Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006748.1 Hibiscus syriacus cultivar Beakdansim tig00016974_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: 64731
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2959 original size:32 final size:32
Alignment explanation
Indices: 2922--3010 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
2912 AAGAAATTTC
*
2922 CTTGGGTAGGCTCTAAGGCCCCAAGGTGC-TT
1 CTTGGGTAGGCTCTAAGGCCCCAAGGTACTTT
* * *
2953 CTTTGGGTAGGCTCTTAGGCCCTAATGTACTTT
1 C-TTGGGTAGGCTCTAAGGCCCCAAGGTACTTT
* *
2986 CTTGGGTAGTCTCTCAGGCCCCAAG
1 CTTGGGTAGGCTCTAAGGCCCCAAG
3011 ATATTCCTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 1 0.02
32 44 0.92
33 3 0.06
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (32 bp):
CTTGGGTAGGCTCTAAGGCCCCAAGGTACTTT
Found at i:6924 original size:18 final size:18
Alignment explanation
Indices: 6897--6939 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
6887 AAGGAGTTAA
*
6897 TCTCAACTTTTAGCTTCC
1 TCTCATCTTTTAGCTTCC
*
6915 TCTCATCTTTTAGCTTTC
1 TCTCATCTTTTAGCTTCC
6933 TCTCATC
1 TCTCATC
6940 CAACGATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.05, T:0.49
Consensus pattern (18 bp):
TCTCATCTTTTAGCTTCC
Found at i:12108 original size:20 final size:20
Alignment explanation
Indices: 12063--12100 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12053 AACGGTCAGA
*
12063 TCGATTTGGGTTGACTCATG
1 TCGATTTGGGTTAACTCATG
*
12083 CCGATTTGGGTTAACTCA
1 TCGATTTGGGTTAACTCA
12101 ATTCGATTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
TCGATTTGGGTTAACTCATG
Found at i:12624 original size:12 final size:12
Alignment explanation
Indices: 12607--12631 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12597 GGGGGTGGCG
12607 AGTGCGCTATAA
1 AGTGCGCTATAA
12619 AGTGCGCTATAA
1 AGTGCGCTATAA
12631 A
1 A
12632 TATCATGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (12 bp):
AGTGCGCTATAA
Found at i:16132 original size:17 final size:17
Alignment explanation
Indices: 16110--16144 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
16100 GAGCTTTGAA
*
16110 ATACACTTACTGCATGT
1 ATACACTTACTACATGT
16127 ATACACTTACTACATGT
1 ATACACTTACTACATGT
16144 A
1 A
16145 ATTTAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (17 bp):
ATACACTTACTACATGT
Found at i:28990 original size:15 final size:16
Alignment explanation
Indices: 28972--29005 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28962 TATGAACATC
*
28972 AAATAAATTAACAA-A
1 AAATAAAATAACAATA
28987 AAATAAAATAACAATA
1 AAATAAAATAACAATA
29003 AAA
1 AAA
29006 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:30473 original size:14 final size:14
Alignment explanation
Indices: 30451--30495 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
30441 GAAGGTAAAA
30451 CTTTCTTTTTTTCT
1 CTTTCTTTTTTTCT
*
30465 CTTTTTTTTTTTCT
1 CTTTCTTTTTTTCT
* **
30479 GTTTCGATTTTTCT
1 CTTTCTTTTTTTCT
30493 CTT
1 CTT
30496 CGTCCCCTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (14 bp):
CTTTCTTTTTTTCT
Found at i:30872 original size:25 final size:25
Alignment explanation
Indices: 30831--30954 Score: 214
Period size: 25 Copynumber: 5.0 Consensus size: 25
30821 AGTTAAGGGA
* *
30831 TTAGGG-TTAAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
30855 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
30880 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
30905 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
30930 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
30955 GGGTTGTTGG
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
