Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008399.1 Hibiscus syriacus cultivar Beakdansim tig00111168_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: 53275
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3844 original size:21 final size:22
Alignment explanation
Indices: 3795--3864 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
3785 AATAACCAAT
* *
3795 AAATTCGCAACGCGAA-CT-CC
1 AAATTCGCAACACGAATTTCCC
* *
3815 AATTTCGCAACAC-AATTTCCT
1 AAATTCGCAACACGAATTTCCC
*
3836 AAATTCGCAACGCGAATTTCCC
1 AAATTCGCAACACGAATTTCCC
3858 AAATTCG
1 AAATTCG
3865 TAACTGAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.05
20 12 0.30
21 12 0.30
22 14 0.35
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.24
Consensus pattern (22 bp):
AAATTCGCAACACGAATTTCCC
Found at i:3853 original size:22 final size:22
Alignment explanation
Indices: 3794--3896 Score: 92
Period size: 21 Copynumber: 4.9 Consensus size: 22
3784 AAATAACCAA
*
3794 TAAATTCGCAACGCGAA-CTCC
1 TAAATTCGCAACGCGAATTTCC
* *
3815 -AATTTCGCAACAC-AATTTCC
1 TAAATTCGCAACGCGAATTTCC
3835 TAAATTCGCAACGCGAATTTCC
1 TAAATTCGCAACGCGAATTTCC
* * * *
3857 CAAATTCGTAAC-TGAGTTT-C
1 TAAATTCGCAACGCGAATTTCC
3877 TGAAA-TCGCAACGCGAATTT
1 T-AAATTCGCAACGCGAATTT
3897 GCACATAAGT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.03
20 21 0.33
21 24 0.38
22 17 0.27
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (22 bp):
TAAATTCGCAACGCGAATTTCC
Found at i:4103 original size:22 final size:22
Alignment explanation
Indices: 4078--4124 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
4068 TCTCTACGAA
*
4078 GACATCCGTCCCCATCTCCGGC
1 GACATCCGTCCCCATATCCGGC
4100 GACATCCGTCCCCATATCCGGC
1 GACATCCGTCCCCATATCCGGC
4122 GAC
1 GAC
4125 CCCCTCTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.47, G:0.19, T:0.17
Consensus pattern (22 bp):
GACATCCGTCCCCATATCCGGC
Found at i:4485 original size:20 final size:20
Alignment explanation
Indices: 4462--4500 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
4452 TTTGAAATTT
4462 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
4482 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
4501 CGCAACGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:4530 original size:20 final size:21
Alignment explanation
Indices: 4510--4560 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
4500 TCGCAACGCG
*
4510 ATTTTAGTTTTCGCGTTGCGA
1 ATTTAAGTTTTCGCGTTGCGA
* *
4531 ATTTCA-TTTTCGTGTTGCGA
1 ATTTAAGTTTTCGCGTTGCGA
4551 ATTTAAGTTT
1 ATTTAAGTTT
4561 CAAAAACTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.51
Consensus pattern (21 bp):
ATTTAAGTTTTCGCGTTGCGA
Found at i:6109 original size:42 final size:42
Alignment explanation
Indices: 6049--6147 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
6039 CCCCCTACTT
* * *
6049 CGAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTAGACAC
*
6091 CGAGAGCCATCACTTGATCGAGCCGATTATACACCTAGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTAGACAC
6133 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
6148 ATTCCATCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.28, C:0.34, G:0.20, T:0.17
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTAGACAC
Found at i:6289 original size:21 final size:21
Alignment explanation
Indices: 6262--6311 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
6252 GTTAGGGGAG
*
6262 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* *
6283 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
6304 TTACGTGA
1 TTACGTGA
6312 CGACAATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:6740 original size:21 final size:21
Alignment explanation
Indices: 6716--6827 Score: 100
Period size: 21 Copynumber: 5.3 Consensus size: 21
6706 AGAGAAGCCC
* *
6716 GATCCACCTGCCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
*
6737 GATCCACCTCCCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* * ** *
6758 GATTCATCTGTCATCGTTCAA
1 GATCCACCTCCCATCGTTCAG
* * *
6779 GAGGCC-CCTCTCATCGTTCAA
1 GA-TCCACCTCCCATCGTTCAG
*
6800 GATCCACCTCCCACCGTTCAG
1 GATCCACCTCCCATCGTTCAG
6821 GATCCAC
1 GATCCAC
6828 ATGGCATACT
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
20 2 0.03
21 71 0.96
22 1 0.01
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.27
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:8367 original size:20 final size:20
Alignment explanation
Indices: 8327--8411 Score: 100
Period size: 20 Copynumber: 4.2 Consensus size: 20
8317 GAAAGTCAAA
* * *
8327 TTCGCATTGCGATTTTTATT
1 TTCGCGTTGCGAATTTGATT
*
8347 TTCGCG-TGTCAAATTTGATT
1 TTCGCGTTG-CGAATTTGATT
*
8367 TTCGTGTTGCGAATTTGATT
1 TTCGCGTTGCGAATTTGATT
*
8387 TTCGCGTTGCGAATTTGACT
1 TTCGCGTTGCGAATTTGATT
8407 TTCGC
1 TTCGC
8412 AATAATCGCA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.04
20 51 0.93
21 2 0.04
ACGTcount: A:0.15, C:0.16, G:0.21, T:0.47
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTGATT
Found at i:10970 original size:24 final size:24
Alignment explanation
Indices: 10936--10989 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
10926 TCAAAACATC
10936 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
10960 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
10984 ATCAAA
1 ATCAAA
10990 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:11936 original size:40 final size:39
Alignment explanation
Indices: 11891--11995 Score: 104
Period size: 40 Copynumber: 2.7 Consensus size: 39
11881 AAATAAAAGC
*
11891 TGTTGCGAATTCGAAAATCGAGTTGCAAAAACAAAATTCG
1 TGTTGCGAATTCGAAAATCCAGTTGCAAAAA-AAAATTCG
* * ** * *
11931 TGTTGCAAATTAGAAAATCTTGTTGCGAAAAGAAATTCG
1 TGTTGCGAATTCGAAAATCCAGTTGCAAAAAAAAATTCG
* *
11970 CGTTACGAATTC-AGAAATCCAGTTGC
1 TGTTGCGAATTCGA-AAATCCAGTTGC
11996 GAATTTGAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.02
39 25 0.48
40 26 0.50
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (39 bp):
TGTTGCGAATTCGAAAATCCAGTTGCAAAAAAAAATTCG
Found at i:11985 original size:21 final size:21
Alignment explanation
