Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007360.1 Hibiscus syriacus cultivar Beakdansim tig00019745_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: 93852
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:10632 original size:54 final size:54
Alignment explanation
Indices: 10573--10859 Score: 405
Period size: 54 Copynumber: 5.3 Consensus size: 54
10563 ATGTGTACTC
*
10573 TAGGCACTTTGTGTGCAACCCATGGAATTCATCATAAGTTGATGAACAACCGTT
1 TAGGCACTATGTGTGCAACCCATGGAATTCATCATAAGTTGATGAACAACCGTT
* *
10627 TAGGCACTATGTGTGCATCCCACGGAATTCATCATAAGTTGATGAACAACCGTT
1 TAGGCACTATGTGTGCAACCCATGGAATTCATCATAAGTTGATGAACAACCGTT
* * *
10681 TTGGCACTATGTGTGCAACCCATGTAATTCATCATAAGTTGATGAACAACTGTT
1 TAGGCACTATGTGTGCAACCCATGGAATTCATCATAAGTTGATGAACAACCGTT
* * * * * *
10735 TTGGCACTATGTGTGAAACCCATCGAATTTATCATATGTTGATGAACAACTGTT
1 TAGGCACTATGTGTGCAACCCATGGAATTCATCATAAGTTGATGAACAACCGTT
* * * * *
10789 TAGGCACTATGTGTGCAACCCACGGAATTCATAATATGTTTATGAATAACCGTAT
1 TAGGCACTATGTGTGCAACCCATGGAATTCATCATAAGTTGATGAACAACCGT-T
10844 T-GGCACTATGTGTGCA
1 TAGGCACTATGTGTGCA
10860 TCTCAACGAA
Statistics
Matches: 210, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
54 208 0.99
55 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (54 bp):
TAGGCACTATGTGTGCAACCCATGGAATTCATCATAAGTTGATGAACAACCGTT
Found at i:14871 original size:17 final size:16
Alignment explanation
Indices: 14849--14882 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
14839 TTCTAAATTT
*
14849 AAAATATAAAATACAAA
1 AAAATAAAAAATA-AAA
14866 AAAATAAAAAATAAAA
1 AAAATAAAAAATAAAA
14882 A
1 A
14883 TATTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAATAAAAAATAAAA
Found at i:14913 original size:38 final size:35
Alignment explanation
Indices: 14870--14956 Score: 86
Period size: 39 Copynumber: 2.3 Consensus size: 35
14860 TACAAAAAAA
14870 TAAAAAATAAAA-ATATTAATAATGAAAATTAAATTGC
1 TAAAAAATAAAATATATT-ATAA--AAAATTAAATTGC
* *
14907 TAAAAAAATTGAACAATATATTTTAAAAAATTTAATTGC
1 T-AAAAAA-T-AA-AATATATTATAAAAAATTAAATTGC
14946 TAAAAAATAAA
1 TAAAAAATAAA
14957 TGCAATTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
35 1 0.02
36 2 0.05
37 2 0.05
38 12 0.28
39 14 0.33
40 2 0.05
41 5 0.12
42 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (35 bp):
TAAAAAATAAAATATATTATAAAAAATTAAATTGC
Found at i:17523 original size:13 final size:13
Alignment explanation
Indices: 17505--17529 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17495 ATTTAGTAAC
17505 AGAAAAAATTTAT
1 AGAAAAAATTTAT
17518 AGAAAAAATTTA
1 AGAAAAAATTTA
17530 GTGACGAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (13 bp):
AGAAAAAATTTAT
Found at i:22241 original size:54 final size:54
Alignment explanation
Indices: 21977--22234 Score: 354
Period size: 54 Copynumber: 4.8 Consensus size: 54
21967 GTACTATAGT
*
21977 CACTATGTGTGTAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
1 CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
* * * *
22031 AACTATGTGTGCAACCCACAAAATTCATCATAAGTTGATGAACAACCATTTTGG
1 CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