24 6 0.06
25 90 0.94
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:31092 original size:3 final size:3
Alignment explanation
Indices: 31084--31147 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
31074 GCAAAAATTG
* **
31084 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31128 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
31148 CGGAAAAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:31139 original size:32 final size:32
Alignment explanation
Indices: 31086--31149 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
31076 AAAAATTGTA
*
31086 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAATAAAATAACG
31118 ATAAT-AATAATAATAATAATAATAAAATAACG
1 ATAATAAATAATAATAA-AATAATAAAATAACG
31150 GAAAAAACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAATAAAATAACG
Found at i:33123 original size:14 final size:15
Alignment explanation
Indices: 33098--33127 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
33088 TAAATTAAAC
33098 AAACATGAAATTTAA
1 AAACATGAAATTTAA
33113 AAACA-GAAATTTAA
1 AAACATGAAATTTAA
33127 A
1 A
33128 TAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (15 bp):
AAACATGAAATTTAA
Found at i:33274 original size:290 final size:285
Alignment explanation
Indices: 32781--33372 Score: 666
Period size: 290 Copynumber: 2.1 Consensus size: 285
32771 CAATTTCTAT
* * * **
32781 TAAAAATACATTTTTAAGGATTAAATTTAGAAAACATAAAATTATAAAATTAAATTTAAATAAAT
1 TAAAAATATAATTTTAAGGATTAAATTTAAAAAACATAAAATTATAAAAAGAAATTTAAATAAAT
* * * *
32846 TAAATAACAAAGTGATCATATTGAAACAATTGTAAAATGTAAAGTTGAAATTAATATAAAAATGG
66 TAAAAAACAAAGTGATCAAATTGAAACAATTGTAAAATATAAAGCTGAAATTAATATAAAAATGG
* *
32911 ACTAACTTCCATTCATTTACAAAATTGGTGAATAAAAGTTTATAAGGTTTGGAGATAATGATATA
131 ACTAACTTCCATTCATTGACAAAATTGGTGAACAAAAGTTTATAAGGTTTGGAGATAATGATATA
*
32976 AGTTATAGGGTTTGAAAT-AAAGTTTATGATGAGAATTATAGGGTTTTG-AGTAAATTACAAAAA
196 AGTTATA-GGTTTGAAATGAAA-TTTATGATGAGAATTATAGAG-TTTGCAGTAAATTA-AAAAA
* * *
33039 ATTA-AAACAATTATGGGCCAAATTTGGA
257 AATAGAAACAATTATAGGCCAAATTTGAA
*
33067 TAAAAATATAATTTTAAGGATTAAA-TTAAACAAACATGAAATT-TAAAAACAGAAATTTAAATA
1 TAAAAATATAATTTTAAGGATTAAATTTAAA-AAACATAAAATTAT-AAAA-AGAAATTTAAATA
* * * *
33130 AATTAAAAAAC-ACGCATGGATCAAATTGAAAGAATTTTAAAAATATAAAGCTGAAATTAATATC
63 AATTAAAAAACAAAG--T-GATCAAATTGAAACAATTGT-AAAATATAAAGCTGAAATTAATATA
* ** * *
33194 AATATGGACTATA-TTGTATTCACTTGA-AAAGTTGGTGAACAAATA-TTTAT-CGAGTTTGGAG
124 AAAATGGACTA-ACTTCCATTCA-TTGACAAAATTGGTGAACAAA-AGTTTATAAG-GTTTGGAG
* * * * *
33255 TTTATGATATAATTTATAGGTTTGAAATGAAATTTATGATGTGATTTATAGAGTTTGCAGTAAAT
185 ATAATGATATAAGTTATAGGTTTGAAATGAAATTTATGATGAGAATTATAGAGTTTGCAGTAAAT
* * **
33320 TAAAAAAAATAGAAATAATTATAGGTCATTTTTGAA
250 TAAAAAAAATAGAAACAATTATAGGCCAAATTTGAA
33356 T-AAAATATAATTTTAAG
1 TAAAAATATAATTTTAAG
33373 AACTAAAAAT
Statistics
Matches: 258, Mismatches: 34, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
285 5 0.02
286 40 0.16
287 21 0.08
288 29 0.11
289 74 0.29
290 84 0.33
291 5 0.02
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (285 bp):
TAAAAATATAATTTTAAGGATTAAATTTAAAAAACATAAAATTATAAAAAGAAATTTAAATAAAT
TAAAAAACAAAGTGATCAAATTGAAACAATTGTAAAATATAAAGCTGAAATTAATATAAAAATGG
ACTAACTTCCATTCATTGACAAAATTGGTGAACAAAAGTTTATAAGGTTTGGAGATAATGATATA
AGTTATAGGTTTGAAATGAAATTTATGATGAGAATTATAGAGTTTGCAGTAAATTAAAAAAAATA
GAAACAATTATAGGCCAAATTTGAA
Found at i:33808 original size:16 final size:16
Alignment explanation
Indices: 33789--33833 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
33779 CATGTATTAG
*
33789 TACATACATGCAT-TCA
1 TACATATATGCATGT-A
*