Indices: 11892--12062 Score: 81
Period size: 20 Copynumber: 8.5 Consensus size: 21
11882 AATAAAAGCT
* *
11892 GTTGCGAATTC-GAAAATCGA
1 GTTGCGAATTCAGAAATTCGC
* ** *
11912 GTTGCAAAAACA-AAATTCGT
1 GTTGCGAATTCAGAAATTCGC
* * **
11932 GTTGCAAATT-AGAAAATCTT
1 GTTGCGAATTCAGAAATTCGC
*
11952 GTTGCGAA--AAGAAATTCGC
1 GTTGCGAATTCAGAAATTCGC
*
11971 GTTACGAATTCAGAAA-TC-C
1 GTTGCGAATTCAGAAATTCGC
* *
11990 AGTTGCGAATT-TGAAATTCCGT
1 -GTTGCGAATTCAGAAATT-CGC
** *
12012 GTTGCGAATTTGGAAATTTGC
1 GTTGCGAATTCAGAAATTCGC
* * *
12033 GTTGCGATTTCAGAAACT-GA
1 GTTGCGAATTCAGAAATTCGC
12053 GTTGCGAATT
1 GTTGCGAATT
12063 TGAAAATTGT
Statistics
Matches: 114, Mismatches: 27, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
19 20 0.18
20 57 0.50
21 31 0.27
22 6 0.05
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (21 bp):
GTTGCGAATTCAGAAATTCGC
Found at i:12035 original size:62 final size:61
Alignment explanation
Indices: 11932--12086 Score: 167
Period size: 62 Copynumber: 2.6 Consensus size: 61
11922 CAAAATTCGT
* * *
11932 GTTGCAAATTAGAAAATCT-TGTTGCGAAA--AGAAATTCGCGTTACGAATTCAGAAA-TCCA
1 GTTGCGAATTTGAAAAT-TGTGTTGCGAAATTGGAAATTCGCGTTACGAATTCAGAAACT-CA
* * * * *
11991 GTTGCGAATTTG-AAATTCCGTGTTGCGAATTTGGAAATTTGCGTTGCGATTTCAGAAACTGA
1 GTTGCGAATTTGAAAATT--GTGTTGCGAAATTGGAAATTCGCGTTACGAATTCAGAAACTCA
12053 GTTGCGAATTTGAAAATTGTGTTGCGAAATTGGA
1 GTTGCGAATTTGAAAATTGTGTTGCGAAATTGGA
12087 GTTCGATTTG
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
57 1 0.01
58 4 0.05
59 10 0.12
60 9 0.11
61 15 0.19
62 35 0.44
63 6 0.08
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (61 bp):
GTTGCGAATTTGAAAATTGTGTTGCGAAATTGGAAATTCGCGTTACGAATTCAGAAACTCA
Found at i:12083 original size:21 final size:20
Alignment explanation
Indices: 11991--12080 Score: 85
Period size: 20 Copynumber: 4.4 Consensus size: 20
11981 CAGAAATCCA
11991 GTTGCGAATTTG-AAATTCCGT
1 GTTGCGAATTTGAAAATT--GT
* *
12012 GTTGCGAATTTGGAAATTTGC
1 GTTGCGAATTT-GAAAATTGT
* * *
12033 GTTGCG-ATTTCAGAAACTGA
1 GTTGCGAATTTGA-AAATTGT
12053 GTTGCGAATTTGAAAATTGT
1 GTTGCGAATTTGAAAATTGT
12073 GTTGCGAA
1 GTTGCGAA
12081 ATTGGAGTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.02
20 27 0.48
21 23 0.41
22 1 0.02
23 4 0.07
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATTGT
Found at i:12300 original size:15 final size:16
Alignment explanation
Indices: 12277--12309 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12267 ATTTTTTAAA
*
12277 ATTATAATAAA-TTTT
1 ATTAAAATAAACTTTT
12292 ATTAAAATAAACTTTT
1 ATTAAAATAAACTTTT
12308 AT
1 AT
12310 CATTAACCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAAAATAAACTTTT
Found at i:12782 original size:29 final size:30
Alignment explanation
Indices: 12750--12825 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
12740 ATAATTTTTT
*
12750 TAATCATTAAAATTTTAAA-ATTTACAAAA
1 TAATCATTAAAATTTTAAACAATTACAAAA
*
12779 TAATCATTAAAATTTTTAAACAATTATAAAA
1 TAATCATTAAAA-TTTTAAACAATTACAAAA
*
12810 TAATCA-TCAAATTTTA
1 TAATCATTAAAATTTTA
