Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009808.1 Kokia drynarioides strain JFW-HI SEQ_124529, 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: 189053
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--27 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 TA 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 TA T
28 TTGTTGACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10198 original size:123 final size:123
Alignment explanation
Indices: 9979--10227 Score: 471
Period size: 123 Copynumber: 2.0 Consensus size: 123
9969 AAGATATTTG
9979 TGCTTTTGAAGAAAATGCATCGAAAAAAGCTTGGAAGGCCAATTTATCAGTGGTAATCATATCTA
1 TGCTTTTGAAGAAAATGCATCGAAAAAAGCTTGGAAGGCCAATTTATCAGTGGTAATCATATCTA
10044 GGCCTAGGGGCAATGAGGTTGTAGAACGAATAACACCATGAGTCATCATTTAGAAACT
66 GGCCTAGGGGCAATGAGGTTGTAGAACGAATAACACCATGAGTCATCATTTAGAAACT
*
10102 TGCTTTTGAAGAAAATGCATCGAAAAAAGCTTGGAAGGCCAATTTATCGGTGGTAATCATATCTA
1 TGCTTTTGAAGAAAATGCATCGAAAAAAGCTTGGAAGGCCAATTTATCAGTGGTAATCATATCTA
* *
10167 GGCCTAGGGGTAATGAGGTTGTAGAATGAATAACACCATGAGTCATCATTTAGAAACT
66 GGCCTAGGGGCAATGAGGTTGTAGAACGAATAACACCATGAGTCATCATTTAGAAACT
10225 TGC
1 TGC
10228 GGTATTTCCT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (123 bp):
TGCTTTTGAAGAAAATGCATCGAAAAAAGCTTGGAAGGCCAATTTATCAGTGGTAATCATATCTA
GGCCTAGGGGCAATGAGGTTGTAGAACGAATAACACCATGAGTCATCATTTAGAAACT
Found at i:17837 original size:18 final size:18
Alignment explanation
Indices: 17816--17852 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17806 AGTGTCATTC
17816 TAATTT-TTACCTTTTATT
1 TAATTTCTT-CCTTTTATT
17834 TAATTTCTTCCTTTTATT
1 TAATTTCTTCCTTTTATT
17852 T
1 T
17853 TGCCCTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.68
Consensus pattern (18 bp):
TAATTTCTTCCTTTTATT
Found at i:18010 original size:12 final size:12
Alignment explanation
Indices: 17993--18024 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
17983 TATTTCTTTT
17993 TTATATTTTTAA
1 TTATATTTTTAA
*
18005 TTATATTATTAA
1 TTATATTTTTAA
18017 TTATATTT
1 TTATATTT
18025 AATTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATATTTTTAA
Found at i:18028 original size:22 final size:22
Alignment explanation
Indices: 18000--18050 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
17990 TTTTTATATT
18000 TTTAATTATA-TTAT-TAATTATA
1 TTTAATTATATTTATCT-ATT-TA
*
18022 TTTAATTGTATTTATCTATTTA
1 TTTAATTATATTTATCTATTTA
18044 TTTAATT
1 TTTAATT
18051 CATGTATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 18 0.69
23 7 0.27
24 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTAATTATATTTATCTATTTA
Found at i:19061 original size:13 final size:13
Alignment explanation
Indices: 19021--19114 Score: 73
Period size: 13 Copynumber: 7.1 Consensus size: 13
19011 TTACAAATAC
* *
19021 TTCATATAAACAC
1 TTCATATAATCAT
19034 TTCATATAATCAT
1 TTCATATAATCAT
* *
19047 TTCATATATTTAT
1 TTCATATAATCAT
* *
19060 TTCCTTATAA-GAT
1 TT-CATATAATCAT
* *
19073 TTCGTATAGTCAT
1 TTCATATAATCAT
19086 TTCATATAATCAT
1 TTCATATAATCAT
*
19099 TTAACACATAATCAT
1 TT--CATATAATCAT
19114 T
1 T
19115 ATGTATAAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
12 5 0.08
13 43 0.67
14 5 0.08
15 11 0.17
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (13 bp):
TTCATATAATCAT
Found at i:19489 original size:45 final size:45
Alignment explanation
Indices: 19416--19903 Score: 146
Period size: 45 Copynumber: 10.8 Consensus size: 45
19406 ATGGTTGAAG
* * * * * *
19416 GATGTCATGGTGTCTTTCAACCAAGGTCTTATTTATTCTCGA-CTT
1 GATGCCATAGTGTCTTTCAA-CATGGTCTTATTCATTCTCCATCGT
*
19461 GATGCCATAGTGTCTTTCAATCATGGTCTTATTCATTTTCCATCGT
1 GATGCCATAGTGTCTTTCAA-CATGGTCTTATTCATTCTCCATCGT
* * * *
19507 GTTGCCATAGCT-TCTTTCAACTATGGTCTTACTCATT-T-GATTGGT
1 GATGCCATAG-TGTCTTTCAAC-ATGGTCTTATTCATTCTCCA-TCGT
* * * *** *
19552 GATGCCACAATGTCTTTCAACTATGGTCTTACTTGA-T-AGAATAGT
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTA-TTCATTCTCCATCGT
* * * * * * *
19597 GATGTCATAATGTCTTTCAACTGTGGTCTTACTCGTT-T-GATTTGT
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTATTCATTCTCCA-TCGT
* * *** *
19642 GATGCCATAGTGTCTTTCAACTATGGTCTTACTCAAT-AGAATAGT
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTATTCATTCTCCATCGT
** * * * * *
19687 GATGCCATAACGTCTTTCAGCTATGGTCTTACTCGTT-T-GATTTGT
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTATTCATTCTCCA-TCGT
* * * *** *
19732 GATGCCATAATGTCTTTCAACTATGGTTTTACTTGA-T-AGAATAGT
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTA-TTCATTCTCCATCGT
* ** * * * **
19777 GATGTCATAACGTCTTTCAGCTATGGTCTTATTCGTT-TCTAGGGT
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTATTCATTCTCCATCGT
* * *
19822 GGTGCCATAGTGTCTTTCAACTATGGCCTTATTTATTCT-CA--GT
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTATTCATTCTCCATCGT
* * * *
19865 ATAGTGTCATAGTGTCTTTTAACTATGGTCTTAATCATT
1 -GA-TGCCATAGTGTCTTTCAAC-ATGGTCTTATTCATT
19904 TCTTTCAAGC
Statistics
Matches: 345, Mismatches: 81, Indels: 34
0.75 0.18 0.07
Matches are distributed among these distances:
43 2 0.01
44 7 0.02
45 295 0.86
46 40 0.12
47 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (45 bp):
GATGCCATAGTGTCTTTCAACATGGTCTTATTCATTCTCCATCGT
Found at i:19637 original size:90 final size:90
Alignment explanation
Indices: 19519--19852 Score: 481
Period size: 90 Copynumber: 3.7 Consensus size: 90
19509 TGCCATAGCT
* *
19519 TCTTTCAACTATGGTCTTACTCATTTGATTGGTGATGCCACAATGTCTTTCAACTATGGTCTTAC
1 TCTTTCAACTATGGTCTTACTCGTTTGATTGGTGATGCCATAATGTCTTTCAACTATGGTCTTAC
*
19584 TTGATAGAATAGTGATGTCATAATG
66 TTGATAGAATAGTGATGTCATAACG
* * *
19609 TCTTTCAACTGTGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTAC
1 TCTTTCAACTATGGTCTTACTCGTTTGATTGGTGATGCCATAATGTCTTTCAACTATGGTCTTAC
** *
19674 TCAATAGAATAGTGATGCCATAACG
66 TTGATAGAATAGTGATGTCATAACG
* * *
19699 TCTTTCAGCTATGGTCTTACTCGTTTGATTTGTGATGCCATAATGTCTTTCAACTATGGTTTTAC
1 TCTTTCAACTATGGTCTTACTCGTTTGATTGGTGATGCCATAATGTCTTTCAACTATGGTCTTAC
19764 TTGATAGAATAGTGATGTCATAACG
66 TTGATAGAATAGTGATGTCATAACG
* * * * * * *
19789 TCTTTCAGCTATGGTCTTATTCGTTT-CTAGGGTGGTGCCATAGTGTCTTTCAACTATGGCCTTA
1 TCTTTCAACTATGGTCTTACTCGTTTGAT-TGGTGATGCCATAATGTCTTTCAACTATGGTCTTA
19853 TTTATTCTCA
Statistics
Matches: 219, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
89 1 0.00
90 218 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (90 bp):
TCTTTCAACTATGGTCTTACTCGTTTGATTGGTGATGCCATAATGTCTTTCAACTATGGTCTTAC
TTGATAGAATAGTGATGTCATAACG
Found at i:19702 original size:135 final size:135
Alignment explanation
Indices: 19509--19807 Score: 366
Period size: 135 Copynumber: 2.2 Consensus size: 135
19499 TCCATCGTGT
* * * * *
19509 TGCCATAGCT-TCTTTCAACTATGGTCTTACTCATTTGATTGGTGATGCCACAATGTCTTTCAAC
1 TGCCATAG-TGTCTTTCAACTATGGTCTTACTCAATAGAATAGTGATGCCACAACGTCTTTCAAC
* * * * * *
19573 TATGGTCTTACTTGATAGAATAGTGATGTCATAATGTCTTTCAACTGTGGTCTTACTCGTTTGAT
65 TATGGTCTTACTCGATAGAATAGTGATGCCATAATGTCTTTCAACTATGGTCTTACTCGATAGAA
*
19638 TTGTGA
130 TAGTGA
* *
19644 TGCCATAGTGTCTTTCAACTATGGTCTTACTCAATAGAATAGTGATGCCATAACGTCTTTCAGCT
1 TGCCATAGTGTCTTTCAACTATGGTCTTACTCAATAGAATAGTGATGCCACAACGTCTTTCAACT
* * * * * *
19709 ATGGTCTTACTCGTTTGATTTGTGATGCCATAATGTCTTTCAACTATGGTTTTACTTGATAGAAT
66 ATGGTCTTACTCGATAGAATAGTGATGCCATAATGTCTTTCAACTATGGTCTTACTCGATAGAAT
19774 AGTGA
131 AGTGA
* ** *
19779 TGTCATAACGTCTTTCAGCTATGGTCTTA
1 TGCCATAGTGTCTTTCAACTATGGTCTTA
19808 TTCGTTTCTA
Statistics
Matches: 139, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
134 1 0.01
135 138 0.99
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (135 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTACTCAATAGAATAGTGATGCCACAACGTCTTTCAACT
ATGGTCTTACTCGATAGAATAGTGATGCCATAATGTCTTTCAACTATGGTCTTACTCGATAGAAT
AGTGA
Found at i:19828 original size:135 final size:135
Alignment explanation
Indices: 19509--19852 Score: 346
Period size: 135 Copynumber: 2.5 Consensus size: 135
19499 TCCATCGTGT
* * * ** ** *
19509 TGCCATAGCTTCTTTCAACTATGGTCTTACTCATTTGATTGGTGATGCCACAATGTCTTTCAACT
