Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 143 of 173
Found at i:43356489 original size:27 final size:27
Alignment explanation
Indices: 43356459--43356510 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
43356449 TTCCATTGAT
43356459 TTTTTTTTTATAGAATAAGAAAAAAGA
1 TTTTTTTTTATAGAATAAGAAAAAAGA
43356486 TTTTTTTTTATAGAATAAGAAAAAA
1 TTTTTTTTTATAGAATAAGAAAAAA
43356511 AATCAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (27 bp):
TTTTTTTTTATAGAATAAGAAAAAAGA
Found at i:43358651 original size:142 final size:144
Alignment explanation
Indices: 43358468--43358821 Score: 515
Period size: 142 Copynumber: 2.5 Consensus size: 144
43358458 ATAAATAATG
* *
43358468 TAAAATAA--TAAAATTAAAAAATAATATATTTTTTGAAAGTAATAAAATTCGAAAAAAAATACG
1 TAAAATAATGTAAAATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAAAAAAAATACG
* * *
43358531 AACAAAGGGCGGAAAT-A-AGGATTTTTTT-AATTTATTTAAAAAATATAGTAAAATAATATATT
66 AACAAAGGGCGGAAATAAGAGGATTTTTTTAAATTTATGT-AAAAACATAGTAAAATAATACATT
*
43358593 TCAAATATAATTTAC
130 TCAAATATAATGTAC
*
43358608 TAAAATAATGTAAAATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATTCG-GAAAAAATACG
1 TAAAATAATGTAAAATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAAAAAAAATACG
* * ** * *
43358672 AATATAGGGTTGAAATAAGAGGTTTTTTTTAAATTTATGTAAAAACATAGTAAATTAATACATTT
66 AACAAAGGGCGGAAATAAGAGGATTTTTTTAAATTTATGTAAAAACATAGTAAAATAATACATTT
43358737 CAAATATAATGTAC
131 CAAATATAATGTAC
*
43358751 TAAAATAATGTAAAA-TAAAAAATAGTATATTTTTTAAAAGTAATAAAATTTGAGAAAAAAATAC
1 TAAAATAATGTAAAATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGA-AAAAAAATAC
43358815 GAACAAA
65 GAACAAA
43358822 TGGTCAAAAT
Statistics
Matches: 190, Mismatches: 17, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
140 8 0.04
141 22 0.12
142 78 0.41
143 60 0.32
144 22 0.12
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (144 bp):
TAAAATAATGTAAAATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAAAAAAAATACG
AACAAAGGGCGGAAATAAGAGGATTTTTTTAAATTTATGTAAAAACATAGTAAAATAATACATTT
CAAATATAATGTAC
Found at i:43358832 original size:19 final size:19
Alignment explanation
Indices: 43358808--43358844 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43358798 ATTTGAGAAA
*
43358808 AAAATACGAACAAATGGTC
1 AAAATAAGAACAAATGGTC
*
43358827 AAAATAAGAACAATTGGT
1 AAAATAAGAACAAATGGT
43358845 GCCGCCTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.11, G:0.16, T:0.19
Consensus pattern (19 bp):
AAAATAAGAACAAATGGTC
Found at i:43360914 original size:47 final size:47
Alignment explanation
Indices: 43360842--43360936 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
43360832 CACTTCTATG
*
43360842 GTGAGTTGTAAGTTGTGTTACAAGGTTTTGCACTGCTGGGAAAGAGA
1 GTGAGTTGTAAGTTGTGTTAAAAGGTTTTGCACTGCTGGGAAAGAGA
43360889 GTGAGTTGTAAGTTGTGTTAAAAGGTTTTGCACTGCTGGGAAAGAGA
1 GTGAGTTGTAAGTTGTGTTAAAAGGTTTTGCACTGCTGGGAAAGAGA
43360936 G
1 G
43360937 CATAACAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.07, G:0.35, T:0.32
Consensus pattern (47 bp):
GTGAGTTGTAAGTTGTGTTAAAAGGTTTTGCACTGCTGGGAAAGAGA
Found at i:43363821 original size:17 final size:16
Alignment explanation
Indices: 43363779--43363821 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
43363769 GATAAAAATT
*
43363779 AAATATTTTATTTTAA
1 AAATATTTTATTTCAA
*
43363795 AAATAATTTATTTCAA
1 AAATATTTTATTTCAA
*
43363811 ATATGATTTTA
1 AAAT-ATTTTA
43363822 AAAAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
AAATATTTTATTTCAA
Found at i:43365355 original size:52 final size:48
Alignment explanation
Indices: 43365277--43365380 Score: 127
Period size: 52 Copynumber: 2.1 Consensus size: 48
43365267 ATTGTCACCT
* *
43365277 TTGATTGATGTAGATAGGATTTTCCTTCCTTCTTAAGATGACTTTGAAATCC
1 TTGATTGATGAAGATAGGATATTCCTT-C-TC--AAGATGACTTTGAAATCC
* * *
43365329 TTGATTGATGAATATGGGATATTCCTTCTCAAGATGACTTTTAAATCC
1 TTGATTGATGAAGATAGGATATTCCTTCTCAAGATGACTTTGAAATCC
43365377 TTGA
1 TTGA
43365381 AGCATGTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 21 0.45
50 2 0.04
51 1 0.02
52 23 0.49
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (48 bp):
TTGATTGATGAAGATAGGATATTCCTTCTCAAGATGACTTTGAAATCC
Found at i:43375569 original size:24 final size:26
Alignment explanation
Indices: 43375524--43375585 Score: 92
Period size: 24 Copynumber: 2.4 Consensus size: 26
43375514 AAATAAAAAA
*
43375524 TTACCAAAATGTTATAATTTTTTTTAT
1 TTACCAAAAT-ATATAATTTTTTTTAT
43375551 TTACCAAAATATAT-A-TTTTTTTAT
1 TTACCAAAATATATAATTTTTTTTAT
43375575 TTACCAAAATA
1 TTACCAAAATA
43375586 CATCAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 20 0.59
25 1 0.03
26 3 0.09
27 10 0.29
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.50
Consensus pattern (26 bp):
TTACCAAAATATATAATTTTTTTTAT
Found at i:43375611 original size:18 final size:18
Alignment explanation
Indices: 43375590--43375627 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
43375580 AAAATACATC
43375590 AAAAAAACA-AAAAACAAA
1 AAAAAAACAGAAAAA-AAA
43375608 AAAAAAACAGAAAAAAAA
1 AAAAAAACAGAAAAAAAA
43375626 AA
1 AA
43375628 CCTAAACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAAAACAGAAAAAAAA
Found at i:43375612 original size:11 final size:11
Alignment explanation
Indices: 43375593--43375626 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
43375583 ATACATCAAA
43375593 AAAACAAAAAAC
1 AAAA-AAAAAAC
43375605 AAAAAAAAAAC
1 AAAAAAAAAAC
43375616 AGAAAAAAAAA
1 A-AAAAAAAAA
43375627 ACCTAAACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:43375760 original size:22 final size:23
Alignment explanation
Indices: 43375729--43375830 Score: 64
Period size: 24 Copynumber: 4.3 Consensus size: 23
43375719 AGGAGAGGGG
*
43375729 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
43375751 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
43375773 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* * ***
43375799 AAGAAGAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
43375823 AAGAAAAA
1 AAGAAAAA
43375831 TAAGCAAAGA
Statistics
Matches: 58, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
22 12 0.21
23 10 0.17
24 30 0.52
25 5 0.09
26 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:43375787 original size:28 final size:28
Alignment explanation
Indices: 43375732--43375811 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
43375722 AGAGGGGAAG
43375732 AAGAA-GAAAGAA-AGG-AAGAAAGAAA
1 AAGAAGGAAAGAAGAGGAAAGAAAGAAA
43375757 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G--A--AGAGGAAAGAAAGAAA
43375791 AAGAAGGAAAGAAGAGGAAAG
1 AAGAAGGAAAGAAGAGGAAAG
43375812 GGGAGGAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 3 0.07
28 10 0.22
30 2 0.04
32 2 0.04
33 6 0.13
34 17 0.37
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAGAGGAAAGAAAGAAA
Found at i:43375808 original size:10 final size:10
Alignment explanation
Indices: 43375729--43375823 Score: 61
Period size: 10 Copynumber: 9.5 Consensus size: 10
43375719 AGGAGAGGGG
*
43375729 AAGAAGAAGA
1 AAGAAGAGGA
*
43375739 AAGAAAGGAAGA
1 AAG-AA-GAGGA
* *
43375751 AAGAAAAAGA
1 AAGAAGAGGA
* *
43375761 AGGAAAAGGA
1 AAGAAGAGGA
*
43375771 AAGGAGAGGA
1 AAGAAGAGGA
43375781 AAGAA-A-GA
1 AAGAAGAGGA
43375789 AA-AAGAAGGA
1 AAGAAG-AGGA
43375799 AAGAAGAGGA
1 AAGAAGAGGA
**
43375809 AAGGGGAGGA
1 AAGAAGAGGA
43375819 AAGAA
1 AAGAA
43375824 AGAAAAATAA
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 2 0.03
10 45 0.66
11 7 0.10
12 8 0.12
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (10 bp):
AAGAAGAGGA
Found at i:43375809 original size:38 final size:38
Alignment explanation
Indices: 43375729--43375890 Score: 160
Period size: 38 Copynumber: 4.4 Consensus size: 38
43375719 AGGAGAGGGG
* *
43375729 AAGAAGAAGAAA-GAAAGG-AAGAAAGAAAAAGAAGG-
1 AAGAAGAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
43375764 -A-AA-AGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
1 AAGAAGAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
* * *
43375799 AAGAAGAGGAAAGGGGAGGAAAGAAAGAAAAATAAGCA
1 AAGAAGAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
* * *
43375837 AAGAAAAGGAAAGGAGAAGAGAA-AAA-AAAAAGAAAGAA
1 AAGAAGAGGAAAGGAGAGGA-AAGAAAGAAAAAG-AAGGA
*
43375875 GAAGAAGAGGGAAGGA
1 -AAGAAGAGGAAAGGA
43375891 AGGGAAAAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
32 5 0.05
33 7 0.07
34 18 0.17
36 1 0.01
37 7 0.07
38 53 0.50
39 15 0.14
ACGTcount: A:0.65, C:0.01, G:0.33, T:0.01
Consensus pattern (38 bp):
AAGAAGAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
Found at i:43375901 original size:71 final size:75
Alignment explanation
Indices: 43375729--43375891 Score: 193
Period size: 72 Copynumber: 2.3 Consensus size: 75
43375719 AGGAGAGGGG
* *
43375729 AAGAAGAAGAAA-GAAAGG-AAGAAAG--AAA-AAG-AAGGAAAAGGAAAGGAGAGGAAAGAAAG
1 AAGAAGAAGAAAGGGAAGGAAAGAAAGAAAAATAAGCAAAGAAAAGGAAAGGAGA-GAAAGAAAG
43375788 AAAAAGAAGGA
65 AAAAAGAAGGA
* * *
43375799 AAGAAGAGGAAAGGGGAGGAAAGAAAGAAAAATAAGCAAAGAAAAGGAAAGGAGA-AGAGAAA-A
1 AAGAAGAAGAAAGGGAAGGAAAGAAAGAAAAATAAGCAAAGAAAAGGAAAGGAGAGAAAGAAAGA
43375862 AAAA-AA-GA
66 AAAAGAAGGA
43375870 AAGAAGAAGAAGAGGGAAGGAA
1 AAGAAGAAGAA-AGGGAAGGAA
43375892 GGGAAAAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
70 11 0.14
71 16 0.20
72 18 0.23
73 5 0.06
74 9 0.11
75 3 0.04
76 17 0.22
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.01
Consensus pattern (75 bp):
