Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 174 of 206
Found at i:53061368 original size:12 final size:11
Alignment explanation
Indices: 53061340--53061379 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
53061330 ACCATTTCTT
* *
53061340 ATTTTTTTTAC
1 ATTTTTTTAAA
53061351 ATTTTTTTAAA
1 ATTTTTTTAAA
53061362 ATATTTTTTAAA
1 AT-TTTTTTAAA
53061374 ATTTTT
1 ATTTTT
53061380 AAACTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTTTTTAAA
Found at i:53068217 original size:52 final size:52
Alignment explanation
Indices: 53068112--53068217 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
53068102 TTCAATGATT
* * * **
53068112 AATTTATTAATAAATTAATGAAAAAATTACTGGTTTAAGTGAAGAAATTGTA
1 AATTTATTAATAAATTAATGAAAAAATTAATAGTTGAAGTGAAGAAACGGTA
* * *
53068164 AATTTATTAATAAATTAGTGAAAAAATTAATAGTTGAAGTGATGAAGCGGTA
1 AATTTATTAATAAATTAATGAAAAAATTAATAGTTGAAGTGAAGAAACGGTA
53068216 AA
1 AA
53068218 ACTAGCAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (52 bp):
AATTTATTAATAAATTAATGAAAAAATTAATAGTTGAAGTGAAGAAACGGTA
Found at i:53069820 original size:20 final size:21
Alignment explanation
Indices: 53069795--53069833 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53069785 TCTATTTGTT
*
53069795 ATTAATTA-TTTTATTATTAA
1 ATTAATTACTTTTACTATTAA
53069815 ATTAATTACTTTTACTATT
1 ATTAATTACTTTTACTATT
53069834 GCTCTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTAATTACTTTTACTATTAA
Found at i:53069846 original size:3 final size:3
Alignment explanation
Indices: 53069838--53069868 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
53069828 ACTATTGCTC
53069838 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
53069869 TCTATACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:53070001 original size:2 final size:2
Alignment explanation
Indices: 53069994--53070020 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53069984 ATACATGATG
53069994 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
53070021 GCATTGACAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53070241 original size:19 final size:20
Alignment explanation
Indices: 53070219--53070268 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
53070209 AAAATTTACT
*
53070219 TATATATCTTACTTT-TAAA
1 TATATATCATACTTTGTAAA
*
53070238 TATACA-CATACTTTGTAAA
1 TATATATCATACTTTGTAAA
*
53070257 TACATATACATA
1 TATATAT-CATA
53070269 TATAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
21 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (20 bp):
TATATATCATACTTTGTAAA
Found at i:53077790 original size:92 final size:92
Alignment explanation
Indices: 53077638--53077815 Score: 320
Period size: 92 Copynumber: 1.9 Consensus size: 92
53077628 GCATTCCAAG
*
53077638 TAGAAGTATCTTCATTAATTAATTGATTCACCATAGTCCATCTAATATCAATGTTCTGACACGAA
1 TAGAAGTATCTTCATTAATTAACTGATTCACCATAGTCCATCTAATATCAATGTTCTGACACGAA
*
53077703 ACCCTCCCATCTCCAGGTTCAAGTATC
66 ACCCTCCCATCTCCAAGTTCAAGTATC
* *
53077730 TAGAAGTATCTTCATTAATTAACTGATTCACCATAGTCCATCTAATATCAATGTTTTGACACGAG
1 TAGAAGTATCTTCATTAATTAACTGATTCACCATAGTCCATCTAATATCAATGTTCTGACACGAA
53077795 ACCCTCCCATCTCCAAGTTCA
66 ACCCTCCCATCTCCAAGTTCA
53077816 GGCAGCTAGA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 82 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (92 bp):
TAGAAGTATCTTCATTAATTAACTGATTCACCATAGTCCATCTAATATCAATGTTCTGACACGAA
ACCCTCCCATCTCCAAGTTCAAGTATC
Found at i:53085834 original size:16 final size:16
Alignment explanation
Indices: 53085813--53085843 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53085803 CACCTAAGAC
53085813 ACACCTCAATCTTATA
1 ACACCTCAATCTTATA
*
53085829 ACACCTTAATCTTAT
1 ACACCTCAATCTTAT
53085844 CAAATTATTA
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:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (16 bp):
ACACCTCAATCTTATA
Found at i:53086627 original size:15 final size:15
Alignment explanation
Indices: 53086607--53086635 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53086597 ATGCCTTACA
53086607 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
53086622 CACCGTGTTATCAA
1 CACCGTGTTATCAA
53086636 GCAACAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:53097187 original size:27 final size:25
Alignment explanation
Indices: 53097125--53097194 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 25
53097115 ATGTACATGT
* *
53097125 ATGCTCACATGAGCTGTGAATTAGA
1 ATGCTCACACGAGCTGTGAATGAGA
*
53097150 ATGCTCACACGAGCTGTGAAAATGAGC
1 ATGCTCACACGAGCTGTG--AATGAGA
* *
53097177 CTGCTCACACGAACTGTG
1 ATGCTCACACGAGCTGTG
53097195 GGTCGGAACG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 17 0.45
27 21 0.55
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAATGAGA
Found at i:53104899 original size:18 final size:20
Alignment explanation
Indices: 53104861--53104910 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
53104851 AATTTATAAT
*
53104861 TTTGTTAAAATATTGTAAAA
1 TTTGTTAAAATATTATAAAA
53104881 TTT-TTAAAA-ATTATAAAA
1 TTTGTTAAAATATTATAAAA
53104899 TTTGTTAAAATA
1 TTTGTTAAAATA
53104911 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 11 0.41
19 12 0.44
20 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
TTTGTTAAAATATTATAAAA
Found at i:53104948 original size:40 final size:40
Alignment explanation
Indices: 53104876--53104956 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
53104866 TAAAATATTG
* * *
53104876 TAAAATTTTTAAAAATTATAAAATTTGTTAAAATAAAAAA
1 TAAAATTATTAAAAATGATAAAATTTATTAAAATAAAAAA
*
53104916 TAAAATTATT-AAAATGATAAAATTTATATAAAATAATAAA
1 TAAAATTATTAAAAATGATAAAATTTAT-TAAAATAAAAAA
53104956 T
1 T
53104957 TGTAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (40 bp):
TAAAATTATTAAAAATGATAAAATTTATTAAAATAAAAAA
Found at i:53104949 original size:19 final size:17
Alignment explanation
Indices: 53104909--53104977 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
53104899 TTTGTTAAAA
53104909 TAAAA-AATAAAATTAT
1 TAAAATAATAAAATTAT
*
53104925 TAAAATGATAAAATTTAT
1 TAAAATAATAAAA-TTAT
*
53104943 ATAAAATAAT-AAATTGT
1 -TAAAATAATAAAATTAT
*
53104960 AAAAATATAATAAAATTA
1 -TAAA-ATAATAAAATTA
53104978 CAGATTTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
16 5 0.12
17 13 0.30
18 12 0.28
19 13 0.30
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATAATAAAATTAT
Found at i:53104956 original size:18 final size:18
Alignment explanation
Indices: 53104908--53104957 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
53104898 ATTTGTTAAA
*
53104908 ATAAAA-AATAAAATTAT
1 ATAAAATAATAAATTTAT
*
53104925 -TAAAATGATAAAATTTAT
1 ATAAAATAAT-AAATTTAT
53104943 ATAAAATAATAAATT
1 ATAAAATAATAAATT
53104958 GTAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 5 0.19
17 2 0.07
18 12 0.44
19 8 0.30
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
ATAAAATAATAAATTTAT
Found at i:53106914 original size:5 final size:5
Alignment explanation
Indices: 53106884--53106913 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
53106874 TATATCCCAA
*
53106884 TTTTC TTTTC TTTTC TTTTC TTTTC ATTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
53106914 AACATCAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:53110743 original size:29 final size:29
Alignment explanation
Indices: 53110701--53110762 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
53110691 ATTAAATTAG
53110701 ATGCTTTTGTTTTTGTCCCTATAGCTCTA
1 ATGCTTTTGTTTTTGTCCCTATAGCTCTA
53110730 ATGCTTTTGTTTTTGTCCCTATAGCTCTA
1 ATGCTTTTGTTTTTGTCCCTATAGCTCTA
53110759 ATGC
1 ATGC
53110763 CCCTTCAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.50
Consensus pattern (29 bp):
ATGCTTTTGTTTTTGTCCCTATAGCTCTA
Found at i:53112302 original size:42 final size:42
Alignment explanation
Indices: 53112255--53112405 Score: 178
Period size: 42 Copynumber: 3.6 Consensus size: 42
53112245 AGGCTGAACT
* * * **
53112255 GAAGCTCATGAGAGCTAAACGGAAACTCGTAAGGGTTGAATG
1 GAAGCTCATAAGAGCTAAACGGAAACTCATAAGGGTTAAACA
* * *
53112297 GAAGCTCGTAAGAGCTGAACGGAAACCCATAAGGGTTAAACA
1 GAAGCTCATAAGAGCTAAACGGAAACTCATAAGGGTTAAACA
* * *
53112339 GAAGCTCA-ATAGAGCTGAACGGAAACTCATATGAGTTAAACA
1 GAAGCTCATA-AGAGCTAAACGGAAACTCATAAGGGTTAAACA
*
53112381 GAAGCTCGTAAGAGCTAAACGGAAA
1 GAAGCTCATAAGAGCTAAACGGAAA
53112406 GTAAACACGA
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 91 0.98
43 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACGGAAACTCATAAGGGTTAAACA
Found at i:53112315 original size:21 final size:21
Alignment explanation
Indices: 53112247--53112404 Score: 93
Period size: 21 Copynumber: 7.5 Consensus size: 21
53112237 AAGCCCGAAG
* * *
53112247 GCTGAACTGAAGCTCATGAGA
1 GCTGAACGGAAGCTCGTAAGA
* * *
53112268 GCTAAACGGAAACTCGTAAGG
1 GCTGAACGGAAGCTCGTAAGA
* *
53112289 GTTGAATGGAAGCTCGTAAGA
1 GCTGAACGGAAGCTCGTAAGA
* * * *
53112310 GCTGAACGGAAACCCATAAGG
1 GCTGAACGGAAGCTCGTAAGA
* * * *
53112331 GTTAAACAGAAGCTC-AATAGA
1 GCTGAACGGAAGCTCGTA-AGA
* * *
53112352 GCTGAACGGAAACTCATATGA
1 GCTGAACGGAAGCTCGTAAGA
* * *
53112373 GTTAAACAGAAGCTCGTAAGA
1 GCTGAACGGAAGCTCGTAAGA
*
53112394 GCTAAACGGAA
1 GCTGAACGGAA
53112405 AGTAAACACG
Statistics
