Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002036.1 Hibiscus syriacus cultivar Beakdansim tig00004151_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: 85332
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1689 original size:30 final size:30
Alignment explanation
Indices: 1612--1697 Score: 122
Period size: 28 Copynumber: 2.9 Consensus size: 30
1602 AGTTGTTGTG
* *
1612 AGTTGTTTATGTCTCCCAAATGCTCCACCA
1 AGTTGTATATGTCTTCCAAATGCTCCACCA
* *
1642 AGCTGTATATG--TTCCAAATGCTCCACTA
1 AGTTGTATATGTCTTCCAAATGCTCCACCA
1670 AGTTGTATATGTCTTCCAAATGCTCCAC
1 AGTTGTATATGTCTTCCAAATGCTCCAC
1698 AAGCTGTCCC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 25 0.51
30 24 0.49
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.34
Consensus pattern (30 bp):
AGTTGTATATGTCTTCCAAATGCTCCACCA
Found at i:5052 original size:31 final size:30
Alignment explanation
Indices: 4997--5116 Score: 168
Period size: 30 Copynumber: 4.0 Consensus size: 30
4987 GTGAGATGTT
* *
4997 TATGTCTCCCAAATGCTCCACTAAGCTGTA
1 TATGTCTTCCAAATGCTCCACTAAGTTGTA
*
5027 AATGTCTTCCAAATGCTCCCACTAAGTTGTA
1 TATGTCTTCCAAATGCT-CCACTAAGTTGTA
* *
5058 TATGTCTTCCAAATTCTCCAGTAAGTTGTA
1 TATGTCTTCCAAATGCTCCACTAAGTTGTA
* *
5088 TATGTCTTCCGAATGCTCCACCAAGTTGT
1 TATGTCTTCCAAATGCTCCACTAAGTTGT
5117 CCCAACGTGT
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 52 0.66
31 27 0.34
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (30 bp):
TATGTCTTCCAAATGCTCCACTAAGTTGTA
Found at i:5093 original size:61 final size:60
Alignment explanation
Indices: 4997--5116 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 60
4987 GTGAGATGTT
*
4997 TATGTCTCCCAAATGCTCCACTAAGCTGTAAATGTCTTCCAAATGCTCCCACTAAGTTGTA
1 TATGTCTCCCAAATGCTCCACTAAGCTGTAAATGTCTTCCAAATGCT-CCACCAAGTTGTA
* * * * * *
5058 TATGTCTTCCAAATTCTCCAGTAAGTTGTATATGTCTTCCGAATGCTCCACCAAGTTGT
1 TATGTCTCCCAAATGCTCCACTAAGCTGTAAATGTCTTCCAAATGCTCCACCAAGTTGT
5117 CCCAACGTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
60 11 0.21
61 41 0.79
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (60 bp):
TATGTCTCCCAAATGCTCCACTAAGCTGTAAATGTCTTCCAAATGCTCCACCAAGTTGTA
Found at i:8693 original size:46 final size:43
Alignment explanation
Indices: 8579--8697 Score: 130
Period size: 46 Copynumber: 2.7 Consensus size: 43
8569 ACCTTCACTC
*
8579 ATTCATCACATAAGGAGTTGGATCAACATCATTGTTTCGTTTG
1 ATTCATCACATAAGGAGTTGGATCAACATCATTGTTTCGCTTG
* * * * * *
8622 ATTCCATCAAAAAAGGAGTTAGATCAGCATCACTCTTTTTTGCTTG
1 ATT-CATCACATAAGGAGTTGGATCAACATCA-T-TGTTTCGCTTG
*
8668 ATTCTATCACATAAGAAGTTGGATCAACAT
1 ATTC-ATCACATAAGGAGTTGGATCAACAT
8698 ATCTCGCTCG
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
43 3 0.05
44 24 0.40
45 2 0.03
46 31 0.52
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (43 bp):
ATTCATCACATAAGGAGTTGGATCAACATCATTGTTTCGCTTG
Found at i:9848 original size:270 final size:270
Alignment explanation
Indices: 9360--9897 Score: 986
Period size: 270 Copynumber: 2.0 Consensus size: 270
9350 CCGTGGCTCA
9360 TCCATCATGTAAGGAGTTGAATCAGTATTTCCAATGAGAATTTCATAATGAGAAGAACTTGTTCG
1 TCCATCATGTAAGGAGTTGAATCAGTATTTCCAATGAGAATTTCATAATGAGAAGAACTTGTTCG
* * * *
9425 ACCTTTTGTTCAAATCTATCATAGAAGGAGATGGATTAATATTTTTAATAGAGGGTTCATAATGA
66 ACCTTTTGTTCAAATCCATCACAGAAGGAGATGGATCAATATTTTCAATAGAGGGTTCATAATGA
9490 TAAGAATTCATCCGATAAGGAAGAAGAAGTCCATATAGGAAAACCTATTCAGCCTTTGGATCAAA
131 TAAGAATTCATCCGATAAGGAAGAAGAAGTCCATATAGGAAAACCTATTCAGCCTTTGGATCAAA
* *
9555 CCCATCACAGAAGAAGGTGGGTCTCCATATCAACATTTCTAGTAGGGGAGTTCATAATAAGAAGA
196 CCCATCACAGAAGAAGATGGGTCTCCATATCAACATTTCTAGTAGAGGAGTTCATAATAAGAAGA
9620 ACTTGTCTCG
261 ACTTGTCTCG
*
9630 TCCATCATGTAAGGAGTTGGATCAGTATTTCCAATGAGAATTTCATAATGAGAAGAACTTGTTCG
1 TCCATCATGTAAGGAGTTGAATCAGTATTTCCAATGAGAATTTCATAATGAGAAGAACTTGTTCG
9695 ACCTTTTGTTCAAATCCATCACAGAAGGAGATGGATCAATATTTTCAATAGAGGGTTCATAATGA
66 ACCTTTTGTTCAAATCCATCACAGAAGGAGATGGATCAATATTTTCAATAGAGGGTTCATAATGA
* *
9760 TAAGAATTCATCCGATGAGGAAGAAGAAGTCCATATAGGAAGACCTATTCAGCCTTTGGATCAAA
131 TAAGAATTCATCCGATAAGGAAGAAGAAGTCCATATAGGAAAACCTATTCAGCCTTTGGATCAAA
*
9825 CCCATCACAGAAGAATATGGGTCTCCATATCAACATTTCTAGTAGAGGAGTTCATAATAAGAAGA
196 CCCATCACAGAAGAAGATGGGTCTCCATATCAACATTTCTAGTAGAGGAGTTCATAATAAGAAGA
9890 ACTTGTCT
261 ACTTGTCT
9898 AGAAAAGAAA
Statistics
Matches: 258, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
270 258 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (270 bp):
TCCATCATGTAAGGAGTTGAATCAGTATTTCCAATGAGAATTTCATAATGAGAAGAACTTGTTCG
