTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTTAAATATATATA
Found at i:119076 original size:31 final size:31
Alignment explanation
Indices: 119038--119138 Score: 139
Period size: 31 Copynumber: 3.3 Consensus size: 31
119028 CATTAAAAAT
* * * *
119038 TTAGGTATTAAATTGAAGTAAAAATTTAATT
1 TTAGGTATTAAAATGAAATAAAAAATTAATA
*
119069 TTGGGTATTAAAATGAAATAAAAAATTAATA
1 TTAGGTATTAAAATGAAATAAAAAATTAATA
* *
119100 TTAGGTATTAAAATGAAATAAAAAGTAAATA
1 TTAGGTATTAAAATGAAATAAAAAATTAATA
119131 TTAGGTAT
1 TTAGGTAT
119139 AATTTTTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (31 bp):
TTAGGTATTAAAATGAAATAAAAAATTAATA
Found at i:119643 original size:24 final size:24
Alignment explanation
Indices: 119609--119677 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
119599 TATTTAAATG
*
119609 ATAAACAAACACAAATGAACGAAC
1 ATAAACGAACACAAATGAACGAAC
*
119633 ATAAACGAACACAAGA-GAACGAAT
1 ATAAACGAACACAA-ATGAACGAAC
* * *
119657 GTAAATGAACATAAATGAACG
1 ATAAACGAACACAAATGAACG
119678 TAAACTAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12
Consensus pattern (24 bp):
ATAAACGAACACAAATGAACGAAC
Found at i:119702 original size:10 final size:10
Alignment explanation
Indices: 119658--119702 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
119648 AGAACGAATG
119658 TAAATGAACA
1 TAAATGAACA
*
119668 TAAATGAACG
1 TAAATGAACA
119678 TAAACT-AACA
1 TAAA-TGAACA
119688 TAAATGAACA
1 TAAATGAACA
119698 TAAAT
1 TAAAT
119703 CACAACAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 1 0.03
10 29 0.94
11 1 0.03
ACGTcount: A:0.58, C:0.11, G:0.09, T:0.22
Consensus pattern (10 bp):
TAAATGAACA
Found at i:120075 original size:14 final size:14
Alignment explanation
Indices: 120053--120096 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
120043 GGCCTAAACC
*
120053 TAAATGAACGAACA
1 TAAACGAACGAACA
120067 TAAACGAACGAA-A
1 TAAACGAACGAACA
*
120080 GTAAACGAACAAACA
1 -TAAACGAACGAACA
120095 TA
1 TA
120097 TTATTGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.11
Consensus pattern (14 bp):
TAAACGAACGAACA
Found at i:121653 original size:21 final size:22
Alignment explanation
Indices: 121628--121686 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
121618 GGTCACTAAT
* *
121628 ATAATTTATCTTTTATTT-TAA
1 ATAATTTATATTTAATTTATAA
121649 ATAATTTATATTTAATTTATAA
1 ATAATTTATATTTAATTTATAA
* *
121671 TTAATTTATAATTAAT
1 ATAATTTATATTTAAT
121687 AGACCATGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATAATTTATATTTAATTTATAA
Found at i:121664 original size:11 final size:11
Alignment explanation
Indices: 121650--121686 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
121640 TTATTTTAAA
*
121650 TAATTTATATT
1 TAATTTATAAT
121661 TAATTTATAAT
1 TAATTTATAAT
121672 TAATTTATAAT
1 TAATTTATAAT
121683 TAAT
1 TAAT
121687 AGACCATGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TAATTTATAAT
Found at i:122040 original size:18 final size:17
Alignment explanation
Indices: 122017--122050 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
122007 CCGTTATTAG
*
122017 TGAACCGGTCAGAACCGT
1 TGAACCGATC-GAACCGT
122035 TGAACCGATCGAACCG
1 TGAACCGATCGAACCG
122051 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.15
Consensus pattern (17 bp):
TGAACCGATCGAACCGT
Found at i:122091 original size:12 final size:10
Alignment explanation
Indices: 122066--122106 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
