Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007861.1 Hibiscus syriacus cultivar Beakdansim tig00110226_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: 673920
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:131612 original size:14 final size:14
Alignment explanation
Indices: 131578--131616 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
131568 TTGGTTATTT
131578 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
131592 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
131606 TGTTGATTTGT
1 AATTGATTTGT
131617 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:131756 original size:20 final size:20
Alignment explanation
Indices: 131714--131758 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
131704 GTTGAAGGCA
*
131714 AAAATGGCTATCGCAACGCG
1 AAAATGGCTATCGCAACGAG
*
131734 AAAATGGCTATCGCAACTAG
1 AAAATGGCTATCGCAACGAG
131754 AAAAT
1 AAAAT
131759 CGCAATGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (20 bp):
AAAATGGCTATCGCAACGAG
Found at i:131777 original size:19 final size:17
Alignment explanation
Indices: 131752--131801 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
131742 TATCGCAACT
131752 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
131770 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
131785 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
131802 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:132206 original size:24 final size:24
Alignment explanation
Indices: 132155--132208 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
132145 GTATTCGAAA
* *
132155 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
132179 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
132203 TTTGAT
1 TTTGAT
132209 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:134714 original size:14 final size:14
Alignment explanation
Indices: 134695--134749 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
134685 GCGAAATGAA
134695 AATCGCAACGAGAT
1 AATCGCAACGAGAT
*
134709 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAT
134728 AATCGCAACGAGAT
1 AATCGCAACGAGAT
134742 AATCGCAA
1 AATCGCAA
134750 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (14 bp):
AATCGCAACGAGAT
Found at i:134723 original size:33 final size:33
Alignment explanation
Indices: 134681--134803 Score: 219
Period size: 33 Copynumber: 3.7 Consensus size: 33
134671 ATTACTATCA
134681 CAATGCGAAATGAAAATCGCAACGAGATAATCG
1 CAATGCGAAATGAAAATCGCAACGAGATAATCG
134714 CAATGCGAAATGAAAATCGCAACGAGATAATCG
1 CAATGCGAAATGAAAATCGCAACGAGATAATCG
**
134747 CAATGCGAAATGAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGATAATCG
*
134780 CAAAGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
134804 CGAATTTAGT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGATAATCG
Found at i:134733 original size:19 final size:18
Alignment explanation
Indices: 134685--134807 Score: 90
Period size: 19 Copynumber: 7.3 Consensus size: 18
134675 CTATCACAAT
134685 GCGAAATGAAAATCGCAA
1 GCGAAATGAAAATCGCAA
*
134703 -CG--A-GATAATCGCAA
1 GCGAAATGAAAATCGCAA
134717 TGCGAAATGAAAATCGCAA
1 -GCGAAATGAAAATCGCAA
*
134736 -CG--A-GATAATCGCAA
1 GCGAAATGAAAATCGCAA
134750 TGCGAAATGAAAATCGCAA
1 -GCGAAATGAAAATCGCAA
**
134769 -CG--A-GGGAATCGCAAA
1 GCGAAATGAAAATCGC-AA
134784 GCGAAATGAAAATCGCAA
1 GCGAAATGAAAATCGCAA
134802 CGCGAA
1 -GCGAA
134808 TTTAGTTTCG
Statistics
Matches: 81, Mismatches: 8, Indels: 31
0.68 0.07 0.26
Matches are distributed among these distances:
14 27 0.33
15 5 0.06
16 6 0.07
17 6 0.07
18 5 0.06
19 32 0.40
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.12
Consensus pattern (18 bp):
GCGAAATGAAAATCGCAA
Found at i:134838 original size:19 final size:19
Alignment explanation
Indices: 134803--134879 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
134793 AAATCGCAAC
*
134803 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
134822 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
134841 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
*
134855 GCGATTTTTA-TTTCGCATT
1 GCGA-TTTTAGTTTCGCGTT
134874 GCGATT
1 GCGATT
134880 CTCTAGTTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
14 8 0.16
15 4 0.08
16 1 0.02
17 1 0.02
18 3 0.06
19 33 0.66
ACGTcount: A:0.13, C:0.16, G:0.25, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:134860 original size:33 final size:33
Alignment explanation
Indices: 134818--134944 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
134808 TTTAGTTTCG
* * *
134818 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTATCT
* *
134851 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
*
134884 AGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
134917 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
134945 AGTAATTTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
33 85 0.99
34 1 0.01
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTATCT
Found at i:134910 original size:19 final size:17
Alignment explanation
Indices: 134886--134944 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 17
134876 GATTCTCTAG
134886 TTGCGATTTTCATTTCGC
1 TTGCGATTTT-ATTTCGC
*
134904 ATTGCGA--TTATCTCG-
1 -TTGCGATTTTATTTCGC
134919 TTGCGATTTTCATTTCGC
1 TTGCGATTTT-ATTTCGC
134937 ATTGCGAT
1 -TTGCGAT
134945 AGTAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (17 bp):
TTGCGATTTTATTTCGC
Found at i:135070 original size:14 final size:15
Alignment explanation
Indices: 135051--135087 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
135041 CATCAATTAA
135051 ACAAATCAAC-TTTT
1 ACAAATCAACATTTT
135065 ACAAATC-ACATTTT
1 ACAAATCAACATTTT
135079 ACAAATCAA
1 ACAAATCAA
135088 TTAAACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACATTTT
Found at i:136522 original size:42 final size:42
Alignment explanation
Indices: 136476--136559 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
136466 CGATGACAGT
* * * *
136476 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATTATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
136518 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
136560 CCAGTTGGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:136952 original size:91 final size:90
Alignment explanation
Indices: 136777--136961 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
136767 ATTTCAAACT
* *
136777 TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
136842 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
136870 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
136934 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
136961 T
1 T
136962 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:138698 original size:20 final size:19
Alignment explanation
Indices: 138653--138713 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
138643 TCTTTTGGTT
138653 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
138672 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
*
138693 GAAATGACTAAT-GCAACGA
1 GAAATGA-AAATCGCAACGA
138712 GA
1 GA
138714 GAATCGCAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.11
20 27 0.75
21 5 0.14
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:138743 original size:19 final size:19
Alignment explanation
Indices: 138716--138776 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
138706 CAACGAGAGA
*
138716 ATCGCAACGCGAAATTACG
1 ATCGTAACGCGAAATTACG
*
138735 ATCGTAACGAGAGAA-T-CG
1 ATCGTAACGCGA-AATTACG
138753 --C--AACGCGAAATTACG
1 ATCGTAACGCGAAATTACG
138768 ATCGTAACG
1 ATCGTAACG
138777 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 14
0.65 0.06 0.29
Matches are distributed among these distances:
13 2 0.06
14 7 0.22
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 15 0.47
20 2 0.06
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGTAACGCGAAATTACG
Found at i:138744 original size:33 final size:33
Alignment explanation
Indices: 138681--138796 Score: 180
Period size: 33 Copynumber: 3.5 Consensus size: 33
138671 AGATAATGAA
* * *
138681 AATCGCAACGCGGAAATGACTAAT-GCAACGAGAG
1 AATCGCAACGC-GAAATTAC-GATCGTAACGAGAG
138715 AATCGCAACGCGAAATTACGATCGTAACGAGAG
1 AATCGCAACGCGAAATTACGATCGTAACGAGAG
138748 AATCGCAACGCGAAATTACGATCGTAACGAGAG
1 AATCGCAACGCGAAATTACGATCGTAACGAGAG
138781 AATCGCAACGCGAAAT
1 AATCGCAACGCGAAAT
138797 GAAAATCGCA
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
32 2 0.03
33 65 0.83
34 11 0.14
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.14
Consensus pattern (33 bp):
AATCGCAACGCGAAATTACGATCGTAACGAGAG
Found at i:138862 original size:19 final size:20
Alignment explanation
Indices: 138838--138892 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
138828 GCGATTATCT
