Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009168.1 Hibiscus syriacus cultivar Beakdansim tig00112715_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: 73156
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1560 original size:20 final size:20
Alignment explanation
Indices: 1535--1602 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1525 ATTGTTCATG
1535 CAATATCGATACTATTAGAA
1 CAATATCGATACTATTAGAA
* * * *
1555 CAATATCGTTATTGCTCATG--
1 CAATATCGATACT-ATTA-GAA
*
1575 CAGTATCGATACTATTAGAA
1 CAATATCGATACTATTAGAA
1595 CAATATCG
1 CAATATCG
1603 TGCTACTTAC
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 28 0.82
21 2 0.06
22 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (20 bp):
CAATATCGATACTATTAGAA
Found at i:1582 original size:40 final size:40
Alignment explanation
Indices: 1512--1603 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
1502 CGGTACTGCA
*
1512 AGAACAATATCG-TATTGTTCATGCAATATCGATACTATT
1 AGAACAATATCGTTATTGCTCATGCAATATCGATACTATT
*
1551 AGAACAATATCGTTATTGCTCATGCAGTATCGATACTATT
1 AGAACAATATCGTTATTGCTCATGCAATATCGATACTATT
1591 AGAACAATATCGT
1 AGAACAATATCGT
1604 GCTACTTACC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 12 0.24
40 38 0.76
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (40 bp):
AGAACAATATCGTTATTGCTCATGCAATATCGATACTATT
Found at i:2232 original size:2 final size:2
Alignment explanation
Indices: 2225--2289 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
2215 ACATGCGTGG
*
2225 AT AT AT AT AT AT AT AT CT 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 AT AT AT
*
2267 AT CT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
2290 GACATATTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10772 original size:182 final size:181
Alignment explanation
Indices: 10465--10895 Score: 596
Period size: 182 Copynumber: 2.4 Consensus size: 181
10455 TGTCGGTTTA
* * *
10465 TGTCGATACTTTATAA-AACTGTATCGATCCACATCAATATAACAGGTAAAAATATGACAAAATC
1 TGTCGATACTTTATAACAA-TGTATCGATCCACAACGATATAACA-GTAAAAATATGACAAAACC
* * *
10529 AGTCTCGAAAAGACAAAACCAATAAAGCGGTACCGAATATATTGAAAGTGTCGATACTTTAATAT
64 GGTCTCGAAAAGACAAAACCAATAAAGCCGTACCGAATATATTGAAAGTGTCGATACTTTAATAC
* *
10594 AAGTATCGACACTTTGTGAAATTAAAAGAGAATCAGTTTTAGAGTCTATAAAG
129 AAGTATCGACACTTTGTGAAATTAAAAGAGAAGCAGTTTTAGAGCCTATAAAG
* * * *
10647 TGTCGATACTTTATAACAATGTATCGATCCAAAACGATATAATATGTACAAATATGACTAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACA-GTAAAAATATGACAAAACCG
* * ** * * *
10712 GTCTCTAAAGGACAAAACCCGTATAGACCG-ATCGGATATATTGAAAGTGTCGATACTTTAATAC
65 GTCTCGAAAAGACAAAACCAATAAAG-CCGTACCGAATATATTGAAAGTGTCGATACTTTAATAC
* * *
10776 AAGTATCGACATTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
129 AAGTATCGACACTTTGTGAAATTAAAAGAGAAGCAGTTTTAGAGCCTATAAAG
*
10829 TGTCGATACTTTATAACAATTTATCGATCCACAACGATATAACAGTTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAG-TAAAAATATGACAAAACCG
10894 GT
65 GT
10896 ATAGAGCGAC
Statistics
Matches: 218, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
181 1 0.00
182 213 0.98
183 4 0.02
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (181 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGTAAAAATATGACAAAACCGG
TCTCGAAAAGACAAAACCAATAAAGCCGTACCGAATATATTGAAAGTGTCGATACTTTAATACAA
GTATCGACACTTTGTGAAATTAAAAGAGAAGCAGTTTTAGAGCCTATAAAG
Found at i:10991 original size:162 final size:162
Alignment explanation
Indices: 10722--11219 Score: 800
Period size: 162 Copynumber: 3.1 Consensus size: 162
10712 GTCTCTAAAG
* * * *
10722 GACAAAACCCGTATAGACCGATCGGATATATTGAAAGTGTCGATACTTTAATACAAGTATCGACA
1 GACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
* *
10787 TTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATTTA
66 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTA
*
10852 TCGATCCACAACGATATAACAGTTAAAAATAT
131 TCGATCCACAACGATATAACAGGTAAAAATAT
*
10884 GACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
1 GACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
** * *
10949 CTTTGTGAATTTAAAAGAGAAATAGTTTTAGCGCCCATAAAGTGACGATACTTTATAACAATGTA
66 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTA
*
11014 TCGATCCAAAACGATATAACAGGTAAAAATAT
131 TCGATCCACAACGATATAACAGGTAAAAATAT
* * * * *
11046 GACAAAACCGGTATAGAGCGACTGGATATATTTAAAGTGTCGATACATTAATATAAGTATTGAGA
1 GACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
*
11111 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCTCCTATAAAGTGTCGATACTTTATAACAATGTA
66 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTA
*
11176 TC-AGTCCACAACAATATAACAGGTAAAAATAT
131 TCGA-TCCACAACGATATAACAGGTAAAAATAT
11208 GACAAAACCGGT
1 GACAAAACCGGT
11220 CTCAAAATGA
Statistics
Matches: 309, Mismatches: 26, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
161 1 0.00
162 308 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (162 bp):
GACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTA
TCGATCCACAACGATATAACAGGTAAAAATAT
Found at i:13285 original size:21 final size:23
Alignment explanation
Indices: 13237--13289 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
13227 TTTTGTTTTT
*
13237 TTTA-TATATAAAATGATAGTATA
1 TTTATTATATAAAAT-ATAGTAAA
13260 TTTATTATATAAAAT-TA-TAAA
1 TTTATTATATAAAATATAGTAAA
13281 TTTATTATA
1 TTTATTATA
13290 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 12 0.43
22 2 0.07
23 4 0.14
24 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTATTATATAAAATATAGTAAA
Found at i:13690 original size:21 final size:21
Alignment explanation
Indices: 13666--13709 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
13656 AAGACAATCA
13666 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
13687 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
13708 AG
1 AG
13710 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:13784 original size:33 final size:33
Alignment explanation
Indices: 13747--13842 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
13737 AGATGGAGTG
* * *
13747 GTGAAAGAAGTTAAGGTGTTGAGGGATGAATTA
1 GTGAAAGAAGTTGAGGTGTTGAGGGGTGAAGTA
13780 GTGAAAGAAGTTGAGGTGTTGAGGGGTGAAGTA
1 GTGAAAGAAGTTGAGGTGTTGAGGGGTGAAGTA
*
13813 GTGAAAGAATTTGAGGTGTTGAGGGGTGAA
1 GTGAAAGAAGTTGAGGTGTTGAGGGGTGAA
13843 CTTAAGATGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.32, C:0.00, G:0.42, T:0.26
Consensus pattern (33 bp):
