Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 50 of 125
Found at i:15414926 original size:59 final size:57
Alignment explanation
Indices: 15414760--15415074 Score: 228
Period size: 59 Copynumber: 5.3 Consensus size: 57
15414750 TTTGAAGTTG
* * * * * ** *
15414760 AAAATGTGACTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTGGATGCACGAGAGC
1 AAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGATGTTCGAGGGC
* *
15414817 AAAATGGTAA-TTTTGGAAAAGTTTG-GGGCCAAAATGGTAATTTTTGGATGTTCGAGGGC
1 AAAAT-GTAATTTTTGG--AAGTTCGAGGG-TAAAATGGTAATTTTTGGATGTTCGAGGGC
* *
15414876 AAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGATGTTTGAGGGTAA
1 --AAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGATGTTCGAGGG--C
* * * * * * *
15414937 AAAATGTGATTTTTGGATGTTCAAGGGTAAAAAT-GTAGTTTTTGAGAAGTTTGGGGGTC
1 AAAATGTAATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTTG-GATGTTCGAGGG-C
* * * *
15414996 AAAATATAATTTTTGAGAAGTT-AAGGGGTTAAAAT-GTAATTTTTGAGAAGTTAG-GGGTC
1 AAAATGTAATTTTTG-GAAGTTCGA-GGG-TAAAATGGTAATTTTTG-GATGTTCGAGGG-C
15415055 AAAATGTAATTTTTAGGAAG
1 AAAATGTAATTTTT-GGAAG
15415075 CTCAGGAGTC
Statistics
Matches: 219, Mismatches: 23, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
57 11 0.05
58 6 0.03
59 137 0.63
60 53 0.24
61 12 0.05
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGATGTTCGAGGGC
Found at i:15415088 original size:30 final size:29
Alignment explanation
Indices: 15414878--15415126 Score: 143
Period size: 30 Copynumber: 8.4 Consensus size: 29
15414868 TCGAGGGCAA
**
15414878 AAAATGTAATTTTTG-GAAGTTCGAGGGT-
1 AAAATGTAATTTTTGAGAAGTAAG-GGGTC
* ** *
15414906 AAAATGGTAATTTTTG-GATGTTTGAGGGTAA
1 AAAAT-GTAATTTTTGAGAAGTAAG-GGGT-C
* * *
15414937 AAAATGTGATTTTTG-GATGTTCAA-GGGTA
1 AAAATGTAATTTTTGAGAAG-T-AAGGGGTC
* **
15414966 AAAATGTAGTTTTTGAGAAGTTTGGGGGTC
1 AAAATGTAATTTTTGAGAAG-TAAGGGGTC
* *
15414996 AAAATATAATTTTTGAGAAGTTAAGGGGTT
1 AAAATGTAATTTTTGAGAAG-TAAGGGGTC
*
15415026 AAAATGTAATTTTTGAGAAGTTAGGGGTC
1 AAAATGTAATTTTTGAGAAGTAAGGGGTC
* *
15415055 AAAATGTAATTTTT-AGGAAGCTCAGGAGTC
1 AAAATGTAATTTTTGA-GAAG-TAAGGGGTC
** * * * *
15415085 AAAATACAATTTTGGAAAAGTTTAGGGATC
1 AAAATGTAATTTTTGAGAAG-TAAGGGGTC
15415115 -AAATGTAATTTT
1 AAAATGTAATTTT
15415127 GAAAAGTTTT
Statistics
Matches: 180, Mismatches: 31, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
28 6 0.03
29 70 0.39
30 97 0.54
31 7 0.04
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGAGAAGTAAGGGGTC
Found at i:15415089 original size:59 final size:58
Alignment explanation
Indices: 15414878--15415126 Score: 240
Period size: 59 Copynumber: 4.2 Consensus size: 58
15414868 TCGAGGGCAA
* * *
15414878 AAAATGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTG-GATGTTT-GAGGGTAA
1 AAAATGTAATTTTTGGAAGTTCAAGGGTAAAAT-GTAATTTTTGAGAAGTTTAG-GGGT-C
* * * *
15414937 AAAATGTGATTTTTGGATGTTCAAGGGTAAAAATGTAGTTTTTGAGAAGTTTGGGGGTC
1 AAAATGTAATTTTTGGAAGTTCAAGGGT-AAAATGTAATTTTTGAGAAGTTTAGGGGTC
*
15414996 AAAATATAATTTTTGAGAAGTT-AAGGGGTTAAAATGTAATTTTTGAGAAG-TTAGGGGTC
1 AAAATGTAATTTTTG-GAAGTTCAA-GGG-TAAAATGTAATTTTTGAGAAGTTTAGGGGTC
* ** * * *
15415055 AAAATGTAATTTTTAGGAAGCTC-AGGAGTCAAAATACAATTTTGGAAAAGTTTAGGGATC
1 AAAATGTAATTTTT-GGAAGTTCAAGG-GT-AAAATGTAATTTTTGAGAAGTTTAGGGGTC
15415115 -AAATGTAATTTT
1 AAAATGTAATTTT
15415127 GAAAAGTTTT
Statistics
Matches: 161, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
58 3 0.02
59 105 0.65
60 51 0.32
61 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAGTTCAAGGGTAAAATGTAATTTTTGAGAAGTTTAGGGGTC
Found at i:15419934 original size:24 final size:24
Alignment explanation
Indices: 15419896--15420065 Score: 223
Period size: 24 Copynumber: 7.1 Consensus size: 24
15419886 TTAATCTGAA
*
15419896 TAGCTGGCGATCGTAAACGCATAT
1 TAGCTGGCGAGCGTAAACGCATAT
* *
15419920 TAGTTGGCGAGCGTAAATGCATAT
1 TAGCTGGCGAGCGTAAACGCATAT
* * *
15419944 TAGTTGACGAGCGTAAACGTATAT
1 TAGCTGGCGAGCGTAAACGCATAT
*
15419968 TAGCTGGCGAGCGTAAAAGCATAT
1 TAGCTGGCGAGCGTAAACGCATAT
* *
15419992 TAGCTAGCGAGTGTAAACGCATAT
1 TAGCTGGCGAGCGTAAACGCATAT
* *
15420016 TAGCTGACGAGCATAAACGCATAT
1 TAGCTGGCGAGCGTAAACGCATAT
* *
15420040 TAGATGGCGAGCGTAAACGAATAT
1 TAGCTGGCGAGCGTAAACGCATAT
15420064 TA
1 TA
15420066 ACTGACAAGA
Statistics
Matches: 125, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 125 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.25
Consensus pattern (24 bp):
TAGCTGGCGAGCGTAAACGCATAT
Found at i:15424900 original size:36 final size:36
Alignment explanation
Indices: 15424859--15424998 Score: 156
Period size: 36 Copynumber: 3.9 Consensus size: 36
15424849 ACTGGCACCC
* *
15424859 TATTTGTCGGTTTTATCAACCAGTGCTTGGCACATT
1 TATTTGTCAGTTTTATCGACCAGTGCTTGGCACATT
* *
15424895 TATTTGTCAGTTTTACCGACTAGTGCTTGGCACATT
1 TATTTGTCAGTTTTATCGACCAGTGCTTGGCACATT
* * * *
15424931 TATTTATCAGTTTTATCGACCAATG-TTGGGCAAAAT
1 TATTTGTCAGTTTTATCGACCAGTGCTT-GGCACATT
* * * *
15424967 TATTTGTCAATTTTCTTGACCAGTGCTAGGCA
1 TATTTGTCAGTTTTATCGACCAGTGCTTGGCA
15424999 TATCGACTAG
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
35 2 0.02
36 83 0.97
37 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.41
Consensus pattern (36 bp):
TATTTGTCAGTTTTATCGACCAGTGCTTGGCACATT
Found at i:15425622 original size:20 final size:18
Alignment explanation
Indices: 15425594--15425670 Score: 60
Period size: 20 Copynumber: 4.4 Consensus size: 18
15425584 TCATATCAGC
*
15425594 AAATAATTTTAAAATTACTA
1 AAATTATTTTAAAA-TA-TA
15425614 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
15425634 AAATT-TTTT-AAAT-T-
1 AAATTATTTTAAAATATA
15425648 --ATT-TTTTAAAATATA
1 AAATTATTTTAAAATATA
15425663 AAATTATT
1 AAATTATT
15425671 AAAATTATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 18
0.72 0.01 0.27
Matches are distributed among these distances:
12 7 0.15
13 4 0.08
14 1 0.02
15 1 0.02
16 4 0.08
17 7 0.15
18 2 0.04
20 12 0.25
21 2 0.04
22 8 0.17
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:15425628 original size:22 final size:19
Alignment explanation
Indices: 15425600--15425642 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 19
15425590 CAGCAAATAA
15425600 TTTTAAAATTACTAAAATTATT
1 TTTTAAAA-TA-TAAAATT-TT
15425622 TTTTAAAATATAAAATTTT
1 TTTTAAAATATAAAATTTT
15425641 TT
1 TT
15425643 AAATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 2 0.10
22 8 0.38
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAAAATATAAAATTTT
Found at i:15425641 original size:17 final size:17
Alignment explanation
Indices: 15425619--15425667 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
15425609 TACTAAAATT
15425619 ATTTTTTAAAATATAAA
1 ATTTTTTAAAATATAAA
15425636 ATTTTTT-AAAT-T---
1 ATTTTTTAAAATATAAA
15425648 ATTTTTTAAAATATAAA
1 ATTTTTTAAAATATAAA
15425665 ATT
1 ATT
15425668 ATTAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
14 1 0.04
15 1 0.04
16 4 0.15
17 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTTAAAATATAAA
Found at i:15425646 original size:29 final size:29
Alignment explanation
Indices: 15425603--15425686 Score: 134
Period size: 29 Copynumber: 2.9 Consensus size: 29
15425593 CAAATAATTT
*
15425603 TAAAATTACTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
* *
15425632 TAAAATTTTTTAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
15425661 TAAAATTATTAAAATTA-TTTTTAAAA
1 TAAAATTATTAAAATTATTTTTTAAAA
15425687 CGTATTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 9 0.18
29 41 0.82
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:15425774 original size:12 final size:12
Alignment explanation
Indices: 15425706--15425811 Score: 92
Period size: 12 Copynumber: 8.8 Consensus size: 12
15425696 ATAACATCCA
15425706 AACAACTAAAAAT
1 AACAAC-AAAAAT
*
15425719 AACATCAAAACA-
1 AACAACAAAA-AT
15425731 AA-AACAAAAAT
1 AACAACAAAAAT
*
15425742 AACAACAAAAAC
1 AACAACAAAAAT
**
15425754 AGTAACAAAAAT
1 AACAACAAAAAT
*
15425766 AACAGCAAAAAT
1 AACAACAAAAAT
*
15425778 AGA-ACCAAAAAT
1 A-ACAACAAAAAT
*
15425790 AACACCAAAAAT
1 AACAACAAAAAT
*
15425802 AACACCAAAA
1 AACAACAAAA
15425812 TAGTAAAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
10 1 0.01
11 9 0.12
12 61 0.78
13 7 0.09
ACGTcount: A:0.70, C:0.19, G:0.03, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:15425864 original size:17 final size:18
Alignment explanation
Indices: 15425839--15425879 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
15425829 AATAGCAACC
*
15425839 AACAGTAAAAAA-ACCAA
1 AACAATAAAAAACACCAA
15425856 AACAATAAAAAAGCACCAA
1 AACAATAAAAAA-CACCAA
15425875 AACAA
1 AACAA
15425880 CAATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
19 10 0.48
ACGTcount: A:0.71, C:0.20, G:0.05, T:0.05
Consensus pattern (18 bp):
AACAATAAAAAACACCAA
Found at i:15426289 original size:20 final size:18
Alignment explanation
Indices: 15426240--15426302 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
15426230 AACATGAGGT
* *
15426240 GAGAGGGAGGGGGAGGGG
1 GAGAGAGAGGGCGAGGGG
* *
15426258 GAGCGAAAAGGGACGATGGGG
1 GAGAG-AGAGGG-CGA-GGGG
*
15426279 GAGAGAGAGGGGGAGGGG
1 GAGAGAGAGGGCGAGGGG
15426297 GAGAGA
1 GAGAGA
15426303 AATATTTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 14 0.40
19 6 0.17
20 7 0.20
21 8 0.23
ACGTcount: A:0.30, C:0.03, G:0.65, T:0.02
Consensus pattern (18 bp):
GAGAGAGAGGGCGAGGGG
Found at i:15428354 original size:112 final size:112
Alignment explanation
Indices: 15428222--15428453 Score: 349
Period size: 112 Copynumber: 2.1 Consensus size: 112
15428212 AAAAATAATT
* * * *
15428222 ATGGTGTAGCCTCCAGTAAAATGAATA-TTGAATTGGCAGATCATGATACATGAATGTGTGTAAT
1 ATGGTGTAGCCTCCAGTAAAATGAAGACTAGAA-TGGCAGAACATGATACATGAATGTGTGTAAG
*
15428286 TCAATGTGGCTGAGACCCATGGAAAAAATTATGATTGTATGAATGTTC
65 TCAATGTGGCTGAGACCCATGGAAAAAATTATGATTATATGAATGTTC
* *
15428334 ATGGTGTAGCCTTCAGTAAAATGAAGACTAGAATGGTAGAACATGATACATGAATGTGTGTAAGT
1 ATGGTGTAGCCTCCAGTAAAATGAAGACTAGAATGGCAGAACATGATACATGAATGTGTGTAAGT
* * * *
15428399 CCATGTGGCTGAGACCCATGGCAAAGATTCTGATTATATGAATGTTC
66 CAATGTGGCTGAGACCCATGGAAAAAATTATGATTATATGAATGTTC
15428446 ATGGTGTA
1 ATGGTGTA
15428454 TTCTTCGATG
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
112 104 0.96
113 4 0.04
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (112 bp):
ATGGTGTAGCCTCCAGTAAAATGAAGACTAGAATGGCAGAACATGATACATGAATGTGTGTAAGT
CAATGTGGCTGAGACCCATGGAAAAAATTATGATTATATGAATGTTC
Found at i:15430864 original size:52 final size:52
Alignment explanation
Indices: 15430786--15431180 Score: 596
Period size: 52 Copynumber: 7.6 Consensus size: 52
15430776 GTAAATGCAA
* *
15430786 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
1 AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* **
15430838 AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTATAGATTAT
1 AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
15430890 AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
*
15430942 AAGG-TCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAA
1 AAGGTTC-GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* *
15430994 AAGGTTCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACGAATTAT
1 AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
15431046 GAGG-TCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTTT
1 AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* ** * *
15431097 GAGGCCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTTCGGATTAT
1 AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
15431149 GAGGTCCGATGACTATGTGTCATCATGAGTAT
1 AAGGTTCGATGACTATGTGTCATCGTGAGTAT
15431181 CAAATGAGAA
Statistics
Matches: 317, Mismatches: 23, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
51 49 0.15
52 266 0.84
53 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:15431147 original size:207 final size:208
Alignment explanation
Indices: 15430784--15431180 Score: 625
Period size: 207 Copynumber: 1.9 Consensus size: 208
15430774 CCGTAAATGC
* *
15430784 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATAAGGTTCGATG
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGGTTCGATG
* * * **
15430849 ACTATGTGTCATCGTGAGTATATGAATCTTTTATAGATTATAAGGTTCGATGACTATGTGTCATC
66 ACTATGTGTCATCATGAGTATATGAATCCTTTACAGATTATAAGGCCCGATGACTATGTGTCATC
* * *
15430914 GTGAGTATATGAATCCTTTACGGATTATAAGGTCTGATGACTATGTGTCATCGTGAGTATATGAA
131 GTGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCATGAGTATATGAA
15430979 TCCTTTACGGATT
196 TCCTTTACGGATT
* * *
15430992 AAAAGGTTCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACGAATTATGAGG-TCGATG
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGGTTCGATG
* * *
15431056 ACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTTTGAGGCCCGATGACTATGTGTCATC
66 ACTATGTGTCATCATGAGTATATGAATCCTTTACAGATTATAAGGCCCGATGACTATGTGTCATC
* *
15431121 GTGAGCATATGAATCCTTTTCGGATTATGAGGTCCGATGACTATGTGTCATCATGAGTAT
