Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002618.1 Hibiscus syriacus cultivar Beakdansim tig00005323_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: 113854
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3951 original size:43 final size:42
Alignment explanation
Indices: 3896--4187 Score: 255
Period size: 43 Copynumber: 6.9 Consensus size: 42
3886 TTTAAACAAA
* * * *
3896 AAACGCCACAATAGGTATTGATATTTAGCGGCGTTTGTGTGAC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTT-TCTCAC
* * * *
3939 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTGTGAC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTT-TCTCAC
* * * * *
3982 AAACGCCGCAATAGGTAATGATATTTAGCAGCGTTTTCCCAT
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTCTCAC
* * * * *
4024 AAACGCCGCACTAGGTGTTGATGTTTTGCGGCATTTTCCCAC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTCTCAC
* ** * * * * *
4066 AAACGCCACCGTAGATTTTGATGTTTTGCGGTGTTTAT-TCCAT
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTT-TCT-CAC
* * *
4109 AAACGCCGCAGTAGGTTTTGATGTTTTGCGGCGTTTTTCTCAC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCG-TTTTCTCAC
*
4152 AAACGCCGCAATATGTATTGAT-TTTTGCGGCGTTTT
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTT
4188 GCTAAAAACA
Statistics
Matches: 211, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
41 4 0.02
42 75 0.36
43 128 0.61
44 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (42 bp):
AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTCTCAC
Found at i:4178 original size:85 final size:84
Alignment explanation
Indices: 3896--4187 Score: 282
Period size: 85 Copynumber: 3.4 Consensus size: 84
3886 TTTAAACAAA
* * *** *
3896 AAACGCCACAATAGGTATTGATATTTAGCGGCGTTTGTGTGACAAACGCCGCAATAGGTGTTGAT
1 AAACGCCGCAATA-GTATTGATATTTTGCGGCGTTT-TCCCATAAACGCCGCAATAGGTGTTGAT
* * * * *
3961 ATTTAGCGGCGTTTGTGTGAC
64 GTTTTGCGGCGTTTTTCTCAC
* * * *
3982 AAACGCCGCAATAGGTAATGATATTTAGCAGCGTTTTCCCATAAACGCCGCACTAGGTGTTGATG
1 AAACGCCGCAATA-GTATTGATATTTTGCGGCGTTTTCCCATAAACGCCGCAATAGGTGTTGATG
* *
4047 TTTTGCGGC-ATTTTCCCAC
65 TTTTGCGGCGTTTTTCTCAC
* ** * * * * * *
4066 AAACGCCACCGTAGATTTTGATGTTTTGCGGTGTTTATTCCATAAACGCCGCAGTAGGTTTTGAT
1 AAACGCCGCAATAG-TATTGATATTTTGCGGCGTTT-TCCCATAAACGCCGCAATAGGTGTTGAT
4131 GTTTTGCGGCGTTTTTCTCAC
64 GTTTTGCGGCGTTTTTCTCAC
4152 AAACGCCGCAATATGTATTGAT-TTTTGCGGCGTTTT
1 AAACGCCGCAATA-GTATTGATATTTTGCGGCGTTTT
4188 GCTAAAAACA
Statistics
Matches: 168, Mismatches: 34, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
83 1 0.01
84 31 0.18
85 78 0.46
86 57 0.34
87 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (84 bp):
AAACGCCGCAATAGTATTGATATTTTGCGGCGTTTTCCCATAAACGCCGCAATAGGTGTTGATGT
TTTGCGGCGTTTTTCTCAC
Found at i:4621 original size:21 final size:21
Alignment explanation
Indices: 4598--4690 Score: 125
Period size: 21 Copynumber: 4.4 Consensus size: 21
4588 GCTGATATGT
*
4598 TGCTTCTCTTTGTGCTGCCGT
1 TGCTTCTCTTTGTGCTGCCGC
*
4619 TGCTTCTCTCTGTGCTGCCGC
1 TGCTTCTCTTTGTGCTGCCGC
4640 TGCTTCTCTTTGTGCTGCCGC
1 TGCTTCTCTTTGTGCTGCCGC
* *
4661 TGCTTCT-TTCTCTGCTTCCGC
1 TGCTTCTCTT-TGTGCTGCCGC
*
4682 TGCTGCTCT
1 TGCTTCTCT
4691 GGCTGCTTCT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
20 2 0.03
21 61 0.95
22 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.22, T:0.44
Consensus pattern (21 bp):
TGCTTCTCTTTGTGCTGCCGC
Found at i:4644 original size:42 final size:42
Alignment explanation
Indices: 4598--4718 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
4588 GCTGATATGT
* *
4598 TGCTTCTCTTTGTGCTGCCGTTGCTTCTCTCTGTGCTGCCGC
1 TGCTTCTCTTTGTGCTGCCGCTGCTTCTCTCTCTGCTGCCGC
* *
4640 TGCTTCTCTTTGTGCTGCCGCTGCTTCTTTCTCTGCTTCCGC
1 TGCTTCTCTTTGTGCTGCCGCTGCTTCTCTCTCTGCTGCCGC
* * * * *
4682 TGCTGCTC-TGGCTGCTTCTGCTGCTGCTCTCTCTGCT
1 TGCTTCTCTTTG-TGCTGCCGCTGCTTCTCTCTCTGCT
4719 TCCCTTGCTT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.03
42 66 0.97
ACGTcount: A:0.00, C:0.35, G:0.22, T:0.43
Consensus pattern (42 bp):
TGCTTCTCTTTGTGCTGCCGCTGCTTCTCTCTCTGCTGCCGC
Found at i:4687 original size:12 final size:12
Alignment explanation
Indices: 4654--4718 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
4644 TCTCTTTGTG
*
4654 CTGCCGCTGCTT
1 CTGCTGCTGCTT