1 TGCCATAACGTCTTTCAACTATGGTCTTACTCAATACAAGGGTGATGCCATAATGTCTTTCAACT
* * * * * *
19574 ATGGTCTTACTTGATAGAATAGTGATGTCATAATGTCTTTCAACTGTGGTCTTACTCGTTTGATT
66 ATGGTCTTACTCGATAGAATAGTGATGCCATAATGTCTTTCAACTATGGTCTTACTCGATAGAAT
*
19639 TGTGA
131 AGTGA
** * ** * *
19644 TGCCATAGTGTCTTTCAACTATGGTCTTACTCAATAGAATAGTGATGCCATAACGTCTTTCAGCT
1 TGCCATAACGTCTTTCAACTATGGTCTTACTCAATACAAGGGTGATGCCATAATGTCTTTCAACT
* * * * * *
19709 ATGGTCTTACTCGTTTGATTTGTGATGCCATAATGTCTTTCAACTATGGTTTTACTTGATAGAAT
66 ATGGTCTTACTCGATAGAATAGTGATGCCATAATGTCTTTCAACTATGGTCTTACTCGATAGAAT
19774 AGTGA
131 AGTGA
* * * ** * * * *
19779 TGTCATAACGTCTTTCAGCTATGGTCTTATTCGTTTCTAGGGTGGTGCCATAGTGTCTTTCAACT
1 TGCCATAACGTCTTTCAACTATGGTCTTACTCAATACAAGGGTGATGCCATAATGTCTTTCAACT
*
19844 ATGGCCTTA
66 ATGGTCTTA
19853 TTTATTCTCA
Statistics
Matches: 170, Mismatches: 39, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
135 170 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (135 bp):
TGCCATAACGTCTTTCAACTATGGTCTTACTCAATACAAGGGTGATGCCATAATGTCTTTCAACT
ATGGTCTTACTCGATAGAATAGTGATGCCATAATGTCTTTCAACTATGGTCTTACTCGATAGAAT
AGTGA
Found at i:19873 original size:90 final size:88
Alignment explanation
Indices: 19519--19897 Score: 351
Period size: 90 Copynumber: 4.2 Consensus size: 88
19509 TGCCATAGCT
* * * *
19519 TCTTTCAACTATGGTCTTACTCATTTGATTGGTGATGCCACAATGTCTTTCAACTATGGTCTTA-
1 TCTTTCAACTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGG-CTTAT
* * *
19583 CT-TGATAGAATAGTGATGTCATAATG
65 TTATTATAGAATA--G-TGTCATAACG
* *
19609 TCTTTCAACTGTGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTAC
1 TCTTTCAACTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGG-CTTAT
*
19674 TCA--ATAGAATAGTGATGCCATAACG
65 TTATTATAGAATAGTG-T--CATAACG
* *
19699 TCTTTCAGCTATGGTCTTACTCGTTTGATTTGTGATGCCATAATGTCTTTCAACTATGG--T-TT
1 TCTTTCAACTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGCTTATT
19761 TACTTGATAGAATAGTGATGTCATAACG
66 TA-TT-ATAGAATA--G-TGTCATAACG
* * * ** *
19789 TCTTTCAGCTATGGTCTTATTCGTTT-CTAGGGTGGTGCCATAGTGTCTTTCAACTATGGCCTTA
1 TCTTTCAACTATGGTCTTACTCGTTTGAT-TTGTGATGCCATAGTGTCTTTCAACTATGG-CTTA
* * **
19853 TTTATTCTCAGTATAGTGTCATAGTG
64 TTTATTAT-AGAATAGTGTCATAACG
*
19879 TCTTTTAACTATGGTCTTA
1 TCTTTCAACTATGGTCTTA
19898 ATCATTTCTT
Statistics
Matches: 246, Mismatches: 25, Indels: 36
0.80 0.08 0.12
Matches are distributed among these distances:
86 2 0.01
87 3 0.01
88 2 0.01
89 1 0.00
90 220 0.89
91 1 0.00
92 3 0.01
93 10 0.04
94 4 0.02
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (88 bp):
TCTTTCAACTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGCTTATT
TATTATAGAATAGTGTCATAACG
Found at i:25521 original size:17 final size:17
Alignment explanation
Indices: 25499--25573 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
25489 GGGCTCAACA
25499 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
25516 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
** * *
25533 AGGTTTAAATTTATGTG
1 AAATTTAAATTTATTTT
* *
25550 AAATTTAAATCTATTAT
1 AAATTTAAATTTATTTT
25567 AAATTTA
1 AAATTTA
25574 TGTTTAAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:26324 original size:3 final size:3
Alignment explanation
Indices: 26316--26382 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
26306 ATAAGTTTAG
* * * *
26316 TAA TAA TAA TAT TAA TAA TAA TAAA TAA CAT TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
26362 TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
26383 ATATACTAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:27518 original size:30 final size:30
Alignment explanation
Indices: 27484--27540 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
27474 TTCTGTAGGT
27484 CCCTAAACTGGTCAAAAATCATATTTTGAC
1 CCCTAAACTGGTCAAAAATCATATTTTGAC
** * *
27514 CCCTAAACTTTTCTAAAATTATATTTT
1 CCCTAAACTGGTCAAAAATCATATTTT
27541 TACTCTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (30 bp):
CCCTAAACTGGTCAAAAATCATATTTTGAC
Found at i:27552 original size:30 final size:29
Alignment explanation
Indices: 27498--27603 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 29
27488 AAACTGGTCA
* * *
27498 AAAATCATATTTTGACCCCTAAACTTTTCT
1 AAAATTATATTTTTACCTC-AAACTTTTCT
27528 AAAATTATATTTTTACTCTCAAACTTTTC-
1 AAAATTATATTTTTAC-CTCAAACTTTTCT
**
27557 AAAATTCCATTTTTGACCTCAAACTTTT-T
1 AAAATTATATTTTT-ACCTCAAACTTTTCT
27586 GAAAATTATATTTTTACC
1 -AAAATTATATTTTTACC
27604 CTCGAGCTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
29 26 0.40
30 37 0.57
31 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (29 bp):
AAAATTATATTTTTACCTCAAACTTTTCT
Found at i:27570 original size:29 final size:28
Alignment explanation
Indices: 27518--27723 Score: 139
Period size: 30 Copynumber: 7.0 Consensus size: 28
27508 TTTGACCCCT
**
27518 AAACTTTTCTAAAATTATATTTTTACTCTC
1 AAACTTTTC-AAAATTCCATTTTTAC-CTC
27548 AAACTTTTCAAAATTCCATTTTTGACCTC
1 AAACTTTTCAAAATTCCATTTTT-ACCTC
* **
27577 AAACTTTTTGAAAATTATATTTTTACCCTC
1 AAAC-TTTTCAAAATTCCATTTTTA-CCTC
* * *
27607 GAGCTTTCCAAAATTCCATTTTTGACC-C
1 AAACTTTTCAAAATTCCATTTTT-ACCTC
* *
27635 TAATTTTTCCAAAAATTACCA-TTTTACCCTC
1 AAACTTTT-C-AAAATT-CCATTTTTA-CCTC
* *
27666 AAAC-TTCCAAAATTCCATTTTTAACCCC
1 AAACTTTTCAAAATTCCATTTTT-ACCTC
* * *
27694 GAACTTTCCAAAAATTACCATTTTAACCTC
1 AAACTTTTC-AAAATT-CCATTTTTACCTC
27724 GGATGTCTAA
Statistics
Matches: 140, Mismatches: 22, Indels: 28
0.74 0.12 0.15
Matches are distributed among these distances:
27 3 0.02
28 21 0.15
29 45 0.32
30 58 0.41
31 13 0.09
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (28 bp):
AAACTTTTCAAAATTCCATTTTTACCTC
Found at i:27702 original size:58 final size:59
Alignment explanation
Indices: 27507--27723 Score: 224
Period size: 59 Copynumber: 3.7 Consensus size: 59
27497 AAAAATCATA
* * * * *
27507 TTTTGACCCCTAAACTTTTCTAAAATTA-TATTTTTACTCTCAAACTTTTCAAAATTCCAT
1 TTTTGACCCC-AAACTTTCCAAAAATTACCA-TTTTACCCTCAAACTTTCCAAAATTCCAT
* *** * * *
27567 TTTTGACCTCAAACTTTTTGAAAATTA-TATTTTTACCCTCGAGCTTTCCAAAATTCCAT
1 TTTTGACCCCAAACTTTCCAAAAATTACCA-TTTTACCCTCAAACTTTCCAAAATTCCAT
* **
27626 TTTTGACCCTAATTTTTCCAAAAATTACCATTTTACCCTCAAAC-TTCCAAAATTCCAT
1 TTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCAT
* * *
27684 TTTTAACCCCGAACTTTCCAAAAATTACCATTTTAACCTC
1 TTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTC
27724 GGATGTCTAA
Statistics
Matches: 133, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
58 48 0.36
59 75 0.56
60 10 0.08
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (59 bp):
TTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCAT
Found at i:27821 original size:27 final size:28
Alignment explanation
Indices: 27761--27821 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
27751 CTAAAATTTC
* *
27761 CCAAAATTACCATTTGGCCCCCGAGTAT
1 CCAAAATTACCATTTGGACCCCGAGCAT
* *
27789 CCAAAATTACCATTT-TACCCCGGGCAT
1 CCAAAATTACCATTTGGACCCCGAGCAT
*
27816 CTAAAA
1 CCAAAA
27822 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.33, C:0.31, G:0.11, T:0.25
Consensus pattern (28 bp):
CCAAAATTACCATTTGGACCCCGAGCAT
Found at i:29425 original size:45 final size:45
Alignment explanation
Indices: 29330--29429 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
29320 ATCATTTTTG
* *
29330 AAGAAGTTGAAAGGTGTGCGCACCTTAATATTCCTAGCTCCAACGG
1 AAGAA-TTGAAAGGTGAGCGCACCTTAATATTCCTAGCTCCAACGA
* * *
29376 AAGAATTGGAAGGTGAGCGCTCCTTAATATTCCTAGCT-CAGCCGA
1 AAGAATTGAAAGGTGAGCGCACCTTAATATTCCTAGCTCCA-ACGA
29421 AAGAATTGA
1 AAGAATTGA
29430 GGGTGATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 2 0.04
45 40 0.85
46 5 0.11
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (45 bp):
AAGAATTGAAAGGTGAGCGCACCTTAATATTCCTAGCTCCAACGA
Found at i:32744 original size:19 final size:18
Alignment explanation
Indices: 32722--32779 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
32712 TGTAAATTGT
32722 TTTAATTATTATAAAATTA
1 TTTAATTATTAT-AAATTA
* * * *
32741 TTTATTTTGTTTTTAATTA
1 TTTA-ATTATTATAAATTA
32760 TTATAATTATTATAAATTA
