Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001928.1 Hibiscus syriacus cultivar Beakdansim tig00003899_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: 89220
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:4858 original size:30 final size:30
Alignment explanation
Indices: 4822--4882 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
4812 TCAGCAGATG
*
4822 TGCATGGAA-GCGTGGATCTCTCCGCGTCTT
1 TGCATGGAAGGC-TGGATATCTCCGCGTCTT
*
4852 TGCATGGAAGGCTGGATATCTCGGCGTCTT
1 TGCATGGAAGGCTGGATATCTCCGCGTCTT
4882 T
1 T
4883 AACGCAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (30 bp):
TGCATGGAAGGCTGGATATCTCCGCGTCTT
Found at i:4991 original size:33 final size:34
Alignment explanation
Indices: 4947--5029 Score: 152
Period size: 33 Copynumber: 2.5 Consensus size: 34
4937 TATGATTGAT
4947 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
4981 CTCTC-GCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
5014 -TCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
5030 GCTGTGCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
32 4 0.08
33 39 0.81
34 5 0.10
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:5151 original size:23 final size:23
Alignment explanation
Indices: 5125--5168 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
5115 TGAGCAGGGG
5125 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
5148 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
5169 GGCATGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:5918 original size:173 final size:173
Alignment explanation
Indices: 5622--5980 Score: 612
Period size: 173 Copynumber: 2.1 Consensus size: 173
5612 TGTAAAGTTG
* *
5622 TAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGATATA
1 TAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGATATA
*
5687 CTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTA-TG
66 CTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT-
*
5751 GATTAAATTGCTAAGTTTGAAAATGTTGAGAACCAAATAGTAAT
130 GATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAAT
* * *
5795 TAGGGATCGTTTTGTAAAATTTGAGGAATTTAAGGAATTAGAGTAAATTATAAAAAGTTGGTATA
1 TAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGATATA
*
5860 CTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGTG
66 CTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGTG
*
5925 ATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAAT
131 ATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAAT
*
5968 TAGGGATCATTTT
1 TAGGGATCGTTTT
5981 ATATTGATGT
Statistics
Matches: 175, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
173 174 0.99
174 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.38
Consensus pattern (173 bp):
TAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGATATA
CTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGTG
ATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAAT
Found at i:7746 original size:18 final size:18
Alignment explanation
Indices: 7705--7746 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
7695 GAAACCAAGA
*
7705 AGGACTGGGACTGGGAGT
1 AGGAGTGGGACTGGGAGT
*
7723 -GAGAGTGGGAGTGGGAGT
1 AG-GAGTGGGACTGGGAGT
7741 AGGAGT
1 AGGAGT
7747 TCTTCTCACC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
17 1 0.05
18 18 0.90
19 1 0.05
ACGTcount: A:0.24, C:0.05, G:0.55, T:0.17
Consensus pattern (18 bp):