Matches: 97, Mismatches: 38, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
20 1 0.01
21 95 0.98
22 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCTGAACGGAAGCTCGTAAGA
Found at i:53115724 original size:9 final size:9
Alignment explanation
Indices: 53115705--53115756 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
53115695 TTTTTTCTCT
*
53115705 AAAACCTTA
1 AAAACCCTA
*
53115714 AAAATCCTA
1 AAAACCCTA
53115723 AAAACCCT-
1 AAAACCCTA
53115731 AAAACCCT-
1 AAAACCCTA
53115739 -AAACCCT-
1 AAAACCCTA
53115746 -AAACCCTA
1 AAAACCCTA
53115754 AAA
1 AAA
53115757 TCCAAAAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
7 14 0.37
8 8 0.21
9 16 0.42
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAACCCTA
Found at i:53115725 original size:8 final size:8
Alignment explanation
Indices: 53115703--53115766 Score: 60
Period size: 8 Copynumber: 8.0 Consensus size: 8
53115693 ACTTTTTTCT
53115703 CTAAAACC
1 CTAAAACC
* *
53115711 TTAAAAATC
1 CT-AAAACC
53115720 CTAAAAACC
1 CT-AAAACC
53115729 CTAAAACC
1 CTAAAACC
53115737 CT-AAACC
1 CTAAAACC
53115744 CT-AAACC
1 CTAAAACC
*
53115751 CTAAAATC
1 CTAAAACC
*
53115759 CAAAAACC
1 CTAAAACC
53115767 TACAAGTCAG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
7 14 0.30
8 19 0.40
9 14 0.30
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.16
Consensus pattern (8 bp):
CTAAAACC
Found at i:53115744 original size:7 final size:7
Alignment explanation
Indices: 53115724--53115755 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
53115714 AAAATCCTAA
53115724 AAACCCT
1 AAACCCT
53115731 AAAACCCT
1 -AAACCCT
53115739 AAACCCT
1 AAACCCT
53115746 AAACCCT
1 AAACCCT
53115753 AAA
1 AAA
53115756 ATCCAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:53115768 original size:22 final size:22
Alignment explanation
Indices: 53115724--53115768 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53115714 AAAATCCTAA
* *
53115724 AAACCCTAAAACCCTAAACCCT
1 AAACCCTAAAACCCAAAAACCT
*
53115746 AAACCCTAAAATCCAAAAACCT
1 AAACCCTAAAACCCAAAAACCT
53115768 A
1 A
53115769 CAAGTCAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.36, G:0.00, T:0.13
Consensus pattern (22 bp):
AAACCCTAAAACCCAAAAACCT
Found at i:53123306 original size:33 final size:33
Alignment explanation
Indices: 53123269--53123416 Score: 91
Period size: 33 Copynumber: 4.3 Consensus size: 33
53123259 ATAACCTAAT
53123269 TATGGTCTTATCATCAAAATGCCATAGCCCAGC
1 TATGGTCTTATCATCAAAATGCCATAGCCCAGC
* * * * *
53123302 TATGGTCTTACACATGTATATATATTGCCATGGTCCAAC
1 TATGGTCTTA-TCAT-CA-A-A-A-TGCCATAGCCCAGC
* * ** * * *
53123341 CATGGTCTTA-CGTTCAAGGTGCCATAACCTAGT
1 TATGGTCTTATC-ATCAAAATGCCATAGCCCAGC
* * *
53123374 TATGGTCTTTTCATTAAAATGCCATAGCCCATC
1 TATGGTCTTATCATCAAAATGCCATAGCCCAGC
53123407 TATGGTCTTA
1 TATGGTCTTA
53123417 CATTTAAGAA
Statistics
Matches: 80, Mismatches: 27, Indels: 16
0.65 0.22 0.13
Matches are distributed among these distances:
33 48 0.60
34 4 0.05
35 1 0.01
36 2 0.03
37 3 0.04
38 2 0.03
39 20 0.25
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (33 bp):
TATGGTCTTATCATCAAAATGCCATAGCCCAGC
Found at i:53123393 original size:105 final size:100
Alignment explanation
Indices: 53123236--53123451 Score: 288
Period size: 105 Copynumber: 2.1 Consensus size: 100
53123226 TATGACCCTG
* **
53123236 CCATGGTCTTACTTTGTAGTGCCATAACCTAATTATGGTCTTATCATCAAAATGCCATAGCCCAG
1 CCATGGTCTTACGTTCAAGTGCCATAACCTAATTATGGTCTTATCATCAAAATGCCATAGCCCAG
* * *
53123301 CTATGGTCTTACACATGTATATATATTGCCATGGTCCAA
66 CTATGGTCTT--ACATGTA-AGA-AATACCATGGTCCAA
* * *
53123340 CCATGGTCTTACGTTCAAGGTGCCATAACCTAGTTATGGTCTTTTCATTAAAATGCCATAGCCCA
1 CCATGGTCTTACGTTCAA-GTGCCATAACCTAATTATGGTCTTATCATCAAAATGCCATAGCCCA
* *
53123405 TCTATGGTCTTACATTTAAGAAATACCATGGTCCAA
65 GCTATGGTCTTACATGTAAGAAATACCATGGTCCAA
53123441 CCATGGTCTTA
1 CCATGGTCTTA
53123452 TCCGCCAATT
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
101 24 0.24
102 2 0.02
103 6 0.06
104 15 0.15
105 53 0.53
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (100 bp):
CCATGGTCTTACGTTCAAGTGCCATAACCTAATTATGGTCTTATCATCAAAATGCCATAGCCCAG
CTATGGTCTTACATGTAAGAAATACCATGGTCCAA
Found at i:53125720 original size:29 final size:29
Alignment explanation
Indices: 53125655--53125714 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
53125645 CTCCACATTG
*
53125655 ACACGAATTCTCAATGAACAAGTTCTTCA
1 ACACGAACTCTCAATGAACAAGTTCTTCA
* *
53125684 TCGCGAACTCTCAATGAACAAGTTC-TCA
1 ACACGAACTCTCAATGAACAAGTTCTTCA
53125712 ACA
1 ACA
53125715 ATGAACACCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.25
Consensus pattern (29 bp):
ACACGAACTCTCAATGAACAAGTTCTTCA
Found at i:53130063 original size:14 final size:14
Alignment explanation
Indices: 53130044--53130093 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
53130034 CTCCTTTTCC
53130044 ATTTATTCTATTCT
1 ATTTATTCTATTCT
53130058 ATTTATAT-TATTCT
1 ATTTAT-TCTATTCT
*
53130072 AATTATTCTAATTCT
1 ATTTATTCT-ATTCT
*
53130087 ATGTATT
1 ATTTATT
53130094 TCTTTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 11 0.37
ACGTcount: A:0.28, C:0.10, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTATTCTATTCT
Found at i:53130367 original size:23 final size:22
Alignment explanation
Indices: 53130326--53130370 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
53130316 AACACTCCTT
*
53130326 TAAACAATAAATAAGAAATAAG
1 TAAACAAGAAATAAGAAATAAG
53130348 TAAACAAGAAATTAAGAAATAAG
1 TAAACAAGAAA-TAAGAAATAAG
53130371 GGGGTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.67, C:0.04, G:0.11, T:0.18
Consensus pattern (22 bp):
TAAACAAGAAATAAGAAATAAG
Found at i:53152403 original size:18 final size:17
Alignment explanation
Indices: 53152382--53152424 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
53152372 AAATTTTTTT
53152382 AAATATAAAAATATAAGAA
1 AAATATAAAAA-ATAA-AA
* *
53152401 AATTTTAAAAAATAAAA
1 AAATATAAAAAATAAAA
53152418 AAATATA
1 AAATATA
53152425 TATACACTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 9 0.45
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAATATAAAAAATAAAA
Found at i:53155432 original size:188 final size:189
Alignment explanation
Indices: 53155115--53155492 Score: 632
Period size: 188 Copynumber: 2.0 Consensus size: 189
53155105 GACTCTTACG
*
53155115 ATTAGCACTAATGTGGAGTTATGCCACACATTTTAGACTAAAAAGTGTGTAACGTCGCAACGATG
1 ATTAGCACTAATGTGGAGTTATGCCACACATTTTAGACTAAAAAGTGTGTAACGTCGCAACGAGG
* **
53155180 AACTGTTCTTTGTCCCAACGAGCAGTCAACGTCACGATGAAAAGAAAGCACTCATCTTCACGATG
66 AACTGTTCTTTGTCCCAACGAGCAGTCAACATCACGACAAAAAGAAAGCACTCATCTTCACGATG
* * * *
53155245 TGATCCTTTTTCGTCCCGATGA-GTAATTCCACGTCACAATGTGGCGACGTGCAGTTCA
131 TGATCCTTTTCCGTCCCGATGACGCAATTCCACCTCACAATGTGGCGACGTACAGTTCA
* *
53155303 ATTAGCACTAATGTGGAGTTATGCCTCGCATTTTAGACTAAAAAGTGTGTAACGTCGCAACGAGG
1 ATTAGCACTAATGTGGAGTTATGCCACACATTTTAGACTAAAAAGTGTGTAACGTCGCAACGAGG
* *
53155368 AAGTGTTCTTTGTCCCAACGAGCAGTCGACATCACGACAAAAAGAAAGCACTCATCTTCACGATG
66 AACTGTTCTTTGTCCCAACGAGCAGTCAACATCACGACAAAAAGAAAGCACTCATCTTCACGATG
*
53155433 TGATCCTTTTCCGTCCCGATGACGCAATTCCACCTCACGATGTGGCGACGTACAGTTCA
131 TGATCCTTTTCCGTCCCGATGACGCAATTCCACCTCACAATGTGGCGACGTACAGTTCA
53155492 A
1 A
53155493 GTTTTTCGAC
Statistics
Matches: 176, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
188 143 0.81
189 33 0.19
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (189 bp):
ATTAGCACTAATGTGGAGTTATGCCACACATTTTAGACTAAAAAGTGTGTAACGTCGCAACGAGG
AACTGTTCTTTGTCCCAACGAGCAGTCAACATCACGACAAAAAGAAAGCACTCATCTTCACGATG
TGATCCTTTTCCGTCCCGATGACGCAATTCCACCTCACAATGTGGCGACGTACAGTTCA
Found at i:53157255 original size:131 final size:131
Alignment explanation
Indices: 53157091--53157352 Score: 443
Period size: 131 Copynumber: 2.0 Consensus size: 131
53157081 GCTCTCAACA
* * *
53157091 TGTCAAGCCTCTTAAGTTTGTGGATTTCCTGCAATTCAGTCAACAAAAAGTGTGAGCTTATAAAT
1 TGTCAAGCCTCTTAAGTCTATAGATTTCCTGCAATTCAGTCAACAAAAAGTGTGAGCTTATAAAT
* * * *
53157156 CAATGTGTGTAGCCTATATATAGGCAAAACAATAATATAGATATAAAAGTAGTTGTCTAAATTCA
66 CAATGTGTGTAGCCGATATATAGGCAAAACAAAAATATAGATATAAAAGTAGTTGCCCAAATTCA
53157221 G
131 G
*
53157222 TGTCAAGCCTCTTAAGTCTATAGATTTCCTGCAATTCAGTCAACAAAAAGTGTGAGCTTATAACT
1 TGTCAAGCCTCTTAAGTCTATAGATTTCCTGCAATTCAGTCAACAAAAAGTGTGAGCTTATAAAT
*
53157287 CAATGTGTGTAGCCGATATATAGGCAAAACAAAAATATAGATATAACAGTAGTTGCCCAAATTCA
66 CAATGTGTGTAGCCGATATATAGGCAAAACAAAAATATAGATATAAAAGTAGTTGCCCAAATTCA
53157352 G
131 G
53157353 ATACGAAATC
Statistics
Matches: 122, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
131 122 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (131 bp):
TGTCAAGCCTCTTAAGTCTATAGATTTCCTGCAATTCAGTCAACAAAAAGTGTGAGCTTATAAAT
CAATGTGTGTAGCCGATATATAGGCAAAACAAAAATATAGATATAAAAGTAGTTGCCCAAATTCA
G
Found at i:53164435 original size:59 final size:62
Alignment explanation
Indices: 53164320--53164435 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
53164310 GTGATTATTG
* ** * * *
53164320 TAATATTAAATTTAATTTAATTTTTATCTTATAGATAAATATTCTATTATTTTAATAAGATT
1 TAATACTAAATTTAACCTAATATTTATCTTATAGATAAATATTATATTAATTTAATAAGATT
53164382 TAATACTAAATTTAACCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATA
1 TAATACTAAATTTAACCTAATATTTATCTTATAGATAAATATTATATTAATTTAATA
53164436 TTAAAGTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 22 0.46
60 1 0.02
61 1 0.02
62 24 0.50
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (62 bp):
TAATACTAAATTTAACCTAATATTTATCTTATAGATAAATATTATATTAATTTAATAAGATT
Found at i:53166434 original size:59 final size:61
Alignment explanation
Indices: 53166260--53166462 Score: 213
Period size: 59 Copynumber: 3.4 Consensus size: 61
53166250 TCATCGATGA
* * * *
53166260 ATGAAAAAGGATGACTTCGGCTA-C-CAATTATGAAAAGGGATGGTGACGACCATCAAATT
1 ATGAAAAGGGATGGCTTCGACTATCATAATTATGAAAAGGGATGGTGACGACCATCAAATT
* * * * * *
53166319 ATGAAAAGGGATGGCTTCGACTATCGT-ATTAAGAAAAGGGATGCCT-TCGGCTATC-AATT
1 ATGAAAAGGGATGGCTTCGACTATCATAATTATGAAAAGGGATG-GTGACGACCATCAAATT
* *
53166378 ATGAAAAGGGATGGCTTTGGCTAT-ATAATTATGAAAAGGGATGGTGACGACCATCAAATT
1 ATGAAAAGGGATGGCTTCGACTATCATAATTATGAAAAGGGATGGTGACGACCATCAAATT
* *
53166438 AT-AAAACAGGATAGCTTCGACTATC
1 ATGAAAA-GGGATGGCTTCGACTATC
53166463 GAGCCATGAA
Statistics
Matches: 115, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
58 2 0.02
59 71 0.62
60 41 0.36
61 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.25
Consensus pattern (61 bp):
ATGAAAAGGGATGGCTTCGACTATCATAATTATGAAAAGGGATGGTGACGACCATCAAATT
Found at i:53166456 original size:89 final size:89
Alignment explanation
Indices: 53166262--53166438 Score: 207
Period size: 89 Copynumber: 2.0 Consensus size: 89
53166252 ATCGATGAAT
* * *
53166262 GAAAAAGGATGACTTCGGCTACCAATTATGAAAAGGGATGGTGACGACCATCAAATTATGAAAAG
1 GAAAAGGGATGCCTTCGGCTATCAATTATGAAAAGGGATGGTGACGACCATCAAATTATGAAAAG
* * **
53166327 GGATGGCTTCGACTATCGTATTAA
66 GGATGGCTACGACCATCAAATTAA
** * *
53166351 GAAAAGGGATGCCTTCGGCTATCAATTATGAAAAGGGATGGCT-TTGGCTAT-ATAATTATGAAA
1 GAAAAGGGATGCCTTCGGCTATCAATTATGAAAAGGGATGG-TGACGACCATCA-AATTATGAAA
53166414 AGGGATGG-TGACGACCATCAAATTA
64 AGGGATGGCT-ACGACCATCAAATTA
53166439 TAAAACAGGA
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
88 2 0.03
89 71 0.96
90 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (89 bp):
GAAAAGGGATGCCTTCGGCTATCAATTATGAAAAGGGATGGTGACGACCATCAAATTATGAAAAG
GGATGGCTACGACCATCAAATTAA
Found at i:53166497 original size:119 final size:119
Alignment explanation
Indices: 53166285--53166508 Score: 319
Period size: 119 Copynumber: 1.9 Consensus size: 119
53166275 TTCGGCTACC
* * **
53166285 AATTATGAAAAGGGATGGTGACGACCATCAAATTATGAAAAGGGATGGCTTCGACTATCGTATTA
1 AATTATGAAAAGGGATGGTGACGACCATCAAATTATGAAAAAGGATAGCTTCGACTATCGTACCA
** *
53166350 AGAAAAGGGATGCCTTCGGCTATCAATTATGAAAAGGGATGGCTTTGGCTATAT
66 AGAAAAGGGATAACTTCGACTATCAATTATGAAAAGGGATGGCTTTGGCTATAT
53166404 AATTATGAAAAGGGATGGTGACGACCATCAAATTAT-AAAACAGGATAGCTTCGACTATCG-AGC
1 AATTATGAAAAGGGATGGTGACGACCATCAAATTATGAAAA-AGGATAGCTTCGACTATCGTA-C
* *
53166467 CATG-AAAGGGATAACTTCGATTATCAAATTATGAAAAGGGAT
64 CAAGAAAAGGGATAACTTCGACTATC-AATTATGAAAAGGGAT
53166509 ATGTTAACCA
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
118 22 0.24
119 71 0.76
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (119 bp):
AATTATGAAAAGGGATGGTGACGACCATCAAATTATGAAAAAGGATAGCTTCGACTATCGTACCA
AGAAAAGGGATAACTTCGACTATCAATTATGAAAAGGGATGGCTTTGGCTATAT
Found at i:53166509 original size:30 final size:30
Alignment explanation
Indices: 53166260--53166509 Score: 167
Period size: 30 Copynumber: 8.4 Consensus size: 30
53166250 TCATCGATGA
* * *
53166260 ATGAAAAAGGAT-GACTTCGGCTA-CCAATT
1 ATGAAAAGGGATAG-CTTCGACTATCAAATT
* * *
53166289 ATGAAAAGGGAT-GGTGACGACCATCAAATT
1 ATGAAAAGGGATAGCT-TCGACTATCAAATT
* **
53166319 ATGAAAAGGGATGGCTTCGACTATCGTATT
1 ATGAAAAGGGATAGCTTCGACTATCAAATT
* *
53166349 AAGAAAAGGGAT-GCCTTCGGCTATC-AATT
1 ATGAAAAGGGATAG-CTTCGACTATCAAATT
* * *
53166378 ATGAAAAGGGATGGCTTTGGCTAT-ATAATT
1 ATGAAAAGGGATAGCTTCGACTATCA-AATT
* * *
53166408 ATGAAAAGGGAT-GGTGACGACCATCAAATT
1 ATGAAAAGGGATAGCT-TCGACTATCAAATT
* * ***
53166438 AT-AAAACAGGATAGCTTCGACTATCGAGCC
1 ATGAAAA-GGGATAGCTTCGACTATCAAATT
* *
53166468 ATG-AAAGGGATAACTTCGATTATCAAATT
1 ATGAAAAGGGATAGCTTCGACTATCAAATT
53166497 ATGAAAAGGGATA
1 ATGAAAAGGGATA
53166510 TGTTAACCAT
Statistics
Matches: 172, Mismatches: 36, Indels: 25
0.74 0.15 0.11
Matches are distributed among these distances:
28 1 0.01
29 65 0.38
30 101 0.59
31 5 0.03
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGACTATCAAATT
Found at i:53173952 original size:30 final size:30
Alignment explanation
Indices: 53173911--53174076 Score: 149
Period size: 30 Copynumber: 5.5 Consensus size: 30
53173901 TTGGGCTATC
* *
53173911 AATTTTGAAAAGGGATAGTGACGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
* * *
53173941 AATTATGAAAAGGGATTGTGACGATCGTCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
** * *
53173971 AATTATGAAAAGGGATGGCT-TTGGCTATCA
1 AATTATGAAAAGGGATGG-TGACGACCATCA
* * *
53174001 TACTATGAAAAGGGATGGTGAC-AGCCATCG
1 AATTATGAAAAGGGATGGTGACGA-CCATCA
* * *
53174031 AATAATGAAATA-GGTTGGTGACGACTATCA
1 AATTATGAAA-AGGGATGGTGACGACCATCA
53174061 AATTATGAAAAGGGAT
1 AATTATGAAAAGGGAT
53174077 AACTTTGGTT
Statistics
Matches: 104, Mismatches: 26, Indels: 12
0.73 0.18 0.08
Matches are distributed among these distances:
29 2 0.02
30 99 0.95
31 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (30 bp):
AATTATGAAAAGGGATGGTGACGACCATCA
Found at i:53174052 original size:90 final size:89
Alignment explanation
Indices: 53173886--53174107 Score: 263
Period size: 90 Copynumber: 2.5 Consensus size: 89
53173876 TCATCGATGA
* * *
53173886 ATGAAAAGGGATGGCTTGGGCTATCAATTTTGAAAAGGGATAGTGACGACCATCAAATTATGAAA
1 ATGAAAAGGGATGGCTTTGGCTATCAATTATGAAAAGGGATAGTGACGACCATCAAATAATGAAA
*
53173951 AGGGATTGTGACGA-TCGTCAAATT
66 AGGGATTGTGACGACT-ATCAAATT
* * *
53173975 ATGAAAAGGGATGGCTTTGGCTATCATACTATGAAAAGGGATGGTGAC-AGCCATCGAATAATGA
1 ATGAAAAGGGATGGCTTTGGCTATCA-ATTATGAAAAGGGATAGTGACGA-CCATCAAATAATGA
53174039 AATA-GG-TTGGTGACGACTATCAAATT
64 AA-AGGGATT-GTGACGACTATCAAATT
** * *
53174065 ATGAAAAGGGATAACTTTGGTTATCAAATTACGAAAAGGGATA
1 ATGAAAAGGGATGGCTTTGGCTATC-AATTATGAAAAGGGATA
53174108 CGTTAACCAT
Statistics
Matches: 114, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
89 28 0.25
90 83 0.73
91 3 0.03
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (89 bp):
ATGAAAAGGGATGGCTTTGGCTATCAATTATGAAAAGGGATAGTGACGACCATCAAATAATGAAA
AGGGATTGTGACGACTATCAAATT
Found at i:53176909 original size:22 final size:22
Alignment explanation
Indices: 53176862--53176913 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
53176852 AGTTCACATA
*
53176862 AGATGCAAAACAAATTGGATAT
1 AGATGCAAAACAAATTAGATAT
* *
53176884 AGATGCAAAATAGATTAGA-AT
1 AGATGCAAAACAAATTAGATAT
53176905 CAGATGCAA
1 -AGATGCAA
53176914 TTTCCTACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (22 bp):
AGATGCAAAACAAATTAGATAT
Found at i:53180497 original size:58 final size:59
Alignment explanation
Indices: 53180401--53180511 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 59
53180391 CATTGACCTG
* * * * *
53180401 TGTGACCCTAAATCCAAAACAGTGAGTCAGACGACCTGGACACATGCTGGTGTAGCTTA
1 TGTGACCCAAAATACAAAACAGTGAGTCACACGACCTGGACACACGCTCGTGTAGCTTA
* * * *
53180460 TGTGACCCAAAATAC-AAGCAGTGAGTTACACGGCCTGGTCACACGCTCGTGT
1 TGTGACCCAAAATACAAAACAGTGAGTCACACGACCTGGACACACGCTCGTGT
53180512 CCCTAGCCCG
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
58 30 0.70
59 13 0.30
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (59 bp):
TGTGACCCAAAATACAAAACAGTGAGTCACACGACCTGGACACACGCTCGTGTAGCTTA
Found at i:53183196 original size:16 final size:17
Alignment explanation
Indices: 53183169--53183206 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
53183159 AATAATTTAA
* *
53183169 AAAATATAAAAATATTT
1 AAAATATAAAAAAATAT
53183186 AAAAT-TAAAAAAATAT
1 AAAATATAAAAAAATAT
53183202 AAAAT
1 AAAAT
53183207 GTTCATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATATAAAAAAATAT
Found at i:53183216 original size:25 final size:26
Alignment explanation
Indices: 53183160--53183216 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
53183150 ATGTCGACAA
* *
53183160 ATAATTTAAAAAATATAAAAATATTT
1 ATAATTAAAAAAATATAAAAATATTC
* *
53183186 AAAATTAAAAAAATAT-AAAATGTTC
1 ATAATTAAAAAAATATAAAAATATTC
53183211 ATAATT
1 ATAATT
53183217 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
ATAATTAAAAAAATATAAAAATATTC
Found at i:53189260 original size:14 final size:14
Alignment explanation
Indices: 53189237--53189270 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
53189227 TGGTATGAGT
53189237 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
53189250 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
53189264 TTATAGG
1 TTATAGG
53189271 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:53189426 original size:24 final size:25
Alignment explanation
Indices: 53189399--53189446 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
53189389 AGAAGAAAGT
53189399 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
53189423 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
53189447 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:53192430 original size:2 final size:2
Alignment explanation