1 TT-TAATTATTATAAATTA
32779 T
1 T
32780 AAAGGCTTGT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTAATTATTATAAATTA
Found at i:34017 original size:43 final size:43
Alignment explanation
Indices: 33956--34053 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
33946 TTATTCCTTG
*
33956 ACATGTTATTAAATTATATTACTTGA-CTCGCGTTAATAGCGTA
1 ACATGTTATTAAATTATATTACTTGACCT-GCGTTAATAGCATA
* * *
33999 ACATGTTATTAAATTATATTACTTGACCTGTGTTAATATCATG
1 ACATGTTATTAAATTATATTACTTGACCTGCGTTAATAGCATA
34042 ACATGTTATTAA
1 ACATGTTATTAA
34054 TTGTGTAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 48 0.96
44 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (43 bp):
ACATGTTATTAAATTATATTACTTGACCTGCGTTAATAGCATA
Found at i:37977 original size:15 final size:15
Alignment explanation
Indices: 37957--37985 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37947 TATCTAAACC
37957 CCTTTTTATAATGTA
1 CCTTTTTATAATGTA
37972 CCTTTTTATAATGT
1 CCTTTTTATAATGT
37986 CCCACGCTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (15 bp):
CCTTTTTATAATGTA
Found at i:44541 original size:22 final size:22
Alignment explanation
Indices: 44509--44558 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
44499 CTTCTTCCTT
*
44509 TTCTTTCTTT-CTTCTCTCTCCC
1 TTCTTTATTTCCTT-TCTCTCCC
* *
44531 TTCTTTATTTCCTTTGTTTCCC
1 TTCTTTATTTCCTTTCTCTCCC
44553 TTCTTT
1 TTCTTT
44559 TTTTTTTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64
Consensus pattern (22 bp):
TTCTTTATTTCCTTTCTCTCCC
Found at i:45364 original size:10 final size:11
Alignment explanation
Indices: 45337--45370 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
45327 ATATGGATGA
45337 TTTAATTGATT
1 TTTAATTGATT
*
45348 CTTAATT-ATT
1 TTTAATTGATT
45358 TTTAATTGATT
1 TTTAATTGATT
45369 TT
1 TT
45371 AAAAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (11 bp):
TTTAATTGATT
Found at i:45411 original size:23 final size:22
Alignment explanation
Indices: 45368--45409 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
45358 TTTAATTGAT
45368 TTTAAAAACTTATAAAAAAATG
1 TTTAAAAACTTATAAAAAAATG
45390 TTTATAAAA-TTATAAAAAAA
1 TTTA-AAAACTTATAAAAAAA
45410 ATTATAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TTTAAAAACTTATAAAAAAATG
Found at i:45423 original size:21 final size:21
Alignment explanation
Indices: 45372--45424 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
45362 ATTGATTTTA
*
45372 AAAACTTATAAAAAAATGTTTAT
1 AAAA-TTATAAAAAAA-GATTAT
45395 AAAATTATAAAAAAA-ATTAT
1 AAAATTATAAAAAAAGATTAT
*
45415 AGAAGTTATA
1 A-AAATTATA
45425 TAAAGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 7 0.26
22 11 0.41
23 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (21 bp):
AAAATTATAAAAAAAGATTAT
Found at i:45559 original size:18 final size:18
Alignment explanation
Indices: 45499--45564 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 18
45489 TCAAAATTTA
*
45499 TAATATTTTAT-A-TTTT
1 TAATAATTTATAATTTTT
*
45515 TAATAATATATATAATTTTC
1 TAATAAT-T-TATAATTTTT
45535 T-AT-ATTTATAATTTTT
1 TAATAATTTATAATTTTT
*
45551 TAATAATTTCTAAT
1 TAATAATTTATAAT
45565 AATTTTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
16 16 0.40
17 4 0.10
18 13 0.32
19 3 0.08
20 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TAATAATTTATAATTTTT
Found at i:45584 original size:20 final size:21
Alignment explanation
Indices: 45542--45586 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
45532 TTCTATATTT
*
45542 ATAATTTTTTAATAATTTCTA
1 ATAATTTTTCAATAATTTCTA
45563 ATAATTTTTCAA-AA-TTCTTA
1 ATAATTTTTCAATAATTTC-TA
45583 ATAA
1 ATAA
45587 AAATTACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 8 0.36
21 11 0.50
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAATTTTTCAATAATTTCTA
Found at i:45814 original size:8 final size:9
Alignment explanation
Indices: 45795--45870 Score: 55
Period size: 9 Copynumber: 8.1 Consensus size: 9
45785 ATACAGTTTT
45795 TTTTTATAA
1 TTTTTATAA
45804 TTTTTAT-A
1 TTTTTATAA
*
45812 TTTTCTAAAA
1 TTTT-TATAA
** *
45822 AATCTATAA
1 TTTTTATAA
*
45831 TTTTTGTAA
1 TTTTTATAA
45840 TTTTTATAA
1 TTTTTATAA
*
45849 TTCTTTCATAT
1 TT-TTT-ATAA
45860 TTTTTCATAA
1 TTTTT-ATAA
45870 T
1 T
45871 ATACTAAAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
8 5 0.10
9 28 0.55
10 13 0.25
11 5 0.10
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:46109 original size:28 final size:27
Alignment explanation
Indices: 46049--46116 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 27
46039 TTTTAGACTT
46049 AAATAATTAAAAAAATGTAACCTCATA
1 AAATAATTAAAAAAATGTAACCTCATA
*
46076 AAATAATTAAAATAAT-TAAATCCTCATA
1 AAATAATTAAAAAAATGT-AA-CCTCATA
*
46104 ACATAATTAAAAA
1 AAATAATTAAAAA
46117 TATTAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 17 0.47
28 18 0.50
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.28
Consensus pattern (27 bp):
AAATAATTAAAAAAATGTAACCTCATA
Found at i:49802 original size:71 final size:71
Alignment explanation
Indices: 49719--49860 Score: 250
Period size: 71 Copynumber: 2.0 Consensus size: 71
49709 TGAATCGGAA
* *
49719 TCGAAATTTGAATCTATATTATCAAAATTATTATGATC-TCTTCCTTTCATGTACTCTATAAAAT
1 TCGAAATTTGAATCTATATTATCAAAATTATCATGATCTTCTT-CTTCCATGTACTCTATAAAAT
49783 ATGAATC
65 ATGAATC
49790 TCGAAATTTGAATCTATATTATCAAAATTATCATGATCTTCTTCTTCCATGTACTCTATAAAATA
1 TCGAAATTTGAATCTATATTATCAAAATTATCATGATCTTCTTCTTCCATGTACTCTATAAAATA
49855 TGAATC
66 TGAATC
49861 ATCCTAATTC
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
71 64 0.94
72 4 0.06
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (71 bp):
TCGAAATTTGAATCTATATTATCAAAATTATCATGATCTTCTTCTTCCATGTACTCTATAAAATA
TGAATC
Found at i:50266 original size:127 final size:129
Alignment explanation
Indices: 50037--50275 Score: 374
Period size: 127 Copynumber: 1.9 Consensus size: 129
50027 GTCCTTGTGC
* *
50037 TTTTTTTAAATTTAAAATTTAGTATCTATAGTTTAATTTCGAAACAATGAGTCCTTATGCTTTTT
1 TTTTTTTAAA-TTAAAATTTAGTATCTATAGTTTAATTTCGAAACAATAAGTCCTCATGC-TTTT
* *
50102 TTTATCAATATGTGTCCACATATTTGTTGGTTTTAATATAGAATTTAAAGGTGCTTGAGTTTTTT
64 TTTATCAATATGTGTCCACATATATGTTGGTGTTAATATAGAATTTAAAGGTGCTTGAGTTTTTT
50167 T
129 T
* * * *
50168 TTTTTTTAAA-TAAAATTTAGTCTCTATAGTTTAATTTTGAAACAATAAGTCGTCGTG-TTTTTT
1 TTTTTTTAAATTAAAATTTAGTATCTATAGTTTAATTTCGAAACAATAAGTCCTCATGCTTTTTT
50231 TATCAATATGTGTCCACATATATGTTGGTGTTAATATAGAATTTA
66 TATCAATATGTGTCCACATATATGTTGGTGTTAATATAGAATTTA
50276 TAAAGTTTAA
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
127 49 0.49
129 41 0.41
131 10 0.10
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (129 bp):
TTTTTTTAAATTAAAATTTAGTATCTATAGTTTAATTTCGAAACAATAAGTCCTCATGCTTTTTT
TATCAATATGTGTCCACATATATGTTGGTGTTAATATAGAATTTAAAGGTGCTTGAGTTTTTTT
Found at i:50525 original size:149 final size:144
Alignment explanation
Indices: 50161--50527 Score: 404
Period size: 149 Copynumber: 2.5 Consensus size: 144
50151 GGTGCTTGAG
* * *
50161 TTTTTTTTTTTTTTAAATAAAATTTAGTCTCTATAGTTTAATTTTGAAACAATAAGT-C--GTCG
1 TTTTTTTTTTTTTTAAATAAAATTTAGTCTCTATAGTTTAATTTTGAGACAATGAGTCCTTGTCT
* *
50223 TGTTT-TTTTATCAATATGTGTCCACATATATGTTGGTGTTAATATAGAATTTATAAAGTTTAAA
66 TGTTTATTTTATCAAAATGTGTCCACATATATGTTGGTGTTAATATAGAATTTATAAAGTCTAAA
** *
50287 TATGCTAATTGTGC
131 TATGCTAAAGGTAC
******* * *
50301 TTTTTAAAAAAAATAAAATAAAATTTAG--TCTATAATTTAATTTTGAGACAATGAGTCCTTGTG
1 TTTTT-TTTTTTTTTAAATAAAATTTAGTCTCTATAGTTTAATTTTGAGACAATGAGTCCTTGT-
* * *
50364 CTTTTTTTTTTATTATTATCAAAATGTGTCCACATATTTGTTGGTGTTAATATAGAATTTATAAG
64 C----TTGTTTATT-TTATCAAAATGTGTCCACATATATGTTGGTGTTAATATAGAATTTATAAA
50429 GTCTAAATATGCTAAAGGTAC
124 GTCTAAATATGCTAAAGGTAC
*
50450 TTGTGTTTTTTTTTTTAATTTAAAATTTAGTCTCTATAGTTTAATTTTGAGACAATGAGTCCTTG
1 TT-T-TTTTTTTTTTTAA-ATAAAATTTAGTCTCTATAGTTTAATTTTGAGACAATGAGTCCTTG
50515 TACTTGTTTATTT
63 T-CTTGTTTATTT
50528 AAAAATTTTG
Statistics
Matches: 179, Mismatches: 32, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
139 25 0.14
140 6 0.03
141 14 0.08
142 2 0.01
143 1 0.01
147 4 0.02
