Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 216 of 311
Found at i:73946144 original size:23 final size:23
Alignment explanation
Indices: 73946117--73946163 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
73946107 GTTAGATTTT
*
73946117 TCCTAAATATTATCACTGAATAA
1 TCCTAAATATTATCACTAAATAA
*
73946140 TCCTAAATATTATCATTAAATAA
1 TCCTAAATATTATCACTAAATAA
73946163 T
1 T
73946164 TCAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:73946170 original size:23 final size:23
Alignment explanation
Indices: 73946121--73946170 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
73946111 GATTTTTCCT
* *
73946121 AAATATTATCACTGAATAATCCT
1 AAATATTATCACTAAATAATCCA
* *
73946144 AAATATTATCATTAAATAATTCA
1 AAATATTATCACTAAATAATCCA
73946167 AAAT
1 AAAT
73946171 TTAAAAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATATTATCACTAAATAATCCA
Found at i:73948496 original size:22 final size:22
Alignment explanation
Indices: 73948465--73948509 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
73948455 GTTCATGGCA
*
73948465 AGAATGAAGGTCGCATACTTTG
1 AGAATAAAGGTCGCATACTTTG
73948487 AGAATAAAGGTCGCATACTTTG
1 AGAATAAAGGTCGCATACTTTG
73948509 A
1 A
73948510 AAATCAGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (22 bp):
AGAATAAAGGTCGCATACTTTG
Found at i:73950511 original size:25 final size:25
Alignment explanation
Indices: 73950482--73950533 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
73950472 AAGAATAATT
**
73950482 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
73950507 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
73950532 TG
1 TG
73950534 TCAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:73956918 original size:18 final size:17
Alignment explanation
Indices: 73956889--73956924 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
73956879 AAATTTTAAT
73956889 AAAATAATAATTAAATA
1 AAAATAATAATTAAATA
*
73956906 AAAATATATAATTTAATA
1 AAAATA-ATAATTAAATA
73956924 A
1 A
73956925 TATTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAATAATTAAATA
Found at i:73956965 original size:25 final size:27
Alignment explanation
Indices: 73956918--73957012 Score: 83
Period size: 32 Copynumber: 3.4 Consensus size: 27
73956908 AATATATAAT
*
73956918 TTAATAATATTTTTATATTAAATTTTA
1 TTAATAATATTTTTATATTAAATTATA
73956945 TTAA-AATA-TTTTAT-TTAAAATTATA
1 TTAATAATATTTTTATATT-AAATTATA
73956970 TTTTGAAATTAA-ATATTTTATATTAAATTATA
1 --TT--AA-TAATAT-TTTTATATTAAATTATA
73957002 TTAA-AATATTT
1 TTAATAATATTT
73957013 CAAATATTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 23
0.70 0.01 0.29
Matches are distributed among these distances:
24 2 0.04
25 13 0.23
26 8 0.14
27 8 0.14
28 2 0.04
29 2 0.04
30 3 0.05
31 2 0.04
32 14 0.25
33 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TTAATAATATTTTTATATTAAATTATA
Found at i:73956996 original size:14 final size:14
Alignment explanation
Indices: 73956923--73956997 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 14
73956913 ATAATTTAAT
73956923 AATATTTTTATATT-
1 AATA-TTTTATATTA
*
73956937 AA-ATTTTAT-TAA
1 AATATTTTATATTA
73956949 AATATTTTAT-TTAAA
1 AATATTTTATATT--A
*
73956964 ATTATATTTTGAAATTA
1 A--ATATTTT-ATATTA
73956981 AATATTTTATATTA
1 AATATTTTATATTA
73956995 AAT
1 AAT
73956998 TATATTAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
11 1 0.02
12 8 0.16
13 9 0.18
14 10 0.20
15 9 0.18
17 9 0.18
18 1 0.02
19 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (14 bp):
AATATTTTATATTA
Found at i:73958495 original size:19 final size:18
Alignment explanation
Indices: 73958473--73958511 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
73958463 TTTAAATGTC
*
73958473 AATTGAATATTAAAATTAA
1 AATTAAATATT-AAATTAA
73958492 AATTAAATATTAAATTAA
1 AATTAAATATTAAATTAA
73958510 AA
1 AA
73958512 CAAAACACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AATTAAATATTAAATTAA
Found at i:73964082 original size:21 final size:22
Alignment explanation
Indices: 73964049--73964089 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
73964039 TTTTATAGAG
*
73964049 AAAATCTTAGGTTTTTACAAGA
1 AAAATCTTAGGTTTTAACAAGA
*
73964071 AAAATC-TGGGTTTTAACAA
1 AAAATCTTAGGTTTTAACAA
73964090 ATCATCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
AAAATCTTAGGTTTTAACAAGA
Found at i:73969911 original size:105 final size:106
Alignment explanation
Indices: 73969786--73969995 Score: 404
Period size: 105 Copynumber: 2.0 Consensus size: 106
73969776 ATCGACACCA
73969786 TAAAATATTTATCAATACCTTTGTTTTGCAAAGAAAACAATAATGAATTTTGGTATCAATTTTCA
1 TAAAATATTTATCAATACCTTTGTTTTGCAAAGAAAACAATAATGAATTTTGGTATCAATTTTCA
73969851 AAAAGGTATCGATTCA-ATCGATACCAACTATAGATTTTCT
66 AAAAGGTATCGATTCATATCGATACCAACTATAGATTTTCT
*
73969891 TAAAATATTTATTAATACCTTTGTTTTGCAAAGAAAACAATAATGAATTTTGGTATCAATTTTCA
1 TAAAATATTTATCAATACCTTTGTTTTGCAAAGAAAACAATAATGAATTTTGGTATCAATTTTCA
73969956 AAAAGGTATCGATTCATATCGATACCAACTATAGATTTTC
66 AAAAGGTATCGATTCATATCGATACCAACTATAGATTTTC
73969996 ATTATTGACC
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
105 80 0.78
106 23 0.22
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (106 bp):
TAAAATATTTATCAATACCTTTGTTTTGCAAAGAAAACAATAATGAATTTTGGTATCAATTTTCA
AAAAGGTATCGATTCATATCGATACCAACTATAGATTTTCT
Found at i:73970782 original size:23 final size:24
Alignment explanation
Indices: 73970756--73970800 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
73970746 TTTTTTTTTA
*
73970756 ATTTTTATGAA-CTTTTTATATTT
1 ATTTTTATGAATATTTTTATATTT
*
73970779 ATTTTTTTGAATATTTTTATAT
1 ATTTTTATGAATATTTTTATAT
73970801 AAATTAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (24 bp):
ATTTTTATGAATATTTTTATATTT
Found at i:73982787 original size:20 final size:19
Alignment explanation
Indices: 73982744--73982810 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
73982734 CACTTTTTGT
73982744 ATTTTTAAAT-TATTTTTA
1 ATTTTTAAATATATTTTTA
* *
73982762 CTTTTTTATATATATTTTATA
1 -ATTTTTAAATATATTTT-TA
*
73982783 A-TTTTAAATATCTTTTTA
1 ATTTTTAAATATATTTTTA
73982801 ATATTTTAAA
1 AT-TTTTAAA
73982811 ATGTGTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.08
19 21 0.54
20 13 0.33
21 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTAAATATATTTTTA
Found at i:73984410 original size:16 final size:18
Alignment explanation
Indices: 73984383--73984415 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
73984373 AAGAATTAGG
73984383 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
73984400 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
73984416 GTGATGTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:73987728 original size:104 final size:104
Alignment explanation
Indices: 73987548--73987765 Score: 355
Period size: 104 Copynumber: 2.1 Consensus size: 104
73987538 CATGGGTTAT
**
73987548 CCACACGACCATGCTCTTCGGTCACACGGGTGTGTGTCATAGTCACATGGTTGTGCGCCTCCTTT
1 CCACACGACCATGCTCTTCGGTCACACGGACGTGTGTCATAGTCACATGGTTGTGCGCCTCCTTT
*
73987613 CACACAGGTGTGTGTCTCTTTCATATAGGCGTGTTGACC
66 CACACAGGTGTGTGTCTCATTCATATAGGCGTGTTGACC
* * * * *
73987652 CCACACGACCATGTTTTTGGGTTACACGGACGTGTGTCATAGTCACATGGTTGTGGGCCTCCTTT
1 CCACACGACCATGCTCTTCGGTCACACGGACGTGTGTCATAGTCACATGGTTGTGCGCCTCCTTT
*
73987717 CACACAGGTGTGTGTCTCATTCATATGGGCGTGTTGACC
66 CACACAGGTGTGTGTCTCATTCATATAGGCGTGTTGACC
73987756 CCACACGACC
1 CCACACGACC
73987766 TAAGCACTTC
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (104 bp):
CCACACGACCATGCTCTTCGGTCACACGGACGTGTGTCATAGTCACATGGTTGTGCGCCTCCTTT
CACACAGGTGTGTGTCTCATTCATATAGGCGTGTTGACC
Found at i:73989349 original size:18 final size:17
Alignment explanation
Indices: 73989330--73989416 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 17
73989320 ATATCTGAAT
73989330 AAAATAAAATAATAAGAT-
1 AAAATAAAATAA-AA-ATA
*
73989348 AAAAT-AACTAAAAATA
1 AAAATAAAATAAAAATA
73989364 AAAATAAAAATAAAAATA
1 AAAAT-AAAATAAAAATA
73989382 AAAATAAAAATAAAAATA
1 AAAAT-AAAATAAAAATA
