Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007342.1 Hibiscus syriacus cultivar Beakdansim tig00019671_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: 77865
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5377 original size:2 final size:2
Alignment explanation
Indices: 5370--5394 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5360 TTATTATTAT
5370 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5395 TACAAGCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6717 original size:12 final size:12
Alignment explanation
Indices: 6700--6787 Score: 72
Period size: 12 Copynumber: 7.2 Consensus size: 12
6690 TTATTTTCTT
*
6700 TTATTTTAATCA
1 TTATTTTAATTA
*
6712 TTATTTGCAA-TA
1 TTATTT-TAATTA
6724 TTATTTT-ATTA
1 TTATTTTAATTA
*
6735 TTATTATTATTTA
1 TTATT-TTAATTA
*
6748 TTACTTTAATTA
1 TTATTTTAATTA
*
6760 TTATTTCATTATTA
1 TTATTT--TAATTA
*
6774 TTATTTTTATTA
1 TTATTTTAATTA
6786 TT
1 TT
6788 TATATAAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
10 1 0.02
11 7 0.11
12 34 0.55
13 9 0.15
14 11 0.18
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.65
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:6735 original size:3 final size:3
Alignment explanation
Indices: 6722--6787 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
6712 TTATTTGCAA
*
6722 TAT TAT T-T TAT TAT TAT TAT TATT TAT TACT T-T AAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT
* *
6766 CAT TAT TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
6788 TATATAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 4 0.08
3 43 0.83
4 5 0.10
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6771 original size:36 final size:34
Alignment explanation
Indices: 6722--6789 Score: 109
Period size: 36 Copynumber: 1.9 Consensus size: 34
6712 TTATTTGCAA
*
6722 TATTATTTTATTATTATTATTATTTATTACTTTAAT
1 TATTATTTCATTATTATTATT-TTTATTA-TTTAAT
6758 TATTATTTCATTATTATTATTTTTATTATTTA
1 TATTATTTCATTATTATTATTTTTATTATTTA
6790 TATAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 4 0.13
35 7 0.23
36 20 0.65
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (34 bp):
TATTATTTCATTATTATTATTTTTATTATTTAAT
Found at i:6813 original size:20 final size:18
Alignment explanation
Indices: 6788--6828 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
6778 TTTTATTATT
6788 TATATAAATAAATAAATATA
1 TATATAAAT-AATAAATA-A
*
6808 TATATATATAATAAATAA
1 TATATAAATAATAAATAA
6826 TAT
1 TAT
6829 TTGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATATAAATAATAAATAA
Found at i:7619 original size:16 final size:15
Alignment explanation
Indices: 7598--7637 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 15
7588 TCTTTCAAAT
7598 TTTTTATTACTTATTA
1 TTTTTATTA-TTATTA
7614 TTTTTATATATTATTA
1 TTTTTAT-TATTATTA
7630 TTTTTATT
1 TTTTTATT
7638 CAAGTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.04
16 20 0.87
17 2 0.09
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTATTATTATTA
Found at i:9967 original size:13 final size:13
Alignment explanation
Indices: 9939--9981 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
9929 AGTAAACACC
*
9939 TTTTCATATATGCA
1 TTTTCAT-TTTGCA
9953 TTTTCATTTTGCA
1 TTTTCATTTTGCA
9966 TTTTTCATTTTGCA
1 -TTTTCATTTTGCA
9980 TT
1 TT
9982 CATACTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (13 bp):
TTTTCATTTTGCA
Found at i:9969 original size:7 final size:7
Alignment explanation
Indices: 9949--9981 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
9939 TTTTCATATA
9949 TGCATTT
1 TGCATTT
9956 T-CATTT
1 TGCATTT
9962 TGCATTT
1 TGCATTT
*
9969 TTCATTT
1 TGCATTT
9976 TGCATT
1 TGCATT
9982 CATACTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.61
Consensus pattern (7 bp):
TGCATTT
Found at i:12188 original size:2 final size:2
Alignment explanation
Indices: 12181--12206 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12171 ATCCTTTCAA
12181 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
12207 CCCTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14642 original size:114 final size:114
Alignment explanation
Indices: 14441--14664 Score: 385
Period size: 114 Copynumber: 2.0 Consensus size: 114
14431 GTGCCACGTT
14441 CTCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTAGAACTGTTCTTCGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTAGAACTGTTCTTCGAGTTATCTGATCTG
*
14506 ATTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTG
66 ATTTGGTATGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
* * * *
14555 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTAGAACTGTTCTTCGAGTTATCTGATCTG
* *
14620 GTTTGGTATGAACCCCAGAACCAATCATTAGAATTGAAAGATGAA
66 ATTTGGTATGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
14665 CTGCATGATC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTAGAACTGTTCTTCGAGTTATCTGATCTG
ATTTGGTATGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
Found at i:17123 original size:22 final size:22
Alignment explanation
Indices: 17094--17148 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
17084 ATCTACACTC
17094 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
17116 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
17138 TTCAAAGATGA
1 TTCAAAGATGA
17149 AAGCTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:17974 original size:166 final size:168
Alignment explanation
Indices: 17660--17992 Score: 546
Period size: 166 Copynumber: 2.0 Consensus size: 168
17650 CCACAAAAAT
17660 TAGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAAACAGAATGAG
1 TAGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-AAAAAAACAGAATGAG
* **
17725 AAAACGATTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAAC
65 AAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAAC
* *
17790 GATTTTCTTAGTTTTTTTTACTTAGTAAACTATTTCCAA
130 GATTTCCTTAGTTTTTTTTACTTAATAAACTATTTCCAA
* ** *
17829 TAGCCTTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAAA-ATAATGAGA
1 TAGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAACAGAATGAGA
17892 AAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAAC
66 AAACGATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAAC
17957 GATTTCCTTAG-TTTTTTTACTTAATAAACTATTTCC
130 GATTTCCTTAGTTTTTTTTACTTAATAAACTATTTCC
17993 CACATCTGTA
Statistics
Matches: 154, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
