Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004448.1 Hibiscus syriacus cultivar Beakdansim tig00009770_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: 83621
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6959 original size:21 final size:23
Alignment explanation
Indices: 6915--6962 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
6905 CGTATAATTA
*
6915 TAAATTAGTTGAAAATTTAAAGG
1 TAAATTAGTTGAAAATTGAAAGG
*
6938 TAAATTA-TTTAAAA-TGAAAGG
1 TAAATTAGTTGAAAATTGAAAGG
6959 TAAA
1 TAAA
6963 ATATAACAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 6 0.26
23 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (23 bp):
TAAATTAGTTGAAAATTGAAAGG
Found at i:11568 original size:2 final size:2
Alignment explanation
Indices: 11561--11602 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
11551 GCATGAAGAA
11561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT GAT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
11602 A
1 A
11603 AATAATTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12457 original size:52 final size:50
Alignment explanation
Indices: 12367--12468 Score: 132
Period size: 52 Copynumber: 2.0 Consensus size: 50
12357 TAAAGCGTGC
* ** *
12367 CCCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTGGGGGTATAGCGCG
1 CCCCCTGAACCGCGCTATACGATGAGCTGGCACCACGT--GGGTATAGCGCG
* *
12419 CCCCCTGAACCGCGCTATACGGTGAGCTGGCACTACGTGGGTATAGCGCG
1 CCCCCTGAACCGCGCTATACGATGAGCTGGCACCACGTGGGTATAGCGCG
12469 GGCCCTACAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
50 12 0.27
52 32 0.73
ACGTcount: A:0.17, C:0.32, G:0.32, T:0.19
Consensus pattern (50 bp):
CCCCCTGAACCGCGCTATACGATGAGCTGGCACCACGTGGGTATAGCGCG
Found at i:12630 original size:20 final size:19
Alignment explanation
Indices: 12599--12637 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
12589 TTATCACACC
*
12599 AAATTTTCTCAAATTCTCT
1 AAATTTTCTCAAATACTCT
12618 AAATTTCTCTCAAATACTCT
1 AAATTT-TCTCAAATACTCT
12638 CTTTTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTTCTCAAATACTCT
Found at i:14753 original size:9 final size:9
Alignment explanation
Indices: 14739--14787 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
14729 ACCTGCGCAA
14739 GACGACGAT
1 GACGACGAT
*
14748 GACGACGAG
1 GACGACGAT
* * *
14757 GATGAGGAC
1 GACGACGAT
14766 GACGACGAT
1 GACGACGAT
14775 GACGACGAT
1 GACGACGAT
14784 GACG
1 GACG
14788 GTGATGATGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.33, C:0.20, G:0.39, T:0.08
Consensus pattern (9 bp):
GACGACGAT
Found at i:14768 original size:15 final size:15
Alignment explanation
Indices: 14739--14787 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
14729 ACCTGCGCAA
14739 GACGACGATGACGAC
1 GACGACGATGACGAC
*
14754 GA-G--GATGAGGAC
1 GACGACGATGACGAC
14766 GACGACGATGACGAC
1 GACGACGATGACGAC
*
14781 GATGACG
1 GACGACG
14788 GTGATGATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
14 1 0.04
15 16 0.57
ACGTcount: A:0.33, C:0.20, G:0.39, T:0.08
Consensus pattern (15 bp):
GACGACGATGACGAC
Found at i:14991 original size:26 final size:24
Alignment explanation
Indices: 14918--14991 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
14908 TTATATTTGT
14918 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
** *
14943 ATTTTTTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
14967 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
14992 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
24 4 0.11
25 17 0.46
26 16 0.43
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.64
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:19670 original size:50 final size:51
Alignment explanation
Indices: 19608--19706 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
19598 GGTATCTGAT
19608 CCGCGCTATATAAAATTATGTC-AGAGTAAAGGTAT-GTCGCGGTACCTGCC
1 CCGCGCTATATAAAATTATGTCGAGAGTAAAGGTATAG-CGCGGTACCTGCC
*
19658 CCGCGCTATATAAAATTATGTCGGGAGTAAAGGTATAGCGCGGTACCTG
1 CCGCGCTATATAAAATTATGTCGAGAGTAAAGGTATAGCGCGGTACCTG
19707 ATCCATGCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