33805 TACATATATGCGTGTA
1 TACATATATGCATGTA
33821 TACATATATGCAT
1 TACATATATGCAT
33834 ACATTCTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (16 bp):
TACATATATGCATGTA
Found at i:33852 original size:4 final size:4
Alignment explanation
Indices: 33843--34165 Score: 141
Period size: 4 Copynumber: 81.5 Consensus size: 4
33833 TACATTCTCT
* * * * *
33843 CATA CATA CATA CATA CATA CATA TAGA TAGA CATA CATA CGCATA CATT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA --CATA CATA
* * *
33893 CACT- CATA CATA CATA TATA TATA CATA CATA CATA CAT- -ATA GATA
1 CA-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
33939 GGCAT- CATA TATA CATA C--A CATA CATT CACT- CATA CATA CATA CATA
1 --CATA CATA CATA CATA CATA CATA CATA CA-TA CATA CATA CATA CATA
* * *
33986 CAT- -ATA GATA GGCATA CATA CATA CATA C--A CATA CATA TATA CACA
1 CATA CATA CATA --CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * * * *
34032 CCCATA CATA CATG TATG CATC CATG CACA CTTA CATA CATC CGTG CACA
1 --CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
34082 CATA CATA CATG CATA CATA C--A CACA CATA CATA CACA CACA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
34128 TATA TATA TATA TATA TATA TATA TATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
34166 CATAAATAGA
Statistics
Matches: 256, Mismatches: 40, Indels: 46
0.75 0.12 0.13
Matches are distributed among these distances:
2 10 0.04
3 5 0.02
4 227 0.89
5 2 0.01
6 12 0.05
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:33928 original size:28 final size:28
Alignment explanation
Indices: 33898--34721 Score: 122
Period size: 28 Copynumber: 29.2 Consensus size: 28
33888 ACATTCACTC
* *
33898 ATACATACATATATATATACATACATAC
1 ATACATATATATATACATACATACATAC
* ** *
33926 ATACATATAGATAGGCAT-CATATATAC
1 ATACATATATATATACATACATACATAC
* *
33953 ATACACATACAT-TCACTCATACATACATAC
1 ATACATATATATAT-A--CATACATACATAC
* **
33983 ATACATATAGATAGGCATACATACATAC
1 ATACATATATATATACATACATACATAC
* * * * **
34011 ATACACATACATATATACACACCCATAC
1 ATACATATATATATACATACATACATAC
* ** * * * *
34039 ATACATGTATGCATCCATGCACACTTAC
1 ATACATATATATATACATACATACATAC
*** ** * *
34067 ATACATCCGTGCACACATACATACATGC
1 ATACATATATATATACATACATACATAC
* * * *
34095 ATAC--ATACACACACATACATACACACAC
1 ATACATATATATATACATACAT--ACATAC
* * * * *
34123 ATATATATATATATATATATATATATAT
1 ATACATATATATATACATACATACATAC
* * * * * * *
34151 ATATACATACATACACATAAATAGACAC
1 ATACATATATATATACATACATACATAC
* * * * * *
34179 AGACATATATGTACACATATACACACACAT
1 ATACATATATATATAC--ATACATACATAC
* * * * *
34209 ATACACATTCACATATACACACATTCACAC
1 ATACATA-T-ATATATACATACATACATAC
* *
34239 ATAC--ACATATATACATATATACATAC
1 ATACATATATATATACATACATACATAC
**
34265 GTATACATAT-TA-GCACATACAT--ATAC
1 --ATACATATATATATACATACATACATAC
* * ** *
34291 ATACACATATATGCATTCATACATACGCAT
1 ATACATATATAT--ATACATACATACATAC
* * * * *
34321 ATACATAAACACACACATACATAAATAC
1 ATACATATATATATACATACATACATAC
* * * * * *
34349 ACACATACATAAATACAAATAGACATAC
1 ATACATATATATATACATACATACATAC
* * * * *
34377 ACACATATACATATACACACATGCACAC
1 ATACATATATATATACATACATACATAC
* * * * * * *
34405 AAATATACACATACACACACATGCATAC
1 ATACATATATATATACATACATACATAC
* * *
34433 --ACATATTTATACACACACATACA-A-
1 ATACATATATATATACATACATACATAC
* * *
34457 AAACACATATACATACATAC--ACATAC
1 ATACATATATATATACATACATACATAC
* * * *
34483 ATAC--ATACACATACATACAGACCCACAC
1 ATACATATATATATACATACATA--CATAC
* ** * * **
34511 ATACATACATGCATGCATACACATGTAC
1 ATACATATATATATACATACATACATAC
* * * * ***
34539 ATACATGTGTGTACACATACATGTGTGTAC
1 ATACATATATATATACATACA--TACATAC
*
34569 ATATACATATATGTATATATGCATATATACATAC