GTGAAAGAAGTTGAGGTGTTGAGGGGTGAAGTA
Found at i:14049 original size:18 final size:18
Alignment explanation
Indices: 14026--14064 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
14016 GAAAAAATAT
* * *
14026 GAAGAATAAAATATGGAG
1 GAAGAAGAAAAGATAGAG
14044 GAAGAAGAAAAGATAGAG
1 GAAGAAGAAAAGATAGAG
14062 GAA
1 GAA
14065 ATGAGGAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.31, T:0.10
Consensus pattern (18 bp):
GAAGAAGAAAAGATAGAG
Found at i:15644 original size:19 final size:19
Alignment explanation
Indices: 15620--15668 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
15610 AATGTAGGGT
15620 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
15639 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
15658 TAATTTTGTAT
1 TAATTTTGTAT
15669 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:16002 original size:15 final size:15
Alignment explanation
Indices: 15979--16011 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
15969 GTCCAGTATG
*
15979 GTTCTCAAACGTAAA
1 GTTCCCAAACGTAAA
15994 GTTCCCAAACGTAAA
1 GTTCCCAAACGTAAA
16009 GTT
1 GTT
16012 TCCATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (15 bp):
GTTCCCAAACGTAAA
Found at i:16515 original size:200 final size:198
Alignment explanation
Indices: 16034--16613 Score: 817
Period size: 200 Copynumber: 2.9 Consensus size: 198
16024 GTAAGCAGAT
* * **
16034 GTGTCGATACATTTATAAAAAGTATCGATCTCAAAAACATTAAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* **
16099 GGTAATTTTGTAAT-TAACCGGCATAAAAATACCGATTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTT-TAATGTAACCGGTATAACTATACCGATTTTATGTGAGAATAGGTCTACATAATGT
* * **
16163 ATCGACACTTTTGAAATTAGTTTCGATACTTTTTGTCCAGAATGAAT-CCCAAAATGGTAAACGC
130 ATCGACAC-TTTGAAATTAGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTAAACAA
16227 ATAAA
194 ATAAA
* *
16232 GTGTCGATACGTTTATAAAAAGTATCGATTCCAGAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
*
16297 GGTAATTTTTCAATGTAACCGGTATAACTATACC-AGTTTTATGAGAGAATAGGTCTACATAATG
66 GGTAATTTTT-AATGTAACCGGTATAACTATACCGA-TTTTATGTGAGAATAGGTCTACATAATG
* * * * **
16361 TATCGACACTTATGGAATTTGTGTCGATACTGTTTGTCCAGAAGGAATGCCCAAAAGGGTGCACA
129 TATCGACACTT-TGAAATTAGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTAAACA
*
16426 AATGAA
193 AATAAA
* * * * *
16432 GTGTCGATACATTTTTTAAAAGTGTCGATCCCAGAGACATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
16497 GGTAATTTTATAATGTAACCGGTAT-ACATATACCGATTTTATGTGAGAATAGGTCTACATAATG
66 GGTAATTTT-TAATGTAACCGGTATAAC-TATACCGATTTTATGTGAGAATAGGTCTACATAATG
*
16561 TATCGACACGTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCCA
129 TATCGACAC-TTTGAAATTAGTGTCGATACTTTTTGTCCAGAATGAATGCCCA
16614 GATTCTGGTA
Statistics
Matches: 340, Mismatches: 33, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
197 1 0.00
198 74 0.22
199 85 0.25
200 176 0.52
201 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (198 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTAATGTAACCGGTATAACTATACCGATTTTATGTGAGAATAGGTCTACATAATGTA
TCGACACTTTGAAATTAGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTAAACAAAT
AAA
Found at i:19279 original size:31 final size:31
