Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008220.1 Hibiscus syriacus cultivar Beakdansim tig00110852_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: 64566
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:843 original size:14 final size:14
Alignment explanation
Indices: 824--878 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
814 ACGTTCGTAA
824 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
838 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
852 CG-T---TTATGTT
1 CGTTCGATTATGTT
862 CGTTCGATTATG-T
1 CGTTCGATTATGTT
875 CGTT
1 CGTT
879 TATGTTCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 6 0.17
14 20 0.56
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:858 original size:24 final size:24
Alignment explanation
Indices: 825--898 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
815 CGTTCGTAAC
* *
825 GTTCGATTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
849 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
873 G-TCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
896 GTT
1 GTT
899 TAACTCAATC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
22 1 0.02
23 20 0.44
24 24 0.53
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.54
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:895 original size:23 final size:22
Alignment explanation
Indices: 831--897 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 22
821 TAACGTTCGA
*
831 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTC-ATTATG-TCGT
855 TTATGTTCGTTCGATTATGTCGT
1 TTATGTTCGTTC-ATTATGTCGT
*
878 TTATGTTCATTCATTTATGT
1 TTATGTTCGTTCA-TTATGT
898 TTAACTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
22 1 0.03
23 21 0.52
24 18 0.45
ACGTcount: A:0.13, C:0.12, G:0.19, T:0.55
Consensus pattern (22 bp):
TTATGTTCGTTCATTATGTCGT
Found at i:1616 original size:16 final size:16
Alignment explanation
Indices: 1593--1647 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
1583 GGGTCTCCAA
1593 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
* *
1609 CATTTATGTTCGTATT
1 CGTTTATGTTCGTGTT
1625 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
1641 CGTTTAT
1 CGTTTAT
1648 TTATTAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.11, C:0.13, G:0.20, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:3973 original size:135 final size:134
Alignment explanation
Indices: 3788--4241 Score: 635
Period size: 134 Copynumber: 3.4 Consensus size: 134
3778 ACTGTCACTC
* *
3788 AGGGAATATTAGATGT-GAGGATGTTGATCCATTCCGCTGTCACTCAGGGAATATTGAATCGGGG
1 AGGGAATATCAGATCTGGAGGA-GTTGATCCATTCCGCTGTCACTCAGGGAATATTGAATCGGGG
* * * *
3852 CAGACTTGTTTTGTTGTCACTCAGGGAATATCAAATCAT-GAAAGAGAGAGATC-TGTTCCGCTT
65 CAGACTTGTTATGCTGTCACTCAGGGAATATCAAATCTTGGAAA-AGAGGGA-CATGTTCCGCTT
3915 CTTTTGA
128 CTTTTGA
* * * *
3922 AGGGAGTATCAGATCTAGGGGGAGTTGATCCATTCCGTTATCACTCAGGGAATATTGAATCGGGG
1 AGGGAATATCAGATCT-GGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAATATTGAATCGGGG
** * *
3987 CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTTCGTTTCT
65 CAGACTTGTTATGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCT
4052 TTTGA
130 TTTGA
* * * *
4057 AGGGAATATCATATTTGGAGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATCGGGGC
1 AGGGAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAATATTGAATCGGGGC
* *
4122 AGACTTGTTATGCTGTCACTCAGGAAATATCAAATCTTGGAAAAAAGGGACATGTTCCGCTTCTT
66 AGACTTGTTATGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTT
*
4187 CTGA
131 TTGA
* * *
4191 AGGGAATATCAGATCTGGAGGAGTTGATACATTCTGCTGTCACTAAGGGAA
1 AGGGAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAA
4242 GATTTCACTG
Statistics
Matches: 282, Mismatches: 34, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
134 165 0.59
135 109 0.39
136 8 0.03