ACCTTTTGTTCAAATCCATCACAGAAGGAGATGGATCAATATTTTCAATAGAGGGTTCATAATGA
TAAGAATTCATCCGATAAGGAAGAAGAAGTCCATATAGGAAAACCTATTCAGCCTTTGGATCAAA
CCCATCACAGAAGAAGATGGGTCTCCATATCAACATTTCTAGTAGAGGAGTTCATAATAAGAAGA
ACTTGTCTCG
Found at i:12646 original size:4 final size:4
Alignment explanation
Indices: 12637--14962 Score: 4471
Period size: 4 Copynumber: 586.8 Consensus size: 4
12627 GATTTTCTTT
12637 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12685 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12733 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12781 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12829 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12877 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12923 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12971 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13019 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13067 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13115 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13163 TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13210 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13258 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13304 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13352 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13400 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13448 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13496 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13544 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13592 TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13638 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13686 TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13732 TATG TATG TATG TATG TA-- TATG TATG TATG TA-G TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13777 TATG TATG TATG TTATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG -TATG TATG TATG TATG TATG TATG TATG TATG TATG
13826 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13874 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13922 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13970 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14018 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14066 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14114 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14162 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14210 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14258 TATG TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14304 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14352 TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14398 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14446 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14494 TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14540 TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14586 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14634 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14682 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14728 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
14776 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
14824 TGTG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14872 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
14920 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
14963 TTTCGATTCA
Statistics
Matches: 2295, Mismatches: 4, Indels: 46
0.98 0.00 0.02
Matches are distributed among these distances:
2 20 0.01
3 6 0.00
4 2265 0.99
5 4 0.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:22620 original size:4 final size:4
Alignment explanation
Indices: 22611--22846 Score: 449
Period size: 4 Copynumber: 59.5 Consensus size: 4
22601 AAAATCATTT
*
22611 TATG TATG TATG TA-- TATA TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
22657 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
22705 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
22753 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
22801 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
22847 CGTGTACGTA
Statistics
Matches: 229, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.01
4 227 0.99
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:22854 original size:6 final size:6
Alignment explanation
