Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 128 of 185
Found at i:39944846 original size:51 final size:50
Alignment explanation
Indices: 39944786--39945174 Score: 350
Period size: 51 Copynumber: 7.7 Consensus size: 50
39944776 GATGAACACG
* *
39944786 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAT-TTGGTCACA
* * * * * * *
39944837 TGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAA-ATTTGGTCACA
* * * *
39944888 TGTGTAGTACTGTGTAAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAT-TTGGTCACA
* * * * * * * * *
39944939 TGTGTAGTTCTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTTGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAA-ATTTGGTCACA
* * * *
39944990 TGTATAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAT-TTGGTCACA
* * * * * *
39945041 TGTGTAGTAGTAAGTGAAGGCTGCTATGTGTA-CCAAAAAGCTTTGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA--TTTGGTCACA
* * * * * *
39945092 TGTATAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAT-AAATTTGGTCACA
39945142 TGTGTAGTACTATGTGAAGGCTACTACGTGTAT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTAT
39945175 GGAATGATAA
Statistics
Matches: 260, Mismatches: 70, Indels: 17
0.75 0.20 0.05
Matches are distributed among these distances:
50 44 0.17
51 209 0.80
52 7 0.03
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATTTGGTCACA
Found at i:39944958 original size:102 final size:102
Alignment explanation
Indices: 39944782--39945165 Score: 572
Period size: 102 Copynumber: 3.8 Consensus size: 102
39944772 TATCGATGAA
* * *
39944782 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTATAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
39944847 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* * *
39944884 CACGTGTGTAGTACTGTGTAAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTTC
1 CACGTGTATAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
39944949 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTTGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
*
39944986 CACGTGTATAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAG
1 CACGTGTATAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* * * *
39945051 TAAGTGAAGGCTGCTATGTGTACCAAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* * * *** * *
39945088 CACATGTATAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTATAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
39945152 TATGTGAAGGCTAC
66 TAAGTGAAGGCTAC
39945166 TACGTGTATG
Statistics
Matches: 257, Mismatches: 25, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
101 31 0.12
102 226 0.88
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
CACGTGTATAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
Found at i:39946731 original size:14 final size:14
Alignment explanation
Indices: 39946714--39946762 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
39946704 GCATGGTTTT
39946714 GGGTTTTGGATTTA
1 GGGTTTTGGATTTA
* *
39946728 GGGTTTAGGGTTTA
1 GGGTTTTGGATTTA
* *
39946742 GTGTTATGGATTTTA
1 GGGTTTTGGA-TTTA
39946757 GGGTTT
1 GGGTTT
39946763 AATTACTTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (14 bp):
GGGTTTTGGATTTA
Found at i:39946740 original size:28 final size:29
Alignment explanation
Indices: 39946708--39946763 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
39946698 TACAATGCAT
* *
39946708 GGTTTTGGGTTTTGGA-TTTAGGGTTTAG
1 GGTTTAGGGTTATGGATTTTAGGGTTTAG
*
39946736 GGTTTAGTGTTATGGATTTTAGGGTTTA
1 GGTTTAGGGTTATGGATTTTAGGGTTTA
39946764 ATTACTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (29 bp):
GGTTTAGGGTTATGGATTTTAGGGTTTAG
Found at i:39948262 original size:31 final size:31
Alignment explanation
Indices: 39948224--39948303 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
39948214 TTGAATTTTA
*
39948224 ATTGGTTTTTGCAGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
39948255 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
*
39948286 ATTGATTTTTGCTGCTAA
1 ATTGGTTTTTGCTGCTAA
39948304 ATCAACCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (31 bp):
ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
Found at i:39951809 original size:43 final size:43
Alignment explanation
Indices: 39951755--39951862 Score: 180
Period size: 43 Copynumber: 2.5 Consensus size: 43
39951745 GACCTTTAAA
* *
39951755 GGCGTTTGTGGGTAAAGCGTCGCTAAAGATAATGTTCTTTAGC
1 GGCGTTTGTGGGTAAAGCGCCGATAAAGATAATGTTCTTTAGC
*
39951798 GGCGTTTGTGGGTAAAGCGCCGATAAAGATCATGTTCTTTAGC
1 GGCGTTTGTGGGTAAAGCGCCGATAAAGATAATGTTCTTTAGC
*
39951841 GGCGTTTGTGGGTAAAACGCCG
1 GGCGTTTGTGGGTAAAGCGCCG
39951863 CAAAAGTTAG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (43 bp):
GGCGTTTGTGGGTAAAGCGCCGATAAAGATAATGTTCTTTAGC
Found at i:39959060 original size:10 final size:9
Alignment explanation
Indices: 39959019--39959083 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
39959009 GATAGATAGA
39959019 AAAAAATGAT
1 AAAAAAT-AT
39959029 -AAAAATA-
1 AAAAAATAT
39959036 AATAAAATAT
1 AA-AAAATAT
39959046 AAAAAATAT
1 AAAAAATAT
* *
39959055 AGAAAATTT
1 AAAAAATAT
* *
39959064 ATAAAATTT
1 AAAAAATAT
39959073 ATAAAAATAT
1 A-AAAAATAT
39959083 A
1 A
39959084 TAGAAAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
8 2 0.04
9 35 0.76
10 9 0.20
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAAAATAT
Found at i:39959085 original size:10 final size:10
Alignment explanation
Indices: 39959027--39959091 Score: 57
Period size: 9 Copynumber: 6.8 Consensus size: 10
39959017 GAAAAAAATG
*
39959027 ATAAAAATAA
1 ATAAAAATAT
39959037 AT-AAAATAT
1 ATAAAAATAT
39959046 A-AAAAATAT
1 ATAAAAATAT
* *
39959055 A-GAAAATTT
1 ATAAAAATAT
*
39959064 AT-AAAATTT
1 ATAAAAATAT
39959073 ATAAAAATAT
1 ATAAAAATAT
39959083 ATAGAAAAT
1 ATA-AAAAT
39959092 TTATTTTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
9 31 0.66
10 11 0.23
11 5 0.11
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:39959589 original size:8 final size:8
Alignment explanation
Indices: 39959576--39959678 Score: 57
Period size: 9 Copynumber: 12.1 Consensus size: 8
39959566 TGTTGGTAAT
39959576 TATTTTTA
1 TATTTTTA
39959584 TATTTTTATA
1 TA-TTTT-TA
39959594 TATTTTTTAA
1 TA-TTTTT-A
* *
39959604 AATTTTAA
1 TATTTTTA
39959612 TAATTTTTAA
1 T-ATTTTT-A
*
39959622 TTTTTTATA
1 TATTTT-TA
39959631 TATTTTTA
1 TATTTTTA
* *
39959639 AATTTTAA
1 TATTTTTA
*
39959647 TATTTGTA
1 TATTTTTA
*
39959655 TA-TATTA
1 TATTTTTA
39959662 TAATTTTTA
1 T-ATTTTTA
39959671 T-TTTTTA
1 TATTTTTA
39959678 T
1 T
39959679 CATATATCAC
Statistics
Matches: 73, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
7 11 0.15
8 19 0.26
9 29 0.40
10 14 0.19
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (8 bp):
TATTTTTA
Found at i:39959597 original size:10 final size:10
Alignment explanation
Indices: 39959578--39959660 Score: 67
Period size: 10 Copynumber: 9.1 Consensus size: 10
39959568 TTGGTAATTA
39959578 TTTT-TATAT
1 TTTTATATAT
39959587 TTTTATATAT
1 TTTTATATAT
* *
39959597 TTTT-TAAAA
1 TTTTATATAT
39959606 TTTTA-ATAAT
1 TTTTATAT-AT
39959616 TTTTA-AT-T
1 TTTTATATAT
39959624 TTTTATATAT
1 TTTTATATAT
39959634 TTTTA-A-A-
1 TTTTATATAT
39959641 TTTTA-ATAT
1 TTTTATATAT
*
39959650 TTGTATATAT
1 TTTTATATAT
39959660 T
1 T
39959661 ATAATTTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
7 6 0.10
8 8 0.13
9 19 0.31
10 28 0.46
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (10 bp):
TTTTATATAT
Found at i:39959599 original size:18 final size:18
Alignment explanation
Indices: 39959576--39959683 Score: 86
Period size: 18 Copynumber: 6.2 Consensus size: 18
39959566 TGTTGGTAAT
39959576 TATTTTTATATTTTTATA
1 TATTTTTATATTTTTATA
* *
39959594 TATTTTTTAAAATTTTA-A
1 TA-TTTTTATATTTTTATA
39959612 TAATTTTTA-ATTTTTTATA
1 T-ATTTTTATA-TTTTTATA
*
39959631 TATTTTTA-AATTTTA-A
1 TATTTTTATATTTTTATA
* *
39959647 TATTTGTATA-TATTATA
1 TATTTTTATATTTTTATA
39959664 -ATTTTTAT-TTTTTATCA
1 TATTTTTATATTTTTAT-A
39959681 TAT
1 TAT
39959684 ATCACAATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
16 24 0.33
17 9 0.12
18 25 0.34
19 15 0.21
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (18 bp):
TATTTTTATATTTTTATA
Found at i:39959627 original size:37 final size:35
Alignment explanation
Indices: 39959572--39959670 Score: 116
Period size: 37 Copynumber: 2.9 Consensus size: 35
39959562 GCTGTGTTGG
*
39959572 TAATTATTTTTATATTTTTATATATTTTTTAAAATTT
1 TAATAATTTTTATATTTTTATATA-TTTTT-AAATTT
39959609 TAATAATTTTTA-ATTTTTTATATATTTTTAAATTT
1 TAATAATTTTTATA-TTTTTATATATTTTTAAATTT
* *
39959644 TAAT-ATTTGTATA-TATTATA-ATTTTTA
1 TAATAATTTTTATATTTTTATATATTTTTA
39959671 TTTTTTATCA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
32 7 0.12
33 6 0.11
34 6 0.11
35 11 0.19
36 6 0.11
37 21 0.37
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (35 bp):
TAATAATTTTTATATTTTTATATATTTTTAAATTT
Found at i:39959683 original size:26 final size:25
Alignment explanation
Indices: 39959594--39959685 Score: 80
Period size: 25 Copynumber: 3.6 Consensus size: 25
39959584 TATTTTTATA
* *
39959594 TATTTTTTA-AAATTTTAATAATTTT
1 TATTTTTTATATATATT-ATAATTTT
* *
39959619 TAATTTTTTATATAT-TTTTAAATTT
1 T-ATTTTTTATATATATTATAATTTT
* * *
39959644 TAATATTTGTATATATTATAATTTT
1 TATTTTTTATATATATTATAATTTT
39959669 TATTTTTTATCATATAT
1 TATTTTTTAT-ATATAT
39959686 CACAATTACA
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
24 10 0.19
25 23 0.44
26 16 0.31
27 3 0.06
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (25 bp):
TATTTTTTATATATATTATAATTTT
Found at i:39962340 original size:26 final size:26
Alignment explanation
Indices: 39962280--39962340 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
39962270 TGGTAAGATA
*
39962280 AAATTTAAAATTTCTTTATTTTTAAT
1 AAATTTAAAATTTATTTATTTTTAAT
* *
39962306 -TATGTTAAAATTTATTTATTTTTGAT
1 AAAT-TTAAAATTTATTTATTTTTAAT
*
39962332 AAATCTAAA
1 AAATTTAAA
39962341 TAATTTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 2 0.07
26 24 0.86
27 2 0.07
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (26 bp):
AAATTTAAAATTTATTTATTTTTAAT