138838 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATTTTCATTTCCG
*
138857 CGTTGCGATAGTT-ATTTCCG
1 CGTTGCGAT-TTTCATTTCCG
138877 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
138893 CTCGAAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:139448 original size:20 final size:20
Alignment explanation
Indices: 139396--139524 Score: 122
Period size: 20 Copynumber: 6.5 Consensus size: 20
139386 GCTATGTAAA
* *
139396 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
139416 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
139436 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
139457 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
* *
139477 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACGTAT
* *
139497 TCGCGTTGCGAATT---TAT
1 TCGCATTGCGATTTACGTAT
139514 TCGCATTGCGA
1 TCGCATTGCGA
139525 ATTGGGAAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
17 13 0.14
19 3 0.03
20 62 0.65
21 18 0.19
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:139466 original size:41 final size:39
Alignment explanation
Indices: 139414--139524 Score: 127
Period size: 41 Copynumber: 2.8 Consensus size: 39
139404 CGATAGTAAG
*
139414 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTAC-TATTCGCATTGCGA-TTTACTA
* * *
139455 ATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTAC-TATTCGCATTGCGATTTACTA
* *
139495 ATTCGCGTTGCGAATT--TATTCGCATTGCGA
1 ATTCGCATTGCGATTTACTATTCGCATTGCGA
139525 ATTGGGAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
37 12 0.20
40 19 0.31
41 30 0.49
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (39 bp):
ATTCGCATTGCGATTTACTATTCGCATTGCGATTTACTA
Found at i:139515 original size:17 final size:17
Alignment explanation
Indices: 139493--139527 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
139483 TGCGATTTAC
*
139493 TTATTCGCGTTGCGAAT
1 TTATTCGCATTGCGAAT
139510 TTATTCGCATTGCGAAT
1 TTATTCGCATTGCGAAT
139527 T
1 T
139528 GGGAAAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (17 bp):
TTATTCGCATTGCGAAT
Found at i:139566 original size:21 final size:22
Alignment explanation
Indices: 139517--139566 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
139507 AATTTATTCG
*
139517 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGGGAAAATCA
**
139538 CAACGCGAAATT-GGAAAATCA
1 CATTGCGAAATTGGGAAAATCA
139559 CATTGCGA
1 CATTGCGA
139567 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGGGAAAATCA
Found at i:139871 original size:24 final size:25
Alignment explanation
Indices: 139827--139883 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
139817 AACTATATTT
*
139827 ATTTTTATATATAATCGTTAAATTA
1 ATTTTTATATATAATCATTAAATTA
*
139852 ATTTTTTTATATAAT-ATTAAATTA
1 ATTTTTATATATAATCATTAAATTA
*
139876 ATTATTAT
1 ATTTTTAT
139884 TTTAAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTTTTATATATAATCATTAAATTA
Found at i:141223 original size:2 final size:2
Alignment explanation
Indices: 141216--141240 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
141206 ATCATACTTT
141216 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
141241 TGGACTCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:150451 original size:22 final size:23
Alignment explanation
Indices: 150408--150462 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
150398 ACCGTTGCCT
150408 GTGGTTTTTACCCTAAATTTTTA
1 GTGGTTTTTACCCTAAATTTTTA
150431 GTGGTTTTTACCCTAAATTTTTA
1 GTGGTTTTTACCCTAAATTTTTA
*
150454 GGGGTTTTT
1 GTGGTTTTT
150463 CACGTAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (23 bp):
GTGGTTTTTACCCTAAATTTTTA
Found at i:154141 original size:78 final size:79
Alignment explanation
Indices: 154053--154207 Score: 267
Period size: 79 Copynumber: 2.0 Consensus size: 79
154043 AGTGCATGTT
*
154053 TAAAAAAACTATATTTAAACATTTT-AAAAACAATCTTAAATTTAGAAATCTCGTAATTAAACCC
1 TAAAAAAACTATATTTAAACATTTTAAAAAACAATCTTAAATTTAAAAATCTCGTAATTAAACCC
* *
154117 ATTGCTTTTGAATA
66 AATACTTTTGAATA
*
154131 TAAAAAAACTATATTTAAACATTTTAAAAAATAATCTTAAATTTAAAAATCTCGTAATTAAACCC
1 TAAAAAAACTATATTTAAACATTTTAAAAAACAATCTTAAATTTAAAAATCTCGTAATTAAACCC
154196 AATACTTTTGAA
66 AATACTTTTGAA
154208 ATATCATAGA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
78 25 0.35
79 47 0.65
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.35
Consensus pattern (79 bp):
TAAAAAAACTATATTTAAACATTTTAAAAAACAATCTTAAATTTAAAAATCTCGTAATTAAACCC
AATACTTTTGAATA
Found at i:165191 original size:23 final size:23
Alignment explanation
Indices: 165154--165218 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
165144 TAGCTCATAT
165154 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * * *
165177 AATTGCACCGTAGTGTCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
165200 AAATGCACCGAAGTGCCAC
1 AAATGCACCGAAGTGCCAC
165219 ATAAGGTTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:170174 original size:23 final size:23
Alignment explanation
Indices: 170138--170206 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
170128 CACCACAGCT
* * *
170138 CGTATAAATACACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
170161 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
170184 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
170207 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:175154 original size:23 final size:23
Alignment explanation
Indices: 175120--175189 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
175110 CACCACAGCT
*
175120 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
175143 CGTAGAATTGCACCGTAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
175166 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
175189 C
1 C
175190 ATAAGGTTGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:193784 original size:32 final size:32
Alignment explanation
Indices: 193743--193831 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
193733 GAGTCGAGGG
**
193743 TTACCTATGTCCTTCGGGATATATGGACATGA
1 TTACCTATGTCCTTCGGGATATATAAACATGA
* * * *
193775 TTACCTATGTTCTTCGGTACATATAAACATGT
1 TTACCTATGTCCTTCGGGATATATAAACATGA
*
193807 TTACCTATG-CCTTTTGGGATATATA
1 TTACCTATGTCC-TTCGGGATATATA
193832 GATAGGTCAT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
31 1 0.02
32 45 0.98
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (32 bp):
TTACCTATGTCCTTCGGGATATATAAACATGA
Found at i:196769 original size:63 final size:64
Alignment explanation
Indices: 196659--196778 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 64
196649 ACATAAATCC
* * * *
196659 CATTCGATGTTTGTATTTTAAGGGGGTGCATCAATGCACTACTTGTGCATCGATACATTGATGG
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACATTGATGG
* * *
196723 CATTCGAT-TTTTTATTTTAAAGGAGTGCATCGATACACTTCATGTGCATCGATACA
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACA
196779 CCTTAAACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 41 0.84
64 8 0.16
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAGGAGTGCATCAATACACTACATGTGCATCGATACATTGATGG
Found at i:200780 original size:22 final size:22
Alignment explanation
Indices: 200745--200798 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
200735 AGTCAAGGGT
200745 TTCATAGGTCCTTCGGAACAAA
1 TTCATAGGTCCTTCGGAACAAA
* * * *
200767 TTCATATGTTCTTCGGGACATA
1 TTCATAGGTCCTTCGGAACAAA
200789 TTCATAGGTC
1 TTCATAGGTC
200799 ATTCAGGATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGAACAAA
Found at i:204349 original size:3 final size:3
Alignment explanation
Indices: 204341--204374 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
204331 CTAGAACAAC
204341 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
204375 CTTCATACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:205460 original size:21 final size:21
Alignment explanation
Indices: 205434--205475 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
205424 AGTGTGATAA
205434 GATATATG-AATTGGTATAAGT
1 GATATATGTAATT-GTATAAGT
*
205455 GATATATGTGATTGTATAAGT
1 GATATATGTAATTGTATAAGT
205476 TACATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (21 bp):
GATATATGTAATTGTATAAGT
Found at i:216500 original size:34 final size:34
Alignment explanation
Indices: 216457--216523 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
216447 TCATTTATAG
216457 AGGCAAAATAAAAGACCGGAGAAAGAGAAGAGAA
1 AGGCAAAATAAAAGACCGGAGAAAGAGAAGAGAA
** *
216491 AGGCAAAATAAAAGATTGGGGAAAGAGAAGAGA
1 AGGCAAAATAAAAGACCGGAGAAAGAGAAGAGA
216524 GAACGACGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.57, C:0.06, G:0.31, T:0.06
Consensus pattern (34 bp):
AGGCAAAATAAAAGACCGGAGAAAGAGAAGAGAA
Found at i:217683 original size:15 final size:15
Alignment explanation
Indices: 217663--217714 Score: 95
Period size: 15 Copynumber: 3.5 Consensus size: 15