148 3 0.02
149 74 0.41
150 4 0.02
151 12 0.07
153 34 0.19
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (144 bp):
TTTTTTTTTTTTTTAAATAAAATTTAGTCTCTATAGTTTAATTTTGAGACAATGAGTCCTTGTCT
TGTTTATTTTATCAAAATGTGTCCACATATATGTTGGTGTTAATATAGAATTTATAAAGTCTAAA
TATGCTAAAGGTAC
Found at i:51062 original size:24 final size:24
Alignment explanation
Indices: 51033--51078 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
51023 TTTCTCTTAG
*
51033 ATTGGTAGTTAATTTTTTTCTCAA
1 ATTGGTAGTTAAATTTTTTCTCAA
*
51057 ATTGGTATTTAAATTTTTTCTC
1 ATTGGTAGTTAAATTTTTTCTC
51079 TATCAACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.57
Consensus pattern (24 bp):
ATTGGTAGTTAAATTTTTTCTCAA
Found at i:54138 original size:6 final size:6
Alignment explanation
Indices: 54124--54157 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
54114 CCTTCCCTTA
54124 CCCTC- CCCTCG CCCTCG CCCTCG CCCTCG CCCTC
1 CCCTCG CCCTCG CCCTCG CCCTCG CCCTCG CCCTC
54158 TCTCTCTCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.00, C:0.71, G:0.12, T:0.18
Consensus pattern (6 bp):
CCCTCG
Found at i:57663 original size:38 final size:38
Alignment explanation
Indices: 57566--57665 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 38
57556 ACATTAGGTC
* * *
57566 TGGTTTTAGGTTATAGCTTGGGTCACTAACATTGGGCT
1 TGGTTTTGGGTTATAGATTGGGTTACTAACATTGGGCT
* * *
57604 TGATTTTGGATTATAGATTGGGTTATTAACATTGGGCT
1 TGGTTTTGGGTTATAGATTGGGTTACTAACATTGGGCT
*
57642 TGGTTTTGGGTCTTTAG-TTGGGTT
1 TGGTTTTGGGT-TATAGATTGGGTT
57666 GCATCTGATG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 48 0.92
39 4 0.08
ACGTcount: A:0.17, C:0.08, G:0.30, T:0.45
Consensus pattern (38 bp):
TGGTTTTGGGTTATAGATTGGGTTACTAACATTGGGCT
Found at i:57906 original size:26 final size:26
Alignment explanation
Indices: 57877--57940 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
57867 AGAAAACCAA
*
57877 ATAATGGGGAAGGTTTTGCTCGCAAG
1 ATAATGGGGAAGGTTTTGCTCGCAAC
57903 ATAATGGGGAAGGTTTTGCTCGCAAC
1 ATAATGGGGAAGGTTTTGCTCGCAAC
57929 ATAATGGGGAAG
1 ATAATGGGGAAG
57941 CCAACGAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (26 bp):
ATAATGGGGAAGGTTTTGCTCGCAAC
Found at i:69524 original size:64 final size:65
Alignment explanation
Indices: 69422--69576 Score: 213
Period size: 64 Copynumber: 2.4 Consensus size: 65
69412 AAGCTATTCC
* * * *
69422 TTCGTGAGGTTTTCACCTCCATGTAGGATAATGAATCGCTTTCGGGATTACATCCATA-CTATGT
1 TTCGTGA-GTTTTCACTTCCATGCAGAATAATAAATCGCTTTCGGGATTACATCCATACCTATGT
69486 T
65 T
* *
69487 TTCGTGAGTTTTTACTTCCATGCAGAATAATAAATCGCTTTCGGGATTACATCCGTACCTATGTT
1 TTCGTGAGTTTTCACTTCCATGCAGAATAATAAATCGCTTTCGGGATTACATCCATACCTATGTT
* *
69552 TTTGTGAAGTTTTCACTTCCGTGCA
1 TTCGTG-AGTTTTCACTTCCATGCA
69577 AACATATGGA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 44 0.56
65 19 0.24
66 16 0.20
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (65 bp):
TTCGTGAGTTTTCACTTCCATGCAGAATAATAAATCGCTTTCGGGATTACATCCATACCTATGTT
Found at i:76412 original size:50 final size:49
Alignment explanation
Indices: 76305--76412 Score: 108
Period size: 50 Copynumber: 2.2 Consensus size: 49
76295 AGAAAGGTCG
* * *
76305 AGGCCGCAACGACGAACCCGGTACCATGAAGATATGAAAGGAAACGTTG
1 AGGCCGCAACGACGAACCCGGTACCATGAAGATATAAAAGGAAACGCTA
* ** * ** * *
76354 AGGTCGCAACGGTGAACCTGGTACTTTAGAAGATGTAAAAGGAAAGGCTA
1 AGGCCGCAACGACGAACCCGGTACCAT-GAAGATATAAAAGGAAACGCTA
76404 AGGCCGCAA
1 AGGCCGCAA
76413 TGGCGAACTC
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
49 21 0.46
50 25 0.54
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.15
Consensus pattern (49 bp):
AGGCCGCAACGACGAACCCGGTACCATGAAGATATAAAAGGAAACGCTA
Found at i:76437 original size:50 final size:50
Alignment explanation
Indices: 76383--76478 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 50
76373 GGTACTTTAG
76383 AAGATGTAAAAGGAAAGGCTAAGGCCGCAATGGCGAACTCGATACCTTAA
1 AAGATGTAAAAGGAAAGGCTAAGGCCGCAATGGCGAACTCGATACCTTAA
* ** * * * * *
76433 AAGATGTGATGGGAAAGGTTGAGGTCGTAATGGTGAACTCGATACC
1 AAGATGTAAAAGGAAAGGCTAAGGCCGCAATGGCGAACTCGATACC
76479 GTGAAGACGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (50 bp):
AAGATGTAAAAGGAAAGGCTAAGGCCGCAATGGCGAACTCGATACCTTAA
Found at i:76505 original size:49 final size:49
Alignment explanation
Indices: 76404--76581 Score: 187
Period size: 49 Copynumber: 3.6 Consensus size: 49
76394 GGAAAGGCTA
* * * * **
76404 AGGCCGCAATGGCGAACTCGATACCTTAAAAGATGTGATGGGAAAGGTTG
1 AGGCCGCAATGGAGAACTCGATACCGT-GAAGACGTGATGGGAAAAATTG
* * *
76454 AGGTCGTAATGGTGAACTCGATACCGTGAAGACGTGATGGGAAAAATTG
1 AGGCCGCAATGGAGAACTCGATACCGTGAAGACGTGATGGGAAAAATTG
* * * **
76503 AGGCCGCAATGGAGAATTTGGTACCGTGAAGACGTGATGGGAAAGGTTG
1 AGGCCGCAATGGAGAACTCGATACCGTGAAGACGTGATGGGAAAAATTG
* *
76552 AGGCCGCAATGGA-AAATCCGGTACCGTGAA
1 AGGCCGCAATGGAGAACT-CGATACCGTGAA
76582 AATATTAAGG
Statistics
Matches: 109, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
48 3 0.03
49 83 0.76
50 23 0.21
ACGTcount: A:0.31, C:0.15, G:0.34, T:0.20
Consensus pattern (49 bp):
AGGCCGCAATGGAGAACTCGATACCGTGAAGACGTGATGGGAAAAATTG
Found at i:76526 original size:149 final size:149
Alignment explanation
Indices: 76245--76518 Score: 332
Period size: 149 Copynumber: 1.8 Consensus size: 149
76235 AAATATGAAG
*
76245 GGAAAGGTTAAGGCCGCAACGACAAACCCGATACCTTAAAAGATGTGATGAGAAAGGTCGAGGCC
1 GGAAAGGCTAAGGCCGCAACGACAAACCCGATACCTTAAAAGATGTGATGAGAAAGGTCGAGGCC
* * ** * *
76310 GCAACGACGAACCCGGTACCATGAAGATATGAAAGGAAACGTTGAGGTCGCAACGGTGAACCTGG
66 GCAACGACGAACCCGATACCATGAAGACATGAAAGGAAAAATTGAGGCCGCAACGGAGAACCTGG
76375 TACTTTAGAAGATGTAAAA
131 TACTTTAGAAGATGTAAAA
* * * * * * *
76394 GGAAAGGCTAAGGCCGCAATGGCGAACTCGATACCTTAAAAGATGTGATGGGAAAGGTTGAGGTC
1 GGAAAGGCTAAGGCCGCAACGACAAACCCGATACCTTAAAAGATGTGATGAGAAAGGTCGAGGCC
* * ** * * * ** *
76459 GTAATGGTGAACTCGATACCGTGAAGACGTGATGGGAAAAATTGAGGCCGCAATGGAGAA
66 GCAACGACGAACCCGATACCATGAAGACATGAAAGGAAAAATTGAGGCCGCAACGGAGAA
76519 TTTGGTACCG
Statistics
Matches: 101, Mismatches: 24, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
149 101 1.00
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.17
Consensus pattern (149 bp):
GGAAAGGCTAAGGCCGCAACGACAAACCCGATACCTTAAAAGATGTGATGAGAAAGGTCGAGGCC
GCAACGACGAACCCGATACCATGAAGACATGAAAGGAAAAATTGAGGCCGCAACGGAGAACCTGG
TACTTTAGAAGATGTAAAA
Found at i:76594 original size:49 final size:49
Alignment explanation
Indices: 76443--76599 Score: 136
Period size: 49 Copynumber: 3.2 Consensus size: 49
76433 AAGATGTGAT
* * ** * * * *
76443 GGGAAAGGTTGAGGTCGTAATGGTGAA-CTCGATACCGTGAAGACGTGAT
1 GGGAAAGGTTGAGGCCGCAATGGAAAATC-CGGTACCGTGAAAACATGAA
** * ** * * *
76492 GGGAAAAATTGAGGCCGCAATGGAGAATTTGGTACCGTGAAGACGTGAT
1 GGGAAAGGTTGAGGCCGCAATGGAAAATCCGGTACCGTGAAAACATGAA
* *
76541 GGGAAAGGTTGAGGCCGCAATGGAAAATCCGGTACCGTGAAAATATTAA
1 GGGAAAGGTTGAGGCCGCAATGGAAAATCCGGTACCGTGAAAACATGAA
76590 GGGAAAGGTT
1 GGGAAAGGTT
76600 AAGACCATAA
Statistics
Matches: 89, Mismatches: 18, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
49 89 1.00
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.20
Consensus pattern (49 bp):
GGGAAAGGTTGAGGCCGCAATGGAAAATCCGGTACCGTGAAAACATGAA
Found at i:76745 original size:39 final size:38
Alignment explanation
Indices: 76684--76804 Score: 122
Period size: 38 Copynumber: 3.2 Consensus size: 38
76674 CATGAAACAG
*
76684 ATTGAAG-CATCCAATCTCTTACCTTAATCAGAAGGCAA
1 ATTGAAGACAT-CAATCTCTTACCCTAATCAGAAGGCAA
* *
76722 ATTGAAGACATACAATTTCTTACCCTGATCATG-AGGCAA
1 ATTGAAGACAT-CAATCTCTTACCCTAATCA-GAAGGCAA
* * * *
76761 ATCGAA-ACACTTAATCTCTTACCCTAATCATAAGGCAG
1 ATTGAAGACA-TCAATCTCTTACCCTAATCAGAAGGCAA
76799 ATTGAA
1 ATTGAA
76805 AACGCCAATC
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
38 36 0.53
39 31 0.46
40 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (38 bp):
ATTGAAGACATCAATCTCTTACCCTAATCAGAAGGCAA
Found at i:78270 original size:27 final size:26
Alignment explanation
Indices: 78224--78292 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
78214 AGACCTTTTT