73989400 AAAATAAAAATAAAAAT
1 AAAAT-AAAATAAAAAT
73989417 TGGGTTGCCT
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
15 2 0.03
16 7 0.11
17 5 0.08
18 50 0.78
ACGTcount: A:0.79, C:0.01, G:0.01, T:0.18
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:73989367 original size:6 final size:6
Alignment explanation
Indices: 73989356--73989416 Score: 122
Period size: 6 Copynumber: 10.2 Consensus size: 6
73989346 ATAAAATAAC
73989356 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
73989404 TAAAAA TAAAAA T
1 TAAAAA TAAAAA T
73989417 TGGGTTGCCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:73995835 original size:27 final size:26
Alignment explanation
Indices: 73995805--73995867 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
73995795 AGATAATTAA
73995805 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
73995832 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
73995859 AATATAAAT
1 AATA-AAAT
73995868 AAAATGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:73995854 original size:15 final size:15
Alignment explanation
Indices: 73995834--73995863 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
73995824 ATAATCCTAA
*
73995834 TAATTATCTTAATAT
1 TAATTATCCTAATAT
73995849 TAATTATCCTAATAT
1 TAATTATCCTAATAT
73995864 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:73997447 original size:51 final size:53
Alignment explanation
Indices: 73997369--73997486 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 53
73997359 AAGTGTCGCC
* * * * *
73997369 TTACTGTTACTGTTCCGGATTCGTTCCGAAGAGGTACTC-TGTACC-TTATTG
1 TTACTGTTACTGTCCCAGATTCATTCCGAAGAGGTACTCGTGTACCGCTACTG
* *
73997420 TTACTGTTACTGTCCCAGATTTATTCCGATGAGGTACTCTGTGTACCGCTACTG
1 TTACTGTTACTGTCCCAGATTCATTCCGAAGAGGTACTC-GTGTACCGCTACTG
73997474 TTACTGTTACTGT
1 TTACTGTTACTGT
73997487 TACCGTTACA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
51 34 0.60
53 6 0.11
54 17 0.30
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (53 bp):
TTACTGTTACTGTCCCAGATTCATTCCGAAGAGGTACTCGTGTACCGCTACTG
Found at i:73997694 original size:18 final size:18
Alignment explanation
Indices: 73997607--73997694 Score: 79
Period size: 18 Copynumber: 4.9 Consensus size: 18
73997597 TAAAAGTACC
* *
73997607 GAATAACTGAATATTACT
1 GAATAACTGACTGTTACT
* *
73997625 GGATAACTGACTGCTACT
1 GAATAACTGACTGTTACT
* *
73997643 AAATAATTGACTGTTACT
1 GAATAACTGACTGTTACT
** *
73997661 GAATAGTTTA-TCGTTACT
1 GAATAACTGACT-GTTACT
73997679 GAATAACTGACTGTTA
1 GAATAACTGACTGTTA
73997695 AAGATTGACT
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
17 1 0.02
18 52 0.96
19 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (18 bp):
GAATAACTGACTGTTACT
Found at i:73997747 original size:18 final size:18
Alignment explanation
Indices: 73997700--73997756 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
73997690 TGTTAAAGAT
*
73997700 TGACTGAATATTATTGAA
1 TGACTGAATGTTATTGAA
*
73997718 CGACT-AATTGTTATTGAA
1 TGACTGAA-TGTTATTGAA
* *
73997736 TGATTGAATGTTACTGAA
1 TGACTGAATGTTATTGAA
73997754 TGA
1 TGA
73997757 AACTGATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 2 0.06
18 28 0.88
19 2 0.06
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (18 bp):
TGACTGAATGTTATTGAA
Found at i:73998600 original size:42 final size:41
Alignment explanation
Indices: 73998548--73998665 Score: 119
Period size: 43 Copynumber: 2.8 Consensus size: 41
73998538 TAAGGTTATT
* **
73998548 TGAGATTTCGTGTAAAACCATATCTGGGATATGTCATCGATA
1 TGAGA-TTCGTGTAAGACCATATCTGGGATATGGAATCGATA
* * *
73998590 TGAGACTTCGTGTGAGACCATAGCTGGGTTATTGGAATCGATA
1 TGAGA-TTCGTGTAAGACCATATCTGGGATA-TGGAATCGATA
* * *
73998633 TGAGATCCCATGTAAGACCATATTTGGGATATG
1 TGAGAT-TCGTGTAAGACCATATCTGGGATATG
73998666 ACATTGGTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 29 0.48
43 32 0.52
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (41 bp):
TGAGATTCGTGTAAGACCATATCTGGGATATGGAATCGATA
Found at i:73999857 original size:20 final size:20
Alignment explanation
Indices: 73999832--73999870 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
73999822 GACCACACGG
*
73999832 CCAAGCCACACGGGCGTGTC
1 CCAAGCCACACAGGCGTGTC
73999852 CCAAGCCACACAGGCGTGT
1 CCAAGCCACACAGGCGTGT
73999871 GACTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.28, T:0.10
Consensus pattern (20 bp):
CCAAGCCACACAGGCGTGTC
Found at i:74005732 original size:20 final size:20
Alignment explanation
Indices: 74005677--74005741 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
74005667 TAATGCAAAT
* * *
74005677 AGGAGCATGAATATGCCATC
1 AGGAGCACGAATGTGCTATC
* *
74005697 AGGAGCACCGTA-GTGCTAAC
1 AGGAGCA-CGAATGTGCTATC
74005717 AGGAGCACGAATGTGCTATC
1 AGGAGCACGAATGTGCTATC
74005737 AGGAG
1 AGGAG
74005742 GAATTATTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
19 3 0.08
20 31 0.86
21 2 0.06
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.17
Consensus pattern (20 bp):
AGGAGCACGAATGTGCTATC
Found at i:74012299 original size:21 final size:21
Alignment explanation
Indices: 74012273--74012313 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
74012263 AAGCCCAAAG
*
74012273 GCTAAACATAAACACATAAGT
1 GCTAAACAGAAACACATAAGT
*
74012294 GCTAAACAGAAACCCATAAG
1 GCTAAACAGAAACACATAAG
74012314 GGTTGAATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.22, G:0.12, T:0.15
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGT
Found at i:74012348 original size:42 final size:42
Alignment explanation
Indices: 74012302--74012422 Score: 134
Period size: 42 Copynumber: 2.9 Consensus size: 42
74012292 GTGCTAAACA
**
74012302 GAAACCCATAAGGGTTGAATGGAAGCTCATAAGAGTTGAACG
1 GAAACCCATAAGGGTTGAACAGAAGCTCATAAGAGTTGAACG
*** * * * *
74012344 GAAACCCATAACTATTAAACAGAAGCTTAAAAGAGCTGAACG
1 GAAACCCATAAGGGTTGAACAGAAGCTCATAAGAGTTGAACG
* * *
74012386 GAAACCCATTAGGGTTGAACAGAAACTCATATGAGTT
1 GAAACCCATAAGGGTTGAACAGAAGCTCATAAGAGTT
74012423 AAACAGAAGC
Statistics
Matches: 60, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (42 bp):
GAAACCCATAAGGGTTGAACAGAAGCTCATAAGAGTTGAACG
Found at i:74012353 original size:21 final size:21
Alignment explanation
Indices: 74012302--74012422 Score: 73
Period size: 21 Copynumber: 5.8 Consensus size: 21
74012292 GTGCTAAACA
* *
74012302 GAAACCCATAAGGGTTGAATG
1 GAAACCCATAAGAGTTGAACG
* *
74012323 GAAGCTCATAAGAGTTGAACG
1 GAAACCCATAAGAGTTGAACG
* * *
74012344 GAAACCCATAACTA-TTAAACA
1 GAAACCCATAA-GAGTTGAACG
* ** * *
74012365 GAAGCTTAAAAGAGCTGAACG
1 GAAACCCATAAGAGTTGAACG
* * *
74012386 GAAACCCATTAGGGTTGAACA
1 GAAACCCATAAGAGTTGAACG
* *
74012407 GAAACTCATATGAGTT
1 GAAACCCATAAGAGTT
74012423 AAACAGAAGC
Statistics
Matches: 69, Mismatches: 29, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
20 1 0.01
21 67 0.97
22 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
GAAACCCATAAGAGTTGAACG
Found at i:74013678 original size:5 final size:5
Alignment explanation
Indices: 74013670--74013709 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
74013660 ATTATTAAGT
74013670 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
74013710 AAGAAATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:74013795 original size:13 final size:13
Alignment explanation
Indices: 74013777--74013801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74013767 AGAAGGAATG
74013777 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
74013790 AAAGAAAGAAAG
1 AAAGAAAGAAAG
74013802 GGAAAATATG
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:74014394 original size:30 final size:30
Alignment explanation
Indices: 74014360--74014422 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
74014350 ACTTAACAAG
74014360 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1 CAAATGTCTT-TAAAATAATAAAAAAATTAA
*
74014390 CAAATGTCTTTAAAATAATAAGAAAATTAA
1 CAAATGTCTTTAAAATAATAAAAAAATTAA
74014420 CAA
1 CAA