Indices: 53192419--53192463 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
53192409 AACACCTCTG
53192419 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53192460 AT AT
1 AT AT
53192464 TTACACAAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:53198735 original size:15 final size:17
Alignment explanation
Indices: 53198701--53198834 Score: 93
Period size: 18 Copynumber: 8.0 Consensus size: 17
53198691 AATATTAAGA
53198701 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
53198718 ATTTTGTTAAA-T-TAT
1 ATTTTATTAAATTATAT
* *
53198733 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* *
53198747 ATTTTAAATTATATTTTAT
1 ATTTT--ATTAAATTATAT
* * *
53198766 AGTATTA-TATATTAT-G
1 A-TTTTATTAAATTATAT
*
53198782 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
53198800 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
53198817 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
53198835 TTAATAATAA
Statistics
Matches: 90, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
13 2 0.02
14 6 0.07
15 12 0.13
16 7 0.08
17 26 0.29
18 32 0.36
19 2 0.02
20 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:53198894 original size:100 final size:99
Alignment explanation
Indices: 53198701--53198895 Score: 227
Period size: 100 Copynumber: 2.0 Consensus size: 99
53198691 AATATTAAGA
* * * **
53198701 ATTTTATTAAATTATATATTTTGTTAAATTATATTTAATAATAATTATTTTAAATTATATTTTAT
1 ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATATTAAAT
* ** **
53198766 AGTATTATATATTATGATTTTAGTAAATTCATAT
66 AGTATTATATATTATGACTAAAAAAAATTCATAT
53198800 ATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAA
1 ATTTTATTAAATTATATA-TTTTATTAAATTATATTTAATAATAATTATGTTAAAATAT-ATTAA
53198865 AT--TATT-TATTATT-TGTACCTAAAAAAAATTC
64 ATAGTATTATA-TATTATG-A-CTAAAAAAAATTC
53198896 TGCTAAGGGT
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
98 4 0.05
99 27 0.33
100 45 0.56
101 5 0.06
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (99 bp):
ATTTTATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATATTAAAT
AGTATTATATATTATGACTAAAAAAAATTCATAT
Found at i:53199025 original size:16 final size:16
Alignment explanation
Indices: 53199004--53199052 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
53198994 TTCGCTGTAT
53199004 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
53199020 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
53199036 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
53199052 T
1 T
53199053 AGCAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.37, C:0.04, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:53199421 original size:16 final size:17
Alignment explanation
Indices: 53199402--53199443 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
53199392 ATAATTAAAT
53199402 ATTAAAATATAT-TTTA
1 ATTAAAATATATATTTA
53199418 ATTAAAATATATGATTTA
1 ATTAAAATATAT-ATTTA
*
53199436 ATAAAAAT
1 ATTAAAAT
53199444 TCTTAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.52
18 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTAAAATATATATTTA
Found at i:53199459 original size:124 final size:122
Alignment explanation
Indices: 53199264--53199584 Score: 456
Period size: 124 Copynumber: 2.6 Consensus size: 122
53199254 ATTTAATCAT
* *
53199264 ATTTAAACATAA-TAATTATTAAATATATTATAATT-AAATATATAATTTAATAAAATTCTTAAT
1 ATTTTAACATAATTAATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATTCTTAAT
53199327 AAGTAATATTCTTATATGAATTTACT-CAAATCATAATATATGATACTATAAAAGATA
66 AA-TAATATTCTTATATGAATTTACTGCAAATCATAATATATGATACTATAAAAGATA
* *
53199384 ATTTTGAA-ATAATTAAATATTAAAATATATTTTAATTAAAATATATGATTTAATAAAAATTCTT
1 ATTTT-AACATAATTAATTATT-AAATATATTATAATTAAAATATATGATTTAAT-AAAATTCTT
* *
53199448 AATAATCAATATTCTTATATGAATTTACTGGAAATCATAATATATGATACTATAAAATATA
63 AATAAT-AATATTCTTATATGAATTTACTGCAAATCATAATATATGATACTATAAAAGATA
* * *
53199509 ATTTTAACATAATT-ATTATTAAATATATTAT-AGTAAAGTAAGATGATTTAATAAAATTCTTAA
1 ATTTTAACATAATTAATTATTAAATATATTATAATTAAAAT-ATATGATTTAATAAAATTCTTAA
53199572 TAATTAATATTCT
65 TAA-TAATATTCT
53199585 NNNNNNNNNN
Statistics
Matches: 180, Mismatches: 11, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
120 8 0.04
121 9 0.05
122 42 0.23
123 38 0.21
124 43 0.24
125 40 0.22
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (122 bp):
ATTTTAACATAATTAATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATTCTTAAT
AATAATATTCTTATATGAATTTACTGCAAATCATAATATATGATACTATAAAAGATA
Found at i:53199912 original size:18 final size:17
Alignment explanation
Indices: 53199889--53199925 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
53199879 AATTATTATT
53199889 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
53199905 AAATATATGATTTAATA
1 AAATATATGATTTAATA
53199922 AAAT
1 AAAT
53199926 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:53200204 original size:47 final size:47
Alignment explanation
Indices: 53200028--53200205 Score: 115
Period size: 47 Copynumber: 3.9 Consensus size: 47
53200018 TTAATTAAAA
* * *
53200028 TATATG-ATTTAATAAAATTTAAAATACTT-ATAAGTAATAAAATTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTAATAATTAAT-AAATTTCT
* ** **
53200075 TATATGAATTTTTATAATTTAAAATAATT-ATTGTTACATATAATTTAA
1 TATATGAATTTATATAATTTAAAATAATTAATAATTA-ATA-AATTTCT
* ** *
53200123 TA-AT-AA--TATATAATTTCATAA-AATTCTTGA-TAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATTAATAATTAATAAA-TTTCT
*
53200166 TATATGAATTTATACAATTTAAAATAATTAAT-ATTAATAA
1 TATATGAATTTATATAATTTAAAATAATTAATAATTAATAA
53200206 GTGAAATGTT
Statistics
Matches: 100, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
42 2 0.02
43 8 0.08
44 17 0.17
45 6 0.06
46 6 0.06
47 48 0.48
48 13 0.13
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (47 bp):
TATATGAATTTATATAATTTAAAATAATTAATAATTAATAAATTTCT
Found at i:53203362 original size:16 final size:16
Alignment explanation
Indices: 53203337--53203374 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
53203327 AGGATTACCT
*
53203337 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
53203353 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
53203369 ATTACA
1 ATTACA
53203375 GCGATCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:53207380 original size:26 final size:26
Alignment explanation
Indices: 53207344--53207396 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
53207334 TTCTTCTAAA
53207344 TCTTCTATGTCTAAGGCTTCATAATC
1 TCTTCTATGTCTAAGGCTTCATAATC
53207370 TCTTCTATGTCTAAGGCTTCATAATC
1 TCTTCTATGTCTAAGGCTTCATAATC
53207396 T
1 T
53207397 ATTTCTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (26 bp):
TCTTCTATGTCTAAGGCTTCATAATC
Found at i:53208744 original size:18 final size:19
Alignment explanation
Indices: 53208721--53208758 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
53208711 TTAAGAATTC
*
53208721 TTCTTT-TTATGTATTTAA
1 TTCTTTGTTATGCATTTAA
*
53208739 TTCTTTGTTCTGCATTTAA
1 TTCTTTGTTATGCATTTAA
53208758 T
1 T
53208759 GTTATAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.18, C:0.11, G:0.08, T:0.63
Consensus pattern (19 bp):
TTCTTTGTTATGCATTTAA
Found at i:53218342 original size:22 final size:22
Alignment explanation
Indices: 53218314--53218356 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
53218304 TTTATTGTTC
53218314 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
53218336 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
53218357 TAGATTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:53222841 original size:2 final size:2
Alignment explanation
Indices: 53222836--53222880 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
53222826 CTTTATCATA
53222836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53222878 AT A
1 AT A
53222881 AAATAGCATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53223697 original size:6 final size:6
Alignment explanation
Indices: 53223686--53223718 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
53223676 GAATTATTGT
53223686 AATTCA AATTCA AATTCA AATTCA AATTCA AAT
1 AATTCA AATTCA AATTCA AATTCA AATTCA AAT
53223719 AAAAGAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTCA
Found at i:53227776 original size:2 final size:2
Alignment explanation
Indices: 53227769--53227794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53227759 TCAGAAATAC
53227769 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
53227795 TAATTATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53230116 original size:2 final size:2
Alignment explanation
Indices: 53230109--53230135 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53230099 GTGGGAAAAC
53230109 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
53230136 AAAGGTTGCT
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:53233532 original size:43 final size:43
Alignment explanation
Indices: 53233471--53233562 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
53233461 GTAATATGGT
* * *
53233471 TTCCACTGATACCCTATTACGTGCAACAGTTGAGTACCATGAA
1 TTCCACTGATACCCTATTAAGTACAACAATTGAGTACCATGAA
*
53233514 TTCCACTGATACCCTATTAAGTACAACAATTGATTACCATGAA
1 TTCCACTGATACCCTATTAAGTACAACAATTGAGTACCATGAA
*