Found at i:39963202 original size:41 final size:40
Alignment explanation
Indices: 39963157--39963290 Score: 153
Period size: 40 Copynumber: 3.4 Consensus size: 40
39963147 AGCGGCGTTT
** *
39963157 TTAGCGGCGCTTGGACAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGCTTTTA-AAAAAACGCCGCTAAAAATCAAGCA
* * ** *
39963198 TTAGCGGCGCTTTTATAAAAACGCTGCTAAAGGTCGAGCA
1 TTAGCGGCGCTTTTAAAAAAACGCCGCTAAAAATCAAGCA
**
39963238 TTAGCGGCGCTTTTAGGAAAACGCCGCTAAAAAT-AAGCA
1 TTAGCGGCGCTTTTAAAAAAACGCCGCTAAAAATCAAGCA
*
39963277 TTAGCGGCGTTTTT
1 TTAGCGGCGCTTTT
39963291 TGAAATGCGC
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 17 0.22
40 48 0.62
41 13 0.17
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (40 bp):
TTAGCGGCGCTTTTAAAAAAACGCCGCTAAAAATCAAGCA
Found at i:39963302 original size:39 final size:40
Alignment explanation
Indices: 39963175--39963308 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 40
39963165 GCTTGGACAA
* *
39963175 AAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTATA
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTATG
* ** * *
39963215 AAAACGCTGCTAAAGGTCGAGCATTAGCGGCGCTTTTAGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTATG
*
39963255 AAAACGCCGCTAAAAAT-AAGCATTAGCGGCG-TTTTTTG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTATG
*
39963293 AAATGCGCCGC-AAAAA
1 AAA-ACGCCGCTAAAAA
39963309 GCCTAAGCCC
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
38 13 0.16
39 19 0.24
40 47 0.59
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTATG
Found at i:39963401 original size:41 final size:41
Alignment explanation
Indices: 39963344--39963577 Score: 324
Period size: 41 Copynumber: 5.7 Consensus size: 41
39963334 TGAGTTTTTG
* ** *
39963344 GGGCCTTTAGTGGCGTTTTTGAGGAAGCGCCGCTAATGCCC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
39963385 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
39963426 AGGCCTTTAGCGGCGTTTTTGAATAAGTGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
39963467 GTGCCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
39963508 GGGCCTTTAGTGGCGTTTTTCAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*** *
39963549 GATTCTTTAGCGGCGTTTTTGAGAAAGCG
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCG
39963578 TTGCTAATAG
Statistics
Matches: 174, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 174 1.00
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:39964880 original size:13 final size:14
Alignment explanation
Indices: 39964849--39964887 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
39964839 CTGATTTAAA
*
39964849 GGTTATAGGTTAGG
1 GGTTAGAGGTTAGG
*
39964863 GGTTAGGGGTTA-G
1 GGTTAGAGGTTAGG
39964876 GGTTAGAGGTTA
1 GGTTAGAGGTTA
39964888 AGATTAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (14 bp):
GGTTAGAGGTTAGG
Found at i:39965040 original size:82 final size:82
Alignment explanation
Indices: 39964927--39965081 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 82
39964917 TTCGGTGTCA
*
39964927 GTTTATGGTTTAGAGTAATTAGTGTGTTTTAATTTATATATTAAATAATGTTT-AGGAGTTAGGG
1 GTTTATGGTTTAGAGTAATTAGTGTGTTTTAATTTATATATTAAATAAGGTTTAAGG-GTTAGGG
*
39964991 ATTCGGGGTCAGGTTAGG
65 ATTAGGGGTCAGGTTAGG
* * *
39965009 GTTTA-GGATTTAGATTAATTAGTTTTTTTTAATTTATATATTAAATAAGGTTTAAGGGTTAGGG
1 GTTTATGG-TTTAGAGTAATTAGTGTGTTTTAATTTATATATTAAATAAGGTTTAAGGGTTAGGG
*
39965073 GTTAGGGGT
65 ATTAGGGGT
39965082 TTGGGGTTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 2 0.03
82 60 0.92
83 3 0.05
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (82 bp):
GTTTATGGTTTAGAGTAATTAGTGTGTTTTAATTTATATATTAAATAAGGTTTAAGGGTTAGGGA
TTAGGGGTCAGGTTAGG
Found at i:39966104 original size:148 final size:146
Alignment explanation
Indices: 39965928--39966269 Score: 481
Period size: 147 Copynumber: 2.3 Consensus size: 146
39965918 AATAAAAGAT
* * * * * *
39965928 TTTTAGCATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTGCGGCGTTTTTGTGA
1 TTTTAGCATAGCAAAACAGTATCGTTTTATTCCAAATAAAATAATTTTTTACGACATTTTTATGA
* *
39965993 AAAACGTCGCAAAAGGTAAGCAATAGCGGCATTTTTATAAAAAACGCCACAAAAAATAATTTTAC
66 AAAACGCCGCAAAAGGTAAGCAATAGCGGCATTTTTATAAAAAACACCAC-AAAAATAATTTTA-
* *
39966058 TTTTAAAAAATAGCGCCC
129 TTTTAAAAAATAGCACCA
* * * *
39966076 TTTTAGCATAGCAAAACACTATCGTTTTATTCCAGATAAAATAA-TTTGTACGACATTTTTATGG
1 TTTTAGCATAGCAAAACAGTATCGTTTTATTCCAAATAAAATAATTTTTTACGACATTTTTATGA
* * *
39966140 AAAACGCCGCAAAAGGTAAGCAATAGCGGCGTTTTTTTAAAAAACATCACAAAAATAATTTTATT
66 AAAACGCCGCAAAAGGTAAGCAATAGCGGCATTTTTATAAAAAACACCACAAAAATAATTTTATT
39966205 TTAAAAAATAGCACCA
131 TTAAAAAATAGCACCA
* *
39966221 TTTTA-TATAGCAAAACAGTATCGTTTTATTCTAAATAAAATAATTTTTT
1 TTTTAGCATAGCAAAACAGTATCGTTTTATTCCAAATAAAATAATTTTTT
39966270 TACGGCAATA
Statistics
Matches: 171, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
144 34 0.20
145 25 0.15
146 13 0.08
147 59 0.35
148 40 0.23
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (146 bp):
TTTTAGCATAGCAAAACAGTATCGTTTTATTCCAAATAAAATAATTTTTTACGACATTTTTATGA
AAAACGCCGCAAAAGGTAAGCAATAGCGGCATTTTTATAAAAAACACCACAAAAATAATTTTATT
TTAAAAAATAGCACCA
Found at i:39969981 original size:35 final size:34
Alignment explanation
Indices: 39969942--39970007 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
39969932 TAATTGTGTT
39969942 ATTAATTTATTAT-TTTAAAATTTAAAATTAAATTC
1 ATTAATTT-TTATATTT-AAATTTAAAATTAAATTC
**
39969977 ATTAATTTTTATATTTAGTTTTAAAATTAAA
1 ATTAATTTTTATATTTAAATTTAAAATTAAA
39970008 ATTTTCATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 17 0.61
35 11 0.39
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (34 bp):
ATTAATTTTTATATTTAAATTTAAAATTAAATTC
Found at i:39970113 original size:24 final size:22
Alignment explanation
Indices: 39970085--39970128 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
39970075 AAATTTAAAA
39970085 CATAAAACATAATATAATATTTAT
1 CATAAAA-ATAA-ATAATATTTAT
*
39970109 CATAAAAATAAATATTATTT
1 CATAAAAATAAATAATATTT
39970129 GATTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
CATAAAAATAAATAATATTTAT
Found at i:39970209 original size:43 final size:43
Alignment explanation
Indices: 39970160--39970407 Score: 311
Period size: 43 Copynumber: 5.7 Consensus size: 43
39970150 GGTTATTTTT
* * *
39970160 TAGCGGCGTTTTTGCGATAAGCGCCGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
*
39970203 TAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
* * * *
39970246 TAGCGGTGTTTGTGGGAAAAGTGCTGCTAAAAGGTTGTGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCT-AAAGGTCGTGGTCTA
* * *
39970290 TAGCGGCGTTT-TCGGGAAGAGCGCCGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
* * * *
39970333 TAGCTGCGTTTGTGGGAAAAGCACTGCTAAAGGT-GATGGTCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCG-TGGTCTA
*
39970376 TAGCGGCGTTTGTGGGAAAAGCGCAGCTAAAG
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
39970408 ACCATGACCT
Statistics
Matches: 177, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
43 140 0.79
44 37 0.21
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTA
Found at i:39970289 original size:87 final size:85
Alignment explanation
Indices: 39970160--39970407 Score: 302
Period size: 87 Copynumber: 2.9 Consensus size: 85
39970150 GGTTATTTTT
* * * * * *
39970160 TAGCGGCGTTTTTGCGATAAGCGCCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCACTGCTAAAGGTTGTGGTCTATAGCGGCGTTTGTGGGAAAAGC
*
39970225 GTCGCTAAAGGTCGTGGTCTA
66 G-CGCTAAAGGTCATGGTCTA
* ** *
39970246 TAGCGGTGTTTGTGGGAAAAGTGCTGCTAAAAGGTTGTGGTCTATAGCGGCGTTT-TCGGGAAGA
1 TAGCGGCGTTTGTGGGAAAAGCACTGCT-AAAGGTTGTGGTCTATAGCGGCGTTTGT-GGGAAAA
*
39970310 GCGCCGCTAAAGGTCATGGTCTT
64 GCG-CGCTAAAGGTCATGGTCTA
* *
39970333 TAGCTGCGTTTGTGGGAAAAGCACTGCTAAAGG-TGATGGTCTTTAGCGGCGTTTGTGGGAAAAG
1 TAGCGGCGTTTGTGGGAAAAGCACTGCTAAAGGTTG-TGGTCTATAGCGGCGTTTGTGGGAAAAG
39970397 CGCAGCTAAAG
65 CGC-GCTAAAG
39970408 ACCATGACCT
Statistics
Matches: 140, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
85 3 0.02
86 61 0.44
87 76 0.54
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.27
Consensus pattern (85 bp):
TAGCGGCGTTTGTGGGAAAAGCACTGCTAAAGGTTGTGGTCTATAGCGGCGTTTGTGGGAAAAGC
GCGCTAAAGGTCATGGTCTA
Found at i:39970393 original size:130 final size:130
Alignment explanation
Indices: 39970160--39970406 Score: 356
Period size: 130 Copynumber: 1.9 Consensus size: 130
39970150 GGTTATTTTT
* *
39970160 TAGCGGCGTTTTTGCGATAAGCGCCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGAAAAGC
1 TAGCGGCGTTTTCGCGATAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAAGC
* * * *
39970225 GTCGCTAAAGGTCGTGGTCTATAGCGGTGTTTGTGGGAAAAGTGCTGCTAAAAGGTTGTGGTCTA
66 CTCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGAAAAGCGCAGCTAAAAGGTTGTGGTCTA
* * *
39970290 TAGCGGCGTTTTCGGGA-AGAGCGCCGCTAAAGGTCATGGTCTTTAGCTGCGTTTGTGGGAAAAG
1 TAGCGGCGTTTTCGCGATA-AGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAAG
*
39970354 CACT-GCTAAAGGT-GATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCAGCTAAA
65 C-CTCGCTAAAGGTCG-TGGTCTATAGCGGCGTTTGTGGGAAAAGCGCAGCTAAA
39970407 GACCATGACC
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
129 2 0.02
130 101 0.97
131 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.27
Consensus pattern (130 bp):
TAGCGGCGTTTTCGCGATAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAAGC
CTCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGGAAAAGCGCAGCTAAAAGGTTGTGGTCTA
Found at i:39971327 original size:11 final size:11
Alignment explanation
Indices: 39971311--39971352 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
39971301 TCCTTTTTCA
39971311 GTTTTTTATTT
1 GTTTTTTATTT
39971322 GTTTTTTA-TT
1 GTTTTTTATTT
* *
39971332 ATTTTTAATTT
1 GTTTTTTATTT
*
39971343 GTTTATTATT
1 GTTTTTTATT
39971353 ATTTTATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (11 bp):
GTTTTTTATTT
Found at i:39971336 original size:21 final size:21
Alignment explanation
Indices: 39971312--39971379 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
39971302 CCTTTTTCAG
* *
39971312 TTTTTTATTTGTTTTTTATTA
1 TTTTTAATTTGTTTATTATTA
39971333 TTTTTAATTTGTTTATTATTA
1 TTTTTAATTTGTTTATTATTA
*
