Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000838.1 Hibiscus syriacus cultivar Beakdansim tig00001620_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: 115034
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4868 original size:43 final size:43
Alignment explanation
Indices: 4781--4869 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 43
4771 ATACGTCTAA
* * * *
4781 CGACGTAATTTTCGTGAGAGTTGATTGGAGGGGAAGGATGGAC
1 CGACGTAATTTTCGTGAGAGTTGATTGGAGAGAAAGCATAGAC
*
4824 CGACGTAATTTTCGTGAGAGTTG-TTCGGAGAGAAATCATAGAC
1 CGACGTAATTTTCGTGAGAGTTGATT-GGAGAGAAAGCATAGAC
4867 CGA
1 CGA
4870 TGTGAGAGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 2 0.05
43 38 0.95
ACGTcount: A:0.28, C:0.12, G:0.34, T:0.26
Consensus pattern (43 bp):
CGACGTAATTTTCGTGAGAGTTGATTGGAGAGAAAGCATAGAC
Found at i:6422 original size:2 final size:2
Alignment explanation
Indices: 6407--6453 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
6397 CTTGAAAAAG
* *
6407 AT AT AT AC AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6449 AT AT A
1 AT AT A
6454 CTGTAGTGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:8315 original size:17 final size:17
Alignment explanation
Indices: 8283--8320 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
8273 AACAACCAAG
8283 AATAAAATATATAAATA
1 AATAAAATATATAAATA
8300 AATATAAATATA-AAATA
1 AATA-AAATATATAAATA
8317 AATA
1 AATA
8321 CAAGGACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAAATATATAAATA
Found at i:9054 original size:2 final size:2
Alignment explanation
Indices: 9047--9075 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9037 AATATGATGT
9047 TA 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 TA T
9076 TGTTTTTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12953 original size:24 final size:20
Alignment explanation
Indices: 12897--12954 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
12887 TCCCCTTTGA
*
12897 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
12917 AGTGCATCAATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
12940 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
12955 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:13009 original size:63 final size:63
Alignment explanation
Indices: 12942--13077 Score: 168
Period size: 63 Copynumber: 2.2 Consensus size: 63
12932 TCTTTAACAT
* * *
12942 GTGCATCGATGCACTACC-CATGCATCGATACACCAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACCAATTACATTCGAT-TTTTCATCTTTAAAGA
* * * * *
13005 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTTCATTCGATTTTTCTTCTTTAAAGA
1 GTGCATCGATGCACTCCTCATGCATCGATACACCAATTACATTCGATTTTTCATCTTTAAAGA
13068 GTGCATCGAT
1 GTGCATCGAT
13078 ACACATTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
62 8 0.13
63 55 0.87
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACCAATTACATTCGATTTTTCATCTTTAAAGA
Found at i:17813 original size:24 final size:20
Alignment explanation
Indices: 17760--17817 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
17750 TCCCCTTTGA
*
17760 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
17780 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
17803 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
17818 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:17940 original size:64 final size:64
Alignment explanation
Indices: 17805--17942 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 64
17795 TCTTTAACAT
* * *
17805 GTGCATCGATGCACTACCCATGCATCGATACACCAATTACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACCAATTACATTCGATGTTTTCATTTTAAGAGA
* * * * * **
17869 GTACATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTTTCTTTAA-AG
1 GTGCATCGATGCACTACC-CATGCATCGATACACCAATTACATTCGATGTTTTCAT-TTTAAGAG
17932 A
64 A
17933 GTGCATCGAT
1 GTGCATCGAT
17943 ACACATTGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
63 2 0.03
64 54 0.89
65 5 0.08
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (64 bp):
GTGCATCGATGCACTACCCATGCATCGATACACCAATTACATTCGATGTTTTCATTTTAAGAGA
Found at i:22055 original size:75 final size:74
Alignment explanation
Indices: 21956--22189 Score: 308
Period size: 75 Copynumber: 3.1 Consensus size: 74
21946 TTACTTGAGG
* *
21956 TTGTTTTTCTTAAAAAAGACTTTGTCTCACTTGAGACAATTTTACTCGAAAGAATACATTTCATT
1 TTGTTTTTCTTAAAAAAGA-TTTGTCTCGCTTGAGACAATTTTACTCGAAAGAAGACATTTCATT
*
22021 TTACTCAAGA
65 TCACTCAAGA
* * *
22031 TTTTTTTTCTTAAAATAAGATTTGTCTCGCTTGAGACAATTTTTACTCGAAACAAGAAATTT-AT
1 TTGTTTTTCTTAAAA-AAGATTTGTCTCGCTTGAGACAA-TTTTACTCGAAAGAAGACATTTCAT
22095 TTCACTCAAGA
64 TTCACTCAAGA
* * * ** *
22106 TTGGTTTTCTTAAAACAATATTTGTCTCGCTTGATACGGTTTTTACTCAAAAGAAGACATTTCAT
1 TTGTTTTTCTTAAAA-AAGATTTGTCTCGCTTGAGAC-AATTTTACTCGAAAGAAGACATTTCAT
22171 TTCACTCAAGA
64 TTCACTCAAGA
22182 TTGTTTTT
1 TTGTTTTT
22190 AAAGAAGTTT