217653 ATATTTAACT
*
217663 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
217678 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
217693 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
217708 GGGCGGG
1 GGGCGGG
217715 TAATGTCTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.06, C:0.17, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:218192 original size:43 final size:40
Alignment explanation
Indices: 218095--218182 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
218085 TATTTACTTT
218095 TTTATTTGTTTTATTATTATTTTCATCATTACTTTACCTA
1 TTTATTTGTTTTATTATTATTTTCATCATTACTTTACCTA
*
218135 TTTATTTGTTTTATTATTATTTTCATCATTATTTTACCTA
1 TTTATTTGTTTTATTATTATTTTCATCATTACTTTACCTA
218175 -TTATTTGT
1 TTTATTTGT
218183 CAATTTTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 8 0.17
40 39 0.83
ACGTcount: A:0.22, C:0.10, G:0.03, T:0.65
Consensus pattern (40 bp):
TTTATTTGTTTTATTATTATTTTCATCATTACTTTACCTA
Found at i:218517 original size:19 final size:19
Alignment explanation
Indices: 218495--218538 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
218485 ATTTTTTGGA
* * *
218495 TTAAAACAAACCAATTTTT
1 TTAAAAAAAAACAATTTTC
*
218514 TTAAAAAAAAATAATTTTC
1 TTAAAAAAAAACAATTTTC
218533 TTAAAA
1 TTAAAA
218539 TTACTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAAAAAAACAATTTTC
Found at i:219471 original size:64 final size:64
Alignment explanation
Indices: 219370--219499 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
219360 TTTTCGTCAG
219370 GCACGAATTTTTTACTTGACGGAAAAAATGATGTGAATAAATGGTTTAAAATAATTTGAGAGTC
1 GCACGAATTTTTTACTTGACGGAAAAAATGATGTGAATAAATGGTTTAAAATAATTTGAGAGTC
*
219434 GCACGAATTTTTTACTTGACGGAAAAAGTGATGTGAATAAATGGTTTAAAATAATTTGAGAGTC
1 GCACGAATTTTTTACTTGACGGAAAAAATGATGTGAATAAATGGTTTAAAATAATTTGAGAGTC
219498 GC
1 GC
219500 CATCGGCCTT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (64 bp):
GCACGAATTTTTTACTTGACGGAAAAAATGATGTGAATAAATGGTTTAAAATAATTTGAGAGTC
Found at i:219808 original size:23 final size:25
Alignment explanation
Indices: 219776--219827 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
219766 TATTTCAAAA
*
219776 TTATAATTAT-GA-AAAATATTAAT
1 TTATAATTATAAATAAAATATTAAT
* *
219799 TTATATTTATAAATAAAATATTTAT
1 TTATAATTATAAATAAAATATTAAT
219824 TTAT
1 TTAT
219828 TTAGAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 1 0.04
25 14 0.58
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTATAATTATAAATAAAATATTAAT
Found at i:219828 original size:23 final size:25
Alignment explanation
Indices: 219788--219836 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
219778 ATAATTATGA
*
219788 AAAATATTAATTTATATTTATAAAT
1 AAAATATTAATTTATATTTAGAAAT
*
219813 AAAATATTTA-TT-TATTTAGAAAT
1 AAAATATTAATTTATATTTAGAAAT
219836 A
1 A
219837 TCAAAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 2 0.09
25 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
AAAATATTAATTTATATTTAGAAAT
Found at i:219921 original size:20 final size:19
Alignment explanation
Indices: 219882--219933 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
219872 TTTCTTTGAT
219882 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
219901 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
219921 ATTTATAAAATAA
1 A-TTAAAAAATAA
219934 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:220003 original size:119 final size:117
Alignment explanation
Indices: 219793--220019 Score: 289
Period size: 119 Copynumber: 1.9 Consensus size: 117
219783 TATGAAAAAT
* * * *
219793 ATTAATTTATATTTATAAATAAAATATTTATTTATTTAGAAATATCAAAAATGACTTCTAGGTGC
1 ATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAATGACATCCAGGTGC
* *
219858 CTTAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAACA
66 CTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACA
*
219910 ATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAG
1 ATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCA-AAAAT-GACATCCAG
* ** *
219975 TTGTTTTAAGACTA-C-CCTTTC-TTAATATTGAAAAATAAATAAATA
62 GTGCCTTAAGAC-AGCTCCTTTCTTTAATATTAAAAAATAAATAAATA
220020 TATATTAAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
117 9 0.10
118 6 0.06
119 51 0.54
120 10 0.11
121 17 0.18
122 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (117 bp):
ATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAATGACATCCAGGTGC
CTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACA
Found at i:220142 original size:14 final size:14
Alignment explanation
Indices: 220123--220154 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
220113 AAATAATAAG
220123 AATAATAATAAAAT
1 AATAATAATAAAAT
220137 AATAATAATAAAAT
1 AATAATAATAAAAT
220151 AATA
1 AATA
220155 TTGCAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:220168 original size:3 final size:3
Alignment explanation
Indices: 220114--220154 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
220104 TATTTATATA
*
220114 AAT AAT AAG AAT AAT AAT AA- AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
220155 TTGCAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:222093 original size:110 final size:110
Alignment explanation
Indices: 221926--222647 Score: 1058
Period size: 113 Copynumber: 6.6 Consensus size: 110
221916 GAATTCGAGC
* *
221926 AACAAGTTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTC
1 AACAAGTTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
221991 GCCCTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTG
63 GACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
* * *
222039 AACAAGTTCTTCTAATTATGAACTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGCC
1 AACAAGTTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
*
222104 CTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTG
66 CTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
222149 AACAAGTTCTTCTCATTATGAACTTCTT-CTTCTTTTCAGATGAGTTCTTCTCATTATGAACTCG
1 AACAAGTTCTTCTCATTATGAACTTCTTCCTTC--TTCAGATGAGTTCTTCTCATTATGAACTCG
* *
222213 ACATGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
64 ACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
222260 AACAAGTTCTTCTCATTATGAA---CTT-CTTCTTC--------T-TTCTCATTATGAACTCGAC
1 AACAAGTTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
*
222312 CTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
66 CTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
222357 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
222422 GACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGTGAAAAGTTG
63 GACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
*
222470 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
222535 GACCTGGTAATACTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
63 GACCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
*
222583 AACAAGTTCTTCTTATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAAC---TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
222648 TTCTACAAAT
Statistics
Matches: 569, Mismatches: 19, Indels: 42
0.90 0.03 0.07
Matches are distributed among these distances:
97 85 0.15
98 1 0.00
103 3 0.01
104 7 0.01
106 3 0.01
108 7 0.01
109 4 0.01
110 115 0.20
111 94 0.17
112 1 0.00
113 249 0.44
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (110 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
CTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAAGTTG
Found at i:222294 original size:111 final size:112
Alignment explanation
Indices: 221926--222293 Score: 643
Period size: 110 Copynumber: 3.3 Consensus size: 112
221916 GAATTCGAGC
*
221926 AACAAGTTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTTATTATGAACTC
221991 GCCCTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTG
65 GCCCTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTG
*
222039 AACAAGTTCTTCTAATTATGAACTTCTTC--CTTCTTCAGATGAGTTCTTCTTATTATGAACTCG
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTATTATGAACTCG
222102 CCCTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTG
66 CCCTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTG
*
222149 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTT-TTCAGATGAGTTCTTCTCATTATGAACTCG
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTATTATGAACTCG
* * * *
222213 ACATGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
66 CCCTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTG
222260 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTT
222294 TCTCATTATG
Statistics
Matches: 245, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
110 108 0.44
111 107 0.44
112 3 0.01
113 27 0.11
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (112 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTATTATGAACTCG
CCCTGGCAATGCTGGTCCATCGAATGATAAATTCAAGCGAAAAGTTG
Found at i:222327 original size:97 final size:97
Alignment explanation
Indices: 222195--222393 Score: 380
Period size: 97 Copynumber: 2.1 Consensus size: 97
222185 CAGATGAGTT
222195 CTTCTCATTATGAACTCGACATGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
1 CTTCTCATTATGAACTCGACATGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
222260 AACAAGTTCTTCTCATTATGAACTTCTTCTTC
66 AACAAGTTCTTCTCATTATGAACTTCTTCTTC
* *
222292 TTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
1 CTTCTCATTATGAACTCGACATGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
222357 AACAAGTTCTTCTCATTATGAACTTCTTCTTC
66 AACAAGTTCTTCTCATTATGAACTTCTTCTTC
222389 CTTCT
1 CTTCT
222394 TCAGATGAGT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 99 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (97 bp):
CTTCTCATTATGAACTCGACATGGCAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
AACAAGTTCTTCTCATTATGAACTTCTTCTTC
Found at i:223106 original size:22 final size:22
Alignment explanation
Indices: 223081--223136 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
223071 GATAAAGCTT
*
223081 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
* *
223103 TCATCTTTTAAAAAGGGAATCTA
1 TCATC-TTTGAAAAGAGAATCTA
223126 TCATCTTTGAA
1 TCATCTTTGAA
223137 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:224564 original size:76 final size:76
Alignment explanation
Indices: 224428--224598 Score: 209
Period size: 76 Copynumber: 2.3 Consensus size: 76
224418 GATGTGGGCC
* * * *
224428 TTCAGCATGCCCCAACA-ATTGCTGATACGAACGTTCAAAATACATCAACATTCTTCATTCTGAT
1 TTCAGCATGCCCCAACATTTTGCTGATACAAACATTCAAAATACATCAACATTCCTCATTCTGAT
*
224492 TGAAAAATACT
66 TGAAAAAGACT
* * * ** *
224503 TTCAGCATGCCCCAGCATTTTGCTGATATAAACATTCAAGATACATCAGTATTCCTGATTCTGAT
1 TTCAGCATGCCCCAACATTTTGCTGATACAAACATTCAAAATACATCAACATTCCTCATTCTGAT
* **
224568 TGAAAAGGGTT
66 TGAAAAAGACT
224579 TTCAGCATGCCCCAACATTT
1 TTCAGCATGCCCCAACATTT
224599 GCCTCTTGTT
Statistics
Matches: 80, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
75 16 0.20
76 64 0.80
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.31
Consensus pattern (76 bp):
TTCAGCATGCCCCAACATTTTGCTGATACAAACATTCAAAATACATCAACATTCCTCATTCTGAT
TGAAAAAGACT
Found at i:230807 original size:14 final size:15
Alignment explanation
Indices: 230773--230811 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
230763 CATAAAAATA
*
230773 CAAATGCAAAGATGC
1 CAAATGTAAAGATGC
*
230788 CAAATGTAAATATG-
1 CAAATGTAAAGATGC
230802 CAAATGTAAA
1 CAAATGTAAA
230812 AATGTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (15 bp):
CAAATGTAAAGATGC
Found at i:230820 original size:14 final size:14
Alignment explanation
Indices: 230765--230820 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
230755 AAAGTAAACA
*
230765 TAAAAATACAAATG
1 TAAAAATGCAAATG
* *
230779 CAAAGATGCCAAATG
1 TAAAAATG-CAAATG
*
230794 TAAATATGCAAATG
1 TAAAAATGCAAATG
*
230808 TAAAAATGTAAAT
1 TAAAAATGCAAAT
230821 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.23
Consensus pattern (14 bp):
TAAAAATGCAAATG
Found at i:233088 original size:20 final size:19
Alignment explanation
Indices: 233049--233090 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
233039 TTTCTTTGAT
233049 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
233068 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
233088 ATT
1 ATT
233091 TATAAAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:233176 original size:120 final size:119
Alignment explanation
Indices: 232957--233186 Score: 279
Period size: 120 Copynumber: 1.9 Consensus size: 119
232947 TATGAAAAAT
* * * *
232957 ATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTATG
1 ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCATG
* *
233022 TGCCTTAAGACAACTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAACA
66 TGCCTTAAGACAACTCCTTTCTTTAATATT-AAAAATAAATAAATAATTAAAACA
*
233077 ATTAATATATA-ATTTATAAAGTAAGATATTTATTTATTTAAAAATATCAGAAAATAGACATCCA
1 ATTAATATATATATTTATAAA-TAAAATATTTATTTATTTAAAAATATCAGAAAAT-GACATCCA
** * **
233141 -GTTGTTTTCAGACTGC-CCTTTC-TTAATATTGAAAAATAAATAAATA
64 TG-TGCCTTAAGACAACTCCTTTCTTTAATATT-AAAAATAAATAAATA
233187 TATATTAAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
119 31 0.33
120 48 0.51
121 15 0.16
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (119 bp):
ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCATG
TGCCTTAAGACAACTCCTTTCTTTAATATTAAAAATAAATAAATAATTAAAACA
Found at i:233297 original size:16 final size:14
Alignment explanation
Indices: 233281--233323 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
233271 TATTTATATA
233281 AATAATAAGAATAAT
1 AATAATAA-AATAAT
*
233296 AATAA-AAAGTAAT
1 AATAATAAAATAAT
233309 AATAATAAAATAAT
1 AATAATAAAATAAT
233323 A
1 A
233324 TTGCAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.40
14 10 0.40
15 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:233337 original size:3 final size:3
Alignment explanation
Indices: 233281--233323 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
233271 TATTTATATA
* *
233281 AAT AAT AAG AAT AAT AAT AAA AAGT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
233324 TTGCAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:233343 original size:12 final size:12
Alignment explanation
Indices: 233281--233345 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
233271 TATTTATATA
233281 AATAA-TAAGAAT
1 AATAATTAA-AAT
*
233293 AATAATAAAAAGT
1 AATAATTAAAA-T
233306 AATAATAATAAAAT
1 AATAAT--TAAAAT
*
233320 AAT-ATTGCAAAT
1 AATAATT-AAAAT
233332 AATAATTAAAAT
1 AATAATTAAAAT
233344 AA
1 AA
233346 AAGGAATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
11 1 0.02
12 20 0.47
13 14 0.33
14 4 0.09
15 4 0.09
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (12 bp):
AATAATTAAAAT
Found at i:234681 original size:22 final size:23
Alignment explanation
Indices: 234653--234697 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
234643 ATAATATAAT
* *
234653 ATAATAAT-ATTATTAAAACAAA
1 ATAATAATAATAAATAAAACAAA
234675 ATAATAATAATAAATAAAACAAA
1 ATAATAATAATAAATAAAACAAA
234698 TGAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAATAATAATAAATAAAACAAA
Found at i:234688 original size:19 final size:19
Alignment explanation
Indices: 234638--234688 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
234628 ATTATTTATT
* * *
234638 TAATAATAATATAATATAA
1 TAATAATAATAAAACAAAA
* *
234657 TAATATTATTAAAACAAAA
1 TAATAATAATAAAACAAAA
234676 TAATAATAATAAA
1 TAATAATAATAAA
234689 TAAAACAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAATAATAAAACAAAA
Found at i:238520 original size:38 final size:38
Alignment explanation
Indices: 238458--238546 Score: 128
Period size: 38 Copynumber: 2.4 Consensus size: 38
238448 ATTTTGTTCG
*
238458 GGTCGGGTCGGG-TTTTTTAAGTGTGATATTCAGGTC-
1 GGTCAGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCA
*
238494 GAGTCAGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCA
1 G-GTCAGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCA
*
238533 GGTCGGGTCGGGTT
1 GGTCAGGTCGGGTT
238547 CGGGTTTAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
36 1 0.02
37 10 0.21
38 35 0.74
39 1 0.02
ACGTcount: A:0.13, C:0.11, G:0.38, T:0.37
Consensus pattern (38 bp):
GGTCAGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCA
Found at i:241123 original size:3 final size:3
Alignment explanation
Indices: 241109--241139 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
241099 TAAAAGTTAA
241109 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
241140 TGTTATGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:241287 original size:37 final size:37
Alignment explanation
Indices: 241237--241341 Score: 167
Period size: 37 Copynumber: 2.8 Consensus size: 37
241227 ATAACGTTAT
**
241237 AGTTTTACTATGATTCAAACTGCTATGAATATGATAG
1 AGTTTTACTATGATTCAAACTGCTAAAAATATGATAG
241274 AGTTTTACTATGATTCAAACT-CTTAAAAATATGATAG
1 AGTTTTACTATGATTCAAACTGC-TAAAAATATGATAG
*
241311 AGTTTTACTAAGATTCAAACTGCTAAAAATA
1 AGTTTTACTATGATTCAAACTGCTAAAAATA
241342 GGATCCATAA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
36 1 0.02
37 61 0.97
38 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (37 bp):
AGTTTTACTATGATTCAAACTGCTAAAAATATGATAG
Found at i:241746 original size:19 final size:19
Alignment explanation
Indices: 241724--241762 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
241714 ATTATATATA
241724 TATATTTCAT-TGTTATTAT
1 TATATTTCATATGTT-TTAT
*
241743 TATATTTTATATGTTTTAT
1 TATATTTCATATGTTTTAT
241762 T
1 T
241763 TTGTTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (19 bp):
TATATTTCATATGTTTTAT