AAGAAGAAGAAAGGGAAGGAAAGAAAGAAAAATAAGCAAAGAAAAGGAAAGGAGAGAAAGAAAGA
AAAAGAAGGA
Found at i:43376612 original size:18 final size:19
Alignment explanation
Indices: 43376589--43376629 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
43376579 AAAATATATA
*
43376589 TAATATTTTGGTATTTTT-
1 TAATATTTTAGTATTTTTG
*
43376607 TAATATTTTATTATTTTTG
1 TAATATTTTAGTATTTTTG
43376626 TAAT
1 TAAT
43376630 GTTTATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (19 bp):
TAATATTTTAGTATTTTTG
Found at i:43376634 original size:18 final size:18
Alignment explanation
Indices: 43376600--43376638 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43376590 AATATTTTGG
*
43376600 TATTTTTTAATATTTTAT
1 TATTTTTTAATAGTTTAT
43376618 TATTTTTGTAAT-GTTTAT
1 TATTTTT-TAATAGTTTAT
43376636 TAT
1 TAT
43376639 GGGTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
TATTTTTTAATAGTTTAT
Found at i:43376729 original size:26 final size:27
Alignment explanation
Indices: 43376673--43376740 Score: 104
Period size: 26 Copynumber: 2.5 Consensus size: 27
43376663 AAATAAAAAA
43376673 TTACCAAAATAT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA--TTTTTTTAT
43376701 TTACCAAAATATATATAA-TTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
43376727 TTACCAAAATATAT
1 TTACCAAAATATAT
43376741 CAAAAAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
26 22 0.56
28 12 0.31
29 5 0.13
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:43379519 original size:18 final size:18
Alignment explanation
Indices: 43379493--43379530 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43379483 ATCCCAATGA
* *
43379493 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
43379511 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
43379529 TC
1 TC
43379531 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:43379537 original size:18 final size:18
Alignment explanation
Indices: 43379496--43379537 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
43379486 CCAATGATCG
* *
43379496 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
43379514 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
43379532 CCACCA
1 CCACCA
43379538 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:43380614 original size:27 final size:27
Alignment explanation
Indices: 43380573--43380646 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
43380563 AACACGAGTA
* ** **
43380573 GTGCCGCCAATCTGGTTGGCAGGACTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
*
43380600 GTGCCGCCAACCTGGTTCCCTCCACTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
*
43380627 GTGCCGCCAACCTGCTTCCC
1 GTGCCGCCAACCTGGTTCCC
43380647 TTGTTTGGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.12, C:0.39, G:0.27, T:0.22
Consensus pattern (27 bp):
GTGCCGCCAACCTGGTTCCCACCACTG
Found at i:43380647 original size:27 final size:27
Alignment explanation
Indices: 43380596--43380678 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 27
43380586 GGTTGGCAGG
*
43380596 ACTGGTGCCGCCAACCTGGTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
**
43380623 ACTGGTGCCGCCAACCTGCTTCCCTTG
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
** *
43380650 TTTGGTGCCGCCAATCTGCTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
43380677 AC
1 AC
43380679 CCAGAGAGTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.11, C:0.42, G:0.20, T:0.27
Consensus pattern (27 bp):
ACTGGTGCCGCCAACCTGCTTCCCTCC
Found at i:43380727 original size:17 final size:18
Alignment explanation
Indices: 43380705--43380739 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
43380695 TCAGTTCAGG
*
43380705 TTTTTTTTCTAT-TTTTA
1 TTTTTTTTATATATTTTA
43380722 TTTTTTTTATATATTTTA
1 TTTTTTTTATATATTTTA
43380740 GTAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTTTATATATTTTA
Found at i:43380759 original size:27 final size:28
Alignment explanation
Indices: 43380729--43380798 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
43380719 TTATTTTTTT
43380729 TATATATTTTAGTAAAT-AAAAAAATTA
1 TATATATTTTAGTAAATAAAAAAAATTA
* *
43380756 TATATTTTTTGGTAAATAAAAAAAAATTA
1 TATATATTTTAGTAAAT-AAAAAAAATTA
43380785 TA-ATATTTTAGTAA
1 TATATATTTTAGTAA
43380799 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 15 0.41
28 10 0.27
29 12 0.32
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (28 bp):
TATATATTTTAGTAAATAAAAAAAATTA
Found at i:43382250 original size:26 final size:27
Alignment explanation
Indices: 43382198--43382260 Score: 103
Period size: 26 Copynumber: 2.4 Consensus size: 27
43382188 ATAAAAAATA
43382198 ATCAAAATATTATAATTTTTTTTATTT
1 ATCAAAATATTATAATTTTTTTTATTT
43382225 A-CTAAAATATTATAA-TTTTTTTATTT
1 ATC-AAAATATTATAATTTTTTTTATTT
43382251 ATCAAAATAT
1 ATCAAAATAT
43382261 ACCAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (27 bp):
ATCAAAATATTATAATTTTTTTTATTT
Found at i:43382578 original size:22 final size:22
Alignment explanation
Indices: 43382553--43382601 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
43382543 ATAACTCTAT
**
43382553 TTTA-ATTTATTAAATTTAATAG
1 TTTATATTTA-TAAATAAAATAG
*
43382575 TTTATGTTTATAAATAAAATAG
1 TTTATATTTATAAATAAAATAG
43382597 TTTAT
1 TTTAT
43382602 GTTTCCATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTATATTTATAAATAAAATAG
Found at i:43382698 original size:19 final size:19
Alignment explanation
Indices: 43382674--43382737 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
43382664 ATTAAAATAG
43382674 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
43382693 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
43382711 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
43382730 TTTAATTT
1 TTTAATTT
43382738 TTAAAAAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:43383021 original size:18 final size:19
Alignment explanation
Indices: 43382972--43383030 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
43382962 ATTTTATATT
43382972 TTAAATAAAAATAGAGTTA
1 TTAAATAAAAATAGAGTTA
* * *
43382991 TTAAATGAGAATAG-TTTA
1 TTAAATAAAAATAGAGTTA
*
43383009 TTAAATTAAAATAGAGTTA
1 TTAAATAAAAATAGAGTTA
43383028 TTA
1 TTA
43383031 CTTAATTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (19 bp):
TTAAATAAAAATAGAGTTA
Found at i:43383690 original size:16 final size:16
Alignment explanation
Indices: 43383669--43383701 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43383659 GCTGTGTCAG
43383669 GTTTTTT-TTTCTTTTT
1 GTTTTTTGTTT-TTTTT
43383685 GTTTTTTGTTTTTTTT
1 GTTTTTTGTTTTTTTT
43383701 G
1 G
43383702 GTATATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (16 bp):
GTTTTTTGTTTTTTTT
Found at i:43383733 original size:26 final size:28
Alignment explanation
Indices: 43383704--43383765 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
43383694 TTTTTTTGGT
43383704 ATATTTTGATAAAT-AA-AAAAATTATA
1 ATATTTTGATAAATAAATAAAAATTATA
43383730 ATATTTTGATAAATAAATAAAAATTATA
1 ATATTTTGATAAATAAATAAAAATTATA
43383758 ATATTTTG
1 ATATTTTG
43383766 GTTATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 14 0.41
27 2 0.06
28 18 0.53
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (28 bp):
ATATTTTGATAAATAAATAAAAATTATA
Found at i:43385123 original size:26 final size:26
Alignment explanation
Indices: 43385089--43385146 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
43385079 ATTTGAATTT
*
43385089 TTTAAATTGAGTTAAGT-GAAATAAAA
1 TTTAAATTGAGTTAAATCG-AATAAAA
* *
43385115 TTTAAATTGATTTAAATCGAGTAAAA
1 TTTAAATTGAGTTAAATCGAATAAAA
43385141 TTTAAA
1 TTTAAA
43385147 AATTAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 27 0.96
27 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (26 bp):
TTTAAATTGAGTTAAATCGAATAAAA
Found at i:43385285 original size:19 final size:20
Alignment explanation
Indices: 43385263--43385313 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
43385253 TTTATATTTT
43385263 TTTTGAA-TTTTTATAAA-TA
1 TTTTGAATTTTTTA-AAATTA
*
43385282 TTTTAAATTTTTTAAAATTA
1 TTTTGAATTTTTTAAAATTA
43385302 TTTTG-ATTTTTT
1 TTTTGAATTTTTT
43385314 TTGTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTGAATTTTTTAAAATTA
Found at i:43388855 original size:30 final size:31
Alignment explanation
Indices: 43388779--43388855 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
43388769 CTCAGATAGC
43388779 AAAAA-CATAGTAAGATTGTGGAATTTATTA
1 AAAAATCATAGTAAGATTGTGGAATTTATTA
43388809 AAAAATCATAGTAAGATTGTGGAATTTATTA
1 AAAAATCATAGTAAGATTGTGGAATTTATTA
*
43388840 AAAAATCTTAG-AAGAT
1 AAAAATCATAGTAAGAT
43388856 CCCAAAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 10 0.22
31 35 0.78
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (31 bp):
AAAAATCATAGTAAGATTGTGGAATTTATTA
Found at i:43394481 original size:24 final size:23
Alignment explanation
Indices: 43394420--43394484 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
43394410 CATTTATTTC
*
43394420 TTAATATAATATTTATATTATAA
1 TTAATATAATATATATATTATAA
*
43394443 TTAATTTAATA-ATATACTTTATAA
1 TTAATATAATATATATA--TTATAA
43394467 TTAATAT-ATATATATATT
1 TTAATATAATATATATATT
43394485 TTTAAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 6 0.17
23 13 0.36
24 17 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATATAATATATATATTATAA
Found at i:43395412 original size:25 final size:25
Alignment explanation
Indices: 43395380--43395516 Score: 102
Period size: 25 Copynumber: 5.5 Consensus size: 25