53233557 CTCCAC
1 TTCCAC
53233563 AACTCATTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (43 bp):
TTCCACTGATACCCTATTAAGTACAACAATTGAGTACCATGAA
Found at i:53241751 original size:23 final size:23
Alignment explanation
Indices: 53241700--53241756 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
53241690 TTCAAACTCG
* *
53241700 TAACTCAAATTATTTATTCGAGT
1 TAACTCAAATAATTGATTCGAGT
*
53241723 TGACTCAAATAACTTGATTCGA-T
1 TAACTCAAATAA-TTGATTCGAGT
53241746 TAACTCGAAAT
1 TAACTC-AAAT
53241757 TCGAAACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (23 bp):
TAACTCAAATAATTGATTCGAGT
Found at i:53241883 original size:15 final size:14
Alignment explanation
Indices: 53241856--53241882 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53241846 AAATATAGTA
53241856 AAATATTAAAAAAT
1 AAATATTAAAAAAT
53241870 AAATATTAAAAAA
1 AAATATTAAAAAA
53241883 AACATAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:53242381 original size:24 final size:24
Alignment explanation
Indices: 53242349--53242400 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53242339 TTAATTTTTG
*
53242349 ATTATTTGTCCCATTCAAACTCTA
1 ATTATTTGTCCCAGTCAAACTCTA
* *
53242373 ATTATTTGTCCCAGTCGAACTTTA
1 ATTATTTGTCCCAGTCAAACTCTA
53242397 ATTA
1 ATTA
53242401 GGGTAGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (24 bp):
ATTATTTGTCCCAGTCAAACTCTA
Found at i:53242658 original size:9 final size:9
Alignment explanation
Indices: 53242644--53242692 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
53242634 GTTAAACGAA
53242644 TCGAGTTAT
1 TCGAGTTAT
*
53242653 TCGAGTTAA
1 TCGAGTTAT
53242662 TCGAGTTAT
1 TCGAGTTAT
*
53242671 TCGAGTTAA
1 TCGAGTTAT
53242680 TCGAGTTAT
1 TCGAGTTAT
53242689 TCGA
1 TCGA
53242693 ATCAACTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:53242665 original size:18 final size:18
Alignment explanation
Indices: 53242642--53242692 Score: 102
Period size: 18 Copynumber: 2.8 Consensus size: 18
53242632 GAGTTAAACG
53242642 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
53242660 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
53242678 AATCGAGTTATTCGA
1 AATCGAGTTATTCGA
53242693 ATCAACTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:53245168 original size:5 final size:5
Alignment explanation
Indices: 53245158--53245183 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53245148 TTCGAAAATT
53245158 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
53245184 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:53245288 original size:20 final size:20
Alignment explanation
Indices: 53245247--53245288 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
53245237 TATAGTGAAA
* *
53245247 TTATCTTTTCCCGTGGTTTT
1 TTATCTTCTCCCGTGGTGTT
53245267 TTATCTTCT-CCGTAGGTGTT
1 TTATCTTCTCCCGT-GGTGTT
53245287 TT
1 TT
53245289 TCCACATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.07, C:0.19, G:0.17, T:0.57
Consensus pattern (20 bp):
TTATCTTCTCCCGTGGTGTT
Found at i:53248544 original size:33 final size:33
Alignment explanation
Indices: 53248462--53248544 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
53248452 TGGTCCAACC
* * ** *
53248462 ATGGTCTTACGTTCAAGGTGTCATAACCCAGTT
1 ATGGTCTTACATTTAAAATGTCATAACCCAGCT
* *
53248495 ATGGTCTTTTCA-TTAAAATGTCATAGCCCAGCT
1 ATGGTC-TTACATTTAAAATGTCATAACCCAGCT
53248528 ATGGTCTTACATTTAAA
1 ATGGTCTTACATTTAAA
53248545 CATTTCCATG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
32 4 0.10
33 33 0.82
34 3 0.08
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATGTCATAACCCAGCT
Found at i:53251092 original size:28 final size:28
Alignment explanation
Indices: 53251052--53251107 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
53251042 ATCCTTACCT
53251052 TTTCTACAAAGATTCAAGGAGAATGAGA
1 TTTCTACAAAGATTCAAGGAGAATGAGA
53251080 TTTCTACAAAGATTCAAGGAGAATGAGA
1 TTTCTACAAAGATTCAAGGAGAATGAGA
53251108 AGGATAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (28 bp):
TTTCTACAAAGATTCAAGGAGAATGAGA
Found at i:53251726 original size:22 final size:22
Alignment explanation
Indices: 53251701--53251745 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
53251691 GCTATTACAT
* *
53251701 AGCCATTAATGAACAGACTTTA
1 AGCCATGAATGAACAAACTTTA
53251723 AGCCATGAATGAACAAACTTTA
1 AGCCATGAATGAACAAACTTTA
53251745 A
1 A
53251746 TACCAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (22 bp):
AGCCATGAATGAACAAACTTTA
Found at i:53255725 original size:38 final size:38
Alignment explanation
Indices: 53255674--53255750 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
53255664 AGCAAGAATG
53255674 AGGACAGCTCAGGAAATTCAGTTCCTACTGTTTGATCA
1 AGGACAGCTCAGGAAATTCAGTTCCTACTGTTTGATCA
53255712 AGGACAGCTCAGGAAATTCAGTTCCTACTGTTTGATCA
1 AGGACAGCTCAGGAAATTCAGTTCCTACTGTTTGATCA
53255750 A
1 A
53255751 AAGTCACCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (38 bp):
AGGACAGCTCAGGAAATTCAGTTCCTACTGTTTGATCA
Found at i:53257887 original size:17 final size:17
Alignment explanation
Indices: 53257865--53257897 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53257855 TGTTAGTTAA
*
53257865 TATTGTCGTTGCATTGC
1 TATTGTCATTGCATTGC
53257882 TATTGTCATTGCATTG
1 TATTGTCATTGCATTG
53257898 TAATCTTAGT
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:0.15, C:0.15, G:0.21, T:0.48
Consensus pattern (17 bp):
TATTGTCATTGCATTGC
Found at i:53260356 original size:41 final size:41
Alignment explanation
Indices: 53260299--53260381 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
53260289 TGATAGGTGT
53260299 ATGGTATTTATAGGTGAAGGTAAGGGGTAGAGTTTGCTAAA
1 ATGGTATTTATAGGTGAAGGTAAGGGGTAGAGTTTGCTAAA
53260340 ATGGTATTTATAGGTGAAGGTAAGGGGTAGAGTTTGCTAAA
1 ATGGTATTTATAGGTGAAGGTAAGGGGTAGAGTTTGCTAAA
53260381 A
1 A
53260382 ATAACATTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.31
Consensus pattern (41 bp):
ATGGTATTTATAGGTGAAGGTAAGGGGTAGAGTTTGCTAAA
Found at i:53261690 original size:42 final size:42
Alignment explanation
Indices: 53261631--53261809 Score: 211
Period size: 42 Copynumber: 4.3 Consensus size: 42
53261621 AAGGAAAGCA
*
53261631 TTCATTGTATTTAGAGGCCCAAGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCTATTTACTT
* * * *
53261673 TTCATTACATTTAGAGGCCC-AGATATGTAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAG-TGTGGAGGTCTATTTACTT
* * *
53261715 TTCATCGTATTTAGA-GCCTCAGGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCC-CAAGTGTGGAGGTCTATTTACTT
* * *
53261757 TTAATTGCATTTAGAGGCTCAGGTGTGGAGGT-TCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCT-ATTTACTT
53261799 TTCATTGCATT
1 TTCATTGCATT
53261810 GTATATAAAG
Statistics
Matches: 115, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
41 6 0.05
42 106 0.92
43 3 0.03
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCTATTTACTT
Found at i:53261772 original size:84 final size:84
Alignment explanation
Indices: 53261631--53261803 Score: 249
Period size: 84 Copynumber: 2.1 Consensus size: 84
53261621 AAGGAAAGCA
* *
53261631 TTCATTGTATTTAGAGGCCCAAGTGTGGAGGTCTATTTACTTTTCATTACATTTAGAGGCCCAGA
1 TTCATCGTATTTAGAGGCCCAAGTGTGGAGGTCTATTTACTTTTAATTACATTTAGAGGCCCAGA
*
53261696 TATGTAGGTCCATTTACTT
66 TATGGAGGTCCATTTACTT
* * *
53261715 TTCATCGTATTTAGA-GCCTCAGGTGTGGAGGTCTATTTACTTTTAATTGCATTTAGAGGCTCAG
1 TTCATCGTATTTAGAGGCC-CAAGTGTGGAGGTCTATTTACTTTTAATTACATTTAGAGGCCCAG
* * *
53261779 GTGTGGAGGTTCATTTACTT
65 ATATGGAGGTCCATTTACTT
53261799 TTCAT
1 TTCAT
53261804 TGCATTGTAT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
83 3 0.04
84 76 0.96
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (84 bp):
TTCATCGTATTTAGAGGCCCAAGTGTGGAGGTCTATTTACTTTTAATTACATTTAGAGGCCCAGA
TATGGAGGTCCATTTACTT
Found at i:53262267 original size:3 final size:3
Alignment explanation
Indices: 53262259--53262303 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
53262249 AAGGGCCCAA
* * *
53262259 ATT ATT ATT ATT ACT ACT ATT ATT ATT ATT AAAT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT AT
53262304 CTTTTTTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.95
4 2 0.05
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:53265168 original size:45 final size:45
Alignment explanation
Indices: 53265104--53265193 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
53265094 AAATAAAAGA
53265104 CTATTAAATCAGAGGCTGGATAGTATGAGCTCCAAGTTGATTCGT
1 CTATTAAATCAGAGGCTGGATAGTATGAGCTCCAAGTTGATTCGT
53265149 CTATTAAATCAGAGGCTGGATAGTATGAGCTCCAAGTTGATTCGT
1 CTATTAAATCAGAGGCTGGATAGTATGAGCTCCAAGTTGATTCGT
53265194 TTGACCCGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (45 bp):
CTATTAAATCAGAGGCTGGATAGTATGAGCTCCAAGTTGATTCGT
Found at i:53266223 original size:44 final size:44
Alignment explanation
Indices: 53266174--53266299 Score: 153
Period size: 44 Copynumber: 2.9 Consensus size: 44
53266164 AAACGGTGTA
*
53266174 ATAGCCAACACCGGTACATAATACCTACTTAATATAAATGGCAC
1 ATAGCCAACACCGGTACATAATACCTACTGAATATAAATGGCAC
*** * * *
53266218 ATAGCCAACATTAGTACATAGTACCTGCTGAATGTAAATGGCAC
1 ATAGCCAACACCGGTACATAATACCTACTGAATATAAATGGCAC
* * **
53266262 ATAGCCAACACCGGTACATAGTACATGTTGAATATAAA
1 ATAGCCAACACCGGTACATAATACCTACTGAATATAAA