12826 TCAACTATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 17 0.40
30 11 0.26
31 14 0.33
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (30 bp):
TAATCATTAAAATTTTAAACAATTACAAAA
Found at i:12813 original size:31 final size:30
Alignment explanation
Indices: 12750--12824 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
12740 ATAATTTTTT
*
12750 TAATCATTAAAA-TTTTAAAATTTACAAAA
1 TAATCATTAAAATTTTTAAAAATTACAAAA
*
12779 TAATCATTAAAATTTTTAAACAATTATAAAA
1 TAATCATTAAAATTTTTAAA-AATTACAAAA
*
12810 TAATCA-TCAAATTTT
1 TAATCATTAAAATTTT
12825 ATCAACTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
29 12 0.29
30 15 0.37
31 14 0.34
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (30 bp):
TAATCATTAAAATTTTTAAAAATTACAAAA
Found at i:18787 original size:17 final size:17
Alignment explanation
Indices: 18761--18799 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
18751 TAAAATTACA
*
18761 AAATTTCAGAAAATACG
1 AAATTACAGAAAATACG
18778 AAATTACAGAAAATACG
1 AAATTACAGAAAATACG
18795 AAATT
1 AAATT
18800 TTATATTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (17 bp):
AAATTACAGAAAATACG
Found at i:23701 original size:118 final size:118
Alignment explanation
Indices: 23493--23730 Score: 476
Period size: 118 Copynumber: 2.0 Consensus size: 118
23483 TAACTAATTT
23493 ATTTTTTTAATTGGGAACATGTCCTTGAATGGACGGAGCACGTAGTTAATCAGTTCATGATGGAC
1 ATTTTTTTAATTGGGAACATGTCCTTGAATGGACGGAGCACGTAGTTAATCAGTTCATGATGGAC
23558 GTCCTGATCTATTAAGCCTTGTGCTTTAGTTGATAGTTTGGACAATGAGCGAC
66 GTCCTGATCTATTAAGCCTTGTGCTTTAGTTGATAGTTTGGACAATGAGCGAC
23611 ATTTTTTTAATTGGGAACATGTCCTTGAATGGACGGAGCACGTAGTTAATCAGTTCATGATGGAC
1 ATTTTTTTAATTGGGAACATGTCCTTGAATGGACGGAGCACGTAGTTAATCAGTTCATGATGGAC
23676 GTCCTGATCTATTAAGCCTTGTGCTTTAGTTGATAGTTTGGACAATGAGCGAC
66 GTCCTGATCTATTAAGCCTTGTGCTTTAGTTGATAGTTTGGACAATGAGCGAC
23729 AT
1 AT
23731 CAAAAGATCC
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 120 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (118 bp):
ATTTTTTTAATTGGGAACATGTCCTTGAATGGACGGAGCACGTAGTTAATCAGTTCATGATGGAC
GTCCTGATCTATTAAGCCTTGTGCTTTAGTTGATAGTTTGGACAATGAGCGAC
Found at i:32996 original size:12 final size:12
Alignment explanation
Indices: 32979--33009 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
32969 TAGCACACTC
32979 GATTGCTTGTTG
1 GATTGCTTGTTG
32991 GATTGCTTGTTG
1 GATTGCTTGTTG
*
33003 GTTTGCT
1 GATTGCT
33010 AGTTTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.10, G:0.32, T:0.52
Consensus pattern (12 bp):
GATTGCTTGTTG
Found at i:38982 original size:2 final size:2
Alignment explanation
Indices: 38969--39015 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
38959 TCCCATAGAT
* *
38969 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39011 AG AG A
1 AG AG A
39016 TATGAAAGCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40952 original size:81 final size:80
Alignment explanation
Indices: 40831--42326 Score: 1454
Period size: 81 Copynumber: 18.6 Consensus size: 80
40821 TCTGAAGACA
* * ** * **