Statistics
Matches: 138, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
75 95 0.69
76 43 0.31
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (74 bp):
TTGTTTTTCTTAAAAAAGATTTGTCTCGCTTGAGACAATTTTACTCGAAAGAAGACATTTCATTT
CACTCAAGA
Found at i:22252 original size:39 final size:39
Alignment explanation
Indices: 22192--22453 Score: 339
Period size: 39 Copynumber: 6.7 Consensus size: 39
22182 TTGTTTTTAA
* * *
22192 AGAAGTTTTTATCTCTCTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
22231 ATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
22270 AGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
22309 AGAAGATTTTATCTCGGTTGA-ATAGTTTCCCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
22347 AGAAGATTTTATCTGGTTTAAGATAGTTTACCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
22386 AGAAGATTTTATCTCACTTGAAATAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
** *
22425 AAGAA-ATTTTATCTTACTTGAGATGGTTT
1 -AGAAGATTTTATCTCGCTTGAGATAGTTT
22454 TTATTAAAAC
Statistics
Matches: 195, Mismatches: 26, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
38 32 0.16
39 159 0.82
40 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:22354 original size:116 final size:118
Alignment explanation
Indices: 22191--22453 Score: 361
Period size: 116 Copynumber: 2.3 Consensus size: 118
22181 ATTGTTTTTA
* * * * *
22191 AAGAAGTTTTTATCTCTCTTGAGATAGTTTCCCTTGAAACATAAGATTTTATCTCGCTTGAGATA
1 AAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTAAGATA
* * * *
22256 GTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCTCTTGAAAC
66 GTTTACCTCGAAACAGAAGATTTTATCTCACTTGAAATAGTTTCCCTTGAAAC
* * * *
22309 -AGAAGATTTTATCTCGGTTGA-ATAGTTTCCCTCGAAATAGAAGATTTTATCTGGTTTAAGATA
1 AAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTAAGATA
22372 GTTTACCTCGAAACAGAAGATTTTATCTCACTTGAAATAGTTTCCCTTGAAAC
66 GTTTACCTCGAAACAGAAGATTTTATCTCACTTGAAATAGTTTCCCTTGAAAC
** *
22425 AAGAA-ATTTTATCTTACTTGAGATGGTTT
1 AAGAAGATTTTATCTCGCTTGAGATAGTTT
22454 TTATTAAAAC
Statistics
Matches: 126, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
116 98 0.78
117 28 0.22
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (118 bp):
AAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTAAGATA
GTTTACCTCGAAACAGAAGATTTTATCTCACTTGAAATAGTTTCCCTTGAAAC
Found at i:23180 original size:87 final size:87
Alignment explanation
Indices: 22976--23219 Score: 373
Period size: 87 Copynumber: 2.8 Consensus size: 87
22966 CAACTTTTAG
* * *
22976 CTCAAATCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTCGATCCCATCACAGAAAGA
1 CTCAAATCTATCACAGATGGAGGTAGATCAGCACCAATATCTCGTTCGATCCCATCACAGAATGA
*** *
23041 TGATAATTGACATTTTCATTTCA
66 -GGGGATCGACATTTTCATTTCA
* *
23064 CTCAAATCTATCAAAGAAT-GAGGTAGATCAGCACCAATATCTCGTTCGATCCCATCACATAATG
1 CTCAAATCTATCACAG-ATGGAGGTAGATCAGCACCAATATCTCGTTCGATCCCATCACAGAATG
23128 AGGGGATCGACATTTTCATTTCA
65 AGGGGATCGACATTTTCATTTCA
*
23151 CTCAAATCTATCACAGATGGAGGTAGATCAGCACCAATATCTCGTTCAATCCCATCACAGAATGA
1 CTCAAATCTATCACAGATGGAGGTAGATCAGCACCAATATCTCGTTCGATCCCATCACAGAATGA
23216 GGGG
66 GGGG
23220 GAAGCTTGAG
Statistics
Matches: 142, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
86 2 0.01
87 81 0.57
88 58 0.41
89 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (87 bp):
CTCAAATCTATCACAGATGGAGGTAGATCAGCACCAATATCTCGTTCGATCCCATCACAGAATGA
GGGGATCGACATTTTCATTTCA
Found at i:23751 original size:21 final size:20
Alignment explanation
Indices: 23678--23752 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 20
23668 GGTCCTTGTA
*
23678 TTTATTTTATATTTATATTT
1 TTTATTTTATTTTTATATTT
*
23698 ATTTATTTTATTCTTAGT-TGTT
1 -TTTATTTTATTTTTA-TAT-TT
*
23720 TTTA--CTATTTTTATACTTT
1 TTTATTTTATTTTTATA-TTT
23739 TTTATTTTATTTTT
1 TTTATTTTATTTTT
23753 TTAAAGTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
18 1 0.02
19 13 0.30
20 1 0.02
21 25 0.58
22 3 0.07
ACGTcount: A:0.20, C:0.04, G:0.03, T:0.73
Consensus pattern (20 bp):
TTTATTTTATTTTTATATTT
Found at i:25165 original size:78 final size:78
Alignment explanation
Indices: 24993--25146 Score: 220
Period size: 78 Copynumber: 2.0 Consensus size: 78
24983 GTGTCGACAG
* * *
24993 TGTGTTTAGCTGGTATACTTAGATGTACTTGATCAAAAATAAGTTTGATCTGTTTTCATACTATG
1 TGTGTTTAGCAGGTACACTTAGATGTACTTGATCAAAAATAAATTTGATCTGTTTTCATACTATG
* *
25058 TTCTCTTCATTGA
66 TACTCTTCACTGA
* * * *
25071 TGTGTTTAGCCGGTACACTTGGATGTACTTGATCAAAAATAAATTTGATGTGTTTTCATACTGTG
1 TGTGTTTAGCAGGTACACTTAGATGTACTTGATCAAAAATAAATTTGATCTGTTTTCATACTATG
25136 TACT-TTCACTG
66 TACTCTTCACTG
25147 TTTTTACGTT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
77 6 0.09
78 62 0.91
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (78 bp):
TGTGTTTAGCAGGTACACTTAGATGTACTTGATCAAAAATAAATTTGATCTGTTTTCATACTATG
TACTCTTCACTGA
Found at i:27536 original size:12 final size:12