122056 GCTGAAAACT
122066 GAAAAAAATC
1 GAAAAAAATC
122076 GAAAAAAATC
1 GAAAAAAATC
* *
122086 GAGAAAAACC
1 GAAAAAAATC
*
122096 GAGAAAAATC
1 GAAAAAAATC
122106 G
1 G
122107 GGAATTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.63, C:0.12, G:0.17, T:0.07
Consensus pattern (10 bp):
GAAAAAAATC
Found at i:128606 original size:33 final size:32
Alignment explanation
Indices: 128563--128642 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 32
128553 AGCCTTGGAT
*
128563 TGTTGTCTTTGCATCGACATTGACATCGACGAC
1 TGTTGCCTTTGCATCGACA-TGACATCGACGAC
128596 TGTTGCCTTTGCAT---C--GACATCGACGAC
1 TGTTGCCTTTGCATCGACATGACATCGACGAC
*
128623 TGTTGCCTTTTCATCGACAT
1 TGTTGCCTTTGCATCGACAT
128643 CGATTGTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
27 25 0.62
30 2 0.05
33 13 0.32
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (32 bp):
TGTTGCCTTTGCATCGACATGACATCGACGAC
Found at i:128614 original size:27 final size:27
Alignment explanation
Indices: 128584--128645 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
128574 CATCGACATT
128584 GACATCGACGACTGTTGCCTTTGCATC
1 GACATCGACGACTGTTGCCTTTGCATC
*
128611 GACATCGACGACTGTTGCCTTTTCATC
1 GACATCGACGACTGTTGCCTTTGCATC
128638 GACATCGA
1 GACATCGA
128646 TTGTTGTCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (27 bp):
GACATCGACGACTGTTGCCTTTGCATC
Found at i:128804 original size:6 final size:6
Alignment explanation
Indices: 128793--128822 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
128783 TAGCACCTGT
*
128793 GGCTTC GGCTTC GGCTTC GGCTCC GGCTTC
1 GGCTTC GGCTTC GGCTTC GGCTTC GGCTTC
128823 AGTTTCGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.37, G:0.33, T:0.30
Consensus pattern (6 bp):
GGCTTC
Found at i:129459 original size:2 final size:2
Alignment explanation
Indices: 129452--129484 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
129442 TTTAATGTTT
129452 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
129485 TCCTTTCCTC
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
Found at i:131493 original size:60 final size:60
Alignment explanation
Indices: 131394--131507 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
131384 ATGAATTTGG
* * * * **
131394 GGATGAAATTATAATATTCAAAAGTTTAGGGACTGATTTAGAAA-GAGAATCATAATTTAT
1 GGATGAAAATAGAATATTAAAAAGTTTAAGGACCAATTTA-AAATGAGAATCATAATTTAT
* *
131454 GGATGAAAATAGAATGTTAAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATA
1 GGATGAAAATAGAATATTAAAAAGTTTAAGGACCAATTTAAAATGAGAATCATA
131508 GTCTGAATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
59 3 0.07
60 42 0.93
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (60 bp):
GGATGAAAATAGAATATTAAAAAGTTTAAGGACCAATTTAAAATGAGAATCATAATTTAT
Found at i:133918 original size:3 final size:3
Alignment explanation
Indices: 133910--133940 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
133900 TTTGCTTTGT
133910 TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
133941 TTTTACTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:144481 original size:19 final size:20
Alignment explanation
Indices: 144440--144479 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
144430 TGAATTCTAG
144440 TAGAAACCATTTCTTATTTT
1 TAGAAACCATTTCTTATTTT
144460 TAGAAACCATTTCTTATTTT
1 TAGAAACCATTTCTTATTTT
144480 AGGGAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.50
Consensus pattern (20 bp):
TAGAAACCATTTCTTATTTT
Done.