50 22 0.48
51 23 0.50
52 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (51 bp):
CCGCGCTATATAAAATTATGTCGAGAGTAAAGGTATAGCGCGGTACCTGCC
Found at i:19718 original size:51 final size:50
Alignment explanation
Indices: 19595--19710 Score: 171
Period size: 50 Copynumber: 2.3 Consensus size: 50
19585 TTATACAAAA
*
19595 CGCGGTATCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGT
1 CGCGGTACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGT
** *
19645 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCGGGAGTAAAGGTATAG-
1 CGCGGTACCTGATCCGCGCTATATAAAATTATGTC-AGAGTAAAGGTAT-GT
19696 CGCGGTACCTGATCC
1 CGCGGTACCTGATCC
19711 ATGCTATACC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 32 0.55
51 25 0.43
52 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (50 bp):
CGCGGTACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGT
Found at i:19824 original size:52 final size:50
Alignment explanation
Indices: 19730--19858 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 50
19720 CCCTACGTGG
* * **
19730 CGTATAGCGCGCTTCAGGGGCCGCGCTATACCCACGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTTCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
*
19780 CGTATAGCGCGGTTCAGGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTTCA-GGGGGCGCGCTATA-CCCACGTGGCGCCAAATCAC
*
19832 CGTATAGCGCGGTGCAGGGGGCGCGCT
1 CGTATAGCGCGGTTCAGGGGGCGCGCT
19859 TTACTGCTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
50 15 0.21
51 24 0.34
52 32 0.45
ACGTcount: A:0.16, C:0.33, G:0.35, T:0.16
Consensus pattern (50 bp):
CGTATAGCGCGGTTCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
Found at i:26153 original size:75 final size:76
Alignment explanation
Indices: 26067--26228 Score: 229
Period size: 76 Copynumber: 2.1 Consensus size: 76
26057 ATCTTATTGG
26067 AGATTGTTTTTCTTAAAAC-AGAATATGTCTCACTTGAGAC-TGTTTTACTCGAAAGAAGACATT
1 AGATTGTTTTTCTTAAAACAAG-ATATGTCTCACTTGAGACATGTTTTACTCGAAAGAAGACATT
* *
26130 TCATTTGACTCA
65 TCATTTCAATCA
* * * * * *
26142 AGATTATTTTTCTTAAAACAAGATTTGTCTCTCTTGAGACATTTTTTACTCGAAATAATACATTT
1 AGATTGTTTTTCTTAAAACAAGATATGTCTCACTTGAGACATGTTTTACTCGAAAGAAGACATTT
26207 CATTTCAATCA
66 CATTTCAATCA
26218 AGATTGTTTTT
1 AGATTGTTTTT
26229 AAAGAATATT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
75 34 0.45
76 42 0.55
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATATGTCTCACTTGAGACATGTTTTACTCGAAAGAAGACATTT
CATTTCAATCA
Found at i:26295 original size:39 final size:39
Alignment explanation
Indices: 26252--26465 Score: 284
Period size: 39 Copynumber: 5.5 Consensus size: 39
26242 TCTTGCTTAT
26252 GATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGA
1 GATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGA
*
26291 GATAGTTTCCCTTGAAACAGAAGATTTTATCTCGGTTGA
1 GATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGA
** * * *
26330 GATAGTTTCCCTCAAAACAGAAGAGTTTGTCTCGTTTGA
1 GATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGA
* * * *
26369 GATAATGTCCCTTGAAACAGAATATTTTATCTCGTTTGA
1 GATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGA
* * * *
26408 GATAGTTTCCCTTGAAACAAAAGATCTTGTCTCTCTTGA
1 GATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGA
**
26447 GGCAGTTTCCCTTGAAACA
1 GATAGTTTCCCTTGAAACA
26466 CCAATCTTTG
Statistics
Matches: 152, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 152 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (39 bp):
GATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGA
Found at i:26712 original size:21 final size:20
Alignment explanation
Indices: 26652--26781 Score: 76
Period size: 21 Copynumber: 7.0 Consensus size: 20
26642 AAAATGTTTC
26652 CCTTGAAACGAA-TTTTGTCT
1 CCTTGAAAC-AAGTTTTGTCT
*
26672 CTCTTGAAAC-CG--TT-TC-
1 C-CTTGAAACAAGTTTTGTCT
26688 CCTTGAAACAAGTTTTGTCT
1 CCTTGAAACAAGTTTTGTCT
*
26708 CCCTTGAGAC-A--TTT-TCT
1 -CCTTGAAACAAGTTTTGTCT
26725 -CTTGAAACAAGTTTTGTCT
1 CCTTGAAACAAGTTTTGTCT
*
26744 CTCTTGAGAC-AG--TT-TCT
1 C-CTTGAAACAAGTTTTGTCT
26761 -CTTGAAACAAAGTTTTGTCT
1 CCTTGAAAC-AAGTTTTGTCT