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (134 bp):
AGGGAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAATATTGAATCGGGGC
AGACTTGTTATGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTT
TTGA
Found at i:6355 original size:15 final size:16
Alignment explanation
Indices: 6327--6365 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
6317 TACATGCAAA
6327 GCTATTTATATTTTTT
1 GCTATTTATATTTTTT
6343 GCTA-TTAT-TTTTTT
1 GCTATTTATATTTTTT
*
6357 ACTATTTAT
1 GCTATTTAT
6366 TCGAACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 8 0.38
16 4 0.19
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (16 bp):
GCTATTTATATTTTTT
Found at i:6986 original size:3 final size:3
Alignment explanation
Indices: 6968--7002 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
6958 TTGTTGGATC
*
6968 ATA AAA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7003 TCGAATGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:16185 original size:18 final size:17
Alignment explanation
Indices: 16162--16285 Score: 62
Period size: 17 Copynumber: 7.2 Consensus size: 17
16152 TTTTAGACAT
16162 TATATTATAATTAAAAAA
1 TATATTA-AATTAAAAAA
* *
16180 TATATT-AA-TATAAAT
1 TATATTAAATTAAAAAA
* * **
16195 TATTTTAAATTTATTAA
1 TATATTAAATTAAAAAA
*
16212 TATTTTAATATATAAAAAA
1 TATATTAA-AT-TAAAAAA
*
16231 TAAATTAAATTATAAAAA
1 TATATTAAATTA-AAAAA
*
16249 -A-ATTAGAAATAAAAAA
1 TATATTA-AATTAAAAAA
16265 TATAATTATAA-T-AAAAA
1 TAT-ATTA-AATTAAAAAA
16282 TATA
1 TATA
16286 AAACGTAAGT
Statistics
Matches: 82, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
15 10 0.12
16 14 0.17
17 26 0.32
18 16 0.20
19 16 0.20
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.40
Consensus pattern (17 bp):
TATATTAAATTAAAAAA
Found at i:16238 original size:19 final size:17
Alignment explanation
Indices: 16223--16287 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
16213 ATTTTAATAT
16223 ATAAAAAATAAATTAAA
1 ATAAAAAATAAATTAAA
* *
16240 TTATAAAA-AAATTAGAA
1 ATAAAAAATAAATTA-AA
*
16257 ATAAAAAATATAATTATA
1 ATAAAAAATA-AATTAAA
16275 ATAAAAATATAAA
1 ATAAAAA-ATAAA
16288 ACGTAAGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 6 0.15
17 14 0.36
18 11 0.28
19 8 0.21
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (17 bp):
ATAAAAAATAAATTAAA
Found at i:19047 original size:11 final size:11
Alignment explanation
Indices: 19008--19063 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
18998 ATAAGAAAGA
19008 AAGAAAGGAAG
1 AAGAAAGGAAG
19019 AAG--A-GAA-
1 AAGAAAGGAAG
* *
19026 AGGAAATGAAG
1 AAGAAAGGAAG
19037 AAGAAAGGAAG
1 AAGAAAGGAAG
*
19048 AAGAAAGGGAG
1 AAGAAAGGAAG
19059 AAGAA
1 AAGAA
19064 GAGATCGGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
9 2 0.05
10 3 0.08
11 27 0.73
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (11 bp):
AAGAAAGGAAG
Found at i:19876 original size:21 final size:21
Alignment explanation
Indices: 19787--19876 Score: 51
Period size: 21 Copynumber: 4.2 Consensus size: 21
19777 ATTATTAGTA
*
19787 ATCATTACTAAATGATT-AAT
1 ATCATTACTAAATCATTAAAT
* *
19807 ATCA-AATCCAAATCATTAAAT
1 ATCATTA-CTAAATCATTAAAT
* * * *
19828 AT-TTATAATAAATAATTATTAGT
1 ATCAT-TACTAAATCATTA--AAT
19851 AATCATTACTAAATCATTAAAT
1 -ATCATTACTAAATCATTAAAT
19873 ATCA
1 ATCA
19877 AATCATTAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 15
0.64 0.17 0.19
Matches are distributed among these distances:
19 1 0.02
20 12 0.24
21 17 0.35
22 3 0.06
23 2 0.04
24 13 0.27
25 1 0.02
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (21 bp):
ATCATTACTAAATCATTAAAT
Found at i:19890 original size:65 final size:61
Alignment explanation
Indices: 19777--19915 Score: 174
Period size: 65 Copynumber: 2.2 Consensus size: 61
19767 ACTAATCATT
* *
19777 ATTATTAGTAATCATTACTAAATGATTAATATCAAATCCAAATCATTAAATATTTATAATAAATA