166 64 0.42
167 43 0.28
169 47 0.31
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (168 bp):
TAGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAAACAGAATGAGA
AAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACG
ATTTCCTTAGTTTTTTTTACTTAATAAACTATTTCCAA
Found at i:18864 original size:76 final size:76
Alignment explanation
Indices: 17995--18862 Score: 1583
Period size: 76 Copynumber: 11.4 Consensus size: 76
17985 CTATTTCCCA
*
17995 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18060 AGCCTTAGGGT
66 AGCCTTAGGGT
*
18071 CATCTGTAAGTCCTGCAGTGCATGATGTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18136 AGCCTTAGGGT
66 AGCCTTAGGGT
18147 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18212 AGCCTTAGGGT
66 AGCCTTAGGGT
18223 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18288 AGCCTTAGGGT
66 AGCCTTAGGGT
18299 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18364 AGCCTTAGGGT
66 AGCCTTAGGGT
18375 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18440 AGCCTTAGGGT
66 AGCCTTAGGGT
18451 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18516 AGCCTTAGGGT
66 AGCCTTAGGGT
18527 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
18592 AACCTTAGGGT
66 AGCCTTAGGGT
**
18603 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAATACTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18668 AGCCTTAGGGT
66 AGCCTTAGGGT
*
18679 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
18744 AGCCTTAGTGT
66 AGCCTTAGGGT
* * **
18755 CATCTGTAAGTCCTGCAATGCATGATGTTTTCAAAAAGCCTTCTAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
** *
18820 AATCTTCGGGT
66 AGCCTTAGGGT
* *
18831 CATCTGTAAGCCCTTCAGTGCATGATGATTTC
1 CATCTGTAAGTCCTGCAGTGCATGATG-TTTC
18863 AATATTTCAT
Statistics
Matches: 767, Mismatches: 24, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
76 764 1.00
77 3 0.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:19020 original size:2 final size:2
Alignment explanation
Indices: 19013--19059 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
19003 TTATTATGAT
19013 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19055 TA TA T
1 TA TA T
19060 TACAAGCCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22155 original size:37 final size:37
Alignment explanation
Indices: 22109--22181 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
22099 TTATCAAAGG
22109 AAAAAATGAATTAAAATTTAATTTAAAAATAAATAGA
1 AAAAAATGAATTAAAATTTAATTTAAAAATAAATAGA
22146 AAAAAATGAATTAAAATTTAATTTAAAAATAAATAG
1 AAAAAATGAATTAAAATTTAATTTAAAAATAAATAG
22182 TAAGTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (37 bp):
AAAAAATGAATTAAAATTTAATTTAAAAATAAATAGA
Found at i:22636 original size:86 final size:85
Alignment explanation
Indices: 22458--22797 Score: 324
Period size: 86 Copynumber: 4.0 Consensus size: 85
22448 CGTTTGTGTG
* ** * * *
22458 ACAAACGCCGTAATAGGTTTTGATATTTAGCGGCGTTTGTCAGAAAAATGCCGTAATAGGTGTTG
1 ACAAACGCCGTAATAGGTTTTGATATTTAGCGGCGTTTTTCTCACAAACGCCGCAATAGGTGTTG
* * **
22523 ATATTTAGCGGCGTTTTTTAG
66 ATGTTTTGCGGCG-TTTTTCC
* * ** * *
22544 ATAAACGCCGCAATAGGTAATGATATTTAGCGGCGTTTTTTCTCTA-AAACGTCGCATTAGGTGT
1 ACAAACGCCGTAATAGGTTTTGATATTTAGCGGCG-TTTTTCTC-ACAAACGCCGCAATAGGTGT
*
22608 TGATGTTTTGCGGCGTTTTCCC
64 TGATGTTTTGCGGCGTTTTTCC
* * * * * * * * * *
22630 ACAAACGCCGTAGTAGATGTTGATGTTTTGCAGCG-TTTTCCCACAAACGCCGCATTAGATTTTG
1 ACAAACGCCGTAATAGGTTTTGATATTTAGCGGCGTTTTTCTCACAAACGCCGCAATAGGTGTTG
22694 ATGTTTTGCGGCGTTTATTCC
66 ATGTTTTGCGGCGTTT-TTCC
* * * * * *
22715 ACAAACGTCGTAGTAGGTTTTGATGTTTTGCGTCGTTTTTCTCACAAACGCCGCAATAGGTATTG
1 ACAAACGCCGTAATAGGTTTTGATATTTAGCGGCGTTTTTCTCACAAACGCCGCAATAGGTGTTG
*
22780 ATTTTTTGCGGCGTTTTT
66 ATGTTTTGCGGCGTTTTT
22798 GCTAAAAACA
Statistics
Matches: 209, Mismatches: 40, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
83 1 0.00
84 39 0.19
85 35 0.17
86 101 0.48
87 32 0.15
88 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (85 bp):
ACAAACGCCGTAATAGGTTTTGATATTTAGCGGCGTTTTTCTCACAAACGCCGCAATAGGTGTTG
ATGTTTTGCGGCGTTTTTCC
Found at i:22651 original size:42 final size:42
Alignment explanation
Indices: 22590--22796 Score: 234
Period size: 42 Copynumber: 4.9 Consensus size: 42
22580 TTTTTCTCTA
* * *
22590 AAACGTCGCATTAGGTGTTGATGTTTTGCGGCGTTTTCCCAC
1 AAACGCCGCAGTAGATGTTGATGTTTTGCGGCGTTTTCCCAC
* *
22632 AAACGCCGTAGTAGATGTTGATGTTTTGCAGCGTTTTCCCAC
1 AAACGCCGCAGTAGATGTTGATGTTTTGCGGCGTTTTCCCAC
* * *
22674 AAACGCCGCATTAGATTTTGATGTTTTGCGGCGTTTATTCCAC
1 AAACGCCGCAGTAGATGTTGATGTTTTGCGGCGTTT-TCCCAC
* * * * * *
22717 AAACGTCGTAGTAGGTTTTGATGTTTTGCGTCGTTTTTCTCAC
1 AAACGCCGCAGTAGATGTTGATGTTTTGCGGCG-TTTTCCCAC
* * * *
22760 AAACGCCGCAATAGGTATTGATTTTTTGCGGCGTTTT
1 AAACGCCGCAGTAGATGTTGATGTTTTGCGGCGTTTT
22797 TGCTAAAAAC
Statistics
Matches: 140, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
42 73 0.52
43 64 0.46
44 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (42 bp):
AAACGCCGCAGTAGATGTTGATGTTTTGCGGCGTTTTCCCAC
Found at i:22764 original size:128 final size:128
Alignment explanation
Indices: 22546--22796 Score: 308
Period size: 128 Copynumber: 2.0 Consensus size: 128
22536 TTTTTTAGAT
* * *
22546 AAACGCCGCAATAGGTAATGATATTTAGCGGCGTTTTTTCTCTAAAACGTCGCATTAGGTGTTGA
1 AAACGCCGCAATAGATAATGATATTTAGCGGCGTTTATTCTCTAAAACGTCGCAGTAGGTGTTGA
* * *
22611 TGTTTTGCGGCGTTTTCCCACAAACGCCGTAGTAGATGTTGATGTTTTGCAGCGTTTTCCCAC
66 TGTTTTGCGGCGTTTTCCCACAAACGCCGCAATAGATATTGATGTTTTGCAGCGTTTTCCCAC
* ** * * * *
22674 AAACGCCGCATTAGATTTTGATGTTTTGCGGCGTTTATTC-C-ACAAACGTCGTAGTAGGTTTTG
1 AAACGCCGCAATAGATAATGATATTTAGCGGCGTTTATTCTCTA-AAACGTCGCAGTAGGTGTTG
* * * * *
22737 ATGTTTTGCGTCGTTTTTCTCACAAACGCCGCAATAGGTATTGATTTTTTGCGGCGTTTT
65 ATGTTTTGCGGCG-TTTTCCCACAAACGCCGCAATAGATATTGATGTTTTGCAGCGTTTT
22797 TGCTAAAAAC
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
126 1 0.01
127 30 0.29
128 72 0.70
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (128 bp):
AAACGCCGCAATAGATAATGATATTTAGCGGCGTTTATTCTCTAAAACGTCGCAGTAGGTGTTGA
TGTTTTGCGGCGTTTTCCCACAAACGCCGCAATAGATATTGATGTTTTGCAGCGTTTTCCCAC
Found at i:22796 original size:43 final size:43
Alignment explanation
Indices: 22424--22797 Score: 281
Period size: 43 Copynumber: 8.7 Consensus size: 43
22414 AAAAAATGCT
* ** * * *
22424 GCAATATGTATTGATATTTAACGGCGTTTGTGTGACAAACGCC