43395370 AATATGCCAT
43395380 AAAGGCTTTTCACAAGATTAACCAC
1 AAAGGCTTTTCACAAGATTAACCAC
* * *
43395405 AAAAGC-TTTC-CAGGTAATAAGCCAC
1 AAAGGCTTTTCACAAG-ATTAA-CCAC
**
43395430 AAAGGCTTTTCACGGGATTAACCAC
1 AAAGGCTTTTCACAAGATTAACCAC
* * * *
43395455 AAAAGATTTTCAGATA-A-TACGCCAC
1 AAAGGCTTTTCACA-AGATTA-ACCAC
* * *
43395480 AAAGGCTTTTTATAAGATTAGCCAC
1 AAAGGCTTTTCACAAGATTAACCAC
43395505 AAAGGCTTTTCA
1 AAAGGCTTTTCA
43395517 GAGAATTCTC
Statistics
Matches: 87, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
23 3 0.03
24 11 0.13
25 60 0.69
26 10 0.11
27 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (25 bp):
AAAGGCTTTTCACAAGATTAACCAC
Found at i:43395435 original size:50 final size:50
Alignment explanation
Indices: 43395368--43395518 Score: 185
Period size: 50 Copynumber: 3.0 Consensus size: 50
43395358 GTCTTTCTAA
* *
43395368 ATAATATGCCATAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCAG
1 ATAATAAGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCAG
* ** * *
43395418 GTAATAAGCCACAAAGGCTTTTCACGGGATTAACCACAAAAGATTTTCAG
1 ATAATAAGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCAG
* * * * * *
43395468 ATAATACGCCACAAAGGCTTTTTATAAGATTAGCCACAAAGGCTTTTCAG
1 ATAATAAGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCAG
43395518 A
1 A
43395519 GAATTCTCGA
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (50 bp):
ATAATAAGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCAG
Found at i:43407115 original size:64 final size:64
Alignment explanation
Indices: 43407014--43407138 Score: 223
Period size: 64 Copynumber: 2.0 Consensus size: 64
43407004 GAAGCGTAAG
*
43407014 ACTATTGCAGGGGTTGTGCACGTCAGTTCTGTGAGTGAGAAAGAAGGAATAATGAACAATTAAA
1 ACTATTGCAGGGGTTGTGCACGTCAGTTCTGCGAGTGAGAAAGAAGGAATAATGAACAATTAAA
* *
43407078 ACTATTGCAGGGGTTGTGCGCGTCAGTTCTGCGAGTGAGAAGGAAGGAATAATGAACAATT
1 ACTATTGCAGGGGTTGTGCACGTCAGTTCTGCGAGTGAGAAAGAAGGAATAATGAACAATT
43407139 GTAGCTACAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (64 bp):
ACTATTGCAGGGGTTGTGCACGTCAGTTCTGCGAGTGAGAAAGAAGGAATAATGAACAATTAAA
Found at i:43408187 original size:140 final size:140
Alignment explanation
Indices: 43407935--43408202 Score: 491
Period size: 140 Copynumber: 1.9 Consensus size: 140
43407925 GGGTAGATAT
* * *
43407935 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGTGTGTGACTCATTTATGTCCATTT
1 GGACAAGCTAGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
*
43408000 GGAAGAACTCTTCAGATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCCTTTG
66 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCCTTTG
43408065 CTGCGAATGA
131 CTGCGAATGA
*
43408075 GGACAAGCTAGGTTTTGAAGTGATTTTTCCTTCTAGCAGTGCGTGTGACTCATTTATGTCCACTT
1 GGACAAGCTAGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
43408140 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCCTT
66 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCCTT
43408203 CTGATAATGC
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 123 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (140 bp):
GGACAAGCTAGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCCTTTG
CTGCGAATGA
Found at i:43408561 original size:58 final size:58
Alignment explanation
Indices: 43408466--43408689 Score: 265
Period size: 58 Copynumber: 3.9 Consensus size: 58
43408456 TGTTAGCTGA
* *
43408466 GGATATGAATCTGTGAGCTATTTTATACTTGTAAAAATTTTGAAAGATAATCAACTGG
1 GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAACTGG
* *
43408524 GGATGTGAATCCGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAATTGG
1 GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAACTGG
* * ** * * *
43408582 GGATGTGAATTTGAGAAATGTTTTATACTTGTGAAAATTTTGAAACATAA-CATATCT-A
1 GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCA-A-CTGG
* * * *
43408640 AGAGTTTGAATCTGCGAGCTGTTTTATACTTGTGAAAATTTTGAAA-ATAA
1 GGA-TGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAA
43408690 CATAGCTGAG
Statistics
Matches: 144, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.01
58 104 0.72
59 38 0.26
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (58 bp):
GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAACTGG
Found at i:43409036 original size:69 final size:69
Alignment explanation
Indices: 43408752--43409037 Score: 225
Period size: 69 Copynumber: 4.1 Consensus size: 69
43408742 ATCCTGCCAA
* ** * * * *
43408752 CCTTAGTATGACAGTTGGGAGTTTTACTCTCTTTAACTGTGTTAGAGGTTGCTGCTATTTGCCTA
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGCGGCTCTTCGCCTA
43408817 CGAG
66 CGAG
* * * * * * * * * *
43408821 CCTAAATATGATAGTTGGGAGTTTTACTCTCATTAACTGTGTTAGAGTCTGCTGCCCTTCGCATG
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGCGGCTCTTCGCCTA
43408886 CGAG
66 CGAG
* * * * * ** * * * * * * *
43408890 CCTCAATATTACAGCTGGGAGCTCTGTTCTCGCTAATTGTGTTGGAGGTTGCGACTTTTCACCTA
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGCGGCTCTTCGCCTA
*
43408955 CAAG
66 CGAG
* *
43408959 CCTTAGTATGACAGTTGGGAGCTTTGCTCTCACTAACTGT-TTTGAAGGCTGCGGCTCTTCG-CT
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAG-AGGCTGCGGCTCTTCGCCT
*
43409022 CGCGAG
65 -ACGAG
43409028 CCTTAGTATG
1 CCTTAGTATG
43409038 GCATAAATGT
Statistics
Matches: 167, Mismatches: 48, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
68 5 0.03
69 162 0.97
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.35
Consensus pattern (69 bp):
CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGCGGCTCTTCGCCTA
CGAG
Found at i:43418643 original size:5 final size:5
Alignment explanation
Indices: 43418633--43418666 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
43418623 GATAATGCAT
*
43418633 GAGAA GAGAA GAGAA GAGAA GAGAA GCGAA GAGA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGA
43418667 GCAGACTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.03, G:0.41, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:43423221 original size:16 final size:16
Alignment explanation
Indices: 43423200--43423231 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43423190 AGAAAGAGAA
43423200 AATAATGAAAAAAGAG
1 AATAATGAAAAAAGAG
43423216 AATAATGAAAAAAGAG
1 AATAATGAAAAAAGAG
43423232 GGCAACAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (16 bp):
AATAATGAAAAAAGAG
Found at i:43424689 original size:17 final size:17
Alignment explanation
Indices: 43424653--43424694 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
43424643 GTAAAGTATG
*
43424653 ATAAAAGAAAAGGGAAA
1 ATAAAAGAAAAGAGAAA
43424670 ATAAAAGAAAA-AGAATA
1 ATAAAAGAAAAGAGAA-A
43424687 ATATAAAG
1 ATA-AAAG
43424695 GGAAGAGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 15 0.68
18 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (17 bp):
ATAAAAGAAAAGAGAAA
Found at i:43426723 original size:16 final size:17
Alignment explanation
Indices: 43426687--43426724 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
43426677 TTTTCAATAA
43426687 TATATTAAGAATATTAGT
1 TATATTAAGAATA-TAGT
*
43426705 TATATTAATAATA-AGT
1 TATATTAAGAATATAGT
43426721 TATA
1 TATA
43426725 GTATTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (17 bp):
TATATTAAGAATATAGT
Found at i:43426948 original size:19 final size:22
Alignment explanation
Indices: 43426902--43426950 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
43426892 AAAAAGAACT
43426902 TATTTTCTGTTGACTTGTAAGTC
1 TATTTTCTGTTGAC-TGTAAGTC
43426925 T-TTTTCTGTTGA-T-TAAG-C
1 TATTTTCTGTTGACTGTAAGTC
43426943 TATTTTCT
1 TATTTTCT
43426951 ATGAAGCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.08
19 10 0.40
20 1 0.04
22 11 0.44
23 1 0.04
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.57
Consensus pattern (22 bp):
TATTTTCTGTTGACTGTAAGTC
Found at i:43427524 original size:23 final size:23
Alignment explanation
Indices: 43427498--43427545 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
43427488 GCCAATATAT
*
43427498 AAATCAAATC-TCTTAAGATTACA
1 AAATCAAATCTTC-TAAAATTACA
43427521 AAATCAAATCTTCTAAAATTACA
1 AAATCAAATCTTCTAAAATTACA
43427544 AA
1 AA
43427546 TCTTCTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (23 bp):
AAATCAAATCTTCTAAAATTACA
Found at i:43428624 original size:13 final size:13
Alignment explanation
Indices: 43428606--43428630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43428596 ATTTTTAATA
43428606 TTATTTTGTGTGT
1 TTATTTTGTGTGT
43428619 TTATTTTGTGTG
1 TTATTTTGTGTG
43428631 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:43430416 original size:41 final size:40
Alignment explanation
Indices: 43430371--43430517 Score: 140
Period size: 41 Copynumber: 3.6 Consensus size: 40
43430361 GGTTATGTAC
*
43430371 CTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAA-TAATTCAGACTTTAAGT
*
43430412 CTAGCAGGCTTAATGCCGGTG-ATACATTTCAGACTATATA-T
1 CTAGCAGGCTTAATGCCGGTGAATA-A-TTCAGACTTTA-AGT
* * *
43430453 CTAGCAGGC-TAAGTGCCGGTGTACTGAA-TCAGGCTTTAAGC
1 CTAGCAGGCTTAA-TGCCGGTG-AAT-AATTCAGACTTTAAGT
* *
43430494 CTAGCAGGCTAAATGCCAGTGAAT
1 CTAGCAGGCTTAATGCCGGTGAAT
43430518 CTGTTTAAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
39 2 0.02
40 8 0.09
41 73 0.83
42 2 0.02
43 2 0.02
44 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAATAATTCAGACTTTAAGT
Found at i:43431224 original size:17 final size:17
Alignment explanation
Indices: 43431191--43431225 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
