Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 106 of 163
Found at i:34166430 original size:15 final size:15
Alignment explanation
Indices: 34166410--34166446 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
34166400 GTTAAGTGTT
34166410 AGGGTTTTTAAGTTA
1 AGGGTTTTTAAGTTA
*
34166425 AGGGTTTTTAGGTTA
1 AGGGTTTTTAAGTTA
34166440 AGGGTTT
1 AGGGTTT
34166447 AGGGTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (15 bp):
AGGGTTTTTAAGTTA
Found at i:34166440 original size:36 final size:36
Alignment explanation
Indices: 34166389--34166467 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
34166379 TTAAGGGTTT
*
34166389 AGGGTTTTTAAGTTAAGTG-TTAGGGTTTTTAAGTTA
1 AGGGTTTTTAAGTTAAGGGTTTAGGG-TTTTAAGTTA
*
34166425 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTAAGTTA
1 AGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAGTTA
34166461 AGGGTTT
1 AGGGTTT
34166468 AGGGTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 34 0.85
37 6 0.15
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.46
Consensus pattern (36 bp):
AGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAGTTA
Found at i:34166931 original size:25 final size:26
Alignment explanation
Indices: 34166900--34166952 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
34166890 AGGGTTTATG
*
34166900 GTTTTTAAGTTAAGGG-TTAGGGTTT
1 GTTTTTAAGTTAAGGGTTTAAGGTTT
*
34166925 GTTTTTAGGTTAAGGGTTTAAGGTTT
1 GTTTTTAAGTTAAGGGTTTAAGGTTT
34166951 GT
1 GT
34166953 CAATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (26 bp):
GTTTTTAAGTTAAGGGTTTAAGGTTT
Found at i:34168158 original size:7 final size:7
Alignment explanation
Indices: 34168148--34168173 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
34168138 TTATATACAT
34168148 AATACTA
1 AATACTA
34168155 AATACTA
1 AATACTA
34168162 AATACTA
1 AATACTA
34168169 AATAC
1 AATAC
34168174 CAATCGGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:34169143 original size:51 final size:51
Alignment explanation
Indices: 34169075--34169174 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
34169065 AATTATTTAA
34169075 AAATAGGAATTTAAGAGAAATTTA-AGAGGAACTTAAGAGCAAATTGAGATT
1 AAATAGGAATTTAAGAGAAATTTAGA-AGGAACTTAAGAGCAAATTGAGATT
* * * * *
34169126 AAATATGG-ATTTGAGAGAAATTTGGAAGGAATTTGAGAGTAAATTGAGA
1 AAATA-GGAATTTAAGAGAAATTTAGAAGGAACTTAAGAGCAAATTGAGA
34169175 GGAAATTTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 39 0.93
52 3 0.07
ACGTcount: A:0.46, C:0.02, G:0.25, T:0.27
Consensus pattern (51 bp):
AAATAGGAATTTAAGAGAAATTTAGAAGGAACTTAAGAGCAAATTGAGATT
Found at i:34169148 original size:11 final size:11
Alignment explanation
Indices: 34169134--34169211 Score: 65
Period size: 11 Copynumber: 7.0 Consensus size: 11
34169124 TTAAATATGG
34169134 ATTTGAGAGAA
1 ATTTGAGAGAA
*
34169145 ATTTG-GAAGGA
1 ATTTGAG-AGAA
34169156 ATTTGAGAGTAA
1 ATTTGAGAG-AA
34169168 A-TTGAGAGGAA
1 ATTTGAGA-GAA
34169179 ATTT-AGAGGAA
1 ATTTGAGA-GAA
*
34169190 A-ATGAGATGAA
1 ATTTGAGA-GAA
34169201 ATTTGAGAGAA
1 ATTTGAGAGAA
34169212 GATTAGTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 2 0.04
11 42 0.76
12 11 0.20
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:34169196 original size:33 final size:35
Alignment explanation
Indices: 34169134--34169209 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 35
34169124 TTAAATATGG
* **
34169134 ATTTGAGA-GAAATTTGGAAGGAATTTGAGA-GTAA
1 ATTTGAGAGGAAATTTAGAAGGAAAATGAGATG-AA
34169168 A-TTGAGAGGAAATTTAG-AGGAAAATGAGATGAA
1 ATTTGAGAGGAAATTTAGAAGGAAAATGAGATGAA
34169201 ATTTGAGAG
1 ATTTGAGAG
34169210 AAGATTAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 19 0.53
34 17 0.47
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.26
Consensus pattern (35 bp):
ATTTGAGAGGAAATTTAGAAGGAAAATGAGATGAA
Found at i:34174596 original size:6 final size:6
Alignment explanation
Indices: 34174587--34174618 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
34174577 AATGCAAGCG
34174587 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AG
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AG
34174619 GGTGATGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.34, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:34176321 original size:91 final size:91
Alignment explanation
Indices: 34176165--34176348 Score: 280
Period size: 91 Copynumber: 2.0 Consensus size: 91
34176155 ATCTATGAGA
* * *
34176165 TTAAGAGAATTTTGTGAGTTCTGGGGAATTTTGGGTTTTAGTTAGAGTACTTTGTTCTTTCGAGA
1 TTAAGAGAATTCTGTGAATTCTGGGGAATTTTGGATTTTAGTTAGAGTACTTTGTTCTTTCGAGA
34176230 TTTCA-GATTTATTTGTTGAGATTATC
66 TTT-AGGATTTATTTGTTGAGATTATC
* * * *
34176256 TTAAGGGAATTCTGTGAATTTTGGGGAATTTTGGATTTTATTTAGAGTACTTTGTTCTTTTGAGA
1 TTAAGAGAATTCTGTGAATTCTGGGGAATTTTGGATTTTAGTTAGAGTACTTTGTTCTTTCGAGA
*
34176321 TTTAGGGTTTATTTGTTGAGATTATC
66 TTTAGGATTTATTTGTTGAGATTATC
34176347 TT
1 TT
34176349 TATCTTATAC
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 1 0.01
91 83 0.99
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (91 bp):
TTAAGAGAATTCTGTGAATTCTGGGGAATTTTGGATTTTAGTTAGAGTACTTTGTTCTTTCGAGA
TTTAGGATTTATTTGTTGAGATTATC
Found at i:34194812 original size:39 final size:39
Alignment explanation
Indices: 34194762--34194840 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
34194752 GTAATGTTTT
* * *
34194762 ACTATCGATCATTGATATCTATATTGATTAATAAAAGCA
1 ACTATCCATCATTGATATCTATATGGATCAATAAAAGCA
34194801 ACTATCCATCATTGATATCTATATGGATCAATAAAAGCA
1 ACTATCCATCATTGATATCTATATGGATCAATAAAAGCA
34194840 A
1 A
34194841 TTTATTAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (39 bp):
ACTATCCATCATTGATATCTATATGGATCAATAAAAGCA
Found at i:34197786 original size:30 final size:30
Alignment explanation
Indices: 34197690--34197792 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
34197680 TATTAAATTA
*
34197690 AATTTAATATTTATCTAGATAATATTTTATT
1 AATTTAATA-TTATCTATATAATATTTTATT
* * * **
34197721 AATTTAGTATTA-ATATGGT-ATATTAAATT
1 AATTTAATATTATCTAT-ATAATATTTTATT
34197750 AAATTTAATATTATCTATATAATATTTTATT
1 -AATTTAATATTATCTATATAATATTTTATT
*
34197781 CATTTAATATTA
1 AATTTAATATTA
34197793 ATGTAATTAA
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
29 10 0.18
30 27 0.48
31 19 0.34
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (30 bp):
AATTTAATATTATCTATATAATATTTTATT
Found at i:34197786 original size:60 final size:61
Alignment explanation
Indices: 34197679--34197794 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 61
34197669 AATGAATTTA
*
34197679 ATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATTTAGTATTAATATGGT
1 ATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATTTAATATTAATATGGT
* *
34197740 ATATTAAATTAAATTTAATA-TTATCTATATAATATTTTATTCATTTAATATTAAT
1 ATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATTTAATATTAAT
34197795 GTAATTAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 32 0.62
61 20 0.38
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (61 bp):
ATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATTTAATATTAATATGGT
Found at i:34198883 original size:40 final size:40
Alignment explanation
Indices: 34198789--34198898 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 40
34198779 CATTTGGATA
*
34198789 AAAAACGCCGCTAAAGATCGAGCATTAGC-GGCACTTTCC
1 AAAAACGCCGCTAAAGATCAAGCATTAGCGGGCACTTTCC
* * *
34198828 AAAAAGCGCCTCTAAAGATCTAGCATTAGCGGTGCA-TTAT-G
1 AAAAA-CGCCGCTAAAGATCAAGCATTAGCGG-GCACTT-TCC
* *
34198869 GAAAACGCCGCTAAAAAT-AAGCATTAGCGG
1 AAAAACGCCGCTAAAGATCAAGCATTAGCGG
34198899 CGCTTTTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
39 16 0.27
40 33 0.55
41 7 0.12
42 4 0.07
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGATCAAGCATTAGCGGGCACTTTCC
Found at i:34199003 original size:41 final size:41
Alignment explanation
Indices: 34198943--34199101 Score: 246
Period size: 41 Copynumber: 3.9 Consensus size: 41
34198933 CTGACCTTTT
* *
34198943 GGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
34198984 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
34199025 TGGGATTTAGCGGCGTTTTTGAAATAGCGCCGCTAATGCTC
1 GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
** *
34199066 TAGGATTTAGCAGCGTTTTTGAAAAAGCGCCGCTAA
1 GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
34199102 AAGCTTTTTA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 111 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (41 bp):
GGGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:34199131 original size:22 final size:21
Alignment explanation
Indices: 34199090--34199132 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
34199080 GTTTTTGAAA
*
34199090 AAGCGCCGCTAAAAGCTTTTT
1 AAGCGCCGCTAAAAACTTTTT
*
34199111 AAGCGCCGCTAAAAACATTTT
1 AAGCGCCGCTAAAAACTTTTT
34199132 A
1 A
34199133 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (21 bp):
AAGCGCCGCTAAAAACTTTTT
Found at i:34199484 original size:22 final size:22
Alignment explanation
Indices: 34199459--34199512 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
34199449 GAGTTATTAT
34199459 TTTAAGGTTTAGGGAGTATGGA
1 TTTAAGGTTTAGGGAGTATGGA
* * * *
34199481 TTTAGGGATTATGGATTATGGA
1 TTTAAGGTTTAGGGAGTATGGA
*
34199503 -TTATGGTTTA
1 TTTAAGGTTTA
34199513 ATTGTTCGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (22 bp):
TTTAAGGTTTAGGGAGTATGGA
Found at i:34199486 original size:15 final size:15
Alignment explanation
Indices: 34199466--34199497 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
34199456 TATTTTAAGG
34199466 TTTAGGGAGTATGGA
1 TTTAGGGAGTATGGA
*
34199481 TTTAGGGATTATGGA
1 TTTAGGGAGTATGGA
34199496 TT
1 TT
34199498 ATGGATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (15 bp):
TTTAGGGAGTATGGA
Found at i:34199498 original size:7 final size:7
Alignment explanation
Indices: 34199475--34199508 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
34199465 GTTTAGGGAG
34199475 TATGGATT
1 TATGGA-T
*
34199483 TAGGGAT
1 TATGGAT
34199490 TATGGAT
1 TATGGAT
34199497 TATGGAT
1 TATGGAT
34199504 TATGG
1 TATGG
34199509 TTTAATTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.41
Consensus pattern (7 bp):
TATGGAT