Alignment explanation
Indices: 27519--27548 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
27509 CCTAAAGTCT
27519 AGAAAATAAAAA
1 AGAAAATAAAAA
*
27531 AGAAAATAGAAA
1 AGAAAATAAAAA
27543 AGAAAA
1 AGAAAA
27549 AGAGGAACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (12 bp):
AGAAAATAAAAA
Found at i:29626 original size:3 final size:3
Alignment explanation
Indices: 29620--29652 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
29610 GGATATAATA
*
29620 ATT ATT ATT ATT ATT A-T ATT ATT AAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
29653 ATACTGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:29642 original size:17 final size:17
Alignment explanation
Indices: 29620--29652 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29610 GGATATAATA
*
29620 ATTATTATTATTATTAT
1 ATTATTAATATTATTAT
29637 ATTATTAATATTATTA
1 ATTATTAATATTATTA
29653 ATACTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATTAATATTATTAT
Found at i:29653 original size:9 final size:9
Alignment explanation
Indices: 29615--29655 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
29605 GTACAGGATA
29615 TAATAATTAT
1 TAAT-ATTAT
*
29625 TATTATTAT
1 TAATATTAT
29634 T-ATATTAT
1 TAATATTAT
29642 TAATATTAT
1 TAATATTAT
29651 TAATA
1 TAATA
29656 CTGTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.25
9 18 0.64
10 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAATATTAT
Found at i:31619 original size:20 final size:20
Alignment explanation
Indices: 31594--31686 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
31584 TTTTCCCAAT
31594 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
31614 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
31634 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
31655 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
31676 TCGCAATGCGA
1 TCGCAATGCGA
31687 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:31636 original size:41 final size:41
Alignment explanation
Indices: 31591--31686 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
31581 CGATTTTCCC
31591 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
31632 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
31673 AAATCGCAATGCGA
1 AATTCGCAATGCGA
31687 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:31640 original size:21 final size:20
Alignment explanation
Indices: 31594--31686 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
31584 TTTTCCCAAT
*
31594 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
31614 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
31634 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
31655 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
31676 TCGCAATGCGA
1 TCGCAATGCGA
31687 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:31699 original size:41 final size:41
Alignment explanation
Indices: 31613--31747 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
31603 GAATAAGTAA
* * *
31613 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
31654 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
31695 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
31736 TTCGCAACGCGA
1 ATCGCAACGCGA
31748 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:31700 original size:20 final size:20
Alignment explanation
Indices: 31675--31769 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
31665 AATTGGGAAA
*
31675 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
31695 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
31716 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
31736 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
31756 TTCGCAACGCGATA
1 ATCGCAACGCGATA
31770 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:31985 original size:22 final size:22
Alignment explanation
Indices: 31957--32000 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31947 CACTCTCTCA
31957 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
31979 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
32001 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:32289 original size:20 final size:20
Alignment explanation
Indices: 32264--32301 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32254 CGATTCTCTC
32264 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
32284 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
32302 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:33643 original size:18 final size:18
Alignment explanation
Indices: 33622--33666 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
33612 TCCACTTCGG
*
33622 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
33640 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
33658 GAGCCATCA
1 GAGCCATCA
33667 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:34177 original size:19 final size:20