* * * *
22085 CACTACGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACTGTTTTGG
1 CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
* * * * *
22139 CACAATATGTGAAACCCACAGAATTCATCATATGTTGATGAGCAACCGTTTAGG
1 CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
* * * *
22193 CACTATGTGTGCAACCCACAAAATTCATAATATGTTTATGAA
1 CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAA
22235 TGACCGTATT
Statistics
Matches: 177, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 177 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (54 bp):
CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
Found at i:22641 original size:54 final size:54
Alignment explanation
Indices: 22581--22863 Score: 318
Period size: 54 Copynumber: 5.2 Consensus size: 54
22571 GTACTCTAGT
* * *
22581 CACTATGTGTGTAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTCAGG
1 CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
* * * *
22635 CACTATGTGTGCAACCCACAAAACTAATCATAAGTTGATGAACAACCGTTTTGG
1 CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
* * *
22689 CACTATATGTGCAACCCACAGAATTTATCATAAGTTGATGAACAACCGTTTTGG
1 CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
* * * * * * *
22743 CAATATGTGTGAAACCCACAAAATTTATTATATGTTGATGAACAACTGTTTAGG
1 CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
* * * * **
22797 AACTATGTGTGTAACCCACAGAATTCAT-AGTATGTTTATGAATGACCGTATT-GG
1 CACTATGTGTGCAACCCACAGAATTCATCA-TAAGTTGATGAACAACCGT-TTAGG
*
22851 CACTACGTGTGCA
1 CACTATGTGTGCA
22864 TCTCAACGAA
Statistics
Matches: 196, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
53 1 0.01
54 193 0.98
55 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (54 bp):
CACTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTAGG
Found at i:22838 original size:108 final size:108
Alignment explanation
Indices: 22582--22861 Score: 355
Period size: 108 Copynumber: 2.6 Consensus size: 108
22572 TACTCTAGTC
* ** *
22582 ACTATGTGTGTAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTATGTGTGC
1 ACTATGTGTGTAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATGTGTGA
* *
22647 AACCCACAAAACTAATCATAAGTTGATGAACAACCGTTTTGGC
66 AACCCACAAAACTAATCATAAGTTGATGAACAACCGTTTAGGA
* * * *
22690 ACTATATGTGCAACCCACAGAATTTATCATAAGTTGATGAACAACCGTTTTGGCAATATGTGTGA
1 ACTATGTGTGTAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATGTGTGA
* * * * *
22755 AACCCACAAAATTTATTATATGTTGATGAACAACTGTTTAGGA
66 AACCCACAAAACTAATCATAAGTTGATGAACAACCGTTTAGGA
* * ** * *
22798 ACTATGTGTGTAACCCACAGAATTCAT-AGTATGTTTATGAATGACCGTATTGGCACTACGTGTG
1 ACTATGTGTGTAACCCACAGAATTCATCA-TAAGTTGATGAACAACCGTTTTGGCACTATGTGTG
22862 CATCTCAACG
Statistics
Matches: 146, Mismatches: 25, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
107 1 0.01
108 145 0.99
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (108 bp):
ACTATGTGTGTAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTTTGGCACTATGTGTGA
AACCCACAAAACTAATCATAAGTTGATGAACAACCGTTTAGGA
Found at i:25546 original size:24 final size:24