Found at i:34199505 original size:14 final size:15
Alignment explanation
Indices: 34199466--34199512 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
34199456 TATTTTAAGG
*
34199466 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
34199481 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
*
34199496 -TTATGGATTATGG-
1 TTTAGGGATTATGGA
34199509 TTTA
1 TTTA
34199513 ATTGTTCGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 15 0.52
15 14 0.48
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.43
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:34199743 original size:58 final size:58
Alignment explanation
Indices: 34199679--34200032 Score: 708
Period size: 58 Copynumber: 6.1 Consensus size: 58
34199669 ATTTTGTTTA
34199679 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
1 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
34199737 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
1 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
34199795 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
1 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
34199853 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
1 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
34199911 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
1 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
34199969 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
1 TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
34200027 TAAATA
1 TAAATA
34200033 AAATAATTTG
Statistics
Matches: 296, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 296 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.40
Consensus pattern (58 bp):
TAAATAGAATTAATAAATAAGTTTAAATAAAATATATTTAAACATTTAAATATTAGTT
Found at i:34204506 original size:43 final size:42
Alignment explanation
Indices: 34204374--34204508 Score: 162
Period size: 43 Copynumber: 3.2 Consensus size: 42
34204364 TGTTTTCAGT
* * * * * *
34204374 GGCGTTTTTGCGAGAAGCGTCGCTAAAGGTTTGTTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTATAGC
* * *
34204416 GGCGCTTGTGGGAAAACCGCTGCTAAAGGTCTCGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-GATCTATAGC
*
34204459 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TGATCTATAGC
34204502 GGCGTTT
1 GGCGTTT
34204509 ATTTTTAAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 24 0.31
43 53 0.68
44 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (42 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTATAGC
Found at i:34207159 original size:18 final size:18
Alignment explanation
Indices: 34207118--34207165 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
34207108 AGGTAGGATT
*
34207118 TGTATCTGTATTCGTATC
1 TGTATCAGTATTCGTATC
**
34207136 AATATCAGTATTCGTATC
1 TGTATCAGTATTCGTATC
*
34207154 TGTATCAATATT
1 TGTATCAGTATT
34207166 TGTAACTATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (18 bp):
TGTATCAGTATTCGTATC
Found at i:34208880 original size:26 final size:25
Alignment explanation
Indices: 34208842--34208920 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
34208832 TATTGGCTAC
* * *
34208842 TTTAAGTTGTTTCATATATTACTTA
1 TTTAAATTTTTTCATATATTATTTA
* *
34208867 TTTAAATTTCTTTC-TATGTTATTTT
1 TTTAAATTT-TTTCATATATTATTTA
*
34208892 TTTAAATTTTTTACATGTATTATTTA
1 TTTAAATTTTTT-CATATATTATTTA
34208918 TTT
1 TTT
34208921 TAGATTTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
24 3 0.07
25 25 0.58
26 15 0.35
ACGTcount: A:0.25, C:0.06, G:0.05, T:0.63
Consensus pattern (25 bp):
TTTAAATTTTTTCATATATTATTTA
Found at i:34214830 original size:45 final size:45
Alignment explanation
Indices: 34214757--34215061 Score: 217
Period size: 45 Copynumber: 6.8 Consensus size: 45
34214747 CATATCCAGC
* ** *
34214757 CTTGCCTTCCTGTACTGGTAGCGGAGCAGA-CTGAAGATAGCAGAT
1 CTTGCCTTCTTGTACTGACAGCGAAGCAGATC-GAAGATAGCAGAT
* * * *
34214802 TTTGCCTTCTTGTACTGACAGTGAAGCAGATCAAAGATAGCATAT
1 CTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGATAGCAGAT
* * * * * * *
34214847 TTTGCCTTTTTGTACCGACAGCGAAGTAGATCGAAGACACCAG-C
1 CTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGATAGCAGAT
* * *
34214891 CTTGCCTTCCTGTACTGACAGTGGAGCAGA-CTGAAGATAGCAGAT
1 CTTGCCTTCTTGTACTGACAGCGAAGCAGATC-GAAGATAGCAGAT
* * * * *
34214936 CCTGCCTTCTTGTACTAACAGCGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGATAGCAGAT
* * * * * * * *
34214980 CTTACCTTCCTG-AGTTTACAGTGGAGCAGATTGAAGATAACAGAT
1 CTTGCCTTCTTGTA-CTGACAGCGAAGCAGATCGAAGATAGCAGAT
* * * *
34215025 CTTGTCTTCCTGTA-TTAGCAGTGAAGCAGATCGAAGA
1 CTTGCCTTCTTGTACTGA-CAGCGAAGCAGATCGAAGA
34215062 CACCAACCTC
Statistics
Matches: 202, Mismatches: 50, Indels: 16
0.75 0.19 0.06
Matches are distributed among these distances:
43 2 0.01
44 66 0.33
45 131 0.65
46 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (45 bp):
CTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGATAGCAGAT
Found at i:34215269 original size:44 final size:44
Alignment explanation
Indices: 34214954--34215269 Score: 164
Period size: 44 Copynumber: 7.1 Consensus size: 44
34214944 CTTGTACTAA
* * *
34214954 CAGCGAAGCAGATCGAAGACACCAGCCTTACCTTCCTGAGTTTA
1 CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTAAGTTTG
* * * * * * *
34214998 CAGTGGAGCAGATTGAAGATAACAGATCTTGTCTTCCT--GTATTAG
1 CAGCGAAGCAGATCGAAGACACCAG-CCTTGCCTTCCTAAGT-TT-G
* * * * *
34215043 CAGTGAAGCAGATCGAAGACACCAACCTCGCCTCCCTAATTTTG
1 CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTAAGTTTG
* * * * *
34215087 CAGCAGAA-CAGATTGAAGATAGCAGATCTTGTCTTCCT--GTATTAG
1 CAGC-GAAGCAGATCGAAGACACCAG-CCTTGCCTTCCTAAGT-TT-G
* * ** *
34215132 CAGCGAAGTAGATCGAAGGCACCAGCCTCACC-TCCTTGAGTTTG
1 CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCC-TAAGTTTG
* * * * * *
34215176 CAGCGGAA-TAGA-CTAAAGATAGCAGACCTTGTCTTCCTATA-TTAG
1 CAGC-GAAGCAGATC-GAAGACACCAG-CCTTGCCTTCCTA-AGTTTG
* *
34215221 CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTAAGTTTG
1 CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTAAGTTTG
34215265 CAGCG
1 CAGCG
34215270 GAGTAGACTG
Statistics
Matches: 196, Mismatches: 55, Indels: 42
0.67 0.19 0.14
Matches are distributed among these distances:
43 8 0.04
44 93 0.47
45 87 0.44
46 8 0.04
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (44 bp):
CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTAAGTTTG
Found at i:34215310 original size:267 final size:267
Alignment explanation
Indices: 34214857--34215683 Score: 1033
Period size: 267 Copynumber: 3.1 Consensus size: 267
34214847 TTTGCCTTTT
* * ** * * * *
34214857 TGTACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCT-TCCTGTA-CTGACAGTGGAGCAG
1 TGTACAGACAGCGAAGCAGATCGAAGACACCAGCCTCACCTCT-CTG-AGTTTACAGCGGAACAG
* * * *
34214920 ACTGAAGATAGCAGATCC-TGCCTTCTTGTACTAACAGCGAAGCAGATCGAAGACACCAGCCTTA
64 ACTGAAGATAGCAGA-CCTTGTCTTCTTGTATTAGCAGCGAAGCAGATCGAAGACACCAGCCTCA
* * * * * * *
34214984 CCTTCCTGAGTTTACAGTGGAGCAGATTGAAGATA-ACAGATCTTGTCTTCCTGTATTAGCAGTG
128 CCTCCCTGAGTTTGCAGCGGAGTAGACTGAAGATAGA-AGATCTTGTCTTCCTATATTAGCAGCG
* * * * *
34215048 AAGCAGATCGAAGACACCAACCTCGCCTCCCTAATTTTGCAGCAGAACAGATTGAAGATAGCAGA
192 AAGCAGATCAAAGACACCAGCCTCGCCTCCCTAAGTTTGCAGCAGAGCAGACTGAAGATAGCAGA
34215113 TCTTGTCTTCC
257 TCTTGTCTTCC
* * * * *
34215124 TGTATTAG-CAGCGAAGTAGATCGAAGGCACCAGCCTCACCTC-CTTGAGTTTGCAGCGGAATAG
1 TGTA-CAGACAGCGAAGCAGATCGAAGACACCAGCCTCACCTCTC-TGAGTTTACAGCGGAACAG
* * * *
34215187 ACTAAAGATAGCAGACCTTGTCTTCCTATATTAGCAGCGAAGCAGATCGAAGACACCAGCCTCGC
64 ACTGAAGATAGCAGACCTTGTCTTCTTGTATTAGCAGCGAAGCAGATCGAAGACACCAGCCTCAC
* *
34215252 CTCCCTAAGTTTGCAGCGGAGTAGACTGAAGATAGAAGATCTTGTCATCCTATATTAGCAGCGAA
129 CTCCCTGAGTTTGCAGCGGAGTAGACTGAAGATAGAAGATCTTGTCTTCCTATATTAGCAGCGAA
* * *
34215317 GCAGATCAAAAACACTC-GCCTCGCCTCCCTGAGTTTACAGCAGAGCAGACTGAAGATAGCAGAT
194 GCAGATCAAAGACAC-CAGCCTCGCCTCCCTAAGTTTGCAGCAGAGCAGACTGAAGATAGCAGAT
*
34215381 CTTGTCTTTC
258 CTTGTCTTCC
*
34215391 TGTACCGACAGCGAAGCAGATCGAAGACACCAGCCTCACCTCTCTGAGTTTACAGCGGAACAGAC
1 TGTACAGACAGCGAAGCAGATCGAAGACACCAGCCTCACCTCTCTGAGTTTACAGCGGAACAGAC
* * *
34215456 TGAAGATAGTAGATCTTGTCTTCTTGTATTAGCAGCGAAGCAGATCGAAGACACTAGCCTCACCT
66 TGAAGATAGCAGACCTTGTCTTCTTGTATTAGCAGCGAAGCAGATCGAAGACACCAGCCTCACCT
* * *
34215521 CCCTGAGTTTGCAGCGGAATA-ACTGAAAATAGTAGATCTTGTCTTCCTATATT-GACAGCGAAG
131 CCCTGAGTTTGCAGCGGAGTAGACTGAAGATAGAAGATCTTGTCTTCCTATATTAG-CAGCGAAG
* ** *
34215584 CAGATCAAAGACACCAGCCTCGCCTCCCTAAGTTTGTAGTGGAGCAGACTGAAGATAGCAGATAT
195 CAGATCAAAGACACCAGCCTCGCCTCCCTAAGTTTGCAGCAGAGCAGACTGAAGATAGCAGATCT
* *
34215649 TATCTTGC
260 TGTCTTCC
* *
34215657 TATACCGACAGCGAAGCAGATCGAAGA
1 TGTACAGACAGCGAAGCAGATCGAAGA
34215684 TACTAATCCT
Statistics
Matches: 484, Mismatches: 65, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
265 2 0.00
266 130 0.27
267 348 0.72
268 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (267 bp):
TGTACAGACAGCGAAGCAGATCGAAGACACCAGCCTCACCTCTCTGAGTTTACAGCGGAACAGAC
TGAAGATAGCAGACCTTGTCTTCTTGTATTAGCAGCGAAGCAGATCGAAGACACCAGCCTCACCT
CCCTGAGTTTGCAGCGGAGTAGACTGAAGATAGAAGATCTTGTCTTCCTATATTAGCAGCGAAGC
AGATCAAAGACACCAGCCTCGCCTCCCTAAGTTTGCAGCAGAGCAGACTGAAGATAGCAGATCTT
GTCTTCC
Found at i:34215516 original size:89 final size:89
Alignment explanation
Indices: 34214865--34215683 Score: 923
Period size: 89 Copynumber: 9.2 Consensus size: 89
34214855 TTTGTACCGA
* * * * *
34214865 CAGCGAAGTAGATCGAAGACACCAGCCTTGCCTTCCT--GTACTGACAGTGGAGCAGACTGAAGA
1 CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGAGT-TTG-CAGCGGAGCAGACTGAAGA
* * * * *
34214928 TAGCAGATCCTGCCTTCTTGTACTAA
64 TAGCAGATCTTGTCTTCCTGTATTAG
** * * * *
34214954 CAGCGAAGCAGATCGAAGACACCAGCCTTACCTTCCTGAGTTTACAGTGGAGCAGATTGAAGATA
1 CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGATA
*
34215019 ACAGATCTTGTCTTCCTGTATTAG
66 GCAGATCTTGTCTTCCTGTATTAG
* * * * * * *
34215043 CAGTGAAGCAGATCGAAGACACCAACCTCGCCTCCCTAATTTTGCAGCAGAACAGATTGAAGATA
1 CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGATA
34215108 GCAGATCTTGTCTTCCTGTATTAG
66 GCAGATCTTGTCTTCCTGTATTAG
* * * * ** *
34215132 CAGCGAAGTAGATCGAAGGCACCAGCCTCACCTCCTTGAGTTTGCAGCGGAATAGACTAAAGATA