53266300 CCCTAATGAC
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (44 bp):
ATAGCCAACACCGGTACATAATACCTACTGAATATAAATGGCAC
Found at i:53268101 original size:13 final size:13
Alignment explanation
Indices: 53268085--53268118 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
53268075 TTTATTTTGG
*
53268085 TTTAATTTTTTAT
1 TTTAATTTTCTAT
53268098 TTTAATTTTCTAT
1 TTTAATTTTCTAT
53268111 TTTAATTT
1 TTTAATTT
53268119 AATCCCCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTAATTTTCTAT
Found at i:53273089 original size:46 final size:46
Alignment explanation
Indices: 53273031--53273308 Score: 504
Period size: 46 Copynumber: 6.0 Consensus size: 46
53273021 ACAATACTAT
*
53273031 AACTGAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
53273077 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
53273123 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCA-
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTAC-TTTTCAC
*
53273169 ACACTCAGTATGATTTTCTTTATTGAAATACCATACCTACTTTTCAC
1 A-ACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
53273216 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
*
53273262 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
53273308 A
1 A
53273309 CTTTGCCATG
Statistics
Matches: 225, Mismatches: 4, Indels: 6
0.96 0.02 0.03
Matches are distributed among these distances:
46 181 0.80
47 44 0.20
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
Found at i:53273203 original size:93 final size:92
Alignment explanation
Indices: 53273031--53273308 Score: 504
Period size: 93 Copynumber: 3.0 Consensus size: 92
53273021 ACAATACTAT
*
53273031 AACTGAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTT
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTT
53273096 TATTGAAATACCATACCTACTTTTCAC
66 TATTGAAATACCATACCTACTTTTCAC
*
53273123 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCA-ACACTCAGTATGATTTTC
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTAC-TTTTCACA-ACTCAGTATGGTTTTC
53273187 TTTATTGAAATACCATACCTACTTTTCAC
64 TTTATTGAAATACCATACCTACTTTTCAC
53273216 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTT
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTT
*
53273281 TATTGAAATACCATACCTACGTTTCAC
66 TATTGAAATACCATACCTACTTTTCAC
53273308 A
1 A
53273309 CTTTGCCATG
Statistics
Matches: 179, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
92 89 0.50
93 90 0.50
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (92 bp):
AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTT
TATTGAAATACCATACCTACTTTTCAC
Found at i:53273286 original size:139 final size:139
Alignment explanation
Indices: 53273036--53273300 Score: 521
Period size: 139 Copynumber: 1.9 Consensus size: 139
53273026 ACTATAACTG
*
53273036 AGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTTTATTG
1 AGTATGATTTTCTTTATTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTTTATTG
53273101 AAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTT
66 AAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTT
53273166 TCAACACTC
131 TCAACACTC
53273175 AGTATGATTTTCTTTATTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTTTATTG
1 AGTATGATTTTCTTTATTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTTTATTG
53273240 AAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTTTATTGAAATACCATACCTAC
66 AAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTTTATTGAAATACCATACCTAC
53273301 GTTTCACACT
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 125 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.42
Consensus pattern (139 bp):
AGTATGATTTTCTTTATTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTTTATTG
AAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTT
TCAACACTC
Found at i:53273427 original size:31 final size:31
Alignment explanation
Indices: 53273389--53273452 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
53273379 TGCGTATCCC
*
53273389 TTAATTTGAGCTTACAAATTGATTTTCACAT
1 TTAATTTGAACTTACAAATTGATTTTCACAT
53273420 TTAATTTGAACTTACAAATTGATTTTCACAT
1 TTAATTTGAACTTACAAATTGATTTTCACAT
53273451 TT
1 TT
53273453 TTACCATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (31 bp):
TTAATTTGAACTTACAAATTGATTTTCACAT
Found at i:53273604 original size:35 final size:35
Alignment explanation
Indices: 53273558--53273627 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
53273548 ACTATTTCAT
53273558 TACCTTTCCACACCCGTTTCCTATGCATATCACAC
1 TACCTTTCCACACCCGTTTCCTATGCATATCACAC
53273593 TACCTTTCCACACCCGTTTCCTATGCATATCACAC
1 TACCTTTCCACACCCGTTTCCTATGCATATCACAC
53273628 AAGACATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.40, G:0.06, T:0.31
Consensus pattern (35 bp):
TACCTTTCCACACCCGTTTCCTATGCATATCACAC
Found at i:53274457 original size:31 final size:32
Alignment explanation
Indices: 53274398--53274462 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
53274388 GGCAAATTAC
53274398 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
53274430 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
53274461 AA
1 AA
53274463 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:53277371 original size:22 final size:22
Alignment explanation
Indices: 53277343--53277387 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
53277333 AAGTTATTAA
*
53277343 ATTAACTGTCTAATATGGGAAG
1 ATTAACTATCTAATATGGGAAG
53277365 ATTAACTATCTAATATGGGAAG
1 ATTAACTATCTAATATGGGAAG
53277387 A
1 A
53277388 GGAAATAGCT
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:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (22 bp):
ATTAACTATCTAATATGGGAAG
Found at i:53277399 original size:22 final size:22
Alignment explanation
Indices: 53277352--53277401 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
53277342 AATTAACTGT
** * *
53277352 CTAATATGGGAAGATTAACTAT
1 CTAATATGGGAAGAGGAAATAG
53277374 CTAATATGGGAAGAGGAAATAG
1 CTAATATGGGAAGAGGAAATAG
53277396 CTAATA
1 CTAATA
53277402 AACATAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (22 bp):
CTAATATGGGAAGAGGAAATAG
Found at i:53283881 original size:40 final size:40
Alignment explanation
Indices: 53283837--53284066 Score: 280
Period size: 40 Copynumber: 5.8 Consensus size: 40
53283827 AATTACTATA
*
53283837 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTATCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
53283877 TGATTGCCCATACGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
53283917 TGATTGCACATATGTGCCCCTGATTGTACTTCGGCACCCT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * * *
53283957 TAATTGCACATATGTGCCCATGGTTGTACTTTGATACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
** *
53283997 TGATTGCACATACGTGCCCCTAATTATACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
53284037 TGAATGCACTTTCGTGCCCCTGTTTATACT
1 TGATTGCACATACGTGCCCCTGTTTGTACT
53284067 CTAACAACTC
Statistics
Matches: 161, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 161 1.00
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:53283897 original size:20 final size:20
Alignment explanation
Indices: 53283837--53284017 Score: 91
Period size: 20 Copynumber: 9.1 Consensus size: 20
53283827 AATTACTATA
53283837 TGATTGCACATACGTGCCCC
1 TGATTGCACATACGTGCCCC
* * * **
53283857 TGTTTGTAC-TTCGGTATCCC
1 TGATTGCACATAC-GTGCCCC
*
53283877 TGATTGCCCATACGTGCCCC
1 TGATTGCACATACGTGCCCC
* * * ** *
53283897 TGTTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCC
*
53283917 TGATTGCACATATGTGCCCC
1 TGATTGCACATACGTGCCCC
* *
53283937 TGATTGTAC-TTCG-GCACCC
1 TGATTGCACATACGTGC-CCC
* * *
53283956 TTAATTGCACATATGTGCCCA
1 -TGATTGCACATACGTGCCCC
* * ** *
53283977 TGGTTGTAC-TTTGATACCCC
1 TGATTGCACATACG-TGCCCC
53283997 TGATTGCACATACGTGCCCC
1 TGATTGCACATACGTGCCCC
53284017 T
1 T
53284018 AATTATACTT
Statistics
Matches: 110, Mismatches: 43, Indels: 16
0.65 0.25 0.09
Matches are distributed among these distances:
18 2 0.02
19 10 0.09
20 88 0.80
21 8 0.07
22 2 0.02
ACGTcount: A:0.17, C:0.30, G:0.19, T:0.34
Consensus pattern (20 bp):
TGATTGCACATACGTGCCCC
Found at i:53285162 original size:48 final size:48
Alignment explanation
Indices: 53285090--53285189 Score: 157
Period size: 48 Copynumber: 2.1 Consensus size: 48
53285080 TATGCATGTG
*
53285090 AATGATTGGTTTATAATAGTATTAACATGTTGAATAATATGAGGTTTA
1 AATGATTGGTTTATAATAGCATTAACATGTTGAATAATATGAGGTTTA
* *
53285138 AATGATTGGTTTATGATTA-CATTAACATGTTGAATCATATGAGGTTTA
1 AATGATTGGTTTAT-AATAGCATTAACATGTTGAATAATATGAGGTTTA
53285186 AATG
1 AATG
53285190 TTTTCAACTG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
48 45 0.94
49 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (48 bp):
AATGATTGGTTTATAATAGCATTAACATGTTGAATAATATGAGGTTTA
Found at i:53299671 original size:6 final size:6
Alignment explanation
Indices: 53299660--53299705 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
53299650 AAGTGCTCGC
* * *
53299660 GATAGA GATAGA GATAGA GATAGG GATAGA GATAGG GATAGG GATA
1 GATAGA GATAGA GATAGA GATAGA GATAGA GATAGA GATAGA GATA
53299706 ATAGAGACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.17
Consensus pattern (6 bp):
GATAGA
Found at i:53299677 original size:12 final size:12