43431181 GATTAAAAGG
43431191 TTATAATATTTATATAT
1 TTATAATATTTATATAT
43431208 TTATATATATTTA-ATAT
1 TTATA-ATATTTATATAT
43431225 T
1 T
43431226 GCTGTAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATAATATTTATATAT
Found at i:43433066 original size:24 final size:24
Alignment explanation
Indices: 43433034--43433087 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
43433024 CACATTGTAG
43433034 AATTGAGAAATTAAGTATAAATGA
1 AATTGAGAAATTAAGTATAAATGA
43433058 AATTGAGAAATTAAGTATAAATGA
1 AATTGAGAAATTAAGTATAAATGA
43433082 AATTGA
1 AATTGA
43433088 AATTAGGGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.30
Consensus pattern (24 bp):
AATTGAGAAATTAAGTATAAATGA
Found at i:43435393 original size:68 final size:68
Alignment explanation
Indices: 43435279--43435428 Score: 221
Period size: 68 Copynumber: 2.2 Consensus size: 68
43435269 CTTAGAATTG
* * * *
43435279 GAAGTCCGTCAAGACAGTAAACATGGGATCATATTCTGTGAGACCATA-ATTGGGCTATGGCAGC
1 GAAGTCCGCCAGGACAGTAAACATGGGATCATATTCTATAAGACCATAGA-TGGGCTATGGCAGC
43435343 ATAT
65 ATAT
* *
43435347 GAAGTCCGCCAGGACAGTAAACATGGGATCATATTGTATAATACCATAGATGGGCTATGGCAGCA
1 GAAGTCCGCCAGGACAGTAAACATGGGATCATATTCTATAAGACCATAGATGGGCTATGGCAGCA
43435412 TAT
66 TAT
*
43435415 GAAGTCCGCTAGGA
1 GAAGTCCGCCAGGA
43435429 TAGAGAACCA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
68 73 0.99
69 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (68 bp):
GAAGTCCGCCAGGACAGTAAACATGGGATCATATTCTATAAGACCATAGATGGGCTATGGCAGCA
TAT
Found at i:43441796 original size:25 final size:24
Alignment explanation
Indices: 43441753--43441803 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
43441743 AAGTTCAAGC
*
43441753 GAGCCATATCAGGAAGCTCATTAA
1 GAGCCATATCAGGAAGCTCATAAA
* *
43441777 GAGCCTATATCGGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
43441802 GA
1 GA
43441804 CCTGTGGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:43441894 original size:64 final size:64
Alignment explanation
Indices: 43441810--43441942 Score: 221
Period size: 64 Copynumber: 2.1 Consensus size: 64
43441800 AAGACCTGTG
43441810 GTATGTCCACATTATATGCAAGATCCATACCAATCATATAACAAGAAGCTCACAAAGAGCTGCA
1 GTATGTCCACATTATATGCAAGATCCATACCAATCATATAACAAGAAGCTCACAAAGAGCTGCA
* * * * *
43441874 GTATGTCCACATTATATGCAATATTCATACCAATCATATAACAGGATGCTCACAAAGAGCTGTA
1 GTATGTCCACATTATATGCAAGATCCATACCAATCATATAACAAGAAGCTCACAAAGAGCTGCA
43441938 GTATG
1 GTATG
43441943 ATCGCAACAC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (64 bp):
GTATGTCCACATTATATGCAAGATCCATACCAATCATATAACAAGAAGCTCACAAAGAGCTGCA
Found at i:43446391 original size:13 final size:13
Alignment explanation
Indices: 43446367--43446402 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
43446357 AAATAAATAA
*
43446367 AAATAAACAAAAC
1 AAATAAAAAAAAC
*
43446380 AATTAAAAAAAAC
1 AAATAAAAAAAAC
43446393 AAATAAAAAA
1 AAATAAAAAA
43446403 GGGGTAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (13 bp):
AAATAAAAAAAAC
Found at i:43451468 original size:18 final size:18
Alignment explanation
Indices: 43451445--43451484 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
43451435 ACCTTGTCTT
43451445 TTCCTTGCTTTATCTCTA
1 TTCCTTGCTTTATCTCTA
43451463 TTCCTTGCTTTATCTCTA
1 TTCCTTGCTTTATCTCTA
43451481 TTCC
1 TTCC
43451485 AAGGAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.30, G:0.05, T:0.55
Consensus pattern (18 bp):
TTCCTTGCTTTATCTCTA
Found at i:43451591 original size:19 final size:19
Alignment explanation
Indices: 43451567--43451606 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
43451557 CCGTTAGTTA
43451567 ATGTTAGTTAAGTCTGTTG
1 ATGTTAGTTAAGTCTGTTG
43451586 ATGTTAGTTAAGTCTGTTG
1 ATGTTAGTTAAGTCTGTTG
43451605 AT
1 AT
43451607 TTGGATTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (19 bp):
ATGTTAGTTAAGTCTGTTG
Found at i:43460975 original size:10 final size:10
Alignment explanation
Indices: 43460950--43461007 Score: 66
Period size: 10 Copynumber: 5.8 Consensus size: 10
43460940 TAGTTAGCTA
*
43460950 TTAGTTAGTCG
1 TTAGTTAAT-G
43460961 TTAGTTAATG
1 TTAGTTAATG
43460971 TTAGTTAATG
1 TTAGTTAATG
43460981 TTAGTTAA-G
1 TTAGTTAATG
*
43460990 TCT-GTTGATG
1 T-TAGTTAATG
43461000 TTAGTTAA
1 TTAGTTAA
43461008 GTCTGTTGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.17
10 26 0.63
11 8 0.20
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.48
Consensus pattern (10 bp):
TTAGTTAATG
Found at i:43461002 original size:19 final size:19
Alignment explanation
Indices: 43460960--43461016 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
43460950 TTAGTTAGTC
*
43460960 GTTAGTTAATGT-TAGTTAAT
1 GTTAGTTAA-GTCT-GTTGAT
43460980 GTTAGTTAAGTCTGTTGAT
1 GTTAGTTAAGTCTGTTGAT
43460999 GTTAGTTAAGTCTGTTGA
1 GTTAGTTAAGTCTGTTGA
43461017 CTTGGATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 25 0.71
20 10 0.29
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.47
Consensus pattern (19 bp):
GTTAGTTAAGTCTGTTGAT
Found at i:43462672 original size:24 final size:24
Alignment explanation
Indices: 43462636--43462698 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
43462626 TGGTATAGGA
* *
43462636 GTCAAAAACTGTATTTGCAGAAAT
1 GTCAAAAATTGTATTTACAGAAAT
*
43462660 GT-AGCAAATTGTATTTACAGAAAT
1 GTCA-AAAATTGTATTTACAGAAAT
43462684 GTCAAAAATTGTATT
1 GTCAAAAATTGTATT
43462699 CTAGAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 31 0.94
25 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (24 bp):
GTCAAAAATTGTATTTACAGAAAT
Found at i:43462885 original size:54 final size:54
Alignment explanation
Indices: 43462839--43463186 Score: 389
Period size: 54 Copynumber: 6.5 Consensus size: 54
43462829 AATCTTGTAT
** * *
43462839 GTAGAAGGTCGTGATCGTAAATCAGTGGACCATGAGATTCGTAAAATCTTGAAA
1 GTAGAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
* ** *
43462893 GTAGAAGGTCGTGATCGTAAATTAGCAGACCGTGAGATTCACAAAATCTCAAAA
1 GTAGAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
* * * ** *
43462947 ATAAAAGGTCGTGATTGTAAATCAGTGGACCGTGAGATTTGTAAAATCTCGAAA
1 GTAGAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
* * * * * *
43463001 GTAAAAGGTCGTGATCATAAATCAACGGATCGTGAGATTTGTAAAATCTCGAAA
1 GTAGAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
*
43463055 GTAGAAGGTC-TGAT-GATAAATCAGCAGACCGTGAGA-TCGT-AAATCTCAAAA
1 GTAGAAGGTCGTGATCG-TAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
* * * * ** * * *
43463106 ATAAAAGGTCGTGATTGTAAATCAGTAGACCAAGAAATTCGTAGAATTTCGAAA
1 GTAGAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
43463160 GTAGAAGGTCGTGATCGTAAATCAGCA
1 GTAGAAGGTCGTGATCGTAAATCAGCA
43463187 TGACAACCCA
Statistics
Matches: 245, Mismatches: 44, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
51 18 0.07
52 23 0.09
53 26 0.11
54 178 0.73
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (54 bp):
GTAGAAGGTCGTGATCGTAAATCAGCAGACCGTGAGATTCGTAAAATCTCGAAA
Found at i:43463168 original size:159 final size:162
Alignment explanation
Indices: 43462839--43463183 Score: 491
Period size: 159 Copynumber: 2.1 Consensus size: 162
43462829 AATCTTGTAT
** *
43462839 GTAGAAGGTCGTGATCGTAAATCAGTGGACCATGAGATTCGTAAAATCTTGAAAGTAGAAGGTCG
1 GTAGAAGGTCGTGATCGTAAATCAACGGACCATGAGATTCGTAAAATCTCGAAAGTAGAAGGTCG
*
43462904 TGATCGTAAATTAGCAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAAT
66 TGATCGTAAATCAGCAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAAT
* ** * *
43462969 CAGTGGACCGTGAGATTTGTAAAATCTCGAAA
131 CAGTAGACCAAGAAATTCGTAAAATCTCGAAA
* * * * *
43463001 GTAAAAGGTCGTGATCATAAATCAACGGATCGTGAGATTTGTAAAATCTCGAAAGTAGAAGGTC-
1 GTAGAAGGTCGTGATCGTAAATCAACGGACCATGAGATTCGTAAAATCTCGAAAGTAGAAGGTCG
**
43463065 TGAT-GATAAATCAGCAGACCGTGAGA-TC-GTAAATCTCAAAAATAAAAGGTCGTGATTGTAAA
66 TGATCG-TAAATCAGCAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAA
* *
43463127 TCAGTAGACCAAGAAATTCGTAGAATTTCGAAA
130 TCAGTAGACCAAGAAATTCGTAAAATCTCGAAA
43463160 GTAGAAGGTCGTGATCGTAAATCA
1 GTAGAAGGTCGTGATCGTAAATCA
43463184 GCATGACAAC
Statistics
Matches: 162, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
159 80 0.49
160 3 0.02
161 23 0.14
162 56 0.35
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (162 bp):
GTAGAAGGTCGTGATCGTAAATCAACGGACCATGAGATTCGTAAAATCTCGAAAGTAGAAGGTCG
TGATCGTAAATCAGCAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAAT
CAGTAGACCAAGAAATTCGTAAAATCTCGAAA
Found at i:43465835 original size:36 final size:35
Alignment explanation
Indices: 43465795--43465866 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
43465785 TGATGATTGT
* *
43465795 TGTGAAAG-AGAATATGTGGGTATGTTATTCATGCCA
1 TGTGAAAGTA-AATATGTGGGTATATT-TTCATACCA
*
43465831 TGTGATAGTAAATATGTGGGTATATTTTCATACCA
1 TGTGAAAGTAAATATGTGGGTATATTTTCATACCA
43465866 T
1 T
43465867 TGACAGTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 9 0.28
36 22 0.69
37 1 0.03
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.38
Consensus pattern (35 bp):
TGTGAAAGTAAATATGTGGGTATATTTTCATACCA
Found at i:43486275 original size:17 final size:17
Alignment explanation
Indices: 43486225--43486282 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
43486215 GGGTGAGAAG
*
43486225 TAAAAGTTTAGAGGAAAAA
1 TAAAAGTTT-GAGG-GAAA
*
43486244 TAAAAAGTTT-TGGGAAA
1 T-AAAAGTTTGAGGGAAA
43486261 TAAAAGTTTGAGGGAAA
1 TAAAAGTTTGAGGGAAA
43486278 GTAAA
1 -TAAA
43486283 TAGGGGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 8 0.24