39971354 TTTTATAATAT-TTTATGTA-TA
1 TTTT-TAATTTGTTTAT-TATTA
39971375 TTTTT
1 TTTTT
39971380 TTGGTGGAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.81
22 7 0.17
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTTAATTTGTTTATTATTA
Found at i:39972163 original size:15 final size:16
Alignment explanation
Indices: 39972143--39972173 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
39972133 ATGTTTGAAA
39972143 TGTAAAAT-TATATTT
1 TGTAAAATATATATTT
39972158 TGTAAAATATATATTT
1 TGTAAAATATATATTT
39972174 GGAATAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TGTAAAATATATATTT
Found at i:39972307 original size:10 final size:10
Alignment explanation
Indices: 39972292--39972334 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
39972282 ACAGAGAAAC
*
39972292 AAAAAATTAA
1 AAAAAATGAA
39972302 AAAAAATGAA
1 AAAAAATGAA
*
39972312 AAACAATGAGA
1 AAAAAATGA-A
39972323 AAAAAAGTGAA
1 AAAAAA-TGAA
39972334 A
1 A
39972335 GCTGAATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 17 0.61
11 8 0.29
12 3 0.11
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:39975933 original size:13 final size:13
Alignment explanation
Indices: 39975915--39975939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39975905 GATATATTTG
39975915 CATATACATAATA
1 CATATACATAATA
39975928 CATATACATAAT
1 CATATACATAAT
39975940 TTTTTTACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
CATATACATAATA
Found at i:39976548 original size:30 final size:30
Alignment explanation
Indices: 39976512--39976569 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
39976502 TACAAGTAAG
39976512 GGGGAGGCTCTCTATTTATAGTTGAGCTAA
1 GGGGAGGCTCTCTATTTATAGTTGAGCTAA
39976542 GGGGAGGCTCTCTATTTATAGTTGAGCT
1 GGGGAGGCTCTCTATTTATAGTTGAGCT
39976570 CCCCTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (30 bp):
GGGGAGGCTCTCTATTTATAGTTGAGCTAA
Found at i:39982783 original size:13 final size:13
Alignment explanation
Indices: 39982765--39982789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39982755 TTCTTTGCGC
39982765 TTGTTTGTTTGTG
1 TTGTTTGTTTGTG
39982778 TTGTTTGTTTGT
1 TTGTTTGTTTGT
39982790 CCTTCTTACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (13 bp):
TTGTTTGTTTGTG
Found at i:39996820 original size:118 final size:113
Alignment explanation
Indices: 39996601--39996837 Score: 402
Period size: 118 Copynumber: 2.1 Consensus size: 113
39996591 CTGCTTCTTG
39996601 ATTTATTTCCTGTGTGCAAAATATGACCTGTGCATATTGGTAACATTCAAAGGTAAAATGGTAAA
1 ATTTATTTCCTGTGTGCAAAATATGACCTGTGCATATTGGTAACATTCAAAGGTAAAATGGTAAA
* *
39996666 AAGATACCAAAAAGAAAAAAGAATGAACCATGGATTTAACCCCTTGGT
66 AAGATACCAAAAACAAAAAAGAATGAACCATGGATTTAACCCCTTCGT
39996714 ATTTATTTCCTGTGTGCAAAATATGACCTGTGCATATTGGTAACATTCAAAGGAAAGGTAAAATG
1 ATTTATTTCCTGTGTGCAAAATATGACCTGTGCATATTGGTAACATTC-----AAAGGTAAAATG
39996779 GTAAAAAGATACCAAAAACAAAAAAGAATGAACCATGGATTTAACCCCTTCGT
61 GTAAAAAGATACCAAAAACAAAAAAGAATGAACCATGGATTTAACCCCTTCGT
*
39996832 TTTTAT
1 ATTTAT
39996838 GGCCACTCTT
Statistics
Matches: 116, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
113 48 0.41
118 68 0.59
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (113 bp):
ATTTATTTCCTGTGTGCAAAATATGACCTGTGCATATTGGTAACATTCAAAGGTAAAATGGTAAA
AAGATACCAAAAACAAAAAAGAATGAACCATGGATTTAACCCCTTCGT
Found at i:40002664 original size:12 final size:13
Alignment explanation
Indices: 40002647--40002676 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40002637 TTATTTAATA
40002647 TTAATAT-AAATT
1 TTAATATAAAATT
40002659 TTAATATAAAATT
1 TTAATATAAAATT
40002672 TTAAT
1 TTAAT
40002677 TTATCATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATATAAAATT
Found at i:40003670 original size:9 final size:9
Alignment explanation
Indices: 40003656--40003713 Score: 89
Period size: 9 Copynumber: 6.4 Consensus size: 9
40003646 GTAGTGATTC
*
40003656 AATTCGGTT
1 AATTCGGGT
40003665 AATTCGGGT
1 AATTCGGGT
40003674 AATTCGGGT
1 AATTCGGGT
*
40003683 AATTCGGTT
1 AATTCGGGT
40003692 AATTCGGGT
1 AATTCGGGT
*
40003701 AATTCGGTT
1 AATTCGGGT
40003710 AATT
1 AATT
40003714 TTTAACAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:40003679 original size:18 final size:18
Alignment explanation
Indices: 40003656--40003713 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
40003646 GTAGTGATTC
* *
40003656 AATTCGGTTAATTCGGGT
1 AATTCGGGTAATTCGGTT
40003674 AATTCGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
40003692 AATTCGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
40003710 AATT
1 AATT
40003714 TTTAACAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (18 bp):
AATTCGGGTAATTCGGTT
Found at i:40003688 original size:27 final size:27
Alignment explanation
Indices: 40003656--40003713 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
40003646 GTAGTGATTC
40003656 AATTCGGTTAATTCGGGTAATTCGGGT
1 AATTCGGTTAATTCGGGTAATTCGGGT
*
40003683 AATTCGGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTCGGGTAATTCGGGT
40003710 AATT
1 AATT
40003714 TTTAACAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (27 bp):
AATTCGGTTAATTCGGGTAATTCGGGT
Found at i:40007120 original size:51 final size:51
Alignment explanation
Indices: 40007051--40007195 Score: 195
Period size: 51 Copynumber: 2.8 Consensus size: 51
40007041 GATACCGGTT
* * *
40007051 CACATAGCAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATA
* * *
40007102 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGATA
*
40007153 CGCATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
40007196 TTCACTTTCA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
50 3 0.04
51 75 0.93
52 3 0.04
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGATA
Found at i:40014573 original size:14 final size:14
Alignment explanation
Indices: 40014551--40014601 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
40014541 TATACAATAT
40014551 ATAAAAATATTCTC
1 ATAAAAATATTCTC
* *
40014565 ATAATAATA-T-TG
1 ATAAAAATATTCTC
*
40014577 ATAAAAATACTCTC
1 ATAAAAATATTCTC
*
40014591 ATAATAATATT
1 ATAAAAATATT
40014602 TTTTACTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
12 9 0.31
13 2 0.07
14 18 0.62
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (14 bp):
ATAAAAATATTCTC
Found at i:40014580 original size:26 final size:26
Alignment explanation
Indices: 40014551--40014601 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
40014541 TATACAATAT
*
40014551 ATAAAAATATTCTCATAATAATATTG
1 ATAAAAATACTCTCATAATAATATTG
40014577 ATAAAAATACTCTCATAATAATATT
1 ATAAAAATACTCTCATAATAATATT
40014602 TTTTACTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (26 bp):
ATAAAAATACTCTCATAATAATATTG
Found at i:40014750 original size:23 final size:23
Alignment explanation
Indices: 40014724--40014770 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
40014714 TAATTACTTG
40014724 TAATATCAACTCCGTCAGAGATT
1 TAATATCAACTCCGTCAGAGATT
40014747 TAATATCAACTCCGTCAGAGATT
1 TAATATCAACTCCGTCAGAGATT
40014770 T
1 T
40014771 TAAGTAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (23 bp):
TAATATCAACTCCGTCAGAGATT
Found at i:40015894 original size:56 final size:56
Alignment explanation
Indices: 40015831--40015950 Score: 150
Period size: 56 Copynumber: 2.1 Consensus size: 56
40015821 GTGTCCATGC
* * * *
40015831 CCGTGTGAATATACTGACTTGGGACACACGGCCAAGCCACACGCCCGTGTGCTAAG
1 CCGTGTGAATATACTGACTTAGGACACACAGCCAAACCACACGCCCATGTGCTAAG
* * * * * *
40015887 CTGTGTGAGTATACTGCCTTAGGTCATACATCCAAACCACACGCCCATGTGCTAAG
1 CCGTGTGAATATACTGACTTAGGACACACAGCCAAACCACACGCCCATGTGCTAAG
40015943 CCGTGTGA
1 CCGTGTGA
40015951 GCAATTTGAG
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (56 bp):
CCGTGTGAATATACTGACTTAGGACACACAGCCAAACCACACGCCCATGTGCTAAG
Found at i:40017011 original size:25 final size:25
Alignment explanation
Indices: 40016936--40017012 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
40016926 GAGTAGTAAA
* *
40016936 CGGGAAGCTCTT-CTGAGCTGAATAA
1 CGGGAAGCTCTTGC-GAGCTAAATAT
* * *
40016961 CGGGAAGCTCATGAGAGCTAAGTAT
1 CGGGAAGCTCTTGCGAGCTAAATAT
40016986 CGGGAAGCTCTTGCGAGCTAAATAT
1 CGGGAAGCTCTTGCGAGCTAAATAT
40017011 CG
1 CG
40017013 AAAAGCTCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (25 bp):
CGGGAAGCTCTTGCGAGCTAAATAT
Found at i:40017018 original size:25 final size:25
Alignment explanation
Indices: 40016965--40017029 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
40016955 GAATAACGGG
* * **
40016965 AAGCTCATGAGAGCTAAGTATCGGG
1 AAGCTCATGCGAGCTAAATATCGAA
*
40016990 AAGCTCTTGCGAGCTAAATATCGAA
1 AAGCTCATGCGAGCTAAATATCGAA
*
40017015 AAGCTCATGCAAGCT
1 AAGCTCATGCGAGCT
40017030 GTGGTGCGTC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (25 bp):
AAGCTCATGCGAGCTAAATATCGAA
Found at i:40023425 original size:55 final size:56
Alignment explanation
Indices: 40023317--40023436 Score: 161
Period size: 55 Copynumber: 2.2 Consensus size: 56
40023307 GTGTCCACGC
* * * *
40023317 CCGTGTGAATATACTGACTTGGGACACACGACCAAGCCACACGCCCATGTGCTAAG
1 CCGTGTGAGTATACTAACTTGGGACACACGACCAAACCACACACCCATGTGCTAAG
* * *
40023373 CCGTGTGAGTATACTAACTT-GGTCACACGGCCAAACCACACACCCGTGTGCTAAG
1 CCGTGTGAGTATACTAACTTGGGACACACGACCAAACCACACACCCATGTGCTAAG
*
40023428 CCGTTTGAG
1 CCGTGTGAG
40023437 CAATTTGAGC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 38 0.68
56 18 0.32
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (56 bp):
CCGTGTGAGTATACTAACTTGGGACACACGACCAAACCACACACCCATGTGCTAAG
Found at i:40024477 original size:25 final size:26
Alignment explanation
Indices: 40024412--40024478 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 26
40024402 CAGTAAACGG
* * *
40024412 GAAGGTCATGAGAGCT-AAGTATCGG
1 GAAGCTCATGCGAGCTGAAGTATCGA
* *
40024437 GAAGCTCTTGCAAGCTGAA-TATCGA
1 GAAGCTCATGCGAGCTGAAGTATCGA
*
40024462 GAAGCTGATGCGAGCTG
1 GAAGCTCATGCGAGCTG
40024479 TGGTGTGTCC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
25 31 0.94
26 2 0.06
ACGTcount: A:0.30, C:0.16, G:0.33, T:0.21
Consensus pattern (26 bp):
GAAGCTCATGCGAGCTGAAGTATCGA
Found at i:40028105 original size:17 final size:17
Alignment explanation