131 GTGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCATGAGTAT
15431181 CAAATGAGAA
Statistics
Matches: 171, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
207 118 0.69
208 53 0.31
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (208 bp):
AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGGTTCGATG
ACTATGTGTCATCATGAGTATATGAATCCTTTACAGATTATAAGGCCCGATGACTATGTGTCATC
GTGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCATCATGAGTATATGAA
TCCTTTACGGATT
Found at i:15435426 original size:43 final size:43
Alignment explanation
Indices: 15435373--15435721 Score: 470
Period size: 43 Copynumber: 8.1 Consensus size: 43
15435363 TTATATGGAA
* * *
15435373 AAACCCCGCTATAGAACATGGTCTTTAGCGATGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCAC
15435416 AAACGCCGCTAAAGAACATGGTCTTTAGC-AGCGC-TTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGA-CGCTTTTCCCAC
15435458 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCAC
* * *
15435501 AAACGCTGCTAAAGAACATGGTCTTTAGCTG-CGCTTTCCCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGC-GACGCTTTTCCCAC
*** * * *
15435544 AAATTTCGTTAAAGAACATGGTCTTTAGCGACGCTTTCCCCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCAC
* * * * *
15435587 AAACACCGCTAAAGACCATGGTCTTTAGTGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCAC
* *
15435630 AAACGCCGCTAAAGAACATGGTCTTTAGCAACGCTTCTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCAC
* *
15435673 AGACACCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCAC
15435716 AAACGC
1 AAACGC
15435722 TGGTAAAATT
Statistics
Matches: 268, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
42 42 0.16
43 225 0.84
44 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTCCCAC
Found at i:15435815 original size:15 final size:15
Alignment explanation
Indices: 15435795--15435827 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
15435785 TTTTCCTGTA
*
15435795 AATTCAAATCTAACC
1 AATTCAAATCCAACC
15435810 AATTCAAATCCAACC
1 AATTCAAATCCAACC
15435825 AAT
1 AAT
15435828 AACTTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTCAAATCCAACC
Found at i:15439697 original size:27 final size:26
Alignment explanation
Indices: 15439661--15439725 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 26
15439651 AAATTAATTT
**
15439661 AAAAAAATAATGGGA-GTAATTTTAA
1 AAAAAAATAAAAGGATGTAATTTTAA
*
15439686 AAAGAAACATAAAAGGATTTAATTTTAA
1 AAA-AAA-ATAAAAGGATGTAATTTTAA
15439714 AAAAAAATAAAA
1 AAAAAAATAAAA
15439726 TGGGCAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 3 0.09
26 9 0.26
27 10 0.29
28 12 0.35
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.25
Consensus pattern (26 bp):
AAAAAAATAAAAGGATGTAATTTTAA
Found at i:15441512 original size:50 final size:50
Alignment explanation
Indices: 15441437--15441749 Score: 313
Period size: 50 Copynumber: 6.3 Consensus size: 50
15441427 AGATCCATTT
* * * * *
15441437 CTCTACAAATTTAAGGGTATAAGATTTGCCCTTATGGGTTCAACCTGCCC
1 CTCTACAACTTTAAGGGTATAAGATTCGCCCTTACGGCTTCAATCTGCCC
* *
15441487 CTCTACAACTTTAAGGGTATAAGATTCGCCTTTACAGCTTCAATCTGCCC
1 CTCTACAACTTTAAGGGTATAAGATTCGCCCTTACGGCTTCAATCTGCCC
* * * **
15441537 CTCTACAACTTTAAGGGTATAAGATTCACTCTTACGGCTTCAATTTGATC
1 CTCTACAACTTTAAGGGTATAAGATTCGCCCTTACGGCTTCAATCTGCCC
* * ** *
15441587 CTCTACAGCTTTAGGGGTATAAGATTCGCCCTTACAACTTCAATCTACCC
1 CTCTACAACTTTAAGGGTATAAGATTCGCCCTTACGGCTTCAATCTGCCC
* * * * ** * *
15441637 CTCTATAGCTTT-AGGTGTATAAGATTCACTCACATGGCTTCAATCTGCTC
1 CTCTACAACTTTAAGG-GTATAAGATTCGCCCTTACGGCTTCAATCTGCCC
* ** * * *
15441687 CTCTACAGCTTTAAGGGTATAAGATTCATCCTTGCAGCTTCAATCTACCC
1 CTCTACAACTTTAAGGGTATAAGATTCGCCCTTACGGCTTCAATCTGCCC
* *
15441737 CTTTACAGCTTTA
1 CTCTACAACTTTA
15441750 GATGGGCTTT
Statistics
Matches: 215, Mismatches: 46, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
49 2 0.01
50 210 0.98
51 3 0.01
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (50 bp):
CTCTACAACTTTAAGGGTATAAGATTCGCCCTTACGGCTTCAATCTGCCC
Found at i:15441610 original size:100 final size:99
Alignment explanation
Indices: 15441437--15441749 Score: 385
Period size: 100 Copynumber: 3.1 Consensus size: 99
15441427 AGATCCATTT
* ** * * * * *
15441437 CTCTACAAATTTAAGGGTATAAGATTTGCCCTTATGGGTTCAACCTGCCCCTCTACAACTTTAAG
1 CTCTACAACTTTAAGGGTATAAGATTCACTCTTATGGCTTCAATCTGCTCCTCTACAGCTTTAAG
*
15441502 GGTATAAGATTCGCCTTTACAGCTTCAATCTGCCC
66 GGTATAAGATTCGCC-TTACAGCTTCAATCTACCC
* * * *
15441537 CTCTACAACTTTAAGGGTATAAGATTCACTCTTACGGCTTCAATTTGATCCTCTACAGCTTTAGG
1 CTCTACAACTTTAAGGGTATAAGATTCACTCTTATGGCTTCAATCTGCTCCTCTACAGCTTTAAG
*
15441602 GGTATAAGATTCGCCCTTACAACTTCAATCTACCC
66 GGTATAAGATTCG-CCTTACAGCTTCAATCTACCC
* * **
15441637 CTCTATAGCTTT-AGGTGTATAAGATTCACTCACATGGCTTCAATCTGCTCCTCTACAGCTTTAA
1 CTCTACAACTTTAAGG-GTATAAGATTCACTCTTATGGCTTCAATCTGCTCCTCTACAGCTTTAA
* *
15441701 GGGTATAAGATTCATCCTTGCAGCTTCAATCTACCC
65 GGGTATAAGATTC-GCCTTACAGCTTCAATCTACCC
* *
15441737 CTTTACAGCTTTA
1 CTCTACAACTTTA
15441750 GATGGGCTTT
Statistics
Matches: 182, Mismatches: 27, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
99 3 0.02
100 177 0.97
101 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (99 bp):
CTCTACAACTTTAAGGGTATAAGATTCACTCTTATGGCTTCAATCTGCTCCTCTACAGCTTTAAG
GGTATAAGATTCGCCTTACAGCTTCAATCTACCC
Found at i:15441814 original size:50 final size:50
Alignment explanation
Indices: 15441760--15441913 Score: 166
Period size: 50 Copynumber: 3.1 Consensus size: 50
15441750 GATGGGCTTT
* * * *
15441760 AATCTGCTCCTCTACAGCTTTAAGGGTATAAGATTCACCCTTACGGCTTC
1 AATCTACTCCTCTATAGCTTTAAGGGTATAAGATTCACCCTTGCGACTTC
* * * * *
15441810 AATCTACCCCTCAATAGCTTT-AGGTGTATAAGATTCGCCCTTGCAACTTT
1 AATCTACTCCTCTATAGCTTTAAGG-GTATAAGATTCACCCTTGCGACTTC
* * * * *
15441860 AATATATTTCTCTATAGCTTTAGGGGTATAAGATTCTCCCTTGCGACTTC
1 AATCTACTCCTCTATAGCTTTAAGGGTATAAGATTCACCCTTGCGACTTC
15441910 AATC
1 AATC
15441914 AACCCCTTTA
Statistics
Matches: 83, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
49 3 0.04
50 78 0.94
51 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (50 bp):
AATCTACTCCTCTATAGCTTTAAGGGTATAAGATTCACCCTTGCGACTTC
Found at i:15441829 original size:82 final size:82
Alignment explanation
Indices: 15441672--15441832 Score: 259
Period size: 82 Copynumber: 2.0 Consensus size: 82
15441662 TCACTCACAT
* *
15441672 GGCTTCAATCTGCTCCTCTACAGCTTTAAGGGTATAAGATTCATCCTTGCAGCTTCAATCTACCC
1 GGCTTCAATCTGCTCCTCTACAGCTTTAAGGGTATAAGATTCACCCTTACAGCTTCAATCTACCC
**
15441737 CTTTACAGCTTTAGATG
66 CTCAACAGCTTTAGATG
* *
15441754 GGCTTTAATCTGCTCCTCTACAGCTTTAAGGGTATAAGATTCACCCTTACGGCTTCAATCTACCC
1 GGCTTCAATCTGCTCCTCTACAGCTTTAAGGGTATAAGATTCACCCTTACAGCTTCAATCTACCC
*
15441819 CTCAATAGCTTTAG
66 CTCAACAGCTTTAG
15441833 GTGTATAAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.34
Consensus pattern (82 bp):
GGCTTCAATCTGCTCCTCTACAGCTTTAAGGGTATAAGATTCACCCTTACAGCTTCAATCTACCC
CTCAACAGCTTTAGATG
Found at i:15441892 original size:182 final size:182
Alignment explanation
Indices: 15441585--15441930 Score: 475
Period size: 182 Copynumber: 1.9 Consensus size: 182
15441575 TTCAATTTGA
* * *
15441585 TCCTCTACAGCTTTAGGGGTATAAGATTCGCCCTTACAACTTCAATCTACCCCTCTATAGCTTTA
1 TCCTCTACAGCTTTAAGGGTATAAGATTCACCCTTACAACTTCAATCTACCCCTCAATAGCTTTA
* * *
15441650 GGTGTATAAGATTCACTCACATGGCTTCAATCTGCTCCTCTACAGCTTTAAGGGTATAAGATTCA
66 GGTGTATAAGATTCACTCACATGACTTCAATATACTCCTCTACAGCTTTAAGGGTATAAGATTC-
* *
15441715 T-CCTTGC-AGCTTCAATCTACCCCTTTACAGCTTTAGATGGGCTTTAATCTGC
130 TCCCTTGCGA-CTTCAATCAACCCCTTTACAACTTTAGATGGGCTTTAATCTGC
**
15441767 TCCTCTACAGCTTTAAGGGTATAAGATTCACCCTTACGGCTTCAATCTACCCCTCAATAGCTTTA
1 TCCTCTACAGCTTTAAGGGTATAAGATTCACCCTTACAACTTCAATCTACCCCTCAATAGCTTTA
* * * * * * *
15441832 GGTGTATAAGATTCGC-C-CTTGCAACTTTAATATATTTCTCTATAGCTTTAGGGGTATAAGATT
66 GGTGTATAAGATTCACTCACATG--ACTTCAATATACTCCTCTACAGCTTTAAGGGTATAAGATT
15441895 CTCCCTTGCGACTTCAATCAACCCCTTTACAACTTT
129 CTCCCTTGCGACTTCAATCAACCCCTTTACAACTTT
15441931 TGTAACTTTA
Statistics
Matches: 143, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
180 3 0.02
181 2 0.01
182 137 0.96
183 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (182 bp):
TCCTCTACAGCTTTAAGGGTATAAGATTCACCCTTACAACTTCAATCTACCCCTCAATAGCTTTA
GGTGTATAAGATTCACTCACATGACTTCAATATACTCCTCTACAGCTTTAAGGGTATAAGATTCT
CCCTTGCGACTTCAATCAACCCCTTTACAACTTTAGATGGGCTTTAATCTGC
Found at i:15442108 original size:99 final size:99
Alignment explanation
Indices: 15441967--15443265 Score: 1019
Period size: 99 Copynumber: 13.2 Consensus size: 99
15441957 CTTTAGGGGT
* * * * * *
15441967 ATAGGATTTGGTGTTGTAA-CTTCACTCCATTCAACTATAACCTTAGGGACATTAAGATCCGTTA
1 ATAGGATTTGTTGTT-TAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGTTA
* * * * *
15442031 CTTATTTTAATCTGCTTCACTGTAACTTAAGAAAG
65 CTTGTTTTAATCCGCTTCACTGCAACTTCAGGAAG
* * * * *
15442066 ATAGGATTTGGTATTAAAGCTTCACTCCATTCCACTGTAACCTCAATGG-CATTGAGATCTACTT
1 ATAGGATTTGTTGTTTAAGCTTCACTCCATTCCACTGTAACCTC-AGGGACATTGAGATCT-GTT
* * * * *
15442130 -CTGGTTTTAATTCGAC-ACATTACAACTTCAGG--G
64 ACTTGTTTTAATCCG-CTTCACTGCAACTTCAGGAAG
* * * * *
15442163 TATAGGATTTGTTGTTGTGA-CTTCATTCCATTCCACTGTAACCTTAGGGACATTGAGATATGCT
1 -ATAGGATTTGTTGTT-TAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGTT
15442227 ACTTGTTTTAATCCGCTTCACTGCAACTTTC-GGAAG
64 ACTTGTTTTAATCCGCTTCACTGCAAC-TTCAGGAAG
* * * * * * *
15442263 ATAAGATTTGTTCTTGAAGCTTTACTCCATTCCACTATAACCTCAAGGACATTGAGATCTACTTA
1 ATAGGATTTGTTGTTTAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCT-GTTA
* * * *
15442328 -TGGTTTTAATCTGAC-CCACTGCAACTTCAGG-GG
65 CTTGTTTTAATCCG-CTTCACTGCAACTTCAGGAAG
* * *
15442361 TATAGGATTTGGTT-TTGTTA-CTTCACTCTATTCCACTATAACCTCAGGGACATTGAGATCTGT
1 -ATAGGATTT-GTTGTT-TAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGT
*
15442424 TACTTGTTTTAATCTGCTTCACTGCAACTTCAGGAAG
63 TACTTGTTTTAATCCGCTTCACTGCAACTTCAGGAAG
* * * *
15442461 ATAGGATTTGTTGTTAAAGCTTCACTCCATTCCACTGTACCCTCAAGGACATTGAGATTTGCTT-
1 ATAGGATTTGTTGTTTAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTG-TTA
* * * * * **
15442525 CTGGCTTTAATTCGAC-CCACTGTAACTTC-GGGGG
65 CTTGTTTTAATCCG-CTTCACTGCAACTTCAGGAAG
* * * * * *
15442559 TACAGGATTTGTTATTGTAA-CTTCACTCCA-TCTACTATAATCTCAGGGACATTGAGATGTGCT
1 -ATAGGATTTGTTGTT-TAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTG-T
* * *
15442622 T-CATGTTTTAATCCACTTCACTGCAACTTTAGGAAG
63 TACTTGTTTTAATCCGCTTCACTGCAACTTCAGGAAG
* * *
15442658 ATAGGATTTCTTGTTAAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGATATCTGCTT-
1 ATAGGATTTGTTGTTTAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTG-TTA
* * * *
15442722 CTAGCTTTAATCCGAC-CCACTGCAACTTCAGG-GG
65 CTTGTTTTAATCCG-CTTCACTGCAACTTCAGGAAG
* * * * ** *
15442756 TATAGGATTTGATGTTGCAA-CTTCACTCCATTCCATTATAACCTCAAAGACATTGAGATCTGCT
1 -ATAGGATTTGTTGTT-TAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGTT
** ** *
15442820 ACTTGTTTTAATAAGCTTCACTTTAACTTCAGAAAG
64 ACTTGTTTTAATCCGCTTCACTGCAACTTCAGGAAG
* *
15442856 ATAGGATTTGTTGTTGAAGCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTGCTT-
1 ATAGGATTTGTTGTTTAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTG-TTA
* * * * *
15442920 CTAGCTTTAATCCGACCT-ACT-AAACTTCAGG-GG
65 CTTGTTTTAATCCG-CTTCACTGCAACTTCAGGAAG
* * * * *
15442953 TATAAGATTTAG-TGTTGTAA-CTTCACTCCATTCCACTGTAACCTTAGGGACATTAAGATTTAT
1 -ATAGGATTT-GTTGTT-TAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGT
* *
15443016 TACTTGTTTTAATCCGTTTCACTACAACTTCAGGAAG
63 TACTTGTTTTAATCCGCTTCACTGCAACTTCAGGAAG
* * * *
15443053 ATAGGATTTGTTGTTGAAGCTTCACTCTATTCCACTGTAACCTTAGGGACATTGAGATCTACTT-
1 ATAGGATTTGTTGTTTAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCT-GTTA
* * * * * * *
15443117 CTGGCTTTAATCCGAC-CCACTGTAATTTTAGG-GG
65 CTTGTTTTAATCCG-CTTCACTGCAACTTCAGGAAG
* * ** * *
15443151 TATAAGATTTGATG-TTACAAATTCACTCCATTCCACTGTAACCTCAAAGG-CATTGAGATCTAT
1 -ATAGGATTTGTTGTTTA-AGCTTCACTCCATTCCACTGTAACCTC-AGGGACATTGAGATCTGT
* * * * * *
15443214 TACTTGTTTTAATCTGCTTTATTACAACTTTAAGAAG
63 TACTTGTTTTAATCCGCTTCACTGCAACTTCAGGAAG
*
15443251 ATAGGATTTGGTGTT
1 ATAGGATTTGTTGTT
15443266 CACTGGTCCA
Statistics
Matches: 949, Mismatches: 192, Indels: 117
0.75 0.15 0.09
Matches are distributed among these distances:
97 13 0.01
98 240 0.25
99 661 0.70
100 35 0.04
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (99 bp):
ATAGGATTTGTTGTTTAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGTTAC
TTGTTTTAATCCGCTTCACTGCAACTTCAGGAAG
Found at i:15442598 original size:296 final size:294
Alignment explanation
Indices: 15441936--15443229 Score: 1133
Period size: 296 Copynumber: 4.4 Consensus size: 294
15441926 ACTTTTGTAA
* ** * *
15441936 CTTTAATCTGACCCACTGTAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCACTCCATTCAA
1 CTTTAATCCGACCCACTGTAACTTCGGGGGTATAGGATTTGTTGTTG-AACTTCACTCCATTCCA
* * * * * *
15442001 CTATAACCTTAGGGACATTAAGATCCGTTACTTA--TTTTAATCTG-CTTCACTGTAACTTAAGA