40831 GTTGTTGTTTCTCTTGAGAAGCTAGCATTGTTGAGTCTTCTTTCTTGGAATCCTCGTCTTGCTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCTTT-TTGGAATCCTCGTCTTGCTGA
* *
40896 GGCTCTGAAGACAATT
65 GGCTCCGAAGACGATT
* * *
40912 GATGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCTTTCTTGGAATCCTTGTCTAGCTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCTTT-TTGGAATCCTCGTCTTGCTGA
* *
40977 CGTTCCGAAGACGATT
65 GGCTCCGAAGACGATT
* * * * *
40993 GCTGTTGGTTCTCTTGAGAAGATGGTGCTGGTGAACCTTCTATTTTGGAATCCTCGTCTTGCTCA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCT-TTTTGGAATCCTCGTCTTGCTGA
*
41058 GGCTCCGAAGACAATT
65 GGCTCCGAAGACGATT
* * * * *
41074 GTTGTTGGTTCTCTTGAGAAGCTAGCGCTGATGAACCTTCTTTCTTGGAATCATTGCCTTGGTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCTTT-TTGGAATCCTCGTCTTGCTGA
* * *
41139 TGCTCCAAAGACGGTT
65 GGCTCCGAAGACGATT
* * * * * ** *
41155 GTTGCTGGTTCTCGTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCAGAATCCTCATCTTGCTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTT-CTTTTTGGAATCCTCGTCTTGCTGA
*
41220 GGCTCCGAAGATGATT
65 GGCTCCGAAGACGATT
* ** ** *
41236 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATAAACCTTCCTTTTCAGAATTGTCATCTTGCTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTT-CTTTTTGGAATCCTCGTCTTGCTGA
* *
41301 GGCTCCGAAAACAATT
65 GGCTCCGAAGACGATT
* * * * * * * *
41317 GCAT-TTGGTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTCGAAATCCTCATCTTGTTG
1 G-TTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTT-CTTTTTGGAATCCTCGTCTTGCTG
* *
41381 AGGCTTCGAAGATGATT
64 AGGCTCCGAAGACGATT
* * * *
41398 GTTGTTGGTTCTCTTGAGAAGCTGGCACTGATGCA-CTTCCCTTTTCGGAA---TCATCTTGCTG
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTT--CTTTTTGGAATCCTCGTCTTGCTG
*
41459 AGGCTCCGAAGACAATT
64 AGGCTCCGAAGACGATT
* * *
41476 GCATT-TT-GTTCTCTTGAGAAGCTGGCTCTAATGATCCTTCCTTTTTGGAATCCTCGTCTTGCT
1 G--TTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTT-CTTTTTGGAATCCTCGTCTTGCT
*
41539 GAGGCTCCCAAGACGATT
63 GAGGCTCCGAAGACGATT
* * * * * * * *
41557 GTTGTTGGTTATATTGACAAGCTGGTGCTGATGAACTTTCCTTTTCGGAATCCTCGGCTTGTTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTT-CTTTTTGGAATCCTCGTCTTGCTGA
* **
41622 GGCTCTGAAGAAAATT
65 GGCTCCGAAGACGATT
* * * * * * *
41638 GCAT-TTGGTTCTCTTGAGAAGCTGGCTCTAAT-AATCCTTCCTTTTCGGAATCCTCATCTAGTT
1 G-TTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAA-CCTT-CTTTTTGGAATCCTCGTCTTGCT
* *
41701 GAGGCTCTGAAGATGATT
63 GAGGCTCCGAAGACGATT
* * * * *
41719 GTTGTTGGTTCTCTTGAGAGGCTGGTGCTGATGATCCTTCCTTTTCGGAATCCTCGTCTTGTTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTT-CTTTTTGGAATCCTCGTCTTGCTGA
*
41784 GGCTCCGAAGATGATT
65 GGCTCCGAAGACGATT
**
41800 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCATTTTTGGAATCCTCACCTTGCTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTC-TTTTTGGAATCCTCGTCTTGCTGA
*
41865 GGCTCTGAAGACGATT
65 GGCTCCGAAGACGATT
* * *
41881 GCTGTTGGTTCTCTTGAGAAGCTGGCGTTGATGAACCTT-TTTTTCCAGAATCCTCGTCTTGCTG