Alignment explanation
Indices: 34123--34189 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
34113 TAGTTTACTT
* *
34123 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
34143 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
34163 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
34182 TCGCAACG
1 TCGCAACG
34190 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:34197 original size:14 final size:14
Alignment explanation
Indices: 34178--34235 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
34168 ATGCGAAATG
34178 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
34192 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
34208 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
34224 AAAATCGCAACG
1 AAAATCGCAACG
34236 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:34220 original size:32 final size:33
Alignment explanation
Indices: 34162--34252 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
34152 GGAAATGGCT
*
34162 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
34195 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
34227 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
34253 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:34246 original size:19 final size:19
Alignment explanation
Indices: 34123--34257 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
34113 TAGTTTACTT
* **
34123 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
34143 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
34163 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34182 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
34196 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
34214 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
34228 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34247 TCGCAATGCGA
1 TCGCAACGCGA
34258 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:34329 original size:50 final size:52
Alignment explanation
Indices: 34264--34380 Score: 184
Period size: 50 Copynumber: 2.3 Consensus size: 52
34254 GCGATTTGTG
* **
34264 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCATTTCGCGTTGCGAT-TTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATAGCCA
34314 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATAGCCA
34366 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
34381 AGTCATTTCG
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
50 27 0.44
51 18 0.30
52 5 0.08
53 11 0.18
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (52 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATAGCCA
Found at i:34359 original size:19 final size:19
Alignment explanation
Indices: 34283--34418 Score: 124
Period size: 18 Copynumber: 7.4 Consensus size: 19
34273 GCGATTTTGT
34283 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
34301 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
34319 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
34333 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
34352 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
34372 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
34391 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
34411 TGTTGCGA
1 CGTTGCGA
34419 AAGTAAACTA
Statistics
Matches: 99, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.08
15 3 0.03
16 2 0.02
17 2 0.02
18 29 0.29
19 26 0.26
20 29 0.29
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:34379 original size:20 final size:19
Alignment explanation
Indices: 34345--34399 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
34335 TTGCGATTTT
*
34345 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
34364 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
34384 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
34400 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:34416 original size:39 final size:37
Alignment explanation
Indices: 34264--34418 Score: 123
Period size: 39 Copynumber: 4.4 Consensus size: 37
34254 GCGATTTGTG
*
34264 TTTCGCGTTGCGATTT--TGT--CGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTCATTTCGCGTTGCGATTTTCA
34296 TTTCGCGTTGCGATTTCATTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTCATTTCGCGTTGCGATTTTCA
* * ***
34330 TGT--CGTTGCGATTTTCATTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGA-TTTCATTTCGCGTTGCGATTTTCA
* *
34366 TTTCCGCGTTGCGATAGTCATTTCGCGTTGCGATTTTAA
1 TTT-CGCGTTGCGAT-TTCATTTCGCGTTGCGATTTTCA
*
34405 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
34419 AAGTAAACTA
Statistics
Matches: 96, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
32 24 0.25
33 17 0.18
34 4 0.04
36 13 0.14
38 1 0.01
39 34 0.35
40 3 0.03
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (37 bp):