26781 C
1 C
26782 TTTAGAGACA
Statistics
Matches: 84, Mismatches: 6, Indels: 39
0.65 0.05 0.30
Matches are distributed among these distances:
15 22 0.26
16 3 0.04
17 10 0.12
18 12 0.14
19 7 0.08
20 7 0.08
21 23 0.27
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (20 bp):
CCTTGAAACAAGTTTTGTCT
Found at i:26794 original size:20 final size:20
Alignment explanation
Indices: 26734--26795 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
26724 TCTTGAAACA
26734 AGTTTTGTCTCTCTT-GAGAC
1 AGTTTTGTCTCT-TTAGAGAC
* * * *
26754 AG--TT-TCTCTTGAAACAA
1 AGTTTTGTCTCTTTAGAGAC
26771 AGTTTTGTCTCTTTAGAGAC
1 AGTTTTGTCTCTTTAGAGAC
26791 AGTTT
1 AGTTT
26796 CCCTCGAAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
16 1 0.03
17 9 0.30
18 2 0.07
19 2 0.07
20 16 0.53
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.44
Consensus pattern (20 bp):
AGTTTTGTCTCTTTAGAGAC
Found at i:26808 original size:37 final size:36
Alignment explanation
Indices: 26647--26807 Score: 218
Period size: 36 Copynumber: 4.4 Consensus size: 36
26637 CTTTGAAAAT
* *
26647 GTTTCCCTTGAAACGAA-TTTTGTCTCTCTTGAAACC
1 GTTTCCCTTGAAAC-AAGTTTTGTCTCTCTTGAGACA
*
26683 GTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
* *
26719 TTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
*
26755 GTTTCTCTTGAAACAAAGTTTTGTCTCT-TTAGAGACA
1 GTTTCCCTTGAAAC-AAGTTTTGTCTCTCTT-GAGACA
*
26792 GTTTCCCTCGAAACAA
1 GTTTCCCTTGAAACAA
26808 ATCTCACTTG
Statistics
Matches: 113, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
35 2 0.02
36 80 0.71
37 31 0.27
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
Found at i:27551 original size:132 final size:131
Alignment explanation
Indices: 27136--28097 Score: 1207
Period size: 132 Copynumber: 7.3 Consensus size: 131
27126 AAGAGATTGT
* * * * * *
27136 TCAACTGTTTGCTTGATTCTATCACAGAAGGAGGTAAATCAGCACCAACATTTCGTTTGATTCCA
1 TCAACT-TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* *
27201 TCACAGAAGGAGGTGGATCGGCA--TTT-GTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
65 TCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
27263 CG
130 CG
* * * * * * * *
27265 TCAACTTTTAGCTTGATTCTATCATAGAACGAGGTATATCAACATCGACGTATCGTTTGATTTCC
1 TCAACTTTT-GCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGA-TTCC
* ** * **
27330 ATAACAGAAATAGGTGGATCGATATTTTTATTTTCGCTCAAATCCATAACAGAAGGAGTTGGATC
64 ATCACAGAAGGAGGTGGATCGACATTTTTA-TTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
27395 AGCG
128 AGCG
* * * * * * *
27399 TCAACGTTTTGCTCGTTTCTATCACAAAATGAGGTAGATCAGCACCAACATCTCATTCGATTTCA
1 TCAAC-TTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
** * * *
27464 TCGTAGAAGGAGGTAGATCGATATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAG
65 TCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
27529 CG
130 CG
* * * *
27531 TCAACTTTTAGCTTGATTCTATCATAGAAGAAGGTAGATCAGCATCGACATCTTGTTCGATTCCA
1 TCAACTTTT-GCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
27596 TCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTT-GATCAG
65 TCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
27660 CG
130 CG
* * * * *
27662 TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACGTCTCGTTCGATTCTA
1 TCAAC-TTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* ** *
27727 TCACAGAAGGAGGTGGATCGATATTTTTATTTAACTCAAATCCATCGCAGAAGAAGTTGGATCAG
65 TCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
27792 CG
130 CG
* *
27794 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTTGTTCGATTCCA
1 TCAAC-TTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
*
27859 TCACACAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
65 TCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
27924 CG
130 CG
* * *
27926 TCAACTTTTTCTCGATTCTATCACCA-AATGAGGTAGATCAGGATCGACATCTCGTTCGATTCCA
1 TCAACTTTTGCTCGATTCTATCA-CAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * * *
27990 TCACAGAAGGAGGTGGATTGACATTTTTATTTTCGCTCAAATCCATCGCAGAAAGAGGTAGATCA
65 TCACAGAAGGAGGTGGATCGACATTTTTA-TTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