Found at i:241866 original size:21 final size:20
Alignment explanation
Indices: 241798--241866 Score: 54
Period size: 22 Copynumber: 3.4 Consensus size: 20
241788 TTTATATGCA
241798 TATTCATTATATTTTTT-TCT
1 TATT-ATTATATTTTTTCTCT
* *
241818 TATT-TTAT-TTCATTTCCCT
1 TATTATTATATT-TTTTCTCT
241837 ATCATTATTATATTTTTTCTCT
1 -T-ATTATTATATTTTTTCTCT
241859 CTATTATT
1 -TATTATT
241867 TAACTATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
17 2 0.05
18 7 0.18
19 2 0.05
20 5 0.13
21 9 0.24
22 11 0.29
23 2 0.05
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTATTATATTTTTTCTCT
Found at i:242030 original size:3 final size:3
Alignment explanation
Indices: 242018--242062 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
242008 CTTTACTTAC
*
242018 TAT T-T TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
242063 CTATTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:242098 original size:14 final size:14
Alignment explanation
Indices: 242058--242097 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
242048 ATTATTATTA
242058 TTATTCTATTTTAT
1 TTATTCTATTTTAT
242072 TTATTCTATTTTAT
1 TTATTCTATTTTAT
242086 TTATTTCTATTT
1 TTA-TTCTATTT
242098 ACCTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTCTATTTTAT
Found at i:242106 original size:23 final size:24
Alignment explanation
Indices: 242053--242115 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
242043 TTATTATTAT
*
242053 TATTATTATTCTATTT-TATTTATTC
1 TATT-TTATT-TATTTCTATTTATCC
242078 TATTTTATTTATTTCTATTTA-CC
1 TATTTTATTTATTTCTATTTATCC
* *
242101 TTTTTTATTTTTTTC
1 TATTTTATTTATTTC
242116 CTCTATTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 19 0.56
24 11 0.32
25 4 0.12
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTTATTTATTTCTATTTATCC
Found at i:242135 original size:19 final size:18
Alignment explanation
Indices: 242107--242151 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
242097 TACCTTTTTT
242107 ATTTTTTTCCTCTAT-TTC
1 ATTTTTTTCCT-TATCTTC
*
242125 ATTTTTATTCCTTATCTTT
1 ATTTTT-TTCCTTATCTTC
242144 ATTTTTTT
1 ATTTTTTT
242152 TATCTTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTTTCCTTATCTTC
Found at i:242228 original size:3 final size:3
Alignment explanation
Indices: 242217--242270 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
242207 ATAATAATAA
* *
242217 TAT TA- TAT TAT TAA TAT TAT T-T TAT T-T TAC TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
242261 TAT TAT TAT T
1 TAT TAT TAT T
242271 TATGTTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 8 0.19
3 35 0.81
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:242233 original size:14 final size:14
Alignment explanation
Indices: 242214--242266 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
242204 TAAATAATAA
242214 TAATATTATATTAT
1 TAATATTATATTAT
*
242228 TAATATTATTTTATTT
1 TAATATTATATTA--T
*
242244 TACTATTATATTAT
1 TAATATTATATTAT
*
242258 TATTATTAT
1 TAATATTAT
242267 TATTTATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 21 0.64
16 12 0.36
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TAATATTATATTAT
Found at i:247770 original size:15 final size:15
Alignment explanation
Indices: 247750--247796 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
247740 GATCAATACC
247750 TTTTGCATACATGCA
1 TTTTGCATACATGCA
247765 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
247780 TTTTGCATACATTCA
1 TTTTGCATACATGCA
247795 TT
1 TT
247797 ATTCATTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:250113 original size:26 final size:26
Alignment explanation
Indices: 250077--250129 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
250067 TAGGTGAAAG
250077 CAAAAGGAAAAGCCATGGTAATACCC
1 CAAAAGGAAAAGCCATGGTAATACCC
250103 CAAAAGGAAAAGCCATGGTAATACCC
1 CAAAAGGAAAAGCCATGGTAATACCC
250129 C
1 C
250130 TCCAACATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.11
Consensus pattern (26 bp):
CAAAAGGAAAAGCCATGGTAATACCC
Found at i:257229 original size:122 final size:123
Alignment explanation
Indices: 256822--257301 Score: 811
Period size: 123 Copynumber: 3.9 Consensus size: 123
256812 TGGATCAGCA
*
256822 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAAAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
*
256887 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACT
66 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACT
* *
256945 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATAAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
257010 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACT
66 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACT
257068 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* * * *
257133 GATCTTGTTCAACC-TTTGCATGACTCTATCATAAAAAGAGATAGATCAACATCAATT
66 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACT
* * *
257190 TTTTCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATCATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* * *
257255 GAGCTTGTTCAACCTTTTG-ATTGATTCTACCACAGAAAGATATAGAT
66 GAGCTTGTTCAACCTTTTGCA-TGACTCTATCACAGAAAGAGATAGAT
257302 GAAGGAGGTA
Statistics
Matches: 336, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
122 116 0.35
123 220 0.65
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACT
Found at i:257257 original size:245 final size:240
Alignment explanation
Indices: 256710--257301 Score: 822
Period size: 245 Copynumber: 2.5 Consensus size: 240
256700 TGGATCAGCA
* *
256710 TTTCCATAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* ** * * ** *
256775 AAATTTGTTCAACCTTTTGCTTCAAT-TCATCAC-----TCGATGGATCAGCATTTCCAGAGAAA
66 GAGCTTGTTCAACCTTTTGCATGAATCT-ATCACAGAAAGAGATAGATCAGCATTTCCAGAGAAA
256834 GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTGTTCAA
130 GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTGTTCAA
* *
256899 CCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACT
195 CCTTTTGCATGACTCTATCACAAAAAGAGATAGATCAACATCAACT
* *
256945 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATAAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* *
257010 GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACTTTTCCAG
66 GAGCTTGTTCAACCTTTTGCATGAATCTATCACAGAAAGAGATAGAT---CAGC-A--TTTCCAG
* *
257075 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGATCTTG
125 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTG
* *
257140 TTCAACC-TTTGCATGACTCTATCATAAAAAGAGATAGATCAACATCAATT
190 TTCAACCTTTTGCATGACTCTATCACAAAAAGAGATAGATCAACATCAACT
* * *
257190 TTTTCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATCATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* * *
257255 GAGCTTGTTCAACCTTTTG-ATTGATTCTACCACAGAAAGATATAGAT
66 GAGCTTGTTCAACCTTTTGCA-TGAATCTATCACAGAAAGAGATAGAT
257302 GAAGGAGGTA
Statistics
Matches: 316, Mismatches: 28, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
235 86 0.27
236 1 0.00
240 6 0.02
243 3 0.01
244 2 0.01
245 141 0.45
246 77 0.24
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (240 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
GAGCTTGTTCAACCTTTTGCATGAATCTATCACAGAAAGAGATAGATCAGCATTTCCAGAGAAAG
TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAAAATGAGAAGAGCTTGTTCAAC
CTTTTGCATGACTCTATCACAAAAAGAGATAGATCAACATCAACT
Found at i:257639 original size:3 final size:3
Alignment explanation
Indices: 257633--257704 Score: 71
Period size: 3 Copynumber: 25.0 Consensus size: 3
257623 AATAATAATC
* *
257633 TTA TTA -TA TTA TTA TTA ATA TTA TT- TTA TT- TTA CTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
257677 TTG TTA TTA TTA TTTA TTA CTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA
257705 ATTAAGTTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
2 8 0.14
3 45 0.80
4 3 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:257676 original size:30 final size:30
Alignment explanation
Indices: 257642--257702 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
257632 CTTATTATAT
*
257642 TATTATTAATATTATT-TTATTTTACTATTA
1 TATTATTAATATTATTATT-TATTACTATTA
**
257672 TATTATTGTTATTATTATTTATTACTATTA
1 TATTATTAATATTATTATTTATTACTATTA
257702 T
1 T
257703 TAATTAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (30 bp):
TATTATTAATATTATTATTTATTACTATTA
Found at i:257704 original size:33 final size:33
Alignment explanation
Indices: 257633--257716 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
257623 AATAATAATC
* * *
257633 TTATTATATTATTATTAATATTATTTTATTTTA
1 TTATTATATTATTGTTATTATTATTTTATTCTA
*
257666 CTATTATATTATTGTTATTATTA-TTTATTACTA
1 TTATTATATTATTGTTATTATTATTTTATT-CTA
*
257699 TTATTA-ATTA-AGTTATTA
1 TTATTATATTATTGTTATTA
257717 CAAACCCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
31 7 0.16