1 ATTATTAGTAATCATTACTAAATCATTAATATCAAATCCAAA-CATT-AATAATTAT--TAAATA
*
19842 ATTATTAGTAATCATTACTAAATCATTAAATATCAAAT-CATTAA-ATTAATAATTATTAAATC
1 ATTATTAGTAATCATTACTAAATCATT-AATATCAAATCCA--AACATTAATAATTATTAAATA
19904 ATTATTAGTAAT
1 ATTATTAGTAAT
19916 GTTAATAATC
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
62 17 0.25
64 8 0.12
65 31 0.46
66 10 0.15
67 2 0.03
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (61 bp):
ATTATTAGTAATCATTACTAAATCATTAATATCAAATCCAAACATTAATAATTATTAAATA
Found at i:27081 original size:21 final size:21
Alignment explanation
Indices: 27044--27129 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 21
27034 TTTTGGTGCA
*
27044 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
27064 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
*
27085 GAAGGGGAACCGATTCCCCCCACA
1 G-A-GGGAACCGATTCCCCCC-CT
* *
27109 G-GGGAATCGATACCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
27129 G
1 G
27130 GGGTTCTGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
20 12 0.23
21 23 0.43
22 1 0.02
23 16 0.30
24 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.26, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:32531 original size:21 final size:23
Alignment explanation
Indices: 32507--32568 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
32497 ATTAAATCGA
32507 ATTTATGTTTTTTTAAAT-AA-T
1 ATTTATGTTTTTTTAAATGAATT
* *
32528 ATTTAAGTTCATTTTTAATTGAATT
1 ATTTATGTT--TTTTTAAATGAATT
*
32553 ATTTATATTTTATTTA
1 ATTTATGTTTT-TTTA
32569 TATTTTATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 8 0.25
23 10 0.31
24 6 0.19
25 8 0.25
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
ATTTATGTTTTTTTAAATGAATT
Found at i:32567 original size:11 final size:11
Alignment explanation
Indices: 32551--32592 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
32541 TTTAATTGAA
32551 TTATTTATATT
1 TTATTTATATT
32562 TTATTTATATT
1 TTATTTATATT
*
32573 TTATCTTAT-TA
1 TTAT-TTATATT
32584 TTATTTATA
1 TTATTTATA
32593 AATAATCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 4 0.14
11 20 0.71
12 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTTATATT
Found at i:32588 original size:16 final size:17
Alignment explanation
Indices: 32550--32592 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
32540 TTTTAATTGA
*
32550 ATTATTTATATTTTATT
1 ATTATTTATATCTTATT
32567 -TATATTT-TATCTTATT
1 AT-TATTTATATCTTATT
32583 ATTATTTATA
1 ATTATTTATA
32593 AATAATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATTTATATCTTATT
Found at i:32633 original size:20 final size:20
Alignment explanation
Indices: 32596--32635 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
32586 ATTTATAAAT
**
32596 AATCAAATTTATTCAATTTA
1 AATCAAATTTATAAAATTTA
*
32616 AATCGAATTTATAAAATTTA
1 AATCAAATTTATAAAATTTA
32636 TGTATGGGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (20 bp):
AATCAAATTTATAAAATTTA
Found at i:33105 original size:15 final size:15
Alignment explanation
Indices: 33085--33113 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33075 TTTATTATTA
33085 ATATTTAATGATTTG
1 ATATTTAATGATTTG
33100 ATATTTAATGATTT
1 ATATTTAATGATTT
33114 ATTAATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
ATATTTAATGATTTG
Found at i:33128 original size:16 final size:16
Alignment explanation
Indices: 33107--33138 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33097 TTGATATTTA
*
33107 ATGATTTATTAATGAT
1 ATGATTTAGTAATGAT
33123 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
33139 TATTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (16 bp):
ATGATTTAGTAATGAT
Found at i:33168 original size:24 final size:25
Alignment explanation
Indices: 33123--33266 Score: 126
Period size: 24 Copynumber: 6.1 Consensus size: 25
33113 TATTAATGAT