74014423 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAAAAAAATTAA
Found at i:74024261 original size:17 final size:17
Alignment explanation
Indices: 74024239--74024272 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
74024229 GAATTGAGCA
*
74024239 GTGTGGGCCACATGGGT
1 GTGTGGGCAACATGGGT
74024256 GTGTGGGCAACATGGGT
1 GTGTGGGCAACATGGGT
74024273 AGTCCACACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.15, G:0.47, T:0.24
Consensus pattern (17 bp):
GTGTGGGCAACATGGGT
Found at i:74024373 original size:18 final size:17
Alignment explanation
Indices: 74024343--74024410 Score: 72
Period size: 18 Copynumber: 4.1 Consensus size: 17
74024333 ATATAGGCCG
74024343 TGTGGGCCACACGGGCA
1 TGTGGGCCACACGGGCA
74024360 TGTGGGCGCACACGGGCA
1 TGTGGGC-CACACGGGCA
**
74024378 --T--GCCACATTGGCA
1 TGTGGGCCACACGGGCA
74024391 TGTGGGCCCACACGGGCA
1 TGTGGG-CCACACGGGCA
74024409 TG
1 TG
74024411 CCATATGGGC
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 1 0.02
16 1 0.02
17 8 0.20
18 21 0.51
ACGTcount: A:0.18, C:0.29, G:0.38, T:0.15
Consensus pattern (17 bp):
TGTGGGCCACACGGGCA
Found at i:74024383 original size:31 final size:31
Alignment explanation
Indices: 74024348--74024425 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
74024338 GGCCGTGTGG
* *
74024348 GCCACACGGGCATGTGGGCGCACACGGGCAT
1 GCCACATGGGCATGTGGGCCCACACGGGCAT
*
74024379 GCCACATTGGCATGTGGGCCCACACGGGCAT
1 GCCACATGGGCATGTGGGCCCACACGGGCAT
*
74024410 GCCATATGGGCATGTG
1 GCCACATGGGCATGTG
74024426 AGTCCATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.29, G:0.36, T:0.15
Consensus pattern (31 bp):
GCCACATGGGCATGTGGGCCCACACGGGCAT
Found at i:74027640 original size:18 final size:17
Alignment explanation
Indices: 74027608--74027641 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
74027598 AGTAACCAAA
*
74027608 CAAAAATACACATCTAC
1 CAAAAATACAAATCTAC
74027625 CAAAAATACCAAATCTA
1 CAAAAATA-CAAATCTA
74027642 AAGGAATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (17 bp):
CAAAAATACAAATCTAC
Found at i:74039669 original size:27 final size:27
Alignment explanation
Indices: 74039631--74039686 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
74039621 TATTTTGGGC
74039631 TTTGCTCTTTGGTTTTTGTGTTGTTTG
1 TTTGCTCTTTGGTTTTTGTGTTGTTTG
74039658 TTTGCTCTTTGGTTTTTGTGTTGTTTG
1 TTTGCTCTTTGGTTTTTGTGTTGTTTG
74039685 TT
1 TT
74039687 GAATTTTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.00, C:0.07, G:0.25, T:0.68
Consensus pattern (27 bp):
TTTGCTCTTTGGTTTTTGTGTTGTTTG
Found at i:74040948 original size:24 final size:24
Alignment explanation
Indices: 74040920--74040965 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
74040910 TAATTGTTAT
74040920 TATTATTATGATT-TTATATTAAAC
1 TATTATTATGATTATTAT-TTAAAC
*
74040944 TATTATTATTATTATTATTTAA
1 TATTATTATGATTATTATTTAA
74040966 TAGGTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
TATTATTATGATTATTATTTAAAC
Found at i:74041403 original size:11 final size:12
Alignment explanation
Indices: 74041373--74041406 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
74041363 GTATGTTTAC
74041373 TTATTATATAAG
1 TTATTATATAAG
74041385 TATATTAT-TAAG
1 T-TATTATATAAG
74041397 TTATTATATA
1 TTATTATATA
74041407 TATATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.30
12 8 0.40
13 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (12 bp):
TTATTATATAAG
Found at i:74041481 original size:18 final size:18
Alignment explanation
Indices: 74041458--74041494 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
74041448 GGTACAAGTG
74041458 TTAAATAAATATTTATTA
1 TTAAATAAATATTTATTA
* *
74041476 TTAAATAGATTTTTATTA
1 TTAAATAAATATTTATTA
74041494 T
1 T
74041495 AGTTATTATT
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:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAATAAATATTTATTA
Found at i:74042887 original size:18 final size:19
Alignment explanation
Indices: 74042866--74042906 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
74042856 AATGAAATGA
74042866 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
74042884 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
74042903 GAAA
1 GAAA
74042907 CATGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:74046696 original size:6 final size:6
Alignment explanation
Indices: 74046670--74046703 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
74046660 CGAAAATAGA
74046670 TTTTA- TTTTAT TTTCTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTT-TAT TTTTAT TTTTAT TTTT
74046704 CCTAAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:74049414 original size:19 final size:19
Alignment explanation
Indices: 74049387--74049432 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
74049377 AGTGTAAATG
74049387 GGCCCAAGGCCCATTACTC
1 GGCCCAAGGCCCATTACTC
*
74049406 GGCCTAAGGCCCATTACTC
1 GGCCCAAGGCCCATTACTC
74049425 GGCCCAAG
1 GGCCCAAG
74049433 TGGGCCAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.22, C:0.39, G:0.24, T:0.15
Consensus pattern (19 bp):
GGCCCAAGGCCCATTACTC
Found at i:74055912 original size:27 final size:27
Alignment explanation
Indices: 74055882--74055940 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
74055872 CAAAGCTGCC
74055882 AGTATCAATATATGTGGCAAAGCCACT
1 AGTATCAATATATGTGGCAAAGCCACT
* * *
74055909 AGTAACAGTATATGTGGCGAAGCCACT
1 AGTATCAATATATGTGGCAAAGCCACT
74055936 AGTAT
1 AGTAT
74055941 AAAACACTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (27 bp):
AGTATCAATATATGTGGCAAAGCCACT
Found at i:74057347 original size:18 final size:17
Alignment explanation
Indices: 74057314--74057352 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
74057304 TTGTATAAAT
74057314 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
74057332 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
74057349 TGTG
1 TGTG
74057353 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:74057470 original size:8 final size:8
Alignment explanation
Indices: 74057457--74057485 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
74057447 CACTAGAGAC
74057457 CAGTGTTA
1 CAGTGTTA
74057465 CAGTGTTA
1 CAGTGTTA
74057473 CAGTGTTA
1 CAGTGTTA
74057481 CAGTG
1 CAGTG
74057486 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:74057650 original size:25 final size:23
Alignment explanation
Indices: 74057572--74057647 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
74057562 AGTGTTATTG
74057572 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
74057595 TTCAGTGGTAGCTTCGGCTATAT
1 ATCAGTGGTAGCTTCGGCTACAT
74057618 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
74057641 ATCAGTG
1 ATCAGTG
74057648 TGGCACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:74060577 original size:6 final size:6
Alignment explanation
Indices: 74060544--74060584 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
74060534 CAAAAATAGA
74060544 TTTTA- TTTTAT TTTCTAT TTTCTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTT-TAT TTT-TAT TTTTAT TTTTAT TTTT
74060585 CCCAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.15
6 16 0.47
7 13 0.38
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:74061330 original size:18 final size:18
Alignment explanation
Indices: 74061302--74061347 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
74061292 CAACCTCTGT
**
74061302 GTGTGGG-CCACATGGGC
1 GTGTGGGCCCACAAAGGC
74061319 GTGTGGGCCCACAAAGGC
1 GTGTGGGCCCACAAAGGC
74061337 GTGTGGGCCCA
1 GTGTGGGCCCA
74061348 TAATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.15, C:0.26, G:0.43, T:0.15
Consensus pattern (18 bp):
GTGTGGGCCCACAAAGGC
Found at i:74064395 original size:23 final size:23
Alignment explanation
Indices: 74064365--74064408 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
74064355 TGCTAAATCT
74064365 GGAGCACCAAAGTGTTAAATTAA
1 GGAGCACCAAAGTGTTAAATTAA
**
74064388 GGAGCACCGGAGTGTTAAATT
1 GGAGCACCAAAGTGTTAAATT