65 CTATAACCTCAAGGACATTGAGAT-C--TACTTATGTTTTAATCTGACTCCACTGCAACTTCAG-
* * *
15442063 AAGATAGGATTTGGTATT-AAAGCTTCACTCCATTCCACTGTAACCTCAATGG-CATTGAGATCT
126 GAGATAGGATTTGGTATTGTAAGCTTCACTCCATTCCACTGTAACCTC-AGGGACATTGAGATCT
* * * * * ** *
15442126 ACTTCTGGTTTTAATTCGACACATTACAACTTCAGG-GTATAGGATTTGTTGTTGTGACTTCATT
190 -GTTCTTGTTTTAATCCGACTCACTACAACTTCAGGAGTATAGGATTTGTTGTTAAG-CTTCACT
* * * *
15442190 CCATTCCACTGTAACCTTAGGGACATTGAGATATGCTACTTG
253 CCATTCCACTGTAACCTCAAGGACATTGAGATCTGCTACTGG
* * * ** * * *
15442232 TTTTAATCCG-CTTCACTGCAACTTTCGGAAG-ATAAGATTTGTTCTTGAAGCTTTACTCCATTC
1 CTTTAATCCGAC-CCACTGTAAC-TTCGGGGGTATAGGATTTGTTGTTGAA-CTTCACTCCATTC
15442295 CACTATAACCTCAAGGACATTGAGATCTACTTATGGTTTTAATCTGAC-CCACTGCAACTTCAGG
63 CACTATAACCTCAAGGACATTGAGATCTACTTAT-GTTTTAATCTGACTCCACTGCAACTTCAGG
* * * * *
15442359 GGTATAGGATTTGGTTTTGTTA-CTTCACTCTATTCCACTATAACCTCAGGGACATTGAGATCTG
127 AG-ATAGGATTTGGTATTGTAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTG
* *
15442423 TTACTTGTTTTAATCTG-CTTCACTGCAACTTCAGGAAG-ATAGGATTTGTTGTTAAAGCTTCAC
191 TT-CTTGTTTTAATCCGAC-TCACTACAACTTCAGG-AGTATAGGATTTGTTGTT-AAGCTTCAC
* * *
15442486 TCCATTCCACTGTACCCTCAAGGACATTGAGATTTGCTTCTGG
252 TCCATTCCACTGTAACCTCAAGGACATTGAGATCTGCTACTGG
* * * *
15442529 CTTTAATTCGACCCACTGTAACTTCGGGGGTACAGGATTTGTTATTGTAACTTCACTCCA-TCTA
1 CTTTAATCCGACCCACTGTAACTTCGGGGGTATAGGATTTGTTGTTG-AACTTCACTCCATTCCA
* * * * * * *
15442593 CTATAATCTCAGGGACATTGAGATGTGCTTCATGTTTTAATC-CACTTCACTGCAACTTTAGGAA
65 CTATAACCTCAAGGACATTGAGATCTACTT-ATGTTTTAATCTGACTCCACTGCAACTTCAGG-A
** * * *
15442657 GATAGGATTTCTTGTT-AAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGATATCTGCT
128 GATAGGATTTGGTATTGTAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTG-T
* * * * * *
15442721 TCTAGCTTTAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTTGCAA-CTTCACTCC
192 TCTTGTTTTAATCCGACTCACTACAACTTCAGGAGTATAGGATTTGTTGTT--AAGCTTCACTCC
* * * *
15442785 ATTCCATTATAACCTCAAAGACATTGAGATCTGCTACTTG
255 ATTCCACTGTAACCTCAAGGACATTGAGATCTGCTACTGG
* ** * * ***
15442825 TTTTAATAAG-CTTCACTTTAACTTCAGAAAG-ATAGGATTTGTTGTTGAAGCTTCACTCCATTC
1 CTTTAATCCGAC-CCACTGTAACTTC-GGGGGTATAGGATTTGTTGTTGAA-CTTCACTCCATTC
* * * * * * *
15442888 CACTGTAACCTCAAGGACATTGAGATCTGCTTCTAGCTTTAATCCGAC-CTACT-AAACTTCAGG
63 CACTATAACCTCAAGGACATTGAGATCTACTTAT-GTTTTAATCTGACTCCACTGCAACTTCAGG
* * * * * * * *
15442951 GGTATAAGATTTAGTGTTGTAA-CTTCACTCCATTCCACTGTAACCTTAGGGACATTAAGATTTA
127 AG-ATAGGATTTGGTATTGTAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTG
**
15443015 TTACTTGTTTTAATCCGTTTCACTACAACTTCAGGAAG-ATAGGATTTGTTGTTGAAGCTTCACT
191 TT-CTTGTTTTAATCCGACTCACTACAACTTCAGG-AGTATAGGATTTGTTGTT-AAGCTTCACT
* * * * *
15443079 CTATTCCACTGTAACCTTAGGGACATTGAGATCTACTTCTGG
253 CCATTCCACTGTAACCTCAAGGACATTGAGATCTGCTACTGG
* ** * * * *
15443121 CTTTAATCCGACCCACTGTAATTTTAGGGGTATAAGATTTGATGTTACAAATTCACTCCATTCCA
1 CTTTAATCCGACCCACTGTAACTTCGGGGGTATAGGATTTGTTGTT-GAACTTCACTCCATTCCA
*
15443186 CTGTAACCTCAAAGG-CATTGAGATCTA-TTACTTGTTTTAATCTG
65 CTATAACCTC-AAGGACATTGAGATCTACTTA--TGTTTTAATCTG
15443230 CTTTATTACA
Statistics
Matches: 802, Mismatches: 153, Indels: 86
0.77 0.15 0.08
Matches are distributed among these distances:
293 6 0.01
295 26 0.03
296 601 0.75
297 162 0.20
298 7 0.01
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (294 bp):
CTTTAATCCGACCCACTGTAACTTCGGGGGTATAGGATTTGTTGTTGAACTTCACTCCATTCCAC
TATAACCTCAAGGACATTGAGATCTACTTATGTTTTAATCTGACTCCACTGCAACTTCAGGAGAT
AGGATTTGGTATTGTAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGTTCTT
GTTTTAATCCGACTCACTACAACTTCAGGAGTATAGGATTTGTTGTTAAGCTTCACTCCATTCCA
CTGTAACCTCAAGGACATTGAGATCTGCTACTGG
Found at i:15442687 original size:395 final size:393
Alignment explanation
Indices: 15441936--15443265 Score: 1734
Period size: 395 Copynumber: 3.4 Consensus size: 393
15441926 ACTTTTGTAA
* * * * * *
15441936 CTTTAATCTGACCCACTGTAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCACTCCATTCAA
1 CTTTAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTTGCAACTTCACTCCATTCCA
* * * * * * *
15442001 CTATAACCTTAGGGACATTAAGATCCGTTACTTATTTTAATCTGCTTCACTGTAACTTAAGAAAG
66 CTATAACCTCAAGGACATTGAGATCTGTTACTTGTTTTAATCTGCTTCACTGCAACTTCAGAAAG
* *
15442066 ATAGGATTTGGTATTAAAGCTTCACTCCATTCCACTGTAACCTCAATGG-CATTGAGATCTACTT
131 ATAGGATTTGGTGTTAAAGCTTCACTCCATTCCACTGTAACCTCAA-GGACATTGAGATCTGCTT
* * * * * *
15442130 CTGGTTTTAATTCGACACATTACAACTTCAGGGTATAGGATTTGTTGTTGTGACTTCATTCCATT
195 CTGGCTTTAATTCGACCCACTA-AACTTCGGGGTATAGGATTTGTTGTTGTAACTTCACTCCATT
* *
15442195 CCACTGTAACCTTAGGGACATTGAGATATGCTACTTGTTTTAATCCGCTTCACTGCAACTTTCGG
259 CCACTGTAACCTTAGGGACATTGAGAT-TGCTTCTTGTTTTAATCCGCTTCACTGCAACTTTAGG
* * * * *
15442260 AAGATAAGATTTGTTCTTGAAGCTTTACTCCATTCCACTATAACCTCAAGGACATTGAGATCTAC
323 AAGATAGGATTTGTTGTTGAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTAC
*
15442325 TTATGG
388 TTCTGG
* * * * ** *
15442331 TTTTAATCTGACCCACTGCAACTTCAGGGGTATAGGATTTGGTTTTGTTACTTCACTCTATTCCA
1 CTTTAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTTGCAACTTCACTCCATTCCA
* *
15442396 CTATAACCTCAGGGACATTGAGATCTGTTACTTGTTTTAATCTGCTTCACTGCAACTTCAGGAAG
66 CTATAACCTCAAGGACATTGAGATCTGTTACTTGTTTTAATCTGCTTCACTGCAACTTCAGAAAG
* * *
15442461 ATAGGATTTGTTGTTAAAGCTTCACTCCATTCCACTGTACCCTCAAGGACATTGAGATTTGCTTC
131 ATAGGATTTGGTGTTAAAGCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTGCTTC
* * *
15442526 TGGCTTTAATTCGACCCACTGTAACTTCGGGGGTACAGGATTTGTTATTGTAACTTCACTCCA-T
196 TGGCTTTAATTCGACCCACT-AAACTTC-GGGGTATAGGATTTGTTGTTGTAACTTCACTCCATT
* * * * * *
15442590 CTACTATAATCTCAGGGACATTGAGATGTGCTTCATGTTTTAATCCACTTCACTGCAACTTTAGG
259 CCACTGTAACCTTAGGGACATTGAGAT-TGCTTCTTGTTTTAATCCGCTTCACTGCAACTTTAGG
* * * *
15442655 AAGATAGGATTTCTTGTTAAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGATATCTGC
323 AAGATAGGATTTGTTGTTGAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTAC
*
15442720 TTCTAG
388 TTCTGG
15442726 CTTTAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTTGCAACTTCACTCCATTCCA
1 CTTTAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTTGCAACTTCACTCCATTCCA
* * * ** **
15442791 TTATAACCTCAAAGACATTGAGATCTGCTACTTGTTTTAATAAGCTTCACTTTAACTTCAGAAAG
66 CTATAACCTCAAGGACATTGAGATCTGTTACTTGTTTTAATCTGCTTCACTGCAACTTCAGAAAG
* *
15442856 ATAGGATTTGTTGTTGAAGCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTGCTTC
131 ATAGGATTTGGTGTTAAAGCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTGCTTC
* * * *
15442921 TAGCTTTAATCCGACCTACTAAACTTCAGGGGTATAAGATTTAG-TGTTGTAACTTCACTCCATT
196 TGGCTTTAATTCGACCCACTAAACTTC-GGGGTATAGGATTT-GTTGTTGTAACTTCACTCCATT
* ** * * *
15442985 CCACTGTAACCTTAGGGACATTAAGATTTATTACTTGTTTTAATCCGTTTCACTACAACTTCAGG
259 CCACTGTAACCTTAGGGACATTGAGATTGCTT-CTTGTTTTAATCCGCTTCACTGCAACTTTAGG
* *
15443050 AAGATAGGATTTGTTGTTGAAGCTTCACTCTATTCCACTGTAACCTTAGGGACATTGAGATCTAC
323 AAGATAGGATTTGTTGTTGAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTAC
15443115 TTCTGG
388 TTCTGG
* * * * * *
15443121 CTTTAATCCGACCCACTGTAATTTTAGGGGTATAAGATTTGATGTTACAAATTCACTCCATTCCA
1 CTTTAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTTGCAACTTCACTCCATTCCA
* * * * * *
15443186 CTGTAACCTCAAAGG-CATTGAGATCTATTACTTGTTTTAATCTGCTTTATTACAACTTTA-AGA
66 CTATAACCTC-AAGGACATTGAGATCTGTTACTTGTTTTAATCTGCTTCACTGCAACTTCAGA-A
15443249 AGATAGGATTTGGTGTT
129 AGATAGGATTTGGTGTT
15443266 CACTGGTCCA
Statistics
Matches: 814, Mismatches: 113, Indels: 16
0.86 0.12 0.02
Matches are distributed among these distances:
394 41 0.05
395 741 0.91
396 32 0.04
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (393 bp):
CTTTAATCCGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTTGCAACTTCACTCCATTCCA
CTATAACCTCAAGGACATTGAGATCTGTTACTTGTTTTAATCTGCTTCACTGCAACTTCAGAAAG
ATAGGATTTGGTGTTAAAGCTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATCTGCTTC
TGGCTTTAATTCGACCCACTAAACTTCGGGGTATAGGATTTGTTGTTGTAACTTCACTCCATTCC
ACTGTAACCTTAGGGACATTGAGATTGCTTCTTGTTTTAATCCGCTTCACTGCAACTTTAGGAAG
ATAGGATTTGTTGTTGAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTACTTC
TGG
Found at i:15444094 original size:7 final size:7
Alignment explanation
Indices: 15444082--15444158 Score: 88
Period size: 7 Copynumber: 11.0 Consensus size: 7
15444072 CTACCTCTCC
15444082 TTTTTCT
1 TTTTTCT
15444089 TTTTTCT
1 TTTTTCT
15444096 TTTTTCT
1 TTTTTCT
*
15444103 TCTTT-T
1 TTTTTCT
*
15444109 TTTCT-T
1 TTTTTCT
15444115 TTTTTC-
1 TTTTTCT
15444121 TTTTTCT
1 TTTTTCT
15444128 TTTTTCT
1 TTTTTCT
15444135 TTTTTCTTT
1 TTTTTC--T
15444144 TCTTTTCT
1 T-TTTTCT
15444152 TTTTTCT
1 TTTTTCT
15444159 CCTTTTTTGG
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
6 15 0.25
7 37 0.61
8 2 0.03
9 2 0.03
10 5 0.08
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:15444124 original size:39 final size:40
Alignment explanation
Indices: 15444077--15444165 Score: 146
Period size: 39 Copynumber: 2.2 Consensus size: 40
15444067 CACCTCTACC
*
15444077 TCTCCTTTTTCTTTTTTCTTTTTTCTTCTTTTTTTCTTTTT
1 TCTCCTTTTTCTTTTTTCTTTTTTCTT-TTCTTTTCTTTTT
15444118 T-T-CTTTTTCTTTTTTCTTTTTTCTTTTCTTTTCTTTTT
1 TCTCCTTTTTCTTTTTTCTTTTTTCTTTTCTTTTCTTTTT
15444156 TCTCCTTTTT
1 TCTCCTTTTT
15444166 TGGGTGAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
38 13 0.29
39 24 0.53
40 7 0.16
41 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (40 bp):
TCTCCTTTTTCTTTTTTCTTTTTTCTTTTCTTTTCTTTTT
Found at i:15444166 original size:1 final size:1
Alignment explanation
Indices: 15444082--15444156 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
15444072 CTACCTCTCC
* * * * * * * * * *
15444082 TTTTTCTTTTTTCTTTTTTCTTCTTTTTTTCTTTTTTTCTTTTTCTTTTTTCTTTTTTCTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
15444147 TTTCTTTTTT
1 TTTTTTTTTT
15444157 CTCCTTTTTT
Statistics
Matches: 52, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:15461485 original size:2 final size:2
Alignment explanation
Indices: 15461478--15461502 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15461468 TTTGGCTATT
15461478 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15461503 TATTACTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15494474 original size:35 final size:36
Alignment explanation
Indices: 15494428--15494504 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
15494418 CAATGATCTT
15494428 TTCAAGTTTCCCAGTAA-TTCAACTCATACGAACCC
1 TTCAAGTTTCCCAGTAATTTCAACTCATACGAACCC
* * *
15494463 TTCAAGTTTCCCTGTAATTTCAACTCATACGAGCTC
1 TTCAAGTTTCCCAGTAATTTCAACTCATACGAACCC
15494499 TTCAAG
1 TTCAAG
15494505 ACTCCCAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 16 0.42
36 22 0.58
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (36 bp):
TTCAAGTTTCCCAGTAATTTCAACTCATACGAACCC
Found at i:15494598 original size:21 final size:20
Alignment explanation
Indices: 15494574--15494618 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
15494564 CAAGCTCAGT
* *
15494574 CAGTAATACGCTCTTGCGAGC
1 CAGTAAT-CGCTCCTACGAGC
15494595 CAGT-ATCGCTCCTACGAGC
1 CAGTAATCGCTCCTACGAGC
15494614 CAGTA
1 CAGTA
15494619 CAGTATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 15 0.71
20 2 0.10
21 4 0.19
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (20 bp):
CAGTAATCGCTCCTACGAGC
Found at i:15500661 original size:17 final size:15
Alignment explanation
Indices: 15500637--15500671 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
15500627 AAGAGGTGTT
* *
15500637 ATAAATATATATTAG
1 ATAAAAATATATTTG
15500652 ATAAAAATATATTTG
1 ATAAAAATATATTTG
15500667 ATAAA
1 ATAAA
15500672 TTATGAGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (15 bp):
ATAAAAATATATTTG
Found at i:15501354 original size:23 final size:23
Alignment explanation
Indices: 15501328--15501373 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
15501318 ACATCTTGAT
*
15501328 GAGAAGAATCGTCACATCCCGAC
1 GAGAAGAATCGCCACATCCCGAC
*
15501351 GAGAAGAATCGCCACGTCCCGAC
1 GAGAAGAATCGCCACATCCCGAC
15501374 AACACAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.24, T:0.11
Consensus pattern (23 bp):
GAGAAGAATCGCCACATCCCGAC
Found at i:15502509 original size:30 final size:31
Alignment explanation
Indices: 15502453--15502544 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 31
15502443 TTTTATTATT
*
15502453 TTAATAATTAATATTTTTA-TAATTTTAAAAAA
1 TTAA-AATTAA-ATTTTTATTATTTTTAAAAAA
*
15502485 TT-AAATTAAATTTTTATTATTTTTAAAAAG
1 TTAAAATTAAATTTTTATTATTTTTAAAAAA
15502515 TTAAAATGT-AA-TTTTATTATTAATTTAAAA
1 TTAAAAT-TAAATTTTTATTATT--TTTAAAA
15502545 TTTTATAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
29 7 0.13
30 29 0.55
31 7 0.13
32 10 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (31 bp):
TTAAAATTAAATTTTTATTATTTTTAAAAAA
Found at i:15506188 original size:13 final size:13
Alignment explanation
Indices: 15506170--15506201 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