*
4666 CTTTCT-CTGCTT
1 C-TGCTGCTGCTT
*
4678 CCGCTGCTGC-T
1 CTGCTGCTGCTT
4689 CTG--GCTGCTT
1 CTGCTGCTGCTT
4699 CTGCTGCTGCTCT
1 CTGCTGCTGCT-T
4712 CT-CTGCT
1 CTGCTGCT
4719 TCCCTTGCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
9 5 0.12
10 4 0.10
11 5 0.12
12 23 0.55
13 5 0.12
ACGTcount: A:0.00, C:0.38, G:0.22, T:0.40
Consensus pattern (12 bp):
CTGCTGCTGCTT
Found at i:4696 original size:21 final size:21
Alignment explanation
Indices: 4652--4721 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
4642 CTTCTCTTTG
* * * *
4652 TGCTGCCGCTGCTTCTTTCTC
1 TGCTTCCGCTGCTGCTCTCGC
*
4673 TGCTTCCGCTGCTGCTCTGGC
1 TGCTTCCGCTGCTGCTCTCGC
* *
4694 TGCTTCTGCTGCTGCTCTCTC
1 TGCTTCCGCTGCTGCTCTCGC
4715 TGCTTCC
1 TGCTTCC
4722 CTTGCTTCAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.00, C:0.39, G:0.21, T:0.40
Consensus pattern (21 bp):
TGCTTCCGCTGCTGCTCTCGC
Found at i:4727 original size:21 final size:20
Alignment explanation
Indices: 4619--4723 Score: 66
Period size: 21 Copynumber: 5.0 Consensus size: 20
4609 GTGCTGCCGT
* * *
4619 TGCTTCTCTCTGTGCTGCCGC
1 TGCTGCTCTCTCTGCTTCC-C
* * * *
4640 TGCTTCTCTTTGTGCTGCCGC
1 TGCTGCTCTCTCTGCTTCC-C
* *
4661 TGCTTCTTTCTCTGCTTCCGC
1 TGCTGCTCTCTCTGCTTCC-C
** *
4682 TGCTGCTCTGGCTGCTTCTGC
1 TGCTGCTCTCTCTGCTTC-CC
4703 TGCTGCTCTCTCTGCTTCCC
1 TGCTGCTCTCTCTGCTTCCC
4723 T
1 T
4724 TGCTTCATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
20 2 0.03
21 68 0.97
ACGTcount: A:0.00, C:0.37, G:0.21, T:0.42
Consensus pattern (20 bp):
TGCTGCTCTCTCTGCTTCCC
Found at i:8152 original size:42 final size:42
Alignment explanation
Indices: 8066--8269 Score: 177
Period size: 41 Copynumber: 5.0 Consensus size: 42
8056 GGCGTTGATA
* * * * *
8066 AAAAAACGTCACTATTGATT-ACACTATTGTGGCATTTGT-T
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTTCT
*
8106 AAAAAATGCCACTATTGATTAAAACTATTGCGGCGTTTTTCT
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTTCT
* * * * *
8148 -AAAAACGCCACTAGTGATTAACACTATTACGACGTTTGTCT
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTTCT
* * ***
8189 -AAAAATGCCACTATTTATTATCACTATTGCGGCGTTTTAAG
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTTCT
* * *
8230 AATAAATGCCACTATATG-TGTAA-TCTATTGCGGTGTTTTT
1 AAAAAATGCCACTAT-TGAT-TAACACTATTGCGGCGTTTTT
8270 GGTATAAACG
Statistics
Matches: 131, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
40 18 0.14
41 81 0.62
42 29 0.22
43 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (42 bp):
AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTTCT
Found at i:8198 original size:82 final size:81
Alignment explanation
Indices: 8067--8226 Score: 214
Period size: 82 Copynumber: 2.0 Consensus size: 81
8057 GCGTTGATAA
* * ** *
8067 AAAAACGTCACTATTGATTACACTATTGTGGCATTTGTTAAAAAATGCCACTATTGATTAAAACT
1 AAAAACGCCACTAGTGATTACACTATTACGACATTTGTTAAAAAATGCCACTATTGATTAAAACT
8132 ATTGCGGCGTTTTTCT
66 ATTGCGGCGTTTTTCT
* * **
8148 AAAAACGCCACTAGTGATTAACACTATTACGACGTTTGTCT-AAAAATGCCACTATTTATTATCA
1 AAAAACGCCACTAGTGATT-ACACTATTACGACATTTGT-TAAAAAATGCCACTATTGATTAAAA
8212 CTATTGCGGCGTTTT
64 CTATTGCGGCGTTTT
8227 AAGAATAAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
81 17 0.25
82 50 0.74
83 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (81 bp):
AAAAACGCCACTAGTGATTACACTATTACGACATTTGTTAAAAAATGCCACTATTGATTAAAACT
ATTGCGGCGTTTTTCT
Found at i:20544 original size:16 final size:17
Alignment explanation
Indices: 20523--20557 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
20513 TACTATACAC
*
20523 GTGAATAGT-GAATTTT
1 GTGAATAGTAAAATTTT
20539 GTGAATAGTAAAATTTT
1 GTGAATAGTAAAATTTT
20556 GT
1 GT
20558 CGGCGATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (17 bp):
GTGAATAGTAAAATTTT
Found at i:24793 original size:11 final size:11
Alignment explanation
Indices: 24777--24801 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24767 TGCTCATAGA
24777 TATTATCAATT
1 TATTATCAATT
24788 TATTATCAATT
1 TATTATCAATT
24799 TAT
1 TAT
24802 AATAAATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTATCAATT
Found at i:26872 original size:15 final size:15
Alignment explanation
Indices: 26826--26872 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
26816 TCGTGGAGGG
26826 GATGCAATCCTCTGA