74064409 CTCAAGTGCT
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:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (23 bp):
GGAGCACCAAAGTGTTAAATTAA
Found at i:74072287 original size:20 final size:19
Alignment explanation
Indices: 74072242--74072289 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
74072232 AATTTATCTA
*
74072242 TATTAACAGTTTTATGCAT
1 TATTAACAGTTTTATACAT
**
74072261 TAGTTAACAGTTTTGATATTT
1 TA-TTAACAGTTTT-ATACAT
74072282 TATTAACA
1 TATTAACA
74072290 AATATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 17 0.71
21 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (19 bp):
TATTAACAGTTTTATACAT
Found at i:74077622 original size:25 final size:25
Alignment explanation
Indices: 74077594--74077730 Score: 143
Period size: 25 Copynumber: 5.5 Consensus size: 25
74077584 CACAGCTCAT
* *
74077594 ATGAGCTTCCCGTTATACAGCTCGC
1 ATGAGCTTCCCGATATTCAGCTCGC
** *
74077619 ATGAGCTTCTTGATATTCAGCTCAC
1 ATGAGCTTCCCGATATTCAGCTCGC
* * *
74077644 ATGAGCTTTCAGATATTCAGCTCAC
1 ATGAGCTTCCCGATATTCAGCTCGC
* *
74077669 ATGAGCTTCCAGATATTCAGCTCGT
1 ATGAGCTTCCCGATATTCAGCTCGC
*
74077694 ATGAGCTTCCC-ATTATTCAGCTCGG
1 ATGAGCTTCCCGA-TATTCAGCTCGC
74077719 A-GAAGCTTCCCG
1 ATG-AGCTTCCCG
74077731 TTTACAGCTC
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
24 2 0.02
25 94 0.98
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCGATATTCAGCTCGC
Found at i:74077648 original size:50 final size:50
Alignment explanation
Indices: 74077586--74077717 Score: 174
Period size: 50 Copynumber: 2.6 Consensus size: 50
74077576 AGACACACCA
* **
74077586 CAGCTCATATGAGCTTCCCGTTATACAGCTCGCATGAGCTTCTTGATATT
1 CAGCTCATATGAGCTTCCCGTTATTCAGCTCGCATGAGCTTCCAGATATT
* * * * *
74077636 CAGCTCACATGAGCTTTCAGATATTCAGCTCACATGAGCTTCCAGATATT
1 CAGCTCATATGAGCTTCCCGTTATTCAGCTCGCATGAGCTTCCAGATATT
* *
74077686 CAGCTCGTATGAGCTTCCCATTATTCAGCTCG
1 CAGCTCATATGAGCTTCCCGTTATTCAGCTCG
74077718 GAGAAGCTTC
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.32
Consensus pattern (50 bp):
CAGCTCATATGAGCTTCCCGTTATTCAGCTCGCATGAGCTTCCAGATATT
Found at i:74080202 original size:31 final size:31
Alignment explanation
Indices: 74080159--74080244 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
74080149 TCAATCTCAG
*
74080159 CATAT-ACTGGGCCGAAGCCTTTACATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* *
74080189 CATGTCACTGGGCCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* **
74080220 CATATCACTGGTCTAAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
74080245 TATAAACGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 4 0.09
31 43 0.91
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:74080490 original size:25 final size:25
Alignment explanation
Indices: 74080462--74080531 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
74080452 CTCTTTTAAT
74080462 AACTGGGGCAAAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
74080487 AACTGGGGCAAAGCCTTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
74080512 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
74080532 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:74080595 original size:16 final size:17
Alignment explanation
Indices: 74080574--74080621 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 17
74080564 GCATATATGA
74080574 ATATCATGTGCA-ATAC
1 ATATCATGTGCACATAC
74080590 ATATCATGTGCATATCATAC
1 ATATCATGTGC--A-CATAC
74080610 ATATCATGTGCA
1 ATATCATGTGCA
74080622 TATCATGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 11 0.39
18 2 0.07
20 15 0.54
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (17 bp):
ATATCATGTGCACATAC
Found at i:74080605 original size:11 final size:11
Alignment explanation
Indices: 74080589--74080639 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
74080579 ATGTGCAATA
74080589 CATATCATGTG
1 CATATCATGTG
*
74080600 CATATCA--TA
1 CATATCATGTG
74080609 CATATCATGTG
1 CATATCATGTG
74080620 CATATCATGT-
1 CATATCATGTG
*
74080630 CAAATCATGT
1 CATATCATGT
74080640 ATATCAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 8 0.23
10 9 0.26
11 18 0.51
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (11 bp):
CATATCATGTG
Found at i:74080611 original size:20 final size:20
Alignment explanation
Indices: 74080586--74080627 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
74080576 ATCATGTGCA
74080586 ATACATATCATGTGCATATC
1 ATACATATCATGTGCATATC
74080606 ATACATATCATGTGCATATC
1 ATACATATCATGTGCATATC
74080626 AT
1 AT
74080628 GTCAAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (20 bp):
ATACATATCATGTGCATATC
Found at i:74088265 original size:31 final size:31
Alignment explanation
Indices: 74088227--74088304 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
74088217 AGCATATACA
* * *
74088227 GGGCCGAAGCCTTTACATTGTTCATGCCATT
1 GGGCCGAAGCCTTTACATTATTCATACCACT
* *
74088258 GGGCCGAAGCCTTTTCATTATTCATATCACT
1 GGGCCGAAGCCTTTACATTATTCATACCACT
74088289 GGGCCGAAGCCTTTAC
1 GGGCCGAAGCCTTTAC
74088305 TGTAAACGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.31
Consensus pattern (31 bp):
GGGCCGAAGCCTTTACATTATTCATACCACT
Found at i:74088629 original size:11 final size:10
Alignment explanation
Indices: 74088613--74088667 Score: 60
Period size: 11 Copynumber: 5.5 Consensus size: 10
74088603 TATATGAATT
74088613 TATCATGTCCA
1 TATCATGT-CA
*
74088624 TATCAT-ACA
1 TATCATGTCA
74088633 TATCATGTGCA
1 TATCATGT-CA
74088644 TATCATGTCA
1 TATCATGTCA
*
74088654 AATCATGT-A
1 TATCATGTCA
74088663 TATCA
1 TATCA
74088668 AAATCTCATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 13 0.34
10 9 0.24
11 16 0.42
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (10 bp):
TATCATGTCA
Found at i:74092858 original size:26 final size:26
Alignment explanation
Indices: 74092823--74092887 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
74092813 TGGCTATCCG
*
74092823 GAGC-TCCTGATTAAAGGTTCTTCGT
1 GAGCTTCCTGATTAAAAGTTCTTCGT
*
74092848 GAGCTTCCTGATTAAAAGTTCTTTGT
1 GAGCTTCCTGATTAAAAGTTCTTCGT
* *
74092874 GAACTTCCTAATTA
1 GAGCTTCCTGATTA
74092888 TGGCTCTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
25 4 0.11
26 31 0.89
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (26 bp):
GAGCTTCCTGATTAAAAGTTCTTCGT
Found at i:74101212 original size:312 final size:314
Alignment explanation
Indices: 74100642--74101242 Score: 845
Period size: 312 Copynumber: 1.9 Consensus size: 314
74100632 TAGAAAATAG
* ** *
74100642 AATAAACAATCTCAAAGCATTGCTGTAAGAAAAAACACCACAAAGAAGTAAGTCCTACAAAACTA
1 AATAAACAATCTCAAAGCATTACTACAAGAAAAAACACCACAAAGAAGCAAGTCCTACAAAACTA
* * *
74100707 CATAAAACATCTCTAGAATGTCGTTGTGTAGGCAATGTTTGCAAGGTGAATGTTATTTGTAGTGG
66 CATAAAACATCTCTAGAATGTCGTTGTGTAGGCAAAGTTTGCAAGGTGAATGTCATTTGCAGTGG
* * *** * * * **
74100772 CAAAGCTAAGAGGGGGAGGTAGGGGCCTCGACCCCCTCTAAAATGGAAAATTTTACATTTAGGCC
131 CAAAGCCAAGAGGGGCAACCAAGGGCCCCGACCCCCTCTAAAATGAAAAAAATTACATTTAGGCC
74100837 TTTTATAAGTTATAAAATTTTAAATTAAAAATGGTAAAATTACACTTTAGCCCCTAAAAATAATA
196 TTTTATAAGTTATAAAATTTTAAATTAAAAATGGTAAAATTACACTTTAGCCCCTAAAAATAATA
74100902 AAAATTTAATTTAATCCTTT-AAAATTATTTAATCTTTAATTCATAAATGAAGT
261 AAAATTTAATTTAATCCTTTGAAAATTATTTAATCTTTAATTCATAAATGAAGT
* *
74100955 AATAAACAATCTCAAAGCATTACTACAA-AAAAAACACCATAAAGAAGCAAGTCCTACAAAATTA
1 AATAAACAATCTCAAAGCATTACTACAAGAAAAAACACCACAAAGAAGCAAGTCCTACAAAACTA
* *
74101019 CATAAAACATTTCTAGAGTGTCGTTGTGTAGGCAAAGTTTG-AAGGGTGAATGTCATTTGCAGTG
66 CATAAAACATCTCTAGAATGTCGTTGTGTAGGCAAAGTTTGCAA-GGTGAATGTCATTTGCAGTG
*
74101083 GCGAAGCCAAGAGGGGCAACCAAGGGCCCCGAGCCACCC-CTAAAATAGAAAAAAATT-CATTTA
130 GCAAAGCCAAGAGGGGCAACCAAGGGCCCCGA-CC-CCCTCTAAAAT-GAAAAAAATTACATTTA
** * ** * *
74101146 GGCCTTTTATAAGTTATAAAATTTTAAATTAGTAATGGTAAAGTTGTATTTTAGCCCCT-CAAAT
192 GGCCTTTTATAAGTTATAAAATTTTAAATTAAAAATGGTAAAATTACACTTTAGCCCCTAAAAAT
* *
74101210 AATAAAAGTTTGATTTAATCCTTTGAAAATTAT
257 AATAAAAATTTAATTTAATCCTTTGAAAATTAT