* * *
33123 ATGATTTAGTAATGATTA-TTAATA
1 ATGATTTACTAATAATGATTTAATA
* *
33147 ATGATTTATTATTAAT-A-TT--TA
1 ATGATTTACTAATAATGATTTAATA
* *
33168 ATGATTTAATACTAATGATTTAATA
1 ATGATTTACTAATAATGATTTAATA
*
33193 ATGA-TTACTAATAATGCAATT-ATA
1 ATGATTTACTAATAATG-ATTTAATA
*
33217 AT-AATTACTAATAATGATTTAATA
1 ATGATTTACTAATAATGATTTAATA
*
33241 ATGA-TTACTAATAATTATTTAATA
1 ATGATTTACTAATAATGATTTAATA
33265 AT
1 AT
33267 AATTAAATAT
Statistics
Matches: 102, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
21 16 0.16
22 1 0.01
23 9 0.09
24 66 0.65
25 10 0.10
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (25 bp):
ATGATTTACTAATAATGATTTAATA
Found at i:33183 original size:21 final size:22
Alignment explanation
Indices: 33145--33191 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
33135 TGATTATTAA
* *
33145 TAATGATTTATTATTAAT-ATT
1 TAATGATTTAATACTAATGATT
33166 TAATGATTTAATACTAATGATT
1 TAATGATTTAATACTAATGATT
33188 TAAT
1 TAAT
33192 AATGATTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (22 bp):
TAATGATTTAATACTAATGATT
Found at i:33185 original size:14 final size:14
Alignment explanation
Indices: 33166--33192 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33156 TATTAATATT
33166 TAATGATTTAATAC
1 TAATGATTTAATAC
33180 TAATGATTTAATA
1 TAATGATTTAATA
33193 ATGATTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
TAATGATTTAATAC
Found at i:33186 original size:59 final size:63
Alignment explanation
Indices: 33069--33245 Score: 179
Period size: 62 Copynumber: 2.9 Consensus size: 63
33059 CTGATGCTAC
* * * *
33069 TAATGATTTATTATTAAT-ATTTAATGATTTGATATTTAATGATTTATTAATGATATGATTTAG
1 TAATGA-TTATTAATAATGATTTAATGATTTAATATTTAATGATTTAATAATGATATGATTTAA
* *
33132 TAATGATTATTAATAATGATTT-ATTA-TTAATATTTAATGATTTAATACT-A-ATGATTTAA
1 TAATGATTATTAATAATGATTTAATGATTTAATATTTAATGATTTAATAATGATATGATTTAA
* * * *
33191 TAATGATTACTAATAATGCAATTATAAT-AATTACTA-ATAATGATTTAATAATGAT
1 TAATGATTATTAATAATG--ATT-TAATGATTTAATATTTAATGATTTAATAATGAT
33246 TACTAATAAT
Statistics
Matches: 96, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
59 25 0.26
60 1 0.01
61 23 0.24
62 29 0.30
63 18 0.19
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (63 bp):
TAATGATTATTAATAATGATTTAATGATTTAATATTTAATGATTTAATAATGATATGATTTAA
Found at i:33201 original size:21 final size:21
Alignment explanation
Indices: 33177--33252 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 21
33167 AATGATTTAA
33177 TACTAATGATTTAATAATGAT
1 TACTAATGATTTAATAATGAT
* *
33198 TACTAATAATGCAATTATAATAATTAC
1 TAC---TAATG--ATT-TAATAATGAT
*
33225 TAATAATGATTTAATAATGAT
1 TACTAATGATTTAATAATGAT
33246 TACTAAT
1 TACTAAT
33253 AATTATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
21 17 0.40
22 3 0.07
24 10 0.23
26 3 0.07
27 10 0.23
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (21 bp):
TACTAATGATTTAATAATGAT
Found at i:33271 original size:24 final size:24
Alignment explanation
Indices: 33180--33271 Score: 132
Period size: 24 Copynumber: 3.8 Consensus size: 24
33170 GATTTAATAC
*
33180 TAATGATTTAATAATGATTACTAA
1 TAATGATTTAATAATAATTACTAA
*
33204 TAATGCAATT-ATAATAATTACTAA
1 TAATG-ATTTAATAATAATTACTAA
*
33228 TAATGATTTAATAATGATTACTAA
1 TAATGATTTAATAATAATTACTAA
*
33252 TAATTATTTAATAATAATTA
1 TAATGATTTAATAATAATTA
33272 AATATTTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
23 3 0.05
24 54 0.90
25 3 0.05
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (24 bp):
TAATGATTTAATAATAATTACTAA
Found at i:33350 original size:22 final size:22
Alignment explanation
Indices: 33322--33364 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
33312 AAATAGTTGA
* *
33322 ATTTATAACTAGTCGAATTTAT
1 ATTTATAAATAGTCAAATTTAT
33344 ATTTATAAATAGTCAAATTTA
1 ATTTATAAATAGTCAAATTTA
33365 AGTTGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTTATAAATAGTCAAATTTAT
Found at i:33363 original size:16 final size:16
Alignment explanation
Indices: 33302--33344 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
33292 TCAATTTAAA
33302 TCGAATTTATAAATAG
1 TCGAATTTATAAATAG
* *
33318 TTGAATTTATAACTAG
1 TCGAATTTATAAATAG
33334 TCGAATTTATA
1 TCGAATTTATA
33345 TTTATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (16 bp):
TCGAATTTATAAATAG
Found at i:33723 original size:11 final size:11
Alignment explanation
Indices: 33707--33832 Score: 60
Period size: 11 Copynumber: 10.7 Consensus size: 11
33697 TATTAATATT
*
33707 TAATGATTTAG
1 TAATGATTTAA
33718 TAATGATTACTAA
1 TAATGATT--TAA
*
33731 TAATGATTTAT
1 TAATGATTTAA
* *
33742 TATTAATATT--
1 TAATGAT-TTAA
33752 TAATGATTTAATA
1 TAATGATTT-A-A
*
33765 CTAATGAGTTAA
1 -TAATGATTTAA
*
33777 TAATAATTACTAA
1 TAATGATT--TAA
33790 TAATGAAATTATAA
1 TAATG--ATT-TAA
* *
33804 TAATTA-CTAA
1 TAATGATTTAA
33814 TAATGATTTAA
1 TAATGATTTAA
33825 TAATGATT
1 TAATGATT
33833 ACTAATAATT
Statistics
Matches: 87, Mismatches: 15, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
9 2 0.02
10 13 0.15
11 32 0.37
12 4 0.05
13 18 0.21
14 15 0.17
15 3 0.03
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:33769 original size:21 final size:21
Alignment explanation
Indices: 33686--33761 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 21
33676 TTTTTACTAC
33686 TAATGATTTATTATTAATATT
1 TAATGATTTATTATTAATATT
* *
33707 TAATGATTTAGTAATGATTACTA-A
1 TAATGATTTA-T--T-ATTAATATT
33731 TAATGATTTATTATTAATATT
1 TAATGATTTATTATTAATATT
33752 TAATGATTTA
1 TAATGATTTA
33762 ATACTAATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
20 6 0.13
21 21 0.46
22 1 0.02
23 1 0.02
24 11 0.24
25 6 0.13
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.51
Consensus pattern (21 bp):
TAATGATTTATTATTAATATT
Found at i:33803 original size:24 final size:24
Alignment explanation
Indices: 33766--33841 Score: 109
Period size: 24 Copynumber: 3.2 Consensus size: 24
33756 GATTTAATAC
*
33766 TAATGAGTTAATAATAATTACTAA
1 TAATGAATTAATAATAATTACTAA
33790 TAATGAAATT-ATAATAATTACTAA
1 TAATG-AATTAATAATAATTACTAA
* *
33814 TAATGATTTAATAATGATTACTAA
1 TAATGAATTAATAATAATTACTAA
33838 TAAT
1 TAAT
33842 TATTAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
23 3 0.06
24 41 0.87
25 3 0.06
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (24 bp):
TAATGAATTAATAATAATTACTAA
Found at i:33850 original size:24 final size:24
Alignment explanation
Indices: 33766--33850 Score: 95
Period size: 24 Copynumber: 3.5 Consensus size: 24
33756 GATTTAATAC
33766 TAATGAGTT-AATAATAATTACTAA
1 TAATGA-TTAAATAATAATTACTAA
33790 TAATGA--AATTATAATAATTACTAA
1 TAATGATTAA--ATAATAATTACTAA
* *
33814 TAATGATTTAATAATGATTACTAA
1 TAATGATTAAATAATAATTACTAA
*
33838 TAATTATTAAATA
1 TAATGATTAAATA
33851 TTAAAATAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.02
24 50 0.96
26 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (24 bp):
TAATGATTAAATAATAATTACTAA
Found at i:33913 original size:22 final size:23
Alignment explanation
Indices: 33885--33929 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
33875 AATCGAATTA
*
33885 ATAAATAGTTGAATTTA-TATTT
1 ATAAATAGTTAAATTTATTATTT
33907 ATAAATAGTTAAATTTATTATTT
1 ATAAATAGTTAAATTTATTATTT
33930 TTACATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (23 bp):
ATAAATAGTTAAATTTATTATTT
Found at i:33987 original size:17 final size:16
Alignment explanation
Indices: 33953--33998 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
33943 AGAGGCATGC
33953 ATATTT-AATATTATA
1 ATATTTAAATATTATA
*
33968 ATATTTAAATTTTAATA
1 ATATTTAAATATT-ATA
33985 ATATTTAACATATT
1 ATATTTAA-ATATT
33999 TAAGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 6 0.23
16 5 0.19
17 11 0.42