1 --ATACATATA--TATATA--CATACATACATAC
* * *
34603 ATACAAATATATATACACATACATGCATAT
1 ATAC--ATATATATATACATACATACATAC
* *
34633 ATACATACACATATATACATACACACATAC
1 ATACAT--ATATATATACATACATACATAC
* * * * *
34663 ATATACACATGTATACAT--ATACATGC
1 ATACATATATATATACATACATACATAC
* *
34689 ATACATATATATATATATACATACACAC
1 ATACATATATATATACATACATACATAC
34717 ATACA
1 ATACA
34722 CACACACACA
Statistics
Matches: 557, Mismatches: 192, Indels: 94
0.66 0.23 0.11
Matches are distributed among these distances:
24 23 0.04
25 4 0.01
26 84 0.15
27 18 0.03
28 267 0.48
29 5 0.01
30 116 0.21
31 1 0.00
32 21 0.04
34 13 0.02
36 5 0.01
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.26
Consensus pattern (28 bp):
ATACATATATATATACATACATACATAC
Found at i:33982 original size:57 final size:58
Alignment explanation
Indices: 33847--34022 Score: 219
Period size: 57 Copynumber: 2.9 Consensus size: 58
33837 TTCTCTCATA
* * * *
33847 CATACATACATACATACATATAGATAGACATACATACGCATACATTCACTCATACATACATATAT
1 CATACATACATACATACATATAGATAGGCATACATA--CATACA-T-ACACATACATTC--A-CT
* *
33912 ATATACATACATACATACATATAGATAGGCAT-CATATATACATACACATACATTCACT
1 -CATACATACATACATACATATAGATAGGCATACATACATACATACACATACATTCACT
33970 CATACATACATACATACATATAGATAGGCATACATACATACATACACATACAT
1 CATACATACATACATACATATAGATAGGCATACATACATACATACACATACAT
34023 ATATACACAC
Statistics
Matches: 101, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
57 30 0.30
58 21 0.21
59 1 0.01
61 10 0.10
62 1 0.01
63 5 0.05
65 4 0.04
66 29 0.29
ACGTcount: A:0.45, C:0.22, G:0.05, T:0.27
Consensus pattern (58 bp):
CATACATACATACATACATATAGATAGGCATACATACATACATACACATACATTCACT
Found at i:34128 original size:2 final size:2
Alignment explanation
Indices: 34123--34155 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34113 ATACACACAC
34123 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
34156 CATACATACA
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:34203 original size:8 final size:8
Alignment explanation
Indices: 34203--34423 Score: 67
Period size: 8 Copynumber: 27.6 Consensus size: 8
34193 ACATATACAC
34203 ACACATAT
1 ACACATAT
34211 ACACAT-T
1 ACACATAT
34218 -CACATAT
1 ACACATAT
*
34225 ACACACAT
1 ACACATAT
* *
34233 TCACACAT
1 ACACATAT
34241 ACACATAT
1 ACACATAT
*
34249 ATACATAT
1 ACACATAT
*
34257 ATACATACGT
1 ACACATA--T
*
34267 ATACATATT
1 ACACATA-T
*
34276 AGCACATAC
1 A-CACATAT
* * *
34285 ATATACAT
1 ACACATAT
34293 ACACATAT
1 ACACATAT
**
34301 ATGCAT-T
1 ACACATAT
* *
34308 -CATACAT
1 ACACATAT
*
34315 ACGCATAT
1 ACACATAT
* * *
34323 ACATAAAC
1 ACACATAT
*
34331 ACACACAT
1 ACACATAT
* *
34339 ACATAAAT
1 ACACATAT
*
34347 ACACACAT
1 ACACATAT
* *
34355 ACATAAAT
1 ACACATAT
34363 ACA-A-AT
1 ACACATAT
* *
34369 AGACATAC
1 ACACATAT
34377 ACACATAT
1 ACACATAT
* *
34385 ACATATAC
1 ACACATAT
*
34393 ACACATGCAC
1 ACACAT--AT
*
34403 ACAAATAT
1 ACACATAT
*
34411 ACACATAC
1 ACACATAT
34419 ACACA
1 ACACA
34424 CATGCATACA
Statistics
Matches: 154, Mismatches: 48, Indels: 22
0.69 0.21 0.10
Matches are distributed among these distances:
6 10 0.06
7 6 0.04
8 115 0.75
9 3 0.02
10 20 0.13
ACGTcount: A:0.49, C:0.25, G:0.03, T:0.23
Consensus pattern (8 bp):
ACACATAT
Found at i:34206 original size:12 final size:12
Alignment explanation
Indices: 34191--34231 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 12
34181 ACATATATGT
34191 ACACATATACAC
1 ACACATATACAC
34203 ACACATATACAC
1 ACACATATACAC
34215 ATTCACATATACAC
1 A--CACATATACAC
34229 ACA
1 ACA
34232 TTCACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 15 0.56
14 12 0.44