Indices: 22843--22939 Score: 185
Period size: 6 Copynumber: 16.2 Consensus size: 6
22833 TATGTATGTA
*
22843 TGTACG TGTACG TATACG TGTACG TGTACG TGTACG TGTACG TGTACG
1 TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG
22891 TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG
1 TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG TGTACG
22939 T
1 T
22940 ATATATGTAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (6 bp):
TGTACG
Found at i:23489 original size:2 final size:2
Alignment explanation
Indices: 23482--23508 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23472 CAAAGTTTTG
23482 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
23509 ACTTGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23745 original size:22 final size:22
Alignment explanation
Indices: 23688--23746 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
23678 ACGCGATTCT
23688 GACTATCGCATTGCGATTTTTC
1 GACTATCGCATTGCGATTTTTC
* * *
23710 AAAT-TCGCGTTGCGATTTTTC
1 GACTATCGCATTGCGATTTTTC
*
23731 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
23747 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTTC
Found at i:23778 original size:20 final size:20
Alignment explanation
Indices: 23731--23822 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
23721 GCGATTTTTC
* *
23731 GACTATCGCAATGCGAATAT
1 GACTATCGCAACGCGATTAT
* *
23751 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAACGCGATTAT
* *
23771 GACTATCGCAACGTGATTCT
1 GACTATCGCAACGCGATTAT
* * *
23791 AACTTTCGCAACGCGATTCT
1 GACTATCGCAACGCGATTAT
*
23811 GACTGTCGCAAC
1 GACTATCGCAAC
23823 ACTGAATTTC
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
19 1 0.02
20 57 0.97
21 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (20 bp):
GACTATCGCAACGCGATTAT
Found at i:24675 original size:24 final size:24
Alignment explanation
Indices: 24643--24696 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
24633 GTATTCGAAA
24643 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
24667 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
24691 TTTGAT
1 TTTGAT
24697 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:27285 original size:140 final size:140
Alignment explanation
Indices: 27030--27299 Score: 495
Period size: 140 Copynumber: 1.9 Consensus size: 140
27020 AAACGTTGTA
* *
27030 TTATGTGTAAACTTTTAACATTTTTAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACCTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* * *
27095 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATTGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACAAATTTGACTAT
27160 TATGTGTATT
131 TATGTGTATT
27170 TTATGTGTAAACCTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACCTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
27235 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACAAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACAAATTTGACTAT
27300 CGCAACGCGA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACCTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACACAAATTTGACTAT
TATGTGTATT
Found at i:27295 original size:20 final size:20
Alignment explanation
Indices: 27270--27583 Score: 274
Period size: 20 Copynumber: 16.6 Consensus size: 20
27260 TTACACATTC
* * *
27270 ATTTGAATATCGCAACACAA
1 ATTTGACTATCGCAACGCGA
27290 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
27310 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
27329 A----A-AATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
*
27344 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
27364 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
27384 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
27404 ATTTGACTATCGCAACGCTA
1 ATTTGACTATCGCAACGCGA
*
27424 ATTTGA-TCATCGCAACG-GCT
1 ATTTGACT-ATCGCAACGCG-A
*
27444 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
27464 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
27478 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
27498 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
*
27518 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
27538 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
27552 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
27572 A-TTGACTTTCGC
1 ATTTGACTATCGC
27584 GTTGCGATTT
Statistics
Matches: 239, Mismatches: 33, Indels: 45
0.75 0.10 0.14
Matches are distributed among these distances:
14 31 0.13
15 3 0.01
16 2 0.01
18 2 0.01
19 13 0.05
20 186 0.78