Alignment explanation
Indices: 19241--19315 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
19231 AAGTGAGATT
19241 TGGTAGGTTGCATAAGCTTGAAGCATGTTCG
1 TGGTAGGTTGCATAAGCTTGAAGCATGTTCG
19272 TGGTAGGTTGCATAAGCTTGAAGCATGTTCG
1 TGGTAGGTTGCATAAGCTTGAAGCATGTTCG
*
19303 TGGTAGATTGCAT
1 TGGTAGGTTGCAT
19316 CGTTTGAGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.23, C:0.12, G:0.32, T:0.33
Consensus pattern (31 bp):
TGGTAGGTTGCATAAGCTTGAAGCATGTTCG
Found at i:22639 original size:26 final size:25
Alignment explanation
Indices: 22600--22649 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
22590 TTAGCATATT
22600 AAAAATAAAACTTGAAAA-TAAAAG
1 AAAAATAAAACTTGAAAAGTAAAAG
22624 AAAAATGAAGAACTTGAAAAGTAAAA
1 AAAAAT-AA-AACTTGAAAAGTAAAA
22650 AGAGAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
26 10 0.43
27 5 0.22
ACGTcount: A:0.68, C:0.04, G:0.12, T:0.16
Consensus pattern (25 bp):
AAAAATAAAACTTGAAAAGTAAAAG
Found at i:22930 original size:27 final size:26
Alignment explanation
Indices: 22899--22961 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
22889 ATGTCTTTTT
*
22899 TTTTCTCTATTTTTCGAACAAC-ATCT
1 TTTTCTCT-TTTTTCGAACAACTATCA
*
22925 TCTTTCTTTCTTTTTTCGAATAACTATCA
1 T-TTTC--TCTTTTTTCGAACAACTATCA
22954 TTTTCTCT
1 TTTTCTCT
22962 CTCTCTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
26 4 0.13
27 4 0.13
28 16 0.52
29 7 0.23
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.56
Consensus pattern (26 bp):
TTTTCTCTTTTTTCGAACAACTATCA
Found at i:27357 original size:19 final size:20
Alignment explanation
Indices: 27335--27375 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
27325 TTTAAATAGT
*
27335 AATAAAAATGATTAAA-TAA
1 AATAAAAATAATTAAAGTAA
*
27354 AATAAAAGTAATTAAAGTAA
1 AATAAAAATAATTAAAGTAA
27374 AA
1 AA
27376 ATAAGAGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
AATAAAAATAATTAAAGTAA
Found at i:29686 original size:14 final size:14
Alignment explanation
Indices: 29667--29694 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29657 CCTCTAAATC
29667 ACCATGCAAAAAAG
1 ACCATGCAAAAAAG
29681 ACCATGCAAAAAAG
1 ACCATGCAAAAAAG
29695 CAGTTTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.21, G:0.14, T:0.07
Consensus pattern (14 bp):
ACCATGCAAAAAAG
Found at i:46047 original size:40 final size:38
Alignment explanation
Indices: 45922--46047 Score: 129
Period size: 40 Copynumber: 3.4 Consensus size: 38
45912 TATAAGTTTT
* *
45922 AAAACATTTTGAAAATTATATAGTATATAGTTTT---G
1 AAAACATTTTGAAAATTATATAATATATAGTTTTAAAA
* *
45957 AAATCATTTTG-AAA--ATATAATATATAATTTTAAAA
1 AAAACATTTTGAAAATTATATAATATATAGTTTTAAAA
**
45992 AAATATTTTTTGAAAATTTATATAATATATAGTTTTAAAA
1 AAA-ACATTTTGAAAA-TTATATAATATATAGTTTTAAAA
46032 AAAACATTTTGGAAAA
1 AAAACATTTT-GAAAA
46048 CATATATTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
32 15 0.21
34 3 0.04
35 13 0.18
36 5 0.07
37 3 0.04
39 5 0.07
40 28 0.39
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (38 bp):
AAAACATTTTGAAAATTATATAATATATAGTTTTAAAA
Found at i:46120 original size:67 final size:67
Alignment explanation
Indices: 45908--46137 Score: 222
Period size: 67 Copynumber: 3.4 Consensus size: 67