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.20
Consensus pattern (12 bp):
ACACATATACAC
Found at i:34228 original size:24 final size:24
Alignment explanation
Indices: 34190--34421 Score: 96
Period size: 26 Copynumber: 9.2 Consensus size: 24
34180 GACATATATG
34190 TACACATATACACACACATATACACA
1 TACACATAT--ACACACATATACACA
*
34216 TTCACATATACACACAT-TCACACA
1 TACACATATACACACATAT-ACACA
* * *
34240 TACACATATATACATATATACATACG
1 TACACATATACACACATATAC--ACA
* * * *
34266 TATACATATTAGCACATACATATACA
1 TACACATA-TA-CACACATATACACA
* * *
34292 TACACATATATGCATTCATACATACGCA
1 TACACATATA--CA--CACATATACACA
* * * *
34320 TATACATAAACACACACATACATAAA
1 TACACATATACACACATATAC--ACA
* * *
34346 TACACACATACATA-A-ATACAAA
1 TACACATATACACACATATACACA
* *
34368 TAGAC--ATACACACATATACATA
1 TACACATATACACACATATACACA
* *
34390 TACACACATGCACACAAATATACACA
1 TACACATAT--ACACACATATACACA
34416 TACACA
1 TACACA
34422 CACATGCATA
Statistics
Matches: 161, Mismatches: 28, Indels: 34
0.72 0.13 0.15
Matches are distributed among these distances:
20 6 0.04
21 1 0.01
22 17 0.11
23 1 0.01
24 43 0.27
25 4 0.02
26 61 0.38
27 2 0.01
28 26 0.16
ACGTcount: A:0.49, C:0.25, G:0.03, T:0.23
Consensus pattern (24 bp):
TACACATATACACACATATACACA
Found at i:34299 original size:16 final size:16
Alignment explanation
Indices: 34237--34499 Score: 74
Period size: 16 Copynumber: 15.9 Consensus size: 16
34227 ACACATTCAC
* *
34237 ACATACACATATATAC
1 ACATACACATACATAT
* * *
34253 ATATATACATACGTAT
1 ACATACACATACATAT
34269 ACATATTAGCACATACATAT
1 AC--A-TA-CACATACATAT
34289 ACATACACATATATGCATTCAT
1 ACATACAC--ATA--CA-T-AT
* *
34311 ACATACGCATATACATAA
1 ACATA--CACATACATAT
* *
34329 ACACACACATACATAA
1 ACATACACATACATAT
* *
34345 ATACACACATACATA-
1 ACATACACATACATAT
* * *
34360 A-ATACAAATAGACAT
1 ACATACACATACATAT
* *
34375 ACACACATATACATAT
1 ACATACACATACATAT
* *
34391 ACACACATGCACACAAATAT
1 ACATACA--CATAC--ATAT
* * * *
34411 ACACATACACACACAT
1 ACATACACATACATAT
* **
34427 GCATACACATATTTAT
1 ACATACACATACATAT
*
34443 ACACACACATACA-A-
1 ACATACACATACATAT
* *
34457 A-A-ACACATATACAT
1 ACATACACATACATAT
34471 ACATACACATAC--AT
1 ACATACACATACATAT
34485 ACATACACATACATA
1 ACATACACATACATA
34500 CAGACCCACA
Statistics
Matches: 185, Mismatches: 38, Indels: 48
0.68 0.14 0.18
Matches are distributed among these distances:
12 8 0.04
13 2 0.01
14 25 0.14
15 4 0.02
16 85 0.46
17 2 0.01
18 18 0.10
19 3 0.02
20 25 0.14
21 1 0.01
22 10 0.05
24 2 0.01
ACGTcount: A:0.50, C:0.25, G:0.03, T:0.23
Consensus pattern (16 bp):
ACATACACATACATAT
Found at i:34339 original size:52 final size:51
Alignment explanation
Indices: 34141--34339 Score: 129
Period size: 52 Copynumber: 3.8 Consensus size: 51
34131 ATATATATAT
* * * * **
34141 ATATATATATATATACATACATACACATAAATAGACACAGACATATATGTACAC
1 ATATATACATATATACATACGTATACAT--ATA-ACACACACATATACATACAC
* * * * * * * *
34195 ATATACACACACATATACACAT-TCACATAT-ACACACA-TTCACACATACAC
1 ATATATACATATATACATACGTAT-ACATATAACACACACAT-ATACATACAC
* *
34245 ATATATACATATATACATACGTATACATATTAGCACATACATATACATACAC
1 ATATATACATATATACATACGTATACATA-TAACACACACATATACATACAC
*
34297 ATATATGCAT-TCATACATACGCATATACATA-AACACACACATA
1 ATATATACATAT-ATACATACG--TATACATATAACACACACATA
34340 CATAAATACA
Statistics
Matches: 111, Mismatches: 25, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
49 1 0.01
50 34 0.31
51 3 0.03
52 44 0.40
53 1 0.01
54 28 0.25
ACGTcount: A:0.47, C:0.23, G:0.04, T:0.27
Consensus pattern (51 bp):
ATATATACATATATACATACGTATACATATAACACACACATATACATACAC
Found at i:34544 original size:4 final size:4