**
78224 ATTTCTTTTCATTTT-AATTCAATCC
1 ATTTCTTTTTTTTTTAAATTCAATCC
* *
78249 ATTTCTTTTTTTTTTAAGATTCGATTC
1 ATTTCTTTTTTTTTTAA-ATTCAATCC
78276 ATTT-TTTTTTTTTTAAA
1 ATTTCTTTTTTTTTTAAA
78293 AGGAAAGGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 14 0.37
26 13 0.34
27 11 0.29
ACGTcount: A:0.22, C:0.12, G:0.03, T:0.64
Consensus pattern (26 bp):
ATTTCTTTTTTTTTTAAATTCAATCC
Found at i:79911 original size:36 final size:36
Alignment explanation
Indices: 79864--79938 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
79854 TCCTTATCAC
*
79864 CTTAGTTCTCGGGTTTTGCAAGACCCTCTCCTGGAT
1 CTTAGTTCTCGGGTTTTGCAAGACCCTCTCCTCGAT
*
79900 CTTAGTTCTCGGGTTTTGCAAGACCCTTTCCTCGAT
1 CTTAGTTCTCGGGTTTTGCAAGACCCTCTCCTCGAT
79936 CTT
1 CTT
79939 TTTCCTCTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.13, C:0.28, G:0.20, T:0.39
Consensus pattern (36 bp):
CTTAGTTCTCGGGTTTTGCAAGACCCTCTCCTCGAT
Found at i:85684 original size:12 final size:12
Alignment explanation
Indices: 85667--85730 Score: 83
Period size: 12 Copynumber: 5.3 Consensus size: 12
85657 ATAACATCCA
*
85667 AACAACCAAAAT
1 AACAACAAAAAT
* *
85679 AACAACTAAAAC
1 AACAACAAAAAT
*
85691 AGCAACAAAAAT
1 AACAACAAAAAT
85703 AACAACAAAAAT
1 AACAACAAAAAT
*
85715 AGCAACAAAAAT
1 AACAACAAAAAT
85727 AACA
1 AACA
85731 GCATTAAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.69, C:0.20, G:0.03, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:85701 original size:24 final size:24
Alignment explanation
Indices: 85669--85730 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
85659 AACATCCAAA
* *
85669 CAACCAAAATAACAACTAAAACAG
1 CAACAAAAATAACAACAAAAACAG
*
85693 CAACAAAAATAACAACAAAAATAG
1 CAACAAAAATAACAACAAAAACAG
85717 CAACAAAAATAACA
1 CAACAAAAATAACA
85731 GCATTAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.68, C:0.21, G:0.03, T:0.08
Consensus pattern (24 bp):
CAACAAAAATAACAACAAAAACAG
Found at i:85792 original size:23 final size:22
Alignment explanation
Indices: 85764--85828 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
85754 ACCAAAGTAG
85764 CAACCAAAATAGT-AAAAAAAA
1 CAACCAAAATAGTAAAAAAAAA
* **
85785 CAATACCAAAACAACAAAAAAAAA
1 C-A-ACCAAAATAGTAAAAAAAAA
85809 CAACCAAAATAGTAAAAAAA
1 CAACCAAAATAGTAAAAAAA
85829 TAGCACCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 1 0.03
22 16 0.46
23 9 0.26
24 9 0.26
ACGTcount: A:0.72, C:0.17, G:0.03, T:0.08
Consensus pattern (22 bp):
CAACCAAAATAGTAAAAAAAAA
Found at i:85814 original size:22 final size:22
Alignment explanation
Indices: 85777--85845 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
85767 CCAAAATAGT
85777 AAAAAAAACAATACCAAAACAACA
1 AAAAAAAAC-A-ACCAAAACAACA
* **
85801 AAAAAAAACAACCAAAATAGTA
1 AAAAAAAACAACCAAAACAACA
*
85823 AAAAAATAGC-ACCAAAACAACA
1 AAAAAA-AACAACCAAAACAACA
85845 A
1 A
85846 TATAATTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 25 0.68
23 3 0.08
24 9 0.24
ACGTcount: A:0.72, C:0.19, G:0.03, T:0.06
Consensus pattern (22 bp):
AAAAAAAACAACCAAAACAACA
Found at i:86965 original size:10 final size:10
Alignment explanation
Indices: 86950--86986 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
86940 AAAATATCAT
86950 ATTAATTTTA
1 ATTAATTTTA
*
86960 ATTAA-TTTG
1 ATTAATTTTA
86969 ATTAATTTTA
1 ATTAATTTTA
86979 ATTAATTT
1 ATTAATTT
86987 GATTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
ATTAATTTTA
Found at i:86974 original size:19 final size:19
Alignment explanation
Indices: 86950--87008 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
86940 AAAATATCAT
86950 ATTAATTTTAATTAATTTG
1 ATTAATTTTAATTAATTTG
86969 ATTAATTTTAATTAATTTG
1 ATTAATTTTAATTAATTTG
* * *
86988 ATTTATTTTATTTTATTTG
1 ATTAATTTTAATTAATTTG
87007 AT
1 AT
87009 CAAAATTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
ATTAATTTTAATTAATTTG
Found at i:87000 original size:9 final size:9
Alignment explanation
Indices: 86949--86999 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
86939 AAAAATATCA
86949 TATTAATTT
1 TATTAATTT
86958 TAATTAATTT
1 T-ATTAATTT
*
86968 GATTAATTT
1 TATTAATTT
86977 TAATTAATTT
1 T-ATTAATTT
* *
86987 GATTTATTT
1 TATTAATTT
86996 TATT
1 TATT
87000 TTATTTGATC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 19 0.54
10 16 0.46
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (9 bp):
TATTAATTT
Found at i:87682 original size:187 final size:179
Alignment explanation
Indices: 87374--87737 Score: 548
Period size: 187 Copynumber: 2.0 Consensus size: 179
87364 AATTCATCTA
* **
87374 ACTGTTTTATTTAATGATGTGGTCACTCTAGTAAGATATTATTATTGTATAACATATTTTTTTGG
1 ACTGTTTTATTTAATGACGTGGTCACTCTAGTAAGATATTATTATTGTATAACATATTACTTTGG
* *
87439 AAAGAAAAACTTTTTTAGAGAGAAAAGGAAAACAATTTTGTTGTAATGCTTTATTTTTTGTCTCA
66 AAAGAAAAACTTTTTTAGAGAGAAAAGGAAAACAATTTTGTCGTAATGCATTATTTTTTGTCTCA
*
87504 ATCATATTCCACTATTTGCAAATTCAAAGCAATGGGGGGTAACTTTGGC
131 ATCATATTCCACTACTTGCAAATTCAAAGCAATGGGGGGTAACTTTGGC
* *
87553 ACTGTTTTATTTAATGACGTGGTCAGTCTTGTAAGATATTATTATTTTATTATGTATAACATATT
1 ACTGTTTTATTTAATGACGTGGTCACTCTAGTAAG--A-TATTA--TTA-T-TGTATAACATATT
** * *
87618 ACTTTGGAAAGTAGGAATTTTTTTATAGAGAAAAGGAAAACAATTTTGTCGTAATGCATTATTTT
59 ACTTTGGAAAG-AAAAACTTTTTTAGAGAGAAAAGGAAAACAATTTTGTCGTAATGCATTATTTT
87683 TTGTCTCAATCATATTCCACTACTTGCAAATTCAAAGCAATGGGGGGTAACTTTG
123 TTGTCTCAATCATATTCCACTACTTGCAAATTCAAAGCAATGGGGGGTAACTTTG
87738 TCTTTTCGGC
Statistics
Matches: 165, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
179 32 0.19
181 1 0.01
182 5 0.03
184 3 0.02
185 1 0.01
186 22 0.13
187 101 0.61
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (179 bp):
ACTGTTTTATTTAATGACGTGGTCACTCTAGTAAGATATTATTATTGTATAACATATTACTTTGG
AAAGAAAAACTTTTTTAGAGAGAAAAGGAAAACAATTTTGTCGTAATGCATTATTTTTTGTCTCA
ATCATATTCCACTACTTGCAAATTCAAAGCAATGGGGGGTAACTTTGGC
Found at i:88992 original size:26 final size:23
Alignment explanation
Indices: 88946--88992 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 23
88936 TTCACATTTT
88946 ACTATTGTTGTTATTTATATGAC
1 ACTATTGTTGTTATTTATATGAC
88969 ACTATTTGTTTGTTATGTTATATG
1 ACTA-TTG-TTGTTAT-TTATATG
88993 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 3 0.14
25 7 0.33
26 7 0.33
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.55
Consensus pattern (23 bp):
ACTATTGTTGTTATTTATATGAC
Found at i:96051 original size:87 final size:87
Alignment explanation
Indices: 95905--96168 Score: 510
Period size: 87 Copynumber: 3.0 Consensus size: 87
95895 GTGAAAGATG
95905 AGGAATCAAAGCCAATGGAGGATATTCTTGATACCGAGGAATTGAAGCCAGTGAAGGAAAAGGAG
1 AGGAATCAAAGCCAATGGAGGATATTCTTGATACCGAGGAATTGAAGCCAGTGAAGGAAAAGGAG
95970 TTCAATGTATTGAAGGATTACA
66 TTCAATGTATTGAAGGATTACA
*
95992 AGGAATCAAAGCCAATGGAGGATATTCTTGATACCGAGGAATTGAAGCCAGCGAAGGAAAAGGAG
1 AGGAATCAAAGCCAATGGAGGATATTCTTGATACCGAGGAATTGAAGCCAGTGAAGGAAAAGGAG
*
96057 TTCAACGTATTGAAGGATTACA
66 TTCAATGTATTGAAGGATTACA
96079 AGGAATCAAAGCCAATGGAGGATATTCTTGATACCGAGGAATTGAAGCCAGTGAAGGAAAAGGAG
1 AGGAATCAAAGCCAATGGAGGATATTCTTGATACCGAGGAATTGAAGCCAGTGAAGGAAAAGGAG
96144 TTCAATGTATTGAAGGATTACA
66 TTCAATGTATTGAAGGATTACA
96166 AGG
1 AGG
96169 TGAAAACATT
Statistics
Matches: 173, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 173 1.00
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (87 bp):
AGGAATCAAAGCCAATGGAGGATATTCTTGATACCGAGGAATTGAAGCCAGTGAAGGAAAAGGAG
TTCAATGTATTGAAGGATTACA
Found at i:103869 original size:77 final size:78
Alignment explanation
Indices: 103731--103885 Score: 285
Period size: 77 Copynumber: 2.0 Consensus size: 78
103721 TATTATCTAT
*
103731 TTTATCTCAACTGTTAGATTTGTTAGAAAAAAAATTTAACCAATTATAACTTGTCACGTAAATCT
1 TTTATCTCAACTGTTAGATTTGTTAGAAAAAAAATTTAACCAATTATAACTTGTCAAGTAAATCT
103796 CTATTTATTTTAC
66 CTATTTATTTTAC
*
103809 TTTATCTCAACTGTTAGATTTGTTAG-AAAAAAATTTAACCAATTATAATTTGTCAAGTAAATCT
1 TTTATCTCAACTGTTAGATTTGTTAGAAAAAAAATTTAACCAATTATAACTTGTCAAGTAAATCT
103873 CTATTTATTTTAC
66 CTATTTATTTTAC
103886 CGATTTTCCT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 49 0.65
78 26 0.35