Alignment explanation
Indices: 25514--25568 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
25504 ACGTTTAGAG
* *
25514 TTTCTACCACCCATTTAGCATCCA
1 TTTCTACCACCCATTGAACATCCA
25538 TTTCTACCACCCATTGAACATCCA
1 TTTCTACCACCCATTGAACATCCA
25562 TTTCTAC
1 TTTCTAC
25569 GATGAACTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.25, C:0.36, G:0.04, T:0.35
Consensus pattern (24 bp):
TTTCTACCACCCATTGAACATCCA
Found at i:37302 original size:9 final size:9
Alignment explanation
Indices: 37288--37316 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
37278 GAAATCGGTT
37288 AATTAACCG
1 AATTAACCG
37297 AATTAACCG
1 AATTAACCG
37306 AATTAACCG
1 AATTAACCG
37315 AA
1 AA
37317 ATAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (9 bp):
AATTAACCG
Found at i:37646 original size:186 final size:186
Alignment explanation
Indices: 37327--37718 Score: 705
Period size: 186 Copynumber: 2.1 Consensus size: 186
37317 ATAAAATTTT
* *
37327 AAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAATCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
* *
37392 TTTAAGATCCAATAATTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
37457 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAA
37513 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
*
37578 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
37643 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTATA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAA
* *
37699 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
37719 AATTAGAAAA
Statistics
Matches: 198, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
185 8 0.04
186 190 0.96
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (186 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAA
Found at i:37685 original size:20 final size:20
Alignment explanation
Indices: 37651--37708 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
37641 TTTTATTTTA
* *
37651 TAATTATATATTATTTAAAT
1 TAATTATAAAATATTTAAAT
* **
37671 TAATTATAAACTATTT-TTT
1 TAATTATAAAATATTTAAAT
37690 TGAATTATAAAATATTTAA
1 T-AATTATAAAATATTTAA
37709 TTTTTATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATTATAAAATATTTAAAT
Found at i:40059 original size:24 final size:26
Alignment explanation
Indices: 40005--40052 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
39995 TTATAATACA
*
40005 TATATTATATACTATTTTGCAAAAAT
1 TATATTATATACTATTTTACAAAAAT
40031 TATATTATATA-TA-TTTACAAAA
1 TATATTATATACTATTTTACAAAA
40053 TCTATATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 2 0.10
26 11 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (26 bp):
TATATTATATACTATTTTACAAAAAT
Found at i:40060 original size:26 final size:27
Alignment explanation
Indices: 40004--40061 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
39994 ATTATAATAC
*
40004 ATATATTATATACTATTTTGCAAAAAT
1 ATATATTATATACTATTTTACAAAAAT
*
40031 -TATATTATATA-TA-TTTACAAAATCT
1 ATATATTATATACTATTTTACAAAA-AT
40056 ATATAT
1 ATATAT
40062 CGTATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 8 0.30
25 3 0.11