AGGAGTGGGACTGGGAGT
Found at i:8189 original size:23 final size:23
Alignment explanation
Indices: 8159--8211 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
8149 TTATTGTAAT
8159 CATTAAAGTAATTATTATTAAAG
1 CATTAAAGTAATTATTATTAAAG
*
8182 CATTAAAGTAATTATTATTAAAT
1 CATTAAAGTAATTATTATTAAAG
8205 CATTAAA
1 CATTAAA
8212 ATTAAATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (23 bp):
CATTAAAGTAATTATTATTAAAG
Found at i:8217 original size:37 final size:37
Alignment explanation
Indices: 8175--8290 Score: 146
Period size: 37 Copynumber: 3.1 Consensus size: 37
8165 AGTAATTATT
*
8175 ATTAAAGCATTAAAGTAATTATTATTAAATCATTAAA
1 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
* * **
8212 ATTAAATCATTAAAGTTAA--ATCATTAAAGTAATTATT
1 ATTAAATCATTAAAG-TAATTATTATTAAA-TCATTAAA
8249 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
1 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
*
8286 GTTAA
1 ATTAA
8291 TTATTATTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
36 11 0.17
37 43 0.66
38 11 0.17
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (37 bp):
ATTAAATCATTAAAGTAATTATTATTAAATCATTAAA
Found at i:8240 original size:14 final size:14
Alignment explanation
Indices: 8199--8290 Score: 87
Period size: 14 Copynumber: 7.3 Consensus size: 14
8189 GTAATTATTA
*
8199 TTAAATCATTAAAA
1 TTAAATCATTAAAG
8213 TTAAATCATTAAAG
1 TTAAATCATTAAAG
8227 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
8241 -T-AATTATT--A-
1 TTAAATCATTAAAG
8250 TTAAATCATTAAAG
1 TTAAATCATTAAAG
*
8264 -T-AATTATT--A-
1 TTAAATCATTAAAG
8273 TTAAATCATTAAAG
1 TTAAATCATTAAAG
8287 TTAA
1 TTAA
8291 TTATTATTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
10 4 0.06
11 12 0.19
12 12 0.19
13 4 0.06
14 31 0.49
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.40
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:8253 original size:23 final size:23
Alignment explanation
Indices: 8227--8299 Score: 137
Period size: 23 Copynumber: 3.1 Consensus size: 23
8217 ATCATTAAAG
8227 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
8250 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
8273 TTAAATCATTAAAGTTAATTATTA
1 TTAAATCATTAAAG-TAATTATTA
8297 TTA
1 TTA
8300 TCCATACTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 37 0.76
24 12 0.24
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAAATCATTAAAGTAATTATTA
Found at i:9247 original size:36 final size:36
Alignment explanation
Indices: 9200--9290 Score: 145
Period size: 36 Copynumber: 2.6 Consensus size: 36
9190 GATGAATGAT
9200 GCTGATGAAGAAGACGCCGAGAACTCCA-CCACCAAG
1 GCTGATGAAGAAGACGCCGAGAACTCCACCCA-CAAG
9236 GCTGATGAAGAAGACGCCGAGAACTCCACCCACAAG
1 GCTGATGAAGAAGACGCCGAGAACTCCACCCACAAG
9272 GC---TGAAGAAGACGCCGAGA
1 GCTGATGAAGAAGACGCCGAGA
9291 GATCCTGCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
33 17 0.31
36 34 0.63
37 3 0.06
ACGTcount: A:0.36, C:0.29, G:0.27, T:0.08
Consensus pattern (36 bp):
GCTGATGAAGAAGACGCCGAGAACTCCACCCACAAG
Found at i:9315 original size:26 final size:26
Alignment explanation
Indices: 9279--9374 Score: 165
Period size: 26 Copynumber: 3.7 Consensus size: 26
9269 AAGGCTGAAG
9279 AAGACGCCGAGAGATCCTGCATGCAC
1 AAGACGCCGAGAGATCCTGCATGCAC
* *
9305 AAGACGCCGAGAGATACTCCATGCAC
1 AAGACGCCGAGAGATCCTGCATGCAC
*
9331 AAGACGCCGAGAGATCCTGCATGCCC
1 AAGACGCCGAGAGATCCTGCATGCAC