32 10 0.23
33 27 0.61
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (33 bp):
TTATTATATTATTGTTATTATTATTTTATTCTA
Found at i:259571 original size:19 final size:19
Alignment explanation
Indices: 259547--259583 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
259537 ATGACCAACA
*
259547 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
259566 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
259584 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:259698 original size:20 final size:20
Alignment explanation
Indices: 259673--259741 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
259663 TTAGATAATT
259673 GCAATGCGAATATGTAAATC
1 GCAATGCGAATATGTAAATC
259693 GCAATGCGAATATGTAAATC
1 GCAATGCGAATATGTAAATC
259713 GCAATGCGAATATGTAAATC
1 GCAATGCGAATATGTAAATC
*
259733 GCAACGCGA
1 GCAATGCGA
259742 TAACACGTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (20 bp):
GCAATGCGAATATGTAAATC
Found at i:259780 original size:20 final size:20
Alignment explanation
Indices: 259755--259898 Score: 166
Period size: 20 Copynumber: 7.1 Consensus size: 20
259745 CACGTGATCA
259755 CAACGCGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
*
259775 CAACGCGATTCGGACTATCG
1 CAACGCGATTCTGACTATCG
**
259795 CAACGCGATAAT-ACGTGATCG
1 CAACGCGATTCTGAC-T-ATCG
259816 CAACGCGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
*
259836 CAACGAGATTCTGACTATCG
1 CAACGCGATTCTGACTATCG
* **
259856 CAACGTGATAAT-ACGTGATCG
1 CAACGCGATTCTGAC-T-ATCG
*
259877 CAACGCGATTCTGACTAACG
1 CAACGCGATTCTGACTATCG
259897 CA
1 CA
259899 TCACTGAATT
Statistics
Matches: 104, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.04
20 67 0.64
21 29 0.28
22 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (20 bp):
CAACGCGATTCTGACTATCG
Found at i:259805 original size:61 final size:61
Alignment explanation
Indices: 259730--259898 Score: 284
Period size: 61 Copynumber: 2.8 Consensus size: 61
259720 GAATATGTAA
* * *
259730 ATCGCAACGCGATAACACGTGATCACAACGCGATTCTGACTATCGCAACGCGATTCGGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCGGACT
*
259791 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCGGACT
* *
259852 ATCGCAACGTGATAATACGTGATCGCAACGCGATTCTGACTAACGCA
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCA
259899 TCACTGAATT
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 102 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (61 bp):
ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCGGACT
Found at i:259877 original size:41 final size:39
Alignment explanation
Indices: 259730--259898 Score: 151
Period size: 41 Copynumber: 4.2 Consensus size: 39
259720 GAATATGTAA
* *
259730 ATCGCAACGCGATAACACGTGATCACAACGCGATTCTGACT
1 ATCGCAACGCGATAATAC-T-ATCGCAACGCGATTCTGACT
*** **
259771 ATCGCAACGCGATTCGGACTATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGA-TAATACTATCGCAACGCGATTCTGAC-T
** *
259811 GATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
1 -ATCGCAACGCGATAAT-ACTATCGCAACGCGATTCTGACT
*
259852 ATCGCAACGTGATAATACGTGATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATAC-T-ATCGCAACGCGATTCTGACT
*
259893 AACGCA
1 ATCGCA
259899 TCACTGAATT
Statistics
Matches: 104, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
39 4 0.04
40 29 0.28
41 66 0.63
42 5 0.05
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (39 bp):
ATCGCAACGCGATAATACTATCGCAACGCGATTCTGACT
Found at i:260729 original size:24 final size:24
Alignment explanation
Indices: 260697--260750 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
260687 GTATTCGAAA
260697 TTTGATCTTGCTCAATACCCGGAC
1 TTTGATCTTGCTCAATACCCGGAC
* * *
260721 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGCTCAATACCCGGAC
260745 TTTGAT
1 TTTGAT
260751 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGCTCAATACCCGGAC
Found at i:263012 original size:12 final size:12
Alignment explanation
Indices: 262995--263025 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
262985 CAAGCAAAAG
262995 GCAATCAAAATC
1 GCAATCAAAATC
263007 GCAATCAAAATC
1 GCAATCAAAATC
*
263019 CCAATCA
1 GCAATCA
263026 CAACCGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.29, G:0.06, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:263232 original size:20 final size:20
Alignment explanation
Indices: 263207--263461 Score: 161
Period size: 20 Copynumber: 13.7 Consensus size: 20
263197 CACATTCATT
263207 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
263227 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
263247 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
263264 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
263281 TGACTATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
263301 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* * *
263318 T-A--ATCACAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* * *
263335 TGACTATCTCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
263355 TGACTATCGCAACGCAAATT
1 TGACTATCGCAACGCGAATA
* *
263375 TGACTATCGCAA--TG-AGA
1 TGACTATCGCAACGCGAATA
263392 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
* *
263408 TGACTATCGCAACGCAAATT
1 TGACTATCGCAACGCGAATA
* * *
263428 TGATTATCGCAACGGGAATT
1 TGACTATCGCAACGCGAATA
263448 TGACTATCGCAACG
1 TGACTATCGCAACG
263462 AGAAAATCGC
Statistics
Matches: 187, Mismatches: 29, Indels: 38
0.74 0.11 0.15
Matches are distributed among these distances:
14 22 0.12
15 2 0.01
16 6 0.03
17 11 0.06
18 2 0.01
19 14 0.07
20 130 0.70
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:263309 original size:54 final size:54
Alignment explanation
Indices: 263212--263368 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 54
263202 TCATTTGACT
* * * * ** *
263212 ATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGGGATA
263266 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGGGATA
* *
263320 ATCACAATGCGAAAATGACTATCTCAATGCGAAAATGACTATCGCAACG
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACG
263369 CAAATTTGAC
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGGGATA
Found at i:263348 original size:74 final size:73
Alignment explanation
Indices: 263266--263469 Score: 250
Period size: 74 Copynumber: 2.8 Consensus size: 73
263256 CAACGGGATA
* * * *
263266 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGGGATAATCACAATGCG
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAATTGACTATCGCAACGAGATAATCACAACGCG
263331 AAAATGACT
66 -AAATGACT
* * *
263340 ATCTCAATGCGAAAATGACTATCGCAACGC-AAATTTGACTATCGCAATGAGATAATCGCAACGC
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAAA-TTGACTATCGCAACGAGATAATCACAACGC
263404 GAAATGACT
65 GAAATGACT
* * * * * *
263413 ATCGCAACGC-AAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAGAAAATC
1 ATCGCAATGCGAAA-ATGACTATCGCAACGCGAAATTGACTATCGCAACGAGATAATC
263470 GCAAAGTGTA
Statistics
Matches: 112, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
72 3 0.03
73 53 0.47
74 56 0.50
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (73 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAAATTGACTATCGCAACGAGATAATCACAACGCG
AAATGACT
Found at i:263639 original size:25 final size:25
Alignment explanation
Indices: 263611--263661 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
263601 TTAAACAAGC
*
263611 ACAAATAATAATTATTTACACATCA
1 ACAAATAAGAATTATTTACACATCA
263636 ACAAATAAGAATTATTTACACATCA
1 ACAAATAAGAATTATTTACACATCA
263661 A
1 A
263662 TTAAACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (25 bp):
ACAAATAAGAATTATTTACACATCA
Found at i:265152 original size:42 final size:42
Alignment explanation
Indices: 265054--265156 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 42
265044 TTGGGAGGGA
* * * * *
265054 CCTCTTCAACGATGACAGTGGCCTCTTGAACGATGGGAGGGG
1 CCTCTTGAACGATGACAGGGGCATCTTGAACGATAGGAGAGG
* * ** *
265096 ACTTTTGAGGGATGATAGGGGCATCTTGAACGATAGGAGAGG
1 CCTCTTGAACGATGACAGGGGCATCTTGAACGATAGGAGAGG
*
265138 CCTCTTGAATGATGACAGG
1 CCTCTTGAACGATGACAGG
265157 TGAGTCGGGC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.23
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGGGGCATCTTGAACGATAGGAGAGG
Found at i:266050 original size:19 final size:19
Alignment explanation
Indices: 266016--266052 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
266006 ATGACCAACA
* *
266016 AAATCGCAATGTGATCTCT
1 AAATCGCAACGCGATCTCT
266035 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
266053 CATTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:266182 original size:20 final size:20
Alignment explanation
Indices: 266159--266223 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
266149 GAATATGTAA
*
266159 ATCGCAACGTGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