26 16 0.59
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (27 bp):
ATATATTATATACTATTTTACAAAAAT
Found at i:42243 original size:26 final size:25
Alignment explanation
Indices: 42214--42300 Score: 90
Period size: 25 Copynumber: 3.4 Consensus size: 25
42204 TATCAGCGTC
42214 GAAAAAGGTATCATTTTCCAATGCCA
1 GAAAAAGGTA-CATTTTCCAATGCCA
** *
42240 GAAAAA-GTACATATTTCCAACACAA
1 GAAAAAGGTACAT-TTTCCAATGCCA
42265 GAAAAAGGTACCAATTTT-CAATGCCA
1 GAAAAAGGTA-C-ATTTTCCAATGCCA
42291 -AAAAAGGTAC
1 GAAAAAGGTAC
42301 TGCTATTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
24 4 0.08
25 27 0.53
26 14 0.27
27 4 0.08
28 2 0.04
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (25 bp):
GAAAAAGGTACATTTTCCAATGCCA
Found at i:43424 original size:32 final size:34
Alignment explanation
Indices: 43381--43451 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
43371 CCTTACAACT
*
43381 CCCTAG-TTTTTACGGGCTAAACTAGAAC-CTTC
1 CCCTAGCTTTTAACGGGCTAAACTAGAACACTTC
* *
43413 CCCTAGCTTTTACACGGGCTAAGCTAGAACATTTC
1 CCCTAGCTTTTA-ACGGGCTAAACTAGAACACTTC
43448 CCCT
1 CCCT
43452 TTACAAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 6 0.18
33 4 0.12
34 16 0.48
35 7 0.21
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (34 bp):
CCCTAGCTTTTAACGGGCTAAACTAGAACACTTC
Found at i:43825 original size:8 final size:8
Alignment explanation
Indices: 43812--43856 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
43802 TTGCAGCCTT
43812 GATGCATG
1 GATGCATG
43820 GATGCAT-
1 GATGCATG
43827 G--GCA-G
1 GATGCATG
*
43832 GATGCATC
1 GATGCATG
43840 GATGCATG
1 GATGCATG
43848 GATGCATG
1 GATGCATG
43856 G
1 G
43857 CAAGGATGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
5 4 0.13
7 4 0.13
8 23 0.74
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (8 bp):
GATGCATG
Found at i:43836 original size:12 final size:12
Alignment explanation
Indices: 43819--43867 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 12
43809 CTTGATGCAT
43819 GGATGCATGGCA
1 GGATGCATGGCA
43831 GGATGCATCGATGCA
1 GGATGCAT-G--GCA
43846 TGGATGCATGGCAA
1 -GGATGCATGGC-A
43860 GGATGCAT
1 GGATGCAT
43868 CGATGCACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 8 0.25
13 11 0.34
14 1 0.03
15 4 0.12
16 8 0.25
ACGTcount: A:0.27, C:0.16, G:0.37, T:0.20
Consensus pattern (12 bp):
GGATGCATGGCA
Found at i:43852 original size:28 final size:29
Alignment explanation
Indices: 43812--43874 Score: 119
Period size: 28 Copynumber: 2.2 Consensus size: 29
43802 TTGCAGCCTT
43812 GATGCATGGATGCATGGC-AGGATGCATC
1 GATGCATGGATGCATGGCAAGGATGCATC
43840 GATGCATGGATGCATGGCAAGGATGCATC
1 GATGCATGGATGCATGGCAAGGATGCATC
43869 GATGCA
1 GATGCA
43875 CTAATTGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 18 0.53
29 16 0.47
ACGTcount: A:0.27, C:0.17, G:0.35, T:0.21
Consensus pattern (29 bp):
GATGCATGGATGCATGGCAAGGATGCATC
Found at i:44113 original size:30 final size:30
Alignment explanation
Indices: 44056--44113 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
44046 AACTTTGAAT
44056 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