28055 GCA
129 GCG
* * * * *
28058 TCGACATCTCGTTCGATT-TCATCACAGAAGGAGGTGGATC
1 TCAAC-TTTTGCTCGATTCT-ATCACAGAAGGAGGTAGATC
28098 GACATTTTTA
Statistics
Matches: 720, Mismatches: 98, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
128 3 0.00
129 48 0.07
130 23 0.03
131 195 0.27
132 320 0.44
133 50 0.07
134 77 0.11
135 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (131 bp):
TCAACTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCAT
CACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGC
G
Found at i:27640 original size:44 final size:44
Alignment explanation
Indices: 27587--28278 Score: 250
Period size: 44 Copynumber: 15.7 Consensus size: 44
27577 GACATCTTGT
27587 TCGATTCCATCACAGAAGGAGGTGGATC-GACATTTTTATTTCGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAG-CATTTTTATTTCGC
* * * * * **
27631 TCAAATCCATCGCAGAAGGA-GTTGATCAGCGTCAACTT-TTT-GC
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCAT--TTTTATTTCGC
* * * ****** * *
27674 TCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACGTCTCGT
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATTTTTATTTCGC
* * **
27718 TCGATTCTATCACAGAAGGAGGTGGATC-GATATTTTTATTTAAC
1 TCGATTCCATCACAGAAGGAGGTGGATCAG-CATTTTTATTTCGC
* * * * * * **
27762 TCAAATCCATCGCAGAAGAAGTTGGATCAGCGTCAACTT-TTT-GC
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCAT--TTTTATTTCGC
* * * **** *
27806 TCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTT-GT
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATTTTTAT-TTCGC
*
27850 TCGATTCCATCACACAAGGAGGTGGATC-GACATTTTTATTTCGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAG-CATTTTTATTTCGC
* * * * * **
27894 TCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTT-TTT--C
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCAT--TTTTATTTCGC
* * * * **** * *
27937 TCGATTCTATCACCA-AATGAGGTAGATCAGGATCGACATCTCGT
1 TCGATTCCATCA-CAGAAGGAGGTGGATCAGCATTTTTATTTCGC
*
27981 TCGATTCCATCACAGAAGGAGGTGGAT-TGACATTTTTATTTTCGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAG-CATTTTTA-TTTCGC
* * * * * **** * *
28026 TCAAATCCATCGCAGAAAGAGGTAGATCAGCATCGACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATTTTTATTTCGC
*
28070 TCGATTTCATCACAGAAGGAGGTGGATC-GACATTTTTATTTTCGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAG-CATTTTTA-TTTCGC
* * * * * ** *
28115 TCAAATCCATCGCAGAAGGAGTTGGATCAGC--GTCAACTTTTGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATTTTTA-TTTCGC
* * * * * **** * *
28158 TAGATTCTATCACAGAAGGAGTTAGATTAGCATCGACATATCGT
1 TCGATTCCATCACAGAAGGAGGTGGATCAGCATTTTTATTTCGC
*
28202 TTGATTTCCATCACAGAAGGAGGTGGATC-GACATTTTTATTTTCGC
1 TCGA-TTCCATCACAGAAGGAGGTGGATCAG-CATTTTTA-TTTCGC
* * * *
28248 TCAAATCCATCGCAGAAGGAGTTGGATCAGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAGC
28279 GTCAACTTCT
Statistics
Matches: 448, Mismatches: 166, Indels: 67
0.66 0.24 0.10
Matches are distributed among these distances:
42 2 0.00
43 88 0.20
44 230 0.51
45 115 0.26
46 13 0.03
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (44 bp):
TCGATTCCATCACAGAAGGAGGTGGATCAGCATTTTTATTTCGC
Found at i:27703 original size:263 final size:263
Alignment explanation
Indices: 27136--28056 Score: 1296
Period size: 263 Copynumber: 3.5 Consensus size: 263
27126 AAGAGATTGT
* * * * *
27136 TCAACTGTTTGCTTGATTCTATCACAGAAGGAGGTAAATCAGCACCAACATTTCGTTTGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
* * *
27201 TCACAGAAGGAGGTGGATCGGCA--TTT-GTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAG
* * * * *
27263 CGTCAACTTTTAGCTTGATTCTATCATAGAACGAGGTATATCAACATCGACGTATCGTTTGATTT
131 CGTCAACTTTTAGCTTGATTCTATCATAGAA-GAGGTAGATCAACATCGACATCTTGTTCGA-TT
* ** * **
27328 CCATAACAGAAATAGGTGGATCGATATTTTTATTTTCGCTCAAATCCATAACAGAAGGAGTTGGA
194 CCATCACAGAAGGAGGTGGATCGACATTTTTA-TTTCGCTCAAATCCATCGCAGAAGGAGTTGGA
27393 TCAGCG
258 TCAGCG
* * * * * *
27399 TCAACGTTTTGCTCGTTTCTATCACAAAATGAGGTAGATCAGCACCAACATCTCATTCGATTTCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