TTTCGCGTTGCGATTTCATTTCGCGTTGCGATTTTCA
Found at i:36289 original size:14 final size:14
Alignment explanation
Indices: 36270--36305 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
36260 ATTGTTTAAT
36270 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
36284 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
36298 TGATTTGT
1 TGATTTGT
36306 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:36444 original size:19 final size:19
Alignment explanation
Indices: 36422--36489 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
36412 ATCGCAACGA
36422 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
36441 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
36460 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
36474 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
36490 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:36533 original size:20 final size:20
Alignment explanation
Indices: 36508--36564 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
36498 TCGCATTGCG
*
36508 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
36528 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
36548 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
36565 GTCAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:36951 original size:14 final size:14
Alignment explanation
Indices: 36932--36967 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
36922 ATTGTTTAAT
36932 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
36946 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
36960 TGATTTGT
1 TGATTTGT
36968 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:38268 original size:24 final size:24
Alignment explanation
Indices: 38212--38270 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
38202 AGTCAGTATT
* *
38212 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
38236 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
38260 CGAATTTTGAT
1 CGAAATTTGAT
38271 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:38461 original size:12 final size:12
Alignment explanation
Indices: 38444--38468 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38434 CATATATCCT
38444 GAAGAAGAAAAA
1 GAAGAAGAAAAA
38456 GAAGAAGAAAAA
1 GAAGAAGAAAAA
38468 G
1 G
38469 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:40785 original size:19 final size:19
Alignment explanation
Indices: 40763--40860 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
40753 GGAAATTACT
40763 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40782 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
40796 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
40815 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
40829 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40848 ATCGCAACGCGAA
1 ATCGCAATGCGAA
40861 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40805 original size:33 final size:33
Alignment explanation
Indices: 40763--40856 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
40753 GGAAATTACT
40763 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
40796 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
40829 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
40857 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:41024 original size:14 final size:14
Alignment explanation
Indices: 41005--41041 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
40995 CATCAATTAA
41005 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
41019 ACAAATCACCTTTT
1 ACAAATCAACTTTT
41033 ACAAATCAA
1 ACAAATCAA
41042 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:42443 original size:21 final size:21
Alignment explanation
Indices: 42414--42494 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
42404 GAATGGTGGG
*
42414 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTCAACGATGAT
* * * **
42435 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAT
* * *
42456 AGGGGACTC-TCGAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAT
42477 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
42495 AGGAGTGGAC
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
20 3 0.07
21 34 0.83
22 4 0.10
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAT
Found at i:42476 original size:42 final size:42
Alignment explanation
Indices: 42430--42521 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
42420 CTCTTCAACG
* * * *
42430 ATGATAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
1 ATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
* * *
42472 ATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGGG
1 ATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
42514 ATGATAGG
1 ATGATAGG
42522 CGACTTAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.23