44086 AAATTCAATTCAAGTCCAAAAACATTTT
1 AAATTCAATTCAAATCCAAAAACATTTT
44114 TCCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:55806 original size:12 final size:12
Alignment explanation
Indices: 55789--55814 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55779 TCTAGGACTC
55789 TAAGTTGTATTA
1 TAAGTTGTATTA
55801 TAAGTTGTATTA
1 TAAGTTGTATTA
55813 TA
1 TA
55815 GGACAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
TAAGTTGTATTA
Found at i:59283 original size:30 final size:30
Alignment explanation
Indices: 59239--59302 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
59229 TTCACTTTAA
* *
59239 TTCATTGTCATTCACTTTGATTTGCACATT
1 TTCATTCTCATTCACTTTGATTTGCACACT
* *
59269 TTCATTCTCTTTCACTTTGCTTTGCACACT
1 TTCATTCTCATTCACTTTGATTTGCACACT
59299 TTCA
1 TTCA
59303 CTTTCTTCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.25, G:0.08, T:0.50
Consensus pattern (30 bp):
TTCATTCTCATTCACTTTGATTTGCACACT
Found at i:59873 original size:45 final size:45
Alignment explanation
Indices: 59795--59880 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
59785 AGTCAAAAAC
*
59795 CAATGTTCAAGGGTTGTGAAAAATCCATGCATAAAATCTATACAA
1 CAATGTTCAAGGGTTATGAAAAATCCATGCATAAAATCTATACAA
* *
59840 CAATGTTCAAGGGTTATGAACAA-CTCATTCATAAAATCTAT
1 CAATGTTCAAGGGTTATGAAAAATC-CATGCATAAAATCTAT
59881 TAAATTCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (45 bp):
CAATGTTCAAGGGTTATGAAAAATCCATGCATAAAATCTATACAA
Found at i:61037 original size:543 final size:542
Alignment explanation
Indices: 59832--61372 Score: 2519
Period size: 543 Copynumber: 2.8 Consensus size: 542
59822 TGCATAAAAT
*
59832 CTATACAACAATGTTCAAGGGTTATGAACAACTCATTCATAAAATCTATTAAATTCATTTGAAAC
1 CTATACAACAATGTTTAAGGGTTATGAACAACTCATTCATAAAATCTATTAAATTCATTTGAAAC
* * *
59897 TCACAAAAACCCAAATATTTCAGAAAATCCATTCGAAAATAAAGAAATATTGGATGATTTGATTC
66 TCACACAAACCCAAATATTTCAGAAAACCCATTCGAAAATAAAGAAATATTGGATGATTCGATTC
* * * * * * * * * *
59962 AAAAAACCAAACTCACCTTCAAAATATGCGATTACATTATCGATGTAAGATCATGGTTCAATGAA
131 AAAAAAACAAACTCACCTTCGAAATATGCAATTACGTGATCTATGGAATATCCTGCTTCAATGAA
* * *
60027 ATTGAAGAAAATGAGAGGGGAAAATATTTGATATATTAGGGTTTAAAAACCCTAATATATTGGGA
196 ATTGAAGAAATTGAGAGGGGAAAAGATTTGATATATTAGGGTTTAAAAACCTTAATAT-TTGGGA
* * *
60092 ATAACCAGGTATCTCTTATTTGAGCATTTTACATAAGATATATACTACATGTGTTTAATTAATTT
260 ATAATCAGGTATCTCCTATTTGAGCATTTTACATAAG----AT-CTACATGTGTTTAATTATTTT
* *
60157 TATTAAATTTAAATATAATGTATATTAAATAAAGATT-TTTCATTATATAACAAAGTAAGCAACT
320 TATTAAATTTAAATATAATATATATTAAATAAAGTTTGTTTCATTATATAACAAAGTAAGCAACT
* **
60221 TGGTGTGGTGGTATGAGACACCTCATTCTATGTCTTTTACCTTAGTTTGATTTCCCTTCCATGTA
385 TGGTGTGGTGGTATGAGACACCTCATTCTATGCCTTTTACCCAAGTTTGATTTCCCTTCCATGTA
*
60286 AAAGAAATGTTCAAGGGTTATGAAACTCAAAGAAAAATCCAAATAAAAAGATTACTCTAATAGAA
450 AAAGAAATGTTCAAGGGTTATGAAACTCAAAGAAAAATCCAAATAAAAAAATTACTCTAATAGAA
*
60351 ACTCAACGAAAAATTAATTCGAGCTAAA
515 ACTCAACGAAAAATTAATTCGAACTAAA
*
60379 CTATACAATAATGTTTAAGGGTTATGAACAACTCATTCATAAAATCTATTAAATTCATTTGAAAC
1 CTATACAACAATGTTTAAGGGTTATGAACAACTCATTCATAAAATCTATTAAATTCATTTGAAAC