9357 AAGACGCCGAGAGATCCT
1 AAGACGCCGAGAGATCCT
9375 TCTCTGCTCA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.31, C:0.31, G:0.26, T:0.11
Consensus pattern (26 bp):
AAGACGCCGAGAGATCCTGCATGCAC
Found at i:10198 original size:39 final size:39
Alignment explanation
Indices: 10144--10224 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
10134 ATTTCACACG
10144 TTTCTAATCATCTCATTAATGTTGGTCCATGCTCTACAA
1 TTTCTAATCATCTCATTAATGTTGGTCCATGCTCTACAA
10183 TTTCTAATCATCTCATTAATGTTGGTCCATGCTCTACAA
1 TTTCTAATCATCTCATTAATGTTGGTCCATGCTCTACAA
10222 TTT
1 TTT
10225 TCTGATGGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (39 bp):
TTTCTAATCATCTCATTAATGTTGGTCCATGCTCTACAA
Found at i:11840 original size:27 final size:27
Alignment explanation
Indices: 11807--11858 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
11797 AATTACGTGT
11807 AAACGTCGACGAATAGTAAAATTATTA
1 AAACGTCGACGAATAGTAAAATTATTA
11834 AAACGTCGACGAATAGTAAAATTAT
1 AAACGTCGACGAATAGTAAAATTAT
11859 ATGGGTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (27 bp):
AAACGTCGACGAATAGTAAAATTATTA
Found at i:13799 original size:12 final size:11
Alignment explanation
Indices: 13784--13862 Score: 54
Period size: 12 Copynumber: 7.0 Consensus size: 11
13774 TAATGAATAT
13784 TAAATTAAATAA
1 TAAATTAAA-AA
*
13796 TAAATTTAGAAA
1 TAAA-TTAAAAA
*
13808 TAAA-TAAAGA
1 TAAATTAAAAA
*
13818 TAAATTTAAAAT
1 TAAA-TTAAAAA
*
13830 TAAATT-AAAT
1 TAAATTAAAAA
*
13840 TAAATTATTAAA
1 TAAATTA-AAAA
*
13852 TAAAATAAAAA
1 TAAATTAAAAA
13863 ATATTTTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
10 18 0.34
11 5 0.09
12 26 0.49
13 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
TAAATTAAAAA
Found at i:13843 original size:22 final size:23
Alignment explanation
Indices: 13782--13845 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
13772 TGTAATGAAT
13782 ATTAAATTAAATAATAAATTTAGAA
1 ATTAAATTAAAT--TAAATTTAGAA
*
13807 A-TAAA-TAAAGATAAATTTA-AA
1 ATTAAATTAAA-TTAAATTTAGAA
13828 ATTAAATTAAATTAAATT
1 ATTAAATTAAATTAAATT
13846 ATTAAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
21 3 0.09
22 18 0.53
23 8 0.24
24 4 0.12
25 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (23 bp):
ATTAAATTAAATTAAATTTAGAA
Found at i:13860 original size:22 final size:20
Alignment explanation
Indices: 13783--13864 Score: 53
Period size: 22 Copynumber: 4.0 Consensus size: 20
13773 GTAATGAATA
*
13783 TTAAATTAAAT-AATAAATT
1 TTAAATAAAATAAATAAATT
*
13802 TAGAAAT-AAATAAAGATAAATT
1 T-TAAATAAAAT-AA-ATAAATT
* *
13824 TAAAATTAAATTAAATTAAATT
1 TTAAA-TAAAATAAA-TAAATT
13846 ATTAAATAAAATAAA-AAAT
1 -TTAAATAAAATAAATAAAT
13865 ATTTTTATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
19 5 0.10
20 8 0.16
21 5 0.10
22 25 0.50
23 7 0.14
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAATAAAATAAATAAATT
Found at i:16569 original size:17 final size:17
Alignment explanation
Indices: 16535--16571 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16525 AAACAAAAAA
*
16535 AAAATTAATTTAATGGT
1 AAAATTAATTTAAGGGT
*
16552 AAAATTAATTTTAGGGT
1 AAAATTAATTTAAGGGT
16569 AAA
1 AAA
16572 CTACTCCAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (17 bp):
AAAATTAATTTAAGGGT
Found at i:20519 original size:11 final size:11
Alignment explanation
Indices: 20482--20520 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
20472 AAACCAATGA
*
20482 TAAACGAACAC