1 CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGATA
* *
34215197 GCAGACCTTGTCTTCCTATATTAG
66 GCAGATCTTGTCTTCCTGTATTAG
* *
34215221 CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTAAGTTTGCAGCGGAGTAGACTGAAGATA
1 CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGATA
* * *
34215286 GAAGATCTTGTCATCCTATATTAG
66 GCAGATCTTGTCTTCCTGTATTAG
* * * *
34215310 CAGCGAAGCAGATCAAAAACACTC-GCCTCGCCTCCCTGAGTTTACAGCAGAGCAGACTGAAGAT
1 CAGCGAAGCAGATCGAAGACAC-CAGCCTCGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGAT
* **
34215374 AGCAGATCTTGTCTTTCTGTA-CCG
65 AGCAGATCTTGTCTTCCTGTATTAG
* * * *
34215398 ACAGCGAAGCAGATCGAAGACACCAGCCTCACCTCTCTGAGTTTACAGCGGAACAGACTGAAGAT
1 -CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGAT
* *
34215463 AGTAGATCTTGTCTTCTTGTATTAG
65 AGCAGATCTTGTCTTCCTGTATTAG
* * ** *
34215488 CAGCGAAGCAGATCGAAGACACTAGCCTCACCTCCCTGAGTTTGCAGCGGAATA-ACTGAAAATA
1 CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGATA
* *
34215552 GTAGATCTTGTCTTCCTATATT-G
66 GCAGATCTTGTCTTCCTGTATTAG
* * * *
34215575 ACAGCGAAGCAGATCAAAGACACCAGCCTCGCCTCCCTAAGTTTGTAGTGGAGCAGACTGAAGAT
1 -CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGAT
* * * * **
34215640 AGCAGATATTATCTTGCTATA-CCG
65 AGCAGATCTTGTCTTCCTGTATTAG
34215664 ACAGCGAAGCAGATCGAAGA
1 -CAGCGAAGCAGATCGAAGA
34215684 TACTAATCCT
Statistics
Matches: 629, Mismatches: 92, Indels: 18
0.85 0.12 0.02
Matches are distributed among these distances:
87 1 0.00
88 77 0.12
89 546 0.87
90 3 0.00
91 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (89 bp):
CAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCCCTGAGTTTGCAGCGGAGCAGACTGAAGATA
GCAGATCTTGTCTTCCTGTATTAG
Found at i:34215768 original size:44 final size:44
Alignment explanation
Indices: 34215688--34215804 Score: 123
Period size: 44 Copynumber: 2.6 Consensus size: 44
34215678 CGAAGATACT
* *
34215688 AATCCTACCTCCTTGAAGTTGCAGTGGAGTGAATTAAA-AT-GA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGAATTAAAGATAGA
* *
34215730 TGGATCCTATCTCCCTGAAGTTGCAGTGGA-TTAGATTAAAGATAGCA
1 --AATCCTATCTCCCTGAAGTTGCAGTGGAGTGA-ATTAAAGATAG-A
* *
34215777 AATCGTATTTCCCTGAAGTTGCAGTGGA
1 AATCCTATCTCCCTGAAGTTGCAGTGGA
34215805 ACAAATTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
43 2 0.03
44 31 0.50
45 27 0.44
46 1 0.02
47 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGTGAATTAAAGATAGA
Found at i:34215994 original size:44 final size:44
Alignment explanation
Indices: 34215872--34216257 Score: 219
Period size: 44 Copynumber: 8.6 Consensus size: 44
34215862 ATATCAAACT
* * * ** **
34215872 TTATCTCTCTGAAGTTGCAATAGAGCAGGTTGAA-ATAACAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-ACAAGTC
* * *
34215916 TTATC-CCCATGAAGTTGTAGTGGGGCA-AGTTGAAGATACAAGTC
1 TTATCTCCC-TGAAGTTGCAGTGGAGCAGA-CTGAAGATACAAGTC
* *
34215960 TTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGTTACTAA-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAC-AAGTC
* * * * * * **
34216004 CTACCTCCCTGAAGTTGCAGTTGAGCGGA-TTAAAATGA-TGGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-ACAAG-TC
* * * *
34216048 CTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-ACAAGTC
* * * * * * * * *
34216093 TTATTTCCCTGAAATTTCAATGGAACAGATTAAATCTATCATAACAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA--GAT-A-CA-AG-TC
* ** * **
34216143 TCATCTTTCTGAAGTTGCAGTGGGGCAGACTGAAGATAGTGAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-CAAGTC
*
34216188 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACTAA-TC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAC-AAGTC
*
34216232 CTATCTCCCTGAAGTTGCAGTGGAGC
1 TTATCTCCCTGAAGTTGCAGTGGAGC
34216258 GGATTAAAAC
Statistics
Matches: 262, Mismatches: 63, Indels: 34
0.73 0.18 0.09
Matches are distributed among these distances:
43 6 0.02
44 141 0.54
45 80 0.31
46 2 0.01
47 4 0.02
48 3 0.01
49 1 0.00
50 25 0.10
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAGTC
Found at i:34216216 original size:45 final size:44
Alignment explanation
Indices: 34215915--34216257 Score: 226
Period size: 44 Copynumber: 7.6 Consensus size: 44
34215905 AATAACAAAC
* * * *
34215915 CTTATC-CCCATGAAGTTGTAGTGGGGCA-AGTTGAAGATACAAGT
1 CTTATCTCCC-TGAAGTTGCAGTGGAGCAGA-CTGAAGATACTAGT
* * *
34215959 CTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGTTACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAGT
* * * * * * *
34216003 CCTACCTCCCTGAAGTTGCAGTTGAGCGGA-TTAAAATGA-TGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-ACTAG-T
* * * * *
34216047 CCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-ACTAGT
* * * * * * * **
34216092 CTTATTTCCCTGAAATTTCAATGGAACAGATTAAATCTATCATAACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-C-T---AG-T
* ** * *
34216142 CTCATCTTTCTGAAGTTGCAGTGGGGCAGACTGAAGATAGTGAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACT-AGT
* *
34216187 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAGT
*
34216231 CCTATCTCCCTGAAGTTGCAGTGGAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGC
34216258 GGATTAAAAC
Statistics
Matches: 230, Mismatches: 57, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
43 5 0.02
44 116 0.50
45 78 0.34
46 2 0.01
48 1 0.00
49 1 0.00
50 27 0.12
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACTAGT
Found at i:34218014 original size:30 final size:30
Alignment explanation
Indices: 34217980--34218039 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
34217970 TCAGATTTTA
34217980 ATTTAATCCTTAACCTCTAATTCTAACCTT
1 ATTTAATCCTTAACCTCTAATTCTAACCTT
34218010 ATTTAATCCTTAACCTCTAATTCTAACCTT
1 ATTTAATCCTTAACCTCTAATTCTAACCTT
34218040 TTACAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (30 bp):
ATTTAATCCTTAACCTCTAATTCTAACCTT
Found at i:34219526 original size:190 final size:190
Alignment explanation
Indices: 34219203--34219583 Score: 753
Period size: 190 Copynumber: 2.0 Consensus size: 190
34219193 TTTCTAAATT
*
34219203 TCGTGGACCAAAATTGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCACTTTTCGAGG
1 TCGTGGACAAAAATTGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCACTTTTCGAGG
34219268 TGATCCGATCACACTTCATCAACAAAAAAGGATTGGTGACGACTTCCATTTTCGTTTTCATCTTT
66 TGATCCGATCACACTTCATCAACAAAAAAGGATTGGTGACGACTTCCATTTTCGTTTTCATCTTT
34219333 AAAAGCCAAGTCGACCCCCTTTTACAAAAAATGGTGTCAACAGGAACTATATGTTTTTTG
131 AAAAGCCAAGTCGACCCCCTTTTACAAAAAATGGTGTCAACAGGAACTATATGTTTTTTG
34219393 TCGTGGACAAAAATTGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCACTTTTCGAGG
1 TCGTGGACAAAAATTGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCACTTTTCGAGG
34219458 TGATCCGATCACACTTCATCAACAAAAAAGGATTGGTGACGACTTCCATTTTCGTTTTCATCTTT
66 TGATCCGATCACACTTCATCAACAAAAAAGGATTGGTGACGACTTCCATTTTCGTTTTCATCTTT
34219523 AAAAGCCAAGTCGACCCCCTTTTACAAAAAATGGTGTCAACAGGAACTATATGTTTTTTG
131 AAAAGCCAAGTCGACCCCCTTTTACAAAAAATGGTGTCAACAGGAACTATATGTTTTTTG
34219583 T
1 T
34219584 TTTTGAATTG
Statistics
Matches: 190, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
190 190 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (190 bp):
TCGTGGACAAAAATTGTTGTTTTAATAAAATCAAATCGTTTATTAAAAACAACCACTTTTCGAGG
TGATCCGATCACACTTCATCAACAAAAAAGGATTGGTGACGACTTCCATTTTCGTTTTCATCTTT
AAAAGCCAAGTCGACCCCCTTTTACAAAAAATGGTGTCAACAGGAACTATATGTTTTTTG
Found at i:34221096 original size:26 final size:26
Alignment explanation
Indices: 34221060--34221111 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
34221050 ATAACTTTTT
34221060 TTTATTTACCAAAATATATAAAAAAA
1 TTTATTTACCAAAATATATAAAAAAA
34221086 TTTATTTACCAAAATATATAAAAAAA
1 TTTATTTACCAAAATATATAAAAAAA
34221112 CCAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (26 bp):
TTTATTTACCAAAATATATAAAAAAA
Found at i:34221204 original size:27 final size:27
Alignment explanation
Indices: 34221174--34221240 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
34221164 CGCCAATGGG
34221174 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* * *
34221201 ATTGGCGGCACCAATGGTGCCAATATC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
34221228 ATTGGCGGCACCA
1 ATTGGCGGCACCA
34221241 GTTAGTAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:34221294 original size:4 final size:4
Alignment explanation
Indices: 34221285--34221353 Score: 61
Period size: 4 Copynumber: 17.2 Consensus size: 4
34221275 GAAGGAGAGG
* * * *
34221285 GAAA GAAA GAAA GAAA GAGA GAAA GAAA GGAA GAAA GGAGAG GGAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA
*
34221335 G-AA -AAA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA G
34221354 GGAAAGGAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
3 4 0.08
4 43 0.84
5 3 0.06
6 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:34221333 original size:38 final size:38
Alignment explanation
Indices: 34221276--34221363 Score: 115
Period size: 42 Copynumber: 2.2 Consensus size: 38
34221266 GGGGGGCCAG
34221276 AAGGAGAGGGAAAGAAAGAAAGAA-AGAGAGAAAGAAAGGAAGA
1 AAGGAGAGGG-AAGAAAGAAA-AAGA-AG-GAAAGAAAGG--GA
34221319 AAGGAGAGGGAAGAAAGAAAAAGAAGGAAAGAAAGGGA
1 AAGGAGAGGGAAGAAAGAAAAAGAAGGAAAGAAAGGGA
34221357 AAGGAGA
1 AAGGAGA
34221364 AGAGAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
38 9 0.20
40 10 0.23
41 4 0.09
42 11 0.25
43 10 0.23
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (38 bp):
AAGGAGAGGGAAGAAAGAAAAAGAAGGAAAGAAAGGGA
Found at i:34235593 original size:16 final size:15
Alignment explanation
Indices: 34235572--34235653 Score: 60
Period size: 16 Copynumber: 5.3 Consensus size: 15
34235562 CTAAGTGGGA
34235572 ATATCCCATTTCAGGG
1 ATATCCCATTT-AGGG
34235588 ATATCCCAATTTTA--G
1 ATATCCC-A-TTTAGGG
**
34235603 ATATCCCAAATAGGG
1 ATATCCCATTTAGGG
* *
34235618 ATATCTCAGTTTGGGG
1 ATATCCCA-TTTAGGG
*
34235634 ATATCCCATTCTAAGG
1 ATATCCCATT-TAGGG
34235650 ATAT
1 ATAT
34235654 TCCGCGTTGG
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
13 2 0.04
14 1 0.02
15 18 0.35
16 25 0.49
17 2 0.04
18 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (15 bp):
ATATCCCATTTAGGG
Found at i:34236266 original size:21 final size:22
Alignment explanation