Indices: 40028080--40028128 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
40028070 TTTAGGGTTT
*
40028080 TTAGGTTTAAGGTTTTG
1 TTAGTTTTAAGGTTTTG
* *
40028097 TTAGTTTTAGGGTTTAG
1 TTAGTTTTAAGGTTTTG
*
40028114 GT-GTTTTAAGGTTTT
1 TTAGTTTTAAGGTTTT
40028129 TGGAATTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (17 bp):
TTAGTTTTAAGGTTTTG
Found at i:40042232 original size:42 final size:43
Alignment explanation
Indices: 40042138--40042250 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
40042128 CAATTCCATC
* * * * *
40042138 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGTCACT
1 GTCCCAGACATGGTCTTACACGAAATCAAATATCGATGCCAAT
* * *
40042181 GTCCTAGACAAGGTCTTACACGAAATCATATA-CGATGCCAAT
1 GTCCCAGACATGGTCTTACACGAAATCAAATATCGATGCCAAT
40042223 GTCCCAGACATGGTCTTACACGTAAATC
1 GTCCCAGACATGGTCTTACACG-AAATC
40042251 TCAAATAGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 28 0.47
43 31 0.53
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGAAATCAAATATCGATGCCAAT
Found at i:40048747 original size:16 final size:15
Alignment explanation
Indices: 40048707--40048748 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
40048697 AGATGATAAT
40048707 TATTAATATATAATTA
1 TATTAAT-TATAATTA
40048723 TA-TACATTATAATATA
1 TATTA-ATTATAAT-TA
40048739 TATTAATTAT
1 TATTAATTAT
40048749 TATCAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.35
16 13 0.57
17 2 0.09
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:40062511 original size:4 final size:4
Alignment explanation
Indices: 40062502--40062545 Score: 81
Period size: 4 Copynumber: 11.2 Consensus size: 4
40062492 ATCTAAGCCC
40062502 CATA CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
40062546 TTATTCATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:40064509 original size:23 final size:20
Alignment explanation
Indices: 40064479--40064522 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 20
40064469 TCCATCCACT
40064479 AGTTTATATATATAGTTAGATTA
1 AGTTTATA-AT-TAGTTA-ATTA
40064502 AGTTTATAATTAGTTAATTA
1 AGTTTATAATTAGTTAATTA
40064522 A
1 A
40064523 TTAGGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 2 0.10
23 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (20 bp):
AGTTTATAATTAGTTAATTA
Found at i:40066619 original size:20 final size:20
Alignment explanation
Indices: 40066594--40066632 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40066584 TTGTTTCTTC
40066594 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
40066614 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
40066633 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:40066977 original size:50 final size:50
Alignment explanation
Indices: 40066923--40067029 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
40066913 ACATAGGAGT
* * * *
40066923 TCTCATATCAGTACCCATGCCATGTCTCAGACATGGTCTTACGGGGGACC
1 TCTCATATCAGTACCAACGCCATGTCCCAGACATGGTCTTACGGGAGACC
* * * *
40066973 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACGTGAGACC
1 TCTCATATCAGTACCAACGCCATGTCCCAGACATGGTCTTACGGGAGACC
40067023 TCTCATA
1 TCTCATA
40067030 AACTCAATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (50 bp):
TCTCATATCAGTACCAACGCCATGTCCCAGACATGGTCTTACGGGAGACC
Found at i:40069106 original size:26 final size:26
Alignment explanation
Indices: 40069076--40069154 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
40069066 TCAAGATAAA
40069076 TATTAGATTAAATTTAATATTAAATT
1 TATTAGATTAAATTTAATATTAAATT
* ** *
40069102 TATTAAATT-AATAGAATATT-TATCT
1 TATTAGATTAAATTTAATATTAAAT-T
40069127 TATATAGA-TAAATATTAA-ATTAAATT
1 TAT-TAGATTAAAT-TTAATATTAAATT
40069153 TA
1 TA
40069155 ATATTAAGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
24 2 0.05
25 14 0.35
26 20 0.50
27 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (26 bp):
TATTAGATTAAATTTAATATTAAATT
Found at i:40069109 original size:58 final size:60
Alignment explanation
Indices: 40069044--40069161 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 60
40069034 ATCACTTTAA
* *
40069044 TATTAAATTAATATAACACTTATC-A-AGATAAATATTAGATTAAATTTAATATTAAATT
1 TATTAAATTAATAGAACACTTATCTATAGATAAATATTAAATTAAATTTAATATTAAATT
* *
40069102 TATTAAATTAATAGAATATTTATCTTATATAGATAAATATTAAATTAAATTTAATATTAA
1 TATTAAATTAATAGAACACTTATC---TATAGATAAATATTAAATTAAATTTAATATTAA
40069162 GATAATCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
58 21 0.41
62 1 0.02
63 29 0.57
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (60 bp):
TATTAAATTAATAGAACACTTATCTATAGATAAATATTAAATTAAATTTAATATTAAATT
Found at i:40069206 original size:39 final size:39
Alignment explanation
Indices: 40069156--40069238 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
40069146 TTAAATTTAA
40069156 TATTAAGATAATCACTTTAATATTAAATTATTAAAATAC
1 TATTAAGATAATCACTTTAATATTAAATTATTAAAATAC
40069195 TATTAAGATAATCACTTTAATATTAAATTATTAAAATAC
1 TATTAAGATAATCACTTTAATATTAAATTATTAAAATAC
40069234 T-TTAA
1 TATTAA
40069239 TATTAAATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 4 0.09
39 40 0.91
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (39 bp):
TATTAAGATAATCACTTTAATATTAAATTATTAAAATAC
Found at i:40069236 original size:63 final size:63
Alignment explanation
Indices: 40069169--40069297 Score: 258
Period size: 63 Copynumber: 2.0 Consensus size: 63
40069159 TAAGATAATC
40069169 ACTTTAATATTAAATTATTAAAATACTATTAAGATAATCACTTTAATATTAAATTATTAAAAT
1 ACTTTAATATTAAATTATTAAAATACTATTAAGATAATCACTTTAATATTAAATTATTAAAAT
40069232 ACTTTAATATTAAATTATTAAAATACTATTAAGATAATCACTTTAATATTAAATTATTAAAAT
1 ACTTTAATATTAAATTATTAAAATACTATTAAGATAATCACTTTAATATTAAATTATTAAAAT
40069295 ACT
1 ACT
40069298 ATCAAGATAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (63 bp):
ACTTTAATATTAAATTATTAAAATACTATTAAGATAATCACTTTAATATTAAATTATTAAAAT
Found at i:40069239 original size:24 final size:24
Alignment explanation
Indices: 40069208--40069263 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
40069198 TAAGATAATC
40069208 ACTTTAATATTAAATTATTAAAAT
1 ACTTTAATATTAAATTATTAAAAT
40069232 ACTTTAATATTAAATTATTAAAAT
1 ACTTTAATATTAAATTATTAAAAT
40069256 ACTATTAA
1 ACT-TTAA
40069264 GATAATCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (24 bp):
ACTTTAATATTAAATTATTAAAAT
Found at i:40069276 original size:39 final size:39
Alignment explanation
Indices: 40069231--40069338 Score: 152
Period size: 39 Copynumber: 2.8 Consensus size: 39
40069221 ATTATTAAAA
40069231 TACTTTAATATTAAATTATTAAAATACTATTAAGATAA-
1 TACTTTAATATTAAATTATTAAAATACTATTAAGATAAG
*
40069269 TCACTTTAATATTAAATTATTAAAATACTATCAAGATAAG
1 T-ACTTTAATATTAAATTATTAAAATACTATTAAGATAAG
*
40069309 TA--TTAA-ATTAAATTTATTAAAATAATATTA
1 TACTTTAATATTAAA-TTATTAAAATACTATTA
40069339 TTTTTGGAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
36 6 0.09
37 19 0.30
38 1 0.02
39 37 0.58
40 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (39 bp):
TACTTTAATATTAAATTATTAAAATACTATTAAGATAAG
Found at i:40070117 original size:49 final size:49
Alignment explanation
Indices: 40070060--40070153 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
40070050 CAATTTACTT
* *
40070060 ATTGAAAACTCCTTATTGTATACTCTTTACAAAAACAATTCATCCCATG
1 ATTGAAAACTCCTTACTGTATACTCTTTACAAAAACAATGCATCCCATG
40070109 ATTGAAAACTCCTTACTGTATACTCTTTACAAAAACAATGCATCC
1 ATTGAAAACTCCTTACTGTATACTCTTTACAAAAACAATGCATCC
40070154 ATCTGTTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.33
Consensus pattern (49 bp):
ATTGAAAACTCCTTACTGTATACTCTTTACAAAAACAATGCATCCCATG
Found at i:40072279 original size:21 final size:20
Alignment explanation
Indices: 40072253--40072294 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
40072243 AACTTTTACC
40072253 ATTTTGAACTTAGGTATCGAT
1 ATTTTGAACTTA-GTATCGAT
* *
40072274 ATTTTGCATTTAGTATCGAT
1 ATTTTGAACTTAGTATCGAT
40072294 A
1 A
40072295 CTTGGCCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.45
Consensus pattern (20 bp):
ATTTTGAACTTAGTATCGAT
Found at i:40073284 original size:174 final size:173
Alignment explanation
Indices: 40072985--40073331 Score: 658
Period size: 174 Copynumber: 2.0 Consensus size: 173
40072975 AAACTCTTAA
40072985 AAGCAATATAAAGCATTACAAGTTAAATCTTTGATAAAATAGAAATATTTGTGGCATGCAATATA
1 AAGCAATATAAAGCATTACAAGTTAAATCTTTGATAAAATAGAAATATTTGTGGCATGCAATATA
40073050 TTCGCCATTTGAAAACATATTCCCAAAAATATCCCTTTGTATGCATAACATCGTACTACGGTCAA
66 TTCGCCATTTGAAAACATATTCCCAAAAATATCCCTTTGTATGCATAACATCGTACTACGGTCAA
40073115 CCACGTTGGTGCATTCATAACTTGGTCCCTTATGGCGAACTGG
131 CCACGTTGGTGCATTCATAACTTGGTCCCTTATGGCGAACTGG
*
40073158 AAGCAATATAAAGCATTACAAGTTAAATCTTTGATAAAATAGACATATTTGTGGCATGCAATACT
1 AAGCAATATAAAGCATTACAAGTTAAATCTTTGATAAAATAGAAATATTTGTGGCATGCAATA-T
*
40073223 ATTCGCCATTTGAAAACATATTCCCCAAAATATCCCTTTGTATGCATAACATCGTACTACGGTCA
65 ATTCGCCATTTGAAAACATATTCCCAAAAATATCCCTTTGTATGCATAACATCGTACTACGGTCA
*
40073288 ACCACGTTGGTGCATTCCTAACTTGGTCCCTTATGGCGAACTGG
130 ACCACGTTGGTGCATTCATAACTTGGTCCCTTATGGCGAACTGG
40073332 TTCAGCTCAA
Statistics
Matches: 170, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
173 62 0.36
174 108 0.64
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (173 bp):
AAGCAATATAAAGCATTACAAGTTAAATCTTTGATAAAATAGAAATATTTGTGGCATGCAATATA
TTCGCCATTTGAAAACATATTCCCAAAAATATCCCTTTGTATGCATAACATCGTACTACGGTCAA
CCACGTTGGTGCATTCATAACTTGGTCCCTTATGGCGAACTGG
Found at i:40074077 original size:25 final size:25
Alignment explanation
Indices: 40074049--40074136 Score: 104
Period size: 25 Copynumber: 3.5 Consensus size: 25
40074039 GACTCACCAA
*
40074049 AAAGGCTTCCCAAGTAAATTGCCAC
1 AAAGGCTTCACAAGTAAATTGCCAC
* * *
40074074 AAAGGCTTTACAAGTGACTTGCCAC
1 AAAGGCTTCACAAGTAAATTGCCAC
** *
40074099 AAAGGCTTCTGAAGTAAATCGCCAC
1 AAAGGCTTCACAAGTAAATTGCCAC
*
40074124 AAAGGCTTTACAA
1 AAAGGCTTCACAA
40074137 ATGACTCATG
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (25 bp):
AAAGGCTTCACAAGTAAATTGCCAC
Found at i:40077680 original size:13 final size:13
Alignment explanation
Indices: 40077662--40077686 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40077652 CAATTAGAGG
40077662 ATATTGTTAATTC
1 ATATTGTTAATTC
40077675 ATATTGTTAATT
1 ATATTGTTAATT