1 GATGCAATCCTCTGA
* **
26841 GAAGCAGCCCT-TGGA
1 GATGCAATCCTCT-GA
26856 GATGCAATCCTCTGA
1 GATGCAATCCTCTGA
26871 GA
1 GA
26873 AAGAACCCGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (15 bp):
GATGCAATCCTCTGA
Found at i:26887 original size:30 final size:30
Alignment explanation
Indices: 26821--26892 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
26811 TAGGCTCGTG
* *
26821 GAGGGGATGCAATCCTCTGAGAAGCAGCCC
1 GAGGAGATGCAATCCTCTGAGAAGCAACCC
**
26851 TTGGAGATGCAATCCTCTGAGAAAG-AACCC
1 GAGGAGATGCAATCCTCTGAG-AAGCAACCC
*
26881 GAGGAGAAGCAA
1 GAGGAGATGCAA
26893 CCCTAGGAGG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 31 0.91
31 3 0.09
ACGTcount: A:0.33, C:0.22, G:0.31, T:0.14
Consensus pattern (30 bp):
GAGGAGATGCAATCCTCTGAGAAGCAACCC
Found at i:27507 original size:4 final size:4
Alignment explanation
Indices: 27498--27530 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
27488 TCAAACTATG
27498 TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA T
27531 GAAAGTACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:29042 original size:12 final size:12
Alignment explanation
Indices: 29025--29049 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29015 CTCCTCTCTA
29025 AGTAGGATTAGG
1 AGTAGGATTAGG
29037 AGTAGGATTAGG
1 AGTAGGATTAGG
29049 A
1 A
29050 TATAGTTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (12 bp):
AGTAGGATTAGG
Found at i:29074 original size:2 final size:2
Alignment explanation
Indices: 29067--29096 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29057 AGAATTTGTA
29067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29097 CGATGATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29450 original size:21 final size:21
Alignment explanation
Indices: 29426--29467 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29416 TTTACTAAAA
* * *
29426 CCTAAACCTTAAATCTTAATC
1 CCTAAAACATAAATCATAATC
29447 CCTAAAACATAAATCATAATC
1 CCTAAAACATAAATCATAATC
29468 AAATCTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (21 bp):
CCTAAAACATAAATCATAATC
Found at i:31220 original size:16 final size:16
Alignment explanation
Indices: 31199--31232 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
31189 ATAAACATCG
*
31199 AGCTTAACGAGTAACA
1 AGCTTAACGAGCAACA
31215 AGCTTAACGAGCAACA
1 AGCTTAACGAGCAACA
31231 AG
1 AG
31233 TTTTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.15
Consensus pattern (16 bp):
AGCTTAACGAGCAACA
Found at i:42879 original size:15 final size:17
Alignment explanation
Indices: 42859--42892 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
42849 TCAAGAATAA
42859 AATAAT-AAACAA-ATT
1 AATAATCAAACAATATT
42874 AATAATCAAACAATATT
1 AATAATCAAACAATATT
42891 AA
1 AA
42893 AATTAGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAATCAAACAATATT
Found at i:43069 original size:49 final size:49
Alignment explanation
Indices: 43005--43128 Score: 185
Period size: 49 Copynumber: 2.5 Consensus size: 49
42995 AAAACTGAAT
*
43005 ACAAAAATCAGAATGAGGATTTAGCCTTTCATAGAGGATTCCAGCAGAA
1 ACAAAAATCAGAATGAGGATTTAGCCATTCATAGAGGATTCCAGCAGAA
* * * * *
43054 ACAGAAATCAAAATGAGGATTTAGCCATTCGTAGAGGTTTCCAGCCGAA
1 ACAAAAATCAGAATGAGGATTTAGCCATTCATAGAGGATTCCAGCAGAA
*
43103 ATAAAAATCAGAATGAGGATTTAGCC
1 ACAAAAATCAGAATGAGGATTTAGCC
43129 CTCTGTAGAG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 66 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (49 bp):
ACAAAAATCAGAATGAGGATTTAGCCATTCATAGAGGATTCCAGCAGAA
Found at i:43267 original size:28 final size:28
Alignment explanation
Indices: 43233--43304 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
43223 GAACGAGGTT
43233 CCATGCAGAATCAGGACGAGGACTAAGC
1 CCATGCAGAATCAGGACGAGGACTAAGC
* * * *
43261 CTATGCAGAATCAAGATGGGGACTAAGC
1 CCATGCAGAATCAGGACGAGGACTAAGC
* *
43289 CCATGCAAAATTAGGA
1 CCATGCAGAATCAGGA
43305 ATGCATCAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (28 bp):
CCATGCAGAATCAGGACGAGGACTAAGC
Found at i:46122 original size:17 final size:16
Alignment explanation
Indices: 46100--46171 Score: 56
Period size: 17 Copynumber: 4.0 Consensus size: 16
46090 TTCGGTTTGC
46100 AAAAAATCCGATTTTTT
1 AAAAAA-CCGATTTTTT
46117 AAAAAACCGGATTTTTT
1 AAAAAACC-GATTTTTT