Indices: 34236242--34236284 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
34236232 ATAATCAATC
34236242 AAATAATACAAT-AT-AATTTAA
1 AAATAATA-AATAATAAATTTAA
*
34236263 AAATTATAAATAATAAATTTAA
1 AAATAATAAATAATAAATTTAA
34236285 TTCACTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 9 0.47
22 7 0.37
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATAATAAATAATAAATTTAA
Found at i:34239394 original size:51 final size:51
Alignment explanation
Indices: 34239317--34239633 Score: 503
Period size: 51 Copynumber: 6.3 Consensus size: 51
34239307 ACTTTTGATC
* * *
34239317 AGTGACAAGTGATAAATGGTACCTTTAGCTACACTTATCTGATTAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
34239368 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
34239419 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
34239470 AGTGACAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATTAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * *
34239520 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * * *
34239571 AATGGCAAGTGATAAGTGGTAGC-TTAGCTATACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
34239621 AGTGATAAGTGAT
1 AGTGACAAGTGAT
34239634 CGTACGCAAG
Statistics
Matches: 247, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
50 80 0.32
51 167 0.68
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:34239550 original size:101 final size:101
Alignment explanation
Indices: 34239317--34239633 Score: 508
Period size: 101 Copynumber: 3.1 Consensus size: 101
34239307 ACTTTTGATC
* * *
34239317 AGTGACAAGTGATAAATGGTACCTTTAGCTACACTTATCTGATTAGTGACAAGTGACAAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
34239382 AGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
66 AGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
34239419 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
* *
34239484 AGTGGTAGCCTAGCTACACTTATCTGATTAGTGACA
66 AGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
* * * * *
34239520 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAATGGCAAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
* *
34239585 AGTGGTAGCTTAGCTATACTTATCTGATCAGGGACA
66 AGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
34239621 AGTGATAAGTGAT
1 AGTGACAAGTGAT
34239634 CGTACGCAAG
Statistics
Matches: 199, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
101 128 0.64
102 71 0.36
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (101 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
AGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:34239582 original size:152 final size:151
Alignment explanation
Indices: 34239317--34239633 Score: 519
Period size: 152 Copynumber: 2.1 Consensus size: 151
34239307 ACTTTTGATC
34239317 AGTGACAAGTGATAAATGGTACCTTTAGCTACACTTATCTGATTAGTGACAAGTGACAAGTGATA
1 AGTGACAAGTGATAAATGGTACC-TTAGCTACACTTATCTGATTAGTGACAAGTGACAAGTGATA
* * *
34239382 AGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAG
65 AGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAATGACAAGTGATAAGTGGTAGC-TTAG
*
34239447 CTACACTTATCTGATCAGTGACA
129 CTACACTTATCTGATCAGGGACA
* *
34239470 AGTGACAAGTGATAAGTGGTAGCC-TAGCTACACTTATCTGATTAGTGACAAGTGGCAAGTGATA
1 AGTGACAAGTGATAAATGGTA-CCTTAGCTACACTTATCTGATTAGTGACAAGTGACAAGTGATA
*
34239534 AGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAATGGCAAGTGATAAGTGGTAGCTTAGC
65 AGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAATGACAAGTGATAAGTGGTAGCTTAGC
*
34239599 TATACTTATCTGATCAGGGACA
130 TACACTTATCTGATCAGGGACA
*
34239621 AGTGATAAGTGAT
1 AGTGACAAGTGAT
34239634 CGTACGCAAG
Statistics
Matches: 154, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
151 37 0.24
152 95 0.62
153 20 0.13
154 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (151 bp):
AGTGACAAGTGATAAATGGTACCTTAGCTACACTTATCTGATTAGTGACAAGTGACAAGTGATAA
GTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAATGACAAGTGATAAGTGGTAGCTTAGCT
ACACTTATCTGATCAGGGACA
Found at i:34242677 original size:26 final size:27
Alignment explanation
Indices: 34242648--34242700 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
34242638 TATAACTTTT
34242648 TTTATTTACCAAAATATAT-AAAAAAA
1 TTTATTTACCAAAATATATCAAAAAAA
34242674 TTTATTTACCAAAATATATCAAAAAAA
1 TTTATTTACCAAAATATATCAAAAAAA
34242701 CTGCAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (27 bp):
TTTATTTACCAAAATATATCAAAAAAA
Found at i:34242707 original size:11 final size:11
Alignment explanation
Indices: 34242693--34242721 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
34242683 CAAAATATAT
34242693 CAAAAAAACTG
1 CAAAAAAACTG
34242704 C-AAAAAACTG
1 CAAAAAAACTG
34242714 CAAAAAAA
1 CAAAAAAA
34242722 TCAGATCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.69, C:0.17, G:0.07, T:0.07
Consensus pattern (11 bp):
CAAAAAAACTG
Found at i:34242718 original size:9 final size:10
Alignment explanation
Indices: 34242695--34242720 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
34242685 AAATATATCA
34242695 AAAAAACTGC
1 AAAAAACTGC
34242705 AAAAAACTGC
1 AAAAAACTGC
34242715 AAAAAA
1 AAAAAA
34242721 ATCAGATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.15, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAACTGC
Found at i:34242781 original size:27 final size:27
Alignment explanation
Indices: 34242751--34242826 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
34242741 AACTGGTCAC
*
34242751 GCCAATGTAATTGGCGGCACCAAAGGT
1 GCCAATGTCATTGGCGGCACCAAAGGT
*** *
34242778 GCCAAAACCATTGGCGGCACCAATGGT
1 GCCAATGTCATTGGCGGCACCAAAGGT
34242805 GCCAATGTCATTGGCGGCACCA
1 GCCAATGTCATTGGCGGCACCA
34242827 CTCGTATTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (27 bp):
GCCAATGTCATTGGCGGCACCAAAGGT
Found at i:34246582 original size:16 final size:16
Alignment explanation
Indices: 34246561--34246610 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
34246551 CCAACGCGGA
34246561 ATATCCTTAGAATGGG
1 ATATCCTTAGAATGGG
* **
34246577 ATATCCCTA-TTTGGG
1 ATATCCTTAGAATGGG
*
34246592 ATAT-CTAAGAATGGG
1 ATATCCTTAGAATGGG
34246607 ATAT
1 ATAT
34246611 TCCCACTTGG
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
14 2 0.08
15 16 0.62
16 8 0.31
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (16 bp):
ATATCCTTAGAATGGG
Found at i:34253534 original size:140 final size:141
Alignment explanation
Indices: 34253256--34253537 Score: 503
Period size: 140 Copynumber: 2.0 Consensus size: 141
34253246 CATCATATTT
* *
34253256 GAGTAGAAATTGCTAATAGTTAAAACGTAAAGTACTTCCAAACATACGTTCTTGATTTAAAGTAA
1 GAGTAGAAATTGCTAATAATTAAAACGTAAAGTACTTCCAAACATACGTTCTTAATTTAAAGT-A
*
34253321 AAAAAACCATGCATTTTTTTCTTCCAAAAAAAGGCTTCAGAATTCTGAAATGTTTTGCTTACAGC
65 AAAAAACCATGCATTTTTTTCTTCCAAAAAAAGGCTTCAGAATTCTAAAATGTTTTGCTTACAGC
34253386 AATAGCAACGAC
130 AATAGCAACGAC
*
34253398 GAGTTGAAATTGCTAATAATTAAAACGTAAAGTACTTCCAAACATACGTTCTTAATTTAAAGT-A
1 GAGTAGAAATTGCTAATAATTAAAACGTAAAGTACTTCCAAACATACGTTCTTAATTTAAAGTAA
*
34253462 AAAAACCGTGCATTTTTTTCTTCCAAAAAAAGGCTTCAGAATTCTAAAATGTTTTGCTTACAGCA
66 AAAAACCATGCATTTTTTTCTTCCAAAAAAAGGCTTCAGAATTCTAAAATGTTTTGCTTACAGCA
34253527 ATAGCAACGAC
131 ATAGCAACGAC
34253538 ACAAAAAAAG
Statistics
Matches: 135, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
140 75 0.56
142 60 0.44
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (141 bp):
GAGTAGAAATTGCTAATAATTAAAACGTAAAGTACTTCCAAACATACGTTCTTAATTTAAAGTAA
AAAAACCATGCATTTTTTTCTTCCAAAAAAAGGCTTCAGAATTCTAAAATGTTTTGCTTACAGCA
ATAGCAACGAC
Found at i:34259005 original size:113 final size:114
Alignment explanation
Indices: 34258865--34259106 Score: 461
Period size: 113 Copynumber: 2.1 Consensus size: 114
34258855 ATTTGACTAA
*
34258865 TAATAATATTAA-AATAAAATAAAAAAAATTGTATTTTATATTTCAAAATTTTCATGACATTTTG
1 TAATAATAATAATAATAAAATAAAAAAAATTGTATTTTATATTTCAAAATTTTCATGACATTTTG
34258929 GTTTACTTTAAGTTATCAAAACTCTATACTCTTAAAAATTTAGTGATTT
66 GTTTACTTTAAGTTATCAAAACTCTATACTCTTAAAAATTTAGTGATTT
34258978 TAATAATAATAATAATAAAAT-AAAAAAATTGTATTTTATATTTCAAAATTTTCATGACATTTTG
1 TAATAATAATAATAATAAAATAAAAAAAATTGTATTTTATATTTCAAAATTTTCATGACATTTTG
34259042 GTTTACTTTAAGTTATCAAAACTCTATACTCTTAAAAATTTAGTGATTT
66 GTTTACTTTAAGTTATCAAAACTCTATACTCTTAAAAATTTAGTGATTT
34259091 TAATAATAATAATAAT
1 TAATAATAATAATAAT
34259107 TTAAAGTTGA
Statistics
Matches: 127, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
113 119 0.94
114 8 0.06
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (114 bp):
TAATAATAATAATAATAAAATAAAAAAAATTGTATTTTATATTTCAAAATTTTCATGACATTTTG
GTTTACTTTAAGTTATCAAAACTCTATACTCTTAAAAATTTAGTGATTT
Found at i:34266723 original size:23 final size:22
Alignment explanation
Indices: 34266692--34266736 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
34266682 TATTATGTAT
34266692 TATTATATTAAGTTTCTTCATA
1 TATTATATTAAGTTTCTTCATA
*
34266714 TATTAATATTTAGTTTCTTCATA
1 TATT-ATATTAAGTTTCTTCATA
34266737 AATCATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (22 bp):
TATTATATTAAGTTTCTTCATA
Found at i:34266950 original size:24 final size:25
Alignment explanation
Indices: 34266905--34266958 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
34266895 ATCTATACAT
34266905 TTTTATAATATATATATGTACATATA
1 TTTTATAATATATATA-GTACATATA
34266931 TTTTATAAT-TCATATA-TACATATA
1 TTTTATAATAT-ATATAGTACATATA
34266955 TTTT
1 TTTT
34266959 TGTTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 12 0.44
25 1 0.04
26 14 0.52
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTTATAATATATATAGTACATATA
Found at i:34267023 original size:4 final size:4
Alignment explanation
Indices: 34267016--34267042 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
34267006 TATATATAGT
34267016 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
34267043 TTATTTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:34271198 original size:43 final size:43
Alignment explanation
Indices: 34271041--34271199 Score: 155
Period size: 43 Copynumber: 3.7 Consensus size: 43
34271031 TATGTGATAT
*
34271041 CGTGTAAGACTACGTCTGGGACATTGGCATCG-ATTTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTT--GATTTA
*** *
34271085 CGTGTAAGACCATACCTGGGACATTGGCATCGTATATGATTT-