** * *
27464 TCGTAGAAGGAGGTAGATCGATATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAG
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAG
*
27529 CGTCAACTTTTAGCTTGATTCTATCATAGAAGAAGGTAGATCAGCATCGACATCTTGTTCGATTC
131 CGTCAACTTTTAGCTTGATTCTATCATAGAAG-AGGTAGATCAACATCGACATCTTGTTCGATTC
27594 CATCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTT-GATC
195 CATCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
27658 AGCG
260 AGCG
* * *
27662 TCAACTTTTTGCTCGTTTCTATCACAGAAGGAGGTAGATCAGCACCAACGTCTCGTTCGATTCTA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
* * *
27727 TCACAGAAGGAGGTGGATCGATATTTTTATTTAACTCAAATCCATCGCAGAAGAAGTTGGATCAG
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAG
* * *
27792 CGTCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTTGTTCGATTC
131 CGTCAACTTTTAGCTTGATTCTATCATAGAA-GAGGTAGATCAACATCGACATCTTGTTCGATTC
*
27857 CATCACACAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
195 CATCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
27922 AGCG
260 AGCG
* * * *
27926 TCAACTTTTT-CTCGATTCTATCACCA-AATGAGGTAGATCAGGATCGACATCTCGTTCGATTCC
1 TCAACTTTTTGCTCGATTCTATCA-CAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCC
* * * * *
27989 ATCACAGAAGGAGGTGGATTGACATTTTTATTTTCGCTCAAATCCATCGCAGAAAGAGGTAGATC
65 ATCACAGAAGGAGGTGGATCGACATTTTTA-TTTCACTCAAATCCATCGCAGAAGGAGTTGGATC
28054 AGC
129 AGC
28057 ATCGACATCT
Statistics
Matches: 588, Mismatches: 62, Indels: 15
0.88 0.09 0.02
Matches are distributed among these distances:
263 387 0.66
264 79 0.13
265 34 0.06
266 88 0.15
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (263 bp):
TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTTTATTTCACTCAAATCCATCGCAGAAGGAGTTGGATCAG
CGTCAACTTTTAGCTTGATTCTATCATAGAAGAGGTAGATCAACATCGACATCTTGTTCGATTCC
ATCACAGAAGGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
GCG
Found at i:28069 original size:89 final size:89
Alignment explanation
Indices: 27955--28145 Score: 328
Period size: 89 Copynumber: 2.1 Consensus size: 89
27945 ATCACCAAAT
* *
27955 GAGGTAGATCAGGATCGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATTGACATTTTTAT
1 GAGGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTAT
28020 TTTCGCTCAAATCCATCGCAGAAA
66 TTTCGCTCAAATCCATCGCAGAAA
*
28044 GAGGTAGATCAGCATCGACATCTCGTTCGATTTCATCACAGAAGGAGGTGGATCGACATTTTTAT
1 GAGGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTAT
*
28109 TTTCGCTCAAATCCATCGCAGAAG
66 TTTCGCTCAAATCCATCGCAGAAA
* *
28133 GAGTTGGATCAGC
1 GAGGTAGATCAGC
28146 GTCAACTTTT
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 96 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (89 bp):
GAGGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTAT
TTTCGCTCAAATCCATCGCAGAAA
Found at i:28241 original size:133 final size:132
Alignment explanation
Indices: 28033--28302 Score: 452
Period size: 133 Copynumber: 2.0 Consensus size: 132
28023 CGCTCAAATC
* *
28033 CATCGCAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTTCATCACAGAAGGAGGTGGATC
1 CATCACAGAAAGAGGTAGATCAGCATCGACATATCGTTCGATTTCATCACAGAAGGAGGTGGATC
28098 GACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTT-TTGCTAGA
66 GACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTCTTGCTAGA
28162 TT
131 TT
* * * *
28164 CTATCACAGAAGGAGTTAGATTAGCATCGACATATCGTTTGATTTCCATCACAGAAGGAGGTGGA
1 C-ATCACAGAAAGAGGTAGATCAGCATCGACATATCGTTCGATTT-CATCACAGAAGGAGGTGGA
*
28229 TCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTCTTGCTC
64 TCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTCTTGCTA
28294 GATT
129 GATT
28298 CATCA
1 CATCA
28303 TATATGGAGT
Statistics
Matches: 129, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
131 1 0.01
132 37 0.29
133 81 0.63
134 10 0.08
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (132 bp):
CATCACAGAAAGAGGTAGATCAGCATCGACATATCGTTCGATTTCATCACAGAAGGAGGTGGATC
GACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTCTTGCTAGA
TT
Found at i:28302 original size:221 final size:219
Alignment explanation
Indices: 27818--28302 Score: 729