1 TAAATGAACAC
* *
20493 TAAAAGAACAT
1 TAAATGAACAC
20504 TAAATGAACAC
1 TAAATGAACAC
20515 TAAATG
1 TAAATG
20521 GACGCTGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.18
Consensus pattern (11 bp):
TAAATGAACAC
Found at i:21894 original size:21 final size:22
Alignment explanation
Indices: 21870--21910 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21860 CATTTCAATT
21870 ATTAAATT-AAAAGAATAAAGG
1 ATTAAATTCAAAAGAATAAAGG
*
21891 ATTAAATTCAAAAGATTAAA
1 ATTAAATTCAAAAGAATAAA
21911 AGTAGAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (22 bp):
ATTAAATTCAAAAGAATAAAGG
Found at i:29821 original size:63 final size:64
Alignment explanation
Indices: 29691--29824 Score: 189
Period size: 63 Copynumber: 2.1 Consensus size: 64
29681 TAAACTACAC
* *
29691 ATTTAATTTACTACTTAAGGTTTTACTTTTTTTTTACATTTTAATACTTAAACTTTTAAAAAATT
1 ATTTAATTTACTACTTAAGGTTTTAC---TTTTATACATTTTAATACTTAAACTTTCAAAAAATT
29756 AT
63 AT
* * *
29758 ATTTAATTTAGTACTTAAGGTTTTAC-TTTATACATTTTAGTACTTAAACTTTCAAAAATTTAT
1 ATTTAATTTACTACTTAAGGTTTTACTTTTATACATTTTAATACTTAAACTTTCAAAAAATTAT
29821 ATTT
1 ATTT
29825 GAAATGGAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
63 37 0.60
67 25 0.40
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.52
Consensus pattern (64 bp):
ATTTAATTTACTACTTAAGGTTTTACTTTTATACATTTTAATACTTAAACTTTCAAAAAATTAT
Found at i:30329 original size:24 final size:23
Alignment explanation
Indices: 30286--30346 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 23
30276 AACAAATATC
*
30286 ATAAAT-TTAATTTTTAAAATAA
1 ATAAATATTAATTTATAAAATAA
* *
30308 ATTAATATTAAGTTTATAAAATAT
1 ATAAATATTAA-TTTATAAAATAA
*
30332 ATAAATATTTATTTA
1 ATAAATATTAATTTA
30347 ATTATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 5 0.16
23 8 0.25
24 19 0.59
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATAAATATTAATTTATAAAATAA
Found at i:31284 original size:28 final size:28
Alignment explanation
Indices: 31244--31309 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
31234 AATGGGAATT
31244 AATCTCTGCAAATCAATCCCTGCGTAAA
1 AATCTCTGCAAATCAATCCCTGCGTAAA
*
31272 AATCTCTGTAAATCAATCCCTGCGTAAA
1 AATCTCTGCAAATCAATCCCTGCGTAAA
31300 AATCTCTGCA
1 AATCTCTGCA
31310 TATAGACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (28 bp):
AATCTCTGCAAATCAATCCCTGCGTAAA
Found at i:31303 original size:14 final size:14
Alignment explanation
Indices: 31258--31308 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
31248 TCTGCAAATC
31258 AATCCCTGCGTAAA
1 AATCCCTGCGTAAA
*
31272 AATCTCT--GTAAA
1 AATCCCTGCGTAAA
31284 TCAATCCCTGCGTAAA
1 --AATCCCTGCGTAAA
*
31300 AATCTCTGC
1 AATCCCTGC
31309 ATATAGACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
12 5 0.17
14 20 0.67
16 5 0.17
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (14 bp):
AATCCCTGCGTAAA
Found at i:36035 original size:39 final size:39
Alignment explanation
Indices: 35966--36102 Score: 184
Period size: 39 Copynumber: 3.5 Consensus size: 39
35956 AACCAAAGCA
* * * * *
35966 GGACTTGCCACTCTTGACGCAGCAGAATGCTCATTATCC
1 GGACTTGCAACTCTCGATGCAGCAGGATGCTCATCATCC
*
36005 GGACTTGCAACTCTCGATGCAACAGGATGCTCATCATCC
1 GGACTTGCAACTCTCGATGCAGCAGGATGCTCATCATCC
* *
36044 GAACTTGCAGCTCTCGATGCAGCAGGATGCTCATCATCC
1 GGACTTGCAACTCTCGATGCAGCAGGATGCTCATCATCC
* *
36083 GGGCTTGCAGCTCTCGATGC
1 GGACTTGCAACTCTCGATGC
36103 TCCATCATGT