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTTA
* * * *
34271127 TGTGTAAGA-CATTGTCTAGGACAATGGCATCGTTATTTG-TTTA
1 CGTGTAAGACCA-CGTCTGGGACATTGGCATCG-TATTTGATTTA
* *
34271170 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACATTGGCAT
34271200 TGTACGAGCT
Statistics
Matches: 93, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
41 2 0.02
42 27 0.29
43 31 0.33
44 30 0.32
45 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTTA
Found at i:34276039 original size:13 final size:13
Alignment explanation
Indices: 34276018--34276050 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
34276008 ATTTATAAGT
34276018 TTATT-ATATATA
1 TTATTAATATATA
34276030 TTATTAATATATA
1 TTATTAATATATA
*
34276043 TTCTTAAT
1 TTATTAAT
34276051 GATTAAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (13 bp):
TTATTAATATATA
Found at i:34276088 original size:9 final size:9
Alignment explanation
Indices: 34276058--34276082 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
34276048 AATGATTAAG
34276058 TATATATAT
1 TATATATAT
34276067 TATATATAT
1 TATATATAT
34276076 TATATAT
1 TATATAT
34276083 TATATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATATATAT
Found at i:34276140 original size:34 final size:34
Alignment explanation
Indices: 34276101--34276176 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
34276091 AAAAACAAAT
*
34276101 AAAGAAATAAAAAGAAATAGAAA-GAACA-AACGAG
1 AAAGAAATAAAAAGAAA-AGAAAGGAA-AGAAAGAG
* * *
34276135 AAAGAAAGAAACAGAAAGGAAAGGAAAGAAAGAG
1 AAAGAAATAAAAAGAAAAGAAAGGAAAGAAAGAG
34276169 AAAGAAAT
1 AAAGAAAT
34276177 GTTAGGGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 5 0.14
34 30 0.86
ACGTcount: A:0.70, C:0.04, G:0.22, T:0.04
Consensus pattern (34 bp):
AAAGAAATAAAAAGAAAAGAAAGGAAAGAAAGAG
Found at i:34276150 original size:10 final size:9
Alignment explanation
Indices: 34276101--34276175 Score: 53
Period size: 10 Copynumber: 7.8 Consensus size: 9
34276091 AAAAACAAAT
*
34276101 AAAGAAATAA
1 AAAGAAA-AG
34276111 AAAGAAATAG
1 AAAGAAA-AG
*
34276121 AAAGAACA-
1 AAAGAAAAG
*
34276129 AACGAGAAAG
1 AAAGA-AAAG
34276139 AAAGAAACAG
1 AAAGAAA-AG
*
34276149 AAAGGAAAGG
1 AAA-GAAAAG
34276159 AAAGAAAGAG
1 AAAGAAA-AG
34276169 AAAGAAA
1 AAAGAAA
34276176 TGTTAGGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
8 4 0.08
9 9 0.17
10 36 0.68
11 4 0.08
ACGTcount: A:0.71, C:0.04, G:0.23, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:34276150 original size:14 final size:14
Alignment explanation
Indices: 34276111--34276167 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
34276101 AAAGAAATAA
*
34276111 AAAGAAATAGAAAG
1 AAAGAAACAGAAAG
*
34276125 -AACAAACGAGAAAG
1 AAAGAAAC-AGAAAG
34276139 AAAGAAACAGAAAGG
1 AAAGAAACAGAAA-G
*
34276154 AAAGGAA-AGAAAG
1 AAAGAAACAGAAAG
34276167 A
1 A
34276168 GAAAGAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
13 7 0.19
14 16 0.44
15 13 0.36
ACGTcount: A:0.68, C:0.05, G:0.25, T:0.02
Consensus pattern (14 bp):
AAAGAAACAGAAAG
Found at i:34276163 original size:20 final size:19
Alignment explanation
Indices: 34276134--34276172 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
34276124 GAACAAACGA
34276134 GAAAGAAAGAAACAGAAAG
1 GAAAGAAAGAAACAGAAAG
*
34276153 GAAAGGAAAGAAAGAGAAAG
1 GAAA-GAAAGAAACAGAAAG
34276173 AAATGTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (19 bp):
GAAAGAAAGAAACAGAAAG
Found at i:34276175 original size:14 final size:14
Alignment explanation
Indices: 34276111--34276175 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
34276101 AAAGAAATAA
*
34276111 AAAGAAATAGAAAG
1 AAAGAAAGAGAAAG
*
34276125 AACA-AACGAGAAAG
1 AA-AGAAAGAGAAAG
*
34276139 AAAGAAACAGAAAGG
1 AAAGAAAGAGAAA-G
34276154 AAAGGAAAGA-AAGAG
1 AAA-GAAAGAGAA-AG
34276169 AAAGAAA
1 AAAGAAA
34276176 TGTTAGGGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 1 0.02
14 23 0.56
15 11 0.27
16 6 0.15
ACGTcount: A:0.69, C:0.05, G:0.25, T:0.02
Consensus pattern (14 bp):
AAAGAAAGAGAAAG
Found at i:34277090 original size:41 final size:41
Alignment explanation
Indices: 34277031--34277144 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 41
34277021 CTCGACTTCA
34277031 AGTCGATGAGACACTGGGTGTCAAATTATTACTTCGGATAT
1 AGTCGATGAGACACTGGGTGTCAAATTATTACTTCGGATAT
* * * * *
34277072 ATTCGATGAGGCATTGGGTG-CCAA-T-TTACTTC-GATTT
1 AGTCGATGAGACACTGGGTGTCAAATTATTACTTCGGATAT
*
34277109 AGCCGATGAGACACTGGGTGTCAAATTATTACTTCG
1 AGTCGATGAGACACTGGGTGTCAAATTATTACTTCG
34277145 AAATATCTGA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
37 20 0.34
38 10 0.17
39 2 0.03
40 10 0.17
41 17 0.29
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (41 bp):
AGTCGATGAGACACTGGGTGTCAAATTATTACTTCGGATAT
Found at i:34277174 original size:40 final size:40
Alignment explanation
Indices: 34277035--34277175 Score: 137
Period size: 40 Copynumber: 3.6 Consensus size: 40
34277025 ACTTCAAGTC
* *
34277035 GATGAGACACTGGGTGTCAAATTATTACTTCGGATATAT-T
1 GATGAGGCACTGGGTGCCAAATTATTACTTC-GATATATCT
* * * *
34277075 CGATGAGGCATTGGGTGCC-AA-T-TTACTTCGATTTAGCC
1 -GATGAGGCACTGGGTGCCAAATTATTACTTCGATATATCT
* * *
34277113 GATGAGACACTGGGTGTCAAATTATTACTTCGAAATATCT
1 GATGAGGCACTGGGTGCCAAATTATTACTTCGATATATCT
* *
34277153 GATAAGGCACTAGGTGCCAAATT
1 GATGAGGCACTGGGTGCCAAATT
34277176 GGTGTATTGG
Statistics
Matches: 79, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
37 20 0.25
38 9 0.11
39 2 0.03
40 33 0.42
41 15 0.19
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (40 bp):
GATGAGGCACTGGGTGCCAAATTATTACTTCGATATATCT
Found at i:34288186 original size:37 final size:37
Alignment explanation
Indices: 34288136--34288209 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
34288126 AATTTTAATA
34288136 ATGATAGTAATAACAATAGTTAAACGGAACTTACAGT
1 ATGATAGTAATAACAATAGTTAAACGGAACTTACAGT
34288173 ATGATAGTAATAACAATAGTTAAACGGAACTTACAGT
1 ATGATAGTAATAACAATAGTTAAACGGAACTTACAGT
34288210 GATGTTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (37 bp):
ATGATAGTAATAACAATAGTTAAACGGAACTTACAGT
Found at i:34292262 original size:25 final size:25
Alignment explanation
Indices: 34292233--34292286 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
34292223 GTTACCAATT
34292233 TCAGCTC-TAATGAGCTTACCGATAC
1 TCAGCTCGT-ATGAGCTTACCGATAC
*
34292258 TCAGCTCGTATGAGCTTACCGTTAC
1 TCAGCTCGTATGAGCTTACCGATAC
34292283 TCAG
1 TCAG
34292287 ATTGGAGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (25 bp):
TCAGCTCGTATGAGCTTACCGATAC
Found at i:34292297 original size:25 final size:25
Alignment explanation
Indices: 34292244--34292300 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
34292234 CAGCTCTAAT
* * *
34292244 GAGCTTACCGATACTCAGCTCGTAT
1 GAGCTTACCGATACTCAGATCGGAG
* *
34292269 GAGCTTACCGTTACTCAGATTGGAG
1 GAGCTTACCGATACTCAGATCGGAG
34292294 GAGCTTA
1 GAGCTTA
34292301 TTGTTATTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (25 bp):
GAGCTTACCGATACTCAGATCGGAG
Found at i:34305377 original size:9 final size:9
Alignment explanation
Indices: 34305285--34305386 Score: 50
Period size: 9 Copynumber: 11.4 Consensus size: 9
34305275 GGGCCAATGA
34305285 TTTTA-AAT
1 TTTTATAAT
34305293 TTTTATAAT
1 TTTTATAAT
* *
34305302 ATTTAACAAT
1 -TTTTATAAT
* *
34305312 TTTAATAAC
1 TTTTATAAT
* *
34305321 TTATGTAATT
1 TTTTATAA-T
34305331 TTTTATAA-
1 TTTTATAAT
* *
34305339 CTTTCT-AT
1 TTTTATAAT
*
34305347 TTTTACAAT
1 TTTTATAAT
*
34305356 TTTCTA-AAA
1 TTT-TATAAT
34305365 TTTTATAAT
1 TTTTATAAT
*
34305374 TTTTTTAAT
1 TTTTATAAT
34305383 TTTT
1 TTTT
34305387 TTAAAAAAAT
Statistics
Matches: 69, Mismatches: 18, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
7 1 0.01
8 14 0.20
9 39 0.57
10 15 0.22
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:34306103 original size:19 final size:20
Alignment explanation
Indices: 34306066--34306103 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34306056 ATAATATTTA
34306066 ATAATATTTATAGTTTTCCT
1 ATAATATTTATAGTTTTCCT
34306086 ATAATATTTATA-TTTTCC
1 ATAATATTTATAGTTTTCC
34306104 AAAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (20 bp):
ATAATATTTATAGTTTTCCT
Found at i:34306170 original size:31 final size:30
Alignment explanation
Indices: 34306135--34306220 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
34306125 TTTTAGACTT
*
34306135 AAATAATTAAAAATCAATTAAGTCTTCCTAA
1 AAATAATTAAAAATCAATTAAGCCTTCCT-A
* * * **
34306166 AAATAAATAAATAAGCAATTAAACCTTTGTA
1 AAATAATTAAA-AATCAATTAAGCCTTCCTA
* *
34306197 AAATAATTAAAGATCATTTAAGCC
1 AAATAATTAAAAATCAATTAAGCC
34306221 CGTTATGTCA
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
30 9 0.21
31 21 0.49
32 13 0.30
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (30 bp):
AAATAATTAAAAATCAATTAAGCCTTCCTA
Found at i:34307727 original size:19 final size:20
Alignment explanation
Indices: 34307695--34307732 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
34307685 TGAAGAATAT
34307695 GAGAAGAGAGAAAAATAAAG
1 GAGAAGAGAGAAAAATAAAG
34307715 GAGAAGA-AGAAAAATAAA
1 GAGAAGAGAGAAAAATAAA
34307733 ATAAAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.05
Consensus pattern (20 bp):
GAGAAGAGAGAAAAATAAAG
Found at i:34311495 original size:123 final size:123
Alignment explanation
Indices: 34311276--34311622 Score: 538
Period size: 123 Copynumber: 2.8 Consensus size: 123
34311266 TTATTTCGAA
*
34311276 TTGACGTTTCTG-GTCAAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
* * *
34311340 GAAATCGCT-CCCTCGTGAACGTGATTTCGCTACAGTAGGTCATGTAAGAAATAATTTTT
65 GAAATCG-TGCCATCGTGGACGCGATTTCGCTACAGTAGGTCATGTAAGAAATAATTTTT
* *
34311399 TTGACGTTTCAGAGCAAATAGTATAAAATTGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
34311464 AAATCGTGCCATCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTT
66 AAATCGTGCCATCGTGGACGCGATTTCGCTACAGTAGGTCATGTAAGAAATAATTTTT
* *
34311522 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTACCAGGATGCTATTTGAGAAGAAAGTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * * *
34311587 AAATCGCGCCTTCGTGGACGCAATTTTGCTA-AGTAG
66 AAATCGTGCCATCGTGGACGCGATTTCGCTACAGTAG
34311623 CAAGTTTGAG
Statistics
Matches: 206, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