15506160 TATAAAAAAA
15506170 TATTTTAATTTTT
1 TATTTTAATTTTT
15506183 TATTTTAATTTTT
1 TATTTTAATTTTT
15506196 TATTTT
1 TATTTT
15506202 TTAATTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTTAATTTTT
Found at i:15513470 original size:60 final size:61
Alignment explanation
Indices: 15513401--15513516 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 61
15513391 CATATTTCTT
* *
15513401 TTTCCTTTTTAATTTC-TTTTTCCATATCATATATTTTAACTTTTTAATTTTAAATAAATA
1 TTTCCTTTTTAATTTCTTTTTTCCATATAATATATTTTAACTTTTTAACTTTAAATAAATA
* * *
15513461 TTTCTTTTTTTATTTCTTTTTTCCATATAATATATTTTAGCTTTTTAACTTTAAAT
1 TTTCCTTTTTAATTTCTTTTTTCCATATAATATATTTTAACTTTTTAACTTTAAAT
15513517 GTTTATATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 14 0.28
61 36 0.72
ACGTcount: A:0.27, C:0.11, G:0.01, T:0.61
Consensus pattern (61 bp):
TTTCCTTTTTAATTTCTTTTTTCCATATAATATATTTTAACTTTTTAACTTTAAATAAATA
Found at i:15513782 original size:18 final size:19
Alignment explanation
Indices: 15513759--15513800 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
15513749 TGTTTTAAAG
15513759 TTTATAG-T-TTAATTTTAT
1 TTTATAGTTATTAATTTT-T
15513777 TTTATAGTTATTAATTTTT
1 TTTATAGTTATTAATTTTT
15513796 TTTAT
1 TTTAT
15513801 CTTTTAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTATAGTTATTAATTTTT
Found at i:15517494 original size:18 final size:18
Alignment explanation
Indices: 15517471--15517517 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
15517461 TCATTCTAGC
15517471 TTATTTTTATTTGTT-AAA
1 TTATTTTTATTT-TTAAAA
15517489 TTATTTTTATTTTTAAAA
1 TTATTTTTATTTTTAAAA
*
15517507 TTATTATTATT
1 TTATTTTTATT
15517518 ATTGTTCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTATTTTTATTTTTAAAA
Found at i:15523935 original size:42 final size:43
Alignment explanation
Indices: 15523841--15523936 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 43
15523831 GAAACACATG
*
15523841 TATATAAATATAAAAGTAGTTTATATAAAAAAAGAAATGTATA
1 TATATATATATAAAAGTAGTTTATATAAAAAAAGAAATGTATA
* * ** * *
15523884 -AAATTTATATAACCGTAGTTTATAT-AAAATAGATATGTATA
1 TATATATATATAAAAGTAGTTTATATAAAAAAAGAAATGTATA
15523925 TATATATATATA
1 TATATATATATA
15523937 TAACAGTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
41 14 0.33
42 29 0.67
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (43 bp):
TATATATATATAAAAGTAGTTTATATAAAAAAAGAAATGTATA
Found at i:15523989 original size:42 final size:41
Alignment explanation
Indices: 15523926--15524022 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 41
15523916 ATATGTATAT
* *
15523926 ATATATATATATAACAGTATATGAAAGTAATTTATAT-AAAAAAA
1 ATATATATATAT-ACAGTATAT--AA-CAATATATATGAAAAAAA
* *
15523970 ATATATATATATAGA-TATATAACAATATATATGTAAAAAA
1 ATATATATATATACAGTATATAACAATATATATGAAAAAAA
*
15524010 ATATATGTATATA
1 ATATATATATATA
15524023 AAATTGATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
39 8 0.17
40 20 0.43
42 5 0.11
43 2 0.04
44 12 0.26
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (41 bp):
ATATATATATATACAGTATATAACAATATATATGAAAAAAA
Found at i:15555091 original size:74 final size:74
Alignment explanation
Indices: 15554970--15555199 Score: 415
Period size: 74 Copynumber: 3.1 Consensus size: 74
15554960 TTGTTTCGGT
* * *
15554970 AGTCTTGGCCAAGGTATCGATAGAAGTCCCAAGCCACAACTTCCTTGCTCATTGGAGTTCATTCT
1 AGTCTTGGCCAAGGTATCGGTAGAAGTCCCAGGCCACAACTTCCTTGCTCACTGGAGTTCATTCT
15555035 ATCGATAGA
66 ATCGATAGA
*
15555044 AGTCTTGGCCAAGGTATCGGTAGAAGTCCCAGGCCACAACTTCCTTGCTCACTAGAGTTCATTCT
1 AGTCTTGGCCAAGGTATCGGTAGAAGTCCCAGGCCACAACTTCCTTGCTCACTGGAGTTCATTCT
15555109 ATCGATAGA
66 ATCGATAGA
*
15555118 AGTCTTGGCCAAGGTATCGGTAGAAGTCCCAGGCCACAACTTCCTTGCTCACTGGAGTTCGTTCT
1 AGTCTTGGCCAAGGTATCGGTAGAAGTCCCAGGCCACAACTTCCTTGCTCACTGGAGTTCATTCT
15555183 ATCGATAGA
66 ATCGATAGA
15555192 AGTCTTGG
1 AGTCTTGG
15555200 TTGTATCGGT
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 150 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (74 bp):
AGTCTTGGCCAAGGTATCGGTAGAAGTCCCAGGCCACAACTTCCTTGCTCACTGGAGTTCATTCT
ATCGATAGA
Found at i:15555841 original size:51 final size:49
Alignment explanation
Indices: 15555742--15555853 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 49
15555732 TAAATTTTAG
* *** ** *
15555742 TGGGCATGCTTAACATGCGTATTGGATTTTATTAGTAGAAGCGTTACAA
1 TGGGCATGCTTAACATGCGAATCAAATTTTATTAAAAGAAGCGATACAA
15555791 TGGGCATGCTTAACATGCGAATCAAAGTATTTATTAAAAGAAGCGATACAA
1 TGGGCATGCTTAACATGCGAATCAAA-T-TTTATTAAAAGAAGCGATACAA
* *
15555842 TAGACATGCTTA
1 TGGGCATGCTTA
15555854 TCAAAACAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 22 0.42
50 1 0.02
51 29 0.56
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (49 bp):
TGGGCATGCTTAACATGCGAATCAAATTTTATTAAAAGAAGCGATACAA
Found at i:15557271 original size:24 final size:24
Alignment explanation
Indices: 15557226--15557272 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
15557216 CAAAGATAAT
*
15557226 AAACCCCAAAACTTGAAAACAAAG
1 AAACCCCAAAACATGAAAACAAAG
*
15557250 AAACCTCAAAACAT-AAACACAAA
1 AAACCCCAAAACATGAAA-ACAAA
15557273 ATTCTCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.62, C:0.26, G:0.04, T:0.09
Consensus pattern (24 bp):
AAACCCCAAAACATGAAAACAAAG
Found at i:15557401 original size:23 final size:23
Alignment explanation
Indices: 15557370--15557413 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
15557360 GTCAAATAAA
* *
15557370 TTATGCTAATAAATGCTAAATAT
1 TTATACTAATAAATACTAAATAT
15557393 TTATACTAATAAATACTAAAT
1 TTATACTAATAAATACTAAAT
15557414 CTTCTAGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (23 bp):
TTATACTAATAAATACTAAATAT
Found at i:15560993 original size:10 final size:10
Alignment explanation
Indices: 15560978--15561003 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
15560968 ATATGACTGA
15560978 ATGTGATTAT
1 ATGTGATTAT
15560988 ATGTGATTAT
1 ATGTGATTAT
15560998 ATGTGA
1 ATGTGA
15561004 CTACTATGTT
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:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:15561803 original size:21 final size:20
Alignment explanation
Indices: 15561777--15561829 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
15561767 TTCCAAACAG
*
15561777 TATCGATACCACTTGTGAAAC
1 TATCGATACCACTT-TAAAAC
* *
15561798 TATCGATACCTCCTTTAAAAT
1 TATCGATACC-ACTTTAAAAC
15561819 TATCGATACCA
1 TATCGATACCA
15561830 GCATAACAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (20 bp):
TATCGATACCACTTTAAAAC
Found at i:15565571 original size:66 final size:67
Alignment explanation
Indices: 15565464--15565597 Score: 225
Period size: 66 Copynumber: 2.0 Consensus size: 67
15565454 TAGGTTTTTC
*
15565464 CACAAAGAGGAATAATCTTGATAGACATATATGTCACTTGAATTATCCTTCGAAGTACCTCTTCT
1 CACAAAGAGGAATAATCTTGATAGAAATATATGTCACTTGAATTATCCTTCGAAGTACCTCTTCT
15565529 TG
66 TG
* * *
15565531 CACAAAGAGG-ATAGTCTTGATAGAAATATTTGTCACTTGAATTATCCTTCGTAGTACCTCTTCT
1 CACAAAGAGGAATAATCTTGATAGAAATATATGTCACTTGAATTATCCTTCGAAGTACCTCTTCT
15565595 TG
66 TG
15565597 C
1 C
15565598 CAATGGGTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 53 0.84
67 10 0.16
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (67 bp):
CACAAAGAGGAATAATCTTGATAGAAATATATGTCACTTGAATTATCCTTCGAAGTACCTCTTCT
TG
Found at i:15566201 original size:67 final size:66
Alignment explanation
Indices: 15566094--15566223 Score: 217
Period size: 67 Copynumber: 2.0 Consensus size: 66
15566084 TAGGTTTTTC
*
15566094 CACAAAGAGGAATATCTTGATAGACATATCTGTCACTTGAATTATCCTTCA-AAGTACCTCTTCT
1 CACAAAGAGGAATATCTTGATAGAAATATCTGTCACTTGAATTATCCTTCATAA-TACCTCTTCT
15566158 TG
65 TG
*
15566160 CACAAAGAGGAATAGTCTTGATAGAAATATTTGTCACTTGAATTATCCTTCATAATACCTCTTC
1 CACAAAGAGGAATA-TCTTGATAGAAATATCTGTCACTTGAATTATCCTTCATAATACCTCTTC
15566224 CTGCCAATGG
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
66 14 0.23
67 44 0.73
68 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (66 bp):
CACAAAGAGGAATATCTTGATAGAAATATCTGTCACTTGAATTATCCTTCATAATACCTCTTCTT
G
Found at i:15569617 original size:22 final size:20
Alignment explanation
Indices: 15569571--15569608 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15569561 TAGTGAAAGA
* *
15569571 TTTATTTTCTAAGTATAAAT
1 TTTATTGTCTAAGAATAAAT
15569591 TTTATTGTCTAAGAATAA
1 TTTATTGTCTAAGAATAA
15569609 TAATTTTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (20 bp):
TTTATTGTCTAAGAATAAAT
Found at i:15575172 original size:15 final size:15
Alignment explanation
Indices: 15575152--15575185 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
15575142 ATTTGCCAAA
15575152 ACCAGAACCAATTTC
1 ACCAGAACCAATTTC
*
15575167 ACCAGAACCAGTTTC
1 ACCAGAACCAATTTC
15575182 ACCA
1 ACCA
15575186 AAATAAGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.35, G:0.09, T:0.18
Consensus pattern (15 bp):
ACCAGAACCAATTTC
Found at i:15576034 original size:21 final size:21
Alignment explanation
Indices: 15575993--15576034 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
15575983 TGTCCAAGTT
* *
15575993 AGAATTCATAGTCATTGAAGA
1 AGAATTCATACTCATTAAAGA
15576014 AGAATTCA-ACTCTATTAAAGA
1 AGAATTCATACTC-ATTAAAGA
15576035 TCCTTTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (21 bp):
AGAATTCATACTCATTAAAGA
Found at i:15579562 original size:19 final size:20
Alignment explanation
Indices: 15579515--15579562 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
15579505 TTGATAATTG
15579515 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
15579533 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
15579552 TTAATTATTAT
1 TTAATTATTAT
15579563 CAAGAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:15579994 original size:20 final size:20
Alignment explanation
Indices: 15579954--15579994 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
15579944 ACCAGCTCCC
* * *
15579954 AATAGCGCCCGATAGCGCCT
1 AATAGCGCCAGAGAGCACCT
15579974 AATAGCGCCAGAGAGCACCT
1 AATAGCGCCAGAGAGCACCT
15579994 A
1 A
15579995 CACGTCCCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (20 bp):
AATAGCGCCAGAGAGCACCT
Found at i:15580169 original size:17 final size:17
Alignment explanation
Indices: 15580144--15580178 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
15580134 AACTTAGGCC
15580144 ATGTACCCCTTACCCAA
1 ATGTACCCCTTACCCAA
*
15580161 ATGTGCCCCTTACCCAA
1 ATGTACCCCTTACCCAA
15580178 A
1 A
15580179 CACTAAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.40, G:0.09, T:0.23
Consensus pattern (17 bp):
ATGTACCCCTTACCCAA
Found at i:15587227 original size:52 final size:52
Alignment explanation
Indices: 15587150--15587380 Score: 399
Period size: 52 Copynumber: 4.4 Consensus size: 52
15587140 TAAATGCAGA
* *
15587150 AGGTCCGATGACTATGTGTTATCGTGAGTATATGAATCCTTTACGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
15587202 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATTCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
15587254 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
15587306 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTTCGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
15587358 AGGTCCGATGACTATGTGTCATC
1 AGGTCCGATGACTATGTGTCATC
15587381 ATGGGTATTA
Statistics
Matches: 168, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 168 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:15602946 original size:107 final size:104
Alignment explanation
Indices: 15602814--15603027 Score: 306
Period size: 108 Copynumber: 2.0 Consensus size: 104
15602804 TAGTGAATTT
*
15602814 TTTAAAAAAAAAGAAAGTTTAGATTTTT-AAAATAAAAATATG-TTTTTAATCATTTTAAAGGAA
1 TTTAAAAAAAAAAAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAATCATTTTAAA-GAA
*
15602877 AAAGTTTAAATTTTATTAAACAAAATTTTGATTTTTTTAACTA
65 AAAGTTTAAA-TTT-TTAAAC-AAAGTTTGATTTTTTTAACTA
* *
15602920 TTTAAAAATAAAAAAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGAG
1 TTTAAAAA-AAAAAAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAATCATTTTAAAGAA
* * *
15602985 AGAGTTTAAATTTTTAAACAAAGTTTGTTTTTTTTAATTA
65 AAAGTTTAAATTTTTAAACAAAGTTTGATTTTTTTAACTA
15603025 TTT
1 TTT
15603028 CGAAATATAA
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
105 21 0.21
106 14 0.14
107 22 0.22
108 25 0.26
109 16 0.16
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.44
Consensus pattern (104 bp):
TTTAAAAAAAAAAAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAATCATTTTAAAGAAA
AAGTTTAAATTTTTAAACAAAGTTTGATTTTTTTAACTA
Found at i:15603187 original size:139 final size:139
Alignment explanation
Indices: 15602928--15603354 Score: 491
Period size: 148 Copynumber: 3.0 Consensus size: 139
15602918 TATTTAAAAA
* *
15602928 TAAAAAAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGAGAGAGTTTA
1 TAAAAAAAAGTTTAGATTTTT--AAA-AAAAA-ATGTTTTTTAGTCATTTTAAAGAAAAAGTTTA
* * * * * *
15602993 AATTTTTAAACAAAGTTTGT-TTTTTTTAATTATTTCGAAATATAATTTTTAATTTTTAAGAAAA