Period size: 221 Copynumber: 2.2 Consensus size: 219
27808 GATTCTATCA
* * *
27818 CAGAAGGAGGTAGATCAACATCGACATCTTGTTCGATTCCATCACACAAGGAGGTGGATCGACAT
1 CAGAAAGAGGTAGATCAGCATCAACATCTTGTTCGATT-CATCACACAAGGAGGTGGATCGACAT
* *
27883 TTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTCTCGATTCTATC
65 TTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTGCTAGATTCTATC
* * * *
27948 ACCAAATGAGGTAGATCAGGATCGACATCTCGTTCGATTCCATCACAGAAGGAGGTGGATTGACA
130 ACCAAAGGAGGTAGATCAGCATCGACATATCGTTCGATTCCATCACAGAAGGAGGTGGATCGACA
28013 TTTTTATTTTCGCTCAAATCCATCG
195 TTTTTATTTTCGCTCAAATCCATCG
* * *
28038 CAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTTCATCACAGAAGGAGGTGGATCGACAT
1 CAGAAAGAGGTAGATCAGCATCAACATCTTGTTCGA-TTCATCACACAAGGAGGTGGATCGACAT
28103 TTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTGCTAGATTCTAT
65 TTTTA-TTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTGCTAGATTCTAT
* * *
28168 CA-CAGAAGGAGTTAGATTAGCATCGACATATCGTTTGATTTCCATCACAGAAGGAGGTGGATCG
129 CACCA-AAGGAGGTAGATCAGCATCGACATATCGTTCGA-TTCCATCACAGAAGGAGGTGGATCG
28232 ACATTTTTATTTTCGCTCAAATCCATCG
192 ACATTTTTATTTTCGCTCAAATCCATCG
* * * * * *
28260 CAGAAGGAGTTGGATCAGCGTCAACTTCTTGCTCGATTCATCA
1 CAGAAAGAGGTAGATCAGCATCAACATCTTGTTCGATTCATCA
28303 TATATGGAGT
Statistics
Matches: 240, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
220 65 0.27
221 95 0.40
222 80 0.33
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (219 bp):
CAGAAAGAGGTAGATCAGCATCAACATCTTGTTCGATTCATCACACAAGGAGGTGGATCGACATT
TTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTGCTAGATTCTATCA
CCAAAGGAGGTAGATCAGCATCGACATATCGTTCGATTCCATCACAGAAGGAGGTGGATCGACAT
TTTTATTTTCGCTCAAATCCATCG
Found at i:32672 original size:16 final size:16
Alignment explanation
Indices: 32648--32685 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
32638 TATTCACATA
*
32648 AATACTGAATTTCATG
1 AATAGTGAATTTCATG
32664 AATAGTGAATTTCATG
1 AATAGTGAATTTCATG
32680 AATAGT
1 AATAGT
32686 AATAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (16 bp):
AATAGTGAATTTCATG
Found at i:45588 original size:19 final size:21
Alignment explanation
Indices: 45564--45604 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
45554 ATTAGTTTAT
45564 TTTATGAA-AAAA-ATAAAAA
1 TTTATGAACAAAAGATAAAAA
45583 TTTATGAATCAAAAGATAAAAA
1 TTTATGAA-CAAAAGATAAAAA
45605 AAAATCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.27
Consensus pattern (21 bp):
TTTATGAACAAAAGATAAAAA
Found at i:45771 original size:19 final size:19
Alignment explanation
Indices: 45747--45784 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
45737 AGGATTGAGA
45747 GCAGCTTCCGTGGGAGACC
1 GCAGCTTCCGTGGGAGACC
45766 GCAGCTTCCGTGGGAGACC
1 GCAGCTTCCGTGGGAGACC
45785 TCTGGCAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.37, T:0.16
Consensus pattern (19 bp):
GCAGCTTCCGTGGGAGACC
Found at i:45878 original size:13 final size:13
Alignment explanation
Indices: 45860--45886 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
45850 AATAGTTGAA
45860 CAGTCTTCATATG
1 CAGTCTTCATATG
45873 CAGTCTTCATATG
1 CAGTCTTCATATG
45886 C
1 C
45887 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:48589 original size:60 final size:59
Alignment explanation
Indices: 48515--48674 Score: 196
Period size: 59 Copynumber: 2.7 Consensus size: 59
48505 ACCTTTATTT
* * *
48515 TAAATTAATCCTTAAACTTTTAAACATTCCAATTTCATCCTCAAACTATGATTCTCATTC
1 TAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCC-CAAACTATAAATCTCATTC
* * * *
48575 TAAATTAGTCCTTAATCTTTTGAACATTCCAAATTCATCCCCAACTATAAATCTCATTC
1 TAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCCCAAACTATAAATCTCATTC
* * * *
48634 TAATTTGGTCCCTAAACTTTTAGATC-TTCCAATTTCATCCC
1 TAAATTAGTCCTTAAACTTTTA-AACATTCCAATTTCATCCC
48675 CGAATTCATG
Statistics
Matches: 85, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 47 0.55
60 38 0.45
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (59 bp):
TAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCCCAAACTATAAATCTCATTC
Found at i:49206 original size:3 final size:3