17 10 0.30
18 6 0.18
19 1 0.03
20 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
TAAAAGTTTGAGGGAAA
Found at i:43486401 original size:30 final size:31
Alignment explanation
Indices: 43486362--43486421 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
43486352 GGAGGTGAGA
*
43486362 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
43486393 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
43486422 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:43486649 original size:9 final size:9
Alignment explanation
Indices: 43486635--43486662 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
43486625 TATAGTTTGA
43486635 TATTCGAAT
1 TATTCGAAT
43486644 TATTCGAAT
1 TATTCGAAT
43486653 TATTCGAAT
1 TATTCGAAT
43486662 T
1 T
43486663 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43486955 original size:31 final size:30
Alignment explanation
Indices: 43486893--43486964 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 30
43486883 TGTATATATG
*
43486893 AACTTTAATTTGGTACAATTATATACGTGA
1 AACTTTAATTTGGTACAAATATATACGTGA
* * *
43486923 AACTCTAATTGTGGTTCAAATATATACTTGA
1 AACTTTAATT-TGGTACAAATATATACGTGA
43486954 AACTTTAATTT
1 AACTTTAATTT
43486965 TGATTTAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (30 bp):
AACTTTAATTTGGTACAAATATATACGTGA
Found at i:43487855 original size:26 final size:26
Alignment explanation
Indices: 43487826--43487875 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
43487816 GTTACGGTAG
*
43487826 ATTTCAACCTATTTTTGTAATTAATA
1 ATTTCAACATATTTTTGTAATTAATA
** *
43487852 ATTTTTATATATTTTTGTAATTAA
1 ATTTCAACATATTTTTGTAATTAA
43487876 CTTTTTGGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (26 bp):
ATTTCAACATATTTTTGTAATTAATA
Found at i:43491418 original size:30 final size:29
Alignment explanation
Indices: 43491384--43491443 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
43491374 AATTTTAAAA
*
43491384 TTTTAAAAATTCAGAAA-CATATAAAATTAT
1 TTTTAAAAATT-AAAAATCAT-TAAAATTAT
43491414 TTTTAAAAATTAAAAATCATTAAAATTAT
1 TTTTAAAAATTAAAAATCATTAAAATTAT
43491443 T
1 T
43491444 AAAAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (29 bp):
TTTTAAAAATTAAAAATCATTAAAATTAT
Found at i:43491421 original size:29 final size:29
Alignment explanation
Indices: 43491383--43491451 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
43491373 TAATTTTAAA
*
43491383 ATTTT-AAAAATTCAGAAA-CATATAAAATT
1 ATTTTAAAAAATT-AAAAATCAT-TAAAATT
*
43491412 ATTTTTAAAAATTAAAAATCATTAAAATT
1 ATTTTAAAAAATTAAAAATCATTAAAATT
*
43491441 A-TTAAAAAAAT
1 ATTTTAAAAAAT
43491452 AAACATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 8 0.23
29 17 0.49
30 10 0.29
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (29 bp):
ATTTTAAAAAATTAAAAATCATTAAAATT
Found at i:43509763 original size:21 final size:22
Alignment explanation
Indices: 43509724--43509769 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
43509714 TTTATATATC
* * *
43509724 AAAGAATTTTTTTTTAAAAA-A
1 AAAGAAATTTTTGTCAAAAATA
43509745 AAAGAAATTTTTGTCAAAAATA
1 AAAGAAATTTTTGTCAAAAATA
43509767 AAA
1 AAA
43509770 ATAAGAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (22 bp):
AAAGAAATTTTTGTCAAAAATA
Found at i:43515447 original size:36 final size:36
Alignment explanation
Indices: 43515400--43515585 Score: 185
Period size: 36 Copynumber: 4.9 Consensus size: 36
43515390 GCTAAGCTAC
*
43515400 CACTTATCACTTTGTCACTTGATCAGATAAGTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTAAAG
* *
43515436 CACTTATCACTTTTTTACTTGATCTGATAAGTATAA-
1 CACTTATCACTTTTTCACTTGATCAGATAAGTA-AAG
* *
43515472 CATTTATCGCTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGAT-A----AG-TAAAG
* * **
43515514 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTAAAG
43515554 CACTTATCACTTTTTCACTTGATCAGATAAGT
1 CACTTATCACTTTTTCACTTGATCAGATAAGT
43515586 GTAGCTAAAG
Statistics
Matches: 123, Mismatches: 15, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
36 84 0.68
37 3 0.02
40 3 0.02
41 6 0.05
42 2 0.02
45 1 0.01
46 24 0.20
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTAAAG
Found at i:43515529 original size:82 final size:82
Alignment explanation
Indices: 43515436--43515626 Score: 303
Period size: 82 Copynumber: 2.3 Consensus size: 82
43515426 ATAAGTAAAG
* * * *
43515436 CACTTATCACTTT-TTTACTTGATCTGATAAGTATAACATTTATCGCTTTTTCACTTGATCAGAT
1 CACTTATCACTTTGTCT-CTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGAT
43515500 AAGTGTAGCTAAAGCTAC
65 AAGTGTAGCTAAAGCTAC
* *
43515518 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
43515583 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
*
43515600 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCTCTTGATCAGA
43515627 AGTACTCAAA
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 99 0.98
83 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (82 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
AGTGTAGCTAAAGCTAC
Found at i:43515532 original size:118 final size:117
Alignment explanation
Indices: 43515374--43515585 Score: 370
Period size: 118 Copynumber: 1.8 Consensus size: 117
43515364 CATTTGTCCC
43515374 TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTAAAGCAC
1 TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTAAAGCAC
* *
43515439 TTATCACTTTTTTACTTGATCTGATAAGTATAACATTTATCGCTTTTTCACT
66 TTATCACTTTTTCACTTGATCAGATAAGTATAACATTTATCGCTTTTTCACT
* **
43515491 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCA
1 TGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTAAAGCA
43515556 CTTATCACTTTTTCACTTGATCAGATAAGT
65 CTTATCACTTTTTCACTTGATCAGATAAGT
43515586 GTAGCTAAAG
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
117 19 0.21
118 70 0.79
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (117 bp):
TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTAAAGCAC
TTATCACTTTTTCACTTGATCAGATAAGTATAACATTTATCGCTTTTTCACT
Found at i:43515542 original size:46 final size:46
Alignment explanation
Indices: 43515475--43515626 Score: 189
Period size: 46 Copynumber: 3.5 Consensus size: 46
43515465 AGTATAACAT
*
43515475 TTATCGCTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
43515521 TTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----CAC
1 TTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
43515557 TTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
43515603 TTATCACTTTATCTCTTGATCAGA
1 TTATCACTTTTTCACTTGATCAGA
43515627 AGTACTCAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
36 28 0.31
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 1 0.01
44 2 0.02
46 49 0.55
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (46 bp):
TTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:43518219 original size:73 final size:73
Alignment explanation
Indices: 43518092--43518239 Score: 242
Period size: 73 Copynumber: 2.0 Consensus size: 73
43518082 CAGAGAATAT
* * *
43518092 TTACTATTCATGCATCTTTTCTTGCAGGGACTATTTACTGTTTACGCCATAGAATATTTCCTGTT
1 TTACTATTCATGCATCTTTTCTTGCAGGGAATATTTACTGCTTACGCCAAAGAATATTTCCTGTT
43518157 CACTTGTC
66 CACTTGTC
* **
43518165 TTACTATTCATGCGTCTTTTCTTGCAGGGAATATTTACTGCTTACGTTAAAGAATATTTCCTGTT
1 TTACTATTCATGCATCTTTTCTTGCAGGGAATATTTACTGCTTACGCCAAAGAATATTTCCTGTT
43518230 CACTTGTC
66 CACTTGTC
43518238 TT
1 TT
43518240 TTCTTGCATC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.45
Consensus pattern (73 bp):
TTACTATTCATGCATCTTTTCTTGCAGGGAATATTTACTGCTTACGCCAAAGAATATTTCCTGTT
CACTTGTC
Found at i:43528922 original size:29 final size:28
Alignment explanation
Indices: 43528880--43528941 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 28
43528870 ATTGGATAGC
43528880 CCACTAAGGAAGGAA-GAAGCCCAAACCGT
1 CCACTAAGGAAGGAATG-AGCCC-AACCGT
43528909 CCACTAAGGAAGGAATGAGCCCAACCGT
1 CCACTAAGGAAGGAATGAGCCCAACCGT
43528937 CCACT
1 CCACT
43528942 TGAGGTGCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 11 0.34
29 20 0.62
30 1 0.03
ACGTcount: A:0.37, C:0.31, G:0.23, T:0.10
Consensus pattern (28 bp):
CCACTAAGGAAGGAATGAGCCCAACCGT
Found at i:43537676 original size:18 final size:18
Alignment explanation
Indices: 43537653--43537715 Score: 76
Period size: 18 Copynumber: 3.5 Consensus size: 18
43537643 AAAACTAAAG
43537653 AAAAATCATTAAAA-TTCA
1 AAAAATCATTAAAACTT-A
43537671 AAAAATCATTAAAACTTA
1 AAAAATCATTAAAACTTA
* *
43537689 AAAAATTATAAAAAC-TA
1 AAAAATCATTAAAACTTA
43537706 AAAGAATCAT
1 AAA-AATCAT
43537716 AATCTATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
17 5 0.12
18 33 0.82
19 2 0.05
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAAATCATTAAAACTTA
Found at i:43537791 original size:18 final size:18
Alignment explanation
Indices: 43537740--43537783 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
43537730 TTTTGTGTGC
* *
43537740 AAAATTTTTTAAAAATTT
1 AAAAATTTTCAAAAATTT
*
43537758 AAAAATTTTCATAAATTT
1 AAAAATTTTCAAAAATTT
*
43537776 TAAAATTT
1 AAAAATTT
43537784 CGAAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AAAAATTTTCAAAAATTT
Found at i:43538010 original size:19 final size:19
Alignment explanation
Indices: 43537969--43538020 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
43537959 TTTTTTTGGG
* *
43537969 ATTTTT-TATTTTTTTAAT
1 ATTTTTATATTTTTTAAAA
*
43537987 GTTTTTATATTTTTTAAAA
1 ATTTTTATATTTTTTAAAA
* *
43538006 ATTTTAAGATTTTTT
1 ATTTTTATATTTTTT
43538021 TTTATTTTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