45898 TCTTATATAC
* * * *
45908 AATATATAAGTTTT-AAAACA-TTTTGAAAATTATATAGTATATAGTTTTGAAATCATTTTGAAA
1 AATATATAA-TTTTAAAAATATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTT-TAA
45971 ATAT
64 ATAT
*
45975 AATATATAATTTTAAAAAAATATTTTTTGAAAATTTATATAATATATAGTTTTAAAAAAAACATT
1 AATATATAATTTT--AAAAATA-TTTTTGAAAA-TTATATAATATATAGTTTT---GAAAACATT
*
46040 TTGGAAA-A-
59 TT-TAAATAT
* *
46048 CATATAT--TTTT-AAAATCATTTTTGAAAACTATATAATATATAGTTTTGAAAACATTTTTAAA
1 AATATATAATTTTAAAAAT-ATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTTAAA
46110 TAT
65 TAT
* *
46113 AATATATAGTTTAAAAAATATTTTT
1 AATATATAATTTTAAAAATATTTTT
46138 TTTGAAACAT
Statistics
Matches: 137, Mismatches: 11, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
63 3 0.02
64 11 0.08
65 6 0.04
66 4 0.03
67 36 0.26
68 20 0.15
69 6 0.04
71 13 0.09
72 18 0.13
73 6 0.04
74 1 0.01
75 13 0.09
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (67 bp):
AATATATAATTTTAAAAATATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTTAAAT
AT
Found at i:46136 original size:31 final size:31
Alignment explanation
Indices: 46078--46137 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
46068 TTTGAAAACT
**
46078 ATATAATATATAGTTTTGAAAACATTTTTAA
1 ATATAATATATAGTTTAAAAAACATTTTTAA
*
46109 ATATAATATATAGTTTAAAAAATATTTTT
1 ATATAATATATAGTTTAAAAAACATTTTT
46138 TTTGAAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (31 bp):
ATATAATATATAGTTTAAAAAACATTTTTAA
Found at i:46217 original size:5 final size:5
Alignment explanation
Indices: 46178--46245 Score: 50
Period size: 5 Copynumber: 14.0 Consensus size: 5
46168 TATTATTATT
* * * * *
46178 ATTT- ATTTT ATTTC ATTTA ATTTC ATTTT A-TTA ATCTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
* * *
46226 ATTTA GTTTC ATTTA TTTTA
1 ATTTA ATTTA ATTTA ATTTA
46246 CTTTTGTCAG
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
4 7 0.14
5 43 0.86
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.63
Consensus pattern (5 bp):
ATTTA
Found at i:47024 original size:9 final size:9
Alignment explanation
Indices: 47012--47045 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
47002 ACAGTAAAAA
47012 AAAATAAAT
1 AAAATAAAT
47021 AAAATAAAT
1 AAAATAAAT
47030 AAAATAAAT
1 AAAATAAAT
47039 AAAATAA
1 AAAATAA
47046 GAAGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATAAAT
Found at i:47025 original size:5 final size:5
Alignment explanation
Indices: 47006--47056 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
46996 GTAAAGACAG
* *
47006 TAAAA AAAAA T-AAA TAAAA T-AAA TAAAA T-AAA TAAAA TAAGAA GAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA TAAAA
47054 TAA
1 TAA
47057 TCATCACGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 12 0.32
5 22 0.58
6 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:50621 original size:18 final size:18
Alignment explanation
Indices: 50598--50639 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
50588 ATGTCCATAA
50598 CATCGGGTCCAAAACCAC
1 CATCGGGTCCAAAACCAC
50616 CATCGGGTCCAAAACCAC
1 CATCGGGTCCAAAACCAC
50634 CATCGG
1 CATCGG
50640 TTTCCTCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.31, C:0.38, G:0.19, T:0.12