Alignment explanation
Indices: 49198--49223 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49188 GTGTGAACCT
49198 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
49224 TACACAGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:63401 original size:12 final size:12
Alignment explanation
Indices: 63386--63413 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
63376 AATTATTAAT
63386 GGAATTTCTGAG
1 GGAATTTCTGAG
63398 GGAATTTCTGAG
1 GGAATTTCTGAG
63410 GGAA
1 GGAA
63414 GAGAGTAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.07, G:0.36, T:0.29
Consensus pattern (12 bp):
GGAATTTCTGAG
Found at i:63624 original size:62 final size:62
Alignment explanation
Indices: 63527--63643 Score: 209
Period size: 62 Copynumber: 1.9 Consensus size: 62
63517 AACTTTAAAA
63527 TCCGTCAGAATGTTATATATAAATAAAATACTATATTTTATGTTT-TCGACGAACATATTTTT
1 TCCGTCAGAATGTTATATATAAATAAAATACTATATTTTATGTTTCT-GACGAACATATTTTT
*
63589 TCCGTCGGAATGTTATATATAAATAAAATACTATATTTTATGTTTCTGACGAACA
1 TCCGTCAGAATGTTATATATAAATAAAATACTATATTTTATGTTTCTGACGAACA
63644 ATCTTTTATA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
62 52 0.98
63 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (62 bp):
TCCGTCAGAATGTTATATATAAATAAAATACTATATTTTATGTTTCTGACGAACATATTTTT
Found at i:63858 original size:33 final size:33
Alignment explanation
Indices: 63785--63861 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
63775 ATACCCGAAA
* * *
63785 AAATTTTCATTCCCTACAAAATATCATGAATCC
1 AAATTTTTATTCCCTACAAAATATCACGAAACC
* *
63818 AAATTTTTATTCCCTCCAAAATATTACGAAACC
1 AAATTTTTATTCCCTACAAAATATCACGAAACC
63851 AAATTTTTATT
1 AAATTTTTATT
63862 TAATTAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.38
Consensus pattern (33 bp):
AAATTTTTATTCCCTACAAAATATCACGAAACC
Found at i:64661 original size:31 final size:31
Alignment explanation
Indices: 64611--64680 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
64601 AAAATAATTT
* *
64611 TTTGTGATAGAACATGTGGACCCATCACAAA
1 TTTGTGACAGAACAGGTGGACCCATCACAAA
* * ** *
64642 TTTGTGACAGAATAGGTGGATCTGTCAGAAA
1 TTTGTGACAGAACAGGTGGACCCATCACAAA
64673 TTTGTGAC
1 TTTGTGAC
64681 GAGTCCACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (31 bp):
TTTGTGACAGAACAGGTGGACCCATCACAAA
Found at i:65280 original size:93 final size:91
Alignment explanation
Indices: 65166--65355 Score: 308
Period size: 93 Copynumber: 2.1 Consensus size: 91
65156 GGTATGTTTG
* * *
65166 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATTAGTGGGTAACTAAAAAAACCTCTAAAT
1 AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGTGGGTAACTAAAAAAA-CTCGAAAT
65231 TTTGTGATGGAACATGTGAACCCATCAC
65 TTTGTGA-GGAACATGTGAACCCATCAC
*
65259 AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGTGGGTAATTAAAAAAACTCGAAATT
1 AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGTGGGTAACTAAAAAAACTCGAAATT
* *
65324 TTGTGAGGAACATGTGGACTCATCAC
66 TTGTGAGGAACATGTGAACCCATCAC
65350 AAATTT
1 AAATTT
65356 GTGACGGAAC
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
91 24 0.26
92 14 0.15
93 53 0.58
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (91 bp):
AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGTGGGTAACTAAAAAAACTCGAAATT
TTGTGAGGAACATGTGAACCCATCAC
Found at i:65354 original size:31 final size:32
Alignment explanation
Indices: 65319--65387 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
65309 AAAAAACTCG
* *
65319 AAATTTTGTGA-GGAACATGTGGACTCATCAC
1 AAATTTTGTGACGGAACATGTGAACCCATCAC
*
65350 AAA-TTTGTGACGGAACATGTGAACCCGTCAC
1 AAATTTTGTGACGGAACATGTGAACCCATCAC
65381 AAATTTT
1 AAATTTT
65388 ATGTTTCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 7 0.21
31 23 0.70
32 3 0.09
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (32 bp):
AAATTTTGTGACGGAACATGTGAACCCATCAC
Found at i:65502 original size:214 final size:215
Alignment explanation
Indices: 65166--65573 Score: 615
Period size: 214 Copynumber: 1.9 Consensus size: 215
65156 GGTATGTTTG
* * * **
65166 AAATTTTATGTTTCAATGGAGGGAAATTGGAGGAAATTAGTGGGTAACTAAAAAAACCTCTAAAT