Consensus pattern (42 bp):
ATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
Found at i:44519 original size:20 final size:19
Alignment explanation
Indices: 44474--44614 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
44464 TCTTTTGGTT
44474 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
44493 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
44514 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
44533 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
44547 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
44566 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
44580 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
44599 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
44615 TGCGATTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 18 0.19
16 4 0.04
17 4 0.04
19 39 0.42
20 26 0.28
21 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:44556 original size:33 final size:33
Alignment explanation
Indices: 44499--44597 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
44489 ACGAGATAAT
* *
44499 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
44533 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
44566 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
44598 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:44591 original size:19 final size:19
Alignment explanation
Indices: 44569--44619 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
44559 GCGACGAGAG
44569 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
44588 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
44607 AATCGCAATGCGA
1 AATCGCAACGCGA
44620 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:44648 original size:19 final size:19
Alignment explanation
Indices: 44615--44681 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
44605 AAAATCGCAA
**
44615 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
44634 TGCGATTTTTATTTCACGT
1 TGCGATTTTTATTTCGCGT
** *
44653 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
44673 TGCGATTTT
1 TGCGATTTT
44682 CATTCTCGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
19 28 0.74
20 10 0.26
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:45275 original size:41 final size:41
Alignment explanation
Indices: 45223--45300 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
45213 CGAAAGTCAG
* * *
45223 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
45264 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
45301 CCCAATTCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:45297 original size:20 final size:20
Alignment explanation
Indices: 45204--45297 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
45194 CGCTAAGTAA
*
45204 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
45224 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
45244 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
45265 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
45285 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
45298 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:45316 original size:41 final size:41
Alignment explanation
Indices: 45286--45381 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
45276 ATAGTCAGTA
* * *
45286 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCACGTTGCGATTCACGTAT
* * *
45327 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCACGTTGCGATTCACGTAT
45368 TCGCATTGCGAATT
1 TCGCATTGCGAATT
45382 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCACGTTGCGATTCACGTAT
Found at i:45317 original size:21 final size:21
Alignment explanation
Indices: 45286--45361 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
45276 ATAGTCAGTA
*
45286 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* * **
45307 TCACGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
* *
45327 TCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
45348 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
45362 ACTTATTCGC
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:45335 original size:20 final size:20
Alignment explanation
Indices: 45312--45378 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
45302 CCAATTCACG
45312 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
45332 TTGCGAATTTCCCAATTCGCG
1 TTGCG-ATTTACTTATTCGCA
45353 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
45373 TTGCGA
1 TTGCGA
45379 ATTGGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:47141 original size:2 final size:2
Alignment explanation
Indices: 47134--47193 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
47124 TGCGCAGATG
47134 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
47176 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