18 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTTAAATATTATA
Found at i:36367 original size:8 final size:8
Alignment explanation
Indices: 36344--36379 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
36334 ACTTATAGTA
*
36344 TAATAAAA
1 TAATAAAC
36352 TAATAAAC
1 TAATAAAC
36360 TAATAAAC
1 TAATAAAC
*
36368 TAACAAAC
1 TAATAAAC
36376 TAAT
1 TAAT
36380 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (8 bp):
TAATAAAC
Found at i:36490 original size:36 final size:35
Alignment explanation
Indices: 36440--36517 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 35
36430 ACTATTTTTT
* *
36440 ATATCACTTAAACTAATAAA-ATATTTATTTATTATA
1 ATATAACTTAAACTAATAAACAAATTT-TTTA-TATA
36476 ATATAACTTAAACTAATAAACTAAATTTTTTATATA
1 ATATAACTTAAACTAATAAAC-AAATTTTTTATATA
36512 ATATAA
1 ATATAA
36518 ATTCAACAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 29 0.76
37 4 0.11
38 5 0.13
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (35 bp):
ATATAACTTAAACTAATAAACAAATTTTTTATATA
Found at i:36658 original size:22 final size:22
Alignment explanation
Indices: 36620--36676 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
36610 TACTTATGTG
36620 TAATATAACTTAAACTAACAAAC
1 TAATATAAC-TAAACTAACAAAC
36643 TAATATAACTAAACTAACAAAC
1 TAATATAACTAAACTAACAAAC
36665 TAAT-TAACTAAA
1 TAATATAACTAAA
36677 ATTTTGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 8 0.24
22 17 0.50
23 9 0.26
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (22 bp):
TAATATAACTAAACTAACAAAC
Found at i:37380 original size:18 final size:18
Alignment explanation
Indices: 37357--37419 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 18
37347 ACATATATCC
37357 TCATTATCAACATCAATA
1 TCATTATCAACATCAATA
** **
37375 TCATTATCATGATCTCTA
1 TCATTATCAACATCAATA
*
37393 TCATTCTCAACATCAATA
1 TCATTATCAACATCAATA
37411 TCATTATCA
1 TCATTATCA
37420 TGTAATACAT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.38
Consensus pattern (18 bp):
TCATTATCAACATCAATA
Found at i:37758 original size:38 final size:38
Alignment explanation
Indices: 37707--37784 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
37697 GGCATATAAA
* * *
37707 ATTATCCCGAAGGATTTCGTATATGTCCCGAAGGACCT
1 ATTATCCCGAAGGATGTCATATATGTCCCGAAGAACCT
*
37745 ATTATCCCGAAGGATGTCATATGTGTCCCGAAGAACCT
1 ATTATCCCGAAGGATGTCATATATGTCCCGAAGAACCT
37783 AT
1 AT
37785 AGAACCCTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (38 bp):
ATTATCCCGAAGGATGTCATATATGTCCCGAAGAACCT
Found at i:37775 original size:21 final size:19
Alignment explanation
Indices: 37711--37777 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 19
37701 TATAAAATTA
*
37711 TCCCGAAGGATTTCGTATATG
1 TCCCGAAGGA-TTCATAT-TG
* *
37732 TCCCGAAGGA--CCTATTA
1 TCCCGAAGGATTCATATTG
37749 TCCCGAAGGATGTCATATGTG
1 TCCCGAAGGAT-TCATAT-TG
37770 TCCCGAAG
1 TCCCGAAG
37778 AACCTATAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.29
18 4 0.11
20 4 0.11
21 19 0.50
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (19 bp):
TCCCGAAGGATTCATATTG
Found at i:38141 original size:26 final size:26
Alignment explanation
Indices: 38103--38153 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
38093 TATGTTCACA
* *
38103 TCAATCATGTCACATAAAATAACATG
1 TCAAACATATCACATAAAATAACATG
*
38129 TCAAACATATCACATATAATAACAT
1 TCAAACATATCACATAAAATAACAT
38154 ATGACACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (26 bp):
TCAAACATATCACATAAAATAACATG
Found at i:38162 original size:26 final size:26
Alignment explanation
Indices: 38102--38164 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
38092 ATATGTTCAC
* *
38102 ATCAATCATGTCACATAAAATAACAT
1 ATCAAACATATCACATAAAATAACAT
* *
38128 GTCAAACATATCACATATAATAACAT
1 ATCAAACATATCACATAAAATAACAT
* *
38154 ATGACACATAT
1 ATCAAACATAT
38165 ACCCATTTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (26 bp):