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCTTTTT--GGAATCCTCGTCTTGCTG
* * *
41945 AGGCTCAGAAGACAACT
64 AGGCTCCGAAGACGATT
* * ** ***
41962 GCTGTTGGTTCTCTTGAGAAACTGGAACTGATGAACCTTCTTTCCAGAATCCTCGTCTTGCTGAG
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCTTTTTGGAATCCTCGTCTTGCTGAG
42027 GCTCCGAAGACGATT
66 GCTCCGAAGACGATT
* * * * * *
42042 GTTTTTGGTTCTCTTCAGAAGTTGGCTCTGATGAACCTTCTTTCTTGGAATCCTTGTTTTGCTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCTTT-TTGGAATCCTCGTCTTGCTGA
* * *
42107 GACTCTGAAGACAATT
65 GGCTCCGAAGACGATT
* * * *
42123 GTTGTTGGTTCTCTTCAGAAGCTGGTGCTGATGAACCTTCTTTAATGGAATCCTTGTCTTGCTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCTTT-TTGGAATCCTCGTCTTGCTGA
* * * *
42188 GCCTCTGAAAATGATT
65 GGCTCCGAAGACGATT
* ** * * * *
42204 GCTGTTGGTTCTCTTGAGAAATTGGCACTGATGAACCTTCTTTTTTGGTATCTTTGTCTTGCTGA
1 GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTC-TTTTTGGAATCCTCGTCTTGCTGA
* *
42269 CGCTCCAAAGACGATT
65 GGCTCCGAAGACGATT
* * *
42285 TTTGTTGGTTCAT-TTTAGAAGCT-GCTCT--TGAACCTTCTTTTT
1 GTTGTTGGTTC-TCTTGAGAAGCTGGCGCTGATGAACCTTCTTTTT
42327 TGGCCTCCTT
Statistics
Matches: 1182, Mismatches: 208, Indels: 54
0.82 0.14 0.04
Matches are distributed among these distances:
77 5 0.00
78 68 0.06
79 12 0.01
80 86 0.07
81 995 0.84
82 16 0.01
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (80 bp):
GTTGTTGGTTCTCTTGAGAAGCTGGCGCTGATGAACCTTCTTTTTGGAATCCTCGTCTTGCTGAG
GCTCCGAAGACGATT
Found at i:42844 original size:18 final size:18
Alignment explanation
Indices: 42821--42860 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
42811 GCCAAGGCTA
42821 GAGCCCTGGCTTGATGAT
1 GAGCCCTGGCTTGATGAT
*
42839 GAGCCCTGGTTTGATGAT
1 GAGCCCTGGCTTGATGAT
42857 GAGC
1 GAGC
42861 GAACACATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.28
Consensus pattern (18 bp):
GAGCCCTGGCTTGATGAT
Found at i:51090 original size:23 final size:23
Alignment explanation
Indices: 51064--51111 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
51054 ATAAAGTACA
* *
51064 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
**
51087 ATAATGTAATAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
51110 AT
1 AT
51112 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:51647 original size:22 final size:23
Alignment explanation
Indices: 51577--51627 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
51567 GATACTTACA
*
51577 ATAT-AACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
51599 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
51622 ATATAA
1 ATATAA
51628 GTGTTACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:52067 original size:22 final size:23
Alignment explanation
Indices: 52006--52077 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
51996 ATAACTTACA
* * *
52006 ATATAAGCACTACCTATTATATT
1 ATATAAACGCTACCTATTACATT
52029 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
52052 ATATAAACG-TACCTATTACATC
1 ATATAAACGCTACCTATTACATT
52074 ATAT
1 ATAT