21 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:27501 original size:74 final size:74
Alignment explanation
Indices: 27392--27574 Score: 312
Period size: 74 Copynumber: 2.5 Consensus size: 74
27382 GAATTTGTCT
*
27392 ATCGCAACGCGAATTTGACTATCGCAACGCTAATTTGATCATCGCAACGGCTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATCATCGCAACGGCTATTTGACTATCGC
27457 AACGAGAAA
66 AACGAGAAA
* *
27466 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATCATCGCAACGGCTATTTGACTATCGC
27531 AACGAGAAA
66 AACGAGAAA
* * *
27540 ATCGCAAAGCGTATTAGACTATCGCAACGCGAATT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATT
27575 GACTTTCGCG
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 103 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATCATCGCAACGGCTATTTGACTATCGC
AACGAGAAA
Found at i:27554 original size:34 final size:34
Alignment explanation
Indices: 27432--27568 Score: 159
Period size: 34 Copynumber: 3.9 Consensus size: 34
27422 TAATTTGATC
27432 ATCGCAACG-GCTATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCG-TATTTGACTATCGCAACGAGAAA
* *
27466 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGA
1 ATCGCAACGCGTATTTGACTATCGCAACGAGAA----A
*
27504 TTATCGCAACGGGTATTTGACTATCGCAACGAGAAA
1 --ATCGCAACGCGTATTTGACTATCGCAACGAGAAA
* *
27540 ATCGCAAAGCGTATTAGACTATCGCAACG
1 ATCGCAACGCGTATTTGACTATCGCAACG
27569 CGAATTGACT
Statistics
Matches: 88, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
34 55 0.62
35 1 0.01
36 1 0.01
38 1 0.01
40 30 0.34
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (34 bp):
ATCGCAACGCGTATTTGACTATCGCAACGAGAAA
Found at i:27602 original size:20 final size:20
Alignment explanation
Indices: 27573--27630 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
27563 GCAACGCGAA
27573 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* * *
27593 TTGTCTTTCGCATTCCGATT
1 TTGACTTTCGCGTTGCGATT
* *
27613 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
27631 AAGTGTACCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:27789 original size:14 final size:14
Alignment explanation
Indices: 27729--27790 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
27719 CACAAATAAG
*
27729 AATTATTTACACATC
1 AATT-TTTACAAATC
**
27744 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
27759 AACTTTTACAAATC
1 AATTTTTACAAATC
*
27773 AATTTTTATAAATC
1 AATTTTTACAAATC
27787 AATT
1 AATT
27791 AAACAACCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:28797 original size:42 final size:42
Alignment explanation
Indices: 28718--28810 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
28708 CCTCTTTAAC
* *
28718 GATGACAGTGGCCTCTTGAACAATGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACAATGGGAGAGGACTCTTGAGG
* * * **
28760 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACAAT-GGGAGAGGACTCTTGAGG
28802 GATGACAGG
1 GATGACAGG
28811 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.25, C:0.17, G:0.38, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACAATGGGAGAGGACTCTTGAGG
Found at i:29332 original size:20 final size:20
Alignment explanation
Indices: 29307--29403 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
29297 ATCGCAACAC
*
29307 AAATGACTATCGCAACGCAA
1 AAATGACTATCGCAACGCGA
* *
29327 AAATGACCATCACAACGCGA
1 AAATGACTATCGCAACGCGA
* *
29347 AAATGACTATCGTAACACGA
1 AAATGACTATCGCAACGCGA
29367 AAATGACTATCGCAACGCGA
1 AAATGACTATCGCAACGCGA
**
29387 ATTTGACTATCGCAACG
1 AAATGACTATCGCAACG
29404 AGAGAATCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGA
Found at i:29685 original size:18 final size:18
Alignment explanation
Indices: 29662--29711 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
29652 TTTACTAAGC
*
29662 AATCTAAGTGAAGTGATT
1 AATCTAAGTGAAATGATT
*
29680 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGATT
29698 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
29712 TACGAGTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGATT
Found at i:31526 original size:19 final size:19
Alignment explanation
Indices: 31439--31545 Score: 90
Period size: 20 Copynumber: 5.5 Consensus size: 19
31429 TCTGAAACTT
* *
31439 AAAATCACAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
**
31459 AAAATCGCAATACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
31479 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
**
31499 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
31518 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
31537 AAAATCGCA
1 AAAATCGCA