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (78 bp):
TTTATCTCAACTGTTAGATTTGTTAGAAAAAAAATTTAACCAATTATAACTTGTCAAGTAAATCT
CTATTTATTTTAC
Found at i:104274 original size:14 final size:13
Alignment explanation
Indices: 104251--104280 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
104241 CAGTTGTGTG
104251 AAATTTAAAATTA
1 AAATTTAAAATTA
104264 AAATCTTAAAATTA
1 AAAT-TTAAAATTA
104278 AAA
1 AAA
104281 AAAAAAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATTTAAAATTA
Found at i:105160 original size:32 final size:33
Alignment explanation
Indices: 105101--105165 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
105091 AAACCCTTAA
105101 AAGTTAGAAAAAAAATTTTAAATCCCTTAAAAG
1 AAGTTAGAAAAAAAATTTTAAATCCCTTAAAAG
*
105134 AAGTT-GACAAAAAAATTTTGAA-CCCTTAAAAG
1 AAGTTAGA-AAAAAAATTTTAAATCCCTTAAAAG
105166 TAAAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (33 bp):
AAGTTAGAAAAAAAATTTTAAATCCCTTAAAAG
Found at i:105994 original size:5 final size:5
Alignment explanation
Indices: 105984--106034 Score: 84
Period size: 5 Copynumber: 10.2 Consensus size: 5
105974 GGATTCGTTA
* *
105984 ACTCG ACTCG ACTCG ATTCG ACTCG ACTCG ACTCG ATTCG ACTCG ACTCG
1 ACTCG ACTCG ACTCG ACTCG ACTCG ACTCG ACTCG ACTCG ACTCG ACTCG
106034 A
1 A
106035 TCAAATACTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.24
Consensus pattern (5 bp):
ACTCG
Found at i:106009 original size:20 final size:20
Alignment explanation
Indices: 105984--106034 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
105974 GGATTCGTTA
105984 ACTCGACTCGACTCGATTCG
1 ACTCGACTCGACTCGATTCG
106004 ACTCGACTCGACTCGATTCG
1 ACTCGACTCGACTCGATTCG
106024 ACTCGACTCGA
1 ACTCGACTCGA
106035 TCAAATACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.24
Consensus pattern (20 bp):
ACTCGACTCGACTCGATTCG
Found at i:115621 original size:24 final size:24
Alignment explanation
Indices: 115594--115663 Score: 140
Period size: 24 Copynumber: 2.9 Consensus size: 24
115584 GTGGAACTTG
115594 TAGAAAATGAAGATCCAACTCCAT
1 TAGAAAATGAAGATCCAACTCCAT
115618 TAGAAAATGAAGATCCAACTCCAT
1 TAGAAAATGAAGATCCAACTCCAT
115642 TAGAAAATGAAGATCCAACTCC
1 TAGAAAATGAAGATCCAACTCC
115664 GTGTATGGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.20
Consensus pattern (24 bp):
TAGAAAATGAAGATCCAACTCCAT
Found at i:118065 original size:14 final size:14
Alignment explanation
Indices: 118028--118066 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
118018 TGATTTCTAA
*
118028 TTTAGGGTTAAGGG
1 TTTAGGGTTTAGGG
118042 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGG
*
118056 TTTAAGGTTTA
1 TTTAGGGTTTA
118067 TAGGTATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (14 bp):
TTTAGGGTTTAGGG
Found at i:118400 original size:45 final size:45
Alignment explanation
Indices: 118332--118422 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
118322 GGGAGGAGCA
* *
118332 GAGTATTGCGGTGACTCGTCAAACTGAGGCTAATATCCTTGGCTT
1 GAGTATTGCGGTGACTCGCCAAACTAAGGCTAATATCCTTGGCTT
* *
118377 GAGTATTGCGGTTG-CTCGCCAAACTAAGGCTGATATCTTTGGCTT
1 GAGTATTGCGG-TGACTCGCCAAACTAAGGCTAATATCCTTGGCTT
118422 G
1 G
118423 GTGAGCTAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 39 0.95
46 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (45 bp):
GAGTATTGCGGTGACTCGCCAAACTAAGGCTAATATCCTTGGCTT
Found at i:119041 original size:43 final size:43
Alignment explanation
Indices: 118993--119082 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
118983 AACTGCACAA
* *
118993 TTAATAACATGTCAA-TATATTAATAAGAGTAAAGTAATATAAT
1 TTAATAACATG-CAACCATATTAACAAGAGTAAAGTAATATAAT
* *
119036 TTAATAACATGCAACCATATTAACATGAGTTAAGTAATATAAT
1 TTAATAACATGCAACCATATTAACAAGAGTAAAGTAATATAAT
119079 TTAA
1 TTAA
119083 CATGTTAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 3 0.07
43 39 0.93
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (43 bp):
TTAATAACATGCAACCATATTAACAAGAGTAAAGTAATATAAT
Found at i:120395 original size:16 final size:16
Alignment explanation
Indices: 120374--120422 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
120364 GGATGAGGAT
*
120374 ATTATTTTGGTAATTA
1 ATTATTTTGTTAATTA
120390 ATTATTTT-TTATATT-
1 ATTATTTTGTTA-ATTA
120405 A-TATTTTGTTAATTA
1 ATTATTTTGTTAATTA
120420 ATT
1 ATT
120423 TAGAGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 9 0.32
15 7 0.25
16 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (16 bp):
ATTATTTTGTTAATTA
Found at i:120440 original size:15 final size:16
Alignment explanation
Indices: 120417--120457 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
120407 ATTTTGTTAA
120417 TTAATTTAGAGTATTT
1 TTAATTTAGAGTATTT
*
120433 TT-ATTTAGA-TTTTT
1 TTAATTTAGAGTATTT
120447 TTAATTTAGAG
1 TTAATTTAGAG
120458 GATATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.27
15 14 0.64
16 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (16 bp):
TTAATTTAGAGTATTT
Found at i:120478 original size:30 final size:30
Alignment explanation
Indices: 120417--120477 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
120407 ATTTTGTTAA
* *
120417 TTAATTTAGAGTATTTTTATTTAGATTTTT
1 TTAATTTAGAGGATTATTATTTAGATTTTT
*
120447 TTAATTTAGAGGA-TATTATTTTGATTTTT
1 TTAATTTAGAGGATTATTATTTAGATTTTT
120476 TT
1 TT
120478 TGAATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.62
Consensus pattern (30 bp):
TTAATTTAGAGGATTATTATTTAGATTTTT
Found at i:120668 original size:16 final size:17
Alignment explanation
Indices: 120640--120690 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
120630 TACTTAAAAG
120640 TAATATAAT-AAATTAT
1 TAATATAATAAAATTAT
120656 TAAT-TAATAAAATTAT
1 TAATATAATAAAATTAT
* * *
120672 AAATCT-ATAAAATCAT
1 TAATATAATAAAATTAT
120688 TAA
1 TAA
120691 ATCATTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 4 0.13
16 25 0.83
17 1 0.03
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATATAATAAAATTAT
Found at i:124967 original size:3 final size:3
Alignment explanation
Indices: 124959--125012 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
124949 TAGGGCAACG
* *
124959 TCT TCT TCT TTT TCT TCCT TC- TCT TCT TCT TTT TCT TCT T-T TCTT
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TC-T
125004 TCT TCT TCT
1 TCT TCT TCT
125013 GCTTTAATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:124985 original size:21 final size:20
Alignment explanation
Indices: 124959--125010 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
124949 TAGGGCAACG
124959 TCTTCTTCTTTTTCTTCCTTC
1 TCTTCTTCTTTTTCTT-CTTC
*
124980 TCTTCTTCTTTTTCTTCTTT
1 TCTTCTTCTTTTTCTTCTTC
125000 TCTTTCTTCTT
1 TC-TTCTTCTT
125011 CTGCTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTCTTCTTTTTCTTCTTC
Found at i:132216 original size:24 final size:24
Alignment explanation
Indices: 132188--132233 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
132178 TCACAATTAT
*
132188 CACACCTTCAAGTGTTGGTAATAC
1 CACACCTTCAAGTGTTGATAATAC
*
132212 CACACCTTTAAGTGTTGATAAT
1 CACACCTTCAAGTGTTGATAAT
132234 GCTTTTCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (24 bp):
CACACCTTCAAGTGTTGATAATAC
Found at i:133367 original size:292 final size:292
Alignment explanation
Indices: 132843--133427 Score: 1082
Period size: 292 Copynumber: 2.0 Consensus size: 292
132833 TATGTTTATC
132843 TTTTTTTATTTATCTTTTAGAGTTTAAATTAGATCCAATTAGGGAAATTAAATGTTAGATATTAT
1 TTTTTTTATTTATCTTTTAGAGTTTAAATTAGATCCAATTAGGGAAATTAAATGTTAGATATTAT
132908 TCTAATTATCTTTTAGAATTTAGATTGGATTCAATTAGGAATATTATGTACTATAAATAGGGGGT
66 TCTAATTATCTTTTAGAATTTAGATTGGATTCAATTAGGAATATTATGTACTATAAATAGGGGGT
132973 AAAGTGATTGAATTATTCATTCCCCATTCATTGAAAAATCCTCATTCTCCCTAAATCCCTAGCTC
131 AAAGTGATTGAATTATTCATTCCCCATTCATTGAAAAATCCTCATTCTCCCTAAATCCCTAGCTC
* *
133038 AATAAAAGCTTTATTTTATTATCTTGTGGTTTTCCCCAAAATCATTAGTAACTAAAAAACCCTTC
196 AATAAAAGCTTTATTTTATTATCTTATGGTTTTCCCCAAAATCATGAGTAACTAAAAAACCCTTC
*
133103 TAGCTAAAGGTTATCAAATATTCCTCCAAGGT
261 TAGCCAAAGGTTATCAAATATTCCTCCAAGGT
*
133135 TTTTTTTATTTATCTTTTAGAGTTTAAATTGGATCCAATTAGGGAAATTAAATGTTAGATATTAT