266179 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
266199 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
266219 ATCGC
1 ATCGC
266224 GTTGCGATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:266388 original size:22 final size:22
Alignment explanation
Indices: 266362--266435 Score: 103
Period size: 22 Copynumber: 3.3 Consensus size: 22
266352 CTACGACGGC
* *
266362 ATCCGTCCCCATCTCTGATGAA
1 ATCCGTCCCCATTTCCGATGAA
**
266384 ATCCGTCCCCATTTCCGGCGAA
1 ATCCGTCCCCATTTCCGATGAA
266406 ATCCGTCCCCCATTTCCGATGAA
1 ATCCGT-CCCCATTTCCGATGAA
266429 ATCCGTC
1 ATCCGTC
266436 TATCTCCATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 25 0.56
23 20 0.44
ACGTcount: A:0.20, C:0.39, G:0.15, T:0.26
Consensus pattern (22 bp):
ATCCGTCCCCATTTCCGATGAA
Found at i:269901 original size:65 final size:63
Alignment explanation
Indices: 269806--269943 Score: 143
Period size: 65 Copynumber: 2.2 Consensus size: 63
269796 CACATTGAAT
* * *
269806 GTGCATCGATACACTCTTTAAAGAAGAAACATCAAACGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATACACCCTTTAAAAAAAAAACATCAAACGCAATTGGTGCATCGATGCAT-AGGTA
* * * * ** * *
269869 GTGCATCGATTCATCCCTTTAAAAATAAAAACATCGAAGGTAATTTTTGTATCGATGCATGGGTA
1 GTGCATCGATACA-CCCTTTAAAAA-AAAAACATCAAACGCAATTGGTGCATCGATGCATAGGTA
269934 GTGCATCGAT
1 GTGCATCGAT
269944 GCACAGGTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
63 12 0.20
64 11 0.18
65 38 0.62
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (63 bp):
GTGCATCGATACACCCTTTAAAAAAAAAACATCAAACGCAATTGGTGCATCGATGCATAGGTA
Found at i:269980 original size:20 final size:20
Alignment explanation
Indices: 269955--269992 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
269945 CACAGGTTAA
*
269955 AGAATGTATCGATACACTGT
1 AGAATGCATCGATACACTGT
*
269975 AGAATGCATCGATGCACT
1 AGAATGCATCGATACACT
269993 TCAAGGGGAA
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:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTGT
Found at i:270786 original size:18 final size:18
Alignment explanation
Indices: 270763--270814 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
270753 GGGTCTACGC
270763 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
270781 GGTCCTTTGGGACATAGT
1 GGTCCTTCGGGACATAGT
270799 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
270815 TGTGTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:273954 original size:65 final size:64
Alignment explanation
Indices: 273859--274000 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 64
273849 CACATTAAAT
* * *
273859 GTGCATCGATGCA-CTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATACAT-AGGTA
* * * *
273922 GTGCATCGATGCACCCCTTTAAA-AATGAAAACATCGAAGGTAATTTGTGTATCGATACATGGGT
1 GTGCATCGATGCACCCCTTTAAAGAA-G-AAACATCGAAGGCAATTGGTGCATCGATACATAGGT
273986 A
64 A
273987 GTGCATCGATGCAC
1 GTGCATCGATGCAC
274001 AGGTTAAAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 15 0.22
64 11 0.16
65 42 0.62
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (64 bp):
GTGCATCGATGCACCCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATACATAGGTA
Found at i:274037 original size:20 final size:20
Alignment explanation
Indices: 274008--274045 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
273998 CACAGGTTAA
274008 AGAATCCATCGATGCACTGT
1 AGAATCCATCGATGCACTGT
*
274028 AGAATGCATCGATGCACT
1 AGAATCCATCGATGCACT
274046 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (20 bp):
AGAATCCATCGATGCACTGT
Found at i:274842 original size:18 final size:18
Alignment explanation
Indices: 274819--274870 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
274809 GGGTCTACGC
274819 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
274837 GGTCC-TCTGGGACATAGT
1 GGTCCTTC-GGGACATAGT
274855 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
274871 TGTGTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.06
18 28 0.88
19 2 0.06
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.27
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:278253 original size:22 final size:22
Alignment explanation
Indices: 278222--278282 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
278212 GCAATATTGA
*
278222 CCTATTGCGGCGTTTTTTTAGT
1 CCTATAGCGGCGTTTTTTTAGT
278244 CCTATAGCGGCGTTTTTTTAGT
1 CCTATAGCGGCGTTTTTTTAGT
*
278266 CTTATAGCGGCGTTTTT
1 CCTATAGCGGCGTTTTT
278283 AAGCGCCGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (22 bp):
CCTATAGCGGCGTTTTTTTAGT
Found at i:278428 original size:43 final size:43
Alignment explanation
Indices: 278378--278644 Score: 392
Period size: 43 Copynumber: 6.2 Consensus size: 43
278368 TGTGAACAAA
278378 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* *
278421 AAACGCCGTAATAGGTCGAGATCTATAGCGGCGTTTTAGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
*
278464 AAACGTCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* *
278507 AAACGCCGCAATAGGTCGAGATCTATAGCGGCATTTTTGGGAT
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* * * *
278550 AAACGCCACAATAGGTCGAGATCTATAGCGACTTTTTTGGAAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
* * * **
278593 AAACGCCACAAAAGGT-TAGATCTATAGCGGCGTTTTTTGATAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCG-TTTTTGGGAC
278636 AAACGCCGC
1 AAACGCCGC
278645 TAATGATCGT
Statistics
Matches: 203, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 13 0.06
43 190 0.94
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
Found at i:282124 original size:41 final size:41
Alignment explanation
Indices: 282078--282304 Score: 129
Period size: 41 Copynumber: 5.3 Consensus size: 41
282068 GTTTGTGTTT
* * * * *
282078 AAAAACTCCACTAACGTATGACTCTTTCGCGGCGTTTTTAC
1 AAAAACGCCACTAAAGTATAAATATTTCGCGGCGTTTTTAC
* **
282119 AAAAACGCCACTAAAGTATAAATATTTTGCGGCGTTTTTTG
1 AAAAACGCCACTAAAGTATAAATATTTCGCGGCGTTTTTAC
* * *
282160 AAATAACGCCACTATATA-TATCAAACCTA-TT-GCGGTGTTTGTAA
1 AAA-AACGCCACTA-A-AGTAT-AAA--TATTTCGCGGCGTTTTTAC
* *
282204 AAAAACGCCGCTAAAGTATAAATATTACTCTTTTGCGGCGTTTTTAT
1 AAAAACGCCACTAAAGTATAAATATT--TC----GCGGCGTTTTTAC
* * * * * *
282251 ACAAACGCCACTAAATTATTACTCTATT-GCGGCGTTTATTAA
1 AAAAACGCCACTAAAGTATAAATAT-TTCGCGGCGTTT-TTAC
282293 AAAAACGCCACT
1 AAAAACGCCACT
282305 GTAAACAAGT
Statistics
Matches: 145, Mismatches: 24, Indels: 33
0.72 0.12 0.16
Matches are distributed among these distances:
39 2 0.01
40 1 0.01
41 49 0.34
42 29 0.20
43 13 0.09
44 16 0.11
45 2 0.01
46 3 0.02
47 29 0.20
48 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTATAAATATTTCGCGGCGTTTTTAC
Found at i:301994 original size:17 final size:17
Alignment explanation
Indices: 301972--302009 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
301962 CTGAGCAACG
301972 AAACCGAGAAAACTGAA
1 AAACCGAGAAAACTGAA
301989 AAACCGAGAAAACTGAA
1 AAACCGAGAAAACTGAA
302006 AAAC
1 AAAC
302010 TGACAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.61, C:0.18, G:0.16, T:0.05
Consensus pattern (17 bp):
AAACCGAGAAAACTGAA
Found at i:302941 original size:37 final size:36
Alignment explanation
Indices: 302859--302962 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
302849 ATTAATCTTC
302859 AATAAG-AAAATACCCAAATTTCTTATGAAACATTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACATTT
* * * *
302894 AATAAGAAAAATACTCAAAATTCTTAAGAAACCTTT
1 AATAAGAAAAATACCCAAATTTCTTATGAAACATTT
302930 AATAAGAAAAAATACCCAAATTTCTTATGAAAC
1 AATAAG-AAAAATACCCAAATTTCTTATGAAAC
302963 TTAAATTGGT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 6 0.10
36 31 0.52
37 23 0.38
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (36 bp):
AATAAGAAAAATACCCAAATTTCTTATGAAACATTT
Found at i:304851 original size:25 final size:25
Alignment explanation
Indices: 304819--304873 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
304809 TCATAAATGG
*
304819 TTCA-AATGCTTAAGCGCTGAATAA
1 TTCAGAATGATTAAGCGCTGAATAA
*
304843 TTCAGAATGATTAAGCGCTGAATGA
1 TTCAGAATGATTAAGCGCTGAATAA
304868 TTCAGA
1 TTCAGA
304874 GGCTCTGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (25 bp):
TTCAGAATGATTAAGCGCTGAATAA
Found at i:305251 original size:14 final size:14
Alignment explanation
Indices: 305232--305263 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
305222 AGACACAATT
305232 AACAGTTTTTAATA
1 AACAGTTTTTAATA
305246 AACAGTTTTTAATA
1 AACAGTTTTTAATA
305260 AACA
1 AACA
305264 AAAGCTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (14 bp):
AACAGTTTTTAATA
Found at i:307703 original size:235 final size:238
Alignment explanation
Indices: 307290--307763 Score: 927
Period size: 235 Copynumber: 2.0 Consensus size: 238
307280 ACTTGACACT
307290 AACACTAAATATCACTATGAATCCCATAAACAAGATTAAACAAGGGGCCTTTTTCTTCTTATTCT
1 AACACTAAATATCACTATGAATCCCATAAACAAGATTAAACAAGGGGCCTTTTTCTTCTTATTCT