62 AAATTTTAAACAAAATTTTTATTTTTTTAACTATTTCGAAATAAAAGTTTTAATTTTTAAGAAAA
15603057 GTAGTGATTTTTT
127 GTAGTGATTTTTT
* * *
15603070 T-AAAAAAAGTTTAGATTTCTAAAAAAAAATGTTTTTTAGTTATTTTACAA-AAAAAATTTAAAA
1 TAAAAAAAAGTTTAGATTTTTAAAAAAAAATGTTTTTTAGTCATTTTA-AAGAAAAAGTTTAAAA
* * * *
15603133 TTTTAAATAAATTTTTTTATTTTTTTAACTATTTCGAAATAAAAGCTTTAATTTTTAAGAAAAAT
65 TTTTAAACAAA-ATTTTTATTTTTTTAACTATTTCGAAATAAAAGTTTTAATTTTTAAGAAAAGT
*
15603198 AGTAATTTTTTT
129 AGTGA-TTTTTT
*
15603210 TAAAAACAGAAATTTTAGATTTTTAAAAATAAAATTTGTTTTTTTAGTCATTTTAAAGGAAAAAG
1 T-AAAA-A-AAAGTTTAGATTTTTAAAAA-AAAA--TG-TTTTTTAGTCATTTTAAA-GAAAAAG
* * * *
15603275 TTTAAAATTTTAAACAAAATTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTTGATCTTTAAG
58 TTTAAAATTTTAAACAAAATTTTTATTTTTTTAACTATTTCGAAATAAAAGTTTTAATTTTTAAG
* *
15603340 AATAGTACTGATTTT
123 AAAAGTAGTGATTTT
15603355 GTTTTTTTTT
Statistics
Matches: 241, Mismatches: 30, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
137 37 0.15
138 11 0.05
139 48 0.20
140 7 0.03
141 18 0.07
142 4 0.02
143 1 0.00
144 18 0.07
145 4 0.02
147 8 0.03
148 63 0.26
149 22 0.09
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (139 bp):
TAAAAAAAAGTTTAGATTTTTAAAAAAAAATGTTTTTTAGTCATTTTAAAGAAAAAGTTTAAAAT
TTTAAACAAAATTTTTATTTTTTTAACTATTTCGAAATAAAAGTTTTAATTTTTAAGAAAAGTAG
TGATTTTTT
Found at i:15603254 original size:22 final size:22
Alignment explanation
Indices: 15603203--15603255 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
15603193 AAAATAGTAA
15603203 TTTTTTTTAAAAACAGAAATTT
1 TTTTTTTTAAAAACAGAAATTT
** *
15603225 TAGATTTTTAAAAATA-AAATTT
1 T-TTTTTTTAAAAACAGAAATTT
*
15603247 GTTTTTTTA
1 TTTTTTTTA
15603256 GTCATTTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
21 6 0.25
22 7 0.29
23 11 0.46
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTTTTTTAAAAACAGAAATTT
Found at i:15604646 original size:3 final size:3
Alignment explanation
Indices: 15604638--15604681 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
15604628 AATATTTTCA
15604638 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
15604682 AAGATTGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:15613529 original size:17 final size:17
Alignment explanation
Indices: 15613507--15613540 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15613497 ATTTTTAAAA
15613507 AAAAAAAATAGATTTTT
1 AAAAAAAATAGATTTTT
* *
15613524 AAAAAATATATATTTTT
1 AAAAAAAATAGATTTTT
15613541 TAATCATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AAAAAAAATAGATTTTT
Found at i:15613705 original size:103 final size:104
Alignment explanation
Indices: 15613515--15613715 Score: 277
Period size: 103 Copynumber: 1.9 Consensus size: 104
15613505 AAAAAAAAAA
*
15613515 TAGATTTTTAAAAAATATATATTTTTTAATCATTTTAAAGGAAAAAGTTTAAATTTTATTAAACA
1 TAGATTTTTAAAAAAAATATATTTTTTAATCATTTTAAAGG-AAAAGTTTAAATTTTATTAAACA
15613580 AAGTTTTGATTTTTTTACTATTTAGAAATAAAAAAAAGTT
65 AAGTTTTGATTTTTTTACTATTTAGAAATAAAAAAAAGTT
* * *
15613620 TAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAA-G-AGAGTTTAAA-TTT-TTAAA
1 TAGATTTTT--AAA-AAAAATATATTTTTTAATCATTTTAAAGGAAAAGTTTAAATTTTATTAAA
*
15613681 CAAAG-TTTGATTTTTTTAACTATTTCGAAATAAAA
63 CAAAGTTTTGATTTTTTT-ACTATTTAGAAATAAAA
15613716 TTTTTAATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
102 12 0.14
103 26 0.30
104 3 0.03
105 18 0.21
107 4 0.05
108 24 0.28
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (104 bp):
TAGATTTTTAAAAAAAATATATTTTTTAATCATTTTAAAGGAAAAGTTTAAATTTTATTAAACAA
AGTTTTGATTTTTTTACTATTTAGAAATAAAAAAAAGTT
Found at i:15613765 original size:22 final size:24
Alignment explanation
Indices: 15613740--15613784 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
15613730 GAAAAGTAGT
*
15613740 GATTTTTAAAAA-AAAAA-GTTTA
1 GATTTCTAAAAATAAAAATGTTTA
15613762 GATTTCTAAAAATAAAAATGTTT
1 GATTTCTAAAAATAAAAATGTTT
15613785 TTTAGTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 5 0.25
24 4 0.20
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (24 bp):
GATTTCTAAAAATAAAAATGTTTA
Found at i:15613843 original size:141 final size:142
Alignment explanation
Indices: 15613609--15614034 Score: 522
Period size: 141 Copynumber: 3.0 Consensus size: 142
15613599 ATTTAGAAAT
* *
15613609 AAAAAAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCA-TTT-TA-AAGAGAGTTTA
1 AAAAAAAAGTTTAGATTTTTAAAAAT-AAAATATGTTTTTTAGTCATTTTATAGAAAAAAGTTTA
* *
15613671 AATTTTTAAACAAAGTTTGATTTTTTTAACTATTTCGAAATAAAATTTTTAATTTTTAAGAAAAG
65 AATTTTTAAACAAATTTTGATTTTTTTAACTATTTCGAAATAAAATTTTTGATTTTTAAGAAAAG
15613736 TAGTGATTTTTAA
130 TAGTGATTTTTAA
* *
15613749 AAAAAAAAGTTTAGATTTCTAAAAATAAAA-ATGTTTTTTAGTCATTTTATAGAAAAAATTTTAA
1 AAAAAAAAGTTTAGATTTTTAAAAATAAAATATGTTTTTTAGTCATTTTATAGAAAAAAGTTTAA
* ** *
15613813 ATTTTTAAACAAATTTT-TTATTTTTTAACTATTTCGAAATAAAAGCTTTGATTTTTAAGAAAAA
66 ATTTTTAAACAAATTTTGAT-TTTTTTAACTATTTCGAAATAAAATTTTTGATTTTTAAGAAAAG
* **
15613877 TGGTTTTTTTTTAA
130 TAG-TGATTTTTAA
* * * * * *
15613891 AAAACAGAAATTTTAAATTTTTAAAAATAAAATTTTATTTTTTAGAT-ATTTTAAAGGAAAAAGT
1 AAAA-A-AAAGTTTAGATTTTTAAAAATAAAA-TATGTTTTTTAG-TCATTTTATAGAAAAAAGT
* *
15613955 TTAAAATTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTTGATCTTTAAG
62 TTAAATTTTTAAAC-AAATTTTGATTTTTTTAACTATTTCGAAATAAAA-TTTTTGATTTTTAAG
* *
15614020 AATAGTACTGATTTT
125 AAAAGTAGTGATTTT
15614035 GTTTTTTTTT
Statistics
Matches: 241, Mismatches: 32, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
138 14 0.06
139 7 0.03
140 28 0.12
141 67 0.28
142 12 0.05
143 1 0.00
144 22 0.09
146 36 0.15
147 37 0.15
148 17 0.07
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (142 bp):
AAAAAAAAGTTTAGATTTTTAAAAATAAAATATGTTTTTTAGTCATTTTATAGAAAAAAGTTTAA
ATTTTTAAACAAATTTTGATTTTTTTAACTATTTCGAAATAAAATTTTTGATTTTTAAGAAAAGT
AGTGATTTTTAA
Found at i:15613933 original size:22 final size:24
Alignment explanation
Indices: 15613882--15613933 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
15613872 AAAAATGGTT
15613882 TTTTTTTAAAAAACAGAAATTTTA
1 TTTTTTTAAAAAACAGAAATTTTA
** *
15613906 AATTTTT-AAAAATA-AAATTTTA
1 TTTTTTTAAAAAACAGAAATTTTA
15613928 TTTTTT
1 TTTTTT
15613934 AGATATTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 12 0.52
23 6 0.26
24 5 0.22
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTTTTAAAAAACAGAAATTTTA
Found at i:15615255 original size:3 final size:3
Alignment explanation
Indices: 15615247--15615275 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15615237 AATATTTCAA
15615247 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
15615276 AAGATTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:15623893 original size:18 final size:18
Alignment explanation
Indices: 15623857--15623908 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 18
15623847 ACCGAGAAGG
15623857 CGAAACCTG-AGAAGAAGAA
1 CGAAA-CTGAAGAAG-AGAA
15623876 CGAAACTGAAGAAGAGAA
1 CGAAACTGAAGAAGAGAA
15623894 -GAAA--GAAGAAGAGAA
1 CGAAACTGAAGAAGAGAA
15623909 GAGTGAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.34
17 4 0.12
18 7 0.22
19 10 0.31
ACGTcount: A:0.58, C:0.10, G:0.29, T:0.04
Consensus pattern (18 bp):
CGAAACTGAAGAAGAGAA
Found at i:15633326 original size:58 final size:58
Alignment explanation
Indices: 15633264--15633455 Score: 232
Period size: 59 Copynumber: 3.3 Consensus size: 58
15633254 GGACATTCGA
* * * *
15633264 GGGTAAAATAGTAGTTTTGGTGGAATCGAGGTCAAAAATGGAAATTTGTAAAGTTTAG
1 GGGTAAAATGGTAATTTTGGTGGAATCGGGGTTAAAAATGGAAATTTGTAAAGTTTAG
15633322 GGGT-AAATGGTAATTTTCGGTGGAATCGGGGTTAAAAAT-GAAATTT-TAGAATGTTTAG
1 GGGTAAAATGGTAATTTT-GGTGGAATCGGGGTTAAAAATGGAAATTTGTA-AA-GTTTAG
* * *
15633380 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGG-AATTTAGGAAAATTTAG
1 GGGTAAAATGGTAA-TTTTGGTGGAATCGGGGTTAAAAATGGAAATTT-GTAAAGTTTAG
*
15633439 GGTTAAAAT-GTAATTTT
1 GGGTAAAATGGTAATTTT
15633456 TAGAAAGTTT
Statistics
Matches: 118, Mismatches: 8, Indels: 17
0.83 0.06 0.12
Matches are distributed among these distances:
56 2 0.02
57 24 0.20
58 37 0.31
59 47 0.40
60 7 0.06
61 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGTGGAATCGGGGTTAAAAATGGAAATTTGTAAAGTTTAG
Found at i:15633396 original size:29 final size:28
Alignment explanation
Indices: 15633356--15633588 Score: 136
Period size: 30 Copynumber: 7.9 Consensus size: 28
15633346 ATCGGGGTTA
* *
15633356 AAAATGAAATTTTAGAATGTTTAGGGGT
1 AAAATGTAATTTTAGAAAGTTTAGGGGT
* *
15633384 AAAATGGTAATTTTTGGTGAAA---TCGGGGTT
1 AAAAT-GTAA-TTTT--AGAAAGTTTAGGGG-T
* * *
15633414 AAAAATGGAA-TTTAGGAAAATTTAGGGTT
1 -AAAATGTAATTTTA-GAAAGTTTAGGGGT
* *
15633443 AAAATGTAATTTTTAGAAAGTTTTGGGATT
1 AAAATGTAA-TTTTAGAAAGTTTAGGG-GT
* *
15633473 AAAATGTAATTTTGGAAAAGTTGTAGGGTT
1 AAAATGTAATTTTAG-AAAGTT-TAGGGGT
*
15633503 AAAATGTAATTTTTA-AAATGTTTTGGGGTT
1 AAAATGTAA-TTTTAGAAA-GTTTAGGGG-T
* * *
15633533 AAAATGTAATTTCCAAAAATTTTA-GGGT
1 AAAATGTAATTT-TAGAAAGTTTAGGGGT
15633561 CAAAATGTAATTTTAGAAAAGTTTAGGG
1 -AAAATGTAATTTTAG-AAAGTTTAGGG
15633589 ACCTACAGAG
Statistics
Matches: 160, Mismatches: 22, Indels: 44
0.71 0.10 0.19
Matches are distributed among these distances:
27 4 0.03
28 18 0.11
29 56 0.35
30 63 0.39
31 16 0.10
32 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTTAGAAAGTTTAGGGGT
Found at i:15633410 original size:59 final size:58
Alignment explanation
Indices: 15633264--15633456 Score: 225
Period size: 58 Copynumber: 3.3 Consensus size: 58
15633254 GGACATTCGA
* * * *
15633264 GGGTAAAATAGT-AGTTTTGGTGGAATCGAGGTCAAAAATGGAAATTTGTA-AAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGGAATCGGGGTTAAAAAT-GAAATTT-TAGAAGTTTAG
*
15633322 GGGT-AAATGGTAATTTTCGGTGGAATCGGGGTTAAAAATGAAATTTTAGAATGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGGAATCGGGGTTAAAAATGAAATTTTAGAA-GTTTAG
* * *
15633380 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAA-TTTAGGAAAATTTAG
1 GGGTAAAATGGTAATTTTTGGTGGAATCGGGGTTAAAAATGAAATTTTA-G-AAGTTTAG
*
15633439 GGTTAAAAT-GTAATTTTT
1 GGGTAAAATGGTAATTTTT
15633457 AGAAAGTTTT
Statistics
Matches: 119, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
56 2 0.02
57 15 0.13
58 50 0.42
59 50 0.42
60 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGTGGAATCGGGGTTAAAAATGAAATTTTAGAAGTTTAG
Found at i:15633514 original size:60 final size:58
Alignment explanation
Indices: 15633415--15633589 Score: 219
Period size: 60 Copynumber: 3.0 Consensus size: 58
15633405 ATCGGGGTTA
* *
15633415 AAAATGGAATTTAGGAAAATTTAGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGATT
1 AAAATGTAATTTTGGAAAATTTAGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGATT
*
15633473 AAAATGTAATTTTGGAAAAGTTGTAGGGTTAAAATGTAATTTTTA-AAATGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAA-TT-TAGGGTTAAAATGTAATTTTTAGAAA-GTTTTGGGATT
*** * *
15633533 AAAATGTAATTTCCAAAAATTTTAGGGTCAAAATGTAA-TTTTAGAAAAGTTTAGGGA
1 AAAATGTAATTTTGGAAAA-TTTAGGGTTAAAATGTAATTTTTAG-AAAGTTTTGGGA
15633590 CCTACAGAGC
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
58 22 0.22
59 27 0.26
60 53 0.52
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.38
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAAATTTAGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGATT
Found at i:15634202 original size:22 final size:22
Alignment explanation
Indices: 15634176--15634219 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
15634166 TCAAGCGCCT
15634176 GCGCC-ACTCCTTCCGTGCTCAC
1 GCGCCTACTCC-TCCGTGCTCAC
*
15634198 GCGCCTCCTCCTCCGTGCTCAC
1 GCGCCTACTCCTCCGTGCTCAC
15634220 ACGCTGGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.07, C:0.52, G:0.18, T:0.23
Consensus pattern (22 bp):
GCGCCTACTCCTCCGTGCTCAC
Found at i:15634340 original size:21 final size:23
Alignment explanation
Indices: 15634309--15634350 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
15634299 TTTTGAAACT
15634309 CTTTTTCTTTT-CTTTTAAAATC
1 CTTTTTCTTTTGCTTTTAAAATC
*
15634331 CTTTTT-TTTTGTTTTTAAAA
1 CTTTTTCTTTTGCTTTTAAAA
15634351 CAACCAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (23 bp):
CTTTTTCTTTTGCTTTTAAAATC
Found at i:15635454 original size:17 final size:16
Alignment explanation
Indices: 15635429--15635478 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
15635419 CAAATTTACT
* *
15635429 AAATCTAAATTTAACAC
1 AAATTTAAATTTAA-AA
15635446 AAATTTAAATTTAAAA
1 AAATTTAAATTTAAAA
15635462 ATTAATTTAAATTTAAA
1 A--AATTTAAATTTAAA
15635479 TTTTAAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 2 0.07
17 13 0.45
18 14 0.48
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTTAAATTTAAAA
Found at i:15635490 original size:18 final size:18
Alignment explanation
Indices: 15635469--15635517 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
15635459 AAAATTAATT
15635469 TAAATTTAAATTT-TAAGA
1 TAAATTTAAATTTGTAA-A
**
15635487 TAAATCCAAATTTGTAAA
1 TAAATTTAAATTTGTAAA
15635505 TAAATTTAGAATT
1 TAAATTTA-AATT
15635518 AACTTAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (18 bp):