Alignment explanation
Indices: 34465--34531 Score: 52
Period size: 4 Copynumber: 17.2 Consensus size: 4
34455 AAAAACACAT
* *
34465 ATAC ATAC ATAC --AC ATAC ATAC ATAC --AC ATAC ATAC AGACCC ACAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA--C ATAC
* *
34511 ATAC ATAC ATGC ATGC ATAC A
1 ATAC ATAC ATAC ATAC ATAC A
34532 CATGTACATA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
2 4 0.08
4 45 0.87
6 3 0.06
ACGTcount: A:0.46, C:0.30, G:0.04, T:0.19
Consensus pattern (4 bp):
ATAC
Found at i:34558 original size:16 final size:16
Alignment explanation
Indices: 34537--34576 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
34527 ATACACATGT
34537 ACATACATGTGTGTAC
1 ACATACATGTGTGTAC
34553 ACATACATGTGTGTAC
1 ACATACATGTGTGTAC
*
34569 ATATACAT
1 ACATACAT
34577 ATATGTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (16 bp):
ACATACATGTGTGTAC
Found at i:34576 original size:20 final size:19
Alignment explanation
Indices: 34531--34582 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
34521 GCATGCATAC
34531 ACATGTACATACATGTGTGT
1 ACAT-TACATACATGTGTGT
34551 AC---ACATACATGTGTGT
1 ACATTACATACATGTGTGT
*
34567 ACATATACATATATGT
1 ACAT-TACATACATGT
34583 ATATATGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 16 0.59
20 11 0.41
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (19 bp):
ACATTACATACATGTGTGT
Found at i:34583 original size:16 final size:16
Alignment explanation
Indices: 34566--34711 Score: 85
Period size: 16 Copynumber: 8.8 Consensus size: 16
34556 TACATGTGTG
*
34566 TACATATACATATATG
1 TACATATACATATATA
* *
34582 TATATATGCATATATACA
1 TACATATACATATAT--A
* *
34600 TACATACAAATATATA
1 TACATATACATATATA
*
34616 TACACATACATGCATATA
1 TACATATACAT--ATATA
*
34634 TACATACACATATATA
1 TACATATACATATATA
* * * * *
34650 CATACACACATACATA
1 TACATATACATATATA
* ** *
34666 TACACATGTATACATA
1 TACATATACATATATA
34682 TACATGCATACATATATA
1 TACAT--ATACATATATA
*
34700 TATATATACATA
1 TACATATACATA
34712 CACACATACA
Statistics
Matches: 98, Mismatches: 26, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
16 61 0.62
18 37 0.38
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.32
Consensus pattern (16 bp):
TACATATACATATATA
Found at i:34604 original size:4 final size:4
Alignment explanation
Indices: 34590--34769 Score: 79
Period size: 4 Copynumber: 47.0 Consensus size: 4
34580 TGTATATATG
* * * * * *
34590 CATA TATA CATA CATA CA-A -ATA TATA TACA CATA CATG CATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
34636 CATA C--A CATA TATA CATA CACA CATA CATA TACA CATG TATA CAT-
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
34681 -ATA CATG CATA CATA TATA TATA TATA CATA CACA CATA C--A CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
34726 CACA CATA CACA CACA CACA CACA CACA CATA CATA AATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
34770 TATAAACACA
Statistics
Matches: 136, Mismatches: 32, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
2 7 0.05
3 2 0.01
4 127 0.93
ACGTcount: A:0.49, C:0.25, G:0.02, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:34616 original size:22 final size:22
Alignment explanation
Indices: 34593--34713 Score: 84
Period size: 22 Copynumber: 5.5 Consensus size: 22
34583 ATATATGCAT
*
34593 ATATACATACATACAAATATAT
1 ATATACATACATACAAATATAC
* * *
34615 ATACACATACATGCATATATAC
1 ATATACATACATACAAATATAC
* * *
34637 ATACACATATATAC--ATACAC
1 ATATACATACATACAAATATAC
* * * **
34657 ACATACATATACACATGTATAC
1 ATATACATACATACAAATATAC
* *
34679 ATATACATGCATACATATATATAT
1 ATATACATACATACA-A-ATATAC
34703 ATATACATACA