Alignment explanation
Indices: 53299660--53299705 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
53299650 AAGTGCTCGC
*
53299660 GATAGAGATAGA
1 GATAGAGATAGG
53299672 GATAGAGATAGG
1 GATAGAGATAGG
53299684 GATAGAGATAGG
1 GATAGAGATAGG
*
53299696 GATAGGGATA
1 GATAGAGATA
53299706 ATAGAGACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.17
Consensus pattern (12 bp):
GATAGAGATAGG
Found at i:53299687 original size:18 final size:18
Alignment explanation
Indices: 53299660--53299705 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
53299650 AAGTGCTCGC
*
53299660 GATAGAGATAGAGATAGA
1 GATAGGGATAGAGATAGA
*
53299678 GATAGGGATAGAGATAGG
1 GATAGGGATAGAGATAGA
53299696 GATAGGGATA
1 GATAGGGATA
53299706 ATAGAGACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.17
Consensus pattern (18 bp):
GATAGGGATAGAGATAGA
Found at i:53304293 original size:24 final size:24
Alignment explanation
Indices: 53304263--53304317 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
53304253 CTGTGGAGAT
* *
53304263 TGATGATGCTT-TGGTGATTGAAGA
1 TGATGATACTTCTGATGA-TGAAGA
*
53304287 TGATGATATTTCTGATGATGAAGA
1 TGATGATACTTCTGATGATGAAGA
53304311 TGATGAT
1 TGATGAT
53304318 CATGAAGACG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (24 bp):
TGATGATACTTCTGATGATGAAGA
Found at i:53311873 original size:11 final size:11
Alignment explanation
Indices: 53311857--53311928 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 11
53311847 TATTTTTTAA
53311857 TTTTAAAATAC
1 TTTTAAAATAC
*
53311868 TTTTAAAATTC
1 TTTTAAAATAC
* *
53311879 TTTTTTAAATTTTTAA
1 --TTTTAAA---ATAC
53311895 TTTTAAAATA-
1 TTTTAAAATAC
53311905 TTTTAAAATA-
1 TTTTAAAATAC
53311915 TTTTAAAATAC
1 TTTTAAAATAC
53311926 TTT
1 TTT
53311929 AAATTTTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
10 20 0.40
11 15 0.30
13 7 0.14
14 7 0.14
16 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:53311884 original size:37 final size:37
Alignment explanation
Indices: 53311842--53311913 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
53311832 AATATAATAA
*
53311842 TTTTTT-ATTTTTTAATTTTAAAATACTTTTAAAATTC
1 TTTTTTAAATTTTTAATTTTAAAATA-TTTTAAAATTC
53311879 TTTTTTAAATTTTTAATTTTAAAATATTTTAAAAT
1 TTTTTTAAATTTTTAATTTTAAAATATTTTAAAAT
53311914 ATTTTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (37 bp):
TTTTTTAAATTTTTAATTTTAAAATATTTTAAAATTC
Found at i:53311907 original size:10 final size:10
Alignment explanation
Indices: 53311894--53311952 Score: 77
Period size: 10 Copynumber: 6.1 Consensus size: 10
53311884 TAAATTTTTA
53311894 ATTTTAAAAT
1 ATTTTAAAAT
53311904 ATTTTAAAAT
1 ATTTTAAAAT
53311914 ATTTTAAAAT
1 ATTTTAAAAT
*
53311924 ACTTT-AAAT
1 ATTTTAAAAT
* *
53311933 TTTTTAATAT
1 ATTTTAAAAT
53311943 -TTTTAAAAT
1 ATTTTAAAAT
53311952 A
1 A
53311953 AAATATTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
9 15 0.36
10 27 0.64
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:53311938 original size:9 final size:9
Alignment explanation
Indices: 53311879--53311951 Score: 62
Period size: 10 Copynumber: 8.1 Consensus size: 9
53311869 TTTAAAATTC
*
53311879 TTTTTTAAA
1 TTTTTAAAA
53311888 TTTTT--AA
1 TTTTTAAAA
53311895 -TTTTAAAA
1 TTTTTAAAA
53311903 TATTTTAAAA
1 T-TTTTAAAA
53311913 TATTTTAAAA
1 T-TTTTAAAA
* *
53311923 TACTTTAAAT
1 T-TTTTAAAA
*
53311933 TTTTTAATA
1 TTTTTAAAA
53311942 TTTTTAAAA
1 TTTTTAAAA
53311951 T
1 T
53311952 AAAATATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
6 4 0.07
7 2 0.04
8 2 0.04
9 19 0.35
10 27 0.50
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:53312000 original size:29 final size:30
Alignment explanation
Indices: 53311943--53312001 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
53311933 TTTTTAATAT
*
53311943 TTTTAAAATAAAATATTTTATTTTGTTTAA
1 TTTTAAAATAAAATATTTTATTTTATTTAA
53311973 TTTT-AAAT-AAAT-TTTTGATATTTATTTAA
1 TTTTAAAATAAAATATTTT-AT-TTTATTTAA
53312002 CAAGCGGGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 4 0.15
28 6 0.23
29 12 0.46
30 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTTAAAATAAAATATTTTATTTTATTTAA
Found at i:53314519 original size:15 final size:16
Alignment explanation
Indices: 53314486--53314530 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
53314476 ACTTTTAGGT
*
53314486 AATAAAATTGTAATGG
1 AATAAAATTGTAATAG
53314502 AATAAAATT-TAATAG
1 AATAAAATTGTAATAG
* *
53314517 AATAGAGTTGTAAT
1 AATAAAATTGTAAT
53314531 TAGTAGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (16 bp):
AATAAAATTGTAATAG
Found at i:53314594 original size:16 final size:16
Alignment explanation
Indices: 53314575--53314620 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
53314565 ACTTTTAGCT
*
53314575 AATAAAATTGTAATGG
1 AATAAAATTGTAATAG
53314591 AATAAAATTGTAATAG
1 AATAAAATTGTAATAG
* *
53314607 AATAGAGTTGTAAT
1 AATAAAATTGTAAT
53314621 TAGTAATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (16 bp):
AATAAAATTGTAATAG
Found at i:53314641 original size:90 final size:89
Alignment explanation
Indices: 53314475--53314647 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 89
53314465 ATTGCTGTTC
* *
53314475 AACTTTTAGGTAATAAAATTGTAATGGAATAAAATTTAATAGAATAGAGTTGTAATTAGTAGTTT
1 AACTTTTAGCTAATAAAATTGTAATGGAATAAAATTTAATAGAATAGAGTTGTAATTAGTAATTT
53314540 CATTATTTGATTGAATGGTTCTAA
66 CATTATTTGATTGAATGGTTCTAA
53314564 AACTTTTAGCTAATAAAATTGTAATGGAATAAAATTGTAATAGAATAGAGTTGTAATTAGTAATT
1 AACTTTTAGCTAATAAAATTGTAATGGAATAAAATT-TAATAGAATAGAGTTGTAATTAGTAATT
*
53314629 TCGTTATTTGATTGAATGG
65 TCATTATTTGATTGAATGG
53314648 AATGAAATAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 35 0.44
90 45 0.56
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.40
Consensus pattern (89 bp):
AACTTTTAGCTAATAAAATTGTAATGGAATAAAATTTAATAGAATAGAGTTGTAATTAGTAATTT
CATTATTTGATTGAATGGTTCTAA
Found at i:53315875 original size:2 final size:2
Alignment explanation
Indices: 53315870--53315909 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
53315860 CTCAAAAAAA
*
53315870 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53315910 TAAATATGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53323472 original size:19 final size:19
Alignment explanation
Indices: 53323448--53323493 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
53323438 AGAGGTGTTT
* *
53323448 AATGCATATG-ATGCAATG
1 AATGCAAATGCATGAAATG
53323466 AAATGCAAATGCATGAAATG
1 -AATGCAAATGCATGAAATG
53323486 AATGCAAA
1 AATGCAAA
53323494 AAAAGACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.22
Consensus pattern (19 bp):
AATGCAAATGCATGAAATG
Found at i:53325783 original size:2 final size:2
Alignment explanation
Indices: 53325778--53325823 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
53325768 AAAACTCAAA
*
53325778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53325820 AT AT
1 AT AT
53325824 TAAATATGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53327176 original size:25 final size:26
Alignment explanation
Indices: 53327148--53327198 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
53327138 ATAATTATTG
*
53327148 TTATTGTT-ATTAAATTTTAATAAAA
1 TTATTGTTAAATAAATTTTAATAAAA
*
53327173 TTATTGTTAAATATATTTTAATAAAA
1 TTATTGTTAAATAAATTTTAATAAAA
53327199 ATAATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
TTATTGTTAAATAAATTTTAATAAAA
Found at i:53327241 original size:58 final size:57
Alignment explanation
Indices: 53327161--53327296 Score: 182
Period size: 57 Copynumber: 2.4 Consensus size: 57
53327151 TTGTTATTAA
* * * * * *
53327161 ATTTTAATAAAATTATTGTTAAATATATTTTAATAAAAATAATAAATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATACAATTTAAT-AAAATAATAAATAATTTAATAAG
* *
53327219 ATTTTAATATAATTTTTATTAAATACAATTTAATAAAATAATATATAATTTAATAAG
1 ATTTTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAAG
*
53327276 ATTCTAATATAATTATTATTA
1 ATTTTAATATAATTATTATTA
53327297 TATGAATTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
57 39 0.57
58 29 0.43
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (57 bp):
ATTTTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAAG
Found at i:53327317 original size:57 final size:57
Alignment explanation
Indices: 53327165--53327324 Score: 171
Period size: 57 Copynumber: 2.8 Consensus size: 57
53327155 TATTAAATTT
* * * * * * * *
53327165 TAATAAAATTATTGTTAAATATATTTTAATAAAAATAATAAATAATTTAATCATATTT
1 TAATATAATTATTATTAAATACAATTTAA-AAAAATAATATATAATTTAATAAGATTC
* *
53327223 TAATATAATTTTTATTAAATACAATTTAATAAAATAATATATAATTTAATAAGATTC
1 TAATATAATTATTATTAAATACAATTTAAAAAAATAATATATAATTTAATAAGATTC
* *
53327280 TAATATAATTATTATTATAT-GAA-TTAAAAAATCATAATATATAAT
1 TAATATAATTATTATTAAATACAATTTAAAAAA--ATAATATATAAT
53327325 ATTATAAAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
55 7 0.08
56 2 0.02
57 53 0.62
58 24 0.28
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (57 bp):
TAATATAATTATTATTAAATACAATTTAAAAAAATAATATATAATTTAATAAGATTC
Found at i:53327970 original size:58 final size:58
Alignment explanation
Indices: 53327880--53327993 Score: 228
Period size: 58 Copynumber: 2.0 Consensus size: 58
53327870 TACTGGCCCT