TAAATTTAAATTTGTAAA
Found at i:15635497 original size:24 final size:24
Alignment explanation
Indices: 15635445--15635499 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
15635435 AAATTTAACA
* *
15635445 CAAATTTAAATTTAAAAATTAATT
1 CAAATTTAAATTTAAAAATAAATC
* * *
15635469 TAAATTTAAATTTTAAGATAAATC
1 CAAATTTAAATTTAAAAATAAATC
15635493 CAAATTT
1 CAAATTT
15635500 GTAAATAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (24 bp):
CAAATTTAAATTTAAAAATAAATC
Found at i:15636575 original size:92 final size:92
Alignment explanation
Indices: 15636410--15636643 Score: 308
Period size: 92 Copynumber: 2.5 Consensus size: 92
15636400 CTTATACAAC
* * * * *
15636410 TTCAGAGGGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAATGATGCTT
1 TTCAGAGAGATAAAGACTTGTCATCCAACTTTACTTCAACTTCAAAAGGATAGGAAATGATGCTT
* *
15636475 GATGCTTTATCTAGTTCTTACTTCAAT
66 GATGCTTTATCTAGCTCGTACTTCAAT
* * * *
15636502 TTTAGAGAGATAAAGACTTGTCATCCTACTTTACTTCAACTTCAAAAGGGTAGGAAATGATGTTT
1 TTCAGAGAGATAAAGACTTGTCATCCAACTTTACTTCAACTTCAAAAGGATAGGAAATGATGCTT
15636567 GATGCTTTATCTAGCTCGTACTTCAAT
66 GATGCTTTATCTAGCTCGTACTTCAAT
* * * * *
15636594 TTCAGAGAGATAAAGATTTGAT-ATCCAGCTCTACTTCAATTTCAAGAGGA
1 TTCAGAGAGATAAAGACTTG-TCATCCAACTTTACTTCAACTTCAAAAGGA
15636644 CAGGGAACGA
Statistics
Matches: 122, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
92 121 0.99
93 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (92 bp):
TTCAGAGAGATAAAGACTTGTCATCCAACTTTACTTCAACTTCAAAAGGATAGGAAATGATGCTT
GATGCTTTATCTAGCTCGTACTTCAAT
Found at i:15636675 original size:38 final size:38
Alignment explanation
Indices: 15636621--15637056 Score: 165
Period size: 38 Copynumber: 11.5 Consensus size: 38
15636611 TTGATATCCA
*
15636621 GCTC-TACTTCAATTTCAAGAGGACAGGGAACGATCTT
1 GCTCTTACTTCAATTTCAAGAGGATAGGGAACGATCTT
** * *
15636658 GCTCTTACTTCAATTTC-AGA-GATAAAGACCTG-TTTAT
1 GCTCTTACTTCAATTTCAAGAGGATAGGGAAC-GATCT-T
* * * *
15636695 CCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTT
1 GC-TCT-TACTTCAATTTCAAGAGGATAGGGAACGATCTT
** *
15636735 GCTCTTACTTCAATTTC-AGA-GATAAAG-ACTTGAT-AT
1 GCTCTTACTTCAATTTCAAGAGGATAGGGAAC--GATCTT
* * * *
15636771 CCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTT
1 GC-TCT-TACTTCAATTTCAAGAGGATAGGGAACGATCTT
* ** **
15636811 ACTCTTACTTCAATTTC-AGA-GATAAAG-ACTTGATATCCA
1 GCTCTTACTTCAATTTCAAGAGGATAGGGAAC--G--ATCTT
* * * *** **
15636850 GCT-GTACTTCATTTTCAAGAGAATAAAAAATTATCTT
1 GCTCTTACTTCAATTTCAAGAGGATAGGGAACGATCTT
* * ** **
15636887 ACTCTTACTTCACTTTC-AGA-GATAAAG-ACTTGATATCCA
1 GCTCTTACTTCAATTTCAAGAGGATAGGGAAC--G--ATCTT
* *
15636926 GCT-TTACTTCAATTTCAAGAGGATAGGAAATGATCTT
1 GCTCTTACTTCAATTTCAAGAGGATAGGGAACGATCTT
** **
15636963 GCTCTTACTTCAATTTC-AGA-GATAAAG-ACTTGTTATCCA
1 GCTCTTACTTCAATTTCAAGAGGATAGGGAAC--G--ATCTT
* *
15637002 ACTC-TACTTCAATTTCAAGAGGATAGGGAATGATCTT
1 GCTCTTACTTCAATTTCAAGAGGATAGGGAACGATCTT
15637039 GCTCTTACTTCAATTTCA
1 GCTCTTACTTCAATTTCA
15637057 GAGATAAAGA
Statistics
Matches: 285, Mismatches: 74, Indels: 79
0.65 0.17 0.18
Matches are distributed among these distances:
35 4 0.01
36 27 0.09
37 46 0.16
38 122 0.43
39 49 0.17
40 26 0.09
41 11 0.04
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (38 bp):
GCTCTTACTTCAATTTCAAGAGGATAGGGAACGATCTT
Found at i:15636802 original size:76 final size:76
Alignment explanation
Indices: 15636575--15637281 Score: 973
Period size: 76 Copynumber: 9.4 Consensus size: 76
15636565 TTGATGCTTT
* * * *
15636575 ATCTAGCTCGTACTTCAATTTCAGAGAGATAAAGATTTGATATCCAGCTCTACTTCAATTTCAAG
1 ATCTTGCTCTTACTTCAATTTC--AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAG
* * *
15636640 AGGACAGGGAACG
64 AGGATAGGAAATG
* *
15636653 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACCTGTTTATCCAACTCTACTTCAATTTCAAGA
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTG-ATATCCAACTCTACTTCAATTTCAAGA
15636718 GGATAGGAAATG
65 GGATAGGAAATG
15636730 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
15636795 GATAGGAAATG
66 GATAGGAAATG
* * * *
15636806 ATCTTACTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTGTACTTCATTTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
* ** *
15636871 AATAAAAAATT
66 GATAGGAAATG
* * * *
15636882 ATCTTACTCTTACTTCACTTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
15636947 GATAGGAAATG
66 GATAGGAAATG
*
15636958 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
15637023 GATAGGGAATG
66 GATAGGAAATG
* * *
15637034 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
* *
15637098 GACAGGAAAAG
66 GATAGGAAATG
* * *
15637109 ATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGATATCCAAGTCTACTTCAATTTCAAGC
1 ATC-TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGA
*
15637174 GGAT--G--ACG
65 GGATAGGAAATG
* * *
15637182 ---TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
*
15637244 GATAGGAAAAG
66 GATAGGAAATG
*
15637255 ATCTTGTTCTTACTAT-AATTTCAGAGA
1 ATCTTGCTCTTACT-TCAATTTCAGAGA
15637282 GATGAAGATT
Statistics
Matches: 569, Mismatches: 49, Indels: 24
0.89 0.08 0.04
Matches are distributed among these distances:
69 61 0.11
71 1 0.00
73 4 0.01
75 32 0.06
76 358 0.63
77 93 0.16
78 20 0.04
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAG
GATAGGAAATG
Found at i:15637652 original size:51 final size:50
Alignment explanation
Indices: 15637500--15637668 Score: 175
Period size: 51 Copynumber: 3.4 Consensus size: 50
15637490 CATGCATCGT
* * * * * * *
15637500 CGTTGCGACTTAGACCTTTCCCTT-T-TGTCTTTGCGATACTGAATCTGC
1 CGTTGCGACTTAGATCTTTCCCTTCTGTATCTTCGTGGTACTGGATCTAC
* * *
15637548 CGTTGCGGGCTTAGATCTTTCCCGTCGTGTA--TTCGTGGTACTAGATCTAC
1 CGTTGC-GACTTAGATCTTTCCCTTC-TGTATCTTCGTGGTACTGGATCTAC
15637598 CGTTGCGACCTTAGATCTTTCCCTTCTGTATCTTCGTGGTACTGGATCTAC
1 CGTTGCGA-CTTAGATCTTTCCCTTCTGTATCTTCGTGGTACTGGATCTAC
*
15637649 CGTTGCGGTCTTAGATCTTT
1 CGTTGC-GACTTAGATCTTT
15637669 TCGGTCCATG
Statistics
Matches: 99, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
48 6 0.06
49 20 0.20
50 35 0.35
51 36 0.36
52 2 0.02
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.39
Consensus pattern (50 bp):
CGTTGCGACTTAGATCTTTCCCTTCTGTATCTTCGTGGTACTGGATCTAC
Found at i:15637712 original size:101 final size:97
Alignment explanation
Indices: 15637501--15637921 Score: 348
Period size: 101 Copynumber: 4.2 Consensus size: 97
15637491 ATGCATCGTC
* * * * * *
15637501 GTTGCGACTTAGACCTTTCCCTTTTGTCTTTGCGATACTGAATCTGCCGTTGCGGGCTTAGATCT
1 GTTGCGACTTAGACCTTTCCCTTCTGT-TTT-CGGTACTGGATCTACCATTGCGGTCTTAGATCT
* * * * * * *
15637566 TTCCCGT-CGTG-TATTCGTGGTACTA-GATCTACC
64 TTCCCATCCATGCT-TTTGAGGTAC-ACGGTCTGCA
* *
15637599 GTTGCGACCTTAGATCTTTCCCTTCTGTATCTTCGTGGTACTGGATCTACCGTTGCGGTCTTAGA
1 GTTGCGA-CTTAGACCTTTCCCTTCTGT-T-TTC--GGTACTGGATCTACCATTGCGGTCTTAGA
* ** *
15637664 TCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCGCA
61 TCTTTCCCATCCATGCTTTTGAGGTACACGGTCTGCA
* * *
15637701 GTTGCGACTTAGACCTTTCCCTTTTTCTGTTTTACGGTACTGGATCTGCCTTTGCGATCTTAGAT
1 GTTGCGACTTAGACCTTTCCC---TTCTGTTTT-CGGTACTGGATCTACCATTGCGGTCTTAGAT
* * * *
15637766 CTTTCCCTTCCATGCTTTTAAGGTACACGATCTGCC
62 CTTTCCCATCCATGCTTTTGAGGTACACGGTCTGCA
* * * * *
15637802 GTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTACGGTACTAGATCCAACATTGCGGTCTTGGAT
1 GTTGCGACTTAGACCTTTCCC--TTCTG-TTTT-CGGTACTGGATCTACCATTGCGGTCTTAGAT
*
15637867 CTTTCCCAT-CATGCTTCTGAGGTACACGGTCTGCCA
62 CTTTCCCATCCATGCTTTTGAGGTACACGGTCTG-CA
*
15637903 -TTGTGACTTAGACCTTTCC
1 GTTGCGACTTAGACCTTTCC
15637922 TTGTTGTGTT
Statistics
Matches: 269, Mismatches: 41, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
98 7 0.03
99 20 0.07
100 47 0.17
101 162 0.60
102 24 0.09
103 3 0.01
104 6 0.02
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (97 bp):
GTTGCGACTTAGACCTTTCCCTTCTGTTTTCGGTACTGGATCTACCATTGCGGTCTTAGATCTTT
CCCATCCATGCTTTTGAGGTACACGGTCTGCA
Found at i:15637740 original size:50 final size:50
Alignment explanation
Indices: 15637677--15637841 Score: 167
Period size: 50 Copynumber: 3.3 Consensus size: 50
15637667 TTTCGGTCCA
* *
15637677 TGCTTTTGA-GGTACACGGTCCGCAGTTGCGACTTAGACCTTTCCCTTTTTC
1 TGCTTTT-ACGGTACACGGTCTGCCGTTGCGACTTAGACCTTTCCC-TTTTC
* * * *
15637728 TG-TTTTACGGTAC-TGGATCTGCCTTTGCGATCTTAGATCTTTCCC-TTCC
1 TGCTTTTACGGTACACGG-TCTGCCGTTGCGA-CTTAGACCTTTCCCTTTTC
* * *
15637777 ATGCTTTTAAGGTACACGATCTGCCGTTGCGACTTAGACCTTTCCCTTTTG
1 -TGCTTTTACGGTACACGGTCTGCCGTTGCGACTTAGACCTTTCCCTTTTC
*
15637828 TGTTTTTACGGTAC
1 TGCTTTTACGGTAC
15637842 TAGATCCAAC
Statistics
Matches: 92, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
49 6 0.07
50 46 0.50
51 39 0.42
52 1 0.01
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (50 bp):
TGCTTTTACGGTACACGGTCTGCCGTTGCGACTTAGACCTTTCCCTTTTC
Found at i:15637770 original size:51 final size:50
Alignment explanation
Indices: 15637701--15637847 Score: 174
Period size: 51 Copynumber: 2.9 Consensus size: 50
15637691 ACGGTCCGCA
*
15637701 GTTGCGACTTAGACCTTTCCCTTTTTCTG-TTTTACGGTACTGGATCTGCC
1 GTTGCGACTTAGACCTTTCCC-TTTTCTGCTTTTACGGTACTAGATCTGCC
* * * *
15637751 TTTGCGATCTTAGATCTTTCCC-TTCCATGCTTTTAAGGTAC-ACGATCTGCC
1 GTTGCGA-CTTAGACCTTTCCCTTTTC-TGCTTTTACGGTACTA-GATCTGCC
* *
15637802 GTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTACGGTACTAGATC
1 GTTGCGACTTAGACCTTTCCCTTTTCTGCTTTTACGGTACTAGATC
15637848 CAACATTGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
49 3 0.04
50 37 0.46
51 40 0.50
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.41
Consensus pattern (50 bp):
GTTGCGACTTAGACCTTTCCCTTTTCTGCTTTTACGGTACTAGATCTGCC
Found at i:15637917 original size:100 final size:101
Alignment explanation
Indices: 15637651--15637933 Score: 349
Period size: 101 Copynumber: 2.8 Consensus size: 101
15637641 GGATCTACCG
* ** *
15637651 TTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCG-CAGTTGCGACTTAGAC
1 TTGCGGTCTTAGATCTTTCCCATCCATGCTTTTGAGGTACACGGTCTGCCA-TTGCGACTTAGAC
* * *** *
15637715 CTTTCCCTTTT-TCTGTTTTACGGTACTGGATCTGCCT
65 CTTTCCCTTTTGTGT-TTTTACGGTACTAGATCCAACA
* * * * *
15637752 TTGCGATCTTAGATCTTTCCCTTCCATGCTTTTAAGGTACACGATCTGCCGTTGCGACTTAGACC
1 TTGCGGTCTTAGATCTTTCCCATCCATGCTTTTGAGGTACACGGTCTGCCATTGCGACTTAGACC
15637817 TTTCCCTTTTGTGTTTTTACGGTACTAGATCCAACA
66 TTTCCCTTTTGTGTTTTTACGGTACTAGATCCAACA
* * *
15637853 TTGCGGTCTTGGATCTTTCCCAT-CATGCTTCTGAGGTACACGGTCTGCCATTGTGACTTAGACC
1 TTGCGGTCTTAGATCTTTCCCATCCATGCTTTTGAGGTACACGGTCTGCCATTGCGACTTAGACC
15637917 TTT-CCTTGTTGTGTTTT
66 TTTCCCTT-TTGTGTTTT
15637934 GTGGTGCTGA
Statistics
Matches: 157, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
99 4 0.03
100 48 0.31
101 102 0.65
102 3 0.02
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (101 bp):
TTGCGGTCTTAGATCTTTCCCATCCATGCTTTTGAGGTACACGGTCTGCCATTGCGACTTAGACC
TTTCCCTTTTGTGTTTTTACGGTACTAGATCCAACA
Found at i:15644790 original size:59 final size:59
Alignment explanation
Indices: 15644705--15644898 Score: 245
Period size: 59 Copynumber: 3.3 Consensus size: 59
15644695 GGACATTCGA
* * * * *
15644705 GGGTAAAATAGT-AGTTTTGGTGGAATCGAGGTCAAAAATGGAAATTTGTAAAGTTCAG
1 GGGTAAAATGGTAATTTTTGGTGGAATCGAGGTTAAAAATGGAAATTTGGAAAGTTTAG
*
15644763 GGGTAAAATGGTAATTTTTGGTGGAATCGAGGTTAAAAAT-GAAATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGGAATCGAGGTTAAAAATGGAAA-TTTGGAAAGTTTAG
* * *
15644822 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGG-AATTTAGGAAAATTTA-
1 GGGTAAAATGGTAATTTTTGGTGGAATCGAGGTTAAAAATGGAAATTT-GGAAAGTTTAG
15644880 GGGTCAAAAT-GTAATTTTT
1 GGGT-AAAATGGTAATTTTT
15644899 AGAAAGTTTT
Statistics
Matches: 121, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
58 31 0.26
59 89 0.74
60 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGGAATCGAGGTTAAAAATGGAAATTTGGAAAGTTTAG
Found at i:15644828 original size:29 final size:29
Alignment explanation
Indices: 15644796--15644937 Score: 85
Period size: 30 Copynumber: 4.8 Consensus size: 29
15644786 GAATCGAGGT
15644796 TAAAAATGAAATTTTGGAAAGTTTGGGGG
1 TAAAAATGAAATTTTGGAAAGTTTGGGGG
* * *
15644825 T-AAAATGGTAATTTTTGGTGAAA--TCGGGGT
1 TAAAAAT-G-AAATTTT-G-GAAAGTTTGGGGG
* * * *
15644855 TAAAAATGGAATTTAGGAAAATTT-AGGG
1 TAAAAATGAAATTTTGGAAAGTTTGGGGG
* * * *
15644883 TCAAAATGTAATTTTTAGAAAGTTTTGGGG
1 TAAAAATG-AAATTTTGGAAAGTTTGGGGG
* *
15644913 TTAAAATGTAATTTTGGAAAAGTTT
1 TAAAAATGAAATTTTGG-AAAGTTT
15644938 TATGGTCAAA
Statistics
Matches: 83, Mismatches: 20, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
27 4 0.05
28 15 0.18
29 24 0.29
30 30 0.36
31 6 0.07
32 4 0.05
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.36
Consensus pattern (29 bp):
TAAAAATGAAATTTTGGAAAGTTTGGGGG
Found at i:15644859 original size:30 final size:30
Alignment explanation
Indices: 15644767--15644868 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 30
15644757 GTTCAGGGGT
* *
15644767 AAAATGGTAATTTTTGGTGGAATCGAGGTTA