40077687 TAAACATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATATTGTTAATTC
Found at i:40084058 original size:22 final size:22
Alignment explanation
Indices: 40084030--40084158 Score: 132
Period size: 22 Copynumber: 5.9 Consensus size: 22
40084020 TACACCATAC
*
40084030 TAGAGAGCACCGTAGTGCTAAA
1 TAGAGAGCACCGAAGTGCTAAA
*
40084052 TAGAGAGCACCAAAGTGCTAAA
1 TAGAGAGCACCGAAGTGCTAAA
** ** * *
40084074 TAGAGAGCACTAAAACGCCAAG
1 TAGAGAGCACCGAAGTGCTAAA
* *
40084096 TAGAGAGCACCGAAGTGTTGAA
1 TAGAGAGCACCGAAGTGCTAAA
* *
40084118 TAGAGAGCATCGAAGTGCTAGA
1 TAGAGAGCACCGAAGTGCTAAA
**
40084140 TAGAGAGCACTAAAGTGCT
1 TAGAGAGCACCGAAGTGCT
40084159 GAATCCATAT
Statistics
Matches: 85, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 85 1.00
ACGTcount: A:0.40, C:0.17, G:0.27, T:0.16
Consensus pattern (22 bp):
TAGAGAGCACCGAAGTGCTAAA
Found at i:40084120 original size:66 final size:66
Alignment explanation
Indices: 40084030--40084153 Score: 194
Period size: 66 Copynumber: 1.9 Consensus size: 66
40084020 TACACCATAC
*
40084030 TAGAGAGCACCGTAGTGCTAAATAGAGAGCACCAAAGTGCTAAATAGAGAGCACTAAAACGCCAA
1 TAGAGAGCACCGAAGTGCTAAATAGAGAGCACCAAAGTGCTAAATAGAGAGCACTAAAACGCCAA
40084095 G
66 G
* * * * *
40084096 TAGAGAGCACCGAAGTGTTGAATAGAGAGCATCGAAGTGCTAGATAGAGAGCACTAAA
1 TAGAGAGCACCGAAGTGCTAAATAGAGAGCACCAAAGTGCTAAATAGAGAGCACTAAA
40084154 GTGCTGAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.41, C:0.17, G:0.27, T:0.15
Consensus pattern (66 bp):
TAGAGAGCACCGAAGTGCTAAATAGAGAGCACCAAAGTGCTAAATAGAGAGCACTAAAACGCCAA
G
Found at i:40085156 original size:11 final size:11
Alignment explanation
Indices: 40085128--40085159 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40085118 TATTAATTTA
40085128 TTATAATTAAC
1 TTATAATTAAC
40085139 -T-TAATTAAC
1 TTATAATTAAC
40085148 TTATAATTAAC
1 TTATAATTAAC
40085159 T
1 T
40085160 AAACTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.42
10 2 0.11
11 9 0.47
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (11 bp):
TTATAATTAAC
Found at i:40093924 original size:39 final size:39
Alignment explanation
Indices: 40093880--40093958 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
40093870 AGAAAATTTC
* *
40093880 AAATCAAGTTAGGATGATAAAATAGGATTCGTCAACTCG
1 AAATCAAGTTAGGATAATAAAATAGGATTCGCCAACTCG
*
40093919 AAATCATGTTAGGATAATAAAATAGGATTCGCCAACTCG
1 AAATCAAGTTAGGATAATAAAATAGGATTCGCCAACTCG
40093958 A
1 A
40093959 TTAATTTAAA
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:0.14, G:0.19, T:0.25
Consensus pattern (39 bp):
AAATCAAGTTAGGATAATAAAATAGGATTCGCCAACTCG
Found at i:40096773 original size:18 final size:18
Alignment explanation
Indices: 40096738--40096773 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40096728 TAAATAGTTC
*
40096738 AAGTTATTTGAGTTAATT
1 AAGTTATTTGAGTCAATT
*
40096756 AAGTTATTTGGGTCAATT
1 AAGTTATTTGAGTCAATT
40096774 CGAATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (18 bp):
AAGTTATTTGAGTCAATT
Found at i:40098875 original size:22 final size:21
Alignment explanation
Indices: 40098845--40098889 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
40098835 ACACCAAAAC
*
40098845 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCG-TTTTTT
40098867 AGGCCTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
40098888 AG
1 AG
40098890 CGTCGCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.42
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGTTTTTT
Found at i:40100753 original size:22 final size:19
Alignment explanation
Indices: 40100726--40100797 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 19
40100716 AAATGAACCC
*
40100726 AAAAAACTTAAGTACTAAATT
1 AAAAAAATTAA-TAC-AAATT
* *
40100747 AAAAAAATCAAACACCAAATT
1 AAAAAAAT-TAATA-CAAATT
40100768 AAAAAAAATTAATAACAAATT
1 -AAAAAAATTAAT-ACAAATT
40100789 AGAAAAAAT
1 A-AAAAAAT
40100798 AAAATAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.02
21 28 0.68
22 12 0.29
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.21
Consensus pattern (19 bp):
AAAAAAATTAATACAAATT
Found at i:40100804 original size:22 final size:20
Alignment explanation
Indices: 40100742--40100800 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
40100732 CTTAAGTACT
* *
40100742 AAATTAAAAAAATCAAACACC
1 AAATTAAAAAAAT-AAATAAC
*
40100763 AAATTAAAAAAAATTAATAAC
1 AAATT-AAAAAAATAAATAAC
40100784 AAATTAGAAAAAATAAA
1 AAATTA-AAAAAATAAA
40100801 ATAATTAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 23 0.72
22 8 0.25
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19
Consensus pattern (20 bp):
AAATTAAAAAAATAAATAAC
Found at i:40103846 original size:7 final size:7
Alignment explanation
Indices: 40103836--40103887 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
40103826 CACTAACTAT
*
40103836 TAACCTC
1 TAACCCC
40103843 TAACCCC
1 TAACCCC
40103850 TAACCCC
1 TAACCCC
*
40103857 AAACCCC
1 TAACCCC
*
40103864 AAACCCC
1 TAACCCC
**
40103871 TAACTAC
1 TAACCCC
40103878 TAACCCC
1 TAACCCC
40103885 TAA
1 TAA
40103888 ACCTTATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.37, C:0.48, G:0.00, T:0.15
Consensus pattern (7 bp):
TAACCCC
Found at i:40103882 original size:21 final size:21
Alignment explanation
Indices: 40103828--40103890 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
40103818 CCTTAAATCA
* * *
40103828 CTAACTATTAACCTCTAACCC
1 CTAACTACTAACCCCAAACCC
** *
40103849 CTAACCCCAAACCCCAAACCC
1 CTAACTACTAACCCCAAACCC
40103870 CTAACTACTAACCCCTAAACC
1 CTAACTACTAACCCC-AAACC
40103891 TTATTTAATA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.37, C:0.46, G:0.00, T:0.17
Consensus pattern (21 bp):
CTAACTACTAACCCCAAACCC
Found at i:40113551 original size:23 final size:23
Alignment explanation
Indices: 40113525--40113571 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40113515 ATTTTTTACA
*
40113525 TTTTAAATTAATCTCTCCATTTT
1 TTTTAAATAAATCTCTCCATTTT
* * *
40113548 TTTTGAGTAAATCTCTCTATTTT
1 TTTTAAATAAATCTCTCCATTTT
40113571 T
1 T
40113572 AATTCACGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTAAATAAATCTCTCCATTTT
Found at i:40120420 original size:20 final size:20
Alignment explanation
Indices: 40120378--40120463 Score: 91
Period size: 20 Copynumber: 4.2 Consensus size: 20
40120368 ACATCATAGA
**
40120378 TGCATAACAGGGGCACCGTAG
1 TGCA-AACAGGGGCACCAAAG
* *
40120399 TGCGAACAGGGACACCAAAG
1 TGCAAACAGGGGCACCAAAG
* *
40120419 TGTATACAGGGGCACCAAAG
1 TGCAAACAGGGGCACCAAAG
* *
40120439 TGCAAATAGGGGCATCAAAG
1 TGCAAACAGGGGCACCAAAG
40120459 TGCAA
1 TGCAA
40120464 GTCTTGTACA
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 50 0.94
21 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.30, T:0.13
Consensus pattern (20 bp):
TGCAAACAGGGGCACCAAAG
Found at i:40123949 original size:14 final size:14
Alignment explanation
Indices: 40123930--40123958 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40123920 GGCTTTTTCC
40123930 ATGGTTAACAACTA
1 ATGGTTAACAACTA
40123944 ATGGTTAACAACTA
1 ATGGTTAACAACTA
40123958 A
1 A
40123959 CATGTCCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
ATGGTTAACAACTA
Found at i:40141266 original size:25 final size:23
Alignment explanation
Indices: 40141228--40141273 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
40141218 ATCTTCTTTC
40141228 GTAAAAAGTCAATTACTATCAAATA
1 GTAAAAAGTCAATT--TATCAAATA
40141253 GTAATAAAGT-AATTTATCAAA
1 GTAA-AAAGTCAATTTATCAAA
40141274 AAAAAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 7 0.35
25 8 0.40
26 5 0.25
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (23 bp):
GTAAAAAGTCAATTTATCAAATA
Found at i:40145288 original size:18 final size:18
Alignment explanation
Indices: 40145267--40145315 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
40145257 TTTGCATAAA
40145267 TAACACAGTTCACCAAAT
1 TAACACAGTTCACCAAAT
* * *
40145285 TAACATAGTTCGCGAAAT
1 TAACACAGTTCACCAAAT
*
40145303 TAACACAATTCAC
1 TAACACAGTTCAC
40145316 ATTATTATAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (18 bp):
TAACACAGTTCACCAAAT
Found at i:40152266 original size:26 final size:26
Alignment explanation
Indices: 40152230--40152282 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40152220 TATATACTAC
40152230 ACTCGTGAGAGGGAAAGAATGATGTA
1 ACTCGTGAGAGGGAAAGAATGATGTA
40152256 ACTCGTGAGAGGGAAAGAATGATGTA
1 ACTCGTGAGAGGGAAAGAATGATGTA
40152282 A
1 A
40152283 ACAATACTTT
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:0.40, C:0.08, G:0.34, T:0.19
Consensus pattern (26 bp):
ACTCGTGAGAGGGAAAGAATGATGTA
Found at i:40155098 original size:14 final size:11
Alignment explanation
Indices: 40155067--40155091 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40155057 GGGGAGGGCA
40155067 AGAAAGGTAGT
1 AGAAAGGTAGT
40155078 AGAAAGGTAGT
1 AGAAAGGTAGT
40155089 AGA
1 AGA
40155092 TCAAAGGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (11 bp):
AGAAAGGTAGT
Found at i:40165314 original size:22 final size:22
Alignment explanation
Indices: 40165286--40165333 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40165276 TGATTGATTA
*
40165286 GGATATTCTATAGG-GTTTTAAG
1 GGATATTCTAT-GGTATTTTAAG
*
40165308 GGATATTTTATGGTATTTTAAG
1 GGATATTCTATGGTATTTTAAG
40165330 GGAT
1 GGAT
40165334 TGATTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (22 bp):
GGATATTCTATGGTATTTTAAG
Found at i:40165338 original size:54 final size:52
Alignment explanation
Indices: 40165215--40165343 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 52
40165205 TTCAAAGCTC
* * *
40165215 TATTTTTAGAGATTGATTAGGATATTTTATAGGATTTATGACATATTTATGG
1 TATTTTAAGAGATTGATTAGGATATTCTATAGGATTTAAGACATATTTATGG
* ** * **
40165267 GATTTTAATTGATTGATTAGGATATTCTATAGGGTTTTAAGGGATATTTTATGG
1 TATTTTAAGAGATTGATTAGGATATTCTATA-GGATTTAAGACATA-TTTATGG
*
40165321 TATTTTAAGGGATTGATTAGGAT
1 TATTTTAAGAGATTGATTAGGAT
40165344 TTTATGGGAT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
52 26 0.41
53 10 0.16
54 27 0.43
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (52 bp):
TATTTTAAGAGATTGATTAGGATATTCTATAGGATTTAAGACATATTTATGG
Found at i:40195510 original size:22 final size:22
Alignment explanation