*
60444 TCACACAAACCCAAATATTTCAGAAAACCCATTCCAAAATAAAGAAATATTGGATGATTCGATTC
66 TCACACAAACCCAAATATTTCAGAAAACCCATTCGAAAATAAAGAAATATTGGATGATTCGATTC
60509 AAAAAAACAAACTCACCTTCGAAATATGCAATTACGTGATCTATGGAATATCCTGCTTCAATGAA
131 AAAAAAACAAACTCACCTTCGAAATATGCAATTACGTGATCTATGGAATATCCTGCTTCAATGAA
* *
60574 AATGAAGAAATTGATAGGGGGAAAAGATTTGATATATTAGGGTTTAAAAACCTTAATATTTGGGA
196 ATTGAAGAAATTGAGA-GGGGAAAAGATTTGATATATTAGGGTTTAAAAACCTTAATATTTGGGA
*
60639 ATAATCTGGTATCTCCTATTTGAGCATTTTACATAAGATCTACATGTGTTTAATTATTTTTATTA
260 ATAATCAGGTATCTCCTATTTGAGCATTTTACATAAGATCTACATGTGTTTAATTATTTTTATTA
*
60704 AATTTAAATATAATATATATTAAATAAAGTTTGTTTCATTATATAACAAAGTAAGCAACTTGCTG
325 AATTTAAATATAATATATATTAAATAAAGTTTGTTTCATTATATAACAAAGTAAGCAACTTGGTG
*
60769 TGGTGGTATGAGACACCTCATTCTATACCTTTTACCCAAGTTTGATTTCCCTTCCATGTAAAAGA
390 TGGTGGTATGAGACACCTCATTCTATGCCTTTTACCCAAGTTTGATTTCCCTTCCATGTAAAAGA
* *
60834 AATGTTCAAGGGTTATGAAACTCAAAGACAAATCCAAATAAAAAAATTACTCTAATAGAATCTCA
455 AATGTTCAAGGGTTATGAAACTCAAAGAAAAATCCAAATAAAAAAATTACTCTAATAGAAACTCA
60899 ACGAAAAATTCAATTCGAACTAAA
520 ACGAAAAATT-AATTCGAACTAAA
60923 CTATACAACAATGTTTAAGGGTTATGAACAACTCATTCATAAAATCTATTAAATTCATTTGAAAC
1 CTATACAACAATGTTTAAGGGTTATGAACAACTCATTCATAAAATCTATTAAATTCATTTGAAAC
*
60988 TCACACAAACCCAAATATTTCAGAAAACCCATTCGAAAATAAA-AAATATTGGATGATTCGATTT
66 TCACACAAACCCAAATATTTCAGAAAACCCATTCGAAAATAAAGAAATATTGGATGATTCGATTC
61052 AAAAAAACAAA-TCCACCTTCGAAATATGCAATTACGTGATCTATGGAATATCCTGCTTCAATGA
131 AAAAAAACAAACT-CACCTTCGAAATATGCAATTACGTGATCTATGGAATATCCTGCTTCAATGA
61116 AATTGAAGAAATTGAGAGGGG-AAAGATTTGATATATTAGGGTTTAAAAACCTTAATATTTGGGA
195 AATTGAAGAAATTGAGAGGGGAAAAGATTTGATATATTAGGGTTTAAAAACCTTAATATTTGGGA
* *
61180 ATAATCAGGTATCTCCTATTTGAGAATTTTACATAAGATCTACACGTGTTTAATTATTTTTTTAT
260 ATAATCAGGTATCTCCTATTTGAGCATTTTACATAAGATCTACATGTGTTTAATTA--TTTTTAT
* *
61245 TAAATTCAAATAAAATATATATTAAATAAAGTTTGTTTCATTATATAACAAAGTAAGCAACTTGG
323 TAAATTTAAATATAATATATATTAAATAAAGTTTGTTTCATTATATAACAAAGTAAGCAACTTGG
* *
61310 TGTGGTGGTAT--G-----TCATTCTATGCCATTTACCCAAGTTTGATTTCCCTTCCATATAAAA
388 TGTGGTGGTATGAGACACCTCATTCTATGCCTTTTACCCAAGTTTGATTTCCCTTCCATGTAAAA
61368 GAAAT
453 GAAAT
61373 TTTAATAATT
Statistics
Matches: 938, Mismatches: 50, Indels: 23
0.93 0.05 0.02
Matches are distributed among these distances:
536 48 0.05
541 97 0.10
542 60 0.06
543 343 0.37
544 118 0.13
547 232 0.25
548 40 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (542 bp):
CTATACAACAATGTTTAAGGGTTATGAACAACTCATTCATAAAATCTATTAAATTCATTTGAAAC
TCACACAAACCCAAATATTTCAGAAAACCCATTCGAAAATAAAGAAATATTGGATGATTCGATTC
AAAAAAACAAACTCACCTTCGAAATATGCAATTACGTGATCTATGGAATATCCTGCTTCAATGAA
ATTGAAGAAATTGAGAGGGGAAAAGATTTGATATATTAGGGTTTAAAAACCTTAATATTTGGGAA
TAATCAGGTATCTCCTATTTGAGCATTTTACATAAGATCTACATGTGTTTAATTATTTTTATTAA
ATTTAAATATAATATATATTAAATAAAGTTTGTTTCATTATATAACAAAGTAAGCAACTTGGTGT
GGTGGTATGAGACACCTCATTCTATGCCTTTTACCCAAGTTTGATTTCCCTTCCATGTAAAAGAA
ATGTTCAAGGGTTATGAAACTCAAAGAAAAATCCAAATAAAAAAATTACTCTAATAGAAACTCAA
CGAAAAATTAATTCGAACTAAA
Found at i:62589 original size:90 final size:90