74101243 AAATACATAG
Statistics
Matches: 252, Mismatches: 31, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
311 2 0.01
312 139 0.55
313 101 0.40
314 10 0.04
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (314 bp):
AATAAACAATCTCAAAGCATTACTACAAGAAAAAACACCACAAAGAAGCAAGTCCTACAAAACTA
CATAAAACATCTCTAGAATGTCGTTGTGTAGGCAAAGTTTGCAAGGTGAATGTCATTTGCAGTGG
CAAAGCCAAGAGGGGCAACCAAGGGCCCCGACCCCCTCTAAAATGAAAAAAATTACATTTAGGCC
TTTTATAAGTTATAAAATTTTAAATTAAAAATGGTAAAATTACACTTTAGCCCCTAAAAATAATA
AAAATTTAATTTAATCCTTTGAAAATTATTTAATCTTTAATTCATAAATGAAGT
Found at i:74102987 original size:21 final size:22
Alignment explanation
Indices: 74102954--74103000 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
74102944 ATATAAAAGC
*
74102954 AAAATGATAGCAAAACAATGAA
1 AAAATGATAGCAAAACAATAAA
*
74102976 AAAAT-ATGGCAAAACAATAAA
1 AAAATGATAGCAAAACAATAAA
74102997 AAAA
1 AAAA
74103001 ACAACAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.68, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAATGATAGCAAAACAATAAA
Found at i:74106177 original size:42 final size:42
Alignment explanation
Indices: 74106130--74106260 Score: 253
Period size: 42 Copynumber: 3.1 Consensus size: 42
74106120 TTATGAGGAA
74106130 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGTTG
1 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGTTG
74106172 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGTTG
1 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGTTG
*
74106214 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGGTG
1 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGTTG
74106256 GTTGA
1 GTTGA
74106261 TTCGGAGTGT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (42 bp):
GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGTTG
Found at i:74107759 original size:20 final size:19
Alignment explanation
Indices: 74107699--74107773 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
74107689 ATATATTTAG
* *
74107699 AATTTTTTTGAAATTTTTATA
1 AATTATTTTGAAA--TTTAAA
*
74107720 AA-TATTCTGAAATTTAAA
1 AATTATTTTGAAATTTAAA
*
74107738 AATTATTTTGAATATTTGAA
1 AATTATTTTGAA-ATTTAAA
74107758 AATTATTTTGAAATTT
1 AATTATTTTGAAATTT
74107774 TTATTGAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
18 7 0.15
19 12 0.26
20 26 0.55
21 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (19 bp):
AATTATTTTGAAATTTAAA
Found at i:74108400 original size:19 final size:19
Alignment explanation
Indices: 74108378--74108421 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
74108368 TCGAGTCAAC
74108378 TCGAATAAGTAATTCGAGT
1 TCGAATAAGTAATTCGAGT
**
74108397 TCGAATCGGTAATTCGAGT
1 TCGAATAAGTAATTCGAGT
74108416 TCGAAT
1 TCGAAT
74108422 CGAGTTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (19 bp):
TCGAATAAGTAATTCGAGT
Found at i:74108422 original size:19 final size:19
Alignment explanation
Indices: 74108386--74108423 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
74108376 ACTCGAATAA
74108386 GTAATTCGAGTTCGAATCG
1 GTAATTCGAGTTCGAATCG
74108405 GTAATTCGAGTTCGAATCG
1 GTAATTCGAGTTCGAATCG
74108424 AGTTGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (19 bp):
GTAATTCGAGTTCGAATCG
Found at i:74108541 original size:21 final size:21
Alignment explanation
Indices: 74108510--74108563 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
74108500 TTGGATTCTC
74108510 TCAACAAAAATTGTAAAATAAT
1 TCAA-AAAAATTGTAAAATAAT
74108532 TCAAAAAAATTGTAAAATAAT
1 TCAAAAAAATTGTAAAATAAT
*
74108553 TCAAAATAATT
1 TCAAAAAAATT
74108564 TTCAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (21 bp):
TCAAAAAAATTGTAAAATAAT
Found at i:74108583 original size:10 final size:10
Alignment explanation
Indices: 74108518--74108620 Score: 70
Period size: 10 Copynumber: 10.2 Consensus size: 10
74108508 TCTCAACAAA
74108518 AATTGTAAAAT
1 AATT-TAAAAT
* *
74108529 AATTCAAAAA
1 AATTTAAAAT
74108539 AATTGTAAAAT
1 AATT-TAAAAT
*
74108550 AATTCAAAAT
1 AATTTAAAAT
*
74108560 AATTTTCAAA-
1 AA-TTTAAAAT
74108570 AATTTAAAAT
1 AATTTAAAAT
**
74108580 AATTTTTAA-
1 AATTTAAAAT
*
74108589 AATTCAAAAT
1 AATTTAAAAT
74108599 -ATTTATAAA-
1 AATTTA-AAAT
74108608 AATTTCAAAAT
1 AATTT-AAAAT
74108619 AA
1 AA
74108621 ATTCTAAAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
9 16 0.23
10 34 0.49
11 20 0.29
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:74108592 original size:19 final size:19
Alignment explanation
Indices: 74108529--74108630 Score: 98
Period size: 20 Copynumber: 5.1 Consensus size: 19
74108519 ATTGTAAAAT
* *
74108529 AATTCAAAAAAATTGTAAAA
1 AATTCAAAATAATT-TTAAA
74108549 TAATTCAAAATAATTTTCAAA
1 -AATTCAAAATAATTTT-AAA
* *
74108570 AATTTAAAATAATTTTTAA
1 AATTCAAAATAATTTTAAA
74108589 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
*
74108608 AATTTCAAAATAAATTCTAAA
1 AA-TTCAAAAT-AATTTTAAA
74108629 AA
1 AA
74108631 ATATATAAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.06
19 16 0.23
20 24 0.35
21 22 0.32
22 3 0.04
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:74108593 original size:39 final size:39
Alignment explanation
Indices: 74108550--74108629 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
74108540 ATTGTAAAAT
* *
74108550 AATTCAAAATAATTT-TCAAAAATTT-AAAATAATTTTTAA
1 AATTCAAAAT-ATTTAT-AAAAATTTCAAAATAAATTCTAA
74108589 AATTCAAAATATTTATAAAAATTTCAAAATAAATTCTAA
1 AATTCAAAATATTTATAAAAATTTCAAAATAAATTCTAA
74108628 AA
1 AA
74108630 AATATATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 25 0.68
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (39 bp):
AATTCAAAATATTTATAAAAATTTCAAAATAAATTCTAA
Found at i:74108617 original size:27 final size:27
Alignment explanation
Indices: 74108564--74108618 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
74108554 CAAAATAATT
*
74108564 TTCAAAAATTTAAAATAATTTTTAAAA
1 TTCAAAAATTTAAAATAATTTTCAAAA
74108591 TTCAAAATATTTATAAA-AA-TTTCAAAA
1 TTCAAAA-ATTTA-AAATAATTTTCAAAA
74108618 T
1 T
74108619 AAATTCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 15 0.60
28 7 0.28
29 3 0.12
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (27 bp):
TTCAAAAATTTAAAATAATTTTCAAAA
Found at i:74108630 original size:21 final size:20
Alignment explanation
Indices: 74108518--74108632 Score: 106
Period size: 21 Copynumber: 5.7 Consensus size: 20
74108508 TCTCAACAAA
*
74108518 AATTGTAAAATAATTCAAAAA
1 AATTGTAAAA-AATTCAAAAT
74108539 AATTGTAAAATAATTCAAAAT
1 AATTGTAAAA-AATTCAAAAT
* * *
74108560 AATTTTCAAAAATTTAAAAT
1 AATTGTAAAAAATTCAAAAT
**
74108580 AATT-TTTAAAATTCAAAAT
1 AATTGTAAAAAATTCAAAAT
* * *
74108599 ATTTATAAAAATTTCAAAAT
1 AATTGTAAAAAATTCAAAAT
*
74108619 AAATTCTAAAAAAT
1 -AATTGTAAAAAAT
74108633 ATATAAAGTT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 15 0.19
20 25 0.32
21 38 0.49
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (20 bp):
AATTGTAAAAAATTCAAAAT
Found at i:74110075 original size:16 final size:16
Alignment explanation
Indices: 74110054--74110087 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
74110044 AAAACAATTC
*
74110054 ATATATAGACTTTTTT
1 ATATATAAACTTTTTT
*
74110070 ATATATAAATTTTTTT
1 ATATATAAACTTTTTT
74110086 AT
1 AT
74110088 CCAATTCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (16 bp):
ATATATAAACTTTTTT
Found at i:74116190 original size:24 final size:25
Alignment explanation
Indices: 74116163--74116210 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
74116153 TGTGTTCACG
74116163 TTATATATT-ATAAAAATAATATAC
1 TTATATATTCATAAAAATAATATAC
*
74116187 TTATATATTCATAAAAATATTATA
1 TTATATATTCATAAAAATAATATA
74116211 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
TTATATATTCATAAAAATAATATAC
Found at i:74116866 original size:43 final size:43
Alignment explanation
Indices: 74116802--74116966 Score: 190
Period size: 43 Copynumber: 3.9 Consensus size: 43
74116792 TTATGTGGGA
* *