307355 TTTGGATTTCTTCCACGCGCTTTTAACATCTTGACCAAACAATATCAACCATCTGTAACATTACC
66 TTTGGATTTCTTCCACGCGCTTTTAACATCTTGACCAAACAATATCAACCATCTGTAACATTACC
307420 ATCATGAATCATCAGTTGCAATTCTTCGTCTAATTGAAAAAGGGTGAATCATCTATAATAACCAC
131 ATCATGAATCATCAGTTGCAATTCTTCGTCTAATTGAAAAAGGGTGAATCATCTATAATAACCAC
307485 ACTCAAATATTACAAACAGGGGC-TATACACTTGGTCCCATAG
196 ACTCAAATATTACAAACAGGGGCATATACACTTGGTCCCATAG
307527 AACACTAAATATCACTATGAATCCCATAAACAAGATTAAACAAGGGGCCTTTTTCTTCTTATTC-
1 AACACTAAATATCACTATGAATCCCATAAACAAGATTAAACAAGGGGCCTTTTTCTTCTTATTCT
307591 TTTGGATTTCTTCCACGCGC-TTTAACATCTTGACCAAACAATATCAACCATCTGTAACATTACC
66 TTTGGATTTCTTCCACGCGCTTTTAACATCTTGACCAAACAATATCAACCATCTGTAACATTACC
307655 ATCATGAATCATCAGTTGCAATTCTTCGTCTAATTGAAAAAGGGTGAATCATCTATAATAACCAC
131 ATCATGAATCATCAGTTGCAATTCTTCGTCTAATTGAAAAAGGGTGAATCATCTATAATAACCAC
307720 ACTCAAATATTACAAACAGGGGCATATACACTTGGTCCCATAG
196 ACTCAAATATTACAAACAGGGGCATATACACTTGGTCCCATAG
307763 A
1 A
307764 GGACAAAATG
Statistics
Matches: 236, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
235 132 0.56
236 40 0.17
237 64 0.27
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (238 bp):
AACACTAAATATCACTATGAATCCCATAAACAAGATTAAACAAGGGGCCTTTTTCTTCTTATTCT
TTTGGATTTCTTCCACGCGCTTTTAACATCTTGACCAAACAATATCAACCATCTGTAACATTACC
ATCATGAATCATCAGTTGCAATTCTTCGTCTAATTGAAAAAGGGTGAATCATCTATAATAACCAC
ACTCAAATATTACAAACAGGGGCATATACACTTGGTCCCATAG
Found at i:308354 original size:30 final size:30
Alignment explanation
Indices: 308320--308422 Score: 138
Period size: 30 Copynumber: 3.4 Consensus size: 30
308310 AATGGGTTCC
308320 TAATAACAAATACTCAAAAAAA-TAGACTCA
1 TAATAACAAATACT-AAAAAAATTAGACTCA
* *
308350 TAATAAAAAATAGTGAAAAAAATTAGAACT-A
1 TAATAACAAATACT-AAAAAAATTAG-ACTCA
*
308381 TAATAACAAATACTAAAAAAATTAGACTCG
1 TAATAACAAATACTAAAAAAATTAGACTCA
308411 TAATAACAAATA
1 TAATAACAAATA
308423 AATATTAGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
29 3 0.05
30 42 0.66
31 16 0.25
32 3 0.05
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (30 bp):
TAATAACAAATACTAAAAAAATTAGACTCA
Found at i:309134 original size:22 final size:22
Alignment explanation
Indices: 309106--309177 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
309096 CGCAAATTCG
309106 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
** * *
309128 CGTTGCGATTTTCCA-AATT-T
1 CGTTGCGATAGTCTACAGTTGT
309148 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
309169 TGTTGCGAT
1 CGTTGCGAT
309178 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 20 0.51
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:309153 original size:19 final size:19
Alignment explanation
Indices: 309129--309196 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
309119 TACAGTTGTC
309129 GTTGCGATTTTCCAAATTT
1 GTTGCGATTTTCCAAATTT
* * **
309148 GTTGCGATAGTCTACAGTTGTT
1 GTTGCGAT--TTTCCAAAT-TT
*
309170 GTTGCGATTTTCCAAATTC
1 GTTGCGATTTTCCAAATTT
309189 GTTGCGAT
1 GTTGCGAT
309197 AGTTAAAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 17 0.46
20 5 0.14
21 5 0.14
22 10 0.27
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (19 bp):
GTTGCGATTTTCCAAATTT
Found at i:309157 original size:41 final size:41
Alignment explanation
Indices: 309106--309199 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
309096 CGCAAATTCG
309106 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
* *
309147 TGTTGCGATAGTCTACAGTTGTTGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
309188 CGTTGCGATAGT
1 CGTTGCGATAGT
309200 TAAAAAAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:309192 original size:22 final size:21
Alignment explanation
Indices: 309124--309192 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
309114 TAGTCTACAG
*
309124 TTGTCGTTGCGATTTTCCAAA
1 TTGTTGTTGCGATTTTCCAAA
** * *
309145 -T-TTGTTGCGATAGTCTACAG
1 TTGTTGTTGCGATTTTCCA-AA
309165 TTGTTGTTGCGATTTTCCAAA
1 TTGTTGTTGCGATTTTCCAAA
309186 TTCGTTG
1 TT-GTTG
309193 CGATAGTTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
19 12 0.34
20 2 0.06
21 4 0.11
22 17 0.49
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.45
Consensus pattern (21 bp):
TTGTTGTTGCGATTTTCCAAA
Found at i:309966 original size:22 final size:22
Alignment explanation
Indices: 309938--309990 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
309928 AATTTGGAAA
*
309938 ATCGCAACGACAACTGTAGAGT
1 ATCGCAACGACAACTGTAGACT
*
309960 ATCGCAATGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
309982 ATCGCAACG
1 ATCGCAACG
309991 CGATTTTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:310005 original size:21 final size:21
Alignment explanation
Indices: 309979--310019 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
309969 ACAACTGTAG
309979 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
**
310000 ACTATCTTAACGCGATTTTC
1 ACTATCGCAACGCGATTTTC
310020 CAGATTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:310077 original size:40 final size:41
Alignment explanation
Indices: 310022--310104 Score: 150
Period size: 40 Copynumber: 2.0 Consensus size: 41
310012 CGATTTTCCA
*
310022 GATTTTCAACTATCGCAACGCGAAATGG-AAATCGCAACGC
1 GATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAAGC
310062 GATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAAGC
1 GATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAAGC
310103 GA
1 GA
310105 AATGGAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 28 0.68
41 13 0.32
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.19
Consensus pattern (41 bp):
GATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAAAGC
Found at i:310078 original size:21 final size:21
Alignment explanation
Indices: 310022--310084 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
310012 CGATTTTCCA
310022 GATTTTCAACTATCGCAACGC
1 GATTTTCAACTATCGCAACGC
** **
310043 GAAATGGAA--ATCGCAACGC
1 GATTTTCAACTATCGCAACGC
310062 GATTTTCAACTATCGCAACGC
1 GATTTTCAACTATCGCAACGC
310083 GA
1 GA
310085 AATGGAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (21 bp):
GATTTTCAACTATCGCAACGC
Found at i:310098 original size:20 final size:20
Alignment explanation
Indices: 310033--310119 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
310023 ATTTTCAACT
310033 ATCGCAACGCGAAATGG-AA
1 ATCGCAACGCGAAATGGAAA
** ** *
310052 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
310073 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
310093 ATCGCAAAGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
310113 ATCGCAA
1 ATCGCAA
310120 TTCAACTATC
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
19 13 0.24
20 27 0.49
21 15 0.27
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:310495 original size:18 final size:18
Alignment explanation
Indices: 310468--310505 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
310458 ATTATTTAAT
* *
310468 AAACACATATAATTATTA
1 AAACAAATATAATAATTA
310486 AAACAAATATAATAATTA
1 AAACAAATATAATAATTA
310504 AA
1 AA
310506 TTATATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (18 bp):
AAACAAATATAATAATTA
Found at i:310691 original size:13 final size:13
Alignment explanation
Indices: 310669--310700 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
310659 TATATTATTT
310669 TTATTT-AAATTA
1 TTATTTAAAATTA
310681 TTATTTAAAATTA
1 TTATTTAAAATTA
310694 TT-TTTAA
1 TTATTTAA
310701 GTAATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATTTAAAATTA
Found at i:327037 original size:3 final size:3
Alignment explanation
Indices: 327029--327068 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
327019 AGGATAAAAA
* *
327029 TAT TAT TAT TA- AAT TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
327069 AGTGTGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:340840 original size:9 final size:9
Alignment explanation
Indices: 340802--340861 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 9
340792 TATGCTTGAA
340802 GAAAAAAA-
1 GAAAAAAAT
* *
340810 GGAACAAAT
1 GAAAAAAAT
*
340819 -AAAAAGAT
1 GAAAAAAAT
340827 G-AAAAAAT
1 GAAAAAAAT
340835 GAAAAAAAATT
1 G-AAAAAAA-T
340846 GAAAAAAAT
1 GAAAAAAAT
340855 GAAAAAA
1 GAAAAAA
340862 TAAAAAGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
8 18 0.44
9 8 0.20
10 13 0.32
11 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.13, T:0.10
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:340841 original size:10 final size:10
Alignment explanation
Indices: 340828--340861 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
340818 TAAAAAGATG
340828 AAAAAATGAA
1 AAAAAATGAA
340838 AAAAAATTG-A
1 AAAAAA-TGAA
340848 AAAAAATGAA
1 AAAAAATGAA
340858 AAAA
1 AAAA
340862 TAAAAAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (10 bp):
AAAAAATGAA
Done.