47194 CATACATGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48569 original size:51 final size:51
Alignment explanation
Indices: 48498--48610 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
48488 TTAATATGAA
*
48498 TCAAGTCATCTCACTAATTAAGAGATTATTATTAACTTTTGAAATATCGAGT
1 TCAAG-CATCGCACTAATTAAGAGATTATTATTAACTTTTGAAATATCGAGT
* ** *
48550 TCGAGCATCGCACTAATTAAGAGATTATTATTATTTTTTGAAATCTCGAGT
1 TCAAGCATCGCACTAATTAAGAGATTATTATTAACTTTTGAAATATCGAGT
48601 TCAAGCATCG
1 TCAAGCATCG
48611 GATACGAACA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
51 51 0.93
52 4 0.07
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (51 bp):
TCAAGCATCGCACTAATTAAGAGATTATTATTAACTTTTGAAATATCGAGT
Found at i:53993 original size:25 final size:24
Alignment explanation
Indices: 53936--53989 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
53926 TAAAAATTAT
* *
53936 AAAAAATGTGCCACAAAAACAAAG
1 AAAAAACGTGCAACAAAAACAAAG
* *
53960 AAAATACGTGCAACAAAAATAAAG
1 AAAAAACGTGCAACAAAAACAAAG
53984 AAAAAA
1 AAAAAA
53990 ACGTTTCACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.67, C:0.13, G:0.11, T:0.09
Consensus pattern (24 bp):
AAAAAACGTGCAACAAAAACAAAG
Found at i:54032 original size:2 final size:2
Alignment explanation
Indices: 54025--54055 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54015 TTAAAATTAA
54025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54056 AGTAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58813 original size:19 final size:19
Alignment explanation
Indices: 58785--58837 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
58775 AATTGAGGTA
*
58785 GTATCAATACTGACTTATC
1 GTATCGATACTGACTTATC
58804 GTATCGATACTGACTTATC
1 GTATCGATACTGACTTATC
58823 GTATCGATACTGACT
1 GTATCGATACTGACT
58838 CAGGAGTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (19 bp):
GTATCGATACTGACTTATC
Found at i:66311 original size:12 final size:12
Alignment explanation
Indices: 66288--66319 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
66278 ATTATTATTT
66288 TTTATGTTTTTTC
1 TTTAT-TTTTTTC
66301 TTTATTTTTTTC
1 TTTATTTTTTTC
66313 TTTATTT
1 TTTATTT
66320 ACTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.81
Consensus pattern (12 bp):
TTTATTTTTTTC
Found at i:67321 original size:106 final size:106
Alignment explanation
Indices: 67131--67328 Score: 333
Period size: 106 Copynumber: 1.9 Consensus size: 106
67121 TCAAGAGATG
*
67131 ACTCTACATGACTAGCTCGGGGGTAGAAAGTATGCTCCCTTTCACTTAGAGTGTGGGATGATAGT
1 ACTCTACATGACTAGCTCGGGGGTAGAAAGTATGCTCCCTTTCACTTAGAGTGTGAGATGATAGT
* *
67196 GTGATGAGCTGACTTCCCTTAAAGTATGCTTAAGAAAAAAA
66 GTGATGAGATGACTCCCCTTAAAGTATGCTTAAGAAAAAAA
* * *
67237 ACTCTACCTGACTAGCTCGGGGGTTGAAGGTATGCTCCCTTTCACTTAGAGTGTGAGATGATAGT
1 ACTCTACATGACTAGCTCGGGGGTAGAAAGTATGCTCCCTTTCACTTAGAGTGTGAGATGATAGT
*
67302 GTGATGAGATGACTCCCCTTGAAGTAT
66 GTGATGAGATGACTCCCCTTAAAGTAT
67329 CAAAAGAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 85 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (106 bp):
ACTCTACATGACTAGCTCGGGGGTAGAAAGTATGCTCCCTTTCACTTAGAGTGTGAGATGATAGT
GTGATGAGATGACTCCCCTTAAAGTATGCTTAAGAAAAAAA
Found at i:71604 original size:13 final size:13
Alignment explanation
Indices: 71588--71614 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
71578 TTTTTGTGTG
71588 TGTTTTTCTTTAT
1 TGTTTTTCTTTAT
71601 TGTTTTTCTTTAT
1 TGTTTTTCTTTAT
71614 T
1 T
71615 TACTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (13 bp):
TGTTTTTCTTTAT
Found at i:72613 original size:105 final size:106
Alignment explanation
Indices: 72430--72626 Score: 324
Period size: 105 Copynumber: 1.9 Consensus size: 106
72420 TCAAGAGATG
* **
72430 ACTCTACATGACTAGCTTGAGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGATAGT
1 ACTCTACATGACTAGCTCGAGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTAAGATGATAGT
*
72495 GTGATGAGCTGACTCCCCTTAAAGTATGCTTAAGAAAAAAA
66 GTGATGAGATGACTCCCCTTAAAGTATGCTTAAGAAAAAAA
* *
72536 ACTCTACCTGACTAGCTCG-GGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTAAGATGGTAGT
1 ACTCTACATGACTAGCTCGAGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTAAGATGATAGT
*
72600 GTGATGAGATGACTCCCCTTGAAGTAT
66 GTGATGAGATGACTCCCCTTAAAGTAT
72627 CAAAAGAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
105 67 0.80
106 17 0.20
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (106 bp):
ACTCTACATGACTAGCTCGAGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTAAGATGATAGT
GTGATGAGATGACTCCCCTTAAAGTATGCTTAAGAAAAAAA
Found at i:80608 original size:15 final size:14
Alignment explanation
Indices: 80588--80618 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
80578 TATTCTTTTG
80588 TTTTTCATTTTCATT
1 TTTTTCATTTTC-TT
80603 TTTTTCATTTTCTT
1 TTTTTCATTTTCTT
80617 TT
1 TT
80619 ATCGTTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTCATTTTCTT
Found at i:80613 original size:27 final size:28