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (39 bp):
GGACTTGCAACTCTCGATGCAGCAGGATGCTCATCATCC
Found at i:43649 original size:16 final size:16
Alignment explanation
Indices: 43628--43662 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
43618 CAACAACTTT
43628 TACCTTATGATATCGA
1 TACCTTATGATATCGA
*
43644 TACCTTATGGTATCGA
1 TACCTTATGATATCGA
43660 TAC
1 TAC
43663 TGCTCATCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (16 bp):
TACCTTATGATATCGA
Found at i:46042 original size:2 final size:2
Alignment explanation
Indices: 46035--46060 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46025 TGCTAAACCG
46035 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
46061 GGAAATGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48474 original size:2 final size:2
Alignment explanation
Indices: 48467--48504 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
48457 AGCAGATAAT
48467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48505 CACACACATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48737 original size:4 final size:4
Alignment explanation
Indices: 48728--48764 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
48718 AGTACTTGTC
48728 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
48765 TATTAGGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:49391 original size:22 final size:23
Alignment explanation
Indices: 49348--49392 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
49338 TACGTGTTCG
49348 ATTCATCTAACATTTGTAAACAT
1 ATTCATCTAACATTTGTAAACAT
* *
49371 ATTCATTTAAC-TTTGTGAACAT
1 ATTCATCTAACATTTGTAAACAT
49393 GATAGCTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.42
Consensus pattern (23 bp):
ATTCATCTAACATTTGTAAACAT
Found at i:78902 original size:36 final size:36
Alignment explanation
Indices: 78830--78902 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
78820 TACTATAATT
**
78830 AATTTATATATTTATTTAAAAAATTTAAATTCATAA
1 AATTTATATATTTATTTAAAAAATTTAAAAACATAA
* * *
78866 AATTTATATAATTTTTTTACAAAA-TTAAAAAGATAA
1 AATTTATAT-ATTTATTTAAAAAATTTAAAAACATAA
78902 A
1 A
78903 TAGATTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 19 0.61
37 12 0.39
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (36 bp):
AATTTATATATTTATTTAAAAAATTTAAAAACATAA
Found at i:81732 original size:37 final size:38
Alignment explanation
Indices: 81646--81739 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
81636 TTTTCACCCT
**
81646 AAACCCGAACCCGACCCGACATGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACACAAATATCACACTTAAAA
* *
81685 AAACCCGACCCGACTCGACCCAAATATCACACTT-AAA
1 AAACCCGACCCGACCCGACACAAATATCACACTTAAAA
*
81722 AAACCCGACCCGAACCGA
1 AAACCCGACCCGACCCGA
81740 ATATTTGAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
37 19 0.39
38 23 0.47
39 7 0.14
ACGTcount: A:0.41, C:0.37, G:0.11, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACCCGACACAAATATCACACTTAAAA
Found at i:86187 original size:63 final size:64
Alignment explanation
Indices: 86119--86383 Score: 195
Period size: 63 Copynumber: 4.1 Consensus size: 64
86109 ATTTATATAT
*
86119 TATATATTTTTTTAAACATTTTGAAAATAATTATAATATATAGTTTTAAAATATTTTTAAAAATA
1 TATATATATTTTTAAACATTTTGAAAA-AATTATAATATATAGTTTTAAAATATTTTTAAAAATA
* ** * ** * * *
86184 TATATTATATTTTTAAACGTTTTGAAAATTTTATAGT-T-T--TTAAAAAAAAGTTTGAAAACAT
1 TATA-TATATTTTTAAACATTTTGAAAAAATTATAATATATAGTTTTAAAATATTTTTAAAA-AT