122 5 0.02
123 200 0.97
124 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGTGCCATCGTGGACGCGATTTCGCTACAGTAGGTCATGTAAGAAATAATTTTT
Found at i:34311989 original size:28 final size:28
Alignment explanation
Indices: 34311957--34312012 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
34311947 GTTCGACATA
*
34311957 AAAGGTGCTCGTAGCTTGGAGGCAATGG
1 AAAGGTGCCCGTAGCTTGGAGGCAATGG
34311985 AAAGGTGCCCGTAGCTTGGAGGCAATGG
1 AAAGGTGCCCGTAGCTTGGAGGCAATGG
34312013 TGCAGACTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.39, T:0.20
Consensus pattern (28 bp):
AAAGGTGCCCGTAGCTTGGAGGCAATGG
Found at i:34314872 original size:55 final size:56
Alignment explanation
Indices: 34314772--34314894 Score: 221
Period size: 55 Copynumber: 2.2 Consensus size: 56
34314762 TATGTAAAAC
*
34314772 TATGTAAAATTATTAAGCCCAAAAAATTTTGTTAATGGTTAGTAAAATTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAT
*
34314828 TATGTAAAATTATTAAGTCC-AAAAATTGTGTTAATGGTTAGTAAAATTATCAAAT
1 TATGTAAAATTATTAAGCCCAAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAT
34314883 TATGTAAAATTA
1 TATGTAAAATTA
34314895 GGTTAGGGTT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
55 46 0.71
56 19 0.29
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (56 bp):
TATGTAAAATTATTAAGCCCAAAAAATTGTGTTAATGGTTAGTAAAATTATCAAAT
Found at i:34314923 original size:29 final size:29
Alignment explanation
Indices: 34314889--34315536 Score: 942
Period size: 29 Copynumber: 22.6 Consensus size: 29
34314879 AAATTATGTA
*
34314889 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
34314918 -AA--A--TTA-GGTTAGGG-TTTTTAGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTTA-TT
*
34314941 AAATTAAGTTAGGGTTAGGG-TTTTTAGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTTA-TT
* *
34314970 AAATTAGGTTAGGGTTATGATTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
* *
34314999 AAATTAGGTTAGGGTTAGGGTTTGTGATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
*
34315028 AAATTAGGTTAGGGTTAGGCTTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
34315057 AAATTAGGTTAGGGTTAGGGTTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
34315086 AAATTAGGTTAGGGTTAGGG-TTTTTAGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTTA-TT
*
34315115 AAATTAGGTTAGGGTTTGGGTTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
34315144 AAATTAGGTTAGGGTTAGGGTTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
34315173 AAATTAGGTTAGGGTTAGGGTTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
* * * *
34315202 AAATTAGATTAAGGTTAGGGTTTGTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
34315231 AAATTAGGTTAGGGTTAGGGTTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
*
34315260 AAATTAGGTTAAGGTTAGGG-TTTTTAGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTTA-TT
* *
34315289 AAATTAGGTTAGGATTAGGGGTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
*
34315318 AAATTAGGTTAGGTTTAGGGTTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
* *
34315347 AAATTAGGTTAGGGTTAGGGTTTGTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
* *
34315376 AAATTAGGTTAAGGTTATGGTTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
34315405 AAATTAGGTTAGGGTTAGGG-TTTTTAGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTTA-TT
****
34315434 AAATTAGGTTAGGGTTAGGGTTTAGGGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
34315463 AAATTAGGTTAGGGTTAGGGTTTTTTATT
1 AAATTAGGTTAGGGTTAGGGTTTTTTATT
34315492 AAATTAGGTTAGGGTTAGGG-TTTTTAGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTTA-TT
34315521 AAATTAGGTTAGGGTT
1 AAATTAGGTTAGGGTT
34315537 TGTAATTAAA
Statistics
Matches: 560, Mismatches: 44, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
22 5 0.01
23 10 0.02
24 5 0.01
26 2 0.00
28 29 0.05
29 489 0.87
30 20 0.04
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTTATT
Found at i:34314931 original size:23 final size:23
Alignment explanation
Indices: 34314901--34314985 Score: 98
Period size: 23 Copynumber: 3.4 Consensus size: 23
34314891 ATTAGGTTAG
34314901 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
34314924 GGTTAGGGTTTTTAGTTAAATTAAGTTA
1 GGTTAGGG--TTT--TT-AATTAAATTA
*
34314952 GGGTTAGGGTTTTTAGTTAAATTA
1 -GGTTAGGGTTTTTAATTAAATTA
34314976 GGTTAGGGTT
1 GGTTAGGGTT
34314986 ATGATTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
23 18 0.34
24 8 0.15
25 5 0.09
27 5 0.09
28 9 0.17
29 8 0.15
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:34316741 original size:7 final size:7
Alignment explanation
Indices: 34316731--34316755 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34316721 TTATATACAT
34316731 AATACTA
1 AATACTA
34316738 AATACTA
1 AATACTA
34316745 AATACTA
1 AATACTA
34316752 AATA
1 AATA
34316756 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:34317702 original size:51 final size:51
Alignment explanation
Indices: 34317647--34317761 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
34317637 TTTAAAAAAT
* * *
34317647 GAAATTGAGGGGAAATTGAAATTAAATATG-GATTTGAGAGATTTTTGGAAG
1 GAAATTGAGAGAAAATTGAAATTAAATATGAG-TTTGAGAGAATTTTGGAAG
34317698 GAAATTGAGAGAAAATTGAAATTAAATATGAGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGAAAATTGAAATTAAATATGAGTTTGAGAGAATTTTGGAAG
34317749 GAAATTGAGAGAA
1 GAAATTGAGAGAA
34317762 TTTTGGAAGG
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 59 0.98
52 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGAAAATTGAAATTAAATATGAGTTTGAGAGAATTTTGGAAG
Found at i:34317756 original size:22 final size:22
Alignment explanation
Indices: 34317731--34317781 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
34317721 AAATATGAGT
34317731 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
34317753 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
34317775 TTGAGAG
1 TTGAGAG
34317782 GATTAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:34318151 original size:20 final size:20
Alignment explanation
Indices: 34318126--34318167 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
34318116 AATAATTTTG
* * *
34318126 TTAAATTAATATATTTACTA
1 TTAAATGAATAAATTTAATA
34318146 TTAAATGAATAAATTTAATA
1 TTAAATGAATAAATTTAATA
34318166 TT
1 TT
34318168 TTATTATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAATGAATAAATTTAATA
Found at i:34318191 original size:28 final size:28
Alignment explanation
Indices: 34318128--34318191 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 28
34318118 TAATTTTGTT
34318128 AAATTAATATATTTACTATTAAATGAATA
1 AAATTAATATATTTACTATTAAA-GAATA
* *
34318157 AATTTAATAT-TTTATTATTAAA-AATA
1 AAATTAATATATTTACTATTAAAGAATA
34318183 TCAAATTAA
1 --AAATTAA
34318192 ATTAAATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.13
28 17 0.57
29 9 0.30
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (28 bp):
AAATTAATATATTTACTATTAAAGAATA
Found at i:34323699 original size:139 final size:139
Alignment explanation
Indices: 34323449--34323727 Score: 558
Period size: 139 Copynumber: 2.0 Consensus size: 139
34323439 GCTATTGGTA
34323449 TAAACGTACCTCGATCGCGATTCCTTCCAGTGAAGGCAACTTCAGATTTGCTTCTTGTTCAGGTC
1 TAAACGTACCTCGATCGCGATTCCTTCCAGTGAAGGCAACTTCAGATTTGCTTCTTGTTCAGGTC
34323514 CTTTTCTTCTTCCCCTGACATCACAATCAATCTTGAATGATAATATGTAGTTTCCTCAACCCATC
66 CTTTTCTTCTTCCCCTGACATCACAATCAATCTTGAATGATAATATGTAGTTTCCTCAACCCATC
34323579 TCTCGTATT
131 TCTCGTATT
34323588 TAAACGTACCTCGATCGCGATTCCTTCCAGTGAAGGCAACTTCAGATTTGCTTCTTGTTCAGGTC
1 TAAACGTACCTCGATCGCGATTCCTTCCAGTGAAGGCAACTTCAGATTTGCTTCTTGTTCAGGTC
34323653 CTTTTCTTCTTCCCCTGACATCACAATCAATCTTGAATGATAATATGTAGTTTCCTCAACCCATC
66 CTTTTCTTCTTCCCCTGACATCACAATCAATCTTGAATGATAATATGTAGTTTCCTCAACCCATC
34323718 TCTCGTATT
131 TCTCGTATT
34323727 T
1 T
34323728 CGTTTGCAGT
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (139 bp):
TAAACGTACCTCGATCGCGATTCCTTCCAGTGAAGGCAACTTCAGATTTGCTTCTTGTTCAGGTC
CTTTTCTTCTTCCCCTGACATCACAATCAATCTTGAATGATAATATGTAGTTTCCTCAACCCATC
TCTCGTATT
Found at i:34326022 original size:17 final size:16
Alignment explanation
Indices: 34325990--34326023 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34325980 TATTATTTTG
*
34325990 AAATTTAAAATATATA
1 AAATTTAAAAAATATA
34326006 AAATTTAAAAAAGTATA
1 AAATTTAAAAAA-TATA
34326023 A
1 A
34326024 GTTTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTTAAAAAATATA
Found at i:34326687 original size:6 final size:6
Alignment explanation
Indices: 34326678--34326711 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
34326668 ATTACATTTA
34326678 CCATGC CCATGC CCATGC CCATGC CCATGC CCAT
1 CCATGC CCATGC CCATGC CCATGC CCATGC CCAT
34326712 ATCCATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.50, G:0.15, T:0.18
Consensus pattern (6 bp):
CCATGC
Found at i:34326717 original size:18 final size:18
Alignment explanation
Indices: 34326678--34326717 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
34326668 ATTACATTTA
*
34326678 CCATGCCCATGCCCATGC
1 CCATGCCCATGCCCATAC
*
34326696 CCATGCCCATGCCCATAT
1 CCATGCCCATGCCCATAC
34326714 CCAT
1 CCAT
34326718 TTTCTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.47, G:0.12, T:0.20
Consensus pattern (18 bp):
CCATGCCCATGCCCATAC
Found at i:34331235 original size:6 final size:6
Alignment explanation
Indices: 34331224--34331251 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
34331214 AGAAAATAAG
34331224 ATCTGA ATCTGA ATCTGA ATCTGA ATCT
1 ATCTGA ATCTGA ATCTGA ATCTGA ATCT
34331252 CAAAGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (6 bp):
ATCTGA
Found at i:34331618 original size:16 final size:16
Alignment explanation
Indices: 34331597--34331630 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
34331587 ATTAAATAAA
34331597 AATATATAA-TATTTAT
1 AATATATAACT-TTTAT
34331613 AATATATAACTTTTAT
1 AATATATAACTTTTAT
34331629 AA
1 AA
34331631 GAAAAGTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATATAACTTTTAT
Found at i:34331815 original size:15 final size:16
Alignment explanation
Indices: 34331785--34331817 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34331775 GTCATGCATC
34331785 TTTTTTAAAATATTTA
1 TTTTTTAAAATATTTA
*
34331801 TTTTTTAATAT-TTTA