1 ATATACATACA
34714 CACATACACA
Statistics
Matches: 75, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
20 16 0.21
22 45 0.60
24 14 0.19
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (22 bp):
ATATACATACATACAAATATAC
Found at i:34629 original size:38 final size:38
Alignment explanation
Indices: 34587--34664 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
34577 ATATGTATAT
* * *
34587 ATGCATATATACATACATACAAATATATATACACATAC
1 ATGCATATATACATACACACAAATACATACACACATAC
* *
34625 ATGCATATATACATACACATATATACATACACACATAC
1 ATGCATATATACATACACACAAATACATACACACATAC
34663 AT
1 AT
34665 ATACACATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.28
Consensus pattern (38 bp):
ATGCATATATACATACACACAAATACATACACACATAC
Found at i:34637 original size:30 final size:30
Alignment explanation
Indices: 34598--34709 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 30
34588 TGCATATATA
* *
34598 CATACATACAAATATATATACACATACATG
1 CATACATACATACATATATACACATACATG
* * * **
34628 CATATATACATACACATATATACATACACA
1 CATACATACATACATATATACACATACATG
* * * *
34658 CATACATATACACATGTATACATATACATG
1 CATACATACATACATATATACACATACATG
* *
34688 CATACATATATATATATATACA
1 CATACATACATACATATATACA
34710 TACACACATA
Statistics
Matches: 63, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.29
Consensus pattern (30 bp):
CATACATACATACATATATACACATACATG
Found at i:34647 original size:14 final size:14
Alignment explanation
Indices: 34613--34743 Score: 91
Period size: 14 Copynumber: 9.1 Consensus size: 14
34603 ATACAAATAT
34613 ATATACACATACATGC
1 ATATACACATACA--C
*
34629 ATATATACATACAC
1 ATATACACATACAC
*
34643 ATATATACATACAC
1 ATATACACATACAC
* *
34657 ACATACATATACAC
1 ATATACACATACAC
* * *
34671 ATGTATACATATAC
1 ATATACACATACAC
* * *
34685 ATGCATACATATATAT
1 AT--ATACACATACAC
*
34701 ATATATACATACAC
1 ATATACACATACAC
* *
34715 ACATACACACACAC
1 ATATACACATACAC
* *
34729 ACATACACACACAC
1 ATATACACATACAC
34743 A
1 A
34744 CACACACACA
Statistics
Matches: 93, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
14 71 0.76
16 22 0.24
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.24
Consensus pattern (14 bp):
ATATACACATACAC
Found at i:34716 original size:2 final size:2
Alignment explanation
Indices: 34711--34755 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
34701 ATATATACAT
* *
34711 AC AC AC AT AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34753 AC A
1 AC A
34756 TACATAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.44, G:0.00, T:0.04
Consensus pattern (2 bp):
AC
Found at i:34804 original size:12 final size:12
Alignment explanation
Indices: 34713--34809 Score: 59
Period size: 12 Copynumber: 7.9 Consensus size: 12
34703 ATATACATAC
34713 ACACATACACACA
1 ACACATACACA-A
*
34726 CACACATACACAC
1 -ACACATACACAA
* *
34739 ACACACACACAC
1 ACACATACACAA
*
34751 ACACATACATAA
1 ACACATACACAA
* * *
34763 ATACATATATAA
1 ACACATACACAA
* * *
34775 ACACAAAAATAA
1 ACACATACACAA
* *
34787 AAACAGACACAA
1 ACACATACACAA
*
34799 ACACAGACACA
1 ACACATACACA
34810 TCATACACAT
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
12 57 0.84
14 11 0.16
ACGTcount: A:0.58, C:0.31, G:0.02, T:0.09
Consensus pattern (12 bp):
ACACATACACAA
Found at i:34893 original size:2 final size:2
Alignment explanation
Indices: 34886--35019 Score: 268
Period size: 2 Copynumber: 67.0 Consensus size: 2
34876 ACATATGTAT
34886 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34928 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34970 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