86245 A
64 A
* * * *
86246 TATTATATAGTTTTGAAATCATTTTG-AAAACTTAT-ATAATATAGTTTTAAAAACATTTTTTAA
1 TA-TATATA-TTTTTAAA-CATTTTGAAAAAATTATAAT-ATATAGTTTT-AAAATATTTTTAAA
*
86309 AA-C
61 AATA
* ** * * * *
86312 TACATA-ATTTGAAAACATTTTTAAAAAATTATAATATATACTTTTAAAATAATTTTGAAAATA
1 TATATATATTTTTAAACATTTTGAAAAAATTATAATATATAGTTTTAAAATATTTTTAAAAATA
86375 TATTATATA
1 TA-TATATA
86384 GATTTTTAGA
Statistics
Matches: 151, Mismatches: 33, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
61 14 0.09
62 29 0.19
63 42 0.28
64 14 0.09
65 15 0.10
66 23 0.15
67 3 0.02
68 11 0.07
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (64 bp):
TATATATATTTTTAAACATTTTGAAAAAATTATAATATATAGTTTTAAAATATTTTTAAAAATA
Found at i:86272 original size:34 final size:34
Alignment explanation
Indices: 86063--86304 Score: 146
Period size: 34 Copynumber: 7.1 Consensus size: 34
86053 ACAAATGGTT
* *
86063 TTTTGAAAAAATATATAAATATAGTTTTGAAAACA
1 TTTTGAAAACATATAT-AATATAGTTTTAAAAACA
* * **
86098 TGTTCGAAAACATTTATATATTATATATTTTTTTAAACA
1 T-TTTGAAAACA--TATATA--ATATAGTTTTAAAAACA
* *
86137 TTTTGAAAATA-ATTATAATATATAGTTTT-AAAATA
1 TTTTGAAAACATA-TAT-A-ATATAGTTTTAAAAACA
* * * *
86172 TTTTTAAAA-ATATATATTATA-TTTT-TAAACG
1 TTTTGAAAACATATATAATATAGTTTTAAAAACA
*
86203 TTTTG-AAA-AT-T-T--TATAGTTTTTAAAAAAAA
1 TTTTGAAAACATATATAATATAG-TTTT-AAAAACA
* * * *
86233 GTTTGAAAACATATATTATATAGTTTTGAAATCA
1 TTTTGAAAACATATATAATATAGTTTTAAAAACA
*
86267 TTTTGAAAACTTATATAATATAGTTTTAAAAACA
1 TTTTGAAAACATATATAATATAGTTTTAAAAACA
86301 TTTT
1 TTTT
86305 TTAAAACTAC
Statistics
Matches: 161, Mismatches: 28, Indels: 37
0.71 0.12 0.16
Matches are distributed among these distances:
26 4 0.02
28 5 0.03
29 1 0.01
30 12 0.07
31 14 0.09
32 6 0.04
33 2 0.01
34 42 0.26
35 19 0.12
36 26 0.16
37 2 0.01
38 13 0.08
39 15 0.09
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (34 bp):
TTTTGAAAACATATATAATATAGTTTTAAAAACA
Found at i:86319 original size:34 final size:34
Alignment explanation
Indices: 86215--86319 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
86205 TTGAAAATTT
* * * * *
86215 TATAGTTTTTAAAAAAAAGTTTGAAAACATATATTA
1 TATAG-TTTT-AAAAACATTTTGAAAACTTACATAA
* * *
86251 TATAGTTTTGAAATCATTTTGAAAACTTATATAA
1 TATAGTTTTAAAAACATTTTGAAAACTTACATAA
*
86285 TATAGTTTTAAAAACATTTTTTAAAAC-TACATAA
1 TATAGTTTTAAAAACA-TTTTGAAAACTTACATAA
86319 T
1 T
86320 TTGAAAACAT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
34 40 0.69
35 13 0.22
36 5 0.09
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.42
Consensus pattern (34 bp):
TATAGTTTTAAAAACATTTTGAAAACTTACATAA
Found at i:86391 original size:34 final size:33
Alignment explanation
Indices: 86113--86397 Score: 93
Period size: 34 Copynumber: 8.8 Consensus size: 33
86103 GAAAACATTT
* * *
86113 ATATATTATATA-TTTTTTTAAACATTTTGAAA
1 ATATATTATATAGATTTTTAAAAAATTTTGAAA
* * *
86145 ATA-ATTATAATATATAGTTTTAAAATATTTTTAAA
1 ATATATTAT-ATAGAT--TTTTAAAAAATTTTGAAA
* **
86180 A-ATA-TATATTATATTTTT-AAACGTTTTG-AA
1 ATATATTATA-TAGATTTTTAAAAAATTTTGAAA
*
86210 A-AT-TT-TATAG-TTTTTAAAAAAAAGTTTGAAAA
1 ATATATTATATAGATTTTT--AAAAAATTTTG-AAA
* **
86242 CATATATTATATAG-TTTTGAAATCATTTTGAAA
1 -ATATATTATATAGATTTTTAAAAAATTTTGAAA
* **
86275 ACTTATATAATATAG--TTTTAAAAACATTTT-TTA
1 A--TATATTATATAGATTTTTAAAAA-ATTTTGAAA
* * * * *
86308 A-A-ACTACATA-A-TTTGAAAACATTTTTAAA