ATTTTTATATTTTTTAAAA
Found at i:43543624 original size:4 final size:4
Alignment explanation
Indices: 43543615--43543645 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
43543605 ATATAAGATT
43543615 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG
43543646 ATGGGTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:43547289 original size:20 final size:19
Alignment explanation
Indices: 43547254--43547292 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
43547244 GTTTATATTC
43547254 TTTACATTCCAGTACACTT
1 TTTACATTCCAGTACACTT
43547273 TTTACCATTACCA-TACACTT
1 TTTA-CATT-CCAGTACACTT
43547293 AATCAGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 11 0.61
21 3 0.17
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (19 bp):
TTTACATTCCAGTACACTT
Found at i:43553731 original size:50 final size:52
Alignment explanation
Indices: 43553677--43553801 Score: 130
Period size: 50 Copynumber: 2.4 Consensus size: 52
43553667 TTCTGCATTT
* *
43553677 AATAAAGTTATGCATTATGTAACTTCTATGCTAG-TTAAGTATGCATCA-GA
1 AATAAAGTTATGCATTATGTAACTCCCATGCTAGTTTAAGTATGCATCATGA
* ** * * *
43553727 AATAATGACATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCATCATTA
1 AATAAAGTTATGCATTATGTAACTCCCATGCTAGTTTAAGTATGCATCATGA
* *
43553779 AATTAAGTCT-TGCATTAAGTAAC
1 AATAAAGT-TATGCATTATGTAAC
43553802 GCATTTAGTT
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
50 28 0.47
51 13 0.22
52 18 0.31
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (52 bp):
AATAAAGTTATGCATTATGTAACTCCCATGCTAGTTTAAGTATGCATCATGA
Found at i:43556268 original size:21 final size:21
Alignment explanation
Indices: 43556242--43556294 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
43556232 TATATGGCTA
*
43556242 GGCCATGTGGCTTAGGGACAT
1 GGCCATGTGGCTCAGGGACAT
43556263 GGCCATGTGGCTCAGGGACAT
1 GGCCATGTGGCTCAGGGACAT
*
43556284 GGCCGTGTGGC
1 GGCCATGTGGC
43556295 CAAACTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.15, C:0.23, G:0.42, T:0.21
Consensus pattern (21 bp):
GGCCATGTGGCTCAGGGACAT
Found at i:43557968 original size:69 final size:70
Alignment explanation
Indices: 43557739--43557971 Score: 342
Period size: 70 Copynumber: 3.3 Consensus size: 70
43557729 TAAAAATGTA
* *
43557739 CAAGACTATGGTTAGACCATGACAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTTT
1 CAAGACCATGGTTGGACCATGACAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTTT
**
43557804 AGATA
66 AGACG
* * *
43557809 CAAGACCATGGTTGGACCATGGCAATGTTTACATAATACCATAGGCTAGGCTATGGCATTTTTTT
1 CAAGACCATGGTTGGACCATGACAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTTT
*
43557874 ATACG
66 AGACG
* * * *
43557879 CAAGACCATGGTTGGACCATGACAATGTTTACGTAAGACCATA-GTTGGGCTATGGCAGTTTTTC
1 CAAGACCATGGTTGGACCATGACAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTTT
43557943 AGACG
66 AGACG
*
43557948 TAAGACCATGGTTGGACCATGACA
1 CAAGACCATGGTTGGACCATGACA
43557972 GTGTATATAT
Statistics
Matches: 146, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
69 44 0.30
70 102 0.70
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (70 bp):
CAAGACCATGGTTGGACCATGACAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTTT
AGACG
Found at i:43561463 original size:16 final size:17
Alignment explanation
Indices: 43561442--43561473 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43561432 TATAAAATAA
43561442 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
43561458 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
43561474 GCTTAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:43562460 original size:22 final size:22
Alignment explanation
Indices: 43562387--43562464 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
43562377 GAACTTTAGC
*
43562387 GTGCTCTCTGATTATTAGCACGTTA
1 GTGCTCTCT-A-TA-TAGCACTTTA
* * * *
43562412 GTGCTCTCTGTTTAGCGCATCTA
1 GTGCTCTCTATATAGCAC-TTTA
43562435 -TGCTCTCTATATAGCACTTTA
1 GTGCTCTCTATATAGCACTTTA
43562456 GTGCTCTCT
1 GTGCTCTCT
43562465 GTTCATTAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
21 3 0.07
22 27 0.64
23 3 0.07
25 9 0.21
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (22 bp):
GTGCTCTCTATATAGCACTTTA
Found at i:43568970 original size:16 final size:16
Alignment explanation
Indices: 43568949--43568979 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43568939 TTCACTATTA
*
43568949 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
43568965 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
43568980 ACATACATGC
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:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:43574007 original size:18 final size:18
Alignment explanation
Indices: 43573984--43574020 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
43573974 GGCGGCCCTA
*
43573984 GTGGATCACGCTTCTTTG
1 GTGGATCAAGCTTCTTTG
*
43574002 GTGGATCAAGTTTCTTTG
1 GTGGATCAAGCTTCTTTG
43574020 G
1 G
43574021 CTTTGATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.41
Consensus pattern (18 bp):
GTGGATCAAGCTTCTTTG
Found at i:43577991 original size:22 final size:22
Alignment explanation
Indices: 43577966--43578047 Score: 76
Period size: 22 Copynumber: 3.6 Consensus size: 22
43577956 GAGATTTCAA
43577966 TAAATTATATTTAAAATTATTT
1 TAAATTATATTTAAAATTATTT
* * *
43577988 TAAATGAAAATTTAATAATTTTTT
1 TAAAT-TATATTTAA-AATTATTT
* * *
43578012 TTAATT-TATCTAAAAATATTTT
1 TAAATTATATTTAAAATTA-TTT
43578034 TAAATTATATTTAA
1 TAAATTATATTTAA
43578048 CTTTTTTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
21 3 0.07
22 18 0.40
23 13 0.29
24 11 0.24
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (22 bp):
TAAATTATATTTAAAATTATTT
Found at i:43588215 original size:20 final size:20
Alignment explanation
Indices: 43588190--43588229 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43588180 CGTAAAATGA
*
43588190 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
43588210 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
43588230 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:43588219 original size:34 final size:35
Alignment explanation
Indices: 43588175--43588241 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
43588165 CAGTAAAATA
*
43588175 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
43588209 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
43588242 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:43588245 original size:14 final size:15
Alignment explanation
Indices: 43588169--43588245 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
43588159 GATTGCCAGT
* *
43588169 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
43588183 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
43588197 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
43588217 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
43588232 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
43588246 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:43588905 original size:98 final size:98
Alignment explanation
Indices: 43588736--43588932 Score: 394
Period size: 98 Copynumber: 2.0 Consensus size: 98
43588726 GATTTTCCGG
43588736 AAAATCAATTCCTTCAATCAAACAGACCCTTAAACTCAATTCATTTGAGCTAAAGCTAGAAATGA
1 AAAATCAATTCCTTCAATCAAACAGACCCTTAAACTCAATTCATTTGAGCTAAAGCTAGAAATGA
43588801 TCCCTAGCTTTTTTGTCCTTTTAAGTCGAATAC
66 TCCCTAGCTTTTTTGTCCTTTTAAGTCGAATAC
43588834 AAAATCAATTCCTTCAATCAAACAGACCCTTAAACTCAATTCATTTGAGCTAAAGCTAGAAATGA
1 AAAATCAATTCCTTCAATCAAACAGACCCTTAAACTCAATTCATTTGAGCTAAAGCTAGAAATGA
43588899 TCCCTAGCTTTTTTGTCCTTTTAAGTCGAATAC
66 TCCCTAGCTTTTTTGTCCTTTTAAGTCGAATAC
43588932 A
1 A
43588933 GATCCATGTT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.32
Consensus pattern (98 bp):
AAAATCAATTCCTTCAATCAAACAGACCCTTAAACTCAATTCATTTGAGCTAAAGCTAGAAATGA
TCCCTAGCTTTTTTGTCCTTTTAAGTCGAATAC
Found at i:43590431 original size:32 final size:28
Alignment explanation
Indices: 43590402--43590465 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
43590392 AACAATTTAA
*
43590402 TTTTTTAAGGGCAGAATGAAACTTTAATT
1 TTTTTTTA-GGCAGAATGAAACTTTAATT
**
43590431 TTTTTTT-TTCAGAATGAAACTTTAATT
1 TTTTTTTAGGCAGAATGAAACTTTAATT
43590458 TTTTTTTA
1 TTTTTTTA
43590466 TAGTTTACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 25 0.81
29 6 0.19
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (28 bp):
TTTTTTTAGGCAGAATGAAACTTTAATT
Found at i:43590462 original size:27 final size:27
Alignment explanation
Indices: 43590413--43590464 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
43590403 TTTTTAAGGG
43590413 CAGAATGAAACTTTAATTTTTTTTTTT
1 CAGAATGAAACTTTAATTTTTTTTTTT
43590440 CAGAATGAAACTTTAATTTTTTTTT
1 CAGAATGAAACTTTAATTTTTTTTT
43590465 ATAGTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (27 bp):
CAGAATGAAACTTTAATTTTTTTTTTT
Found at i:43598807 original size:2 final size:2
Alignment explanation
Indices: 43598800--43598826 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43598790 CAATATAGAA
43598800 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
43598827 AAAGAAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43604056 original size:20 final size:19
Alignment explanation
Indices: 43603994--43604060 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
43603984 AAATATAAAA
* *
43603994 TTTGAAATTTTAAGAAATAT
1 TTTGAATTTTTAA-AATTAT
* *