1 TTTTTTTATTTATCTTTTAGAGTTTAAATTAGATCCAATTAGGGAAATTAAATGTTAGATATTAT
133200 TCTAATTATCTTTTAGAATTTAGATTGGATTCAATTAGGAATATTATGTACTATAAATAGGGGGT
66 TCTAATTATCTTTTAGAATTTAGATTGGATTCAATTAGGAATATTATGTACTATAAATAGGGGGT
**
133265 GGAGTGATTGAATTATTCATTCCCCATTCATTGAAAAATCCTTCA-TCTCCCTAAATCCCTAGCT
131 AAAGTGATTGAATTATTCATTCCCCATTCATTGAAAAATCC-TCATTCTCCCTAAATCCCTAGCT
* *
133329 CAATAAAAGCTTTATTTTATTATCTTATGTTTTTCCCCAAAATCATGAGTAACTAAAAATCCCTT
195 CAATAAAAGCTTTATTTTATTATCTTATGGTTTTCCCCAAAATCATGAGTAACTAAAAAACCCTT
133394 CTAGCCAAAGGTTATCAAATATTCCTCCAAGGT
260 CTAGCCAAAGGTTATCAAATATTCCTCCAAGGT
133427 T
1 T
133428 CATGAGGTTT
Statistics
Matches: 284, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
292 281 0.99
293 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (292 bp):
TTTTTTTATTTATCTTTTAGAGTTTAAATTAGATCCAATTAGGGAAATTAAATGTTAGATATTAT
TCTAATTATCTTTTAGAATTTAGATTGGATTCAATTAGGAATATTATGTACTATAAATAGGGGGT
AAAGTGATTGAATTATTCATTCCCCATTCATTGAAAAATCCTCATTCTCCCTAAATCCCTAGCTC
AATAAAAGCTTTATTTTATTATCTTATGGTTTTCCCCAAAATCATGAGTAACTAAAAAACCCTTC
TAGCCAAAGGTTATCAAATATTCCTCCAAGGT
Found at i:135765 original size:24 final size:22
Alignment explanation
Indices: 135713--135761 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 22
135703 TTTAATTAGT
135713 AAATATATATTTTTAAAATTATA
1 AAAT-TATATTTTTAAAATTATA
135736 AAATTATATTATTTATAAATT-TA
1 AAATTATATT-TTTA-AAATTATA
135759 AAA
1 AAA
135762 ATTAAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.25
23 13 0.54
24 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATTATATTTTTAAAATTATA
Found at i:137902 original size:35 final size:35
Alignment explanation
Indices: 137863--137929 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
137853 CTTAAACTGT
*
137863 TTTTTTTTTTTTTATAT-TAAAATTGTTATTTTTAC
1 TTTTTTTTTTTTTAAATATAAAATT-TTATTTTTAC
*
137898 TTTTTTTTTTTTTAAATATAAAGTTTTATTTT
1 TTTTTTTTTTTTTAAATATAAAATTTTATTTT
137930 ATCATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 23 0.79
36 6 0.21
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (35 bp):
TTTTTTTTTTTTTAAATATAAAATTTTATTTTTAC
Found at i:141983 original size:10 final size:10
Alignment explanation
Indices: 141970--142008 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
141960 ATAAATAGAT
141970 ATAAAAATAA
1 ATAAAAATAA
*
141980 ATAAAGATGAA
1 ATAAAAAT-AA
*
141991 ATAAGAATAA
1 ATAAAAATAA
142001 ATAAAAAT
1 ATAAAAAT
142009 TATACGATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:142880 original size:21 final size:20
Alignment explanation
Indices: 142843--142882 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
142833 AAAACGCATA
* *
142843 AAAAATAATAGCCAAACAAT
1 AAAAATAAAAGCAAAACAAT
142863 AAAAATAACAAGCAAAACAA
1 AAAAATAA-AAGCAAAACAA
142883 CAGCAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.70, C:0.15, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAAATAAAAGCAAAACAAT
Found at i:143000 original size:21 final size:21
Alignment explanation
Indices: 142974--143046 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 21
142964 GAGTAAAAAA
142974 ACCAAAACAATAAAAAATAAC
1 ACCAAAACAATAAAAAATAAC
142995 ACCAAAA-AAGTAAAAAACATAA-
1 ACCAAAACAA-T-AAAAA-ATAAC
* *
143017 ACCAAAACAGTTAAAAA-AAC
1 ACCAAAACAATAAAAAATAAC
143037 ACCAAAACAA
1 ACCAAAACAA
143047 CAATATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.05
20 12 0.27
21 12 0.27
22 13 0.30
23 5 0.11
ACGTcount: A:0.70, C:0.19, G:0.03, T:0.08
Consensus pattern (21 bp):
ACCAAAACAATAAAAAATAAC
Found at i:143040 original size:20 final size:21
Alignment explanation
Indices: 142974--143045 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
142964 GAGTAAAAAA
* *
142974 ACCAAAACAATAAAAAATAAC
1 ACCAAAACAGTAAAAAACAAC
* *
142995 ACCAAAAAAGTAAAAAACATAA
1 ACCAAAACAGTAAAAAACA-AC
*
143017 ACCAAAACAGTTAAAAA-AAC
1 ACCAAAACAGTAAAAAACAAC
143037 ACCAAAACA
1 ACCAAAACA
143046 ACAATATAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 10 0.23
21 17 0.40
22 16 0.37
ACGTcount: A:0.69, C:0.19, G:0.03, T:0.08
Consensus pattern (21 bp):
ACCAAAACAGTAAAAAACAAC
Found at i:143400 original size:2 final size:2
Alignment explanation
Indices: 143395--143420 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
143385 AAGGACTAAA
143395 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
143421 TTAAAACCCT
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:143745 original size:148 final size:151
Alignment explanation
Indices: 143462--143745 Score: 351
Period size: 148 Copynumber: 1.9 Consensus size: 151
143452 TACTATTTTT
* * **
143462 CTTAAAAATCAAAGTTTTTATTTCAAAATAGTTAAAAAAATCAAAATTTTATTTTTAAAAAATTT
1 CTTAAAAATCAAAATTTTTATTTCAAAATAATT-AAAAAATC-AAATTTTATTTAAAAAAAATTT
* * * ********
143527 AATTTTTTCCTTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATTTGAACTTTCTTTTTT
64 AATTTTTTCCTTTAAAATGACTAAAAAACATATTCTTATTTTTAAAAATCTAAACTTAAAAAAAA
*
143592 GAAAAAATAAAAATAAATGACTA
129 AAAAAAATAAAAATAAATGACTA
*
143615 CTTAAAAATCAAAATTTTTATTTTAAAATAATT-AAAAATC-AATTTT-TTTAAAAAAAA-TTAT
1 CTTAAAAATCAAAATTTTTATTTCAAAATAATTAAAAAATCAAATTTTATTTAAAAAAAATTTA-
*
143676 TTTTTTTCCTTTAAAATGACTAAAAAACATATTCTTATTTTTAAAAATCTAAACTTAAAAAAAAA
65 ATTTTTTCCTTTAAAATGACTAAAAAACATATTCTTATTTTTAAAAATCTAAACTTAAAAAAAAA
143741 AAAAA
130 AAAAA
143746 TCACTACTTT
Statistics
Matches: 112, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
147 3 0.03
148 66 0.59
149 6 0.05
151 7 0.06
153 30 0.27
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (151 bp):
CTTAAAAATCAAAATTTTTATTTCAAAATAATTAAAAAATCAAATTTTATTTAAAAAAAATTTAA
TTTTTTCCTTTAAAATGACTAAAAAACATATTCTTATTTTTAAAAATCTAAACTTAAAAAAAAAA
AAAAATAAAAATAAATGACTA
Found at i:144228 original size:30 final size:31
Alignment explanation
Indices: 144176--144233 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
144166 ACTCAAATTT
*
144176 GACACTTTCTTCTAATTTGGTACCTAAATCC
1 GACACTTTCTTCTAAGTTGGTACCTAAATCC
* *
144207 GACACTTT-TTTTAAGTTGGTACTTAAA
1 GACACTTTCTTCTAAGTTGGTACCTAAA
144234 CTTTTTGGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (31 bp):
GACACTTTCTTCTAAGTTGGTACCTAAATCC
Found at i:144504 original size:31 final size:31
Alignment explanation
Indices: 144468--144571 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
144458 AAAAAAAAGC
144468 TTAGGTACCAGAA-TAAGAAAAAATGTTAAGT
1 TTAGGTACCA-AATTAAGAAAAAATGTTAAGT
* **
144499 TTAGGTAACAAATTGGGTAAAAAA----AAGT
1 TTAGGTACCAAATTAAG-AAAAAATGTTAAGT
* *
144527 TTAGGTACCAAATTAAGAAAAAGTGTTAAAT
1 TTAGGTACCAAATTAAGAAAAAATGTTAAGT
*
144558 TCAGGTACCAAATT
1 TTAGGTACCAAATT
144572 GGGTAAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
27 5 0.09
28 18 0.31
30 2 0.03
31 27 0.47
32 6 0.10
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (31 bp):
TTAGGTACCAAATTAAGAAAAAATGTTAAGT
Found at i:144534 original size:59 final size:59
Alignment explanation
Indices: 144457--144628 Score: 204
Period size: 59 Copynumber: 2.9 Consensus size: 59
144447 AAATTGAATC
* * *
144457 TAAAAAAAAGCTTAGGTACCAGAA-TAAGAAAAAATGTTAAGTTTAGGTAACAAATTGGG
1 TAAAAAAAAGTTTAGGTACCA-AATTAAGAAAAAATGTTAAATTCAGGTAACAAATTGGG
* *
144516 TAAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTTAAATTCAGGTACCAAATTGGG
1 TAAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTTAAATTCAGGTAACAAATTGGG
** * * * * * *
144575 TAAAAAAAAGTTTAAATATCAAATTTA-AAAAAATATCAAGTTCAGGTACCAAAT
1 TAAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTTAAATTCAGGTAACAAAT
144629 ACTATATTAA
Statistics
Matches: 99, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
58 25 0.25
59 74 0.75
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.26
Consensus pattern (59 bp):
TAAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTTAAATTCAGGTAACAAATTGGG
Found at i:144538 original size:28 final size:28
Alignment explanation
Indices: 144495--144588 Score: 93
Period size: 28 Copynumber: 3.2 Consensus size: 28
144485 AAAAAATGTT
*
144495 AAGTTTAGGTAACAAATTGGGTAAAAAA
1 AAGTTTAGGTACCAAATTGGGTAAAAAA