46134 CGGATAAAAATCC-AGTTTTTT
1 ---A-AAAAA-CCGA-TTTTTT
46155 AAAAAACCGAATTTTTT
1 AAAAAACCG-ATTTTTT
46172 CCGGATAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
16 4 0.09
17 25 0.54
18 2 0.04
20 2 0.04
21 11 0.24
22 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (16 bp):
AAAAAACCGATTTTTT
Found at i:46154 original size:39 final size:39
Alignment explanation
Indices: 46101--46194 Score: 147
Period size: 38 Copynumber: 2.4 Consensus size: 39
46091 TCGGTTTGCA
*
46101 AAAAATCC-GATTTTTTAAAAAACCGGATTTTTT-CGGAT
1 AAAAATCCAG-TTTTTTAAAAAACCGAATTTTTTCCGGAT
46139 AAAAATCCAGTTTTTTAAAAAACCGAATTTTTTCCGGAT
1 AAAAATCCAGTTTTTTAAAAAACCGAATTTTTTCCGGAT
*
46178 AAAAAACCAGTTTTTTA
1 AAAAATCCAGTTTTTTA
46195 TCCGGTTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
38 30 0.58
39 22 0.42
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (39 bp):
AAAAATCCAGTTTTTTAAAAAACCGAATTTTTTCCGGAT
Found at i:46236 original size:24 final size:26
Alignment explanation
Indices: 46178--46239 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
46168 TTTTCCGGAT
* *
46178 AAAAAACCAGTTTTTTATCCGGTTTAA
1 AAAAAACCGGTTTTTAATCCGG-TTAA
46205 AAAAAACCGGTTTTTAATCCGG-T-A
1 AAAAAACCGGTTTTTAATCCGGTTAA
46229 AAAAAACCGGT
1 AAAAAACCGGT
46240 CGTTCAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 12 0.36
25 1 0.03
27 20 0.61
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (26 bp):
AAAAAACCGGTTTTTAATCCGGTTAA
Found at i:46950 original size:119 final size:119
Alignment explanation
Indices: 46721--46952 Score: 317
Period size: 119 Copynumber: 1.9 Consensus size: 119
46711 CTTTATTATT
*
46721 TTTTCTTTTCTTATATCACATCTCTATTTTCTTTTGTTTTTTAATCTTCAATAAGCATGTCTTTA
1 TTTTCTTTTCTTATATCACATCTCTATTTTCTTTTGTTTTTTAATCTTCAATAAGCATATCTTTA
* * * *
46786 TGACACATTTTCATCTACCTTTATAATACGATTTGATCTACCTTTATGGCATCC
66 TGACACATTTTCATCCACCTTTATAACAAGATTTAATCTACCTTTATGGCATCC
* *
46840 TTTTCTTTTCTTATATCACATCTCTATTTTCTTTTGTTTTTTAATGTTCAATAAATC-TATCTTT
1 TTTTCTTTTCTTATATCACATCTCTATTTTCTTTTGTTTTTTAATCTTCAAT-AAGCATATCTTT
* * * *
46904 ATGACACGTTTTTATCCA-CTATTATAACAAGTTTTTAAT-TATCTTTATG
65 ATGACACATTTTCATCCACCT-TTATAACAAG-ATTTAATCTACCTTTATG
46953 ACACATTATC
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
118 2 0.02
119 89 0.90
120 8 0.08
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (119 bp):
TTTTCTTTTCTTATATCACATCTCTATTTTCTTTTGTTTTTTAATCTTCAATAAGCATATCTTTA
TGACACATTTTCATCCACCTTTATAACAAGATTTAATCTACCTTTATGGCATCC
Found at i:47158 original size:18 final size:18
Alignment explanation
Indices: 47135--47202 Score: 127
Period size: 18 Copynumber: 3.8 Consensus size: 18
47125 ATATAAATAG
47135 AAAAATCTTATTTTTCAT
1 AAAAATCTTATTTTTCAT
47153 AAAAATCTTATTTTTCAT
1 AAAAATCTTATTTTTCAT
47171 AAAAATCTTATTTTTCAT
1 AAAAATCTTATTTTTCAT
*
47189 AAAAATCTAATTTT
1 AAAAATCTTATTTT
47203 CTTTTTATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAAATCTTATTTTTCAT
Found at i:50258 original size:2 final size:2
Alignment explanation
Indices: 50251--50280 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
50241 GGTTTATTAG
50251 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50281 TATTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50398 original size:38 final size:39
Alignment explanation
Indices: 50314--50423 Score: 138
Period size: 38 Copynumber: 2.8 Consensus size: 39
50304 TTATTTATAA
* *
50314 TTCTCAAATTATTTCAC-TCTAACATTCTAGATTCCTAAT
1 TTCTTAAATTATTTCACAT-TAACATTCTAAATTCCTAAT
*
50353 TTCTTAAATT-TTTCCACCA-TAACATT-TAAATTCTTAAT
1 TTCTTAAATTATTT-CA-CATTAACATTCTAAATTCCTAAT
50391 TTCTTAAATTATTTCACATTAACATTCTAAATT
1 TTCTTAAATTATTTCACATTAACATTCTAAATT
50424 ATTTTTTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
37 2 0.03
38 32 0.52
39 27 0.44
40 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.01, T:0.46
Consensus pattern (39 bp):
TTCTTAAATTATTTCACATTAACATTCTAAATTCCTAAT
Found at i:50486 original size:18 final size:18
Alignment explanation
Indices: 50465--50509 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
50455 ACATTTGAAA
50465 TTTAATTATAAT-TTTTGT
1 TTTAATTATAATATTTT-T
*
50483 TTTAATTTTAATATTTTT
1 TTTAATTATAATATTTTT
*
50501 TTCAATTAT
1 TTTAATTAT
50510 GTAATTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTAATTATAATATTTTT
Found at i:51259 original size:22 final size:20
Alignment explanation
Indices: 51225--51269 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
51215 TAGTATATAT
51225 TATATTTTAATTAATGATAA
1 TATATTTTAATTAATGATAA
* *
51245 TATATATTTATATTATTGTTAA
1 TATAT-TTTA-ATTAATGATAA
51267 TAT
1 TAT
51270 TCAAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
TATATTTTAATTAATGATAA
Found at i:56617 original size:13 final size:12
Alignment explanation
Indices: 56599--56631 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
56589 GTTAAAAAAA
56599 TAAAAATATAATT
1 TAAAAATAT-ATT
56612 TAAAAAT-TATT
1 TAAAAATATATT
56623 TAAAAATAT
1 TAAAAATAT
56632 TAAAAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 2 0.11
13 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAAAATATATT
Found at i:57860 original size:17 final size:17
Alignment explanation
Indices: 57834--57866 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
57824 TTTTGTTTTT
57834 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
57852 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
57867 TATTTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:57868 original size:17 final size:19
Alignment explanation
Indices: 57829--57868 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
57819 TAATATTTTG
*
57829 TTTTTAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
57848 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
57864 TTTTA
1 TTTTA
57869 TTTAATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:58130 original size:13 final size:13
Alignment explanation
Indices: 58112--58139 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
58102 CCTTAAGTTA
58112 GTGATACCTAGCC
1 GTGATACCTAGCC
58125 GTGATACCTAGCC
1 GTGATACCTAGCC
58138 GT
1 GT
58140 ATCTTGCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (13 bp):
GTGATACCTAGCC
Found at i:58989 original size:24 final size:24
Alignment explanation
Indices: 58957--59002 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
58947 AGATTATAGT
58957 TATATAATTAGATTATTATTTTGA
1 TATATAATTAGATTATTATTTTGA
58981 TATATAATTAGATTATTATTTT
1 TATATAATTAGATTATTATTTT
59003 AATAGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (24 bp):
TATATAATTAGATTATTATTTTGA
Found at i:59021 original size:24 final size:24
Alignment explanation
Indices: 58960--59013 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
58950 TTATAGTTAT
* *
58960 ATAATTAGATTATTATTTTGATAT
1 ATAATTAGATTATTATTTTAATAG
58984 ATAATTAGATTATTATTTTAATAG
1 ATAATTAGATTATTATTTTAATAG
59008 A-AATTA
1 ATAATTA
59014 TATATATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (24 bp):
ATAATTAGATTATTATTTTAATAG
Found at i:59688 original size:33 final size:33
Alignment explanation
Indices: 59633--59697 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
59623 CCTGATGTCA
** *
59633 CCGCCGCCACCATCACCTAGTTTTATGACCCCG
1 CCGCCGCCACCATCACAGAGTTTTATAACCCCG
**
59666 CCGCCGCCACTGTCACAGAGTTTTATAACCCC
1 CCGCCGCCACCATCACAGAGTTTTATAACCCC
59698 TCATAGAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.15, T:0.22
Consensus pattern (33 bp):
CCGCCGCCACCATCACAGAGTTTTATAACCCCG
Found at i:60123 original size:13 final size:14
Alignment explanation
Indices: 60105--60137 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
60095 TATTTAGTTG
60105 TTTATTGGAC-TTT
1 TTTATTGGACATTT
*
60118 TTTATTGTACATTT
1 TTTATTGGACATTT
60132 TTTATT
1 TTTATT
60138 ATTTATCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (14 bp):
TTTATTGGACATTT
Found at i:60195 original size:33 final size:33
Alignment explanation
Indices: 60158--60241 Score: 109
Period size: 34 Copynumber: 2.5 Consensus size: 33
60148 TAATACTTAC
60158 TTTATTTTGTTAATTTGGTTGGA-TTTATT-TTAA
1 TTTATTTTGTTAATTT-GTTGGACTTT-TTGTTAA
60191 TTTATTTTGTTAAATTTGTTGGACTTTTTGTTAA
1 TTTATTTTGTT-AATTTGTTGGACTTTTTGTTAA
*
60225 TGTATTTTGGTTAATTT
1 TTTATTTT-GTTAATTT
60242 TGTTTATTAC
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
33 19 0.41
34 24 0.52
35 3 0.07
ACGTcount: A:0.20, C:0.01, G:0.15, T:0.63
Consensus pattern (33 bp):
TTTATTTTGTTAATTTGTTGGACTTTTTGTTAA
Found at i:60225 original size:34 final size:33
Alignment explanation