1 GCAATAGGTATTGATATTTTGCGGCGTTTTTCTCACAAACGCC
* * * * ** * *
22467 GTAATAGGTTTTGATATTTAGCGGCGTTTGTCAGAAAAATGCC
1 GCAATAGGTATTGATATTTTGCGGCGTTTTTCTCACAAACGCC
* * * * *
22510 GTAATAGGTGTTGATATTTAGCGGCGTTTTT-TAGATAAACGCC
1 GCAATAGGTATTGATATTTTGCGGCGTTTTTCT-CACAAACGCC
* * *
22553 GCAATAGGTAATGATATTTAGCGGCGTTTTTTCTCTA-AAACGTC
1 GCAATAGGTATTGATATTTTGCGGCG-TTTTTCTC-ACAAACGCC
* * * *
22597 GCATTAGGTGTTGATGTTTTGCGGCG-TTTTCCCACAAACGCC
1 GCAATAGGTATTGATATTTTGCGGCGTTTTTCTCACAAACGCC
* * * * * * *
22639 GTAGTAGATGTTGATGTTTTGCAGCG-TTTTCCCACAAACGCC
1 GCAATAGGTATTGATATTTTGCGGCGTTTTTCTCACAAACGCC
* * * * *
22681 GCATTAGATTTTGATGTTTTGCGGCGTTTATTC-CACAAACGTC
1 GCAATAGGTATTGATATTTTGCGGCGTTT-TTCTCACAAACGCC
* * * * *
22724 GTAGTAGGTTTTGATGTTTTGCGTCGTTTTTCTCACAAACGCC
1 GCAATAGGTATTGATATTTTGCGGCGTTTTTCTCACAAACGCC
*
22767 GCAATAGGTATTGATTTTTTGCGGCGTTTTT
1 GCAATAGGTATTGATATTTTGCGGCGTTTTT
22798 GCTAAAAACA
Statistics
Matches: 279, Mismatches: 44, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.00
42 75 0.27
43 166 0.59
44 35 0.13
45 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (43 bp):
GCAATAGGTATTGATATTTTGCGGCGTTTTTCTCACAAACGCC
Found at i:23220 original size:21 final size:19
Alignment explanation
Indices: 23195--23242 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
23185 ATTCTTCATA
23195 TCTCTGCTGATATACTGCTTC
1 TCTCTGCTG-T-TACTGCTTC
*
23216 TCTCTGTGCTGTTGCTGCTTC
1 TCTC--TGCTGTTACTGCTTC
23237 TCTCTG
1 TCTCTG
23243 TGCTGCCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
21 16 0.67
22 1 0.04
23 5 0.21
ACGTcount: A:0.06, C:0.29, G:0.19, T:0.46
Consensus pattern (19 bp):
TCTCTGCTGTTACTGCTTC
Found at i:23254 original size:21 final size:21
Alignment explanation
Indices: 23208--23281 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
23198 CTGCTGATAT
*
23208 ACTGCTTCTCTCTGTGCTGTT
1 ACTGCTTCTCTCTGTGCTGTC
* *
23229 GCTGCTTCTCTCTGTGCTGCC
1 ACTGCTTCTCTCTGTGCTGTC
* * *
23250 ACTGCTTCTTTCTCTGCTTTC
1 ACTGCTTCTCTCTGTGCTGTC
*
23271 ACTGCTGCTCT
1 ACTGCTTCTCT
23282 AGCTGCTTCT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.04, C:0.34, G:0.18, T:0.45
Consensus pattern (21 bp):
ACTGCTTCTCTCTGTGCTGTC
Found at i:23318 original size:21 final size:20
Alignment explanation
Indices: 23230--23311 Score: 65
Period size: 21 Copynumber: 4.0 Consensus size: 20
23220 TGTGCTGTTG
* * *
23230 CTGCTTCTCTCTGTGCTGCCA
1 CTGCTGCTCTCTCTGCT-TCA
* *
23251 CTGCTTCTTTCTCTGCTTTCA
1 CTGCTGCTCTCTCTGC-TTCA
** *
23272 CTGCTGCTCTAGCTGCTTCTG
1 CTGCTGCTCTCTCTGCTTC-A
23293 CTGCTGCTCTCTCTGCTTC
1 CTGCTGCTCTCTCTGCTTC
23312 CCTTGCTTCA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 3 0.06
21 45 0.92
22 1 0.02
ACGTcount: A:0.04, C:0.37, G:0.17, T:0.43
Consensus pattern (20 bp):
CTGCTGCTCTCTCTGCTTCA
Found at i:31583 original size:42 final size:41
Alignment explanation
Indices: 31533--31625 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
31523 TGTTTATATT
**
31533 AAAAATGCCACAAAGGAACTATTCTACTACGGCGTTTATTAC
1 AAAAATGCCACAAAGGAAC-ACACTACTACGGCGTTTATTAC
* * * *
31575 AAAAATGCCACTAAGGGACACACTATTGCGGCGTTTATTAC
1 AAAAATGCCACAAAGGAACACACTACTACGGCGTTTATTAC
31616 AAAAA-GCCAC
1 AAAAATGCCAC
31626 TAAATTACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 5 0.11
41 23 0.51
42 17 0.38
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAAATGCCACAAAGGAACACACTACTACGGCGTTTATTAC
Found at i:31613 original size:41 final size:41
Alignment explanation
Indices: 31562--31677 Score: 137
Period size: 41 Copynumber: 2.8 Consensus size: 41
31552 TATTCTACTA
*
31562 CGGCGTTTATTACAAAAATGCCACTAAGGGAC-ACACTATTG
1 CGGCGTTTATTACAAAAA-GCCACTAAAGGACAACACTATTG
** *
31603 CGGCGTTTATTACAAAAAGCCACTAAATTACAACTCTATTG
1 CGGCGTTTATTACAAAAAGCCACTAAAGGACAACACTATTG
* *
31644 CGGCGTTTATGT-CAAAAACACCACTAAAGTACAA
1 CGGCGTTTAT-TACAAAAA-GCCACTAAAGGACAA
31678 ATTTTTAGCG
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
40 10 0.15
41 42 0.64
42 14 0.21
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (41 bp):
CGGCGTTTATTACAAAAAGCCACTAAAGGACAACACTATTG
Found at i:31689 original size:42 final size:41
Alignment explanation
Indices: 31562--31693 Score: 135
Period size: 41 Copynumber: 3.2 Consensus size: 41
31552 TATTCTACTA
* * * *
31562 CGGCGTTTATTACAAAAATGCCACTAAGGGACACA-CTATTG
1 CGGCGTTTATTACAAAAA-ACCACTAAAGTACAAATCTATTG
* * *
31603 CGGCGTTTATTACAAAAAGCCACTAAATTACAACTCTATTG
1 CGGCGTTTATTACAAAAAACCACTAAAGTACAAATCTATTG
*
31644 CGGCGTTTATGT-CAAAAACACCACTAAAGTACAAAT-TTTTAG
1 CGGCGTTTAT-TACAAAAA-ACCACTAAAGTACAAATCTATT-G
31686 CGGCGTTT
1 CGGCGTTT
31694 GGTAACGGCG
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
40 11 0.14
41 43 0.55
42 24 0.31
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (41 bp):
CGGCGTTTATTACAAAAAACCACTAAAGTACAAATCTATTG
Found at i:32179 original size:15 final size:15
Alignment explanation
Indices: 32159--32188 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32149 GTTATGCATA
32159 AAAATACTTAACAAT
1 AAAATACTTAACAAT
*
32174 AAAATACTTTACAAT
1 AAAATACTTAACAAT
32189 TTAGAAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATACTTAACAAT
Found at i:33296 original size:40 final size:40
Alignment explanation
Indices: 33244--33422 Score: 173
Period size: 41 Copynumber: 4.4 Consensus size: 40
33234 GCGTTTATAA
**
33244 AAAAAATGCCACTATTGATT-ACACTATTATGGCGTTTGTT
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTT-TT
* * **
33284 AAAAAATGCCACTGTTGATTAAAACTATTGCAACGTTTTT
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTT
* * *
33324 CTAAAAACGCCACTAGTGATTAACACTATTGCGGCGTTTGTCT
1 -AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTT-T-T
* * * *
33367 -AAAAACGCCACTATTTATTATCACTATTGCGGCGTTTTA
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTT
33406 AGAATAAATGCCACTAT
1 A-AA-AAATGCCACTAT
33423 ATGTGTAATC
Statistics
Matches: 114, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
40 22 0.19
41 79 0.69
42 12 0.11
43 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (40 bp):
AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTT
Found at i:33404 original size:82 final size:81
Alignment explanation
Indices: 33245--33396 Score: 198
Period size: 82 Copynumber: 1.9 Consensus size: 81
33235 CGTTTATAAA
* * * * *
33245 AAAAATGCCACTATTGATTACACTATTATGGCGTTTGTTAAAAAATGCCACTGTTGATTAAAACT