53327880 CAAAAGAAAGAAATGGGAACTATTGTCAAATGTTCAGCTTACATGTCGTATTCTCAGC
1 CAAAAGAAAGAAATGGGAACTATTGTCAAATGTTCAGCTTACATGTCGTATTCTCAGC
53327938 CAAAAGAAAGAAATGGGAACTATTGTCAAATGTTCAGCTTACATGTCGTATTCTCA
1 CAAAAGAAAGAAATGGGAACTATTGTCAAATGTTCAGCTTACATGTCGTATTCTCA
53327994 ATACAGAAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (58 bp):
CAAAAGAAAGAAATGGGAACTATTGTCAAATGTTCAGCTTACATGTCGTATTCTCAGC
Found at i:53331284 original size:10 final size:10
Alignment explanation
Indices: 53331269--53331326 Score: 55
Period size: 10 Copynumber: 5.4 Consensus size: 10
53331259 TCTTTATCCC
53331269 TTTTCTTTCT
1 TTTTCTTTCT
53331279 TTTTCTTTCT
1 TTTTCTTTCT
*
53331289 GTTTCGTTT-T
1 TTTTC-TTTCT
53331299 GGTTTTCTATTCCT
1 --TTTTCT-TT-CT
53331313 TTTTCTTTCT
1 TTTTCTTTCT
53331323 TTTT
1 TTTT
53331327 TTTTATTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
10 21 0.52
11 6 0.15
12 12 0.30
14 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.07, T:0.74
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:53336762 original size:46 final size:45
Alignment explanation
Indices: 53336693--53336792 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 45
53336683 GGAAAATGAT
* * * *
53336693 TAAGACCATCGTTGAAAGGCACTATGGCACTATACCAGAGAATAAA
1 TAAGACCATAGTTGAAAGACACTATGACACCATACCAGA-AATAAA
* * *
53336739 TAAGACCATAGTTGAAAGACACTATGACACCATACTAGAAATGAG
1 TAAGACCATAGTTGAAAGACACTATGACACCATACCAGAAATAAA
53336784 TAAGACCAT
1 TAAGACCAT
53336793 GACTGAAAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 13 0.28
46 34 0.72
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGACACCATACCAGAAATAAA
Found at i:53336801 original size:45 final size:45
Alignment explanation
Indices: 53336686--53336803 Score: 123
Period size: 46 Copynumber: 2.6 Consensus size: 45
53336676 TCTTGAAGGA
* * * *
53336686 AAATGATTAAGACCATCG-TTGAAAGGCACTATGGCACTATACCAG
1 AAATGAATAAGACCAT-GATTGAAAGACACTATGACACCATACCAG
* *
53336731 AGAATAAATAAGACCAT-AGTTGAAAGACACTATGACACCATACTAG
1 A-AATGAATAAGACCATGA-TTGAAAGACACTATGACACCATACCAG
* *
53336777 AAATGAGTAAGACCATGACTGAAAGAC
1 AAATGAATAAGACCATGATTGAAAGAC
53336804 GTTATGGCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
45 22 0.37
46 38 0.63
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (45 bp):
AAATGAATAAGACCATGATTGAAAGACACTATGACACCATACCAG
Found at i:53336829 original size:45 final size:45
Alignment explanation
Indices: 53336780--53336951 Score: 240
Period size: 45 Copynumber: 3.8 Consensus size: 45
53336770 ATACTAGAAA
* *
53336780 TGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
1 TGAGTAAGACCATGACTGAAAGACGTTATGGCTTCACAATTCTAT
* *
53336825 TGAGTAAGATCATGACTGAAAGATGTTATGGCTTCACAAATT-TAT
1 TGAGTAAGACCATGACTGAAAGACGTTATGGCTTCAC-AATTCTAT
** *
53336870 CAAGTAAGACCATGACTGAAAGACGTTATGGCGTCACAATTCTAT
1 TGAGTAAGACCATGACTGAAAGACGTTATGGCTTCACAATTCTAT
*
53336915 TGAGTAAGACCAT-AGCTGAAAGACGCTATGGCTTCAC
1 TGAGTAAGACCATGA-CTGAAAGACGTTATGGCTTCAC
53336952 GAATCAAACG
Statistics
Matches: 111, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
44 5 0.05
45 103 0.93
46 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (45 bp):
TGAGTAAGACCATGACTGAAAGACGTTATGGCTTCACAATTCTAT
Found at i:53336881 original size:90 final size:90
Alignment explanation
Indices: 53336782--53336951 Score: 279
Period size: 90 Copynumber: 1.9 Consensus size: 90
53336772 ACTAGAAATG
* *
53336782 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATTGAGTAAGATCAT-GACTGAAA
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATTGAGTAAGACCATAG-CTGAAA
* *
53336846 GATGTTATGGCTTCACAAATTTATCA
65 GACGCTATGGCTTCACAAATTTATCA
*
53336872 AGTAAGACCATGACTGAAAGACGTTATGGCGTCACAATTCTATTGAGTAAGACCATAGCTGAAAG
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATTGAGTAAGACCATAGCTGAAAG
53336937 ACGCTATGGCTTCAC
66 ACGCTATGGCTTCAC
53336952 GAATCAAACG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
90 73 0.99
91 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (90 bp):
AGTAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATTGAGTAAGACCATAGCTGAAAG
ACGCTATGGCTTCACAAATTTATCA
Found at i:53336974 original size:45 final size:45
Alignment explanation
Indices: 53336784--53336972 Score: 204
Period size: 45 Copynumber: 4.2 Consensus size: 45
53336774 TAGAAATGAG
* * * *
53336784 TAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATTGAG
1 TAAGACCATGACTGAAAGACGTTATGGCTTCACGAATCTATCGAA
* * * *
53336829 TAAGATCATGACTGAAAGATGTTATGGCTTCACAAATTTATC-AA
1 TAAGACCATGACTGAAAGACGTTATGGCTTCACGAATCTATCGAA
* * *
53336873 GTAAGACCATGACTGAAAGACGTTATGGCGTCAC-AATTCTATTGAG
1 -TAAGACCATGACTGAAAGACGTTATGGCTTCACGAA-TCTATCGAA
* * *
53336919 TAAGACCAT-AGCTGAAAGACGCTATGGCTTCACGAATCAAACGAA
1 TAAGACCATGA-CTGAAAGACGTTATGGCTTCACGAATCTATCGAA
53336964 TAAGACCAT
1 TAAGACCAT
53336973 AGTTGAAAGA
Statistics
Matches: 119, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
44 4 0.03
45 112 0.94
46 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (45 bp):
TAAGACCATGACTGAAAGACGTTATGGCTTCACGAATCTATCGAA
Found at i:53336983 original size:90 final size:90
Alignment explanation
Indices: 53336782--53336972 Score: 269
Period size: 90 Copynumber: 2.1 Consensus size: 90
53336772 ACTAGAAATG
* *
53336782 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATTGAGTAAGATCATGACTGAAAG
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATTGAGTAAGACCATGACTGAAAG
* * ** *
53336847 ATGTTATGGCTTCACAAATTTATCA
66 ACGCTATGGCTTCACAAATCAAACA
*
53336872 AGTAAGACCATGACTGAAAGACGTTATGGCGTCACAATTCTATTGAGTAAGACCAT-AGCTGAAA
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATTGAGTAAGACCATGA-CTGAAA
*
53336936 GACGCTATGGCTTCACGAATCAAACGA
65 GACGCTATGGCTTCACAAATCAAAC-A
53336963 A-TAAGACCAT
1 AGTAAGACCAT
53336973 AGTTGAAAGA
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
89 1 0.01
90 87 0.97
91 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (90 bp):
AGTAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATTGAGTAAGACCATGACTGAAAG
ACGCTATGGCTTCACAAATCAAACA
Found at i:53336998 original size:45 final size:45
Alignment explanation
Indices: 53336919--53337076 Score: 147
Period size: 45 Copynumber: 3.5 Consensus size: 45
53336909 TTCTATTGAG
* * * ** *
53336919 TAAGACCATAGCTGAAAGACGCTATGGCTTCACGA-ATCAAACGAA
1 TAAGACCATAGTTGAAAGACACTATGACAACACGACA-AAAACGAA
*
53336964 TAAGACCATAGTTGAAAGACACTATGACAACACGACGAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAACACGAC-AAAAACGAA
* * * * * * **
53337010 TAAGACCATGGTTTAAAGACACTATGGCATCAAGACAAGAATAAA
1 TAAGACCATAGTTGAAAGACACTATGACAACACGACAAAAACGAA
*
53337055 TAAGACCATGGTTGAAAGACAC
1 TAAGACCATAGTTGAAAGACAC
53337077 CATGGTACAC
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
45 58 0.60
46 37 0.39
47 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGACAACACGACAAAAACGAA
Found at i:53337028 original size:46 final size:45
Alignment explanation
Indices: 53336961--53337076 Score: 160
Period size: 46 Copynumber: 2.6 Consensus size: 45
53336951 CGAATCAAAC
* *
53336961 GAATAAGACCATAGTTGAAAGACACTATGACAACACGACGAAAAAT
1 GAATAAGACCATGGTTGAAAGACACTATGACAACAAGAC-AAAAAT
* * * *
53337007 GAATAAGACCATGGTTTAAAGACACTATGGCATCAAGACAAGAAT
1 GAATAAGACCATGGTTGAAAGACACTATGACAACAAGACAAAAAT
*
53337052 AAATAAGACCATGGTTGAAAGACAC
1 GAATAAGACCATGGTTGAAAGACAC
53337077 CATGGTACAC
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
45 28 0.45
46 34 0.55
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.17
Consensus pattern (45 bp):
GAATAAGACCATGGTTGAAAGACACTATGACAACAAGACAAAAAT
Found at i:53344165 original size:43 final size:43
Alignment explanation
Indices: 53344117--53344266 Score: 137
Period size: 43 Copynumber: 3.5 Consensus size: 43
53344107 GTGAAAAAAT
* *
53344117 GCCGCTAAATATCTTGACCTTTAGCGGCCCTTTTA-TCACAAAC
1 GCCGCTAAAGATCATGACCTTTAGCGGCCC-TTTAGTCACAAAC
*
53344160 GCCGCTAAAGATCATGACCTTTAGCGGCGCTTTAGTCACAAAC
1 GCCGCTAAAGATCATGACCTTTAGCGGCCCTTTAGTCACAAAC
** * * * * * *
53344203 GCTACGAAAGAACA-AACCTTTAGCGGCGCTTCTCG-CAAAAAC
1 GCCGCTAAAGATCATGACCTTTAGCGGCCCTT-TAGTCACAAAC
* *
53344245 GCCGCTAAA-AACATAACCTTTA
1 GCCGCTAAAGATCATGACCTTTA
53344267 AAAATATATA
Statistics
Matches: 91, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
41 4 0.04
42 40 0.44
43 47 0.52
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (43 bp):
GCCGCTAAAGATCATGACCTTTAGCGGCCCTTTAGTCACAAAC
Found at i:53344232 original size:42 final size:42
Alignment explanation
Indices: 53344133--53344266 Score: 128
Period size: 42 Copynumber: 3.2 Consensus size: 42
53344123 AAATATCTTG
* * * * *
53344133 ACCTTTAGCGGCCCTTTTATCACAAACGCCGCTAAAGATCATG
1 ACCTTTAGCGGCGC-TTTATCACAAACGCCACGAAAGAACATA
*
53344176 ACCTTTAGCGGCGCTTTAGTCACAAACGCTACGAAAGAACA-A
1 ACCTTTAGCGGCGCTTTA-TCACAAACGCCACGAAAGAACATA
** * * *
53344218 ACCTTTAGCGGCGCTTCTCGCAAAAACGCCGCTAAA-AACATA
1 ACCTTTAGCGGCGCTT-TATCACAAACGCCACGAAAGAACATA
53344260 ACCTTTA
1 ACCTTTA
53344267 AAAATATATA
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.05
42 40 0.53
43 32 0.42
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.22
Consensus pattern (42 bp):
ACCTTTAGCGGCGCTTTATCACAAACGCCACGAAAGAACATA
Done.