Indices: 60158--60245 Score: 108
Period size: 33 Copynumber: 2.6 Consensus size: 33
60148 TAATACTTAC
60158 TTTATTTTGTT-AATTTGGTTGGATTTATTTTAA
1 TTTATTTTGTTAAATTT-GTTGGATTTATTTTAA
60191 TTTATTTTGTTAAATTTGTTGGACTTT-TTGTTAA
1 TTTATTTTGTTAAATTTGTTGGA-TTTATT-TTAA
* *
60225 TGTATTTTGGTTAATTTTGTT
1 TTTATTTT-GTTAAATTTGTT
60246 TATTACCATT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
33 19 0.39
34 19 0.39
35 11 0.22
ACGTcount: A:0.19, C:0.01, G:0.16, T:0.64
Consensus pattern (33 bp):
TTTATTTTGTTAAATTTGTTGGATTTATTTTAA
Found at i:60275 original size:35 final size:32
Alignment explanation
Indices: 60240--60320 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 32
60230 TTTGGTTAAT
60240 TTTGTT-TATTACCATTTAATATCAATTATTGTAA
1 TTTGTTATATTACCATTTAATA-C--TTATTGTAA
60274 TTTGTTTATCATTTACCATTTAATACTTATTGTAA
1 TTTG-TTAT-A-TTACCATTTAATACTTATTGTAA
*
60309 GTTTGTTGTATT
1 -TTTGTTATATT
60321 TAAAATCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
33 2 0.05
34 5 0.12
35 14 0.34
36 5 0.12
37 2 0.05
38 13 0.32
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.56
Consensus pattern (32 bp):
TTTGTTATATTACCATTTAATACTTATTGTAA
Found at i:64466 original size:97 final size:97
Alignment explanation
Indices: 64320--64514 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
64310 GATTGAAGAG
64320 CATTTTAAAGTCATGGGTATTAGGGCGATGGGAAGTTTGAGCATGGGTTCAAAATAGGGATGGCA
1 CATTTTAAAGTCATGGGTATTAGGGCGATGGGAAGTTTGAGCATGGGTTCAAAATAGGGATGGCA
64385 AATGGACGGATCGGGTGCGGATACCTCCTCCC
66 AATGGACGGATCGGGTGCGGATACCTCCTCCC
64417 CATTTTAAAGTCATGGGTATTAGGGCGATGGGAAGTTTGAGCATGGGTTCAAAATAGGGATGGCA
1 CATTTTAAAGTCATGGGTATTAGGGCGATGGGAAGTTTGAGCATGGGTTCAAAATAGGGATGGCA
64482 AATGGACGGATCGGGTGCGGATACCTCCTCCC
66 AATGGACGGATCGGGTGCGGATACCTCCTCCC
64514 C
1 C
64515 CATCCCCATA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.25
Consensus pattern (97 bp):
CATTTTAAAGTCATGGGTATTAGGGCGATGGGAAGTTTGAGCATGGGTTCAAAATAGGGATGGCA
AATGGACGGATCGGGTGCGGATACCTCCTCCC
Found at i:65713 original size:15 final size:16
Alignment explanation
Indices: 65694--65734 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
65684 CCTTTACGCT
*
65694 CTTTATTTTTTAATTA
1 CTTTATTTTTTAAATA
*
65710 -TTTA-TATTTAAATA
1 CTTTATTTTTTAAATA
65724 CTTTATTTTTT
1 CTTTATTTTTT
65735 TTGTTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 4
0.74 0.11 0.15
Matches are distributed among these distances:
14 8 0.40
15 8 0.40
16 4 0.20
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
CTTTATTTTTTAAATA
Found at i:65742 original size:31 final size:31
Alignment explanation
Indices: 65694--65781 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
65684 CCTTTACGCT
** *
65694 CTTTA-TTTTTTAATTATTTATATTTAAATA
1 CTTTATTTTTTTTGTTATTTACATTTAAATA
**
65724 CTTTATTTTTTTTGTTATTTACATTTTCATA
1 CTTTATTTTTTTTGTTATTTACATTTAAATA
*
65755 CTTTATTTTTTCTGTTATTTACATTTA
1 CTTTATTTTTTTTGTTATTTACATTTA
65782 TGCCTTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (31 bp):
CTTTATTTTTTTTGTTATTTACATTTAAATA
Found at i:65791 original size:31 final size:29
Alignment explanation
Indices: 65731--65925 Score: 134
Period size: 29 Copynumber: 6.7 Consensus size: 29
65721 ATACTTTATT
* * *
65731 TTTTTTGTTATTTACATTTTCAT-ACTTTATT
1 TTTTCTGTTATTTACA-TTT-ATGCCTTT-TA
65762 TTTTCTGTTATTTACATTTATGCCTTTTA
1 TTTTCTGTTATTTACATTTATGCCTTTTA
** * *
65791 TTTTCTCATATTTATATTTCA-GTCCTTTCA
1 TTTTCTGTTATTTACATTT-ATG-CCTTTTA
65821 TTTTCTGTT-TTTACA-TTATTG-CTTTTA
1 TTTTCTGTTATTTACATTTA-TGCCTTTTA
* *
65848 TTTTCTGTTATTTACATTTCTGTCCTTTAA
1 TTTTCTGTTATTTACATTTATG-CCTTTTA
* *
65878 TTTTATG-TACTTTA-ATTTATGTCCTTTAA
1 TTTTCTGTTA-TTTACATTTATG-CCTTTTA
* **
65907 ATTTCTGGCATTTACATTT
1 TTTTCTGTTATTTACATTT
65926 CAGCCATTTA
Statistics
Matches: 134, Mismatches: 18, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
27 15 0.11
28 10 0.07
29 53 0.40
30 41 0.31
31 15 0.11
ACGTcount: A:0.19, C:0.14, G:0.06, T:0.61
Consensus pattern (29 bp):
TTTTCTGTTATTTACATTTATGCCTTTTA
Found at i:65860 original size:57 final size:59
Alignment explanation
Indices: 65739--65928 Score: 176
Period size: 57 Copynumber: 3.2 Consensus size: 59
65729 TTTTTTTTGT
* *
65739 TATTTACATTTTCA-TACTTTATTTTTTCTGTTATTTACATTTATGCCTTTTATTTTCTCA