31546 TTGCGATTCT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
19 28 0.37
20 47 0.63
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:31958 original size:22 final size:22
Alignment explanation
Indices: 31931--31973 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31921 GAGATAGACA
*
31931 GATTTCGCCGGAGATGGGGACT
1 GATTTCGCCAGAGATGGGGACT
*
31953 GATTTCGTCAGAGATGGGGAC
1 GATTTCGCCAGAGATGGGGAC
31974 GGATGTCGGC
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:0.21, C:0.16, G:0.40, T:0.23
Consensus pattern (22 bp):
GATTTCGCCAGAGATGGGGACT
Found at i:32180 original size:20 final size:20
Alignment explanation
Indices: 32157--32263 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
32147 GAAAATCGTA
* *
32157 TTGCGATAGTCGGCATCGCG
1 TTGCGATAGTCAGAATCGCG
*
32177 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
32197 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
* *
32217 TTGCGATAGTCATAATCGTG
1 TTGCGATAGTCAGAATCGCG
* *
32237 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCG
32257 TTGCGAT
1 TTGCGAT
32264 TTACATATTC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:32281 original size:40 final size:40
Alignment explanation
Indices: 32157--32287 Score: 138
Period size: 40 Copynumber: 3.3 Consensus size: 40
32147 GAAAATCGTA
* * * * *
32157 TTGCGATAGTCGGCATCGCGTTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCATTGCGATAGTCATAATCGCG
* * *
32197 TTGCGATAGTCAGAATCTCGTTGCGATAGTCATAATCGTG
1 TTGCGATAGTCAGAATCGCATTGCGATAGTCATAATCGCG
* * * *
32237 TTGCGATAGTCATAATCGCATTGCGAT-TTACATATTCGCA
1 TTGCGATAGTCAGAATCGCATTGCGATAGT-CATAATCGCG
32277 TTGCGATAGTC
1 TTGCGATAGTC
32288 GGAAAGTCAC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 76 0.99
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (40 bp):
TTGCGATAGTCAGAATCGCATTGCGATAGTCATAATCGCG
Found at i:45707 original size:12 final size:13
Alignment explanation
Indices: 45681--45713 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
45671 TTCTCGAATG
*
45681 TAAAGTTATTTAA
1 TAAAGTTATTAAA
45694 TAAA-TTATTAAA
1 TAAAGTTATTAAA
45706 TAAAGTTA
1 TAAAGTTA
45714 AGATTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (13 bp):
TAAAGTTATTAAA
Found at i:46613 original size:20 final size:21
Alignment explanation
Indices: 46574--46614 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
46564 CAAAACATAG
*
46574 AAGGGATCGATCCTTTTCTCC
1 AAGGAATCGATCCTTTTCTCC
46595 AAGGAATCGATCC-TTTCTCC
1 AAGGAATCGATCCTTTTCTCC
46615 CGATGGATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (21 bp):
AAGGAATCGATCCTTTTCTCC
Found at i:46626 original size:21 final size:20
Alignment explanation
Indices: 46577--46614 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46567 AACATAGAAG
46577 GGATCGATCCTTTTCTCCAA
1 GGATCGATCCTTTTCTCCAA
46597 GGAATCGATCC-TTTCTCC
1 GG-ATCGATCCTTTTCTCC
46615 CGATGGATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (20 bp):
GGATCGATCCTTTTCTCCAA
Found at i:47172 original size:22 final size:22
Alignment explanation
Indices: 47119--47174 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
47109 AGGAAATGAA
*
47119 GAAAGAAAAAGGGAAGGAAAAT
1 GAAAGAAGAAGGGAAGGAAAAT
47141 GAAAGAAGAAGGGAAGGAAAAT
1 GAAAGAAGAAGGGAAGGAAAAT
*
47163 GAAAGGAGAAGG
1 GAAAGAAGAAGG
47175 TGAAATAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.04
Consensus pattern (22 bp):
GAAAGAAGAAGGGAAGGAAAAT
Found at i:49563 original size:31 final size:31
Alignment explanation
Indices: 49525--49585 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
49515 TGGGGCAATG
**
49525 TATAATTAATTATAGAAAATGAGGGAGAAAA
1 TATAATTAAACATAGAAAATGAGGGAGAAAA
*
49556 TATAATTAAACATAGAAAATGAGGGGGAAA
1 TATAATTAAACATAGAAAATGAGGGAGAAA
49586 TCAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.02, G:0.21, T:0.23
Consensus pattern (31 bp):
TATAATTAAACATAGAAAATGAGGGAGAAAA
Found at i:50735 original size:2 final size:2
Alignment explanation
Indices: 50728--50752 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50718 AATCCATAGG
50728 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
50753 TCATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57547 original size:38 final size:38
Alignment explanation
Indices: 57504--57583 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
57494 AAATATAACG
*
57504 TTAAGTATCTAAAAGTGTAACTGAAAAAATGTTAAGTA
1 TTAAGTATCTAAAAGTGCAACTGAAAAAATGTTAAGTA
57542 TTAAGTATCTAAAAGTGCAACTGAAAAAATGTTAAGTA
1 TTAAGTATCTAAAAGTGCAACTGAAAAAATGTTAAGTA