1 ATATATTATATAGATTTTTAAAAAATTTTGAAA
* * * *
86337 AAATTATAATATATACTTTTAAAATAATTTTGAAA
1 ATA-TATTATATAGATTTTTAAAA-AATTTTGAAA
*
86372 ATATATTATATAGATTTTTAGAAAAT
1 ATATATTATATAGATTTTTAAAAAAT
86398 AGTTATATAT
Statistics
Matches: 187, Mismatches: 39, Indels: 53
0.67 0.14 0.19
Matches are distributed among these distances:
27 5 0.03
28 7 0.04
29 16 0.09
30 15 0.08
31 12 0.06
32 18 0.10
33 18 0.10
34 58 0.31
35 29 0.16
36 9 0.05
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (33 bp):
ATATATTATATAGATTTTTAAAAAATTTTGAAA
Found at i:86391 original size:97 final size:98
Alignment explanation
Indices: 86132--86396 Score: 242
Period size: 97 Copynumber: 2.7 Consensus size: 98
86122 ATATTTTTTT
* * *
86132 AAACATTTTGAAAATAATTATAATATATAGTTTTAAAATATTTTTAAAAATATA-TAT-TATATT
1 AAACATTTTGAAAA-AATTATAATATATAGTTTTAAAATAATTTTGAAAATATATTATATAGATT
* ** *
86195 TTT--AAACGTTTTGAAAATTTTATAGTTTTTAAA
65 TTTAAAAACGTTTTGAAAACTACATAG-ATTTAAA
* * * * * * *
86228 AAAAAGTTTGAAAACA-TATATTATATAGTTTTGAAATCATTTTGAAAACTTATATAATATAG--
1 AAACATTTTGAAAAAATTATAATATATAGTTTTAAAATAATTTTGAAAA--TATATTATATAGAT
* * *
86290 TTTTAAAAACATTTTTTAAAACTACATA-ATTT-GA
64 TTTTAAAAAC-GTTTTGAAAACTACATAGATTTAAA
* *
86324 AAACATTTTTAAAAAATTATAATATATACTTTTAAAATAATTTTGAAAATATATTATATAGATTT
1 AAACATTTTGAAAAAATTATAATATATAGTTTTAAAATAATTTTGAAAATATATTATATAGATTT
86389 TTAGAAAA
66 TTA-AAAA
86397 TAGTTATATA
Statistics
Matches: 132, Mismatches: 26, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
94 27 0.20
95 12 0.09
96 33 0.25
97 38 0.29
98 10 0.08
99 12 0.09
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (98 bp):
AAACATTTTGAAAAAATTATAATATATAGTTTTAAAATAATTTTGAAAATATATTATATAGATTT
TTAAAAACGTTTTGAAAACTACATAGATTTAAA
Found at i:87374 original size:31 final size:31
Alignment explanation
Indices: 87351--87516 Score: 281
Period size: 31 Copynumber: 5.5 Consensus size: 31
87341 CATAGATTCT
*
87351 GAAGAACCTAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
87382 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
87413 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
87444 GAAG-ACATAGGT-AA-AGTCCATATGT-CC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
87471 G-A-AACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
87500 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
87517 CCTCGACCCT
Statistics
Matches: 128, Mismatches: 1, Indels: 12
0.91 0.01 0.09
Matches are distributed among these distances:
26 9 0.07
27 5 0.04
28 22 0.17
29 5 0.04
30 9 0.07
31 78 0.61
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:88287 original size:64 final size:63
Alignment explanation
Indices: 88158--88381 Score: 242
Period size: 64 Copynumber: 3.5 Consensus size: 63
88148 TAATGAAGGT
* ** **
88158 ATGCATCGATGCACTACTGATGCATCTG-TGCA--AAAAGCATTCGATGTTGTATTATTGCTGAG
1 ATGCATCGATGCACTACTTATGCATC-GATGCACCAATTGCATTCGATGTT-TATTATTAATGAG
* *
88220 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTT-ATTATTAATGAG
** *
88284 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATG--TTTATTATTAATGAG
** *
88347 AGTGCATCGATGCACTACCAATGCATCGATACACC
1 A-TGCATCGATGCACTACTTATGCATCGATGCACC
88382 TTCAAACAAA
Statistics
Matches: 138, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
61 1 0.01
62 28 0.20
63 3 0.02
64 100 0.72
65 3 0.02
66 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTATTATTAATGAG
Done.