1 TATTTACA-TTTCAGTCCTTTA-ATTTTCTGTTATTTACATTTATGCCTTTTATTTTCTCA
* * **
65799 TATTTATATTTCAGTCCTTTCATTTTCTGTT-TTTACA-TTATTG-CTTTTATTTTCTGT
1 TATTTACATTTCAGTCCTTTAATTTTCTGTTATTTACATTTA-TGCCTTTTATTTTCTCA
* * * * **
65856 TATTTACATTTCTGTCCTTTAATTTTATG-TACTTTA-ATTTATGTCCTTTAAATTTCTGG
1 TATTTACATTTCAGTCCTTTAATTTTCTGTTA-TTTACATTTATG-CCTTTTATTTTCTCA
*
65915 CATTTACATTTCAG
1 TATTTACATTTCAG
65929 CCATTTACAC
Statistics
Matches: 108, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
56 1 0.01
57 43 0.40
58 15 0.14
59 37 0.34
60 12 0.11
ACGTcount: A:0.20, C:0.15, G:0.06, T:0.59
Consensus pattern (59 bp):
TATTTACATTTCAGTCCTTTAATTTTCTGTTATTTACATTTATGCCTTTTATTTTCTCA
Found at i:65880 original size:14 final size:14
Alignment explanation
Indices: 65844--65913 Score: 59
Period size: 15 Copynumber: 4.8 Consensus size: 14
65834 CATTATTGCT
* **
65844 TTTATTTTCTGTTA
1 TTTAATTTCTGTCC
65858 TTTACATTTCTGTCC
1 TTTA-ATTTCTGTCC
* *
65873 TTTAATTTTATGTAC
1 TTTAA-TTTCTGTCC
*
65888 TTTAATTTATGTCC
1 TTTAATTTCTGTCC
65902 TTTAAATTTCTG
1 TTT-AATTTCTG
65914 GCATTTACAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
14 16 0.35
15 30 0.65
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTAATTTCTGTCC
Found at i:67699 original size:93 final size:93
Alignment explanation
Indices: 67532--67750 Score: 312
Period size: 93 Copynumber: 2.4 Consensus size: 93
67522 CTCGTGTTTG
** * * *
67532 CTTGCGTACTCGTTAAATTAAACTAAATAAATTCATGTTTCCTCAGTGGAAGCATTGTGTGCTAA
1 CTTGCGTACTTATTAAATTAAACTAAATAAATTAATGTTTCCTCAGTGGAAACATTGAGTGCTAA
* *
67597 TAAGATTGTAGGTTTGTCATTTGTGTGT
66 TAAGATTGTAGGGTCGTCATTTGTGTGT
* *
67625 CTTGCGTACTTATTAAACTAAACTAAATAAATTAATGTTTCCTCAGTGGAAACATTGAGTGGTAA
1 CTTGCGTACTTATTAAATTAAACTAAATAAATTAATGTTTCCTCAGTGGAAACATTGAGTGCTAA
* *
67690 TGAGCTTGTAGGGTCGTCATTTGTGTGT
66 TAAGATTGTAGGGTCGTCATTTGTGTGT
* * *
67718 GTTGCGTACTTATTCAATTATACTAAATAAATT
1 CTTGCGTACTTATTAAATTAAACTAAATAAATT
67751 CGTGTAAACA
Statistics
Matches: 111, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 111 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (93 bp):
CTTGCGTACTTATTAAATTAAACTAAATAAATTAATGTTTCCTCAGTGGAAACATTGAGTGCTAA
TAAGATTGTAGGGTCGTCATTTGTGTGT
Found at i:69521 original size:26 final size:25
Alignment explanation
Indices: 69491--69543 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 25
69481 GTTGTCAACC
69491 ATGCAAGCACCAAATTGGTTTCAATA
1 ATGC-AGCACCAAATTGGTTTCAATA
69517 AT---GCACCAAATTGGTTTCAATA
1 ATGCAGCACCAAATTGGTTTCAATA
69539 ATGCA
1 ATGCA
69544 CCGAAAGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
22 22 0.92
26 2 0.08
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (25 bp):
ATGCAGCACCAAATTGGTTTCAATA
Found at i:69525 original size:22 final size:22
Alignment explanation
Indices: 69497--69545 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
69487 AACCATGCAA
69497 GCACCAAATTGGTTTCAATAAT
1 GCACCAAATTGGTTTCAATAAT
69519 GCACCAAATTGGTTTCAATAAT
1 GCACCAAATTGGTTTCAATAAT
69541 GCACC
1 GCACC
69546 GAAAGTGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (22 bp):
GCACCAAATTGGTTTCAATAAT
Found at i:76143 original size:3 final size:3
Alignment explanation
Indices: 76135--76248 Score: 198
Period size: 3 Copynumber: 38.7 Consensus size: 3
76125 ACACATAATT
76135 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
76180 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
76227 TTA -TA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
76249 CTCATGATTG
Statistics
Matches: 107, Mismatches: 0, Indels: 8
0.93 0.00 0.07
Matches are distributed among these distances:
2 6 0.06
3 98 0.92
4 3 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:80874 original size:43 final size:43
Alignment explanation
Indices: 80826--80912 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
80816 TCACTAAGAA
80826 AACAAACTCGATCACTAAGAATCCTTGCTCCATAAATTTTCTT
1 AACAAACTCGATCACTAAGAATCCTTGCTCCATAAATTTTCTT
80869 AACAAACTCGATCACTAAGAATCCTTGCTCCATAAATTTTCTT
1 AACAAACTCGATCACTAAGAATCCTTGCTCCATAAATTTTCTT
80912 A
1 A
80913 CCTAAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (43 bp):
AACAAACTCGATCACTAAGAATCCTTGCTCCATAAATTTTCTT
Found at i:83065 original size:30 final size:30
Alignment explanation