57580 TTAA
1 TTAA
57584 TTTTTAACGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.31
Consensus pattern (38 bp):
TTAAGTATCTAAAAGTGCAACTGAAAAAATGTTAAGTA
Found at i:59206 original size:15 final size:14
Alignment explanation
Indices: 59186--59268 Score: 64
Period size: 13 Copynumber: 5.9 Consensus size: 14
59176 AACACACAAG
59186 ATAAATATAAAATTT
1 ATAAATATAAAA-TT
*
59201 ATAAATATTCAAATT
1 ATAAATA-TAAAATT
* *
59216 ATAGAATCTAAAACT
1 ATA-AATATAAAATT
*
59231 A-AAATATAAAAAT
1 ATAAATATAAAATT
*
59244 ATAAAAATAAAA-T
1 ATAAATATAAAATT
59257 A-AAATTATAAAA
1 ATAAA-TATAAAA
59269 AATGTATAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
12 3 0.05
13 18 0.32
14 10 0.18
15 18 0.32
16 7 0.12
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (14 bp):
ATAAATATAAAATT
Found at i:60098 original size:73 final size:73
Alignment explanation
Indices: 59974--60118 Score: 220
Period size: 73 Copynumber: 2.0 Consensus size: 73
59964 CCATCTTTCT
* * * * *
59974 ACTAGTAGAGTGGGATGAGATTTAAAGTTTAAGCTAACCATATACTTTCGAGAAACACAATTATT
1 ACTAATAGAGTGGGATGAGATCTAAAATTTAAACTAACCATATACTTTCGAGAAACACAATTATC
60039 ATAATATG
66 ATAATATG
*
60047 ACTAATAGAGTGGGATGAGATCTAAAATTTAAATTAATCC-TATACTTTCGAGAAACACAATTAT
1 ACTAATAGAGTGGGATGAGATCTAAAATTTAAACTAA-CCATATACTTTCGAGAAACACAATTAT
60111 CATAATAT
65 CATAATAT
60119 TATCACATGT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 63 0.97
74 2 0.03
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (73 bp):
ACTAATAGAGTGGGATGAGATCTAAAATTTAAACTAACCATATACTTTCGAGAAACACAATTATC
ATAATATG
Found at i:64409 original size:40 final size:40
Alignment explanation
Indices: 64365--64456 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
64355 AGAACAATAA
*
64365 GTTATTTAGAAAAACTCGATCTGAAGAAGTAAAAAATGAT
1 GTTATTTAGAAAAACTCAATCTGAAGAAGTAAAAAATGAT
64405 GTTATTTAGAAAAACTCAATCTGAAGAAGTAAAAAATGAT
1 GTTATTTAGAAAAACTCAATCTGAAGAAGTAAAAAATGAT
*
64445 GTCATTTA-AAAA
1 GTTATTTAGAAAA
64457 TTATTGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 4 0.08
40 46 0.92
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (40 bp):
GTTATTTAGAAAAACTCAATCTGAAGAAGTAAAAAATGAT
Found at i:70011 original size:55 final size:54
Alignment explanation
Indices: 69942--70269 Score: 182
Period size: 55 Copynumber: 6.1 Consensus size: 54
69932 GGGATAAATG
* * *
69942 AGACTTGAAAAATCTTCAAATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGTATA
1 AGACTTGAACAATCTTCAAA-AACGAGCCTGCTCCCTATTCATTCAGAG-AGTATA
* * * * *
69997 AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTATTCATTCAGAGAGTATA
1 AGACTTGAACAATCTTCA-AAAACGAGCCTGCTCCCTATTCATTCAGAGAGTATA
* * * * *
70052 AGAATTGAACAATCTTCAATAAAACGGGTAC-GCTCTCTATTCCTTCAGAGAGTAT-
1 AGACTTGAACAATCTTC-A-AAAACGAG-CCTGCTCCCTATTCATTCAGAGAGTATA
* *
70107 AGAACTCGGAA-AATCTTCAATAAAC-AGGTCC-GCTCCCTATTCTTTCAGAGAGTATA
1 AG-ACT-TGAACAATCTTCAA-AAACGA-G-CCTGCTCCCTATTCATTCAGAGAGTATA
* * * * *
70163 GGAC-T---CAATCTTTAATAAACGTGTCC-ACTCCCTATTCCTTCAGAGAGTATA
1 AGACTTGAACAATCTTCAA-AAACGAG-CCTGCTCCCTATTCATTCAGAGAGTATA
* * * * * *
70214 GGAC-T---CGATCTTCATAAAATGTGTCTGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTTGAACAATCTTCA-AAAACGAGCCTGCTCCCTATTCATTCAGAGAGTATA
*
70265 GGACT
1 AGACT
70270 CGATCTTCAT
Statistics
Matches: 228, Mismatches: 31, Indels: 31
0.79 0.11 0.11
Matches are distributed among these distances:
50 1 0.00
51 86 0.38
52 1 0.00
54 1 0.00
55 91 0.40
56 44 0.19
57 4 0.02
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (54 bp):
AGACTTGAACAATCTTCAAAAACGAGCCTGCTCCCTATTCATTCAGAGAGTATA
Found at i:70114 original size:111 final size:106
Alignment explanation
Indices: 69972--70282 Score: 336
Period size: 111 Copynumber: 2.9 Consensus size: 106
69962 TGACGAGCCT
*
69972 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAA-AATCTTCATAAAATGTGTCTGCTCCCTA
*
70035 TTCATTCAGAGAGTATAAGAATTGAACAATCTTCAATAAAACGGGTAC
63 TTCATTCAGAGAGTATAAGAACT---CAATCTTCAAT-AAACGGGTAC
* *
70083 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAACA-G-GTCCGCTCCCTA
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC-GAAAATCTTC-ATAAA-ATGTGTCTGCTCCCTA
* * * * *
70146 TTCTTTCAGAGAGTAT-AGGACTCAATCTTTAATAAACGTGTCC
63 TTCATTCAGAGAGTATAAGAACTCAATCTTCAATAAACGGGTAC
* *
70189 ACTCCCTATTCCTTCAGAGAGTATAGGACTCG---ATCTTCATAAAATGTGTCTGCTCCCTATTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAAATCTTCATAAAATGTGTCTGCTCCCTATTC
* * *
70251 CTTCAGAGAGTAT-AGGACTCGATCTTC-ATAAA
66 ATTCAGAGAGTATAAGAACTCAATCTTCAATAAA