1 TTTTTTAAAATATTTA
34331816 TT
1 TT
34331818 ATGCCTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTAAAATATTTA
Found at i:34333071 original size:23 final size:22
Alignment explanation
Indices: 34333023--34333071 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
34333013 GTCATTTAAC
* *
34333023 TATTAAATTTTTTAAATTCAAT
1 TATTAAATTTTTTAAATTAAAA
34333045 TATT-AATTTTTTAAAAATTAAAA
1 TATTAAATTTTTT--AAATTAAAA
34333068 TATT
1 TATT
34333072 TTAATCACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
23 11 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTAAATTTTTTAAATTAAAA
Found at i:34333795 original size:17 final size:16
Alignment explanation
Indices: 34333765--34333807 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
34333755 CAATTAAGTT
* *
34333765 ATTTTTGAAGTTTTAA
1 ATTTTTTAAATTTTAA
34333781 AGTTTTTTAAATTTTAA
1 A-TTTTTTAAATTTTAA
34333798 ATTTTTTAAA
1 ATTTTTTAAA
34333808 ATTATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (16 bp):
ATTTTTTAAATTTTAA
Found at i:34333810 original size:17 final size:17
Alignment explanation
Indices: 34333775--34333807 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
34333765 ATTTTTGAAG
34333775 TTTTAAAGTTTTTTAAA
1 TTTTAAAGTTTTTTAAA
34333792 TTTTAAA-TTTTTTAAA
1 TTTTAAAGTTTTTTAAA
34333808 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTAAAGTTTTTTAAA
Found at i:34336307 original size:15 final size:15
Alignment explanation
Indices: 34336272--34336313 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
34336262 TGATAAATTA
34336272 ATATTTT-TATGTATT
1 ATATTTTATAT-TATT
34336287 -TATTTTATATTATT
1 ATATTTTATATTATT
34336301 ATATTTTATATTA
1 ATATTTTATATTA
34336314 GATCATGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
ATATTTTATATTATT
Found at i:34339360 original size:26 final size:26
Alignment explanation
Indices: 34339331--34339380 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
34339321 TTCGGTTTTA
*
34339331 TTTAAAAT-ATTTATTTTGATTTTAAT
1 TTTAAAATGATTT-CTTTGATTTTAAT
*
34339357 TTTAAATTGATTTCTTTGATTTTA
1 TTTAAAATGATTTCTTTGATTTTA
34339381 CCTTGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (26 bp):
TTTAAAATGATTTCTTTGATTTTAAT
Found at i:34340702 original size:319 final size:319
Alignment explanation
Indices: 34340074--34340702 Score: 1034
Period size: 318 Copynumber: 2.0 Consensus size: 319
34340064 TTATAAATTT
*
34340074 AACAGATATCCTTTCATCAAGCTGTAATGAAAGAAAATAATTGAATTTCAAGATTTTTCCTCTTC
1 AACAGATATCCTTTCATCAAGCTGTAATGAAAGAAAAGAATTGAATTTCAAGATTTTTCCTCTTC
*
34340139 TTTTTTTTTTCCCTTTATCAAGCTGTAATGAAACAGATATCCATATAAAGAAATGAATTTTAAGT
66 TTTTTTTTTTCCCTTTATCAAGCTGTAATGAAACAGATATCCATATAAAGAAATGAATTTCAAGT
*
34340204 TGCAAAGATAATTTTAATTTCTATTTTTTGCCTCGTAAAGATTTTAAATTTGTATTGTTCATTTT
131 TGCAAAGATAATTTTAATTTCTATTTTTTGCCTCGTAAAGATTCTAAATTTGTATTGTTCATTTT
**
34340269 TCTTTGATAGTGTGTTATTGCTTCCTATTGAAGCGGCTTGTTTGATTGCTTCCTCCACCCACAGT
196 TCTTTGATAGTGTGTTATTGCTAAC-ATTGAAGCGGCTTGTTTGATTGCTTCCTCCACCCACAGT
* *
34340334 TGAGTGTCTTGTATTCACACAAACACTGTAAGTTCTTTGGCAATTAAATTATTACAGAAA
260 TGAGCGTCTTGTATTCACACAAACACTGTAAGTTCTTTGACAATTAAATTATTACAGAAA
* *
34340394 AACATATATCCTTTCATTAAGCTGTAATGAAA-AAAAGAATTGAATTTCAAGATTTTTCCTCTTC
1 AACAGATATCCTTTCATCAAGCTGTAATGAAAGAAAAGAATTGAATTTCAAGATTTTTCCTCTTC
34340458 -TTTTTTTTTCCCTTTATCAAGCTGTAATGAAACAGATATCCATATAAAGAAATGAATTTCAAGT
66 TTTTTTTTTTCCCTTTATCAAGCTGTAATGAAACAGATATCCATATAAAGAAATGAATTTCAAGT
* *
34340522 TGCAAAGATAATTTTAATTTCTATTTTTTGCTTCGTAAATATTCTAAATTTGTATTGTTCATTTT
131 TGCAAAGATAATTTTAATTTCTATTTTTTGCCTCGTAAAGATTCTAAATTTGTATTGTTCATTTT
* *
34340587 TCTTTGATAGTGTGTTATTGC-AAC-TTGAATTCTTTGGCTTGTTTGATTGCTTCCTCCATCCAC
196 TCTTTGATAGTGTGTTATTGCTAACATTGAA-GC---GGCTTGTTTGATTGCTTCCTCCACCCAC
* *
34340650 AGTTGAGCGTCTTGTATTCACTA-AATCACTGTAAGTTTTTTGACAATTAAATT
257 AGTTGAGCGTCTTGTATTCAC-ACAAACACTGTAAGTTCTTTGACAATTAAATT
34340703 CTTTAATTTT
Statistics
Matches: 289, Mismatches: 15, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
315 5 0.02
316 1 0.00
317 1 0.00
318 146 0.51
319 105 0.36
320 31 0.11
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (319 bp):
AACAGATATCCTTTCATCAAGCTGTAATGAAAGAAAAGAATTGAATTTCAAGATTTTTCCTCTTC
TTTTTTTTTTCCCTTTATCAAGCTGTAATGAAACAGATATCCATATAAAGAAATGAATTTCAAGT
TGCAAAGATAATTTTAATTTCTATTTTTTGCCTCGTAAAGATTCTAAATTTGTATTGTTCATTTT
TCTTTGATAGTGTGTTATTGCTAACATTGAAGCGGCTTGTTTGATTGCTTCCTCCACCCACAGTT
GAGCGTCTTGTATTCACACAAACACTGTAAGTTCTTTGACAATTAAATTATTACAGAAA
Found at i:34342396 original size:49 final size:49
Alignment explanation
Indices: 34342323--34342427 Score: 183
Period size: 49 Copynumber: 2.1 Consensus size: 49
34342313 TCATGTGTTA
* * *
34342323 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
34342372 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
34342421 TAATTTT
1 TAATTTT
34342428 TTTTCTTAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:34343886 original size:10 final size:10
Alignment explanation
Indices: 34343868--34343940 Score: 52
Period size: 10 Copynumber: 7.9 Consensus size: 10
34343858 ATATAAGAAT
*
34343868 AATTATATTG
1 AATTATATTA
*
34343878 AATTTTATTA
1 AATTATATTA
34343888 AATTATA-T-
1 AATTATATTA
34343896 -ATTATTATTA
1 AATTA-TATTA
*
34343906 AATTATATTT
1 AATTATATTA
34343916 AA-TA-A-T-
1 AATTATATTA
*
34343922 AATTATTTTA
1 AATTATATTA
34343932 AATTATATT
1 AATTATATT
34343941 TTATAGTATT
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
6 2 0.04
7 7 0.14
8 3 0.06
9 5 0.10
10 28 0.57
11 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (10 bp):
AATTATATTA
Found at i:34343905 original size:18 final size:18
Alignment explanation
Indices: 34343882--34344013 Score: 111
Period size: 18 Copynumber: 7.8 Consensus size: 18
34343872 ATATTGAATT
34343882 TTATTAAATTATATATTA
1 TTATTAAATTATATATTA
34343900 TTATTAAATTATAT-TTA
1 TTATTAAATTATATATTA
* *
34343917 ATAAT-AATTAT-T-TTA
1 TTATTAAATTATATATTA
* * * *
34343932 -AATTATATTTTATAGTA
1 TTATTAAATTATATATTA
* *
34343949 TTA-TATATTAT-GATT-
1 TTATTAAATTATATATTA
*
34343964 TTAGTAAATTCATATATT-
1 TTATTAAATT-ATATATTA
34343982 TTATTAAATTATATATTA
1 TTATTAAATTATATATTA
34344000 TTATTAAATTATAT
1 TTATTAAATTATAT
34344014 TTAATAATAA
Statistics
Matches: 92, Mismatches: 14, Indels: 16
0.75 0.11 0.13
Matches are distributed among these distances:
14 2 0.02
15 11 0.12
16 14 0.15
17 24 0.26
18 41 0.45
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (18 bp):
TTATTAAATTATATATTA
Found at i:34344073 original size:40 final size:37
Alignment explanation
Indices: 34344002--34344075 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 37
34343992 ATATATTATT
*
34344002 ATTAAATTATATTTAATAATAATTATGTTAAAATATG
1 ATTAAATTATATTTAATAATAATTATATTAAAATATG
34344039 ATTAAATTATTATTTATATTAATAATCT-TATTAAAAT
1 ATTAAATTA-TATTTA-A-TAATAAT-TATATTAAAAT
34344076 TTAATAACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
37 9 0.28
38 6 0.19
39 1 0.03
40 15 0.47
41 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
ATTAAATTATATTTAATAATAATTATATTAAAATATG
Found at i:34344256 original size:45 final size:44
Alignment explanation
Indices: 34344167--34344259 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
34344157 ATTACAACAT
*
34344167 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
*
34344211 CATTCCATTCAACCAAACA-ATTGAATTACTATTAC-GCCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAG-CTCTATTC
34344256 CATT
1 CATT
34344260 ACAGCGAACC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 20 0.45
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.32
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:34347148 original size:63 final size:63
Alignment explanation
Indices: 34347067--34347223 Score: 183
Period size: 63 Copynumber: 2.5 Consensus size: 63
34347057 ACATAATAAG
* * * * * * *
34347067 ACACACAATAATTCCCTGCATCAACACCTTCAGCTCTAGTTTATTTTACATAAGCAT-CACAAC
1 ACACACAATCATTTCCTGCATCAACACATTCAACACCAGTTTATTTTACACAAGC-TCCACAAC
* *
34347130 ACACACAATCATTTCCTGCATCAGCACATTTAACACCAGTTTATTTTACACAAGCTCCACAAC
1 ACACACAATCATTTCCTGCATCAACACATTCAACACCAGTTTATTTTACACAAGCTCCACAAC
* *
34347193 ACGCACAATCA-TTCTTTGCATCAACACATTC
1 ACACACAATCATTTC-CTGCATCAACACATTC
34347224 TCCATGGGTA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
62 4 0.05
63 75 0.95
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.28
Consensus pattern (63 bp):
ACACACAATCATTTCCTGCATCAACACATTCAACACCAGTTTATTTTACACAAGCTCCACAAC
Found at i:34349613 original size:9 final size:9
Alignment explanation
Indices: 34349599--34349629 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34349589 GTTAAACGAA
34349599 TCGAGTTAT
1 TCGAGTTAT
*
34349608 TCGAGTTAA
1 TCGAGTTAT
34349617 TCGAGTTAT
1 TCGAGTTAT
34349626 TCGA
1 TCGA
34349630 ATTAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:34349620 original size:18 final size:18
Alignment explanation
Indices: 34349597--34349639 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
34349587 GAGTTAAACG
*
34349597 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAATT
34349615 AATCGAGTTATTCGAATT
1 AATCGAGTTATTCGAATT
34349633 AACTCGA
1 AA-TCGA
34349640 ATTTTTTTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (18 bp):
AATCGAGTTATTCGAATT
Found at i:34349710 original size:9 final size:9
Alignment explanation
Indices: 34349681--34349717 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
34349671 TGAGTTTTCG
34349681 AATTCGAAT
1 AATTCGAAT
*
34349690 AACTCGAAT
1 AATTCGAAT
34349699 AATTCGAAT
1 AATTCGAAT
*
34349708 AATTCAAAT
1 AATTCGAAT
34349717 A
1 A
34349718 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34351882 original size:2 final size:2
Alignment explanation
Indices: 34351875--34351902 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34351865 GTGCGCGTGC
34351875 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34351903 CGTACTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34351941 original size:42 final size:42
Alignment explanation
Indices: 34351882--34351974 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
34351872 TGCGAGAGAG
34351882 AGAGAGAGAGAGAGAGAGAGACGTACTCAAATTGGTCAAGAA