1 AAAAACGCCACTAGTGATTACACTATTACGGCGTTTGTTAAAAAACGCCACTATTGATTAAAACT
33310 ATTGCAACGTTTTTCT
66 ATTGCAACGTTTTTCT
* * **
33326 AAAAACGCCACTAGTGATTAACACTATTGCGGCGTTTGTCT-AAAAACGCCACTATTTATTATCA
1 AAAAACGCCACTAGTGATT-ACACTATTACGGCGTTTGT-TAAAAAACGCCACTATTGATTAAAA
33390 CTATTGC
64 CTATTGC
33397 GGCGTTTTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
81 17 0.28
82 42 0.70
83 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (81 bp):
AAAAACGCCACTAGTGATTACACTATTACGGCGTTTGTTAAAAAACGCCACTATTGATTAAAACT
ATTGCAACGTTTTTCT
Found at i:33436 original size:42 final size:40
Alignment explanation
Indices: 33390--33527 Score: 95
Period size: 42 Copynumber: 3.4 Consensus size: 40
33380 TTTATTATCA
*
33390 CTATTGCGGCGTTTTAAGAATAAATGCCACTATATGTGTAAT
1 CTATTACGGCGTTTTAAG-ATAAATGCCACTATATGT-TAAT
* * * *
33432 CTATTACGACG-TTTATGGTATAAATACCGCTA-AT-TTACTGAT
1 CTATTACGGCGTTTTA-AG-ATAAATGCCACTATATGTTA---AT
* * *
33474 CTATTGCGGCGTTTT-AGCTAAAACGCCACTATATGTTAAT
1 CTATTACGGCGTTTTAAGAT-AAATGCCACTATATGTTAAT
*
33514 ATATTACGGCGTTT
1 CTATTACGGCGTTT
33528 GTGGTATAAA
Statistics
Matches: 73, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
39 2 0.03
40 16 0.22
41 15 0.21
42 34 0.47
43 6 0.08
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (40 bp):
CTATTACGGCGTTTTAAGATAAATGCCACTATATGTTAAT
Found at i:33568 original size:42 final size:40
Alignment explanation
Indices: 33430--33570 Score: 117
Period size: 42 Copynumber: 3.4 Consensus size: 40
33420 TATATGTGTA
* * **
33430 ATCTATTACGACGTTTATGGTATAAATACCGCTAATTTAC
1 ATCTATTACGGCGTTTGTGGTATAAACGCCGCTAATTTAC
* * *
33470 TGATCTATTGCGGCGTTT-TAGCTA-AAACGCCACTATATGTTA-
1 --ATCTATTACGGCGTTTGT-GGTATAAACGCCGCTA-AT-TTAC
*
33512 ATATATTACGGCGTTTGTGGTATAAACGCCGCTAATTTACC
1 ATCTATTACGGCGTTTGTGGTATAAACGCCGCTAATTTA-C
*
33553 ACTCTATTGCGGCGTTTG
1 A-TCTATTACGGCGTTTG
33571 GTAAAAAACG
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
39 3 0.04
40 19 0.24
41 21 0.27
42 33 0.42
43 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (40 bp):
ATCTATTACGGCGTTTGTGGTATAAACGCCGCTAATTTAC
Found at i:33579 original size:82 final size:82
Alignment explanation
Indices: 33390--33584 Score: 243
Period size: 82 Copynumber: 2.3 Consensus size: 82
33380 TTTATTATCA
* *
33390 CTATTGCGGCGTTTTAAGAATAAATGCCACTATATGTGTAATCTATTACGACGTTTATGGTATAA
1 CTATTGCGGCGTTTT-AGAA-AAACGCCACTATATGTGTAATATATTACGACGTTTATGGTATAA
* *
33455 ATACCGCTAATTTACTGAT
64 ACACCGCTAATTTACTCAT
* * *
33474 CTATTGCGGCGTTTTAGCTAAAACGCCACTATATGT-TAATATATTACGGCGTTTGTGGTATAAA
1 CTATTGCGGCGTTTTAG-AAAAACGCCACTATATGTGTAATATATTACGACGTTTATGGTATAAA
*
33538 CGCCGCTAATTTAC-CACT
65 CACCGCTAATTTACTCA-T
33556 CTATTGCGGCGTTTGGTA-AAAAACGCCAC
1 CTATTGCGGCGTTT--TAGAAAAACGCCAC
33585 AATAAACCAC
Statistics
Matches: 98, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
81 1 0.01
82 62 0.63
83 17 0.17
84 18 0.18
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (82 bp):
CTATTGCGGCGTTTTAGAAAAACGCCACTATATGTGTAATATATTACGACGTTTATGGTATAAAC
ACCGCTAATTTACTCAT
Found at i:33665 original size:28 final size:27
Alignment explanation
Indices: 33603--33667 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
33593 ACCCTATTAC
33603 GGCGTTTTTCTATATGTCAACTTTATT
1 GGCGTTTTTCTATATGTCAACTTTATT
*
33630 GCAGCGTTTTTCTATATGTTTAACTTT-TAT
1 G--GCGTTTTTCTATATG-TCAACTTTAT-T
33660 GGCGTTTT
1 GGCGTTTT
33668 CTCTCCAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 1 0.03
28 7 0.21
29 16 0.48
30 9 0.27
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (27 bp):
GGCGTTTTTCTATATGTCAACTTTATT
Found at i:37644 original size:20 final size:20
Alignment explanation
Indices: 37612--37724 Score: 172
Period size: 20 Copynumber: 5.7 Consensus size: 20
37602 TTTTCCGAAT
37612 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
37632 TTGTAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
37652 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
37672 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
37692 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
37712 TCGCAACGCGAAT
1 TCGCAATGCGAAT
37725 CTGACTATCG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:37986 original size:22 final size:22
Alignment explanation
Indices: 37921--37986 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
37911 GGCGACATCT
*
37921 GTCCCCATCTCCGACGAAAGCA
1 GTCCCCATCTCCGACGAAATCA
*
37943 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
37965 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
37987 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:38390 original size:20 final size:20
Alignment explanation
Indices: 38327--38392 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
38317 TCTGTCATTA
*
38327 CGATTTTCATTTT-GCGTTG
1 CGATTTTCATTTTCGTGTTG
**
38346 CGATAGTCATTTTCGTGTTG
1 CGATTTTCATTTTCGTGTTG
38366 CGATTTTCATTTTCGTGTTG
1 CGATTTTCATTTTCGTGTTG
38386 CGATTTT
1 CGATTTT
38393 AAGTTTCAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 11 0.27
20 30 0.73
ACGTcount: A:0.12, C:0.15, G:0.21, T:0.52
Consensus pattern (20 bp):
CGATTTTCATTTTCGTGTTG
Found at i:38399 original size:20 final size:20
Alignment explanation
Indices: 38356--38399 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
38346 CGATAGTCAT
* *
38356 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
38376 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
38396 TTTC
1 TTTC
38400 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:40305 original size:20 final size:20
Alignment explanation
Indices: 40280--40476 Score: 170
Period size: 20 Copynumber: 10.5 Consensus size: 20
40270 AGAATAATTT
40280 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
40300 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
40320 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
40336 A--ATCGCAATGTG-AAATG
1 ACTATCGCAATGCGAAAATG
** *
40353 AAAATCGTAA--C-AATAA--
1 ACTATCGCAATGCGAA-AATG
*
40369 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
40387 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
** *
40407 ACTATCGCAACACAAAAATG
1 ACTATCGCAATGCGAAAATG
40427 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
40447 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
40467 ACTATCGCAA
1 ACTATCGCAA
40477 CGAGAGAATC
Statistics