70283 ATGAGTTTGC
Statistics
Matches: 177, Mismatches: 16, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
100 1 0.01
101 11 0.06
102 44 0.25
105 1 0.01
106 36 0.20
107 10 0.06
110 4 0.02
111 58 0.33
112 11 0.06
113 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (106 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAAATCTTCATAAAATGTGTCTGCTCCCTATTC
ATTCAGAGAGTATAAGAACTCAATCTTCAATAAACGGGTAC
Found at i:70194 original size:51 final size:52
Alignment explanation
Indices: 69972--70283 Score: 287
Period size: 51 Copynumber: 5.9 Consensus size: 52
69962 TGACGAGCCT
* * *
69972 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTC-ATAAAATGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCAATAAAACGTGTCC
* * * * * *
70027 GCTCTCTATTCATTCAGAGAGTATAAGAATTGAACAATCTTCAATAAAACGGGTAC
1 GCTCCCTATTCCTTCAGAGAGTAT-AGGACT---CAATCTTCAATAAAACGTGTCC
* *
70083 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAAAATCTTCAAT-AAACAG-GTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAATAAAAC-GTGTCC
* *
70138 GCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAAT-AAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATAAAACGTGTCC
* * * *
70189 ACTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTC-ATAAAATGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATAAAACGTGTCC
*
70240 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTC-ATAAAA
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATAAAA
70284 TGAGTTTGCT
Statistics
Matches: 224, Mismatches: 23, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
50 3 0.01
51 102 0.46
52 1 0.00
55 71 0.32
56 47 0.21
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (52 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAATAAAACGTGTCC
Found at i:70328 original size:37 final size:36
Alignment explanation
Indices: 70287--70358 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
70277 CATAAAATGA
70287 GTTTGCTTCACTAATCTTCCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTA-AGATG
*
70324 GTTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGAT
70359 TGACCTGCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGATG
Found at i:71716 original size:27 final size:27
Alignment explanation
Indices: 71669--71813 Score: 70
Period size: 27 Copynumber: 5.2 Consensus size: 27
71659 TGTTTTTCTC
* *
71669 TTTCAT-TTTTTCTTCCATTTTCCATTT
1 TTTCATCTTTTTTTTTCATTTT-CATTT
*
71696 TTTCATCTTTTTTTTTC-TTTTCGTTT
1 TTTCATCTTTTTTTTTCATTTTCATTT
* *
71722 TTCCATCATTTTTCTTTT--TTATCATTT
1 TTTCATC-TTTTT-TTTTCATTTTCATTT
** *
71749 TTCTTTTCTTATTTTTCTTC-TTCTCATTAT
1 TT-TCATCTT-TTTTT-TTCATTTTCATT-T
71779 TATT-AT-TTTTTTTTTCATTTTTTTCATTT
1 T-TTCATCTTTTTTTTTCA---TTTTCATTT
71808 TTTCAT
1 TTTCAT
71814 TTTCTCTTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
26 13 0.14
27 33 0.36
28 23 0.25
29 12 0.13
30 10 0.11
31 1 0.01
ACGTcount: A:0.11, C:0.17, G:0.01, T:0.72
Consensus pattern (27 bp):
TTTCATCTTTTTTTTTCATTTTCATTT
Found at i:71723 original size:45 final size:44
Alignment explanation
Indices: 71647--71758 Score: 111
Period size: 44 Copynumber: 2.5 Consensus size: 44
71637 TTTTTTTTCA
* * * *
71647 TTTTCCTCTTTTTGTTTTTCTCTTTCATTTTTTCTTCCATTTTCCATT
1 TTTTCATCATTTT-TTTTTCT-TTTCATTTTTCCAT-CATTTTCC-TT
* *
71695 TTTTCATC-TTTTTTTTTCTTTTCGTTTTTCCATCATTTTTCTT
1 TTTTCATCATTTTTTTTTCTTTTCATTTTTCCATCATTTTCCTT
71738 TTTT-ATCATTTTTCTTTTCTT
1 TTTTCATCATTTTT-TTTTCTT
71759 ATTTTTCTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
42 3 0.05
43 11 0.19
44 14 0.25
45 11 0.19
46 7 0.12
47 4 0.07
48 7 0.12
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (44 bp):
TTTTCATCATTTTTTTTTCTTTTCATTTTTCCATCATTTTCCTT
Found at i:71733 original size:26 final size:27
Alignment explanation
Indices: 71691--71751 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
71681 TTCCATTTTC
* *
71691 CATTTTTTCATC-TTTTT-TTTTCTTTT
1 CATTTTTCCATCATTTTTCTTTT-TTAT
*
71717 CGTTTTTCCATCATTTTTCTTTTTTAT
1 CATTTTTCCATCATTTTTCTTTTTTAT
71744 CATTTTTC
1 CATTTTTC
71752 TTTTCTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 10 0.34
27 15 0.52
28 4 0.14
ACGTcount: A:0.10, C:0.18, G:0.02, T:0.70
Consensus pattern (27 bp):
CATTTTTCCATCATTTTTCTTTTTTAT
Found at i:71739 original size:16 final size:16
Alignment explanation
Indices: 71720--71756 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
71710 TTCTTTTCGT
71720 TTTTCCATCATTTTTC
1 TTTTCCATCATTTTTC
**
71736 TTTTTTATCATTTTTC
1 TTTTCCATCATTTTTC