Alignment explanation
Indices: 62433--62604 Score: 299
Period size: 90 Copynumber: 1.9 Consensus size: 90
62423 CCTAACACAC
* * * *
62433 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
62498 ATTTAATTAATTGAAATCTAATAAT
66 ATTTAATTAATTGAAATCTAATAAT
*
62523 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
62588 ATTTAATTAATTGAAAT
66 ATTTAATTAATTGAAAT
62605 AAATATTCGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 77 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
ATTTAATTAATTGAAATCTAATAAT
Found at i:66742 original size:14 final size:14
Alignment explanation
Indices: 66725--66761 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
66715 TGCTTGTTCA
66725 TTTATGTTCGTTTG
1 TTTATGTTCGTTTG
* *
66739 TTTATATTTGTTTG
1 TTTATGTTCGTTTG
66753 TTTATGTTC
1 TTTATGTTC
66762 ATTTATGTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.16, T:0.68
Consensus pattern (14 bp):
TTTATGTTCGTTTG
Found at i:67294 original size:19 final size:19
Alignment explanation
Indices: 67249--67287 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
67239 TACCGATGCA
67249 GAGACTCGGGCGTAGTGAT
1 GAGACTCGGGCGTAGTGAT
67268 GAGACTCGGGCGTAGTGAT
1 GAGACTCGGGCGTAGTGAT
67287 G
1 G
67288 TTACTCGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.44, T:0.21
Consensus pattern (19 bp):
GAGACTCGGGCGTAGTGAT
Found at i:78239 original size:17 final size:17
Alignment explanation
Indices: 78219--78252 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
78209 AGATTGCCAT
78219 GGCAATTCAATTGAATC
1 GGCAATTCAATTGAATC
78236 GGCAATTCAATTGAATC
1 GGCAATTCAATTGAATC
78253 ACAAAGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (17 bp):
GGCAATTCAATTGAATC
Found at i:88568 original size:60 final size:60
Alignment explanation
Indices: 88460--88702 Score: 330
Period size: 60 Copynumber: 4.1 Consensus size: 60
88450 CTGTTCTAAA
* * *
88460 ATGAAAAGTTAAATGCCTAACAGTGCATTTTGG-AAGAAAGGTGTCACTAATGCAAGTTAG
1 ATGAAAAGTTAAATGCCTAACAGTGCATTTTGGCAA-AAATGTGCCACTAATACAAGTTAG
* * *
88520 ATGAAAAGTTAAACGCCTAACGGTGCATTTTGGCAAAAATGTGCCACTAATGCAAGTTAG
1 ATGAAAAGTTAAATGCCTAACAGTGCATTTTGGCAAAAATGTGCCACTAATACAAGTTAG
* * * *
88580 ATGACAAGTTAAATGCCTAACAGTGCATTTTGGTAGAAATATGCCACTAATACAAGTTAG
1 ATGAAAAGTTAAATGCCTAACAGTGCATTTTGGCAAAAATGTGCCACTAATACAAGTTAG
* * *
88640 ATGAAAAGTTAAATGCCTAACGGTGCATTTT-GCAGAAAA-GTGCCATTAATACAAGTTAT
1 ATGAAAAGTTAAATGCCTAACAGTGCATTTTGGCA-AAAATGTGCCACTAATACAAGTTAG
88699 ATGA
1 ATGA
88703 CAAATGGTGC
Statistics
Matches: 163, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
59 23 0.14
60 138 0.85
61 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (60 bp):
ATGAAAAGTTAAATGCCTAACAGTGCATTTTGGCAAAAATGTGCCACTAATACAAGTTAG
Found at i:88758 original size:46 final size:46
Alignment explanation
Indices: 88705--88792 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
88695 TTATATGACA
* *
88705 AATGGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGCAT
1 AATGGTGCATAATCGACATGAAAGGATGCCACAAATGAAAATGCAT
*
88751 AATGGTGCATAATCGACATGAACGGATGCCACAAATGAAAAT