1 AAATTTTATGTTTCAATGGAGGAAAATTAGAGGAAATGAACGGGTAACTAAAAAAACCTCTAAAT
* *
65231 TTTGTGATGGAACATGTGAACCCATCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAAT
66 TTTATGACGGAACATGTGAACCCATCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAAT
* *
65296 GAGTGGGTAATTAAAAAAACTCGAAATTTTGTGA-GGAACATGTGGACTCA-TCACAAATTTGTG
131 GAGCGGG-AATGAAAAAAACTCGAAATTTTGTGACGGAACATGTGGAC-CAGTCACAAATTTGTG
65359 ACGGAACATGTGAACCCGTCAC
194 ACGGAACATGTGAACCCGTCAC
*
65381 AAATTTTATGTTTCAATGGAGGAAAATTAGAGGAAATGAACGGGTAATTAAAAAAA-CTCTAAAT
1 AAATTTTATGTTTCAATGGAGGAAAATTAGAGGAAATGAACGGGTAACTAAAAAAACCTCTAAAT
* * * * * * *
65445 TTTATGACGGAACTTGTGGACCCGTTACAAATTTTATGTTTTAATGGAGGTAAATTGGAGGTAAT
66 TTTATGACGGAACATGTGAACCCATCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAAT
*
65510 GAGCGGGAATGAAAAAAACTCTAAATTTTGTGACGGAACATGTGGACCAGTCACAAATTTGTGA
131 GAGCGGGAATGAAAAAAACTCGAAATTTTGTGACGGAACATGTGGACCAGTCACAAATTTGTGA
65574 TGGGTCCGCA
Statistics
Matches: 173, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
213 26 0.15
214 97 0.56
215 50 0.29
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (215 bp):
AAATTTTATGTTTCAATGGAGGAAAATTAGAGGAAATGAACGGGTAACTAAAAAAACCTCTAAAT
TTTATGACGGAACATGTGAACCCATCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAAT
GAGCGGGAATGAAAAAAACTCGAAATTTTGTGACGGAACATGTGGACCAGTCACAAATTTGTGAC
GGAACATGTGAACCCGTCAC
Found at i:65566 original size:91 final size:92
Alignment explanation
Indices: 65353--65569 Score: 328
Period size: 92 Copynumber: 2.4 Consensus size: 92
65343 TCATCACAAA
*
65353 TTTGTGACGGAACATGTGAACCCGTCACAAATTTTATGTTTCAATGGAGGAAAATTAGAGGAAAT
1 TTTGTGACGGAACATGTGGACCCGTCACAAATTTTATGTTTCAATGGAGGAAAATTAGAGGAAAT
*
65418 GAACGGGTAATTAAAAAAACTCTAAAT
66 GAACGGGTAATGAAAAAAACTCTAAAT
* * * * * * *
65445 TTTATGACGGAACTTGTGGACCCGTTACAAATTTTATGTTTTAATGGAGGTAAATTGGAGGTAAT
1 TTTGTGACGGAACATGTGGACCCGTCACAAATTTTATGTTTCAATGGAGGAAAATTAGAGGAAAT
*
65510 GAGCGGG-AATGAAAAAAACTCTAAAT
66 GAACGGGTAATGAAAAAAACTCTAAAT
*
65536 TTTGTGACGGAACATGTGGACCAGTCACAAATTT
1 TTTGTGACGGAACATGTGGACCCGTCACAAATTT
65570 GTGATGGGTC
Statistics
Matches: 111, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
91 48 0.43
92 63 0.57
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (92 bp):
TTTGTGACGGAACATGTGGACCCGTCACAAATTTTATGTTTCAATGGAGGAAAATTAGAGGAAAT
GAACGGGTAATGAAAAAAACTCTAAAT
Found at i:67208 original size:31 final size:30
Alignment explanation
Indices: 67166--67266 Score: 104
Period size: 31 Copynumber: 3.5 Consensus size: 30
67156 TAAAAAAGAA
67166 AAATGCATATAAATAAAAAAAAGTAAAGGAT
1 AAATGCATATAAAT-AAAAAAAGTAAAGGAT
* * * **
67197 AAATGCGTATAAAT-----CAGTATATTAT
1 AAATGCATATAAATAAAAAAAGTAAAGGAT
67222 AAATGCATATAAATTAAAAAAAGTAAAGGAT
1 AAATGCATATAAA-TAAAAAAAGTAAAGGAT
67253 AAATGCATATAAAT
1 AAATGCATATAAAT
67267 GGTAATTGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
25 19 0.35
26 1 0.02
30 1 0.02
31 33 0.61
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.26
Consensus pattern (30 bp):
AAATGCATATAAATAAAAAAAGTAAAGGAT
Found at i:68155 original size:40 final size:41
Alignment explanation
Indices: 68070--68155 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 41
68060 GAGTGTAACC
* *
68070 TTTGAAATTATGATAATTATAAACGATTCATCCATTTTTGA
1 TTTGAAATTATGATAATTATAAACAATTCATCCATTTGTGA
* ** * *
68111 -TTGAAATTTTGATGGTTATAAATAATTTATCCA-TTGTGA
1 TTTGAAATTATGATAATTATAAACAATTCATCCATTTGTGA
68150 TTTGAA
1 TTTGAA
68156 CGAAGAGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
39 5 0.14
40 32 0.86
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (41 bp):
TTTGAAATTATGATAATTATAAACAATTCATCCATTTGTGA
Found at i:78383 original size:19 final size:18
Alignment explanation
Indices: 78359--78394 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
78349 TTAAAGGCTA
*
78359 TTTGTAATCTTTCTCTCTC
1 TTTGTAATATTTC-CTCTC
78378 TTTGTAATATTTCCTCT
1 TTTGTAATATTTCCTCT
78395 ATTAGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.14, C:0.22, G:0.06, T:0.58
Consensus pattern (18 bp):
TTTGTAATATTTCCTCTC
Done.