Consensus pattern (18 bp):
CATCGGGTCCAAAACCAC
Found at i:59547 original size:2 final size:2
Alignment explanation
Indices: 59542--59587 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
59532 TTTTTCATTC
*
59542 AT AT AT AT AT AT AT AC 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 AT AT AT
59584 AT AT
1 AT AT
59588 TAACTTTAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62677 original size:21 final size:21
Alignment explanation
Indices: 62653--62694 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
62643 AAATCTAATT
*
62653 ATTTTTTCTTT-TCCAAATATC
1 ATTTTTTATTTAT-CAAATATC
62674 ATTTTTTATTTATCAAATATC
1 ATTTTTTATTTATCAAATATC
62695 CTTTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTTATTTATCAAATATC
Found at i:68909 original size:15 final size:15
Alignment explanation
Indices: 68891--68941 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
68881 GTTTAGGGAC
68891 CAAAAGTGTAAATTT
1 CAAAAGTGTAAATTT
* ***
68906 CAAAAGT-TCAAGGA
1 CAAAAGTGTAAATTT
*
68920 CCAAAGTGTAAATTT
1 CAAAAGTGTAAATTT
68935 CAAAAGT
1 CAAAAGT
68942 ATGTATTTTA
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (15 bp):
CAAAAGTGTAAATTT
Found at i:68935 original size:29 final size:29
Alignment explanation
Indices: 68859--68941 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
68849 AGTTTAGTAG
* * * *
68859 CCAAAGTATAAAGTTTGGAAAAGTTTAGGGA
1 CCAAAGTGTAAA-TTT-CAAAAGTTCAAGGA
68890 CCAAAAGTGTAAATTTCAAAAGTTCAAGGA
1 CC-AAAGTGTAAATTTCAAAAGTTCAAGGA
68920 CCAAAGTGTAAATTTCAAAAGT
1 CCAAAGTGTAAATTTCAAAAGT
68942 ATGTATTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 20 0.43
30 13 0.28
31 5 0.11
32 9 0.19
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (29 bp):
CCAAAGTGTAAATTTCAAAAGTTCAAGGA
Found at i:71738 original size:175 final size:175
Alignment explanation
Indices: 71409--71754 Score: 489
Period size: 175 Copynumber: 2.0 Consensus size: 175
71399 AGTATGATGA
* * * * * * *
71409 TTATCGATCGATTTGGTTTGATTCATTATTTCGTTCTTGTAGTAGTACATTTTTTTTACTATGGC
1 TTATCGATCGATTTGGTTTAATGCATTATTGCGTTCTTGTAGTAGTACATTTGTTGTACCATAGC
* * * *
71474 ACTATGTGTGCTAGGATGGGTTCATAATGAATTACCACTCTGTAATTGTTAGTTAGTGTCGTTGT
66 ACTATGTGTGCAAGGATGGGTTCATAATGAATTACCACTATGGAATTGTTAGTTAGAGTCGTTGT
* * *
71539 GTACTACAATTCCTATATGTCATTGTAGCACTTAAGTACTACATG
131 GGACTACAATACCTATACGTCATTGTAGCACTTAAGTACTACATG
* * *
71584 TTATCTATCGATTT-GTTTAATGCATTATTGCGTTTTTGTAGTAGTATATTTGTTGTACCATAGC
1 TTATCGATCGATTTGGTTTAATGCATTATTGCGTTCTTGTAGTAGTACATTTGTTGTACCATAGC
*
71648 ACTATGTGTGCAAGGATGGTGTTCATAATGAATTACCATTATGGAATTGTTAGTATAGAGTCGTT
66 ACTATGTGTGCAAGGATGG-GTTCATAATGAATTACCACTATGGAATTGTTAGT-TAGAGTCGTT
*
71713 GTGGACTA-AATACCTATACGTCATTGTAGCACTTAGGTACTA
129 GTGGACTACAATACCTATACGTCATTGTAGCACTTAAGTACTA
71755 ATTGTGTACC
Statistics
Matches: 150, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
174 59 0.39
175 75 0.50
176 16 0.11
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (175 bp):
TTATCGATCGATTTGGTTTAATGCATTATTGCGTTCTTGTAGTAGTACATTTGTTGTACCATAGC
ACTATGTGTGCAAGGATGGGTTCATAATGAATTACCACTATGGAATTGTTAGTTAGAGTCGTTGT
GGACTACAATACCTATACGTCATTGTAGCACTTAAGTACTACATG
Done.