**
144523 AAGTTTAGGTACCAAATTAAG-AAAAAGTGTTA
1 AAGTTTAGGTACCAAATTGGGTAAAAA-----A
*
144555 AA-TTCAGGTACCAAATTGGGTAAAAAA
1 AAGTTTAGGTACCAAATTGGGTAAAAAA
144582 AAGTTTA
1 AAGTTTA
144589 AATATCAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
27 8 0.15
28 21 0.40
31 15 0.29
32 8 0.15
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (28 bp):
AAGTTTAGGTACCAAATTGGGTAAAAAA
Found at i:151360 original size:12 final size:12
Alignment explanation
Indices: 151343--151378 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
151333 TTCACGAACA
151343 AGCTCGTTTATT
1 AGCTCGTTTATT
151355 AGCTCGTTTATT
1 AGCTCGTTTATT
151367 -GACTCGTTTATT
1 AG-CTCGTTTATT
151379 TATTAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 1 0.04
12 22 0.96
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (12 bp):
AGCTCGTTTATT
Found at i:151497 original size:24 final size:23
Alignment explanation
Indices: 151470--151533 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
151460 TCATCAACAT
*
151470 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
**
151494 TGTTCATGAACATGTTCGTTTAA
1 TGTTCATGAACATGTTCAATTAA
*
151517 TGTTCTTGAACATGTTC
1 TGTTCATGAACATGTTC
151534 GATAAAGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:151508 original size:12 final size:12
Alignment explanation
Indices: 151459--151564 Score: 51
Period size: 12 Copynumber: 8.9 Consensus size: 12
151449 TTGTTTGTTA
*
151459 TTCATCAACATTG
1 TTCATGAACA-TG
*
151472 TTCGTGAACATG
1 TTCATGAACATG
* *
151484 TTCAAT-TATATG
1 TTC-ATGAACATG
151496 TTCATGAACATG
1 TTCATGAACATG
* **
151508 TTCGTTTA-ATG
1 TTCATGAACATG
*
151519 TTCTTGAACATG
1 TTCATGAACATG
151531 TTCGAT-AA-A-G
1 TTC-ATGAACATG
* *
151541 TTAAATGAACAAG
1 TT-CATGAACATG
151554 TTCATGAACAT
1 TTCATGAACAT
151565 TAAACAAACG
Statistics
Matches: 68, Mismatches: 17, Indels: 17
0.67 0.17 0.17
Matches are distributed among these distances:
10 5 0.07
11 13 0.19
12 37 0.54
13 13 0.19
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:151526 original size:23 final size:24
Alignment explanation
Indices: 151470--151536 Score: 91
Period size: 23 Copynumber: 2.8 Consensus size: 24
151460 TCATCAACAT
* *
151470 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCGATTATA
*
151494 TGTTCATGAACATGTTCGTTTA-A
1 TGTTCATGAACATGTTCGATTATA
*
151517 TGTTCTTGAACATGTTCGAT
1 TGTTCATGAACATGTTCGAT
151537 AAAGTTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.43
Consensus pattern (24 bp):
TGTTCATGAACATGTTCGATTATA
Found at i:151965 original size:21 final size:20
Alignment explanation
Indices: 151932--151982 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
151922 TCAAATTGAT
*
151932 TTTTTTAAATTATACTTTTG
1 TTTTTTAAATTATAATTTTG
*
151952 TTTTTTATATTTATAATTTTG
1 TTTTTTA-AATTATAATTTTG
*
151973 ATATTTTAAA
1 -TTTTTTAAA
151983 AAAATTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 7 0.28
21 12 0.48
22 6 0.24
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTTTAAATTATAATTTTG
Found at i:162652 original size:18 final size:20
Alignment explanation
Indices: 162629--162669 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
162619 TATCGGTTTT
162629 TTAAAAAAATT-GAA-AATA
1 TTAAAAAAATTCGAATAATA
*
162647 TTAAAAAATTTCGAATAATA
1 TTAAAAAAATTCGAATAATA
162667 TTA
1 TTA
162670 TATATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 3 0.15
20 7 0.35
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (20 bp):
TTAAAAAAATTCGAATAATA
Found at i:168828 original size:49 final size:50
Alignment explanation
Indices: 168678--168911 Score: 191
Period size: 49 Copynumber: 4.8 Consensus size: 50
168668 AGATTCGTCA
* *
168678 TTGCGGCTTAAATCTTTCCCTCCATG--CTTC-TGAGGTACAAGGTTTGCCG
1 TTGCGGCTTAAATCTTTCCCTTCATGATCTTCAT--GGTACAAGGTTCGCCG
* * * * * *
168727 TTG-GGACTTAAACCTTTCCCTT--TGTATTTTCATGGTACTAGATTTGTCG
1 TTGCGG-CTTAAATCTTTCCCTTCATG-ATCTTCATGGTACAAGGTTCGCCG
* * *
168776 TTGCGGCTTAAATCTTTCCCTTCATGCTCTTAAT-GTACAAGGTTCGCTG
1 TTGCGGCTTAAATCTTTCCCTTCATGATCTTCATGGTACAAGGTTCGCCG
** * * * *
168825 TTGCAACTTAAACCTTT-CCTTCCATTATCTTCGTGGTAC-TGGATTCGCCG
1 TTGCGGCTTAAATCTTTCCCTT-CATGATCTTCATGGTACAAGG-TTCGCCG
168875 TTGCGGCTTAAATCTTTCCCTTCATG-TCTTCATGGTA
1 TTGCGGCTTAAATCTTTCCCTTCATGATCTTCATGGTA
168912 ATGAAACCTG
Statistics
Matches: 144, Mismatches: 29, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
47 2 0.01
48 6 0.04
49 92 0.64
50 37 0.26
51 7 0.05
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (50 bp):
TTGCGGCTTAAATCTTTCCCTTCATGATCTTCATGGTACAAGGTTCGCCG
Found at i:168895 original size:99 final size:98
Alignment explanation
Indices: 168655--168904 Score: 310
Period size: 98 Copynumber: 2.6 Consensus size: 98
168645 GGCTTCAATG
* * * *
168655 TCTTTGTGGTACTAGATTCGTCATTGCGGCTTAAATCTTTCCCTCCATGCT-TCTGAGGTACAAG
1 TCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTCT-TAAGGTACAAG
* **
168719 GTTTGCCGTTGGGACTTAAACCTTTCCCTTTGTA
65 GTTCGCCGTTGCAACTTAAACCTTTCCCTTTGTA
* * * *
168753 TTTTCATGGTACTAGATTTGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTCTTAATGTACAAGG
1 TCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTCTTAAGGTACAAGG
*
168818 TTCGCTGTTGCAACTTAAACCTTT-CCTTCCAT-TA
66 TTCGCCGTTGCAACTTAAACCTTTCCCTT---TGTA
* *
168852 TCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-TCTT
1 TCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTCTT
168905 CATGGTAATG
Statistics
Matches: 131, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
97 4 0.03
98 79 0.60
99 47 0.36
100 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.40
Consensus pattern (98 bp):
TCTTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGCTCTTAAGGTACAAGG
TTCGCCGTTGCAACTTAAACCTTTCCCTTTGTA
Found at i:173114 original size:78 final size:78
Alignment explanation
Indices: 173023--173175 Score: 297
Period size: 78 Copynumber: 2.0 Consensus size: 78
173013 AGAATGATTG
*
173023 TATGGTATGAGTATGAGTATTTGTATACAAAATTTAAGAATGATTAATTATGTAGATTAAGTGTA
1 TATGGTATGAGTATGAGTATATGTATACAAAATTTAAGAATGATTAATTATGTAGATTAAGTGTA
173088 AACAAATTGTTTT
66 AACAAATTGTTTT
173101 TATGGTATGAGTATGAGTATATGTATACAAAATTTAAGAATGATTAATTATGTAGATTAAGTGTA
1 TATGGTATGAGTATGAGTATATGTATACAAAATTTAAGAATGATTAATTATGTAGATTAAGTGTA
173166 AACAAATTGT
66 AACAAATTGT
173176 CTGAATGGAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (78 bp):
TATGGTATGAGTATGAGTATATGTATACAAAATTTAAGAATGATTAATTATGTAGATTAAGTGTA
AACAAATTGTTTT
Found at i:173171 original size:40 final size:40
Alignment explanation
Indices: 173044--173171 Score: 113
Period size: 40 Copynumber: 3.2 Consensus size: 40
173034 TATGAGTATT
*
173044 TGTATACAAAATTTAAGAATGATTAATTATGTAGATTAAG
1 TGTAAACAAAATTTAAGAATGATTAATTATGTAGATTAAG
**** * * *
173084 TGTAAAC-AAATTGTTTTTATG-GT-ATGA-GTATGAGTATA-
1 TGTAAACAAAATT-TAAGAATGATTAATTATGTA-GATTA-AG
*
173122 TGTATACAAAATTTAAGAATGATTAATTATGTAGATTAAG
1 TGTAAACAAAATTTAAGAATGATTAATTATGTAGATTAAG
173162 TGTAAACAAA
1 TGTAAACAAA
173172 TTGTCTGAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 16
0.66 0.18 0.17
Matches are distributed among these distances:
37 3 0.05
38 17 0.27
39 14 0.22
40 26 0.41
41 3 0.05
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (40 bp):
TGTAAACAAAATTTAAGAATGATTAATTATGTAGATTAAG
Found at i:184255 original size:71 final size:70
Alignment explanation
Indices: 184134--184273 Score: 235
Period size: 71 Copynumber: 2.0 Consensus size: 70
184124 TCTTTCTCTA
*
184134 CAGGTGTGTGCTTTGGAAGAAGAGTTGATAAGTGGAACAAGGGTTGATGGGTGAGGGGTGCTCAG
1 CAGGCGTGTGCTTTGGAAGAAGAGTTGATAAGTGGAACAAGGGTTGATGGGTG-GGGGTGCTCAG
184199 GTTTTG
65 GTTTTG
* * *
184205 CAGGCGTGTGTTTTGGAGGAAGAGTTGATAGGTGGAACAAGGGTTGATGGGTGGGGGTGCTCAGG
1 CAGGCGTGTGCTTTGGAAGAAGAGTTGATAAGTGGAACAAGGGTTGATGGGTGGGGGTGCTCAGG
184270 TTTT
66 TTTT
184274 AAGTTGGTCA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 16 0.25
71 49 0.75
ACGTcount: A:0.21, C:0.07, G:0.44, T:0.29
Consensus pattern (70 bp):
CAGGCGTGTGCTTTGGAAGAAGAGTTGATAAGTGGAACAAGGGTTGATGGGTGGGGGTGCTCAGG
TTTTG
Done.