74116802 AAACGCCGTTATAGAACATGATCTTTAGCAACACTTTTCCTAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGACACTTTTCCTAC
* *
74116845 AAACGCCGCTATAGAATATGATCTTTAG-GTCACTTTTCCTAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGACACTTTTCCTAC
* * * * * **
74116887 AAATGCTGCTATAGAACATGATATTTAGCGGCGCTTTTATTAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGACACTTTTCCTAC
* * *
74116930 AAACGCCACTAAAGAACATGATTTTTAGCGAC-CTTTT
1 AAACGCCGCTATAGAACATGATCTTTAGCGACACTTTT
74116967 TTTTTTACAA
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 41 0.40
43 62 0.60
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGATCTTTAGCGACACTTTTCCTAC
Found at i:74116966 original size:85 final size:85
Alignment explanation
Indices: 74116811--74116966 Score: 197
Period size: 85 Copynumber: 1.8 Consensus size: 85
74116801 AAAACGCCGT
* * * * * *
74116811 TATAGAACATGATCTTTAGCAACACTTTTCCTACAAACGCCGCTATAGAATATGATCTTTAGGTC
1 TATAGAACATGATATTTAGCAACACTTTTACTACAAACGCCACTAAAGAACATGATCTTTAGGAC
74116876 ACTTTTCCTACAAATGCTGC
66 ACTTTTCCTACAAATGCTGC
** * * *
74116896 TATAGAACATGATATTTAGCGGCGCTTTTATTACAAACGCCACTAAAGAACATGATTTTTAGCGA
1 TATAGAACATGATATTTAGCAACACTTTTACTACAAACGCCACTAAAGAACATGATCTTTAG-GA
74116961 C-CTTTT
65 CACTTTT
74116967 TTTTTTACAA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
85 57 0.97
86 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (85 bp):
TATAGAACATGATATTTAGCAACACTTTTACTACAAACGCCACTAAAGAACATGATCTTTAGGAC
ACTTTTCCTACAAATGCTGC
Found at i:74117385 original size:21 final size:21
Alignment explanation
Indices: 74117343--74117395 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
74117333 ATTTTCTTGT
* * *
74117343 TGCCTCTGCTGCCTTTGCTGC
1 TGCCTCTGCTTCCCTCGCTGC
*
74117364 TGCCTCTGCTTCCCTCGTTGC
1 TGCCTCTGCTTCCCTCGCTGC
*
74117385 TGCCTCCGCTT
1 TGCCTCTGCTT
74117396 TAAGTTTTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.00, C:0.42, G:0.21, T:0.38
Consensus pattern (21 bp):
TGCCTCTGCTTCCCTCGCTGC
Found at i:74120720 original size:17 final size:17
Alignment explanation
Indices: 74120700--74120732 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
74120690 TTTTGCACCT
74120700 CCCACCATTTTCAACTC
1 CCCACCATTTTCAACTC
*
74120717 CCCACTATTTTCAACT
1 CCCACCATTTTCAACT
74120733 AAAAAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.42, G:0.00, T:0.33
Consensus pattern (17 bp):
CCCACCATTTTCAACTC
Found at i:74125338 original size:21 final size:21
Alignment explanation
Indices: 74125314--74125353 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
74125304 TTACCTTCTA
*
74125314 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
74125335 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
74125354 CATTGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:74133907 original size:30 final size:30
Alignment explanation
Indices: 74133871--74133932 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
74133861 CAAGTAGCCG
* *
74133871 AAGCTAGTTTAAATCGCACATTTAGTGTCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
74133901 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
74133931 AA
1 AA
74133933 ACTTCCGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (30 bp):
AAGCTAGTTTAAATCGCACACTTAGTGCCA
Found at i:74136249 original size:39 final size:39
Alignment explanation
Indices: 74136045--74136267 Score: 232
Period size: 40 Copynumber: 5.6 Consensus size: 39
74136035 TTGAATGCTG
* * * * * *
74136045 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
74136085 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
*
74136125 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
74136165 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
* *
74136205 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
74136244 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
74136268 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 109 0.69
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:74136287 original size:79 final size:80
Alignment explanation
Indices: 74136120--74136302 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
74136110 GTGCGAGATA
* * *
74136120 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
74136185 CAGTCGTGCGAGTTG
66 CAGTCGAACGAGGAG
* * * *
74136200 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
74136264 CATTTGAACGAGGAG
66 CAGTCGAACGAGGAG
* *
74136279 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
74136303 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGGAG
Found at i:74144161 original size:39 final size:39
Alignment explanation
Indices: 74143957--74144179 Score: 232
Period size: 40 Copynumber: 5.6 Consensus size: 39
74143947 TTGAATGCTG
* * * * * *
74143957 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
74143997 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
*
74144037 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
74144077 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
* *
74144117 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
74144156 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
74144180 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 109 0.69
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:74144199 original size:79 final size:80
Alignment explanation
Indices: 74144032--74144214 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
74144022 GTGCGAGATA
* * *
74144032 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
74144097 CAGTCGTGCGAGTTG
66 CAGTCGAACGAGGAG
* * * *
74144112 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
74144176 CATTTGAACGAGGAG
66 CAGTCGAACGAGGAG
* *
74144191 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
74144215 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGGAG
Found at i:74148522 original size:22 final size:22
Alignment explanation
Indices: 74148495--74148539 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
74148485 ATATAATTCG
74148495 TAATAAAGGTAATTTTAGTCTA
1 TAATAAAGGTAATTTTAGTCTA
74148517 TAATAAAGGTAATTTTAGTCTA
1 TAATAAAGGTAATTTTAGTCTA
74148539 T
1 T
74148540 GTATATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (22 bp):
TAATAAAGGTAATTTTAGTCTA
Found at i:74161472 original size:27 final size:27
Alignment explanation
Indices: 74161420--74161498 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
74161410 CCCTTCACGT
* *
74161420 TTCTTTTC-TTTCTTTCTTTT-TATCTA
1 TTCTCTTCTTTTC-TTCTTTTCTTTCTA
74161446 TTCTCTTCTTTTCTTCTTTTCTTTCTA
1 TTCTCTTCTTTTCTTCTTTTCTTTCTA
*
74161473 TTCCCTTCTTTTCTTCTTTTCTTTCT
1 TTCTCTTCTTTTCTTCTTTTCTTTCT
74161499 CTGTTTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
26 14 0.29
27 34 0.71
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (27 bp):
TTCTCTTCTTTTCTTCTTTTCTTTCTA
Found at i:74164050 original size:21 final size:20
Alignment explanation
Indices: 74164022--74164063 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
74164012 CAAAACTTGT
74164022 ATAACTATAATCAAA-CATTC
1 ATAACTATAAT-AAATCATTC
*
74164042 ATAATCTATCATAAATCATTC
1 ATAA-CTATAATAAATCATTC
74164063 A
1 A
74164064 AGCTCATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATAATAAATCATTC
Found at i:74169298 original size:21 final size:21
Alignment explanation
Indices: 74169280--74169320 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
74169270 AGCTATGGTC
*
74169280 GTGGTCGAGCAGGACATGGCA
1 GTGGTCGAGCAGGAAATGGCA
*
74169301 GTGGTCGAGTAGGAAATGGC
1 GTGGTCGAGCAGGAAATGGC
74169321 TGTCGTGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.44, T:0.17
Consensus pattern (21 bp):
GTGGTCGAGCAGGAAATGGCA
Found at i:74177718 original size:20 final size:20
Alignment explanation
Indices: 74177689--74177733 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
74177679 AATGACGGAC
74177689 TTTT-GGACTTTTAATTTTG-
1 TTTTGGGAC-TTTAATTTTGA
74177708 TTTTGGGACTTTAATTTTGA
1 TTTTGGGACTTTAATTTTGA
74177728 TTTTGG
1 TTTTGG