Indices: 40195476--40195519 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
40195466 CAAATTTATG
* *
40195476 AAAATTTATTATAAAAATAATT
1 AAAATTCAATATAAAAATAATT
**
40195498 AAAATTCAATATATTAATAATT
1 AAAATTCAATATAAAAATAATT
40195520 TAAGTGGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTCAATATAAAAATAATT
Found at i:40199966 original size:26 final size:25
Alignment explanation
Indices: 40199913--40199973 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
40199903 CAATAATTTT
**
40199913 ATATATTATATAATAAAACCCATGC
1 ATATATTATATAATAAAACCCACAC
* *
40199938 ATATATGTATATAGTAAGACCCACAC
1 ATATAT-TATATAATAAAACCCACAC
*
40199964 ATATAATATA
1 ATATATTATA
40199974 ATTTATGTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.31
Consensus pattern (25 bp):
ATATATTATATAATAAAACCCACAC
Found at i:40201310 original size:13 final size:13
Alignment explanation
Indices: 40201292--40201342 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
40201282 ATTAATACCA
40201292 TAATTATTTATTT
1 TAATTATTTATTT
40201305 TAATTA-TTATTT
1 TAATTATTTATTT
* *
40201317 TTACTATTT-TTAAT
1 TAATTATTTATT--T
40201331 TAATTATTTATT
1 TAATTATTTATT
40201343 GTATCCTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 12 0.40
13 8 0.27
14 8 0.27
15 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TAATTATTTATTT
Found at i:40201835 original size:31 final size:31
Alignment explanation
Indices: 40201799--40201865 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
40201789 GACGATTTTC
*
40201799 CTTTTCCTTCAAAGTATTTCTTTAGTTCTTT
1 CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
*
40201830 GTTTTCCTTCAAAGTATTTCTTTAATTCTTT
1 CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
40201861 CTTTT
1 CTTTT
40201866 TCTTAAGTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.16, C:0.18, G:0.06, T:0.60
Consensus pattern (31 bp):
CTTTTCCTTCAAAGTATTTCTTTAATTCTTT
Found at i:40202843 original size:22 final size:22
Alignment explanation
Indices: 40202785--40202892 Score: 80
Period size: 22 Copynumber: 5.0 Consensus size: 22
40202775 TACTCTAATT
*
40202785 TGGCCTTTAAGGCACATTTTGTTA
1 TGGCCTTTATGG--CATTTTGTTA
*
40202809 --GTCTTTATGGCATTTTGTTA
1 TGGCCTTTATGGCATTTTGTTA
*
40202829 TGGCCTTTATGGCATTCTGTTA
1 TGGCCTTTATGGCATTTTGTTA
* * ** *
40202851 --ACCTTTGTAACATTTTGATA
1 TGGCCTTTATGGCATTTTGTTA
* *
40202871 TGGCCTTTATGGAATTATGTTA
1 TGGCCTTTATGGCATTTTGTTA
40202893 AATTTGTGGC
Statistics
Matches: 63, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
20 24 0.38
22 39 0.62
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.46
Consensus pattern (22 bp):
TGGCCTTTATGGCATTTTGTTA
Found at i:40210073 original size:22 final size:21
Alignment explanation
Indices: 40210038--40210114 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 21
40210028 AAAGGGTATC
* *
40210038 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
40210059 TACAAAATCATATCTTTTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
40210082 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
40210101 TATATATCATATCT
1 TACAAATCATATCT
40210115 AAGACTGCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
19 16 0.36
21 4 0.09
22 15 0.34
23 9 0.20
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:40210100 original size:19 final size:19
Alignment explanation
Indices: 40210076--40210184 Score: 155
Period size: 19 Copynumber: 5.7 Consensus size: 19
40210066 TCATATCTTT
40210076 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
**
40210095 TAAGATTATATATCATATC
1 TAAGATTGCATATCATATC
* *
40210114 TAAGACTGCATATTATATC
1 TAAGATTGCATATCATATC
** *
40210133 TAAGATTATATATTATATC
1 TAAGATTGCATATCATATC
40210152 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
40210171 TAAGATTGCATATC
1 TAAGATTGCATATC
40210185 CCTGAAGATT
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 78 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Found at i:40210124 original size:38 final size:38
Alignment explanation
Indices: 40210076--40210177 Score: 177
Period size: 38 Copynumber: 2.7 Consensus size: 38
40210066 TCATATCTTT
40210076 TAAGATTGCATATCATATCTAAGATTATATATCATATC
1 TAAGATTGCATATCATATCTAAGATTATATATCATATC
* * *
40210114 TAAGACTGCATATTATATCTAAGATTATATATTATATC
1 TAAGATTGCATATCATATCTAAGATTATATATCATATC
40210152 TAAGATTGCATATCATATCTAAGATT
1 TAAGATTGCATATCATATCTAAGATT
40210178 GCATATCCCT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (38 bp):
TAAGATTGCATATCATATCTAAGATTATATATCATATC
Found at i:40210736 original size:132 final size:132
Alignment explanation
Indices: 40210511--40211271 Score: 1272
Period size: 132 Copynumber: 5.8 Consensus size: 132
40210501 TAGGACTTAC
40210511 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* *
40210576 AACCACAGAGAGGTAAAATCCGTCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
40210641 GA
131 GA
*
40210643 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* * * * * *
40210708 AACCACAGGAAGGTAAAATCCGCGATCTTTGATCTGCTCCACTATTGCTTAGGGAAATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
40210773 GA
131 GA
40210775 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* * *
40210840 AACCACAGGGAGGTAAAATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
40210905 GA
131 GA
*
40210907 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGACTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* *
40210972 AACCATAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
40211037 GA
131 GA
* * * *
40211039 AATCTTCAATCTATTCCACTGTTGTTCAGGGAAGTAGAATTACTGGCTTCAATTTACTGCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* * * *
40211104 AACCACATGGAGGTAAAATCCGTCATTTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
40211169 GA
131 GA
* *
40211171 ATTCTTCAATCTATTCCACGGTTG-CCTAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTA
1 AATCTTCAATCTATTCCACTGTTGTCC-AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTA
*
40211235 TAACCACAGGGAGGTAAAATCCACCATCTTCGATCTG
65 TAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTG
40211272 TTTCGCTGTC
Statistics
Matches: 584, Mismatches: 44, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
131 1 0.00
132 583 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (132 bp):
AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
GA
Found at i:40218154 original size:22 final size:21
Alignment explanation
Indices: 40218119--40218214 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 21
40218109 AAAGGGTATC
* *
40218119 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
40218140 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
40218163 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
40218182 TATATAT--TATATCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
40218201 TGCATATCATATCT
1 TACAAATCATATCT
40218215 AAGATTGCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
17 2 0.03
19 26 0.43
21 7 0.12
22 15 0.25
23 10 0.17
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:40218162 original size:23 final size:22
Alignment explanation
Indices: 40218119--40218176 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40218109 AAAGGGTATC
* *
40218119 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40218140 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40218163 TGCATATCATATCT
1 TACAAATCATATCT
40218177 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40218179 original size:19 final size:19
Alignment explanation
Indices: 40218155--40218227 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
40218145 AATCATATCT
40218155 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
40218174 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
40218193 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40218212 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
40218228 CCTGAAGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40219734 original size:3 final size:3
Alignment explanation
Indices: 40219726--40219774 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
40219716 AAAACAATTA
*
40219726 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
40219774 T
1 T
40219775 TCTTTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:40221322 original size:22 final size:22
Alignment explanation
Indices: 40221283--40221368 Score: 93
Period size: 22 Copynumber: 3.8 Consensus size: 22
40221273 TTCTTCTTTC
*
40221283 AGAGAATATTCACTGTTCAAGCT
1 AGAGAAT-TTTACTGTTCAAGCT
*
40221306 AGATAATTTTACTGTTCAAGCT
1 AGAGAATTTTACTGTTCAAGCT
* *
40221328 AGAGAATTTTATTGTTCATCGC-
1 AGAGAATTTTACTGTTCA-AGCT
*
40221350 AGAGAATCTTCACTGTTCA
1 AGAGAAT-TTTACTGTTCA
40221369 TTCTCATTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
22 37 0.69
23 17 0.31
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
AGAGAATTTTACTGTTCAAGCT
Found at i:40232189 original size:105 final size:108
Alignment explanation
Indices: 40231996--40232192 Score: 301
Period size: 105 Copynumber: 1.9 Consensus size: 108
40231986 AAAAATAATA
* * *
40231996 AAGGTAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATTTGCTGGGTTTCGATTTTTC
1 AAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATATTTC
*
40232061 TCGTTCAACCAAATAGCCGAATATCCTTCCAAAAATTCCAAAT
66 TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAT
* *
40232104 AAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAATGTGCTGGGTTTC-A-ATTTC
1 AAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATATTTC
* *
40232166 TCGTTTAACTAAATAGCCAAATATCCT
66 TCGTTCAACCAAATAGCCAAATATCCT
40232193 CTTGAATTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
105 28 0.35
106 1 0.01
107 24 0.30
108 28 0.35
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (108 bp):
AAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATATTTC
TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAT
Found at i:40238020 original size:86 final size:87
Alignment explanation
Indices: 40237839--40238540 Score: 797
Period size: 86 Copynumber: 8.1 Consensus size: 87
40237829 GATCAGTGAG
* * * * *
40237839 GATC-AAAGACAAAGCCTTGCCTCCATCGATCGCAGTGGAGCTGGTTGAAGATAGTAGATCTTGC