Matches: 147, Mismatches: 16, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
14 13 0.09
16 9 0.06
17 7 0.05
18 5 0.03
19 6 0.04
20 107 0.73
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:40548 original size:20 final size:21
Alignment explanation
Indices: 40523--40629 Score: 143
Period size: 20 Copynumber: 5.3 Consensus size: 21
40513 GATTCTTTCG
*
40523 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTCAATTTTCGCA
*
40543 TTGCGATAGT-TATTTTCGCA
1 TTGCGATAGTCAATTTTCGCA
40563 TTGCGATAGTC-ATTTTCGCA
1 TTGCGATAGTCAATTTTCGCA
*
40583 TTGCGATAGTC-ATTTTTGCA
1 TTGCGATAGTCAATTTTCGCA
*
40603 TTGCGATAGTC-ATTTTCGCG
1 TTGCGATAGTCAATTTTCGCA
40623 TTGCGAT
1 TTGCGAT
40630 TTTAAGTTTC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
19 4 0.05
20 76 0.95
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (21 bp):
TTGCGATAGTCAATTTTCGCA
Found at i:42621 original size:14 final size:14
Alignment explanation
Indices: 42602--42637 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
42592 ATTGTTTAAT
42602 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
42616 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
42630 TGATTTGT
1 TGATTTGT
42638 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:42781 original size:14 final size:14
Alignment explanation
Indices: 42762--42813 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
42752 CGGAAATGAC
42762 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
42776 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
42795 AATCGCAACGAGAG
1 AATCGCAACGAGAG
42809 AATCG
1 AATCG
42814 TAATGCGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 15 0.48
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.32
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:42793 original size:33 final size:33
Alignment explanation
Indices: 42743--42838 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
42733 AAAACAGACT
* *
42743 ATCGCAACGCGGAAATGACAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
42777 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
42810 ATCGTAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
42839 CGAAACTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.55
34 26 0.45
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:42912 original size:20 final size:20
Alignment explanation
Indices: 42887--42980 Score: 122
Period size: 20 Copynumber: 4.7 Consensus size: 20
42877 GCGATTCTCT
42887 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCA
42907 CGTTGCGATAGTCAATTTCGCA
1 CGTTGCGATAGTC-ATTTC-CA
42929 --TTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCA
* *
42947 GGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCA
42967 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
42981 AATGAATGTC
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
18 2 0.03
19 5 0.07
20 51 0.76
21 7 0.10
22 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCA
Found at i:42944 original size:40 final size:40
Alignment explanation
Indices: 42889--42980 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
42879 GATTCTCTCG
42889 TTGCGATAGTCATTTCCACGTTGCGATAGTCA-ATTTCGCA
1 TTGCGATAGTCATTTCCACGTTGCGATAGTCATA-TTCGCA
* *
42929 TTGCGATAGTCATTTCCAGGTTGCGATAGTCATATTCGCG
1 TTGCGATAGTCATTTCCACGTTGCGATAGTCATATTCGCA
42969 TTGCGATAGTCA
1 TTGCGATAGTCA
42981 AATGAATGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 48 0.98
41 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (40 bp):
TTGCGATAGTCATTTCCACGTTGCGATAGTCATATTCGCA
Found at i:42981 original size:60 final size:54
Alignment explanation
Indices: 42848--42981 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 54
42838 GCGAAACTAA
** *
42848 ATTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 ATTCGCGTTGCGATAGTCAATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
* *
42902 -TTCCACGTTGCGATAGTCAATTTCGCATTGCGATAGTCATTTCCAGGTTGCGATAGTCAT
1 ATT-CGCGTTGCGATAGTCAATTTCGCATTGCGAT--TC-TCT-C--GTTGCGATAGTCAT
42962 ATTCGCGTTGCGATAGTCAA
1 ATTCGCGTTGCGATAGTCAA
42982 ATGAATGTCT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
53 2 0.03
54 27 0.41
56 2 0.03
57 2 0.03
58 1 0.02
60 30 0.45
61 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (54 bp):
ATTCGCGTTGCGATAGTCAATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
Found at i:45189 original size:14 final size:14
Alignment explanation
Indices: 45170--45206 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
45160 TCCCGTGGCA
45170 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
45184 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
45198 TTCTTCTTC
1 TT-TTCTTC
45207 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:46356 original size:20 final size:20
Alignment explanation
Indices: 46289--46343 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
46279 GAAATTCAGT
46289 ATTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCTC
46309 ATTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCTC
46329 ATTGCGATAGTCAGA
1 ATTGCGATAGTCAGA
46344 TTCGCGTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (20 bp):
ATTGCGATAGTCAGAATCTC
Found at i:46366 original size:20 final size:20
Alignment explanation
Indices: 46343--46432 Score: 162
Period size: 20 Copynumber: 4.5 Consensus size: 20
46333 CGATAGTCAG
*
46343 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
46363 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
46383 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
46403 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
46423 ATTCGCATTG
1 ATTCGCATTG
46433 TGAATTAGGA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:49374 original size:22 final size:22
Alignment explanation
Indices: 49326--49377 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
49316 TACACCTCAA
*
49326 TATCAATACTTCTTTAAATCGG
1 TATCGATACTTCTTTAAATCGG
49348 TATCGATACTTCTTTAAATCGG
1 TATCGATACTTCTTTAAATCGG
49370 TATCGATA
1 TATCGATA
49378 TTGTTCATCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (22 bp):
TATCGATACTTCTTTAAATCGG
Found at i:50341 original size:31 final size:31
Alignment explanation
Indices: 50306--50374 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
50296 AAGTTACTGA
50306 TTTGATGTTGATGATATAAGGGTTGTTCTGG
1 TTTGATGTTGATGATATAAGGGTTGTTCTGG