52078 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 16 0.36
23 29 0.64
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:52273 original size:430 final size:423
Alignment explanation
Indices: 51472--52315 Score: 1409
Period size: 429 Copynumber: 2.0 Consensus size: 423
51462 ATACATATAA
* * *
51472 TTACTAAATTGATATTTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCACAGTGAA
1 TTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
* *
51537 ATAAGTATGTACACTTTTATAAAAATGATAGATACTTACAATATAACACTACCTATTACATTATA
66 AAAAGTATGGACACTTTTATAAAAATGATAGATACTTACAATATAACACTACCTATTACATTATA
**
51602 TAAACGCTACCTATTACATTATATAAGTGTTACTATTACATCATATTTTTACCTATTATATTGAA
131 TAAACGCTACCTATTACATTATATAAACGTTACTATTACATCATATTTTTACCTATTATATTGAA
* *
51667 AGTGTCCATACTTTTATAAAAAGAATCGATATTTTTTTTAAAGTTATGTAATTATGTTTCAATTT
196 AGTGTCCATACTTTTATAAAAAGAATCGATACTTTTTTTAAAGTTATATAATTATGTTTCAATTT
51732 TTTTTAATAGTGTTTCATGTTTTCCACTAACAATATTAATTTAATAATTTCATTTGCACAAAAAA
261 TTTTTAATAGTGTTTCATGTTTTCCACTAACAATATTAATTTAATAATTTCATTTGCAC--AAAA
51797 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCA
324 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTAAATTTAACAATATTAACCA
51862 AAGATAATAATAAATATGTAATATATGTTTATTTTTAAT
388 AAG---ATAATAAATATGTAATATATGTTTATTTTTAAT
51901 TTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
1 TTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
* *
51966 AAAAGTATGGACACTTTTATAAAAGT-ATAGATAACTTACAATATAAGCACTACCTATTATATTA
66 AAAAGTATGGACACTTTTATAAAAATGATAGAT-ACTTACAATATAA-CACTACCTATTACATTA
52030 TATAAACGCTACCTATTACATTATATAAACG-TACCTATTACATCATATTTTTACCTATTATATT
129 TATAAACGCTACCTATTACATTATATAAACGTTA-CTATTACATCATATTTTTACCTATTATATT
52094 GAAAGTGTCCATACTTTTTATAAAAATG-ATCGATACTTTTTTTAAAGTTATATAATTTATGTTT
193 GAAAGTGTCCATAC-TTTTATAAAAA-GAATCGATACTTTTTTTAAAGTTATATAA-TTATGTTT
52158 CAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCT-ACAATATTAATTTAATAATTTCATTTGCA
255 CAATTTTTTTTAATAGTGTTTCATGTTTTCCA-CTAACAATATTAATTTAATAATTTCATTTGCA
52221 C-AAAATTATTTGATTGTTTTGATA-TTTAT-AAA-AATATTTAGAATTAAATTTAACAATATTA
319 CAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTAAATTTAACAATATTA
52282 ACCAAAGATAATAAATATGTAATATATGTTTATT
384 ACCAAAGATAATAAATATGTAATATATGTTTATT
52316 GTTTTTAATT
Statistics
Matches: 397, Mismatches: 11, Indels: 22
0.92 0.03 0.05
Matches are distributed among these distances:
421 27 0.07
424 25 0.06
425 11 0.03
426 3 0.01
427 5 0.01
428 29 0.07
429 100 0.25
430 89 0.22
431 94 0.24
432 14 0.04
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (423 bp):
TTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
AAAAGTATGGACACTTTTATAAAAATGATAGATACTTACAATATAACACTACCTATTACATTATA
TAAACGCTACCTATTACATTATATAAACGTTACTATTACATCATATTTTTACCTATTATATTGAA
AGTGTCCATACTTTTATAAAAAGAATCGATACTTTTTTTAAAGTTATATAATTATGTTTCAATTT
TTTTTAATAGTGTTTCATGTTTTCCACTAACAATATTAATTTAATAATTTCATTTGCACAAAAAT
TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTAAATTTAACAATATTAACCAAAG
ATAATAAATATGTAATATATGTTTATTTTTAAT
Done.