1 AAAATGG-AATTTTTGGTGAAATCGGGGTTA
* * *
15644798 AAAAT-GAAATTTT-G-GAAAGTTTGGGGGT-
1 AAAATGGAATTTTTGGTGAAA--TCGGGGTTA
15644826 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTTGGTGAAATCGGGGTTA
15644857 AAAATGGAATTT
1 AAAATGGAATTT
15644869 AGGAAAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
27 3 0.05
28 6 0.11
29 12 0.21
30 18 0.32
31 13 0.23
32 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGTGAAATCGGGGTTA
Found at i:15645024 original size:30 final size:30
Alignment explanation
Indices: 15644851--15645031 Score: 201
Period size: 30 Copynumber: 6.1 Consensus size: 30
15644841 GGTGAAATCG
* *
15644851 GGGTTAAAAATGGAATTTAGGAAAA--TTTA
1 GGGTT-AAAATGTAATTTTGGAAAAGTTTTA
* * *
15644880 GGGTCAAAATGTAATTTT-TAGAAAGTTTTG
1 GGGTTAAAATGTAATTTTGGA-AAAGTTTTA
15644910 GGGTTAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTTA
* * *
15644940 TGGTCAAAATGTAATTTT-CAAAATGTTTTA
1 GGGTTAAAATGTAATTTTGGAAAA-GTTTTA
***
15644970 GGGTTAAAATGTAATTTCCAAAAAGTTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTTA
15645000 GGGTTAAAATGTAATTTTGGAAAAG-TTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTTA
15645029 GGG
1 GGG
15645032 ACCTACAGAG
Statistics
Matches: 128, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
27 1 0.01
28 14 0.11
29 15 0.12
30 93 0.73
31 5 0.04
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTTA
Found at i:15652780 original size:16 final size:16
Alignment explanation
Indices: 15652759--15652789 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15652749 AACAACACGA
*
15652759 TGAAAAGTGAAATAAC
1 TGAAAAGTAAAATAAC
15652775 TGAAAAGTAAAATAA
1 TGAAAAGTAAAATAA
15652790 AAAATTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.16, T:0.19
Consensus pattern (16 bp):
TGAAAAGTAAAATAAC
Found at i:15662194 original size:17 final size:17
Alignment explanation
Indices: 15662172--15662210 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
15662162 TAGTGAATTT
15662172 TTTTTAAAAAAAATAGA
1 TTTTTAAAAAAAATAGA
* *
15662189 TTTTTAAAAAATATATA
1 TTTTTAAAAAAAATAGA
15662206 TTTTT
1 TTTTT
15662211 TAATCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTTTTAAAAAAAATAGA
Found at i:15662302 original size:103 final size:102
Alignment explanation
Indices: 15662185--15662385 Score: 264
Period size: 107 Copynumber: 1.9 Consensus size: 102
15662175 TTAAAAAAAA
15662185 TAGATTTTTAAAAAAT-ATATATTTTTTAATCATTTTAAAGGAAAAAGTTTAAATTTTATTAAAC
1 TAGATTTTTAAAAAATAATATATTTTTTAATCATTTTAAA-G--AAAGTTTAAA-TTT-TTAAAC
15662249 AAAGTTTTGA-TTTTTTT-ACTATTTAGAAATAAAAAAAAGTT
61 AAAG-TTTGATTTTTTTTAACTATTTAGAAATAAAAAAAAGTT
* * * * *
15662290 TAGATTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGAGAGTTTAAATTTTTAAACAAAG
1 TAGATTTTTAAAA-AATAATATATTTTTTAATCATTTTAAAGAAAGTTTAAATTTTTAAACAAAG
*
15662355 TTTGATTTTTTTTAACTATTTCGAAATAAAA
65 TTTGATTTTTTTTAACTATTTAGAAATAAAA
15662386 TTTTTAATTT
Statistics
Matches: 86, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
101 5 0.06
102 17 0.20
103 19 0.22
104 9 0.10
105 12 0.14
106 3 0.03
107 21 0.24
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (102 bp):
TAGATTTTTAAAAAATAATATATTTTTTAATCATTTTAAAGAAAGTTTAAATTTTTAAACAAAGT
TTGATTTTTTTTAACTATTTAGAAATAAAAAAAAGTT
Found at i:15662435 original size:22 final size:24
Alignment explanation
Indices: 15662410--15662454 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
15662400 GAAAAGTAGT
*
15662410 GATTTTTAAAAA-AAAAA-GTTTA
1 GATTTCTAAAAATAAAAATGTTTA
15662432 GATTTCTAAAAATAAAAATGTTT
1 GATTTCTAAAAATAAAAATGTTT
15662455 TTTAGTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 5 0.25
24 4 0.20
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (24 bp):
GATTTCTAAAAATAAAAATGTTTA
Found at i:15662450 original size:141 final size:139
Alignment explanation
Indices: 15662279--15662704 Score: 491
Period size: 141 Copynumber: 3.0 Consensus size: 139
15662269 ATTTAGAAAT
*
15662279 AAAAAAAAGTTTAGATTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGAGAGTTTAAATT
1 AAAAAAAAGTTTAGATTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGAAAGTTTAAATT
*
15662344 TTTAAACAAAGTTTGATTTTTTTTAACTATTTCGAAATAAAATTTTTAATTTTTAAGAAAAGTAG
66 TTTAAACAAA-TTTGATTTTTTTTAACTATTTCGAAATAAAATTTTTGATTTTTAAGAAAAGTAG
15662409 TGATTTTTAA
130 TGATTTTTAA
* *
15662419 AAAAAAAAGTTTAGATTTCTAAAAAT-AAAA-ATGTTTTTTAGTCATTTTATAGAAAAAATTTTA
1 AAAAAAAAGTTTAGATTT-TAAAAATAAAAATATGTTTTTTAGTCA-TTT-TA-AAGAAAGTTTA
* **
15662482 AATTTTTAAACAAATTT-TTTATTTTTTAACTATTTCGAAATAAAAGCTTTGATTTTTAAGAAAA
62 AATTTTTAAACAAATTTGATT-TTTTTTAACTATTTCGAAATAAAATTTTTGATTTTTAAGAAAA
* * **
15662546 ATGGTTTTTTTTTAA
126 GTAG-TGATTTTTAA
* * * * * *
15662561 AAAACAGAAATTTTAAATTTTTAAAAATAAAATTTTATTTTTTAGACATTTTAAAGGAAAAAGTT
1 AAAA-A-AAAGTTTAGA-TTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAA-G--AAAGTT
* *
15662626 TAAAATTTTAAACAAAATTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTTTGATCTTTAAG
60 TAAATTTTTAAAC-AAA-TTTGATTTTTTTTAACTATTTCGAAATAAAA-TTTTTGATTTTTAAG
* *
15662690 AATAGTACTGATTTT
122 AAAAGTAGTGATTTT
15662705 GTTTTTTTTT
Statistics
Matches: 238, Mismatches: 30, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
139 14 0.06
140 27 0.11
141 54 0.23
142 34 0.14
143 3 0.01
144 17 0.07
145 9 0.04
146 28 0.12
147 32 0.13
148 20 0.08
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (139 bp):
AAAAAAAAGTTTAGATTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGAAAGTTTAAATT
TTTAAACAAATTTGATTTTTTTTAACTATTTCGAAATAAAATTTTTGATTTTTAAGAAAAGTAGT
GATTTTTAA
Found at i:15662603 original size:22 final size:24
Alignment explanation
Indices: 15662552--15662603 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
15662542 AAAAATGGTT
15662552 TTTTTTTAAAAAACAGAAATTTTA
1 TTTTTTTAAAAAACAGAAATTTTA
** *
15662576 AATTTTT-AAAAATA-AAATTTTA
1 TTTTTTTAAAAAACAGAAATTTTA
15662598 TTTTTT
1 TTTTTT
15662604 AGACATTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 12 0.52
23 6 0.26
24 5 0.22
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTTTTAAAAAACAGAAATTTTA
Found at i:15666700 original size:13 final size:14
Alignment explanation
Indices: 15666671--15666703 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
15666661 TGGAAAGGGA
15666671 AAAAATTAATGCAT
1 AAAAATTAATGCAT
*
15666685 AAAAATTAATTC-T
1 AAAAATTAATGCAT
15666698 AAAAAT
1 AAAAAT
15666704 AAAAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (14 bp):
AAAAATTAATGCAT
Found at i:15670474 original size:17 final size:16
Alignment explanation
Indices: 15670431--15670481 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
15670421 TTAAAATTAT
15670431 AATTTTAAAAATAAAA
1 AATTTTAAAAATAAAA
*
15670447 AATTATGAAAAATAAAA
1 AATT-TTAAAAATAAAA
*
15670464 ACTCTTT-AAAATAAAA
1 AAT-TTTAAAAATAAAA
15670480 AA
1 AA
15670482 AATAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 14 0.48
17 14 0.48
18 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (16 bp):
AATTTTAAAAATAAAA
Found at i:15670485 original size:9 final size:9
Alignment explanation
Indices: 15670471--15670499 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
15670461 AAAACTCTTT
15670471 AAAATAAAA
1 AAAATAAAA
15670480 AAAAT-AAA
1 AAAATAAAA
15670488 AAAATAAAA
1 AAAATAAAA
15670497 AAA
1 AAA
15670500 TTCTAGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAATAAAA
Found at i:15670488 original size:8 final size:8
Alignment explanation
Indices: 15670471--15670500 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
15670461 AAAACTCTTT
15670471 AAAATAAAA
1 AAAAT-AAA
15670480 AAAATAAA
1 AAAATAAA
15670488 AAAATAAA
1 AAAATAAA
15670496 AAAAT
1 AAAAT
15670501 TCTAGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAATAAA
Found at i:15670816 original size:32 final size:32
Alignment explanation
Indices: 15670775--15670840 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
15670765 AGTTTTAATA
*
15670775 TAAGTAGTAGGGATTCGCAGATCCTCTAGACG
1 TAAGTAGTAGGGATTCGCAAATCCTCTAGACG
15670807 TAAGTAGTAGGGATTCGCAAATCCTCTAGACG
1 TAAGTAGTAGGGATTCGCAAATCCTCTAGACG
15670839 TA
1 TA
15670841 GGGCTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (32 bp):
TAAGTAGTAGGGATTCGCAAATCCTCTAGACG
Found at i:15671423 original size:24 final size:22
Alignment explanation
Indices: 15671395--15671449 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
15671385 AATTATATTT
15671395 TTTTAAAATAAAAAATGAAAATC
1 TTTTAAAATAAAAAAT-AAAATC
* * *
15671418 TCTTTAGAATTCAAAAATAAAATG
1 T-TTTA-AAATAAAAAATAAAATC
15671442 TTTTAAAA
1 TTTTAAAA
15671450 ATCTAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
22 2 0.08
23 5 0.19
24 10 0.38
25 9 0.35
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (22 bp):
TTTTAAAATAAAAAATAAAATC
Found at i:15676553 original size:11 final size:11
Alignment explanation
Indices: 15676483--15676557 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
15676473 TTTTAAAATA
15676483 TAAAATT-TTT
1 TAAAATTATTT
15676493 T-AAATTATTT
1 TAAAATTATTT
* *
15676503 TTAAATTAATT
1 TAAAATTATTT
*
15676514 T--AATTTTTT
1 TAAAATTATTT
*
15676523 TAAATATAAAATTAT
1 TAAA-AT--TATT-T
15676538 TAAAATTATTT
1 TAAAATTATTT
15676549 TAAAATTAT
1 TAAAATTAT
15676558 AATCATCATT
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
9 12 0.24
10 5 0.10
11 20 0.39
12 5 0.10
14 4 0.08
15 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:15678417 original size:18 final size:18
Alignment explanation
Indices: 15678395--15678447 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
15678385 GCCACGTCAG
*
15678395 TAAAAAAAT--TTAAACT
1 TAAAAAAATAATTAAAAT
15678411 TAAAAAAATAATTAAAAT
1 TAAAAAAATAATTAAAAT
* *
15678429 TAAAAAAACAGTTAAAAT
1 TAAAAAAATAATTAAAAT
15678447 T
1 T
15678448 TTTAATGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 9 0.28
18 23 0.72
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (18 bp):
TAAAAAAATAATTAAAAT
Found at i:15679139 original size:23 final size:23
Alignment explanation
Indices: 15679113--15679160 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
15679103 ACCCACCCAA
15679113 AACCCAAAATCCCCAAATTCAAC
1 AACCCAAAATCCCCAAATTCAAC
* * * *
15679136 AACCTAAAATCTCTAAATTCGAC
1 AACCCAAAATCCCCAAATTCAAC
15679159 AA
1 AA
15679161 TCATAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (23 bp):
AACCCAAAATCCCCAAATTCAAC
Found at i:15688225 original size:24 final size:24
Alignment explanation
Indices: 15688172--15688228 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
15688162 TTTAGAAGAT
*
15688172 TTAG-TATTTATTAGTATAATATA
1 TTAGTTATTTATTAGTATAAAATA
* *
15688195 TTTGTTATTTATTAGCT-TAAAATC
1 TTAGTTATTTATTAG-TATAAAATA
15688219 TTAGTTATTT
1 TTAGTTATTT
15688229 CTTTTCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 3 0.11
24 24 0.86
25 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.56
Consensus pattern (24 bp):
TTAGTTATTTATTAGTATAAAATA
Found at i:15692900 original size:29 final size:31
Alignment explanation
Indices: 15692844--15692908 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 31
15692834 ATTTTTGAGG
* *
15692844 AATTTAGGGATCAAAATTGAAATTTTTGGAA
1 AATTTAGGGATCAAAATTCAAACTTTTGGAA
*
15692875 AATTTA-GGATTAAAA-TCAAACTTTTGGAA
1 AATTTAGGGATCAAAATTCAAACTTTTGGAA
15692904 AATTT
1 AATTT
15692909 GAAGCTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 17 0.55
30 8 0.26
31 6 0.19
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.37
Consensus pattern (31 bp):
AATTTAGGGATCAAAATTCAAACTTTTGGAA
Found at i:15692956 original size:29 final size:28
Alignment explanation
Indices: 15692916--15692986 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
15692906 TTTGAAGCTG
*
15692916 AAAATGTGATTTTTAGAAATTTAGAGGC
1 AAAATGTAATTTTTAGAAATTTAGAGGC
* * * *
15692944 AAAATGGTAATTTTTGGATATTTAGGGGT
1 AAAAT-GTAATTTTTAGAAATTTAGAGGC
15692973 AAAATAGTAATTTT
1 AAAAT-GTAATTTT
15692987 GAATGTTCGG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.39
Consensus pattern (28 bp):
AAAATGTAATTTTTAGAAATTTAGAGGC
Found at i:15692999 original size:28 final size:30
Alignment explanation
Indices: 15692968--15693190 Score: 139
Period size: 29 Copynumber: 7.7 Consensus size: 30
15692958 TGGATATTTA
*
15692968 GGGGTAAAATA-GTAA-TTTTGAATGTTCG
1 GGGGTAAAATATGTAATTTTTGAAAGTTCG
* *
15692996 GGGGAAAAATA-G-AATTTTT-AAATATTC-
1 GGGGTAAAATATGTAATTTTTGAAA-GTTCG
*
15693023 GAGGT-AAATATGTAATTTTTGAGAAGTTCG
1 GGGGTAAAATATGTAATTTTTGA-AAGTTCG
* *
15693053 AGGGTAAAA-ATGTGATTTTTGAAAGTTCG
1 GGGGTAAAATATGTAATTTTTGAAAGTTCG
* * *
15693082 GGGGTAAAAAAATG--ATTTTTGGAAGTTTG
1 GGGGT-AAAATATGTAATTTTTGAAAGTTCG
* * *
15693111 AGGGTAAAA-ATGTAATTTTTAAAAGTTTG
1 GGGGTAAAATATGTAATTTTTGAAAGTTCG
* * * * * **
15693140 AGAGTAAAA-ATGTGATTTTGGAAAAATTTA
1 GGGGTAAAATATGTAATTTTTG-AAAGTTCG
15693170 GGGGTCAAAA-ATGTAATTTTT
1 GGGGT-AAAATATGTAATTTTT
15693191 AGACAAAATA
Statistics
Matches: 156, Mismatches: 25, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