43604014 TTTAAAATTTTAAAATTAT
1 TTTGAATTTTTAAAATTAT
43604033 TTTGAATTTTTGAAAATTAT
1 TTTGAATTTTT-AAAATTAT
43604053 TTTGAATT
1 TTTGAATT
43604061 ATTTTGTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.33
20 28 0.67
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTGAATTTTTAAAATTAT
Found at i:43604224 original size:23 final size:23
Alignment explanation
Indices: 43604198--43604253 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
43604188 TCAAATTTGA
* *
43604198 AACTTAAATTACT-TATTCAATTT
1 AACTTAAATTACTCAATGCAA-TT
* *
43604221 AACTCAAATAACTCAATGCAATT
1 AACTTAAATTACTCAATGCAATT
43604244 AACTTAAATT
1 AACTTAAATT
43604254 TTGATTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.38
Consensus pattern (23 bp):
AACTTAAATTACTCAATGCAATT
Found at i:43604799 original size:19 final size:20
Alignment explanation
Indices: 43604775--43604820 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
43604765 TTTTTTTTAA
*
43604775 AATTTTTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
43604794 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
43604813 AATCTTTT
1 AAT-TTTT
43604821 TTGTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
21 4 0.17
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:43606655 original size:23 final size:23
Alignment explanation
Indices: 43606626--43606769 Score: 184
Period size: 23 Copynumber: 6.3 Consensus size: 23
43606616 ATAAGTGCCA
43606626 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * * *
43606649 CATTGATATGTAGACGTAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
*
43606672 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
43606695 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
43606718 CACTGATAT-TAGTCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
43606740 CACTGGA-ATGTAGCCGAAGCTAC
1 CACT-GATATGTAGCCGAAGCTAC
43606763 CACTGAT
1 CACTGAT
43606770 CAATAACACT
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
22 18 0.18
23 84 0.82
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:43606761 original size:68 final size:69
Alignment explanation
Indices: 43606626--43606768 Score: 225
Period size: 68 Copynumber: 2.1 Consensus size: 69
43606616 ATAAGTGCCA
* * *
43606626 CACTGATATGTAGCCGAAGCTACCATTGATATGTAGACGTAGTTACCACTGAAATGTAGCCGAAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGACGTAGCTACCACTGAAATGTAGCCGAAG
43606691 CTAC
66 CTAC
* * *
43606695 CACTGAAATGTAGCTGAAGCTACCACTGATAT-TAGTCGTAGCTACCACTGGAATGTAGCCGAAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGACGTAGCTACCACTGAAATGTAGCCGAAG
43606759 CTAC
66 CTAC
43606763 CACTGA
1 CACTGA
43606769 TCAATAACAC
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
68 39 0.57
69 29 0.43
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (69 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGACGTAGCTACCACTGAAATGTAGCCGAAG
CTAC
Found at i:43610295 original size:16 final size:18
Alignment explanation
Indices: 43610256--43610289 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43610246 TAAGTTTATA
43610256 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
43610273 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
43610290 AATTTAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:43622437 original size:5 final size:5
Alignment explanation
Indices: 43622429--43622461 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
43622419 ATTTTATTTG
43622429 ATAAA ATAAA ATAAA ATAAA ATAAA AGTAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA A-TAAA AT
43622462 CTCTGTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:43624694 original size:33 final size:33
Alignment explanation
Indices: 43624652--43624715 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
43624642 AGAAGTAAGT
43624652 AAATATATTTTAGAATTTATTAGAGCTTGATTG
1 AAATATATTTTAGAATTTATTAGAGCTTGATTG
43624685 AAATATATTTTAGAATTTATTAGAGCTTGAT
1 AAATATATTTTAGAATTTATTAGAGCTTGAT
43624716 AGACTTACGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (33 bp):
AAATATATTTTAGAATTTATTAGAGCTTGATTG
Found at i:43627335 original size:25 final size:24
Alignment explanation
Indices: 43627307--43627368 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
43627297 TGGTGGTGTA
*
43627307 AATTTGGGTTTTATTTTTGGGTTTG
1 AATTTGGGTTTTA-TGTTGGGTTTG
*
43627332 AATTTGGGTTGGTATGTTGGGTTTG
1 AATTTGGGTT-TTATGTTGGGTTTG
*
43627357 GATTTGGGTTTT
1 AATTTGGGTTTT
43627369 GGTTAATGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 1 0.03
25 29 0.91
26 2 0.06
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.55
Consensus pattern (24 bp):
AATTTGGGTTTTATGTTGGGTTTG
Found at i:43627339 original size:12 final size:12
Alignment explanation
Indices: 43627307--43627367 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
43627297 TGGTGGTGTA
*
43627307 AATTTGGGTTTT
1 AATTTGGGTTTG
*
43627319 ATTTTTGGGTTTG
1 A-ATTTGGGTTTG
*
43627332 AATTTGGGTTGG
1 AATTTGGGTTTG
*
43627344 TATGTTGGGTTTG
1 AAT-TTGGGTTTG
*
43627357 GATTTGGGTTT
1 AATTTGGGTTT
43627368 TGGTTAATGG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
12 20 0.50
13 20 0.50
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.54
Consensus pattern (12 bp):
AATTTGGGTTTG
Found at i:43627532 original size:14 final size:14
Alignment explanation
Indices: 43627497--43627545 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
43627487 GTTTCCCTGC
43627497 AAAAATAAAAT-AA
1 AAAAATAAAATAAA
*
43627510 AAATA-AAAATAAA
1 AAAAATAAAATAAA
**
43627523 AAAAATAAAATAGT
1 AAAAATAAAATAAA
43627537 AAAAATAAA
1 AAAAATAAA
43627546 TAATAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 5 0.17
13 10 0.33
14 15 0.50
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAAATAAAATAAA
Found at i:43627554 original size:6 final size:6
Alignment explanation
Indices: 43627497--43627551 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
43627487 GTTTCCCTGC
43627497 AAAAAT -AAAAT AAAAAT AAAAAT --AAA- AAAAAT AAAATAGT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT
43627543 AAATAAT AA
1 AAA-AAT AA
43627552 TAAAAGGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
4 3 0.07
5 8 0.19
6 19 0.45
7 7 0.17
8 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:43627563 original size:30 final size:29
Alignment explanation
Indices: 43627507--43627563 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
43627497 AAAAATAAAA
*
43627507 TAAAAATAAAAATAAAAAAAATAAAATAG
1 TAAAAATAAAAATAAAAAAAAGAAAATAG
* *
43627536 TAAAAATAAATAATAATAAAAGGAAAAT
1 TAAAAATAAA-AATAAAAAAAAGAAAAT
43627564 TAAAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.19
Consensus pattern (29 bp):
TAAAAATAAAAATAAAAAAAAGAAAATAG
Found at i:43637747 original size:2 final size:2
Alignment explanation
Indices: 43637740--43637766 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43637730 CAATATAGAA
43637740 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
43637767 AAAGAAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43644272 original size:11 final size:10
Alignment explanation
Indices: 43644256--43644280 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43644246 AGTTAGCTTC
43644256 AAAAAAAAAG
1 AAAAAAAAAG
43644266 AAAAAAAAAG
1 AAAAAAAAAG
43644276 AAAAA
1 AAAAA
43644281 GGGAGTCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:43645020 original size:51 final size:51
Alignment explanation
Indices: 43644941--43645038 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
43644931 ATTAATGTAC
* *
43644941 AATTAGGACCAAGTTGACATCATATGTAAATTTTTAGGGCTAAATTTGTTA
1 AATTAAGACCAAGTTGACATCATATGTAAATTTTGAGGGCTAAATTTGTTA
*
43644992 AATTAAGACCAAGTTGACATCATTTGTAAATTTTGAGGGCTAAATTT
1 AATTAAGACCAAGTTGACATCATATGTAAATTTTGAGGGCTAAATTT
43645039 ATTATATCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (51 bp):
AATTAAGACCAAGTTGACATCATATGTAAATTTTGAGGGCTAAATTTGTTA
Found at i:43649522 original size:15 final size:15
Alignment explanation
Indices: 43649487--43649538 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
43649477 TTAATAATTT
*
43649487 TATTAAATTAT-ATA
1 TATTTAATTATAATA
43649501 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
43649515 TATTTAATAATAAT-
1 TATTTAATTATAATA
43649529 TATGTTAATT
1 TAT-TTAATT
43649539 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:43649637 original size:16 final size:16
Alignment explanation
Indices: 43649616--43649657 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
43649606 TTACTAAATT
*
43649616 ATATATTTTAATTATA
1 ATATATTTTAATAATA
43649632 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
43649647 AT-TATGTTTAA
1 ATATAT-TTTAA
43649658 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:43649889 original size:16 final size:16
Alignment explanation
Indices: 43649868--43649903 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
43649858 GATTTGCTAT
*
43649868 TACACCTCTAATCCAA
1 TACACCCCTAATCCAA
43649884 TACACCCCTAATCCAA
1 TACACCCCTAATCCAA
43649900 TACA
1 TACA
43649904 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (16 bp):
TACACCCCTAATCCAA
Found at i:43650711 original size:15 final size:15
Alignment explanation
Indices: 43650691--43650725 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43650681 TATATATGCC
43650691 ACAATAAGAAATACA
1 ACAATAAGAAATACA
* *
43650706 ACAATAATAAATATA
1 ACAATAAGAAATACA
43650721 ACAAT
1 ACAAT
43650726 GTCATAGAAA