74177734 TATTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.60
Consensus pattern (20 bp):
TTTTGGGACTTTAATTTTGA
Found at i:74186383 original size:68 final size:68
Alignment explanation
Indices: 74186309--74186445 Score: 195
Period size: 68 Copynumber: 2.0 Consensus size: 68
74186299 AATTGATAGC
* * * *
74186309 TAATCTACCCTAAAACCCAAATTCAAAGTTAGTTACAAACCCT-GAACTGAGTTAATCTTCTTGA
1 TAATCTACCATAAAACCCAAATTCAAAGTTAGTTACAAACCCTAAAAC-GAGTTAATATTCATGA
74186373 TTGG
65 TTGG
* * *
74186377 TAATCTACCATAAATCTCAAATTCAAAGTTAGTTACAAACCTTAAAACGAGTTAATATTCATGAT
1 TAATCTACCATAAAACCCAAATTCAAAGTTAGTTACAAACCCTAAAACGAGTTAATATTCATGAT
74186442 TGG
66 TGG
74186445 T
1 T
74186446 TTATTGATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 58 0.95
69 3 0.05
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (68 bp):
TAATCTACCATAAAACCCAAATTCAAAGTTAGTTACAAACCCTAAAACGAGTTAATATTCATGAT
TGG
Found at i:74195557 original size:26 final size:26
Alignment explanation
Indices: 74195521--74195572 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
74195511 CACACAAGAG
74195521 TAAGCTTATGAAAGCTTAGTAAGCTC
1 TAAGCTTATGAAAGCTTAGTAAGCTC
74195547 TAAGCTTATGAAAGCTTAGTAAGCTC
1 TAAGCTTATGAAAGCTTAGTAAGCTC
74195573 ATAGGCATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (26 bp):
TAAGCTTATGAAAGCTTAGTAAGCTC
Found at i:74195585 original size:26 final size:26
Alignment explanation
Indices: 74195521--74195585 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
74195511 CACACAAGAG
*
74195521 TAAGCTTATGAAAGCTTAGTAAGCTC
1 TAAGCATATGAAAGCTTAGTAAGCTC
*
74195547 TAAGCTTATGAAAGCTTAGTAAGCTC
1 TAAGCATATGAAAGCTTAGTAAGCTC
*
74195573 ATAGGCATA-GAAA
1 -TAAGCATATGAAA
74195586 AATAAATCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 30 0.83
27 6 0.17
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (26 bp):
TAAGCATATGAAAGCTTAGTAAGCTC
Found at i:74195952 original size:39 final size:39
Alignment explanation
Indices: 74195814--74195953 Score: 181
Period size: 39 Copynumber: 3.6 Consensus size: 39
74195804 ATCATGATTT
* * *
74195814 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
* * * * *
74195853 GAAGCCCGTAGGCTAACTAAAGAAAACAAGTGTTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
* * *
74195892 GAAGCCCGAAGGCTCATTGAAGCACACAAGTGCTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
74195931 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
74195954 TCATCAGAGC
Statistics
Matches: 83, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 83 1.00
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:74196473 original size:9 final size:9
Alignment explanation
Indices: 74196459--74196487 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
74196449 TTGCCCCAAA
74196459 TTTTACAAT
1 TTTTACAAT
74196468 TTTTACAAT
1 TTTTACAAT
74196477 TTTTACAAT
1 TTTTACAAT
74196486 TT
1 TT
74196488 AGTCCCTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTACAAT
Found at i:74197809 original size:21 final size:20
Alignment explanation
Indices: 74197794--74197832 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
74197784 GATAAAATTG
74197794 GAAAAATAA-AAAATAAAGAT
1 GAAAAATAATAAAATAAA-AT
*
74197814 GATAAATAATAAAATAAAA
1 GAAAAATAATAAAATAAAA
74197833 CAAAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (20 bp):
GAAAAATAATAAAATAAAAT
Found at i:74198868 original size:26 final size:26
Alignment explanation
Indices: 74198839--74198889 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
74198829 CCCATTATAT
74198839 GGCTCTTCATGAGCTTCCTGATTAAA
1 GGCTCTTCATGAGCTTCCTGATTAAA
**
74198865 GGCTCTTTGTGAGCTTCCTGATTAA
1 GGCTCTTCATGAGCTTCCTGATTAA
74198890 TGACTGGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCTGATTAAA
Found at i:74205362 original size:23 final size:24
Alignment explanation
Indices: 74205335--74205386 Score: 97
Period size: 23 Copynumber: 2.2 Consensus size: 24
74205325 TGAAGAGGTT
74205335 GATAGAGAAAATTAAAGAGACT-G
1 GATAGAGAAAATTAAAGAGACTGG
74205358 GATAGAGAAAATTAAAGAGACTGG
1 GATAGAGAAAATTAAAGAGACTGG
74205382 GATAG
1 GATAG
74205387 GGAAGTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.50, C:0.04, G:0.29, T:0.17
Consensus pattern (24 bp):
GATAGAGAAAATTAAAGAGACTGG
Found at i:74206484 original size:40 final size:38
Alignment explanation
Indices: 74206439--74206537 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 38
74206429 ACGGTACTCT
* * *
74206439 ATGGTGCGTAGGGTTGAATGGGTTGATTTTATCCCCAT
1 ATGGTGTGTAGGGTTGAATGGGTCGATTTTATCCCCAC
* * **
74206477 ATTTGGTGTGTAGAGATGGGTGGGTCGATTTTATCCCCAC
1 A--TGGTGTGTAGGGTTGAATGGGTCGATTTTATCCCCAC
*
74206517 ATGGTGTGTTGGGTTGAATGG
1 ATGGTGTGTAGGGTTGAATGG
74206538 AGATGGTGTG
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
38 16 0.34
40 31 0.66
ACGTcount: A:0.17, C:0.11, G:0.35, T:0.36
Consensus pattern (38 bp):
ATGGTGTGTAGGGTTGAATGGGTCGATTTTATCCCCAC
Found at i:74212816 original size:8 final size:8
Alignment explanation
Indices: 74212802--74212834 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
74212792 ATTTAAGTAA
74212802 ATATTATT
1 ATATTATT
*
74212810 TTATTATT
1 ATATTATT
74212818 ATATTATT
1 ATATTATT
74212826 ATATT-TT
1 ATATTATT
74212833 AT
1 AT
74212835 TAATTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
ATATTATT
Found at i:74213003 original size:18 final size:18
Alignment explanation
Indices: 74212960--74212997 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
74212950 ATATATATTA
*
74212960 TAAT-ATAATAATATAAC
1 TAATAATAATAATACAAC
74212977 TAATAATAATAATACAAC
1 TAATAATAATAATACAAC
74212995 TAA
1 TAA
74212998 ACATAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATACAAC
Found at i:74213024 original size:14 final size:15
Alignment explanation
Indices: 74212985--74213027 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
74212975 ACTAATAATA
* *
74212985 ATAATACAACTAAAC
1 ATAAAACAAATAAAC
74213000 ATAAAACAAATAAAC
1 ATAAAACAAATAAAC
*
74213015 -TAAAAGAAATAAA
1 ATAAAACAAATAAA
74213028 AGATAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.70, C:0.12, G:0.02, T:0.16
Consensus pattern (15 bp):
ATAAAACAAATAAAC
Found at i:74215818 original size:42 final size:42
Alignment explanation
Indices: 74215707--74215861 Score: 206
Period size: 42 Copynumber: 3.7 Consensus size: 42
74215697 TATCATACCA
* *
74215707 ATGCCATATCCCAGATATGGTCTTACATGTAA-TCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACG-AAGTCTCATATCG
* *
74215749 ATGCCAATAGCCCAGCTATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
* *
74215792 ATGCCATATCCCAGATATGGTCTTACAC-ACAGTCTTATATTG
1 ATGCCATATCCCAGATATGGTCTTACACGA-AGTCTCATATCG
*
74215834 ATGTCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
74215862 ATAGTATTTG
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 65 0.64
43 35 0.35
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
Found at i:74218973 original size:129 final size:129
Alignment explanation
Indices: 74218743--74218999 Score: 496
Period size: 129 Copynumber: 2.0 Consensus size: 129
74218733 AATATAATTA
74218743 AATCAATGCATTATTTACATAAGAACTTACCTCGATACAAAATAGTAGAAATAGGACCTACTCGT
1 AATCAATGCATTATTTACATAAGAACTTACCTCGATACAAAATAGTAGAAATAGGACCTACTCGT
*
74218808 CAAACACCTTGTTTTTCCTCCAATCTAGGTCCAAACCTTGTTTCTCTTGATAATCGAGCTTGAT
66 CAAACACCTTGTTTTTCCTCCAATCTAGGTCCAAACCTTGTTTCTCTTGATAATCAAGCTTGAT
74218872 AATCAATGCATTATTTACATAAGAACTTACCTCGATACAAAATAGTAGAAATAGGACCTACTCGT
1 AATCAATGCATTATTTACATAAGAACTTACCTCGATACAAAATAGTAGAAATAGGACCTACTCGT
*
74218937 CAAACACTTTGTTTTTCCTCCAATCTAGGTCCAAACCTTGTTTCTCTTGATAATCAAGCTTGA
66 CAAACACCTTGTTTTTCCTCCAATCTAGGTCCAAACCTTGTTTCTCTTGATAATCAAGCTTGA
74219000 AAAGTTTTGA
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 126 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (129 bp):
AATCAATGCATTATTTACATAAGAACTTACCTCGATACAAAATAGTAGAAATAGGACCTACTCGT
CAAACACCTTGTTTTTCCTCCAATCTAGGTCCAAACCTTGTTTCTCTTGATAATCAAGCTTGAT