ATCAAACATATCACATAAAATAACAT
Found at i:40727 original size:18 final size:18
Alignment explanation
Indices: 40704--40741 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40694 GGCATTTTAA
40704 AAAATATATATATTA-ATT
1 AAAATAT-TATATTACATT
*
40722 AAAATATTTTATTACATT
1 AAAATATTATATTACATT
40740 AA
1 AA
40742 CTCAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATATTATATTACATT
Found at i:42416 original size:5 final size:5
Alignment explanation
Indices: 42406--42497 Score: 184
Period size: 5 Copynumber: 18.4 Consensus size: 5
42396 AATTGTTATT
42406 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
42456 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC AT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC AT
42498 CACATTAGAC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 87 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATC
Found at i:47403 original size:23 final size:22
Alignment explanation
Indices: 47377--47445 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
47367 CACCACAGCT
*
47377 CGTATAAATGCACAGGAGTGCCA
1 CGTATAAATGCAC-GAAGTGCCA
* *
47400 CGTATAATTGCATCGAAGTGCCG
1 CGTATAAATGCA-CGAAGTGCCA
* *
47423 CGTAGAAATGCACTGTAGTGCCA
1 CGTATAAATGCAC-GAAGTGCCA
47446 TATAAGATGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (22 bp):
CGTATAAATGCACGAAGTGCCA
Found at i:48106 original size:2 final size:2
Alignment explanation
Indices: 48099--48131 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48089 ACTTATAAAC
48099 AT 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 AT A
48132 CTTATATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54527 original size:23 final size:23
Alignment explanation
Indices: 54501--54568 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
54491 ACCACAGCTC
*
54501 GTATAAATGCACCGGAGTGCCAA
1 GTATAAATGCACCGAAGTGCCAA
* * **
54524 GTATAATTGCATCGAAGTGCCGC
1 GTATAAATGCACCGAAGTGCCAA
* *
54547 GTAGAAATGCACCGTAGTGCCA
1 GTATAAATGCACCGAAGTGCCA
54569 TATAAGATGT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (23 bp):
GTATAAATGCACCGAAGTGCCAA
Found at i:55223 original size:2 final size:2
Alignment explanation
Indices: 55218--55249 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
55208 TACTTATAAA
55218 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
55250 TACTTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61593 original size:23 final size:23
Alignment explanation
Indices: 61567--61634 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
61557 ACCACAGCTC
*
61567 GTATAAATGCACCGGAGTGCCAA
1 GTATAAATGCACCGAAGTGCCAA
* * **
61590 GTATAATTGCATCGAAGTGCCGC
1 GTATAAATGCACCGAAGTGCCAA
* *
61613 GTAGAAATGCACCGTAGTGCCA
1 GTATAAATGCACCGAAGTGCCA
61635 TATAGATGAT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (23 bp):
GTATAAATGCACCGAAGTGCCAA
Found at i:62291 original size:2 final size:2
Alignment explanation
Indices: 62284--62333 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
62274 ACTTATAAAC
62284 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT -T ACT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
62323 AT TT AT AT AT A
1 AT AT AT AT AT A
62334 AAAATTAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
1 4 0.10
2 36 0.88
3 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:62307 original size:11 final size:11
Alignment explanation
Indices: 62284--62333 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
62274 ACTTATAAAC
62284 ATATATA-TAT
1 ATATATATTAT
62294 ATATATATTAT
1 ATATATATTAT
62305 ATATATATTACT
1 ATATATATTA-T
62317 -TATATTATT-T
1 ATATA-TATTAT
62327 ATATATA
1 ATATATA
62334 AAAATTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.28
11 21 0.58
12 5 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATATATTAT
Done.