26 5 0.03
27 11 0.07
28 29 0.19
29 62 0.40
30 30 0.19
31 19 0.12
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (30 bp):
GGGGTAAAATATGTAATTTTTGAAAGTTCG
Found at i:15693071 original size:30 final size:30
Alignment explanation
Indices: 15693020--15693158 Score: 160
Period size: 29 Copynumber: 4.8 Consensus size: 30
15693010 TTTTTAAATA
* *
15693020 TTCGA-GGTAAATATGTAATTTTTGAGAAG
1 TTCGAGGGTAAAAATGTGATTTTTGAGAAG
15693049 TTCGAGGGTAAAAATGTGATTTTTGA-AAG
1 TTCGAGGGTAAAAATGTGATTTTTGAGAAG
* **
15693078 TTCGGGGGTAAAAAAATGATTTTTG-GAAG
1 TTCGAGGGTAAAAATGTGATTTTTGAGAAG
* * *
15693107 TTTGAGGGTAAAAATGTAATTTTT-AAAAG
1 TTCGAGGGTAAAAATGTGATTTTTGAGAAG
* *
15693136 TTTGAGAGTAAAAATGTGATTTT
1 TTCGAGGGTAAAAATGTGATTTT
15693159 GGAAAAATTT
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
29 76 0.81
30 18 0.19
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TTCGAGGGTAAAAATGTGATTTTTGAGAAG
Found at i:15693147 original size:58 final size:58
Alignment explanation
Indices: 15693037--15693191 Score: 170
Period size: 58 Copynumber: 2.6 Consensus size: 58
15693027 TAAATATGTA
* * * * *
15693037 ATTTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGAAAGTTCGGGGGTAAAAAAATG
1 ATTTTTG-GAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTCGAGAGTAAAAAAATG
* **
15693096 ATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTTGAGAGTAAAAATGTG
1 ATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTCGAGAGTAAAAAAATG
*
15693154 A-TTTTGGAAAAATTT-AGGGGTCAAAAATGTAATTTTTA
1 ATTTTTGG--AAGTTTGA-GGGT-AAAAATGTAATTTTTA
15693192 GACAAAATAG
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
57 6 0.07
58 45 0.54
59 16 0.19
60 16 0.19
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (58 bp):
ATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTCGAGAGTAAAAAAATG
Found at i:15700719 original size:28 final size:28
Alignment explanation
Indices: 15700560--15700755 Score: 130
Period size: 29 Copynumber: 6.8 Consensus size: 28
15700550 AGAAAAGCTG
* * *
15700560 AAAAT-GTGATTTTTGGAAATTTGGGGGC
1 AAAATGGTAATTTTTGGATATTT-GGGGT
* ** *
15700588 AAAACGGTAAATTTTTTTATGTTTGAGAGG-
1 AAAATGGT-AATTTTTGGATATTTG-G-GGT
* * *
15700618 AAAATGGTAATTTTTGGATGTTCGACGGT
1 AAAATGGTAATTTTTGGATATTTG-GGGT
* *
15700647 AAAATGGTAATTTTTGGAAAAGTTTGAGGT
1 AAAATGGTAATTTTTGG-ATA-TTTGGGGT
15700677 CAAAAT-GTAATTTTTGGATATTTAGGGGT
1 -AAAATGGTAATTTTTGGATATTT-GGGGT
* * *
15700706 AAAATGGTAA-TTTTGGATGTTCGGGGGA
1 AAAATGGTAATTTTTGGATATT-TGGGGT
*
15700734 AAAATGGTAATTTTCGGATATT
1 AAAATGGTAATTTTTGGATATT
15700756 CGAGGGCAAA
Statistics
Matches: 134, Mismatches: 22, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
28 38 0.28
29 53 0.40
30 33 0.25
31 10 0.07
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.38
Consensus pattern (28 bp):
AAAATGGTAATTTTTGGATATTTGGGGT
Found at i:15700793 original size:87 final size:88
Alignment explanation
Indices: 15700618--15700824 Score: 233
Period size: 87 Copynumber: 2.4 Consensus size: 88
15700608 GTTTGAGAGG
* * * * *
15700618 AAAATGGTAATTTTTGGATGTTCGACGGTAAAATGGTAATTTTTGGAAAAGTTTGAGGTCAAAAT
1 AAAATGGTAA-TTTTGGATGTTCGAGGGAAAAATGGTAATTTTCGGAAAAGTTCGAGGGCAAAAT
* * * *
15700683 GTAATTTTTGGATATTTAGGGGT-
65 ATAATTTTTGAAAAGTTAGGGGTA
* *
15700706 AAAATGGTAATTTTGGATGTTCGGGGGAAAAATGGTAATTTTCGG-ATA-TTCGAGGGCAAAAAT
1 AAAATGGTAATTTTGGATGTTCGAGGGAAAAATGGTAATTTTCGGAAAAGTTCGAGGGC-AAAAT
15700769 ATAATTTTTGAAAAGTTAGAGGGTA
65 ATAATTTTTGAAAAGTTAG-GGGTA
* * *
15700794 AAAAT-GTATTTTTGGAAGTTCAAGGGAAAAA
1 AAAATGGTAATTTTGGATGTTCGAGGGAAAAA
15700825 ATGTGATTTT
Statistics
Matches: 101, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
85 7 0.07
86 22 0.22
87 57 0.56
88 15 0.15
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (88 bp):
AAAATGGTAATTTTGGATGTTCGAGGGAAAAATGGTAATTTTCGGAAAAGTTCGAGGGCAAAATA
TAATTTTTGAAAAGTTAGGGGTA
Found at i:15700796 original size:29 final size:29
Alignment explanation
Indices: 15700618--15701011 Score: 156
Period size: 29 Copynumber: 13.5 Consensus size: 29
15700608 GTTTGAGAGG
* * * *
15700618 AAAATGGTAATTTTTG-GATGTTCGACGGT
1 AAAAT-GTAATTTTTGAAAAGTTAGAGGGT
*
15700647 AAAATGGTAATTTTTGGAAAAGTTTGA-GGT
1 AAAAT-GTAATTTTT-GAAAAGTTAGAGGGT
* * *
15700677 CAAAATGTAATTTTTGGATATTTAG-GGGT
1 -AAAATGTAATTTTTGAAAAGTTAGAGGGT
* * * * *
15700706 AAAATGGTAA-TTTTG-GATGTTCGGGGGA
1 AAAAT-GTAATTTTTGAAAAGTTAGAGGGT
* * * * *
15700734 AAAATGGTAATTTTCGGATA-TTCGAGGGCA
1 AAAAT-GTAATTTTTGAAAAGTTAGAGGG-T
*
15700764 AAAATATAATTTTTGAAAAGTTAGAGGGT
1 AAAATGTAATTTTTGAAAAGTTAGAGGGT
* *
15700793 AAAAATGT-ATTTTTG-GAAGTTCA-AGGGAA
1 -AAAATGTAATTTTTGAAAAGTT-AGAGGG-T
*
15700822 AAAATGTGATTTTTG-AAAGTTCA-AGGGT
1 AAAATGTAATTTTTGAAAAGTT-AGAGGGT
* * *
15700850 AAATATGTGATTTTAGAGAAA-TTCGAGGGT
1 AAA-ATGTAATTTTTGA-AAAGTTAGAGGGT
* * *
15700880 AAATATGTGATTTTAGAGAAA-TTCGAGGGT
1 AAA-ATGTAATTTTTGA-AAAGTTAGAGGGT
* * * *
15700910 AAAAATGTGATTTTTTG--AAGTTTGGGGGA
1 -AAAATGT-AATTTTTGAAAAGTTAGAGGGT
* *
15700939 AAAATATAATTTTT-AAGAAGTTCGAGGGT
1 AAAATGTAATTTTTGAA-AAGTTAGAGGGT
* * *
15700968 AAAAATGTAATTTTAGAAAAATT-TAGGGT
1 -AAAATGTAATTTTTGAAAAGTTAGAGGGT
15700997 CAAAATGTAATTTTT
1 -AAAATGTAATTTTT
15701012 AGACAAAATA
Statistics
Matches: 291, Mismatches: 48, Indels: 52
0.74 0.12 0.13
Matches are distributed among these distances:
27 9 0.03
28 50 0.17
29 119 0.41
30 89 0.31
31 24 0.08
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAAGTTAGAGGGT
Found at i:15700805 original size:58 final size:59
Alignment explanation
Indices: 15700618--15700981 Score: 225
Period size: 58 Copynumber: 6.2 Consensus size: 59
15700608 GTTTGAGAGG
* * * * * *
15700618 AAAATGGTAATTTTTGGATGTTCGACGG-TAAAATGGTAATTTTTGGAAAAGTTTGA-GGTC
1 AAAAT-GTAATTTTTGGAAGTTCGAGGGAAAAAAT-ATAATTTTT-GAAAAGTTAGAGGGTA
* ** * * * * *
15700678 AAAATGTAATTTTTGGATA-TT-TAGGGGTAAAATGGTAA-TTTTG-GATGTTCG-GGGGA
1 AAAATGTAATTTTTGGA-AGTTCGAGGGAAAAAAT-ATAATTTTTGAAAAGTTAGAGGGTA
* *
15700734 AAAATGGTAATTTTCGGATA-TTCGAGGGCAAAAATATAATTTTTGAAAAGTTAGAGGGTA
1 AAAAT-GTAATTTTTGGA-AGTTCGAGGGAAAAAATATAATTTTTGAAAAGTTAGAGGGTA
* * *
15700794 AAAATGT-ATTTTTGGAAGTTCAAGGGAAAAAATGTGATTTTTG-AAAGTTCA-AGGGTA
1 AAAATGTAATTTTTGGAAGTTCGAGGGAAAAAATATAATTTTTGAAAAGTT-AGAGGGTA
* * * * * * * * * *
15700851 AATATGTGATTTTAGAGAAATTCGAGGGTAAATATGTGATTTTAGAGAAA-TTCGAGGGTA
1 AAAATGTAATTTTTG-GAAGTTCGAGGGAAAAAATATAATTTTTGA-AAAGTTAGAGGGTA
* * * * *
15700911 AAAATGTGATTTTTTGAAGTTTG-GGGGAAAAATATAATTTTT-AAGAAGTTCGAGGGTA
1 AAAATGTAATTTTTGGAAGTTCGAGGGAAAAAATATAATTTTTGAA-AAGTTAGAGGGTA
15700969 AAAATGTAATTTT
1 AAAATGTAATTTT
15700982 AGAAAAATTT
Statistics
Matches: 246, Mismatches: 41, Indels: 36
0.76 0.13 0.11
Matches are distributed among these distances:
56 13 0.05
57 41 0.17
58 93 0.38
59 62 0.25
60 34 0.14
61 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGAAAAAATATAATTTTTGAAAAGTTAGAGGGTA
Found at i:15700819 original size:28 final size:29
Alignment explanation
Indices: 15700618--15700981 Score: 208
Period size: 30 Copynumber: 12.4 Consensus size: 29
15700608 GTTTGAGAGG
* * *
15700618 AAAATGGTAATTTTTGGATGTTCGACGGT-
1 AAAAT-GTAATTTTTGGAAGTTCAAGGGTA
** *
15700647 AAAATGGTAATTTTTGGAAAAGTTTGA-GGTC
1 AAAAT-GTAATTTTTGG--AAGTTCAAGGGTA
* *
15700678 AAAATGTAATTTTTGGATA-TTTAGGGGT-
1 AAAATGTAATTTTTGGA-AGTTCAAGGGTA
* * *
15700706 AAAATGGTAA-TTTTGGATGTTC-GGGGGA
1 AAAAT-GTAATTTTTGGAAGTTCAAGGGTA
* * *
15700734 AAAATGGTAATTTTCGGATA-TTCGAGGGCA
1 AAAAT-GTAATTTTTGGA-AGTTCAAGGGTA
* *
15700764 AAAATATAATTTTTGAAAAGTT-AGAGGGTA
1 AAAATGTAATTTTTG-GAAGTTCA-AGGGTA
*
15700794 AAAATGT-ATTTTTGGAAGTTCAAGGGAA
1 AAAATGTAATTTTTGGAAGTTCAAGGGTA
* *
15700822 AAAATGTGATTTTTGAAAGTTCAAGGGTA
1 AAAATGTAATTTTTGGAAGTTCAAGGGTA
* * * * *
15700851 AATATGTGATTTTAGAGAAATTCGAGGGTA
1 AAAATGTAATTTTTG-GAAGTTCAAGGGTA
* * * * *
15700881 AATATGTGATTTTAGAGAAATTCGAGGGTA
1 AAAATGTAATTTTTG-GAAGTTCAAGGGTA
* * ** *
15700911 AAAATGTGATTTTTTGAAGTT-TGGGGGA
1 AAAATGTAATTTTTGGAAGTTCAAGGGTA
* * *
15700939 AAAATATAATTTTTAAGAAGTTCGAGGGTA
1 AAAATGTAATTTTT-GGAAGTTCAAGGGTA
15700969 AAAATGTAATTTT
1 AAAATGTAATTTT
15700982 AGAAAAATTT
Statistics
Matches: 276, Mismatches: 40, Indels: 37
0.78 0.11 0.10
Matches are distributed among these distances:
27 4 0.01
28 61 0.22
29 94 0.34
30 106 0.38
31 11 0.04
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTCAAGGGTA
Found at i:15700918 original size:30 final size:30
Alignment explanation
Indices: 15700725--15701010 Score: 205
Period size: 29 Copynumber: 9.8 Consensus size: 30
15700715 ATTTTGGATG
* * *
15700725 TTCG-GGGGAAAAATGGTAATTTTCG-GATA
1 TTCGAGGGTAAAAAT-GTAATTTTAGAGAAA
* * *
15700754 TTCGAGGGCAAAAATATAATTTTTGA-AAA
1 TTCGAGGGTAAAAATGTAATTTTAGAGAAA
* * *
15700783 GTTAGAGGGTAAAAATGT-ATTTTTG-GAAG
1 -TTCGAGGGTAAAAATGTAATTTTAGAGAAA
* * * * *
15700812 TTCAAGGGAAAAAATGTGATTTTTGA-AAG
1 TTCGAGGGTAAAAATGTAATTTTAGAGAAA
* * *
15700841 TTCAAGGGTAAATATGTGATTTTAGAGAAA
1 TTCGAGGGTAAAAATGTAATTTTAGAGAAA
* *
15700871 TTCGAGGGTAAATATGTGATTTTAGAGAAA
1 TTCGAGGGTAAAAATGTAATTTTAGAGAAA
* ** *
15700901 TTCGAGGGTAAAAATGTGATTTT-TTGAAG
1 TTCGAGGGTAAAAATGTAATTTTAGAGAAA
* * * *
15700930 TTTG-GGGGAAAAATATAATTTTTA-AGAAG
1 TTCGAGGGTAAAAATGTAA-TTTTAGAGAAA
*
15700959 TTCGAGGGTAAAAATGTAATTTTAGAAAAA
1 TTCGAGGGTAAAAATGTAATTTTAGAGAAA
* *
15700989 TT-TAGGGTCAAAATGTAATTTT
1 TTCGAGGGTAAAAATGTAATTTT
15701011 TAGACAAAAT
Statistics
Matches: 214, Mismatches: 32, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
28 25 0.12
29 96 0.45
30 93 0.43
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
TTCGAGGGTAAAAATGTAATTTTAGAGAAA
Found at i:15701012 original size:30 final size:30
Alignment explanation
Indices: 15700963--15701020 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
15700953 AAGAAGTTCG
15700963 AGGGTAAAAATGTAATTTTAGA-AAAATTT
1 AGGGTAAAAATGTAATTTTAGACAAAATTT
*
15700992 AGGGTCAAAATGTAATTTTTAGACAAAAT
1 AGGGTAAAAATGTAA-TTTTAGACAAAAT
15701021 AGGGACCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 7 0.27
31 5 0.19
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (30 bp):
AGGGTAAAAATGTAATTTTAGACAAAATTT
Found at i:15701023 original size:29 final size:28
Alignment explanation
Indices: 15700758--15701024 Score: 96
Period size: 30 Copynumber: 9.1 Consensus size: 28
15700748 CGGATATTCG
* * * *
15700758 AGGGCAAAAATATAATTTTTGAAAAGTT
1 AGGGTAAAAATGTAATTTTAGAAAAATT
* * *
15700786 AGAGGGTAAAAATGT-ATTTTTG-GAAGTT
1 --AGGGTAAAAATGTAATTTTAGAAAAATT
* * * *
15700814 CAAGGGAAAAAATGTGATTTTTG-AAAGTT
1 --AGGGTAAAAATGTAATTTTAGAAAAATT
* * *
15700843 CAAGGGTAAATATGTGATTTTAGAGAAATT
1 --AGGGTAAAAATGTAATTTTAGAAAAATT
* * *
15700873 CGAGGGTAAATATGTGATTTTAGAGAAATT
1 --AGGGTAAAAATGTAATTTTAGAAAAATT
* * **
15700903 CGAGGGTAAAAATGTGATTTTTTG-AAGTTT
1 --AGGGTAAAAATGT-AATTTTAGAAAAATT
* * * * *
15700933 GGGGGAAAAATATAATTTTTA-AGAAGTT
1 AGGGTAAAAATGTAA-TTTTAGAAAAATT
15700961 CGAGGGTAAAAATGTAATTTTAGAAAAATTT
1 --AGGGTAAAAATGTAATTTTAGAAAAA-TT
*
15700992 AGGGTCAAAATGTAATTTTTAGACAAAA-T
1 AGGGTAAAAATGTAA-TTTTAGA-AAAATT
15701021 AGGG
1 AGGG
15701025 ACCTTATGCA
Statistics
Matches: 192, Mismatches: 34, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
27 1 0.01
28 34 0.18
29 63 0.33
30 83 0.43
31 11 0.06
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (28 bp):
AGGGTAAAAATGTAATTTTAGAAAAATT
Found at i:15702161 original size:30 final size:30
Alignment explanation
Indices: 15702124--15702192 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
15702114 GTAGAAAATG
15702124 ATAAATAAGTAATTAATGAATATATTAATATATA
1 ATAAATAA-T-ATTAAT--ATATATTAATATATA
*
15702158 ATAAATAATATTAATATATATTTATATATA
1 ATAAATAATATTAATATATATTAATATATA
*
15702188 TTAAA
1 ATAAA
15702193 ACGTTTTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 18 0.55
32 6 0.18
33 1 0.03
34 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (30 bp):
ATAAATAATATTAATATATATTAATATATA
Found at i:15702184 original size:10 final size:10
Alignment explanation
Indices: 15702143--15702191 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
15702133 TAATTAATGA
15702143 ATATATTAAT
1 ATATATTAAT
*
15702153 ATATAATAA-
1 ATATATTAAT
15702162 ATAATATTAAT
1 AT-ATATTAAT
*
15702173 ATATATTTAT
1 ATATATTAAT
15702183 ATATATTAA
1 ATATATTAA
15702192 AACGTTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATATATTAAT
Found at i:15702188 original size:20 final size:19
Alignment explanation
Indices: 15702137--15702191 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
15702127 AATAAGTAAT
*
15702137 TAATGAATATATTAATATA
1 TAATAAATATATTAATATA
15702156 TAATAAATAATATTAATATA
1 TAATAAAT-ATATTAATATA
* *
15702176 TATTTATATATATTAA
1 TA-ATAAATATATTAA
15702192 AACGTTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.23
20 20 0.65
21 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TAATAAATATATTAATATA
Done.