Alignment explanation
Indices: 80565--80633 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
80555 ATTTATTCGC
*
80565 TCATTTT-ATTTGTTATTCTTTTGTTTT-
1 TCATTTTCATTT-TTATTCTTTTCTTTTA
80592 TCATTTTCATTTTT-TTCATTTTCTTTTA
1 TCATTTTCATTTTTATTC-TTTTCTTTTA
*
80620 TCGTTCTTCATTTT
1 TCATT-TTCATTTT
80634 CTCCTTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 3 0.08
27 17 0.47
28 8 0.22
29 8 0.22
ACGTcount: A:0.12, C:0.13, G:0.04, T:0.71
Consensus pattern (28 bp):
TCATTTTCATTTTTATTCTTTTCTTTTA
Found at i:91493 original size:28 final size:27
Alignment explanation
Indices: 91442--91494 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
91432 GAAGGGTTTC
*
91442 TTTTTTTAAAAAAAATATTATTAAATA
1 TTTTTTTAAAAAAAATAGTATTAAATA
* *
91469 TTTTATTTAAAAAAAGTAGTGTTAAA
1 TTTT-TTTAAAAAAAATAGTATTAAA
91495 GTGGGATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (27 bp):
TTTTTTTAAAAAAAATAGTATTAAATA
Found at i:92557 original size:23 final size:23
Alignment explanation
Indices: 92489--92561 Score: 105
Period size: 23 Copynumber: 3.2 Consensus size: 23
92479 AACATAAAAT
92489 ATTATA-ATTTT-TTAATTTTTTAA
1 ATTATATATTTTATTAA--TTTTAA
*
92512 ATTATATATTTTATTAATCTTAA
1 ATTATATATTTTATTAATTTTAA
92535 ATTATATATTTTATTAATTTTAA
1 ATTATATATTTTATTAATTTTAA
92558 ATTA
1 ATTA
92562 AATTATCGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 37 0.80
24 5 0.11
25 4 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTATATATTTTATTAATTTTAA
Found at i:92664 original size:17 final size:17
Alignment explanation
Indices: 92642--92677 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
92632 TGGATGATAG
92642 TAATGATTGGTGGAGAA
1 TAATGATTGGTGGAGAA
92659 TAATGATTGGTGGAGAA
1 TAATGATTGGTGGAGAA
92676 TA
1 TA
92678 GAGATAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (17 bp):
TAATGATTGGTGGAGAA
Found at i:103220 original size:6 final size:7
Alignment explanation
Indices: 103204--103231 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
103194 GGCAGAAGGC
103204 AAAAAGA
1 AAAAAGA
103211 AAAAAGA
1 AAAAAGA
103218 AAAAAGA
1 AAAAAGA
103225 AAAAAGA
1 AAAAAGA
103232 TCAAGGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:109623 original size:310 final size:309
Alignment explanation
Indices: 109039--109646 Score: 1164
Period size: 310 Copynumber: 2.0 Consensus size: 309
109029 TTCAACTTGC
109039 GTTGTCCCTTGGTATGCTTTAAAGCTTCATGGTCTGTATGAATAACAAATTCTTTGGCAAAAGGT
1 GTTGTCCCTTGGTATGCTTTAAAGCTTCATGGTCTGTATGAATAACAAATTCTTTGGCAAAAGGT
* *
109104 AATGTTGCCAAACTTTAAGTGCCCTGATGAGAGAATACATATTTTTGTCATAAGTTGGGTAGTTT
66 AATGTTGCCAAACTTCAAGTGCCCTGATCAGAGAATACATATTTTTGTCATAAGTTGGGTAGTTT
*
109169 AGTGAAGCACCACTTAGTTTTTCACTAAAGTATGCAATGAGTCGTTCTTCTTGAGTTAGAACTGC
131 AGTGAAGCACCACTTAGTTTTTCACTAAAGTATGCAATGAGTCGCTCTTCTTGAGTTAGAACTGC
109234 TCCAATCCTATTTCGGATGCATCACATTCCACTTCAAAAGTCTTATCAAAGTTAGGTAATACAAG
196 TCCAATCCTATTTCGGATGCATCACATTCCACTTCAAAAGTCTTATCAAAGTTAGGTAATACAAG
109299 TAAAGGTGACTTTGTCAAACACTCATTCATTTCTTTGAGAAAAGGTAAT
261 TAAAGGTGACTTTGTCAAACACTCATTCATTTCTTTGAGAAAAGGTAAT
109348 GTTGTCCCTTGGTATGCTTTAAAGCTTCATGGTCTGTATGAATAACAAATTCTTTTGGCAAAAGG
1 GTTGTCCCTTGGTATGCTTTAAAGCTTCATGGTCTGTATGAATAACAAATTC-TTTGGCAAAAGG
109413 TAATGTTGCCAAACTTCAAGTGCCCTGATCAGAGAATACATATTTTTGTCATAA-TTGGGTAGTT
65 TAATGTTGCCAAACTTCAAGTGCCCTGATCAGAGAATACATATTTTTGTCATAAGTTGGGTAGTT
109477 TAGTGAAGCACCACTTAGTTTTTCACTAAAGTATGCAATGAGTCGCTCTTCTTGAGTTAGAACTG
130 TAGTGAAGCACCACTTAGTTTTTCACTAAAGTATGCAATGAGTCGCTCTTCTTGAGTTAGAACTG
109542 CTCCAATCCCTATTTCGGATGCATCACATTCCACTTCAAAAGTCTTATCAAAGTTAGGTAATACA
195 CTCCAAT-CCTATTTCGGATGCATCACATTCCACTTCAAAAGTCTTATCAAAGTTAGGTAATACA
109607 AGTAAAGGTGACTTTGTCAAACACTCATTCATTTCTTTGA
259 AGTAAAGGTGACTTTGTCAAACACTCATTCATTTCTTTGA
109647 AGGCATCTTC
Statistics
Matches: 294, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
309 133 0.45
310 161 0.55
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (309 bp):
GTTGTCCCTTGGTATGCTTTAAAGCTTCATGGTCTGTATGAATAACAAATTCTTTGGCAAAAGGT
AATGTTGCCAAACTTCAAGTGCCCTGATCAGAGAATACATATTTTTGTCATAAGTTGGGTAGTTT
AGTGAAGCACCACTTAGTTTTTCACTAAAGTATGCAATGAGTCGCTCTTCTTGAGTTAGAACTGC
TCCAATCCTATTTCGGATGCATCACATTCCACTTCAAAAGTCTTATCAAAGTTAGGTAATACAAG
TAAAGGTGACTTTGTCAAACACTCATTCATTTCTTTGAGAAAAGGTAAT
Found at i:114713 original size:23 final size:25
Alignment explanation
Indices: 114686--114739 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
114676 CGTTATGTTT
114686 AATTTTG-TTGGACATTA-AACTTA
1 AATTTTGTTTGGACATTAGAACTTA
*
114709 AATTTTGTTTGGACATTAGAACTTG
1 AATTTTGTTTGGACATTAGAACTTA
114734 AATTTT
1 AATTTT
114740 AAATTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 7 0.25
24 10 0.36
25 11 0.39
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.46
Consensus pattern (25 bp):
AATTTTGTTTGGACATTAGAACTTA
Done.