1 GATCGAAA-ACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGC
40237903 CTTCCTGCGTTAACAGCGAAGCA
65 CTTCCTGCGTTAACAGCGAAGCA
* * *
40237926 GATTGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGA-ACCTGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCC
* * *
40237990 TTCCTACATTAACAGAGAAGCA
66 TTCCTGCGTTAACAGCGAAGCA
* * * * * *
40238012 GATCGAAAACAAAGCCTTGCCTCCCTCGGTCGCAGTCGAGCTAGTTGAAGATAGCAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCC
* * *
40238077 TTACTGTGTTAACAGCGAAACA
66 TTCCTGCGTTAACAGCGAAGCA
*
40238099 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCC
** *
40238163 TTCCTATGTTAACAGCGAAGAA
66 TTCCTGCGTTAACAGCGAAGCA
* * * *
40238185 GATCGAAAATAAAGTCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGA-AGCAGGTCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCC
40238249 TTCCTGCGTTAACAGCGAAGCA
66 TTCCTGCGTTAACAGCGAAGCA
* * * *
40238271 GATCAAAAACAAAACCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGACAACAGATCTTGCC
1 GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCC
* * *
40238336 TTCCTGCCTTGACAACGAAGCA
66 TTCCTGCGTTAACAGCGAAGCA
* ** * * *
40238358 GATCGAAGACACAAA-CCTTGCCTCTC-TCGGTTGTAGCAGAGCTGGTTGAAGACAACATATCTT
1 GATCGAA-A-ACAAAGCCTTGCCTC-CATCGGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTT
* * *
40238421 GCCTTCCTGCATTGACAGTGAAGCA
63 GCCTTCCTGCGTTAACAGCGAAGCA
* * * * * * * * *
40238446 TATCGAAGACACAAA-ACTTTCCTCCCTCAGTTGTAGTGGAGCTGGTTGAGGACAACAGATCTTG
1 GATCGAA-A-ACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTG
* * *
40238510 CCTTCCTGCATTGACAGCGAAGTA
64 CCTTCCTGCGTTAACAGCGAAGCA
40238534 GATCGAA
1 GATCGAA
40238541 GTTACAAATC
Statistics
Matches: 538, Mismatches: 70, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
86 230 0.43
87 152 0.28
88 150 0.28
89 6 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (87 bp):
GATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCC
TTCCTGCGTTAACAGCGAAGCA
Found at i:40238138 original size:173 final size:175
Alignment explanation
Indices: 40237839--40238540 Score: 814
Period size: 173 Copynumber: 4.0 Consensus size: 175
40237829 GATCAGTGAG
* * * *
40237839 GATC-AAAGACAAAGCCTTGCCTCCATCGATCGCAGTGGAGCTGGTTGAAGATAGTAGATCTTGC
1 GATCGAAACACAAAGCCTTGCCTCCATCGGTCGCAGTCGAGCTGGTTGAAGATAGCAGATCTTGC
*
40237903 CTTCCTGCGTTAACAGCGAAGCAGATTGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
* *
40237968 GGTTAAAGA-ACCTGATCTTGCCTTCCTACATTAACAGAGAAGCA
131 GGTTAAAGACAACAGATCTTGCCTTCCTACATTAACAGAGAAGCA
* *
40238012 GATCGAAA-ACAAAGCCTTGCCTCCCTCGGTCGCAGTCGAGCTAGTTGAAGATAGCAGATCTTGC
1 GATCGAAACACAAAGCCTTGCCTCCATCGGTCGCAGTCGAGCTGGTTGAAGATAGCAGATCTTGC
* * * *
40238076 CTTACTGTGTTAACAGCGAAACAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCT
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
* ** * *
40238141 GGTTAAAGA-AGCAGATCTTGCCTTCCTATGTTAACAGCGAAGAA
131 GGTTAAAGACAACAGATCTTGCCTTCCTACATTAACAGAGAAGCA
* * * * * * *
40238185 GATCGAAA-ATAAAGTCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGA-AGCAGGTCTTGC
1 GATCGAAACACAAAGCCTTGCCTCCATCGGTCGCAGTCGAGCTGGTTGAAGATAGCAGATCTTGC
* *
40238248 CTTCCTGCGTTAACAGCGAAGCAGATCAAAAACAAAACCTTGCCTCCATCGGTTGCAGTGGAGCT
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
* * * *
40238313 GGTTGAAGACAACAGATCTTGCCTTCCTGCCTTGACA-ACGAAGCA
131 GGTTAAAGACAACAGATCTTGCCTTCCTACATTAACAGA-GAAGCA
* * * * *
40238358 GATCGAAGACACAAA-CCTTGCCTCTC-TCGGTTGTAG-CAGAGCTGGTTGAAGACAACATATCT
1 GATCGAA-ACACAAAGCCTTGCCTC-CATCGGTCGCAGTC-GAGCTGGTTGAAGATAGCAGATCT
* * * * * * * * *
40238420 TGCCTTCCTGCATTGACAGTGAAGCATATCGAAGACACAAA-ACTTTCCTCCCTCAGTTGTAGTG
63 TGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTCCATCGGTTGCAGTG
* * * * * *
40238484 GAGCTGGTTGAGGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGTA
126 GAGCTGGTTAAAGACAACAGATCTTGCCTTCCTACATTAACAGAGAAGCA
40238534 GATCGAA
1 GATCGAA
40238541 GTTACAAATC
Statistics
Matches: 458, Mismatches: 60, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
172 78 0.17
173 230 0.50
174 35 0.08
175 39 0.09
176 71 0.16
177 5 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (175 bp):
GATCGAAACACAAAGCCTTGCCTCCATCGGTCGCAGTCGAGCTGGTTGAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
GGTTAAAGACAACAGATCTTGCCTTCCTACATTAACAGAGAAGCA
Found at i:40238161 original size:43 final size:42
Alignment explanation
Indices: 40238114--40238249 Score: 102
Period size: 43 Copynumber: 3.2 Consensus size: 42
40238104 AAAACAAAGC
40238114 CTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGAAGCAGAT
1 CTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGAAGCAG-T
** * * * * *
40238157 CTTGCCTTCCTAT--GTTAACAGCGAAGAAGATCG-AAAATAA--AGT
1 CTTGCC-TCC-ATCGGTT-GTAGTG--G-AGCTGGTTAAAGAAGCAGT
40238200 CTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGAAGCAGGT
1 CTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGAAGCA-GT
40238243 CTTGCCT
1 CTTGCCT
40238250 TCCTGCGTTA
Statistics
Matches: 67, Mismatches: 14, Indels: 24
0.64 0.13 0.23
Matches are distributed among these distances:
39 4 0.06
40 6 0.09
41 2 0.03
42 7 0.10
43 28 0.42
44 8 0.12
45 2 0.03
46 6 0.09
47 4 0.06
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (42 bp):
CTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGAAGCAGT
Found at i:40238320 original size:259 final size:261
Alignment explanation
Indices: 40237839--40238537 Score: 852
Period size: 259 Copynumber: 2.7 Consensus size: 261
40237829 GATCAGTGAG
* * * * * *
40237839 GATC-AAAGACAAAGCCTTGCCTCCATCGATCGCAGTGGAGCTGGTTGAAGATAGTAGATCTTGC
1 GATCGAAACACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGC
* * *
40237903 CTTCCTGCGTTAACAGCGAAGCAGATTGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGACTTGCCTCCATCGGTTGTAGTGGAGCT
* * * * * *
40237968 GGTTAAAGAACCTGATCTTGCCTTCCTACATTAACAGAGAAGCAGATCGAAAACAAAGCCTTGCC
131 GGTTAAAGAAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAACCTTGCC
* * * ** *
40238033 TCCCTCGGTCGCAGTCGAGCTAGTTGAAGATAGCAGATCTTGCCTTACTGTGTTAACAGCGAAAC
196 TCCATCGGTCGCAGTCGAGCTAGTTGAAGACAACAGATCTTGCCTTACTGCCTTAACAACGAAAC
40238098 A
261 A
*
40238099 GATCGAAA-ACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGA-AGCAGATCTTGC
1 GATCGAAACACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGC
** * * *
40238162 CTTCCTATGTTAACAGCGAAGAAGATCGAAAATAAAGTCTTGCCTCCATCGGTTGTAGTGGAGCT
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGACTTGCCTCCATCGGTTGTAGTGGAGCT
* * *
40238227 GGTTAAAGAAGCAGGTCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCAAAAACAAAACCTTGCC
131 GGTTAAAGAAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAACCTTGCC
* * * * * *
40238292 TCCATCGGTTGCAGTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCCTTGACAACGAAGC
196 TCCATCGGTCGCAGTCGAGCTAGTTGAAGACAACAGATCTTGCCTTACTGCCTTAACAACGAAAC
40238357 A
261 A
** * *
40238358 GATCGAAGACACAAA-CCTTGCCTCTC-TCGGTTGTAGCAGAGCTGGTTGAAGACAACATATCTT
1 GATCGAA-ACACAAAGCCTTGCCTC-CATCGGTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTT
* * * * * * *
40238421 GCCTTCCTGCATTGACAGTGAAGCATATCGAAGACACAAA-ACTTTCCTCCCTCAGTTGTAGTGG
64 GCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGACTTGCCTCCATCGGTTGTAGTGG
* * * *
40238485 AGCTGGTTGAGGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGTAGATC
127 AGCTGGTTAAAGA-AACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC
40238538 GAAGTTACAA
Statistics
Matches: 375, Mismatches: 56, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
259 187 0.50
260 76 0.20
261 42 0.11
262 32 0.09
263 38 0.10
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (261 bp):
GATCGAAACACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGACAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGACTTGCCTCCATCGGTTGTAGTGGAGCT
GGTTAAAGAAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAAACAAAACCTTGCC
TCCATCGGTCGCAGTCGAGCTAGTTGAAGACAACAGATCTTGCCTTACTGCCTTAACAACGAAAC
A
Found at i:40238692 original size:132 final size:131
Alignment explanation
Indices: 40238549--40238916 Score: 472
Period size: 132 Copynumber: 2.8 Consensus size: 131
40238539 AAGTTACAAA
* * * * *
40238549 TCCTATCTCCCTGGCCAGCAGTGGAATAGGTTGGAA-ATTGTAGGTCTTGTCTCCCTAAGTAGTA
1 TCCTATCTCCCTAG-TAGTAGTGGAATAGGTT-GAAGATTGTAGATCTTGTCTCCCTAAGCAGTA
* * *
40238613 GCGGAGCAGATCGAAGATGTTGAATCTTATCTTCCCAAGACAGTGGAGAAGCAGATTTAAGTCAT
64 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGCAGATTTAAGCCAT
40238678 TAG
129 TAG
** * * *
40238681 TTTTATCTCCCTTAGTAGTAGTGGAGTAGGTTGAAGATTGCAGAATC-TGTCACCCTAAGCAGTA
1 TCCTATCTCCC-TAGTAGTAGTGGAATAGGTTGAAGATTGTAG-ATCTTGTCTCCCTAAGCAGTA
*
40238745 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGTAGATTTAAGCCAT
64 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGCAGATTTAAGCCAT
40238810 TAG
129 TAG
* ** *
40238813 TCCTATCTCCCTAAGTAGTAGTGGAATATGTCAAAGATTGTAGAT-TCTGTATCCCTAAGCAGTA
1 TCCTATCTCCCT-AGTAGTAGTGGAATAGGTTGAAGATTGTAGATCT-TGTCTCCCTAAGCAGTA
* * *
40238877 GTGGAGCAGAACAAAGACGGTGAATCTTATCTTCCCAAGA
64 GTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGA
40238917 TAGTAGGGAA
Statistics
Matches: 204, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
131 6 0.03
132 194 0.95
133 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (131 bp):
TCCTATCTCCCTAGTAGTAGTGGAATAGGTTGAAGATTGTAGATCTTGTCTCCCTAAGCAGTAGT
GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGCAGATTTAAGCCATTA
G
Found at i:40238928 original size:132 final size:133
Alignment explanation
Indices: 40238596--40238936 Score: 474
Period size: 132 Copynumber: 2.6 Consensus size: 133
40238586 TTGTAGGTCT
* * *
40238596 TGTC-TCCCTAAGTAGTAGCGGAGCAGATCGAAGATGTTGAATCTTATCTTCCCAAGACAGTGGA
1 TGTCATCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGA
* * ** * * **
40238660 GAAGCAGATTTAAGTCATTAGTTTTATCTCCCTTAGTAGTAGTGGAGTAGGTTGAAGATTGCAGA
66 GAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAATAGGTCAAAGATTGCAGA
40238725 ATC
131 ATC
40238728 TGTCA-CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGA
1 TGTCATCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGA
* *
40238792 GAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAATATGTCAAAGATTGTAGA
66 GAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAATAGGTCAAAGATTGCAGA
*
40238857 TTC
131 ATC
* * * *
40238860 TGT-ATCCCTAAGCAGTAGTGGAGCAGAACAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGG
1 TGTCATCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGT-GG
*
40238924 -GAAGTAAATTTAA
65 AGAAGTAGATTTAA
40238937 ACTACAAACA
Statistics
Matches: 187, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
131 1 0.01
132 184 0.98
133 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (133 bp):
TGTCATCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGA
GAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAATAGGTCAAAGATTGCAGA
ATC
Found at i:40241416 original size:107 final size:106
Alignment explanation
Indices: 40241189--40241386 Score: 301
Period size: 105 Copynumber: 1.9 Consensus size: 106
40241179 AAAAATAATA
* * *
40241189 AAGGTAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
1 AAGGCAATGTTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA-TTTTC
*
40241254 TCATTCAACCAAATAGCCGAATATCCTGCCAAAAATTTCAAAT
65 TCATTCAACCAAATAGCCAAATATCCT-CCAAAAATTTCAAAT
*
40241297 AAGGCAATGTTTTACGTTTGGAAATTCGAG-GAACGTGCCCTAATGTGCTGGGTTTCGA-TTTCT
1 AAGGCAATGTTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTCT
* *
40241360 CGTTTAACCAAATAGCCAAATATCCTC
66 CATTCAACCAAATAGCCAAATATCCTC
40241387 TTGAATTTCA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
104 1 0.01
105 28 0.34
107 27 0.33
108 27 0.33
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (106 bp):
AAGGCAATGTTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTCT
CATTCAACCAAATAGCCAAATATCCTCCAAAAATTTCAAAT
Found at i:40251690 original size:18 final size:18
Alignment explanation
Indices: 40251667--40251706 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40251657 CTCACAATAC
40251667 ACAGTTTGACAAATTAAT
1 ACAGTTTGACAAATTAAT
* *
40251685 ACAGTTTGCCATATTAAT
1 ACAGTTTGACAAATTAAT
40251703 ACAG
1 ACAG
40251707 ATCACCGAAT
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:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (18 bp):
ACAGTTTGACAAATTAAT
Found at i:40255365 original size:43 final size:42
Alignment explanation
Indices: 40255310--40255420 Score: 143
Period size: 43 Copynumber: 2.6 Consensus size: 42
40255300 TTTTAGAAAT
* * *
40255310 AAACGCCTCTAAAGGTCATGACTTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGGACATGACTTTTAGCGACGCTTTTT-CAC
* * *
40255353 AAACGCCGCTAAAGGCCAGGACCTTTAGCGACGCTTTTTCAC
1 AAACGCCGCTAAAGGACATGACTTTTAGCGACGCTTTTTCAC
*
40255395 AAACGCCGCTAAA-AACATGACTTTTA
1 AAACGCCGCTAAAGGACATGACTTTTA
40255421 AAAAAATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 9 0.15
42 16 0.27
43 34 0.58
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGGACATGACTTTTAGCGACGCTTTTTCAC
Found at i:40259235 original size:21 final size:21
Alignment explanation
Indices: 40259211--40259256 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
40259201 CCTTAAATCA
* * * *
40259211 TTAACTCTTAATCTCTAACCT
1 TTAACCCTTAACCCCTAACCC
40259232 TTAACCCTTAACCCCTAACCC
1 TTAACCCTTAACCCCTAACCC
40259253 TTAA
1 TTAA
40259257 ACATTATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (21 bp):
TTAACCCTTAACCCCTAACCC
Found at i:40259331 original size:130 final size:132
Alignment explanation
Indices: 40259137--40259383 Score: 293
Period size: 130 Copynumber: 1.9 Consensus size: 132
40259127 CTTAATTGAT
* * * * * * *
40259137 ATATAAATTAAAAAATACTAACTAATTTAAAGCTTAAACCTTAACCTGACCCCGAATCTCTAAAC
1 ATATAAATTAAAAAACACTAACTAATCTAAACCCTAAACCCTAACCTGACACCAAATCTCTAAAC
* * * **
40259202 CTTAAA-TCAT-TAACTCTTAATCTCTAACCTTTAACCCTTAACCCCTAACCCTTAAACATTATT
66 CCTAAATTAATCTAACTCTTAATCCCTAACCCCTAACCCTTAACCCCTAACCCTTAAACATTATT
40259265 TA
131 TA
* * * *
40259267 ATATAAATTAAAACACATTAATTAATCTAAACCCTAAACCCTAACTTGACACCAAATC-CATAAA
1 ATATAAATTAAAAAACACTAACTAATCTAAACCCTAAACCCTAACCTGACACCAAATCTC-TAAA
*
40259331 CCCTAAATTAATCCCTAACTCTTAATCCCTAACCCCTAACCCTTACCCCCTAA
65 CCCTAAATTAAT--CTAACTCTTAATCCCTAACCCCTAACCCTTAACCCCTAA
40259384 ATTACAACCC
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
129 1 0.01
130 57 0.60
131 3 0.03
134 34 0.36
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.29
Consensus pattern (132 bp):
ATATAAATTAAAAAACACTAACTAATCTAAACCCTAAACCCTAACCTGACACCAAATCTCTAAAC
CCTAAATTAATCTAACTCTTAATCCCTAACCCCTAACCCTTAACCCCTAACCCTTAAACATTATT
TA
Found at i:40259381 original size:21 final size:21
Alignment explanation
Indices: 40259343--40259383 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40259333 CTAAATTAAT
* *
40259343 CCCTAACTCTTAATCCCTAAC
1 CCCTAACCCTTAACCCCTAAC
*
40259364 CCCTAACCCTTACCCCCTAA
1 CCCTAACCCTTAACCCCTAA
40259384 ATTACAACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.49, G:0.00, T:0.24
Consensus pattern (21 bp):
CCCTAACCCTTAACCCCTAAC
Found at i:40259983 original size:41 final size:41
Alignment explanation
Indices: 40259832--40259984 Score: 164
Period size: 41 Copynumber: 3.7 Consensus size: 41
40259822 AAATGTTTTT
* * * **
40259832 GCGGCGCTTTTTCAAAAGCGCCGCTAAATC-CCGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTTTGAGCATTA
* * * **
40259872 GCAGCGCTTTTCCAAAAAACGCCACTAAAGCTTTAAGCGCTA
1 GCGGCGCTTTTCC-AAAAACGCCGCTAAAGCTTTGAGCATTA
* *
40259914 GCGACGCTTTTCCAAAAACGCTGCTAAAGCTTTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTTTGAGCATTA
* *
40259955 GCGGCGCTTTTTCAAAAACGCCGTTAAAGC
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGC
40259985 CTCGAAAGGT
Statistics
Matches: 90, Mismatches: 21, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
40 11 0.12
41 63 0.70
42 16 0.18
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGCTTTGAGCATTA
Found at i:40260116 original size:40 final size:40
Alignment explanation
Indices: 40260022--40260151 Score: 140
Period size: 40 Copynumber: 3.3 Consensus size: 40
40260012 TGGGCTTAGG
* * *
40260022 TTTTTTGCGGCGCTTTTCTAAACAA-CGCTGCTAATGCTC--
1 TTTTTAGCGGCGTTTTTC-AAA-AAGCGCCGCTAATGCTCGA
40260061 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGA
* * ** * *
40260101 TCTTTAGCGGTGTTTTTTGAAAAGCGCCTCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGA
40260141 TTTTTAGCGGC
1 TTTTTAGCGGC
40260152 AATTTTTATC
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
37 2 0.03
38 16 0.21
39 16 0.21
40 43 0.56
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGA
Found at i:40262405 original size:20 final size:20
Alignment explanation
Indices: 40262361--40262432 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
40262351 CTTTTATGGC
* * *
40262361 GCATTTTGTTAGCCTTTTTT
1 GCATTTTATTAGCCTTTGTG
*
40262381 TCATTTTATTAGCCTTTGTG
1 GCATTTTATTAGCCTTTGTG
*
40262401 GCATTTTGGATGA-CCTTTGTG
1 GCATTTT--ATTAGCCTTTGTG
*
40262422 GCATTCTATTA
1 GCATTTTATTA
40262433 AAATTTTGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.07
20 22 0.52
21 14 0.33
22 3 0.07
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
GCATTTTATTAGCCTTTGTG
Found at i:40265022 original size:28 final size:28
Alignment explanation
Indices: 40264991--40265046 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
40264981 ATTCCAAAAG
40264991 AACACTATTAGGATAACATTAGATTTAT
1 AACACTATTAGGATAACATTAGATTTAT
40265019 AACACTATTAGGATAACATTAGATTTAT
1 AACACTATTAGGATAACATTAGATTTAT
40265047 GTAATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (28 bp):
AACACTATTAGGATAACATTAGATTTAT
Found at i:40265592 original size:14 final size:14
Alignment explanation
Indices: 40265573--40265620 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
40265563 TAAGTTAAAA
40265573 ATAATATAAAATTT
1 ATAATATAAAATTT
*
40265587 ATAATATATAACCTTT
1 ATAATATA-AA-ATTT
* *
40265603 ATAAAAAAAAATTT
1 ATAATATAAAATTT
40265617 ATAA
1 ATAA
40265621 AGTGTCCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 15 0.54
15 4 0.14
16 9 0.32
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATAAAATTT
Found at i:40265597 original size:16 final size:15
Alignment explanation
Indices: 40265575--40265621 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
40265565 AGTTAAAAAT
40265575 AATATAAAATTTATA
1 AATATAAAATTTATA
**
40265590 ATATATAACCTTTATA
1 A-ATATAAAATTTATA
*
40265606 AA-AAAAAATTTATA
1 AATATAAAATTTATA
40265620 AA
1 AA
40265622 GTGTCCAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 11 0.42
15 2 0.08
16 13 0.50
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATAAAATTTATA
Found at i:40266247 original size:4 final size:4
Alignment explanation
Indices: 40266233--40266262 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
40266223 ATTTTAAAAT
40266233 ATTA TATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA -ATTA ATTA ATTA ATTA ATTA ATTA A
40266263 CGAGAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:40272968 original size:12 final size:12
Alignment explanation
Indices: 40272951--40272975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40272941 CAAATTTTAG
40272951 ATTTTAAAATTT
1 ATTTTAAAATTT
40272963 ATTTTAAAATTT
1 ATTTTAAAATTT
40272975 A
1 A
40272976 GAATTTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTAAAATTT
Found at i:40277123 original size:6 final size:6
Alignment explanation
Indices: 40277109--40277186 Score: 147
Period size: 6 Copynumber: 13.0 Consensus size: 6
40277099 GCAAATGGAT
*
40277109 CATTTC CATTCC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
40277157 CATTTC CATTTC CATTTC CATTTC CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC
40277187 AAAATGATTC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.17, C:0.35, G:0.00, T:0.49
Consensus pattern (6 bp):
CATTTC
Found at i:40277599 original size:12 final size:12
Alignment explanation
Indices: 40277579--40277609 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40277569 CAAATGAATA
40277579 ATTTCCATTTTC
1 ATTTCCATTTTC
*
40277591 ATTTTCATTTTC
1 ATTTCCATTTTC
40277603 ATTTCCA
1 ATTTCCA
40277610 AATGATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTCCATTTTC
Done.