Indices: 83029--83088 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
83019 TTCCTTTCAT
*
83029 GGAACCTAACGTGTCTTTTCCTTTAATGTA
1 GGAACCTAACGTCTCTTTTCCTTTAATGTA
* * *
83059 GGAACCTAATGTCTGTTTTCCTTTTATGTA
1 GGAACCTAACGTCTCTTTTCCTTTAATGTA
83089 TTAATAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (30 bp):
GGAACCTAACGTCTCTTTTCCTTTAATGTA
Found at i:87485 original size:21 final size:21
Alignment explanation
Indices: 87443--87489 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
87433 CCTACGGCGA
* *
87443 GGCATCTGAACTGACTGTGGT
1 GGCATCTGAAATGACTGCGGT
87464 GGCATCTGAAATGGA-TGCGGT
1 GGCATCTGAAAT-GACTGCGGT
87485 GGCAT
1 GGCAT
87490 TGACTCGGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.26
Consensus pattern (21 bp):
GGCATCTGAAATGACTGCGGT
Found at i:93852 original size:21 final size:21
Alignment explanation
Indices: 93826--93889 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
93816 TTTTGGTGCA
*
93826 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATCCCCCCCAT
* **
93847 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCAT
*
93868 GAAGGGGAACCGATTCCCCCCA
1 G-A-GGGAACCGATCCCCCCCA
93890 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCAT
Found at i:93896 original size:21 final size:21
Alignment explanation
Indices: 93828--93908 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
93818 TTGGTGCAGA
*
93828 GGGAATCGA-TCCCCCC-CATG
1 GGGAACCGATTCCCCCCACA-G
*
93848 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
93872 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
93893 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
93909 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 1 0.02
21 24 0.49
22 6 0.12
23 16 0.33
24 1 0.02
25 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:98590 original size:32 final size:34
Alignment explanation
Indices: 98549--98616 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
98539 TAATAAAATA
*
98549 ATAATAATAATGT-AATATATTA-TATA-TTATAT
1 ATAATAATAAT-TAAATATATAAGTATACTTATAT
98581 ATAATAATAATTAAATATATAAGTATACTTATAT
1 ATAATAATAATTAAATATATAAGTATACTTATAT
98615 AT
1 AT
98617 TTTTTAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 1 0.03
32 19 0.59
33 4 0.12
34 8 0.25
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (34 bp):
ATAATAATAATTAAATATATAAGTATACTTATAT
Found at i:98616 original size:18 final size:18
Alignment explanation
Indices: 98536--98616 Score: 50
Period size: 18 Copynumber: 4.8 Consensus size: 18
98526 TAAAATAAAT
* *
98536 TAATAATAAAATA-ATAA
1 TAATAATTATATATATAA
*
98553 TAATAATGTA-ATATATTA
1 TAATAAT-TATATATATAA
98571 T-AT-A-T-TATATATAA
1 TAATAATTATATATATAA
*
98585 TAATAATTAAATATATAA
1 TAATAATTATATATATAA
*
98603 GT-ATACTTATATAT
1 -TAATAATTATATAT
98617 TTTTTAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
14 9 0.18
15 2 0.04
16 2 0.04
17 13 0.26
18 23 0.46
19 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (18 bp):
TAATAATTATATATATAA
Found at i:98638 original size:19 final size:19
Alignment explanation
Indices: 98610--98654 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
98600 TAAGTATACT
98610 TATATATTTTTTAAAAAAC
1 TATATATTTTTTAAAAAAC
* *
98629 TATATCTTTTTTCAAAAAC
1 TATATATTTTTTAAAAAAC
98648 TATATAT
1 TATATAT
98655 ATACTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATTTTTTAAAAAAC
Found at i:98661 original size:30 final size:30
Alignment explanation
Indices: 98627--98684 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
98617 TTTTTAAAAA
98627 ACTATAT-CTTTTTTCAAAAACTATATATAT
1 ACTATATACTTTTTTC-AAAACTATATATAT
*
98657 ACTATATATTTTTTTCAAAACTATATAT
1 ACTATATACTTTTTTCAAAACTATATAT
98685 TTTCATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (30 bp):
ACTATATACTTTTTTCAAAACTATATATAT
Found at i:103992 original size:18 final size:18
Alignment explanation
Indices: 103969--104011 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
103959 GGTCCACTTT
*
103969 CGGCACCGGGTACAGGAC
1 CGGCACCAGGTACAGGAC
* *
103987 CGGCACCAGGTGCAGGTC
1 CGGCACCAGGTACAGGAC
104005 CGGCACC
1 CGGCACC
104012 CGGTTGGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.37, G:0.37, T:0.07
Consensus pattern (18 bp):
CGGCACCAGGTACAGGAC
Done.