1 AATGGTGCATAATCGACATGAAAGGATGCCACAAATGAAAAT
88793 ATATAACAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.22
Consensus pattern (46 bp):
AATGGTGCATAATCGACATGAAAGGATGCCACAAATGAAAATGCAT
Found at i:88814 original size:46 final size:46
Alignment explanation
Indices: 88709--88821 Score: 129
Period size: 46 Copynumber: 2.5 Consensus size: 46
88699 ATGACAAATG
* * * **
88709 GTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAATG
1 GTGCATTAACGACATGAAAGGATGCCACAAATGAAAATACATAACA
* *
88755 GTGCA-TAATCGACATGAACGGATGCCACAAATGAAAATATATAACA
1 GTGCATTAA-CGACATGAAAGGATGCCACAAATGAAAATACATAACA
* *
88801 GTGTATTAACGACATAAAAGG
1 GTGCATTAACGACATGAAAGG
88822 TGTTACTCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
45 2 0.04
46 50 0.91
47 3 0.05
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (46 bp):
GTGCATTAACGACATGAAAGGATGCCACAAATGAAAATACATAACA
Found at i:92543 original size:60 final size:58
Alignment explanation
Indices: 92452--92692 Score: 302
Period size: 60 Copynumber: 4.0 Consensus size: 58
92442 TCTAAAATGA
*
92452 AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGAGGTCACTAATGATAGTTAGATG
1 AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAG-GGCCACTAATGA-AGTTAGATG
* * *
92512 AAAAGTTAAATGTCTAACGGTGCATTATGGCAGAAATGTGCCACTAATGGAAGTTAGATG
1 AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAA-GGGCCACTAAT-GAAGTTAGATG
* **
92572 AAAAGCTAAATGCCTAACGGTGCATTTTGGCAGAAAGGTGCCACTAACACAAGTTAGATG
1 AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGG-GCCACTAA-TGAAGTTAGATG
* * * * *
92632 AAAAGTTAAATGCCCAACGATGTATTTTGGAAGAAATGTGCCACTAATGCAAGTTAGATG
1 AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAA-GGGCCACTAATG-AAGTTAGATG
92692 A
1 A
92693 CAAATGTTGC
Statistics
Matches: 157, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
59 1 0.01
60 152 0.97
61 4 0.03
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (58 bp):
AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGGGCCACTAATGAAGTTAGATG
Found at i:92667 original size:120 final size:120
Alignment explanation
Indices: 92452--92692 Score: 351
Period size: 120 Copynumber: 2.0 Consensus size: 120
92442 TCTAAAATGA
* * * *
92452 AAAAGTTAAATGCCTAACGGTGCATTTTGGCAGAAAGAGGTCACTAATGATAGTTAGATGAAAAG
1 AAAAGCTAAATGCCTAACGGTGCATTTTGGCAGAAAGAGGCCACTAATCAAAGTTAGATGAAAAG
* * * * *
92517 TTAAATGTCTAACGGTGCATTATGGCAGAAATGTGCCACTAATGGAAGTTAGATG
66 TTAAATGCCCAACGATGCATTATGGAAGAAATGTGCCACTAATGCAAGTTAGATG
92572 AAAAGCTAAATGCCTAACGGTGCATTTTGGCAGAAAG-GTGCCACTAA-CACAAGTTAGATGAAA
1 AAAAGCTAAATGCCTAACGGTGCATTTTGGCAGAAAGAG-GCCACTAATCA-AAGTTAGATGAAA
* *
92635 AGTTAAATGCCCAACGATGTATTTTGGAAGAAATGTGCCACTAATGCAAGTTAGATG
64 AGTTAAATGCCCAACGATGCATTATGGAAGAAATGTGCCACTAATGCAAGTTAGATG
92692 A
1 A
92693 CAAATGTTGC
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
119 2 0.02
120 106 0.98
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (120 bp):
AAAAGCTAAATGCCTAACGGTGCATTTTGGCAGAAAGAGGCCACTAATCAAAGTTAGATGAAAAG
TTAAATGCCCAACGATGCATTATGGAAGAAATGTGCCACTAATGCAAGTTAGATG
Done.