Found at i:74230785 original size:3 final size:3
Alignment explanation
Indices: 74230779--74230807 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
74230769 TTGTTGTTGT
74230779 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
74230808 TACCGAATCA
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:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:74231191 original size:2 final size:2
Alignment explanation
Indices: 74231186--74231228 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
74231176 TTATTTTTTG
74231186 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
74231228 T
1 T
74231229 AAGAATCCGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:74232196 original size:66 final size:66
Alignment explanation
Indices: 74232090--74232214 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
74232080 ATAATGCATT
* * * *
74232090 ATGTCAAAATTAACCCTTAACGTTTACATTTTTTATCAATTTGGCTCTTATTCTTTTTTTGGTAT
1 ATGTCAAAATTAACCCTTAACGTTTACATCTTTTATCAATTTAGCCCTTATTATTTTTTTGGTAT
74232155 A
66 A
* * *
74232156 ATGTCAAATTTTACCCTTAATGTTTACATCTTTTATCAATTTAGCCCTTATTATTTTTT
1 ATGTCAAAATTAACCCTTAACGTTTACATCTTTTATCAATTTAGCCCTTATTATTTTTT
74232215 AAAATTACTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (66 bp):
ATGTCAAAATTAACCCTTAACGTTTACATCTTTTATCAATTTAGCCCTTATTATTTTTTTGGTAT
A
Found at i:74233559 original size:13 final size:12
Alignment explanation
Indices: 74233537--74233570 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
74233527 GACCCGCCTG
74233537 TATTAATTTTTTA
1 TATT-ATTTTTTA
74233550 TATTA-TTTTTA
1 TATTATTTTTTA
74233561 TATTATTTTT
1 TATTATTTTT
74233571 AAATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 5 0.25
13 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:74233576 original size:13 final size:11
Alignment explanation
Indices: 74233544--74233571 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
74233534 CTGTATTAAT
74233544 TTTTTATATTA
1 TTTTTATATTA
74233555 TTTTTATATTA
1 TTTTTATATTA
74233566 TTTTTA
1 TTTTTA
74233572 AATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:74233752 original size:30 final size:31
Alignment explanation
Indices: 74233693--74233756 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
74233683 ACTTAGCAAG
74233693 CAAATGCCTCTAAAATAATAATAAAAATTAA
1 CAAATGCCTCTAAAATAATAATAAAAATTAA
* *
74233724 CAAATGCCTTTAAAATAATAA-CAAAATTAA
1 CAAATGCCTCTAAAATAATAATAAAAATTAA
74233754 CAA
1 CAA
74233757 TATACAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (31 bp):
CAAATGCCTCTAAAATAATAATAAAAATTAA
Found at i:74237948 original size:16 final size:16
Alignment explanation
Indices: 74237923--74237961 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
74237913 TGTAAAGTTA
*
74237923 CTAATAATATCAATTT
1 CTAATTATATCAATTT
74237939 CTAATTATATCAATTT
1 CTAATTATATCAATTT
74237955 CGTAATT
1 C-TAATT
74237962 TTCCTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (16 bp):
CTAATTATATCAATTT
Found at i:74238954 original size:16 final size:16
Alignment explanation
Indices: 74238933--74238970 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
74238923 TCGAAGTACA
*
74238933 ATTTTATCATTATATT
1 ATTTTATAATTATATT
*
74238949 ATTTTATAATTCTATT
1 ATTTTATAATTATATT
74238965 ATTTTA
1 ATTTTA
74238971 GAGGAGACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTATAATTATATT
Found at i:74241681 original size:13 final size:13
Alignment explanation
Indices: 74241663--74241687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74241653 CCTCACACAG
74241663 CCGTGTCATGCGC
1 CCGTGTCATGCGC
74241676 CCGTGTCATGCG
1 CCGTGTCATGCG
74241688 TACACTGTAA
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:0.36, G:0.32, T:0.24
Consensus pattern (13 bp):
CCGTGTCATGCGC
Found at i:74245827 original size:23 final size:23
Alignment explanation
Indices: 74245801--74245851 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
74245791 TTCTGAGAGG
74245801 TTAAAACATAATTTTATC-ATTT
1 TTAAAACATAATTTTATCAATTT
***
74245823 ATTAATTTATAATTTTATCAATTT
1 -TTAAAACATAATTTTATCAATTT
74245847 TTAAA
1 TTAAA
74245852 GGAATTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAAACATAATTTTATCAATTT
Found at i:74246961 original size:21 final size:21
Alignment explanation
Indices: 74246914--74246963 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
74246904 TGCGTATAAT
* * *
74246914 AAAATATATATACTAATACTA
1 AAAATAAATATACTAAGAATA
* *
74246935 ATAATAAATATACTAGGAATA
1 AAAATAAATATACTAAGAATA
74246956 AAAATAAA
1 AAAATAAA
74246964 ATAATAGTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAATAAATATACTAAGAATA
Found at i:74247636 original size:26 final size:27
Alignment explanation
Indices: 74247592--74247645 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
74247582 TTGCATAAAC
*
74247592 ATATACATATATATATTAAAGATATAT
1 ATATACATATATATATTAAAAATATAT
74247619 ATATACATA-ATATATTAAAAATATAT
1 ATATACATATATATATTAAAAATATAT
74247645 A
1 A
74247646 CAATATATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATACATATATATATTAAAAATATAT
Found at i:74247659 original size:26 final size:25
Alignment explanation
Indices: 74247598--74247659 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
74247588 AAACATATAC
* *
74247598 ATATATATATTAAAGATATATATAT
1 ATATATATATTAAAAATATATAAAT
*
74247623 ACATAATATATTAAAAATATATACAAT
1 ATAT-ATATATTAAAAATATATA-AAT
*
74247650 ATATACATAT
1 ATATATATAT
74247660 ATTGGAAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 3 0.10
26 22 0.73
27 5 0.17
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATATATATTAAAAATATATAAAT
Found at i:74247774 original size:21 final size:21
Alignment explanation
Indices: 74247740--74247779 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
74247730 ATATGTAATA
*
74247740 ATAGTGTTAAAAATATACAAT
1 ATAGTATTAAAAATATACAAT
*
74247761 ATAGTATTAGAAATATACA
1 ATAGTATTAAAAATATACA
74247780 TACAATAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
ATAGTATTAAAAATATACAAT
Found at i:74248558 original size:13 final size:13
Alignment explanation
Indices: 74248542--74248582 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
74248532 AGAAAAAAAA
*
74248542 AGAGAGAAAAGGG
1 AGAGAGGAAAGGG
74248555 AGAG-GGAAAGGG
1 AGAGAGGAAAGGG
*
74248567 AGAAAGGAAAGGG
1 AGAGAGGAAAGGG
74248580 AGA
1 AGA
74248583 AGGGATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (13 bp):
AGAGAGGAAAGGG
Found at i:74248564 original size:12 final size:13
Alignment explanation
Indices: 74248549--74248587 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
74248539 AAAAGAGAGA
74248549 AAAGGGAG-AGGG
1 AAAGGGAGAAGGG
*
74248561 AAAGGGAGAAAGG
1 AAAGGGAGAAGGG
74248574 AAAGGGAGAAGGG
1 AAAGGGAGAAGGG
74248587 A
1 A
74248588 TTTTCAGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (13 bp):
AAAGGGAGAAGGG
Found at i:74257615 original size:16 final size:16
Alignment explanation
Indices: 74257570--74257617 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
74257560 TATTGCAACC
*
74257570 AAATTTATAATTAAACT
1 AAATTTATAA-TAAAAT
74257587 AAATTTA-AATAAAAT
1 AAATTTATAATAAAAT
*
74257602 ATATTTATAATAAAAT
1 AAATTTATAATAAAAT
74257618 TTAGAGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 11 0.39
16 10 0.36
17 7 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTATAATAAAAT
Found at i:74258065 original size:29 final size:32
Alignment explanation
Indices: 74258004--74258066 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 32
74257994 CAAGATGAAT
* **
74258004 TTATAAATTTTTTTAGAAAGGTCAAAATTTAA
1 TTATAAATTTTTTGAGAAAGGTCAAAACATAA
74258036 TTAT-AATTTTTTGAG-AA-GTCAAAACATAA
1 TTATAAATTTTTTGAGAAAGGTCAAAACATAA
74258065 TT
1 TT
74258067 TTACCATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.43
30 2 0.07
31 10 0.36
32 4 0.14
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (32 bp):
TTATAAATTTTTTGAGAAAGGTCAAAACATAA
Done.