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:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (15 bp):
ACAATAAGAAATACA
Found at i:43651146 original size:30 final size:30
Alignment explanation
Indices: 43651110--43651168 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
43651100 GTATAAATAT
43651110 AAAAATATTCATTTAAAAAA-ACAAATATAG
1 AAAAATATTCA-TTAAAAAATACAAATATAG
* *
43651140 AAAAATATTTATTAAAAAATAGAAATATA
1 AAAAATATTCATTAAAAAATACAAATATA
43651169 TATATATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (30 bp):
AAAAATATTCATTAAAAAATACAAATATAG
Found at i:43651203 original size:22 final size:21
Alignment explanation
Indices: 43651177--43651222 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
43651167 TATATATATG
43651177 CATATATAGATAAGAAAAATTA
1 CATATATAGATAA-AAAAATTA
* *
43651199 CATATATATATAAAATAATTA
1 CATATATAGATAAAAAAATTA
43651220 CAT
1 CAT
43651223 TATCAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (21 bp):
CATATATAGATAAAAAAATTA
Found at i:43653483 original size:133 final size:131
Alignment explanation
Indices: 43653261--43653982 Score: 362
Period size: 133 Copynumber: 5.4 Consensus size: 131
43653251 ATCTACTATT
* * *** *
43653261 TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGATTTCTTCGATTTTCTTCGCCACCAG
1 TTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGA-TTATTCGATCCACTTCGCCACCAA
* * * * * * ** *
43653326 TATGGGAAGACAAGATCTACATCTTTGATCCACTTCGCTAGCAATATAGGAAGACAGGATCTGTT
65 TATAGGAAAACAAGATCTACATCTTCGATCCACTTCACCACCAATATAGGAAGACAAAATCTG-C
43653391 ATC
129 ATC
* * *
43653394 TTCGATCTACTTCACGCCAATACGGGAAGATAAGATCTGCA-TATTCGATCCACTTCGCTACCAA
1 TTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTG-ATTATTCGATCCACTTCGCCACCAA
* * ** * *
43653458 TATAGGAAAATAGGATCTGTTATCTTCGATCTACTTCACCACCAGTATAGGAAGACAAAATCTGC
65 TATAGGAAAACAAGATCT-ACATCTTCGATCCACTTCACCACCAATATAGGAAGACAAAATCTGC
43653523 ATC
129 ATC
* * * * * * * ***
43653526 TTCGATCCACTTCACTACTAATATAGGAAGATAGGATCTG-TTATCTTCGATCTACTTC-ATGCC
1 TTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGATTA--TTCGATCCACTTCGCCACC
* * * * * * * * * * * *
43653589 AATACATGAAGACAAGATTTGCTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT
63 AATATAGGAAAACAAGATCTAC-ATCTTCGATCCACTTCACCACCAATATAGGAAGACAAAATCT
43653654 GCATC
127 GCATC
* * * * * ** * * * *
43653659 TTCAATCCACTTCGCTACCAATATAGGAAGACGGGATCT-ACTATCTTCGATCTACTTC-ACGCC
1 TTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGA-T-TATTCGATCCACTTCGCCACC
* * * * * * * * * * * *
43653722 AATACATGAAGACAATATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCT
63 AATATAGGAAAACAAGATCTAC-ATCTTCGATCCACTTCACCACCAATATAGGAAGACAAAATCT
43653787 GCATC
127 GCATC
* * * * * * * * * *
43653792 TTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTG-TTATCTTTGATCTACTTC-ACGCT
1 TTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGATTA--TTCGATCCACTTCGCCACC
* * * * * * * * * *
43653855 AATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCTCCAATATGGGAAGACAAGATCT
63 AATATAGGAAAACAAGATCTAC-ATCTTCGATCCACTTCACCACCAATATAGGAAGACAAAATCT
43653920 GCATC
127 GCATC
* * * * * *
43653925 TTCGGTCCACTTCGCTACCAATATAGGAAGACAGGATCTG-TTATCTTCGATCCACTTC
1 TTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGATTA--TTCGATCCACTTC
43653983 ACGCCAATAC
Statistics
Matches: 507, Mismatches: 69, Indels: 26
0.84 0.11 0.04
Matches are distributed among these distances:
131 1 0.00
132 51 0.10
133 440 0.87
134 14 0.03
135 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (131 bp):
TTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGATTATTCGATCCACTTCGCCACCAAT
ATAGGAAAACAAGATCTACATCTTCGATCCACTTCACCACCAATATAGGAAGACAAAATCTGCAT
C
Found at i:43653551 original size:177 final size:177
Alignment explanation
Indices: 43653214--43654008 Score: 708
Period size: 177 Copynumber: 4.5 Consensus size: 177
43653204 ATGACTGATG
* * * * * * * *
43653214 TCTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTACTATTTTCGATCTACTTCAC-GC
1 TCTTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCTAC
* * * * * *
43653278 CAATACATGAAGACAAGATCTGATT-TCTTCGATTTTCTTCGCCACCAGTATGGGAAGACAAGAT
65 CAATATAGGAAGACAAGATCTG-TTATCTTCGATCTACTTCACCACCAGTATAGGAAGACAAGAT
* *
43653342 CTACATCTTTGATCCACTTCGCTAGCAATATAGGAAGACAGGATCTGTTA
129 CTACATCTTCGATCCACTTCACTA-CAATATAGGAAGACAGGATCTGTTA
* * *
43653392 TCTTCGATCTACTTCACGCCAATACGGGAAGATAAGATCTGC-ATATTCGATCCACTTCGCTACC
1 TCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCTACC
* * * *
43653456 AATATAGGAAAATAGGATCTGTTATCTTCGATCTACTTCACCACCAGTATAGGAAGACAAAATCT
66 AATATAGGAAGACAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATAGGAAGACAAGATCT
* *
43653521 GCATCTTCGATCCACTTCACTACTAATATAGGAAGATAGGATCTGTTA
131 ACATCTTCGATCCACTTCACTAC-AATATAGGAAGACAGGATCTGTTA
* * * * * * *
43653569 TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATTTGCTTTCTTTGATCTACTTCGCCACC
1 TCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCTACC
* * * * * * * * **
43653634 AGTATGGGAAGACAAGATCTG-CATCTTCAATCCACTTCGCTACCAATATAGGAAGACGGGATCT
66 AATATAGGAAGACAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATAGGAAGACAAGATCT
* ** * * **
43653698 ACTATCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTGCTT-
131 AC-ATCTTCGATCCACTTCACTACAATATAGGAAGACAGGATCTG-TTA
* * * ** *
43653746 TCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGC-ATCTTCGATCCACTTCGCTAC
1 TCTTCGATCTACTTC-ACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCTAC
* * * * * * *
43653810 CAATATAGGAAGACAGGATCTGTTATCTTTGATCTACTTCA-CGCTAATACATGAAGACAAGATC
65 CAATATAGGAAGACAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATAGGAAGACAAGATC
* * * * * * * *
43653874 TGCTTTCTTCGATCTACTTCGCCTCCAATATGGGAAGACAAGATCTG-CA
130 TAC-ATCTTCGATCCACTTC-ACTACAATATAGGAAGACAGGATCTGTTA
* * * * * * * * *
43653923 TCTTCGGTCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCCACTTCAC-GC
1 TCTTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCTAC
* *
43653987 CAATACATGAAGACAAGATCTG
65 CAATATAGGAAGACAAGATCTG
43654009 CTATTTTCTA
Statistics
Matches: 498, Mismatches: 107, Indels: 25
0.79 0.17 0.04
Matches are distributed among these distances:
176 19 0.04
177 342 0.69
178 137 0.28
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (177 bp):
TCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCCACTTCGCTACC
AATATAGGAAGACAAGATCTGTTATCTTCGATCTACTTCACCACCAGTATAGGAAGACAAGATCT
ACATCTTCGATCCACTTCACTACAATATAGGAAGACAGGATCTGTTA
Found at i:43653754 original size:266 final size:267
Alignment explanation
Indices: 43653214--43654010 Score: 888
Period size: 266 Copynumber: 3.0 Consensus size: 267
43653204 ATGACTGATG
* ** * * * * * * *
43653214 TCTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTACTATTTTCGATCTACTTCAC-GC
1 TCTTCGATCTACTTCACCACCAGTATAGGAAGACAAAATCTGC-ATCTTCGATCCACTTCACTAC
* * * * * * * * ***
43653278 CAATACATGAAGACAAGATCTGATT-TCTTCGATTTTCTTCGCCACCAGTATGGGAAGACAAGAT
65 CAATATAGGAAGACAGGATCTG-TTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGAT
* * * * * * * * * * *
43653342 CTAC-ATCTTTGATCCACTTCGCTAGCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTT
128 CTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTG-CATCTTCAATCCACTT
* * ** * * * * * * * * * *
43653406 CAC-GCCAATACGGGAAGATAAGATCTGC-ATATTCGATCCACTTCGCTACCAATATAGGAAAAT
192 CGCTACCAATATAGGAAGACAGGATCTACTATCTTCGATCCACTTCAC-GCCAATACATGAAGAC
*
43653469 AGGATCTG-TTA
256 AAGATCTGCTTA
*
43653480 TCTTCGATCTACTTCACCACCAGTATAGGAAGACAAAATCTGCATCTTCGATCCACTTCACTACT
1 TCTTCGATCTACTTCACCACCAGTATAGGAAGACAAAATCTGCATCTTCGATCCACTTCACTACC
* * *
43653545 AATATAGGAAGATAGGATCTGTTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATTTG
66 AATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
* *
43653610 CTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCAATCCACTTCGCT
131 CTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCAATCCACTTCGCT
* * *
43653675 ACCAATATAGGAAGACGGGATCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAATAT
196 ACCAATATAGGAAGACAGGATCTACTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGAT
43653740 CTGCTT-
261 CTGCTTA
* * * * *
43653746 TCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGCATCTTCGATCCACTTCGCTACC
1 TCTTCGATCTACTTCACCACCAGTATAGGAAGACAAAATCTGCATCTTCGATCCACTTCACTACC
* *
43653811 AATATAGGAAGACAGGATCTGTTATCTTTGATCTACTTCACGCTAATACATGAAGACAAGATCTG
66 AATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
* **
43653876 CTTTCTTCGATCTACTTCGCCTCCAATATGGGAAGACAAGATCTGCATCTTCGGTCCACTTCGCT
131 CTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCAATCCACTTCGCT
**
43653941 ACCAATATAGGAAGACAGGATCTGTTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGAT
196 ACCAATATAGGAAGACAGGATCTACTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGAT
43654006 CTGCT
261 CTGCT
43654011 ATTTTCTAGT
Statistics
Matches: 450, Mismatches: 75, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
265 51 0.11
266 382 0.85
267 17 0.04
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (267 bp):
TCTTCGATCTACTTCACCACCAGTATAGGAAGACAAAATCTGCATCTTCGATCCACTTCACTACC
AATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
CTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCAATCCACTTCGCT
ACCAATATAGGAAGACAGGATCTACTATCTTCGATCCACTTCACGCCAATACATGAAGACAAGAT
CTGCTTA
Done.