35012 AC AC AC AC
1 AC AC AC AC
35020 GTGTGTGCAC
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 132 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:35033 original size:4 final size:4
Alignment explanation
Indices: 35026--35060 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
35016 ACACGTGTGT
35026 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCA
1 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCA
35061 TACATACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.49, G:0.26, T:0.00
Consensus pattern (4 bp):
GCAC
Found at i:35313 original size:19 final size:20
Alignment explanation
Indices: 35278--35325 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
35268 TTCAAAATTA
*
35278 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATTCCATTTTG
35298 TTTTTCAAAA-TCCATTTTG
1 TTTTTCAAAATTCCATTTTG
35317 TTTTT-AAAA
1 TTTTTCAAAA
35326 AGAAAAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 4 0.15
19 13 0.48
20 10 0.37
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTCAAAATTCCATTTTG
Found at i:36895 original size:10 final size:10
Alignment explanation
Indices: 36842--36888 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
36832 GCTGCTGGAA
36842 ACCGGTTT-G
1 ACCGGTTTCG
*
36851 ACCGGTTTTCA
1 ACCGG-TTTCG
*
36862 ACCGGTTTTG
1 ACCGGTTTCG
36872 ACCGGTTTCG
1 ACCGGTTTCG
36882 ACCGGTT
1 ACCGGTT
36889 CGAACCGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 5 0.16
10 22 0.69
11 5 0.16
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.34
Consensus pattern (10 bp):
ACCGGTTTCG
Found at i:36895 original size:20 final size:20
Alignment explanation
Indices: 36841--36888 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
36831 CGCTGCTGGA
36841 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTTTC
36861 AACCGGTTTTGACCGG-TTTC
1 AACCGG-TTTGACCGGTTTTC
*
36881 GACCGGTT
1 AACCGGTT
36889 CGAACCGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 15 0.58
21 9 0.35
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTTTC
Found at i:36945 original size:17 final size:17
Alignment explanation
Indices: 36907--36957 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
36897 TACCGGTCTT
*
36907 ACCCGACCCGACC-CT-
1 ACCCGACCCGACCGTTG
36922 A-CCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
36938 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
36955 ACC
1 ACC
36958 GTTGACAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 11 0.34
15 2 0.06
16 1 0.03
17 18 0.56
ACGTcount: A:0.20, C:0.51, G:0.20, T:0.10
Consensus pattern (17 bp):
ACCCGACCCGACCGTTG
Found at i:44130 original size:9 final size:9
Alignment explanation
Indices: 44116--44169 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
44106 CGCTGCTGGA
44116 AACCGGTTT
1 AACCGGTTT
44125 AACCGGTTCT
1 AACCGGTT-T
*
44135 AACCGTTTT
1 AACCGGTTT
* *
44144 GACCGGTCTG
1 AACCGGT-TT
44154 AACCGGTTT
1 AACCGGTTT
*
44163 AGCCGGT
1 AACCGGT
44170 CTGACCCGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
9 21 0.58
10 15 0.42
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:44157 original size:19 final size:18
Alignment explanation
Indices: 44116--44173 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
44106 CGCTGCTGGA
44116 AACCGGTTTAACCGGTTCT-
1 AACCGGTTT-ACCGG-TCTG
*
44135 AACCGTTTTGACCGGTCTG
1 AACCGGTTT-ACCGGTCTG
44154 AACCGGTTTAGCCGGTCTG
1 AACCGGTTTA-CCGGTCTG
44173 A
1 A
44174 CCCGACCCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.12
19 30 0.88
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (18 bp):
AACCGGTTTACCGGTCTG
Done.