1 AGAGAGAGAGAGAGAGAGAGACGTACTCAAATTGGTCAAGAA
*
34351924 AGAGAGAGAGAGAGAGAGAGACGTACTGAAATTGGTCAAGAA
1 AGAGAGAGAGAGAGAGAGAGACGTACTCAAATTGGTCAAGAA
*
34351966 A-AGAAAGAG
1 AGAGAGAGAG
34351975 TAAAGCAACA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 7 0.14
42 42 0.86
ACGTcount: A:0.47, C:0.08, G:0.34, T:0.11
Consensus pattern (42 bp):
AGAGAGAGAGAGAGAGAGAGACGTACTCAAATTGGTCAAGAA
Found at i:34352925 original size:77 final size:78
Alignment explanation
Indices: 34352821--34352975 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
34352811 ACTATTTAAA
34352821 TTAATTAATTACGTTACAAAAATATTAAACTAATTAATAATATTATAAAAATATAAAGACTGAAT
1 TTAATTAATTACGTTACAAAAATATTAAACTAATTAATAATATTATAAAAATATAAAGACTGAAT
34352886 TATATTAACAATT
66 TATATTAACAATT
34352899 TTAATTAATT-CGTTACAAAAATATTAAACTAATTAATAATATTATAAAAATATAAAGACTGAAT
1 TTAATTAATTACGTTACAAAAATATTAAACTAATTAATAATATTATAAAAATATAAAGACTGAAT
34352963 TATATTAACAATT
66 TATATTAACAATT
34352976 GAAGTATAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 67 0.87
78 10 0.13
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.37
Consensus pattern (78 bp):
TTAATTAATTACGTTACAAAAATATTAAACTAATTAATAATATTATAAAAATATAAAGACTGAAT
TATATTAACAATT
Found at i:34354086 original size:19 final size:20
Alignment explanation
Indices: 34354050--34354093 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
34354040 TAAAAACTTT
*
34354050 ATTTTAATGTTTTTTTATAC
1 ATTTTAATGTTTTGTTATAC
*
34354070 ATTTTAAT-TTTTGTTATGC
1 ATTTTAATGTTTTGTTATAC
34354089 ATTTT
1 ATTTT
34354094 GTTACCTCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.66
Consensus pattern (20 bp):
ATTTTAATGTTTTGTTATAC
Found at i:34357459 original size:13 final size:14
Alignment explanation
Indices: 34357431--34357459 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34357421 TCACCTTACC
34357431 TTGAAAAACTTAGT
1 TTGAAAAACTTAGT
34357445 TTGAAAAACTT-GT
1 TTGAAAAACTTAGT
34357458 TT
1 TT
34357460 ACTTACAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (14 bp):
TTGAAAAACTTAGT
Found at i:34358050 original size:14 final size:15
Alignment explanation
Indices: 34358026--34358057 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
34358016 ATATGAGGGC
34358026 ATTTTTATATAAAAT
1 ATTTTTATATAAAAT
34358041 ATTTTT-TATAAAAT
1 ATTTTTATATAAAAT
34358055 ATT
1 ATT
34358058 ACTATGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTTATATAAAAT
Found at i:34360043 original size:30 final size:30
Alignment explanation
Indices: 34360007--34360074 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
34359997 AGATACAAGG
* *
34360007 GACACATGGCCATGTGTCATACACGGTTGA
1 GACACATGGCCATGTGTCACACACGGCTGA
34360037 GACACATGGCCATGTGTCACACACGGCTGA
1 GACACATGGCCATGTGTCACACACGGCTGA
34360067 GACACATG
1 GACACATG
34360075 TCCGTGTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19
Consensus pattern (30 bp):
GACACATGGCCATGTGTCACACACGGCTGA
Found at i:34360082 original size:28 final size:29
Alignment explanation
Indices: 34360007--34360082 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
34359997 AGATACAAGG
* *
34360007 GACACATGGCCATGTGTCATACACGGTTGA
1 GACACATGGCCA-GTGTCACACACGGCTGA
34360037 GACACATGGCCATGTGTCACACACGGCTGA
1 GACACATGGCCA-GTGTCACACACGGCTGA
*
34360067 GACACATGTCC-GTGTC
1 GACACATGGCCAGTGTC
34360083 TCTGCCCGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 5 0.12
30 38 0.88
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (29 bp):
GACACATGGCCAGTGTCACACACGGCTGA
Found at i:34361759 original size:25 final size:25
Alignment explanation
Indices: 34361707--34361781 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
34361697 GTACATGTAT
*
34361707 GCTCATACGAGCTGAATATCGGTTA
1 GCTCATACGAGCTGAATATCGGTAA
* *
34361732 GCTCATGCGAGTTGAATA-CTGGTAA
1 GCTCATACGAGCTGAATATC-GGTAA
*
34361757 GCTC-TCTCGAGCTGAGA-ATCGGTAA
1 GCTCAT-ACGAGCTGA-ATATCGGTAA
34361782 ACCTAATGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
24 2 0.05
25 37 0.90
26 2 0.05
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTGAATATCGGTAA
Found at i:34362638 original size:21 final size:21
Alignment explanation
Indices: 34362600--34362641 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34362590 GAAATTAAAG
*
34362600 TGTTTTAATTTTACTTTAATT
1 TGTTTTAATTTCACTTTAATT
34362621 TGTTTTAATTTC-CATTTAATT
1 TGTTTTAATTTCAC-TTTAATT
34362642 ACAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (21 bp):
TGTTTTAATTTCACTTTAATT
Found at i:34364870 original size:22 final size:23
Alignment explanation
Indices: 34364839--34364921 Score: 62
Period size: 24 Copynumber: 3.6 Consensus size: 23
34364829 AGGAGAGGGG
*
34364839 AAGAAGAAGAAAG-AAAGGAAGC
1 AAGAAAAAGAAAGAAAAGGAAGC
*
34364861 AAGAAAAAGAAGGAAAAGGAAAG-
1 AAGAAAAAGAAAGAAAAGG-AAGC
* * * *
34364884 GAGAGGAAAGAAAGAAAAAGAAGGA
1 AAGA-AAAAGAAAGAAAAGGAA-GC
*
34364909 AAGAAAAGGAAAG
1 AAGAAAAAGAAAG
34364922 GGGAGGAAAG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
22 11 0.23
23 10 0.21
24 23 0.49
25 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGC
Found at i:34364890 original size:10 final size:10
Alignment explanation
Indices: 34364870--34364960 Score: 57
Period size: 10 Copynumber: 9.4 Consensus size: 10
34364860 CAAGAAAAAG
34364870 AAGGAAAAGGA
1 AAGG-AAAGGA
*
34364881 AAGGAGAGGA
1 AAGGAAAGGA
*
34364891 AA-GAAAGAA
1 AAGGAAAGGA
*
34364900 AAAG-AAGGA
1 AAGGAAAGGA
*
34364909 AAGAAAAGGA
1 AAGGAAAGGA
**
34364919 AAGGGGAGGA
1 AAGGAAAGGA
34364929 AA-GAAA-GA
1 AAGGAAAGGA
*
34364937 AA-AATAAGGA
1 AAGGA-AAGGA
*
34364947 AAGAAAAGGA
1 AAGGAAAGGA
34364957 AAGG
1 AAGG
34364961 GGAAGAGAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
8 5 0.08
9 17 0.27
10 34 0.55
11 6 0.10
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (10 bp):
AAGGAAAGGA
Found at i:34364897 original size:28 final size:28
Alignment explanation
Indices: 34364842--34364921 Score: 76
Period size: 34 Copynumber: 2.8 Consensus size: 28
34364832 AGAGGGGAAG
*
34364842 AAGAA-GAAAG-AAAGG-AAGCAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
34364867 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
34364901 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
34364922 GGGAGGAAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 3 0.07
28 8 0.18
29 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 6 0.13
34 16 0.36
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:34364915 original size:38 final size:38
Alignment explanation
Indices: 34364873--34365014 Score: 159
Period size: 38 Copynumber: 3.8 Consensus size: 38
34364863 GAAAAAGAAG
34364873 GAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAA
1 GAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAA
* *
34364911 GAAAAGGAAAGGGGAGGAAAGAAAGAAAAATAAGGAAA
1 GAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAA
*
34364949 GAAAAGGAAA-G-G-GGAAGAGAAA-AAAAAGAAAGAAGAA
1 GAAAAGGAAAGGAGAGGAA-AGAAAGAAAAAG-AAGGA-AA
* * *
34364986 GAAGAGGGAAGGA-AGGAAAAAAAAGAAAA
1 GAAAAGGAAAGGAGAGG-AAAGAAAGAAAA
34365015 TAAGGTATTT
Statistics
Matches: 89, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
35 9 0.10
36 10 0.11
37 11 0.12
38 47 0.53
39 6 0.07
40 6 0.07
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (38 bp):
GAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAA
Found at i:34364986 original size:21 final size:22
Alignment explanation
Indices: 34364945--34364987 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
34364935 GAAAAATAAG
* **
34364945 GAAAGAAAAGGAAAGGGGAAGA
1 GAAAGAAAAAGAAAGAAGAAGA
34364967 GAAA-AAAAAGAAAGAAGAAGA
1 GAAAGAAAAAGAAAGAAGAAGA
34364988 AGAGGGAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (22 bp):
GAAAGAAAAAGAAAGAAGAAGA
Found at i:34365991 original size:19 final size:19
Alignment explanation
Indices: 34365967--34366009 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
34365957 CCATAACGAA
34365967 AGCCCTCGTCAAAACTTTG
1 AGCCCTCGTCAAAACTTTG
*
34365986 AGCCCTCGTCAAACCTTTG
1 AGCCCTCGTCAAAACTTTG
34366005 AGCCC
1 AGCCC
34366010 ATTGCCACGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.23
Consensus pattern (19 bp):
AGCCCTCGTCAAAACTTTG
Found at i:34366354 original size:40 final size:40
Alignment explanation
Indices: 34366294--34366375 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
34366284 CGAATGCAGT
* *
34366294 AAACGGATCTCCACGGCACACCGGAACGCCTAATAGCTGC
1 AAACGGATCTCCACGACACACCGAAACGCCTAATAGCTGC
* *
34366334 AAACGGATCTCCACGACACACCGAAACGCCTGATTGCTGC
1 AAACGGATCTCCACGACACACCGAAACGCCTAATAGCTGC
34366374 AA
1 AA
34366376 TTAAACCCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.32, C:0.34, G:0.21, T:0.13
Consensus pattern (40 bp):
AAACGGATCTCCACGACACACCGAAACGCCTAATAGCTGC
Found at i:34367481 original size:18 final size:18
Alignment explanation
Indices: 34367455--34367492 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
34367445 ATCCCAATGA
* *
34367455 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
34367473 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
34367491 TC
1 TC
34367493 ACCACCAACC
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:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:34367499 original size:18 final size:18
Alignment explanation
Indices: 34367458--34367499 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
34367448 CCAATGATCG
* *
34367458 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
34367476 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
34367494 CCACCA
1 CCACCA
34367500 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:34368434 original size:27 final size:27
Alignment explanation
Indices: 34368361--34368440 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
34368351 ATAACACGAG
**
34368361 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
34368388 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
34368415 TGGTGCCGCCAACAGTGTTCCCTTGT
1 TGGTGCCGCCAACAGGGTTCCCTTGT
34368441 CCCAGGGAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.14, C:0.30, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Done.