50337 TTTGATGTTGATGATATAAGGGTTGTTCTGG
1 TTTGATGTTGATGATATAAGGGTTGTTCTGG
50368 TTTGATG
1 TTTGATG
50375 GTTCAGATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (31 bp):
TTTGATGTTGATGATATAAGGGTTGTTCTGG
Found at i:52649 original size:79 final size:79
Alignment explanation
Indices: 52530--52686 Score: 242
Period size: 79 Copynumber: 2.0 Consensus size: 79
52520 TTAATATTTT
* * *
52530 TTTAACATTTTCGATAAAACGCTACCTAAAATATTATTTTTTCTACCAAAAATGTTAATATTGAG
1 TTTAACATTTTCGATAAAAAGCTACCTAAAACATTATTTTTTCTACCAAAAATATTAATATTGAG
*
52595 CGCTACCTAAAATA
66 CACTACCTAAAATA
* * **
52609 TTTAACATTTTCGGTAAAAAGTTACCTAAAACATTATTTTTTCTACCGTAAATATTAATATTGAG
1 TTTAACATTTTCGATAAAAAGCTACCTAAAACATTATTTTTTCTACCAAAAATATTAATATTGAG
52674 CACTACCTAAAAT
66 CACTACCTAAAAT
52687 GTTATTTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 70 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.38
Consensus pattern (79 bp):
TTTAACATTTTCGATAAAAAGCTACCTAAAACATTATTTTTTCTACCAAAAATATTAATATTGAG
CACTACCTAAAATA
Found at i:53301 original size:19 final size:19
Alignment explanation
Indices: 53277--53324 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
53267 ATGACCAACA
* * *
53277 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATATCC
53296 AAATCGCAACGCGATATCC
1 AAATCGCAACGCGATATCC
53315 AATATCGCAA
1 AA-ATCGCAA
53325 ATCAGTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.21
Consensus pattern (19 bp):
AAATCGCAACGCGATATCC
Found at i:53464 original size:41 final size:41
Alignment explanation
Indices: 53418--53505 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
53408 GCGAATATGT
*
53418 AAATCGCAACGCGATTCTGATTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
* * * ***
53459 TAATCGCGACGCTATTCTGACTATCGCGTTGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
53500 AAATCG
1 AAATCG
53506 TAATACGATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (41 bp):
AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
Found at i:53680 original size:22 final size:22
Alignment explanation
Indices: 53665--53710 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
53655 GCGACTTCCG
53665 TCCCCATCTCCGGCGAAATCCA
1 TCCCCATCTCCGGCGAAATCCA
53687 TCCCCATCTCCGGCGAAATCCA
1 TCCCCATCTCCGGCGAAATCCA
53709 TC
1 TC
53711 TATCTCCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.46, G:0.13, T:0.20
Consensus pattern (22 bp):
TCCCCATCTCCGGCGAAATCCA
Found at i:54103 original size:19 final size:19
Alignment explanation
Indices: 54081--54124 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
54071 AAATCGCAAC
*
54081 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGAGTT
54100 GCGATTTTCATTTCGAGTT
1 GCGATTTTCATTTCGAGTT
54119 GCGATT
1 GCGATT
54125 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (19 bp):
GCGATTTTCATTTCGAGTT
Found at i:54154 original size:20 final size:20
Alignment explanation
Indices: 54129--54177 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
54119 GCGATTATCT
54129 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
54149 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
54169 TGTTGCGAT
1 CGTTGCGAT
54178 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:56122 original size:20 final size:20
Alignment explanation
Indices: 56099--56187 Score: 151
Period size: 20 Copynumber: 4.5 Consensus size: 20
56089 GAAACTTAAA
56099 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
56119 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
56139 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
56159 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
56179 ATCGCAACG
1 ATCGCAACG
56188 GGATAATCGC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:56229 original size:33 final size:33
Alignment explanation
Indices: 56179--56285 Score: 178
Period size: 33 Copynumber: 3.2 Consensus size: 33
56169 GAATTTGACT
* *
56179 ATCGCAACGGGATAATCGCAATGCGAAATAAAA
1 ATCGCAACGTGAAAATCGCAATGCGAAATAAAA
56212 ATCGCAACGTGAAAATCGCAATGCGAAATAAAA
1 ATCGCAACGTGAAAATCGCAATGCGAAATAAAA
*
56245 ATCGCAACGTGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGTGAAAATCGCAATGCG-AAATAAAA
56279 ATCGCAA
1 ATCGCAA
56286 TGCGAATTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 56 0.80
34 14 0.20
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.15
Consensus pattern (33 bp):
ATCGCAACGTGAAAATCGCAATGCGAAATAAAA
Found at i:56277 original size:20 final size:19
Alignment explanation
Indices: 56192--56291 Score: 103
Period size: 14 Copynumber: 5.7 Consensus size: 19
56182 GCAACGGGAT
*
56192 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
56211 AATCGCAA--CG---TGAA
1 AATCGCAATGCGAAATGAA
*
56225 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
56244 AATCGCAA--CG---TGAA
1 AATCGCAATGCGAAATGAA
56258 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
56278 AATCGCAATGCGAA
1 AATCGCAATGCGAA
56292 TTTAGTTTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
14 22 0.33
16 4 0.06
17 4 0.06
19 21 0.31
20 16 0.24
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:56318 original size:19 final size:19
Alignment explanation
Indices: 56286--56332 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
56276 AAAATCGCAA
*
56286 TGCGAATTTAGTTTCACGT
1 TGCGATTTTAGTTTCACGT
* *
56305 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAGTTTCACGT
56324 TGCGATTTT
1 TGCGATTTT
56333 TATTTCGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.26, T:0.47
Consensus pattern (19 bp):
TGCGATTTTAGTTTCACGT
Found at i:56338 original size:19 final size:19
Alignment explanation
Indices: 56292--56345 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
56282 GCAATGCGAA
*
56292 TTTAGTTTCACGTTGCGATT
1 TTTA-TTTCGCGTTGCGATT
**
56312 TTGGTTTCGCGTTGCGATT
1 TTTATTTCGCGTTGCGATT
*
56331 TTTATTTCGCATTGC
1 TTTATTTCGCGTTGC
56346 AATTATCTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 26 0.93
20 2 0.07
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (19 bp):
TTTATTTCGCGTTGCGATT
Found at i:56392 original size:20 final size:20
Alignment explanation
Indices: 56369--56412 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
56359 CGATAGCCAT
56369 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
56389 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
56409 TTTC
1 TTTC