71752 TTTTC
1 TTTTC
71757 TTATTTTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTCCATCATTTTTC
Found at i:71739 original size:17 final size:16
Alignment explanation
Indices: 71713--71776 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 16
71703 TTTTTTTTTC
71713 TTTTCGTTTTTCCATCAT
1 TTTTC-TTTTT-CATCAT
*
71731 TTTTCTTTTTTATCAT
1 TTTTCTTTTTCATCAT
*
71747 TTTTC-TTTTC-TTAT
1 TTTTCTTTTTCATCAT
*
71761 TTTTCTTCTTC-TCAT
1 TTTTCTTTTTCATCAT
71776 T
1 T
71777 ATTATTATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.20
15 12 0.30
16 10 0.25
17 5 0.12
18 5 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTTCTTTTTCATCAT
Found at i:71741 original size:25 final size:26
Alignment explanation
Indices: 71647--71751 Score: 66
Period size: 26 Copynumber: 3.8 Consensus size: 26
71637 TTTTTTTTCA
* * *
71647 TTTTCCTCTTTTTGTTTTTCTCTTTCATT
1 TTTTCTTCTTTTCGTTTTTC-C-ATCA-T
* * *
71676 TTTTCTTCCATTTTCCATTTTTTCATCTT
1 TTTTCTT-C-TTTT-CGTTTTTCCATCAT
*
71705 TTTTTTTCTTTTCGTTTTTCCATCAT
1 TTTTCTTCTTTTCGTTTTTCCATCAT
* *
71731 TTTTCTTTTTTATCATTTTTC
1 TTTTCTTCTTT-TCGTTTTTC
71752 TTTTCTTATT
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
26 20 0.34
27 12 0.20
28 1 0.02
29 13 0.22
30 3 0.05
31 5 0.08
32 5 0.08
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTCTTCTTTTCGTTTTTCCATCAT
Found at i:71757 original size:21 final size:21
Alignment explanation
Indices: 71731--71825 Score: 58
Period size: 22 Copynumber: 4.6 Consensus size: 21
71721 TTTCCATCAT
71731 TTTTCTTTTTTATCATTTTTC
1 TTTTCTTTTTTATCATTTTTC
71752 TTTTCTTATTTT-TC----TTC
1 TTTTCTT-TTTTATCATTTTTC
* * * * *
71769 TTCTCATTATTATTATTTTTT
1 TTTTCTTTTTTATCATTTTTC
71790 TTTTCATTTTTT-TCATTTTTTC
1 TTTTC-TTTTTTATCA-TTTTTC
*
71812 ATTTTCTCTTTTAT
1 -TTTTCTTTTTTAT
71826 TTCTTCTTCA
Statistics
Matches: 53, Mismatches: 11, Indels: 18
0.65 0.13 0.22
Matches are distributed among these distances:
16 3 0.06
17 9 0.17
21 17 0.32
22 18 0.34
23 6 0.11
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTCTTTTTTATCATTTTTC
Found at i:71801 original size:9 final size:9
Alignment explanation
Indices: 71787--71816 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
71777 ATTATTATTT
71787 TTTTTTTCA
1 TTTTTTTCA
71796 TTTTTTTCA
1 TTTTTTTCA
71805 -TTTTTTCA
1 TTTTTTTCA
71813 TTTT
1 TTTT
71817 CTCTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:71814 original size:38 final size:37
Alignment explanation
Indices: 71730--71814 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 37
71720 TTTTCCATCA
* *
71730 TTTTTCTTTTTTATCATTTTTCTTTTCTTATTTTTCT
1 TTTTTCATTATTATCATTTTTCTTTTCTTATTTTTCT
* * *
71767 TCTTCTCATTATTATTATTTTTTTTTTCATT-TTTTTCAT
1 T-TTTTCATTATTATCATTTTTCTTTTC-TTATTTTTC-T
71806 TTTTTCATT
1 TTTTTCATT
71815 TTCTCTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
37 1 0.03
38 34 0.87
39 4 0.10
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (37 bp):
TTTTTCATTATTATCATTTTTCTTTTCTTATTTTTCT
Found at i:71828 original size:17 final size:17
Alignment explanation
Indices: 71787--71828 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
71777 ATTATTATTT
*
71787 TTTTTTTCATTTTTTTC
1 TTTTTTTCATTTTTCTC
*
71804 ATTTTTTCA-TTTTCTC
1 TTTTTTTCATTTTTCTC
71820 TTTTATTTC
1 TTTT-TTTC
71829 TTCTTCAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTCATTTTTCTC
Found at i:81535 original size:45 final size:46
Alignment explanation
Indices: 81468--81572 Score: 169
Period size: 45 Copynumber: 2.3 Consensus size: 46
81458 CCATGCTTTG
81468 TTATTCACAAAAATAAATCCTAA-CTGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAATCCTAATC-GCATGATATCTAATTCGCATGC
*
81515 TTATTCAAAAAATAAA-CCTAATCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAATCCTAATCGCATGATATCTAATTCGCATGC
81560 TTATTCAAAAAAT
1 TTATTCAAAAAAT
81573 GAAAATAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
45 39 0.70
46 10 0.18
47 7 0.12
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAATCGCATGATATCTAATTCGCATGC
Found at i:85272 original size:23 final size:25
Alignment explanation
Indices: 85242--85292 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
85232 TCTAATGTGC
85242 ATCATGCAT-TACCT-GGAAACAAG
1 ATCATGCATATACCTAGGAAACAAG
85265 ATCATGCATACTACCTAGGAAACAAG
1 ATCATGCATA-TACCTAGGAAACAAG
85291 AT
1 AT
85293 GGGATGGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 9 0.36
25 5 0.20
26 11 0.44
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (25 bp):
ATCATGCATATACCTAGGAAACAAG
Done.