56413 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:56961 original size:42 final size:42
Alignment explanation
Indices: 56910--57010 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
56900 CAAGAGGCTT
*
56910 CTCCTATCGTTCAAGAGGCCCCTATCATCCCTT-AAGA-GTCCC
1 CTCCCATCGTTCAAGAGGCCCCTATCAT-CCTTGAAGAGGT-CC
* * *
56952 CTCCCATCGTTTAAGAGGCCCCTGTCATCGTTGAAGAGGTCC
1 CTCCCATCGTTCAAGAGGCCCCTATCATCCTTGAAGAGGTCC
* *
56994 CTCCCACCATTCAAGAG
1 CTCCCATCGTTCAAGAG
57011 CCCGATTCAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 3 0.06
42 45 0.90
43 2 0.04
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.25
Consensus pattern (42 bp):
CTCCCATCGTTCAAGAGGCCCCTATCATCCTTGAAGAGGTCC
Found at i:56981 original size:21 final size:21
Alignment explanation
Indices: 56888--56995 Score: 85
Period size: 21 Copynumber: 5.1 Consensus size: 21
56878 GCTCGACTCA
*
56888 CCTGTCATCGTTCAAGAGGCT
1 CCTGTCATCGTTCAAGAGGCC
* *
56909 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* * *
56930 CCTATCATCCCTT-AAGAGTCC
1 CCTGTCAT-CGTTCAAGAGGCC
** *
56951 CCTCCCATCGTTTAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
56972 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
56993 CCT
1 CCT
56996 CCCACCATTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
20 4 0.06
21 60 0.88
22 4 0.06
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.28
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:58411 original size:14 final size:14
Alignment explanation
Indices: 58392--58428 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
58382 GCTTGTTTAA
58392 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
58406 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
58420 TTGATTTGT
1 TTGATTTGT
58429 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:58587 original size:20 final size:20
Alignment explanation
Indices: 58548--58625 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
58538 AGGTACACTT
* * *
58548 TCGCAACGCTAAACTCAAAA
1 TCGCAATGCGAAAGTCAAAA
*
58568 TCGTAATGCGAAAGTCAAAA
1 TCGCAATGCGAAAGTCAAAA
*
58588 TCGCAATGCGAAAGCCAAAA
1 TCGCAATGCGAAAGTCAAAA
*
58608 TCGCAACGCGAAAGTCAA
1 TCGCAATGCGAAAGTCAA
58626 TTCGCGTTAC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (20 bp):
TCGCAATGCGAAAGTCAAAA
Found at i:58692 original size:20 final size:20
Alignment explanation
Indices: 58664--58834 Score: 165
Period size: 20 Copynumber: 8.8 Consensus size: 20
58654 GCGATTTTCT
*
58664 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
* *
58684 CGTTACGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
58704 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
**
58724 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCA
* * **
58744 TGTTGTGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCA
*
58758 CGTTGCGATAGTCATATTCA
1 CGTTGCGATAGTCAAATTCA
* *
58778 CGTTGCGATAGTGAAATTCG
1 CGTTGCGATAGTCAAATTCA
*
58798 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
*
58818 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
58835 GAATGTGTAA
Statistics
Matches: 127, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
14 11 0.09
16 1 0.01
18 1 0.01
20 114 0.90
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:58719 original size:40 final size:40
Alignment explanation
Indices: 58664--58834 Score: 192
Period size: 40 Copynumber: 4.4 Consensus size: 40
58654 GCGATTTTCT
* * *
58664 CGTTGCGATAGTCAAATTCCCGTTACGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCA
**
58704 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCA
* * * *
58744 TGTTGTGAT--T----TTTGCGTTGCGATAGTCATATTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCA
* *
58778 CGTTGCGATAGTGAAATTCGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCA
*
58818 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
58835 GAATGTGTAA
Statistics
Matches: 107, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
34 27 0.25
36 1 0.01
38 1 0.01
40 78 0.73
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCA
Found at i:58736 original size:94 final size:94
Alignment explanation
Indices: 58615--58834 Score: 275
Period size: 94 Copynumber: 2.4 Consensus size: 94
58605 AAATCGCAAC
* * * *
58615 GCGAAAGTC-AATTCGCGTTACGTTAGTCTAATACGCT-TTGCGATTTTCT-CGTTGCGATAGTC
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATACG-TGTTGCGATTTT-TGCGTTGCGATAGTC
*
58677 AAATTCCCGTTACGATAATCAAATTCACGTT
64 AAATTCACGTTACGATAATCAAATTCACGTT
** * *
58708 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGTGTTGTGATTTTTGCGTTGCGATAGTCAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATACGTGTTGCGATTTTTGCGTTGCGATAGTCAA
* * * *
58773 ATTCACGTTGCGATAGTGAAATTCGCGTT
66 ATTCACGTTACGATAATCAAATTCACGTT
*
58802 GCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
58835 GAATGTGTAA
Statistics
Matches: 110, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
93 10 0.09
94 100 0.91
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (94 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATACGTGTTGCGATTTTTGCGTTGCGATAGTCAA
ATTCACGTTACGATAATCAAATTCACGTT
Found at i:59057 original size:140 final size:140
Alignment explanation
Indices: 58805--59087 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
58795 TCGCGTTGCG
58805 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
* *
58870 TATCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAATTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
58935 AATACACATA
131 AATACACATA
58945 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
59010 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
59075 AATACACATA
131 AATACACATA
59085 ATA
1 ATA
59088 CAACGTTTGC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:59160 original size:12 final size:12
Alignment explanation
Indices: 59145--59187 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
59135 AAGCCGGTTG
*
59145 TGATTGGGATTT
1 TGATTGCGATTT
**
59157 TGATTTTGATTT
1 TGATTGCGATTT
59169 TGATTGCGATTT
1 TGATTGCGATTT
59181 TGATTGC
1 TGATTGC
59188 CTTTTTCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:59161 original size:6 final size:6
Alignment explanation
Indices: 59152--59185 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
59142 TTGTGATTGG
**
59152 GATTTT GATTTT GATTTT GATTGC GATTTT GATT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATT
59186 GCCTTTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.59
Consensus pattern (6 bp):
GATTTT
Found at i:61240 original size:14 final size:14
Alignment explanation
Indices: 61221--61257 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
61211 TCCCGTGGCA
61221 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
61235 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
61249 TTCTTCTTC
1 TT-TTCTTC
61258 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:61485 original size:24 final size:24
Alignment explanation
Indices: 61447--61500 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
61437 CTGAAACATC
61447 ATCAAAATCCAAGTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
* *
61471 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCAAGTATTGACCAAG
61495 ATCAAA
1 ATCAAA
61501 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCAAGTATTGACCAAG
Found at i:61514 original size:24 final size:24
Alignment explanation
Indices: 61463--61514 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
61453 ATCCAAGTAT
* *
61463 TGACCAAGATCAAAGTCCGAGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
61487 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
61511 TGAC
1 TGAC
61515 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:62250 original size:20 final size:20
Alignment explanation
Indices: 62217--62326 Score: 184
Period size: 20 Copynumber: 5.5 Consensus size: 20
62207 TTCAAATTCA
* *
62217 GCGTTGTGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
62237 ACGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
62257 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
62277 GAGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
62297 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
62317 GCGTTGCGAT
1 GCGTTGCGAT
62327 GCGATAGTCA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:62371 original size:45 final size:45
Alignment explanation
Indices: 62241--62350 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 45
62231 AGAATCACGT
* *
62241 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGAG-T----
1 TGCGATAGTCAAAATCGCGTTGCGATAGTCAGAAACGAGTTGCGA
* * *
62281 TGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGA
1 TGCGATAGTCAAAATCGCGTTGCGATAGTCAGAAACGAGTTGCGA
62326 TGCGATAGTCAAAATCGCGTTGCGA
1 TGCGATAGTCAAAATCGCGTTGCGA
62351 ATCTGGAAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
40 38 0.60
41 1 0.02
45 24 0.38
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (45 bp):
TGCGATAGTCAAAATCGCGTTGCGATAGTCAGAAACGAGTTGCGA
Found at i:62400 original size:19 final size:19
Alignment explanation
Indices: 62365--62412 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
62355 GGAAACTGAT
* *
62365 TTGCGATATTGGAGATCGCG
1 TTGCGAT-TTAGAGATCGCA
62385 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
62404 TTGCGATTT
1 TTGCGATTT
62413 TGTTGGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCA
Found at i:65590 original size:44 final size:44
Alignment explanation
Indices: 65513--65608 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 44
65503 ATGAGAACAA
* * * *
65513 GATATAAGCTATGTGATATGATCTACGTGATTACATGAATATGT
1 GATATAAGCCATGTGACATGACCTACATGATTACATGAATATGT
* * ** *
65557 GATATAAGCCATGTGACATGACCTACATTATTACTTGTCTATTT
1 GATATAAGCCATGTGACATGACCTACATGATTACATGAATATGT
65601 GATATAAG
1 GATATAAG
65609 ATACAATAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (44 bp):
GATATAAGCCATGTGACATGACCTACATGATTACATGAATATGT
Found at i:65728 original size:23 final size:23
Alignment explanation
Indices: 65695--65743 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
65685 TCGAGGGTTC
65695 TACGTGCTCCTTCGGAACAATTA
1 TACGTGCTCCTTCGGAACAATTA
* * *
65718 TACGTGGTCCTTCGGGACATTTA
1 TACGTGCTCCTTCGGAACAATTA
65741 TAC
1 TAC
65744 ACTATCTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (23 bp):
TACGTGCTCCTTCGGAACAATTA
Found at i:70957 original size:44 final size:44
Alignment explanation
Indices: 70907--71002 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
70897 ATGAGAAAAA
* * *
70907 GATATAAGCTATCTGATATGATCTACGTGATTACATGAAC-ATGT
1 GATATAAGCCATCTGACATGACCTACGTGATTACATG-ACTATGT
* * *
70951 GATATAAGCCATGTGACATGACCTACGTGATTACTTGTCTATGT
1 GATATAAGCCATCTGACATGACCTACGTGATTACATGACTATGT
70995 GATATAAG
1 GATATAAG
71003 ATACAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 1 0.02
44 44 0.98
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (44 bp):
GATATAAGCCATCTGACATGACCTACGTGATTACATGACTATGT
Found at i:71120 original size:23 final size:23
Alignment explanation
Indices: 71094--71188 Score: 84
Period size: 23 Copynumber: 4.1 Consensus size: 23
71084 GGTTCTACGC
* *
71094 GGTCCTTCGGGACAATTCTATAT
1 GGTCCTTCAGGACAATTCTATGT
* * * *
71117 GGTCTTTCAGGACATTTCTACGC
1 GGTCCTTCAGGACAATTCTATGT
* * *
71140 GGTCATTCAGGACAATACTATTT
1 GGTCCTTCAGGACAATTCTATGT
*
71163 GGTCCTTC-GTGACATTTCTATGT
1 GGTCCTTCAG-GACAATTCTATGT
71186 GGT
1 GGT
71189 ACTTTGGTGC
Statistics
Matches: 55, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
22 1 0.02
23 54 0.98
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (23 bp):
GGTCCTTCAGGACAATTCTATGT
Found at i:71153 original size:46 final size:46
Alignment explanation
Indices: 71086--71182 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
71076 GAGTCGAGGG
* * * *
71086 TTCTACGCGGTCCTTCGGGACAATTCTATATGGTCTTTCAG-GACAT
1 TTCTACGCGGTCATTCAGGACAATACTATATGGTCCTTC-GTGACAT
*
71132 TTCTACGCGGTCATTCAGGACAATACTATTTGGTCCTTCGTGACAT
1 TTCTACGCGGTCATTCAGGACAATACTATATGGTCCTTCGTGACAT
71178 TTCTA
1 TTCTA
71183 TGTGGTACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
45 1 0.02
46 44 0.98
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (46 bp):
TTCTACGCGGTCATTCAGGACAATACTATATGGTCCTTCGTGACAT
Found at i:72290 original size:23 final size:23
Alignment explanation
Indices: 72264--72327 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
72254 AACTCGTATA
72264 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
72287 AAATACATCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
72310 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
72328 TATAAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.14
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Done.